#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_Mutation_Status	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964409	37964429	+	In_Frame_Del	DEL	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	-	rs13056859|rs13055845|rs77417880|rs62235033|rs62235034|rs187761157|rs66468174|rs200195385	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:37964409_37964429delCAGCGCCTGCTGCAAACCCCT	ENST00000249014.4	+	3	1178_1198	c.758_778delCAGCGCCTGCTGCAAACCCCT	c.(757-780)ccagcgcctgctgcaaacccctca>cca	p.APAANPS254del		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	254	8 X 7 AA tandem repeats of [PT]-[AT]-A- [ENT]-[PT]-[PTS]-[AG].				positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.N258_A264delNPSAPAA(3)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					GCAAACCCCCCAGCGCCTGCTGCAAACCCCTCAGCACCTGC	0.665																																					p.253_259del		Atlas-Indel	.											.	CDC42EP1	53	.	3	Deletion - In frame(3)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(1)	c.757_777del						PASS	.			868,3338		98,672,1333						1.5	0.0		dbSNP_130	10	4310,3696		1298,1714,991	no	coding	CDC42EP1	NM_152243.2		1396,2386,2324	A1A1,A1R,RR		46.1654,20.6372,42.4009				5178,7034				SO:0001651	inframe_deletion	11135	exon3			.	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.758_778delCAGCGCCTGCTGCAAACCCCT	22.37:g.37964409_37964429delCAGCGCCTGCTGCAAACCCCT	ENSP00000249014:p.Ala254_Ser260del	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	102	37	0.362745	NM_152243	A8K825|Q96GN1	In_Frame_Del	DEL	ENST00000249014.4	37	CCDS13949.1																																																																																			CAGCGCCTGCTGCAAACCCCT|0.610;-|0.390	0.390	strong		0.665	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
ABCF1	23	hgsc.bcm.edu	37	6	30558477	30558478	+	Stop_Codon_Ins	INS	-	-	A	rs76018112|rs548415581	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30558477_30558478insA	ENST00000326195.8	+	0	2649_2650				ABCF1_ENST00000396515.4_Stop_Codon_Ins|ABCF1_ENST00000376545.3_Stop_Codon_Ins	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1						inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						CCCCGAGAGTGAGCTTTCCTTC	0.564													A|A|AA|insertion	3576	0.714058	0.73	0.5937	5008	,	,		19175	0.6736		0.6789	False		,,,				2504	0.8558				p.X846delinsX		Pindel,Atlas-Indel	.											.	ABCF1	61	.	0			c.2537_2538insA						PASS	.		,	2545,933		984,577,178					,	5.4	1.0		dbSNP_130	106	4558,2170		1686,1186,492	no	frameshift,frameshift	ABCF1	NM_001090.2,NM_001025091.1	,	2670,1763,670	A1A1,A1R,RR		32.2533,26.8258,30.4037	,	,		7103,3103				SO:0001567	stop_retained_variant	23	exon25			.	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.2536dupA	6.37:g.30558478_30558478dupA		Somatic	160	.	.		WXS	Illumina HiSeq	Phase_I	184	72	0.391	NM_001025091	A2BF75|O14897|Q69YP6	Frame_Shift_Ins	INS	ENST00000326195.8	37	CCDS34380.1																																																																																			A|1.000;|0.000	1.000	strong		0.564	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3		
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586676	+	Frame_Shift_Del	DEL	TTTTA	TTTTA	-	rs201063949|rs199927874	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTTTA	TTTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145586672_145586676delTTTTA	ENST00000334513.5	-	8	911_915	c.900_904delTAAAA	c.(898-906)tgtaaaagtfs	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)					TAAGCTGCACTTTTACACGGTGGGG	0.532														72	0.014377	0.0015	0.0303	5008	,	,		19363	0.0		0.0398	False		,,,				2504	0.0092				p.301_302del		Atlas-Indel	.											.	NUDT17	25	.	0			c.901_905del						PASS	.			14,4252		0,14,2119						-1.1	0.0			111	162,8092		2,158,3967	no	frameshift	NUDT17	NM_001012758.2		2,172,6086	A1A1,A1R,RR		1.9627,0.3282,1.4058				176,12344				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.900_904delTAAAA	1.37:g.145586672_145586676delTTTTA	ENSP00000334437:p.Cys300fs	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	81	18	0.222222	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			TTTTA|0.983;-|0.017	0.017	strong		0.532	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395	
SYNPO2	171024	hgsc.bcm.edu	37	4	119947962	119947964	+	In_Frame_Del	DEL	AAG	AAG	-	rs70944826	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:119947962_119947964delAAG	ENST00000429713.2	+	3	620_622	c.438_440delAAG	c.(436-441)caaaga>caa	p.R147del	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_In_Frame_Del_p.R147del|SYNPO2_ENST00000434046.2_In_Frame_Del_p.R147del	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	147				Missing (in Ref. 3; AL832031). {ECO:0000305}.		actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CTGAGAACCAAAGAAGTGGTCCC	0.552														1780	0.355431	0.2375	0.4654	5008	,	,		17830	0.496		0.3489	False		,,,				2504	0.2986				p.146_147del		Pindel,Atlas-Indel	.											.	SYNPO2	353	.	0			c.437_439del						PASS	.		,,	1140,3126		155,830,1148					,,	2.9	0.4		dbSNP_130	44	3087,5167		549,1989,1589	no	coding,coding,coding	SYNPO2	NM_133477.2,NM_001128934.1,NM_001128933.1	,,	704,2819,2737	A1A1,A1R,RR		37.4,26.7229,33.762	,,	,,		4227,8293				SO:0001651	inframe_deletion	171024	exon3			.	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.438_440delAAG	4.37:g.119947965_119947967delAAG	ENSP00000395143:p.Arg147del	Somatic	78	.	.		WXS	Illumina HiSeq	Phase_I	70	20	0.286	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	In_Frame_Del	DEL	ENST00000429713.2	37	CCDS47129.1																																																																																			AAG|0.631;-|0.369	0.369	strong		0.552	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
C11orf40	143501	hgsc.bcm.edu	37	11	4592706	4592707	+	Frame_Shift_Ins	INS	-	-	AC	rs80310454|rs67702097|rs141600462	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:4592706_4592707insAC	ENST00000307616.1	-	4	599_600	c.600_601insGT	c.(598-603)tgtatgfs	p.M201fs		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	201										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		acacgatccatacagtttttcc	0.426																																					p.M201fs		Pindel,Atlas-Indel	.											.	C11orf40	37	.	0			c.601_602insGT						PASS	.			2670,1456		925,820,318						-0.7	0.0		dbSNP_130	78	4274,3706		1320,1634,1036	no	frameshift	C11orf40	NM_144663.1		2245,2454,1354	A1A1,A1R,RR		46.4411,35.2884,42.64				6944,5162				SO:0001589	frameshift_variant	143501	exon4			.		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.599_600dupGT	11.37:g.4592707_4592708dupAC	ENSP00000302918:p.Met201fs	Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	115	29	0.252	NM_144663		Frame_Shift_Ins	INS	ENST00000307616.1	37	CCDS31354.1																																																																																			-|0.377;AC|0.623	0.623	strong		0.426	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
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 GAIIx	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	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	110	16	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 GAIIx	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	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	157	33	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	
P2RX5	5026	hgsc.bcm.edu	37	17	3594277	3594277	+	Frame_Shift_Del	DEL	G	G	-	rs138772680|rs397743686|rs3215407	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3594277delG	ENST00000225328.5	-	3	731	c.333delC	c.(331-333)cccfs	p.P111fs	P2RX5_ENST00000550772.1_5'Flank|P2RX5_ENST00000552276.1_Frame_Shift_Del_p.P111fs|P2RX5_ENST00000435558.1_Frame_Shift_Del_p.P111fs|P2RX5_ENST00000551178.1_Intron|P2RX5_ENST00000547178.1_Frame_Shift_Del_p.P111fs|P2RX5_ENST00000345901.3_Intron|P2RX5_ENST00000552050.1_Intron|P2RX5-TAX1BP3_ENST00000550383.1_Frame_Shift_Del_p.P111fs	NM_001204519.1|NM_002561.3	NP_001191448.1|NP_002552.2	Q93086	P2RX5_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 5	111					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transport (GO:0006810)	integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|ion channel activity (GO:0005216)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						GCCGCTGGTTGGGGGTCACAA	0.597													GGGGG|GGGGG|GGGG|deletion	2872	0.573482	0.1702	0.7767	5008	,	,		18534	0.8145		0.6918	False		,,,				2504	0.6043				p.N112fs		Pindel,Atlas-Indel	.											.	P2RX5	36	.	0			c.334delA	GRCh37	CD054974	P2RX5	D	rs5818907	PASS	.		,,,	1161,3103		165,831,1136	47.0	23.0	32.0		,,,	3.9	1.0	17	dbSNP_114	59	5647,2607		1943,1761,423	yes	intron,frameshift,intron,frameshift	P2RX5	NM_175080.2,NM_002561.3,NM_001204520.1,NM_001204519.1	,,,	2108,2592,1559	A1A1,A1R,RR		31.5847,27.228,45.6143	,,,	,,,	3594277	6808,5710	2191	4147	6338	SO:0001589	frameshift_variant	5026	exon3			.	AF016709	CCDS11034.1, CCDS11035.1, CCDS56014.1, CCDS56015.1	17p13.3	2012-01-17			ENSG00000083454	ENSG00000083454		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8536	protein-coding gene	gene with protein product		602836				9414125	Standard	NM_002561		Approved	P2X5	uc002fwi.3	Q93086	OTTHUMG00000090700	ENST00000225328.5:c.333delC	17.37:g.3594277delG	ENSP00000225328:p.Pro111fs	Somatic	53	.	.		WXS	Illumina HiSeq	Phase_I	34	18	0.529	NM_001204519	G5E981|O43450|O75540|Q308M5|Q59F38|Q8IXW4|Q93087|Q9NZV0	Frame_Shift_Del	DEL	ENST00000225328.5	37	CCDS11034.1																																																																																			G|0.374;-|0.626	0.626	strong		0.597	P2RX5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207388.3	NM_002561, NM_175080, NM_175081	
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 GAIIx	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_ENST00000411935.1_Frame_Shift_Del_p.L254fs|FAM115C_ENST00000409703.3_Frame_Shift_Del_p.L254fs|FAM115C_ENST00000357344.4_Frame_Shift_Del_p.L418fs|FAM115C_ENST00000444908.2_Frame_Shift_Del_p.L418fs|FAM115C_ENST00000425618.2_Frame_Shift_Del_p.L137fs|FAM115C_ENST00000411497.2_Frame_Shift_Del_p.L137fs			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	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	87	16	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	
HRCT1	646962	hgsc.bcm.edu	37	9	35906584	35906586	+	In_Frame_Del	DEL	CCA	CCA	-	rs143611048	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:35906584_35906586delCCA	ENST00000354323.2	+	1	396_398	c.300_302delCCA	c.(298-303)ctccac>ctc	p.H105del	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	105	His-rich.					integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						ctcaccacctccaccaccaccac	0.66														929	0.185503	0.1619	0.1268	5008	,	,		6334	0.3085		0.1213	False		,,,				2504	0.1984				p.100_101del		Atlas-Indel	.											HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	0			c.299_301del						PASS	.																																			SO:0001651	inframe_deletion	646962	exon1			.		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.300_302delCCA	9.37:g.35906593_35906595delCCA	ENSP00000346283:p.His105del	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_001039792	B7ZBJ1	In_Frame_Del	DEL	ENST00000354323.2	37	CCDS35012.1																																																																																			.	.	strong		0.660	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
HOMEZ	57594	hgsc.bcm.edu	37	14	23744827	23744829	+	In_Frame_Del	DEL	TCC	TCC	-	rs79723196|rs35076736|rs67447855	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:23744827_23744829delTCC	ENST00000357460.5	-	2	1772_1774	c.1608_1610delGGA	c.(1606-1611)gaggaa>gaa	p.536_537EE>E	HOMEZ_ENST00000431326.2_In_Frame_Del_p.538_539EE>E|HOMEZ_ENST00000561013.1_In_Frame_Del_p.538_539EE>E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	536	Glu-rich.|Poly-Asp.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		atcatcatcttcctcctcctcct	0.483														1763	0.352037	0.3949	0.3386	5008	,	,		20301	0.1974		0.3738	False		,,,				2504	0.4407				p.537_537del		Pindel,Atlas-Indel	.											.	HOMEZ	80	.	0			c.1609_1611del						PASS	.																																			SO:0001651	inframe_deletion	57594	exon2			.	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1608_1610delGGA	14.37:g.23744836_23744838delTCC	ENSP00000350049:p.Glu537del	Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	69	21	0.304	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	In_Frame_Del	DEL	ENST00000357460.5	37	CCDS45085.1																																																																																			TCC|0.500;-|0.500	0.500	weak		0.483	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
STRBP	55342	hgsc.bcm.edu	37	9	125876697	125876697	+	Intron	DEL	G	G	-	rs149751997	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:125876697delG	ENST00000530364.1	-	2	31				MIR600HG_ENST00000385007.1_RNA			Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein						cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						TCCAACCCTTGCTTAGGTTAA	0.483													G|G|-|deletion	6	0.00119808	0.0	0.0029	5008	,	,		23033	0.0		0.004	False		,,,				2504	0.0				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																			SO:0001627	intron_variant	81571	.			.	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000530364.1:c.255-4665C>-	9.37:g.125876697delG		Somatic	73	.	.		WXS	Illumina HiSeq	Phase_I	47	16	0.340	.	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	RNA	DEL	ENST00000530364.1	37																																																																																				.	.	strong		0.483	STRBP-009	PUTATIVE	basic	processed_transcript	protein_coding	OTTHUMT00000392598.1		
ACIN1	22985	hgsc.bcm.edu	37	14	23548787	23548788	+	In_Frame_Ins	INS	-	-	GTGAAT	rs55838227|rs34870944|rs61741619	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:23548787_23548788insGTGAAT	ENST00000262710.1	-	6	2257_2258	c.1930_1931insATTCAC	c.(1930-1932)cgt>cATTCACgt	p.643_644insHS	ACIN1_ENST00000555053.1_In_Frame_Ins_p.643_644insHS|ACIN1_ENST00000605057.1_In_Frame_Ins_p.585_586insHS|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000457657.1_In_Frame_Ins_p.603_604insHS	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	643	Ser-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S643_R644insHS(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TGAACGAGAACGTGAACGTGAC	0.49																																					p.R644delinsHSR		Pindel,Atlas-Indel	.											.	ACIN1	147	.	1	Insertion - In frame(1)	upper_aerodigestive_tract(1)	c.1931_1932insATTCAC						PASS	.																																			SO:0001652	inframe_insertion	22985	exon6			.	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1930_1931insATTCAC	14.37:g.23548787_23548788insGTGAAT	ENSP00000262710:p.Ser643_Arg644insHisSer	Somatic	177	.	.		WXS	Illumina HiSeq	Phase_I	154	34	0.221	NM_014977	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	In_Frame_Ins	INS	ENST00000262710.1	37	CCDS9587.1																																																																																			-|0.604;GTGAAT|0.396	0.396	strong		0.490	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
GNLY	10578	hgsc.bcm.edu	37	2	85922121	85922122	+	Intron	INS	-	-	A	rs113717357	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85922121_85922122insA	ENST00000263863.4	+	2	180				GNLY_ENST00000533041.1_Splice_Site|GNLY_ENST00000524600.1_Splice_Site|GNLY_ENST00000409696.3_Splice_Site	NM_006433.3	NP_006424.2	P22749	GNLY_HUMAN	granulysin						cellular defense response (GO:0006968)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular space (GO:0005615)				endometrium(4)|kidney(10)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	19						GGATGGAAGGTAAAAAAAGAAA	0.52													AAAAAAA|AAAAAAA|AAAAAAAA|insertion	1149	0.229433	0.6172	0.098	5008	,	,		20731	0.0337		0.0765	False		,,,				2504	0.1575				.		Pindel,Atlas-Indel	.											.	GNLY	29	.	0			c.7+2->A						PASS	.		,	2025,1655		575,875,390					,	-1.7	0.0		dbSNP_132	60	669,7245		29,611,3317	no	splice-5,intron	GNLY	NM_012483.2,NM_006433.3	,	604,1486,3707	A1A1,A1R,RR		8.4534,44.9728,23.2362	,	,		2694,8900				SO:0001627	intron_variant	10578	exon2			.	X54101	CCDS1984.1, CCDS46354.1	2p12-q11	2008-02-05			ENSG00000115523	ENSG00000115523			4414	protein-coding gene	gene with protein product	"""T-lymphocyte activation gene 519"""	188855		LAG2		2212946, 2434598	Standard	NM_012483		Approved	NKG5, LAG-2, D2S69E, TLA519	uc002sql.4	P22749	OTTHUMG00000130179	ENST00000263863.4:c.53-321->A	2.37:g.85922128_85922128dupA		Somatic	25	.	.		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_012483	P09325|Q6GU08	Splice_Site	INS	ENST00000263863.4	37	CCDS1984.1																																																																																			-|0.808;A|0.192	0.192	strong		0.520	GNLY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252497.1	NM_006433	
OR13C2	392376	hgsc.bcm.edu	37	9	107367665	107367666	+	Frame_Shift_Del	DEL	GC	GC	-	rs377668801|rs143760725|rs144815315|rs140970710	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107367665_107367666delGC	ENST00000542196.1	-	1	285_286	c.243_244delGC	c.(241-246)acgctafs	p.L82fs		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	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(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						AAGCTCACTAGCGTGGAGGGAA	0.515														1574	0.314297	0.4138	0.2003	5008	,	,		20880	0.4097		0.16	False		,,,				2504	0.3211				p.82_82del		Atlas-Indel	.											.	OR13C2	46	.	0			c.244_245del						PASS	.			2387,1861		730,927,467						2.2	0.0		dbSNP_134	35	1565,6681		171,1223,2729	no	frameshift	OR13C2	NM_001004481.1		901,2150,3196	A1A1,A1R,RR		18.9789,43.8089,31.6312				3952,8542				SO:0001589	frameshift_variant	392376	exon1			.		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.243_244delGC	9.37:g.107367665_107367666delGC	ENSP00000438815:p.Leu82fs	Somatic	399	0	0		WXS	Illumina HiSeq	Phase_I	372	113	0.303763	NM_001004481	B9EGV8|Q6IF54	Frame_Shift_Del	DEL	ENST00000542196.1	37	CCDS35092.1																																																																																			.	.	strong		0.515	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
WDR81	124997	hgsc.bcm.edu	37	17	1631341	1631343	+	In_Frame_Del	DEL	GAG	GAG	-	rs577690948|rs200758098|rs35048651	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1631341_1631343delGAG	ENST00000409644.1	+	1	3088_3090	c.3088_3090delGAG	c.(3088-3090)gagdel	p.E1033del	WDR81_ENST00000419248.1_Intron|WDR81_ENST00000545662.1_5'Flank|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_5'UTR|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000437219.2_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1033				Missing (in Ref. 1; BAB84937). {ECO:0000305}.	negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGGGGCTGCTGAGGAGGAGGAGA	0.695														1061	0.211861	0.115	0.196	5008	,	,		16982	0.1835		0.1948	False		,,,				2504	0.4008				p.1029_1030del		Pindel,Atlas-Indel	.											.	WDR81	180	.	0			c.3087_3089del						PASS	.		,,,	549,3367		98,353,1507					,,,	-11.3	0.0		dbSNP_130	17	1642,6232		262,1118,2557	no	utr-5,intron,coding,intron	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	,,,	360,1471,4064	A1A1,A1R,RR		20.8534,14.0194,18.5835	,,,	,,,		2191,9599				SO:0001651	inframe_deletion	124997	exon1			.	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3088_3090delGAG	17.37:g.1631350_1631352delGAG	ENSP00000386609:p.Glu1033del	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	43	12	0.279	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	In_Frame_Del	DEL	ENST00000409644.1	37	CCDS54062.1																																																																																			-|0.172;GAG|0.828	0.172	strong		0.695	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
RTKN2	219790	hgsc.bcm.edu	37	10	63976913	63976918	+	In_Frame_Del	DEL	AGCTTC	AGCTTC	-	rs115357868|rs201442319|rs149331212|rs59044276|rs76810894	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AGCTTC	AGCTTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:63976913_63976918delAGCTTC	ENST00000373789.3	-	9	1075_1080	c.979_984delGAAGCT	c.(979-984)gaagctdel	p.EA327del	RTKN2_ENST00000395265.1_In_Frame_Del_p.EA327del|RTKN2_ENST00000315289.2_In_Frame_Del_p.EA108del	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	327	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					GTTCCACTTTAGCTTCAATTTCCTCT	0.354														704	0.140575	0.295	0.1066	5008	,	,		17288	0.005		0.16	False		,,,				2504	0.0757				p.327_329del		Pindel,Atlas-Indel	.											.	RTKN2	68	.	0			c.980_985del						PASS	.			1087,3173		162,763,1205						6.0	1.0		dbSNP_129	131	1232,7022		103,1026,2998	no	coding	RTKN2	NM_145307.2		265,1789,4203	A1A1,A1R,RR		14.9261,25.5164,18.5312				2319,10195				SO:0001651	inframe_deletion	219790	exon9			.	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"""Pleckstrin homology (PH) domain containing"""	19364	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family K member 1"""	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.979_984delGAAGCT	10.37:g.63976913_63976918delAGCTTC	ENSP00000362894:p.Glu327_Ala328del	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	21	18	0.857	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	In_Frame_Del	DEL	ENST00000373789.3	37	CCDS7263.1																																																																																			AGCTTC|0.861;-|0.139	0.139	strong		0.354	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307	
PDE6G	5148	hgsc.bcm.edu	37	17	79614933	79614936	+	IGR	DEL	TAAC	TAAC	-	rs34872037|rs10536197|rs397693108	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TAAC	TAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79614933_79614936delTAAC	ENST00000331056.5	-	0	1023				TSPAN10_ENST00000572675.1_RNA|TSPAN10_ENST00000328585.4_RNA|PDE6G_ENST00000574777.1_5'Flank	NM_002602.3	NP_002593.1	P18545	CNRG_HUMAN	phosphodiesterase 6G, cGMP-specific, rod, gamma						activation of MAPK activity (GO:0000187)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|enzyme inhibitor activity (GO:0004857)			lung(2)|urinary_tract(1)	3	all_neural(118;0.0878)|all_lung(278;0.175)|Lung NSC(278;0.192)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)		Sildenafil(DB00203)|Vardenafil(DB00862)	GCAGGTACTTTAACTAACTGCAGC	0.637														4228	0.844249	0.947	0.7738	5008	,	,		14523	0.997		0.6441	False		,,,				2504	0.8037				.	GBM(189;38 2147 16440 40945 46567)	Pindel,Atlas-Indel	.											.	TSPAN10	21	.	0			.						PASS	.			3258,464		1461,336,64						4.3	0.8		dbSNP_126	13	4943,2891		1640,1663,614	no	frameshift	TSPAN10	NM_031945.3		3101,1999,678	A1A1,A1R,RR		36.9032,12.4664,29.0325				8201,3355				SO:0001628	intergenic_variant	83882	.			.		CCDS11783.1	17q21.1	2014-01-28				ENSG00000185527	3.1.4.17	"""Phosphodiesterases"""	8789	protein-coding gene	gene with protein product		180073		PDEG		2155175	Standard	NM_002602		Approved	RP57	uc002kay.3	P18545			17.37:g.79614937_79614940delTAAC		Somatic	36	.	.		WXS	Illumina HiSeq	Phase_I	23	10	0.435	.	Q3KP63|Q7Z3U8	Splice_Site	DEL	ENST00000331056.5	37	CCDS11783.1																																																																																			TAAC|0.198;-|0.802	0.802	strong		0.637	PDE6G-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440314.1		
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 GAIIx	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	Somatic	190	.	.		WXS	Illumina HiSeq	Phase_I	222	69	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	
CAPN11	11131	hgsc.bcm.edu	37	6	44140054	44140055	+	Frame_Shift_Ins	INS	-	-	GGCTGCC	rs397947482|rs57288791|rs111320370	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:44140054_44140055insGGCTGCC	ENST00000398776.1	+	5	463_464	c.425_426insGGCTGCC	c.(424-429)ctggctfs	p.-143fs	CAPN11_ENST00000542245.1_Frame_Shift_Ins_p.-143fs	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11						proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGCTGGCTGCTGGCTGCCATCG	0.584											OREG0017466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		330	0.0658946	0.1256	0.0519	5008	,	,		15212	0.0		0.0736	False		,,,				2504	0.0552				p.L142fs		Pindel,Atlas-Indel	.											CAPN11,colon,carcinoma,0,1	CAPN11	66	1	0			c.425_426insGGCTGCC						PASS	.			348,3260		52,244,1508						4.1	1.0		dbSNP_134	14	387,7195		36,315,3440	yes	frameshift	CAPN11	NM_007058.3		88,559,4948	A1A1,A1R,RR		5.1042,9.6452,6.5684				735,10455				SO:0001589	frameshift_variant	11131	exon5			.	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.426_432dupGGCTGCC	6.37:g.44140055_44140061dupGGCTGCC	ENSP00000381758:p.Ala143fs	Somatic	59	.	.	921	WXS	Illumina HiSeq	Phase_I	48	11	0.229	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Frame_Shift_Ins	INS	ENST00000398776.1	37	CCDS47436.1																																																																																			-|0.944;GGCTGCC|0.056	0.056	strong		0.584	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		
CLDN16	10686	hgsc.bcm.edu	37	3	190106072	190106072	+	Frame_Shift_Del	DEL	G	G	-	rs386669518|rs201380153|rs56086318|rs368234054	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:190106072delG	ENST00000264734.2	+	1	412	c.164delG	c.(163-165)aggfs	p.R55fs	CLDN16_ENST00000456423.1_Frame_Shift_Del_p.R55fs|CLDN16_ENST00000468220.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	55					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		AGTGGGGCCAGGGCTGGTGTC	0.512													GGG|GGG|GG|deletion	586	0.117013	0.0681	0.1455	5008	,	,		21539	0.0208		0.2336	False		,,,				2504	0.1421				p.R55fs		Atlas-Indel	.											.	CLDN16	59	.	0			c.163delA						PASS	.						145.0	107.0	120.0					3																	190106072		2203	4291	6494	SO:0001589	frameshift_variant	10686	exon1			.	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"""Claudins"""	2037	protein-coding gene	gene with protein product	"""paracellin-1"", ""hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"""	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.164delG	3.37:g.190106072delG	ENSP00000264734:p.Arg55fs	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_006580		Frame_Shift_Del	DEL	ENST00000264734.2	37	CCDS3296.1																																																																																			.	.	strong		0.512	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121653375	121653377	+	In_Frame_Del	DEL	TGA	TGA	-	rs80103123|rs35947407|rs398111797	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:121653375_121653377delTGA	ENST00000393386.2	+	12	4686_4688	c.4275_4277delTGA	c.(4273-4278)ggtgat>ggt	p.D1431del	PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1431					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)	p.G1425G(1)		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						atgatgatggtgatgatgatgat	0.424														2357	0.470647	0.559	0.464	5008	,	,		22105	0.3542		0.3708	False		,,,				2504	0.5787				p.1425_1426del		Pindel,Atlas-Indel	.											PTPRZ1,leg,malignant_melanoma,-1,1	PTPRZ1	605	1	1	Substitution - coding silent(1)	skin(1)	c.4274_4276del						PASS	.																																			SO:0001651	inframe_deletion	5803	exon12			.	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.4275_4277delTGA	7.37:g.121653384_121653386delTGA	ENSP00000377047:p.Asp1431del	Somatic	123	.	.		WXS	Illumina HiSeq	Phase_I	94	26	0.277	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	In_Frame_Del	DEL	ENST00000393386.2	37	CCDS34740.1																																																																																			TGA|0.585;-|0.415	0.415	strong		0.424	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
RIC8A	60626	hgsc.bcm.edu	37	11	209895	209897	+	In_Frame_Del	DEL	CCC	CCC	-	rs201633036|rs200641500|rs3832797|rs398102296|rs571957041	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:209895_209897delCCC	ENST00000526104.1	+	3	1965_1967	c.621_623delCCC	c.(619-624)aacccc>aac	p.P210del	BET1L_ENST00000486280.1_5'Flank|BET1L_ENST00000382762.3_5'Flank|BET1L_ENST00000529614.2_5'Flank|BET1L_ENST00000325147.9_5'Flank|RIC8A_ENST00000527696.1_In_Frame_Del_p.P204del|BET1L_ENST00000332865.6_5'Flank|RIC8A_ENST00000325207.5_In_Frame_Del_p.P210del|BET1L_ENST00000410108.1_5'Flank			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	210					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CTGAAGGGAACCCCCCACCCACG	0.601														2073	0.413938	0.2519	0.428	5008	,	,		21433	0.7629		0.327	False		,,,				2504	0.3528				p.207_208del		Atlas-Indel	.											.	RIC8A	45	.	0			c.620_622del						PASS	.			1167,8,3089		173,0,821,4,0,1134						1.2	0.0		dbSNP_107	49	2820,12,5422		493,0,1834,6,0,1794	no	codingComplex	RIC8A	NM_021932.4		666,0,2655,10,0,2928	A1A1,A1A2,A1R,A2A2,A2R,RR		34.3106,27.5563,32.0099				3987,20,8511				SO:0001651	inframe_deletion	60626	exon3			.	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.621_623delCCC	11.37:g.209898_209900delCCC	ENSP00000432008:p.Pro210del	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	In_Frame_Del	DEL	ENST00000526104.1	37																																																																																				CCC|0.579;-|0.421	0.421	strong		0.601	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932	
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 GAIIx	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	Somatic	82	.	.		WXS	Illumina HiSeq	Phase_I	62	17	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 GAIIx	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	Somatic	154	.	.		WXS	Illumina HiSeq	Phase_I	153	34	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106158509_106158510insT	ENST00000540549.1	+	3	4269		c.e3+1		TET2_ENST00000513237.1_Splice_Site|TET2_ENST00000413648.2_Splice_Site|TET2_ENST00000380013.4_Splice_Site|TET2_ENST00000394764.1_Frame_Shift_Ins_p.K1138fs|TET2_ENST00000305737.2_Frame_Shift_Ins_p.K1138fs|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		Somatic	250	.	.		WXS	Illumina HiSeq	Phase_I	272	55	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
ZNF250	58500	hgsc.bcm.edu	37	8	146112247	146112249	+	In_Frame_Del	DEL	TTG	TTG	-	rs138214845	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:146112247_146112249delTTG	ENST00000292579.7	-	5	453_455	c.337_339delCAA	c.(337-339)caadel	p.Q113del	ZNF250_ENST00000543949.1_In_Frame_Del_p.Q113del|ZNF250_ENST00000417550.2_In_Frame_Del_p.Q108del|ZNF250_ENST00000342660.6_In_Frame_Del_p.Q108del	NM_001109689.3|NM_021061.4	NP_001103159.1|NP_066405.1	P15622	ZN250_HUMAN	zinc finger protein 250	113					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(4)|kidney(2)|lung(8)|skin(1)	15	all_cancers(97;8.72e-12)|all_epithelial(106;1.07e-10)|Lung NSC(106;7.18e-05)|all_lung(105;0.00021)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;2.53e-38)|OV - Ovarian serous cystadenocarcinoma(54;4.07e-38)|all cancers(56;2.27e-33)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;0.0654)		ATAAACTGTCTTGTTGTGTACAG	0.379														44	0.00878594	0.0333	0.0	5008	,	,		19534	0.0		0.0	False		,,,				2504	0.0				p.113_114del	NSCLC(16;520 556 24096 40084 43446)	Pindel,Atlas-Indel	.											.	ZNF250	37	.	0			c.338_340del						PASS	.		,	100,4164		1,98,2033					,	3.5	0.9		dbSNP_134	182	5,8249		0,5,4122	no	coding,coding	ZNF250	NM_021061.4,NM_001109689.3	,	1,103,6155	A1A1,A1R,RR		0.0606,2.3452,0.8388	,	,		105,12413				SO:0001651	inframe_deletion	58500	exon5			.	AK095705	CCDS34972.1, CCDS55282.1	8q24.3	2013-01-08	2004-11-08			ENSG00000196150		"""Zinc fingers, C2H2-type"", ""-"""	13044	protein-coding gene	gene with protein product			"""zinc finger protein 647"""	ZNF647		12477932	Standard	NM_021061		Approved	MGC9718, ZFP647	uc003zer.4	P15622		ENST00000292579.7:c.337_339delCAA	8.37:g.146112250_146112252delTTG	ENSP00000292579:p.Gln113del	Somatic	155	.	.		WXS	Illumina HiSeq	Phase_I	173	57	0.329	NM_021061	D3DWP1|Q59HE9|Q8N942|Q96AH9	In_Frame_Del	DEL	ENST00000292579.7	37	CCDS34972.1																																																																																			TTG|0.994;-|0.006	0.006	strong		0.379	ZNF250-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382968.1	NM_021061	
SLC7A7	9056	hgsc.bcm.edu	37	14	23240713	23240714	+	IGR	INS	-	-	AGC	rs397761468|rs57267429|rs148216086|rs200470407|rs36078271	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:23240713_23240714insAGC	ENST00000397532.3	-	0	2447				OXA1L_ENST00000412791.1_In_Frame_Ins_p.392_392S>SS|SLC7A7_ENST00000554061.1_5'Flank|OXA1L_ENST00000285848.5_In_Frame_Ins_p.479_479S>SS|OXA1L_ENST00000358043.5_In_Frame_Ins_p.403_403S>SS|OXA1L_ENST00000604262.1_In_Frame_Ins_p.419_419S>SS			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7						amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		CCAATATCCCTAGCAGCAGCAG	0.48														1057	0.211062	0.1596	0.2133	5008	,	,		22040	0.1458		0.2396	False		,,,				2504	0.317				p.P478delinsPS		Pindel,Atlas-Indel	.											.	OXA1L	49	.	0			c.1434_1435insAGC						PASS	.			857,3407		86,685,1361						-4.3	0.0		dbSNP_130	182	2307,5947		310,1687,2130	no	coding	OXA1L	NM_005015.3		396,2372,3491	A1A1,A1R,RR		27.9501,20.0985,25.2756				3164,9354				SO:0001628	intergenic_variant	5018	exon10			.	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"""Solute carriers"""	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692		14.37:g.23240720_23240722dupAGC		Somatic	103	.	.		WXS	Illumina HiSeq	Phase_I	110	31	0.282	NM_005015	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	In_Frame_Ins	INS	ENST00000397532.3	37	CCDS9574.1																																																																																			-|0.809;AGC|0.191	0.191	strong		0.480	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3		
CYP2D6	1565	hgsc.bcm.edu	37	22	42524176	42524178	+	Splice_Site	DEL	CTT	CTT	-	rs28371720|rs587777919|rs5030656	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:42524176_42524178delCTT	ENST00000360608.5	-	5	955_957	c.841_843delAAG	c.(841-843)aagdel	p.K281del	NDUFA6-AS1_ENST00000417327.1_RNA|CYP2D6_ENST00000389970.3_Splice_Site_p.K281del|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Splice_Site_p.K230del|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	281			Missing (in allele CYP2D6*9). {ECO:0000269|PubMed:1844820}.		alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CCACTCTCACCTTCTCCATCTCT	0.64														36	0.0071885	0.0008	0.013	5008	,	,		19102	0.0		0.0258	False		,,,				2504	0.0				p.281_281del		Pindel,Atlas-Indel	.											.	CYP2D6	104	.	0			c.842_843del	GRCh37	CD033535	CYP2D6	D	rs5030656	PASS	.		,	25,4223		2,21,2101					,	4.0	1.0		dbSNP_113	19	223,8021		12,199,3911	no	coding-near-splice,coding-near-splice	CYP2D6	NM_001025161.1,NM_000106.4	,	14,220,6012	A1A1,A1R,RR		2.705,0.5885,1.9853	,	,		248,12244				SO:0001630	splice_region_variant	1565	exon5			.	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.843+1AAG>-	22.37:g.42524176_42524178delCTT		Somatic	153	.	.		WXS	Illumina HiSeq	Phase_I	163	40	0.245	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Frame_Shift_Del	DEL	ENST00000360608.5	37	CCDS46721.1																																																																																			CTT|0.989;-|0.011	0.011	strong		0.640	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		In_Frame_Del
PRSS16	10279	hgsc.bcm.edu	37	6	27223065	27223079	+	In_Frame_Del	DEL	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	-	rs199705677|rs201493618|rs144604424|rs140280737|rs371606222|rs147170589|rs143492910|rs200987021|rs141138864|rs142712601	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAGGAGAGCCAGATT	AAGGAGAGCCAGATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27223065_27223079delAAGGAGAGCCAGATT	ENST00000230582.3	+	12	1531_1545	c.1516_1530delAAGGAGAGCCAGATT	c.(1516-1530)aaggagagccagattdel	p.KESQI506del	PRSS16_ENST00000377456.2_3'UTR|PRSS16_ENST00000421826.2_In_Frame_Del_p.KESQI249del	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	506					protein catabolic process (GO:0030163)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|lysosome (GO:0005764)	serine-type peptidase activity (GO:0008236)	p.K506_I510delKESQI(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CAAGCTGGCAAAGGAGAGCCAGATTAAGGGTGAAG	0.479														511	0.102037	0.1135	0.1124	5008	,	,		20927	0.0139		0.174	False		,,,				2504	0.0961				p.505_510del	NSCLC(178;1118 2105 17078 23587 44429)	Pindel,Atlas-Indel	.											.	PRSS16	66	.	1	Deletion - In frame(1)	ovary(1)	c.1515_1529del						PASS	.			514,3748		27,460,1644						-5.7	0.0		dbSNP_113	73	1519,6735		166,1187,2774	no	coding	PRSS16	NM_005865.3		193,1647,4418	A1A1,A1R,RR		18.4032,12.0601,16.2432				2033,10483				SO:0001651	inframe_deletion	10279	exon12			.	AF052514	CCDS4623.1	6p21	2010-05-07			ENSG00000112812	ENSG00000112812		"""Serine peptidases / Serine peptidases"""	9480	protein-coding gene	gene with protein product		607169				10527559	Standard	NM_005865		Approved	TSSP	uc003nja.3	Q9NQE7	OTTHUMG00000016167	ENST00000230582.3:c.1516_1530delAAGGAGAGCCAGATT	6.37:g.27223065_27223079delAAGGAGAGCCAGATT	ENSP00000230582:p.Lys506_Ile510del	Somatic	119	.	.		WXS	Illumina HiSeq	Phase_I	52	30	0.577	NM_005865	O75416	In_Frame_Del	DEL	ENST00000230582.3	37	CCDS4623.1																																																																																			AAGGAGAGCCAGATT|0.883;-|0.117	0.117	strong		0.479	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2		
ITGB5	3693	hgsc.bcm.edu	37	3	124482495	124482503	+	In_Frame_Del	DEL	TTGTTGAAC	TTGTTGAAC	-	rs144662766|rs150512726|rs149489624|rs140998759|rs547715576	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTGTTGAAC	TTGTTGAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:124482495_124482503delTTGTTGAAC	ENST00000296181.4	-	15	2663_2671	c.2367_2375delGTTCAACAA	c.(2365-2376)aagttcaacaaa>aaa	p.789_792KFNK>K	ITGB5_ENST00000461306.1_5'Flank	NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	789				Missing (in Ref. 2; AAA52707). {ECO:0000305}.	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-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		ATTGTAGGATTTGTTGAACTTGTTGAAGG	0.512														437	0.0872604	0.0053	0.0821	5008	,	,		26574	0.0486		0.1282	False		,,,				2504	0.1994				p.790_792del		Pindel,Atlas-Indel	.											.	ITGB5	66	.	0			c.2368_2376del						PASS	.			191,4075		46,99,1988						-3.5	1.0		dbSNP_129	167	1165,7089		151,863,3113	no	coding	ITGB5	NM_002213.3		197,962,5101	A1A1,A1R,RR		14.1144,4.4773,10.8307				1356,11164				SO:0001651	inframe_deletion	3693	exon15			.	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"""Integrins"""	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.2367_2375delGTTCAACAA	3.37:g.124482495_124482503delTTGTTGAAC	ENSP00000296181:p.Lys789_Asn791del	Somatic	159	.	.		WXS	Illumina HiSeq	Phase_I	101	62	0.614	NM_002213	B0LPF8|B2RD70	In_Frame_Del	DEL	ENST00000296181.4	37	CCDS3030.1																																																																																			TTGTTGAAC|0.922;-|0.078	0.078	strong		0.512	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	
PTPRQ	374462	hgsc.bcm.edu	37	12	80943506	80943523	+	Splice_Site	DEL	TGAAACAGGTAACTAACG	TGAAACAGGTAACTAACG	-	rs141686707|rs190917077	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGAAACAGGTAACTAACG	TGAAACAGGTAACTAACG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:80943506_80943523delTGAAACAGGTAACTAACG	ENST00000266688.5	+	30	4266_4273	c.4266_4273delTGAAACAGGTAACTAACG	c.(4264-4275)cctgaaacaggt>ccgt	p.ETG1423del				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	1469	Fibronectin type-III 15. {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						GCACACTACCTGAAACAGGTAACTAACGTGAAACAGGT	0.381																																					p.1254_1257del		Pindel,Atlas-Indel	.											.	PTPRQ	119	.	0			c.3761_3769del						PASS	.			21,2253		2,17,1118						3.6	1.0		dbSNP_134	53	261,3959		31,199,1880	no	coding-near-splice	PTPRQ	NM_001145026.1		33,216,2998	A1A1,A1R,RR		6.1848,0.9235,4.3425				282,6212				SO:0001630	splice_region_variant	374462	exon22			.	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.4273+1TGAAACAGGTAACTAACG>-	12.37:g.80943506_80943523delTGAAACAGGTAACTAACG		Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	85	28	0.329	NM_001145026		In_Frame_Del	DEL	ENST00000266688.5	37																																																																																				.	.	strong		0.381	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	In_Frame_Del
METTL21A	151194	hgsc.bcm.edu	37	2	208477923	208477924	+	Frame_Shift_Del	DEL	CA	CA	-	rs548492945		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:208477923_208477924delCA	ENST00000411432.1	-	4	719_720	c.503_504delTG	c.(502-504)gtgfs	p.V168fs	METTL21A_ENST00000448007.2_Frame_Shift_Del_p.V168fs|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000272839.3_Frame_Shift_Del_p.V186fs|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000406927.2_Frame_Shift_Del_p.V168fs|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000426075.1_Frame_Shift_Del_p.V168fs|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000442521.1_Frame_Shift_Del_p.V168fs|METTL21A_ENST00000432416.1_Intron	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	168					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						CTAAAAGAATCACAGAGTGATT	0.396																																					p.168_169del		Pindel,Atlas-Indel	.											.	METTL21A	24	.	0			c.504_505del						PASS	.		,	0,4266		0,0,2133					,	4.2	1.0			146	4,8250		0,4,4123	no	frameshift,frameshift	METTL21A	NM_145280.4,NM_001127395.1	,	0,4,6256	A1A1,A1R,RR		0.0485,0.0,0.0319	,	,		4,12516				SO:0001589	frameshift_variant	151194	exon4			.	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 557b"", ""heat shock protein 70kDa lysine (K) methyltransferase"""	615257	"""family with sequence similarity 119, member A"""	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.503_504delTG	2.37:g.208477925_208477926delCA	ENSP00000415115:p.Val168fs	Somatic	128	.	.		WXS	Illumina HiSeq	Phase_I	103	22	0.214	NM_001127395	Q53RV0|Q8N1Z9|Q96GH6	Frame_Shift_Del	DEL	ENST00000411432.1	37	CCDS2376.1																																																																																			.	.	none		0.396	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280	
DMKN	93099	hgsc.bcm.edu	37	19	36002419	36002421	+	In_Frame_Del	DEL	CCA	CCA	-	rs72334573	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36002419_36002421delCCA	ENST00000339686.3	-	5	986_988	c.810_812delTGG	c.(808-813)ggtggc>ggc	p.270_271GG>G	DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000424570.2_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000440396.1_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000451297.2_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000418261.1_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000462126.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	270	Gly-rich.			Missing (in Ref. 3; ABN11273/ABN11274). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			actgctgctgccaccactgctgc	0.655														1022	0.204073	0.2405	0.1369	5008	,	,		13814	0.3403		0.172	False		,,,				2504	0.0951				p.271_271del		Atlas-Indel	.											DMKN,colon,carcinoma,-2,1	DMKN	116	1	0			c.811_813del						PASS	.		,,,,,,	945,3305		85,775,1265					,,,,,,	-1.4	0.0		dbSNP_132	28	1553,6687		146,1261,2713	no	coding,coding,coding,intron,coding,coding,intron	DMKN	NM_033317.4,NM_001190349.1,NM_001190348.1,NM_001190347.1,NM_001126058.2,NM_001126057.2,NM_001126056.2	,,,,,,	231,2036,3978	A1A1,A1R,RR		18.8471,22.2353,20.0	,,,,,,	,,,,,,		2498,9992				SO:0001651	inframe_deletion	93099	exon5			.	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.810_812delTGG	19.37:g.36002422_36002424delCCA	ENSP00000342012:p.Gly271del	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	50	16	0.32	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			CCA|0.786;-|0.214	0.214	strong		0.655	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75816814	75816815	+	Intron	INS	-	-	ACA	rs199738162|rs397750292|rs144850646|rs59277111	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:75816814_75816815insACA	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000320460.4_In_Frame_Ins_p.239_240insN|GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000378692.3_Intron|GLIPR1L2_ENST00000441218.1_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						TAATGGATTGGACAAGAAAAAT	0.312														1714	0.342252	0.2511	0.2622	5008	,	,		17045	0.4683		0.3767	False		,,,				2504	0.3569				p.D239delinsDN		Pindel,Atlas-Indel	.											.	GLIPR1L2	54	.	0			c.715_716insACA						PASS	.			1181,3083		163,855,1114						0.0	0.0		dbSNP_130	117	3246,5006		650,1946,1530	no	coding	GLIPR1L2	NM_152436.1		813,2801,2644	A1A1,A1R,RR		39.3359,27.697,35.3707				4427,8089				SO:0001627	intron_variant	144321	exon4			.	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+45->ACA	12.37:g.75816815_75816817dupACA		Somatic	58	.	.		WXS	Illumina HiSeq	Phase_I	48	20	0.417	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	In_Frame_Ins	INS	ENST00000550916.1	37	CCDS58258.1																																																																																			.	.	strong		0.312	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
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 GAIIx	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_ENST00000475231.1_Frame_Shift_Ins_p.S4229fs|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	68	10	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	
CPNE2	221184	hgsc.bcm.edu	37	16	57153565	57153565	+	Intron	DEL	G	G	-	rs200482251|rs529228251	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57153565delG	ENST00000535318.2	+	8	1042				CPNE2_ENST00000565874.1_Intron|CPNE2_ENST00000290776.8_Intron|CPNE2_ENST00000537605.1_Intron			Q96FN4	CPNE2_HUMAN	copine II							extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				CCATCCAGGTGAGGGGGCTCT	0.587													G|G|-|deletion	14	0.00279553	0.0	0.0043	5008	,	,		20331	0.0		0.008	False		,,,				2504	0.0031				.		Atlas-Indel	.											.	CPNE2	48	.	0			c.681+2G>-						PASS	.			12,4252		0,12,2120	52.0	45.0	48.0			4.6	1.0	16		49	114,8140		0,114,4013	no	intron	CPNE2	NM_152727.5		0,126,6133	A1A1,A1R,RR		1.3811,0.2814,1.0066			57153565	126,12392	2198	4300	6498	SO:0001627	intron_variant	221184	exon7			.		CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.681+3G>-	16.37:g.57153565delG		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	28	0.325581	NM_152727	Q68D19|Q719H8|Q86XP9	Splice_Site	DEL	ENST00000535318.2	37	CCDS10774.1																																																																																			.	.	none		0.587	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727	
GATAD2A	54815	hgsc.bcm.edu	37	19	19612012	19612014	+	In_Frame_Del	DEL	GGA	GGA	-	rs372055939	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:19612012_19612014delGGA	ENST00000360315.3	+	9	1599_1601	c.1287_1289delGGA	c.(1285-1290)cgggag>cgg	p.E431del	GATAD2A_ENST00000537887.1_In_Frame_Del_p.E60del|GATAD2A_ENST00000429563.2_In_Frame_Del_p.E259del|GATAD2A_ENST00000252577.5_In_Frame_Del_p.E431del|GATAD2A_ENST00000358713.3_In_Frame_Del_p.E431del|GATAD2A_ENST00000404158.1_In_Frame_Del_p.E432del	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	431	CR2; histone tail-binding.				anterior neuropore closure (GO:0021506)|blood vessel development (GO:0001568)|DNA methylation (GO:0006306)|embryonic body morphogenesis (GO:0010172)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|neural fold formation (GO:0001842)|programmed cell death (GO:0012501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|NuRD complex (GO:0016581)	protein binding, bridging (GO:0030674)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	13						GCCGCTGGCGGGAGGAGAAGAGC	0.621														4	0.000798722	0.0	0.0014	5008	,	,		19532	0.0		0.003	False		,,,				2504	0.0				p.429_430del		Pindel,Atlas-Indel	.											.	GATAD2A	81	.	0			c.1286_1288del						PASS	.			5,4259		2,1,2129						4.7	1.0			44	11,8241		2,7,4117	no	coding	GATAD2A	NM_017660.3		4,8,6246	A1A1,A1R,RR		0.1333,0.1173,0.1278				16,12500				SO:0001651	inframe_deletion	54815	exon9			.	AL390164	CCDS12402.2	19p13.11	2013-01-25			ENSG00000167491	ENSG00000167491		"""GATA zinc finger domain containing"""	29989	protein-coding gene	gene with protein product	"""p66 alpha"""	614997				12183469	Standard	NM_017660		Approved	p66alpha	uc010xqt.2	Q86YP4	OTTHUMG00000152541	ENST00000360315.3:c.1287_1289delGGA	19.37:g.19612015_19612017delGGA	ENSP00000353463:p.Glu431del	Somatic	146	.	.		WXS	Illumina HiSeq	Phase_I	120	30	0.250	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	In_Frame_Del	DEL	ENST00000360315.3	37	CCDS12402.2																																																																																			.	.	weak		0.621	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660	
EIF4EBP3	8637	hgsc.bcm.edu	37	5	139931628	139931629	+	IGR	INS	-	-	GT	rs5871740|rs3085220|rs368142622|rs202193903	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139931628_139931629insGT	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Frame_Shift_Ins_p.V110fs	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATCCTCCATCACAGCCTCAGAC	0.589														2174	0.434105	0.2194	0.5144	5008	,	,		18017	0.5645		0.4831	False		,,,				2504	0.4826				p.V110fs		Atlas-Indel	.											SRA1,NS,carcinoma,0,2	SRA1	24	2	0			c.329_330insAC						PASS	.																																			SO:0001628	intergenic_variant	10011	exon3			.	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931628_139931629insGT		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	109	31	0.284404	NM_001035235		Frame_Shift_Ins	INS	ENST00000310331.2	37	CCDS4226.1																																																																																			.	.	strong		0.589	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732	
TSPYL1	7259	hgsc.bcm.edu	37	6	116600465	116600466	+	In_Frame_Ins	INS	-	-	CAC	rs76746450|rs397735194|rs78371471|rs56100880	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:116600465_116600466insCAC	ENST00000368608.3	-	1	600_601	c.528_529insGTG	c.(526-531)gtgaag>gtgGTGaag	p.176_177insV	RP1-93H18.1_ENST00000449314.1_lincRNA|DSE_ENST00000540275.1_Intron|DSE_ENST00000452085.3_5'Flank	NM_003309.3	NP_003300.1	Q9H0U9	TSYL1_HUMAN	TSPY-like 1	176					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.V176_K177insV(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(3)|urinary_tract(1)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.0235)|OV - Ovarian serous cystadenocarcinoma(136;0.0469)|GBM - Glioblastoma multiforme(226;0.0503)|Epithelial(106;0.094)		aggccttccttcaccacctcAG	0.614														4368	0.872204	0.9592	0.7839	5008	,	,		18686	0.9772		0.6521	False		,,,				2504	0.9356				p.K177delinsVK		Pindel,Atlas-Indel	.											.	TSPYL1	28	.	1	Insertion - In frame(1)	ovary(1)	c.529_530insGTG						PASS	.			3880,384		1772,336,24						-8.3	0.0		dbSNP_131	62	5244,3010		1653,1938,536	no	coding	TSPYL1	NM_003309.3		3425,2274,560	A1A1,A1R,RR		36.4672,9.0056,27.113				9124,3394				SO:0001652	inframe_insertion	7259	exon1			.	AF042181	CCDS34518.1	6q22.1	2014-09-17	2004-04-05	2004-04-07	ENSG00000189241	ENSG00000189241			12382	protein-coding gene	gene with protein product		604714	"""TSPY-like"""	TSPYL		9730615	Standard	NM_003309		Approved		uc003pwp.4	Q9H0U9	OTTHUMG00000015427	ENST00000368608.3:c.526_528dupGTG	6.37:g.116600469_116600471dupCAC	ENSP00000357597:p.Val176_Val176dup	Somatic	31	.	.		WXS	Illumina HiSeq	Phase_I	29	16	0.552	NM_003309	O75885|Q5TFE6	In_Frame_Ins	INS	ENST00000368608.3	37	CCDS34518.1																																																																																			.	.	strong		0.614	TSPYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041929.1		
DHDH	27294	hgsc.bcm.edu	37	19	49442849	49442850	+	Frame_Shift_Ins	INS	-	-	G	rs3830420|rs397960489|rs78637763	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49442849_49442850insG	ENST00000221403.2	+	4	550_551	c.510_511insG	c.(511-513)gggfs	p.G171fs	DHDH_ENST00000523250.1_Intron|DHDH_ENST00000522614.1_Frame_Shift_Ins_p.G171fs	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	171					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		GGGCCCAGGCTGGGGGGGCCCT	0.604													GGGGGGG|GGGGGGG|GGGGGGGG|insertion	1276	0.254792	0.0575	0.232	5008	,	,		18577	0.5417		0.1759	False		,,,				2504	0.3231				p.A170fs		Pindel,Atlas-Indel	.											.	DHDH	35	.	0			c.510_511insG						PASS	.																																			SO:0001589	frameshift_variant	27294	exon4			.	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.517dupG	19.37:g.49442856_49442856dupG	ENSP00000221403:p.Gly171fs	Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	56	19	0.339	NM_014475		Frame_Shift_Ins	INS	ENST00000221403.2	37	CCDS12741.1																																																																																			-|0.754;G|0.246	0.246	strong		0.604	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
AAK1	22848	hgsc.bcm.edu	37	2	69741754	69741756	+	In_Frame_Del	DEL	TGT	TGT	-	rs66931661|rs3832159|rs55712143	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:69741754_69741756delTGT	ENST00000409085.4	-	13	1999_2001	c.1623_1625delACA	c.(1621-1626)caacag>cag	p.541_542QQ>Q	AAK1_ENST00000406297.3_In_Frame_Del_p.541_542QQ>Q|AAK1_ENST00000409068.1_In_Frame_Del_p.541_542QQ>Q|RN7SL604P_ENST00000492589.2_RNA	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	541	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						ttgctgttgctgttgttgttgct	0.547														1782	0.355831	0.1755	0.4755	5008	,	,		19080	0.5129		0.3897	False		,,,				2504	0.318				p.542_542del		Atlas-Indel	.											.	AAK1	121	.	0			c.1624_1626del						PASS	.			952,3280		126,700,1290						3.2	1.0		dbSNP_107	34	3317,4915		696,1925,1495	no	coding	AAK1	NM_014911.3		822,2625,2785	A1A1,A1R,RR		40.294,22.4953,34.2506				4269,8195				SO:0001651	inframe_deletion	22848	exon13			.	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1623_1625delACA	2.37:g.69741760_69741762delTGT	ENSP00000386456:p.Gln546del	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	57	12	0.210526	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	In_Frame_Del	DEL	ENST00000409085.4	37	CCDS1893.2																																																																																			TGT|0.607;-|0.393	0.393	strong		0.547	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
OR52B4	143496	hgsc.bcm.edu	37	11	4389405	4389405	+	Frame_Shift_Del	DEL	G	G	-	rs398075683|rs397699893|rs201331071|rs11310407	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:4389405delG	ENST00000408920.2	-	1	211	c.121delC	c.(121-123)cttfs	p.L42fs		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	42					cognition (GO:0050890)	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(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTCCCAAGAAGGGCGGTGACA	0.522													GGG|GGG|GG|deletion	1601	0.319688	0.1422	0.4193	5008	,	,		24468	0.4157		0.3499	False		,,,				2504	0.3589				p.L41fs		Pindel,Atlas-Indel	.											.	OR52B4	56	.	0			c.122delT	GRCh37	CD035871	OR52B4	D	rs80193749	PASS	.			717,3355		101,515,1420	55.0	47.0	50.0			4.9	0.0	11	dbSNP_131	68	2865,5269		532,1801,1734	no	frameshift	OR52B4	NM_001005161.3		633,2316,3154	A1A1,A1R,RR		35.2225,17.6081,29.3462			4389405	3582,8624	2066	4141	6207	SO:0001589	frameshift_variant	143496	exon1			.	AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"""GPCR / Class A : Olfactory receptors"""	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.121delC	11.37:g.4389405delG	ENSP00000386160:p.Leu42fs	Somatic	94	.	.		WXS	Illumina HiSeq	Phase_I	95	24	0.253	NM_001005161	A6NP68|Q6IFK6	Frame_Shift_Del	DEL	ENST00000408920.2	37	CCDS41609.1																																																																																			G|0.671;-|0.329	0.329	strong		0.522	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161	
C14orf23	387978	hgsc.bcm.edu	37	14	29261305	29261305	+	Frame_Shift_Del	DEL	A	A	-	rs202195469|rs200251419		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:29261305delA	ENST00000399387.4	+	3	446	c.342delA	c.(340-342)ctafs	p.L114fs	C14orf23_ENST00000550266.1_Intron|C14orf23_ENST00000548213.1_Intron					chromosome 14 open reading frame 23											central_nervous_system(1)	1						CTTCAGCACTAAAAAAAACAA	0.378																																					.		Atlas-Indel	.											.	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	ENST00000399387.4:c.342delA	14.37:g.29261305delA	ENSP00000382318:p.Leu114fs	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	15	0.227273	.		RNA	DEL	ENST00000399387.4	37																																																																																				A|0.648;-|0.352	0.352	strong		0.378	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000134019.2	NR_026731	
TBCK	93627	hgsc.bcm.edu	37	4	107171638	107171642	+	Intron	DEL	AAATA	AAATA	-	rs139991421	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAATA	AAATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:107171638_107171642delAAATA	ENST00000273980.5	-	8	1045				TBCK_ENST00000394708.2_Intron|TBCK_ENST00000361687.4_Intron|TBCK_ENST00000432496.2_Intron|TBCK_ENST00000394706.3_Intron					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TTTCTTCCCTAAATAAAATGAGAAA	0.273														684	0.136581	0.0076	0.1167	5008	,	,		15823	0.1468		0.1789	False		,,,				2504	0.271				.		Pindel,Atlas-Indel	.											.	TBCK	89	.	0			.						PASS	.		,,,	130,3952		3,124,1914					,,,	5.8	1.0		dbSNP_106	22	1346,6704		147,1052,2826	no	intron,intron,intron,intron	TBCK	NM_033115.3,NM_001163437.1,NM_001163436.1,NM_001163435.1	,,,	150,1176,4740	A1A1,A1R,RR		16.7205,3.1847,12.1662	,,,	,,,		1476,10656				SO:0001627	intron_variant	93627	.			.		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.598-3TATTT>-	4.37:g.107171638_107171642delAAATA		Somatic	68	.	.		WXS	Illumina HiSeq	Phase_I	60	22	0.367	.		Splice_Site	DEL	ENST00000273980.5	37	CCDS54788.1																																																																																			AAATA|0.864;-|0.136	0.136	strong		0.273	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
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 GAIIx	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	Somatic	41	.	.		WXS	Illumina HiSeq	Phase_I	38	13	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	
GPSM1	26086	hgsc.bcm.edu	37	9	139235482	139235482	+	Intron	DEL	C	C	-	rs374298038|rs145729152	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139235482delC	ENST00000440944.1	+	9	1427				GPSM1_ENST00000392945.3_Frame_Shift_Del_p.L413fs	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GGGTCTTGCTCCCCACAGGCA	0.687													?|CCCC|CCC|unsure	747	0.149161	0.0961	0.0793	5008	,	,		14952	0.252		0.1372	False		,,,				2504	0.1769				p.L413fs		Pindel,Atlas-Indel	.											.	GPSM1	50	.	0			c.1238delT						PASS	.		,	494,3628		54,386,1621	12.0	14.0	14.0		,	0.3	0.0	9	dbSNP_134	15	1203,6943		136,931,3006	no	frameshift,intron	GPSM1	NM_015597.4,NM_001145638.1	,	190,1317,4627	A1A1,A1R,RR		14.768,11.9845,13.8327	,	,	139235482	1697,10571	2116	4195	6311	SO:0001627	intron_variant	26086	exon9			.	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1207+32C>-	9.37:g.139235482delC		Somatic	70	.	.		WXS	Illumina HiSeq	Phase_I	67	43	0.642	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Frame_Shift_Del	DEL	ENST00000440944.1	37	CCDS48055.1																																																																																			C|0.857;-|0.143	0.143	strong		0.687	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597	
CHEK1	1111	hgsc.bcm.edu	37	11	125505377	125505378	+	Frame_Shift_Ins	INS	-	-	A	rs35817404		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:125505377_125505378insA	ENST00000534070.1	+	7	922_923	c.667_668insA	c.(667-669)gaafs	p.E223fs	CHEK1_ENST00000427383.2_Frame_Shift_Ins_p.E239fs|CHEK1_ENST00000278916.3_Frame_Shift_Ins_p.E223fs|CHEK1_ENST00000532449.1_3'UTR|CHEK1_ENST00000428830.2_Frame_Shift_Ins_p.E223fs|CHEK1_ENST00000438015.1_Frame_Shift_Ins_p.E223fs|CHEK1_ENST00000544373.1_Frame_Shift_Ins_p.E223fs|CHEK1_ENST00000524737.1_Frame_Shift_Ins_p.E223fs	NM_001274.5	NP_001265.2	O14757	CHK1_HUMAN	checkpoint kinase 1	223	Interaction with CLSPN. {ECO:0000250}.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> V (in dbSNP:rs35817404). {ECO:0000269|PubMed:17344846}.		cellular response to caffeine (GO:0071313)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to mechanical stimulus (GO:0071260)|chromatin-mediated maintenance of transcription (GO:0048096)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of mitosis (GO:0045839)|peptidyl-threonine phosphorylation (GO:0018107)|regulation of cell proliferation (GO:0042127)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of histone H3-K9 acetylation (GO:2000615)|regulation of mitotic centrosome separation (GO:0046602)|regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010767)|replicative senescence (GO:0090399)	centrosome (GO:0005813)|chromatin (GO:0000785)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	ATP binding (GO:0005524)|histone kinase activity (H3-T11 specific) (GO:0035402)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(3)|endometrium(3)|large_intestine(2)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	26	all_hematologic(175;0.228)	Breast(109;0.0021)|Lung NSC(97;0.0126)|all_lung(97;0.0132)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0748)		TGACTGGAAAGAAAAAAAAACA	0.361								Other conserved DNA damage response genes																													p.E223fs		Atlas-Indel	.											CHEK1,colon,carcinoma,-1,1	CHEK1	44	1	0			c.667_668insA						PASS	.																																			SO:0001589	frameshift_variant	1111	exon7			.	AF016582, BC017575	CCDS8459.1, CCDS58191.1	11q24.2	2011-11-11	2011-11-11		ENSG00000149554	ENSG00000149554			1925	protein-coding gene	gene with protein product		603078	"""CHK1 (checkpoint, S.pombe) homolog"", ""CHK1 checkpoint homolog (S. pombe)"""			9278511, 9382850	Standard	NM_001114121		Approved	CHK1	uc001qcg.4	O14757	OTTHUMG00000165853	ENST00000534070.1:c.676dupA	11.37:g.125505386_125505386dupA	ENSP00000435371:p.Glu223fs	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	87	10	0.114943	NM_001114122	A8K934|B4DDD0|B4DSK3|B5BTY6|F5H7S4|H2BI51	Frame_Shift_Ins	INS	ENST00000534070.1	37	CCDS8459.1																																																																																			.	.	none		0.361	CHEK1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386714.1	NM_001274	
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 GAIIx	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	Somatic	152	.	.		WXS	Illumina HiSeq	Phase_I	179	56	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	
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511804	99511805	+	Frame_Shift_Ins	INS	-	-	C	rs398043625|rs5814919	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:99511804_99511805insC	ENST00000378919.6	-	5	698_699	c.493_494insG	c.(493-495)gtcfs	p.V165fs	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_Frame_Shift_Ins_p.V111fs	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	165							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						CTGGATGATGACTCTCAAGGCT	0.574													C|C|CC|insertion	2217	0.442692	0.1558	0.4914	5008	,	,		17754	0.4841		0.5716	False		,,,				2504	0.6207				p.V165fs		Pindel,Atlas-Indel	.											.	PGPEP1L	26	.	0			c.494_495insG						PASS	.		,	816,2946		112,592,1177					,	1.6	0.2		dbSNP_114	44	4130,3796		1081,1968,914	no	frameshift,frameshift	PGPEP1L	NM_001167902.1,NM_001102612.2	,	1193,2560,2091	A1A1,A1R,RR		47.893,21.6906,42.3169	,	,		4946,6742				SO:0001589	frameshift_variant	145814	exon5			.		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.494dupG	15.37:g.99511805_99511805dupC	ENSP00000368199:p.Val165fs	Somatic	117	.	.		WXS	Illumina HiSeq	Phase_I	120	37	0.308	NM_001102612	H0YF86	Frame_Shift_Ins	INS	ENST00000378919.6	37	CCDS53977.1																																																																																			-|0.556;C|0.444	0.444	strong		0.574	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
PIEZO1	9780	hgsc.bcm.edu	37	16	88780635	88780636	+	IGR	INS	-	-	GTGT	rs397761749|rs149847195|rs571090098|rs562672342|rs11278302	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88780635_88780636insGTGT	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Splice_Site_p.R366fs|CTU2_ENST00000567949.1_Splice_Site_p.R437fs|CTU2_ENST00000378384.3_Splice_Site_p.R279fs|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Splice_Site_p.R366fs	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						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						ACtgtgtacaggtgtgggtgtg	0.644																																					p.R366fs		Pindel,Atlas-Indel	.											.	CTU2	66	.	0			c.1097_1098insGTGT						PASS	.																																			SO:0001628	intergenic_variant	348180	exon10			.	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		16.37:g.88780636_88780639dupGTGT		Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	59	14	0.237	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Frame_Shift_Ins	INS	ENST00000301015.9	37	CCDS54058.1																																																																																			.	.	weak		0.644	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
NINL	22981	hgsc.bcm.edu	37	20	25457050	25457055	+	In_Frame_Del	DEL	CTCCCA	CTCCCA	-	rs68078266|rs146288604|rs200097181|rs34410422|rs201074890	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTCCCA	CTCCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:25457050_25457055delCTCCCA	ENST00000278886.6	-	17	2945_2950	c.2872_2877delTGGGAG	c.(2872-2877)tgggagdel	p.WE958del	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	958				Missing (in Ref. 4; AAH36380). {ECO:0000305}.	G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						TCAGGGGTGGCTCCCACATCCGTGGC	0.689														2791	0.557308	0.5356	0.3559	5008	,	,		14584	0.9067		0.4304	False		,,,				2504	0.5				p.958_960del		Atlas-Indel	.											.	NINL	148	.	0			c.2873_2878del						PASS	.			1921,2191		513,895,648						0.3	0.0		dbSNP_130	17	3184,4816		750,1684,1566	no	coding	NINL	NM_025176.4		1263,2579,2214	A1A1,A1R,RR		39.8,46.7169,42.1483				5105,7007				SO:0001651	inframe_deletion	22981	exon17			.		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.2872_2877delTGGGAG	20.37:g.25457050_25457055delCTCCCA	ENSP00000278886:p.Trp958_Glu959del	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	54	15	0.277778	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	In_Frame_Del	DEL	ENST00000278886.6	37	CCDS33452.1																																																																																			CTCCCA|0.450;-|0.550	0.550	strong		0.689	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
BDNF	627	hgsc.bcm.edu	37	11	27681176	27681177	+	5'UTR	INS	-	-	TG	rs149254890|rs397725548|rs28722151	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:27681176_27681177insTG	ENST00000525528.1	-	0	28_29				BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000584049.1_Intron|BDNF_ENST00000420794.1_Intron|BDNF-AS_ENST00000532965.1_RNA|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000530861.1_Intron|BDNF_ENST00000532997.1_Intron|BDNF-AS_ENST00000499568.2_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000395983.3_Intron|BDNF_ENST00000533246.1_Intron|BDNF_ENST00000439476.2_5'UTR|BDNF_ENST00000395980.2_Intron|BDNF_ENST00000314915.6_Intron|BDNF_ENST00000438929.1_Intron|BDNF_ENST00000525950.1_Intron|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000356660.4_Intron|BDNF_ENST00000533131.1_Intron|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000395986.2_Intron|BDNF_ENST00000418212.1_Intron|BDNF_ENST00000395981.3_Intron|BDNF_ENST00000395978.3_Intron	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor						axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						GATGTTCTCTCtgtgtgtgtgt	0.446																																					.		Atlas-Indel	.											.	BDNF	63	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	627	.			.	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"""Endogenous ligands"""	1033	protein-coding gene	gene with protein product	"""neurotrophin"""	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.-1066->CA	11.37:g.27681185_27681186dupTG		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	147	68	0.462585	.	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	RNA	INS	ENST00000525528.1	37	CCDS7866.1																																																																																			.	.	strong		0.446	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
CNDP1	84735	hgsc.bcm.edu	37	18	72223591	72223592	+	In_Frame_Ins	INS	-	-	TGC	rs10663835|rs60017744|rs67791561	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72223591_72223592insTGC	ENST00000358821.3	+	2	271_272	c.43_44insTGC	c.(43-45)gtg>gTGCtg	p.20_21insL	CNDP1_ENST00000582365.1_Intron|CNDP1_ENST00000585136.1_3'UTR	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	20			L -> LL. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16046297}.			extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.L20_E21insL(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		CCTGCTGGCTGTGCTGCTGCTG	0.559																																					p.V15delinsVL	Melanoma(32;1029 1042 25286 38395 44237)	Pindel,Atlas-Indel	.											.	CNDP1	98	.	1	Insertion - In frame(1)	kidney(1)	c.43_44insTGC						PASS	.																																			SO:0001652	inframe_insertion	84735	exon2			.		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.56_58dupTGC	18.37:g.72223598_72223600dupTGC	ENSP00000351682:p.Leu20_Leu20dup	Somatic	64	.	.		WXS	Illumina HiSeq	Phase_I	69	16	0.232	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	In_Frame_Ins	INS	ENST00000358821.3	37	CCDS12007.1																																																																																			-|0.500;TGC|0.500	0.500	strong		0.559	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
A2M	2	hgsc.bcm.edu	37	12	9246177	9246181	+	Splice_Site	DEL	TATGG	TATGG	-	rs1799759|rs3832852		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TATGG	TATGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9246177_9246181delTATGG	ENST00000318602.7	-	18	2433		c.e18-2			NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin						blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	CATCTGACTCTATGGTGAGTGAGGA	0.42														734	0.146565	0.211	0.0965	5008	,	,		18777	0.0456		0.175	False		,,,				2504	0.1697				.		Pindel,Atlas-Indel	.											.	A2M	180	.	0			.	GRCh37	CD984159	A2M	D	rs3832852	PASS	.			640,3002		64,512,1245				http://www.ncbi.nlm.nih.gov/sites/varvu?gene		3.6	0.0		dbSNP_107	59	1227,6665		106,1015,2825	no	splice-3	A2M	NM_000014.4		170,1527,4070	A1A1,A1R,RR		15.5474,17.5728,16.1869				1867,9667				SO:0001630	splice_region_variant	2	.			.	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2126-2CCATA>-	12.37:g.9246177_9246181delTATGG		Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	59	16	0.271	.	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Splice_Site	DEL	ENST00000318602.7	37	CCDS44827.1																																																																																			TATGG|0.860;-|0.140	0.140	strong		0.420	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	Intron
EPSTI1	94240	hgsc.bcm.edu	37	13	43462434	43462435	+	IGR	INS	-	-	TCAGG	rs397971974|rs61389340|rs76888419|rs375469696	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:43462434_43462435insTCAGG	ENST00000398762.3	-	0	957				EPSTI1_ENST00000313624.7_3'UTR|EPSTI1_ENST00000313640.7_Frame_Shift_Ins_p.E395fs			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)									p.E395D(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		TAAATATGAGTTCAGGAATCAG	0.406														631	0.125998	0.1914	0.0605	5008	,	,		17089	0.1597		0.0348	False		,,,				2504	0.1431				p.E395fs		Pindel,Atlas-Indel	.											EPSTI1,NS,carcinoma,0,1	EPSTI1	47	1	1	Substitution - Missense(1)	kidney(1)	c.1185_1186insCCTGA						PASS	.		,	657,3605		44,569,1518					,	-0.9	0.0		dbSNP_132	43	215,8037		4,207,3915	no	utr-3,frameshift	EPSTI1	NM_033255.2,NM_001002264.1	,	48,776,5433	A1A1,A1R,RR		2.6054,15.4153,6.9682	,	,		872,11642				SO:0001628	intergenic_variant	94240	exon13			.	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"""epithelial stromal interaction protein 1"""	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814		13.37:g.43462435_43462439dupTCAGG		Somatic	179	.	.		WXS	Illumina HiSeq	Phase_I	223	81	0.363	NM_001002264	Q8IVC7|Q8NDQ7	Frame_Shift_Ins	INS	ENST00000398762.3	37	CCDS9387.1																																																																																			-|0.890;TCAGG|0.110	0.110	strong		0.406	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264	
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 GAIIx	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		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	153	38	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 GAIIx	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	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	31	17	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		
HAVCR1	26762	hgsc.bcm.edu	37	5	156479568	156479569	+	In_Frame_Ins	INS	-	-	GTT	rs386693994|rs139041445|rs6149307|rs10068551|rs141023871|rs77147640|rs376729615	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:156479568_156479569insGTT	ENST00000339252.3	-	3	1008_1009	c.476_477insAAC	c.(475-477)acg>acAACg	p.159_159T>TT	HAVCR1_ENST00000522693.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000425854.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000544197.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000523175.1_In_Frame_Ins_p.159_159T>TT	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)	p.T160_V161insT(1)		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)			TTGGAACAGTCGTCATTGGAAC	0.49														1655	0.330471	0.6165	0.2363	5008	,	,		22483	0.2232		0.2097	False		,,,				2504	0.2454				p.T159delinsTT		Pindel,Atlas-Indel	.											.	HAVCR1	84	.	1	Insertion - In frame(1)	ovary(1)	c.477_478insAAC						PASS	.																																			SO:0001652	inframe_insertion	26762	exon4			.	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.476_477insAAC	5.37:g.156479568_156479569insGTT	ENSP00000344844:p.Thr160dup	Somatic	233	.	.		WXS	Illumina HiSeq	Phase_I	257	54	0.210	NM_001099414	O43656	In_Frame_Ins	INS	ENST00000339252.3	37	CCDS43392.1																																																																																			.	.	strong		0.490	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
SLC3A1	6519	hgsc.bcm.edu	37	2	44528268	44528268	+	Splice_Site	DEL	T	T	-	rs556841667|rs61179824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44528268delT	ENST00000260649.6	+	6	1212		c.e6+2		SLC3A1_ENST00000409294.1_Intron|SLC3A1_ENST00000409380.1_Splice_Site|SLC3A1_ENST00000409740.3_5'Flank|SLC3A1_ENST00000409741.1_Splice_Site|SLC3A1_ENST00000409229.3_Splice_Site|SLC3A1_ENST00000410056.3_Frame_Shift_Del_p.L380fs|SLC3A1_ENST00000409387.1_Splice_Site	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1						amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	CAGATACAGGTTGACCACGGC	0.507													T|TT|T|insertion	560	0.111821	0.2708	0.0821	5008	,	,		20412	0.001		0.1243	False		,,,				2504	0.0194				.		Pindel,Atlas-Indel	.											.	SLC3A1	62	.	0			c.1136+1T>-	GRCh37	CS013629	SLC3A1	S	rs146125507	PASS	.			1011,3255		126,759,1248	78.0	75.0	76.0			5.3	1.0	2	dbSNP_134	89	935,7319		49,837,3241	no	splice-5	SLC3A1	NM_000341.3		175,1596,4489	A1A1,A1R,RR		11.3278,23.699,15.5431			44528268	1946,10574	2170	4288	6458	SO:0001630	splice_region_variant	6519	exon6			.		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"""Solute carriers"""	11025	protein-coding gene	gene with protein product		104614	"""solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"""			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.1136+2T>-	2.37:g.44528268delT		Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	94	24	0.255	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Splice_Site	DEL	ENST00000260649.6	37	CCDS1819.1																																																																																			T|0.888;-|0.112	0.112	strong		0.507	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	Intron
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 GAIIx	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	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	108	16	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39784005_39784008delTATA	ENST00000280083.3	+	15	1670		c.e15+2		CTAGE5_ENST00000348007.3_Splice_Site|RP11-407N17.3_ENST00000603904.1_Splice_Site|CTAGE5_ENST00000396158.2_Splice_Site|CTAGE5_ENST00000556148.1_Splice_Site|CTAGE5_ENST00000341502.5_Splice_Site|CTAGE5_ENST00000341749.3_Splice_Site|CTAGE5_ENST00000553352.1_Splice_Site|CTAGE5_ENST00000557038.1_Splice_Site|CTAGE5_ENST00000396165.4_Splice_Site|RP11-407N17.3_ENST00000553728.1_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		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	131	79	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
LCE4A	199834	hgsc.bcm.edu	37	1	152681680	152681681	+	In_Frame_Ins	INS	-	-	AGCTCTGGGGGCTGCTGT	rs6143428|rs11269814|rs200890315|rs33921874	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152681680_152681681insAGCTCTGGGGGCTGCTGT	ENST00000368777.1	+	2	385_386	c.129_130insAGCTCTGGGGGCTGCTGT	c.(130-132)agc>AGCTCTGGGGGCTGCTGTagc	p.44_44S>SSGGCCS	LCE4A_ENST00000335535.3_In_Frame_Ins_p.44_44S>SSGGCCS			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	44	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			GCTGTGGCTCCAGCTCTGGGGG	0.599														4009	0.800519	0.9758	0.853	5008	,	,		18534	0.6855		0.7177	False		,,,				2504	0.7301				p.S43delinsSSSGGCC		Pindel,Atlas-Indel	.											LCE4A,rectum,carcinoma,+1,3	LCE4A	37	3	0			c.129_130insAGCTCTGGGGGCTGCTGT						PASS	.																																			SO:0001652	inframe_insertion	199834	exon1			.	BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"""Late cornified envelopes"""	16613	protein-coding gene	gene with protein product		612618	"""small proline rich-like (epidermal differentiation complex) 4A"""	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	Exception_encountered	1.37:g.152681680_152681681insAGCTCTGGGGGCTGCTGT	Exception_encountered	Somatic	143	.	.		WXS	Illumina HiSeq	Phase_I	147	31	0.211	NM_178356	Q14D97	In_Frame_Ins	INS	ENST00000368777.1	37	CCDS1022.1																																																																																			.	.	strong		0.599	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356	
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 GAIIx	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_ENST00000377861.3_Frame_Shift_Del_p.I128fs|PCDH9_ENST00000544246.1_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	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	154	12	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	
IL33	90865	hgsc.bcm.edu	37	9	6254555	6254556	+	Splice_Site	INS	-	-	A	rs113609242|rs60420792		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6254555_6254556insA	ENST00000381434.3	+	6	625		c.e6+2		IL33_ENST00000456383.2_Splice_Site|IL33_ENST00000417746.2_Splice_Site	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33						extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)			breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		TCTGTGGAGGTAAAAAAAAAAA	0.371																																					.		Atlas-Indel	.											.	IL33	27	.	0			c.612+2->A						PASS	.																																			SO:0001630	splice_region_variant	90865	exon7			.	AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.612+2->A	9.37:g.6254566_6254566dupA		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	27	10	0.37037	NM_033439	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Splice_Site	INS	ENST00000381434.3	37	CCDS6468.1																																																																																			A|1.000;|0.000	1.000	weak		0.371	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439	Intron
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 GAIIx	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		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	195	52	0.266667	NM_001136234		In_Frame_Del	DEL		37																																																																																				.	.	alt	0	0.577								
PBOV1	59351	hgsc.bcm.edu	37	6	138539183	138539184	+	Frame_Shift_Ins	INS	-	-	G	rs397781314|rs3841283|rs397886596	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:138539183_138539184insG	ENST00000527246.2	-	1	443_444	c.349_350insC	c.(349-351)ctafs	p.L117fs	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	117						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		TTCCAGACCTAGGGTCTGAGTT	0.386													GGGG|GGG|GGGG|deletion	781	0.15595	0.1498	0.1556	5008	,	,		21295	0.3581		0.0616	False		,,,				2504	0.0532				p.L117fs		Pindel,Atlas-Indel	.											PBOV1_ENST00000527246,bladder,carcinoma,-1,2	PBOV1	12	2	0			c.350_351insC						PASS	.		,	649,3615		49,551,1532					,	-0.7	0.0		dbSNP_107	157	566,7688		18,530,3579	no	frameshift,intron	KIAA1244,PBOV1	NM_021635.2,NM_020340.4	,	67,1081,5111	A1A1,A1R,RR		6.8573,15.2205,9.706	,	,		1215,11303				SO:0001589	frameshift_variant	59351	exon1			.	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.350dupC	6.37:g.138539186_138539186dupG	ENSP00000432353:p.Leu117fs	Somatic	208	.	.		WXS	Illumina HiSeq	Phase_I	213	58	0.272	NM_021635		Frame_Shift_Ins	INS	ENST00000527246.2	37	CCDS5190.1																																																																																			-|0.811;G|0.189	0.189	strong		0.386	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635	
GJB4	127534	hgsc.bcm.edu	37	1	35227008	35227011	+	Frame_Shift_Del	DEL	TGTC	TGTC	-	rs146812843		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:35227008_35227011delTGTC	ENST00000339480.1	+	2	523_526	c.153_156delTGTC	c.(151-156)tttgtcfs	p.FV51fs	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	51					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				AGAAGGACTTTGTCTGCAACACCA	0.603																																					p.51_52del		Pindel,Atlas-Indel	.											.	GJB4	51	.	0			c.152_155del						PASS	.			53,4213		0,53,2080						5.6	0.9		dbSNP_134	192	376,7878		3,370,3754	no	frameshift	GJB4	NM_153212.2		3,423,5834	A1A1,A1R,RR		4.5554,1.2424,3.4265				429,12091				SO:0001589	frameshift_variant	127534	exon2			.		CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"""Ion channels / Gap junction proteins (connexins)"""	4286	protein-coding gene	gene with protein product	"""connexin 30.3"""	605425	"""gap junction protein, beta 4 (connexin 30.3)"", ""gap junction protein, beta 4"""				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.153_156delTGTC	1.37:g.35227008_35227011delTGTC	ENSP00000345868:p.Phe51fs	Somatic	125	.	.		WXS	Illumina HiSeq	Phase_I	118	44	0.373	NM_153212	B3KQ82	Frame_Shift_Del	DEL	ENST00000339480.1	37	CCDS383.1																																																																																			TGTC|0.987;-|0.013	0.013	strong		0.603	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
PVRL1	5818	hgsc.bcm.edu	37	11	119535677	119535678	+	In_Frame_Ins	INS	-	-	CCT	rs539461545|rs137909701|rs369523216|rs375181781|rs3833765		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119535677_119535678insCCT	ENST00000264025.3	-	6	1863_1864	c.1333_1334insAGG	c.(1333-1335)ggc>gAGGgc	p.444_445insE	PVRL1_ENST00000341398.2_Intron	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	444	Poly-Glu.|Poly-Gly.				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)	p.E444fs*>73(1)		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)		CCCTCCACCGCcctcctcctcc	0.658																																					p.G445delinsEG		Atlas-Indel	.											PVRL1,colon,carcinoma,+1,1	PVRL1	133	1	1	Deletion - Frameshift(1)	kidney(1)	c.1334_1335insAGG	GRCh37	HI030001	PVRL1	I	rs137909701	PASS	.																																			SO:0001652	inframe_insertion	5818	exon6			.	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.1331_1333dupAGG	11.37:g.119535684_119535686dupCCT	ENSP00000264025:p.Glu444_Glu444dup	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	11	0.125	NM_002855	O75465|Q2M3D3|Q9HBE6|Q9HBW2	In_Frame_Ins	INS	ENST00000264025.3	37	CCDS8426.1																																																																																			-|0.937;CCT|0.063	0.063	strong		0.658	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1		
SYNJ1	8867	hgsc.bcm.edu	37	21	34003928	34003929	+	In_Frame_Ins	INS	-	-	AGTATT	rs57257560|rs71640263	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:34003928_34003929insAGTATT	ENST00000322229.7	-	31	4097_4098	c.4098_4099insAATACT	c.(4096-4101)gttttg>gttAATACTttg	p.1366_1367VL>VNTL	SYNJ1_ENST00000357345.3_3'UTR|SYNJ1_ENST00000382499.2_3'UTR|SYNJ1_ENST00000433931.2_In_Frame_Ins_p.1405_1406VL>VNTL|SYNJ1_ENST00000382491.3_In_Frame_Ins_p.1319_1320VL>VNTL			O43426	SYNJ1_HUMAN	synaptojanin 1	1366	Pro-rich.		V -> A (in dbSNP:rs9980589).	V -> VNT (in Ref. 1; AAC51922). {ECO:0000305}.	cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						ACAGAACTCAAAACATTACTTT	0.45														2860	0.571086	0.7269	0.4755	5008	,	,		21036	0.4712		0.5268	False		,,,				2504	0.5767				p.L1406delinsNTL		Pindel,Atlas-Indel	.											.	SYNJ1	253	.	0			c.4216_4217insAATACT						PASS	.		,,,	2849,1415		970,909,253					,,,	-0.8	0.3		dbSNP_130	73	4172,4082		1048,2076,1003	no	utr-3,coding,coding,utr-3	SYNJ1	NM_203446.2,NM_003895.3,NM_001160306.1,NM_001160302.1	,,,	2018,2985,1256	A1A1,A1R,RR		49.4548,33.1848,43.9128	,,,	,,,		7021,5497				SO:0001652	inframe_insertion	8867	exon32			.	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.4098_4099insAATACT	21.37:g.34003928_34003929insAGTATT	ENSP00000322234:p.Val1366_Leu1367insAsnThr	Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	93	57	0.613	NM_003895	O43425|O94984|Q4KMR1	In_Frame_Ins	INS	ENST00000322229.7	37	CCDS54484.1																																																																																			-|0.489;AGTATT|0.511	0.511	strong		0.450	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
CYP2F1	1572	hgsc.bcm.edu	37	19	41622107	41622108	+	Frame_Shift_Ins	INS	-	-	C	rs79512346|rs79756737|rs3833221	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41622107_41622108insC	ENST00000331105.2	+	2	86_87	c.14_15insC	c.(13-18)agcacafs	p.T6fs		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	6					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|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)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						GACAGCATAAGCACAGCCATCT	0.574													C|C|CC|insertion	1362	0.271965	0.4251	0.1873	5008	,	,		21760	0.251		0.1799	False		,,,				2504	0.2413				p.S5fs		Pindel,Atlas-Indel	.											.	CYP2F1	60	.	0			c.14_15insC	GRCh37	CI071425	CYP2F1	I	rs3833221	PASS	.			1649,2615		313,1023,796						-0.3	0.0		dbSNP_107	110	1550,6704		137,1276,2714	yes	frameshift	CYP2F1	NM_000774.3		450,2299,3510	A1A1,A1R,RR		18.7788,38.6726,25.5552				3199,9319				SO:0001589	frameshift_variant	1572	exon2			.	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.15dupC	19.37:g.41622108_41622108dupC	ENSP00000333534:p.Thr6fs	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	66	25	0.379	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Frame_Shift_Ins	INS	ENST00000331105.2	37	CCDS12572.1																																																																																			-|0.741;C|0.259	0.259	strong		0.574	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
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 GAIIx	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	Somatic	46	.	.		WXS	Illumina HiSeq	Phase_I	36	13	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	
HAVCR1	26762	hgsc.bcm.edu	37	5	156479444	156479446	+	In_Frame_Del	DEL	TTG	TTG	-	rs45439103|rs74944471|rs398065342|rs386693990	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:156479444_156479446delTTG	ENST00000339252.3	-	3	1131_1133	c.599_601delCAA	c.(598-603)acaagt>agt	p.T200del	HAVCR1_ENST00000522693.1_In_Frame_Del_p.T200del|HAVCR1_ENST00000425854.1_In_Frame_Del_p.T200del|HAVCR1_ENST00000544197.1_In_Frame_Del_p.T200del|HAVCR1_ENST00000523175.1_In_Frame_Del_p.T200del	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				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)			ACTGGAACACTTGTTGTTGTTGG	0.463														1221	0.24381	0.385	0.1873	5008	,	,		28364	0.2034		0.1869	False		,,,				2504	0.1933				p.200_201del		Pindel,Atlas-Indel	.											HAVCR1,NS,carcinoma,-1,1	HAVCR1	84	1	0			c.600_602del						PASS	.		,,	1271,2705		243,785,960					,,	-1.7	0.0		dbSNP_131	374	1639,6415		165,1309,2553	no	coding,coding,coding	HAVCR1	NM_012206.2,NM_001173393.1,NM_001099414.1	,,	408,2094,3513	A1A1,A1R,RR		20.3501,31.9668,24.1895	,,	,,		2910,9120				SO:0001651	inframe_deletion	26762	exon4			.	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.599_601delCAA	5.37:g.156479453_156479455delTTG	ENSP00000344844:p.Thr200del	Somatic	236	.	.		WXS	Illumina HiSeq	Phase_I	250	64	0.256	NM_001099414	O43656	In_Frame_Del	DEL	ENST00000339252.3	37	CCDS43392.1																																																																																			TTG|0.766;-|0.234	0.234	strong		0.463	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
CNKSR1	10256	hgsc.bcm.edu	37	1	26510311	26510311	+	Frame_Shift_Del	DEL	C	C	-	rs201305445	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26510311delC	ENST00000374253.5	+	9	905	c.866delC	c.(865-867)accfs	p.T289fs	CNKSR1_ENST00000531191.1_Frame_Shift_Del_p.T24fs|CNKSR1_ENST00000361530.6_Frame_Shift_Del_p.T282fs	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	289	Pro-rich.				Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		ATACCGGAGACCCCCCCACAG	0.667														59	0.0117812	0.0008	0.0202	5008	,	,		6575	0.001		0.0348	False		,,,				2504	0.0082				p.T282fs	NSCLC(180;1396 2109 28270 30756 34275)	Pindel,Atlas-Indel	.											.	CNKSR1	66	.	0			c.844delA						PASS	.			5,37,4224		0,0,5,0,37,2091	44.0	46.0	45.0			-0.5	0.0	1		47	1,431,7822		0,0,1,13,405,3708	no	codingComplex	CNKSR1	NM_006314.2		0,0,6,13,442,5799	A1A1,A1A2,A1R,A2A2,A2R,RR		5.2338,0.9845,3.7859			26510311	6,468,12046	2203	4300	6503	SO:0001589	frameshift_variant	10256	exon9			.	AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.866delC	1.37:g.26510311delC	ENSP00000363371:p.Thr289fs	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	81	21	0.259	NM_006314	B1AMW9|O95381	Frame_Shift_Del	DEL	ENST00000374253.5	37																																																																																				C|0.980;-|0.020	0.020	strong		0.667	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314	
A2ML1	144568	hgsc.bcm.edu	37	12	9016563	9016564	+	Frame_Shift_Del	DEL	GC	GC	-	rs144686314		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9016563_9016564delGC	ENST00000299698.7	+	29	3856_3857	c.3676_3677delGC	c.(3676-3678)gccfs	p.A1226fs	A2ML1_ENST00000539547.1_Frame_Shift_Del_p.A735fs	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						GGCTTGGTTGGCCAAGCAACAC	0.485														135	0.0269569	0.0023	0.0432	5008	,	,		15031	0.002		0.0447	False		,,,				2504	0.0562				p.1225_1226del		Pindel,Atlas-Indel	.											.	A2ML1	199	.	0			c.3675_3676del						PASS	.			39,3661		1,37,1812						1.6	0.3		dbSNP_134	52	418,7468		17,384,3542	no	frameshift	A2ML1	NM_144670.3		18,421,5354	A1A1,A1R,RR		5.3005,1.0541,3.9444				457,11129				SO:0001589	frameshift_variant	144568	exon29			.	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.3676_3677delGC	12.37:g.9016563_9016564delGC	ENSP00000299698:p.Ala1226fs	Somatic	89	.	.		WXS	Illumina HiSeq	Phase_I	70	14	0.200	NM_144670		Frame_Shift_Del	DEL	ENST00000299698.7	37	CCDS8596.2																																																																																			GC|0.979;-|0.021	0.021	strong		0.485	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
GRWD1	83743	hgsc.bcm.edu	37	19	48950002	48950004	+	In_Frame_Del	DEL	GAA	GAA	-	rs141552216	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48950002_48950004delGAA	ENST00000253237.5	+	3	603_605	c.370_372delGAA	c.(370-372)gaadel	p.E129del		NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	129	Asp/Glu-rich (acidic).					cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E124delE(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		GGGCAGTGATgaagaagaagagg	0.527														247	0.0493211	0.0219	0.049	5008	,	,		20564	0.0694		0.0547	False		,,,				2504	0.0603				p.123_124del		Pindel,Atlas-Indel	.											.	GRWD1	41	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.369_371del						PASS	.			132,4132		2,128,2002						1.0	1.0		dbSNP_134	86	362,7892		8,346,3773	no	coding	GRWD1	NM_031485.3		10,474,5775	A1A1,A1R,RR		4.3858,3.0957,3.9463				494,12024				SO:0001651	inframe_deletion	83743	exon3			.	AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"""WD repeat domain containing"""	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.370_372delGAA	19.37:g.48950008_48950010delGAA	ENSP00000253237:p.Glu129del	Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	65	16	0.246	NM_031485	Q8TF59	In_Frame_Del	DEL	ENST00000253237.5	37	CCDS12720.1																																																																																			GAA|0.945;-|0.055	0.055	strong		0.527	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466122.1	NM_031485	
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 GAIIx	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	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	75	14	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	
CTDP1	9150	hgsc.bcm.edu	37	18	77475187	77475188	+	In_Frame_Ins	INS	-	-	GGA	rs35893234|rs3833180|rs376153496	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:77475187_77475188insGGA	ENST00000299543.7	+	8	1874_1875	c.1727_1728insGGA	c.(1726-1731)atggag>atGGAggag	p.582_583insE	CTDP1_ENST00000075430.7_In_Frame_Ins_p.582_583insE	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	582	Poly-Glu.				exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		GACCAGAGCATggaggaggagg	0.609														299	0.0597045	0.0045	0.0951	5008	,	,		17334	0.1736		0.0239	False		,,,				2504	0.0286				p.M576delinsME		Pindel,Atlas-Indel	.											.	CTDP1	67	.	0			c.1727_1728insGGA						PASS	.																																			SO:0001652	inframe_insertion	9150	exon8			.	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.1746_1748dupGGA	18.37:g.77475194_77475196dupGGA	ENSP00000299543:p.Glu582_Glu582dup	Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	100	23	0.230	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	In_Frame_Ins	INS	ENST00000299543.7	37	CCDS12017.1																																																																																			-|0.926;GGA|0.074	0.074	strong		0.609	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427650	70427652	+	Stop_Codon_Del	DEL	CAG	CAG	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:70427650_70427652delCAG	ENST00000377413.1	-	0	2079_2081					NM_199244.2	NP_954714.2	Q8WXT5	FX4L4_HUMAN	forkhead box D4-like 4						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C416delC(1)							GBM - Glioblastoma multiforme(29;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		CCTGATACCTCAGCAGCGCCGAC	0.65																																					p.417_417del		Pindel,Atlas-Indel	.											.	FOXD4L2	4	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.1249_1251del						PASS	.																																			SO:0001567	stop_retained_variant	100036519	exon1			.		CCDS75845.1	9q13	2007-03-19			ENSG00000184659	ENSG00000184659			23762	protein-coding gene	gene with protein product		611085					Standard	NM_199244		Approved	bA460E7.2, OTTHUMG00000013337		Q8WXT5	OTTHUMG00000013337	Exception_encountered	9.37:g.70427653_70427655delCAG	Exception_encountered	Somatic	215	.	.		WXS	Illumina HiSeq	Phase_I	111	22	0.198	NM_001099279	Q5RIB4	In_Frame_Del	DEL	ENST00000377413.1	37	CCDS6621.1																																																																																			.	.	none		0.650	FOXD4L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037143.2		
WT1-AS	51352	hgsc.bcm.edu	37	11	32461025	32461026	+	RNA	INS	-	-	AG	rs373529925|rs386373507|rs57991818|rs113953318|rs199598071|rs144116821|rs59966210	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:32461025_32461026insAG	ENST00000395900.1	+	0	1903_1904				WT1-AS_ENST00000525436.1_RNA|WT1-AS_ENST00000494911.1_RNA|WT1-AS_ENST00000459866.1_RNA|WT1-AS_ENST00000478367.1_RNA|WT1-AS_ENST00000426618.2_RNA|WT1-AS_ENST00000442957.1_RNA	NR_023920.1		Q06250	WIT1_HUMAN	WT1 antisense RNA											endometrium(1)|large_intestine(2)|lung(2)|prostate(1)	6						AATTAAAAAAAGGGGGGGGCAA	0.485														2251	0.449481	0.2799	0.4063	5008	,	,		12882	0.7391		0.2694	False		,,,				2504	0.5961				.		Atlas-Indel	.											.	WT1-AS	7	.	0			.						PASS	.																																					51352	.			.	BC002734		11p13	2012-10-19	2012-08-15	2012-01-25	ENSG00000183242	ENSG00000183242		"""Long non-coding RNAs"", ""-"""	18135	non-coding RNA	RNA, long non-coding	"""Wilms tumor associated protein"""	607899	"""Wilms tumor upstream neighbor 1"", ""WT1 antisense RNA (non-protein coding)"""	WIT1		2173145, 8406502, 17210670	Standard	NR_120546		Approved	WIT-1, WT1AS, WT1-AS1	uc010red.2	Q06250	OTTHUMG00000039557		11.37:g.32461025_32461026insAG		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	.	Q4KMY0|Q96A27	RNA	INS	ENST00000395900.1	37																																																																																				.	.	strong		0.485	WT1-AS-001	KNOWN	basic	antisense	antisense	OTTHUMT00000095437.1	NR_023920	
NKAP	79576	hgsc.bcm.edu	37	X	119070328	119070330	+	In_Frame_Del	DEL	GAT	GAT	-	rs10577974		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:119070328_119070330delGAT	ENST00000371410.3	-	4	769_771	c.603_605delATC	c.(601-606)tcatcg>tcg	p.201_202SS>S	NKAP_ENST00000477789.1_5'UTR	NM_024528.3	NP_078804.2	Q8N5F7	NKAP_HUMAN	NFKB activating protein	201	Lys-rich.|Necessary for interaction with CIR1.				granulocyte differentiation (GO:0030851)|hematopoietic stem cell proliferation (GO:0071425)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|stem cell maintenance (GO:0019827)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)	p.S202L(1)		breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)	20						TTTTCTTTTCGATGATTTTTTCT	0.34														357	0.0945695	0.1747	0.0476	3775	,	,		11854	0.001		0.0388	False		,,,				2504	0.0542				p.202_202del		Pindel,Atlas-Indel	.											.	NKAP	53	.	1	Substitution - Missense(1)	large_intestine(1)	c.604_606del						PASS	.			823,2898		78,555,112,959,425						-0.6	1.0		dbSNP_119	144	341,6143		8,230,95,2119,1675	no	coding	NKAP	NM_024528.3		86,785,207,3078,2100	A1A1,A1R,A1,RR,R		5.2591,22.1177,11.4062				1164,9041				SO:0001651	inframe_deletion	79576	exon4			.	BC012770	CCDS14592.1	Xq24	2010-07-20			ENSG00000101882	ENSG00000101882			29873	protein-coding gene	gene with protein product	"""NF kappaB activating protein"""	300766				14550261	Standard	NM_024528		Approved	FLJ22626	uc004esh.3	Q8N5F7	OTTHUMG00000022284	ENST00000371410.3:c.603_605delATC	X.37:g.119070331_119070333delGAT	ENSP00000360464:p.Ser202del	Somatic	202	.	.		WXS	Illumina HiSeq	Phase_I	238	76	0.319	NM_024528	Q6IPW6|Q96BQ2|Q9H638	In_Frame_Del	DEL	ENST00000371410.3	37	CCDS14592.1																																																																																			.	.	weak		0.340	NKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058072.1	NM_024528	
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 GAIIx	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_ENST00000574563.1_5'Flank|TSR1_ENST00000576112.2_In_Frame_Del_p.V253del|SGSM2_ENST00000268989.3_5'Flank|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	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	87	29	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	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084943	31084945	+	Intron	DEL	CTT	CTT	-	rs57244323|rs540877039	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31084943_31084945delCTT	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_In_Frame_Del_p.S153del|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGAGCTGCTGCTTCCCGAGTGAG	0.571														939	0.1875	0.2065	0.1527	5008	,	,		17220	0.1637		0.1869	False		,,,				2504	0.2117				p.150_150del		Pindel,Atlas-Indel	.											.	CDSN	48	.	0			c.448_450del						PASS	.		,	950,3314		87,776,1269					,	2.5	0.2		dbSNP_126	37	1846,6398		222,1402,2498	no	intron,coding	CDSN,PSORS1C1	NM_014068.2,NM_001264.4	,	309,2178,3767	A1A1,A1R,RR		22.392,22.2795,22.3537	,	,		2796,9712				SO:0001627	intron_variant	1041	exon2			.	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2275CTT>-	6.37:g.31084943_31084945delCTT		Somatic	49	.	.		WXS	Illumina HiSeq	Phase_I	50	13	0.260	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	In_Frame_Del	DEL	ENST00000259881.9	37	CCDS34390.1																																																																																			CTT|0.500;-|0.500	0.500	strong		0.571	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
OR4L1	122742	hgsc.bcm.edu	37	14	20528449	20528467	+	Frame_Shift_Del	DEL	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	-	rs145273733|rs111945603|rs112516164|rs75613488|rs139767954|rs112425920|rs33965693|rs112192573|rs200018603|rs201521851	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CATAGATTTGCTCACTGAC	CATAGATTTGCTCACTGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20528449_20528467delCATAGATTTGCTCACTGAC	ENST00000315683.1	+	1	246_264	c.246_264delCATAGATTTGCTCACTGAC	c.(244-264)atcatagatttgctcactgacfs	p.IIDLLTD82fs		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L85F(1)|p.I83fs*10(1)		central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		CCAAGATGATCATAGATTTGCTCACTGACCACAAGACCA	0.466														2665	0.532149	0.4849	0.5562	5008	,	,		20575	0.5734		0.3837	False		,,,				2504	0.6892				p.82_88del		Pindel,Atlas-Indel	.											.	OR4L1	98	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	upper_aerodigestive_tract(1)|lung(1)	c.245_263del						PASS	.																																			SO:0001589	frameshift_variant	122742	exon1			.		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.246_264delCATAGATTTGCTCACTGAC	14.37:g.20528449_20528467delCATAGATTTGCTCACTGAC	ENSP00000319217:p.Ile82fs	Somatic	184	.	.		WXS	Illumina HiSeq	Phase_I	141	32	0.227	NM_001004717	Q6IEZ5	Frame_Shift_Del	DEL	ENST00000315683.1	37	CCDS32029.1																																																																																			CATAGATTTGCTCACTGAC|0.504;-|0.496	0.496	strong		0.466	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
C11orf40	143501	hgsc.bcm.edu	37	11	4592708	4592709	+	Frame_Shift_Ins	INS	-	-	AG	rs67037861|rs71280817|rs3064108|rs79804156	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:4592708_4592709insAG	ENST00000307616.1	-	4	597_598	c.598_599insCT	c.(598-600)tgtfs	p.C200fs		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	200										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		acgatccatacagtttttccCT	0.431																																					p.C200fs		Pindel,Atlas-Indel	.											.	C11orf40	37	.	0			c.599_600insCT						PASS	.			1965,709,1460		611,170,573,143,253,317						-1.1	0.0		dbSNP_102	79	1984,2343,3691		483,304,714,544,951,1013	no	codingComplex	C11orf40	NM_144663.1		1094,474,1287,687,1204,1330	A1A1,A1A2,A1R,A2A2,A2R,RR		53.9661,52.4673,57.6119				3949,3052,5151				SO:0001589	frameshift_variant	143501	exon4			.		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.597_598dupCT	11.37:g.4592709_4592710dupAG	ENSP00000302918:p.Cys200fs	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	118	33	0.280	NM_144663		Frame_Shift_Ins	INS	ENST00000307616.1	37	CCDS31354.1																																																																																			-|0.378;AC|0.622	.	strong		0.431	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
MUC20	200958	hgsc.bcm.edu	37	3	195453018	195453018	+	Frame_Shift_Del	DEL	C	C	-	rs144288174	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195453018delC	ENST00000447234.2	+	2	1670	c.1544delC	c.(1543-1545)gccfs	p.A515fs	MUC20_ENST00000436408.1_Frame_Shift_Del_p.A515fs|MUC20_ENST00000445522.2_Frame_Shift_Del_p.A480fs|MUC20_ENST00000320736.6_Frame_Shift_Del_p.A344fs	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	515	Involved in oligomerization.		Missing. {ECO:0000269|PubMed:14702039}.		activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.T516fs*39(2)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		GCACCCGGGGCCACGACCCTC	0.577													cc|CC|C|deletion	439	0.0876597	0.0295	0.1398	5008	,	,		26511	0.0377		0.169	False		,,,				2504	0.0971				p.A344fs		Atlas-Indel	.											.	MUC20	84	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1030delG						PASS	.		,	185,3935		1,183,1876	54.0	47.0	49.0		,	-0.7	0.0	3	dbSNP_134	54	1243,6833		18,1207,2813	no	frameshift,frameshift	MUC20	NM_152673.2,NM_001098516.1	,	19,1390,4689	A1A1,A1R,RR		15.3913,4.4903,11.7088	,	,	195453018	1428,10768	2136	4208	6344	SO:0001589	frameshift_variant	200958	exon3			.	AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1544delC	3.37:g.195453018delC	ENSP00000414350:p.Ala515fs	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	417	93	0.223022	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Frame_Shift_Del	DEL	ENST00000447234.2	37																																																																																				C|0.915;-|0.085	0.085	strong		0.577	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
NPVF	64111	hgsc.bcm.edu	37	7	25266570	25266572	+	In_Frame_Del	DEL	TAA	TAA	-	rs3216928	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TAA	TAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:25266570_25266572delTAA	ENST00000222674.2	-	2	258_260	c.212_214delTTA	c.(211-216)attaag>aag	p.I71del		NM_022150.3	NP_071433	Q9HCQ7	NPVF_HUMAN	neuropeptide VF precursor	71					negative regulation of gonadotropin secretion (GO:0032277)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						GTACTCATCTTAATAACATTTTT	0.394														733	0.146366	0.1626	0.1455	5008	,	,		19000	0.1448		0.1004	False		,,,				2504	0.1738				p.71_72del		Pindel,Atlas-Indel	.											.	NPVF	36	.	0			c.213_215del						PASS	.			692,3570		80,532,1519						5.7	1.0		dbSNP_106	140	1051,7199		149,753,3223	no	coding	NPVF	NM_022150.3		229,1285,4742	A1A1,A1R,RR		12.7394,16.2365,13.9306				1743,10769				SO:0001651	inframe_deletion	64111	exon2			.	AB040290	CCDS5395.1	7p21-p15	2013-02-28	2006-10-06	2006-10-06	ENSG00000105954	ENSG00000105954		"""Endogenous ligands"""	13782	protein-coding gene	gene with protein product	"""RFamide-related peptide precursor"", ""FMRFamide-related peptide precursor"""		"""chromosome 7 open reading frame 9"""	C7orf9		11951088, 11173868	Standard	NM_022150		Approved	RFRP	uc003sxo.3	Q9HCQ7	OTTHUMG00000128509	ENST00000222674.2:c.212_214delTTA	7.37:g.25266573_25266575delTAA	ENSP00000222674:p.Ile71del	Somatic	179	.	.		WXS	Illumina HiSeq	Phase_I	124	27	0.218	NM_022150	A4D164|Q7LE27|Q96PI9	In_Frame_Del	DEL	ENST00000222674.2	37	CCDS5395.1																																																																																			TAA|0.862;-|0.138	0.138	strong		0.394	NPVF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250315.1	NM_022150	
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 GAIIx	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	Somatic	109	.	.		WXS	Illumina HiSeq	Phase_I	83	24	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	
KRT36	8689	hgsc.bcm.edu	37	17	39642658	39642660	+	In_Frame_Del	DEL	GGA	GGA	-	rs565828637	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39642658_39642660delGGA	ENST00000328119.6	-	7	1371_1373	c.1372_1374delTCC	c.(1372-1374)tccdel	p.S458del	KRT36_ENST00000393986.2_In_Frame_Del_p.S408del	NM_003771.4	NP_003762.1	O76013	KRT36_HUMAN	keratin 36	458	Tail.				regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of epidermis (GO:0030280)			breast(2)|cervix(1)|kidney(2)|large_intestine(3)|lung(8)|skin(1)	17		Breast(137;0.000286)				CGTGCTCCCTGGAGGAGATGACT	0.66														28	0.00559105	0.0023	0.0072	5008	,	,		17908	0.0		0.0139	False		,,,				2504	0.0061				p.458_459del		Pindel,Atlas-Indel	.											.	KRT36	52	.	0			c.1373_1375del						PASS	.			12,4252		1,10,2121						0.4	1.0			53	115,8139		1,113,4013	no	coding	KRT36	NM_003771.4		2,123,6134	A1A1,A1R,RR		1.3933,0.2814,1.0145				127,12391				SO:0001651	inframe_deletion	8689	exon7			.	Y16792	CCDS11395.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000126337	ENSG00000126337		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6454	protein-coding gene	gene with protein product		604540	"""keratin, hair, acidic, 6"""	KRTHA6		9756910, 16831889	Standard	XM_005257762		Approved		uc002hwt.3	O76013	OTTHUMG00000133431	ENST00000328119.6:c.1372_1374delTCC	17.37:g.39642661_39642663delGGA	ENSP00000329165:p.Ser458del	Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	71	25	0.352	NM_003771	Q86XG4	In_Frame_Del	DEL	ENST00000328119.6	37	CCDS11395.1																																																																																			.	.	none		0.660	KRT36-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259508.1	NM_003771	
GPSM2	29899	hgsc.bcm.edu	37	1	109465166	109465168	+	In_Frame_Del	DEL	CTT	CTT	-	rs374875864|rs79761186|rs35029887|rs201481482	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109465166_109465168delCTT	ENST00000406462.2	+	14	2341_2343	c.1568_1570delCTT	c.(1567-1572)acttct>act	p.S525del	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_In_Frame_Del_p.S525del			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	525					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		TCAACAACAACTTCTTCCACTCC	0.374																																					p.523_523del		Pindel,Atlas-Indel	.											.	GPSM2	56	.	0			c.1567_1569del						PASS	.			2409,1857		681,1047,405						-3.5	0.0		dbSNP_126	157	2331,5923		336,1659,2132	no	coding	GPSM2	NM_013296.4		1017,2706,2537	A1A1,A1R,RR		28.2409,43.5302,37.8594				4740,7780				SO:0001651	inframe_deletion	29899	exon13			.	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1568_1570delCTT	1.37:g.109465169_109465171delCTT	ENSP00000385510:p.Ser525del	Somatic	156	.	.		WXS	Illumina HiSeq	Phase_I	140	41	0.293	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	In_Frame_Del	DEL	ENST00000406462.2	37	CCDS792.2																																																																																			CTT|0.700;-|0.300	0.300	strong		0.374	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296	
GTF2I	2969	hgsc.bcm.edu	37	7	74149837	74149840	+	Frame_Shift_Del	DEL	AAGA	AAGA	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAGA	AAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:74149837_74149840delAAGA	ENST00000324896.4	+	17	1787_1790	c.1398_1401delAAGA	c.(1396-1401)ttaagafs	p.LR466fs	GTF2I_ENST00000353920.4_Frame_Shift_Del_p.LR446fs|GTF2I_ENST00000416070.1_Frame_Shift_Del_p.LR425fs|GTF2I_ENST00000346152.4_Frame_Shift_Del_p.LR445fs	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	466					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						TCACTAAATTAAGAAAGATGGTGG	0.275																																					p.466_467del		Atlas-Indel	.											.	GTF2I	40	.	0			c.1397_1400del						PASS	.		,,,,	4,1578		1,2,788					,,,,	4.4	0.1			2	20,2954		3,14,1470	no	frameshift,frameshift,frameshift,frameshift,frameshift	GTF2I	NM_033001.2,NM_033000.2,NM_032999.2,NM_001518.3,NM_001163636.1	,,,,	4,16,2258	A1A1,A1R,RR		0.6725,0.2528,0.5268	,,,,	,,,,		24,4532				SO:0001589	frameshift_variant	2969	exon17			.	U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.1398_1401delAAGA	7.37:g.74149841_74149844delAAGA	ENSP00000322542:p.Leu466fs	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	122	12	0.0983607	NM_032999	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Frame_Shift_Del	DEL	ENST00000324896.4	37	CCDS5573.1																																																																																			.	.	none		0.275	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999	
GLT6D1	360203	hgsc.bcm.edu	37	9	138516347	138516347	+	Frame_Shift_Del	DEL	A	A	-	rs34217442	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138516347delA	ENST00000371763.1	-	5	680	c.427delT	c.(427-429)tggfs	p.W143fs		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	143					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		CCATCGAGCCACCACCTCTCG	0.552													A|A|-|deletion	860	0.171725	0.09	0.1888	5008	,	,		16603	0.2103		0.1839	False		,,,				2504	0.2178				p.W143fs		Pindel,Atlas-Indel	.											.	GLT6D1	56	.	0			c.428delG						PASS	.			334,3488		26,282,1603	39.0	36.0	37.0			-1.0	0.0	9	dbSNP_126	43	1598,6358		173,1252,2553	yes	frameshift	GLT6D1	NM_182974.2		199,1534,4156	A1A1,A1R,RR		20.0855,8.7389,16.4035			138516347	1932,9846	1961	4021	5982	SO:0001589	frameshift_variant	360203	exon5			.	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.427delT	9.37:g.138516347delA	ENSP00000360829:p.Trp143fs	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	68	20	0.294	NM_182974		Frame_Shift_Del	DEL	ENST00000371763.1	37	CCDS43900.1																																																																																			A|0.829;-|0.171	0.171	strong		0.552	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
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 GAIIx	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_ENST00000513237.1_Frame_Shift_Del_p.G1641fs|TET2_ENST00000380013.4_Frame_Shift_Del_p.G1620fs|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	Somatic	96	.	.		WXS	Illumina HiSeq	Phase_I	76	13	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	
GDPD4	220032	hgsc.bcm.edu	37	11	76954788	76954789	+	Frame_Shift_Ins	INS	-	-	A	rs34784710|rs76229203	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:76954788_76954789insA	ENST00000376217.2	-	12	1441_1442	c.1191_1192insT	c.(1189-1194)aatatcfs	p.I398fs	GDPD4_ENST00000315938.4_Frame_Shift_Ins_p.I398fs			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	398	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						ATTATACTGATATTGTTTTTAG	0.416													A|A|AA|insertion	1272	0.253994	0.0514	0.1916	5008	,	,		16545	0.256		0.3718	False		,,,				2504	0.4489				p.I398fs		Atlas-Indel	.											.	GDPD4	49	.	0			c.1192_1193insT						PASS	.			442,3822		29,384,1719						1.2	0.7		dbSNP_126	119	2948,5306		503,1942,1682	no	frameshift	GDPD4	NM_182833.1		532,2326,3401	A1A1,A1R,RR		35.716,10.3659,27.081				3390,9128				SO:0001589	frameshift_variant	220032	exon12			.	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1192dupT	11.37:g.76954789_76954789dupA	ENSP00000365390:p.Ile398fs	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	115	19	0.165217	NM_182833	Q7Z5B0	Frame_Shift_Ins	INS	ENST00000376217.2	37																																																																																				-|0.773;A|0.227	0.227	strong		0.416	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
USP40	55230	hgsc.bcm.edu	37	2	234429739	234429740	+	In_Frame_Ins	INS	-	-	TTC	rs141501074|rs59586144|rs397953463	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:234429739_234429740insTTC	ENST00000427112.2	-	16	2254_2255	c.2219_2220insGAA	c.(2218-2220)aaa>aaGAAa	p.740_740K>KK	USP40_ENST00000251722.6_In_Frame_Ins_p.740_740K>KK|USP40_ENST00000450966.1_In_Frame_Ins_p.752_752K>KK			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	740					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		TAGTGACCCATTTCTCTTCCTT	0.361														749	0.149561	0.1967	0.1326	5008	,	,		19239	0.0456		0.2425	False		,,,				2504	0.1094				p.K752delinsKK		Pindel,Atlas-Indel	.											.	USP40	174	.	0			c.2256_2257insGAA						PASS	.			676,2890		63,550,1170						-1.6	0.8		dbSNP_130	84	1690,6138		187,1316,2411	no	coding	USP40	NM_018218.2		250,1866,3581	A1A1,A1R,RR		21.5892,18.9568,20.7653				2366,9028				SO:0001652	inframe_insertion	55230	exon16			.	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.2217_2219dupGAA	2.37:g.234429740_234429742dupTTC	ENSP00000387898:p.Lys740dup	Somatic	62	.	.		WXS	Illumina HiSeq	Phase_I	47	29	0.617	NM_018218	Q6NX38|Q70EL0	In_Frame_Ins	INS	ENST00000427112.2	37	CCDS46547.1																																																																																			-|0.837;TTC|0.163	0.163	strong		0.361	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496323	39496325	+	In_Frame_Del	DEL	AAC	AAC	-	rs140936762|rs139292|rs201177427	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39496323_39496325delAAC	ENST00000401756.1	+	2	116_118	c.40_42delAAC	c.(40-42)aacdel	p.N15del	APOBEC3H_ENST00000348946.4_In_Frame_Del_p.N15del|APOBEC3H_ENST00000421988.2_In_Frame_Del_p.N15del|APOBEC3H_ENST00000442487.3_In_Frame_Del_p.N15del	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	15			Missing (decreases protein stability). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					CTTACAGTTTAACAACAAGCGCC	0.532														1590	0.317492	0.3071	0.2795	5008	,	,		17995	0.2579		0.339	False		,,,				2504	0.3978				p.13_14del		Pindel,Atlas-Indel	.											.	APOBEC3H	28	.	0			c.39_41del						PASS	.		,,,	1382,2882		240,902,990					,,,	-1.8	0.2		dbSNP_129	82	2684,5570		426,1832,1869	no	coding,coding,coding,coding	APOBEC3H	NM_181773.3,NM_001166004.1,NM_001166003.1,NM_001166002.1	,,,	666,2734,2859	A1A1,A1R,RR		32.5176,32.4109,32.4812	,,,	,,,		4066,8452				SO:0001651	inframe_deletion	164668	exon2			.	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.40_42delAAC	22.37:g.39496326_39496328delAAC	ENSP00000385741:p.Asn15del	Somatic	131	.	.		WXS	Illumina HiSeq	Phase_I	123	42	0.341	NM_181773	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	In_Frame_Del	DEL	ENST00000401756.1	37	CCDS54530.1																																																																																			AAC|0.696;-|0.304	0.304	strong		0.532	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
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 GAIIx	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_ENST00000423743.3_Frame_Shift_Del_p.R46fs|KIAA0586_ENST00000261244.5_Frame_Shift_Del_p.R131fs	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	Somatic	170	.	.		WXS	Illumina HiSeq	Phase_I	152	56	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	
FOXD4L2	100036519	hgsc.bcm.edu	37	9	42719309	42719311	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:42719309_42719311delGCT	ENST00000377590.1	+	1	2076_2078	c.1244_1246delGCT	c.(1243-1248)cgctgc>cgc	p.C416del		NM_001099279.1	NP_001092749.1	Q6VB85	FX4L2_HUMAN	forkhead box D4-like 2	416					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		CCTCGTCGGCGCTGCTGAGGTAT	0.64																																					p.415_415del		Atlas-Indel	.											.	FOXD4L2	4	.	0			c.1243_1245del						PASS	.																																			SO:0001651	inframe_deletion	100036519	exon1			.			9p12	2008-07-21			ENSG00000204828				24813	protein-coding gene	gene with protein product						12421752	Standard			Approved	OTTHUMG00000066752	uc004acn.3	Q6VB85	OTTHUMG00000066752	ENST00000377590.1:c.1244_1246delGCT	9.37:g.42719312_42719314delGCT	ENSP00000366814:p.Cys416del	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	127	18	0.141732	NM_001099279		In_Frame_Del	DEL	ENST00000377590.1	37	CCDS43817.1																																																																																			.	.	none		0.640	FOXD4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143077.1	NM_001099279	
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Frame_Shift_Del	DEL	A	A	-	rs398101268|rs34470614		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52887146delA	ENST00000422689.2	+	4	328	c.313delA	c.(313-315)aaafs	p.K105fs	ZNF880_ENST00000424032.2_3'UTR	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	105					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CAAGTCTCTTAAAAATCAACT	0.368																																					p.L104fs		Pindel,Atlas-Indel	.											.	ZNF880	45	.	0			c.312delT						PASS	.			1094,2682		234,626,1028	61.0	45.0	50.0			-2.8	0.0	19	dbSNP_126	72	3080,4810		677,1726,1542	no	frameshift	ZNF880	NM_001145434.1		911,2352,2570	A1A1,A1R,RR		39.0368,28.9725,35.7792			52887146	4174,7492	690	1569	2259	SO:0001589	frameshift_variant	400713	exon4			.	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.313delA	19.37:g.52887146delA	ENSP00000406318:p.Lys105fs	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	87	52	0.598	NM_001145434	B4DNA6	Frame_Shift_Del	DEL	ENST00000422689.2	37	CCDS46164.1																																																																																			A|0.672;-|0.328	0.328	strong		0.368	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
RETNLB	84666	hgsc.bcm.edu	37	3	108475993	108475994	+	Frame_Shift_Ins	INS	-	-	GGGGATTA	rs5851607|rs368497660	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:108475993_108475994insGGGGATTA	ENST00000295755.6	-	1	237_238	c.39_40insTAATCCCC	c.(37-42)ccccttfs	p.L14fs	RETNLB_ENST00000482939.1_5'Flank	NM_032579.2	NP_115968.1	Q9BQ08	RETNB_HUMAN	resistin like beta	14					cell proliferation (GO:0008283)	extracellular region (GO:0005576)				endometrium(1)|kidney(3)|lung(10)|prostate(1)|skin(1)	16						AGCTGGAGAAGGGGGATTAGGA	0.51														459	0.0916534	0.0893	0.1239	5008	,	,		19161	0.0		0.1909	False		,,,				2504	0.0644				p.L14_L15delinsX		Pindel,Atlas-Indel	.											.	RETNLB	38	.	0			c.40_41insTAATCCCC						PASS	.			420,3846		19,382,1732						2.2	0.4		dbSNP_114	65	1534,6720		140,1254,2733	no	frameshift	RETNLB	NM_032579.2		159,1636,4465	A1A1,A1R,RR		18.5849,9.8453,15.607				1954,10566				SO:0001589	frameshift_variant	84666	exon1			.	AF290873	CCDS2953.1	3q13.1	2008-02-05			ENSG00000163515	ENSG00000163515			20388	protein-coding gene	gene with protein product		605645				10921885, 12574343	Standard	NM_032579		Approved	HXCP2, FIZZ2, RELMb	uc003dxh.2	Q9BQ08	OTTHUMG00000159393	ENST00000295755.6:c.32_39dupTAATCCCC	3.37:g.108475994_108476001dupGGGGATTA	ENSP00000295755:p.Leu14fs	Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	50	17	0.340	NM_032579	Q14D27	Frame_Shift_Ins	INS	ENST00000295755.6	37	CCDS2953.1																																																																																			-|0.879;GGGGATTA|0.121	0.121	strong		0.510	RETNLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355093.1		
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 GAIIx	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	Somatic	144	.	.		WXS	Illumina HiSeq	Phase_I	45	10	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	
CREB3L2	64764	hgsc.bcm.edu	37	7	137612914	137612916	+	In_Frame_Del	DEL	TGG	TGG	-	rs565336947|rs3217268|rs66593747	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:137612914_137612916delTGG	ENST00000330387.6	-	2	650_652	c.299_301delCCA	c.(298-303)accagt>agt	p.T100del	CREB3L2_ENST00000458726.1_In_Frame_Del_p.T37del|CREB3L2_ENST00000452463.1_In_Frame_Del_p.T100del|CREB3L2_ENST00000456390.1_In_Frame_Del_p.T100del	NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	100			Missing. {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:12915480, ECO:0000269|PubMed:15489334}.		cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|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)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						AAGCTGTCACTGGTGGTAATGTG	0.571			T	FUS	fibromyxoid sarcoma									3459	0.690695	0.6876	0.6571	5008	,	,		19457	0.8244		0.6362	False		,,,				2504	0.637				p.100_101del		Pindel,Atlas-Indel	.		Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	CREB3L2	62	.	0			c.300_302del						PASS	.			2862,1400		963,936,232						3.5	0.5		dbSNP_130	42	5143,3109		1603,1937,586	no	coding	CREB3L2	NM_194071.2		2566,2873,818	A1A1,A1R,RR		37.6757,32.8484,36.0316				8005,4509				SO:0001651	inframe_deletion	64764	exon2			.	AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"""basic leucine zipper proteins"""	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.299_301delCCA	7.37:g.137612917_137612919delTGG	ENSP00000329140:p.Thr100del	Somatic	246	.	.		WXS	Illumina HiSeq	Phase_I	168	83	0.494	NM_001253775	Q6P454|Q6ZMR6	In_Frame_Del	DEL	ENST00000330387.6	37	CCDS34760.1																																																																																			TGG|0.250;-|0.750	0.750	strong		0.571	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071	
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 GAIIx	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_ENST00000475231.1_Frame_Shift_Del_p.L4230fs|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	68	10	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	
OR13C5	138799	hgsc.bcm.edu	37	9	107360769	107360769	+	Frame_Shift_Del	DEL	T	T	-	rs78341003|rs11314210	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107360769delT	ENST00000374779.2	-	1	1019	c.926delA	c.(925-927)cacfs	p.H309fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						TCTCAGTAGGTGTTTTACTGC	0.323													T|T|-|deletion	2184	0.436102	0.6475	0.2277	5008	,	,		19983	0.5754		0.1789	False		,,,				2504	0.4192				p.H309fs		Pindel,Atlas-Indel	.											.	OR13C5	60	.	0			c.927delC						PASS	.			2496,1768		742,1012,378	57.0	85.0	77.0			-8.0	0.0	9	dbSNP_120	94	1603,6651		175,1253,2699	no	frameshift	OR13C5	NM_001004482.1		917,2265,3077	A1A1,A1R,RR		19.4209,41.4634,32.7448			107360769	4099,8419	1566	4154	5720	SO:0001589	frameshift_variant	138799	exon1			.		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.926delA	9.37:g.107360769delT	ENSP00000363911:p.His309fs	Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	94	33	0.351	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	CCDS35091.1																																																																																			T|0.620;-|0.380	0.380	strong		0.323	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
MYO5B	4645	hgsc.bcm.edu	37	18	47405425	47405426	+	In_Frame_Ins	INS	-	-	GAG	rs33910398|rs3841750|rs200219597|rs397841722	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:47405425_47405426insGAG	ENST00000285039.7	-	24	3464_3465	c.3165_3166insCTC	c.(3163-3168)ctcatg>ctcCTCatg	p.1055_1056insL	MYO5B_ENST00000324581.6_In_Frame_Ins_p.196_197insL|MYO5B_ENST00000587895.1_5'Flank	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1055			L -> LL (in dbSNP:rs72530399). {ECO:0000269|PubMed:10574461, ECO:0000269|Ref.4}.		endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)	p.M1056L(1)		NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TCTTTCTTCATGAGATTTTCCT	0.45														2027	0.404752	0.3638	0.268	5008	,	,		21517	0.5685		0.3002	False		,,,				2504	0.4959				p.M1056delinsLM		Pindel,Atlas-Indel	.											MYO5B,NS,carcinoma,0,1	MYO5B	178	1	1	Substitution - Missense(1)	pancreas(1)	c.3166_3167insCTC						PASS	.			1273,2303		242,789,757						2.8	0.9		dbSNP_119	77	2176,5680		316,1544,2068	no	coding	MYO5B	NM_001080467.2		558,2333,2825	A1A1,A1R,RR		27.6986,35.5984,30.1697				3449,7983				SO:0001652	inframe_insertion	4645	exon24			.	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3163_3165dupCTC	18.37:g.47405426_47405428dupGAG	ENSP00000285039:p.Leu1055_Leu1055dup	Somatic	131	.	.		WXS	Illumina HiSeq	Phase_I	144	42	0.292	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	In_Frame_Ins	INS	ENST00000285039.7	37	CCDS42436.1																																																																																			-|0.623;GAG|0.377	0.377	strong		0.450	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
OR10AD1	121275	hgsc.bcm.edu	37	12	48596875	48596876	+	Frame_Shift_Ins	INS	-	-	A	rs79650217|rs144247841	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48596875_48596876insA	ENST00000310248.2	-	1	294_295	c.200_201insT	c.(199-201)ctgfs	p.L67fs		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						CCAGGAGAGACAGATGGCCGAG	0.525													A|A|AA|insertion	1017	0.203075	0.2716	0.1326	5008	,	,		22247	0.128		0.2346	False		,,,				2504	0.2055				p.L67fs		Pindel,Atlas-Indel	.											.	OR10AD1	24	.	0			c.201_202insT						PASS	.			1181,3083		178,825,1129						-0.6	1.0		dbSNP_129	109	1745,6509		176,1393,2558	no	frameshift	OR10AD1	NM_001004134.1		354,2218,3687	A1A1,A1R,RR		21.1413,27.697,23.3743				2926,9592				SO:0001589	frameshift_variant	121275	exon1			.		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.201dupT	12.37:g.48596876_48596876dupA	ENSP00000308689:p.Leu67fs	Somatic	176	.	.		WXS	Illumina HiSeq	Phase_I	166	48	0.289	NM_001004134	B9EGT9|Q6IFA8	Frame_Shift_Ins	INS	ENST00000310248.2	37	CCDS31787.1																																																																																			-|0.791;A|0.209	0.209	strong		0.525	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
LMOD3	56203	hgsc.bcm.edu	37	3	69171497	69171499	+	In_Frame_Del	DEL	AGA	AGA	-	rs139192915|rs398105991	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:69171497_69171499delAGA	ENST00000420581.2	-	1	218_220	c.39_41delTCT	c.(37-42)cttctc>ctc	p.13_14LL>L	LMOD3_ENST00000489031.1_In_Frame_Del_p.13_14LL>L|LMOD3_ENST00000475434.1_In_Frame_Del_p.13_14LL>L	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	13						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.L14delL(2)		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)		CTCCTCATCGAGAAGTTCTTCTT	0.36														58	0.0115815	0.0	0.0115	5008	,	,		17202	0.001		0.0298	False		,,,				2504	0.0194				p.14_14del		Pindel,Atlas-Indel	.											.	LMOD3	92	.	2	Deletion - In frame(2)	kidney(2)	c.40_42del						PASS	.			14,3540		1,12,1764						-0.2	0.0		dbSNP_134	42	225,7605		5,215,3695	no	coding	LMOD3	NM_198271.3		6,227,5459	A1A1,A1R,RR		2.8736,0.3939,2.0994				239,11145				SO:0001651	inframe_deletion	56203	exon1			.	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.39_41delTCT	3.37:g.69171497_69171499delAGA	ENSP00000414670:p.Leu14del	Somatic	105	.	.		WXS	Illumina HiSeq	Phase_I	92	27	0.293	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	In_Frame_Del	DEL	ENST00000420581.2	37	CCDS46862.1																																																																																			AGA|0.988;-|0.012	0.012	strong		0.360	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529	
C14orf23	387978	hgsc.bcm.edu	37	14	29261307	29261308	+	Frame_Shift_Ins	INS	-	-	C	rs56363493|rs34203558	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:29261307_29261308insC	ENST00000399387.4	+	3	448_449	c.344_345insC	c.(343-348)aaaaaafs	p.K115fs	C14orf23_ENST00000550266.1_Intron|C14orf23_ENST00000548213.1_Intron					chromosome 14 open reading frame 23											central_nervous_system(1)	1						TCAGCACTAAAAAAAACAAACA	0.381																																					.		Atlas-Indel	.											.	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.29261307_29261308insC	ENSP00000382318:p.Lys115fs	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	67	11	0.164179	.		RNA	INS	ENST00000399387.4	37																																																																																				-|0.736;C|0.264	0.264	strong		0.381	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000134019.2	NR_026731	
RP1L1	94137	hgsc.bcm.edu	37	8	10466004	10466024	+	In_Frame_Del	DEL	CTGGGCCTCCCCTTCAGCCTC	CTGGGCCTCCCCTTCAGCCTC	-	rs199577777|rs199959237|rs535482422|rs558932296|rs181718385|rs542254783	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTGGGCCTCCCCTTCAGCCTC	CTGGGCCTCCCCTTCAGCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:10466004_10466024delCTGGGCCTCCCCTTCAGCCTC	ENST00000382483.3	-	4	5807_5827	c.5584_5604delGAGGCTGAAGGGGAGGCCCAG	c.(5584-5604)gaggctgaaggggaggcccagdel	p.EAEGEAQ1862del		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1942					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)		p.E1862E(1)|p.A1863D(1)		breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CTGACTCTGGCTGGGCCTCCCCTTCAGCCTCCTGGGCATCC	0.633																																					p.1862_1869del		Atlas-Indel	.											RP1L1,lower_third,carcinoma,+2,1	RP1L1	453	1	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)	c.5585_5605del						PASS	.			85,3535		3,79,1728						0.5	0.0			170	854,7024		39,776,3124	no	coding	RP1L1	NM_178857.5		42,855,4852	A1A1,A1R,RR		10.8403,2.3481,8.1666				939,10559				SO:0001651	inframe_deletion	94137	exon4			.	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5584_5604delGAGGCTGAAGGGGAGGCCCAG	8.37:g.10466004_10466024delCTGGGCCTCCCCTTCAGCCTC	ENSP00000371923:p.Glu1862_Gln1868del	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	29	26	0.896552	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Del	DEL	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	none		0.633	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SERINC2	347735	hgsc.bcm.edu	37	1	31905889	31905890	+	In_Frame_Ins	INS	-	-	CAG	rs33956499|rs3050461|rs5773362	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:31905889_31905890insCAG	ENST00000373709.3	+	9	1239_1240	c.1089_1090insCAG	c.(1090-1092)cag>CAGcag	p.364_364Q>QQ	SERINC2_ENST00000491976.1_3'UTR|SERINC2_ENST00000536859.1_In_Frame_Ins_p.368_368Q>QQ|SERINC2_ENST00000373710.1_In_Frame_Ins_p.373_373Q>QQ|SERINC2_ENST00000536384.1_In_Frame_Ins_p.368_368Q>QQ	NM_178865.4	NP_849196.2	Q96SA4	SERC2_HUMAN	serine incorporator 2	364					phosphatidylserine metabolic process (GO:0006658)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	L-serine transmembrane transporter activity (GO:0015194)			cervix(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	12		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0629)|Breast(348;0.0707)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0541)|READ - Rectum adenocarcinoma(331;0.151)		TAGACGCCACACAGCAGCAGCA	0.634														3701	0.739018	0.7617	0.7363	5008	,	,		17436	0.63		0.8598	False		,,,				2504	0.6984				p.T372delinsTQ		Pindel,Atlas-Indel	.											.	SERINC2	44	.	0			c.1116_1117insCAG						PASS	.																																			SO:0001652	inframe_insertion	347735	exon10			.	AY094595	CCDS30662.1, CCDS55583.1, CCDS55584.1, CCDS55585.1	1p35.1	2008-02-05	2005-11-01	2005-11-01	ENSG00000168528	ENSG00000168528			23231	protein-coding gene	gene with protein product		614549	"""tumor differentially expressed 2-like"""	TDE2L		12949800	Standard	NM_178865		Approved	FKSG84, PRO0899, TDE2	uc010ogh.2	Q96SA4	OTTHUMG00000003796	ENST00000373709.3:c.1102_1104dupCAG	1.37:g.31905896_31905898dupCAG	ENSP00000362813:p.Gln368dup	Somatic	93	.	.		WXS	Illumina HiSeq	Phase_I	84	45	0.536	NM_001199038	A0AVB4|B4DJK5|B7Z567|B7ZAP2|E7EUZ9|Q86Y23	In_Frame_Ins	INS	ENST00000373709.3	37	CCDS30662.1																																																																																			.	.	strong		0.634	SERINC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010680.1	NM_018565	
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 GAIIx	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	Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	47	20	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	
NUDT17	200035	hgsc.bcm.edu	37	1	145586679	145586679	+	Frame_Shift_Del	DEL	C	C	-	rs199513201|rs150364859	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145586679delC	ENST00000334513.5	-	8	908	c.897delG	c.(895-897)ccgfs	p.P299fs	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	299							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)					CACTTTTACACGGTGGGGGTG	0.522													C|C|-|deletion	72	0.014377	0.0015	0.0303	5008	,	,		18793	0.0		0.0398	False		,,,				2504	0.0092				p.C300fs		Atlas-Indel	.											.	NUDT17	25	.	0			c.898delT						PASS	.			11,4255		0,11,2122	106.0	107.0	107.0			-8.2	0.0	1		106	142,8112		2,138,3987	no	frameshift	NUDT17	NM_001012758.2		2,149,6109	A1A1,A1R,RR		1.7204,0.2579,1.222			145586679	153,12367	2203	4300	6503	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.897delG	1.37:g.145586679delC	ENSP00000334437:p.Pro299fs	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	80	18	0.225	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			C|0.983;-|0.017	0.017	strong		0.522	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395	
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 GAIIx	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_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000547395.1_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	Somatic	41	.	.		WXS	Illumina HiSeq	Phase_I	52	11	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		
CHRFAM7A	89832	hgsc.bcm.edu	37	15	30665281	30665282	+	Frame_Shift_Del	DEL	CA	CA	-	rs200872014|rs201490160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:30665281_30665282delCA	ENST00000299847.2	-	6	680_681	c.227_228delTG	c.(226-228)ctgfs	p.L76fs	CHRFAM7A_ENST00000397827.3_5'UTR|CHRFAM7A_ENST00000401522.3_5'UTR|CHRFAM7A_ENST00000567722.1_5'Flank	NM_139320.1	NP_647536.1	Q494W8	CRFM7_HUMAN	CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion	76						integral component of membrane (GO:0016021)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(1)|skin(2)	6		all_lung(180;3.42e-11)|Breast(32;0.000153)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		ACCCAAACTTCAGTTTGCAGTG	0.505														1938	0.386981	0.0817	0.4409	5008	,	,		21827	0.6647		0.3777	False		,,,				2504	0.4847				p.76_77del		Atlas-Indel	.											.	CHRFAM7A	15	.	0			c.228_229del	GRCh37	CD025514	CHRFAM7A	D		PASS	.		,	570,2490		43,484,1003					,	2.1	1.0			64	2874,4020		317,2240,890	no	utr-5,frameshift	CHRFAM7A	NM_148911.1,NM_139320.1	,	360,2724,1893	A1A1,A1R,RR		41.6884,18.6275,34.5992	,	,		3444,6510				SO:0001589	frameshift_variant	89832	exon6			.	AF029838	CCDS32184.1, CCDS42008.1	15q13.2	2013-04-24	2006-02-01		ENSG00000166664	ENSG00000166664			15781	protein-coding gene	gene with protein product		609756				11829490	Standard	NM_139320		Approved	D-10, CHRNA7-DR1	uc001zdt.1	Q494W8	OTTHUMG00000175645	ENST00000299847.2:c.227_228delTG	15.37:g.30665281_30665282delCA	ENSP00000299847:p.Leu76fs	Somatic	1086	0	0		WXS	Illumina HiSeq	Phase_I	1183	697	0.58918	NM_139320	A8KAB9	Frame_Shift_Del	DEL	ENST00000299847.2	37	CCDS32184.1																																																																																			.	.	strong		0.505	CHRFAM7A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430700.1	NM_148911	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129924	175129925	+	In_Frame_Ins	INS	-	-	CTT	rs150137790|rs374766108		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:175129924_175129925insCTT	ENST00000423313.1	-	4	761_762	c.225_226insAAG	c.(223-228)aaggat>aagAAGgat	p.75_76insK	KIAA0040_ENST00000444639.1_In_Frame_Ins_p.75_76insK|KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000545251.2_In_Frame_Ins_p.75_76insK	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tcttcttcatccttcttcttct	0.505																																					p.D76delinsKD		Pindel,Atlas-Indel	.											.	KIAA0040	2	.	0			c.226_227insAAG						PASS	.																																			SO:0001652	inframe_insertion	9674	exon5			.	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.223_225dupAAG	1.37:g.175129931_175129933dupCTT	ENSP00000462172:p.Lys75_Lys75dup	Somatic	78	.	.		WXS	Illumina HiSeq	Phase_I	93	15	0.161	NM_001162893	A8K9H6|Q2NKQ0	In_Frame_Ins	INS	ENST00000423313.1	37																																																																																				.	.	alt		0.505	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
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 GAIIx	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		Somatic	145	.	.		WXS	Illumina HiSeq	Phase_I	143	57	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	
OR2W3	343171	hgsc.bcm.edu	37	1	248059353	248059355	+	In_Frame_Del	DEL	CTC	CTC	-	rs147816311|rs201631118	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248059353_248059355delCTC	ENST00000360358.3	+	1	465_467	c.465_467delCTC	c.(463-468)aactcc>aac	p.S156del	OR2W3_ENST00000537741.1_In_Frame_Del_p.S156del	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	156						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S156F(1)		breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GGGTGGCCAACTCCTTGGCCATG	0.64														104	0.0207668	0.0023	0.036	5008	,	,		19811	0.0		0.0477	False		,,,				2504	0.0286				p.155_156del		Pindel,Atlas-Indel	.											.	OR2W3	113	.	1	Substitution - Missense(1)	skin(1)	c.464_466del						PASS	.			41,4225		0,41,2092						2.8	1.0		dbSNP_134	74	413,7841		5,403,3719	no	coding	OR2W3	NM_001001957.2		5,444,5811	A1A1,A1R,RR		5.0036,0.9611,3.6262				454,12066				SO:0001651	inframe_deletion	343171	exon1			.	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.465_467delCTC	1.37:g.248059353_248059355delCTC	ENSP00000353516:p.Ser156del	Somatic	171	.	.		WXS	Illumina HiSeq	Phase_I	170	45	0.265	NM_001001957	Q6IF06|Q8NG86	In_Frame_Del	DEL	ENST00000360358.3	37	CCDS31099.1																																																																																			CTC|0.980;-|0.020	0.020	strong		0.640	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
LRRC17	10234	hgsc.bcm.edu	37	7	102575000	102575002	+	In_Frame_Del	DEL	GAA	GAA	-	rs3832497|rs77576273|rs531650613	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:102575000_102575002delGAA	ENST00000339431.4	+	2	935_937	c.640_642delGAA	c.(640-642)gaadel	p.E216del	FBXL13_ENST00000455112.2_Intron|FBXL13_ENST00000379305.3_Intron|FBXL13_ENST00000313221.4_Intron|FBXL13_ENST00000393772.2_Intron|FBXL13_ENST00000456695.1_Intron|FBXL13_ENST00000436908.1_Intron|FBXL13_ENST00000379308.3_Intron|FBXL13_ENST00000379306.3_Intron|LRRC17_ENST00000249377.4_In_Frame_Del_p.E216del	NM_001031692.2	NP_001026862.1	Q8N6Y2	LRC17_HUMAN	leucine rich repeat containing 17	216					bone marrow development (GO:0048539)|negative regulation of osteoclast differentiation (GO:0045671)|ossification (GO:0001503)	extracellular space (GO:0005615)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	17						GTTGTGTAATGAAGAAGAAAAGG	0.438														3164	0.631789	0.5416	0.7882	5008	,	,		18402	0.4375		0.8598	False		,,,				2504	0.6084				p.213_214del		Pindel,Atlas-Indel	.											.	LRRC17	45	.	0			c.639_641del						PASS	.		,,,	2463,1663		787,889,387					,,,	-1.8	0.4		dbSNP_107	39	6708,1498		2766,1176,161	no	intron,coding,intron,coding	LRRC17,FBXL13	NM_145032.3,NM_005824.2,NM_001111038.1,NM_001031692.2	,,,	3553,2065,548	A1A1,A1R,RR		18.2549,40.3054,25.6325	,,,	,,,		9171,3161				SO:0001651	inframe_deletion	10234	exon2			.	U32907	CCDS5727.1, CCDS34721.1	7q22.1	2009-05-26			ENSG00000128606	ENSG00000128606			16895	protein-coding gene	gene with protein product						8982252, 19336404	Standard	NM_005824		Approved	P37NB, H_RG318M05.3	uc003vau.3	Q8N6Y2	OTTHUMG00000157210	ENST00000339431.4:c.640_642delGAA	7.37:g.102575006_102575008delGAA	ENSP00000344242:p.Glu216del	Somatic	41	.	.		WXS	Illumina HiSeq	Phase_I	63	38	0.603	NM_005824	Q13288|Q6UWA7|Q75MG5	In_Frame_Del	DEL	ENST00000339431.4	37	CCDS34721.1																																																																																			GAA|0.331;-|0.669	0.669	strong		0.438	LRRC17-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347930.1	NM_005824	
TOP3A	7156	hgsc.bcm.edu	37	17	18205751	18205760	+	Intron	DEL	GGAGAGTGAA	GGAGAGTGAA	-	rs398030477|rs56191269|rs376457096|rs66697088	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGAGAGTGAA	GGAGAGTGAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18205751_18205760delGGAGAGTGAA	ENST00000321105.5	-	7	858				TOP3A_ENST00000540524.1_5'Flank|TOP3A_ENST00000542570.1_Intron	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha						DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						GGCAGCTCCTGGAGAGTGAAGGAGAGTGAA	0.51														1135	0.226637	0.3275	0.268	5008	,	,		22295	0.0605		0.3082	False		,,,				2504	0.1483				.		Pindel,Atlas-Indel	.											.	TOP3A	85	.	0			.						PASS	.			1400,2860		219,962,949						6.1	1.0		dbSNP_126	37	2430,5820		352,1726,2047	no	intron	TOP3A	NM_004618.3		571,2688,2996	A1A1,A1R,RR		29.4545,32.8638,30.6155				3830,8680				SO:0001627	intron_variant	7156	.			.	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.644-3TTCACTCTCC>-	17.37:g.18205761_18205770delGGAGAGTGAA		Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	64	19	0.297	.	A8KA61|B4DK80|D3DXC7|Q13473	Splice_Site	DEL	ENST00000321105.5	37	CCDS11194.1																																																																																			GGAGAGTGAA|0.758;-|0.242	0.242	strong		0.510	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
CCDC37	348807	hgsc.bcm.edu	37	3	126142434	126142436	+	In_Frame_Del	DEL	GGA	GGA	-	rs140223152|rs398102320|rs35657615|rs200815085	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:126142434_126142436delGGA	ENST00000352312.1	+	13	1332_1334	c.1233_1235delGGA	c.(1231-1236)acggag>acg	p.E412del	CCDC37_ENST00000393425.1_In_Frame_Del_p.E413del|CCDC37_ENST00000505024.1_In_Frame_Del_p.E413del	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	412				Missing (in Ref. 3; AAI01370/AAI01368). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		GCCAGGAGACGGAGAAGACCCTG	0.611														272	0.0543131	0.0068	0.0605	5008	,	,		17424	0.003		0.1223	False		,,,				2504	0.0971				p.411_412del		Pindel,Atlas-Indel	.											.	CCDC37	69	.	0			c.1232_1234del						PASS	.			125,4141		4,117,2012						2.6	1.0		dbSNP_134	96	1085,7169		63,959,3105	no	coding	CCDC37	NM_182628.2		67,1076,5117	A1A1,A1R,RR		13.1451,2.9301,9.6645				1210,11310				SO:0001651	inframe_deletion	348807	exon13			.	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1233_1235delGGA	3.37:g.126142434_126142436delGGA	ENSP00000344749:p.Glu412del	Somatic	111	.	.		WXS	Illumina HiSeq	Phase_I	108	29	0.269	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	In_Frame_Del	DEL	ENST00000352312.1	37	CCDS3037.1																																																																																			GGA|0.949;-|0.051	0.051	strong		0.611	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
OR13C2	392376	hgsc.bcm.edu	37	9	107367393	107367396	+	Frame_Shift_Del	DEL	GTTA	GTTA	-	rs112364120|rs143198170	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GTTA	GTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107367393_107367396delGTTA	ENST00000542196.1	-	1	555_558	c.513_516delTAAC	c.(511-516)aataacfs	p.NN171fs		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	171						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(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GATTGATGATGTTATTCCTGCAGA	0.451														1868	0.373003	0.4304	0.2161	5008	,	,		20908	0.5665		0.1789	False		,,,				2504	0.407				p.172_173del		Atlas-Indel	.											.	OR13C2	46	.	0			c.514_517del						PASS	.			1624,2632		344,936,848						1.3	0.3		dbSNP_129	138	1571,6681		165,1241,2720	no	frameshift	OR13C2	NM_001004481.1		509,2177,3568	A1A1,A1R,RR		19.0378,38.1579,25.5437				3195,9313				SO:0001589	frameshift_variant	392376	exon1			.		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.513_516delTAAC	9.37:g.107367393_107367396delGTTA	ENSP00000438815:p.Asn171fs	Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	267	93	0.348315	NM_001004481	B9EGV8|Q6IF54	Frame_Shift_Del	DEL	ENST00000542196.1	37	CCDS35092.1																																																																																			.	.	strong		0.451	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
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 GAIIx	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_ENST00000492597.1_Frame_Shift_Del_p.C400fs|MCCC1_ENST00000489909.1_5'UTR|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	Somatic	122	.	.		WXS	Illumina HiSeq	Phase_I	131	39	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	
EIF4EBP3	8637	hgsc.bcm.edu	37	5	139931629	139931630	+	IGR	INS	-	-	G	rs5871740|rs368142622|rs202193903	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139931629_139931630insG	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Frame_Shift_Ins_p.V110fs	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTCCATCACAGCCTCAGACT	0.594													-|-|G|insertion	2174	0.434105	0.2194	0.5144	5008	,	,		17103	0.5645		0.4831	False		,,,				2504	0.4826				p.V110fs		Atlas-Indel	.											SRA1,NS,carcinoma,+1,2	SRA1	24	2	0			c.328_329insC						PASS	.																																			SO:0001628	intergenic_variant	10011	exon3			.	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931629_139931630insG		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	106	31	0.292453	NM_001035235		Frame_Shift_Ins	INS	ENST00000310331.2	37	CCDS4226.1																																																																																			.	.	weak		0.594	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732	
DSPP	1834	hgsc.bcm.edu	37	4	88536543	88536551	+	In_Frame_Del	DEL	ACAGCAGTG	ACAGCAGTG	-	rs111215872|rs111456637	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	ACAGCAGTG	ACAGCAGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88536543_88536551delACAGCAGTG	ENST00000282478.7	+	4	2762_2770	c.2729_2737delACAGCAGTG	c.(2728-2739)aacagcagtgac>aac	p.SSD914del	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Del_p.SSD914del			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	914	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.S912S(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gatagcagcaacagcagtgacagcagtga	0.483														645	0.128794	0.3858	0.049	5008	,	,		40749	0.0109		0.0567	False		,,,				2504	0.0337				p.910_912del		Atlas-Indel	.											.	DSPP	174	.	1	Substitution - coding silent(1)	stomach(1)	c.2728_2736del						PASS	.			772,2314		137,498,908						-0.3	0.4		dbSNP_132	85	410,5168		83,244,2462	no	coding	DSPP	NM_014208.3		220,742,3370	A1A1,A1R,RR		7.3503,25.0162,13.6427				1182,7482				SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2729_2737delACAGCAGTG	4.37:g.88536552_88536560delACAGCAGTG	ENSP00000282478:p.Ser914_Asp916del	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	82	13	0.158537	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	37	CCDS43248.1																																																																																			ACAGCAGTG|0.500;-|0.500	0.500	weak		0.483	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
QRICH2	84074	hgsc.bcm.edu	37	17	74288565	74288567	+	In_Frame_Del	DEL	TGA	TGA	-	rs35035566|rs79093440|rs34007000	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74288565_74288567delTGA	ENST00000262765.5	-	4	1922_1924	c.1743_1745delTCA	c.(1741-1746)catcag>cag	p.H581del		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	581	Gln-rich.							p.H581Q(5)|p.Q582R(1)		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						CAAACCACGCTGATGATCTGCAC	0.537														2352	0.469649	0.7073	0.3098	5008	,	,		27303	0.5734		0.2753	False		,,,				2504	0.3548				p.582_582del		Atlas-Indel	.											QRICH2,NS,carcinoma,-1,1	QRICH2	143	1	6	Substitution - Missense(6)	kidney(4)|lung(2)	c.1744_1746del						PASS	.			2830,1434		943,944,245						1.4	0.0		dbSNP_126	148	2377,5877		324,1729,2074	no	coding	QRICH2	NM_032134.1		1267,2673,2319	A1A1,A1R,RR		28.7982,33.6304,41.5961				5207,7311				SO:0001651	inframe_deletion	84074	exon4			.	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.1743_1745delTCA	17.37:g.74288568_74288570delTGA	ENSP00000262765:p.His581del	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_032134	A2RRE1|Q96LM3	In_Frame_Del	DEL	ENST00000262765.5	37	CCDS32741.1																																																																																			TGA|0.548;-|0.452	0.452	strong		0.537	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
DMTF1	9988	hgsc.bcm.edu	37	7	86795881	86795883	+	In_Frame_Del	DEL	TGA	TGA	-	rs148453627	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGA	TGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:86795881_86795883delTGA	ENST00000394703.5	+	6	755_757	c.192_194delTGA	c.(190-195)attgat>att	p.D66del	DMTF1_ENST00000411766.2_Intron|DMTF1_ENST00000414194.2_5'UTR|DMTF1_ENST00000331242.7_In_Frame_Del_p.D66del|DMTF1_ENST00000394702.3_In_Frame_Del_p.D66del|DMTF1_ENST00000432937.2_5'UTR|DMTF1_ENST00000413276.2_In_Frame_Del_p.D66del	NM_021145.3	NP_066968.3	Q9Y222	DMTF1_HUMAN	cyclin D binding myb-like transcription factor 1	66	Interaction with CCND2. {ECO:0000250}.				cell cycle (GO:0007049)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)	16	Esophageal squamous(14;0.0058)					ATCAGAGTATTGATGATTCTACT	0.374														43	0.00858626	0.0015	0.0159	5008	,	,		18701	0.0		0.0298	False		,,,				2504	0.0				p.64_65del		Pindel,Atlas-Indel	.											.	DMTF1	48	.	0			c.191_193del						PASS	.																																			SO:0001651	inframe_deletion	9988	exon4			.	AF084530	CCDS5601.1, CCDS47633.1	7q21	2014-06-25			ENSG00000135164	ENSG00000135164			14603	protein-coding gene	gene with protein product	"""cyclin D-binding Myb-like protein"""	608491				10095122, 24958102	Standard	NR_024549		Approved	DMP1, DMTF, hDMP1, MRUL	uc003uih.3	Q9Y222	OTTHUMG00000154135	ENST00000394703.5:c.192_194delTGA	7.37:g.86795884_86795886delTGA	ENSP00000378193:p.Asp66del	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	91	23	0.253	NM_001142327	B2RBE1|B4DJS5|Q05C48|Q59G79|Q6IS13|Q969T2|Q9H2Z2|Q9H2Z3	In_Frame_Del	DEL	ENST00000394703.5	37	CCDS5601.1																																																																																			TGA|0.983;-|0.017	0.017	strong		0.374	DMTF1-002	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334025.5	NM_021145	
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176734	70176736	+	Stop_Codon_Del	DEL	CAG	CAG	-			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:70176734_70176736delCAG	ENST00000377420.1	-	0	2079_2081					NM_001126334.1	NP_001119806.1	Q5VV16	FX4L5_HUMAN	forkhead box D4-like 5						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|lung(2)	7						CCTGATACCTCAGCAGCGCCGAC	0.65																																					p.417_417del		Atlas-Indel	.											.	FOXD4L5	27	.	0			c.1249_1251del						PASS	.																																			SO:0001567	stop_retained_variant	653427	exon1			.		CCDS47977.1	9q13	2008-07-21			ENSG00000204779	ENSG00000204779			18522	protein-coding gene	gene with protein product						12234674	Standard	NM_001126334		Approved	bA15J10.2, OTTHUMG00000013332	uc010moc.3	Q5VV16	OTTHUMG00000013332	Exception_encountered	9.37:g.70176737_70176739delCAG	Exception_encountered	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	125	17	0.136	NM_001126334		In_Frame_Del	DEL	ENST00000377420.1	37	CCDS47977.1																																																																																			.	.	none		0.650	FOXD4L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037122.1	NM_001126334	
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 GAIIx	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_ENST00000503919.1_5'Flank|SLC23A1_ENST00000353963.3_Frame_Shift_Ins_p.G316fs	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	Somatic	85	.	.		WXS	Illumina HiSeq	Phase_I	99	16	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	
ZNF880	400713	hgsc.bcm.edu	37	19	52887246	52887247	+	In_Frame_Ins	INS	-	-	CAA	rs398071206|rs71836013|rs34678014		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52887246_52887247insCAA	ENST00000422689.2	+	4	428_429	c.413_414insCAA	c.(412-417)atcaac>atCAAcaac	p.140_141insN		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	140					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GAAAAACCTATCAACAATTCCT	0.312																																					p.I138delinsIN		Pindel,Atlas-Indel	.											.	ZNF880	45	.	0			c.413_414insCAA						PASS	.			958,2510		225,508,1001						-0.9	0.0		dbSNP_126	61	2771,4597		695,1381,1608	no	coding	ZNF880	NM_001145434.1		920,1889,2609	A1A1,A1R,RR		37.6086,27.624,34.4131				3729,7107				SO:0001652	inframe_insertion	400713	exon4			.	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.417_419dupCAA	19.37:g.52887250_52887252dupCAA	ENSP00000406318:p.Asn140_Asn140dup	Somatic	118	.	.		WXS	Illumina HiSeq	Phase_I	137	78	0.569	NM_001145434	B4DNA6	In_Frame_Ins	INS	ENST00000422689.2	37	CCDS46164.1																																																																																			-|0.657;CAA|0.343	0.343	strong		0.312	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057613	46057627	+	In_Frame_Del	DEL	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	-	rs66931310|rs375198526|rs56249559|rs55677560|rs77286437	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTGCTGTGTGCCTGT	CTGCTGTGTGCCTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46057613_46057627delCTGCTGTGTGCCTGT	ENST00000380095.1	+	1	341_355	c.279_293delCTGCTGTGTGCCTGT	c.(277-294)gcctgctgtgtgcctgtc>gcc	p.CCVPV104del	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	104	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						gccagcaggcctgctgtgtgcctgtctgctgtgtg	0.628														2493	0.497804	0.5575	0.6153	5008	,	,		22046	0.37		0.5736	False		,,,				2504	0.3875				p.93_98del		Atlas-Indel	.											.	KRTAP10-10	37	.	0			c.278_292del						PASS	.		,	2335,1929		615,1105,412					,	-1.6	0.0		dbSNP_130	113	4575,3679		1191,2193,743	no	coding,intron	TSPEAR,KRTAP10-10	NM_181688.1,NM_144991.2	,	1806,3298,1155	A1A1,A1R,RR		44.5723,45.2392,44.7995	,	,		6910,5608				SO:0001651	inframe_deletion	353333	exon1			.	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.279_293delCTGCTGTGTGCCTGT	21.37:g.46057613_46057627delCTGCTGTGTGCCTGT	ENSP00000369438:p.Cys104_Val108del	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	145	43	0.296552	NM_181688		In_Frame_Del	DEL	ENST00000380095.1	37	CCDS33585.1																																																																																			CTGCTGTGTGCCTGT|0.469;-|0.531	0.531	strong		0.628	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
ASMTL	8623	hgsc.bcm.edu	37	X	1522164	1522164	+	Stop_Codon_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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:1522164delA	ENST00000381317.3	-	0	1896				ASMTL-AS1_ENST00000425740.2_RNA|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL_ENST00000534940.1_Stop_Codon_Del|ASMTL_ENST00000381333.4_Stop_Codon_Del|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000443929.1_RNA|ASMTL_ENST00000416733.2_Stop_Codon_Del|ASMTL-AS1_ENST00000602357.1_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like							cytoplasm (GO:0005737)	O-methyltransferase activity (GO:0008171)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(9)|pancreas(1)|soft_tissue(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)				CCTGGGCTTCAGGGGGCCACT	0.607													a|A|-|deletion	385	0.076877	0.025	0.1427	5008	,	,		16677	0.0635		0.1074	False		,,,				2504	0.0828				p.X622X		Pindel,Atlas-Indel	.											.	ASMTL	56	.	0			c.1865delG						PASS	.		,,	176,3578		9,158,1710	47.0	49.0	49.0		,,	0.8	0.0	X		52	1024,6896		69,886,3005	no	frameshift,frameshift,frameshift	ASMTL	NM_004192.3,NM_001173474.1,NM_001173473.1	,,	78,1044,4715	A1A1,A1R,RR		12.9293,4.6883,10.2793	,,	,,	1522164	1200,10474	1952	4068	6020	SO:0001567	stop_retained_variant	8623	exon13			.	Y15521	CCDS43917.1, CCDS55362.1, CCDS55363.1	Xp22.3 and Yp11.3	2008-02-05			ENSG00000169093	ENSG00000169093		"""Pseudoautosomal regions / PAR1"""	751	protein-coding gene	gene with protein product		300162, 400011				9736779	Standard	NM_004192		Approved		uc004cpx.2	O95671	OTTHUMG00000021057	Exception_encountered	X.37:g.1522164delA	Exception_encountered	Somatic	112	.	.		WXS	Illumina HiSeq	Phase_I	61	15	0.246	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	In_Frame_Del	DEL	ENST00000381317.3	37	CCDS43917.1																																																																																			A|0.500;-|0.500	0.500	weak		0.607	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
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 GAIIx	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	RFC4_ENST00000296273.2_Frame_Shift_Del_p.V293fs|SNORA4_ENST00000584302.1_RNA|SNORA63_ENST00000363450.1_RNA|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	Somatic	134	.	.		WXS	Illumina HiSeq	Phase_I	112	24	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 GAIIx	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	Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	36	18	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	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482704	54482709	+	In_Frame_Del	DEL	GGGCCC	GGGCCC	-	rs76397255|rs398060196	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGGCCC	GGGCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54482704_54482709delGGGCCC	ENST00000317802.7	-	1	700_705	c.580_585delGGGCCC	c.(580-585)gggcccdel	p.GP194del	ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000303536.4_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	194					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						CCACGTTCAGGGGCCCGGGCCCGGGC	0.626														798	0.159345	0.1921	0.111	5008	,	,		19038	0.1865		0.1143	False		,,,				2504	0.1677				p.194_196del		Pindel,Atlas-Indel	.											.	TSPYL6	54	.	0			c.581_586del						PASS	.		,	65,738,2585		2,12,49,141,444,1046					,	0.3	0.0		dbSNP_134	31	3,1183,6334		0,1,2,162,858,2737	no	intron,codingComplex	ACYP2,TSPYL6	NM_138448.3,NM_001003937.2	,	2,13,51,303,1302,3783	A1A1,A1A2,A1R,A2A2,A2R,RR		15.7713,23.7013,18.2343	,	,		68,1921,8919				SO:0001651	inframe_deletion	388951	exon1			.	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.580_585delGGGCCC	2.37:g.54482710_54482715delGGGCCC	ENSP00000417919:p.Gly194_Pro195del	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	64	20	0.312	NM_001003937	Q6NUJ3	In_Frame_Del	DEL	ENST00000317802.7	37	CCDS42682.1																																																																																			GGGCCC|0.831;-|0.169	0.169	strong		0.626	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361452	+	Frame_Shift_Del	DEL	GC	GC	-	rs376107801|rs201540433|rs377523807|rs199665292	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107361451_107361452delGC	ENST00000374779.2	-	1	336_337	c.243_244delGC	c.(241-246)acgctafs	p.L82fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AAGCTCACTAGCGTGGAGGGAA	0.51																																					p.82_82del		Atlas-Indel	.											.	OR13C5	60	.	0			c.244_245del						PASS	.																																			SO:0001589	frameshift_variant	138799	exon1			.		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.243_244delGC	9.37:g.107361451_107361452delGC	ENSP00000363911:p.Leu82fs	Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	325	50	0.153846	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	CCDS35091.1																																																																																			GC|0.500;-|0.500	0.500	strong		0.510	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
WDR73	84942	hgsc.bcm.edu	37	15	85186877	85186894	+	In_Frame_Del	DEL	CTTGGCTCCGTGTTCCAT	CTTGGCTCCGTGTTCCAT	-	rs370347033|rs373448317|rs11267906|rs372798651|rs199676984	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTTGGCTCCGTGTTCCAT	CTTGGCTCCGTGTTCCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:85186877_85186894delCTTGGCTCCGTGTTCCAT	ENST00000434634.2	-	8	1004_1021	c.944_961delATGGAACACGGAGCCAAG	c.(943-963)gatggaacacggagccaagta>gta	p.DGTRSQ315del	SCAND2P_ENST00000348993.5_RNA|WDR73_ENST00000398528.3_5'UTR	NM_032856.2	NP_116245.2	Q6P4I2	WDR73_HUMAN	WD repeat domain 73	315										cervix(1)|large_intestine(1)|lung(1)	3						AGAGGTTCTACTTGGCTCCGTGTTCCATCTTGGCTCCG	0.509														794	0.158546	0.1399	0.1383	5008	,	,		21272	0.0843		0.2038	False		,,,				2504	0.228				p.315_321del		Pindel,Atlas-Indel	.											.	WDR73	15	.	0			c.945_962del						PASS	.			344,3500		48,248,1626						-0.4	0.0		dbSNP_120	111	1220,6750		177,866,2942	no	coding	WDR73	NM_032856.2		225,1114,4568	A1A1,A1R,RR		15.3074,8.949,13.2385				1564,10250				SO:0001651	inframe_deletion	84942	exon8			.	AK027200	CCDS45339.1	15q25.2	2013-01-09				ENSG00000177082		"""WD repeat domain containing"""	25928	protein-coding gene	gene with protein product						12477932	Standard	NM_032856		Approved	FLJ14888, HSPC264	uc002bkw.2	Q6P4I2		ENST00000434634.2:c.944_961delATGGAACACGGAGCCAAG	15.37:g.85186877_85186894delCTTGGCTCCGTGTTCCAT	ENSP00000387982:p.Asp315_Gln320del	Somatic	120	.	.		WXS	Illumina HiSeq	Phase_I	88	26	0.295	NM_032856	Q96JZ1|Q9P0B7	In_Frame_Del	DEL	ENST00000434634.2	37	CCDS45339.1																																																																																			.	.	strong		0.509	WDR73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418195.1	NM_032856	
IL32	9235	hgsc.bcm.edu	37	16	3119297	3119298	+	Frame_Shift_Ins	INS	-	-	G	rs71818662|rs531600758	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3119297_3119298insG	ENST00000534507.1	+	6	857_858	c.646_647insG	c.(646-648)cggfs	p.R216fs	IL32_ENST00000396887.3_Frame_Shift_Ins_p.R113fs|IL32_ENST00000549213.1_Frame_Shift_Ins_p.R113fs|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000552356.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000526464.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000551513.1_Frame_Shift_Ins_p.R207fs|IL32_ENST00000530538.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000008180.9_Frame_Shift_Ins_p.R150fs|IL32_ENST00000533097.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000440815.3_Frame_Shift_Ins_p.R170fs|IL32_ENST00000325568.5_Frame_Shift_Ins_p.R170fs|IL32_ENST00000525643.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000552664.1_Frame_Shift_Ins_p.R170fs|IL32_ENST00000396890.2_Frame_Shift_Ins_p.R216fs|IL32_ENST00000548652.1_Frame_Shift_Ins_p.R161fs|IL32_ENST00000528163.2_Frame_Shift_Ins_p.R170fs|IL32_ENST00000529550.1_Frame_Shift_Ins_p.R170fs|IL32_ENST00000529699.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000382213.3_Frame_Shift_Ins_p.R161fs|IL32_ENST00000548246.1_Frame_Shift_Ins_p.R130fs|IL32_ENST00000444393.3_Frame_Shift_Ins_p.R170fs|IL32_ENST00000552936.1_Frame_Shift_Ins_p.R194fs|IL32_ENST00000548476.1_Frame_Shift_Ins_p.R216fs|IL32_ENST00000530890.1_Frame_Shift_Ins_p.R150fs|IL32_ENST00000551122.1_Frame_Shift_Ins_p.R113fs|IL32_ENST00000531965.1_Frame_Shift_Ins_p.R160fs			P24001	IL32_HUMAN	interleukin 32	216					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)		p.D172fs*12(3)		breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CGGAGCCCCACGGGGGGACAAG	0.579																																					p.R170fs		Pindel,Atlas-Indel	.											IL32,NS,carcinoma,0,1	IL32	32	1	3	Insertion - Frameshift(3)	urinary_tract(1)|breast(1)|pancreas(1)	c.508_509insG						PASS	.																																			SO:0001589	frameshift_variant	9235	exon7			.	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.652dupG	16.37:g.3119303_3119303dupG	ENSP00000431775:p.Arg216fs	Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	172	27	0.157	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Frame_Shift_Ins	INS	ENST00000534507.1	37																																																																																				.	.	strong		0.579	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
OR52A1	23538	hgsc.bcm.edu	37	11	5172795	5172796	+	Frame_Shift_Ins	INS	-	-	C	rs112098990	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5172795_5172796insC	ENST00000380367.1	-	2	1221_1222	c.804_805insG	c.(802-807)gggtctfs	p.S269fs	OR52A1_ENST00000328942.1_Frame_Shift_Ins_p.S269fs			Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A, member 1	269					sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	19		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGATGTGAGACCCAAACCTAT	0.436													CCC|CCC|CCCC|insertion	980	0.195687	0.1399	0.2738	5008	,	,		18188	0.0278		0.2445	False		,,,				2504	0.3384				p.S269fs		Pindel,Atlas-Indel	.											OR52A1,NS,carcinoma,+1,1	OR52A1	58	1	0			c.805_806insG						PASS	.			597,3667		41,515,1576						-1.6	0.3		dbSNP_132	163	2117,6137		287,1543,2297	no	frameshift	OR52A1	NM_012375.2		328,2058,3873	A1A1,A1R,RR		25.6482,14.0009,21.6808				2714,9804				SO:0001589	frameshift_variant	23538	exon1			.	AF154673	CCDS31374.1	11p15.4	2012-08-09			ENSG00000182070	ENSG00000182070		"""GPCR / Class A : Olfactory receptors"""	8318	protein-coding gene	gene with protein product						10512676	Standard	NM_012375		Approved	HPFH1OR	uc010qyy.2	Q9UKL2	OTTHUMG00000066603	ENST00000380367.1:c.805dupG	11.37:g.5172798_5172798dupC	ENSP00000369725:p.Ser269fs	Somatic	76	.	.		WXS	Illumina HiSeq	Phase_I	81	28	0.346	NM_012375	Q6IF31	Frame_Shift_Ins	INS	ENST00000380367.1	37	CCDS31374.1																																																																																			-|0.838;C|0.162	0.162	strong		0.436	OR52A1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142810.2	NM_012375	
TRIM52	84851	hgsc.bcm.edu	37	5	180687429	180687431	+	In_Frame_Del	DEL	TCT	TCT	-	rs200454506|rs78075294|rs3073543|rs33972170	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180687429_180687431delTCT	ENST00000327767.4	-	1	688_690	c.384_386delAGA	c.(382-387)gaagag>gag	p.128_129EE>E	TRIM52_ENST00000514805.1_5'UTR|TRIM52-AS1_ENST00000507434.1_RNA|CTC-338M12.4_ENST00000505151.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA|TRIM52-AS1_ENST00000509252.1_RNA|CTC-338M12.4_ENST00000511331.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	128	Glu-rich.				positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		CTGATCTTCCTCTTCTTCTTCTT	0.453														2462	0.491613	0.916	0.304	5008	,	,		21160	0.3393		0.2773	False		,,,				2504	0.4284				p.129_129del		Pindel	.											.	TRIM52	20	.	0			c.385_387del						PASS	.																																			SO:0001651	inframe_deletion	84851	exon1			.		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19024	protein-coding gene	gene with protein product			"""tripartite motif-containing 52"""				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.384_386delAGA	5.37:g.180687438_180687440delTCT	ENSP00000332152:p.Glu130del	Somatic	131	.	.		WXS	Illumina HiSeq	Phase_I	114	54	0.474	NM_032765		In_Frame_Del	DEL	ENST00000327767.4	37	CCDS4467.1																																																																																			TCT|0.580;-|0.420	0.420	strong		0.453	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765	
KLF17	128209	hgsc.bcm.edu	37	1	44596380	44596382	+	In_Frame_Del	DEL	CAA	CAA	-	rs200059598|rs34057178	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:44596380_44596382delCAA	ENST00000372299.3	+	3	1180_1182	c.1122_1124delCAA	c.(1120-1125)gccaac>gcc	p.N378del	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	378					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					ACCCACAGGCCAACAACAACAAT	0.493														1153	0.230232	0.0719	0.2723	5008	,	,		21631	0.2887		0.175	False		,,,				2504	0.411				p.374_375del		Pindel	.											.	KLF17	92	.	0			c.1121_1123del						PASS	.			430,3836		27,376,1730						-0.7	0.0		dbSNP_126	87	1593,6661		149,1295,2683	no	coding	KLF17	NM_173484.3		176,1671,4413	A1A1,A1R,RR		19.2997,10.0797,16.1581				2023,10497				SO:0001651	inframe_deletion	128209	exon3			.	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.1122_1124delCAA	1.37:g.44596389_44596391delCAA	ENSP00000361373:p.Asn378del	Somatic	81	.	.		WXS	Illumina HiSeq	Phase_I	65	18	0.277	NM_173484	Q86VQ7|Q8N805	In_Frame_Del	DEL	ENST00000372299.3	37	CCDS508.1																																																																																			CAA|0.811;-|0.189	0.189	strong		0.493	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
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 GAIIx	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_ENST00000559916.1_Frame_Shift_Del_p.IV112fs|B2M_ENST00000559220.1_Intron|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	Somatic	71	.	.		WXS	Illumina HiSeq	Phase_I	51	17	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	
LINC00238	440184	hgsc.bcm.edu	37	14	66953309	66953310	+	lincRNA	DEL	TC	TC	-	rs147152268|rs10569333	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:66953309_66953310delTC	ENST00000556874.1	-	0	643				LINC00238_ENST00000389594.3_RNA																							GAAAAGAGGGtctctctctctc	0.416														1824	0.364217	0.7383	0.3487	5008	,	,		19252	0.1389		0.2386	False		,,,				2504	0.2311				.		Pindel	.											.	.	.	.	0			.						PASS	.																																					440184	.			.																													14.37:g.66953319_66953320delTC		Somatic	37	.	.		WXS	Illumina HiSeq	Phase_I	52	14	0.269	.		RNA	DEL	ENST00000556874.1	37																																																																																				TC|0.500;-|0.500	0.500	strong		0.416	RP11-72M17.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000412209.1		
OR5P2	120065	hgsc.bcm.edu	37	11	7818383	7818384	+	In_Frame_Ins	INS	-	-	ATATGGTTACCAGGTAGATGC	rs138967151	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7818383_7818384insATATGGTTACCAGGTAGATGC	ENST00000329434.2	-	1	136_137	c.106_107insGCATCTACCTGGTAACCATAT	c.(106-108)tct>tGCATCTACCTGGTAACCATATct	p.35_36insCIYLVTI	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAGATTACCAGATAGGATGATC	0.436														1170	0.233626	0.3404	0.2896	5008	,	,		17899	0.128		0.2763	False		,,,				2504	0.1145				p.S36delinsCIYLVTIS		Pindel	.											.	OR5P2	68	.	0			c.107_108insGCATCTACCTGGTAACCATAT						PASS	.																																			SO:0001652	inframe_insertion	120065	exon1			.	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.106_107insGCATCTACCTGGTAACCATAT	11.37:g.7818383_7818384insATATGGTTACCAGGTAGATGC	ENSP00000331823:p.Leu35_Ser36insCysIleTyrLeuValThrIle	Somatic	51	.	.		WXS	Illumina HiSeq	Phase_I	27	13	0.481	NM_153444	Q3MIS8	In_Frame_Ins	INS	ENST00000329434.2	37	CCDS7782.1																																																																																			.	.	strong		0.436	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
TNRC6B	23112	hgsc.bcm.edu	37	22	40697177	40697179	+	In_Frame_Del	DEL	GCA	GCA	-	rs66700157|rs10617561|rs139908	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:40697177_40697179delGCA	ENST00000454349.2	+	15	4171_4173	c.3960_3962delGCA	c.(3958-3963)ctgcag>ctg	p.Q1328del	TNRC6B_ENST00000301923.9_In_Frame_Del_p.Q524del|TNRC6B_ENST00000402203.1_In_Frame_Del_p.Q524del|TNRC6B_ENST00000335727.9_In_Frame_Del_p.Q1218del	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1328	Silencing domain; interaction with CNOT1 and PAN3.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						TGAGTGCACTgcagcagcagcag	0.596														1289	0.257388	0.4622	0.1499	5008	,	,		20853	0.0179		0.2396	False		,,,				2504	0.3221				p.1320_1321del		Pindel	.											.	TNRC6B	195	.	0			c.3959_3961del						PASS	.																																			SO:0001651	inframe_deletion	23112	exon15			.	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"""Trinucleotide (CAG) repeat containing"""	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.3960_3962delGCA	22.37:g.40697186_40697188delGCA	ENSP00000401946:p.Gln1328del	Somatic	27	.	.		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	In_Frame_Del	DEL	ENST00000454349.2	37	CCDS54533.1																																																																																			GCA|0.779;-|0.221	0.221	strong		0.596	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding			
PI4KAP2	375133	hgsc.bcm.edu	37	22	21829514	21829517	+	RNA	DEL	TGTC	TGTC	-	rs113567369|rs57294418	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:21829514_21829517delTGTC	ENST00000450651.1	-	0	1821_1824							A4QPH2	PI4P2_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha pseudogene 2						phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(3)|urinary_tract(1)	4						AGAGCTTGATTGTCTGGCCGCGAA	0.564														3270	0.652955	0.8162	0.5865	5008	,	,		11476	0.4454		0.8708	False		,,,				2504	0.4693				.		Pindel	.											.	PI4KAP2	11	.	0			.						PASS	.			3028,976		1236,556,210						2.4	1.0		dbSNP_132	21	6139,1303		2723,693,305	no	intergenic				3959,1249,515	A1A1,A1R,RR		17.5087,24.3756,19.9109				9167,2279						375133	.			.			22q11.21	2014-03-20	2007-08-14		ENSG00000183506	ENSG00000183506			33577	pseudogene	pseudogene							Standard	NR_003700		Approved		uc011aie.1	A4QPH2	OTTHUMG00000150827		22.37:g.21829514_21829517delTGTC		Somatic	155	.	.		WXS	Illumina HiSeq	Phase_I	97	29	0.299	.	Q6ICJ0|Q6ZT68|Q8WUK7	RNA	DEL	ENST00000450651.1	37																																																																																				TGTC|0.500;-|0.500	0.500	strong		0.564	PI4KAP2-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000334908.1		
EVA1A	84141	hgsc.bcm.edu	37	2	75720569	75720577	+	In_Frame_Del	DEL	GCTGTCGCT	GCTGTCGCT	-	rs201833026|rs148155576	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GCTGTCGCT	GCTGTCGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:75720569_75720577delGCTGTCGCT	ENST00000233712.1	-	4	681_689	c.244_252delAGCGACAGC	c.(244-252)agcgacagcdel	p.SDS82del	EVA1A_ENST00000490746.1_Intron|EVA1A_ENST00000393913.3_In_Frame_Del_p.SDS82del|EVA1A_ENST00000410071.1_In_Frame_Del_p.SDS82del|EVA1A_ENST00000410113.1_In_Frame_Del_p.SDS82del|EVA1A_ENST00000410010.1_In_Frame_Del_p.SDS70del	NM_032181.2	NP_115557.1	Q9H8M9	EVA1A_HUMAN	eva-1 homolog A (C. elegans)	82					apoptotic process (GO:0006915)|autophagy (GO:0006914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.D83N(2)									TGCCATCCTCGCTGTCGCTGCTGTCGCTG	0.603														221	0.0441294	0.0772	0.036	5008	,	,		20655	0.001		0.0537	False		,,,				2504	0.0399				p.82_85del		Pindel	.											.	.	.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.245_253del						PASS	.		,	303,3963		17,269,1847					,	5.1	1.0		dbSNP_130	60	438,7816		26,386,3715	no	coding,coding	FAM176A	NM_032181.2,NM_001135032.1	,	43,655,5562	A1A1,A1R,RR		5.3065,7.1027,5.9185	,	,		741,11779				SO:0001651	inframe_deletion	84141	exon4			.	BC016157	CCDS1959.1	2p12	2012-11-05	2012-11-05	2012-11-05	ENSG00000115363	ENSG00000115363			25816	protein-coding gene	gene with protein product			"""transmembrane protein 166"", ""family with sequence similarity 176, member A"""	TMEM166, FAM176A		12477932	Standard	NM_001135032		Approved	FLJ13391	uc002sni.2	Q9H8M9	OTTHUMG00000129991	ENST00000233712.1:c.244_252delAGCGACAGC	2.37:g.75720578_75720586delGCTGTCGCT	ENSP00000233712:p.Ser82_Ser84del	Somatic	62	.	.		WXS	Illumina HiSeq	Phase_I	55	11	0.200	NM_001135032	D6W5J3|Q9HC41	In_Frame_Del	DEL	ENST00000233712.1	37	CCDS1959.1																																																																																			GCTGTCGCT|0.959;-|0.041	0.041	strong		0.603	EVA1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328707.1	NM_032181	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026115	176026138	+	In_Frame_Del	DEL	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	-	rs3797464|rs200519605|rs386695335|rs550332435|rs142779818|rs371149640|rs199714570|rs373697082|rs201635586	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176026115_176026138delCCTTTCTCAAAGACCCAGGATCCT	ENST00000303991.4	-	2	875_898	c.698_721delAGGATCCTGGGTCTTTGAGAAAGG	c.(697-723)gaggatcctgggtctttgagaaaggtg>gtg	p.EDPGSLRK233del		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	233				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)		p.L238L(1)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAGGATCCACCTTTCTCAAAGACCCAGGATCCTCCTTCCTCGG	0.496																																					p.233_241del		Pindel	.											.	GPRIN1	77	.	1	Substitution - coding silent(1)	lung(1)	c.699_722del						PASS	.																																			SO:0001651	inframe_deletion	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.698_721delAGGATCCTGGGTCTTTGAGAAAGG	5.37:g.176026115_176026138delCCTTTCTCAAAGACCCAGGATCCT	ENSP00000305839:p.Glu233_Lys240del	Somatic	141	.	.		WXS	Illumina HiSeq	Phase_I	104	26	0.250	NM_052899	C9JM70|Q8ND74|Q96PZ4	In_Frame_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	none		0.496	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
RBM27	54439	hgsc.bcm.edu	37	5	145647319	145647320	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:145647319_145647320insA	ENST00000265271.5	+	15	2605_2606	c.2439_2440insA	c.(2440-2442)aaafs	p.K814fs	RBM27_ENST00000506502.1_Frame_Shift_Ins_p.K759fs	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	814					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K816fs*5(1)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AAGAAGTGCTTAAAAAAAAACA	0.351																																					p.L813fs		Pindel	.											.	RBM27	119	.	1	Deletion - Frameshift(1)	ovary(1)	c.2439_2440insA						PASS	.																																			SO:0001589	frameshift_variant	54439	exon15			.	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.2448dupA	5.37:g.145647328_145647328dupA	ENSP00000265271:p.Lys814fs	Somatic	220	.	.		WXS	Illumina HiSeq	Phase_I	266	41	0.154	NM_018989	Q8IYW9	Frame_Shift_Ins	INS	ENST00000265271.5	37	CCDS43378.1																																																																																			.	.	none		0.351	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
EIF4EBP3	8637	hgsc.bcm.edu	37	5	139931629	139931629	+	IGR	DEL	C	C	-	rs5871740|rs368142622|rs202193903	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139931629delC	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Frame_Shift_Del_p.V110fs	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTCCATCACAGCCTCAGAC	0.592																																					p.V110fs		Pindel	.											SRA1,NS,carcinoma,0,2	SRA1	24	2	0			c.329delT						PASS	.						82.0	59.0	67.0					5																	139931629		2202	4295	6497	SO:0001628	intergenic_variant	10011	exon3			.	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931629delC		Somatic	153	.	.		WXS	Illumina HiSeq	Phase_I	108	17	0.157	NM_001035235		Frame_Shift_Del	DEL	ENST00000310331.2	37	CCDS4226.1																																																																																			.	.	strong		0.592	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732	
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 GAIIx	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	Somatic	116	.	.		WXS	Illumina HiSeq	Phase_I	84	21	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 GAIIx	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	Somatic	86	.	.		WXS	Illumina HiSeq	Phase_I	67	12	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	
MAB21L1	4081	hgsc.bcm.edu	37	13	36050434	36050451	+	5'UTR	DEL	CTGCTGCTGCTGCTGCTG	CTGCTGCTGCTGCTGCTG	-	rs146621732|rs376319884|rs372625772	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTGCTGCTGCTGCTGCTG	CTGCTGCTGCTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:36050434_36050451delCTGCTGCTGCTGCTGCTG	ENST00000379919.4	-	0	381_398				NBEA_ENST00000540320.1_Intron|NBEA_ENST00000379939.2_Intron|NBEA_ENST00000400445.3_Intron|NBEA_ENST00000310336.4_Intron|NBEA_ENST00000537702.1_5'Flank	NM_005584.4	NP_005575.1	Q13394	MB211_HUMAN	mab-21-like 1 (C. elegans)						anatomical structure morphogenesis (GO:0009653)|camera-type eye development (GO:0043010)|positive regulation of cell proliferation (GO:0008284)	nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	20		Breast(139;0.014)|Lung SC(185;0.051)|Prostate(109;0.202)		all cancers(112;9.63e-08)|Epithelial(112;1.37e-06)|BRCA - Breast invasive adenocarcinoma(63;0.000659)|OV - Ovarian serous cystadenocarcinoma(117;0.00372)|GBM - Glioblastoma multiforme(144;0.115)		GTTGGTTTCCctgctgctgctgctgctgctgctgctgc	0.56																																					.		Pindel	.											.	MAB21L1	52	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	4081	.			.	BC028170	CCDS9353.1	13q13.3	2008-02-05	2001-11-28		ENSG00000180660	ENSG00000180660			6757	protein-coding gene	gene with protein product		601280	"""mab-21 (C. elegans)-like 1"""			8733127	Standard	NM_005584		Approved	CAGR1		Q13394	OTTHUMG00000016723	ENST00000379919.4:c.-176CAGCAGCAGCAGCAGCAG>-	13.37:g.36050434_36050451delCTGCTGCTGCTGCTGCTG		Somatic	73	.	.		WXS	Illumina HiSeq	Phase_I	59	11	0.186	.	Q6I9T5	RNA	DEL	ENST00000379919.4	37	CCDS9353.1																																																																																			.	.	alt		0.560	MAB21L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044459.3	NM_005584	
CACNA1B	774	hgsc.bcm.edu	37	9	140918171	140918185	+	In_Frame_Del	DEL	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	-	rs145816559|rs11137342|rs370787788|rs551405755	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GGAGAAGGAGACCAC	GGAGAAGGAGACCAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:140918171_140918185delGGAGAAGGAGACCAC	ENST00000371372.1	+	19	3121_3135	c.2976_2990delGGAGAAGGAGACCAC	c.(2974-2991)gtggagaaggagaccacg>gtg	p.EKETT993del	CACNA1B_ENST00000277549.5_In_Frame_Del_p.EKETT185del|CACNA1B_ENST00000277551.2_In_Frame_Del_p.EKETT993del|CACNA1B_ENST00000371367.5_5'UTR|CACNA1B_ENST00000545473.1_5'Flank|CACNA1B_ENST00000371363.1_In_Frame_Del_p.EKETT993del|CACNA1B_ENST00000371355.4_In_Frame_Del_p.EKETT994del|CACNA1B_ENST00000371357.1_In_Frame_Del_p.EKETT994del	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	993					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.T996_E1000delTTEKE(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	ACGAGGCTGTGGAGAAGGAGACCACGGAGAAGGAG	0.735														1990	0.397364	0.6225	0.1282	5008	,	,		9031	0.6349		0.1521	False		,,,				2504	0.2914				p.992_997del		Pindel	.											.	CACNA1B	266	.	1	Deletion - In frame(1)	breast(1)	c.2975_2989del						PASS	.			1091,1197		364,363,417						-1.3	0.0		dbSNP_134	8	691,4399		126,439,1980	no	coding	CACNA1B	NM_000718.3		490,802,2397	A1A1,A1R,RR		13.5756,47.6836,24.1529				1782,5596				SO:0001651	inframe_deletion	774	exon19			.	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.2976_2990delGGAGAAGGAGACCAC	9.37:g.140918171_140918185delGGAGAAGGAGACCAC	ENSP00000360423:p.Glu993_Thr997del	Somatic	87	.	.		WXS	Illumina HiSeq	Phase_I	72	17	0.236	NM_001243812	B1AQK5	In_Frame_Del	DEL	ENST00000371372.1	37	CCDS59522.1																																																																																			GGAGAAGGAGACCAC|0.621;-|0.379	0.379	strong		0.735	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
NRD1	4898	hgsc.bcm.edu	37	1	52306064	52306066	+	In_Frame_Del	DEL	TCT	TCT	-	rs397701944|rs35723519|rs72663147|rs60220085	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:52306064_52306066delTCT	ENST00000354831.7	-	2	651_653	c.462_464delAGA	c.(460-465)gaagat>gat	p.E154del	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_In_Frame_Del_p.E22del|NRD1_ENST00000539524.1_In_Frame_Del_p.E22del|NRD1_ENST00000352171.7_In_Frame_Del_p.E154del	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	0	Asp/Glu-rich (highly acidic).				cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.E154D(1)		NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						ttcatcatcatcttcttcttctt	0.384														2813	0.561701	0.3132	0.6888	5008	,	,		19365	0.9256		0.5457	False		,,,				2504	0.4489				p.155_155del		Pindel	.											NRD1,caecum,carcinoma,0,1	NRD1	89	1	1	Substitution - Missense(1)	pancreas(1)	c.463_465del						PASS	.																																			SO:0001651	inframe_deletion	4898	exon2			.	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.462_464delAGA	1.37:g.52306073_52306075delTCT	ENSP00000346890:p.Glu154del	Somatic	229	.	.		WXS	Illumina HiSeq	Phase_I	242	76	0.314	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	In_Frame_Del	DEL	ENST00000354831.7	37	CCDS559.1																																																																																			TCT|0.388;-|0.612	0.612	strong		0.384	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
PLD1	5337	hgsc.bcm.edu	37	3	171455452	171455452	+	Intron	DEL	A	A	-	rs545683379		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:171455452delA	ENST00000351298.4	-	3	287				PLD1_ENST00000356327.5_Intron|PLD1_ENST00000342215.6_Intron|PLD1_ENST00000340989.4_Intron	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific						chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GATATACACTAAAAAAAAAAG	0.323																																					.	NSCLC(149;2174 3517 34058)	Pindel	.											.	PLD1	134	.	0			c.161-2T>-						PASS	.		,	25,150,4089		0,0,25,0,150,1957	43.0	44.0	44.0		,	5.4	0.9	3	dbSNP_130	48	26,282,7944		0,0,26,1,280,3819	no	intron,intron	PLD1	NM_002662.4,NM_001130081.2	,	0,0,51,1,430,5776	A1A1,A1A2,A1R,A2A2,A2R,RR		3.7324,4.1041,3.8591	,	,	171455452	51,432,12033	2203	4299	6502	SO:0001627	intron_variant	5337	exon4			.	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.161-3T>-	3.37:g.171455452delA		Somatic	39	.	.		WXS	Illumina HiSeq	Phase_I	56	14	0.250	NM_001130081		Splice_Site	DEL	ENST00000351298.4	37	CCDS3216.1																																																																																			.	.	none		0.323	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
LRRC37A3	374819	hgsc.bcm.edu	37	17	62882286	62882287	+	Splice_Site	INS	-	-	A			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:62882286_62882287insA	ENST00000584306.1	-	7	3356		c.e7-2		LRRC37A3_ENST00000339474.5_Intron|LRRC37A3_ENST00000319651.5_Splice_Site|LRRC37A3_ENST00000400877.3_Splice_Site	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3							integral component of membrane (GO:0016021)				NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						CTAAGATTTCTAAAAAAAAAAG	0.307																																					.		Pindel	.											.	LRRC37A3	75	.	0			c.2826-2->T						PASS	.																																			SO:0001630	splice_region_variant	374819	exon8			.	AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.2826-2->T	17.37:g.62882296_62882296dupA		Somatic	93	.	.		WXS	Illumina HiSeq	Phase_I	100	21	0.210	NM_199340	Q49A01|Q49A80|Q8NB33	Splice_Site	INS	ENST00000584306.1	37	CCDS32708.1																																																																																			.	.	none		0.307	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	Intron
HLA-B	3106	hgsc.bcm.edu	37	6	31324525	31324531	+	Frame_Shift_Del	DEL	CCTGGGC	CCTGGGC	-	rs41546313|rs41548914|rs1140404|rs1131212|rs1131204|rs1131213|rs1071817|rs71533898	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCTGGGC	CCTGGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31324525_31324531delCCTGGGC	ENST00000412585.2	-	2	305_311	c.277_283delGCCCAGG	c.(277-285)gcccaggcafs	p.AQA93fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	93	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						TCAGTCTGTGCCTGGGCCTTGTAGATC	0.676									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.93_95del		Pindel	.											.	HLA-B	54	.	0			c.278_284del						PASS	.																																			SO:0001589	frameshift_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	.	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.277_283delGCCCAGG	6.37:g.31324525_31324531delCCTGGGC	ENSP00000399168:p.Ala93fs	Somatic	37	.	.		WXS	Illumina HiSeq	Phase_I	98	39	0.398	NM_005514	Q29764	Frame_Shift_Del	DEL	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	none		0.676	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
RTN1	6252	hgsc.bcm.edu	37	14	60063508	60063508	+	Intron	DEL	A	A	-	rs529779690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:60063508delA	ENST00000267484.5	-	9	2624				RTN1_ENST00000557422.1_Intron|RTN1_ENST00000395090.1_Intron|RTN1_ENST00000342503.4_Intron	NM_021136.2	NP_066959.1	Q16799	RTN1_HUMAN	reticulon 1						neuron differentiation (GO:0030182)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(30)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(108;0.0968)		CCTGAATCCTAAAAAGACAGT	0.383													AAAAA|AAAAA|AAAA|deletion	3	0.000599042	0.0	0.0	5008	,	,		19776	0.0		0.003	False		,,,				2504	0.0				.		Pindel	.											.	RTN1	139	.	0			c.2289-2T>-						PASS	.		,,	3,4259		0,3,2128	120.0	113.0	115.0		,,	5.7	1.0	14		116	31,8223		0,31,4096	no	intron,intron,intron	RTN1	NM_206857.1,NM_206852.2,NM_021136.2	,,	0,34,6224	A1A1,A1R,RR		0.3756,0.0704,0.2717	,,	,,	60063508	34,12482	2203	4300	6503	SO:0001627	intron_variant	6252	exon10			.	L10333	CCDS9740.1, CCDS9741.1	14q21-q22	2008-08-29			ENSG00000139970	ENSG00000139970			10467	protein-coding gene	gene with protein product		600865	"""neuroendocrine-specific protein"""	NSP		8275708	Standard	NM_206852		Approved		uc001xen.1	Q16799	OTTHUMG00000028947	ENST00000267484.5:c.2289-3T>-	14.37:g.60063508delA		Somatic	104	.	.		WXS	Illumina HiSeq	Phase_I	109	34	0.312	NM_021136	Q16800|Q16801|Q5BKZ4|Q9BQ59	Splice_Site	DEL	ENST00000267484.5	37	CCDS9740.1																																																																																			.	.	none		0.383	RTN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000072278.2		
DMKN	93099	hgsc.bcm.edu	37	19	36002362	36002412	+	In_Frame_Del	DEL	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	-	rs112672248|rs142519211|rs144877871|rs544198244|rs199498909|rs11667007|rs12981076|rs146822312|rs148799704|rs138902616|rs56743379|rs140071083|rs371511253|rs117522133|rs59309505|rs113540509|rs111543270|rs58579970|rs201369392	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	CTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36002362_36002412delCTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	ENST00000339686.3	-	5	995_1045	c.819_869delCAGTGGCAGCAGCAGTGGCGGCAGCAGTGGCGGCAGCAGTGGTGGCAGCAG	c.(817-870)agcagtggcagcagcagtggcggcagcagtggcggcagcagtggtggcagcagt>agt	p.273_290SSGSSSGGSSGGSSGGSS>S	DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000424570.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000440396.1_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000451297.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000418261.1_In_Frame_Del_p.273_290SSGSSSGGSSGGSSGGSS>S|DMKN_ENST00000462126.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	273	Gly-rich.		G -> S (in dbSNP:rs11667007). {ECO:0000269|PubMed:17380110}.	G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			actgttgccactgctgccaccactgctgccgccactgctgccgccactgctgctgccactgctgctgccac	0.641																																					p.274_290del		Pindel	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.820_870del						PASS	.		,,,,,,	1051,3093		133,785,1154					,,,,,,	-3.2	0.0		dbSNP_130	28	1360,6640		184,992,2824	no	coding,coding,coding,intron,coding,coding,intron	DMKN	NM_033317.4,NM_001190349.1,NM_001190348.1,NM_001190347.1,NM_001126058.2,NM_001126057.2,NM_001126056.2	,,,,,,	317,1777,3978	A1A1,A1R,RR		17.0,25.362,19.8534	,,,,,,	,,,,,,		2411,9733				SO:0001651	inframe_deletion	93099	exon5			.	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.819_869delCAGTGGCAGCAGCAGTGGCGGCAGCAGTGGCGGCAGCAGTGGTGGCAGCAG	19.37:g.36002362_36002412delCTGCTGCCACCACTGCTGCCGCCACTGCTGCCGCCACTGCTGCTGCCACTG	ENSP00000342012:p.Ser273_Ser289del	Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	49	14	0.286	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.641	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
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 GAIIx	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		Somatic	84	.	.		WXS	Illumina HiSeq	Phase_I	68	15	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
CHIT1	1118	hgsc.bcm.edu	37	1	203186950	203186951	+	In_Frame_Ins	INS	-	-	AGACCATGGCCCCGCCCAGTCCCT	rs201320385|rs386369359|rs3831317|rs150192398	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203186950_203186951insAGACCATGGCCCCGCCCAGTCCCT	ENST00000367229.1	-	10	1106_1107	c.1072_1073insAGGGACTGGGCGGGGCCATGGTCT	c.(1072-1074)tgg>tAGGGACTGGGCGGGGCCATGGTCTgg	p.357_358ins*GLGGAMV	CHIT1_ENST00000484834.1_De_novo_Start_OutOfFrame|CHIT1_ENST00000535569.1_In_Frame_Ins_p.348_349ins*GLGGAMV|CHIT1_ENST00000255427.3_In_Frame_Ins_p.338_339ins*GLGGAMV	NM_001270509.1|NM_003465.2	NP_001257438.1|NP_003456.1	Q13231	CHIT1_HUMAN	chitinase 1 (chitotriosidase)	357					chitin catabolic process (GO:0006032)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|lysosome (GO:0005764)	chitin binding (GO:0008061)|chitinase activity (GO:0004568)|endochitinase activity (GO:0008843)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|stomach(2)	27						GTCCAGTGCCCAGACCATGGCC	0.634														1448	0.289137	0.0242	0.2983	5008	,	,		19472	0.5704		0.1839	False		,,,				2504	0.4591				p.W358delinsX		Pindel	.											CHIT1,colon,carcinoma,0,2	CHIT1	61	2	0			c.1073_1074insAGGGACTGGGCGGGGCCATGGTCT						PASS	.																																			SO:0001652	inframe_insertion	1118	exon10			.	U29615	CCDS1436.1, CCDS58057.1	1q32.1	2013-06-06			ENSG00000133063	ENSG00000133063			1936	protein-coding gene	gene with protein product		600031				9748235, 9492324	Standard	NM_003465		Approved	CHIT, CHI3	uc001gzn.2	Q13231	OTTHUMG00000042126	ENST00000367229.1:c.1049_1072dupAGGGACTGGGCGGGGCCATGGTCT	1.37:g.203186950_203186951insAGACCATGGCCCCGCCCAGTCCCT	ENSP00000356198:p.Val357_Trp358ins*GlyLeuGlyGlyAlaMetVal	Somatic	62	.	.		WXS	Illumina HiSeq	Phase_I	35	19	0.543	NM_003465	B3KNW6|J3KN09|Q0VGG5|Q0VGG6|Q3ZAR1|Q6ISC2|Q9H3V8|Q9UDJ8	In_Frame_Ins	INS	ENST00000367229.1	37	CCDS1436.1																																																																																			.	.	strong		0.634	CHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100275.2	NM_003465	
CLDN16	10686	hgsc.bcm.edu	37	3	190106073	190106074	+	Frame_Shift_Del	DEL	GG	GG	-	rs386669518|rs3214506	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:190106073_190106074delGG	ENST00000264734.2	+	1	413_414	c.165_166delGG	c.(163-168)agggctfs	p.RA55fs	CLDN16_ENST00000456423.1_Frame_Shift_Del_p.RA55fs|CLDN16_ENST00000468220.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	55					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		GTGGGGCCAGGGCTGGTGTCTG	0.505																																					p.55_55del		Pindel	.											.	CLDN16	59	.	0			c.164_165del	GRCh37	CX001601	CLDN16	X		PASS	.																																			SO:0001589	frameshift_variant	10686	exon1			.	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"""Claudins"""	2037	protein-coding gene	gene with protein product	"""paracellin-1"", ""hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"""	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.165_166delGG	3.37:g.190106073_190106074delGG	ENSP00000264734:p.Arg55fs	Somatic	180	.	.		WXS	Illumina HiSeq	Phase_I	155	25	0.161	NM_006580		Frame_Shift_Del	DEL	ENST00000264734.2	37	CCDS3296.1																																																																																			.	.	none		0.505	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580	
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 GAIIx	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	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	52	20	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 GAIIx	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		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	30	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	
SEC14L3	266629	hgsc.bcm.edu	37	22	30860830	30860830	+	Missense_Mutation	SNP	C	C	T	rs2269961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30860830C>T	ENST00000215812.4	-	8	731	c.641G>A	c.(640-642)cGc>cAc	p.R214H	SEC14L3_ENST00000539629.1_Missense_Mutation_p.R155H|SEC14L3_ENST00000403066.1_Missense_Mutation_p.R155H|SEC14L3_ENST00000402286.1_Missense_Mutation_p.R137H|SEC14L3_ENST00000401751.1_Missense_Mutation_p.R155H|SEC14L3_ENST00000415957.2_Missense_Mutation_p.R155H|SEC14L3_ENST00000540910.1_Missense_Mutation_p.R137H	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	214	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		R -> H (in dbSNP:rs2269961).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	AATTTTCCTGCGAGTGTCCTC	0.443													C|||	1102	0.220048	0.2209	0.1427	5008	,	,		23188	0.3194		0.2167	False		,,,				2504	0.1748				p.R214H	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.G641A						PASS	.	C	HIS/ARG	1012,3394	374.9+/-321.4	117,778,1308	176.0	151.0	160.0		641	4.5	1.0	22	dbSNP_100	160	1833,6767	328.2+/-318.2	187,1459,2654	yes	missense	SEC14L3	NM_174975.4	29	304,2237,3962	TT,TC,CC		21.314,22.9687,21.8745	probably-damaging	214/401	30860830	2845,10161	2203	4300	6503	SO:0001583	missense	266629	exon8			TTCCTGCGAGTGT	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.641G>A	22.37:g.30860830C>T	ENSP00000215812:p.Arg214His	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	502|502	0.22985347985347984|0.22985347985347984	94|94	0.1910569105691057|0.1910569105691057	60|60	0.16574585635359115|0.16574585635359115	182|182	0.3181818181818182|0.3181818181818182	166|166	0.21899736147757257|0.21899736147757257	C|C	24.0|24.0	4.480823|4.480823	0.84747|0.84747	0.229687|0.229687	0.21314|0.21314	ENSG00000100012|ENSG00000100012	ENST00000435069|ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	.|T;T;T;T;T;T;T	.|0.79352	.|-1.26;-1.26;-1.26;-1.26;-1.26;-1.26;-1.26	5.5|5.5	4.49|4.49	0.54785|0.54785	.|Cellular retinaldehyde-binding/triple function, C-terminal (5);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.80982|0.80982	2.52|2.52	0.09310|0.09310	P|P	1.0|1.0	.|D;D	.|0.76494	.|0.974;0.999	.|B;D	.|0.63597	.|0.419;0.916	T|T	0.00001|0.00001	-1.2690|-1.2690	4|9	.|0.72032	.|D	.|0.01	-11.635|-11.635	14.2373|14.2373	0.65934|0.65934	0.0:0.9272:0.0:0.0728|0.0:0.9272:0.0:0.0728	rs2269961;rs17659246;rs52827962;rs61243443;rs2269961|rs2269961;rs17659246;rs52827962;rs61243443;rs2269961	.|137;214	.|E9PE57;Q9UDX4	.|.;S14L3_HUMAN	T|H	180|155;155;214;137;155;155;137	.|ENSP00000385941:R155H;ENSP00000401864:R155H;ENSP00000215812:R214H;ENSP00000385004:R137H;ENSP00000383896:R155H;ENSP00000444691:R155H;ENSP00000439752:R137H	.|ENSP00000215812:R214H	A|R	-|-	1|2	0|0	SEC14L3|SEC14L3	29190830|29190830	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.701000|0.701000	0.40568|0.40568	4.589000|4.589000	0.61006|0.61006	1.334000|1.334000	0.45468|0.45468	0.655000|0.655000	0.94253|0.94253	GCA|CGC	C|0.774;N|0.001	.	strong		0.443	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
FKBP10	60681	hgsc.bcm.edu	37	17	39974642	39974642	+	Missense_Mutation	SNP	A	A	G	rs34764749	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39974642A>G	ENST00000321562.4	+	4	694	c.590A>G	c.(589-591)aAg>aGg	p.K197R	FKBP10_ENST00000544340.1_5'Flank	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	197	PPIase FKBP-type 2. {ECO:0000255|PROSITE- ProRule:PRU00277}.		K -> R (in dbSNP:rs34764749).		chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			cervix(1)|endometrium(3)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(137;0.00122)		BRCA - Breast invasive adenocarcinoma(366;0.148)		AGCTACAGTAAGGGCGGCACT	0.612													G|||	372	0.0742812	0.1082	0.0346	5008	,	,		17653	0.1071		0.0457	False		,,,				2504	0.0521				p.K197R		Atlas-SNP	.											.	FKBP10	57	.	0			c.A590G						PASS	.	G	ARG/LYS	484,3922	779.9+/-414.4	29,426,1748	82.0	73.0	76.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	590	1.4	0.0	17	dbSNP_126	76	336,8264	803.5+/-407.3	6,324,3970	yes	missense	FKBP10	NM_021939.3	26	35,750,5718	GG,GA,AA		3.907,10.985,6.3048	benign	197/583	39974642	820,12186	2203	4300	6503	SO:0001583	missense	60681	exon4			ACAGTAAGGGCGG	AB045981	CCDS11409.1	17q21.2	2014-09-17	2002-08-29		ENSG00000141756	ENSG00000141756		"""EF-hand domain containing"""	18169	protein-coding gene	gene with protein product		607063	"""FK506 binding protein 10 (65 kDa)"""			11071917, 18786928	Standard	NM_021939		Approved	hFKBP65, FLJ22041, FKBP6, FLJ20683, FLJ23833	uc002hxv.2	Q96AY3	OTTHUMG00000133497	ENST00000321562.4:c.590A>G	17.37:g.39974642A>G	ENSP00000317232:p.Lys197Arg	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	152	85	0.559211	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Missense_Mutation	SNP	ENST00000321562.4	37	CCDS11409.1	150	0.06868131868131869	46	0.09349593495934959	13	0.03591160220994475	56	0.0979020979020979	35	0.04617414248021108	G	0.007	-1.947993	0.00475	0.10985	0.03907	ENSG00000141756	ENST00000321562;ENST00000414352	T	0.48201	0.82	5.53	1.37	0.22104	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.376195	0.24141	N	0.041166	T	0.00241	0.0007	N	0.00251	-1.775	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.34428	-0.9829	9	0.02654	T	1	-17.991	11.5403	0.50663	0.42:0.0:0.58:0.0	rs34764749;rs61749878	197	Q96AY3	FKB10_HUMAN	R	197	ENSP00000317232:K197R	ENSP00000317232:K197R	K	+	2	0	FKBP10	37228168	0.831000	0.29352	0.023000	0.16930	0.118000	0.20060	2.163000	0.42377	-0.123000	0.11745	-2.304000	0.00258	AAG	A|0.935;G|0.065	0.065	strong		0.612	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939	
SLC2A9	56606	hgsc.bcm.edu	37	4	10027542	10027542	+	Missense_Mutation	SNP	C	C	T	rs6820230	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:10027542C>T	ENST00000506583.1	-	3	266	c.49G>A	c.(49-51)Gcg>Acg	p.A17T	SLC2A9_ENST00000309065.3_Missense_Mutation_p.A17T			Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	46					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)	TTCTTTTTCGCTGAATCACTT	0.423													C|||	1345	0.26857	0.5507	0.2205	5008	,	,		20219	0.0972		0.2972	False		,,,				2504	0.0685				p.A17T		Atlas-SNP	.											SLC2A9,NS,carcinoma,+2,1	SLC2A9	158	1	0			c.G49A						PASS	.	C	THR/ALA	2173,2233	585.0+/-386.2	526,1121,556	130.0	131.0	131.0		49	0.9	0.0	4	dbSNP_116	131	2340,6260	390.9+/-343.5	333,1674,2293	yes	missense	SLC2A9	NM_001001290.1	58	859,2795,2849	TT,TC,CC		27.2093,49.3191,34.6994		17/512	10027542	4513,8493	2203	4300	6503	SO:0001583	missense	56606	exon2			TTTTCGCTGAATC	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	ENST00000506583.1:c.49G>A	4.37:g.10027542C>T	ENSP00000422209:p.Ala17Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_001001290	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000506583.1	37	CCDS3406.1	617	0.2825091575091575	269	0.5467479674796748	85	0.23480662983425415	50	0.08741258741258741	213	0.28100263852242746	C	3.384	-0.125708	0.06795	0.493191	0.272093	ENSG00000109667	ENST00000506583;ENST00000309065;ENST00000513129	D;D;D	0.87334	-1.62;-1.62;-2.24	3.59	0.892	0.19230	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40098	-0.9581	7	.	.	.	.	3.6186	0.08086	0.0:0.5531:0.2107:0.2362	rs6820230;rs52816748;rs56455102;rs56938107;rs6820230	17	Q9NRM0-2	.	T	17	ENSP00000422209:A17T;ENSP00000311383:A17T;ENSP00000426800:A17T	.	A	-	1	0	SLC2A9	9636640	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.100000	0.10990	0.155000	0.19261	0.561000	0.74099	GCG	C|0.682;T|0.318	0.318	strong		0.423	SLC2A9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207054.2		
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 GAIIx	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	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	20	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	
ZNF239	8187	hgsc.bcm.edu	37	10	44053013	44053013	+	Missense_Mutation	SNP	G	G	C	rs2230660	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:44053013G>C	ENST00000306006.6	-	2	1167	c.515C>G	c.(514-516)gCt>gGt	p.A172G	ZNF239_ENST00000491188.1_5'UTR|ZNF239_ENST00000535642.1_Missense_Mutation_p.A172G|ZNF239_ENST00000426961.1_Missense_Mutation_p.A172G|ZNF239_ENST00000374446.2_Missense_Mutation_p.A172G	NM_005674.2	NP_005665.2	Q16600	ZN239_HUMAN	zinc finger protein 239	172			A -> G (in dbSNP:rs2230660). {ECO:0000269|PubMed:8587123}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CTCTGTATGAGCTCTCTGCTG	0.428																																					p.A172G		Atlas-SNP	.											.	ZNF239	45	.	0			c.C515G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	2065,1845		561,943,451	149.0	135.0	140.0		515,515,515,515	0.3	0.0	10	dbSNP_98	140	4459,3863		1201,2057,903	yes	missense,missense,missense,missense	ZNF239	NM_001099282.1,NM_001099283.1,NM_001099284.1,NM_005674.2	60,60,60,60	1762,3000,1354	CC,CG,GG		46.4191,47.1867,46.6645	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	172/459,172/459,172/459,172/459	44053013	6524,5708	1955	4161	6116	SO:0001583	missense	8187	exon2			GTATGAGCTCTCT	X82125	CCDS41502.1	10q11.22-q11.23	2013-01-08			ENSG00000196793	ENSG00000196793		"""Zinc fingers, C2H2-type"""	13031	protein-coding gene	gene with protein product		601069				8903737, 8587123	Standard	NM_005674		Approved	MOK2, HOK-2	uc009xmk.3	Q16600	OTTHUMG00000018033	ENST00000306006.6:c.515C>G	10.37:g.44053013G>C	ENSP00000307774:p.Ala172Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_001099283	Q5T1G9|Q8TAS5	Missense_Mutation	SNP	ENST00000306006.6	37	CCDS41502.1	1136	0.5201465201465202	221	0.4491869918699187	173	0.47790055248618785	327	0.5716783216783217	415	0.5474934036939314	G	14.55	2.569341	0.45798	0.528133	0.535809	ENSG00000196793	ENST00000306006;ENST00000374446;ENST00000426961;ENST00000535642;ENST00000339962	T;T;T;T	0.06371	3.31;3.31;3.31;3.31	4.3	0.271	0.15640	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	P	0.35433	0.501	B	0.30646	0.118	T	0.32107	-0.9919	8	0.66056	D	0.02	-0.2564	4.3439	0.11124	0.2806:0.0:0.5532:0.1661	rs2230660;rs3750892;rs17153875;rs17843212;rs52799439;rs2230660	172	Q16600	ZN239_HUMAN	G	172	ENSP00000307774:A172G;ENSP00000363569:A172G;ENSP00000398202:A172G;ENSP00000443907:A172G	ENSP00000307774:A172G	A	-	2	0	ZNF239	43373019	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.510000	0.06328	0.051000	0.15978	-0.140000	0.14226	GCT	G|0.474;C|0.525	0.525	strong		0.428	ZNF239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047710.1		
VWA7	80737	hgsc.bcm.edu	37	6	31734345	31734345	+	Silent	SNP	G	G	T	rs3115671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31734345G>T	ENST00000375688.4	-	14	2279	c.2079C>A	c.(2077-2079)tcC>tcA	p.S693S	VWA7_ENST00000375686.3_Silent_p.S693S|VWA7_ENST00000447450.1_Missense_Mutation_p.H687N|VWA7_ENST00000467576.1_5'UTR|SAPCD1-AS1_ENST00000419679.1_RNA			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	693						extracellular region (GO:0005576)											GTCTAGGGGTGGACAGCAGCG	0.692													G|||	170	0.0339457	0.0575	0.0274	5008	,	,		15534	0.0		0.0746	False		,,,				2504	0.0				p.S693S		Atlas-SNP	.											.	.	.	.	0			c.C2079A						PASS	.	G		203,2815		7,189,1313	34.0	34.0	34.0		2079	0.8	0.0	6	dbSNP_103	34	557,4857		33,491,2183	yes	coding-synonymous	C6orf27	NM_025258.2		40,680,3496	TT,TG,GG		10.2881,6.7263,9.0133		693/892	31734345	760,7672	1509	2707	4216	SO:0001819	synonymous_variant	80737	exon14			AGGGGTGGACAGC		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"""chromosome 6 open reading frame 27"""	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.2079C>A	6.37:g.31734345G>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	30	28	0.933333	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Silent	SNP	ENST00000375688.4	37	CCDS4721.2	96	0.04395604395604396	28	0.056910569105691054	11	0.03038674033149171	0	0.0	57	0.07519788918205805	G	8.875	0.950281	0.18431	0.067263	0.102881	ENSG00000204396	ENST00000447450	T	0.30714	1.52	5.64	0.78	0.18556	.	.	.	.	.	T	0.02970	0.0088	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.44421	-0.9329	6	0.08837	T	0.75	-14.6053	3.73	0.08489	0.237:0.0:0.47:0.2929	rs3115671;rs3115671	.	.	.	N	687	ENSP00000390554:H687N	ENSP00000390554:H687N	H	-	1	0	C6orf27	31842324	0.024000	0.19004	0.007000	0.13788	0.760000	0.43138	0.056000	0.14256	-0.150000	0.11195	-0.261000	0.10672	CAC	G|0.932;T|0.068	0.068	strong		0.692	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258	
KRT23	25984	hgsc.bcm.edu	37	17	39092735	39092735	+	Missense_Mutation	SNP	C	C	A	rs34861030	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39092735C>A	ENST00000209718.3	-	2	545	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	AC004231.2_ENST00000418393.1_RNA|KRT23_ENST00000582283.1_5'Flank|KRT23_ENST00000436344.3_Intron	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	41	Head.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				GAGATGCGGGCTCCCCCCGCA	0.706													C|||	170	0.0339457	0.0091	0.0043	5008	,	,		14025	0.0744		0.0109	False		,,,				2504	0.0706				p.A41S		Atlas-SNP	.											.	KRT23	59	.	0			c.G121T						PASS	.	C	SER/ALA	47,4359	46.7+/-81.2	0,47,2156	30.0	36.0	34.0		121	-1.0	0.0	17	dbSNP_126	34	84,8514	45.4+/-104.0	0,84,4215	no	missense	KRT23	NM_015515.3	99	0,131,6371	AA,AC,CC		0.977,1.0667,1.0074	benign	41/423	39092735	131,12873	2203	4299	6502	SO:0001583	missense	25984	exon2			TGCGGGCTCCCCC	AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.121G>T	17.37:g.39092735C>A	ENSP00000209718:p.Ala41Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	40	26	0.65	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Missense_Mutation	SNP	ENST00000209718.3	37	CCDS11380.1	54	0.024725274725274724	5	0.01016260162601626	2	0.0055248618784530384	41	0.07167832167832168	6	0.0079155672823219	C	0.616	-0.823001	0.02755	0.010667	0.00977	ENSG00000108244	ENST00000209718	D	0.81739	-1.53	5.59	-1.03	0.10102	.	1.322140	0.05102	N	0.487397	T	0.09247	0.0228	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15983	-1.0418	10	0.08381	T	0.77	.	9.5324	0.39202	0.0:0.479:0.0:0.521	rs34861030	41	Q9C075	K1C23_HUMAN	S	41	ENSP00000209718:A41S	ENSP00000209718:A41S	A	-	1	0	KRT23	36346261	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.850000	0.04317	-0.144000	0.11314	-1.360000	0.01215	GCC	C|0.987;A|0.013	0.013	strong		0.706	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1		
KIF23	9493	hgsc.bcm.edu	37	15	69709792	69709792	+	Missense_Mutation	SNP	C	C	T	rs61751119	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:69709792C>T	ENST00000260363.4	+	3	269	c.152C>T	c.(151-153)aCt>aTt	p.T51I	KIF23_ENST00000559279.1_Missense_Mutation_p.T51I|KIF23_ENST00000352331.4_Missense_Mutation_p.T51I|KIF23_ENST00000395392.2_Missense_Mutation_p.T51I|RP11-253M7.1_ENST00000558617.1_RNA|RP11-253M7.1_ENST00000560539.1_RNA	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	51	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						AATAATACAACTGTTCAGCTT	0.413													C|||	130	0.0259585	0.0008	0.0274	5008	,	,		17840	0.001		0.0646	False		,,,				2504	0.045				p.T51I		Atlas-SNP	.											.	KIF23	57	.	0			c.C152T						PASS	.	C	ILE/THR,ILE/THR	77,4321	67.6+/-105.2	1,75,2123	149.0	135.0	140.0		152,152	4.8	0.4	15	dbSNP_129	140	603,7993	159.2+/-212.6	21,561,3716	yes	missense,missense	KIF23	NM_004856.5,NM_138555.2	89,89	22,636,5839	TT,TC,CC		7.0149,1.7508,5.2332	possibly-damaging,possibly-damaging	51/857,51/961	69709792	680,12314	2199	4298	6497	SO:0001583	missense	9493	exon3			ATACAACTGTTCA	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"""Kinesins"""	6392	protein-coding gene	gene with protein product		605064	"""kinesin-like 5 (mitotic kinesin-like protein 1)"""	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.152C>T	15.37:g.69709792C>T	ENSP00000260363:p.Thr51Ile	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_138555	Q8WVP0	Missense_Mutation	SNP	ENST00000260363.4	37	CCDS32278.1	64	0.029304029304029304	0	0.0	12	0.03314917127071823	0	0.0	52	0.06860158311345646	C	24.0	4.477433	0.84640	0.017508	0.070149	ENSG00000137807	ENST00000260363;ENST00000352331;ENST00000395392	T;T;T	0.72725	-0.68;-0.68;-0.68	4.75	4.75	0.60458	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.29684	0.0741	M	0.68593	2.085	0.80722	D	1	D;P	0.67145	0.996;0.931	P;P	0.59948	0.866;0.742	T	0.66834	-0.5823	10	0.87932	D	0	.	16.6698	0.85263	0.0:1.0:0.0:0.0	rs61751119	51;51	Q02241-2;Q02241	.;KIF23_HUMAN	I	51	ENSP00000260363:T51I;ENSP00000304978:T51I;ENSP00000378790:T51I	ENSP00000260363:T51I	T	+	2	0	KIF23	67496846	1.000000	0.71417	0.431000	0.26735	0.982000	0.71751	5.853000	0.69496	2.335000	0.79485	0.561000	0.74099	ACT	C|0.956;T|0.044	0.044	strong		0.413	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
CCDC93	54520	hgsc.bcm.edu	37	2	118771566	118771566	+	Silent	SNP	C	C	A	rs11545372	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:118771566C>A	ENST00000376300.2	-	1	143	c.6G>T	c.(4-6)ggG>ggT	p.G2G	AC009303.1_ENST00000590516.1_RNA|RN7SL111P_ENST00000468841.2_RNA|AC009303.1_ENST00000588042.1_RNA|CCDC93_ENST00000319432.5_Silent_p.G2G	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	2								p.G2G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						CCCTGGGCAACCCCATGATCC	0.692													C|||	1604	0.320288	0.4894	0.2421	5008	,	,		10351	0.1409		0.3459	False		,,,				2504	0.3057				p.G2G		Atlas-SNP	.											CCDC93,NS,carcinoma,0,1	CCDC93	70	1	1	Substitution - coding silent(1)	prostate(1)	c.G6T						PASS	.	C		1828,2574		393,1042,766	20.0	23.0	22.0		6	2.0	1.0	2	dbSNP_120	22	2829,5755		508,1813,1971	no	coding-synonymous	CCDC93	NM_019044.4		901,2855,2737	AA,AC,CC		32.9567,41.5266,35.8617		2/632	118771566	4657,8329	2201	4292	6493	SO:0001819	synonymous_variant	54520	exon1			GGGCAACCCCATG	BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.6G>T	2.37:g.118771566C>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Silent	SNP	ENST00000376300.2	37	CCDS2121.2																																																																																			C|0.673;A|0.327	0.327	strong		0.692	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044	
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 GAIIx	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	ILK_ENST00000528995.1_5'Flank|RP11-732A19.8_ENST00000527191.1_RNA|RRP8_ENST00000534343.1_Intron|ILK_ENST00000299421.4_5'Flank|ILK_ENST00000396751.2_5'Flank|ILK_ENST00000537806.1_5'Flank|ILK_ENST00000420936.2_5'Flank	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	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	91	39	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	
RTTN	25914	hgsc.bcm.edu	37	18	67687860	67687860	+	Silent	SNP	T	T	C	rs2304378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:67687860T>C	ENST00000255674.6	-	45	6430	c.6144A>G	c.(6142-6144)gtA>gtG	p.V2048V	RTTN_ENST00000579986.1_5'UTR|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	2048					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CCTTCTGAATTACTCCTTTAC	0.393													T|||	763	0.152356	0.0605	0.1311	5008	,	,		19560	0.1806		0.2286	False		,,,				2504	0.184				p.V2048V		Atlas-SNP	.											.	RTTN	184	.	0			c.A6144G						PASS	.	T		329,3529		12,305,1612	152.0	145.0	147.0		6144	-4.0	1.0	18	dbSNP_100	147	1719,6509		172,1375,2567	no	coding-synonymous	RTTN	NM_173630.3		184,1680,4179	CC,CT,TT		20.8921,8.5277,16.9452		2048/2227	67687860	2048,10038	1929	4114	6043	SO:0001819	synonymous_variant	25914	exon45			CTGAATTACTCCT	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.6144A>G	18.37:g.67687860T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	37	CCDS42443.1																																																																																			T|0.826;C|0.174	0.174	strong		0.393	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
MAP7D2	256714	hgsc.bcm.edu	37	X	20134902	20134902	+	Silent	SNP	C	C	G	rs142065916	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:20134902C>G	ENST00000379651.3	-	1	114	c.96G>C	c.(94-96)gcG>gcC	p.A32A	MAP7D2_ENST00000443379.3_Silent_p.A32A|MAP7D2_ENST00000452324.3_5'Flank|MAP7D2_ENST00000379643.5_Silent_p.A32A	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	32			A -> P (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						AGGTCCGCACCGCGCCCGGTT	0.731													C|||	26	0.00688742	0.0053	0.0144	3775	,	,		7138	0.0		0.008	False		,,,				2504	0.001				p.A32A		Atlas-SNP	.											.	MAP7D2	165	.	0			c.G96C						PASS	.	C	,,	29,3798		0,26,3,1604,564	18.0	19.0	19.0		96,96,96	-2.4	0.0	X	dbSNP_134	19	98,6621		1,57,39,2369,1826	no	coding-synonymous,coding-synonymous,coding-synonymous	MAP7D2	NM_001168465.1,NM_001168466.1,NM_152780.3	,,	1,83,42,3973,2390	GG,GC,G,CC,C		1.4586,0.7578,1.2042	,,	32/774,32/688,32/733	20134902	127,10419	2197	4292	6489	SO:0001819	synonymous_variant	256714	exon1			CCGCACCGCGCCC	BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.96G>C	X.37:g.20134902C>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	49	0.680556	NM_001168466	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Silent	SNP	ENST00000379651.3	37	CCDS14195.1																																																																																			C|0.990;G|0.010	0.010	strong		0.731	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780	
ZNF79	7633	hgsc.bcm.edu	37	9	130206762	130206762	+	Silent	SNP	C	C	T	rs2248025	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:130206762C>T	ENST00000342483.5	+	5	1189	c.783C>T	c.(781-783)aaC>aaT	p.N261N	ZNF79_ENST00000543471.1_Silent_p.N237N	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N261N(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						TCAGCCAGAACGCCAACCTCA	0.537													C|||	1663	0.332069	0.3215	0.2853	5008	,	,		21490	0.1647		0.5318	False		,,,				2504	0.3466				p.N261N		Atlas-SNP	.											ZNF79,NS,carcinoma,0,1	ZNF79	47	1	1	Substitution - coding silent(1)	stomach(1)	c.C783T						PASS	.	C		1541,2865	487.8+/-361.0	259,1023,921	116.0	103.0	107.0		783	-5.3	0.9	9	dbSNP_100	107	4161,4439	567.3+/-388.8	1037,2087,1176	no	coding-synonymous	ZNF79	NM_007135.2		1296,3110,2097	TT,TC,CC		48.3837,34.975,43.8413		261/499	130206762	5702,7304	2203	4300	6503	SO:0001819	synonymous_variant	7633	exon5			CCAGAACGCCAAC	X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"""Zinc fingers, C2H2-type"""	13153	protein-coding gene	gene with protein product		194552	"""zinc finger protein 79 (pT7)"""			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.783C>T	9.37:g.130206762C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	50	21	0.42	NM_007135	Q5VVW1|Q96NV1	Silent	SNP	ENST00000342483.5	37	CCDS6871.1																																																																																			C|0.612;T|0.388	0.388	strong		0.537	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135	
ATP13A2	23400	hgsc.bcm.edu	37	1	17312743	17312743	+	Silent	SNP	C	C	T	rs3170740	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17312743C>T	ENST00000326735.8	-	29	3549	c.3516G>A	c.(3514-3516)ccG>ccA	p.P1172P	ATP13A2_ENST00000341676.5_Missense_Mutation_p.A1072T|ATP13A2_ENST00000452699.1_Silent_p.P1167P|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	1172					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CGGGCAGCGGCGGCCAGGGCT	0.711													C|||	1659	0.33127	0.1445	0.4553	5008	,	,		12200	0.246		0.5099	False		,,,				2504	0.3998				p.A1072T		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G3214A						PASS	.	C	,THR/ALA,	944,3410		135,674,1368	16.0	24.0	22.0		3501,3214,3516	-7.1	0.0	1	dbSNP_105	22	4491,4055		1201,2089,983	yes	coding-synonymous,missense,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,58,	1336,2763,2351	TT,TC,CC		47.4491,21.6812,42.1318	,,	1167/1176,1072/1159,1172/1181	17312743	5435,7465	2177	4273	6450	SO:0001819	synonymous_variant	23400	exon27			CAGCGGCGGCCAG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.3516G>A	1.37:g.17312743C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_001141974	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Missense_Mutation	SNP	ENST00000326735.8	37	CCDS175.1	773	0.35393772893772896	65	0.13211382113821138	158	0.43646408839779005	161	0.28146853146853146	389	0.5131926121372031	C	0.008	-1.900646	0.00517	0.216812	0.525509	ENSG00000159363	ENST00000341676;ENST00000502418	D;D	0.96967	-3.3;-4.19	3.56	-7.11	0.01542	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.26789	P	0.9694444	B	0.06786	0.001	B	0.04013	0.001	T	0.18681	-1.0329	7	0.02654	T	1	-23.2806	7.7309	0.28786	0.0:0.2877:0.2133:0.499	rs3170740	1072	Q5JXY1	.	T	1072;312	ENSP00000341115:A1072T;ENSP00000423065:A312T	ENSP00000341115:A1072T	A	-	1	0	ATP13A2	17185330	0.001000	0.12720	0.015000	0.15790	0.046000	0.14306	-2.548000	0.00930	-1.707000	0.01402	-0.914000	0.02751	GCC	C|0.645;T|0.355	0.355	strong		0.711	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
NIPBL	25836	hgsc.bcm.edu	37	5	36985303	36985303	+	Missense_Mutation	SNP	A	A	G	rs3822471	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:36985303A>G	ENST00000282516.8	+	10	2520	c.2021A>G	c.(2020-2022)aAt>aGt	p.N674S	NIPBL_ENST00000448238.2_Missense_Mutation_p.N674S|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	674			N -> S (in dbSNP:rs3822471). {ECO:0000269|PubMed:15318302}.		brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CCTAAACAAAATGAAAATAGA	0.373													A|||	627	0.1252	0.1021	0.1888	5008	,	,		19832	0.1329		0.1054	False		,,,				2504	0.1237				p.N674S		Atlas-SNP	.											NIPBL_ENST00000448238,NS,carcinoma,-1,2	NIPBL	513	2	0			c.A2021G						PASS	.	A	SER/ASN,SER/ASN	406,4000	203.1+/-225.7	23,360,1820	88.0	86.0	87.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2021,2021	2.3	1.0	5	dbSNP_107	87	1074,7526	223.1+/-260.0	55,964,3281	yes	missense,missense	NIPBL	NM_015384.4,NM_133433.3	46,46	78,1324,5101	GG,GA,AA		12.4884,9.2147,11.3794	benign,benign	674/2698,674/2805	36985303	1480,11526	2203	4300	6503	SO:0001583	missense	25836	exon10			AACAAAATGAAAA	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.2021A>G	5.37:g.36985303A>G	ENSP00000282516:p.Asn674Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	259	0.11858974358974358	55	0.11178861788617886	73	0.20165745856353592	51	0.08916083916083917	80	0.10554089709762533	A	4.339	0.062284	0.08388	0.092147	0.124884	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.93859	-3.27;-3.3	5.98	2.31	0.28768	.	0.180790	0.47455	N	0.000240	T	0.00356	0.0011	N	0.24115	0.695	0.33515	P	0.408377	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.27739	-1.0065	9	0.07325	T	0.83	-7.3863	4.765	0.13128	0.6002:0.1633:0.2365:0.0	rs61259989	674;674	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	S	674	ENSP00000282516:N674S;ENSP00000406266:N674S	ENSP00000282516:N674S	N	+	2	0	NIPBL	37021060	0.250000	0.23951	0.999000	0.59377	0.987000	0.75469	0.421000	0.21280	0.160000	0.19432	0.528000	0.53228	AAT	A|0.879;G|0.121	0.121	strong		0.373	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
KANSL1	284058	hgsc.bcm.edu	37	17	44111613	44111613	+	Silent	SNP	A	A	G	rs17574604	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44111613A>G	ENST00000262419.6	-	11	3050	c.2580T>C	c.(2578-2580)ttT>ttC	p.F860F	KANSL1_ENST00000575318.1_Silent_p.F796F|KANSL1_ENST00000432791.1_Silent_p.F860F|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000393476.3_Silent_p.F154F|KANSL1_ENST00000574590.1_Silent_p.F860F|KANSL1_ENST00000572904.1_Silent_p.F860F	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	860	Required for activation of KAT8 histone acetyltransferase activity.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.F860F(2)									TGTTAATATCAAATGAGCTCT	0.398													G|||	432	0.086262	0.0151	0.1571	5008	,	,		21592	0.001		0.2406	False		,,,				2504	0.0613				p.F860F		Atlas-SNP	.											KIAA1267,NS,carcinoma,0,1	.	.	1	2	Substitution - coding silent(2)	prostate(2)	c.T2580C						PASS	.	G	,,	202,4204	807.7+/-415.9	5,192,2006	187.0	157.0	167.0		2577,2580,2580	-6.8	0.2	17	dbSNP_123	167	1928,6672	726.2+/-406.6	220,1488,2592	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	225,1680,4598	GG,GA,AA		22.4186,4.5847,16.3771	,,	859/1105,860/1106,860/1106	44111613	2130,10876	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon11			AATATCAAATGAG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2580T>C	17.37:g.44111613A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.853;G|0.147	0.147	strong		0.398	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
DEFB136	613210	hgsc.bcm.edu	37	8	11832079	11832079	+	Silent	SNP	A	A	G	rs10108075	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11832079A>G	ENST00000382209.2	-	1	29	c.30T>C	c.(28-30)ttT>ttC	p.F10F		NM_001033018.2	NP_001028190.2	Q30KP8	DB136_HUMAN	defensin, beta 136	10					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(4)	7			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.163)		TCACCAGGAAAAAGAGTAATG	0.488													G|||	3866	0.771965	0.8555	0.6945	5008	,	,		21049	0.9851		0.5159	False		,,,				2504	0.7577				p.F10F		Atlas-SNP	.											.	DEFB136	16	.	0			c.T30C						PASS	.	G		3186,740		1304,578,81	135.0	137.0	136.0		30	3.1	0.1	8	dbSNP_119	136	4384,3930		1174,2036,947	no	coding-synonymous	DEFB136	NM_001033018.2		2478,2614,1028	GG,GA,AA		47.2697,18.8487,38.1536		10/79	11832079	7570,4670	1963	4157	6120	SO:0001819	synonymous_variant	613210	exon1			CAGGAAAAAGAGT	DQ012026	CCDS43709.1	8p23.1	2011-07-19			ENSG00000205884	ENSG00000205884		"""Defensins, beta"""	34433	protein-coding gene	gene with protein product						16033865	Standard	NM_001033018		Approved	DEFB137	uc011kxm.2	Q30KP8	OTTHUMG00000158720	ENST00000382209.2:c.30T>C	8.37:g.11832079A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_001033018	Q4QY36	Silent	SNP	ENST00000382209.2	37	CCDS43709.1																																																																																			A|0.331;G|0.669	0.669	strong		0.488	DEFB136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351889.1	NM_001033018	
GIMAP5	55340	hgsc.bcm.edu	37	7	150439500	150439500	+	Silent	SNP	C	C	T	rs759011	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150439500C>T	ENST00000358647.3	+	3	640	c.273C>T	c.(271-273)gcC>gcT	p.A91A	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	91	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		AGTCACAGGCCGATACCCAAG	0.597													T|||	1953	0.389976	0.5696	0.2651	5008	,	,		18052	0.3006		0.3082	False		,,,				2504	0.4121				p.A295A		Atlas-SNP	.											GIMAP5,NS,carcinoma,0,1	.	.	1	0			c.C885T						PASS	.	T	,	2405,2001	560.3+/-380.4	672,1061,470	111.0	99.0	103.0		885,273	1.4	0.0	7	dbSNP_86	103	2642,5958	686.6+/-404.1	390,1862,2048	no	coding-synonymous,coding-synonymous	GIMAP5,GIMAP1-GIMAP5	NM_001199577.1,NM_018384.4	,	1062,2923,2518	TT,TC,CC		30.7209,45.4153,38.8052	,	295/512,91/308	150439500	5047,7959	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			ACAGGCCGATACC	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"""GTPases, IMAP"""	18005	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 5"""	608086	"""immune associated nucleotide 4 like 1 (mouse)"""	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.273C>T	7.37:g.150439500C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Silent	SNP	ENST00000358647.3	37	CCDS5907.1																																																																																			T|0.385;G|0.004	0.385	strong		0.597	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384	
OR4L1	122742	hgsc.bcm.edu	37	14	20528505	20528505	+	Missense_Mutation	SNP	T	T	A	rs2775253	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20528505T>A	ENST00000315683.1	+	1	302	c.302T>A	c.(301-303)aTg>aAg	p.M101K		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	101			M -> K (in dbSNP:rs2775253).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		GTGACCCAGATGTTCTTCATG	0.473													t|||	2135	0.426318	0.3623	0.3934	5008	,	,		19257	0.5357		0.3221	False		,,,				2504	0.5307				p.M101K		Atlas-SNP	.											.	OR4L1	98	.	0			c.T302A						PASS	.		LYS/MET	1574,2832		284,1006,913	151.0	136.0	141.0		302	4.0	1.0	14	dbSNP_100	141	2755,5845		481,1793,2026	yes	missense	OR4L1	NM_001004717.1	95	765,2799,2939	AA,AT,TT		32.0349,35.724,33.2846	probably-damaging	101/313	20528505	4329,8677	2203	4300	6503	SO:0001583	missense	122742	exon1			CCCAGATGTTCTT		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.302T>A	14.37:g.20528505T>A	ENSP00000319217:p.Met101Lys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	102	45	0.441176	NM_001004717	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	889	0.40705128205128205	184	0.37398373983739835	140	0.3867403314917127	303	0.5297202797202797	262	0.34564643799472294	.	19.10	3.761031	0.69763	0.35724	0.320349	ENSG00000176246	ENST00000315683	T	0.06687	3.27	3.97	3.97	0.46021	GPCR, rhodopsin-like superfamily (1);	0.164442	0.43110	D	0.000618	T	0.00012	0.0000	M	0.83312	2.635	0.29923	P	0.8226100000000001	P	0.49862	0.929	P	0.49012	0.598	T	0.44498	-0.9324	9	0.87932	D	0	.	11.1491	0.48447	0.0:0.0:0.0:1.0	rs2775253;rs2994401;rs2775253	101	Q8NH43	OR4L1_HUMAN	K	101	ENSP00000319217:M101K	ENSP00000319217:M101K	M	+	2	0	OR4L1	19598345	0.001000	0.12720	1.000000	0.80357	0.960000	0.62799	0.887000	0.28254	1.793000	0.52555	0.524000	0.50904	ATG	T|0.639;A|0.361	0.361	strong		0.473	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
CALCOCO2	10241	hgsc.bcm.edu	37	17	46929908	46929908	+	Missense_Mutation	SNP	T	T	C	rs2303015	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:46929908T>C	ENST00000258947.3	+	8	844	c.743T>C	c.(742-744)gTt>gCt	p.V248A	CALCOCO2_ENST00000508679.1_Missense_Mutation_p.V176A|CALCOCO2_ENST00000448105.2_Missense_Mutation_p.V272A|CALCOCO2_ENST00000416445.2_Missense_Mutation_p.V206A|CALCOCO2_ENST00000509507.1_Missense_Mutation_p.V269A	NM_001261390.1|NM_001261391.1|NM_001261393.1|NM_001261395.1|NM_005831.4	NP_001248319.1|NP_001248320.1|NP_001248322.1|NP_001248324.1|NP_005822.1	Q13137	CACO2_HUMAN	calcium binding and coiled-coil domain 2	248			V -> A (in dbSNP:rs2303015). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		response to interferon-gamma (GO:0034341)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	15						GAGAAGCTTGTTCAGGGAGAT	0.378													T|||	756	0.150958	0.3245	0.0533	5008	,	,		20544	0.0675		0.0467	False		,,,				2504	0.1789				p.V272A		Atlas-SNP	.											.	CALCOCO2	29	.	0			c.T815C						PASS	.	T	ALA/VAL	1183,3223	414.6+/-336.9	155,873,1175	74.0	74.0	74.0		743	4.2	0.2	17	dbSNP_100	74	324,8276	114.6+/-174.5	5,314,3981	yes	missense	CALCOCO2	NM_005831.3	64	160,1187,5156	CC,CT,TT		3.7674,26.8498,11.587	possibly-damaging	248/447	46929908	1507,11499	2203	4300	6503	SO:0001583	missense	10241	exon9			AGCTTGTTCAGGG	BC004130	CCDS11538.1, CCDS58558.1, CCDS58559.1, CCDS58560.1, CCDS58561.1	17q21.32	2006-02-09				ENSG00000136436			29912	protein-coding gene	gene with protein product		604587				7540613	Standard	NM_001261390		Approved	MGC17318, NDP52	uc010wlr.3	Q13137		ENST00000258947.3:c.743T>C	17.37:g.46929908T>C	ENSP00000258947:p.Val248Ala	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	223	106	0.475336	NM_001261390	B2RBT0|B4DDC4|B4DDT4|B4DP36|B4E0C0|E7ENK0|E7ETP5|E9PBE5|Q53FQ5|Q53HB5|Q6IBN9|Q9BTF7	Missense_Mutation	SNP	ENST00000258947.3	37	CCDS11538.1	267	0.12225274725274725	181	0.3678861788617886	21	0.058011049723756904	33	0.057692307692307696	32	0.04221635883905013	T	9.801	1.180618	0.21787	0.268498	0.037674	ENSG00000136436	ENST00000258947;ENST00000509507;ENST00000448105;ENST00000513119;ENST00000416445;ENST00000508679	T;T;T;T;T;T	0.17854	2.92;2.92;2.92;2.25;3.04;2.45	5.33	4.22	0.49857	.	1.445420	0.04399	N	0.363956	T	0.00012	0.0000	M	0.70595	2.14	0.80722	P	0.0	B;B;B;B	0.31125	0.309;0.098;0.202;0.095	B;B;B;B	0.31946	0.138;0.076;0.113;0.053	T	0.48559	-0.9025	9	0.09084	T	0.74	0.3295	2.6261	0.04930	0.3817:0.1311:0.0:0.4872	rs2303015;rs52825110;rs58716116;rs2303015	206;272;269;248	E7ETP5;B4DP36;E9PBE5;Q13137	.;.;.;CACO2_HUMAN	A	248;269;272;176;206;176	ENSP00000258947:V248A;ENSP00000424352:V269A;ENSP00000398523:V272A;ENSP00000425090:V176A;ENSP00000406974:V206A;ENSP00000423437:V176A	ENSP00000258947:V248A	V	+	2	0	CALCOCO2	44284907	0.004000	0.15560	0.227000	0.23927	0.963000	0.63663	0.138000	0.16016	2.013000	0.59113	0.528000	0.53228	GTT	T|0.868;G|0.001	.	strong		0.378	CALCOCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360866.1	NM_005831	
MMP27	64066	hgsc.bcm.edu	37	11	102576358	102576358	+	Missense_Mutation	SNP	T	T	C	rs2846707	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102576358T>C	ENST00000260229.4	-	1	179	c.88A>G	c.(88-90)Atg>Gtg	p.M30V		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	30			M -> V (in dbSNP:rs2846707). {ECO:0000269|Ref.1}.		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GCCAGTTGCATATTTTCTTCA	0.343													C|||	4086	0.815895	0.9213	0.7233	5008	,	,		19293	0.8839		0.6799	False		,,,				2504	0.8088				p.M30V		Atlas-SNP	.											.	MMP27	84	.	0			c.A88G						PASS	.	C	VAL/MET	3846,560	249.3+/-256.8	1677,492,34	96.0	102.0	100.0		88	0.2	0.0	11	dbSNP_100	100	5673,2925	457.4+/-364.3	1876,1921,502	yes	missense	MMP27	NM_022122.2	21	3553,2413,536	CC,CT,TT		34.0195,12.7099,26.7994	benign	30/514	102576358	9519,3485	2203	4299	6502	SO:0001583	missense	64066	exon1			GTTGCATATTTTC	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.88A>G	11.37:g.102576358T>C	ENSP00000260229:p.Met30Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	231	23	0.0995671	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	1728	0.7912087912087912	455	0.9247967479674797	270	0.7458563535911602	510	0.8916083916083916	493	0.6503957783641161	C	0.010	-1.767913	0.00645	0.872901	0.659805	ENSG00000137675	ENST00000260229	T	0.18657	2.2	5.22	0.184	0.15086	Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1);	2.099370	0.01609	N	0.022433	T	0.00012	0.0000	N	0.17278	0.47	0.80722	P	0.0	B	0.09022	0.002	B	0.15052	0.012	T	0.33189	-0.9878	9	0.06236	T	0.91	.	7.2012	0.25881	0.0:0.2001:0.1148:0.6851	rs2846707;rs17357793;rs61659932;rs2846707	30	Q9H306	MMP27_HUMAN	V	30	ENSP00000260229:M30V	ENSP00000260229:M30V	M	-	1	0	MMP27	102081568	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.323000	0.07997	-0.282000	0.09128	-1.881000	0.00545	ATG	T|0.229;C|0.771	0.771	strong		0.343	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
OR10H2	26538	hgsc.bcm.edu	37	19	15838967	15838967	+	Silent	SNP	G	G	A	rs2285955	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15838967G>A	ENST00000305899.3	+	1	134	c.114G>A	c.(112-114)acG>acA	p.T38T		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	38						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)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					ACCTGTTCACGCTGCTGGGCA	0.587													G|||	1755	0.350439	0.233	0.3112	5008	,	,		22410	0.3135		0.4394	False		,,,				2504	0.4836				p.T38T		Atlas-SNP	.											OR10H2,NS,carcinoma,+1,1	OR10H2	59	1	0			c.G114A						PASS	.	G		1225,3181		174,877,1152	237.0	198.0	211.0		114	-5.8	1.0	19	dbSNP_100	211	3845,4751		870,2105,1323	no	coding-synonymous	OR10H2	NM_013939.2		1044,2982,2475	AA,AG,GG		44.7301,27.803,38.994		38/316	15838967	5070,7932	2203	4298	6501	SO:0001819	synonymous_variant	26538	exon1			GTTCACGCTGCTG	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.114G>A	19.37:g.15838967G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	189	78	0.412698	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			G|0.611;A|0.389	0.389	strong		0.587	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
FAM71D	161142	hgsc.bcm.edu	37	14	67671293	67671293	+	3'UTR	SNP	T	T	C	rs17836680	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:67671293T>C	ENST00000556046.1	+	0	940							Q8N9W8	FA71D_HUMAN	family with sequence similarity 71, member D							cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)	13		all_hematologic(31;0.0116)		all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012)		CTGTGCATGATGCGGAGAACA	0.468													C|||	201	0.0401358	0.059	0.0346	5008	,	,		18115	0.0288		0.0427	False		,,,				2504	0.0276				p.D133D		Atlas-SNP	.											.	FAM71D	33	.	0			c.T399C						PASS	.	C		239,4167	804.0+/-415.7	7,225,1971	89.0	74.0	79.0		399	-0.3	0.0	14	dbSNP_123	79	379,8221	801.2+/-407.4	10,359,3931	no	coding-synonymous	FAM71D	NM_173526.3		17,584,5902	CC,CT,TT		4.407,5.4244,4.7517		133/423	67671293	618,12388	2203	4300	6503	SO:0001624	3_prime_UTR_variant	161142	exon5			GCATGATGCGGAG		CCDS9778.1	14q23.3	2007-11-20	2007-11-20	2007-11-20		ENSG00000172717			20101	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 54"""	C14orf54			Standard	NM_173526		Approved		uc001xja.2	Q8N9W8		ENST00000556046.1:c.*455T>C	14.37:g.67671293T>C		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	229	117	0.510917	NM_173526	Q86VN4	Silent	SNP	ENST00000556046.1	37																																																																																				T|0.957;C|0.043	0.043	strong		0.468	FAM71D-009	KNOWN	not_organism_supported|basic|appris_candidate	nonsense_mediated_decay	protein_coding	OTTHUMT00000412390.1	NM_173526	
CCDC176	80127	hgsc.bcm.edu	37	14	74523869	74523869	+	Missense_Mutation	SNP	A	A	G	rs3742809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74523869A>G	ENST00000394009.3	+	11	1609	c.1486A>G	c.(1486-1488)Aaa>Gaa	p.K496E	ALDH6A1_ENST00000553458.1_3'UTR|CCDC176_ENST00000553773.1_Missense_Mutation_p.K221E|AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000492247.2_Missense_Mutation_p.K40E	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	496			K -> E (in dbSNP:rs3742809).		motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											GCTTCAAGATAAAATCTTCAT	0.398													A|||	1210	0.241613	0.1566	0.1671	5008	,	,		19313	0.2371		0.1849	False		,,,				2504	0.4724				p.K496E		Atlas-SNP	.											.	.	.	.	0			c.A1486G						PASS	.	A	GLU/LYS	733,3673	301.0+/-286.6	66,601,1536	76.0	76.0	76.0		1486	2.7	0.8	14	dbSNP_107	76	1566,7034	292.6+/-300.9	136,1294,2870	yes	missense	C14orf45	NM_025057.2	56	202,1895,4406	GG,GA,AA		18.2093,16.6364,17.6765	benign	496/530	74523869	2299,10707	2203	4300	6503	SO:0001583	missense	80127	exon11			CAAGATAAAATCT	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 45"""	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.1486A>G	14.37:g.74523869A>G	ENSP00000377577:p.Lys496Glu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_025057	Q0P604|Q9H5P8	Missense_Mutation	SNP	ENST00000394009.3	37	CCDS32119.2	408	0.18681318681318682	70	0.14227642276422764	64	0.17679558011049723	137	0.2395104895104895	137	0.18073878627968337	A	9.915	1.210595	0.22289	0.166364	0.182093	ENSG00000119636	ENST00000394009;ENST00000553773;ENST00000492247	T;T;T	0.49720	2.29;0.94;0.77	4.59	2.71	0.32032	.	0.659026	0.12998	N	0.421864	T	0.00012	0.0000	N	0.22421	0.69	0.29472	P	0.8569869999999999	B	0.02656	0.0	B	0.04013	0.001	T	0.22521	-1.0214	9	0.22109	T	0.4	1.0849	8.9085	0.35539	0.1716:0.6698:0.1585:0.0	rs3742809;rs52797532;rs59742664;rs3742809	496	Q8ND07	CN045_HUMAN	E	496;221;40	ENSP00000377577:K496E;ENSP00000451097:K221E;ENSP00000451020:K40E	ENSP00000377577:K496E	K	+	1	0	C14orf45	73593622	0.912000	0.30974	0.783000	0.31826	0.680000	0.39746	0.991000	0.29654	0.640000	0.30582	-1.290000	0.01357	AAA	G|0.185;N|0.001	0.185	strong		0.398	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
CCDC53	51019	hgsc.bcm.edu	37	12	102455729	102455729	+	Silent	SNP	G	G	A	rs3751129	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:102455729G>A	ENST00000240079.6	-	1	173	c.12C>T	c.(10-12)gaC>gaT	p.D4D	RP11-554E23.4_ENST00000552707.1_RNA|CCDC53_ENST00000545679.1_Silent_p.D4D|CCDC53_ENST00000539515.1_Intron	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	4						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						GAGGAAGCCCGTCCTCATCCA	0.612													G|||	1404	0.280351	0.3003	0.2464	5008	,	,		16728	0.4276		0.2157	False		,,,				2504	0.1922				p.D4D		Atlas-SNP	.											.	CCDC53	14	.	0			c.C12T						PASS	.	G		1183,2651		195,793,929	26.0	31.0	29.0		12	-0.9	1.0	12	dbSNP_107	29	1782,6448		209,1364,2542	no	coding-synonymous	CCDC53	NM_016053.2		404,2157,3471	AA,AG,GG		21.6525,30.8555,24.5773		4/195	102455729	2965,9099	1917	4115	6032	SO:0001819	synonymous_variant	51019	exon1			AAGCCCGTCCTCA	AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.12C>T	12.37:g.102455729G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_016053	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Silent	SNP	ENST00000240079.6	37	CCDS44959.1																																																																																			G|0.694;A|0.306	0.306	strong		0.612	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1	NM_016053	
EXOC1	55763	hgsc.bcm.edu	37	4	56756531	56756531	+	Silent	SNP	T	T	C	rs2290016	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:56756531T>C	ENST00000381295.2	+	12	1866	c.1518T>C	c.(1516-1518)gcT>gcC	p.A506A	EXOC1_ENST00000349598.6_Silent_p.A491A|EXOC1_ENST00000346134.7_Silent_p.A506A	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	506					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	35	Glioma(25;0.08)|all_neural(26;0.101)					TCGATGTTGCTGACAGGACCA	0.388													C|||	1632	0.325879	0.2617	0.281	5008	,	,		18688	0.5278		0.2843	False		,,,				2504	0.2791				p.A506A		Atlas-SNP	.											.	EXOC1	103	.	0			c.T1518C						PASS	.	C	,,	1235,3171	704.5+/-407.1	169,897,1137	130.0	115.0	120.0		1518,1518,1473	-10.9	0.1	4	dbSNP_100	120	2500,6100	695.2+/-404.8	371,1758,2171	no	coding-synonymous,coding-synonymous,coding-synonymous	EXOC1	NM_001024924.1,NM_018261.3,NM_178237.2	,,	540,2655,3308	CC,CT,TT		29.0698,28.03,28.7175	,,	506/895,506/895,491/880	56756531	3735,9271	2203	4300	6503	SO:0001819	synonymous_variant	55763	exon12			TGTTGCTGACAGG	AK027047	CCDS3502.1, CCDS3503.1	4q12	2013-01-22	2005-11-01	2005-11-01	ENSG00000090989	ENSG00000090989			30380	protein-coding gene	gene with protein product		607879	"""SEC3-like 1 (S. cerevisiae)"""	SEC3L1		11042152, 11406615	Standard	XM_005265747		Approved	SEC3, FLJ10893, BM-102, Sec3p	uc003hbf.1	Q9NV70	OTTHUMG00000102165	ENST00000381295.2:c.1518T>C	4.37:g.56756531T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Silent	SNP	ENST00000381295.2	37	CCDS3502.1																																																																																			T|0.688;C|0.312	0.312	strong		0.388	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46058060	46058060	+	Silent	SNP	C	C	T	rs13051517	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46058060C>T	ENST00000380095.1	+	1	788	c.726C>T	c.(724-726)agC>agT	p.S242S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	242						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCTGCTACAGCCTCTGCTCTG	0.687													C|||	1782	0.355831	0.2799	0.4813	5008	,	,		18886	0.3333		0.4364	False		,,,				2504	0.3098				p.S242S		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C726T						PASS	.	C	,	1303,3099	389.3+/-327.3	187,929,1085	37.0	41.0	40.0		,726	2.0	0.0	21	dbSNP_121	40	3267,5325	463.0+/-365.8	638,1991,1667	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	825,2920,2752	TT,TC,CC		38.0237,29.6002,35.1701	,	,242/252	46058060	4570,8424	2201	4296	6497	SO:0001819	synonymous_variant	353333	exon1			CTACAGCCTCTGC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.726C>T	21.37:g.46058060C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	177	58	0.327684	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			T|1.000;|0.000	1.000	weak		0.687	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394239	103394239	+	RNA	SNP	C	C	T	rs16960471	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103394239C>T	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		TAATCCTTAACGGTCCAATAT	0.358													C|||	348	0.0694888	0.1399	0.0159	5008	,	,		21957	0.1052		0.0268	False		,,,				2504	0.0194				p.P2936P		Atlas-SNP	.											.	.	.	.	0			c.G8808A						PASS	.	C		158,1226		10,138,544	91.0	76.0	81.0		8808	-7.1	0.0	13	dbSNP_123	81	66,3116		2,62,1527	no	coding-synonymous	CCDC168	NM_001146197.1		12,200,2071	TT,TC,CC		2.0742,11.4162,4.9058		2936/7082	103394239	224,4342	692	1591	2283			643677	exon4			CCTTAACGGTCCA			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103394239C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	74	26	0.351351	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				C|0.924;T|0.076	0.076	strong		0.358	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
CNDP2	55748	hgsc.bcm.edu	37	18	72176083	72176083	+	Missense_Mutation	SNP	T	T	C	rs2278161	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72176083T>C	ENST00000324262.4	+	5	692	c.376T>C	c.(376-378)Tat>Cat	p.Y126H	CNDP2_ENST00000579847.1_Missense_Mutation_p.Y126H|CNDP2_ENST00000324301.8_Intron	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	126			Y -> H (in dbSNP:rs2278161). {ECO:0000269|Ref.2}.		cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.Y126H(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		AGGCAAGCTGTATGGGAGAGG	0.522													T|||	1081	0.215855	0.0802	0.3156	5008	,	,		18577	0.3006		0.1899	False		,,,				2504	0.2679				p.Y126H		Atlas-SNP	.											CNDP2,NS,carcinoma,0,1	CNDP2	55	1	1	Substitution - Missense(1)	stomach(1)	c.T376C						scavenged	.	T	,HIS/TYR	521,3885	239.0+/-250.2	41,439,1723	83.0	76.0	78.0		,376	5.6	0.9	18	dbSNP_100	78	1919,6681	340.5+/-323.6	190,1539,2571	yes	intron,missense	CNDP2	NM_001168499.1,NM_018235.2	,83	231,1978,4294	CC,CT,TT		22.314,11.8248,18.7606	,probably-damaging	,126/476	72176083	2440,10566	2203	4300	6503	SO:0001583	missense	55748	exon5			AAGCTGTATGGGA	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.376T>C	18.37:g.72176083T>C	ENSP00000325548:p.Tyr126His	Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	37	CCDS12006.1	435	0.19917582417582416	37	0.07520325203252033	95	0.26243093922651933	170	0.2972027972027972	133	0.17546174142480211	T	13.04	2.119143	0.37436	0.118248	0.22314	ENSG00000133313	ENST00000324262	T	0.53640	0.61	5.57	5.57	0.84162	.	0.055379	0.85682	D	0.000000	T	0.00012	0.0000	H	0.97516	4.02	0.09310	P	1.0	P;P	0.36065	0.535;0.535	P;P	0.55545	0.778;0.778	T	0.01420	-1.1359	9	0.72032	D	0.01	-29.6742	15.7428	0.77914	0.0:0.0:0.0:1.0	rs2278161;rs11539408;rs17816172;rs52835248;rs60808093;rs2278161	114;126	B4DV28;Q96KP4	.;CNDP2_HUMAN	H	126	ENSP00000325548:Y126H	ENSP00000325548:Y126H	Y	+	1	0	CNDP2	70327063	1.000000	0.71417	0.950000	0.38849	0.459000	0.32528	7.629000	0.83207	2.114000	0.64651	0.533000	0.62120	TAT	T|0.801;C|0.198	0.198	strong		0.522	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
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 GAIIx	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_ENST00000395575.2_Missense_Mutation_p.P424S|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.P424S|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.P424S|ALDH3A2_ENST00000579855.1_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	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	50	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		
SPRR1B	6699	hgsc.bcm.edu	37	1	153004983	153004983	+	Silent	SNP	C	C	T	rs12195	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153004983C>T	ENST00000307098.4	+	2	227	c.162C>T	c.(160-162)ccC>ccT	p.P54P	SPRR1B_ENST00000392661.3_Intron	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	54	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCAAAGTGCCCGAGCCCTGCC	0.627													T|||	2492	0.497604	0.441	0.4265	5008	,	,		14910	0.5923		0.5179	False		,,,				2504	0.5061				p.P54P		Atlas-SNP	.											.	SPRR1B	18	.	1	Deletion - In frame(1)	ovary(1)	c.C162T						PASS	.	T		2076,2330	605.2+/-390.5	490,1096,617	113.0	114.0	113.0		162	0.6	1.0	1	dbSNP_52	113	4494,4102	561.2+/-387.7	1233,2028,1037	no	coding-synonymous	SPRR1B	NM_003125.2		1723,3124,1654	TT,TC,CC		47.7199,47.1176,49.4693		54/90	153004983	6570,6432	2203	4298	6501	SO:0001819	synonymous_variant	6699	exon2			AGTGCCCGAGCCC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.162C>T	1.37:g.153004983C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_003125	B2R5H7|P22529|P22530|Q5T524	Silent	SNP	ENST00000307098.4	37	CCDS30863.1																																																																																			C|0.493;T|0.507	0.507	strong		0.627	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
AFF3	3899	hgsc.bcm.edu	37	2	100210074	100210074	+	Silent	SNP	G	G	C	rs1047281	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:100210074G>C	ENST00000409236.2	-	13	2161	c.2049C>G	c.(2047-2049)tcC>tcG	p.S683S	AFF3_ENST00000409579.1_Silent_p.S708S|AFF3_ENST00000356421.2_Silent_p.S708S|AFF3_ENST00000317233.4_Silent_p.S683S			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	683					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						CCTCCTGCTCGGACTCCAGGT	0.617													G|||	735	0.146765	0.087	0.1239	5008	,	,		13756	0.0843		0.2038	False		,,,				2504	0.2495				p.S708S		Atlas-SNP	.											AFF3,NS,carcinoma,0,1	AFF3	164	1	0			c.C2124G						PASS	.	G	,	506,3890		38,430,1730	48.0	57.0	54.0		2124,2049	-9.3	0.5	2	dbSNP_86	54	1710,6866		170,1370,2748	no	coding-synonymous,coding-synonymous	AFF3	NM_001025108.1,NM_002285.2	,	208,1800,4478	CC,CG,GG		19.9394,11.5105,17.0829	,	708/1252,683/1227	100210074	2216,10756	2198	4288	6486	SO:0001819	synonymous_variant	3899	exon14			CTGCTCGGACTCC	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.2049C>G	2.37:g.100210074G>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	37	CCDS42723.1																																																																																			G|0.832;C|0.168	0.168	strong		0.617	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
METTL13	51603	hgsc.bcm.edu	37	1	171763549	171763549	+	Silent	SNP	C	C	T	rs2232825	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171763549C>T	ENST00000361735.3	+	7	1973	c.1707C>T	c.(1705-1707)taC>taT	p.Y569Y	METTL13_ENST00000458517.1_Silent_p.Y568Y|METTL13_ENST00000362019.3_Silent_p.Y483Y|METTL13_ENST00000466643.1_3'UTR|METTL13_ENST00000367737.5_Silent_p.Y413Y	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	569							methyltransferase activity (GO:0008168)	p.Y569Y(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GGCCTTGCTACGATGTCATAA	0.418													C|||	583	0.116414	0.0234	0.1556	5008	,	,		21017	0.1329		0.2177	False		,,,				2504	0.093				p.Y569Y		Atlas-SNP	.											METTL13,NS,carcinoma,0,1	METTL13	67	1	1	Substitution - coding silent(1)	stomach(1)	c.C1707T						PASS	.	C	,,	234,4172		7,220,1976	100.0	88.0	92.0		1239,1449,1707	-7.1	0.0	1	dbSNP_98	92	1791,6809		196,1399,2705	no	coding-synonymous,coding-synonymous,coding-synonymous	METTL13	NM_001007239.1,NM_014955.2,NM_015935.4	,,	203,1619,4681	TT,TC,CC		20.8256,5.3109,15.5697	,,	413/544,483/614,569/700	171763549	2025,10981	2203	4300	6503	SO:0001819	synonymous_variant	51603	exon7			TTGCTACGATGTC	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1707C>T	1.37:g.171763549C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Silent	SNP	ENST00000361735.3	37	CCDS1299.1																																																																																			C|0.859;T|0.141	0.141	strong		0.418	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39498038	39498038	+	Missense_Mutation	SNP	G	G	C	rs139302	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39498038G>C	ENST00000401756.1	+	4	610	c.534G>C	c.(532-534)gaG>gaC	p.E178D	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.E178D|APOBEC3H_ENST00000421988.2_Intron|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.E178D	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	178			E -> D (in allele A3H-Var; haplotype 2; allele presenting a higher expression and more effective in retrotransposons and HIV-1 restriction; dbSNP:rs139302). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					GACGGCTTGAGAGGATAAAGG	0.562													G|||	2582	0.515575	0.8472	0.3458	5008	,	,		13390	0.3313		0.4632	False		,,,				2504	0.4315				p.E178D		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G534C						PASS	.	G	ASP/GLU,ASP/GLU,,ASP/GLU	3461,945		1362,737,104	55.0	46.0	49.0		534,534,,534	-6.1	0.0	22	dbSNP_78	49	3964,4636		887,2190,1223	yes	missense,missense,intron,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	45,45,,45	2249,2927,1327	CC,CG,GG		46.093,21.448,42.911	possibly-damaging,possibly-damaging,,possibly-damaging	178/183,178/201,,178/184	39498038	7425,5581	2203	4300	6503	SO:0001583	missense	164668	exon4			GCTTGAGAGGATA	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.534G>C	22.37:g.39498038G>C	ENSP00000385741:p.Glu178Asp	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	31	30	0.967742	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	1082	0.49542124542124544	411	0.8353658536585366	122	0.3370165745856354	186	0.32517482517482516	363	0.4788918205804749	.	2.255	-0.370687	0.05069	0.78552	0.46093	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000401756	T;T;T	0.64438	-0.08;-0.08;-0.1	3.06	-6.12	0.02124	.	.	.	.	.	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.12630	0.006	B	0.16722	0.016	T	0.25710	-1.0124	8	0.30078	T	0.28	.	1.9922	0.03448	0.1454:0.3233:0.309:0.2223	rs139302;rs52796542;rs58930549;rs139302	178	B7TQM3	.	D	178	ENSP00000216123:E178D;ENSP00000411754:E178D;ENSP00000385741:E178D	ENSP00000216123:E178D	E	+	3	2	APOBEC3H	37827984	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.286000	0.02788	-2.277000	0.00677	-2.185000	0.00314	GAG	G|0.460;C|0.540	0.540	strong		0.562	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
ZNF630	57232	hgsc.bcm.edu	37	X	47918160	47918160	+	Silent	SNP	A	A	G	rs61736415	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:47918160A>G	ENST00000409324.3	-	5	1897	c.1671T>C	c.(1669-1671)caT>caC	p.H557H	ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000442455.3_Silent_p.H543H|ZNF630_ENST00000276054.4_Silent_p.H433H	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	557					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(1)|large_intestine(6)|lung(11)|ovary(1)	19						GTAGAATGAGATGTGACTTCA	0.448													A|||	27	0.00715232	0.0008	0.0058	3775	,	,		15133	0.0		0.0189	False		,,,				2504	0.0031				p.H557H		Atlas-SNP	.											.	ZNF630	71	.	0			c.T1671C						PASS	.	A	,	12,3811		0,9,3,1622,558	57.0	50.0	53.0		1671,1629	-4.1	0.9	X	dbSNP_129	53	133,6582		1,92,39,2335,1820	no	coding-synonymous,coding-synonymous	ZNF630	NM_001037735.2,NM_001190255.1	,	1,101,42,3957,2378	GG,GA,G,AA,A		1.9806,0.3139,1.376	,	557/658,543/644	47918160	145,10393	2192	4287	6479	SO:0001819	synonymous_variant	57232	exon5			AATGAGATGTGAC	AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.1671T>C	X.37:g.47918160A>G		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	31	8	0.258065	NM_001037735	F8WAG4|Q5H8Z5	Silent	SNP	ENST00000409324.3	37	CCDS35237.2																																																																																			A|0.987;G|0.013	0.013	strong		0.448	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735	
ZNF880	400713	hgsc.bcm.edu	37	19	52887904	52887904	+	Silent	SNP	T	T	C	rs2042913	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52887904T>C	ENST00000422689.2	+	4	1086	c.1071T>C	c.(1069-1071)tgT>tgC	p.C357C		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	357					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GTAATAAATGTGGCAAGGTCT	0.403																																					p.C357C		Atlas-SNP	.											ZNF880,colon,carcinoma,0,1	ZNF880	45	1	0			c.T1071C						PASS	.						41.0	38.0	39.0					19																	52887904		1568	3582	5150	SO:0001819	synonymous_variant	400713	exon4			TAAATGTGGCAAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1071T>C	19.37:g.52887904T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	33	28	0.848485	NM_001145434	B4DNA6	Silent	SNP	ENST00000422689.2	37	CCDS46164.1																																																																																			T|0.637;C|0.363	0.363	strong		0.403	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
RASGRF1	5923	hgsc.bcm.edu	37	15	79277391	79277391	+	Silent	SNP	T	T	G	rs117481060	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:79277391T>G	ENST00000419573.3	-	24	3694	c.3420A>C	c.(3418-3420)gcA>gcC	p.A1140A	RP11-16K12.1_ENST00000316148.4_RNA|RASGRF1_ENST00000394745.3_Silent_p.A356A|RASGRF1_ENST00000558480.2_Silent_p.A1124A|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1140	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GCCGGAAGATTGCACTGCGGT	0.597													T|||	25	0.00499201	0.0061	0.0029	5008	,	,		19444	0.0		0.0119	False		,,,				2504	0.0031				p.A1140A		Atlas-SNP	.											.	RASGRF1	168	.	0			c.A3420C						PASS	.	T	,,	48,4344	50.2+/-85.5	0,48,2148	128.0	96.0	107.0		3372,3420,1068	-7.8	0.8	15	dbSNP_132	107	179,8407	81.5+/-144.1	5,169,4119	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRF1	NM_001145648.1,NM_002891.4,NM_153815.2	,,	5,217,6267	GG,GT,TT		2.0848,1.0929,1.7491	,,	1124/1258,1140/1274,356/490	79277391	227,12751	2196	4293	6489	SO:0001819	synonymous_variant	5923	exon24			GAAGATTGCACTG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3420A>C	15.37:g.79277391T>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	154	63	0.409091	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																			T|0.986;G|0.014	0.014	strong		0.597	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
SERPINB10	5273	hgsc.bcm.edu	37	18	61582751	61582751	+	Missense_Mutation	SNP	T	T	G	rs17072097	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61582751T>G	ENST00000238508.3	+	2	66	c.7T>G	c.(7-9)Tct>Gct	p.S3A		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	3			S -> A (in dbSNP:rs17072097).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S3A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				CTCAATGGACTCTCTAGCAAC	0.348													G|||	1402	0.279952	0.4123	0.3127	5008	,	,		19162	0.248		0.1998	False		,,,				2504	0.1933				p.S3A		Atlas-SNP	.											SERPINB10,colon,carcinoma,0,2	SERPINB10	53	2	1	Substitution - Missense(1)	stomach(1)	c.T7G						PASS	.	G	ALA/SER	1734,2672	647.9+/-398.6	341,1052,810	82.0	82.0	82.0		7	0.6	0.0	18	dbSNP_123	82	1617,6983	741.1+/-407.1	145,1327,2828	yes	missense	SERPINB10	NM_005024.1	99	486,2379,3638	GG,GT,TT		18.8023,39.3554,25.765		3/398	61582751	3351,9655	2203	4300	6503	SO:0001583	missense	5273	exon1			ATGGACTCTCTAG	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.7T>G	18.37:g.61582751T>G	ENSP00000238508:p.Ser3Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	147	91	0.619048	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	550|550	0.2518315018315018|0.2518315018315018	186|186	0.3780487804878049|0.3780487804878049	107|107	0.2955801104972376|0.2955801104972376	115|115	0.20104895104895104|0.20104895104895104	142|142	0.18733509234828497|0.18733509234828497	G|G	0.005|0.005	-2.159978|-2.159978	0.00321|0.00321	0.393554|0.393554	0.188023|0.188023	ENSG00000242550|ENSG00000242550	ENST00000397996;ENST00000418725|ENST00000238508	.|D	.|0.82433	.|-1.61	5.97|5.97	0.577|0.577	0.17385|0.17385	.|Serpin domain (1);	.|0.538205	.|0.21214	.|N	.|0.078260	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.41124|0.41124	1.26|1.26	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.06786	.|0.001;0.0	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.21008|0.21008	-1.0258|-1.0258	4|9	.|0.11182	.|T	.|0.66	.|.	1.6638|1.6638	0.02797|0.02797	0.1955:0.1217:0.2005:0.4822|0.1955:0.1217:0.2005:0.4822	rs17072097;rs52808370;rs57746168;rs17072097|rs17072097;rs52808370;rs57746168;rs17072097	.|3;3	.|P48595;B2RC45	.|SPB10_HUMAN;.	R|A	215;188|3	.|ENSP00000238508:S3A	.|ENSP00000238508:S3A	L|S	+|+	2|1	0|0	SERPINB10|SERPINB10	59733731|59733731	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.156000|-0.156000	0.10100|0.10100	-0.300000|-0.300000	0.08895|0.08895	-4.888000|-4.888000	0.00002|0.00002	CTC|TCT	T|0.744;G|0.256	0.256	strong		0.348	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
ZBTB22	9278	hgsc.bcm.edu	37	6	33283766	33283766	+	Missense_Mutation	SNP	T	T	C	rs3130100	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33283766T>C	ENST00000431845.2	-	2	1079	c.928A>G	c.(928-930)Aca>Gca	p.T310A	TAPBP_ENST00000434618.2_5'Flank|TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000456592.2_5'Flank|TAPBP_ENST00000489157.1_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.T310A	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	310			T -> A (in dbSNP:rs3130100). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						ACCAGGGGTGTTGGCGCTGGG	0.567													C|||	2676	0.534345	0.5734	0.549	5008	,	,		18569	0.3899		0.5288	False		,,,				2504	0.6258				p.T310A		Atlas-SNP	.											.	ZBTB22	48	.	0			c.A928G						PASS	.	C	ALA/THR,ALA/THR	2459,1947	544.3+/-376.5	691,1077,435	110.0	91.0	98.0		928,928	3.0	0.6	6	dbSNP_103	98	4652,3948	536.7+/-383.1	1265,2122,913	yes	missense,missense	ZBTB22	NM_001145338.1,NM_005453.4	58,58	1956,3199,1348	CC,CT,TT		45.907,44.1897,45.3252	benign,benign	310/635,310/635	33283766	7111,5895	2203	4300	6503	SO:0001583	missense	9278	exon2			GGGGTGTTGGCGC	Z97183	CCDS4775.1	6p21.3	2013-01-09	2006-04-12	2006-04-12	ENSG00000236104	ENSG00000236104		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13085	protein-coding gene	gene with protein product		611439	"""zinc finger protein 297"""	ZNF297			Standard	NM_005453		Approved	BING1, ZNF297A, fruitless, fru, ZBTB22A	uc010juu.3	O15209	OTTHUMG00000031110	ENST00000431845.2:c.928A>G	6.37:g.33283766T>C	ENSP00000407545:p.Thr310Ala	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	54	0.675	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	37	CCDS4775.1	1141	0.5224358974358975	305	0.6199186991869918	218	0.6022099447513812	222	0.3881118881118881	396	0.5224274406332454	C	0	-2.636134	0.00114	0.558103	0.54093	ENSG00000236104	ENST00000418724;ENST00000431845	T;T	0.04234	3.67;3.67	3.88	3.0	0.34707	.	.	.	.	.	T	0.00440	0.0014	N	0.02011	-0.69	0.54753	P	1.0999999999983245E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	8	0.05620	T	0.96	.	5.3554	0.16057	0.0:0.6798:0.206:0.1142	rs3130100;rs17856567;rs57230775;rs3130100	310	O15209	ZBT22_HUMAN	A	310	ENSP00000404403:T310A;ENSP00000407545:T310A	ENSP00000404403:T310A	T	-	1	0	ZBTB22	33391744	1.000000	0.71417	0.563000	0.28383	0.381000	0.30169	1.935000	0.40173	0.327000	0.23409	-1.568000	0.00874	ACA	T|0.467;C|0.533	0.533	strong		0.567	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2		
MYOCD	93649	hgsc.bcm.edu	37	17	12656417	12656417	+	Silent	SNP	T	T	C	rs28730824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:12656417T>C	ENST00000343344.4	+	10	1812	c.1812T>C	c.(1810-1812)gcT>gcC	p.A604A	AC005358.1_ENST00000609971.1_Silent_p.A508A|MYOCD_ENST00000425538.1_Silent_p.A604A|MYOCD_ENST00000395988.1_3'UTR			Q8IZQ8	MYCD_HUMAN	myocardin	604					cardiac muscle cell differentiation (GO:0055007)|cardiac ventricle development (GO:0003231)|cardiocyte differentiation (GO:0035051)|cell growth involved in cardiac muscle cell development (GO:0061049)|cellular component maintenance (GO:0043954)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|hepatic stellate cell activation (GO:0035733)|lung alveolus development (GO:0048286)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of skeletal muscle cell differentiation (GO:2001015)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of cardiac vascular smooth muscle cell differentiation (GO:2000724)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of histone acetylation (GO:0035065)|regulation of myoblast differentiation (GO:0045661)|regulation of smooth muscle cell differentiation (GO:0051150)|response to hypoxia (GO:0001666)|smooth muscle cell differentiation (GO:0051145)|urinary bladder development (GO:0060157)|uterus development (GO:0060065)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|protein domain specific binding (GO:0019904)|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 transcription factor binding transcription factor activity (GO:0001076)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(2)|lung(33)|ovary(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	70				UCEC - Uterine corpus endometrioid carcinoma (92;0.0969)		GTGAAGCTGCTCAACTCCAGC	0.507													T|||	89	0.0177716	0.0015	0.0231	5008	,	,		15492	0.0		0.0557	False		,,,				2504	0.0153				p.A604A		Atlas-SNP	.											.	MYOCD	291	.	0			c.T1812C						PASS	.	T	,,	58,4348	55.5+/-91.7	0,58,2145	89.0	97.0	94.0		1812,1524,1812	-0.4	0.0	17	dbSNP_125	94	534,8066	149.1+/-204.2	14,506,3780	no	coding-synonymous,coding-synonymous,coding-synonymous	MYOCD	NM_001146312.1,NM_001146313.1,NM_153604.2	,,	14,564,5925	CC,CT,TT		6.2093,1.3164,4.5517	,,	604/987,508/685,604/939	12656417	592,12414	2203	4300	6503	SO:0001819	synonymous_variant	93649	exon10			AGCTGCTCAACTC	AF532596	CCDS11163.1, CCDS54091.1	17p11.2	2004-03-01			ENSG00000141052	ENSG00000141052			16067	protein-coding gene	gene with protein product		606127				11439182, 12397177	Standard	XM_005256863		Approved	MYCD	uc002gno.2	Q8IZQ8	OTTHUMG00000058767	ENST00000343344.4:c.1812T>C	17.37:g.12656417T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_001146312	Q5UBU5|Q8N7Q1	Silent	SNP	ENST00000343344.4	37	CCDS11163.1																																																																																			T|0.963;C|0.037	0.037	strong		0.507	MYOCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129950.1	NM_153604	
MUC2	4583	hgsc.bcm.edu	37	11	1088815	1088815	+	Silent	SNP	A	A	G	rs7103978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1088815A>G	ENST00000441003.2	+	26	3627	c.3600A>G	c.(3598-3600)gcA>gcG	p.A1200A	MUC2_ENST00000359061.5_Silent_p.A1200A	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1200					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)	CACCTGGAGCATCGGTTCCCA	0.592													G|||	326	0.0650958	0.053	0.0591	5008	,	,		22307	0.0556		0.0974	False		,,,				2504	0.0624				p.A1200A		Atlas-SNP	.											.	MUC2	614	.	0			c.A3600G						PASS	.	G		223,3987		5,213,1887	59.0	64.0	62.0		3600	-7.2	0.0	11	dbSNP_116	62	784,7636		37,710,3463	no	coding-synonymous	MUC2	NM_002457.2		42,923,5350	GG,GA,AA		9.3112,5.2969,7.9731		1200/2813	1088815	1007,11623	2105	4210	6315	SO:0001819	synonymous_variant	4583	exon26			TGGAGCATCGGTT	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.3600A>G	11.37:g.1088815A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				A|0.939;G|0.061	0.061	strong		0.592	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
N4BP2	55728	hgsc.bcm.edu	37	4	40103817	40103817	+	Missense_Mutation	SNP	G	G	A	rs61748746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:40103817G>A	ENST00000261435.6	+	4	768	c.352G>A	c.(352-354)Gaa>Aaa	p.E118K		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	118				E -> K (in Ref. 2; AAI26467). {ECO:0000305}.	nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TAAAATAATGGAAAAACGTCC	0.363													G|||	216	0.043131	0.034	0.0231	5008	,	,		16779	0.0407		0.0815	False		,,,				2504	0.0327				p.E118K		Atlas-SNP	.											.	N4BP2	166	.	0			c.G352A						PASS	.	G	LYS/GLU	137,4269	94.8+/-133.5	2,133,2068	94.0	91.0	92.0		352	6.1	1.0	4	dbSNP_129	92	728,7872	175.5+/-225.5	26,676,3598	yes	missense	N4BP2	NM_018177.4	56	28,809,5666	AA,AG,GG		8.4651,3.1094,6.6508	possibly-damaging	118/1771	40103817	865,12141	2203	4300	6503	SO:0001583	missense	55728	exon4			ATAATGGAAAAAC	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.352G>A	4.37:g.40103817G>A	ENSP00000261435:p.Glu118Lys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	91	32	0.351648	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	95	0.043498168498168496	16	0.032520325203252036	4	0.011049723756906077	18	0.03146853146853147	57	0.07519788918205805	G	15.02	2.708557	0.48517	0.031094	0.084651	ENSG00000078177	ENST00000261435;ENST00000381804;ENST00000515550	T;T	0.80480	-1.38;-1.38	6.08	6.08	0.98989	.	0.349077	0.26489	N	0.024097	T	0.15652	0.0377	L	0.29908	0.895	0.29193	N	0.8757	P;P	0.46142	0.873;0.799	P;B	0.44990	0.466;0.276	T	0.51196	-0.8736	10	0.32370	T	0.25	-9.3661	15.2685	0.73681	0.0:0.0:0.8605:0.1395	rs61748746	118;118	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	K	118;38;38	ENSP00000261435:E118K;ENSP00000422057:E38K	ENSP00000261435:E118K	E	+	1	0	N4BP2	39780212	0.998000	0.40836	0.994000	0.49952	0.330000	0.28571	1.989000	0.40707	2.894000	0.99253	0.591000	0.81541	GAA	G|0.938;A|0.062	0.062	strong		0.363	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
TAX1BP1	8887	hgsc.bcm.edu	37	7	27827103	27827103	+	Missense_Mutation	SNP	T	T	A	rs11540483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:27827103T>A	ENST00000396319.2	+	8	1007	c.919T>A	c.(919-921)Tta>Ata	p.L307I	TAX1BP1_ENST00000265393.6_Missense_Mutation_p.L307I|TAX1BP1_ENST00000409980.1_Missense_Mutation_p.L307I|TAX1BP1_ENST00000543117.1_Missense_Mutation_p.L307I|TAX1BP1_ENST00000433216.2_Missense_Mutation_p.L150I	NM_006024.6	NP_006015.4	Q86VP1	TAXB1_HUMAN	Tax1 (human T-cell leukemia virus type I) binding protein 1	307			L -> I (in dbSNP:rs11540483). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)	cytosol (GO:0005829)	kinase binding (GO:0019900)			breast(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(8)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31			GBM - Glioblastoma multiforme(3;0.0823)			TTTAAAAAATTTAGATGGGAA	0.343													T|||	190	0.0379393	0.0061	0.0663	5008	,	,		16596	0.001		0.1173	False		,,,				2504	0.0174				p.L307I		Atlas-SNP	.											TAX1BP1,NS,carcinoma,-1,1	TAX1BP1	71	1	0			c.T919A						scavenged	.	T	ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU	106,4300	83.4+/-121.9	1,104,2098	73.0	78.0	76.0		919,919,448,919	2.3	1.0	7	dbSNP_120	76	1011,7589	215.3+/-254.7	58,895,3347	yes	missense,missense,missense,missense	TAX1BP1	NM_001079864.2,NM_001206901.1,NM_001206902.1,NM_006024.6	5,5,5,5	59,999,5445	AA,AT,TT		11.7558,2.4058,8.5883	benign,benign,benign,benign	307/748,307/748,150/591,307/790	27827103	1117,11889	2203	4300	6503	SO:0001583	missense	8887	exon8			AAAAATTTAGATG	U33821	CCDS5415.1, CCDS43561.1, CCDS56471.1	7p15	2010-08-05			ENSG00000106052	ENSG00000106052			11575	protein-coding gene	gene with protein product		605326				10435631	Standard	NM_006024		Approved	TXBP151, CALCOCO3	uc003szl.3	Q86VP1	OTTHUMG00000023377	ENST00000396319.2:c.919T>A	7.37:g.27827103T>A	ENSP00000379612:p.Leu307Ile	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	72	51	0.708333	NM_006024	B4DKU7|E7ENV2|O60398|O95770|Q13311|Q9BQG5|Q9UI88	Missense_Mutation	SNP	ENST00000396319.2	37	CCDS5415.1	119	0.05448717948717949	4	0.008130081300813009	30	0.08287292817679558	0	0.0	85	0.11213720316622691	T	15.47	2.843571	0.51057	0.024058	0.117558	ENSG00000106052	ENST00000543117;ENST00000265393;ENST00000409980;ENST00000433216;ENST00000396319	T;T;T;T;T	0.32988	2.83;2.83;2.79;1.43;2.8	5.98	2.28	0.28536	.	0.170216	0.27500	N	0.019093	T	0.00412	0.0013	L	0.47716	1.5	0.26996	P	0.9650325	P;B;B	0.40431	0.717;0.122;0.112	P;B;B	0.48089	0.566;0.2;0.167	T	0.05566	-1.0877	9	0.32370	T	0.25	-1.4847	2.9897	0.05979	0.1204:0.1207:0.1255:0.6334	rs11540483;rs17854622	150;307;307	E7ENV2;Q86VP1;Q86VP1-2	.;TAXB1_HUMAN;.	I	307;307;307;150;307	ENSP00000444811:L307I;ENSP00000265393:L307I;ENSP00000386515:L307I;ENSP00000391907:L150I;ENSP00000379612:L307I	ENSP00000265393:L307I	L	+	1	2	TAX1BP1	27793628	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.318000	0.43779	0.460000	0.27045	0.528000	0.53228	TTA	A|0.078;T|0.922	0.078	strong		0.343	TAX1BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214142.1	NM_006024	
PPL	5493	hgsc.bcm.edu	37	16	4947748	4947748	+	Silent	SNP	T	T	C	rs61734748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4947748T>C	ENST00000345988.2	-	9	989	c.900A>G	c.(898-900)gcA>gcG	p.A300A	PPL_ENST00000590782.2_Silent_p.A298A	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	300					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CCTTCCAGTCTGCGTGCACAG	0.597													T|||	45	0.00898562	0.0008	0.0043	5008	,	,		19379	0.0		0.0229	False		,,,				2504	0.0184				p.A300A		Atlas-SNP	.											PPL,NS,carcinoma,-2,1	PPL	168	1	0			c.A900G						PASS	.	T		12,4382	19.1+/-41.9	0,12,2185	89.0	68.0	75.0		900	-9.0	0.9	16	dbSNP_129	75	167,8433	77.8+/-140.4	1,165,4134	no	coding-synonymous	PPL	NM_002705.4		1,177,6319	CC,CT,TT		1.9419,0.2731,1.3776		300/1757	4947748	179,12815	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon9			CCAGTCTGCGTGC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.900A>G	16.37:g.4947748T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			T|0.988;C|0.012	0.012	strong		0.597	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
MUC16	94025	hgsc.bcm.edu	37	19	9049910	9049910	+	Missense_Mutation	SNP	C	C	T	rs56307190	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9049910C>T	ENST00000397910.4	-	5	31924	c.31721G>A	c.(31720-31722)cGt>cAt	p.R10574H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10576	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGCCCCAGAACGAGAGACCAG	0.498													C|||	928	0.185304	0.0628	0.2752	5008	,	,		20093	0.3363		0.167	False		,,,				2504	0.1503				p.R10574H		Atlas-SNP	.											.	MUC16	4315	.	0			c.G31721A						PASS	.		HIS/ARG	303,3471		14,275,1598	134.0	124.0	127.0		31721	-0.1	0.0	19	dbSNP_129	127	1499,6711		137,1225,2743	yes	missense	MUC16	NM_024690.2	29	151,1500,4341	TT,TC,CC		18.2582,8.0286,15.0367	benign	10574/14508	9049910	1802,10182	1887	4105	5992	SO:0001583	missense	94025	exon5			CCAGAACGAGAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.31721G>A	19.37:g.9049910C>T	ENSP00000381008:p.Arg10574His	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	255	141	0.552941	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	462	0.21153846153846154	32	0.06504065040650407	91	0.2513812154696133	213	0.3723776223776224	126	0.1662269129287599	c	6.957	0.546438	0.13312	0.080286	0.182582	ENSG00000181143	ENST00000397910	T	0.02916	4.11	3.2	-0.111	0.13576	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	.	.	.	B	0.14012	0.009	B	0.09377	0.004	T	0.42849	-0.9427	8	0.87932	D	0	.	5.6847	0.17797	0.0:0.6388:0.0:0.3612	rs56307190;rs61748894	10574	B5ME49	.	H	10574	ENSP00000381008:R10574H	ENSP00000381008:R10574H	R	-	2	0	MUC16	8910910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.183000	0.16919	0.055000	0.16094	-0.711000	0.03637	CGT	C|0.794;T|0.206	0.206	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
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 GAIIx	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*	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	87	47	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	
SEL1L2	80343	hgsc.bcm.edu	37	20	13830137	13830137	+	Missense_Mutation	SNP	A	A	C	rs2073290	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:13830137A>C	ENST00000284951.5	-	20	2135	c.2061T>G	c.(2059-2061)caT>caG	p.H687Q	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Missense_Mutation_p.H574Q			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	687			H -> Q (in dbSNP:rs2073290).			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						CATCCTACCCATGGTGATTTC	0.473													A|||	713	0.142372	0.0121	0.2363	5008	,	,		16950	0.0903		0.2594	False		,,,				2504	0.1851				p.H574Q		Atlas-SNP	.											.	SEL1L2	103	.	0			c.T1722G						PASS	.	A	GLN/HIS	185,3631		3,179,1726	141.0	132.0	135.0		2061	-10.9	0.0	20	dbSNP_96	135	2104,6128		278,1548,2290	yes	missense	SEL1L2	NM_025229.1	24	281,1727,4016	CC,CA,AA		25.5588,4.848,18.999	benign	687/689	13830137	2289,9759	1908	4116	6024	SO:0001583	missense	80343	exon18			CTACCCATGGTGA	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.2061T>G	20.37:g.13830137A>C	ENSP00000284951:p.His687Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		349	0.15979853479853479	9	0.018292682926829267	85	0.23480662983425415	52	0.09090909090909091	203	0.2678100263852243	A	7.546	0.661779	0.14645	0.04848	0.255588	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.26223	1.75;2.21	5.43	-10.9	0.00192	.	0.775970	0.11646	N	0.543298	T	0.00012	0.0000	N	0.04063	-0.285	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16012	-1.0417	9	0.02654	T	1	5.1932	4.1043	0.10030	0.1721:0.101:0.477:0.2499	rs2073290;rs17226810;rs52832304;rs61566789;rs2073290	574;687	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	Q	574;687	ENSP00000367312:H574Q;ENSP00000284951:H687Q	ENSP00000284951:H687Q	H	-	3	2	SEL1L2	13778137	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.060000	0.03475	-1.893000	0.01106	-1.272000	0.01410	CAT	A|0.837;C|0.163	0.163	strong		0.473	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
ALOX15	246	hgsc.bcm.edu	37	17	4536241	4536241	+	Silent	SNP	T	T	C	rs743646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4536241T>C	ENST00000570836.1	-	12	1551	c.1455A>G	c.(1453-1455)acA>acG	p.T485T	ALOX15_ENST00000545513.1_Silent_p.T507T|ALOX15_ENST00000293761.3_Silent_p.T485T|ALOX15_ENST00000574640.1_Silent_p.T446T			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	485	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		CAGCCACGTCTGTCTTATAGT	0.592													T|||	232	0.0463259	0.0045	0.0648	5008	,	,		18952	0.001		0.1342	False		,,,				2504	0.046				p.T485T		Atlas-SNP	.											.	ALOX15	70	.	0			c.A1455G						PASS	.	T		89,4317	73.6+/-111.7	1,87,2115	93.0	85.0	88.0		1455	-3.2	0.0	17	dbSNP_86	88	1057,7543	222.7+/-259.7	66,925,3309	no	coding-synonymous	ALOX15	NM_001140.3		67,1012,5424	CC,CT,TT		12.2907,2.02,8.8113		485/663	4536241	1146,11860	2203	4300	6503	SO:0001819	synonymous_variant	246	exon11			CACGTCTGTCTTA	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"""Arachidonate lipoxygenases"""	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.1455A>G	17.37:g.4536241T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Silent	SNP	ENST00000570836.1	37	CCDS11049.1																																																																																			T|0.920;C|0.080	0.080	strong		0.592	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2		
IFITM2	10581	hgsc.bcm.edu	37	11	308314	308314	+	Missense_Mutation	SNP	T	T	C	rs14408	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:308314T>C	ENST00000399817.4	+	1	152	c.122T>C	c.(121-123)aTg>aCg	p.M41T	RP11-326C3.7_ENST00000526612.1_RNA|IFITM2_ENST00000533141.1_Missense_Mutation_p.M21T|IFITM2_ENST00000602569.1_Missense_Mutation_p.M21T	NM_006435.2	NP_006426.2	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2	41			M -> T (in dbSNP:rs14408). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1906403}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-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;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCTCCCCCGATGTCCACCGTG	0.607													t|||	3531	0.705072	0.7617	0.6657	5008	,	,		14037	0.9593		0.3787	False		,,,				2504	0.7301				p.M41T		Atlas-SNP	.											IFITM2,rectum,carcinoma,0,1	IFITM2	21	1	0			c.T122C						PASS	.	T	THR/MET	2520,1396		857,806,295	63.0	88.0	80.0		122	-2.8	0.0	11	dbSNP_52	80	3019,5275		590,1839,1718	no	missense	IFITM2	NM_006435.2	81	1447,2645,2013	CC,CT,TT		36.3998,35.6486,45.3645	benign	41/133	308314	5539,6671	1958	4147	6105	SO:0001583	missense	10581	exon1			CCCCGATGTCCAC	X57351	CCDS41583.1	11p15.5	2012-03-13	2012-03-13		ENSG00000185201	ENSG00000185201			5413	protein-coding gene	gene with protein product		605578	"""interferon induced transmembrane protein 2 (1-8D)"""			1906403	Standard	NM_006435		Approved	1-8D	uc001lox.4	Q01629		ENST00000399817.4:c.122T>C	11.37:g.308314T>C	ENSP00000382714:p.Met41Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	112	46	0.410714	NM_006435	Q6FH82|Q96DA8	Missense_Mutation	SNP	ENST00000399817.4	37	CCDS41583.1	1298	0.5943223443223443	337	0.6849593495934959	199	0.5497237569060773	523	0.9143356643356644	239	0.3153034300791557	T	0.004	-2.266536	0.00259	0.643514	0.363998	ENSG00000185201	ENST00000533141;ENST00000399817;ENST00000327366	T;T	0.76709	-1.04;-0.8	2.59	-2.76	0.05896	.	1.327100	0.06148	N	0.673694	T	0.00012	0.0000	N	0.00010	-3.02	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45644	-0.9247	9	0.02654	T	1	2.4836	3.407	0.07344	0.3221:0.496:0.0:0.1819	rs14408;rs3179090;rs17850538;rs58885107;rs14408	41	Q01629	IFM2_HUMAN	T	21;41;41	ENSP00000434443:M21T;ENSP00000382714:M41T	ENSP00000327996:M41T	M	+	2	0	IFITM2	298314	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-2.620000	0.00879	-0.998000	0.03446	-3.056000	0.00068	ATG	.	.	weak		0.607	IFITM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383591.1	NM_006435	
FAM196A	642938	hgsc.bcm.edu	37	10	128974220	128974220	+	Missense_Mutation	SNP	G	G	A	rs11594560	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:128974220G>A	ENST00000522781.1	-	4	995	c.440C>T	c.(439-441)gCg>gTg	p.A147V	DOCK1_ENST00000280333.6_Intron|FAM196A_ENST00000424811.2_Missense_Mutation_p.A147V	NM_001039762.2	NP_001034851.1	Q6ZSG2	F196A_HUMAN	family with sequence similarity 196, member A	147			A -> V (in dbSNP:rs11594560).							breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CTTCTCTTTCGCATCTGTTAG	0.547													G|||	830	0.165735	0.0446	0.2133	5008	,	,		17929	0.0347		0.2793	False		,,,				2504	0.3139				p.A147V		Atlas-SNP	.											.	FAM196A	55	.	0			c.C440T						PASS	.	G	VAL/ALA,	341,4065	178.0+/-206.8	14,313,1876	90.0	85.0	87.0		440,	2.6	0.0	10	dbSNP_120	87	2355,6245	393.7+/-344.5	324,1707,2269	yes	missense,intron	DOCK1,FAM196A	NM_001039762.2,NM_001380.3	64,	338,2020,4145	AA,AG,GG		27.3837,7.7394,20.7289	benign,	147/480,	128974220	2696,10310	2203	4300	6503	SO:0001583	missense	642938	exon4			TCTTTCGCATCTG		CCDS31312.1	10q26.2	2009-09-11	2009-09-11	2009-09-11		ENSG00000188916			33859	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 141"""	C10orf141			Standard	NM_001039762		Approved	FLJ45557	uc001ljv.1	Q6ZSG2		ENST00000522781.1:c.440C>T	10.37:g.128974220G>A	ENSP00000429763:p.Ala147Val	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_001039762	B2RNT4|B7ZME7	Missense_Mutation	SNP	ENST00000522781.1	37	CCDS31312.1	346	0.15842490842490842	27	0.054878048780487805	92	0.2541436464088398	12	0.02097902097902098	215	0.2836411609498681	G	0.008	-1.931052	0.00488	0.077394	0.273837	ENSG00000188916	ENST00000522781;ENST00000424811	T;T	0.42513	0.97;0.97	4.46	2.58	0.30949	.	1.061370	0.07259	N	0.867102	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B	0.13145	0.007;0.003	B;B	0.09377	0.001;0.004	T	0.35375	-0.9791	9	0.02654	T	1	.	6.43	0.21790	0.3258:0.0:0.6742:0.0	rs11594560;rs56480626;rs60757760;rs11594560	147;147	B7ZME7;Q6ZSG2	.;F196A_HUMAN	V	147	ENSP00000429763:A147V;ENSP00000428730:A147V	ENSP00000428730:A147V	A	-	2	0	FAM196A	128864210	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	0.577000	0.23758	1.180000	0.42898	0.563000	0.77884	GCG	G|0.829;A|0.171	0.171	strong		0.547	FAM196A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050978.2	NM_001039762	
RPL7L1	285855	hgsc.bcm.edu	37	6	42852357	42852357	+	Silent	SNP	C	C	T	rs16896142	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42852357C>T	ENST00000493763.1	+	4	594	c.291C>T	c.(289-291)gaC>gaT	p.D97D	RPL7L1_ENST00000602561.1_Silent_p.D97D|RPL7L1_ENST00000304734.5_Silent_p.D97D|RPL7L1_ENST00000397415.3_3'UTR|RPL7L1_ENST00000424341.2_Silent_p.D97D	NM_198486.2	NP_940888.2	Q6DKI1	RL7L_HUMAN	ribosomal protein L7-like 1	97						ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)	6	Colorectal(47;0.196)		Colorectal(64;0.00237)|all cancers(41;0.00288)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.088)			TCAGGATTGACGGCGTGAGTT	0.448													T|||	65	0.0129792	0.0151	0.0231	5008	,	,		21528	0.001		0.0149	False		,,,				2504	0.0133				p.D97D		Atlas-SNP	.											.	RPL7L1	20	.	0			c.C291T						PASS	.	T		73,4333	819.7+/-416.4	1,71,2131	125.0	121.0	122.0		291	-9.1	0.0	6	dbSNP_123	122	256,8344	807.8+/-407.2	5,246,4049	no	coding-synonymous	RPL7L1	NM_198486.2		6,317,6180	TT,TC,CC		2.9767,1.6568,2.5296		97/247	42852357	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	285855	exon4			GATTGACGGCGTG		CCDS4873.1	6p21.1	2011-01-14			ENSG00000146223	ENSG00000146223		"""L ribosomal proteins"""	21370	protein-coding gene	gene with protein product							Standard	NM_198486		Approved	dJ475N16.4	uc003osq.1	Q6DKI1	OTTHUMG00000014710	ENST00000493763.1:c.291C>T	6.37:g.42852357C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	81	49	0.604938	NM_198486	A8K7D4|B7Z652|Q5TFZ5|Q6PEK3	Silent	SNP	ENST00000493763.1	37	CCDS4873.1																																																																																			C|0.975;T|0.025	0.025	strong		0.448	RPL7L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314417.1	XM_209769	
PLCB3	5331	hgsc.bcm.edu	37	11	64034911	64034911	+	Silent	SNP	G	G	A	rs28395877	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64034911G>A	ENST00000540288.1	+	31	3691	c.3588G>A	c.(3586-3588)ccG>ccA	p.P1196P	PLCB3_ENST00000325234.5_Silent_p.P1129P|PLCB3_ENST00000279230.6_Silent_p.P1196P	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	1196					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						GCGAGATGCCGGAGGGGCTGG	0.726													G|||	602	0.120208	0.0023	0.1182	5008	,	,		11849	0.4861		0.0219	False		,,,				2504	0.0051				p.P1196P		Atlas-SNP	.											PLCB3,colon,carcinoma,0,1	PLCB3	103	1	0			c.G3588A						PASS	.	G	,	45,4171		0,45,2063	5.0	6.0	6.0		3588,3387	-3.3	0.0	11	dbSNP_126	6	103,8121		0,103,4009	no	coding-synonymous,coding-synonymous	PLCB3	NM_000932.2,NM_001184883.1	,	0,148,6072	AA,AG,GG		1.2524,1.0674,1.1897	,	1196/1235,1129/1168	64034911	148,12292	2108	4112	6220	SO:0001819	synonymous_variant	5331	exon31			GATGCCGGAGGGG	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.3588G>A	11.37:g.64034911G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	19	14	0.736842	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																			G|0.845;A|0.155	0.155	strong		0.726	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
APOH	350	hgsc.bcm.edu	37	17	64210580	64210580	+	Missense_Mutation	SNP	A	A	C	rs1801689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:64210580A>C	ENST00000205948.6	-	7	1010	c.973T>G	c.(973-975)Tgc>Ggc	p.C325G		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	325	Sushi-like.		C -> G (loss of phosphatidylserine- binding; dbSNP:rs1801689). {ECO:0000269|PubMed:9063752}.		blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			CCCTTGAAGCATTTGGGGACT	0.403													A|||	82	0.0163738	0.0015	0.036	5008	,	,		19294	0.001		0.0408	False		,,,				2504	0.0133				p.C325G	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.T973G	GRCh37	CM970094	APOH	M	rs1801689	PASS	.	A	GLY/CYS	37,4369	40.8+/-73.8	0,37,2166	182.0	143.0	156.0		973	5.5	1.0	17	dbSNP_89	156	313,8287	112.3+/-172.5	7,299,3994	yes	missense	APOH	NM_000042.2	159	7,336,6160	CC,CA,AA		3.6395,0.8398,2.6911	probably-damaging	325/346	64210580	350,12656	2203	4300	6503	SO:0001583	missense	350	exon7			TGAAGCATTTGGG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.973T>G	17.37:g.64210580A>C	ENSP00000205948:p.Cys325Gly	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	146	79	0.541096	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	44	0.020146520146520148	0	0.0	16	0.04419889502762431	0	0.0	28	0.036939313984168866	a	18.07	3.541861	0.65198	0.008398	0.036395	ENSG00000091583	ENST00000205948	D	0.99422	-5.88	5.5	5.5	0.81552	Complement control module (2);Beta-2-glycoprotein-1 fifth domain (2);	0.000000	0.85682	D	0.000000	D	0.97766	0.9267	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88767	0.3261	10	0.87932	D	0	.	14.6578	0.68847	1.0:0.0:0.0:0.0	rs1801689;rs4791077;rs17690416;rs52792576;rs1801689	325	P02749	APOH_HUMAN	G	325	ENSP00000205948:C325G	ENSP00000205948:C325G	C	-	1	0	APOH	61641042	1.000000	0.71417	0.952000	0.39060	0.842000	0.47809	6.439000	0.73430	2.104000	0.64026	0.529000	0.55759	TGC	A|0.976;C|0.024	0.024	strong		0.403	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
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 GAIIx	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-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TT_ENST00000387460.2_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		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	19	19	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 GAIIx	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_ENST00000379711.2_Splice_Site_p.H65H|SFMBT2_ENST00000397167.1_Splice_Site_p.H65H|SFMBT2_ENST00000379713.3_Splice_Site_p.H65H|SFMBT2_ENST00000397160.3_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		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	73	32	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
SYCE1	93426	hgsc.bcm.edu	37	10	135370639	135370639	+	Missense_Mutation	SNP	C	C	A	rs8181357	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135370639C>A	ENST00000343131.5	-	7	500	c.396G>T	c.(394-396)gaG>gaT	p.E132D	SYCE1_ENST00000432597.2_Missense_Mutation_p.E96D|SYCE1_ENST00000368517.3_Missense_Mutation_p.E96D|SPRN_ENST00000541506.1_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	132			E -> D (in dbSNP:rs8181357). {ECO:0000269|PubMed:15489334}.		synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.E96D(1)|p.E132D(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TCTCCTTGCACTCCTGCAACA	0.552													C|||	775	0.154752	0.0454	0.1715	5008	,	,		21943	0.2698		0.1093	False		,,,				2504	0.2188				p.E132D		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	2	Substitution - Missense(2)	stomach(2)	c.G396T						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	274,4132	151.4+/-185.3	6,262,1935	253.0	239.0	244.0		396,396,288	0.2	0.9	10	dbSNP_117	244	822,7778	189.1+/-236.0	45,732,3523	yes	missense,missense,missense	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	45,45,45	51,994,5458	AA,AC,CC		9.5581,6.2188,8.4269	probably-damaging,probably-damaging,probably-damaging	132/319,132/352,96/283	135370639	1096,11910	2203	4300	6503	SO:0001583	missense	93426	exon7			CTTGCACTCCTGC	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.396G>T	10.37:g.135370639C>A	ENSP00000341282:p.Glu132Asp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	114	50	0.438596	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	329	0.15064102564102563	24	0.04878048780487805	62	0.1712707182320442	153	0.2674825174825175	90	0.11873350923482849	C	12.63	1.996834	0.35226	0.062188	0.095581	ENSG00000171772	ENST00000303903;ENST00000432597;ENST00000368517;ENST00000343131	T;T;T;T	0.32272	1.46;3.12;3.12;3.12	4.3	0.217	0.15264	.	0.389128	0.24176	N	0.040858	T	0.00012	0.0000	L	0.44542	1.39	0.42354	P	0.00761400000000001	B;B;B	0.15930	0.015;0.015;0.015	B;B;B	0.19946	0.016;0.027;0.016	T	0.30822	-0.9965	9	0.38643	T	0.18	-1.8451	5.4635	0.16630	0.0:0.5252:0.306:0.1688	rs8181357;rs11537981;rs17857024;rs52803233;rs8181357	4;132;96	Q8N0S2-3;Q8N0S2;Q8N0S2-2	.;SYCE1_HUMAN;.	D	132;96;96;132	ENSP00000303978:E132D;ENSP00000411779:E96D;ENSP00000357503:E96D;ENSP00000341282:E132D	ENSP00000303978:E132D	E	-	3	2	SYCE1	135220629	0.154000	0.22792	0.912000	0.35992	0.873000	0.50193	-0.666000	0.05280	0.050000	0.15949	0.655000	0.94253	GAG	C|0.892;A|0.108	0.108	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
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 GAIIx	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	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	124	61	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	
IL16	3603	hgsc.bcm.edu	37	15	81582868	81582868	+	Silent	SNP	G	G	A	rs8031107	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:81582868G>A	ENST00000302987.4	+	10	1407	c.1407G>A	c.(1405-1407)caG>caA	p.Q469Q	IL16_ENST00000394660.2_Silent_p.Q469Q			Q14005	IL16_HUMAN	interleukin 16	469					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						AGAGGCATCAGTGGAGTCTGG	0.413													G|||	2932	0.585463	0.7474	0.4222	5008	,	,		18859	0.5407		0.4801	False		,,,				2504	0.637				p.Q469Q		Atlas-SNP	.											IL16_ENST00000302987,right_upper_lobe,carcinoma,+1,2	IL16	254	2	0			c.G1407A						PASS	.	G	,	2604,1200		910,784,208	131.0	138.0	136.0		1407,1407	-0.4	1.0	15	dbSNP_116	136	3677,4575		821,2035,1270	no	coding-synonymous,coding-synonymous	IL16	NM_001172128.1,NM_172217.3	,	1731,2819,1478	AA,AG,GG		44.5589,31.5457,47.9015	,	469/1332,469/1333	81582868	6281,5775	1902	4126	6028	SO:0001819	synonymous_variant	3603	exon11			GCATCAGTGGAGT	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1407G>A	15.37:g.81582868G>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			G|0.455;A|0.545	0.545	strong		0.413	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
OBSCN	84033	hgsc.bcm.edu	37	1	228412308	228412308	+	Silent	SNP	G	G	A	rs1757152	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228412308G>A	ENST00000422127.1	+	9	2846	c.2802G>A	c.(2800-2802)tcG>tcA	p.S934S	OBSCN_ENST00000570156.2_Silent_p.S1026S|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.S934S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	934	Ig-like 9.|Poly-Ser.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTCCAGCTCGAAAGTGTGCA	0.662													G|||	2066	0.41254	0.5885	0.402	5008	,	,		19773	0.3839		0.3678	False		,,,				2504	0.2577				p.S1026S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G3078A						PASS	.	G	,	2342,1864		643,1056,404	58.0	59.0	59.0		2802,2802	-9.0	0.0	1	dbSNP_89	59	3317,5133		663,1991,1571	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1306,3047,1975	AA,AG,GG		39.2544,44.3176,44.714	,	934/7969,934/6621	228412308	5659,6997	2103	4225	6328	SO:0001819	synonymous_variant	84033	exon10			CAGCTCGAAAGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2802G>A	1.37:g.228412308G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	165	76	0.460606	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.567;A|0.433	0.433	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
BTNL8	79908	hgsc.bcm.edu	37	5	180376972	180376972	+	Missense_Mutation	SNP	C	C	G	rs142207026|rs386695831	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180376972C>G	ENST00000340184.4	+	8	1137	c.931C>G	c.(931-933)Cat>Gat	p.H311D	BTNL8_ENST00000511704.1_Missense_Mutation_p.H195D|BTNL8_ENST00000508408.1_3'UTR|BTNL8_ENST00000231229.4_3'UTR|BTNL8_ENST00000505126.1_Missense_Mutation_p.H104D|BTNL8_ENST00000400707.3_Missense_Mutation_p.H186D|BTNL8_ENST00000533815.2_Missense_Mutation_p.H127D	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	311	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		H -> Q (in dbSNP:rs146303629). {ECO:0000269|PubMed:15489334}.	H -> E (in Ref. 2; BAH12847). {ECO:0000305}.	immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AACTGTAACCCATAGAAAAGC	0.527													c|||	1447	0.288938	0.4796	0.1527	5008	,	,		14296	0.1825		0.2266	False		,,,				2504	0.3016				p.H311D		Atlas-SNP	.											.	BTNL8	114	.	0			c.C931G						PASS	.						36.0	36.0	36.0					5																	180376972		2111	3895	6006	SO:0001583	missense	79908	exon8			GTAACCCATAGAA	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.931C>G	5.37:g.180376972C>G	ENSP00000342197:p.His311Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	48	38	0.791667	NM_001040462	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	621	0.28434065934065933	259	0.5264227642276422	67	0.1850828729281768	108	0.1888111888111888	187	0.24670184696569922	c	9.646	1.140294	0.21205	.	.	ENSG00000113303	ENST00000340184;ENST00000400707;ENST00000511704;ENST00000505126;ENST00000533815	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	1.89	-3.78	0.04333	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.39514	1.22	0.80722	P	0.0	D;P;D	0.58268	0.961;0.666;0.982	P;B;P	0.57204	0.462;0.184;0.815	T	0.38156	-0.9674	8	0.36615	T	0.2	.	3.5092	0.07701	0.0:0.2805:0.1999:0.5196	.	186;195;311	E9PG07;E9PEF6;Q6UX41	.;.;BTNL8_HUMAN	D	311;186;195;104;127	ENSP00000342197:H311D;ENSP00000383543:H186D;ENSP00000425207:H195D;ENSP00000427441:H104D;ENSP00000435098:H127D	ENSP00000342197:H311D	H	+	1	0	BTNL8	180309578	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.624000	0.05540	-1.168000	0.02776	-1.417000	0.01113	CAT	C|1.000;|0.000	.	weak		0.527	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
TLR10	81793	hgsc.bcm.edu	37	4	38775040	38775040	+	Silent	SNP	A	A	G	rs10776483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38775040A>G	ENST00000308973.4	-	4	2777	c.2172T>C	c.(2170-2172)caT>caC	p.H724H	TLR10_ENST00000508334.1_Silent_p.H724H|TLR10_ENST00000506111.1_Silent_p.H724H|TLR10_ENST00000361424.2_Silent_p.H724H|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	724	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						TAAGAATTATATGATCAGAAT	0.388													A|||	1496	0.298722	0.2126	0.3184	5008	,	,		19051	0.4325		0.2495	False		,,,				2504	0.3139				p.H724H		Atlas-SNP	.											.	TLR10	87	.	0			c.T2172C						PASS	.	A	,,,,	981,3425	352.6+/-311.8	101,779,1323	91.0	96.0	94.0		2172,2172,2172,2130,2172	-2.2	0.0	4	dbSNP_120	94	1746,6854	315.3+/-312.2	187,1372,2741	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	,,,,	288,2151,4064	GG,GA,AA		20.3023,22.2651,20.9672	,,,,	724/812,724/812,724/812,710/798,724/812	38775040	2727,10279	2203	4300	6503	SO:0001819	synonymous_variant	81793	exon2			AATTATATGATCA	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.2172T>C	4.37:g.38775040A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			A|0.738;G|0.262	0.262	strong		0.388	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
MAPK6	5597	hgsc.bcm.edu	37	15	52353498	52353498	+	Missense_Mutation	SNP	C	C	G	rs17853426|rs35697691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:52353498C>G	ENST00000261845.5	+	5	1675	c.868C>G	c.(868-870)Ctg>Gtg	p.L290V	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> V (in dbSNP:rs35697691). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)	p.L290V(2)		breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CTCTGCAGCACTGGATTTCCT	0.358													C|||	164	0.0327476	0.0061	0.0735	5008	,	,		18672	0.0		0.0875	False		,,,				2504	0.0174				p.L290V		Atlas-SNP	.											MAPK6,face,carcinoma,0,5	MAPK6	70	5	2	Substitution - Missense(2)	lung(1)|skin(1)	c.C868G						PASS	.	C	VAL/LEU	100,4290	77.8+/-116.1	4,92,2099	93.0	89.0	91.0		868	5.1	1.0	15	dbSNP_126	91	794,7792	182.5+/-230.9	35,724,3534	yes	missense	MAPK6	NM_002748.3	32	39,816,5633	GG,GC,CC		9.2476,2.2779,6.8896	probably-damaging	290/722	52353498	894,12082	2195	4293	6488	SO:0001583	missense	5597	exon5			GCAGCACTGGATT	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"""Mitogen-activated protein kinase cascade / Kinases"""	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.868C>G	15.37:g.52353498C>G	ENSP00000261845:p.Leu290Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	196	103	0.52551	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	37	CCDS10147.1	93	0.042582417582417584	4	0.008130081300813009	25	0.06906077348066299	0	0.0	64	0.08443271767810026	C	16.84	3.233417	0.58886	0.022779	0.092476	ENSG00000069956	ENST00000261845	T	0.66099	-0.19	5.13	5.13	0.70059	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	0.07007	0.0178	N	0.17379	0.485	0.09310	P	0.999999574787	D	0.69078	0.997	D	0.79108	0.992	T	0.47341	-0.9125	9	0.37606	T	0.19	-0.3463	18.5662	0.91118	0.0:1.0:0.0:0.0	rs35697691	290	Q16659	MK06_HUMAN	V	290	ENSP00000261845:L290V	ENSP00000261845:L290V	L	+	1	2	MAPK6	50140790	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.015000	0.40961	2.399000	0.81585	0.585000	0.79938	CTG	C|0.939;G|0.061	0.061	strong		0.358	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748	
B3GALTL	145173	hgsc.bcm.edu	37	13	31848657	31848657	+	Silent	SNP	C	C	T	rs35019745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:31848657C>T	ENST00000343307.4	+	9	821	c.672C>T	c.(670-672)taC>taT	p.Y224Y	B3GALTL_ENST00000461652.2_3'UTR	NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	224					fucose metabolic process (GO:0006004)|protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Lung SC(185;0.0257)		all cancers(112;0.00436)|Epithelial(112;0.0285)|OV - Ovarian serous cystadenocarcinoma(117;0.0512)|GBM - Glioblastoma multiforme(144;0.184)		TTGCCCTCTACATCTGGGACA	0.483													C|||	28	0.00559105	0.0	0.0043	5008	,	,		19440	0.0		0.0219	False		,,,				2504	0.0031				p.Y224Y		Atlas-SNP	.											.	B3GALTL	48	.	0			c.C672T						PASS	.	C		21,4385	29.0+/-57.7	1,19,2183	136.0	114.0	122.0		672	3.9	1.0	13	dbSNP_126	122	196,8404	85.6+/-148.0	0,196,4104	no	coding-synonymous	B3GALTL	NM_194318.3		1,215,6287	TT,TC,CC		2.2791,0.4766,1.6685		224/499	31848657	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	145173	exon9			CCTCTACATCTGG	AB101481	CCDS9341.1	13q12.3	2014-03-24			ENSG00000187676	ENSG00000187676		"""Beta 3-glycosyltransferases"""	20207	protein-coding gene	gene with protein product		610308				12943678, 16899492, 17032646	Standard	NM_194318		Approved	B3GTL, B3Glc-T	uc010aaz.3	Q6Y288	OTTHUMG00000016688	ENST00000343307.4:c.672C>T	13.37:g.31848657C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_194318	A8K5F8|Q5W0H2|Q6NUI3	Silent	SNP	ENST00000343307.4	37	CCDS9341.1																																																																																			C|0.985;T|0.015	0.015	strong		0.483	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318	
CEACAM5	1048	hgsc.bcm.edu	37	19	42213782	42213782	+	Missense_Mutation	SNP	T	T	C	rs28683503	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:42213782T>C	ENST00000221992.6	+	2	362	c.248T>C	c.(247-249)gTa>gCa	p.V83A	CEA_ENST00000598976.1_Missense_Mutation_p.V83A|CEACAM5_ENST00000405816.1_Missense_Mutation_p.V83A|CEACAM7_ENST00000599715.1_5'Flank|CEACAM5_ENST00000398599.4_Missense_Mutation_p.V83A	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	83	Ig-like 1.		V -> A (in dbSNP:rs28683503).		homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		ATAGGATATGTAATAGGAACT	0.473													t|||	813	0.16234	0.3949	0.1037	5008	,	,		18311	0.0		0.1958	False		,,,				2504	0.0225				p.V83A		Atlas-SNP	.											.	CEACAM5	84	.	0			c.T248C						PASS	.	T	ALA/VAL	1345,3061		301,743,1159	164.0	173.0	170.0		248	-4.7	0.0	19	dbSNP_125	170	1139,7461		117,905,3278	no	missense	CEACAM5	NM_004363.2	64	418,1648,4437	CC,CT,TT		13.2442,30.5266,19.0989	benign	83/703	42213782	2484,10522	2203	4300	6503	SO:0001583	missense	1048	exon2			GATATGTAATAGG	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.248T>C	19.37:g.42213782T>C	ENSP00000221992:p.Val83Ala	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	162	100	0.617284	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	304	0.1391941391941392	132	0.2682926829268293	40	0.11049723756906077	0	0.0	132	0.1741424802110818	-	3.830	-0.035887	0.07497	0.305266	0.132442	ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181	T;T	0.67523	-0.27;-0.27	2.56	-4.68	0.03309	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.66506	2.035	0.80722	P	0.0	B;B;B	0.16166	0.016;0.0;0.0	B;B;B	0.27887	0.084;0.016;0.011	T	0.35301	-0.9794	8	0.46703	T	0.11	.	1.288	0.02055	0.177:0.3815:0.1797:0.2618	rs28683503	83;83;83	Q8N4D0;P06731;Q53G30	.;CEAM5_HUMAN;.	A	83	ENSP00000221992:V83A;ENSP00000385072:V83A	ENSP00000221992:V83A	V	+	2	0	CEACAM5	46905622	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.465000	0.00995	-1.374000	0.02131	0.254000	0.18369	GTA	T|0.810;C|0.190	0.190	strong		0.473	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
SPAG17	200162	hgsc.bcm.edu	37	1	118565953	118565953	+	Missense_Mutation	SNP	G	G	A	rs10923472	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:118565953G>A	ENST00000336338.5	-	28	4108	c.4043C>T	c.(4042-4044)cCa>cTa	p.P1348L		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1348			P -> L (in dbSNP:rs10923472).			cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		AATCTCAGATGGTATCGTTTC	0.383													G|||	1439	0.28734	0.1551	0.4107	5008	,	,		15600	0.1567		0.4314	False		,,,				2504	0.365				p.P1348L		Atlas-SNP	.											.	SPAG17	263	.	0			c.C4043T						PASS	.	G	LEU/PRO	897,3509	347.5+/-309.5	89,719,1395	118.0	109.0	112.0		4043	5.6	0.1	1	dbSNP_120	112	3857,4743	540.4+/-383.8	875,2107,1318	yes	missense	SPAG17	NM_206996.2	98	964,2826,2713	AA,AG,GG		44.8488,20.3586,36.5524	probably-damaging	1348/2224	118565953	4754,8252	2203	4300	6503	SO:0001583	missense	200162	exon28			TCAGATGGTATCG		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.4043C>T	1.37:g.118565953G>A	ENSP00000337804:p.Pro1348Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	71	26	0.366197	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	634	0.2902930402930403	73	0.1483739837398374	156	0.430939226519337	71	0.12412587412587413	334	0.44063324538258575	G	18.18	3.566922	0.65651	0.203586	0.448488	ENSG00000155761	ENST00000336338	T	0.20463	2.07	5.63	5.63	0.86233	.	0.431247	0.25529	N	0.030042	T	0.37100	0.0991	M	0.66939	2.045	0.30462	P	0.774151	D	0.89917	1.0	D	0.87578	0.998	T	0.16541	-1.0399	9	0.72032	D	0.01	.	15.1893	0.73032	0.0:0.0:1.0:0.0	rs10923472;rs17257687;rs52828260;rs57051065;rs10923472	1348	Q6Q759	SPG17_HUMAN	L	1348	ENSP00000337804:P1348L	ENSP00000337804:P1348L	P	-	2	0	SPAG17	118367476	0.936000	0.31750	0.132000	0.22025	0.085000	0.17905	2.084000	0.41625	2.669000	0.90835	0.591000	0.81541	CCA	G|0.682;A|0.318	0.318	strong		0.383	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
LRRK2	120892	hgsc.bcm.edu	37	12	40716260	40716260	+	Silent	SNP	T	T	C	rs10878371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:40716260T>C	ENST00000298910.7	+	37	5515	c.5457T>C	c.(5455-5457)ggT>ggC	p.G1819G		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1819					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TTAATGATGGTGAAGAACATC	0.353													C|||	2931	0.585264	0.5862	0.6037	5008	,	,		16965	0.501		0.5427	False		,,,				2504	0.7014				p.G1819G		Atlas-SNP	.											.	LRRK2	763	.	0			c.T5457C						PASS	.	C		2541,1865	538.1+/-374.9	739,1063,401	130.0	130.0	130.0		5457	-1.3	1.0	12	dbSNP_120	130	4657,3943	547.8+/-385.2	1244,2169,887	no	coding-synonymous	LRRK2	NM_198578.3		1983,3232,1288	CC,CT,TT		45.8488,42.3286,44.6563		1819/2528	40716260	7198,5808	2203	4300	6503	SO:0001819	synonymous_variant	120892	exon37			TGATGGTGAAGAA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.5457T>C	12.37:g.40716260T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																			T|0.448;C|0.552	0.552	strong		0.353	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577602	90577602	+	RNA	SNP	C	C	T	rs60966143	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90577602C>T	ENST00000551025.1	+	0	6030									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		CTATGCATGCCGTCATAATGG	0.418													C|||	602	0.120208	0.0923	0.0764	5008	,	,		22458	0.0069		0.1948	False		,,,				2504	0.229				p.A1531A	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.C4593T						PASS	.	C	,,	326,3508		12,302,1603	110.0	98.0	102.0		4593,4593,4593	0.0	1.0	6	dbSNP_129	102	1510,6756		133,1244,2756	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP8AP2	NM_001137667.1,NM_001137668.1,NM_012115.3	,,	145,1546,4359	TT,TC,CC		18.2676,8.5029,15.1736	,,	1531/1967,1531/1967,1531/1967	90577602	1836,10264	1917	4133	6050			9994	exon8			GCATGCCGTCATA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90577602C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_001137667		Silent	SNP	ENST00000551025.1	37																																																																																				C|0.879;T|0.121	0.121	strong		0.418	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
ATP13A4	84239	hgsc.bcm.edu	37	3	193209178	193209178	+	Missense_Mutation	SNP	T	T	C	rs6788448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193209178T>C	ENST00000342695.4	-	6	865	c.543A>G	c.(541-543)atA>atG	p.I181M	ATP13A4_ENST00000392443.3_Missense_Mutation_p.I181M|ATP13A4_ENST00000295548.3_Missense_Mutation_p.I181M	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	181			I -> M (in dbSNP:rs6788448). {ECO:0000269|PubMed:15925480}.			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)		TAGGCCCACATATTAACCTCC	0.358													T|||	2361	0.471446	0.5318	0.4928	5008	,	,		18519	0.4673		0.3946	False		,,,				2504	0.4581				p.I181M		Atlas-SNP	.											.	ATP13A4	154	.	0			c.A543G						PASS	.	T	MET/ILE	2270,2136	597.1+/-388.8	571,1128,504	101.0	100.0	101.0		543	4.6	1.0	3	dbSNP_116	101	3476,5124	508.3+/-377.0	727,2022,1551	yes	missense	ATP13A4	NM_032279.2	10	1298,3150,2055	CC,CT,TT		40.4186,48.4793,44.1796	probably-damaging	181/1197	193209178	5746,7260	2203	4300	6503	SO:0001583	missense	84239	exon6			CCCACATATTAAC	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.543A>G	3.37:g.193209178T>C	ENSP00000339182:p.Ile181Met	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	37	CCDS3304.2	989	0.45283882783882784	260	0.5284552845528455	179	0.494475138121547	257	0.4493006993006993	293	0.3865435356200528	T	17.12	3.308038	0.60305	0.515207	0.404186	ENSG00000127249	ENST00000392443;ENST00000342695;ENST00000295548	T;T;T	0.78707	-1.2;-1.2;-1.2	5.81	4.63	0.57726	ATPase, P-type cation-transporter, N-terminal (2);	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	M	0.79123	2.44	0.28947	P	0.890639	D;D	0.76494	0.998;0.999	D;D	0.77004	0.981;0.989	T	0.44065	-0.9352	9	0.48119	T	0.1	-19.2398	9.3177	0.37943	0.287:0.0:0.0:0.713	rs6788448;rs56481856;rs60242198;rs6788448	181;181	Q4VNC1-2;Q4VNC1	.;AT134_HUMAN	M	181	ENSP00000376238:I181M;ENSP00000339182:I181M;ENSP00000295548:I181M	ENSP00000295548:I181M	I	-	3	3	ATP13A4	194691872	0.701000	0.27806	1.000000	0.80357	0.947000	0.59692	-0.447000	0.06828	0.992000	0.38840	0.482000	0.46254	ATA	T|0.559;C|0.441	0.441	strong		0.358	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
ELMOD3	84173	hgsc.bcm.edu	37	2	85617327	85617327	+	Silent	SNP	C	C	T	rs17850708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85617327C>T	ENST00000409890.2	+	13	1549	c.882C>T	c.(880-882)caC>caT	p.H294H	ELMOD3_ENST00000315658.7_Silent_p.H294H|ELMOD3_ENST00000409344.3_Silent_p.H294H|ELMOD3_ENST00000409013.3_Silent_p.H294H|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000393852.4_Silent_p.H294H			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	294	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						CATTCCTCCACCTCGCACATG	0.562													C|||	214	0.0427316	0.0439	0.0432	5008	,	,		19935	0.006		0.0656	False		,,,				2504	0.0552				p.H294H		Atlas-SNP	.											.	ELMOD3	53	.	0			c.C882T						PASS	.	C	,,,	206,4200	127.8+/-164.7	5,196,2002	118.0	90.0	100.0		882,882,882,882	1.9	0.9	2	dbSNP_123	100	583,8017	156.3+/-210.2	17,549,3734	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ELMOD3	NM_001135021.1,NM_001135022.1,NM_001135023.1,NM_032213.4	,,,	22,745,5736	TT,TC,CC		6.7791,4.6754,6.0664	,,,	294/382,294/382,294/382,294/392	85617327	789,12217	2203	4300	6503	SO:0001819	synonymous_variant	84173	exon13			CCTCCACCTCGCA	AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"""RNA binding motif (RRM) containing"""	26158	protein-coding gene	gene with protein product		615427	"""RNA binding motif protein 29"", ""RNA binding motif and ELMO/CED-12 domain 1"", ""deafness, autosomal recessive 88"""	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.882C>T	2.37:g.85617327C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	116	87	0.75	NM_001135022	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Silent	SNP	ENST00000409890.2	37	CCDS46352.1																																																																																			C|0.951;T|0.049	0.049	strong		0.562	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213	
PDK2	5164	hgsc.bcm.edu	37	17	48174908	48174908	+	Silent	SNP	C	C	T	rs9839	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48174908C>T	ENST00000503176.1	+	2	401	c.240C>T	c.(238-240)tcC>tcT	p.S80S	PDK2_ENST00000007708.3_Silent_p.S16S	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	80				S -> T (in Ref. 1; AAC42010). {ECO:0000305}.	cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						GCACACCCTCCGTGCAGCTGG	0.607									Autosomal Dominant Polycystic Kidney Disease				T|||	2179	0.435104	0.4932	0.4395	5008	,	,		22189	0.38		0.2783	False		,,,				2504	0.5716				p.S80S		Atlas-SNP	.											PDK2,NS,carcinoma,0,1	PDK2	41	1	0			c.C240T						PASS	.	T	,,,	2092,2314	605.2+/-390.5	499,1094,610	78.0	65.0	69.0		48,48,240,240	-7.4	0.8	17	dbSNP_105	69	2532,6068	692.8+/-404.6	370,1792,2138	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDK2	NM_001199898.1,NM_001199899.1,NM_001199900.1,NM_002611.4	,,,	869,2886,2748	TT,TC,CC		29.4419,47.4807,35.5528	,,,	16/344,16/344,80/200,80/408	48174908	4624,8382	2203	4300	6503	SO:0001819	synonymous_variant	5164	exon2	Familial Cancer Database	ADPKD	ACCCTCCGTGCAG	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"""pyruvate dehydrogenase kinase, isoenzyme 2"""			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.240C>T	17.37:g.48174908C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	26	16	0.615385	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Silent	SNP	ENST00000503176.1	37	CCDS11559.1																																																																																			C|0.639;T|0.361	0.361	strong		0.607	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611	
DUSP13	51207	hgsc.bcm.edu	37	10	76867899	76867899	+	Missense_Mutation	SNP	T	T	C	rs7912300	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:76867899T>C	ENST00000372702.3	-	2	281	c.218A>G	c.(217-219)aAg>aGg	p.K73R	DUSP13_ENST00000607009.1_5'UTR|DUSP13_ENST00000491677.2_5'UTR|DUSP13_ENST00000372700.3_Intron|DUSP13_ENST00000607131.1_Intron			Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	81					meiotic nuclear division (GO:0007126)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	8	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GTAGAGGCCCTTGTGGGCGGC	0.632													C|||	2271	0.453474	0.5348	0.4452	5008	,	,		18611	0.6438		0.2823	False		,,,				2504	0.3292				p.K73R	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.A218G						PASS	.	C	ARG/LYS,,	1971,2081		500,971,555	48.0	56.0	53.0		218,,	4.9	1.0	10	dbSNP_116	53	2211,6115		294,1623,2246	yes	missense,intron,intron	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1	26,,	794,2594,2801	CC,CT,TT		26.5554,48.6426,33.7857	,,	73/189,,	76867899	4182,8196	2026	4163	6189	SO:0001583	missense	51207	exon2			AGGCCCTTGTGGG	AB027004	CCDS7346.1, CCDS31224.1, CCDS53542.1	10q23.1	2013-10-25			ENSG00000079393	ENSG00000079393		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	19681	protein-coding gene	gene with protein product		613191				10585869	Standard	XM_005269883		Approved	BEDP, TMDP, FLJ32450, DUSP13A, DUSP13B	uc001jwu.3	Q6B8I1	OTTHUMG00000018516	ENST00000372702.3:c.218A>G	10.37:g.76867899T>C	ENSP00000361787:p.Lys73Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_001007271	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Missense_Mutation	SNP	ENST00000372702.3	37	CCDS53542.1	980	0.44871794871794873	257	0.5223577235772358	134	0.3701657458563536	362	0.6328671328671329	227	0.2994722955145119	C	24.0	4.482367	0.84747	0.486426	0.265554	ENSG00000079393	ENST00000372702	D	0.85629	-2.01	4.93	4.93	0.64822	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	.	.	.	.	T	0.00012	0.0000	N	0.05306	-0.075	0.09310	P	1.0	B	0.10296	0.003	B	0.10450	0.005	T	0.47355	-0.9124	8	0.42905	T	0.14	.	12.5486	0.56214	0.0:0.9181:0.0:0.0819	rs7912300;rs57157460;rs7912300	73	Q6B8I1	MDSP_HUMAN	R	73	ENSP00000361787:K73R	ENSP00000361787:K73R	K	-	2	0	DUSP13	76537905	0.996000	0.38824	0.994000	0.49952	0.992000	0.81027	5.371000	0.66150	1.312000	0.45043	-0.119000	0.15052	AAG	T|0.574;C|0.426	0.426	strong		0.632	DUSP13-012	KNOWN	NMD_exception|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401503.3		
DNAH5	1767	hgsc.bcm.edu	37	5	13865980	13865980	+	Silent	SNP	T	T	C	rs7703349	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:13865980T>C	ENST00000265104.4	-	27	4256	c.4152A>G	c.(4150-4152)acA>acG	p.T1384T	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1384	Stem. {ECO:0000250}.				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)	p.T1384T(1)		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)					CTCCAGTATATGTGATGTATT	0.318									Kartagener syndrome				C|||	2347	0.46865	0.5968	0.3401	5008	,	,		18627	0.3323		0.4652	False		,,,				2504	0.5307				p.T1384T		Atlas-SNP	.											DNAH5,NS,carcinoma,0,1	DNAH5	868	1	1	Substitution - coding silent(1)	stomach(1)	c.A4152G						PASS	.	C		2506,1892		718,1070,411	49.0	55.0	53.0		4152	1.8	1.0	5	dbSNP_116	53	4011,4581		985,2041,1270	no	coding-synonymous	DNAH5	NM_001369.2		1703,3111,1681	CC,CT,TT		46.683,43.0196,49.8306		1384/4625	13865980	6517,6473	2199	4296	6495	SO:0001819	synonymous_variant	1767	exon27	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTATATGTGATG	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.4152A>G	5.37:g.13865980T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.533;C|0.467	0.467	strong		0.318	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
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 GAIIx	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	LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000358394.3_Missense_Mutation_p.T100I|CEACAM1_ENST00000403444.3_Missense_Mutation_p.T100I|CEACAM1_ENST00000599389.1_Missense_Mutation_p.T100I|CEACAM1_ENST00000403461.1_Missense_Mutation_p.T100I|CEACAM1_ENST00000351134.3_Missense_Mutation_p.T100I|CEACAM1_ENST00000352591.5_Missense_Mutation_p.T100I|LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000308072.4_Missense_Mutation_p.T60I	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	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	313	13	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	
PCSK5	5125	hgsc.bcm.edu	37	9	78925765	78925765	+	Silent	SNP	G	G	A	rs61744750	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:78925765G>A	ENST00000545128.1	+	29	4339	c.3801G>A	c.(3799-3801)ccG>ccA	p.P1267P		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1267	CRM (Cys-rich motif).				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						CCAAGTGCCCGGAGTAAGTTT	0.473													G|||	195	0.0389377	0.0318	0.0403	5008	,	,		17508	0.003		0.0457	False		,,,				2504	0.0777				p.P1267P		Atlas-SNP	.											.	PCSK5	329	.	0			c.G3801A						PASS	.	G		59,1693		2,55,819	16.0	15.0	15.0		3801	-9.2	0.3	9	dbSNP_129	15	263,3719		13,237,1741	no	coding-synonymous	PCSK5	NM_001190482.1		15,292,2560	AA,AG,GG		6.6047,3.3676,5.6156		1267/1861	78925765	322,5412	876	1991	2867	SO:0001819	synonymous_variant	5125	exon29			GTGCCCGGAGTAA		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.3801G>A	9.37:g.78925765G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	38	0.655172	NM_001190482	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			G|0.966;A|0.034	0.034	strong		0.473	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FOLR4	390243	hgsc.bcm.edu	37	11	94040783	94040783	+	Silent	SNP	C	C	T	rs367878279		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:94040783C>T	ENST00000440961.2	+	4	701	c.657C>T	c.(655-657)ttC>ttT	p.F219F		NM_001199206.1	NP_001186135.1	A6ND01	JUNO_HUMAN	folate receptor 4, delta (putative)	226					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)	p.F220fs*>22(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14						CCCGCCTCTTCGCCAGCTCTG	0.602																																					p.F226F		Atlas-SNP	.											FOLR4,NS,carcinoma,0,2	FOLR4	31	2	1	Deletion - Frameshift(1)	breast(1)	c.C678T						scavenged	.	C		0,4160		0,0,2080	176.0	186.0	183.0		678	-8.5	0.0	11		183	1,8409		0,1,4204	no	coding-synonymous	FOLR4	NM_001199206.1		0,1,6284	TT,TC,CC		0.0119,0.0,0.0080		226/251	94040783	1,12569	2080	4205	6285	SO:0001819	synonymous_variant	390243	exon4			CCTCTTCGCCAGC			11q14	2014-07-23	2012-12-07		ENSG00000183560	ENSG00000183560			32565	protein-coding gene	gene with protein product		615737	"""folate receptor 4 (delta) homolog (mouse)"""			11111049, 24739963	Standard	NM_001199206		Approved	Folbp3, JUNO	uc021qou.1	A6ND01		ENST00000440961.2:c.657C>T	11.37:g.94040783C>T		Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	125	28	0.224	NM_001199206		Silent	SNP	ENST00000440961.2	37																																																																																				.	.	weak		0.602	FOLR4-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000396420.1	NM_001080486	
TSC22D2	9819	hgsc.bcm.edu	37	3	150128484	150128484	+	Silent	SNP	C	C	A	rs3749400	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:150128484C>A	ENST00000361875.3	+	1	2363	c.1347C>A	c.(1345-1347)gtC>gtA	p.V449V	TSC22D2_ENST00000361136.2_Silent_p.V449V	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	449					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GCGGGCAGGTCGCGCCTTGTC	0.731													C|||	635	0.126797	0.1921	0.1052	5008	,	,		13898	0.0317		0.173	False		,,,				2504	0.1043				p.V449V		Atlas-SNP	.											.	TSC22D2	42	.	0			c.C1347A						PASS	.	C		826,3416		95,636,1390	5.0	7.0	6.0		1347	-5.9	0.1	3	dbSNP_107	6	1577,6731		174,1229,2751	no	coding-synonymous	TSC22D2	NM_014779.2		269,1865,4141	AA,AC,CC		18.9817,19.4719,19.1474		449/781	150128484	2403,10147	2121	4154	6275	SO:0001819	synonymous_variant	9819	exon1			GCAGGTCGCGCCT	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1347C>A	3.37:g.150128484C>A		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	22	16	0.727273	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	37	CCDS3149.1																																																																																			C|0.879;A|0.121	0.121	strong		0.731	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
SCYL2	55681	hgsc.bcm.edu	37	12	100732327	100732327	+	Silent	SNP	C	C	T	rs10860580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:100732327C>T	ENST00000360820.2	+	18	2604	c.2167C>T	c.(2167-2169)Ctg>Ttg	p.L723L		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	723	Necessary for interaction with AP2 complex and clathrin, interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes.				endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						GACAGACACACTGATGGATAA	0.328													T|||	1184	0.236422	0.3933	0.1945	5008	,	,		16782	0.0585		0.2674	False		,,,				2504	0.2055				p.L723L		Atlas-SNP	.											.	SCYL2	99	.	0			c.C2167T						PASS	.	T		1560,2846	668.4+/-402.0	274,1012,917	116.0	109.0	111.0		2167	-0.6	0.2	12	dbSNP_120	111	2222,6378	708.6+/-405.7	287,1648,2365	no	coding-synonymous	SCYL2	NM_017988.4		561,2660,3282	TT,TC,CC		25.8372,35.4063,29.0789		723/930	100732327	3782,9224	2203	4300	6503	SO:0001819	synonymous_variant	55681	exon18			GACACACTGATGG	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.2167C>T	12.37:g.100732327C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	24	0.380952	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Silent	SNP	ENST00000360820.2	37	CCDS9076.1																																																																																			C|0.721;T|0.279	0.279	strong		0.328	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988	
SYNJ1	8867	hgsc.bcm.edu	37	21	34059352	34059352	+	Missense_Mutation	SNP	T	T	C	rs2254562	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:34059352T>C	ENST00000322229.7	-	7	883	c.884A>G	c.(883-885)aAa>aGa	p.K295R	SYNJ1_ENST00000357345.3_Missense_Mutation_p.K295R|SYNJ1_ENST00000382499.2_Missense_Mutation_p.K334R|SYNJ1_ENST00000433931.2_Missense_Mutation_p.K334R|SYNJ1_ENST00000382491.3_Missense_Mutation_p.K295R			O43426	SYNJ1_HUMAN	synaptojanin 1	295	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.		K -> R (in dbSNP:rs2254562). {ECO:0000269|PubMed:9428629}.		cell death (GO:0008219)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of synaptic vesicle uncoating (GO:1903390)|regulation of synaptic vesicle membrane organization (GO:1901632)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)	cytosol (GO:0005829)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|lung(11)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	57						TATTATTTGTTTACCATATAA	0.289													T|||	1523	0.304113	0.2988	0.2882	5008	,	,		16567	0.3284		0.2873	False		,,,				2504	0.3149				p.K334R		Atlas-SNP	.											.	SYNJ1	253	.	0			c.A1001G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	1307,3093	435.9+/-344.5	198,911,1091	100.0	96.0	98.0		1001,1001,884,884	5.8	1.0	21	dbSNP_100	98	2559,6031	414.9+/-351.6	365,1829,2101	yes	missense,missense,missense,missense	SYNJ1	NM_203446.2,NM_003895.3,NM_001160306.1,NM_001160302.1	26,26,26,26	563,2740,3192	CC,CT,TT		29.7905,29.7045,29.7614	benign,benign,benign,benign	334/1351,334/1613,295/1527,295/1296	34059352	3866,9124	2200	4295	6495	SO:0001583	missense	8867	exon8			ATTTGTTTACCAT	AF009040	CCDS33539.1, CCDS33540.1, CCDS33539.2, CCDS33540.2, CCDS54483.1	21q22.2	2008-06-23			ENSG00000159082	ENSG00000159082			11503	protein-coding gene	gene with protein product		604297				9428629, 10773674	Standard	NM_203446		Approved	INPP5G	uc002yqh.2	O43426	OTTHUMG00000064926	ENST00000322229.7:c.884A>G	21.37:g.34059352T>C	ENSP00000322234:p.Lys295Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_203446	O43425|O94984|Q4KMR1	Missense_Mutation	SNP	ENST00000322229.7	37	CCDS54484.1	639	0.2925824175824176	123	0.25	100	0.27624309392265195	193	0.3374125874125874	223	0.2941952506596306	T	32	5.106299	0.94292	0.297045	0.297905	ENSG00000159082	ENST00000382491;ENST00000357345;ENST00000382499;ENST00000433931;ENST00000322229;ENST00000429236	T;T;T;T;T;T	0.59083	0.29;0.29;0.29;0.29;0.29;0.29	5.85	5.85	0.93711	Synaptojanin, N-terminal (2);	0.143592	0.64402	D	0.000005	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	0.9999999116388	B;P;B;D	0.63046	0.425;0.835;0.261;0.992	B;P;B;P	0.58660	0.221;0.471;0.324;0.843	T	0.04203	-1.0969	9	0.62326	D	0.03	.	16.2392	0.82399	0.0:0.0:0.0:1.0	rs2254562;rs52814583;rs61140656;rs2254562	334;295;295;295	C9JFZ1;O43426-2;O43426;O43426-4	.;.;SYNJ1_HUMAN;.	R	295;295;334;334;295;295	ENSP00000371931:K295R;ENSP00000349903:K295R;ENSP00000371939:K334R;ENSP00000409667:K334R;ENSP00000322234:K295R;ENSP00000413649:K295R	ENSP00000322234:K295R	K	-	2	0	SYNJ1	32981223	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.888000	0.87302	2.239000	0.73571	0.383000	0.25322	AAA	T|0.699;C|0.301	0.301	strong		0.289	SYNJ1-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
OR2F1	26211	hgsc.bcm.edu	37	7	143657427	143657427	+	Missense_Mutation	SNP	C	C	T	rs2072164	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143657427C>T	ENST00000392899.1	+	1	401	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	122			R -> C (in dbSNP:rs2072164).		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(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					GGCCTATGACCGCTATGTGGC	0.547													C|||	573	0.114417	0.0908	0.1744	5008	,	,		20383	0.1617		0.0706	False		,,,				2504	0.1002				p.R122C		Atlas-SNP	.											.	OR2F1	71	.	0			c.C364T						PASS	.	C	CYS/ARG	371,4035	189.9+/-215.9	16,339,1848	197.0	165.0	176.0		364	4.5	1.0	7	dbSNP_96	176	540,8060	149.7+/-204.7	15,510,3775	yes	missense	OR2F1	NM_012369.2	180	31,849,5623	TT,TC,CC		6.2791,8.4203,7.0045	possibly-damaging	122/318	143657427	911,12095	2203	4300	6503	SO:0001583	missense	26211	exon1			TATGACCGCTATG	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"""GPCR / Class A : Olfactory receptors"""	8246	protein-coding gene	gene with protein product		608497	"""olfactory receptor, family 2, subfamily F, member 1"""	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.364C>T	7.37:g.143657427C>T	ENSP00000376633:p.Arg122Cys	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	37	CCDS5887.1	263	0.12042124542124542	44	0.08943089430894309	58	0.16022099447513813	102	0.17832167832167833	59	0.07783641160949868	C	14.46	2.542464	0.45280	0.084203	0.062791	ENSG00000213215	ENST00000392899	T	0.77358	-1.09	5.41	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000045	T	0.00552	0.0018	M	0.89163	3.01	0.20307	P	0.9999113421	B	0.15719	0.014	B	0.14023	0.01	T	0.51787	-0.8661	9	0.87932	D	0	-13.4453	12.1368	0.53977	0.0:0.9174:0.0:0.0826	rs2072164;rs52837212;rs61344302;rs2072164	122	Q13607	OR2F1_HUMAN	C	122	ENSP00000376633:R122C	ENSP00000376633:R122C	R	+	1	0	OR2F1	143288360	0.996000	0.38824	1.000000	0.80357	0.990000	0.78478	2.186000	0.42593	1.513000	0.48852	0.655000	0.94253	CGC	C|0.910;T|0.090	0.090	strong		0.547	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1		
ZNF717	100131827	hgsc.bcm.edu	37	3	75786685	75786685	+	Missense_Mutation	SNP	T	T	A	rs201963249	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:75786685T>A	ENST00000478296.1	-	4	2215	c.1939A>T	c.(1939-1941)Aca>Tca	p.T647S	MIR4273_ENST00000582824.1_RNA|ZNF717_ENST00000400845.3_Missense_Mutation_p.T690S|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.T697S			Q9BY31	ZN717_HUMAN	zinc finger protein 717	687					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)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TTCCCCGGTGTGAGTTCTCTG	0.408													t|||	38	0.00758786	0.0	0.0014	5008	,	,		8414	0.0		0.0169	False		,,,				2504	0.0204				p.T697S		Atlas-SNP	.											.	ZNF717	160	.	0			c.A2089T						PASS	.						4.0	4.0	4.0					3																	75786685		568	1417	1985	SO:0001583	missense	100131827	exon5			CCGGTGTGAGTTC	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1939A>T	3.37:g.75786685T>A	ENSP00000419377:p.Thr647Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	14	11	0.785714	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		.	.	.	.	.	.	.	.	.	.	.	12.71	2.020326	0.35606	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.06449	3.3;3.45;3.46	1.63	1.63	0.23807	.	.	.	.	.	T	0.15089	0.0364	L	0.49350	1.555	0.25562	N	0.986984	D	0.76494	0.999	D	0.66979	0.948	T	0.06917	-1.0800	9	0.66056	D	0.02	.	7.2918	0.26370	0.0:0.0:0.0:1.0	.	697	C9JSV9	.	S	647;697;690	ENSP00000419377:T647S;ENSP00000409514:T697S;ENSP00000383643:T690S	ENSP00000383643:T690S	T	-	1	0	ZNF717	75869375	1.000000	0.71417	0.020000	0.16555	0.002000	0.02628	5.444000	0.66587	1.012000	0.39366	0.451000	0.29950	ACA	.	.	weak		0.408	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
MXRA5	25878	hgsc.bcm.edu	37	X	3241317	3241317	+	Silent	SNP	T	T	C	rs1635249	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3241317T>C	ENST00000217939.6	-	5	2563	c.2409A>G	c.(2407-2409)ccA>ccG	p.P803P		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	803						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TTTTAATCAATGGGGGTACTT	0.473													C|||	2833	0.750464	0.6868	0.5216	3775	,	,		13934	0.5595		0.5278	False		,,,				2504	0.4785				p.P803P		Atlas-SNP	.											.	MXRA5	815	.	0			c.A2409G						PASS	.	C		3376,459		1280,321,495,31,76	141.0	140.0	140.0		2409	-1.1	0.0	X	dbSNP_89	140	4342,2386		1019,1110,1194,299,678	no	coding-synonymous	MXRA5	NM_015419.3		2299,1431,1689,330,754	CC,CT,C,TT,T		35.4637,11.9687,26.9336		803/2829	3241317	7718,2845	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			AATCAATGGGGGT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2409A>G	X.37:g.3241317T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			0|0.003;C|0.737	0.737	strong		0.473	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
NAP1L3	4675	hgsc.bcm.edu	37	X	92927634	92927634	+	Missense_Mutation	SNP	G	G	C	rs1045686	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:92927634G>C	ENST00000373079.3	-	1	933	c.670C>G	c.(670-672)Cct>Gct	p.P224A	FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000538690.1_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.P217A|FAM133A_ENST00000322139.4_5'Flank|FAM133A_ENST00000355813.5_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	224	Glu-rich.		P -> A (in dbSNP:rs1045686). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8976385}.		nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	34						ATTTCTTTAGGAACTTCCTTT	0.408													G|||	2286	0.605563	0.4107	0.487	3775	,	,		12236	0.4315		0.492	False		,,,				2504	0.4857				p.P224A		Atlas-SNP	.											.	NAP1L3	81	.	0			c.C670G						PASS	.	G	ALA/PRO	2117,1718		493,805,326,334,245	109.0	111.0	110.0		670	3.3	0.0	X	dbSNP_86	110	4341,2387		1009,1120,1203,299,669	yes	missense	NAP1L3	NM_004538.5	27	1502,1925,1529,633,914	CC,CG,C,GG,G		35.4786,44.7979,38.8621	benign	224/507	92927634	6458,4105	2203	4300	6503	SO:0001583	missense	4675	exon1			CTTTAGGAACTTC		CCDS14465.1	Xq21.3-q22	2008-08-01			ENSG00000186310	ENSG00000186310			7639	protein-coding gene	gene with protein product		300117				8976385	Standard	NM_004538		Approved	MB20, NPL3, MGC26312	uc004efq.3	Q99457	OTTHUMG00000021974	ENST00000373079.3:c.670C>G	X.37:g.92927634G>C	ENSP00000362171:p.Pro224Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	98	24	0.244898	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	945	0.569620253164557	144	0.37894736842105264	115	0.4356060606060606	137	0.33414634146341465	247	0.4695817490494297	G	1.796	-0.478383	0.04414	0.552021	0.645214	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.22945	1.93	3.29	3.29	0.37713	.	0.715244	0.11488	N	0.559020	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.29835	0.258	B	0.26202	0.067	T	0.32079	-0.9920	9	0.28530	T	0.3	.	11.8227	0.52247	0.0:0.0:1.0:0.0	rs1045686;rs3174472;rs3813175;rs17846115;rs17859119;rs52800074;rs1045686	224	Q99457	NP1L3_HUMAN	A	224;217	ENSP00000362171:P224A	ENSP00000362171:P224A	P	-	1	0	NAP1L3	92814290	0.001000	0.12720	0.015000	0.15790	0.516000	0.34256	0.625000	0.24477	1.928000	0.55862	0.529000	0.55759	CCT	G|0.390;0|0.015	.	strong		0.408	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538	
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 GAIIx	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		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	252	105	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		
OR2W5	441932	hgsc.bcm.edu	37	1	247654993	247654993	+	RNA	SNP	T	T	C	rs10925061	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247654993T>C	ENST00000522351.1	+	0	624							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)			TTGCCATGTCTTGTGAGGAAA	0.562													C|||	1621	0.323682	0.4546	0.2536	5008	,	,		18968	0.2659		0.3231	False		,,,				2504	0.2566				p.S188S		Atlas-SNP	.											.	OR2W5	97	.	0			c.T564C						PASS	.	C		1929,2477	624.9+/-394.4	429,1071,703	141.0	141.0	141.0		564	-0.5	0.5	1	dbSNP_120	141	2608,5992	688.5+/-404.3	394,1820,2086	no	coding-synonymous	OR2W5	NM_001004698.2		823,2891,2789	CC,CT,TT		30.3256,43.7812,34.8839		188/321	247654993	4537,8469	2203	4300	6503			441932	exon1			CATGTCTTGTGAG			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.247654993T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	29	0.345238	NM_001004698	B9EH85	Silent	SNP	ENST00000522351.1	37																																																																																				T|0.645;C|0.355	0.355	strong		0.562	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
SLC9C1	285335	hgsc.bcm.edu	37	3	111996554	111996554	+	Missense_Mutation	SNP	T	T	C	rs9828502	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111996554T>C	ENST00000305815.5	-	5	724	c.472A>G	c.(472-474)Ata>Gta	p.I158V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I158V|SLC9C1_ENST00000467397.1_5'Flank	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	158			I -> V (in dbSNP:rs9828502). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										AGGTCTCTTATAGCAGCTGCG	0.333													T|||	1557	0.310903	0.3116	0.4006	5008	,	,		17507	0.2976		0.2346	False		,,,				2504	0.3384				p.I158V		Atlas-SNP	.											.	.	.	.	0			c.A472G						PASS	.	T	VAL/ILE	1392,3014	448.5+/-348.7	219,954,1030	72.0	77.0	75.0		472	-1.3	0.3	3	dbSNP_119	75	2333,6267	386.0+/-341.7	321,1691,2288	yes	missense	SLC9A10	NM_183061.1	29	540,2645,3318	CC,CT,TT		27.1279,31.5933,28.6406	possibly-damaging	158/1178	111996554	3725,9281	2203	4300	6503	SO:0001583	missense	285335	exon5			CTCTTATAGCAGC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.472A>G	3.37:g.111996554T>C	ENSP00000306627:p.Ile158Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	67	0.544715	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	649	0.29716117216117216	157	0.31910569105691056	137	0.3784530386740331	173	0.30244755244755245	182	0.24010554089709762	T	0.080	-1.185856	0.01620	0.315933	0.271279	ENSG00000172139	ENST00000305815;ENST00000487372;ENST00000486574	T;T;T	0.13420	2.59;2.59;3.95	5.45	-1.34	0.09143	Cation/H+ exchanger (1);	0.188565	0.36854	N	0.002361	T	0.00012	0.0000	L	0.53249	1.67	0.58432	P	6.999999999979245E-6	B;B	0.10296	0.002;0.003	B;B	0.14578	0.005;0.011	T	0.44174	-0.9345	9	0.56958	D	0.05	.	5.697	0.17861	0.1198:0.302:0.0:0.5782	rs9828502;rs9828502	158;158	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	158;158;85	ENSP00000306627:I158V;ENSP00000420688:I158V;ENSP00000417274:I85V	ENSP00000306627:I158V	I	-	1	0	SLC9A10	113479244	0.992000	0.36948	0.281000	0.24762	0.037000	0.13140	0.134000	0.15932	-0.872000	0.04037	-2.485000	0.00197	ATA	T|0.713;C|0.287	0.287	strong		0.333	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
MOS	4342	hgsc.bcm.edu	37	8	57026229	57026229	+	Missense_Mutation	SNP	C	C	A	rs35392772	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:57026229C>A	ENST00000311923.1	-	1	312	c.313G>T	c.(313-315)Gct>Tct	p.A105S		NM_005372.1	NP_005363.1	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene homolog	105	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> S (in dbSNP:rs35392772). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|chromatin organization (GO:0006325)|establishment of meiotic spindle orientation (GO:0051296)|MAPK cascade (GO:0000165)|meiotic spindle organization (GO:0000212)|negative regulation of metaphase/anaphase transition of meiotic cell cycle (GO:1902103)|protein autophosphorylation (GO:0046777)|regulation of meiosis (GO:0040020)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(12)|ovary(1)|urinary_tract(2)	22			Epithelial(17;0.00117)|all cancers(17;0.00879)			TTGAGCTCAGCCCAGAAACTC	0.592													C|||	295	0.0589058	0.0083	0.1182	5008	,	,		19021	0.002		0.163	False		,,,				2504	0.0368				p.A105S	Esophageal Squamous(124;373 2870 4778)	Atlas-SNP	.											.	MOS	63	.	0			c.G313T						PASS	.	C	SER/ALA	162,4244	107.3+/-145.7	2,158,2043	120.0	108.0	112.0		313	5.4	1.0	8	dbSNP_126	112	1459,7141	280.1+/-294.3	129,1201,2970	yes	missense	MOS	NM_005372.1	99	131,1359,5013	AA,AC,CC		16.9651,3.6768,12.4635	probably-damaging	105/347	57026229	1621,11385	2203	4300	6503	SO:0001583	missense	4342	exon1			GCTCAGCCCAGAA		CCDS6164.1	8q11	2012-10-02			ENSG00000172680	ENSG00000172680			7199	protein-coding gene	gene with protein product		190060				9552420	Standard	NM_005372		Approved		uc011leb.2	P00540	OTTHUMG00000164299	ENST00000311923.1:c.313G>T	8.37:g.57026229C>A	ENSP00000310722:p.Ala105Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_005372	Q3KPG9|Q3KPH0	Missense_Mutation	SNP	ENST00000311923.1	37	CCDS6164.1	174	0.07967032967032966	5	0.01016260162601626	53	0.1464088397790055	0	0.0	116	0.15303430079155672	C	33	5.255099	0.95336	0.036768	0.169651	ENSG00000172680	ENST00000311923	D	0.93426	-3.22	5.37	5.37	0.77165	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.05044	0.0135	L	0.27944	0.81	0.09310	P	0.99999894481	D	0.89917	1.0	D	0.91635	0.999	T	0.58763	-0.7579	9	0.87932	D	0	.	19.1728	0.93585	0.0:1.0:0.0:0.0	rs35392772;rs35392772	105	P00540	MOS_HUMAN	S	105	ENSP00000310722:A105S	ENSP00000310722:A105S	A	-	1	0	MOS	57188783	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.855000	0.69510	2.533000	0.85409	0.551000	0.68910	GCT	C|0.888;A|0.112	0.112	strong		0.592	MOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378174.1	NM_005372	
GLDC	2731	hgsc.bcm.edu	37	9	6620216	6620216	+	Silent	SNP	C	C	T	rs13289273	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6620216C>T	ENST00000321612.6	-	3	588	c.438G>A	c.(436-438)acG>acA	p.T146T		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	146					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	TCCGCAAAATCGTCTGTGGCA	0.418													C|||	149	0.0297524	0.0038	0.0447	5008	,	,		20847	0.0		0.1004	False		,,,				2504	0.0123				p.T146T		Atlas-SNP	.											.	GLDC	118	.	0			c.G438A						PASS	.	C		80,4326	69.2+/-107.0	0,80,2123	166.0	138.0	147.0		438	-4.3	1.0	9	dbSNP_121	147	798,7802	186.9+/-234.3	46,706,3548	no	coding-synonymous	GLDC	NM_000170.2		46,786,5671	TT,TC,CC		9.2791,1.8157,6.7507		146/1021	6620216	878,12128	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon3			CAAAATCGTCTGT	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"""glycine cleavage system protein P"", ""glycine decarboxylase"""	238300	"""glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"""			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.438G>A	9.37:g.6620216C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	138	57	0.413043	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			C|0.941;T|0.059	0.059	strong		0.418	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
RGPD4	285190	hgsc.bcm.edu	37	2	108475968	108475968	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:108475968C>T	ENST00000408999.3	+	11	1669	c.1592C>T	c.(1591-1593)tCt>tTt	p.S531F	RGPD4_ENST00000354986.4_Missense_Mutation_p.S531F	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	531					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						AGACAAAAATCTTGGTGGGAT	0.388																																					p.S531F		Atlas-SNP	.											RGPD4,NS,carcinoma,0,1	RGPD4	112	1	0			c.C1592T						scavenged	.						60.0	55.0	56.0					2																	108475968		692	1591	2283	SO:0001583	missense	285190	exon11			AAAAATCTTGGTG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.1592C>T	2.37:g.108475968C>T	ENSP00000386810:p.Ser531Phe	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	196	4	0.0204082	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	7.859	0.725728	0.15439	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.48522	0.81;0.81	2.6	2.6	0.31112	.	.	.	.	.	T	0.42449	0.1203	L	0.57536	1.79	0.20926	N	0.999821	P	0.41041	0.736	B	0.35550	0.205	T	0.39354	-0.9618	9	0.87932	D	0	-9.068	11.8656	0.52490	0.0:1.0:0.0:0.0	.	531	Q7Z3J3	RGPD4_HUMAN	F	531;531;289	ENSP00000347081:S531F;ENSP00000386810:S531F	ENSP00000347081:S531F	S	+	2	0	RGPD4	107842400	0.027000	0.19231	0.084000	0.20598	0.209000	0.24338	2.391000	0.44424	1.299000	0.44798	0.152000	0.16155	TCT	.	.	none		0.388	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
CPNE8	144402	hgsc.bcm.edu	37	12	39087609	39087609	+	Silent	SNP	G	G	A	rs3759139	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:39087609G>A	ENST00000331366.5	-	15	1089	c.993C>T	c.(991-993)taC>taT	p.Y331Y	CPNE8_ENST00000360449.3_Silent_p.Y319Y|CPNE8_ENST00000538596.2_5'UTR	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	331	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular vesicular exosome (GO:0070062)		p.Y331Y(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				AAGGATTCATGTAGTGGAGGG	0.378													G|||	1314	0.26238	0.0477	0.2997	5008	,	,		17328	0.2331		0.4493	False		,,,				2504	0.364				p.Y331Y		Atlas-SNP	.											CPNE8,NS,carcinoma,0,1	CPNE8	66	1	1	Substitution - coding silent(1)	stomach(1)	c.C993T						PASS	.	G		450,3956	215.1+/-234.2	21,408,1774	120.0	99.0	106.0		993	-0.0	1.0	12	dbSNP_107	106	3855,4745	543.3+/-384.4	843,2169,1288	no	coding-synonymous	CPNE8	NM_153634.2		864,2577,3062	AA,AG,GG		44.8256,10.2133,33.1001		331/565	39087609	4305,8701	2203	4300	6503	SO:0001819	synonymous_variant	144402	exon15			ATTCATGTAGTGG	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.993C>T	12.37:g.39087609G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_153634	Q2TB41|Q86VY2	Silent	SNP	ENST00000331366.5	37	CCDS8733.1																																																																																			G|0.695;A|0.305	0.305	strong		0.378	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	NM_153634	
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 GAIIx	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	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	178	9	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		
APEH	327	hgsc.bcm.edu	37	3	49722303	49722303	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49722303G>A	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Missense_Mutation_p.T546M	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.T532M(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CTCATAGCCCGTGAGAGGCAT	0.572																																					p.T546M		Atlas-SNP	.											MST1,NS,carcinoma,0,2	MST1	84	2	1	Substitution - Missense(1)	breast(1)	c.C1637T						scavenged	.						38.0	41.0	40.0					3																	49722303		2199	4292	6491	SO:0001628	intergenic_variant	4485	exon15			TAGCCCGTGAGAG	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49722303G>A		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	168	10	0.0595238	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	8.833	0.940436	0.18281	.	.	ENSG00000173531	ENST00000449682	D	0.88896	-2.44	5.5	-6.04	0.02178	.	1.359990	0.05409	N	0.542101	D	0.85150	0.5631	L	0.48642	1.525	0.09310	N	1	B	0.17465	0.022	B	0.19391	0.025	T	0.69247	-0.5195	10	0.39692	T	0.17	.	15.5487	0.76129	0.119:0.0907:0.7903:0.0	.	546	G3XAK1	.	M	546	ENSP00000414287:T546M	ENSP00000414287:T546M	T	-	2	0	MST1	49697307	0.000000	0.05858	0.000000	0.03702	0.623000	0.37688	0.518000	0.22847	-1.219000	0.02597	-1.119000	0.02030	ACG	.	.	none		0.572	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
SEMA5B	54437	hgsc.bcm.edu	37	3	122632436	122632436	+	Missense_Mutation	SNP	A	A	G	rs2276781	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:122632436A>G	ENST00000357599.3	-	16	2611	c.2225T>C	c.(2224-2226)aTg>aCg	p.M742T	SEMA5B_ENST00000451055.2_Missense_Mutation_p.M796T|SEMA5B_ENST00000195173.4_Missense_Mutation_p.M742T	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	742	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		M -> T (in dbSNP:rs2276781). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		CCGCGACTGCATGCCCCCTCC	0.677													A|||	310	0.061901	0.062	0.0735	5008	,	,		14567	0.0546		0.0398	False		,,,				2504	0.0838				p.M796T		Atlas-SNP	.											SEMA5B_ENST00000451055,NS,carcinoma,0,2	SEMA5B	303	2	0			c.T2387C						PASS	.	A	THR/MET	230,4176		7,216,1980	18.0	20.0	19.0		2225	4.6	1.0	3	dbSNP_100	19	396,8198		7,382,3908	yes	missense	SEMA5B	NM_001031702.2	81	14,598,5888	GG,GA,AA		4.6079,5.2202,4.8154	benign	742/1152	122632436	626,12374	2203	4297	6500	SO:0001583	missense	54437	exon16			GACTGCATGCCCC	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.2225T>C	3.37:g.122632436A>G	ENSP00000350215:p.Met742Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	112	0.05128205128205128	29	0.05894308943089431	22	0.06077348066298342	29	0.050699300699300696	32	0.04221635883905013	A	12.79	2.042881	0.36085	0.052202	0.046079	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.51817	0.69;0.69;0.69;0.69	4.56	4.56	0.56223	.	0.416572	0.25704	N	0.028841	T	0.01287	0.0042	N	0.00152	-1.975	0.09310	N	0.999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.06607	-1.0817	10	0.54805	T	0.06	.	8.0133	0.30365	0.9088:0.0:0.0912:0.0	rs2276781	684;742;742	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	T	742;742;684;796;742	ENSP00000350215:M742T;ENSP00000195173:M742T;ENSP00000389588:M796T;ENSP00000377208:M742T	ENSP00000195173:M742T	M	-	2	0	SEMA5B	124115126	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.116000	0.71571	1.905000	0.55150	0.459000	0.35465	ATG	A|0.949;G|0.051	0.051	strong		0.677	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
HDAC6	10013	hgsc.bcm.edu	37	X	48681187	48681187	+	Missense_Mutation	SNP	G	G	A	rs61735967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:48681187G>A	ENST00000334136.5	+	24	2673	c.2495G>A	c.(2494-2496)cGc>cAc	p.R832H	HDAC6_ENST00000444343.2_Missense_Mutation_p.R846H|HDAC6_ENST00000376619.2_Missense_Mutation_p.R832H			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	832					aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	AGATACTGGCGCAGCTTACGG	0.622													G|||	31	0.00821192	0.0	0.0072	3775	,	,		13125	0.0		0.0229	False		,,,				2504	0.0031				p.R832H	Pancreas(112;205 1675 2305 8976 15959)	Atlas-SNP	.											.	HDAC6	111	.	0			c.G2495A						PASS	.	G	HIS/ARG	20,3815		0,16,4,1616,567	37.0	34.0	35.0		2495	2.8	1.0	X	dbSNP_129	35	219,6509		3,153,60,2272,1812	yes	missense	HDAC6	NM_006044.2	29	3,169,64,3888,2379	AA,AG,A,GG,G		3.2551,0.5215,2.2626	probably-damaging	832/1216	48681187	239,10324	2203	4300	6503	SO:0001583	missense	10013	exon24			ACTGGCGCAGCTT	AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.2495G>A	X.37:g.48681187G>A	ENSP00000334061:p.Arg832His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	98	18	0.183673	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	37	CCDS14306.1	20	0.012055455093429777	0	0.0	1	0.002793296089385475	0	0.0	18	0.023872679045092837	G	18.61	3.661801	0.67700	0.005215	0.032551	ENSG00000094631	ENST00000444343;ENST00000334136;ENST00000376619	T;T;T	0.60424	0.19;0.19;0.19	5.89	2.84	0.33178	Histone deacetylase domain (1);	0.340463	0.28859	N	0.013918	T	0.42966	0.1226	M	0.64997	1.995	0.40692	D	0.982406	D;D;D;D	0.76494	0.972;0.999;0.998;0.972	B;P;D;B	0.66351	0.406;0.891;0.943;0.406	T	0.57087	-0.7871	10	0.48119	T	0.1	-16.5194	7.4397	0.27176	0.3456:0.0:0.6544:0.0	rs61735967	822;195;480;832	B4DZN1;B3KY98;B3KVK5;Q9UBN7	.;.;.;HDAC6_HUMAN	H	846;832;832	ENSP00000398566:R846H;ENSP00000334061:R832H;ENSP00000365804:R832H	ENSP00000334061:R832H	R	+	2	0	HDAC6	48566131	0.328000	0.24687	0.970000	0.41538	0.966000	0.64601	1.046000	0.30354	0.633000	0.30452	0.600000	0.82982	CGC	G|0.983;A|0.017	0.017	strong		0.622	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
COL2A1	1280	hgsc.bcm.edu	37	12	48391416	48391416	+	Silent	SNP	G	G	T	rs3737548	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48391416G>T	ENST00000380518.3	-	7	668	c.504C>A	c.(502-504)ggC>ggA	p.G168G	COL2A1_ENST00000337299.6_Silent_p.G99G	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	168					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)	gaccaggggggccgggaggac	0.562													G|||	1098	0.219249	0.146	0.2277	5008	,	,		17261	0.3036		0.2356	False		,,,				2504	0.2086				p.G168G		Atlas-SNP	.											.	COL2A1	368	.	0			c.C504A						PASS	.	G	,	693,3713	269.8+/-269.2	52,589,1562	31.0	35.0	34.0		504,297	-0.7	1.0	12	dbSNP_107	34	1927,6673	319.5+/-314.2	209,1509,2582	no	coding-synonymous,coding-synonymous	COL2A1	NM_001844.4,NM_033150.2	,	261,2098,4144	TT,TG,GG		22.407,15.7286,20.1445	,	168/1488,99/1419	48391416	2620,10386	2203	4300	6503	SO:0001819	synonymous_variant	1280	exon7			AGGGGGGCCGGGA	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.504C>A	12.37:g.48391416G>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	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|0.784;T|0.216	0.216	strong		0.562	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
SBF1	6305	hgsc.bcm.edu	37	22	50901009	50901009	+	Silent	SNP	C	C	T	rs5771037	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50901009C>T	ENST00000390679.3	-	18	2290	c.2106G>A	c.(2104-2106)acG>acA	p.T702T	SBF1_ENST00000348911.6_Silent_p.T703T|SBF1_ENST00000380817.3_Silent_p.T702T			O95248	MTMR5_HUMAN	SET binding factor 1	702					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)		CCAGGTCCTCCGTGGGCTCCA	0.701													c|||	842	0.168131	0.0053	0.1686	5008	,	,		12036	0.4425		0.0606	False		,,,				2504	0.2157				p.T702T		Atlas-SNP	.											SBF1_ENST00000380817,NS,carcinoma,0,2	SBF1	211	2	0			c.G2106A						PASS	.	C		57,3819		0,57,1881	14.0	17.0	16.0		2106	-9.3	0.0	22	dbSNP_114	16	501,7745		15,471,3637	no	coding-synonymous	SBF1	NM_002972.2		15,528,5518	TT,TC,CC		6.0757,1.4706,4.6032		702/1894	50901009	558,11564	1938	4123	6061	SO:0001819	synonymous_variant	6305	exon18			GTCCTCCGTGGGC	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.2106G>A	22.37:g.50901009C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				C|0.857;T|0.143	0.143	strong		0.701	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
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 GAIIx	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_ENST00000584337.1_Missense_Mutation_p.A105S|CDH8_ENST00000299345.6_Missense_Mutation_p.A105S|CDH8_ENST00000577730.1_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	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	20	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	
ANAPC4	29945	hgsc.bcm.edu	37	4	25408838	25408838	+	Missense_Mutation	SNP	G	G	A	rs34811474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:25408838G>A	ENST00000315368.3	+	20	1536	c.1394G>A	c.(1393-1395)cGa>cAa	p.R465Q	ANAPC4_ENST00000510092.1_Missense_Mutation_p.R466Q	NM_013367.2	NP_037499.2	Q9UJX5	APC4_HUMAN	anaphase promoting complex subunit 4	465			R -> Q (in dbSNP:rs34811474).		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	27		Breast(46;0.0503)				CTTTATAATCGAAAAGGAAAA	0.323													G|||	371	0.0740815	0.0189	0.1239	5008	,	,		16203	0.0		0.2167	False		,,,				2504	0.0429				p.R465Q		Atlas-SNP	.											ANAPC4,NS,carcinoma,+1,1	ANAPC4	61	1	0			c.G1394A						PASS	.	G	GLN/ARG	180,4226	101.6+/-140.2	7,166,2030	53.0	56.0	55.0		1394	5.1	1.0	4	dbSNP_126	55	1886,6710	323.5+/-316.1	207,1472,2619	yes	missense	ANAPC4	NM_013367.2	43	214,1638,4649	AA,AG,GG		21.9404,4.0853,15.8899	benign	465/809	25408838	2066,10936	2203	4298	6501	SO:0001583	missense	29945	exon20			ATAATCGAAAAGG	AF191338	CCDS3434.1, CCDS68684.1	4p15.31	2011-06-15			ENSG00000053900	ENSG00000053900		"""Anaphase promoting complex subunits"""	19990	protein-coding gene	gene with protein product		606947				6180011	Standard	NM_013367		Approved	APC4	uc003gro.3	Q9UJX5	OTTHUMG00000097753	ENST00000315368.3:c.1394G>A	4.37:g.25408838G>A	ENSP00000318775:p.Arg465Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	77	33	0.428571	NM_013367	A8K8H1|E9PCR4|Q6PCC6|Q9NSH6	Missense_Mutation	SNP	ENST00000315368.3	37	CCDS3434.1	223	0.1021062271062271	10	0.02032520325203252	54	0.14917127071823205	0	0.0	159	0.20976253298153033	G	13.01	2.110474	0.37242	0.040853	0.219404	ENSG00000053900	ENST00000315368;ENST00000510092	T;T	0.32023	1.47;1.47	5.13	5.13	0.70059	.	0.059354	0.64402	D	0.000001	T	0.00012	0.0000	L	0.27053	0.805	0.21445	P	0.999685615	B	0.25312	0.123	B	0.13407	0.009	T	0.21143	-1.0254	9	0.10377	T	0.69	-6.5303	12.3291	0.55028	0.078:0.0:0.922:0.0	rs34811474;rs61748742	465	Q9UJX5	APC4_HUMAN	Q	465;466	ENSP00000318775:R465Q;ENSP00000426654:R466Q	ENSP00000318775:R465Q	R	+	2	0	ANAPC4	25017936	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	6.177000	0.71961	2.569000	0.86673	0.591000	0.81541	CGA	G|0.858;A|0.142	0.142	strong		0.323	ANAPC4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214986.1	NM_013367	
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 GAIIx	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_ENST00000400423.2_3'UTR|UMODL1_ENST00000400424.2_Silent_p.A1216A|UMODL1_ENST00000408989.2_Silent_p.A1416A|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		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	205	127	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 GAIIx	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	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	73	35	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	
C9orf89	84270	hgsc.bcm.edu	37	9	95872885	95872885	+	Silent	SNP	C	C	T	rs17593496	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:95872885C>T	ENST00000375464.2	+	3	314	c.186C>T	c.(184-186)ctC>ctT	p.L62L	C9orf89_ENST00000488630.1_3'UTR	NM_032310.3	NP_115686.3	Q96LW7	BINCA_HUMAN	chromosome 9 open reading frame 89	62	CARD.				negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	CARD domain binding (GO:0050700)			endometrium(1)|kidney(1)|lung(3)|ovary(1)|skin(1)	7						GTGTGCGGCTCTGTGACCTCC	0.667													C|||	298	0.0595048	0.0356	0.062	5008	,	,		18997	0.002		0.161	False		,,,				2504	0.045				p.L62L		Atlas-SNP	.											C9orf89,NS,adenoma,0,1	C9orf89	12	1	0			c.C186T						PASS	.	C		207,4199	127.4+/-164.3	4,199,2000	93.0	93.0	93.0		186	-0.8	1.0	9	dbSNP_123	93	1267,7333	253.6+/-279.2	82,1103,3115	no	coding-synonymous	C9orf89	NM_032310.3		86,1302,5115	TT,TC,CC		14.7326,4.6981,11.3332		62/184	95872885	1474,11532	2203	4300	6503	SO:0001819	synonymous_variant	84270	exon3			GCGGCTCTGTGAC	AK057716	CCDS6702.2	9q22.32	2012-03-16			ENSG00000165233	ENSG00000165233			28148	protein-coding gene	gene with protein product	"""Bcl10-interacting protein with CARD"""					12477932	Standard	XM_005252273		Approved	MGC11115, bA370F5.1, BinCARD	uc004atd.3	Q96LW7	OTTHUMG00000020243	ENST00000375464.2:c.186C>T	9.37:g.95872885C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_032310	Q5BJH8|Q9BSY2	Silent	SNP	ENST00000375464.2	37	CCDS6702.2																																																																																			C|0.908;T|0.092	0.092	strong		0.667	C9orf89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053128.1	NM_032310	
HRG	3273	hgsc.bcm.edu	37	3	186395113	186395113	+	Missense_Mutation	SNP	A	A	G	rs2228243	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:186395113A>G	ENST00000232003.4	+	7	1099	c.1019A>G	c.(1018-1020)cAt>cGt	p.H340R		NM_000412.2	NP_000403.1	P04196	HRG_HUMAN	histidine-rich glycoprotein	340			H -> R (in dbSNP:rs2228243).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|defense response to fungus (GO:0050832)|fibrinolysis (GO:0042730)|heme export (GO:0097037)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel remodeling (GO:2000504)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of immune response to tumor cell (GO:0002839)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet activation (GO:0010543)|regulation of protein complex assembly (GO:0043254)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|response to organic cyclic compound (GO:0014070)	blood microparticle (GO:0072562)|endolysosome (GO:0036019)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|phagolysosome membrane (GO:0061474)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|heme binding (GO:0020037)|heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)|immunoglobulin binding (GO:0019865)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)	p.H340R(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(12)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_cancers(143;6.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.73e-20)	GBM - Glioblastoma multiforme(93;0.0683)		GCCCAAAGACATTCTCATAAT	0.498													A|||	1026	0.204872	0.0303	0.2147	5008	,	,		20524	0.4137		0.1819	False		,,,				2504	0.2423				p.H340R		Atlas-SNP	.											HRG,NS,adenoma,0,2	HRG	81	2	1	Substitution - Missense(1)	stomach(1)	c.A1019G						PASS	.	A	ARG/HIS	280,4126	153.3+/-186.9	15,250,1938	144.0	138.0	140.0		1019	-1.9	0.0	3	dbSNP_98	140	1752,6848	317.6+/-313.3	191,1370,2739	yes	missense	HRG	NM_000412.2	29	206,1620,4677	GG,GA,AA		20.3721,6.355,15.6236	benign	340/526	186395113	2032,10974	2203	4300	6503	SO:0001583	missense	3273	exon7			AAAGACATTCTCA		CCDS3280.1	3q27	2008-07-18			ENSG00000113905	ENSG00000113905			5181	protein-coding gene	gene with protein product	"""histidine-proline rich glycoprotein"", ""thrombophilia due to elevated HRG"""	142640				1678514	Standard	NM_000412		Approved	HRGP, HPRG	uc003fqq.3	P04196	OTTHUMG00000156578	ENST00000232003.4:c.1019A>G	3.37:g.186395113A>G	ENSP00000232003:p.His340Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_000412	B9EK35|D3DNU7	Missense_Mutation	SNP	ENST00000232003.4	37	CCDS3280.1	458	0.2097069597069597	12	0.024390243902439025	80	0.22099447513812154	224	0.3916083916083916	142	0.18733509234828497	A	9.261	1.043188	0.19748	0.06355	0.203721	ENSG00000113905	ENST00000232003	T	0.14640	2.49	4.55	-1.9	0.07665	.	0.903725	0.09359	N	0.812968	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	P	0.38978	0.652	B	0.31614	0.133	T	0.48175	-0.9058	9	0.20046	T	0.44	0.0549	7.2636	0.26217	0.6619:0.2388:0.0:0.0994	rs2228243;rs3733014;rs16860998;rs58808959;rs2228243	340	P04196	HRG_HUMAN	R	340	ENSP00000232003:H340R	ENSP00000232003:H340R	H	+	2	0	HRG	187877807	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.010000	0.03656	-0.477000	0.06832	0.374000	0.22700	CAT	A|0.768;G|0.232	0.232	strong		0.498	HRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344655.1	NM_000412	
RGS17	26575	hgsc.bcm.edu	37	6	153365112	153365112	+	Silent	SNP	G	G	A	rs41292882	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:153365112G>A	ENST00000367225.2	-	1	66	c.42C>T	c.(40-42)gcC>gcT	p.A14A	RGS17_ENST00000206262.1_Silent_p.A14A			Q9UGC6	RGS17_HUMAN	regulator of G-protein signaling 17	14					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(2)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	14		Ovarian(120;0.126)		OV - Ovarian serous cystadenocarcinoma(155;1.09e-09)|BRCA - Breast invasive adenocarcinoma(81;0.0429)		CTTGAGACACGGCAGGTGTTC	0.463													G|||	117	0.0233626	0.0	0.0317	5008	,	,		16874	0.002		0.0437	False		,,,				2504	0.0501				p.A14A	Esophageal Squamous(78;500 1236 6775 24364 49058)	Atlas-SNP	.											.	RGS17	32	.	0			c.C42T						PASS	.	G		41,4365	43.1+/-76.7	0,41,2162	173.0	173.0	173.0		42	-0.4	1.0	6	dbSNP_127	173	403,8197	128.5+/-186.7	7,389,3904	no	coding-synonymous	RGS17	NM_012419.4		7,430,6066	AA,AG,GG		4.686,0.9305,3.4138		14/211	153365112	444,12562	2203	4300	6503	SO:0001819	synonymous_variant	26575	exon2			AGACACGGCAGGT	AF202257	CCDS5244.1	6q25-q26	2009-05-29	2007-08-14		ENSG00000091844	ENSG00000091844		"""Regulators of G-protein signaling"""	14088	protein-coding gene	gene with protein product		607191	"""regulator of G-protein signalling 17"""			10419452	Standard	NM_012419		Approved	RGSZ2, RGS-17	uc003qpm.3	Q9UGC6	OTTHUMG00000015858	ENST00000367225.2:c.42C>T	6.37:g.153365112G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_012419	Q5TF49|Q8TD61|Q9UJS8	Silent	SNP	ENST00000367225.2	37	CCDS5244.1																																																																																			G|0.971;A|0.029	0.029	strong		0.463	RGS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042773.2		
PCK1	5105	hgsc.bcm.edu	37	20	56138621	56138621	+	Splice_Site	SNP	A	A	G	rs8192708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:56138621A>G	ENST00000319441.4	+	6	963	c.799A>G	c.(799-801)Att>Gtt	p.I267V	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Splice_Site_p.I135V	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	267			I -> V (in dbSNP:rs8192708). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TCCCCAACAGATTCTGGGTAT	0.522													A|||	289	0.0577077	0.0408	0.0922	5008	,	,		18039	0.001		0.1203	False		,,,				2504	0.0501				p.I267V		Atlas-SNP	.											.	PCK1	95	.	0			c.A799G						PASS	.	A	VAL/ILE	195,4211	122.9+/-160.3	3,189,2011	56.0	56.0	56.0		799	5.4	1.0	20	dbSNP_117	56	1089,7511	226.9+/-262.5	56,977,3267	yes	missense-near-splice	PCK1	NM_002591.3	29	59,1166,5278	GG,GA,AA		12.6628,4.4258,9.8724	possibly-damaging	267/623	56138621	1284,11722	2203	4300	6503	SO:0001630	splice_region_variant	5105	exon6			CAACAGATTCTGG		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.799-1A>G	20.37:g.56138621A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Missense_Mutation	SNP	ENST00000319441.4	37	CCDS13460.1	148	0.06776556776556776	20	0.04065040650406504	39	0.10773480662983426	0	0.0	89	0.11741424802110818	A	15.76	2.929262	0.52759	0.044258	0.126628	ENSG00000124253	ENST00000319441;ENST00000535860	T;T	0.06528	3.29;3.29	5.43	5.43	0.79202	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00300	0.0009	M	0.91510	3.215	0.09310	P	0.999999999558022	D	0.63046	0.992	P	0.61003	0.882	T	0.01613	-1.1312	9	0.66056	D	0.02	-33.4337	15.4961	0.75653	1.0:0.0:0.0:0.0	rs8192708;rs17412388;rs56732547;rs8192708	267	P35558	PCKGC_HUMAN	V	267;135	ENSP00000319814:I267V;ENSP00000444342:I135V	ENSP00000319814:I267V	I	+	1	0	PCK1	55572027	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	8.832000	0.92079	2.072000	0.62099	0.459000	0.35465	ATT	A|0.915;G|0.085	0.085	strong		0.522	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		Missense_Mutation
PTGER3	5733	hgsc.bcm.edu	37	1	71512643	71512643	+	Silent	SNP	C	C	A	rs5671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:71512643C>A	ENST00000306666.5	-	1	828	c.618G>T	c.(616-618)acG>acT	p.T206T	PTGER3_ENST00000370931.3_Silent_p.T206T|PTGER3_ENST00000414819.1_Silent_p.T206T|PTGER3_ENST00000354608.5_Silent_p.T206T|ZRANB2-AS1_ENST00000450461.1_RNA|PTGER3_ENST00000460330.1_Silent_p.T206T|PTGER3_ENST00000370932.2_Silent_p.T206T|PTGER3_ENST00000356595.4_Silent_p.T206T|PTGER3_ENST00000370924.4_Silent_p.T206T|PTGER3_ENST00000351052.5_Silent_p.T206T	NM_198719.1	NP_942012.1	P43115	PE2R3_HUMAN	prostaglandin E receptor 3 (subtype EP3)	206					cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of fever generation (GO:0031622)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|prostaglandin E receptor activity (GO:0004957)			endometrium(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25					Bimatoprost(DB00905)|Dinoprostone(DB00917)|Misoprostol(DB00929)	TGAAGCACCACGTCCCGGGCC	0.677													C|||	355	0.0708866	0.1589	0.0706	5008	,	,		15416	0.0		0.0845	False		,,,				2504	0.0112				p.T206T		Atlas-SNP	.											PTGER3_ENST00000460330,NS,carcinoma,0,5	PTGER3	246	5	0			c.G618T						scavenged	.	C	,,,,,,	692,3712	279.9+/-275.1	44,604,1554	55.0	57.0	57.0		618,618,618,618,618,618,618	-1.9	1.0	1	dbSNP_52	57	731,7869	174.5+/-224.7	37,657,3606	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTGER3	NM_001126044.1,NM_198714.1,NM_198715.2,NM_198716.1,NM_198717.1,NM_198718.1,NM_198719.1	,,,,,,	81,1261,5160	AA,AC,CC		8.5,15.713,10.9428	,,,,,,	206/391,206/391,206/389,206/375,206/366,206/419,206/391	71512643	1423,11581	2202	4300	6502	SO:0001819	synonymous_variant	5733	exon1			GCACCACGTCCCG	X83863	CCDS652.1, CCDS655.1, CCDS656.1, CCDS657.1, CCDS658.1	1p31.2	2012-08-08			ENSG00000050628	ENSG00000050628		"""GPCR / Class A : Prostanoid receptors"""	9595	protein-coding gene	gene with protein product		176806				7759114, 9073510	Standard	NM_001126044		Approved	EP3	uc001dfo.3	P43115	OTTHUMG00000009399	ENST00000306666.5:c.618G>T	1.37:g.71512643C>A		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_001126044	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Silent	SNP	ENST00000306666.5	37	CCDS657.1																																																																																			C|0.893;A|0.107	0.107	strong		0.677	PTGER3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026076.1	NM_000957	
AIRE	326	hgsc.bcm.edu	37	21	45717550	45717550	+	Silent	SNP	T	T	C	rs1133779	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45717550T>C	ENST00000291582.5	+	14	1705	c.1578T>C	c.(1576-1578)gaT>gaC	p.D526D	AIRE_ENST00000329347.4_3'UTR|AIRE_ENST00000355347.4_Silent_p.D319D|PFKL_ENST00000349048.4_5'Flank	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	526					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)	p.D526D(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		ACACCTTCGATGGCATCCTGC	0.637									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy		OREG0026249	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2656	0.530351	0.6694	0.4841	5008	,	,		14233	0.6369		0.4056	False		,,,				2504	0.3937				p.D526D		Atlas-SNP	.											AIRE,NS,lymphoid_neoplasm,0,1	AIRE	61	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1578C						PASS	.	C	,	2858,1548	479.0+/-358.4	920,1018,265	46.0	45.0	45.0		1578,987	0.5	1.0	21	dbSNP_86	45	3568,5024	625.6+/-397.7	730,2108,1458	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	1650,3126,1723	CC,CT,TT		41.527,35.1339,49.4384	,	526/546,329/349	45717550	6426,6572	2203	4296	6499	SO:0001819	synonymous_variant	326	exon14	Familial Cancer Database	APECED	CTTCGATGGCATC	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.1578T>C	21.37:g.45717550T>C		Somatic	82	0	0	933	WXS	Illumina HiSeq	Phase_I	89	57	0.640449	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.483;C|0.517	0.517	strong		0.637	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
GPANK1	7918	hgsc.bcm.edu	37	6	31632134	31632134	+	Missense_Mutation	SNP	C	C	A	rs3130618	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31632134C>A	ENST00000375906.1	-	3	806	c.122G>T	c.(121-123)cGa>cTa	p.R41L	CSNK2B_ENST00000375866.2_5'Flank|GPANK1_ENST00000375893.2_Missense_Mutation_p.R41L|GPANK1_ENST00000375895.2_Missense_Mutation_p.R41L|GPANK1_ENST00000375900.4_Missense_Mutation_p.R41L|CSNK2B_ENST00000375865.2_5'Flank|CSNK2B_ENST00000375885.4_5'Flank|Y_RNA_ENST00000364337.1_RNA|GPANK1_ENST00000375896.4_Missense_Mutation_p.R41L|CSNK2B_ENST00000375882.2_5'Flank|CSNK2B-LY6G5B-1181_ENST00000375880.2_5'Flank	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	41			R -> L (in dbSNP:rs3130618). {ECO:0000269|PubMed:14574404}.				nucleic acid binding (GO:0003676)			central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						ATAGAAAGCTCGGGCTGCAGC	0.582													C|||	668	0.133387	0.2126	0.0793	5008	,	,		16816	0.0714		0.1461	False		,,,				2504	0.1155				p.R41L		Atlas-SNP	.											GPANK1,colon,carcinoma,0,1	GPANK1	19	1	0			c.G122T	GRCh37	CM062443	GPANK1	M	rs3130618	PASS	.	C	LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG	881,3525	341.5+/-306.7	85,711,1407	45.0	50.0	48.0		122,122,122,122,122	5.2	1.0	6	dbSNP_103	48	1541,7059	288.9+/-299.0	146,1249,2905	yes	missense,missense,missense,missense,missense	GPANK1	NM_001199237.1,NM_001199238.1,NM_001199239.1,NM_001199240.1,NM_033177.3	102,102,102,102,102	231,1960,4312	AA,AC,CC		17.9186,19.9955,18.6222	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	41/357,41/357,41/357,41/357,41/357	31632134	2422,10584	2203	4300	6503	SO:0001583	missense	7918	exon3			AAAGCTCGGGCTG		CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.122G>T	6.37:g.31632134C>A	ENSP00000365071:p.Arg41Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	58	0.725	NM_001199238	A6NG25|B0UXA2|Q5SQ49	Missense_Mutation	SNP	ENST00000375906.1	37	CCDS4711.1	285	0.1304945054945055	112	0.22764227642276422	30	0.08287292817679558	33	0.057692307692307696	110	0.14511873350923482	C	16.43	3.121880	0.56613	0.199955	0.179186	ENSG00000204438	ENST00000375906;ENST00000375896;ENST00000375893;ENST00000375895;ENST00000375900;ENST00000440842;ENST00000458083;ENST00000445768;ENST00000432291;ENST00000456540	T;T;T;T;T;T;T;T	0.61392	2.66;2.66;2.66;2.66;2.66;0.79;0.82;0.11	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.59609	0.2206	L	0.34521	1.04	0.09310	P	0.999999151211	D	0.89917	1.0	D	0.85130	0.997	T	0.63225	-0.6685	9	0.51188	T	0.08	-0.4689	16.1888	0.81972	0.0:1.0:0.0:0.0	rs3130618;rs34603477;rs59584303;rs3130618	41	O95872	GPAN1_HUMAN	L	41	ENSP00000365071:R41L;ENSP00000365060:R41L;ENSP00000365057:R41L;ENSP00000365059:R41L;ENSP00000365065:R41L;ENSP00000395307:R41L;ENSP00000409349:R41L;ENSP00000395484:R41L	ENSP00000365057:R41L	R	-	2	0	GPANK1	31740113	0.989000	0.36119	0.996000	0.52242	0.994000	0.84299	3.194000	0.51005	2.415000	0.81967	0.561000	0.74099	CGA	C|0.839;A|0.161	0.161	strong		0.582	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2	NM_033177	
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 GAIIx	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		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	123	51	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	
BPIFB1	92747	hgsc.bcm.edu	37	20	31897554	31897554	+	Missense_Mutation	SNP	G	G	C	rs1999663	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:31897554G>C	ENST00000253354.1	+	16	1597	c.1436G>C	c.(1435-1437)aGc>aCc	p.S479T		NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	479			S -> T (in dbSNP:rs1999663). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										TGGAAACCCAGCTCTCCTGTC	0.522													C|||	3382	0.675319	0.8018	0.5807	5008	,	,		21096	0.7669		0.498	False		,,,				2504	0.6595				p.S479T		Atlas-SNP	.											.	.	.	.	0			c.G1436C						PASS	.	C	THR/SER	3221,1185	415.0+/-337.0	1179,863,161	90.0	77.0	81.0		1436	-1.9	0.0	20	dbSNP_92	81	4164,4436	587.6+/-392.2	1024,2116,1160	yes	missense	BPIFB1	NM_033197.2	58	2203,2979,1321	CC,CG,GG		48.4186,26.8951,43.2185	benign	479/485	31897554	7385,5621	2203	4300	6503	SO:0001583	missense	92747	exon16			AACCCAGCTCTCC	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"""BPI fold containing"""	16108	protein-coding gene	gene with protein product	"""von Ebner minor salivary gland protein"""		"""chromosome 20 open reading frame 114"""	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.1436G>C	20.37:g.31897554G>C	ENSP00000253354:p.Ser479Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	37	CCDS13218.1	1459	0.668040293040293	390	0.7926829268292683	211	0.5828729281767956	459	0.8024475524475524	399	0.5263852242744064	C	0.162	-1.080191	0.01888	0.731049	0.484186	ENSG00000125999	ENST00000253354	T	0.03468	3.92	3.77	-1.88	0.07713	.	3.103030	0.01200	N	0.007552	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.42207	-0.9465	9	0.02654	T	1	4.1796	7.3845	0.26874	0.178:0.4384:0.3836:0.0	rs1999663;rs17856250;rs52837668;rs56899864;rs1999663	479	Q8TDL5	BPIB1_HUMAN	T	479	ENSP00000253354:S479T	ENSP00000253354:S479T	S	+	2	0	BPIFB1	31361215	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.239000	0.18023	-0.594000	0.05836	-2.116000	0.00351	AGC	G|0.390;C|0.610	0.610	strong		0.522	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	
AIFM2	84883	hgsc.bcm.edu	37	10	71880858	71880858	+	Missense_Mutation	SNP	A	A	G	rs10999147	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:71880858A>G	ENST00000307864.1	-	4	617	c.404T>C	c.(403-405)aTg>aCg	p.M135T	AIFM2_ENST00000482166.1_5'Flank|AIFM2_ENST00000373248.1_Missense_Mutation_p.M135T	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	135			M -> T (in dbSNP:rs10999147).		apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						CTGCCTCACCATGTCCTCATA	0.617													A|||	465	0.0928514	0.0129	0.0576	5008	,	,		15284	0.1637		0.0835	False		,,,				2504	0.1626				p.M135T		Atlas-SNP	.											.	AIFM2	33	.	0			c.T404C						PASS	.	A	THR/MET,THR/MET	110,4296	83.9+/-122.4	1,108,2094	92.0	84.0	87.0		404,404	6.2	1.0	10	dbSNP_120	87	756,7844	180.0+/-229.1	29,698,3573	yes	missense,missense	AIFM2	NM_001198696.1,NM_032797.5	81,81	30,806,5667	GG,GA,AA		8.7907,2.4966,6.6585	benign,benign	135/374,135/374	71880858	866,12140	2203	4300	6503	SO:0001583	missense	84883	exon4			CTCACCATGTCCT	AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"""apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"""	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.404T>C	10.37:g.71880858A>G	ENSP00000312370:p.Met135Thr	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_001198696	B3KXI0|Q63Z39	Missense_Mutation	SNP	ENST00000307864.1	37	CCDS7297.1	179	0.08195970695970696	7	0.014227642276422764	23	0.06353591160220995	88	0.15384615384615385	61	0.08047493403693931	A	17.46	3.394955	0.62066	0.024966	0.087907	ENSG00000042286	ENST00000373248;ENST00000307864	T;T	0.44881	0.91;0.91	6.17	6.17	0.99709	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.213826	0.51477	D	0.000096	T	0.00241	0.0007	L	0.39397	1.21	0.22127	P	0.99934758	B	0.25235	0.121	B	0.29942	0.109	T	0.06917	-1.0800	9	0.22109	T	0.4	-38.7414	16.4957	0.84242	1.0:0.0:0.0:0.0	rs10999147;rs52808584;rs57546560;rs10999147	135	Q9BRQ8	AIFM2_HUMAN	T	135	ENSP00000362345:M135T;ENSP00000312370:M135T	ENSP00000312370:M135T	M	-	2	0	AIFM2	71550864	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.930000	0.87610	2.371000	0.80710	0.533000	0.62120	ATG	A|0.920;G|0.080	0.080	strong		0.617	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797	
OR4N4	283694	hgsc.bcm.edu	37	15	22383249	22383249	+	Missense_Mutation	SNP	G	G	A	rs112081824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:22383249G>A	ENST00000328795.4	+	1	868	c.777G>A	c.(775-777)atG>atA	p.M259I	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	259						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(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		TCATCTACATGTGCCCTTTCA	0.453													g|||	41	0.0081869	0.0	0.013	5008	,	,		29574	0.0		0.0229	False		,,,				2504	0.0092				p.M259I		Atlas-SNP	.											.	OR4N4	108	.	0			c.G777A						PASS	.	G	ILE/MET	33,4347		2,29,2159	228.0	202.0	211.0		777	-6.4	0.0	15	dbSNP_132	211	274,8250		18,238,4006	yes	missense	OR4N4	NM_001005241.2	10	20,267,6165	AA,AG,GG		3.2145,0.7534,2.3791	benign	259/317	22383249	307,12597	2190	4262	6452	SO:0001583	missense	283694	exon1			CTACATGTGCCCT	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"""GPCR / Class A : Olfactory receptors"""	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.777G>A	15.37:g.22383249G>A	ENSP00000332500:p.Met259Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	170	53	0.311765	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	22	0.010073260073260074	0	0.0	5	0.013812154696132596	0	0.0	17	0.022427440633245383	.	0.019	-1.461475	0.01062	0.007534	0.032145	ENSG00000183706	ENST00000328795	T	0.34859	1.34	3.2	-6.41	0.01938	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000178	T	0.03520	0.0101	N	0.13327	0.33	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27806	-1.0063	10	0.07644	T	0.81	-1.7405	2.6751	0.05079	0.3035:0.1655:0.4088:0.1222	.	259	Q8N0Y3	OR4N4_HUMAN	I	259	ENSP00000332500:M259I	ENSP00000332500:M259I	M	+	3	0	OR4N4	19884613	0.000000	0.05858	0.049000	0.19019	0.010000	0.07245	-5.448000	0.00121	-2.894000	0.00314	-2.355000	0.00241	ATG	G|0.983;A|0.017	0.017	strong		0.453	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
TPTE	7179	hgsc.bcm.edu	37	21	10959771	10959771	+	Missense_Mutation	SNP	A	A	T	rs111657679	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:10959771A>T	ENST00000361285.4	-	8	532	c.203T>A	c.(202-204)gTt>gAt	p.V68D	TPTE_ENST00000298232.7_Missense_Mutation_p.V50D|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Intron	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	68					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AGCATCTTCAACTTCAAACTT	0.333																																					p.V68D		Atlas-SNP	.											.	TPTE	513	.	0			c.T203A						PASS	.	A	ASP/VAL,,ASP/VAL	54,4352		0,54,2149	95.0	92.0	93.0		149,,203	-3.0	0.0	21	dbSNP_132	93	562,8038		1,560,3739	no	missense,intron,missense	TPTE	NM_199259.2,NM_199260.2,NM_199261.2	152,,152	1,614,5888	TT,TA,AA		6.5349,1.2256,4.7363	benign,,benign	50/534,,68/552	10959771	616,12390	2203	4300	6503	SO:0001583	missense	7179	exon8			TCTTCAACTTCAA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.203T>A	21.37:g.10959771A>T	ENSP00000355208:p.Val68Asp	Somatic	433	0	0		WXS	Illumina HiSeq	Phase_I	441	121	0.274376	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	64	0.029304029304029304	3	0.006097560975609756	17	0.04696132596685083	0	0.0	44	0.05804749340369393	A	4.598	0.111032	0.08831	0.012256	0.065349	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000328758	D;D	0.94931	-3.39;-3.56	1.49	-2.99	0.05497	.	0.427833	0.20668	N	0.087887	T	0.31765	0.0807	N	0.11064	0.09	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.61267	-0.7097	10	0.51188	T	0.08	-0.0112	0.0434	0.00009	0.2665:0.1846:0.2078:0.341	.	50;68	P56180-2;P56180	.;TPTE_HUMAN	D	50;68;50	ENSP00000298232:V50D;ENSP00000355208:V68D	ENSP00000298232:V50D	V	-	2	0	TPTE	9981642	0.002000	0.14202	0.000000	0.03702	0.090000	0.18270	0.045000	0.14013	-1.680000	0.01450	0.333000	0.21579	GTT	A|0.964;T|0.036	0.036	strong		0.333	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
UBAC1	10422	hgsc.bcm.edu	37	9	138831567	138831567	+	Silent	SNP	T	T	C	rs1044193	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138831567T>C	ENST00000371756.3	-	8	1132	c.915A>G	c.(913-915)aaA>aaG	p.K305K	UBAC1_ENST00000465873.1_5'UTR	NM_016172.2	NP_057256.2	Q9BSL1	UBAC1_HUMAN	UBA domain containing 1	305	UBA 2. {ECO:0000255|PROSITE- ProRule:PRU00212}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				NS(1)|biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;1.1e-06)|Epithelial(140;7.79e-06)		CTATCACCTCTTTCTCGTCGA	0.592													C|||	205	0.0409345	0.0068	0.0605	5008	,	,		20341	0.001		0.1252	False		,,,				2504	0.0276				p.K305K	NSCLC(78;973 1398 27381 29552 42415)	Atlas-SNP	.											.	UBAC1	40	.	0			c.A915G						PASS	.	C		94,4312	818.1+/-416.3	1,92,2110	340.0	264.0	290.0		915	4.3	1.0	9	dbSNP_86	290	1126,7474	767.2+/-407.6	78,970,3252	no	coding-synonymous	UBAC1	NM_016172.2		79,1062,5362	CC,CT,TT		13.093,2.1335,9.3803		305/406	138831567	1220,11786	2203	4300	6503	SO:0001819	synonymous_variant	10422	exon8			CACCTCTTTCTCG	AF176796	CCDS35177.1	9q34.3	2008-02-05	2007-04-20	2007-04-20	ENSG00000130560	ENSG00000130560			30221	protein-coding gene	gene with protein product		608129	"""ubiquitin associated domain containing 1"""	UBADC1		10857748, 8619474	Standard	NM_016172		Approved	GBDR1	uc004cgt.3	Q9BSL1	OTTHUMG00000020920	ENST00000371756.3:c.915A>G	9.37:g.138831567T>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	163	75	0.460123	NM_016172	O75500|Q9UMW7	Silent	SNP	ENST00000371756.3	37	CCDS35177.1																																																																																			T|0.917;C|0.083	0.083	strong		0.592	UBAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055034.1	NM_016172	
LRIG2	9860	hgsc.bcm.edu	37	1	113657233	113657233	+	Missense_Mutation	SNP	T	T	G	rs41296184	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:113657233T>G	ENST00000361127.5	+	15	2463	c.2265T>G	c.(2263-2265)gaT>gaG	p.D755E	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	755	Ig-like C2-type 3.				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)		TCATTGTAGATGCCGGGCTAG	0.473													T|||	89	0.0177716	0.0053	0.0101	5008	,	,		19619	0.0496		0.0099	False		,,,				2504	0.0153				p.D755E		Atlas-SNP	.											.	LRIG2	67	.	0			c.T2265G						PASS	.	T	GLU/ASP	35,4371	39.2+/-71.8	0,35,2168	139.0	129.0	132.0		2265	1.8	1.0	1	dbSNP_127	132	103,8497	56.4+/-117.6	0,103,4197	yes	missense	LRIG2	NM_014813.1	45	0,138,6365	GG,GT,TT		1.1977,0.7944,1.061	probably-damaging	755/1066	113657233	138,12868	2203	4300	6503	SO:0001583	missense	9860	exon15			TGTAGATGCCGGG	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.2265T>G	1.37:g.113657233T>G	ENSP00000355396:p.Asp755Glu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	37	CCDS30808.1	21	0.009615384615384616	0	0.0	4	0.011049723756906077	10	0.017482517482517484	7	0.009234828496042216	T	15.11	2.736885	0.49045	0.007944	0.011977	ENSG00000198799	ENST00000361127	T	0.30182	1.54	5.39	1.8	0.24995	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.10465	0.0256	N	0.17922	0.545	0.42466	D	0.992809	B	0.33379	0.41	B	0.41174	0.349	T	0.11991	-1.0565	10	0.35671	T	0.21	.	8.8436	0.35157	0.0:0.2162:0.0:0.7838	rs41296184;rs61751734	755	O94898	LRIG2_HUMAN	E	755	ENSP00000355396:D755E	ENSP00000355396:D755E	D	+	3	2	LRIG2	113458756	0.998000	0.40836	0.998000	0.56505	0.996000	0.88848	0.413000	0.21148	0.053000	0.16036	0.459000	0.35465	GAT	T|0.990;G|0.010	0.010	strong		0.473	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813	
CPA6	57094	hgsc.bcm.edu	37	8	68536470	68536470	+	Missense_Mutation	SNP	A	A	G	rs10957393	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:68536470A>G	ENST00000297770.4	-	2	348	c.133T>C	c.(133-135)Ttt>Ctt	p.F45L	CPA6_ENST00000518549.1_Missense_Mutation_p.F45L|CPA6_ENST00000297769.4_5'UTR	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	45			F -> L (in dbSNP:rs10957393).			proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(5)	26			Epithelial(68;0.04)|OV - Ovarian serous cystadenocarcinoma(28;0.0593)|all cancers(69;0.136)			TTGGGAATAAATCTTATCACT	0.299													A|||	1163	0.232228	0.3449	0.2421	5008	,	,		15219	0.0923		0.2227	False		,,,				2504	0.227				p.F45L		Atlas-SNP	.											CPA6,NS,adenoma,0,1	CPA6	69	1	0			c.T133C						PASS	.	A	LEU/PHE	1408,2996	458.2+/-351.9	217,974,1011	157.0	136.0	143.0		133	4.5	1.0	8	dbSNP_120	143	2025,6573	352.6+/-328.8	220,1585,2494	yes	missense	CPA6	NM_020361.4	22	437,2559,3505	GG,GA,AA		23.552,31.9709,26.4036	benign	45/438	68536470	3433,9569	2202	4299	6501	SO:0001583	missense	57094	exon2			GAATAAATCTTAT	AF221594	CCDS6200.1	8q12.3	2012-02-10			ENSG00000165078	ENSG00000165078			17245	protein-coding gene	gene with protein product		609562				11836249	Standard	NM_020361		Approved	CPAH	uc003xxq.4	Q8N4T0	OTTHUMG00000164575	ENST00000297770.4:c.133T>C	8.37:g.68536470A>G	ENSP00000297770:p.Phe45Leu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	37	CCDS6200.1	477	0.2184065934065934	166	0.33739837398373984	84	0.23204419889502761	61	0.10664335664335664	166	0.21899736147757257	A	12.60	1.987604	0.35036	0.319709	0.23552	ENSG00000165078	ENST00000297770;ENST00000518549	T;T	0.35789	1.29;1.29	5.42	4.54	0.55810	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.211058	0.29646	N	0.011573	T	0.00012	0.0000	N	0.02011	-0.69	0.09310	P	0.9999999999999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39272	-0.9622	9	0.30078	T	0.28	.	9.7063	0.40218	0.0986:0.0:0.9014:0.0	rs10957393;rs52833473;rs57275145;rs10957393	45;45	Q8N4T0-2;Q8N4T0	.;CBPA6_HUMAN	L	45	ENSP00000297770:F45L;ENSP00000431112:F45L	ENSP00000297770:F45L	F	-	1	0	CPA6	68699024	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	2.986000	0.49370	1.398000	0.46701	-0.242000	0.12053	TTT	A|0.750;G|0.249	0.249	strong		0.299	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361	
ICAM5	7087	hgsc.bcm.edu	37	19	10407169	10407169	+	Silent	SNP	G	G	C	rs710845	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10407169G>C	ENST00000221980.4	+	11	2715	c.2652G>C	c.(2650-2652)ctG>ctC	p.L884L		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	884					phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CCGTGTGTCTGAACGGAgcgg	0.771													C|||	2557	0.510583	0.5681	0.6455	5008	,	,		6247	0.3313		0.5895	False		,,,				2504	0.4407				p.L884L		Atlas-SNP	.											.	ICAM5	53	.	0			c.G2652C						PASS	.	C		1682,962		566,550,206	4.0	3.0	3.0		2652	0.5	1.0	19	dbSNP_86	3	2905,1749		979,947,401	no	coding-synonymous	ICAM5	NM_003259.3		1545,1497,607	CC,CG,GG		37.5806,36.3843,37.1472		884/925	10407169	4587,2711	1322	2327	3649	SO:0001819	synonymous_variant	7087	exon11			GTGTCTGAACGGA	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.2652G>C	19.37:g.10407169G>C		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	13	4	0.307692	NM_003259	Q9Y6F3	Silent	SNP	ENST00000221980.4	37	CCDS12233.1																																																																																			G|0.499;C|0.501	0.501	strong		0.771	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
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 GAIIx	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	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	67	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	
SLC5A9	200010	hgsc.bcm.edu	37	1	48695081	48695081	+	Missense_Mutation	SNP	G	G	A	rs212989	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:48695081G>A	ENST00000438567.2	+	4	506	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	SLC5A9_ENST00000420136.2_Missense_Mutation_p.V145M|RP5-1024N4.4_ENST00000606809.1_RNA|SLC5A9_ENST00000533824.1_Missense_Mutation_p.V173M|SLC5A9_ENST00000236495.5_Missense_Mutation_p.V177M	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	152			V -> M (in dbSNP:rs212989).		sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						GAGGATCCAGGTGTACATGTC	0.527													G|||	848	0.169329	0.3109	0.1225	5008	,	,		18036	0.0109		0.161	False		,,,				2504	0.183				p.V177M		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G529A						PASS	.	G	MET/VAL,MET/VAL	1337,3069	447.5+/-348.4	212,913,1078	180.0	158.0	166.0		454,529	1.7	1.0	1	dbSNP_79	166	1348,7252	265.2+/-286.0	102,1144,3054	yes	missense,missense	SLC5A9	NM_001011547.2,NM_001135181.1	21,21	314,2057,4132	AA,AG,GG		15.6744,30.345,20.6443	benign,benign	152/682,177/707	48695081	2685,10321	2203	4300	6503	SO:0001583	missense	200010	exon5			ATCCAGGTGTACA	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.454G>A	1.37:g.48695081G>A	ENSP00000401730:p.Val152Met	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	329	0.15064102564102563	155	0.3150406504065041	48	0.13259668508287292	3	0.005244755244755245	123	0.16226912928759896	G	12.97	2.096458	0.36952	0.30345	0.156744	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495;ENST00000420136	D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49	5.74	1.73	0.24493	.	0.106808	0.64402	D	0.000006	T	0.00012	0.0000	N	0.21583	0.68	0.30894	P	0.730067	B;B;B	0.23990	0.095;0.011;0.025	B;B;B	0.30105	0.111;0.026;0.062	T	0.05209	-1.0899	9	0.35671	T	0.21	.	3.5787	0.07943	0.3682:0.0:0.4666:0.1652	rs212989;rs559015;rs58564219;rs212989	173;152;177	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	M	173;152;177;145	ENSP00000431900:V173M;ENSP00000401730:V152M;ENSP00000236495:V177M;ENSP00000408881:V145M	ENSP00000236495:V177M	V	+	1	0	SLC5A9	48467668	0.494000	0.26043	1.000000	0.80357	0.999000	0.98932	0.864000	0.27926	0.439000	0.26476	0.655000	0.94253	GTG	G|0.805;A|0.195	0.195	strong		0.527	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
ZNF30	90075	hgsc.bcm.edu	37	19	35434582	35434582	+	Missense_Mutation	SNP	G	G	T	rs142299823	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35434582G>T	ENST00000601142.1	+	5	949	c.712G>T	c.(712-714)Ggg>Tgg	p.G238W	ZNF30_ENST00000426813.2_Missense_Mutation_p.G157W|ZNF30_ENST00000303586.7_Missense_Mutation_p.G239W|ZNF30_ENST00000439785.1_Missense_Mutation_p.G239W|ZNF30_ENST00000601957.1_3'UTR			P17039	ZNF30_HUMAN	zinc finger protein 30	238				G -> W (in Ref. 2; CAE45802). {ECO:0000305}.	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)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		CGGGGAATGTGGGAAAGCTTT	0.433													G|||	34	0.00678914	0.0008	0.0115	5008	,	,		21880	0.0		0.0229	False		,,,				2504	0.002				p.G239W		Atlas-SNP	.											.	ZNF30	44	.	0			c.G715T						PASS	.	G	TRP/GLY,TRP/GLY,TRP/GLY	16,4142		0,16,2063	40.0	45.0	43.0		715,715,712	2.1	0.8	19	dbSNP_134	43	234,8208		6,222,3993	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	184,184,184	6,238,6056	TT,TG,GG		2.7719,0.3848,1.9841	probably-damaging,probably-damaging,probably-damaging	239/625,239/625,238/624	35434582	250,12350	2079	4221	6300	SO:0001583	missense	90075	exon5			GAATGTGGGAAAG	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.712G>T	19.37:g.35434582G>T	ENSP00000469954:p.Gly238Trp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	22	0.010073260073260074	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	17	0.022427440633245383	G	17.77	3.471586	0.63737	0.003848	0.027719	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813	T;T	0.03717	3.83;3.83	2.12	2.12	0.27331	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09468	0.0233	H	0.96748	3.875	0.34652	D	0.721748	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.42649	-0.9439	9	0.87932	D	0	.	9.8645	0.41134	0.0:0.0:1.0:0.0	.	239;238	P17039-2;P17039	.;ZNF30_HUMAN	W	239;238;157	ENSP00000403441:G239W;ENSP00000416457:G157W	ENSP00000303889:G238W	G	+	1	0	ZNF30	40126422	1.000000	0.71417	0.826000	0.32828	0.181000	0.23173	3.863000	0.56016	1.178000	0.42870	0.404000	0.27445	GGG	G|0.983;T|0.017	0.017	strong		0.433	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
ASPM	259266	hgsc.bcm.edu	37	1	197072420	197072420	+	Silent	SNP	T	T	C	rs41310925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:197072420T>C	ENST00000367409.4	-	18	6217	c.5961A>G	c.(5959-5961)caA>caG	p.Q1987Q	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1987	IQ 13. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TCCACTTCTTTTGTTGCACAT	0.333													t|||	1067	0.213059	0.0386	0.2262	5008	,	,		21160	0.1637		0.4115	False		,,,				2504	0.2863				p.Q1987Q		Atlas-SNP	.											.	ASPM	444	.	0			c.A5961G						PASS	.		,	440,3966	211.2+/-231.4	24,392,1787	147.0	147.0	147.0		,5961	-8.9	0.0	1	dbSNP_127	147	3738,4858	529.5+/-381.6	817,2104,1377	no	intron,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	841,2496,3164	CC,CT,TT		43.4853,9.9864,32.1335	,	,1987/3478	197072420	4178,8824	2203	4298	6501	SO:0001819	synonymous_variant	259266	exon18			CTTCTTTTGTTGC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.5961A>G	1.37:g.197072420T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	179	178	0.994413	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			T|0.699;C|0.301	0.301	strong		0.333	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964299	37964299	+	Silent	SNP	C	C	G	rs2281098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:37964299C>G	ENST00000249014.4	+	3	1068	c.648C>G	c.(646-648)ctC>ctG	p.L216L		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	216					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					TCATGAGCCTCCCAGAAGCCC	0.662													C|||	2300	0.459265	0.3154	0.6297	5008	,	,		11542	0.3204		0.5626	False		,,,				2504	0.5695				p.L216L		Atlas-SNP	.											.	CDC42EP1	53	.	0			c.C648G						PASS	.	C		1510,2894		282,946,974	33.0	36.0	35.0		648	-0.5	1.0	22	dbSNP_100	35	4908,3690		1434,2040,825	no	coding-synonymous	CDC42EP1	NM_152243.2		1716,2986,1799	GG,GC,CC		42.917,34.287,49.3616		216/392	37964299	6418,6584	2202	4299	6501	SO:0001819	synonymous_variant	11135	exon3			GAGCCTCCCAGAA	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.648C>G	22.37:g.37964299C>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_152243	A8K825|Q96GN1	Silent	SNP	ENST00000249014.4	37	CCDS13949.1																																																																																			C|0.541;G|0.459	0.459	strong		0.662	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
PEAK1	79834	hgsc.bcm.edu	37	15	77472871	77472871	+	Silent	SNP	G	G	A	rs10519162	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:77472871G>A	ENST00000560626.2	-	4	1873	c.1398C>T	c.(1396-1398)aaC>aaT	p.N466N	PEAK1_ENST00000312493.4_Silent_p.N466N|PEAK1_ENST00000558305.1_Silent_p.N466N			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	466					cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCTGTTCCAGGTTCACAACTC	0.498													A|||	288	0.057508	0.0522	0.1225	5008	,	,		17870	0.0139		0.0746	False		,,,				2504	0.046				p.N466N		Atlas-SNP	.											.	.	.	.	0			c.C1398T						PASS	.	A		186,3878		4,178,1850	134.0	135.0	135.0		1398	-3.8	0.6	15	dbSNP_119	135	796,7596		49,698,3449	no	coding-synonymous	PEAK1	NM_024776.3		53,876,5299	AA,AG,GG		9.4852,4.5768,7.8838		466/1747	77472871	982,11474	2032	4196	6228	SO:0001819	synonymous_variant	0	exon5			TTCCAGGTTCACA		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.1398C>T	15.37:g.77472871G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	180	71	0.394444	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Silent	SNP	ENST00000560626.2	37	CCDS42062.1																																																																																			G|0.935;A|0.065	0.065	strong		0.498	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
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 GAIIx	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_ENST00000605860.1_Missense_Mutation_p.R357W|UPP2_ENST00000409859.4_Missense_Mutation_p.R357W|UPP2-IT1_ENST00000439185.1_RNA|UPP2_ENST00000460456.1_3'UTR	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	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	91	20	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	
SAMD12	401474	hgsc.bcm.edu	37	8	119452073	119452073	+	Missense_Mutation	SNP	G	G	A	rs117020479	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:119452073G>A	ENST00000314727.4	-	3	456	c.320C>T	c.(319-321)aCt>aTt	p.T107I	SAMD12_ENST00000409003.4_Missense_Mutation_p.T107I	NM_207506.2	NP_997389.2	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12	107	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			TACTTTACCAGTTATGTCATG	0.438													G|||	8	0.00159744	0.0	0.0014	5008	,	,		21162	0.0		0.007	False		,,,				2504	0.0				p.T107I		Atlas-SNP	.											.	SAMD12	24	.	0			c.C320T						PASS	.	G	ILE/THR,ILE/THR	2,4404	6.2+/-15.9	0,2,2201	237.0	201.0	213.0		320,320	5.7	1.0	8	dbSNP_132	213	57,8543	35.9+/-90.5	0,57,4243	yes	missense,missense	SAMD12	NM_001101676.1,NM_207506.2	89,89	0,59,6444	AA,AG,GG		0.6628,0.0454,0.4536	probably-damaging,probably-damaging	107/162,107/202	119452073	59,12947	2203	4300	6503	SO:0001583	missense	401474	exon3			TTACCAGTTATGT	AK096777	CCDS6325.1, CCDS47913.1	8q24.12	2013-01-10			ENSG00000177570	ENSG00000177570		"""Sterile alpha motif (SAM) domain containing"""	31750	protein-coding gene	gene with protein product							Standard	NM_207506		Approved	FLJ39458	uc003yom.2	Q8N8I0	OTTHUMG00000059817	ENST00000314727.4:c.320C>T	8.37:g.119452073G>A	ENSP00000314173:p.Thr107Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_207506	Q0P502	Missense_Mutation	SNP	ENST00000314727.4	37	CCDS6325.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	27.2	4.810354	0.90707	4.54E-4	0.006628	ENSG00000177570	ENST00000409003;ENST00000524796;ENST00000314727;ENST00000526328	T;T;T;T	0.34275	1.37;1.37;1.37;1.37	5.68	5.68	0.88126	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.85682	D	0.000000	T	0.57110	0.2031	M	0.80616	2.505	0.58432	D	0.999997	D;D	0.89917	0.999;1.0	D;D	0.97110	0.995;1.0	T	0.62431	-0.6856	9	.	.	.	-13.0268	19.778	0.96402	0.0:0.0:1.0:0.0	.	107;107	B8ZZB7;Q8N8I0	.;SAM12_HUMAN	I	107;99;107;107	ENSP00000387133:T107I;ENSP00000435927:T99I;ENSP00000314173:T107I;ENSP00000431360:T107I	.	T	-	2	0	SAMD12	119521254	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.475000	0.97721	2.677000	0.91161	0.561000	0.74099	ACT	G|0.997;A|0.003	0.003	strong		0.438	SAMD12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132989.3	NM_207506	
SUSD2	56241	hgsc.bcm.edu	37	22	24581207	24581207	+	Silent	SNP	C	C	T	rs3752497	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:24581207C>T	ENST00000358321.3	+	6	1189	c.928C>T	c.(928-930)Ctg>Ttg	p.L310L		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	310	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						CCTGGAGGAGCTGCCGGACTG	0.672													c|||	483	0.0964457	0.1044	0.1124	5008	,	,		15550	0.0764		0.0606	False		,,,				2504	0.1319				p.L310L		Atlas-SNP	.											.	SUSD2	68	.	0			c.C928T						PASS	.	C		476,3930	209.2+/-230.0	22,432,1749	26.0	26.0	26.0		928	0.6	1.0	22	dbSNP_107	26	539,8061	143.1+/-199.2	16,507,3777	no	coding-synonymous	SUSD2	NM_019601.3		38,939,5526	TT,TC,CC		6.2674,10.8034,7.8041		310/823	24581207	1015,11991	2203	4300	6503	SO:0001819	synonymous_variant	56241	exon6			GAGGAGCTGCCGG	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.928C>T	22.37:g.24581207C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_019601	Q9H5Y6	Silent	SNP	ENST00000358321.3	37	CCDS13824.1																																																																																			C|0.922;T|0.078	0.078	strong		0.672	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601	
MUT	4594	hgsc.bcm.edu	37	6	49412433	49412433	+	Missense_Mutation	SNP	C	C	T	rs1141321	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:49412433C>T	ENST00000274813.3	-	9	1722	c.1595G>A	c.(1594-1596)cGt>cAt	p.R532H		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	532			R -> H (in dbSNP:rs1141321). {ECO:0000269|PubMed:16281286, ECO:0000269|PubMed:1980486, ECO:0000269|PubMed:2567699, ECO:0000269|PubMed:7912889}.		cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AGCAAGACAACGTTCAGCCAA	0.428													C|||	1330	0.265575	0.174	0.2104	5008	,	,		16274	0.2063		0.331	False		,,,				2504	0.4223				p.R532H		Atlas-SNP	.											.	MUT	70	.	0			c.G1595A						PASS	.	C	HIS/ARG	929,3477	352.6+/-311.8	88,753,1362	163.0	155.0	158.0		1595	1.4	0.1	6	dbSNP_86	158	3148,5452	479.1+/-370.0	578,1992,1730	yes	missense	MUT	NM_000255.3	29	666,2745,3092	TT,TC,CC		36.6047,21.0849,31.3471	possibly-damaging	532/751	49412433	4077,8929	2203	4300	6503	SO:0001583	missense	4594	exon9			AGACAACGTTCAG		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"""methylmalonyl Coenzyme A mutase"""			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1595G>A	6.37:g.49412433C>T	ENSP00000274813:p.Arg532His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	48	27	0.5625	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	37	CCDS4924.1	573	0.2623626373626374	94	0.1910569105691057	83	0.2292817679558011	112	0.1958041958041958	284	0.37467018469656993	C	8.081	0.772374	0.16051	0.210849	0.366047	ENSG00000146085	ENST00000274813	D	0.98280	-4.84	5.31	1.44	0.22558	Cobalamin (vitamin B12)-dependent enzyme, catalytic (1);Methylmalonyl-CoA mutase, alpha/beta chain, catalytic (1);Methylmalonyl-CoA mutase, alpha chain, catalytic (1);	0.336740	0.30028	N	0.010596	D	0.95739	0.8614	M	0.78916	2.43	0.80722	P	0.0	B	0.28850	0.225	B	0.35931	0.214	D	0.92245	0.5804	9	0.44086	T	0.13	-7.7706	9.9771	0.41791	0.0:0.5716:0.0:0.4284	rs1141321;rs2229386;rs3205245;rs9473558;rs17246003;rs17405002;rs56630024;rs9473558	532	P22033	MUTA_HUMAN	H	532	ENSP00000274813:R532H	ENSP00000274813:R532H	R	-	2	0	MUT	49520392	0.003000	0.15002	0.070000	0.20053	0.139000	0.21198	-0.018000	0.12568	0.310000	0.22990	-0.237000	0.12165	CGT	T|0.242;G|0.135;C|0.582;A|0.041	0.242	strong		0.428	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
DYRK4	8798	hgsc.bcm.edu	37	12	4705317	4705317	+	Silent	SNP	C	C	T	rs3741925|rs17845948	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4705317C>T	ENST00000540757.2	+	5	445	c.285C>T	c.(283-285)gtC>gtT	p.V95V	DYRK4_ENST00000010132.5_Silent_p.V95V|DYRK4_ENST00000543431.1_Silent_p.V95V	NM_001282285.1|NM_001282286.1|NM_003845.1	NP_001269214.1|NP_001269215.1|NP_003836.1	Q9NR20	DYRK4_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 4	95			V -> I. {ECO:0000269|PubMed:11062477}.			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27			Colorectal(7;0.103)			TTCCACAGGTCCTGCATGATC	0.552													C|||	1183	0.236222	0.1044	0.2867	5008	,	,		19972	0.3135		0.2992	False		,,,				2504	0.2342				p.V95V		Atlas-SNP	.											.	DYRK4	75	.	0			c.C285T						PASS	.	C		518,3888	239.3+/-250.5	32,454,1717	120.0	125.0	123.0		285	1.7	1.0	12	dbSNP_107	123	2440,6160	404.9+/-348.3	366,1708,2226	no	coding-synonymous	DYRK4	NM_003845.1		398,2162,3943	TT,TC,CC		28.3721,11.7567,22.7433		95/521	4705317	2958,10048	2203	4300	6503	SO:0001819	synonymous_variant	8798	exon5			ACAGGTCCTGCAT	Y09305	CCDS8530.1	12p13.32	2014-09-11			ENSG00000010219	ENSG00000010219			3095	protein-coding gene	gene with protein product		609181				9748265	Standard	NM_003845		Approved		uc001qmx.3	Q9NR20	OTTHUMG00000168204	ENST00000540757.2:c.285C>T	12.37:g.4705317C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_003845	A8K8F7|Q8NEF2|Q92631	Silent	SNP	ENST00000540757.2	37	CCDS8530.1																																																																																			C|0.758;T|0.242	0.242	strong		0.552	DYRK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398780.2		
BOLA1	51027	hgsc.bcm.edu	37	1	149871905	149871905	+	Missense_Mutation	SNP	G	G	C	rs1044808	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:149871905G>C	ENST00000369153.2	+	3	957	c.293G>C	c.(292-294)gGa>gCa	p.G98A	BOLA1_ENST00000369150.1_Missense_Mutation_p.G98A|BOLA1_ENST00000369152.5_Missense_Mutation_p.G98A|BOLA1_ENST00000476344.1_3'UTR			Q9Y3E2	BOLA1_HUMAN	bolA family member 1	98			G -> A (in dbSNP:rs1044808).			extracellular region (GO:0005576)|mitochondrion (GO:0005739)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	10	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GAGGAGCTGGGAGGTCCGGTC	0.662													C|||	116	0.0231629	0.0008	0.0288	5008	,	,		13942	0.0		0.0865	False		,,,				2504	0.0082				p.G98A		Atlas-SNP	.											.	BOLA1	24	.	0			c.G293C						PASS	.	C	ALA/GLY	57,4349	792.1+/-415.1	0,57,2146	30.0	31.0	31.0		293	5.5	0.9	1	dbSNP_86	31	646,7954	763.9+/-407.6	33,580,3687	no	missense	BOLA1	NM_016074.3	60	33,637,5833	CC,CG,GG		7.5116,1.2937,5.4052	benign	98/138	149871905	703,12303	2203	4300	6503	SO:0001583	missense	51027	exon2			AGCTGGGAGGTCC	AF151901	CCDS939.1	1q21	2013-09-02	2013-09-02		ENSG00000178096	ENSG00000178096			24263	protein-coding gene	gene with protein product		613181	"""bolA-like 1 (E. coli)"", ""bolA homolog 1 (E. coli)"""			14718656	Standard	NM_016074		Approved	CGI-143	uc001etf.3	Q9Y3E2	OTTHUMG00000012087	ENST00000369153.2:c.293G>C	1.37:g.149871905G>C	ENSP00000358149:p.Gly98Ala	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_016074	B2R7K2|D3DUZ4|Q5QNY0	Missense_Mutation	SNP	ENST00000369153.2	37	CCDS939.1	88	0.040293040293040296	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	75	0.09894459102902374	C	1.110	-0.658420	0.03454	0.012937	0.075116	ENSG00000178096	ENST00000369153;ENST00000369152;ENST00000369150	T;T;T	0.61040	0.14;0.14;0.14	5.48	5.48	0.80851	.	0.117392	0.64402	N	0.000017	T	0.08537	0.0212	N	0.00869	-1.13	0.20074	N	0.999938	B	0.02656	0.0	B	0.04013	0.001	T	0.24621	-1.0155	10	0.02654	T	1	-24.8322	14.5927	0.68378	0.0:0.8529:0.1471:0.0	rs1044808;rs3170700;rs52795365;rs1044808	98	Q9Y3E2	BOLA1_HUMAN	A	98	ENSP00000358149:G98A;ENSP00000358148:G98A;ENSP00000358146:G98A	ENSP00000358146:G98A	G	+	2	0	BOLA1	148138529	1.000000	0.71417	0.945000	0.38365	0.017000	0.09413	4.116000	0.57871	1.468000	0.48064	-0.216000	0.12614	GGA	G|0.951;C|0.049	0.049	strong		0.662	BOLA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033443.2	NM_016074	
PTGIS	5740	hgsc.bcm.edu	37	20	48129706	48129706	+	Silent	SNP	G	G	T	rs5629	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:48129706G>T	ENST00000244043.4	-	8	1146	c.1117C>A	c.(1117-1119)Cga>Aga	p.R373R	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	373					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	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 (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	TTGAATTCTCGCCCGTCTGCC	0.602													G|||	1103	0.220248	0.1248	0.2723	5008	,	,		16672	0.2321		0.2604	False		,,,				2504	0.2587				p.R373R		Atlas-SNP	.											PTGIS,colon,carcinoma,+1,2	PTGIS	60	2	0			c.C1117A						PASS	.	G		582,3824	257.4+/-261.8	38,506,1659	101.0	90.0	94.0		1117	2.6	1.0	20	dbSNP_52	94	2247,6353	380.0+/-339.5	285,1677,2338	no	coding-synonymous	PTGIS	NM_000961.3		323,2183,3997	TT,TG,GG		26.1279,13.2093,21.7515		373/501	48129706	2829,10177	2203	4300	6503	SO:0001819	synonymous_variant	5740	exon8			ATTCTCGCCCGTC		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.1117C>A	20.37:g.48129706G>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																			G|0.782;T|0.218	0.218	strong		0.602	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
FAM47E	100129583	hgsc.bcm.edu	37	4	77192838	77192838	+	Missense_Mutation	SNP	A	A	C	rs3733251	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:77192838A>C	ENST00000424749.2	+	5	793	c.787A>C	c.(787-789)Aag>Cag	p.K263Q	FAM47E_ENST00000510197.1_Missense_Mutation_p.K165Q|FAM47E_ENST00000339906.6_Missense_Mutation_p.K165Q|FAM47E_ENST00000515604.1_Missense_Mutation_p.K263Q|FAM47E-STBD1_ENST00000539752.1_5'UTR	NM_001136570.2	NP_001130042.1	Q6ZV65	FA47E_HUMAN	family with sequence similarity 47, member E	263																	TCTGGAGCTAAAGCGTAGTGT	0.463													A|||	729	0.145567	0.2837	0.0937	5008	,	,		18076	0.0526		0.1571	False		,,,				2504	0.0798				p.K263Q		Atlas-SNP	.											.	.	.	.	0			c.A787C						PASS	.	A	GLN/LYS	387,997		53,281,358	124.0	105.0	111.0		787	2.1	0.0	4	dbSNP_107	111	561,2621		56,449,1086	yes	missense	FAM47E	NM_001136570.2	53	109,730,1444	CC,CA,AA		17.6304,27.9624,20.7622	probably-damaging	263/394	77192838	948,3618	692	1591	2283	SO:0001583	missense	0	exon5			GAGCTAAAGCGTA	AC034139, AK124936, CR591456, CR627383	CCDS47081.1, CCDS58907.1	4q21.1	2013-04-23			ENSG00000189157	ENSG00000189157			34343	protein-coding gene	gene with protein product	"""similar to genethonin 1"""						Standard	NM_001136570		Approved	FLJ42946, LOC100129583	uc003hjx.3	Q6ZV65	OTTHUMG00000185390	ENST00000424749.2:c.787A>C	4.37:g.77192838A>C	ENSP00000409423:p.Lys263Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001242939	D6R8Y4	Missense_Mutation	SNP	ENST00000424749.2	37	CCDS47081.1	322	0.14743589743589744	134	0.27235772357723576	41	0.1132596685082873	35	0.06118881118881119	112	0.14775725593667546	A	15.01	2.707469	0.48412	0.279624	0.176304	ENSG00000189157	ENST00000510197;ENST00000339906;ENST00000515604;ENST00000509377;ENST00000424749;ENST00000514140	T;T;T;T	0.48522	0.81;0.81;1.4;1.4	4.59	2.1	0.27182	.	0.604497	0.13746	N	0.365599	T	0.00012	0.0000	L	0.55103	1.725	0.58432	P	2.9999999999752447E-6	P;D;P;P;P	0.64830	0.949;0.994;0.879;0.879;0.949	P;D;P;P;P	0.64410	0.738;0.925;0.656;0.656;0.575	T	0.07654	-1.0761	9	0.46703	T	0.11	-8.3688	8.9641	0.35865	0.5868:0.4132:0.0:0.0	rs3733251;rs52792112;rs60191153;rs3733251	110;263;263;263;165	D6RCS4;Q6ZV65-1;Q6ZV65;C9JTC9;Q6ZV65-2	.;.;FA47E_HUMAN;.;.	Q	165;165;263;110;263;71	ENSP00000422262:K165Q;ENSP00000340401:K165Q;ENSP00000422067:K263Q;ENSP00000409423:K263Q	ENSP00000340401:K165Q	K	+	1	0	FAM47E	77411862	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.961000	0.29267	0.354000	0.24105	-0.313000	0.08912	AAG	A|0.845;C|0.155	0.155	strong		0.463	FAM47E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362528.2	NM_001136570	
GPRC5A	9052	hgsc.bcm.edu	37	12	13061294	13061294	+	Silent	SNP	C	C	T	rs2075288	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:13061294C>T	ENST00000014914.5	+	2	1001	c.111C>T	c.(109-111)gcC>gcT	p.A37A	GPRC5A_ENST00000542056.1_Intron	NM_003979.3	NP_003970.1	Q8NFJ5	RAI3_HUMAN	G protein-coupled receptor, class C, group 5, member A	37					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	18		Prostate(47;0.141)		BRCA - Breast invasive adenocarcinoma(232;0.0708)	Tretinoin(DB00755)	TGGCCACAGCCGGGGTTGTGA	0.547													C|||	1811	0.361621	0.0401	0.4481	5008	,	,		20094	0.7173		0.331	False		,,,				2504	0.3998				p.A37A		Atlas-SNP	.											.	GPRC5A	38	.	0			c.C111T						PASS	.	C		323,4083	171.6+/-201.8	12,299,1892	94.0	87.0	89.0		111	-10.7	0.0	12	dbSNP_96	89	2406,6194	401.0+/-347.0	336,1734,2230	no	coding-synonymous	GPRC5A	NM_003979.3		348,2033,4122	TT,TC,CC		27.9767,7.3309,20.9826		37/358	13061294	2729,10277	2203	4300	6503	SO:0001819	synonymous_variant	9052	exon2			CACAGCCGGGGTT	AF095448	CCDS8657.1	12p13-p12.3	2014-01-30	2014-01-30	2005-05-03		ENSG00000013588		"""GPCR / Class C : Orphans"""	9836	protein-coding gene	gene with protein product		604138	"""retinoic acid induced 3"", ""G protein-coupled receptor, family C, group 5, member A"""	RAI3, GPCR5A		9857033	Standard	NM_003979		Approved	RAIG1	uc001rba.3	Q8NFJ5		ENST00000014914.5:c.111C>T	12.37:g.13061294C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_003979	B3KV45|O95357	Silent	SNP	ENST00000014914.5	37	CCDS8657.1																																																																																			C|0.726;T|0.274	0.274	strong		0.547	GPRC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400682.1		
NDFIP2	54602	hgsc.bcm.edu	37	13	80095030	80095030	+	Missense_Mutation	SNP	C	C	T	rs11549502	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:80095030C>T	ENST00000218652.7	+	2	459	c.407C>T	c.(406-408)gCg>gTg	p.A136V	NDFIP2_ENST00000494647.1_3'UTR	NM_001161407.1|NM_019080.2	NP_001154879.1|NP_061953.2	Q9NV92	NFIP2_HUMAN	Nedd4 family interacting protein 2	136			A -> V (in dbSNP:rs11549502). {ECO:0000269|PubMed:10574461, ECO:0000269|PubMed:12761501, ECO:0000269|PubMed:15489334}.		negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of transporter activity (GO:0032410)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			NS(1)|breast(1)|endometrium(2)|kidney(3)|lung(3)|ovary(2)|prostate(1)|skin(1)	14		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0196)		GTGCAGGCTGCGTCTTCAGCA	0.443													C|||	307	0.0613019	0.0287	0.0749	5008	,	,		15400	0.0		0.1223	False		,,,				2504	0.0961				p.A136V		Atlas-SNP	.											NDFIP2,NS,carcinoma,-1,1	NDFIP2	23	1	0			c.C407T						PASS	.	C	VAL/ALA,VAL/ALA	211,4195	130.2+/-166.9	7,197,1999	102.0	92.0	95.0		407,407	1.9	0.0	13	dbSNP_120	95	1175,7425	239.6+/-270.6	80,1015,3205	yes	missense,missense	NDFIP2	NM_001161407.1,NM_019080.2	64,64	87,1212,5204	TT,TC,CC		13.6628,4.7889,10.6566	benign,benign	136/317,136/337	80095030	1386,11620	2203	4300	6503	SO:0001583	missense	54602	exon2			AGGCTGCGTCTTC	AB032991	CCDS31998.1	13q22.1	2011-05-18			ENSG00000102471	ENSG00000102471			18537	protein-coding gene	gene with protein product		610041				10574461, 12050153	Standard	NM_019080		Approved	KIAA1165, N4wbp5a	uc001vlf.3	Q9NV92	OTTHUMG00000017136	ENST00000218652.7:c.407C>T	13.37:g.80095030C>T	ENSP00000218652:p.Ala136Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	160	82	0.5125	NM_019080	Q7Z2H3|Q7Z428|Q8TAR3|Q9ULQ5	Missense_Mutation	SNP	ENST00000218652.7	37	CCDS31998.1	149	0.06822344322344322	17	0.034552845528455285	35	0.09668508287292818	0	0.0	97	0.1279683377308707	C	9.329	1.059920	0.19987	0.047889	0.136628	ENSG00000102471	ENST00000218652;ENST00000487865	T;T	0.33654	1.4;1.46	5.75	1.86	0.25419	.	0.719210	0.14146	N	0.338351	T	0.00178	0.0005	L	0.43152	1.355	0.80722	P	0.0	B;P	0.34892	0.24;0.474	B;B	0.23716	0.048;0.038	T	0.07597	-1.0764	9	0.35671	T	0.21	4.0E-4	7.5368	0.27714	0.0:0.5994:0.2558:0.1448	rs11549502;rs17852355;rs52798056;rs11549502	42;136	B4DGY6;Q9NV92	.;NFIP2_HUMAN	V	136;53	ENSP00000218652:A136V;ENSP00000419200:A53V	ENSP00000218652:A136V	A	+	2	0	NDFIP2	78993031	0.087000	0.21565	0.001000	0.08648	0.012000	0.07955	2.041000	0.41213	0.335000	0.23614	0.655000	0.94253	GCG	C|0.910;G|0.000;T|0.090	0.090	strong		0.443	NDFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045380.2		
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 GAIIx	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	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	18	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	
MANBA	4126	hgsc.bcm.edu	37	4	103611845	103611845	+	Missense_Mutation	SNP	C	C	T	rs227368	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:103611845C>T	ENST00000226578.4	-	6	856	c.757G>A	c.(757-759)Gta>Ata	p.V253I	MANBA_ENST00000505239.1_Missense_Mutation_p.V196I	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	253			V -> I (in dbSNP:rs227368). {ECO:0000269|PubMed:9384606}.|V -> L (in dbSNP:rs227368).		cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		GGGATGGCTACGATCACTTGA	0.393													C|||	1886	0.376597	0.1195	0.3545	5008	,	,		12527	0.4732		0.497	False		,,,				2504	0.5164				p.V253I		Atlas-SNP	.											.	MANBA	78	.	0			c.G757A						PASS	.	C	ILE/VAL	929,3477	354.1+/-312.5	107,715,1381	271.0	229.0	243.0		757	1.3	0.0	4	dbSNP_79	243	4081,4519	560.9+/-387.7	967,2147,1186	yes	missense	MANBA	NM_005908.3	29	1074,2862,2567	TT,TC,CC		47.4535,21.0849,38.5207	benign	253/880	103611845	5010,7996	2203	4300	6503	SO:0001583	missense	4126	exon6			TGGCTACGATCAC		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.757G>A	4.37:g.103611845C>T	ENSP00000226578:p.Val253Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	865	0.39606227106227104	58	0.11788617886178862	137	0.3784530386740331	288	0.5034965034965035	382	0.503957783641161	C	7.365	0.625609	0.14257	0.210849	0.474535	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.55760	0.5;0.5	4.93	1.29	0.21616	.	0.358272	0.29342	N	0.012434	T	0.00012	0.0000	L	0.37800	1.135	0.48830	P	2.8799999999995496E-4	B;B	0.19583	0.037;0.016	B;B	0.08055	0.003;0.003	T	0.48536	-0.9027	9	0.25751	T	0.34	-10.9971	8.9216	0.35615	0.0:0.702:0.0:0.298	rs227368;rs3912789;rs52818263;rs58634559;rs227368	196;253	E9PFW2;O00462	.;MANBA_HUMAN	I	253;196	ENSP00000226578:V253I;ENSP00000427322:V196I	ENSP00000226578:V253I	V	-	1	0	MANBA	103830893	0.000000	0.05858	0.007000	0.13788	0.915000	0.54546	-0.243000	0.08915	0.016000	0.14998	-0.143000	0.13931	GTA	T|0.377;G|0.002;C|0.617;A|0.004	0.377	strong		0.393	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
SLC14A2	8170	hgsc.bcm.edu	37	18	43262359	43262359	+	Missense_Mutation	SNP	G	G	A	rs3745009	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:43262359G>A	ENST00000255226.6	+	20	3454	c.2638G>A	c.(2638-2640)Gcc>Acc	p.A880T	SLC14A2_ENST00000589658.1_Missense_Mutation_p.A357T|RP11-116O18.3_ENST00000589510.1_RNA|SLC14A2_ENST00000586448.1_Missense_Mutation_p.A880T	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	880			A -> T (in dbSNP:rs3745009). {ECO:0000269|PubMed:15489334}.		transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)	p.A880T(1)		NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAATAACCCCGCCATCTACAA	0.527													G|||	2142	0.427716	0.4024	0.3761	5008	,	,		19225	0.3869		0.4404	False		,,,				2504	0.5276				p.A880T		Atlas-SNP	.											SLC14A2,NS,carcinoma,0,2	SLC14A2	121	2	1	Substitution - Missense(1)	prostate(1)	c.G2638A	GRCh37	CM013794	SLC14A2	M	rs3745009	PASS	.	G	THR/ALA,THR/ALA	1720,2686	517.8+/-369.5	354,1012,837	271.0	262.0	265.0		2638,2638	5.1	1.0	18	dbSNP_107	265	3870,4730	544.3+/-384.6	862,2146,1292	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	58,58	1216,3158,2129	AA,AG,GG		45.0,39.0377,42.9802	benign,benign	880/921,880/921	43262359	5590,7416	2203	4300	6503	SO:0001583	missense	8170	exon21			AACCCCGCCATCT	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.2638G>A	18.37:g.43262359G>A	ENSP00000255226:p.Ala880Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	161	76	0.47205	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	880	0.40293040293040294	196	0.3983739837398374	127	0.35082872928176795	223	0.38986013986013984	334	0.44063324538258575	G	15.21	2.766981	0.49574	0.390377	0.45	ENSG00000132874	ENST00000255226	T	0.51071	0.72	5.14	5.14	0.70334	.	0.110360	0.39687	N	0.001291	T	0.00012	0.0000	L	0.48877	1.53	0.09310	P	0.9999999999999103	B	0.16396	0.017	B	0.19148	0.024	T	0.43360	-0.9396	9	0.23302	T	0.38	-11.6177	18.2166	0.89887	0.0:0.0:1.0:0.0	rs3745009;rs52819242;rs58066525;rs3745009	880	Q15849	UT2_HUMAN	T	880	ENSP00000255226:A880T	ENSP00000255226:A880T	A	+	1	0	SLC14A2	41516357	0.978000	0.34361	0.967000	0.41034	0.993000	0.82548	1.970000	0.40520	2.390000	0.81377	0.561000	0.74099	GCC	G|0.573;A|0.427	0.427	strong		0.527	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
MGAT5B	146664	hgsc.bcm.edu	37	17	74921129	74921129	+	Silent	SNP	C	C	T	rs34056052	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74921129C>T	ENST00000569840.2	+	9	1681	c.1107C>T	c.(1105-1107)caC>caT	p.H369H	MGAT5B_ENST00000428789.2_Silent_p.H380H|MGAT5B_ENST00000301618.4_Silent_p.H369H	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	369					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)	p.H369H(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCGACTACCACGGCCTGCAGC	0.627													C|||	295	0.0589058	0.0166	0.072	5008	,	,		10333	0.0784		0.0954	False		,,,				2504	0.0491				p.H380H		Atlas-SNP	.											MGAT5B,NS,carcinoma,0,2	MGAT5B	98	2	1	Substitution - coding silent(1)	stomach(1)	c.C1140T						PASS	.	C	,,	111,4295	84.4+/-122.9	0,111,2092	94.0	86.0	89.0		1107,1107,1140	-4.1	1.0	17	dbSNP_126	89	773,7827	181.8+/-230.4	39,695,3566	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	39,806,5658	TT,TC,CC		8.9884,2.5193,6.7969	,,	369/793,369/791,380/802	74921129	884,12122	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon8			CTACCACGGCCTG	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1107C>T	17.37:g.74921129C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			C|0.932;T|0.068	0.068	strong		0.627	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
EPPK1	83481	hgsc.bcm.edu	37	8	144941181	144941181	+	Missense_Mutation	SNP	G	G	C	rs7839934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144941181G>C	ENST00000525985.1	-	2	6312	c.6241C>G	c.(6241-6243)Ctg>Gtg	p.L2081V				P58107	EPIPL_HUMAN	epiplakin 1	2081						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)			GGGAACAGCAGCCAGCCCGTG	0.592													g|||	1432	0.285942	0.2254	0.2997	5008	,	,		20148	0.2669		0.2575	False		,,,				2504	0.407				p.L2081V		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6241G						PASS	.	C	VAL/LEU	960,3348		104,752,1298	66.0	73.0	71.0		6241	-1.8	0.0	8	dbSNP_116	71	2179,6351		285,1609,2371	yes	missense	EPPK1	NM_031308.1	32	389,2361,3669	CC,CG,GG		25.5451,22.2841,24.4508	benign	2081/2420	144941181	3139,9699	2154	4265	6419	SO:0001583	missense	83481	exon1			ACAGCAGCCAGCC	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.6241C>G	8.37:g.144941181G>C	ENSP00000436337:p.Leu2081Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	106	0.972477	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		567	0.25961538461538464	116	0.23577235772357724	104	0.287292817679558	148	0.25874125874125875	199	0.262532981530343	g	3.474	-0.107219	0.06924	0.222841	0.255451	ENSG00000227184	ENST00000525985	T	0.69040	-0.37	4.41	-1.77	0.07982	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17440	-1.0369	7	0.15952	T	0.53	.	5.5162	0.16908	0.0:0.3982:0.2789:0.3229	rs7839934;rs7839934	2081	E9PPU0	.	V	2081	ENSP00000436337:L2081V	ENSP00000436337:L2081V	L	-	1	2	EPPK1	145013169	0.000000	0.05858	0.005000	0.12908	0.000000	0.00434	-2.297000	0.01141	-0.861000	0.04094	-3.661000	0.00025	CTG	G|0.737;C|0.263	0.263	strong		0.592	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634313	32634313	+	Missense_Mutation	SNP	C	C	G	rs1049059	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32634313C>G	ENST00000399082.3	-	1	116	c.72G>C	c.(70-72)atG>atC	p.M24I	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.M24I|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.M24I|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.M24I|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.M24I			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	24			M -> I (in allele DQB1*05:01 and allele DQB1*05:02; dbSNP:rs1049059).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GGGAGCTCAGCATCGCCAGCA	0.592									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1079	0.215455	0.2292	0.1556	5008	,	,		9016	0.246		0.1998	False		,,,				2504	0.2239				p.M24I	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G72C						PASS	.	C	ILE/MET	827,3095		135,557,1269	53.0	51.0	52.0		72	3.3	0.8	6	dbSNP_86	52	1504,6734		266,972,2881	yes	missense	HLA-DQB1	NM_002123.4	10	401,1529,4150	GG,GC,CC		18.2569,21.0862,19.1694	benign	24/262	32634313	2331,9829	1961	4119	6080	SO:0001583	missense	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GCTCAGCATCGCC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.72G>C	6.37:g.32634313C>G	ENSP00000382032:p.Met24Ile	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		452	0.20695970695970695	119	0.241869918699187	68	0.1878453038674033	95	0.1660839160839161	170	0.22427440633245382	.	11.84	1.758307	0.31137	0.210862	0.182569	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T;T	0.05319	3.84;3.46;3.46;3.46;3.46	4.16	3.26	0.37387	.	1626.350000	0.00559	U	0.000273	T	0.03095	0.0091	L	0.45581	1.43	0.58432	P	6.999999999979245E-6	B;B;B;B	0.11235	0.004;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.0;0.0;0.0	T	0.33879	-0.9851	9	0.72032	D	0.01	.	8.968	0.35887	0.2209:0.7791:0.0:0.0	rs1049059;rs3189135;rs12722100;rs17416190;rs35062088	34;24;24;24	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	I	24	ENSP00000382032:M24I;ENSP00000382029:M24I;ENSP00000364080:M24I;ENSP00000407332:M24I;ENSP00000382034:M24I	ENSP00000364080:M24I	M	-	3	0	HLA-DQB1	32742291	0.969000	0.33509	0.824000	0.32777	0.039000	0.13416	0.620000	0.24403	0.933000	0.37291	0.298000	0.19748	ATG	C|0.813;G|0.187	0.187	strong		0.592	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
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 GAIIx	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_ENST00000372988.4_Intron|CCND3_ENST00000372987.4_5'Flank|CCND3_ENST00000510503.1_Intron|CCND3_ENST00000511642.1_Intron|CCND3_ENST00000415497.2_Intron|CCND3_ENST00000414200.2_Missense_Mutation_p.V39I|CCND3_ENST00000511686.1_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	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	72	22	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	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75406912	75406912	+	Missense_Mutation	SNP	G	G	T	rs34163229	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:75406912G>T	ENST00000394810.2	-	4	2647	c.2498C>A	c.(2497-2499)tCc>tAc	p.S833Y	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.S609Y	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	833	Pro-rich.		S -> Y (in dbSNP:rs34163229).			cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					AGGCCCCTGGGATTGGGCCTT	0.537													G|||	853	0.170327	0.2065	0.111	5008	,	,		15950	0.1845		0.1332	False		,,,				2504	0.1871				p.S833Y		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.C2498A						PASS	.	G	TYR/SER,TYR/SER	826,3562		74,678,1442	50.0	61.0	58.0		2498,1826	5.1	1.0	10	dbSNP_126	58	1275,7315		96,1083,3116	yes	missense,missense	SYNPO2L	NM_001114133.1,NM_024875.3	144,144	170,1761,4558	TT,TG,GG		14.8428,18.8241,16.1889	possibly-damaging,possibly-damaging	833/978,609/754	75406912	2101,10877	2194	4295	6489	SO:0001583	missense	79933	exon4			CCCTGGGATTGGG	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.2498C>A	10.37:g.75406912G>T	ENSP00000378289:p.Ser833Tyr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	353	0.16163003663003664	91	0.18495934959349594	40	0.11049723756906077	119	0.20804195804195805	103	0.1358839050131926	G	14.66	2.602697	0.46423	0.188241	0.148428	ENSG00000166317	ENST00000372873;ENST00000394810	T;T	0.25912	1.77;2.1	5.08	5.08	0.68730	.	0.918728	0.09391	N	0.808558	T	0.00039	0.0001	L	0.56769	1.78	0.80722	P	0.0	P;D	0.59767	0.956;0.986	P;P	0.54100	0.459;0.742	T	0.04811	-1.0925	9	0.59425	D	0.04	-13.6833	12.8662	0.57941	0.0:0.2968:0.7032:0.0	rs34163229	833;609	Q9H987;Q9H987-2	SYP2L_HUMAN;.	Y	609;833	ENSP00000361964:S609Y;ENSP00000378289:S833Y	ENSP00000361964:S609Y	S	-	2	0	SYNPO2L	75076918	0.009000	0.17119	1.000000	0.80357	0.959000	0.62525	0.716000	0.25836	2.633000	0.89246	0.561000	0.74099	TCC	G|0.842;T|0.158	0.158	strong		0.537	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
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 GAIIx	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	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	147	71	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	
EFCAB7	84455	hgsc.bcm.edu	37	1	64021096	64021096	+	Missense_Mutation	SNP	G	G	A	rs2273367	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:64021096G>A	ENST00000371088.4	+	9	1370	c.1124G>A	c.(1123-1125)aGg>aAg	p.R375K	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	375			R -> K (in dbSNP:rs2273367). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.				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						ACTGGCTGTAGGCTGAGGAAA	0.358													G|||	701	0.139976	0.0673	0.1585	5008	,	,		15942	0.1855		0.1441	False		,,,				2504	0.1738				p.R375K		Atlas-SNP	.											EFCAB7,right_upper_lobe,carcinoma,-1,1	EFCAB7	45	1	0			c.G1124A						scavenged	.	G	LYS/ARG	348,4058	179.7+/-208.2	8,332,1863	140.0	138.0	139.0		1124	4.0	1.0	1	dbSNP_100	139	1326,7274	260.9+/-283.5	93,1140,3067	yes	missense	EFCAB7	NM_032437.2	26	101,1472,4930	AA,AG,GG		15.4186,7.8983,12.871	benign	375/630	64021096	1674,11332	2203	4300	6503	SO:0001583	missense	84455	exon9			GCTGTAGGCTGAG	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.1124G>A	1.37:g.64021096G>A	ENSP00000360129:p.Arg375Lys	Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	315	0.14423076923076922	41	0.08333333333333333	61	0.1685082872928177	105	0.18356643356643357	108	0.1424802110817942	G	13.30	2.196337	0.38806	0.078983	0.154186	ENSG00000203965	ENST00000371088	T	0.44881	0.91	5.96	4.04	0.47022	.	0.214437	0.53938	N	0.000044	T	0.20618	0.0496	L	0.57536	1.79	0.09310	P	0.9999999999995571	B	0.06786	0.001	B	0.06405	0.002	T	0.05435	-1.0885	9	0.32370	T	0.25	-6.8388	10.965	0.47408	0.1579:0.0:0.8421:0.0	rs2273367;rs17851338;rs52834573;rs61180196;rs2273367	375	A8K855	EFCB7_HUMAN	K	375	ENSP00000360129:R375K	ENSP00000360129:R375K	R	+	2	0	EFCAB7	63793684	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	4.663000	0.61532	0.773000	0.33404	0.655000	0.94253	AGG	G|0.849;A|0.151	0.151	strong		0.358	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
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 GAIIx	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_ENST00000409412.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000444522.2_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409206.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000468301.1_3'UTR|ZFAND2B_ENST00000409217.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409594.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409097.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409336.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409319.1_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	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	28	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 GAIIx	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	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	91	4	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	
EIF3F	8665	hgsc.bcm.edu	37	11	8009241	8009241	+	Silent	SNP	C	C	T	rs12421289	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:8009241C>T	ENST00000533626.1	+	3	968	c.342C>T	c.(340-342)gcC>gcT	p.A114A	EIF3F_ENST00000309828.4_Silent_p.A114A|EIF3F_ENST00000449102.2_5'UTR|EIF3F_ENST00000537635.1_Silent_p.A129A					eukaryotic translation initiation factor 3, subunit F											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)	13				Epithelial(150;1.44e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGGGTGCTGCCCGAGTTATCG	0.542											OREG0020726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	338	0.067492	0.0424	0.0994	5008	,	,		19051	0.001		0.1829	False		,,,				2504	0.0286				p.A114A		Atlas-SNP	.											.	EIF3F	23	.	0			c.C342T						PASS	.	C		253,4147		8,237,1955	14.0	15.0	15.0		342	2.9	1.0	11	dbSNP_120	15	1506,7080		132,1242,2919	no	coding-synonymous	EIF3F	NM_003754.2		140,1479,4874	TT,TC,CC		17.5402,5.75,13.5454		114/358	8009241	1759,11227	2200	4293	6493	SO:0001819	synonymous_variant	8665	exon1			TGCTGCCCGAGTT	U94855, AK093511	CCDS7785.1	11p15.4	2010-03-10	2007-07-27	2007-07-27	ENSG00000175390	ENSG00000175390			3275	protein-coding gene	gene with protein product		603914	"""eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa"""	EIF3S5		9341143	Standard	NM_003754		Approved	eIF3-epsilon, eIF3-p47, eIF3f	uc001mfw.3	O00303		ENST00000533626.1:c.342C>T	11.37:g.8009241C>T		Somatic	97	0	0	646	WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_003754		Silent	SNP	ENST00000533626.1	37	CCDS7785.1																																																																																			C|0.889;T|0.111	0.111	strong		0.542	EIF3F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385713.2	NM_003754	
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 GAIIx	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	54	5	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	
SLC34A2	10568	hgsc.bcm.edu	37	4	25669530	25669530	+	Silent	SNP	T	T	C	rs77319279	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:25669530T>C	ENST00000382051.3	+	6	602	c.552T>C	c.(550-552)atT>atC	p.I184I	SLC34A2_ENST00000503434.1_Silent_p.I183I|SLC34A2_ENST00000504570.1_Silent_p.I183I|SLC34A2_ENST00000510033.2_3'UTR	NM_001177998.1|NM_006424.2	NP_001171469.1|NP_006415	O95436	NPT2B_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 2	184					aging (GO:0007568)|cellular phosphate ion homeostasis (GO:0030643)|in utero embryonic development (GO:0001701)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|response to fructose (GO:0009750)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	phosphate ion binding (GO:0042301)|sodium ion binding (GO:0031402)|sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)		SLC34A2/ROS1(14)	breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(4)	41		Breast(46;0.0503)				CCATCCCCATTATCATGGGGG	0.502			T	ROS1	NSCLC								T|||	51	0.0101837	0.0053	0.0231	5008	,	,		22345	0.0		0.0239	False		,,,				2504	0.0041				p.I184I		Atlas-SNP	.		Dom	yes		4	4p15.2	10568	"""solute carrier family 34 (sodium phosphate), member 2"""		E	.	SLC34A2	93	.	0			c.T552C						PASS	.	T	,,	27,4379	32.6+/-62.9	0,27,2176	112.0	95.0	101.0		549,549,552	-1.5	0.9	4	dbSNP_131	101	267,8333	102.7+/-163.9	6,255,4039	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC34A2	NM_001177998.1,NM_001177999.1,NM_006424.2	,,	6,282,6215	CC,CT,TT		3.1047,0.6128,2.2605	,,	183/690,183/690,184/691	25669530	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	10568	exon6			CCCCATTATCATG	AF111856	CCDS3435.1, CCDS54750.1	4p15.2	2013-07-17	2013-07-17		ENSG00000157765	ENSG00000157765		"""Solute carriers"""	11020	protein-coding gene	gene with protein product		604217	"""solute carrier family 34 (sodium phosphate), member 2"""			10329428, 10610722	Standard	NM_006424		Approved	NAPI-3B	uc003grr.3	O95436	OTTHUMG00000097757	ENST00000382051.3:c.552T>C	4.37:g.25669530T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_006424	A5PL17|Q8N2K2|Q8WYA9|Q9P0V7	Silent	SNP	ENST00000382051.3	37	CCDS3435.1																																																																																			T|0.980;C|0.020	0.020	strong		0.502	SLC34A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214990.1	NM_006424	
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 GAIIx	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_ENST00000492590.1_Silent_p.S13S|FHIT_ENST00000476844.1_Silent_p.S13S|FHIT_ENST00000341848.4_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		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	59	13	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	
MTTP	4547	hgsc.bcm.edu	37	4	100516022	100516022	+	Missense_Mutation	SNP	C	C	G	rs2306985	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100516022C>G	ENST00000265517.5	+	7	1094	c.891C>G	c.(889-891)caC>caG	p.H297Q	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.H297Q|MTTP_ENST00000511045.1_Missense_Mutation_p.H324Q			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	297	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		H -> Q (in dbSNP:rs2306985). {ECO:0000269|PubMed:11792722, ECO:0000269|PubMed:14732481, ECO:0000269|PubMed:8939939}.		cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	TCCAGAGCCACTGTAAAGGAT	0.443													G|||	2716	0.542332	0.8169	0.3069	5008	,	,		20048	0.6706		0.3151	False		,,,				2504	0.4397				p.H297Q		Atlas-SNP	.											.	MTTP	127	.	0			c.C891G						PASS	.	G	GLN/HIS	3237,1169	409.7+/-335.1	1192,853,158	102.0	95.0	97.0		891	-2.7	0.0	4	dbSNP_100	97	3130,5470	656.8+/-401.4	598,1934,1768	yes	missense	MTTP	NM_000253.2	24	1790,2787,1926	GG,GC,CC		36.3953,26.532,48.9543	benign	297/895	100516022	6367,6639	2203	4300	6503	SO:0001583	missense	4547	exon8			GAGCCACTGTAAA		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.891C>G	4.37:g.100516022C>G	ENSP00000265517:p.His297Gln	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	160	67	0.41875	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	1108	0.5073260073260073	384	0.7804878048780488	105	0.2900552486187845	388	0.6783216783216783	231	0.30474934036939316	G	0.006	-2.082567	0.00371	0.73468	0.363953	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.38077	1.16;1.16;1.16	4.96	-2.65	0.06095	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (1);	0.983377	0.08358	N	0.958193	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30707	-0.9969	9	0.15499	T	0.54	-7.5323	4.8904	0.13724	0.2481:0.4492:0.2164:0.0863	rs2306985;rs17599155;rs52823538;rs56751900;rs2306985	324;297	E9PBP6;P55157	.;MTP_HUMAN	Q	324;297;297;297	ENSP00000427679:H324Q;ENSP00000400821:H297Q;ENSP00000265517:H297Q	ENSP00000265517:H297Q	H	+	3	2	MTTP	100735045	0.035000	0.19736	0.002000	0.10522	0.010000	0.07245	-0.390000	0.07332	-1.251000	0.02494	-4.627000	0.00004	CAC	C|0.483;G|0.516	0.516	strong		0.443	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
UBASH3B	84959	hgsc.bcm.edu	37	11	122665437	122665437	+	Silent	SNP	A	A	G	rs872414	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:122665437A>G	ENST00000284273.5	+	7	1383	c.1008A>G	c.(1006-1008)tcA>tcG	p.S336S		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	336					negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		ATACATCGTCATCCAACTCTC	0.512													G|||	2816	0.5623	0.7602	0.5317	5008	,	,		19279	0.5615		0.3917	False		,,,				2504	0.4928				p.S336S		Atlas-SNP	.											.	UBASH3B	73	.	0			c.A1008G						PASS	.	G		3077,1327	447.7+/-348.4	1079,919,204	153.0	157.0	156.0		1008	-7.8	0.0	11	dbSNP_86	156	3446,5152	637.3+/-399.2	704,2038,1557	no	coding-synonymous	UBASH3B	NM_032873.4		1783,2957,1761	GG,GA,AA		40.0791,30.1317,49.8308		336/650	122665437	6523,6479	2202	4299	6501	SO:0001819	synonymous_variant	84959	exon7			ATCGTCATCCAAC	AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"""SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"""	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1008A>G	11.37:g.122665437A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	104	90	0.865385	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Silent	SNP	ENST00000284273.5	37	CCDS31694.1																																																																																			A|0.478;G|0.522	0.522	strong		0.512	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873	
C5orf60	285679	hgsc.bcm.edu	37	5	179071836	179071836	+	Silent	SNP	C	C	T	rs4990391	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:179071836C>T	ENST00000448248.2	-	1	211	c.186G>A	c.(184-186)ccG>ccA	p.P62P	C5orf60_ENST00000506142.1_Intron	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	62						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						GCACTGAGGACGGCTCCCTGG	0.532													-|||	717	0.143171	0.171	0.0951	5008	,	,		22464	0.0546		0.2256	False		,,,				2504	0.1462				p.P62P		Atlas-SNP	.											C5orf60,colon,carcinoma,0,1	C5orf60	24	1	0			c.G186A						scavenged	.						64.0	60.0	62.0					5																	179071836		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			TGAGGACGGCTCC	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.186G>A	5.37:g.179071836C>T		Somatic	129	4	0.0310078		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			C|0.848;T|0.152	0.152	strong		0.532	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
MUC2	4583	hgsc.bcm.edu	37	11	1103873	1103873	+	Silent	SNP	C	C	T	rs11245957	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1103873C>T	ENST00000441003.2	+	48	8199	c.8172C>T	c.(8170-8172)taC>taT	p.Y2724Y		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5086					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)	AGGTTTCGTACGCCGGCTGCA	0.657													c|||	753	0.150359	0.385	0.072	5008	,	,		14924	0.0357		0.0934	False		,,,				2504	0.0654				p.Y2720Y		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.C8160T						PASS	.	T		1236,2906		166,904,1001	26.0	30.0	28.0		8157	-7.6	0.0	11	dbSNP_120	28	693,7677		30,633,3522	no	coding-synonymous	MUC2	NM_002457.2		196,1537,4523	TT,TC,CC		8.2796,29.8407,15.4172		2719/2813	1103873	1929,10583	2071	4185	6256	SO:0001819	synonymous_variant	4583	exon49			TTCGTACGCCGGC	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.8172C>T	11.37:g.1103873C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.867;T|0.133	0.133	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SYNJ2	8871	hgsc.bcm.edu	37	6	158497717	158497717	+	Silent	SNP	T	T	C	rs2296508	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:158497717T>C	ENST00000355585.4	+	17	2427	c.2352T>C	c.(2350-2352)gtT>gtC	p.V784V	SYNJ2_ENST00000367112.1_5'Flank|SYNJ2_ENST00000367122.2_Silent_p.V784V|SYNJ2_ENST00000367121.3_Silent_p.V784V	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	784					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		AGTATGACGTTGGCTCAGCCG	0.493													C|||	2896	0.578275	0.7587	0.3545	5008	,	,		15458	0.5883		0.5139	False		,,,				2504	0.5491				p.V784V		Atlas-SNP	.											.	SYNJ2	111	.	0			c.T2352C						PASS	.	C	,	3104,1302	439.0+/-345.5	1095,914,194	64.0	65.0	64.0		1641,2352	-10.6	0.9	6	dbSNP_100	64	4427,4173	568.4+/-389.0	1141,2145,1014	no	coding-synonymous,coding-synonymous	SYNJ2	NM_001178088.1,NM_003898.3	,	2236,3059,1208	CC,CT,TT		48.5233,29.5506,42.096	,	547/1260,784/1497	158497717	7531,5475	2203	4300	6503	SO:0001819	synonymous_variant	8871	exon17			TGACGTTGGCTCA	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.2352T>C	6.37:g.158497717T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	37	CCDS5254.1																																																																																			T|0.420;C|0.580	0.580	strong		0.493	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2		
PKD1L1	168507	hgsc.bcm.edu	37	7	47854956	47854956	+	Silent	SNP	C	C	T	rs17545564	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:47854956C>T	ENST00000289672.2	-	47	7115	c.7065G>A	c.(7063-7065)ccG>ccA	p.P2355P	C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2355					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CACGGGCTGACGGGGTGCCTC	0.557													c|||	739	0.147564	0.0174	0.2017	5008	,	,		18335	0.2153		0.173	False		,,,				2504	0.1892				p.P2355P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G7065A						PASS	.	C	,	222,4184	132.5+/-169.0	4,214,1985	59.0	56.0	57.0		,7065	-7.9	0.0	7	dbSNP_123	57	1338,7262	262.5+/-284.5	96,1146,3058	no	intron,coding-synonymous	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,	100,1360,5043	TT,TC,CC		15.5581,5.0386,11.9945	,	,2355/2850	47854956	1560,11446	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon47			GGCTGACGGGGTG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7065G>A	7.37:g.47854956C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			C|0.867;T|0.133	0.133	strong		0.557	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
NID2	22795	hgsc.bcm.edu	37	14	52481917	52481917	+	Silent	SNP	C	C	T	rs946615	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:52481917C>T	ENST00000216286.5	-	15	3104	c.3105G>A	c.(3103-3105)cgG>cgA	p.R1035R	NID2_ENST00000541773.1_Silent_p.R934R	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1035	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					ACTGGTCATCCCGGGGGGTGC	0.627													c|||	2301	0.459465	0.5045	0.5245	5008	,	,		16732	0.7063		0.2406	False		,,,				2504	0.3231				p.R1035R		Atlas-SNP	.											NID2,NS,carcinoma,0,1	NID2	201	1	0			c.G3105A						PASS	.	C		2082,2324	542.5+/-376.0	485,1112,606	52.0	48.0	50.0		3105	2.8	0.6	14	dbSNP_86	50	2315,6285	359.1+/-331.4	338,1639,2323	no	coding-synonymous	NID2	NM_007361.3		823,2751,2929	TT,TC,CC		26.9186,47.2537,33.8075		1035/1376	52481917	4397,8609	2203	4300	6503	SO:0001819	synonymous_variant	22795	exon15			GTCATCCCGGGGG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3105G>A	14.37:g.52481917C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	50	48	0.96	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1	1004	0.4597069597069597	237	0.4817073170731707	184	0.5082872928176796	407	0.7115384615384616	176	0.23218997361477572	C	8.058	0.767452	0.15983	0.472537	0.269186	ENSG00000087303	ENST00000556572	.	.	.	5.67	2.8	0.32819	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25093	P	0.99084443	.	.	.	.	.	.	T	0.33752	-0.9856	3	.	.	.	.	4.7078	0.12858	0.3472:0.4462:0.1361:0.0705	rs946615;rs57980038;rs946615	.	.	.	R	304	.	.	G	-	1	0	NID2	51551667	0.000000	0.05858	0.556000	0.28293	0.731000	0.41821	-1.434000	0.02425	0.285000	0.22329	0.655000	0.94253	GGA	C|0.604;T|0.396	0.396	strong		0.627	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
HLA-G	3135	hgsc.bcm.edu	37	6	29796327	29796327	+	Silent	SNP	C	C	T	rs1130356	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29796327C>T	ENST00000360323.6	+	3	375	c.351C>T	c.(349-351)caC>caT	p.H117H	HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376818.3_Intron|HLA-G_ENST00000376828.2_Silent_p.H122H|HLA-G_ENST00000428701.1_Silent_p.H117H			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	117	Alpha-2.				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 peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CAGGTTCTCACACCCTCCAGT	0.662													c|||	1253	0.2502	0.2625	0.2565	5008	,	,		13097	0.1141		0.2763	False		,,,				2504	0.3425				p.H117H		Atlas-SNP	.											.	HLA-G	90	.	0			c.C351T						PASS	.	C		823,2195		112,599,798	68.0	72.0	71.0		351	0.8	0.2	6	dbSNP_86	71	1692,3724		272,1148,1288	no	coding-synonymous	HLA-G	NM_002127.5		384,1747,2086	TT,TC,CC		31.2408,27.2697,29.8198		117/339	29796327	2515,5919	1509	2708	4217	SO:0001819	synonymous_variant	3135	exon4			TTCTCACACCCTC		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.351C>T	6.37:g.29796327C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	86	73	0.848837	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.734;T|0.266	0.266	strong		0.662	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
SLC22A2	6582	hgsc.bcm.edu	37	6	160679400	160679400	+	Silent	SNP	C	C	A	rs624249	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:160679400C>A	ENST00000366953.3	-	1	648	c.390G>T	c.(388-390)acG>acT	p.T130T	SLC22A2_ENST00000491092.1_5'UTR|SLC22A2_ENST00000366952.1_Silent_p.T109T	NM_003058.3	NP_003049.2	O15244	S22A2_HUMAN	solute carrier family 22 (organic cation transporter), member 2	130					body fluid secretion (GO:0007589)|drug transmembrane transport (GO:0006855)|histamine transport (GO:0051608)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|organic cation transport (GO:0015695)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|steroid binding (GO:0005496)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(16)|prostate(2)|skin(1)	27		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.28e-17)|BRCA - Breast invasive adenocarcinoma(81;6.29e-06)	Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Chlorphenamine(DB01114)|Choline(DB00122)|Cimetidine(DB00501)|Cisplatin(DB00515)|Cladribine(DB00242)|Cocaine(DB00907)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Desipramine(DB01151)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Famotidine(DB00927)|Flurazepam(DB00690)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Lamivudine(DB00709)|Levofloxacin(DB01137)|Memantine(DB01043)|Metformin(DB00331)|Metoprolol(DB00264)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Oxprenolol(DB01580)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Propranolol(DB00571)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Reserpine(DB00206)|Thiamine(DB00152)|Tubocurarine(DB01199)|Vinblastine(DB00570)|Zidovudine(DB00495)	ACGAGCCAGGCGTCTCGTACA	0.627													C|||	1324	0.264377	0.2663	0.268	5008	,	,		15695	0.1498		0.3926	False		,,,				2504	0.2454				p.T130T		Atlas-SNP	.											.	SLC22A2	78	.	0			c.G390T						PASS	.	C		1083,3321	359.4+/-314.8	129,825,1248	59.0	67.0	64.0		390	0.7	1.0	6	dbSNP_83	64	3496,5104	486.5+/-371.9	706,2084,1510	no	coding-synonymous	SLC22A2	NM_003058.3		835,2909,2758	AA,AC,CC		40.6512,24.5913,35.2122		130/556	160679400	4579,8425	2202	4300	6502	SO:0001819	synonymous_variant	6582	exon1			GCCAGGCGTCTCG	X98333	CCDS5276.1	6q25.3	2013-05-22			ENSG00000112499	ENSG00000112499		"""Solute carriers"""	10966	protein-coding gene	gene with protein product		602608				9605850	Standard	NM_003058		Approved	OCT2	uc003qtf.3	O15244	OTTHUMG00000015950	ENST00000366953.3:c.390G>T	6.37:g.160679400C>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_003058	Q5T7Q6|Q6PIQ8|Q8NG62|Q9NQB9	Silent	SNP	ENST00000366953.3	37	CCDS5276.1																																																																																			C|0.673;A|0.327	0.327	strong		0.627	SLC22A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042943.1	NM_003058	
DSC3	1825	hgsc.bcm.edu	37	18	28611061	28611061	+	Missense_Mutation	SNP	A	A	T	rs276937	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:28611061A>T	ENST00000360428.4	-	3	312	c.232T>A	c.(232-234)Tca>Aca	p.S78T	DSC3_ENST00000434452.1_Missense_Mutation_p.S78T	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	78			S -> T (in dbSNP:rs276937).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			GTGTACACTGACCCATCATTT	0.413													A|||	2178	0.434904	0.3132	0.3401	5008	,	,		13475	0.6835		0.3549	False		,,,				2504	0.4928				p.S78T		Atlas-SNP	.											.	DSC3	225	.	0			c.T232A						PASS	.	A	THR/SER,THR/SER	1465,2941	469.0+/-355.3	240,985,978	73.0	65.0	67.0		232,232	2.8	0.0	18	dbSNP_79	67	2764,5836	439.1+/-359.1	443,1878,1979	yes	missense,missense	DSC3	NM_001941.3,NM_024423.2	58,58	683,2863,2957	TT,TA,AA		32.1395,33.2501,32.5158	possibly-damaging,possibly-damaging	78/897,78/840	28611061	4229,8777	2203	4300	6503	SO:0001583	missense	1825	exon3			ACACTGACCCATC	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.232T>A	18.37:g.28611061A>T	ENSP00000353608:p.Ser78Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_024423	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	942	0.43131868131868134	158	0.32113821138211385	127	0.35082872928176795	397	0.6940559440559441	260	0.34300791556728233	A	8.716	0.913305	0.17907	0.332501	0.321395	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.38560	1.13;1.13	5.26	2.83	0.33086	Cadherin prodomain-like (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	M	0.62266	1.93	0.58432	P	5.000000000032756E-6	B;P	0.38335	0.267;0.627	B;B	0.40940	0.344;0.329	T	0.36696	-0.9737	8	0.26408	T	0.33	.	7.2036	0.25895	0.7754:0.147:0.0776:0.0	rs276937;rs1098249;rs1303278;rs1602889;rs17799213;rs52793945;rs59695561;rs276937	78;78	Q14574;Q14574-2	DSC3_HUMAN;.	T	78	ENSP00000353608:S78T;ENSP00000392068:S78T	ENSP00000353608:S78T	S	-	1	0	DSC3	26865059	0.998000	0.40836	0.005000	0.12908	0.004000	0.04260	3.054000	0.49908	0.442000	0.26555	-0.256000	0.11100	TCA	A|0.626;T|0.374	0.374	strong		0.413	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
CLCC1	23155	hgsc.bcm.edu	37	1	109479978	109479978	+	Missense_Mutation	SNP	G	G	T	rs168107	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109479978G>T	ENST00000369971.2	-	10	1233	c.1104C>A	c.(1102-1104)agC>agA	p.S368R	CLCC1_ENST00000369976.1_Intron|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000369970.3_Missense_Mutation_p.S318R|CLCC1_ENST00000302500.4_Missense_Mutation_p.S247R|CLCC1_ENST00000369968.2_Missense_Mutation_p.S183R|CLCC1_ENST00000415331.1_Missense_Mutation_p.S318R|CLCC1_ENST00000356970.2_Missense_Mutation_p.S368R|CLCC1_ENST00000369969.2_Missense_Mutation_p.S247R|CLCC1_ENST00000348264.2_Missense_Mutation_p.S183R	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	368			S -> R (in dbSNP:rs168107).			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)		GGGGAGGTTCGCTCTCAGGAC	0.478													T|||	1538	0.307109	0.6233	0.2147	5008	,	,		15929	0.0377		0.2803	False		,,,				2504	0.2505				p.S368R		Atlas-SNP	.											.	CLCC1	55	.	0			c.C1104A						PASS	.	T	ARG/SER,ARG/SER	2484,1922	543.3+/-376.2	707,1070,426	62.0	66.0	65.0		1104,954	1.7	0.4	1	dbSNP_79	65	2297,6303	702.0+/-405.3	320,1657,2323	yes	missense,missense	CLCC1	NM_001048210.1,NM_015127.3	110,110	1027,2727,2749	TT,TG,GG		26.7093,43.6223,36.76	benign,benign	368/552,318/502	109479978	4781,8225	2203	4300	6503	SO:0001583	missense	23155	exon10			AGGTTCGCTCTCA	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.1104C>A	1.37:g.109479978G>T	ENSP00000358988:p.Ser368Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Missense_Mutation	SNP	ENST00000369971.2	37	CCDS41362.1	631	0.2889194139194139	305	0.6199186991869918	92	0.2541436464088398	20	0.03496503496503497	214	0.28232189973614774	T	0.006	-2.059776	0.00386	0.563777	0.267093	ENSG00000121940	ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369969;ENST00000369968;ENST00000369970;ENST00000348264;ENST00000302500	T;T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.57	1.71	0.24356	.	0.242200	0.43579	N	0.000553	T	0.01976	0.0062	N	0.00152	-1.975	0.80722	P	0.0	B;B;B;B	0.10296	0.001;0.003;0.001;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.43798	-0.9369	9	0.02654	T	1	-2.9609	8.4464	0.32845	0.0:0.1013:0.4688:0.4299	rs168107;rs17565258;rs52797843;rs60258424;rs168107	183;247;318;368	Q96S66-4;Q96S66-3;Q96S66-2;Q96S66	.;.;.;CLCC1_HUMAN	R	368;368;318;247;183;318;183;247	ENSP00000349456:S368R;ENSP00000358988:S368R;ENSP00000411591:S318R;ENSP00000358986:S247R;ENSP00000358985:S183R;ENSP00000358987:S318R;ENSP00000337243:S183R;ENSP00000306552:S247R	ENSP00000306552:S247R	S	-	3	2	CLCC1	109281501	0.554000	0.26522	0.375000	0.26029	0.021000	0.10359	0.381000	0.20619	-0.136000	0.11475	-0.256000	0.11100	AGC	A|0.000;C|0.006	.	strong		0.478	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127	
ABCA5	23461	hgsc.bcm.edu	37	17	67267317	67267317	+	Missense_Mutation	SNP	T	T	C	rs557491	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:67267317T>C	ENST00000392676.3	-	21	2942	c.2878A>G	c.(2878-2880)Atg>Gtg	p.M960V	ABCA5_ENST00000392677.2_Missense_Mutation_p.M961V|ABCA5_ENST00000588877.1_Missense_Mutation_p.M960V			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	960			M -> V (in dbSNP:rs557491). {ECO:0000269|PubMed:11572484}.		cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TCTGAATGCATCACATTTAAA	0.348													T|||	2491	0.497404	0.4327	0.5893	5008	,	,		16231	0.6002		0.4404	False		,,,				2504	0.4724				p.M960V		Atlas-SNP	.											.	ABCA5	162	.	0			c.A2878G						PASS	.	T	VAL/MET,VAL/MET	1989,2417	557.9+/-379.9	441,1107,655	106.0	92.0	97.0		2878,2878	2.0	0.9	17	dbSNP_83	97	3967,4633	551.1+/-385.9	897,2173,1230	yes	missense,missense	ABCA5	NM_018672.3,NM_172232.2	21,21	1338,3280,1885	CC,CT,TT		46.1279,45.143,45.7942	benign,benign	960/1643,960/1643	67267317	5956,7050	2203	4300	6503	SO:0001583	missense	23461	exon20			AATGCATCACATT	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.2878A>G	17.37:g.67267317T>C	ENSP00000376443:p.Met960Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	1106	0.5064102564102564	228	0.4634146341463415	183	0.505524861878453	362	0.6328671328671329	333	0.4393139841688654	T	0.009	-1.827882	0.00584	0.45143	0.461279	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.86497	-2.13;-2.13	5.5	1.95	0.26073	.	0.388405	0.24861	N	0.035020	T	0.00012	0.0000	N	0.13043	0.29	0.51482	P	7.199999999996098E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46442	-0.9191	8	.	.	.	.	3.3547	0.07164	0.2829:0.3545:0.0:0.3626	rs557491;rs52818855;rs60930051;rs557491	960	Q8WWZ7	ABCA5_HUMAN	V	961;960	ENSP00000376444:M961V;ENSP00000376443:M960V	.	M	-	1	0	ABCA5	64778912	0.058000	0.20735	0.853000	0.33588	0.149000	0.21700	0.306000	0.19279	0.057000	0.16193	0.482000	0.46254	ATG	T|0.519;C|0.481	0.481	strong		0.348	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
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 GAIIx	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_ENST00000400186.3_Silent_p.P1944P|CSMD1_ENST00000542608.1_Silent_p.P1943P|CSMD1_ENST00000602557.1_Silent_p.P1944P|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000539096.1_Silent_p.P1943P|CSMD1_ENST00000537824.1_Silent_p.P1943P|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		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	45	18	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	
BTBD11	121551	hgsc.bcm.edu	37	12	107713696	107713696	+	Missense_Mutation	SNP	G	G	A	rs111260184	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:107713696G>A	ENST00000280758.5	+	1	1507	c.979G>A	c.(979-981)Gca>Aca	p.A327T	BTBD11_ENST00000490090.2_Missense_Mutation_p.A327T|BTBD11_ENST00000420571.2_Missense_Mutation_p.A327T	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	327	Ala-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						agtcccgccggcagccgccgc	0.746													G|||	1976	0.394569	0.2201	0.4539	5008	,	,		7762	0.4127		0.492	False		,,,				2504	0.4693				p.A327T		Atlas-SNP	.											.	BTBD11	122	.	0			c.G979A						PASS	.	G	THR/ALA	899,2583		155,589,997	5.0	6.0	6.0		979	3.1	0.1	12	dbSNP_132	6	3803,3633		1025,1753,940	no	missense	BTBD11	NM_001018072.1	58	1180,2342,1937	AA,AG,GG		48.8569,25.8185,43.0665	benign	327/1105	107713696	4702,6216	1741	3718	5459	SO:0001583	missense	121551	exon1			CCGCCGGCAGCCG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.979G>A	12.37:g.107713696G>A	ENSP00000280758:p.Ala327Thr	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	884	0.40476190476190477	116	0.23577235772357724	158	0.43646408839779005	233	0.40734265734265734	377	0.4973614775725594	G	12.78	2.040605	0.35989	0.258185	0.511431	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000550706	T;T;T;T	0.55930	1.32;1.39;1.36;0.49	3.99	3.06	0.35304	Histone-fold (1);	0.780131	0.10817	N	0.630929	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	1.0	P;B;B	0.35745	0.518;0.259;0.376	B;B;B	0.29524	0.103;0.032;0.071	T	0.41270	-0.9518	9	0.09590	T	0.72	.	10.0955	0.42473	0.1003:0.0:0.8997:0.0	.	327;327;327	A6QL63-2;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	T	327;327;327;8	ENSP00000280758:A327T;ENSP00000413889:A327T;ENSP00000447319:A327T;ENSP00000447606:A8T	ENSP00000280758:A327T	A	+	1	0	BTBD11	106237826	.	.	0.088000	0.20740	0.468000	0.32798	.	.	2.030000	0.59900	0.561000	0.74099	GCA	G|0.595;A|0.405	0.405	strong		0.746	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
GJB7	375519	hgsc.bcm.edu	37	6	87994504	87994504	+	Missense_Mutation	SNP	C	C	T	rs35259282	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:87994504C>T	ENST00000525899.1	-	3	472	c.127G>A	c.(127-129)Gtg>Atg	p.V43M	GJB7_ENST00000296882.3_Missense_Mutation_p.V43M	NM_198568.2	NP_940970.1	Q6PEY0	CXB7_HUMAN	gap junction protein, beta 7, 25kDa	43				V -> M (in Ref. 1; CAC93845). {ECO:0000305}.	cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)	5		all_cancers(76;1.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;7.38e-10)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00323)		BRCA - Breast invasive adenocarcinoma(108;0.0167)		TCTTTCCACACGTGCTCTGCT	0.478													C|||	177	0.0353435	0.0061	0.0591	5008	,	,		19784	0.0188		0.0895	False		,,,				2504	0.0194				p.V43M		Atlas-SNP	.											.	GJB7	28	.	0			c.G127A						PASS	.	C	MET/VAL	80,4326	68.1+/-105.8	0,80,2123	117.0	105.0	109.0		127	4.1	0.3	6	dbSNP_126	109	779,7821	183.6+/-231.8	35,709,3556	yes	missense	GJB7	NM_198568.2	21	35,789,5679	TT,TC,CC		9.0581,1.8157,6.6046	probably-damaging	43/224	87994504	859,12147	2203	4300	6503	SO:0001583	missense	375519	exon3			TCCACACGTGCTC	AJ414563	CCDS5008.1	6q15	2008-02-05	2007-11-06			ENSG00000164411		"""Ion channels / Gap junction proteins (connexins)"""	16690	protein-coding gene	gene with protein product	"""connexin 25"""	611921	"""gap junction protein, beta 7"""				Standard	NM_198568		Approved	CX25, bA136M9.1	uc003plo.2	Q6PEY0		ENST00000525899.1:c.127G>A	6.37:g.87994504C>T	ENSP00000435355:p.Val43Met	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	199	87	0.437186	NM_198568	B3KXL0|Q96KP0	Missense_Mutation	SNP	ENST00000525899.1	37	CCDS5008.1	110	0.05036630036630037	6	0.012195121951219513	23	0.06353591160220995	12	0.02097902097902098	69	0.09102902374670185	C	13.99	2.401570	0.42613	0.018157	0.090581	ENSG00000164411	ENST00000525899;ENST00000296882;ENST00000369576	D;D;D	0.99399	-5.83;-5.83;-5.83	4.99	4.13	0.48395	Connexin, N-terminal (2);	0.000000	0.64402	U	0.000006	D	0.99302	0.9756	M	0.83774	2.66	0.35760	D	0.820096	D	0.89917	1.0	D	0.80764	0.994	D	0.99901	1.1163	10	0.72032	D	0.01	.	9.7652	0.40557	0.0:0.8299:0.0:0.1701	rs35259282;rs62441378	43	Q6PEY0	CXB7_HUMAN	M	43	ENSP00000435355:V43M;ENSP00000296882:V43M;ENSP00000358589:V43M	ENSP00000296882:V43M	V	-	1	0	GJB7	88051223	0.998000	0.40836	0.343000	0.25615	0.250000	0.25880	3.751000	0.55165	1.105000	0.41606	-0.224000	0.12420	GTG	C|0.939;T|0.061	0.061	strong		0.478	GJB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394780.1		
GRIN3B	116444	hgsc.bcm.edu	37	19	1008683	1008683	+	Missense_Mutation	SNP	G	G	A	rs2285906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1008683G>A	ENST00000234389.3	+	7	2552	c.2533G>A	c.(2533-2535)Gct>Act	p.A845T		NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	845			A -> T (in dbSNP:rs2285906).		ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCTGGGCAGCGCTCTGCTCAG	0.677													g|||	545	0.108826	0.0378	0.1383	5008	,	,		11007	0.1329		0.161	False		,,,				2504	0.1053				p.A845T		Atlas-SNP	.											GRIN3B,NS,carcinoma,0,1	GRIN3B	46	1	0			c.G2533A						PASS	.	G	THR/ALA	261,4145	146.1+/-180.8	8,245,1950	41.0	35.0	37.0		2533	1.2	1.0	19	dbSNP_100	37	1416,7184	268.7+/-288.0	121,1174,3005	yes	missense	GRIN3B	NM_138690.1	58	129,1419,4955	AA,AG,GG		16.4651,5.9237,12.894	possibly-damaging	845/1044	1008683	1677,11329	2203	4300	6503	SO:0001583	missense	116444	exon7			GGCAGCGCTCTGC		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.2533G>A	19.37:g.1008683G>A	ENSP00000234389:p.Ala845Thr	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	35	34	0.971429	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	259	0.11858974358974358	21	0.042682926829268296	47	0.1298342541436464	70	0.12237762237762238	121	0.15963060686015831	G	21.1	4.091740	0.76756	0.059237	0.164651	ENSG00000116032	ENST00000234389	T	0.16073	2.37	3.78	1.22	0.21188	.	0.136063	0.49305	U	0.000143	T	0.00073	0.0002	L	0.55481	1.735	0.09310	P	0.9999999999999997	D	0.62365	0.991	P	0.50314	0.637	T	0.11665	-1.0578	9	0.72032	D	0.01	.	9.4558	0.38753	0.0:0.0:0.548:0.452	rs2285906	845	O60391	NMD3B_HUMAN	T	845	ENSP00000234389:A845T	ENSP00000234389:A845T	A	+	1	0	GRIN3B	959683	0.994000	0.37717	0.954000	0.39281	0.981000	0.71138	2.365000	0.44196	1.661000	0.50771	0.462000	0.41574	GCT	G|0.875;A|0.125	0.125	strong		0.677	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
CEACAM5	1048	hgsc.bcm.edu	37	19	42213868	42213868	+	Missense_Mutation	SNP	A	A	G	rs34155934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:42213868A>G	ENST00000221992.6	+	2	448	c.334A>G	c.(334-336)Atc>Gtc	p.I112V	CEA_ENST00000598976.1_Missense_Mutation_p.I112V|CEACAM5_ENST00000405816.1_Missense_Mutation_p.I112V|CEACAM7_ENST00000599715.1_5'Flank|CEACAM5_ENST00000398599.4_Missense_Mutation_p.I112V	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	112	Ig-like 1.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		GATCCAGAACATCATCCAGAA	0.453													a|||	649	0.129593	0.2799	0.0865	5008	,	,		19981	0.0		0.1958	False		,,,				2504	0.0225				p.I112V		Atlas-SNP	.											.	CEACAM5	84	.	0			c.A334G						PASS	.	A	VAL/ILE	1093,3313		181,731,1291	230.0	234.0	233.0		334	-0.9	0.0	19	dbSNP_126	233	1294,7306		115,1064,3121	no	missense	CEACAM5	NM_004363.2	29	296,1795,4412	GG,GA,AA		15.0465,24.8071,18.3531	benign	112/703	42213868	2387,10619	2203	4300	6503	SO:0001583	missense	1048	exon2			CAGAACATCATCC	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.334A>G	19.37:g.42213868A>G	ENSP00000221992:p.Ile112Val	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	175	92	0.525714	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	261|261	0.11950549450549451|0.11950549450549451	96|96	0.1951219512195122|0.1951219512195122	34|34	0.09392265193370165|0.09392265193370165	0|0	0.0|0.0	131|131	0.17282321899736147|0.17282321899736147	-|-	0.008|0.008	-1.883991|-1.883991	0.00532|0.00532	0.248071|0.248071	0.150465|0.150465	ENSG00000105388|ENSG00000105388	ENST00000398599|ENST00000221992;ENST00000405816;ENST00000378181	.|T;T	.|0.63255	.|-0.03;-0.03	3.09|3.09	-0.944|-0.944	0.10392|0.10392	.|Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00026|0.00026	-2.66|-2.66	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.18741	.|0.03;0.0;0.0	.|B;B;B	.|0.28305	.|0.088;0.002;0.002	T|T	0.30563|0.30563	-0.9974|-0.9974	4|8	.|0.02654	.|T	.|1	.|.	3.103|3.103	0.06333|0.06333	0.3082:0.2268:0.465:0.0|0.3082:0.2268:0.465:0.0	rs34155934|rs34155934	.|112;112;112	.|Q8N4D0;P06731;Q53G30	.|.;CEAM5_HUMAN;.	R|V	108|112	.|ENSP00000221992:I112V;ENSP00000385072:I112V	.|ENSP00000221992:I112V	H|I	+|+	2|1	0|0	CEACAM5|CEACAM5	46905708|46905708	0.000000|0.000000	0.05858|0.05858	0.006000|0.006000	0.13384|0.13384	0.011000|0.011000	0.07611|0.07611	-0.152000|-0.152000	0.10159|0.10159	0.127000|0.127000	0.18452|0.18452	-0.769000|-0.769000	0.03391|0.03391	CAT|ATC	A|0.834;G|0.166	0.166	strong		0.453	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
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 GAIIx	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	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	258	72	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	
CEP120	153241	hgsc.bcm.edu	37	5	122718736	122718736	+	Missense_Mutation	SNP	G	G	C	rs6595440	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:122718736G>C	ENST00000306467.5	-	12	2108	c.1804C>G	c.(1804-1806)Cta>Gta	p.L602V	CEP120_ENST00000328236.5_Missense_Mutation_p.L602V|CEP120_ENST00000306481.6_Missense_Mutation_p.L576V			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	602			L -> V (in dbSNP:rs6595440). {ECO:0000269|PubMed:14702039}.		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						TAATCTTCTAGAGTCACTGTG	0.254													G|||	2065	0.41234	0.2935	0.4078	5008	,	,		17690	0.506		0.4453	False		,,,				2504	0.4458				p.L602V		Atlas-SNP	.											.	CEP120	72	.	0			c.C1804G						PASS	.	G	VAL/LEU,VAL/LEU	1415,2985	427.0+/-341.4	238,939,1023	43.0	44.0	44.0		1726,1804	1.9	0.7	5	dbSNP_116	44	3666,4926	507.5+/-376.8	780,2106,1410	yes	missense,missense	CEP120	NM_001166226.1,NM_153223.3	32,32	1018,3045,2433	CC,CG,GG		42.6676,32.1591,39.1087	probably-damaging,probably-damaging	576/961,602/987	122718736	5081,7911	2200	4296	6496	SO:0001583	missense	153241	exon13			CTTCTAGAGTCAC	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.1804C>G	5.37:g.122718736G>C	ENSP00000303058:p.Leu602Val	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	37	CCDS4134.2	955	0.43727106227106227	149	0.30284552845528456	146	0.40331491712707185	295	0.5157342657342657	365	0.4815303430079156	G	16.01	3.001820	0.54254	0.321591	0.426676	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481;ENST00000508442	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.92	1.93	0.25924	.	0.080760	0.51477	N	0.000094	T	0.00012	0.0000	M	0.73962	2.25	0.09310	P	0.9999999999999104	D	0.89917	1.0	D	0.91635	0.999	T	0.47661	-0.9100	9	0.72032	D	0.01	-12.0814	6.9203	0.24385	0.2901:0.1153:0.5945:0.0	rs6595440;rs17474014;rs52804850;rs57437586;rs6595440	602	Q8N960	CE120_HUMAN	V	602;602;576;576	ENSP00000303058:L602V;ENSP00000327504:L602V;ENSP00000307419:L576V;ENSP00000421620:L576V	ENSP00000303058:L602V	L	-	1	2	CEP120	122746635	1.000000	0.71417	0.710000	0.30468	0.945000	0.59286	2.765000	0.47621	0.058000	0.16222	-0.142000	0.14014	CTA	G|0.598;C|0.402	0.402	strong		0.254	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
ABCC8	6833	hgsc.bcm.edu	37	11	17419279	17419279	+	Silent	SNP	C	C	T	rs1799859	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:17419279C>T	ENST00000389817.3	-	31	3887	c.3819G>A	c.(3817-3819)agG>agA	p.R1273R	ABCC8_ENST00000302539.4_Silent_p.R1274R			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	1273	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	CAGAGAGCTCCCTGTGCAGGG	0.652													C|||	1958	0.390974	0.77	0.4236	5008	,	,		18243	0.0873		0.2704	False		,,,				2504	0.2924				p.R1273R		Atlas-SNP	.											.	ABCC8	170	.	0			c.G3819A	GRCh37	CM981881	ABCC8	M	rs1799859	PASS	.	C		3006,1394	686.5+/-404.7	1022,962,216	90.0	84.0	86.0		3819	-0.4	1.0	11	dbSNP_89	86	2314,6272	389.5+/-342.9	307,1700,2286	no	coding-synonymous	ABCC8	NM_000352.3		1329,2662,2502	TT,TC,CC		26.9509,31.6818,40.9672		1273/1582	17419279	5320,7666	2200	4293	6493	SO:0001819	synonymous_variant	6833	exon31			GAGCTCCCTGTGC	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.3819G>A	11.37:g.17419279C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Silent	SNP	ENST00000389817.3	37	CCDS31437.1	723	0.33104395604395603	322	0.6544715447154471	144	0.39779005524861877	56	0.0979020979020979	201	0.26517150395778366	C	9.687	1.150834	0.21371	0.683182	0.269509	ENSG00000006071	ENST00000528374	.	.	.	5.12	-0.368	0.12537	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27281	P	0.9580932	.	.	.	.	.	.	T	0.35549	-0.9784	3	.	.	.	.	0.9041	0.01281	0.1595:0.2632:0.1952:0.3822	rs1799859;rs2229689;rs4148643;rs12787564;rs17846763;rs57092202;rs1799859	.	.	.	R	97	.	.	G	-	1	0	ABCC8	17375855	0.983000	0.35010	0.977000	0.42913	0.974000	0.67602	0.311000	0.19380	0.034000	0.15491	0.555000	0.69702	GGA	C|0.611;T|0.389	0.389	strong		0.652	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
TNFSF13	8741	hgsc.bcm.edu	37	17	7462555	7462555	+	Missense_Mutation	SNP	G	G	A	rs11552708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7462555G>A	ENST00000338784.4	+	1	642	c.199G>A	c.(199-201)Ggg>Agg	p.G67R	TNFSF13_ENST00000349228.4_Missense_Mutation_p.G67R|TNFSF12_ENST00000557233.1_Intron|TNFSF13_ENST00000396542.1_Missense_Mutation_p.G50R|TNFSF12-TNFSF13_ENST00000293826.4_Intron|TNFSF13_ENST00000483039.1_Intron|SENP3_ENST00000321337.7_5'Flank|TNFSF13_ENST00000380535.4_Missense_Mutation_p.G67R|SENP3_ENST00000429205.2_5'Flank|TNFSF13_ENST00000396545.4_Missense_Mutation_p.G67R	NM_003808.3	NP_003799.1	O75888	TNF13_HUMAN	tumor necrosis factor (ligand) superfamily, member 13	67			G -> R (in dbSNP:rs11552708). {ECO:0000269|Ref.9}.		gene expression (GO:0010467)|immunoglobulin production in mucosal tissue (GO:0002426)|mRNA metabolic process (GO:0016071)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of isotype switching to IgA isotypes (GO:0048298)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	receptor binding (GO:0005102)			large_intestine(2)|lung(2)|skin(1)	5		Prostate(122;0.157)				CCGGCTGCAGGGGACAGGAGG	0.647													A|||	690	0.13778	0.084	0.1499	5008	,	,		15359	0.3026		0.1004	False		,,,				2504	0.0706				p.G67R		Atlas-SNP	.											.	TNFSF13	12	.	0			c.G199A						PASS	.	A	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,	356,3942		14,328,1807	11.0	11.0	11.0		199,199,148,199,199,199,	2.2	1.0	17	dbSNP_120	11	932,7508		61,810,3349	yes	missense,missense,missense,missense,missense,missense,intron	TNFSF13,TNFSF12-TNFSF13	NM_001198622.1,NM_001198623.1,NM_001198624.1,NM_003808.3,NM_172087.2,NM_172088.2,NM_172089.3	125,125,125,125,125,125,	75,1138,5156	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	11.0427,8.2829,10.1115	,,,,,,	67/224,67/223,50/206,67/251,67/235,67/248,	7462555	1288,11450	2149	4220	6369	SO:0001583	missense	8741	exon1			CTGCAGGGGACAG	AF046888	CCDS11111.1, CCDS11112.1, CCDS42256.1, CCDS56019.1, CCDS73957.1	17p13.1	2007-07-23			ENSG00000161955	ENSG00000161955		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11928	protein-coding gene	gene with protein product		604472				9743536	Standard	NM_172088		Approved	APRIL, CD256		O75888	OTTHUMG00000108145	ENST00000338784.4:c.199G>A	17.37:g.7462555G>A	ENSP00000343505:p.Gly67Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	127	61	0.480315	NM_001198623	A8MYD5|B4DVT2|Q541E1|Q5U0G8|Q96HV6|Q9P1M8|Q9P1M9	Missense_Mutation	SNP	ENST00000338784.4	37	CCDS11111.1	378	0.17307692307692307	34	0.06910569105691057	55	0.15193370165745856	209	0.36538461538461536	80	0.10554089709762533	A	0.101	-1.151752	0.01700	0.082829	0.110427	ENSG00000161955	ENST00000396542;ENST00000438470;ENST00000436057;ENST00000349228;ENST00000338784;ENST00000380535;ENST00000396545	D;T;T;D;D;D;D	0.97016	-4.2;1.66;1.65;-3.64;-3.7;-4.21;-3.7	4.88	2.21	0.28008	.	.	.	.	.	T	0.00012	0.0000	N	0.00419	-1.52	0.53688	P	2.2999999999995246E-5	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.06405	0.0;0.0;0.002;0.001;0.001	T	0.37220	-0.9715	8	0.13853	T	0.58	-2.4838	3.3198	0.07047	0.5011:0.2259:0.273:0.0	rs11552708;rs58340751;rs11552708	67;67;67;67;67	B4DVT2;Q2QBA2;O75888-2;O75888;O75888-3	.;.;.;TNF13_HUMAN;.	R	50;50;50;67;67;67;67	ENSP00000379792:G50R;ENSP00000390771:G50R;ENSP00000410094:G50R;ENSP00000314455:G67R;ENSP00000343505:G67R;ENSP00000369908:G67R;ENSP00000379794:G67R	ENSP00000343505:G67R	G	+	1	0	TNFSF13	7403279	1.000000	0.71417	0.998000	0.56505	0.674000	0.39518	1.442000	0.35046	0.285000	0.22329	-0.361000	0.07541	GGG	G|0.857;A|0.143	0.143	strong		0.647	TNFSF13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226948.2	NM_003808	
NECAB3	63941	hgsc.bcm.edu	37	20	32248163	32248163	+	Silent	SNP	C	C	T	rs3746460	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:32248163C>T	ENST00000246190.6	-	6	481	c.426G>A	c.(424-426)acG>acA	p.T142T	C20orf144_ENST00000375222.3_5'Flank|RP1-63M2.6_ENST00000607224.1_RNA|NECAB3_ENST00000375238.4_Silent_p.T142T|NECAB3_ENST00000606525.1_5'UTR	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	142					protein metabolic process (GO:0019538)|protein secretion (GO:0009306)|regulation of amyloid precursor protein biosynthetic process (GO:0042984)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|Golgi cis cisterna (GO:0000137)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			large_intestine(3)|lung(5)|skin(2)	10						GCAGGAAGCGCGTCACAAACT	0.652													c|||	1479	0.295327	0.2769	0.2104	5008	,	,		19779	0.3909		0.3181	False		,,,				2504	0.2587				p.T142T		Atlas-SNP	.											.	NECAB3	27	.	0			c.G426A						PASS	.	T	,	1104,3052		145,814,1119	49.0	55.0	53.0		426,426	-10.2	0.3	20	dbSNP_107	53	2492,5940		385,1722,2109	no	coding-synonymous,coding-synonymous	NECAB3	NM_031231.3,NM_031232.3	,	530,2536,3228	TT,TC,CC		29.5541,26.564,28.5669	,	142/363,142/397	32248163	3596,8992	2078	4216	6294	SO:0001819	synonymous_variant	63941	exon6			GAAGCGCGTCACA	AB039947	CCDS42866.1, CCDS42867.1	20q11.21	2013-01-10	2007-12-06	2007-12-06	ENSG00000125967	ENSG00000125967		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	15851	protein-coding gene	gene with protein product	"""EF-hand calcium binding protein 3"""	612478	"""amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein"""	SYTIP2, APBA2BP		10833507	Standard	NM_031232		Approved	XB51, dJ63M2.4, NIP1, dJ63M2.5, EFCBP3	uc002wzn.4	Q96P71	OTTHUMG00000032264	ENST00000246190.6:c.426G>A	20.37:g.32248163C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_031232	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Silent	SNP	ENST00000246190.6	37	CCDS42866.1																																																																																			C|0.701;T|0.299	0.299	strong		0.652	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2		
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 GAIIx	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	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	215	50	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	
MAPK12	6300	hgsc.bcm.edu	37	22	50695370	50695370	+	Silent	SNP	G	G	A	rs2072876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50695370G>A	ENST00000215659.8	-	5	765	c.450C>T	c.(448-450)atC>atT	p.I150I	MAPK12_ENST00000497036.1_5'UTR|MAPK12_ENST00000395780.1_Intron	NM_002969.3	NP_002960.2	P53778	MK12_HUMAN	mitogen-activated protein kinase 12	150	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle arrest (GO:0007050)|DNA damage induced protein phosphorylation (GO:0006975)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of peptidase activity (GO:0010952)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCACTCTGTGGATGATGCCGG	0.657													G|||	191	0.038139	0.0008	0.0317	5008	,	,		15337	0.0913		0.0318	False		,,,				2504	0.045				p.I150I		Atlas-SNP	.											.	MAPK12	43	.	0			c.C450T						PASS	.	G		18,4366		0,18,2174	28.0	29.0	28.0		450	3.7	1.0	22	dbSNP_96	28	199,8391		1,197,4097	no	coding-synonymous	MAPK12	NM_002969.3		1,215,6271	AA,AG,GG		2.3166,0.4106,1.6726		150/368	50695370	217,12757	2192	4295	6487	SO:0001819	synonymous_variant	6300	exon5			TCTGTGGATGATG	U66243	CCDS14089.1	22q13.3	2012-05-08			ENSG00000188130	ENSG00000188130	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6874	protein-coding gene	gene with protein product		602399		SAPK3		9169156	Standard	NM_002969		Approved	ERK6, PRKM12, p38gamma, SAPK-3	uc003bkm.1	P53778	OTTHUMG00000030145	ENST00000215659.8:c.450C>T	22.37:g.50695370G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_002969	Q14260|Q6IC53|Q99588|Q99672	Silent	SNP	ENST00000215659.8	37	CCDS14089.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	MAPK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074999.2	NM_002969	
TNRC18	84629	hgsc.bcm.edu	37	7	5353344	5353344	+	Missense_Mutation	SNP	G	G	A	rs12532973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:5353344G>A	ENST00000430969.1	-	27	7526	c.7178C>T	c.(7177-7179)cCg>cTg	p.P2393L	TNRC18_ENST00000399537.4_Missense_Mutation_p.P2393L	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2393	Pro-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGGCTGCGGCGGTGCCGGGCG	0.711													g|||	449	0.0896565	0.0605	0.1758	5008	,	,		11080	0.0605		0.1044	False		,,,				2504	0.0828				p.P2393L		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7178T						PASS	.	A	LEU/PRO	195,2925		8,179,1373	11.0	13.0	13.0		7178	2.9	0.0	7	dbSNP_120	13	764,6376		35,694,2841	no	missense	TNRC18	NM_001080495.2	98	43,873,4214	AA,AG,GG		10.7003,6.25,9.347	benign	2393/2969	5353344	959,9301	1560	3570	5130	SO:0001583	missense	84629	exon27			TGCGGCGGTGCCG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7178C>T	7.37:g.5353344G>A	ENSP00000395538:p.Pro2393Leu	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	16	13	0.8125	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	203	0.09294871794871795	34	0.06910569105691057	51	0.1408839779005525	33	0.057692307692307696	85	0.11213720316622691	g	0.006	-2.116432	0.00349	0.0625	0.107003	ENSG00000182095	ENST00000399537;ENST00000430969	T;T	0.12361	2.69;2.71	4.73	2.94	0.34122	.	0.800836	0.10212	N	0.701975	T	0.00109	0.0003	L	0.46157	1.445	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.26780	-1.0093	9	0.20519	T	0.43	.	9.7442	0.40437	0.1538:0.0:0.8462:0.0	rs12532973	2393	O15417	TNC18_HUMAN	L	2393	ENSP00000382452:P2393L;ENSP00000395538:P2393L	ENSP00000382452:P2393L	P	-	2	0	TNRC18	5319870	0.730000	0.28100	0.001000	0.08648	0.000000	0.00434	4.155000	0.58131	0.442000	0.26555	-0.927000	0.02713	CCG	G|0.908;A|0.092	0.092	strong		0.711	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
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 GAIIx	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		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	112	50	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	
MYBPH	4608	hgsc.bcm.edu	37	1	203143725	203143725	+	Splice_Site	SNP	G	G	C	rs2642531	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203143725G>C	ENST00000255416.4	-	3	398	c.341C>G	c.(340-342)gCc>gGc	p.A114G		NM_004997.2	NP_004988.2	Q13203	MYBPH_HUMAN	myosin binding protein H	114	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		A -> G (in dbSNP:rs2642531).		cell adhesion (GO:0007155)|regulation of striated muscle contraction (GO:0006942)	myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			endometrium(5)|large_intestine(6)|lung(7)|skin(1)|urinary_tract(1)	20			BRCA - Breast invasive adenocarcinoma(75;0.153)	Colorectal(1306;0.0306)		CCACTCCGAGGCTGAGGGGAT	0.612													g|||	1271	0.253794	0.528	0.2522	5008	,	,		17735	0.1468		0.1352	False		,,,				2504	0.1166				p.A114G	NSCLC(32;174 1025 14462 23899 42933)	Atlas-SNP	.											.	MYBPH	41	.	0			c.C341G						PASS	.	C	GLY/ALA	2143,2263		534,1075,594	28.0	23.0	25.0		341	4.6	1.0	1	dbSNP_100	25	1124,7476		86,952,3262	yes	missense-near-splice	MYBPH	NM_004997.2	60	620,2027,3856	CC,CG,GG		13.0698,48.6382,25.1192	benign	114/478	203143725	3267,9739	2203	4300	6503	SO:0001630	splice_region_variant	4608	exon3			TCCGAGGCTGAGG	BC044226	CCDS30975.1	1q32.1	2013-02-11	2001-11-28		ENSG00000133055	ENSG00000133055		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7552	protein-coding gene	gene with protein product		160795	"""myosin-binding protein H"""			8486381	Standard	NM_004997		Approved		uc001gzh.1	Q13203	OTTHUMG00000042121	ENST00000255416.4:c.341-1C>G	1.37:g.203143725G>C		Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	299	157	0.525084	NM_004997	Q16886|Q86YC5	Missense_Mutation	SNP	ENST00000255416.4	37	CCDS30975.1	536	0.2454212454212454	263	0.5345528455284553	85	0.23480662983425415	91	0.1590909090909091	97	0.1279683377308707	g	10.09	1.255596	0.22965	0.486382	0.130698	ENSG00000133055	ENST00000255416	T	0.54866	0.55	5.53	4.62	0.57501	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.133482	0.34245	N	0.004140	T	0.00012	0.0000	N	0.17872	0.535	0.30470	P	0.773413	B	0.20780	0.048	B	0.25614	0.062	T	0.45600	-0.9250	9	0.45353	T	0.12	.	12.5921	0.56449	0.0:0.1669:0.8331:0.0	rs2642531;rs3820146;rs59912116;rs2642531	114	Q13203	MYBPH_HUMAN	G	114	ENSP00000255416:A114G	ENSP00000255416:A114G	A	-	2	0	MYBPH	201410348	0.997000	0.39634	1.000000	0.80357	0.037000	0.13140	1.982000	0.40638	1.346000	0.45694	-0.121000	0.15023	GCC	G|0.736;C|0.264	0.264	strong		0.612	MYBPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100264.1	NM_004997	Missense_Mutation
GRID2IP	392862	hgsc.bcm.edu	37	7	6550584	6550584	+	Missense_Mutation	SNP	G	G	A	rs61732374	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6550584G>A	ENST00000457091.2	-	9	1509	c.1510C>T	c.(1510-1512)Cgc>Tgc	p.R504C	GRID2IP_ENST00000435185.1_Missense_Mutation_p.R320C|GRID2IP_ENST00000452113.1_Missense_Mutation_p.R313C	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	504					long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						AGGCTGCGGCGGCACATGGAG	0.682													G|||	22	0.00439297	0.0008	0.0072	5008	,	,		14795	0.0		0.0139	False		,,,				2504	0.002				p.R504C		Atlas-SNP	.											.	GRID2IP	82	.	0			c.C1510T						PASS	.	G	CYS/ARG	1,1383		0,1,691	21.0	22.0	22.0		1510	4.5	1.0	7	dbSNP_129	22	57,3125		0,57,1534	no	missense	GRID2IP	NM_001145118.1	180	0,58,2225	AA,AG,GG		1.7913,0.0723,1.2703	probably-damaging	504/1212	6550584	58,4508	692	1591	2283	SO:0001583	missense	392862	exon9			TGCGGCGGCACAT		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.1510C>T	7.37:g.6550584G>A	ENSP00000397351:p.Arg504Cys	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_001145118		Missense_Mutation	SNP	ENST00000457091.2	37	CCDS47537.1	21	0.009615384615384616	10	0.02032520325203252	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	16.92	3.254730	0.59212	7.23E-4	0.017913	ENSG00000215045	ENST00000452113;ENST00000435185;ENST00000457091	T;T;T	0.50001	0.76;0.76;0.77	4.5	4.5	0.54988	.	0.190440	0.31210	U	0.008044	T	0.46502	0.1396	L	0.53249	1.67	0.58432	D	0.999996	D	0.89917	1.0	D	0.77557	0.99	T	0.60094	-0.7330	10	0.87932	D	0	.	13.4216	0.61001	0.0:0.0:1.0:0.0	.	504	A4D2P6	GRD2I_HUMAN	C	313;320;504	ENSP00000397887:R313C;ENSP00000408364:R320C;ENSP00000397351:R504C	ENSP00000408364:R320C	R	-	1	0	GRID2IP	6517109	1.000000	0.71417	1.000000	0.80357	0.409000	0.31022	2.872000	0.48467	2.452000	0.82932	0.462000	0.41574	CGC	G|0.990;A|0.010	0.010	strong		0.682	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
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 GAIIx	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_ENST00000348007.3_Intron|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.P492A|CTAGE5_ENST00000396158.2_Missense_Mutation_p.P526A|CTAGE5_ENST00000556148.1_Missense_Mutation_p.P446A|CTAGE5_ENST00000341502.5_Missense_Mutation_p.P521A|CTAGE5_ENST00000341749.3_Missense_Mutation_p.P509A|CTAGE5_ENST00000553352.1_Missense_Mutation_p.P492A|CTAGE5_ENST00000557038.1_Missense_Mutation_p.P441A|CTAGE5_ENST00000396165.4_Missense_Mutation_p.P492A|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.P1056A			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	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	100	52	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	
RHCG	51458	hgsc.bcm.edu	37	15	90023558	90023558	+	Missense_Mutation	SNP	G	G	A	rs17807723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90023558G>A	ENST00000268122.4	-	4	672	c.604C>T	c.(604-606)Cgc>Tgc	p.R202C	RHCG_ENST00000544600.1_Missense_Mutation_p.R202C	NM_016321.1	NP_057405.1	Q9UBD6	RHCG_HUMAN	Rh family, C glycoprotein	202			R -> C (in dbSNP:rs17807723).		amine transport (GO:0015837)|ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|cellular ion homeostasis (GO:0006873)|epithelial cell differentiation (GO:0030855)|homeostatic process (GO:0042592)|regulation of pH (GO:0006885)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Lung NSC(78;0.0237)|all_lung(78;0.0478)					TCTAGGTTGCGTCGGTAGAGG	0.567													G|||	398	0.0794728	0.0318	0.1023	5008	,	,		21861	0.0437		0.162	False		,,,				2504	0.0798				p.R202C		Atlas-SNP	.											.	RHCG	49	.	0			c.C604T						PASS	.	G	CYS/ARG	173,4227	114.6+/-152.6	5,163,2032	225.0	203.0	210.0		604	3.4	0.1	15	dbSNP_123	210	1165,7433	238.1+/-269.7	92,981,3226	yes	missense	RHCG	NM_016321.1	180	97,1144,5258	AA,AG,GG		13.5497,3.9318,10.2939	possibly-damaging	202/480	90023558	1338,11660	2200	4299	6499	SO:0001583	missense	51458	exon4			GGTTGCGTCGGTA	AF081497	CCDS10351.1	15q25	2013-05-22	2006-02-23		ENSG00000140519	ENSG00000140519		"""Solute carriers"""	18140	protein-coding gene	gene with protein product		605381	"""chromosome 15 open reading frame 6"", ""Rhesus blood group, C glycoprotein"""	C15orf6		10852913	Standard	NM_016321		Approved	RHGK, PDRC2, SLC42A3	uc002bnz.2	Q9UBD6	OTTHUMG00000149647	ENST00000268122.4:c.604C>T	15.37:g.90023558G>A	ENSP00000268122:p.Arg202Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	80	46	0.575	NM_016321	A8K4D4|Q6X3Y4	Missense_Mutation	SNP	ENST00000268122.4	37	CCDS10351.1	196	0.08974358974358974	21	0.042682926829268296	35	0.09668508287292818	19	0.033216783216783216	121	0.15963060686015831	G	17.65	3.441389	0.63067	0.039318	0.135497	ENSG00000140519	ENST00000544600;ENST00000268122;ENST00000536247	T;T	0.44482	0.92;0.92	5.34	3.39	0.38822	Ammonium transporter AmtB-like (3);	0.416227	0.29093	N	0.013167	T	0.00241	0.0007	L	0.34521	1.04	0.36478	P	0.13232100000000002	D;D	0.76494	0.999;0.999	P;P	0.58970	0.849;0.849	T	0.02698	-1.1122	8	.	.	.	-5.9769	14.093	0.65002	0.0:0.0:0.7168:0.2832	rs17807723;rs52804243;rs17807723	202;202	A8K4D4;Q9UBD6	.;RHCG_HUMAN	C	202;202;193	ENSP00000438123:R202C;ENSP00000268122:R202C	.	R	-	1	0	RHCG	87824562	1.000000	0.71417	0.099000	0.21106	0.604000	0.37047	6.523000	0.73787	0.593000	0.29745	-0.318000	0.08688	CGC	G|0.905;A|0.095	0.095	strong		0.567	RHCG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000312855.2	NM_016321	
GJB3	2707	hgsc.bcm.edu	37	1	35250457	35250457	+	Missense_Mutation	SNP	C	C	T	rs1805063	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:35250457C>T	ENST00000373366.2	+	2	709	c.94C>T	c.(94-96)Cgg>Tgg	p.R32W	RP1-34M23.5_ENST00000542839.1_RNA|GJB3_ENST00000373362.3_Missense_Mutation_p.R32W	NM_024009.2	NP_076872.1	O75712	CXB3_HUMAN	gap junction protein, beta 3, 31kDa	32			R -> W (in dbSNP:rs1805063). {ECO:0000269|PubMed:10757647, ECO:0000269|PubMed:10790215, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19283857}.		cell communication (GO:0007154)|in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|sensory perception of sound (GO:0007605)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	connexon complex (GO:0005922)|cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|prostate(3)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GTTCGTCTTCCGGGTGCTGGT	0.607													c|||	65	0.0129792	0.0008	0.0202	5008	,	,		20216	0.0		0.0378	False		,,,				2504	0.0123				p.R32W		Atlas-SNP	.											.	GJB3	40	.	0			c.C94T	GRCh37	CM001173	GJB3	M	rs1805063	PASS	.	C	TRP/ARG,TRP/ARG	36,4370	41.6+/-74.8	0,36,2167	162.0	120.0	134.0		94,94	5.8	1.0	1	dbSNP_89	134	264,8336	101.9+/-163.1	4,256,4040	yes	missense,missense	GJB3	NM_001005752.1,NM_024009.2	101,101	4,292,6207	TT,TC,CC		3.0698,0.8171,2.3066	probably-damaging,probably-damaging	32/271,32/271	35250457	300,12706	2203	4300	6503	SO:0001583	missense	2707	exon2			GTCTTCCGGGTGC	BC012918	CCDS384.1	1p34	2008-05-14	2007-01-16		ENSG00000188910	ENSG00000188910		"""Ion channels / Gap junction proteins (connexins)"""	4285	protein-coding gene	gene with protein product	"""connexin 31"""	603324	"""gap junction protein, beta 3, 31kD (connexin 31)"", ""gap junction protein, beta 3, 31kDa (connexin 31)"", ""erythrokeratodermia variabilis"""	DFNA2, EKV		9843210, 9704026	Standard	NM_024009		Approved	CX31	uc001bxy.3	O75712	OTTHUMG00000004051	ENST00000373366.2:c.94C>T	1.37:g.35250457C>T	ENSP00000362464:p.Arg32Trp	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	118	43	0.364407	NM_001005752	B2R790|Q2TAZ8	Missense_Mutation	SNP	ENST00000373366.2	37	CCDS384.1	32	0.014652014652014652	0	0.0	7	0.019337016574585635	0	0.0	25	0.032981530343007916	c	15.63	2.890415	0.52014	0.008171	0.030698	ENSG00000188910	ENST00000373366;ENST00000373362;ENST00000543647	D;D	0.99695	-6.43;-6.43	5.85	5.85	0.93711	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99462	0.9809	H	0.97186	3.955	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.90794	0.4689	10	0.87932	D	0	.	19.7879	0.96445	0.0:1.0:0.0:0.0	rs1805063;rs52821309	32	O75712	CXB3_HUMAN	W	32	ENSP00000362464:R32W;ENSP00000362460:R32W	ENSP00000362460:R32W	R	+	1	2	GJB3	35023044	1.000000	0.71417	0.996000	0.52242	0.022000	0.10575	1.086000	0.30853	2.771000	0.95319	0.561000	0.74099	CGG	C|0.980;T|0.020	0.020	strong		0.607	GJB3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011559.1	NM_024009	
SYNGR2	9144	hgsc.bcm.edu	37	17	76167047	76167047	+	Silent	SNP	C	C	T	rs1062668	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:76167047C>T	ENST00000225777.3	+	2	308	c.249C>T	c.(247-249)gcC>gcT	p.A83A	SYNGR2_ENST00000592456.1_3'UTR|SYNGR2_ENST00000590201.1_Silent_p.A27A|SYNGR2_ENST00000588282.1_Silent_p.A83A|SYNGR2_ENST00000589711.1_Intron|SYNGR2_ENST00000585591.1_Silent_p.A83A			O43760	SNG2_HUMAN	synaptogyrin 2	83	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				protein targeting (GO:0006605)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)				endometrium(2)|large_intestine(1)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	7			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.0994)			TGGCCTCGGCCTTCTTCTTGG	0.582													C|||	383	0.0764776	0.0386	0.1153	5008	,	,		19484	0.002		0.1203	False		,,,				2504	0.1319				p.A83A		Atlas-SNP	.											SYNGR2,NS,carcinoma,+2,1	SYNGR2	17	1	0			c.C249T						PASS	.	C		252,4154	146.5+/-181.1	7,238,1958	121.0	98.0	106.0		249	3.9	1.0	17	dbSNP_86	106	1254,7346	250.7+/-277.5	87,1080,3133	no	coding-synonymous	SYNGR2	NM_004710.3		94,1318,5091	TT,TC,CC		14.5814,5.7195,11.5793		83/225	76167047	1506,11500	2203	4300	6503	SO:0001819	synonymous_variant	9144	exon2			CTCGGCCTTCTTC	AJ002308	CCDS11753.1	17q25.3	2014-09-11			ENSG00000108639	ENSG00000108639			11499	protein-coding gene	gene with protein product	"""cellugyrin"""	603926				9760194	Standard	NM_004710		Approved		uc002juu.1	O43760	OTTHUMG00000177457	ENST00000225777.3:c.249C>T	17.37:g.76167047C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_004710	O43762|Q3KQZ2|Q658S7	Silent	SNP	ENST00000225777.3	37	CCDS11753.1																																																																																			C|0.889;T|0.111	0.111	strong		0.582	SYNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437009.2		
PLOD1	5351	hgsc.bcm.edu	37	1	12009956	12009956	+	Missense_Mutation	SNP	G	G	A	rs7551175	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12009956G>A	ENST00000196061.4	+	3	322	c.295G>A	c.(295-297)Gca>Aca	p.A99T	PLOD1_ENST00000485046.1_3'UTR|PLOD1_ENST00000376369.3_Missense_Mutation_p.A146T	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	99			A -> T (in dbSNP:rs7551175). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1577494}.		cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	CATTCTCTTCGCAGACAGGTA	0.572													A|||	1500	0.299521	0.5749	0.1282	5008	,	,		17892	0.2698		0.1461	False		,,,				2504	0.2372				p.A99T		Atlas-SNP	.											.	PLOD1	75	.	0			c.G295A						PASS	.	A	THR/ALA	2356,2050	568.0+/-382.3	639,1078,486	118.0	122.0	121.0		295	2.9	1.0	1	dbSNP_116	121	1293,7307	758.8+/-407.5	99,1095,3106	yes	missense	PLOD1	NM_000302.3	58	738,2173,3592	AA,AG,GG		15.0349,46.5275,28.0563	benign	99/728	12009956	3649,9357	2203	4300	6503	SO:0001583	missense	5351	exon3			CTCTTCGCAGACA	BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"""lysyl hydroxlase 1"""	153454	"""procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"""	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.295G>A	1.37:g.12009956G>A	ENSP00000196061:p.Ala99Thr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_000302	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	37	CCDS142.1	544	0.2490842490842491	253	0.5142276422764228	48	0.13259668508287292	133	0.23251748251748253	110	0.14511873350923482	A	1.515	-0.548384	0.04024	0.534725	0.150349	ENSG00000083444	ENST00000449038;ENST00000414311;ENST00000358133;ENST00000376369;ENST00000429000;ENST00000196061	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	4.02	2.9	0.33743	.	0.556046	0.18333	N	0.144421	T	0.00012	0.0000	N	0.00028	-2.63	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46373	-0.9196	9	0.02654	T	1	.	7.7151	0.28700	0.7311:0.0:0.2689:0.0	rs7551175;rs11553678;rs17856510;rs56973305;rs7551175	146;99	B4DR87;Q02809	.;PLOD1_HUMAN	T	146;99;99;146;99;99	ENSP00000414443:A146T;ENSP00000365548:A146T;ENSP00000405372:A99T;ENSP00000196061:A99T	ENSP00000196061:A99T	A	+	1	0	PLOD1	11932543	0.531000	0.26338	0.990000	0.47175	0.965000	0.64279	1.447000	0.35101	0.163000	0.19507	-0.269000	0.10298	GCA	G|0.733;A|0.267	0.267	strong		0.572	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302	
GLT6D1	360203	hgsc.bcm.edu	37	9	138515991	138515991	+	Silent	SNP	A	A	G	rs12351198	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138515991A>G	ENST00000371763.1	-	5	1036	c.783T>C	c.(781-783)acT>acC	p.T261T		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	261					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		GCTTTTCATAAGTGCTATTGA	0.388													G|||	822	0.164137	0.1694	0.1902	5008	,	,		20043	0.2183		0.1362	False		,,,				2504	0.1115				p.T261T		Atlas-SNP	.											.	GLT6D1	56	.	0			c.T783C						PASS	.	G		542,3134		42,458,1338	174.0	172.0	172.0		783	-1.6	0.0	9	dbSNP_120	172	1144,7040		94,956,3042	no	coding-synonymous	GLT6D1	NM_182974.2		136,1414,4380	GG,GA,AA		13.9785,14.7443,14.2159		261/277	138515991	1686,10174	1838	4092	5930	SO:0001819	synonymous_variant	360203	exon5			TTCATAAGTGCTA	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.783T>C	9.37:g.138515991A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	158	64	0.405063	NM_182974		Silent	SNP	ENST00000371763.1	37	CCDS43900.1																																																																																			A|0.850;G|0.150	0.150	strong		0.388	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
ACAN	176	hgsc.bcm.edu	37	15	89398407	89398407	+	Missense_Mutation	SNP	C	C	T	rs3743398	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89398407C>T	ENST00000561243.1	+	11	2591	c.2591C>T	c.(2590-2592)cCt>cTt	p.P864L	ACAN_ENST00000559004.1_Missense_Mutation_p.P864L|ACAN_ENST00000439576.2_Missense_Mutation_p.P864L|ACAN_ENST00000352105.7_Missense_Mutation_p.P864L			P16112	PGCA_HUMAN	aggrecan	863	CS-1.				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)			TCTGGGGCCCCTGATGTCAGT	0.607													C|||	409	0.0816693	0.0151	0.1081	5008	,	,		19429	0.0952		0.1909	False		,,,				2504	0.0266				p.P864L		Atlas-SNP	.											.	ACAN	220	.	0			c.C2591T						PASS	.	C	LEU/PRO,LEU/PRO	138,3846		4,130,1858	47.0	53.0	51.0		2591,2591	4.9	0.5	15	dbSNP_107	51	1673,6659		152,1369,2645	yes	missense,missense	ACAN	NM_001135.3,NM_013227.3	98,98	156,1499,4503	TT,TC,CC		20.0792,3.4639,14.7044	probably-damaging,probably-damaging	864/2432,864/2531	89398407	1811,10505	1992	4166	6158	SO:0001583	missense	176	exon12			GGGCCCCTGATGT	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.2591C>T	15.37:g.89398407C>T	ENSP00000453342:p.Pro864Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	256	0.11721611721611722	11	0.022357723577235773	49	0.13535911602209943	55	0.09615384615384616	141	0.18601583113456466	C	15.30	2.793935	0.50102	0.034639	0.200792	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.03468	4.19;3.92	5.79	4.87	0.63330	.	0.000000	0.32343	N	0.006224	T	0.00012	0.0000	M	0.65975	2.015	0.53005	P	3.799999999998249E-5	P;D	0.76494	0.584;0.999	B;D	0.71184	0.16;0.972	T	0.33599	-0.9862	9	0.09338	T	0.73	-12.1183	9.3039	0.37863	0.1416:0.7849:0.0:0.0735	rs3743398;rs60866336;rs3743398	864;864	E7ENV9;E7EX88	.;.	L	864	ENSP00000387356:P864L;ENSP00000341615:P864L	ENSP00000268134:P864L	P	+	2	0	ACAN	87199411	0.372000	0.25064	0.480000	0.27341	0.521000	0.34408	1.014000	0.29950	2.722000	0.93159	0.655000	0.94253	CCT	C|0.871;T|0.129	0.129	strong		0.607	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
CLDN6	9074	hgsc.bcm.edu	37	16	3065596	3065596	+	Missense_Mutation	SNP	T	T	C	rs2257295	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3065596T>C	ENST00000396925.1	-	3	855	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	TNFRSF12A_ENST00000573001.1_5'Flank|CLDN6_ENST00000328796.4_Missense_Mutation_p.I143V|CLDN6_ENST00000572154.1_Intron			P56747	CLD6_HUMAN	claudin 6	143			I -> V (in dbSNP:rs2257295). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		calcium-independent cell-cell adhesion (GO:0016338)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TCCCGGATGATGGCATGCGCC	0.617													T|||	1497	0.298922	0.3548	0.3343	5008	,	,		18815	0.1925		0.3708	False		,,,				2504	0.2342				p.I143V		Atlas-SNP	.											CLDN6,rectum,carcinoma,0,3	CLDN6	31	3	0			c.A427G						PASS	.	T	VAL/ILE	1631,2761		311,1009,876	23.0	25.0	25.0		427	2.5	0.9	16	dbSNP_100	25	3379,5217		688,2003,1607	no	missense	CLDN6	NM_021195.4	29	999,3012,2483	CC,CT,TT		39.309,37.1357,38.5741	benign	143/221	3065596	5010,7978	2196	4298	6494	SO:0001583	missense	9074	exon2			GGATGATGGCATG	AJ249735	CCDS10488.1	16p13.3	2008-08-01			ENSG00000184697	ENSG00000184697		"""Claudins"""	2048	protein-coding gene	gene with protein product		615798				9892664, 18234789	Standard	NM_021195		Approved		uc002csu.4	P56747	OTTHUMG00000128999	ENST00000396925.1:c.427A>G	16.37:g.3065596T>C	ENSP00000380131:p.Ile143Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	100	32	0.32	NM_021195	B3KQP9|D3DUA5	Missense_Mutation	SNP	ENST00000396925.1	37	CCDS10488.1	695	0.3182234432234432	179	0.3638211382113821	122	0.3370165745856354	124	0.21678321678321677	270	0.3562005277044855	T	6.973	0.549571	0.13374	0.371357	0.39309	ENSG00000184697	ENST00000396925;ENST00000328796	D;D	0.89270	-2.49;-2.49	4.76	2.51	0.30379	.	0.125321	0.52532	N	0.000076	T	0.00012	0.0000	L	0.33245	0.995	0.32491	P	0.540211	B	0.22276	0.067	B	0.27500	0.08	T	0.10776	-1.0615	9	0.23302	T	0.38	.	7.5467	0.27770	0.0:0.1806:0.0:0.8194	rs2257295;rs17850428;rs61137178;rs2257295	143	P56747	CLD6_HUMAN	V	143	ENSP00000380131:I143V;ENSP00000328674:I143V	ENSP00000328674:I143V	I	-	1	0	CLDN6	3005597	1.000000	0.71417	0.941000	0.38009	0.114000	0.19823	1.726000	0.38085	0.423000	0.26033	0.533000	0.62120	ATC	T|0.645;C|0.355	0.355	strong		0.617	CLDN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250988.1	NM_021195	
STK17B	9262	hgsc.bcm.edu	37	2	197021372	197021372	+	Silent	SNP	T	T	A	rs12478353	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:197021372T>A	ENST00000263955.4	-	3	412	c.126A>T	c.(124-126)ggA>ggT	p.G42G	RP11-347P5.1_ENST00000606818.1_RNA|STK17B_ENST00000409228.1_Silent_p.G42G	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	42	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)			CAGCAAATTTTCCTCTGGGGG	0.348													T|||	3256	0.65016	0.4266	0.7003	5008	,	,		16560	0.9028		0.6243	False		,,,				2504	0.683				p.G42G		Atlas-SNP	.											.	STK17B	28	.	0			c.A126T						PASS	.	T		2049,2357	536.4+/-374.5	476,1097,630	70.0	74.0	73.0		126	5.1	1.0	2	dbSNP_120	73	5085,3515	615.3+/-396.4	1500,2085,715	no	coding-synonymous	STK17B	NM_004226.3		1976,3182,1345	AA,AT,TT		40.8721,46.5048,45.1484		42/373	197021372	7134,5872	2203	4300	6503	SO:0001819	synonymous_variant	9262	exon3			AAATTTTCCTCTG	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.126A>T	2.37:g.197021372T>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_004226		Silent	SNP	ENST00000263955.4	37	CCDS2315.1																																																																																			T|0.406;A|0.594	0.594	strong		0.348	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2		
POLR2B	5431	hgsc.bcm.edu	37	4	57881715	57881715	+	Silent	SNP	G	G	A	rs1713982	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57881715G>A	ENST00000381227.1	+	15	2261	c.1848G>A	c.(1846-1848)acG>acA	p.T616T	POLR2B_ENST00000441246.2_Silent_p.T609T|POLR2B_ENST00000510355.1_3'UTR|POLR2B_ENST00000431623.2_Silent_p.T541T|POLR2B_ENST00000314595.5_Silent_p.T616T			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	616					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					GGATCTATACGGATGCAGGCC	0.333													A|||	1934	0.386182	0.4342	0.2954	5008	,	,		10572	0.2986		0.3469	False		,,,				2504	0.5164				p.T616T		Atlas-SNP	.											POLR2B,colon,carcinoma,0,1	POLR2B	108	1	0			c.G1848A						scavenged	.	A		1882,2524	629.0+/-395.2	403,1076,724	119.0	125.0	123.0		1848	-2.7	1.0	4	dbSNP_89	123	2939,5661	667.8+/-402.5	487,1965,1848	no	coding-synonymous	POLR2B	NM_000938.1		890,3041,2572	AA,AG,GG		34.1744,42.7145,37.0675		616/1175	57881715	4821,8185	2203	4300	6503	SO:0001819	synonymous_variant	5431	exon14			CTATACGGATGCA		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1848G>A	4.37:g.57881715G>A		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			G|0.634;A|0.366	0.366	strong		0.333	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
ARMC4	55130	hgsc.bcm.edu	37	10	28228865	28228865	+	Silent	SNP	A	A	G	rs7893462	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:28228865A>G	ENST00000305242.5	-	14	2150	c.2058T>C	c.(2056-2058)aaT>aaC	p.N686N	ARMC4_ENST00000537576.1_Silent_p.N378N|ARMC4_ENST00000545014.1_Silent_p.N211N	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	686					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						GCAGCTGCTCATTCTCACTAT	0.438													G|||	2670	0.533147	0.469	0.5764	5008	,	,		14602	0.5		0.5477	False		,,,				2504	0.6084				p.N686N		Atlas-SNP	.											.	ARMC4	177	.	0			c.T2058C						PASS	.	G		2030,2376	613.0+/-392.1	484,1062,657	104.0	93.0	97.0		2058	-2.7	0.8	10	dbSNP_116	97	4578,4022	556.4+/-386.8	1223,2132,945	yes	coding-synonymous	ARMC4	NM_018076.2		1707,3194,1602	GG,GA,AA		46.7674,46.0735,49.1927		686/1045	28228865	6608,6398	2203	4300	6503	SO:0001819	synonymous_variant	55130	exon14			CTGCTCATTCTCA	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.2058T>C	10.37:g.28228865A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_018076	A8K906|B7Z7I1|Q9H0C0	Silent	SNP	ENST00000305242.5	37	CCDS7157.1																																																																																			A|0.488;G|0.512	0.512	strong		0.438	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	
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 GAIIx	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_ENST00000455345.2_Missense_Mutation_p.S557R|ZBBX_ENST00000392767.2_Missense_Mutation_p.S557R|ZBBX_ENST00000307529.5_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	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	169	37	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	
CR1	1378	hgsc.bcm.edu	37	1	207790088	207790088	+	Missense_Mutation	SNP	C	C	G	rs3811381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207790088C>G	ENST00000367049.4	+	41	6830	c.6830C>G	c.(6829-6831)cCt>cGt	p.P2277R	CR1_ENST00000367052.1_Missense_Mutation_p.P1827R|CR1_ENST00000367051.1_Missense_Mutation_p.P1827R|CR1_ENST00000367053.1_Missense_Mutation_p.P1827R|CR1_ENST00000400960.2_Missense_Mutation_p.P1827R	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1827					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACAAGTGACCCTCAAGGGAAT	0.517													C|||	1316	0.26278	0.1172	0.2608	5008	,	,		19452	0.3224		0.1809	False		,,,				2504	0.4836				p.P2277R		Atlas-SNP	.											.	CR1	354	.	0			c.C6830G	GRCh37	CM025385	CR1	M	rs3811381	PASS	.	C	ARG/PRO,ARG/PRO	498,3414		34,430,1492	146.0	147.0	147.0		5480,6830	-5.6	0.0	1	dbSNP_107	147	1508,6762		125,1258,2752	no	missense,missense	CR1	NM_000573.3,NM_000651.4	103,103	159,1688,4244	GG,GC,CC		18.2346,12.7301,16.4669	benign,benign	1827/2040,2277/2490	207790088	2006,10176	1956	4135	6091	SO:0001583	missense	1378	exon41			GTGACCCTCAAGG	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6830C>G	1.37:g.207790088C>G	ENSP00000356016:p.Pro2277Arg	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	212	212	1	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	429|429	0.19642857142857142|0.19642857142857142	64|64	0.13008130081300814|0.13008130081300814	102|102	0.281767955801105|0.281767955801105	131|131	0.229020979020979|0.229020979020979	132|132	0.1741424802110818|0.1741424802110818	C|C	0.010|0.010	-1.745772|-1.745772	0.00669|0.00669	0.127301|0.127301	0.182346|0.182346	ENSG00000203710|ENSG00000203710	ENST00000529814|ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	.|T;T;T;T;T	.|0.21543	.|2.0;2.0;2.0;2.0;2.0	4.15|4.15	-5.58|-5.58	0.02512|0.02512	.|Complement control module (2);Sushi/SCR/CCP (3);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.05078|0.05078	-0.115|-0.115	0.80722|0.80722	P|P	0.0|0.0	.|B;P	.|0.38711	.|0.005;0.643	.|B;B	.|0.32211	.|0.032;0.142	T|T	0.39643|0.39643	-0.9604|-0.9604	4|8	.|0.11794	.|T	.|0.64	.|.	3.1972|3.1972	0.06637|0.06637	0.5482:0.1261:0.1987:0.127|0.5482:0.1261:0.1987:0.127	rs3811381;rs56791502|rs3811381;rs56791502	.|1827;2277	.|P17927;E9PDY4	.|CR1_HUMAN;.	V|R	450|1827;1827;1827;1827;2277	.|ENSP00000356019:P1827R;ENSP00000356018:P1827R;ENSP00000356020:P1827R;ENSP00000383744:P1827R;ENSP00000356016:P2277R	.|ENSP00000356016:P2277R	L|P	+|+	1|2	0|0	CR1|CR1	205856711|205856711	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.021000|0.021000	0.10359|0.10359	-0.775000|-0.775000	0.04679|0.04679	-1.266000|-1.266000	0.02446|0.02446	-2.118000|-2.118000	0.00350|0.00350	CTC|CCT	C|0.800;G|0.200	0.200	strong		0.517	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84651185	84651185	+	Silent	SNP	C	C	A	rs8031704	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:84651185C>A	ENST00000286744.5	+	21	3029	c.2805C>A	c.(2803-2805)ccC>ccA	p.P935P	ADAMTSL3_ENST00000567476.1_Silent_p.P935P	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	935	Ig-like C2-type 1.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P935P(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TTAAGTGCCCCGTGCGACGAT	0.493													A|||	1883	0.375998	0.5681	0.2536	5008	,	,		18791	0.38		0.3419	False		,,,				2504	0.2342				p.P935P		Atlas-SNP	.											ADAMTSL3,NS,adenoma,0,2	ADAMTSL3	290	2	1	Substitution - coding silent(1)	stomach(1)	c.C2805A						PASS	.	A		2372,2034	563.1+/-381.1	649,1074,480	148.0	137.0	141.0		2805	-2.1	1.0	15	dbSNP_116	141	2959,5641	666.8+/-402.4	512,1935,1853	no	coding-synonymous	ADAMTSL3	NM_207517.2		1161,3009,2333	AA,AC,CC		34.407,46.1643,40.9888		935/1692	84651185	5331,7675	2203	4300	6503	SO:0001819	synonymous_variant	57188	exon21			GTGCCCCGTGCGA	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2805C>A	15.37:g.84651185C>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	128	126	0.984375	NM_207517	A1A566|A1A567|Q9ULI7	Silent	SNP	ENST00000286744.5	37	CCDS10326.1																																																																																			C|0.593;A|0.407	0.407	strong		0.493	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
MAGEC3	139081	hgsc.bcm.edu	37	X	140967195	140967195	+	Missense_Mutation	SNP	T	T	A	rs11095910	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:140967195T>A	ENST00000298296.1	+	3	493	c.493T>A	c.(493-495)Ttg>Atg	p.L165M	MAGEC3_ENST00000536088.1_5'Flank|MAGEC3_ENST00000443323.2_5'Flank|MAGEC3_ENST00000448920.1_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	165			L -> M (in dbSNP:rs11095910).							NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					TGGAAAAAGGTTGTGGGGGGA	0.572													t|||	1395	0.369536	0.348	0.3314	3775	,	,		10454	0.3651		0.0676	False		,,,				2504	0.2751				p.L165M		Atlas-SNP	.											.	MAGEC3	228	.	0			c.T493A						PASS	.	T	MET/LEU	1596,2227		297,764,238,570,323	26.0	21.0	23.0		493	-0.4	0.0	X	dbSNP_120	23	569,6148		19,382,149,2027,1712	yes	missense	MAGEC3	NM_138702.1	15	316,1146,387,2597,2035	AA,AT,A,TT,T		8.471,41.7473,20.5408	benign	165/644	140967195	2165,8375	2192	4289	6481	SO:0001583	missense	139081	exon3			AAAAGGTTGTGGG	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.493T>A	X.37:g.140967195T>A	ENSP00000298296:p.Leu165Met	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	163	117	0.717791	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	525	0.31645569620253167	121	0.3151041666666667	72	0.23529411764705882	136	0.3090909090909091	37	0.05096418732782369	A	0.001	-4.228477	0.00001	0.417473	0.08471	ENSG00000165509	ENST00000298296	T	0.07908	3.15	0.225	-0.451	0.12214	.	.	.	.	.	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	0.48340	-0.9044	7	0.42905	T	0.14	.	.	.	.	rs11095910;rs11095910	165	Q8TD91	MAGC3_HUMAN	M	165	ENSP00000298296:L165M	ENSP00000298296:L165M	L	+	1	2	MAGEC3	140794861	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.506000	0.00223	-2.698000	0.00400	-2.905000	0.00092	TTG	T|0.739;A|0.261	0.261	strong		0.572	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
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 GAIIx	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	PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_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	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	27	9	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	
MAML1	9794	hgsc.bcm.edu	37	5	179193598	179193598	+	Silent	SNP	C	C	T	rs3797776	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:179193598C>T	ENST00000292599.3	+	2	1850	c.1587C>T	c.(1585-1587)agC>agT	p.S529S	MAML1_ENST00000503050.1_3'UTR	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCAAGGCAGCCCGGGGTCTG	0.532													C|||	831	0.165935	0.0257	0.2161	5008	,	,		18528	0.1488		0.3231	False		,,,				2504	0.1759				p.S529S		Atlas-SNP	.											.	MAML1	118	.	0			c.C1587T						PASS	.	C		314,4092	168.7+/-199.5	17,280,1906	62.0	61.0	62.0		1587	1.2	0.4	5	dbSNP_107	62	2556,6044	416.9+/-352.3	391,1774,2135	no	coding-synonymous	MAML1	NM_014757.4		408,2054,4041	TT,TC,CC		29.7209,7.1266,22.0667		529/1017	179193598	2870,10136	2203	4300	6503	SO:0001819	synonymous_variant	9794	exon2			AGGCAGCCCGGGG	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.1587C>T	5.37:g.179193598C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_014757		Silent	SNP	ENST00000292599.3	37	CCDS34315.1																																																																																			C|0.800;T|0.200	0.200	strong		0.532	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
FAT3	120114	hgsc.bcm.edu	37	11	92088177	92088177	+	Silent	SNP	C	C	T	rs7479732	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:92088177C>T	ENST00000298047.6	+	1	2916	c.2899C>T	c.(2899-2901)Ctg>Ttg	p.L967L	FAT3_ENST00000541502.1_Silent_p.L967L|FAT3_ENST00000525166.1_Silent_p.L817L|FAT3_ENST00000409404.2_Silent_p.L967L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	967	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGATCTTGGACTGGGGGGTCA	0.458										TCGA Ovarian(4;0.039)			T|||	1758	0.351038	0.8079	0.1801	5008	,	,		19090	0.1746		0.2038	False		,,,				2504	0.1881				p.L967L		Atlas-SNP	.											FAT3_ENST00000409404,colon,carcinoma,0,2	FAT3	1822	2	0			c.C2899T						PASS	.	T		2521,1247		857,807,220	71.0	70.0	70.0		2899	2.5	1.0	11	dbSNP_116	70	1774,6460		199,1376,2542	no	coding-synonymous	FAT3	NM_001008781.2		1056,2183,2762	TT,TC,CC		21.5448,33.0945,35.7857		967/4558	92088177	4295,7707	1884	4117	6001	SO:0001819	synonymous_variant	120114	exon1			CTTGGACTGGGGG	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.2899C>T	11.37:g.92088177C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	110	99	0.9	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.697;T|0.303	0.303	strong		0.458	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
MGAT5B	146664	hgsc.bcm.edu	37	17	74936576	74936576	+	Silent	SNP	G	G	A	rs8081793	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74936576G>A	ENST00000569840.2	+	14	2251	c.1677G>A	c.(1675-1677)ccG>ccA	p.P559P	MGAT5B_ENST00000428789.2_Silent_p.P568P|MGAT5B_ENST00000301618.4_Silent_p.P557P	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	559					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCTTCAGCCCGCCCCACAGCT	0.647													G|||	1327	0.264976	0.2451	0.1744	5008	,	,		16308	0.371		0.2674	False		,,,				2504	0.2444				p.P568P		Atlas-SNP	.											.	MGAT5B	98	.	0			c.G1704A						PASS	.	G	,,	1125,3281	401.3+/-331.9	145,835,1223	76.0	69.0	71.0		1677,1671,1704	-8.8	0.6	17	dbSNP_116	71	2155,6445	370.6+/-335.9	294,1567,2439	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	439,2402,3662	AA,AG,GG		25.0581,25.5334,25.2191	,,	559/793,557/791,568/802	74936576	3280,9726	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon12			CAGCCCGCCCCAC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1677G>A	17.37:g.74936576G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			G|0.734;A|0.266	0.266	strong		0.647	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
MYOM2	9172	hgsc.bcm.edu	37	8	2041894	2041894	+	Missense_Mutation	SNP	G	G	A	rs35335787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:2041894G>A	ENST00000262113.4	+	17	2242	c.2101G>A	c.(2101-2103)Gtc>Atc	p.V701I	MYOM2_ENST00000523438.1_Missense_Mutation_p.V126I	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	701	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs35335787).		muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GGAATCAGACGTCATAAAAGT	0.498													G|||	99	0.0197684	0.0045	0.0418	5008	,	,		18692	0.0		0.0487	False		,,,				2504	0.0153				p.V701I		Atlas-SNP	.											.	MYOM2	251	.	0			c.G2101A						PASS	.	G	ILE/VAL	53,4353	54.9+/-90.9	2,49,2152	171.0	139.0	150.0		2101	1.7	0.1	8	dbSNP_126	150	504,8096	144.0+/-200.0	15,474,3811	yes	missense	MYOM2	NM_003970.2	29	17,523,5963	AA,AG,GG		5.8605,1.2029,4.2826	benign	701/1466	2041894	557,12449	2203	4300	6503	SO:0001583	missense	9172	exon17			TCAGACGTCATAA		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2101G>A	8.37:g.2041894G>A	ENSP00000262113:p.Val701Ile	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	65	0.02976190476190476	3	0.006097560975609756	17	0.04696132596685083	0	0.0	45	0.059366754617414245	G	7.286	0.610110	0.14066	0.012029	0.058605	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.55234	0.53;0.53	5.44	1.69	0.24217	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.460476	0.22308	N	0.061773	T	0.04407	0.0121	N	0.22421	0.69	0.21604	N	0.999626	B	0.06786	0.001	B	0.08055	0.003	T	0.05616	-1.0874	10	0.46703	T	0.11	.	6.9791	0.24694	0.2456:0.1192:0.6351:0.0	rs35335787;rs62478386	701	P54296	MYOM2_HUMAN	I	701;126	ENSP00000262113:V701I;ENSP00000428396:V126I	ENSP00000262113:V701I	V	+	1	0	MYOM2	2029301	0.575000	0.26692	0.090000	0.20809	0.003000	0.03518	1.416000	0.34759	0.036000	0.15547	-0.136000	0.14681	GTC	G|0.958;A|0.042	0.042	strong		0.498	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
ATG4D	84971	hgsc.bcm.edu	37	19	10664661	10664661	+	IGR	SNP	C	C	T	rs34495400	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10664661C>T	ENST00000309469.4	+	0	1949				MIR1238_ENST00000408483.1_RNA|KRI1_ENST00000312962.6_Missense_Mutation_p.R699Q|KRI1_ENST00000361821.5_Missense_Mutation_p.R695Q|RNU7-140P_ENST00000459546.1_RNA	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase						apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			TTGTTTCCTCCGCTGCCGGCC	0.637													C|||	39	0.00778754	0.003	0.0058	5008	,	,		17810	0.0		0.0179	False		,,,				2504	0.0133				p.R699Q		Atlas-SNP	.											.	KRI1	65	.	0			c.G2096A						PASS	.	C	GLN/ARG	18,4388	22.3+/-47.3	0,18,2185	22.0	22.0	22.0		2096	-2.8	0.0	19	dbSNP_126	22	131,8469	61.0+/-122.8	0,131,4169	yes	missense	KRI1	NM_023008.3	43	0,149,6354	TT,TC,CC		1.5233,0.4085,1.1456	benign	699/710	10664661	149,12857	2203	4300	6503	SO:0001628	intergenic_variant	65095	exon19			TTCCTCCGCTGCC	AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"""AUT-like 4, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog D (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog D (S. cerevisiae)"""	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582		19.37:g.10664661C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_023008	Q969K0	Missense_Mutation	SNP	ENST00000309469.4	37	CCDS12241.1	18	0.008241758241758242	3	0.006097560975609756	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	16.53	3.150273	0.57151	0.004085	0.015233	ENSG00000129347	ENST00000312962;ENST00000361821	T;T	0.10288	3.09;2.89	4.97	-2.78	0.05859	.	0.395446	0.21720	N	0.070125	T	0.02767	0.0083	L	0.38531	1.155	0.09310	N	1	B;B	0.22480	0.041;0.07	B;B	0.08055	0.003;0.003	T	0.24404	-1.0161	10	0.39692	T	0.17	-10.2205	5.3979	0.16278	0.1263:0.4773:0.0:0.3964	rs34495400	699;695	Q8N9T8;D3YTE0	KRI1_HUMAN;.	Q	699;695	ENSP00000320917:R699Q;ENSP00000355366:R695Q	ENSP00000320917:R699Q	R	-	2	0	KRI1	10525661	0.000000	0.05858	0.000000	0.03702	0.574000	0.36063	0.004000	0.13106	-0.388000	0.07797	-0.793000	0.03317	CGG	C|0.991;T|0.009	0.009	strong		0.637	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885	
KDM2B	84678	hgsc.bcm.edu	37	12	121880520	121880520	+	Silent	SNP	G	G	A	rs3751131	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121880520G>A	ENST00000377071.4	-	19	2796	c.2724C>T	c.(2722-2724)gaC>gaT	p.D908D	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Silent_p.D839D|KDM2B_ENST00000542973.1_Silent_p.D276D	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	908					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						AGCGGGAGTGGTCGCTCTCCC	0.706													G|||	1675	0.334465	0.1566	0.4006	5008	,	,		12186	0.4534		0.4046	False		,,,				2504	0.3333				p.D908D		Atlas-SNP	.											KDM2B_ENST00000377071,colon,carcinoma,-2,2	KDM2B	218	2	0			c.C2724T						scavenged	.	G	,	708,3046		79,550,1248	12.0	13.0	13.0		2517,2724	2.2	1.0	12	dbSNP_107	13	3078,5096		591,1896,1600	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	670,2446,2848	AA,AG,GG		37.656,18.8599,31.7404	,	839/1266,908/1337	121880520	3786,8142	1877	4087	5964	SO:0001819	synonymous_variant	84678	exon19			GGAGTGGTCGCTC	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2724C>T	12.37:g.121880520G>A		Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.651;A|0.349	0.349	strong		0.706	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
CAPG	822	hgsc.bcm.edu	37	2	85629256	85629256	+	Missense_Mutation	SNP	T	T	C	rs113987685	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85629256T>C	ENST00000409921.1	-	2	79	c.13A>G	c.(13-15)Att>Gtt	p.I5V	CAPG_ENST00000263867.4_Missense_Mutation_p.I5V|CAPG_ENST00000483659.1_5'Flank|CAPG_ENST00000409670.1_Missense_Mutation_p.I5V|CAPG_ENST00000409724.1_Missense_Mutation_p.I5V			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						CTCTGGGGAATGGCTGTGTAC	0.522													T|||	3	0.000599042	0.0	0.0029	5008	,	,		18368	0.0		0.001	False		,,,				2504	0.0				p.I5V		Atlas-SNP	.											.	CAPG	32	.	0			c.A13G						PASS	.	T	VAL/ILE	3,4403	4.2+/-10.8	0,3,2200	65.0	56.0	59.0		13	0.1	0.8	2	dbSNP_132	59	43,8557	27.9+/-77.7	0,43,4257	yes	missense	CAPG	NM_001747.2	29	0,46,6457	CC,CT,TT		0.5,0.0681,0.3537	benign	5/349	85629256	46,12960	2203	4300	6503	SO:0001583	missense	822	exon2			GGGGAATGGCTGT	M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"""macrophage capping protein"""	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.13A>G	2.37:g.85629256T>C	ENSP00000387063:p.Ile5Val	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	155	37	0.23871	NM_001256140	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000409921.1	37	CCDS58715.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	6.832	0.522629	0.13066	6.81E-4	0.005	ENSG00000042493	ENST00000542681;ENST00000263867;ENST00000409921;ENST00000409670;ENST00000409724;ENST00000439385;ENST00000449030;ENST00000447219;ENST00000409275	T;T;T;T;T;T;T;T	0.19938	2.42;2.42;2.42;2.42;2.11;2.11;2.11;2.12	5.02	0.0637	0.14350	.	1.504410	0.03839	N	0.270319	T	0.08758	0.0217	N	0.14661	0.345	0.22954	N	0.998518	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28073	-1.0055	10	0.48119	T	0.1	.	3.881	0.09079	0.0:0.2886:0.186:0.5254	.	5;5	B8ZZS7;P40121	.;CAPG_HUMAN	V	5	ENSP00000263867:I5V;ENSP00000387063:I5V;ENSP00000386315:I5V;ENSP00000386965:I5V;ENSP00000391923:I5V;ENSP00000403330:I5V;ENSP00000398232:I5V;ENSP00000386596:I5V	ENSP00000263867:I5V	I	-	1	0	CAPG	85482767	0.989000	0.36119	0.827000	0.32855	0.678000	0.39670	0.195000	0.17155	0.112000	0.17975	0.459000	0.35465	ATT	T|0.997;C|0.003	0.003	strong		0.522	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747	
RALB	5899	hgsc.bcm.edu	37	2	121036333	121036333	+	Silent	SNP	G	G	A	rs11545293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:121036333G>A	ENST00000272519.5	+	2	363	c.93G>A	c.(91-93)acG>acA	p.T31T	RALB_ENST00000404963.3_Silent_p.T31T|RALB_ENST00000474855.2_Silent_p.T53T|RALB_ENST00000420510.1_Silent_p.T31T|RALB_ENST00000470417.1_Intron	NM_002881.2	NP_002872.1	P11234	RALB_HUMAN	v-ral simian leukemia viral oncogene homolog B	31					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of exocyst assembly (GO:0001928)|regulation of exocyst localization (GO:0060178)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(154;0.122)				CAGCCCTGACGCTTCAGTTCA	0.592													g|||	221	0.0441294	0.0008	0.0634	5008	,	,		19749	0.003		0.1064	False		,,,				2504	0.0675				p.T31T		Atlas-SNP	.											.	RALB	27	.	0			c.G93A						PASS	.			88,4318	75.2+/-113.4	1,86,2116	104.0	80.0	88.0		93	-10.3	0.3	2	dbSNP_120	88	933,7667	205.1+/-247.6	65,803,3432	no	coding-synonymous	RALB	NM_002881.2		66,889,5548	AA,AG,GG		10.8488,1.9973,7.8502		31/207	121036333	1021,11985	2203	4300	6503	SO:0001819	synonymous_variant	5899	exon2			CCTGACGCTTCAG		CCDS2131.1	2q14.2	2014-05-09	2013-07-09		ENSG00000144118	ENSG00000144118			9840	protein-coding gene	gene with protein product	"""ras related GTP binding protein B"""	179551					Standard	NM_002881		Approved		uc002tmk.3	P11234	OTTHUMG00000131435	ENST00000272519.5:c.93G>A	2.37:g.121036333G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	40	27	0.675	NM_002881	B4E040|Q53T32|Q6ZS74	Silent	SNP	ENST00000272519.5	37	CCDS2131.1																																																																																			G|0.926;A|0.074	0.074	strong		0.592	RALB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254232.3	NM_002881	
MKL1	57591	hgsc.bcm.edu	37	22	40814636	40814636	+	Silent	SNP	C	C	T	rs4821944	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:40814636C>T	ENST00000355630.3	-	12	2396	c.1806G>A	c.(1804-1806)gcG>gcA	p.A602A	MKL1_ENST00000396617.3_Silent_p.A602A|MKL1_ENST00000402042.1_Silent_p.A552A|MKL1_ENST00000407029.1_Silent_p.A602A	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	602	Pro-rich.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						TGGCTGGGGCCGCCAGGCTGG	0.701			T	RBM15	acute megakaryocytic leukemia								C|||	983	0.196286	0.1324	0.1988	5008	,	,		10064	0.0099		0.3052	False		,,,				2504	0.3609				p.A602A		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1	69	.	0			c.G1806A						PASS	.	C		645,3593		64,517,1538	7.0	10.0	9.0		1806	-9.1	0.0	22	dbSNP_111	9	2472,5952		376,1720,2116	no	coding-synonymous	MKL1	NM_020831.3		440,2237,3654	TT,TC,CC		29.3447,15.2194,24.617		602/932	40814636	3117,9545	2119	4212	6331	SO:0001819	synonymous_variant	57591	exon12			TGGGGCCGCCAGG	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1806G>A	22.37:g.40814636C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Silent	SNP	ENST00000355630.3	37	CCDS14003.1																																																																																			C|0.829;T|0.171	0.171	strong		0.701	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
CPO	130749	hgsc.bcm.edu	37	2	207820276	207820276	+	Missense_Mutation	SNP	G	G	A	rs13420911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:207820276G>A	ENST00000272852.3	+	3	301	c.255G>A	c.(253-255)atG>atA	p.M85I		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	85			M -> I (in dbSNP:rs13420911). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		CCCACCCCATGTATTATCTGA	0.438													G|||	1915	0.382388	0.3843	0.2579	5008	,	,		20214	0.4067		0.4553	False		,,,				2504	0.3681				p.M85I		Atlas-SNP	.											.	CPO	42	.	0			c.G255A						PASS	.	G	ILE/MET	1709,2697	515.5+/-368.9	344,1021,838	148.0	130.0	136.0		255	5.1	1.0	2	dbSNP_121	136	4090,4510	560.3+/-387.6	975,2140,1185	yes	missense	CPO	NM_173077.2	10	1319,3161,2023	AA,AG,GG		47.5581,38.788,44.5871	benign	85/375	207820276	5799,7207	2203	4300	6503	SO:0001583	missense	130749	exon3			CCCCATGTATTAT		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.255G>A	2.37:g.207820276G>A	ENSP00000272852:p.Met85Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_173077	Q2M277|Q7RTW7	Missense_Mutation	SNP	ENST00000272852.3	37	CCDS2372.1	859	0.3933150183150183	190	0.3861788617886179	107	0.2955801104972376	222	0.3881118881118881	340	0.44854881266490765	G	1.814	-0.473902	0.04414	0.38788	0.475581	ENSG00000144410	ENST00000272852	T	0.08193	3.12	5.11	5.11	0.69529	Peptidase M14, carboxypeptidase A (3);	0.087737	0.85682	D	0.000000	T	0.00012	0.0000	N	0.00783	-1.19	0.39286	P	0.03534300000000001	B	0.17268	0.021	B	0.15870	0.014	T	0.39542	-0.9609	9	0.10111	T	0.7	.	11.0191	0.47707	0.0:0.0:0.8145:0.1855	rs13420911;rs52809631;rs60385629;rs13420911	85	Q8IVL8	CBPO_HUMAN	I	85	ENSP00000272852:M85I	ENSP00000272852:M85I	M	+	3	0	CPO	207528521	1.000000	0.71417	0.999000	0.59377	0.267000	0.26476	1.092000	0.30927	2.660000	0.90430	0.561000	0.74099	ATG	G|0.569;A|0.431	0.431	strong		0.438	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
HRNR	388697	hgsc.bcm.edu	37	1	152186837	152186837	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152186837C>T	ENST00000368801.2	-	3	7343	c.7268G>A	c.(7267-7269)cGa>cAa	p.R2423Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2423					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R2423Q(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACCCATGTCGGCCACGGCT	0.612																																					p.R2423Q		Atlas-SNP	.											HRNR,NS,carcinoma,0,4	HRNR	403	4	1	Substitution - Missense(1)	ovary(1)	c.G7268A						scavenged	.						1.0	1.0	1.0					1																	152186837		251	755	1006	SO:0001583	missense	388697	exon3			CCATGTCGGCCAC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7268G>A	1.37:g.152186837C>T	ENSP00000357791:p.Arg2423Gln	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	516	30	0.0581395	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	6.285	0.420671	0.11928	.	.	ENSG00000197915	ENST00000368801	T	0.02974	4.09	2.94	-5.88	0.02290	.	.	.	.	.	T	0.00328	0.0010	N	0.03115	-0.41	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.45293	-0.9271	9	0.10636	T	0.68	.	7.9897	0.30233	0.1213:0.2056:0.0:0.673	.	2423	Q86YZ3	HORN_HUMAN	Q	2423	ENSP00000357791:R2423Q	ENSP00000357791:R2423Q	R	-	2	0	HRNR	150453461	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.624000	0.02038	-2.325000	0.00638	-0.762000	0.03455	CGA	.	.	none		0.612	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
UCK2	7371	hgsc.bcm.edu	37	1	165865478	165865478	+	Silent	SNP	G	G	A	rs11553301	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:165865478G>A	ENST00000367879.4	+	4	711	c.408G>A	c.(406-408)ggG>ggA	p.G136G	UCK2_ENST00000462329.1_3'UTR|RP11-525G13.2_ENST00000455257.2_RNA|UCK2_ENST00000470820.1_5'UTR|UCK2_ENST00000372212.4_Intron|UCK2_ENST00000469256.2_5'UTR	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	136					cellular response to oxygen levels (GO:0071453)|CTP salvage (GO:0044211)|feeding behavior (GO:0007631)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to axon injury (GO:0048678)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					TCTTTGAAGGGATCCTGGCCT	0.552													G|||	436	0.0870607	0.0348	0.0836	5008	,	,		21179	0.0823		0.1521	False		,,,				2504	0.0982				p.G136G		Atlas-SNP	.											.	UCK2	31	.	0			c.G408A						PASS	.	G		207,4199	127.8+/-164.7	7,193,2003	218.0	203.0	208.0		408	0.9	1.0	1	dbSNP_120	208	1308,7292	257.7+/-281.7	104,1100,3096	no	coding-synonymous	UCK2	NM_012474.4		111,1293,5099	AA,AG,GG		15.2093,4.6981,11.6485		136/262	165865478	1515,11491	2203	4300	6503	SO:0001819	synonymous_variant	7371	exon4			TGAAGGGATCCTG	AF236637	CCDS1252.1	1p32	2012-10-02	2004-07-13	2004-07-14	ENSG00000143179	ENSG00000143179	2.7.1.48		12562	protein-coding gene	gene with protein product		609329	"""uridine monophosphate kinase"""	UMPK			Standard	NM_012474		Approved		uc001gdp.3	Q9BZX2	OTTHUMG00000040117	ENST00000367879.4:c.408G>A	1.37:g.165865478G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_012474	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Silent	SNP	ENST00000367879.4	37	CCDS1252.1																																																																																			G|0.887;A|0.113	0.113	strong		0.552	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096753.1	NM_012474	
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 GAIIx	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	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	36	14	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	
C3	718	hgsc.bcm.edu	37	19	6710782	6710782	+	Silent	SNP	G	G	T	rs2230203	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:6710782G>T	ENST00000245907.6	-	13	1646	c.1554C>A	c.(1552-1554)ccC>ccA	p.P518P		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	518					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGATGGACAGGGGCAGCACCA	0.657													G|||	319	0.0636981	0.0098	0.0807	5008	,	,		17642	0.003		0.1859	False		,,,				2504	0.0613				p.P518P		Atlas-SNP	.											.	C3	192	.	0			c.C1554A						PASS	.	G		159,4247	104.7+/-143.2	1,157,2045	64.0	63.0	63.0		1554	-10.4	0.0	19	dbSNP_98	63	1579,7021	287.5+/-298.3	136,1307,2857	no	coding-synonymous	C3	NM_000064.2		137,1464,4902	TT,TG,GG		18.3605,3.6087,13.3631		518/1664	6710782	1738,11268	2203	4300	6503	SO:0001819	synonymous_variant	718	exon13			GGACAGGGGCAGC	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1554C>A	19.37:g.6710782G>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	42	0.4	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																			G|0.888;T|0.112	0.112	strong		0.657	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
SPRR2E	6704	hgsc.bcm.edu	37	1	153066067	153066067	+	Missense_Mutation	SNP	C	C	T	rs75229137		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153066067C>T	ENST00000368751.1	-	2	235	c.161G>A	c.(160-162)tGt>tAt	p.C54Y	SPRR2E_ENST00000368750.3_Missense_Mutation_p.C54Y|SPRR2B_ENST00000368752.4_Intron			P22531	SPR2E_HUMAN	small proline-rich protein 2E	54					epidermis development (GO:0008544)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	structural molecule activity (GO:0005198)	p.C54Y(2)		NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CACAGGAGGACATTTTTGCTG	0.557																																					p.C54Y		Atlas-SNP	.											SPRR2E,NS,malignant_melanoma,0,1	SPRR2E	21	1	2	Substitution - Missense(2)	NS(1)|lung(1)	c.G161A						scavenged	.						244.0	237.0	239.0					1																	153066067		2203	4300	6503	SO:0001583	missense	6704	exon2			GGAGGACATTTTT	AF333955	CCDS30866.1	1q21-q22	2008-02-05			ENSG00000203785	ENSG00000203785			11265	protein-coding gene	gene with protein product						8325635	Standard	NM_001024209		Approved		uc001fbh.3	P22531	OTTHUMG00000014397	ENST00000368751.1:c.161G>A	1.37:g.153066067C>T	ENSP00000357740:p.Cys54Tyr	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	134	5	0.0373134	NM_001024209	Q5T9T4|Q96RM2	Missense_Mutation	SNP	ENST00000368751.1	37	CCDS30866.1	.	.	.	.	.	.	.	.	.	.	C	5.236	0.228966	0.09916	.	.	ENSG00000203785	ENST00000368751;ENST00000368750	T;T	0.32023	1.47;1.47	3.54	2.62	0.31277	.	0.000000	0.38272	N	0.001755	T	0.35219	0.0924	.	.	.	0.23585	N	0.997357	D	0.69078	0.997	D	0.83275	0.996	T	0.15665	-1.0429	9	0.87932	D	0	.	7.9404	0.29955	0.0:0.874:0.0:0.126	.	54	P22531	SPR2E_HUMAN	Y	54	ENSP00000357740:C54Y;ENSP00000357739:C54Y	ENSP00000357739:C54Y	C	-	2	0	SPRR2E	151332691	0.473000	0.25878	0.693000	0.30195	0.002000	0.02628	0.164000	0.16542	0.408000	0.25621	-1.111000	0.02071	TGT	C|0.500;T|0.500	0.500	weak		0.557	SPRR2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040054.1		
ZNF880	400713	hgsc.bcm.edu	37	19	52888245	52888245	+	Missense_Mutation	SNP	A	A	G	rs55748277	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52888245A>G	ENST00000422689.2	+	4	1427	c.1412A>G	c.(1411-1413)aAg>aGg	p.K471R		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	471					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GAATGTGGCAAGGACTTCACT	0.388													A|||	2061	0.411542	0.3555	0.3919	5008	,	,		22737	0.3492		0.4205	False		,,,				2504	0.5562				p.K471R		Atlas-SNP	.											.	ZNF880	45	.	0			c.A1412G						PASS	.	A	ARG/LYS	529,855		102,325,265	83.0	75.0	77.0		1412	-0.5	0.0	19	dbSNP_129	77	1216,1966		222,772,597	no	missense	ZNF880	NM_001145434.1	26	324,1097,862	GG,GA,AA		38.215,38.2225,38.2173	possibly-damaging	471/578	52888245	1745,2821	692	1591	2283	SO:0001583	missense	400713	exon4			GTGGCAAGGACTT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1412A>G	19.37:g.52888245A>G	ENSP00000406318:p.Lys471Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	51	48	0.941176	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	802	0.36721611721611724	164	0.3333333333333333	148	0.4088397790055249	179	0.3129370629370629	311	0.4102902374670185	A	13.64	2.296527	0.40594	0.382225	0.38215	ENSG00000221923	ENST00000422689	T	0.26223	1.75	2.03	-0.46	0.12175	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.35854	1.095	0.58432	P	9.99999999995449E-6	D	0.62365	0.991	D	0.63703	0.917	T	0.43750	-0.9372	7	.	.	.	.	6.4253	0.21766	0.7772:0.0:0.2228:0.0	rs55748277;rs62108357	471	Q6PDB4	ZN880_HUMAN	R	471	ENSP00000406318:K471R	.	K	+	2	0	ZNF880	57580057	0.060000	0.20803	0.007000	0.13788	0.010000	0.07245	1.664000	0.37439	-0.387000	0.07809	0.450000	0.29827	AAG	A|0.631;G|0.369	0.369	strong		0.388	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
PWWP2B	170394	hgsc.bcm.edu	37	10	134218175	134218175	+	Silent	SNP	C	C	T	rs111647732	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:134218175C>T	ENST00000305233.5	+	2	230	c.171C>T	c.(169-171)gtC>gtT	p.V57V	PWWP2B_ENST00000368609.4_Silent_p.V57V	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	57										central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		TGCCCCAGGTCGATGAGTCCC	0.672													C|||	148	0.0295527	0.0076	0.0476	5008	,	,		11697	0.001		0.0646	False		,,,				2504	0.0399				p.V57V		Atlas-SNP	.											.	PWWP2B	33	.	0			c.C171T						PASS	.	C	,	64,4216		0,64,2076	112.0	123.0	119.0		171,171	-0.6	0.0	10	dbSNP_132	119	530,8000		16,498,3751	no	coding-synonymous,coding-synonymous	PWWP2B	NM_001098637.1,NM_138499.3	,	16,562,5827	TT,TC,CC		6.2134,1.4953,4.637	,	57/500,57/591	134218175	594,12216	2140	4265	6405	SO:0001819	synonymous_variant	170394	exon2			CCAGGTCGATGAG	AK128663	CCDS7667.2	10q26.3	2009-06-03	2007-10-22	2007-10-22	ENSG00000171813	ENSG00000171813			25150	protein-coding gene	gene with protein product			"""PWWP domain containing 2"""	PWWP2			Standard	NM_001098637		Approved	bA432J24.1, FLJ46823	uc001lll.4	Q6NUJ5	OTTHUMG00000019286	ENST00000305233.5:c.171C>T	10.37:g.134218175C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	37	CCDS7667.2																																																																																			C|0.954;T|0.046	0.046	strong		0.672	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499	
SPTBN5	51332	hgsc.bcm.edu	37	15	42149596	42149596	+	Missense_Mutation	SNP	C	C	G	rs1197675	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42149596C>G	ENST00000320955.6	-	51	8688	c.8461G>C	c.(8461-8463)Ggg>Cgg	p.G2821R		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2821					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		TCGCCCACCCCAGGCAGGGCC	0.677													C|||	1270	0.253594	0.3812	0.2133	5008	,	,		17337	0.0377		0.333	False		,,,				2504	0.2505				p.G2786R		Atlas-SNP	.											SPTBN5,colon,carcinoma,+1,1	SPTBN5	171	1	0			c.G8356C						PASS	.	C	ARG/GLY	1387,2701		243,901,900	12.0	15.0	14.0		8356	2.4	0.0	15	dbSNP_87	14	2539,5805		396,1747,2029	yes	missense	SPTBN5	NM_016642.2	125	639,2648,2929	GG,GC,CC		30.4291,33.9286,31.5798	benign	2786/3640	42149596	3926,8506	2044	4172	6216	SO:0001583	missense	51332	exon51			CCACCCCAGGCAG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8461G>C	15.37:g.42149596C>G	ENSP00000317790:p.Gly2821Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		499	0.22847985347985347	169	0.3434959349593496	79	0.21823204419889503	11	0.019230769230769232	240	0.316622691292876	.	0.157	-1.085141	0.01873	0.339286	0.304291	ENSG00000137877	ENST00000320955	T	0.51817	0.69	4.31	2.42	0.29668	.	0.828045	0.10605	N	0.655213	T	0.00012	0.0000	L	0.28192	0.835	0.80722	P	0.0	B	0.30686	0.29	B	0.32022	0.139	T	0.40627	-0.9553	9	0.14656	T	0.56	.	3.84	0.08911	0.1727:0.563:0.0:0.2644	rs1197675;rs1648825;rs58159504;rs1197675	2821	Q9NRC6	SPTN5_HUMAN	R	2821	ENSP00000317790:G2821R	ENSP00000317790:G2821R	G	-	1	0	SPTBN5	39936888	0.001000	0.12720	0.002000	0.10522	0.017000	0.09413	0.435000	0.21510	0.443000	0.26582	-0.366000	0.07423	GGG	C|0.770;G|0.230	0.230	strong		0.677	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
RIMS2	9699	hgsc.bcm.edu	37	8	105263979	105263979	+	Silent	SNP	C	C	T	rs10461	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:105263979C>T	ENST00000436393.2	+	28	4276	c.4035C>T	c.(4033-4035)gcC>gcT	p.A1345A	RIMS2_ENST00000406091.3_Silent_p.A1327A|RIMS2_ENST00000507740.1_Silent_p.A1141A|RIMS2_ENST00000339750.2_Silent_p.A263A|RIMS2_ENST00000262231.10_Silent_p.A1166A			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1389	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			CAACCTTGGCCCCTCTGACAA	0.448										HNSCC(12;0.0054)			C|||	2394	0.478035	0.5227	0.536	5008	,	,		16632	0.6498		0.3529	False		,,,				2504	0.3282				p.A1327A		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C3981T						PASS	.	C	,	1859,1877		476,907,485	149.0	149.0	149.0		3981,3423	0.4	1.0	8	dbSNP_52	149	2858,5328		525,1808,1760	no	coding-synonymous,coding-synonymous	RIMS2	NM_001100117.2,NM_014677.4	,	1001,2715,2245	TT,TC,CC		34.9133,49.7591,39.5655	,	1327/1350,1141/1164	105263979	4717,7205	1868	4093	5961	SO:0001819	synonymous_variant	9699	exon24			CTTGGCCCCTCTG	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.4035C>T	8.37:g.105263979C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	37																																																																																				C|0.553;T|0.447	0.447	strong		0.448	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	
ILK	3611	hgsc.bcm.edu	37	11	6629665	6629665	+	Silent	SNP	C	C	T	rs1043388	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6629665C>T	ENST00000396751.2	+	3	753	c.297C>T	c.(295-297)caC>caT	p.H99H	TAF10_ENST00000531760.1_5'Flank|ILK_ENST00000528995.1_Silent_p.H99H|RP11-732A19.2_ENST00000527398.1_RNA|ILK_ENST00000299421.4_Silent_p.H99H|ILK_ENST00000537806.1_5'UTR|ILK_ENST00000420936.2_Silent_p.H99H	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	99	Interaction with LIMS1.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell junction assembly (GO:0034329)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|extracellular fibril organization (GO:0043206)|fibroblast migration (GO:0010761)|integrin-mediated signaling pathway (GO:0007229)|myelin assembly (GO:0032288)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|peptidyl-serine phosphorylation (GO:0018105)|platelet aggregation (GO:0070527)|positive regulation of axon extension (GO:0045773)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|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 dendrite morphogenesis (GO:0050775)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		TGAATGAACACGGGAATGTGC	0.483													T|||	1576	0.314696	0.4153	0.2608	5008	,	,		24191	0.3512		0.2535	False		,,,				2504	0.2423				p.H99H		Atlas-SNP	.											.	ILK	41	.	0			c.C297T						PASS	.	T	,,	1685,2717	654.2+/-399.7	315,1055,831	138.0	118.0	124.0		297,297,297	2.4	1.0	11	dbSNP_86	124	2148,6444	713.9+/-406.0	260,1628,2408	no	coding-synonymous,coding-synonymous,coding-synonymous	ILK	NM_001014794.1,NM_001014795.1,NM_004517.2	,,	575,2683,3239	TT,TC,CC		25.0,38.2781,29.4982	,,	99/453,99/453,99/453	6629665	3833,9161	2201	4296	6497	SO:0001819	synonymous_variant	3611	exon4			TGAACACGGGAAT	U40282	CCDS7768.1, CCDS60712.1, CCDS60713.1	11p15.4	2014-09-17			ENSG00000166333	ENSG00000166333		"""Ankyrin repeat domain containing"""	6040	protein-coding gene	gene with protein product		602366				8538749	Standard	NM_004517		Approved		uc001mef.3	Q13418	OTTHUMG00000133407	ENST00000396751.2:c.297C>T	11.37:g.6629665C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_001014794	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Silent	SNP	ENST00000396751.2	37	CCDS7768.1																																																																																			C|0.690;T|0.310	0.310	strong		0.483	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517	
NRP1	8829	hgsc.bcm.edu	37	10	33510663	33510663	+	Silent	SNP	G	G	A	rs2229935	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:33510663G>A	ENST00000265371.4	-	9	1791	c.1266C>T	c.(1264-1266)taC>taT	p.Y422Y	NRP1_ENST00000374823.5_Silent_p.Y422Y|NRP1_ENST00000432372.2_Silent_p.Y422Y|NRP1_ENST00000395995.1_Silent_p.Y422Y|NRP1_ENST00000374875.1_Silent_p.Y241Y|NRP1_ENST00000374822.4_Silent_p.Y422Y|NRP1_ENST00000374867.2_Silent_p.Y422Y|NRP1_ENST00000374816.3_Silent_p.Y422Y|NRP1_ENST00000374821.5_Silent_p.Y422Y			O14786	NRP1_HUMAN	neuropilin 1	422	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	TCTTGCAACCGTATACTTCAA	0.393													A|||	1798	0.359026	0.1793	0.4337	5008	,	,		18709	0.623		0.2485	False		,,,				2504	0.3906				p.Y422Y	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.C1266T						PASS	.	A	,,	917,3489	738.2+/-411.0	99,719,1385	150.0	145.0	146.0		1266,1266,1266	-0.6	0.8	10	dbSNP_111	146	2285,6315	706.9+/-405.6	302,1681,2317	no	coding-synonymous,coding-synonymous,coding-synonymous	NRP1	NM_001024628.2,NM_001024629.2,NM_003873.5	,,	401,2400,3702	AA,AG,GG		26.5698,20.8125,24.6194	,,	422/645,422/610,422/924	33510663	3202,9804	2203	4300	6503	SO:0001819	synonymous_variant	8829	exon8			GCAACCGTATACT	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.1266C>T	10.37:g.33510663G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	37	CCDS7177.1																																																																																			G|0.708;A|0.292	0.292	strong		0.393	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
FBN3	84467	hgsc.bcm.edu	37	19	8161450	8161450	+	Missense_Mutation	SNP	C	C	T	rs3829817	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8161450C>T	ENST00000600128.1	-	44	5831	c.5417G>A	c.(5416-5418)cGg>cAg	p.R1806Q	FBN3_ENST00000601739.1_Missense_Mutation_p.R1806Q|FBN3_ENST00000270509.2_Missense_Mutation_p.R1806Q			Q75N90	FBN3_HUMAN	fibrillin 3	1806	EGF-like 28. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> Q (in dbSNP:rs3829817). {ECO:0000269|PubMed:11347906}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						ACACTCATTCCGTCCTGGGGG	0.562													C|||	920	0.183706	0.1346	0.1988	5008	,	,		19629	0.1687		0.2406	False		,,,				2504	0.1963				p.R1806Q		Atlas-SNP	.											.	FBN3	300	.	0			c.G5417A						PASS	.	C	GLN/ARG	673,3733	284.6+/-277.7	60,553,1590	102.0	77.0	85.0		5417	-1.5	0.3	19	dbSNP_107	85	1952,6648	344.1+/-325.2	228,1496,2576	yes	missense	FBN3	NM_032447.3	43	288,2049,4166	TT,TC,CC		22.6977,15.2746,20.183	benign	1806/2810	8161450	2625,10381	2203	4300	6503	SO:0001583	missense	84467	exon43			TCATTCCGTCCTG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5417G>A	19.37:g.8161450C>T	ENSP00000470498:p.Arg1806Gln	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	44	43	0.977273	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	410	0.18772893772893773	64	0.13008130081300814	70	0.19337016574585636	92	0.16083916083916083	184	0.24274406332453827	C	9.888	1.203326	0.22121	0.152746	0.226977	ENSG00000142449	ENST00000270509	D	0.87179	-2.22	3.63	-1.51	0.08664	Epidermal growth factor-like, type 3 (1);	0.135938	0.50627	N	0.000110	T	0.00073	0.0002	L	0.45352	1.415	0.21984	P	0.999431471	B	0.16396	0.017	B	0.13407	0.009	T	0.05370	-1.0889	9	0.26408	T	0.33	.	8.5647	0.33531	0.0:0.6604:0.0:0.3396	rs3829817;rs52826609;rs56512420;rs59040820;rs3829817	1806	Q75N90	FBN3_HUMAN	Q	1806	ENSP00000270509:R1806Q	ENSP00000270509:R1806Q	R	-	2	0	FBN3	8067450	0.909000	0.30893	0.265000	0.24526	0.173000	0.22820	1.282000	0.33226	-0.474000	0.06862	-0.140000	0.14226	CGG	C|0.810;T|0.190	0.190	strong		0.562	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188709	140188709	+	Missense_Mutation	SNP	G	G	T	rs147674000	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140188709G>T	ENST00000530339.1	+	1	1937	c.1937G>T	c.(1936-1938)cGc>cTc	p.R646L	PCDHA4_ENST00000356878.4_Missense_Mutation_p.R646L|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.R646L|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	646	Cadherin 6. {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)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCGCCACCGCCTACTGGTA	0.687													.|||	19	0.00379393	0.0	0.0159	5008	,	,		17402	0.0		0.008	False		,,,				2504	0.0				p.R646L		Atlas-SNP	.											PCDHA4_ENST00000530339,colon,carcinoma,0,2	PCDHA4	419	2	0			c.G1937T						PASS	.	G	,,,LEU/ARG,,LEU/ARG	8,4398	15.5+/-35.6	0,8,2195	73.0	76.0	75.0		,,,1937,,1937	3.1	1.0	5	dbSNP_134	75	78,8522	45.8+/-104.6	0,78,4222	no	intron,intron,intron,missense,intron,missense	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,102,,102	0,86,6417	TT,TG,GG		0.907,0.1816,0.6612	,,,,,	,,,646/948,,646/799	140188709	86,12920	2203	4300	6503	SO:0001583	missense	56144	exon1			GCCACCGCCTACT	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1937G>T	5.37:g.140188709G>T	ENSP00000435300:p.Arg646Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	10	0.004578754578754579	0	0.0	6	0.016574585635359115	0	0.0	4	0.005277044854881266	g	5.871	0.344818	0.11126	0.001816	0.00907	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.52983	0.64;0.64;0.64	4.08	3.12	0.35913	Cadherin (4);Cadherin-like (1);	0.217766	0.20330	U	0.094451	T	0.34337	0.0894	L	0.60957	1.885	0.09310	N	1	P;B;B	0.42337	0.776;0.299;0.432	P;B;P	0.48815	0.511;0.214;0.591	T	0.31420	-0.9944	10	0.72032	D	0.01	.	9.1337	0.36861	0.0909:0.2074:0.7016:0.0	.	646;646;646	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	L	646	ENSP00000423470:R646L;ENSP00000349344:R646L;ENSP00000435300:R646L	ENSP00000349344:R646L	R	+	2	0	PCDHA4	140168893	0.000000	0.05858	0.975000	0.42487	0.040000	0.13550	-0.737000	0.04877	2.006000	0.58801	0.484000	0.47621	CGC	G|0.993;T|0.007	0.007	strong		0.687	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
CDH4	1002	hgsc.bcm.edu	37	20	60509209	60509209	+	Silent	SNP	C	C	T	rs3753045	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60509209C>T	ENST00000360469.5	+	15	2563	c.2475C>T	c.(2473-2475)ggC>ggT	p.G825G	CDH4_ENST00000543233.1_Silent_p.G751G	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	825					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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GGCCGGTGGGCGCTGAGCCCC	0.687													C|||	808	0.161342	0.0287	0.1988	5008	,	,		14233	0.1498		0.2535	False		,,,				2504	0.2311				p.G825G		Atlas-SNP	.											CDH4,colon,carcinoma,0,1	CDH4	172	1	0			c.C2475T						scavenged	.	C		285,4119		8,269,1925	27.0	31.0	29.0		2475	-8.7	0.7	20	dbSNP_107	29	2147,6445		274,1599,2423	no	coding-synonymous	CDH4	NM_001794.2		282,1868,4348	TT,TC,CC		24.9884,6.4714,18.7135		825/917	60509209	2432,10564	2202	4296	6498	SO:0001819	synonymous_variant	1002	exon15			GGTGGGCGCTGAG	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.2475C>T	20.37:g.60509209C>T		Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Silent	SNP	ENST00000360469.5	37	CCDS13488.1																																																																																			C|0.826;T|0.174	0.174	strong		0.687	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
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 GAIIx	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_ENST00000259075.2_Nonsense_Mutation_p.Q8*|TANK_ENST00000403609.1_Nonsense_Mutation_p.Q8*|TANK_ENST00000457476.1_Nonsense_Mutation_p.Q8*|TANK_ENST00000405852.1_Nonsense_Mutation_p.Q8*|TANK_ENST00000402568.1_Nonsense_Mutation_p.Q66*|TANK_ENST00000406287.1_Nonsense_Mutation_p.Q66*	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*	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	100	41	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	
MARK1	4139	hgsc.bcm.edu	37	1	220791729	220791729	+	Silent	SNP	G	G	T	rs36024488	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:220791729G>T	ENST00000366917.4	+	8	896	c.630G>T	c.(628-630)ggG>ggT	p.G210G	MARK1_ENST00000366918.4_Silent_p.G188G|MARK1_ENST00000402574.1_Silent_p.G75G					MAP/microtubule affinity-regulating kinase 1									p.G210G(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		TTACAGTTGGGAACAAATTGG	0.403													G|||	78	0.0155751	0.0	0.0173	5008	,	,		16051	0.001		0.0099	False		,,,				2504	0.0562				p.G210G		Atlas-SNP	.											MARK1,NS,carcinoma,0,1	MARK1	161	1	1	Substitution - coding silent(1)	stomach(1)	c.G630T						PASS	.	G		25,4381	29.9+/-59.1	0,25,2178	61.0	64.0	63.0		630	2.3	1.0	1	dbSNP_126	63	177,8423	80.9+/-143.5	3,171,4126	no	coding-synonymous	MARK1	NM_018650.3		3,196,6304	TT,TG,GG		2.0581,0.5674,1.5531		210/796	220791729	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	4139	exon8			AGTTGGGAACAAA	AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.630G>T	1.37:g.220791729G>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	84	31	0.369048	NM_018650		Silent	SNP	ENST00000366917.4	37	CCDS31029.2																																																																																			G|0.985;T|0.015	0.015	strong		0.403	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1		
SP100	6672	hgsc.bcm.edu	37	2	231333763	231333763	+	Missense_Mutation	SNP	A	A	G	rs12724|rs57377576	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:231333763A>G	ENST00000264052.5	+	14	1652	c.1297A>G	c.(1297-1299)Atg>Gtg	p.M433V	SP100_ENST00000409341.1_Missense_Mutation_p.M433V|SP100_ENST00000341950.4_Missense_Mutation_p.M433V|SP100_ENST00000409112.1_Missense_Mutation_p.M433V|SP100_ENST00000409897.1_Missense_Mutation_p.M398V|SP100_ENST00000427101.2_Missense_Mutation_p.M405V|SP100_ENST00000340126.4_Missense_Mutation_p.M433V|SP100_ENST00000409824.1_Missense_Mutation_p.M408V	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	433	Sufficient to mediate interaction with ETS1.		M -> V (in HeLa cells; dbSNP:rs12724).		cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TCTAGCTCCTATGACTTCTAG	0.323													A|||	901	0.179912	0.0688	0.1729	5008	,	,		15981	0.0635		0.3221	False		,,,				2504	0.3088				p.M433V		Atlas-SNP	.											.	SP100	167	.	0			c.A1297G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	440,3966	214.8+/-234.0	19,402,1782	110.0	107.0	108.0		1297,1297,1297,1213,1192,1297	-4.2	0.0	2	dbSNP_52	108	2764,5834	437.2+/-358.5	452,1860,1987	yes	missense,missense,missense,missense,missense,missense	SP100	NM_001080391.1,NM_001206701.1,NM_001206702.1,NM_001206703.1,NM_001206704.1,NM_003113.3	21,21,21,21,21,21	471,2262,3769	GG,GA,AA		32.147,9.9864,24.6386	benign,benign,benign,benign,benign,benign	433/886,433/689,433/481,405/453,398/446,433/880	231333763	3204,9800	2203	4299	6502	SO:0001583	missense	6672	exon14			GCTCCTATGACTT	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"""Zinc fingers, PHD-type"""	11206	protein-coding gene	gene with protein product		604585	"""nuclear antigen Sp100"""			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1297A>G	2.37:g.231333763A>G	ENSP00000264052:p.Met433Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_001206702	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	390	0.17857142857142858	50	0.1016260162601626	69	0.19060773480662985	34	0.05944055944055944	237	0.31266490765171506	A	0.003	-2.414046	0.00191	0.099864	0.32147	ENSG00000067066	ENST00000264052;ENST00000427101;ENST00000409824;ENST00000409341;ENST00000409112;ENST00000340126;ENST00000341950;ENST00000409897;ENST00000452345	T;T;T;T;T;T;T;T;T	0.78364	2.48;2.37;2.37;2.37;-1.17;0.41;2.38;2.37;1.04	3.33	-4.21	0.03812	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.16689	-1.0394	8	0.18276	T	0.48	.	0.2456	0.00198	0.3195:0.1348:0.2204:0.3253	rs12724;rs1131025;rs1678160;rs3190536;rs3731730;rs11555637;rs17274178;rs17296406;rs17357235;rs52837394;rs1678160	405;398;433;433;433;408;433	F8WFE2;B8ZZD8;P23497-4;P23497;E7EUA7;E9PHV6;P23497-2	.;.;.;SP100_HUMAN;.;.;.	V	433;405;408;433;433;433;433;398;98	ENSP00000264052:M433V;ENSP00000399389:M405V;ENSP00000387311:M408V;ENSP00000386404:M433V;ENSP00000386427:M433V;ENSP00000343023:M433V;ENSP00000342729:M433V;ENSP00000386998:M398V;ENSP00000416563:M98V	ENSP00000264052:M433V	M	+	1	0	SP100	231042007	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-0.538000	0.06120	-1.007000	0.03408	-1.032000	0.02404	ATG	A|0.778;G|0.221;N|0.000;T|0.000	0.221	strong		0.323	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
FAT2	2196	hgsc.bcm.edu	37	5	150901597	150901597	+	Silent	SNP	G	G	C	rs3734047	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150901597G>C	ENST00000261800.5	-	18	10569	c.10557C>G	c.(10555-10557)gtC>gtG	p.V3519V		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3519	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGTGACATGGACACGGACAG	0.542													G|||	488	0.0974441	0.0083	0.1585	5008	,	,		20790	0.126		0.1948	False		,,,				2504	0.045				p.V3519V		Atlas-SNP	.											.	FAT2	465	.	0			c.C10557G						PASS	.	G		164,4242	107.8+/-146.2	6,152,2045	57.0	51.0	53.0		10557	2.3	0.1	5	dbSNP_107	53	1829,6771	328.1+/-318.2	206,1417,2677	no	coding-synonymous	FAT2	NM_001447.2		212,1569,4722	CC,CG,GG		21.2674,3.7222,15.3237		3519/4350	150901597	1993,11013	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon18			GACATGGACACGG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10557C>G	5.37:g.150901597G>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	30	12	0.4	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	290	0.13278388278388278	6	0.012195121951219513	65	0.17955801104972377	82	0.14335664335664336	137	0.18073878627968337	G	0.017	-1.494745	0.01009	0.037222	0.212674	ENSG00000086570	ENST00000520200	.	.	.	5.14	2.3	0.28687	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999996599	.	.	.	.	.	.	T	0.14531	-1.0469	3	.	.	.	.	4.8548	0.13554	0.0715:0.1279:0.5208:0.2799	rs3734047;rs3734047	.	.	.	A	378	.	.	P	-	1	0	FAT2	150881790	0.998000	0.40836	0.059000	0.19551	0.012000	0.07955	0.818000	0.27295	0.246000	0.21394	-0.261000	0.10672	CCA	G|0.858;C|0.142	0.142	strong		0.542	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
INPP5J	27124	hgsc.bcm.edu	37	22	31529463	31529463	+	Silent	SNP	C	C	A	rs35342535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:31529463C>A	ENST00000331075.5	+	11	2452	c.2403C>A	c.(2401-2403)acC>acA	p.T801T	INPP5J_ENST00000412277.2_Silent_p.T734T|INPP5J_ENST00000405300.1_Silent_p.T434T|INPP5J_ENST00000402238.1_Intron|INPP5J_ENST00000404453.1_Silent_p.T166T|INPP5J_ENST00000401755.1_Silent_p.T166T|INPP5J_ENST00000400294.2_Silent_p.T434T|INPP5J_ENST00000404390.3_Silent_p.T433T	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J	801	Required for ruffle localization. {ECO:0000250}.				inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						ATGGGAATACCTACCAGGTAC	0.537													C|||	1301	0.259784	0.1906	0.281	5008	,	,		19967	0.0208		0.3877	False		,,,				2504	0.453				p.T433T		Atlas-SNP	.											.	INPP5J	94	.	0			c.C1299A						PASS	.	C		834,3112		86,662,1225	97.0	95.0	95.0		1299	2.3	1.0	22	dbSNP_126	95	3215,5099		632,1951,1574	no	coding-synonymous	INPP5J	NM_001002837.1		718,2613,2799	AA,AC,CC		38.6697,21.1353,33.0261		433/639	31529463	4049,8211	1973	4157	6130	SO:0001819	synonymous_variant	27124	exon11			GAATACCTACCAG	U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"""phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"""	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.2403C>A	22.37:g.31529463C>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_001002837	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Silent	SNP	ENST00000331075.5	37																																																																																				C|0.726;A|0.274	0.274	strong		0.537	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837	
CDKAL1	54901	hgsc.bcm.edu	37	6	21065450	21065450	+	Silent	SNP	A	A	G	rs56087852	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:21065450A>G	ENST00000378610.1	+	10	1237	c.1227A>G	c.(1225-1227)ccA>ccG	p.P409P	CDKAL1_ENST00000378624.4_Silent_p.P339P|CDKAL1_ENST00000274695.4_Silent_p.P409P			Q5VV42	CDKAL_HUMAN	CDK5 regulatory subunit associated protein 1-like 1	409					maintenance of translational fidelity (GO:1990145)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)|N6-threonylcarbomyladenosine methylthiotransferase activity (GO:0035598)	p.P409P(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(2)|stomach(1)	29	all_epithelial(95;0.0708)|Breast(50;0.131)|Ovarian(93;0.227)		OV - Ovarian serous cystadenocarcinoma(7;0.0241)|all cancers(50;0.123)|Epithelial(50;0.248)			AACAAGTTCCAGCACAAGTGG	0.388													A|||	941	0.187899	0.239	0.1369	5008	,	,		16097	0.1627		0.1998	False		,,,				2504	0.1687				p.P409P		Atlas-SNP	.											CDKAL1,NS,carcinoma,0,1	CDKAL1	55	1	1	Substitution - coding silent(1)	stomach(1)	c.A1227G						PASS	.	A		963,3443	359.1+/-314.7	114,735,1354	90.0	87.0	88.0		1227	-0.0	1.0	6	dbSNP_129	88	1633,6967	298.3+/-303.9	147,1339,2814	no	coding-synonymous	CDKAL1	NM_017774.3		261,2074,4168	GG,GA,AA		18.9884,21.8566,19.96		409/580	21065450	2596,10410	2203	4300	6503	SO:0001819	synonymous_variant	54901	exon12			AGTTCCAGCACAA	AK000349	CCDS4546.1	6p22.2	2008-02-05			ENSG00000145996	ENSG00000145996			21050	protein-coding gene	gene with protein product		611259					Standard	NM_017774		Approved	FLJ20342	uc003ndd.2	Q5VV42	OTTHUMG00000014340	ENST00000378610.1:c.1227A>G	6.37:g.21065450A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	56	15	0.267857	NM_017774	A8K6S0|Q6P385|Q6ZR27|Q9NXB3	Silent	SNP	ENST00000378610.1	37	CCDS4546.1																																																																																			A|0.809;G|0.191	0.191	strong		0.388	CDKAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039986.1	NM_017774	
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 GAIIx	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	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	73	39	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		
LRPPRC	10128	hgsc.bcm.edu	37	2	44201376	44201376	+	Silent	SNP	T	T	C	rs4953042	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44201376T>C	ENST00000260665.7	-	9	1125	c.1068A>G	c.(1066-1068)caA>caG	p.Q356Q	LRPPRC_ENST00000409659.1_Silent_p.Q356Q|LRPPRC_ENST00000409946.1_Silent_p.Q356Q	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	356					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CTAGTAAAATTTGCAACGCTA	0.373													T|||	1281	0.255791	0.025	0.2666	5008	,	,		19268	0.5198		0.1521	False		,,,				2504	0.3947				p.Q356Q		Atlas-SNP	.											.	LRPPRC	105	.	0			c.A1068G						PASS	.	T		212,4194	129.4+/-166.1	4,204,1995	76.0	76.0	76.0		1068	-3.3	0.0	2	dbSNP_111	76	1286,7314	254.0+/-279.5	89,1108,3103	no	coding-synonymous	LRPPRC	NM_133259.3		93,1312,5098	CC,CT,TT		14.9535,4.8116,11.5178		356/1395	44201376	1498,11508	2203	4300	6503	SO:0001819	synonymous_variant	10128	exon9			TAAAATTTGCAAC	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1068A>G	2.37:g.44201376T>C		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	300	148	0.493333	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			T|0.840;C|0.160	0.160	strong		0.373	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
PRSS55	203074	hgsc.bcm.edu	37	8	10390452	10390452	+	Missense_Mutation	SNP	C	C	T	rs4406360	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:10390452C>T	ENST00000328655.3	+	4	675	c.635C>T	c.(634-636)gCg>gTg	p.A212V	PRSS55_ENST00000522210.1_Missense_Mutation_p.A212V|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	212	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		A -> V (in dbSNP:rs4406360). {ECO:0000269|PubMed:12975309}.			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						CTGATGAAAGCGCCAATGGTC	0.478													C|||	1709	0.341254	0.2224	0.3329	5008	,	,		20467	0.4266		0.334	False		,,,				2504	0.4274				p.A212V		Atlas-SNP	.											.	PRSS55	67	.	0			c.C635T						PASS	.	C	VAL/ALA,VAL/ALA	1085,3321	393.3+/-328.8	113,859,1231	115.0	107.0	110.0		635,635	-4.1	0.6	8	dbSNP_111	110	2962,5638	460.7+/-365.2	476,2010,1814	yes	missense,missense	PRSS55	NM_001197020.1,NM_198464.3	64,64	589,2869,3045	TT,TC,CC		34.4419,24.6255,31.1164	benign,benign	212/277,212/353	10390452	4047,8959	2203	4300	6503	SO:0001583	missense	203074	exon4			TGAAAGCGCCAAT	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"""Serine peptidases / Serine peptidases"""	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.635C>T	8.37:g.10390452C>T	ENSP00000333003:p.Ala212Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_001197020	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	749	0.34294871794871795	126	0.25609756097560976	128	0.35359116022099446	232	0.40559440559440557	263	0.3469656992084433	C	7.360	0.624582	0.14193	0.246255	0.344419	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.92446	-3.04;-3.04	5.27	-4.08	0.03963	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.552989	0.13570	N	0.378158	T	0.00012	0.0000	N	0.05280	-0.08	0.80722	P	0.0	B	0.24651	0.108	B	0.16289	0.015	T	0.14200	-1.0481	9	0.20519	T	0.43	.	7.1514	0.25612	0.0:0.4539:0.1334:0.4127	rs4406360;rs61420274;rs4406360	212	Q6UWB4	PRS55_HUMAN	V	212	ENSP00000333003:A212V;ENSP00000430459:A212V	ENSP00000333003:A212V	A	+	2	0	PRSS55	10427862	0.002000	0.14202	0.642000	0.29436	0.005000	0.04900	-0.579000	0.05834	-0.461000	0.06993	-0.218000	0.12543	GCG	C|0.668;T|0.332	0.332	strong		0.478	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
ACSM5	54988	hgsc.bcm.edu	37	16	20442608	20442608	+	Missense_Mutation	SNP	C	C	A	rs79364355		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20442608C>A	ENST00000331849.4	+	10	1420	c.1273C>A	c.(1273-1275)Ccc>Acc	p.P425T		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	425					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						CCGTATCAGACCCACTCGGCC	0.507																																					p.P425T		Atlas-SNP	.											ACSM5,NS,NS,0,1	ACSM5	101	1	0			c.C1273A						PASS	.						181.0	152.0	162.0					16																	20442608		2203	4300	6503	SO:0001583	missense	54988	exon10			ATCAGACCCACTC		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1273C>A	16.37:g.20442608C>A	ENSP00000327916:p.Pro425Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	119	14	0.117647	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.211007	0.58343	.	.	ENSG00000183549	ENST00000331849	T	0.46063	0.88	4.37	4.37	0.52481	AMP-dependent synthetase/ligase (1);	0.000000	0.52532	D	0.000068	T	0.42899	0.1223	L	0.41573	1.285	0.51482	D	0.999926	B	0.27700	0.186	B	0.37346	0.247	T	0.49679	-0.8914	10	0.87932	D	0	-15.5986	16.0686	0.80907	0.0:1.0:0.0:0.0	.	425	Q6NUN0	ACSM5_HUMAN	T	425	ENSP00000327916:P425T	ENSP00000327916:P425T	P	+	1	0	ACSM5	20350109	0.980000	0.34600	0.744000	0.31058	0.954000	0.61252	3.276000	0.51646	2.119000	0.64992	0.650000	0.86243	CCC	C|0.500;A|0.500	0.500	weak		0.507	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
SMCR8	140775	hgsc.bcm.edu	37	17	18226177	18226177	+	Silent	SNP	G	G	T	rs4925171	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18226177G>T	ENST00000406438.3	+	2	3087	c.2607G>T	c.(2605-2607)ctG>ctT	p.L869L	RP1-178F10.3_ENST00000577764.1_lincRNA	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	869						nucleus (GO:0005634)		p.L869L(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						ACCTGCACCTGCCTACCCACG	0.587													G|||	1152	0.230032	0.3396	0.2695	5008	,	,		18525	0.0605		0.3082	False		,,,				2504	0.1483				p.L869L		Atlas-SNP	.											SMCR8,NS,carcinoma,0,1	SMCR8	62	1	1	Substitution - coding silent(1)	stomach(1)	c.G2607T						PASS	.	G		1386,2802		206,974,914	61.0	64.0	63.0		2607	5.2	1.0	17	dbSNP_111	63	2552,5914		369,1814,2050	no	coding-synonymous	SMCR8	NM_144775.2		575,2788,2964	TT,TG,GG		30.1441,33.0946,31.1206		869/938	18226177	3938,8716	2094	4233	6327	SO:0001819	synonymous_variant	140775	exon2			GCACCTGCCTACC	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2607G>T	17.37:g.18226177G>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			G|0.744;T|0.256	0.256	strong		0.587	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
HIST1H2BE	8344	hgsc.bcm.edu	37	6	26184102	26184102	+	Missense_Mutation	SNP	G	G	A	rs7766641	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26184102G>A	ENST00000356530.3	+	1	145	c.79G>A	c.(79-81)Ggc>Agc	p.G27S		NM_003523.2	NP_003514.2	P62807	H2B1C_HUMAN	histone cluster 1, H2be	27			G -> S (in dbSNP:rs7766641). {ECO:0000269|PubMed:9119399}.		antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(1)	4						GAAGAAGGACGGCAAGAAGCG	0.582													G|||	1767	0.352835	0.0204	0.3732	5008	,	,		18763	0.7579		0.2833	False		,,,				2504	0.4417				p.G27S		Atlas-SNP	.											.	HIST1H2BE	10	.	0			c.G79A						PASS	.	G	SER/GLY	287,4119		7,273,1923	141.0	129.0	133.0		79	4.2	1.0	6	dbSNP_116	133	2418,6182		325,1768,2207	no	missense	HIST1H2BE	NM_003523.2	56	332,2041,4130	AA,AG,GG		28.1163,6.5138,20.7981	benign	27/127	26184102	2705,10301	2203	4300	6503	SO:0001583	missense	8344	exon1			AAGGACGGCAAGA	Z80780	CCDS4588.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197697	ENSG00000274290		"""Histones / Replication-dependent"""	4753	protein-coding gene	gene with protein product		602805	"""H2B histone family, member H"", ""histone 1, H2be"""	H2BFH		9119399, 12408966	Standard	NM_003523		Approved	H2B/h, H2B.h	uc003ngt.3	P62807	OTTHUMG00000014427	ENST00000356530.3:c.79G>A	6.37:g.26184102G>A	ENSP00000348924:p.Gly27Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	73	59	0.808219	NM_003523	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000356530.3	37	CCDS4588.1	797	0.3649267399267399	17	0.034552845528455285	119	0.3287292817679558	441	0.7709790209790209	220	0.29023746701846964	.	15.08	2.728194	0.48833	0.065138	0.281163	ENSG00000197697	ENST00000356530	T	0.22539	1.95	5.05	4.18	0.49190	.	0.000000	0.34700	U	0.003742	T	0.20455	0.0492	.	.	.	0.28334	P	0.9216307	.	.	.	.	.	.	T	0.02477	-1.1153	6	0.46703	T	0.11	.	12.9072	0.58160	0.0791:0.0:0.9209:0.0	rs7766641;rs58684673	.	.	.	S	27	ENSP00000348924:G27S	ENSP00000348924:G27S	G	+	1	0	HIST1H2BE	26292081	1.000000	0.71417	0.986000	0.45419	0.042000	0.13812	7.554000	0.82212	1.280000	0.44463	-0.199000	0.12753	GGC	G|0.744;A|0.256	0.256	strong		0.582	HIST1H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040090.1	NM_003523	
VPS13C	54832	hgsc.bcm.edu	37	15	62243197	62243197	+	Missense_Mutation	SNP	T	T	C	rs11629598	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62243197T>C	ENST00000261517.5	-	40	4556	c.4483A>G	c.(4483-4485)Att>Gtt	p.I1495V	VPS13C_ENST00000395896.4_Missense_Mutation_p.I1495V|VPS13C_ENST00000395898.3_Missense_Mutation_p.I1452V|VPS13C_ENST00000249837.3_Missense_Mutation_p.I1452V	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.I1495V(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GAAGAGTTAATAATGTGAAGA	0.323													T|||	233	0.0465256	0.0159	0.0447	5008	,	,		15840	0.0387		0.0746	False		,,,				2504	0.0685				p.I1495V		Atlas-SNP	.											VPS13C,NS,carcinoma,0,1	VPS13C	506	1	1	Substitution - Missense(1)	stomach(1)	c.A4483G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	115,4283	84.4+/-122.9	0,115,2084	42.0	43.0	43.0		4483,4354,4354,4483	4.4	1.0	15	dbSNP_120	43	691,7897	165.8+/-217.9	31,629,3634	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	29,29,29,29	31,744,5718	CC,CT,TT		8.0461,2.6148,6.2067	benign,benign,benign,benign	1495/3629,1452/3711,1452/3586,1495/3754	62243197	806,12180	2199	4294	6493	SO:0001583	missense	54832	exon40			AGTTAATAATGTG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.4483A>G	15.37:g.62243197T>C	ENSP00000261517:p.Ile1495Val	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	212	106	0.5	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	98	0.04487179487179487	6	0.012195121951219513	17	0.04696132596685083	27	0.0472027972027972	48	0.0633245382585752	T	10.81	1.454534	0.26161	0.026148	0.080461	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.20200	2.09;2.09;2.09	5.5	4.38	0.52667	.	0.062159	0.64402	N	0.000006	T	0.00695	0.0023	L	0.39898	1.24	0.44702	D	0.997698	B;B;B;B	0.17852	0.01;0.004;0.024;0.008	B;B;B;B	0.23150	0.028;0.028;0.044;0.009	T	0.25813	-1.0121	10	0.20046	T	0.44	.	3.9809	0.09495	0.0:0.1266:0.2103:0.663	rs11629598;rs52793992;rs61379117;rs11629598	1452;1495;1452;1495	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	V	1452;1495;1495;1495	ENSP00000249837:I1452V;ENSP00000261517:I1495V;ENSP00000379233:I1495V	ENSP00000249837:I1452V	I	-	1	0	VPS13C	60030489	0.961000	0.32948	0.974000	0.42286	0.896000	0.52359	1.033000	0.30191	0.942000	0.37525	0.477000	0.44152	ATT	T|0.946;C|0.054	0.054	strong		0.323	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
CCL14	6358	hgsc.bcm.edu	37	17	34311387	34311387	+	Missense_Mutation	SNP	T	T	C	rs16971802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:34311387T>C	ENST00000394509.4	-	2	289	c.181A>G	c.(181-183)Aag>Gag	p.K61E	CTB-186H2.3_ENST00000593057.1_Intron|CCL14_ENST00000536149.1_Missense_Mutation_p.K77E|CCL14_ENST00000480944.2_Missense_Mutation_p.K83E|CCL14_ENST00000586216.1_Missense_Mutation_p.K61E|CCL14_ENST00000435911.2_Missense_Mutation_p.K77E|CCL16_ENST00000293275.3_5'Flank|CCL15-CCL14_ENST00000481427.2_3'UTR|CTB-186H2.3_ENST00000591669.1_5'Flank			Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14	61			K -> E (in dbSNP:rs16971802).		cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)	extracellular space (GO:0005615)				large_intestine(1)|lung(6)	7		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATTCCGGGCTTGGAGCACTGG	0.577													T|||	318	0.0634984	0.1536	0.0576	5008	,	,		20801	0.0		0.0537	False		,,,				2504	0.0215				p.K77E		Atlas-SNP	.											.	CCL14	22	.	0			c.A229G						PASS	.	T	GLU/LYS,GLU/LYS	595,3811	263.1+/-265.3	42,511,1650	102.0	87.0	92.0		229,181	4.1	0.7	17	dbSNP_123	92	449,8151	135.4+/-192.6	7,435,3858	yes	missense,missense	CCL14	NM_032962.4,NM_032963.3	56,56	49,946,5508	CC,CT,TT		5.2209,13.5043,8.0271	possibly-damaging,possibly-damaging	77/110,61/94	34311387	1044,11962	2203	4300	6503	SO:0001583	missense	6358	exon3			CGGGCTTGGAGCA	Z49270	CCDS32624.1, CCDS45652.1	17q11.2	2014-04-10	2002-08-22	2002-08-23	ENSG00000213494	ENSG00000276409		"""Chemokine ligands"", ""Endogenous ligands"""	10612	protein-coding gene	gene with protein product		601392	"""small inducible cytokine subfamily A (Cys-Cys), member 14"""	SCYA14		8661057	Standard	NM_032963		Approved	HCC-1, HCC-3, NCC-2, SCYL2, CKb1, MCIF	uc010wcq.1	Q16627	OTTHUMG00000188403	ENST00000394509.4:c.181A>G	17.37:g.34311387T>C	ENSP00000378017:p.Lys61Glu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_032962	E1P649|E1P650|Q13954	Missense_Mutation	SNP	ENST00000394509.4	37	CCDS32624.1	133	0.060897435897435896	79	0.16056910569105692	19	0.052486187845303865	0	0.0	35	0.04617414248021108	T	16.19	3.052917	0.55218	0.135043	0.052209	ENSG00000213494	ENST00000394509;ENST00000536149;ENST00000435911	T;T;T	0.05447	3.44;3.44;3.44	5.14	4.05	0.47172	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.192216	0.31358	U	0.007781	T	0.00073	0.0002	.	.	.	0.51482	P	7.40000000000185E-5	P;D	0.56035	0.943;0.974	P;P	0.54544	0.755;0.641	T	0.11397	-1.0589	8	0.66056	D	0.02	.	9.4164	0.38523	0.0:0.0:0.1787:0.8213	rs16971802;rs56435289;rs16971802	61;77	Q16627;Q16627-2	CCL14_HUMAN;.	E	61;77;77	ENSP00000378017:K61E;ENSP00000441771:K77E;ENSP00000409197:K77E	ENSP00000378017:K61E	K	-	1	0	CCL14	31335500	0.304000	0.24472	0.688000	0.30117	0.690000	0.40134	0.521000	0.22893	0.863000	0.35553	0.460000	0.39030	AAG	T|0.925;C|0.075	0.075	strong		0.577	CCL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272892.2	NM_032962	
CCL4	6351	hgsc.bcm.edu	37	17	34432663	34432663	+	Silent	SNP	A	A	G	rs1049807|rs386796798	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:34432663A>G	ENST00000250151.4	+	3	553	c.237A>G	c.(235-237)gaA>gaG	p.E79E	CCL4_ENST00000394495.1_Missense_Mutation_p.N41S	NM_002984.2	NP_002975.1	P13236	CCL4_HUMAN	chemokine (C-C motif) ligand 4	79					cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|establishment or maintenance of cell polarity (GO:0007163)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of natural killer cell chemotaxis (GO:2000503)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemokine activity (GO:0008009)|cytokine activity (GO:0005125)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(1)|lung(2)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATCCCAGTGAATCCTGGGTCC	0.498													G|||	1096	0.21885	0.1732	0.1254	5008	,	,		21052	0.3036		0.2485	False		,,,				2504	0.229				p.E79E	Colon(139;824 1752 21188 21615 24765)	Atlas-SNP	.											.	CCL4	14	.	0			c.A237G						PASS	.	G		480,3926		54,372,1777	200.0	184.0	190.0		237	-10.1	0.0	17	dbSNP_86	190	278,8322		96,86,4118	no	coding-synonymous	CCL4	NM_002984.2		150,458,5895	GG,GA,AA		3.2326,10.8942,5.8281		79/93	34432663	758,12248	2203	4300	6503	SO:0001819	synonymous_variant	6351	exon3			CAGTGAATCCTGG	M23502	CCDS11308.1	17q21-q23	2014-05-06	2002-08-22	2002-08-23	ENSG00000129277	ENSG00000275302		"""Chemokine ligands"", ""Endogenous ligands"""	10630	protein-coding gene	gene with protein product		182284	"""small inducible cytokine A4 (homologous to mouse Mip-1b)"""	LAG1, SCYA4		1972563	Standard	NM_002984		Approved	MIP-1-beta, Act-2, AT744.1	uc002hkw.1	P13236	OTTHUMG00000188414	ENST00000250151.4:c.237A>G	17.37:g.34432663A>G		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	380	379	0.997368	NM_002984	P22617|Q13704|Q3SXL8|Q6FGI8	Silent	SNP	ENST00000250151.4	37	CCDS11308.1	380	0.17399267399267399	58	0.11788617886178862	48	0.13259668508287292	137	0.2395104895104895	137	0.18073878627968337	.	0.859	-0.736020	0.03111	0.108942	0.032326	ENSG00000129277	ENST00000394495	T	0.71222	-0.55	5.03	-10.1	0.00402	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.29822	-0.9999	5	0.87932	D	0	.	2.3631	0.04312	0.1849:0.3061:0.1036:0.4054	rs1049807;rs1719151;rs52827317;rs56801182;rs1049807	.	.	.	S	41	ENSP00000378004:N41S	ENSP00000378004:N41S	N	+	2	0	CCL4	31456776	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.376000	0.01070	-3.251000	0.00204	-0.768000	0.03414	AAT	A|0.816;G|0.184	0.184	strong		0.498	CCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256592.2	NM_002984	
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 GAIIx	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		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	23	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	
SIGLEC6	946	hgsc.bcm.edu	37	19	52033158	52033158	+	Missense_Mutation	SNP	C	C	T	rs35931837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52033158C>T	ENST00000425629.3	-	5	986	c.832G>A	c.(832-834)Ggc>Agc	p.G278S	SIGLEC6_ENST00000436458.1_Missense_Mutation_p.G226S|SIGLEC6_ENST00000343300.4_Missense_Mutation_p.G278S|SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000391797.3_Missense_Mutation_p.G267S|SIGLEC6_ENST00000359982.4_Missense_Mutation_p.G289S|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.G262S	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	278	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GGGGGGTTGCCGTCAGCATCA	0.622													C|||	368	0.0734824	0.0038	0.2363	5008	,	,		15730	0.002		0.1183	False		,,,				2504	0.0798				p.G289S		Atlas-SNP	.											SIGLEC6_ENST00000425629,NS,carcinoma,+2,2	SIGLEC6	142	2	0			c.G865A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	116,4288	82.9+/-121.4	2,112,2088	76.0	86.0	83.0		676,865,799,832,784,832	1.5	0.9	19	dbSNP_126	83	938,7662	203.2+/-246.3	62,814,3424	no	missense,missense,missense,missense,missense,missense	SIGLEC6	NM_001177547.1,NM_001177548.1,NM_001177549.1,NM_001245.5,NM_198845.4,NM_198846.4	56,56,56,56,56,56	64,926,5512	TT,TC,CC		10.907,2.634,8.1052	benign,benign,benign,benign,benign,benign	226/402,289/390,267/343,278/454,262/438,278/354	52033158	1054,11950	2202	4300	6502	SO:0001583	missense	946	exon5			GGTTGCCGTCAGC	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.832G>A	19.37:g.52033158C>T	ENSP00000401502:p.Gly278Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_001177548	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	37	CCDS12834.3	178	0.0815018315018315	4	0.008130081300813009	71	0.19613259668508287	0	0.0	103	0.1358839050131926	C	0.011	-1.691978	0.00731	0.02634	0.10907	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000359982;ENST00000436458;ENST00000343300	T;T;T;T;T	0.81163	-1.46;-1.29;-1.29;-1.29;-1.29	3.71	1.55	0.23275	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.297955	0.23995	N	0.042527	T	0.00073	0.0002	N	0.03917	-0.325	0.38054	P	0.06411100000000003	B;B;B;B;B;B	0.17852	0.002;0.0;0.016;0.007;0.024;0.009	B;B;B;B;B;B	0.09377	0.002;0.002;0.004;0.003;0.004;0.002	T	0.05451	-1.0884	9	0.02654	T	1	.	5.3372	0.15965	0.0:0.254:0.0:0.746	rs35931837	289;226;267;278;262;278	F8WA78;C9JBE5;O43699-4;O43699-2;O43699-3;O43699	.;.;.;.;.;SIGL6_HUMAN	S	251;262;278;289;226;278	ENSP00000344064:G251S;ENSP00000401502:G278S;ENSP00000353071:G289S;ENSP00000410679:G226S;ENSP00000345907:G278S	ENSP00000345907:G278S	G	-	1	0	SIGLEC6	56724970	0.083000	0.21467	0.902000	0.35471	0.038000	0.13279	-0.302000	0.08221	0.150000	0.19136	-0.492000	0.04666	GGC	C|0.914;T|0.086	0.086	strong		0.622	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
SLC25A32	81034	hgsc.bcm.edu	37	8	104427541	104427541	+	5'Flank	SNP	C	C	T	rs3134296	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:104427541C>T	ENST00000297578.4	-	0	0				DCAF13_ENST00000297579.5_Missense_Mutation_p.P108L|DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|SLC25A32_ENST00000543107.1_5'Flank	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	CCAGTTGAGCCAGCAGGCCGC	0.642													C|||	1112	0.222045	0.1626	0.2262	5008	,	,		16959	0.3323		0.168	False		,,,				2504	0.2413				p.P108L		Atlas-SNP	.											DCAF13,NS,carcinoma,-1,1	DCAF13	66	1	0			c.C323T						PASS	.	C	LEU/PRO	734,3668		49,636,1516	31.0	40.0	37.0		323	0.6	0.0	8	dbSNP_103	37	1117,7477		83,951,3263	yes	missense	DCAF13	NM_015420.6	98	132,1587,4779	TT,TC,CC		12.9974,16.6742,14.2428	benign	108/598	104427541	1851,11145	2201	4297	6498	SO:0001631	upstream_gene_variant	25879	exon1			TTGAGCCAGCAGG	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		8.37:g.104427541C>T	Exception_encountered	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_015420	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	CCDS6300.1	489	0.2239010989010989	86	0.17479674796747968	76	0.20994475138121546	196	0.34265734265734266	131	0.17282321899736147	C	12.25	1.882032	0.33255	0.166742	0.129974	ENSG00000164934	ENST00000297579	T	0.78126	-1.15	4.55	0.585	0.17428	.	1.567910	0.04564	U	0.392106	T	0.00012	0.0000	.	.	.	0.58432	P	4.000000000004E-6	.	.	.	.	.	.	T	0.04178	-1.0971	6	0.25106	T	0.35	.	2.547	0.04739	0.1381:0.4278:0.2698:0.1642	rs3134296;rs3736048;rs28364768;rs3134296	.	.	.	L	108	ENSP00000297579:P108L	ENSP00000297579:P108L	P	+	2	0	DCAF13	104496717	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.198000	0.09505	0.226000	0.20979	-0.253000	0.11424	CCA	C|0.817;T|0.183	0.183	strong		0.642	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
ZNF700	90592	hgsc.bcm.edu	37	19	12059467	12059467	+	Missense_Mutation	SNP	C	C	G	rs73509026	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:12059467C>G	ENST00000254321.5	+	4	771	c.628C>G	c.(628-630)Cga>Gga	p.R210G	CTD-2006C1.12_ENST00000586394.1_RNA|ZNF700_ENST00000482090.1_Missense_Mutation_p.R192G|ZNF763_ENST00000590798.1_Intron|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	210					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						TTCAAGCATTCGAAGACACAT	0.383													c|||	318	0.0634984	0.1505	0.0288	5008	,	,		21685	0.0218		0.0378	False		,,,				2504	0.0399				p.R213G		Atlas-SNP	.											ZNF700,NS,carcinoma,-1,1	ZNF700	81	1	0			c.C637G						PASS	.	C	GLY/ARG	584,3822	254.0+/-259.7	38,508,1657	89.0	93.0	92.0		628	0.6	0.0	19	dbSNP_130	92	256,8344	99.7+/-161.2	2,252,4046	yes	missense	ZNF700	NM_144566.1	125	40,760,5703	GG,GC,CC		2.9767,13.2547,6.4586	probably-damaging	210/743	12059467	840,12166	2203	4300	6503	SO:0001583	missense	90592	exon4			AGCATTCGAAGAC	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"""Zinc fingers, C2H2-type"", ""-"""	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.628C>G	19.37:g.12059467C>G	ENSP00000254321:p.Arg210Gly	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_001271848	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	123	0.05631868131868132	67	0.13617886178861788	13	0.03591160220994475	16	0.027972027972027972	27	0.03562005277044855	c	9.486	1.099434	0.20552	0.132547	0.029767	ENSG00000196757	ENST00000254321	T	0.07114	3.22	0.554	0.554	0.17241	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	M	0.63169	1.94	0.09310	N	1	P	0.51057	0.941	P	0.50708	0.648	T	0.31110	-0.9955	9	0.21540	T	0.41	.	3.5609	0.07882	0.4412:0.5587:1.0E-4:0.0	.	210	Q9H0M5	ZN700_HUMAN	G	210	ENSP00000254321:R210G	ENSP00000254321:R210G	R	+	1	2	ZNF700	11920467	0.000000	0.05858	0.032000	0.17829	0.334000	0.28698	-1.823000	0.01710	0.535000	0.28714	0.305000	0.20034	CGA	C|0.940;G|0.060	0.060	strong		0.383	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566	
SYNRG	11276	hgsc.bcm.edu	37	17	35937637	35937637	+	Missense_Mutation	SNP	T	T	C	rs12602536	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:35937637T>C	ENST00000339208.6	-	7	804	c.664A>G	c.(664-666)Act>Gct	p.T222A	SYNRG_ENST00000585472.1_Intron|SYNRG_ENST00000591288.1_Intron|SYNRG_ENST00000394378.2_Intron|SYNRG_ENST00000502449.2_Intron|SYNRG_ENST00000345615.4_Intron|SYNRG_ENST00000588194.1_Intron|SYNRG_ENST00000346661.4_Missense_Mutation_p.T222A	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	222			T -> A (in dbSNP:rs12602536).		endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)	p.T222A(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						ACTTCAGAAGTATTTAATTTA	0.428													T|||	849	0.169529	0.0877	0.2176	5008	,	,		16631	0.1389		0.2097	False		,,,				2504	0.2362				p.T222A		Atlas-SNP	.											SYNRG,NS,carcinoma,0,1	SYNRG	101	1	1	Substitution - Missense(1)	prostate(1)	c.A664G						PASS	.	T	,,,,ALA/THR,,	442,3964	213.5+/-233.1	19,404,1780	154.0	161.0	159.0		,,,,664,,	2.0	0.9	17	dbSNP_120	159	1525,7075	288.1+/-298.6	127,1271,2902	yes	intron,intron,intron,intron,missense,intron,intron	SYNRG	NM_001163544.1,NM_001163545.1,NM_001163546.1,NM_001163547.1,NM_007247.4,NM_080550.3,NM_198882.1	,,,,58,,	146,1675,4682	CC,CT,TT		17.7326,10.0318,15.1238	,,,,benign,,	,,,,222/1315,,	35937637	1967,11039	2203	4300	6503	SO:0001583	missense	11276	exon7			CAGAAGTATTTAA	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.664A>G	17.37:g.35937637T>C	ENSP00000343610:p.Thr222Ala	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	152	82	0.539474	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	353	0.16163003663003664	40	0.08130081300813008	72	0.19889502762430938	77	0.1346153846153846	164	0.21635883905013192	T	11.99	1.802382	0.31869	0.100318	0.177326	ENSG00000006114	ENST00000346661;ENST00000345615;ENST00000394379	T	0.30182	1.54	5.46	1.97	0.26223	.	0.346213	0.30302	N	0.009933	T	0.00012	0.0000	L	0.41236	1.265	0.35584	P	0.193465	P;B;B	0.37207	0.587;0.004;0.004	B;B;B	0.32724	0.151;0.006;0.006	T	0.28996	-1.0026	9	0.09590	T	0.72	-9.3107	4.795	0.13269	0.291:0.0787:0.0:0.6303	rs12602536;rs52810147;rs59102053;rs12602536	323;222;222	A8MYE0;Q9UMZ2-5;Q9UMZ2	.;.;SYNRG_HUMAN	A	222;222;323	ENSP00000005279:T222A	ENSP00000315722:T222A	T	-	1	0	SYNRG	33011750	0.997000	0.39634	0.931000	0.37212	0.899000	0.52679	0.400000	0.20932	0.320000	0.23234	0.482000	0.46254	ACT	C|0.151;T|0.849	0.151	strong		0.428	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	
PARP15	165631	hgsc.bcm.edu	37	3	122296647	122296647	+	Missense_Mutation	SNP	G	G	A	rs7632426	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:122296647G>A	ENST00000464300.2	+	1	199	c.133G>A	c.(133-135)Gcc>Acc	p.A45T	PARP15_ENST00000483793.1_Missense_Mutation_p.A45T	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	45					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		CGTGCTGCCGGCCGGGAACCG	0.692													G|||	847	0.169129	0.1528	0.0908	5008	,	,		14070	0.2331		0.1193	False		,,,				2504	0.2321				p.A45T		Atlas-SNP	.											.	PARP15	115	.	0			c.G133A						PASS	.						24.0	27.0	26.0					3																	122296647		692	1591	2283	SO:0001583	missense	165631	exon1			CTGCCGGCCGGGA	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.133G>A	3.37:g.122296647G>A	ENSP00000417214:p.Ala45Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	63	41	0.650794	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	325	0.1488095238095238	74	0.15040650406504066	25	0.06906077348066299	125	0.21853146853146854	101	0.13324538258575197	G	9.266	1.044407	0.19748	.	.	ENSG00000173200	ENST00000464300;ENST00000483793	T;T	0.18016	2.63;2.24	2.55	-2.4	0.06583	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	4.000000000004E-6	B;B	0.11235	0.004;0.004	B;B	0.08055	0.003;0.003	T	0.45145	-0.9281	8	0.11182	T	0.66	.	3.3144	0.07027	0.3969:0.0:0.4141:0.189	rs7632426;rs7632426	45;23	C9J7L3;Q460N3	.;PAR15_HUMAN	T	45	ENSP00000417214:A45T;ENSP00000417785:A45T	ENSP00000417214:A45T	A	+	1	0	PARP15	123779337	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.172000	0.09868	-0.618000	0.05656	-0.367000	0.07326	GCC	G|0.835;A|0.165	0.165	strong		0.692	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
GP1BA	2811	hgsc.bcm.edu	37	17	4836381	4836381	+	Missense_Mutation	SNP	C	C	T	rs6065	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4836381C>T	ENST00000329125.5	+	2	557	c.482C>T	c.(481-483)aCg>aTg	p.T161M		NM_000173.5	NP_000164.5	P07359	GP1BA_HUMAN	glycoprotein Ib (platelet), alpha polypeptide	161			T -> M (in Siba(+); dbSNP:rs6065). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:1586750, ECO:0000269|PubMed:7632942, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|fibrinolysis (GO:0042730)|platelet activation (GO:0030168)|regulation of blood coagulation (GO:0030193)|thrombin receptor signaling pathway (GO:0070493)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						GGGCTCCTGACGCCCACACCC	0.597													C|||	659	0.131589	0.2511	0.1542	5008	,	,		19329	0.0704		0.0875	False		,,,				2504	0.0624				p.T161M		Atlas-SNP	.											GP1BA,colon,carcinoma,-1,1	GP1BA	53	1	0			c.C482T	GRCh37	CM032257	GP1BA	M	rs6065	PASS	.	C	MET/THR	856,3152		105,646,1253	67.0	68.0	68.0	http://www.ncbi.nlm.nih.gov/pubmed?term	482	-9.6	0.0	17	dbSNP_52	68	663,7663		32,599,3532	yes	missense	GP1BA	NM_000173.5	81	137,1245,4785	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	7.963,21.3573,12.3156	possibly-damaging	161/653	4836381	1519,10815	2004	4163	6167	SO:0001583	missense	2811	exon2			TCCTGACGCCCAC		CCDS54068.1	17p13.2	2014-09-17			ENSG00000185245	ENSG00000185245		"""CD molecules"""	4439	protein-coding gene	gene with protein product		606672		GP1B		3353370	Standard	NM_000173		Approved	CD42b	uc021tnz.1	P07359	OTTHUMG00000177946	ENST00000329125.5:c.482C>T	17.37:g.4836381C>T	ENSP00000329380:p.Thr161Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	89	32	0.359551	NM_000173	E7ES66|Q14441|Q16469|Q8N1F3|Q8NG39|Q9HDC7|Q9UEK1|Q9UQS4	Missense_Mutation	SNP	ENST00000329125.5	37	CCDS54068.1	282	0.12912087912087913	130	0.26422764227642276	51	0.1408839779005525	40	0.06993006993006994	61	0.08047493403693931	C	11.30	1.596638	0.28445	0.213573	0.07963	ENSG00000185245	ENST00000329125;ENST00000438881	T	0.57907	0.37	4.81	-9.62	0.00547	.	1.499870	0.04549	N	0.389490	T	0.00012	0.0000	L	0.28274	0.84	0.80722	P	0.0	P	0.34629	0.46	B	0.33196	0.159	T	0.03259	-1.1055	9	0.40728	T	0.16	1.2474	1.5063	0.02487	0.4764:0.1156:0.1575:0.2505	rs6065;rs61370736;rs6065	161	A5CKE2	.	M	161	ENSP00000329380:T161M	ENSP00000329380:T161M	T	+	2	0	GP1BA	4777161	0.000000	0.05858	0.000000	0.03702	0.533000	0.34776	-2.797000	0.00763	-2.443000	0.00548	-0.657000	0.03884	ACG	C|0.878;T|0.122	0.122	strong		0.597	GP1BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439889.1		
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815522	23815522	+	Silent	SNP	C	C	T	rs3755863	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:23815522C>T	ENST00000264867.2	-	8	1703	c.1584G>A	c.(1582-1584)acG>acA	p.T528T	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	528	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				AATAGGATTGCGTGCCATCCC	0.408													C|||	1764	0.352236	0.239	0.3343	5008	,	,		19235	0.4454		0.4284	False		,,,				2504	0.3436				p.T528T	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											PPARGC1A,colon,carcinoma,0,1	PPARGC1A	129	1	0			c.G1584A	GRCh37	CM035706	PPARGC1A	M	rs3755863	PASS	.	C		1052,3354	384.2+/-325.2	120,812,1271	145.0	138.0	140.0		1584	3.2	1.0	4	dbSNP_107	140	3512,5088	512.9+/-378.0	695,2122,1483	no	coding-synonymous	PPARGC1A	NM_013261.3		815,2934,2754	TT,TC,CC		40.8372,23.8765,35.0915		528/799	23815522	4564,8442	2203	4300	6503	SO:0001819	synonymous_variant	10891	exon8			GGATTGCGTGCCA	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.1584G>A	4.37:g.23815522C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	37	CCDS3429.1																																																																																			C|0.640;T|0.360	0.360	strong		0.408	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
COL20A1	57642	hgsc.bcm.edu	37	20	61929348	61929348	+	Missense_Mutation	SNP	C	C	A	rs144861412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61929348C>A	ENST00000358894.6	+	3	269	c.169C>A	c.(169-171)Ctg>Atg	p.L57M	COL20A1_ENST00000422202.1_Missense_Mutation_p.L57M|COL20A1_ENST00000326996.6_Missense_Mutation_p.L57M|COL20A1_ENST00000435874.1_Missense_Mutation_p.L57M	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	57	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					CCTCGGCTACCTGGTGCAGGT	0.652													C|||	21	0.00419329	0.0	0.0014	5008	,	,		14571	0.0		0.0119	False		,,,				2504	0.0082				p.L57M		Atlas-SNP	.											.	COL20A1	137	.	0			c.C169A						PASS	.	C	MET/LEU	10,4012		0,10,2001	35.0	46.0	42.0		169	1.7	1.0	20	dbSNP_134	42	75,8235		1,73,4081	yes	missense	COL20A1	NM_020882.2	15	1,83,6082	AA,AC,CC		0.9025,0.2486,0.6893	probably-damaging	57/1285	61929348	85,12247	2011	4155	6166	SO:0001583	missense	57642	exon3			GGCTACCTGGTGC	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.169C>A	20.37:g.61929348C>A	ENSP00000351767:p.Leu57Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	C	12.63	1.995970	0.35226	0.002486	0.009025	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	T;T;T;T	0.58060	0.36;0.36;0.36;0.36	3.95	1.69	0.24217	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.140637	0.45126	U	0.000387	T	0.37571	0.1008	N	0.14661	0.345	0.24214	N	0.995468	D	0.67145	0.996	D	0.64877	0.93	T	0.13710	-1.0499	10	0.51188	T	0.08	.	4.5613	0.12161	0.5055:0.3578:0.0:0.1366	.	57	Q9P218	COKA1_HUMAN	M	57	ENSP00000351767:L57M;ENSP00000323077:L57M;ENSP00000408690:L57M;ENSP00000414753:L57M	ENSP00000323077:L57M	L	+	1	2	COL20A1	61399793	1.000000	0.71417	0.988000	0.46212	0.005000	0.04900	2.148000	0.42235	0.621000	0.30232	0.591000	0.81541	CTG	C|0.995;A|0.005	0.005	strong		0.652	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
NEK10	152110	hgsc.bcm.edu	37	3	27326451	27326451	+	Splice_Site	SNP	A	A	G	rs10510594	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:27326451A>G	ENST00000429845.2	-	22	2153	c.1791T>C	c.(1789-1791)aaT>aaC	p.N597N	NEK10_ENST00000357467.2_5'UTR|NEK10_ENST00000341435.5_Splice_Site_p.N597N			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	597	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.N597N(3)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						ACAACCTATCATCTATATAAA	0.383													A|||	1052	0.210064	0.1067	0.3516	5008	,	,		17244	0.1002		0.2793	False		,,,				2504	0.2914				p.N597N		Atlas-SNP	.											NEK10_ENST00000429845,NS,carcinoma,0,3	NEK10	271	3	3	Substitution - coding silent(3)	kidney(3)	c.T1791C						PASS	.	A		631,3741		55,521,1610	49.0	52.0	51.0		1791	5.7	1.0	3	dbSNP_119	51	2393,6199		365,1663,2268	yes	coding-synonymous-near-splice	NEK10	NM_199347.2		420,2184,3878	GG,GA,AA		27.8515,14.4328,23.3261		597/713	27326451	3024,9940	2186	4296	6482	SO:0001630	splice_region_variant	152110	exon22			CCTATCATCTATA	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1790-1T>C	3.37:g.27326451A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	42	15	0.357143	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	37		459|459	0.21016483516483517|0.21016483516483517	54|54	0.10975609756097561|0.10975609756097561	133|133	0.3674033149171271|0.3674033149171271	58|58	0.10139860139860139|0.10139860139860139	214|214	0.28232189973614774|0.28232189973614774	A|A	14.32|14.32	2.500023|2.500023	0.44455|0.44455	0.144328|0.144328	0.278515|0.278515	ENSG00000163491|ENSG00000163491	ENST00000424275|ENST00000435584	.|.	.|.	.|.	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.05386|.	-1.0888|.	3|.	.|.	.|.	.|.	.|.	15.9466|15.9466	0.79799|0.79799	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs10510594;rs17681232;rs10510594|rs10510594;rs17681232;rs10510594	.|.	.|.	.|.	T|R	84|54	.|.	.|.	M|X	-|-	2|1	0|0	NEK10|NEK10	27301455|27301455	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.852000|0.852000	0.48524|0.48524	3.860000|3.860000	0.55995|0.55995	2.175000|2.175000	0.68902|0.68902	0.397000|0.397000	0.26171|0.26171	ATG|TGA	A|0.792;G|0.208	0.208	strong		0.383	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	Silent
SLC52A3	113278	hgsc.bcm.edu	37	20	741847	741847	+	Silent	SNP	A	A	G	rs910857	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:741847A>G	ENST00000217254.7	-	5	1474	c.1233T>C	c.(1231-1233)agT>agC	p.S411S	SLC52A3_ENST00000381944.3_3'UTR|SLC52A3_ENST00000473664.1_5'UTR	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	411			S -> R (in dbSNP:rs910857).		cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										CCTTGACGTAACTGAGGCAGC	0.706													A|||	3282	0.655351	0.6399	0.647	5008	,	,		14258	0.5238		0.7217	False		,,,				2504	0.7495				p.S411S		Atlas-SNP	.											.	.	.	.	0			c.T1233C						PASS	.	A		2795,1505		950,895,305	9.0	10.0	9.0		1233	4.2	1.0	20	dbSNP_86	9	6097,2265		2271,1555,355	no	coding-synonymous	C20orf54	NM_033409.3		3221,2450,660	GG,GA,AA		27.0868,35.0,29.7741		411/470	741847	8892,3770	2150	4181	6331	SO:0001819	synonymous_variant	113278	exon5			GACGTAACTGAGG	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.1233T>C	20.37:g.741847A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			A|0.391;G|0.609	0.609	strong		0.706	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
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 GAIIx	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	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	180	106	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 GAIIx	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_ENST00000564537.1_Silent_p.A27A|HAGHL_ENST00000389703.3_Silent_p.A27A|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000564545.1_Silent_p.A27A|HAGHL_ENST00000561546.1_Silent_p.A27A			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		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	45	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 GAIIx	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	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	265	53	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	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559914	140559914	+	Missense_Mutation	SNP	T	T	C	rs2740583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140559914T>C	ENST00000239444.2	+	1	2544	c.2299T>C	c.(2299-2301)Ttc>Ctc	p.F767L	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	767			F -> L (in dbSNP:rs2740583). {ECO:0000269|PubMed:11322959, ECO:0000269|PubMed:15489334}.		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAGTTCCAGTTCCTGAAACC	0.502													T|||	973	0.194289	0.0197	0.2939	5008	,	,		16792	0.1171		0.3449	False		,,,				2504	0.2843				p.F767L		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T2299C						PASS	.	T	LEU/PHE	301,4105	162.9+/-194.8	17,267,1919	99.0	102.0	101.0		2299	4.5	0.3	5	dbSNP_100	101	2995,5605	464.0+/-366.1	532,1931,1837	yes	missense	PCDHB8	NM_019120.3	22	549,2198,3756	CC,CT,TT		34.8256,6.8316,25.3421	benign	767/802	140559914	3296,9710	2203	4300	6503	SO:0001583	missense	56128	exon1			TTCCAGTTCCTGA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.2299T>C	5.37:g.140559914T>C	ENSP00000239444:p.Phe767Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	467	0.21382783882783882	13	0.026422764227642278	121	0.3342541436464088	71	0.12412587412587413	262	0.34564643799472294	T	22.2	4.258002	0.80246	0.068316	0.348256	ENSG00000120322	ENST00000239444	T	0.18657	2.2	4.53	4.53	0.55603	.	.	.	.	.	T	0.00012	0.0000	M	0.88105	2.93	0.36688	P	0.12056599999999995	B	0.24132	0.098	B	0.29942	0.109	T	0.23190	-1.0195	8	0.66056	D	0.02	.	13.5476	0.61713	0.0:0.0:0.0:1.0	rs2740583;rs17697117;rs17844510;rs61661593;rs2740583	767	Q9UN66	PCDB8_HUMAN	L	767	ENSP00000239444:F767L	ENSP00000239444:F767L	F	+	1	0	PCDHB8	140540098	0.998000	0.40836	0.332000	0.25469	0.020000	0.10135	3.378000	0.52432	1.673000	0.50895	0.455000	0.32223	TTC	A|0.000;C|0.223;N|0.000;T|0.776	0.223	strong		0.502	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
TEP1	7011	hgsc.bcm.edu	37	14	20863677	20863677	+	Silent	SNP	C	C	A	rs2228036	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20863677C>A	ENST00000262715.5	-	12	1900	c.1860G>T	c.(1858-1860)cgG>cgT	p.R620R	TEP1_ENST00000556935.1_Silent_p.R512R	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	620	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TCATTGCCATCCGAAGCTGCT	0.502													C|||	983	0.196286	0.0893	0.2954	5008	,	,		20960	0.1379		0.3111	False		,,,				2504	0.2127				p.R620R		Atlas-SNP	.											.	TEP1	224	.	0			c.G1860T						PASS	.	C		577,3829	259.5+/-263.1	40,497,1666	144.0	119.0	128.0		1860	0.8	0.2	14	dbSNP_98	128	2846,5754	448.3+/-361.8	492,1862,1946	no	coding-synonymous	TEP1	NM_007110.4		532,2359,3612	AA,AC,CC		33.093,13.0958,26.3186		620/2628	20863677	3423,9583	2203	4300	6503	SO:0001819	synonymous_variant	7011	exon12			TGCCATCCGAAGC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.1860G>T	14.37:g.20863677C>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	184	79	0.429348	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																			C|0.753;A|0.247	0.247	strong		0.502	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
C9orf171	389799	hgsc.bcm.edu	37	9	135413085	135413085	+	Missense_Mutation	SNP	A	A	C	rs34650498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135413085A>C	ENST00000343036.2	+	5	778	c.730A>C	c.(730-732)Aag>Cag	p.K244Q	C9orf171_ENST00000393216.2_Missense_Mutation_p.K208Q	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	244			K -> Q (in dbSNP:rs34650498).							large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						ACTGGAGAAGAAGCAGAAGGT	0.552													A|||	119	0.023762	0.0106	0.0432	5008	,	,		19241	0.0		0.0646	False		,,,				2504	0.0102				p.K244Q		Atlas-SNP	.											C9orf171,colon,carcinoma,-1,1	C9orf171	53	1	0			c.A730C						PASS	.	A	GLN/LYS	84,4322	70.3+/-108.2	0,84,2119	87.0	90.0	89.0		730	5.7	1.0	9	dbSNP_126	89	621,7979	161.7+/-214.6	26,569,3705	yes	missense	C9orf171	NM_207417.1	53	26,653,5824	CC,CA,AA		7.2209,1.9065,5.4206	probably-damaging	244/321	135413085	705,12301	2203	4300	6503	SO:0001583	missense	389799	exon5			GAGAAGAAGCAGA	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.730A>C	9.37:g.135413085A>C	ENSP00000343290:p.Lys244Gln	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_207417	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	37	CCDS6949.1	70	0.03205128205128205	10	0.02032520325203252	15	0.04143646408839779	0	0.0	45	0.059366754617414245	A	16.85	3.235663	0.58886	0.019065	0.072209	ENSG00000188523	ENST00000343036;ENST00000393216	T;T	0.22945	1.93;1.93	5.65	5.65	0.86999	.	0.479549	0.19860	N	0.104451	T	0.01353	0.0044	L	0.27053	0.805	0.29949	N	0.820413	B;B	0.33637	0.42;0.42	B;B	0.32928	0.099;0.155	T	0.02909	-1.1095	10	0.29301	T	0.29	.	13.6318	0.62200	1.0:0.0:0.0:0.0	rs34650498	208;244	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	Q	244;208	ENSP00000343290:K244Q;ENSP00000376909:K208Q	ENSP00000343290:K244Q	K	+	1	0	C9orf171	134402906	1.000000	0.71417	0.995000	0.50966	0.978000	0.69477	3.201000	0.51059	2.146000	0.66826	0.533000	0.62120	AAG	A|0.952;C|0.048	0.048	strong		0.552	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417	
LBP	3929	hgsc.bcm.edu	37	20	36979265	36979265	+	Silent	SNP	T	T	C	rs2232582	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:36979265T>C	ENST00000217407.2	+	3	452	c.291T>C	c.(289-291)ccT>ccC	p.P97P		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	97					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				GGCCTGTCCCTGGCCAGGGCC	0.617													C|||	1068	0.213259	0.4221	0.1023	5008	,	,		21538	0.0734		0.1322	False		,,,				2504	0.2372				p.P97P		Atlas-SNP	.											.	LBP	60	.	0			c.T291C						PASS	.	C		1635,2771	658.5+/-400.4	306,1023,874	88.0	80.0	83.0		291	-9.4	0.0	20	dbSNP_98	83	1364,7236	755.0+/-407.5	111,1142,3047	no	coding-synonymous	LBP	NM_004139.2		417,2165,3921	CC,CT,TT		15.8605,37.1085,23.0586		97/482	36979265	2999,10007	2203	4300	6503	SO:0001819	synonymous_variant	3929	exon3			TGTCCCTGGCCAG		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.291T>C	20.37:g.36979265T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																			T|0.792;C|0.208	0.208	strong		0.617	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
TMEM63A	9725	hgsc.bcm.edu	37	1	226041438	226041438	+	Silent	SNP	C	C	T	rs2292556	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226041438C>T	ENST00000366835.3	-	19	1959	c.1689G>A	c.(1687-1689)tcG>tcA	p.S563S		NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	563					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					CGATGAAGGCCGAGGCGATGA	0.597													C|||	344	0.0686901	0.0045	0.0735	5008	,	,		20098	0.1567		0.0497	False		,,,				2504	0.0808				p.S563S		Atlas-SNP	.											TMEM63A,NS,carcinoma,0,1	TMEM63A	75	1	0			c.G1689A						PASS	.	C		43,4363	43.1+/-76.7	0,43,2160	53.0	40.0	45.0		1689	-4.4	1.0	1	dbSNP_100	45	349,8249	110.2+/-170.6	3,343,3953	no	coding-synonymous	TMEM63A	NM_014698.2		3,386,6113	TT,TC,CC		4.0591,0.9759,3.0145		563/808	226041438	392,12612	2203	4299	6502	SO:0001819	synonymous_variant	9725	exon19			GAAGGCCGAGGCG		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.1689G>A	1.37:g.226041438C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	137	61	0.445255	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			C|0.960;T|0.040	0.040	strong		0.597	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
B4GALT4	8702	hgsc.bcm.edu	37	3	118948716	118948716	+	Silent	SNP	G	G	A	rs4422294	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:118948716G>A	ENST00000483209.1	-	3	872	c.231C>T	c.(229-231)tgC>tgT	p.C77C	B4GALT4_ENST00000471675.1_Silent_p.C30C|B4GALT4_ENST00000467604.1_Silent_p.C77C|B4GALT4-AS1_ENST00000470790.1_RNA|B4GALT4_ENST00000359213.3_Silent_p.C77C|B4GALT4_ENST00000460321.1_Intron|B4GALT4_ENST00000393765.2_Silent_p.C77C			O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4	77					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|membrane lipid metabolic process (GO:0006643)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)	p.C77C(1)		breast(2)|endometrium(1)|large_intestine(1)|lung(6)|skin(2)|stomach(2)	14				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)	ACACAGAAGGGCAGTTGTCAA	0.373													G|||	968	0.193291	0.0378	0.3084	5008	,	,		20926	0.246		0.3022	False		,,,				2504	0.1554				p.C77C		Atlas-SNP	.											B4GALT4,NS,carcinoma,0,1	B4GALT4	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C231T						PASS	.	G	,	342,4064	177.6+/-206.5	17,308,1878	138.0	128.0	132.0		231,231	-2.9	0.8	3	dbSNP_111	132	2540,6060	414.1+/-351.3	372,1796,2132	no	coding-synonymous,coding-synonymous	B4GALT4	NM_003778.3,NM_212543.1	,	389,2104,4010	AA,AG,GG		29.5349,7.7621,22.159	,	77/345,77/345	118948716	2882,10124	2203	4300	6503	SO:0001819	synonymous_variant	8702	exon4			AGAAGGGCAGTTG	AF022367	CCDS2986.1	3q13.3	2013-02-19			ENSG00000121578	ENSG00000121578		"""Beta 4-glycosyltransferases"""	927	protein-coding gene	gene with protein product		604015				9597550	Standard	NM_003778		Approved	beta4Gal-T4	uc003eci.3	O60513	OTTHUMG00000159358	ENST00000483209.1:c.231C>T	3.37:g.118948716G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_212543	Q68D68|Q9BSW3|Q9C078	Silent	SNP	ENST00000483209.1	37	CCDS2986.1																																																																																			G|0.776;A|0.224	0.224	strong		0.373	B4GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354925.2	NM_003778	
ZNF792	126375	hgsc.bcm.edu	37	19	35449486	35449486	+	Missense_Mutation	SNP	T	T	C	rs34687332	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35449486T>C	ENST00000404801.1	-	4	1659	c.1273A>G	c.(1273-1275)Aac>Gac	p.N425D	ZNF792_ENST00000605484.1_Missense_Mutation_p.N358D	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	425					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(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CCACATTCGTTACACTTGTAA	0.478													T|||	192	0.0383387	0.0038	0.0403	5008	,	,		21899	0.004		0.0457	False		,,,				2504	0.1115				p.N425D	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											.	ZNF792	46	.	0			c.A1273G						PASS	.	T	ASP/ASN	39,4367	42.3+/-75.8	3,33,2167	99.0	93.0	95.0		1273	1.7	0.0	19	dbSNP_126	95	449,8151	135.7+/-192.9	17,415,3868	yes	missense	ZNF792	NM_175872.4	23	20,448,6035	CC,CT,TT		5.2209,0.8852,3.7521	probably-damaging	425/633	35449486	488,12518	2203	4300	6503	SO:0001583	missense	126375	exon4			ATTCGTTACACTT	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1273A>G	19.37:g.35449486T>C	ENSP00000385099:p.Asn425Asp	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Missense_Mutation	SNP	ENST00000404801.1	37	CCDS12440.2	56	0.02564102564102564	4	0.008130081300813009	16	0.04419889502762431	0	0.0	36	0.047493403693931395	t	13.75	2.329287	0.41197	0.008852	0.052209	ENSG00000180884	ENST00000404801;ENST00000379189	T	0.15952	2.38	2.77	1.74	0.24563	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01156	0.0038	N	0.12831	0.26	0.25574	N	0.986865	B	0.30211	0.273	B	0.26202	0.067	T	0.32268	-0.9913	9	0.40728	T	0.16	.	6.0896	0.19987	0.0:0.1351:0.0:0.8649	rs34687332;rs34687332	425	Q3KQV3	ZN792_HUMAN	D	425;185	ENSP00000385099:N425D	ENSP00000368487:N185D	N	-	1	0	ZNF792	40141326	0.000000	0.05858	0.009000	0.14445	0.840000	0.47671	-0.270000	0.08584	0.479000	0.27511	0.460000	0.39030	AAC	T|0.966;C|0.034	0.034	strong		0.478	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
SETD4	54093	hgsc.bcm.edu	37	21	37410477	37410477	+	Missense_Mutation	SNP	T	T	C	rs2835239	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:37410477T>C	ENST00000399215.1	-	9	2531	c.1159A>G	c.(1159-1161)Ata>Gta	p.I387V	SETD4_ENST00000399212.1_Missense_Mutation_p.I363V|SETD4_ENST00000481477.1_5'UTR|SETD4_ENST00000332131.4_Missense_Mutation_p.I387V|AP000688.1_ENST00000600312.1_Intron			Q9NVD3	SETD4_HUMAN	SET domain containing 4	387			I -> V (in dbSNP:rs2835239).	EILVKYLPSTDKQMDKKISILKDHGYIENLTFGWDGPSWRL LTALKLLCLEAEKFTCWKKVLLGEVISDTNEKTSLDIAQKI CYYFIEETNAVLQKVSHMKDEKEALINQLTLVESLWTEELK ILRASAETLHSLQTAFT -> GWNQLCS (in Ref. 5; AAH02898). {ECO:0000305}.			methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GTCTCTTCTATGAAATAATAG	0.348													T|||	128	0.0255591	0.0	0.036	5008	,	,		19033	0.002		0.0636	False		,,,				2504	0.0378				p.I387V		Atlas-SNP	.											.	SETD4	37	.	0			c.A1159G						PASS	.	T	VAL/ILE	56,4348	54.9+/-90.9	2,52,2148	164.0	159.0	161.0		1159	3.2	0.2	21	dbSNP_100	161	498,8102	144.3+/-200.2	8,482,3810	yes	missense	SETD4	NM_017438.3	29	10,534,5958	CC,CT,TT		5.7907,1.2716,4.2602	possibly-damaging	387/441	37410477	554,12450	2202	4300	6502	SO:0001583	missense	54093	exon10			CTTCTATGAAATA	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.1159A>G	21.37:g.37410477T>C	ENSP00000382163:p.Ile387Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_017438	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	37	CCDS13640.1	62	0.028388278388278388	0	0.0	13	0.03591160220994475	0	0.0	49	0.06464379947229551	T	14.91	2.676807	0.47886	0.012716	0.057907	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131	T;T;T	0.18016	2.24;2.24;2.24	5.79	3.22	0.36961	Rubisco LS methyltransferase, substrate-binding domain (1);	0.377760	0.30762	N	0.008935	T	0.02083	0.0065	M	0.70595	2.14	0.38358	D	0.94451	B;P	0.36789	0.27;0.57	B;B	0.41202	0.151;0.35	T	0.04294	-1.0962	10	0.24483	T	0.36	-25.5361	7.6719	0.28463	0.1314:0.0:0.2735:0.5951	rs2835239;rs17228507;rs52822224;rs59296148;rs2835239	363;387	Q9NVD3-3;Q9NVD3	.;SETD4_HUMAN	V	387;363;387	ENSP00000382163:I387V;ENSP00000382161:I363V;ENSP00000329189:I387V	ENSP00000329189:I387V	I	-	1	0	SETD4	36332347	0.986000	0.35501	0.209000	0.23619	0.729000	0.41735	0.337000	0.19841	0.970000	0.38263	0.459000	0.35465	ATA	T|0.963;C|0.037	0.037	strong		0.348	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438	
ADAM19	8728	hgsc.bcm.edu	37	5	156917340	156917340	+	Missense_Mutation	SNP	A	A	C	rs10067096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:156917340A>C	ENST00000517905.1	-	19	2262	c.2218T>G	c.(2218-2220)Tcc>Gcc	p.S740A	ADAM19_ENST00000257527.4_Missense_Mutation_p.S740A|ADAM19_ENST00000430702.2_Missense_Mutation_p.S473A|ADAM19_ENST00000394020.1_Missense_Mutation_p.S742A			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	740					heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTCAGCTTGGAAGGGAGAGCT	0.493													A|||	603	0.120407	0.205	0.1124	5008	,	,		18142	0.005		0.1968	False		,,,				2504	0.0521				p.S740A		Atlas-SNP	.											.	ADAM19	216	.	0			c.T2218G						PASS	.	A	ALA/SER	852,3554	334.4+/-303.4	79,694,1430	180.0	156.0	164.0		2218	4.2	1.0	5	dbSNP_119	164	1705,6895	312.3+/-310.8	186,1333,2781	yes	missense	ADAM19	NM_033274.3	99	265,2027,4211	CC,CA,AA		19.8256,19.3373,19.6602	benign	740/919	156917340	2557,10449	2203	4300	6503	SO:0001583	missense	8728	exon19			GCTTGGAAGGGAG	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.2218T>G	5.37:g.156917340A>C	ENSP00000428654:p.Ser740Ala	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		300	0.13736263736263737	94	0.1910569105691057	42	0.11602209944751381	4	0.006993006993006993	160	0.21108179419525067	A	12.44	1.939797	0.34189	0.193373	0.198256	ENSG00000135074	ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	T;T;T;T	0.01685	4.69;4.83;4.85;4.82	5.41	4.24	0.50183	.	0.207319	0.34700	N	0.003743	T	0.00012	0.0000	L	0.56769	1.78	0.43073	P	0.005283999999999955	B;B;B	0.34015	0.417;0.435;0.149	B;B;B	0.30495	0.116;0.078;0.098	T	0.28933	-1.0028	9	0.07325	T	0.83	.	4.8818	0.13683	0.7489:0.0:0.0864:0.1647	rs10067096;rs61143303;rs10067096	740;740;473	Q9H013-2;Q9H013;E9PD32	.;ADA19_HUMAN;.	A	473;740;742;740	ENSP00000414088:S473A;ENSP00000257527:S740A;ENSP00000377588:S742A;ENSP00000428654:S740A	ENSP00000257527:S740A	S	-	1	0	ADAM19	156849918	0.980000	0.34600	0.974000	0.42286	0.617000	0.37484	2.373000	0.44266	0.866000	0.35629	0.533000	0.62120	TCC	A|0.827;C|0.173	0.173	strong		0.493	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
PNN	5411	hgsc.bcm.edu	37	14	39644498	39644498	+	Silent	SNP	G	G	A	rs11558738|rs1061583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39644498G>A	ENST00000216832.4	+	1	82	c.15G>A	c.(13-15)gtG>gtA	p.V5V	RP11-407N17.4_ENST00000556537.1_lincRNA|PNN_ENST00000556530.1_Silent_p.V5V|PNN_ENST00000553331.1_Silent_p.V5V	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	5	Necessary for interaction with RNPS1.|Necessary for interactions with KRT8, KRT18 and KRT19.|Necessary for mediating alternative 5' splicing.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		CGGTCGCCGTGAGAACTTTGC	0.602													G|||	935	0.186701	0.0091	0.2017	5008	,	,		14330	0.2321		0.2783	False		,,,				2504	0.2751				p.V5V		Atlas-SNP	.											PNN,right_upper_lobe,carcinoma,+2,1	PNN	67	1	0			c.G15A						PASS	.	G		228,4178	133.7+/-170.0	6,216,1981	53.0	45.0	48.0		15	5.2	1.0	14	dbSNP_86	48	2255,6345	377.2+/-338.5	290,1675,2335	no	coding-synonymous	PNN	NM_002687.3		296,1891,4316	AA,AG,GG		26.2209,5.1748,19.0912		5/718	39644498	2483,10523	2203	4300	6503	SO:0001819	synonymous_variant	5411	exon1			CGCCGTGAGAACT	U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.15G>A	14.37:g.39644498G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	50	17	0.34	NM_002687	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Silent	SNP	ENST00000216832.4	37	CCDS9671.1																																																																																			G|0.804;A|0.196	0.196	strong		0.602	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687	
INMT	11185	hgsc.bcm.edu	37	7	30795331	30795331	+	Missense_Mutation	SNP	A	A	G	rs2302340	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:30795331A>G	ENST00000013222.5	+	3	672	c.656A>G	c.(655-657)gAg>gGg	p.E219G	INMT_ENST00000484180.1_3'UTR|INMT-FAM188B_ENST00000458257.1_Intron|INMT_ENST00000409539.1_Missense_Mutation_p.E218G	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	219			E -> G (in dbSNP:rs2302340). {ECO:0000269|PubMed:10552930, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)	p.E219G(1)		kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						CTGGAGAAAGAGGAGGTGGAG	0.587													A|||	1649	0.329273	0.059	0.5086	5008	,	,		20038	0.5476		0.4294	False		,,,				2504	0.2393				p.E219G		Atlas-SNP	.											INMT,NS,carcinoma,0,1	INMT	38	1	1	Substitution - Missense(1)	stomach(1)	c.A656G						scavenged	.	A	GLY/GLU,GLY/GLU	553,3853	247.8+/-255.9	34,485,1684	109.0	102.0	104.0		653,656	3.7	1.0	7	dbSNP_100	104	3577,5023	517.9+/-379.1	768,2041,1491	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	98,98	802,2526,3175	GG,GA,AA		41.593,12.5511,31.7546	possibly-damaging,possibly-damaging	218/263,219/264	30795331	4130,8876	2203	4300	6503	SO:0001583	missense	11185	exon3			AGAAAGAGGAGGT		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.656A>G	7.37:g.30795331A>G	ENSP00000013222:p.Glu219Gly	Somatic	78	2	0.025641		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	857	0.3923992673992674	41	0.08333333333333333	178	0.49171270718232046	314	0.548951048951049	324	0.42744063324538256	A	16.68	3.190717	0.58017	0.125511	0.41593	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.11495	2.77;2.77	3.67	3.67	0.42095	.	0.170656	0.37530	N	0.002047	T	0.00012	0.0000	M	0.73598	2.24	0.25776	P	0.9847839	D;D	0.54964	0.969;0.969	P;P	0.58873	0.847;0.847	T	0.45411	-0.9263	9	0.52906	T	0.07	-16.1597	10.6007	0.45365	1.0:0.0:0.0:0.0	rs2302340;rs52838184;rs56784180;rs2302340	218;219	B8ZZ69;O95050	.;INMT_HUMAN	G	219;218	ENSP00000013222:E219G;ENSP00000386961:E218G	ENSP00000013222:E219G	E	+	2	0	INMT	30761856	0.986000	0.35501	0.998000	0.56505	0.625000	0.37756	3.452000	0.52971	1.635000	0.50512	0.459000	0.35465	GAG	A|0.661;G|0.339	0.339	strong		0.587	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
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 GAIIx	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_ENST00000446742.1_Missense_Mutation_p.S13G|PAX5_ENST00000520281.1_Missense_Mutation_p.S13G|PAX5_ENST00000377847.2_Missense_Mutation_p.S13G|PAX5_ENST00000377852.2_Missense_Mutation_p.S13G|PAX5_ENST00000414447.1_Missense_Mutation_p.S13G|PAX5_ENST00000523241.1_Missense_Mutation_p.S13G|PAX5_ENST00000377853.2_Missense_Mutation_p.S13G|PAX5_ENST00000520154.1_Missense_Mutation_p.S13G|PAX5_ENST00000522003.1_5'UTR|PAX5_ENST00000523145.1_5'UTR	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	89	41	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		
TTN	7273	hgsc.bcm.edu	37	2	179413110	179413110	+	Silent	SNP	G	G	A	rs3731748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179413110G>A	ENST00000591111.1	-	289	88544	c.88320C>T	c.(88318-88320)gcC>gcT	p.A29440A	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.A31081A|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.A22208A|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.A22141A|TTN_ENST00000460472.2_Silent_p.A22016A|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN_ENST00000342992.6_Silent_p.A28513A			Q8WZ42	TITIN_HUMAN	titin	29440	Fibronectin type-III 114. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GAACACCTTCGGCCAGGTCAT	0.468													G|||	1173	0.234225	0.1483	0.1571	5008	,	,		23794	0.4514		0.1382	False		,,,				2504	0.2802				p.A31081A		Atlas-SNP	.											.	TTN	18412	.	0			c.C93243T						PASS	.	G	,,,	563,3493		40,483,1505	221.0	222.0	222.0		66048,85539,66423,66624	2.0	0.9	2	dbSNP_107	222	1222,7148		92,1038,3055	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	132,1521,4560	AA,AG,GG		14.5998,13.8807,14.365	,,,	22016/26927,28513/33424,22141/27052,22208/27119	179413110	1785,10641	2028	4185	6213	SO:0001819	synonymous_variant	7273	exon339			ACCTTCGGCCAGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.88320C>T	2.37:g.179413110G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.798;A|0.202	0.202	strong		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
HERC1	8925	hgsc.bcm.edu	37	15	63988400	63988400	+	Missense_Mutation	SNP	G	G	C	rs74814914	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:63988400G>C	ENST00000443617.2	-	27	5131	c.5044C>G	c.(5044-5046)Cta>Gta	p.L1682V	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	1682					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CACCCTGCTAGGAACTGCAGC	0.512													G|||	51	0.0101837	0.0023	0.0202	5008	,	,		16282	0.0		0.0288	False		,,,				2504	0.0051				p.L1682V		Atlas-SNP	.											.	HERC1	624	.	0			c.C5044G						PASS	.	G	VAL/LEU	30,3990		0,30,1980	87.0	86.0	86.0		5044	5.5	1.0	15	dbSNP_132	86	304,8028		5,294,3867	yes	missense	HERC1	NM_003922.3	32	5,324,5847	CC,CG,GG		3.6486,0.7463,2.704	possibly-damaging	1682/4862	63988400	334,12018	2010	4166	6176	SO:0001583	missense	8925	exon27			CTGCTAGGAACTG	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.5044C>G	15.37:g.63988400G>C	ENSP00000390158:p.Leu1682Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	27	0.012362637362637362	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	19	0.025065963060686015	G	22.5	4.299964	0.81136	0.007463	0.036486	ENSG00000103657	ENST00000443617;ENST00000425434	T	0.49139	0.79	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000019	T	0.24661	0.0598	L	0.34521	1.04	0.58432	D	0.999997	D;D	0.67145	0.996;0.993	D;D	0.72625	0.978;0.967	T	0.45425	-0.9262	10	0.87932	D	0	.	12.7906	0.57530	0.0749:0.0:0.9251:0.0	.	666;1682	B4DKS2;Q15751	.;HERC1_HUMAN	V	1682;666	ENSP00000390158:L1682V	ENSP00000389613:L666V	L	-	1	2	HERC1	61775453	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.658000	0.68003	2.607000	0.88179	0.650000	0.86243	CTA	G|0.985;C|0.015	0.015	strong		0.512	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
ABCD4	5826	hgsc.bcm.edu	37	14	74759301	74759301	+	Silent	SNP	G	G	T	rs4148078	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74759301G>T	ENST00000356924.4	-	10	1124	c.981C>A	c.(979-981)ctC>ctA	p.L327L	ABCD4_ENST00000557554.1_Intron|AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000298816.7_Silent_p.L223L	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	327	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		ACAGGTCGATGAGCTGGGTGA	0.592													G|||	1317	0.262979	0.121	0.2695	5008	,	,		22556	0.247		0.3857	False		,,,				2504	0.3405				p.L327L		Atlas-SNP	.											.	ABCD4	54	.	0			c.C981A						PASS	.	G		765,3641	310.2+/-291.5	64,637,1502	83.0	68.0	73.0		981	4.7	1.0	14	dbSNP_110	73	3127,5473	474.3+/-368.8	552,2023,1725	no	coding-synonymous	ABCD4	NM_005050.3		616,2660,3227	TT,TG,GG		36.3605,17.3627,29.9247		327/607	74759301	3892,9114	2203	4300	6503	SO:0001819	synonymous_variant	5826	exon10			GTCGATGAGCTGG	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.981C>A	14.37:g.74759301G>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Silent	SNP	ENST00000356924.4	37	CCDS9828.1																																																																																			G|0.719;T|0.281	0.281	strong		0.592	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
NPLOC4	55666	hgsc.bcm.edu	37	17	79589242	79589242	+	Silent	SNP	G	G	A	rs6565604	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79589242G>A	ENST00000331134.6	-	3	374	c.159C>T	c.(157-159)acC>acT	p.T53T	NPLOC4_ENST00000539314.1_5'UTR|NPLOC4_ENST00000374747.5_Silent_p.T53T	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	53					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			TTATCTCTCCGGTCTTGTTTC	0.433													G|||	3219	0.642772	0.7065	0.6628	5008	,	,		17313	0.7768		0.4076	False		,,,				2504	0.6462				p.T53T		Atlas-SNP	.											.	NPLOC4	27	.	0			c.C159T						PASS	.	G		2526,1202		854,818,192	113.0	108.0	110.0		159	-7.4	1.0	17	dbSNP_116	110	3762,4440		868,2026,1207	no	coding-synonymous	NPLOC4	NM_017921.2		1722,2844,1399	AA,AG,GG		45.8669,32.2425,47.2925		53/609	79589242	6288,5642	1864	4101	5965	SO:0001819	synonymous_variant	55666	exon3			CTCTCCGGTCTTG	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.159C>T	17.37:g.79589242G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Silent	SNP	ENST00000331134.6	37	CCDS45812.1																																																																																			G|0.403;A|0.597	0.597	strong		0.433	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
ZNF441	126068	hgsc.bcm.edu	37	19	11890921	11890921	+	Silent	SNP	C	C	T	rs33949590	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:11890921C>T	ENST00000357901.4	+	4	384	c.282C>T	c.(280-282)aaC>aaT	p.N94N	ZNF441_ENST00000454339.2_Silent_p.N27N	NM_152355.2	NP_689568.2	Q8N8Z8	ZN441_HUMAN	zinc finger protein 441	94					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)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GTATTGTGAACGAGAAAATAC	0.408													C|||	165	0.0329473	0.0045	0.0548	5008	,	,		18888	0.0		0.0855	False		,,,				2504	0.0358				p.N94N		Atlas-SNP	.											.	ZNF441	123	.	0			c.C282T						PASS	.	C		89,4317	72.5+/-110.5	1,87,2115	87.0	85.0	85.0		282	-2.1	0.0	19	dbSNP_126	85	786,7814	186.7+/-234.1	32,722,3546	no	coding-synonymous	ZNF441	NM_152355.2		33,809,5661	TT,TC,CC		9.1395,2.02,6.7277		94/694	11890921	875,12131	2203	4300	6503	SO:0001819	synonymous_variant	126068	exon4			TGTGAACGAGAAA	AK095956	CCDS12266.2	19p13.13	2013-01-08			ENSG00000197044	ENSG00000197044		"""Zinc fingers, C2H2-type"", ""-"""	20875	protein-coding gene	gene with protein product							Standard	NM_152355		Approved	FLJ38637	uc010dyj.3	Q8N8Z8	OTTHUMG00000154449	ENST00000357901.4:c.282C>T	19.37:g.11890921C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_152355		Silent	SNP	ENST00000357901.4	37	CCDS12266.2																																																																																			C|0.939;T|0.061	0.061	strong		0.408	ZNF441-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335273.3	NM_152355	
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44028013	44028013	+	Missense_Mutation	SNP	A	A	T	rs11556157	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44028013A>T	ENST00000260605.8	+	9	788	c.688A>T	c.(688-690)Ata>Tta	p.I230L	DYNC2LI1_ENST00000489222.2_3'UTR|DYNC2LI1_ENST00000443170.3_Missense_Mutation_p.I104L|DYNC2LI1_ENST00000605786.1_Missense_Mutation_p.I231L	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1	230			I -> L (in dbSNP:rs11556157). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				ATTACTAAAAATACGTGGAGT	0.303													A|||	1177	0.235024	0.3427	0.1844	5008	,	,		12055	0.0258		0.2386	False		,,,				2504	0.3374				p.I231L		Atlas-SNP	.											.	DYNC2LI1	46	.	0			c.A691T						PASS	.	A	LEU/ILE,LEU/ILE	1423,2983	460.2+/-352.5	247,929,1027	90.0	95.0	94.0		691,688	3.9	1.0	2	dbSNP_120	94	2100,6498	359.4+/-331.5	266,1568,2465	yes	missense,missense	DYNC2LI1	NM_001193464.1,NM_016008.3	5,5	513,2497,3492	TT,TA,AA		24.4243,32.2969,27.0917	benign,benign	231/353,230/352	44028013	3523,9481	2203	4299	6502	SO:0001583	missense	51626	exon9			CTAAAAATACGTG		CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"""Cytoplasmic dyneins"""	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.688A>T	2.37:g.44028013A>T	ENSP00000260605:p.Ile230Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_001193464	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Missense_Mutation	SNP	ENST00000260605.8	37	CCDS1813.1	432|432	0.1978021978021978|0.1978021978021978	163|163	0.3313008130081301|0.3313008130081301	81|81	0.22375690607734808|0.22375690607734808	16|16	0.027972027972027972|0.027972027972027972	172|172	0.22691292875989447|0.22691292875989447	A|A	7.886|7.886	0.731358|0.731358	0.15507|0.15507	0.322969|0.322969	0.244243|0.244243	ENSG00000138036|ENSG00000138036	ENST00000260605;ENST00000443170|ENST00000378587	T;T|T	0.05319|0.15834	3.46;3.46|2.39	5.09|5.09	3.94|3.94	0.45596|0.45596	.|.	0.315054|.	0.36703|.	N|.	0.002460|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04297|0.04297	-0.235|-0.235	0.40481|0.40481	P|P	0.019550999999999985|0.019550999999999985	B;B;B|.	0.06786|.	0.001;0.001;0.001|.	B;B;B|.	0.06405|.	0.002;0.001;0.002|.	T|T	0.49485|0.49485	-0.8935|-0.8935	9|6	0.02654|0.25106	T|T	1|0.35	-8.7008|-8.7008	8.7254|8.7254	0.34467|0.34467	0.8337:0.0:0.1663:0.0|0.8337:0.0:0.1663:0.0	rs11556157;rs52837792;rs56458012;rs11556157|rs11556157;rs52837792;rs56458012;rs11556157	231;230;230|.	Q8TCX1-2;Q8TCX1;Q8TCX1-3|.	.;DC2L1_HUMAN;.|.	L|N	230;104|213	ENSP00000260605:I230L;ENSP00000388941:I104L|ENSP00000367850:K213N	ENSP00000260605:I230L|ENSP00000367850:K213N	I|K	+|+	1|3	0|2	DYNC2LI1|DYNC2LI1	43881517|43881517	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	2.364000|2.364000	0.44187|0.44187	0.952000|0.952000	0.37798|0.37798	0.477000|0.477000	0.44152|0.44152	ATA|AAA	A|0.758;T|0.242	0.242	strong		0.303	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008	
AGPAT4	56895	hgsc.bcm.edu	37	6	161557662	161557662	+	Silent	SNP	G	G	A	rs3734462	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:161557662G>A	ENST00000320285.4	-	9	1259	c.1047C>T	c.(1045-1047)tcC>tcT	p.S349S	AGPAT4_ENST00000457520.2_Silent_p.S187S|AGPAT4_ENST00000366911.5_3'UTR	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	349					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(10)|lung(10)|ovary(2)|skin(2)	25		Breast(66;0.000289)|Ovarian(120;0.0266)|Prostate(117;0.0285)		OV - Ovarian serous cystadenocarcinoma(65;2.23e-17)|BRCA - Breast invasive adenocarcinoma(81;3.58e-05)		GAACTCCCACGGAGGCTGCAG	0.542													G|||	687	0.137181	0.0204	0.33	5008	,	,		19489	0.1825		0.1899	False		,,,				2504	0.0573				p.S349S		Atlas-SNP	.											AGPAT4,brain,glioma,-1,1	AGPAT4	50	1	0			c.C1047T						scavenged	.	G		214,4192	130.6+/-167.2	5,204,1994	102.0	88.0	93.0		1047	-1.3	0.8	6	dbSNP_107	93	1631,6969	301.4+/-305.4	159,1313,2828	no	coding-synonymous	AGPAT4	NM_020133.2		164,1517,4822	AA,AG,GG		18.9651,4.857,14.1858		349/379	161557662	1845,11161	2203	4300	6503	SO:0001819	synonymous_variant	56895	exon9			TCCCACGGAGGCT	AF156776	CCDS5280.1	6q25.3	2013-02-05	2013-02-05		ENSG00000026652	ENSG00000026652	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20885	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, delta"""	614795	"""1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid acyltransferase, delta)"""				Standard	XM_005267052		Approved	LPAAT-delta, dJ473J16.2	uc003qtr.1	Q9NRZ5	OTTHUMG00000015966	ENST00000320285.4:c.1047C>T	6.37:g.161557662G>A		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_020133	B4DSF9|Q5TEF0	Silent	SNP	ENST00000320285.4	37	CCDS5280.1																																																																																			G|0.858;A|0.142	0.142	strong		0.542	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133	
UAP1L1	91373	hgsc.bcm.edu	37	9	139975195	139975195	+	Silent	SNP	C	C	T	rs41302685	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139975195C>T	ENST00000409858.3	+	7	1265	c.1233C>T	c.(1231-1233)aaC>aaT	p.N411N	UAP1L1_ENST00000360271.3_Silent_p.N288N	NM_207309.2	NP_997192.2	Q3KQV9	UAP1L_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1 like 1	411							uridylyltransferase activity (GO:0070569)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CACTGAAGAACGCAGAGCCAG	0.662													C|||	399	0.0796725	0.0431	0.0519	5008	,	,		17273	0.0853		0.0755	False		,,,				2504	0.1472				p.N411N		Atlas-SNP	.											UAP1L1_ENST00000409858,NS,carcinoma,0,2	UAP1L1	46	2	0			c.C1233T						PASS	.	C		225,4181	128.2+/-165.1	2,221,1980	71.0	74.0	73.0		1233	-8.2	0.0	9	dbSNP_127	73	748,7852	173.2+/-223.7	29,690,3581	no	coding-synonymous	UAP1L1	NM_207309.2		31,911,5561	TT,TC,CC		8.6977,5.1067,7.4812		411/508	139975195	973,12033	2203	4300	6503	SO:0001819	synonymous_variant	91373	exon7			GAAGAACGCAGAG	AK022632	CCDS7028.2	9q34.3	2014-07-31	2014-07-31		ENSG00000197355	ENSG00000197355			28082	protein-coding gene	gene with protein product							Standard	NM_207309		Approved		uc010ncb.3	Q3KQV9	OTTHUMG00000020962	ENST00000409858.3:c.1233C>T	9.37:g.139975195C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_207309	A2AMJ8|Q5SPZ2|Q69YQ3|Q6ZR38	Silent	SNP	ENST00000409858.3	37	CCDS7028.2																																																																																			C|0.927;T|0.073	0.073	strong		0.662	UAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055216.2	XM_038063	
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 GAIIx	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	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	170	85	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	
AAMDC	28971	hgsc.bcm.edu	37	11	77583266	77583266	+	Missense_Mutation	SNP	G	G	A	rs2186564	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77583266G>A	ENST00000526415.1	+	5	447	c.274G>A	c.(274-276)Gtg>Atg	p.V92M	AAMDC_ENST00000393427.2_Missense_Mutation_p.V92M|AAMDC_ENST00000525409.1_Missense_Mutation_p.V60M|AAMDC_ENST00000304716.8_Intron|RP11-91P24.6_ENST00000530972.1_RNA|AAMDC_ENST00000532481.1_Intron|AAMDC_ENST00000533193.1_Missense_Mutation_p.V138M|RP11-91P24.7_ENST00000525594.1_RNA|AAMDC_ENST00000527134.1_Intron|AAMDC_ENST00000525034.1_Missense_Mutation_p.V111M			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	92	MTH138-like domain. {ECO:0000250}.		V -> M (in dbSNP:rs2186564).		negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)		p.V92M(1)									TGGCATTGATGTGCGGGTCCT	0.552													G|||	706	0.140974	0.1286	0.1888	5008	,	,		20307	0.1766		0.1004	False		,,,				2504	0.1288				p.V92M		Atlas-SNP	.											C11orf67,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.G274A						scavenged	.	G	MET/VAL	526,3874	239.9+/-250.9	28,470,1702	114.0	103.0	107.0		274	5.3	1.0	11	dbSNP_96	107	827,7757	191.1+/-237.4	37,753,3502	yes	missense	C11orf67	NM_024684.2	21	65,1223,5204	AA,AG,GG		9.6342,11.9545,10.4205	probably-damaging	92/123	77583266	1353,11631	2200	4292	6492	SO:0001583	missense	28971	exon4			ATTGATGTGCGGG	BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884			30205	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 67"""	C11orf67		12477932	Standard	NM_024684		Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000526415.1:c.274G>A	11.37:g.77583266G>A	ENSP00000431808:p.Val92Met	Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	115	88	0.765217	NM_024684	Q96AQ4|Q9Y6B1	Missense_Mutation	SNP	ENST00000526415.1	37	CCDS8254.1	320	0.14652014652014653	76	0.15447154471544716	56	0.15469613259668508	112	0.1958041958041958	76	0.10026385224274406	G	22.1	4.244571	0.79912	0.119545	0.096342	ENSG00000087884	ENST00000526415;ENST00000393427;ENST00000525409;ENST00000533193;ENST00000525034	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000001	T	0.00552	0.0018	M	0.74881	2.28	0.20074	P	0.9999344981	D	0.71674	0.998	D	0.67725	0.953	T	0.03887	-1.0995	9	0.54805	T	0.06	-10.6555	14.3405	0.66622	0.0:0.1481:0.8519:0.0	rs2186564;rs52804138;rs57349472;rs2186564	92	Q9H7C9	CK067_HUMAN	M	92;92;60;138;111	ENSP00000431808:V92M;ENSP00000377078:V92M;ENSP00000433956:V60M;ENSP00000436086:V138M;ENSP00000432830:V111M	ENSP00000377078:V92M	V	+	1	0	C11orf67	77260914	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	6.493000	0.73658	2.746000	0.94184	0.655000	0.94253	GTG	G|0.876;N|0.000	.	strong		0.552	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684	
CACNG5	27091	hgsc.bcm.edu	37	17	64873552	64873552	+	Silent	SNP	G	G	A	rs11652480	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:64873552G>A	ENST00000533854.1	+	2	339	c.102G>A	c.(100-102)ctG>ctA	p.L34L	CACNG5_ENST00000307139.3_Silent_p.L34L|CACNG5_ENST00000169565.3_Silent_p.L34L			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5	34					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			ACTACTGGCTGTACCTGGAGG	0.612													G|||	314	0.0626997	0.0507	0.1095	5008	,	,		19281	0.0139		0.1064	False		,,,				2504	0.0511				p.L34L		Atlas-SNP	.											.	CACNG5	77	.	0			c.G102A						PASS	.	G		213,4193	131.4+/-167.9	3,207,1993	172.0	132.0	146.0		102	-1.4	1.0	17	dbSNP_120	146	804,7796	187.6+/-234.8	33,738,3529	no	coding-synonymous	CACNG5	NM_145811.2		36,945,5522	AA,AG,GG		9.3488,4.8343,7.8195		34/276	64873552	1017,11989	2203	4300	6503	SO:0001819	synonymous_variant	27091	exon1			CTGGCTGTACCTG	AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"""Calcium channel subunits"""	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.102G>A	17.37:g.64873552G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_145811	A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Silent	SNP	ENST00000533854.1	37	CCDS11665.1																																																																																			G|0.922;A|0.078	0.078	strong		0.612	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811	
OR8B4	283162	hgsc.bcm.edu	37	11	124294349	124294349	+	Missense_Mutation	SNP	C	C	A	rs7116575	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124294349C>A	ENST00000356130.3	-	1	440	c.419G>T	c.(418-420)tGc>tTc	p.C140F		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	140			C -> F (in dbSNP:rs7116575). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CAGCAGAAAGCAGACCCTTGG	0.517													C|||	805	0.160743	0.2648	0.111	5008	,	,		21230	0.1984		0.0875	False		,,,				2504	0.092				p.C140F		Atlas-SNP	.											OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	0			c.G419T						PASS	.	C	PHE/CYS	986,3416	368.6+/-318.7	111,764,1326	79.0	70.0	73.0		419	4.6	0.1	11	dbSNP_116	73	920,7678	203.1+/-246.2	38,844,3417	yes	missense	OR8B4	NM_001005196.1	205	149,1608,4743	AA,AC,CC		10.7002,22.3989,14.6615	probably-damaging	140/310	124294349	1906,11094	2201	4299	6500	SO:0001583	missense	283162	exon1			AGAAAGCAGACCC	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.419G>T	11.37:g.124294349C>A	ENSP00000348449:p.Cys140Phe	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	87	77	0.885057	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	336	0.15384615384615385	139	0.28252032520325204	29	0.08011049723756906	101	0.17657342657342656	67	0.08839050131926121	c	11.45	1.641959	0.29157	0.223989	0.107002	ENSG00000198657	ENST00000356130	T	0.00220	8.52	4.62	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000020	T	0.00012	0.0000	M	0.94142	3.5	0.20638	P	0.999879906	P	0.35944	0.529	B	0.44163	0.443	T	0.48536	-0.9027	9	0.72032	D	0.01	.	17.6029	0.88030	0.0:1.0:0.0:0.0	rs7116575;rs52820733;rs7116575	140	Q96RC9	OR8B4_HUMAN	F	140	ENSP00000348449:C140F	ENSP00000348449:C140F	C	-	2	0	OR8B4	123799559	0.919000	0.31177	0.107000	0.21349	0.018000	0.09664	2.958000	0.49145	2.564000	0.86499	0.655000	0.94253	TGC	C|0.845;A|0.155	0.155	strong		0.517	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
CARD9	64170	hgsc.bcm.edu	37	9	139266496	139266496	+	Missense_Mutation	SNP	C	C	T	rs4077515	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139266496C>T	ENST00000371732.5	-	2	200	c.35G>A	c.(34-36)aGc>aAc	p.S12N	CARD9_ENST00000371734.3_Missense_Mutation_p.S12N|CARD9_ENST00000315908.7_Missense_Mutation_p.S12N	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	12	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		S -> N (in dbSNP:rs4077515). {ECO:0000269|PubMed:11053425, ECO:0000269|PubMed:14702039}.		defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		CTCCAGGACGCTCCAGCACTC	0.647													C|||	1836	0.366613	0.2519	0.5706	5008	,	,		18895	0.3214		0.3966	False		,,,				2504	0.3926				p.S12N		Atlas-SNP	.											CARD9,NS,carcinoma,0,1	CARD9	47	1	0			c.G35A						PASS	.	C	ASN/SER,ASN/SER	1227,3179	422.3+/-339.7	165,897,1141	116.0	80.0	92.0	http://www.ncbi.nlm.nih.gov/pubmed?term	35,35	-0.6	0.1	9	dbSNP_108	92	3625,4975	521.0+/-379.8	760,2105,1435	yes	missense,missense	CARD9	NM_052813.4,NM_052814.3	46,46	925,3002,2576	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	42.1512,27.8484,37.3059	benign,benign	12/537,12/493	139266496	4852,8154	2203	4300	6503	SO:0001583	missense	64170	exon2			AGGACGCTCCAGC	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.35G>A	9.37:g.139266496C>T	ENSP00000360797:p.Ser12Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Missense_Mutation	SNP	ENST00000371732.5	37	CCDS6997.1	803	0.3676739926739927	144	0.2926829268292683	170	0.4696132596685083	177	0.3094405594405594	312	0.41160949868073876	C	6.546	0.468978	0.12461	0.278484	0.421512	ENSG00000187796	ENST00000371734;ENST00000371732;ENST00000315908	T;T;T	0.20463	2.07;2.07;2.07	4.88	-0.553	0.11815	DEATH-like (2);Caspase Recruitment (2);	0.565475	0.18338	N	0.144278	T	0.00012	0.0000	N	0.03115	-0.41	0.54753	P	1.399999999995849E-5	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.08055	0.002;0.003;0.003	T	0.46400	-0.9194	9	0.27082	T	0.32	-14.5962	4.5111	0.11912	0.0:0.2509:0.3177:0.4314	rs4077515;rs60359505;rs4077515	12;12;12	Q9H257-2;Q5SXM5;Q9H257	.;.;CARD9_HUMAN	N	12	ENSP00000360799:S12N;ENSP00000360797:S12N;ENSP00000323719:S12N	ENSP00000323719:S12N	S	-	2	0	CARD9	138386317	0.005000	0.15991	0.100000	0.21137	0.252000	0.25951	-0.134000	0.10436	0.013000	0.14918	-0.326000	0.08463	AGC	C|0.634;T|0.366	0.366	strong		0.647	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
PLCXD1	55344	hgsc.bcm.edu	37	X	207362	207362	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:207362C>T	ENST00000381657.2	+	4	826	c.312C>T	c.(310-312)gaC>gaT	p.D104D	PLCXD1_ENST00000399012.1_Silent_p.D104D|PLCXD1_ENST00000484611.2_3'UTR|PLCXD1_ENST00000381663.3_Silent_p.D104D	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	104	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid metabolic process (GO:0006629)		phosphoric diester hydrolase activity (GO:0008081)			endometrium(3)|large_intestine(1)|lung(7)	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)				GGTACCTGGACCTGCGGATAG	0.647																																					p.D104D		Atlas-SNP	.											.	PLCXD1	18	.	0			c.C312T						PASS	.	C		1608,2798		304,1000,899	218.0	185.0	196.0		312	1.2	1.0	X	dbSNP_134	196	5047,3545		1497,2053,746	no	coding-synonymous	PLCXD1	NM_018390.3		1801,3053,1645	TT,TC,CC		41.2593,36.4957,48.7998		104/324	207362	6655,6343	2203	4296	6499	SO:0001819	synonymous_variant	55344	exon4			CCTGGACCTGCGG	AK002185	CCDS14103.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000182378	ENSG00000182378		"""Pseudoautosomal regions / PAR1"""	23148	protein-coding gene	gene with protein product							Standard	NM_018390		Approved	FLJ11323	uc004cpc.3	Q9NUJ7	OTTHUMG00000022693	ENST00000381657.2:c.312C>T	X.37:g.207362C>T		Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	207	56	0.270531	NM_018390	A2BH51|A2BH52	Silent	SNP	ENST00000381657.2	37	CCDS14103.1																																																																																			T|0.530;G|0.000;C|0.470	0.530	strong		0.647	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390	
ZNF860	344787	hgsc.bcm.edu	37	3	32032397	32032397	+	Missense_Mutation	SNP	G	G	T	rs4955216	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:32032397G>T	ENST00000360311.4	+	2	2375	c.1826G>T	c.(1825-1827)cGc>cTc	p.R609L		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	609					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(3)|lung(4)|ovary(1)	8						CATTCACATCGCATTAGACAT	0.398													T|||	2157	0.430711	0.7988	0.3573	5008	,	,		22192	0.3006		0.1928	False		,,,				2504	0.364				p.R609L		Atlas-SNP	.											.	ZNF860	96	.	0			c.G1826T						PASS	.	T	LEU/ARG	935,449		322,291,79	43.0	36.0	38.0		1826	0.3	0.0	3	dbSNP_111	38	610,2572		58,494,1039	no	missense	ZNF860	NM_001137674.2	102	380,785,1118	TT,TG,GG		19.1703,32.4422,33.8371	benign	609/633	32032397	1545,3021	692	1591	2283	SO:0001583	missense	344787	exon2			CACATCGCATTAG	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1826G>T	3.37:g.32032397G>T	ENSP00000373274:p.Arg609Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	836	0.38278388278388276	385	0.782520325203252	125	0.3453038674033149	176	0.3076923076923077	150	0.19788918205804748	T	0.004	-2.318068	0.00235	0.675578	0.191703	ENSG00000197385	ENST00000360311	T	0.06687	3.27	0.314	0.314	0.15847	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00186	-1.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09122	-1.0689	7	.	.	.	.	5.1539	0.15025	0.0:0.0:0.6429:0.357	rs4955216;rs17028702;rs52831549;rs59940424;rs4955216	609	A6NHJ4	ZN860_HUMAN	L	609	ENSP00000373274:R609L	.	R	+	2	0	ZNF860	32007401	0.275000	0.24201	0.001000	0.08648	0.001000	0.01503	1.189000	0.32114	-0.768000	0.04626	-0.930000	0.02707	CGC	G|0.644;T|0.356	0.356	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
HDAC4	9759	hgsc.bcm.edu	37	2	240003870	240003870	+	Silent	SNP	G	G	A	rs1063639	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:240003870G>A	ENST00000345617.3	-	21	3356	c.2565C>T	c.(2563-2565)ccC>ccT	p.P855P	HDAC4_ENST00000543185.1_Silent_p.P439P	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	855	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|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)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		ACAGGACGCTGGGGTCGCTGT	0.592													G|||	2981	0.595248	0.59	0.6499	5008	,	,		15729	0.6885		0.4414	False		,,,				2504	0.6258				p.P855P		Atlas-SNP	.											.	HDAC4	127	.	0			c.C2565T						PASS	.	G		2499,1907	626.5+/-394.7	713,1073,417	171.0	155.0	160.0		2565	-3.0	0.0	2	dbSNP_86	160	4083,4517	561.0+/-387.7	958,2167,1175	no	coding-synonymous	HDAC4	NM_006037.3		1671,3240,1592	AA,AG,GG		47.4767,43.2819,49.3926		855/1085	240003870	6582,6424	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon21			GACGCTGGGGTCG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2565C>T	2.37:g.240003870G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	212	103	0.485849	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.456;A|0.544	0.544	strong		0.592	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
CYP11B2	1585	hgsc.bcm.edu	37	8	143994702	143994702	+	Splice_Site	SNP	G	G	T	rs4538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143994702G>T	ENST00000323110.2	-	6	1122	c.1120C>A	c.(1120-1122)Cgg>Agg	p.R374R		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	374					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	AGCACCCACCGCAAGGTCTCC	0.677									Familial Hyperaldosteronism type I				.|||	3043	0.607628	0.4743	0.585	5008	,	,		16613	0.8065		0.5815	False		,,,				2504	0.6258				p.R374R		Atlas-SNP	.											CYP11B2,NS,carcinoma,0,2	CYP11B2	107	2	0			c.C1120A						PASS	.	T		2166,2240		514,1138,551	29.0	32.0	31.0		1120	1.4	1.0	8	dbSNP_52	31	4778,3816		1342,2094,861	no	coding-synonymous-near-splice	CYP11B2	NM_000498.3		1856,3232,1412	TT,TG,GG		44.4031,49.1602,46.5846		374/504	143994702	6944,6056	2203	4297	6500	SO:0001630	splice_region_variant	1585	exon6	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CCCACCGCAAGGT	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"""Cytochrome P450s"""	2592	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	124080	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"""	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.1121+1C>A	8.37:g.143994702G>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	117	43	0.367521	NM_000498	B0ZBE4|Q16726	Silent	SNP	ENST00000323110.2	37	CCDS6393.1																																																																																			G|0.462;T|0.538	0.538	strong		0.677	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		Silent
SEC14L6	730005	hgsc.bcm.edu	37	22	30934887	30934887	+	Silent	SNP	G	G	A	rs5753191	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30934887G>A	ENST00000402034.2	-	2	56	c.57C>T	c.(55-57)ttC>ttT	p.F19F		NM_001193336.2	NP_001180265.2	B5MCN3	S14L6_HUMAN	SEC14-like 6 (S. cerevisiae)	19						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			lung(3)	3						TGTTCTCCCGGAACTGAGGAC	0.577													.|||	2664	0.531949	0.702	0.4496	5008	,	,		17077	0.4107		0.492	False		,,,				2504	0.5266				p.F19F		Atlas-SNP	.											.	SEC14L6	6	.	0			c.C57T						PASS	.																																			SO:0001819	synonymous_variant	730005	exon2			CTCCCGGAACTGA		CCDS54518.1	22q12.2	2011-05-06			ENSG00000214491	ENSG00000214491			40047	protein-coding gene	gene with protein product							Standard	NM_001193336		Approved		uc021wnu.1	B5MCN3	OTTHUMG00000151267	ENST00000402034.2:c.57C>T	22.37:g.30934887G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_001193336		Silent	SNP	ENST00000402034.2	37	CCDS54518.1																																																																																			G|0.494;A|0.506	0.506	strong		0.577	SEC14L6-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000322022.2		
B4GALNT4	338707	hgsc.bcm.edu	37	11	372157	372157	+	Missense_Mutation	SNP	C	C	T	rs34063493	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:372157C>T	ENST00000329962.6	+	2	200	c.200C>T	c.(199-201)gCg>gTg	p.A67V		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	67			A -> V (in dbSNP:rs34063493).		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)		GTCCACGCTGCGCCATCCACA	0.647													.|||	1881	0.375599	0.4887	0.3098	5008	,	,		19615	0.3859		0.2952	False		,,,				2504	0.3415				p.A67V		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.C200T						PASS	.	T	VAL/ALA	1576,1900		360,856,522	65.0	57.0	60.0		200	-4.0	0.0	11	dbSNP_126	60	1762,4752		249,1264,1744	yes	missense	B4GALNT4	NM_178537.4	64	609,2120,2266	TT,TC,CC		27.0494,45.3395,33.4134	benign	67/1040	372157	3338,6652	1738	3257	4995	SO:0001583	missense	338707	exon2			ACGCTGCGCCATC	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.200C>T	11.37:g.372157C>T	ENSP00000328277:p.Ala67Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	68	0.944444	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	817	0.3740842490842491	223	0.4532520325203252	119	0.3287292817679558	245	0.42832167832167833	230	0.3034300791556728	c	3.145	-0.175445	0.06421	0.453395	0.270494	ENSG00000182272	ENST00000329962	T	0.04862	3.54	3.52	-3.99	0.04069	.	2.616520	0.02606	N	0.101596	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.46610	-0.9179	9	0.02654	T	1	-0.5022	10.2695	0.43475	0.0:0.4536:0.0:0.5464	rs34063493;rs59064726	67	Q76KP1	B4GN4_HUMAN	V	67	ENSP00000328277:A67V	ENSP00000328277:A67V	A	+	2	0	B4GALNT4	362157	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.321000	0.08018	-0.770000	0.04614	-1.740000	0.00687	GCG	A|0.000;C|0.629;G|0.000;T|0.371	0.371	strong		0.647	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
COL12A1	1303	hgsc.bcm.edu	37	6	75844458	75844458	+	Silent	SNP	C	C	T	rs77425231	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:75844458C>T	ENST00000322507.8	-	32	5817	c.5508G>A	c.(5506-5508)acG>acA	p.T1836T	COL12A1_ENST00000416123.2_Silent_p.T1836T|COL12A1_ENST00000483888.2_Silent_p.T1836T|COL12A1_ENST00000345356.6_Silent_p.T672T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1836	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)			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						TGCCTCTTCCCGTCATCCGAC	0.463													C|||	21	0.00419329	0.0008	0.0029	5008	,	,		15447	0.001		0.0109	False		,,,				2504	0.0061				p.T1836T		Atlas-SNP	.											.	COL12A1	385	.	0			c.G5508A						PASS	.	C	,	10,3836		0,10,1913	124.0	121.0	122.0		5508,2016	-11.7	0.2	6	dbSNP_132	122	108,8154		1,106,4024	no	coding-synonymous,coding-synonymous	COL12A1	NM_004370.5,NM_080645.2	,	1,116,5937	TT,TC,CC		1.3072,0.26,0.9746	,	1836/3064,672/1900	75844458	118,11990	1923	4131	6054	SO:0001819	synonymous_variant	1303	exon32			TCTTCCCGTCATC	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.5508G>A	6.37:g.75844458C>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	207	98	0.47343	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1	13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	4.779	0.144796	0.09134	0.0026	0.013072	ENSG00000111799	ENST00000419671	.	.	.	5.87	-11.7	0.00046	.	.	.	.	.	T	0.13586	0.0329	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44498	-0.9324	4	.	.	.	.	1.0297	0.01535	0.2525:0.1443:0.1932:0.4101	.	.	.	.	R	571	.	.	G	-	1	0	COL12A1	75901178	0.000000	0.05858	0.205000	0.23548	0.828000	0.46876	-3.808000	0.00361	-2.770000	0.00365	-0.909000	0.02823	GGG	C|0.993;T|0.007	0.007	strong		0.463	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
THBS1	7057	hgsc.bcm.edu	37	15	39882178	39882178	+	Missense_Mutation	SNP	A	A	G	rs2228262	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:39882178A>G	ENST00000260356.5	+	13	2264	c.2099A>G	c.(2098-2100)aAt>aGt	p.N700S		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	700			N -> S (in dbSNP:rs2228262). {ECO:0000269|Ref.4}.		activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		GGCTGGCCCAATGAGAACCTG	0.572													A|||	201	0.0401358	0.0136	0.0533	5008	,	,		18546	0.002		0.1064	False		,,,				2504	0.0378				p.N700S		Atlas-SNP	.											THBS1,NS,carcinoma,0,3	THBS1	106	3	0			c.A2099G	GRCh37	CM043345	THBS1	M	rs2228262	PASS	.	A	SER/ASN	159,4241	106.9+/-145.3	4,151,2045	90.0	72.0	78.0		2099	6.0	1.0	15	dbSNP_98	78	982,7612	206.2+/-248.4	49,884,3364	yes	missense	THBS1	NM_003246.2	46	53,1035,5409	GG,GA,AA		11.4266,3.6136,8.781	probably-damaging	700/1171	39882178	1141,11853	2200	4297	6497	SO:0001583	missense	7057	exon13			GGCCCAATGAGAA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2099A>G	15.37:g.39882178A>G	ENSP00000260356:p.Asn700Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	116	0.05311355311355311	6	0.012195121951219513	24	0.06629834254143646	3	0.005244755244755245	83	0.10949868073878628	A	32	5.127644	0.94473	0.036136	0.114266	ENSG00000137801	ENST00000260356	D	0.97870	-4.58	5.99	5.99	0.97316	.	0.000000	0.38381	N	0.001703	T	0.66954	0.2842	M	0.71036	2.16	0.09310	P	0.99999145411	D;D	0.69078	0.994;0.997	P;D	0.65010	0.894;0.931	T	0.67321	-0.5700	9	0.72032	D	0.01	-31.7732	16.4645	0.84074	1.0:0.0:0.0:0.0	rs2228262;rs17632786;rs52798888;rs59160172;rs2228262	615;700	B4E3J7;P07996	.;TSP1_HUMAN	S	700	ENSP00000260356:N700S	ENSP00000260356:N700S	N	+	2	0	THBS1	37669470	1.000000	0.71417	0.978000	0.43139	0.991000	0.79684	9.339000	0.96797	2.292000	0.77174	0.533000	0.62120	AAT	A|0.930;G|0.070	0.070	strong		0.572	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
HLA-A	3105	hgsc.bcm.edu	37	6	29910731	29910731	+	Missense_Mutation	SNP	G	G	A	rs79361534|rs281864737	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29910731G>A	ENST00000396634.1	+	4	612	c.271G>A	c.(271-273)Gtg>Atg	p.V91M	HLA-A_ENST00000376806.5_Missense_Mutation_p.V91M|HLA-A_ENST00000376802.2_Missense_Mutation_p.V91M|HLA-A_ENST00000376809.5_Missense_Mutation_p.V91M			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	91	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GACACGGAATGTGAAGGCCCA	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	454	0.090655	0.0847	0.0476	5008	,	,		12317	0.0188		0.1262	False		,,,				2504	0.1667				p.V91M		Atlas-SNP	.											.	HLA-A	89	.	0			c.G271A						PASS	.	G	MET/VAL	353,4047		18,317,1865	80.0	84.0	82.0		271	-6.4	0.0	6	dbSNP_127	82	1485,7097		170,1145,2976	no	missense	HLA-A	NM_002116.7	21	188,1462,4841	AA,AG,GG		17.3037,8.0227,14.1581	benign	91/366	29910731	1838,11144	2200	4291	6491	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGGAATGTGAAGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.271G>A	6.37:g.29910731G>A	ENSP00000379873:p.Val91Met	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	145	133	0.917241	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	198	0.09065934065934066	45	0.09146341463414634	19	0.052486187845303865	12	0.02097902097902098	122	0.16094986807387862	.	5.403	0.259593	0.10239	0.080227	0.173037	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00010	9.4;9.4;9.4;9.4	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	754.410000	0.00447	U	0.000088	T	0.00039	0.0001	L	0.28054	0.825	0.80722	P	0.0	B;B;B;B;B	0.17667	0.002;0.023;0.002;0.011;0.002	B;B;B;B;B	0.23419	0.005;0.046;0.005;0.012;0.005	T	0.09207	-1.0685	9	0.41790	T	0.15	.	4.2384	0.10637	0.2942:0.0:0.1814:0.5244	rs41564215	91;91;91;91;91	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	M	91	ENSP00000379873:V91M;ENSP00000366002:V91M;ENSP00000366005:V91M;ENSP00000365998:V91M	ENSP00000348012:V91M	V	+	1	0	HLA-A	30018710	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.711000	0.00195	-1.498000	0.01824	-1.251000	0.01509	GTG	A|0.124;G|0.876	0.124	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84639350	84639350	+	Missense_Mutation	SNP	C	C	T	rs2277849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:84639350C>T	ENST00000286744.5	+	20	2829	c.2605C>T	c.(2605-2607)Ctc>Ttc	p.L869F	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.L869F|ADAMTSL3_ENST00000567716.1_3'UTR	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	869	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.		L -> F (in dbSNP:rs2277849). {ECO:0000269|PubMed:15489334}.			proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.L869F(1)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TCTACCAGGGCTCCCTCTTGT	0.522													C|||	1304	0.260383	0.3714	0.1571	5008	,	,		20793	0.3442		0.2714	False		,,,				2504	0.0859				p.L869F		Atlas-SNP	.											ADAMTSL3,NS,carcinoma,0,1	ADAMTSL3	290	1	1	Substitution - Missense(1)	stomach(1)	c.C2605T						PASS	.	C	PHE/LEU	1537,2869	486.2+/-360.5	252,1033,918	184.0	161.0	169.0		2605	2.4	0.1	15	dbSNP_100	169	2269,6331	383.0+/-340.6	291,1687,2322	yes	missense	ADAMTSL3	NM_207517.2	22	543,2720,3240	TT,TC,CC		26.3837,34.8842,29.2634	possibly-damaging	869/1692	84639350	3806,9200	2203	4300	6503	SO:0001583	missense	57188	exon20			CCAGGGCTCCCTC	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2605C>T	15.37:g.84639350C>T	ENSP00000286744:p.Leu869Phe	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	638	0.29212454212454214	158	0.32113821138211385	64	0.17679558011049723	199	0.3479020979020979	217	0.2862796833773087	C	19.35	3.810236	0.70797	0.348842	0.263837	ENSG00000156218	ENST00000286744	T	0.62232	0.04	4.39	2.38	0.29361	.	0.810196	0.10421	N	0.676704	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	P;P	0.42941	0.606;0.794	B;P	0.45998	0.435;0.5	T	0.17501	-1.0367	9	0.54805	T	0.06	.	8.0735	0.30704	0.0:0.6773:0.1475:0.1752	rs2277849;rs17370789;rs52816289;rs61270368;rs2277849	869;869	P82987-2;P82987	.;ATL3_HUMAN	F	869	ENSP00000286744:L869F	ENSP00000286744:L869F	L	+	1	0	ADAMTSL3	82430354	0.428000	0.25522	0.121000	0.21740	0.978000	0.69477	1.014000	0.29950	1.043000	0.40175	0.650000	0.86243	CTC	C|0.712;T|0.288	0.288	strong		0.522	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
RNF152	220441	hgsc.bcm.edu	37	18	59483508	59483508	+	Silent	SNP	G	G	T	rs116886631	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:59483508G>T	ENST00000312828.3	-	2	1288	c.189C>A	c.(187-189)ggC>ggA	p.G63G		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	63					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				ACACGGAGAAGCCGGGAGGCA	0.627													G|||	112	0.0223642	0.0106	0.0187	5008	,	,		18383	0.0		0.0746	False		,,,				2504	0.0102				p.G63G		Atlas-SNP	.											.	RNF152	37	.	0			c.C189A						PASS	.	G		112,4294	84.8+/-123.5	0,112,2091	55.0	60.0	58.0		189	4.1	1.0	18	dbSNP_132	58	538,8062	147.9+/-203.2	19,500,3781	no	coding-synonymous	RNF152	NM_173557.2		19,612,5872	TT,TG,GG		6.2558,2.542,4.9977		63/204	59483508	650,12356	2203	4300	6503	SO:0001819	synonymous_variant	220441	exon2			GGAGAAGCCGGGA	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"""RING-type (C3HC4) zinc fingers"""	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.189C>A	18.37:g.59483508G>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_173557	B3KV99|Q52LA4	Silent	SNP	ENST00000312828.3	37	CCDS11978.1																																																																																			G|0.958;T|0.042	0.042	strong		0.627	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557	
COBLL1	22837	hgsc.bcm.edu	37	2	165586466	165586466	+	Silent	SNP	T	T	C	rs13392281	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:165586466T>C	ENST00000392717.2	-	4	508	c.504A>G	c.(502-504)ccA>ccG	p.P168P	COBLL1_ENST00000409184.3_Silent_p.P168P|COBLL1_ENST00000491126.2_Intron|COBLL1_ENST00000375458.2_Silent_p.P130P|COBLL1_ENST00000194871.6_Silent_p.P183P|COBLL1_ENST00000342193.4_Silent_p.P130P			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	168						extracellular vesicular exosome (GO:0070062)		p.M132fs*4(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						CCAACATTTTTGGCTTTAAAA	0.338													t|||	864	0.172524	0.329	0.111	5008	,	,		16790	0.1052		0.1571	False		,,,				2504	0.09				p.P130P		Atlas-SNP	.											.	COBLL1	122	.	1	Insertion - Frameshift(1)	prostate(1)	c.A390G						PASS	.	C		1366,3038	450.4+/-349.3	213,940,1049	162.0	155.0	157.0		390	1.9	1.0	2	dbSNP_121	157	1270,7330	250.7+/-277.5	101,1068,3131	no	coding-synonymous	COBLL1	NM_014900.3		314,2008,4180	CC,CT,TT		14.7674,31.0173,20.2707		130/1167	165586466	2636,10368	2202	4300	6502	SO:0001819	synonymous_variant	22837	exon3			CATTTTTGGCTTT	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.504A>G	2.37:g.165586466T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	71	18	0.253521	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Silent	SNP	ENST00000392717.2	37		387	0.1771978021978022	158	0.32113821138211385	40	0.11049723756906077	70	0.12237762237762238	119	0.15699208443271767	t	9.165	1.019676	0.19355	0.310173	0.147674	ENSG00000082438	ENST00000452626	.	.	.	5.83	1.87	0.25490	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999672	.	.	.	.	.	.	T	0.35126	-0.9801	3	.	.	.	-13.5306	7.1454	0.25581	0.0:0.1311:0.1232:0.7457	rs13392281;rs58993873;rs13392281	.	.	.	E	133	.	.	K	-	1	0	COBLL1	165294712	0.999000	0.42202	1.000000	0.80357	0.896000	0.52359	0.487000	0.22356	0.449000	0.26747	-0.266000	0.10368	AAA	T|0.804;C|0.196	0.196	strong		0.338	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
CIT	11113	hgsc.bcm.edu	37	12	120156141	120156141	+	Silent	SNP	G	G	A	rs278102	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:120156141G>A	ENST00000261833.7	-	31	4003	c.3951C>T	c.(3949-3951)tcC>tcT	p.S1317S	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Silent_p.S1359S	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1317					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)		GCACGATGGCGGACATGGCGA	0.642													G|||	914	0.182508	0.2383	0.1916	5008	,	,		13978	0.0109		0.2843	False		,,,				2504	0.1728				p.S1359S		Atlas-SNP	.											.	CIT	535	.	0			c.C4077T						PASS	.	G	,	1056,3350	385.6+/-325.8	134,788,1281	69.0	79.0	76.0		4077,3951	-8.0	0.9	12	dbSNP_79	76	2485,6113	407.8+/-349.3	358,1769,2172	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	492,2557,3453	AA,AG,GG		28.9021,23.9673,27.2301	,	1359/2070,1317/2028	120156141	3541,9463	2203	4299	6502	SO:0001819	synonymous_variant	11113	exon32			GATGGCGGACATG	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.3951C>T	12.37:g.120156141G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	409	0.18727106227106227	115	0.23373983739837398	73	0.20165745856353592	5	0.008741258741258742	216	0.2849604221635884	G	11.45	1.641188	0.29157	0.239673	0.289021	ENSG00000122966	ENST00000392520	.	.	.	5.74	-8.01	0.01122	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17410	-1.0370	3	.	.	.	.	8.9636	0.35863	0.439:0.1088:0.4522:0.0	rs278102;rs17409026;rs278102	.	.	.	L	930	.	.	P	-	2	0	CIT	118640524	0.307000	0.24500	0.876000	0.34364	0.986000	0.74619	-0.263000	0.08670	-1.770000	0.01295	-0.345000	0.07892	CCG	G|0.760;A|0.240	0.240	strong		0.642	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
FBXL5	26234	hgsc.bcm.edu	37	4	15640168	15640168	+	Silent	SNP	C	C	T	rs3182730	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:15640168C>T	ENST00000341285.3	-	4	670	c.546G>A	c.(544-546)aaG>aaA	p.K182K	FBXL5_ENST00000412094.2_Silent_p.K165K|FBXL5_ENST00000382358.4_Silent_p.K56K	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	182					iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						ATTTAAAAAACTTCTGTCGCT	0.338													C|||	481	0.0960463	0.0696	0.0807	5008	,	,		17245	0.0337		0.1581	False		,,,				2504	0.1431				p.K182K		Atlas-SNP	.											.	FBXL5	52	.	0			c.G546A						PASS	.	C	,,	325,4079	169.8+/-200.3	11,303,1888	71.0	66.0	68.0		546,495,546	1.8	1.0	4	dbSNP_105	68	1251,7349	250.0+/-277.0	99,1053,3148	no	coding-synonymous,coding-synonymous,coding-synonymous	FBXL5	NM_001193534.1,NM_001193535.1,NM_012161.3	,,	110,1356,5036	TT,TC,CC		14.5465,7.3797,12.1193	,,	182/691,165/675,182/692	15640168	1576,11428	2202	4300	6502	SO:0001819	synonymous_variant	26234	exon4			AAAAAACTTCTGT	AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"""F-boxes / Leucine-rich repeats"""	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.546G>A	4.37:g.15640168C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	69	26	0.376812	NM_001193534	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Silent	SNP	ENST00000341285.3	37	CCDS3415.1	212	0.09706959706959707	50	0.1016260162601626	35	0.09668508287292818	18	0.03146853146853147	109	0.1437994722955145	C	7.981	0.751222	0.15778	0.073797	0.145465	ENSG00000118564	ENST00000513163	.	.	.	5.49	1.79	0.24919	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09574	-1.0668	3	.	.	.	-22.075	10.3944	0.44192	0.0:0.6401:0.0:0.3599	rs3182730;rs17418670	.	.	.	I	103	.	.	V	-	1	0	FBXL5	15249266	0.999000	0.42202	0.996000	0.52242	0.856000	0.48823	0.528000	0.23002	0.080000	0.16959	-0.961000	0.02630	GTT	T|0.112;G|0.000;C|0.888	0.112	strong		0.338	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2		
TGS1	96764	hgsc.bcm.edu	37	8	56708701	56708701	+	Missense_Mutation	SNP	T	T	C	rs10100659	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:56708701T>C	ENST00000260129.5	+	7	2009	c.1532T>C	c.(1531-1533)aTt>aCt	p.I511T		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	511			I -> T (in dbSNP:rs10100659).		7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			AAAAGCAAAATTCTGAGTAAG	0.299													C|||	720	0.14377	0.2784	0.121	5008	,	,		18664	0.0099		0.1103	False		,,,				2504	0.1503				p.I511T	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.T1532C						PASS	.	C	THR/ILE	1140,3266	696.3+/-406.1	160,820,1223	40.0	39.0	39.0		1532	4.4	0.4	8	dbSNP_119	39	923,7675	767.4+/-407.6	48,827,3424	yes	missense	TGS1	NM_024831.6	89	208,1647,4647	CC,CT,TT		10.7351,25.8738,15.8643	benign	511/854	56708701	2063,10941	2203	4299	6502	SO:0001583	missense	96764	exon7			GCAAAATTCTGAG	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.1532T>C	8.37:g.56708701T>C	ENSP00000260129:p.Ile511Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	281	0.12866300366300365	153	0.31097560975609756	43	0.11878453038674033	0	0.0	85	0.11213720316622691	C	1.497	-0.552964	0.03996	0.258738	0.107351	ENSG00000137574	ENST00000260129	T	0.37235	1.21	6.17	4.37	0.52481	.	0.572044	0.20332	N	0.094404	T	0.00012	0.0000	N	0.00104	-2.125	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40794	-0.9544	9	0.02654	T	1	-0.0665	9.9018	0.41353	0.0:0.7887:0.0:0.2113	rs10100659;rs52810778;rs59983864;rs10100659	511;511	B2RBJ7;Q96RS0	.;TGS1_HUMAN	T	511	ENSP00000260129:I511T	ENSP00000260129:I511T	I	+	2	0	TGS1	56871255	0.999000	0.42202	0.442000	0.26870	0.941000	0.58515	2.096000	0.41738	0.486000	0.27676	-0.766000	0.03442	ATT	T|0.847;C|0.153	0.153	strong		0.299	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
ANKK1	255239	hgsc.bcm.edu	37	11	113266821	113266821	+	Missense_Mutation	SNP	G	G	A	rs7118900	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:113266821G>A	ENST00000303941.3	+	5	809	c.715G>A	c.(715-717)Gcg>Acg	p.A239T		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs7118900). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		TATCCGAGTGGCGGCAGGCAT	0.607													G|||	1605	0.320487	0.3744	0.3069	5008	,	,		16275	0.4058		0.1819	False		,,,				2504	0.3119				p.A239T		Atlas-SNP	.											.	ANKK1	83	.	0			c.G715A						PASS	.	G	THR/ALA	1246,2802		199,848,977	61.0	65.0	63.0		715	2.5	0.0	11	dbSNP_116	63	1518,6826		149,1220,2803	yes	missense	ANKK1	NM_178510.1	58	348,2068,3780	AA,AG,GG		18.1927,30.7806,22.3047	possibly-damaging	239/766	113266821	2764,9628	2024	4172	6196	SO:0001583	missense	255239	exon5			CGAGTGGCGGCAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.715G>A	11.37:g.113266821G>A	ENSP00000306678:p.Ala239Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	99	77	0.777778	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	634	0.2902930402930403	178	0.3617886178861789	98	0.27071823204419887	223	0.38986013986013984	135	0.17810026385224276	G	12.52	1.963618	0.34659	0.307806	0.181927	ENSG00000170209	ENST00000303941	D	0.82619	-1.63	4.44	2.55	0.30701	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.266529	0.24912	U	0.034605	T	0.00012	0.0000	L	0.31578	0.945	0.44006	P	0.0032879999999999576	B	0.26547	0.152	B	0.37304	0.246	T	0.21484	-1.0244	9	0.44086	T	0.13	-1.7695	12.3831	0.55317	0.157:0.0:0.843:0.0	rs7118900;rs59912012;rs7118900	239	Q8NFD2	ANKK1_HUMAN	T	239	ENSP00000306678:A239T	ENSP00000306678:A239T	A	+	1	0	ANKK1	112772031	0.948000	0.32251	0.002000	0.10522	0.001000	0.01503	2.088000	0.41663	0.150000	0.19136	-1.598000	0.00824	GCG	G|0.714;A|0.286	0.286	strong		0.607	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
IGFBP1	3484	hgsc.bcm.edu	37	7	45932669	45932669	+	Missense_Mutation	SNP	A	A	G	rs4619	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:45932669A>G	ENST00000275525.3	+	4	1055	c.759A>G	c.(757-759)atA>atG	p.I253M	IGFBP1_ENST00000468955.1_Missense_Mutation_p.I210M|IGFBP1_ENST00000457280.1_Missense_Mutation_p.I251M	NM_000596.2	NP_000587.1	P08833	IBP1_HUMAN	insulin-like growth factor binding protein 1	253			I -> M (in dbSNP:rs4619). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.10}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)|tissue regeneration (GO:0042246)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	insulin-like growth factor binding (GO:0005520)			large_intestine(2)|lung(4)	6						ACTGCCAGATATATTTTAATG	0.418													G|||	1883	0.375998	0.444	0.3588	5008	,	,		15297	0.5268		0.334	False		,,,				2504	0.184				p.I253M		Atlas-SNP	.											.	IGFBP1	19	.	0			c.A759G	GRCh37	CM055287	IGFBP1	M	rs4619	PASS	.	G	MET/ILE	1998,2408	613.7+/-392.2	469,1060,674	53.0	54.0	54.0		759	1.5	0.0	7	dbSNP_52	54	3041,5559	662.6+/-402.0	526,1989,1785	yes	missense	IGFBP1	NM_000596.2	10	995,3049,2459	GG,GA,AA		35.3605,45.3473,38.7437	benign	253/260	45932669	5039,7967	2203	4300	6503	SO:0001583	missense	3484	exon4			CCAGATATATTTT		CCDS5504.1	7p12.3	2014-09-16			ENSG00000146678	ENSG00000146678			5469	protein-coding gene	gene with protein product	"""placental protein 12"", ""amniotic fluid binding protein"", ""alpha-pregnancy-associated endometrial globulin"", ""growth hormone independent-binding protein"", ""binding protein-28"", ""binding protein-26"", ""binding protein-25"", ""IGF-binding protein 1"""	146730		IBP1		2461294	Standard	NM_000596		Approved	IGF-BP25, AFBP, hIGFBP-1, PP12	uc003tnp.3	P08833	OTTHUMG00000152343	ENST00000275525.3:c.759A>G	7.37:g.45932669A>G	ENSP00000275525:p.Ile253Met	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_000596	A4D2F4|D3DVL9|Q8IYP5	Missense_Mutation	SNP	ENST00000275525.3	37	CCDS5504.1	882	0.40384615384615385	242	0.491869918699187	102	0.281767955801105	280	0.48951048951048953	258	0.3403693931398417	G	1.240	-0.621478	0.03636	0.453473	0.353605	ENSG00000146678	ENST00000275525;ENST00000457280;ENST00000468955	T;T;T	0.62941	-0.01;-0.01;-0.01	5.44	1.51	0.23008	Thyroglobulin type-1 (2);	0.547615	0.20243	N	0.096243	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.10450	0.0;0.005;0.005	T	0.43410	-0.9393	9	0.59425	D	0.04	-20.5084	6.1715	0.20421	0.2899:0.1242:0.5859:0.0	rs4619;rs3173754;rs9658226;rs10464236;rs11539263;rs17846130;rs17859136;rs58707225;rs4619	210;253;251	C9J6H2;P08833;C9JXF9	.;IBP1_HUMAN;.	M	253;251;210	ENSP00000275525:I253M;ENSP00000413511:I251M;ENSP00000417069:I210M	ENSP00000275525:I253M	I	+	3	3	IGFBP1	45899194	0.934000	0.31675	0.004000	0.12327	0.000000	0.00434	1.012000	0.29924	0.045000	0.15804	-1.889000	0.00537	ATA	A|0.602;G|0.397	0.397	strong		0.418	IGFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251355.2	NM_000596	
OR2F1	26211	hgsc.bcm.edu	37	7	143657801	143657801	+	Silent	SNP	A	A	G	rs2072166	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143657801A>G	ENST00000392899.1	+	1	775	c.738A>G	c.(736-738)acA>acG	p.T246T	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	246					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(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					CTCACCTCACAGTGGTTGCCC	0.488													a|||	2291	0.457468	0.6687	0.415	5008	,	,		22020	0.5744		0.3231	False		,,,				2504	0.2198				p.T246T		Atlas-SNP	.											.	OR2F1	71	.	0			c.A738G						PASS	.	G		2672,1734	519.3+/-369.9	816,1040,347	158.0	130.0	140.0		738	-11.1	0.0	7	dbSNP_96	140	2839,5761	675.2+/-403.2	481,1877,1942	no	coding-synonymous	OR2F1	NM_012369.2		1297,2917,2289	GG,GA,AA		33.0116,39.3554,42.3728		246/318	143657801	5511,7495	2203	4300	6503	SO:0001819	synonymous_variant	26211	exon1			CCTCACAGTGGTT	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"""GPCR / Class A : Olfactory receptors"""	8246	protein-coding gene	gene with protein product		608497	"""olfactory receptor, family 2, subfamily F, member 1"""	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.738A>G	7.37:g.143657801A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Silent	SNP	ENST00000392899.1	37	CCDS5887.1																																																																																			A|0.568;G|0.432	0.432	strong		0.488	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1		
OR2L3	391192	hgsc.bcm.edu	37	1	248224216	248224216	+	Missense_Mutation	SNP	C	C	T	rs6658227	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248224216C>T	ENST00000359959.3	+	1	233	c.233C>T	c.(232-234)cCt>cTt	p.P78L	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	78			P -> L (in dbSNP:rs6658227).			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)			ACCATTGTTCCTAAGATGGCA	0.443													c|||	941	0.187899	0.298	0.098	5008	,	,		22692	0.254		0.1441	False		,,,				2504	0.0798				p.P78L		Atlas-SNP	.											.	OR2L3	97	.	0			c.C233T						PASS	.	C	LEU/PRO,	1206,3200		158,890,1155	298.0	275.0	283.0		233,	2.0	0.9	1	dbSNP_116	283	1187,7413		90,1007,3203	no	missense,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	98,	248,1897,4358	TT,TC,CC		13.8023,27.3718,18.3992	probably-damaging,	78/313,	248224216	2393,10613	2203	4300	6503	SO:0001583	missense	391192	exon1			TTGTTCCTAAGAT	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.233C>T	1.37:g.248224216C>T	ENSP00000353044:p.Pro78Leu	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	223	110	0.493274	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	465	0.2129120879120879	148	0.3008130081300813	37	0.10220994475138122	172	0.3006993006993007	108	0.1424802110817942	.	14.47	2.544357	0.45280	0.273718	0.138023	ENSG00000198128	ENST00000359959	T	0.01854	4.6	2.05	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31697	U	0.007204	T	0.00012	0.0000	M	0.93854	3.465	0.09310	P	0.99999426361	D	0.54964	0.969	P	0.61070	0.883	T	0.31943	-0.9925	9	0.87932	D	0	.	11.9647	0.53027	0.0:1.0:0.0:0.0	rs6658227;rs59129511;rs6658227	78	Q8NG85	OR2L3_HUMAN	L	78	ENSP00000353044:P78L	ENSP00000353044:P78L	P	+	2	0	OR2L3	246290839	0.991000	0.36638	0.866000	0.34008	0.388000	0.30384	2.852000	0.48310	1.124000	0.41980	0.462000	0.41574	CCT	C|0.801;T|0.199	0.199	strong		0.443	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
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 GAIIx	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	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	43	20	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		
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 GAIIx	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_ENST00000469823.1_3'UTR|MCMDC2_ENST00000396592.3_Missense_Mutation_p.T94M|MCMDC2_ENST00000313616.5_Missense_Mutation_p.T94M|MCMDC2_ENST00000541540.1_Missense_Mutation_p.T31M|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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	50	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	
PRDM11	56981	hgsc.bcm.edu	37	11	45245778	45245778	+	Missense_Mutation	SNP	G	G	T	rs35090414	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:45245778G>T	ENST00000530656.1	+	7	855	c.855G>T	c.(853-855)agG>agT	p.R285S	CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000528980.1_Intron|PRDM11_ENST00000424263.2_Missense_Mutation_p.R251S|PRDM11_ENST00000263765.4_Missense_Mutation_p.R285S			Q9NQV5	PRD11_HUMAN	PR domain containing 11	285							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						GAGAGAAGAGGTTGCAGAGGG	0.502													G|||	228	0.0455272	0.0015	0.1441	5008	,	,		18715	0.0		0.0835	False		,,,				2504	0.0429				p.R251S	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											PRDM11,caecum,carcinoma,0,2	PRDM11	53	2	0			c.G753T						PASS	.	G	SER/ARG	93,4307		1,91,2108	101.0	111.0	107.0		855	1.9	1.0	11	dbSNP_126	107	732,7866		36,660,3603	yes	missense	PRDM11	NM_020229.2	110	37,751,5711	TT,TG,GG		8.5136,2.1136,6.3471	benign	285/512	45245778	825,12173	2200	4299	6499	SO:0001583	missense	56981	exon7			GAAGAGGTTGCAG	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"""PR-domain containing protein 11"""						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.855G>T	11.37:g.45245778G>T	ENSP00000435976:p.Arg285Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_001256695	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	37		108	0.04945054945054945	3	0.006097560975609756	47	0.1298342541436464	0	0.0	58	0.07651715039577836	G	13.22	2.170746	0.38315	0.021136	0.085136	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000424263	T;T;T	0.47177	0.85;0.85;0.85	5.82	1.88	0.25563	.	0.391190	0.24818	N	0.035341	T	0.00241	0.0007	N	0.08118	0	0.39765	P	0.02791699999999997	B	0.17667	0.023	B	0.18561	0.022	T	0.13415	-1.0510	9	0.11485	T	0.65	-23.2779	10.403	0.44241	0.3803:0.0:0.6197:0.0	rs35090414;rs61880321	285	Q9NQV5	PRD11_HUMAN	S	285;285;251	ENSP00000263765:R285S;ENSP00000435976:R285S;ENSP00000394314:R251S	ENSP00000263765:R285S	R	+	3	2	PRDM11	45202354	0.999000	0.42202	0.999000	0.59377	0.998000	0.95712	0.657000	0.24963	0.373000	0.24621	0.655000	0.94253	AGG	G|0.940;T|0.060	0.060	strong		0.502	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388759	1388759	+	Missense_Mutation	SNP	C	C	T	rs112233131	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:1388759C>T	ENST00000324803.4	+	1	3420	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	154					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R154W(2)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCCATGCGGAGTGCCCG	0.701																																					p.R154W		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,3	CRIPAK	185	3	2	Substitution - Missense(2)	NS(1)|skin(1)	c.C460T						PASS	.						84.0	72.0	76.0					4																	1388759		2202	4282	6484	SO:0001583	missense	285464	exon1			CCCATGCGGAGTG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.460C>T	4.37:g.1388759C>T	ENSP00000323978:p.Arg154Trp	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	21	6	0.285714	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.074|0.074	-1.196289|-1.196289	0.01594|0.01594	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000382944|ENST00000324803	.|T	.|0.19806	.|2.12	0.948|0.948	-1.9|-1.9	0.07665|0.07665	.|.	.|.	.|.	.|.	.|.	T|T	0.07908|0.07908	0.0198|0.0198	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.22851	.|0.076	.|B	.|0.04013	.|0.001	T|T	0.18116|0.18116	-1.0347|-1.0347	6|9	0.02654|0.49607	T|T	1|0.09	.|.	0.8279|0.8279	0.01124|0.01124	0.1649:0.1747:0.3249:0.3355|0.1649:0.1747:0.3249:0.3355	.|.	.|154	.|Q8N1N5	.|CRPAK_HUMAN	V|W	137|154	.|ENSP00000323978:R154W	ENSP00000372402:A137V|ENSP00000323978:R154W	A|R	+|+	2|1	0|2	CRIPAK|CRIPAK	1378759|1378759	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.017000|0.017000	0.09413|0.09413	-2.063000|-2.063000	0.01388|0.01388	-3.215000|-3.215000	0.00213|0.00213	-1.709000|-1.709000	0.00716|0.00716	GCG|CGG	C|0.966;T|0.034	0.034	strong		0.701	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559029	140559029	+	Missense_Mutation	SNP	G	G	C	rs139165988	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140559029G>C	ENST00000239444.2	+	1	1659	c.1414G>C	c.(1414-1416)Ggc>Cgc	p.G472R	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	472	Cadherin 5. {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)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTGCACATCGGCAGCGTCAG	0.667													G|||	39	0.00778754	0.0076	0.0231	5008	,	,		24409	0.0		0.0119	False		,,,				2504	0.001				p.G472R		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G1414C						PASS	.	G	ARG/GLY	26,4380	32.6+/-62.9	0,26,2177	80.0	123.0	108.0		1414	4.3	1.0	5	dbSNP_134	108	94,8494	46.7+/-105.8	0,94,4200	no	missense	PCDHB8	NM_019120.3	125	0,120,6377	CC,CG,GG		1.0946,0.5901,0.9235	possibly-damaging	472/802	140559029	120,12874	2203	4294	6497	SO:0001583	missense	56128	exon1			CACATCGGCAGCG	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1414G>C	5.37:g.140559029G>C	ENSP00000239444:p.Gly472Arg	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	234	56	0.239316	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	23	0.010531135531135532	4	0.008130081300813009	11	0.03038674033149171	0	0.0	8	0.010554089709762533	G	16.19	3.052256	0.55218	0.005901	0.010946	ENSG00000120322	ENST00000239444	T	0.04502	3.61	4.26	4.26	0.50523	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.06600	0.0169	M	0.91459	3.21	0.18873	N	0.999987	P	0.43169	0.8	P	0.50570	0.644	T	0.01858	-1.1259	9	0.48119	T	0.1	.	11.5582	0.50761	0.0:0.0:0.8211:0.1789	.	472	Q9UN66	PCDB8_HUMAN	R	472	ENSP00000239444:G472R	ENSP00000239444:G472R	G	+	1	0	PCDHB8	140539213	0.194000	0.23325	1.000000	0.80357	0.972000	0.66771	0.602000	0.24134	1.920000	0.55613	0.305000	0.20034	GGC	G|0.991;C|0.009	0.009	strong		0.667	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
Unknown	0	hgsc.bcm.edu	37	13	103410782	103410782	+	IGR	SNP	T	T	C	rs1375719	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103410782T>C								LINC00283 (13208 upstream) : TEX30 (7557 downstream)																							GATGAATTAATAACTGACCAA	0.294													T|||	1911	0.381589	0.1044	0.5043	5008	,	,		17536	0.4097		0.5089	False		,,,				2504	0.5092				p.I96V		Atlas-SNP	.											.	.	.	.	0			c.A286G						PASS	.	T	VAL/ILE	262,1122		28,206,458	81.0	69.0	73.0		286	2.1	0.0	13	dbSNP_88	73	1591,1581		410,771,405	yes	missense	CCDC168	NM_001146197.1	29	438,977,863	CC,CT,TT		49.8424,18.9306,40.6716		96/7082	103410782	1853,2703	692	1586	2278	SO:0001628	intergenic_variant	643677	exon3			AATTAATAACTGA																													13.37:g.103410782T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	57	40	0.701754	NM_001146197		Missense_Mutation	SNP		37																																																																																				A|0.014;C|0.352	0.352	strong	0	0.294								
CBY1	25776	hgsc.bcm.edu	37	22	39069181	39069181	+	Silent	SNP	T	T	C	rs3747174	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39069181T>C	ENST00000216029.3	+	5	455	c.321T>C	c.(319-321)gcT>gcC	p.A107A	RP3-508I15.9_ENST00000422408.2_RNA|RP3-508I15.9_ENST00000444381.1_RNA|RP3-508I15.9_ENST00000431924.2_RNA|RP3-508I15.9_ENST00000412067.1_RNA	NM_015373.3	NP_056188.1	Q9Y3M2	CBY1_HUMAN	chibby homolog 1 (Drosophila)	107	Minimal region for the interaction with PKD2.				cardiac muscle cell differentiation (GO:0055007)|cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|protein localization (GO:0008104)	ciliary basal body (GO:0036064)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	beta-catenin binding (GO:0008013)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|ovary(1)	4	Melanoma(58;0.04)					AGTCCACTGCTGAATCCCACT	0.498													C|||	1431	0.285743	0.2897	0.2032	5008	,	,		20300	0.3502		0.2932	False		,,,				2504	0.2648				p.A150A		Atlas-SNP	.											.	CBY1	10	.	0			c.T450C						PASS	.	C	,	1279,3127	700.4+/-406.6	186,907,1110	71.0	65.0	67.0		321,321	-10.1	0.1	22	dbSNP_107	67	2514,6086	693.3+/-404.6	362,1790,2148	no	coding-synonymous,coding-synonymous	CBY1	NM_001002880.1,NM_015373.3	,	548,2697,3258	CC,CT,TT		29.2326,29.0286,29.1635	,	107/127,107/127	39069181	3793,9213	2203	4300	6503	SO:0001819	synonymous_variant	25776	exon6			CACTGCTGAATCC	BK005534	CCDS13974.1, CCDS74861.1	22q12	2014-02-06	2007-01-26	2007-01-26	ENSG00000100211	ENSG00000100211			1307	protein-coding gene	gene with protein product	"""chibby CTNNB1-mediated transcription inhibitor"""	607757	"""chromosome 22 open reading frame 2"", ""PKD2 interactor, golgi and endoplasmic reticulum associated 1"""	C22orf2, PGEA1		10591208, 15194699	Standard	NM_015373		Approved	PIGEA14, PIGEA-14, Chibby, Cby	uc003awb.4	Q9Y3M2	OTTHUMG00000150990	ENST00000216029.3:c.321T>C	22.37:g.39069181T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_001002880	B2R4S2|Q66GT6|Q9UIK9	Silent	SNP	ENST00000216029.3	37	CCDS13974.1																																																																																			T|0.702;C|0.298	0.298	strong		0.498	CBY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320832.1	NM_015373	
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 GAIIx	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	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	33	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	
JARID2	3720	hgsc.bcm.edu	37	6	15496662	15496662	+	Silent	SNP	C	C	T	rs742099	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:15496662C>T	ENST00000341776.2	+	7	1450	c.1206C>T	c.(1204-1206)ccC>ccT	p.P402P	JARID2_ENST00000397311.3_Silent_p.P230P|JARID2_ENST00000541660.1_Silent_p.P364P	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	402					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				CCACTGGGCCCGCCGTCAATG	0.612													C|||	940	0.1877	0.056	0.2147	5008	,	,		15542	0.3056		0.2515	False		,,,				2504	0.1595				p.P402P		Atlas-SNP	.											.	JARID2	135	.	0			c.C1206T						PASS	.	C		378,4028	181.9+/-209.8	14,350,1839	53.0	62.0	59.0		1206	2.9	1.0	6	dbSNP_86	59	2188,6412	362.0+/-332.6	292,1604,2404	no	coding-synonymous	JARID2	NM_004973.2		306,1954,4243	TT,TC,CC		25.4419,8.5792,19.7294		402/1247	15496662	2566,10440	2203	4300	6503	SO:0001819	synonymous_variant	3720	exon7			TGGGCCCGCCGTC	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.1206C>T	6.37:g.15496662C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	40	0.754717	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																			C|0.798;T|0.202	0.202	strong		0.612	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
GREB1	9687	hgsc.bcm.edu	37	2	11736305	11736305	+	Missense_Mutation	SNP	G	G	A	rs36030386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:11736305G>A	ENST00000381486.2	+	13	2194	c.1894G>A	c.(1894-1896)Gct>Act	p.A632T	GREB1_ENST00000234142.5_Missense_Mutation_p.A632T	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	632			A -> T (in dbSNP:rs36030386).			integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TTCCTCACTCGCTGCCTCTTC	0.478													A|||	1079	0.215455	0.5696	0.1182	5008	,	,		15567	0.0317		0.1362	False		,,,				2504	0.0767				p.A632T	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.G1894A						PASS	.	A	THR/ALA	1771,2279		397,977,651	118.0	111.0	113.0		1894	1.4	0.1	2	dbSNP_126	113	1194,7216		93,1008,3104	yes	missense	GREB1	NM_014668.3	58	490,1985,3755	AA,AG,GG		14.1974,43.7284,23.7961	benign	632/1950	11736305	2965,9495	2025	4205	6230	SO:0001583	missense	9687	exon13			TCACTCGCTGCCT		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.1894G>A	2.37:g.11736305G>A	ENSP00000370896:p.Ala632Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	111	65	0.585586	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	422	0.19322344322344323	253	0.5142276422764228	44	0.12154696132596685	20	0.03496503496503497	105	0.13852242744063326	A	1.886	-0.456552	0.04540	0.437284	0.141974	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000432985	T;T;T	0.43294	3.29;3.29;0.95	4.63	1.38	0.22167	.	1.029010	0.07715	N	0.942640	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45906	-0.9229	9	0.08599	T	0.76	-34.9125	0.7537	0.00995	0.458:0.129:0.2244:0.1886	rs36030386	266;632	C9JIG0;Q4ZG55	.;GREB1_HUMAN	T	632;632;266	ENSP00000370896:A632T;ENSP00000234142:A632T;ENSP00000403886:A266T	ENSP00000234142:A632T	A	+	1	0	GREB1	11653756	0.010000	0.17322	0.058000	0.19502	0.940000	0.58332	-0.047000	0.11963	-0.071000	0.12886	-1.189000	0.01698	GCT	G|0.826;A|0.174	0.174	strong		0.478	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
MUC16	94025	hgsc.bcm.edu	37	19	9086318	9086318	+	Missense_Mutation	SNP	G	G	A	rs4520945	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9086318G>A	ENST00000397910.4	-	1	5700	c.5497C>T	c.(5497-5499)Ctc>Ttc	p.L1833F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1833	Ser-rich.|Thr-rich.		L -> F (in dbSNP:rs4520945).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGAGAGTGAGAGAAATCCAT	0.478													G|||	952	0.190096	0.0711	0.2709	5008	,	,		22597	0.3036		0.172	False		,,,				2504	0.1953				p.L1833F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C5497T						PASS	.	G	PHE/LEU	280,3662		5,270,1696	146.0	141.0	142.0		5497	0.7	0.0	19	dbSNP_111	142	1489,6845		126,1237,2804	yes	missense	MUC16	NM_024690.2	22	131,1507,4500	AA,AG,GG		17.8666,7.103,14.4102	probably-damaging	1833/14508	9086318	1769,10507	1971	4167	6138	SO:0001583	missense	94025	exon1			GAGTGAGAGAAAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5497C>T	19.37:g.9086318G>A	ENSP00000381008:p.Leu1833Phe	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	g	2.939	-0.219341	0.06061	0.07103	0.178666	ENSG00000181143	ENST00000397910	T	0.03124	4.04	0.732	0.732	0.18283	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.62365	0.991	D	0.65323	0.934	T	0.55159	-0.8184	7	0.87932	D	0	.	.	.	.	rs4520945;rs52791576;rs60060127;rs4520945	1833	B5ME49	.	F	1833	ENSP00000381008:L1833F	ENSP00000381008:L1833F	L	-	1	0	MUC16	8947318	0.000000	0.05858	0.002000	0.10522	0.158000	0.22134	0.004000	0.13106	0.648000	0.30732	0.305000	0.20034	CTC	G|0.812;A|0.188	0.188	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
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 GAIIx	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	SYMPK_ENST00000598155.1_5'UTR|RSPH6A_ENST00000597055.1_5'Flank|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		Somatic	110	0	0	938	WXS	Illumina HiSeq	Phase_I	92	47	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	
SMG6	23293	hgsc.bcm.edu	37	17	2203175	2203175	+	Missense_Mutation	SNP	C	C	G	rs1885986	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2203175C>G	ENST00000263073.6	-	2	922	c.872G>C	c.(871-873)cGa>cCa	p.R291P	SMG6_ENST00000544865.1_Missense_Mutation_p.R260P	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	291	Interaction with telomeric DNA.		R -> P (in dbSNP:rs1885986). {ECO:0000269|PubMed:9872452}.		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTTCTTCAGTCGTGGCCTCTC	0.552													C|||	925	0.184704	0.0318	0.4222	5008	,	,		17225	0.0893		0.3569	False		,,,				2504	0.1442				p.R291P	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G872C						PASS	.	C	PRO/ARG,PRO/ARG	321,4085	169.4+/-200.1	15,291,1897	84.0	74.0	78.0		779,872	5.3	1.0	17	dbSNP_92	78	3091,5509	473.3+/-368.6	554,1983,1763	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	103,103	569,2274,3660	GG,GC,CC		35.9419,7.2855,26.234	probably-damaging,probably-damaging	260/1389,291/1420	2203175	3412,9594	2203	4300	6503	SO:0001583	missense	23293	exon2			TTCAGTCGTGGCC	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.872G>C	17.37:g.2203175C>G	ENSP00000263073:p.Arg291Pro	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	512	0.23443223443223443	21	0.042682926829268296	155	0.4281767955801105	75	0.13111888111888112	261	0.34432717678100266	C	15.57	2.871802	0.51695	0.072855	0.359419	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.10288	2.89;2.89	5.35	5.35	0.76521	.	0.282865	0.34245	N	0.004131	T	0.00012	0.0000	L	0.29908	0.895	0.46011	P	0.0011879999999999669	D	0.71674	0.998	D	0.64042	0.921	T	0.55283	-0.8165	9	0.54805	T	0.06	-3.0807	19.0567	0.93069	0.0:1.0:0.0:0.0	rs1885986;rs3744273;rs1885986	291	Q86US8	EST1A_HUMAN	P	291;260	ENSP00000263073:R291P;ENSP00000443920:R260P	ENSP00000263073:R291P	R	-	2	0	SMG6	2149925	0.963000	0.33076	0.997000	0.53966	0.976000	0.68499	3.931000	0.56529	2.490000	0.84030	0.655000	0.94253	CGA	C|0.743;G|0.257	0.257	strong		0.552	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
CPZ	8532	hgsc.bcm.edu	37	4	8613867	8613867	+	Silent	SNP	G	G	A	rs2302573	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:8613867G>A	ENST00000360986.4	+	8	1515	c.1341G>A	c.(1339-1341)gcG>gcA	p.A447A	CPZ_ENST00000382480.2_Silent_p.A310A|CPZ_ENST00000315782.6_Silent_p.A436A|CPZ_ENST00000429646.2_Silent_p.A55A	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	447					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.A447A(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TCAACGGGGCGGACTGGTACA	0.652													G|||	408	0.0814696	0.0545	0.0086	5008	,	,		8298	0.2669		0.005	False		,,,				2504	0.0573				p.A447A		Atlas-SNP	.											CPZ,NS,carcinoma,+1,2	CPZ	95	2	1	Substitution - coding silent(1)	stomach(1)	c.G1341A						PASS	.	G	,,	282,4120	153.7+/-187.2	7,268,1926	52.0	48.0	49.0		1341,930,1308	-7.3	0.8	4	dbSNP_100	49	29,8569	19.8+/-62.0	0,29,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	7,297,6196	AA,AG,GG		0.3373,6.4062,2.3923	,,	447/653,310/516,436/642	8613867	311,12689	2201	4299	6500	SO:0001819	synonymous_variant	8532	exon8			CGGGGCGGACTGG	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"""metallocarboxypeptidase Z"""	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.1341G>A	4.37:g.8613867G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			G|0.956;A|0.044	0.044	strong		0.652	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
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 GAIIx	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	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	84	28	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	
APBB3	10307	hgsc.bcm.edu	37	5	139936980	139936980	+	IGR	SNP	A	A	G	rs250427	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139936980A>G	ENST00000357560.4	-	0	2218				SRA1_ENST00000520427.1_Intron|SRA1_ENST00000336283.6_Intron	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGGGGCGACAACCTAGTGCC	0.667													G|||	3551	0.709065	0.5696	0.7493	5008	,	,		14128	0.8254		0.7187	False		,,,				2504	0.7393				p.C20R		Atlas-SNP	.											.	SRA1	24	.	0			c.T58C						PASS	.	G		2750,1578		886,978,300	8.0	10.0	9.0			-3.3	0.0	5	dbSNP_79	9	6054,2436		2195,1664,386	no	intron	SRA1	NM_001035235.2		3081,2642,686	GG,GA,AA		28.6926,36.4603,31.3153			139936980	8804,4014	2164	4245	6409	SO:0001628	intergenic_variant	10011	exon1			GGCGACAACCTAG	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504		5.37:g.139936980A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	52	50	0.961538	NM_001253764	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	37	CCDS4229.1																																																																																			A|0.290;G|0.710	0.710	strong		0.667	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
ERCC6	2074	hgsc.bcm.edu	37	10	50681033	50681033	+	Silent	SNP	G	G	A	rs2229760	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50681033G>A	ENST00000355832.5	-	15	2829	c.2751C>T	c.(2749-2751)ggC>ggT	p.G917G	ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000542458.1_Silent_p.G287G	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	917	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)	p.G917G(1)		breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CACCTAAGCCGCCCACCCGCG	0.473								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	1273	0.254193	0.0893	0.2968	5008	,	,		14918	0.3155		0.3926	False		,,,				2504	0.2413				p.R917R		Atlas-SNP	.											ERCC6,NS,carcinoma,0,1	ERCC6	162	1	1	Substitution - coding silent(1)	stomach(1)	c.G2751T						PASS	.	G		659,3747	281.4+/-275.9	47,565,1591	67.0	62.0	64.0		2751	-8.2	0.5	10	dbSNP_98	64	3552,5048	516.8+/-378.9	720,2112,1468	no	coding-synonymous	ERCC6	NM_000124.2		767,2677,3059	AA,AG,GG		41.3023,14.9569,32.3774		917/1494	50681033	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	2074	exon15			TAAGCCGCCCACC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.2751C>T	10.37:g.50681033G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			G|0.702;A|0.298	0.298	strong		0.473	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
TYK2	7297	hgsc.bcm.edu	37	19	10477206	10477206	+	Silent	SNP	G	G	A	rs280523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10477206G>A	ENST00000525621.1	-	6	997	c.516C>T	c.(514-516)acC>acT	p.T172T	TYK2_ENST00000524462.1_5'UTR|TYK2_ENST00000264818.6_Silent_p.T172T|TYK2_ENST00000529370.1_Silent_p.T172T	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	172	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|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 tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			TCTCCTCCTCGGTCGACAGCT	0.562													G|||	417	0.0832668	0.1634	0.0403	5008	,	,		17246	0.0308		0.0775	False		,,,				2504	0.0654				p.T172T		Atlas-SNP	.											.	TYK2	126	.	0			c.C516T						PASS	.	G		776,3630	314.7+/-293.7	58,660,1485	171.0	157.0	162.0		516	-2.5	0.0	19	dbSNP_79	162	566,8034	154.3+/-208.6	22,522,3756	no	coding-synonymous	TYK2	NM_003331.4		80,1182,5241	AA,AG,GG		6.5814,17.6123,10.3183		172/1188	10477206	1342,11664	2203	4300	6503	SO:0001819	synonymous_variant	7297	exon6			CTCCTCGGTCGAC		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.516C>T	19.37:g.10477206G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_003331	Q6QB10|Q96CH0	Silent	SNP	ENST00000525621.1	37	CCDS12236.1																																																																																			G|0.905;A|0.095	0.095	strong		0.562	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
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 GAIIx	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	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	50	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	
CCDC27	148870	hgsc.bcm.edu	37	1	3669205	3669205	+	Missense_Mutation	SNP	C	C	G	rs10910021	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3669205C>G	ENST00000294600.2	+	1	244	c.160C>G	c.(160-162)Cag>Gag	p.Q54E		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	54			Q -> E (in dbSNP:rs10910021). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		CAGCCCATCTCAGAGGCACAG	0.602													G|||	1939	0.387181	0.4017	0.4078	5008	,	,		17772	0.2897		0.3946	False		,,,				2504	0.4458				p.Q54E		Atlas-SNP	.											.	CCDC27	79	.	0			c.C160G						PASS	.	G	GLU/GLN	1728,2678	648.5+/-398.7	345,1038,820	132.0	113.0	119.0		160	-5.5	0.0	1	dbSNP_120	119	3176,5424	653.6+/-401.1	589,1998,1713	yes	missense	CCDC27	NM_152492.2	29	934,3036,2533	GG,GC,CC		36.9302,39.2192,37.7057	benign	54/657	3669205	4904,8102	2203	4300	6503	SO:0001583	missense	148870	exon1			CCATCTCAGAGGC		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.160C>G	1.37:g.3669205C>G	ENSP00000294600:p.Gln54Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	97	34	0.350515	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	790	0.3617216117216117	200	0.4065040650406504	135	0.3729281767955801	159	0.27797202797202797	296	0.39050131926121373	G	5.832	0.337707	0.11013	0.392192	0.369302	ENSG00000162592	ENST00000294600	T	0.17691	2.26	3.95	-5.54	0.02544	.	1.231100	0.06015	N	0.650230	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47341	-0.9125	9	0.08179	T	0.78	-5.2542	7.9089	0.29778	0.3185:0.4778:0.2037:0.0	rs10910021	54	Q2M243	CCD27_HUMAN	E	54	ENSP00000294600:Q54E	ENSP00000294600:Q54E	Q	+	1	0	CCDC27	3659065	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.374000	0.02566	-1.647000	0.01511	-0.829000	0.03081	CAG	C|0.625;G|0.375	0.375	strong		0.602	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
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 GAIIx	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_ENST00000530267.1_Intron|USP35_ENST00000441408.2_5'UTR|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	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	119	95	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	
EVC2	132884	hgsc.bcm.edu	37	4	5690902	5690902	+	Missense_Mutation	SNP	T	T	C	rs4689278	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:5690902T>C	ENST00000344408.5	-	5	741	c.688A>G	c.(688-690)Agc>Ggc	p.S230G	EVC2_ENST00000344938.1_Missense_Mutation_p.S230G|EVC2_ENST00000310917.2_Missense_Mutation_p.S150G	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	230			S -> G (in dbSNP:rs4689278).		smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S230G(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						AACTTCTTGCTAAAAGCCTGG	0.493													T|||	1328	0.265176	0.1914	0.2896	5008	,	,		20409	0.4028		0.2097	False		,,,				2504	0.2628				p.S230G		Atlas-SNP	.											EVC2,NS,carcinoma,0,1	EVC2	202	1	1	Substitution - Missense(1)	stomach(1)	c.A688G						PASS	.	T	GLY/SER,GLY/SER	887,3519	342.5+/-307.2	86,715,1402	88.0	84.0	85.0		448,688	1.9	0.5	4	dbSNP_111	85	1856,6744	332.4+/-320.1	202,1452,2646	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	56,56	288,2167,4048	CC,CT,TT		21.5814,20.1316,21.0903	benign,benign	150/1229,230/1309	5690902	2743,10263	2203	4300	6503	SO:0001583	missense	132884	exon5			TCTTGCTAAAAGC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.688A>G	4.37:g.5690902T>C	ENSP00000342144:p.Ser230Gly	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	517	0.2367216117216117	80	0.16260162601626016	91	0.2513812154696133	183	0.31993006993006995	163	0.21503957783641162	T	3.322	-0.138455	0.06669	0.201316	0.215814	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.74315	-0.83;-0.81;-0.82	4.54	1.94	0.25998	.	0.628224	0.16647	N	0.205392	T	0.00012	0.0000	N	0.22421	0.69	0.47476	P	5.619999999999514E-4	B	0.23185	0.081	B	0.20184	0.028	T	0.14200	-1.0481	9	0.23891	T	0.37	-10.6293	9.0029	0.36092	0.0:0.0:0.3622:0.6378	rs4689278;rs58994043;rs4689278	230	Q86UK5	LBN_HUMAN	G	230;150;230	ENSP00000339954:S230G;ENSP00000311683:S150G;ENSP00000342144:S230G	ENSP00000311683:S150G	S	-	1	0	EVC2	5741803	0.926000	0.31397	0.461000	0.27105	0.160000	0.22226	0.997000	0.29731	0.190000	0.20209	-0.488000	0.04728	AGC	T|0.776;C|0.224	0.224	strong		0.493	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
OR10H1	26539	hgsc.bcm.edu	37	19	15918654	15918654	+	Missense_Mutation	SNP	G	G	A	rs4808382	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15918654G>A	ENST00000334920.2	-	1	282	c.194C>T	c.(193-195)gCc>gTc	p.A65V		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	65			A -> V (in dbSNP:rs4808382).			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(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						GACGGAGAGGGCGCACAGGAA	0.647													.|||	767	0.153155	0.1369	0.1153	5008	,	,		20012	0.119		0.1769	False		,,,				2504	0.2127				p.A65V		Atlas-SNP	.											OR10H1,colon,carcinoma,-1,2	OR10H1	59	2	0			c.C194T						scavenged	.						114.0	99.0	104.0					19																	15918654		2203	4297	6500	SO:0001583	missense	26539	exon1			GAGAGGGCGCACA	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.194C>T	19.37:g.15918654G>A	ENSP00000335596:p.Ala65Val	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	87	16	0.183908	NM_013940	Q6IFQ2|Q96R59	Missense_Mutation	SNP	ENST00000334920.2	37	CCDS12335.1	271	0.12408424908424909	53	0.10772357723577236	34	0.09392265193370165	62	0.10839160839160839	122	0.16094986807387862	g	2.686	-0.274334	0.05679	.	.	ENSG00000186723	ENST00000334920	T	0.03065	4.06	4.71	4.71	0.59529	GPCR, rhodopsin-like superfamily (1);	0.271882	0.26200	N	0.025747	T	0.00012	0.0000	N	0.01771	-0.73	0.39146	P	0.037856	B	0.11235	0.004	B	0.15052	0.012	T	0.39881	-0.9592	9	0.02654	T	1	.	15.1534	0.72720	0.0:0.0:1.0:0.0	rs4808382	65	Q9Y4A9	O10H1_HUMAN	V	65	ENSP00000335596:A65V	ENSP00000335596:A65V	A	-	2	0	OR10H1	15779654	0.589000	0.26807	0.964000	0.40570	0.471000	0.32888	1.685000	0.37659	2.169000	0.68431	0.643000	0.83706	GCC	A|1.000;|0.000	1.000	weak		0.647	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
LRRC47	57470	hgsc.bcm.edu	37	1	3700618	3700618	+	Silent	SNP	G	G	A	rs74764187	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3700618G>A	ENST00000378251.1	-	4	1279	c.1252C>T	c.(1252-1254)Ctg>Ttg	p.L418L	RP1-286D6.5_ENST00000607459.1_RNA|RN7SL574P_ENST00000581512.1_RNA	NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	418							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)	p.L418L(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		TCGGCCTCCAGCTGCAGCTGC	0.662													G|||	35	0.00698882	0.0	0.0115	5008	,	,		14207	0.001		0.0239	False		,,,				2504	0.002				p.L418L		Atlas-SNP	.											LRRC47,NS,haematopoietic_neoplasm,0,1	LRRC47	42	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1252T						PASS	.	G		8,4398	12.9+/-30.5	0,8,2195	34.0	34.0	34.0		1252	3.0	1.0	1	dbSNP_133	34	128,8470	61.7+/-123.6	1,126,4172	no	coding-synonymous	LRRC47	NM_020710.2		1,134,6367	AA,AG,GG		1.4887,0.1816,1.0458		418/584	3700618	136,12868	2203	4299	6502	SO:0001819	synonymous_variant	57470	exon4			CCTCCAGCTGCAG	AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.1252C>T	1.37:g.3700618G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_020710	Q9ULN5	Silent	SNP	ENST00000378251.1	37	CCDS51.1																																																																																			G|0.987;A|0.013	0.013	strong		0.662	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710	
PARP4	143	hgsc.bcm.edu	37	13	25075859	25075859	+	Silent	SNP	C	C	T	rs1539096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25075859C>T	ENST00000381989.3	-	3	351	c.246G>A	c.(244-246)agG>agA	p.R82R		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	82	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GTCTCTTTTCCCTGATAGATT	0.398													.|||	3031	0.605232	0.618	0.6037	5008	,	,		16368	0.6062		0.5119	False		,,,				2504	0.684				p.R82R		Atlas-SNP	.											.	PARP4	142	.	0			c.G246A						PASS	.	T		2558,1848	536.5+/-374.5	738,1082,383	125.0	130.0	128.0		246	1.5	0.3	13	dbSNP_88	128	4634,3966	551.8+/-386.0	1240,2154,906	no	coding-synonymous	PARP4	NM_006437.3		1978,3236,1289	TT,TC,CC		46.1163,41.9428,44.7024		82/1725	25075859	7192,5814	2203	4300	6503	SO:0001819	synonymous_variant	143	exon3			CTTTTCCCTGATA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.246G>A	13.37:g.25075859C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.431;T|0.569	0.569	strong		0.398	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
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 GAIIx	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	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	75	17	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	
RUFY1	80230	hgsc.bcm.edu	37	5	179025789	179025789	+	Silent	SNP	G	G	A	rs72824522	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:179025789G>A	ENST00000319449.4	+	14	1740	c.1728G>A	c.(1726-1728)agG>agA	p.R576R	RP11-1379J22.2_ENST00000500262.1_RNA|RUFY1_ENST00000377001.2_3'UTR|RUFY1_ENST00000393438.2_Silent_p.R468R|RUFY1_ENST00000437570.2_Silent_p.R468R	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	576					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCTACTCAGGATGGAGCTGC	0.522										HNSCC(44;0.11)			G|||	361	0.0720847	0.0378	0.0764	5008	,	,		19945	0.0853		0.1064	False		,,,				2504	0.0665				p.R576R		Atlas-SNP	.											.	RUFY1	101	.	0			c.G1728A						PASS	.	G	,,	194,4212	122.9+/-160.3	6,182,2015	113.0	110.0	111.0		1404,1404,1728	-2.1	0.0	5	dbSNP_130	111	956,7644	208.4+/-249.9	60,836,3404	no	coding-synonymous,coding-synonymous,coding-synonymous	RUFY1	NM_001040451.1,NM_001040452.1,NM_025158.3	,,	66,1018,5419	AA,AG,GG		11.1163,4.4031,8.8421	,,	468/601,468/601,576/709	179025789	1150,11856	2203	4300	6503	SO:0001819	synonymous_variant	80230	exon14			ACTCAGGATGGAG	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.1728G>A	5.37:g.179025789G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	167	82	0.491018	NM_025158	Q59FF3|Q71S93|Q9H6I3	Silent	SNP	ENST00000319449.4	37	CCDS4445.2	173	0.07921245421245421	23	0.046747967479674794	28	0.07734806629834254	47	0.08216783216783216	75	0.09894459102902374	G	0.032	-1.325400	0.01309	0.044031	0.111163	ENSG00000176783	ENST00000502434	.	.	.	4.98	-2.1	0.07210	.	.	.	.	.	T	0.00608	0.0020	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.21143	-1.0254	3	.	.	.	-1.642	6.3823	0.21542	0.4772:0.1314:0.3914:0.0	.	.	.	.	N	254	.	.	D	+	1	0	RUFY1	178958395	0.235000	0.23794	0.001000	0.08648	0.019000	0.09904	0.424000	0.21330	-0.693000	0.05121	-0.459000	0.05422	GAT	G|0.912;A|0.088	0.088	strong		0.522	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
C8A	731	hgsc.bcm.edu	37	1	57383358	57383358	+	Missense_Mutation	SNP	C	C	T	rs17300936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:57383358C>T	ENST00000361249.3	+	11	1820	c.1724C>T	c.(1723-1725)cCa>cTa	p.P575L		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	575	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		P -> L (in dbSNP:rs17300936).	P -> S (in Ref. 3; AAA82124). {ECO:0000305}.	complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	43						GCCTCGTGTCCAGGGCGGAAA	0.567													C|||	307	0.0613019	0.0174	0.0432	5008	,	,		17737	0.0585		0.1233	False		,,,				2504	0.0726				p.P575L		Atlas-SNP	.											.	C8A	103	.	0			c.C1724T						PASS	.	C	LEU/PRO	151,4255	104.7+/-143.2	2,147,2054	57.0	57.0	57.0		1724	1.6	0.5	1	dbSNP_123	57	1084,7516	227.5+/-262.8	75,934,3291	yes	missense	C8A	NM_000562.2	98	77,1081,5345	TT,TC,CC		12.6047,3.4271,9.4956	benign	575/585	57383358	1235,11771	2203	4300	6503	SO:0001583	missense	731	exon11			CGTGTCCAGGGCG	M16974	CCDS606.1	1p32.2	2014-09-17			ENSG00000157131	ENSG00000157131		"""Complement system"""	1352	protein-coding gene	gene with protein product		120950					Standard	NM_000562		Approved		uc001cyo.2	P07357	OTTHUMG00000008306	ENST00000361249.3:c.1724C>T	1.37:g.57383358C>T	ENSP00000354458:p.Pro575Leu	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	239	239	1	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	159	0.07280219780219781	12	0.024390243902439025	19	0.052486187845303865	33	0.057692307692307696	95	0.12532981530343007	C	0.124	-1.122112	0.01785	0.034271	0.126047	ENSG00000157131	ENST00000361249	T	0.54071	0.59	4.82	1.63	0.23807	.	0.346426	0.30879	N	0.008683	T	0.00271	0.0008	N	0.12471	0.22	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.06643	-1.0815	9	0.21540	T	0.41	-1.0877	6.014	0.19592	0.1444:0.5988:0.0:0.2568	rs17300936;rs58858987;rs17300936	575	P07357	CO8A_HUMAN	L	575	ENSP00000354458:P575L	ENSP00000354458:P575L	P	+	2	0	C8A	57155946	0.150000	0.22732	0.470000	0.27216	0.009000	0.06853	0.722000	0.25925	0.611000	0.30052	-0.251000	0.11542	CCA	C|0.917;N|0.000	.	strong		0.567	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562	
ZNFX1	57169	hgsc.bcm.edu	37	20	47865784	47865784	+	Missense_Mutation	SNP	C	C	T	rs6512577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47865784C>T	ENST00000396105.1	-	14	4023	c.3777G>A	c.(3775-3777)atG>atA	p.M1259I	ZNFX1_ENST00000371754.4_Intron|ZNFX1_ENST00000371752.1_Missense_Mutation_p.M1259I	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1259			M -> I (in dbSNP:rs6512577).				metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			AGAGCCGGAGCATGGGGCCTA	0.532													C|||	671	0.133986	0.1778	0.1686	5008	,	,		20164	0.0427		0.2018	False		,,,				2504	0.0746				p.M1259I		Atlas-SNP	.											.	ZNFX1	194	.	0			c.G3777A						PASS	.	C	ILE/MET	753,3653	308.8+/-290.8	62,629,1512	71.0	71.0	71.0		3777	-12.3	0.0	20	dbSNP_116	71	1926,6674	340.3+/-323.5	203,1520,2577	yes	missense	ZNFX1	NM_021035.2	10	265,2149,4089	TT,TC,CC		22.3953,17.0903,20.5982	benign	1259/1919	47865784	2679,10327	2203	4300	6503	SO:0001583	missense	57169	exon14			CCGGAGCATGGGG	AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.3777G>A	20.37:g.47865784C>T	ENSP00000379412:p.Met1259Ile	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	128	71	0.554688	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	335	0.1533882783882784	91	0.18495934959349594	64	0.17679558011049723	28	0.04895104895104895	152	0.20052770448548812	C	1.356	-0.590167	0.03799	0.170903	0.223953	ENSG00000124201	ENST00000371752;ENST00000396105	D;D	0.86030	-2.06;-2.06	6.17	-12.3	0.00002	.	0.790063	0.12288	N	0.482275	T	0.00039	0.0001	N	0.02539	-0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.13495	-1.0507	9	0.22706	T	0.39	-0.0137	7.3514	0.26693	0.0641:0.3567:0.3897:0.1895	rs6512577;rs17778787;rs52817512;rs57225169;rs6512577	1259	Q9P2E3	ZNFX1_HUMAN	I	1259	ENSP00000360817:M1259I;ENSP00000379412:M1259I	ENSP00000360817:M1259I	M	-	3	0	ZNFX1	47299191	0.000000	0.05858	0.000000	0.03702	0.301000	0.27625	-2.653000	0.00856	-3.493000	0.00153	-0.150000	0.13652	ATG	C|0.824;T|0.176	0.176	strong		0.532	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407649	75407649	+	Silent	SNP	A	A	C	rs4746139	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:75407649A>C	ENST00000394810.2	-	4	1910	c.1761T>G	c.(1759-1761)ccT>ccG	p.P587P	SYNPO2L_ENST00000372873.4_Silent_p.P363P	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	587	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					AGGGTCGCAAAGGCGCAGATA	0.701													A|||	774	0.154553	0.1483	0.1052	5008	,	,		11160	0.1845		0.1332	False		,,,				2504	0.1892				p.P587P		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.T1761G						PASS	.	A	,	582,3772		39,504,1634	13.0	17.0	16.0		1761,1089	1.3	1.0	10	dbSNP_111	16	1226,7312		94,1038,3137	no	coding-synonymous,coding-synonymous	SYNPO2L	NM_001114133.1,NM_024875.3	,	133,1542,4771	CC,CA,AA		14.3593,13.367,14.0242	,	587/978,363/754	75407649	1808,11084	2177	4269	6446	SO:0001819	synonymous_variant	79933	exon4			TCGCAAAGGCGCA	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.1761T>G	10.37:g.75407649A>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_001114133	A5PKV9|Q68A20	Silent	SNP	ENST00000394810.2	37	CCDS44438.1																																																																																			A|0.855;C|0.145	0.145	strong		0.701	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
RP1	6101	hgsc.bcm.edu	37	8	55541450	55541450	+	Missense_Mutation	SNP	G	G	A	rs446227	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:55541450G>A	ENST00000220676.1	+	4	5156	c.5008G>A	c.(5008-5010)Gca>Aca	p.A1670T		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1670			A -> T (in dbSNP:rs446227). {ECO:0000269|PubMed:10391212, ECO:0000269|PubMed:11095597, ECO:0000269|PubMed:11527933, ECO:0000269|PubMed:20664799}.		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)			TTCCAGGAAAGCAAGTCTTTA	0.398													G|||	1243	0.248203	0.0772	0.2824	5008	,	,		21103	0.4415		0.2614	False		,,,				2504	0.2423				p.A1670T	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G5008A						PASS	.	G	THR/ALA	474,3932	213.1+/-232.8	27,420,1756	142.0	146.0	145.0		5008	-0.3	0.0	8	dbSNP_80	145	2199,6401	372.4+/-336.6	274,1651,2375	yes	missense	RP1	NM_006269.1	58	301,2071,4131	AA,AG,GG		25.5698,10.7581,20.5521	benign	1670/2157	55541450	2673,10333	2203	4300	6503	SO:0001583	missense	6101	exon4			AGGAAAGCAAGTC	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.5008G>A	8.37:g.55541450G>A	ENSP00000220676:p.Ala1670Thr	Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	125	122	0.976	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	601	0.2751831501831502	66	0.13414634146341464	94	0.2596685082872928	250	0.4370629370629371	191	0.2519788918205805	G	3.593	-0.083196	0.07141	0.107581	0.255698	ENSG00000104237	ENST00000220676	T	0.19394	2.15	5.86	-0.331	0.12679	.	1.243950	0.05754	N	0.603645	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.14805	0.011	B	0.08055	0.003	T	0.48175	-0.9058	9	0.18276	T	0.48	4.0012	1.8554	0.03177	0.4247:0.1285:0.3156:0.1312	rs446227;rs16920623;rs59806829;rs446227	1670	P56715	RP1_HUMAN	T	1670	ENSP00000220676:A1670T	ENSP00000220676:A1670T	A	+	1	0	RP1	55704003	0.007000	0.16637	0.003000	0.11579	0.722000	0.41435	0.010000	0.13242	-0.379000	0.07906	-0.182000	0.12963	GCA	G|0.766;A|0.233	0.233	strong		0.398	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
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 GAIIx	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		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	224	12	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	
CAPG	822	hgsc.bcm.edu	37	2	85628745	85628745	+	Silent	SNP	C	C	T	rs2229669	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85628745C>T	ENST00000409921.1	-	4	324	c.258G>A	c.(256-258)acG>acA	p.T86T	CAPG_ENST00000263867.4_Silent_p.T86T|CAPG_ENST00000483659.1_5'UTR|CAPG_ENST00000409670.1_Silent_p.T86T|CAPG_ENST00000409724.1_Silent_p.T86T			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						CTCCCAGCAGCGTGTTGAGGT	0.642													C|||	265	0.0529153	0.0809	0.0461	5008	,	,		16368	0.006		0.0656	False		,,,				2504	0.0552				p.T86T		Atlas-SNP	.											CAPG,colon,carcinoma,0,1	CAPG	32	1	0			c.G258A						PASS	.	C		353,4053	182.2+/-210.1	12,329,1862	52.0	52.0	52.0		258	-0.8	1.0	2	dbSNP_98	52	585,8015	156.4+/-210.3	17,551,3732	no	coding-synonymous	CAPG	NM_001747.2		29,880,5594	TT,TC,CC		6.8023,8.0118,7.2121		86/349	85628745	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	822	exon4			CAGCAGCGTGTTG	M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"""macrophage capping protein"""	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.258G>A	2.37:g.85628745C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	89	71	0.797753	NM_001256140	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Silent	SNP	ENST00000409921.1	37	CCDS58715.1																																																																																			C|0.940;T|0.060	0.060	strong		0.642	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747	
PAMR1	25891	hgsc.bcm.edu	37	11	35456085	35456085	+	Missense_Mutation	SNP	T	T	A	rs138978009	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:35456085T>A	ENST00000378880.2	-	10	2046	c.1601A>T	c.(1600-1602)gAt>gTt	p.D534V	PAMR1_ENST00000378878.3_Missense_Mutation_p.D423V|PAMR1_ENST00000532848.1_Missense_Mutation_p.D494V|PAMR1_ENST00000278360.3_Missense_Mutation_p.D551V	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	534	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						GGTCTTCTCATCCCGGTCATC	0.517													T|||	8	0.00159744	0.0008	0.0029	5008	,	,		18967	0.0		0.004	False		,,,				2504	0.001				p.D551V		Atlas-SNP	.											PAMR1,NS,malignant_melanoma,-1,1	PAMR1	85	1	0			c.A1652T						PASS	.	T	VAL/ASP,VAL/ASP	9,4395	16.8+/-37.8	0,9,2193	124.0	109.0	114.0		1601,1652	5.5	1.0	11	dbSNP_134	114	38,8558	26.3+/-74.7	0,38,4260	yes	missense,missense	PAMR1	NM_001001991.1,NM_015430.2	152,152	0,47,6453	AA,AT,TT		0.4421,0.2044,0.3615	probably-damaging,probably-damaging	534/721,551/738	35456085	47,12953	2202	4298	6500	SO:0001583	missense	25891	exon11			TTCTCATCCCGGT		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.1601A>T	11.37:g.35456085T>A	ENSP00000368158:p.Asp534Val	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	25.0	4.590479	0.86851	0.002044	0.004421	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	D;D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4;-3.4	5.52	5.52	0.82312	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.184737	0.52532	D	0.000066	D	0.95037	0.8393	L	0.46614	1.455	0.80722	D	1	D;D;P	0.76494	0.999;0.999;0.573	D;D;B	0.68039	0.946;0.955;0.369	D	0.95618	0.8678	10	0.87932	D	0	.	15.6335	0.76929	0.0:0.0:0.0:1.0	.	423;534;551	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	V	551;534;423;494;511	ENSP00000278360:D551V;ENSP00000368158:D534V;ENSP00000368156:D423V;ENSP00000433868:D494V;ENSP00000432591:D511V	ENSP00000278360:D551V	D	-	2	0	PAMR1	35412661	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.999000	0.63934	2.103000	0.63969	0.454000	0.30748	GAT	T|0.997;A|0.003	0.003	strong		0.517	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	
ECE1	1889	hgsc.bcm.edu	37	1	21564631	21564631	+	Missense_Mutation	SNP	C	C	T	rs141146885	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:21564631C>T	ENST00000374893.6	-	11	1459	c.1385G>A	c.(1384-1386)aGc>aAc	p.S462N	ECE1_ENST00000436918.2_Missense_Mutation_p.S462N|ECE1_ENST00000264205.6_Missense_Mutation_p.S459N|ECE1_ENST00000357071.4_Missense_Mutation_p.S450N|ECE1_ENST00000528294.1_5'Flank|ECE1_ENST00000415912.2_Missense_Mutation_p.S446N	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	462					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		ACTTACTATGCTCTTGCTGTC	0.562													C|||	11	0.00219649	0.0	0.0029	5008	,	,		20400	0.0		0.005	False		,,,				2504	0.0041				p.S462N		Atlas-SNP	.											.	ECE1	76	.	0			c.G1385A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER,ASN/SER	4,4402	8.1+/-20.4	0,4,2199	99.0	84.0	89.0		1349,1337,1376,1385	0.5	1.0	1	dbSNP_134	89	34,8566	22.2+/-67.0	0,34,4266	yes	missense,missense,missense,missense	ECE1	NM_001113347.1,NM_001113348.1,NM_001113349.1,NM_001397.2	46,46,46,46	0,38,6465	TT,TC,CC		0.3953,0.0908,0.2922	benign,benign,benign,benign	450/759,446/755,459/768,462/771	21564631	38,12968	2203	4300	6503	SO:0001583	missense	1889	exon11			ACTATGCTCTTGC	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.1385G>A	1.37:g.21564631C>T	ENSP00000364028:p.Ser462Asn	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	42	0.636364	NM_001397	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Missense_Mutation	SNP	ENST00000374893.6	37	CCDS215.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	10.13	1.264616	0.23136	9.08E-4	0.003953	ENSG00000117298	ENST00000415912;ENST00000357071;ENST00000374893;ENST00000436918;ENST00000264205	T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79;-0.79	5.55	0.51	0.16983	Peptidase M13 (1);Metallopeptidase, catalytic domain (1);	0.508327	0.24544	N	0.037610	T	0.37433	0.1003	N	0.11064	0.09	0.25372	N	0.988695	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.0	T	0.12604	-1.0541	10	0.29301	T	0.29	-25.8126	1.2783	0.02035	0.1351:0.2448:0.14:0.4801	.	462;446;462;450;459	B4DKB2;Q2Z2K8;P42892;P42892-2;P42892-4	.;.;ECE1_HUMAN;.;.	N	446;450;462;462;459	ENSP00000405088:S446N;ENSP00000349581:S450N;ENSP00000364028:S462N;ENSP00000388439:S462N;ENSP00000264205:S459N	ENSP00000264205:S459N	S	-	2	0	ECE1	21437218	0.967000	0.33354	0.994000	0.49952	0.749000	0.42624	0.750000	0.26334	-0.090000	0.12462	-0.302000	0.09304	AGC	C|0.997;T|0.003	0.003	strong		0.562	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397	
PRSS58	136541	hgsc.bcm.edu	37	7	141952110	141952110	+	Silent	SNP	G	G	A	rs1052406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:141952110G>A	ENST00000552471.1	-	5	976	c.657C>T	c.(655-657)gcC>gcT	p.A219A	PRSS58_ENST00000547058.2_Silent_p.A219A			Q8IYP2	PRS58_HUMAN	protease, serine, 58	219	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						TGCCAACATCGGCTCTCAAAA	0.428													G|||	1030	0.205671	0.2088	0.2277	5008	,	,		17409	0.0089		0.3469	False		,,,				2504	0.2434				p.A219A		Atlas-SNP	.											.	PRSS58	41	.	0			c.C657T						PASS	.	G		1072,3334	390.7+/-327.8	121,830,1252	61.0	66.0	64.0		657	-4.1	1.0	7	dbSNP_86	64	3212,5388	484.6+/-371.4	603,2006,1691	no	coding-synonymous	PRSS58	NM_001001317.3		724,2836,2943	AA,AG,GG		37.3488,24.3305,32.9386		219/242	141952110	4284,8722	2203	4300	6503	SO:0001819	synonymous_variant	136541	exon6			AACATCGGCTCTC		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.657C>T	7.37:g.141952110G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_001001317	B3KVJ6|D3DXD2	Silent	SNP	ENST00000552471.1	37	CCDS5871.1																																																																																			G|0.709;A|0.291	0.291	strong		0.428	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317	
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 GAIIx	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	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	110	65	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		
ZFPM1	161882	hgsc.bcm.edu	37	16	88599659	88599659	+	Missense_Mutation	SNP	G	G	T	rs71395304	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88599659G>T	ENST00000319555.3	+	10	1615	c.1293G>T	c.(1291-1293)aaG>aaT	p.K431N	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	431					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	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)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		TGGACAGAAAGGCCCTGGCCG	0.721													G|||	612	0.122204	0.0091	0.1398	5008	,	,		9175	0.3294		0.0915	False		,,,				2504	0.0808				p.K431N	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											.	ZFPM1	32	.	0			c.G1293T						PASS	.	G	ASN/LYS	61,3871		0,61,1905	4.0	5.0	4.0		1293	-1.2	0.1	16	dbSNP_130	4	544,7434		10,524,3455	yes	missense	ZFPM1	NM_153813.2	94	10,585,5360	TT,TG,GG		6.8188,1.5514,5.0798	probably-damaging	431/1007	88599659	605,11305	1966	3989	5955	SO:0001583	missense	161882	exon10			CAGAAAGGCCCTG	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.1293G>T	16.37:g.88599659G>T	ENSP00000326630:p.Lys431Asn	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_153813		Missense_Mutation	SNP	ENST00000319555.3	37	CCDS32502.1	308	0.14102564102564102	9	0.018292682926829267	49	0.13535911602209943	192	0.3356643356643357	58	0.07651715039577836	G	10.12	1.262467	0.23051	0.015514	0.068188	ENSG00000179588	ENST00000319555	T	0.08008	3.14	3.39	-1.17	0.09648	.	1.163550	0.06454	U	0.728227	T	0.00012	0.0000	L	0.60455	1.87	0.40357	P	0.02080599999999999	D	0.69078	0.997	P	0.57911	0.829	T	0.41161	-0.9524	9	0.42905	T	0.14	-7.9024	6.4423	0.21856	0.5249:0.0:0.4751:0.0	.	431	Q8IX07	FOG1_HUMAN	N	431	ENSP00000326630:K431N	ENSP00000326630:K431N	K	+	3	2	ZFPM1	87127160	0.522000	0.26266	0.089000	0.20774	0.599000	0.36880	0.335000	0.19806	-0.105000	0.12132	0.289000	0.19496	AAG	G|0.858;T|0.142	0.142	strong		0.721	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		
STX2	2054	hgsc.bcm.edu	37	12	131306314	131306314	+	Missense_Mutation	SNP	C	C	G	rs17564	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:131306314C>G	ENST00000392373.2	-	3	219	c.125G>C	c.(124-126)aGt>aCt	p.S42T	STX2_ENST00000261653.6_Missense_Mutation_p.S42T	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	42			S -> T (in dbSNP:rs6486602).		acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		TTTATCAATACTGTTTCTAAT	0.383													C|||	3025	0.604034	0.2141	0.6499	5008	,	,		17814	0.872		0.6571	False		,,,				2504	0.7679				p.S42T		Atlas-SNP	.											.	STX2	66	.	0			c.G125C						PASS	.	C	THR/SER,THR/SER	1217,3189	421.9+/-339.5	176,865,1162	148.0	133.0	138.0		125,125	-0.5	0.0	12	dbSNP_116	138	5651,2949	667.2+/-402.4	1856,1939,505	yes	missense,missense	STX2	NM_001980.2,NM_194356.1	58,58	2032,2804,1667	GG,GC,CC		34.2907,27.6214,47.1936	benign,benign	42/288,42/289	131306314	6868,6138	2203	4300	6503	SO:0001583	missense	2054	exon3			TCAATACTGTTTC	D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"""epimorphin"""	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.125G>C	12.37:g.131306314C>G	ENSP00000376178:p.Ser42Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_194356	Q86VW8	Missense_Mutation	SNP	ENST00000392373.2	37	CCDS9270.1	1345	0.6158424908424909	110	0.22357723577235772	223	0.6160220994475138	501	0.8758741258741258	511	0.6741424802110818	C	2.614	-0.290165	0.05568	0.276214	0.657093	ENSG00000111450	ENST00000261653;ENST00000392373	T;T	0.17370	2.28;2.28	4.48	-0.508	0.11980	t-SNARE (1);Syntaxin, N-terminal (2);	0.633406	0.17716	N	0.164408	T	0.00012	0.0000	N	0.25485	0.75	0.80722	P	0.0	B;B;B	0.32893	0.332;0.185;0.389	B;B;B	0.36766	0.076;0.034;0.232	T	0.18023	-1.0350	9	0.15499	T	0.54	-21.5042	5.4155	0.16372	0.0:0.5118:0.1425:0.3457	rs6486602;rs11551010;rs52823741;rs6486602	42;42;42	P32856-3;P32856-2;P32856	.;.;STX2_HUMAN	T	42	ENSP00000261653:S42T;ENSP00000376178:S42T	ENSP00000261653:S42T	S	-	2	0	STX2	129872267	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.070000	0.11523	0.006000	0.14734	-1.786000	0.00637	AGT	C|0.443;G|0.557	0.557	strong		0.383	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356	
NUAK2	81788	hgsc.bcm.edu	37	1	205273100	205273100	+	Silent	SNP	G	G	A	rs56091501	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205273100G>A	ENST00000367157.3	-	7	1491	c.1365C>T	c.(1363-1365)cgC>cgT	p.R455R		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AGCCAGACTCGCGCTGTCGGG	0.637													G|||	130	0.0259585	0.0008	0.0576	5008	,	,		16471	0.003		0.0586	False		,,,				2504	0.0276				p.R455R		Atlas-SNP	.											NUAK2_ENST00000367157,NS,carcinoma,0,2	NUAK2	107	2	0			c.C1365T						scavenged	.	G		46,4360	42.3+/-75.8	1,44,2158	29.0	29.0	29.0		1365	-0.7	1.0	1	dbSNP_129	29	488,8112	136.5+/-193.6	13,462,3825	no	coding-synonymous	NUAK2	NM_030952.1		14,506,5983	AA,AG,GG		5.6744,1.044,4.1058		455/629	205273100	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	81788	exon7			AGACTCGCGCTGT	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1365C>T	1.37:g.205273100G>A		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_030952		Silent	SNP	ENST00000367157.3	37	CCDS1453.1																																																																																			G|0.962;A|0.038	0.038	strong		0.637	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
IRX3	79191	hgsc.bcm.edu	37	16	54318172	54318172	+	Missense_Mutation	SNP	C	C	A	rs1126960	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:54318172C>A	ENST00000329734.3	-	3	2149	c.1437G>T	c.(1435-1437)caG>caT	p.Q479H		NM_024336.2	NP_077312.2	P78415	IRX3_HUMAN	iroquois homeobox 3	479			Q -> H (in dbSNP:rs1126960).		mesoderm development (GO:0007498)|metanephros development (GO:0001656)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of neuron differentiation (GO:0045666)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|soft_tissue(1)|urinary_tract(1)	14						TGGGCACGGGCTGGAAAGCTG	0.607													C|||	774	0.154553	0.1732	0.1931	5008	,	,		14474	0.0169		0.2455	False		,,,				2504	0.1503				p.Q479H	GBM(143;1830 1866 4487 4646 37383)	Atlas-SNP	.											.	IRX3	25	.	0			c.G1437T						PASS	.	C	HIS/GLN	850,3546	322.9+/-297.8	83,684,1431	49.0	45.0	46.0		1437	4.1	1.0	16	dbSNP_86	46	2090,6510	346.1+/-326.1	244,1602,2454	yes	missense	IRX3	NM_024336.2	24	327,2286,3885	AA,AC,CC		24.3023,19.3358,22.6223	benign	479/502	54318172	2940,10056	2198	4300	6498	SO:0001583	missense	79191	exon3			CACGGGCTGGAAA	U90308	CCDS10750.1	16q12.2	2011-06-20	2007-07-13		ENSG00000177508	ENSG00000177508		"""Homeoboxes / TALE class"""	14360	protein-coding gene	gene with protein product		612985					Standard	NM_024336		Approved	IRX-1	uc002eht.1	P78415	OTTHUMG00000133200	ENST00000329734.3:c.1437G>T	16.37:g.54318172C>A	ENSP00000331608:p.Gln479His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_024336	Q7Z4A4|Q7Z4A5|Q8IVC6	Missense_Mutation	SNP	ENST00000329734.3	37	CCDS10750.1	366	0.16758241758241757	87	0.17682926829268292	78	0.2154696132596685	9	0.015734265734265736	192	0.2532981530343008	C	14.42	2.529864	0.45073	0.193358	0.243023	ENSG00000177508	ENST00000329734	T	0.54279	0.58	5.19	4.1	0.47936	.	0.637907	0.15331	N	0.268038	T	0.00012	0.0000	L	0.35854	1.095	0.35136	P	0.23153999999999997	B	0.21225	0.053	B	0.16722	0.016	T	0.07520	-1.0768	9	0.51188	T	0.08	-3.0069	7.686	0.28540	0.0:0.7114:0.0:0.2886	rs1126960;rs3182332;rs16953308;rs17366063;rs17416771	479	P78415	IRX3_HUMAN	H	479	ENSP00000331608:Q479H	ENSP00000331608:Q479H	Q	-	3	2	IRX3	52875673	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.377000	0.20552	1.058000	0.40530	0.555000	0.69702	CAG	T|0.000;G|0.000;C|0.792;A|0.208	0.208	strong		0.607	IRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256910.2		
FRAS1	80144	hgsc.bcm.edu	37	4	79385632	79385632	+	Silent	SNP	C	C	T	rs13123710	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:79385632C>T	ENST00000264895.6	+	49	7364	c.6924C>T	c.(6922-6924)gtC>gtT	p.V2308V		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2308					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTCACCCTGTCGATGATTCGC	0.527													C|||	122	0.024361	0.0061	0.036	5008	,	,		22333	0.001		0.0646	False		,,,				2504	0.0235				p.V2308V		Atlas-SNP	.											.	FRAS1	779	.	0			c.C6924T						PASS	.	C		69,4059		2,65,1997	133.0	128.0	129.0		6924	3.8	1.0	4	dbSNP_121	129	679,7745		31,617,3564	no	coding-synonymous	FRAS1	NM_025074.6		33,682,5561	TT,TC,CC		8.0603,1.6715,5.9592		2308/4013	79385632	748,11804	2064	4212	6276	SO:0001819	synonymous_variant	80144	exon49			CCCTGTCGATGAT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.6924C>T	4.37:g.79385632C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	71	0.03250915750915751	3	0.006097560975609756	14	0.03867403314917127	0	0.0	54	0.0712401055408971	C	1.028	-0.682839	0.03353	0.016715	0.080603	ENSG00000138759	ENST00000512123	.	.	.	5.48	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6598	0.51339	0.0:0.2548:0.6168:0.1283	rs13123710;rs13123710	.	.	.	X	537	.	.	R	+	1	2	FRAS1	79604656	1.000000	0.71417	1.000000	0.80357	0.002000	0.02628	2.680000	0.46918	0.702000	0.31825	-0.839000	0.03059	CGA	C|0.962;T|0.038	0.038	strong		0.527	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MUC2	4583	hgsc.bcm.edu	37	11	1075747	1075747	+	Missense_Mutation	SNP	T	T	C	rs2856111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1075747T>C	ENST00000441003.2	+	2	200	c.173T>C	c.(172-174)cTc>cCc	p.L58P	MUC2_ENST00000359061.5_Missense_Mutation_p.L58P	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	58	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.		L -> P (in dbSNP:rs2856111).		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)	TTCCCCGGCCTCTGCGACTAC	0.647													T|||	1359	0.271366	0.4062	0.1052	5008	,	,		16777	0.4375		0.1362	False		,,,				2504	0.1748				p.L58P		Atlas-SNP	.											.	MUC2	614	.	0			c.T173C						PASS	.	T	PRO/LEU	1396,2748		255,886,931	24.0	29.0	27.0		173	3.9	1.0	11	dbSNP_100	27	1082,7336		79,924,3206	yes	missense	MUC2	NM_002457.2	98	334,1810,4137	CC,CT,TT		12.8534,33.6873,19.7262	probably-damaging	58/2813	1075747	2478,10084	2072	4209	6281	SO:0001583	missense	4583	exon2			CCGGCCTCTGCGA	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.173T>C	11.37:g.1075747T>C	ENSP00000415183:p.Leu58Pro	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	109	63	0.577982	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		589	0.2696886446886447	214	0.4349593495934959	33	0.09116022099447514	237	0.4143356643356643	105	0.13852242744063326	T	11.43	1.637716	0.29157	0.336873	0.128534	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.58210	0.35;0.35	3.94	3.94	0.45596	.	0.806126	0.10627	U	0.652652	T	0.00012	0.0000	M	0.78456	2.415	0.22199	P	0.999297546	D	0.69078	0.997	D	0.75484	0.986	T	0.31447	-0.9943	9	0.46703	T	0.11	.	12.7996	0.57578	0.0:0.0:0.0:1.0	rs2856111;rs60177945;rs2856111	58	E7EUV1	.	P	58	ENSP00000415183:L58P;ENSP00000351956:L58P	ENSP00000351956:L58P	L	+	2	0	MUC2	1065747	0.013000	0.17824	0.998000	0.56505	0.622000	0.37654	1.613000	0.36900	1.429000	0.47314	0.459000	0.35465	CTC	T|0.739;C|0.261	0.261	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZNF211	10520	hgsc.bcm.edu	37	19	58153009	58153009	+	Silent	SNP	C	C	T	rs3746217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58153009C>T	ENST00000347302.3	+	3	1334	c.1155C>T	c.(1153-1155)atC>atT	p.I385I	ZNF211_ENST00000299871.5_Silent_p.I450I|ZNF211_ENST00000254182.7_Silent_p.I376I|ZNF211_ENST00000420680.1_Silent_p.I389I|ZNF211_ENST00000240731.4_Silent_p.I398I|ZNF211_ENST00000544273.1_Silent_p.I397I|ZNF211_ENST00000541801.1_Silent_p.I376I|ZNF211_ENST00000391703.3_Silent_p.I324I	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	385					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(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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;0.026)		TTAGCCTGATCTACCACCAGA	0.473													T|||	1072	0.214058	0.2352	0.1297	5008	,	,		22138	0.3214		0.159	False		,,,				2504	0.1912				p.I450I		Atlas-SNP	.											.	ZNF211	78	.	0			c.C1350T						PASS	.	T	,	979,3427	731.6+/-410.3	117,745,1341	70.0	76.0	74.0		1194,1155	-1.4	0.0	19	dbSNP_107	74	1346,7254	756.1+/-407.5	97,1152,3051	no	coding-synonymous,coding-synonymous	ZNF211	NM_006385.3,NM_198855.2	,	214,1897,4392	TT,TC,CC		15.6512,22.2197,17.8764	,	398/578,385/565	58153009	2325,10681	2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			CCTGATCTACCAC	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1155C>T	19.37:g.58153009C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	37	CCDS12957.1																																																																																			C|0.789;T|0.211	0.211	strong		0.473	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
SNX30	401548	hgsc.bcm.edu	37	9	115598610	115598610	+	Missense_Mutation	SNP	A	A	G	rs76424583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:115598610A>G	ENST00000374232.3	+	5	899	c.735A>G	c.(733-735)atA>atG	p.I245M		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	245					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)			large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						TTGCTGCCATAGGTGACTACT	0.498													A|||	283	0.0565096	0.0023	0.0793	5008	,	,		21203	0.0655		0.1093	False		,,,				2504	0.0501				p.I245M		Atlas-SNP	.											.	SNX30	32	.	0			c.A735G						PASS	.	A	MET/ILE	95,3805		1,93,1856	116.0	114.0	115.0		735	-8.6	0.3	9	dbSNP_131	115	800,7484		41,718,3383	yes	missense	SNX30	NM_001012994.1	10	42,811,5239	GG,GA,AA		9.6572,2.4359,7.3457	benign	245/438	115598610	895,11289	1950	4142	6092	SO:0001583	missense	401548	exon5			TGCCATAGGTGAC	AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"""Sorting nexins"""	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.735A>G	9.37:g.115598610A>G	ENSP00000363349:p.Ile245Met	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_001012994		Missense_Mutation	SNP	ENST00000374232.3	37	CCDS43865.1	143	0.06547619047619048	1	0.0020325203252032522	29	0.08011049723756906	30	0.05244755244755245	83	0.10949868073878628	A	3.654	-0.070970	0.07228	0.024359	0.096572	ENSG00000148158	ENST00000374232	T	0.23754	1.89	5.8	-8.61	0.00885	.	0.139939	0.64402	D	0.000007	T	0.00109	0.0003	N	0.02539	-0.55	0.23758	P	0.99692116	B	0.10296	0.003	B	0.09377	0.004	T	0.11494	-1.0585	9	0.31617	T	0.26	.	2.4477	0.04510	0.3115:0.3028:0.0648:0.3209	.	245	Q5VWJ9	SNX30_HUMAN	M	245	ENSP00000363349:I245M	ENSP00000363349:I245M	I	+	3	3	SNX30	114638431	0.037000	0.19845	0.311000	0.25182	0.711000	0.40976	-0.830000	0.04410	-1.388000	0.02092	-0.327000	0.08410	ATA	A|0.922;G|0.078	0.078	strong		0.498	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31238929	31238929	+	Silent	SNP	C	C	G	rs2308592	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31238929C>G	ENST00000376228.5	-	3	554	c.540G>C	c.(538-540)ctG>ctC	p.L180L	HLA-C_ENST00000383329.3_Silent_p.L180L	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	180	Alpha-2.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGTAGGCTCTCAGCTGCTCCG	0.692																																					p.L180L		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,-1,2	HLA-C	92	2	0			c.G540C						scavenged	.						44.0	31.0	36.0					6																	31238929		2196	4292	6488	SO:0001819	synonymous_variant	3107	exon3			GGCTCTCAGCTGC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.540G>C	6.37:g.31238929C>G		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	155	14	0.0903226	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	5.596	0.294742	0.10567	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	-5.62	0.02481	.	.	.	.	.	T	0.06600	0.0169	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.26744	-1.0094	4	.	.	.	.	3.9618	0.09413	0.0987:0.4803:0.1638:0.2572	rs41547419	.	.	.	Q	180	.	.	E	-	1	0	HLA-C	31346908	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.653000	0.00856	-1.717000	0.01385	0.305000	0.20034	GAG	CCG|0.500;GTC|0.500	.	alt		0.692	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
UNC13A	23025	hgsc.bcm.edu	37	19	17746940	17746940	+	Silent	SNP	C	C	T	rs77267738	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17746940C>T	ENST00000519716.2	-	26	3107	c.3108G>A	c.(3106-3108)gaG>gaA	p.E1036E	UNC13A_ENST00000551649.1_Silent_p.E1036E|UNC13A_ENST00000252773.7_Silent_p.E1036E|UNC13A_ENST00000552293.1_Silent_p.E1036E|UNC13A_ENST00000428389.2_Silent_p.E1124E|UNC13A_ENST00000550896.1_Silent_p.E1034E	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1036					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GCCCCTGTTCCTCTGGGAGAA	0.517													c|||	116	0.0231629	0.0061	0.0504	5008	,	,		19614	0.001		0.0656	False		,,,				2504	0.0061				p.E1036E		Atlas-SNP	.											.	UNC13A	299	.	0			c.G3108A						PASS	.	C		56,3772		0,56,1858	64.0	61.0	62.0		3108	3.5	1.0	19	dbSNP_132	62	498,7780		16,466,3657	no	coding-synonymous	UNC13A	NM_001080421.2		16,522,5515	TT,TC,CC		6.0159,1.4629,4.5762		1036/1704	17746940	554,11552	1914	4139	6053	SO:0001819	synonymous_variant	23025	exon25			CTGTTCCTCTGGG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3108G>A	19.37:g.17746940C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	152	77	0.506579	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			C|0.958;T|0.042	0.042	strong		0.517	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
NHLRC2	374354	hgsc.bcm.edu	37	10	115644040	115644040	+	Missense_Mutation	SNP	G	G	A	rs7913176	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:115644040G>A	ENST00000369301.3	+	5	1152	c.940G>A	c.(940-942)Gta>Ata	p.V314I		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	314			V -> I (in dbSNP:rs7913176).							breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		GGTGAGCACTGTAGCTGGTAT	0.388													G|||	1119	0.223442	0.121	0.2291	5008	,	,		15051	0.3125		0.2932	False		,,,				2504	0.1943				p.V314I		Atlas-SNP	.											NHLRC2,NS,carcinoma,0,1	NHLRC2	56	1	0			c.G940A						PASS	.	G	ILE/VAL	684,3722	289.8+/-280.6	64,556,1583	137.0	126.0	130.0		940	5.0	1.0	10	dbSNP_116	130	2422,6178	400.6+/-346.9	361,1700,2239	yes	missense	NHLRC2	NM_198514.3	29	425,2256,3822	AA,AG,GG		28.1628,15.5243,23.8813	benign	314/727	115644040	3106,9900	2203	4300	6503	SO:0001583	missense	374354	exon5			AGCACTGTAGCTG	AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.940G>A	10.37:g.115644040G>A	ENSP00000358307:p.Val314Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_198514	Q8N1H1|Q8N5A6	Missense_Mutation	SNP	ENST00000369301.3	37	CCDS7585.1	525	0.2403846153846154	59	0.11991869918699187	71	0.19613259668508287	178	0.3111888111888112	217	0.2862796833773087	G	13.78	2.338147	0.41398	0.155243	0.281628	ENSG00000196865	ENST00000369301	D	0.89939	-2.59	5.03	5.03	0.67393	Six-bladed beta-propeller, TolB-like (1);	0.155986	0.44285	D	0.000462	T	0.00012	0.0000	L	0.35723	1.085	0.27849	P	0.9408216	P	0.36412	0.552	B	0.25884	0.064	T	0.33599	-0.9862	9	0.07990	T	0.79	-18.5562	16.5886	0.84759	0.0:0.0:1.0:0.0	rs7913176;rs52796392;rs56430477;rs61476386;rs7913176	314	Q8NBF2	NHLC2_HUMAN	I	314	ENSP00000358307:V314I	ENSP00000358307:V314I	V	+	1	0	NHLRC2	115634030	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.574000	0.46016	2.345000	0.79718	0.479000	0.44913	GTA	G|0.771;A|0.229	0.229	strong		0.388	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514	
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 GAIIx	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-AS1_ENST00000519140.1_RNA|KIAA0196_ENST00000517845.1_Silent_p.A795A	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		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	137	70	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	
ACSM5	54988	hgsc.bcm.edu	37	16	20442562	20442562	+	Silent	SNP	C	C	T	rs78006992	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20442562C>T	ENST00000331849.4	+	10	1374	c.1227C>T	c.(1225-1227)aaC>aaT	p.N409N		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	409					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.N409N(1)		breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						ATGAGGGCAACGTCCTGCCTC	0.557																																					p.N409N		Atlas-SNP	.											ACSM5,NS,carcinoma,0,1	ACSM5	101	1	1	Substitution - coding silent(1)	kidney(1)	c.C1227T						PASS	.						157.0	135.0	142.0					16																	20442562		2203	4300	6503	SO:0001819	synonymous_variant	54988	exon10			GGGCAACGTCCTG		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1227C>T	16.37:g.20442562C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	91	8	0.0879121	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Silent	SNP	ENST00000331849.4	37	CCDS10585.1																																																																																			C|0.500;T|0.500	0.500	strong		0.557	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
POM121L2	94026	hgsc.bcm.edu	37	6	27278020	27278020	+	Missense_Mutation	SNP	C	C	A	rs16897515	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27278020C>A	ENST00000444565.1	-	1	1929	c.1930G>T	c.(1930-1932)Ggt>Tgt	p.G644C	POM121L2_ENST00000377451.2_Missense_Mutation_p.G580C	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	644										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						TTCACTACACCAAAATCCAAA	0.517													C|||	723	0.144369	0.2443	0.147	5008	,	,		21112	0.0288		0.168	False		,,,				2504	0.1022				p.G644C		Atlas-SNP	.											.	POM121L2	61	.	0			c.G1930T						PASS	.	C	CYS/GLY	346,1038		41,264,387	54.0	51.0	52.0		1930	0.8	0.0	6	dbSNP_123	52	577,2605		45,487,1059	yes	missense	POM121L2	NM_033482.3	159	86,751,1446	AA,AC,CC		18.1332,25.0,20.2146	probably-damaging	644/1036	27278020	923,3643	692	1591	2283	SO:0001583	missense	94026	exon1			CTACACCAAAATC	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.1930G>T	6.37:g.27278020C>A	ENSP00000392726:p.Gly644Cys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	55	35	0.636364	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	320	0.14652014652014653	128	0.2601626016260163	59	0.16298342541436464	10	0.017482517482517484	123	0.16226912928759896	C	15.86	2.958304	0.53400	0.25	0.181332	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.17054	2.3;2.31	3.96	0.825	0.18824	.	0.890845	0.09283	N	0.823423	T	0.15478	0.0373	L	0.42245	1.32	0.80722	P	0.0	D	0.89917	1.0	D	0.74023	0.982	T	0.08146	-1.0736	9	0.72032	D	0.01	.	5.5069	0.16858	0.0:0.5474:0.0:0.4526	rs16897515;rs16897515	644	C9J1I7	.	C	580;644	ENSP00000366671:G580C;ENSP00000392726:G644C	ENSP00000366671:G580C	G	-	1	0	POM121L2	27385999	0.002000	0.14202	0.000000	0.03702	0.640000	0.38277	1.292000	0.33342	0.148000	0.19059	-0.350000	0.07774	GGT	C|0.850;A|0.150	0.150	strong		0.517	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
VWF	7450	hgsc.bcm.edu	37	12	6153534	6153534	+	Missense_Mutation	SNP	T	T	C	rs1063856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6153534T>C	ENST00000261405.5	-	18	2619	c.2365A>G	c.(2365-2367)Acc>Gcc	p.T789A		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	789	E1.|TIL 3.		T -> A (in dbSNP:rs1063856). {ECO:0000269|PubMed:2864688}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CACGTTTTGGTACACTCGAGC	0.602													C|||	1684	0.336262	0.6377	0.2406	5008	,	,		20583	0.0913		0.3668	False		,,,				2504	0.2178				p.T789A		Atlas-SNP	.											.	VWF	338	.	0			c.A2365G						PASS	.	C	ALA/THR	2504,1902	544.9+/-376.7	701,1102,400	109.0	91.0	97.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2365	2.2	1.0	12	dbSNP_86	97	3074,5526	660.4+/-401.8	546,1982,1772	yes	missense	VWF	NM_000552.3	58	1247,3084,2172	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	35.7442,43.1684,42.8879	benign	789/2814	6153534	5578,7428	2203	4300	6503	SO:0001583	missense	7450	exon18			TTTTGGTACACTC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2365A>G	12.37:g.6153534T>C	ENSP00000261405:p.Thr789Ala	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	749	0.34294871794871795	321	0.6524390243902439	98	0.27071823204419887	46	0.08041958041958042	284	0.37467018469656993	C	3.009	-0.204232	0.06180	0.568316	0.357442	ENSG00000110799	ENST00000261405	D	0.90261	-2.64	4.19	2.17	0.27698	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.206482	0.24238	N	0.040287	T	0.00012	0.0000	N	0.01352	-0.895	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40459	-0.9562	9	0.02654	T	1	.	9.2439	0.37513	0.0:0.6494:0.0:0.3506	rs1063856;rs2228318;rs3204894;rs52799826;rs61544748;rs1063856	789	P04275	VWF_HUMAN	A	789	ENSP00000261405:T789A	ENSP00000261405:T789A	T	-	1	0	VWF	6023795	0.995000	0.38212	0.995000	0.50966	0.907000	0.53573	0.890000	0.28295	0.446000	0.26666	-0.213000	0.12676	ACC	T|0.617;C|0.383;N|0.000	0.383	strong		0.602	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
SPPL2C	162540	hgsc.bcm.edu	37	17	43922942	43922942	+	Missense_Mutation	SNP	T	T	C	rs62621252	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43922942T>C	ENST00000329196.5	+	1	687	c.670T>C	c.(670-672)Tct>Cct	p.S224P	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	224						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										AGGAGGGGGGTCTGGTGGTCA	0.647													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		18327	0.001		0.2396	False		,,,				2504	0.0613				p.S224P		Atlas-SNP	.											.	.	.	.	0			c.T670C						PASS	.	C	PRO/SER	202,4204		5,192,2006	37.0	39.0	38.0		670	0.8	0.0	17	dbSNP_129	38	1909,6689		217,1475,2607	yes	missense	IMP5	NM_175882.2	74	222,1667,4613	CC,CT,TT		22.2028,4.5847,16.2335	benign	224/685	43922942	2111,10893	2203	4299	6502	SO:0001583	missense	162540	exon1			GGGGGGTCTGGTG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.670T>C	17.37:g.43922942T>C	ENSP00000332488:p.Ser224Pro	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	33	32	0.969697	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	0.013	-1.632921	0.00806	0.045847	0.222028	ENSG00000185294	ENST00000329196	T	0.05258	3.47	5.24	0.827	0.18835	.	0.807093	0.10116	N	0.714047	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48885	-0.8995	9	0.26408	T	0.33	-34.9333	1.2817	0.02042	0.1516:0.4416:0.1475:0.2594	rs62621252	224	Q8IUH8	IMP5_HUMAN	P	224	ENSP00000332488:S224P	ENSP00000332488:S224P	S	+	1	0	AC217771.1	41278722	0.062000	0.20869	0.006000	0.13384	0.004000	0.04260	0.475000	0.22164	0.358000	0.24211	-0.119000	0.15052	TCT	T|0.851;C|0.149	0.149	strong		0.647	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
COL24A1	255631	hgsc.bcm.edu	37	1	86590948	86590948	+	Silent	SNP	A	A	G	rs11161746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:86590948A>G	ENST00000370571.2	-	3	1437	c.1071T>C	c.(1069-1071)agT>agC	p.S357S	COL24A1_ENST00000436319.1_Silent_p.S357S	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	357					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)		TTTTTGCCTCACTGATGCGAT	0.408													A|||	692	0.138179	0.0794	0.1614	5008	,	,		18266	0.0605		0.165	False		,,,				2504	0.2536				p.S357S		Atlas-SNP	.											.	COL24A1	202	.	0			c.T1071C						PASS	.	A		333,3541		16,301,1620	147.0	129.0	135.0		1071	-5.3	0.0	1	dbSNP_120	135	1232,7022		102,1028,2997	no	coding-synonymous	COL24A1	NM_152890.5		118,1329,4617	GG,GA,AA		14.9261,8.5958,12.904		357/1715	86590948	1565,10563	1937	4127	6064	SO:0001819	synonymous_variant	255631	exon3			TGCCTCACTGATG	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.1071T>C	1.37:g.86590948A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	184	87	0.472826	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	37	CCDS41353.1																																																																																			A|0.886;G|0.114	0.114	strong		0.408	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
KIF13A	63971	hgsc.bcm.edu	37	6	17781450	17781450	+	Silent	SNP	G	G	A	rs942376	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:17781450G>A	ENST00000259711.6	-	30	3732	c.3627C>T	c.(3625-3627)agC>agT	p.S1209S	KIF13A_ENST00000378843.2_Silent_p.S1196S|KIF13A_ENST00000378816.5_Silent_p.S1209S|KIF13A_ENST00000378826.2_Silent_p.S1209S|KIF13A_ENST00000378814.5_Silent_p.S1196S	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1209					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			AGAAAAACTGGCTGCCATGCT	0.512													G|||	822	0.164137	0.0598	0.2997	5008	,	,		15964	0.2014		0.2097	False		,,,				2504	0.1237				p.S1209S		Atlas-SNP	.											.	KIF13A	276	.	0			c.C3627T						PASS	.	G	,,,	349,3525		18,313,1606	93.0	93.0	93.0		3627,3588,3588,3627	3.1	1.0	6	dbSNP_86	93	1579,6727		160,1259,2734	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	178,1572,4340	AA,AG,GG		19.0104,9.0088,15.8292	,,,	1209/1771,1196/1758,1196/1750,1209/1806	17781450	1928,10252	1937	4153	6090	SO:0001819	synonymous_variant	63971	exon30			AAACTGGCTGCCA	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.3627C>T	6.37:g.17781450G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	31	21	0.677419	NM_001105566	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1	419	0.19184981684981686	37	0.07520325203252033	94	0.2596685082872928	137	0.2395104895104895	151	0.19920844327176782	G	10.33	1.320761	0.23994	0.090088	0.190104	ENSG00000137177	ENST00000358380	.	.	.	5.29	3.07	0.35406	.	.	.	.	.	T	0.26702	0.0653	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09662	-1.0664	3	.	.	.	.	7.1879	0.25809	0.3069:0.0:0.6931:0.0	rs942376;rs3734233;rs58734397;rs942376	.	.	.	V	603	.	.	A	-	2	0	KIF13A	17889429	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.524000	0.35942	1.333000	0.45449	0.561000	0.74099	GCC	G|0.825;A|0.175	0.175	strong		0.512	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
IQCA1	79781	hgsc.bcm.edu	37	2	237374309	237374309	+	Silent	SNP	C	C	T	rs35432941	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:237374309C>T	ENST00000409907.3	-	6	1039	c.765G>A	c.(763-765)caG>caA	p.Q255Q	IQCA1_ENST00000431676.2_Silent_p.Q255Q|IQCA1_ENST00000309507.5_Silent_p.Q251Q	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	255							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						CCTTTTCAGCCTGGATTACTG	0.428													C|||	372	0.0742812	0.0076	0.0764	5008	,	,		19184	0.001		0.1849	False		,,,				2504	0.1247				p.Q262Q		Atlas-SNP	.											.	IQCA1	170	.	0			c.G786A						PASS	.	C		140,3670		5,130,1770	105.0	93.0	97.0		765	-0.5	0.1	2	dbSNP_126	97	1735,6525		174,1387,2569	no	coding-synonymous	IQCA1	NM_024726.3		179,1517,4339	TT,TC,CC		21.0048,3.6745,15.5344		255/823	237374309	1875,10195	1905	4130	6035	SO:0001819	synonymous_variant	79781	exon6			TTCAGCCTGGATT	AK026180	CCDS46549.1, CCDS59441.1, CCDS74677.1	2q37.3	2014-07-18	2008-07-02	2008-07-02	ENSG00000132321	ENSG00000132321		"""ATPases / AAA-type"""	26195	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 11"""		"""IQ motif containing with AAA domain"""	IQCA		23427265	Standard	NM_024726		Approved	FLJ22527, DRC11	uc002vwb.3	Q86XH1	OTTHUMG00000153058	ENST00000409907.3:c.765G>A	2.37:g.237374309C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	130	60	0.461538	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Silent	SNP	ENST00000409907.3	37	CCDS46549.1	177	0.08104395604395605	6	0.012195121951219513	26	0.0718232044198895	0	0.0	145	0.19129287598944592	C	0.806	-0.753650	0.03041	0.036745	0.210048	ENSG00000132321	ENST00000418802	.	.	.	5.37	-0.467	0.12150	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.50313	P	1.32000000000021E-4	.	.	.	.	.	.	T	0.29181	-1.0020	3	.	.	.	.	0.1116	0.00057	0.2791:0.2582:0.2037:0.259	rs35432941;rs62189792	.	.	.	S	274	.	.	G	-	1	0	IQCA1	237039048	0.928000	0.31464	0.108000	0.21378	0.302000	0.27658	0.225000	0.17757	-0.011000	0.14247	0.563000	0.77884	GGC	C|0.896;T|0.104	0.104	strong		0.428	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726	
MXRA5	25878	hgsc.bcm.edu	37	X	3239545	3239545	+	Missense_Mutation	SNP	C	C	T	rs1726199	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3239545C>T	ENST00000217939.6	-	5	4335	c.4181G>A	c.(4180-4182)gGc>gAc	p.G1394D		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1394			G -> D (in dbSNP:rs1726199). {ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				AACAGGTATGCCTGTCTGTAG	0.488													T|||	2723	0.721325	0.6104	0.5115	3775	,	,		14108	0.5595		0.5268	False		,,,				2504	0.4775				p.G1394D		Atlas-SNP	.											.	MXRA5	815	.	0			c.G4181A						PASS	.	T	ASP/GLY	2945,890		969,569,438,94,133	34.0	33.0	33.0		4181	1.7	0.1	X	dbSNP_89	33	4340,2388		1020,1107,1193,301,679	yes	missense	MXRA5	NM_015419.3	94	1989,1676,1631,395,812	TT,TC,T,CC,C		35.4935,23.2073,31.0329	benign	1394/2829	3239545	7285,3278	2203	4300	6503	SO:0001583	missense	25878	exon5			GGTATGCCTGTCT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.4181G>A	X.37:g.3239545C>T	ENSP00000217939:p.Gly1394Asp	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	1198	0.7221217600964437	214	0.6993464052287581	129	0.49615384615384617	206	0.5885714285714285	272	0.5291828793774319	t	0.001	-3.030648	0.00041	0.767927	0.645065	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.61158	0.13	2.92	1.69	0.24217	.	0.413025	0.17741	N	0.163572	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42849	-0.9427	9	0.02654	T	1	.	7.3365	0.26613	0.0:0.7527:0.0:0.2473	rs1726199;rs60762451;rs1726199	1394	Q9NR99	MXRA5_HUMAN	D	1394	ENSP00000217939:G1394D	ENSP00000217939:G1394D	G	-	2	0	MXRA5	3249545	0.001000	0.12720	0.127000	0.21898	0.068000	0.16541	-0.017000	0.12590	-0.241000	0.09681	-0.573000	0.04149	GGC	0|0.013;T|0.704	0.704	strong		0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
REG1B	5968	hgsc.bcm.edu	37	2	79313990	79313990	+	Missense_Mutation	SNP	C	C	T	rs62640882	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:79313990C>T	ENST00000305089.3	-	3	211	c.131G>A	c.(130-132)cGc>cAc	p.R44H		NM_006507.3	NP_006498.1	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta	44	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell proliferation (GO:0008283)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						GCAGTAGGAGCGATAGGCATT	0.507													C|||	57	0.0113818	0.0	0.0086	5008	,	,		17949	0.0		0.0437	False		,,,				2504	0.0072				p.R44H		Atlas-SNP	.											.	REG1B	83	.	0			c.G131A						PASS	.	C	HIS/ARG	25,4381	31.7+/-61.6	0,25,2178	156.0	152.0	154.0		131	-0.3	0.0	2	dbSNP_129	154	330,8270	115.2+/-175.0	12,306,3982	yes	missense	REG1B	NM_006507.3	29	12,331,6160	TT,TC,CC		3.8372,0.5674,2.7295	benign	44/167	79313990	355,12651	2203	4300	6503	SO:0001583	missense	5968	exon3			TAGGAGCGATAGG		CCDS1963.1	2p12	2008-06-04	2008-06-04		ENSG00000172023	ENSG00000172023			9952	protein-coding gene	gene with protein product	"""lithostathine 1 beta"", ""secretory pancreatic stone protein 2"""	167771	"""regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)"""			8110835	Standard	NM_006507		Approved	REGL, PSPS2, REGH, REGI-BETA	uc002sny.2	P48304	OTTHUMG00000130019	ENST00000305089.3:c.131G>A	2.37:g.79313990C>T	ENSP00000303206:p.Arg44His	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	113	31	0.274336	NM_006507		Missense_Mutation	SNP	ENST00000305089.3	37	CCDS1963.1	42	0.019230769230769232	0	0.0	5	0.013812154696132596	0	0.0	37	0.048812664907651716	c	10.83	1.459885	0.26248	0.005674	0.038372	ENSG00000172023	ENST00000305089	T	0.08370	3.1	3.74	-0.261	0.12963	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.582077	0.14158	N	0.337555	T	0.00724	0.0024	L	0.45352	1.415	0.09310	N	1	P;P	0.35348	0.496;0.496	B;B	0.15870	0.014;0.014	T	0.37361	-0.9709	10	0.40728	T	0.16	.	3.4587	0.07524	0.0:0.4497:0.1989:0.3515	.	44;44	Q6ICS1;P48304	.;REG1B_HUMAN	H	44	ENSP00000303206:R44H	ENSP00000303206:R44H	R	-	2	0	REG1B	79167498	0.000000	0.05858	0.001000	0.08648	0.778000	0.44026	-0.670000	0.05256	0.044000	0.15775	-0.224000	0.12420	CGC	C|0.975;T|0.025	0.025	strong		0.507	REG1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252292.2	NM_006507	
NCOA3	8202	hgsc.bcm.edu	37	20	46268493	46268493	+	Silent	SNP	A	A	G	rs2076546	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:46268493A>G	ENST00000371998.3	+	15	3071	c.2880A>G	c.(2878-2880)acA>acG	p.T960T	NCOA3_ENST00000341724.6_Silent_p.T890T|NCOA3_ENST00000372004.3_Silent_p.T960T|NCOA3_ENST00000371997.3_Silent_p.T955T			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	960					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CTATTCCCACATTGCCTCTTC	0.488													G|||	673	0.134385	0.2549	0.0879	5008	,	,		20124	0.0933		0.0845	False		,,,				2504	0.0982				p.T960T		Atlas-SNP	.											.	NCOA3	156	.	0			c.A2880G						PASS	.	G	,,,	1039,3367	722.1+/-409.2	123,793,1287	91.0	93.0	92.0		2880,2865,2880,2880	-0.8	0.0	20	dbSNP_96	92	752,7848	784.0+/-407.6	43,666,3591	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	166,1459,4878	GG,GA,AA		8.7442,23.5815,13.7706	,,,	960/1424,955/1416,960/1421,960/1425	46268493	1791,11215	2203	4300	6503	SO:0001819	synonymous_variant	8202	exon15			TCCCACATTGCCT	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.2880A>G	20.37:g.46268493A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			A|0.863;G|0.137	0.137	strong		0.488	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
IRF1	3659	hgsc.bcm.edu	37	5	131822055	131822055	+	Silent	SNP	T	T	C	rs9282762	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131822055T>C	ENST00000245414.4	-	7	813	c.555A>G	c.(553-555)ccA>ccG	p.P185P	IRF1_ENST00000405885.2_Silent_p.P185P|IRF1_ENST00000463784.1_5'Flank	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1	185					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)		TGACAGCACATGGCGACAGTG	0.577													C|||	2036	0.40655	0.4758	0.3588	5008	,	,		19987	0.3829		0.3449	False		,,,				2504	0.4346				p.P185P		Atlas-SNP	.											.	IRF1	26	.	0			c.A555G						PASS	.	C	,	2158,2248	588.0+/-386.8	521,1116,566	72.0	70.0	71.0		,555	-7.7	0.0	5	dbSNP_118	71	2806,5794	672.0+/-402.9	460,1886,1954	no	utr-3,coding-synonymous	IRF1,C5orf56	NM_001207002.1,NM_002198.2	,	981,3002,2520	CC,CT,TT		32.6279,48.9787,38.167	,	,185/326	131822055	4964,8042	2203	4300	6503	SO:0001819	synonymous_variant	3659	exon7			AGCACATGGCGAC		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.555A>G	5.37:g.131822055T>C		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	35	22	0.628571	NM_002198	Q96GG7	Silent	SNP	ENST00000245414.4	37	CCDS4155.1																																																																																			T|0.623;C|0.377	0.377	strong		0.577	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198	
HIST3H3	8290	hgsc.bcm.edu	37	1	228612892	228612892	+	Silent	SNP	G	G	A	rs56336130	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228612892G>A	ENST00000366696.1	-	1	134	c.135C>T	c.(133-135)ggC>ggT	p.G45G		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	45					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				GCGCCACCGTGCCGGGCCGGT	0.677													g|||	217	0.0433307	0.0061	0.0519	5008	,	,		13044	0.0139		0.0746	False		,,,				2504	0.0859				p.G45G		Atlas-SNP	.											.	HIST3H3	20	.	0			c.C135T						PASS	.	G		76,4330	61.1+/-98.1	1,74,2128	52.0	58.0	56.0		135	-0.3	0.3	1	dbSNP_129	56	746,7854	172.5+/-223.2	39,668,3593	no	coding-synonymous	HIST3H3	NM_003493.2		40,742,5721	AA,AG,GG		8.6744,1.7249,6.3202		45/137	228612892	822,12184	2203	4300	6503	SO:0001819	synonymous_variant	8290	exon1			CACCGTGCCGGGC	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"""Histones / Replication-dependent"""	4778	protein-coding gene	gene with protein product		602820	"""H3 histone family, member T"", ""histone 3, H3"""	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.135C>T	1.37:g.228612892G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			G|0.942;A|0.058	0.058	strong		0.677	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493	
TLR1	7096	hgsc.bcm.edu	37	4	38798935	38798935	+	Silent	SNP	C	C	T	rs5743614	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38798935C>T	ENST00000502213.2	-	3	1747	c.1518G>A	c.(1516-1518)tcG>tcA	p.S506S	TLR1_ENST00000510552.1_5'Flank|TLR1_ENST00000308979.2_Silent_p.S506S			Q15399	TLR1_HUMAN	toll-like receptor 1	506					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						AGAAATCAGCCGATGGGTGGG	0.418													c|||	2802	0.559505	0.8404	0.4654	5008	,	,		18263	0.5992		0.2744	False		,,,				2504	0.499				p.S506S	GBM(5;216 373 40795 46382)	Atlas-SNP	.											TLR1,NS,carcinoma,-1,1	TLR1	70	1	0			c.G1518A						PASS	.						75.0	79.0	78.0					4																	38798935		2202	4280	6482	SO:0001819	synonymous_variant	7096	exon4			ATCAGCCGATGGG	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1518G>A	4.37:g.38798935C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	213	102	0.478873	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	37	CCDS33973.1																																																																																			C|0.575;T|0.425	0.425	strong		0.418	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
TMEM45B	120224	hgsc.bcm.edu	37	11	129722553	129722553	+	Missense_Mutation	SNP	C	C	T	rs558813	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:129722553C>T	ENST00000524567.1	+	2	457	c.176C>T	c.(175-177)aCt>aTt	p.T59I	TMEM45B_ENST00000281441.3_Missense_Mutation_p.T59I			Q96B21	TM45B_HUMAN	transmembrane protein 45B	59			T -> I (in dbSNP:rs558813).			integral component of membrane (GO:0016021)		p.T59I(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		TTTTCCGTCACTGGTAAGAGC	0.478													c|||	1129	0.225439	0.4539	0.1974	5008	,	,		20778	0.0952		0.165	False		,,,				2504	0.1329				p.T59I		Atlas-SNP	.											TMEM45B,NS,carcinoma,0,1	TMEM45B	25	1	1	Substitution - Missense(1)	stomach(1)	c.C176T						PASS	.	C	ILE/THR	1888,2514	544.5+/-376.5	397,1094,710	110.0	104.0	106.0		176	3.3	0.1	11	dbSNP_83	106	1571,7023	294.6+/-302.0	143,1285,2869	yes	missense	TMEM45B	NM_138788.3	89	540,2379,3579	TT,TC,CC		18.2802,42.8896,26.6159	benign	59/276	129722553	3459,9537	2201	4297	6498	SO:0001583	missense	120224	exon2			CCGTCACTGGTAA	AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.176C>T	11.37:g.129722553C>T	ENSP00000436293:p.Thr59Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	244	206	0.844262	NM_138788	A8K2L8	Missense_Mutation	SNP	ENST00000524567.1	37	CCDS8482.1	471	0.21565934065934067	219	0.4451219512195122	65	0.17955801104972377	61	0.10664335664335664	126	0.1662269129287599	c	0.672	-0.801700	0.02841	0.428896	0.182802	ENSG00000151715	ENST00000281441;ENST00000524567	T;T	0.26810	1.71;1.71	5.64	3.34	0.38264	.	0.201259	0.51477	N	0.000099	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.02654	T	1	-15.493	9.4769	0.38878	0.0:0.146:0.0:0.854	rs558813;rs3205706;rs11552100;rs17401429;rs52814728;rs57773245;rs558813	59	Q96B21	TM45B_HUMAN	I	59	ENSP00000281441:T59I;ENSP00000436293:T59I	ENSP00000281441:T59I	T	+	2	0	TMEM45B	129227763	0.311000	0.24536	0.103000	0.21229	0.003000	0.03518	2.306000	0.43673	0.411000	0.25702	-1.137000	0.01932	ACT	C|0.754;T|0.246	0.246	strong		0.478	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788	
NNT	23530	hgsc.bcm.edu	37	5	43656024	43656024	+	Silent	SNP	T	T	C	rs56193661	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:43656024T>C	ENST00000264663.5	+	15	2363	c.2142T>C	c.(2140-2142)gcT>gcC	p.A714A	NNT_ENST00000344920.4_Silent_p.A714A|NNT_ENST00000512996.2_Silent_p.A583A	NM_012343.3	NP_036475.3	Q13423	NNTM_HUMAN	nicotinamide nucleotide transhydrogenase	714					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)|proton transport (GO:0015992)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrion (GO:0005739)	NAD binding (GO:0051287)|NAD(P)+ transhydrogenase (AB-specific) activity (GO:0008750)|NAD(P)+ transhydrogenase (B-specific) activity (GO:0003957)|NAD(P)+ transhydrogenase activity (GO:0008746)|NADP binding (GO:0050661)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(7)|large_intestine(6)|liver(2)|lung(20)|ovary(3)|prostate(2)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(6;2.58e-06)					GTTTGGCAGCTGTACTTACTT	0.413													T|||	317	0.0632987	0.146	0.0375	5008	,	,		19258	0.0		0.0497	False		,,,				2504	0.0491				p.A714A		Atlas-SNP	.											.	NNT	92	.	0			c.T2142C						PASS	.	T	,	645,3761	277.5+/-273.7	40,565,1598	126.0	116.0	119.0		2142,2142	-1.0	0.9	5	dbSNP_129	119	298,8302	109.8+/-170.3	7,284,4009	no	coding-synonymous,coding-synonymous	NNT	NM_012343.3,NM_182977.2	,	47,849,5607	CC,CT,TT		3.4651,14.6391,7.2505	,	714/1087,714/1087	43656024	943,12063	2203	4300	6503	SO:0001819	synonymous_variant	23530	exon15			GGCAGCTGTACTT	U40490	CCDS3949.1	5p12	2008-02-05			ENSG00000112992	ENSG00000112992	1.6.1.1		7863	protein-coding gene	gene with protein product		607878				9271681, 9524818	Standard	NM_182977		Approved		uc003jof.3	Q13423	OTTHUMG00000096961	ENST00000264663.5:c.2142T>C	5.37:g.43656024T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_182977	Q16796|Q2TB60|Q8N3V4	Silent	SNP	ENST00000264663.5	37	CCDS3949.1																																																																																			T|0.933;C|0.067	0.067	strong		0.413	NNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214026.1	NM_182977	
UNC45A	55898	hgsc.bcm.edu	37	15	91486305	91486305	+	Silent	SNP	C	C	T	rs8034551	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:91486305C>T	ENST00000418476.2	+	8	1060	c.1020C>T	c.(1018-1020)atC>atT	p.I340I	UNC45A_ENST00000394275.2_Silent_p.I325I|UNC45A_ENST00000553671.2_3'UTR	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	340					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TCTGGGTCATCGACCAAGGTA	0.502													T|||	293	0.0585064	0.0045	0.0331	5008	,	,		19221	0.0		0.0915	False		,,,				2504	0.1759				p.I340I		Atlas-SNP	.											.	UNC45A	57	.	0			c.C1020T						PASS	.	T	,	91,4305	816.1+/-416.2	0,91,2107	61.0	65.0	63.0		975,1020	1.0	1.0	15	dbSNP_116	63	824,7772	780.0+/-407.7	40,744,3514	no	coding-synonymous,coding-synonymous	UNC45A	NM_001039675.1,NM_018671.3	,	40,835,5621	TT,TC,CC		9.5859,2.0701,7.0428	,	325/930,340/945	91486305	915,12077	2198	4298	6496	SO:0001819	synonymous_variant	55898	exon8			GGTCATCGACCAA		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.1020C>T	15.37:g.91486305C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Silent	SNP	ENST00000418476.2	37	CCDS10367.1																																																																																			C|0.944;T|0.056	0.056	strong		0.502	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
C12orf71	728858	hgsc.bcm.edu	37	12	27234200	27234200	+	Silent	SNP	T	T	C	rs708165	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27234200T>C	ENST00000429849.2	-	2	747	c.717A>G	c.(715-717)aaA>aaG	p.K239K		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	239										endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						GATGGGGACTTTTGGTGGCAT	0.522													C|||	1003	0.20028	0.1316	0.2176	5008	,	,		19100	0.0357		0.4433	False		,,,				2504	0.2004				p.K239K		Atlas-SNP	.											.	C12orf71	20	.	0			c.A717G						PASS	.	C		744,3398		66,612,1393	89.0	87.0	88.0		717	0.2	0.0	12	dbSNP_86	88	3764,4680		843,2078,1301	no	coding-synonymous	C12orf71	NM_001080406.1		909,2690,2694	CC,CT,TT		44.576,17.9623,35.8176		239/270	27234200	4508,8078	2071	4222	6293	SO:0001819	synonymous_variant	728858	exon2			GGGACTTTTGGTG		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.717A>G	12.37:g.27234200T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_001080406		Silent	SNP	ENST00000429849.2	37	CCDS44851.1																																																																																			T|0.739;C|0.261	0.261	strong		0.522	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
LILRB5	10990	hgsc.bcm.edu	37	19	54755923	54755923	+	Silent	SNP	A	A	G	rs34889610|rs12976868	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54755923A>G	ENST00000316219.5	-	12	1727	c.1620T>C	c.(1618-1620)gaT>gaC	p.D540D	LILRB5_ENST00000449561.2_Silent_p.D541D|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_Silent_p.D532D|LILRB5_ENST00000345866.6_Silent_p.D441D	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	540					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCACCCGAGCATCCATCTCCA	0.632													.|||	1056	0.210863	0.2284	0.1556	5008	,	,		14747	0.0992		0.2525	False		,,,				2504	0.2986				p.D541D		Atlas-SNP	.											.	LILRB5	176	.	0			c.T1623C						PASS	.	G	,,	853,3553		78,697,1428	112.0	110.0	111.0		1623,1323,1620	0.5	0.0	19	dbSNP_121	111	1842,6758		243,1356,2701	no	coding-synonymous,coding-synonymous,coding-synonymous	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	,,	321,2053,4129	GG,GA,AA		21.4186,19.36,20.7212	,,	541/592,441/492,540/591	54755923	2695,10311	2203	4300	6503	SO:0001819	synonymous_variant	10990	exon12			CCGAGCATCCATC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1620T>C	19.37:g.54755923A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	125	48	0.384	NM_001081442	Q8N760	Silent	SNP	ENST00000316219.5	37	CCDS12885.1																																																																																			A|0.786;G|0.214	0.214	strong		0.632	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
MYOM3	127294	hgsc.bcm.edu	37	1	24421474	24421474	+	Missense_Mutation	SNP	G	G	A	rs6678540	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:24421474G>A	ENST00000374434.3	-	9	959	c.797C>T	c.(796-798)aCg>aTg	p.T266M	MYOM3_ENST00000330966.7_Missense_Mutation_p.T267M|MYOM3_ENST00000329601.7_Missense_Mutation_p.T266M|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	266			T -> M (in dbSNP:rs6678540). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GGGGCCAAACGTCGATCCTGG	0.532													A|||	1602	0.319888	0.2746	0.2911	5008	,	,		18851	0.3383		0.4771	False		,,,				2504	0.2209				p.T266M		Atlas-SNP	.											.	MYOM3	131	.	0			c.C797T						PASS	.	A	MET/THR	1045,2801		156,733,1034	45.0	46.0	45.0		797	4.1	0.7	1	dbSNP_116	45	3747,4489		855,2037,1226	yes	missense	MYOM3	NM_152372.3	81	1011,2770,2260	AA,AG,GG		45.4954,27.1711,39.6623	benign	266/1438	24421474	4792,7290	1923	4118	6041	SO:0001583	missense	127294	exon9			CCAAACGTCGATC	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.797C>T	1.37:g.24421474G>A	ENSP00000363557:p.Thr266Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	820	0.37545787545787546	141	0.2865853658536585	116	0.32044198895027626	179	0.3129370629370629	384	0.5065963060686016	A	7.540	0.660523	0.14645	0.271711	0.454954	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.55930	0.53;0.53;0.49	5.18	4.06	0.47325	.	0.579783	0.19017	N	0.124919	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.0	T	0.46484	-0.9188	9	0.12430	T	0.62	.	7.2915	0.26368	0.8218:0.0:0.1782:0.0	rs6678540;rs17184616;rs52794525;rs58002450;rs6678540	266;266	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	M	266;267;266	ENSP00000363557:T266M;ENSP00000332670:T267M;ENSP00000328415:T266M	ENSP00000328415:T266M	T	-	2	0	MYOM3	24294061	0.108000	0.22018	0.674000	0.29902	0.591000	0.36615	2.024000	0.41049	0.810000	0.34279	-0.381000	0.06696	ACG	G|0.633;A|0.367	0.367	strong		0.532	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
NBPF10	100132406	hgsc.bcm.edu	37	1	145323656	145323656	+	Missense_Mutation	SNP	A	A	T	rs75252120	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145323656A>T	ENST00000342960.5	+	27	3528	c.3493A>T	c.(3493-3495)Att>Ttt	p.I1165F	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	752						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.I1165F(3)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TATTGCAGGAATTAAAAAGGA	0.473																																					p.I1165F		Atlas-SNP	.											NBPF10,NS,carcinoma,0,7	NBPF10	221	7	3	Substitution - Missense(3)	endometrium(2)|kidney(1)	c.A3493T						scavenged	.																																			SO:0001583	missense	100132406	exon27			GCAGGAATTAAAA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.3493A>T	1.37:g.145323656A>T	ENSP00000345684:p.Ile1165Phe	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	24	6	0.25	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	7.524	0.657305	0.14580	.	.	ENSG00000163386	ENST00000342960	T	0.03441	3.93	.	.	.	.	.	.	.	.	T	0.02342	0.0072	M	0.67953	2.075	0.09310	N	1	.	.	.	.	.	.	T	0.44065	-0.9352	5	0.28530	T	0.3	.	.	.	.	.	.	.	.	F	1165	ENSP00000345684:I1165F	ENSP00000345684:I1165F	I	+	1	0	NBPF10	144035013	0.353000	0.24904	0.005000	0.12908	0.123000	0.20343	1.122000	0.31295	0.386000	0.24997	0.128000	0.15822	ATT	A|0.625;T|0.375	0.375	strong		0.473	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
ANK3	288	hgsc.bcm.edu	37	10	61868716	61868716	+	Silent	SNP	C	C	A	rs3750800	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:61868716C>A	ENST00000280772.2	-	27	3236	c.3045G>T	c.(3043-3045)acG>acT	p.T1015T	ANK3_ENST00000373827.2_Silent_p.T1009T|ANK3_ENST00000503366.1_Silent_p.T1016T|ANK3_ENST00000355288.2_Silent_p.T149T	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1015	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						GAGTGGGGGCCGTACACTTGC	0.542													C|||	897	0.179113	0.0272	0.2262	5008	,	,		15374	0.0704		0.3221	False		,,,				2504	0.316				p.T1016T		Atlas-SNP	.											.	ANK3	703	.	0			c.G3048T						PASS	.	C	,,,	309,4097	168.0+/-198.9	12,285,1906	67.0	72.0	70.0		447,3027,3048,3045	-9.9	0.3	10	dbSNP_107	70	2807,5793	443.0+/-360.3	468,1871,1961	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	480,2156,3867	AA,AC,CC		32.6395,7.0132,23.9582	,,,	149/1002,1009/1862,1016/1869,1015/4378	61868716	3116,9890	2203	4300	6503	SO:0001819	synonymous_variant	288	exon28			GGGGGCCGTACAC	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.3045G>T	10.37:g.61868716C>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_001204404	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1	392	0.1794871794871795	18	0.036585365853658534	97	0.26795580110497236	40	0.06993006993006994	237	0.31266490765171506	C	5.518	0.280589	0.10458	0.070132	0.326395	ENSG00000151150	ENST00000467420	.	.	.	6.04	-9.89	0.00464	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999998	.	.	.	.	.	.	T	0.08638	-1.0712	3	.	.	.	.	10.7989	0.46476	0.153:0.2378:0.0:0.6092	rs3750800;rs17803381;rs3750800	.	.	.	L	40	.	.	R	-	2	0	ANK3	61538722	0.000000	0.05858	0.333000	0.25482	0.987000	0.75469	-2.374000	0.01072	-2.001000	0.00964	-0.251000	0.11542	CGG	C|0.791;A|0.209	0.209	strong		0.542	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
UBE4B	10277	hgsc.bcm.edu	37	1	10190575	10190575	+	Missense_Mutation	SNP	G	G	C	rs61760196	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10190575G>C	ENST00000253251.8	+	12	2165	c.1326G>C	c.(1324-1326)ttG>ttC	p.L442F	UBE4B_ENST00000343090.6_Missense_Mutation_p.L571F|UBE4B_ENST00000377157.3_Missense_Mutation_p.L326F|UBE4B_ENST00000475795.1_3'UTR					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CTTTGCGGTTGTGGTTGCCGA	0.507													G|||	219	0.04373	0.0658	0.0432	5008	,	,		14036	0.0526		0.0288	False		,,,				2504	0.0204				p.L571F		Atlas-SNP	.											.	UBE4B	233	.	0			c.G1713C						PASS	.	G	PHE/LEU,PHE/LEU	233,4173	136.5+/-172.5	8,217,1978	132.0	136.0	135.0		1713,1326	5.9	1.0	1	dbSNP_129	135	216,8384	91.4+/-153.5	2,212,4086	yes	missense,missense	UBE4B	NM_001105562.2,NM_006048.4	22,22	10,429,6064	CC,CG,GG		2.5116,5.2882,3.4523	probably-damaging,probably-damaging	571/1303,442/1174	10190575	449,12557	2203	4300	6503	SO:0001583	missense	10277	exon13			GCGGTTGTGGTTG	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.1326G>C	1.37:g.10190575G>C	ENSP00000253251:p.Leu442Phe	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	167	70	0.419162	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	37	CCDS110.1	99	0.04532967032967033	32	0.06504065040650407	19	0.052486187845303865	28	0.04895104895104895	20	0.026385224274406333	G	16.44	3.125167	0.56721	0.052882	0.025116	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.51325	0.71;0.71;0.71	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.08088	0.0202	L	0.56769	1.78	0.53688	D	0.999974	D;D	0.64830	0.99;0.994	P;P	0.59703	0.731;0.862	T	0.18871	-1.0323	10	0.09843	T	0.71	-16.7783	9.9867	0.41846	0.071:0.1392:0.7898:0.0	rs61760196	571;442	O95155;O95155-2	UBE4B_HUMAN;.	F	442;326;571	ENSP00000253251:L442F;ENSP00000366362:L326F;ENSP00000343001:L571F	ENSP00000253251:L442F	L	+	3	2	UBE4B	10113162	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	4.043000	0.57354	2.826000	0.97356	0.655000	0.94253	TTG	G|0.961;C|0.039	0.039	strong		0.507	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:31348076G>A	ENST00000349752.5	-	1	769				GALNT14_ENST00000406653.1_5'UTR|GALNT14_ENST00000356174.3_Intron|GALNT14_ENST00000324589.5_Missense_Mutation_p.A58V|GALNT14_ENST00000420311.2_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		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	15	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	
CFHR3	10878	hgsc.bcm.edu	37	1	196759282	196759282	+	Missense_Mutation	SNP	C	C	T	rs138675433		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196759282C>T	ENST00000367425.4	+	5	813	c.721C>T	c.(721-723)Ccc>Tcc	p.P241S	CFHR3_ENST00000391985.3_Missense_Mutation_p.P180S	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	241	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.			P -> S (in Ref. 1; CAA48639). {ECO:0000305}.		blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.P241S(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						CCAATGCCAGCCCTACTATGA	0.428																																					p.P241S		Atlas-SNP	.											CFHR3,NS,carcinoma,0,1	CFHR3	52	1	1	Substitution - Missense(1)	prostate(1)	c.C721T						scavenged	.						101.0	148.0	134.0					1																	196759282		1754	4010	5764	SO:0001583	missense	10878	exon5			TGCCAGCCCTACT	X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"""Complement system"""	16980	protein-coding gene	gene with protein product	"""complement factor H related 3"""	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.721C>T	1.37:g.196759282C>T	ENSP00000356395:p.Pro241Ser	Somatic	318	2	0.00628931		WXS	Illumina HiSeq	Phase_I	301	9	0.0299003	NM_021023	B4DPR0|Q9UJ16	Missense_Mutation	SNP	ENST00000367425.4	37	CCDS30958.1	487	0.222985347985348	102	0.2073170731707317	61	0.1685082872928177	231	0.40384615384615385	93	0.12269129287598944	T	0.008	-1.884513	0.00532	.	.	ENSG00000116785	ENST00000367425;ENST00000391985	T;T	0.65178	-0.14;-0.14	3.27	-6.54	0.01860	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.01668	-0.77	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.02398	-1.1165	8	0.06757	T	0.87	.	1.7706	0.03011	0.5551:0.1977:0.1048:0.1423	.	180;241	B4DPR0;Q02985	.;FHR3_HUMAN	S	241;180	ENSP00000356395:P241S;ENSP00000375845:P180S	ENSP00000356395:P241S	P	+	1	0	CFHR3	195025905	0.000000	0.05858	0.001000	0.08648	0.042000	0.13812	-3.343000	0.00504	-3.939000	0.00089	-1.461000	0.01025	CCC	T|0.236;G|0.236	0.236	strong		0.428	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023	
TCEB3B	51224	hgsc.bcm.edu	37	18	44561630	44561630	+	Silent	SNP	C	C	T	rs61746775	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44561630C>T	ENST00000332567.4	-	1	358	c.6G>A	c.(4-6)gcG>gcA	p.A2A	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	2					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TGGACCCTGCCGCCATCTCAC	0.622													c|||	190	0.0379393	0.0499	0.0418	5008	,	,		16629	0.0069		0.0835	False		,,,				2504	0.0041				p.A2A		Atlas-SNP	.											.	TCEB3B	141	.	0			c.G6A						PASS	.	T	,	262,4140		9,244,1948	47.0	45.0	45.0		6,	-2.0	0.0	18	dbSNP_129	45	619,7975		24,571,3702	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	33,815,5650	TT,TC,CC		7.2027,5.9518,6.779	,	2/754,	44561630	881,12115	2201	4297	6498	SO:0001819	synonymous_variant	51224	exon1			CCCTGCCGCCATC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.6G>A	18.37:g.44561630C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			C|0.933;T|0.067	0.067	strong		0.622	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
LRRC16A	55604	hgsc.bcm.edu	37	6	25600968	25600968	+	Silent	SNP	G	G	A	rs10456324	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:25600968G>A	ENST00000329474.6	+	33	3914	c.3546G>A	c.(3544-3546)gcG>gcA	p.A1182A		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1182					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.A1182A(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						CTGCGTGTGCGCAGAAGGTAA	0.453													A|||	2030	0.405351	0.3404	0.4179	5008	,	,		18673	0.372		0.4632	False		,,,				2504	0.4591				p.A1182A		Atlas-SNP	.											LRRC16A_ENST00000329474,NS,carcinoma,0,1	LRRC16A	168	1	1	Substitution - coding silent(1)	prostate(1)	c.G3546A						PASS	.	A	,	1375,2629		246,883,873	34.0	40.0	38.0		3546,3546	-10.1	0.0	6	dbSNP_119	38	3864,4496		908,2048,1224	no	coding-synonymous,coding-synonymous	LRRC16A	NM_001173977.1,NM_017640.5	,	1154,2931,2097	AA,AG,GG		46.2201,34.3407,42.373	,	1182/1366,1182/1372	25600968	5239,7125	2002	4180	6182	SO:0001819	synonymous_variant	55604	exon33			GTGTGCGCAGAAG	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.3546G>A	6.37:g.25600968G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Silent	SNP	ENST00000329474.6	37	CCDS54973.1																																																																																			G|0.607;A|0.393	0.393	strong		0.453	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
SPSB1	80176	hgsc.bcm.edu	37	1	9416151	9416151	+	Silent	SNP	G	G	A	rs9435243	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:9416151G>A	ENST00000328089.6	+	2	542	c.201G>A	c.(199-201)gtG>gtA	p.V67V	SPSB1_ENST00000377399.2_Silent_p.V67V|SPSB1_ENST00000357898.3_Silent_p.V67V	NM_025106.3	NP_079382.2	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box containing 1	67	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(2)|lung(5)|prostate(2)	13	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)		ATGTCTTTGTGAAGGAGGACG	0.582													G|||	1299	0.259385	0.2368	0.3401	5008	,	,		20489	0.2748		0.1998	False		,,,				2504	0.2781				p.V67V		Atlas-SNP	.											.	SPSB1	22	.	0			c.G201A						PASS	.	G		1056,3350	387.7+/-326.6	147,762,1294	174.0	169.0	170.0		201	2.2	1.0	1	dbSNP_119	170	1998,6602	350.7+/-328.0	230,1538,2532	no	coding-synonymous	SPSB1	NM_025106.3		377,2300,3826	AA,AG,GG		23.2326,23.9673,23.4815		67/274	9416151	3054,9952	2203	4300	6503	SO:0001819	synonymous_variant	80176	exon2			CTTTGTGAAGGAG		CCDS102.1	1p36.22	2008-02-05			ENSG00000171621	ENSG00000171621			30628	protein-coding gene	gene with protein product		611657				15713673, 12076535	Standard	NM_025106		Approved	SSB-1	uc010oae.2	Q96BD6	OTTHUMG00000001279	ENST00000328089.6:c.201G>A	1.37:g.9416151G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_025106	A2A275|Q59FA1|Q5TIH9|Q9BRY9|Q9H6C5	Silent	SNP	ENST00000328089.6	37	CCDS102.1																																																																																			G|0.765;A|0.235	0.235	strong		0.582	SPSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003727.2	NM_025106	
ZNF880	400713	hgsc.bcm.edu	37	19	52888049	52888049	+	Missense_Mutation	SNP	C	C	A	rs75346003	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52888049C>A	ENST00000422689.2	+	4	1231	c.1216C>A	c.(1216-1218)Caa>Aaa	p.Q406K		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	406					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						CACGGGAGAGCAACCTTACAA	0.398																																					p.Q406K		Atlas-SNP	.											ZNF880,colon,carcinoma,-1,2	ZNF880	45	2	0			c.C1216A						PASS	.						69.0	63.0	65.0					19																	52888049		1568	3582	5150	SO:0001583	missense	400713	exon4			GGAGAGCAACCTT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1216C>A	19.37:g.52888049C>A	ENSP00000406318:p.Gln406Lys	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	7	4	0.571429	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.634723	0.00114	.	.	ENSG00000221923	ENST00000422689	T	0.10860	2.83	1.84	0.731	0.18277	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01835	0.0058	N	0.00128	-2.045	0.20638	N	0.999879	B	0.17667	0.023	B	0.14023	0.01	T	0.46105	-0.9215	8	.	.	.	.	6.7224	0.23338	0.7399:0.2601:0.0:0.0	.	406	Q6PDB4	ZN880_HUMAN	K	406	ENSP00000406318:Q406K	.	Q	+	1	0	ZNF880	57579861	0.006000	0.16342	0.407000	0.26434	0.151000	0.21798	0.708000	0.25719	0.007000	0.14760	-0.493000	0.04662	CAA	C|0.872;A|0.128	0.128	strong		0.398	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
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 GAIIx	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	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	34	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	
NRAP	4892	hgsc.bcm.edu	37	10	115412793	115412793	+	Silent	SNP	A	A	G	rs3737322	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:115412793A>G	ENST00000359988.3	-	6	715	c.471T>C	c.(469-471)taT>taC	p.Y157Y	NRAP_ENST00000360478.3_Silent_p.Y157Y|NRAP_ENST00000369358.4_Silent_p.Y157Y|NRAP_ENST00000369360.3_Silent_p.Y157Y	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		AGTCTTCTGTATATTCCTGTT	0.443													A|||	1543	0.308107	0.4887	0.2378	5008	,	,		16745	0.2173		0.2664	False		,,,				2504	0.2505				p.Y157Y		Atlas-SNP	.											.	NRAP	208	.	0			c.T471C						PASS	.	A	,	1969,2435		499,971,732	157.0	139.0	145.0		471,471	-1.3	0.2	10	dbSNP_107	145	2390,6210		336,1718,2246	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	835,2689,2978	GG,GA,AA		27.7907,44.7094,33.5205	,	157/1696,157/1731	115412793	4359,8645	2202	4300	6502	SO:0001819	synonymous_variant	4892	exon6			TTCTGTATATTCC		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.471T>C	10.37:g.115412793A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	90	52	0.577778	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			A|0.676;G|0.324	0.324	strong		0.443	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
MUC2	4583	hgsc.bcm.edu	37	11	1084821	1084821	+	Silent	SNP	T	T	C	rs10794288	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1084821T>C	ENST00000441003.2	+	20	2643	c.2616T>C	c.(2614-2616)gaT>gaC	p.D872D	MUC2_ENST00000359061.5_Silent_p.D872D	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	872	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	TCACCTTTGATGGGAAGTACT	0.592													C|||	1697	0.338858	0.4259	0.3646	5008	,	,		18680	0.3919		0.2167	False		,,,				2504	0.274				p.D872D		Atlas-SNP	.											.	MUC2	614	.	0			c.T2616C						PASS	.	C		1735,2589		356,1023,783	86.0	88.0	87.0		2616	-6.2	0.1	11	dbSNP_120	87	1719,6787		185,1349,2719	no	coding-synonymous	MUC2	NM_002457.2		541,2372,3502	CC,CT,TT		20.2093,40.1249,26.9213		872/2813	1084821	3454,9376	2162	4253	6415	SO:0001819	synonymous_variant	4583	exon20			CTTTGATGGGAAG	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.2616T>C	11.37:g.1084821T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.699;C|0.301	0.301	strong		0.592	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
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 GAIIx	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_ENST00000414515.3_RNA|MAMDC2-AS1_ENST00000591368.1_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	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	125	63	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	
C9orf84	158401	hgsc.bcm.edu	37	9	114490229	114490229	+	Silent	SNP	T	T	G	rs10512411	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:114490229T>G	ENST00000318737.4	-	11	1454	c.1326A>C	c.(1324-1326)gcA>gcC	p.A442A	C9orf84_ENST00000394779.3_Silent_p.A403A|C9orf84_ENST00000394777.4_Silent_p.A403A|C9orf84_ENST00000374287.3_Silent_p.A442A	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	442										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						GTACTTCTTTTGCCAGAGATG	0.343													T|||	719	0.14357	0.1422	0.196	5008	,	,		18422	0.0278		0.2286	False		,,,				2504	0.1401				p.A442A		Atlas-SNP	.											C9orf84_ENST00000374287,NS,carcinoma,-2,2	C9orf84	207	2	0			c.A1326C						PASS	.	T	,	767,3637	308.0+/-290.3	67,633,1502	79.0	79.0	79.0		1209,1326	3.9	0.3	9	dbSNP_119	79	1992,6604	344.4+/-325.3	228,1536,2534	no	coding-synonymous,coding-synonymous	C9orf84	NM_001080551.1,NM_173521.3	,	295,2169,4036	GG,GT,TT		23.1736,17.416,21.2231	,	403/1406,442/1445	114490229	2759,10241	2202	4298	6500	SO:0001819	synonymous_variant	158401	exon11			TTCTTTTGCCAGA	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.1326A>C	9.37:g.114490229T>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	37	CCDS6781.3																																																																																			T|0.852;G|0.148	0.148	strong		0.343	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496412	39496412	+	Silent	SNP	G	G	C	rs139294	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39496412G>C	ENST00000401756.1	+	2	205	c.129G>C	c.(127-129)acG>acC	p.T43T	APOBEC3H_ENST00000348946.4_Silent_p.T43T|APOBEC3H_ENST00000421988.2_Silent_p.T43T|APOBEC3H_ENST00000442487.3_Silent_p.T43T	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	43					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					CCACGCCCACGAGAGGCTACT	0.562													C|||	2578	0.514776	0.8275	0.3775	5008	,	,		16490	0.3333		0.4543	False		,,,				2504	0.4387				p.T43T		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G129C						PASS	.	C	,,,	3359,1047		1289,781,133	43.0	42.0	43.0		129,129,129,129	2.9	0.0	22	dbSNP_78	43	3925,4675		874,2177,1249	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	,,,	2163,2958,1382	CC,CG,GG		45.6395,23.7631,43.9951	,,,	43/183,43/201,43/155,43/184	39496412	7284,5722	2203	4300	6503	SO:0001819	synonymous_variant	164668	exon2			GCCCACGAGAGGC	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.129G>C	22.37:g.39496412G>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Silent	SNP	ENST00000401756.1	37	CCDS54530.1																																																																																			G|0.464;C|0.536	0.536	strong		0.562	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
CCDC38	120935	hgsc.bcm.edu	37	12	96292170	96292170	+	Missense_Mutation	SNP	C	C	G	rs75959092	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:96292170C>G	ENST00000344280.3	-	7	1164	c.607G>C	c.(607-609)Gtg>Ctg	p.V203L	SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	203										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CACCTTTTCACTGCTTGTACC	0.428													C|||	282	0.0563099	0.0045	0.0706	5008	,	,		19368	0.0278		0.1342	False		,,,				2504	0.0654				p.V203L		Atlas-SNP	.											.	CCDC38	45	.	0			c.G607C						PASS	.	C	LEU/VAL	102,4304	80.9+/-119.3	2,98,2103	346.0	261.0	290.0		607	0.7	0.1	12	dbSNP_132	290	1073,7527	225.1+/-261.3	70,933,3297	yes	missense	CCDC38	NM_182496.2	32	72,1031,5400	GG,GC,CC		12.4767,2.315,9.0343	benign	203/564	96292170	1175,11831	2203	4300	6503	SO:0001583	missense	120935	exon7			TTTTCACTGCTTG	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.607G>C	12.37:g.96292170C>G	ENSP00000345470:p.Val203Leu	Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	289	137	0.474048	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	139	0.06364468864468864	6	0.012195121951219513	24	0.06629834254143646	10	0.017482517482517484	99	0.13060686015831136	C	5.900	0.350137	0.11182	0.02315	0.124767	ENSG00000165972	ENST00000344280	T	0.07688	3.17	5.4	0.671	0.17929	.	0.361234	0.28062	N	0.016743	T	0.00039	0.0001	L	0.28556	0.865	0.42212	P	0.008184999999999998	B	0.23128	0.08	B	0.23419	0.046	T	0.42749	-0.9433	9	0.07325	T	0.83	-3.5442	4.7641	0.13123	0.0:0.3797:0.1564:0.4638	.	203	Q502W7	CCD38_HUMAN	L	203	ENSP00000345470:V203L	ENSP00000345470:V203L	V	-	1	0	CCDC38	94816301	0.010000	0.17322	0.129000	0.21949	0.024000	0.10985	-0.125000	0.10579	0.055000	0.16094	-0.424000	0.05967	GTG	C|0.917;G|0.083	0.083	strong		0.428	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
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 GAIIx	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_ENST00000375226.2_Silent_p.L1004L|UBR4_ENST00000375267.2_Silent_p.L1004L|UBR4_ENST00000375217.2_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		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	112	59	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	
RSBN1L	222194	hgsc.bcm.edu	37	7	77365770	77365770	+	Silent	SNP	A	A	G	rs3764824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:77365770A>G	ENST00000334955.8	+	2	657	c.630A>G	c.(628-630)gaA>gaG	p.E210E	RSBN1L_ENST00000445288.1_5'UTR	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	210	Lys-rich.					nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						aagaaaaagaaagagaaaaaa	0.249													G|||	2892	0.577476	0.8979	0.4481	5008	,	,		15634	0.3095		0.5219	False		,,,				2504	0.5695				p.E210E		Atlas-SNP	.											.	RSBN1L	74	.	0			c.A630G						PASS	.	G		2886,600		1200,486,57	51.0	53.0	53.0		630	2.8	1.0	7	dbSNP_107	53	4049,3933		1084,1881,1026	no	coding-synonymous	RSBN1L	NM_198467.2		2284,2367,1083	GG,GA,AA		49.2734,17.2117,39.5274		210/847	77365770	6935,4533	1743	3991	5734	SO:0001819	synonymous_variant	222194	exon2			AAAAGAAAGAGAA	AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.630A>G	7.37:g.77365770A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Silent	SNP	ENST00000334955.8	37	CCDS43607.1																																																																																			A|0.466;G|0.534	0.534	strong		0.249	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467	
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 GAIIx	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		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	32	8	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	
OR2T34	127068	hgsc.bcm.edu	37	1	248737595	248737595	+	Missense_Mutation	SNP	A	A	G	rs150601708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248737595A>G	ENST00000328782.2	-	1	485	c.464T>C	c.(463-465)gTt>gCt	p.V155A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V155A(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	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)			CATTCCCAAAACCCAGCAGGC	0.522																																					p.V155A		Atlas-SNP	.											OR2T34,NS,carcinoma,0,2	OR2T34	72	2	1	Substitution - Missense(1)	ovary(1)	c.T464C						scavenged	.						17.0	23.0	21.0					1																	248737595		2143	4273	6416	SO:0001583	missense	127068	exon1			CCCAAAACCCAGC	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.464T>C	1.37:g.248737595A>G	ENSP00000330904:p.Val155Ala	Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	448	94	0.209821	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	602	0.27564102564102566	196	0.3983739837398374	85	0.23480662983425415	151	0.263986013986014	170	0.22427440633245382	.	5.973	0.363525	0.11296	.	.	ENSG00000183310	ENST00000328782	T	0.38722	1.12	2.34	0.992	0.19819	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B	0.15930	0.015	B	0.19666	0.026	T	0.47522	-0.9111	8	0.28530	T	0.3	.	6.4829	0.22073	0.7538:0.2461:0.0:0.0	.	155	Q8NGX1	O2T34_HUMAN	A	155	ENSP00000330904:V155A	ENSP00000330904:V155A	V	-	2	0	OR2T34	246804218	0.000000	0.05858	0.011000	0.14972	0.090000	0.18270	-0.276000	0.08514	0.953000	0.37825	0.319000	0.21371	GTT	A|0.500;G|0.500	0.500	weak		0.522	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
ZNF280C	55609	hgsc.bcm.edu	37	X	129349295	129349295	+	Silent	SNP	T	T	G	rs209238	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:129349295T>G	ENST00000370978.4	-	15	2004	c.1851A>C	c.(1849-1851)ggA>ggC	p.G617G		NM_017666.4	NP_060136.1	Q8ND82	Z280C_HUMAN	zinc finger protein 280C	617					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(3)|kidney(4)|large_intestine(9)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26						ACTTGTGAATTCCCCGACGAC	0.318													T|||	1969	0.521589	0.5681	0.353	3775	,	,		12569	0.2738		0.3151	False		,,,				2504	0.3885				p.G617G		Atlas-SNP	.											.	ZNF280C	63	.	0			c.A1851C						PASS	.	T		2618,1217		769,679,401,184,170	77.0	81.0	80.0		1851	3.2	0.8	X	dbSNP_79	80	2698,4030		394,1164,746,870,1126	no	coding-synonymous	ZNF280C	NM_017666.4		1163,1843,1147,1054,1296	GG,GT,G,TT,T		40.1011,31.734,49.6734		617/738	129349295	5316,5247	2203	4300	6503	SO:0001819	synonymous_variant	55609	exon15			GTGAATTCCCCGA	AL834333	CCDS14622.1	Xq25	2008-05-02	2007-09-20	2007-09-20	ENSG00000056277	ENSG00000056277			25955	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 3 (Drosophila)"""	SUHW3		12477932	Standard	NM_017666		Approved	FLJ20095, ZNF633	uc004evm.3	Q8ND82	OTTHUMG00000022393	ENST00000370978.4:c.1851A>C	X.37:g.129349295T>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	21	0.259259	NM_017666	A8K2V8|Q9NXR3	Silent	SNP	ENST00000370978.4	37	CCDS14622.1																																																																																			0|0.003;G|0.509	0.509	strong		0.318	ZNF280C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058251.1	NM_017666	
TACC2	10579	hgsc.bcm.edu	37	10	123846860	123846860	+	Silent	SNP	C	C	T	rs11599291	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123846860C>T	ENST00000369005.1	+	4	5185	c.4845C>T	c.(4843-4845)ccC>ccT	p.P1615P	TACC2_ENST00000334433.3_Silent_p.P1615P|TACC2_ENST00000515603.1_Silent_p.P1615P|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Silent_p.P1615P|TACC2_ENST00000515273.1_Silent_p.P1615P	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1615					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				AAGATGGTCCCGGGGACTTTG	0.567													C|||	996	0.198882	0.2859	0.1844	5008	,	,		21091	0.1002		0.2107	False		,,,				2504	0.181				p.P1615P		Atlas-SNP	.											TACC2,colon,carcinoma,0,1	TACC2	271	1	0			c.C4845T						PASS	.	C	,	1406,3000	460.9+/-352.8	223,960,1020	82.0	81.0	81.0		,4845	1.6	0.0	10	dbSNP_120	81	1930,6670	340.3+/-323.5	214,1502,2584	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	437,2462,3604	TT,TC,CC		22.4419,31.911,25.6497	,	,1615/2949	123846860	3336,9670	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			TGGTCCCGGGGAC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.4845C>T	10.37:g.123846860C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			C|0.767;T|0.233	0.233	strong		0.567	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
PRKCI	5584	hgsc.bcm.edu	37	3	169988286	169988286	+	Silent	SNP	C	C	T	rs56257047	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:169988286C>T	ENST00000295797.4	+	6	833	c.528C>T	c.(526-528)ctC>ctT	p.L176L		NM_002740.5	NP_002731.4	P41743	KPCI_HUMAN	protein kinase C, iota	176	Regulatory domain.				actin filament organization (GO:0007015)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell junction organization (GO:0045216)|cellular response to insulin stimulus (GO:0032869)|cytoskeleton organization (GO:0007010)|establishment of apical/basal cell polarity (GO:0035089)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|eye photoreceptor cell development (GO:0042462)|Golgi vesicle budding (GO:0048194)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of glucose import (GO:0046326)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|protein targeting to membrane (GO:0006612)|response to interleukin-1 (GO:0070555)|secretion (GO:0046903)|tight junction assembly (GO:0070830)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|Schmidt-Lanterman incisure (GO:0043220)	ATP binding (GO:0005524)|phospholipid binding (GO:0005543)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	36	all_cancers(22;6.45e-23)|all_epithelial(15;8.52e-28)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)		Tamoxifen(DB00675)	ACTGCAAACTCTTGGTTCATA	0.403													C|||	378	0.0754792	0.0204	0.1225	5008	,	,		19057	0.0645		0.1541	False		,,,				2504	0.047				p.L176L		Atlas-SNP	.											.	PRKCI	82	.	0			c.C528T						PASS	.	C		176,4230	116.3+/-154.2	5,166,2032	115.0	106.0	109.0		528	-3.1	0.6	3	dbSNP_129	109	1299,7301	256.8+/-281.1	102,1095,3103	no	coding-synonymous	PRKCI	NM_002740.5		107,1261,5135	TT,TC,CC		15.1047,3.9946,11.3409		176/597	169988286	1475,11531	2203	4300	6503	SO:0001819	synonymous_variant	5584	exon6			CAAACTCTTGGTT		CCDS3212.2	3q26.3	2008-07-18			ENSG00000163558	ENSG00000163558	2.7.11.13		9404	protein-coding gene	gene with protein product		600539		DXS1179E		7607695, 11978974	Standard	NM_002740		Approved	PKCI	uc003fgs.2	P41743	OTTHUMG00000150214	ENST00000295797.4:c.528C>T	3.37:g.169988286C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_002740	D3DNQ4|Q8WW06	Silent	SNP	ENST00000295797.4	37	CCDS3212.2																																																																																			C|0.886;T|0.114	0.114	strong		0.403	PRKCI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316866.3	NM_002740	
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 GAIIx	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	Y_RNA_ENST00000383990.1_RNA|UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.L20V	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	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	114	14	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	
COL20A1	57642	hgsc.bcm.edu	37	20	61944253	61944253	+	Silent	SNP	G	G	A	rs376373104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61944253G>A	ENST00000358894.6	+	16	2143	c.2043G>A	c.(2041-2043)acG>acA	p.T681T	COL20A1_ENST00000422202.1_Silent_p.T688T|COL20A1_ENST00000326996.6_Silent_p.T681T|COL20A1_ENST00000435874.1_Silent_p.T688T	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	681	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					ACCAGATCACGTGGACGCCCC	0.677													g|||	2	0.000399361	0.0	0.0	5008	,	,		15665	0.0		0.002	False		,,,				2504	0.0				p.T681T		Atlas-SNP	.											.	COL20A1	137	.	0			c.G2043A						PASS	.	A		4,3830		0,4,1913	19.0	27.0	24.0		2043	0.6	1.0	20		24	23,8115		0,23,4046	no	coding-synonymous	COL20A1	NM_020882.2		0,27,5959	AA,AG,GG		0.2826,0.1043,0.2255		681/1285	61944253	27,11945	1917	4069	5986	SO:0001819	synonymous_variant	57642	exon16			GATCACGTGGACG	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.2043G>A	20.37:g.61944253G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	156	73	0.467949	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Silent	SNP	ENST00000358894.6	37	CCDS46628.1																																																																																			.	.	weak		0.677	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
MEGF11	84465	hgsc.bcm.edu	37	15	66411441	66411441	+	Missense_Mutation	SNP	C	C	T	rs16949528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:66411441C>T	ENST00000409699.2	-	4	456	c.284G>A	c.(283-285)aGc>aAc	p.S95N	MEGF11_ENST00000422354.1_Missense_Mutation_p.S95N|MEGF11_ENST00000288745.3_Intron|MEGF11_ENST00000395625.2_Intron|MEGF11_ENST00000360698.4_Missense_Mutation_p.S95N|MEGF11_ENST00000395614.1_5'UTR			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	95	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.|EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.		S -> N (in dbSNP:rs16949528). {ECO:0000269|PubMed:15489334}.		homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						GAAGTCTCCGCTCTCATAGTA	0.607													T|||	2141	0.427516	0.5545	0.2867	5008	,	,		15476	0.4762		0.2555	False		,,,				2504	0.4826				p.S95N		Atlas-SNP	.											.	MEGF11	70	.	0			c.G284A						PASS	.	T	ASN/SER	732,648		187,358,145	68.0	70.0	70.0		284	1.7	0.3	15	dbSNP_123	70	889,2291		135,619,836	yes	missense	MEGF11	NM_032445.2	46	322,977,981	TT,TC,CC		27.956,46.9565,35.5482	benign	95/1045	66411441	1621,2939	690	1590	2280	SO:0001583	missense	84465	exon4			TCTCCGCTCTCAT	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.284G>A	15.37:g.66411441C>T	ENSP00000386908:p.Ser95Asn	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	34	22	0.647059	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	37	CCDS10213.2	834	0.38186813186813184	278	0.5650406504065041	95	0.26243093922651933	268	0.46853146853146854	193	0.2546174142480211	T	11.20	1.569365	0.28003	0.530435	0.27956	ENSG00000157890	ENST00000409699;ENST00000422354;ENST00000360698	D;D;D	0.87029	-2.2;-2.2;-2.13	5.29	1.74	0.24563	EMI domain (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.00012	0.0000	M	0.65498	2.005	0.44798	P	0.0021970000000000045	B	0.02656	0.0	B	0.08055	0.003	T	0.45600	-0.9250	8	0.20046	T	0.44	.	9.9341	0.41541	0.0:0.4872:0.0:0.5128	rs16949528;rs56708944	95	A6BM72	MEG11_HUMAN	N	95	ENSP00000386908:S95N;ENSP00000414475:S95N;ENSP00000353919:S95N	ENSP00000353919:S95N	S	-	2	0	MEGF11	64198495	0.920000	0.31207	0.279000	0.24732	0.913000	0.54294	1.643000	0.37217	-0.184000	0.10567	-0.269000	0.10298	AGC	C|0.642;T|0.358	0.358	strong		0.607	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445	
DNAH6	1768	hgsc.bcm.edu	37	2	84880695	84880695	+	Silent	SNP	G	G	A	rs12992282	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:84880695G>A	ENST00000237449.6	+	33	5339	c.5331G>A	c.(5329-5331)ggG>ggA	p.G1777G	DNAH6_ENST00000398278.2_Silent_p.G1777G|DNAH6_ENST00000389394.3_Silent_p.G1777G			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1777	AAA 2. {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(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AAAAACTTGGGATAGAAAATT	0.383													G|||	201	0.0401358	0.0106	0.0533	5008	,	,		20330	0.0		0.1421	False		,,,				2504	0.0072				p.G1777G		Atlas-SNP	.											.	DNAH6	194	.	0			c.G5331A						PASS	.	G		37,1347		0,37,655	71.0	64.0	66.0		5331	-7.3	0.0	2	dbSNP_121	66	489,2693		40,409,1142	no	coding-synonymous	DNAH6	NM_001370.1		40,446,1797	AA,AG,GG		15.3677,2.6734,11.5199		1777/4159	84880695	526,4040	692	1591	2283	SO:0001819	synonymous_variant	1768	exon34			ACTTGGGATAGAA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.5331G>A	2.37:g.84880695G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			G|0.925;A|0.075	0.075	strong		0.383	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
AHRR	57491	hgsc.bcm.edu	37	5	434722	434722	+	Missense_Mutation	SNP	G	G	C	rs34453673	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:434722G>C	ENST00000505113.1	+	11	1923	c.1879G>C	c.(1879-1881)Gac>Cac	p.D627H	AHRR_ENST00000512529.1_Missense_Mutation_p.D473H|AHRR_ENST00000316418.5_Missense_Mutation_p.D645H|AHRR_ENST00000506456.1_Missense_Mutation_p.D483H	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	627	Needed for transcriptional repression. {ECO:0000250}.		D -> H (in dbSNP:rs34453673).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			GGAGCCCACAGACGGCCTTCC	0.701													C|||	776	0.154952	0.0113	0.2363	5008	,	,		18582	0.004		0.4036	False		,,,				2504	0.1912				p.D645H		Atlas-SNP	.											AHRR,colon,carcinoma,0,1	AHRR	67	1	0			c.G1933C						PASS	.	C	HIS/ASP,HIS/ASP	288,3746		12,264,1741	11.0	15.0	13.0		1879,1933	3.3	0.0	5	dbSNP_126	13	3041,5303		580,1881,1711	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	81,81	592,2145,3452	CC,CG,GG		36.4453,7.1393,26.8945	benign,benign	627/702,645/720	434722	3329,9049	2017	4172	6189	SO:0001583	missense	57491	exon12			CCCACAGACGGCC	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.1879G>C	5.37:g.434722G>C	ENSP00000424601:p.Asp627His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	413	0.1891025641025641	7	0.014227642276422764	97	0.26795580110497236	0	0.0	309	0.4076517150395778	C	0.012	-1.666056	0.00765	0.071393	0.364453	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456	T;T;T;T	0.21734	2.33;2.31;1.99;1.99	3.32	3.32	0.38043	.	0.872680	0.09850	N	0.747721	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48559	-0.9025	9	0.13470	T	0.59	.	5.0538	0.14522	0.0:0.6575:0.2193:0.1232	rs34453673	483;627;645	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	H	627;645;473;483	ENSP00000424601:D627H;ENSP00000323816:D645H;ENSP00000424880:D473H;ENSP00000426932:D483H	ENSP00000323816:D645H	D	+	1	0	AHRR	487722	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.329000	0.19698	0.508000	0.28173	-0.216000	0.12614	GAC	G|0.808;C|0.192	0.192	strong		0.701	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
QRICH2	84074	hgsc.bcm.edu	37	17	74289908	74289908	+	Silent	SNP	A	A	G	rs6501883	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74289908A>G	ENST00000262765.5	-	4	581	c.402T>C	c.(400-402)agT>agC	p.S134S		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	134										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						TTTGTTCCCTACTGGAAACCC	0.582													A|||	2351	0.469449	0.7073	0.3098	5008	,	,		18812	0.5724		0.2753	False		,,,				2504	0.3548				p.S134S		Atlas-SNP	.											.	QRICH2	143	.	0			c.T402C						PASS	.	A		2926,1480	679.0+/-403.6	977,972,254	59.0	60.0	60.0		402	-0.2	0.0	17	dbSNP_116	60	2485,6115	407.1+/-349.0	347,1791,2162	no	coding-synonymous	QRICH2	NM_032134.1		1324,2763,2416	GG,GA,AA		28.8953,33.5906,41.6039		134/1664	74289908	5411,7595	2203	4300	6503	SO:0001819	synonymous_variant	84074	exon4			TTCCCTACTGGAA	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.402T>C	17.37:g.74289908A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			A|0.557;G|0.443	0.443	strong		0.582	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
CALD1	800	hgsc.bcm.edu	37	7	134645319	134645319	+	Silent	SNP	C	C	T	rs2230186	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:134645319C>T	ENST00000361675.2	+	13	2464	c.2235C>T	c.(2233-2235)cgC>cgT	p.R745R	CALD1_ENST00000361901.2_Silent_p.R490R|CALD1_ENST00000424922.1_Silent_p.R484R|CALD1_ENST00000466704.1_3'UTR|CALD1_ENST00000417172.1_Silent_p.R490R|CALD1_ENST00000495522.1_Silent_p.R509R|CALD1_ENST00000543443.1_Silent_p.R495R|CALD1_ENST00000361388.2_Silent_p.R516R|CALD1_ENST00000422748.1_Silent_p.R515R|CALD1_ENST00000393118.2_Silent_p.R510R			Q05682	CALD1_HUMAN	caldesmon 1	745					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|calmodulin binding (GO:0005516)|tropomyosin binding (GO:0005523)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(15)|lung(10)	43						TTTCTAGCCGCATCAATGAAT	0.413													C|||	120	0.0239617	0.0091	0.0346	5008	,	,		18624	0.0		0.0656	False		,,,				2504	0.0184				p.R745R		Atlas-SNP	.											.	CALD1	150	.	0			c.C2235T						PASS	.	C	,,,,	60,4346	58.1+/-94.6	1,58,2144	101.0	96.0	97.0		1470,2235,1530,1452,1545	3.8	1.0	7	dbSNP_98	97	498,8102	142.0+/-198.3	15,468,3817	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CALD1	NM_004342.6,NM_033138.3,NM_033139.3,NM_033140.3,NM_033157.3	,,,,	16,526,5961	TT,TC,CC		5.7907,1.3618,4.2903	,,,,	490/539,745/794,510/559,484/533,515/564	134645319	558,12448	2203	4300	6503	SO:0001819	synonymous_variant	800	exon13			TAGCCGCATCAAT	M64110	CCDS5834.1, CCDS5835.1, CCDS5836.1, CCDS47716.1, CCDS47717.1, CCDS5836.2	7q33	2007-04-23			ENSG00000122786	ENSG00000122786			1441	protein-coding gene	gene with protein product		114213				1885618	Standard	NM_004342		Approved	CDM, H-CAD, L-CAD	uc003vrz.3	Q05682	OTTHUMG00000155407	ENST00000361675.2:c.2235C>T	7.37:g.134645319C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_033138	A8K0X1|Q13978|Q13979|Q14741|Q14742|Q9UD91	Silent	SNP	ENST00000361675.2	37	CCDS5835.1																																																																																			C|0.964;T|0.036	0.036	strong		0.413	CALD1-005	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339939.1	NM_033138	
ZNF461	92283	hgsc.bcm.edu	37	19	37129806	37129806	+	Missense_Mutation	SNP	G	G	A	rs61746529	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:37129806G>A	ENST00000588268.1	-	6	1668	c.1441C>T	c.(1441-1443)Cat>Tat	p.H481Y	ZNF461_ENST00000360357.4_Missense_Mutation_p.H458Y|ZNF461_ENST00000540605.2_5'UTR	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	481					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(4)|kidney(1)|large_intestine(4)|lung(17)|prostate(1)|urinary_tract(2)	29	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			AGGTGTGAATGAAGTCTAAAG	0.388													G|||	107	0.0213658	0.0015	0.0648	5008	,	,		20624	0.0		0.0487	False		,,,				2504	0.0112				p.H481Y		Atlas-SNP	.											.	ZNF461	73	.	0			c.C1441T						PASS	.	G	TYR/HIS	51,4349	46.0+/-80.4	0,51,2149	65.0	69.0	67.0		1441	2.4	0.8	19	dbSNP_129	67	471,8125	135.9+/-193.0	18,435,3845	yes	missense	ZNF461	NM_153257.2	83	18,486,5994	AA,AG,GG		5.4793,1.1591,4.0166	benign	481/564	37129806	522,12474	2200	4298	6498	SO:0001583	missense	92283	exon6			GTGAATGAAGTCT	BX649031	CCDS54257.1, CCDS74348.1	19q13.13	2013-01-08				ENSG00000197808		"""Zinc fingers, C2H2-type"", ""-"""	21629	protein-coding gene	gene with protein product		608640				11579202, 15004467	Standard	XM_005259402		Approved	GIOT-1, MGC33911	uc002oem.3	Q8TAF7		ENST00000588268.1:c.1441C>T	19.37:g.37129806G>A	ENSP00000467931:p.His481Tyr	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	37	CCDS54257.1	60	0.027472527472527472	3	0.006097560975609756	19	0.052486187845303865	0	0.0	38	0.05013192612137203	G	0.346	-0.947456	0.02304	0.011591	0.054793	ENSG00000197808	ENST00000396893;ENST00000396896;ENST00000360357;ENST00000540605;ENST00000396892	T	0.07567	3.18	3.48	2.41	0.29592	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01029	0.0034	N	0.21240	0.645	0.09310	N	1	D;D;P	0.58268	0.982;0.96;0.812	P;B;B	0.51701	0.677;0.358;0.373	T	0.03384	-1.1042	9	0.02654	T	1	.	8.0191	0.30398	0.0:0.1739:0.6475:0.1786	rs61746529	458;403;481	B4DRP8;Q59G30;Q8TAF7	.;.;ZN461_HUMAN	Y	481;212;458;354;175	ENSP00000353515:H458Y	ENSP00000353515:H458Y	H	-	1	0	ZNF461	41821646	0.000000	0.05858	0.774000	0.31636	0.986000	0.74619	-0.110000	0.10824	0.782000	0.33613	0.491000	0.48974	CAT	G|0.967;A|0.033	0.033	strong		0.388	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257	
SDC2	6383	hgsc.bcm.edu	37	8	97605800	97605800	+	Silent	SNP	C	C	T	rs1126681	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:97605800C>T	ENST00000302190.4	+	2	1074	c.153C>T	c.(151-153)taC>taT	p.Y51Y	SDC2_ENST00000518385.1_Intron|SDC2_ENST00000522911.1_Silent_p.Y22Y|SDC2_ENST00000519914.1_Silent_p.Y22Y	NM_002998.3	NP_002989.2	P34741	SDC2_HUMAN	syndecan 2	51					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dendrite morphogenesis (GO:0048813)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|regulation of dendrite morphogenesis (GO:0048814)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)	p.Y51Y(2)		breast(1)|cervix(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|stomach(2)	16	Breast(36;3.41e-05)				Sargramostim(DB00020)	ACGATGACTACGCTTCTGCGT	0.473													C|||	1132	0.226038	0.0484	0.1628	5008	,	,		21516	0.3591		0.2217	False		,,,				2504	0.3783				p.Y51Y		Atlas-SNP	.											SDC2,NS,carcinoma,0,2	SDC2	33	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.C153T						PASS	.	C		362,4044	186.0+/-213.0	14,334,1855	142.0	108.0	119.0		153	-6.0	0.9	8	dbSNP_86	119	1894,6706	335.6+/-321.5	207,1480,2613	no	coding-synonymous	SDC2	NM_002998.3		221,1814,4468	TT,TC,CC		22.0233,8.2161,17.3458		51/202	97605800	2256,10750	2203	4300	6503	SO:0001819	synonymous_variant	6383	exon2			TGACTACGCTTCT	BC030133	CCDS6272.1	8q22-q23	2011-08-11	2007-02-15		ENSG00000169439	ENSG00000169439		"""Proteoglycans / Cell Surface : Syndecans"", ""CD molecules"""	10659	protein-coding gene	gene with protein product	"""syndecan proteoglycan 2"""	142460	"""heparan sulfate proteoglycan 1, cell surface-associated"""	HSPG, HSPG1		8187643	Standard	NM_002998		Approved	fibroglycan, SYND2, CD362	uc003yhv.1	P34741	OTTHUMG00000164689	ENST00000302190.4:c.153C>T	8.37:g.97605800C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_002998	B3KQA3|Q6PIS6|Q9H6V1	Silent	SNP	ENST00000302190.4	37	CCDS6272.1																																																																																			C|0.804;T|0.196	0.196	strong		0.473	SDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379750.1	NM_002998	
TTI1	9675	hgsc.bcm.edu	37	20	36624780	36624780	+	Missense_Mutation	SNP	C	C	T	rs34900517	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:36624780C>T	ENST00000373448.2	-	8	3321	c.3083G>A	c.(3082-3084)aGg>aAg	p.R1028K	TTI1_ENST00000449821.1_Missense_Mutation_p.R1028K|TTI1_ENST00000373447.3_Missense_Mutation_p.R1028K	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	1028			R -> K (in dbSNP:rs34900517).		regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						GACGTACCTCCTGGCAGCCTC	0.458													C|||	82	0.0163738	0.0	0.0202	5008	,	,		20369	0.0		0.0348	False		,,,				2504	0.0337				p.R1028K		Atlas-SNP	.											.	TTI1	104	.	0			c.G3083A						PASS	.	C	LYS/ARG	30,4376	35.2+/-66.4	0,30,2173	97.0	90.0	93.0		3083	5.3	1.0	20	dbSNP_126	93	289,8311	106.6+/-167.4	6,277,4017	yes	missense	TTI1	NM_014657.1	26	6,307,6190	TT,TC,CC		3.3605,0.6809,2.4527	benign	1028/1090	36624780	319,12687	2203	4300	6503	SO:0001583	missense	9675	exon8			TACCTCCTGGCAG	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"""smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	614425	"""KIAA0406"", ""Tel2 interacting protein 1 homolog (S. pombe)"""	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.3083G>A	20.37:g.36624780C>T	ENSP00000362547:p.Arg1028Lys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	CCDS13300.1	42	0.019230769230769232	0	0.0	13	0.03591160220994475	0	0.0	29	0.03825857519788918	C	7.314	0.615633	0.14129	0.006809	0.033605	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.65732	-0.17;-0.17;-0.17	5.3	5.3	0.74995	Armadillo-type fold (1);	0.315894	0.35970	N	0.002874	T	0.22085	0.0532	M	0.63428	1.95	0.33917	D	0.640416	B	0.02656	0.0	B	0.06405	0.002	T	0.50750	-0.8791	10	0.29301	T	0.29	.	6.2312	0.20736	0.1868:0.7196:0.0:0.0936	rs34900517	1028	O43156	TTI1_HUMAN	K	1028	ENSP00000362547:R1028K;ENSP00000362546:R1028K;ENSP00000407270:R1028K	ENSP00000362546:R1028K	R	-	2	0	TTI1	36058194	0.984000	0.35163	1.000000	0.80357	0.970000	0.65996	0.975000	0.29449	2.756000	0.94617	0.563000	0.77884	AGG	C|0.975;T|0.025	0.025	strong		0.458	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657	
CFHR1	3078	hgsc.bcm.edu	37	1	196801078	196801078	+	Silent	SNP	A	A	T	rs414628	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196801078A>T	ENST00000320493.5	+	6	1030	c.942A>T	c.(940-942)cgA>cgT	p.R314R	CFHR2_ENST00000367421.3_Intron|CFHR1_ENST00000367424.4_Silent_p.R255R	NM_002113.2	NP_002104.2	Q03591	FHR1_HUMAN	complement factor H-related 1	314	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|kidney(1)|large_intestine(2)|lung(7)	11						ACACATTGCGAACAACATGTT	0.383													-|||	2122	0.423722	0.326	0.5072	5008	,	,		13037	0.5228		0.4433	False		,,,				2504	0.3742				p.R314R		Atlas-SNP	.											CFHR1,right_upper_lobe,carcinoma,+1,1	CFHR1	47	1	0			c.A942T						PASS	.	A		1425,2329		530,365,982	77.0	82.0	80.0		942	1.1	0.0	1	dbSNP_80	80	3341,4909		1008,1325,1792	no	coding-synonymous	CFHR1	NM_002113.2		1538,1690,2774	TT,TA,AA		40.497,37.9595,39.7034		314/331	196801078	4766,7238	1877	4125	6002	SO:0001819	synonymous_variant	3078	exon6			ATTGCGAACAACA	M65292	CCDS1386.1	1q32	2014-09-17	2004-08-09	2006-02-28	ENSG00000244414	ENSG00000244414		"""Complement system"""	4888	protein-coding gene	gene with protein product		134371	"""H factor (complement)-like 1"", ""complement factor H-related 1 pseudogene"", ""H factor (complement)-like 2"""	HFL1, CFHL1, CFHR1P, HFL2, CFHL1P		1711047, 1826708	Standard	NM_002113		Approved	H36-1, FHR1, CFHL, H36-2		Q03591	OTTHUMG00000036276	ENST00000320493.5:c.942A>T	1.37:g.196801078A>T		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	494	205	0.41498	NM_002113	A8K465|Q3B774|Q9UJ17	Silent	SNP	ENST00000320493.5	37	CCDS1386.1																																																																																			A|0.604;T|0.396	0.396	strong		0.383	CFHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088251.2	NM_002113	
LGALS9	3965	hgsc.bcm.edu	37	17	25970642	25970642	+	Missense_Mutation	SNP	A	A	T	rs361498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:25970642A>T	ENST00000395473.2	+	5	2004	c.536A>T	c.(535-537)cAa>cTa	p.Q179L	LGALS9_ENST00000413914.2_Missense_Mutation_p.Q122L|LGALS9_ENST00000302228.5_Intron|LGALS9_ENST00000313648.6_Intron|LGALS9_ENST00000310394.5_Intron	NM_009587.2	NP_033665.1	O00182	LEG9_HUMAN	lectin, galactoside-binding, soluble, 9	179					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|galactose binding (GO:0005534)|signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(12)|skin(1)	18	Lung NSC(42;0.0103)		BRCA - Breast invasive adenocarcinoma(3;0.0141)	UCEC - Uterine corpus endometrioid carcinoma (53;0.155)		GGGCGCAGACAAAAAGTGAGT	0.627													A|||	309	0.0617013	0.0121	0.0965	5008	,	,		17794	0.0		0.1998	False		,,,				2504	0.0256				p.Q179L	Melanoma(106;677 1527 28724 29571 46552)|Ovarian(193;263 2088 2118 29005 43023)	Atlas-SNP	.											.	LGALS9	29	.	0			c.A536T						PASS	.	A	,LEU/GLN	180,4226		2,176,2025	20.0	20.0	20.0		,536	-0.1	0.0	17	dbSNP_79	20	1755,6819		190,1375,2722	no	intron,missense	LGALS9	NM_002308.3,NM_009587.2	,113	192,1551,4747	TT,TA,AA		20.4689,4.0853,14.9076	,benign	,179/356	25970642	1935,11045	2203	4287	6490	SO:0001583	missense	3965	exon5			GCAGACAAAAAGT	AB006782	CCDS11222.1, CCDS32592.1	17q11.2	2013-03-28	2008-07-25		ENSG00000168961	ENSG00000168961		"""Lectins, galactoside-binding"""	6570	protein-coding gene	gene with protein product	"""galectin 9"""	601879				9045665	Standard	NM_009587		Approved	LGALS9A	uc002gzp.3	O00182	OTTHUMG00000179831	ENST00000395473.2:c.536A>T	17.37:g.25970642A>T	ENSP00000378856:p.Gln179Leu	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	259	120	0.46332	NM_009587	A7VJG6|O14532|O75028|Q3B8N1|Q53FQ0|Q9NQ58	Missense_Mutation	SNP	ENST00000395473.2	37	CCDS11222.1	222	0.10164835164835165	14	0.028455284552845527	40	0.11049723756906077	4	0.006993006993006993	164	0.21635883905013192	A	12.31	1.899332	0.33535	0.040853	0.204689	ENSG00000168961	ENST00000395473;ENST00000413914	T;T	0.14893	3.89;2.47	3.53	-0.0973	0.13633	.	0.488214	0.17273	N	0.180295	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.21905	0.062;0.017	B;B	0.18871	0.023;0.004	T	0.45963	-0.9225	9	0.10902	T	0.67	.	9.0558	0.36405	0.6141:0.3859:0.0:0.0	rs361498;rs17399029	122;179	B4DWP7;O00182	.;LEG9_HUMAN	L	179;122	ENSP00000378856:Q179L;ENSP00000393695:Q122L	ENSP00000378856:Q179L	Q	+	2	0	LGALS9	22994769	0.000000	0.05858	0.022000	0.16811	0.614000	0.37383	-0.053000	0.11846	-0.054000	0.13266	-0.262000	0.10625	CAA	A|0.874;T|0.126	0.126	strong		0.627	LGALS9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255583.1	NM_009587	
WDR62	284403	hgsc.bcm.edu	37	19	36593915	36593915	+	Missense_Mutation	SNP	T	T	G	rs61741470	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36593915T>G	ENST00000270301.7	+	28	3386	c.3386T>G	c.(3385-3387)aTg>aGg	p.M1129R	WDR62_ENST00000401500.2_Missense_Mutation_p.M1134R			O43379	WDR62_HUMAN	WD repeat domain 62	1129					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GTCAAGCTCATGGACCGAGGC	0.632													T|||	275	0.0549121	0.0159	0.036	5008	,	,		19098	0.1062		0.0358	False		,,,				2504	0.0879				p.M1134R		Atlas-SNP	.											.	WDR62	102	.	0			c.T3401G						PASS	.	T	ARG/MET,ARG/MET	112,4294	83.4+/-121.9	0,112,2091	50.0	50.0	50.0		3401,3386	-5.3	0.0	19	dbSNP_129	50	337,8263	112.5+/-172.7	4,329,3967	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	91,91	4,441,6058	GG,GT,TT		3.9186,2.542,3.4523	benign,benign	1134/1524,1129/1519	36593915	449,12557	2203	4300	6503	SO:0001583	missense	284403	exon28			AGCTCATGGACCG	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.3386T>G	19.37:g.36593915T>G	ENSP00000270301:p.Met1129Arg	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	99	0.04532967032967033	9	0.018292682926829267	16	0.04419889502762431	45	0.07867132867132867	29	0.03825857519788918	T	6.810	0.518486	0.13005	0.02542	0.039186	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.44482	1.0;0.92	4.68	-5.29	0.02747	.	2.109050	0.01890	N	0.038466	T	0.01092	0.0036	N	0.08118	0	0.09310	N	1	B;B	0.17852	0.024;0.014	B;B	0.23150	0.044;0.019	T	0.12915	-1.0529	10	0.11794	T	0.64	2.1238	11.0584	0.47933	0.0:0.3636:0.0:0.6364	rs61741470	1134;1129	O43379-4;O43379	.;WDR62_HUMAN	R	1134;1129	ENSP00000384792:M1134R;ENSP00000270301:M1129R	ENSP00000270301:M1129R	M	+	2	0	WDR62	41285755	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-1.463000	0.02361	-0.706000	0.05028	-0.182000	0.12963	ATG	T|0.959;G|0.041	0.041	strong		0.632	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
ZNF567	163081	hgsc.bcm.edu	37	19	37209866	37209866	+	Silent	SNP	T	T	C	rs34642314	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:37209866T>C	ENST00000536254.2	+	6	462	c.240T>C	c.(238-240)gcT>gcC	p.A80A	ZNF567_ENST00000392163.2_Silent_p.A49A|ZNF850_ENST00000589390.1_Intron|ZNF567_ENST00000360729.4_Silent_p.A49A|ZNF567_ENST00000588311.1_Silent_p.A49A|ZNF567_ENST00000585696.1_Silent_p.A49A			Q8N184	ZN567_HUMAN	zinc finger protein 567	80					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)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Esophageal squamous(110;0.198)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ACTGGAAAGCTGAAGACTTTT	0.328													T|||	262	0.0523163	0.0061	0.1297	5008	,	,		17030	0.003		0.1083	False		,,,				2504	0.0532				p.A49A		Atlas-SNP	.											.	ZNF567	61	.	0			c.T147C						PASS	.	T		110,4258		1,108,2075	36.0	39.0	38.0		147	1.4	1.0	19	dbSNP_126	38	1018,7554		59,900,3327	no	coding-synonymous	ZNF567	NM_152603.2		60,1008,5402	CC,CT,TT		11.8759,2.5183,8.7172		49/617	37209866	1128,11812	2184	4286	6470	SO:0001819	synonymous_variant	163081	exon4			GAAAGCTGAAGAC	AK093034	CCDS12495.1, CCDS74349.1	19q13.12	2013-10-08				ENSG00000189042		"""Zinc fingers, C2H2-type"", ""-"""	28696	protein-coding gene	gene with protein product						12477932	Standard	XM_006723064		Approved	MGC45586	uc002oep.4	Q8N184		ENST00000536254.2:c.240T>C	19.37:g.37209866T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_152603	B3KX49|Q6N044	Silent	SNP	ENST00000536254.2	37																																																																																				T|0.917;C|0.083	0.083	strong		0.328	ZNF567-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000453549.1	NM_152603	
TOP3A	7156	hgsc.bcm.edu	37	17	18193941	18193941	+	Silent	SNP	G	G	A	rs2230154	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18193941G>A	ENST00000321105.5	-	13	1741	c.1527C>T	c.(1525-1527)gaC>gaT	p.D509D	TOP3A_ENST00000540524.1_Silent_p.D39D|TOP3A_ENST00000542570.1_Silent_p.D414D	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	509					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)	p.D509D(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TGGTCTCCCCGTCCACCATCT	0.582													g|||	896	0.178914	0.1611	0.2421	5008	,	,		20534	0.0605		0.3062	False		,,,				2504	0.1493				p.D509D		Atlas-SNP	.											TOP3A,NS,carcinoma,0,1	TOP3A	85	1	1	Substitution - coding silent(1)	stomach(1)	c.C1527T						PASS	.	A		901,3505	348.5+/-309.9	83,735,1385	88.0	62.0	71.0		1527	-6.1	1.0	17	dbSNP_98	71	2600,6000	422.0+/-353.9	383,1834,2083	no	coding-synonymous	TOP3A	NM_004618.3		466,2569,3468	AA,AG,GG		30.2326,20.4494,26.9183		509/1002	18193941	3501,9505	2203	4300	6503	SO:0001819	synonymous_variant	7156	exon13			CTCCCCGTCCACC	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.1527C>T	17.37:g.18193941G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	37	CCDS11194.1																																																																																			G|0.757;A|0.243	0.243	strong		0.582	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
SACS	26278	hgsc.bcm.edu	37	13	23930055	23930055	+	Missense_Mutation	SNP	A	A	T	rs2031640	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:23930055A>T	ENST00000382292.3	-	7	969	c.696T>A	c.(694-696)aaT>aaA	p.N232K	SACS_ENST00000382298.3_Missense_Mutation_p.N232K|SACS_ENST00000402364.1_5'UTR|SACS_ENST00000476776.1_5'Flank			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	232			N -> K (in dbSNP:rs2031640).		cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CATCTTTGAGATTCCAACATT	0.393													A|||	433	0.0864617	0.0068	0.0922	5008	,	,		18517	0.121		0.1292	False		,,,				2504	0.1104				p.N232K		Atlas-SNP	.											.	SACS	871	.	0			c.T696A						PASS	.	A	LYS/ASN	103,4303	79.9+/-118.3	2,99,2102	87.0	81.0	83.0		696	0.7	1.0	13	dbSNP_94	83	1002,7598	216.2+/-255.3	49,904,3347	yes	missense	SACS	NM_014363.4	94	51,1003,5449	TT,TA,AA		11.6512,2.3377,8.4961	probably-damaging	232/4580	23930055	1105,11901	2203	4300	6503	SO:0001583	missense	26278	exon8			TTTGAGATTCCAA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.696T>A	13.37:g.23930055A>T	ENSP00000371729:p.Asn232Lys	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	200	94	0.47	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	208|208	0.09523809523809523|0.09523809523809523	2|2	0.0040650406504065045|0.0040650406504065045	32|32	0.08839779005524862|0.08839779005524862	74|74	0.12937062937062938|0.12937062937062938	100|100	0.13192612137203166|0.13192612137203166	A|A	19.71|19.71	3.877814|3.877814	0.72294|0.72294	0.023377|0.023377	0.116512|0.116512	ENSG00000151835|ENSG00000151835	ENST00000382292;ENST00000382298|ENST00000455470	D;D|.	0.84146|.	-1.81;-1.81|.	5.94|5.94	0.714|0.714	0.18180|0.18180	ATPase-like, ATP-binding domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00300|0.00300	0.0009|0.0009	L|L	0.31420|0.31420	0.93|0.93	0.27070|0.27070	P|P	0.9633483|0.9633483	D;P;P|.	0.54601|.	0.967;0.767;0.787|.	P;P;B|.	0.57101|.	0.813;0.661;0.345|.	T|T	0.16217|0.16217	-1.0410|-1.0410	9|4	0.22706|.	T|.	0.39|.	.|.	5.7211|5.7211	0.17988|0.17988	0.6049:0.1294:0.2657:0.0|0.6049:0.1294:0.2657:0.0	rs2031640;rs17378785;rs2031640|rs2031640;rs17378785;rs2031640	131;19;232|.	B2REB1;E9PAL4;Q9NZJ4|.	.;.;SACS_HUMAN|.	K|T	232|132	ENSP00000371729:N232K;ENSP00000371735:N232K|.	ENSP00000371729:N232K|.	N|S	-|-	3|1	2|0	SACS|SACS	22828055|22828055	0.995000|0.995000	0.38212|0.38212	0.998000|0.998000	0.56505|0.56505	0.997000|0.997000	0.91878|0.91878	0.536000|0.536000	0.23129|0.23129	-0.073000|-0.073000	0.12842|0.12842	0.528000|0.528000	0.53228|0.53228	AAT|TCT	A|0.907;T|0.093	0.093	strong		0.393	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
INTS1	26173	hgsc.bcm.edu	37	7	1533513	1533513	+	Silent	SNP	A	A	G	rs2251226	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:1533513A>G	ENST00000404767.3	-	15	2030	c.1945T>C	c.(1945-1947)Ttg>Ctg	p.L649L	INTS1_ENST00000389470.4_Silent_p.L777L	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	649					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		GTGTCCTCCAAAATGGGCACC	0.677													G|||	3083	0.615615	0.8419	0.4236	5008	,	,		16908	0.7123		0.4662	False		,,,				2504	0.5				p.L649L		Atlas-SNP	.											.	INTS1	145	.	0			c.T1945C						PASS	.			3083,975		1206,671,152	17.0	24.0	22.0		1945	2.8	1.0	7	dbSNP_100	22	3480,4846		768,1944,1451	no	coding-synonymous	INTS1	NM_001080453.2		1974,2615,1603	GG,GA,AA		41.7968,24.0266,47.0042		649/2191	1533513	6563,5821	2029	4163	6192	SO:0001819	synonymous_variant	26173	exon15			CCTCCAAAATGGG	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1945T>C	7.37:g.1533513A>G		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	188	95	0.505319	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			A|0.379;G|0.621	0.621	strong		0.677	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
HSD17B14	51171	hgsc.bcm.edu	37	19	49339098	49339098	+	Missense_Mutation	SNP	T	T	C	rs8110220	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49339098T>C	ENST00000263278.4	-	2	357	c.91A>G	c.(91-93)Aac>Gac	p.N31D	HSD17B14_ENST00000599157.1_Missense_Mutation_p.N31D	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	31			N -> D (in dbSNP:rs8110220).		steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GCCCCGCTGTTCACTGAGAAT	0.607											OREG0025610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	1722	0.34385	0.6165	0.2867	5008	,	,		16704	0.0893		0.2674	False		,,,				2504	0.3569				p.N31D		Atlas-SNP	.											.	HSD17B14	25	.	0			c.A91G						PASS	.		ASP/ASN	2378,2028		645,1088,470	87.0	73.0	78.0		91	-1.8	0.1	19	dbSNP_116	78	2126,6472		258,1610,2431	yes	missense	HSD17B14	NM_016246.2	23	903,2698,2901	CC,CT,TT		24.7267,46.0281,34.6355	benign	31/271	49339098	4504,8500	2203	4299	6502	SO:0001583	missense	51171	exon2			CGCTGTTCACTGA	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.91A>G	19.37:g.49339098T>C	ENSP00000263278:p.Asn31Asp	Somatic	49	0	0	961	WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	665	0.30448717948717946	285	0.5792682926829268	115	0.31767955801104975	67	0.11713286713286714	198	0.2612137203166227	-	0.019	-1.451578	0.01080	0.539719	0.247267	ENSG00000087076	ENST00000263278	T	0.21031	2.03	3.1	-1.77	0.07982	NAD(P)-binding domain (1);	0.876083	0.09791	N	0.755389	T	0.00012	0.0000	N	0.03891	-0.335	0.52099	P	5.500000000002725E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41538	-0.9503	9	0.21540	T	0.41	.	4.0567	0.09819	0.0:0.3503:0.3462:0.3035	rs8110220;rs52799828;rs61231150;rs8110220	31	Q9BPX1	DHB14_HUMAN	D	31	ENSP00000263278:N31D	ENSP00000263278:N31D	N	-	1	0	HSD17B14	54030910	0.109000	0.22037	0.063000	0.19743	0.073000	0.16967	-0.043000	0.12043	-0.518000	0.06452	-0.382000	0.06688	AAC	C|0.335;N|0.001	0.335	strong		0.607	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
C2orf54	79919	hgsc.bcm.edu	37	2	241834907	241834907	+	Missense_Mutation	SNP	C	C	T	rs4359646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:241834907C>T	ENST00000388934.4	-	1	666	c.508G>A	c.(508-510)Gca>Aca	p.A170T		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	170			A -> T (in dbSNP:rs4359646).							haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GTACCTGGTGCGATGAGACTG	0.587													C|||	977	0.195088	0.3828	0.0793	5008	,	,		23936	0.1776		0.0954	False		,,,				2504	0.1442				p.A170T		Atlas-SNP	.											.	C2orf54	14	.	0			c.G508A						PASS	.	C	THR/ALA	1498,2888		255,988,950	20.0	22.0	22.0		508	-10.6	0.0	2	dbSNP_111	22	782,7804		43,696,3554	yes	missense	C2orf54	NM_001085437.1	58	298,1684,4504	TT,TC,CC		9.1078,34.1541,17.5763	benign	170/448	241834907	2280,10692	2193	4293	6486	SO:0001583	missense	79919	exon1			CTGGTGCGATGAG	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.508G>A	2.37:g.241834907C>T	ENSP00000373586:p.Ala170Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Missense_Mutation	SNP	ENST00000388934.4	37	CCDS42839.1	384	0.17582417582417584	200	0.4065040650406504	29	0.08011049723756906	81	0.14160839160839161	74	0.09762532981530343	C	0.326	-0.958772	0.02267	0.341541	0.091078	ENSG00000172478	ENST00000388934	T	0.11712	2.75	5.32	-10.6	0.00265	.	1.233210	0.05820	N	0.615553	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.48525	-0.9028	9	0.12103	T	0.63	-3.7009	12.4655	0.55755	0.0:0.4379:0.3889:0.1732	rs4359646;rs57803936;rs4359646	170	Q08AI8	CB054_HUMAN	T	170	ENSP00000373586:A170T	ENSP00000373586:A170T	A	-	1	0	C2orf54	241483580	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.769000	0.00780	-2.080000	0.00870	-1.564000	0.00881	GCA	C|0.838;T|0.162	0.162	strong		0.587	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
PSMD3	5709	hgsc.bcm.edu	37	17	38146154	38146154	+	Silent	SNP	T	T	C	rs9916279	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38146154T>C	ENST00000264639.4	+	5	1023	c.849T>C	c.(847-849)aaT>aaC	p.N283N	PSMD3_ENST00000541736.1_Silent_p.N145N	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	283					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)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Colorectal(19;0.000442)					CCAACAACAATGAGTGGGCCA	0.537													T|||	844	0.16853	0.3805	0.1398	5008	,	,		18840	0.0069		0.165	False		,,,				2504	0.0726				p.N283N	Ovarian(186;531 2051 6385 19668 48409)	Atlas-SNP	.											.	PSMD3	56	.	0			c.T849C						PASS	.	T		1483,2923	476.4+/-357.6	248,987,968	71.0	57.0	62.0		849	-8.4	0.5	17	dbSNP_119	62	1416,7184	272.8+/-290.3	116,1184,3000	no	coding-synonymous	PSMD3	NM_002809.2		364,2171,3968	CC,CT,TT		16.4651,33.6586,22.2897		283/535	38146154	2899,10107	2203	4300	6503	SO:0001819	synonymous_variant	5709	exon5			CAACAATGAGTGG	D67025	CCDS11356.1	17q21.2	2010-07-23			ENSG00000108344	ENSG00000108344		"""Proteasome (prosome, macropain) subunits"""	9560	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 2"""	TSTA2		9017604	Standard	NM_002809		Approved	S3, P58, Rpn3	uc002htn.2	O43242	OTTHUMG00000133251	ENST00000264639.4:c.849T>C	17.37:g.38146154T>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	40	28	0.7	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Silent	SNP	ENST00000264639.4	37	CCDS11356.1																																																																																			T|0.798;C|0.202	0.202	strong		0.537	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809	
TULP3	7289	hgsc.bcm.edu	37	12	3049698	3049698	+	3'UTR	SNP	T	T	C	rs998814	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:3049698T>C	ENST00000448120.2	+	0	2468				TULP3_ENST00000397132.2_Missense_Mutation_p.C438R	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3						anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CTTCCCAGAATGTATCCAAAC	0.498													C|||	1389	0.277356	0.4085	0.2046	5008	,	,		20215	0.2183		0.2058	False		,,,				2504	0.2863				p.C438R		Atlas-SNP	.											.	TULP3	45	.	0			c.T1312C						PASS	.	C	,ARG/CYS	517,867		96,325,271	49.0	44.0	46.0		,1312	-0.3	0.0	12	dbSNP_86	46	691,2491		69,553,969	yes	utr-3,missense	TULP3	NM_003324.4,NM_001160408.1	,180	165,878,1240	CC,CT,TT		21.7159,37.3555,26.4564	,benign	,438/502	3049698	1208,3358	692	1591	2283	SO:0001624	3_prime_UTR_variant	7289	exon12			CCAGAATGTATCC	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.*1088T>C	12.37:g.3049698T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_001160408	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	37	CCDS8519.1	537	0.24587912087912087	186	0.3780487804878049	75	0.20718232044198895	110	0.19230769230769232	166	0.21899736147757257	C	0.107	-1.143619	0.01728	0.373555	0.217159	ENSG00000078246	ENST00000397132	D	0.91351	-2.83	3.48	-0.313	0.12754	.	.	.	.	.	T	0.00012	0.0000	N	0.04090	-0.28	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10314	-1.0635	8	0.46703	T	0.11	.	4.1363	0.10172	0.0:0.2335:0.1803:0.5862	rs998814;rs3210448;rs998814	438	F8WBZ9	.	R	438	ENSP00000380321:C438R	ENSP00000380321:C438R	C	+	1	0	TULP3	2919959	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.057000	0.03486	-0.212000	0.10109	-1.259000	0.01468	TGT	A|0.008;C|0.256	0.256	strong		0.498	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
LLGL1	3996	hgsc.bcm.edu	37	17	18137141	18137141	+	Missense_Mutation	SNP	A	A	G	rs2290505	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18137141A>G	ENST00000316843.4	+	5	538	c.442A>G	c.(442-444)Agc>Ggc	p.S148G		NM_004140.3	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1 (Drosophila)	148			S -> G (in dbSNP:rs2290505). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7542763, ECO:0000269|PubMed:8565641}.		axonogenesis (GO:0007409)|cortical actin cytoskeleton organization (GO:0030866)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|maintenance of apical/basal cell polarity (GO:0035090)|positive regulation of Rab GTPase activity (GO:0032851)|protein complex assembly (GO:0006461)	cell projection (GO:0042995)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome membrane (GO:0031901)|Golgi cis cisterna (GO:0000137)|myelin sheath abaxonal region (GO:0035748)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)|structural molecule activity (GO:0005198)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_neural(463;0.228)					GGTGGCTGCCAGCGACATAGC	0.632													G|||	3918	0.782348	0.848	0.7493	5008	,	,		11652	0.6786		0.7614	False		,,,				2504	0.8456				p.S148G		Atlas-SNP	.											LLGL1,rectum,carcinoma,0,1	LLGL1	61	1	0			c.A442G						PASS	.	G	GLY/SER	3690,716	298.1+/-285.1	1556,578,69	89.0	80.0	83.0		442	2.6	0.0	17	dbSNP_100	83	6459,2141	365.6+/-334.0	2422,1615,263	yes	missense	LLGL1	NM_004140.3	56	3978,2193,332	GG,GA,AA		24.8953,16.2506,21.9668	benign	148/1065	18137141	10149,2857	2203	4300	6503	SO:0001583	missense	3996	exon5			GCTGCCAGCGACA		CCDS32586.1	17p11.2	2013-01-10	2001-11-28		ENSG00000131899	ENSG00000131899		"""WD repeat domain containing"""	6628	protein-coding gene	gene with protein product		600966	"""lethal giant larvae (Drosophila) homolog 1"""	DLG4, LLGL, HUGL, HUGL-1		7542763, 8565641	Standard	XM_005256643		Approved		uc002gsp.3	Q15334	OTTHUMG00000059396	ENST00000316843.4:c.442A>G	17.37:g.18137141A>G	ENSP00000321537:p.Ser148Gly	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_004140	A7MBM7|O00188|Q58F11|Q86UK6	Missense_Mutation	SNP	ENST00000316843.4	37	CCDS32586.1	1650	0.7554945054945055	406	0.8252032520325203	274	0.7569060773480663	402	0.7027972027972028	568	0.7493403693931399	G	0.008	-1.867144	0.00547	0.837494	0.751047	ENSG00000131899	ENST00000316843	T	0.05139	3.49	5.87	2.63	0.31362	WD40 repeat-like-containing domain (1);	0.357650	0.36444	N	0.002589	T	0.00012	0.0000	N	0.11341	0.13	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07673	-1.0760	9	0.16896	T	0.51	-8.2838	7.0524	0.25081	0.2156:0.0:0.6055:0.1788	rs2290505;rs58954283;rs2290505	148	Q15334	L2GL1_HUMAN	G	148	ENSP00000321537:S148G	ENSP00000321537:S148G	S	+	1	0	LLGL1	18077866	0.002000	0.14202	0.001000	0.08648	0.033000	0.12548	-0.023000	0.12456	0.428000	0.26173	-0.748000	0.03510	AGC	A|0.229;G|0.771	0.771	strong		0.632	LLGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132067.3		
TACC2	10579	hgsc.bcm.edu	37	10	123846485	123846485	+	Silent	SNP	A	A	G	rs4751871	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123846485A>G	ENST00000369005.1	+	4	4810	c.4470A>G	c.(4468-4470)caA>caG	p.Q1490Q	TACC2_ENST00000334433.3_Silent_p.Q1490Q|TACC2_ENST00000515603.1_Silent_p.Q1490Q|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Silent_p.Q1490Q|TACC2_ENST00000515273.1_Silent_p.Q1490Q	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1490					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGGCTCTGCAAGATCCAGCTT	0.597													G|||	1026	0.204872	0.3071	0.1844	5008	,	,		19551	0.1012		0.2117	False		,,,				2504	0.181				p.Q1490Q		Atlas-SNP	.											.	TACC2	271	.	0			c.A4470G						PASS	.	G	,	1515,2891	667.9+/-401.9	257,1001,945	48.0	45.0	46.0		,4470	3.0	0.2	10	dbSNP_111	46	1931,6669	721.9+/-406.4	215,1501,2584	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	472,2502,3529	GG,GA,AA		22.4535,34.3849,26.4955	,	,1490/2949	123846485	3446,9560	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			TCTGCAAGATCCA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.4470A>G	10.37:g.123846485A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			A|0.762;G|0.238	0.238	strong		0.597	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
MOB3C	148932	hgsc.bcm.edu	37	1	47080665	47080665	+	Intron	SNP	C	C	T	rs11211328	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47080665C>T	ENST00000319928.3	-	2	181				MOB3C_ENST00000477318.1_Intron|MOB3C_ENST00000271139.8_Missense_Mutation_p.M28I|MKNK1_ENST00000545730.1_Intron|MOB3C_ENST00000371940.1_5'UTR	NM_201403.2	NP_958805.1	Q70IA8	MOB3C_HUMAN	MOB kinase activator 3C								metal ion binding (GO:0046872)										TCATCTCATCCATCCCGACTC	0.463													C|||	1275	0.254593	0.2413	0.3271	5008	,	,		15620	0.246		0.2654	False		,,,				2504	0.2188				p.M28I		Atlas-SNP	.											.	MOB3C	1	.	0			c.G84A						PASS	.	C	ILE/MET,	1074,3332	391.0+/-327.9	143,788,1272	80.0	79.0	79.0		84,	-0.1	0.0	1	dbSNP_120	79	2166,6434	370.3+/-335.8	254,1658,2388	yes	missense,intron	MOB3C	NM_145279.4,NM_201403.2	10,	397,2446,3660	TT,TC,CC		25.186,24.3759,24.9116	,	28/269,	47080665	3240,9766	2203	4300	6503	SO:0001627	intron_variant	148932	exon1			CTCATCCATCCCG	AK091808	CCDS539.1, CCDS540.1	1p34.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000142961	ENSG00000142961		"""MOB kinase activators"""	29800	protein-coding gene	gene with protein product			"""MOB1, Mps One Binder kinase activator-like 2C (yeast)"""	MOBKL2C		12477932	Standard	NM_145279		Approved	MOB1E	uc001cqe.4	Q70IA8	OTTHUMG00000007989	ENST00000319928.3:c.50-1622G>A	1.37:g.47080665C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_145279	D3DQ22|Q0VA98|Q5TC10|Q5TC11|Q8NAZ2|Q8NF28	Missense_Mutation	SNP	ENST00000319928.3	37	CCDS540.1	585	0.26785714285714285	128	0.2601626016260163	122	0.3370165745856354	146	0.25524475524475526	189	0.24934036939313983	C	10.54	1.377711	0.24944	0.243759	0.25186	ENSG00000142961	ENST00000271139	.	.	.	3.5	-0.136	0.13473	.	3.731830	0.01478	U	0.016542	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.30621	-0.9972	5	0.11794	T	0.64	-1.6724	5.769	0.18243	0.0:0.527:0.0:0.473	rs11211328;rs52833882;rs58382771;rs11211328	.	.	.	I	28	.	ENSP00000271139:M28I	M	-	3	0	MOBKL2C	46853252	0.002000	0.14202	0.000000	0.03702	0.020000	0.10135	0.609000	0.24238	-0.020000	0.14032	-0.136000	0.14681	ATG	C|0.743;T|0.257	0.257	strong		0.463	MOB3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145279	
RTN3	10313	hgsc.bcm.edu	37	11	63449125	63449125	+	Missense_Mutation	SNP	C	C	A	rs11551944	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:63449125C>A	ENST00000377819.5	+	1	171	c.17C>A	c.(16-18)gCg>gAg	p.A6E	RTN3_ENST00000356000.3_Missense_Mutation_p.A6E|RTN3_ENST00000540798.1_Missense_Mutation_p.A6E|RTN3_ENST00000341307.2_Missense_Mutation_p.A6E|RTN3_ENST00000538995.1_3'UTR|RTN3_ENST00000339997.4_Missense_Mutation_p.A6E|RTN3_ENST00000354497.4_Missense_Mutation_p.A6E|RTN3_ENST00000537981.1_Missense_Mutation_p.A6E	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	6			A -> E (in dbSNP:rs11551944). {ECO:0000269|PubMed:15946766}.		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						GAGCCGTCGGCGGCCACTCAG	0.687													C|||	380	0.0758786	0.0295	0.0648	5008	,	,		13038	0.003		0.1332	False		,,,				2504	0.1626				p.A6E		Atlas-SNP	.											RTN3_ENST00000356000,NS,carcinoma,0,3	RTN3	104	3	0			c.C17A						PASS	.	C	GLU/ALA,GLU/ALA,GLU/ALA,GLU/ALA	234,4126		8,218,1954	27.0	33.0	31.0		17,17,17,17	3.4	1.0	11	dbSNP_120	31	1271,7283		98,1075,3104	yes	missense,missense,missense,missense	RTN3	NM_006054.2,NM_201428.1,NM_201429.1,NM_201430.1	107,107,107,107	106,1293,5058	AA,AC,CC		14.8585,5.367,11.654	probably-damaging,probably-damaging,probably-damaging,probably-damaging	6/237,6/1014,6/256,6/242	63449125	1505,11409	2180	4277	6457	SO:0001583	missense	10313	exon1			CGTCGGCGGCCAC	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.17C>A	11.37:g.63449125C>A	ENSP00000367050:p.Ala6Glu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_201428	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	143	0.06547619047619048	15	0.03048780487804878	27	0.07458563535911603	1	0.0017482517482517483	100	0.13192612137203166	C	17.49	3.403311	0.62288	0.05367	0.148585	ENSG00000133318	ENST00000341307;ENST00000356000;ENST00000542238;ENST00000377819;ENST00000339997;ENST00000540798;ENST00000545432;ENST00000543552;ENST00000537981;ENST00000354497	T;T;T;T;T;T;T;T;T;T	0.60548	0.55;0.58;0.65;1.1;1.01;0.97;0.22;0.26;0.76;0.18	4.33	3.42	0.39159	.	0.599771	0.13805	N	0.361511	T	0.00524	0.0017	L	0.27053	0.805	0.45930	P	0.0012349999999999861	P;D;D;P;D;D;D	0.65815	0.856;0.992;0.987;0.613;0.995;0.992;0.995	B;P;P;B;D;P;D	0.69142	0.434;0.906;0.807;0.298;0.962;0.906;0.962	T	0.23404	-1.0189	9	0.87932	D	0	-2.6338	8.4535	0.32884	0.0:0.8889:0.0:0.1111	rs11551944;rs17249377;rs11551944	6;6;6;6;6;6;6	B7Z4M0;F5H774;O95197;O95197-5;O95197-3;O95197-2;O95197-4	.;.;RTN3_HUMAN;.;.;.;.	E	6	ENSP00000340903:A6E;ENSP00000348279:A6E;ENSP00000437971:A6E;ENSP00000367050:A6E;ENSP00000344106:A6E;ENSP00000442733:A6E;ENSP00000441614:A6E;ENSP00000442080:A6E;ENSP00000440874:A6E;ENSP00000346492:A6E	ENSP00000344106:A6E	A	+	2	0	RTN3	63205701	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	0.821000	0.27338	0.819000	0.34492	0.462000	0.41574	GCG	C|0.903;A|0.097	0.097	strong		0.687	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183708	11183708	+	Missense_Mutation	SNP	T	T	C	rs80125932	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11183708T>C	ENST00000390675.2	-	1	298	c.227A>G	c.(226-228)tAt>tGt	p.Y76C	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	76					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						TTCTACACTATAAAAAGCTGG	0.408																																					p.Y76C		Atlas-SNP	.											.	TAS2R31	24	.	0			c.A227G						PASS	.	T	CYS/TYR	98,4028		0,98,1965	81.0	95.0	91.0		227	1.1	0.0	12	dbSNP_131	91	880,7650		0,880,3385	no	missense	TAS2R31	NM_176885.2	194	0,978,5350	CC,CT,TT		10.3165,2.3752,7.7276	benign	76/310	11183708	978,11678	2063	4265	6328	SO:0001583	missense	259290	exon1			ACACTATAAAAAG	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.227A>G	12.37:g.11183708T>C	ENSP00000375093:p.Tyr76Cys	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	158	25	0.158228	NM_176885	P59547|Q17R84|Q645X5	Missense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	T	5.935	0.356563	0.11239	0.023752	0.103165	ENSG00000256436	ENST00000390675	T	0.38240	1.15	2.45	1.15	0.20763	.	.	.	.	.	T	0.01061	0.0035	M	0.75777	2.31	0.09310	N	1	B	0.18863	0.031	B	0.27262	0.078	T	0.16541	-1.0399	9	0.54805	T	0.06	.	5.2988	0.15766	0.0:0.0:0.2988:0.7012	.	76	P59538	T2R31_HUMAN	C	76	ENSP00000375093:Y76C	ENSP00000375093:Y76C	Y	-	2	0	TAS2R31	11074975	0.001000	0.12720	0.005000	0.12908	0.116000	0.19942	0.134000	0.15932	0.151000	0.19162	0.163000	0.16589	TAT	T|0.871;C|0.129	0.129	strong		0.408	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
AKAP6	9472	hgsc.bcm.edu	37	14	33293531	33293531	+	Missense_Mutation	SNP	T	T	A	rs4647899	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:33293531T>A	ENST00000280979.4	+	13	6682	c.6512T>A	c.(6511-6513)tTc>tAc	p.F2171Y	AKAP6_ENST00000557272.1_Intron	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	2171			F -> Y (in dbSNP:rs4647899).		action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		GAGCCTTGTTTCTCTAGTGCT	0.468													T|||	1344	0.268371	0.2012	0.4035	5008	,	,		21217	0.3413		0.2843	False		,,,				2504	0.1718				p.F2171Y	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.T6512A						PASS	.	T	TYR/PHE	936,3470	355.6+/-313.1	90,756,1357	87.0	77.0	81.0		6512	4.6	0.0	14	dbSNP_111	81	2467,6133	405.6+/-348.5	347,1773,2180	yes	missense	AKAP6	NM_004274.4	22	437,2529,3537	AA,AT,TT		28.686,21.2438,26.1648	benign	2171/2320	33293531	3403,9603	2203	4300	6503	SO:0001583	missense	9472	exon13			CTTGTTTCTCTAG	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.6512T>A	14.37:g.33293531T>A	ENSP00000280979:p.Phe2171Tyr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	680	0.31135531135531136	102	0.2073170731707317	155	0.4281767955801105	212	0.3706293706293706	211	0.2783641160949868	T	12.47	1.948868	0.34377	0.212438	0.28686	ENSG00000151320	ENST00000280979	T	0.04970	3.52	5.83	4.64	0.57946	.	0.764012	0.12553	N	0.458849	T	0.00012	0.0000	L	0.41236	1.265	0.58432	P	8.000000000008E-6	B	0.16802	0.019	B	0.11329	0.006	T	0.43686	-0.9376	9	0.30078	T	0.28	0.3775	6.9522	0.24552	0.0:0.0811:0.146:0.7728	rs4647899;rs17099592;rs4647899	2171	Q13023	AKAP6_HUMAN	Y	2171	ENSP00000280979:F2171Y	ENSP00000280979:F2171Y	F	+	2	0	AKAP6	32363282	0.171000	0.23029	0.001000	0.08648	0.186000	0.23388	2.140000	0.42159	0.973000	0.38340	0.533000	0.62120	TTC	T|0.722;A|0.278	0.278	strong		0.468	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
TGFBI	7045	hgsc.bcm.edu	37	5	135388663	135388663	+	Silent	SNP	A	A	G	rs1054124	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:135388663A>G	ENST00000442011.2	+	8	1142	c.981A>G	c.(979-981)gtA>gtG	p.V327V	TGFBI_ENST00000305126.8_Silent_p.V327V	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	327	FAS1 2. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GGCTGTCTGTAGAGACCCTGG	0.557													G|||	1939	0.387181	0.5446	0.3631	5008	,	,		21375	0.3433		0.2594	False		,,,				2504	0.3681				p.V327V		Atlas-SNP	.											.	TGFBI	76	.	0			c.A981G						PASS	.	G		2109,2145		546,1017,564	74.0	84.0	81.0		981	5.7	1.0	5	dbSNP_86	81	2293,6195		329,1635,2280	no	coding-synonymous	TGFBI	NM_000358.2		875,2652,2844	GG,GA,AA		27.0146,49.5769,34.5472		327/684	135388663	4402,8340	2127	4244	6371	SO:0001819	synonymous_variant	7045	exon8			GTCTGTAGAGACC	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.981A>G	5.37:g.135388663A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	58	0.43609	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1	779	0.3566849816849817	259	0.5264227642276422	124	0.3425414364640884	195	0.3409090909090909	201	0.26517150395778366	G	5.696	0.312930	0.10789	0.495769	0.270146	ENSG00000120708	ENST00000514554	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48603	-0.9021	3	.	.	.	-4.4285	15.1618	0.72791	0.0679:0.0:0.932:0.0	rs1054124;rs2228405;rs3173020;rs3749783;rs7723764;rs17849889;rs17857531;rs61124579;rs1054124	.	.	.	G	45	.	.	R	+	1	2	TGFBI	135416562	1.000000	0.71417	0.987000	0.45799	0.302000	0.27658	5.704000	0.68347	1.532000	0.49169	-0.119000	0.15052	AGA	A|0.650;G|0.350	0.350	strong		0.557	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
CYP4A22	284541	hgsc.bcm.edu	37	1	47607281	47607281	+	Missense_Mutation	SNP	C	C	T	rs12564525	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47607281C>T	ENST00000371891.3	+	3	407	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	CYP4A22_ENST00000294337.3_Missense_Mutation_p.R126W|CYP4A22_ENST00000371890.3_Missense_Mutation_p.R126W|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000485117.1_3'UTR	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	126			R -> W (in allele CYP4A22*8, allele CYP4A22*9, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs12564525). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCTGGCTCCACGGATTGGTAT	0.453													c|||	1859	0.371206	0.2254	0.2867	5008	,	,		23221	0.6141		0.2058	False		,,,				2504	0.5481				p.R126W	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.C376T						PASS	.	T	TRP/ARG	1099,3307	720.2+/-409.0	129,841,1233	132.0	122.0	125.0		376	1.7	0.7	1	dbSNP_120	125	1802,6798	732.5+/-406.8	197,1408,2695	yes	missense	CYP4A22	NM_001010969.2	101	326,2249,3928	TT,TC,CC		20.9535,24.9433,22.3051	benign	126/520	47607281	2901,10105	2203	4300	6503	SO:0001583	missense	284541	exon3			GCTCCACGGATTG		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.376C>T	1.37:g.47607281C>T	ENSP00000360958:p.Arg126Trp	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	146	72	0.493151	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	682	0.31227106227106227	103	0.20934959349593496	90	0.24861878453038674	342	0.5979020979020979	147	0.19393139841688653	t	0.721	-0.783423	0.02907	0.249433	0.209535	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.67865	-0.27;-0.29;-0.29	1.66	1.66	0.24008	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00003	-3.465	0.51482	P	7.900000000005125E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48514	-0.9029	9	0.02654	T	1	.	6.8608	0.24066	0.0:0.126:0.0:0.874	rs12564525;rs57365220	126;126	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	W	126	ENSP00000360957:R126W;ENSP00000360958:R126W;ENSP00000294337:R126W	ENSP00000294337:R126W	R	+	1	2	CYP4A22	47379868	1.000000	0.71417	0.697000	0.30258	0.155000	0.21991	2.836000	0.48183	0.117000	0.18138	-0.665000	0.03846	CGG	C|0.715;T|0.285	0.285	strong		0.453	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
COL18A1	80781	hgsc.bcm.edu	37	21	46924389	46924389	+	Silent	SNP	C	C	T	rs11544971	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46924389C>T	ENST00000359759.4	+	33	4053	c.4032C>T	c.(4030-4032)ggC>ggT	p.G1344G	COL18A1_ENST00000355480.5_Silent_p.G1109G|COL18A1_ENST00000400337.2_Silent_p.G929G|SLC19A1_ENST00000567670.1_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1344	Triple-helical region 8 (COL8).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		AGCCCGGGGGCGGCGGTTTCT	0.687													C|||	56	0.0111821	0.0121	0.0231	5008	,	,		12520	0.001		0.0179	False		,,,				2504	0.0051				p.G1109G		Atlas-SNP	.											.	COL18A1	129	.	0			c.C3327T						PASS	.	C	,	27,3073		0,27,1523	9.0	11.0	10.0		3327,2787	-6.8	0.0	21	dbSNP_120	10	116,7186		0,116,3535	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	0,143,5058	TT,TC,CC		1.5886,0.871,1.3747	,	1109/1520,929/1340	46924389	143,10259	1550	3651	5201	SO:0001819	synonymous_variant	80781	exon33			CGGGGGCGGCGGT		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.4032C>T	21.37:g.46924389C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	18	11	0.611111	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.985;T|0.015	0.015	strong		0.687	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
CLPSL1	340204	hgsc.bcm.edu	37	6	35755658	35755658	+	Silent	SNP	A	A	G	rs12211728	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:35755658A>G	ENST00000373861.5	+	3	331	c.237A>G	c.(235-237)caA>caG	p.Q79Q	CLPSL1_ENST00000542261.1_Silent_p.Q78Q			A2RUU4	COLL1_HUMAN	colipase-like 1	79					digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										TCTTTGGCCAATATAGAGCGT	0.542													A|||	1827	0.364816	0.3298	0.3847	5008	,	,		26184	0.2649		0.4324	False		,,,				2504	0.4315				p.Q79Q		Atlas-SNP	.											.	.	.	.	0			c.A237G						PASS	.	A		1278,2802		87,1104,849	137.0	133.0	134.0		237	-1.1	0.0	6	dbSNP_120	134	3481,4915		151,3179,868	no	coding-synonymous	C6orf127	NM_001010886.3		238,4283,1717	GG,GA,AA		41.4602,31.3235,38.1452		79/122	35755658	4759,7717	2040	4198	6238	SO:0001819	synonymous_variant	340204	exon3			TGGCCAATATAGA		CCDS43456.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000204140	ENSG00000204140			21251	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 127"""	C6orf127			Standard	NM_001010886		Approved	dJ510O8.6	uc003old.4	A2RUU4	OTTHUMG00000014582	ENST00000373861.5:c.237A>G	6.37:g.35755658A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	45	0.833333	NM_001010886	A7E2T6|B2RPE2|B5G4V2|B6ZDM9|Q5T9G1	Silent	SNP	ENST00000373861.5	37	CCDS43456.1																																																																																			A|0.641;G|0.359	0.359	strong		0.542	CLPSL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040317.2	NM_001010886	
ULK4	54986	hgsc.bcm.edu	37	3	41952852	41952852	+	Missense_Mutation	SNP	T	T	C	rs35263917	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:41952852T>C	ENST00000301831.4	-	11	1504	c.1042A>G	c.(1042-1044)Agt>Ggt	p.S348G	ULK4_ENST00000420927.1_Missense_Mutation_p.S348G	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	348			S -> G (in dbSNP:rs35263917). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCAAGAGTACTCTTAGGCCGA	0.343													T|||	421	0.0840655	0.0635	0.0908	5008	,	,		20625	0.002		0.166	False		,,,				2504	0.1074				p.S348G		Atlas-SNP	.											ULK4_ENST00000301831,colon,carcinoma,+1,2	ULK4	150	2	0			c.A1042G						PASS	.	T	GLY/SER	283,3385		9,265,1560	94.0	88.0	90.0		1042	5.2	0.9	3	dbSNP_126	90	1227,6941		90,1047,2947	yes	missense	ULK4	NM_017886.2	56	99,1312,4507	CC,CT,TT		15.022,7.7154,12.7577	possibly-damaging	348/1276	41952852	1510,10326	1834	4084	5918	SO:0001583	missense	54986	exon11			GAGTACTCTTAGG	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1042A>G	3.37:g.41952852T>C	ENSP00000301831:p.Ser348Gly	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	195	97	0.497436	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	198	0.09065934065934066	31	0.06300813008130081	32	0.08839779005524862	2	0.0034965034965034965	133	0.17546174142480211	T	21.5	4.164150	0.78339	0.077154	0.15022	ENSG00000168038	ENST00000301831;ENST00000420927	T;T	0.69040	0.42;-0.37	5.22	5.22	0.72569	.	0.707959	0.15193	N	0.275422	T	0.00300	0.0009	M	0.71581	2.175	0.09310	P	1.0	P	0.48911	0.917	B	0.43950	0.437	T	0.20907	-1.0261	9	0.62326	D	0.03	.	14.1258	0.65219	0.0:0.0:0.0:1.0	rs35263917;rs61740620	348	Q96C45	ULK4_HUMAN	G	348	ENSP00000301831:S348G;ENSP00000412187:S348G	ENSP00000301831:S348G	S	-	1	0	ULK4	41927856	1.000000	0.71417	0.918000	0.36340	0.766000	0.43426	5.411000	0.66386	1.979000	0.57680	0.529000	0.55759	AGT	T|0.887;C|0.113	0.113	strong		0.343	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
PCDHGB3	56102	hgsc.bcm.edu	37	5	140750517	140750517	+	Silent	SNP	C	C	T	rs78666647	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140750517C>T	ENST00000576222.1	+	1	687	c.556C>T	c.(556-558)Ctg>Ttg	p.L186L	PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	186	Cadherin 2. {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)			GAAGGAGAACCTGGATGGCAG	0.552													.|||	70	0.0139776	0.0015	0.0346	5008	,	,		19811	0.0		0.0378	False		,,,				2504	0.0061				p.L186L		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.C556T						PASS	.	C	,,,,,,,,	30,4020		0,30,1995	143.0	141.0	142.0		,,,,,,,556,556	5.4	1.0	5	dbSNP_132	142	359,8061		13,333,3864	no	intron,intron,intron,intron,intron,intron,intron,coding-synonymous,coding-synonymous	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032097.1	,,,,,,,,	13,363,5859	TT,TC,CC		4.2637,0.7407,3.1195	,,,,,,,,	,,,,,,,186/930,186/815	140750517	389,12081	2025	4210	6235	SO:0001819	synonymous_variant	56102	exon1			GAGAACCTGGATG	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.556C>T	5.37:g.140750517C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_018924	A7E229|Q9Y5C7	Silent	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			C|0.977;T|0.023	0.023	strong		0.552	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
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 GAIIx	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_ENST00000524510.1_5'UTR|PVRL1_ENST00000340882.2_Missense_Mutation_p.V28I|PVRL1_ENST00000341398.2_Missense_Mutation_p.V28I	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	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	40	9	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		
ABRA	137735	hgsc.bcm.edu	37	8	107782335	107782335	+	Silent	SNP	G	G	A	rs11996457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:107782335G>A	ENST00000311955.3	-	1	138	c.84C>T	c.(82-84)agC>agT	p.S28S		NM_139166.4	NP_631905.1			actin-binding Rho activating protein											breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			CTCGGGCCAAGCTGATGACCA	0.647													G|||	1405	0.280551	0.5378	0.1686	5008	,	,		17334	0.1944		0.2247	False		,,,				2504	0.1585				p.S28S		Atlas-SNP	.											ABRA,NS,adenoma,0,1	ABRA	57	1	0			c.C84T						scavenged	.	G		2079,2327	567.8+/-382.2	499,1081,623	61.0	65.0	64.0		84	0.7	0.5	8	dbSNP_120	64	1815,6785	324.5+/-316.5	182,1451,2667	no	coding-synonymous	ABRA	NM_139166.4		681,2532,3290	AA,AG,GG		21.1047,47.1857,29.94		28/382	107782335	3894,9112	2203	4300	6503	SO:0001819	synonymous_variant	137735	exon1			GGCCAAGCTGATG	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"""striated muscle activator of Rho-dependent signaling"""	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.84C>T	8.37:g.107782335G>A		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_139166		Silent	SNP	ENST00000311955.3	37	CCDS6305.1																																																																																			G|0.710;A|0.290	0.290	strong		0.647	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166	
ITSN1	6453	hgsc.bcm.edu	37	21	35239562	35239562	+	Missense_Mutation	SNP	A	A	G	rs56279221	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:35239562A>G	ENST00000381318.3	+	33	4388	c.4100A>G	c.(4099-4101)aAa>aGa	p.K1367R	ITSN1_ENST00000437442.2_Missense_Mutation_p.K1362R|ITSN1_ENST00000381285.4_Missense_Mutation_p.K1367R|ITSN1_ENST00000399367.3_Missense_Mutation_p.K1362R|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399326.3_3'UTR	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1367	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.			K -> R (in Ref. 7; AAI16187). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						CCTCGGTGTAAAGGGATGCCA	0.373													A|||	260	0.0519169	0.0303	0.036	5008	,	,		21499	0.0685		0.0765	False		,,,				2504	0.0501				p.K1367R		Atlas-SNP	.											.	ITSN1	166	.	0			c.A4100G						PASS	.	A	ARG/LYS	185,4221	118.4+/-156.1	3,179,2021	148.0	141.0	144.0		4100	5.5	1.0	21	dbSNP_129	144	634,7966	162.9+/-215.5	22,590,3688	yes	missense	ITSN1	NM_003024.2	26	25,769,5709	GG,GA,AA		7.3721,4.1988,6.2971	probably-damaging	1367/1722	35239562	819,12187	2203	4300	6503	SO:0001583	missense	6453	exon33			GGTGTAAAGGGAT	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.4100A>G	21.37:g.35239562A>G	ENSP00000370719:p.Lys1367Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	NM_003024	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	129	0.059065934065934064	10	0.02032520325203252	11	0.03038674033149171	46	0.08041958041958042	62	0.08179419525065963	A	28.2	4.898779	0.91962	0.041988	0.073721	ENSG00000205726	ENST00000381318;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000437442	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	5.51	5.51	0.81932	Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	T	0.10508	0.0257	N	0.20574	0.59	0.80722	D	1	B;D;D	0.69078	0.021;0.997;0.997	B;D;D	0.77557	0.023;0.99;0.99	T	0.54576	-0.8273	10	0.72032	D	0.01	.	15.9211	0.79575	1.0:0.0:0.0:0.0	rs56279221	1362;1362;1367	A8CTY3;A8CTX8;Q15811	.;.;ITSN1_HUMAN	R	1367;1367;1296;1362;1362	ENSP00000370719:K1367R;ENSP00000370685:K1367R;ENSP00000382301:K1362R;ENSP00000387377:K1362R	ENSP00000370685:K1367R	K	+	2	0	ITSN1	34161432	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.055000	0.76656	2.210000	0.71456	0.533000	0.62120	AAA	A|0.937;G|0.063	0.063	strong		0.373	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	
USP36	57602	hgsc.bcm.edu	37	17	76814782	76814782	+	Silent	SNP	G	G	A	rs35273233	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:76814782G>A	ENST00000542802.3	-	10	1433	c.990C>T	c.(988-990)cgC>cgT	p.R330R	USP36_ENST00000312010.6_Silent_p.R330R|USP36_ENST00000588467.1_5'UTR|USP36_ENST00000449938.2_Silent_p.R30R			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	330	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)			AGTTGGCAAAGCGCTTGAGGG	0.532													G|||	579	0.115615	0.0855	0.1297	5008	,	,		18769	0.0863		0.1988	False		,,,				2504	0.091				p.R330R		Atlas-SNP	.											.	USP36	243	.	0			c.C990T						PASS	.	G		438,3968	210.8+/-231.2	10,418,1775	187.0	162.0	170.0		990	3.1	1.0	17	dbSNP_126	170	1639,6961	303.7+/-306.6	150,1339,2811	no	coding-synonymous	USP36	NM_025090.3		160,1757,4586	AA,AG,GG		19.0581,9.941,15.9696		330/1124	76814782	2077,10929	2203	4300	6503	SO:0001819	synonymous_variant	57602	exon10			GGCAAAGCGCTTG	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.990C>T	17.37:g.76814782G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	37	CCDS32755.1																																																																																			G|0.848;A|0.152	0.152	strong		0.532	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090	
LAMA5	3911	hgsc.bcm.edu	37	20	60897772	60897772	+	Missense_Mutation	SNP	T	T	C	rs6143021	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60897772T>C	ENST00000252999.3	-	46	6173	c.6107A>G	c.(6106-6108)cAc>cGc	p.H2036R		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2036	Laminin EGF-like 20. {ECO:0000255|PROSITE-ProRule:PRU00460}.		H -> R (in dbSNP:rs6143021).		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)			GTGCCCGCTGTGGGGGTCGCA	0.711													.|||	994	0.198482	0.1634	0.232	5008	,	,		9144	0.1885		0.2644	False		,,,				2504	0.1646				p.H2036R		Atlas-SNP	.											.	LAMA5	268	.	0			c.A6107G						PASS	.	T	ARG/HIS	784,3420		82,620,1400	9.0	7.0	8.0		6107	-2.6	0.0	20	dbSNP_114	8	1799,6529		217,1365,2582	yes	missense	LAMA5	NM_005560.3	29	299,1985,3982	CC,CT,TT		21.6018,18.6489,20.6112	benign	2036/3696	60897772	2583,9949	2102	4164	6266	SO:0001583	missense	3911	exon46			CCGCTGTGGGGGT	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.6107A>G	20.37:g.60897772T>C	ENSP00000252999:p.His2036Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	22	0.305556	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	458	0.2097069597069597	84	0.17073170731707318	83	0.2292817679558011	102	0.17832167832167833	189	0.24934036939313983	t	0.008	-1.930680	0.00488	0.186489	0.216018	ENSG00000130702	ENST00000252999	T	0.33654	1.4	4.12	-2.6	0.06190	EGF-like, laminin (3);	0.504726	0.20835	N	0.084806	T	0.00012	0.0000	N	0.04335	-0.225	0.38604	P	0.049277000000000015	B	0.02656	0.0	B	0.04013	0.001	T	0.40270	-0.9572	9	0.22109	T	0.4	.	10.9539	0.47345	0.0:0.5633:0.0:0.4367	rs6143021	2036	O15230	LAMA5_HUMAN	R	2036	ENSP00000252999:H2036R	ENSP00000252999:H2036R	H	-	2	0	LAMA5	60331167	0.011000	0.17503	0.026000	0.17262	0.049000	0.14656	0.205000	0.17356	-0.425000	0.07371	0.397000	0.26171	CAC	T|0.787;C|0.213	0.213	strong		0.711	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
HSPG2	3339	hgsc.bcm.edu	37	1	22163390	22163390	+	Silent	SNP	G	G	A	rs35444472	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22163390G>A	ENST00000374695.3	-	75	10339	c.10260C>T	c.(10258-10260)caC>caT	p.H3420H		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3420	Ig-like C2-type 20.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCACAGCACAGTGGAACTCAA	0.657													G|||	431	0.0860623	0.1664	0.0519	5008	,	,		16913	0.001		0.0676	False		,,,				2504	0.1084				p.H3420H		Atlas-SNP	.											.	HSPG2	311	.	0			c.C10260T						PASS	.	G		729,3651		59,611,1520	51.0	42.0	45.0		10260	2.6	1.0	1	dbSNP_126	45	633,7953		25,583,3685	no	coding-synonymous	HSPG2	NM_005529.5		84,1194,5205	AA,AG,GG		7.3725,16.6438,10.5044		3420/4392	22163390	1362,11604	2190	4293	6483	SO:0001819	synonymous_variant	3339	exon75			AGCACAGTGGAAC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10260C>T	1.37:g.22163390G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			A|0.098;C|0.000;G|0.902;T|0.000	0.098	strong		0.657	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
ACSF2	80221	hgsc.bcm.edu	37	17	48539035	48539035	+	Silent	SNP	T	T	C	rs9674937	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48539035T>C	ENST00000300441.4	+	4	599	c.495T>C	c.(493-495)taT>taC	p.Y165Y	ACSF2_ENST00000502667.1_Silent_p.Y152Y|ACSF2_ENST00000427954.2_Silent_p.Y190Y|ACSF2_ENST00000541920.1_Silent_p.Y5Y|ACSF2_ENST00000504392.1_Silent_p.Y122Y	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	165					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			AACTGGAGTATGTCCTCAAGA	0.607													T|||	1723	0.34405	0.705	0.2824	5008	,	,		18866	0.0863		0.2545	False		,,,				2504	0.2577				p.Y165Y		Atlas-SNP	.											.	ACSF2	46	.	0			c.T495C						PASS	.	T		2719,1687	653.9+/-399.7	849,1021,333	83.0	79.0	80.0		495	-0.4	1.0	17	dbSNP_119	80	2180,6420	373.2+/-336.9	300,1580,2420	no	coding-synonymous	ACSF2	NM_025149.4		1149,2601,2753	CC,CT,TT		25.3488,38.2887,37.6672		165/616	48539035	4899,8107	2203	4300	6503	SO:0001819	synonymous_variant	80221	exon4			GGAGTATGTCCTC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"""Acyl-CoA synthetase family"""	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.495T>C	17.37:g.48539035T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	140	61	0.435714	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Silent	SNP	ENST00000300441.4	37	CCDS11567.1	664	0.304029304029304	324	0.6585365853658537	103	0.2845303867403315	47	0.08216783216783216	190	0.25065963060686014	T	11.10	1.538263	0.27475	0.617113	0.253488	ENSG00000167107	ENST00000506582	T	0.55760	0.5	5.49	-0.363	0.12556	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999525967	.	.	.	.	.	.	T	0.47156	-0.9139	5	0.87932	D	0	-3.9033	10.1911	0.43028	0.0:0.4557:0.0:0.5443	rs9674937;rs11546317;rs56922985;rs9674937	.	.	.	R	138	ENSP00000424842:C138R	ENSP00000424842:C138R	C	+	1	0	ACSF2	45894034	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	1.020000	0.30027	-0.127000	0.11661	0.533000	0.62120	TGT	T|0.644;C|0.356	0.356	strong		0.607	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907533	12907533	+	Missense_Mutation	SNP	T	T	C	rs141872266	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907533T>C	ENST00000317869.6	-	2	835	c.610A>G	c.(610-612)Att>Gtt	p.I204V		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	204						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						TCCTTTTCAATTTTTTCCAGG	0.423																																					p.I204V		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	0			c.A610G						PASS	.	T	VAL/ILE	46,4284		1,44,2120	92.0	102.0	99.0		610	1.1	0.9	1	dbSNP_134	99	191,8303		4,183,4060	no	missense	HNRNPCL1	NM_001013631.1	29	5,227,6180	CC,CT,TT		2.2486,1.0624,1.8481	benign	204/294	12907533	237,12587	2165	4247	6412	SO:0001583	missense	343069	exon2			TTTCAATTTTTTC	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.610A>G	1.37:g.12907533T>C	ENSP00000365370:p.Ile204Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	197	49	0.248731	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	164	0.07509157509157509	4	0.008130081300813009	9	0.024861878453038673	118	0.2062937062937063	33	0.04353562005277045	.	5.008	0.187087	0.09547	0.010624	0.022486	ENSG00000179172	ENST00000317869	T	0.12255	2.7	1.09	1.09	0.20402	.	0.071260	0.53938	U	0.000057	T	0.00012	0.0000	M	0.76838	2.35	0.31515	N	0.663119	B	0.15719	0.014	B	0.13407	0.009	T	0.10753	-1.0616	10	0.72032	D	0.01	.	6.3584	0.21414	0.0:0.0:0.0:1.0	.	204	O60812	HNRCL_HUMAN	V	204	ENSP00000365370:I204V	ENSP00000365370:I204V	I	-	1	0	HNRNPCL1	12830120	1.000000	0.71417	0.927000	0.36925	0.130000	0.20726	3.089000	0.50183	0.759000	0.33084	0.341000	0.21757	ATT	T|0.959;C|0.041	0.041	strong		0.423	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
FFAR3	2865	hgsc.bcm.edu	37	19	35850520	35850520	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35850520T>C	ENST00000327809.4	+	2	929	c.728T>C	c.(727-729)gTg>gCg	p.V243A	FFAR3_ENST00000594310.1_Missense_Mutation_p.V243A	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	243					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			CCCTACAACGTGTCCCATGTC	0.627																																					p.V243A	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											FFAR3,NS,carcinoma,-1,1	FFAR3	40	1	0			c.T728C						scavenged	.						180.0	135.0	150.0					19																	35850520		2201	4298	6499	SO:0001583	missense	2865	exon2			ACAACGTGTCCCA	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"""GPCR / Class A : Fatty acid receptors"""	4499	protein-coding gene	gene with protein product		603821	"""G protein-coupled receptor 41"""	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.728T>C	19.37:g.35850520T>C	ENSP00000328230:p.Val243Ala	Somatic	723	2	0.00276625		WXS	Illumina HiSeq	Phase_I	932	10	0.0107296	NM_005304	B2RWM8|Q14CM7	Missense_Mutation	SNP	ENST00000327809.4	37	CCDS12459.1	.	.	.	.	.	.	.	.	.	.	T	3.050	-0.195609	0.06259	.	.	ENSG00000185897	ENST00000327809	T	0.73575	-0.76	5.13	2.87	0.33458	GPCR, rhodopsin-like superfamily (1);	0.791425	0.11559	U	0.551938	T	0.60366	0.2263	L	0.28054	0.825	0.09310	N	1	B	0.15141	0.012	B	0.20384	0.029	T	0.52457	-0.8573	10	0.52906	T	0.07	-4.756	6.3104	0.21161	0.0:0.26:0.0:0.74	.	243	O14843	FFAR3_HUMAN	A	243	ENSP00000328230:V243A	ENSP00000328230:V243A	V	+	2	0	FFAR3	40542360	0.025000	0.19082	0.637000	0.29366	0.068000	0.16541	1.317000	0.33631	0.800000	0.34041	0.374000	0.22700	GTG	.	.	none		0.627	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304	
RPAP1	26015	hgsc.bcm.edu	37	15	41829230	41829230	+	Silent	SNP	A	A	G	rs721772	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:41829230A>G	ENST00000304330.4	-	2	210	c.94T>C	c.(94-96)Ttg>Ctg	p.L32L	RPAP1_ENST00000561603.1_Silent_p.L32L	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	32						nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TTCTTCACCAACTGCACTGCT	0.592													A|||	1960	0.391374	0.1528	0.3862	5008	,	,		18053	0.4464		0.5199	False		,,,				2504	0.5286				p.L32L		Atlas-SNP	.											.	RPAP1	111	.	0			c.T94C						PASS	.	A		1020,3386	377.8+/-322.6	111,798,1294	121.0	104.0	110.0		94	-9.6	0.0	15	dbSNP_86	110	4485,4115	592.2+/-392.9	1161,2163,976	no	coding-synonymous	RPAP1	NM_015540.2		1272,2961,2270	GG,GA,AA		47.8488,23.1502,42.3266		32/1394	41829230	5505,7501	2203	4300	6503	SO:0001819	synonymous_variant	26015	exon2			TCACCAACTGCAC	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.94T>C	15.37:g.41829230A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	71	16	0.225352	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	37	CCDS10079.1																																																																																			A|0.592;G|0.408	0.408	strong		0.592	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
ENTPD6	955	hgsc.bcm.edu	37	20	25187213	25187213	+	Missense_Mutation	SNP	G	G	A	rs2076559	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:25187213G>A	ENST00000376652.4	+	2	204	c.41G>A	c.(40-42)aGc>aAc	p.S14N	ENTPD6_ENST00000354989.5_Intron|ENTPD6_ENST00000433259.2_Missense_Mutation_p.S14N|ENTPD6_ENST00000360031.2_Missense_Mutation_p.S14N			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	14			S -> N (in dbSNP:rs2076559). {ECO:0000269|PubMed:14529283}.		response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						AGAAAAACGAGCTACATTTTT	0.403													G|||	1562	0.311901	0.0983	0.2349	5008	,	,		20423	0.5903		0.3469	False		,,,				2504	0.3323				p.S14N		Atlas-SNP	.											.	ENTPD6	57	.	0			c.G41A						PASS	.	G	,ASN/SER	621,3785	269.5+/-269.1	42,537,1624	104.0	97.0	100.0		,41	-0.2	0.0	20	dbSNP_96	100	2767,5833	439.7+/-359.3	431,1905,1964	yes	intron,missense	ENTPD6	NM_001114089.1,NM_001247.2	,46	473,2442,3588	AA,AG,GG		32.1744,14.0944,26.0495	,benign	,14/485	25187213	3388,9618	2203	4300	6503	SO:0001583	missense	955	exon2			AAACGAGCTACAT	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.41G>A	20.37:g.25187213G>A	ENSP00000365840:p.Ser14Asn	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	77	27	0.350649	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	37	CCDS13170.1	755	0.3456959706959707	59	0.11991869918699187	94	0.2596685082872928	344	0.6013986013986014	258	0.3403693931398417	G	8.922	0.961415	0.18583	0.140944	0.321744	ENSG00000197586	ENST00000360031;ENST00000376652;ENST00000433259;ENST00000435520;ENST00000425813	T;T;T;T;T	0.34275	2.18;2.18;2.05;1.37;2.35	2.98	-0.162	0.13367	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B;B	0.30482	0.281;0.18;0.18;0.18;0.18	B;B;B;B;B	0.22152	0.038;0.038;0.038;0.017;0.017	T	0.44283	-0.9338	8	0.19590	T	0.45	.	3.4656	0.07549	0.2556:0.2143:0.5302:0.0	rs2076559;rs11539327;rs17829504;rs52811761;rs60671666;rs2076559	14;14;14;14;14	E7EP89;Q5QPI9;D3DW49;Q5QPJ2;O75354	.;.;.;.;ENTP6_HUMAN	N	14	ENSP00000353131:S14N;ENSP00000365840:S14N;ENSP00000401895:S14N;ENSP00000398844:S14N;ENSP00000390646:S14N	ENSP00000353131:S14N	S	+	2	0	ENTPD6	25135213	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.214000	0.17541	0.004000	0.14682	-0.172000	0.13284	AGC	G|0.702;A|0.298	0.298	strong		0.403	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
ZNF366	167465	hgsc.bcm.edu	37	5	71757266	71757266	+	Missense_Mutation	SNP	T	T	C	rs74460472	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:71757266T>C	ENST00000318442.5	-	2	548	c.58A>G	c.(58-60)Aag>Gag	p.K20E		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	20					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		GGGGTCTTCTTCACAGCCAAG	0.502													T|||	244	0.048722	0.0401	0.0231	5008	,	,		16625	0.0546		0.0298	False		,,,				2504	0.092				p.K20E		Atlas-SNP	.											.	ZNF366	108	.	0			c.A58G						PASS	.						64.0	61.0	62.0					5																	71757266		2203	4300	6503	SO:0001583	missense	167465	exon2			TCTTCTTCACAGC	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.58A>G	5.37:g.71757266T>C	ENSP00000313158:p.Lys20Glu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	T	7.158	0.585103	0.13749	.	.	ENSG00000178175	ENST00000318442;ENST00000414109	T;T	0.44881	0.91;0.91	5.7	3.31	0.37934	.	0.245070	0.36268	N	0.002681	T	0.28134	0.0694	L	0.32530	0.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20438	-1.0275	10	0.14252	T	0.57	-24.8326	10.0189	0.42031	0.0:0.1368:0.0:0.8632	.	20	Q8N895	ZN366_HUMAN	E	20	ENSP00000313158:K20E;ENSP00000391333:K20E	ENSP00000313158:K20E	K	-	1	0	ZNF366	71793022	0.763000	0.28462	0.012000	0.15200	0.298000	0.27526	4.471000	0.60182	0.439000	0.26476	0.459000	0.35465	AAG	T|0.950;C|0.050	0.050	strong		0.502	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815662	23815662	+	Missense_Mutation	SNP	C	C	T	rs8192678	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:23815662C>T	ENST00000264867.2	-	8	1563	c.1444G>A	c.(1444-1446)Ggt>Agt	p.G482S	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	482	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.		G -> S (in dbSNP:rs8192678). {ECO:0000269|PubMed:10643692}.		androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				CTCAGTTCACCGGTCTTGTCT	0.463													T|||	1331	0.265775	0.0454	0.2565	5008	,	,		19910	0.4425		0.3608	False		,,,				2504	0.2904				p.G482S	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.G1444A	GRCh37	CM013959	PPARGC1A	M	rs8192678	PASS	.	T	SER/GLY	455,3951	785.2+/-414.7	22,411,1770	129.0	118.0	122.0		1444	6.0	1.0	4	dbSNP_117	122	2988,5612	666.0+/-402.3	484,2020,1796	yes	missense	PPARGC1A	NM_013261.3	56	506,2431,3566	TT,TC,CC		34.7442,10.3268,26.4724	benign	482/799	23815662	3443,9563	2203	4300	6503	SO:0001583	missense	10891	exon8			GTTCACCGGTCTT	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.1444G>A	4.37:g.23815662C>T	ENSP00000264867:p.Gly482Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	37	CCDS3429.1	635	0.2907509157509158	23	0.046747967479674794	84	0.23204419889502761	256	0.44755244755244755	272	0.35883905013192613	T	3.141	-0.176377	0.06380	0.103268	0.347442	ENSG00000109819	ENST00000264867	T	0.20200	2.09	6.02	6.02	0.97574	.	0.241030	0.49305	N	0.000156	T	0.00012	0.0000	N	0.01576	-0.805	0.09310	P	1.0	B	0.21225	0.053	B	0.09377	0.004	T	0.42716	-0.9435	9	0.02654	T	1	-1.3449	10.8867	0.46971	0.0:0.1297:0.0:0.8703	rs8192678;rs17847358;rs52829424;rs56570248;rs56707915;rs8192678	482	Q9UBK2	PRGC1_HUMAN	S	482	ENSP00000264867:G482S	ENSP00000264867:G482S	G	-	1	0	PPARGC1A	23424760	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.170000	0.42443	1.099000	0.41499	-0.269000	0.10298	GGT	C|0.724;T|0.276	0.276	strong		0.463	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
SYNDIG1L	646658	hgsc.bcm.edu	37	14	74876181	74876181	+	Silent	SNP	T	T	G	rs12590672	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74876181T>G	ENST00000554823.1	-	1	328	c.267A>C	c.(265-267)acA>acC	p.T89T	SYNDIG1L_ENST00000331628.3_Silent_p.T89T			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	89					response to biotic stimulus (GO:0009607)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(8)|pancreas(1)|prostate(1)|skin(1)	14						CTGTGAAGCTTGTCTCACAGC	0.647													G|||	2307	0.460663	0.472	0.4222	5008	,	,		14317	0.4454		0.494	False		,,,				2504	0.454				p.T89T		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.A267C						PASS	.	G		1773,2063		420,933,565	42.0	45.0	44.0		267	1.7	1.0	14	dbSNP_120	44	4113,4145		1033,2047,1049	no	coding-synonymous	SYNDIG1L	NM_001105579.1		1453,2980,1614	GG,GT,TT		49.8062,46.22,48.6688		89/239	74876181	5886,6208	1918	4129	6047	SO:0001819	synonymous_variant	646658	exon2			GAAGCTTGTCTCA		CCDS41970.1	14q24.3	2011-06-30	2011-06-30	2011-06-30		ENSG00000183379			32388	protein-coding gene	gene with protein product	"""caudate-and putamen-enriched sequence"", ""interferon induced transmembrane protein domain containing 4"""	609999	"""transmembrane protein 90A"""	TMEM90A		16359841	Standard	NM_001105579		Approved	capucin, IFITMD4	uc001xpx.2	A6NDD5		ENST00000554823.1:c.267A>C	14.37:g.74876181T>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_001105579		Silent	SNP	ENST00000554823.1	37	CCDS41970.1																																																																																			T|0.508;G|0.492	0.492	strong		0.647	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515	
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 GAIIx	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_ENST00000389562.2_Silent_p.T1440T|EP400_ENST00000332482.4_Silent_p.T1404T			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		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	30	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	
ZNF860	344787	hgsc.bcm.edu	37	3	32031962	32031962	+	Missense_Mutation	SNP	A	A	G	rs1808125	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:32031962A>G	ENST00000360311.4	+	2	1940	c.1391A>G	c.(1390-1392)cAt>cGt	p.H464R		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	464					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(3)|lung(4)|ovary(1)	8						AAGACCTTCCATCACAATTCA	0.418													a|||	3114	0.621805	0.9054	0.4813	5008	,	,		19471	0.7599		0.2773	False		,,,				2504	0.5501				p.H464R		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	0			c.A1391G						PASS	.						22.0	58.0	48.0					3																	32031962		627	1568	2195	SO:0001583	missense	344787	exon2			CCTTCCATCACAA	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1391A>G	3.37:g.32031962A>G	ENSP00000373274:p.His464Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	27	26	0.962963	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	991	0.45375457875457875	324	0.6585365853658537	145	0.4005524861878453	368	0.6433566433566433	154	0.20316622691292877	a	0.169	-1.073378	0.01918	.	.	ENSG00000197385	ENST00000360311	T	0.17370	2.28	0.3	-0.599	0.11645	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.42032	-0.9475	7	.	.	.	.	4.0852	0.09943	0.2146:0.4157:0.3696:0.0	rs1808125;rs60384157	464	A6NHJ4	ZN860_HUMAN	R	464	ENSP00000373274:H464R	.	H	+	2	0	ZNF860	32006966	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.083000	0.03397	-3.961000	0.00087	-3.988000	0.00014	CAT	A|0.545;G|0.455	0.455	strong		0.418	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
VPS13C	54832	hgsc.bcm.edu	37	15	62253791	62253791	+	Missense_Mutation	SNP	T	T	C	rs2303405	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62253791T>C	ENST00000261517.5	-	35	3978	c.3905A>G	c.(3904-3906)tAt>tGt	p.Y1302C	VPS13C_ENST00000395896.4_Missense_Mutation_p.Y1302C|VPS13C_ENST00000395898.3_Missense_Mutation_p.Y1259C|VPS13C_ENST00000249837.3_Missense_Mutation_p.Y1259C	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.Y1302C(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						AGCATACCTATAAAGTGTAAG	0.308													T|||	247	0.0493211	0.031	0.0403	5008	,	,		17448	0.0377		0.0726	False		,,,				2504	0.0685				p.Y1302C		Atlas-SNP	.											VPS13C,NS,carcinoma,0,1	VPS13C	506	1	1	Substitution - Missense(1)	stomach(1)	c.A3905G						scavenged	.	T	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	167,4239	110.4+/-148.6	1,165,2037	56.0	53.0	54.0		3905,3776,3776,3905	3.8	1.0	15	dbSNP_100	54	686,7914	169.9+/-221.1	32,622,3646	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	194,194,194,194	33,787,5683	CC,CT,TT		7.9767,3.7903,6.5585	benign,benign,benign,benign	1302/3629,1259/3711,1259/3586,1302/3754	62253791	853,12153	2203	4300	6503	SO:0001583	missense	54832	exon35			TACCTATAAAGTG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.3905A>G	15.37:g.62253791T>C	ENSP00000261517:p.Tyr1302Cys	Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	103	0.04716117216117216	12	0.024390243902439025	16	0.04419889502762431	27	0.0472027972027972	48	0.0633245382585752	T	11.47	1.649675	0.29336	0.037903	0.079767	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.15139	2.45;2.45;2.45	5.76	3.85	0.44370	.	0.230587	0.36034	N	0.002821	T	0.00695	0.0023	L	0.38175	1.15	0.32403	N	0.551729	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.03139	-1.1068	10	0.41790	T	0.15	.	12.3558	0.55174	0.0:0.1257:0.7391:0.1352	rs2303405;rs59137518;rs2303405	1259;1302;1259;1302	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	C	1259;1302;1302;1302	ENSP00000249837:Y1259C;ENSP00000261517:Y1302C;ENSP00000379233:Y1302C	ENSP00000249837:Y1259C	Y	-	2	0	VPS13C	60041083	1.000000	0.71417	0.956000	0.39512	0.883000	0.51084	3.499000	0.53310	0.746000	0.32786	-0.286000	0.09958	TAT	T|0.942;C|0.058	0.058	strong		0.308	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
ITIH5	80760	hgsc.bcm.edu	37	10	7622009	7622009	+	Missense_Mutation	SNP	G	G	A	rs41298373	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:7622009G>A	ENST00000256861.6	-	9	1205	c.1127C>T	c.(1126-1128)gCc>gTc	p.A376V	ITIH5_ENST00000397145.2_Missense_Mutation_p.A376V|ITIH5_ENST00000397146.2_Missense_Mutation_p.A376V|ITIH5_ENST00000446830.2_Missense_Mutation_p.A158V|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000298441.6_Missense_Mutation_p.A162V	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	376	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CCTCTGCAGGGCCCCGTTGAT	0.577													G|||	297	0.0593051	0.0144	0.1052	5008	,	,		18218	0.004		0.1113	False		,,,				2504	0.091				p.A376V		Atlas-SNP	.											.	ITIH5	343	.	0			c.C1127T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	103,4303	78.3+/-116.7	2,99,2102	32.0	31.0	31.0		1127,1127,485	5.2	1.0	10	dbSNP_127	31	928,7672	192.7+/-238.6	59,810,3431	yes	missense,missense,missense	ITIH5	NM_001001851.2,NM_030569.6,NM_032817.5	64,64,64	61,909,5533	AA,AG,GG		10.7907,2.3377,7.9271	probably-damaging,probably-damaging,probably-damaging	376/703,376/943,162/729	7622009	1031,11975	2203	4300	6503	SO:0001583	missense	80760	exon9			TGCAGGGCCCCGT			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1127C>T	10.37:g.7622009G>A	ENSP00000256861:p.Ala376Val	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		130	0.05952380952380952	6	0.012195121951219513	41	0.1132596685082873	4	0.006993006993006993	79	0.10422163588390501	G	18.10	3.549070	0.65311	0.023377	0.107907	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54;-2.54	5.23	5.23	0.72850	von Willebrand factor, type A (3);	0.097454	0.64402	D	0.000001	T	0.35038	0.0918	.	.	.	0.23010	P	0.99843691	D;D;D	0.89917	1.0;0.998;0.998	D;D;D	0.91635	0.999;0.974;0.956	T	0.69359	-0.5166	8	0.87932	D	0	-31.7952	14.4073	0.67090	0.0:0.1477:0.8523:0.0	rs41298373;rs61731878	376;376;162	G5E9D8;Q86UX2;Q86UX2-3	.;ITIH5_HUMAN;.	V	376;376;162;158;376	ENSP00000256861:A376V;ENSP00000380333:A376V;ENSP00000298441:A162V;ENSP00000387969:A158V;ENSP00000380332:A376V	ENSP00000256861:A376V	A	-	2	0	ITIH5	7662015	1.000000	0.71417	1.000000	0.80357	0.418000	0.31294	5.883000	0.69721	2.443000	0.82685	0.491000	0.48974	GCC	G|0.929;A|0.071	0.071	strong		0.577	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
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 GAIIx	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	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	92	56	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	
MCM9	254394	hgsc.bcm.edu	37	6	119137011	119137011	+	Missense_Mutation	SNP	G	G	A	rs35917528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:119137011G>A	ENST00000316316.6	-	13	2694	c.2408C>T	c.(2407-2409)cCa>cTa	p.P803L		NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	803					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		TGTCTCTCCTGGTGATGGAAG	0.468													G|||	245	0.0489217	0.0265	0.072	5008	,	,		20834	0.0		0.1133	False		,,,				2504	0.047				p.P803L		Atlas-SNP	.											.	MCM9	73	.	0			c.C2408T						PASS	.																																			SO:0001583	missense	254394	exon12			TCTCCTGGTGATG	BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"""minichromosome maintenance deficient domain containing 1"", ""chromosome 6 open reading frame 61"""	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.2408C>T	6.37:g.119137011G>A	ENSP00000314505:p.Pro803Leu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_017696	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	134	0.06135531135531135	20	0.04065040650406504	34	0.09392265193370165	0	0.0	80	0.10554089709762533	G	11.85	1.763174	0.31228	.	.	ENSG00000111877	ENST00000316316;ENST00000243218	T	0.03689	3.84	6.17	3.26	0.37387	.	0.238047	0.43416	D	0.000564	T	0.01387	0.0045	L	0.57536	1.79	0.47407	P	5.889999999999507E-4	P	0.38922	0.651	B	0.27887	0.084	T	0.53287	-0.8460	9	0.25106	T	0.35	.	10.9587	0.47372	0.0:0.1264:0.6107:0.2629	rs35917528	803	Q9NXL9	MCM9_HUMAN	L	803;422	ENSP00000314505:P803L	ENSP00000243218:P422L	P	-	2	0	MCM9	119243714	0.661000	0.27430	0.192000	0.23308	0.096000	0.18686	0.747000	0.26290	0.880000	0.35969	0.655000	0.94253	CCA	G|0.926;A|0.074	0.074	strong		0.468	MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
BCL2A1	597	hgsc.bcm.edu	37	15	80263217	80263217	+	Missense_Mutation	SNP	C	C	T	rs3826007	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:80263217C>T	ENST00000267953.3	-	1	571	c.245G>A	c.(244-246)gGc>gAc	p.G82D	BCL2A1_ENST00000335661.6_Missense_Mutation_p.G82D	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	82			G -> D (in dbSNP:rs3826007). {ECO:0000269|Ref.6}.		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)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						GTTAATGATGCCGTCTTCAAA	0.403													C|||	1019	0.203474	0.0703	0.1599	5008	,	,		21004	0.2063		0.2545	False		,,,				2504	0.3589				p.G82D		Atlas-SNP	.											.	BCL2A1	28	.	0			c.G245A	GRCh37	CM064994	BCL2A1	M	rs3826007	PASS	.	C	ASP/GLY,ASP/GLY	406,4000	200.8+/-224.0	20,366,1817	207.0	193.0	197.0		245,245	5.6	0.8	15	dbSNP_107	197	2186,6414	373.7+/-337.1	259,1668,2373	yes	missense,missense	BCL2A1	NM_001114735.1,NM_004049.3	94,94	279,2034,4190	TT,TC,CC		25.4186,9.2147,19.9293	probably-damaging,probably-damaging	82/164,82/176	80263217	2592,10414	2203	4300	6503	SO:0001583	missense	597	exon1			ATGATGCCGTCTT		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.245G>A	15.37:g.80263217C>T	ENSP00000267953:p.Gly82Asp	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	209	115	0.550239	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	421	0.19276556776556777	31	0.06300813008130081	69	0.19060773480662985	128	0.22377622377622378	193	0.2546174142480211	C	16.22	3.062546	0.55432	0.092147	0.254186	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.54279	0.58;0.58	5.63	5.63	0.86233	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);Apoptosis regulator, Bcl-2, BH1 motif, conserved site (1);	1.583130	0.03463	N	0.212436	T	0.00073	0.0002	M	0.87328	2.875	0.18873	P	0.9999886628	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.39313	-0.9620	9	0.72032	D	0.01	-20.7853	17.8901	0.88869	0.0:1.0:0.0:0.0	rs3826007;rs60753792;rs3826007	82;82	Q86W13;Q16548	.;B2LA1_HUMAN	D	82	ENSP00000267953:G82D;ENSP00000335250:G82D	ENSP00000267953:G82D	G	-	2	0	BCL2A1	78050272	1.000000	0.71417	0.824000	0.32777	0.019000	0.09904	4.115000	0.57865	2.652000	0.90054	0.655000	0.94253	GGC	C|0.805;T|0.195	0.195	strong		0.403	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
PIK3CG	5294	hgsc.bcm.edu	37	7	106524689	106524689	+	Silent	SNP	C	C	T	rs2230460	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:106524689C>T	ENST00000359195.3	+	9	3160	c.2850C>T	c.(2848-2850)gaC>gaT	p.D950D	PIK3CG_ENST00000496166.1_Silent_p.D950D|PIK3CG_ENST00000440650.2_Silent_p.D950D	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	950	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						GACACAATGACAATATTATGA	0.333													C|||	594	0.11861	0.0144	0.0504	5008	,	,		18934	0.1925		0.1123	False		,,,				2504	0.2382				p.D950D		Atlas-SNP	.											.	PIK3CG	279	.	0			c.C2850T						PASS	.	C		144,4262	101.6+/-140.2	1,142,2060	160.0	156.0	157.0		2850	3.5	1.0	7	dbSNP_98	157	928,7672	205.8+/-248.1	47,834,3419	no	coding-synonymous	PIK3CG	NM_002649.2		48,976,5479	TT,TC,CC		10.7907,3.2683,8.2423		950/1103	106524689	1072,11934	2203	4300	6503	SO:0001819	synonymous_variant	5294	exon9			CAATGACAATATT		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.2850C>T	7.37:g.106524689C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Silent	SNP	ENST00000359195.3	37	CCDS5739.1																																																																																			C|0.901;N|0.000	.	strong		0.333	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
DNASE1L3	1776	hgsc.bcm.edu	37	3	58191266	58191266	+	Silent	SNP	C	C	T	rs2070117	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:58191266C>T	ENST00000394549.2	-	3	568	c.252G>A	c.(250-252)acG>acA	p.T84T	DNASE1L3_ENST00000318316.3_Silent_p.T84T|DNASE1L3_ENST00000486455.1_Intron|DNASE1L3_ENST00000483681.1_Silent_p.T84T	NM_004944.3	NP_004935.1	Q13609	DNSL3_HUMAN	deoxyribonuclease I-like 3	84					apoptotic DNA fragmentation (GO:0006309)|developmental programmed cell death (GO:0010623)|DNA metabolic process (GO:0006259)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			breast(2)|large_intestine(4)|lung(6)	12				BRCA - Breast invasive adenocarcinoma(55;0.00021)|KIRC - Kidney renal clear cell carcinoma(284;0.0445)|Kidney(284;0.0556)|OV - Ovarian serous cystadenocarcinoma(275;0.202)		CATAGTTGTACGTTATGCCTC	0.388													C|||	1812	0.361821	0.1664	0.2997	5008	,	,		22701	0.6429		0.2237	False		,,,				2504	0.5225				p.T84T	Esophageal Squamous(96;1069 1424 4841 43466 52325)	Atlas-SNP	.											.	DNASE1L3	36	.	0			c.G252A						PASS	.	C		728,3676	300.4+/-286.3	54,620,1528	186.0	182.0	183.0		252	3.4	0.2	3	dbSNP_96	183	1709,6891	313.0+/-311.1	166,1377,2757	no	coding-synonymous	DNASE1L3	NM_004944.2		220,1997,4285	TT,TC,CC		19.8721,16.5304,18.7404		84/306	58191266	2437,10567	2202	4300	6502	SO:0001819	synonymous_variant	1776	exon3			GTTGTACGTTATG	AF047354	CCDS2886.1, CCDS58836.1	3p14.3	2008-05-15			ENSG00000163687	ENSG00000163687			2959	protein-coding gene	gene with protein product	"""DNase gamma"""	602244				9205125, 9714828, 14646506	Standard	NM_004944		Approved	DNAS1L3, LSD	uc003djo.2	Q13609	OTTHUMG00000159153	ENST00000394549.2:c.252G>A	3.37:g.58191266C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_004944	B2R8B1|B7Z707|O75803	Silent	SNP	ENST00000394549.2	37	CCDS2886.1																																																																																			C|0.747;T|0.253	0.253	strong		0.388	DNASE1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353533.1	NM_004944	
LRRC37A2	474170	hgsc.bcm.edu	37	17	44626866	44626866	+	Missense_Mutation	SNP	T	T	C	rs202051157	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44626866T>C	ENST00000576629.1	+	10	4856	c.4361T>C	c.(4360-4362)cTg>cCg	p.L1454P	LRRC37A2_ENST00000333412.3_Missense_Mutation_p.L1454P|ARL17A_ENST00000337845.7_Intron|ARL17A_ENST00000573185.1_Intron|ARL17A_ENST00000445552.2_Intron|ARL17A_ENST00000329240.4_Intron			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	1454						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		GGCACTGACCTGTCCCCCGAG	0.498																																					p.L1454P		Atlas-SNP	.											LRRC37A2,NS,carcinoid-endocrine_tumour,0,1	LRRC37A2	37	1	0			c.T4361C						scavenged	.						2.0	1.0	1.0					17																	44626866		598	1214	1812	SO:0001583	missense	474170	exon9			CTGACCTGTCCCC	AY386262	CCDS42353.1	17q21.31	2013-05-14			ENSG00000238083	ENSG00000238083			32404	protein-coding gene	gene with protein product	"""c114 SLIT-like testicular protein"""						Standard	NM_001006607		Approved	FLJ45049	uc002ikn.1	A6NM11	OTTHUMG00000178032	ENST00000576629.1:c.4361T>C	17.37:g.44626866T>C	ENSP00000459551:p.Leu1454Pro	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	158	61	0.386076	NM_001006607	B7ZMC3	Missense_Mutation	SNP	ENST00000576629.1	37	CCDS42353.1	.	.	.	.	.	.	.	.	.	.	t	8.780	0.927936	0.18056	.	.	ENSG00000238083	ENST00000333412	T	0.59638	0.25	3.02	-1.85	0.07784	.	.	.	.	.	T	0.62744	0.2453	L	0.59436	1.845	0.09310	N	1	D;D;B	0.69078	0.995;0.997;0.158	D;D;B	0.72982	0.979;0.964;0.074	T	0.52335	-0.8589	9	0.33141	T	0.24	.	3.1977	0.06639	0.0:0.358:0.2285:0.4136	.	1454;415;1454	C9JSP5;B3KRJ4;A6NM11	.;.;L37A2_HUMAN	P	1454	ENSP00000333071:L1454P	ENSP00000333071:L1454P	L	+	2	0	LRRC37A2	41982182	0.000000	0.05858	0.000000	0.03702	0.158000	0.22134	0.101000	0.15251	-0.073000	0.12842	0.147000	0.16070	CTG	.	.	weak		0.498	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	
IPO4	79711	hgsc.bcm.edu	37	14	24653523	24653523	+	Missense_Mutation	SNP	G	G	C	rs11550452	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24653523G>C	ENST00000354464.6	-	17	1914	c.1738C>G	c.(1738-1740)Cct>Gct	p.P580A	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	580			P -> A (in dbSNP:rs11550452). {ECO:0000269|PubMed:11823430, ECO:0000269|PubMed:14702039}.		DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CGCAAGTCAGGGTCGTCTACC	0.672													G|||	1580	0.315495	0.1831	0.2493	5008	,	,		15854	0.4196		0.2922	False		,,,				2504	0.4581				p.P580A		Atlas-SNP	.											.	IPO4	74	.	0			c.C1738G						PASS	.	G	ALA/PRO	1023,3323		149,725,1299	15.0	21.0	19.0		1738	5.4	1.0	14	dbSNP_120	19	2806,5736		475,1856,1940	yes	missense	IPO4	NM_024658.3	27	624,2581,3239	CC,CG,GG		32.8494,23.5389,29.7098	probably-damaging	580/1082	24653523	3829,9059	2173	4271	6444	SO:0001583	missense	79711	exon17			AGTCAGGGTCGTC	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1738C>G	14.37:g.24653523G>C	ENSP00000346453:p.Pro580Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	37	CCDS9616.1	660	0.3021978021978022	96	0.1951219512195122	96	0.26519337016574585	250	0.4370629370629371	218	0.287598944591029	G	24.1	4.495905	0.85069	0.235389	0.328494	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.50277	0.75	5.4	5.4	0.78164	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66297	2.02	0.09310	P	0.999999999258	D;P	0.76494	0.999;0.953	D;P	0.71414	0.973;0.867	T	0.37776	-0.9691	9	0.40728	T	0.16	-14.7544	18.116	0.89555	0.0:0.0:1.0:0.0	rs11550452;rs12586264;rs17184519;rs11550452	580;580	Q8TEX9;Q8TEX9-2	IPO4_HUMAN;.	A	580;256	ENSP00000346453:P580A	ENSP00000346453:P580A	P	-	1	0	IPO4	23723363	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.795000	0.85887	2.814000	0.96858	0.655000	0.94253	CCT	G|0.693;C|0.307	0.307	strong		0.672	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
DNAH5	1767	hgsc.bcm.edu	37	5	13864728	13864728	+	Silent	SNP	C	C	A	rs6554827	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:13864728C>A	ENST00000265104.4	-	28	4478	c.4374G>T	c.(4372-4374)cgG>cgT	p.R1458R	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1458	Stem. {ECO:0000250}.				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)	p.R1458R(1)		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)					CCTTCAAGGCCCGGGGAAGCT	0.478									Kartagener syndrome																												p.R1458R		Atlas-SNP	.											DNAH5,NS,carcinoma,0,1	DNAH5	868	1	1	Substitution - coding silent(1)	stomach(1)	c.G4374T						PASS	.	C		1386,3020	457.5+/-351.6	229,928,1046	59.0	60.0	60.0		4374	0.9	1.0	5	dbSNP_116	60	3807,4793	537.7+/-383.3	893,2021,1386	no	coding-synonymous	DNAH5	NM_001369.2		1122,2949,2432	AA,AC,CC		44.2674,31.4571,39.9277		1458/4625	13864728	5193,7813	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon28	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAAGGCCCGGGGA	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.4374G>T	5.37:g.13864728C>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			C|0.626;A|0.374	0.374	strong		0.478	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
LGMN	5641	hgsc.bcm.edu	37	14	93199080	93199080	+	Missense_Mutation	SNP	C	C	T	rs2236264	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:93199080C>T	ENST00000393218.2	-	3	389	c.52G>A	c.(52-54)Gtt>Att	p.V18I	LGMN_ENST00000555699.1_Missense_Mutation_p.V18I|LGMN_ENST00000334869.4_Missense_Mutation_p.V18I|LGMN_ENST00000557434.1_Missense_Mutation_p.V18I	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	18			V -> I (in dbSNP:rs2236264). {ECO:0000269|PubMed:15489334}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		TCTATAGGAACGGCACCAATG	0.483													C|||	1171	0.233826	0.326	0.2118	5008	,	,		19183	0.2371		0.1571	False		,,,				2504	0.2004				p.V18I		Atlas-SNP	.											.	LGMN	28	.	0			c.G52A						PASS	.	C	ILE/VAL,ILE/VAL	1303,3103	439.4+/-345.7	182,939,1082	151.0	126.0	134.0		52,52	-9.4	0.0	14	dbSNP_98	134	1418,7182	273.1+/-290.5	96,1226,2978	yes	missense,missense	LGMN	NM_001008530.2,NM_005606.6	29,29	278,2165,4060	TT,TC,CC		16.4884,29.5733,20.9211	benign,benign	18/434,18/434	93199080	2721,10285	2203	4300	6503	SO:0001583	missense	5641	exon2			TAGGAACGGCACC	D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"""protease, cysteine, 1 (legumain)"""	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.52G>A	14.37:g.93199080C>T	ENSP00000376911:p.Val18Ile	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_005606	O00123|Q86TV2|Q86TV3|Q9BTY1	Missense_Mutation	SNP	ENST00000393218.2	37	CCDS9904.1	420	0.19230769230769232	130	0.26422764227642276	72	0.19889502762430938	109	0.19055944055944055	109	0.1437994722955145	C	10.96	1.498046	0.26861	0.295733	0.164884	ENSG00000100600	ENST00000555699;ENST00000334869;ENST00000557434;ENST00000334864;ENST00000262004;ENST00000393218;ENST00000535855;ENST00000553802;ENST00000554397;ENST00000554919;ENST00000554080;ENST00000553371;ENST00000553918	T;T;T;T;T;T;T;T;T;T	0.69685	0.9;0.93;0.93;0.93;0.91;0.89;0.89;0.87;0.87;-0.42	4.68	-9.35	0.00633	.	1.897820	0.02448	N	0.085289	T	0.00012	0.0000	L	0.45581	1.43	0.80722	P	0.0	B;B;B	0.12013	0.0;0.005;0.001	B;B;B	0.04013	0.0;0.001;0.0	T	0.05852	-1.0860	9	0.17369	T	0.5	-0.0458	2.4853	0.04597	0.1656:0.1265:0.3872:0.3207	rs2236264;rs17849714;rs58212475;rs2236264	18;18;18	Q99538;Q86TV2;Q86TV3	LGMN_HUMAN;.;.	I	18	ENSP00000451861:V18I;ENSP00000334052:V18I;ENSP00000452572:V18I;ENSP00000376911:V18I;ENSP00000450854:V18I;ENSP00000450677:V18I;ENSP00000451916:V18I;ENSP00000452268:V18I;ENSP00000451797:V18I;ENSP00000450619:V18I	ENSP00000262004:V18I	V	-	1	0	LGMN	92268833	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-2.629000	0.00872	-2.287000	0.00669	-0.485000	0.04761	GTT	T|0.202;G|0.005	0.202	strong		0.483	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606	
TRPV1	7442	hgsc.bcm.edu	37	17	3486702	3486702	+	Missense_Mutation	SNP	G	G	A	rs224534	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3486702G>A	ENST00000571088.1	-	9	1619	c.1406C>T	c.(1405-1407)aCt>aTt	p.T469I	TRPV1_ENST00000399756.4_Missense_Mutation_p.T469I|TRPV1_ENST00000399759.3_Missense_Mutation_p.T469I|TRPV1_ENST00000174621.6_Missense_Mutation_p.T467I|TRPV1_ENST00000425167.2_Missense_Mutation_p.T480I|SHPK_ENST00000572705.1_Missense_Mutation_p.T469I|TRPV1_ENST00000310522.5_Missense_Mutation_p.T409I|TRPV1_ENST00000576351.1_Missense_Mutation_p.T459I	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	469			T -> I (in dbSNP:rs224534). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:11243859}.		calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	ATAGTCTCCAGTTTTTTCCAT	0.448													G|||	1893	0.377995	0.0378	0.353	5008	,	,		21155	0.7679		0.3718	False		,,,				2504	0.4601				p.T469I	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.C1406T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	325,3491		18,289,1601	60.0	57.0	58.0		1406,1406,1406,1406	4.1	0.1	17	dbSNP_79	58	2842,5430		493,1856,1787	yes	missense,missense,missense,missense	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	89,89,89,89	511,2145,3388	AA,AG,GG		34.3569,8.5168,26.1995	benign,benign,benign,benign	469/840,469/840,469/840,469/840	3486702	3167,8921	1908	4136	6044	SO:0001583	missense	7442	exon9			TCTCCAGTTTTTT	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1406C>T	17.37:g.3486702G>A	ENSP00000461007:p.Thr469Ile	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	37	CCDS45576.1	881	0.4033882783882784	26	0.052845528455284556	137	0.3784530386740331	428	0.7482517482517482	290	0.38258575197889183	G	5.282	0.237389	0.10023	0.085168	0.343569	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88	5.12	4.12	0.48240	.	0.568097	0.19342	N	0.116624	T	0.00012	0.0000	M	0.67397	2.05	0.80722	P	0.0	B;B;B;B	0.34181	0.025;0.083;0.042;0.44	B;B;B;B	0.31016	0.056;0.025;0.025;0.123	T	0.50127	-0.8864	9	0.42905	T	0.14	-23.1286	3.7328	0.08499	0.0975:0.1713:0.5771:0.1541	rs224534;rs60157790;rs224534	469;467;409;480	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	I	469;469;467;480;409	ENSP00000382661:T469I;ENSP00000382659:T469I;ENSP00000174621:T467I;ENSP00000409627:T480I;ENSP00000311692:T409I	ENSP00000174621:T467I	T	-	2	0	TRPV1	3433451	0.947000	0.32204	0.080000	0.20451	0.060000	0.15804	2.864000	0.48404	1.225000	0.43566	0.655000	0.94253	ACT	G|0.613;A|0.387	0.387	strong		0.448	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
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 GAIIx	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		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	119	33	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	
PBOV1	59351	hgsc.bcm.edu	37	6	138539315	138539315	+	Missense_Mutation	SNP	A	A	G	rs6927706	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:138539315A>G	ENST00000527246.2	-	1	312	c.218T>C	c.(217-219)aTa>aCa	p.I73T	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	73			I -> T (in dbSNP:rs6927706).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		TGACTGTTCTATGGAATAATC	0.378													A|||	781	0.15595	0.1498	0.1556	5008	,	,		21690	0.3581		0.0616	False		,,,				2504	0.0532				p.I73T		Atlas-SNP	.											.	PBOV1	12	.	0			c.T218C						PASS	.	A	,THR/ILE	668,3738	284.3+/-277.5	52,564,1587	277.0	274.0	275.0		,218	-6.2	0.0	6	dbSNP_116	275	589,8011	157.5+/-211.1	18,553,3729	yes	intron,missense	KIAA1244,PBOV1	NM_020340.4,NM_021635.2	,89	70,1117,5316	GG,GA,AA		6.8488,15.1611,9.6648	,benign	,73/136	138539315	1257,11749	2203	4300	6503	SO:0001583	missense	59351	exon1			TGTTCTATGGAAT	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.218T>C	6.37:g.138539315A>G	ENSP00000432353:p.Ile73Thr	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	236	110	0.466102	NM_021635		Missense_Mutation	SNP	ENST00000527246.2	37	CCDS5190.1	408	0.18681318681318682	89	0.18089430894308944	51	0.1408839779005525	218	0.3811188811188811	50	0.06596306068601583	A	0.276	-0.989605	0.02162	0.151611	0.068488	ENSG00000254440	ENST00000527246	T	0.43294	0.95	3.1	-6.21	0.02065	.	.	.	.	.	T	0.07458	0.0188	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32079	-0.9920	8	0.87932	D	0	.	11.5379	0.50648	0.196:0.1308:0.6731:0.0	rs6927706;rs52793958;rs61006697;rs6927706	73	Q9GZY1	PBOV1_HUMAN	T	73	ENSP00000432353:I73T	ENSP00000432353:I73T	I	-	2	0	PBOV1	138581008	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.868000	0.00346	-2.939000	0.00298	-1.948000	0.00487	ATA	A|0.855;G|0.145	0.145	strong		0.378	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635	
WAPAL	23063	hgsc.bcm.edu	37	10	88277457	88277457	+	Missense_Mutation	SNP	C	C	T	rs10887621	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:88277457C>T	ENST00000298767.5	-	2	842	c.370G>A	c.(370-372)Gtt>Att	p.V124I		NM_015045.2	NP_055860.1	Q7Z5K2	WAPL_HUMAN	wings apart-like homolog (Drosophila)	124	Mediates interaction with the cohesin complex.		V -> I (in dbSNP:rs10887621).		mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA replication (GO:0008156)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of fibroblast proliferation (GO:0048146)|protein localization to chromatin (GO:0071168)|regulation of chromosome condensation (GO:0060623)|regulation of cohesin localization to chromatin (GO:0071922)|response to toxic substance (GO:0009636)|viral process (GO:0016032)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)				breast(2)|endometrium(2)|kidney(5)|large_intestine(6)|lung(13)|ovary(2)|stomach(1)	31						GTGTCTTCAACGACCACATGA	0.408													C|||	964	0.192492	0.0643	0.1239	5008	,	,		18371	0.1776		0.2803	False		,,,				2504	0.3395				p.V124I		Atlas-SNP	.											.	WAPAL	81	.	0			c.G370A						PASS	.	C	ILE/VAL	462,3944	218.7+/-236.7	20,422,1761	136.0	124.0	128.0		370	1.1	0.4	10	dbSNP_120	128	2426,6174	402.3+/-347.4	348,1730,2222	yes	missense	WAPAL	NM_015045.2	29	368,2152,3983	TT,TC,CC		28.2093,10.4857,22.2051	benign	124/1191	88277457	2888,10118	2203	4300	6503	SO:0001583	missense	23063	exon2			CTTCAACGACCAC	AB065003	CCDS7375.1	10q23.31	2006-12-08	2006-03-16	2006-03-16	ENSG00000062650	ENSG00000062650			23293	protein-coding gene	gene with protein product	"""friend of EBNA2"""	610754	"""KIAA0261"""	KIAA0261		9039502, 17112726	Standard	XM_006717726		Approved	FOE, WAPL	uc001kdo.3	Q7Z5K2	OTTHUMG00000018651	ENST00000298767.5:c.370G>A	10.37:g.88277457C>T	ENSP00000298767:p.Val124Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_015045	A7E2B5|Q5VSK5|Q8IX10|Q92549	Missense_Mutation	SNP	ENST00000298767.5	37	CCDS7375.1	397	0.18177655677655677	37	0.07520325203252033	48	0.13259668508287292	100	0.17482517482517482	212	0.2796833773087071	C	8.675	0.903750	0.17760	0.104857	0.282093	ENSG00000062650	ENST00000342368;ENST00000298767;ENST00000372076	T	0.22336	1.96	5.57	1.12	0.20585	.	0.771843	0.11847	N	0.523732	T	0.00012	0.0000	N	0.08118	0	0.27768	P	0.9435937	B;B;B;B	0.21753	0.06;0.014;0.014;0.024	B;B;B;B	0.17979	0.02;0.005;0.002;0.01	T	0.41448	-0.9508	9	0.51188	T	0.08	.	10.0746	0.42353	0.0:0.5265:0.0:0.4735	rs10887621;rs52791504;rs60591557;rs10887621	209;124;124;167	Q7Z5K2-3;B2RTX8;Q7Z5K2;Q7Z5K2-2	.;.;WAPL_HUMAN;.	I	209;124;209	ENSP00000298767:V124I	ENSP00000298767:V124I	V	-	1	0	WAPAL	88267437	0.966000	0.33281	0.383000	0.26132	0.254000	0.26022	1.529000	0.35996	0.323000	0.23307	0.655000	0.94253	GTT	C|0.796;T|0.204	0.204	strong		0.408	WAPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049151.2	NM_015045	
TTN	7273	hgsc.bcm.edu	37	2	179406191	179406191	+	Missense_Mutation	SNP	C	C	T	rs3731749	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179406191C>T	ENST00000591111.1	-	300	92914	c.92690G>A	c.(92689-92691)cGc>cAc	p.R30897H	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R32538H|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R23665H|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|RP11-65L3.4_ENST00000604692.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R23598H|TTN_ENST00000460472.2_Missense_Mutation_p.R23473H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R29970H|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000585358.1_RNA			Q8WZ42	TITIN_HUMAN	titin	30897	Fibronectin type-III 125. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CACTTCTTTGCGCTCCACAAT	0.468													C|||	1048	0.209265	0.0666	0.1484	5008	,	,		15530	0.4514		0.1382	False		,,,				2504	0.2689				p.R32538H		Atlas-SNP	.											.	TTN	18412	.	0			c.G97613A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	289,3661		10,269,1696	129.0	122.0	125.0		70418,89909,70793,70994	5.7	1.0	2	dbSNP_107	125	1206,7092		90,1026,3033	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	100,1295,4729	TT,TC,CC		14.5336,7.3165,12.2061	probably-damaging,probably-damaging,probably-damaging,probably-damaging	23473/26927,29970/33424,23598/27052,23665/27119	179406191	1495,10753	1975	4149	6124	SO:0001583	missense	7273	exon350			TCTTTGCGCTCCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.92690G>A	2.37:g.179406191C>T	ENSP00000465570:p.Arg30897His	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	179	95	0.530726	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		415	0.190018315018315	30	0.06097560975609756	43	0.11878453038674033	238	0.4160839160839161	104	0.13720316622691292	C	34	5.412118	0.96072	0.073165	0.145336	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.72	5.72	0.89469	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.71206	2.165	0.09310	P	0.9999999321613	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.999	T	0.17899	-1.0354	8	0.87932	D	0	.	19.8706	0.96849	0.0:1.0:0.0:0.0	rs3731749;rs58471840;rs3731749	23473;23598;23665;30897	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	29970;23473;23665;23598;23470	ENSP00000343764:R29970H;ENSP00000434586:R23473H;ENSP00000340554:R23665H;ENSP00000352154:R23598H	ENSP00000340554:R23665H	R	-	2	0	TTN	179114437	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.814000	0.86154	2.692000	0.91855	0.561000	0.74099	CGC	C|0.822;T|0.178	0.178	strong		0.468	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OR51G1	79324	hgsc.bcm.edu	37	11	4945233	4945233	+	Missense_Mutation	SNP	C	C	T	rs35264256	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:4945233C>T	ENST00000321961.2	-	1	404	c.337G>A	c.(337-339)Gag>Aag	p.E113K	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	113						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)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACTGATGACTCCATTGAAGAC	0.502													C|||	385	0.076877	0.062	0.1527	5008	,	,		22495	0.0079		0.1083	False		,,,				2504	0.0818				p.E113K		Atlas-SNP	.											.	OR51G1	74	.	0			c.G337A						PASS	.	C	LYS/GLU	277,4125	154.8+/-188.1	3,271,1927	101.0	94.0	97.0		337	4.2	0.5	11	dbSNP_126	97	930,7666	206.2+/-248.4	61,808,3429	no	missense	OR51G1	NM_001005237.1	56	64,1079,5356	TT,TC,CC		10.819,6.2926,9.286	probably-damaging	113/322	4945233	1207,11791	2201	4298	6499	SO:0001583	missense	79324	exon1			ATGACTCCATTGA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.337G>A	11.37:g.4945233C>T	ENSP00000322546:p.Glu113Lys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	171	0.0782967032967033	34	0.06910569105691057	30	0.08287292817679558	5	0.008741258741258742	102	0.1345646437994723	C	12.66	2.005934	0.35415	0.062926	0.10819	ENSG00000176879	ENST00000321961	T	0.40225	1.04	4.2	4.2	0.49525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39475	U	0.001355	T	0.02119	0.0066	H	0.95504	3.68	0.36263	P	0.145324	D	0.89917	1.0	D	0.91635	0.999	T	0.58092	-0.7697	9	0.87932	D	0	.	15.2651	0.73654	0.0:1.0:0.0:0.0	rs35264256;rs61737945	113	Q8NGK1	O51G1_HUMAN	K	113	ENSP00000322546:E113K	ENSP00000322546:E113K	E	-	1	0	OR51G1	4901809	0.634000	0.27190	0.508000	0.27688	0.043000	0.13939	1.261000	0.32980	2.169000	0.68431	0.557000	0.71058	GAG	C|0.912;T|0.088	0.088	strong		0.502	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
SYT15	83849	hgsc.bcm.edu	37	10	46969312	46969312	+	Missense_Mutation	SNP	G	G	A	rs55894256	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:46969312G>A	ENST00000374321.4	-	2	215	c.149C>T	c.(148-150)aCa>aTa	p.T50I	SYT15_ENST00000374323.4_Intron|SYT15_ENST00000374325.3_Missense_Mutation_p.T50I|SYT15_ENST00000503753.1_Missense_Mutation_p.T50I|RP11-38L15.3_ENST00000506914.1_RNA	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						GGAGGCAGCTGTGGTGGCCAT	0.642													G|||	240	0.0479233	0.0038	0.0793	5008	,	,		34618	0.0		0.1153	False		,,,				2504	0.0654				p.T50I	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											SYT15_ENST00000416127,NS,carcinoma,0,3	SYT15	165	3	0			c.C149T						PASS	.	G	ILE/THR,ILE/THR	65,4257		0,65,2096	36.0	47.0	43.0		149,149	0.3	0.0	10	dbSNP_129	43	869,7679		0,869,3405	yes	missense,missense	SYT15	NM_031912.4,NM_181519.2	89,89	0,934,5501	AA,AG,GG		10.1661,1.5039,7.2572	benign,benign	50/422,50/391	46969312	934,11936	2161	4274	6435	SO:0001583	missense	83849	exon2			GCAGCTGTGGTGG	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.149C>T	10.37:g.46969312G>A	ENSP00000363441:p.Thr50Ile	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	65	17	0.261538	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	107	0.04899267399267399	3	0.006097560975609756	24	0.06629834254143646	0	0.0	80	0.10554089709762533	g	9.886	1.203012	0.22121	0.015039	0.101661	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374321	T;T;T	0.13778	2.56;2.56;2.79	4.08	0.285	0.15705	.	.	.	.	.	T	0.00178	0.0005	N	0.16478	0.41	0.09310	N	1	B;B	0.10296	0.0;0.003	B;B	0.08055	0.001;0.003	T	0.40384	-0.9566	9	0.34782	T	0.22	.	7.0107	0.24861	0.1047:0.3786:0.5167:0.0	rs55894256;rs61854277	50;50	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	I	50	ENSP00000363445:T50I;ENSP00000427607:T50I;ENSP00000363441:T50I	ENSP00000363441:T50I	T	-	2	0	SYT15	46389318	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.305000	0.08188	-0.039000	0.13602	0.467000	0.42956	ACA	G|0.950;A|0.050	0.050	strong		0.642	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629868	32629868	+	Silent	SNP	A	A	G	rs1049088	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32629868A>G	ENST00000399082.3	-	2	311	c.267T>C	c.(265-267)ctT>ctC	p.L89L	HLA-DQB1_ENST00000399079.3_Silent_p.L179L|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1_ENST00000374943.4_Silent_p.L179L|HLA-DQB1_ENST00000399084.1_Silent_p.L179L|HLA-DQB1-AS1_ENST00000419852.1_RNA|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.L179L			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	179	Beta-1.		D -> A (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:04, allele DQB1*03:05, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:14, allele DQB1*03:18 and allele DQB1*06:29; dbSNP:rs1071637).|D -> S (in allele DQB1*05:02, allele DQB1*05:04, allele DQB1*05:05, allele DQB1*06:10 and allele DQB1*06:25; requires 2 nucleotide substitutions).|D -> V (in allele DQB1*05:01, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:27, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:38 and allele DQB1*06:39).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	CATTCCTAATAAGGGGGGTGG	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1027	0.205072	0.2201	0.1484	5008	,	,		17034	0.2331		0.1909	False		,,,				2504	0.2106				p.L179L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.T537C						PASS	.	A		849,3543		81,687,1428	52.0	56.0	55.0		537	-4.1	0.2	6	dbSNP_86	55	1396,7202		112,1172,3015	no	coding-synonymous	HLA-DQB1	NM_002123.4		193,1859,4443	GG,GA,AA		16.2363,19.3306,17.2825		179/262	32629868	2245,10745	2196	4299	6495	SO:0001819	synonymous_variant	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CCTAATAAGGGGG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.267T>C	6.37:g.32629868A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	72	16	0.222222	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				G|0.171;A|0.829	0.171	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
KLHL38	340359	hgsc.bcm.edu	37	8	124663987	124663987	+	Missense_Mutation	SNP	C	C	G	rs16898691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124663987C>G	ENST00000325995.7	-	1	1203	c.1180G>C	c.(1180-1182)Ggg>Cgg	p.G394R	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	394			G -> R (in dbSNP:rs16898691).							breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						AGCTCCTGCCCTTCTCCAATC	0.602													C|||	583	0.116414	0.0461	0.0836	5008	,	,		21826	0.2192		0.0408	False		,,,				2504	0.2065				p.G394R		Atlas-SNP	.											.	KLHL38	81	.	0			c.G1180C						PASS	.	C	ARG/GLY	164,3860		4,156,1852	65.0	65.0	65.0		1180	3.2	0.8	8	dbSNP_123	65	370,7990		14,342,3824	yes	missense	KLHL38	NM_001081675.2	125	18,498,5676	GG,GC,CC		4.4258,4.0755,4.312	probably-damaging	394/582	124663987	534,11850	2012	4180	6192	SO:0001583	missense	340359	exon1			CCTGCCCTTCTCC		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1180G>C	8.37:g.124663987C>G	ENSP00000321475:p.Gly394Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	211	0.09661172161172162	25	0.0508130081300813	26	0.0718232044198895	128	0.22377622377622378	32	0.04221635883905013	C	10.04	1.240664	0.22711	0.040755	0.044258	ENSG00000175946	ENST00000325995	T	0.71103	-0.54	5.18	3.18	0.36537	Kelch-type beta propeller (1);	0.367273	0.33691	N	0.004655	T	0.00073	0.0002	L	0.49778	1.585	0.39734	P	0.02834700000000001	B	0.02656	0.0	B	0.06405	0.002	T	0.06935	-1.0799	9	0.72032	D	0.01	.	5.0825	0.14664	0.0:0.3131:0.0:0.6869	rs16898691;rs52812544;rs16898691	394	Q2WGJ6	KLH38_HUMAN	R	394	ENSP00000321475:G394R	ENSP00000321475:G394R	G	-	1	0	KLHL38	124733168	0.978000	0.34361	0.777000	0.31699	0.732000	0.41865	3.219000	0.51200	0.571000	0.29365	0.561000	0.74099	GGG	C|0.903;G|0.097	0.097	strong		0.602	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
PTGS2	5743	hgsc.bcm.edu	37	1	186648197	186648197	+	Silent	SNP	C	C	G	rs5277	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186648197C>G	ENST00000367468.5	-	3	442	c.306G>C	c.(304-306)gtG>gtC	p.V102V	RP5-973M2.2_ENST00000608917.1_lincRNA|PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	102					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.V102V(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	TACATGTCAACACATAACTCA	0.348													C|||	380	0.0758786	0.0129	0.1095	5008	,	,		20438	0.0437		0.1819	False		,,,				2504	0.0613				p.V102V		Atlas-SNP	.											PTGS2_ENST00000367468,NS,carcinoma,0,1	PTGS2	144	1	1	Substitution - coding silent(1)	stomach(1)	c.G306C						scavenged	.	C		168,4238	111.2+/-149.4	7,154,2042	67.0	66.0	66.0		306	3.0	0.6	1	dbSNP_52	66	1327,7273	259.5+/-282.7	94,1139,3067	no	coding-synonymous	PTGS2	NM_000963.2		101,1293,5109	GG,GC,CC		15.4302,3.813,11.4947		102/605	186648197	1495,11511	2203	4300	6503	SO:0001819	synonymous_variant	5743	exon3			TGTCAACACATAA	D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.306G>C	1.37:g.186648197C>G		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_000963	A8K802|Q16876	Silent	SNP	ENST00000367468.5	37	CCDS1371.1																																																																																			C|0.882;G|0.118	0.118	strong		0.348	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963	
AKAP1	8165	hgsc.bcm.edu	37	17	55182878	55182878	+	Missense_Mutation	SNP	C	C	T	rs17761023	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:55182878C>T	ENST00000337714.3	+	2	286	c.53C>T	c.(52-54)gCg>gTg	p.A18V	AKAP1_ENST00000571629.1_Missense_Mutation_p.A18V|AKAP1_ENST00000314126.3_Missense_Mutation_p.A18V|AKAP1_ENST00000572557.1_Missense_Mutation_p.A18V|AKAP1_ENST00000539273.1_Missense_Mutation_p.A18V	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	18			A -> V (in dbSNP:rs17761023).		blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					GGGATGCTGGCGCTCCTCGGC	0.582													C|||	305	0.0609026	0.0643	0.0476	5008	,	,		20923	0.005		0.1143	False		,,,				2504	0.0685				p.A18V		Atlas-SNP	.											AKAP1,NS,carcinoma,-1,1	AKAP1	73	1	0			c.C53T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	304,4102	162.9+/-194.8	8,288,1907	64.0	60.0	61.0		53,53,53	3.7	0.5	17	dbSNP_123	61	879,7721	198.6+/-242.9	45,789,3466	yes	missense,missense,missense	AKAP1	NM_001242902.1,NM_001242903.1,NM_003488.3	64,64,64	53,1077,5373	TT,TC,CC		10.2209,6.8997,9.0958	probably-damaging,probably-damaging,probably-damaging	18/904,18/904,18/904	55182878	1183,11823	2203	4300	6503	SO:0001583	missense	8165	exon3			TGCTGGCGCTCCT	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.53C>T	17.37:g.55182878C>T	ENSP00000337736:p.Ala18Val	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	127	0.05815018315018315	23	0.046747967479674794	16	0.04419889502762431	5	0.008741258741258742	83	0.10949868073878628	C	14.55	2.567697	0.45798	0.068997	0.102209	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.18502	2.21;2.21;2.21	5.62	3.65	0.41850	.	0.051862	0.85682	D	0.000000	T	0.00271	0.0008	L	0.41961	1.31	0.21802	P	0.999537472	P	0.36249	0.545	B	0.26310	0.068	T	0.09618	-1.0666	9	0.87932	D	0	-12.041	11.4341	0.50058	0.0:0.8543:0.0:0.1457	rs17761023;rs52795163;rs17761023	18	Q92667	AKAP1_HUMAN	V	18;18;60;18	ENSP00000337736:A18V;ENSP00000314075:A18V;ENSP00000443139:A18V	ENSP00000314075:A18V	A	+	2	0	AKAP1	52537877	0.995000	0.38212	0.490000	0.27465	0.453000	0.32348	3.292000	0.51772	0.737000	0.32582	-0.137000	0.14449	GCG	C|0.928;T|0.072	0.072	strong		0.582	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1		
LANCL3	347404	hgsc.bcm.edu	37	X	37518806	37518806	+	Silent	SNP	C	C	T	rs12009345	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:37518806C>T	ENST00000378619.3	+	3	1008	c.789C>T	c.(787-789)agC>agT	p.S263S	TM4SF2_ENST00000465127.1_Intron|LANCL3_ENST00000378621.3_Silent_p.S263S	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)	263							catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						TATGGCAGAGCGTGGACTTTC	0.522													C|||	1121	0.296954	0.5197	0.147	3775	,	,		12831	0.0496		0.1113	False		,,,				2504	0.1738				p.S263S		Atlas-SNP	.											.	LANCL3	42	.	0			c.C789T						PASS	.	C	,	2413,1420		652,750,359,229,212	79.0	67.0	71.0		789,789	-0.3	1.0	X	dbSNP_120	71	1158,5570		84,684,306,1660,1566	no	coding-synonymous,coding-synonymous	LANCL3	NM_001170331.1,NM_198511.2	,	736,1434,665,1889,1778	TT,TC,T,CC,C		17.2117,37.0467,33.8131	,	263/421,263/389	37518806	3571,6990	2202	4300	6502	SO:0001819	synonymous_variant	347404	exon3			GCAGAGCGTGGAC	AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.789C>T	X.37:g.37518806C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	72	18	0.25	NM_001170331	A6NHE3	Silent	SNP	ENST00000378619.3	37	CCDS55398.1																																																																																			C|0.681;0|0.003	.	strong		0.522	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511	
PPP2R5A	5525	hgsc.bcm.edu	37	1	212515613	212515613	+	Silent	SNP	C	C	T	rs1774249	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:212515613C>T	ENST00000261461.2	+	4	1138	c.564C>T	c.(562-564)ttC>ttT	p.F188F	PPP2R5A_ENST00000537030.3_Silent_p.F131F|PPP2R5A_ENST00000498129.2_3'UTR	NM_006243.3	NP_006234.1	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B', alpha	188					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of lipid kinase activity (GO:0090219)|positive regulation of protein dephosphorylation (GO:0035307)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|M band (GO:0031430)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)|Z disc (GO:0030018)	kinase binding (GO:0019900)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		ATCAGAAATTCGTACAACAGG	0.313													C|||	1410	0.28155	0.1853	0.33	5008	,	,		15520	0.2837		0.34	False		,,,				2504	0.3149				p.F188F		Atlas-SNP	.											.	PPP2R5A	48	.	0			c.C564T						PASS	.	C	,	936,3470	354.1+/-312.5	99,738,1366	108.0	103.0	105.0		393,564	4.7	1.0	1	dbSNP_89	105	3045,5555	468.4+/-367.3	542,1961,1797	no	coding-synonymous,coding-synonymous	PPP2R5A	NM_001199756.1,NM_006243.3	,	641,2699,3163	TT,TC,CC		35.407,21.2438,30.6089	,	131/430,188/487	212515613	3981,9025	2203	4300	6503	SO:0001819	synonymous_variant	5525	exon4			GAAATTCGTACAA	BC022474	CCDS1503.1, CCDS55686.1	1q32.2-q32.3	2010-06-18	2010-04-14		ENSG00000066027	ENSG00000066027		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9309	protein-coding gene	gene with protein product		601643	"""protein phosphatase 2, regulatory subunit B (B56), alpha isoform"", ""protein phosphatase 2, regulatory subunit B', alpha isoform"""			7592815	Standard	NM_006243		Approved	PR61A, B56A	uc001hjb.3	Q15172	OTTHUMG00000036750	ENST00000261461.2:c.564C>T	1.37:g.212515613C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_006243	B2R6D2|B7Z7L2|D3DT99|Q2NL72|Q5VVB2|Q8TBI9	Silent	SNP	ENST00000261461.2	37	CCDS1503.1																																																																																			C|0.701;T|0.299	0.299	strong		0.313	PPP2R5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089302.1	NM_006243	
ANAPC1	64682	hgsc.bcm.edu	37	2	112615933	112615933	+	Silent	SNP	T	T	C	rs72936244	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:112615933T>C	ENST00000341068.3	-	11	2080	c.1308A>G	c.(1306-1308)ctA>ctG	p.L436L		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	436					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						TTTGCCCACATAGGTCAGATG	0.378																																					p.L436L		Atlas-SNP	.											ANAPC1,NS,carcinoma,0,1	ANAPC1	116	1	0			c.A1308G						PASS	.						97.0	91.0	93.0					2																	112615933		2203	4300	6503	SO:0001819	synonymous_variant	64682	exon11			CCCACATAGGTCA	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.1308A>G	2.37:g.112615933T>C		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	211	66	0.312796	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Silent	SNP	ENST00000341068.3	37	CCDS2093.1																																																																																			.	.	weak		0.378	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	
SEC24C	9632	hgsc.bcm.edu	37	10	75506674	75506674	+	Silent	SNP	T	T	C	rs2306325	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:75506674T>C	ENST00000339365.2	+	3	246	c.84T>C	c.(82-84)taT>taC	p.Y28Y	SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000411652.2_5'UTR|SEC24C_ENST00000345254.4_Silent_p.Y28Y|SEC24C_ENST00000546025.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	28					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.Y28Y(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					AGTCCAGCTATGGTGGGCAAT	0.542													c|||	765	0.152756	0.1528	0.1182	5008	,	,		15519	0.1587		0.1332	False		,,,				2504	0.1912				p.Y28Y		Atlas-SNP	.											SEC24C,NS,carcinoma,0,1	SEC24C	86	1	1	Substitution - coding silent(1)	stomach(1)	c.T84C						PASS	.	C	,	653,3753	765.4+/-413.4	55,543,1605	97.0	84.0	88.0		84,84	1.1	1.0	10	dbSNP_100	88	1233,7367	762.0+/-407.6	85,1063,3152	no	coding-synonymous,coding-synonymous	SEC24C	NM_004922.3,NM_198597.2	,	140,1606,4757	CC,CT,TT		14.3372,14.8207,14.501	,	28/1095,28/1095	75506674	1886,11120	2203	4300	6503	SO:0001819	synonymous_variant	9632	exon2			CAGCTATGGTGGG	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.84T>C	10.37:g.75506674T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_198597	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	37	CCDS7332.1																																																																																			T|0.851;C|0.149	0.149	strong		0.542	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
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 GAIIx	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_ENST00000529824.2_Silent_p.T482T|TIAM2_ENST00000456144.1_Silent_p.T482T|TIAM2_ENST00000318981.5_Silent_p.T482T|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000360366.4_Silent_p.T482T			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		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	86	33	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 GAIIx	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	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	132	43	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	
AOC1	26	hgsc.bcm.edu	37	7	150557622	150557622	+	Silent	SNP	G	G	A	rs12179	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150557622G>A	ENST00000493429.1	+	6	2474	c.1890G>A	c.(1888-1890)tcG>tcA	p.S630S	AOC1_ENST00000467291.1_Silent_p.S630S|AOC1_ENST00000360937.4_Silent_p.S630S|AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000416793.2_Silent_p.S649S			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	630					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)	p.S630S(1)								Amiloride(DB00594)	ACCGGGAGTCGGAGCTGTGCA	0.622													G|||	2270	0.453275	0.5446	0.3977	5008	,	,		17441	0.4802		0.2694	False		,,,				2504	0.5307				p.S649S		Atlas-SNP	.											ABP1,NS,carcinoma,0,1	ABP1	92	1	1	Substitution - coding silent(1)	stomach(1)	c.G1947A						PASS	.	G		2025,2247		505,1015,616	74.0	85.0	81.0		1890	-10.1	0.0	7	dbSNP_52	81	2557,5915		415,1727,2094	no	coding-synonymous	ABP1	NM_001091.2		920,2742,2710	AA,AG,GG		30.1818,47.4017,35.9542		630/752	150557622	4582,8162	2136	4236	6372	SO:0001819	synonymous_variant	26	exon4			GGAGTCGGAGCTG	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1890G>A	7.37:g.150557622G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	21	0.333333	NM_001272072	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																			G|0.580;A|0.420	0.420	strong		0.622	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
FANCI	55215	hgsc.bcm.edu	37	15	89804043	89804043	+	Missense_Mutation	SNP	C	C	T	rs17803620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89804043C>T	ENST00000310775.7	+	4	343	c.257C>T	c.(256-258)gCg>gTg	p.A86V	FANCI_ENST00000451393.2_5'UTR|FANCI_ENST00000567996.1_Missense_Mutation_p.A86V|FANCI_ENST00000300027.8_Missense_Mutation_p.A86V	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	86			A -> V (in dbSNP:rs17803620). {ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					AAAGAAATAGCGTCTGAGATC	0.438								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	1301	0.259784	0.0393	0.3458	5008	,	,		17597	0.3036		0.3787	False		,,,				2504	0.3292				p.A86V		Atlas-SNP	.											.	FANCI	129	.	0			c.C257T						PASS	.	C	VAL/ALA,VAL/ALA	417,3983	205.2+/-227.1	19,379,1802	124.0	118.0	120.0		257,257	4.4	1.0	15	dbSNP_123	120	3304,5294	493.6+/-373.6	635,2034,1630	yes	missense,missense	FANCI	NM_001113378.1,NM_018193.2	64,64	654,2413,3432	TT,TC,CC		38.4275,9.4773,28.6275	benign,benign	86/1329,86/1269	89804043	3721,9277	2200	4299	6499	SO:0001583	missense	55215	exon4	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAATAGCGTCTGA	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.257C>T	15.37:g.89804043C>T	ENSP00000310842:p.Ala86Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	623	0.28525641025641024	29	0.05894308943089431	120	0.3314917127071823	173	0.30244755244755245	301	0.3970976253298153	C	15.55	2.866199	0.51588	0.094773	0.384275	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	T;T;T	0.43294	0.95;0.95;0.95	5.43	4.45	0.53987	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	L	0.38838	1.175	0.09310	P	1.0	B;P	0.41345	0.191;0.746	B;B	0.25614	0.055;0.062	T	0.39375	-0.9617	9	0.08381	T	0.77	-8.5811	9.6142	0.39681	0.0:0.7708:0.1457:0.0835	rs17803620;rs17803620	86;86	Q9NVI1;Q9NVI1-1	FANCI_HUMAN;.	V	86	ENSP00000300027:A86V;ENSP00000310842:A86V;ENSP00000413249:A86V	ENSP00000300027:A86V	A	+	2	0	FANCI	87605047	0.997000	0.39634	1.000000	0.80357	0.955000	0.61496	1.970000	0.40520	2.534000	0.85438	0.655000	0.94253	GCG	C|0.726;T|0.274	0.274	strong		0.438	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
HIST1H2BK	85236	hgsc.bcm.edu	37	6	27114488	27114488	+	Silent	SNP	G	G	C	rs12207760	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27114488G>C	ENST00000356950.1	-	1	89	c.90C>G	c.(88-90)cgC>cgG	p.R30R	MIR3143_ENST00000584253.1_RNA|HIST1H2BK_ENST00000396891.4_Silent_p.R30R|HIST1H2AH_ENST00000377459.1_5'Flank			O60814	H2B1K_HUMAN	histone cluster 1, H2bk	30					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R30R(2)		breast(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						GGCTGCGCTTGCGCTTCTTGC	0.592													G|||	60	0.0119808	0.0015	0.0058	5008	,	,		21167	0.001		0.0477	False		,,,				2504	0.0051				p.R30R		Atlas-SNP	.											HIST1H2BK_ENST00000396891,NS,carcinoma,0,2	HIST1H2BK	68	2	2	Substitution - coding silent(2)	ovary(2)	c.C90G						PASS	.	G		31,4375		0,31,2172	176.0	143.0	154.0		90	2.9	1.0	6	dbSNP_120	154	340,8260		4,332,3964	no	coding-synonymous	HIST1H2BK	NM_080593.2		4,363,6136	CC,CG,GG		3.9535,0.7036,2.8525		30/127	27114488	371,12635	2203	4300	6503	SO:0001819	synonymous_variant	85236	exon1			GCGCTTGCGCTTC	AJ223352	CCDS4621.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000197903	ENSG00000197903		"""Histones / Replication-dependent"""	13954	protein-coding gene	gene with protein product		615045	"""H2B histone family, member T"", ""histone 1, H2bk"""	H2BFT		12408966	Standard	NM_080593		Approved	H2BFAiii	uc003nix.2	O60814	OTTHUMG00000014473	ENST00000356950.1:c.90C>G	6.37:g.27114488G>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	12	0.116505	NM_080593	A8K7P7|Q2VPI7	Silent	SNP	ENST00000356950.1	37	CCDS4621.1																																																																																			G|0.965;C|0.035	0.035	strong		0.592	HIST1H2BK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040141.1	NM_080593	
PCNXL4	64430	hgsc.bcm.edu	37	14	60591887	60591887	+	Missense_Mutation	SNP	G	G	A	rs167437	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:60591887G>A	ENST00000406854.1	+	9	3552	c.2998G>A	c.(2998-3000)Ggt>Agt	p.G1000S	PCNXL4_ENST00000535349.1_Missense_Mutation_p.G207S|PCNXL4_ENST00000406949.1_Missense_Mutation_p.G766S|PCNXL4_ENST00000404681.2_Missense_Mutation_p.G1000S|PCNXL4_ENST00000317623.4_Missense_Mutation_p.G766S			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	1000			G -> S (in dbSNP:rs167437). {ECO:0000269|PubMed:17974005}.			integral component of membrane (GO:0016021)											GAGAGTTTACGGTGGTGTTTT	0.363													A|||	1747	0.348842	0.6082	0.1412	5008	,	,		19049	0.3472		0.1183	False		,,,				2504	0.3845				p.G766S		Atlas-SNP	.											.	.	.	.	0			c.G2296A						PASS	.	A	SER/GLY	2375,2031	558.0+/-379.9	630,1115,458	52.0	52.0	52.0		2296	5.2	1.0	14	dbSNP_79	52	1103,7497	763.8+/-407.6	75,953,3272	yes	missense	C14orf135	NM_022495.5	56	705,2068,3730	AA,AG,GG		12.8256,46.0962,26.7415	benign	766/939	60591887	3478,9528	2203	4300	6503	SO:0001583	missense	64430	exon8			GTTTACGGTGGTG	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.2998G>A	14.37:g.60591887G>A	ENSP00000384801:p.Gly1000Ser	Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	284	282	0.992958	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		610	0.2793040293040293	277	0.5630081300813008	57	0.1574585635359116	196	0.34265734265734266	80	0.10554089709762533	A	3.746	-0.052626	0.07362	0.539038	0.128256	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681;ENST00000535349	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	5.18	5.18	0.71444	.	0.472372	0.27100	N	0.020923	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	1.0000000000287557E-6	B;B	0.11235	0.004;0.0	B;B	0.06405	0.002;0.001	T	0.44892	-0.9298	9	0.07482	T	0.82	.	6.5552	0.22456	0.7897:0.0:0.0736:0.1367	rs167437;rs3737079;rs52795398;rs61537067;rs167437	1000;766	Q63HM2;B5MC47	CN135_HUMAN;.	S	766;1000;766;1000;207	ENSP00000317396:G766S;ENSP00000384801:G1000S;ENSP00000385201:G766S;ENSP00000385713:G1000S;ENSP00000445644:G207S	ENSP00000317396:G766S	G	+	1	0	C14orf135	59661640	0.999000	0.42202	0.998000	0.56505	0.729000	0.41735	4.470000	0.60175	0.914000	0.36822	-0.893000	0.02921	GGT	G|0.700;A|0.300	0.300	strong		0.363	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
SPESP1	246777	hgsc.bcm.edu	37	15	69238392	69238392	+	Silent	SNP	T	T	C	rs3743092	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:69238392T>C	ENST00000310673.3	+	2	673	c.519T>C	c.(517-519)taT>taC	p.Y173Y	NOX5_ENST00000448182.3_Intron|NOX5_ENST00000455873.3_Intron|NOX5_ENST00000260364.5_Intron|RP11-809H16.2_ENST00000557966.1_RNA|SPESP1_ENST00000560188.1_3'UTR	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	173					acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						CAAGTCCATATGTTACCTCAT	0.453													T|||	88	0.0175719	0.0	0.0043	5008	,	,		18038	0.0437		0.0109	False		,,,				2504	0.0307				p.Y173Y		Atlas-SNP	.											.	SPESP1	39	.	0			c.T519C						PASS	.	T	,	13,4387	20.2+/-43.8	0,13,2187	122.0	120.0	120.0		,519	-6.0	0.0	15	dbSNP_107	120	84,8512	49.4+/-109.1	1,82,4215	no	intron,coding-synonymous	NOX5,SPESP1	NM_001184780.1,NM_145658.3	,	1,95,6402	CC,CT,TT		0.9772,0.2955,0.7464	,	,173/351	69238392	97,12899	2200	4298	6498	SO:0001819	synonymous_variant	246777	exon2			TCCATATGTTACC	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.519T>C	15.37:g.69238392T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	156	66	0.423077	NM_145658	Q8NG22|Q8WVH8	Silent	SNP	ENST00000310673.3	37	CCDS10230.1																																																																																			T|0.988;C|0.012	0.012	strong		0.453	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658	
CARD9	64170	hgsc.bcm.edu	37	9	139266405	139266405	+	Silent	SNP	G	G	A	rs10781499	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139266405G>A	ENST00000371732.5	-	2	291	c.126C>T	c.(124-126)ccC>ccT	p.P42P	CARD9_ENST00000371734.3_Silent_p.P42P|CARD9_ENST00000315908.7_Silent_p.P42P	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	42	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		CCTCATCATCGGGGTTCAGGA	0.642													G|||	1834	0.366214	0.2504	0.572	5008	,	,		17535	0.3185		0.3976	False		,,,				2504	0.3937				p.P42P		Atlas-SNP	.											CARD9,NS,carcinoma,0,1	CARD9	47	1	0			c.C126T						PASS	.	G	,	1227,3179	424.7+/-340.5	166,895,1142	171.0	150.0	157.0	http://www.ncbi.nlm.nih.gov/pubmed?term	126,126	-2.2	0.8	9	dbSNP_120	157	3641,4959	523.9+/-380.4	767,2107,1426	yes	coding-synonymous,coding-synonymous	CARD9	NM_052813.4,NM_052814.3	,	933,3002,2568	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	42.3372,27.8484,37.4289	,	42/537,42/493	139266405	4868,8138	2203	4300	6503	SO:0001819	synonymous_variant	64170	exon2			ATCATCGGGGTTC	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.126C>T	9.37:g.139266405G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			G|0.634;A|0.366	0.366	strong		0.642	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
EXD3	54932	hgsc.bcm.edu	37	9	140262426	140262426	+	Missense_Mutation	SNP	C	C	T	rs11533158	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:140262426C>T	ENST00000340951.4	-	6	673	c.478G>A	c.(478-480)Gcg>Acg	p.A160T	EXD3_ENST00000475006.1_5'UTR|EXD3_ENST00000479452.1_Missense_Mutation_p.A160T|EXD3_ENST00000342129.4_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						TTCAACGTCGCGCCCAGCGTG	0.562													T|||	3536	0.70607	0.5356	0.7089	5008	,	,		20820	0.8522		0.659	False		,,,				2504	0.8323				p.A160T		Atlas-SNP	.											EXD3_ENST00000340951,colon,carcinoma,0,2	EXD3	86	2	0			c.G478A						PASS	.	C	THR/ALA	2192,1800		629,934,433	37.0	37.0	37.0		478	-1.5	0.1	9	dbSNP_120	37	5815,2529		2040,1735,397	yes	missense	EXD3	NM_017820.3	58	2669,2669,830	TT,TC,CC		30.3092,45.0902,35.0924	benign	160/877	140262426	8007,4329	1996	4172	6168	SO:0001583	missense	54932	exon6			ACGTCGCGCCCAG		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.478G>A	9.37:g.140262426C>T	ENSP00000340474:p.Ala160Thr	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	1516	0.6941391941391941	255	0.5182926829268293	259	0.7154696132596685	494	0.8636363636363636	508	0.6701846965699209	T	1.921	-0.448390	0.04572	0.549098	0.696908	ENSG00000187609	ENST00000340951;ENST00000479452	T;T	0.49432	0.78;1.61	2.85	-1.53	0.08611	.	0.580226	0.18378	N	0.143056	T	0.00012	0.0000	N	0.00246	-1.78	0.45066	P	0.0019120000000000248	B;B	0.09022	0.0;0.002	B;B	0.01281	0.0;0.0	T	0.29941	-0.9995	9	0.02654	T	1	.	2.5199	0.04677	0.2044:0.2595:0.0:0.5362	rs11533158	160;160	Q8N9H8-4;Q8N9H8	.;MUT7_HUMAN	T	160	ENSP00000340474:A160T;ENSP00000431859:A160T	ENSP00000340474:A160T	A	-	1	0	EXD3	139382247	0.004000	0.15560	0.118000	0.21660	0.196000	0.23810	0.014000	0.13333	-0.453000	0.07076	-0.959000	0.02639	GCG	C|0.308;T|0.692	0.692	strong		0.562	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
SBNO2	22904	hgsc.bcm.edu	37	19	1127615	1127615	+	Silent	SNP	G	G	C	rs2074915	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1127615G>C	ENST00000361757.3	-	5	666	c.429C>G	c.(427-429)tcC>tcG	p.S143S	SBNO2_ENST00000438103.2_Silent_p.S86S|SBNO2_ENST00000587024.1_Silent_p.S143S	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	143					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)		TATCGTGGGTGGAGGGGGCAG	0.682													G|||	877	0.17512	0.0136	0.304	5008	,	,		15747	0.1875		0.1958	False		,,,				2504	0.2679				p.S143S		Atlas-SNP	.											SBNO2_ENST00000250872,NS,carcinoma,0,2	SBNO2	112	2	0			c.C429G						PASS	.	G	,	197,4059		2,193,1933	62.0	73.0	69.0		258,429	-1.9	0.0	19	dbSNP_96	69	1774,6678		187,1400,2639	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	189,1593,4572	CC,CG,GG		20.9891,4.6288,15.5099	,	86/1310,143/1367	1127615	1971,10737	2128	4226	6354	SO:0001819	synonymous_variant	22904	exon5			GTGGGTGGAGGGG	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.429C>G	19.37:g.1127615G>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			G|0.810;C|0.190	0.190	strong		0.682	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
ARNTL2	56938	hgsc.bcm.edu	37	12	27540204	27540204	+	Missense_Mutation	SNP	A	A	G	rs71541528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27540204A>G	ENST00000266503.5	+	7	626	c.608A>G	c.(607-609)aAa>aGa	p.K203R	RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000395901.2_Missense_Mutation_p.K166R|ARNTL2_ENST00000546179.1_Missense_Mutation_p.K166R|ARNTL2_ENST00000544915.1_Missense_Mutation_p.K169R|ARNTL2_ENST00000542388.1_Missense_Mutation_p.K118R|ARNTL2_ENST00000311001.5_Missense_Mutation_p.K189R|ARNTL2_ENST00000261178.5_Missense_Mutation_p.K155R			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	203	Interaction with PER2. {ECO:0000250|UniProtKB:Q2VPD4}.|PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|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)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					GAAAGAGGAAAAATTCTCTTC	0.294													A|||	101	0.0201677	0.0015	0.013	5008	,	,		18717	0.006		0.0388	False		,,,				2504	0.046				p.K203R		Atlas-SNP	.											.	ARNTL2	54	.	0			c.A608G						PASS	.	A	ARG/LYS	33,4373	39.2+/-71.8	0,33,2170	114.0	117.0	116.0		608	1.3	1.0	12	dbSNP_130	116	428,8172	131.7+/-189.4	10,408,3882	yes	missense	ARNTL2	NM_020183.3	26	10,441,6052	GG,GA,AA		4.9767,0.749,3.5445	benign	203/637	27540204	461,12545	2203	4300	6503	SO:0001583	missense	56938	exon7			GAGGAAAAATTCT	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"""Basic helix-loop-helix proteins"""	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.608A>G	12.37:g.27540204A>G	ENSP00000266503:p.Lys203Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_020183	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	37	CCDS8712.1	39|39	0.017857142857142856|0.017857142857142856	1|1	0.0020325203252032522|0.0020325203252032522	5|5	0.013812154696132596|0.013812154696132596	1|1	0.0017482517482517483|0.0017482517482517483	32|32	0.04221635883905013|0.04221635883905013	A|A	5.024|5.024	0.190026|0.190026	0.09547|0.09547	0.00749|0.00749	0.049767|0.049767	ENSG00000029153|ENSG00000029153	ENST00000457040|ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388	T|T;T;T;T;T;T;T	0.18502|0.15256	2.21|2.44;2.44;2.44;2.44;2.44;2.44;2.44	3.79|3.79	1.33|1.33	0.21861|0.21861	.|PAS (2);PAS fold (1);	0.174816|0.174816	0.49916|0.49916	D|N	0.000130|0.000130	T|T	0.00967|0.00967	0.0032|0.0032	N|N	0.10685|0.10685	0.025|0.025	0.36059|0.36059	D|D	0.841313|0.841313	.|B;B;B;B;B;B	.|0.30664	.|0.289;0.007;0.282;0.282;0.122;0.024	.|B;B;B;B;B;B	.|0.36244	.|0.17;0.036;0.22;0.22;0.081;0.074	T|T	0.36286|0.36286	-0.9754|-0.9754	8|10	0.59425|0.02654	D|T	0.04|1	.|.	6.369|6.369	0.21471|0.21471	0.6447:0.0:0.3553:0.0|0.6447:0.0:0.3553:0.0	.|.	.|166;169;166;155;189;203	.|F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1	.|.;.;.;.;.;BMAL2_HUMAN	E|R	155|169;166;166;189;155;203;118	ENSP00000400185:K155E|ENSP00000442438:K169R;ENSP00000379238:K166R;ENSP00000438545:K166R;ENSP00000312247:K189R;ENSP00000261178:K155R;ENSP00000266503:K203R;ENSP00000445836:K118R	ENSP00000400185:K155E|ENSP00000261178:K155R	K|K	+|+	1|2	0|0	ARNTL2|ARNTL2	27431471|27431471	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	4.177000|4.177000	0.58276|0.58276	0.162000|0.162000	0.19483|0.19483	-0.408000|-0.408000	0.06270|0.06270	AAA|AAA	A|0.970;G|0.030	0.030	strong		0.294	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183	
SPTBN1	6711	hgsc.bcm.edu	37	2	54858664	54858664	+	Silent	SNP	C	C	T	rs2229503	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54858664C>T	ENST00000356805.4	+	16	3761	c.3480C>T	c.(3478-3480)aaC>aaT	p.N1160N	SPTBN1_ENST00000333896.5_Silent_p.N1147N	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1160					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			TGTGGGAGAACAGACAAAATC	0.547													C|||	578	0.115415	0.1339	0.0951	5008	,	,		19822	0.0813		0.174	False		,,,				2504	0.0798				p.N1160N		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C3480T						PASS	.	C	,	573,3833	257.0+/-261.6	33,507,1663	101.0	100.0	100.0		3480,3441	3.5	1.0	2	dbSNP_98	100	1594,7006	297.1+/-303.3	160,1274,2866	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	193,1781,4529	TT,TC,CC		18.5349,13.005,16.6615	,	1160/2365,1147/2156	54858664	2167,10839	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon16			GGAGAACAGACAA		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3480C>T	2.37:g.54858664C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.857;T|0.143	0.143	strong		0.547	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
FRMPD1	22844	hgsc.bcm.edu	37	9	37745413	37745413	+	Silent	SNP	G	G	A	rs3747541	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:37745413G>A	ENST00000539465.1	+	16	3977	c.3384G>A	c.(3382-3384)gaG>gaA	p.E1128E	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Silent_p.E1128E			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1128						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TTCAGGAGGAGTCTAGGAAGG	0.428													A|||	1935	0.386382	0.5847	0.4193	5008	,	,		20725	0.2024		0.332	False		,,,				2504	0.3405				p.E1128E		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G3384A						PASS	.	A		2298,2108	576.3+/-384.2	614,1070,519	69.0	72.0	71.0		3384	-1.8	0.0	9	dbSNP_107	71	3005,5595	664.5+/-402.2	526,1953,1821	no	coding-synonymous	FRMPD1	NM_014907.2		1140,3023,2340	AA,AG,GG		34.9419,47.8438,40.7735		1128/1579	37745413	5303,7703	2203	4300	6503	SO:0001819	synonymous_variant	22844	exon16			GGAGGAGTCTAGG	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3384G>A	9.37:g.37745413G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Silent	SNP	ENST00000539465.1	37	CCDS6612.1																																																																																			G|0.618;A|0.382	0.382	strong		0.428	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
PRKX	5613	hgsc.bcm.edu	37	X	3592797	3592797	+	Silent	SNP	C	C	A	rs56037462	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3592797C>A	ENST00000262848.5	-	2	531	c.177G>T	c.(175-177)acG>acT	p.T59T		NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	59	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				CCCGCCCGAACGTCCCAGTGC	0.557													C|||	32	0.00847682	0.0	0.0	3775	,	,		13926	0.0		0.006	False		,,,				2504	0.0266				p.T59T		Atlas-SNP	.											.	PRKX	29	.	0			c.G177T						PASS	.	C		6,3829		0,6,0,1626,571	118.0	93.0	101.0		177	-5.2	0.1	X	dbSNP_129	101	73,6650		1,51,20,2374,1851	no	coding-synonymous	PRKX	NM_005044.4		1,57,20,4000,2422	AA,AC,A,CC,C		1.0858,0.1565,0.7482		59/359	3592797	79,10479	2203	4297	6500	SO:0001819	synonymous_variant	5613	exon2			CCCGAACGTCCCA		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.177G>T	X.37:g.3592797C>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	101	27	0.267327	NM_005044		Silent	SNP	ENST00000262848.5	37	CCDS14125.1																																																																																			C|0.992;A|0.008	0.008	strong		0.557	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044	
CPNE7	27132	hgsc.bcm.edu	37	16	89662990	89662990	+	Silent	SNP	T	T	C	rs694285	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89662990T>C	ENST00000268720.5	+	17	1993	c.1863T>C	c.(1861-1863)ggT>ggC	p.G621G	CPNE7_ENST00000319518.8_Silent_p.G546G|CPNE7_ENST00000566398.1_3'UTR	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	621					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		GAAGCCTGGGTGTCCCTGCCG	0.667													C|||	2364	0.472045	0.5658	0.3963	5008	,	,		17717	0.8333		0.1948	False		,,,				2504	0.3119				p.G621G		Atlas-SNP	.											CPNE7,caecum,carcinoma,0,1	CPNE7	56	1	0			c.T1863C						PASS	.	C	,	2129,2263	580.9+/-385.2	516,1097,583	45.0	46.0	46.0		1863,1638	-2.7	0.0	16	dbSNP_83	46	1596,7000	734.9+/-406.9	158,1280,2860	no	coding-synonymous,coding-synonymous	CPNE7	NM_014427.4,NM_153636.2	,	674,2377,3443	CC,CT,TT		18.5668,48.4745,28.6803	,	621/634,546/559	89662990	3725,9263	2196	4298	6494	SO:0001819	synonymous_variant	27132	exon17			CCTGGGTGTCCCT	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.1863T>C	16.37:g.89662990T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	29	28	0.965517	NM_014427		Silent	SNP	ENST00000268720.5	37	CCDS10980.1	1015	0.46474358974358976	259	0.5264227642276422	126	0.34806629834254144	474	0.8286713286713286	156	0.20580474934036938	C	5.609	0.297052	0.10622	0.484745	0.185668	ENSG00000178773	ENST00000526232	.	.	.	3.79	-2.66	0.06077	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.23404	-1.0189	3	.	.	.	-21.8946	5.9551	0.19269	0.0:0.2364:0.3748:0.3888	rs694285;rs3751683;rs17853416;rs17855267;rs56830719;rs694285	.	.	.	A	74	.	.	V	+	2	0	CPNE7	88190491	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.151000	0.03175	-0.392000	0.07751	-1.103000	0.02113	GTG	T|0.654;C|0.346	0.346	strong		0.667	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
FLT1	2321	hgsc.bcm.edu	37	13	28964198	28964198	+	Silent	SNP	C	C	T	rs17537350	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:28964198C>T	ENST00000282397.4	-	13	1955	c.1704G>A	c.(1702-1704)acG>acA	p.T568T	FLT1_ENST00000541932.1_Silent_p.T568T	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	568	Ig-like C2-type 6.				blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|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 MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCTCTCCTTCCGTCGGCATTT	0.363													C|||	301	0.0601038	0.003	0.2248	5008	,	,		21422	0.0139		0.0626	False		,,,				2504	0.0654				p.T568T		Atlas-SNP	.											FLT1_ENST00000541932,colon,carcinoma,-1,2	FLT1	393	2	0			c.G1704A						PASS	.	C	,,	65,4341	58.1+/-94.6	2,61,2140	125.0	117.0	120.0		1704,1704,1704	-6.8	0.1	13	dbSNP_123	120	564,8036	153.3+/-207.7	22,520,3758	no	coding-synonymous,coding-synonymous,coding-synonymous	FLT1	NM_001159920.1,NM_001160030.1,NM_002019.4	,,	24,581,5898	TT,TC,CC		6.5581,1.4753,4.8362	,,	568/688,568/734,568/1339	28964198	629,12377	2203	4300	6503	SO:0001819	synonymous_variant	2321	exon13			TCCTTCCGTCGGC	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.1704G>A	13.37:g.28964198C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	52	0.597701	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Silent	SNP	ENST00000282397.4	37	CCDS9330.1																																																																																			C|0.951;T|0.049	0.049	strong		0.363	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
GPR98	84059	hgsc.bcm.edu	37	5	90024735	90024735	+	Missense_Mutation	SNP	G	G	A	rs2366928	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:90024735G>A	ENST00000405460.2	+	49	10507	c.10411G>A	c.(10411-10413)Gaa>Aaa	p.E3471K		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3471			E -> K (in dbSNP:rs2366928). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14740321}.		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		AATATTTGCCGAAAATGTCTT	0.338													A|||	4152	0.829073	0.941	0.8285	5008	,	,		17416	0.8155		0.6978	False		,,,				2504	0.8272				p.E3471K		Atlas-SNP	.											.	GPR98	605	.	0			c.G10411A						PASS	.	A	LYS/GLU	3307,353		1496,315,19	50.0	49.0	49.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	10411	5.6	1.0	5	dbSNP_100	49	5602,2570		1912,1778,396	yes	missense	GPR98	NM_032119.3	56	3408,2093,415	AA,AG,GG		31.4488,9.6448,24.7042	benign	3471/6307	90024735	8909,2923	1830	4086	5916	SO:0001583	missense	84059	exon49			TTTGCCGAAAATG	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.10411G>A	5.37:g.90024735G>A	ENSP00000384582:p.Glu3471Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	1744	0.7985347985347986	469	0.9532520325203252	291	0.8038674033149171	449	0.784965034965035	535	0.7058047493403694	A	2.502	-0.315021	0.05422	0.903552	0.685512	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.25250	1.81	5.6	5.6	0.85130	.	0.373305	0.33496	N	0.004852	T	0.00012	0.0000	N	0.00197	-1.87	0.09310	P	0.9999999999999984	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39643	-0.9604	9	0.02654	T	1	.	11.6426	0.51242	0.9304:0.0:0.0696:0.0	rs2366928;rs17553075;rs52826499;rs59791227;rs2366928	3471;3471	E7ETI5;Q8WXG9	.;GPR98_HUMAN	K	3471	ENSP00000384582:E3471K	ENSP00000296619:E3471K	E	+	1	0	GPR98	90060491	1.000000	0.71417	0.995000	0.50966	0.276000	0.26787	4.384000	0.59607	0.961000	0.38030	-0.254000	0.11334	GAA	G|0.203;A|0.797	0.797	strong		0.338	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
DCAF13	25879	hgsc.bcm.edu	37	8	104432545	104432545	+	Missense_Mutation	SNP	A	A	G	rs3134253	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:104432545A>G	ENST00000297579.5	+	2	857	c.580A>G	c.(580-582)Ata>Gta	p.I194V	DCAF13_ENST00000521999.1_Intron|DCAF13_ENST00000519682.1_Missense_Mutation_p.I38V|DCAF13_ENST00000521716.1_Missense_Mutation_p.I38V|DCAF13_ENST00000521971.1_Missense_Mutation_p.I38V	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	42					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ACGAGAATATATAAGAGCTTT	0.383													G|||	1269	0.253395	0.202	0.268	5008	,	,		19647	0.3313		0.2316	False		,,,				2504	0.2546				p.I194V		Atlas-SNP	.											.	DCAF13	66	.	0			c.A580G						PASS	.	G	VAL/ILE	964,3442	734.4+/-410.6	104,756,1343	98.0	92.0	94.0		580	-0.4	0.3	8	dbSNP_103	94	1830,6770	731.0+/-406.8	191,1448,2661	no	missense	DCAF13	NM_015420.6	29	295,2204,4004	GG,GA,AA		21.2791,21.8793,21.4824	benign	194/598	104432545	2794,10212	2203	4300	6503	SO:0001583	missense	25879	exon2			GAATATATAAGAG	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	24535	protein-coding gene	gene with protein product			"""WD repeats and SOF1 domain containing"""	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.580A>G	8.37:g.104432545A>G	ENSP00000297579:p.Ile194Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_015420	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	577	0.2641941391941392	106	0.21544715447154472	93	0.2569060773480663	196	0.34265734265734266	182	0.24010554089709762	G	7.825	0.718601	0.15372	0.218793	0.212791	ENSG00000164934	ENST00000297579;ENST00000521716;ENST00000521971;ENST00000388778;ENST00000519682	T;T;T;T	0.01252	5.1;5.1;5.1;5.1	5.26	-0.374	0.12512	.	0.522492	0.21591	N	0.072093	T	0.00012	0.0000	N	0.00046	-2.44	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21211	-1.0252	9	0.10902	T	0.67	-5.3123	11.2365	0.48944	0.6324:0.0:0.3676:0.0	rs3134253;rs52822106;rs3134253	42	B3KME9	.	V	194;38;38;42;38	ENSP00000297579:I194V;ENSP00000430645:I38V;ENSP00000430883:I38V;ENSP00000430411:I38V	ENSP00000297579:I194V	I	+	1	0	DCAF13	104501721	0.000000	0.05858	0.294000	0.24946	0.994000	0.84299	0.477000	0.22196	-0.208000	0.10171	-0.119000	0.15052	ATA	A|0.768;G|0.232	0.232	strong		0.383	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420	
TGIF1	7050	hgsc.bcm.edu	37	18	3457539	3457539	+	Silent	SNP	A	A	G	rs2229337	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:3457539A>G	ENST00000330513.5	+	3	1110	c.807A>G	c.(805-807)ccA>ccG	p.P269P	TGIF1_ENST00000405385.3_Silent_p.P120P|TGIF1_ENST00000407501.2_Silent_p.P140P|TGIF1_ENST00000472042.1_Silent_p.P120P|TGIF1_ENST00000548489.2_Silent_p.P154P|TGIF1_ENST00000345133.5_Silent_p.P120P|TGIF1_ENST00000551541.1_Silent_p.P120P|TGIF1_ENST00000343820.5_Silent_p.P140P|TGIF1_ENST00000577543.1_3'UTR|TGIF1_ENST00000400167.2_Silent_p.P120P|TGIF1_ENST00000401449.1_Silent_p.P120P	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	269					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				AGGAGACCCCATTTCATTCCT	0.537													G|||	959	0.191494	0.3116	0.0922	5008	,	,		17980	0.2778		0.0696	False		,,,				2504	0.136				p.P269P		Atlas-SNP	.											.	TGIF1	41	.	0			c.A807G						PASS	.	G	,,,,,,,	1242,3164	705.0+/-407.2	170,902,1131	52.0	50.0	50.0		420,807,462,420,360,360,360,360	-10.8	0.1	18	dbSNP_98	50	648,7952	790.1+/-407.6	23,602,3675	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_173211.1,NM_174886.1	,,,,,,,	193,1504,4806	GG,GA,AA		7.5349,28.1888,14.5318	,,,,,,,	140/273,269/402,154/287,140/273,120/253,120/253,120/253,120/253	3457539	1890,11116	2203	4300	6503	SO:0001819	synonymous_variant	7050	exon3			GACCCCATTTCAT	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.807A>G	18.37:g.3457539A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	37	CCDS11834.1																																																																																			A|0.856;G|0.144	0.144	strong		0.537	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
LMNTD2	256329	hgsc.bcm.edu	37	11	557584	557584	+	Silent	SNP	G	G	A	rs11822657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:557584G>A	ENST00000329451.3	-	6	674	c.612C>T	c.(610-612)gcC>gcT	p.A204A	RP11-496I9.1_ENST00000527113.1_RNA|RP11-496I9.1_ENST00000527620.1_RNA|RASSF7_ENST00000431809.1_5'Flank	NM_173573.2	NP_775844.2	Q8IXW0	LMTD2_HUMAN		204										NS(1)|breast(1)|central_nervous_system(1)|lung(4)|pancreas(1)	8		all_cancers(49;2.16e-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;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCCGGTGGGGGCCTGAATGT	0.642													G|||	272	0.0543131	0.0522	0.0504	5008	,	,		18168	0.0466		0.0606	False		,,,				2504	0.0613				p.A204A		Atlas-SNP	.											.	C11orf35	22	.	0			c.C612T						PASS	.	G		291,4113	158.5+/-191.2	11,269,1922	63.0	61.0	62.0		612	-0.3	0.0	11	dbSNP_120	62	517,8083	145.1+/-200.9	20,477,3803	no	coding-synonymous	C11orf35	NM_173573.2		31,746,5725	AA,AG,GG		6.0116,6.6076,6.2135		204/635	557584	808,12196	2202	4300	6502	SO:0001819	synonymous_variant	256329	exon6			GGTGGGGGCCTGA																												ENST00000329451.3:c.612C>T	11.37:g.557584G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_173573		Silent	SNP	ENST00000329451.3	37	CCDS7701.1																																																																																			G|0.939;A|0.061	0.061	strong		0.642	C11orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254973.2		
TNFRSF4	7293	hgsc.bcm.edu	37	1	1147422	1147422	+	Silent	SNP	C	C	T	rs17568	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1147422C>T	ENST00000379236.3	-	5	538	c.534G>A	c.(532-534)gaG>gaA	p.E178E	TNFRSF4_ENST00000453580.1_5'UTR	NM_003327.3	NP_003318.1	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily, member 4	178					cellular defense response (GO:0006968)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin secretion (GO:0051024)|regulation of apoptotic process (GO:0042981)|regulation of protein kinase activity (GO:0045859)|T cell proliferation (GO:0042098)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			large_intestine(1)|lung(2)|urinary_tract(1)	4	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGCCCTGGGTCTCCTGGGGCT	0.701													c|||	2496	0.498403	0.4297	0.5043	5008	,	,		13575	0.7837		0.2117	False		,,,				2504	0.5879				p.E178E		Atlas-SNP	.											.	TNFRSF4	12	.	0			c.G534A						PASS	.	C		1662,2718		306,1050,834	16.0	20.0	18.0		534	0.3	0.9	1	dbSNP_63	18	1756,6800		195,1366,2717	no	coding-synonymous	TNFRSF4	NM_003327.3		501,2416,3551	TT,TC,CC		20.5236,37.9452,26.4224		178/278	1147422	3418,9518	2190	4278	6468	SO:0001819	synonymous_variant	7293	exon5			CTGGGTCTCCTGG	X75962	CCDS11.1	1p36	2008-02-05			ENSG00000186827	ENSG00000186827		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11918	protein-coding gene	gene with protein product		600315		TXGP1L		7510240, 2828930	Standard	NM_003327		Approved	ACT35, OX40, CD134	uc001ade.3	P43489	OTTHUMG00000001415	ENST00000379236.3:c.534G>A	1.37:g.1147422C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_003327	Q13663|Q2M312|Q5T7M0	Silent	SNP	ENST00000379236.3	37	CCDS11.1	993	0.45467032967032966	231	0.4695121951219512	172	0.47513812154696133	433	0.756993006993007	157	0.20712401055408972	C	5.772	0.326856	0.10900	0.379452	0.205236	ENSG00000186827	ENST00000453580	.	.	.	3.47	0.346	0.16017	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20764	P	0.999857777	.	.	.	.	.	.	T	0.25152	-1.0140	3	.	.	.	-12.4998	2.9742	0.05932	0.1675:0.5134:0.2059:0.1132	rs17568;rs62648068	.	.	.	N	124	.	.	D	-	1	0	TNFRSF4	1137285	0.461000	0.25783	0.890000	0.34922	0.026000	0.11368	0.431000	0.21444	0.250000	0.21479	0.491000	0.48974	GAC	C|0.674;T|0.326	0.326	strong		0.701	TNFRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004086.1		
PRR22	163154	hgsc.bcm.edu	37	19	5783634	5783634	+	Silent	SNP	T	T	C	rs2446210	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5783634T>C	ENST00000419421.2	-	3	728	c.624A>G	c.(622-624)ccA>ccG	p.P208P		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	208	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						TGTAGGCGTCTGGGGGCAGTG	0.706													C|||	2259	0.451078	0.7769	0.2334	5008	,	,		11349	0.5496		0.1928	False		,,,				2504	0.3292				p.P208P		Atlas-SNP	.											.	PRR22	25	.	0			c.A624G						PASS	.	C		2924,1454		1004,916,269	13.0	16.0	15.0		624	-7.8	0.0	19	dbSNP_100	15	1601,6985		129,1343,2821	no	coding-synonymous	PRR22	NM_001134316.1		1133,2259,3090	CC,CT,TT		18.6466,33.2115,34.9044		208/423	5783634	4525,8439	2189	4293	6482	SO:0001819	synonymous_variant	163154	exon3			GGCGTCTGGGGGC	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.624A>G	19.37:g.5783634T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_001134316	E9PB31	Silent	SNP	ENST00000419421.2	37	CCDS45933.1																																																																																			T|0.612;C|0.388	0.388	strong		0.706	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
CD101	9398	hgsc.bcm.edu	37	1	117576522	117576522	+	Missense_Mutation	SNP	A	A	T	rs34223095	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117576522A>T	ENST00000256652.4	+	9	2923	c.2865A>T	c.(2863-2865)ttA>ttT	p.L955F	CD101_ENST00000467588.1_3'UTR|CD101_ENST00000369470.1_Missense_Mutation_p.L955F|RP11-27K13.3_ENST00000445523.1_RNA|RP11-27K13.3_ENST00000421254.1_RNA	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	955			L -> F (in dbSNP:rs34223095).		cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CGGCCCCTTTACTCTATTTCC	0.488													A|||	228	0.0455272	0.0008	0.0663	5008	,	,		19332	0.002		0.0477	False		,,,				2504	0.1339				p.L955F		Atlas-SNP	.											.	CD101	95	.	0			c.A2865T						PASS	.	A	PHE/LEU	50,4356	49.6+/-84.7	0,50,2153	114.0	109.0	110.0		2865	-8.2	0.0	1	dbSNP_126	110	508,8092	145.0+/-200.8	19,470,3811	yes	missense	CD101	NM_004258.3	22	19,520,5964	TT,TA,AA		5.907,1.1348,4.2903	benign	955/1022	117576522	558,12448	2203	4300	6503	SO:0001583	missense	9398	exon9			CCCTTTACTCTAT	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.2865A>T	1.37:g.117576522A>T	ENSP00000256652:p.Leu955Phe	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	66	0.03021978021978022	0	0.0	26	0.0718232044198895	1	0.0017482517482517483	39	0.051451187335092345	A	13.23	2.174648	0.38413	0.011348	0.05907	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.07800	3.16;3.16	5.83	-8.22	0.01037	.	0.215398	0.23342	N	0.049224	T	0.01800	0.0057	L	0.36672	1.1	0.09310	N	1	B	0.32829	0.386	B	0.29353	0.101	T	0.11717	-1.0576	10	0.87932	D	0	-6.8302	12.1392	0.53989	0.2715:0.1188:0.6097:0.0	rs34223095	955	Q93033	IGSF2_HUMAN	F	955	ENSP00000256652:L955F;ENSP00000358482:L955F	ENSP00000256652:L955F	L	+	3	2	CD101	117378045	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.784000	0.01769	-1.695000	0.01423	-0.468000	0.05107	TTA	A|0.960;T|0.040	0.040	strong		0.488	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
ITGAX	3687	hgsc.bcm.edu	37	16	31374535	31374535	+	Missense_Mutation	SNP	C	C	G	rs2230429	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31374535C>G	ENST00000268296.4	+	14	1671	c.1550C>G	c.(1549-1551)cCc>cGc	p.P517R	ITGAX_ENST00000562522.1_Missense_Mutation_p.P517R	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	517			P -> R (in dbSNP:rs2230429).		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CAGGGCCACCCCTGGGGTCGC	0.637													C|||	1496	0.298722	0.1014	0.3184	5008	,	,		13794	0.6766		0.339	False		,,,				2504	0.1207				p.P517R		Atlas-SNP	.											.	ITGAX	198	.	0			c.C1550G						PASS	.	C	ARG/PRO	685,3709	284.3+/-277.5	55,575,1567	100.0	109.0	106.0		1550	4.0	1.0	16	dbSNP_98	106	3143,5457	472.8+/-368.4	592,1959,1749	yes	missense	ITGAX	NM_000887.3	103	647,2534,3316	GG,GC,CC		36.5465,15.5894,29.4598	possibly-damaging	517/1164	31374535	3828,9166	2197	4300	6497	SO:0001583	missense	3687	exon14			GCCACCCCTGGGG	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1550C>G	16.37:g.31374535C>G	ENSP00000268296:p.Pro517Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_000887	Q8IVA6	Missense_Mutation	SNP	ENST00000268296.4	37	CCDS10711.1	886	0.4056776556776557	64	0.13008130081300814	130	0.35911602209944754	426	0.7447552447552448	266	0.35092348284960423	C	14.93	2.681501	0.47991	0.155894	0.365465	ENSG00000140678	ENST00000268296	T	0.34667	1.35	4.03	4.03	0.46877	.	.	.	.	.	T	0.00012	0.0000	L	0.60904	1.88	0.37094	P	0.10040199999999999	D	0.67145	0.996	P	0.53490	0.727	T	0.19095	-1.0316	8	0.87932	D	0	.	13.447	0.61146	0.0:1.0:0.0:0.0	rs2230429;rs3087447;rs59868842	517	P20702	ITAX_HUMAN	R	517	ENSP00000268296:P517R	ENSP00000268296:P517R	P	+	2	0	ITGAX	31282036	0.951000	0.32395	1.000000	0.80357	0.965000	0.64279	0.907000	0.28531	1.952000	0.56665	0.460000	0.39030	CCC	C|0.671;G|0.329	0.329	strong		0.637	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
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 GAIIx	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	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	28	17	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	
BMS1	9790	hgsc.bcm.edu	37	10	43316099	43316099	+	Silent	SNP	T	T	C	rs61736599	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:43316099T>C	ENST00000374518.5	+	17	2976	c.2913T>C	c.(2911-2913)taT>taC	p.Y971Y		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	971					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TTCTAAAGTATACCCCACAGC	0.428													T|||	299	0.0597045	0.0961	0.0591	5008	,	,		18769	0.002		0.1044	False		,,,				2504	0.0245				p.Y971Y		Atlas-SNP	.											.	BMS1	132	.	0			c.T2913C						PASS	.	T		496,3900		35,426,1737	47.0	51.0	49.0		2913	-1.5	1.0	10	dbSNP_129	49	772,7818		31,710,3554	no	coding-synonymous	BMS1	NM_014753.3		66,1136,5291	CC,CT,TT		8.9872,11.283,9.7644		971/1283	43316099	1268,11718	2198	4295	6493	SO:0001819	synonymous_variant	9790	exon17			AAAGTATACCCCA	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.2913T>C	10.37:g.43316099T>C		Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	322	171	0.531056	NM_014753	Q5QPT5|Q86XJ9	Silent	SNP	ENST00000374518.5	37	CCDS7199.1																																																																																			T|0.913;C|0.087	0.087	strong		0.428	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
CYP2C8	1558	hgsc.bcm.edu	37	10	96798749	96798749	+	Missense_Mutation	SNP	T	T	C	rs10509681	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96798749T>C	ENST00000371270.3	-	8	1290	c.1196A>G	c.(1195-1197)aAa>aGa	p.K399R	CYP2C8_ENST00000535898.1_Missense_Mutation_p.K297R	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	399			K -> R (in allele CYP2C8*3; dbSNP:rs10509681). {ECO:0000269|PubMed:11668219, ECO:0000269|PubMed:12429347, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:2216732, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	AGGAAATTCTTTGTCATCATG	0.383													T|||	229	0.0457268	0.0083	0.0994	5008	,	,		22146	0.001		0.1183	False		,,,				2504	0.0297				p.K399R		Atlas-SNP	.											.	CYP2C8	73	.	0			c.A1196G	GRCh37	CM014701	CYP2C8	M	rs10509681	PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	108,4298	83.9+/-122.4	2,104,2097	133.0	124.0	127.0		1196,986,890,986	-1.4	0.0	10	dbSNP_119	127	1003,7597	215.5+/-254.8	67,869,3364	yes	missense,missense,missense,missense	CYP2C8	NM_000770.3,NM_001198853.1,NM_001198854.1,NM_001198855.1	26,26,26,26	69,973,5461	CC,CT,TT		11.6628,2.4512,8.5422	benign,benign,benign,benign	399/491,329/421,297/389,329/421	96798749	1111,11895	2203	4300	6503	SO:0001583	missense	1558	exon8			AATTCTTTGTCAT	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"""Cytochrome P450s"""	2622	protein-coding gene	gene with protein product		601129	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"""			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.1196A>G	10.37:g.96798749T>C	ENSP00000360317:p.Lys399Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	141	0.06456043956043957	6	0.012195121951219513	46	0.1270718232044199	2	0.0034965034965034965	87	0.11477572559366754	T	10.51	1.369107	0.24771	0.024512	0.116628	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898	T;T	0.70516	-0.49;-0.49	3.96	-1.44	0.08856	.	0.504809	0.19644	U	0.109394	T	0.01061	0.0035	M	0.62016	1.91	0.80722	P	0.0	B;B;B	0.17268	0.02;0.021;0.021	B;B;B	0.27380	0.079;0.063;0.078	T	0.15752	-1.0426	9	0.46703	T	0.11	.	4.629	0.12491	0.0:0.2844:0.1588:0.5567	rs10509681;rs17522568;rs56435423;rs61450273;rs10509681	297;367;399	B7Z1F6;B7Z8S1;P10632	.;.;CP2C8_HUMAN	R	399;366;297	ENSP00000360317:K399R;ENSP00000445062:K297R	ENSP00000360317:K399R	K	-	2	0	CYP2C8	96788739	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-0.030000	0.12308	-0.368000	0.08040	0.402000	0.26972	AAA	T|0.946;C|0.054	0.054	strong		0.383	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
OR6B1	135946	hgsc.bcm.edu	37	7	143701516	143701516	+	Missense_Mutation	SNP	C	C	T	rs7787378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143701516C>T	ENST00000408922.2	+	1	495	c.427C>T	c.(427-429)Cgc>Tgc	p.R143C		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	143			R -> C (in dbSNP:rs7787378).			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(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					GCTCTGCTTCCGCCTCGCTCT	0.562													C|||	813	0.16234	0.0764	0.3674	5008	,	,		21958	0.2411		0.0885	False		,,,				2504	0.1278				p.R143C		Atlas-SNP	.											OR6B1,NS,carcinoma,-1,3	OR6B1	60	3	0			c.C427T						PASS	.	C	CYS/ARG	303,3985		11,281,1852	80.0	83.0	82.0		427	5.3	0.5	7	dbSNP_116	82	796,7768		49,698,3535	yes	missense	OR6B1	NM_001005281.1	180	60,979,5387	TT,TC,CC		9.2947,7.0662,8.5512	benign	143/312	143701516	1099,11753	2144	4282	6426	SO:0001583	missense	135946	exon1			TGCTTCCGCCTCG		CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"""GPCR / Class A : Olfactory receptors"""	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.427C>T	7.37:g.143701516C>T	ENSP00000386151:p.Arg143Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_001005281	A4D2G2|B9EH47|Q6IFP6|Q96R38	Missense_Mutation	SNP	ENST00000408922.2	37	CCDS43667.1	358	0.16391941391941392	38	0.07723577235772358	111	0.30662983425414364	141	0.2465034965034965	68	0.08970976253298153	C	8.409	0.843804	0.16963	0.070662	0.092947	ENSG00000221813	ENST00000408922	T	0.00123	8.7	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.415982	0.17515	U	0.171466	T	0.00012	0.0000	L	0.28458	0.855	0.41184	P	0.013746000000000036	B	0.09022	0.002	B	0.18561	0.022	T	0.50955	-0.8766	9	0.34782	T	0.22	.	14.2547	0.66043	0.0:1.0:0.0:0.0	rs7787378;rs52795515;rs7787378	143	O95007	OR6B1_HUMAN	C	143	ENSP00000386151:R143C	ENSP00000386151:R143C	R	+	1	0	OR6B1	143332449	0.022000	0.18835	0.511000	0.27724	0.142000	0.21351	1.965000	0.40471	2.739000	0.93911	0.655000	0.94253	CGC	C|0.853;N|0.000	.	strong		0.562	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1		
ZNF99	7652	hgsc.bcm.edu	37	19	22940899	22940899	+	Silent	SNP	G	G	A	rs59017672	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:22940899G>A	ENST00000596209.1	-	4	1902	c.1812C>T	c.(1810-1812)caC>caT	p.H604H	ZNF99_ENST00000397104.3_Silent_p.H513H	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	604					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				GGGCTGAGAAGTGGTTAAAAG	0.383													g|||	1838	0.367013	0.5378	0.3256	5008	,	,		19631	0.3452		0.2783	False		,,,				2504	0.2791				p.H604H		Atlas-SNP	.											.	ZNF99	273	.	0			c.C1812T						PASS	.	A		1886,2154		462,962,596	41.0	47.0	45.0		1539	-2.3	0.0	19	dbSNP_129	45	2325,6129		325,1675,2227	no	coding-synonymous	ZNF99	NM_001080409.2		787,2637,2823	AA,AG,GG		27.5018,46.6832,33.7042		513/912	22940899	4211,8283	2020	4227	6247	SO:0001819	synonymous_variant	7652	exon4			TGAGAAGTGGTTA	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1812C>T	19.37:g.22940899G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_001080409	M0R335	Silent	SNP	ENST00000596209.1	37	CCDS59369.1																																																																																			A|0.316;G|0.683;T|0.001	0.316	strong		0.383	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
FYCO1	79443	hgsc.bcm.edu	37	3	46008087	46008087	+	Silent	SNP	G	G	A	rs13079869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46008087G>A	ENST00000296137.2	-	8	2944	c.2739C>T	c.(2737-2739)tgC>tgT	p.C913C	FYCO1_ENST00000535325.1_Silent_p.C913C	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	913					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)		CGGTCAGTGCGCAAACCTGGA	0.632													G|||	529	0.105631	0.0076	0.0605	5008	,	,		20768	0.004		0.1223	False		,,,				2504	0.3579				p.C913C		Atlas-SNP	.											.	FYCO1	115	.	0			c.C2739T						PASS	.	G		109,4297	83.9+/-122.4	0,109,2094	50.0	47.0	48.0		2739	-5.3	0.0	3	dbSNP_121	48	947,7653	205.8+/-248.1	48,851,3401	no	coding-synonymous	FYCO1	NM_024513.2		48,960,5495	AA,AG,GG		11.0116,2.4739,8.1193		913/1479	46008087	1056,11950	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			CAGTGCGCAAACC	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.2739C>T	3.37:g.46008087G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	166	88	0.53012	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			G|0.920;A|0.080	0.080	strong		0.632	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
CD200R1	131450	hgsc.bcm.edu	37	3	112643952	112643952	+	Silent	SNP	C	C	T	rs72491121	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112643952C>T	ENST00000471858.1	-	5	1021	c.789G>A	c.(787-789)ttG>ttA	p.L263L	CD200R1_ENST00000295863.4_Intron|CD200R1_ENST00000308611.3_Silent_p.L286L	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	263					regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGACTTTCAACAACCAAATGA	0.333													T|||	417	0.0832668	0.0189	0.0159	5008	,	,		19595	0.2272		0.0328	False		,,,				2504	0.1217				p.L286L		Atlas-SNP	.											.	CD200R1	91	.	0			c.G858A						PASS	.	T	,	85,4321	810.1+/-416.0	0,85,2118	66.0	69.0	68.0		858,789	-1.4	0.0	3	dbSNP_130	68	326,8274	801.0+/-407.4	6,314,3980	no	coding-synonymous,coding-synonymous	CD200R1	NM_138806.3,NM_170780.2	,	6,399,6098	TT,TC,CC		3.7907,1.9292,3.1601	,	286/349,263/326	112643952	411,12595	2203	4300	6503	SO:0001819	synonymous_variant	131450	exon6			TTTCAACAACCAA	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.789G>A	3.37:g.112643952C>T		Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	191	89	0.465969	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Silent	SNP	ENST00000471858.1	37	CCDS2970.1																																																																																			C|0.954;T|0.046	0.046	strong		0.333	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
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 GAIIx	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		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	48	30	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	
MRPL23	6150	hgsc.bcm.edu	37	11	1977552	1977552	+	Missense_Mutation	SNP	G	G	A	rs12812	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1977552G>A	ENST00000397298.3	+	5	449	c.364G>A	c.(364-366)Gct>Act	p.A122T	MRPL23_ENST00000381519.1_Missense_Mutation_p.A122T|MRPL23_ENST00000397297.3_Intron|MRPL23_ENST00000381514.3_Intron|MRPL23_ENST00000397294.3_Intron	NM_021134.3	NP_066957.3	Q16540	RM23_HUMAN	mitochondrial ribosomal protein L23	122			A -> T (in dbSNP:rs12812). {ECO:0000269|PubMed:11543634}.		translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(1)|ovary(1)	4		all_epithelial(84;6.24e-05)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.0026)|Lung(200;0.0171)|LUSC - Lung squamous cell carcinoma(625;0.0842)		TGAAGGCAGCGCTGCCGACGA	0.647													G|||	715	0.142772	0.0121	0.2032	5008	,	,		12924	0.1389		0.169	False		,,,				2504	0.2536				p.A122T		Atlas-SNP	.											MRPL23,NS,carcinoma,0,1	MRPL23	14	1	0			c.G364A						PASS	.	G	THR/ALA	203,4199	126.1+/-163.2	4,195,2002	83.0	83.0	83.0		364	-6.5	0.0	11	dbSNP_52	83	1296,7302	255.4+/-280.3	91,1114,3094	yes	missense	MRPL23	NM_021134.3	58	95,1309,5096	AA,AG,GG		15.0733,4.6115,11.5308	benign	122/154	1977552	1499,11501	2201	4299	6500	SO:0001583	missense	6150	exon5			GGCAGCGCTGCCG	AB051340	CCDS31336.1	11p15.5	2012-09-13			ENSG00000214026	ENSG00000214026		"""Mitochondrial ribosomal proteins / large subunits"""	10322	protein-coding gene	gene with protein product		600789		RPL23L		8541832	Standard	NM_021134		Approved	L23MRP	uc001lux.3	Q16540	OTTHUMG00000012476	ENST00000397298.3:c.364G>A	11.37:g.1977552G>A	ENSP00000380466:p.Ala122Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_021134	A8MT29|Q96Q71	Missense_Mutation	SNP	ENST00000397298.3	37	CCDS31336.1	318	0.14560439560439561	13	0.026422764227642278	68	0.1878453038674033	88	0.15384615384615385	149	0.19656992084432717	G	5.460	0.269875	0.10349	0.046115	0.150733	ENSG00000214026	ENST00000397298;ENST00000381519	T;T	0.14266	2.52;2.52	3.24	-6.48	0.01896	.	.	.	.	.	T	0.00012	0.0000	N	0.11560	0.145	0.50813	P	1.0900000000002574E-4	B	0.06786	0.001	B	0.01281	0.0	T	0.31943	-0.9925	8	0.15499	T	0.54	.	3.0296	0.06102	0.2037:0.1638:0.4707:0.1619	rs12812;rs217212;rs3168309;rs12812	122	Q16540	RM23_HUMAN	T	122	ENSP00000380466:A122T;ENSP00000370930:A122T	ENSP00000370930:A122T	A	+	1	0	MRPL23	1934128	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.103000	0.03329	-3.533000	0.00145	-2.560000	0.00174	GCT	G|0.874;A|0.126	0.126	strong		0.647	MRPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034765.2	NM_021134	
VSIG10	54621	hgsc.bcm.edu	37	12	118506186	118506186	+	Silent	SNP	A	A	T	rs67405503	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:118506186A>T	ENST00000359236.5	-	8	1839	c.1563T>A	c.(1561-1563)ctT>ctA	p.L521L		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	521						integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GCTTACCTTGAAGATCCTGGA	0.448													T|||	2110	0.421326	0.4516	0.4582	5008	,	,		18101	0.372		0.4036	False		,,,				2504	0.4233				p.L521L		Atlas-SNP	.											.	VSIG10	41	.	0			c.T1563A						PASS	.	T		1649,2181		344,961,610	187.0	183.0	184.0		1563	-8.2	0.3	12	dbSNP_130	184	3170,5072		618,1934,1569	no	coding-synonymous	VSIG10	NM_019086.5		962,2895,2179	TT,TA,AA		38.4615,43.0548,39.9188		521/541	118506186	4819,7253	1915	4121	6036	SO:0001819	synonymous_variant	54621	exon8			ACCTTGAAGATCC		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.1563T>A	12.37:g.118506186A>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	190	97	0.510526	NM_019086	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																			A|0.602;T|0.398	0.398	strong		0.448	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
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 GAIIx	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_ENST00000357258.3_Silent_p.T617T|ZBTB20_ENST00000471418.1_Silent_p.T617T|ZBTB20_ENST00000462705.1_Silent_p.T617T|ZBTB20_ENST00000481632.1_Silent_p.T617T|ZBTB20_ENST00000393785.2_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		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	104	45	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	
TNRC18	84629	hgsc.bcm.edu	37	7	5353253	5353253	+	Silent	SNP	G	G	T	rs140781391	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:5353253G>T	ENST00000430969.1	-	27	7617	c.7269C>A	c.(7267-7269)gcC>gcA	p.A2423A	TNRC18_ENST00000399537.4_Silent_p.A2423A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2423	Pro-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGGGTGCTGGGGCCAGGGAGG	0.731													G|||	449	0.0896565	0.062	0.1758	5008	,	,		12013	0.0605		0.1034	False		,,,				2504	0.0818				p.A2423A		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7269A						PASS	.	G		203,2919		10,183,1368	11.0	12.0	11.0		7269	2.4	0.3	7	dbSNP_134	11	767,6389		35,697,2846	no	coding-synonymous	TNRC18	NM_001080495.2		45,880,4214	TT,TG,GG		10.7183,6.5022,9.4376		2423/2969	5353253	970,9308	1561	3578	5139	SO:0001819	synonymous_variant	84629	exon27			TGCTGGGGCCAGG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7269C>A	7.37:g.5353253G>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	53	0.638554	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1	203	0.09294871794871795	34	0.06910569105691057	51	0.1408839779005525	33	0.057692307692307696	85	0.11213720316622691	g	0.025	-1.377010	0.01214	0.065022	0.107183	ENSG00000182095	ENST00000328270	.	.	.	3.33	2.43	0.29744	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.46185	P	0.0010879999999999779	.	.	.	.	.	.	T	0.09357	-1.0678	3	.	.	.	.	5.1903	0.15207	0.1266:0.2132:0.6602:0.0	.	.	.	.	T	237	.	.	P	-	1	0	TNRC18	5319779	0.770000	0.28543	0.332000	0.25469	0.057000	0.15508	0.143000	0.16115	0.682000	0.31407	0.313000	0.20887	CCC	G|0.907;T|0.093	0.093	strong		0.731	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
CARD8	22900	hgsc.bcm.edu	37	19	48722180	48722180	+	Silent	SNP	C	C	T	rs10500299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48722180C>T	ENST00000359009.4	-	8	1245	c.933G>A	c.(931-933)gaG>gaA	p.E311E	CARD8_ENST00000391898.3_Silent_p.E417E|CARD8_ENST00000520753.1_Intron|CARD8_ENST00000447740.2_Silent_p.E367E|CARD8_ENST00000520153.1_Silent_p.E367E|CARD8_ENST00000520015.1_Intron|CARD8_ENST00000357778.5_Silent_p.E142E|CARD8_ENST00000521613.1_Silent_p.E367E|CARD8_ENST00000519940.1_Silent_p.E417E|ZNF114_ENST00000597695.1_Intron			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	311					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		TTTCAGTAATCTCAAGTTGAA	0.463													T|||	1300	0.259585	0.2042	0.3487	5008	,	,		17821	0.1766		0.2465	False		,,,				2504	0.3701				p.E417E		Atlas-SNP	.											.	CARD8	53	.	0			c.G1251A						PASS	.	T	,,,,	920,3486	739.1+/-411.0	92,736,1375	157.0	149.0	151.0		1251,1101,,,1101	1.2	0.0	19	dbSNP_119	151	2429,6171	699.2+/-405.1	379,1671,2250	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	,,,,	471,2407,3625	TT,TC,CC		28.2442,20.8806,25.7497	,,,,	417/538,367/488,,,367/488	48722180	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	22900	exon9			AGTAATCTCAAGT	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.933G>A	19.37:g.48722180C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Silent	SNP	ENST00000359009.4	37																																																																																				C|0.758;T|0.242	0.242	strong		0.463	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150214	11150214	+	Silent	SNP	G	G	A	rs11054142	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11150214G>A	ENST00000538986.1	-	1	260	c.261C>T	c.(259-261)gcC>gcT	p.A87A	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	87					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TTACTGCCCAGGCATTAGAAA	0.343													G|||	2118	0.422923	0.0651	0.3847	5008	,	,		19034	0.755		0.3817	False		,,,				2504	0.6339				p.A87A		Atlas-SNP	.											.	TAS2R20	17	.	0			c.C261T						PASS	.	G		431,3969		22,387,1791	57.0	63.0	61.0		261	-0.3	0.0	12	dbSNP_120	61	2982,5612		533,1916,1848	no	coding-synonymous	TAS2R20	NM_176889.2		555,2303,3639	AA,AG,GG		34.6986,9.7955,26.266		87/310	11150214	3413,9581	2200	4297	6497	SO:0001819	synonymous_variant	259295	exon1			TGCCCAGGCATTA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.261C>T	12.37:g.11150214G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Silent	SNP	ENST00000538986.1	37	CCDS8639.1																																																																																			G|0.672;A|0.328	0.328	strong		0.343	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
FLNC	2318	hgsc.bcm.edu	37	7	128477472	128477472	+	Silent	SNP	T	T	C	rs2291560	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128477472T>C	ENST00000325888.8	+	4	981	c.720T>C	c.(718-720)atT>atC	p.I240I	FLNC_ENST00000346177.6_Silent_p.I240I	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	240	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CTGAGGAGATTGTGGACCCCA	0.577													C|||	610	0.121805	0.1248	0.062	5008	,	,		15037	0.121		0.1093	False		,,,				2504	0.1738				p.I240I		Atlas-SNP	.											.	FLNC	339	.	0			c.T720C						PASS	.	C	,	553,3797	223.3+/-239.8	39,475,1661	149.0	157.0	155.0		720,720	-9.7	0.6	7	dbSNP_100	155	952,7628	202.8+/-246.0	49,854,3387	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	88,1329,5048	CC,CT,TT		11.0956,12.7126,11.6396	,	240/2693,240/2726	128477472	1505,11425	2175	4290	6465	SO:0001819	synonymous_variant	2318	exon4			GGAGATTGTGGAC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.720T>C	7.37:g.128477472T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	15	0.306122	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			T|0.879;C|0.121	0.121	strong		0.577	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
UBASH3A	53347	hgsc.bcm.edu	37	21	43824106	43824106	+	Missense_Mutation	SNP	A	A	G	rs2277798	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43824106A>G	ENST00000319294.6	+	1	83	c.52A>G	c.(52-54)Agc>Ggc	p.S18G	UBASH3A_ENST00000450356.1_Missense_Mutation_p.S18G|UBASH3A_ENST00000291535.6_Missense_Mutation_p.S18G|UBASH3A_ENST00000398367.1_Missense_Mutation_p.S18G	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	18	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.		S -> G (in dbSNP:rs2277798). {ECO:0000269|PubMed:15489334}.		negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						CAAGCTCAAGAGCCGCAGCAG	0.647													G|||	2731	0.545327	0.5666	0.4899	5008	,	,		14655	0.4643		0.6262	False		,,,				2504	0.5562				p.S18G		Atlas-SNP	.											.	UBASH3A	72	.	0			c.A52G						PASS	.	G	GLY/SER,GLY/SER	2467,1817		742,983,417	21.0	19.0	20.0		52,52	3.4	1.0	21	dbSNP_100	20	5382,2884		1823,1736,574	yes	missense,missense	UBASH3A	NM_001001895.2,NM_018961.3	56,56	2565,2719,991	GG,GA,AA		34.8899,42.4136,37.4582	benign,benign	18/624,18/662	43824106	7849,4701	2142	4133	6275	SO:0001583	missense	53347	exon1			CTCAAGAGCCGCA	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.52A>G	21.37:g.43824106A>G	ENSP00000317327:p.Ser18Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Missense_Mutation	SNP	ENST00000319294.6	37	CCDS13687.1	1198	0.5485347985347986	275	0.5589430894308943	190	0.5248618784530387	258	0.45104895104895104	475	0.6266490765171504	G	9.126	1.010149	0.19277	0.575864	0.651101	ENSG00000160185	ENST00000291535;ENST00000450356;ENST00000319294;ENST00000398367	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	5.22	3.39	0.38822	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);	0.719731	0.13078	N	0.415485	T	0.00012	0.0000	N	0.00538	-1.39	0.53688	P	2.199999999996649E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.33599	-0.9862	9	0.11485	T	0.65	-17.7595	8.3647	0.32380	0.3659:0.0:0.6341:0.0	rs2277798;rs17856790;rs56722954;rs2277798	18;18;18	G5E9E4;P57075-2;P57075	.;.;UBS3A_HUMAN	G	18	ENSP00000291535:S18G;ENSP00000407179:S18G;ENSP00000317327:S18G;ENSP00000381408:S18G	ENSP00000291535:S18G	S	+	1	0	UBASH3A	42697175	0.985000	0.35326	0.990000	0.47175	0.859000	0.49053	0.556000	0.23438	0.588000	0.29660	-0.677000	0.03784	AGC	A|0.427;G|0.573	0.573	strong		0.647	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
RNF213	57674	hgsc.bcm.edu	37	17	78355494	78355494	+	Missense_Mutation	SNP	C	C	G	rs61745599	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78355494C>G	ENST00000582970.1	+	57	14088	c.13945C>G	c.(13945-13947)Ctt>Gtt	p.L4649V	CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.L2722V|RNF213_ENST00000508628.2_Missense_Mutation_p.L4698V|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4649					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CCTGCGCAGGCTTCTCCAAGA	0.622													C|||	152	0.0303514	0.0061	0.0461	5008	,	,		19280	0.0		0.0895	False		,,,				2504	0.0225				p.L4649V		Atlas-SNP	.											.	RNF213	766	.	0			c.C13945G						PASS	.	C	VAL/LEU	102,4304	80.9+/-119.3	3,96,2104	55.0	45.0	48.0		14092	4.2	0.2	17	dbSNP_129	48	864,7736	195.6+/-240.8	54,756,3490	yes	missense	RNF213	NM_020914.4	32	57,852,5594	GG,GC,CC		10.0465,2.315,7.4273	probably-damaging	4698/5257	78355494	966,12040	2203	4300	6503	SO:0001583	missense	57674	exon57			CGCAGGCTTCTCC	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.13945C>G	17.37:g.78355494C>G	ENSP00000464087:p.Leu4649Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	35	22	0.628571	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	99	0.04532967032967033	4	0.008130081300813009	23	0.06353591160220995	0	0.0	72	0.09498680738786279	C	17.82	3.483798	0.63962	0.02315	0.100465	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.53206	0.63	5.2	4.23	0.50019	.	0.077056	0.53938	D	0.000057	T	0.03263	0.0095	M	0.61703	1.905	0.31465	N	0.6691	D;D	0.76494	0.999;0.983	D;P	0.69654	0.965;0.656	T	0.17107	-1.0380	10	0.44086	T	0.13	.	10.16	0.42847	0.0:0.9074:0.0:0.0926	rs61745599	4698;2722	C9JCP4;Q63HN8	.;RN213_HUMAN	V	4649;4698;2722	ENSP00000338218:L2722V	ENSP00000338218:L2722V	L	+	1	0	RNF213	75970089	0.999000	0.42202	0.243000	0.24186	0.009000	0.06853	1.768000	0.38511	2.419000	0.82065	0.655000	0.94253	CTT	C|0.938;G|0.062	0.062	strong		0.622	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
SSR3	6747	hgsc.bcm.edu	37	3	156266774	156266774	+	Silent	SNP	C	C	T	rs9296	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:156266774C>T	ENST00000265044.2	-	3	373	c.279G>A	c.(277-279)gaG>gaA	p.E93E	SSR3_ENST00000467789.1_Silent_p.E93E|SSR3_ENST00000496050.1_Silent_p.E41E|SSR3_ENST00000476217.1_Silent_p.E93E|SSR3_ENST00000478842.1_5'UTR|SSR3_ENST00000463503.1_Silent_p.E41E	NM_007107.3	NP_009038.1	Q9UNL2	SSRG_HUMAN	signal sequence receptor, gamma (translocon-associated protein gamma)	93					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	integral component of endoplasmic reticulum membrane (GO:0030176)|Sec61 translocon complex (GO:0005784)				endometrium(1)|prostate(2)	3			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			AAACAGCATCCTCCCTCTTCT	0.393													C|||	878	0.175319	0.1543	0.1542	5008	,	,		18154	0.2312		0.1481	False		,,,				2504	0.1892				p.E93E		Atlas-SNP	.											.	SSR3	17	.	0			c.G279A						PASS	.	C		601,3805	260.4+/-263.7	40,521,1642	95.0	93.0	93.0		279	3.6	1.0	3	dbSNP_52	93	1068,7532	223.3+/-260.1	68,932,3300	no	coding-synonymous	SSR3	NM_007107.3		108,1453,4942	TT,TC,CC		12.4186,13.6405,12.8325		93/186	156266774	1669,11337	2203	4300	6503	SO:0001819	synonymous_variant	6747	exon3			AGCATCCTCCCTC	BC017203	CCDS3176.1	3q25.31	2004-02-27			ENSG00000114850	ENSG00000114850			11325	protein-coding gene	gene with protein product		606213					Standard	NM_007107		Approved	TRAPG	uc003fau.3	Q9UNL2	OTTHUMG00000158632	ENST00000265044.2:c.279G>A	3.37:g.156266774C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_007107	B2R7D0|B4E2P2|D3DNK5|Q549M4	Silent	SNP	ENST00000265044.2	37	CCDS3176.1																																																																																			C|0.865;T|0.135	0.135	strong		0.393	SSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351521.1	NM_007107	
OR2T34	127068	hgsc.bcm.edu	37	1	248737511	248737511	+	Missense_Mutation	SNP	A	A	G	rs150608839	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248737511A>G	ENST00000328782.2	-	1	569	c.548T>C	c.(547-549)tTc>tCc	p.F183S		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F183S(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	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)			AGTCTCACAGAAAAAACTCAG	0.517													a|||	776	0.154952	0.2935	0.111	5008	,	,		20908	0.0942		0.1034	False		,,,				2504	0.1145				p.F183S		Atlas-SNP	.											OR2T34,NS,haematopoietic_neoplasm,0,2	OR2T34	72	2	1	Substitution - Missense(1)	stomach(1)	c.T548C						scavenged	.	A	SER/PHE	894,3422		141,612,1405	67.0	84.0	78.0		548	-0.6	0.2	1	dbSNP_134	78	279,8315		1,277,4019	no	missense	OR2T34	NM_001001821.1	155	142,889,5424	GG,GA,AA		3.2465,20.7136,9.086	probably-damaging	183/319	248737511	1173,11737	2158	4297	6455	SO:0001583	missense	127068	exon1			TCACAGAAAAAAC	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.548T>C	1.37:g.248737511A>G	ENSP00000330904:p.Phe183Ser	Somatic	319	1	0.0031348		WXS	Illumina HiSeq	Phase_I	361	93	0.257618	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	316	0.1446886446886447	135	0.27439024390243905	47	0.1298342541436464	51	0.08916083916083917	83	0.10949868073878628	.	12.99	2.104183	0.37145	0.207136	0.032465	ENSG00000183310	ENST00000328782	T	0.00258	8.41	2.37	-0.608	0.11611	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.88570	2.965	0.48288	P	3.769999999999607E-4	D	0.76494	0.999	D	0.79784	0.993	T	0.50110	-0.8866	8	0.87932	D	0	.	3.4931	0.07645	0.6779:0.0:0.1275:0.1946	.	183	Q8NGX1	O2T34_HUMAN	S	183	ENSP00000330904:F183S	ENSP00000330904:F183S	F	-	2	0	OR2T34	246804134	1.000000	0.71417	0.152000	0.22495	0.007000	0.05969	1.350000	0.34010	0.088000	0.17205	0.104000	0.15600	TTC	.	.	weak		0.517	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
LRP1B	53353	hgsc.bcm.edu	37	2	141259283	141259283	+	Silent	SNP	G	G	A	rs35296183	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:141259283G>A	ENST00000389484.3	-	55	9794	c.8823C>T	c.(8821-8823)gaC>gaT	p.D2941D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2941	EGF-like 11. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		GGTCTTGACAGTCTTGAGAAC	0.378										TSP Lung(27;0.18)			G|||	523	0.104433	0.0401	0.1066	5008	,	,		16546	0.0188		0.1988	False		,,,				2504	0.181				p.D2941D	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C8823T						PASS	.	G		283,4123	158.5+/-191.2	7,269,1927	115.0	118.0	117.0		8823	1.2	1.0	2	dbSNP_126	117	1947,6653	343.9+/-325.1	215,1517,2568	no	coding-synonymous	LRP1B	NM_018557.2		222,1786,4495	AA,AG,GG		22.6395,6.4231,17.1459		2941/4600	141259283	2230,10776	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon55			TTGACAGTCTTGA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8823C>T	2.37:g.141259283G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	27	22	0.814815	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.847;A|0.153	0.153	strong		0.378	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
SCN9A	6335	hgsc.bcm.edu	37	2	167145142	167145142	+	Silent	SNP	A	A	G	rs13414203	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:167145142A>G	ENST00000409435.1	-	9	1118	c.1119T>C	c.(1117-1119)gcT>gcC	p.A373A	SCN9A_ENST00000375387.4_Silent_p.A374A|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.A374A|SCN9A_ENST00000409672.1_Silent_p.A373A			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	373					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTTGCCAGCAGCACGCAGCG	0.378													A|||	1775	0.354433	0.357	0.3242	5008	,	,		15731	0.3065		0.4036	False		,,,				2504	0.3712				p.A373A		Atlas-SNP	.											.	SCN9A	296	.	0			c.T1119C						PASS	.	A		1388,2274		279,830,722	62.0	58.0	59.0		1119	4.7	1.0	2	dbSNP_121	59	3180,5018		598,1984,1517	no	coding-synonymous	SCN9A	NM_002977.3		877,2814,2239	GG,GA,AA		38.7899,37.9028,38.516		373/1978	167145142	4568,7292	1831	4099	5930	SO:0001819	synonymous_variant	6335	exon10			GCCAGCAGCACGC	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1119T>C	2.37:g.167145142A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	13	11	0.846154	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			A|0.652;G|0.348	0.348	strong		0.378	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
DUSP10	11221	hgsc.bcm.edu	37	1	221912808	221912808	+	Silent	SNP	T	T	C	rs1136448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:221912808T>C	ENST00000366899.3	-	2	517	c.279A>G	c.(277-279)caA>caG	p.Q93Q	DUSP10_ENST00000323825.3_Intron|DUSP10_ENST00000544095.1_5'Flank|DUSP10_ENST00000468085.1_5'Flank	NM_007207.4	NP_009138.1	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10	93					inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|oligodendrocyte differentiation (GO:0048709)|protein dephosphorylation (GO:0006470)|regulation of adaptive immune response (GO:0002819)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	MAP kinase phosphatase activity (GO:0033549)|MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(131;0.0103)		TGGCTTGGGTTTGGGCCTGAT	0.567													T|||	1719	0.343251	0.0961	0.4179	5008	,	,		20999	0.4484		0.3777	False		,,,				2504	0.4806				p.Q93Q		Atlas-SNP	.											.	DUSP10	64	.	0			c.A279G						PASS	.	T	,	638,3768	274.3+/-271.8	48,542,1613	102.0	69.0	80.0		279,	-4.4	0.9	1	dbSNP_86	80	3506,5094	510.5+/-377.5	684,2138,1478	no	coding-synonymous,intron	DUSP10	NM_007207.4,NM_144729.2	,	732,2680,3091	CC,CT,TT		40.7674,14.4803,31.8622	,	93/483,	221912808	4144,8862	2203	4300	6503	SO:0001819	synonymous_variant	11221	exon2			TTGGGTTTGGGCC	AB026436	CCDS1528.1	1q41	2011-06-09			ENSG00000143507	ENSG00000143507		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3065	protein-coding gene	gene with protein product		608867				10391943, 10597297	Standard	NM_007207		Approved	MKP-5, MKP5	uc001hmy.2	Q9Y6W6	OTTHUMG00000037269	ENST00000366899.3:c.279A>G	1.37:g.221912808T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	130	127	0.976923	NM_007207	D3DTB4|Q6GSI4|Q9H9Z5	Silent	SNP	ENST00000366899.3	37	CCDS1528.1																																																																																			T|0.678;C|0.322	0.322	strong		0.567	DUSP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090716.1	NM_007207	
CEP44	80817	hgsc.bcm.edu	37	4	175238508	175238508	+	Silent	SNP	C	C	T	rs17358230	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:175238508C>T	ENST00000503780.1	+	12	1561	c.1147C>T	c.(1147-1149)Ctg>Ttg	p.L383L	CEP44_ENST00000296519.4_Silent_p.L383L|CEP44_ENST00000457424.2_Intron|CEP44_ENST00000426172.1_Intron	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	383						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						TGCAGAGTTACTGAAATGTCC	0.244													C|||	96	0.0191693	0.0008	0.0058	5008	,	,		11848	0.002		0.0398	False		,,,				2504	0.0501				p.L383L		Atlas-SNP	.											.	CEP44	35	.	0			c.C1147T						PASS	.	C	,	19,4347		0,19,2164	31.0	35.0	33.0		1147,	3.0	1.0	4	dbSNP_123	33	302,8212		0,302,3955	no	coding-synonymous,intron	CEP44	NM_001040157.2,NM_001145314.1	,	0,321,6119	TT,TC,CC		3.5471,0.4352,2.4922	,	383/391,	175238508	321,12559	2183	4257	6440	SO:0001819	synonymous_variant	80817	exon12			GAGTTACTGAAAT	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"""KIAA1712"""	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.1147C>T	4.37:g.175238508C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Silent	SNP	ENST00000503780.1	37	CCDS34106.1																																																																																			C|0.975;T|0.025	0.025	strong		0.244	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633	
ICAM5	7087	hgsc.bcm.edu	37	19	10402938	10402938	+	Missense_Mutation	SNP	G	G	A	rs1056538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10402938G>A	ENST00000221980.4	+	4	964	c.901G>A	c.(901-903)Gtc>Atc	p.V301I		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	301	Ig-like C2-type 3.		V -> I (in dbSNP:rs1056538). {ECO:0000269|PubMed:8995416}.		phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CAGGCAGCTGGTCTGCAACGT	0.642													G|||	1450	0.289537	0.0439	0.5202	5008	,	,		16487	0.2371		0.4056	False		,,,				2504	0.3926				p.V301I		Atlas-SNP	.											.	ICAM5	53	.	0			c.G901A						PASS	.	G	ILE/VAL	436,3970	202.8+/-225.5	19,398,1786	36.0	29.0	31.0		901	3.3	1.0	19	dbSNP_86	31	3345,5253	473.0+/-368.5	669,2007,1623	no	missense	ICAM5	NM_003259.3	29	688,2405,3409	AA,AG,GG		38.9044,9.8956,29.0757	benign	301/925	10402938	3781,9223	2203	4299	6502	SO:0001583	missense	7087	exon4			CAGCTGGTCTGCA	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.901G>A	19.37:g.10402938G>A	ENSP00000221980:p.Val301Ile	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	641	0.2934981684981685	11	0.022357723577235773	175	0.48342541436464087	145	0.2534965034965035	310	0.40897097625329815	G	16.96	3.265958	0.59540	0.098956	0.389044	ENSG00000105376	ENST00000221980	T	0.05447	3.44	5.54	3.27	0.37495	Immunoglobulin-like fold (1);	0.652062	0.14359	N	0.324603	T	0.00012	0.0000	L	0.60455	1.87	0.45867	P	0.0012799999999999478	B	0.12630	0.006	B	0.11329	0.006	T	0.41395	-0.9511	9	0.30078	T	0.28	-22.8733	5.0439	0.14473	0.3049:0.0:0.6951:0.0	rs1056538;rs2228616;rs11549918;rs17845811;rs17858776;rs61530381	301	Q9UMF0	ICAM5_HUMAN	I	301	ENSP00000221980:V301I	ENSP00000221980:V301I	V	+	1	0	ICAM5	10263938	0.401000	0.25303	1.000000	0.80357	0.884000	0.51177	0.359000	0.20233	1.336000	0.45506	0.485000	0.47835	GTC	G|0.719;A|0.281	0.281	strong		0.642	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
NOP9	161424	hgsc.bcm.edu	37	14	24773387	24773387	+	Silent	SNP	T	T	C	rs2144494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24773387T>C	ENST00000267425.3	+	8	1644	c.1551T>C	c.(1549-1551)ctT>ctC	p.L517L	NOP9_ENST00000396802.3_Silent_p.L517L	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	517							poly(A) RNA binding (GO:0044822)										TTCTGTCCCTTGCCCAAAGTC	0.587													G|||	720	0.14377	0.1346	0.3444	5008	,	,		19048	0.004		0.1849	False		,,,				2504	0.1155				p.L517L		Atlas-SNP	.											.	.	.	.	0			c.T1551C						PASS	.	G		650,3756		54,542,1607	64.0	55.0	58.0		1551	1.5	1.0	14	dbSNP_96	58	1782,6818		188,1406,2706	no	coding-synonymous	C14orf21	NM_174913.1		242,1948,4313	CC,CT,TT		20.7209,14.7526,18.6991		517/637	24773387	2432,10574	2203	4300	6503	SO:0001819	synonymous_variant	161424	exon8			GTCCCTTGCCCAA		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.1551T>C	14.37:g.24773387T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			T|0.835;C|0.165	0.165	strong		0.587	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
MBD3L2	125997	hgsc.bcm.edu	37	19	7051588	7051588	+	Silent	SNP	G	G	A	rs76206324	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:7051588G>A	ENST00000381393.3	+	2	635	c.582G>A	c.(580-582)caG>caA	p.Q194Q		NM_144614.3	NP_653215.2	Q8NHZ7	MB3L2_HUMAN	methyl-CpG binding domain protein 3-like 2	194										endometrium(1)	1	all_hematologic(4;0.166)			Lung(535;0.179)		AGGCCTTGCAGGCAGACAGGC	0.577													-|||	365	0.0728834	0.0076	0.0677	5008	,	,		22456	0.0853		0.1392	False		,,,				2504	0.0838				p.Q194Q		Atlas-SNP	.											.	MBD3L2	2	.	0			c.G582A						PASS	.						8.0	9.0	9.0					19																	7051588		1771	3878	5649	SO:0001819	synonymous_variant	125997	exon2			CTTGCAGGCAGAC	AF503919	CCDS42483.1	19p13.3	2011-01-31			ENSG00000230522	ENSG00000230522			18532	protein-coding gene	gene with protein product		607964					Standard	NM_144614		Approved		uc010dvf.1	Q8NHZ7		ENST00000381393.3:c.582G>A	19.37:g.7051588G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	178	77	0.432584	NM_144614		Silent	SNP	ENST00000381393.3	37	CCDS42483.1																																																																																			G|0.855;A|0.145	0.145	strong		0.577	MBD3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458499.1	NM_144614	
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 GAIIx	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	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	41	19	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	
SWT1	54823	hgsc.bcm.edu	37	1	185240474	185240474	+	Missense_Mutation	SNP	A	A	G	rs12041704	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:185240474A>G	ENST00000367500.4	+	17	2626	c.2461A>G	c.(2461-2463)Aat>Gat	p.N821D	SWT1_ENST00000367501.3_Missense_Mutation_p.N821D	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	821			N -> D (in dbSNP:rs12041704). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						CCCAAACAGTAATTATCAAGA	0.284													A|||	1743	0.348043	0.2428	0.3963	5008	,	,		13198	0.245		0.4433	False		,,,				2504	0.4642				p.N821D		Atlas-SNP	.											SWT1,NS,carcinoma,0,1	SWT1	88	1	0			c.A2461G						PASS	.	A	ASP/ASN,ASP/ASN	1203,3175	380.2+/-323.6	164,875,1150	38.0	39.0	39.0		2461,2461	4.8	1.0	1	dbSNP_120	39	3641,4921	504.5+/-376.2	786,2069,1426	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	23,23	950,2944,2576	GG,GA,AA		42.5251,27.4783,37.4343	benign,benign	821/901,821/901	185240474	4844,8096	2189	4281	6470	SO:0001583	missense	54823	exon17			AACAGTAATTATC	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.2461A>G	1.37:g.185240474A>G	ENSP00000356470:p.Asn821Asp	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	763	0.34935897435897434	132	0.2682926829268293	134	0.3701657458563536	170	0.2972027972027972	327	0.4313984168865435	A	16.44	3.123324	0.56613	0.274783	0.425251	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.20200	2.09;2.09	6.02	4.8	0.61643	.	0.263012	0.43747	D	0.000535	T	0.00012	0.0000	N	0.24115	0.695	0.41524	P	0.011584000000000039	P	0.49090	0.919	B	0.42692	0.395	T	0.42068	-0.9473	9	0.11794	T	0.64	.	9.9289	0.41510	0.838:0.0:0.0:0.162	rs12041704;rs12756341;rs17578728;rs17852826;rs52806916;rs60303559;rs12041704	821	Q5T5J6	SWT1_HUMAN	D	821	ENSP00000356471:N821D;ENSP00000356470:N821D	ENSP00000356470:N821D	N	+	1	0	SWT1	183507097	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.076000	0.50081	2.299000	0.77371	0.528000	0.53228	AAT	A|0.637;G|0.363	0.363	strong		0.284	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
ZNF763	284390	hgsc.bcm.edu	37	19	12089903	12089903	+	Silent	SNP	G	G	A	rs112017572	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:12089903G>A	ENST00000358987.3	+	4	1291	c.1164G>A	c.(1162-1164)gcG>gcA	p.A388A	ZNF763_ENST00000590798.1_Silent_p.A408A|ZNF763_ENST00000545530.1_Silent_p.A266A|ZNF763_ENST00000538752.1_Silent_p.A408A|ZNF763_ENST00000343949.5_Silent_p.A391A			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	388					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)	p.A390A(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						CTAAGAATGCGCTCTGGAGAA	0.393													a|||	398	0.0794728	0.2103	0.0317	5008	,	,		22553	0.0218		0.0378	False		,,,				2504	0.0389				p.A391A		Atlas-SNP	.											ZNF763,caecum,carcinoma,+2,3	ZNF763	31	3	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G1173A						PASS	.	A		819,3565	683.6+/-404.3	81,657,1454	59.0	65.0	63.0		1173	1.4	0.0	19	dbSNP_132	63	256,8336	789.1+/-407.6	3,250,4043	no	coding-synonymous	ZNF763	NM_001012753.1		84,907,5497	AA,AG,GG		2.9795,18.6816,8.2845		391/398	12089903	1075,11901	2192	4296	6488	SO:0001819	synonymous_variant	284390	exon4			GAATGCGCTCTGG	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.1164G>A	19.37:g.12089903G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				G|0.941;A|0.059	0.059	strong		0.393	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	
SLC4A7	9497	hgsc.bcm.edu	37	3	27442336	27442336	+	Silent	SNP	G	G	A	rs3736312	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:27442336G>A	ENST00000295736.5	-	16	2389	c.2319C>T	c.(2317-2319)aaC>aaT	p.N773N	SLC4A7_ENST00000446700.1_Silent_p.N765N|SLC4A7_ENST00000454389.1_Silent_p.N782N|SLC4A7_ENST00000428386.1_Silent_p.N649N|SLC4A7_ENST00000435667.2_Silent_p.N658N|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000388777.4_Silent_p.N323N|SLC4A7_ENST00000437179.1_Silent_p.N654N|SLC4A7_ENST00000445684.1_Silent_p.N769N|SLC4A7_ENST00000440156.1_Silent_p.N769N|SLC4A7_ENST00000455077.1_Silent_p.N654N	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	773					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CATTGCTGGGGTTTGGAGGTT	0.313													G|||	642	0.128195	0.0446	0.1614	5008	,	,		17831	0.0565		0.2247	False		,,,				2504	0.1922				p.N773N		Atlas-SNP	.											.	SLC4A7	119	.	0			c.C2319T						PASS	.	G		354,4052	182.6+/-210.3	9,336,1858	152.0	149.0	150.0		2319	1.3	1.0	3	dbSNP_107	150	2129,6465	365.1+/-333.8	264,1601,2432	no	coding-synonymous	SLC4A7	NM_003615.3		273,1937,4290	AA,AG,GG		24.7731,8.0345,19.1		773/1215	27442336	2483,10517	2203	4297	6500	SO:0001819	synonymous_variant	9497	exon16			GCTGGGGTTTGGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2319C>T	3.37:g.27442336G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	63	0.480916	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			G|0.828;A|0.172	0.172	strong		0.313	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
PRX	57716	hgsc.bcm.edu	37	19	40901614	40901614	+	Missense_Mutation	SNP	A	A	G	rs268671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40901614A>G	ENST00000324001.7	-	7	2915	c.2645T>C	c.(2644-2646)gTg>gCg	p.V882A	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	882			V -> A (in dbSNP:rs268671). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:11133365}.		axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			AGGGCCCTCCACCCGCTCTCC	0.627													G|||	2664	0.531949	0.8427	0.4784	5008	,	,		17084	0.2401		0.506	False		,,,				2504	0.4775				p.V882A		Atlas-SNP	.											.	PRX	151	.	0			c.T2645C						PASS	.	G	,ALA/VAL	3477,929	343.1+/-307.5	1384,709,110	38.0	46.0	43.0		,2645	2.7	0.0	19	dbSNP_79	43	4453,4147	555.8+/-386.7	1152,2149,999	yes	utr-3,missense	PRX	NM_020956.2,NM_181882.2	,64	2536,2858,1109	GG,GA,AA		48.2209,21.0849,39.0281	,benign	,882/1462	40901614	7930,5076	2203	4300	6503	SO:0001583	missense	57716	exon7			CCCTCCACCCGCT	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.2645T>C	19.37:g.40901614A>G	ENSP00000326018:p.Val882Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	37	CCDS33028.1	1082	0.49542124542124544	391	0.7947154471544715	193	0.5331491712707183	123	0.21503496503496503	375	0.4947229551451187	G	0.016	-1.538715	0.00942	0.789151	0.517791	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.01113	5.32	4.88	2.7	0.31948	.	0.563419	0.14794	N	0.298050	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.01360	-1.1375	9	0.17832	T	0.49	0.0625	7.2297	0.26036	0.1619:0.1377:0.7004:0.0	rs268671;rs3745204;rs52793723;rs60720056;rs268671	882	Q9BXM0	PRAX_HUMAN	A	882	ENSP00000326018:V882A	ENSP00000326018:V882A	V	-	2	0	PRX	45593454	0.346000	0.24844	0.033000	0.17914	0.004000	0.04260	2.680000	0.46918	0.119000	0.18210	-0.900000	0.02857	GTG	A|0.446;G|0.554	0.554	strong		0.627	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
LXN	56925	hgsc.bcm.edu	37	3	158388780	158388780	+	Missense_Mutation	SNP	T	T	C	rs8455	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:158388780T>C	ENST00000264265.3	-	2	372	c.158A>G	c.(157-159)cAc>cGc	p.H53R	GFM1_ENST00000486715.1_Intron|GFM1_ENST00000478576.1_Intron|GFM1_ENST00000264263.5_Intron	NM_020169.3	NP_064554.3	Q9BS40	LXN_HUMAN	latexin	53	Cystatin-like fold 1. {ECO:0000250}.		H -> R (in dbSNP:rs8455). {ECO:0000269|PubMed:11455960}.		detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|metalloendopeptidase inhibitor activity (GO:0008191)			breast(2)|endometrium(1)|kidney(2)	5			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			AAATTTAAGGTGATACTTATG	0.323													C|||	2888	0.576677	0.7474	0.5288	5008	,	,		19706	0.3839		0.5437	False		,,,				2504	0.6125				p.H53R		Atlas-SNP	.											.	LXN	14	.	0			c.A158G						PASS	.	C	ARG/HIS,	3060,1296		1084,892,202	34.0	40.0	38.0		158,	-2.5	0.5	3	dbSNP_52	38	4622,3966		1234,2154,906	yes	missense,intron	LXN,GFM1	NM_020169.3,NM_024996.5	29,	2318,3046,1108	CC,CT,TT		46.1807,29.7521,40.652	benign,	53/223,	158388780	7682,5262	2178	4294	6472	SO:0001583	missense	56925	exon2			TTAAGGTGATACT	AF087851	CCDS3183.1	3q25.32	2004-05-10			ENSG00000079257	ENSG00000079257			13347	protein-coding gene	gene with protein product		609305					Standard	NM_020169		Approved		uc003fch.3	Q9BS40	OTTHUMG00000158807	ENST00000264265.3:c.158A>G	3.37:g.158388780T>C	ENSP00000264265:p.His53Arg	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	190	57	0.3	NM_020169	Q96PN2|Q9NQS6	Missense_Mutation	SNP	ENST00000264265.3	37	CCDS3183.1	1190	0.5448717948717948	361	0.733739837398374	191	0.5276243093922652	215	0.3758741258741259	423	0.558047493403694	C	9.858	1.195620	0.22037	0.702479	0.538193	ENSG00000079257	ENST00000264265	T	0.23552	1.9	5.39	-2.53	0.06326	.	0.764210	0.12723	N	0.444503	T	0.00012	0.0000	N	0.16307	0.4	0.44275	P	0.002870000000000039	B	0.06786	0.001	B	0.04013	0.001	T	0.29971	-0.9994	9	0.23891	T	0.37	1.6545	12.0573	0.53542	0.0:0.2303:0.0:0.7697	rs8455;rs1132811;rs3193979;rs6788438;rs11549295;rs17295118;rs17349641;rs17630531;rs17856146;rs52825353;rs59364417;rs8455	53	Q9BS40	LXN_HUMAN	R	53	ENSP00000264265:H53R	ENSP00000264265:H53R	H	-	2	0	LXN	159871474	0.958000	0.32768	0.485000	0.27403	0.955000	0.61496	0.105000	0.15333	-0.464000	0.06963	-1.133000	0.01973	CAC	C|0.557;N|0.000	0.557	strong		0.323	LXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352284.1	NM_020169	
ZNF705B	100132396	hgsc.bcm.edu	37	8	7808219	7808219	+	Missense_Mutation	SNP	A	A	T	rs2740676	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:7808219A>T	ENST00000400120.3	+	6	550	c.268A>T	c.(268-270)Ata>Tta	p.I90L	ZNF705B_ENST00000443676.1_Missense_Mutation_p.I90L	NM_001193630.1	NP_001180559.1	P0CI00	Z705B_HUMAN	zinc finger protein 705B	90					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.I90L(4)		kidney(2)|lung(2)	4						AAAACACATGATATCCATGCA	0.328													a|||	611	0.122005	0.3215	0.098	5008	,	,		8921	0.0476		0.0368	False		,,,				2504	0.0337				p.I90L		Atlas-SNP	.											ZNF705B_ENST00000443676,NS,carcinoma,0,4	ZNF705B	10	4	4	Substitution - Missense(4)	kidney(4)	c.A268T						scavenged	.																																			SO:0001583	missense	100132396	exon6			CACATGATATCCA		CCDS55194.1	8p23.1	2013-01-08			ENSG00000215356	ENSG00000215356		"""Zinc fingers, C2H2-type"", ""-"""	32284	protein-coding gene	gene with protein product							Standard	NM_001193630		Approved		uc010lro.1	P0CI00	OTTHUMG00000165401	ENST00000400120.3:c.268A>T	8.37:g.7808219A>T	ENSP00000382987:p.Ile90Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	182	79	0.434066	NM_001193630	A8K971|A8MY01	Missense_Mutation	SNP	ENST00000400120.3	37	CCDS55194.1	.	.	.	.	.	.	.	.	.	.	A	5.923	0.354401	0.11239	.	.	ENSG00000215356	ENST00000400120;ENST00000443676	T;T	0.10477	2.87;2.87	1.03	-0.278	0.12894	.	.	.	.	.	T	0.04182	0.0116	N	0.12182	0.205	0.80722	P	0.0	P	0.42692	0.787	B	0.38056	0.264	T	0.36016	-0.9765	8	0.13470	T	0.59	.	4.1796	0.10369	0.5061:0.0:0.4939:0.0	.	90	P0CI00	Z705L_HUMAN	L	90	ENSP00000382987:I90L;ENSP00000411618:I90L	ENSP00000382987:I90L	I	+	1	0	ZNF705B	7845629	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.124000	0.15728	-0.074000	0.12820	0.155000	0.16302	ATA	T|1.000;|0.000	1.000	weak		0.328	ZNF705B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383804.1	NM_001193630	
ZNF799	90576	hgsc.bcm.edu	37	19	12502787	12502787	+	Missense_Mutation	SNP	G	G	A	rs12974755	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:12502787G>A	ENST00000430385.3	-	4	625	c.425C>T	c.(424-426)aCg>aTg	p.T142M	CTD-3105H18.16_ENST00000595562.1_Missense_Mutation_p.T142M|ZNF799_ENST00000419318.1_Missense_Mutation_p.T110M|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	142					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)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						TTGTTTATGCGTATCTGGCTT	0.423													G|||	443	0.0884585	0.0174	0.0793	5008	,	,		22280	0.0585		0.1501	False		,,,				2504	0.1585				p.T142M		Atlas-SNP	.											.	ZNF799	111	.	0			c.C425T						PASS	.	G	MET/THR	191,4215	123.7+/-161.0	5,181,2017	163.0	154.0	158.0		425	-0.8	0.0	19	dbSNP_121	158	1319,7281	260.2+/-283.1	101,1117,3082	no	missense	ZNF799	NM_001080821.2	81	106,1298,5099	AA,AG,GG		15.3372,4.335,11.61	possibly-damaging	142/644	12502787	1510,11496	2203	4300	6503	SO:0001583	missense	90576	exon4			TTATGCGTATCTG	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.425C>T	19.37:g.12502787G>A	ENSP00000411084:p.Thr142Met	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	234	121	0.517094	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	185	0.08470695970695971	11	0.022357723577235773	33	0.09116022099447514	26	0.045454545454545456	115	0.1517150395778364	G	11.07	1.529300	0.27387	0.04335	0.153372	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.08458	3.09;3.22	1.0	-0.771	0.11002	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	M	0.64997	1.995	0.80722	P	0.0	D	0.65815	0.995	P	0.54060	0.741	T	0.16041	-1.0416	8	0.72032	D	0.01	.	6.2771	0.20987	0.0:0.0:0.6435:0.3565	rs12974755	142	Q96GE5	ZN799_HUMAN	M	110;142	ENSP00000415278:T110M;ENSP00000411084:T142M	ENSP00000415278:T110M	T	-	2	0	ZNF799	12363787	0.001000	0.12720	0.005000	0.12908	0.287000	0.27160	-0.024000	0.12435	-0.311000	0.08754	0.430000	0.28490	ACG	G|0.898;A|0.102	0.102	strong		0.423	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
TMC1	117531	hgsc.bcm.edu	37	9	75303653	75303653	+	Silent	SNP	C	C	T	rs2589615	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:75303653C>T	ENST00000297784.5	+	6	585	c.45C>T	c.(43-45)gaC>gaT	p.D15D	TMC1_ENST00000396237.3_Silent_p.D15D|TMC1_ENST00000340019.3_Silent_p.D15D	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	15	Arg/Asp/Glu/Lys-rich (highly charged).				auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						AAAAAGAAGACGAGACTGAGG	0.368													C|||	2558	0.510783	0.77	0.4496	5008	,	,		19992	0.4187		0.4085	False		,,,				2504	0.4039				p.D15D	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.C45T						PASS	.	C		3161,1245	694.7+/-405.8	1149,863,191	90.0	90.0	90.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	45	-5.3	0.2	9	dbSNP_100	90	3698,4902	521.2+/-379.8	775,2148,1377	no	coding-synonymous	TMC1	NM_138691.2		1924,3011,1568	TT,TC,CC		43.0,28.2569,47.2628		15/761	75303653	6859,6147	2203	4300	6503	SO:0001819	synonymous_variant	117531	exon6			AGAAGACGAGACT	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"""transmembrane, cochlear expressed, 1"""	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.45C>T	9.37:g.75303653C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	27	0.5625	NM_138691	A8MVZ2|B1AM91	Silent	SNP	ENST00000297784.5	37	CCDS6643.1																																																																																			C|0.478;T|0.522	0.522	strong		0.368	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		
DNHD1	144132	hgsc.bcm.edu	37	11	6524072	6524072	+	Missense_Mutation	SNP	A	A	C	rs11605196	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6524072A>C	ENST00000527990.2	+	2	836	c.836A>C	c.(835-837)cAg>cCg	p.Q279P	DNHD1_ENST00000354685.3_Missense_Mutation_p.Q279P|DNHD1_ENST00000254579.6_Missense_Mutation_p.Q279P			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	279			Q -> P (in dbSNP:rs11605196).		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)		CTGGATAGCCAGGTGATGACT	0.502													A|||	499	0.0996406	0.0408	0.147	5008	,	,		20522	0.0169		0.1789	False		,,,				2504	0.1493				p.Q279P		Atlas-SNP	.											.	DNHD1	198	.	0			c.A836C						PASS	.	A	PRO/GLN,PRO/GLN	277,4125	155.2+/-188.4	10,257,1934	122.0	102.0	109.0		836,836	4.5	0.0	11	dbSNP_120	109	1636,6956	302.2+/-305.8	165,1306,2825	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	76,76	175,1563,4759	CC,CA,AA		19.041,6.2926,14.7222	benign,benign	279/4754,279/598	6524072	1913,11081	2201	4296	6497	SO:0001583	missense	144132	exon3			ATAGCCAGGTGAT	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.836A>C	11.37:g.6524072A>C	ENSP00000436180:p.Gln279Pro	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	224	0.10256410256410256	26	0.052845528455284556	46	0.1270718232044199	11	0.019230769230769232	141	0.18601583113456466	A	11.40	1.627054	0.28978	0.062926	0.19041	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.27890	1.64;2.65;1.64	5.64	4.52	0.55395	.	0.540708	0.18166	N	0.149607	T	0.00039	0.0001	L	0.40543	1.245	0.80722	P	0.0	P;B	0.44578	0.838;0.004	B;B	0.41813	0.367;0.004	T	0.18178	-1.0345	9	0.28530	T	0.3	.	8.2343	0.31616	0.9095:0.0:0.0905:0.0	rs11605196;rs52824639;rs11605196	279;279	Q96M86;Q96M86-4	DNHD1_HUMAN;.	P	279	ENSP00000254579:Q279P;ENSP00000346716:Q279P;ENSP00000436180:Q279P	ENSP00000254579:Q279P	Q	+	2	0	DNHD1	6480648	0.000000	0.05858	0.019000	0.16419	0.032000	0.12392	0.115000	0.15540	0.971000	0.38288	0.460000	0.39030	CAG	A|0.862;C|0.138	0.138	strong		0.502	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
LBP	3929	hgsc.bcm.edu	37	20	36989381	36989381	+	Silent	SNP	G	G	A	rs2232596	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:36989381G>A	ENST00000217407.2	+	6	773	c.612G>A	c.(610-612)tcG>tcA	p.S204S		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	204					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TCCAGAAATCGGTGTCCTCCG	0.473													A|||	3252	0.649361	0.6498	0.5375	5008	,	,		15930	0.8819		0.4901	False		,,,				2504	0.6524				p.S204S		Atlas-SNP	.											.	LBP	60	.	0			c.G612A						PASS	.	A		2716,1690	511.7+/-367.9	830,1056,317	179.0	177.0	178.0		612	-8.4	0.0	20	dbSNP_98	178	4410,4190	568.8+/-389.1	1124,2162,1014	no	coding-synonymous	LBP	NM_004139.2		1954,3218,1331	AA,AG,GG		48.7209,38.3568,45.2099		204/482	36989381	7126,5880	2203	4300	6503	SO:0001819	synonymous_variant	3929	exon6			GAAATCGGTGTCC		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.612G>A	20.37:g.36989381G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	95	55	0.578947	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																			G|0.400;A|0.599	0.599	strong		0.473	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
MAGEC3	139081	hgsc.bcm.edu	37	X	140967165	140967165	+	Missense_Mutation	SNP	T	T	C	rs372869684|rs11095909	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:140967165T>C	ENST00000298296.1	+	3	463	c.463T>C	c.(463-465)Tcc>Ccc	p.S155P	MAGEC3_ENST00000536088.1_5'Flank|MAGEC3_ENST00000443323.2_5'Flank|MAGEC3_ENST00000448920.1_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	155			S -> P (in dbSNP:rs11095909).							NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					CTACACCCTTTCCCTTCCTGC	0.572													C|||	1658	0.439205	0.5348	0.3458	3775	,	,		10239	0.3651		0.0676	False		,,,				2504	0.2812				p.S155P		Atlas-SNP	.											.	MAGEC3	228	.	0			c.T463C						PASS	.	C	PRO/SER	2201,1453		686,544,285,357,195	37.0	32.0	33.0		463	-1.4	0.0	X	dbSNP_120	33	564,6162		18,376,152,2034,1718	yes	missense	MAGEC3	NM_138702.1	74	704,920,437,2391,1913	CC,CT,C,TT,T		8.3854,39.7646,26.6378	benign	155/644	140967165	2765,7615	2067	4298	6365	SO:0001583	missense	139081	exon3			ACCCTTTCCCTTC	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.463T>C	X.37:g.140967165T>C	ENSP00000298296:p.Ser155Pro	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	191	137	0.717277	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	594	0.35804701627486435	178	0.5028248587570622	77	0.2532894736842105	130	0.29545454545454547	37	0.05096418732782369	C	0.009	-1.811288	0.00600	0.602354	0.083854	ENSG00000165509	ENST00000298296	T	0.06528	3.29	0.994	-1.44	0.08856	.	.	.	.	.	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	0.34054	-0.9844	8	0.20519	T	0.43	.	0.3624	0.00366	0.2444:0.308:0.2421:0.2055	rs11095909	155	Q8TD91	MAGC3_HUMAN	P	155	ENSP00000298296:S155P	ENSP00000298296:S155P	S	+	1	0	MAGEC3	140794831	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.198000	0.01239	-1.544000	0.01721	-2.375000	0.00234	TCC	T|0.639;C|0.361	0.361	strong		0.572	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
TAF1L	138474	hgsc.bcm.edu	37	9	32631369	32631369	+	Silent	SNP	C	C	T	rs10971047	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:32631369C>T	ENST00000242310.4	-	1	4298	c.4209G>A	c.(4207-4209)acG>acA	p.T1403T	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1403					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGGATGACAGCGTCACCATAG	0.458													C|||	809	0.161542	0.1097	0.1182	5008	,	,		21985	0.3095		0.1034	False		,,,				2504	0.1697				p.T1403T		Atlas-SNP	.											TAF1L,NS,carcinoma,-1,1	TAF1L	382	1	0			c.G4209A						PASS	.	C		374,4032	188.5+/-214.9	13,348,1842	297.0	272.0	280.0		4209	-0.9	0.9	9	dbSNP_120	280	893,7707	201.1+/-244.7	44,805,3451	no	coding-synonymous	TAF1L	NM_153809.2		57,1153,5293	TT,TC,CC		10.3837,8.4884,9.7417		1403/1827	32631369	1267,11739	2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			TGACAGCGTCACC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4209G>A	9.37:g.32631369C>T		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	328	162	0.493902	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			C|0.873;T|0.127	0.127	strong		0.458	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
QRICH2	84074	hgsc.bcm.edu	37	17	74288421	74288421	+	Missense_Mutation	SNP	A	A	G	rs6501878	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74288421A>G	ENST00000262765.5	-	4	2068	c.1889T>C	c.(1888-1890)aTa>aCa	p.I630T		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	630	Gln-rich.		I -> T (in dbSNP:rs6501878).|I -> V (in dbSNP:rs6501879).					p.I630_G639delIVQRGLVQPG(3)		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						acgctgaactataccaggttg	0.537													a|||	2303	0.459864	0.6861	0.3084	5008	,	,		23715	0.5665		0.2734	False		,,,				2504	0.3436				p.I630T		Atlas-SNP	.											.	QRICH2	143	.	3	Deletion - In frame(3)	stomach(3)	c.T1889C						PASS	.	G	THR/ILE	1346,2454		623,100,1177	73.0	84.0	81.0		1889	-9.4	0.0	17	dbSNP_116	81	535,7851		209,117,3867	no	missense	QRICH2	NM_032134.1	89	832,217,5044	GG,GA,AA		6.3797,35.4211,15.4357	benign	630/1664	74288421	1881,10305	1900	4193	6093	SO:0001583	missense	84074	exon4			TGAACTATACCAG	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.1889T>C	17.37:g.74288421A>G	ENSP00000262765:p.Ile630Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	713	0.32646520146520147	254	0.516260162601626	85	0.23480662983425415	267	0.46678321678321677	107	0.14116094986807387	a	4.894	0.166137	0.09339	0.354211	0.063797	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.21361	2.01	4.72	-9.44	0.00603	.	.	.	.	.	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41466	-0.9507	8	0.11794	T	0.64	0.5378	13.5155	0.61539	0.7104:0.0815:0.2081:0.0	rs6501878;rs6501878	630;630	B5MD94;Q9H0J4	.;QRIC2_HUMAN	T	630	ENSP00000262765:I630T	ENSP00000262765:I630T	I	-	2	0	QRICH2	71800016	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.857000	0.00016	-3.030000	0.00266	-2.691000	0.00139	ATA	A|0.636;G|0.364	0.364	strong		0.537	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
PREX1	57580	hgsc.bcm.edu	37	20	47258763	47258763	+	Missense_Mutation	SNP	C	C	T	rs16993997	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47258763C>T	ENST00000371941.3	-	29	3740	c.3718G>A	c.(3718-3720)Gtc>Atc	p.V1240I	PREX1_ENST00000496915.1_5'UTR|PREX1_ENST00000396220.1_Missense_Mutation_p.V1240I	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1240			V -> I (in dbSNP:rs16993997). {ECO:0000269|PubMed:17974005}.		actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			CGGCTCATGACTGGCCCCTTG	0.582													.|||	755	0.150759	0.0182	0.2133	5008	,	,		16987	0.1528		0.1849	False		,,,				2504	0.2485				p.V1240I		Atlas-SNP	.											PREX1,NS,carcinoma,+2,1	PREX1	441	1	0			c.G3718A						PASS	.	C	ILE/VAL	251,4155	144.6+/-179.5	10,231,1962	91.0	87.0	88.0		3718	3.5	0.8	20	dbSNP_123	88	1623,6977	300.5+/-305.0	148,1327,2825	yes	missense	PREX1	NM_020820.3	29	158,1558,4787	TT,TC,CC		18.8721,5.6968,14.4087	benign	1240/1660	47258763	1874,11132	2203	4300	6503	SO:0001583	missense	57580	exon29			TCATGACTGGCCC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3718G>A	20.37:g.47258763C>T	ENSP00000361009:p.Val1240Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	313	0.1433150183150183	12	0.024390243902439025	81	0.22375690607734808	85	0.1486013986013986	135	0.17810026385224276	c	11.01	1.512329	0.27036	0.056968	0.188721	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.37235	1.21;1.21	5.4	3.47	0.39725	.	0.585620	0.14633	U	0.307705	T	0.00012	0.0000	N	0.17474	0.49	0.43334	P	0.0046279999999999655	B;B	0.12013	0.001;0.005	B;B	0.12837	0.003;0.008	T	0.15492	-1.0435	9	0.39692	T	0.17	.	10.6574	0.45684	0.0:0.7903:0.0:0.2097	rs16993997;rs16993997	1240;537	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	I	1240	ENSP00000361009:V1240I;ENSP00000379522:V1240I	ENSP00000361009:V1240I	V	-	1	0	PREX1	46692170	0.920000	0.31207	0.829000	0.32907	0.411000	0.31082	2.936000	0.48971	1.292000	0.44672	0.639000	0.83563	GTC	C|0.855;N|0.001	.	strong		0.582	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
LRRC38	126755	hgsc.bcm.edu	37	1	13802325	13802325	+	Missense_Mutation	SNP	T	T	C	rs3013105	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:13802325T>C	ENST00000376085.3	-	2	1328	c.874A>G	c.(874-876)Aag>Gag	p.K292E		NM_001010847.1	NP_001010847.1	Q5VT99	LRC38_HUMAN	leucine rich repeat containing 38	292			K -> E (in dbSNP:rs3013105).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)											CAGTCATCCTTGTCCTCGTCT	0.557													C|||	2314	0.462061	0.5242	0.3357	5008	,	,		20308	0.62		0.3837	False		,,,				2504	0.3855				p.K292E		Atlas-SNP	.											LRRC38,NS,meningioma,0,1	LRRC38	12	1	0			c.A874G						PASS	.																																			SO:0001583	missense	126755	exon2			CATCCTTGTCCTC	BC016048	CCDS53269.1	1p36.21	2008-02-05			ENSG00000162494	ENSG00000162494			27005	protein-coding gene	gene with protein product		615212				12477932	Standard	NM_001010847		Approved		uc001avb.3	Q5VT99	OTTHUMG00000007918	ENST00000376085.3:c.874A>G	1.37:g.13802325T>C	ENSP00000365253:p.Lys292Glu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_001010847	Q96B32	Missense_Mutation	SNP	ENST00000376085.3	37	CCDS53269.1	1039	0.4757326007326007	254	0.516260162601626	134	0.3701657458563536	362	0.6328671328671329	289	0.3812664907651715	.	0.018	-1.483234	0.01027	.	.	ENSG00000162494	ENST00000376085	T	0.59224	0.28	5.25	5.25	0.73442	.	0.491849	0.20946	N	0.082822	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46005	-0.9222	9	0.02654	T	1	.	5.2956	0.15751	0.1637:0.6687:0.0:0.1676	rs3013105;rs3795751;rs60739508;rs3013105	292	Q5VT99	LRC38_HUMAN	E	292	ENSP00000365253:K292E	ENSP00000365253:K292E	K	-	1	0	LRRC38	13674912	0.048000	0.20356	0.701000	0.30321	0.084000	0.17831	1.002000	0.29796	1.225000	0.43566	-0.215000	0.12644	AAG	C|0.487;N|0.000	0.487	strong		0.557	LRRC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021793.1		
CLEC10A	10462	hgsc.bcm.edu	37	17	6979179	6979179	+	Silent	SNP	A	A	G	rs364569	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6979179A>G	ENST00000254868.4	-	7	874	c.546T>C	c.(544-546)ccT>ccC	p.P182P	CLEC10A_ENST00000576617.1_Silent_p.P155P|CLEC10A_ENST00000571664.1_Silent_p.P158P|CLEC10A_ENST00000416562.2_Silent_p.P155P	NM_182906.2	NP_878910.1	Q8IUN9	CLC10_HUMAN	C-type lectin domain family 10, member A	182					endocytosis (GO:0006897)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						CCCAGTTGACAGGGCAGCAGG	0.597													g|||	2125	0.424321	0.6936	0.3127	5008	,	,		18008	0.3294		0.3569	False		,,,				2504	0.3067				p.P182P		Atlas-SNP	.											.	CLEC10A	40	.	0			c.T546C						PASS	.	G	,	2888,1518	481.2+/-359.0	945,998,260	78.0	76.0	77.0		474,546	-1.1	0.0	17	dbSNP_80	77	3040,5560	661.6+/-401.9	546,1948,1806	no	coding-synonymous,coding-synonymous	CLEC10A	NM_006344.2,NM_182906.2	,	1491,2946,2066	GG,GA,AA		35.3488,34.453,45.579	,	158/293,182/317	6979179	5928,7078	2203	4300	6503	SO:0001819	synonymous_variant	10462	exon7			GTTGACAGGGCAG	D50532	CCDS11087.1, CCDS45597.1	17p13.2	2014-05-20	2005-02-09	2005-02-11		ENSG00000132514		"""C-type lectin domain containing"", ""CD molecules"""	16916	protein-coding gene	gene with protein product	"""macrophage lectin 2 (calcium dependent)"""	605999	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 14 (macrophage-derived)"""	CLECSF13, CLECSF14		8598452	Standard	XM_005256411		Approved	HML2, HML, CD301	uc002gej.3	Q8IUN9		ENST00000254868.4:c.546T>C	17.37:g.6979179A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_182906	A8K8J8|Q14538|Q6PIW3	Silent	SNP	ENST00000254868.4	37	CCDS11087.1																																																																																			A|0.544;G|0.456	0.456	strong		0.597	CLEC10A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439837.2	NM_006344	
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 GAIIx	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	AC010646.3_ENST00000594059.1_5'Flank|USHBP1_ENST00000431146.2_Silent_p.L402L	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		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	54	31	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	
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17981184	17981184	+	Silent	SNP	A	A	C	rs35255680	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17981184A>C	ENST00000361221.3	+	23	2607	c.2448A>C	c.(2446-2448)gcA>gcC	p.A816A	ARHGEF10L_ENST00000167825.4_Silent_p.A519A|ARHGEF10L_ENST00000434513.1_Silent_p.A811A|ARHGEF10L_ENST00000375408.3_Silent_p.A589A|ARHGEF10L_ENST00000375415.1_Silent_p.A777A|ARHGEF10L_ENST00000452522.1_Silent_p.A777A|ARHGEF10L_ENST00000469726.1_3'UTR	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	816						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GTTTCTCAGCAGTCAGCACCT	0.612													C|||	953	0.190296	0.298	0.17	5008	,	,		18637	0.1667		0.163	False		,,,				2504	0.1115				p.A816A		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.A2448C						PASS	.	C	,	1281,3125	700.3+/-406.6	183,915,1105	191.0	185.0	187.0		2331,2448	-8.7	0.1	1	dbSNP_126	187	1346,7254	756.3+/-407.5	114,1118,3068	no	coding-synonymous,coding-synonymous	ARHGEF10L	NM_001011722.2,NM_018125.3	,	297,2033,4173	CC,CA,AA		15.6512,29.074,20.1984	,	777/1241,816/1280	17981184	2627,10379	2203	4300	6503	SO:0001819	synonymous_variant	55160	exon23			CTCAGCAGTCAGC	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.2448A>C	1.37:g.17981184A>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Silent	SNP	ENST00000361221.3	37	CCDS182.1																																																																																			A|0.800;C|0.200	0.200	strong		0.612	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
ZNF808	388558	hgsc.bcm.edu	37	19	53056953	53056953	+	Missense_Mutation	SNP	G	G	A	rs329965	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:53056953G>A	ENST00000359798.4	+	5	964	c.784G>A	c.(784-786)Gat>Aat	p.D262N		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	262			D -> N (in dbSNP:rs329965).		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(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		ATATAAATGTGATGTATGTGG	0.393													G|||	1088	0.217252	0.1831	0.2983	5008	,	,		22090	0.0754		0.3022	False		,,,				2504	0.2648				p.D262N		Atlas-SNP	.											.	ZNF808	81	.	0			c.G784A						PASS	.	G	ASN/ASP	855,3551		79,697,1427	158.0	157.0	158.0		784	-1.5	0.0	19	dbSNP_79	158	2468,6132		351,1766,2183	no	missense	ZNF808	NM_001039886.3	23	430,2463,3610	AA,AG,GG		28.6977,19.4054,25.5497	possibly-damaging	262/904	53056953	3323,9683	2203	4300	6503	SO:0001583	missense	388558	exon5			AAATGTGATGTAT	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"""Zinc fingers, C2H2-type"", ""-"""	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.784G>A	19.37:g.53056953G>A	ENSP00000352846:p.Asp262Asn	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	84	69	0.821429	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	465	0.2129120879120879	91	0.18495934959349594	109	0.3011049723756906	37	0.06468531468531469	228	0.3007915567282322	.	9.422	1.083267	0.20309	0.194054	0.286977	ENSG00000198482	ENST00000359798	T	0.07567	3.18	1.57	-1.46	0.08800	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.28458	0.855	0.58432	P	5.000000000032756E-6	P	0.39022	0.655	P	0.47786	0.557	T	0.16660	-1.0395	8	0.02654	T	1	.	2.604	0.04873	0.3051:0.0:0.3404:0.3545	rs329965;rs489728;rs1300305	262	Q8N4W9	ZN808_HUMAN	N	262	ENSP00000352846:D262N	ENSP00000352846:D262N	D	+	1	0	ZNF808	57748765	0.000000	0.05858	0.023000	0.16930	0.168000	0.22595	-2.115000	0.01328	-0.660000	0.05352	0.305000	0.20034	GAT	G|0.792;A|0.208	0.208	strong		0.393	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886	
AXDND1	126859	hgsc.bcm.edu	37	1	179452275	179452275	+	Silent	SNP	G	G	A	rs10494520	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:179452275G>A	ENST00000367618.3	+	18	2397	c.2010G>A	c.(2008-2010)gcG>gcA	p.A670A	AL160286.1_ENST00000600581.1_Intron|AXDND1_ENST00000457238.2_3'UTR	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	670										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						TACTCCAAGCGTATATATTTA	0.338													g|||	978	0.195288	0.1399	0.196	5008	,	,		18554	0.3284		0.1183	False		,,,				2504	0.2117				p.A670A		Atlas-SNP	.											AXDND1,colon,carcinoma,+1,1	AXDND1	142	1	0			c.G2010A						PASS	.	G		614,3792	266.2+/-267.1	44,526,1633	129.0	127.0	128.0		2010	-5.0	0.0	1	dbSNP_119	128	998,7602	215.0+/-254.5	47,904,3349	no	coding-synonymous	AXDND1	NM_144696.4		91,1430,4982	AA,AG,GG		11.6047,13.9355,12.3943		670/1013	179452275	1612,11394	2203	4300	6503	SO:0001819	synonymous_variant	126859	exon18			CCAAGCGTATATA	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2010G>A	1.37:g.179452275G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	113	45	0.39823	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Silent	SNP	ENST00000367618.3	37	CCDS30948.1																																																																																			G|0.807;A|0.193	0.193	strong		0.338	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
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 GAIIx	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	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	41	20	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	
PTGFR	5737	hgsc.bcm.edu	37	1	78958491	78958491	+	Silent	SNP	C	C	T	rs35227129	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:78958491C>T	ENST00000370757.3	+	2	300	c.63C>T	c.(61-63)acC>acT	p.T21T	PTGFR_ENST00000370756.3_Silent_p.T21T|PTGFR_ENST00000370758.1_Silent_p.T21T	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	21					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	CAAACACAACCTGCCAGACGG	0.453													C|||	157	0.0313498	0.0076	0.0476	5008	,	,		20761	0.001		0.0944	False		,,,				2504	0.0184				p.T21T		Atlas-SNP	.											.	PTGFR	121	.	0			c.C63T						PASS	.	C	,	73,4333	66.4+/-103.9	0,73,2130	75.0	79.0	78.0		63,63	2.4	1.0	1	dbSNP_126	78	831,7769	191.5+/-237.7	32,767,3501	no	coding-synonymous,coding-synonymous	PTGFR	NM_000959.3,NM_001039585.1	,	32,840,5631	TT,TC,CC		9.6628,1.6568,6.9506	,	21/360,21/298	78958491	904,12102	2203	4300	6503	SO:0001819	synonymous_variant	5737	exon2			CACAACCTGCCAG	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"""GPCR / Class A : Prostanoid receptors"""	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.63C>T	1.37:g.78958491C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Silent	SNP	ENST00000370757.3	37	CCDS686.1																																																																																			C|0.937;T|0.063	0.063	strong		0.453	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959	
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 GAIIx	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		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	38	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 GAIIx	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_ENST00000406593.1_Intron|MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000407095.3_Missense_Mutation_p.R41C|MTERFD2_ENST00000495694.1_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	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	42	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		
FOXN3	1112	hgsc.bcm.edu	37	14	89878620	89878620	+	Silent	SNP	G	G	A	rs148222339	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:89878620G>A	ENST00000345097.4	-	2	317	c.201C>T	c.(199-201)caC>caT	p.H67H	FOXN3_ENST00000555353.1_Silent_p.H67H|FOXN3_ENST00000557258.1_Silent_p.H67H|RP11-33N16.3_ENST00000555070.1_RNA|FOXN3_ENST00000261302.5_Silent_p.H67H|RP11-33N16.2_ENST00000556383.1_RNA	NM_001085471.1	NP_001078940.1	O00409	FOXN3_HUMAN	forkhead box N3	67					mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCTTGCTCTCGTGCAGCCAGT	0.577													G|||	7	0.00139776	0.0	0.0	5008	,	,		17490	0.0		0.007	False		,,,				2504	0.0				p.H67H		Atlas-SNP	.											.	FOXN3	78	.	0			c.C201T						PASS	.	G	,	0,4406		0,0,2203	94.0	80.0	85.0		201,201	-2.1	1.0	14	dbSNP_134	85	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous,coding-synonymous	FOXN3	NM_001085471.1,NM_005197.3	,	0,26,6477	AA,AG,GG		0.3023,0.0,0.1999	,	67/491,67/469	89878620	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	1112	exon2			GCTCTCGTGCAGC		CCDS32138.1, CCDS41977.1	14q32.11	2012-04-17	2007-05-02	2007-05-02	ENSG00000053254	ENSG00000053254		"""Forkhead boxes"""	1928	protein-coding gene	gene with protein product		602628	"""chromosome 14 open reading frame 116"", ""checkpoint suppressor 1"""	C14orf116, CHES1		9154802	Standard	NM_005197		Approved		uc001xxo.4	O00409	OTTHUMG00000170898	ENST00000345097.4:c.201C>T	14.37:g.89878620G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_005197	Q96II7|Q9UIE7	Silent	SNP	ENST00000345097.4	37	CCDS41977.1																																																																																			G|0.997;A|0.003	0.003	strong		0.577	FOXN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410902.2	NM_005197	
OR4D6	219983	hgsc.bcm.edu	37	11	59224885	59224885	+	Missense_Mutation	SNP	G	G	C	rs1453542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:59224885G>C	ENST00000300127.2	+	1	475	c.452G>C	c.(451-453)aGt>aCt	p.S151T		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	151			S -> T (in dbSNP:rs1453542).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						TCTTGGGTGAGTGGTGGTTTG	0.517													G|||	888	0.177316	0.0477	0.2305	5008	,	,		19531	0.1746		0.2793	False		,,,				2504	0.2127				p.S151T		Atlas-SNP	.											.	OR4D6	65	.	0			c.G452C						PASS	.	G	THR/SER	329,4073	176.2+/-205.4	11,307,1883	283.0	250.0	261.0		452	5.0	1.0	11	dbSNP_88	261	2540,6050	415.1+/-351.7	365,1810,2120	yes	missense	OR4D6	NM_001004708.1	58	376,2117,4003	CC,CG,GG		29.5693,7.4739,22.0828	benign	151/315	59224885	2869,10123	2201	4295	6496	SO:0001583	missense	219983	exon1			GGGTGAGTGGTGG	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.452G>C	11.37:g.59224885G>C	ENSP00000300127:p.Ser151Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	460	0.21062271062271062	28	0.056910569105691054	95	0.26243093922651933	114	0.1993006993006993	223	0.2941952506596306	G	12.41	1.928327	0.34002	0.074739	0.295693	ENSG00000166884	ENST00000300127	T	0.36699	1.24	6.0	5.04	0.67666	GPCR, rhodopsin-like superfamily (1);	0.374604	0.22876	N	0.054573	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.17465	0.022	B	0.28305	0.088	T	0.27400	-1.0075	9	0.87932	D	0	-5.4983	15.5056	0.75739	0.0:0.1386:0.8614:0.0	rs1453542;rs17500408;rs1453542	151	Q8NGJ1	OR4D6_HUMAN	T	151	ENSP00000300127:S151T	ENSP00000300127:S151T	S	+	2	0	OR4D6	58981461	0.000000	0.05858	0.956000	0.39512	0.935000	0.57460	-0.059000	0.11731	2.846000	0.97976	0.650000	0.86243	AGT	G|0.782;C|0.218	0.218	strong		0.517	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
TRAF3	7187	hgsc.bcm.edu	37	14	103371930	103371930	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:103371930C>T	ENST00000560371.1	+	11	1733	c.1516C>T	c.(1516-1518)Cgt>Tgt	p.R506C	TRAF3_ENST00000392745.2_Missense_Mutation_p.R506C|TRAF3_ENST00000347662.4_Missense_Mutation_p.R481C|TRAF3_ENST00000351691.5_Missense_Mutation_p.R481C|TRAF3_ENST00000539721.1_Missense_Mutation_p.R423C	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	506	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|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)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		GTCCTCTCGACGTCATTTGGG	0.522																																					p.R506C		Atlas-SNP	.											TRAF3,colon,carcinoma,-1,1	TRAF3	60	1	0			c.C1516T						scavenged	.						154.0	146.0	149.0					14																	103371930		2203	4300	6503	SO:0001583	missense	7187	exon12			TCTCGACGTCATT	U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.1516C>T	14.37:g.103371930C>T	ENSP00000454207:p.Arg506Cys	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	102	3	0.0294118	NM_145725	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Missense_Mutation	SNP	ENST00000560371.1	37	CCDS9975.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.432540	0.25813	.	.	ENSG00000131323	ENST00000392745;ENST00000347662;ENST00000351691;ENST00000539721	T;T;T	0.31769	1.48;1.48;1.48	5.56	5.56	0.83823	TRAF-type (1);TRAF-like (1);MATH (3);	0.051191	0.85682	D	0.000000	T	0.46268	0.1384	L	0.35644	1.08	0.58432	D	0.999995	D;P;D	0.89917	1.0;0.931;1.0	D;B;P	0.62955	0.909;0.247;0.882	T	0.34576	-0.9823	10	0.56958	D	0.05	-23.6137	19.6059	0.95582	0.0:1.0:0.0:0.0	.	423;481;506	Q13114-2;A6NHG8;Q13114	.;.;TRAF3_HUMAN	C	506;481;506;423	ENSP00000376500:R506C;ENSP00000328003:R481C;ENSP00000445998:R423C	ENSP00000328003:R481C	R	+	1	0	TRAF3	102441683	1.000000	0.71417	0.160000	0.22671	0.005000	0.04900	4.768000	0.62293	2.658000	0.90341	0.650000	0.86243	CGT	.	.	none		0.522	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
ERMARD	55780	hgsc.bcm.edu	37	6	170181516	170181516	+	Silent	SNP	A	A	G	rs2274952	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:170181516A>G	ENST00000366773.3	+	18	1977	c.1944A>G	c.(1942-1944)acA>acG	p.T648T	ERMARD_ENST00000366772.2_Silent_p.T601T|ERMARD_ENST00000392095.4_Silent_p.T522T|ERMARD_ENST00000588451.1_Silent_p.T512T|ERMARD_ENST00000418781.3_Silent_p.T575T	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	648					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TCAATCTTACACATACAGCTT	0.348													A|||	245	0.0489217	0.0015	0.0375	5008	,	,		17763	0.0188		0.0199	False		,,,				2504	0.182				p.T648T		Atlas-SNP	.											.	C6orf70	63	.	0			c.A1944G						PASS	.	A		33,4373	39.2+/-71.8	0,33,2170	95.0	86.0	89.0		1944	-6.7	0.0	6	dbSNP_100	89	253,8347	99.5+/-161.0	5,243,4052	no	coding-synonymous	C6orf70	NM_018341.1		5,276,6222	GG,GA,AA		2.9419,0.749,2.199		648/679	170181516	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	55780	exon18			TCTTACACATACA	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.1944A>G	6.37:g.170181516A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Silent	SNP	ENST00000366773.3	37	CCDS34576.1																																																																																			A|0.974;G|0.026	0.026	strong		0.348	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
PAK7	57144	hgsc.bcm.edu	37	20	9520142	9520142	+	Silent	SNP	G	G	A	rs12329540	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:9520142G>A	ENST00000378429.3	-	11	2673	c.2127C>T	c.(2125-2127)atC>atT	p.I709I	PAK7_ENST00000353224.5_Silent_p.I709I|PAK7_ENST00000378423.1_Silent_p.I709I	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	709					apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			TGAGGGGGACGATGCAAGACG	0.493													G|||	215	0.0429313	0.0015	0.0735	5008	,	,		19431	0.0		0.1322	False		,,,				2504	0.0297				p.I709I		Atlas-SNP	.											.	PAK7	194	.	0			c.C2127T						PASS	.	G	,	150,4256	101.2+/-139.8	3,144,2056	241.0	220.0	227.0		2127,2127	-3.4	1.0	20	dbSNP_120	227	1375,7225	267.9+/-287.5	117,1141,3042	no	coding-synonymous,coding-synonymous	PAK7	NM_020341.3,NM_177990.2	,	120,1285,5098	AA,AG,GG		15.9884,3.4044,11.7254	,	709/720,709/720	9520142	1525,11481	2203	4300	6503	SO:0001819	synonymous_variant	57144	exon10			GGGGACGATGCAA	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"""p21(CDKN1A)-activated kinase 7"""			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.2127C>T	20.37:g.9520142G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	109	42	0.385321	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Silent	SNP	ENST00000378429.3	37	CCDS13107.1																																																																																			G|0.907;A|0.093	0.093	strong		0.493	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
SOWAHD	347454	hgsc.bcm.edu	37	X	118893413	118893413	+	Silent	SNP	T	T	C	rs2782225		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:118893413T>C	ENST00000343905.3	+	1	838	c.783T>C	c.(781-783)agT>agC	p.S261S		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	261																	ACAACAGCAGTGGCACCACTG	0.687													C|||	2433	0.644503	0.559	0.5072	3775	,	,		11187	0.374		0.495	False		,,,				2504	0.4775				p.S261S		Atlas-SNP	.											.	.	.	.	0			c.T783C						PASS	.	C		2802,848		940,530,392,82,154	8.0	11.0	10.0		783	2.1	0.2	X	dbSNP_100	10	4152,2337		967,1078,1140,321,617	no	coding-synonymous	ANKRD58	NM_001105576.2		1907,1608,1532,403,771	CC,CT,C,TT,T		36.0148,23.2329,31.4134		261/316	118893413	6954,3185	2098	4123	6221	SO:0001819	synonymous_variant	347454	exon1			CAGCAGTGGCACC		CCDS43984.1	Xq24	2013-01-10	2012-01-12	2012-01-12	ENSG00000187808	ENSG00000187808		"""Ankyrin repeat domain containing"""	32960	protein-coding gene	gene with protein product			"""ankyrin repeat domain 58"""	ANKRD58		22234889	Standard	NM_001105576		Approved		uc010nql.3	A6NJG2	OTTHUMG00000159606	ENST00000343905.3:c.783T>C	X.37:g.118893413T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_001105576		Silent	SNP	ENST00000343905.3	37	CCDS43984.1																																																																																			T|0.366;C|0.634	0.634	strong		0.687	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576	
SAGE1	55511	hgsc.bcm.edu	37	X	134994005	134994005	+	Missense_Mutation	SNP	T	T	C	rs4829799	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:134994005T>C	ENST00000370709.3	+	17	2414	c.2414T>C	c.(2413-2415)tTg>tCg	p.L805S	SAGE1_ENST00000535938.1_Missense_Mutation_p.L805S|SAGE1_ENST00000537770.1_Missense_Mutation_p.L429S|SAGE1_ENST00000324447.3_Missense_Mutation_p.L805S			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	805			L -> S (in dbSNP:rs4829799). {ECO:0000269|PubMed:10919659}.			nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GTAATGTCTTTGGTGGAAACT	0.373													N|||	611	0.161854	0.0681	0.1585	3775	,	,		15825	0.1012		0.2058	False		,,,				2504	0.1043				p.L805S		Atlas-SNP	.											.	SAGE1	160	.	0			c.T2414C						PASS	.	C	SER/LEU	557,3278		30,426,71,1176,500	95.0	86.0	89.0		2414	2.7	0.0	X	dbSNP_111	89	1753,4975		188,922,455,1318,1417	yes	missense	SAGE1	NM_018666.2	145	218,1348,526,2494,1917	CC,CT,C,TT,T		26.0553,14.5241,21.8688	benign	805/905	134994005	2310,8253	2203	4300	6503	SO:0001583	missense	55511	exon18			TGTCTTTGGTGGA	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.2414T>C	X.37:g.134994005T>C	ENSP00000359743:p.Leu805Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	115	25	0.217391	NM_018666	Q5JNW0	Missense_Mutation	SNP	ENST00000370709.3	37	CCDS14652.1	310	0.18685955394816153	24	0.05	41	0.12732919254658384	38	0.07196969696969698	105	0.16153846153846155	C	0.014	-1.605379	0.00842	0.145241	0.260553	ENSG00000181433	ENST00000324447;ENST00000535938;ENST00000537770;ENST00000370709	T;T;T;T	0.29397	1.57;1.57;1.62;1.57	2.67	2.67	0.31697	.	0.944741	0.08754	N	0.898686	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.42155	-0.9468	9	0.07482	T	0.82	.	8.6217	0.33864	0.0:0.8737:0.0:0.1263	rs4829799;rs17221796;rs52801822;rs61577447;rs4829799	429;805	F5H2Z8;Q9NXZ1	.;SAGE1_HUMAN	S	805;805;429;805	ENSP00000323191:L805S;ENSP00000445959:L805S;ENSP00000438276:L429S;ENSP00000359743:L805S	ENSP00000323191:L805S	L	+	2	0	SAGE1	134821671	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	0.100000	0.15231	0.146000	0.19002	-1.150000	0.01838	TTG	0|0.015;C|0.189	0.189	strong		0.373	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
WDR92	116143	hgsc.bcm.edu	37	2	68364478	68364478	+	Missense_Mutation	SNP	T	T	C	rs13009282	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:68364478T>C	ENST00000295121.6	-	6	837	c.721A>G	c.(721-723)Atg>Gtg	p.M241V	WDR92_ENST00000409164.1_Missense_Mutation_p.M241V|WDR92_ENST00000406245.2_Missense_Mutation_p.M140V|WDR92_ENST00000492039.2_5'UTR|RP11-474G23.1_ENST00000406334.3_3'UTR	NM_138458.3	NP_612467.1	Q96MX6	WDR92_HUMAN	WD repeat domain 92	241			M -> V (in dbSNP:rs13009282).		apoptotic process (GO:0006915)|histone lysine methylation (GO:0034968)		methylated histone binding (GO:0035064)	p.M241V(1)		endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|stomach(1)	12						TGTGTTCTCATGTCAAAAACA	0.373													T|||	888	0.177316	0.1641	0.1988	5008	,	,		18917	0.1538		0.2177	False		,,,				2504	0.1626				p.M241V		Atlas-SNP	.											WDR92,NS,carcinoma,0,1	WDR92	21	1	1	Substitution - Missense(1)	stomach(1)	c.A721G						scavenged	.	T	VAL/MET	703,3703	293.6+/-282.7	62,579,1562	148.0	141.0	143.0		721	4.8	1.0	2	dbSNP_121	143	2215,6385	376.4+/-338.1	274,1667,2359	yes	missense	WDR92	NM_138458.2	21	336,2246,3921	CC,CT,TT		25.7558,15.9555,22.4358	benign	241/358	68364478	2918,10088	2203	4300	6503	SO:0001583	missense	116143	exon6			TTCTCATGTCAAA	AK056303	CCDS1884.1, CCDS58712.1	2p14	2013-01-09			ENSG00000243667	ENSG00000243667		"""WD repeat domain containing"""	25176	protein-coding gene	gene with protein product		610729				16487927	Standard	NM_138458		Approved	FLJ31741, Monad	uc002see.2	Q96MX6	OTTHUMG00000152561	ENST00000295121.6:c.721A>G	2.37:g.68364478T>C	ENSP00000295121:p.Met241Val	Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	107	58	0.542056	NM_001256476	Q96CR6	Missense_Mutation	SNP	ENST00000295121.6	37	CCDS1884.1	379	0.17353479853479853	64	0.13008130081300814	60	0.16574585635359115	89	0.1555944055944056	166	0.21899736147757257	T	12.86	2.063138	0.36373	0.159555	0.257558	ENSG00000243667	ENST00000295121;ENST00000406245;ENST00000409164	D;T;T	0.89552	-2.53;1.71;-0.02	6.03	4.81	0.61882	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.132323	0.47852	D	0.000212	T	0.00073	0.0002	L	0.45137	1.4	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.04961	-1.0915	9	0.33940	T	0.23	.	12.2344	0.54508	0.1273:0.0:0.0:0.8727	rs13009282;rs17589505;rs52821939;rs60739059;rs13009282	241	Q96MX6	WDR92_HUMAN	V	241;140;241	ENSP00000295121:M241V;ENSP00000384518:M140V;ENSP00000386746:M241V	ENSP00000295121:M241V	M	-	1	0	WDR92	68217982	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.431000	0.52814	2.308000	0.77769	0.533000	0.62120	ATG	T|0.804;C|0.196	0.196	strong		0.373	WDR92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251754.2	NM_138458	
TACC2	10579	hgsc.bcm.edu	37	10	123842523	123842523	+	Missense_Mutation	SNP	G	G	A	rs11200385	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123842523G>A	ENST00000369005.1	+	4	848	c.508G>A	c.(508-510)Gtc>Atc	p.V170I	TACC2_ENST00000334433.3_Missense_Mutation_p.V170I|TACC2_ENST00000515603.1_Missense_Mutation_p.V170I|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.V170I|TACC2_ENST00000515273.1_Missense_Mutation_p.V170I	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	170			V -> I (in dbSNP:rs11200385).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GATTGCTGCCGTCCCCAGTGC	0.587													A|||	1028	0.205272	0.3101	0.1902	5008	,	,		18513	0.0992		0.2087	False		,,,				2504	0.18				p.V170I		Atlas-SNP	.											.	TACC2	271	.	0			c.G508A						PASS	.	A	,ILE/VAL	1503,2903	661.7+/-400.9	258,987,958	30.0	30.0	30.0		,508	-0.5	0.0	10	dbSNP_120	30	1917,6683	713.6+/-406.0	212,1493,2595	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,29	470,2480,3553	AA,AG,GG		22.2907,34.1126,26.2956	,benign	,170/2949	123842523	3420,9586	2203	4300	6503	SO:0001583	missense	10579	exon4			GCTGCCGTCCCCA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.508G>A	10.37:g.123842523G>A	ENSP00000358001:p.Val170Ile	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	456	0.2087912087912088	153	0.31097560975609756	80	0.22099447513812154	69	0.12062937062937062	154	0.20316622691292877	A	1.688	-0.504694	0.04261	0.341126	0.222907	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03801	3.87;3.8;3.8;3.87;3.8	5.07	-0.534	0.11883	.	0.920070	0.08828	N	0.887732	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.04013	0.001;0.001;0.001	T	0.46162	-0.9211	9	0.10902	T	0.67	-1.1282	5.5726	0.17204	0.3491:0.0:0.5201:0.1308	rs11200385;rs57010222;rs11200385	170;170;170	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	I	170;170;170;170;170;160	ENSP00000358001:V170I;ENSP00000424467:V170I;ENSP00000427618:V170I;ENSP00000334280:V170I;ENSP00000395048:V170I	ENSP00000334280:V170I	V	+	1	0	TACC2	123832513	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.846000	0.04336	-0.347000	0.08299	-1.266000	0.01441	GTC	G|0.763;A|0.237	0.237	strong		0.587	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
OR10A2	341276	hgsc.bcm.edu	37	11	6891113	6891113	+	Missense_Mutation	SNP	A	A	G	rs3930075	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6891113A>G	ENST00000307322.4	+	1	190	c.128A>G	c.(127-129)cAc>cGc	p.H43R		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	43			H -> R (in dbSNP:rs3930075).			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)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCCATGCTACACAGCCCCATG	0.483													-|||	1624	0.324281	0.2073	0.3732	5008	,	,		22090	0.3135		0.3569	False		,,,				2504	0.4254				p.H43R		Atlas-SNP	.											.	OR10A2	55	.	0			c.A128G						PASS	.	A	ARG/HIS	885,3517	341.8+/-306.9	89,707,1405	183.0	174.0	177.0		128	4.3	1.0	11	dbSNP_108	177	3209,5383	485.7+/-371.7	606,1997,1693	no	missense	OR10A2	NM_001004460.1	29	695,2704,3098	GG,GA,AA		37.3487,20.1045,31.5068	benign	43/304	6891113	4094,8900	2201	4296	6497	SO:0001583	missense	341276	exon1			TGCTACACAGCCC	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"""GPCR / Class A : Olfactory receptors"""	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.128A>G	11.37:g.6891113A>G	ENSP00000303862:p.His43Arg	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	227	87	0.38326	NM_001004460	B2RNL9|Q6IFG9	Missense_Mutation	SNP	ENST00000307322.4	37	CCDS31415.1	671	0.30723443223443225	97	0.19715447154471544	128	0.35359116022099446	176	0.3076923076923077	270	0.3562005277044855	a	6.758	0.508631	0.12883	0.201045	0.373487	ENSG00000170790	ENST00000307322	T	0.15952	2.38	4.3	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.117044	0.38897	N	0.001530	T	0.00012	0.0000	M	0.74467	2.265	0.38045	P	0.06440299999999999	B	0.06786	0.001	B	0.06405	0.002	T	0.37314	-0.9711	9	0.66056	D	0.02	.	6.6225	0.22810	0.8936:0.0:0.1064:0.0	rs3930075;rs3963528	43	Q9H208	O10A2_HUMAN	R	43	ENSP00000303862:H43R	ENSP00000303862:H43R	H	+	2	0	OR10A2	6847689	0.681000	0.27614	1.000000	0.80357	0.165000	0.22458	5.036000	0.64164	1.942000	0.56320	0.491000	0.48974	CAC	.	.	weak		0.483	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460	
POU5F1B	5462	hgsc.bcm.edu	37	8	128428638	128428638	+	Missense_Mutation	SNP	G	G	A	rs6998061	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:128428638G>A	ENST00000465342.2	+	2	1684	c.527G>A	c.(526-528)gGg>gAg	p.G176E	POU5F1B_ENST00000391675.1_Missense_Mutation_p.G176E|CASC8_ENST00000502082.1_RNA|CASC8_ENST00000501396.1_RNA|CASC8_ENST00000523825.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	176	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.		G -> E (in dbSNP:rs6998061). {ECO:0000269|PubMed:21341266}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						GTTCTATTTGGGAAGGTGTTC	0.532													g|||	1870	0.373403	0.1172	0.3991	5008	,	,		17368	0.5565		0.4314	False		,,,				2504	0.453				p.G176E		Atlas-SNP	.											.	POU5F1B	32	.	0			c.G527A	GRCh37	CM073275	POU5F1B	M	rs6998061	PASS	.	G	GLU/GLY	198,1186		14,170,508	77.0	88.0	85.0		527	1.1	1.0	8	dbSNP_116	85	1316,1866		261,794,536	no	missense	POU5F1B	NM_001159542.1	98	275,964,1044	AA,AG,GG		41.3576,14.3064,33.1581	probably-damaging	176/360	128428638	1514,3052	692	1591	2283	SO:0001583	missense	5462	exon1			TATTTGGGAAGGT	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"""Homeoboxes / POU class"""	9223	protein-coding gene	gene with protein product		615739	"""POU domain class 5, transcription factor 1 pseudogene 1"", ""POU class 5 homeobox 1 pseudogene 1"""	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.527G>A	8.37:g.128428638G>A	ENSP00000419298:p.Gly176Glu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	50	0.769231	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Missense_Mutation	SNP	ENST00000465342.2	37	CCDS55274.1	894	0.40934065934065933	74	0.15040650406504066	136	0.3756906077348066	336	0.5874125874125874	348	0.45910290237467016	G	21.1	4.092755	0.76756	0.143064	0.413576	ENSG00000212993	ENST00000465342;ENST00000391675	D;D	0.82803	-1.65;-1.65	1.14	1.14	0.20703	POU-specific (3);Lambda repressor-like, DNA-binding (2);	0.000000	0.50627	D	0.000108	T	0.00012	0.0000	M	0.79258	2.445	0.09310	P	0.999999568388	P	0.46457	0.878	P	0.54706	0.759	T	0.43925	-0.9361	9	0.56958	D	0.05	.	8.3083	0.32055	0.0:0.0:1.0:0.0	rs6998061;rs60145230	176	Q06416	P5F1B_HUMAN	E	176	ENSP00000419298:G176E;ENSP00000375557:G176E	ENSP00000375557:G176E	G	+	2	0	POU5F1B	128497820	1.000000	0.71417	0.997000	0.53966	0.578000	0.36192	4.714000	0.61902	0.968000	0.38212	0.134000	0.15878	GGG	.	.	weak		0.532	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720673	135720673	+	Silent	SNP	T	T	C	rs9872542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:135720673T>C	ENST00000264977.3	+	2	950	c.333T>C	c.(331-333)gaT>gaC	p.D111D	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	111					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ACTTAAAGGATATTGCAGGAG	0.423													C|||	936	0.186901	0.202	0.1455	5008	,	,		21751	0.0288		0.2783	False		,,,				2504	0.2648				p.D111D		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T333C						PASS	.	C	,	954,3452	727.3+/-409.8	99,756,1348	42.0	43.0	43.0		,333	5.8	1.0	3	dbSNP_119	43	2713,5885	678.3+/-403.4	417,1879,2003	no	intron,coding-synonymous	PPP2R3A	NM_001190447.1,NM_002718.4	,	516,2635,3351	CC,CT,TT		31.5538,21.6523,28.199	,	,111/1151	135720673	3667,9337	2203	4299	6502	SO:0001819	synonymous_variant	5523	exon2			AAAGGATATTGCA	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.333T>C	3.37:g.135720673T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	37	CCDS3087.1																																																																																			T|0.802;C|0.198	0.198	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
ZNF880	400713	hgsc.bcm.edu	37	19	52887437	52887437	+	Missense_Mutation	SNP	A	A	C	rs8104812	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52887437A>C	ENST00000422689.2	+	4	619	c.604A>C	c.(604-606)Aat>Cat	p.N202H		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	202					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						ACTTGCTAACAATCAAGTAAT	0.373													C|||	1897	0.378794	0.2405	0.379	5008	,	,		20813	0.3462		0.4205	False		,,,				2504	0.5562				p.N202H		Atlas-SNP	.											.	ZNF880	45	.	0			c.A604C						PASS	.	C	HIS/ASN	392,992		53,286,353	47.0	46.0	46.0		604	0.7	0.0	19	dbSNP_116	46	1214,1968		222,770,599	yes	missense	ZNF880	NM_001145434.1	68	275,1056,952	CC,CA,AA		38.1521,28.3237,35.173	benign	202/578	52887437	1606,2960	692	1591	2283	SO:0001583	missense	400713	exon4			GCTAACAATCAAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.604A>C	19.37:g.52887437A>C	ENSP00000406318:p.Asn202His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	745	0.3411172161172161	119	0.241869918699187	138	0.3812154696132597	177	0.3094405594405594	311	0.4102902374670185	C	0.005	-2.223193	0.00283	0.283237	0.381521	ENSG00000221923	ENST00000422689	T	0.12879	2.64	1.84	0.682	0.17992	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00005	-3.26	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41698	-0.9494	7	.	.	.	.	5.3499	0.16030	0.2302:0.5451:0.2247:0.0	rs8104812;rs17736363;rs8104812	202	Q6PDB4	ZN880_HUMAN	H	202	ENSP00000406318:N202H	.	N	+	1	0	ZNF880	57579249	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.069000	0.14552	-0.288000	0.09051	-1.160000	0.01791	AAT	A|0.655;C|0.345	0.345	strong		0.373	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
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 GAIIx	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	RP11-380L11.3_ENST00000602292.1_RNA|DNAH10_ENST00000538983.1_3'UTR|DNAH10OS_ENST00000514254.2_Intron|CCDC92_ENST00000544798.1_Intron	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		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	57	27	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		
CPA4	51200	hgsc.bcm.edu	37	7	129950740	129950740	+	Missense_Mutation	SNP	G	G	T	rs2171492	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:129950740G>T	ENST00000222482.4	+	9	935	c.907G>T	c.(907-909)Ggc>Tgc	p.G303C	CPA4_ENST00000445470.2_Missense_Mutation_p.G270C|CPA4_ENST00000493259.1_Missense_Mutation_p.G199C	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	303			G -> C (in dbSNP:rs2171492).		histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					GAATTTCAAGGGCTTCATCGA	0.512													T|||	1586	0.316693	0.2065	0.3156	5008	,	,		20193	0.374		0.3638	False		,,,				2504	0.3589				p.G303C		Atlas-SNP	.											.	CPA4	47	.	0			c.G907T						PASS	.	T	CYS/GLY,CYS/GLY	1003,3403	730.5+/-410.2	123,757,1323	148.0	142.0	144.0		808,907	0.5	1.0	7	dbSNP_96	144	3310,5290	645.2+/-400.1	644,2022,1634	yes	missense,missense	CPA4	NM_001163446.1,NM_016352.3	159,159	767,2779,2957	TT,TG,GG		38.4884,22.7644,33.1616	benign,benign	270/389,303/422	129950740	4313,8693	2203	4300	6503	SO:0001583	missense	51200	exon9			TTCAAGGGCTTCA	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.907G>T	7.37:g.129950740G>T	ENSP00000222482:p.Gly303Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	37	CCDS5818.1	719	0.3292124542124542	108	0.21951219512195122	122	0.3370165745856354	227	0.3968531468531469	262	0.34564643799472294	T	12.75	2.032247	0.35893	0.227644	0.384884	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.11063	2.81;2.81;2.81	6.17	0.479	0.16796	Peptidase M14, carboxypeptidase A (2);	0.437819	0.26746	N	0.022720	T	0.00012	0.0000	N	0.16130	0.375	0.52099	P	5.100000000002325E-5	B;B	0.15141	0.012;0.004	B;B	0.28849	0.095;0.021	T	0.49031	-0.8981	9	0.51188	T	0.08	.	11.7939	0.52088	0.1397:0.0:0.6312:0.2291	rs2171492;rs17327657;rs52837974;rs58222478;rs2171492	270;303	B7Z576;Q9UI42	.;CBPA4_HUMAN	C	270;303;108;199	ENSP00000412947:G270C;ENSP00000222482:G303C;ENSP00000419660:G199C	ENSP00000222482:G303C	G	+	1	0	CPA4	129737976	0.998000	0.40836	0.992000	0.48379	0.691000	0.40173	0.552000	0.23376	-0.068000	0.12953	-1.131000	0.01979	GGC	G|0.677;T|0.323	0.323	strong		0.512	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
C1orf101	257044	hgsc.bcm.edu	37	1	244735858	244735858	+	Silent	SNP	A	A	G	rs10927267	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:244735858A>G	ENST00000366534.4	+	11	1788	c.1734A>G	c.(1732-1734)acA>acG	p.T578T	C1orf101_ENST00000473875.1_3'UTR|C1orf101_ENST00000366533.4_Silent_p.T578T|C1orf101_ENST00000366531.3_Silent_p.T427T	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	578						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)			TAGCTTTCACAACAAAAGACA	0.393													a|||	1362	0.271965	0.4289	0.2464	5008	,	,		18269	0.373		0.0785	False		,,,				2504	0.1728				p.T578T		Atlas-SNP	.											C1orf101_ENST00000366534,NS,carcinoma,0,2	C1orf101	158	2	0			c.A1734G						PASS	.	A	,,	1693,2713	512.9+/-368.2	326,1041,836	120.0	107.0	111.0		1734,1281,1734	-4.1	0.0	1	dbSNP_120	111	765,7835	181.3+/-230.0	26,713,3561	no	coding-synonymous,coding-synonymous,coding-synonymous	C1orf101	NM_001130957.1,NM_001242340.1,NM_173807.4	,,	352,1754,4397	GG,GA,AA		8.8953,38.4249,18.899	,,	578/952,427/801,578/833	244735858	2458,10548	2203	4300	6503	SO:0001819	synonymous_variant	257044	exon11			TTTCACAACAAAA	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.1734A>G	1.37:g.244735858A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																			A|0.783;G|0.217	0.217	strong		0.393	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68041061	68041061	+	Missense_Mutation	SNP	G	G	A	rs61534804	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:68041061G>A	ENST00000329153.5	+	14	2161	c.2029G>A	c.(2029-2031)Ggg>Agg	p.G677R		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	677						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		GCAGGCCACCGGGCCTCCAGC	0.617													G|||	537	0.107228	0.0938	0.2046	5008	,	,		18719	0.0625		0.0905	False		,,,				2504	0.1196				p.G677R		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G2029A						PASS	.	G	ARG/GLY	294,3622		14,266,1678	24.0	24.0	24.0		2029	4.5	0.9	14	dbSNP_129	24	688,7544		32,624,3460	yes	missense	PLEKHH1	NM_020715.2	125	46,890,5138	AA,AG,GG		8.3576,7.5077,8.0836	benign	677/1365	68041061	982,11166	1958	4116	6074	SO:0001583	missense	57475	exon14			GCCACCGGGCCTC	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.2029G>A	14.37:g.68041061G>A	ENSP00000330278:p.Gly677Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	220	0.10073260073260074	42	0.08536585365853659	82	0.2265193370165746	30	0.05244755244755245	66	0.0870712401055409	G	17.79	3.475788	0.63737	0.075077	0.083576	ENSG00000054690	ENST00000329153	T	0.72394	-0.65	5.41	4.51	0.55191	.	0.174933	0.52532	N	0.000063	T	0.00073	0.0002	L	0.44542	1.39	0.09310	P	0.9999999999999999	D;B	0.64830	0.994;0.259	P;B	0.60286	0.872;0.018	T	0.08106	-1.0738	9	0.35671	T	0.21	.	8.6628	0.34103	0.2123:0.0:0.7877:0.0	rs61534804	192;677	Q9ULM0-2;Q9ULM0	.;PKHH1_HUMAN	R	677	ENSP00000330278:G677R	ENSP00000330278:G677R	G	+	1	0	PLEKHH1	67110814	0.963000	0.33076	0.918000	0.36340	0.734000	0.41952	1.912000	0.39946	1.507000	0.48752	0.591000	0.81541	GGG	G|0.898;A|0.102	0.102	strong		0.617	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
CATSPERD	257062	hgsc.bcm.edu	37	19	5778597	5778597	+	Silent	SNP	C	C	G	rs2305926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5778597C>G	ENST00000381624.3	+	22	2368	c.2307C>G	c.(2305-2307)gtC>gtG	p.V769V	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	769					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)		p.V769V(1)									GCAAGACGGTCTGCCAGTTCA	0.652													C|||	156	0.0311502	0.0	0.013	5008	,	,		15814	0.0843		0.0179	False		,,,				2504	0.045				p.V769V		Atlas-SNP	.											TMEM146,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.C2307G						PASS	.	C		20,4264		0,20,2122	55.0	63.0	60.0		2307	-5.7	0.0	19	dbSNP_100	60	123,8337		1,121,4108	no	coding-synonymous	TMEM146	NM_152784.3		1,141,6230	GG,GC,CC		1.4539,0.4669,1.1221		769/799	5778597	143,12601	2142	4230	6372	SO:0001819	synonymous_variant	257062	exon22			GACGGTCTGCCAG	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.2307C>G	19.37:g.5778597C>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	130	55	0.423077	NM_152784	Q6ZRP1	Silent	SNP	ENST00000381624.3	37	CCDS12149.2																																																																																			C|0.978;G|0.022	0.022	strong		0.652	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
OCA2	4948	hgsc.bcm.edu	37	15	28235773	28235773	+	Silent	SNP	C	C	T	rs1800404	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:28235773C>T	ENST00000354638.3	-	10	1220	c.1065G>A	c.(1063-1065)gcG>gcA	p.A355A	OCA2_ENST00000353809.5_Intron|OCA2_ENST00000382996.2_Silent_p.A355A	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	355					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CCAGCATGGCCGCCAGAGTTC	0.552									Oculocutaneous Albinism				C|||	2057	0.410743	0.1271	0.5793	5008	,	,		20099	0.3859		0.7863	False		,,,				2504	0.3139				p.A355A		Atlas-SNP	.											OCA2,colon,adenoma,-1,1	OCA2	173	1	0			c.G1065A						PASS	.	C		997,3409	370.3+/-319.5	125,747,1331	153.0	132.0	139.0		1065	-5.6	1.0	15	dbSNP_89	139	6792,1808	732.7+/-406.9	2672,1448,180	no	coding-synonymous	OCA2	NM_000275.2		2797,2195,1511	TT,TC,CC		21.0233,22.6282,40.1123		355/839	28235773	7789,5217	2203	4300	6503	SO:0001819	synonymous_variant	4948	exon10	Familial Cancer Database		CATGGCCGCCAGA		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1065G>A	15.37:g.28235773C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	51	0.944444	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																			C|0.469;T|0.530	0.530	strong		0.552	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919064	12919064	+	Missense_Mutation	SNP	T	T	G	rs3204790	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12919064T>G	ENST00000240189.2	+	2	287	c.200T>G	c.(199-201)gTa>gGa	p.V67G		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	67			V -> G (in dbSNP:rs3204790).		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)			p.V67G(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCCTCTGGTATCGCTGATG	0.557													.|||	934	0.186502	0.1437	0.1297	5008	,	,		22643	0.3333		0.1531	False		,,,				2504	0.1677				p.V67G		Atlas-SNP	.											PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	1	Substitution - Missense(1)	prostate(1)	c.T200G						scavenged	.	G	GLY/VAL	705,3697	757.4+/-412.7	76,553,1572	144.0	150.0	148.0		200	0.8	0.1	1	dbSNP_105	148	1295,7297	751.5+/-407.4	117,1061,3118	no	missense	PRAMEF2	NM_023014.1	109	193,1614,4690	GG,GT,TT		15.0722,16.0154,15.3917	benign	67/475	12919064	2000,10994	2201	4296	6497	SO:0001583	missense	65122	exon2			CTCTGGTATCGCT		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.200T>G	1.37:g.12919064T>G	ENSP00000240189:p.Val67Gly	Somatic	161	3	0.0186335		WXS	Illumina HiSeq	Phase_I	219	70	0.319635	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	480	0.21978021978021978	76	0.15447154471544716	59	0.16298342541436464	188	0.32867132867132864	157	0.20712401055408972	G	0.004	-2.285905	0.00251	0.160154	0.150722	ENSG00000120952	ENST00000240189	T	0.04049	3.72	0.842	0.842	0.18927	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00004	-3.36	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.37220	-0.9715	9	0.02654	T	1	.	4.0419	0.09755	0.0:0.0:0.5905:0.4095	rs3204790;rs17038653	67	O60811	PRAM2_HUMAN	G	67	ENSP00000240189:V67G	ENSP00000240189:V67G	V	+	2	0	PRAMEF2	12841651	0.017000	0.18338	0.148000	0.22405	0.037000	0.13140	-0.608000	0.05641	-0.047000	0.13423	-1.044000	0.02363	GTA	T|0.824;G|0.176	0.176	strong		0.557	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
SMEK1	55671	hgsc.bcm.edu	37	14	91948043	91948043	+	Silent	SNP	T	T	C	rs17127374	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:91948043T>C	ENST00000554943.1	-	4	907	c.792A>G	c.(790-792)acA>acG	p.T264T	SMEK1_ENST00000428424.2_Intron|SMEK1_ENST00000555462.1_Intron|SMEK1_ENST00000337238.4_Silent_p.T264T|SMEK1_ENST00000554684.1_Silent_p.T264T			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	264					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		GAACTCTGTATGTCTGATGAA	0.348													T|||	233	0.0465256	0.0204	0.0605	5008	,	,		17946	0.003		0.1163	False		,,,				2504	0.045				p.T264T		Atlas-SNP	.											.	SMEK1	94	.	0			c.A792G						PASS	.	T		163,4243	109.5+/-147.8	6,151,2046	158.0	147.0	151.0		792	-2.8	1.0	14	dbSNP_123	151	896,7704	199.7+/-243.7	53,790,3457	yes	coding-synonymous	SMEK1	NM_032560.4		59,941,5503	CC,CT,TT		10.4186,3.6995,8.1424		264/821	91948043	1059,11947	2203	4300	6503	SO:0001819	synonymous_variant	55671	exon5			TCTGTATGTCTGA	AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"""KIAA2010"""	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.792A>G	14.37:g.91948043T>C		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	229	228	0.995633	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Silent	SNP	ENST00000554943.1	37		113	0.051739926739926737	10	0.02032520325203252	24	0.06629834254143646	3	0.005244755244755245	76	0.10026385224274406	T	8.401	0.841920	0.16963	0.036995	0.104186	ENSG00000100796	ENST00000555470	.	.	.	6.03	-2.82	0.05787	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18840	-1.0324	4	.	.	.	-14.8432	1.3143	0.02104	0.1967:0.2318:0.1018:0.4697	rs17127374;rs52791686;rs59536884;rs17127374	.	.	.	V	59	.	.	I	-	1	0	SMEK1	91017796	0.980000	0.34600	0.992000	0.48379	0.977000	0.68977	0.101000	0.15251	-0.337000	0.08426	-0.313000	0.08912	ATA	T|0.932;C|0.068	0.068	strong		0.348	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560	
KRTAP12-1	353332	hgsc.bcm.edu	37	21	46101934	46101934	+	Silent	SNP	G	G	A	rs56135164	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46101934G>A	ENST00000391617.1	-	1	144	c.105C>T	c.(103-105)tgC>tgT	p.C35C	TSPEAR_ENST00000323084.4_Intron	NM_181686.1	NP_859014.1	P59990	KR121_HUMAN	keratin associated protein 12-1	35	14 X 5 AA approximate repeats.					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|skin(2)	5						TCACGGGCACGCACACGGAGG	0.687													A|||	171	0.0341454	0.0234	0.0476	5008	,	,		17071	0.001		0.0736	False		,,,				2504	0.0327				p.C35C		Atlas-SNP	.											.	KRTAP12-1	9	.	0			c.C105T						PASS	.	A	,	100,4278		1,98,2090	58.0	68.0	64.0		,105	-1.7	0.0	21	dbSNP_129	64	553,7991		19,515,3738	no	intron,coding-synonymous	TSPEAR,KRTAP12-1	NM_144991.2,NM_181686.1	,	20,613,5828	AA,AG,GG		6.4724,2.2841,5.0534	,	,35/97	46101934	653,12269	2189	4272	6461	SO:0001819	synonymous_variant	353332	exon1			GGGCACGCACACG	AJ566388	CCDS42966.1	21q22.3	2006-03-13			ENSG00000187175	ENSG00000187175		"""Keratin associated proteins"""	20529	protein-coding gene	gene with protein product							Standard	NM_181686		Approved	KRTAP12.1, KAP12.1	uc002zfv.3	P59990	OTTHUMG00000057639	ENST00000391617.1:c.105C>T	21.37:g.46101934G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_181686	Q0VAS3	Silent	SNP	ENST00000391617.1	37	CCDS42966.1																																																																																			G|0.954;A|0.046	0.046	strong		0.687	KRTAP12-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128043.1	NM_181686	
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	rs28989168	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152975715C>T	ENST00000295367.4	+	2	261	c.219C>T	c.(217-219)ggC>ggT	p.G73G	SPRR3_ENST00000542696.1_Silent_p.G73G|SPRR3_ENST00000331860.3_Silent_p.G73G	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	73	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGAGCCAGGCTGTACCAAGG	0.577													T|||	2	0.000399361	0.0015	0.0	5008	,	,		14904	0.0		0.0	False		,,,				2504	0.0				p.G73G		Atlas-SNP	.											SPRR3,colon,carcinoma,0,3	SPRR3	45	3	0			c.C219T						PASS	.						42.0	39.0	40.0					1																	152975715		2182	4268	6450	SO:0001819	synonymous_variant	6707	exon2			GCCAGGCTGTACC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.219C>T	1.37:g.152975715C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	55	14	0.254545	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			.	.	none		0.577	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
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 GAIIx	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		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	29	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	
GM2A	2760	hgsc.bcm.edu	37	5	150639409	150639409	+	Missense_Mutation	SNP	A	A	G	rs153477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150639409A>G	ENST00000357164.3	+	2	500	c.175A>G	c.(175-177)Atc>Gtc	p.I59V		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	59			I -> V (in dbSNP:rs153477). {ECO:0000269|PubMed:10364519, ECO:0000269|PubMed:1427911, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1915857, ECO:0000269|PubMed:2059210, ECO:0000269|PubMed:2753159}.		ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGACCCCATCATCGTTCCTGG	0.582													A|||	3325	0.663938	0.5666	0.7392	5008	,	,		17677	0.6637		0.6471	False		,,,				2504	0.7597				p.I59V		Atlas-SNP	.											.	GM2A	24	.	0			c.A175G						PASS	.	A	VAL/ILE,VAL/ILE	2528,1878	630.9+/-395.5	735,1058,410	67.0	58.0	61.0		175,175	-0.6	0.0	5	dbSNP_79	61	5388,3212	651.7+/-400.9	1685,2018,597	yes	missense,missense	GM2A	NM_000405.4,NM_001167607.1	29,29	2420,3076,1007	GG,GA,AA		37.3488,42.6237,39.1358	benign,benign	59/194,59/187	150639409	7916,5090	2203	4300	6503	SO:0001583	missense	2760	exon2			CCCATCATCGTTC		CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"""cerebroside sulfate activator protein"", ""sphingolipid activator protein 3"""	613109	"""GM2 ganglioside activator protein"""			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.175A>G	5.37:g.150639409A>G	ENSP00000349687:p.Ile59Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_001167607	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Missense_Mutation	SNP	ENST00000357164.3	37	CCDS4313.1	1393|1393	0.6378205128205128|0.6378205128205128	265|265	0.5386178861788617|0.5386178861788617	255|255	0.7044198895027625|0.7044198895027625	389|389	0.6800699300699301|0.6800699300699301	484|484	0.6385224274406333|0.6385224274406333	A|A	4.333|4.333	0.061288|0.061288	0.08339|0.08339	0.573763|0.573763	0.626512|0.626512	ENSG00000196743|ENSG00000196743	ENST00000523004|ENST00000523466;ENST00000357164	.|T;T	.|0.73681	.|-0.77;-0.77	5.36|5.36	-0.554|-0.554	0.11811|0.11811	.|MD-2-related lipid-recognition (1);	.|1.307600	.|0.04943	.|N	.|0.458931	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03324|0.03324	-0.35|-0.35	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.40590|0.40590	-0.9555|-0.9555	4|9	.|0.02654	.|T	.|1	0.5447|0.5447	2.2769|2.2769	0.04104|0.04104	0.2498:0.3408:0.2956:0.1138|0.2498:0.3408:0.2956:0.1138	rs153477;rs976512;rs3188751;rs17850475;rs52834919;rs59024596;rs153477|rs153477;rs976512;rs3188751;rs17850475;rs52834919;rs59024596;rs153477	.|59	.|P17900	.|SAP3_HUMAN	R|V	17|74;59	.|ENSP00000429100:I74V;ENSP00000349687:I59V	.|ENSP00000349687:I59V	H|I	+|+	2|1	0|0	GM2A|GM2A	150619602|150619602	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.998000|-0.998000	0.03701|0.03701	-0.230000|-0.230000	0.09840|0.09840	-1.999000|-1.999000	0.00445|0.00445	CAT|ATC	A|0.380;G|0.620	0.620	strong		0.582	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405	
HN1	51155	hgsc.bcm.edu	37	17	73142764	73142764	+	Missense_Mutation	SNP	G	G	A	rs62620707	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73142764G>A	ENST00000409753.3	-	4	598	c.313C>T	c.(313-315)Cat>Tat	p.H105Y	Y_RNA_ENST00000516233.1_RNA|HN1_ENST00000405458.3_Missense_Mutation_p.H59Y|HN1_ENST00000465454.1_5'Flank|HN1_ENST00000392566.2_Intron|HN1_ENST00000581874.1_3'UTR|RP11-649A18.4_ENST00000579554.1_RNA|HN1_ENST00000470924.1_Missense_Mutation_p.H59Y|HN1_ENST00000482348.1_Missense_Mutation_p.H59Y|HN1_ENST00000476258.1_Missense_Mutation_p.H59Y|HN1_ENST00000481647.1_Missense_Mutation_p.H59Y|HN1_ENST00000356033.4_Intron	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	105					developmental process (GO:0032502)	nucleus (GO:0005634)		p.H105Y(1)	HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					TACTTACCATGAATATCACCT	0.358													G|||	51	0.0101837	0.0008	0.013	5008	,	,		18869	0.0		0.0328	False		,,,				2504	0.0082				p.H105Y		Atlas-SNP	.											HN1_ENST00000409753,NS,carcinoma,0,1	HN1	17	1	1	Substitution - Missense(1)	prostate(1)	c.C313T						PASS	.	G	,TYR/HIS,TYR/HIS	19,3599		0,19,1790	39.0	37.0	38.0		,175,313	5.4	1.0	17	dbSNP_129	38	221,7881		1,219,3831	yes	intron,missense,missense	HN1	NM_001002032.1,NM_001002033.1,NM_016185.2	,83,83	1,238,5621	AA,AG,GG		2.7277,0.5252,2.0478	,,	,59/109,105/155	73142764	240,11480	1809	4051	5860	SO:0001583	missense	51155	exon4			TACCATGAATATC	AF086910	CCDS32729.1, CCDS45771.1, CCDS45772.1	17q25.1	2013-09-20			ENSG00000189159	ENSG00000189159			14569	protein-coding gene	gene with protein product	"""androgen-regulated protein 2"""					15094197	Standard	NM_001002032		Approved	ARM2, HN1A	uc002jnb.1	Q9UK76	OTTHUMG00000154521	ENST00000409753.3:c.313C>T	17.37:g.73142764G>A	ENSP00000387059:p.His105Tyr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_016185	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	37	CCDS45771.1	31	0.014194139194139194	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	24	0.0316622691292876	G	4.680	0.126358	0.08931	0.005252	0.027277	ENSG00000189159	ENST00000405458;ENST00000409753	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	T	0.16428	0.0395	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10314	-1.0635	8	0.13470	T	0.59	.	14.937	0.70964	0.0:0.0:1.0:0.0	rs62620707	105	Q9UK76	HN1_HUMAN	Y	59;105	.	ENSP00000384619:H59Y	H	-	1	0	HN1	70654359	1.000000	0.71417	0.990000	0.47175	0.934000	0.57294	4.164000	0.58190	2.662000	0.90505	0.555000	0.69702	CAT	G|0.983;A|0.017	0.017	strong		0.358	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032	
FREM1	158326	hgsc.bcm.edu	37	9	14801710	14801710	+	Missense_Mutation	SNP	C	C	A	rs35870000	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:14801710C>A	ENST00000380880.3	-	20	4417	c.3634G>T	c.(3634-3636)Gcc>Tcc	p.A1212S	FREM1_ENST00000422223.2_Missense_Mutation_p.A1212S|FREM1_ENST00000380881.4_Missense_Mutation_p.A1213S			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1212					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)		TGAGGGTTGGCTGGCTGCTTA	0.488													C|||	1302	0.259984	0.0681	0.3991	5008	,	,		18978	0.2321		0.3579	False		,,,				2504	0.3487				p.A1212S		Atlas-SNP	.											.	FREM1	261	.	0			c.G3634T						PASS	.	C	SER/ALA	472,3482		41,390,1546	146.0	143.0	144.0		3634	1.8	0.0	9	dbSNP_126	144	2824,5528		465,1894,1817	yes	missense	FREM1	NM_144966.5	99	506,2284,3363	AA,AC,CC		33.8123,11.9373,26.7837	benign	1212/2180	14801710	3296,9010	1977	4176	6153	SO:0001583	missense	158326	exon21			GGTTGGCTGGCTG	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.3634G>T	9.37:g.14801710C>A	ENSP00000370262:p.Ala1212Ser	Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	219	112	0.511416	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	591	0.2706043956043956	43	0.08739837398373984	158	0.43646408839779005	127	0.22202797202797203	263	0.3469656992084433	C	9.841	1.191048	0.21954	0.119373	0.338123	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.10860	2.83;2.83;2.83	5.12	1.79	0.24919	.	1.028690	0.07657	N	0.932920	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.10296	0.003	B	0.14578	0.011	T	0.47086	-0.9144	9	0.09338	T	0.73	-0.03	2.6233	0.04922	0.0:0.376:0.2601:0.3638	rs35870000;rs61737620	1212	Q5H8C1	FREM1_HUMAN	S	1213;1212;1212	ENSP00000370263:A1213S;ENSP00000412940:A1212S;ENSP00000370262:A1212S	ENSP00000370257:A1215S	A	-	1	0	FREM1	14791710	0.003000	0.15002	0.001000	0.08648	0.084000	0.17831	0.988000	0.29616	0.542000	0.28846	0.591000	0.81541	GCC	C|0.719;A|0.281	0.281	strong		0.488	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
OR52N1	79473	hgsc.bcm.edu	37	11	5809548	5809548	+	Missense_Mutation	SNP	G	G	A	rs7948009	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5809548G>A	ENST00000317078.1	-	1	498	c.499C>T	c.(499-501)Cgc>Tgc	p.R167C	TRIM5_ENST00000380027.1_Intron	NM_001001913.1	NP_001001913.1	Q8NH53	O52N1_HUMAN	olfactory receptor, family 52, subfamily N, member 1	167			R -> C (in dbSNP:rs7948009).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(15)|prostate(2)|skin(3)	31		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.05e-11)|LUSC - Lung squamous cell carcinoma(625;0.112)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.195)		TATGGAAGGCGCTTGGTGAGG	0.478													G|||	2763	0.551717	0.2458	0.5908	5008	,	,		22784	0.7054		0.6382	False		,,,				2504	0.6902				p.R167C		Atlas-SNP	.											.	OR52N1	70	.	0			c.C499T						PASS	.	G	CYS/ARG	1436,2966	466.6+/-354.6	240,956,1005	135.0	115.0	122.0		499	1.4	1.0	11	dbSNP_116	122	5686,2906	671.1+/-402.8	1876,1934,486	yes	missense	OR52N1	NM_001001913.1	180	2116,2890,1491	AA,AG,GG		33.8222,32.6215,45.1901	benign	167/321	5809548	7122,5872	2201	4296	6497	SO:0001583	missense	79473	exon1			GAAGGCGCTTGGT	AB065538	CCDS31398.1	11p15.4	2012-08-09			ENSG00000181001	ENSG00000181001		"""GPCR / Class A : Olfactory receptors"""	14853	protein-coding gene	gene with protein product							Standard	NM_001001913		Approved		uc010qzo.2	Q8NH53	OTTHUMG00000168800	ENST00000317078.1:c.499C>T	11.37:g.5809548G>A	ENSP00000322823:p.Arg167Cys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_001001913	Q6IFF6	Missense_Mutation	SNP	ENST00000317078.1	37	CCDS31398.1	1248	0.5714285714285714	113	0.22967479674796748	230	0.6353591160220995	414	0.7237762237762237	491	0.6477572559366754	G	7.954	0.745558	0.15710	0.326215	0.661778	ENSG00000181001	ENST00000317078	T	0.00188	8.59	4.59	1.38	0.22167	GPCR, rhodopsin-like superfamily (1);	0.134990	0.31177	N	0.008107	T	0.00012	0.0000	M	0.75085	2.285	0.34260	P	0.320248	B	0.23128	0.08	B	0.27715	0.082	T	0.43829	-0.9367	9	0.72032	D	0.01	.	3.8534	0.08965	0.0884:0.1355:0.5257:0.2504	rs7948009;rs52796900;rs61678687;rs7948009	167	Q8NH53	O52N1_HUMAN	C	167	ENSP00000322823:R167C	ENSP00000322823:R167C	R	-	1	0	OR52N1	5766124	0.000000	0.05858	0.979000	0.43373	0.182000	0.23217	-2.131000	0.01311	0.618000	0.30179	0.609000	0.83330	CGC	G|0.440;A|0.560	0.560	strong		0.478	OR52N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401142.1	NM_001001913	
C1QTNF6	114904	hgsc.bcm.edu	37	22	37581422	37581422	+	Missense_Mutation	SNP	G	G	C	rs229526	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:37581422G>C	ENST00000337843.2	-	2	200	c.125C>G	c.(124-126)cCt>cGt	p.P42R	C1QTNF6_ENST00000397110.2_Missense_Mutation_p.P42R|RP1-151B14.6_ENST00000419128.1_RNA|C1QTNF6_ENST00000255836.6_5'Flank|C1QTNF6_ENST00000470655.1_5'UTR	NM_031910.3	NP_114116.3	Q9BXI9	C1QT6_HUMAN	C1q and tumor necrosis factor related protein 6	23					protein heterotrimerization (GO:0070208)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)				breast(1)|large_intestine(2)|lung(6)|stomach(1)|upper_aerodigestive_tract(1)	11						CTCCACCATAGGGATCTCACA	0.612													G|||	947	0.189097	0.2769	0.1369	5008	,	,		18321	0.1071		0.2068	False		,,,				2504	0.1738				p.P42R		Atlas-SNP	.											.	C1QTNF6	32	.	0			c.C125G						PASS	.	G	ARG/PRO,ARG/PRO	1169,3237	404.6+/-333.2	155,859,1189	40.0	40.0	40.0	http://www.ncbi.nlm.nih.gov/pubmed?term	125,125	4.5	0.2	22	dbSNP_79	40	1919,6681	338.1+/-322.6	217,1485,2598	yes	missense,missense	C1QTNF6	NM_031910.3,NM_182486.1	103,103	372,2344,3787	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	22.314,26.532,23.7429	probably-damaging,probably-damaging	42/279,42/279	37581422	3088,9918	2203	4300	6503	SO:0001583	missense	114904	exon2			ACCATAGGGATCT	AF329842	CCDS13943.1	22q13.1	2014-02-21			ENSG00000133466	ENSG00000133466			14343	protein-coding gene	gene with protein product		614910				12975309	Standard	NM_031910		Approved	CTRP6, ZACRP6	uc003aqy.1	Q9BXI9	OTTHUMG00000150538	ENST00000337843.2:c.125C>G	22.37:g.37581422G>C	ENSP00000338812:p.Pro42Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_182486	Q5H9G8|Q6ZRM7	Missense_Mutation	SNP	ENST00000337843.2	37	CCDS13943.1	394	0.1804029304029304	136	0.2764227642276423	58	0.16022099447513813	55	0.09615384615384616	145	0.19129287598944592	G	11.16	1.557493	0.27827	0.26532	0.22314	ENSG00000133466	ENST00000397110;ENST00000337843	T;T	0.39406	1.08;1.08	4.49	4.49	0.54785	.	0.162471	0.41097	D	0.000960	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	0.9999999999995662	P;P	0.49090	0.919;0.718	P;B	0.45506	0.483;0.387	T	0.12243	-1.0555	9	0.44086	T	0.13	.	15.3686	0.74545	0.0:0.0:1.0:0.0	rs229526;rs17812735;rs52834593;rs59914011;rs229526	42;23	Q9BXI9-2;Q9BXI9	.;C1QT6_HUMAN	R	42	ENSP00000380299:P42R;ENSP00000338812:P42R	ENSP00000338812:P42R	P	-	2	0	C1QTNF6	35911368	1.000000	0.71417	0.229000	0.23960	0.004000	0.04260	3.883000	0.56168	2.039000	0.60335	0.491000	0.48974	CCT	G|0.791;C|0.208	0.208	strong		0.612	C1QTNF6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318807.1	NM_182486	
CACNA1B	774	hgsc.bcm.edu	37	9	140918181	140918181	+	Missense_Mutation	SNP	A	A	G	rs145816559|rs370787788|rs11137342	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:140918181A>G	ENST00000371372.1	+	19	3131	c.2986A>G	c.(2986-2988)Acc>Gcc	p.T996A	CACNA1B_ENST00000277549.5_Missense_Mutation_p.T188A|CACNA1B_ENST00000277551.2_Missense_Mutation_p.T996A|CACNA1B_ENST00000371367.5_5'UTR|CACNA1B_ENST00000545473.1_5'Flank|CACNA1B_ENST00000371363.1_Missense_Mutation_p.T996A|CACNA1B_ENST00000371355.4_Missense_Mutation_p.T997A|CACNA1B_ENST00000371357.1_Missense_Mutation_p.T997A	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	996			T -> A (in dbSNP:rs11137342).		calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)	p.T996_E1000delTTEKE(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GGAGAAGGAGACCACGGAGAA	0.716													g|||	533	0.10643	0.3563	0.0331	5008	,	,		7452	0.0089		0.0139	False		,,,				2504	0.0164				p.T996A		Atlas-SNP	.											.	CACNA1B	266	.	1	Deletion - In frame(1)	breast(1)	c.A2986G						PASS	.						6.0	10.0	9.0					9																	140918181		1177	2761	3938	SO:0001583	missense	774	exon19			AAGGAGACCACGG	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.2986A>G	9.37:g.140918181A>G	ENSP00000360423:p.Thr996Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	71	18	0.253521	NM_001243812	B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	g	0.004	-2.282231	0.00251	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D;D;D;D;D;D	0.96745	-3.87;-3.88;-4.11;-3.87;-3.85;-3.86	0.483	0.483	0.16820	.	28.367200	0.00166	N	0.000003	D	0.88833	0.6544	N	0.08118	0	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	0.83160	-0.0099	9	0.08599	T	0.76	.	.	.	.	rs11137342	996;997;996	B1AQK4;B1AQK7;B1AQK6	.;.;.	A	996;996;188;996;997;997	ENSP00000360423:T996A;ENSP00000277551:T996A;ENSP00000277549:T188A;ENSP00000360414:T996A;ENSP00000360408:T997A;ENSP00000360406:T997A	ENSP00000277549:T188A	T	+	1	0	CACNA1B	140038002	0.937000	0.31787	0.008000	0.14137	0.014000	0.08584	-0.405000	0.07196	-0.342000	0.08363	-0.795000	0.03280	ACC	A|0.972;G|0.028	0.028	strong		0.716	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	
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 GAIIx	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	Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	138	74	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	
MUC16	94025	hgsc.bcm.edu	37	19	9060125	9060125	+	Silent	SNP	G	G	A	rs12972088	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9060125G>A	ENST00000397910.4	-	3	27524	c.27321C>T	c.(27319-27321)caC>caT	p.H9107H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9109	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATGCAGTTGAGTGGGTCCCTG	0.483													G|||	1053	0.210264	0.2595	0.2118	5008	,	,		23165	0.0099		0.3121	False		,,,				2504	0.2444				p.H9107H		Atlas-SNP	.											.	MUC16	4315	.	0			c.C27321T						PASS	.	G		945,2921		98,749,1086	126.0	116.0	119.0		27321	-3.1	0.0	19	dbSNP_121	119	2804,5482		499,1806,1838	no	coding-synonymous	MUC16	NM_024690.2		597,2555,2924	AA,AG,GG		33.8402,24.4439,30.8509		9107/14508	9060125	3749,8403	1933	4143	6076	SO:0001819	synonymous_variant	94025	exon3			AGTTGAGTGGGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27321C>T	19.37:g.9060125G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.760;A|0.240	0.240	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GGCX	2677	hgsc.bcm.edu	37	2	85780107	85780107	+	Silent	SNP	G	G	A	rs10179904	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85780107G>A	ENST00000233838.4	-	9	1322	c.1242C>T	c.(1240-1242)acC>acT	p.T414T	GGCX_ENST00000430215.3_Silent_p.T357T|GGCX_ENST00000473665.1_5'UTR	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	414					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	CATCACGGTAGGTGATCTTCA	0.547													G|||	596	0.11901	0.1157	0.098	5008	,	,		19792	0.0704		0.1123	False		,,,				2504	0.1953				p.T414T		Atlas-SNP	.											.	GGCX	44	.	0			c.C1242T						PASS	.	G	,	508,3898	235.2+/-247.8	30,448,1725	189.0	173.0	178.0		1242,1071	5.5	1.0	2	dbSNP_119	178	1009,7591	217.7+/-256.3	56,897,3347	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	86,1345,5072	AA,AG,GG		11.7326,11.5297,11.6638	,	414/759,357/702	85780107	1517,11489	2203	4300	6503	SO:0001819	synonymous_variant	2677	exon9			ACGGTAGGTGATC		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.1242C>T	2.37:g.85780107G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	131	91	0.694656	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			G|0.893;A|0.107	0.107	strong		0.547	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
INPP4A	3631	hgsc.bcm.edu	37	2	99149946	99149946	+	Silent	SNP	G	G	A	rs2278211	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:99149946G>A	ENST00000523221.1	+	3	258	c.258G>A	c.(256-258)acG>acA	p.T86T	INPP4A_ENST00000074304.5_Silent_p.T86T|INPP4A_ENST00000545415.1_Silent_p.T86T|INPP4A_ENST00000409851.3_Silent_p.T86T|INPP4A_ENST00000409540.3_Silent_p.T86T|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409016.4_Silent_p.T86T			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	86	C2.				inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						ATGCACAGACGGAGATCATTG	0.522													G|||	1154	0.230431	0.0749	0.304	5008	,	,		18892	0.2956		0.2674	False		,,,				2504	0.2832				p.T86T		Atlas-SNP	.											.	INPP4A	205	.	0			c.G258A						PASS	.	G	,,,	479,3711		32,415,1648	112.0	112.0	112.0		258,258,258,258	-2.2	1.0	2	dbSNP_100	112	2216,6242		296,1624,2309	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	328,2039,3957	AA,AG,GG		26.2,11.432,21.3077	,,,	86/978,86/973,86/955,86/939	99149946	2695,9953	2095	4229	6324	SO:0001819	synonymous_variant	3631	exon5			ACAGACGGAGATC	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.258G>A	2.37:g.99149946G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_004027	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			G|0.779;N|0.000	.	strong		0.522	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
AKAP1	8165	hgsc.bcm.edu	37	17	55183792	55183792	+	Missense_Mutation	SNP	G	G	A	rs35359994	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:55183792G>A	ENST00000337714.3	+	2	1200	c.967G>A	c.(967-969)Ggc>Agc	p.G323S	AKAP1_ENST00000571629.1_Missense_Mutation_p.G323S|AKAP1_ENST00000314126.3_Missense_Mutation_p.G323S|AKAP1_ENST00000572557.1_Missense_Mutation_p.G323S|AKAP1_ENST00000539273.1_Missense_Mutation_p.G323S	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	323					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					AAATGAGGAGGGCTTGGATAG	0.498													G|||	242	0.0483227	0.0189	0.0432	5008	,	,		18051	0.006		0.1133	False		,,,				2504	0.0685				p.G323S		Atlas-SNP	.											.	AKAP1	73	.	0			c.G967A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	83,4323		0,83,2120	95.0	103.0	100.0		967,967,967	-0.3	0.0	17	dbSNP_126	100	607,7993		0,607,3693	no	missense,missense,missense	AKAP1	NM_001242902.1,NM_001242903.1,NM_003488.3	56,56,56	0,690,5813	AA,AG,GG		7.0581,1.8838,5.3052	benign,benign,benign	323/904,323/904,323/904	55183792	690,12316	2203	4300	6503	SO:0001583	missense	8165	exon3			GAGGAGGGCTTGG	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.967G>A	17.37:g.55183792G>A	ENSP00000337736:p.Gly323Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	41	0.630769	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	83	0.038003663003663	6	0.012195121951219513	11	0.03038674033149171	5	0.008741258741258742	61	0.08047493403693931	G	8.381	0.837457	0.16891	0.018838	0.070581	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.18960	2.24;2.18;2.24	1.16	-0.285	0.12866	.	.	.	.	.	T	0.00440	0.0014	N	0.08118	0	0.09310	N	1	B	0.17667	0.023	B	0.09377	0.004	T	0.35919	-0.9769	9	0.27082	T	0.32	.	3.7756	0.08659	0.3336:0.0:0.6664:0.0	rs35359994;rs61742672	323	Q92667	AKAP1_HUMAN	S	323;323;365;323	ENSP00000337736:G323S;ENSP00000314075:G323S;ENSP00000443139:G323S	ENSP00000314075:G323S	G	+	1	0	AKAP1	52538791	0.500000	0.26091	0.008000	0.14137	0.135000	0.20990	-1.247000	0.02893	0.202000	0.20498	0.205000	0.17691	GGC	G|0.949;A|0.051	0.051	strong		0.498	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1		
ACSM2A	123876	hgsc.bcm.edu	37	16	20488696	20488696	+	Silent	SNP	A	A	G	rs1700805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20488696A>G	ENST00000573854.1	+	9	1218	c.1104A>G	c.(1102-1104)ttA>ttG	p.L368L	ACSM2A_ENST00000417235.2_Silent_p.L289L|ACSM2A_ENST00000396104.2_Silent_p.L368L|ACSM2A_ENST00000536134.1_Silent_p.L140L|ACSM2A_ENST00000575690.1_Silent_p.L368L|ACSM2A_ENST00000575558.1_3'UTR|ACSM2A_ENST00000219054.6_Silent_p.L368L	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	368					fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						CACAGGGATTAACTTGCATGG	0.463													a|||	2428	0.484824	0.5454	0.2695	5008	,	,		20036	0.7748		0.2654	False		,,,				2504	0.4826				p.L368L		Atlas-SNP	.											.	ACSM2A	120	.	0			c.A1104G						PASS	.	A		2241,2163	579.2+/-384.9	590,1061,551	46.0	43.0	44.0		1104	-5.9	0.0	16	dbSNP_89	44	2422,6138	394.4+/-344.7	337,1748,2195	no	coding-synonymous	ACSM2A	NM_001010845.2		927,2809,2746	GG,GA,AA		28.2944,49.1144,35.9688		368/578	20488696	4663,8301	2202	4280	6482	SO:0001819	synonymous_variant	123876	exon10			GGGATTAACTTGC	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"""Acyl-CoA synthetase family"""	32017	protein-coding gene	gene with protein product		614358	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1104A>G	16.37:g.20488696A>G		Somatic	533	0	0		WXS	Illumina HiSeq	Phase_I	535	171	0.319626	NM_001010845	B3KTT9|O75202	Silent	SNP	ENST00000573854.1	37	CCDS32401.1																																																																																			A|0.333;G|0.667	0.667	strong		0.463	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
MKRN1	23608	hgsc.bcm.edu	37	7	140158851	140158851	+	Missense_Mutation	SNP	C	C	G	rs2272095	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:140158851C>G	ENST00000255977.2	-	4	951	c.727G>C	c.(727-729)Gtc>Ctc	p.V243L	MKRN1_ENST00000480552.1_Intron|MKRN1_ENST00000443720.2_Missense_Mutation_p.V243L|MKRN1_ENST00000481705.1_5'Flank|MKRN1_ENST00000437223.2_Intron|MKRN1_ENST00000474576.1_Missense_Mutation_p.V179L	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	243	Makorin-type Cys-His.		V -> L (in dbSNP:rs2272095). {ECO:0000269|PubMed:10843807, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					GGATGCAGGACCTGCAGCCCA	0.488													c|||	620	0.123802	0.0204	0.1527	5008	,	,		19731	0.0913		0.2893	False		,,,				2504	0.1063				p.V243L		Atlas-SNP	.											.	MKRN1	35	.	0			c.G727C						PASS	.	C	LEU/VAL,LEU/VAL	246,4160	143.8+/-178.8	10,226,1967	95.0	90.0	92.0		727,727	4.9	1.0	7	dbSNP_100	92	2247,6353	381.6+/-340.1	303,1641,2356	yes	missense,missense	MKRN1	NM_001145125.1,NM_013446.3	32,32	313,1867,4323	GG,GC,CC		26.1279,5.5833,19.1681	benign,benign	243/330,243/483	140158851	2493,10513	2203	4300	6503	SO:0001583	missense	23608	exon4			GCAGGACCTGCAG	AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"""RING-type (C3HC4) zinc fingers"""	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.727G>C	7.37:g.140158851C>G	ENSP00000255977:p.Val243Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_013446	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Missense_Mutation	SNP	ENST00000255977.2	37	CCDS5860.1	337	0.1543040293040293	15	0.03048780487804878	56	0.15469613259668508	61	0.10664335664335664	205	0.2704485488126649	C	24.5	4.534295	0.85812	0.055833	0.261279	ENSG00000133606	ENST00000255977;ENST00000539898;ENST00000474576;ENST00000443720;ENST00000471104	T;T;T;T	0.24723	2.87;2.22;2.45;1.84	4.91	4.91	0.64330	.	0.057098	0.64402	D	0.000001	T	0.00012	0.0000	M	0.74647	2.275	0.09310	P	1.0	P	0.38420	0.63	B	0.35770	0.21	T	0.17167	-1.0378	9	0.52906	T	0.07	.	18.2987	0.90155	0.0:1.0:0.0:0.0	rs2272095;rs9648841;rs17852313;rs2272095	243	Q9UHC7	MKRN1_HUMAN	L	243;179;179;243;179	ENSP00000255977:V243L;ENSP00000417863:V179L;ENSP00000416369:V243L;ENSP00000418864:V179L	ENSP00000255977:V243L	V	-	1	0	MKRN1	139805320	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.223000	0.78033	2.556000	0.86216	0.555000	0.69702	GTC	C|0.819;G|0.181	0.181	strong		0.488	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446	
ARFGAP3	26286	hgsc.bcm.edu	37	22	43203137	43203137	+	Silent	SNP	C	C	T	rs738535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:43203137C>T	ENST00000263245.5	-	14	1572	c.1353G>A	c.(1351-1353)tcG>tcA	p.S451S	ARFGAP3_ENST00000429508.2_Silent_p.S379S|ARFGAP3_ENST00000437119.2_Silent_p.S407S	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	451					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						AGGAACTTGCCGACAGCCTCT	0.522													C|||	1553	0.310104	0.289	0.366	5008	,	,		17906	0.0853		0.4364	False		,,,				2504	0.4008				p.S451S	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.G1353A						PASS	.	C	,	1535,2871	481.0+/-359.0	273,989,941	41.0	35.0	37.0		1221,1353	-6.2	0.0	22	dbSNP_86	37	3892,4708	533.8+/-382.5	907,2078,1315	no	coding-synonymous,coding-synonymous	ARFGAP3	NM_001142293.1,NM_014570.4	,	1180,3067,2256	TT,TC,CC		45.2558,34.8389,41.7269	,	407/473,451/517	43203137	5427,7579	2203	4300	6503	SO:0001819	synonymous_variant	26286	exon14			ACTTGCCGACAGC	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.1353G>A	22.37:g.43203137C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	36	35	0.972222	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Silent	SNP	ENST00000263245.5	37	CCDS14042.1	651	0.2980769230769231	145	0.29471544715447157	149	0.4116022099447514	36	0.06293706293706294	321	0.4234828496042216	C	0.050	-1.253780	0.01457	0.348389	0.452558	ENSG00000242247	ENST00000453516	.	.	.	4.94	-6.15	0.02105	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20403	P	0.9999019985	.	.	.	.	.	.	T	0.48801	-0.9003	3	.	.	.	-8.7248	1.6031	0.02679	0.3155:0.3219:0.2148:0.1478	rs738535;rs1044700;rs3171717;rs17405155;rs17409171;rs17849916;rs60500703;rs738535	.	.	.	S	254	.	.	G	-	1	0	ARFGAP3	41533081	0.156000	0.22821	0.015000	0.15790	0.006000	0.05464	-0.630000	0.05502	-0.428000	0.07339	-0.923000	0.02734	GGC	C|0.641;T|0.359	0.359	strong		0.522	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570	
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 GAIIx	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_ENST00000541064.1_Missense_Mutation_p.K71R|NPC2_ENST00000557510.1_Missense_Mutation_p.K71R|NPC2_ENST00000238633.2_Missense_Mutation_p.K71R|NPC2_ENST00000434013.2_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	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	47	25	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	
GRM4	2914	hgsc.bcm.edu	37	6	34003685	34003685	+	Silent	SNP	T	T	C	rs2228623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:34003685T>C	ENST00000538487.2	-	9	2645	c.2202A>G	c.(2200-2202)acA>acG	p.T734T	GRM4_ENST00000535756.1_Silent_p.T601T|GRM4_ENST00000374181.4_Silent_p.T734T|GRM4_ENST00000455714.2_Silent_p.T594T|GRM4_ENST00000374177.3_Silent_p.T618T|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000609222.1_Silent_p.T601T|GRM4_ENST00000544773.2_Silent_p.T565T	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	734					activation of MAPK activity (GO:0000187)|adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|learning (GO:0007612)|neurotransmitter secretion (GO:0007269)|positive regulation of MAPK cascade (GO:0043410)|regulation of neuron apoptotic process (GO:0043523)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	cytoplasmic vesicle (GO:0031410)|dendritic shaft (GO:0043198)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic active zone membrane (GO:0048787)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GGGGGTCGAGTGTCCGCTGGT	0.617													T|||	1207	0.241014	0.2118	0.1772	5008	,	,		17178	0.3581		0.1571	False		,,,				2504	0.2914				p.T734T		Atlas-SNP	.											.	GRM4	317	.	0			c.A2202G						PASS	.	T		931,3475	354.4+/-312.6	88,755,1360	88.0	83.0	85.0		2202	-0.6	1.0	6	dbSNP_98	85	1347,7253	262.4+/-284.4	118,1111,3071	no	coding-synonymous	GRM4	NM_000841.1		206,1866,4431	CC,CT,TT		15.6628,21.1303,17.515		734/913	34003685	2278,10728	2203	4300	6503	SO:0001819	synonymous_variant	2914	exon9			GTCGAGTGTCCGC	U92457	CCDS4787.1, CCDS59010.1, CCDS59011.1, CCDS59012.1, CCDS75432.1	6p21.3	2012-08-29			ENSG00000124493	ENSG00000124493		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4596	protein-coding gene	gene with protein product		604100				8738157, 9473604	Standard	NM_000841		Approved	GPRC1D, mGlu4, MGLUR4	uc010jvh.4	Q14833	OTTHUMG00000014538	ENST00000538487.2:c.2202A>G	6.37:g.34003685T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	84	13	0.154762	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Silent	SNP	ENST00000538487.2	37	CCDS4787.1																																																																																			T|0.822;C|0.178	0.178	strong		0.617	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2		
TPPP	11076	hgsc.bcm.edu	37	5	665295	665295	+	Silent	SNP	A	A	G	rs61731455	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:665295A>G	ENST00000360578.5	-	4	703	c.582T>C	c.(580-582)gaT>gaC	p.D194D	AC026740.1_ENST00000594226.1_5'Flank|CEP72_ENST00000514507.1_3'UTR	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	194					microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		CGTCCACCAGATCCACGCGGC	0.652													G|||	481	0.0960463	0.0061	0.1599	5008	,	,		18022	0.0208		0.1909	False		,,,				2504	0.1524				p.D194D		Atlas-SNP	.											TPPP,caecum,carcinoma,0,1	TPPP	24	1	0			c.T582C						PASS	.	G		169,4237	809.7+/-416.0	0,169,2034	86.0	75.0	79.0		582	4.2	1.0	5	dbSNP_129	79	1686,6914	738.4+/-407.1	171,1344,2785	no	coding-synonymous	TPPP	NM_007030.2		171,1513,4819	GG,GA,AA		19.6047,3.8357,14.2626		194/220	665295	1855,11151	2203	4300	6503	SO:0001819	synonymous_variant	11076	exon4			CACCAGATCCACG	AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368			24164	protein-coding gene	gene with protein product	"""brain specific protein p25 alpha"""	608773				10083737, 12093283, 15590652, 17105200	Standard	NM_007030		Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.582T>C	5.37:g.665295A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_007030		Silent	SNP	ENST00000360578.5	37	CCDS3856.1																																																																																			A|0.870;G|0.130	0.130	strong		0.652	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253645.3	NM_007030	
GPR112	139378	hgsc.bcm.edu	37	X	135431358	135431358	+	Silent	SNP	C	C	T	rs5930933	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135431358C>T	ENST00000394143.1	+	6	5784	c.5493C>T	c.(5491-5493)ccC>ccT	p.P1831P	GPR112_ENST00000394141.1_Silent_p.P1626P|GPR112_ENST00000370652.1_Silent_p.P1831P|GPR112_ENST00000287534.4_Silent_p.P1768P|GPR112_ENST00000412101.1_Silent_p.P1626P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1831					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(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CAACTCTACCCTCTTTGACAT	0.433													c|||	1787	0.473377	0.4236	0.3573	3775	,	,		16215	0.2778		0.3797	False		,,,				2504	0.3241				p.P1831P		Atlas-SNP	.											.	GPR112	459	.	0			c.C5493T						PASS	.			2112,1723		495,811,311,326,260	143.0	125.0	131.0		5493	0.4	0.0	X	dbSNP_114	131	3228,3500		567,1180,914,681,958	yes	coding-synonymous	GPR112	NM_153834.3		1062,1991,1225,1007,1218	TT,TC,T,CC,C		47.9786,44.9283,49.4462		1831/3081	135431358	5340,5223	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			TCTACCCTCTTTG	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5493C>T	X.37:g.135431358C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	58	0.698795	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			C|0.507;0|0.003	.	strong		0.433	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
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 GAIIx	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	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	97	4	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	
TRIM27	5987	hgsc.bcm.edu	37	6	28891176	28891176	+	Silent	SNP	T	T	C	rs2230683	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:28891176T>C	ENST00000377199.3	-	1	590	c.234A>G	c.(232-234)gtA>gtG	p.V78V	TRIM27_ENST00000498117.1_5'Flank|TRIM27_ENST00000377194.3_Silent_p.V78V	NM_006510.4	NP_006501.1	P14373	TRI27_HUMAN	tripartite motif containing 27	78					Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell proliferation (GO:0008283)|innate immune response (GO:0045087)|interferon-gamma secretion (GO:0072643)|negative regulation of adaptive immune response (GO:0002820)|negative regulation of calcium ion import (GO:0090281)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(6)|ovary(1)	10						GCAGCTGCTTTACCAGTTGGG	0.687			T	RET	papillary thyroid								T|||	93	0.0185703	0.0045	0.0245	5008	,	,		13739	0.0		0.0696	False		,,,				2504	0.0				p.V78V		Atlas-SNP	.		Dom	yes		6	6p22	5987	tripartite motif-containing 27		E	.	TRIM27	26	.	0			c.A234G						PASS	.	T		101,4299		3,95,2102	27.0	27.0	27.0		234	2.3	1.0	6	dbSNP_98	27	769,7825		40,689,3568	no	coding-synonymous	TRIM27	NM_006510.4		43,784,5670	CC,CT,TT		8.9481,2.2955,6.6954		78/514	28891176	870,12124	2200	4297	6497	SO:0001819	synonymous_variant	5987	exon1			CTGCTTTACCAGT	Z58939	CCDS4654.1	6p22	2013-01-09	2011-01-25	2006-09-26	ENSG00000204713	ENSG00000204713		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9975	protein-coding gene	gene with protein product		602165	"""ret finger protein"", ""tripartite motif-containing 27"""	RFP		8114113	Standard	NM_006510		Approved	RNF76	uc003nlr.3	P14373	OTTHUMG00000031215	ENST00000377199.3:c.234A>G	6.37:g.28891176T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_006510	A2BE15|Q5RJA8|Q5ST26|Q6LA73|Q6NXR9|Q9BZY6|Q9UJL3	Silent	SNP	ENST00000377199.3	37	CCDS4654.1																																																																																			T|0.950;C|0.050	0.050	strong		0.687	TRIM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076442.2	NM_030950	
TYR	7299	hgsc.bcm.edu	37	11	89017961	89017961	+	Missense_Mutation	SNP	G	G	A	rs1126809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:89017961G>A	ENST00000263321.5	+	4	1707	c.1205G>A	c.(1204-1206)cGa>cAa	p.R402Q		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	402			R -> G (in OCA1B).|R -> L (in OCA1A). {ECO:0000269|PubMed:15146472}.|R -> Q (in dbSNP:rs1126809). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:15146472, ECO:0000269|PubMed:2342539, ECO:0000269|PubMed:7955413, ECO:0000269|PubMed:9158138}.		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CAGTGGCTCCGAAGGCACCGT	0.368													G|||	407	0.08127	0.0091	0.1254	5008	,	,		15773	0.001		0.2525	False		,,,				2504	0.0542				p.R402Q		Atlas-SNP	.											TYR,NS,carcinoma,+1,1	TYR	130	1	0			c.G1205A	GRCh37	CM041478|CM971555	TYR	M	rs1126809	PASS	.	G	GLN/ARG	223,4179	130.2+/-166.9	8,207,1986	60.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1205	4.7	1.0	11	dbSNP_86	61	2418,6180	399.1+/-346.3	322,1774,2203	yes	missense	TYR	NM_000372.4	43	330,1981,4189	AA,AG,GG		28.1228,5.0659,20.3154	probably-damaging	402/530	89017961	2641,10359	2201	4299	6500	SO:0001583	missense	7299	exon4			GGCTCCGAAGGCA	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1205G>A	11.37:g.89017961G>A	ENSP00000263321:p.Arg402Gln	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	162	159	0.981481	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	244	0.11172161172161173	5	0.01016260162601626	53	0.1464088397790055	0	0.0	186	0.24538258575197888	G	29.5	5.013726	0.93404	0.050659	0.281228	ENSG00000077498	ENST00000263321	D	0.98234	-4.81	4.68	4.68	0.58851	Tyrosinase (1);Uncharacterised domain, di-copper centre (2);	0.000000	0.85682	D	0.000000	T	0.00440	0.0014	M	0.66378	2.025	0.09310	P	0.999999826736	D	0.76494	0.999	D	0.80764	0.994	T	0.00000	-1.7609	8	.	.	.	.	17.6247	0.88091	0.0:0.0:1.0:0.0	rs62645918	402	P14679	TYRO_HUMAN	Q	402	ENSP00000263321:R402Q	.	R	+	2	0	TYR	88657609	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	7.499000	0.81566	2.166000	0.68216	0.555000	0.69702	CGA	G|0.831;A|0.169	0.169	strong		0.368	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
LRSAM1	90678	hgsc.bcm.edu	37	9	130219669	130219669	+	Silent	SNP	C	C	T	rs2243906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:130219669C>T	ENST00000323301.4	+	5	853	c.249C>T	c.(247-249)atC>atT	p.I83I	LRSAM1_ENST00000373324.4_Silent_p.I83I|LRSAM1_ENST00000300417.6_Silent_p.I83I|LRSAM1_ENST00000373322.1_Silent_p.I83I	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif containing 1	83					cell death (GO:0008219)|negative regulation of endocytosis (GO:0045806)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent endocytosis (GO:0070086)|viral budding (GO:0046755)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						TGGCAACCATCAAGGTACTGG	0.612													C|||	2792	0.557508	0.6067	0.6499	5008	,	,		19717	0.4137		0.6322	False		,,,				2504	0.4969				p.I83I		Atlas-SNP	.											.	LRSAM1	40	.	0			c.C249T						PASS	.	C	,,,	2817,1589	665.6+/-401.6	890,1037,276	114.0	79.0	91.0		249,249,249,249	5.1	1.0	9	dbSNP_100	91	5058,3542	629.5+/-398.2	1498,2062,740	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRSAM1	NM_001005373.2,NM_001005374.2,NM_001190723.1,NM_138361.4	,,,	2388,3099,1016	TT,TC,CC		41.186,36.0645,39.451	,,,	83/724,83/724,83/697,83/724	130219669	7875,5131	2203	4300	6503	SO:0001819	synonymous_variant	90678	exon6			AACCATCAAGGTA	AK056203	CCDS6873.1, CCDS55347.1	9q34.13	2014-09-17			ENSG00000148356	ENSG00000148356		"""Sterile alpha motif (SAM) domain containing"""	25135	protein-coding gene	gene with protein product		610933				12975309	Standard	NM_001005373		Approved	FLJ31641	uc004brd.2	Q6UWE0	OTTHUMG00000020701	ENST00000323301.4:c.249C>T	9.37:g.130219669C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	32	0.395062	NM_001005373	Q5VVV0|Q8NB40|Q96GT5|Q96MX5|Q96MZ7	Silent	SNP	ENST00000323301.4	37	CCDS6873.1																																																																																			C|0.416;T|0.584	0.584	strong		0.612	LRSAM1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054164.1	NM_138361	
SCPEP1	59342	hgsc.bcm.edu	37	17	55079471	55079471	+	Silent	SNP	T	T	C	rs12940187	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:55079471T>C	ENST00000262288.3	+	12	1280	c.1225T>C	c.(1225-1227)Ttg>Ctg	p.L409L	AC007114.1_ENST00000580911.1_RNA	NM_021626.2	NP_067639.1	Q9HB40	RISC_HUMAN	serine carboxypeptidase 1	409					negative regulation of blood pressure (GO:0045776)|positive regulation of vasodilation (GO:0045909)|retinoic acid metabolic process (GO:0042573)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	14	Breast(9;2.86e-08)					CCCTAAATCTTTGGAAACATC	0.463													T|||	379	0.0756789	0.0098	0.1671	5008	,	,		19712	0.002		0.17	False		,,,				2504	0.0787				p.L409L		Atlas-SNP	.											.	SCPEP1	35	.	0			c.T1225C						PASS	.	T		188,4218	119.2+/-156.9	5,178,2020	131.0	117.0	122.0		1225	0.9	0.0	17	dbSNP_121	122	1568,7032	292.8+/-301.0	158,1252,2890	no	coding-synonymous	SCPEP1	NM_021626.2		163,1430,4910	CC,CT,TT		18.2326,4.2669,13.5015		409/453	55079471	1756,11250	2203	4300	6503	SO:0001819	synonymous_variant	59342	exon12			AAATCTTTGGAAA	AF282618	CCDS11593.1	17q22	2012-09-20			ENSG00000121064	ENSG00000121064			29507	protein-coding gene	gene with protein product	"""retinoid inducible serine carboxypeptidase"""					11447226, 12975309	Standard	NM_021626		Approved	RISC	uc002iuv.4	Q9HB40	OTTHUMG00000178129	ENST00000262288.3:c.1225T>C	17.37:g.55079471T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_021626	Q96A94|Q9H3F0	Silent	SNP	ENST00000262288.3	37	CCDS11593.1																																																																																			T|0.884;C|0.116	0.116	strong		0.463	SCPEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440622.1	NM_021626	
LMF1	64788	hgsc.bcm.edu	37	16	920870	920870	+	Missense_Mutation	SNP	C	C	T	rs35168378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:920870C>T	ENST00000262301.11	-	8	1109	c.1091G>A	c.(1090-1092)cGg>cAg	p.R364Q	LMF1_ENST00000568268.1_5'UTR|LMF1_ENST00000568897.1_Missense_Mutation_p.R147Q|LMF1_ENST00000543238.1_Missense_Mutation_p.R127Q|LMF1_ENST00000399843.2_Missense_Mutation_p.R364Q	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	364			R -> Q (in dbSNP:rs35168378).		chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				GGCTGCACGCCGCACCACGGA	0.677													C|||	128	0.0255591	0.0484	0.0159	5008	,	,		14741	0.0		0.0298	False		,,,				2504	0.0235				p.R364Q		Atlas-SNP	.											.	LMF1	42	.	0			c.G1091A						PASS	.	C	GLN/ARG	155,4087		2,151,1968	37.0	43.0	41.0		1091	5.5	0.8	16	dbSNP_126	41	213,8277		4,205,4036	yes	missense	LMF1	NM_022773.2	43	6,356,6004	TT,TC,CC		2.5088,3.6539,2.8904	probably-damaging	364/568	920870	368,12364	2121	4245	6366	SO:0001583	missense	64788	exon8			GCACGCCGCACCA	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.1091G>A	16.37:g.920870C>T	ENSP00000262301:p.Arg364Gln	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Missense_Mutation	SNP	ENST00000262301.11	37	CCDS45373.1	58	0.026556776556776556	25	0.0508130081300813	8	0.022099447513812154	0	0.0	25	0.032981530343007916	C	35	5.560510	0.96527	0.036539	0.025088	ENSG00000103227	ENST00000262301;ENST00000399843;ENST00000540070;ENST00000545827;ENST00000543238	T;T;T	0.22134	1.97;1.97;1.97	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.07324	0.0185	M	0.66939	2.045	0.80722	D	1	D	0.56746	0.977	P	0.50405	0.64	T	0.00294	-1.1840	10	0.54805	T	0.06	-11.7191	17.8997	0.88900	0.0:1.0:0.0:0.0	rs35168378	364	Q96S06	LMF1_HUMAN	Q	364;364;147;118;127	ENSP00000262301:R364Q;ENSP00000382737:R364Q;ENSP00000437418:R127Q	ENSP00000262301:R364Q	R	-	2	0	LMF1	860871	1.000000	0.71417	0.819000	0.32651	0.024000	0.10985	6.183000	0.72002	2.588000	0.87417	0.561000	0.74099	CGG	C|0.976;T|0.024	0.024	strong		0.677	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
KIF4A	24137	hgsc.bcm.edu	37	X	69573639	69573639	+	Silent	SNP	C	C	T	rs1199429	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:69573639C>T	ENST00000374403.3	+	15	1738	c.1656C>T	c.(1654-1656)ccC>ccT	p.P552P	KIF4A_ENST00000374388.3_Silent_p.P552P	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	552					anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						AACTGCAGCCCATTCAGTACC	0.428													C|||	450	0.119205	0.2791	0.0375	3775	,	,		13843	0.0		0.0398	False		,,,				2504	0.0153				p.P552P		Atlas-SNP	.											.	KIF4A	118	.	0			c.C1656T						PASS	.	C		1337,2496		210,717,200,705,369	46.0	39.0	41.0		1656	-0.2	1.0	X	dbSNP_87	41	323,6400		4,225,90,2199,1777	no	coding-synonymous	KIF4A	NM_012310.4		214,942,290,2904,2146	TT,TC,T,CC,C		4.8044,34.8813,15.7257		552/1233	69573639	1660,8896	2201	4295	6496	SO:0001819	synonymous_variant	24137	exon15			GCAGCCCATTCAG	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1656C>T	X.37:g.69573639C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	145	101	0.696552	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Silent	SNP	ENST00000374403.3	37	CCDS14401.1																																																																																			0|0.003;T|0.145	0.145	strong		0.428	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	
ZNF30	90075	hgsc.bcm.edu	37	19	35422808	35422808	+	Missense_Mutation	SNP	C	C	T	rs10422961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35422808C>T	ENST00000601142.1	+	3	308	c.71C>T	c.(70-72)tCc>tTc	p.S24F	ZNF30_ENST00000426813.2_5'UTR|ZNF30_ENST00000303586.7_Missense_Mutation_p.S24F|ZNF30_ENST00000439785.1_Missense_Mutation_p.S24F|ZNF30_ENST00000601957.1_Missense_Mutation_p.S24F			P17039	ZNF30_HUMAN	zinc finger protein 30	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.			S -> F (in Ref. 1; BAG58432). {ECO:0000305}.	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)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		ATAGCCTTCTCCCAGCAGGAG	0.463													C|||	1443	0.288139	0.2693	0.232	5008	,	,		20449	0.2202		0.3618	False		,,,				2504	0.3476				p.S24F		Atlas-SNP	.											ZNF30,colon,carcinoma,0,1	ZNF30	44	1	0			c.C71T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	1094,3212		155,784,1214	79.0	85.0	83.0		71,71,71	1.5	1.0	19	dbSNP_119	83	2777,5777		466,1845,1966	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	155,155,155	621,2629,3180	TT,TC,CC		32.4643,25.4064,30.1011	benign,benign,benign	24/625,24/625,24/624	35422808	3871,8989	2153	4277	6430	SO:0001583	missense	90075	exon3			CCTTCTCCCAGCA	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.71C>T	19.37:g.35422808C>T	ENSP00000469954:p.Ser24Phe	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	637	0.2916666666666667	128	0.2601626016260163	93	0.2569060773480663	136	0.23776223776223776	280	0.36939313984168864	C	11.43	1.637390	0.29157	0.254064	0.324643	ENSG00000168661	ENST00000439785;ENST00000303586	T;T	0.02944	4.1;4.1	1.55	1.55	0.23275	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	H	0.98701	4.305	0.09310	P	0.999999999831031	P;B	0.39903	0.694;0.031	B;B	0.41236	0.351;0.021	T	0.15235	-1.0444	8	0.72032	D	0.01	.	6.5714	0.22541	0.0:1.0:0.0:0.0	rs10422961;rs10422961	24;24	P17039-2;P17039	.;ZNF30_HUMAN	F	24	ENSP00000403441:S24F;ENSP00000303889:S24F	ENSP00000303889:S24F	S	+	2	0	ZNF30	40114648	0.676000	0.27567	0.991000	0.47740	0.971000	0.66376	1.149000	0.31626	1.167000	0.42706	0.514000	0.50259	TCC	C|0.700;T|0.300	0.300	strong		0.463	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
EMILIN3	90187	hgsc.bcm.edu	37	20	39991171	39991171	+	Silent	SNP	G	G	A	rs61739307	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:39991171G>A	ENST00000332312.3	-	4	1230	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	346						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TCCGGCTGGCGGCCTGACCCT	0.672													G|||	405	0.0808706	0.059	0.1225	5008	,	,		14633	0.003		0.1799	False		,,,				2504	0.0593				p.A346A		Atlas-SNP	.											EMILIN3,rectum,carcinoma,0,1	EMILIN3	63	1	0			c.C1038T						PASS	.	G		390,4012		16,358,1827	15.0	17.0	16.0		1038	-10.3	0.2	20	dbSNP_129	16	1433,7165		130,1173,2996	no	coding-synonymous	EMILIN3	NM_052846.1		146,1531,4823	AA,AG,GG		16.6667,8.8596,14.0231		346/767	39991171	1823,11177	2201	4299	6500	SO:0001819	synonymous_variant	90187	exon4			GCTGGCGGCCTGA	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1038C>T	20.37:g.39991171G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			G|0.883;A|0.117	0.117	strong		0.672	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
SOGA3	387104	hgsc.bcm.edu	37	6	127797374	127797374	+	Silent	SNP	G	G	A	rs3734450	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:127797374G>A	ENST00000525778.1	-	6	2542	c.1797C>T	c.(1795-1797)aaC>aaT	p.N599N	SOGA3_ENST00000556132.1_Silent_p.N599N|SOGA3_ENST00000465909.2_Silent_p.N599N|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000481848.2_Silent_p.N599N|SOGA3_ENST00000368268.2_Silent_p.N599N			Q5TF21	SOGA3_HUMAN	SOGA family member 3	599					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											TGCCCAGGATGTTGGCTTCTT	0.597													G|||	1753	0.35004	0.1309	0.4424	5008	,	,		19251	0.7371		0.2416	False		,,,				2504	0.2935				p.N599N		Atlas-SNP	.											C6orf174,colon,carcinoma,0,1	.	.	1	0			c.C1797T						PASS	.	G		560,3716		36,488,1614	140.0	149.0	146.0		1797	4.6	1.0	6	dbSNP_107	146	2044,6460		257,1530,2465	no	coding-synonymous	C6orf174	NM_001012279.2		293,2018,4079	AA,AG,GG		24.0357,13.0964,20.3756		599/948	127797374	2604,10176	2138	4252	6390	SO:0001819	synonymous_variant	387104	exon6			CAGGATGTTGGCT	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1797C>T	6.37:g.127797374G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	75	47	0.626667	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																			G|0.678;A|0.322	0.322	strong		0.597	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
CXXC5	51523	hgsc.bcm.edu	37	5	139060486	139060486	+	Silent	SNP	G	G	A	rs356445	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139060486G>A	ENST00000302517.3	+	2	1092	c.378G>A	c.(376-378)gcG>gcA	p.A126A	CXXC5_ENST00000511048.1_Silent_p.A126A	NM_016463.7	NP_057547.5	Q7LFL8	CXXC5_HUMAN	CXXC finger protein 5	126					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	12			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCCATGGCGGTGGACAAAA	0.652													G|||	957	0.191094	0.5015	0.0634	5008	,	,		16819	0.0585		0.0517	False		,,,				2504	0.1421				p.A126A		Atlas-SNP	.											CXXC5,NS,carcinoma,0,1	CXXC5	27	1	0			c.G378A						PASS	.						68.0	83.0	78.0					5																	139060486		2111	4242	6353	SO:0001819	synonymous_variant	51523	exon2			CATGGCGGTGGAC	AK024338	CCDS43370.1	5q31.3	2014-02-18	2011-12-01						26943	protein-coding gene	gene with protein product	"""retinoid-inducible nuclear factor"", ""WT1-induced Inhibitor of Dishevelled"""	612752				11042152, 19001364, 19182210, 20220130	Standard	NM_016463		Approved	HSPC195, RINF, WID	uc010jfg.1	Q7LFL8		ENST00000302517.3:c.378G>A	5.37:g.139060486G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_016463	B3KND0|C8CBA8|Q8TB79|Q9NV51|Q9P0S8	Silent	SNP	ENST00000302517.3	37	CCDS43370.1																																																																																			G|0.837;A|0.163	0.163	strong		0.652	CXXC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372744.1	NM_016463	
EFHB	151651	hgsc.bcm.edu	37	3	19961331	19961331	+	Silent	SNP	T	T	C	rs2929362|rs386659061	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:19961331T>C	ENST00000295824.9	-	3	1151	c.990A>G	c.(988-990)tcA>tcG	p.S330S	EFHB_ENST00000498089.1_5'UTR|EFHB_ENST00000344838.4_Silent_p.S200S	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	330							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						TTACCAGTACTGAAATTTTAG	0.338													T|||	983	0.196286	0.3177	0.1153	5008	,	,		16733	0.1081		0.1481	False		,,,				2504	0.2301				p.S330S		Atlas-SNP	.											.	EFHB	186	.	0			c.A990G						PASS	.	T		24,4380		4,16,2182	84.0	94.0	90.0		990	1.3	0.0	3	dbSNP_101	90	14,8586		2,10,4288	no	coding-synonymous	EFHB	NM_144715.3		6,26,6470	CC,CT,TT		0.1628,0.545,0.2922		330/834	19961331	38,12966	2202	4300	6502	SO:0001819	synonymous_variant	151651	exon3			CAGTACTGAAATT	AK122616	CCDS33715.2	3p24.3	2014-07-18			ENSG00000163576	ENSG00000163576		"""EF-hand domain containing"""	26330	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 21"""					12477932	Standard	NM_144715		Approved	FLJ25200, CFAP21	uc003cbl.4	Q8N7U6	OTTHUMG00000150505	ENST00000295824.9:c.990A>G	3.37:g.19961331T>C		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	168	76	0.452381	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Silent	SNP	ENST00000295824.9	37	CCDS33715.2																																																																																			T|0.652;G|0.040;C|0.133;A|0.175	0.133	strong		0.338	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
AKAP3	10566	hgsc.bcm.edu	37	12	4735737	4735737	+	Silent	SNP	A	A	G	rs2072358	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4735737A>G	ENST00000545990.2	-	5	2855	c.2331T>C	c.(2329-2331)ctT>ctC	p.L777L	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Silent_p.L777L	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	777					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						CTACCCATTGAAGGACGGCTT	0.493													A|||	1323	0.264177	0.1475	0.3256	5008	,	,		21345	0.3621		0.3022	False		,,,				2504	0.2382				p.L777L		Atlas-SNP	.											.	AKAP3	212	.	0			c.T2331C						PASS	.	A		706,3700	295.0+/-283.4	50,606,1547	155.0	142.0	146.0		2331	-2.0	1.0	12	dbSNP_96	146	2518,6082	414.1+/-351.3	408,1702,2190	no	coding-synonymous	AKAP3	NM_006422.2		458,2308,3737	GG,GA,AA		29.2791,16.0236,24.7886		777/854	4735737	3224,9782	2203	4300	6503	SO:0001819	synonymous_variant	10566	exon4			CCATTGAAGGACG	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.2331T>C	12.37:g.4735737A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	178	85	0.477528	NM_006422	O75945|Q86X01|Q9UM61	Silent	SNP	ENST00000545990.2	37	CCDS8531.1																																																																																			G|0.259;A|0.741	0.259	strong		0.493	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422	
DUSP27	92235	hgsc.bcm.edu	37	1	167097739	167097739	+	Missense_Mutation	SNP	C	C	A	rs2281959	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:167097739C>A	ENST00000361200.2	+	6	3537	c.3371C>A	c.(3370-3372)aCt>aAt	p.T1124N	DUSP27_ENST00000443333.1_Missense_Mutation_p.T1124N|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.T1124N			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	1124			T -> N (in dbSNP:rs2281959).		protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CGGAGAAGCACTGACAGGGAG	0.517													C|||	1914	0.382188	0.2776	0.2867	5008	,	,		20287	0.7431		0.3141	False		,,,				2504	0.2894				p.T1124N		Atlas-SNP	.											.	DUSP27	235	.	0			c.C3371A						PASS	.	C	ASN/THR	1248,3158	428.7+/-342.0	181,886,1136	46.0	42.0	43.0		3371	0.9	0.4	1	dbSNP_100	43	2668,5932	425.7+/-355.0	433,1802,2065	yes	missense	DUSP27	NM_001080426.1	65	614,2688,3201	AA,AC,CC		31.0233,28.325,30.1092	probably-damaging	1124/1159	167097739	3916,9090	2203	4300	6503	SO:0001583	missense	92235	exon5			GAAGCACTGACAG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.3371C>A	1.37:g.167097739C>A	ENSP00000354483:p.Thr1124Asn	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	917	0.4198717948717949	142	0.2886178861788618	117	0.32320441988950277	435	0.7604895104895105	223	0.2941952506596306	C	5.249	0.231340	0.09969	0.28325	0.310233	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03580	3.88;3.88;3.88	5.4	0.916	0.19373	.	0.385319	0.22313	N	0.061703	T	0.01523	0.0049	M	0.63428	1.95	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.33085	-0.9882	9	0.87932	D	0	-3.2628	4.6731	0.12699	0.3827:0.4217:0.1241:0.0714	rs2281959;rs52811569;rs60867293;rs2281959	1124	Q5VZP5	DUS27_HUMAN	N	1124	ENSP00000354483:T1124N;ENSP00000271385:T1124N;ENSP00000404874:T1124N	ENSP00000271385:T1124N	T	+	2	0	DUSP27	165364363	0.002000	0.14202	0.363000	0.25875	0.335000	0.28730	0.036000	0.13819	0.198000	0.20407	-0.335000	0.08231	ACT	C|0.639;A|0.361	0.361	strong		0.517	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
NVL	4931	hgsc.bcm.edu	37	1	224482084	224482084	+	Missense_Mutation	SNP	C	C	T	rs34631151	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:224482084C>T	ENST00000281701.6	-	12	1469	c.1210G>A	c.(1210-1212)Gtc>Atc	p.V404I	NVL_ENST00000361463.3_Missense_Mutation_p.V298I|NVL_ENST00000340871.4_Missense_Mutation_p.V215I|NVL_ENST00000391875.2_Missense_Mutation_p.V298I|NVL_ENST00000469075.1_Missense_Mutation_p.V313I|NVL_ENST00000482491.1_Missense_Mutation_p.V128I	NM_002533.3	NP_002524.2	O15381	NVL_HUMAN	nuclear VCP-like	404			V -> I (in dbSNP:rs34631151).			membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|prostate(1)|skin(4)|soft_tissue(1)|urinary_tract(1)	42				GBM - Glioblastoma multiforme(131;0.00501)		ATAACTAGGACCCGGGCTGTA	0.463													C|||	84	0.0167732	0.0015	0.0187	5008	,	,		17146	0.0		0.0427	False		,,,				2504	0.0266				p.V404I		Atlas-SNP	.											.	NVL	74	.	0			c.G1210A						PASS	.	C	ILE/VAL,ILE/VAL	38,4368	40.8+/-73.8	0,38,2165	59.0	58.0	58.0		1210,892	4.7	0.9	1	dbSNP_126	58	385,8215	125.0+/-183.6	13,359,3928	yes	missense,missense	NVL	NM_002533.3,NM_206840.2	29,29	13,397,6093	TT,TC,CC		4.4767,0.8625,3.2523	probably-damaging,probably-damaging	404/857,298/751	224482084	423,12583	2203	4300	6503	SO:0001583	missense	4931	exon12			CTAGGACCCGGGC	U78772	CCDS1541.1, CCDS1542.1, CCDS58062.1, CCDS58063.1	1q41-q42.2	2010-04-21			ENSG00000143748	ENSG00000143748		"""ATPases / AAA-type"""	8070	protein-coding gene	gene with protein product	"""Nuclear valosin-containing protein-like"", ""nuclear VCP-like protein"""	602426				9286697	Standard	NM_002533		Approved		uc001hok.3	O15381	OTTHUMG00000037536	ENST00000281701.6:c.1210G>A	1.37:g.224482084C>T	ENSP00000281701:p.Val404Ile	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_002533	B4DMC4|B4DP98|Q96EM7	Missense_Mutation	SNP	ENST00000281701.6	37	CCDS1541.1	37|37	0.01694139194139194|0.01694139194139194	1|1	0.0020325203252032522|0.0020325203252032522	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	30|30	0.0395778364116095|0.0395778364116095	C|C	29.8|29.8	5.035457|5.035457	0.93630|0.93630	0.008625|0.008625	0.044767|0.044767	ENSG00000143748|ENSG00000143748	ENST00000469968|ENST00000281701;ENST00000391875;ENST00000469075;ENST00000482491;ENST00000340871;ENST00000361463	.|D;D;D;D;D;D	.|0.94376	.|-3.41;-3.41;-3.41;-3.41;-3.41;-3.41	5.65|5.65	4.74|4.74	0.60224|0.60224	.|ATPase, AAA-type, conserved site (1);ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.82898|0.82898	0.5137|0.5137	L|L	0.35288|0.35288	1.05|1.05	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.71674	.|0.993;0.998;0.995	.|D;D;D	.|0.67382	.|0.923;0.951;0.951	D|D	0.87143|0.87143	0.2204|0.2204	5|10	.|0.51188	.|T	.|0.08	-10.0212|-10.0212	14.8777|14.8777	0.70507|0.70507	0.0:0.9309:0.0:0.0691|0.0:0.9309:0.0:0.0691	rs34631151|rs34631151	.|215;313;404	.|B4DMC4;B4DP98;O15381	.|.;.;NVL_HUMAN	D|I	286|404;298;313;128;215;298	.|ENSP00000281701:V404I;ENSP00000375747:V298I;ENSP00000417826:V313I;ENSP00000417213:V128I;ENSP00000341362:V215I;ENSP00000354779:V298I	.|ENSP00000281701:V404I	G|V	-|-	2|1	0|0	NVL|NVL	222548707|222548707	1.000000|1.000000	0.71417|0.71417	0.941000|0.941000	0.38009|0.38009	0.948000|0.948000	0.59901|0.59901	5.856000|5.856000	0.69518|0.69518	1.532000|1.532000	0.49169|0.49169	0.491000|0.491000	0.48974|0.48974	GGT|GTC	C|0.969;T|0.031	0.031	strong		0.463	NVL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091453.2	NM_002533	
MYO3A	53904	hgsc.bcm.edu	37	10	26286159	26286159	+	Silent	SNP	G	G	T	rs12257119	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:26286159G>T	ENST00000265944.5	+	6	646	c.480G>T	c.(478-480)acG>acT	p.T160T	MYO3A_ENST00000376302.1_Silent_p.T160T|MYO3A_ENST00000376301.1_Silent_p.T160T|MYO3A_ENST00000543632.1_Silent_p.T160T	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	160	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TATTGACCACGGAAGGTGGAG	0.318													T|||	458	0.0914537	0.2526	0.0548	5008	,	,		20309	0.004		0.0626	False		,,,				2504	0.0194				p.T160T		Atlas-SNP	.											.	MYO3A	371	.	0			c.G480T						PASS	.	T		956,3450	734.1+/-410.5	95,766,1342	84.0	77.0	79.0		480	-4.3	0.7	10	dbSNP_120	79	469,8123	795.6+/-407.5	17,435,3844	no	coding-synonymous	MYO3A	NM_017433.4		112,1201,5186	TT,TG,GG		5.4586,21.6977,10.9632		160/1617	26286159	1425,11573	2203	4296	6499	SO:0001819	synonymous_variant	53904	exon6			GACCACGGAAGGT	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.480G>T	10.37:g.26286159G>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	145	65	0.448276	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																			G|0.902;T|0.098	0.098	strong		0.318	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
MIOX	55586	hgsc.bcm.edu	37	22	50926768	50926768	+	Silent	SNP	C	C	T	rs2232883	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50926768C>T	ENST00000216075.6	+	5	479	c.405C>T	c.(403-405)ccC>ccT	p.P135P	MIOX_ENST00000395732.3_Silent_p.P135P|MIOX_ENST00000395733.3_Missense_Mutation_p.P146L	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	135					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCGGGGAGCCCCAGGTAAGAG	0.647													c|||	427	0.0852636	0.093	0.0908	5008	,	,		14186	0.0278		0.1392	False		,,,				2504	0.0746				p.P135P		Atlas-SNP	.											.	MIOX	21	.	0			c.C405T						PASS	.	C		450,3956	211.5+/-231.7	30,390,1783	55.0	57.0	56.0		405	-2.2	1.0	22	dbSNP_98	56	1244,7356	245.7+/-274.4	101,1042,3157	no	coding-synonymous	MIOX	NM_017584.5		131,1432,4940	TT,TC,CC		14.4651,10.2133,13.0248		135/286	50926768	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	55586	exon5			GGAGCCCCAGGTA	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"""kidney-specific protein 32"""	606774	"""aldehyde reductase (aldose reductase) like 6"""	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.405C>T	22.37:g.50926768C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Silent	SNP	ENST00000216075.6	37	CCDS14092.1	212	0.09706959706959707	48	0.0975609756097561	38	0.10497237569060773	16	0.027972027972027972	110	0.14511873350923482	C	10.08	1.251662	0.22880	0.102133	0.144651	ENSG00000100253	ENST00000395733	.	.	.	4.29	-2.17	0.07059	.	0.057262	0.64402	D	0.000001	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	B	0.09022	0.002	B	0.09377	0.004	T	0.07366	-1.0776	7	0.72032	D	0.01	-9.7685	0.8144	0.01099	0.163:0.2381:0.3211:0.2778	rs2232883	146	Q9UGB7-2	.	L	146	.	ENSP00000379082:P146L	P	+	2	0	MIOX	49273634	0.009000	0.17119	1.000000	0.80357	0.751000	0.42716	-0.849000	0.04322	0.058000	0.16222	0.436000	0.28706	CCC	C|0.878;T|0.122	0.122	strong		0.647	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584	
PITRM1	10531	hgsc.bcm.edu	37	10	3200292	3200292	+	Missense_Mutation	SNP	G	G	A	rs3182535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:3200292G>A	ENST00000224949.4	-	11	1224	c.1190C>T	c.(1189-1191)gCg>gTg	p.A397V	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380994.1_5'Flank|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.A397V|PITRM1_ENST00000451104.2_Missense_Mutation_p.A365V			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	397			A -> V (in dbSNP:rs3182535). {ECO:0000269|PubMed:10360838, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						GTCTTTCTCCGCAATCCCTTG	0.463													G|||	3135	0.625998	0.5719	0.5677	5008	,	,		17501	0.6022		0.7097	False		,,,				2504	0.6789				p.A397V		Atlas-SNP	.											.	PITRM1	109	.	0			c.C1190T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	2447,1427		788,871,278	106.0	100.0	102.0		1190,1094,1190	4.7	0.0	10	dbSNP_105	102	5828,2432		2037,1754,339	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	64,64,64	2825,2625,617	AA,AG,GG		29.4431,36.8353,31.8032	benign,benign,benign	397/1039,365/940,397/1038	3200292	8275,3859	1937	4130	6067	SO:0001583	missense	10531	exon11			TTCTCCGCAATCC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1190C>T	10.37:g.3200292G>A	ENSP00000224949:p.Ala397Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	1411	0.6460622710622711	279	0.5670731707317073	231	0.638121546961326	353	0.6171328671328671	548	0.7229551451187335	g	13.46	2.243903	0.39697	0.631647	0.705569	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.08282	3.11;3.11;3.11	5.58	4.66	0.58398	.	0.212459	0.49305	D	0.000155	T	0.00012	0.0000	.	.	.	0.48901	P	2.76000000000054E-4	B;B;B	0.28933	0.008;0.228;0.005	B;B;B	0.33254	0.006;0.16;0.032	T	0.01596	-1.1316	8	0.29301	T	0.29	-13.1671	13.3929	0.60834	0.0:0.0:0.7137:0.2863	rs3182535;rs17133337;rs17855374;rs58562123;rs3182535	390;365;397	E9PDX6;E7ES23;C9JSL2	.;.;.	V	397;390;397;365	ENSP00000224949:A397V;ENSP00000370377:A397V;ENSP00000401201:A365V	ENSP00000224949:A397V	A	-	2	0	PITRM1	3190292	0.999000	0.42202	0.002000	0.10522	0.010000	0.07245	5.411000	0.66386	1.319000	0.45190	0.563000	0.77884	GCG	G|0.356;A|0.644	0.644	strong		0.463	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
IGHMBP2	3508	hgsc.bcm.edu	37	11	68705674	68705674	+	Missense_Mutation	SNP	C	C	A	rs17612126	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:68705674C>A	ENST00000255078.3	+	14	2747	c.2636C>A	c.(2635-2637)aCg>aAg	p.T879K		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	879			T -> K (in HMN6; dbSNP:rs17612126). {ECO:0000269|PubMed:15797190}.		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)			GATCTGCCCACGGAGGAGGAC	0.562													C|||	987	0.197085	0.0166	0.438	5008	,	,		17099	0.2212		0.2654	False		,,,				2504	0.1748				p.T879K		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.C2636A	GRCh37	CM055288	IGHMBP2	M	rs17612126	PASS	.	C	LYS/THR	342,4058	176.6+/-205.7	17,308,1875	68.0	72.0	71.0		2636	-3.6	0.0	11	dbSNP_123	71	2387,6201	396.4+/-345.4	341,1705,2248	yes	missense	IGHMBP2	NM_002180.2	78	358,2013,4123	AA,AC,CC		27.7946,7.7727,21.0117	benign	879/994	68705674	2729,10259	2200	4294	6494	SO:0001583	missense	3508	exon14			TGCCCACGGAGGA	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.2636C>A	11.37:g.68705674C>A	ENSP00000255078:p.Thr879Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	13	0.142857	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	493	0.22573260073260074	9	0.018292682926829267	139	0.3839779005524862	144	0.2517482517482518	201	0.26517150395778366	C	0.585	-0.835530	0.02713	0.077727	0.277946	ENSG00000132740	ENST00000255078	D	0.89415	-2.51	3.9	-3.62	0.04543	Zinc finger, AN1-type (1);	7.534400	0.00166	N	0.000004	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	1.0000000000287557E-6	B	0.28552	0.215	B	0.20577	0.03	T	0.44651	-0.9314	9	0.05959	T	0.93	-10.2922	0.3694	0.00377	0.2403:0.26:0.2553:0.2443	rs17612126;rs52812152;rs61068197;rs17612126	879	P38935	SMBP2_HUMAN	K	879	ENSP00000255078:T879K	ENSP00000255078:T879K	T	+	2	0	IGHMBP2	68462250	0.523000	0.26274	0.000000	0.03702	0.020000	0.10135	0.878000	0.28126	-0.893000	0.03930	0.462000	0.41574	ACG	C|0.791;A|0.209	0.209	strong		0.562	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
PIGB	9488	hgsc.bcm.edu	37	15	55619796	55619796	+	Missense_Mutation	SNP	T	T	C	rs2290344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:55619796T>C	ENST00000164305.5	+	4	776	c.485T>C	c.(484-486)aTg>aCg	p.M162T	PIGB_ENST00000539642.1_Intron	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	162			M -> T (in dbSNP:rs2290344).		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		TACTCATTAATGAAGCAACTA	0.388													T|||	1152	0.230032	0.0189	0.2118	5008	,	,		15519	0.5635		0.1203	False		,,,				2504	0.2975				p.M162T		Atlas-SNP	.											.	PIGB	36	.	0			c.T485C						PASS	.	T	THR/MET	144,3558		1,142,1708	93.0	87.0	89.0		485	3.2	1.0	15	dbSNP_100	89	889,7313		59,771,3271	yes	missense	PIGB	NM_004855.4	81	60,913,4979	CC,CT,TT		10.8388,3.8898,8.6778	benign	162/555	55619796	1033,10871	1851	4101	5952	SO:0001583	missense	9488	exon4			CATTAATGAAGCA	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8959	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 3"", ""dol-P-Man dependent GPI mannosyltransferase"""	604122	"""phosphatidylinositol glycan, class B"""			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.485T>C	15.37:g.55619796T>C	ENSP00000164305:p.Met162Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	47	0.594937	NM_004855	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	37		454	0.2078754578754579	8	0.016260162601626018	73	0.20165745856353592	292	0.5104895104895105	81	0.10686015831134564	T	10.78	1.446235	0.25987	0.038898	0.108388	ENSG00000069943	ENST00000164305	T	0.63580	-0.05	5.57	3.23	0.37069	.	0.408765	0.30392	N	0.009732	T	0.00012	0.0000	N	0.00237	-1.79	0.09310	P	0.9999999999999959	B	0.02656	0.0	B	0.06405	0.002	T	0.44513	-0.9323	9	0.23302	T	0.38	-6.9731	8.8825	0.35382	0.0:0.1556:0.0:0.8444	rs2290344;rs52791382;rs59002340;rs2290344	162	Q92521	PIGB_HUMAN	T	162	ENSP00000164305:M162T	ENSP00000164305:M162T	M	+	2	0	PIGB	53407088	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	2.727000	0.47311	0.912000	0.36772	0.533000	0.62120	ATG	T|0.805;C|0.195	0.195	strong		0.388	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855	
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 GAIIx	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		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	79	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	
DNALI1	7802	hgsc.bcm.edu	37	1	38023316	38023316	+	Missense_Mutation	SNP	C	C	T	rs11749	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:38023316C>T	ENST00000296218.7	+	2	270	c.260C>T	c.(259-261)gCa>gTa	p.A87V	DNALI1_ENST00000541606.1_5'UTR	NM_003462.3	NP_003453.2	O14645	IDLC_HUMAN	dynein, axonemal, light intermediate chain 1	65					cellular component movement (GO:0006928)|metabolic process (GO:0008152)|single fertilization (GO:0007338)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|filopodium (GO:0030175)	microtubule motor activity (GO:0003777)			breast(1)|kidney(1)|large_intestine(2)|ovary(1)	5		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ACAAAGCAGGCAGAAGAAATC	0.537													C|||	1023	0.204273	0.0681	0.2046	5008	,	,		20615	0.3502		0.2535	False		,,,				2504	0.1871				p.A87V		Atlas-SNP	.											.	DNALI1	25	.	0			c.C260T						PASS	.	C	VAL/ALA	427,3979	208.8+/-229.8	19,389,1795	176.0	170.0	172.0		260	5.8	1.0	1	dbSNP_52	172	2211,6389	376.5+/-338.2	297,1617,2386	yes	missense	DNALI1	NM_003462.3	64	316,2006,4181	TT,TC,CC		25.7093,9.6913,20.2829	possibly-damaging	87/281	38023316	2638,10368	2203	4300	6503	SO:0001583	missense	7802	exon2			AGCAGGCAGAAGA	AF006386	CCDS420.1	1p35.1	2008-07-18	2006-09-04		ENSG00000163879	ENSG00000163879		"""Axonemal dyneins"""	14353	protein-coding gene	gene with protein product	"""inner dynein arm, homolog of clamydomonas"", ""dJ423B22.5 (axonemal dynein light chain (hp28))"""	602135	"""dynein, axonemal, light intermediate polypeptide 1"""			9284741	Standard	NM_003462		Approved	P28, hp28, dJ423B22.5	uc001cbj.3	O14645	OTTHUMG00000004222	ENST00000296218.7:c.260C>T	1.37:g.38023316C>T	ENSP00000296218:p.Ala87Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	18	0.339623	NM_003462	A8K387|B4DHN6|Q05BL9|Q5HYE2|Q5TGH0|Q7L0I5	Missense_Mutation	SNP	ENST00000296218.7	37	CCDS420.1	522	0.23901098901098902	34	0.06910569105691057	83	0.2292817679558011	216	0.3776223776223776	189	0.24934036939313983	C	22.9	4.346647	0.82022	0.096913	0.257093	ENSG00000163879	ENST00000296218	T	0.42513	0.97	5.76	5.76	0.90799	.	0.313134	0.38663	N	0.001610	T	0.00012	0.0000	N	0.12182	0.205	0.09310	P	1.0	P	0.41420	0.749	P	0.45753	0.492	T	0.47812	-0.9088	9	0.27082	T	0.32	-6.8937	17.4499	0.87589	0.0:1.0:0.0:0.0	rs11749;rs1047072;rs3170935;rs11540746;rs17350512;rs52811198;rs60888941;rs11540746	65	O14645	IDLC_HUMAN	V	87	ENSP00000296218:A87V	ENSP00000296218:A87V	A	+	2	0	DNALI1	37795903	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.974000	0.56852	2.725000	0.93324	0.591000	0.81541	GCA	C|0.786;G|0.000;N|0.000;T|0.213	0.213	strong		0.537	DNALI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012159.1	NM_003462	
ARMS2	387715	hgsc.bcm.edu	37	10	124214355	124214355	+	Nonsense_Mutation	SNP	C	C	T	rs2736911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124214355C>T	ENST00000528446.1	+	1	187	c.112C>T	c.(112-114)Cga>Tga	p.R38*		NM_001099667.1	NP_001093137.1	P0C7Q2	ARMS2_HUMAN	age-related maculopathy susceptibility 2	38					retina homeostasis (GO:0001895)	mitochondrion (GO:0005739)|photoreceptor inner segment (GO:0001917)				ovary(1)	1		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				TTCCACTCTGCGAGAGTCTGT	0.542													C|||	573	0.114417	0.056	0.0908	5008	,	,		19861	0.1905		0.173	False		,,,				2504	0.0716				p.R38X		Atlas-SNP	.											ARMS2_ENST00000528446,NS,carcinoma,-1,1	ARMS2	7	1	0			c.C112T	GRCh37	CM083592	ARMS2	M	rs2736911	PASS	.	C	stop/ARG	288,3772		14,260,1756	142.0	147.0	145.0		112	-2.2	0.0	10	dbSNP_100	145	1274,7116		105,1064,3026	yes	stop-gained	ARMS2	NM_001099667.1		119,1324,4782	TT,TC,CC		15.1847,7.0936,12.5462		38/108	124214355	1562,10888	2030	4195	6225	SO:0001587	stop_gained	387715	exon1			ACTCTGCGAGAGT	BC066349	CCDS53585.1	10q26.13	2013-01-23			ENSG00000254636	ENSG00000254636			32685	protein-coding gene	gene with protein product		611313				16080115, 16174643	Standard	NM_001099667		Approved	LOC387715, ARMD8	uc001lgi.3	P0C7Q2	OTTHUMG00000048232	ENST00000528446.1:c.112C>T	10.37:g.124214355C>T	ENSP00000436682:p.Arg38*	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_001099667	B2Y7I5	Nonsense_Mutation	SNP	ENST00000528446.1	37	CCDS53585.1	283	0.1295787545787546	32	0.06504065040650407	32	0.08839779005524862	101	0.17657342657342656	118	0.15567282321899736	C	12.36	1.914830	0.33815	0.070936	0.151847	ENSG00000254636	ENST00000528446	.	.	.	1.45	-2.21	0.06973	.	.	.	.	.	.	.	.	.	.	.	0.20307	P	0.9999111937	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	0.5279	0.00623	0.1922:0.2562:0.3244:0.2272	rs2736911;rs2736911	.	.	.	X	38	.	ENSP00000436682:R38X	R	+	1	2	ARMS2	124204345	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.426000	0.07008	-0.730000	0.04869	-1.080000	0.02220	CGA	C|0.869;T|0.131	0.131	strong		0.542	ARMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109727.2		
PGBD1	84547	hgsc.bcm.edu	37	6	28268824	28268824	+	Missense_Mutation	SNP	A	A	G	rs33932084	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:28268824A>G	ENST00000405948.2	+	7	1613	c.1193A>G	c.(1192-1194)aAt>aGt	p.N398S	PGBD1_ENST00000259883.3_Missense_Mutation_p.N398S	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	398			N -> S (in dbSNP:rs33932084).			membrane (GO:0016020)|nucleus (GO:0005634)	scavenger receptor activity (GO:0005044)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(2)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	41						ATTAAACCCAATTTTCCAAGC	0.383													A|||	121	0.0241613	0.0257	0.0216	5008	,	,		19621	0.001		0.0706	False		,,,				2504	0.0				p.N398S		Atlas-SNP	.											.	PGBD1	106	.	0			c.A1193G						PASS	.	A	SER/ASN,SER/ASN	250,4156	140.4+/-175.9	6,238,1959	66.0	71.0	69.0		1193,1193	-0.6	1.0	6	dbSNP_126	69	755,7845	176.3+/-226.2	35,685,3580	yes	missense,missense	PGBD1	NM_001184743.1,NM_032507.3	46,46	41,923,5539	GG,GA,AA		8.7791,5.6741,7.7272	benign,benign	398/810,398/810	28268824	1005,12001	2203	4300	6503	SO:0001583	missense	84547	exon7			AACCCAATTTTCC	D88259	CCDS4648.1	6p22.1	2013-01-09			ENSG00000137338	ENSG00000137338		"""-"""	19398	protein-coding gene	gene with protein product							Standard	NM_001184743		Approved	HUCEP-4, dJ874C20.4, SCAND4	uc003nkz.3	Q96JS3	OTTHUMG00000014520	ENST00000405948.2:c.1193A>G	6.37:g.28268824A>G	ENSP00000385213:p.Asn398Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	44	0.709677	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	83	0.038003663003663	18	0.036585365853658534	7	0.019337016574585635	0	0.0	58	0.07651715039577836	A	8.244	0.807549	0.16467	0.056741	0.087791	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01388	4.95;4.95	4.54	-0.61	0.11604	.	0.439561	0.19459	N	0.113751	T	0.00271	0.0008	N	0.12182	0.205	0.25988	N	0.982283	B	0.10296	0.003	B	0.06405	0.002	T	0.31364	-0.9946	10	0.10902	T	0.67	-19.5486	7.3919	0.26915	0.5566:0.0:0.4434:0.0	rs33932084	398	Q96JS3	PGBD1_HUMAN	S	398	ENSP00000385213:N398S;ENSP00000259883:N398S	ENSP00000259883:N398S	N	+	2	0	PGBD1	28376803	0.064000	0.20934	0.992000	0.48379	0.995000	0.86356	-0.220000	0.09215	-0.170000	0.10816	0.533000	0.62120	AAT	A|0.939;G|0.061	0.061	strong		0.383	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2		
LEPR	3953	hgsc.bcm.edu	37	1	66102257	66102257	+	Silent	SNP	G	G	A	rs1805096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:66102257G>A	ENST00000349533.6	+	20	3242	c.3057G>A	c.(3055-3057)ccG>ccA	p.P1019P	LEPR_ENST00000406510.3_Silent_p.P86P	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)		AAAATTCTCCGTTGAAGGATT	0.413													A|||	2653	0.529752	0.4478	0.4841	5008	,	,		18263	0.869		0.3797	False		,,,				2504	0.4775				p.P1019P		Atlas-SNP	.											.	LEPR	284	.	0			c.G3057A						PASS	.	A		2073,2329		506,1061,634	66.0	72.0	70.0		3057	-11.9	0.0	1	dbSNP_89	70	3222,5370		624,1974,1698	no	coding-synonymous	LEPR	NM_002303.5		1130,3035,2332	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	37.5,47.0922,40.7496		1019/1166	66102257	5295,7699	2201	4296	6497	SO:0001819	synonymous_variant	3953	exon20			TTCTCCGTTGAAG	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.3057G>A	1.37:g.66102257G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_002303	Q6FHL5	Silent	SNP	ENST00000349533.6	37	CCDS631.1																																																																																			G|0.516;A|0.484	0.484	strong		0.413	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
ZNF414	84330	hgsc.bcm.edu	37	19	8578035	8578035	+	Missense_Mutation	SNP	T	T	C	rs8100431	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8578035T>C	ENST00000255616.8	-	2	295	c.194A>G	c.(193-195)cAg>cGg	p.Q65R	ZNF414_ENST00000393927.4_Missense_Mutation_p.Q65R	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	65			Q -> R (in dbSNP:rs8100431). {ECO:0000269|PubMed:15489334}.		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						GGAGCCCTGCTGCATCCCTCC	0.706													T|||	1544	0.308307	0.1415	0.2709	5008	,	,		15055	0.5357		0.3082	False		,,,				2504	0.3262				p.Q65R		Atlas-SNP	.											.	ZNF414	25	.	0			c.A194G						PASS	.	T	ARG/GLN,ARG/GLN	655,3647		61,533,1557	8.0	8.0	8.0		194,194	2.0	0.4	19	dbSNP_116	8	2293,6123		349,1595,2264	yes	missense,missense	ZNF414	NM_001146175.1,NM_032370.2	43,43	410,2128,3821	CC,CT,TT		27.2457,15.2255,23.1797	benign,benign	65/391,65/313	8578035	2948,9770	2151	4208	6359	SO:0001583	missense	84330	exon2			CCCTGCTGCATCC	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.194A>G	19.37:g.8578035T>C	ENSP00000255616:p.Gln65Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	37	CCDS12205.1	713	0.32646520146520147	69	0.1402439024390244	113	0.31215469613259667	297	0.5192307692307693	234	0.3087071240105541	T	13.78	2.338251	0.41398	0.152255	0.272457	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.08546	3.08;3.08	4.13	1.95	0.26073	.	0.000000	0.33438	N	0.004910	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D;D	0.57899	0.981;0.981	D;D	0.70487	0.969;0.954	T	0.47459	-0.9116	9	0.66056	D	0.02	-9.8746	3.2547	0.06827	0.2039:0.1132:0.0:0.6829	rs8100431;rs17355273;rs17855387	65;65	Q96IQ9;A8MY94	ZN414_HUMAN;.	R	65	ENSP00000377504:Q65R;ENSP00000255616:Q65R	ENSP00000255616:Q65R	Q	-	2	0	ZNF414	8484035	0.982000	0.34865	0.422000	0.26621	0.367000	0.29736	0.944000	0.29043	0.223000	0.20920	0.533000	0.62120	CAG	T|0.673;C|0.327	0.327	strong		0.706	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370	
RYR3	6263	hgsc.bcm.edu	37	15	33905410	33905410	+	Missense_Mutation	SNP	A	A	G	rs2229116	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:33905410A>G	ENST00000389232.4	+	19	2261	c.2191A>G	c.(2191-2193)Atc>Gtc	p.I731V	RYR3_ENST00000415757.3_Missense_Mutation_p.I731V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	731	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.		I -> V (in dbSNP:rs2229116). {ECO:0000269|PubMed:9515741}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGTGGCTTCCATCAACCAGCA	0.602													A|||	1012	0.202077	0.1271	0.3314	5008	,	,		18103	0.1587		0.2247	False		,,,				2504	0.2331				p.I731V		Atlas-SNP	.											RYR3,colon,carcinoma,0,1	RYR3	760	1	0			c.A2191G						PASS	.	A	VAL/ILE	576,3604		30,516,1544	38.0	41.0	40.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2191	3.1	1.0	15	dbSNP_98	40	1824,6658		203,1418,2620	yes	missense	RYR3	NM_001036.3	29	233,1934,4164	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	21.5044,13.7799,18.9544	benign	731/4871	33905410	2400,10262	2090	4241	6331	SO:0001583	missense	6263	exon19			GCTTCCATCAACC		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.2191A>G	15.37:g.33905410A>G	ENSP00000373884:p.Ile731Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	477	0.2184065934065934	89	0.18089430894308944	114	0.3149171270718232	98	0.17132867132867133	176	0.23218997361477572	A	8.841	0.942258	0.18281	0.137799	0.215044	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.68331	-0.32;-0.32	5.4	3.06	0.35304	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.296753	0.33457	N	0.004896	T	0.00012	0.0000	N	0.19112	0.55	0.39187	P	0.037104000000000026	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18147	-1.0346	9	0.15952	T	0.53	.	2.9905	0.05981	0.4962:0.232:0.2718:0.0	rs2229116;rs2277889;rs8042362;rs17817397;rs52825179;rs58186010;rs2229116	731;731	Q15413-2;Q15413	.;RYR3_HUMAN	V	731	ENSP00000373884:I731V;ENSP00000399610:I731V	ENSP00000354735:I731V	I	+	1	0	RYR3	31692702	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.792000	0.26929	1.079000	0.41038	0.529000	0.55759	ATC	A|0.790;G|0.210	0.210	strong		0.602	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
MCRS1	10445	hgsc.bcm.edu	37	12	49952668	49952668	+	Silent	SNP	G	G	A	rs2303305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49952668G>A	ENST00000550165.1	-	15	1526	c.1260C>T	c.(1258-1260)ctC>ctT	p.L420L	MCRS1_ENST00000343810.4_Silent_p.L420L|MCRS1_ENST00000546244.1_Silent_p.L229L|MCRS1_ENST00000547182.1_5'UTR|MCRS1_ENST00000357123.4_Silent_p.L433L			Q96EZ8	MCRS1_HUMAN	microspherule protein 1	420					cellular protein modification process (GO:0006464)|chromatin organization (GO:0006325)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)	23						TGGAGCCACAGAGCACCGGCC	0.567													G|||	544	0.108626	0.1891	0.0836	5008	,	,		20234	0.0823		0.0875	False		,,,				2504	0.0665				p.L433L		Atlas-SNP	.											.	MCRS1	40	.	0			c.C1299T						PASS	.	G	,	748,3658	305.8+/-289.2	61,626,1516	61.0	58.0	59.0		1299,1260	-2.7	1.0	12	dbSNP_100	59	720,7880	174.8+/-225.0	30,660,3610	no	coding-synonymous,coding-synonymous	MCRS1	NM_001012300.1,NM_006337.3	,	91,1286,5126	AA,AG,GG		8.3721,16.9768,11.2871	,	433/476,420/463	49952668	1468,11538	2203	4300	6503	SO:0001819	synonymous_variant	10445	exon13			GCCACAGAGCACC	BC011794	CCDS8787.1, CCDS31795.1, CCDS61118.1	12q13.12	2011-07-06				ENSG00000187778		"""INO80 complex subunits"""	6960	protein-coding gene	gene with protein product	"""INO80 complex subunit Q"""	609504				9765390, 9654073	Standard	NM_006337		Approved	ICP22BP, MSP58, P78, MCRS2, INO80Q	uc001rui.1	Q96EZ8		ENST00000550165.1:c.1260C>T	12.37:g.49952668G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_001012300	O14742|O75497|Q6VN53|Q7Z372	Silent	SNP	ENST00000550165.1	37	CCDS8787.1																																																																																			G|0.892;A|0.108	0.108	strong		0.567	MCRS1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405102.1	NM_006337	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103229027	103229027	+	Silent	SNP	T	T	C	rs2566913	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:103229027T>C	ENST00000375735.2	+	83	12240	c.12096T>C	c.(12094-12096)gaT>gaC	p.D4032D	DYNC2H1_ENST00000398093.3_Silent_p.D4039D|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4032					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CCAAATTTGATAGAGAAATCT	0.328													T|||	2479	0.495008	0.2481	0.6816	5008	,	,		17239	0.4871		0.661	False		,,,				2504	0.5337				p.D4039D		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T12117C						PASS	.	T	,	1161,2485		199,763,861	83.0	71.0	75.0		12117,12096	0.5	1.0	11	dbSNP_100	75	5435,2731		1804,1827,452	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	2003,2590,1313	CC,CT,TT		33.4435,31.8431,44.1585	,	4039/4315,4032/4308	103229027	6596,5216	1823	4083	5906	SO:0001819	synonymous_variant	79659	exon84			ATTTGATAGAGAA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.12096T>C	11.37:g.103229027T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	99	87	0.878788	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			T|0.488;C|0.512	0.512	strong		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
FN1	2335	hgsc.bcm.edu	37	2	216229692	216229692	+	Silent	SNP	A	A	G	rs11651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:216229692A>G	ENST00000359671.1	-	43	7153	c.6888T>C	c.(6886-6888)taT>taC	p.Y2296Y	FN1_ENST00000357867.4_Silent_p.Y2086Y|FN1_ENST00000432072.2_Silent_p.Y2177Y|FN1_ENST00000354785.4_Silent_p.Y2387Y|FN1_ENST00000323926.6_Silent_p.Y2356Y|FN1_ENST00000421182.1_Silent_p.Y2150Y|FN1_ENST00000346544.3_Silent_p.Y2121Y|FN1_ENST00000443816.1_Silent_p.Y2175Y|FN1_ENST00000356005.4_Silent_p.Y2206Y|FN1_ENST00000357009.2_3'UTR|FN1_ENST00000336916.4_Silent_p.Y2265Y|FN1_ENST00000446046.1_Silent_p.Y2240Y|FN1_ENST00000345488.5_Silent_p.Y2094Y			P02751	FINC_HUMAN	fibronectin 1	2296	Fibrin-binding 2.|Fibronectin type-I 12. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TCCCATCATCATAACACGTTG	0.488													A|||	1416	0.282748	0.0651	0.3127	5008	,	,		23128	0.2986		0.3141	False		,,,				2504	0.5072				p.Y2387Y		Atlas-SNP	.											FN1_ENST00000354785,NS,carcinoma,0,2	FN1	521	2	0			c.T7161C						PASS	.	A	,,,,	445,3959		25,395,1782	152.0	92.0	112.0		6795,6258,6618,6720,7161	-8.3	0.1	2	dbSNP_52	112	2780,5816		463,1854,1981	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FN1	NM_002026.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	,,,,	488,2249,3763	GG,GA,AA		32.3406,10.1045,24.8077	,,,,	2265/2356,2086/2177,2206/2297,2240/2331,2387/2478	216229692	3225,9775	2202	4298	6500	SO:0001819	synonymous_variant	2335	exon44			ATCATCATAACAC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.6888T>C	2.37:g.216229692A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																				A|0.771;G|0.229	0.229	strong		0.488	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
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 GAIIx	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	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	104	52	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		
ACSM2A	123876	hgsc.bcm.edu	37	16	20494408	20494408	+	Missense_Mutation	SNP	C	C	T	rs1133607	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20494408C>T	ENST00000573854.1	+	13	1652	c.1538C>T	c.(1537-1539)tCg>tTg	p.S513L	ACSM2A_ENST00000417235.2_Missense_Mutation_p.S434L|ACSM2A_ENST00000396104.2_Missense_Mutation_p.S513L|ACSM2A_ENST00000536134.1_Missense_Mutation_p.S285L|ACSM2A_ENST00000575690.1_Missense_Mutation_p.S513L|ACSM2A_ENST00000219054.6_Missense_Mutation_p.S513L	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	513			S -> L (in dbSNP:rs1133607). {ECO:0000269|PubMed:10493829, ECO:0000269|PubMed:12654705, ECO:0000269|PubMed:16521160}.		fatty acid metabolic process (GO:0006631)|glucose homeostasis (GO:0042593)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|triglyceride homeostasis (GO:0070328)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						GTCCTGGCCTCGCAGTTCCTG	0.502													c|||	705	0.140775	0.1301	0.1369	5008	,	,		17954	0.1984		0.0746	False		,,,				2504	0.1667				p.S513L		Atlas-SNP	.											ACSM2A,NS,carcinoma,+1,1	ACSM2A	120	1	0			c.C1538T						PASS	.	C	LEU/SER	551,3855	250.0+/-257.2	33,485,1685	199.0	178.0	185.0		1538	3.3	1.0	16	dbSNP_86	185	872,7728	197.6+/-242.2	31,810,3459	no	missense	ACSM2A	NM_001010845.2	145	64,1295,5144	TT,TC,CC		10.1395,12.5057,10.9411	benign	513/578	20494408	1423,11583	2203	4300	6503	SO:0001583	missense	123876	exon14			TGGCCTCGCAGTT	AK091878, AK096039	CCDS32401.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000183747	ENSG00000183747		"""Acyl-CoA synthetase family"""	32017	protein-coding gene	gene with protein product		614358	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2			Standard	NM_001010845		Approved	A-923A4.1, MGC150530	uc010bwe.3	Q08AH3	OTTHUMG00000177401	ENST00000573854.1:c.1538C>T	16.37:g.20494408C>T	ENSP00000459451:p.Ser513Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	177	89	0.502825	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	312	0.14285714285714285	74	0.15040650406504066	52	0.143646408839779	115	0.20104895104895104	71	0.09366754617414248	C	14.03	2.414161	0.42817	0.125057	0.101395	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000536134;ENST00000396104	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	3.26	3.26	0.37387	.	0.461328	0.18403	N	0.142287	T	0.00073	0.0002	L	0.51914	1.62	0.09310	P	0.999999999999518	B	0.06786	0.001	B	0.04013	0.001	T	0.13415	-1.0510	9	0.66056	D	0.02	-0.9891	14.417	0.67158	0.0:1.0:0.0:0.0	rs1133607;rs1634313;rs3195484;rs16970281;rs52800134;rs1133607	513	Q08AH3	ACS2A_HUMAN	L	434;513;285;513	ENSP00000392169:S434L;ENSP00000219054:S513L;ENSP00000445082:S285L;ENSP00000379411:S513L	ENSP00000219054:S513L	S	+	2	0	ACSM2A	20401909	0.171000	0.23029	0.987000	0.45799	0.913000	0.54294	4.507000	0.60434	1.507000	0.48752	0.305000	0.20034	TCG	C|0.880;T|0.120	0.120	strong		0.502	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
OR13H1	347468	hgsc.bcm.edu	37	X	130678596	130678596	+	Silent	SNP	C	C	G	rs17316625	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:130678596C>G	ENST00000338616.3	+	1	647	c.549C>G	c.(547-549)ctC>ctG	p.L183L		NM_001004486.1	NP_001004486.1	Q8NG92	O13H1_HUMAN	olfactory receptor, family 13, subfamily H, member 1	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	15	Acute lymphoblastic leukemia(192;0.000636)					TTCTCTCCCTCATTAAGCTGA	0.473													C|||	684	0.181192	0.0151	0.1369	3775	,	,		17026	0.0446		0.2654	False		,,,				2504	0.2628				p.L183L		Atlas-SNP	.											.	OR13H1	41	.	0			c.C549G						PASS	.	C		209,3626		6,171,26,1455,545	256.0	220.0	232.0		549	0.6	0.0	X	dbSNP_123	232	2432,4296		293,1132,714,1003,1158	no	coding-synonymous	OR13H1	NM_001004486.1		299,1303,740,2458,1703	GG,GC,G,CC,C		36.1474,5.4498,25.0024		183/309	130678596	2641,7922	2203	4300	6503	SO:0001819	synonymous_variant	347468	exon1			CTCCCTCATTAAG		CCDS35396.1	Xq26.2	2012-08-23			ENSG00000171054	ENSG00000171054		"""GPCR / Class A : Olfactory receptors"""	14755	protein-coding gene	gene with protein product							Standard	NM_001004486		Approved		uc011muw.2	Q8NG92	OTTHUMG00000022411	ENST00000338616.3:c.549C>G	X.37:g.130678596C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	167	114	0.682635	NM_001004486	B2RNQ3|Q6IET8|Q96R12	Silent	SNP	ENST00000338616.3	37	CCDS35396.1																																																																																			C|0.787;0|0.015	.	strong		0.473	OR13H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058297.1		
DND1	373863	hgsc.bcm.edu	37	5	140050894	140050894	+	Missense_Mutation	SNP	G	G	C	rs201638404		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140050894G>C	ENST00000542735.1	-	4	1089	c.1046C>G	c.(1045-1047)aCc>aGc	p.T349S	WDR55_ENST00000358337.5_3'UTR|WDR55_ENST00000520764.1_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	349					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTAACCATGGTACCTGCCTC	0.602																																					p.T349S		Atlas-SNP	.											DND1,NS,carcinoma,-1,1	DND1	15	1	0			c.C1046G						scavenged	.						75.0	61.0	66.0					5																	140050894		1959	3964	5923	SO:0001583	missense	373863	exon4			ACCATGGTACCTG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1046C>G	5.37:g.140050894G>C	ENSP00000445366:p.Thr349Ser	Somatic	332	1	0.00301205		WXS	Illumina HiSeq	Phase_I	470	105	0.223404	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	G	9.262	1.043394	0.19748	.	.	ENSG00000256453	ENST00000542735	T	0.30182	1.54	4.97	0.117	0.14652	.	1.006470	0.07994	N	0.987573	T	0.16769	0.0403	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29518	-1.0009	10	0.27082	T	0.32	0.0017	3.9136	0.09213	0.3271:0.0:0.5115:0.1614	.	349	Q8IYX4	DND1_HUMAN	S	349	ENSP00000445366:T349S	ENSP00000445366:T349S	T	-	2	0	DND1	140031078	0.002000	0.14202	0.000000	0.03702	0.312000	0.27988	0.583000	0.23849	0.101000	0.17610	0.551000	0.68910	ACC	G|0.979;C|0.021	0.021	strong		0.602	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
LTF	4057	hgsc.bcm.edu	37	3	46480801	46480801	+	Silent	SNP	A	A	G	rs9110	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46480801A>G	ENST00000231751.4	-	15	2189	c.1894T>C	c.(1894-1896)Ttg>Ctg	p.L632L	LTF_ENST00000426532.2_Silent_p.L588L|LTF_ENST00000493056.1_5'UTR|LTF_ENST00000417439.1_Silent_p.L630L	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	632	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		TGGTGGAGCAACACCTGTTTC	0.552													G|||	2617	0.522564	0.6452	0.3991	5008	,	,		21524	0.6349		0.3131	False		,,,				2504	0.544				p.L632L		Atlas-SNP	.											.	LTF	98	.	0			c.T1894C	GRCh37	CM073189	LTF	M	rs9110	PASS	.	G	,	2549,1857	537.9+/-374.9	733,1083,387	139.0	106.0	117.0		1762,1894	5.1	0.3	3	dbSNP_52	117	2432,6168	698.1+/-405.0	347,1738,2215	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	1080,2821,2602	GG,GA,AA		28.2791,42.1471,38.2977	,	588/667,632/711	46480801	4981,8025	2203	4300	6503	SO:0001819	synonymous_variant	4057	exon15			GGAGCAACACCTG		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1894T>C	3.37:g.46480801A>G		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	195	97	0.497436	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			T|0.000;G|0.435;C|0.000;A|0.565	0.435	strong		0.552	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377657	138377657	+	Missense_Mutation	SNP	T	T	C	rs1808998	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138377657T>C	ENST00000356818.2	+	4	1850	c.1301T>C	c.(1300-1302)aTg>aCg	p.M434T	PPP1R26_ENST00000605286.1_Missense_Mutation_p.M434T|PPP1R26_ENST00000605660.1_Missense_Mutation_p.M434T|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Missense_Mutation_p.M434T|PPP1R26_ENST00000401470.3_Missense_Mutation_p.M434T	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	434			M -> T (in dbSNP:rs1808998). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										ACCAAGACCATGGACCCTGGT	0.592													C|||	2324	0.464058	0.4183	0.5231	5008	,	,		18270	0.6825		0.2147	False		,,,				2504	0.5153				p.M434T		Atlas-SNP	.											.	.	.	.	0			c.T1301C						PASS	.	C	THR/MET	1645,2761	636.1+/-396.5	304,1037,862	33.0	37.0	36.0		1301	-2.0	0.0	9	dbSNP_92	36	1822,6778	713.3+/-405.9	201,1420,2679	yes	missense	KIAA0649	NM_014811.3	81	505,2457,3541	CC,CT,TT		21.186,37.3355,26.6569	benign	434/1210	138377657	3467,9539	2203	4300	6503	SO:0001583	missense	9858	exon4			AGACCATGGACCC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1301T>C	9.37:g.138377657T>C	ENSP00000349274:p.Met434Thr	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	908	0.4157509157509158	168	0.34146341463414637	163	0.45027624309392267	416	0.7272727272727273	161	0.21240105540897097	C	0.016	-1.520221	0.00967	0.373355	0.21186	ENSG00000196422	ENST00000356818	T	0.08102	3.13	5.06	-1.98	0.07480	.	1.322620	0.05171	N	0.499637	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39921	-0.9590	9	0.02654	T	1	0.4383	1.8933	0.03252	0.1239:0.3712:0.1217:0.3833	rs1808998;rs3748193;rs17846421;rs17859466;rs1808998	434	Q5T8A7	PPR26_HUMAN	T	434	ENSP00000349274:M434T	ENSP00000349274:M434T	M	+	2	0	KIAA0649	137517478	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.935000	0.03950	-1.293000	0.02362	-1.859000	0.00561	ATG	T|0.653;C|0.347	0.347	strong		0.592	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
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 GAIIx	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_ENST00000475231.1_Silent_p.T4235T|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	70	21	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	
TAS1R2	80834	hgsc.bcm.edu	37	1	19175846	19175846	+	Missense_Mutation	SNP	T	T	C	rs28374389	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19175846T>C	ENST00000375371.3	-	4	1477	c.1456A>G	c.(1456-1458)Atc>Gtc	p.I486V	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	486			I -> V (in dbSNP:rs28374389). {ECO:0000269|PubMed:11917125}.		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)	GTGTTGTTGATGGTGTGCCAG	0.637													T|||	631	0.125998	0.1369	0.245	5008	,	,		14893	0.002		0.2087	False		,,,				2504	0.0695				p.I486V		Atlas-SNP	.											.	TAS1R2	134	.	0			c.A1456G						PASS	.	T	VAL/ILE	654,3752	277.8+/-273.9	50,554,1599	80.0	70.0	73.0		1456	-1.9	0.1	1	dbSNP_125	73	1769,6831	319.0+/-313.9	210,1349,2741	yes	missense	TAS1R2	NM_152232.2	29	260,1903,4340	CC,CT,TT		20.5698,14.8434,18.6299	benign	486/840	19175846	2423,10583	2203	4300	6503	SO:0001583	missense	80834	exon4			TGTTGATGGTGTG		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.1456A>G	1.37:g.19175846T>C	ENSP00000364520:p.Ile486Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	318	0.14560439560439561	71	0.1443089430894309	94	0.2596685082872928	1	0.0017482517482517483	152	0.20052770448548812	T	2.501	-0.315238	0.05422	0.148434	0.205698	ENSG00000179002	ENST00000375371	D	0.88124	-2.34	4.4	-1.92	0.07618	.	0.473418	0.17601	N	0.168433	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03287	-1.1052	9	0.16896	T	0.51	.	9.8404	0.40996	0.0:0.5455:0.3022:0.1523	rs28374389	486	Q8TE23	TS1R2_HUMAN	V	486	ENSP00000364520:I486V	ENSP00000364520:I486V	I	-	1	0	TAS1R2	19048433	0.000000	0.05858	0.093000	0.20910	0.133000	0.20885	-0.359000	0.07632	-0.169000	0.10834	-0.396000	0.06452	ATC	T|0.832;C|0.168	0.168	strong		0.637	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
RAD9A	5883	hgsc.bcm.edu	37	11	67164791	67164791	+	Silent	SNP	T	T	C	rs872110	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67164791T>C	ENST00000307980.2	+	10	1107	c.1014T>C	c.(1012-1014)ggT>ggC	p.G338G	RAD9A_ENST00000535644.1_3'UTR|RNU6-1238P_ENST00000517215.1_RNA|PPP1CA_ENST00000532446.1_5'Flank	NM_001243224.1|NM_004584.2	NP_001230153.1|NP_004575.1	Q99638	RAD9A_HUMAN	RAD9 homolog A (S. pombe)	338	Sufficient for interaction with ABL1.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|intra-S DNA damage checkpoint (GO:0031573)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|enzyme binding (GO:0019899)|exodeoxyribonuclease III activity (GO:0008853)|histone deacetylase binding (GO:0042826)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			lung(7)|upper_aerodigestive_tract(1)	8			BRCA - Breast invasive adenocarcinoma(15;8.53e-07)			AGAGCCCCGGTCCCCACTCCG	0.632								Other conserved DNA damage response genes					C|||	1760	0.351438	0.8253	0.4063	5008	,	,		7858	0.2599		0.0805	False		,,,				2504	0.045				p.G338G		Atlas-SNP	.											.	RAD9A	15	.	0			c.T1014C						PASS	.	C		2635,1735		890,855,440	10.0	14.0	12.0		1014	-2.9	0.0	11	dbSNP_86	12	508,8080		17,474,3803	no	coding-synonymous	RAD9A	NM_004584.2		907,1329,4243	CC,CT,TT		5.9152,39.7025,24.2553		338/392	67164791	3143,9815	2185	4294	6479	SO:0001819	synonymous_variant	5883	exon10			CCCCGGTCCCCAC	U53174	CCDS8159.1	11q13.1-q13.2	2008-02-05	2003-07-21	2003-07-23	ENSG00000172613	ENSG00000172613			9827	protein-coding gene	gene with protein product		603761	"""RAD9 (S. pombe) homolog"""	RAD9		8943031	Standard	NM_004584		Approved		uc001okr.3	Q99638	OTTHUMG00000167670	ENST00000307980.2:c.1014T>C	11.37:g.67164791T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	53	11	0.207547	NM_004584	B2RCZ8|Q6FI29|Q96C41	Silent	SNP	ENST00000307980.2	37	CCDS8159.1																																																																																			T|0.653;C|0.347	0.347	strong		0.632	RAD9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395481.2	NM_004584	
GAB4	128954	hgsc.bcm.edu	37	22	17450929	17450929	+	Missense_Mutation	SNP	C	C	T	rs61741409	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:17450929C>T	ENST00000400588.1	-	4	948	c.841G>A	c.(841-843)Gca>Aca	p.A281T	GAB4_ENST00000523144.1_Intron	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	281										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				CTGAATTCTGCATTGTGCTGG	0.572													T|||	205	0.0409345	0.0749	0.0274	5008	,	,		20118	0.0069		0.0268	False		,,,				2504	0.0542				p.A281T		Atlas-SNP	.											.	GAB4	95	.	0			c.G841A						PASS	.	T	THR/ALA	282,4094		10,262,1916	87.0	100.0	96.0		841	-1.6	0.8	22	dbSNP_129	96	258,8328		2,254,4037	yes	missense	GAB4	NM_001037814.1	58	12,516,5953	TT,TC,CC		3.0049,6.4442,4.166	benign	281/575	17450929	540,12422	2188	4293	6481	SO:0001583	missense	128954	exon4			ATTCTGCATTGTG	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.841G>A	22.37:g.17450929C>T	ENSP00000383431:p.Ala281Thr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	37	CCDS42976.1	70	0.03205128205128205	38	0.07723577235772358	11	0.03038674033149171	1	0.0017482517482517483	20	0.026385224274406333	T	0.001	-2.987626	0.00046	0.064442	0.030049	ENSG00000215568	ENST00000400588	T	0.29917	1.55	1.97	-1.58	0.08479	.	0.633137	0.16165	N	0.226569	T	0.00440	0.0014	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23940	-1.0174	10	0.13853	T	0.58	.	5.0141	0.14328	0.1844:0.5376:0.0:0.2779	.	281	Q2WGN9	GAB4_HUMAN	T	281	ENSP00000383431:A281T	ENSP00000383431:A281T	A	-	1	0	GAB4	15830929	0.000000	0.05858	0.834000	0.33040	0.005000	0.04900	-0.662000	0.05305	-1.062000	0.03181	-1.557000	0.00889	GCA	C|0.972;T|0.028	0.028	strong		0.572	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
CYP2C8	1558	hgsc.bcm.edu	37	10	96827030	96827030	+	Missense_Mutation	SNP	C	C	T	rs11572080	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96827030C>T	ENST00000371270.3	-	3	510	c.416G>A	c.(415-417)aGg>aAg	p.R139K	CYP2C8_ENST00000539050.1_Missense_Mutation_p.R53K|CYP2C8_ENST00000535898.1_Missense_Mutation_p.R37K	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	139			R -> K (in allele CYP2C8*3; dbSNP:rs11572080). {ECO:0000269|PubMed:11668219, ECO:0000269|PubMed:12429347, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:2729895, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	CTCAATGCTCCTCTTCCCCAT	0.483													C|||	229	0.0457268	0.0083	0.0994	5008	,	,		20114	0.001		0.1183	False		,,,				2504	0.0297				p.R139K		Atlas-SNP	.											.	CYP2C8	73	.	0			c.G416A	GRCh37	CM014700	CYP2C8	M	rs11572080	PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	108,4298	83.9+/-122.4	2,104,2097	209.0	188.0	195.0		416,206,110,206	2.8	1.0	10	dbSNP_120	195	1002,7598	215.5+/-254.8	67,868,3365	yes	missense,missense,missense,missense	CYP2C8	NM_000770.3,NM_001198853.1,NM_001198854.1,NM_001198855.1	26,26,26,26	69,972,5462	TT,TC,CC		11.6512,2.4512,8.5345	benign,benign,benign,benign	139/491,69/421,37/389,69/421	96827030	1110,11896	2203	4300	6503	SO:0001583	missense	1558	exon3			ATGCTCCTCTTCC	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"""Cytochrome P450s"""	2622	protein-coding gene	gene with protein product		601129	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"""			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.416G>A	10.37:g.96827030C>T	ENSP00000360317:p.Arg139Lys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	141	0.06456043956043957	6	0.012195121951219513	46	0.1270718232044199	2	0.0034965034965034965	87	0.11477572559366754	C	15.48	2.845990	0.51164	0.024512	0.116512	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.11712	2.75;2.75;2.75	4.64	2.8	0.32819	.	0.133357	0.49305	U	0.000147	T	0.00109	0.0003	L	0.42529	1.33	0.31880	P	0.618617	B;B;B;B	0.22080	0.052;0.015;0.064;0.015	B;B;B;B	0.33295	0.027;0.15;0.161;0.15	T	0.25117	-1.0141	9	0.30078	T	0.28	.	9.4607	0.38783	0.0:0.8256:0.0:0.1744	rs11572080;rs60090616	53;37;107;139	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	K	139;106;37;53	ENSP00000360317:R139K;ENSP00000445062:R37K;ENSP00000442343:R53K	ENSP00000360317:R139K	R	-	2	0	CYP2C8	96817020	0.078000	0.21339	0.992000	0.48379	0.983000	0.72400	0.356000	0.20181	0.594000	0.29761	0.561000	0.74099	AGG	C|0.931;T|0.069	0.069	strong		0.483	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
Unknown	0	hgsc.bcm.edu	37	11	124095884	124095884	+	IGR	SNP	A	A	G	rs2466614	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124095884A>G								OR10D3 (38932 upstream) : OR8G1 (24538 downstream)																							GGGAGTTTACATTTTAGGCAT	0.433													a|||	504	0.100639	0.0174	0.1585	5008	,	,		23282	0.131		0.1441	False		,,,				2504	0.0961				p.I163V		Atlas-SNP	.											.	.	.	.	0			c.A487G						PASS	.	A	VAL/ILE	168,4040		4,160,1940	255.0	264.0	261.0		487	-4.2	0.0	11	dbSNP_100	261	1339,7207		97,1145,3031	yes	missense	OR8G2	NM_001007249.1	29	101,1305,4971	GG,GA,AA		15.6681,3.9924,11.8159	benign	163/305	124095884	1507,11247	2104	4273	6377	SO:0001628	intergenic_variant	26492	exon1			GTTTACATTTTAG																													11.37:g.124095884A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	150	122	0.813333	NM_001007249		Missense_Mutation	SNP		37																																																																																				A|0.893;G|0.107	0.107	strong	0	0.433								
CCDC132	55610	hgsc.bcm.edu	37	7	92985252	92985252	+	Silent	SNP	T	T	C	rs2374639	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92985252T>C	ENST00000305866.5	+	27	2763	c.2635T>C	c.(2635-2637)Ttg>Ctg	p.L879L	CCDC132_ENST00000474412.1_3'UTR|CCDC132_ENST00000544910.1_Silent_p.L849L|CCDC132_ENST00000541136.1_3'UTR|CCDC132_ENST00000535481.1_Silent_p.L599L	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	879						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			CCTGATGCAATTGGATTTTCA	0.289													T|||	1652	0.329872	0.385	0.3199	5008	,	,		17277	0.2788		0.2942	False		,,,				2504	0.3517				p.L879L		Atlas-SNP	.											.	CCDC132	136	.	0			c.T2635C						PASS	.	T		1225,2391		199,827,782	47.0	44.0	45.0		2635	1.7	1.0	7	dbSNP_100	45	2352,5786		334,1684,2051	no	coding-synonymous	CCDC132	NM_017667.2		533,2511,2833	CC,CT,TT		28.9014,33.8772,30.4322		879/965	92985252	3577,8177	1808	4069	5877	SO:0001819	synonymous_variant	55610	exon27			ATGCAATTGGATT	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.2635T>C	7.37:g.92985252T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Silent	SNP	ENST00000305866.5	37	CCDS43617.1	705	0.3228021978021978	193	0.39227642276422764	122	0.3370165745856354	170	0.2972027972027972	220	0.29023746701846964	T	9.201	1.028464	0.19512	0.338772	0.289014	ENSG00000004766	ENST00000443443	.	.	.	5.77	1.71	0.24356	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45041	-0.9288	3	.	.	.	-7.5805	3.1241	0.06401	0.0:0.3575:0.2366:0.406	rs2374639;rs57945507;rs2374639	.	.	.	T	103	.	.	I	+	2	0	CCDC132	92823188	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.791000	0.62460	0.521000	0.28445	-0.256000	0.11100	ATT	C|0.320;N|0.000	0.320	strong		0.289	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
SALL4	57167	hgsc.bcm.edu	37	20	50407966	50407966	+	Silent	SNP	C	C	T	rs13038893	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:50407966C>T	ENST00000217086.4	-	2	1167	c.1056G>A	c.(1054-1056)gcG>gcA	p.A352A	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Silent_p.A352A	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	352					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ATGTGTCTAGCGCCACAGTGG	0.612													C|||	1048	0.209265	0.3071	0.2046	5008	,	,		17598	0.0278		0.328	False		,,,				2504	0.1452				p.A352A		Atlas-SNP	.											SALL4,NS,carcinoma,-1,2	SALL4	168	2	0			c.G1056A						PASS	.	C		1466,2940	464.0+/-353.7	232,1002,969	44.0	46.0	45.0		1056	-3.9	0.0	20	dbSNP_121	45	2894,5706	447.8+/-361.6	488,1918,1894	no	coding-synonymous	SALL4	NM_020436.3		720,2920,2863	TT,TC,CC		33.6512,33.2728,33.523		352/1054	50407966	4360,8646	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			GTCTAGCGCCACA	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1056G>A	20.37:g.50407966C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	46	14	0.304348	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			C|0.725;T|0.275	0.275	strong		0.612	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
NEK10	152110	hgsc.bcm.edu	37	3	27326097	27326097	+	Silent	SNP	G	G	T	rs11129280	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:27326097G>T	ENST00000429845.2	-	23	2372	c.2010C>A	c.(2008-2010)acC>acA	p.T670T	NEK10_ENST00000357467.2_Silent_p.T67T|NEK10_ENST00000341435.5_Silent_p.T670T			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	670	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						ACTTACTAACGGTTACTTTGT	0.378													T|||	1061	0.211861	0.1218	0.3516	5008	,	,		15934	0.1002		0.2734	False		,,,				2504	0.2863				p.T670T		Atlas-SNP	.											.	NEK10	271	.	0			c.C2010A						PASS	.	T		716,3690	757.8+/-412.8	69,578,1556	123.0	115.0	117.0		2010	-5.8	0.6	3	dbSNP_120	117	2329,6271	703.8+/-405.4	349,1631,2320	yes	coding-synonymous	NEK10	NM_199347.2		418,2209,3876	TT,TG,GG		27.0814,16.2506,23.4123		670/713	27326097	3045,9961	2203	4300	6503	SO:0001819	synonymous_variant	152110	exon23			ACTAACGGTTACT	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.2010C>A	3.37:g.27326097G>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	69	22	0.318841	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Silent	SNP	ENST00000429845.2	37		464|464	0.21245421245421245|0.21245421245421245	64|64	0.13008130081300814|0.13008130081300814	132|132	0.36464088397790057|0.36464088397790057	58|58	0.10139860139860139|0.10139860139860139	210|210	0.2770448548812665|0.2770448548812665	T|T	9.473|9.473	1.096174|1.096174	0.20552|0.20552	0.162506|0.162506	0.270814|0.270814	ENSG00000163491|ENSG00000163491	ENST00000424275|ENST00000435584	.|.	.|.	.|.	6.02|6.02	-5.81|-5.81	0.02340|0.02340	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999993107|0.9999999999993107	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24190|0.24190	-1.0167|-1.0167	3|3	.|.	.|.	.|.	.|.	17.0958|17.0958	0.86634|0.86634	0.0781:0.0:0.624:0.2978|0.0781:0.0:0.624:0.2978	rs11129280;rs17681183;rs11129280|rs11129280;rs17681183;rs11129280	.|.	.|.	.|.	Q|S	157|127	.|.	.|.	P|R	-|-	2|1	0|0	NEK10|NEK10	27301101|27301101	0.190000|0.190000	0.23276|0.23276	0.621000|0.621000	0.29145|0.29145	0.956000|0.956000	0.61745|0.61745	-0.757000|-0.757000	0.04772|0.04772	-0.744000|-0.744000	0.04778|0.04778	-0.264000|-0.264000	0.10439|0.10439	CCG|CGT	G|0.774;T|0.226	0.226	strong		0.378	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	
TMEM176B	28959	hgsc.bcm.edu	37	7	150493495	150493495	+	Missense_Mutation	SNP	G	G	A	rs11546671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150493495G>A	ENST00000447204.2	-	2	535	c.163C>T	c.(163-165)Cct>Tct	p.P55S	TMEM176B_ENST00000492607.1_Missense_Mutation_p.P55S|TMEM176B_ENST00000429904.2_Missense_Mutation_p.P55S|TMEM176B_ENST00000434545.1_Missense_Mutation_p.P55S|TMEM176B_ENST00000450753.2_Missense_Mutation_p.P55S|TMEM176B_ENST00000326442.5_Missense_Mutation_p.P55S	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	55			P -> S (in dbSNP:rs11546671). {ECO:0000269|PubMed:9922225}.		cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCTGTGGAAGGCACAGTGTCC	0.537													G|||	66	0.0131789	0.0023	0.0317	5008	,	,		16243	0.0		0.0348	False		,,,				2504	0.0061				p.P55S		Atlas-SNP	.											.	TMEM176B	36	.	0			c.C163T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	39,4367	43.1+/-76.7	0,39,2164	73.0	70.0	71.0		163,163,163,163	0.7	0.0	7	dbSNP_120	71	369,8231	122.0+/-181.0	7,355,3938	yes	missense,missense,missense,missense	TMEM176B	NM_001101311.1,NM_001101312.1,NM_001101314.1,NM_014020.3	74,74,74,74	7,394,6102	AA,AG,GG		4.2907,0.8852,3.137	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	55/271,55/271,55/234,55/271	150493495	408,12598	2203	4300	6503	SO:0001583	missense	28959	exon2			TGGAAGGCACAGT	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.163C>T	7.37:g.150493495G>A	ENSP00000410269:p.Pro55Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	47	0.02152014652014652	3	0.006097560975609756	17	0.04696132596685083	0	0.0	27	0.03562005277044855	G	12.68	2.012058	0.35511	0.008852	0.042907	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	T;T;T;T;T;T	0.08282	3.25;3.25;3.25;3.25;3.25;3.11	3.82	0.672	0.17935	.	3.130830	0.01716	N	0.028014	T	0.02533	0.0077	L	0.45581	1.43	0.09310	N	1	D;D	0.89917	1.0;0.959	D;P	0.74348	0.983;0.556	T	0.41928	-0.9481	10	0.09084	T	0.74	-2.2578	3.3595	0.07181	0.252:0.2217:0.5263:0.0	rs11546671;rs52825959;rs11546671	55;55	E9PAV4;Q3YBM2	.;T176B_HUMAN	S	55	ENSP00000419258:P55S;ENSP00000318409:P55S;ENSP00000410269:P55S;ENSP00000413531:P55S;ENSP00000397810:P55S;ENSP00000404831:P55S	ENSP00000318409:P55S	P	-	1	0	TMEM176B	150124428	0.019000	0.18553	0.001000	0.08648	0.017000	0.09413	0.824000	0.27379	0.368000	0.24481	0.467000	0.42956	CCT	G|0.973;A|0.027	0.027	strong		0.537	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020	
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 GAIIx	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	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	141	93	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	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592576	167592576	+	Silent	SNP	G	G	A	rs60976240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:167592576G>A	ENST00000366832.2	+	6	866	c.735G>A	c.(733-735)acG>acA	p.T245T		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	245										endometrium(1)|kidney(2)|lung(3)	6						AGGCCGCCACGCTGCAGGAGC	0.582													G|||	3206	0.640176	0.7617	0.6614	5008	,	,		17779	0.5694		0.5984	False		,,,				2504	0.5767				p.T245T		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G735A						PASS	.						23.0	28.0	27.0					6																	167592576		692	1591	2283	SO:0001819	synonymous_variant	401285	exon6			CGCCACGCTGCAG		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.735G>A	6.37:g.167592576G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001145121		Silent	SNP	ENST00000366832.2	37	CCDS47514.1																																																																																			G|0.424;A|0.576	0.576	strong		0.582	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
TUBA3E	112714	hgsc.bcm.edu	37	2	130952725	130952725	+	Missense_Mutation	SNP	C	C	T	rs3863907	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:130952725C>T	ENST00000312988.7	-	3	402	c.302G>A	c.(301-303)aGt>aAt	p.S101N		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	101			S -> N (in dbSNP:rs3863907).		microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GGCGTAATTACTGGCTGCATC	0.532													.|||	2731	0.545327	0.8366	0.5216	5008	,	,		19056	0.4425		0.3787	False		,,,				2504	0.4458				p.S101N		Atlas-SNP	.											.	TUBA3E	73	.	0			c.G302A						PASS	.						74.0	128.0	110.0					2																	130952725		2192	4289	6481	SO:0001583	missense	112714	exon3			TAATTACTGGCTG	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.302G>A	2.37:g.130952725C>T	ENSP00000318197:p.Ser101Asn	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	129	17	0.131783	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	1006	0.4606227106227106	363	0.7378048780487805	172	0.47513812154696133	243	0.42482517482517484	228	0.3007915567282322	N	8.309	0.821757	0.16678	.	.	ENSG00000152086	ENST00000312988	T	0.62105	0.05	2.95	2.95	0.34219	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.52532	N	0.000066	T	0.00012	0.0000	N	0.00001	-3.66	0.51012	P	9.999999999998899E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.47071	-0.9145	9	0.02654	T	1	.	6.4475	0.21885	0.0:0.1291:0.0:0.8709	rs3863907;rs6745966;rs17016706;rs60742675	101	Q6PEY2	TBA3E_HUMAN	N	101	ENSP00000318197:S101N	ENSP00000318197:S101N	S	-	2	0	TUBA3E	130669195	1.000000	0.71417	0.960000	0.40013	0.492000	0.33523	4.020000	0.57189	0.350000	0.24002	-0.556000	0.04195	AGT	C|0.500;T|0.500	0.500	strong		0.532	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
Unknown	0	hgsc.bcm.edu	37	11	124096275	124096275	+	IGR	SNP	T	T	C	rs2512268	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124096275T>C								OR10D3 (39323 upstream) : OR8G1 (24147 downstream)																							TTTTATACTATTGTTGTGCCC	0.448													N|||	504	0.100639	0.0174	0.1585	5008	,	,		20278	0.131		0.1441	False		,,,				2504	0.0961				p.I293T		Atlas-SNP	.											.	.	.	.	0			c.T878C						PASS	.	C	THR/ILE	136,3726		3,130,1798	73.0	67.0	69.0		878	-4.1	0.0	11	dbSNP_100	69	1122,7182		95,932,3125	no	missense	OR8G2	NM_001007249.1	89	98,1062,4923	CC,CT,TT		13.5116,3.5215,10.3403	benign	293/305	124096275	1258,10908	1931	4152	6083	SO:0001628	intergenic_variant	26492	exon1			ATACTATTGTTGT																													11.37:g.124096275T>C		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	199	162	0.81407	NM_001007249		Missense_Mutation	SNP		37																																																																																				T|0.891;C|0.109	0.109	strong	0	0.448								
C3orf30	152405	hgsc.bcm.edu	37	3	118865801	118865801	+	Silent	SNP	C	C	T	rs4077931	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:118865801C>T	ENST00000295622.1	+	1	805	c.765C>T	c.(763-765)tcC>tcT	p.S255S	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000425327.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	255										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)		AAAGACCTTCCGTACAGATTG	0.502													C|||	1129	0.225439	0.2118	0.196	5008	,	,		24314	0.1994		0.2346	False		,,,				2504	0.2822				p.S255S		Atlas-SNP	.											C3orf30,NS,malignant_melanoma,+1,1	C3orf30	64	1	0			c.C765T						PASS	.	C		1073,3333	389.8+/-327.4	128,817,1258	92.0	92.0	92.0		765	-7.1	0.0	3	dbSNP_108	92	2446,6154	404.2+/-348.1	345,1756,2199	no	coding-synonymous	C3orf30	NM_152539.2		473,2573,3457	TT,TC,CC		28.4419,24.3532,27.0567		255/537	118865801	3519,9487	2203	4300	6503	SO:0001819	synonymous_variant	152405	exon1			ACCTTCCGTACAG	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.765C>T	3.37:g.118865801C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_152539	A1L4B7	Silent	SNP	ENST00000295622.1	37	CCDS2984.1	480	0.21978021978021978	103	0.20934959349593496	76	0.20994475138121546	120	0.2097902097902098	181	0.23878627968337732	C	3.881	-0.026039	0.07589	0.243532	0.284419	ENSG00000163424	ENST00000460150;ENST00000473121	.	.	.	4.45	-7.09	0.01553	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.41413	-0.9510	3	.	.	.	-0.3947	0.2055	0.00150	0.2265:0.2212:0.2309:0.3213	rs4077931;rs4077931	.	.	.	C	219;48	.	.	R	+	1	0	C3orf30	120348491	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.902000	0.04088	-1.239000	0.02532	-1.769000	0.00663	CGT	C|0.750;T|0.250	0.250	strong		0.502	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
KRT3	3850	hgsc.bcm.edu	37	12	53186088	53186088	+	Missense_Mutation	SNP	G	G	C	rs3887954	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53186088G>C	ENST00000417996.2	-	5	1197	c.1123C>G	c.(1123-1125)Cgt>Ggt	p.R375G	KRT3_ENST00000309505.3_Missense_Mutation_p.R375G	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	375	Coil 2.|Rod.		R -> G (in dbSNP:rs3887954). {ECO:0000269|PubMed:2439698}.		epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						TACTGTGCACGAACTTCAGCA	0.537													G|||	1892	0.377796	0.3775	0.4539	5008	,	,		22988	0.1369		0.672	False		,,,				2504	0.2699				p.R375G		Atlas-SNP	.											.	KRT3	65	.	0			c.C1123G						PASS	.	G	GLY/ARG	1902,2502	542.4+/-376.0	413,1076,713	81.0	79.0	80.0		1123	0.7	0.9	12	dbSNP_108	80	5703,2897	671.2+/-402.8	1905,1893,502	yes	missense	KRT3	NM_057088.2	125	2318,2969,1215	CC,CG,GG		33.686,43.188,41.518	probably-damaging	375/629	53186088	7605,5399	2202	4300	6502	SO:0001583	missense	3850	exon5			GTGCACGAACTTC		CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1123C>G	12.37:g.53186088G>C	ENSP00000413479:p.Arg375Gly	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	948	0.4340659340659341	178	0.3617886178861789	183	0.505524861878453	74	0.12937062937062938	513	0.6767810026385225	G	11.35	1.612222	0.28712	0.43188	0.66314	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.93366	-3.21;-3.21	4.41	0.697	0.18081	Filament (1);	0.437683	0.17428	N	0.174598	T	0.00012	0.0000	M	0.93150	3.385	0.80722	P	0.0	D	0.67145	0.996	D	0.66497	0.944	T	0.43212	-0.9405	9	0.87932	D	0	.	14.7673	0.69648	0.0:0.0:0.6335:0.3665	rs3887954;rs52801567;rs3887954	375	P12035	K2C3_HUMAN	G	375	ENSP00000413479:R375G;ENSP00000312206:R375G	ENSP00000312206:R375G	R	-	1	0	KRT3	51472355	0.000000	0.05858	0.870000	0.34147	0.032000	0.12392	0.076000	0.14712	0.289000	0.22422	0.491000	0.48974	CGT	G|0.565;C|0.435	0.435	strong		0.537	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
TAS2R1	50834	hgsc.bcm.edu	37	5	9629529	9629529	+	Missense_Mutation	SNP	G	G	A	rs2234233	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:9629529G>A	ENST00000382492.2	-	1	934	c.616C>T	c.(616-618)Cgg>Tgg	p.R206W	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	206			R -> W (in dbSNP:rs2234233).		chemosensory behavior (GO:0007635)|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)	p.R206W(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(19)|ovary(3)|prostate(1)|skin(1)|stomach(1)	39						CTCATTTGCCGGGTGTGCCTC	0.507													G|||	572	0.114217	0.028	0.1268	5008	,	,		17670	0.1071		0.1521	False		,,,				2504	0.1902				p.R206W		Atlas-SNP	.											TAS2R1,NS,carcinoma,0,1	TAS2R1	84	1	1	Substitution - Missense(1)	stomach(1)	c.C616T						PASS	.	G	TRP/ARG	216,4190	121.3+/-158.8	8,200,1995	47.0	55.0	53.0		616	-11.3	0.0	5	dbSNP_98	53	1422,7178	266.3+/-286.6	113,1196,2991	yes	missense	TAS2R1	NM_019599.2	101	121,1396,4986	AA,AG,GG		16.5349,4.9024,12.5942	benign	206/300	9629529	1638,11368	2203	4300	6503	SO:0001583	missense	50834	exon1			TTTGCCGGGTGTG	AF227129	CCDS3876.1	5p15	2012-08-22			ENSG00000169777	ENSG00000169777		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14909	protein-coding gene	gene with protein product		604796				10761934, 10766242	Standard	NM_019599		Approved	T2R1, TRB7	uc003jem.1	Q9NYW7	OTTHUMG00000090500	ENST00000382492.2:c.616C>T	5.37:g.9629529G>A	ENSP00000371932:p.Arg206Trp	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_019599	Q646G8	Missense_Mutation	SNP	ENST00000382492.2	37	CCDS3876.1	255	0.11675824175824176	15	0.03048780487804878	48	0.13259668508287292	75	0.13111888111888112	117	0.15435356200527706	G	11.62	1.692461	0.30052	0.049024	0.165349	ENSG00000169777	ENST00000382492	T	0.00986	5.47	5.65	-11.3	0.00108	.	1.250620	0.06042	N	0.655136	T	0.00012	0.0000	N	0.05574	-0.02	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.48559	-0.9025	8	.	.	.	.	2.3549	0.04293	0.2929:0.0693:0.3959:0.242	rs2234233;rs52805045;rs60592533;rs2234233	206	Q9NYW7	TA2R1_HUMAN	W	206	ENSP00000371932:R206W	.	R	-	1	2	TAS2R1	9682529	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.202000	0.09451	-2.320000	0.00642	-0.880000	0.02959	CGG	G|0.878;A|0.122	0.122	strong		0.507	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2		
KIAA2026	158358	hgsc.bcm.edu	37	9	5969249	5969249	+	Silent	SNP	A	A	G	rs10739080	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:5969249A>G	ENST00000399933.3	-	3	981	c.982T>C	c.(982-984)Ttg>Ctg	p.L328L	KIAA2026_ENST00000381461.2_Silent_p.L328L	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	328										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		CAACGTTCCAATTCGTAAAAG	0.398													A|||	2552	0.509585	0.3238	0.5605	5008	,	,		19352	0.5427		0.6869	False		,,,				2504	0.5082				p.L328L		Atlas-SNP	.											.	KIAA2026	231	.	0			c.T982C						PASS	.	A		1465,2287		284,897,695	81.0	74.0	77.0		982	1.0	1.0	9	dbSNP_120	77	5897,2309		2103,1691,309	no	coding-synonymous	KIAA2026	NM_001017969.2		2387,2588,1004	GG,GA,AA		28.1379,39.0458,38.4345		328/2104	5969249	7362,4596	1876	4103	5979	SO:0001819	synonymous_variant	158358	exon3			GTTCCAATTCGTA	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.982T>C	9.37:g.5969249A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	37																																																																																				A|0.421;G|0.579	0.579	strong		0.398	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
RNF183	138065	hgsc.bcm.edu	37	9	116060124	116060124	+	Missense_Mutation	SNP	T	T	C	rs3750534	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:116060124T>C	ENST00000478815.1	-	1	1921	c.341A>G	c.(340-342)cAa>cGa	p.Q114R	RNF183_ENST00000416588.2_Missense_Mutation_p.Q114R|RNF183_ENST00000441031.3_Missense_Mutation_p.Q114R|RNF183_ENST00000297894.5_Missense_Mutation_p.Q114R|RNF183_ENST00000478493.1_5'Flank			Q96D59	RN183_HUMAN	ring finger protein 183	114			Q -> R (in dbSNP:rs3750534). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			lung(1)|prostate(1)|skin(1)	3						CGTGTAGACTTGAGGCTGGCG	0.677													C|||	2046	0.408546	0.4486	0.2061	5008	,	,		17546	0.4246		0.3181	False		,,,				2504	0.5746				p.Q114R		Atlas-SNP	.											.	RNF183	11	.	0			c.A341G						PASS	.	C	ARG/GLN	1682,2254		372,938,658	34.0	41.0	39.0		341	3.2	1.0	9	dbSNP_107	39	2814,5520		491,1832,1844	yes	missense	RNF183	NM_145051.3	43	863,2770,2502	CC,CT,TT		33.7653,42.7337,36.6422	benign	114/193	116060124	4496,7774	1968	4167	6135	SO:0001583	missense	138065	exon2			TAGACTTGAGGCT		CCDS43866.1	9q32	2007-04-24			ENSG00000165188	ENSG00000165188		"""RING-type (C3HC4) zinc fingers"""	28721	protein-coding gene	gene with protein product						12477932	Standard	NM_145051		Approved	MGC4734	uc004bgz.3	Q96D59	OTTHUMG00000020520	ENST00000478815.1:c.341A>G	9.37:g.116060124T>C	ENSP00000419454:p.Gln114Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	147	77	0.52381	NM_145051		Missense_Mutation	SNP	ENST00000478815.1	37	CCDS43866.1	818	0.37454212454212454	238	0.483739837398374	85	0.23480662983425415	248	0.43356643356643354	247	0.3258575197889182	C	0.018	-1.471647	0.01044	0.427337	0.337653	ENSG00000165188	ENST00000441031;ENST00000416588;ENST00000478815;ENST00000297894	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	4.98	3.16	0.36331	.	0.563466	0.16985	N	0.191541	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.43556	-0.9384	6	0.14252	T	0.57	-22.1071	4.7681	0.13142	0.0:0.5873:0.1556:0.257	rs3750534;rs17856416;rs59531625;rs3750534	.	.	.	R	114	ENSP00000417176:Q114R;ENSP00000420740:Q114R;ENSP00000419454:Q114R;ENSP00000417943:Q114R	ENSP00000417943:Q114R	Q	-	2	0	RNF183	115099945	0.097000	0.21791	0.998000	0.56505	0.110000	0.19582	0.059000	0.14322	0.318000	0.23185	-0.119000	0.15052	CAA	T|0.603;C|0.397	0.397	strong		0.677	RNF183-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356360.1	NM_145051	
DCHS2	54798	hgsc.bcm.edu	37	4	155410909	155410909	+	Silent	SNP	A	A	G	rs35172627	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:155410909A>G	ENST00000339452.1	-	1	1959	c.1599T>C	c.(1597-1599)aaT>aaC	p.N533N	DCHS2_ENST00000456341.2_Silent_p.N526N|DCHS2_ENST00000443500.1_Silent_p.N533N	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1678	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)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GTGGTTGGTCATTGAGGTCAG	0.637													A|||	568	0.113419	0.0567	0.1571	5008	,	,		16044	0.0109		0.2445	False		,,,				2504	0.1299				p.N533N		Atlas-SNP	.											.	DCHS2	594	.	0			c.T1599C						PASS	.	A	,	135,1249		6,123,563	103.0	106.0	105.0		1599,1599	-4.0	0.8	4	dbSNP_126	105	842,2340		114,614,863	no	coding-synonymous,coding-synonymous	DCHS2	NM_001142552.1,NM_001142553.1	,	120,737,1426	GG,GA,AA		26.4613,9.7543,21.3973	,	533/1370,533/710	155410909	977,3589	692	1591	2283	SO:0001819	synonymous_variant	54798	exon1			TTGGTCATTGAGG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.1599T>C	4.37:g.155410909A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000339452.1	37	CCDS47150.1																																																																																			A|0.843;G|0.157	0.157	strong		0.637	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
IQUB	154865	hgsc.bcm.edu	37	7	123097468	123097468	+	Silent	SNP	T	T	C	rs10234745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:123097468T>C	ENST00000466202.1	-	12	2736	c.2160A>G	c.(2158-2160)gcA>gcG	p.A720A	IQUB_ENST00000324698.6_Silent_p.A720A|RP11-332K15.1_ENST00000419832.1_RNA|RNU6-296P_ENST00000384608.1_RNA	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	720					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.A720A(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						GATGAGCAGCTGCTTCATCTT	0.403													C|||	1688	0.337061	0.3926	0.2781	5008	,	,		16262	0.3909		0.2972	False		,,,				2504	0.2894				p.A720A		Atlas-SNP	.											IQUB,colon,carcinoma,0,2	IQUB	117	2	1	Substitution - coding silent(1)	stomach(1)	c.A2160G						PASS	.	C		1779,2627	642.8+/-397.7	372,1035,796	98.0	102.0	100.0		2160	-11.7	0.0	7	dbSNP_119	100	2376,6224	700.4+/-405.1	324,1728,2248	no	coding-synonymous	IQUB	NM_178827.4		696,2763,3044	CC,CT,TT		27.6279,40.3768,31.9468		720/792	123097468	4155,8851	2203	4300	6503	SO:0001819	synonymous_variant	154865	exon12			AGCAGCTGCTTCA	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.2160A>G	7.37:g.123097468T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																			T|0.682;C|0.318	0.318	strong		0.403	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
SLIT3	6586	hgsc.bcm.edu	37	5	168093522	168093522	+	Silent	SNP	G	G	A	rs1048307	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:168093522G>A	ENST00000519560.1	-	36	4928	c.4509C>T	c.(4507-4509)gaC>gaT	p.D1503D	SLIT3_ENST00000332966.8_Silent_p.D1510D|CTC-558O2.2_ENST00000520041.1_RNA	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1503	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACGAGGAGCCGTCCGTGCACT	0.642													G|||	1032	0.20607	0.0431	0.2061	5008	,	,		14738	0.4206		0.174	False		,,,				2504	0.2382				p.D1510D	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.C4530T						PASS	.	G		358,4048	182.9+/-210.6	20,318,1865	47.0	39.0	42.0		4509	2.3	1.0	5	dbSNP_86	42	1589,7011	293.4+/-301.3	153,1283,2864	no	coding-synonymous	SLIT3	NM_003062.2		173,1601,4729	AA,AG,GG		18.4767,8.1253,14.97		1503/1524	168093522	1947,11059	2203	4300	6503	SO:0001819	synonymous_variant	6586	exon36			GGAGCCGTCCGTG	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.4509C>T	5.37:g.168093522G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			G|0.834;A|0.166	0.166	strong		0.642	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
SPNS3	201305	hgsc.bcm.edu	37	17	4391153	4391153	+	Silent	SNP	A	A	G	rs333122	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4391153A>G	ENST00000355530.2	+	12	1783	c.1503A>G	c.(1501-1503)ctA>ctG	p.L501L	RP13-580F15.2_ENST00000576086.1_RNA|SPNS3_ENST00000333476.2_Silent_p.L374L	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	501					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.L501L(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						GACAAGGCCTACTTTCGGGCG	0.622													G|||	869	0.173522	0.1256	0.1729	5008	,	,		18292	0.0446		0.3171	False		,,,				2504	0.2239				p.L501L		Atlas-SNP	.											SPNS3,NS,carcinoma,0,1	SPNS3	52	1	1	Substitution - coding silent(1)	stomach(1)	c.A1503G						scavenged	.	G		626,3780	767.8+/-413.5	50,526,1627	114.0	104.0	107.0		1503	1.2	0.0	17	dbSNP_79	107	2537,6063	692.6+/-404.6	364,1809,2127	no	coding-synonymous	SPNS3	NM_182538.4		414,2335,3754	GG,GA,AA		29.5,14.2079,24.3195		501/513	4391153	3163,9843	2203	4300	6503	SO:0001819	synonymous_variant	201305	exon12			AGGCCTACTTTCG		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.1503A>G	17.37:g.4391153A>G		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	96	34	0.354167	NM_182538	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																			A|0.784;G|0.216	0.216	strong		0.622	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
MZF1	7593	hgsc.bcm.edu	37	19	59082605	59082605	+	Missense_Mutation	SNP	C	C	T	rs3752109	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:59082605C>T	ENST00000215057.2	-	2	712	c.152G>A	c.(151-153)cGc>cAc	p.R51H	MZF1_ENST00000594234.1_Missense_Mutation_p.R51H|AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|MZF1_ENST00000599369.1_Missense_Mutation_p.R51H|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000594108.1_Missense_Mutation_p.R51H	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	51	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.		R -> H (in dbSNP:rs3752109). {ECO:0000269|PubMed:10974541, ECO:0000269|PubMed:15489334}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|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(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0443)|all cancers(4;7.92e-14)|Epithelial(4;5.57e-11)|OV - Ovarian serous cystadenocarcinoma(4;1.13e-09)|GBM - Glioblastoma multiforme(193;0.0108)|Lung(386;0.182)		CTCCTCATAGCGGAAGCACCG	0.647													.|||	1037	0.207069	0.0688	0.2378	5008	,	,		18124	0.2996		0.2744	False		,,,				2504	0.2076				p.R51H		Atlas-SNP	.											.	MZF1	37	.	0			c.G152A						PASS	.	C	HIS/ARG,HIS/ARG	411,3995		22,367,1814	21.0	22.0	22.0		152,152	-1.9	0.0	19	dbSNP_107	22	2432,6166		334,1764,2201	yes	missense,missense	MZF1	NM_003422.2,NM_198055.1	29,29	356,2131,4015	TT,TC,CC		28.2856,9.3282,21.8625	benign,benign	51/735,51/735	59082605	2843,10161	2203	4299	6502	SO:0001583	missense	7593	exon2			TCATAGCGGAAGC	M58297	CCDS12988.1, CCDS59427.1	19q13.43	2014-08-22	2006-06-15	2006-06-15	ENSG00000099326	ENSG00000099326		"""-"", ""Zinc fingers, C2H2-type"""	13108	protein-coding gene	gene with protein product		194550	"""zinc finger protein 42 (myeloid-specific retinoic acid-responsive)"""	ZNF42		1860835	Standard	NM_198055		Approved	ZSCAN6, MZF1B, MZF-1, Zfp98	uc002qtn.3	P28698	OTTHUMG00000183550	ENST00000215057.2:c.152G>A	19.37:g.59082605C>T	ENSP00000215057:p.Arg51His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	511	0.23397435897435898	38	0.07723577235772358	86	0.23756906077348067	169	0.29545454545454547	218	0.287598944591029	.	9.266	1.044385	0.19748	0.093282	0.282856	ENSG00000099326	ENST00000215057	T	0.04317	3.65	4.35	-1.86	0.07760	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.997429	0.08115	N	0.995595	T	0.00012	0.0000	L	0.43646	1.37	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.46190	-0.9209	8	.	.	.	-6.6894	7.7165	0.28708	0.0:0.4866:0.0:0.5134	rs3752109;rs17846501;rs17859570;rs58492417;rs3752109	51	P28698	MZF1_HUMAN	H	51	ENSP00000215057:R51H	.	R	-	2	0	MZF1	63774417	0.000000	0.05858	0.008000	0.14137	0.493000	0.33554	-2.046000	0.01409	-0.298000	0.08921	-0.253000	0.11424	CGC	C|0.795;T|0.205	0.205	strong		0.647	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055	
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 GAIIx	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	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	24	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		
USP40	55230	hgsc.bcm.edu	37	2	234432017	234432017	+	Missense_Mutation	SNP	A	A	G	rs838543	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:234432017A>G	ENST00000427112.2	-	15	2032	c.1997T>C	c.(1996-1998)gTc>gCc	p.V666A	USP40_ENST00000251722.6_Missense_Mutation_p.V666A|USP40_ENST00000450966.1_Missense_Mutation_p.V678A			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	666			V -> A (in dbSNP:rs838543).		ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		AGCTGGAAAGACATGTGGAGA	0.468													A|||	902	0.180112	0.2284	0.134	5008	,	,		19676	0.1458		0.2435	False		,,,				2504	0.1176				p.V678A		Atlas-SNP	.											.	USP40	174	.	0			c.T2033C						PASS	.	A	ALA/VAL	848,3170		86,676,1247	179.0	169.0	172.0		2033	5.6	0.9	2	dbSNP_86	172	1761,6597		188,1385,2606	yes	missense	USP40	NM_018218.2	64	274,2061,3853	GG,GA,AA		21.0696,21.105,21.0811	benign	678/1248	234432017	2609,9767	2009	4179	6188	SO:0001583	missense	55230	exon15			GGAAAGACATGTG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1997T>C	2.37:g.234432017A>G	ENSP00000387898:p.Val666Ala	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	131	129	0.984733	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	410	0.18772893772893773	121	0.2459349593495935	48	0.13259668508287292	66	0.11538461538461539	175	0.23087071240105542	A	12.61	1.989024	0.35131	0.21105	0.210696	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.53206	0.63;0.63;0.63	5.57	5.57	0.84162	.	.	.	.	.	T	0.00012	0.0000	L	0.55103	1.725	0.25118	P	0.99066606	B;B	0.24618	0.036;0.107	B;B	0.18871	0.01;0.023	T	0.05419	-1.0886	8	0.44086	T	0.13	.	14.3088	0.66403	1.0:0.0:0.0:0.0	rs838543;rs17669447;rs52822056;rs61311513;rs838543	666;678	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	A	678;666;666	ENSP00000415434:V678A;ENSP00000251722:V666A;ENSP00000387898:V666A	ENSP00000251722:V666A	V	-	2	0	USP40	234096756	0.966000	0.33281	0.948000	0.38648	0.956000	0.61745	2.928000	0.48908	2.119000	0.64992	0.533000	0.62120	GTC	T|0.001;G|0.188	0.188	strong		0.468	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
FSIP1	161835	hgsc.bcm.edu	37	15	39910404	39910404	+	Missense_Mutation	SNP	G	G	A	rs12908846	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:39910404G>A	ENST00000350221.3	-	11	1440	c.1231C>T	c.(1231-1233)Ctt>Ttt	p.L411F		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	411			L -> F (in dbSNP:rs12908846).							NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCATCCAGAAGACACTTTAAC	0.353													G|||	788	0.157348	0.0333	0.1196	5008	,	,		19671	0.2907		0.1471	False		,,,				2504	0.2249				p.L411F		Atlas-SNP	.											.	FSIP1	53	.	0			c.C1231T						PASS	.	G	PHE/LEU	230,4164		3,224,1970	51.0	54.0	53.0		1231	5.1	1.0	15	dbSNP_121	53	1107,7475		65,977,3249	yes	missense	FSIP1	NM_152597.4	22	68,1201,5219	AA,AG,GG		12.8991,5.2344,10.3036	probably-damaging	411/582	39910404	1337,11639	2197	4291	6488	SO:0001583	missense	161835	exon11			CCAGAAGACACTT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1231C>T	15.37:g.39910404G>A	ENSP00000280236:p.Leu411Phe	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	349	0.15979853479853479	16	0.032520325203252036	48	0.13259668508287292	178	0.3111888111888112	107	0.14116094986807387	G	20.4	3.987146	0.74589	0.052344	0.128991	ENSG00000150667	ENST00000350221	T	0.35789	1.29	5.06	5.06	0.68205	.	0.104654	0.38217	N	0.001773	T	0.00012	0.0000	L	0.29908	0.895	0.27465	P	0.9530472	D	0.89917	1.0	D	0.91635	0.999	T	0.18808	-1.0325	8	.	.	.	-7.7703	17.1261	0.86714	0.0:0.0:1.0:0.0	rs12908846;rs59692160;rs12908846	411	Q8NA03	FSIP1_HUMAN	F	411	ENSP00000280236:L411F	.	L	-	1	0	FSIP1	37697696	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.542000	0.67218	2.785000	0.95823	0.655000	0.94253	CTT	G|0.862;A|0.138	0.138	strong		0.353	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
MED13L	23389	hgsc.bcm.edu	37	12	116403920	116403920	+	Silent	SNP	G	G	A	rs3088260	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:116403920G>A	ENST00000281928.3	-	29	6560	c.6354C>T	c.(6352-6354)ccC>ccT	p.P2118P		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	2118						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TTTGAGCCTGGGGACACGATG	0.448													G|||	180	0.0359425	0.0129	0.036	5008	,	,		17606	0.0		0.0845	False		,,,				2504	0.0542				p.P2118P		Atlas-SNP	.											.	MED13L	193	.	0			c.C6354T						PASS	.	G		93,4313	75.7+/-113.9	1,91,2111	136.0	142.0	140.0		6354	-3.8	1.0	12	dbSNP_102	140	818,7782	190.7+/-237.1	40,738,3522	no	coding-synonymous	MED13L	NM_015335.4		41,829,5633	AA,AG,GG		9.5116,2.1108,7.0045		2118/2211	116403920	911,12095	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon29			AGCCTGGGGACAC	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.6354C>T	12.37:g.116403920G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																			G|0.936;A|0.064	0.064	strong		0.448	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
PLEC	5339	hgsc.bcm.edu	37	8	144993377	144993377	+	Silent	SNP	A	A	G	rs6992333	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144993377A>G	ENST00000322810.4	-	32	11192	c.11023T>C	c.(11023-11025)Ttg>Ctg	p.L3675L	PLEC_ENST00000354589.3_Silent_p.L3538L|PLEC_ENST00000357649.2_Silent_p.L3542L|PLEC_ENST00000436759.2_Silent_p.L3565L|PLEC_ENST00000354958.2_Silent_p.L3516L|PLEC_ENST00000527096.1_Silent_p.L3561L|PLEC_ENST00000345136.3_Silent_p.L3538L|PLEC_ENST00000356346.3_Silent_p.L3524L|PLEC_ENST00000398774.2_Silent_p.L3506L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3675	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AGAAGGCGCAAGCCCGTCTCG	0.607													G|||	2363	0.471845	0.8918	0.3746	5008	,	,		16831	0.1438		0.4324	False		,,,				2504	0.3517				p.L3675L		Atlas-SNP	.											.	PLEC	1144	.	0			c.T11023C						PASS	.	G	,,,,,,,	3429,675		1444,541,67	73.0	89.0	84.0		10693,10570,10546,11023,10516,10612,10624,10612	2.9	0.8	8	dbSNP_116	84	3601,4801		800,2001,1400	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	2244,2542,1467	GG,GA,AA		42.8588,16.4474,43.787	,,,,,,,	3565/4575,3524/4534,3516/4526,3675/4685,3506/4516,3538/4548,3542/4552,3538/4548	144993377	7030,5476	2052	4201	6253	SO:0001819	synonymous_variant	5339	exon32			GGCGCAAGCCCGT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11023T>C	8.37:g.144993377A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.544;G|0.456	0.456	strong		0.607	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
TAP2	6891	hgsc.bcm.edu	37	6	32797297	32797297	+	Silent	SNP	T	T	C	rs241441	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32797297T>C	ENST00000452392.2	-	11	1985	c.1812A>G	c.(1810-1812)ggA>ggG	p.G604G	TAP2_ENST00000374899.4_Silent_p.G604G|TAP2_ENST00000485701.1_5'Flank|TAP2_ENST00000374897.2_Silent_p.G604G			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	CCAGCTGGCTTCCCTTCTCCC	0.552													C|||	1498	0.299121	0.1551	0.304	5008	,	,		20092	0.3621		0.2783	False		,,,				2504	0.4468				p.G604G		Atlas-SNP	.											.	TAP2	98	.	0			c.A1812G						PASS	.	C	,	815,3591	317.7+/-295.3	77,661,1465	70.0	72.0	71.0		1812,1812	-2.5	0.1	6	dbSNP_79	71	2259,6341	376.1+/-338.0	292,1675,2333	no	coding-synonymous,coding-synonymous	TAP2	NM_000544.3,NM_018833.2	,	369,2336,3798	CC,CT,TT		26.2674,18.4975,23.6352	,	604/704,604/654	32797297	3074,9932	2203	4300	6503	SO:0001819	synonymous_variant	6891	exon11			CTGGCTTCCCTTC	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.1812A>G	6.37:g.32797297T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	12	0.169014	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000452392.2	37																																																																																				T|0.748;C|0.252	0.252	strong		0.552	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
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 GAIIx	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	RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000544413.1_Silent_p.L459L|HNF1A_ENST00000541395.1_Silent_p.L459L|HNF1A_ENST00000400024.2_Silent_p.L459L|HNF1A_ENST00000538626.1_Silent_p.L41L			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		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	117	116	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	
ANGPTL4	51129	hgsc.bcm.edu	37	19	8436164	8436164	+	Missense_Mutation	SNP	C	C	T	rs1044250	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8436164C>T	ENST00000301455.2	+	6	968	c.797C>T	c.(796-798)aCg>aTg	p.T266M	ANGPTL4_ENST00000541807.1_Missense_Mutation_p.T99M|ANGPTL4_ENST00000393962.2_Missense_Mutation_p.T228M	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	266	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		T -> M (in dbSNP:rs1044250). {ECO:0000269|PubMed:10698685, ECO:0000269|PubMed:17322881, ECO:0000269|Ref.8}.		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						CATAGCATCACGGGGGACCGC	0.667													C|||	1200	0.239617	0.2564	0.3285	5008	,	,		18038	0.0595		0.331	False		,,,				2504	0.2454				p.T266M		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.C797T	GRCh37	CM086232	ANGPTL4	M	rs1044250	PASS	.	C	MET/THR,MET/THR	1123,3283	393.7+/-329.0	132,859,1212	43.0	44.0	44.0		683,797	-1.3	0.0	19	dbSNP_86	44	2667,5933	418.0+/-352.6	419,1829,2052	yes	missense,missense	ANGPTL4	NM_001039667.1,NM_139314.1	81,81	551,2688,3264	TT,TC,CC		31.0116,25.488,29.1404	benign,benign	228/369,266/407	8436164	3790,9216	2203	4300	6503	SO:0001583	missense	51129	exon6			GCATCACGGGGGA	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"""Fibrinogen C domain containing"""	16039	protein-coding gene	gene with protein product	"""fasting-induced adipose factor"", ""hepatic angiopoietin-related protein"", ""PPARG angiopoietin related protein"", ""hepatic fibrinogen/angiopoietin-related protein"", ""peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein"", ""angiopoietin-related protein 4"""	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.797C>T	19.37:g.8436164C>T	ENSP00000301455:p.Thr266Met	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_139314	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	37	CCDS12200.1	555	0.2541208791208791	139	0.28252032520325204	116	0.32044198895027626	44	0.07692307692307693	256	0.33773087071240104	C	6.884	0.532489	0.13127	0.25488	0.310116	ENSG00000167772	ENST00000301455;ENST00000393962;ENST00000541807	T;T;T	0.33865	1.39;1.39;1.39	5.09	-1.27	0.09347	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	1.836750	0.02798	N	0.122905	T	0.00012	0.0000	M	0.92412	3.305	0.80722	P	0.0	B;B	0.25563	0.129;0.129	B;B	0.24848	0.056;0.056	T	0.36383	-0.9750	9	0.51188	T	0.08	.	6.5885	0.22634	0.112:0.6775:0.0:0.2105	rs1044250;rs3183947;rs17305531;rs52807441;rs59900793;rs1044250	228;266	A8MY84;Q9BY76	.;ANGL4_HUMAN	M	266;228;99	ENSP00000301455:T266M;ENSP00000377534:T228M;ENSP00000439833:T99M	ENSP00000301455:T266M	T	+	2	0	ANGPTL4	8342164	0.001000	0.12720	0.000000	0.03702	0.239000	0.25481	0.761000	0.26489	-0.515000	0.06479	-0.263000	0.10527	ACG	C|0.730;T|0.270	0.270	strong		0.667	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314	
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 GAIIx	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		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	54	24	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
GRM1	2911	hgsc.bcm.edu	37	6	146755324	146755324	+	Missense_Mutation	SNP	T	T	C	rs6923492	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:146755324T>C	ENST00000282753.1	+	8	3212	c.2977T>C	c.(2977-2979)Tcc>Ccc	p.S993P	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000361719.2_Missense_Mutation_p.S993P|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000492807.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	993			S -> P (in dbSNP:rs6923492). {ECO:0000269|PubMed:7476890, ECO:0000269|PubMed:9076744}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GCCTCTGCCGTCCCACCTGAC	0.687													C|||	3025	0.604034	0.7421	0.4726	5008	,	,		15666	0.5466		0.5457	False		,,,				2504	0.6299				p.S993P		Atlas-SNP	.											.	GRM1	419	.	0			c.T2977C						PASS	.	C	PRO/SER,	3129,1277	424.7+/-340.5	1114,901,188	55.0	64.0	61.0		2977,	3.4	0.7	6	dbSNP_116	61	4581,4019	542.2+/-384.1	1242,2097,961	yes	missense,utr-3	GRM1	NM_000838.3,NM_001114329.1	74,	2356,2998,1149	CC,CT,TT		46.7326,28.9832,40.7197	benign,	993/1195,	146755324	7710,5296	2203	4300	6503	SO:0001583	missense	2911	exon9			CTGCCGTCCCACC	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2977T>C	6.37:g.146755324T>C	ENSP00000282753:p.Ser993Pro	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	1239	0.5673076923076923	353	0.717479674796748	175	0.48342541436464087	305	0.5332167832167832	406	0.5356200527704486	C	1.636	-0.517781	0.04171	0.710168	0.532674	ENSG00000152822	ENST00000361719;ENST00000282753	D;D	0.88277	-2.36;-2.36	5.38	3.42	0.39159	.	0.585264	0.18293	N	0.145675	T	0.45736	0.1357	N	0.01874	-0.695	0.48632	P	3.189999999999582E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.15407	-1.0438	9	0.02654	T	1	.	8.5533	0.33465	0.0:0.6009:0.3095:0.0895	rs6923492;rs52837655;rs58247061;rs6923492	993	Q13255	GRM1_HUMAN	P	993	ENSP00000354896:S993P;ENSP00000282753:S993P	ENSP00000282753:S993P	S	+	1	0	GRM1	146797017	0.000000	0.05858	0.720000	0.30636	0.571000	0.35966	0.444000	0.21661	0.607000	0.29982	-0.642000	0.03964	TCC	T|0.420;C|0.580	0.580	strong		0.687	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
FAM220A	84792	hgsc.bcm.edu	37	7	6370406	6370406	+	Missense_Mutation	SNP	C	C	T	rs3750040	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6370406C>T	ENST00000313324.4	-	2	847	c.380G>A	c.(379-381)cGg>cAg	p.R127Q	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	127			R -> Q (in dbSNP:rs3750040). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			nucleus (GO:0005634)											CCAGTCTCGCCGCCCCAGAGC	0.632													C|||	3621	0.723043	0.8669	0.6571	5008	,	,		17256	0.8839		0.4543	False		,,,				2504	0.6861				p.R127Q		Atlas-SNP	.											.	.	.	.	0			c.G380A						PASS	.	C	GLN/ARG	3590,816	736.7+/-410.8	1483,624,96	38.0	40.0	39.0		380	4.2	0.0	7	dbSNP_107	39	4105,4495	553.0+/-386.2	972,2161,1167	no	missense	C7orf70	NM_001037163.1	43	2455,2785,1263	TT,TC,CC		47.7326,18.5202,40.835	probably-damaging	127/260	6370406	7695,5311	2203	4300	6503	SO:0001583	missense	84792	exon2			TCTCGCCGCCCCA	BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"""STAT3-interacting protein as a repressor"""		"""chromosome 7 open reading frame 70"""	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.380G>A	7.37:g.6370406C>T	ENSP00000317289:p.Arg127Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	Missense_Mutation	SNP	ENST00000313324.4	37	CCDS34599.1	1497	0.6854395604395604	420	0.8536585365853658	228	0.6298342541436464	505	0.8828671328671329	344	0.45382585751978893	C	8.298	0.819362	0.16607	0.814798	0.477326	ENSG00000178397	ENST00000313324	T	0.08370	3.1	5.12	4.23	0.50019	.	0.754743	0.11509	U	0.556900	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	D	0.64830	0.994	P	0.51193	0.662	T	0.16867	-1.0388	9	0.13108	T	0.6	-5.6486	8.367	0.32393	0.3083:0.5423:0.1494:0.0	rs3750040;rs10304769;rs11550273;rs17775294;rs52813284;rs57990713;rs3750040	127	Q7Z4H9	SIPAR_HUMAN	Q	127	ENSP00000317289:R127Q	ENSP00000317289:R127Q	R	-	2	0	C7orf70	6336931	0.002000	0.14202	0.023000	0.16930	0.004000	0.04260	0.772000	0.26647	1.144000	0.42321	0.655000	0.94253	CGG	C|0.381;T|0.619	0.619	strong		0.632	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163	
LPPR3	79948	hgsc.bcm.edu	37	19	814680	814680	+	Intron	SNP	G	G	T	rs56944467	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:814680G>T	ENST00000520876.3	-	6	736				MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Silent_p.A223A	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN								integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										GGCAGTGAGGGGCCGGACTCA	0.662													G|||	676	0.134984	0.0764	0.2565	5008	,	,		14874	0.0208		0.1312	False		,,,				2504	0.2495				p.A223A		Atlas-SNP	.											.	.	.	.	0			c.C669A						PASS	.	G		359,4033	179.7+/-208.2	15,329,1852	54.0	50.0	51.0		669	0.9	0.0	19	dbSNP_129	51	1094,7502	225.7+/-261.6	62,970,3266	no	coding-synonymous	LPPR3	NM_024888.1		77,1299,5118	TT,TG,GG		12.7268,8.174,11.1872		223/747	814680	1453,11535	2196	4298	6494	SO:0001627	intron_variant	0	exon6			GTGAGGGGCCGGA																												ENST00000520876.3:c.657+11C>A	19.37:g.814680G>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Silent	SNP	ENST00000520876.3	37	CCDS58636.1																																																																																			G|0.886;T|0.114	0.114	strong		0.662	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3		
PREX1	57580	hgsc.bcm.edu	37	20	47273726	47273726	+	Splice_Site	SNP	C	C	T	rs55904123	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47273726C>T	ENST00000371941.3	-	18	1997	c.1975G>A	c.(1975-1977)Gtg>Atg	p.V659M	PREX1_ENST00000396220.1_Splice_Site_p.V659M	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	659	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.		V -> M (in dbSNP:rs55904123). {ECO:0000269|PubMed:17974005}.		actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGGCCAGCCACCTGGGTAGGG	0.572											OREG0026010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	803	0.160343	0.0363	0.2133	5008	,	,		21050	0.1587		0.1839	False		,,,				2504	0.2679				p.V659M		Atlas-SNP	.											PREX1_ENST00000396220,NS,adenoma,0,2	PREX1	441	2	0			c.G1975A						PASS	.	T	MET/VAL	341,4065	792.8+/-415.2	13,315,1875	75.0	58.0	64.0		1975	2.8	1.0	20	dbSNP_129	64	1617,6983	740.3+/-407.1	147,1323,2830	yes	missense-near-splice	PREX1	NM_020820.3	21	160,1638,4705	TT,TC,CC		18.8023,7.7394,15.0546	benign	659/1660	47273726	1958,11048	2203	4300	6503	SO:0001630	splice_region_variant	57580	exon18			CAGCCACCTGGGT	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.1975-1G>A	20.37:g.47273726C>T		Somatic	38	0	0	945	WXS	Illumina HiSeq	Phase_I	40	24	0.6	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	325	0.1488095238095238	21	0.042682926829268296	81	0.22375690607734808	88	0.15384615384615385	135	0.17810026385224276	T	0.007	-1.987474	0.00443	0.077394	0.188023	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.17213	2.29;2.29	5.12	2.8	0.32819	PDZ/DHR/GLGF (3);	0.079540	0.51477	N	0.000100	T	0.00012	0.0000	N	0.01352	-0.895	0.33382	P	0.42501999999999995	B	0.02656	0.0	B	0.04013	0.001	T	0.46400	-0.9194	9	0.02654	T	1	.	8.5258	0.33304	0.0:0.1263:0.1111:0.7626	rs55904123;rs62621373	659	Q8TCU6	PREX1_HUMAN	M	659	ENSP00000361009:V659M;ENSP00000379522:V659M	ENSP00000361009:V659M	V	-	1	0	PREX1	46707133	1.000000	0.71417	0.981000	0.43875	0.047000	0.14425	3.541000	0.53618	-0.281000	0.09141	-2.680000	0.00142	GTG	C|0.849;T|0.151	0.151	strong		0.572	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	Missense_Mutation
ACO1	48	hgsc.bcm.edu	37	9	32425910	32425910	+	Silent	SNP	A	A	G	rs3780473	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:32425910A>G	ENST00000309951.6	+	11	1401	c.1263A>G	c.(1261-1263)gaA>gaG	p.E421E	ACO1_ENST00000541043.1_Silent_p.E322E|ACO1_ENST00000379923.1_Silent_p.E421E	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	421					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		ATAACACTGAATTCACCCTTG	0.393													A|||	1772	0.353834	0.2632	0.3386	5008	,	,		17408	0.5516		0.336	False		,,,				2504	0.3016				p.E421E		Atlas-SNP	.											.	ACO1	149	.	0			c.A1263G						PASS	.	A		1204,3202	417.8+/-338.1	167,870,1166	142.0	110.0	121.0		1263	0.7	1.0	9	dbSNP_107	121	3048,5552	468.5+/-367.3	566,1916,1818	no	coding-synonymous	ACO1	NM_002197.2		733,2786,2984	GG,GA,AA		35.4419,27.3264,32.6926		421/890	32425910	4252,8754	2203	4300	6503	SO:0001819	synonymous_variant	48	exon11			CACTGAATTCACC	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1263A>G	9.37:g.32425910A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	37	CCDS6525.1																																																																																			G|0.346;N|0.000	0.346	strong		0.393	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
NANS	54187	hgsc.bcm.edu	37	9	100823135	100823135	+	Missense_Mutation	SNP	G	G	C	rs1058446	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:100823135G>C	ENST00000210444.5	+	2	274	c.204G>C	c.(202-204)gaG>gaC	p.E68D		NM_018946.3	NP_061819.2	Q9NR45	SIAS_HUMAN	N-acetylneuraminic acid synthase	68			E -> D (in dbSNP:rs1058446). {ECO:0000269|PubMed:15489334}.		lipopolysaccharide biosynthetic process (GO:0009103)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	N-acetylneuraminate synthase activity (GO:0050462)|N-acylneuraminate cytidylyltransferase activity (GO:0008781)|N-acylneuraminate-9-phosphate synthase activity (GO:0047444)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	11		Acute lymphoblastic leukemia(62;0.0559)				AAGCCTTGGAGAGGCCATACA	0.502													G|||	963	0.192292	0.2224	0.2622	5008	,	,		18731	0.2004		0.2207	False		,,,				2504	0.0644				p.E68D		Atlas-SNP	.											.	NANS	24	.	0			c.G204C						PASS	.	G	ASP/GLU	937,3469	357.4+/-313.9	105,727,1371	182.0	180.0	181.0		204	3.0	1.0	9	dbSNP_86	181	2075,6525	359.9+/-331.7	269,1537,2494	yes	missense	NANS	NM_018946.3	45	374,2264,3865	CC,CG,GG		24.1279,21.2665,23.1585	benign	68/360	100823135	3012,9994	2203	4300	6503	SO:0001583	missense	54187	exon2			CTTGGAGAGGCCA	AF161387	CCDS6733.1	9p24.1-p23	2008-07-31	2008-07-31		ENSG00000095380	ENSG00000095380			19237	protein-coding gene	gene with protein product	"""sialic acid synthase"""	605202				10749855	Standard	NM_018946		Approved	SAS	uc004ayc.3	Q9NR45	OTTHUMG00000020341	ENST00000210444.5:c.204G>C	9.37:g.100823135G>C	ENSP00000210444:p.Glu68Asp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	NM_018946	B2RE98|Q8WUV9|Q9BWS6|Q9NVD4	Missense_Mutation	SNP	ENST00000210444.5	37	CCDS6733.1	498	0.22802197802197802	120	0.24390243902439024	88	0.2430939226519337	125	0.21853146853146854	165	0.21767810026385223	G	12.90	2.077207	0.36662	0.212665	0.241279	ENSG00000095380	ENST00000210444	T	0.43294	0.95	5.73	2.95	0.34219	Aldolase-type TIM barrel (1);N-acetylneuraminic acid synthase, N-terminal (1);	0.043833	0.85682	D	0.000000	T	0.00012	0.0000	N	0.02751	-0.505	0.22754	P	0.99877242	B	0.02656	0.0	B	0.11329	0.006	T	0.29150	-1.0021	9	0.27082	T	0.32	-17.3272	9.6941	0.40147	0.2239:0.0:0.7761:0.0	rs1058446;rs3199071;rs17858509;rs52795099;rs1058446	68	Q9NR45	SIAS_HUMAN	D	68	ENSP00000210444:E68D	ENSP00000210444:E68D	E	+	3	2	NANS	99862956	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	2.315000	0.43752	0.470000	0.27294	0.655000	0.94253	GAG	G|0.775;C|0.225	0.225	strong		0.502	NANS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053359.1	NM_018946	
C1orf94	84970	hgsc.bcm.edu	37	1	34663208	34663208	+	Missense_Mutation	SNP	C	C	G	rs1382602	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:34663208C>G	ENST00000488417.1	+	2	823	c.703C>G	c.(703-705)Caa>Gaa	p.Q235E	C1orf94_ENST00000373374.3_Missense_Mutation_p.Q45E	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	235			Q -> E (in dbSNP:rs1382602). {ECO:0000269|PubMed:15489334}.							central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CTCCAACTTGCAAGTCAGCAA	0.542													G|||	1903	0.379992	0.7632	0.3617	5008	,	,		20334	0.1409		0.2376	False		,,,				2504	0.2679				p.Q235E		Atlas-SNP	.											.	C1orf94	156	.	0			c.C703G						PASS	.	G	GLU/GLN,GLU/GLN	2938,1468	470.7+/-355.8	991,956,256	85.0	76.0	79.0		703,133	3.1	0.5	1	dbSNP_88	79	2284,6316	707.0+/-405.6	317,1650,2333	yes	missense,missense	C1orf94	NM_001134734.1,NM_032884.3	29,29	1308,2606,2589	GG,GC,CC		26.5581,33.3182,40.1507	benign,benign	235/599,45/409	34663208	5222,7784	2203	4300	6503	SO:0001583	missense	84970	exon2			AACTTGCAAGTCA	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.703C>G	1.37:g.34663208C>G	ENSP00000435634:p.Gln235Glu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	37	CCDS44108.1	752	0.3443223443223443	378	0.7682926829268293	128	0.35359116022099446	72	0.1258741258741259	174	0.22955145118733508	G	0.004	-2.343661	0.00222	0.666818	0.265581	ENSG00000142698	ENST00000373374;ENST00000488417	T;T	0.17528	2.27;2.27	4.98	3.09	0.35607	.	0.320719	0.26979	N	0.021522	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33650	-0.9860	9	0.02654	T	1	-10.8271	4.6061	0.12378	0.1965:0.1836:0.6199:0.0	rs1382602;rs3795413;rs17845123;rs17857923;rs52817485;rs61292196;rs1382602	235	Q6P1W5	CA094_HUMAN	E	45;235	ENSP00000362472:Q45E;ENSP00000435634:Q235E	ENSP00000362472:Q45E	Q	+	1	0	C1orf94	34435795	0.977000	0.34250	0.525000	0.27900	0.047000	0.14425	1.778000	0.38614	0.516000	0.28340	-0.215000	0.12644	CAA	C|0.612;G|0.387	0.387	strong		0.542	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
CCDC144NL	339184	hgsc.bcm.edu	37	17	20798992	20798992	+	Silent	SNP	C	C	T	rs8073465	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:20798992C>T	ENST00000327925.5	-	1	461	c.342G>A	c.(340-342)aaG>aaA	p.K114K	RP11-344E13.3_ENST00000577537.1_RNA|RP11-344E13.3_ENST00000417232.2_RNA|RP11-344E13.3_ENST00000583962.1_RNA|RNU6-1178P_ENST00000516674.1_RNA|RP11-344E13.3_ENST00000582324.1_RNA|RP11-344E13.3_ENST00000439794.2_RNA|RP11-344E13.3_ENST00000577860.1_RNA	NM_001004306.1	NP_001004306.1	Q6NUI1	C144L_HUMAN	coiled-coil domain containing 144 family, N-terminal like	114										large_intestine(3)|lung(3)|skin(1)	7						GCCATTACCTCTTCTTCCTAT	0.652													c|||	497	0.0992412	0.0212	0.0865	5008	,	,		14967	0.1766		0.1501	False		,,,				2504	0.0818				p.K114K		Atlas-SNP	.											.	CCDC144NL	34	.	0			c.G342A						PASS	.	C		228,4178	130.2+/-166.9	12,204,1987	74.0	79.0	77.0		342	-1.8	0.0	17	dbSNP_116	77	1217,7383	229.0+/-263.8	74,1069,3157	no	coding-synonymous	CCDC144NL	NM_001004306.1		86,1273,5144	TT,TC,CC		14.1512,5.1748,11.1103		114/222	20798992	1445,11561	2203	4300	6503	SO:0001819	synonymous_variant	339184	exon1			TTACCTCTTCTTC		CCDS32591.1	17p11.2	2009-01-15			ENSG00000205212	ENSG00000205212			33735	protein-coding gene	gene with protein product							Standard	NM_001004306		Approved	MGC87631	uc002gyf.3	Q6NUI1	OTTHUMG00000132271	ENST00000327925.5:c.342G>A	17.37:g.20798992C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_001004306		Silent	SNP	ENST00000327925.5	37	CCDS32591.1																																																																																			C|0.883;T|0.117	0.117	strong		0.652	CCDC144NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255361.2	NM_001004306	
CWC27	10283	hgsc.bcm.edu	37	5	64267595	64267595	+	Silent	SNP	T	T	C	rs2278351	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:64267595T>C	ENST00000381070.3	+	12	1325	c.1108T>C	c.(1108-1110)Ttg>Ctg	p.L370L	CWC27_ENST00000545000.1_3'UTR	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	370					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						GTATGAAGCTTTGAGGAAGCA	0.373													T|||	1700	0.339457	0.4123	0.1772	5008	,	,		16092	0.4653		0.2435	False		,,,				2504	0.3252				p.L370L		Atlas-SNP	.											.	CWC27	47	.	0			c.T1108C						PASS	.	T		1483,2923	473.1+/-356.6	265,953,985	61.0	63.0	62.0		1108	1.0	1.0	5	dbSNP_100	62	1995,6605	347.4+/-326.6	240,1515,2545	no	coding-synonymous	CWC27	NM_005869.2		505,2468,3530	CC,CT,TT		23.1977,33.6586,26.7415		370/473	64267595	3478,9528	2203	4300	6503	SO:0001819	synonymous_variant	10283	exon12			GAAGCTTTGAGGA	AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"""serologically defined colon cancer antigen 10"""	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.1108T>C	5.37:g.64267595T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	119	73	0.613445	NM_005869	O60529|O60530|Q96EM3	Silent	SNP	ENST00000381070.3	37	CCDS3982.2																																																																																			T|0.708;C|0.292	0.292	strong		0.373	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
LIPC	3990	hgsc.bcm.edu	37	15	58860963	58860963	+	Silent	SNP	C	C	A	rs6074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:58860963C>A	ENST00000356113.6	+	11	2052	c.1437C>A	c.(1435-1437)acC>acA	p.T479T	LIPC_ENST00000299022.5_Silent_p.T479T|LIPC_ENST00000433326.2_Silent_p.T418T			P11150	LIPC_HUMAN	lipase, hepatic	479	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		TTCGCCCAACCCAGGAAAAAA	0.348													C|||	1009	0.201478	0.0817	0.196	5008	,	,		19374	0.249		0.1561	False		,,,				2504	0.365				p.T479T		Atlas-SNP	.											.	LIPC	56	.	0			c.C1437A						PASS	.	C		432,3952	207.2+/-228.6	27,378,1787	85.0	80.0	81.0		1437	4.6	1.0	15	dbSNP_52	81	1220,7364	244.0+/-273.4	88,1044,3160	no	coding-synonymous	LIPC	NM_000236.2		115,1422,4947	AA,AC,CC		14.2125,9.854,12.739		479/500	58860963	1652,11316	2192	4292	6484	SO:0001819	synonymous_variant	3990	exon9			CCCAACCCAGGAA		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.1437C>A	15.37:g.58860963C>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	52	32	0.615385	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Silent	SNP	ENST00000356113.6	37	CCDS10166.1																																																																																			C|0.856;A|0.144	0.144	strong		0.348	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1		
CYP2D6	1565	hgsc.bcm.edu	37	22	42523539	42523539	+	Silent	SNP	A	A	G	rs28371726	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:42523539A>G	ENST00000360608.5	-	7	1197	c.1083T>C	c.(1081-1083)caT>caC	p.H361H	NDUFA6-AS1_ENST00000417327.1_RNA|CYP2D6_ENST00000389970.3_Silent_p.H361H|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Silent_p.H310H|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	361					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GCTGCACCTCATGAATCACGG	0.602																																					p.H361H		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,4	CYP2D6	104	4	0			c.T1083C						scavenged	.						119.0	93.0	102.0					22																	42523539		2202	4299	6501	SO:0001819	synonymous_variant	1565	exon7			CACCTCATGAATC	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1083T>C	22.37:g.42523539A>G		Somatic	267	4	0.0149813		WXS	Illumina HiSeq	Phase_I	217	5	0.0230415	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	37	CCDS46721.1																																																																																			A|0.959;G|0.041	0.041	strong		0.602	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
MLF1	4291	hgsc.bcm.edu	37	3	158320597	158320597	+	Splice_Site	SNP	T	T	C	rs4875	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:158320597T>C	ENST00000355893.5	+	6	708	c.570T>C	c.(568-570)agT>agC	p.S190S	MLF1_ENST00000392822.3_Splice_Site_p.S221S|MLF1_ENST00000469452.1_Splice_Site_p.S122S|MLF1_ENST00000497004.1_3'UTR|MLF1_ENST00000478894.2_Splice_Site_p.S180S|MLF1_ENST00000471745.1_Splice_Site_p.S180S|MLF1_ENST00000359117.5_Splice_Site_p.S165S|MLF1_ENST00000482628.1_Splice_Site_p.S165S|MLF1_ENST00000484955.1_Splice_Site_p.S165S	NM_022443.4	NP_071888.1	P58340	MLF1_HUMAN	myeloid leukemia factor 1	190					cell cycle arrest (GO:0007050)|myeloid progenitor cell differentiation (GO:0002318)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)			large_intestine(3)	3		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			TTGACATAGGTGATGCTCATG	0.398			T	NPM1	AML								T|||	2887	0.576478	0.7595	0.5303	5008	,	,		17790	0.381		0.5437	False		,,,				2504	0.5971				p.S221S		Atlas-SNP	.		Dom	yes		3	3q25.1	4291	myeloid leukemia factor 1		L	.	MLF1	62	.	0			c.T663C						PASS	.	T	,,,,,	3124,1280	699.7+/-406.5	1107,910,185	97.0	97.0	97.0		495,495,663,366,540,570	0.2	0.8	3	dbSNP_52	97	4634,3966	601.5+/-394.4	1240,2154,906	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	MLF1	NM_001130156.2,NM_001130157.2,NM_001195432.1,NM_001195433.1,NM_001195434.1,NM_022443.4	,,,,,	2347,3064,1091	CC,CT,TT		46.1163,29.0645,40.3414	,,,,,	165/244,165/244,221/300,122/201,180/259,190/269	158320597	7758,5246	2202	4300	6502	SO:0001630	splice_region_variant	4291	exon8			CATAGGTGATGCT	L49054	CCDS3182.1, CCDS46945.1, CCDS56286.1, CCDS56287.1, CCDS56288.1	3q25	2008-07-18			ENSG00000178053	ENSG00000178053			7125	protein-coding gene	gene with protein product	"""myeloid leukemia factor 1 variant 1"", ""myeloid leukemia factor 1 variant 2"", ""myeloid leukemia factor 1 variant 3"""	601402				8570204	Standard	NM_022443		Approved		uc003fcb.3	P58340	OTTHUMG00000158775	ENST00000355893.5:c.569-1T>C	3.37:g.158320597T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_001195432	E9PEU9|Q2TLE3|Q2TLE5|Q8N8F8|Q96MH1	Silent	SNP	ENST00000355893.5	37	CCDS3182.1																																																																																			T|0.426;C|0.574	0.574	strong		0.398	MLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352164.3	NM_022443	Silent
GAREM	64762	hgsc.bcm.edu	37	18	30050356	30050356	+	Silent	SNP	C	C	T	rs11664566	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:30050356C>T	ENST00000269209.6	-	1	39	c.36G>A	c.(34-36)aaG>aaA	p.K12K	GAREM_ENST00000399218.4_Silent_p.K12K			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	12	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										ACTTCACATCCTTGAGGCTGC	0.726													c|||	1280	0.255591	0.298	0.2161	5008	,	,		8443	0.3869		0.162	False		,,,				2504	0.1871				p.K12K		Atlas-SNP	.											.	.	.	.	0			c.G36A						PASS	.		,	1195,3201		164,867,1167	16.0	18.0	17.0		36,36	3.5	1.0	18	dbSNP_120	17	1361,7229		122,1117,3056	no	coding-synonymous,coding-synonymous	FAM59A	NM_001242409.1,NM_022751.2	,	286,1984,4223	TT,TC,CC		15.844,27.1838,19.6827	,	12/877,12/876	30050356	2556,10430	2198	4295	6493	SO:0001819	synonymous_variant	64762	exon1			CACATCCTTGAGG	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.36G>A	18.37:g.30050356C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																			C|0.784;T|0.216	0.216	strong		0.726	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751	
NGEF	25791	hgsc.bcm.edu	37	2	233785015	233785015	+	Silent	SNP	G	G	A	rs778354	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233785015G>A	ENST00000264051.3	-	5	1085	c.807C>T	c.(805-807)ccC>ccT	p.P269P	NGEF_ENST00000373552.4_Silent_p.P177P|NGEF_ENST00000409079.1_Silent_p.P177P	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	269	Regulatory region; modulates activity toward RHOA, RAC1 and CDC42. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		TAATCTCCTCGGGCTGTAGGA	0.647													G|||	3592	0.717252	0.8359	0.8156	5008	,	,		16171	0.5625		0.7565	False		,,,				2504	0.6063				p.P269P		Atlas-SNP	.											NGEF_ENST00000264051,colon,carcinoma,0,2	NGEF	198	2	0			c.C807T						PASS	.	G	,	3710,696	759.1+/-412.9	1555,600,48	47.0	53.0	51.0		531,807	-10.5	0.0	2	dbSNP_86	51	6584,2016	719.9+/-406.3	2552,1480,268	no	coding-synonymous,coding-synonymous	NGEF	NM_001114090.1,NM_019850.2	,	4107,2080,316	AA,AG,GG		23.4419,15.7966,20.8519	,	177/619,269/711	233785015	10294,2712	2203	4300	6503	SO:0001819	synonymous_variant	25791	exon5			CTCCTCGGGCTGT	AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"""Rho guanine nucleotide exchange factors"""	7807	protein-coding gene	gene with protein product	"""ephexin"""	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.807C>T	2.37:g.233785015G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Silent	SNP	ENST00000264051.3	37	CCDS2500.1																																																																																			G|0.244;A|0.756	0.756	strong		0.647	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799	
USHBP1	83878	hgsc.bcm.edu	37	19	17366278	17366278	+	Silent	SNP	T	T	C	rs4430871	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17366278T>C	ENST00000252597.3	-	10	1781	c.1608A>G	c.(1606-1608)gcA>gcG	p.A536A	AC010646.3_ENST00000594059.1_5'Flank|USHBP1_ENST00000431146.2_Silent_p.A472A	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						CCTGGAGCTCTGCCCGTTCCC	0.682													C|||	3903	0.779353	0.9766	0.7709	5008	,	,		15195	0.7996		0.5805	False		,,,				2504	0.7025				p.A536A		Atlas-SNP	.											.	USHBP1	85	.	0			c.A1608G						PASS	.	C		4049,357	180.1+/-208.5	1861,327,15	53.0	57.0	56.0		1608	-9.9	0.0	19	dbSNP_111	56	5186,3414	495.0+/-374.0	1575,2036,689	no	coding-synonymous	USHBP1	NM_031941.3		3436,2363,704	CC,CT,TT		39.6977,8.1026,28.9943		536/704	17366278	9235,3771	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon10			GAGCTCTGCCCGT	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.1608A>G	19.37:g.17366278T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			T|0.284;C|0.716	0.716	strong		0.682	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
KIAA1217	56243	hgsc.bcm.edu	37	10	24790393	24790393	+	Silent	SNP	A	A	G	rs1112284	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:24790393A>G	ENST00000376454.3	+	9	1950	c.1920A>G	c.(1918-1920)tcA>tcG	p.S640S	KIAA1217_ENST00000376452.3_Silent_p.S605S|KIAA1217_ENST00000458595.1_Silent_p.S605S|KIAA1217_ENST00000376462.1_Silent_p.S560S|KIAA1217_ENST00000430453.2_Silent_p.S526S|KIAA1217_ENST00000376451.2_Silent_p.S323S|KIAA1217_ENST00000396445.1_Silent_p.S323S|KIAA1217_ENST00000307544.6_Silent_p.S323S|KIAA1217_ENST00000396446.1_Silent_p.S323S	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	640					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						TGGGCACCTCAGCCATCCACA	0.617													G|||	2003	0.39996	0.6815	0.2983	5008	,	,		15614	0.2123		0.3439	False		,,,				2504	0.3425				p.S640S		Atlas-SNP	.											.	KIAA1217	235	.	0			c.A1920G						PASS	.	G	,,	2768,1638	503.9+/-365.7	870,1028,305	73.0	64.0	67.0		1680,1815,1920	-7.3	0.0	10	dbSNP_86	67	2835,5765	674.9+/-403.2	470,1895,1935	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	1340,2923,2240	GG,GA,AA		32.9651,37.1766,43.0801	,,	560/1265,605/1310,640/1944	24790393	5603,7403	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon9			CACCTCAGCCATC	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.1920A>G	10.37:g.24790393A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			A|0.581;C|0.007	.	strong		0.617	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
MKRN3	7681	hgsc.bcm.edu	37	15	23811592	23811592	+	Silent	SNP	C	C	T	rs2239669	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:23811592C>T	ENST00000314520.3	+	1	1139	c.663C>T	c.(661-663)ccC>ccT	p.P221P	MKRN3_ENST00000564592.1_Intron|MKRN3_ENST00000568252.1_Intron|RP11-73C9.1_ENST00000563044.1_RNA	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	221					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		CATCTGCCCCCGAGGCTCCTC	0.592													C|||	1051	0.209864	0.1596	0.1715	5008	,	,		17393	0.1875		0.3161	False		,,,				2504	0.2188				p.P221P		Atlas-SNP	.											.	MKRN3	155	.	0			c.C663T						PASS	.	C		794,3612	313.3+/-293.0	58,678,1467	47.0	52.0	50.0		663	-8.1	0.0	15	dbSNP_98	50	2651,5949	420.5+/-353.4	421,1809,2070	no	coding-synonymous	MKRN3	NM_005664.3		479,2487,3537	TT,TC,CC		30.8256,18.0209,26.4878		221/508	23811592	3445,9561	2203	4300	6503	SO:0001819	synonymous_variant	7681	exon1			TGCCCCCGAGGCT	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"""RING-type (C3HC4) zinc fingers"""	7114	protein-coding gene	gene with protein product	"""zinc finger protein 127"""	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.663C>T	15.37:g.23811592C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	32	0.581818	NM_005664		Silent	SNP	ENST00000314520.3	37	CCDS10013.1																																																																																			C|0.745;A|0.002	.	strong		0.592	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664	
RAI1	10743	hgsc.bcm.edu	37	17	17707105	17707105	+	Silent	SNP	T	T	C	rs3818717	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:17707105T>C	ENST00000353383.1	+	4	6070	c.5601T>C	c.(5599-5601)atT>atC	p.I1867I	RAI1_ENST00000261641.6_Intron	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1867					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GGGCCACCATTGGGTGCTGCC	0.597													T|||	1205	0.240615	0.1248	0.3847	5008	,	,		19451	0.0754		0.5318	False		,,,				2504	0.1656				p.I1867I		Atlas-SNP	.											.	RAI1	121	.	0			c.T5601C						PASS	.	T		836,3570	325.6+/-299.2	77,682,1444	91.0	76.0	81.0		5601	-7.0	0.9	17	dbSNP_107	81	4832,3768	611.6+/-395.8	1361,2110,829	no	coding-synonymous	RAI1	NM_030665.3		1438,2792,2273	CC,CT,TT		43.814,18.9741,43.5799		1867/1907	17707105	5668,7338	2203	4300	6503	SO:0001819	synonymous_variant	10743	exon4			CACCATTGGGTGC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.5601T>C	17.37:g.17707105T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1	649	0.29716117216117216	57	0.11585365853658537	153	0.42265193370165743	35	0.06118881118881119	404	0.5329815303430079	T	10.79	1.450792	0.26074	0.189741	0.56186	ENSG00000108557	ENST00000395776;ENST00000315321	.	.	.	5.46	-6.98	0.01611	.	0.293540	0.29760	N	0.011262	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999982953	.	.	.	.	.	.	T	0.30001	-0.9993	5	0.39692	T	0.17	.	6.6284	0.22843	0.0819:0.5328:0.1606:0.2247	rs3818717;rs52832780;rs57642502;rs3818717	.	.	.	S	1911;1780	.	ENSP00000322928:L1780S	L	+	2	0	RAI1	17647830	0.036000	0.19791	0.900000	0.35374	0.987000	0.75469	-1.200000	0.03029	-1.125000	0.02932	-0.256000	0.11100	TTG	T|0.635;C|0.365	0.365	strong		0.597	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
KRT1	3848	hgsc.bcm.edu	37	12	53072370	53072370	+	Silent	SNP	C	C	T	rs2741155	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53072370C>T	ENST00000252244.3	-	2	820	c.762G>A	c.(760-762)tcG>tcA	p.S254S		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	254	Coil 1B.|Rod.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)	p.S254S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						TCTTCAGTTCCGAATCCAACC	0.453													C|||	14	0.00279553	0.0015	0.0043	5008	,	,		22193	0.0		0.0089	False		,,,				2504	0.0				p.S254S		Atlas-SNP	.											KRT1,NS,carcinoma,0,1	KRT1	110	1	1	Substitution - coding silent(1)	endometrium(1)	c.G762A						PASS	.	C		13,4393	20.2+/-43.8	0,13,2190	182.0	162.0	169.0		762	-10.0	0.0	12	dbSNP_100	169	110,8490	58.3+/-119.8	0,110,4190	no	coding-synonymous	KRT1	NM_006121.3		0,123,6380	TT,TC,CC		1.2791,0.2951,0.9457		254/645	53072370	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	3848	exon2			CAGTTCCGAATCC	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.762G>A	12.37:g.53072370C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	195	90	0.461538	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Silent	SNP	ENST00000252244.3	37	CCDS8836.1																																																																																			C|0.994;T|0.006	0.006	strong		0.453	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
DAXX	1616	hgsc.bcm.edu	37	6	33288271	33288271	+	Silent	SNP	A	A	G	rs1059231	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33288271A>G	ENST00000374542.5	-	4	1341	c.1137T>C	c.(1135-1137)taT>taC	p.Y379Y	DAXX_ENST00000414083.2_Silent_p.Y304Y|DAXX_ENST00000266000.6_Silent_p.Y379Y|ZBTB22_ENST00000431845.2_5'Flank|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000477162.1_5'UTR	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	379	Interaction with histone H3.3.|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						GCAACATTGCATATTTGGAGA	0.552			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM								A|||	1106	0.220847	0.0182	0.3415	5008	,	,		18188	0.2619		0.2922	False		,,,				2504	0.2935				p.Y391Y		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.T1173C						PASS	.	A	,,	277,4129	154.4+/-187.8	5,267,1931	94.0	87.0	90.0		1137,1173,1137	2.1	1.0	6	dbSNP_86	90	2570,6030	417.9+/-352.6	398,1774,2128	no	coding-synonymous,coding-synonymous,coding-synonymous	DAXX	NM_001141969.1,NM_001141970.1,NM_001350.4	,,	403,2041,4059	GG,GA,AA		29.8837,6.2869,21.8899	,,	379/741,391/753,379/741	33288271	2847,10159	2203	4300	6503	SO:0001819	synonymous_variant	1616	exon4			CATTGCATATTTG	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1137T>C	6.37:g.33288271A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	30	22	0.733333	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	37	CCDS4776.1																																																																																			A|0.778;G|0.222	0.222	strong		0.552	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1		
PM20D1	148811	hgsc.bcm.edu	37	1	205819039	205819039	+	Silent	SNP	C	C	T	rs11540016	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205819039C>T	ENST00000367136.4	-	1	206	c.162G>A	c.(160-162)gcG>gcA	p.A54A	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	54					negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CACCTTTCAGCGCCTCTTTCA	0.617													C|||	802	0.160144	0.053	0.0605	5008	,	,		17728	0.4246		0.0964	False		,,,				2504	0.1687				p.A54A		Atlas-SNP	.											.	PM20D1	56	.	0			c.G162A						PASS	.	C		265,4141	149.9+/-184.0	8,249,1946	78.0	86.0	83.0		162	-1.3	1.0	1	dbSNP_120	83	647,7953	165.7+/-217.8	20,607,3673	no	coding-synonymous	PM20D1	NM_152491.4		28,856,5619	TT,TC,CC		7.5233,6.0145,7.0121		54/503	205819039	912,12094	2203	4300	6503	SO:0001819	synonymous_variant	148811	exon1			TTTCAGCGCCTCT		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.162G>A	1.37:g.205819039C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_152491	Q6P4E3|Q96DM4	Silent	SNP	ENST00000367136.4	37	CCDS1460.1																																																																																			C|0.902;T|0.098	0.098	strong		0.617	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
ZFYVE1	53349	hgsc.bcm.edu	37	14	73459917	73459917	+	Silent	SNP	C	C	T	rs2333016	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:73459917C>T	ENST00000556143.1	-	4	1857	c.1137G>A	c.(1135-1137)gaG>gaA	p.E379E	ZFYVE1_ENST00000553891.1_Silent_p.E379E|ZFYVE1_ENST00000318876.5_Silent_p.E379E	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	379					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		CTAGTAGCTGCTCCAAAGCAC	0.552													C|||	1387	0.276957	0.1921	0.2176	5008	,	,		16874	0.3542		0.3608	False		,,,				2504	0.2679				p.E379E		Atlas-SNP	.											.	ZFYVE1	67	.	0			c.G1137A						PASS	.	C		978,3428	365.4+/-317.4	115,748,1340	69.0	74.0	72.0		1137	3.5	1.0	14	dbSNP_100	72	3104,5496	475.0+/-369.0	555,1994,1751	no	coding-synonymous	ZFYVE1	NM_021260.2		670,2742,3091	TT,TC,CC		36.093,22.197,31.3855		379/778	73459917	4082,8924	2203	4300	6503	SO:0001819	synonymous_variant	53349	exon4			TAGCTGCTCCAAA	AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.1137G>A	14.37:g.73459917C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	17	0.288136	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Silent	SNP	ENST00000556143.1	37	CCDS9811.1																																																																																			C|0.689;T|0.311	0.311	strong		0.552	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
PZP	5858	hgsc.bcm.edu	37	12	9334571	9334571	+	Splice_Site	SNP	C	C	T	rs3741849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9334571C>T	ENST00000261336.2	-	14	1717	c.1689G>A	c.(1687-1689)aaG>aaA	p.K563K	PZP_ENST00000381997.2_Splice_Site_p.K432K	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	563					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						AATCGCTCACCTTGTTGGCTA	0.358													C|||	475	0.0948482	0.1831	0.0548	5008	,	,		-128	0.0337		0.0934	False		,,,				2504	0.0685				p.K563K	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,colon,carcinoma,-1,2	PZP	422	2	0			c.G1689A						PASS	.	C		696,3710	266.8+/-267.5	51,594,1558	48.0	51.0	50.0		1689	3.9	0.9	12	dbSNP_107	50	872,7728	186.3+/-233.8	42,788,3470	yes	coding-synonymous-near-splice	PZP	NM_002864.2		93,1382,5028	TT,TC,CC		10.1395,15.7966,12.056		563/1483	9334571	1568,11438	2203	4300	6503	SO:0001630	splice_region_variant	5858	exon14			GCTCACCTTGTTG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.1689+1G>A	12.37:g.9334571C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Silent	SNP	ENST00000261336.2	37	CCDS8600.1																																																																																			C|0.886;T|0.114	0.114	strong		0.358	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	Silent
ADAM28	10863	hgsc.bcm.edu	37	8	24171051	24171051	+	Silent	SNP	C	C	T	rs6996616	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:24171051C>T	ENST00000265769.4	+	6	644	c.534C>T	c.(532-534)caC>caT	p.H178H	ADAM28_ENST00000540823.1_Intron|ADAM28_ENST00000437154.2_Silent_p.H178H|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	178					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGTGGGCCCACGATTTGCAGC	0.448													T|||	932	0.186102	0.152	0.0965	5008	,	,		16774	0.3621		0.1571	False		,,,				2504	0.1442				p.H178H	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.C534T						PASS	.	T	,	754,3652	755.8+/-412.6	65,624,1514	208.0	181.0	190.0		534,534	0.0	0.0	8	dbSNP_116	190	1315,7285	758.0+/-407.5	104,1107,3089	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	169,1731,4603	TT,TC,CC		15.2907,17.113,15.908	,	178/776,178/541	24171051	2069,10937	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon6			GGCCCACGATTTG	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.534C>T	8.37:g.24171051C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	169	82	0.485207	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			C|0.809;T|0.191	0.191	strong		0.448	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
CIITA	4261	hgsc.bcm.edu	37	16	11001691	11001691	+	Missense_Mutation	SNP	C	C	T	rs13330686	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11001691C>T	ENST00000324288.8	+	11	2475	c.2342C>T	c.(2341-2343)tCg>tTg	p.S781L	CIITA_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	781			S -> L (in dbSNP:rs13330686).		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						GCGGCTGCCTCGGTGGACAGG	0.697			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								T|||	199	0.0397364	0.0348	0.0389	5008	,	,		12614	0.0		0.0944	False		,,,				2504	0.0317				p.S781L		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.C2342T						PASS	.	T	LEU/SER	159,4219		2,155,2032	24.0	31.0	29.0		2342	-7.7	0.0	16	dbSNP_121	29	705,7879		29,647,3616	no	missense	CIITA	NM_000246.3	145	31,802,5648	TT,TC,CC		8.213,3.6318,6.6656	benign	781/1131	11001691	864,12098	2189	4292	6481	SO:0001583	missense	4261	exon11			CTGCCTCGGTGGA	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.2342C>T	16.37:g.11001691C>T	ENSP00000316328:p.Ser781Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	111	0.050824175824175824	26	0.052845528455284556	14	0.03867403314917127	0	0.0	71	0.09366754617414248	T	0.013	-1.611856	0.00835	0.036318	0.08213	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.73047	-0.71	5.15	-7.67	0.01272	.	3.735610	0.00702	N	0.000782	T	0.01454	0.0047	N	0.01109	-1.01	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.38415	-0.9662	9	0.06625	T	0.88	.	11.5043	0.50456	0.0897:0.6552:0.0:0.2551	rs13330686	781;781;733;781	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	L	781;733	ENSP00000316328:S781L	ENSP00000316328:S781L	S	+	2	0	CIITA	10909192	0.991000	0.36638	0.000000	0.03702	0.001000	0.01503	-0.287000	0.08388	-1.777000	0.01283	-0.254000	0.11334	TCG	C|0.935;T|0.065	0.065	strong		0.697	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
Unknown	0	hgsc.bcm.edu	37	13	103400729	103400729	+	IGR	SNP	G	G	A	rs12583104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103400729G>A								LINC00283 (3155 upstream) : TEX30 (17610 downstream)																							TTTGCTTCCTGGGGAAATGAG	0.353													A|||	3597	0.718251	0.6324	0.7536	5008	,	,		20444	0.5883		0.826	False		,,,				2504	0.8323				p.P773L		Atlas-SNP	.											.	.	.	.	0			c.C2318T						PASS	.	A	LEU/PRO	898,486		293,312,87	87.0	67.0	73.0		2318	0.6	0.0	13	dbSNP_120	73	2546,634		1026,494,70	yes	missense	CCDC168	NM_001146197.1	98	1319,806,157	AA,AG,GG		19.9371,35.1156,24.5399		773/7082	103400729	3444,1120	692	1590	2282	SO:0001628	intergenic_variant	643677	exon4			CTTCCTGGGGAAA																													13.37:g.103400729G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_001146197		Missense_Mutation	SNP		37																																																																																				G|0.314;A|0.686	0.686	strong	0	0.353								
AMPD1	270	hgsc.bcm.edu	37	1	115236057	115236057	+	Splice_Site	SNP	G	G	A	rs17602729	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:115236057G>A	ENST00000520113.2	-	2	148	c.133C>T	c.(133-135)Caa>Taa	p.Q45*	AMPD1_ENST00000353928.6_Splice_Site_p.Q12*|AMPD1_ENST00000369538.3_Intron			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	45					IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-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)	Adenosine monophosphate(DB00131)	CAATACTCACGTTTCTCTTCA	0.323													G|||	191	0.038139	0.0045	0.0576	5008	,	,		12866	0.001		0.1233	False		,,,				2504	0.0204				p.Q45X		Atlas-SNP	.											AMPD1_ENST00000520113,NS,carcinoma,0,2	AMPD1	223	2	0			c.C133T	GRCh37	CM920025	AMPD1	M	rs17602729	PASS	.	G	stop/GLN,	104,4302	81.9+/-120.4	2,100,2101	85.0	90.0	89.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	133,	2.8	1.0	1	dbSNP_123	89	1126,7472	232.6+/-266.2	89,948,3262	yes	stop-gained-near-splice,intron	AMPD1	NM_000036.2,NM_001172626.1	,	91,1048,5363	AA,AG,GG		13.0961,2.3604,9.4586	,	45/781,	115236057	1230,11774	2203	4299	6502	SO:0001630	splice_region_variant	270	exon2			ACTCACGTTTCTC	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.133+1C>T	1.37:g.115236057G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Nonsense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	117	0.05357142857142857	3	0.006097560975609756	30	0.08287292817679558	0	0.0	84	0.11081794195250659	G	29.9	5.043403	0.93685	0.023604	0.130961	ENSG00000116748	ENST00000520113;ENST00000353928	.	.	.	4.91	2.84	0.33178	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.6038	0.62035	0.0:0.2934:0.7066:0.0	rs17602729;rs52833197;rs17602729	.	.	.	X	45;12	.	.	Q	-	1	0	AMPD1	115037580	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.265000	0.43311	1.143000	0.42306	0.650000	0.86243	CAA	G|0.923;A|0.077	0.077	strong		0.323	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		Nonsense_Mutation
STX6	10228	hgsc.bcm.edu	37	1	180953853	180953853	+	Silent	SNP	A	A	G	rs3747957	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:180953853A>G	ENST00000258301.5	-	7	888	c.651T>C	c.(649-651)aaT>aaC	p.N217N	STX6_ENST00000469135.1_5'UTR|STX6_ENST00000542060.1_Silent_p.N116N	NM_005819.4	NP_005810.1	O43752	STX6_HUMAN	syntaxin 6	217	t-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00202}.				endosome organization (GO:0007032)|Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)|vesicle fusion (GO:0006906)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|trans-Golgi network membrane (GO:0032588)	SNAP receptor activity (GO:0005484)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	10						TCTTCATCACATTGTCCAGCC	0.433													A|||	2626	0.524361	0.4486	0.6282	5008	,	,		20709	0.631		0.5686	False		,,,				2504	0.3978				p.N217N		Atlas-SNP	.											.	STX6	21	.	0			c.T651C						PASS	.	A		2130,2276	578.0+/-384.6	522,1086,595	96.0	91.0	93.0		651	-3.1	1.0	1	dbSNP_107	93	5057,3543	631.1+/-398.4	1509,2039,752	no	coding-synonymous	STX6	NM_005819.4		2031,3125,1347	GG,GA,AA		41.1977,48.3432,44.7409		217/256	180953853	7187,5819	2203	4300	6503	SO:0001819	synonymous_variant	10228	exon7			CATCACATTGTCC	AJ002078	CCDS1341.1, CCDS65738.1	1q25.3	2008-02-05			ENSG00000135823	ENSG00000135823			11441	protein-coding gene	gene with protein product		603944				10080545	Standard	XM_005244824		Approved		uc021pfr.1	O43752	OTTHUMG00000035179	ENST00000258301.5:c.651T>C	1.37:g.180953853A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_005819	B2R652|B4DR17|Q5VY08|Q6FH83	Silent	SNP	ENST00000258301.5	37	CCDS1341.1																																																																																			A|0.439;G|0.561	0.561	strong		0.433	STX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085143.1	NM_005819	
ZBTB4	57659	hgsc.bcm.edu	37	17	7366619	7366619	+	Missense_Mutation	SNP	T	T	C	rs34914463	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7366619T>C	ENST00000311403.4	-	4	2021	c.1682A>G	c.(1681-1683)aAt>aGt	p.N561S	ZBTB4_ENST00000380599.4_Missense_Mutation_p.N561S	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	561			N -> S (in dbSNP:rs34914463).		cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		AGCCCGTGGATTCCGGCCCTT	0.701													T|||	140	0.0279553	0.0038	0.0418	5008	,	,		13314	0.0		0.0994	False		,,,				2504	0.0061				p.N561S		Atlas-SNP	.											.	ZBTB4	163	.	0			c.A1682G						PASS	.	T	SER/ASN,SER/ASN	118,4284		3,112,2086	16.0	18.0	18.0		1682,1682	3.9	1.0	17	dbSNP_126	18	1028,7564		77,874,3345	yes	missense,missense	ZBTB4	NM_001128833.1,NM_020899.3	46,46	80,986,5431	CC,CT,TT		11.9646,2.6806,8.8195	possibly-damaging,possibly-damaging	561/1014,561/1014	7366619	1146,11848	2201	4296	6497	SO:0001583	missense	57659	exon4			CGTGGATTCCGGC	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.1682A>G	17.37:g.7366619T>C	ENSP00000307858:p.Asn561Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	37	CCDS11107.1	96	0.04395604395604396	5	0.01016260162601626	13	0.03591160220994475	0	0.0	78	0.10290237467018469	T	14.22	2.471484	0.43942	0.026806	0.119646	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.03580	3.88;3.88	4.97	3.86	0.44501	.	0.262110	0.31531	N	0.007500	T	0.00039	0.0001	N	0.19112	0.55	0.26391	N	0.976573	P	0.34977	0.478	B	0.31442	0.13	T	0.45934	-0.9227	10	0.07813	T	0.8	-7.9164	8.5092	0.33206	0.0:0.0:0.1964:0.8036	rs34914463	561	Q9P1Z0	ZBTB4_HUMAN	S	561	ENSP00000307858:N561S;ENSP00000369973:N561S	ENSP00000307858:N561S	N	-	2	0	ZBTB4	7307343	0.033000	0.19621	0.998000	0.56505	0.990000	0.78478	0.346000	0.19997	0.885000	0.36088	0.379000	0.24179	AAT	T|0.942;C|0.058	0.058	strong		0.701	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
CEP44	80817	hgsc.bcm.edu	37	4	175225452	175225452	+	Missense_Mutation	SNP	G	G	A	rs4695918	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:175225452G>A	ENST00000503780.1	+	6	853	c.439G>A	c.(439-441)Ggc>Agc	p.G147S	CEP44_ENST00000296519.4_Missense_Mutation_p.G147S|CEP44_ENST00000457424.2_Missense_Mutation_p.G147S|CEP44_ENST00000426172.1_Missense_Mutation_p.G147S	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	147			G -> S (in dbSNP:rs4695918). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:14702039}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)				endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						ACCTCCTTTGGGCAATGAGAA	0.358													A|||	2205	0.440296	0.5809	0.3184	5008	,	,		14793	0.1597		0.5477	False		,,,				2504	0.5153				p.G147S		Atlas-SNP	.											.	CEP44	35	.	0			c.G439A						PASS	.	A	SER/GLY,SER/GLY	2511,1895	544.9+/-376.7	710,1091,402	70.0	74.0	73.0		439,439	0.7	0.0	4	dbSNP_111	73	4647,3953	549.9+/-385.6	1245,2157,898	yes	missense,missense	CEP44	NM_001040157.2,NM_001145314.1	56,56	1955,3248,1300	AA,AG,GG		45.9651,43.0095,44.9639	benign,benign	147/391,147/400	175225452	7158,5848	2203	4300	6503	SO:0001583	missense	80817	exon6			CCTTTGGGCAATG	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"""KIAA1712"""	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.439G>A	4.37:g.175225452G>A	ENSP00000423153:p.Gly147Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	126	47	0.373016	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Missense_Mutation	SNP	ENST00000503780.1	37	CCDS34106.1	906	0.41483516483516486	272	0.5528455284552846	129	0.356353591160221	91	0.1590909090909091	414	0.5461741424802111	A	0.007	-1.935401	0.00484	0.569905	0.540349	ENSG00000164118	ENST00000503780;ENST00000457424;ENST00000515299;ENST00000426172;ENST00000296519	T;T;T;T;T	0.39997	1.08;1.05;1.07;1.05;1.08	5.01	0.671	0.17929	.	0.724351	0.13541	N	0.380212	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46830	-0.9163	9	0.02654	T	1	.	8.8488	0.35188	0.7002:0.0:0.2998:0.0	rs4695918;rs60445014;rs4695918	147;147	Q9C0F1-2;Q9C0F1	.;CEP44_HUMAN	S	147	ENSP00000423153:G147S;ENSP00000389427:G147S;ENSP00000421128:G147S;ENSP00000408221:G147S;ENSP00000296519:G147S	ENSP00000296519:G147S	G	+	1	0	CEP44	175462027	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.070000	0.11523	-0.181000	0.10619	-1.390000	0.01156	GGC	G|0.520;A|0.480	0.480	strong		0.358	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633	
C12orf71	728858	hgsc.bcm.edu	37	12	27235279	27235279	+	Silent	SNP	G	G	A	rs12228215	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27235279G>A	ENST00000429849.2	-	1	168	c.138C>T	c.(136-138)tcC>tcT	p.S46S		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	46										endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						AAGGACCCTTGGAAGGTGCAT	0.542													G|||	126	0.0251597	0.0045	0.0216	5008	,	,		18205	0.0288		0.0676	False		,,,				2504	0.0082				p.S46S		Atlas-SNP	.											.	C12orf71	20	.	0			c.C138T						PASS	.	G		76,3790		0,76,1857	56.0	55.0	55.0		138	-3.6	0.0	12	dbSNP_120	55	763,7493		39,685,3404	no	coding-synonymous	C12orf71	NM_001080406.1		39,761,5261	AA,AG,GG		9.2418,1.9659,6.9213		46/270	27235279	839,11283	1933	4128	6061	SO:0001819	synonymous_variant	728858	exon1			ACCCTTGGAAGGT		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.138C>T	12.37:g.27235279G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	198	96	0.484848	NM_001080406		Silent	SNP	ENST00000429849.2	37	CCDS44851.1																																																																																			G|0.955;A|0.045	0.045	strong		0.542	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
MLPH	79083	hgsc.bcm.edu	37	2	238434434	238434434	+	Missense_Mutation	SNP	C	C	T	rs11883500	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238434434C>T	ENST00000264605.3	+	7	1160	c.866C>T	c.(865-867)aCt>aTt	p.T289I	MLPH_ENST00000338530.4_Missense_Mutation_p.T289I|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Missense_Mutation_p.T289I|MLPH_ENST00000409373.1_Missense_Mutation_p.T249I|MLPH_ENST00000410032.1_Intron	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	289			T -> I (in dbSNP:rs11883500).		melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		GCCCTGGGGACTGCTGCTGCA	0.657													C|||	657	0.13119	0.2352	0.0778	5008	,	,		17959	0.0675		0.1421	False		,,,				2504	0.0828				p.T289I		Atlas-SNP	.											.	MLPH	41	.	0			c.C866T						PASS	.	C	ILE/THR,ILE/THR	1044,3360	350.3+/-310.7	122,800,1280	28.0	29.0	29.0		866,866	-4.4	0.0	2	dbSNP_120	29	1434,7166	257.9+/-281.7	118,1198,2984	yes	missense,missense	MLPH	NM_001042467.1,NM_024101.5	89,89	240,1998,4264	TT,TC,CC		16.6744,23.7057,19.0557	benign,benign	289/573,289/601	238434434	2478,10526	2202	4300	6502	SO:0001583	missense	79083	exon7			TGGGGACTGCTGC	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.866C>T	2.37:g.238434434C>T	ENSP00000264605:p.Thr289Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	107	36	0.336449	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	293	0.13415750915750915	108	0.21951219512195122	30	0.08287292817679558	43	0.07517482517482517	112	0.14775725593667546	C	5.026	0.190481	0.09547	0.237057	0.166744	ENSG00000115648	ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T;T;T;T	0.26810	2.07;2.06;1.92;1.71	3.09	-4.43	0.03568	.	3.607730	0.00757	N	0.001103	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B;B;B	0.15719	0.014;0.011;0.004;0.004;0.007;0.004	B;B;B;B;B;B	0.19391	0.007;0.005;0.011;0.007;0.025;0.007	T	0.27839	-1.0062	9	0.24483	T	0.36	5.367	5.7615	0.18203	0.1637:0.6192:0.0:0.2171	rs11883500;rs52823878;rs57325617;rs11883500	289;173;289;249;289;289	B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36	.;.;.;.;.;MELPH_HUMAN	I	289;289;289;249	ENSP00000264605:T289I;ENSP00000414849:T289I;ENSP00000341845:T289I;ENSP00000386780:T249I	ENSP00000264605:T289I	T	+	2	0	MLPH	238099173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.252000	0.01185	-1.022000	0.03346	-0.471000	0.05019	ACT	C|0.832;T|0.168	0.168	strong		0.657	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
MMRN2	79812	hgsc.bcm.edu	37	10	88717154	88717154	+	Missense_Mutation	SNP	C	C	T	rs3750823	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:88717154C>T	ENST00000372027.5	-	1	466	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	SNCG_ENST00000348795.4_5'Flank|SNCG_ENST00000372017.3_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	49			G -> S (in dbSNP:rs3750823). {ECO:0000269|PubMed:11559704}.		angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.G49S(1)		breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						GGGTCCTTGCCGGTGTCCTCA	0.622													C|||	2121	0.423522	0.1899	0.4179	5008	,	,		17586	0.7113		0.4742	False		,,,				2504	0.3947				p.G49S		Atlas-SNP	.											MMRN2,NS,carcinoma,0,1	MMRN2	49	1	1	Substitution - Missense(1)	stomach(1)	c.G145A						PASS	.	C	SER/GLY	998,3408	372.0+/-320.2	122,754,1327	111.0	108.0	109.0		145	-5.3	0.0	10	dbSNP_107	109	4016,4584	555.5+/-386.7	923,2170,1207	yes	missense	MMRN2	NM_024756.2	56	1045,2924,2534	TT,TC,CC		46.6977,22.6509,38.5514	benign	49/950	88717154	5014,7992	2203	4300	6503	SO:0001583	missense	79812	exon1			CCTTGCCGGTGTC	AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.145G>A	10.37:g.88717154C>T	ENSP00000361097:p.Gly49Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_024756	Q504V7|Q6P2N2	Missense_Mutation	SNP	ENST00000372027.5	37	CCDS7379.1	994	0.4551282051282051	94	0.1910569105691057	134	0.3701657458563536	408	0.7132867132867133	358	0.47229551451187335	C	3.925	-0.017394	0.07681	0.226509	0.466977	ENSG00000173269	ENST00000372027;ENST00000443699	T	0.13196	2.61	3.93	-5.26	0.02772	.	1.607910	0.03256	N	0.182630	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.35525	-0.9785	9	0.07482	T	0.82	-3.0939	6.0887	0.19983	0.0:0.4018:0.1377:0.4604	rs3750823;rs3750823	49	Q9H8L6	MMRN2_HUMAN	S	49	ENSP00000361097:G49S	ENSP00000361097:G49S	G	-	1	0	MMRN2	88707134	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-1.357000	0.02607	-0.985000	0.03503	-0.379000	0.06801	GGC	C|0.595;T|0.405	0.405	strong		0.622	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
PLEC	5339	hgsc.bcm.edu	37	8	144995494	144995494	+	Missense_Mutation	SNP	C	C	T	rs6558407	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144995494C>T	ENST00000322810.4	-	32	9075	c.8906G>A	c.(8905-8907)cGc>cAc	p.R2969H	PLEC_ENST00000354589.3_Missense_Mutation_p.R2832H|PLEC_ENST00000357649.2_Missense_Mutation_p.R2836H|PLEC_ENST00000436759.2_Missense_Mutation_p.R2859H|PLEC_ENST00000354958.2_Missense_Mutation_p.R2810H|PLEC_ENST00000527096.1_Missense_Mutation_p.R2855H|PLEC_ENST00000345136.3_Missense_Mutation_p.R2832H|PLEC_ENST00000356346.3_Missense_Mutation_p.R2818H|PLEC_ENST00000398774.2_Missense_Mutation_p.R2800H	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2969	Globular 2.		R -> H (in dbSNP:rs6558407).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GAAGTAGCCGCGCCGGTAGGC	0.682													C|||	1155	0.230631	0.028	0.2939	5008	,	,		19137	0.1419		0.4294	False		,,,				2504	0.3466				p.R2969H		Atlas-SNP	.											.	PLEC	1144	.	0			c.G8906A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	368,3618		24,320,1649	60.0	66.0	64.0		8576,8453,8429,8906,8399,8495,8507,8495	2.1	1.0	8	dbSNP_116	64	3412,4876		720,1972,1452	no	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	29,29,29,29,29,29,29,29	744,2292,3101	TT,TC,CC		41.168,9.2323,30.7968	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	2859/4575,2818/4534,2810/4526,2969/4685,2800/4516,2832/4548,2836/4552,2832/4548	144995494	3780,8494	1993	4144	6137	SO:0001583	missense	5339	exon32			TAGCCGCGCCGGT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8906G>A	8.37:g.144995494C>T	ENSP00000323856:p.Arg2969His	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	24	0.685714	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	538	0.24633699633699635	15	0.03048780487804878	108	0.2983425414364641	94	0.16433566433566432	321	0.4234828496042216	C	9.838	1.190145	0.21954	0.092323	0.41168	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25;-1.25	4.95	2.11	0.27256	.	0.205118	0.33591	U	0.004744	T	0.00012	0.0000	M	0.92412	3.305	0.30565	P	0.76412	B;B;B;B;B;B;B;B	0.25007	0.095;0.095;0.095;0.116;0.095;0.095;0.095;0.095	B;B;B;B;B;B;B;B	0.14023	0.006;0.006;0.006;0.01;0.006;0.006;0.006;0.006	T	0.09015	-1.0694	9	0.54805	T	0.06	.	7.3802	0.26851	0.1365:0.7151:0.0:0.1483	rs6558407;rs6558407	2859;2818;2810;2969;2800;2832;2836;2832	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	H	2832;2836;2832;2800;2969;2810;2818;2859;2855	ENSP00000344848:R2832H;ENSP00000350277:R2836H;ENSP00000346602:R2832H;ENSP00000381756:R2800H;ENSP00000323856:R2969H;ENSP00000347044:R2810H;ENSP00000348702:R2818H;ENSP00000388180:R2859H;ENSP00000434583:R2855H	ENSP00000323856:R2969H	R	-	2	0	PLEC	145067482	0.993000	0.37304	0.985000	0.45067	0.496000	0.33645	2.910000	0.48766	0.222000	0.20900	-0.538000	0.04264	CGC	.	.	weak		0.682	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
TACC2	10579	hgsc.bcm.edu	37	10	123845211	123845211	+	Missense_Mutation	SNP	G	G	A	rs11200387	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123845211G>A	ENST00000369005.1	+	4	3536	c.3196G>A	c.(3196-3198)Gcc>Acc	p.A1066T	TACC2_ENST00000334433.3_Missense_Mutation_p.A1066T|TACC2_ENST00000515603.1_Missense_Mutation_p.A1066T|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.A1066T|TACC2_ENST00000515273.1_Missense_Mutation_p.A1066T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1066					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CCTGGCGCCCGCCAGCCCCGG	0.647													G|||	694	0.138578	0.1929	0.1499	5008	,	,		15541	0.0913		0.17	False		,,,				2504	0.0736				p.A1066T		Atlas-SNP	.											.	TACC2	271	.	0			c.G3196A						PASS	.	G	,THR/ALA	992,3414	350.3+/-310.7	115,762,1326	37.0	43.0	41.0		,3196	2.5	0.0	10	dbSNP_120	41	1441,7157	262.0+/-284.2	117,1207,2975	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	232,1969,4301	AA,AG,GG		16.7597,22.5148,18.7096	,benign	,1066/2949	123845211	2433,10571	2203	4299	6502	SO:0001583	missense	10579	exon4			GCGCCCGCCAGCC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.3196G>A	10.37:g.123845211G>A	ENSP00000358001:p.Ala1066Thr	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	349	0.15979853479853479	92	0.18699186991869918	63	0.17403314917127072	66	0.11538461538461539	128	0.16886543535620052	G	11.06	1.528723	0.27387	0.225148	0.167597	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03242	4.06;4.01;4.0;4.06;4.01	5.37	2.46	0.29980	.	0.496053	0.15164	N	0.276983	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	P;P;P	0.35872	0.525;0.525;0.525	B;B;B	0.28638	0.092;0.092;0.092	T	0.46359	-0.9197	9	0.12430	T	0.62	-0.0562	5.8983	0.18951	0.1754:0.1576:0.667:0.0	rs11200387;rs58225650	1066;1066;1066	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1066;1066;1066;1066;1066;1056	ENSP00000358001:A1066T;ENSP00000424467:A1066T;ENSP00000427618:A1066T;ENSP00000334280:A1066T;ENSP00000395048:A1066T	ENSP00000334280:A1066T	A	+	1	0	TACC2	123835201	0.001000	0.12720	0.005000	0.12908	0.048000	0.14542	0.705000	0.25675	0.240000	0.21263	0.478000	0.44815	GCC	G|0.826;A|0.174	0.174	strong		0.647	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
AKAP6	9472	hgsc.bcm.edu	37	14	33014869	33014869	+	Missense_Mutation	SNP	C	C	T	rs3742926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:33014869C>T	ENST00000280979.4	+	4	1180	c.1010C>T	c.(1009-1011)gCt>gTt	p.A337V	AKAP6_ENST00000557354.1_Missense_Mutation_p.A337V|AKAP6_ENST00000557272.1_Missense_Mutation_p.A337V	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	337			A -> V (in dbSNP:rs3742926).		action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		ACAAATGCTGCTCAACCCTCC	0.493													T|||	881	0.175919	0.233	0.1859	5008	,	,		20444	0.1815		0.1004	False		,,,				2504	0.1636				p.A337V	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.C1010T						PASS	.	T	VAL/ALA	887,3519	741.1+/-411.2	78,731,1394	73.0	64.0	67.0		1010	-5.0	0.0	14	dbSNP_107	67	804,7796	781.9+/-407.6	37,730,3533	yes	missense	AKAP6	NM_004274.4	64	115,1461,4927	TT,TC,CC		9.3488,20.1316,13.0017	benign	337/2320	33014869	1691,11315	2203	4300	6503	SO:0001583	missense	9472	exon4			ATGCTGCTCAACC	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.1010C>T	14.37:g.33014869C>T	ENSP00000280979:p.Ala337Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_004274	A7E242|A7E2D4|O15028	Missense_Mutation	SNP	ENST00000280979.4	37	CCDS9644.1	367	0.16804029304029305	121	0.2459349593495935	62	0.1712707182320442	97	0.16958041958041958	87	0.11477572559366754	T	0.013	-1.629818	0.00813	0.201316	0.093488	ENSG00000151320	ENST00000280979;ENST00000557354;ENST00000557272;ENST00000553547	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.61	-4.96	0.03038	.	1.589520	0.03277	N	0.185626	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29458	-1.0011	9	0.16420	T	0.52	1.892	0.6198	0.00776	0.2906:0.2271:0.3018:0.1805	rs3742926;rs52801792;rs61666772;rs3742926	337;337	A7E242;Q13023	.;AKAP6_HUMAN	V	337;337;337;95	ENSP00000280979:A337V;ENSP00000450531:A337V;ENSP00000451247:A337V;ENSP00000451239:A95V	ENSP00000280979:A337V	A	+	2	0	AKAP6	32084620	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.734000	0.04893	-0.707000	0.05022	-0.254000	0.11334	GCT	C|0.859;T|0.141	0.141	strong		0.493	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
ALMS1	7840	hgsc.bcm.edu	37	2	73829372	73829372	+	Silent	SNP	C	C	T	rs1052162	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73829372C>T	ENST00000264448.6	+	20	12283	c.12172C>T	c.(12172-12174)Ctg>Ttg	p.L4058L	ALMS1_ENST00000409009.1_Silent_p.L4016L|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4058	ALMS motif.				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						GATAAAGCGCCTGAAGTTAAT	0.493													C|||	1711	0.341653	0.8011	0.3804	5008	,	,		20743	0.0089		0.2276	False		,,,				2504	0.1534				p.L4058L		Atlas-SNP	.											.	ALMS1	384	.	0			c.C12172T						PASS	.	C		3092,1314	677.6+/-403.4	1083,926,194	53.0	58.0	56.0		12172	3.6	1.0	2	dbSNP_86	56	2027,6573	351.2+/-328.2	228,1571,2501	no	coding-synonymous	ALMS1	NM_015120.4		1311,2497,2695	TT,TC,CC		23.5698,29.823,39.3588		4058/4168	73829372	5119,7887	2203	4300	6503	SO:0001819	synonymous_variant	7840	exon20			AAGCGCCTGAAGT	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.12172C>T	2.37:g.73829372C>T		Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	132	89	0.674242	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			C|0.663;T|0.337	0.337	strong		0.493	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
CCDC137	339230	hgsc.bcm.edu	37	17	79638805	79638805	+	Missense_Mutation	SNP	C	C	T	rs11150805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79638805C>T	ENST00000329214.8	+	4	932	c.529C>T	c.(529-531)Cgg>Tgg	p.R177W		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	177			R -> W (in dbSNP:rs11150805).				poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			TAAAGTCCGACGGAAAAAGGA	0.572													C|||	535	0.106829	0.1467	0.0951	5008	,	,		18674	0.002		0.1918	False		,,,				2504	0.0818				p.R177W		Atlas-SNP	.											.	CCDC137	27	.	0			c.C529T						PASS	.	C	TRP/ARG	735,3227		70,595,1316	54.0	60.0	58.0		529	4.1	0.0	17	dbSNP_120	58	1368,6950		126,1116,2917	yes	missense	CCDC137	NM_199287.2	101	196,1711,4233	TT,TC,CC		16.4463,18.5512,17.1254	probably-damaging	177/290	79638805	2103,10177	1981	4159	6140	SO:0001583	missense	339230	exon4			GTCCGACGGAAAA	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.529C>T	17.37:g.79638805C>T	ENSP00000329360:p.Arg177Trp	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_199287		Missense_Mutation	SNP	ENST00000329214.8	37	CCDS42400.1	243	0.11126373626373626	72	0.14634146341463414	41	0.1132596685082873	0	0.0	130	0.17150395778364116	C	12.18	1.859126	0.32884	0.185512	0.164463	ENSG00000185298	ENST00000329214	D	0.90385	-2.66	5.12	4.12	0.48240	.	0.496261	0.21184	N	0.078761	T	0.01061	0.0035	L	0.47716	1.5	0.80722	P	0.0	D	0.71674	0.998	P	0.53861	0.736	T	0.20140	-1.0284	9	0.72032	D	0.01	-9.5786	11.4747	0.50291	0.4593:0.5407:0.0:0.0	rs11150805;rs57790847;rs11150805	177	Q6PK04	CC137_HUMAN	W	177	ENSP00000329360:R177W	ENSP00000329360:R177W	R	+	1	2	CCDC137	77249210	0.000000	0.05858	0.010000	0.14722	0.041000	0.13682	0.509000	0.22707	1.082000	0.41137	0.655000	0.94253	CGG	C|0.863;T|0.137	0.137	strong		0.572	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
KDELC1	79070	hgsc.bcm.edu	37	13	103450973	103450973	+	Silent	SNP	T	T	C	rs7994595	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103450973T>C	ENST00000376004.4	-	1	384	c.48A>G	c.(46-48)ccA>ccG	p.P16P	KDELC1_ENST00000460338.1_5'UTR|BIVM_ENST00000448849.2_5'Flank|BIVM_ENST00000257336.1_5'Flank|BIVM_ENST00000419638.1_5'Flank	NM_024089.2	NP_076994.2	Q6UW63	KDEL1_HUMAN	KDEL (Lys-Asp-Glu-Leu) containing 1	16						endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CGGCGAGTGCTGGAACTGTCG	0.522													T|||	428	0.0854633	0.1513	0.0231	5008	,	,		16117	0.1121		0.0507	False		,,,				2504	0.0491				p.P16P		Atlas-SNP	.											.	KDELC1	66	.	0			c.A48G						PASS	.	T		587,3819	257.4+/-261.8	41,505,1657	58.0	58.0	58.0		48	-0.4	0.3	13	dbSNP_116	58	337,8263	116.3+/-176.0	9,319,3972	no	coding-synonymous	KDELC1	NM_024089.2		50,824,5629	CC,CT,TT		3.9186,13.3227,7.1044		16/503	103450973	924,12082	2203	4300	6503	SO:0001819	synonymous_variant	79070	exon1			GAGTGCTGGAACT	BC001297	CCDS9504.1	13q33	2010-11-18			ENSG00000134901	ENSG00000134901			19350	protein-coding gene	gene with protein product		611613					Standard	NM_024089		Approved	MGC5302, EP58	uc001vpq.4	Q6UW63	OTTHUMG00000017307	ENST00000376004.4:c.48A>G	13.37:g.103450973T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_024089	Q53HL3|Q9BVD2	Silent	SNP	ENST00000376004.4	37	CCDS9504.1																																																																																			T|0.916;C|0.084	0.084	strong		0.522	KDELC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045699.1		
LILRB5	10990	hgsc.bcm.edu	37	19	54755922	54755922	+	Missense_Mutation	SNP	C	C	T	rs34889610|rs12977062	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54755922C>T	ENST00000316219.5	-	12	1728	c.1621G>A	c.(1621-1623)Gct>Act	p.A541T	LILRB5_ENST00000449561.2_Missense_Mutation_p.A542T|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_Missense_Mutation_p.A533T|LILRB5_ENST00000345866.6_Missense_Mutation_p.A442T	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	541					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTCACCCGAGCATCCATCTCC	0.627													.|||	896	0.178914	0.1112	0.1484	5008	,	,		14643	0.0992		0.2525	False		,,,				2504	0.2986				p.A542T		Atlas-SNP	.											.	LILRB5	176	.	0			c.G1624A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	478,3928		27,424,1752	111.0	110.0	110.0		1624,1324,1621	-2.3	0.0	19	dbSNP_121	110	1746,6854		240,1266,2794	no	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	58,58,58	267,1690,4546	TT,TC,CC		20.3023,10.8488,17.0998	benign,benign,benign	542/592,442/492,541/591	54755922	2224,10782	2203	4300	6503	SO:0001583	missense	10990	exon12			CCCGAGCATCCAT	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1621G>A	19.37:g.54755922C>T	ENSP00000320390:p.Ala541Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	123	45	0.365854	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	275	0.1259157509157509	59	0.11991869918699187	60	0.16574585635359115	23	0.04020979020979021	133	0.17546174142480211	C	0.189	-1.054678	0.01965	0.108488	0.203023	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00466	7.33;7.23;7.33;7.33	1.7	-2.32	0.06745	.	.	.	.	.	T	0.00012	0.0000	N	0.00413	-1.525	0.80722	P	0.0	B;B;B;B	0.15473	0.001;0.013;0.0;0.0	B;B;B;B	0.15052	0.001;0.012;0.002;0.001	T	0.23332	-1.0191	8	0.02654	T	1	.	3.7856	0.08698	0.0:0.3933:0.2823:0.3244	rs12977062;rs12977062	533;442;542;541	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	T	541;533;542;442	ENSP00000320390:A541T;ENSP00000414225:A533T;ENSP00000406478:A542T;ENSP00000263430:A442T	ENSP00000320390:A541T	A	-	1	0	LILRB5	59447734	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	-0.640000	0.05440	-0.658000	0.05366	-0.606000	0.04082	GCT	TG|1.000;|0.000	.	alt		0.627	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
POLR2B	5431	hgsc.bcm.edu	37	4	57876955	57876955	+	Silent	SNP	G	G	A	rs1718878	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57876955G>A	ENST00000381227.1	+	13	2003	c.1590G>A	c.(1588-1590)gcG>gcA	p.A530A	POLR2B_ENST00000441246.2_Silent_p.A523A|POLR2B_ENST00000510355.1_3'UTR|POLR2B_ENST00000431623.2_Silent_p.A455A|POLR2B_ENST00000314595.5_Silent_p.A530A			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	530					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					CCTTGATGGCGTATATTTCAG	0.353													A|||	1937	0.386781	0.4365	0.2954	5008	,	,		16271	0.2986		0.3469	False		,,,				2504	0.5164				p.A530A		Atlas-SNP	.											.	POLR2B	108	.	0			c.G1590A						PASS	.	A		1880,2526	624.5+/-394.3	400,1080,723	117.0	124.0	121.0		1590	2.0	1.0	4	dbSNP_89	121	2935,5661	666.9+/-402.4	487,1961,1850	no	coding-synonymous	POLR2B	NM_000938.1		887,3041,2573	AA,AG,GG		34.1438,42.6691,37.0328		530/1175	57876955	4815,8187	2203	4298	6501	SO:0001819	synonymous_variant	5431	exon12			GATGGCGTATATT		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.1590G>A	4.37:g.57876955G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	207	98	0.47343	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			G|0.635;A|0.365	0.365	strong		0.353	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
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 GAIIx	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_ENST00000452935.2_Missense_Mutation_p.N254S|ATL2_ENST00000546051.1_Missense_Mutation_p.N101S|ATL2_ENST00000332337.4_Missense_Mutation_p.N254S|ATL2_ENST00000402054.1_Missense_Mutation_p.N101S|ATL2_ENST00000406122.1_Missense_Mutation_p.N101S|ATL2_ENST00000539122.1_Missense_Mutation_p.N101S|ATL2_ENST00000419554.2_Missense_Mutation_p.N272S	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	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	97	58	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	
ZNF587	84914	hgsc.bcm.edu	37	19	58371259	58371259	+	Silent	SNP	A	A	G	rs75951435	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58371259A>G	ENST00000339656.5	+	3	1661	c.1479A>G	c.(1477-1479)gaA>gaG	p.E493E	ZNF814_ENST00000597652.1_5'Flank|ZNF587_ENST00000419854.1_Silent_p.E450E|ZNF814_ENST00000595295.1_Intron|ZNF587_ENST00000423137.1_Silent_p.E492E|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	493					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E493E(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		GGCCGTATGAATGCAGTGAAT	0.423																																					p.E493E	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											ZNF587,NS,carcinoma,0,1	ZNF587	53	1	1	Substitution - coding silent(1)	stomach(1)	c.A1479G						PASS	.						145.0	149.0	148.0					19																	58371259		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			GTATGAATGCAGT	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1479A>G	19.37:g.58371259A>G		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	224	20	0.0892857	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			A|0.963;G|0.037	0.037	strong		0.423	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
KIAA1731	85459	hgsc.bcm.edu	37	11	93460160	93460160	+	Missense_Mutation	SNP	A	A	C	rs67879380	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:93460160A>C	ENST00000325212.6	+	24	6680	c.6518A>C	c.(6517-6519)gAa>gCa	p.E2173A	KIAA1731_ENST00000411936.1_Missense_Mutation_p.E2173A|KIAA1731_ENST00000531700.1_Missense_Mutation_p.E353A|KIAA1731_ENST00000344196.4_Missense_Mutation_p.E353A			Q9C0D2	K1731_HUMAN	KIAA1731	2173						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CAATGTTTTGAACAGCTTCAG	0.363													A|||	756	0.150958	0.1566	0.0778	5008	,	,		18658	0.2718		0.0974	False		,,,				2504	0.1258				p.E2173A		Atlas-SNP	.											.	KIAA1731	173	.	0			c.A6518C						PASS	.	A	ALA/GLU	217,1167		16,185,491	89.0	74.0	78.0		6518	0.5	0.9	11	dbSNP_130	78	274,2908		10,254,1327	yes	missense	KIAA1731	NM_033395.1	107	26,439,1818	CC,CA,AA		8.6109,15.6792,10.7534	possibly-damaging	2173/2602	93460160	491,4075	692	1591	2283	SO:0001583	missense	85459	exon24			GTTTTGAACAGCT	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.6518A>C	11.37:g.93460160A>C	ENSP00000316681:p.Glu2173Ala	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	210	172	0.819048	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	37	CCDS44708.1	336	0.15384615384615385	75	0.1524390243902439	29	0.08011049723756906	153	0.2674825174825175	79	0.10422163588390501	A	17.36	3.369075	0.61624	0.156792	0.086109	ENSG00000166004	ENST00000325212;ENST00000411936;ENST00000344196;ENST00000531700;ENST00000531404;ENST00000529185	T;T	0.09911	2.93;2.93	5.61	0.522	0.17053	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.48087	P	4.1199999999996795E-4	B;B;B	0.25667	0.056;0.131;0.131	B;B;B	0.21151	0.015;0.033;0.033	T	0.44862	-0.9300	8	0.66056	D	0.02	.	5.2387	0.15460	0.6285:0.1395:0.2319:0.0	.	2173;2173;353	Q9C0D2;Q9C0D2-3;Q9C0D2-2	K1731_HUMAN;.;.	A	2173;2173;353;353;185;39	ENSP00000316681:E2173A;ENSP00000406505:E2173A	ENSP00000316681:E2173A	E	+	2	0	KIAA1731	93099808	0.267000	0.24122	0.924000	0.36721	0.903000	0.53119	1.359000	0.34113	0.080000	0.16959	0.477000	0.44152	GAA	A|0.852;C|0.148	0.148	strong		0.363	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
LOXL2	4017	hgsc.bcm.edu	37	8	23225559	23225559	+	Silent	SNP	G	G	A	rs1063577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:23225559G>A	ENST00000389131.3	-	2	675	c.306C>T	c.(304-306)taC>taT	p.Y102Y	RP11-177H13.2_ENST00000519692.1_RNA	NM_002318.2	NP_002309.1	Q9Y4K0	LOXL2_HUMAN	lysyl oxidase-like 2	102	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.				aging (GO:0007568)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial to mesenchymal transition (GO:0001837)|histone modification (GO:0016570)|negative regulation of transcription, DNA-templated (GO:0045892)|oxidation-reduction process (GO:0055114)|positive regulation of chondrocyte differentiation (GO:0032332)|protein deamination (GO:0018277)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)|sprouting angiogenesis (GO:0002040)|transcription, DNA-templated (GO:0006351)	basement membrane (GO:0005604)|chromosome (GO:0005694)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|methylated histone binding (GO:0035064)|oligosaccharide binding (GO:0070492)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)|transcription corepressor activity (GO:0003714)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(5)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(55;0.0453)|Breast(100;0.143)		Colorectal(74;0.0288)|COAD - Colon adenocarcinoma(73;0.096)		TGGCCTCCACGTAGCCCAGCT	0.627													G|||	509	0.101637	0.0076	0.2349	5008	,	,		20116	0.0585		0.2048	False		,,,				2504	0.0726				p.Y102Y		Atlas-SNP	.											.	LOXL2	97	.	0			c.C306T						PASS	.	G		200,4206	121.3+/-158.8	8,184,2011	81.0	62.0	68.0		306	-3.7	0.9	8	dbSNP_86	68	1585,7015	289.0+/-299.1	141,1303,2856	no	coding-synonymous	LOXL2	NM_002318.2		149,1487,4867	AA,AG,GG		18.4302,4.5393,13.7244		102/775	23225559	1785,11221	2203	4300	6503	SO:0001819	synonymous_variant	4017	exon2			CTCCACGTAGCCC	U89942	CCDS34864.1	8p21.3	2008-05-15				ENSG00000134013			6666	protein-coding gene	gene with protein product		606663				9722957	Standard	NM_002318		Approved	WS9-14	uc003xdh.1	Q9Y4K0		ENST00000389131.3:c.306C>T	8.37:g.23225559G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_002318	B2R5Q0|Q53HV3|Q9BW70|Q9Y5Y8	Silent	SNP	ENST00000389131.3	37	CCDS34864.1																																																																																			G|0.861;A|0.139	0.139	strong		0.627	LOXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375603.1		
PSMB9	5698	hgsc.bcm.edu	37	6	32825090	32825090	+	Missense_Mutation	SNP	G	G	A	rs17587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32825090G>A	ENST00000374859.2	+	3	248	c.179G>A	c.(178-180)cGc>cAc	p.R60H	PSMB9_ENST00000453265.2_Intron|PSMB9_ENST00000395330.1_Missense_Mutation_p.R37H	NM_002800.4	NP_002791.1	P28065	PSB9_HUMAN	proteasome (prosome, macropain) subunit, beta type, 9	60			R -> H (in dbSNP:rs17587). {ECO:0000269|PubMed:10924276, ECO:0000269|PubMed:1922385}.		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)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|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)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			large_intestine(4)|lung(4)|skin(1)	9					Carfilzomib(DB08889)	CTGCACGAGCGCATCTACTGT	0.557													G|||	1124	0.224441	0.2322	0.2233	5008	,	,		17369	0.2123		0.2565	False		,,,				2504	0.1943				p.R60H		Atlas-SNP	.											.	PSMB9	16	.	0			c.G179A						PASS	.	G	HIS/ARG	649,2373		81,487,943	109.0	96.0	101.0		179	-3.8	0.4	6	dbSNP_63	101	1444,3972		218,1008,1482	yes	missense	PSMB9	NM_002800.4	29	299,1495,2425	AA,AG,GG		26.6617,21.4758,24.8045	benign	60/220	32825090	2093,6345	1511	2708	4219	SO:0001583	missense	5698	exon3			ACGAGCGCATCTA		CCDS4759.1	6p21.3	2013-03-27	2013-03-27		ENSG00000240065	ENSG00000240065		"""Proteasome (prosome, macropain) subunits"""	9546	protein-coding gene	gene with protein product		177045	"""proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2)"", ""large multifunctional peptidase 2"""	LMP2		1922385, 1529427	Standard	NM_002800		Approved	RING12, beta1i, PSMB6i	uc003sga.3	P28065	OTTHUMG00000031287	ENST00000374859.2:c.179G>A	6.37:g.32825090G>A	ENSP00000363993:p.Arg60His	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	41	37	0.902439	NM_002800	B0V0T1|Q16523|Q5JNW4	Missense_Mutation	SNP	ENST00000374859.2	37	CCDS4759.1	486	0.22252747252747251	95	0.19308943089430894	83	0.2292817679558011	114	0.1993006993006993	194	0.2559366754617414	G	13.16	2.154819	0.38021	0.214758	0.266617	ENSG00000240065	ENST00000395330;ENST00000414474;ENST00000374859	T;T;T	0.19938	2.11;2.11;2.11	5.68	-3.82	0.04281	Proteasome, beta-type subunit, conserved site (1);	0.654017	0.15104	N	0.280372	T	0.05731	0.0150	L	0.37507	1.11	0.32374	P	0.5554250000000001	B	0.06786	0.001	B	0.06405	0.002	T	0.35992	-0.9766	9	0.34782	T	0.22	-7.1336	12.9288	0.58275	0.5927:0.0:0.4073:0.0	rs17587;rs1044244;rs2070254;rs3173317;rs9276814;rs17398467;rs17501771;rs52789962;rs60495382;rs17587	60	P28065	PSB9_HUMAN	H	37;37;60	ENSP00000378739:R37H;ENSP00000394363:R37H;ENSP00000363993:R60H	ENSP00000363993:R60H	R	+	2	0	PSMB9	32933068	0.003000	0.15002	0.413000	0.26509	0.677000	0.39632	0.081000	0.14823	-0.559000	0.06110	-0.154000	0.13518	CGC	G|0.760;A|0.240	0.240	strong		0.557	PSMB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076624.5	NM_002800	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150319	11150319	+	Silent	SNP	T	T	C	rs11054143	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11150319T>C	ENST00000538986.1	-	1	155	c.156A>G	c.(154-156)gcA>gcG	p.A52A	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	52					sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						CTCTGGAGACTGCCAGAGCAG	0.343													C|||	2118	0.422923	0.0651	0.3847	5008	,	,		18136	0.755		0.3817	False		,,,				2504	0.6339				p.A52A		Atlas-SNP	.											.	TAS2R20	17	.	0			c.A156G						PASS	.	C		433,3971	729.6+/-410.1	18,397,1787	40.0	46.0	44.0		156	-5.5	0.0	12	dbSNP_120	44	3001,5597	650.8+/-400.8	539,1923,1837	no	coding-synonymous	TAS2R20	NM_176889.2		557,2320,3624	CC,CT,TT		34.9035,9.832,26.4113		52/310	11150319	3434,9568	2202	4299	6501	SO:0001819	synonymous_variant	259295	exon1			GGAGACTGCCAGA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.156A>G	12.37:g.11150319T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	192	80	0.416667	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Silent	SNP	ENST00000538986.1	37	CCDS8639.1																																																																																			T|0.678;C|0.322	0.322	strong		0.343	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047418	46047418	+	Silent	SNP	C	C	T	rs8126553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46047418C>T	ENST00000397911.3	+	1	379	c.330C>T	c.(328-330)tgC>tgT	p.C110C	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	110	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						ctgtgtgctgcgtgcccgtct	0.667													T|||	3942	0.787141	0.9123	0.745	5008	,	,		20271	0.6746		0.7714	False		,,,				2504	0.7802				p.C110C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.C330T						PASS	.	T	,	3913,489	215.8+/-234.7	1747,419,35	100.0	113.0	108.0		,330	-7.1	0.0	21	dbSNP_116	108	6219,2379	388.3+/-342.5	2266,1687,346	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	4013,2106,381	TT,TC,CC		27.6692,11.1086,22.0615	,	,110/293	46047418	10132,2868	2201	4299	6500	SO:0001819	synonymous_variant	386676	exon1			GTGCTGCGTGCCC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.330C>T	21.37:g.46047418C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	134	53	0.395522	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			C|0.234;T|0.766	0.766	strong		0.667	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
TNXB	7148	hgsc.bcm.edu	37	6	32035694	32035694	+	Silent	SNP	C	C	T	rs1150756	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32035694C>T	ENST00000375244.3	-	18	6489	c.6288G>A	c.(6286-6288)ccG>ccA	p.P2096P	TNXB_ENST00000375247.2_Silent_p.P2096P			P22105	TENX_HUMAN	tenascin XB	2168	Fibronectin type-III 13. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCCCCAGGAGCGGCTCCTCAG	0.647													C|||	96	0.0191693	0.0023	0.0231	5008	,	,		13995	0.001		0.0755	False		,,,				2504	0.0				p.P2096P		Atlas-SNP	.											.	TNXB	553	.	0			c.G6288A						PASS	.	C		67,3425		1,65,1680	35.0	39.0	38.0		6288	-9.4	0.7	6	dbSNP_87	38	757,6943		32,693,3125	no	coding-synonymous	TNXB	NM_019105.6		33,758,4805	TT,TC,CC		9.8312,1.9187,7.3624		2096/4243	32035694	824,10368	1746	3850	5596	SO:0001819	synonymous_variant	7148	exon18			CAGGAGCGGCTCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.6288G>A	6.37:g.32035694C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	103	78	0.757282	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				C|0.959;T|0.041	0.041	strong		0.647	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
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 GAIIx	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|KLHDC4_ENST00000353170.5_Missense_Mutation_p.L98V|RP11-278A23.2_ENST00000563036.1_RNA	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	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	70	28	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	
INTS1	26173	hgsc.bcm.edu	37	7	1542697	1542697	+	Silent	SNP	G	G	A	rs3752714	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:1542697G>A	ENST00000404767.3	-	3	274	c.189C>T	c.(187-189)gcC>gcT	p.A63A	INTS1_ENST00000493531.1_5'Flank|INTS1_ENST00000389470.4_Silent_p.A191A	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	63	Poly-Ala.				inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TGGACAACGCGGCCGCCGCAT	0.667													A|||	2933	0.585663	0.7746	0.4179	5008	,	,		15450	0.7123		0.4642	False		,,,				2504	0.4438				p.A63A		Atlas-SNP	.											INTS1,NS,carcinoma,0,1	INTS1	145	1	0			c.C189T						PASS	.			2854,1190		1030,794,198	55.0	69.0	65.0		189	-3.4	0.0	7	dbSNP_107	65	3508,4828		740,2028,1400	no	coding-synonymous	INTS1	NM_001080453.2		1770,2822,1598	AA,AG,GG		42.0825,29.4263,48.6107		63/2191	1542697	6362,6018	2022	4168	6190	SO:0001819	synonymous_variant	26173	exon3			CAACGCGGCCGCC	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.189C>T	7.37:g.1542697G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	137	73	0.532847	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			G|0.412;A|0.588	0.588	strong		0.667	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
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 GAIIx	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	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	138	56	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	
RRP7A	27341	hgsc.bcm.edu	37	22	42912097	42912097	+	Missense_Mutation	SNP	C	C	T	rs11553441	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:42912097C>T	ENST00000323013.6	-	3	277	c.262G>A	c.(262-264)Gta>Ata	p.V88I		NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	88	RRM.		V -> I (in dbSNP:rs11553441).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						TGCAACTCTACAGACTGGACG	0.627													C|||	381	0.0760783	0.0567	0.1772	5008	,	,		19105	0.003		0.1461	False		,,,				2504	0.0337				p.V88I		Atlas-SNP	.											.	RRP7A	25	.	0			c.G262A						PASS	.	C	ILE/VAL	342,4064	174.1+/-203.8	13,316,1874	53.0	50.0	51.0		262	2.9	0.1	22	dbSNP_120	51	1182,7418	238.1+/-269.7	92,998,3210	yes	missense	RRP7A	NM_015703.4	29	105,1314,5084	TT,TC,CC		13.7442,7.7621,11.7177	benign	88/281	42912097	1524,11482	2203	4300	6503	SO:0001583	missense	27341	exon3			ACTCTACAGACTG	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.262G>A	22.37:g.42912097C>T	ENSP00000321449:p.Val88Ile	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Missense_Mutation	SNP	ENST00000323013.6	37	CCDS14036.1	204	0.09340659340659341	25	0.0508130081300813	71	0.19613259668508287	1	0.0017482517482517483	107	0.14116094986807387	C	9.919	1.211667	0.22289	0.077621	0.137442	ENSG00000189306	ENST00000323013	T	0.18502	2.21	3.93	2.9	0.33743	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.65320	2	0.09310	P	0.9999962723	P	0.51057	0.941	B	0.42030	0.373	T	0.28618	-1.0038	9	0.45353	T	0.12	-21.505	12.1146	0.53858	0.0:0.9124:0.0:0.0876	rs11553441;rs11553441	88	Q9Y3A4	RRP7A_HUMAN	I	88	ENSP00000321449:V88I	ENSP00000321449:V88I	V	-	1	0	RRP7A	41242041	0.994000	0.37717	0.050000	0.19076	0.004000	0.04260	3.845000	0.55880	0.946000	0.37632	-0.346000	0.07831	GTA	C|0.893;T|0.107	0.107	strong		0.627	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
NUP153	9972	hgsc.bcm.edu	37	6	17688798	17688798	+	Silent	SNP	G	G	A	rs1065057	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:17688798G>A	ENST00000262077.2	-	2	162	c.163C>T	c.(163-165)Cta>Tta	p.L55L	NUP153_ENST00000537253.1_Silent_p.L55L	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	55					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of RNA export from nucleus (GO:0046832)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)|viral penetration into host nucleus (GO:0075732)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleocytoplasmic transporter activity (GO:0005487)|protein anchor (GO:0043495)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			NS(2)|breast(6)|endometrium(4)|kidney(3)|large_intestine(7)|lung(23)|ovary(3)|skin(3)|urinary_tract(2)	53	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.125)	all cancers(50;0.0981)|Epithelial(50;0.112)			TATCTTTGTAGCCACCCTGGC	0.383													G|||	1362	0.271965	0.0431	0.3184	5008	,	,		19289	0.2431		0.4006	False		,,,				2504	0.4458				p.L55L		Atlas-SNP	.											.	NUP153	116	.	0			c.C163T						PASS	.	G		408,3998	200.4+/-223.7	21,366,1816	137.0	130.0	132.0		163	3.0	1.0	6	dbSNP_120	132	3044,5556	468.3+/-367.3	542,1960,1798	no	coding-synonymous	NUP153	NM_005124.2		563,2326,3614	AA,AG,GG		35.3953,9.2601,26.5416		55/1476	17688798	3452,9554	2203	4300	6503	SO:0001819	synonymous_variant	9972	exon2			TTTGTAGCCACCC	Z25535	CCDS4541.1, CCDS64359.1, CCDS75407.1	6p22.3	2008-07-29	2002-08-29		ENSG00000124789	ENSG00000124789			8062	protein-coding gene	gene with protein product		603948	"""nucleoporin 153kD"""			8110839	Standard	NM_001278209		Approved	HNUP153	uc003ncd.2	P49790	OTTHUMG00000014312	ENST00000262077.2:c.163C>T	6.37:g.17688798G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	87	17	0.195402	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Silent	SNP	ENST00000262077.2	37	CCDS4541.1																																																																																			G|0.720;C|0.000;N|0.000;A|0.279	0.279	strong		0.383	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		
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 GAIIx	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		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	140	140	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	
TDRD10	126668	hgsc.bcm.edu	37	1	154516477	154516477	+	Missense_Mutation	SNP	G	G	A	rs12750774	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:154516477G>A	ENST00000368480.3	+	9	627	c.542G>A	c.(541-543)cGa>cAa	p.R181Q	TDRD10_ENST00000368482.4_Missense_Mutation_p.R181Q|TDRD10_ENST00000479937.1_3'UTR			Q5VZ19	TDR10_HUMAN	tudor domain containing 10	181			R -> Q (in dbSNP:rs12750774).				nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.R181Q(1)		breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)			GAATGCTTCCGAGACCTGAGC	0.602													G|||	658	0.13139	0.0144	0.2522	5008	,	,		20020	0.0308		0.3082	False		,,,				2504	0.1258				p.R181Q		Atlas-SNP	.											TDRD10,NS,carcinoma,+1,3	TDRD10	48	3	1	Substitution - Missense(1)	stomach(1)	c.G542A						PASS	.	G	GLN/ARG,GLN/ARG	270,4136	152.2+/-185.9	13,244,1946	159.0	140.0	147.0		542,542	-1.6	0.0	1	dbSNP_121	147	2637,5963	426.1+/-355.2	425,1787,2088	yes	missense,missense	TDRD10	NM_001098475.1,NM_182499.3	43,43	438,2031,4034	AA,AG,GG		30.6628,6.128,22.3512	benign,benign	181/367,181/352	154516477	2907,10099	2203	4300	6503	SO:0001583	missense	126668	exon9			GCTTCCGAGACCT	AL713777	CCDS30878.2, CCDS41406.1	1q21.3	2013-02-12			ENSG00000163239	ENSG00000163239		"""Tudor domain containing"", ""RNA binding motif (RRM) containing"""	25316	protein-coding gene	gene with protein product						12975309	Standard	NM_182499		Approved	DKFZp434M202	uc009wow.3	Q5VZ19	OTTHUMG00000037264	ENST00000368480.3:c.542G>A	1.37:g.154516477G>A	ENSP00000357465:p.Arg181Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_182499	A4FU09|B0QZ53|B4DXV4|Q3ZCP1|Q3ZCS7|Q5SXY7|Q6UXV2|Q8TCN3	Missense_Mutation	SNP	ENST00000368480.3	37	CCDS41406.1	352	0.16117216117216118	10	0.02032520325203252	84	0.23204419889502761	23	0.04020979020979021	235	0.3100263852242744	G	3.590	-0.083717	0.07141	0.06128	0.306628	ENSG00000163239	ENST00000368482;ENST00000368480	T;T	0.22539	1.97;1.95	4.07	-1.63	0.08345	.	0.697753	0.11381	N	0.569811	T	0.03434	0.0099	N	0.17082	0.46	0.80722	P	0.0	B;B	0.30686	0.29;0.078	B;B	0.17979	0.015;0.02	T	0.36114	-0.9761	9	0.49607	T	0.09	0.0401	8.5311	0.33335	0.2944:0.0:0.7056:0.0	rs12750774;rs12750774	181;181	Q5VZ19;Q5VZ19-2	TDR10_HUMAN;.	Q	181	ENSP00000357467:R181Q;ENSP00000357465:R181Q	ENSP00000357465:R181Q	R	+	2	0	TDRD10	152783101	0.015000	0.18098	0.002000	0.10522	0.036000	0.12997	-0.475000	0.06599	-0.453000	0.07076	-0.391000	0.06502	CGA	G|0.809;A|0.191	0.191	strong		0.602	TDRD10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090700.2	NM_182499	
NLRP4	147945	hgsc.bcm.edu	37	19	56369313	56369313	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56369313C>T	ENST00000301295.6	+	3	976	c.554C>T	c.(553-555)aCg>aTg	p.T185M	NLRP4_ENST00000587891.1_Missense_Mutation_p.T110M|NLRP4_ENST00000346986.5_Missense_Mutation_p.T185M	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	185	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		TTCCTGTACACGTTCTATTTC	0.498																																					p.T185M		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,-1,1	NLRP4	331	1	0			c.C554T						scavenged	.						110.0	109.0	109.0					19																	56369313		2203	4300	6503	SO:0001583	missense	147945	exon3			TGTACACGTTCTA	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.554C>T	19.37:g.56369313C>T	ENSP00000301295:p.Thr185Met	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	152	2	0.0131579	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	C	13.23	2.174762	0.38413	.	.	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.78481	-1.18;-1.18	4.24	3.22	0.36961	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.65863	0.2732	N	0.14661	0.345	0.09310	N	1	D;D;D	0.59767	0.967;0.986;0.975	P;P;B	0.47981	0.52;0.563;0.397	T	0.56823	-0.7915	9	0.72032	D	0.01	.	7.421	0.27071	0.0:0.1096:0.0:0.8904	.	185;110;185	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	M	185	ENSP00000301295:T185M;ENSP00000344787:T185M	ENSP00000301295:T185M	T	+	2	0	NLRP4	61061125	0.025000	0.19082	0.002000	0.10522	0.001000	0.01503	2.346000	0.44027	0.787000	0.33731	-0.302000	0.09304	ACG	.	.	none		0.498	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573709	140573709	+	Missense_Mutation	SNP	G	G	C	rs17844577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140573709G>C	ENST00000239446.4	+	1	1768	c.1584G>C	c.(1582-1584)gaG>gaC	p.E528D		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E528D(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGCTTTCGAGTTCCGCGTGG	0.697													G|||	320	0.0638978	0.202	0.0447	5008	,	,		19700	0.0		0.0129	False		,,,				2504	0.0092				p.E528D		Atlas-SNP	.											PCDHB10,NS,carcinoma,+2,2	PCDHB10	177	2	1	Substitution - Missense(1)	lung(1)	c.G1584C						PASS	.	G	ASP/GLU	678,3728	251.2+/-258.0	40,598,1565	77.0	95.0	89.0		1584	3.5	1.0	5	dbSNP_123	89	106,8494	52.3+/-112.8	0,106,4194	no	missense	PCDHB10	NM_018930.3	45	40,704,5759	CC,CG,GG		1.2326,15.3881,6.028	benign	528/801	140573709	784,12222	2203	4300	6503	SO:0001583	missense	56126	exon1			TTTCGAGTTCCGC	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1584G>C	5.37:g.140573709G>C	ENSP00000239446:p.Glu528Asp	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	155	38	0.245161	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	107	0.04899267399267399	82	0.16666666666666666	17	0.04696132596685083	0	0.0	8	0.010554089709762533	g	12.76	2.036005	0.35893	0.153881	0.012326	ENSG00000120324	ENST00000239446	T	0.01745	4.66	3.53	3.53	0.40419	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.35723	1.085	0.36543	P	0.12861299999999998	B	0.17268	0.021	B	0.30029	0.11	T	0.40459	-0.9562	8	0.52906	T	0.07	.	4.8909	0.13726	0.2896:0.0:0.7104:0.0	rs17844577	528	Q9UN67	PCDBA_HUMAN	D	528	ENSP00000239446:E528D	ENSP00000239446:E528D	E	+	3	2	PCDHB10	140553893	0.056000	0.20664	1.000000	0.80357	0.978000	0.69477	0.144000	0.16135	1.994000	0.58287	0.549000	0.68633	GAG	G|0.943;C|0.057	0.057	strong		0.697	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
DISP1	84976	hgsc.bcm.edu	37	1	223178478	223178478	+	Missense_Mutation	SNP	G	G	A	rs9441940	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:223178478G>A	ENST00000284476.6	+	8	3903	c.3739G>A	c.(3739-3741)Gct>Act	p.A1247T		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1247				A -> T (in Ref. 3; CAB61406). {ECO:0000305}.	determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		TGAAAGTGACGCTGGCTCTGC	0.473													A|||	349	0.0696885	0.0151	0.0937	5008	,	,		21371	0.0		0.1829	False		,,,				2504	0.0818				p.A1247T		Atlas-SNP	.											.	DISP1	145	.	0			c.G3739A						PASS	.	A	THR/ALA	206,4200	807.8+/-415.9	7,192,2004	125.0	120.0	122.0		3739	-11.0	0.0	1	dbSNP_119	122	1567,7033	745.0+/-407.3	137,1293,2870	yes	missense	DISP1	NM_032890.3	58	144,1485,4874	AA,AG,GG		18.2209,4.6754,13.6322	benign	1247/1525	223178478	1773,11233	2203	4300	6503	SO:0001583	missense	84976	exon10			AGTGACGCTGGCT	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.3739G>A	1.37:g.223178478G>A	ENSP00000284476:p.Ala1247Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	117	41	0.350427	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	182	0.08333333333333333	14	0.028455284552845527	37	0.10220994475138122	0	0.0	131	0.17282321899736147	A	0.143	-1.100258	0.01843	0.046754	0.182209	ENSG00000154309	ENST00000284476	D	0.91631	-2.88	5.48	-11.0	0.00169	.	1.581290	0.03198	N	0.174310	T	0.00412	0.0013	N	0.04880	-0.145	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.12766	T	0.61	4.78	2.8562	0.05573	0.1563:0.3499:0.2777:0.2162	rs9441940	1247	Q96F81	DISP1_HUMAN	T	1247	ENSP00000284476:A1247T	ENSP00000284476:A1247T	A	+	1	0	DISP1	221245101	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-3.127000	0.00592	-7.105000	0.00001	-3.472000	0.00035	GCT	A|0.123;G|0.877;T|0.000	0.123	strong		0.473	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
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 GAIIx	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_ENST00000287701.10_Missense_Mutation_p.K131M|HMBOX1_ENST00000403668.2_Missense_Mutation_p.K131M|HMBOX1_ENST00000444075.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000558662.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000355231.5_Missense_Mutation_p.K131M|HMBOX1_ENST00000519047.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000524238.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000523613.1_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	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	87	4	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	
CILP2	148113	hgsc.bcm.edu	37	19	19654117	19654117	+	Silent	SNP	G	G	C	rs7252453	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:19654117G>C	ENST00000291495.5	+	7	1123	c.1038G>C	c.(1036-1038)ctG>ctC	p.L346L	CILP2_ENST00000586018.1_Silent_p.L352L	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	346	Ig-like C2-type.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						ACCTGGAGCTGCGGGGACTGC	0.652													C|||	1277	0.254992	0.4947	0.2248	5008	,	,		16755	0.0308		0.173	False		,,,				2504	0.2679				p.L346L		Atlas-SNP	.											.	CILP2	84	.	0			c.G1038C						PASS	.	C		1950,2456	604.8+/-390.4	430,1090,683	44.0	49.0	47.0		1038	-9.6	0.0	19	dbSNP_116	47	1516,7084	738.0+/-407.0	125,1266,2909	no	coding-synonymous	CILP2	NM_153221.2		555,2356,3592	CC,CG,GG		17.6279,44.2578,26.6492		346/1157	19654117	3466,9540	2203	4300	6503	SO:0001819	synonymous_variant	148113	exon7			GGAGCTGCGGGGA	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1038G>C	19.37:g.19654117G>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			G|0.754;C|0.246	0.246	strong		0.652	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
MFHAS1	9258	hgsc.bcm.edu	37	8	8749729	8749729	+	Silent	SNP	G	G	C	rs3748141	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:8749729G>C	ENST00000276282.6	-	1	1426	c.840C>G	c.(838-840)ctC>ctG	p.L280L		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	280										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		GGTTGGAGGAGAGGTTGAGCA	0.627													G|||	713	0.142372	0.2663	0.1138	5008	,	,		17476	0.0079		0.1531	False		,,,				2504	0.1227				p.L280L	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.C840G						PASS	.	G		1085,3321	361.9+/-315.9	132,821,1250	30.0	33.0	32.0		840	0.4	1.0	8	dbSNP_107	32	1202,7394	230.5+/-264.8	87,1028,3183	no	coding-synonymous	MFHAS1	NM_004225.2		219,1849,4433	CC,CG,GG		13.9832,24.6255,17.5896		280/1053	8749729	2287,10715	2203	4298	6501	SO:0001819	synonymous_variant	9258	exon1			GGAGGAGAGGTTG	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.840C>G	8.37:g.8749729G>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			G|0.840;C|0.160	0.160	strong		0.627	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
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 GAIIx	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	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	28	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	
TNFRSF8	943	hgsc.bcm.edu	37	1	12198297	12198297	+	Silent	SNP	T	T	C	rs476488	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12198297T>C	ENST00000263932.2	+	14	1569	c.1347T>C	c.(1345-1347)agT>agC	p.S449S	TNFRSF8_ENST00000417814.2_Silent_p.S337S|TNFRSF8_ENST00000479933.2_Intron|TNFRSF8_ENST00000413146.2_5'UTR	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	449					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	AGCTGAGGAGTGGTGCGTCGG	0.612													T|||	1460	0.291534	0.5053	0.1801	5008	,	,		14226	0.3988		0.1292	False		,,,				2504	0.138				p.S449S		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.T1347C						PASS	.	T	,	1939,2449		436,1067,691	31.0	35.0	34.0		1347,	-8.3	0.0	1	dbSNP_83	34	1166,7424		89,988,3218	no	coding-synonymous,utr-5	TNFRSF8	NM_001243.3,NM_152942.2	,	525,2055,3909	CC,CT,TT		13.5739,44.1887,23.9251	,	449/596,	12198297	3105,9873	2194	4295	6489	SO:0001819	synonymous_variant	943	exon14			GAGGAGTGGTGCG	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.1347T>C	1.37:g.12198297T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Silent	SNP	ENST00000263932.2	37	CCDS144.1																																																																																			A|0.005;C|0.259	0.259	strong		0.612	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1		
SLC37A2	219855	hgsc.bcm.edu	37	11	124947149	124947149	+	Silent	SNP	G	G	A	rs12276567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124947149G>A	ENST00000403796.2	+	3	466	c.165G>A	c.(163-165)tcG>tcA	p.S55S	SLC37A2_ENST00000298280.5_Silent_p.S55S|SLC37A2_ENST00000308074.4_Silent_p.S55S|SLC37A2_ENST00000407458.1_Silent_p.S55S	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	55					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.S55S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		AGAACTGCTCGGAGCAGATCA	0.542													G|||	1687	0.336861	0.5242	0.2925	5008	,	,		21821	0.1419		0.2634	False		,,,				2504	0.3916				p.S55S	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											SLC37A2_ENST00000403796,NS,adenoma,0,3	SLC37A2	105	3	1	Substitution - coding silent(1)	prostate(1)	c.G165A						PASS	.	G	,	2062,2340	569.4+/-382.6	486,1090,625	186.0	182.0	183.0		165,165	-8.6	0.0	11	dbSNP_120	183	2197,6401	374.0+/-337.2	264,1669,2366	no	coding-synonymous,coding-synonymous	SLC37A2	NM_001145290.1,NM_198277.2	,	750,2759,2991	AA,AG,GG		25.5525,46.8423,32.7615	,	55/502,55/506	124947149	4259,8741	2201	4299	6500	SO:0001819	synonymous_variant	219855	exon3			CTGCTCGGAGCAG	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.165G>A	11.37:g.124947149G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	144	128	0.888889	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Silent	SNP	ENST00000403796.2	37	CCDS44757.1																																																																																			G|0.679;A|0.321	0.321	strong		0.542	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
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 GAIIx	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	CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'Flank|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	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	98	43	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	
TTN	7273	hgsc.bcm.edu	37	2	179583496	179583496	+	Missense_Mutation	SNP	T	T	G	rs16866465	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179583496T>G	ENST00000591111.1	-	82	23704	c.23480A>C	c.(23479-23481)gAa>gCa	p.E7827A	TTN_ENST00000589042.1_Missense_Mutation_p.E8144A|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E6900A			Q8WZ42	TITIN_HUMAN	titin	13366	Ig-like 60.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCTCCACTTTCTAATGGCTG	0.453													T|||	1196	0.238818	0.1732	0.183	5008	,	,		20020	0.4375		0.1571	False		,,,				2504	0.2464				p.E8144A		Atlas-SNP	.											.	TTN	18412	.	0			c.A24431C						PASS	.	T	,,,ALA/GLU	590,3382		38,514,1434	75.0	76.0	76.0		,,,20699	6.0	0.5	2	dbSNP_123	76	1266,7082		97,1072,3005	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,107	135,1586,4439	GG,GT,TT		15.1653,14.854,15.0649	,,,benign	,,,6900/33424	179583496	1856,10464	1986	4174	6160	SO:0001583	missense	7273	exon84			CCACTTTCTAATG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.23480A>C	2.37:g.179583496T>G	ENSP00000465570:p.Glu7827Ala	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		500	0.22893772893772893	86	0.17479674796747968	54	0.14917127071823205	244	0.42657342657342656	116	0.15303430079155672	T	7.627	0.678028	0.14841	0.14854	0.151653	ENSG00000155657	ENST00000342992	T	0.67865	-0.29	6.01	6.01	0.97437	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B	0.10296	0.003	B	0.15870	0.014	T	0.29366	-1.0014	8	0.87932	D	0	.	16.5285	0.84344	0.0:0.0:0.0:1.0	rs16866465;rs52832346;rs16866465	7827	Q8WZ42	TITIN_HUMAN	A	6900	ENSP00000343764:E6900A	ENSP00000343764:E6900A	E	-	2	0	TTN	179291741	1.000000	0.71417	0.490000	0.27465	0.387000	0.30353	5.942000	0.70203	2.307000	0.77673	0.528000	0.53228	GAA	T|0.778;G|0.222	0.222	strong		0.453	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF804A	91752	hgsc.bcm.edu	37	2	185801756	185801756	+	Missense_Mutation	SNP	G	G	A	rs61739288	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:185801756G>A	ENST00000302277.6	+	4	2227	c.1633G>A	c.(1633-1635)Ggt>Agt	p.G545S		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	545				G -> S (in Ref. 3; AAI50199). {ECO:0000305}.			metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						TGAGAACACAGGTCAGAGGTA	0.328													G|||	156	0.0311502	0.0008	0.0317	5008	,	,		17535	0.0159		0.0666	False		,,,				2504	0.0511				p.G545S		Atlas-SNP	.											.	ZNF804A	322	.	0			c.G1633A						PASS	.						44.0	47.0	46.0					2																	185801756		2163	4286	6449	SO:0001583	missense	91752	exon4			AACACAGGTCAGA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1633G>A	2.37:g.185801756G>A	ENSP00000303252:p.Gly545Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	G	6.433	0.448103	0.12223	.	.	ENSG00000170396	ENST00000302277	T	0.05786	3.39	5.5	3.67	0.42095	.	0.821339	0.10727	N	0.641090	T	0.06508	0.0167	L	0.46157	1.445	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.45687	-0.9244	10	0.16420	T	0.52	0.1666	7.0843	0.25249	0.0874:0.0:0.7437:0.1688	rs61739288	545	Q7Z570	Z804A_HUMAN	S	545	ENSP00000303252:G545S	ENSP00000303252:G545S	G	+	1	0	ZNF804A	185510001	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.568000	0.23623	0.657000	0.30906	0.650000	0.86243	GGT	G|0.932;A|0.068	0.068	strong		0.328	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
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 GAIIx	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_ENST00000429677.3_Silent_p.K216K|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000342836.4_Silent_p.K237K|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		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	210	9	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228505739	228505739	+	Missense_Mutation	SNP	G	G	A	rs3795801	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228505739G>A	ENST00000422127.1	+	53	14040	c.13996G>A	c.(13996-13998)Ggt>Agt	p.G4666S	OBSCN_ENST00000284548.11_Missense_Mutation_p.G4666S|OBSCN_ENST00000366709.4_Missense_Mutation_p.G1785S|OBSCN_ENST00000366707.4_Missense_Mutation_p.G2300S|OBSCN_ENST00000570156.2_Missense_Mutation_p.G5623S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4666	Ig-like 47.		G -> S (in dbSNP:rs3795801).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CATCCAGCCCGGTGGGCGGTT	0.627													g|||	867	0.173123	0.2216	0.2435	5008	,	,		18063	0.1518		0.159	False		,,,				2504	0.0941				p.G5623S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G16867A						PASS	.		SER/GLY,SER/GLY	1019,3243		112,795,1224	87.0	97.0	94.0		13996,13996	-5.4	0.0	1	dbSNP_107	94	1469,6999		133,1203,2898	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	56,56	245,1998,4122	AA,AG,GG		17.3477,23.909,19.5444	benign,benign	4666/7969,4666/6621	228505739	2488,10242	2131	4234	6365	SO:0001583	missense	84033	exon64			CAGCCCGGTGGGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13996G>A	1.37:g.228505739G>A	ENSP00000409493:p.Gly4666Ser	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	183	64	0.349727	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	393	0.17994505494505494	94	0.1910569105691057	89	0.24585635359116023	87	0.1520979020979021	123	0.16226912928759896	g	13.43	2.235989	0.39498	0.23909	0.173477	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	4.51	-5.37	0.02681	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.102050	0.06837	N	0.794996	T	0.00012	0.0000	N	0.17800	0.525	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.002	T	0.41484	-0.9506	9	0.07175	T	0.84	.	20.2526	0.98410	0.1567:0.0:0.8433:0.0	rs3795801;rs52803091;rs58512327;rs3795801	4666;4666	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	4666;4666;2300;1785	ENSP00000284548:G4666S;ENSP00000409493:G4666S;ENSP00000355668:G2300S;ENSP00000355670:G1785S	ENSP00000284548:G4666S	G	+	1	0	OBSCN	226572362	0.020000	0.18652	0.000000	0.03702	0.151000	0.21798	0.239000	0.18023	-1.559000	0.01688	-0.565000	0.04167	GGT	G|0.828;A|0.172	0.172	strong		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
RBM19	9904	hgsc.bcm.edu	37	12	114386639	114386639	+	Splice_Site	SNP	A	A	G	rs7966348|rs17849837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:114386639A>G	ENST00000545145.2	-	10	1353	c.1275T>C	c.(1273-1275)taT>taC	p.Y425Y	RBM19_ENST00000392561.3_Splice_Site_p.Y425Y|RBM19_ENST00000261741.5_Splice_Site_p.Y425Y	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	425	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Y425Y(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					CACCCCTACCATATTTGGAGA	0.607													G|||	992	0.198083	0.3457	0.0764	5008	,	,		18272	0.1885		0.1133	False		,,,				2504	0.182				p.Y425Y		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - coding silent(1)	stomach(1)	c.T1275C						PASS	.	G	,,	1441,2965	683.3+/-404.2	253,935,1015	76.0	66.0	69.0		1275,1275,1275	0.8	0.8	12	dbSNP_116	69	887,7713	778.8+/-407.7	38,811,3451	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	291,1746,4466	GG,GA,AA		10.314,32.7054,17.8994	,,	425/961,425/961,425/961	114386639	2328,10678	2203	4300	6503	SO:0001630	splice_region_variant	9904	exon10			CCTACCATATTTG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1276+1T>C	12.37:g.114386639A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			A|0.823;G|0.177	0.177	strong		0.607	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	Silent
ZFYVE26	23503	hgsc.bcm.edu	37	14	68252852	68252852	+	Missense_Mutation	SNP	A	A	T	rs112787369	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:68252852A>T	ENST00000347230.4	-	17	3256	c.3118T>A	c.(3118-3120)Tca>Aca	p.S1040T	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.S1040T	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	1040				S -> T (in Ref. 1; BAG11658). {ECO:0000305}.	cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		TGACTGGCTGACATAAGCAGA	0.408													A|||	136	0.0271565	0.0015	0.1297	5008	,	,		20207	0.0		0.0368	False		,,,				2504	0.0072				p.S1040T		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.T3118A						PASS	.	A	THR/SER	44,4362	46.0+/-80.4	0,44,2159	113.0	111.0	112.0		3118	-0.6	0.0	14	dbSNP_132	112	361,8239	120.6+/-179.8	6,349,3945	yes	missense	ZFYVE26	NM_015346.3	58	6,393,6104	TT,TA,AA		4.1977,0.9986,3.1139	benign	1040/2540	68252852	405,12601	2203	4300	6503	SO:0001583	missense	23503	exon17			TGGCTGACATAAG	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.3118T>A	14.37:g.68252852A>T	ENSP00000251119:p.Ser1040Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	53	36	0.679245	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	81	0.03708791208791209	2	0.0040650406504065045	52	0.143646408839779	0	0.0	27	0.03562005277044855	A	3.840	-0.033966	0.07543	0.009986	0.041977	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.27890	1.78;1.64	5.24	-0.567	0.11763	.	0.916560	0.09281	N	0.823737	T	0.00144	0.0004	L	0.50333	1.59	0.80722	P	0.0	B;B	0.26547	0.152;0.094	B;B	0.28011	0.085;0.016	T	0.29397	-1.0013	9	0.12430	T	0.62	0.4195	2.5106	0.04656	0.5276:0.2173:0.1461:0.109	.	1040;1040	G3V2D8;Q68DK2	.;ZFY26_HUMAN	T	1040;1019;1040	ENSP00000251119:S1040T;ENSP00000450603:S1040T	ENSP00000251119:S1040T	S	-	1	0	ZFYVE26	67322605	0.000000	0.05858	0.002000	0.10522	0.079000	0.17450	0.343000	0.19944	-0.009000	0.14296	0.533000	0.62120	TCA	A|0.967;T|0.033	0.033	strong		0.408	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
WDR81	124997	hgsc.bcm.edu	37	17	1640793	1640793	+	Silent	SNP	C	C	T	rs587780510|rs8077638	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1640793C>T	ENST00000409644.1	+	10	5640	c.5640C>T	c.(5638-5640)agC>agT	p.S1880S	WDR81_ENST00000419248.1_Silent_p.S653S|WDR81_ENST00000545662.1_Silent_p.S511S|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.S829S|WDR81_ENST00000446363.1_Silent_p.S519S|WDR81_ENST00000437219.2_Silent_p.S677S	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1880					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TGTACGGCAGCGAGGTGGTCA	0.597													C|||	1210	0.241613	0.23	0.2075	5008	,	,		22298	0.1865		0.1988	False		,,,				2504	0.3824				p.S1880S		Atlas-SNP	.											WDR81_ENST00000437219,colon,carcinoma,0,6	WDR81	180	6	0			c.C5640T						PASS	.	C	,,,	986,3418	366.8+/-318.0	106,774,1322	229.0	137.0	168.0		2031,5640,1959,2487	2.0	1.0	17	dbSNP_116	168	1799,6801	323.9+/-316.2	186,1427,2687	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	292,2201,4009	TT,TC,CC		20.9186,22.3887,21.4165	,,,	677/739,1880/1942,653/715,829/891	1640793	2785,10219	2202	4300	6502	SO:0001819	synonymous_variant	124997	exon10			CGGCAGCGAGGTG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5640C>T	17.37:g.1640793C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	142	77	0.542253	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.789;T|0.211	0.211	strong		0.597	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
OTOP1	133060	hgsc.bcm.edu	37	4	4199083	4199083	+	Missense_Mutation	SNP	T	T	G	rs34666677	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:4199083T>G	ENST00000296358.4	-	5	1502	c.1478A>C	c.(1477-1479)aAg>aCg	p.K493T		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	493			K -> T (in dbSNP:rs34666677).		biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TGGCATGTCCTTGCCCTGGGG	0.592													t|||	304	0.0607029	0.0113	0.0591	5008	,	,		15180	0.0298		0.1093	False		,,,				2504	0.1104				p.K493T		Atlas-SNP	.											.	OTOP1	118	.	0			c.A1478C						PASS	.	T	THR/LYS	140,4266	90.6+/-129.3	2,136,2065	51.0	54.0	53.0		1478	-0.2	0.0	4	dbSNP_126	53	951,7649	193.7+/-239.3	68,815,3417	yes	missense	OTOP1	NM_177998.1	78	70,951,5482	GG,GT,TT		11.0581,3.1775,8.3884	benign	493/613	4199083	1091,11915	2203	4300	6503	SO:0001583	missense	133060	exon5			ATGTCCTTGCCCT	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.1478A>C	4.37:g.4199083T>G	ENSP00000296358:p.Lys493Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	128	0.05860805860805861	8	0.016260162601626018	21	0.058011049723756904	18	0.03146853146853147	81	0.10686015831134564	t	4.779	0.144914	0.09134	0.031775	0.110581	ENSG00000163982	ENST00000296358	T	0.08458	3.09	4.92	-0.201	0.13212	.	2.641920	0.01146	N	0.006318	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	B	0.21071	0.051	B	0.16722	0.016	T	0.36456	-0.9747	10	0.13470	T	0.59	-0.0401	3.7221	0.08460	0.2674:0.4424:0.0:0.2903	rs34666677	493	Q7RTM1	OTOP1_HUMAN	T	493	ENSP00000296358:K493T	ENSP00000296358:K493T	K	-	2	0	OTOP1	4249984	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.700000	0.25601	-0.303000	0.08856	-0.308000	0.09152	AAG	T|0.925;G|0.075	0.075	strong		0.592	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998	
LRIG3	121227	hgsc.bcm.edu	37	12	59282702	59282702	+	Silent	SNP	T	T	C	rs17533647	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:59282702T>C	ENST00000320743.3	-	6	988	c.702A>G	c.(700-702)acA>acG	p.T234T	LRIG3_ENST00000379141.4_Silent_p.T174T	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	234					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			GGCCTTGGAATGTCAGTCCAT	0.378			T	ROS1	NSCLC								T|||	306	0.0611022	0.0129	0.0461	5008	,	,		19089	0.0397		0.1163	False		,,,				2504	0.1022				p.T234T		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	LRIG3,NS,carcinoma,-2,1	LRIG3	120	1	0			c.A702G						PASS	.	T	,	148,4258	101.2+/-139.8	4,140,2059	198.0	185.0	189.0		522,702	-11.0	0.8	12	dbSNP_123	189	995,7605	214.6+/-254.2	51,893,3356	no	coding-synonymous,coding-synonymous	LRIG3	NM_001136051.1,NM_153377.3	,	55,1033,5415	CC,CT,TT		11.5698,3.3591,8.7883	,	174/1060,234/1120	59282702	1143,11863	2203	4300	6503	SO:0001819	synonymous_variant	121227	exon6			TTGGAATGTCAGT	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.702A>G	12.37:g.59282702T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_153377	Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																			T|0.928;C|0.072	0.072	strong		0.378	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377	
FAM120AOS	158293	hgsc.bcm.edu	37	9	96209943	96209943	+	Missense_Mutation	SNP	T	T	C	rs10821128	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:96209943T>C	ENST00000375412.5	-	3	1603	c.721A>G	c.(721-723)Aag>Gag	p.K241E	FAM120AOS_ENST00000479094.1_5'UTR|FAM120AOS_ENST00000423591.1_Missense_Mutation_p.K59E	NM_198841.2	NP_942138.2	Q5T036	F120S_HUMAN	family with sequence similarity 120A opposite strand	241			K -> E (in dbSNP:rs10821128). {ECO:0000269|PubMed:14702039}.							kidney(1)|large_intestine(1)|lung(3)|skin(1)	6						GTGGTTTTCTTTGAGACTTTG	0.338													T|||	1138	0.227236	0.0363	0.3069	5008	,	,		20145	0.4117		0.3479	False		,,,				2504	0.1145				p.K241E		Atlas-SNP	.											.	FAM120AOS	13	.	0			c.A721G						PASS	.	-	GLU/LYS	403,4003	197.1+/-221.3	22,359,1822	224.0	207.0	213.0		721	-1.4	0.0	9	dbSNP_120	213	2898,5702	453.0+/-363.1	507,1884,1909	yes	missense	FAM120AOS	NM_198841.2	56	529,2243,3731	CC,CT,TT		33.6977,9.1466,25.3806	benign	241/257	96209943	3301,9705	2203	4300	6503	SO:0001583	missense	158293	exon3			TTTTCTTTGAGAC	AK056096	CCDS6705.1	9q22.32	2008-02-05	2006-07-04	2006-07-04	ENSG00000188938	ENSG00000188938			23389	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 10 opposite strand"""	C9orf10OS		14585507	Standard	NM_198841		Approved		uc004atu.4	Q5T036	OTTHUMG00000020251	ENST00000375412.5:c.721A>G	9.37:g.96209943T>C	ENSP00000364561:p.Lys241Glu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_198841	A6NN20	Missense_Mutation	SNP	ENST00000375412.5	37	CCDS6705.1	686	0.3141025641025641	26	0.052845528455284556	132	0.36464088397790057	257	0.4493006993006993	271	0.3575197889182058	T	2.509	-0.313505	0.05422	0.091466	0.336977	ENSG00000188938	ENST00000423591;ENST00000375412;ENST00000375409;ENST00000428378	T;T;T	0.57595	0.44;0.63;0.39	1.77	-1.41	0.08941	.	.	.	.	.	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	0.43458	-0.9390	8	0.87932	D	0	.	5.3583	0.16073	0.0:0.5975:0.0:0.4025	rs10821128;rs10821128	241	Q5T036	F120S_HUMAN	E	59;241;58;58	ENSP00000414298:K59E;ENSP00000364561:K241E;ENSP00000416978:K58E	ENSP00000364558:K58E	K	-	1	0	FAM120AOS	95249764	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.584000	0.02114	-0.371000	0.08004	-0.280000	0.10049	AAG	T|0.734;C|0.266	0.266	strong		0.338	FAM120AOS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053154.1		
CD8A	925	hgsc.bcm.edu	37	2	87016506	87016506	+	Silent	SNP	A	A	G	rs3020726	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:87016506A>G	ENST00000409511.2	-	7	1595	c.565T>C	c.(565-567)Ttg>Ctg	p.L189L	CD8A_ENST00000283635.3_Silent_p.L189L|CD8A_ENST00000409781.1_Silent_p.L152L|CD8A_ENST00000538832.1_Silent_p.L230L|CD8A_ENST00000352580.3_Intron|CD8A_ENST00000456996.2_Intron	NM_001145873.1	NP_001139345.1	P01732	CD8A_HUMAN	CD8a molecule	189					antigen processing and presentation (GO:0019882)|cytotoxic T cell differentiation (GO:0045065)|defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of calcium-mediated signaling (GO:0050850)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|T cell mediated immunity (GO:0002456)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)			lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	8						GTCCCGGCCAAGGGCGCCCAG	0.612													A|||	411	0.0820687	0.0893	0.062	5008	,	,		13566	0.0744		0.1412	False		,,,				2504	0.0337				p.L189L		Atlas-SNP	.											.	CD8A	28	.	0			c.T565C						PASS	.	A	,,	351,4055	175.9+/-205.1	11,329,1863	84.0	87.0	86.0		565,565,	-3.2	0.0	2	dbSNP_101	86	1414,7186	269.0+/-288.2	122,1170,3008	no	coding-synonymous,coding-synonymous,intron	CD8A	NM_001145873.1,NM_001768.6,NM_171827.3	,,	133,1499,4871	GG,GA,AA		16.4419,7.9664,13.5707	,,	189/236,189/236,	87016506	1765,11241	2203	4300	6503	SO:0001819	synonymous_variant	925	exon7			CGGCCAAGGGCGC		CCDS1992.1, CCDS1993.1	2p12	2014-09-17	2006-03-28		ENSG00000153563	ENSG00000153563		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1706	protein-coding gene	gene with protein product		186910	"""CD8 antigen, alpha polypeptide (p32)"", ""T-cell surface glycoprotein CD8 alpha chain"""	CD8		1541829	Standard	NM_171827		Approved		uc002sru.3	P01732	OTTHUMG00000130265	ENST00000409511.2:c.565T>C	2.37:g.87016506A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	46	0.741935	NM_001145873	B4DT80|D6W5M8|Q13970|Q4ZG17	Silent	SNP	ENST00000409511.2	37	CCDS1992.1																																																																																			A|0.873;G|0.127	0.127	strong		0.612	CD8A-006	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330784.3	NM_001768	
SPAG16	79582	hgsc.bcm.edu	37	2	214794743	214794743	+	Missense_Mutation	SNP	A	A	C	rs12623569	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:214794743A>C	ENST00000331683.5	+	12	1369	c.1274A>C	c.(1273-1275)aAa>aCa	p.K425T	SPAG16_ENST00000374309.3_Missense_Mutation_p.K331T	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	425			K -> T (in dbSNP:rs12623569). {ECO:0000269|PubMed:11867345, ECO:0000269|PubMed:12391165}.		cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		GATCTATGTAAAGGCGATTGC	0.428													A|||	1386	0.276757	0.2738	0.3112	5008	,	,		17159	0.4067		0.2843	False		,,,				2504	0.1145				p.K425T		Atlas-SNP	.											.	SPAG16	134	.	0			c.A1274C						PASS	.	A	THR/LYS	1197,3209	419.6+/-338.7	147,903,1153	119.0	117.0	118.0		1274	4.3	0.6	2	dbSNP_120	118	2253,6347	382.3+/-340.3	295,1663,2342	yes	missense	SPAG16	NM_024532.3	78	442,2566,3495	CC,CA,AA		26.1977,27.1675,26.5262	benign	425/632	214794743	3450,9556	2203	4300	6503	SO:0001583	missense	79582	exon12			TATGTAAAGGCGA	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1274A>C	2.37:g.214794743A>C	ENSP00000332592:p.Lys425Thr	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	653	0.298992673992674	114	0.23170731707317074	110	0.30386740331491713	220	0.38461538461538464	209	0.2757255936675462	A	9.017	0.983924	0.18889	0.271675	0.261977	ENSG00000144451	ENST00000331683;ENST00000374309	T;T	0.78707	-1.2;-1.2	5.48	4.29	0.51040	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.277074	0.29466	N	0.012065	T	0.00012	0.0000	N	0.02181	-0.65	0.27912	P	0.9385632	B;B;B;B	0.17667	0.008;0.023;0.002;0.008	B;B;B;B	0.19391	0.011;0.025;0.002;0.011	T	0.12708	-1.0537	9	0.02654	T	1	.	11.4259	0.50009	0.8484:0.1516:0.0:0.0	rs12623569;rs52808897;rs59619307;rs12623569	331;276;365;425	B4DYB5;Q8N0X2-2;Q4G1A2;Q8N0X2	.;.;.;SPG16_HUMAN	T	425;331	ENSP00000332592:K425T;ENSP00000363428:K331T	ENSP00000332592:K425T	K	+	2	0	SPAG16	214502988	0.999000	0.42202	0.563000	0.28383	0.260000	0.26232	2.907000	0.48743	0.864000	0.35578	0.533000	0.62120	AAA	A|0.722;C|0.278	0.278	strong		0.428	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
SLC5A9	200010	hgsc.bcm.edu	37	1	48708278	48708278	+	Silent	SNP	G	G	A	rs75538709	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:48708278G>A	ENST00000438567.2	+	13	1879	c.1827G>A	c.(1825-1827)gaG>gaA	p.E609E	SLC5A9_ENST00000533824.1_Silent_p.E630E|SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000236495.5_Silent_p.E634E	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	609					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						TGGGCCAGGAGCAGCCTGAAG	0.642													G|||	253	0.0505192	0.0129	0.0648	5008	,	,		15903	0.001		0.1113	False		,,,				2504	0.0798				p.E634E		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G1902A						PASS	.	G	,	113,4293		1,111,2091	21.0	25.0	24.0		1827,1902	0.4	0.0	1	dbSNP_132	24	1005,7589		60,885,3352	no	coding-synonymous,coding-synonymous	SLC5A9	NM_001011547.2,NM_001135181.1	,	61,996,5443	AA,AG,GG		11.6942,2.5647,8.6	,	609/682,634/707	48708278	1118,11882	2203	4297	6500	SO:0001819	synonymous_variant	200010	exon14			CCAGGAGCAGCCT	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.1827G>A	1.37:g.48708278G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Silent	SNP	ENST00000438567.2	37	CCDS30709.2																																																																																			G|0.920;A|0.080	0.080	strong		0.642	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
GABRG2	2566	hgsc.bcm.edu	37	5	161528280	161528280	+	Silent	SNP	C	C	T	rs211037	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:161528280C>T	ENST00000361925.4	+	5	808	c.588C>T	c.(586-588)aaC>aaT	p.N196N	GABRG2_ENST00000393933.4_Silent_p.N101N|GABRG2_ENST00000414552.2_Silent_p.N196N|GABRG2_ENST00000356592.3_Silent_p.N196N			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	196					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.N196N(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AATTGCACAACTTTCCAATGG	0.358													C|||	1861	0.371605	0.4682	0.2507	5008	,	,		17256	0.6012		0.2435	False		,,,				2504	0.2219				p.N196N		Atlas-SNP	.											GABRG2,NS,carcinoma,0,1	GABRG2	142	1	1	Substitution - coding silent(1)	stomach(1)	c.C588T						scavenged	.	C	,,	1906,2500	545.1+/-376.7	413,1080,710	112.0	104.0	106.0		588,588,588	3.5	1.0	5	dbSNP_79	106	2088,6512	358.8+/-331.3	269,1550,2481	no	coding-synonymous,coding-synonymous,coding-synonymous	GABRG2	NM_000816.3,NM_198903.2,NM_198904.2	,,	682,2630,3191	TT,TC,CC		24.2791,43.2592,30.7089	,,	196/468,196/516,196/476	161528280	3994,9012	2203	4300	6503	SO:0001819	synonymous_variant	2566	exon5			GCACAACTTTCCA		CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.588C>T	5.37:g.161528280C>T		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	83	26	0.313253	NM_198904	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Silent	SNP	ENST00000361925.4	37	CCDS4358.1																																																																																			C|0.648;T|0.352	0.352	strong		0.358	GABRG2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252706.1		
PIGQ	9091	hgsc.bcm.edu	37	16	630902	630902	+	Silent	SNP	C	C	G	rs1045274	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:630902C>G	ENST00000026218.5	+	9	1549	c.1461C>G	c.(1459-1461)ctC>ctG	p.L487L	PIGQ_ENST00000321878.5_Silent_p.L487L|PIGQ_ENST00000409527.2_Silent_p.L487L	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	487	Leu-rich.				C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				TCCATCTGCTCGTGGACCTCA	0.667													C|||	691	0.137979	0.1369	0.0807	5008	,	,		17865	0.0248		0.1759	False		,,,				2504	0.2577				p.L487L		Atlas-SNP	.											PIGQ,NS,carcinoma,0,1	PIGQ	43	1	0			c.C1461G						PASS	.	C	,	690,3712	289.5+/-280.5	49,592,1560	143.0	136.0	139.0		1461,1461	-4.0	1.0	16	dbSNP_86	139	1588,7012	296.3+/-302.9	149,1290,2861	no	coding-synonymous,coding-synonymous	PIGQ	NM_004204.3,NM_148920.1	,	198,1882,4421	GG,GC,CC		18.4651,15.6747,17.5204	,	487/582,487/761	630902	2278,10724	2201	4300	6501	SO:0001819	synonymous_variant	9091	exon9			TCTGCTCGTGGAC	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.1461C>G	16.37:g.630902C>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Silent	SNP	ENST00000026218.5	37	CCDS10411.1																																																																																			C|0.846;G|0.154	0.154	strong		0.667	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
TACC2	10579	hgsc.bcm.edu	37	10	123844503	123844503	+	Missense_Mutation	SNP	C	C	T	rs10887063	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123844503C>T	ENST00000369005.1	+	4	2828	c.2488C>T	c.(2488-2490)Ctc>Ttc	p.L830F	TACC2_ENST00000334433.3_Missense_Mutation_p.L830F|TACC2_ENST00000515603.1_Missense_Mutation_p.L830F|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.L830F|TACC2_ENST00000515273.1_Missense_Mutation_p.L830F	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	830			L -> F (in dbSNP:rs10887063). {ECO:0000269|PubMed:12620397}.		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGAGAAGCATCTCCAGCCATC	0.557													C|||	922	0.184105	0.2882	0.17	5008	,	,		19229	0.0982		0.1829	False		,,,				2504	0.1431				p.L830F		Atlas-SNP	.											.	TACC2	271	.	0			c.C2488T						PASS	.	C	,PHE/LEU	1381,3025	455.7+/-351.1	210,961,1032	125.0	126.0	126.0		,2488	4.6	0.0	10	dbSNP_120	126	1595,7005	295.9+/-302.6	142,1311,2847	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,22	352,2272,3879	TT,TC,CC		18.5465,31.3436,22.8817	,benign	,830/2949	123844503	2976,10030	2203	4300	6503	SO:0001583	missense	10579	exon4			AAGCATCTCCAGC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.2488C>T	10.37:g.123844503C>T	ENSP00000358001:p.Leu830Phe	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	24	0.6	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	417	0.19093406593406592	141	0.2865853658536585	73	0.20165745856353592	68	0.11888111888111888	135	0.17810026385224276	C	14.53	2.561552	0.45590	0.313436	0.185465	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.04970	3.62;3.52;3.56;3.62;3.52	5.66	4.57	0.56435	.	0.260219	0.20581	N	0.089522	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P;P;P	0.47106	0.89;0.89;0.89	B;B;B	0.38954	0.286;0.286;0.286	T	0.54866	-0.8229	9	0.46703	T	0.11	-5.2727	12.3263	0.55013	0.0:0.9063:0.0:0.0937	rs10887063;rs52822997;rs10887063	830;830;830	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	F	830;830;830;830;830;820	ENSP00000358001:L830F;ENSP00000424467:L830F;ENSP00000427618:L830F;ENSP00000334280:L830F;ENSP00000395048:L830F	ENSP00000334280:L830F	L	+	1	0	TACC2	123834493	0.001000	0.12720	0.008000	0.14137	0.034000	0.12701	0.982000	0.29539	2.660000	0.90430	0.549000	0.68633	CTC	C|0.791;T|0.209	0.209	strong		0.557	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
CERS5	91012	hgsc.bcm.edu	37	12	50529736	50529736	+	Silent	SNP	G	G	A	rs3741562	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:50529736G>A	ENST00000317551.6	-	7	877	c.753C>T	c.(751-753)gaC>gaT	p.D251D	CERS5_ENST00000422340.2_Silent_p.D193D	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	251	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				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)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										CCAGCAAGAAGTCTGAGACAT	0.423													G|||	1577	0.314896	0.3162	0.3026	5008	,	,		19360	0.1806		0.3479	False		,,,				2504	0.4264				p.D251D		Atlas-SNP	.											.	.	.	.	0			c.C753T						PASS	.	G		1420,2986	463.4+/-353.5	235,950,1018	123.0	113.0	116.0		753	4.6	1.0	12	dbSNP_107	116	3100,5500	474.5+/-368.9	556,1988,1756	no	coding-synonymous	CERS5	NM_147190.2		791,2938,2774	AA,AG,GG		36.0465,32.2288,34.7532		251/393	50529736	4520,8486	2203	4300	6503	SO:0001819	synonymous_variant	91012	exon7			CAAGAAGTCTGAG		CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"""Homeoboxes / CERS class"""	23749	protein-coding gene	gene with protein product		615335	"""LAG1 longevity assurance homolog 5 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 5"""	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.753C>T	12.37:g.50529736G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_147190	B4DV54	Silent	SNP	ENST00000317551.6	37	CCDS8801.1	631|631	0.2889194139194139|0.2889194139194139	153|153	0.31097560975609756|0.31097560975609756	109|109	0.3011049723756906|0.3011049723756906	110|110	0.19230769230769232|0.19230769230769232	259|259	0.341688654353562|0.341688654353562	G|G	8.269|8.269	0.812981|0.812981	0.16537|0.16537	0.322288|0.322288	0.360465|0.360465	ENSG00000139624|ENSG00000139624	ENST00000550919|ENST00000550547;ENST00000547800	.|.	.|.	.|.	4.63|4.63	4.63|4.63	0.57726|0.57726	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.41875|0.41875	-0.9484|-0.9484	3|3	.|.	.|.	.|.	-16.8045|-16.8045	8.5384|8.5384	0.33377|0.33377	0.1764:0.0:0.8236:0.0|0.1764:0.0:0.8236:0.0	rs3741562;rs59016377;rs3741562|rs3741562;rs59016377;rs3741562	.|.	.|.	.|.	F|I	21|53;155	.|.	.|.	L|T	-|-	1|2	0|0	CERS5|CERS5	48816003|48816003	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	3.398000|3.398000	0.52579|0.52579	2.567000|2.567000	0.86603|0.86603	0.655000|0.655000	0.94253|0.94253	CTT|ACT	G|0.679;A|0.321	0.321	strong		0.423	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190	
AKAP13	11214	hgsc.bcm.edu	37	15	86122875	86122875	+	Missense_Mutation	SNP	A	A	C	rs34434221	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:86122875A>C	ENST00000394518.2	+	7	1671	c.1576A>C	c.(1576-1578)Aag>Cag	p.K526Q	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.K526Q	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	526			K -> Q (in dbSNP:rs34434221).		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						CGTCACAAGTAAGCCTGTGGA	0.458													A|||	66	0.0131789	0.0038	0.0317	5008	,	,		20928	0.0		0.0368	False		,,,				2504	0.002				p.K526Q	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A1576C	GRCh37	CM063842	AKAP13	M	rs34434221	PASS	.	A	GLN/LYS,GLN/LYS	23,4381	29.9+/-59.1	0,23,2179	79.0	85.0	83.0		1576,1576	-4.9	0.0	15	dbSNP_126	83	266,8332	101.4+/-162.7	3,260,4036	yes	missense,missense	AKAP13	NM_006738.4,NM_007200.3	53,53	3,283,6215	CC,CA,AA		3.0937,0.5223,2.2227	benign,benign	526/2818,526/2814	86122875	289,12713	2202	4299	6501	SO:0001583	missense	11214	exon7			ACAAGTAAGCCTG	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.1576A>C	15.37:g.86122875A>C	ENSP00000378026:p.Lys526Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	46	0.021062271062271064	3	0.006097560975609756	17	0.04696132596685083	0	0.0	26	0.03430079155672823	A	10.65	1.409294	0.25378	0.005223	0.030937	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.09817	2.94;2.95	5.41	-4.86	0.03132	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	0.999999	B;B	0.13145	0.004;0.007	B;B	0.12156	0.003;0.007	T	0.43507	-0.9387	9	0.31617	T	0.26	.	8.6836	0.34223	0.1731:0.2688:0.5581:0.0	rs34434221	526;526	Q12802;Q12802-2	AKP13_HUMAN;.	Q	526;526;525;525	ENSP00000354718:K526Q;ENSP00000378026:K526Q	ENSP00000354718:K526Q	K	+	1	0	AKAP13	83923879	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-0.739000	0.04866	-0.685000	0.05177	0.533000	0.62120	AAG	A|0.978;C|0.022	0.022	strong		0.458	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
FUT8	2530	hgsc.bcm.edu	37	14	66136163	66136163	+	Missense_Mutation	SNP	C	C	A	rs35949016	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:66136163C>A	ENST00000360689.5	+	7	2527	c.800C>A	c.(799-801)aCa>aAa	p.T267K	FUT8_ENST00000394586.2_Missense_Mutation_p.T267K|FUT8_ENST00000554765.1_3'UTR|FUT8_ENST00000557164.1_Missense_Mutation_p.T104K|FUT8_ENST00000417683.1_Missense_Mutation_p.H2Q|FUT8_ENST00000394585.1_Missense_Mutation_p.T267K|FUT8_ENST00000358307.2_Missense_Mutation_p.T138K	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	267	GT23. {ECO:0000255|PROSITE- ProRule:PRU00992}.		T -> K (in dbSNP:rs35949016).		cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)	p.T267K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		GAGACATGCACAGACAGATCT	0.473													C|||	748	0.149361	0.0136	0.1095	5008	,	,		17709	0.1022		0.2157	False		,,,				2504	0.3415				p.T267K		Atlas-SNP	.											FUT8,NS,carcinoma,0,1	FUT8	101	1	1	Substitution - Missense(1)	stomach(1)	c.C800A						scavenged	.	C	LYS/THR,LYS/THR,LYS/THR	143,4263	99.8+/-138.5	2,139,2062	151.0	133.0	139.0		311,800,800	5.8	1.0	14	dbSNP_126	139	1433,7167	274.1+/-291.0	125,1183,2992	yes	missense,missense,missense	FUT8	NM_004480.4,NM_178155.2,NM_178156.2	78,78,78	127,1322,5054	AA,AC,CC		16.6628,3.2456,12.1175	probably-damaging,probably-damaging,probably-damaging	104/413,267/576,267/576	66136163	1576,11430	2203	4300	6503	SO:0001583	missense	2530	exon7			CATGCACAGACAG	AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"""Fucosyltransferases"""	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000360689.5:c.800C>A	14.37:g.66136163C>A	ENSP00000353910:p.Thr267Lys	Somatic	169	3	0.0177515		WXS	Illumina HiSeq	Phase_I	167	81	0.48503	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Missense_Mutation	SNP	ENST00000360689.5	37	CCDS9775.1	287|287	0.13141025641025642|0.13141025641025642	10|10	0.02032520325203252|0.02032520325203252	41|41	0.1132596685082873|0.1132596685082873	64|64	0.11188811188811189|0.11188811188811189	172|172	0.22691292875989447|0.22691292875989447	C|C	6.902|6.902	0.536045|0.536045	0.13188|0.13188	0.032456|0.032456	0.166628|0.166628	ENSG00000033170|ENSG00000033170	ENST00000417683|ENST00000360689;ENST00000394586;ENST00000557164;ENST00000394585;ENST00000358307	T|T;T;T;T;T	0.43294|0.21734	0.95|1.99;1.99;1.99;1.99;1.99	5.85|5.85	5.85|5.85	0.93711|0.93711	.|.	.|0.046256	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.62723|0.62723	1.935|1.935	0.40642|0.40642	P|P	0.018046000000000006|0.018046000000000006	B|B;P	0.02656|0.51791	0.0|0.289;0.948	B|B;B	0.01281|0.37267	0.0|0.042;0.245	T|T	0.46569|0.46569	-0.9182|-0.9182	8|9	0.87932|0.19147	D|T	0|0.46	-10.6644|-10.6644	17.6669|17.6669	0.88205|0.88205	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs35949016;rs35949016|rs35949016;rs35949016	2|138;267	Q8IUA5|G3XAD2;Q9BYC5	.|.;FUT8_HUMAN	Q|K	2|267;267;104;267;138	ENSP00000396770:H2Q|ENSP00000353910:T267K;ENSP00000378087:T267K;ENSP00000452433:T104K;ENSP00000378086:T267K;ENSP00000351057:T138K	ENSP00000396770:H2Q|ENSP00000345865:T267K	H|T	+|+	3|2	2|0	FUT8|FUT8	65205916|65205916	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.863000|4.863000	0.62983|0.62983	2.768000|2.768000	0.95171|0.95171	0.655000|0.655000	0.94253|0.94253	CAC|ACA	C|0.875;A|0.125	0.125	strong		0.473	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480	
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 GAIIx	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	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	35	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	
AIPL1	23746	hgsc.bcm.edu	37	17	6331803	6331803	+	Silent	SNP	T	T	C	rs8075035	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6331803T>C	ENST00000381129.3	-	3	380	c.300A>G	c.(298-300)ctA>ctG	p.L100L	AIPL1_ENST00000570466.1_Silent_p.L78L|AIPL1_ENST00000576776.1_Silent_p.L100L|AIPL1_ENST00000576307.1_Silent_p.L40L|AIPL1_ENST00000575265.1_Silent_p.L100L|AIPL1_ENST00000250087.5_Intron|AIPL1_ENST00000571740.1_Silent_p.L100L|AIPL1_ENST00000574506.1_Silent_p.L88L	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	100	PPIase FKBP-type.				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)		GGCTCCGGGATAGGATGGGGT	0.627													C|||	2884	0.575879	0.4569	0.6758	5008	,	,		19343	0.5367		0.6759	False		,,,				2504	0.6033				p.L100L		Atlas-SNP	.											.	AIPL1	34	.	0			c.A300G						PASS	.	C	,,	2203,2203	584.9+/-386.1	556,1091,556	75.0	62.0	67.0		,120,300	1.1	1.0	17	dbSNP_116	67	5669,2931	453.4+/-363.2	1859,1951,490	no	intron,coding-synonymous,coding-synonymous	AIPL1	NM_001033054.1,NM_001033055.1,NM_014336.3	,,	2415,3042,1046	CC,CT,TT		34.0814,50.0,39.4741	,,	,40/325,100/385	6331803	7872,5134	2203	4300	6503	SO:0001819	synonymous_variant	23746	exon3			CCGGGATAGGATG	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.300A>G	17.37:g.6331803T>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	46	31	0.673913	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Silent	SNP	ENST00000381129.3	37	CCDS11075.1																																																																																			T|0.391;C|0.609	0.609	strong		0.627	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336	
MCAM	4162	hgsc.bcm.edu	37	11	119181170	119181170	+	Silent	SNP	T	T	C	rs2249466	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119181170T>C	ENST00000264036.4	-	15	1814	c.1800A>G	c.(1798-1800)ctA>ctG	p.L600L	MCAM_ENST00000392814.1_3'UTR	NM_006500.2	NP_006491.2	P43121	MUC18_HUMAN	melanoma cell adhesion molecule	600					anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|glomerular filtration (GO:0003094)|vascular wound healing (GO:0061042)	external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|skin(1)	22		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.78e-05)		GAGACGGGGGTAGCGTGCTGG	0.577													C|||	3747	0.748203	0.767	0.7695	5008	,	,		18536	0.6577		0.7107	False		,,,				2504	0.8395				p.L600L		Atlas-SNP	.											MCAM,NS,carcinoma,0,1	MCAM	57	1	0			c.A1800G						PASS	.	C		3310,1088	393.1+/-328.7	1242,826,131	100.0	104.0	102.0		1800	5.1	1.0	11	dbSNP_100	102	6115,2475	406.4+/-348.8	2169,1777,349	no	coding-synonymous	MCAM	NM_006500.2		3411,2603,480	CC,CT,TT		28.8126,24.7385,27.433		600/647	119181170	9425,3563	2199	4295	6494	SO:0001819	synonymous_variant	4162	exon15			CGGGGGTAGCGTG	X68264	CCDS31690.1	11q23.3	2013-01-29				ENSG00000076706		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6934	protein-coding gene	gene with protein product	"""Gicerin"""	155735				2602381, 10702685	Standard	XM_005271552		Approved	MUC18, CD146	uc001pwf.3	P43121		ENST00000264036.4:c.1800A>G	11.37:g.119181170T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_006500	O95812|Q59E86|Q6PHR3|Q6ZTR2	Silent	SNP	ENST00000264036.4	37	CCDS31690.1																																																																																			T|0.279;C|0.721	0.721	strong		0.577	MCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388332.2		
SPANXN2	494119	hgsc.bcm.edu	37	X	142795438	142795438	+	Silent	SNP	G	G	T	rs5908761	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:142795438G>T	ENST00000370498.1	-	2	993	c.240C>A	c.(238-240)ccC>ccA	p.P80P		NM_001009615.1	NP_001009615.1	Q5MJ10	SPXN2_HUMAN	SPANX family, member N2	80										NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)					CCTCTTGGACGGGATTGATGG	0.453													T|||	892	0.236291	0.3343	0.1196	3775	,	,		15309	0.1677		0.0676	False		,,,				2504	0.1329				p.P80P		Atlas-SNP	.											.	SPANXN2	67	.	0			c.C240A						PASS	.	T		1597,2238		291,780,235,561,336	304.0	278.0	287.0		240	-0.4	0.0	X	dbSNP_114	287	796,5932		33,516,214,1879,1658	no	coding-synonymous	SPANXN2	NM_001009615.1		324,1296,449,2440,1994	TT,TG,T,GG,G		11.8312,41.6428,22.6545		80/181	142795438	2393,8170	2203	4300	6503	SO:0001819	synonymous_variant	494119	exon2			TTGGACGGGATTG		CCDS35419.1	Xq27.3	2012-06-12			ENSG00000203924	ENSG00000268988			33175	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 7"""	300665				14973187, 17012309	Standard	NM_001009615		Approved	SPANX-N2, CT11.7	uc004fbz.3	Q5MJ10	OTTHUMG00000022583	ENST00000370498.1:c.240C>A	X.37:g.142795438G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	139	50	0.359712	NM_001009615	Q0ZNM2	Silent	SNP	ENST00000370498.1	37	CCDS35419.1																																																																																			G|0.764;T|0.236	0.236	strong		0.453	SPANXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058621.2	NM_001009615	
STAB2	55576	hgsc.bcm.edu	37	12	104136316	104136316	+	Silent	SNP	C	C	T	rs2292688	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:104136316C>T	ENST00000388887.2	+	56	6219	c.6015C>T	c.(6013-6015)ttC>ttT	p.F2005F		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						CGGGGAGATTCGGGCCTGATT	0.577													C|||	671	0.133986	0.0446	0.1787	5008	,	,		20976	0.252		0.0964	False		,,,				2504	0.1401				p.F2005F		Atlas-SNP	.											.	STAB2	370	.	0			c.C6015T						PASS	.	C		218,4188	134.1+/-170.4	6,206,1991	196.0	176.0	183.0		6015	0.7	1.0	12	dbSNP_100	183	865,7735	197.6+/-242.2	44,777,3479	no	coding-synonymous	STAB2	NM_017564.9		50,983,5470	TT,TC,CC		10.0581,4.9478,8.3269		2005/2552	104136316	1083,11923	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon56			GAGATTCGGGCCT	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.6015C>T	12.37:g.104136316C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.892;T|0.108	0.108	strong		0.577	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
LILRB3	11025	hgsc.bcm.edu	37	19	54725913	54725913	+	Missense_Mutation	SNP	C	C	T	rs199822090	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54725913C>T	ENST00000391750.1	-	5	581	c.445G>A	c.(445-447)Gga>Aga	p.G149R	LILRB3_ENST00000407860.2_Missense_Mutation_p.G149R|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000391735.3_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000245620.9_Missense_Mutation_p.G149R|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000346401.6_Missense_Mutation_p.G149R|LILRB3_ENST00000424807.1_Missense_Mutation_p.G149R|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	149	Ig-like C2-type 2.			G -> R (in Ref. 2; AAB87667). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGTGATATCCCTTCTGTGAG	0.597													.|||	783	0.15635	0.3411	0.1715	5008	,	,		12077	0.002		0.1362	False		,,,				2504	0.0757				p.G149R		Atlas-SNP	.											.	LILRB3	67	.	0			c.G445A						PASS	.						23.0	15.0	18.0					19																	54725913		2079	3867	5946	SO:0001583	missense	11025	exon4			GATATCCCTTCTG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.445G>A	19.37:g.54725913C>T	ENSP00000375630:p.Gly149Arg	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	131	69	0.526718	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	6.911	0.537697	0.13188	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;5.76	2.87	-5.75	0.02384	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.07683	0.0193	L	0.37800	1.135	0.80722	P	0.0	B;B;P;P;P	0.41546	0.218;0.08;0.555;0.754;0.68	B;B;B;B;B	0.39094	0.271;0.132;0.29;0.049;0.209	T	0.17258	-1.0375	9	0.41790	T	0.15	.	1.2731	0.02025	0.1365:0.1909:0.2699:0.4027	.	149;149;149;149;149	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	R	149	ENSP00000375630:G149R;ENSP00000412771:G149R;ENSP00000345184:G149R;ENSP00000245620:G149R;ENSP00000384274:G149R;ENSP00000388199:G149R	ENSP00000245620:G149R	G	-	1	0	LILRB3	59417725	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.520000	0.00951	-1.631000	0.01543	-0.510000	0.04470	GGA	C|0.931;T|0.069	0.069	strong		0.597	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
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 GAIIx	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		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	33	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	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135745762	135745762	+	Missense_Mutation	SNP	C	C	T	rs9826032	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:135745762C>T	ENST00000264977.3	+	3	2701	c.2084C>T	c.(2083-2085)cCc>cTc	p.P695L	PPP2R3A_ENST00000492624.2_5'Flank|PPP2R3A_ENST00000490467.1_5'UTR|PPP2R3A_ENST00000334546.2_Missense_Mutation_p.P74L	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	695	Pro-rich.		P -> L (in dbSNP:rs9826032).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TCCCCGGTTCCCCATGTGAAT	0.448													C|||	20	0.00399361	0.0015	0.0086	5008	,	,		15312	0.0		0.0109	False		,,,				2504	0.001				p.P695L		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.C2084T						PASS	.	C	,LEU/PRO,LEU/PRO	14,4392	21.2+/-45.6	0,14,2189	95.0	95.0	95.0		,2084,221	4.6	0.9	3	dbSNP_119	95	109,8491	59.1+/-120.7	1,107,4192	yes	utr-5,missense,missense	PPP2R3A	NM_001190447.1,NM_002718.4,NM_181897.2	,98,98	1,121,6381	TT,TC,CC		1.2674,0.3177,0.9457	,benign,benign	,695/1151,74/530	135745762	123,12883	2203	4300	6503	SO:0001583	missense	5523	exon3			CGGTTCCCCATGT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.2084C>T	3.37:g.135745762C>T	ENSP00000264977:p.Pro695Leu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	14	0.00641025641025641	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	13.07	2.126608	0.37533	0.003177	0.012674	ENSG00000073711	ENST00000264977;ENST00000334546	T;T	0.16897	2.31;2.31	5.52	4.63	0.57726	.	0.445759	0.21636	N	0.071420	T	0.06645	0.0170	N	0.11927	0.2	0.80722	D	1	B;B	0.10296	0.0;0.003	B;B	0.10450	0.001;0.005	T	0.12142	-1.0559	10	0.44086	T	0.13	.	8.987	0.35999	0.0:0.8336:0.0:0.1664	rs9826032;rs9826032	74;695	Q06190-2;Q06190	.;P2R3A_HUMAN	L	695;74	ENSP00000264977:P695L;ENSP00000334748:P74L	ENSP00000264977:P695L	P	+	2	0	PPP2R3A	137228452	1.000000	0.71417	0.878000	0.34440	0.547000	0.35210	1.903000	0.39858	2.757000	0.94681	0.585000	0.79938	CCC	C|0.992;T|0.008	0.008	strong		0.448	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
KANSL1	284058	hgsc.bcm.edu	37	17	44248814	44248814	+	Silent	SNP	G	G	A	rs535019273	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44248814G>A	ENST00000262419.6	-	2	1166	c.696C>T	c.(694-696)tcC>tcT	p.S232S	KANSL1_ENST00000575318.1_Silent_p.S232S|KANSL1_ENST00000432791.1_Silent_p.S232S|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.S232S|KANSL1_ENST00000572904.1_Silent_p.S232S|KANSL1_ENST00000576248.1_5'Flank	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	232					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											AATTGACAGAGGATTTGTTTG	0.458													A|||	433	0.0864617	0.0151	0.1571	5008	,	,		24585	0.001		0.2406	False		,,,				2504	0.0624				p.S232S		Atlas-SNP	.											.	.	.	.	0			c.C696T						PASS	.	A	,,	203,4203	807.8+/-415.9	5,193,2005	118.0	146.0	136.0		696,696,696	5.0	1.0	17	dbSNP_92	136	1935,6665	725.7+/-406.6	220,1495,2585	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	225,1688,4590	AA,AG,GG		22.5,4.6074,16.4386	,,	232/1105,232/1106,232/1106	44248814	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			GACAGAGGATTTG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.696C>T	17.37:g.44248814G>A		Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	384	384	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			G|0.848;A|0.152	0.152	strong		0.458	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
SPON2	10417	hgsc.bcm.edu	37	4	1165764	1165764	+	Silent	SNP	C	C	T	rs11538062	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:1165764C>T	ENST00000290902.5	-	2	428	c.96G>A	c.(94-96)gaG>gaA	p.E32E	SPON2_ENST00000431380.1_Silent_p.E32E	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	32	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		AACAGATGGACTCTCCCCCAA	0.682													C|||	674	0.134585	0.1233	0.0965	5008	,	,		12032	0.1815		0.1133	False		,,,				2504	0.1503				p.E32E		Atlas-SNP	.											.	SPON2	22	.	0			c.G96A						PASS	.	C	,,	496,3890		34,428,1731	28.0	39.0	35.0		96,96,96	-1.9	0.0	4	dbSNP_120	35	1132,7418		80,972,3223	no	coding-synonymous,coding-synonymous,coding-synonymous	SPON2	NM_001128325.2,NM_001199021.1,NM_012445.3	,,	114,1400,4954	TT,TC,CC		13.2398,11.3087,12.585	,,	32/332,32/332,32/332	1165764	1628,11308	2193	4275	6468	SO:0001819	synonymous_variant	10417	exon2			GATGGACTCTCCC	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"""Mindin"", ""M-spondin"""	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.96G>A	4.37:g.1165764C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Silent	SNP	ENST00000290902.5	37	CCDS3347.1																																																																																			C|0.870;T|0.130	0.130	strong		0.682	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2		
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 GAIIx	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_ENST00000528778.1_5'UTR|DUSP8_ENST00000331588.4_Silent_p.L161L	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		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	119	34	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	
MMP3	4314	hgsc.bcm.edu	37	11	102713620	102713620	+	Missense_Mutation	SNP	T	T	C	rs679620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102713620T>C	ENST00000299855.5	-	2	389	c.133A>G	c.(133-135)Aaa>Gaa	p.K45E		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	45			K -> E (in dbSNP:rs679620). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6, ECO:0000269|Ref.7}.		cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	ACATCTTTTTTGAGGTCGTAG	0.333													C|||	3266	0.652157	0.671	0.6787	5008	,	,		18508	0.6657		0.5278	False		,,,				2504	0.7219				p.K45E		Atlas-SNP	.											MMP3,NS,carcinoma,0,1	MMP3	60	1	0			c.A133G						PASS	.	C	GLU/LYS	2815,1591	483.9+/-359.9	907,1001,295	30.0	30.0	30.0		133	-0.2	0.0	11	dbSNP_83	30	4301,4297	567.7+/-388.9	1067,2167,1065	yes	missense	MMP3	NM_002422.3	56	1974,3168,1360	CC,CT,TT		49.9767,36.1099,45.2784	benign	45/478	102713620	7116,5888	2203	4299	6502	SO:0001583	missense	4314	exon2			CTTTTTTGAGGTC	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.133A>G	11.37:g.102713620T>C	ENSP00000299855:p.Lys45Glu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Missense_Mutation	SNP	ENST00000299855.5	37	CCDS8323.1	1373	0.6286630036630036	348	0.7073170731707317	231	0.638121546961326	384	0.6713286713286714	410	0.5408970976253298	C	1.799	-0.477598	0.04414	0.638901	0.500233	ENSG00000149968	ENST00000299855	T	0.34859	1.34	6.16	-0.221	0.13126	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	2.486670	0.02224	N	0.064238	T	0.00012	0.0000	N	0.10733	0.035	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39502	-0.9611	9	0.02654	T	1	.	6.9869	0.24733	0.0:0.2794:0.318:0.4026	rs679620;rs1051161;rs3168234;rs56822421;rs679620	45	P08254	MMP3_HUMAN	E	45	ENSP00000299855:K45E	ENSP00000299855:K45E	K	-	1	0	MMP3	102218830	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.578000	0.02125	-0.250000	0.09555	-2.364000	0.00238	AAA	T|0.428;C|0.572	0.572	strong		0.333	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
SYNJ2	8871	hgsc.bcm.edu	37	6	158499302	158499302	+	Silent	SNP	G	G	T	rs2296507	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:158499302G>T	ENST00000355585.4	+	18	2631	c.2556G>T	c.(2554-2556)gcG>gcT	p.A852A	SYNJ2_ENST00000367112.1_5'UTR|SYNJ2_ENST00000367122.2_Silent_p.A852A|SYNJ2_ENST00000367121.3_Silent_p.A852A	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	852					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		AGCTACAAGCGTCTGATCACA	0.532													g|||	2769	0.552915	0.6732	0.353	5008	,	,		18405	0.5833		0.5099	False		,,,				2504	0.545				p.A852A		Atlas-SNP	.											.	SYNJ2	111	.	0			c.G2556T						PASS	.	A	,	2820,1586	667.1+/-401.8	899,1022,282	198.0	170.0	179.0		1845,2556	-10.9	0.9	6	dbSNP_100	179	4382,4218	582.9+/-391.5	1108,2166,1026	no	coding-synonymous,coding-synonymous	SYNJ2	NM_001178088.1,NM_003898.3	,	2007,3188,1308	TT,TG,GG		49.0465,35.9964,44.6256	,	615/1260,852/1497	158499302	7202,5804	2203	4300	6503	SO:0001819	synonymous_variant	8871	exon18			ACAAGCGTCTGAT	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.2556G>T	6.37:g.158499302G>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	37	CCDS5254.1																																																																																			G|0.446;T|0.554	0.554	strong		0.532	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2		
PRR14L	253143	hgsc.bcm.edu	37	22	32112461	32112461	+	Missense_Mutation	SNP	T	T	C	rs140081	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:32112461T>C	ENST00000327423.6	-	4	1553	c.1364A>G	c.(1363-1365)aAc>aGc	p.N455S	PRR14L_ENST00000434485.1_Missense_Mutation_p.N455S|PRR14L_ENST00000461722.1_5'Flank|PRR14L_ENST00000397493.2_Missense_Mutation_p.N455S	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	455			N -> S (in dbSNP:rs140081).							endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						AGAACTAGAGTTCCCTGTATG	0.358													C|||	1740	0.347444	0.5862	0.3098	5008	,	,		17728	0.1895		0.2058	False		,,,				2504	0.3599				p.N455S		Atlas-SNP	.											.	PRR14L	198	.	0			c.A1364G						PASS	.	C	SER/ASN	729,655		195,339,158	106.0	98.0	100.0		1364	2.9	0.0	22	dbSNP_78	100	680,2502		80,520,991	yes	missense	PRR14L	NM_173566.2	46	275,859,1149	CC,CT,TT		21.3702,47.3266,30.8585	benign	455/2152	32112461	1409,3157	692	1591	2283	SO:0001583	missense	253143	exon4			CTAGAGTTCCCTG	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.1364A>G	22.37:g.32112461T>C	ENSP00000331845:p.Asn455Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	653	0.298992673992674	288	0.5853658536585366	106	0.292817679558011	105	0.18356643356643357	154	0.20316622691292877	C	0	-2.639341	0.00112	0.526734	0.213702	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.04551	3.6;3.61;3.62	5.32	2.88	0.33553	.	0.477523	0.20890	N	0.083854	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.17048	-1.0382	8	.	.	.	-0.2648	6.6956	0.23197	0.0:0.6952:0.0:0.3048	rs140081;rs58959236;rs140081	455;455;455	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	S	455	ENSP00000380630:N455S;ENSP00000331845:N455S;ENSP00000388314:N455S	.	N	-	2	0	PRR14L	30442461	0.000000	0.05858	0.013000	0.15412	0.009000	0.06853	-0.401000	0.07232	0.763000	0.33175	-0.722000	0.03604	AAC	T|0.684;C|0.316	0.316	strong		0.358	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
ZNF518B	85460	hgsc.bcm.edu	37	4	10447907	10447907	+	Missense_Mutation	SNP	C	C	T	rs72648876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:10447907C>T	ENST00000326756.3	-	3	484	c.46G>A	c.(46-48)Gga>Aga	p.G16R		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	16					regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)	p.G16*(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						GAATTATGTCCGCCGTTCAAG	0.413													C|||	35	0.00698882	0.0008	0.0159	5008	,	,		20730	0.0		0.0199	False		,,,				2504	0.0031				p.G16R		Atlas-SNP	.											.	ZNF518B	116	.	1	Substitution - Nonsense(1)	lung(1)	c.G46A						PASS	.	C	ARG/GLY	23,4383	29.9+/-59.1	0,23,2180	206.0	179.0	188.0		46	1.4	0.0	4	dbSNP_130	188	234,8366	96.6+/-158.3	4,226,4070	yes	missense	ZNF518B	NM_053042.2	125	4,249,6250	TT,TC,CC		2.7209,0.522,1.976	probably-damaging	16/1075	10447907	257,12749	2203	4300	6503	SO:0001583	missense	85460	exon3			TATGTCCGCCGTT	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.46G>A	4.37:g.10447907C>T	ENSP00000317614:p.Gly16Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	22	0.010073260073260074	0	0.0	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	0.154	-1.088391	0.01873	0.00522	0.027209	ENSG00000178163	ENST00000326756;ENST00000507515	T	0.01495	4.83	5.76	1.39	0.22231	.	0.274240	0.19473	N	0.113409	T	0.00496	0.0016	N	0.19112	0.55	0.09310	N	1	B	0.16396	0.017	B	0.08055	0.003	T	0.48906	-0.8993	10	0.33940	T	0.23	-9.3433	7.915	0.29812	0.0:0.5041:0.0:0.4959	.	16	Q9C0D4	Z518B_HUMAN	R	16	ENSP00000317614:G16R	ENSP00000317614:G16R	G	-	1	0	ZNF518B	10057005	0.087000	0.21565	0.010000	0.14722	0.260000	0.26232	0.489000	0.22387	0.313000	0.23062	0.650000	0.86243	GGA	C|0.983;T|0.017	0.017	strong		0.413	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
MTDH	92140	hgsc.bcm.edu	37	8	98725970	98725970	+	Silent	SNP	G	G	A	rs2331652	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:98725970G>A	ENST00000336273.3	+	9	1681	c.1353G>A	c.(1351-1353)aaG>aaA	p.K451K	MTDH_ENST00000519934.1_Silent_p.K395K	NM_178812.3	NP_848927.2	Q86UE4	LYRIC_HUMAN	metadherin	451	Poly-Lys.				lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of angiogenesis (GO:0045766)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)	double-stranded RNA binding (GO:0003725)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|transcription coactivator activity (GO:0003713)	p.K451K(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Breast(36;2.56e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.178)			aaaagaagaagcaaggtgaag	0.363													G|||	539	0.107628	0.0023	0.1931	5008	,	,		15239	0.2411		0.0199	False		,,,				2504	0.1421				p.K451K		Atlas-SNP	.											MTDH,NS,carcinoma,0,1	MTDH	54	1	1	Substitution - coding silent(1)	stomach(1)	c.G1353A						PASS	.	G		22,4384	27.2+/-55.0	0,22,2181	43.0	43.0	43.0		1353	5.5	1.0	8	dbSNP_100	43	122,8474	62.4+/-124.4	1,120,4177	no	coding-synonymous	MTDH	NM_178812.3		1,142,6358	AA,AG,GG		1.4193,0.4993,1.1075		451/583	98725970	144,12858	2203	4298	6501	SO:0001819	synonymous_variant	92140	exon9			GAAGAAGCAAGGT	AF411226	CCDS6274.1	8q22.1	2014-07-14			ENSG00000147649	ENSG00000147649			29608	protein-coding gene	gene with protein product	"""astrocyte elevated gene 1"""	610323				15093543	Standard	NM_178812		Approved	LYRIC, 3D3, AEG-1	uc003yhz.3	Q86UE4	OTTHUMG00000164692	ENST00000336273.3:c.1353G>A	8.37:g.98725970G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_178812	Q05DH2|Q52QU9|Q6PK07|Q8TCX3	Silent	SNP	ENST00000336273.3	37	CCDS6274.1																																																																																			G|0.950;A|0.050	0.050	strong		0.363	MTDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379772.2		
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 GAIIx	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_ENST00000534366.1_Missense_Mutation_p.P22S|MROH1_ENST00000398656.4_Missense_Mutation_p.P22S|MROH1_ENST00000326134.5_Missense_Mutation_p.P22S|MROH1_ENST00000423230.2_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	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	9	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	
MUC21	394263	hgsc.bcm.edu	37	6	30954709	30954709	+	Missense_Mutation	SNP	G	G	A	rs11756238	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30954709G>A	ENST00000376296.3	+	2	998	c.757G>A	c.(757-759)Ggc>Agc	p.G253S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	253	28 X 15 AA approximate tandem repeats.|Ser-rich.		G -> S (in dbSNP:rs41288655). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G253S(1)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CAGTGGGGCCGGCACAGCCAC	0.637													A|||	193	0.0385383	0.0356	0.062	5008	,	,		20371	0.0208		0.0467	False		,,,				2504	0.0358				p.G253S		Atlas-SNP	.											MUC21,colon,carcinoma,-1,2	MUC21	98	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.G757A						scavenged	.						135.0	138.0	137.0					6																	30954709		2203	4300	6503	SO:0001583	missense	394263	exon2			GGGGCCGGCACAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.757G>A	6.37:g.30954709G>A	ENSP00000365473:p.Gly253Ser	Somatic	99	3	0.030303		WXS	Illumina HiSeq	Phase_I	95	6	0.0631579	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	1.863	-0.462214	0.04508	.	.	ENSG00000204544	ENST00000376296	T	0.01265	5.08	4.3	1.82	0.25136	.	.	.	.	.	T	0.00210	0.0006	N	0.01576	-0.805	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.18366	-1.0339	8	.	.	.	.	7.3667	0.26776	0.6106:0.0:0.3894:0.0	rs41288655	253	Q5SSG8	MUC21_HUMAN	S	253	ENSP00000365473:G253S	.	G	+	1	0	MUC21	31062688	0.000000	0.05858	0.003000	0.11579	0.041000	0.13682	-0.706000	0.05047	-0.001000	0.14495	-0.490000	0.04691	GGC	G|0.989;A|0.011	0.011	strong		0.637	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
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 GAIIx	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	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	79	38	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	
CCDC88C	440193	hgsc.bcm.edu	37	14	91760522	91760522	+	Silent	SNP	C	C	T	rs12891713	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:91760522C>T	ENST00000389857.6	-	23	4193	c.4107G>A	c.(4105-4107)caG>caA	p.Q1369Q		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1369					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				CTTACATGTACTGCTTCTGCT	0.567													C|||	1015	0.202676	0.4856	0.1412	5008	,	,		21614	0.0843		0.1193	False		,,,				2504	0.0716				p.Q1369Q		Atlas-SNP	.											.	CCDC88C	192	.	0			c.G4107A						PASS	.	C		1763,2535		364,1035,750	260.0	275.0	270.0		4107	3.1	1.0	14	dbSNP_121	270	948,7556		64,820,3368	no	coding-synonymous	CCDC88C	NM_001080414.3		428,1855,4118	TT,TC,CC		11.1477,41.0191,21.1764		1369/2029	91760522	2711,10091	2149	4252	6401	SO:0001819	synonymous_variant	440193	exon23			CATGTACTGCTTC		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.4107G>A	14.37:g.91760522C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	164	68	0.414634	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.823;T|0.177	0.177	strong		0.567	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
DPP3	10072	hgsc.bcm.edu	37	11	66276576	66276576	+	Missense_Mutation	SNP	G	G	A	rs12421620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:66276576G>A	ENST00000360510.2	+	18	2133	c.2068G>A	c.(2068-2070)Gag>Aag	p.E690K	DPP3_ENST00000532677.1_Missense_Mutation_p.E709K|DPP3_ENST00000530165.1_Missense_Mutation_p.E660K|DPP3_ENST00000531863.1_Missense_Mutation_p.E710K|BBS1_ENST00000393994.2_5'Flank|DPP3_ENST00000453114.1_Missense_Mutation_p.E690K|CTD-3074O7.11_ENST00000419755.3_5'UTR|DPP3_ENST00000541961.1_Missense_Mutation_p.E690K|BBS1_ENST00000537537.1_5'Flank|BBS1_ENST00000318312.7_5'Flank|BBS1_ENST00000455748.2_5'Flank			Q9NY33	DPP3_HUMAN	dipeptidyl-peptidase 3	690			E -> K (in dbSNP:rs12421620).		proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)	23						TCTGGAATACGAGGCGTCAGC	0.527													G|||	252	0.0503195	0.003	0.2939	5008	,	,		18106	0.0		0.0288	False		,,,				2504	0.0153				p.E690K		Atlas-SNP	.											.	DPP3	61	.	0			c.G2068A						PASS	.	G	LYS/GLU,LYS/GLU	33,4367	36.0+/-67.5	0,33,2167	82.0	80.0	81.0		2068,2068	5.3	1.0	11	dbSNP_120	81	153,8437	71.0+/-133.6	5,143,4147	yes	missense,missense	DPP3	NM_005700.3,NM_130443.2	56,56	5,176,6314	AA,AG,GG		1.7811,0.75,1.4319	benign,benign	690/738,690/738	66276576	186,12804	2200	4295	6495	SO:0001583	missense	10072	exon18			GAATACGAGGCGT	AB017970	CCDS8141.1, CCDS58147.1	11q12-q13.1	2008-02-05	2006-01-12		ENSG00000254986	ENSG00000254986	3.4.14.4		3008	protein-coding gene	gene with protein product		606818	"""dipeptidylpeptidase III"", ""dipeptidylpeptidase 3"""			10773679	Standard	NM_005700		Approved		uc001oif.2	Q9NY33	OTTHUMG00000167143	ENST00000360510.2:c.2068G>A	11.37:g.66276576G>A	ENSP00000353701:p.Glu690Lys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	10	0.169492	NM_130443	B2RDB5|B4DLX4|F5H8L6|O95748|Q969H2|Q9BV67|Q9HAL6	Missense_Mutation	SNP	ENST00000360510.2	37	CCDS8141.1	108	0.04945054945054945	4	0.008130081300813009	76	0.20994475138121546	0	0.0	28	0.036939313984168866	G	19.16	3.773660	0.69992	0.0075	0.017811	ENSG00000254986	ENST00000531863;ENST00000532677;ENST00000360510;ENST00000453114;ENST00000541961;ENST00000530165;ENST00000543807;ENST00000347422	T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.82056	2.57	0.21256	P	0.999746047	P;P	0.37663	0.604;0.522	B;B	0.35039	0.091;0.194	T	0.08046	-1.0741	9	0.66056	D	0.02	.	14.5126	0.67797	0.0:0.0:1.0:0.0	rs12421620;rs56529436;rs59164997;rs12421620	709;690	G3V1D3;Q9NY33	.;DPP3_HUMAN	K	710;709;690;690;690;660;588;270	ENSP00000432782:E710K;ENSP00000435284:E709K;ENSP00000353701:E690K;ENSP00000389943:E690K;ENSP00000440502:E690K;ENSP00000436941:E660K	ENSP00000309957:E270K	E	+	1	0	DPP3	66033152	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	6.043000	0.71004	2.498000	0.84270	0.555000	0.69702	GAG	G|0.975;A|0.025	0.025	strong		0.527	DPP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393424.2		
POR	5447	hgsc.bcm.edu	37	7	75615287	75615287	+	Silent	SNP	G	G	A	rs1057870	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:75615287G>A	ENST00000461988.1	+	14	1821	c.1716G>A	c.(1714-1716)tcG>tcA	p.S572S	POR_ENST00000450476.1_Silent_p.S471S|TMEM120A_ENST00000338761.4_RNA|POR_ENST00000439269.1_Silent_p.S310S|TMEM120A_ENST00000493111.2_RNA|POR_ENST00000419840.1_Intron|POR_ENST00000394893.1_Silent_p.S572S|POR_ENST00000545601.1_Silent_p.S380S	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	569					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GCCGCCGCTCGGATGAGGACT	0.697													G|||	978	0.195288	0.1256	0.2133	5008	,	,		15903	0.0377		0.341	False		,,,				2504	0.2894				p.S572S		Atlas-SNP	.											.	POR	46	.	0			c.G1716A						PASS	.	G		610,3330		41,528,1401	10.0	16.0	14.0		1716	-7.2	0.0	7	dbSNP_86	14	2849,5335		524,1801,1767	no	coding-synonymous	POR	NM_000941.2		565,2329,3168	AA,AG,GG		34.8118,15.4822,28.5302		572/681	75615287	3459,8665	1970	4092	6062	SO:0001819	synonymous_variant	5447	exon14			CCGCTCGGATGAG	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1716G>A	7.37:g.75615287G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	51	32	0.627451	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	37	CCDS5579.1	402	0.18406593406593408	53	0.10772357723577236	79	0.21823204419889503	20	0.03496503496503497	250	0.32981530343007914	G	4.067	0.010290	0.07912	0.154822	0.348118	ENSG00000127948	ENST00000447222	.	.	.	3.59	-7.18	0.01505	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.4999999999987246E-5	.	.	.	.	.	.	T	0.15752	-1.0426	3	.	.	.	-21.412	3.4043	0.07335	0.339:0.1397:0.4265:0.0949	rs1057870;rs2228105;rs3198404;rs10954733;rs11540676;rs17148959;rs56753821;rs1057870	.	.	.	R	623	.	.	G	+	1	0	POR	75453223	0.000000	0.05858	0.020000	0.16555	0.705000	0.40729	-2.390000	0.01057	-3.492000	0.00153	-2.868000	0.00100	GGA	G|0.826;A|0.174	0.174	strong		0.697	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
ATP1A4	480	hgsc.bcm.edu	37	1	160134056	160134056	+	Missense_Mutation	SNP	G	G	A	rs17368402	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:160134056G>A	ENST00000368081.4	+	7	1360	c.889G>A	c.(889-891)Gaa>Aaa	p.E297K		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	297			E -> K (in dbSNP:rs17368402).		ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGCTGAGATCGAACACTTCAT	0.537													G|||	225	0.0449281	0.0023	0.0562	5008	,	,		18832	0.002		0.0974	False		,,,				2504	0.0849				p.E297K		Atlas-SNP	.											.	ATP1A4	167	.	0			c.G889A						PASS	.	G	LYS/GLU	100,4306	79.9+/-118.3	0,100,2103	283.0	224.0	244.0		889	1.6	0.0	1	dbSNP_123	244	985,7615	214.2+/-253.9	45,895,3360	yes	missense	ATP1A4	NM_144699.3	56	45,995,5463	AA,AG,GG		11.4535,2.2696,8.3423	benign	297/1030	160134056	1085,11921	2203	4300	6503	SO:0001583	missense	480	exon7			GAGATCGAACACT	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.889G>A	1.37:g.160134056G>A	ENSP00000357060:p.Glu297Lys	Somatic	443	1	0.00225734		WXS	Illumina HiSeq	Phase_I	444	215	0.484234	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	37	CCDS1197.1	99	0.04532967032967033	1	0.0020325203252032522	21	0.058011049723756904	1	0.0017482517482517483	76	0.10026385224274406	G	9.009	0.982061	0.18812	0.022696	0.114535	ENSG00000132681	ENST00000368081	D	0.90732	-2.72	4.54	1.62	0.23740	ATPase, P-type, ATPase-associated domain (1);	0.158645	0.53938	N	0.000056	T	0.82148	0.4974	L	0.58302	1.8	0.80722	D	1	B	0.31910	0.346	B	0.34536	0.185	T	0.78209	-0.2293	10	0.87932	D	0	.	10.4681	0.44620	0.0777:0.2542:0.6681:0.0	rs17368402;rs56500076;rs57880353;rs17368402	297	Q13733	AT1A4_HUMAN	K	297	ENSP00000357060:E297K	ENSP00000357060:E297K	E	+	1	0	ATP1A4	158400680	1.000000	0.71417	0.010000	0.14722	0.050000	0.14768	3.911000	0.56378	0.013000	0.14918	-2.387000	0.00228	GAA	G|0.934;A|0.066	0.066	strong		0.537	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
PTER	9317	hgsc.bcm.edu	37	10	16547058	16547058	+	Silent	SNP	A	A	G	rs7904014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:16547058A>G	ENST00000378000.1	+	5	984	c.738A>G	c.(736-738)caA>caG	p.Q246Q	PTER_ENST00000298942.3_Silent_p.Q246Q|PTER_ENST00000535784.2_Silent_p.Q246Q|PTER_ENST00000423462.2_Intron	NM_001001484.2|NM_001261838.1|NM_030664.4	NP_001001484.1|NP_001248767.1|NP_109589.2	Q96BW5	PTER_HUMAN	phosphotriesterase related	246					catabolic process (GO:0009056)|epithelial cell differentiation (GO:0030855)	extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on ester bonds (GO:0016788)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)	15						AGTTTGCTCAACTTGGCTGCT	0.383													A|||	3287	0.65635	0.6392	0.5793	5008	,	,		18810	0.8264		0.4771	False		,,,				2504	0.7434				p.Q246Q	Ovarian(2;46 150 15648 38137 47908)	Atlas-SNP	.											.	PTER	40	.	0			c.A738G						PASS	.	A	,	2616,1790	641.4+/-397.5	768,1080,355	191.0	184.0	186.0		738,738	-1.6	1.0	10	dbSNP_116	186	3997,4603	554.1+/-386.4	932,2133,1235	no	coding-synonymous,coding-synonymous	PTER	NM_001001484.1,NM_030664.3	,	1700,3213,1590	GG,GA,AA		46.4767,40.6264,49.1542	,	246/350,246/350	16547058	6613,6393	2203	4300	6503	SO:0001819	synonymous_variant	9317	exon5			TGCTCAACTTGGC	BC015092	CCDS7111.1, CCDS58070.1, CCDS73070.1	10p12	2003-11-05			ENSG00000165983	ENSG00000165983			9590	protein-coding gene	gene with protein product		604446				9925913	Standard	NM_001001484		Approved		uc001ioi.2	Q96BW5	OTTHUMG00000017737	ENST00000378000.1:c.738A>G	10.37:g.16547058A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	147	61	0.414966	NM_030664	B0YJ77|B3KTF5|D3DRU0|Q9BY46	Silent	SNP	ENST00000378000.1	37	CCDS7111.1																																																																																			A|0.428;G|0.572	0.572	strong		0.383	PTER-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047001.2	NM_030664	
TAF1C	9013	hgsc.bcm.edu	37	16	84212779	84212779	+	Missense_Mutation	SNP	G	G	A	rs2230131	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84212779G>A	ENST00000567759.1	-	14	2560	c.2378C>T	c.(2377-2379)cCg>cTg	p.P793L	TAF1C_ENST00000378541.4_Missense_Mutation_p.P793L|TAF1C_ENST00000341690.6_Missense_Mutation_p.P699L|TAF1C_ENST00000541676.1_Missense_Mutation_p.P700L|TAF1C_ENST00000570117.1_Missense_Mutation_p.P461L|TAF1C_ENST00000566732.1_Missense_Mutation_p.P767L	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	793			P -> L (in dbSNP:rs2230131). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						CTGGGAGGGCGGGGTCGTGGG	0.647													G|||	795	0.158746	0.208	0.0648	5008	,	,		14150	0.1508		0.1103	False		,,,				2504	0.2168				p.P793L		Atlas-SNP	.											.	TAF1C	60	.	0			c.C2378T						PASS	.	G	LEU/PRO,LEU/PRO	861,3537		79,703,1417	20.0	17.0	18.0		2378,2096	2.2	0.0	16	dbSNP_98	18	804,7788		46,712,3538	yes	missense,missense	TAF1C	NM_005679.3,NM_139353.2	98,98	125,1415,4955	AA,AG,GG		9.3575,19.5771,12.8176	possibly-damaging,possibly-damaging	793/870,699/776	84212779	1665,11325	2199	4296	6495	SO:0001583	missense	9013	exon14			GAGGGCGGGGTCG	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.2378C>T	16.37:g.84212779G>A	ENSP00000455265:p.Pro793Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	37	CCDS32496.1	296	0.13553113553113552	105	0.21341463414634146	29	0.08011049723756906	78	0.13636363636363635	84	0.11081794195250659	G	11.18	1.563138	0.27915	0.195771	0.093575	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	T;T;T	0.02579	4.24;4.24;4.24	5.3	2.21	0.28008	.	0.366869	0.21074	N	0.080606	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B;B;B;B	0.32717	0.078;0.381;0.007;0.032	B;B;B;B	0.26202	0.014;0.067;0.006;0.01	T	0.45220	-0.9276	9	0.72032	D	0.01	-8.6675	4.7623	0.13113	0.1809:0.0:0.6479:0.1712	rs2230131;rs3743641	767;316;793;699	Q15572-6;F5H0H4;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	L	793;700;699;316	ENSP00000367802:P793L;ENSP00000437900:P700L;ENSP00000345305:P699L	ENSP00000345305:P699L	P	-	2	0	TAF1C	82770280	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	1.120000	0.31271	0.219000	0.20840	-0.136000	0.14681	CCG	G|0.840;A|0.160	0.160	strong		0.647	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
NCOA7	135112	hgsc.bcm.edu	37	6	126249914	126249914	+	Missense_Mutation	SNP	T	T	G	rs1567|rs386705611	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:126249914T>G	ENST00000368357.3	+	17	3178	c.2826T>G	c.(2824-2826)gaT>gaG	p.D942E	NCOA7_ENST00000392477.2_Missense_Mutation_p.D942E|NCOA7_ENST00000229634.9_Missense_Mutation_p.D827E	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	942	TLD.		D -> E (in dbSNP:rs1567).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		GGGCATTTGATTGAAATTCAG	0.433													G|||	827	0.165136	0.2617	0.0764	5008	,	,		16628	0.2401		0.1153	False		,,,				2504	0.0716				p.D942E		Atlas-SNP	.											.	NCOA7	92	.	0			c.T2826G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	1109,3297	715.1+/-408.4	152,805,1246	76.0	78.0	77.0		2793,2826,2826,2481,657,2826	4.1	1.0	6	dbSNP_36	77	1106,7494	768.0+/-407.6	64,978,3258	yes	missense,missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_001199622.1,NM_181782.4	45,45,45,45,45,45	216,1783,4504	GG,GT,TT		12.8605,25.1702,17.0306	benign,benign,benign,benign,benign,benign	931/932,942/943,942/943,827/828,219/220,942/943	126249914	2215,10791	2203	4300	6503	SO:0001583	missense	135112	exon17			ATTTGATTGAAAT	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.2826T>G	6.37:g.126249914T>G	ENSP00000357341:p.Asp942Glu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	55	20	0.363636	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	343|343	0.15705128205128205|0.15705128205128205	116|116	0.23577235772357724|0.23577235772357724	24|24	0.06629834254143646|0.06629834254143646	115|115	0.20104895104895104|0.20104895104895104	88|88	0.11609498680738786|0.11609498680738786	G|G	1.772|1.772	-0.484123|-0.484123	0.04383|0.04383	0.251702|0.251702	0.128605|0.128605	ENSG00000111912|ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634|ENST00000438495	T;T;T|.	0.06933|.	3.26;3.26;3.24|.	6.17|6.17	4.1|4.1	0.47936|0.47936	TLDc (1);|.	0.000000|.	0.85682|.	N|.	0.000000|.	T|T	0.03305|0.03305	0.0096|0.0096	N|N	0.01202|0.01202	-0.96|-0.96	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.0;0.001;0.0;0.0|.	T|T	0.38265|0.38265	-0.9669|-0.9669	9|4	0.02654|.	T|.	1|.	.|.	6.2777|6.2777	0.20989|0.20989	0.2432:0.0:0.6121:0.1447|0.2432:0.0:0.6121:0.1447	rs1567;rs52814580;rs59469171;rs1567|rs1567;rs52814580;rs59469171;rs1567	931;236;931;942|.	B3KXK4;Q5JVL0;Q8NI08-2;Q8NI08|.	.;.;.;NCOA7_HUMAN|.	E|V	942;942;827|237	ENSP00000357341:D942E;ENSP00000376269:D942E;ENSP00000229634:D827E|.	ENSP00000229634:D827E|.	D|L	+|+	3|1	2|2	NCOA7|NCOA7	126291607|126291607	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.734000|0.734000	0.41952|0.41952	1.200000|1.200000	0.32247|0.32247	0.952000|0.952000	0.37798|0.37798	-0.121000|-0.121000	0.15023|0.15023	GAT|TTG	T|0.829;G|0.171	0.171	strong		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
EIF2S3	1968	hgsc.bcm.edu	37	X	24073761	24073761	+	Silent	SNP	C	C	T	rs36018672	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:24073761C>T	ENST00000253039.4	+	2	352	c.99C>T	c.(97-99)caC>caT	p.H33H		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	33					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						CACTTTCACACGAAGTTATCA	0.358													C|||	1371	0.363179	0.0877	0.4625	3775	,	,		13244	0.2698		0.5328	False		,,,				2504	0.1288				p.H33H		Atlas-SNP	.											.	EIF2S3	31	.	0			c.C99T						PASS	.	C		743,3092		73,484,113,1075,458	92.0	73.0	80.0		99	-5.6	1.0	X	dbSNP_126	80	4540,2188		1094,1070,1282,264,590	no	coding-synonymous	EIF2S3	NM_001415.3		1167,1554,1395,1339,1048	TT,TC,T,CC,C		32.5208,19.3742,49.9858		33/473	24073761	5283,5280	2203	4300	6503	SO:0001819	synonymous_variant	1968	exon2			TTCACACGAAGTT	L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"""eukaryotic translation initiation factor 2G"""	300161	"""eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"""	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.99C>T	X.37:g.24073761C>T		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	182	176	0.967033	NM_001415	B5BTZ4	Silent	SNP	ENST00000253039.4	37	CCDS14210.1	789	0.4755877034358047	30	0.0641025641025641	113	0.452	119	0.26327433628318586	274	0.5393700787401575	C	9.857	1.195295	0.22037	0.193742	0.674792	ENSG00000130741	ENST00000423068	.	.	.	4.68	-5.59	0.02505	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999898	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.8051	0.05425	0.2206:0.1277:0.0905:0.5612	rs36018672;rs60195265;rs62585018	.	.	.	X	33	.	.	R	+	1	2	EIF2S3	23983682	0.963000	0.33076	0.958000	0.39756	0.969000	0.65631	0.070000	0.14573	-0.749000	0.04747	-0.458000	0.05436	CGA	C|0.514;T|0.486	0.486	strong		0.358	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415	
MANSC4	100287284	hgsc.bcm.edu	37	12	27915944	27915944	+	Silent	SNP	A	A	G	rs11049124	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27915944A>G	ENST00000381273.3	-	3	749	c.750T>C	c.(748-750)ccT>ccC	p.P250P		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	250						integral component of membrane (GO:0016021)				kidney(1)	1						TGTTGAGTCCAGGTGGAACAG	0.373													G|||	625	0.1248	0.0234	0.1023	5008	,	,		22025	0.2044		0.173	False		,,,				2504	0.1462				p.P250P		Atlas-SNP	.											.	MANSC4	9	.	0			c.T750C						PASS	.	G		63,1321		1,61,630	301.0	225.0	248.0		750	1.7	0.0	12	dbSNP_120	248	485,2697		36,413,1142	no	coding-synonymous	MANSC4	NM_001146221.1		37,474,1772	GG,GA,AA		15.242,4.552,12.0018		250/341	27915944	548,4018	692	1591	2283	SO:0001819	synonymous_variant	100287284	exon3			GAGTCCAGGTGGA		CCDS53770.1	12p11.22	2011-05-05			ENSG00000205693	ENSG00000205693			40023	protein-coding gene	gene with protein product							Standard	NM_001146221		Approved		uc010sjs.1	A6NHS7	OTTHUMG00000169216	ENST00000381273.3:c.750T>C	12.37:g.27915944A>G		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	273	126	0.461538	NM_001146221		Silent	SNP	ENST00000381273.3	37	CCDS53770.1																																																																																			A|0.859;G|0.141	0.141	strong		0.373	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
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 GAIIx	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	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	28	17	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	
COL22A1	169044	hgsc.bcm.edu	37	8	139824057	139824057	+	Silent	SNP	G	G	A	rs10101430	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:139824057G>A	ENST00000303045.6	-	9	1880	c.1434C>T	c.(1432-1434)tgC>tgT	p.C478C	COL22A1_ENST00000435777.1_Silent_p.C478C	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	478	Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CTCCAGCTGGGCAGGAGCAGT	0.592										HNSCC(7;0.00092)			G|||	2407	0.480631	0.4062	0.4438	5008	,	,		12375	0.5694		0.5527	False		,,,				2504	0.4417				p.C478C		Atlas-SNP	.											.	COL22A1	390	.	0			c.C1434T						PASS	.	G		1849,2557	534.8+/-374.1	387,1075,741	76.0	65.0	69.0		1434	1.2	1.0	8	dbSNP_119	69	4608,3992	598.7+/-394.0	1275,2058,967	no	coding-synonymous	COL22A1	NM_152888.1		1662,3133,1708	AA,AG,GG		46.4186,41.9655,49.6463		478/1627	139824057	6457,6549	2203	4300	6503	SO:0001819	synonymous_variant	169044	exon9			AGCTGGGCAGGAG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1434C>T	8.37:g.139824057G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			G|0.507;A|0.493	0.493	strong		0.592	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43876040	43876040	+	Missense_Mutation	SNP	C	C	A	rs62536540	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:43876040C>A	ENST00000377564.3	+	14	2525	c.2132C>A	c.(2131-2133)tCc>tAc	p.S711Y		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	711	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						ACACACACTTCCTGGGGAGGT	0.453													c|||	2144	0.428115	0.3797	0.4323	5008	,	,		12033	0.5575		0.4563	False		,,,				2504	0.3282				p.S711Y		Atlas-SNP	.											CNTNAP3B,NS,carcinoma,0,1	CNTNAP3B	37	1	0			c.C2132A						scavenged	.																																			SO:0001583	missense	728577	exon14			ACACTTCCTGGGG	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.2132C>A	9.37:g.43876040C>A	ENSP00000366787:p.Ser711Tyr	Somatic	891	12	0.013468		WXS	Illumina HiSeq	Phase_I	524	277	0.528626	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.005|0.005	-2.125372|-2.125372	0.00342|0.00342	.|.	.|.	ENSG00000154529|ENSG00000154529	ENST00000377561|ENST00000377564;ENST00000341990	.|T	.|0.04083	.|3.71	2.5|2.5	2.5|2.5	0.30297|0.30297	.|.	.|.	.|.	.|.	.|.	T|T	0.00936|0.00936	0.0031|0.0031	N|N	0.00095|0.00095	-2.16|-2.16	0.19300|0.19300	N|N	0.999976|0.999976	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.44081|0.44081	-0.9351|-0.9351	5|7	.|0.02654	.|T	.|1	.|.	7.8062|7.8062	0.29204|0.29204	0.7873:0.2127:0.0:0.0|0.7873:0.2127:0.0:0.0	.|.	.|.	.|.	.|.	T|Y	760|711	.|ENSP00000366787:S711Y	.|ENSP00000340890:S711Y	P|S	+|+	1|2	0|0	CNTNAP3B|CNTNAP3B	43816036|43816036	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.374000|0.374000	0.29953|0.29953	3.305000|3.305000	0.51873|0.51873	0.226000|0.226000	0.20979|0.20979	-2.210000|-2.210000	0.00300|0.00300	CCT|TCC	A|1.000;|0.000	1.000	weak		0.453	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
TTLL10	254173	hgsc.bcm.edu	37	1	1115503	1115503	+	Missense_Mutation	SNP	T	T	C	rs111751804	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1115503T>C	ENST00000379290.1	+	6	462	c.289T>C	c.(289-291)Tgt>Cgt	p.C97R	TTLL10_ENST00000379289.1_Missense_Mutation_p.C97R|TTLL10_ENST00000379288.3_Missense_Mutation_p.C24R|TTLL10-AS1_ENST00000379317.1_RNA			Q6ZVT0	TTL10_HUMAN	tubulin tyrosine ligase-like family, member 10	97					cellular protein modification process (GO:0006464)					haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(2)|skin(1)	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;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|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;0.199)		AGATGGACACTGTGGGCCGGA	0.677													T|||	53	0.0105831	0.0038	0.0072	5008	,	,		11056	0.0		0.0308	False		,,,				2504	0.0123				p.C97R		Atlas-SNP	.											.	TTLL10	66	.	0			c.T289C						PASS	.	T	ARG/CYS,ARG/CYS	18,4382		0,18,2182	25.0	31.0	29.0		289,70	-3.2	0.0	1	dbSNP_132	29	217,8375		6,205,4085	yes	missense,missense	TTLL10	NM_001130045.1,NM_153254.2	180,180	6,223,6267	CC,CT,TT		2.5256,0.4091,1.8088	benign,benign	97/674,24/405	1115503	235,12757	2200	4296	6496	SO:0001583	missense	254173	exon6			GGACACTGTGGGC	AK093438	CCDS8.1, CCDS44036.1	1p36.33	2014-01-28	2005-07-29	2005-07-29	ENSG00000162571	ENSG00000162571		"""Tubulin tyrosine ligase-like family"""	26693	protein-coding gene	gene with protein product			"""tubulin tyrosine ligase-like family, member 5"""	TTLL5		15890843	Standard	NM_153254		Approved	FLJ36119	uc001acy.2	Q6ZVT0	OTTHUMG00000000851	ENST00000379290.1:c.289T>C	1.37:g.1115503T>C	ENSP00000368592:p.Cys97Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_001130045	B1AMF6|Q5T2W4|Q5T2W5|Q8N9X2	Missense_Mutation	SNP	ENST00000379290.1	37	CCDS44036.1	28	0.01282051282051282	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	23	0.030343007915567283	T	2.361	-0.346594	0.05208	0.004091	0.025256	ENSG00000162571	ENST00000379290;ENST00000379289;ENST00000379288	T;T;T	0.16743	3.39;3.39;2.32	3.4	-3.17	0.05202	.	.	.	.	.	T	0.02888	0.0086	N	0.22421	0.69	0.09310	N	1	B;B	0.22683	0.073;0.044	B;B	0.22753	0.041;0.025	T	0.32188	-0.9916	9	0.52906	T	0.07	.	5.0326	0.14417	0.0:0.4086:0.1734:0.418	.	24;97	Q6ZVT0-3;Q6ZVT0	.;TTL10_HUMAN	R	97;97;24	ENSP00000368592:C97R;ENSP00000368591:C97R;ENSP00000368590:C24R	ENSP00000368590:C24R	C	+	1	0	TTLL10	1105366	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.367000	0.07553	-0.708000	0.05015	-1.055000	0.02315	TGT	T|0.985;C|0.015	0.015	strong		0.677	TTLL10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002421.3	NM_153254	
DLEC1	9940	hgsc.bcm.edu	37	3	38125705	38125705	+	Silent	SNP	G	G	A	rs7652276	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:38125705G>A	ENST00000308059.6	+	7	1251	c.1230G>A	c.(1228-1230)ccG>ccA	p.P410P	DLEC1_ENST00000346219.3_Silent_p.P410P|DLEC1_ENST00000469151.1_3'UTR|DLEC1_ENST00000452631.2_Silent_p.P410P					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		GAGTCCTCCCGCCTTCCACGC	0.448													g|||	1880	0.375399	0.4145	0.3818	5008	,	,		25644	0.5387		0.3012	False		,,,				2504	0.226				p.P410P		Atlas-SNP	.											.	DLEC1	278	.	0			c.G1230A						PASS	.		,	1644,2520		332,980,770	110.0	120.0	117.0		1230,1230	-10.8	0.0	3	dbSNP_116	117	2535,5901		412,1711,2095	no	coding-synonymous,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	744,2691,2865	AA,AG,GG		30.0498,39.4813,33.1667	,	410/1756,410/1779	38125705	4179,8421	2082	4218	6300	SO:0001819	synonymous_variant	9940	exon7			CCTCCCGCCTTCC	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.1230G>A	3.37:g.38125705G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_007337		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			G|0.644;A|0.356	0.356	strong		0.448	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
MIA3	375056	hgsc.bcm.edu	37	1	222833538	222833538	+	Silent	SNP	C	C	G	rs2291835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:222833538C>G	ENST00000344922.5	+	24	5020	c.4995C>G	c.(4993-4995)ggC>ggG	p.G1665G	RP11-378J18.8_ENST00000608771.1_RNA|MIA3_ENST00000344507.1_Intron|MIA3_ENST00000344441.6_Silent_p.G1665G|MIA3_ENST00000340535.7_Silent_p.G543G	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1665	Pro-rich.				chondrocyte development (GO:0002063)|collagen fibril organization (GO:0030199)|exocytosis (GO:0006887)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|positive regulation of bone mineralization (GO:0030501)|positive regulation of leukocyte migration (GO:0002687)|protein transport (GO:0015031)|wound healing (GO:0042060)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.G1665G(1)		breast(5)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(15)|lung(37)|ovary(5)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|urinary_tract(1)	80				GBM - Glioblastoma multiforme(131;0.0199)		GCCAGAATGGCTCTTTTGGCC	0.468													C|||	635	0.126797	0.087	0.1311	5008	,	,		17069	0.1607		0.1988	False		,,,				2504	0.0685				p.G1665G		Atlas-SNP	.											MIA3,NS,carcinoma,0,1	MIA3	167	1	1	Substitution - coding silent(1)	stomach(1)	c.C4995G						PASS	.	C		330,3474		14,302,1586	92.0	95.0	94.0		4995	4.1	1.0	1	dbSNP_100	94	1579,6659		147,1285,2687	no	coding-synonymous	MIA3	NM_198551.2		161,1587,4273	GG,GC,CC		19.1673,8.6751,15.8528		1665/1908	222833538	1909,10133	1902	4119	6021	SO:0001819	synonymous_variant	375056	exon24			GAATGGCTCTTTT		CCDS41470.1, CCDS73035.1	1p36.33	2012-12-13		2006-07-25	ENSG00000154305	ENSG00000154305			24008	protein-coding gene	gene with protein product	"""C219 reactive peptide"", ""transport and golgi organization"""	613455				15183315	Standard	XM_005273121		Approved	UNQ6077, FLJ39207, KIAA0268, TANGO	uc001hnl.3	Q5JRA6	OTTHUMG00000037543	ENST00000344922.5:c.4995C>G	1.37:g.222833538C>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Silent	SNP	ENST00000344922.5	37	CCDS41470.1																																																																																			C|0.832;G|0.168	0.168	strong		0.468	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
PPL	5493	hgsc.bcm.edu	37	16	4933939	4933939	+	Missense_Mutation	SNP	G	G	C	rs2037912	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4933939G>C	ENST00000345988.2	-	22	4806	c.4717C>G	c.(4717-4719)Caa>Gaa	p.Q1573E	PPL_ENST00000590782.2_Missense_Mutation_p.Q1571E	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1573			Q -> E (in dbSNP:rs2037912). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9628581, ECO:0000269|Ref.5}.		keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						TGCAGGTTTTGCCTCTCCAGC	0.537													G|||	2017	0.402756	0.0303	0.4712	5008	,	,		20646	0.6518		0.5318	False		,,,				2504	0.4683				p.Q1573E		Atlas-SNP	.											.	PPL	168	.	0			c.C4717G						PASS	.	G	GLU/GLN	513,3881	233.6+/-246.7	36,441,1720	110.0	110.0	110.0		4717	5.8	1.0	16	dbSNP_94	110	4748,3852	609.1+/-395.5	1310,2128,862	yes	missense	PPL	NM_002705.4	29	1346,2569,2582	CC,CG,GG		44.7907,11.675,40.4879	possibly-damaging	1573/1757	4933939	5261,7733	2197	4300	6497	SO:0001583	missense	5493	exon22			GGTTTTGCCTCTC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.4717C>G	16.37:g.4933939G>C	ENSP00000340510:p.Gln1573Glu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	151	69	0.456954	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	972	0.44505494505494503	20	0.04065040650406504	166	0.4585635359116022	376	0.6573426573426573	410	0.5408970976253298	G	17.76	3.469610	0.63625	0.11675	0.552093	ENSG00000118898	ENST00000345988	T	0.45276	0.9	5.83	5.83	0.93111	.	0.066791	0.64402	D	0.000009	T	0.00012	0.0000	M	0.70595	2.14	0.09310	P	0.99999843917	D	0.64830	0.994	D	0.72338	0.977	T	0.27938	-1.0059	9	0.02654	T	1	.	20.1184	0.97949	0.0:0.0:1.0:0.0	rs2037912;rs52812562;rs2037912	1573	O60437	PEPL_HUMAN	E	1573	ENSP00000340510:Q1573E	ENSP00000340510:Q1573E	Q	-	1	0	PPL	4873940	1.000000	0.71417	0.998000	0.56505	0.919000	0.55068	9.428000	0.97476	2.769000	0.95229	0.655000	0.94253	CAA	G|0.581;C|0.419	0.419	strong		0.537	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
DDX60L	91351	hgsc.bcm.edu	37	4	169279364	169279364	+	Silent	SNP	C	C	T	rs11736382	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:169279364C>T	ENST00000511577.1	-	38	5302	c.5055G>A	c.(5053-5055)ttG>ttA	p.L1685L	DDX60L_ENST00000260184.7_Silent_p.L1685L			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1685							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AGGTTTGACTCAATTGTTTAA	0.299													C|||	109	0.0217652	0.0038	0.0346	5008	,	,		15501	0.0		0.0706	False		,,,				2504	0.0092				p.L1685L		Atlas-SNP	.											.	DDX60L	116	.	0			c.G5055A						PASS	.	C		43,3569		0,43,1763	121.0	113.0	115.0		5055	0.4	0.0	4	dbSNP_120	115	541,7617		17,507,3555	no	coding-synonymous	DDX60L	NM_001012967.1		17,550,5318	TT,TC,CC		6.6315,1.1905,4.9618		1685/1707	169279364	584,11186	1806	4079	5885	SO:0001819	synonymous_variant	91351	exon38			TTGACTCAATTGT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.5055G>A	4.37:g.169279364C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.960;T|0.040	0.040	strong		0.299	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
FUT3	2525	hgsc.bcm.edu	37	19	5844792	5844792	+	Missense_Mutation	SNP	A	A	C	rs28362459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5844792A>C	ENST00000303225.6	-	3	693	c.59T>G	c.(58-60)cTg>cGg	p.L20R	FUT3_ENST00000589918.1_Missense_Mutation_p.L20R|FUT3_ENST00000593144.1_5'Flank|AC024592.9_ENST00000589276.1_RNA|FUT3_ENST00000458379.2_Missense_Mutation_p.L20R|FUT3_ENST00000589620.1_Missense_Mutation_p.L20R	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	20			L -> R (in Le(-); dbSNP:rs28362459). {ECO:0000269|PubMed:8063716, ECO:0000269|PubMed:8219240, ECO:0000269|PubMed:8240337, ECO:0000269|PubMed:8801770, ECO:0000269|Ref.5}.		cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						CTGAAATAGCAGTGCGGCCAG	0.612													A|||	1266	0.252796	0.3374	0.2709	5008	,	,		15473	0.2956		0.0984	False		,,,				2504	0.2403				p.L20R	Esophageal Squamous(82;745 1728 24593 44831)	Atlas-SNP	.											FUT3,NS,carcinoma,0,1	FUT3	30	1	0			c.T59G	GRCh37	CM930258	FUT3	M	rs28362459	PASS	.	A	ARG/LEU,ARG/LEU,ARG/LEU,ARG/LEU	1244,3162	381.8+/-324.2	181,882,1140	28.0	26.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	59,59,59,59	2.3	0.0	19	dbSNP_125	27	846,7754	179.8+/-228.8	43,760,3497	yes	missense,missense,missense,missense	FUT3	NM_000149.3,NM_001097639.1,NM_001097640.1,NM_001097641.1	102,102,102,102	224,1642,4637	CC,CA,AA		9.8372,28.2342,16.0695	probably-damaging,probably-damaging,probably-damaging,probably-damaging	20/362,20/362,20/362,20/362	5844792	2090,10916	2203	4300	6503	SO:0001583	missense	2525	exon3			AATAGCAGTGCGG		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.59T>G	19.37:g.5844792A>C	ENSP00000305603:p.Leu20Arg	Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	457	0.20924908424908426	156	0.3170731707317073	79	0.21823204419889503	141	0.2465034965034965	81	0.10686015831134564	A	15.12	2.738382	0.49045	0.282342	0.098372	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.26810	1.71;1.71	2.33	2.33	0.28932	.	0.909833	0.09089	N	0.850153	T	0.00012	0.0000	M	0.79475	2.455	0.32237	P	0.573249	D;D;D;D	0.69078	0.997;0.997;0.997;0.997	D;D;D;D	0.70227	0.968;0.968;0.968;0.968	T	0.22034	-1.0228	9	0.29301	T	0.29	.	8.4913	0.33102	1.0:0.0:0.0:0.0	rs28362459;rs60711378	20;20;20;20	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	R	20	ENSP00000305603:L20R;ENSP00000416443:L20R	ENSP00000305603:L20R	L	-	2	0	FUT3	5795792	0.002000	0.14202	0.024000	0.17045	0.030000	0.12068	0.986000	0.29590	1.010000	0.39314	0.172000	0.16884	CTG	A|0.832;C|0.168	0.168	strong		0.612	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149	
SEZ6L	23544	hgsc.bcm.edu	37	22	26688838	26688838	+	Silent	SNP	C	C	T	rs17304075	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:26688838C>T	ENST00000248933.6	+	2	656	c.561C>T	c.(559-561)gaC>gaT	p.D187D	SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000360929.3_Silent_p.D187D|SEZ6L_ENST00000343706.4_Silent_p.D187D|SEZ6L_ENST00000529632.2_Silent_p.D187D|SEZ6L_ENST00000404234.3_Silent_p.D187D|SEZ6L_ENST00000402979.1_5'UTR			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	187					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TTTGGCTGGACCGAAAGGAGA	0.642													C|||	267	0.0533147	0.0083	0.0576	5008	,	,		17473	0.0		0.1362	False		,,,				2504	0.0808				p.D187D		Atlas-SNP	.											SEZ6L,NS,carcinoma,+2,1	SEZ6L	174	1	0			c.C561T						PASS	.	C	,,,,,	94,4312	75.7+/-113.9	1,92,2110	53.0	54.0	54.0		561,561,561,561,561,561	-6.2	0.0	22	dbSNP_123	54	1025,7575	213.6+/-253.5	53,919,3328	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	54,1011,5438	TT,TC,CC		11.9186,2.1335,8.6037	,,,,,	187/1024,187/1014,187/1012,187/950,187/949,187/1025	26688838	1119,11887	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon2			GCTGGACCGAAAG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.561C>T	22.37:g.26688838C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	28	0.368421	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			C|0.919;T|0.081	0.081	strong		0.642	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
SAMM50	25813	hgsc.bcm.edu	37	22	44379822	44379822	+	Silent	SNP	T	T	C	rs10452	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44379822T>C	ENST00000350028.4	+	12	1174	c.1017T>C	c.(1015-1017)ctT>ctC	p.L339L	SAMM50_ENST00000396202.3_Silent_p.L129L	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	339					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)				endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				GGTTTTACCTTGGGGGACCCA	0.552													C|||	3644	0.727636	0.7973	0.6254	5008	,	,		18591	0.8165		0.5984	False		,,,				2504	0.7474				p.L339L		Atlas-SNP	.											.	SAMM50	30	.	0			c.T1017C						PASS	.	C		3341,1065	387.9+/-326.7	1267,807,129	169.0	156.0	160.0		1017	-7.6	0.4	22	dbSNP_52	160	4864,3736	532.2+/-382.1	1374,2116,810	no	coding-synonymous	SAMM50	NM_015380.4		2641,2923,939	CC,CT,TT		43.4419,24.1716,36.9137		339/470	44379822	8205,4801	2203	4300	6503	SO:0001819	synonymous_variant	25813	exon12			TTACCTTGGGGGA	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.1017T>C	22.37:g.44379822T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	125	66	0.528	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Silent	SNP	ENST00000350028.4	37	CCDS14055.1																																																																																			T|0.352;C|0.648	0.648	strong		0.552	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
PARP3	10039	hgsc.bcm.edu	37	3	51978552	51978552	+	Silent	SNP	C	C	T	rs142065339	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:51978552C>T	ENST00000417220.2	+	5	947	c.459C>T	c.(457-459)atC>atT	p.I153I	PARP3_ENST00000431474.1_Silent_p.I153I|RRP9_ENST00000232888.6_5'Flank|PARP3_ENST00000398755.3_Silent_p.I160I			Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	153					DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|positive regulation of DNA ligation (GO:0051106)|protein ADP-ribosylation (GO:0006471)|protein localization to site of double-strand break (GO:1990166)|regulation of mitotic spindle organization (GO:0060236)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	catalytic activity (GO:0003824)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		ACACACTTATCGAAGTACAGG	0.542													C|||	9	0.00179712	0.0008	0.0014	5008	,	,		22157	0.0		0.007	False		,,,				2504	0.0				p.I160I		Atlas-SNP	.											PARP3_ENST00000398755,right_lower_lobe,carcinoma,+1,2	PARP3	90	2	0			c.C480T						PASS	.	C	,	7,4215		0,7,2104	112.0	129.0	123.0		480,459	-1.1	0.1	3	dbSNP_134	123	72,8390		0,72,4159	no	coding-synonymous,coding-synonymous	PARP3	NM_001003931.2,NM_005485.4	,	0,79,6263	TT,TC,CC		0.8509,0.1658,0.6228	,	160/541,153/534	51978552	79,12605	2111	4231	6342	SO:0001819	synonymous_variant	10039	exon4			ACTTATCGAAGTA	AF083068	CCDS43097.1, CCDS46839.1	3p22.2-p21.1	2010-07-14	2004-08-20	2004-08-26	ENSG00000041880	ENSG00000041880	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	273	protein-coding gene	gene with protein product	"""poly(ADP-ribose) synthetase-3"", ""NAD+ ADP-ribosyltransferase 3"", ""poly(ADP-ribose) polymerase 3"""	607726	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 3"""	ADPRTL3		10329013	Standard	NM_001003931		Approved	ADPRT3, IRT1, hPARP-3, pADPRT-3	uc003dbz.3	Q9Y6F1	OTTHUMG00000156931	ENST00000417220.2:c.459C>T	3.37:g.51978552C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001003931	Q8NER9|Q96CG2|Q9UG81	Silent	SNP	ENST00000417220.2	37	CCDS43097.1																																																																																			C|0.996;T|0.004	0.004	strong		0.542	PARP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348612.2	NM_005485.4	
APCDD1	147495	hgsc.bcm.edu	37	18	10487918	10487918	+	Silent	SNP	C	C	T	rs3185480	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:10487918C>T	ENST00000355285.5	+	5	1782	c.1428C>T	c.(1426-1428)ctC>ctT	p.L476L		NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CAGAGGACCTCGCAGAAGACA	0.647													C|||	2053	0.409944	0.205	0.4769	5008	,	,		14532	0.6181		0.4304	False		,,,				2504	0.4039				p.L476L		Atlas-SNP	.											.	APCDD1	57	.	0			c.C1428T						PASS	.	C		1073,3333	373.7+/-320.9	132,809,1262	62.0	63.0	63.0		1428	-3.8	0.0	18	dbSNP_105	63	3515,5085	490.0+/-372.7	713,2089,1498	no	coding-synonymous	APCDD1	NM_153000.4		845,2898,2760	TT,TC,CC		40.8721,24.3532,35.276		476/515	10487918	4588,8418	2203	4300	6503	SO:0001819	synonymous_variant	147495	exon5			GGACCTCGCAGAA	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1428C>T	18.37:g.10487918C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_153000		Silent	SNP	ENST00000355285.5	37	CCDS11849.1																																																																																			C|0.613;T|0.387	0.387	strong		0.647	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
TEX10	54881	hgsc.bcm.edu	37	9	103064530	103064530	+	Silent	SNP	G	G	A	rs7472	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:103064530G>A	ENST00000374902.4	-	15	2909	c.2733C>T	c.(2731-2733)ttC>ttT	p.F911F	TEX10_ENST00000477648.1_5'UTR|TEX10_ENST00000535814.1_Silent_p.F895F	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	911						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		TATACACGTTGAAGCAGTAAT	0.448													G|||	3140	0.626997	0.6188	0.611	5008	,	,		18565	0.8542		0.329	False		,,,				2504	0.7219				p.F911F		Atlas-SNP	.											.	TEX10	99	.	0			c.C2733T						PASS	.	G	,	2581,1825	638.1+/-396.9	750,1081,372	153.0	130.0	137.0		2685,2733	5.3	1.0	9	dbSNP_52	137	2933,5667	456.2+/-364.0	503,1927,1870	no	coding-synonymous,coding-synonymous	TEX10	NM_001161584.1,NM_017746.3	,	1253,3008,2242	AA,AG,GG		34.1047,41.4208,42.3958	,	895/914,911/930	103064530	5514,7492	2203	4300	6503	SO:0001819	synonymous_variant	54881	exon15			CACGTTGAAGCAG	AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"""testis expressed gene 10"", ""testis expressed sequence 10"""			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.2733C>T	9.37:g.103064530G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_017746	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Silent	SNP	ENST00000374902.4	37	CCDS6748.1																																																																																			G|0.502;A|0.498	0.498	strong		0.448	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746	
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 GAIIx	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	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	132	6	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	
LAIR1	3903	hgsc.bcm.edu	37	19	54867572	54867572	+	Silent	SNP	C	C	T	rs7257187	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54867572C>T	ENST00000391742.2	-	9	860	c.708G>A	c.(706-708)acG>acA	p.T236T	LAIR1_ENST00000391743.3_Silent_p.T218T|LAIR1_ENST00000434277.2_Silent_p.T235T|LAIR1_ENST00000313038.6_Silent_p.T229T|LAIR1_ENST00000474878.1_Silent_p.T218T|CTD-2587H19.1_ENST00000596234.1_lincRNA|LAIR1_ENST00000348231.4_Silent_p.T219T|LAIR1_ENST00000463489.1_5'Flank			Q6GTX8	LAIR1_HUMAN	leukocyte-associated immunoglobulin-like receptor 1	236					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(4)|prostate(1)|stomach(3)	26	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0573)		CCGAGGTGTCCGTCTCTCTGT	0.468													C|||	1172	0.234026	0.1006	0.2695	5008	,	,		17217	0.2808		0.3708	False		,,,				2504	0.2004				p.T236T		Atlas-SNP	.											.	LAIR1	44	.	0			c.G708A						PASS	.	C	,	579,3827		47,485,1671	131.0	127.0	128.0		708,657	0.4	0.0	19	dbSNP_116	128	3027,5573		543,1941,1816	no	coding-synonymous,coding-synonymous	LAIR1	NM_002287.3,NM_021706.2	,	590,2426,3487	TT,TC,CC		35.1977,13.1412,27.7257	,	236/288,219/271	54867572	3606,9400	2203	4300	6503	SO:0001819	synonymous_variant	3903	exon9			GGTGTCCGTCTCT	AF013249	CCDS12891.1, CCDS12892.1, CCDS74448.1, CCDS74449.1, CCDS74450.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167613	ENSG00000167613		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6477	protein-coding gene	gene with protein product		602992	"""leukocyte-associated Ig-like receptor 1"""			9285412	Standard	XM_005258924		Approved	CD305	uc002qfk.1	Q6GTX8	OTTHUMG00000065545	ENST00000391742.2:c.708G>A	19.37:g.54867572C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_002287		Silent	SNP	ENST00000391742.2	37	CCDS12891.1																																																																																			C|0.734;T|0.266	0.266	strong		0.468	LAIR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140506.1		
TF	7018	hgsc.bcm.edu	37	3	133474328	133474328	+	Silent	SNP	G	G	A	rs12769	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:133474328G>A	ENST00000402696.3	+	5	1109	c.624G>A	c.(622-624)tcG>tcA	p.S208S	TF_ENST00000264998.3_Silent_p.S81S|TFP1_ENST00000460564.1_RNA	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	208	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	TCGGCTACTCGGGAGCCTTCA	0.582													G|||	1559	0.311302	0.087	0.3775	5008	,	,		19938	0.4454		0.3211	False		,,,				2504	0.4192				p.S208S		Atlas-SNP	.											.	TF	116	.	0			c.G624A						PASS	.	G		592,3814	260.4+/-263.7	34,524,1645	77.0	66.0	70.0		624	-10.2	0.0	3	dbSNP_52	70	2787,5813	442.2+/-360.0	473,1841,1986	no	coding-synonymous	TF	NM_001063.3		507,2365,3631	AA,AG,GG		32.407,13.4362,25.9803		208/699	133474328	3379,9627	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon5			CTACTCGGGAGCC		CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.624G>A	3.37:g.133474328G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			G|0.727;A|0.273	0.273	strong		0.582	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
IL9R	3581	hgsc.bcm.edu	37	X	155239827	155239827	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:155239827A>G	ENST00000244174.5	+	9	1498	c.1319A>G	c.(1318-1320)aAc>aGc	p.N440S	IL9R_ENST00000540897.1_3'UTR|IL9R_ENST00000369423.2_3'UTR|IL9R_ENST00000424344.3_Missense_Mutation_p.N419S	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	440	Poly-Asn.				cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)	p.N440S(1)		NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					agcagcaacaacaacaACTAC	0.642													a|||	523	0.104433	0.0136	0.0605	5008	,	,		13185	0.0298		0.1471	False		,,,				2504	0.2914				p.N440S		Atlas-SNP	.											.	IL9R	73	.	1	Substitution - Missense(1)	kidney(1)	c.A1319G						PASS	.						7.0	13.0	11.0					X																	155239827		2072	4217	6289	SO:0001583	missense	3581	exon9			GCAACAACAACAA	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"""Pseudoautosomal regions / PAR2"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.1319A>G	X.37:g.155239827A>G	ENSP00000244174:p.Asn440Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	90	38	0.422222	NM_002186	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Missense_Mutation	SNP	ENST00000244174.5	37	CCDS14771.4	.	.	.	.	.	.	.	.	.	.	a	0	-2.858724	0.00065	.	.	ENSG00000124334	ENST00000244174;ENST00000424344	T;T	0.07908	3.16;3.15	.	.	.	.	12.144800	0.00166	N	0.000006	T	0.03827	0.0108	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33317	-0.9873	5	0.10636	T	0.68	.	.	.	.	.	440	Q01113	IL9R_HUMAN	S	440;419	ENSP00000244174:N440S;ENSP00000388918:N419S	ENSP00000244174:N440S	N	+	2	0	IL9R	154893021	0.004000	0.15560	0.007000	0.13788	0.007000	0.05969	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	AAC	.	.	weak		0.642	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186	
PSG5	5673	hgsc.bcm.edu	37	19	43680037	43680037	+	Missense_Mutation	SNP	T	T	A	rs1135901	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43680037T>A	ENST00000366175.3	-	3	824	c.694A>T	c.(694-696)Acc>Tcc	p.T232S	PSG5_ENST00000342951.6_Missense_Mutation_p.T232S|PSG5_ENST00000599812.1_Missense_Mutation_p.T325S|PSG5_ENST00000404580.1_Missense_Mutation_p.T232S|PSG5_ENST00000407356.1_Missense_Mutation_p.T232S|PSG5_ENST00000407568.1_Intron			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	232	Ig-like C2-type 1.			T -> S (in Ref. 2; AAA60205 and 3; AAA36514). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				ACATTCAGGGTGACTGGGTCA	0.493													T|||	621	0.124002	0.1687	0.1383	5008	,	,		19877	0.0		0.2614	False		,,,				2504	0.0399				p.T232S		Atlas-SNP	.											PSG5,colon,carcinoma,0,2	PSG5	58	2	0			c.A694T						PASS	.	T	SER/THR,SER/THR	850,3552	334.7+/-303.5	100,650,1451	142.0	139.0	140.0		694,694	-2.2	0.1	19	dbSNP_86	140	2225,6365	378.7+/-339.0	338,1549,2408	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	58,58	438,2199,3859	AA,AT,TT		25.9022,19.3094,23.6684	probably-damaging,probably-damaging	232/336,232/336	43680037	3075,9917	2201	4295	6496	SO:0001583	missense	5673	exon3			TCAGGGTGACTGG		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.694A>T	19.37:g.43680037T>A	ENSP00000382334:p.Thr232Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	331	0.15155677655677655	78	0.15853658536585366	51	0.1408839779005525	0	0.0	202	0.26649076517150394	t	11.12	1.544429	0.27563	0.193094	0.259022	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951;ENST00000404580	T;T;T;T	0.12774	2.65;2.65;2.65;2.65	1.08	-2.17	0.07059	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.79258	2.445	0.51012	P	9.700000000001374E-5	B;B	0.33739	0.272;0.422	B;P	0.45712	0.189;0.491	T	0.35500	-0.9786	8	0.45353	T	0.12	.	2.8794	0.05642	0.4002:0.0:0.0:0.5998	rs1135901;rs3179037;rs3198898	325;232	Q15228;Q15238	.;PSG5_HUMAN	S	232	ENSP00000382334:T232S;ENSP00000386008:T232S;ENSP00000344413:T232S;ENSP00000385250:T232S	ENSP00000344413:T232S	T	-	1	0	PSG5	48371877	0.004000	0.15560	0.075000	0.20258	0.024000	0.10985	-0.018000	0.12568	-0.711000	0.04995	0.155000	0.16302	ACC	T|0.792;A|0.208	0.208	strong		0.493	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
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 GAIIx	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	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	237	66	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	
PLXNC1	10154	hgsc.bcm.edu	37	12	94642023	94642023	+	Silent	SNP	C	C	T	rs2230756	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:94642023C>T	ENST00000258526.4	+	14	2862	c.2613C>T	c.(2611-2613)aaC>aaT	p.N871N		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	871					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						ACAACTTCAACATTTCCAAAA	0.343													C|||	277	0.0553115	0.0348	0.0461	5008	,	,		19648	0.0		0.1243	False		,,,				2504	0.0757				p.N871N		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C2613T						PASS	.	C		167,4239	105.2+/-143.6	7,153,2043	34.0	35.0	35.0		2613	5.0	1.0	12	dbSNP_98	35	948,7652	203.7+/-246.6	54,840,3406	no	coding-synonymous	PLXNC1	NM_005761.2		61,993,5449	TT,TC,CC		11.0233,3.7903,8.573		871/1569	94642023	1115,11891	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon14			CTTCAACATTTCC	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.2613C>T	12.37:g.94642023C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			C|0.932;T|0.068	0.068	strong		0.343	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
RTP5	285093	hgsc.bcm.edu	37	2	242814009	242814009	+	Missense_Mutation	SNP	G	G	A	rs7420371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242814009G>A	ENST00000343216.3	+	2	330	c.302G>A	c.(301-303)gGg>gAg	p.G101E		NM_173821.2	NP_776182.2																					CCCGCACCCGGGGACTGCCAG	0.716													G|||	1361	0.271765	0.1051	0.2925	5008	,	,		15254	0.1925		0.4384	False		,,,				2504	0.3926				p.G101E		Atlas-SNP	.											.	.	.	.	0			c.G302A						PASS	.	G	GLU/GLY	551,3197		64,423,1387	7.0	9.0	9.0		302	-0.6	0.0	2	dbSNP_116	9	3443,4677		801,1841,1418	no	missense	C2orf85	NM_173821.2	98	865,2264,2805	AA,AG,GG		42.4015,14.7012,33.6535	probably-damaging	101/573	242814009	3994,7874	1874	4060	5934	SO:0001583	missense	285093	exon2			CACCCGGGGACTG																												ENST00000343216.3:c.302G>A	2.37:g.242814009G>A	ENSP00000345374:p.Gly101Glu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	31	20	0.645161	NM_173821		Missense_Mutation	SNP	ENST00000343216.3	37	CCDS42843.1	589	0.2696886446886447	50	0.1016260162601626	112	0.30939226519337015	87	0.1520979020979021	340	0.44854881266490765	.	7.227	0.598459	0.13939	0.147012	0.424015	ENSG00000188011	ENST00000343216	T	0.19532	2.14	2.67	-0.573	0.11742	.	.	.	.	.	T	0.00012	0.0000	N	0.00313	-1.665	0.80722	P	0.0	D	0.89917	1.0	D	0.75020	0.985	T	0.17048	-1.0382	8	0.02654	T	1	.	5.7222	0.17992	0.0:0.4141:0.3743:0.2115	rs7420371	101	Q14D33	CB085_HUMAN	E	101	ENSP00000345374:G101E	ENSP00000345374:G101E	G	+	2	0	C2orf85	242462682	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.950000	0.03889	-0.117000	0.11872	-0.552000	0.04208	GGG	G|0.729;A|0.271	0.271	strong		0.716	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552921	43552921	+	Silent	SNP	C	C	T	rs12452273	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43552921C>T	ENST00000430334.3	-	4	601	c.468G>A	c.(466-468)cgG>cgA	p.R156R	PLEKHM1_ENST00000421073.2_Silent_p.R67R	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	156	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CCTCAGCATCCCGGAGCAGGG	0.602													C|||	412	0.0822684	0.0378	0.1556	5008	,	,		19188	0.001		0.1958	False		,,,				2504	0.0573				p.R156R		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.G468A						PASS	.	C		276,4128	141.9+/-177.2	10,256,1936	43.0	42.0	42.0		468	-4.5	0.2	17	dbSNP_120	42	1606,6992	272.0+/-289.9	155,1296,2848	no	coding-synonymous	PLEKHM1	NM_014798.2		165,1552,4784	TT,TC,CC		18.6788,6.267,14.4747		156/1057	43552921	1882,11120	2202	4299	6501	SO:0001819	synonymous_variant	9842	exon4			AGCATCCCGGAGC	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.468G>A	17.37:g.43552921C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			C|0.865;T|0.135	0.135	strong		0.602	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
ZSCAN20	7579	hgsc.bcm.edu	37	1	33957130	33957130	+	Silent	SNP	C	C	A	rs3795419	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:33957130C>A	ENST00000361328.3	+	6	1425	c.1272C>A	c.(1270-1272)gcC>gcA	p.A424A	ZSCAN20_ENST00000373413.2_Silent_p.A370A	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	424					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A424A(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(2)|pancreas(1)|stomach(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CAGGAGAGGCCGTGGCACTTC	0.612													C|||	974	0.194489	0.0204	0.2104	5008	,	,		17850	0.3651		0.162	False		,,,				2504	0.2761				p.A424A		Atlas-SNP	.											ZSCAN20,NS,carcinoma,0,1	ZSCAN20	107	1	1	Substitution - coding silent(1)	stomach(1)	c.C1272A						PASS	.	C		175,3689		2,171,1759	59.0	66.0	64.0		1272	-8.6	0.0	1	dbSNP_107	64	1422,6836		136,1150,2843	no	coding-synonymous	ZSCAN20	NM_145238.3		138,1321,4602	AA,AC,CC		17.2197,4.529,13.1744		424/1044	33957130	1597,10525	1932	4129	6061	SO:0001819	synonymous_variant	7579	exon6			AGAGGCCGTGGCA	X52360	CCDS41300.1	1p34.3	2013-01-08	2007-02-20	2007-02-20	ENSG00000121903	ENSG00000121903		"""-"", ""Zinc fingers, C2H2-type"""	13093	protein-coding gene	gene with protein product		611315	"""zinc finger protein 31 (KOX 29)"", ""zinc finger protein 31"""	ZNF360, ZNF31		2288909	Standard	NM_145238		Approved	KOX29	uc001bxj.4	P17040	OTTHUMG00000004173	ENST00000361328.3:c.1272C>A	1.37:g.33957130C>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	37	CCDS41300.1																																																																																			C|0.824;A|0.176	0.176	strong		0.612	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238	
CIT	11113	hgsc.bcm.edu	37	12	120148363	120148363	+	Silent	SNP	C	C	T	rs35490437	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:120148363C>T	ENST00000261833.7	-	37	4843	c.4791G>A	c.(4789-4791)acG>acA	p.T1597T	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Silent_p.T1639T	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1597	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				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)		TGAAGGGCAGCGTGCAGTTCA	0.498													T|||	135	0.0269569	0.0537	0.013	5008	,	,		21292	0.0238		0.0169	False		,,,				2504	0.0143				p.T1639T		Atlas-SNP	.											.	CIT	535	.	0			c.G4917A						PASS	.	T	,	229,4177	805.5+/-415.8	6,217,1980	183.0	163.0	169.0		4917,4791	-7.1	0.9	12	dbSNP_126	169	182,8418	811.3+/-407.1	0,182,4118	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	6,399,6098	TT,TC,CC		2.1163,5.1975,3.1601	,	1639/2070,1597/2028	120148363	411,12595	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon38			GGGCAGCGTGCAG	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.4791G>A	12.37:g.120148363C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	66	0.03021978021978022	30	0.06097560975609756	6	0.016574585635359115	16	0.027972027972027972	14	0.018469656992084433	T	9.253	1.041191	0.19669	0.051975	0.021163	ENSG00000122966	ENST00000392520	.	.	.	6.17	-7.05	0.01573	.	.	.	.	.	T	0.04998	0.0134	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35025	-0.9805	4	.	.	.	.	3.0135	0.06052	0.1076:0.3388:0.1832:0.3704	rs35490437	.	.	.	H	1210	.	.	R	-	2	0	CIT	118632746	0.018000	0.18449	0.864000	0.33941	0.991000	0.79684	-1.008000	0.03663	-1.016000	0.03371	-0.254000	0.11334	CGC	C|0.969;T|0.031	0.031	strong		0.498	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
GYPB	2994	hgsc.bcm.edu	37	4	144918712	144918712	+	Missense_Mutation	SNP	C	C	G	rs1132783	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:144918712C>G	ENST00000502664.1	-	4	302	c.251G>C	c.(250-252)aGt>aCt	p.S84T	GYPB_ENST00000283126.7_Missense_Mutation_p.S84T|GYPB_ENST00000510196.2_5'UTR|GYPB_ENST00000429670.2_Splice_Site|RP11-673E1.4_ENST00000506982.1_RNA|GYPB_ENST00000513128.1_Missense_Mutation_p.S51T	NM_002100.4	NP_002091	P06028	GLPB_HUMAN	glycophorin B (MNS blood group)	84			S -> T (in dbSNP:rs1132783). {ECO:0000269|PubMed:11239234, ECO:0000269|PubMed:2734312, ECO:0000269|PubMed:3477806}.			integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					TCGGCGAATACTGTAAGAAAT	0.358													C|||	882	0.176118	0.0666	0.1354	5008	,	,		16638	0.2054		0.1839	False		,,,				2504	0.3149				p.S84T		Atlas-SNP	.											.	GYPB	17	.	0			c.G251C						PASS	.	C	THR/SER	348,4036	162.5+/-194.5	32,284,1876	82.0	89.0	86.0		251	-4.2	0.0	4	dbSNP_86	86	1961,6639	340.1+/-323.5	234,1493,2573	yes	missense	GYPB	NM_002100.4	58	266,1777,4449	GG,GC,CC		22.8023,7.938,17.7834		84/92	144918712	2309,10675	2192	4300	6492	SO:0001583	missense	2994	exon4			CGAATACTGTAAG		CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"""CD molecules"", ""Blood group antigens"""	4703	protein-coding gene	gene with protein product		111740	"""glycophorin B (includes Ss blood group)"", ""glycophorin B (Ss blood group)"""	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000502664.1:c.251G>C	4.37:g.144918712C>G	ENSP00000427690:p.Ser84Thr	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	258	134	0.51938	NM_002100	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000502664.1	37	CCDS54809.1	343|343	0.15705128205128205|0.15705128205128205	35|35	0.07113821138211382|0.07113821138211382	48|48	0.13259668508287292|0.13259668508287292	116|116	0.20279720279720279|0.20279720279720279	144|144	0.18997361477572558|0.18997361477572558	C|C	0.744|0.744	-0.775236|-0.775236	0.02951|0.02951	0.07938|0.07938	0.228023|0.228023	ENSG00000250361|ENSG00000250361	ENST00000429670|ENST00000283126;ENST00000502664;ENST00000513128	.|T;T;T	.|0.14391	.|2.51;2.51;2.51	2.35|2.35	-4.16|-4.16	0.03869|0.03869	.|.	.|1.115970	.|0.06874	.|N	.|0.801295	.|T	.|0.00012	.|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.17852	.|0.024;0.024	.|B;B	.|0.14023	.|0.01;0.01	.|T	.|0.47328	.|-0.9126	.|8	.|0.14252	.|T	.|0.57	.|.	5.1875|5.1875	0.15191|0.15191	0.5316:0.2872:0.1813:0.0|0.5316:0.2872:0.1813:0.0	rs1132783;rs3193923;rs17418147|rs1132783;rs3193923;rs17418147	.|116;84	.|Q16336;E2QBW7	.|.;.	.|T	-1|84;84;51	.|ENSP00000283126:S84T;ENSP00000427690:S84T;ENSP00000425244:S51T	.|ENSP00000283126:S84T	.|S	-|-	.|2	.|0	GYPB|GYPB	145138162|145138162	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.043000|0.043000	0.13939|0.13939	-1.527000|-1.527000	0.02227|0.02227	-0.582000|-0.582000	0.05929|0.05929	0.184000|0.184000	0.17185|0.17185	.|AGT	C|0.822;G|0.178	0.178	strong		0.358	GYPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364791.1	NM_002100	
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 GAIIx	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	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	49	20	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	
MDFI	4188	hgsc.bcm.edu	37	6	41621271	41621271	+	Silent	SNP	G	G	A	rs2230088	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41621271G>A	ENST00000373050.4	+	4	703	c.516G>A	c.(514-516)ctG>ctA	p.L172L				Q99750	MDFI_HUMAN	MyoD family inhibitor	233	Cys-rich.				activation of JUN kinase activity (GO:0007257)|cytoplasmic sequestering of transcription factor (GO:0042994)|dorsal/ventral axis specification (GO:0009950)|embryo development (GO:0009790)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|prostate(2)|skin(1)|urinary_tract(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.121)		Colorectal(64;0.0123)|COAD - Colon adenocarcinoma(64;0.0264)|KIRC - Kidney renal clear cell carcinoma(1;0.138)			CGGACTGCCTGGAGATCTGCA	0.667													G|||	326	0.0650958	0.0098	0.098	5008	,	,		16244	0.004		0.1471	False		,,,				2504	0.0951				p.L233L		Atlas-SNP	.											.	MDFI	19	.	0			c.G699A						PASS	.	G		168,4238	111.2+/-149.4	4,160,2039	90.0	91.0	91.0		699	3.1	1.0	6	dbSNP_98	91	1428,7172	274.1+/-291.0	128,1172,3000	no	coding-synonymous	MDFI	NM_005586.3		132,1332,5039	AA,AG,GG		16.6047,3.813,12.2713		233/247	41621271	1596,11410	2203	4300	6503	SO:0001819	synonymous_variant	4188	exon5			CTGCCTGGAGATC	U78313	CCDS4857.1, CCDS75451.1	6p21	2008-08-29			ENSG00000112559	ENSG00000112559			6967	protein-coding gene	gene with protein product	"""inhibitor of MyoD family a"""	604971				9250874, 17289077	Standard	NM_005586		Approved	I-mfa	uc003oqq.4	Q99750	OTTHUMG00000014681	ENST00000373050.4:c.516G>A	6.37:g.41621271G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	36	7	0.194444	NM_005586		Silent	SNP	ENST00000373050.4	37																																																																																				G|0.892;A|0.108	0.108	strong		0.667	MDFI-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000040519.2	NM_005586	
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 GAIIx	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|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Missense_Mutation_p.E592K	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	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	100	15	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 GAIIx	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	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	11	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	
PRC1	9055	hgsc.bcm.edu	37	15	91513674	91513674	+	Missense_Mutation	SNP	T	T	C	rs12911192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:91513674T>C	ENST00000361188.5	-	12	2743	c.1532A>G	c.(1531-1533)tAc>tGc	p.Y511C	PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000442656.2_Missense_Mutation_p.Y470C|PRC1_ENST00000361919.3_Missense_Mutation_p.Y511C|PRC1_ENST00000394249.3_Missense_Mutation_p.Y511C|PRC1-AS1_ENST00000556200.1_RNA					protein regulator of cytokinesis 1											endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					GGGGGAGTGGTAGACTGTCCC	0.537													T|||	265	0.0529153	0.0038	0.0317	5008	,	,		21738	0.002		0.0746	False		,,,				2504	0.1646				p.Y511C		Atlas-SNP	.											.	PRC1	51	.	0			c.A1532G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	67,4329	61.7+/-98.7	0,67,2131	295.0	225.0	249.0		1532,1532,1532	-1.8	0.4	15	dbSNP_121	249	632,7964	164.6+/-216.9	22,588,3688	yes	missense,missense,missense	PRC1	NM_003981.2,NM_199413.1,NM_199414.1	194,194,194	22,655,5819	CC,CT,TT		7.3523,1.5241,5.3802	benign,benign,benign	511/621,511/607,511/567	91513674	699,12293	2198	4298	6496	SO:0001583	missense	9055	exon12			GAGTGGTAGACTG	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"""anaphase spindle elongation 1 homolog (S. cerevisiae)"""	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.1532A>G	15.37:g.91513674T>C	ENSP00000354679:p.Tyr511Cys	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_199413		Missense_Mutation	SNP	ENST00000361188.5	37	CCDS45352.1	74	0.03388278388278388	4	0.008130081300813009	12	0.03314917127071823	0	0.0	58	0.07651715039577836	T	7.540	0.660401	0.14645	0.015241	0.073523	ENSG00000198901	ENST00000394249;ENST00000361919;ENST00000361188;ENST00000555455;ENST00000442656	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	6.05	-1.79	0.07932	.	0.507032	0.24154	N	0.041050	T	0.00580	0.0019	N	0.05124	-0.11	0.31816	N	0.626667	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.11329	0.003;0.002;0.002;0.006	T	0.12041	-1.0563	10	0.36615	T	0.2	.	6.8145	0.23822	0.144:0.4969:0.0:0.3591	rs12911192;rs52793325;rs61491082;rs12911192	470;511;481;511	O43663-3;F8W9B5;O43663-2;O43663	.;.;.;PRC1_HUMAN	C	511;511;511;114;470	ENSP00000377793:Y511C;ENSP00000354618:Y511C;ENSP00000354679:Y511C;ENSP00000409549:Y470C	ENSP00000354679:Y511C	Y	-	2	0	PRC1	89314678	0.998000	0.40836	0.353000	0.25747	0.007000	0.05969	0.334000	0.19787	-0.318000	0.08665	-0.263000	0.10527	TAC	T|0.954;C|0.046	0.046	strong		0.537	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981	
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 GAIIx	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	84	49	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 GAIIx	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_ENST00000545409.1_Missense_Mutation_p.S271L|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Missense_Mutation_p.S400L	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	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	116	107	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		
SH2D4B	387694	hgsc.bcm.edu	37	10	82331292	82331292	+	Silent	SNP	G	G	A	rs72805712	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:82331292G>A	ENST00000470604.2	+	3	450	c.450G>A	c.(448-450)aaG>aaA	p.K150K	SH2D4B_ENST00000339284.2_Silent_p.K151K|SH2D4B_ENST00000313455.4_Silent_p.K102K			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	150	Glu-rich.									endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			AAGACCGCAAGGCTGCCAAAG	0.587													G|||	470	0.0938498	0.1785	0.0879	5008	,	,		15438	0.004		0.1203	False		,,,				2504	0.0491				p.K151K		Atlas-SNP	.											.	SH2D4B	44	.	0			c.G453A						PASS	.	G	,	748,3658	306.0+/-289.3	56,636,1511	77.0	73.0	74.0		306,453	5.6	1.0	10	dbSNP_130	74	1146,7454	235.1+/-267.8	77,992,3231	no	coding-synonymous,coding-synonymous	SH2D4B	NM_001145719.1,NM_207372.2	,	133,1628,4742	AA,AG,GG		13.3256,16.9768,14.5625	,	102/310,151/358	82331292	1894,11112	2203	4300	6503	SO:0001819	synonymous_variant	387694	exon3			CCGCAAGGCTGCC		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"""SH2 domain containing"""	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.450G>A	10.37:g.82331292G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Silent	SNP	ENST00000470604.2	37																																																																																				G|0.869;A|0.131	0.131	strong		0.587	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
CEP192	55125	hgsc.bcm.edu	37	18	13095609	13095609	+	Missense_Mutation	SNP	T	T	C	rs474337	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:13095609T>C	ENST00000325971.8	+	33	6167	c.4574T>C	c.(4573-4575)cTg>cCg	p.L1525P	CEP192_ENST00000506447.1_Missense_Mutation_p.L2121P|CEP192_ENST00000430049.2_Missense_Mutation_p.L1646P|CEP192_ENST00000540847.2_3'UTR			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1525			L -> P (in dbSNP:rs474337). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12693554, ECO:0000269|PubMed:14702039}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CGCCCGCCTCTGGATCAGCTG	0.557													C|||	3856	0.769968	0.9486	0.6455	5008	,	,		15198	0.8105		0.6193	False		,,,				2504	0.7301				p.L2121P		Atlas-SNP	.											.	CEP192	340	.	0			c.T6362C						PASS	.	C	PRO/LEU	3887,519	236.5+/-248.6	1714,459,30	78.0	78.0	78.0		6362	3.4	0.0	18	dbSNP_83	78	5330,3270	490.1+/-372.8	1665,2000,635	yes	missense	CEP192	NM_032142.3	98	3379,2459,665	CC,CT,TT		38.0233,11.7794,29.1327	benign	2121/2538	13095609	9217,3789	2203	4300	6503	SO:0001583	missense	55125	exon35			CGCCTCTGGATCA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.4574T>C	18.37:g.13095609T>C	ENSP00000317156:p.Leu1525Pro	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1634	0.7481684981684982	461	0.9369918699186992	238	0.6574585635359116	464	0.8111888111888111	471	0.6213720316622692	C	11.01	1.512281	0.27036	0.882206	0.619767	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	T;T;T	0.28895	1.59;1.59;1.59	5.91	3.43	0.39272	.	0.361134	0.29034	N	0.013343	T	0.00012	0.0000	N	0.03608	-0.345	0.40733	P	0.017239000000000004	B;B;B;B	0.10296	0.0;0.003;0.0;0.0	B;B;B;B	0.08055	0.0;0.003;0.0;0.0	T	0.18903	-1.0322	9	0.29301	T	0.29	-0.5414	8.7751	0.34756	0.6244:0.2595:0.0:0.116	rs474337;rs1786266;rs17603435;rs58740087;rs474337	1646;2121;125;723	C9JT09;E9PF99;F5GZ47;Q9HCK3	.;.;.;.	P	2121;1525;1525;1646;125	ENSP00000427550:L2121P;ENSP00000317156:L1525P;ENSP00000389190:L1646P	ENSP00000317156:L1525P	L	+	2	0	CEP192	13085609	0.013000	0.17824	0.039000	0.18376	0.002000	0.02628	1.599000	0.36751	0.506000	0.28125	-1.068000	0.02270	CTG	T|0.259;C|0.741	0.741	strong		0.557	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
HGD	3081	hgsc.bcm.edu	37	3	120369683	120369683	+	Silent	SNP	G	G	A	rs140977117	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:120369683G>A	ENST00000283871.5	-	6	831	c.372C>T	c.(370-372)gaC>gaT	p.D124D	HGD_ENST00000488183.1_5'Flank	NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	124					cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		TAGACTTTATGTCTCCAGCTC	0.517													G|||	48	0.00958466	0.0015	0.0072	5008	,	,		20552	0.001		0.0278	False		,,,				2504	0.0123				p.D124D		Atlas-SNP	.											HGD,NS,carcinoma,0,1	HGD	65	1	0			c.C372T						PASS	.	G		21,4385	29.0+/-57.7	1,19,2183	176.0	158.0	164.0		372	3.3	1.0	3	dbSNP_134	164	229,8363	94.0+/-155.9	1,227,4068	no	coding-synonymous	HGD	NM_000187.3		2,246,6251	AA,AG,GG		2.6653,0.4766,1.9234		124/446	120369683	250,12748	2203	4296	6499	SO:0001819	synonymous_variant	3081	exon6			CTTTATGTCTCCA		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"""homogentisate oxidase"""	607474	"""homogentisate 1,2-dioxygenase (homogentisate oxidase)"""	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.372C>T	3.37:g.120369683G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	110	62	0.563636	NM_000187	A8K417|B2R8Z0	Silent	SNP	ENST00000283871.5	37	CCDS3000.1																																																																																			G|0.985;A|0.015	0.015	strong		0.517	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1		
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 GAIIx	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	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	28	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	
GPR112	139378	hgsc.bcm.edu	37	X	135430044	135430044	+	Silent	SNP	T	T	C	rs877761	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135430044T>C	ENST00000394143.1	+	6	4470	c.4179T>C	c.(4177-4179)acT>acC	p.T1393T	GPR112_ENST00000394141.1_Silent_p.T1188T|GPR112_ENST00000370652.1_Silent_p.T1393T|GPR112_ENST00000287534.4_Silent_p.T1330T|GPR112_ENST00000412101.1_Silent_p.T1188T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1393					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(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CTCCCAGGACTGTGGAAATGA	0.448													c|||	2014	0.53351	0.5983	0.3847	3775	,	,		16408	0.255		0.3817	False		,,,				2504	0.3221				p.T1393T		Atlas-SNP	.											.	GPR112	459	.	0			c.T4179C						PASS	.			2878,957		910,628,430,94,141	170.0	160.0	163.0		4179	-1.4	0.0	X	dbSNP_86	163	3231,3497		571,1175,914,682,958	no	coding-synonymous	GPR112	NM_153834.3		1481,1803,1344,776,1099	CC,CT,C,TT,T		48.0232,24.9544,42.1661		1393/3081	135430044	6109,4454	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			CAGGACTGTGGAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4179T>C	X.37:g.135430044T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	114	75	0.657895	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			T|0.432;0|0.003	.	strong		0.448	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
GID4	79018	hgsc.bcm.edu	37	17	17948475	17948475	+	Silent	SNP	G	G	A	rs2955355	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:17948475G>A	ENST00000268719.4	+	2	626	c.453G>A	c.(451-453)ggG>ggA	p.G151G	GID4_ENST00000376345.3_Silent_p.G151G	NM_024052.4	NP_076957.3	Q8IVV7	GID4_HUMAN	GID complex subunit 4	151																	TGGACACGGGGAACTCTTACC	0.478													G|||	1833	0.366014	0.4327	0.4625	5008	,	,		21071	0.0952		0.6233	False		,,,				2504	0.2219				p.G151G		Atlas-SNP	.											C17orf39,right_upper_lobe,carcinoma,+2,1	.	.	1	0			c.G453A						PASS	.	G		2041,2365	566.4+/-381.9	456,1129,618	161.0	136.0	144.0		453	1.9	1.0	17	dbSNP_101	144	5727,2873	672.8+/-403.0	1903,1921,476	no	coding-synonymous	C17orf39	NM_024052.4		2359,3050,1094	AA,AG,GG		33.407,46.3232,40.2737		151/301	17948475	7768,5238	2203	4300	6503	SO:0001819	synonymous_variant	79018	exon2			CACGGGGAACTCT	AK127580	CCDS11190.1	17p11.2	2013-07-31	2013-07-31	2012-07-20	ENSG00000141034	ENSG00000141034			28453	protein-coding gene	gene with protein product	"""vacuolar import and degradation 24"""		"""chromosome 17 open reading frame 39"", ""GID complex subunit 4, VID24 homolog (S. cerevisiae)"""	C17orf39		11997338	Standard	NM_024052		Approved	VID24	uc002gsg.1	Q8IVV7	OTTHUMG00000059398	ENST00000268719.4:c.453G>A	17.37:g.17948475G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_024052	Q8TEB5|Q9BW50	Silent	SNP	ENST00000268719.4	37	CCDS11190.1																																																																																			G|0.483;A|0.517	0.517	strong		0.478	GID4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132071.2	NM_024052	
PSG5	5673	hgsc.bcm.edu	37	19	43679410	43679410	+	Silent	SNP	A	A	G	rs1058467	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43679410A>G	ENST00000366175.3	-	4	1051	c.921T>C	c.(919-921)gcT>gcC	p.A307A	PSG5_ENST00000342951.6_Silent_p.A307A|PSG5_ENST00000599812.1_Silent_p.A400A|PSG5_ENST00000404580.1_Silent_p.A307A|PSG5_ENST00000407356.1_Silent_p.A307A|PSG5_ENST00000407568.1_Intron			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	307	Ig-like C2-type 2.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				CCTTGCCAGTAGCTGAGTTAC	0.453													G|||	3840	0.766773	0.8396	0.5836	5008	,	,		18569	0.9851		0.6133	False		,,,				2504	0.7311				p.A307A		Atlas-SNP	.											.	PSG5	58	.	0			c.T921C						PASS	.	G	,	3467,937		1434,599,169	120.0	147.0	138.0		921,921	1.2	0.0	19	dbSNP_86	138	5075,3515		1606,1863,826	no	coding-synonymous,coding-synonymous	PSG5	NM_001130014.1,NM_002781.3	,	3040,2462,995	GG,GA,AA		40.9197,21.2761,34.262	,	307/336,307/336	43679410	8542,4452	2202	4295	6497	SO:0001819	synonymous_variant	5673	exon4			GCCAGTAGCTGAG		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.921T>C	19.37:g.43679410A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_002781	Q15239|Q96QJ1|Q9UQ75	Silent	SNP	ENST00000366175.3	37	CCDS12617.1																																																																																			A|0.331;G|0.669	0.669	strong		0.453	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
SLC2A2	6514	hgsc.bcm.edu	37	3	170724955	170724955	+	Silent	SNP	C	C	T	rs5404	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:170724955C>T	ENST00000314251.3	-	5	673	c.594G>A	c.(592-594)acG>acA	p.T198T	SLC2A2_ENST00000382808.4_Silent_p.T79T	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	198					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TAAGAATGCCCGTGACGATGG	0.488													C|||	759	0.151558	0.3086	0.1254	5008	,	,		19830	0.0159		0.1103	False		,,,				2504	0.1401				p.T198T		Atlas-SNP	.											.	SLC2A2	71	.	0			c.G594A	GRCh37	CM052367	SLC2A2	M	rs5404	PASS	.	C		1242,3164	426.6+/-341.2	174,894,1135	104.0	93.0	97.0		594	-11.5	0.0	3	dbSNP_52	97	874,7726	196.8+/-241.6	42,790,3468	no	coding-synonymous	SLC2A2	NM_000340.1		216,1684,4603	TT,TC,CC		10.1628,28.1888,16.2694		198/525	170724955	2116,10890	2203	4300	6503	SO:0001819	synonymous_variant	6514	exon5			AATGCCCGTGACG	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.594G>A	3.37:g.170724955C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	89	28	0.314607	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	37	CCDS3215.1																																																																																			C|0.847;T|0.153	0.153	strong		0.488	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
ZNF669	79862	hgsc.bcm.edu	37	1	247267274	247267274	+	Missense_Mutation	SNP	C	C	A	rs4925692	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247267274C>A	ENST00000343381.6	-	1	400	c.228G>T	c.(226-228)gaG>gaT	p.E76D	ZNF669_ENST00000448299.2_Intron|ZNF669_ENST00000366500.1_Intron|ZNF669_ENST00000358785.4_Missense_Mutation_p.E76D|ZNF669_ENST00000366501.1_Intron	NM_024804.2	NP_079080.2	Q96BR6	ZN669_HUMAN	zinc finger protein 669	76			E -> D (in dbSNP:rs4925692). {ECO:0000269|PubMed:15489334}.		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(3)|kidney(4)|large_intestine(2)|lung(6)	17	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			CCCGACAGGGCTCCGGCCGGC	0.711													C|||	1260	0.251597	0.1172	0.2925	5008	,	,		12776	0.123		0.332	False		,,,				2504	0.454				p.E76D		Atlas-SNP	.											.	ZNF669	46	.	0			c.G228T						PASS	.	C	,ASP/GLU	605,3555		61,483,1536	7.0	10.0	9.0		,228	0.3	0.1	1	dbSNP_111	9	2506,5700		406,1694,2003	yes	intron,missense	ZNF669	NM_001142572.1,NM_024804.2	,45	467,2177,3539	AA,AC,CC		30.5386,14.5433,25.1577	,benign	,76/465	247267274	3111,9255	2080	4103	6183	SO:0001583	missense	79862	exon1			ACAGGGCTCCGGC		CCDS31088.1, CCDS44345.1	1q44	2013-01-08			ENSG00000188295	ENSG00000188295		"""Zinc fingers, C2H2-type"", ""-"""	25736	protein-coding gene	gene with protein product						12477932	Standard	NM_024804		Approved	FLJ12606	uc001ice.2	Q96BR6	OTTHUMG00000040869	ENST00000343381.6:c.228G>T	1.37:g.247267274C>A	ENSP00000342818:p.Glu76Asp	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	30	9	0.3	NM_024804	B3KP94|Q5VT39|Q9H9Q6	Missense_Mutation	SNP	ENST00000343381.6	37	CCDS31088.1	484	0.2216117216117216	58	0.11788617886178862	109	0.3011049723756906	69	0.12062937062937062	248	0.32717678100263853	C	15.19	2.758708	0.49468	0.145433	0.305386	ENSG00000188295	ENST00000358785;ENST00000343381;ENST00000476158	T;T;T	0.05925	4.79;3.37;4.75	0.342	0.342	0.15996	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.47511	P	5.560000000000009E-4	P	0.46578	0.88	P	0.50270	0.636	T	0.44174	-0.9345	8	0.17832	T	0.49	.	2.7626	0.05311	0.0:0.5869:0.0:0.4131	rs4925692;rs17855457;rs4925692	76	Q96BR6	ZN669_HUMAN	D	76	ENSP00000351636:E76D;ENSP00000342818:E76D;ENSP00000429550:E76D	ENSP00000342818:E76D	E	-	3	2	ZNF669	245333897	0.005000	0.15991	0.066000	0.19879	0.068000	0.16541	-1.229000	0.02945	0.392000	0.25172	0.397000	0.26171	GAG	C|0.780;A|0.220	0.220	strong		0.711	ZNF669-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000098394.4	NM_024804	
PIK3R2	5296	hgsc.bcm.edu	37	19	18273013	18273013	+	Splice_Site	SNP	G	G	A	rs28730848	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:18273013G>A	ENST00000593731.1	+	8	1463	c.903G>A	c.(901-903)gcG>gcA	p.A301A	PIK3R2_ENST00000222254.8_Splice_Site_p.A301A			O00459	P85B_HUMAN	phosphoinositide-3-kinase, regulatory subunit 2 (beta)	301					blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	phosphatidylinositol 3-kinase regulator activity (GO:0035014)|receptor tyrosine kinase binding (GO:0030971)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(3)|pancreas(1)|stomach(1)	24					Isoprenaline(DB01064)	GTCCCCCAGCGCTGCCGCCTA	0.627													g|||	129	0.0257588	0.0038	0.0331	5008	,	,		17055	0.0		0.0437	False		,,,				2504	0.0583				p.A301A		Atlas-SNP	.											.	PIK3R2	48	.	0			c.G903A						PASS	.	G		42,4360	42.3+/-75.8	0,42,2159	25.0	25.0	25.0		903	-8.3	0.9	19	dbSNP_125	25	508,8088	137.8+/-194.7	16,476,3806	yes	coding-synonymous-near-splice	PIK3R2	NM_005027.2		16,518,5965	AA,AG,GG		5.9097,0.9541,4.2314		301/729	18273013	550,12448	2201	4298	6499	SO:0001630	splice_region_variant	5296	exon8			CCCAGCGCTGCCG		CCDS12371.1	19p13.11	2013-03-28	2008-02-04		ENSG00000105647	ENSG00000105647		"""SH2 domain containing"""	8980	protein-coding gene	gene with protein product		603157				1314371	Standard	NM_005027		Approved	P85B, p85	uc002nia.2	O00459	OTTHUMG00000183383	ENST00000593731.1:c.902-1G>A	19.37:g.18273013G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_005027	Q5EAT5|Q9UPH9	Silent	SNP	ENST00000593731.1	37	CCDS12371.1																																																																																			G|0.964;A|0.036	0.036	strong		0.627	PIK3R2-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000466386.2	NM_005027	Silent
FCGRT	2217	hgsc.bcm.edu	37	19	50017724	50017724	+	Silent	SNP	C	C	T	rs2878342	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50017724C>T	ENST00000221466.5	+	4	1068	c.582C>T	c.(580-582)cgC>cgT	p.R194R	FCGRT_ENST00000599988.1_Intron|FCGRT_ENST00000596975.1_Intron|FCGRT_ENST00000426395.3_Silent_p.R194R|FCGRT_ENST00000594823.1_3'UTR	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	194	Alpha-2.				antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		AGAGGGGCCGCGGAAACCTGG	0.662													C|||	735	0.146765	0.348	0.1023	5008	,	,		14689	0.0238		0.0855	False		,,,				2504	0.0961				p.R194R		Atlas-SNP	.											FCGRT,NS,carcinoma,0,1	FCGRT	23	1	0			c.C582T						PASS	.	C	,	1477,2929		246,985,972	19.0	22.0	21.0		582,582	-8.6	0.0	19	dbSNP_101	21	718,7874		30,658,3608	no	coding-synonymous,coding-synonymous	FCGRT	NM_001136019.2,NM_004107.4	,	276,1643,4580	TT,TC,CC		8.3566,33.5225,16.8872	,	194/366,194/366	50017724	2195,10803	2203	4296	6499	SO:0001819	synonymous_variant	2217	exon4			GGGCCGCGGAAAC	U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"""Immunoglobulin superfamily / C1-set domain containing"""	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.582C>T	19.37:g.50017724C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_001136019	Q5HYM5|Q9HBV7|Q9NZ19	Silent	SNP	ENST00000221466.5	37	CCDS12770.1	277	0.12683150183150182	165	0.3353658536585366	37	0.10220994475138122	17	0.02972027972027972	58	0.07651715039577836	C	5.219	0.225948	0.09916	0.335225	0.083566	ENSG00000104870	ENST00000415900	.	.	.	4.3	-8.6	0.00889	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.40526	P	0.01911099999999999	.	.	.	.	.	.	T	0.18461	-1.0336	4	0.87932	D	0	.	3.8572	0.08981	0.231:0.5127:0.1636:0.0928	rs2878342;rs2878342	.	.	.	V	140	.	ENSP00000391574:A140V	A	+	2	0	FCGRT	54709536	0.000000	0.05858	0.000000	0.03702	0.689000	0.40095	-4.406000	0.00239	-4.568000	0.00042	-1.203000	0.01651	GCG	C|0.846;T|0.154	0.154	strong		0.662	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1		
CYP11B1	1584	hgsc.bcm.edu	37	8	143960597	143960597	+	Silent	SNP	G	G	A	rs5283	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143960597G>A	ENST00000292427.4	-	2	278	c.246C>T	c.(244-246)gaC>gaT	p.D82D	CYP11B1_ENST00000517471.1_Silent_p.D82D|CYP11B1_ENST00000377675.3_Silent_p.D127D	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	82					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CTCCTCCCAAGTCGTACCTGT	0.632									Familial Hyperaldosteronism type I				.|||	1516	0.302716	0.0356	0.4582	5008	,	,		19293	0.3115		0.4602	False		,,,				2504	0.3824				p.D82D		Atlas-SNP	.											.	CYP11B1	128	.	0			c.C246T						PASS	.	G	,	492,3914	228.1+/-243.1	37,418,1748	141.0	112.0	122.0		246,246	-2.1	0.0	8	dbSNP_52	122	3778,4822	536.4+/-383.0	822,2134,1344	no	coding-synonymous,coding-synonymous	CYP11B1	NM_000497.3,NM_001026213.1	,	859,2552,3092	AA,AG,GG		43.9302,11.1666,32.831	,	82/504,82/438	143960597	4270,8736	2203	4300	6503	SO:0001819	synonymous_variant	1584	exon2	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TCCCAAGTCGTAC	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.246C>T	8.37:g.143960597G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			G|0.668;A|0.332	0.332	strong		0.632	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248924	48248924	+	Silent	SNP	G	G	A	rs3181870	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48248924G>A	ENST00000246802.5	+	1	146	c.108G>A	c.(106-108)cgG>cgA	p.R36R	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	36						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CGCTGAGGCGGCGGCGGCGAG	0.667													G|||	61	0.0121805	0.0008	0.0216	5008	,	,		9559	0.0		0.0338	False		,,,				2504	0.0112				p.R36R	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.G108A						PASS	.	G		13,4393		0,13,2190	35.0	43.0	40.0		108	4.6	1.0	19	dbSNP_105	40	182,8414		5,172,4121	no	coding-synonymous	GLTSCR2	NM_015710.4		5,185,6311	AA,AG,GG		2.1173,0.2951,1.4998		36/479	48248924	195,12807	2203	4298	6501	SO:0001819	synonymous_variant	29997	exon1			GAGGCGGCGGCGG	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.108G>A	19.37:g.48248924G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	136	75	0.551471	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			G|0.981;A|0.019	0.019	strong		0.667	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
CPZ	8532	hgsc.bcm.edu	37	4	8605818	8605818	+	Silent	SNP	C	C	T	rs6852001	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:8605818C>T	ENST00000360986.4	+	4	786	c.612C>T	c.(610-612)tgC>tgT	p.C204C	CPZ_ENST00000382480.2_Silent_p.C67C|CPZ_ENST00000315782.6_Silent_p.C193C|CPZ_ENST00000429646.2_5'UTR	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	204					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						CCTCCCGCTGCGCCCACGTGG	0.692													C|||	807	0.161142	0.0204	0.1988	5008	,	,		16720	0.2976		0.2465	False		,,,				2504	0.0961				p.C204C		Atlas-SNP	.											CPZ,NS,carcinoma,0,1	CPZ	95	1	0			c.C612T						PASS	.	C	,,	237,4125		10,217,1954	19.0	16.0	17.0		612,201,579	1.0	1.0	4	dbSNP_116	17	2178,6368		284,1610,2379	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	294,1827,4333	TT,TC,CC		25.4856,5.4333,18.7093	,,	204/653,67/516,193/642	8605818	2415,10493	2181	4273	6454	SO:0001819	synonymous_variant	8532	exon4			CCGCTGCGCCCAC	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"""metallocarboxypeptidase Z"""	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.612C>T	4.37:g.8605818C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			C|0.812;T|0.188	0.188	strong		0.692	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
WDR44	54521	hgsc.bcm.edu	37	X	117566782	117566782	+	Silent	SNP	C	C	T	rs10521584	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:117566782C>T	ENST00000254029.3	+	13	2171	c.1776C>T	c.(1774-1776)aaC>aaT	p.N592N	WDR44_ENST00000371822.5_Silent_p.N567N|WDR44_ENST00000371825.3_Silent_p.N592N	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	592						endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						ATGATAAAAACGCACCCTTTC	0.353													C|||	615	0.162914	0.0772	0.2464	3775	,	,		15880	0.127		0.0974	False		,,,				2504	0.1186				p.N592N		Atlas-SNP	.											.	WDR44	188	.	0			c.C1776T						PASS	.	C	,,	420,3415		20,317,63,1295,508	171.0	153.0	159.0		1776,1701,1776	-1.6	1.0	X	dbSNP_119	159	865,5863		31,546,257,1851,1615	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR44	NM_001184965.1,NM_001184966.1,NM_019045.4	,,	51,863,320,3146,2123	TT,TC,T,CC,C		12.8567,10.9518,12.1651	,,	592/906,567/825,592/914	117566782	1285,9278	2203	4300	6503	SO:0001819	synonymous_variant	54521	exon13			TAAAAACGCACCC	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"""WD repeat domain containing"""	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.1776C>T	X.37:g.117566782C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	193	133	0.689119	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Silent	SNP	ENST00000254029.3	37	CCDS14572.1	283	0.17058468957203135	31	0.06595744680851064	58	0.1870967741935484	49	0.09645669291338582	58	0.08033240997229917	C	8.285	0.816421	0.16607	0.109518	0.128567	ENSG00000131725	ENST00000371848	.	.	.	5.44	-1.56	0.08532	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999999999281	.	.	.	.	.	.	T	0.19582	-1.0301	3	.	.	.	-3.5768	10.8482	0.46754	0.0:0.4423:0.0:0.5577	rs10521584;rs10521584	.	.	.	C	492	.	.	R	+	1	0	WDR44	117450810	0.571000	0.26659	0.995000	0.50966	0.948000	0.59901	-0.271000	0.08572	-0.315000	0.08703	-1.366000	0.01203	CGC	C|0.842;0|0.014	.	strong		0.353	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045	
IKBKAP	8518	hgsc.bcm.edu	37	9	111663793	111663793	+	Silent	SNP	C	C	T	rs10979605	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:111663793C>T	ENST00000374647.5	-	18	2233	c.1926G>A	c.(1924-1926)acG>acA	p.T642T	IKBKAP_ENST00000537196.1_Silent_p.T293T	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	642					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CTGCAAATGACGTGATATTTG	0.418													C|||	396	0.0790735	0.1755	0.0346	5008	,	,		19704	0.0		0.0915	False		,,,				2504	0.0491				p.T642T		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G1926A						PASS	.	C		654,3752	279.9+/-275.1	53,548,1602	129.0	109.0	116.0		1926	-6.5	0.9	9	dbSNP_120	116	702,7898	173.9+/-224.3	30,642,3628	no	coding-synonymous	IKBKAP	NM_003640.3		83,1190,5230	TT,TC,CC		8.1628,14.8434,10.426		642/1333	111663793	1356,11650	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon18			AAATGACGTGATA	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.1926G>A	9.37:g.111663793C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			C|0.909;T|0.091	0.091	strong		0.418	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
ERBB3	2065	hgsc.bcm.edu	37	12	56494991	56494991	+	Silent	SNP	G	G	A	rs2271189	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:56494991G>A	ENST00000267101.3	+	27	3788	c.3348G>A	c.(3346-3348)agG>agA	p.R1116R	ERBB3_ENST00000415288.2_Silent_p.R1057R|RP11-603J24.9_ENST00000548861.1_5'Flank|ERBB3_ENST00000450146.2_Silent_p.R473R|ERBB3_ENST00000549832.1_Silent_p.R236R|ERBB3_ENST00000553131.1_Silent_p.R357R	NM_001982.3	NP_001973.2	P21860	ERBB3_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 3	1116					cranial nerve development (GO:0021545)|endocardial cushion development (GO:0003197)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of cell adhesion (GO:0007162)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of secretion (GO:0051048)|negative regulation of signal transduction (GO:0009968)|neuron apoptotic process (GO:0051402)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell proliferation (GO:0042127)|Schwann cell differentiation (GO:0014037)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein tyrosine kinase activator activity (GO:0030296)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	8			OV - Ovarian serous cystadenocarcinoma(18;0.112)			CAATGTGTAGGAGCCGGAGCA	0.617													G|||	1263	0.252196	0.0734	0.3718	5008	,	,		13537	0.2887		0.4036	False		,,,				2504	0.2157				p.R1116R		Atlas-SNP	.											.	ERBB3	350	.	0			c.G3348A						PASS	.	G		620,3786	269.8+/-269.2	44,532,1627	54.0	52.0	52.0		3348	-0.8	1.0	12	dbSNP_100	52	3413,5187	503.3+/-375.9	692,2029,1579	no	coding-synonymous	ERBB3	NM_001982.3		736,2561,3206	AA,AG,GG		39.686,14.0717,31.0088		1116/1343	56494991	4033,8973	2203	4300	6503	SO:0001819	synonymous_variant	2065	exon27			GTGTAGGAGCCGG	M34309	CCDS31833.1, CCDS44918.1	12q13	2013-07-09	2013-07-09			ENSG00000065361			3431	protein-coding gene	gene with protein product		190151	"""lethal congenital contracture syndrome 2"""	LCCS2			Standard	NM_001982		Approved	HER3	uc001sjh.3	P21860	OTTHUMG00000170140	ENST00000267101.3:c.3348G>A	12.37:g.56494991G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_001982	A8K6L6|B4DIK7|B4DV32|E9PDT8|Q9BUD7	Silent	SNP	ENST00000267101.3	37	CCDS31833.1																																																																																			G|0.703;A|0.297	0.297	strong		0.617	ERBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407619.3		
ZNF117	51351	hgsc.bcm.edu	37	7	64439701	64439701	+	Missense_Mutation	SNP	C	C	T	rs3807069	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:64439701C>T	ENST00000282869.6	-	4	1532	c.248G>A	c.(247-249)tGt>tAt	p.C83Y		NM_015852.3	NP_056936.2	Q03924	ZN117_HUMAN	zinc finger protein 117	83			C -> Y (in dbSNP:rs3807069).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(1)|skin(1)	22		Lung NSC(55;0.0295)|all_lung(88;0.0691)				ATATTTATTACATTGAAATAT	0.289													C|||	1939	0.387181	0.3964	0.2637	5008	,	,		17591	0.4058		0.4016	False		,,,				2504	0.4284				p.C83Y		Atlas-SNP	.											.	ZNF117	56	.	0			c.G248A						PASS	.	C	TYR/CYS	1446,2376		281,884,746	43.0	41.0	42.0		248	0.2	0.0	7	dbSNP_107	42	3086,5238		576,1934,1652	no	missense	ZNF117	NM_015852.3	194	857,2818,2398	TT,TC,CC		37.0735,37.8336,37.3127	benign	83/484	64439701	4532,7614	1911	4162	6073	SO:0001583	missense	51351	exon4			TTATTACATTGAA	M27879	CCDS43593.1	7q11.2	2013-01-08	2006-06-12		ENSG00000152926	ENSG00000152926		"""Zinc fingers, C2H2-type"""	12897	protein-coding gene	gene with protein product		194624	"""zinc finger protein 117 (HPF9)"""			1427907	Standard	NM_015852		Approved	HPF9, H-plk	uc003ttr.2	Q03924	OTTHUMG00000156631	ENST00000282869.6:c.248G>A	7.37:g.64439701C>T	ENSP00000282869:p.Cys83Tyr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_015852	Q02313|Q7Z7Q7	Missense_Mutation	SNP	ENST00000282869.6	37	CCDS43593.1	856	0.39194139194139194	196	0.3983739837398374	116	0.32044198895027626	223	0.38986013986013984	321	0.4234828496042216	.	10.52	1.374106	0.24857	0.378336	0.370735	ENSG00000152926	ENST00000398695;ENST00000282869	T	0.35421	1.31	1.29	0.163	0.14986	.	.	.	.	.	T	0.00012	0.0000	M	0.91561	3.22	0.80722	P	0.0	B	0.26672	0.156	B	0.24701	0.055	T	0.20806	-1.0264	8	0.59425	D	0.04	.	5.9854	0.19432	0.3063:0.6937:0.0:0.0	rs3807069;rs59205936;rs3807069	83	Q03924	ZN117_HUMAN	Y	83	ENSP00000282869:C83Y	ENSP00000282869:C83Y	C	-	2	0	ZNF117	64077136	0.094000	0.21725	0.000000	0.03702	0.018000	0.09664	1.008000	0.29872	-0.224000	0.09928	0.305000	0.20034	TGT	C|0.612;T|0.388	0.388	strong		0.289	ZNF117-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344863.3	NM_024498	
TAS2R16	50833	hgsc.bcm.edu	37	7	122634843	122634843	+	Silent	SNP	C	C	T	rs1204014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:122634843C>T	ENST00000249284.2	-	1	911	c.846G>A	c.(844-846)acG>acA	p.T282T		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	282					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	bitter taste receptor activity (GO:0033038)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TCCTTTTCAACGTAGGGCTGC	0.423													T|||	501	0.10004	0.323	0.0432	5008	,	,		21099	0.0		0.0378	False		,,,				2504	0.0061				p.T282T		Atlas-SNP	.											TAS2R16,right_lower_lobe,carcinoma,-1,2	TAS2R16	57	2	0			c.G846A						PASS	.	T		1246,3160	700.8+/-406.7	171,904,1128	110.0	113.0	112.0		846	0.5	0.0	7	dbSNP_87	112	367,8233	800.7+/-407.4	11,345,3944	no	coding-synonymous	TAS2R16	NM_016945.2		182,1249,5072	TT,TC,CC		4.2674,28.2796,12.402		282/292	122634843	1613,11393	2203	4300	6503	SO:0001819	synonymous_variant	50833	exon1			TTTCAACGTAGGG	AF227139	CCDS5785.1	7q31.1-q31.3	2012-08-22			ENSG00000128519	ENSG00000128519		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14921	protein-coding gene	gene with protein product		604867				10761934	Standard	NM_016945		Approved	T2R16	uc003vkl.1	Q9NYV7	OTTHUMG00000157090	ENST00000249284.2:c.846G>A	7.37:g.122634843C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Silent	SNP	ENST00000249284.2	37	CCDS5785.1																																																																																			C|0.884;T|0.116	0.116	strong		0.423	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945	
EBI3	10148	hgsc.bcm.edu	37	19	4237067	4237067	+	Silent	SNP	A	A	G	rs4905	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4237067A>G	ENST00000221847.5	+	5	725	c.672A>G	c.(670-672)acA>acG	p.T224T		NM_005755.2	NP_005746.2	Q14213	IL27B_HUMAN	Epstein-Barr virus induced 3	224	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|humoral immune response (GO:0006959)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|T-helper 1 type immune response (GO:0042088)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)		CCACTGCCACAATGAGCCTGG	0.657													G|||	2308	0.460863	0.6679	0.2767	5008	,	,		15560	0.4435		0.3052	False		,,,				2504	0.4898				p.T224T		Atlas-SNP	.											.	EBI3	15	.	0			c.A672G						PASS	.	G		2725,1681	481.7+/-359.2	844,1037,322	40.0	40.0	40.0		672	-7.3	0.0	19	dbSNP_52	40	2457,6143	665.9+/-402.3	372,1713,2215	no	coding-synonymous	EBI3	NM_005755.2		1216,2750,2537	GG,GA,AA		28.5698,38.1525,39.8431		224/230	4237067	5182,7824	2203	4300	6503	SO:0001819	synonymous_variant	10148	exon5			TGCCACAATGAGC	L08187	CCDS12123.1	19p13	2013-02-11	2008-09-12		ENSG00000105246	ENSG00000105246		"""Fibronectin type III domain containing"""	3129	protein-coding gene	gene with protein product	"""IL27 subunit"", ""IL35 subunit"""	605816				8551575	Standard	NM_005755		Approved		uc002lzu.3	Q14213		ENST00000221847.5:c.672A>G	19.37:g.4237067A>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_005755	A0N0N2|O75269	Silent	SNP	ENST00000221847.5	37	CCDS12123.1																																																																																			A|0.585;G|0.415	0.415	strong		0.657	EBI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458005.1		
QRICH2	84074	hgsc.bcm.edu	37	17	74290097	74290097	+	Silent	SNP	T	T	A	rs7225131	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74290097T>A	ENST00000262765.5	-	4	392	c.213A>T	c.(211-213)tcA>tcT	p.S71S		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	71										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						TAAGTGTTTCTGAGCCCTGGT	0.428													T|||	2352	0.469649	0.7073	0.3098	5008	,	,		20370	0.5724		0.2753	False		,,,				2504	0.3558				p.S71S		Atlas-SNP	.											QRICH2,NS,adenoma,0,1	QRICH2	143	1	0			c.A213T						PASS	.	T		2922,1482	654.3+/-399.7	975,972,255	63.0	71.0	69.0		213	-1.3	0.1	17	dbSNP_116	69	2487,6111	384.7+/-341.2	349,1789,2161	no	coding-synonymous	QRICH2	NM_032134.1		1324,2761,2416	AA,AT,TT		28.9253,33.6512,41.6013		71/1664	74290097	5409,7593	2202	4299	6501	SO:0001819	synonymous_variant	84074	exon4			TGTTTCTGAGCCC	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.213A>T	17.37:g.74290097T>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			T|0.574;A|0.426	0.426	strong		0.428	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
ZDHHC11	79844	hgsc.bcm.edu	37	5	801252	801252	+	Missense_Mutation	SNP	C	C	T	rs142091140	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:801252C>T	ENST00000283441.8	-	12	1592	c.1209G>A	c.(1207-1209)atG>atA	p.M403I	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.M403I	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	403						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.M403I(2)		haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			TGTCAGTTTTCATGGGCTCTG	0.413																																					p.M403I		Atlas-SNP	.											ZDHHC11_ENST00000424784,NS,carcinoma,0,3	ZDHHC11	97	3	2	Substitution - Missense(2)	prostate(2)	c.G1209A						scavenged	.	C	ILE/MET	6,4398		0,6,2196	147.0	108.0	121.0		1209	-0.4	0.0	5	dbSNP_134	121	6,8584		0,6,4289	no	missense	ZDHHC11	NM_024786.2	10	0,12,6485	TT,TC,CC		0.0698,0.1362,0.0924	benign	403/413	801252	12,12982	2202	4295	6497	SO:0001583	missense	79844	exon12			AGTTTTCATGGGC	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1209G>A	5.37:g.801252C>T	ENSP00000283441:p.Met403Ile	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	137	10	0.0729927	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	N	6.779	0.512644	0.12944	0.001362	6.98E-4	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.36520	1.25;1.25	1.57	-0.362	0.12560	.	.	.	.	.	T	0.14098	0.0341	N	0.08118	0	0.09310	N	1	B	0.18968	0.032	B	0.09377	0.004	T	0.29549	-1.0008	9	0.14656	T	0.56	-9.9532	3.9839	0.09507	0.0:0.5594:0.0:0.4406	.	403	Q9H8X9	ZDH11_HUMAN	I	403	ENSP00000397719:M403I;ENSP00000283441:M403I	ENSP00000283441:M403I	M	-	3	0	ZDHHC11	854252	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.366000	0.07563	-0.120000	0.11809	0.384000	0.25694	ATG	C|0.999;T|0.001	0.001	strong		0.413	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
RPS6KA4	8986	hgsc.bcm.edu	37	11	64127744	64127744	+	Silent	SNP	A	A	G	rs521950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64127744A>G	ENST00000334205.4	+	3	302	c.237A>G	c.(235-237)caA>caG	p.Q79Q	RPS6KA4_ENST00000528057.1_Silent_p.Q79Q|RPS6KA4_ENST00000294261.4_Silent_p.Q79Q	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	79	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						CCAAGACGCAAGAGCACACGC	0.687													G|||	1350	0.269569	0.0499	0.4078	5008	,	,		15083	0.2083		0.4324	False		,,,				2504	0.364				p.Q79Q		Atlas-SNP	.											.	RPS6KA4	85	.	0			c.A237G						PASS	.	G	,	434,3564		35,364,1600	12.0	10.0	10.0		237,237	3.1	1.0	11	dbSNP_83	10	2989,4947		559,1871,1538	no	coding-synonymous,coding-synonymous	RPS6KA4	NM_001006944.1,NM_003942.2	,	594,2235,3138	GG,GA,AA		37.6638,10.8554,28.6828	,	79/767,79/773	64127744	3423,8511	1999	3968	5967	SO:0001819	synonymous_variant	8986	exon3			GACGCAAGAGCAC	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"""ribosomal protein S6 kinase, 90kD, polypeptide 4"""			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.237A>G	11.37:g.64127744A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_001006944	A8K7Z8|O75585|Q53ES8	Silent	SNP	ENST00000334205.4	37	CCDS8073.1																																																																																			A|0.713;G|0.287	0.287	strong		0.687	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942	
FGD5	152273	hgsc.bcm.edu	37	3	14861103	14861103	+	Missense_Mutation	SNP	G	G	C	rs144016950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:14861103G>C	ENST00000285046.5	+	1	635	c.525G>C	c.(523-525)gaG>gaC	p.E175D	FGD5_ENST00000543601.1_5'UTR	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	175	Glu-rich.				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						CACACAGGGAGTGCAGCCTGG	0.627																																					p.E175D		Atlas-SNP	.											.	FGD5	248	.	0			c.G525C						PASS	.	G	ASP/GLU	0,1384		0,0,692	27.0	34.0	32.0		525	-7.4	0.0	3	dbSNP_134	32	3,3179		0,3,1588	no	missense	FGD5	NM_152536.3	45	0,3,2280	CC,CG,GG		0.0943,0.0,0.0657	benign	175/1463	14861103	3,4563	692	1591	2283	SO:0001583	missense	152273	exon1			CAGGGAGTGCAGC	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.525G>C	3.37:g.14861103G>C	ENSP00000285046:p.Glu175Asp	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	185	87	0.47027	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.746518	0.30955	0.0	9.43E-4	ENSG00000154783	ENST00000285046	T	0.75260	-0.92	5.6	-7.42	0.01388	.	2.542450	0.01537	N	0.019062	T	0.49012	0.1532	N	0.14661	0.345	0.09310	N	1	B	0.27498	0.18	B	0.23018	0.043	T	0.41466	-0.9507	10	0.12766	T	0.61	0.0593	5.131	0.14909	0.203:0.448:0.2583:0.0908	.	175	Q6ZNL6	FGD5_HUMAN	D	175	ENSP00000285046:E175D	ENSP00000285046:E175D	E	+	3	2	FGD5	14836107	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.106000	0.03319	-1.080000	0.03109	0.591000	0.81541	GAG	G|0.999;T|0.001	.	strong		0.627	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
MCF2L	23263	hgsc.bcm.edu	37	13	113728781	113728781	+	Silent	SNP	G	G	A	rs3814264	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:113728781G>A	ENST00000375608.3	+	11	1168	c.1110G>A	c.(1108-1110)gcG>gcA	p.A370A	MCF2L_ENST00000535094.2_Silent_p.A340A|MCF2L_ENST00000375604.2_Silent_p.A397A|MCF2L_ENST00000423482.2_Silent_p.A338A|MCF2L_ENST00000375601.3_Silent_p.A344A|MCF2L_ENST00000421756.1_Silent_p.A344A|MCF2L_ENST00000397030.1_Silent_p.A373A|MCF2L_ENST00000434480.2_Silent_p.A346A|MCF2L_ENST00000375597.4_Silent_p.A338A|MCF2L_ENST00000442652.2_Silent_p.A370A			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	370					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	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)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				TGGACGCAGCGTCCCAGAAGA	0.582													G|||	1103	0.220248	0.0356	0.3314	5008	,	,		16659	0.4593		0.2237	False		,,,				2504	0.1411				p.A340A		Atlas-SNP	.											.	MCF2L	182	.	0			c.G1020A						PASS	.	G	,	314,4092	167.6+/-198.6	13,288,1902	81.0	76.0	78.0		1020,1014	2.8	0.9	13	dbSNP_107	78	1839,6761	330.1+/-319.0	182,1475,2643	yes	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	195,1763,4545	AA,AG,GG		21.3837,7.1266,16.5539	,	340/1126,338/1124	113728781	2153,10853	2203	4300	6503	SO:0001819	synonymous_variant	23263	exon10			CGCAGCGTCCCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.1110G>A	13.37:g.113728781G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	93	30	0.322581	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37		569	0.26053113553113555	26	0.052845528455284556	107	0.2955801104972376	264	0.46153846153846156	172	0.22691292875989447	G	2.214	-0.379936	0.05000	0.071266	0.213837	ENSG00000126217	ENST00000397017	.	.	.	4.87	2.81	0.32909	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999963344	.	.	.	.	.	.	T	0.50162	-0.8860	3	.	.	.	.	9.4825	0.38908	0.0868:0.0:0.7666:0.1465	rs3814264;rs3814264	.	.	.	I	1	.	.	V	+	1	0	MCF2L	112776782	1.000000	0.71417	0.908000	0.35775	0.007000	0.05969	2.757000	0.47557	2.234000	0.73211	0.655000	0.94253	GTC	G|0.809;A|0.191	0.191	strong		0.582	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
RPN1	6184	hgsc.bcm.edu	37	3	128344786	128344786	+	Silent	SNP	G	G	A	rs1126828	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:128344786G>A	ENST00000296255.3	-	7	1254	c.1206C>T	c.(1204-1206)gaC>gaT	p.D402D	RPN1_ENST00000497289.1_Silent_p.D230D|RPN1_ENST00000490166.1_5'Flank	NM_002950.3	NP_002941.1	P04843	RPN1_HUMAN	ribophorin I	402					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)|poly(A) RNA binding (GO:0044822)	p.D402D(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|stomach(2)	13				GBM - Glioblastoma multiforme(114;0.189)		GGCCAAATGTGTCCAGATAGG	0.468			T	EVI1	AML								G|||	1192	0.238019	0.143	0.2003	5008	,	,		19302	0.4147		0.2137	False		,,,				2504	0.2362				p.D402D		Atlas-SNP	.		Dom	yes		3	3q21.3-q25.2	6184	ribophorin I		L	RPN1,NS,carcinoma,0,1	RPN1	39	1	1	Substitution - coding silent(1)	stomach(1)	c.C1206T						PASS	.	G		627,3779	270.1+/-269.4	48,531,1624	135.0	124.0	128.0		1206	3.1	1.0	3	dbSNP_86	128	1950,6650	343.9+/-325.1	237,1476,2587	no	coding-synonymous	RPN1	NM_002950.3		285,2007,4211	AA,AG,GG		22.6744,14.2306,19.8139		402/608	128344786	2577,10429	2203	4300	6503	SO:0001819	synonymous_variant	6184	exon7			AAATGTGTCCAGA		CCDS3051.1	3q21.3	2013-03-06			ENSG00000163902	ENSG00000163902			10381	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 1 homolog (S. cerevisiae)"", ""oligosaccharyltransferase complex subunit (non-catalytic)"""	180470					Standard	NM_002950		Approved	OST1	uc003ekr.1	P04843	OTTHUMG00000159691	ENST00000296255.3:c.1206C>T	3.37:g.128344786G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_002950	B2R5Z0|D3DNB6|Q68DT1	Silent	SNP	ENST00000296255.3	37	CCDS3051.1																																																																																			G|0.779;A|0.221	0.221	strong		0.468	RPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356934.2	NM_002950	
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:115931703G>A	ENST00000238256.3	-	26	3403	c.3286C>T	c.(3286-3288)Ctg>Ttg	p.L1096L		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1096					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GTCAGGGACAGTCTTGTGGAG	0.577													G|||	1420	0.283546	0.3351	0.2954	5008	,	,		17925	0.1617		0.3489	False		,,,				2504	0.2638				p.L1096L		Atlas-SNP	.											.	FKBP15	128	.	0			c.C3286T						PASS	.	G		1174,2710		177,820,945	96.0	98.0	98.0		3286	3.5	0.0	9	dbSNP_107	98	2704,5574		443,1818,1878	no	coding-synonymous	FKBP15	NM_015258.1		620,2638,2823	AA,AG,GG		32.6649,30.2266,31.8862		1096/1220	115931703	3878,8284	1942	4139	6081	SO:0001819	synonymous_variant	23307	exon26			GGGACAGTCTTGT	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.3286C>T	9.37:g.115931703G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			G|0.712;A|0.288	0.288	strong		0.577	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
RGS3	5998	hgsc.bcm.edu	37	9	116346287	116346287	+	Silent	SNP	C	C	T	rs3810927	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:116346287C>T	ENST00000374140.2	+	21	2804	c.2595C>T	c.(2593-2595)taC>taT	p.Y865Y	RGS3_ENST00000462143.1_Silent_p.Y186Y|RGS3_ENST00000374134.3_Silent_p.Y186Y|RGS3_ENST00000350696.5_Silent_p.Y865Y|RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000343817.5_Silent_p.Y584Y	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	865					inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.Y865Y(1)|p.Y761Y(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						ATAGCACCTACAGCCAGAAGG	0.662													C|||	850	0.169728	0.1082	0.2421	5008	,	,		17767	0.2103		0.1869	False		,,,				2504	0.1421				p.Y865Y		Atlas-SNP	.											RGS3_ENST00000374140,NS,carcinoma,0,2	RGS3	251	2	2	Substitution - coding silent(2)	stomach(2)	c.C2595T						PASS	.	C	,,,	591,3815	259.5+/-263.1	55,481,1667	54.0	53.0	54.0		558,1752,,2595	2.6	1.0	9	dbSNP_107	54	1577,7023	290.5+/-299.9	144,1289,2867	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4	,,,	199,1770,4534	TT,TC,CC		18.3372,13.4135,16.6692	,,,	186/520,584/918,,865/1199	116346287	2168,10838	2203	4300	6503	SO:0001819	synonymous_variant	5998	exon21			CACCTACAGCCAG	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.2595C>T	9.37:g.116346287C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	37	CCDS43869.1																																																																																			C|0.832;T|0.168	0.168	strong		0.662	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
MATN1	4146	hgsc.bcm.edu	37	1	31188901	31188901	+	Silent	SNP	A	A	G	rs20566	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:31188901A>G	ENST00000373765.4	-	5	1097	c.1062T>C	c.(1060-1062)acT>acC	p.T354T	MATN1-AS1_ENST00000414532.2_RNA|MATN1-AS1_ENST00000454613.1_RNA|MATN1_ENST00000477320.1_5'UTR|MATN1-AS1_ENST00000414763.1_RNA	NM_002379.3	NP_002370.1	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein	354	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|growth plate cartilage chondrocyte morphogenesis (GO:0003429)|protein complex assembly (GO:0006461)|regulation of bone mineralization (GO:0030500)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		GAGCAGCCCCAGTCATTGTGC	0.582													G|||	3026	0.604233	0.8411	0.6787	5008	,	,		20847	0.6052		0.4682	False		,,,				2504	0.3701				p.T354T		Atlas-SNP	.											.	MATN1	28	.	0			c.T1062C						PASS	.	G		3404,1002	372.5+/-320.4	1310,784,109	120.0	129.0	126.0		1062	-10.7	0.1	1	dbSNP_67	126	3899,4701	607.3+/-395.2	892,2115,1293	no	coding-synonymous	MATN1	NM_002379.3		2202,2899,1402	GG,GA,AA		45.3372,22.7417,43.849		354/497	31188901	7303,5703	2203	4300	6503	SO:0001819	synonymous_variant	4146	exon5			AGCCCCAGTCATT	M55675	CCDS336.1	1p35	2008-02-05			ENSG00000162510	ENSG00000162510			6907	protein-coding gene	gene with protein product		115437		CRTM, CMP		2246248, 9083061	Standard	NM_002379		Approved		uc001brz.3	P21941	OTTHUMG00000003705	ENST00000373765.4:c.1062T>C	1.37:g.31188901A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_002379	B2R7E3|Q5TBB9	Silent	SNP	ENST00000373765.4	37	CCDS336.1																																																																																			A|0.426;G|0.574	0.574	strong		0.582	MATN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010458.1	NM_002379	
IRAK2	3656	hgsc.bcm.edu	37	3	10276185	10276185	+	Missense_Mutation	SNP	C	C	G	rs11465927	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:10276185C>G	ENST00000256458.4	+	11	1405	c.1315C>G	c.(1315-1317)Ctc>Gtc	p.L439V		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	439	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> V (in dbSNP:rs11465927). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						CACCGCCTCGCTCTGCTCCAG	0.597													C|||	73	0.0145767	0.0008	0.0288	5008	,	,		18858	0.0		0.0388	False		,,,				2504	0.0133				p.L439V		Atlas-SNP	.											.	IRAK2	113	.	0			c.C1315G						PASS	.	C	VAL/LEU	29,4377	34.3+/-65.2	0,29,2174	80.0	76.0	77.0		1315	1.8	0.0	3	dbSNP_120	77	301,8299	109.2+/-169.8	7,287,4006	yes	missense	IRAK2	NM_001570.3	32	7,316,6180	GG,GC,CC		3.5,0.6582,2.5373	benign	439/626	10276185	330,12676	2203	4300	6503	SO:0001583	missense	3656	exon11			GCCTCGCTCTGCT	AF026273	CCDS33697.1	3p25.2	2008-08-18			ENSG00000134070	ENSG00000134070			6113	protein-coding gene	gene with protein product		603304				9374458	Standard	XR_245126		Approved		uc003bve.1	O43187	OTTHUMG00000155358	ENST00000256458.4:c.1315C>G	3.37:g.10276185C>G	ENSP00000256458:p.Leu439Val	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_001570	B4DQZ6|Q08AG6|Q5K546	Missense_Mutation	SNP	ENST00000256458.4	37	CCDS33697.1	34	0.015567765567765568	0	0.0	11	0.03038674033149171	0	0.0	23	0.030343007915567283	C	2.991	-0.208091	0.06180	0.006582	0.035	ENSG00000134070	ENST00000256458	T	0.65549	-0.16	4.6	1.76	0.24704	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	1.715730	0.03293	N	0.187951	T	0.24275	0.0588	L	0.54863	1.705	0.09310	N	1	B	0.13145	0.007	B	0.18263	0.021	T	0.06991	-1.0796	10	0.25751	T	0.34	-0.61	4.7177	0.12903	0.0:0.6103:0.1862:0.2035	rs11465927;rs11465927	439	O43187	IRAK2_HUMAN	V	439	ENSP00000256458:L439V	ENSP00000256458:L439V	L	+	1	0	IRAK2	10251185	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.047000	0.11963	0.158000	0.19367	0.655000	0.94253	CTC	C|0.976;G|0.024	0.024	strong		0.597	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		
MFAP2	4237	hgsc.bcm.edu	37	1	17301780	17301780	+	Silent	SNP	A	A	G	rs761422	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17301780A>G	ENST00000375535.3	-	8	721	c.432T>C	c.(430-432)caT>caC	p.H144H	MFAP2_ENST00000438542.1_Silent_p.H143H|MFAP2_ENST00000375534.3_Silent_p.H143H|MFAP2_ENST00000490075.1_5'UTR			P55001	MFAP2_HUMAN	microfibrillar-associated protein 2	144					extracellular matrix organization (GO:0030198)|platelet formation (GO:0030220)	extracellular region (GO:0005576)|microfibril (GO:0001527)				kidney(1)|lung(1)	2		Colorectal(325;3.46e-05)|Breast(348;0.000118)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000538)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|COAD - Colon adenocarcinoma(227;1.07e-05)|BRCA - Breast invasive adenocarcinoma(304;3.04e-05)|Kidney(64;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00544)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GGAGCTCCTCATGGGCACACA	0.602													a|||	2080	0.415335	0.4743	0.4582	5008	,	,		17372	0.2401		0.4861	False		,,,				2504	0.4131				p.H144H		Atlas-SNP	.											.	MFAP2	8	.	0			c.T432C						PASS	.	G	,,,	1980,2426	558.0+/-379.9	469,1042,692	104.0	80.0	88.0		429,429,432,432	-4.4	0.8	1	dbSNP_86	88	4076,4524	559.4+/-387.4	995,2086,1219	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MFAP2	NM_001135247.1,NM_001135248.1,NM_002403.3,NM_017459.2	,,,	1464,3128,1911	GG,GA,AA		47.3953,44.9387,46.5631	,,,	143/183,143/183,144/184,144/184	17301780	6056,6950	2203	4300	6503	SO:0001819	synonymous_variant	4237	exon8			CTCCTCATGGGCA	BC015039	CCDS174.1, CCDS44071.1	1p36.1-p35	2008-02-05			ENSG00000117122	ENSG00000117122			7033	protein-coding gene	gene with protein product		156790				7759096	Standard	NM_017459		Approved	MAGP, MAGP-1	uc001azw.3	P55001	OTTHUMG00000002290	ENST00000375535.3:c.432T>C	1.37:g.17301780A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	140	60	0.428571	NM_017459	Q53X60|Q5JXY0	Silent	SNP	ENST00000375535.3	37	CCDS174.1																																																																																			G|0.440;N|0.000	0.440	strong		0.602	MFAP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006609.1	NM_002403	
SLC25A46	91137	hgsc.bcm.edu	37	5	110079450	110079450	+	Silent	SNP	T	T	C	rs17446534	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:110079450T>C	ENST00000355943.3	+	3	472	c.346T>C	c.(346-348)Ttg>Ctg	p.L116L	SLC25A46_ENST00000509442.2_Silent_p.L25L|SLC25A46_ENST00000504098.1_5'UTR|SLC25A46_ENST00000513807.1_5'UTR|SLC25A46_ENST00000447245.2_Silent_p.L116L	NM_138773.1	NP_620128.1	Q96AG3	S2546_HUMAN	solute carrier family 25, member 46	116					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10		all_cancers(142;0.00203)|all_epithelial(76;4.52e-05)|Prostate(80;0.0115)|Colorectal(57;0.0676)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;2.58e-09)|Epithelial(69;7.29e-08)|all cancers(49;9.35e-06)|COAD - Colon adenocarcinoma(37;0.211)		AGAAAATGTATTGGCACATCC	0.313													T|||	202	0.0403355	0.0234	0.0519	5008	,	,		14586	0.0188		0.0905	False		,,,				2504	0.0256				p.L116L		Atlas-SNP	.											.	SLC25A46	33	.	0			c.T346C						PASS	.	T		163,4241	107.3+/-145.7	2,159,2041	81.0	70.0	74.0		346	1.3	1.0	5	dbSNP_123	74	786,7810	183.6+/-231.8	36,714,3548	no	coding-synonymous	SLC25A46	NM_138773.1		38,873,5589	CC,CT,TT		9.1438,3.7012,7.3		116/419	110079450	949,12051	2202	4298	6500	SO:0001819	synonymous_variant	91137	exon3			AATGTATTGGCAC	BC017169	CCDS4100.1	5q22.1	2013-05-22			ENSG00000164209	ENSG00000164209		"""Solute carriers"""	25198	protein-coding gene	gene with protein product		610826				1651562, 1651563, 16949250	Standard	NM_138773		Approved		uc003koz.3	Q96AG3	OTTHUMG00000128794	ENST00000355943.3:c.346T>C	5.37:g.110079450T>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	249	122	0.48996	NM_138773	A8K2F2|B3KRE6|B4DTA3|D3DSZ6|D6R9W7|Q04197	Silent	SNP	ENST00000355943.3	37	CCDS4100.1																																																																																			T|0.938;C|0.062	0.062	strong		0.313	SLC25A46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250721.5	NM_138773	
TAP1	6890	hgsc.bcm.edu	37	6	32816772	32816772	+	Missense_Mutation	SNP	C	C	A	rs41550019	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32816772C>A	ENST00000354258.4	-	6	1713	c.1552G>T	c.(1552-1554)Gtg>Ttg	p.V518L	TAPSAR1_ENST00000453426.1_lincRNA|PSMB9_ENST00000395330.1_Intron|TAP1_ENST00000425148.2_Missense_Mutation_p.V257L	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	518	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.|Involved in peptide-binding site.		V -> L (in allele TAP1*04:01; dbSNP:rs41550019). {ECO:0000269|PubMed:11250043, ECO:0000269|PubMed:12878362, ECO:0000269|PubMed:8248212}.		antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|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)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CTCACCTCCACAGCCTGGGTG	0.542													C|||	296	0.0591054	0.171	0.049	5008	,	,		20359	0.001		0.0338	False		,,,				2504	0.001				p.V518L		Atlas-SNP	.											.	TAP1	39	.	0			c.G1552T						PASS	.	C	LEU/VAL	376,2646		22,332,1157	78.0	52.0	61.0		1552	4.1	1.0	6	dbSNP_127	61	158,5260		2,154,2553	yes	missense	TAP1	NM_000593.5	32	24,486,3710	AA,AC,CC		2.9162,12.4421,6.327	possibly-damaging	518/809	32816772	534,7906	1511	2709	4220	SO:0001583	missense	6890	exon6			CCTCCACAGCCTG		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.1552G>T	6.37:g.32816772C>A	ENSP00000346206:p.Val518Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	97	15	0.154639	NM_000593	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	132	0.06043956043956044	95	0.19308943089430894	16	0.04419889502762431	1	0.0017482517482517483	20	0.026385224274406333	C	15.34	2.804766	0.50315	0.124421	0.029162	ENSG00000168394	ENST00000354258;ENST00000425148	D;D	0.86769	-2.17;-2.17	5.02	4.05	0.47172	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	2.649620	0.01818	N	0.033862	T	0.78578	0.4305	L	0.42245	1.32	0.19300	P	0.9999799193	B	0.33135	0.399	B	0.39531	0.302	T	0.62163	-0.6912	9	0.34782	T	0.22	-15.3442	10.8749	0.46904	0.0:0.9001:0.0:0.0999	rs41550019;rs60844934;rs62621091	518	Q03518	TAP1_HUMAN	L	518;257	ENSP00000346206:V518L;ENSP00000401919:V257L	ENSP00000346206:V518L	V	-	1	0	TAP1	32924750	0.344000	0.24827	0.994000	0.49952	0.339000	0.28857	0.669000	0.25142	1.178000	0.42870	0.643000	0.83706	GTG	G|0.000;C|0.939;A|0.061	0.061	strong		0.542	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
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 GAIIx	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	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	73	4	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	
ZCCHC16	340595	hgsc.bcm.edu	37	X	111698463	111698463	+	Silent	SNP	C	C	T	rs112035132	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:111698463C>T	ENST00000340433.2	+	1	737	c.507C>T	c.(505-507)ctC>ctT	p.L169L		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	169							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						TCCACCTCCTCGCTCAAAATC	0.448													T||||T|||	107|107	0.0283444|0.0283444	0.0008|0.0008	0.0288|0.0288	3775|3775	,|,	,|,		15526|15526	0.0|0.0		0.0666|0.0666	False|False		,,,|,,,				2504|2504	0.0194|0.0194				p.L169L		Atlas-SNP	.											.	ZCCHC16	66	.	0			c.C507T						PASS	.	T		63,3772		0,54,9,1578,562	75.0	73.0	73.0		507	2.4	0.0	X	dbSNP_132	73	680,6048		21,456,182,1951,1690	no	coding-synonymous	ZCCHC16	NM_001004308.2		21,510,191,3529,2252	TT,TC,T,CC,C		10.107,1.6428,7.034		169/311	111698463	743,9820	2203	4300	6503	SO:0001819	synonymous_variant	340595	exon3			CCTCCTCGCTCAA	AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"""Zinc fingers, CCHC domain containing"""	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.507C>T	X.37:g.111698463C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	146	32	0.219178	NM_001004308	B2RPG1	Silent	SNP	ENST00000340433.2	37	CCDS35369.1																																																																																			C|0.941;T|0.059	0.059	strong		0.448	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1	NM_001004308	
PIEZO1	9780	hgsc.bcm.edu	37	16	88781073	88781073	+	IGR	SNP	G	G	A	rs11549835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88781073G>A	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Missense_Mutation_p.R427Q|CTU2_ENST00000567949.1_Missense_Mutation_p.R498Q|CTU2_ENST00000378384.3_Missense_Mutation_p.R340Q|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.R427Q	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						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						ACTGAGACCCGGACACCCCCG	0.687													G|||	199	0.0397364	0.0234	0.0375	5008	,	,		13888	0.0		0.1292	False		,,,				2504	0.0123				p.R427Q		Atlas-SNP	.											.	CTU2	66	.	0			c.G1280A						PASS	.	G	GLN/ARG,GLN/ARG	154,4216	101.2+/-139.8	4,146,2035	27.0	30.0	29.0		1280,1280	0.2	0.0	16	dbSNP_120	29	1165,7419	229.3+/-264.0	80,1005,3207	yes	missense,missense	CTU2	NM_001012759.1,NM_001012762.1	43,43	84,1151,5242	AA,AG,GG		13.5718,3.524,10.1822	benign,benign	427/516,427/486	88781073	1319,11635	2185	4292	6477	SO:0001628	intergenic_variant	348180	exon12			AGACCCGGACACC	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		16.37:g.88781073G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	144	0.06593406593406594	16	0.032520325203252036	13	0.03591160220994475	0	0.0	115	0.1517150395778364	G	4.011	-0.000621	0.07819	0.03524	0.135718	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.16597	2.33;2.59;2.59	2.67	0.244	0.15507	.	0.997056	0.08125	N	0.994048	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	P;P;P	0.39131	0.477;0.661;0.53	B;B;B	0.24848	0.056;0.056;0.025	T	0.35724	-0.9777	9	0.15066	T	0.55	.	4.2804	0.10829	0.1651:0.2812:0.5537:0.0	rs11549835	340;427;427	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	Q	340;427;427	ENSP00000367635:R340Q;ENSP00000308617:R427Q;ENSP00000388320:R427Q	ENSP00000308617:R427Q	R	+	2	0	CTU2	87308574	0.001000	0.12720	0.001000	0.08648	0.036000	0.12997	0.029000	0.13666	-0.031000	0.13781	0.462000	0.41574	CGG	G|0.914;A|0.086	0.086	strong		0.687	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
DDX20	11218	hgsc.bcm.edu	37	1	112308972	112308972	+	Silent	SNP	G	G	A	rs197413	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:112308972G>A	ENST00000369702.4	+	11	2546	c.1926G>A	c.(1924-1926)gtG>gtA	p.V642V	DDX20_ENST00000475700.1_Silent_p.V250V	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	642					ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GAGTCCCTGTGTTGGCAAGTA	0.443													A|||	2403	0.479832	0.7428	0.5115	5008	,	,		19455	0.3403		0.4185	False		,,,				2504	0.3088				p.V642V		Atlas-SNP	.											.	DDX20	50	.	0			c.G1926A						PASS	.	A		2992,1414	455.7+/-351.1	1018,956,229	47.0	48.0	48.0		1926	-2.6	0.0	1	dbSNP_79	48	3349,5251	639.0+/-399.4	671,2007,1622	no	coding-synonymous	DDX20	NM_007204.4		1689,2963,1851	AA,AG,GG		38.9419,32.0926,48.7544		642/825	112308972	6341,6665	2203	4300	6503	SO:0001819	synonymous_variant	11218	exon11			CCCTGTGTTGGCA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1926G>A	1.37:g.112308972G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Silent	SNP	ENST00000369702.4	37	CCDS842.1																																																																																			G|0.512;A|0.488	0.488	strong		0.443	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
CARS	833	hgsc.bcm.edu	37	11	3028140	3028140	+	Silent	SNP	G	G	A	rs729662	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:3028140G>A	ENST00000397111.5	-	18	2114	c.1869C>T	c.(1867-1869)ccC>ccT	p.P623P	CARS_ENST00000397114.3_Silent_p.P613P|CARS_ENST00000278224.9_Silent_p.P623P|CARS_ENST00000470221.2_5'UTR|CARS_ENST00000380525.4_Silent_p.P706P|CARS_ENST00000401769.3_Silent_p.P636P			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	623					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)		CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	CCCCAAGCTCGGGCAGGATGT	0.587			T	ALK	ALCL								G|||	1757	0.350839	0.0303	0.4957	5008	,	,		20311	0.6627		0.2922	False		,,,				2504	0.4202				p.P706P	Ovarian(61;932 1157 5961 20446 52152)	Atlas-SNP	.		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	CARS	114	.	0			c.C2118T						PASS	.	G	,,,	333,4071	174.4+/-204.0	12,309,1881	177.0	169.0	172.0		2118,2118,1869,1869	-4.1	1.0	11	dbSNP_86	172	2504,6092	409.7+/-349.9	363,1778,2157	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CARS	NM_001014437.2,NM_001194997.1,NM_001751.5,NM_139273.3	,,,	375,2087,4038	AA,AG,GG		29.1298,7.5613,21.8231	,,,	706/832,706/810,623/749,623/727	3028140	2837,10163	2202	4298	6500	SO:0001819	synonymous_variant	833	exon19			AAGCTCGGGCAGG	AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	1493	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 1, cytoplasmic"""	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.1869C>T	11.37:g.3028140G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Silent	SNP	ENST00000397111.5	37	CCDS7742.1																																																																																			G|0.727;A|0.273	0.273	strong		0.587	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751	
GJA9	81025	hgsc.bcm.edu	37	1	39341749	39341749	+	Missense_Mutation	SNP	C	C	T	rs61732191	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:39341749C>T	ENST00000360786.3	-	1	274	c.22G>A	c.(22-24)Gga>Aga	p.G8R	RP5-864K19.4_ENST00000456813.1_RNA|MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000454994.2_Missense_Mutation_p.G8R|MYCBP_ENST00000397572.2_5'Flank|GJA9_ENST00000357771.3_Missense_Mutation_p.G8R|RP5-864K19.4_ENST00000433671.2_RNA			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	8					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			AGAGTATCTCCAAGGAGATTC	0.448													C|||	7	0.00139776	0.0	0.0043	5008	,	,		19977	0.0		0.004	False		,,,				2504	0.0				p.G8R		Atlas-SNP	.											GJA9,NS,malignant_melanoma,+1,1	GJA9	55	1	0			c.G22A						scavenged	.	C	ARG/GLY	3,4403	4.2+/-10.8	0,3,2200	126.0	129.0	128.0		22	4.8	1.0	1	dbSNP_129	128	30,8570	21.0+/-64.5	0,30,4270	yes	missense	GJA9	NM_030772.4	125	0,33,6470	TT,TC,CC		0.3488,0.0681,0.2537	probably-damaging	8/516	39341749	33,12973	2203	4300	6503	SO:0001583	missense	81025	exon2			TATCTCCAAGGAG	AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"""Ion channels / Gap junction proteins (connexins)"""	19155	protein-coding gene	gene with protein product	"""connexin 59"""	611923	"""gap junction protein, alpha 10, 59kDa"""	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.22G>A	1.37:g.39341749C>T	ENSP00000354020:p.Gly8Arg	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	160	2	0.0125	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Missense_Mutation	SNP	ENST00000360786.3	37	CCDS432.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	25.5	4.642899	0.87859	6.81E-4	0.003488	ENSG00000131233	ENST00000454994;ENST00000357771;ENST00000360786	D;D;D	0.99060	-5.38;-5.38;-5.38	4.83	4.83	0.62350	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98604	0.9533	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96352	0.9259	10	0.66056	D	0.02	.	17.3659	0.87364	0.0:1.0:0.0:0.0	.	8	P57773	CXA9_HUMAN	R	8	ENSP00000406846:G8R;ENSP00000350415:G8R;ENSP00000354020:G8R	ENSP00000350415:G8R	G	-	1	0	GJA9	39114336	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.766000	0.68843	2.612000	0.88384	0.655000	0.94253	GGA	C|0.999;T|0.001	0.001	strong		0.448	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
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 GAIIx	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|MCF2L2_ENST00000473233.1_Intron|B3GNT5_ENST00000465010.1_Missense_Mutation_p.Y182C|B3GNT5_ENST00000460419.1_Missense_Mutation_p.Y182C	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	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	156	69	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	
TACC2	10579	hgsc.bcm.edu	37	10	123903133	123903133	+	Missense_Mutation	SNP	G	G	A	rs12765679	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123903133G>A	ENST00000369005.1	+	7	6086	c.5746G>A	c.(5746-5748)Gaa>Aaa	p.E1916K	TACC2_ENST00000334433.3_Missense_Mutation_p.E1916K|TACC2_ENST00000369001.1_Intron|TACC2_ENST00000515603.1_Intron|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000493951.1_3'UTR|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Intron|TACC2_ENST00000369000.1_Intron|TACC2_ENST00000515273.1_Intron	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1916			E -> K (in dbSNP:rs12765679).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CTCGGCTGCAGAACACATAGT	0.577											OREG0020589	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	453	0.0904553	0.0688	0.1138	5008	,	,		14875	0.0		0.2286	False		,,,				2504	0.0542				p.E1916K		Atlas-SNP	.											.	TACC2	271	.	0			c.G5746A						PASS	.	G	,LYS/GLU	361,4045	185.7+/-212.7	15,331,1857	103.0	89.0	94.0		,5746	3.5	0.0	10	dbSNP_121	94	1929,6671	341.6+/-324.1	219,1491,2590	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,56	234,1822,4447	AA,AG,GG		22.4302,8.1934,17.6073	,probably-damaging	,1916/2949	123903133	2290,10716	2203	4300	6503	SO:0001583	missense	10579	exon7			GCTGCAGAACACA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5746G>A	10.37:g.123903133G>A	ENSP00000358001:p.Glu1916Lys	Somatic	44	0	0	1530	WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	268	0.1227106227106227	31	0.06300813008130081	55	0.15193370165745856	0	0.0	182	0.24010554089709762	G	14.03	2.413032	0.42817	0.081934	0.224302	ENSG00000138162	ENST00000369005;ENST00000334433;ENST00000340076	T;T	0.57907	0.37;0.37	4.45	3.53	0.40419	.	0.443678	0.16781	N	0.199795	T	0.00012	0.0000	L	0.32530	0.975	0.48571	P	3.269999999999662E-4	P	0.37061	0.58	B	0.37601	0.254	T	0.11665	-1.0578	9	0.72032	D	0.01	-4.7039	10.6039	0.45384	0.0:0.1948:0.8052:0.0	rs12765679;rs17551488;rs52820192;rs57234473;rs12765679	1916	O95359	TACC2_HUMAN	K	1916;1916;1906	ENSP00000358001:E1916K;ENSP00000334280:E1916K	ENSP00000334280:E1916K	E	+	1	0	TACC2	123893123	0.032000	0.19561	0.003000	0.11579	0.003000	0.03518	2.480000	0.45206	1.209000	0.43321	-0.304000	0.09214	GAA	G|0.854;A|0.146	0.146	strong		0.577	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
ARHGAP33	115703	hgsc.bcm.edu	37	19	36273308	36273308	+	Silent	SNP	G	G	A	rs35297478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36273308G>A	ENST00000007510.4	+	13	1263	c.1119G>A	c.(1117-1119)ctG>ctA	p.L373L	ARHGAP33_ENST00000314737.5_Silent_p.L373L|ARHGAP33_ENST00000378944.5_Silent_p.L237L			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	373	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						TCCCGGAGCTGTCTGGCCCTG	0.597													G|||	599	0.119609	0.0598	0.1916	5008	,	,		18912	0.1488		0.1123	False		,,,				2504	0.1268				p.L373L		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.G1119A						PASS	.		,	310,4096	167.3+/-198.3	7,296,1900	120.0	104.0	110.0		711,1119	4.3	1.0	19	dbSNP_126	110	845,7755	194.2+/-239.7	36,773,3491	no	coding-synonymous,coding-synonymous	ARHGAP33	NM_001172630.1,NM_052948.3	,	43,1069,5391	AA,AG,GG		9.8256,7.0359,8.8805	,	237/1124,373/1127	36273308	1155,11851	2203	4300	6503	SO:0001819	synonymous_variant	115703	exon13			GGAGCTGTCTGGC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1119G>A	19.37:g.36273308G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				G|0.905;A|0.095	0.095	strong		0.597	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847069	100847069	+	Missense_Mutation	SNP	G	G	A	rs569336	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:100847069G>A	ENST00000298815.8	+	20	2140	c.2137G>A	c.(2137-2139)Gtt>Att	p.V713I	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.V679I	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	713	Ser-rich.			V -> I (in Ref. 3; BAB71456). {ECO:0000305}.	signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						CCCAGGAGACGTTTCCCCACC	0.488													G|||	2485	0.496206	0.1505	0.5274	5008	,	,		21331	0.997		0.2883	False		,,,				2504	0.6391				p.V713I		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G2137A						PASS	.	G	ILE/VAL	307,1077		34,239,419	64.0	49.0	54.0		2137	2.4	0.0	11	dbSNP_83	54	987,2195		160,667,764	yes	missense	ARHGAP42	NM_152432.2	29	194,906,1183	AA,AG,GG		31.0182,22.1821,28.3399	benign	713/875	100847069	1294,3272	692	1591	2283	SO:0001583	missense	143872	exon20			GGAGACGTTTCCC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2137G>A	11.37:g.100847069G>A	ENSP00000298815:p.Val713Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_152432	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	37		1052	0.4816849816849817	87	0.17682926829268292	168	0.46408839779005523	572	1.0	225	0.29683377308707126	G	3.367	-0.129186	0.06753	0.221821	0.310182	ENSG00000165895	ENST00000524892;ENST00000298815	T;T	0.06849	3.25;3.34	5.7	2.36	0.29203	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37753	-0.9692	8	0.33141	T	0.24	.	12.4883	0.55885	0.2148:0.0:0.7852:0.0	rs569336;rs52827090;rs58116702;rs569336	713	A6NI28	RHG42_HUMAN	I	679;713	ENSP00000431776:V679I;ENSP00000298815:V713I	ENSP00000298815:V713I	V	+	1	0	ARHGAP42	100352279	0.011000	0.17503	0.008000	0.14137	0.397000	0.30659	1.390000	0.34464	0.760000	0.33108	0.655000	0.94253	GTT	G|0.552;A|0.448	0.448	strong		0.488	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
LIPK	643414	hgsc.bcm.edu	37	10	90490921	90490921	+	Silent	SNP	G	G	A	rs412227	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:90490921G>A	ENST00000404190.1	+	3	405	c.405G>A	c.(403-405)ccG>ccA	p.P135P		NM_001080518.1	NP_001073987.1	Q5VXJ0	LIPK_HUMAN	lipase, family member K	135					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	12		Colorectal(252;0.0381)		Colorectal(12;7.03e-05)|COAD - Colon adenocarcinoma(12;8.33e-05)		CGAAATCACCGGAATACTGGG	0.413													A|||	1288	0.257188	0.1899	0.2853	5008	,	,		21082	0.3462		0.2137	False		,,,				2504	0.2812				p.P135P		Atlas-SNP	.											.	LIPK	50	.	0			c.G405A						PASS	.	A		729,3079		70,589,1245	49.0	47.0	48.0		405	0.0	0.0	10	dbSNP_80	48	1786,6516		224,1338,2589	no	coding-synonymous	LIPK	NM_001080518.1		294,1927,3834	AA,AG,GG		21.5129,19.1439,20.768		135/400	90490921	2515,9595	1904	4151	6055	SO:0001819	synonymous_variant	643414	exon3			ATCACCGGAATAC		CCDS44455.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000204021	ENSG00000204021			23444	protein-coding gene	gene with protein product		613922	"""lipase-like, ab-hydrolase domain containing 2"""	LIPL2			Standard	NM_001080518		Approved	bA186O14.2	uc010qmv.2	Q5VXJ0	OTTHUMG00000018693	ENST00000404190.1:c.405G>A	10.37:g.90490921G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001080518	A7KIH8	Silent	SNP	ENST00000404190.1	37	CCDS44455.1																																																																																			G|0.756;A|0.244	0.244	strong		0.413	LIPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049253.2	XM_061222	
CCDC183	84960	hgsc.bcm.edu	37	9	139694569	139694569	+	Missense_Mutation	SNP	A	A	C	rs7859194	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139694569A>C	ENST00000338005.6	+	4	421	c.386A>C	c.(385-387)gAc>gCc	p.D129A	RP11-216L13.18_ENST00000471502.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.D159A|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		129			D -> A (in dbSNP:rs7859194).							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CTGGAGCTGGACAGCCTGCGG	0.682													C|||	1376	0.27476	0.3381	0.2968	5008	,	,		9043	0.2421		0.2157	False		,,,				2504	0.2679				p.D129A		Atlas-SNP	.											.	KIAA1984	39	.	0			c.A386C						PASS	.	C	ALA/ASP	963,2909		140,683,1113	10.0	12.0	12.0		386	-3.1	0.0	9	dbSNP_116	12	1531,6531		185,1161,2685	no	missense	KIAA1984	NM_001039374.4	126	325,1844,3798	CC,CA,AA		18.9903,24.8709,20.8983	benign	129/535	139694569	2494,9440	1936	4031	5967	SO:0001583	missense	84960	exon4			AGCTGGACAGCCT																												ENST00000338005.6:c.386A>C	9.37:g.139694569A>C	ENSP00000338013:p.Asp129Ala	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	13	7	0.538462	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	535	0.24496336996336995	158	0.32113821138211385	97	0.26795580110497236	122	0.21328671328671328	158	0.20844327176781002	C	5.124	0.208555	0.09757	0.248709	0.189903	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.11604	2.76	4.95	-3.07	0.05363	.	0.822281	0.09595	N	0.780992	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45145	-0.9281	9	0.09843	T	0.71	-0.1055	5.2268	0.15399	0.6236:0.1793:0.1142:0.0829	rs7859194;rs60792782;rs7859194	129	Q5T5S1	K1984_HUMAN	A	129	ENSP00000338013:D129A	ENSP00000338013:D129A	D	+	2	0	KIAA1984	138814390	0.000000	0.05858	0.004000	0.12327	0.086000	0.17979	-0.016000	0.12613	-0.448000	0.07128	-0.358000	0.07595	GAC	A|0.754;C|0.246	0.246	strong		0.682	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
TMEM5	10329	hgsc.bcm.edu	37	12	64173807	64173807	+	Missense_Mutation	SNP	G	G	A	rs61935924	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:64173807G>A	ENST00000261234.6	+	1	225	c.67G>A	c.(67-69)Gct>Act	p.A23T	TMEM5_ENST00000537373.1_5'Flank|RP11-415I12.3_ENST00000509615.2_RNA	NM_014254.1	NP_055069.1	Q9Y2B1	TMEM5_HUMAN	transmembrane protein 5	23						integral component of plasma membrane (GO:0005887)				breast(1)|large_intestine(3)|liver(2)|lung(7)|prostate(1)|skin(1)	15		Myeloproliferative disorder(1001;0.0255)	BRCA - Breast invasive adenocarcinoma(9;0.0985)	GBM - Glioblastoma multiforme(28;9e-08)|BRCA - Breast invasive adenocarcinoma(357;0.000175)		CTCCCTCTACGCTGCCTACCA	0.716													G|||	262	0.0523163	0.0166	0.0562	5008	,	,		8945	0.0129		0.1044	False		,,,				2504	0.0849				p.A23T		Atlas-SNP	.											.	TMEM5	35	.	0			c.G67A						PASS	.	G	THR/ALA	125,4281	91.1+/-129.8	0,125,2078	51.0	48.0	49.0		67	2.5	1.0	12	dbSNP_129	49	903,7697	200.7+/-244.4	41,821,3438	yes	missense	TMEM5	NM_014254.1	58	41,946,5516	AA,AG,GG		10.5,2.837,7.904	possibly-damaging	23/444	64173807	1028,11978	2203	4300	6503	SO:0001583	missense	10329	exon1			CTCTACGCTGCCT	AB015633	CCDS8966.1, CCDS61179.1	12q14.1	2013-05-07			ENSG00000118600	ENSG00000118600			13530	protein-coding gene	gene with protein product		605862				10072769, 23217329	Standard	NM_014254		Approved	HP10481	uc001srq.2	Q9Y2B1	OTTHUMG00000168730	ENST00000261234.6:c.67G>A	12.37:g.64173807G>A	ENSP00000261234:p.Ala23Thr	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_014254	A8K017|Q6PKD6	Missense_Mutation	SNP	ENST00000261234.6	37	CCDS8966.1	121	0.0554029304029304	12	0.024390243902439025	25	0.06906077348066299	6	0.01048951048951049	78	0.10290237467018469	G	24.5	4.540086	0.85917	0.02837	0.105	ENSG00000118600	ENST00000261234	T	0.32023	1.47	3.39	2.5	0.30297	.	0.000000	0.85682	D	0.000000	T	0.01353	0.0044	L	0.49350	1.555	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00123	-1.2026	9	.	.	.	-23.3885	6.7536	0.23501	0.1293:0.0:0.8707:0.0	rs61935924	23	Q9Y2B1	TMEM5_HUMAN	T	23	ENSP00000261234:A23T	.	A	+	1	0	TMEM5	62460074	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.363000	0.59473	1.009000	0.39289	0.462000	0.41574	GCT	G|0.927;A|0.073	0.073	strong		0.716	TMEM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400821.1	NM_014254	
PPP1R18	170954	hgsc.bcm.edu	37	6	30652781	30652781	+	Missense_Mutation	SNP	C	C	T	rs9262143	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30652781C>T	ENST00000274853.3	-	1	2891	c.1015G>A	c.(1015-1017)Ggg>Agg	p.G339R	PPP1R18_ENST00000399199.3_Missense_Mutation_p.G339R|PPP1R18_ENST00000488324.1_Intron	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	339			G -> R (in dbSNP:rs9262143). {ECO:0000269|PubMed:14574404}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CGAGCCTTCCCGGAGTTCAGG	0.567													C|||	97	0.019369	0.0023	0.0202	5008	,	,		14981	0.0		0.0795	False		,,,				2504	0.0				p.G339R		Atlas-SNP	.											.	.	.	.	0			c.G1015A						PASS	.	C	ARG/GLY,ARG/GLY	54,2818		1,52,1383	120.0	143.0	135.0		1015,1015	5.1	1.0	6	dbSNP_118	135	551,4765		32,487,2139	yes	missense,missense	KIAA1949	NM_001134870.1,NM_133471.3	125,125	33,539,3522	TT,TC,CC		10.3649,1.8802,7.3889	probably-damaging,probably-damaging	339/614,339/614	30652781	605,7583	1436	2658	4094	SO:0001583	missense	170954	exon2			CCTTCCCGGAGTT	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29413	protein-coding gene	gene with protein product	"""protein phosphatase 1 F-actin cytoskeleton targeting subunit"""	610990	"""KIAA1949"""	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.1015G>A	6.37:g.30652781C>T	ENSP00000274853:p.Gly339Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	115	89	0.773913	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	79	0.036172161172161175	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	66	0.0870712401055409	C	20.5	4.006971	0.74932	0.018802	0.103649	ENSG00000146112	ENST00000274853;ENST00000399199	T;T	0.55588	0.51;0.51	5.1	5.1	0.69264	.	0.378221	0.21808	N	0.068801	T	0.50837	0.1639	L	0.32530	0.975	0.38584	D	0.950265	D	0.76494	0.999	D	0.64595	0.927	T	0.45101	-0.9284	10	0.28530	T	0.3	-24.1078	17.2657	0.87086	0.0:1.0:0.0:0.0	rs9262143;rs17189267;rs52821119;rs57338511;rs9262143	339	Q6NYC8	PPR18_HUMAN	R	339	ENSP00000274853:G339R;ENSP00000382150:G339R	ENSP00000274853:G339R	G	-	1	0	KIAA1949	30760760	0.995000	0.38212	1.000000	0.80357	0.967000	0.64934	3.624000	0.54231	2.369000	0.80426	0.561000	0.74099	GGG	C|0.942;T|0.058	0.058	strong		0.567	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471	
MUC5B	727897	hgsc.bcm.edu	37	11	1246941	1246941	+	Missense_Mutation	SNP	A	A	G	rs2672785	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1246941A>G	ENST00000529681.1	+	2	159	c.101A>G	c.(100-102)gAg>gGg	p.E34G	MUC5B_ENST00000447027.1_Missense_Mutation_p.E34G	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	34			E -> G (in dbSNP:rs2672785). {ECO:0000269|PubMed:11713095, ECO:0000269|PubMed:9804771}.		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)		CCGAGCTGGGAGAATGCAGGG	0.642													g|||	1640	0.327476	0.3434	0.2767	5008	,	,		17181	0.4365		0.2406	False		,,,				2504	0.319				p.E34G		Atlas-SNP	.											MUC5B,NS,malignant_melanoma,-1,4	MUC5B	473	4	0			c.A101G						PASS	.	G	GLY/GLU	1174,2798		178,818,990	26.0	34.0	31.0		101	0.0	0.0	11	dbSNP_100	31	1699,6603		201,1297,2653	yes	missense	MUC5B	NM_002458.2	98	379,2115,3643	GG,GA,AA		20.4649,29.5569,23.4072	benign	34/5763	1246941	2873,9401	1986	4151	6137	SO:0001583	missense	727897	exon2			GCTGGGAGAATGC	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.101A>G	11.37:g.1246941A>G	ENSP00000436812:p.Glu34Gly	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	218	114	0.522936	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	708	0.3241758241758242	177	0.3597560975609756	108	0.2983425414364641	246	0.43006993006993005	177	0.23350923482849603	G	7.391	0.630737	0.14322	0.295569	0.204649	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637	T;T	0.20069	2.1;2.29	3.05	0.0329	0.14177	.	.	.	.	.	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.47328	-0.9126	8	0.87932	D	0	.	0.5156	0.00603	0.2992:0.2414:0.2905:0.1689	rs2672785;rs61649189;rs2672785	34;660;34	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	G	34	ENSP00000436812:E34G;ENSP00000415793:E34G	ENSP00000343037:E34G	E	+	2	0	MUC5B	1203517	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.925000	0.03992	-0.216000	0.10048	-0.215000	0.12644	GAG	A|0.673;G|0.327	0.327	strong		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TSSK1B	83942	hgsc.bcm.edu	37	5	112770027	112770027	+	Silent	SNP	T	T	G	rs26980	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:112770027T>G	ENST00000390666.3	-	1	701	c.510A>C	c.(508-510)gcA>gcC	p.A170A	MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000416046.2_RNA|CTD-2201G3.1_ENST00000510381.2_RNA|CTD-2201G3.1_ENST00000383058.4_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	170	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		TCTTGCTTAATGCCATTCGAC	0.562													T|||	257	0.0513179	0.0204	0.0317	5008	,	,		20598	0.0288		0.1243	False		,,,				2504	0.0552				p.A170A		Atlas-SNP	.											.	TSSK1B	89	.	0			c.A510C						PASS	.	T	,	152,4252	101.6+/-140.2	2,148,2052	75.0	72.0	73.0		,510	-0.0	0.6	5	dbSNP_76	73	1022,7578	218.0+/-256.5	46,930,3324	no	intron,coding-synonymous	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,	48,1078,5376	GG,GT,TT		11.8837,3.4514,9.028	,	,170/368	112770027	1174,11830	2202	4300	6502	SO:0001819	synonymous_variant	83942	exon1			GCTTAATGCCATT	AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"""serine/threonine kinase 22D (spermiogenesis associated)"", ""testis-specific serine kinase 1"""	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.510A>C	5.37:g.112770027T>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_032028	B2R8D9	Silent	SNP	ENST00000390666.3	37	CCDS4112.1																																																																																			T|0.931;G|0.069	0.069	strong		0.562	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028	
SLC17A9	63910	hgsc.bcm.edu	37	20	61588865	61588865	+	Silent	SNP	C	C	T	rs76379118	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61588865C>T	ENST00000370351.4	+	3	461	c.330C>T	c.(328-330)ctC>ctT	p.L110L	SLC17A9_ENST00000488738.1_3'UTR|SLC17A9_ENST00000370349.3_Silent_p.L104L	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	110					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						CCCCACTGCTCGCCCACCTGA	0.632													C|||	127	0.0253594	0.0045	0.0389	5008	,	,		23715	0.001		0.0716	False		,,,				2504	0.0215				p.L110L		Atlas-SNP	.											.	SLC17A9	54	.	0			c.C330T						PASS	.	C		61,4227		1,59,2084	69.0	75.0	73.0		330	-5.2	0.0	20	dbSNP_132	73	580,7922		21,538,3692	no	coding-synonymous	SLC17A9	NM_022082.3		22,597,5776	TT,TC,CC		6.8219,1.4226,5.0117		110/437	61588865	641,12149	2144	4251	6395	SO:0001819	synonymous_variant	63910	exon3			ACTGCTCGCCCAC	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"""Solute carriers"""	16192	protein-coding gene	gene with protein product		612107	"""chromosome 20 open reading frame 59"", ""solute carrier family 17, member 9"""	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.330C>T	20.37:g.61588865C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Silent	SNP	ENST00000370351.4	37	CCDS42901.1																																																																																			C|0.958;T|0.042	0.042	strong		0.632	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
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 GAIIx	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		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	189	92	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	
ANKRD26	22852	hgsc.bcm.edu	37	10	27303605	27303605	+	Missense_Mutation	SNP	A	A	T	rs2274741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27303605A>T	ENST00000376087.4	-	31	4707	c.4542T>A	c.(4540-4542)ttT>ttA	p.F1514L	ANKRD26_ENST00000436985.2_Missense_Mutation_p.F1530L|ANKRD26_ENST00000376070.3_Missense_Mutation_p.F1071L	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1513					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TATTCTCTCTAAACTGCTCTA	0.318													T|||	1589	0.317292	0.236	0.1758	5008	,	,		16688	0.5506		0.1928	False		,,,				2504	0.4151				p.F1514L		Atlas-SNP	.											.	ANKRD26	179	.	0			c.T4542A						PASS	.	T	LEU/PHE	841,2775		97,647,1064	57.0	51.0	53.0		4542	1.3	0.0	10	dbSNP_100	53	1181,6977		78,1025,2976	yes	missense	ANKRD26	NM_014915.2	22	175,1672,4040	TT,TA,AA		14.4766,23.2577,17.1734	benign	1514/1711	27303605	2022,9752	1808	4079	5887	SO:0001583	missense	22852	exon31			CTCTCTAAACTGC	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4542T>A	10.37:g.27303605A>T	ENSP00000365255:p.Phe1514Leu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	660|660	0.3021978021978022|0.3021978021978022	109|109	0.22154471544715448|0.22154471544715448	63|63	0.17403314917127072|0.17403314917127072	340|340	0.5944055944055944|0.5944055944055944	148|148	0.19525065963060687|0.19525065963060687	T|T	1.260|1.260	-0.616082|-0.616082	0.03663|0.03663	0.232577|0.232577	0.144766|0.144766	ENSG00000107890|ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985|ENST00000445828	T;T;T|.	0.23348|.	4.39;1.92;1.91|.	5.13|5.13	1.33|1.33	0.21861|0.21861	.|.	0.158842|.	0.28425|.	N|.	0.015397|.	T|.	0.00012|.	0.0000|.	N|N	0.00080|0.00080	-2.225|-2.225	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|.	0.38972|.	-0.9636|.	9|.	0.02654|.	T|.	1|.	.|.	2.8736|2.8736	0.05624|0.05624	0.1342:0.0773:0.2793:0.5092|0.1342:0.0773:0.2793:0.5092	rs2274741;rs52820176;rs2274741|rs2274741;rs52820176;rs2274741	1514;1513;1530|.	Q9UPS8-3;Q9UPS8;A1L497|.	.;ANR26_HUMAN;.|.	L|K	1071;1514;1530|2	ENSP00000365238:F1071L;ENSP00000365255:F1514L;ENSP00000405112:F1530L|.	ENSP00000365238:F1071L|.	F|X	-|-	3|1	2|0	ANKRD26|ANKRD26	27343611|27343611	1.000000|1.000000	0.71417|0.71417	0.001000|0.001000	0.08648|0.08648	0.691000|0.691000	0.40173|0.40173	0.535000|0.535000	0.23114|0.23114	-0.287000|-0.287000	0.09064|0.09064	-0.827000|-0.827000	0.03088|0.03088	TTT|TAG	A|0.712;T|0.288	0.288	strong		0.318	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
ESPL1	9700	hgsc.bcm.edu	37	12	53662624	53662624	+	Missense_Mutation	SNP	C	C	A	rs6580942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53662624C>A	ENST00000257934.4	+	2	165	c.74C>A	c.(73-75)gCc>gAc	p.A25D	ESPL1_ENST00000552462.1_Missense_Mutation_p.A25D	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	25				A -> D (in Ref. 1; AAR18247). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TTGCTGCCCGCCTTGAAGGTG	0.527													A|||	4449	0.888379	0.9841	0.7954	5008	,	,		17314	0.999		0.673	False		,,,				2504	0.9325				p.A25D	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C74A						PASS	.	A	ASP/ALA	4135,271	151.0+/-185.0	1946,243,14	35.0	34.0	34.0	http://omim.org/entry/606257	74	4.8	0.1	12	dbSNP_116	34	5835,2765	433.7+/-357.5	1997,1841,462	yes	missense	ESPL1	NM_012291.4	126	3943,2084,476	AA,AC,CC		32.1512,6.1507,23.3431	benign	25/2121	53662624	9970,3036	2203	4300	6503	SO:0001583	missense	9700	exon2			TGCCCGCCTTGAA	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.74C>A	12.37:g.53662624C>A	ENSP00000257934:p.Ala25Asp	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	40	39	0.975	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	1822	0.8342490842490843	475	0.9654471544715447	281	0.7762430939226519	572	1.0	494	0.6517150395778364	A	1.127	-0.653471	0.03480	0.938493	0.678488	ENSG00000135476	ENST00000257934;ENST00000552462	T;T	0.10668	2.85;2.85	5.95	4.79	0.61399	.	0.227922	0.36519	N	0.002552	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37753	-0.9692	9	0.02654	T	1	.	11.3037	0.49323	0.7081:0.2919:0.0:0.0	rs6580942;rs17750752;rs52806931;rs60259413;rs6580942	25	Q14674	ESPL1_HUMAN	D	25	ENSP00000257934:A25D;ENSP00000449831:A25D	ENSP00000257934:A25D	A	+	2	0	ESPL1	51948891	0.995000	0.38212	0.137000	0.22149	0.354000	0.29330	3.448000	0.52943	0.492000	0.27815	-0.256000	0.11100	GCC	C|0.192;A|0.808	0.808	strong		0.527	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
QSOX1	5768	hgsc.bcm.edu	37	1	180159654	180159654	+	Silent	SNP	C	C	T	rs7521513	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:180159654C>T	ENST00000367602.3	+	10	1301	c.1227C>T	c.(1225-1227)gtC>gtT	p.V409V	QSOX1_ENST00000367600.5_Silent_p.V409V			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	409	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						CCCTGTGGGTCCTCTTCCACT	0.592													C|||	630	0.125799	0.0832	0.1556	5008	,	,		18817	0.0744		0.1581	False		,,,				2504	0.182				p.V409V		Atlas-SNP	.											.	QSOX1	79	.	0			c.C1227T						PASS	.	C	,	388,4018		27,334,1842	135.0	121.0	126.0		1227,1227	3.7	1.0	1	dbSNP_116	126	1340,7260		121,1098,3081	no	coding-synonymous,coding-synonymous	QSOX1	NM_001004128.2,NM_002826.4	,	148,1432,4923	TT,TC,CC		15.5814,8.8062,13.2862	,	409/605,409/748	180159654	1728,11278	2203	4300	6503	SO:0001819	synonymous_variant	5768	exon10			GTGGGTCCTCTTC	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1227C>T	1.37:g.180159654C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Silent	SNP	ENST00000367602.3	37	CCDS1337.1																																																																																			C|0.863;T|0.137	0.137	strong		0.592	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
GABRB1	2560	hgsc.bcm.edu	37	4	47322219	47322219	+	Silent	SNP	C	C	A	rs6284	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:47322219C>A	ENST00000295454.3	+	5	829	c.537C>A	c.(535-537)atC>atA	p.I179I	GABRB1_ENST00000538619.1_Silent_p.I109I	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	179					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CCCTGGAGATCGAAAGTTGTG	0.423													C|||	634	0.126597	0.1074	0.1282	5008	,	,		17941	0.1101		0.1968	False		,,,				2504	0.0961				p.I179I		Atlas-SNP	.											.	GABRB1	107	.	0			c.C537A						PASS	.	C		553,3853	247.8+/-255.9	39,475,1689	111.0	96.0	101.0		537	-2.5	1.0	4	dbSNP_52	101	1727,6873	313.1+/-311.2	146,1435,2719	no	coding-synonymous	GABRB1	NM_000812.3		185,1910,4408	AA,AC,CC		20.0814,12.5511,17.5304		179/475	47322219	2280,10726	2203	4300	6503	SO:0001819	synonymous_variant	2560	exon5			GGAGATCGAAAGT		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4081	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 1"""	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.537C>A	4.37:g.47322219C>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Silent	SNP	ENST00000295454.3	37	CCDS3474.1																																																																																			C|0.849;A|0.151	0.151	strong		0.423	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1		
TRIM45	80263	hgsc.bcm.edu	37	1	117656088	117656088	+	Missense_Mutation	SNP	A	A	G	rs1289658	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117656088A>G	ENST00000256649.4	-	5	2013	c.1487T>C	c.(1486-1488)aTg>aCg	p.M496T	TRIM45_ENST00000369461.3_Missense_Mutation_p.M439T|TRIM45_ENST00000369464.3_Missense_Mutation_p.M478T	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	496			M -> T (in dbSNP:rs1289658). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15351693, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		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)		TCTCCTCACCATCACAGTGAA	0.557													G|||	2229	0.445088	0.6793	0.4755	5008	,	,		22011	0.1865		0.4364	False		,,,				2504	0.3824				p.M496T		Atlas-SNP	.											.	TRIM45	55	.	0			c.T1487C						PASS	.	G	THR/MET,THR/MET	2732,1674	508.8+/-367.0	873,986,344	66.0	61.0	62.0		1433,1487	4.0	0.6	1	dbSNP_87	62	3455,5145	636.3+/-399.1	680,2095,1525	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	81,81	1553,3081,1869	GG,GA,AA		40.1744,37.9936,47.5704	benign,benign	478/563,496/581	117656088	6187,6819	2203	4300	6503	SO:0001583	missense	80263	exon5			CTCACCATCACAG		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.1487T>C	1.37:g.117656088A>G	ENSP00000256649:p.Met496Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_025188	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	909	0.41620879120879123	317	0.6443089430894309	169	0.46685082872928174	93	0.16258741258741258	330	0.43535620052770446	G	0.005	-2.228181	0.00280	0.620064	0.401744	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	T;T;T	0.39406	2.08;1.08;2.08	4.96	3.99	0.46301	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.522971	0.20258	N	0.095923	T	0.02929	0.0087	N	0.00823	-1.155	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39663	-0.9603	9	0.07030	T	0.85	-10.0408	3.8833	0.09088	0.1845:0.0:0.4103:0.4052	rs1289658;rs17524007;rs52814348;rs60516003;rs1289658	478;496	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	T	496;478;439	ENSP00000256649:M496T;ENSP00000358476:M478T;ENSP00000358473:M439T	ENSP00000256649:M496T	M	-	2	0	TRIM45	117457611	0.023000	0.18921	0.629000	0.29254	0.342000	0.28953	0.149000	0.16243	0.562000	0.29204	-0.213000	0.12676	ATG	A|0.549;G|0.451	0.451	strong		0.557	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
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 GAIIx	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	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	11	6	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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.I71M|SGK1_ENST00000367857.5_Missense_Mutation_p.I47M|SGK1_ENST00000475719.2_Missense_Mutation_p.I57M|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367858.5_Missense_Mutation_p.I152M|SGK1_ENST00000528577.1_Missense_Mutation_p.I85M	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	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	5	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:10258375G>A	ENST00000254976.2	+	3	325		c.e3+1		SNAP25-AS1_ENST00000453544.1_RNA|SNAP25_ENST00000304886.2_Splice_Site|SNAP25-AS1_ENST00000421143.2_RNA	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		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	20	5	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
SLCO4C1	353189	hgsc.bcm.edu	37	5	101575091	101575091	+	Splice_Site	SNP	C	C	T	rs62370437	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:101575091C>T	ENST00000310954.6	-	12	2164	c.1878G>A	c.(1876-1878)ggG>ggA	p.G626G		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		CAGGAATTGTCCCTAAAAGAA	0.284													T|||	1651	0.329673	0.3434	0.2738	5008	,	,		15098	0.2589		0.4592	False		,,,				2504	0.2904				p.G626G		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.G1878A						PASS	.	T		1589,2817	632.7+/-395.9	295,999,909	50.0	52.0	51.0		1878	-1.1	1.0	5	dbSNP_129	51	3928,4670	586.9+/-392.1	910,2108,1281	yes	coding-synonymous-near-splice	SLCO4C1	NM_180991.4		1205,3107,2190	TT,TC,CC		45.685,36.0645,42.4254		626/725	101575091	5517,7487	2203	4299	6502	SO:0001630	splice_region_variant	353189	exon12			AATTGTCCCTAAA	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.1877-1G>A	5.37:g.101575091C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_180991		Silent	SNP	ENST00000310954.6	37	CCDS34205.1																																																																																			C|0.597;T|0.403	0.403	strong		0.284	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	Silent
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 GAIIx	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_ENST00000389272.3_Missense_Mutation_p.D468Y|STAT3_ENST00000404395.3_Missense_Mutation_p.D566Y|STAT3_ENST00000588969.1_Missense_Mutation_p.D566Y|STAT3_ENST00000585517.1_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	Somatic	87	0	0	893	WXS	Illumina HiSeq	Phase_I	102	33	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	
CFHR2	3080	hgsc.bcm.edu	37	1	196884258	196884258	+	Intron	SNP	A	A	T	rs150845796		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196884258A>T	ENST00000367421.3	+	2	135				CFHR4_ENST00000608469.1_Silent_p.P133P|CFHR4_ENST00000367416.2_Silent_p.P509P|CFHR4_ENST00000251424.4_Silent_p.P263P|CFHR4_ENST00000367418.2_Silent_p.P263P			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						CGGAACCACCAAGATGCATAC	0.358																																					p.P510P		Atlas-SNP	.											CFHR4_ENST00000367416,right_lower_lobe,carcinoma,+1,2	CFHR4	141	2	0			c.A1530T						scavenged	.						67.0	69.0	68.0					1																	196884258		2199	4295	6494	SO:0001627	intron_variant	10877	exon9			ACCACCAAGATGC	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	ENST00000367421.3:c.59-34327A>T	1.37:g.196884258A>T		Somatic	354	1	0.00282486		WXS	Illumina HiSeq	Phase_I	509	143	0.280943	NM_001201550	Q14310|Q5T9T1	Silent	SNP	ENST00000367421.3	37																																																																																				.	.	weak		0.358	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666	
IRS2	8660	hgsc.bcm.edu	37	13	110435914	110435914	+	Silent	SNP	G	G	A	rs12853546	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:110435914G>A	ENST00000375856.3	-	1	3001	c.2487C>T	c.(2485-2487)ccC>ccT	p.P829P		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	829					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TGCGCCCCACGGGGGAGCTCA	0.731													.|||	1127	0.22504	0.2027	0.1542	5008	,	,		8938	0.2173		0.2565	False		,,,				2504	0.2812				p.P829P	Melanoma(100;613 2409 40847)	Atlas-SNP	.											IRS2,NS,carcinoma,0,1	IRS2	44	1	0			c.C2487T						PASS	.	G		757,3251		86,585,1333	4.0	6.0	5.0		2487	-10.3	0.3	13	dbSNP_121	5	1742,6278		224,1294,2492	no	coding-synonymous	IRS2	NM_003749.2		310,1879,3825	AA,AG,GG		21.7207,18.8872,20.7765		829/1339	110435914	2499,9529	2004	4010	6014	SO:0001819	synonymous_variant	8660	exon1			CCCCACGGGGGAG	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2487C>T	13.37:g.110435914G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Silent	SNP	ENST00000375856.3	37	CCDS9510.1																																																																																			G|0.788;A|0.212	0.212	strong		0.731	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749	
C3orf20	84077	hgsc.bcm.edu	37	3	14724413	14724413	+	Missense_Mutation	SNP	G	G	A	rs9821143	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:14724413G>A	ENST00000253697.3	+	3	645	c.193G>A	c.(193-195)Gac>Aac	p.D65N	C3orf20_ENST00000435614.1_Intron|C3orf20_ENST00000412910.1_Intron	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	65			D -> N (in dbSNP:rs9821143).			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						TACCCCGTCCGACATCTTGGG	0.552													G|||	1491	0.297724	0.2806	0.4438	5008	,	,		19624	0.2252		0.3658	False		,,,				2504	0.2219				p.D65N		Atlas-SNP	.											.	C3orf20	109	.	0			c.G193A						PASS	.	G	,,ASN/ASP	1359,3047	451.6+/-349.7	215,929,1059	111.0	110.0	110.0		,,193	0.6	0.0	3	dbSNP_119	110	2990,5610	463.5+/-366.0	486,2018,1796	yes	intron,intron,missense	C3orf20	NM_001184957.1,NM_001184958.1,NM_032137.4	,,23	701,2947,2855	AA,AG,GG		34.7674,30.8443,33.4384	,,benign	,,65/905	14724413	4349,8657	2203	4300	6503	SO:0001583	missense	84077	exon3			CCGTCCGACATCT	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.193G>A	3.37:g.14724413G>A	ENSP00000253697:p.Asp65Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Missense_Mutation	SNP	ENST00000253697.3	37	CCDS33706.1	732	0.33516483516483514	159	0.3231707317073171	154	0.425414364640884	139	0.243006993006993	280	0.36939313984168864	G	9.562	1.118756	0.20877	0.308443	0.347674	ENSG00000131379	ENST00000253697	T	0.06449	3.3	5.28	0.576	0.17380	.	0.883554	0.09670	N	0.771197	T	0.00012	0.0000	L	0.29908	0.895	0.48901	P	2.7800000000000047E-4	B	0.32800	0.385	B	0.21360	0.034	T	0.45056	-0.9287	9	0.37606	T	0.19	-8.4977	1.4841	0.02443	0.3045:0.1444:0.4042:0.1469	rs9821143;rs52827165;rs57810074;rs9821143	65	Q8ND61	CC020_HUMAN	N	65	ENSP00000253697:D65N	ENSP00000253697:D65N	D	+	1	0	C3orf20	14699417	0.000000	0.05858	0.003000	0.11579	0.024000	0.10985	-0.301000	0.08232	0.166000	0.19597	0.591000	0.81541	GAC	G|0.672;A|0.328	0.328	strong		0.552	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
MUC2	4583	hgsc.bcm.edu	37	11	1101649	1101649	+	Silent	SNP	T	T	C	rs7480563	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1101649T>C	ENST00000441003.2	+	42	7689	c.7662T>C	c.(7660-7662)ccT>ccC	p.P2554P		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4916					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)	GGTGCTGTCCTTTCTACTGGT	0.627													C|||	3492	0.697284	0.6808	0.6196	5008	,	,		15474	0.9931		0.5219	False		,,,				2504	0.6503				p.P2550P		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.T7650C						PASS	.	C		2577,1589		802,973,308	93.0	103.0	100.0		7647	-5.3	0.0	11	dbSNP_116	100	4354,4066		1136,2082,992	no	coding-synonymous	MUC2	NM_002457.2		1938,3055,1300	CC,CT,TT		48.2898,38.1421,44.9309		2549/2813	1101649	6931,5655	2083	4210	6293	SO:0001819	synonymous_variant	4583	exon43			CTGTCCTTTCTAC	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.7662T>C	11.37:g.1101649T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.346;C|0.654	0.654	strong		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
DHX9	1660	hgsc.bcm.edu	37	1	182844020	182844020	+	Silent	SNP	C	C	T	rs11332	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:182844020C>T	ENST00000367549.3	+	16	1856	c.1746C>T	c.(1744-1746)acC>acT	p.T582T		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	582					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TTCAGATGACCCACTTTGTTC	0.383													C|||	900	0.179712	0.3449	0.1254	5008	,	,		19735	0.1181		0.0746	False		,,,				2504	0.1667				p.T582T	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.C1746T						PASS	.	C		1131,2635		160,811,912	129.0	134.0	132.0		1746	3.5	1.0	1	dbSNP_52	132	652,7578		23,606,3486	no	coding-synonymous	DHX9	NM_001357.4		183,1417,4398	TT,TC,CC		7.9222,30.0319,14.8633		582/1271	182844020	1783,10213	1883	4115	5998	SO:0001819	synonymous_variant	1660	exon16			GATGACCCACTTT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1746C>T	1.37:g.182844020C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	55	30	0.545455	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																			C|0.865;T|0.135	0.135	strong		0.383	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
OR10H1	26539	hgsc.bcm.edu	37	19	15918434	15918434	+	Silent	SNP	C	C	A	rs1859299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15918434C>A	ENST00000334920.2	-	1	502	c.414G>T	c.(412-414)ccG>ccT	p.P138P		NM_013940.2	NP_039228.1	Q9Y4A9	O10H1_HUMAN	olfactory receptor, family 10, subfamily H, member 1	138						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(4)|large_intestine(6)|lung(8)|ovary(4)|skin(2)|urinary_tract(1)	29						CGCAGCCCCGCGGGCTCATGA	0.647													.|||	65	0.0129792	0.0053	0.0216	5008	,	,		19364	0.0		0.0398	False		,,,				2504	0.0031				p.P138P		Atlas-SNP	.											.	OR10H1	59	.	0			c.G414T						PASS	.	T		44,4362		0,44,2159	87.0	71.0	76.0		414	-6.2	0.0	19	dbSNP_92	76	452,8148		12,428,3860	no	coding-synonymous	OR10H1	NM_013940.2		12,472,6019	AA,AC,CC		5.2558,0.9986,3.8136		138/319	15918434	496,12510	2203	4300	6503	SO:0001819	synonymous_variant	26539	exon1			GCCCCGCGGGCTC	AC004510	CCDS12335.1	19p13.1	2012-08-09				ENSG00000186723		"""GPCR / Class A : Olfactory receptors"""	8172	protein-coding gene	gene with protein product							Standard	NM_013940		Approved		uc002nbq.2	Q9Y4A9		ENST00000334920.2:c.414G>T	19.37:g.15918434C>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_013940	Q6IFQ2|Q96R59	Silent	SNP	ENST00000334920.2	37	CCDS12335.1																																																																																			A|0.032;C|0.968	0.032	strong		0.647	OR10H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460364.1		
ALPPL2	251	hgsc.bcm.edu	37	2	233274509	233274509	+	Missense_Mutation	SNP	C	C	G	rs1048995	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233274509C>G	ENST00000295453.3	+	11	1578	c.1526C>G	c.(1525-1527)cCg>cGg	p.P509R		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	509					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		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;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	CACCCGGGGCCGTCCGTGGTC	0.726													c|||	554	0.110623	0.1679	0.0519	5008	,	,		10598	0.128		0.0875	False		,,,				2504	0.0808				p.P509R		Atlas-SNP	.											ALPPL2,NS,carcinoma,0,2	ALPPL2	36	2	0			c.C1526G						scavenged	.						8.0	11.0	10.0					2																	233274509		2137	4190	6327	SO:0001583	missense	251	exon11			CGGGGCCGTCCGT	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.1526C>G	2.37:g.233274509C>G	ENSP00000295453:p.Pro509Arg	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	37	CCDS2491.1	231	0.10576923076923077	68	0.13821138211382114	22	0.06077348066298342	70	0.12237762237762238	71	0.09366754617414248	c	0.410	-0.913674	0.02415	.	.	ENSG00000163286	ENST00000295453	D	0.95377	-3.69	2.44	-2.3	0.06785	.	1.123750	0.06665	N	0.765198	T	0.03390	0.0098	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.58160	-0.7685	9	0.10636	T	0.68	.	0.9298	0.01332	0.1568:0.3069:0.1599:0.3764	rs1048995;rs3189068;rs16828989	509	P10696	PPBN_HUMAN	R	509	ENSP00000295453:P509R	ENSP00000295453:P509R	P	+	2	0	ALPPL2	232982753	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.789000	0.04609	-1.031000	0.03308	-1.087000	0.02190	CCG	C|0.899;G|0.101	0.101	strong		0.726	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313	
SNAPC4	6621	hgsc.bcm.edu	37	9	139289825	139289825	+	Silent	SNP	A	A	G	rs4266763	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139289825A>G	ENST00000298532.2	-	4	764	c.396T>C	c.(394-396)gaT>gaC	p.D132D		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GGCTTTTGCCATCTTTCACCT	0.567													a|||	1983	0.395966	0.3593	0.5793	5008	,	,		18187	0.3214		0.3907	False		,,,				2504	0.3978				p.D132D		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T396C						PASS	.	G		1553,2853	666.9+/-401.8	266,1021,916	114.0	102.0	106.0		396	-9.4	0.0	9	dbSNP_111	106	3587,5013	626.9+/-397.9	742,2103,1455	no	coding-synonymous	SNAPC4	NM_003086.2		1008,3124,2371	GG,GA,AA		41.7093,35.2474,39.5202		132/1470	139289825	5140,7866	2203	4300	6503	SO:0001819	synonymous_variant	6621	exon4			TTTGCCATCTTTC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.396T>C	9.37:g.139289825A>G		Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.611;G|0.388	0.388	strong		0.567	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
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 GAIIx	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		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	20	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	
IDO2	169355	hgsc.bcm.edu	37	8	39840234	39840234	+	Missense_Mutation	SNP	A	A	G	rs4736794	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:39840234A>G	ENST00000389060.4	+	4	379	c.379A>G	c.(379-381)Atc>Gtc	p.I127V	RP11-44K6.3_ENST00000517623.1_RNA|IDO2_ENST00000343295.4_3'UTR|IDO2_ENST00000502986.2_Missense_Mutation_p.I140V			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	127					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						GCTCCCTCCTATCCTGGTCCA	0.463													A|||	800	0.159744	0.0227	0.2118	5008	,	,		17762	0.3343		0.1014	False		,,,				2504	0.1881				p.I140V		Atlas-SNP	.											.	IDO2	78	.	0			c.A418G						PASS	.	A	VAL/ILE	115,3659		3,109,1775	66.0	66.0	66.0		418	5.3	1.0	8	dbSNP_111	66	780,7436		28,724,3356	yes	missense	IDO2	NM_194294.2	29	31,833,5131	GG,GA,AA		9.4937,3.0472,7.4646	probably-damaging	140/421	39840234	895,11095	1887	4108	5995	SO:0001583	missense	169355	exon5			CCTCCTATCCTGG	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.379A>G	8.37:g.39840234A>G	ENSP00000426447:p.Ile127Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	36	0.6	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		358	0.16391941391941392	10	0.02032520325203252	67	0.1850828729281768	207	0.3618881118881119	74	0.09762532981530343	A	20.8	4.056992	0.76074	0.030472	0.094937	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.41758	0.99;0.99	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.37850	1.14	0.25863	P	0.9838042	D	0.76494	0.999	D	0.83275	0.996	T	0.38757	-0.9646	8	.	.	.	.	11.6398	0.51227	1.0:0.0:0.0:0.0	rs4736794;rs52790922;rs57148239;rs4736794	140	F5H5G0	.	V	140;127	ENSP00000443432:I140V;ENSP00000426447:I127V	.	I	+	1	0	IDO2	39959391	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	6.903000	0.75703	2.009000	0.58944	0.377000	0.23210	ATC	A|0.845;G|0.155	0.155	strong		0.463	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
STT3B	201595	hgsc.bcm.edu	37	3	31667621	31667621	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:31667621T>C	ENST00000295770.2	+	13	2282		c.e13+2			NM_178862.1	NP_849193.1	Q8TCJ2	STT3B_HUMAN	STT3B, subunit of the oligosaccharyltransferase complex (catalytic)						co-translational protein modification (GO:0043686)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to unfolded protein (GO:0006986)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			autonomic_ganglia(1)|biliary_tract(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	19						GACATTCGGGTAAGAAACTAG	0.383																																					.		Atlas-SNP	.											STT3B,NS,carcinoma,0,1	STT3B	52	1	0			c.2073+2T>C						scavenged	.						105.0	99.0	101.0					3																	31667621		2203	4300	6503	SO:0001630	splice_region_variant	201595	exon13			TTCGGGTAAGAAA	AK027789	CCDS2650.1	3p24.1	2013-03-06	2013-03-06		ENSG00000163527	ENSG00000163527	2.4.99.18		30611	protein-coding gene	gene with protein product	"""source of immunodominant MHC associated peptides"", ""dolichyl-diphosphooligosaccharide protein glycotransferase"""	608605	"""STT3, subunit of the oligosaccharyltransferase complex, homolog B (S. cerevisiae)"""			12887896, 12439619	Standard	XM_006713017		Approved	SIMP, FLJ90106, STT3-B	uc011axe.2	Q8TCJ2	OTTHUMG00000130673	ENST00000295770.2:c.2073+2T>C	3.37:g.31667621T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	96	2	0.0208333	NM_178862	Q96JZ4|Q96KY7	Splice_Site	SNP	ENST00000295770.2	37	CCDS2650.1	.	.	.	.	.	.	.	.	.	.	T	16.44	3.122966	0.56613	.	.	ENSG00000163527	ENST00000295770	.	.	.	5.36	4.18	0.49190	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.8342	0.52314	0.1314:0.0:0.0:0.8685	.	.	.	.	.	-1	.	.	.	+	.	.	STT3B	31642625	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	7.986000	0.88173	0.958000	0.37956	0.260000	0.18958	.	.	.	none		0.383	STT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253166.2	NM_178862	Intron
OR2T33	391195	hgsc.bcm.edu	37	1	248436655	248436655	+	Silent	SNP	C	C	G	rs140771747		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248436655C>G	ENST00000318021.2	-	1	483	c.462G>C	c.(460-462)ggG>ggC	p.G154G		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	154						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G154G(1)		NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|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;0.0245)			CCTGCAGGAGCCCGTCAGCTG	0.587																																					p.G154G		Atlas-SNP	.											OR2T33,NS,carcinoma,0,3	OR2T33	133	3	1	Substitution - coding silent(1)	large_intestine(1)	c.G462C						PASS	.						98.0	95.0	96.0					1																	248436655		2203	4300	6503	SO:0001819	synonymous_variant	391195	exon1			CAGGAGCCCGTCA		CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"""GPCR / Class A : Olfactory receptors"""	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.462G>C	1.37:g.248436655C>G		Somatic	412	0	0		WXS	Illumina HiSeq	Phase_I	516	41	0.0794574	NM_001004695	B2RNN0	Silent	SNP	ENST00000318021.2	37	CCDS31109.1																																																																																			C|0.999;G|0.001	0.001	weak		0.587	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695	
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 GAIIx	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		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	155	40	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	
PJA1	64219	hgsc.bcm.edu	37	X	68381912	68381912	+	Silent	SNP	G	G	A	rs3761646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:68381912G>A	ENST00000361478.1	-	2	1547	c.1170C>T	c.(1168-1170)ggC>ggT	p.G390G	PJA1_ENST00000374583.1_Silent_p.G390G|PJA1_ENST00000374584.3_Silent_p.G202G|PJA1_ENST00000477231.1_5'Flank|PJA1_ENST00000374571.4_Silent_p.G335G	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	390					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						CCCAGCTTTCGCCACTGGAGG	0.577													g|||	516	0.136689	0.053	0.2205	3775	,	,		12786	0.0774		0.1173	False		,,,				2504	0.0992				p.G390G		Atlas-SNP	.											.	PJA1	106	.	0			c.C1170T						PASS	.		,,	405,3430		20,295,70,1317,501	34.0	34.0	34.0		1005,606,1170	-6.7	0.0	X	dbSNP_107	34	1134,5593		78,681,297,1669,1574	no	coding-synonymous,coding-synonymous,coding-synonymous	PJA1	NM_001032396.2,NM_022368.4,NM_145119.3	,,	98,976,367,2986,2075	AA,AG,A,GG,G		16.8574,10.5606,14.5711	,,	335/589,202/456,390/644	68381912	1539,9023	2203	4299	6502	SO:0001819	synonymous_variant	64219	exon2			GCTTTCGCCACTG	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"""RING-type (C3HC4) zinc fingers"""	16648	protein-coding gene	gene with protein product		300420	"""praja 1"", ""praja ring finger 1"""			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.1170C>T	X.37:g.68381912G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	46	31	0.673913	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Silent	SNP	ENST00000361478.1	37	CCDS14393.1																																																																																			G|0.863;0|0.003	.	strong		0.577	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119	
FAM208B	54906	hgsc.bcm.edu	37	10	5781802	5781802	+	Missense_Mutation	SNP	C	C	A	rs41310221	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:5781802C>A	ENST00000328090.5	+	13	2294	c.1669C>A	c.(1669-1671)Ctt>Att	p.L557I	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	557																	GGCTAGAAATCTTCACTGTTC	0.403													C|||	14	0.00279553	0.0	0.0029	5008	,	,		20244	0.0		0.0089	False		,,,				2504	0.0031				p.L557I		Atlas-SNP	.											.	.	.	.	0			c.C1669A						PASS	.	C	ILE/LEU	8,3744		0,8,1868	102.0	94.0	97.0		1669	-3.0	0.0	10	dbSNP_127	97	89,8135		0,89,4023	yes	missense	FAM208B	NM_017782.4	5	0,97,5891	AA,AC,CC		1.0822,0.2132,0.81	possibly-damaging	557/2431	5781802	97,11879	1876	4112	5988	SO:0001583	missense	54906	exon13			AGAAATCTTCACT	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.1669C>A	10.37:g.5781802C>A	ENSP00000328426:p.Leu557Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	105	58	0.552381	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	7.876	0.729256	0.15507	0.002132	0.010822	ENSG00000108021	ENST00000328090	D	0.97772	-4.53	5.16	-2.97	0.05530	.	0.945549	0.08827	N	0.887882	D	0.92077	0.7489	L	0.50333	1.59	0.09310	N	1	P	0.37708	0.606	B	0.38985	0.287	D	0.86836	0.2014	10	0.18710	T	0.47	.	2.6594	0.05021	0.1114:0.4802:0.1088:0.2995	rs41310221	557	Q5VWN6	F208B_HUMAN	I	557	ENSP00000328426:L557I	ENSP00000328426:L557I	L	+	1	0	C10orf18	5821808	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-1.397000	0.02511	-1.064000	0.03172	0.491000	0.48974	CTT	C|0.994;A|0.006	0.006	strong		0.403	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
CCDC105	126402	hgsc.bcm.edu	37	19	15131330	15131330	+	Missense_Mutation	SNP	G	G	A	rs35352238	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15131330G>A	ENST00000292574.3	+	3	815	c.733G>A	c.(733-735)Gtg>Atg	p.V245M		NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	245			V -> M (in dbSNP:rs35352238).			extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						GCTCCAAGCCGTGGACCTCAT	0.622													G|||	1574	0.314297	0.0666	0.4496	5008	,	,		15408	0.5367		0.2535	False		,,,				2504	0.3865				p.V245M		Atlas-SNP	.											.	CCDC105	53	.	0			c.G733A						PASS	.	G	MET/VAL	489,3917	224.6+/-240.7	31,427,1745	52.0	47.0	49.0		733	4.1	0.9	19	dbSNP_126	49	2261,6339	380.0+/-339.5	286,1689,2325	yes	missense	CCDC105	NM_173482.2	21	317,2116,4070	AA,AG,GG		26.2907,11.0985,21.1441	probably-damaging	245/500	15131330	2750,10256	2203	4300	6503	SO:0001583	missense	126402	exon3			CAAGCCGTGGACC	AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.733G>A	19.37:g.15131330G>A	ENSP00000292574:p.Val245Met	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_173482	Q8N7T5|Q8NDL5	Missense_Mutation	SNP	ENST00000292574.3	37	CCDS12322.1	683	0.31272893772893773	38	0.07723577235772358	149	0.4116022099447514	294	0.513986013986014	202	0.26649076517150394	G	11.76	1.735569	0.30774	0.110985	0.262907	ENSG00000160994	ENST00000292574	T	0.02606	4.23	4.09	4.09	0.47781	.	0.160493	0.28225	N	0.016126	T	0.00012	0.0000	L	0.53249	1.67	0.42004	P	0.009095999999999993	D	0.89917	1.0	D	0.67900	0.954	T	0.48502	-0.9030	9	0.33940	T	0.23	-24.6107	12.2139	0.54396	0.0:0.0:1.0:0.0	rs35352238	245	Q8IYK2	CC105_HUMAN	M	245	ENSP00000292574:V245M	ENSP00000292574:V245M	V	+	1	0	CCDC105	14992330	0.983000	0.35010	0.881000	0.34555	0.082000	0.17680	2.069000	0.41481	1.982000	0.57802	0.558000	0.71614	GTG	G|0.758;A|0.242	0.242	strong		0.622	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482	
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 GAIIx	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_ENST00000356435.5_Missense_Mutation_p.P1311S|PTPRD_ENST00000397611.3_Missense_Mutation_p.P901S|PTPRD_ENST00000358503.5_Missense_Mutation_p.P1289S|PTPRD_ENST00000537002.1_Missense_Mutation_p.P901S|PTPRD_ENST00000360074.4_Missense_Mutation_p.P1298S|PTPRD_ENST00000486161.1_Missense_Mutation_p.P904S|PTPRD_ENST00000540109.1_Missense_Mutation_p.P1311S|PTPRD_ENST00000397617.3_Missense_Mutation_p.P890S|PTPRD_ENST00000397606.3_Missense_Mutation_p.P890S|PTPRD_ENST00000355233.5_Missense_Mutation_p.P905S	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	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	189	57	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		
SIPA1L3	23094	hgsc.bcm.edu	37	19	38673298	38673298	+	Missense_Mutation	SNP	C	C	G	rs3745945	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38673298C>G	ENST00000222345.6	+	16	4857	c.4348C>G	c.(4348-4350)Cct>Gct	p.P1450A	CTB-102L5.7_ENST00000594299.1_RNA	NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1450			P -> A (in dbSNP:rs3745945).		hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CTCCAAGCAGCCTGTACGCAA	0.617													C|||	262	0.0523163	0.0008	0.0893	5008	,	,		13199	0.0466		0.0835	False		,,,				2504	0.0695				p.P1450A		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C4348G						PASS	.	C	ALA/PRO	68,4338	63.5+/-100.7	0,68,2135	64.0	73.0	70.0		4348	4.4	1.0	19	dbSNP_107	70	632,7968	161.7+/-214.6	24,584,3692	yes	missense	SIPA1L3	NM_015073.1	27	24,652,5827	GG,GC,CC		7.3488,1.5433,5.3821	possibly-damaging	1450/1782	38673298	700,12306	2203	4300	6503	SO:0001583	missense	23094	exon16			AAGCAGCCTGTAC	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.4348C>G	19.37:g.38673298C>G	ENSP00000222345:p.Pro1450Ala	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	126	0.057692307692307696	1	0.0020325203252032522	35	0.09668508287292818	30	0.05244755244755245	60	0.079155672823219	C	13.53	2.265710	0.40095	0.015433	0.073488	ENSG00000105738	ENST00000222345	T	0.74209	-0.82	5.48	4.39	0.52855	.	0.177792	0.37095	N	0.002245	T	0.02380	0.0073	N	0.14661	0.345	0.32284	N	0.567252	B	0.11235	0.004	B	0.08055	0.003	T	0.14144	-1.0483	10	0.36615	T	0.2	-5.8179	8.1936	0.31383	0.2752:0.5798:0.145:0.0	rs3745945;rs17640341;rs3745945	1450	O60292	SI1L3_HUMAN	A	1450	ENSP00000222345:P1450A	ENSP00000222345:P1450A	P	+	1	0	SIPA1L3	43365138	0.875000	0.30112	1.000000	0.80357	0.987000	0.75469	1.042000	0.30303	2.562000	0.86427	0.555000	0.69702	CCT	C|0.942;G|0.058	0.058	strong		0.617	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
ADIRF	10974	hgsc.bcm.edu	37	10	88730312	88730312	+	Silent	SNP	T	T	C	rs4869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:88730312T>C	ENST00000372013.3	+	3	557	c.204T>C	c.(202-204)atT>atC	p.I68I	ADIRF-AS1_ENST00000440490.1_RNA|RP11-96C23.15_ENST00000609363.1_RNA|RP11-96C23.5_ENST00000433214.2_RNA|ADIRF-AS1_ENST00000609111.1_RNA|ADIRF-AS1_ENST00000418273.2_RNA	NM_006829.2	NP_006820.1	Q15847	ADIRF_HUMAN	adipogenesis regulatory factor	68					cell differentiation (GO:0030154)|cellular response to cisplatin (GO:0072719)|cellular response to radiation (GO:0071478)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of response to drug (GO:2001023)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.I68I(1)									TCTCTGGGATTGGGAAAAAAT	0.587													N|||	2640	0.527157	0.3585	0.4308	5008	,	,		17157	0.8095		0.6014	False		,,,				2504	0.456				p.I68I		Atlas-SNP	.											C10orf116,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.T204C						scavenged	.	C		1662,2744	652.1+/-399.3	341,980,882	77.0	70.0	72.0	http://omim.org/entry/178500	204	-8.6	0.0	10	dbSNP_52	72	4610,3990	546.5+/-385.0	1229,2152,919	no	coding-synonymous	C10orf116	NM_006829.2		1570,3132,1801	CC,CT,TT		46.3953,37.7213,48.2239		68/77	88730312	6272,6734	2203	4300	6503	SO:0001819	synonymous_variant	10974	exon3			TGGGATTGGGAAA	BC004471	CCDS7381.1	10q23.31	2013-02-20	2013-02-20	2013-02-20	ENSG00000148671	ENSG00000148671			24043	protein-coding gene	gene with protein product	"""adipose specific 2"", ""adipose most abundant gene transcript 2"", ""adipogenesis factor rich in obesity"""		"""chromosome 10 open reading frame 116"""	C10orf116		8619847, 23239344	Standard	NM_006829		Approved	APM2, AFRO	uc001ked.2	Q15847	OTTHUMG00000018668	ENST00000372013.3:c.204T>C	10.37:g.88730312T>C		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_006829		Silent	SNP	ENST00000372013.3	37	CCDS7381.1																																																																																			T|0.489;C|0.511	0.511	strong		0.587	ADIRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049194.1	NM_006829	
GABBR2	9568	hgsc.bcm.edu	37	9	101340316	101340316	+	Silent	SNP	T	T	C	rs3750344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:101340316T>C	ENST00000259455.2	-	2	819	c.360A>G	c.(358-360)gcA>gcG	p.A120A		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	120					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CGTATTTTATTGCATCGTAGA	0.493													t|||	807	0.161142	0.236	0.0908	5008	,	,		21374	0.1508		0.1799	False		,,,				2504	0.1012				p.A120A		Atlas-SNP	.											.	GABBR2	126	.	0			c.A360G						PASS	.			996,3410	373.0+/-320.6	113,770,1320	181.0	165.0	171.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	360	2.2	1.0	9	dbSNP_107	171	1435,7165	274.9+/-291.5	123,1189,2988	no	coding-synonymous	GABBR2	NM_005458.7		236,1959,4308	CC,CT,TT		16.686,22.6055,18.6914		120/942	101340316	2431,10575	2203	4300	6503	SO:0001819	synonymous_variant	9568	exon2			TTTTATTGCATCG	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.360A>G	9.37:g.101340316T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																			T|0.809;C|0.191	0.191	strong		0.493	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
OR1S2	219958	hgsc.bcm.edu	37	11	57971201	57971201	+	Silent	SNP	G	G	A	rs11229280	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57971201G>A	ENST00000302592.6	-	1	452	c.453C>T	c.(451-453)gcC>gcT	p.A151A		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	151						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A151A(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGCCGAACCTGGCCCGCATGA	0.478													G|||	2575	0.514177	0.2806	0.4971	5008	,	,		22031	0.7927		0.4245	False		,,,				2504	0.6472				p.A151A		Atlas-SNP	.											OR1S2,NS,carcinoma,-2,3	OR1S2	119	3	1	Substitution - coding silent(1)	stomach(1)	c.C453T						PASS	.	G		1327,3075	446.5+/-348.0	200,927,1074	165.0	156.0	159.0		453	-1.2	0.0	11	dbSNP_120	159	3639,4953	524.0+/-380.4	784,2071,1441	no	coding-synonymous	OR1S2	NM_001004459.1		984,2998,2515	AA,AG,GG		42.3534,30.1454,38.2176		151/326	57971201	4966,8028	2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			GAACCTGGCCCGC	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.453C>T	11.37:g.57971201G>A		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	139	129	0.928058	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			G|0.585;A|0.415	0.415	strong		0.478	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
OGFOD3	79701	hgsc.bcm.edu	37	17	80350331	80350331	+	Silent	SNP	G	G	A	rs11903	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:80350331G>A	ENST00000313056.5	-	9	1054	c.903C>T	c.(901-903)atC>atT	p.I301I	OGFOD3_ENST00000329197.5_3'UTR|OGFOD3_ENST00000578287.1_5'UTR	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	301	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)										AGGCGATGGTGATGGCGTAAC	0.637													g|||	1602	0.319888	0.2118	0.4409	5008	,	,		16096	0.3581		0.2117	False		,,,				2504	0.4519				p.I301I		Atlas-SNP	.											.	.	.	.	0			c.C903T						PASS	.	G	,	931,3475	342.3+/-307.1	106,719,1378	113.0	86.0	95.0		903,	5.2	1.0	17	dbSNP_52	95	1659,6939	294.8+/-302.1	174,1311,2814	no	coding-synonymous,utr-3	C17orf101	NM_024648.2,NM_175902.4	,	280,2030,4192	AA,AG,GG		19.2952,21.1303,19.9169	,	301/320,	80350331	2590,10414	2203	4299	6502	SO:0001819	synonymous_variant	79701	exon9			GATGGTGATGGCG	BC023602	CCDS11811.1, CCDS11812.1	17q25.3	2012-10-23	2012-10-23	2012-10-23	ENSG00000181396	ENSG00000181396			26174	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 101"""	C17orf101		12477932	Standard	NM_175902		Approved	FLJ22222	uc002keu.2	Q6PK18		ENST00000313056.5:c.903C>T	17.37:g.80350331G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_024648	C9JDC8|Q8IZ37|Q9H6J2	Silent	SNP	ENST00000313056.5	37	CCDS11811.1																																																																																			G|0.764;A|0.236	0.236	strong		0.637	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
LMF1	64788	hgsc.bcm.edu	37	16	921179	921179	+	Missense_Mutation	SNP	G	G	A	rs143076454	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:921179G>A	ENST00000262301.11	-	7	1078	c.1060C>T	c.(1060-1062)Cgg>Tgg	p.R354W	LMF1_ENST00000568268.1_5'UTR|LMF1_ENST00000568897.1_Missense_Mutation_p.R137W|LMF1_ENST00000543238.1_Missense_Mutation_p.R117W|LMF1_ENST00000399843.2_Missense_Mutation_p.R354W	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	354					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				GGCTCGGGCCGGGCCCCTCGG	0.667													G|||	41	0.0081869	0.003	0.0115	5008	,	,		17181	0.0		0.0249	False		,,,				2504	0.0041				p.R354W		Atlas-SNP	.											.	LMF1	42	.	0			c.C1060T						PASS	.	G	TRP/ARG	16,3798		0,16,1891	20.0	24.0	23.0		1060	-1.7	0.0	16	dbSNP_134	23	99,8121		0,99,4011	yes	missense	LMF1	NM_022773.2	101	0,115,5902	AA,AG,GG		1.2044,0.4195,0.9556	benign	354/568	921179	115,11919	1907	4110	6017	SO:0001583	missense	64788	exon7			CGGGCCGGGCCCC	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.1060C>T	16.37:g.921179G>A	ENSP00000262301:p.Arg354Trp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Missense_Mutation	SNP	ENST00000262301.11	37	CCDS45373.1	26	0.011904761904761904	0	0.0	7	0.019337016574585635	0	0.0	19	0.025065963060686015	G	9.472	1.095775	0.20552	0.004195	0.012044	ENSG00000103227	ENST00000262301;ENST00000399843;ENST00000540070;ENST00000545827;ENST00000543238	T;T;T	0.22945	1.93;1.93;1.93	4.46	-1.66	0.08265	.	1.240890	0.05458	N	0.550696	T	0.04452	0.0122	N	0.16656	0.425	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.27938	-1.0059	10	0.52906	T	0.07	-10.8533	2.3657	0.04318	0.1629:0.2602:0.4327:0.1442	.	354	Q96S06	LMF1_HUMAN	W	354;354;137;108;117	ENSP00000262301:R354W;ENSP00000382737:R354W;ENSP00000437418:R117W	ENSP00000262301:R354W	R	-	1	2	LMF1	861180	0.009000	0.17119	0.000000	0.03702	0.002000	0.02628	-0.063000	0.11655	-0.324000	0.08589	-0.304000	0.09214	CGG	G|0.988;A|0.012	0.012	strong		0.667	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
TCF7L1	83439	hgsc.bcm.edu	37	2	85536415	85536415	+	Missense_Mutation	SNP	G	G	A	rs11547160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85536415G>A	ENST00000282111.3	+	12	1872	c.1597G>A	c.(1597-1599)Ggg>Agg	p.G533R		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	533			G -> R (in dbSNP:rs11547160). {ECO:0000269|PubMed:15489334}.		anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CTCCTCCTCTGGGCAGATGGG	0.697													G|||	146	0.0291534	0.0023	0.0461	5008	,	,		13772	0.0		0.0636	False		,,,				2504	0.0481				p.G533R		Atlas-SNP	.											.	TCF7L1	44	.	0			c.G1597A						PASS	.	G	ARG/GLY	59,4345		0,59,2143	25.0	26.0	25.0		1597	0.1	0.9	2	dbSNP_120	25	534,8066		17,500,3783	yes	missense	TCF7L1	NM_031283.2	125	17,559,5926	AA,AG,GG		6.2093,1.3397,4.5601	benign	533/589	85536415	593,12411	2202	4300	6502	SO:0001583	missense	83439	exon12			TCCTCTGGGCAGA	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.1597G>A	2.37:g.85536415G>A	ENSP00000282111:p.Gly533Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	53	38	0.716981	NM_031283	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	37	CCDS1971.1	62	0.028388278388278388	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	43	0.05672823218997362	G	13.66	2.302718	0.40795	0.013397	0.062093	ENSG00000152284	ENST00000282111	D	0.98474	-4.95	5.21	0.0841	0.14436	.	0.850756	0.11006	N	0.609952	T	0.71187	0.3310	L	0.29908	0.895	0.36271	D	0.855176	B	0.25169	0.119	B	0.23574	0.047	T	0.80473	-0.1367	10	0.16896	T	0.51	.	3.6426	0.08173	0.5239:0.0:0.2946:0.1815	rs11547160;rs17854976;rs59819155;rs11547160	533	Q9HCS4	TF7L1_HUMAN	R	533	ENSP00000282111:G533R	ENSP00000282111:G533R	G	+	1	0	TCF7L1	85389926	0.542000	0.26426	0.904000	0.35570	0.876000	0.50452	0.877000	0.28106	0.108000	0.17862	0.655000	0.94253	GGG	G|0.963;A|0.037	0.037	strong		0.697	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283	
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 GAIIx	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*	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	4	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		
CD276	80381	hgsc.bcm.edu	37	15	73996066	73996066	+	Missense_Mutation	SNP	G	G	A	rs11574483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:73996066G>A	ENST00000318443.5	+	5	1102	c.800G>A	c.(799-801)cGc>cAc	p.R267H	CD276_ENST00000537340.2_Missense_Mutation_p.R121H|CD276_ENST00000318424.5_Intron|CD276_ENST00000561213.1_Missense_Mutation_p.R267H|CD276_ENST00000564751.1_Intron	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	267	Ig-like V-type 2.		R -> H (in dbSNP:rs11574483).		cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GCCACCCTGCGCTGCTCCTTC	0.667													G|||	606	0.121006	0.1467	0.0793	5008	,	,		15361	0.127		0.0944	False		,,,				2504	0.137				p.R267H		Atlas-SNP	.											CD276,NS,carcinoma,0,1	CD276	29	1	0			c.G800A						PASS	.	G	HIS/ARG,	643,3753	268.6+/-268.5	49,545,1604	32.0	31.0	31.0		800,	1.7	1.0	15	dbSNP_120	31	827,7767	187.3+/-234.6	34,759,3504	no	missense,intron	CD276	NM_001024736.1,NM_025240.2	29,	83,1304,5108	AA,AG,GG		9.623,14.6269,11.3164	benign,	267/535,	73996066	1470,11520	2198	4297	6495	SO:0001583	missense	80381	exon5			CCCTGCGCTGCTC	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.800G>A	15.37:g.73996066G>A	ENSP00000320084:p.Arg267His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	232	0.10622710622710622	60	0.12195121951219512	33	0.09116022099447514	66	0.11538461538461539	73	0.09630606860158311	G	12.83	2.054435	0.36277	0.146269	0.09623	ENSG00000103855	ENST00000318443;ENST00000379823;ENST00000537340	T;T	0.65549	-0.16;-0.16	4.84	1.73	0.24493	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.373446	0.29579	N	0.011760	T	0.00210	0.0006	N	0.12637	0.245	0.09310	P	0.9999999999929695	B;B;B	0.17465	0.022;0.002;0.001	B;B;B	0.11329	0.004;0.006;0.001	T	0.03394	-1.1041	9	0.38643	T	0.18	-27.5137	6.0698	0.19883	0.2493:0.1388:0.6119:0.0	rs11574483	213;267;267	B4DK26;Q5ZPR3;Q5ZPR3-4	.;CD276_HUMAN;.	H	267;267;121	ENSP00000320084:R267H;ENSP00000441087:R121H	ENSP00000320084:R267H	R	+	2	0	CD276	71783119	0.307000	0.24500	0.976000	0.42696	0.970000	0.65996	0.403000	0.20982	0.574000	0.29417	0.561000	0.74099	CGC	G|0.889;A|0.111	0.111	strong		0.667	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
MMP3	4314	hgsc.bcm.edu	37	11	102713447	102713447	+	Silent	SNP	G	G	C	rs41380244	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102713447G>C	ENST00000299855.5	-	2	562	c.306C>G	c.(304-306)acC>acG	p.T102T		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	102					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	TGCCAGGAAAGGTTCTGAAGT	0.478													T|||	314	0.0626997	0.0968	0.0476	5008	,	,		17480	0.006		0.0915	False		,,,				2504	0.0562				p.T102T		Atlas-SNP	.											.	MMP3	60	.	0			c.C306G						PASS	.	T		423,3983		19,385,1799	72.0	66.0	68.0		306	-0.3	0.2	11	dbSNP_127	68	838,7760		41,756,3502	no	coding-synonymous	MMP3	NM_002422.3		60,1141,5301	CC,CG,GG		9.7465,9.6005,9.697		102/478	102713447	1261,11743	2203	4299	6502	SO:0001819	synonymous_variant	4314	exon2			AGGAAAGGTTCTG	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.306C>G	11.37:g.102713447G>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	124	15	0.120968	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Silent	SNP	ENST00000299855.5	37	CCDS8323.1																																																																																			G|0.915;C|0.085	0.085	strong		0.478	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
SOX30	11063	hgsc.bcm.edu	37	5	157078475	157078475	+	Silent	SNP	C	C	G	rs3749797	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:157078475C>G	ENST00000265007.6	-	1	953	c.612G>C	c.(610-612)ccG>ccC	p.P204P	SOX30_ENST00000311371.5_Silent_p.P204P|SOX30_ENST00000519442.1_Intron	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	204					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	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)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGATGGCTGCCGGGCTTTTGC	0.657													.|||	830	0.165735	0.2912	0.1326	5008	,	,		15560	0.0724		0.1571	False		,,,				2504	0.1247				p.P204P	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											SOX30,NS,carcinoma,0,1	SOX30	67	1	0			c.G612C						scavenged	.	C	,	1112,3290		124,864,1213	64.0	74.0	71.0		612,612	1.9	0.0	5	dbSNP_107	71	1095,7499		75,945,3277	no	coding-synonymous,coding-synonymous	SOX30	NM_007017.2,NM_178424.1	,	199,1809,4490	GG,GC,CC		12.7414,25.2612,16.9821	,	204/502,204/754	157078475	2207,10789	2201	4297	6498	SO:0001819	synonymous_variant	11063	exon1			GGCTGCCGGGCTT	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.612G>C	5.37:g.157078475C>G		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	195	85	0.435897	NM_178424	O94995|Q8IYX6	Silent	SNP	ENST00000265007.6	37	CCDS4339.1																																																																																			C|0.825;G|0.175	0.175	strong		0.657	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835272	27835272	+	Silent	SNP	T	T	C	rs200948	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27835272T>C	ENST00000331442.3	-	1	87	c.36A>G	c.(34-36)ccA>ccG	p.P12P		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	12					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CCACCGGCGCTGGGGTGGCTG	0.587													T|||	561	0.112021	0.1793	0.1383	5008	,	,		15202	0.0645		0.0875	False		,,,				2504	0.0767				p.P12P		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.A36G						PASS	.	T		580,3690		40,500,1595	20.0	25.0	23.0		36	-1.9	0.4	6	dbSNP_79	23	830,7498		44,742,3378	no	coding-synonymous	HIST1H1B	NM_005322.2		84,1242,4973	CC,CT,TT		9.9664,13.5831,11.1923		12/227	27835272	1410,11188	2135	4164	6299	SO:0001819	synonymous_variant	3009	exon1			CGGCGCTGGGGTG	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.36A>G	6.37:g.27835272T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	66	0.868421	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			T|0.896;C|0.104	0.104	strong		0.587	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
PCNXL4	64430	hgsc.bcm.edu	37	14	60591829	60591829	+	Silent	SNP	T	T	C	rs308990	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:60591829T>C	ENST00000406854.1	+	9	3494	c.2940T>C	c.(2938-2940)ttT>ttC	p.F980F	PCNXL4_ENST00000535349.1_Silent_p.F187F|PCNXL4_ENST00000406949.1_Silent_p.F746F|PCNXL4_ENST00000404681.2_Silent_p.F980F|PCNXL4_ENST00000317623.4_Silent_p.F746F			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	980						integral component of membrane (GO:0016021)											CTTGTTATTTTAGTTTATTTG	0.373													T|||	1635	0.326478	0.5787	0.1369	5008	,	,		20338	0.2946		0.1153	False		,,,				2504	0.3701				p.F746F		Atlas-SNP	.											.	.	.	.	0			c.T2238C						PASS	.	T		2207,2197	583.5+/-385.8	543,1121,538	74.0	76.0	76.0		2238	2.8	0.8	14	dbSNP_79	76	1097,7503	224.3+/-260.7	75,947,3278	no	coding-synonymous	C14orf135	NM_022495.5		618,2068,3816	CC,CT,TT		12.7558,49.8865,25.4076		746/939	60591829	3304,9700	2202	4300	6502	SO:0001819	synonymous_variant	64430	exon8			TTATTTTAGTTTA	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.2940T>C	14.37:g.60591829T>C		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	261	258	0.988506	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Silent	SNP	ENST00000406854.1	37																																																																																				T|0.723;C|0.277	0.277	strong		0.373	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
ZNF99	7652	hgsc.bcm.edu	37	19	22941191	22941191	+	Missense_Mutation	SNP	T	T	A	rs11667397	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:22941191T>A	ENST00000596209.1	-	4	1610	c.1520A>T	c.(1519-1521)aAa>aTa	p.K507I	ZNF99_ENST00000397104.3_Missense_Mutation_p.K416I	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	507					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTTGCAAGGTTTCTCTTCCAT	0.348													T|||	749	0.149561	0.118	0.1931	5008	,	,		19973	0.1716		0.1421	False		,,,				2504	0.1462				p.K507I		Atlas-SNP	.											.	ZNF99	273	.	0			c.A1520T						PASS	.	T	ILE/LYS	504,3640		26,452,1594	43.0	45.0	44.0		1247	-0.1	0.0	19	dbSNP_120	44	1372,7068		93,1186,2941	no	missense	ZNF99	NM_001080409.2	102	119,1638,4535	AA,AT,TT		16.2559,12.1622,14.9078	probably-damaging	416/912	22941191	1876,10708	2072	4220	6292	SO:0001583	missense	7652	exon4			CAAGGTTTCTCTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1520A>T	19.37:g.22941191T>A	ENSP00000472969:p.Lys507Ile	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	344	0.1575091575091575	62	0.12601626016260162	65	0.17955801104972377	103	0.18006993006993008	114	0.1503957783641161	-	11.30	1.596585	0.28445	0.121622	0.162559	ENSG00000213973	ENST00000397104	T	0.33654	1.4	1.16	-0.143	0.13444	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00144	0.0004	H	0.94734	3.575	0.39932	P	0.025704999999999978	P	0.45902	0.868	P	0.46452	0.517	T	0.04115	-1.0976	8	0.87932	D	0	.	5.0822	0.14663	0.0:0.1911:0.0:0.8089	rs11667397;rs35159026	416	A8MXY4	ZNF99_HUMAN	I	416	ENSP00000380293:K416I	ENSP00000380293:K416I	K	-	2	0	ZNF99	22733031	0.001000	0.12720	0.004000	0.12327	0.075000	0.17131	-0.278000	0.08490	-0.345000	0.08325	0.163000	0.16589	AAA	T|0.834;A|0.166	0.166	strong		0.348	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
DCHS2	54798	hgsc.bcm.edu	37	4	155412464	155412464	+	Missense_Mutation	SNP	C	C	T	rs13149269	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:155412464C>T	ENST00000339452.1	-	1	404	c.44G>A	c.(43-45)cGg>cAg	p.R15Q	DCHS2_ENST00000456341.2_Missense_Mutation_p.R8Q|DCHS2_ENST00000443500.1_Missense_Mutation_p.R15Q	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	491					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CGGAGCCCGCCGCTGCTGACG	0.672													C|||	1867	0.372804	0.3502	0.4885	5008	,	,		16047	0.1647		0.4612	False		,,,				2504	0.4448				p.R15Q		Atlas-SNP	.											.	DCHS2	594	.	0			c.G44A						PASS	.						7.0	14.0	12.0					4																	155412464		678	1559	2237	SO:0001583	missense	54798	exon1			GCCCGCCGCTGCT	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.44G>A	4.37:g.155412464C>T	ENSP00000345062:p.Arg15Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	68	66	0.970588	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	37	CCDS47150.1	785	0.35943223443223443	177	0.3597560975609756	173	0.47790055248618785	82	0.14335664335664336	353	0.4656992084432718	C	10.79	1.450518	0.26074	.	.	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.58506	0.33;0.38;0.39	5.35	-10.7	0.00240	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.17268	0.021;0.021	B;B	0.08055	0.003;0.003	T	0.04607	-1.0939	7	0.18710	T	0.47	.	5.0984	0.14747	0.3583:0.1213:0.4102:0.1103	rs13149269;rs17373888	15;15	E9PG03;E9PC11	.;.	Q	15;15;8;15	ENSP00000345062:R15Q;ENSP00000408543:R8Q;ENSP00000395539:R15Q	ENSP00000345062:R15Q	R	-	2	0	DCHS2	155631914	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.236000	0.00268	-4.157000	0.00069	-2.548000	0.00178	CGG	C|0.653;N|0.001	.	strong		0.672	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
COL18A1	80781	hgsc.bcm.edu	37	21	46924383	46924383	+	Silent	SNP	C	C	T	rs11544970	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46924383C>T	ENST00000359759.4	+	33	4047	c.4026C>T	c.(4024-4026)ccC>ccT	p.P1342P	COL18A1_ENST00000355480.5_Silent_p.P1107P|COL18A1_ENST00000400337.2_Silent_p.P927P|SLC19A1_ENST00000567670.1_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1342	Triple-helical region 8 (COL8).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGGGGGAGCCCGGGGGCGGCG	0.682													C|||	138	0.0275559	0.0068	0.0389	5008	,	,		12931	0.0367		0.0239	False		,,,				2504	0.0419				p.P1107P		Atlas-SNP	.											.	COL18A1	129	.	0			c.C3321T						PASS	.	C	,	20,3170		0,20,1575	10.0	13.0	12.0		3321,2781	-6.8	0.0	21	dbSNP_120	12	180,7224		0,180,3522	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	0,200,5097	TT,TC,CC		2.4311,0.627,1.8879	,	1107/1520,927/1340	46924383	200,10394	1595	3702	5297	SO:0001819	synonymous_variant	80781	exon33			GGAGCCCGGGGGC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.4026C>T	21.37:g.46924383C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.975;T|0.025	0.025	strong		0.682	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
SLC2A4RG	56731	hgsc.bcm.edu	37	20	62373707	62373707	+	Missense_Mutation	SNP	G	G	T	rs8957	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62373707G>T	ENST00000266077.2	+	6	751	c.699G>T	c.(697-699)gaG>gaT	p.E233D	RP4-583P15.10_ENST00000447343.2_RNA|SLC2A4RG_ENST00000493772.1_3'UTR	NM_020062.3	NP_064446.2	Q9NR83	S2A4R_HUMAN	SLC2A4 regulator	233			E -> D (in dbSNP:rs8957). {ECO:0000269|PubMed:10825161, ECO:0000269|PubMed:14625278, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|kidney(1)|lung(2)|prostate(2)|skin(1)	7	all_cancers(38;1.13e-12)|all_epithelial(29;2.64e-14)|Lung NSC(23;4.79e-10)|all_lung(23;1.7e-09)					CAGAGCCTGAGCAGAGTGATG	0.662													G|||	3601	0.71905	0.9614	0.7089	5008	,	,		10581	0.371		0.7475	False		,,,				2504	0.728				p.E233D		Atlas-SNP	.											SLC2A4RG,NS,carcinoma,0,1	SLC2A4RG	20	1	0			c.G699T						PASS	.	G	ASP/GLU	4017,381	761.4+/-413.0	1833,351,15	50.0	35.0	40.0		699	1.3	0.8	20	dbSNP_52	40	6286,2312	686.7+/-404.1	2316,1654,329	yes	missense	SLC2A4RG	NM_020062.3	45	4149,2005,344	TT,TG,GG		26.89,8.663,20.7218	benign	233/388	62373707	10303,2693	2199	4299	6498	SO:0001583	missense	56731	exon6			GCCTGAGCAGAGT	AF249267	CCDS13537.1	20q13.33	2010-03-11			ENSG00000125520	ENSG00000125520			15930	protein-coding gene	gene with protein product	"""GLUT4 enhancer factor"", ""Huntington's disease gene regulatory region-binding protein 1"""	609493				10825161	Standard	NM_020062		Approved	GEF, HDBP1, Si-1-2, Si-1-2-19	uc002ygq.3	Q9NR83	OTTHUMG00000032997	ENST00000266077.2:c.699G>T	20.37:g.62373707G>T	ENSP00000266077:p.Glu233Asp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_020062	Q2PHL5|Q6F6I6|Q6F6I7|Q6GTK5|Q8TAH5|Q8WVW7|Q96QD3|Q9BV85	Missense_Mutation	SNP	ENST00000266077.2	37	CCDS13537.1	1522	0.6968864468864469	469	0.9532520325203252	278	0.7679558011049724	211	0.3688811188811189	564	0.7440633245382586	G	3.376	-0.127362	0.06753	0.91337	0.7311	ENSG00000125520	ENST00000266077	D	0.86769	-2.17	3.5	1.27	0.21489	.	0.239901	0.24730	U	0.036069	T	0.00012	0.0000	N	0.16037	0.36	0.45216	P	0.0017730000000000246	B;B	0.17038	0.02;0.02	B;B	0.12837	0.008;0.008	T	0.47661	-0.9100	9	0.02654	T	1	.	2.5318	0.04704	0.1211:0.1828:0.5098:0.1864	rs8957;rs1129074;rs3177459;rs3186572;rs17295251;rs17353769;rs57099542;rs8957	128;233	Q2PHL5;Q9NR83	.;S2A4R_HUMAN	D	233	ENSP00000266077:E233D	ENSP00000266077:E233D	E	+	3	2	SLC2A4RG	61844151	0.947000	0.32204	0.762000	0.31397	0.533000	0.34776	0.036000	0.13819	1.496000	0.48567	0.313000	0.20887	GAG	G|0.242;T|0.758	0.758	strong		0.662	SLC2A4RG-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080202.1	NM_020062	
SGK223	157285	hgsc.bcm.edu	37	8	8176554	8176554	+	Missense_Mutation	SNP	C	C	T	rs12549973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:8176554C>T	ENST00000520004.1	-	6	3595	c.3331G>A	c.(3331-3333)Gcg>Acg	p.A1111T	SGK223_ENST00000330777.4_Missense_Mutation_p.A1111T			Q86YV5	SG223_HUMAN		1113	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TCGGGCTCCGCCTGGTGGCTG	0.682													C|||	1496	0.298722	0.0825	0.3429	5008	,	,		10743	0.5446		0.2505	False		,,,				2504	0.3558				p.A1111T	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3331A						PASS	.	C	THR/ALA	473,3653		34,405,1624	67.0	75.0	73.0		3331	3.5	0.0	8	dbSNP_120	73	2333,6071		306,1721,2175	yes	missense	SGK223	NM_001080826.1	58	340,2126,3799	TT,TC,CC		27.7606,11.4639,22.3943	probably-damaging	1111/1403	8176554	2806,9724	2063	4202	6265	SO:0001583	missense	0	exon5			GCTCCGCCTGGTG																												ENST00000520004.1:c.3331G>A	8.37:g.8176554C>T	ENSP00000428054:p.Ala1111Thr	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	690	0.3159340659340659	57	0.11585365853658537	98	0.27071823204419887	344	0.6013986013986014	191	0.2519788918205805	C	13.13	2.145121	0.37825	0.114639	0.277606	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.65732	-0.17;-0.17	5.48	3.53	0.40419	Serine/threonine-protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.791425	0.12206	N	0.489775	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.26935	0.164	B	0.28465	0.09	T	0.46707	-0.9172	9	0.18710	T	0.47	.	10.1238	0.42637	0.2011:0.6845:0.1144:0.0	rs12549973	1111	Q86YV5	SG223_HUMAN	T	1111	ENSP00000330930:A1111T;ENSP00000428054:A1111T	ENSP00000330930:A1111T	A	-	1	0	AC068353.1	8213964	0.000000	0.05858	0.001000	0.08648	0.812000	0.45895	0.043000	0.13971	0.661000	0.30985	0.467000	0.42956	GCG	C|0.701;T|0.299	0.299	strong		0.682	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
KLHL26	55295	hgsc.bcm.edu	37	19	18775077	18775077	+	Silent	SNP	C	C	T	rs1076235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:18775077C>T	ENST00000300976.4	+	2	180	c.90C>T	c.(88-90)gcC>gcT	p.A30A	KLHL26_ENST00000595182.1_Silent_p.A30A|KLHL26_ENST00000596843.1_3'UTR|KLHL26_ENST00000599006.1_Silent_p.A30A	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	30										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GCAGCACGGCCGACAAGAACG	0.622													C|||	2193	0.437899	0.5136	0.4251	5008	,	,		13998	0.4365		0.3091	False		,,,				2504	0.4785				p.A30A		Atlas-SNP	.											KLHL26,NS,carcinoma,0,1	KLHL26	43	1	0			c.C90T						PASS	.	C		2177,2229	580.5+/-385.1	553,1071,579	87.0	101.0	96.0		90	-8.3	0.0	19	dbSNP_86	96	2460,6140	404.2+/-348.1	333,1794,2173	no	coding-synonymous	KLHL26	NM_018316.1		886,2865,2752	TT,TC,CC		28.6047,49.4099,35.6528		30/616	18775077	4637,8369	2203	4300	6503	SO:0001819	synonymous_variant	55295	exon2			CACGGCCGACAAG		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"""Kelch-like"", ""BTB/POZ domain containing"""	25623	protein-coding gene	gene with protein product			"""kelch-like 26 (Drosophila)"""				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.90C>T	19.37:g.18775077C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	26	16	0.615385	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.625;T|0.375	0.375	strong		0.622	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
GIMAP2	26157	hgsc.bcm.edu	37	7	150389593	150389593	+	Silent	SNP	T	T	C	rs1860871	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150389593T>C	ENST00000223293.5	+	3	313	c.219T>C	c.(217-219)atT>atC	p.I73I		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	73	AIG1-type G.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATAGAGAGATTGTCATTATTG	0.483													T|||	496	0.0990415	0.0348	0.0821	5008	,	,		21860	0.2163		0.0865	False		,,,				2504	0.09				p.I73I		Atlas-SNP	.											.	GIMAP2	39	.	0			c.T219C						PASS	.	T		190,4216	120.0+/-157.7	8,174,2021	92.0	86.0	88.0		219	1.8	0.0	7	dbSNP_92	88	766,7834	182.6+/-231.0	42,682,3576	no	coding-synonymous	GIMAP2	NM_015660.2		50,856,5597	CC,CT,TT		8.907,4.3123,7.3505		73/338	150389593	956,12050	2203	4300	6503	SO:0001819	synonymous_variant	26157	exon3			AGAGATTGTCATT	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"""GTPases, IMAP"""	21789	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 12"""	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.219T>C	7.37:g.150389593T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_015660	Q96L25	Silent	SNP	ENST00000223293.5	37	CCDS5905.1																																																																																			T|0.910;C|0.090	0.090	strong		0.483	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660	
RBMXL3	139804	hgsc.bcm.edu	37	X	114426385	114426385	+	Missense_Mutation	SNP	G	G	A	rs80194951		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:114426385G>A	ENST00000424776.3	+	1	2423	c.2381G>A	c.(2380-2382)cGc>cAc	p.R794H	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	794	Gly-rich.			R -> H (in Ref. 1; AK097568). {ECO:0000305}.			nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						AGCGGAGGCCGCTCACCCAAT	0.662													G|||	220	0.0582781	0.0038	0.0533	3775	,	,		13082	0.002		0.1123	False		,,,				2504	0.0644				p.R794H		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G2381A						PASS	.	G	HIS/ARG,	34,1175		1,25,7,491,168	30.0	32.0	32.0		2381,	0.9	0.0	X	dbSNP_131	32	387,2004		18,212,139,570,652	yes	missense,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	29,	19,237,146,1061,820	AA,AG,A,GG,G		16.1857,2.8122,11.6944	possibly-damaging,	794/1068,	114426385	421,3179	692	1591	2283	SO:0001583	missense	139804	exon1			GAGGCCGCTCACC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.2381G>A	X.37:g.114426385G>A	ENSP00000417451:p.Arg794His	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	160	48	0.3	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	37	CCDS55478.1	117	0.0705244122965642	3	0.006122448979591836	20	0.056179775280898875	2	0.0034965034965034965	53	0.07703488372093023	G	14.93	2.683230	0.47991	0.028122	0.161857	ENSG00000175718	ENST00000424776	T	0.05996	3.36	0.92	0.92	0.19397	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.45567	P	0.0014840000000000408	D	0.56521	0.976	P	0.46629	0.522	T	0.49844	-0.8896	8	0.87932	D	0	.	7.6329	0.28249	1.0E-4:0.0:0.9999:0.0	.	794	Q8N7X1	RMXL3_HUMAN	H	794	ENSP00000417451:R794H	ENSP00000417451:R794H	R	+	2	0	RBMXL3	114332641	0.003000	0.15002	0.013000	0.15412	0.014000	0.08584	0.066000	0.14489	0.179000	0.19938	0.181000	0.17075	CGC	G|0.929;A|0.071	0.071	strong		0.662	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
MTHFR	4524	hgsc.bcm.edu	37	1	11854896	11854896	+	Silent	SNP	G	G	A	rs2066462	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11854896G>A	ENST00000376592.1	-	6	1184	c.1056C>T	c.(1054-1056)agC>agT	p.S352S	MTHFR_ENST00000376585.1_Silent_p.S393S|MTHFR_ENST00000376583.3_Silent_p.S393S|MTHFR_ENST00000376590.3_Silent_p.S352S			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	352					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	TGGGGTGGGCGCTGAGAGCCC	0.607													G|||	518	0.103435	0.0772	0.0576	5008	,	,		20032	0.1181		0.1024	False		,,,				2504	0.1575				p.S352S		Atlas-SNP	.											.	MTHFR	65	.	0			c.C1056T						PASS	.	G		387,4019	189.9+/-215.9	20,347,1836	47.0	49.0	48.0		1056	-5.1	0.9	1	dbSNP_94	48	835,7765	189.8+/-236.5	41,753,3506	no	coding-synonymous	MTHFR	NM_005957.4		61,1100,5342	AA,AG,GG		9.7093,8.7835,9.3957		352/657	11854896	1222,11784	2203	4300	6503	SO:0001819	synonymous_variant	4524	exon7			GTGGGCGCTGAGA	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.1056C>T	1.37:g.11854896G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	122	68	0.557377	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Silent	SNP	ENST00000376592.1	37	CCDS137.1																																																																																			G|0.910;A|0.090	0.090	strong		0.607	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
SLC4A7	9497	hgsc.bcm.edu	37	3	27472936	27472936	+	Missense_Mutation	SNP	C	C	T	rs3755652	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:27472936C>T	ENST00000295736.5	-	7	1046	c.976G>A	c.(976-978)Gag>Aag	p.E326K	SLC4A7_ENST00000446700.1_Missense_Mutation_p.E318K|SLC4A7_ENST00000454389.1_Missense_Mutation_p.E335K|SLC4A7_ENST00000428386.1_Intron|SLC4A7_ENST00000435667.2_Intron|SLC4A7_ENST00000425128.2_Missense_Mutation_p.E318K|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000437179.1_Intron|SLC4A7_ENST00000445684.1_Missense_Mutation_p.E322K|SLC4A7_ENST00000440156.1_Missense_Mutation_p.E322K|SLC4A7_ENST00000455077.1_Intron	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	326			E -> K (in dbSNP:rs3755652). {ECO:0000269|PubMed:10347222, ECO:0000269|Ref.4}.		auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CGCTGACTCTCTTGGGAACTT	0.542													c|||	647	0.129193	0.0461	0.1643	5008	,	,		15813	0.0565		0.2266	False		,,,				2504	0.1912				p.E326K		Atlas-SNP	.											.	SLC4A7	119	.	0			c.G976A						PASS	.	C	LYS/GLU	359,4047	184.3+/-211.7	10,339,1854	108.0	113.0	111.0		976	5.1	0.8	3	dbSNP_107	111	2159,6441	369.3+/-335.4	270,1619,2411	yes	missense	SLC4A7	NM_003615.3	56	280,1958,4265	TT,TC,CC		25.1047,8.148,19.3603	benign	326/1215	27472936	2518,10488	2203	4300	6503	SO:0001583	missense	9497	exon7			GACTCTCTTGGGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.976G>A	3.37:g.27472936C>T	ENSP00000295736:p.Glu326Lys	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	147	78	0.530612	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	276	0.12637362637362637	21	0.042682926829268296	70	0.19337016574585636	19	0.033216783216783216	166	0.21899736147757257	c	4.815	0.151530	0.09185	0.08148	0.251047	ENSG00000033867	ENST00000295736;ENST00000454389;ENST00000440156;ENST00000446700;ENST00000445684;ENST00000425128	T;T;T;T;T;T	0.77489	-1.01;-1.02;-1.1;-1.1;-1.1;0.42	5.98	5.12	0.69794	Bicarbonate transporter, cytoplasmic (1);	0.315954	0.28284	N	0.015915	T	0.00039	0.0001	N	0.11560	0.145	0.38427	P	0.053651000000000004	B;B;B;B;B	0.15141	0.012;0.012;0.012;0.012;0.005	B;B;B;B;B	0.21917	0.037;0.037;0.037;0.037;0.025	T	0.03576	-1.1023	9	0.06757	T	0.87	.	15.793	0.78380	0.0:0.2578:0.7422:0.0	rs3755652;rs17682585;rs56593324;rs57811624;rs3755652	322;318;322;335;326	E9PFN4;E9PGC1;B5M453;E9PDL9;Q9Y6M7	.;.;.;.;S4A7_HUMAN	K	326;335;322;318;322;318	ENSP00000295736:E326K;ENSP00000390394:E335K;ENSP00000414797:E322K;ENSP00000406605:E318K;ENSP00000406804:E322K;ENSP00000401949:E318K	ENSP00000295736:E326K	E	-	1	0	SLC4A7	27447940	0.996000	0.38824	0.793000	0.32043	0.844000	0.47949	2.454000	0.44979	1.560000	0.49568	-0.191000	0.12829	GAG	C|0.843;T|0.157	0.157	strong		0.542	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
TMEM261	90871	hgsc.bcm.edu	37	9	7799606	7799606	+	Silent	SNP	C	C	A	rs14059	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:7799606C>A	ENST00000358227.4	-	1	461	c.129G>T	c.(127-129)ctG>ctT	p.L43L	TMEM261_ENST00000484082.1_Intron	NM_033428.1	NP_219500.1	Q96GE9	TM261_HUMAN	transmembrane protein 261	43						integral component of membrane (GO:0016021)											AGGTCTTCAACAGGCGGTGTT	0.667													c|||	1889	0.377196	0.267	0.5389	5008	,	,		10006	0.38		0.3897	False		,,,				2504	0.3957				p.L43L		Atlas-SNP	.											.	C9orf123	7	.	0			c.G129T						PASS	.	C		1229,3177	409.7+/-335.1	176,877,1150	36.0	39.0	38.0		129	-7.3	0.0	9	dbSNP_52	38	3407,5193	485.0+/-371.5	668,2071,1561	no	coding-synonymous	C9orf123	NM_033428.1		844,2948,2711	AA,AC,CC		39.6163,27.8938,35.6451		43/113	7799606	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	90871	exon1			CTTCAACAGGCGG	BC009510	CCDS34989.1	9p24.1	2014-02-21	2013-09-11	2013-09-11	ENSG00000137038	ENSG00000137038			30536	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 123"""	C9orf123		21666724	Standard	NM_033428		Approved	MGC4730	uc003zkj.3	Q96GE9	OTTHUMG00000019539	ENST00000358227.4:c.129G>T	9.37:g.7799606C>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_033428	A8K9B7|Q5T6Y9|Q9NT74	Silent	SNP	ENST00000358227.4	37	CCDS34989.1																																																																																			C|0.639;A|0.361	0.361	strong		0.667	TMEM261-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051705.1	NM_033428	
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 GAIIx	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		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	94	60	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	
SPDYE1	285955	hgsc.bcm.edu	37	7	44047066	44047066	+	Missense_Mutation	SNP	T	T	C	rs78424385	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:44047066T>C	ENST00000258704.3	+	5	969	c.832T>C	c.(832-834)Tgc>Cgc	p.C278R	AC004951.6_ENST00000447643.1_lincRNA|RP5-1165K10.2_ENST00000454572.1_RNA|POLR2J4_ENST00000427076.1_RNA	NM_001099435.2|NM_175064.2	NP_001092905.2|NP_778234.2	Q8NFV5	SPDE1_HUMAN	speedy/RINGO cell cycle regulator family member E1	278	Arg-rich.									endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	11						GTTACGCCGTTGCATGAACCC	0.552													t|||	2127	0.42472	0.4531	0.3818	5008	,	,		18930	0.4474		0.329	False		,,,				2504	0.4918				p.C278R		Atlas-SNP	.											.	SPDYE1	29	.	0			c.T832C						PASS	.	T	ARG/CYS	1870,2536		396,1078,729	130.0	139.0	136.0		832		0.1	7	dbSNP_131	136	3026,5572		546,1934,1819	no	missense	SPDYE1	NM_175064.2	180	942,3012,2548	CC,CT,TT		35.1942,42.4421,37.65	possibly-damaging	278/337	44047066	4896,8108	2203	4299	6502	SO:0001583	missense	285955	exon5			CGCCGTTGCATGA	AF412027	CCDS5475.1	7q11.23	2013-05-08	2013-05-08	2009-02-17	ENSG00000136206	ENSG00000136206		"""Speedy homologs"""	16408	protein-coding gene	gene with protein product	"""Speedy E"""		"""Williams Beuren syndrome chromosome region 19"", ""speedy homolog E1 (Xenopus laevis)"""	WBSCR19		12073013	Standard	NM_175064		Approved	Ringo1, SPDYE	uc003tjf.3	Q8NFV5	OTTHUMG00000128985	ENST00000258704.3:c.832T>C	7.37:g.44047066T>C	ENSP00000258704:p.Cys278Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	127	29	0.228346	NM_175064	Q9NTH5	Missense_Mutation	SNP	ENST00000258704.3	37	CCDS5475.1	846	0.3873626373626374	211	0.42886178861788615	141	0.38950276243093923	237	0.4143356643356643	257	0.3390501319261214	.	4.489	0.090703	0.08632	0.424421	0.351942	ENSG00000136206	ENST00000258704	.	.	.	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.48670	-0.9015	5	0.24483	T	0.36	.	.	.	.	.	278	Q8NFV5	SPDE1_HUMAN	R	278	.	ENSP00000258704:C278R	C	+	1	0	SPDYE1	44013591	0.169000	0.23002	0.117000	0.21633	0.117000	0.20001	0.077000	0.14738	0.077000	0.16863	0.076000	0.15429	TGC	.	.	weak		0.552	SPDYE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250974.1	NM_175064	
FBN3	84467	hgsc.bcm.edu	37	19	8159339	8159339	+	Missense_Mutation	SNP	G	G	C	rs34167077	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8159339G>C	ENST00000600128.1	-	47	6310	c.5896C>G	c.(5896-5898)Cac>Gac	p.H1966D	FBN3_ENST00000601739.1_Missense_Mutation_p.H1966D|FBN3_ENST00000270509.2_Missense_Mutation_p.H1966D			Q75N90	FBN3_HUMAN	fibrillin 3	1966	EGF-like 31; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		H -> D (in dbSNP:rs34167077).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCAATGCAGTGGTCACTCTGC	0.592													G|||	271	0.0541134	0.0068	0.0663	5008	,	,		19075	0.0		0.1163	False		,,,				2504	0.1012				p.H1966D		Atlas-SNP	.											.	FBN3	300	.	0			c.C5896G						PASS	.	G	ASP/HIS	84,4322	73.1+/-111.1	0,84,2119	69.0	53.0	58.0		5896	2.4	0.1	19	dbSNP_126	58	923,7677	203.1+/-246.2	59,805,3436	yes	missense	FBN3	NM_032447.3	81	59,889,5555	CC,CG,GG		10.7326,1.9065,7.7426	benign	1966/2810	8159339	1007,11999	2203	4300	6503	SO:0001583	missense	84467	exon46			TGCAGTGGTCACT		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5896C>G	19.37:g.8159339G>C	ENSP00000470498:p.His1966Asp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	113	0.051739926739926737	2	0.0040650406504065045	26	0.0718232044198895	0	0.0	85	0.11213720316622691	G	9.353	1.066075	0.20067	0.019065	0.107326	ENSG00000142449	ENST00000270509	D	0.87256	-2.23	4.69	2.4	0.29515	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.613082	0.15924	U	0.237993	T	0.04861	0.0131	N	0.13003	0.285	0.47037	P	7.009999999999517E-4	B	0.31193	0.312	B	0.30251	0.113	T	0.49133	-0.8971	9	0.20046	T	0.44	.	10.7785	0.46363	0.0:0.0:0.3634:0.6366	rs34167077	1966	Q75N90	FBN3_HUMAN	D	1966	ENSP00000270509:H1966D	ENSP00000270509:H1966D	H	-	1	0	FBN3	8065339	1.000000	0.71417	0.139000	0.22197	0.818000	0.46254	2.275000	0.43399	0.921000	0.36994	0.462000	0.41574	CAC	G|0.937;C|0.063	0.063	strong		0.592	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
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 GAIIx	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_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Missense_Mutation_p.R1021C			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	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	68	26	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		
GPRIN1	114787	hgsc.bcm.edu	37	5	176026143	176026143	+	Silent	SNP	C	C	T	rs142779818|rs550332435|rs77245696|rs371149640|rs386695335	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176026143C>T	ENST00000303991.4	-	2	870	c.693G>A	c.(691-693)agG>agA	p.R231R		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	231				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GATCCTCCTTCCTCGGTGACA	0.493																																					p.R231R		Atlas-SNP	.											.	GPRIN1	77	.	0			c.G693A						PASS	.						84.0	86.0	85.0					5																	176026143		2157	4218	6375	SO:0001819	synonymous_variant	114787	exon2			CTCCTTCCTCGGT	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.693G>A	5.37:g.176026143C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	94	30	0.319149	NM_052899	C9JM70|Q8ND74|Q96PZ4	Silent	SNP	ENST00000303991.4	37	CCDS4405.1																																																																																			C|0.778;T|0.222	0.222	strong		0.493	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
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 GAIIx	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	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	38	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	
SPNS3	201305	hgsc.bcm.edu	37	17	4391132	4391132	+	Silent	SNP	C	C	T	rs2291743	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4391132C>T	ENST00000355530.2	+	12	1762	c.1482C>T	c.(1480-1482)aaC>aaT	p.N494N	RP13-580F15.2_ENST00000576086.1_RNA|SPNS3_ENST00000333476.2_Silent_p.N367N	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	494					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.N494N(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						TGGACAGCAACGACCTGGAGA	0.622													C|||	775	0.154752	0.0567	0.1715	5008	,	,		18930	0.0437		0.3171	False		,,,				2504	0.2229				p.N494N		Atlas-SNP	.											SPNS3,NS,carcinoma,0,1	SPNS3	52	1	1	Substitution - coding silent(1)	stomach(1)	c.C1482T						PASS	.	C		402,4004	200.4+/-223.7	21,360,1822	130.0	119.0	123.0		1482	-3.1	0.0	17	dbSNP_100	123	2582,6018	419.5+/-353.1	371,1840,2089	no	coding-synonymous	SPNS3	NM_182538.4		392,2200,3911	TT,TC,CC		30.0233,9.1239,22.9433		494/513	4391132	2984,10022	2203	4300	6503	SO:0001819	synonymous_variant	201305	exon12			CAGCAACGACCTG		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.1482C>T	17.37:g.4391132C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_182538	Q8IZ31	Silent	SNP	ENST00000355530.2	37	CCDS11045.1																																																																																			C|0.793;T|0.207	0.207	strong		0.622	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
OR2F2	135948	hgsc.bcm.edu	37	7	143632618	143632618	+	Missense_Mutation	SNP	C	C	T	rs2240359	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143632618C>T	ENST00000408955.2	+	1	360	c.293C>T	c.(292-294)gCa>gTa	p.A98V		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	98			A -> V (in dbSNP:rs2240359).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					CAGAGCTGTGCAGCCCAGTTA	0.542													C|||	2180	0.435304	0.6974	0.4006	5008	,	,		21952	0.5397		0.2783	False		,,,				2504	0.1595				p.A98V		Atlas-SNP	.											.	OR2F2	63	.	0			c.C293T						PASS	.	C	VAL/ALA	2758,1648	659.2+/-400.5	855,1048,300	128.0	125.0	126.0		293	3.7	1.0	7	dbSNP_98	126	2501,6093	409.6+/-349.9	376,1749,2172	no	missense	OR2F2	NM_001004685.1	64	1231,2797,2472	TT,TC,CC		29.1017,37.4035,40.4538	benign	98/318	143632618	5259,7741	2203	4297	6500	SO:0001583	missense	135948	exon1			GCTGTGCAGCCCA		CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"""GPCR / Class A : Olfactory receptors"""	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.293C>T	7.37:g.143632618C>T	ENSP00000386222:p.Ala98Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	96	92	0.958333	NM_001004685	A4D2G0|Q6IFP8	Missense_Mutation	SNP	ENST00000408955.2	37	CCDS43666.1	999	0.4574175824175824	338	0.6869918699186992	155	0.4281767955801105	301	0.5262237762237763	205	0.2704485488126649	C	4.540	0.100329	0.08731	0.625965	0.291017	ENSG00000221910	ENST00000408955	T	0.00662	5.93	3.66	3.66	0.41972	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000089	T	0.00012	0.0000	N	0.16478	0.41	0.33205	P	0.447315	P	0.40909	0.732	B	0.33254	0.16	T	0.00563	-1.1669	9	0.02654	T	1	-20.4853	7.147	0.25589	0.0:0.8772:0.0:0.1228	rs2240359;rs10381441;rs57849346;rs2240359	98	O95006	OR2F2_HUMAN	V	98	ENSP00000386222:A98V	ENSP00000386222:A98V	A	+	2	0	OR2F2	143263551	0.089000	0.21612	1.000000	0.80357	0.802000	0.45316	2.487000	0.45268	2.048000	0.60808	0.491000	0.48974	GCA	C|0.403;T|0.597	0.597	strong		0.542	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1		
ACOXL	55289	hgsc.bcm.edu	37	2	111691147	111691147	+	Silent	SNP	G	G	A	rs3761711	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:111691147G>A	ENST00000389811.4	+	12	1211	c.987G>A	c.(985-987)gcG>gcA	p.A329A	ACOXL_ENST00000439055.1_Silent_p.A329A			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	329					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						CTCTGGTGGCGGGGCTGAAGG	0.642													G|||	333	0.0664936	0.0189	0.1614	5008	,	,		16259	0.1766		0.0	False		,,,				2504	0.0184				p.A329A		Atlas-SNP	.											.	ACOXL	93	.	0			c.G987A						PASS	.	G		100,4306	80.9+/-119.3	0,100,2103	43.0	42.0	42.0		987	-10.9	0.1	2	dbSNP_107	42	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	ACOXL	NM_001142807.1		0,106,6397	AA,AG,GG		0.0698,2.2696,0.815		329/581	111691147	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	55289	exon12			GGTGGCGGGGCTG		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"""acyl-Coenzyme A oxidase-like"""				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.987G>A	2.37:g.111691147G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Silent	SNP	ENST00000389811.4	37		177	0.08104395604395605	10	0.02032520325203252	47	0.1298342541436464	120	0.2097902097902098	0	0.0	G	3.489	-0.104271	0.06967	0.022696	6.98E-4	ENSG00000153093	ENST00000433706	.	.	.	5.46	-10.9	0.00192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.33388	P	0.424245	.	.	.	.	.	.	T	0.09997	-1.0649	3	.	.	.	-42.45	1.1336	0.01750	0.1777:0.2488:0.3174:0.2561	rs3761711;rs61540468	.	.	.	Q	65	.	.	R	+	2	0	ACOXL	111407618	0.004000	0.15560	0.087000	0.20705	0.360000	0.29518	-3.106000	0.00602	-3.360000	0.00179	-0.658000	0.03865	CGG	G|0.971;A|0.029	0.029	strong		0.642	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308	
CCDC122	160857	hgsc.bcm.edu	37	13	44411421	44411421	+	Missense_Mutation	SNP	C	C	T	rs79782223	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:44411421C>T	ENST00000444614.3	-	7	1075	c.817G>A	c.(817-819)Gag>Aag	p.E273K		NM_144974.3	NP_659411.2	Q5T0U0	CC122_HUMAN	coiled-coil domain containing 122	273										endometrium(1)|large_intestine(2)|lung(5)|stomach(1)	9		Lung NSC(96;7.5e-06)|Breast(139;0.00765)|Hepatocellular(98;0.00826)|Prostate(109;0.0143)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;0.000767)|BRCA - Breast invasive adenocarcinoma(63;0.128)		CAATGTTACTCTTGCATTCCA	0.373													C|||	91	0.0181709	0.0023	0.0187	5008	,	,		19462	0.001		0.0676	False		,,,				2504	0.0061				p.E273K		Atlas-SNP	.											.	CCDC122	21	.	0			c.G817A						PASS	.	C	LYS/GLU	46,3678		0,46,1816	147.0	131.0	136.0		817	4.2	0.5	13	dbSNP_131	136	476,7700		19,438,3631	yes	missense	CCDC122	NM_144974.3	56	19,484,5447	TT,TC,CC		5.8219,1.2352,4.3866	benign	273/274	44411421	522,11378	1862	4088	5950	SO:0001583	missense	160857	exon7			GTTACTCTTGCAT	AK056408	CCDS9390.2	13q14.11	2008-10-30			ENSG00000151773	ENSG00000151773			26478	protein-coding gene	gene with protein product		613408					Standard	NM_144974		Approved	FLJ31846	uc010acf.3	Q5T0U0	OTTHUMG00000017413	ENST00000444614.3:c.817G>A	13.37:g.44411421C>T	ENSP00000407763:p.Glu273Lys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	232	57	0.24569	NM_144974	B2RP70|B7ZMI9|Q96MV0	Missense_Mutation	SNP	ENST00000444614.3	37	CCDS9390.2	60	0.027472527472527472	2	0.0040650406504065045	10	0.027624309392265192	1	0.0017482517482517483	47	0.06200527704485488	C	16.17	3.045981	0.55110	0.012352	0.058219	ENSG00000151773	ENST00000444614	T	0.52526	0.66	5.09	4.24	0.50183	.	.	.	.	.	T	0.04048	0.0113	N	0.24115	0.695	0.58432	D	0.999999	B	0.34290	0.447	B	0.30646	0.118	T	0.02505	-1.1149	9	0.62326	D	0.03	.	10.7217	0.46044	0.0:0.91:0.0:0.09	.	273	Q5T0U0	CC122_HUMAN	K	273	ENSP00000407763:E273K	ENSP00000407763:E273K	E	-	1	0	CCDC122	43309421	0.043000	0.20138	0.460000	0.27093	0.164000	0.22412	0.570000	0.23653	1.256000	0.44068	0.585000	0.79938	GAG	C|0.963;T|0.037	0.037	strong		0.373	CCDC122-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276172.4	NM_144974	
KCNQ2	3785	hgsc.bcm.edu	37	20	62046278	62046278	+	Silent	SNP	G	G	C	rs1801545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62046278G>C	ENST00000359125.2	-	13	1677	c.1503C>G	c.(1501-1503)gcC>gcG	p.A501A	KCNQ2_ENST00000344462.4_Silent_p.A471A|KCNQ2_ENST00000354587.3_Silent_p.A473A|KCNQ2_ENST00000357249.2_Silent_p.A483A|KCNQ2_ENST00000370224.1_Silent_p.A473A|KCNQ2_ENST00000359689.1_Silent_p.A501A|KCNQ2_ENST00000360480.3_Silent_p.A473A	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	501					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GCCGTGACGCGGCACCCTTGA	0.672													G|||	347	0.0692891	0.143	0.072	5008	,	,		10683	0.0		0.0905	False		,,,				2504	0.0174				p.A501A		Atlas-SNP	.											.	KCNQ2	201	.	0			c.C1503G						PASS	.	G	,,,	593,3813	255.8+/-260.9	42,509,1652	70.0	79.0	76.0		1419,1449,1503,1413	-6.3	0.4	20	dbSNP_89	76	754,7846	179.0+/-228.3	29,696,3575	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNQ2	NM_004518.4,NM_172106.1,NM_172107.2,NM_172108.3	,,,	71,1205,5227	CC,CG,GG		8.7674,13.4589,10.3568	,,,	473/845,483/855,501/873,471/842	62046278	1347,11659	2203	4300	6503	SO:0001819	synonymous_variant	3785	exon13			TGACGCGGCACCC	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1503C>G	20.37:g.62046278G>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	37	CCDS13520.1																																																																																			G|0.911;C|0.089;A|0.000	0.089	strong		0.672	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
SERPINA9	327657	hgsc.bcm.edu	37	14	94933695	94933695	+	Missense_Mutation	SNP	G	G	A	rs17090921	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94933695G>A	ENST00000380365.3	-	3	731	c.653C>T	c.(652-654)cCt>cTt	p.P218L	SERPINA9_ENST00000448305.2_Missense_Mutation_p.P138L|SERPINA9_ENST00000337425.5_Missense_Mutation_p.P236L|SERPINA9_ENST00000424550.2_Missense_Mutation_p.P87L|SERPINA9_ENST00000539349.1_5'Flank|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000546329.1_Missense_Mutation_p.P200L|SERPINA9_ENST00000298845.7_Missense_Mutation_p.P136L			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	218			P -> L (in dbSNP:rs17090921). {ECO:0000269|PubMed:12975309}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TGTATATTCAGGGTGAAAGGG	0.468													G|||	1615	0.322484	0.146	0.3847	5008	,	,		21030	0.4643		0.3101	False		,,,				2504	0.3834				p.P236L		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C707T						PASS	.	G	LEU/PRO,LEU/PRO	622,3220		53,516,1352	66.0	63.0	64.0		407,707	1.9	0.0	14	dbSNP_123	64	2486,5780		375,1736,2022	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	98,98	428,2252,3374	AA,AG,GG		30.075,16.1895,25.669	benign,benign	136/336,236/436	94933695	3108,9000	1921	4133	6054	SO:0001583	missense	327657	exon3			TATTCAGGGTGAA	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.653C>T	14.37:g.94933695G>A	ENSP00000369723:p.Pro218Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		721	0.3301282051282051	79	0.16056910569105692	127	0.35082872928176795	275	0.4807692307692308	240	0.316622691292876	G	10.74	1.435279	0.25813	0.161895	0.30075	ENSG00000170054	ENST00000448305;ENST00000298845;ENST00000424550;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01;-2.01	3.73	1.87	0.25490	Serpin domain (3);	34.778500	0.00166	N	0.000009	T	0.00012	0.0000	M	0.67517	2.055	0.80722	P	0.0	B;B;B;B;P	0.42203	0.168;0.44;0.391;0.386;0.773	B;B;B;B;B	0.39068	0.092;0.21;0.092;0.092;0.289	T	0.12066	-1.0562	9	0.48119	T	0.1	.	5.0016	0.14268	0.1832:0.0:0.6521:0.1647	rs17090921;rs52803409;rs17090921	200;218;138;236;136	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7;Q86WD7-2	.;SPA9_HUMAN;.;.;.	L	138;136;87;236;218;200	ENSP00000414092:P138L;ENSP00000298845:P136L;ENSP00000409012:P87L;ENSP00000337133:P236L;ENSP00000369723:P218L;ENSP00000445476:P200L	ENSP00000298845:P136L	P	-	2	0	SERPINA9	94003448	0.001000	0.12720	0.004000	0.12327	0.120000	0.20174	0.933000	0.28897	0.390000	0.25115	0.462000	0.41574	CCT	G|0.689;A|0.311	0.311	strong		0.468	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
HIST1H3I	8354	hgsc.bcm.edu	37	6	27839746	27839746	+	Silent	SNP	T	T	C	rs200956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27839746T>C	ENST00000328488.2	-	1	353	c.348A>G	c.(346-348)aaA>aaG	p.K116K		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	116					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)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TAGTGACGCGTTTGGCGTGAA	0.572													C|||	1273	0.254193	0.4758	0.2305	5008	,	,		18092	0.1389		0.1511	False		,,,				2504	0.1963				p.K116K		Atlas-SNP	.											.	HIST1H3I	28	.	0			c.A348G						PASS	.	C		1856,2550	634.1+/-396.1	405,1046,752	125.0	136.0	133.0		348	2.3	1.0	6	dbSNP_79	133	1396,7204	754.3+/-407.5	114,1168,3018	no	coding-synonymous	HIST1H3I	NM_003533.2		519,2214,3770	CC,CT,TT		16.2326,42.1244,25.0038		116/137	27839746	3252,9754	2203	4300	6503	SO:0001819	synonymous_variant	8354	exon1			GACGCGTTTGGCG	X83550	CCDS4636.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000182572	ENSG00000275379		"""Histones / Replication-dependent"""	4771	protein-coding gene	gene with protein product		602814	"""H3 histone family, member F"", ""histone 1, H3i"""	H3FF		9031620, 9439656, 12408966	Standard	NM_003533		Approved	H3/f, H3.f	uc003njy.3	P68431	OTTHUMG00000016184	ENST00000328488.2:c.348A>G	6.37:g.27839746T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	111	88	0.792793	NM_003533	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000328488.2	37	CCDS4636.1																																																																																			A|0.004;C|0.245	0.245	strong		0.572	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1	NM_003533	
PYGL	5836	hgsc.bcm.edu	37	14	51383432	51383432	+	Silent	SNP	G	G	A	rs2075643	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:51383432G>A	ENST00000216392.7	-	9	1352	c.1020C>T	c.(1018-1020)gaC>gaT	p.D340D	PYGL_ENST00000532462.1_Silent_p.D340D|PYGL_ENST00000544180.2_Silent_p.D306D	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	340					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)	CAGGGTGAGTGTCATTCAGCT	0.498													G|||	1179	0.235423	0.0431	0.3501	5008	,	,		19495	0.4365		0.1829	False		,,,				2504	0.2607				p.D340D		Atlas-SNP	.											.	PYGL	77	.	0			c.C1020T						PASS	.	G	,	294,4112	160.3+/-192.7	11,272,1920	115.0	105.0	108.0		918,1020	4.6	1.0	14	dbSNP_96	108	1503,7097	284.6+/-296.7	132,1239,2929	no	coding-synonymous,coding-synonymous	PYGL	NM_001163940.1,NM_002863.4	,	143,1511,4849	AA,AG,GG		17.4767,6.6727,13.8167	,	306/814,340/848	51383432	1797,11209	2203	4300	6503	SO:0001819	synonymous_variant	5836	exon9			GTGAGTGTCATTC		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.1020C>T	14.37:g.51383432G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Silent	SNP	ENST00000216392.7	37	CCDS32080.1																																																																																			G|0.807;A|0.193	0.193	strong		0.498	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	
CAB39L	81617	hgsc.bcm.edu	37	13	49951193	49951193	+	Silent	SNP	T	T	C	rs8002858	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:49951193T>C	ENST00000355854.4	-	3	683	c.186A>G	c.(184-186)ccA>ccG	p.P62P	CAB39L_ENST00000347776.5_Silent_p.P62P|CAB39L_ENST00000410043.1_Silent_p.P62P|CAB39L_ENST00000409308.1_Silent_p.P62P	NM_030925.2	NP_112187.2	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	62					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|stomach(1)	12		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)		CTGCTTCTGTTGGGGGTTCTT	0.473													C|||	2483	0.495807	0.7436	0.4784	5008	,	,		15244	0.1448		0.5139	False		,,,				2504	0.5164				p.P62P		Atlas-SNP	.											.	CAB39L	35	.	0			c.A186G						PASS	.	C	,	3193,1213	423.2+/-340.0	1159,875,169	124.0	118.0	120.0		186,186	-11.1	0.0	13	dbSNP_116	120	4368,4232	572.0+/-389.6	1136,2096,1068	no	coding-synonymous,coding-synonymous	CAB39L	NM_001079670.1,NM_030925.2	,	2295,2971,1237	CC,CT,TT		49.2093,27.5306,41.8653	,	62/338,62/338	49951193	7561,5445	2203	4300	6503	SO:0001819	synonymous_variant	81617	exon3			TTCTGTTGGGGGT	AK022639	CCDS9416.2	13q14.11	2008-02-05			ENSG00000102547	ENSG00000102547			20290	protein-coding gene	gene with protein product		612175					Standard	NM_030925		Approved	bA103J18.3, FLJ12577, MO2L	uc001vcw.3	Q9H9S4	OTTHUMG00000016914	ENST00000355854.4:c.186A>G	13.37:g.49951193T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	219	119	0.543379	NM_030925	Q5TAW6|Q6WG71|Q96FG1|Q9BZ33	Silent	SNP	ENST00000355854.4	37	CCDS9416.2																																																																																			T|0.454;C|0.546	0.546	strong		0.473	CAB39L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044908.3	NM_030925	
COL4A1	1282	hgsc.bcm.edu	37	13	110838814	110838814	+	Silent	SNP	A	A	G	rs61749897	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:110838814A>G	ENST00000375820.4	-	26	1936	c.1815T>C	c.(1813-1815)ccT>ccC	p.P605P		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	605	Triple-helical region.				axon guidance (GO:0007411)|basement membrane organization (GO:0071711)|blood vessel morphogenesis (GO:0048514)|brain development (GO:0007420)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)|patterning of blood vessels (GO:0001569)|renal tubule morphogenesis (GO:0061333)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)|platelet-derived growth factor binding (GO:0048407)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	105	all_cancers(4;9.8e-13)|all_epithelial(4;9.66e-08)|all_lung(23;3.75e-06)|Lung NSC(43;0.000274)|Colorectal(4;0.00178)|all_neural(89;0.00459)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0604)	Breast(118;0.2)	BRCA - Breast invasive adenocarcinoma(86;0.11)|all cancers(43;0.145)			CATATCCTGGAGGCCCAGGGG	0.607													A|||	482	0.096246	0.0923	0.0793	5008	,	,		16093	0.1379		0.0924	False		,,,				2504	0.0746				p.P605P		Atlas-SNP	.											.	COL4A1	372	.	0			c.T1815C						PASS	.	A		349,4057		12,325,1866	38.0	45.0	42.0		1815	-8.2	0.4	13	dbSNP_129	42	577,8023		22,533,3745	no	coding-synonymous	COL4A1	NM_001845.4		34,858,5611	GG,GA,AA		6.7093,7.921,7.1198		605/1670	110838814	926,12080	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon26			TCCTGGAGGCCCA	J04217	CCDS9511.1	13q34	2013-09-05			ENSG00000187498	ENSG00000187498		"""Collagens"""	2202	protein-coding gene	gene with protein product		120130				3691802	Standard	NM_001845		Approved		uc001vqw.4	P02462	OTTHUMG00000017342	ENST00000375820.4:c.1815T>C	13.37:g.110838814A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			A|0.900;G|0.100	0.100	strong		0.607	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
ESPNL	339768	hgsc.bcm.edu	37	2	239039183	239039183	+	Missense_Mutation	SNP	G	G	A	rs73102303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:239039183G>A	ENST00000343063.3	+	9	2091	c.1828G>A	c.(1828-1830)Gtg>Atg	p.V610M	ESPNL_ENST00000409169.1_Missense_Mutation_p.V566M|ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.V242M	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	610				V -> M (in Ref. 1; BAC85884 and 3; AAH42051). {ECO:0000305}.						endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GCTGAAGGGCGTGCATGGGCT	0.711													G|||	658	0.13139	0.2413	0.085	5008	,	,		16293	0.0526		0.1113	False		,,,				2504	0.1176				p.V610M		Atlas-SNP	.											ESPNL,NS,carcinoma,0,1	ESPNL	63	1	0			c.G1828A						PASS	.	G	MET/VAL	862,3504		81,700,1402	10.0	11.0	11.0		1828	-2.3	0.3	2	dbSNP_130	11	920,7564		49,822,3371	yes	missense	ESPNL	NM_194312.2	21	130,1522,4773	AA,AG,GG		10.8439,19.7435,13.8677	benign	610/1006	239039183	1782,11068	2183	4242	6425	SO:0001583	missense	339768	exon9			AAGGGCGTGCATG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1828G>A	2.37:g.239039183G>A	ENSP00000339115:p.Val610Met	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	249	0.11401098901098901	97	0.19715447154471544	35	0.09668508287292818	41	0.07167832167832168	76	0.10026385224274406	G	0.031	-1.332649	0.01298	0.197435	0.108439	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.63580	-0.05;1.04;0.61	3.78	-2.26	0.06867	.	0.423150	0.21191	N	0.078648	T	0.00039	0.0001	N	0.05124	-0.11	0.80722	P	0.0	B;B	0.33494	0.414;0.291	B;B	0.20384	0.029;0.013	T	0.19031	-1.0318	9	0.19147	T	0.46	-12.2189	9.0509	0.36376	0.6378:0.0:0.3622:0.0	.	566;610	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	M	610;566;242	ENSP00000339115:V610M;ENSP00000386577:V566M;ENSP00000386579:V242M	ENSP00000339115:V610M	V	+	1	0	ESPNL	238703922	0.016000	0.18221	0.297000	0.24988	0.220000	0.24768	-0.513000	0.06305	-0.396000	0.07703	0.205000	0.17691	GTG	G|0.871;A|0.129	0.129	strong		0.711	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
DTYMK	1841	hgsc.bcm.edu	37	2	242618050	242618050	+	Silent	SNP	A	A	G	rs1131195	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242618050A>G	ENST00000305784.2	-	4	552	c.345T>C	c.(343-345)gaT>gaC	p.D115D		NM_001165031.1|NM_012145.3	NP_001158503.1|NP_036277.2	P23919	KTHY_HUMAN	deoxythymidylate kinase (thymidylate kinase)	115					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|cellular response to growth factor stimulus (GO:0071363)|dTDP biosynthetic process (GO:0006233)|dTTP biosynthetic process (GO:0006235)|myoblast differentiation (GO:0045445)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside monophosphate phosphorylation (GO:0046940)|nucleotide phosphorylation (GO:0046939)|response to cadmium ion (GO:0046686)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|nucleoside phosphate kinase activity (GO:0050145)|thymidylate kinase activity (GO:0004798)			NS(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.6e-33)|all cancers(36;3.57e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.23e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		GTTTACACCAATCTAGGGAAA	0.488													A|||	1703	0.340056	0.357	0.5	5008	,	,		17644	0.1994		0.4324	False		,,,				2504	0.2536				p.D115D		Atlas-SNP	.											.	DTYMK	9	.	0			c.T345C						PASS	.	A	,	1510,2896	478.8+/-358.3	252,1006,945	40.0	47.0	45.0		,345	-5.3	0.7	2	dbSNP_86	45	3658,4934	521.5+/-379.9	806,2046,1444	no	intron,coding-synonymous	DTYMK	NM_001165031.1,NM_012145.3	,	1058,3052,2389	GG,GA,AA		42.5745,34.2714,39.76	,	,115/213	242618050	5168,7830	2203	4296	6499	SO:0001819	synonymous_variant	1841	exon4			ACACCAATCTAGG	X54729	CCDS2552.1	2q37	2008-02-05			ENSG00000168393	ENSG00000168393	2.7.4.9		3061	protein-coding gene	gene with protein product	"""dTMP kinase"", ""thymidylate (dTMP) kinase"""	188345				2017365, 8024690	Standard	NM_001165031		Approved	CDC8, TYMK, TMPK	uc002wbz.2	P23919	OTTHUMG00000133409	ENST00000305784.2:c.345T>C	2.37:g.242618050A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	57	18	0.315789	NM_012145	B7ZW70|Q6FGX1|Q9BUX4	Silent	SNP	ENST00000305784.2	37	CCDS2552.1	783	0.3585164835164835	176	0.35772357723577236	175	0.48342541436464087	112	0.1958041958041958	320	0.42216358839050133	A	1.800	-0.477370	0.04414	0.342714	0.425745	ENSG00000168393	ENST00000420144	.	.	.	5.35	-5.33	0.02713	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999672201	.	.	.	.	.	.	T	0.43669	-0.9377	3	.	.	.	-24.1626	5.232	0.15426	0.5787:0.1843:0.1573:0.0798	rs1131195;rs1803264;rs3190874;rs4675906;rs17413605;rs17572987;rs17849537	.	.	.	T	111	.	.	I	-	2	0	DTYMK	242266723	0.003000	0.15002	0.743000	0.31040	0.340000	0.28889	-1.710000	0.01888	-1.261000	0.02462	-0.290000	0.09829	ATT	A|0.622;G|0.378	0.378	strong		0.488	DTYMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257266.2	NM_012145	
TMEM254	80195	hgsc.bcm.edu	37	10	81841692	81841692	+	Silent	SNP	G	G	T	rs1932574	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:81841692G>T	ENST00000372281.3	+	2	213	c.183G>T	c.(181-183)ctG>ctT	p.L61L	TMEM254_ENST00000467529.1_3'UTR|TMEM254_ENST00000372275.1_Silent_p.L61L|TMEM254_ENST00000372274.1_Silent_p.L61L|TMEM254_ENST00000372277.3_Silent_p.L61L	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254	61						integral component of membrane (GO:0016021)											ACACCCTCCTGTGCAATGGGT	0.547													.|||	2109	0.421126	0.2345	0.3372	5008	,	,		15872	0.6865		0.4125	False		,,,				2504	0.4683				p.C93F		Atlas-SNP	.											.	TMEM254	1	.	0			c.G278T						PASS	.	G		1179,3227	414.8+/-337.0	170,839,1194	96.0	96.0	96.0		183	1.3	0.1	10	dbSNP_92	96	3678,4922	526.1+/-380.9	779,2120,1401	no	coding-synonymous	C10orf57	NM_025125.2		949,2959,2595	TT,TG,GG		42.7674,26.759,37.3443		61/124	81841692	4857,8149	2203	4300	6503	SO:0001819	synonymous_variant	80195	exon3			CCTCCTGTGCAAT	BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 57"""	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.183G>T	10.37:g.81841692G>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	NM_001270371	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	37	CCDS7363.1	925|925	0.42353479853479853|0.42353479853479853	102|102	0.2073170731707317|0.2073170731707317	119|119	0.3287292817679558|0.3287292817679558	391|391	0.6835664335664335|0.6835664335664335	313|313	0.4129287598944591|0.4129287598944591	G|G	3.937|3.937	-0.014996|-0.014996	0.07681|0.07681	0.26759|0.26759	0.427674|0.427674	ENSG00000133678|ENSG00000133678	ENST00000372273|ENST00000450179	.|.	.|.	.|.	5.34|5.34	1.28|1.28	0.21552|0.21552	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.48135|0.48135	P|P	4.0200000000001346E-4|4.0200000000001346E-4	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39961|0.39961	-0.9588|-0.9588	3|3	.|.	.|.	.|.	-19.6002|-19.6002	8.5308|8.5308	0.33333|0.33333	0.3419:0.0:0.6581:0.0|0.3419:0.0:0.6581:0.0	rs1932574;rs11559166;rs1932574|rs1932574;rs11559166;rs1932574	.|.	.|.	.|.	F|L	82|39	.|.	.|.	C|V	+|+	2|1	0|0	C10orf57|C10orf57	81831672|81831672	0.000000|0.000000	0.05858|0.05858	0.062000|0.062000	0.19696|0.19696	0.682000|0.682000	0.39822|0.39822	-0.437000|-0.437000	0.06914|0.06914	0.318000|0.318000	0.23185|0.23185	0.655000|0.655000	0.94253|0.94253	TGT|GTG	G|0.607;T|0.393	0.393	strong		0.547	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1	NM_025125	
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 GAIIx	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	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	80	54	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 GAIIx	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		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	205	95	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		
KLK1	3816	hgsc.bcm.edu	37	19	51323676	51323676	+	Missense_Mutation	SNP	C	C	T	rs5515	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51323676C>T	ENST00000301420.2	-	3	265	c.230G>A	c.(229-231)cGc>cAc	p.R77H	KLK1_ENST00000448701.2_5'UTR|CTD-2568A17.5_ENST00000326989.5_lincRNA	NM_002257.2	NP_002248.1	P06870	KLK1_HUMAN	kallikrein 1	77	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> H (in dbSNP:rs5515).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(4)|lung(7)|urinary_tract(1)	13		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Aprotinin(DB06692)	CAAGTTGTGGCGACCCAGCCA	0.567													c|||	208	0.0415335	0.1044	0.0375	5008	,	,		15605	0.0		0.0348	False		,,,				2504	0.0092				p.R77H		Atlas-SNP	.											.	KLK1	27	.	0			c.G230A	GRCh37	CM022221	KLK1	M	rs5515	PASS	.		HIS/ARG	428,3978	208.8+/-229.8	26,376,1801	138.0	137.0	137.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	230	-0.9	0.0	19	dbSNP_52	137	310,8290	111.0+/-171.3	4,302,3994	yes	missense	KLK1	NM_002257.2	29	30,678,5795	TT,TC,CC		3.6047,9.714,5.6743	possibly-damaging	77/263	51323676	738,12268	2203	4300	6503	SO:0001583	missense	3816	exon3			TTGTGGCGACCCA	L10038	CCDS12804.1	19q13.3	2008-02-05	2006-10-27			ENSG00000167748	3.4.21.35	"""Kallikreins"""	6357	protein-coding gene	gene with protein product		147910	"""kallikrein 1, renal/pancreas/salivary"""			1684954, 16800724, 16800723	Standard	NM_002257		Approved	Klk6	uc002ptk.1	P06870		ENST00000301420.2:c.230G>A	19.37:g.51323676C>T	ENSP00000301420:p.Arg77His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_002257	Q66US9|Q86U61|Q8TCV8|Q9BS53|Q9NQU4|Q9UD19|Q9UMJ1	Missense_Mutation	SNP	ENST00000301420.2	37	CCDS12804.1	92	0.04212454212454213	51	0.10365853658536585	18	0.049723756906077346	0	0.0	23	0.030343007915567283	c	14.82	2.650665	0.47362	0.09714	0.036047	ENSG00000167748	ENST00000301420	D	0.88975	-2.45	3.02	-0.916	0.10489	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.08447	0.0210	N	0.15975	0.35	0.18873	N	0.999989	P	0.43662	0.814	B	0.40165	0.321	T	0.47275	-0.9130	9	0.87932	D	0	.	4.7384	0.13001	0.5398:0.3445:0.0:0.1157	rs5515;rs16987491;rs5515	77	P06870	KLK1_HUMAN	H	77	ENSP00000301420:R77H	ENSP00000301420:R77H	R	-	2	0	KLK1	56015488	0.008000	0.16893	0.001000	0.08648	0.135000	0.20990	0.005000	0.13129	-0.064000	0.13043	0.306000	0.20318	CGC	C|0.947;T|0.053	0.053	strong		0.567	KLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464135.2	NM_002257	
BPI	671	hgsc.bcm.edu	37	20	36946848	36946848	+	Missense_Mutation	SNP	G	G	A	rs4358188	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:36946848G>A	ENST00000262865.4	+	6	735	c.646G>A	c.(646-648)Gag>Aag	p.E216K	CTD-2308N23.2_ENST00000437016.1_RNA|BPI_ENST00000489102.1_3'UTR	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	216			E -> K (in dbSNP:rs4358188). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2722846, ECO:0000269|Ref.7}.		defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)	p.E216K(1)		kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				TGTATCCTCCGAGCTGCAACC	0.483													G|||	2179	0.435104	0.5356	0.4323	5008	,	,		19870	0.2173		0.4632	False		,,,				2504	0.4969				p.E216K		Atlas-SNP	.											BPI,NS,carcinoma,0,1	BPI	67	1	1	Substitution - Missense(1)	stomach(1)	c.G646A						PASS	.	G	LYS/GLU	2214,2192	589.5+/-387.1	540,1134,529	153.0	144.0	147.0		646	0.6	0.2	20	dbSNP_111	147	4228,4372	571.4+/-389.5	1080,2068,1152	yes	missense	BPI	NM_001725.2	56	1620,3202,1681	AA,AG,GG		49.1628,49.7503,49.531	benign	216/488	36946848	6442,6564	2203	4300	6503	SO:0001583	missense	671	exon6			TCCTCCGAGCTGC	J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"""BPI fold containing"""	1095	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 1"""	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.646G>A	20.37:g.36946848G>A	ENSP00000262865:p.Glu216Lys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	151	149	0.986755	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Missense_Mutation	SNP	ENST00000262865.4	37	CCDS13303.1	888	0.4065934065934066	259	0.5264227642276422	151	0.4171270718232044	116	0.20279720279720279	362	0.47757255936675463	G	0.708	-0.788261	0.02884	0.502497	0.491628	ENSG00000101425	ENST00000262865	T	0.04015	3.73	4.34	0.595	0.17490	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.490320	0.03671	N	0.243958	T	0.00012	0.0000	N	0.00104	-2.125	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.47971	-0.9075	9	0.02654	T	1	-2.5832	3.8847	0.09093	0.647:0.0:0.1929:0.1601	rs4358188;rs17773743;rs17854060;rs52793514;rs60579548;rs4358188	216	P17213	BPI_HUMAN	K	216	ENSP00000262865:E216K	ENSP00000262865:E216K	E	+	1	0	BPI	36380262	0.000000	0.05858	0.201000	0.23476	0.023000	0.10783	-0.543000	0.06084	0.316000	0.23135	-0.351000	0.07748	GAG	G|0.558;A|0.442	0.442	strong		0.483	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	
MEF2D	4209	hgsc.bcm.edu	37	1	156446903	156446903	+	Silent	SNP	T	T	C	rs2274317	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156446903T>C	ENST00000348159.4	-	7	1236	c.756A>G	c.(754-756)ccA>ccG	p.P252P	MEF2D_ENST00000340875.5_Silent_p.P251P|MEF2D_ENST00000464356.2_Silent_p.P251P|MEF2D_ENST00000368240.2_Silent_p.P252P|MEF2D_ENST00000353795.3_Silent_p.P206P|MEF2D_ENST00000360595.3_Silent_p.P252P	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	252	Poly-Pro.				adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TAGGTGGGGGTGGAGACTTGG	0.612													T|||	2863	0.571685	0.2368	0.5951	5008	,	,		16626	0.756		0.672	False		,,,				2504	0.7147				p.P252P		Atlas-SNP	.											MEF2D,colon,adenoma,-1,1	MEF2D	43	1	0			c.A756G						scavenged	.	T		1389,3017	458.6+/-352.0	238,913,1052	82.0	75.0	77.0		756	-8.0	0.9	1	dbSNP_100	77	5651,2949	668.0+/-402.5	1850,1951,499	no	coding-synonymous	MEF2D	NM_005920.2		2088,2864,1551	CC,CT,TT		34.2907,31.5252,45.8711		252/522	156446903	7040,5966	2203	4300	6503	SO:0001819	synonymous_variant	4209	exon7			TGGGGGTGGAGAC	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.756A>G	1.37:g.156446903T>C		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	85	80	0.941176	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	37	CCDS1143.1																																																																																			A|0.000;C|0.551;T|0.449	0.551	strong		0.612	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
KIAA0556	23247	hgsc.bcm.edu	37	16	27752135	27752135	+	Silent	SNP	C	C	T	rs12447120	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:27752135C>T	ENST00000261588.4	+	15	2536	c.2517C>T	c.(2515-2517)gaC>gaT	p.D839D		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	839						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						ATGACTCAGACATCTTTAACC	0.607													C|||	669	0.133586	0.2496	0.1931	5008	,	,		19590	0.001		0.162	False		,,,				2504	0.0419				p.D839D		Atlas-SNP	.											.	KIAA0556	348	.	0			c.C2517T						PASS	.	C		1055,3339	382.3+/-324.4	121,813,1263	48.0	48.0	48.0		2517	4.2	1.0	16	dbSNP_120	48	1285,7315	252.9+/-278.8	85,1115,3100	no	coding-synonymous	KIAA0556	NM_015202.2		206,1928,4363	TT,TC,CC		14.9419,24.01,18.0083		839/1619	27752135	2340,10654	2197	4300	6497	SO:0001819	synonymous_variant	23247	exon15			CTCAGACATCTTT	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2517C>T	16.37:g.27752135C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																			C|0.837;T|0.163	0.163	strong		0.607	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
PALLD	23022	hgsc.bcm.edu	37	4	169606649	169606649	+	Missense_Mutation	SNP	C	C	A	rs62333891	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:169606649C>A	ENST00000505667.1	+	6	1447	c.1274C>A	c.(1273-1275)aCt>aAt	p.T425N	PALLD_ENST00000512127.1_Missense_Mutation_p.T43N|RNU6-1336P_ENST00000383886.1_RNA|PALLD_ENST00000333488.4_Missense_Mutation_p.T302N|PALLD_ENST00000261509.6_Missense_Mutation_p.T425N|PALLD_ENST00000335742.7_Missense_Mutation_p.T43N			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	425					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		CACAGTCCAACTTCATATCTC	0.403									Pancreatic Cancer, Familial Clustering of				C|||	646	0.128994	0.208	0.196	5008	,	,		19036	0.0804		0.0785	False		,,,				2504	0.0767				p.T425N	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C1274A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR	807,3599	322.6+/-297.7	79,649,1475	219.0	213.0	215.0		1274,128,1274	5.8	1.0	4	dbSNP_129	215	642,7958	165.4+/-217.5	15,612,3673	yes	missense,missense,missense	PALLD	NM_001166108.1,NM_001166109.1,NM_016081.3	65,65,65	94,1261,5148	AA,AC,CC		7.4651,18.3159,11.141	probably-damaging,probably-damaging,probably-damaging	425/1124,43/778,425/1107	169606649	1449,11557	2203	4300	6503	SO:0001583	missense	23022	exon6	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GTCCAACTTCATA	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.1274C>A	4.37:g.169606649C>A	ENSP00000425556:p.Thr425Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	262	0.11996336996336997	78	0.15853658536585366	69	0.19060773480662985	46	0.08041958041958042	69	0.09102902374670185	C	18.88	3.716838	0.68844	0.183159	0.074651	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000508898;ENST00000333488;ENST00000504519;ENST00000512127;ENST00000513245;ENST00000503457	T;T;T;T;T;T;T;D	0.91295	-0.21;-0.27;0.06;-0.25;-0.1;-1.42;-0.2;-2.82	5.77	5.77	0.91146	.	0.000000	0.32901	U	0.005513	T	0.02494	0.0076	M	0.73598	2.24	0.28329	P	0.9218524	D;D;D	0.76494	0.998;0.997;0.999	P;P;D	0.64410	0.852;0.879;0.925	T	0.12268	-1.0554	9	0.62326	D	0.03	.	19.9947	0.97381	0.0:1.0:0.0:0.0	rs62333891	425;43;425	B7ZMM5;B3KTG2;B2RTX2	.;.;.	N	425;43;425;404;302;43;43;43;43	ENSP00000261509:T425N;ENSP00000336735:T43N;ENSP00000425556:T425N;ENSP00000423063:T404N;ENSP00000328945:T302N;ENSP00000424121:T43N;ENSP00000426947:T43N;ENSP00000424288:T43N	ENSP00000261509:T425N	T	+	2	0	PALLD	169843224	1.000000	0.71417	0.984000	0.44739	0.788000	0.44548	3.600000	0.54052	2.736000	0.93811	0.305000	0.20034	ACT	C|0.887;A|0.113	0.113	strong		0.403	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
DSC3	1825	hgsc.bcm.edu	37	18	28586964	28586964	+	Silent	SNP	A	A	G	rs1313586	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:28586964A>G	ENST00000360428.4	-	12	1877	c.1797T>C	c.(1795-1797)ccT>ccC	p.P599P	DSC3_ENST00000434452.1_Silent_p.P599P	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	599	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.P599P(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			CAGGTTCATCAGGATCAACAG	0.368													G|||	2976	0.594249	0.8268	0.3833	5008	,	,		14919	0.7917		0.3121	False		,,,				2504	0.5164				p.P599P		Atlas-SNP	.											DSC3,NS,carcinoma,0,1	DSC3	225	1	1	Substitution - coding silent(1)	stomach(1)	c.T1797C						PASS	.	G	,	3339,1067	388.6+/-327.0	1275,789,139	118.0	113.0	115.0		1797,1797	-10.2	0.0	18	dbSNP_87	115	2767,5833	679.2+/-403.5	434,1899,1967	no	coding-synonymous,coding-synonymous	DSC3	NM_001941.3,NM_024423.2	,	1709,2688,2106	GG,GA,AA		32.1744,24.217,46.9476	,	599/897,599/840	28586964	6106,6900	2203	4300	6503	SO:0001819	synonymous_variant	1825	exon12			TTCATCAGGATCA	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.1797T>C	18.37:g.28586964A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_024423	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	37	CCDS32810.1																																																																																			A|0.478;G|0.521	0.521	strong		0.368	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
INPP5E	56623	hgsc.bcm.edu	37	9	139328551	139328551	+	Silent	SNP	T	T	C	rs10870199	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139328551T>C	ENST00000371712.3	-	3	1374	c.972A>G	c.(970-972)ccA>ccG	p.P324P		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		CGGCCTCGGCTGGGAGCAGGA	0.677													T|||	620	0.123802	0.0068	0.245	5008	,	,		15559	0.1587		0.1292	False		,,,				2504	0.1544				p.P324P		Atlas-SNP	.											.	INPP5E	18	.	0			c.A972G						PASS	.	T		135,4261	92.5+/-131.2	1,133,2064	40.0	35.0	37.0		972	-5.7	0.0	9	dbSNP_120	37	1173,7419	222.2+/-259.3	73,1027,3196	no	coding-synonymous	INPP5E	NM_019892.4		74,1160,5260	CC,CT,TT		13.6522,3.071,10.0708		324/645	139328551	1308,11680	2198	4296	6494	SO:0001819	synonymous_variant	56623	exon3			CTCGGCTGGGAGC	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.972A>G	9.37:g.139328551T>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			T|0.894;C|0.106	0.106	strong		0.677	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
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 GAIIx	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		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	49	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		
ALMS1	7840	hgsc.bcm.edu	37	2	73680508	73680508	+	Missense_Mutation	SNP	G	G	C	rs6546839	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73680508G>C	ENST00000264448.6	+	8	6962	c.6851G>C	c.(6850-6852)cGt>cCt	p.R2284P	ALMS1_ENST00000409009.1_Missense_Mutation_p.R2242P|ALMS1_ENST00000377715.1_Missense_Mutation_p.R2284P	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2284			R -> P (in dbSNP:rs6546839).		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						CCCCTTGCCCGTTTCAGAGAT	0.398													C|||	1825	0.364417	0.8782	0.3919	5008	,	,		20366	0.0089		0.2276	False		,,,				2504	0.1575				p.R2284P		Atlas-SNP	.											.	ALMS1	384	.	0			c.G6851C						PASS	.	C	PRO/ARG	2723,947		1024,675,136	72.0	73.0	73.0		6851	5.5	1.0	2	dbSNP_116	73	1952,6200		222,1508,2346	yes	missense	ALMS1	NM_015120.4	103	1246,2183,2482	CC,CG,GG		23.945,25.8038,39.5449	benign	2284/4168	73680508	4675,7147	1835	4076	5911	SO:0001583	missense	7840	exon8			TTGCCCGTTTCAG	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.6851G>C	2.37:g.73680508G>C	ENSP00000264448:p.Arg2284Pro	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	43	32	0.744186	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	737	0.3374542124542125	425	0.8638211382113821	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	C	3.609	-0.079949	0.07141	0.741962	0.23945	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.11385	3.65;3.65;2.78	5.49	5.49	0.81192	.	0.132997	0.35291	N	0.003301	T	0.00012	0.0000	N	0.00413	-1.525	0.49299	P	2.2900000000003473E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32295	-0.9912	9	0.02654	T	1	.	12.855	0.57880	0.0:0.8363:0.1637:0.0	rs6546839;rs17434138;rs17848860;rs61596780;rs6546839	2284;2242;2284	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	P	2242;2284;2284	ENSP00000386627:R2242P;ENSP00000264448:R2284P;ENSP00000366944:R2284P	ENSP00000264448:R2284P	R	+	2	0	ALMS1	73534016	0.983000	0.35010	1.000000	0.80357	0.958000	0.62258	2.660000	0.46749	1.481000	0.48307	-0.120000	0.15030	CGT	G|0.687;C|0.313	0.313	strong		0.398	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
STK17B	9262	hgsc.bcm.edu	37	2	197021276	197021276	+	Silent	SNP	T	T	C	rs10931726	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:197021276T>C	ENST00000263955.4	-	3	508	c.222A>G	c.(220-222)cgA>cgG	p.R74R	RP11-347P5.1_ENST00000606818.1_RNA|STK17B_ENST00000409228.1_Silent_p.R74R	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	74	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)			AAATTTCTGCTCGACAATCCT	0.358													T|||	2355	0.470248	0.1006	0.5893	5008	,	,		16480	0.5536		0.6103	False		,,,				2504	0.6554				p.R74R		Atlas-SNP	.											STK17B,NS,carcinoma,-1,1	STK17B	28	1	0			c.A222G						PASS	.	T		817,3589	325.9+/-299.3	84,649,1470	97.0	91.0	93.0		222	1.4	1.0	2	dbSNP_120	93	5060,3540	630.1+/-398.3	1482,2096,722	no	coding-synonymous	STK17B	NM_004226.3		1566,2745,2192	CC,CT,TT		41.1628,18.5429,45.1868		74/373	197021276	5877,7129	2203	4300	6503	SO:0001819	synonymous_variant	9262	exon3			TTCTGCTCGACAA	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.222A>G	2.37:g.197021276T>C		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	229	84	0.366812	NM_004226		Silent	SNP	ENST00000263955.4	37	CCDS2315.1																																																																																			T|0.540;C|0.460	0.460	strong		0.358	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2		
CDRT1	374286	hgsc.bcm.edu	37	17	15496727	15496727	+	Missense_Mutation	SNP	T	T	G	rs79385100	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:15496727T>G	ENST00000395906.3	-	11	1929	c.1930A>C	c.(1930-1932)Aat>Cat	p.N644H	CDRT1_ENST00000583965.1_Intron|RP11-385D13.1_ENST00000455584.2_Intron|CDRT1_ENST00000354433.3_Missense_Mutation_p.N144H	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	644				N -> H (in Ref. 1; AAC52034/AAD10830). {ECO:0000305}.						endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		CAGTTCCCATTGAAGAAATTG	0.512													.|||	987	0.197085	0.1936	0.281	5008	,	,		17558	0.2331		0.1213	False		,,,				2504	0.183				p.N644H		Atlas-SNP	.											.	CDRT1	83	.	0			c.A1930C						PASS	.	T	HIS/ASN	830,3576	318.5+/-295.7	75,680,1448	229.0	240.0	236.0		1930	3.6	1.0	17	dbSNP_131	236	1103,7497	221.0+/-258.6	72,959,3269	yes	missense	CDRT1	NM_006382.3	68	147,1639,4717	GG,GT,TT		12.8256,18.8379,14.8624	probably-damaging	644/753	15496727	1933,11073	2203	4300	6503	SO:0001583	missense	374286	exon11			TCCCATTGAAGAA	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1930A>C	17.37:g.15496727T>G	ENSP00000379242:p.Asn644His	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	174	101	0.58046	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	398	0.18223443223443223	82	0.16666666666666666	94	0.2596685082872928	126	0.2202797202797203	96	0.1266490765171504	t	17.55	3.416430	0.62511	0.188379	0.128256	ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000354433;ENST00000261644;ENST00000395906	T;T	0.19669	2.13;2.13	4.74	3.61	0.41365	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.00012	0.0000	M	0.61703	1.905	0.09310	P	0.9999999999999785	D	0.65815	0.995	P	0.62885	0.908	T	0.15521	-1.0434	7	.	.	.	.	9.886	0.41262	0.1521:0.0:0.0:0.8479	.	644	O95170	CDRT1_HUMAN	H	144;674;644	ENSP00000346416:N144H;ENSP00000379242:N644H	.	N	-	1	0	CDRT1;RP11-385D13.1	15437452	0.999000	0.42202	0.988000	0.46212	0.915000	0.54546	4.784000	0.62411	1.781000	0.52344	0.528000	0.53228	AAT	T|0.825;G|0.175	0.175	strong		0.512	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
SPATA4	132851	hgsc.bcm.edu	37	4	177113836	177113836	+	Silent	SNP	C	C	T	rs6832177	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:177113836C>T	ENST00000280191.2	-	4	738	c.630G>A	c.(628-630)gcG>gcA	p.A210A	SPATA4_ENST00000515234.1_Silent_p.A37A	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	210						cytoplasm (GO:0005737)				NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		TGAGGAACTCCGCTTTAAGTT	0.373													c|||	1416	0.282748	0.2239	0.3646	5008	,	,		17787	0.255		0.3708	False		,,,				2504	0.2423				p.A210A		Atlas-SNP	.											SPATA4,NS,carcinoma,-1,1	SPATA4	44	1	0			c.G630A						scavenged	.	C		1120,3286	398.3+/-330.8	147,826,1230	88.0	91.0	90.0		630	-3.7	0.0	4	dbSNP_116	90	3042,5558	466.9+/-366.9	551,1940,1809	no	coding-synonymous	SPATA4	NM_144644.2		698,2766,3039	TT,TC,CC		35.3721,25.4199,32.0006		210/306	177113836	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	132851	exon4			GAACTCCGCTTTA	AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.630G>A	4.37:g.177113836C>T		Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_144644	Q8NCS5|Q8WW15	Silent	SNP	ENST00000280191.2	37	CCDS3826.1																																																																																			C|0.701;T|0.299	0.299	strong		0.373	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644	
GAD1	2571	hgsc.bcm.edu	37	2	171678625	171678625	+	Silent	SNP	T	T	C	rs769404	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:171678625T>C	ENST00000358196.3	+	3	661	c.111T>C	c.(109-111)caT>caC	p.H37H	GAD1_ENST00000429023.1_3'UTR|GAD1_ENST00000375272.1_Silent_p.H37H|GAD1_ENST00000344257.5_Silent_p.H37H	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	37					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						GCGTGGCCCATGGATGCACCA	0.642													T|||	1789	0.357228	0.1596	0.3703	5008	,	,		14360	0.506		0.4324	False		,,,				2504	0.3845				p.H37H		Atlas-SNP	.											GAD1,colon,carcinoma,0,1	GAD1	79	1	0			c.T111C						PASS	.	T	,	828,3578	312.7+/-292.7	72,684,1447	48.0	42.0	44.0		111,111	-1.7	1.0	2	dbSNP_120	44	3568,5030	494.0+/-373.7	731,2106,1462	no	coding-synonymous,coding-synonymous	GAD1	NM_000817.2,NM_013445.3	,	803,2790,2909	CC,CT,TT		41.498,18.7926,33.805	,	37/595,37/225	171678625	4396,8608	2203	4299	6502	SO:0001819	synonymous_variant	2571	exon3			GGCCCATGGATGC		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.111T>C	2.37:g.171678625T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Silent	SNP	ENST00000358196.3	37	CCDS2239.1																																																																																			T|0.654;C|0.346	0.346	strong		0.642	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
POC5	134359	hgsc.bcm.edu	37	5	75003678	75003678	+	Missense_Mutation	SNP	T	T	C	rs2307111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:75003678T>C	ENST00000428202.2	-	3	296	c.107A>G	c.(106-108)cAt>cGt	p.H36R	POC5_ENST00000504862.1_5'UTR|RNU6-680P_ENST00000384603.1_RNA|POC5_ENST00000510798.1_5'UTR|POC5_ENST00000446329.2_Missense_Mutation_p.H11R|POC5_ENST00000514838.2_Missense_Mutation_p.H36R|POC5_ENST00000380475.2_5'UTR	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	36			H -> R (in dbSNP:rs2307111). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TATAGCATAATGAAGCAGTTC	0.333													C|||	3083	0.615615	0.9244	0.4798	5008	,	,		16489	0.5347		0.3956	False		,,,				2504	0.6043				p.H36R		Atlas-SNP	.											.	POC5	82	.	0			c.A107G						PASS	.	C	ARG/HIS,ARG/HIS	3158,526		1353,452,37	41.0	40.0	40.0		107,32	5.8	0.9	5	dbSNP_100	40	3295,4875		661,1973,1451	yes	missense,missense	POC5	NM_001099271.1,NM_152408.2	29,29	2014,2425,1488	CC,CT,TT		40.3305,14.278,45.5627	benign,benign	36/576,11/551	75003678	6453,5401	1842	4085	5927	SO:0001583	missense	134359	exon3			GCATAATGAAGCA	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.107A>G	5.37:g.75003678T>C	ENSP00000410216:p.His36Arg	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	180	180	1	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	1228	0.5622710622710623	442	0.8983739837398373	169	0.46685082872928174	305	0.5332167832167832	312	0.41160949868073876	C	0.187	-1.056591	0.01965	0.85722	0.403305	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000446329	T;T;T	0.19938	2.53;2.11;2.51	5.85	5.85	0.93711	.	0.053444	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00063	-2.32	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37103	-0.9720	9	0.02654	T	1	-4.8718	12.2646	0.54670	0.0:0.9214:0.0:0.0786	rs2307111;rs3186857;rs17411855;rs17563925;rs58982046;rs2307111	36;11	Q8NA72;Q8NA72-3	POC5_HUMAN;.	R	36;36;11	ENSP00000410216:H36R;ENSP00000420971:H36R;ENSP00000399481:H11R	ENSP00000410216:H36R	H	-	2	0	POC5	75039434	1.000000	0.71417	0.937000	0.37676	0.006000	0.05464	2.176000	0.42500	1.483000	0.48342	-0.119000	0.15052	CAT	T|0.429;C|0.571	0.571	strong		0.333	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
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 GAIIx	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	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	8	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		
QRICH2	84074	hgsc.bcm.edu	37	17	74289839	74289839	+	Silent	SNP	G	G	A	rs6501881	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74289839G>A	ENST00000262765.5	-	4	650	c.471C>T	c.(469-471)ggC>ggT	p.G157G		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	157										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						GTCGTGGCACGCCAGCTTCAT	0.532													G|||	2351	0.469449	0.7073	0.3098	5008	,	,		21092	0.5724		0.2753	False		,,,				2504	0.3548				p.G157G		Atlas-SNP	.											.	QRICH2	143	.	0			c.C471T						PASS	.	G		2926,1480	678.2+/-403.5	977,972,254	74.0	71.0	72.0		471	0.9	0.0	17	dbSNP_116	72	2485,6115	407.0+/-349.0	348,1789,2163	no	coding-synonymous	QRICH2	NM_032134.1		1325,2761,2417	AA,AG,GG		28.8953,33.5906,41.6039		157/1664	74289839	5411,7595	2203	4300	6503	SO:0001819	synonymous_variant	84074	exon4			TGGCACGCCAGCT	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.471C>T	17.37:g.74289839G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			G|0.579;A|0.421	0.421	strong		0.532	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
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 GAIIx	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	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	25	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	
NUGGC	389643	hgsc.bcm.edu	37	8	27903069	27903069	+	Missense_Mutation	SNP	C	C	T	rs13279787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27903069C>T	ENST00000413272.2	-	12	1563	c.1421G>A	c.(1420-1422)aGt>aAt	p.S474N	NUGGC_ENST00000341513.6_Missense_Mutation_p.S474N	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	474			S -> N (in dbSNP:rs13279787). {ECO:0000269|PubMed:15221005}.		cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										GGAGTTGAAACTATCTGTGAG	0.448													C|||	1894	0.378195	0.4304	0.4092	5008	,	,		17688	0.4375		0.2972	False		,,,				2504	0.3078				p.S474N		Atlas-SNP	.											.	.	.	.	0			c.G1421A						PASS	.	C	ASN/SER	1458,2390		292,874,758	120.0	124.0	123.0		1421	2.3	0.6	8	dbSNP_121	123	2321,5933		327,1667,2133	yes	missense	C8orf80	NM_001010906.1	46	619,2541,2891	TT,TC,CC		28.1197,37.8898,31.2262	benign	474/797	27903069	3779,8323	1924	4127	6051	SO:0001583	missense	389643	exon12			TTGAAACTATCTG	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1421G>A	8.37:g.27903069C>T	ENSP00000408697:p.Ser474Asn	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	833	0.3814102564102564	218	0.44308943089430897	135	0.3729281767955801	256	0.44755244755244755	224	0.2955145118733509	C	7.315	0.615758	0.14129	0.378898	0.281197	ENSG00000189233	ENST00000413272;ENST00000341513	T;T	0.31510	1.49;1.49	5.31	2.29	0.28610	.	0.348037	0.33180	N	0.005190	T	0.00012	0.0000	N	0.14661	0.345	0.41786	P	0.010159000000000029	B	0.06786	0.001	B	0.04013	0.001	T	0.48768	-0.9006	9	0.22706	T	0.39	-5.1026	6.5726	0.22547	0.0:0.4918:0.4051:0.1031	rs13279787;rs52823771;rs57973781;rs13279787	474	Q68CJ6	SLIP_HUMAN	N	474	ENSP00000408697:S474N;ENSP00000345031:S474N	ENSP00000345031:S474N	S	-	2	0	C8orf80	27958988	0.946000	0.32159	0.643000	0.29450	0.322000	0.28314	0.340000	0.19892	1.181000	0.42912	0.650000	0.86243	AGT	C|0.625;N|0.000	.	strong		0.448	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
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 GAIIx	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_ENST00000323022.5_Missense_Mutation_p.V624I|CACNA1F_ENST00000376251.1_Missense_Mutation_p.V570I|CACNA1F_ENST00000480889.1_5'Flank	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	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	69	47	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	
LILRA6	79168	hgsc.bcm.edu	37	19	54745665	54745665	+	Missense_Mutation	SNP	C	C	T	rs1052966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54745665C>T	ENST00000396365.2	-	4	484	c.445G>A	c.(445-447)Gga>Aga	p.G149R	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.G149R|LILRA6_ENST00000391735.3_Missense_Mutation_p.G149R|LILRA6_ENST00000270464.5_Missense_Mutation_p.G149R|LILRA6_ENST00000245621.5_Missense_Mutation_p.G149R|LILRA6_ENST00000419410.2_Missense_Mutation_p.G149R	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	149			G -> R (in dbSNP:rs1052966).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.G149R(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGTGATATCCCTTCTGTGAG	0.582																																					p.G149R		Atlas-SNP	.											LILRA6,NS,carcinoma,+1,4	LILRA6	75	4	2	Substitution - Missense(2)	large_intestine(2)	c.G445A						scavenged	.						25.0	40.0	35.0					19																	54745665		2106	4268	6374	SO:0001583	missense	79168	exon4			GATATCCCTTCTG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.445G>A	19.37:g.54745665C>T	ENSP00000379651:p.Gly149Arg	Somatic	661	0	0		WXS	Illumina HiSeq	Phase_I	537	63	0.117318	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825878	0.32237	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;3.85;2.76;2.76	3.1	-6.21	0.02065	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.12050	0.0293	L	0.39326	1.205	0.09310	N	1	P;B;P;P;B;P	0.41978	0.64;0.037;0.767;0.555;0.383;0.716	P;B;B;B;B;B	0.47044	0.535;0.085;0.444;0.211;0.344;0.276	T	0.27773	-1.0064	10	0.44086	T	0.13	.	4.765	0.13128	0.0:0.4155:0.3207:0.2638	rs1052966;rs3193450;rs13346484	149;149;149;149;149;149	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	R	149	ENSP00000390120:G149R;ENSP00000270464:G149R;ENSP00000411227:G149R;ENSP00000375615:G149R;ENSP00000379651:G149R;ENSP00000245621:G149R	ENSP00000245621:G149R	G	-	1	0	LILRA6	59437477	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-2.553000	0.00927	-1.315000	0.02297	0.162000	0.16502	GGA	C|0.972;T|0.028	0.028	strong		0.582	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
SMCR8	140775	hgsc.bcm.edu	37	17	18219742	18219742	+	Silent	SNP	G	G	A	rs34824853	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18219742G>A	ENST00000406438.3	+	1	1119	c.639G>A	c.(637-639)acG>acA	p.T213T	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	213						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						ACACAGAAACGGAGATCCAGA	0.458													G|||	123	0.0245607	0.003	0.0634	5008	,	,		22129	0.0		0.0696	False		,,,				2504	0.0051				p.T213T		Atlas-SNP	.											.	SMCR8	62	.	0			c.G639A						PASS	.	G		68,4338	61.7+/-98.7	0,68,2135	62.0	61.0	61.0		639	-11.9	0.2	17	dbSNP_126	61	681,7919	169.4+/-220.8	32,617,3651	no	coding-synonymous	SMCR8	NM_144775.2		32,685,5786	AA,AG,GG		7.9186,1.5433,5.7589		213/938	18219742	749,12257	2203	4300	6503	SO:0001819	synonymous_variant	140775	exon1			AGAAACGGAGATC	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.639G>A	17.37:g.18219742G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			G|0.950;A|0.050	0.050	strong		0.458	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
PCDHB7	56129	hgsc.bcm.edu	37	5	140554481	140554481	+	Missense_Mutation	SNP	G	G	T	rs1811237	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140554481G>T	ENST00000231137.3	+	1	2239	c.2065G>T	c.(2065-2067)Gtg>Ttg	p.V689L	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	689					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGTCTACCTGGTGGTGGCGTT	0.711													G|||	1672	0.333866	0.2504	0.3516	5008	,	,		22188	0.5278		0.2465	False		,,,				2504	0.3241				p.V689L		Atlas-SNP	.											PCDHB7,NS,carcinoma,0,1	PCDHB7	231	1	0			c.G2065T						PASS	.	G	LEU/VAL	958,3440		139,680,1380	63.0	100.0	87.0		2065	2.9	0.5	5	dbSNP_92	87	1772,6820		228,1316,2752	no	missense	PCDHB7	NM_018940.2	32	367,1996,4132	TT,TG,GG		20.6238,21.7826,21.0162	probably-damaging	689/794	140554481	2730,10260	2199	4296	6495	SO:0001583	missense	56129	exon1			TACCTGGTGGTGG	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2065G>T	5.37:g.140554481G>T	ENSP00000231137:p.Val689Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	125	36	0.288	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	704	0.32234432234432236	117	0.23780487804878048	106	0.292817679558011	301	0.5262237762237763	180	0.23746701846965698	G	21.8	4.203707	0.79127	0.217826	0.206238	ENSG00000113212	ENST00000231137	T	0.46819	0.86	3.77	2.86	0.33363	.	.	.	.	.	T	0.00012	0.0000	H	0.97682	4.055	0.32646	P	0.520018	D	0.76494	0.999	D	0.85130	0.997	T	0.45702	-0.9243	8	0.87932	D	0	.	7.7855	0.29089	0.2703:0.0:0.7297:0.0	rs62378900	689	Q9Y5E2	PCDB7_HUMAN	L	689	ENSP00000231137:V689L	ENSP00000231137:V689L	V	+	1	0	PCDHB7	140534665	1.000000	0.71417	0.546000	0.28166	0.957000	0.61999	1.707000	0.37888	1.808000	0.52836	0.449000	0.29647	GTG	G|0.758;T|0.242	0.242	strong		0.711	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
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 GAIIx	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	Somatic	34	0	0	1504	WXS	Illumina HiSeq	Phase_I	51	20	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	
DSPP	1834	hgsc.bcm.edu	37	4	88536460	88536460	+	Silent	SNP	C	C	T	rs199691318		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88536460C>T	ENST00000282478.7	+	4	2679	c.2646C>T	c.(2644-2646)agC>agT	p.S882S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S882S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	882	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgatagcagtgacagca	0.498																																					p.S882S		Atlas-SNP	.											.	DSPP	174	.	0			c.C2646T						PASS	.						73.0	87.0	82.0					4																	88536460		1617	2929	4546	SO:0001819	synonymous_variant	1834	exon5			TGATAGCAGTGAC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2646C>T	4.37:g.88536460C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	12	0.157895	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
CPNE7	27132	hgsc.bcm.edu	37	16	89661807	89661807	+	Silent	SNP	C	C	T	rs12445560	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89661807C>T	ENST00000268720.5	+	16	1690	c.1560C>T	c.(1558-1560)ggC>ggT	p.G520G	CPNE7_ENST00000319518.8_Silent_p.G445G|CPNE7_ENST00000566398.1_3'UTR	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	520	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		TGACGGACGGCGTGGTGACCG	0.632													C|||	436	0.0870607	0.0053	0.2536	5008	,	,		18215	0.1181		0.0855	False		,,,				2504	0.0491				p.G520G		Atlas-SNP	.											.	CPNE7	56	.	0			c.C1560T						PASS	.	C	,	64,4330	58.1+/-94.6	0,64,2133	73.0	52.0	59.0		1560,1335	-5.0	0.9	16	dbSNP_120	59	500,8090	142.0+/-198.3	23,454,3818	no	coding-synonymous,coding-synonymous	CPNE7	NM_014427.4,NM_153636.2	,	23,518,5951	TT,TC,CC		5.8207,1.4565,4.3438	,	520/634,445/559	89661807	564,12420	2197	4295	6492	SO:0001819	synonymous_variant	27132	exon16			GGACGGCGTGGTG	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.1560C>T	16.37:g.89661807C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_014427		Silent	SNP	ENST00000268720.5	37	CCDS10980.1																																																																																			C|0.937;T|0.063	0.063	strong		0.632	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
DHX32	55760	hgsc.bcm.edu	37	10	127530325	127530325	+	Silent	SNP	T	T	C	rs3208565	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127530325T>C	ENST00000284690.3	-	7	2020	c.1530A>G	c.(1528-1530)gcA>gcG	p.A510A	BCCIP_ENST00000429863.2_3'UTR|BCCIP_ENST00000299130.3_3'UTR|DHX32_ENST00000368721.1_Silent_p.A134A|BCCIP_ENST00000368759.5_Intron|DHX32_ENST00000284688.6_Silent_p.A429A|AL360176.1_ENST00000401153.1_RNA	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	510						mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)	p.A510A(1)		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)				TTACCATGGCTGCGATTGTTA	0.368													C|||	2274	0.454073	0.5961	0.3487	5008	,	,		18241	0.3234		0.4443	False		,,,				2504	0.4816				p.A510A		Atlas-SNP	.											DHX32,NS,carcinoma,0,1	DHX32	67	1	1	Substitution - coding silent(1)	stomach(1)	c.A1530G						PASS	.	C	,,	2532,1874	542.2+/-376.0	738,1056,409	73.0	69.0	70.0		,1530,	-0.5	1.0	10	dbSNP_105	70	3952,4648	602.5+/-394.5	917,2118,1265	no	intron,coding-synonymous,utr-3	DHX32,BCCIP	NM_016567.3,NM_018180.2,NM_078469.2	,,	1655,3174,1674	CC,CT,TT		45.9535,42.5329,49.8539	,,	,510/744,	127530325	6484,6522	2203	4300	6503	SO:0001819	synonymous_variant	55760	exon7			CATGGCTGCGATT		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.1530A>G	10.37:g.127530325T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Silent	SNP	ENST00000284690.3	37	CCDS7652.1																																																																																			T|0.521;C|0.479	0.479	strong		0.368	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180	
ZHX3	23051	hgsc.bcm.edu	37	20	39831725	39831725	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:39831725A>G	ENST00000309060.3	-	4	2247	c.1832T>C	c.(1831-1833)tTc>tCc	p.F611S	ZHX3_ENST00000560361.1_Missense_Mutation_p.F611S|ZHX3_ENST00000540170.1_Missense_Mutation_p.F611S|ZHX3_ENST00000432768.2_Missense_Mutation_p.F611S|ZHX3_ENST00000544979.2_Missense_Mutation_p.F611S|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000559234.1_Missense_Mutation_p.F611S			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	611					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				GGTTGGTGTGAAGTCAGGAGT	0.542																																					p.F611S		Atlas-SNP	.											ZHX3,lower_third,carcinoma,-1,1	ZHX3	78	1	0			c.T1832C						scavenged	.						181.0	166.0	171.0					20																	39831725		2203	4300	6503	SO:0001583	missense	23051	exon3			GGTGTGAAGTCAG	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.1832T>C	20.37:g.39831725A>G	ENSP00000312222:p.Phe611Ser	Somatic	296	2	0.00675676		WXS	Illumina HiSeq	Phase_I	340	5	0.0147059	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.968565	0.74131	.	.	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262	T;T;T	0.14144	2.76;2.76;2.53	6.06	6.06	0.98353	Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.34629	0.0904	L	0.59436	1.845	0.58432	D	0.999997	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.76071	0.96;0.968;0.987	T	0.01156	-1.1434	10	0.41790	T	0.15	-20.5076	16.6127	0.84892	1.0:0.0:0.0:0.0	.	611;611;611	A8K8Q0;Q9H4I2;F5H820	.;ZHX3_HUMAN;.	S	611;611;611;611;389	ENSP00000362360:F611S;ENSP00000442290:F611S;ENSP00000443783:F611S	ENSP00000312222:F611S	F	-	2	0	ZHX3	39265139	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.585000	0.67497	2.322000	0.78497	0.528000	0.53228	TTC	.	.	none		0.542	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
HLA-A	3105	hgsc.bcm.edu	37	6	29912098	29912098	+	Silent	SNP	G	G	A	rs142475339	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29912098G>A	ENST00000396634.1	+	6	1160	c.819G>A	c.(817-819)gtG>gtA	p.V273V	HLA-A_ENST00000376806.5_Silent_p.V273V|HLA-A_ENST00000376802.2_Silent_p.V273V|HLA-A_ENST00000376809.5_Silent_p.V273V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	273	Alpha-3.|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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CTGTGGTGGTGCCTTCTGGAG	0.637									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	776	0.154952	0.1354	0.1758	5008	,	,		17674	0.2034		0.1123	False		,,,				2504	0.1605				p.V273V		Atlas-SNP	.											.	HLA-A	89	.	0			c.G819A						PASS	.	A		410,2612		28,354,1129	36.0	34.0	35.0		819	2.8	1.0	6	dbSNP_127	35	582,4828		35,512,2158	no	coding-synonymous	HLA-A	NM_002116.7		63,866,3287	AA,AG,GG		10.7579,13.5672,11.7647		273/366	29912098	992,7440	1511	2705	4216	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGTGGTGCCTTCT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.819G>A	6.37:g.29912098G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	124	26	0.209677	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.871;A|0.129	0.129	strong		0.637	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
BRF1	2972	hgsc.bcm.edu	37	14	105722726	105722726	+	Intron	SNP	T	T	C	rs1008628	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105722726T>C	ENST00000546474.1	-	4	15431				BRF1_ENST00000440513.3_Intron|BRF1_ENST00000327359.3_Intron|BRF1_ENST00000548421.1_Silent_p.P200P|BRF1_ENST00000379937.2_Intron	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit						gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		ACTTCCTGACTGGGCAGGCAG	0.622													C|||	1115	0.222644	0.1989	0.1916	5008	,	,		15484	0.123		0.2903	False		,,,				2504	0.3098				p.P200P		Atlas-SNP	.											.	BRF1	102	.	0			c.A600G						PASS	.																																			SO:0001627	intron_variant	2972	exon4			CCTGACTGGGCAG	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.471+128A>G	14.37:g.105722726T>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_001242790	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Silent	SNP	ENST00000546474.1	37	CCDS10001.1	492	0.22527472527472528	100	0.2032520325203252	80	0.22099447513812154	87	0.1520979020979021	225	0.29683377308707126	C	2.261	-0.369157	0.05069	.	.	ENSG00000185024	ENST00000345053	.	.	.	1.08	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.36915	-0.9728	4	0.30854	T	0.27	.	0.1578	0.00100	0.336:0.246:0.2015:0.2165	rs1008628;rs17845500;rs17858387;rs52792575;rs57994825;rs1008628	.	.	.	G	200	.	ENSP00000339442:S200G	S	-	1	0	BRF1	104793771	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.214000	0.01223	-1.634000	0.01537	-1.464000	0.01018	AGT	T|0.783;C|0.217	0.217	strong		0.622	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519	
KRT6C	286887	hgsc.bcm.edu	37	12	52863213	52863213	+	Missense_Mutation	SNP	C	C	T	rs412533	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52863213C>T	ENST00000252250.6	-	8	1488	c.1441G>A	c.(1441-1443)Gtt>Att	p.V481I		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	481	Tail.		V -> I (in dbSNP:rs412533). {ECO:0000269|PubMed:7543104}.		intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		ACTTGTCCAACGCCTTCGCCA	0.607													C|||	1250	0.249601	0.0242	0.2637	5008	,	,		21887	0.4812		0.3628	False		,,,				2504	0.1892				p.V481I		Atlas-SNP	.											.	KRT6C	55	.	0			c.G1441A						PASS	.	C	ILE/VAL	316,4090	170.5+/-200.9	15,286,1902	140.0	109.0	119.0		1441	3.6	1.0	12	dbSNP_80	119	3163,5437	480.9+/-370.5	583,1997,1720	no	missense	KRT6C	NM_173086.4	29	598,2283,3622	TT,TC,CC		36.7791,7.172,26.7492	possibly-damaging	481/565	52863213	3479,9527	2203	4300	6503	SO:0001583	missense	286887	exon8			GTCCAACGCCTTC	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.1441G>A	12.37:g.52863213C>T	ENSP00000252250:p.Val481Ile	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	730	0.3342490842490842	19	0.03861788617886179	116	0.32044198895027626	320	0.5594405594405595	275	0.3627968337730871	C	12.01	1.809706	0.31961	0.07172	0.367791	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.92495	-3.05	3.57	3.57	0.40892	.	0.000000	0.49305	D	0.000143	T	0.00012	0.0000	L	0.54323	1.7	0.40382	P	0.020545000000000035	P	0.44006	0.824	B	0.27500	0.08	T	0.42766	-0.9432	9	0.39692	T	0.17	.	11.8038	0.52143	0.1761:0.8239:0.0:0.0	rs412533	481	P48668	K2C6C_HUMAN	I	481;466	ENSP00000252250:V481I	ENSP00000252250:V481I	V	-	1	0	KRT6C	51149480	0.007000	0.16637	0.994000	0.49952	0.774000	0.43823	0.864000	0.27926	1.983000	0.57843	0.448000	0.29417	GTT	C|0.723;T|0.277	0.277	strong		0.607	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
DDX55	57696	hgsc.bcm.edu	37	12	124104049	124104049	+	Silent	SNP	A	A	G	rs15587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:124104049A>G	ENST00000238146.4	+	13	1454	c.1404A>G	c.(1402-1404)ggA>ggG	p.G468G	DDX55_ENST00000421670.3_Silent_p.G75G|SNORA9_ENST00000384170.1_RNA|DDX55_ENST00000538744.1_Silent_p.G437G|DDX55_ENST00000541259.1_3'UTR	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	468						membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		AATTGAGAGGAAAGCAGTTTC	0.458													A|||	1266	0.252796	0.4486	0.2205	5008	,	,		15634	0.0159		0.2654	False		,,,				2504	0.2423				p.G468G		Atlas-SNP	.											.	DDX55	51	.	0			c.A1404G						PASS	.	A		1835,2571	536.7+/-374.5	386,1063,754	124.0	122.0	123.0		1404	-0.9	1.0	12	dbSNP_52	123	2376,6224	394.7+/-344.8	341,1694,2265	no	coding-synonymous	DDX55	NM_020936.1		727,2757,3019	GG,GA,AA		27.6279,41.6478,32.3774		468/601	124104049	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	57696	exon13			GAGAGGAAAGCAG	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.1404A>G	12.37:g.124104049A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	35	8	0.228571	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Silent	SNP	ENST00000238146.4	37	CCDS9251.1																																																																																			A|0.701;G|0.299	0.299	strong		0.458	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
CCDC102A	92922	hgsc.bcm.edu	37	16	57552088	57552088	+	Silent	SNP	T	T	C	rs28756858	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57552088T>C	ENST00000258214.2	-	6	1386	c.1140A>G	c.(1138-1140)gcA>gcG	p.A380A		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	380										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						CTCCGACCTGTGCCCGCAGCT	0.701													T|||	1078	0.215256	0.413	0.1585	5008	,	,		15230	0.0288		0.2445	False		,,,				2504	0.1503				p.A380A		Atlas-SNP	.											.	CCDC102A	22	.	0			c.A1140G						PASS	.	T		1718,2678		343,1032,823	50.0	63.0	58.0		1140	-6.6	0.8	16	dbSNP_125	58	2031,6563		240,1551,2506	no	coding-synonymous	CCDC102A	NM_033212.3		583,2583,3329	CC,CT,TT		23.6328,39.081,28.8607		380/551	57552088	3749,9241	2198	4297	6495	SO:0001819	synonymous_variant	92922	exon6			GACCTGTGCCCGC	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.1140A>G	16.37:g.57552088T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_033212	Q9BT74	Silent	SNP	ENST00000258214.2	37	CCDS10784.1																																																																																			A|0.000;C|0.268;T|0.732	0.268	strong		0.701	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212	
FAM110D	79927	hgsc.bcm.edu	37	1	26488019	26488019	+	Silent	SNP	G	G	A	rs3748857	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26488019G>A	ENST00000374268.3	+	2	424	c.237G>A	c.(235-237)ccG>ccA	p.P79P		NM_024869.2	NP_079145.2	Q8TAY7	F110D_HUMAN	family with sequence similarity 110, member D	79																	GGCGGCTGCCGAGGCCTGATT	0.697													G|||	1413	0.282149	0.0076	0.389	5008	,	,		12069	0.5794		0.1133	False		,,,				2504	0.4448				p.P79P		Atlas-SNP	.											.	.	.	.	0			c.G237A						PASS	.	G		82,2872		1,80,1396	2.0	3.0	3.0		237	-3.1	1.0	1	dbSNP_107	3	504,6034		12,480,2777	no	coding-synonymous	GRRP1	NM_024869.2		13,560,4173	AA,AG,GG		7.7088,2.7759,6.1736		79/272	26488019	586,8906	1477	3269	4746	SO:0001819	synonymous_variant	79927	exon2			GCTGCCGAGGCCT		CCDS41285.1	1p36.11	2011-12-01	2011-12-01	2011-12-01	ENSG00000197245	ENSG00000197245			25860	protein-coding gene	gene with protein product			"""glycine/arginine rich protein 1"""	GRRP1		12477932	Standard	NM_024869		Approved	FLJ14050	uc001blk.3	Q8TAY7	OTTHUMG00000007537	ENST00000374268.3:c.237G>A	1.37:g.26488019G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	29	28	0.965517	NM_024869	A8K3V0|Q9H7Z4	Silent	SNP	ENST00000374268.3	37	CCDS41285.1																																																																																			G|0.753;A|0.247	0.247	strong		0.697	FAM110D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019841.1	NM_024869	
TMCC2	9911	hgsc.bcm.edu	37	1	205238530	205238530	+	Silent	SNP	C	C	T	rs1779411	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205238530C>T	ENST00000358024.3	+	3	1589	c.1200C>T	c.(1198-1200)ggC>ggT	p.G400G	TMCC2_ENST00000329800.7_Silent_p.G160G|TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000330675.7_Silent_p.G175G|TMCC2_ENST00000545499.1_Silent_p.G322G	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	400						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			GCTTTGGGGGCGGCGTGGTGG	0.706													C|||	630	0.125799	0.0287	0.1816	5008	,	,		14780	0.0377		0.3549	False		,,,				2504	0.0726				p.G400G		Atlas-SNP	.											.	TMCC2	89	.	0			c.C1200T						PASS	.	C	,	329,4069		20,289,1890	27.0	30.0	29.0		966,1200	-4.8	0.9	1	dbSNP_89	29	3031,5563		539,1953,1805	no	coding-synonymous,coding-synonymous	TMCC2	NM_001242925.1,NM_014858.3	,	559,2242,3695	TT,TC,CC		35.2688,7.4807,25.8621	,	322/632,400/710	205238530	3360,9632	2199	4297	6496	SO:0001819	synonymous_variant	9911	exon3			TGGGGGCGGCGTG	AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"""Transmembrane and coiled-coil domain containing"""	24239	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 2"""			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.1200C>T	1.37:g.205238530C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	46	26	0.565217	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Silent	SNP	ENST00000358024.3	37	CCDS30984.1																																																																																			C|0.784;T|0.216	0.216	strong		0.706	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858	
RBM23	55147	hgsc.bcm.edu	37	14	23371055	23371055	+	Missense_Mutation	SNP	G	G	C	rs1127066	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:23371055G>C	ENST00000359890.3	-	13	1479	c.1284C>G	c.(1282-1284)ttC>ttG	p.F428L	RBM23_ENST00000399922.2_Missense_Mutation_p.F412L|RBM23_ENST00000346528.5_Missense_Mutation_p.F394L|RBM23_ENST00000542016.2_Missense_Mutation_p.F258L|RBM23_ENST00000555209.1_Missense_Mutation_p.F178L	NM_001077351.1	NP_001070819.1	Q86U06	RBM23_HUMAN	RNA binding motif protein 23	428			F -> L (in dbSNP:rs1127066).		mRNA processing (GO:0006397)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|lung(3)|prostate(1)|skin(1)	10	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.0128)		TGGAGAGCTGGAAACACTGGG	0.527													G|||	1076	0.214856	0.053	0.2983	5008	,	,		19620	0.2649		0.2853	False		,,,				2504	0.2505				p.F428L		Atlas-SNP	.											.	RBM23	44	.	0			c.C1284G						PASS	.	G	LEU/PHE,LEU/PHE,LEU/PHE	381,3653		20,341,1656	166.0	176.0	173.0		1284,1182,1236	2.3	1.0	14	dbSNP_86	173	2510,5860		387,1736,2062	yes	missense,missense,missense	RBM23	NM_001077351.1,NM_001077352.1,NM_018107.4	22,22,22	407,2077,3718	CC,CG,GG		29.9881,9.4447,23.307	possibly-damaging,possibly-damaging,possibly-damaging	428/440,394/406,412/424	23371055	2891,9513	2017	4185	6202	SO:0001583	missense	55147	exon13			GAGCTGGAAACAC	AF275678	CCDS41919.1, CCDS41920.1, CCDS41921.1	14q11.1	2014-07-03	2004-04-23	2004-04-23		ENSG00000100461		"""RNA binding motif (RRM) containing"""	20155	protein-coding gene	gene with protein product	"""coactivator of activating protein-1 and estrogen recep- tors beta"""		"""RNA-binding region (RNP1, RRM) containing 4"""	RNPC4		15694343	Standard	NM_018107		Approved	FLJ10482, CAPERbeta	uc001whg.3	Q86U06		ENST00000359890.3:c.1284C>G	14.37:g.23371055G>C	ENSP00000352956:p.Phe428Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_001077351	D3DS32|Q8ND16|Q8TB88|Q8WY40|Q9BUJ1|Q9NVV7	Missense_Mutation	SNP	ENST00000359890.3	37	CCDS41921.1	509|509	0.23305860805860806|0.23305860805860806	37|37	0.07520325203252033|0.07520325203252033	107|107	0.2955801104972376|0.2955801104972376	154|154	0.2692307692307692|0.2692307692307692	211|211	0.2783641160949868|0.2783641160949868	G|G	12.07|12.07	1.826883|1.826883	0.32329|0.32329	0.094447|0.094447	0.299881|0.299881	ENSG00000100461|ENSG00000100461	ENST00000555209;ENST00000359890;ENST00000338980;ENST00000399922;ENST00000346528;ENST00000542016;ENST00000557245|ENST00000553884	T;T;T;T;T;T|.	0.47528|.	0.84;0.84;0.84;0.84;0.84;0.84|.	5.34|5.34	2.35|2.35	0.29111|0.29111	.|.	0.314942|.	0.26072|.	N|.	0.026512|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.35854|0.35854	1.095|1.095	0.23298|0.23298	P|P	0.9979592|0.9979592	B;B;B|.	0.23735|.	0.002;0.002;0.09|.	B;B;B|.	0.23574|.	0.019;0.019;0.047|.	T|T	0.26360|0.26360	-1.0105|-1.0105	9|4	0.15066|.	T|.	0.55|.	-0.3141|-0.3141	10.3266|10.3266	0.43796|0.43796	0.0:0.1306:0.599:0.2704|0.0:0.1306:0.599:0.2704	rs1127066;rs1242630;rs1742324;rs3182572;rs11557897;rs17124077;rs52811176;rs59971662;rs1127066|rs1127066;rs1242630;rs1742324;rs3182572;rs11557897;rs17124077;rs52811176;rs59971662;rs1127066	394;412;428|.	Q86U06-4;Q86U06-2;Q86U06|.	.;.;RBM23_HUMAN|.	L|A	178;428;405;412;394;258;71|203	ENSP00000452602:F178L;ENSP00000352956:F428L;ENSP00000382806:F412L;ENSP00000339220:F394L;ENSP00000438504:F258L;ENSP00000451838:F71L|.	ENSP00000345496:F405L|.	F|P	-|-	3|1	2|0	RBM23|RBM23	22440895|22440895	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.982000|0.982000	0.71751|0.71751	0.348000|0.348000	0.20031|0.20031	0.190000|0.190000	0.20209|0.20209	0.561000|0.561000	0.74099|0.74099	TTC|CCA	G|0.760;C|0.240	0.240	strong		0.527	RBM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413545.3		
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 GAIIx	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	54	29	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	
TTN	7273	hgsc.bcm.edu	37	2	179412966	179412966	+	Silent	SNP	G	G	A	rs35445420	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179412966G>A	ENST00000591111.1	-	289	88688	c.88464C>T	c.(88462-88464)tcC>tcT	p.S29488S	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.S31129S|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Silent_p.S22256S|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.S22189S|TTN_ENST00000460472.2_Silent_p.S22064S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN_ENST00000342992.6_Silent_p.S28561S			Q8WZ42	TITIN_HUMAN	titin	29488	Fibronectin type-III 115. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTAAGACTGCGGAGGATTTGC	0.493													G|||	45	0.00898562	0.0015	0.0245	5008	,	,		22476	0.0		0.0229	False		,,,				2504	0.0031				p.S31129S		Atlas-SNP	.											.	TTN	18412	.	0			c.C93387T						PASS	.	G	,,,	15,4015		0,15,2000	163.0	160.0	161.0		66192,85683,66567,66768	-1.6	0.9	2	dbSNP_126	161	238,8146		4,230,3958	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	4,245,5958	AA,AG,GG		2.8387,0.3722,2.038	,,,	22064/26927,28561/33424,22189/27052,22256/27119	179412966	253,12161	2015	4192	6207	SO:0001819	synonymous_variant	7273	exon339			GACTGCGGAGGAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.88464C>T	2.37:g.179412966G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.985;A|0.015	0.015	strong		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
GPR139	124274	hgsc.bcm.edu	37	16	20043236	20043236	+	Missense_Mutation	SNP	T	T	C	rs149441644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20043236T>C	ENST00000570682.1	-	2	1183	c.883A>G	c.(883-885)Atg>Gtg	p.M295V		NM_001002911.2	NP_001002911.1	Q6DWJ6	GP139_HUMAN	G protein-coupled receptor 139	295					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	30						GCGGCTGCCATGGTGCGGAAC	0.502													T|||	7	0.00139776	0.0	0.0029	5008	,	,		19554	0.0		0.004	False		,,,				2504	0.001				p.M295V		Atlas-SNP	.											.	GPR139	75	.	0			c.A883G						PASS	.	T	VAL/MET	2,4404	6.2+/-15.9	0,2,2201	114.0	112.0	112.0		883	4.4	0.9	16	dbSNP_134	112	53,8547	34.3+/-88.2	0,53,4247	yes	missense	GPR139	NM_001002911.2	21	0,55,6448	CC,CT,TT		0.6163,0.0454,0.4229	benign	295/354	20043236	55,12951	2203	4300	6503	SO:0001583	missense	124274	exon2			CTGCCATGGTGCG	AY255545	CCDS32398.1	16p13.11	2012-08-21						"""GPCR / Class A : Orphans"""	19995	protein-coding gene	gene with protein product						12679517	Standard	XM_005255114		Approved	PGR3	uc002dgu.1	Q6DWJ6		ENST00000570682.1:c.883A>G	16.37:g.20043236T>C	ENSP00000458791:p.Met295Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_001002911	A8K5R9|Q86SP2|Q8TDU8	Missense_Mutation	SNP	ENST00000570682.1	37	CCDS32398.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	9.109	1.005968	0.19199	4.54E-4	0.006163	ENSG00000180269	ENST00000326571	.	.	.	5.52	4.4	0.53042	.	0.040495	0.85682	D	0.000000	T	0.32406	0.0828	N	0.19112	0.55	0.49051	D	0.999748	B	0.21071	0.051	B	0.14023	0.01	T	0.09862	-1.0655	9	0.28530	T	0.3	-42.6744	11.9001	0.52678	0.0:0.0:0.146:0.854	.	295	Q6DWJ6	GP139_HUMAN	V	295	.	ENSP00000370779:M295V	M	-	1	0	GPR139	19950737	1.000000	0.71417	0.937000	0.37676	0.997000	0.91878	5.975000	0.70475	0.891000	0.36235	0.533000	0.62120	ATG	T|0.996;C|0.004	0.004	strong		0.502	GPR139-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438522.1	NM_001002911	
PRDM16	63976	hgsc.bcm.edu	37	1	3328659	3328659	+	Missense_Mutation	SNP	C	C	T	rs2493292	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3328659C>T	ENST00000270722.5	+	9	1947	c.1898C>T	c.(1897-1899)cCt>cTt	p.P633L	PRDM16_ENST00000378398.3_Missense_Mutation_p.P634L|PRDM16_ENST00000441472.2_Missense_Mutation_p.P633L|PRDM16_ENST00000514189.1_Missense_Mutation_p.P634L|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000442529.2_Missense_Mutation_p.P633L|PRDM16_ENST00000511072.1_Missense_Mutation_p.P634L|PRDM16_ENST00000378391.2_Missense_Mutation_p.P633L			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	633			P -> L (in dbSNP:rs2493292).		brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		GACAGCGACCCTGACAAGGAC	0.697			T	EVI1	"""MDS, AML"""								C|||	531	0.10603	0.1634	0.121	5008	,	,		13011	0.006		0.166	False		,,,				2504	0.0593				p.P633L		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C1898T						PASS	.	C	LEU/PRO,LEU/PRO	659,3627		61,537,1545	55.0	66.0	62.0		1898,1898	4.2	0.9	1	dbSNP_100	62	1283,7181		100,1083,3049	yes	missense,missense	PRDM16	NM_199454.2,NM_022114.3	98,98	161,1620,4594	TT,TC,CC		15.1583,15.3756,15.2314	benign,benign	633/1258,633/1277	3328659	1942,10808	2143	4232	6375	SO:0001583	missense	63976	exon9			GCGACCCTGACAA	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1898C>T	1.37:g.3328659C>T	ENSP00000270722:p.Pro633Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	242	0.1108058608058608	75	0.1524390243902439	52	0.143646408839779	4	0.006993006993006993	111	0.14643799472295516	C	15.56	2.871058	0.51695	0.153756	0.151583	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.04917	3.54;3.57;3.58;3.58;3.57;3.57;3.58;3.53;3.53	5.09	4.18	0.49190	.	0.125337	0.29046	N	0.013308	T	0.00039	0.0001	N	0.08118	0	0.28723	P	0.9029207	B;B;B;B	0.31383	0.039;0.066;0.321;0.039	B;B;B;B	0.26969	0.016;0.036;0.075;0.016	T	0.48163	-0.9059	9	0.52906	T	0.07	.	14.9602	0.71151	0.0:0.1609:0.8391:0.0	rs2493292;rs57392481;rs2493292	633;633;633;633	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	L	634;634;633;633;633;634;633;449;449;442	ENSP00000426975:P634L;ENSP00000367651:P634L;ENSP00000407968:P633L;ENSP00000405253:P633L;ENSP00000367643:P633L;ENSP00000421400:P634L;ENSP00000270722:P633L;ENSP00000422504:P449L;ENSP00000425796:P442L	ENSP00000270722:P633L	P	+	2	0	PRDM16	3318519	1.000000	0.71417	0.921000	0.36526	0.851000	0.48451	4.782000	0.62396	1.153000	0.42468	0.603000	0.83216	CCT	C|0.868;T|0.132	0.132	strong		0.697	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
GNPTAB	79158	hgsc.bcm.edu	37	12	102224436	102224436	+	Silent	SNP	C	C	T	rs4764655	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:102224436C>T	ENST00000299314.7	-	1	280	c.18G>A	c.(16-18)ctG>ctA	p.L6L	GNPTAB_ENST00000549940.1_Silent_p.L6L|GNPTAB_ENST00000549165.1_Silent_p.L6L|GNPTAB_ENST00000392919.4_Silent_p.L6L	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	6					carbohydrate phosphorylation (GO:0046835)|cell differentiation (GO:0030154)|lysosome organization (GO:0007040)|protein secretion (GO:0009306)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(8)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	37						TCTGTCTCTGCAGGAGCTTGA	0.662													C|||	490	0.0978435	0.0182	0.1657	5008	,	,		8386	0.1637		0.1133	False		,,,				2504	0.0736				p.L6L		Atlas-SNP	.											.	GNPTAB	120	.	0			c.G18A						PASS	.	C		176,4230	110.8+/-149.0	4,168,2031	90.0	70.0	77.0		18	-3.7	0.1	12	dbSNP_111	77	1019,7581	209.0+/-250.3	61,897,3342	no	coding-synonymous	GNPTAB	NM_024312.4		65,1065,5373	TT,TC,CC		11.8488,3.9946,9.1881		6/1257	102224436	1195,11811	2203	4300	6503	SO:0001819	synonymous_variant	79158	exon1			TCTCTGCAGGAGC	AY687932	CCDS9088.1	12q23.3	2013-01-10				ENSG00000111670		"""EF-hand domain containing"""	29670	protein-coding gene	gene with protein product		607840		GNPTA		10574462, 16116615	Standard	NM_024312		Approved	KIAA1208, MGC4170	uc001tit.3	Q3T906	OTTHUMG00000170444	ENST00000299314.7:c.18G>A	12.37:g.102224436C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Silent	SNP	ENST00000299314.7	37	CCDS9088.1																																																																																			C|0.900;T|0.100	0.100	strong		0.662	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1		
EFCAB7	84455	hgsc.bcm.edu	37	1	63999868	63999868	+	Missense_Mutation	SNP	T	T	C	rs6657480	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:63999868T>C	ENST00000371088.4	+	6	1031	c.785T>C	c.(784-786)aTg>aCg	p.M262T	RNU7-123P_ENST00000515911.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	262			M -> T (in dbSNP:rs6657480). {ECO:0000269|PubMed:15489334}.				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						TCAAAGTTAATGGAGCCAAAT	0.343													C|||	1440	0.28754	0.5825	0.196	5008	,	,		15429	0.1925		0.1491	False		,,,				2504	0.1943				p.M262T		Atlas-SNP	.											.	EFCAB7	45	.	0			c.T785C						PASS	.	C	THR/MET	2103,2303	597.0+/-388.8	514,1075,614	64.0	65.0	65.0		785	2.3	1.0	1	dbSNP_116	65	1344,7256	754.1+/-407.5	94,1156,3050	yes	missense	EFCAB7	NM_032437.2	81	608,2231,3664	CC,CT,TT		15.6279,47.7304,26.5032	benign	262/630	63999868	3447,9559	2203	4300	6503	SO:0001583	missense	84455	exon6			AGTTAATGGAGCC	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.785T>C	1.37:g.63999868T>C	ENSP00000360129:p.Met262Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	561	0.25686813186813184	267	0.5426829268292683	74	0.20441988950276244	110	0.19230769230769232	110	0.14511873350923482	C	0.003	-2.489623	0.00161	0.477304	0.156279	ENSG00000203965	ENST00000371088	T	0.55588	0.51	5.65	2.32	0.28847	.	0.671131	0.16090	N	0.230086	T	0.04363	0.0120	N	0.00538	-1.39	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35276	-0.9795	9	0.08381	T	0.77	-6.203	4.47	0.11708	0.1582:0.5267:0.0:0.3151	rs6657480;rs17845480;rs17858360;rs52835496;rs60937630;rs6657480	262	A8K855	EFCB7_HUMAN	T	262	ENSP00000360129:M262T	ENSP00000360129:M262T	M	+	2	0	EFCAB7	63772456	0.083000	0.21467	0.980000	0.43619	0.037000	0.13140	0.268000	0.18571	0.346000	0.23899	-0.767000	0.03436	ATG	T|0.741;C|0.259	0.259	strong		0.343	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
STRN3	29966	hgsc.bcm.edu	37	14	31381351	31381351	+	Missense_Mutation	SNP	T	T	C	rs2273171	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:31381351T>C	ENST00000357479.5	-	11	1608	c.1412A>G	c.(1411-1413)aAt>aGt	p.N471S	STRN3_ENST00000366206.2_5'UTR|STRN3_ENST00000355683.5_Missense_Mutation_p.N387S	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	471			N -> S (in dbSNP:rs2273171). {ECO:0000269|PubMed:10748158, ECO:0000269|PubMed:7864889}.		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)	p.N387S(1)		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)		ATACTTGGGATTCCATGTCTT	0.423													T|||	1948	0.388978	0.3139	0.4553	5008	,	,		17850	0.4692		0.4632	False		,,,				2504	0.2843				p.N471S		Atlas-SNP	.											STRN3,NS,carcinoma,0,1	STRN3	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1412G						PASS	.	T	SER/ASN,SER/ASN	1515,2891	481.2+/-359.0	271,973,959	130.0	124.0	126.0		1412,1160	5.6	1.0	14	dbSNP_100	126	3983,4617	552.8+/-386.2	904,2175,1221	yes	missense,missense	STRN3	NM_001083893.1,NM_014574.3	46,46	1175,3148,2180	CC,CT,TT		46.314,34.3849,42.2728	possibly-damaging,possibly-damaging	471/798,387/714	31381351	5498,7508	2203	4300	6503	SO:0001583	missense	29966	exon11			TTGGGATTCCATG		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.1412A>G	14.37:g.31381351T>C	ENSP00000350071:p.Asn471Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	37	CCDS41938.1	941	0.4308608058608059	165	0.3353658536585366	166	0.4585635359116022	250	0.4370629370629371	360	0.47493403693931396	T	24.6	4.544097	0.86022	0.343849	0.46314	ENSG00000196792	ENST00000355683;ENST00000357479	T;T	0.59772	0.24;0.24	5.63	5.63	0.86233	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.083501	0.85682	D	0.000000	T	0.00012	0.0000	L	0.28400	0.85	0.09310	P	0.99999999782838	B;B	0.33135	0.029;0.399	B;B	0.31946	0.037;0.138	T	0.44922	-0.9296	9	0.72032	D	0.01	-10.5307	15.7875	0.78319	0.0:0.0:0.0:1.0	rs2273171;rs57146647;rs2273171	387;471	Q13033-2;Q13033	.;STRN3_HUMAN	S	387;471	ENSP00000347909:N387S;ENSP00000350071:N471S	ENSP00000347909:N387S	N	-	2	0	STRN3	30451102	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.153000	0.71819	2.257000	0.74773	0.533000	0.62120	AAT	C|0.414;N|0.000	0.414	strong		0.423	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394003	103394003	+	RNA	SNP	G	G	A	rs1449707	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103394003G>A	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		CTCCTGGCAAGTCTTCTGTTG	0.403													G|||	3476	0.694089	0.5408	0.7493	5008	,	,		19700	0.5913		0.826	False		,,,				2504	0.8323				p.T3015I		Atlas-SNP	.											.	.	.	.	0			c.C9044T						PASS	.	G	ILE/THR	773,611		217,339,136	63.0	52.0	55.0		9044	-2.2	0.0	13	dbSNP_88	55	2543,637		1023,497,70	yes	missense	CCDC168	NM_001146197.1	89	1240,836,206	AA,AG,GG		20.0314,44.1474,27.3444		3015/7082	103394003	3316,1248	692	1590	2282			643677	exon4			TGGCAAGTCTTCT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103394003G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				G|0.336;A|0.664	0.664	strong		0.403	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
TMEM63A	9725	hgsc.bcm.edu	37	1	226034774	226034774	+	Silent	SNP	C	C	T	rs2292559	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226034774C>T	ENST00000366835.3	-	24	2661	c.2391G>A	c.(2389-2391)acG>acA	p.T797T	RP11-285F7.2_ENST00000424332.1_RNA	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	797					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					CCACACTGCCCGTGGCGCTCT	0.662													C|||	353	0.0704872	0.0008	0.0735	5008	,	,		18801	0.1587		0.0487	False		,,,				2504	0.0941				p.T797T		Atlas-SNP	.											.	TMEM63A	75	.	0			c.G2391A						PASS	.	C		32,4372	36.8+/-68.6	0,32,2170	51.0	52.0	52.0		2391	0.3	0.0	1	dbSNP_100	52	349,8251	114.8+/-174.7	4,341,3955	no	coding-synonymous	TMEM63A	NM_014698.2		4,373,6125	TT,TC,CC		4.0581,0.7266,2.9299		797/808	226034774	381,12623	2202	4300	6502	SO:0001819	synonymous_variant	9725	exon24			ACTGCCCGTGGCG		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.2391G>A	1.37:g.226034774C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			C|0.957;T|0.043	0.043	strong		0.662	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
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 GAIIx	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_ENST00000543612.1_Silent_p.L784L|EPS8_ENST00000543523.1_Silent_p.L784L|EPS8_ENST00000542903.1_Silent_p.L524L|EPS8_ENST00000540613.1_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		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	129	63	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		
XIRP2	129446	hgsc.bcm.edu	37	2	168108357	168108357	+	Silent	SNP	A	A	G	rs1842233	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:168108357A>G	ENST00000409195.1	+	9	10544	c.10455A>G	c.(10453-10455)caA>caG	p.Q3485Q	XIRP2_ENST00000409273.1_Silent_p.Q3263Q|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000295237.9_Silent_p.Q3485Q|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3310					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGACGTGGCAAGAGAGTGGAA	0.413													G|||	1729	0.345248	0.5477	0.2522	5008	,	,		19870	0.3284		0.169	False		,,,				2504	0.3364				p.Q3485Q		Atlas-SNP	.											.	XIRP2	914	.	0			c.A10455G						PASS	.	G	,,,,	1743,1959		418,907,526	61.0	63.0	62.0		,,9789,,10455	1.4	1.0	2	dbSNP_92	62	1282,6876		99,1084,2896	yes	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	517,1991,3422	GG,GA,AA		15.7146,47.0827,25.5059	,,,,	,,3263/3328,,3485/3550	168108357	3025,8835	1851	4079	5930	SO:0001819	synonymous_variant	129446	exon9			GTGGCAAGAGAGT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.10455A>G	2.37:g.168108357A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			G|0.309;N|0.001	0.309	strong		0.413	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905132	1905132	+	Silent	SNP	G	G	A	rs3735876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:1905132G>A	ENST00000398564.1	+	29	3813	c.3813G>A	c.(3811-3813)tcG>tcA	p.S1271S	ARHGEF10_ENST00000349830.3_Silent_p.S1246S|ARHGEF10_ENST00000262112.6_Silent_p.S1242S|ARHGEF10_ENST00000520359.1_Silent_p.S1208S|ARHGEF10_ENST00000518288.1_Silent_p.S1270S|ARHGEF10_ENST00000521927.1_3'UTR			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1271	Ser-rich.				centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		TGGGAGATTCGCTGGGATCGA	0.577													G|||	1843	0.368011	0.2133	0.2349	5008	,	,		18564	0.5714		0.4016	False		,,,				2504	0.4274				p.S1246S		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.G3738A						PASS	.	G		1172,3234	413.7+/-336.6	160,852,1191	134.0	127.0	129.0		3738	-11.2	0.0	8	dbSNP_107	129	3323,5277	495.2+/-374.0	630,2063,1607	no	coding-synonymous	ARHGEF10	NM_014629.2		790,2915,2798	AA,AG,GG		38.6395,26.6001,34.561		1246/1345	1905132	4495,8511	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon29			AGATTCGCTGGGA	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3813G>A	8.37:g.1905132G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				G|0.648;A|0.352	0.352	strong		0.577	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
MAGEB6	158809	hgsc.bcm.edu	37	X	26212477	26212477	+	Missense_Mutation	SNP	G	G	C	rs145782491	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:26212477G>C	ENST00000379034.1	+	2	663	c.514G>C	c.(514-516)Ggt>Cgt	p.G172R		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	172				G -> R (in Ref. 1; BAC05102). {ECO:0000305}.						breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						GGCTGCCGAGGGTGAAGATGA	0.502													.|||	51	0.0135099	0.0	0.0072	3775	,	,		13896	0.0		0.0189	False		,,,				2504	0.0276				p.G172R		Atlas-SNP	.											.	MAGEB6	91	.	0			c.G514C						PASS	.	G	ARG/GLY	6,3827		0,5,1,1626,570	55.0	49.0	51.0		514	-2.6	0.0	X	dbSNP_134	51	112,6616		0,84,28,2344,1844	yes	missense	MAGEB6	NM_173523.2	125	0,89,29,3970,2414	CC,CG,C,GG,G		1.6647,0.1565,1.1173	probably-damaging	172/408	26212477	118,10443	2202	4300	6502	SO:0001583	missense	158809	exon2			GCCGAGGGTGAAG	AF320514	CCDS14217.1	Xp22.12	2009-03-17			ENSG00000176746	ENSG00000176746			23796	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 4"""	300467				10861452	Standard	NM_173523		Approved	FLJ40242, MAGE-B6, MAGEB6A, CT3.4	uc004dbr.3	Q8N7X4	OTTHUMG00000021285	ENST00000379034.1:c.514G>C	X.37:g.26212477G>C	ENSP00000368320:p.Gly172Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	67	44	0.656716	NM_173523	Q6GS19|Q9H219	Missense_Mutation	SNP	ENST00000379034.1	37	CCDS14217.1	13	0.007836045810729355	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011936339522546418	G	6.633	0.485291	0.12641	0.001565	0.016647	ENSG00000176746	ENST00000379034	T	0.01902	4.57	1.83	-2.56	0.06268	.	1.004860	0.08007	U	0.989793	T	0.01061	0.0035	N	0.24115	0.695	0.09310	N	1	P	0.48503	0.911	P	0.48166	0.569	T	0.34329	-0.9833	10	0.44086	T	0.13	.	2.5024	0.04637	0.3012:0.0:0.4394:0.2594	.	172	Q8N7X4	MAGB6_HUMAN	R	172	ENSP00000368320:G172R	ENSP00000368320:G172R	G	+	1	0	MAGEB6	26122398	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.905000	0.04075	-0.833000	0.04245	-0.386000	0.06593	GGT	G|0.990;C|0.010	0.010	strong		0.502	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523	
SUN2	25777	hgsc.bcm.edu	37	22	39134715	39134715	+	Silent	SNP	T	T	C	rs1062687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39134715T>C	ENST00000405510.1	-	17	2182	c.1824A>G	c.(1822-1824)caA>caG	p.Q608Q	SUN2_ENST00000411587.2_Silent_p.Q597Q|SUN2_ENST00000216064.4_Silent_p.Q608Q|RP3-508I15.14_ENST00000416406.1_RNA|RP3-508I15.20_ENST00000609428.1_RNA|RP3-508I15.18_ENST00000420118.1_RNA|SUN2_ENST00000406622.1_Silent_p.Q608Q|SUN2_ENST00000405018.1_Silent_p.Q629Q|RP3-508I15.19_ENST00000418803.1_RNA	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	608	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						CGGCGAAGCCTTGTGGCCCCT	0.622													C|||	1923	0.383986	0.556	0.2046	5008	,	,		17697	0.4603		0.2982	False		,,,				2504	0.2883				p.Q629Q		Atlas-SNP	.											.	SUN2	59	.	0			c.A1887G						PASS	.	C	,,	2258,2148	573.8+/-383.6	577,1104,522	66.0	70.0	69.0		1887,1824,1824	2.4	1.0	22	dbSNP_86	69	2565,6035	685.2+/-404.0	375,1815,2110	no	coding-synonymous,coding-synonymous,coding-synonymous	SUN2	NM_001199579.1,NM_001199580.1,NM_015374.2	,,	952,2919,2632	CC,CT,TT		29.8256,48.7517,37.0829	,,	629/739,608/718,608/718	39134715	4823,8183	2203	4300	6503	SO:0001819	synonymous_variant	25777	exon16			GAAGCCTTGTGGC	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"""unc-84 homolog B (C. elegans)"""	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.1824A>G	22.37:g.39134715T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001199579	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Silent	SNP	ENST00000405510.1	37	CCDS13978.1																																																																																			T|0.620;C|0.380;A|0.000	0.380	strong		0.622	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332	
LAMTOR2	28956	hgsc.bcm.edu	37	1	156025096	156025096	+	Silent	SNP	C	C	T	rs7541	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156025096C>T	ENST00000368305.4	+	2	249	c.111C>T	c.(109-111)taC>taT	p.Y37Y	LAMTOR2_ENST00000489664.1_3'UTR|LAMTOR2_ENST00000368304.5_Silent_p.Y37Y|LAMTOR2_ENST00000368302.3_Silent_p.Y37Y|UBQLN4_ENST00000472638.1_5'Flank|UBQLN4_ENST00000368309.3_5'Flank	NM_014017.3	NP_054736.1	Q9Y2Q5	LTOR2_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2	37					activation of MAPKK activity (GO:0000186)|cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|positive regulation of GTPase activity (GO:0043547)|positive regulation of TOR signaling (GO:0032008)	extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|Ragulator complex (GO:0071986)				breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7						ACTCTGGTTACGGGGACACTG	0.582													C|||	359	0.0716853	0.0333	0.1297	5008	,	,		16935	0.001		0.1581	False		,,,				2504	0.0665				p.Y37Y		Atlas-SNP	.											.	LAMTOR2	13	.	0			c.C111T						PASS	.	C	,	252,4154	146.1+/-180.8	6,240,1957	99.0	104.0	102.0		111,111	-4.7	0.9	1	dbSNP_52	102	1400,7200	270.9+/-289.3	128,1144,3028	no	coding-synonymous,coding-synonymous	LAMTOR2	NM_001145264.1,NM_014017.3	,	134,1384,4985	TT,TC,CC		16.2791,5.7195,12.7018	,	37/96,37/126	156025096	1652,11354	2203	4300	6503	SO:0001819	synonymous_variant	28956	exon2			TGGTTACGGGGAC	BC024190	CCDS1128.1, CCDS44243.1	1q22	2014-09-17	2011-02-15	2011-02-15	ENSG00000116586	ENSG00000116586			29796	protein-coding gene	gene with protein product	"""mitogen activated protein binding protein interacting protein"", ""MAPKSP1 adaptor protein"", ""endosomal adaptor protein"""	610389	"""roadblock domain containing 3"""	ROBLD3		11042152	Standard	NM_014017		Approved	MAPBPIP, MAPKSP1AP, p14, ENDAP, Ragulator2	uc001fnb.3	Q9Y2Q5	OTTHUMG00000017462	ENST00000368305.4:c.111C>T	1.37:g.156025096C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_001145264	Q5VY97|Q5VY98|Q5VY99	Silent	SNP	ENST00000368305.4	37	CCDS1128.1																																																																																			C|0.895;T|0.105	0.105	strong		0.582	LAMTOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046197.1	NM_014017	
RPH3AL	9501	hgsc.bcm.edu	37	17	63683	63683	+	Missense_Mutation	SNP	G	G	A	rs117190076	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:63683G>A	ENST00000331302.7	-	10	1215	c.908C>T	c.(907-909)gCt>gTt	p.A303V	RPH3AL_ENST00000323434.8_Missense_Mutation_p.A274V|RPH3AL_ENST00000536489.2_Missense_Mutation_p.A274V|RPH3AL_ENST00000576001.1_5'Flank	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	303					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of protein secretion (GO:0050714)|regulation of calcium ion-dependent exocytosis (GO:0017158)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|secretory granule membrane (GO:0030667)	cytoskeletal protein binding (GO:0008092)|metal ion binding (GO:0046872)			NS(2)|breast(1)|kidney(1)|large_intestine(1)|skin(1)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		AGCTGCGTCAGCAGCGGGGGC	0.637													G|||	151	0.0301518	0.0076	0.0317	5008	,	,		15515	0.0		0.0596	False		,,,				2504	0.0603				p.A303V		Atlas-SNP	.											.	RPH3AL	18	.	0			c.C908T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	68,4338	59.3+/-96.0	1,66,2136	22.0	26.0	25.0		908,821,821,908	1.0	0.3	17	dbSNP_132	25	563,8037	149.8+/-204.8	17,529,3754	yes	missense,missense,missense,missense	RPH3AL	NM_001190411.1,NM_001190412.1,NM_001190413.1,NM_006987.3	64,64,64,64	18,595,5890	AA,AG,GG		6.5465,1.5433,4.8516	benign,benign,benign,benign	303/316,274/287,274/287,303/316	63683	631,12375	2203	4300	6503	SO:0001583	missense	9501	exon10			GCGTCAGCAGCGG		CCDS10994.1, CCDS54059.1	17p13.3	2014-07-02			ENSG00000181031	ENSG00000181031		"""Synaptotagmins"""	10296	protein-coding gene	gene with protein product		604881				10395805	Standard	NM_006987		Approved	Noc2	uc021tmx.1	Q9UNE2	OTTHUMG00000090273	ENST00000331302.7:c.908C>T	17.37:g.63683G>A	ENSP00000328977:p.Ala303Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_006987	D3DTG7|Q9BSB3	Missense_Mutation	SNP	ENST00000331302.7	37	CCDS10994.1	70	0.03205128205128205	6	0.012195121951219513	14	0.03867403314917127	0	0.0	50	0.06596306068601583	G	16.52	3.147380	0.57151	0.015433	0.065465	ENSG00000181031	ENST00000323434;ENST00000331302;ENST00000536489	.	.	.	4.08	0.976	0.19727	.	0.829708	0.10311	N	0.689920	T	0.01222	0.0040	N	0.19112	0.55	0.19945	N	0.999941	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.22034	-1.0228	9	0.15499	T	0.54	.	2.557	0.04763	0.3105:0.0:0.4724:0.2171	.	274;303	Q9UNE2-2;Q9UNE2	.;RPH3L_HUMAN	V	303;274;274	.	ENSP00000319210:A303V	A	-	2	0	RPH3AL	63683	1.000000	0.71417	0.252000	0.24328	0.005000	0.04900	1.759000	0.38420	0.486000	0.27676	0.555000	0.69702	GCT	G|0.957;A|0.043	0.043	strong		0.637	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987	
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 GAIIx	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	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	140	64	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	
PTCRA	171558	hgsc.bcm.edu	37	6	42891022	42891022	+	Missense_Mutation	SNP	G	G	A	rs9471966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42891022G>A	ENST00000304672.1	+	2	397	c.316G>A	c.(316-318)Gtc>Atc	p.V106I	PTCRA_ENST00000446507.1_Intron|PTCRA_ENST00000441198.1_Missense_Mutation_p.V81I	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	106			V -> I (in dbSNP:rs9471966). {ECO:0000269|PubMed:15489334}.		negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			GGAGCCTTTGGTCTGCCACAC	0.632													G|||	1204	0.240415	0.3994	0.2133	5008	,	,		21832	0.0238		0.2893	False		,,,				2504	0.2178				p.V106I		Atlas-SNP	.											.	PTCRA	24	.	0			c.G316A						PASS	.	G	ILE/VAL	1522,2884	483.3+/-359.7	264,994,945	82.0	68.0	73.0		316	4.8	1.0	6	dbSNP_119	73	2278,6322	383.5+/-340.8	285,1708,2307	yes	missense	PTCRA	NM_138296.2	29	549,2702,3252	AA,AG,GG		26.4884,34.5438,29.2173	benign	106/282	42891022	3800,9206	2203	4300	6503	SO:0001583	missense	171558	exon2			CCTTTGGTCTGCC	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.316G>A	6.37:g.42891022G>A	ENSP00000304447:p.Val106Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	149	70	0.469799	NM_138296	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	511	0.23397435897435898	201	0.40853658536585363	83	0.2292817679558011	15	0.026223776223776224	212	0.2796833773087071	G	23.0	4.362653	0.82353	0.345438	0.264884	ENSG00000171611	ENST00000304672;ENST00000441198	T;T	0.54279	0.58;0.58	5.69	4.82	0.62117	Immunoglobulin-like fold (1);	0.000000	0.42682	D	0.000670	T	0.46698	0.1406	L	0.36672	1.1	0.09310	P	0.9999999999999986	D;D	0.65815	0.995;0.98	P;P	0.61800	0.894;0.691	T	0.51919	-0.8644	9	0.52906	T	0.07	-35.6978	9.6018	0.39609	0.0925:0.0:0.9075:0.0	rs9471966;rs52795622;rs58242015;rs9471966	81;106	Q6ISU1-3;Q6ISU1	.;PTCRA_HUMAN	I	106;81	ENSP00000304447:V106I;ENSP00000409550:V81I	ENSP00000304447:V106I	V	+	1	0	PTCRA	42999000	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	3.635000	0.54309	2.668000	0.90789	0.650000	0.86243	GTC	G|0.729;A|0.271	0.271	strong		0.632	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296	
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 GAIIx	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_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_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	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	25	9	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
GIPC1	10755	hgsc.bcm.edu	37	19	14589378	14589378	+	Splice_Site	SNP	C	C	T	rs1127307	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:14589378C>T	ENST00000393033.4	-	9	1121	c.852G>A	c.(850-852)gcG>gcA	p.A284A	GIPC1_ENST00000345425.2_Splice_Site_p.A284A|GIPC1_ENST00000586027.1_Splice_Site_p.A284A|GIPC1_ENST00000591349.1_Splice_Site_p.A187A|GIPC1_ENST00000393028.1_Splice_Site_p.A187A|GIPC1_ENST00000393029.3_Splice_Site_p.A187A	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	284					endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						CCATGGTGGCCGCTATTGGGG	0.637													C|||	1243	0.248203	0.27	0.2651	5008	,	,		16097	0.3036		0.2217	False		,,,				2504	0.1769				p.A284A	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											.	GIPC1	21	.	0			c.G852A						PASS	.		,,,,,	1186,3220	409.7+/-335.1	158,870,1175	45.0	49.0	47.0		852,561,852,561,852,561	-0.7	1.0	19	dbSNP_86	47	1786,6814	316.8+/-312.9	196,1394,2710	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	GIPC1	NM_005716.2,NM_202467.1,NM_202468.1,NM_202469.1,NM_202470.1,NM_202494.1	,,,,,	354,2264,3885	TT,TC,CC		20.7674,26.9178,22.851	,,,,,	284/334,187/237,284/334,187/237,284/334,187/237	14589378	2972,10034	2203	4300	6503	SO:0001630	splice_region_variant	10755	exon8			GGTGGCCGCTATT	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"""chromosome 19 open reading frame 3"", ""regulator of G-protein signalling 19 interacting protein 1"""	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.851-1G>A	19.37:g.14589378C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Silent	SNP	ENST00000393033.4	37	CCDS12310.1																																																																																			T|0.235;G|0.000;C|0.765	0.235	strong		0.637	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		Silent
CD226	10666	hgsc.bcm.edu	37	18	67531642	67531642	+	Missense_Mutation	SNP	T	T	C	rs763361	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:67531642T>C	ENST00000280200.4	-	7	1187	c.919A>G	c.(919-921)Agt>Ggt	p.S307G	CD226_ENST00000581982.1_Missense_Mutation_p.S152G|CD226_ENST00000582621.1_Missense_Mutation_p.S307G|CD226_ENST00000577287.1_Missense_Mutation_p.S152G	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	307			S -> G (in dbSNP:rs763361). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19690332, ECO:0000269|PubMed:8673704, ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				GTAGGTTGACTGGTAGAGATG	0.383													T|||	2351	0.469449	0.2632	0.5476	5008	,	,		19506	0.6121		0.5268	False		,,,				2504	0.4867				p.S307G	NSCLC(184;838 2130 8673 21498 50749)	Atlas-SNP	.											CD226,NS,adenoma,0,1	CD226	51	1	0			c.A919G						PASS	.	T	GLY/SER	1403,3003	460.2+/-352.5	222,959,1022	232.0	205.0	214.0	http://www.ncbi.nlm.nih.gov/pubmed?term	919	0.2	0.0	18	dbSNP_86	214	4477,4123	591.1+/-392.8	1185,2107,1008	yes	missense	CD226	NM_006566.2	56	1407,3066,2030	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	47.9419,31.8429,45.2099	benign	307/337	67531642	5880,7126	2203	4300	6503	SO:0001583	missense	10666	exon7			GTTGACTGGTAGA	U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	16961	protein-coding gene	gene with protein product		605397	"""CD226 antigen"""			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.919A>G	18.37:g.67531642T>C	ENSP00000280200:p.Ser307Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_006566	B2R818	Missense_Mutation	SNP	ENST00000280200.4	37	CCDS11997.1	1075	0.49221611721611724	126	0.25609756097560976	200	0.5524861878453039	361	0.6311188811188811	388	0.5118733509234829	T	0.051	-1.250683	0.01469	0.318429	0.520581	ENSG00000150637	ENST00000280200	T	0.23552	1.9	0.225	0.225	0.15325	.	1.124220	0.06665	N	0.765093	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.43228	-0.9404	8	0.54805	T	0.06	.	.	.	.	rs763361;rs1790587;rs17800796;rs52822910;rs57176311;rs763361	307	Q15762	CD226_HUMAN	G	307	ENSP00000280200:S307G	ENSP00000280200:S307G	S	-	1	0	CD226	65682622	0.000000	0.05858	0.004000	0.12327	0.010000	0.07245	-0.188000	0.09642	0.257000	0.21650	0.254000	0.18369	AGT	C|0.456;N|0.000	0.456	strong		0.383	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566	
DHX34	9704	hgsc.bcm.edu	37	19	47883126	47883126	+	Missense_Mutation	SNP	C	C	T	rs151213663	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47883126C>T	ENST00000328771.4	+	14	3215	c.2866C>T	c.(2866-2868)Cgg>Tgg	p.R956W		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	956					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)		TGCCCTGGACCGGCAGCTGGC	0.667													C|||	12	0.00239617	0.0008	0.0043	5008	,	,		17242	0.0		0.005	False		,,,				2504	0.0031				p.R956W		Atlas-SNP	.											.	DHX34	98	.	0			c.C2866T						PASS	.	C	TRP/ARG	8,4398		0,8,2195	32.0	34.0	34.0		2866	2.4	1.0	19	dbSNP_134	34	32,8566		0,32,4267	no	missense	DHX34	NM_014681.5	101	0,40,6462	TT,TC,CC		0.3722,0.1816,0.3076	probably-damaging	956/1144	47883126	40,12964	2203	4299	6502	SO:0001583	missense	9704	exon14			CTGGACCGGCAGC	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.2866C>T	19.37:g.47883126C>T	ENSP00000331907:p.Arg956Trp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_014681	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	24	0.01098901098901099	1	0.0020325203252032522	9	0.024861878453038673	4	0.006993006993006993	10	0.013192612137203167	C	10.88	1.474686	0.26511	0.001816	0.003722	ENSG00000134815	ENST00000328771	T	0.02890	4.12	4.54	2.39	0.29439	.	0.602245	0.14742	N	0.301092	T	0.00998	0.0033	L	0.29908	0.895	0.35294	D	0.782401	D	0.54047	0.964	B	0.36766	0.232	T	0.57997	-0.7714	10	0.66056	D	0.02	-9.1206	6.2329	0.20744	0.1862:0.7151:0.0:0.0988	.	956	Q14147	DHX34_HUMAN	W	956	ENSP00000331907:R956W	ENSP00000331907:R956W	R	+	1	2	DHX34	52574957	1.000000	0.71417	0.999000	0.59377	0.034000	0.12701	1.258000	0.32944	0.895000	0.36342	-0.268000	0.10319	CGG	C|0.994;T|0.006	0.006	strong		0.667	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
TMEM2	23670	hgsc.bcm.edu	37	9	74360234	74360234	+	Missense_Mutation	SNP	C	C	T	rs25688	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:74360234C>T	ENST00000377044.4	-	4	1273	c.734G>A	c.(733-735)aGg>aAg	p.R245K	TMEM2_ENST00000377066.5_Missense_Mutation_p.R245K	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	245	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.		R -> K (in dbSNP:rs25688).		multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		ATTCAGGGTCCTTGCCAACAA	0.512													C|||	403	0.0804712	0.0424	0.0461	5008	,	,		18087	0.0208		0.0755	False		,,,				2504	0.2229				p.R245K		Atlas-SNP	.											.	TMEM2	112	.	0			c.G734A						PASS	.	C	LYS/ARG,LYS/ARG	184,4222	118.4+/-156.1	9,166,2028	95.0	85.0	89.0		734,734	1.7	0.8	9	dbSNP_72	89	669,7931	168.0+/-219.6	25,619,3656	yes	missense,missense	TMEM2	NM_001135820.1,NM_013390.2	26,26	34,785,5684	TT,TC,CC		7.7791,4.1761,6.5585	benign,benign	245/1321,245/1384	74360234	853,12153	2203	4300	6503	SO:0001583	missense	23670	exon4			AGGGTCCTTGCCA		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.734G>A	9.37:g.74360234C>T	ENSP00000366243:p.Arg245Lys	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	121	0.0554029304029304	29	0.05894308943089431	21	0.058011049723756904	14	0.024475524475524476	57	0.07519788918205805	C	0.108	-1.142768	0.01728	0.041761	0.077791	ENSG00000135048	ENST00000377044;ENST00000377066	D;D	0.89343	-2.5;-2.5	6.03	1.74	0.24563	G8 domain (2);	0.323928	0.38111	N	0.001809	T	0.09512	0.0234	N	0.02192	-0.645	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45542	-0.9254	10	0.02654	T	1	.	6.6351	0.22879	0.0:0.4262:0.0:0.5738	rs25688;rs52809947;rs57404035;rs25688	245;245	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	K	245	ENSP00000366243:R245K;ENSP00000366266:R245K	ENSP00000366243:R245K	R	-	2	0	TMEM2	73550054	1.000000	0.71417	0.829000	0.32907	0.069000	0.16628	1.754000	0.38369	0.458000	0.26988	-0.751000	0.03497	AGG	C|0.937;T|0.063	0.063	strong		0.512	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
LRRC8B	23507	hgsc.bcm.edu	37	1	90049040	90049040	+	Silent	SNP	A	A	G	rs36084789	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:90049040A>G	ENST00000330947.2	+	5	1191	c.831A>G	c.(829-831)ccA>ccG	p.P277P	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.P277P|LRRC8B_ENST00000439853.1_Silent_p.P277P	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	277					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		CTTATGTTCCATATTTTTTAA	0.378													A|||	809	0.161542	0.034	0.1225	5008	,	,		22995	0.1677		0.2117	False		,,,				2504	0.3037				p.P277P		Atlas-SNP	.											.	LRRC8B	49	.	0			c.A831G						PASS	.	A	,	341,4065	180.5+/-208.7	12,317,1874	120.0	116.0	117.0		831,831	-10.6	0.3	1	dbSNP_126	117	2230,6370	377.5+/-338.5	281,1668,2351	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	293,1985,4225	GG,GA,AA		25.9302,7.7394,19.7678	,	277/804,277/804	90049040	2571,10435	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			TGTTCCATATTTT	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"""T cell activation leucine repeat rich protein"""	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.831A>G	1.37:g.90049040A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	113	63	0.557522	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			A|0.813;G|0.187	0.187	strong		0.378	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
KIAA0556	23247	hgsc.bcm.edu	37	16	27772880	27772880	+	Missense_Mutation	SNP	G	G	A	rs61742593	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:27772880G>A	ENST00000261588.4	+	19	3797	c.3778G>A	c.(3778-3780)Gag>Aag	p.E1260K		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	1260						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TGAGCTCCCCGAGTACTCTGA	0.577													G|||	69	0.013778	0.0008	0.0245	5008	,	,		18106	0.001		0.0477	False		,,,				2504	0.002				p.E1260K		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G3778A						PASS	.	G	LYS/GLU	37,4357	41.6+/-74.8	0,37,2160	52.0	54.0	53.0		3778	4.6	1.0	16	dbSNP_129	53	301,8299	110.0+/-170.5	6,289,4005	yes	missense	KIAA0556	NM_015202.2	56	6,326,6165	AA,AG,GG		3.5,0.8421,2.6012	benign	1260/1619	27772880	338,12656	2197	4300	6497	SO:0001583	missense	23247	exon19			CTCCCCGAGTACT	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.3778G>A	16.37:g.27772880G>A	ENSP00000261588:p.Glu1260Lys	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	33	12	0.363636	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	45	0.020604395604395604	1	0.0020325203252032522	9	0.024861878453038673	1	0.0017482517482517483	34	0.044854881266490766	G	29.1	4.979953	0.92982	0.008421	0.035	ENSG00000047578	ENST00000261588	T	0.14022	2.54	4.56	4.56	0.56223	.	0.159395	0.53938	D	0.000046	T	0.12390	0.0301	M	0.83012	2.62	0.58432	D	0.999993	D	0.76494	0.999	D	0.65874	0.939	T	0.08638	-1.0712	10	0.49607	T	0.09	.	16.9555	0.86258	0.0:0.0:1.0:0.0	rs61742593	1260	O60303	K0556_HUMAN	K	1260	ENSP00000261588:E1260K	ENSP00000261588:E1260K	E	+	1	0	KIAA0556	27680381	1.000000	0.71417	0.958000	0.39756	0.929000	0.56500	9.692000	0.98682	2.086000	0.62901	0.561000	0.74099	GAG	G|0.975;A|0.025	0.025	strong		0.577	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
PISD	23761	hgsc.bcm.edu	37	22	32015766	32015766	+	Silent	SNP	G	G	A	rs41282571	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:32015766G>A	ENST00000439502.2	-	8	1285	c.1062C>T	c.(1060-1062)ttC>ttT	p.F354F	PISD_ENST00000397500.1_3'UTR|PISD_ENST00000266095.5_Silent_p.F320F|PISD_ENST00000478893.1_5'Flank|PISD_ENST00000336566.4_Silent_p.F353F|PISD_ENST00000382151.2_Silent_p.F320F			Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	354					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylserine decarboxylase activity (GO:0004609)			central_nervous_system(3)|endometrium(2)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	12					Phosphatidylserine(DB00144)	TGTGCGTCACGAAGCTGAAGT	0.612													G|||	181	0.0361422	0.0234	0.0187	5008	,	,		20115	0.0069		0.0368	False		,,,				2504	0.0951				p.F320F		Atlas-SNP	.											.	PISD	53	.	0			c.C960T						PASS	.	G		90,4316	76.2+/-114.5	0,90,2113	163.0	125.0	138.0		960	-1.6	1.0	22	dbSNP_127	138	245,8355	97.2+/-158.9	3,239,4058	no	coding-synonymous	PISD	NM_014338.3		3,329,6171	AA,AG,GG		2.8488,2.0427,2.5757		320/376	32015766	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	23761	exon9			CGTCACGAAGCTG		CCDS13899.1	22q12.2	2011-01-25			ENSG00000241878	ENSG00000241878	4.1.1.65		8999	protein-coding gene	gene with protein product		612770				10591208	Standard	NM_014338		Approved	dJ858B16.2, PSDC	uc003alk.2	Q9UG56	OTTHUMG00000030252	ENST00000439502.2:c.1062C>T	22.37:g.32015766G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	187	97	0.518717	NM_014338	B1AKM7|O43207|O95535|Q6IC28|Q96GQ2|Q9UGA9	Silent	SNP	ENST00000439502.2	37		58	0.026556776556776556	15	0.03048780487804878	10	0.027624309392265192	3	0.005244755244755245	30	0.0395778364116095	G	4.359	0.066221	0.08388	0.020427	0.028488	ENSG00000241878	ENST00000435900	.	.	.	4.88	-1.64	0.08318	.	.	.	.	.	T	0.22704	0.0548	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29274	-1.0017	4	.	.	.	-24.3787	9.3904	0.38370	0.5267:0.0:0.4733:0.0	rs41282571;rs61747366	.	.	.	L	307	.	.	S	-	2	0	PISD	30345766	1.000000	0.71417	0.970000	0.41538	0.458000	0.32498	0.891000	0.28309	-0.578000	0.05959	-0.216000	0.12614	TCG	A|0.028;C|0.000;G|0.972	0.028	strong		0.612	PISD-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000075106.4		
GJB3	2707	hgsc.bcm.edu	37	1	35250840	35250840	+	Silent	SNP	G	G	A	rs61732640	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:35250840G>A	ENST00000373366.2	+	2	1092	c.477G>A	c.(475-477)ccG>ccA	p.P159P	RP1-34M23.5_ENST00000542839.1_RNA|GJB3_ENST00000373362.3_Silent_p.P159P	NM_024009.2	NP_076872.1	O75712	CXB3_HUMAN	gap junction protein, beta 3, 31kDa	159					cell communication (GO:0007154)|in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|sensory perception of sound (GO:0007605)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	connexon complex (GO:0005922)|cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|prostate(3)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TCAATATGCCGCGCCTGGTGC	0.552													g|||	179	0.0357428	0.1248	0.0173	5008	,	,		20586	0.0		0.001	False		,,,				2504	0.001				p.P159P		Atlas-SNP	.											GJB3,NS,carcinoma,+1,1	GJB3	40	1	0			c.G477A						scavenged	.		,	380,4026	193.0+/-218.2	20,340,1843	157.0	167.0	163.0		477,477	-10.1	0.5	1	dbSNP_129	163	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	GJB3	NM_001005752.1,NM_024009.2	,	20,352,6131	AA,AG,GG		0.1395,8.6246,3.014	,	159/271,159/271	35250840	392,12614	2203	4300	6503	SO:0001819	synonymous_variant	2707	exon2			TATGCCGCGCCTG	BC012918	CCDS384.1	1p34	2008-05-14	2007-01-16		ENSG00000188910	ENSG00000188910		"""Ion channels / Gap junction proteins (connexins)"""	4285	protein-coding gene	gene with protein product	"""connexin 31"""	603324	"""gap junction protein, beta 3, 31kD (connexin 31)"", ""gap junction protein, beta 3, 31kDa (connexin 31)"", ""erythrokeratodermia variabilis"""	DFNA2, EKV		9843210, 9704026	Standard	NM_024009		Approved	CX31	uc001bxy.3	O75712	OTTHUMG00000004051	ENST00000373366.2:c.477G>A	1.37:g.35250840G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	223	3	0.0134529	NM_001005752	B2R790|Q2TAZ8	Silent	SNP	ENST00000373366.2	37	CCDS384.1																																																																																			G|0.969;A|0.031	0.031	strong		0.552	GJB3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011559.1	NM_024009	
CACNA1F	778	hgsc.bcm.edu	37	X	49081291	49081291	+	Silent	SNP	G	G	A	rs2235127	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49081291G>A	ENST00000376265.2	-	14	1903	c.1842C>T	c.(1840-1842)ggC>ggT	p.G614G	CACNA1F_ENST00000323022.5_Silent_p.G603G|CACNA1F_ENST00000376251.1_Silent_p.G549G|CACNA1F_ENST00000480889.1_5'Flank	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	614					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)	GCTGCATGGCGCCCACCTCCA	0.582													g|||	1663	0.44053	0.3585	0.366	3775	,	,		13422	0.5188		0.2028	False		,,,				2504	0.2127				p.G614G		Atlas-SNP	.											.	CACNA1F	218	.	0			c.C1842T						PASS	.			1651,2184		306,806,233,520,338	74.0	47.0	56.0		1842	-6.8	0.9	X	dbSNP_98	56	1874,4853		193,968,520,1267,1351	no	coding-synonymous	CACNA1F	NM_005183.2		499,1774,753,1787,1689	AA,AG,A,GG,G		27.8579,43.0508,33.3744		614/1978	49081291	3525,7037	2203	4299	6502	SO:0001819	synonymous_variant	778	exon14			CATGGCGCCCACC	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.1842C>T	X.37:g.49081291G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	110	32	0.290909	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	37	CCDS35253.1																																																																																			G|0.623;A|0.377	0.377	strong		0.582	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
TTLL10	254173	hgsc.bcm.edu	37	1	1120431	1120431	+	Missense_Mutation	SNP	G	G	A	rs1320571	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1120431G>A	ENST00000379290.1	+	13	1516	c.1343G>A	c.(1342-1344)aGt>aAt	p.S448N	TTLL10_ENST00000379289.1_Missense_Mutation_p.S448N|TTLL10_ENST00000379288.3_Missense_Mutation_p.S375N			Q6ZVT0	TTL10_HUMAN	tubulin tyrosine ligase-like family, member 10	448	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.		S -> N (in dbSNP:rs1320571).		cellular protein modification process (GO:0006464)					haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(2)|skin(1)	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;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|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;0.199)		CGCTACATCAGTGACACGTTC	0.607													A|||	928	0.185304	0.3608	0.0562	5008	,	,		19922	0.1478		0.0517	False		,,,				2504	0.2157				p.S448N		Atlas-SNP	.											TTLL10_ENST00000379290,NS,haematopoietic_neoplasm,0,6	TTLL10	66	6	0			c.G1343A						scavenged	.	A	ASN/SER,ASN/SER	1416,2990	681.9+/-404.1	235,946,1022	97.0	75.0	83.0		1343,1124	4.5	0.7	1	dbSNP_88	83	452,8148	797.6+/-407.4	16,420,3864	yes	missense,missense	TTLL10	NM_001130045.1,NM_153254.2	46,46	251,1366,4886	AA,AG,GG		5.2558,32.138,14.3626	benign,benign	448/674,375/405	1120431	1868,11138	2203	4300	6503	SO:0001583	missense	254173	exon13			ACATCAGTGACAC	AK093438	CCDS8.1, CCDS44036.1	1p36.33	2014-01-28	2005-07-29	2005-07-29	ENSG00000162571	ENSG00000162571		"""Tubulin tyrosine ligase-like family"""	26693	protein-coding gene	gene with protein product			"""tubulin tyrosine ligase-like family, member 5"""	TTLL5		15890843	Standard	NM_153254		Approved	FLJ36119	uc001acy.2	Q6ZVT0	OTTHUMG00000000851	ENST00000379290.1:c.1343G>A	1.37:g.1120431G>A	ENSP00000368592:p.Ser448Asn	Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	163	87	0.533742	NM_001130045	B1AMF6|Q5T2W4|Q5T2W5|Q8N9X2	Missense_Mutation	SNP	ENST00000379290.1	37	CCDS44036.1	347	0.15888278388278387	199	0.40447154471544716	23	0.06353591160220995	89	0.1555944055944056	36	0.047493403693931395	A	8.390	0.839575	0.16891	0.32138	0.052558	ENSG00000162571	ENST00000379290;ENST00000379289;ENST00000379288	T;T;T	0.05580	3.42;3.42;3.42	4.54	4.54	0.55810	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00972	-1.085	0.41513	P	0.011647999999999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42032	-0.9475	9	0.07644	T	0.81	.	8.3694	0.32406	0.9052:0.0:0.0948:0.0	rs1320571;rs1320571	375;448	Q6ZVT0-3;Q6ZVT0	.;TTL10_HUMAN	N	448;448;375	ENSP00000368592:S448N;ENSP00000368591:S448N;ENSP00000368590:S375N	ENSP00000368590:S375N	S	+	2	0	TTLL10	1110294	1.000000	0.71417	0.746000	0.31095	0.003000	0.03518	6.435000	0.73412	0.789000	0.33779	-0.360000	0.07572	AGT	G|0.839;A|0.161	0.161	strong		0.607	TTLL10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002421.3	NM_153254	
POTEC	388468	hgsc.bcm.edu	37	18	14542931	14542931	+	Missense_Mutation	SNP	C	C	T	rs45554841	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:14542931C>T	ENST00000358970.5	-	1	214	c.215G>A	c.(214-216)tGc>tAc	p.C72Y	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	72			C -> Y (in dbSNP:rs45554841).					p.C72Y(1)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GCTCCCCCTGCAGCAGGGGAA	0.567																																					p.C72Y		Atlas-SNP	.											POTEC,NS,carcinoma,0,1	POTEC	129	1	1	Substitution - Missense(1)	kidney(1)	c.G215A						PASS	.						46.0	57.0	53.0					18																	14542931		692	1591	2283	SO:0001583	missense	388468	exon1			CCCCTGCAGCAGG	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.215G>A	18.37:g.14542931C>T	ENSP00000351856:p.Cys72Tyr	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	234	43	0.183761	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	314	0.14377289377289376	36	0.07317073170731707	62	0.1712707182320442	149	0.26048951048951047	67	0.08839050131926121	C	10.16	1.272916	0.23221	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.39592	1.07	0.429	0.429	0.16506	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	D	0.63046	0.992	D	0.74023	0.982	T	0.14172	-1.0482	7	0.87932	D	0	.	.	.	.	rs45554841;rs60359173	72	B2RU33	POTEC_HUMAN	Y	72	ENSP00000351856:C72Y	ENSP00000351856:C72Y	C	-	2	0	POTEC	14532931	0.007000	0.16637	0.005000	0.12908	0.090000	0.18270	-0.364000	0.07583	0.472000	0.27344	0.175000	0.17021	TGC	C|0.857;T|0.143	0.143	strong		0.567	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
TLR10	81793	hgsc.bcm.edu	37	4	38774889	38774889	+	Missense_Mutation	SNP	T	T	C	rs4129009	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38774889T>C	ENST00000308973.4	-	4	2928	c.2323A>G	c.(2323-2325)Att>Gtt	p.I775V	TLR10_ENST00000508334.1_Missense_Mutation_p.I775V|TLR10_ENST00000506111.1_Missense_Mutation_p.I775V|TLR10_ENST00000361424.2_Missense_Mutation_p.I775V|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	775	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.		I -> F (in dbSNP:rs4129009).|I -> L (in dbSNP:rs4129009).|I -> V (in dbSNP:rs4129009). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						TTAACATTAATAGCAGCTCGA	0.408													T|||	734	0.146565	0.0106	0.1398	5008	,	,		18119	0.2688		0.2068	False		,,,				2504	0.1472				p.I775V		Atlas-SNP	.											.	TLR10	87	.	0			c.A2323G	GRCh37	CM057767	TLR10	M	rs4129009	PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	129,4277	93.0+/-131.7	4,121,2078	84.0	83.0	84.0		2323,2323,2323,2281,2323	-5.3	0.0	4	dbSNP_108	84	1492,7108	283.2+/-296.0	126,1240,2934	yes	missense,missense,missense,missense,missense	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	29,29,29,29,29	130,1361,5012	CC,CT,TT		17.3488,2.9278,12.4635	benign,benign,benign,benign,benign	775/812,775/812,775/812,761/798,775/812	38774889	1621,11385	2203	4300	6503	SO:0001583	missense	81793	exon2			CATTAATAGCAGC	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.2323A>G	4.37:g.38774889T>C	ENSP00000308925:p.Ile775Val	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	178	76	0.426966	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	412	0.18864468864468864	8	0.016260162601626018	51	0.1408839779005525	215	0.3758741258741259	138	0.1820580474934037	T	3.040	-0.197715	0.06219	0.029278	0.173488	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.25085	1.82;1.82;1.82;1.82	5.38	-5.34	0.02705	Toll/interleukin-1 receptor homology (TIR) domain (3);	0.420019	0.19121	N	0.122185	T	0.00012	0.0000	L	0.35854	1.095	0.43364	P	0.0045600000000000085	B	0.02656	0.0	B	0.01281	0.0	T	0.44467	-0.9326	9	0.34782	T	0.22	.	7.1692	0.25708	0.0:0.3023:0.2997:0.398	rs4129009;rs52824627;rs4129009	775	Q9BXR5	TLR10_HUMAN	V	775	ENSP00000308925:I775V;ENSP00000421483:I775V;ENSP00000354459:I775V;ENSP00000424923:I775V	ENSP00000308925:I775V	I	-	1	0	TLR10	38451284	0.006000	0.16342	0.010000	0.14722	0.011000	0.07611	0.012000	0.13287	-0.961000	0.03609	-1.221000	0.01599	ATT	T|0.840;C|0.160	0.160	strong		0.408	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
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 GAIIx	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_ENST00000420078.1_Missense_Mutation_p.L334V|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000439316.2_Missense_Mutation_p.L291V|CLCNKA_ENST00000375692.1_Missense_Mutation_p.L334V			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	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	60	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		
MUC4	4585	hgsc.bcm.edu	37	3	195511686	195511686	+	Silent	SNP	G	G	T	rs71291862|rs201950480		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195511686G>T	ENST00000463781.3	-	2	7224	c.6765C>A	c.(6763-6765)acC>acA	p.T2255T	MUC4_ENST00000475231.1_Silent_p.T2255T|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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)		CAGGAAGAGGGGTGGTGTCAC	0.582																																					p.T2255T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.C6765A						scavenged	.						30.0	28.0	29.0					3																	195511686		686	1584	2270	SO:0001819	synonymous_variant	4585	exon2			AAGAGGGGTGGTG	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.6765C>A	3.37:g.195511686G>T		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	190	31	0.163158	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|0.998;T|0.002	0.002	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GLT1D1	144423	hgsc.bcm.edu	37	12	129360498	129360498	+	Silent	SNP	G	G	A	rs482401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:129360498G>A	ENST00000442111.2	+	2	196	c.108G>A	c.(106-108)aaG>aaA	p.K36K	GLT1D1_ENST00000537468.1_Silent_p.K25K|GLT1D1_ENST00000281703.6_Silent_p.K36K|GLT1D1_ENST00000542193.1_5'UTR			Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	36					biosynthetic process (GO:0009058)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		GCGTTTTGAAGGATGCCTTTG	0.478													A|||	1704	0.340256	0.4803	0.304	5008	,	,		16962	0.2361		0.2256	False		,,,				2504	0.4018				p.K36K		Atlas-SNP	.											.	GLT1D1	48	.	0			c.G108A						PASS	.	A		1921,2485	625.8+/-394.6	405,1111,687	158.0	159.0	159.0		108	4.4	1.0	12	dbSNP_83	159	1699,6901	738.4+/-407.1	185,1329,2786	no	coding-synonymous	GLT1D1	NM_144669.1		590,2440,3473	AA,AG,GG		19.7558,43.5996,27.8333		36/267	129360498	3620,9386	2203	4300	6503	SO:0001819	synonymous_variant	144423	exon2			TTTGAAGGATGCC		CCDS9265.1	12q24.32	2013-02-22			ENSG00000151948	ENSG00000151948		"""Glycosyltransferase group 1 domain containing"""	26483	protein-coding gene	gene with protein product							Standard	NM_144669		Approved	FLJ31978	uc001uhx.1	Q96MS3	OTTHUMG00000168437	ENST00000442111.2:c.108G>A	12.37:g.129360498G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_144669	Q86XG8	Silent	SNP	ENST00000442111.2	37																																																																																				G|0.706;A|0.294	0.294	strong		0.478	GLT1D1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000399740.1	NM_144669	
HTR1D	3352	hgsc.bcm.edu	37	1	23519633	23519633	+	Silent	SNP	A	A	G	rs6300	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:23519633A>G	ENST00000374619.1	-	1	1589	c.1080T>C	c.(1078-1080)aaT>aaC	p.N360N	HTR1D_ENST00000314113.3_Silent_p.N360N	NM_000864.4	NP_000855.1	P28221	5HT1D_HUMAN	5-hydroxytryptamine (serotonin) receptor 1D, G protein-coupled	360					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intestine smooth muscle contraction (GO:0014827)|regulation of behavior (GO:0050795)|regulation of locomotion (GO:0040012)|response to toxic substance (GO:0009636)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|large_intestine(3)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000779)|all_lung(284;0.00135)|Breast(348;0.0385)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0561)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;4.69e-27)|Colorectal(126;4.86e-08)|COAD - Colon adenocarcinoma(152;2.86e-06)|GBM - Glioblastoma multiforme(114;0.00012)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(1967;0.00122)|STAD - Stomach adenocarcinoma(196;0.0123)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.083)|LUSC - Lung squamous cell carcinoma(448;0.185)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Naratriptan(DB00952)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GAAACTCTTCATTAAACACAG	0.463													A|||	1033	0.20627	0.1581	0.2709	5008	,	,		14943	0.1845		0.0934	False		,,,				2504	0.364				p.N360N		Atlas-SNP	.											.	HTR1D	36	.	0			c.T1080C						PASS	.	A		786,3620	311.1+/-291.9	74,638,1491	62.0	67.0	65.0		1080	-6.8	0.8	1	dbSNP_52	65	903,7697	199.0+/-243.2	45,813,3442	no	coding-synonymous	HTR1D	NM_000864.4		119,1451,4933	GG,GA,AA		10.5,17.8393,12.9863		360/378	23519633	1689,11317	2203	4300	6503	SO:0001819	synonymous_variant	3352	exon1			CTCTTCATTAAAC	M89955	CCDS231.1	1p36.3-p34.3	2012-08-08	2012-02-03		ENSG00000179546	ENSG00000179546		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5289	protein-coding gene	gene with protein product		182133	"""5-hydroxytryptamine (serotonin) receptor 1D"""	HTRL		2541503, 1662665	Standard	NM_000864		Approved	RDC4, HT1DA, 5-HT1D	uc001bgn.3	P28221	OTTHUMG00000003235	ENST00000374619.1:c.1080T>C	1.37:g.23519633A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_000864		Silent	SNP	ENST00000374619.1	37	CCDS231.1																																																																																			A|0.854;G|0.146	0.146	strong		0.463	HTR1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008924.1	NM_000864	
VASH2	79805	hgsc.bcm.edu	37	1	213147400	213147400	+	Missense_Mutation	SNP	G	G	A	rs35976699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:213147400G>A	ENST00000517399.1	+	6	983	c.983G>A	c.(982-984)cGg>cAg	p.R328Q	VASH2_ENST00000366965.2_Missense_Mutation_p.R284Q|VASH2_ENST00000366966.2_Missense_Mutation_p.R263Q|VASH2_ENST00000366967.2_Missense_Mutation_p.R224Q|VASH2_ENST00000271776.4_3'UTR|VASH2_ENST00000366968.4_Missense_Mutation_p.R263Q			Q86V25	VASH2_HUMAN	vasohibin 2	328					positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)	cytoplasm (GO:0005737)				endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(81;0.00479)|all cancers(67;0.00844)|GBM - Glioblastoma multiforme(131;0.0496)|Epithelial(68;0.0986)		AGGCTCGGCCGGCGAGAGAAG	0.577													G|||	116	0.0231629	0.0015	0.0303	5008	,	,		17751	0.002		0.0378	False		,,,				2504	0.0542				p.R284Q		Atlas-SNP	.											.	VASH2	55	.	0			c.G851A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	34,4372	38.4+/-70.7	0,34,2169	38.0	43.0	41.0		788,671,851	4.0	1.0	1	dbSNP_126	41	247,8353	97.0+/-158.7	6,235,4059	yes	missense,missense,missense	VASH2	NM_001136474.1,NM_001136475.1,NM_024749.3	43,43,43	6,269,6228	AA,AG,GG		2.8721,0.7717,2.1605	possibly-damaging,possibly-damaging,possibly-damaging	263/291,224/252,284/312	213147400	281,12725	2203	4300	6503	SO:0001583	missense	79805	exon5			TCGGCCGGCGAGA	AK022567	CCDS1511.1, CCDS44315.1, CCDS44316.1, CCDS73026.1	1q23	2008-02-05			ENSG00000143494	ENSG00000143494			25723	protein-coding gene	gene with protein product		610471				16528006	Standard	XR_247041		Approved	FLJ12505	uc001hjw.3	Q86V25	OTTHUMG00000036925	ENST00000517399.1:c.983G>A	1.37:g.213147400G>A	ENSP00000428324:p.Arg328Gln	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	48	28	0.583333	NM_024749	B4DYZ5|Q2VT46|Q5VTE7|Q5VTE9|Q7Z6E3|Q8IZ24|Q9H9W5	Missense_Mutation	SNP	ENST00000517399.1	37	CCDS1511.1	44	0.020146520146520148	1	0.0020325203252032522	17	0.04696132596685083	1	0.0017482517482517483	25	0.032981530343007916	G	17.05	3.290116	0.59976	0.007717	0.028721	ENSG00000143494	ENST00000366966;ENST00000366968;ENST00000366965;ENST00000366967;ENST00000517399	.	.	.	5.81	3.96	0.45880	.	0.203721	0.48767	N	0.000177	T	0.15349	0.0370	L	0.45137	1.4	0.80722	D	1	B;D	0.61080	0.028;0.989	B;P	0.51170	0.005;0.661	T	0.14896	-1.0456	9	0.54805	T	0.06	-11.8379	11.5695	0.50826	0.1391:0.0:0.8609:0.0	rs35976699	328;284	Q86V25;Q86V25-5	VASH2_HUMAN;.	Q	263;263;284;224;328	.	ENSP00000355932:R284Q	R	+	2	0	VASH2	211214023	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	3.020000	0.49643	0.932000	0.37266	-0.126000	0.14955	CGG	G|0.977;A|0.023	0.023	strong		0.577	VASH2-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381686.1	NM_024749	
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 GAIIx	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	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	56	23	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	
FAM66D	100132923	hgsc.bcm.edu	37	8	11989986	11989986	+	RNA	SNP	G	G	C	rs9694757	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11989986G>C	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		ATCTCCTGGTGCTCCCTTGCA	0.512													-|||	581	0.116014	0.3298	0.0634	5008	,	,		23213	0.0437		0.0318	False		,,,				2504	0.0256				p.S511R		Atlas-SNP	.											.	.	.	.	0			c.C1533G						PASS	.																																					392197	exon1			CCTGGTGCTCCCT			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11989986G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	32	0.266667	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				G|0.910;C|0.090	0.090	strong		0.512	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
CLPSL1	340204	hgsc.bcm.edu	37	6	35748931	35748931	+	Missense_Mutation	SNP	T	T	C	rs34109614	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:35748931T>C	ENST00000373861.5	+	1	138	c.44T>C	c.(43-45)tTc>tCc	p.F15S	CLPSL1_ENST00000542261.1_Missense_Mutation_p.F14S			A2RUU4	COLL1_HUMAN	colipase-like 1	15			F -> S (in dbSNP:rs34109614).		digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										CTTCTCTTCTTCTTTCTCTTC	0.532													c|||	1485	0.296526	0.3351	0.2522	5008	,	,		19574	0.2917		0.2992	False		,,,				2504	0.2781				p.F15S		Atlas-SNP	.											.	.	.	.	0			c.T44C						PASS	.	T	SER/PHE	1350,2706		224,902,902	161.0	176.0	171.0		44	-0.4	0.0	6	dbSNP_126	171	2676,5686		429,1818,1934	yes	missense	C6orf127	NM_001010886.3	155	653,2720,2836	CC,CT,TT		32.0019,33.284,32.4207	benign	15/122	35748931	4026,8392	2028	4181	6209	SO:0001583	missense	340204	exon1			TCTTCTTCTTTCT		CCDS43456.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000204140	ENSG00000204140			21251	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 127"""	C6orf127			Standard	NM_001010886		Approved	dJ510O8.6	uc003old.4	A2RUU4	OTTHUMG00000014582	ENST00000373861.5:c.44T>C	6.37:g.35748931T>C	ENSP00000362968:p.Phe15Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	131	99	0.755725	NM_001010886	A7E2T6|B2RPE2|B5G4V2|B6ZDM9|Q5T9G1	Missense_Mutation	SNP	ENST00000373861.5	37	CCDS43456.1	635	0.2907509157509158	173	0.3516260162601626	89	0.24585635359116023	147	0.256993006993007	226	0.29815303430079154	c	0.006	-2.049623	0.00394	0.33284	0.320019	ENSG00000204140	ENST00000373861;ENST00000373860;ENST00000542261	T;T	0.31769	1.48;1.49	1.62	-0.45	0.12223	.	1.624490	0.04724	N	0.419874	T	0.02767	0.0083	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30966	-0.9960	9	0.48119	T	0.1	.	2.9097	0.05733	0.0:0.5052:0.2934:0.2014	rs34109614;rs58544058	15	A2RUU4	CF127_HUMAN	S	15;15;14	ENSP00000362968:F15S;ENSP00000438478:F14S	ENSP00000362967:F15S	F	+	2	0	C6orf127	35856909	0.010000	0.17322	0.000000	0.03702	0.038000	0.13279	-0.240000	0.08952	-0.170000	0.10816	-0.741000	0.03529	TTC	C|0.301;G|0.000;T|0.698	0.301	strong		0.532	CLPSL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040317.2	NM_001010886	
KIF1B	23095	hgsc.bcm.edu	37	1	10397567	10397567	+	Missense_Mutation	SNP	A	A	G	rs2297881	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10397567A>G	ENST00000377086.1	+	31	3600	c.3398A>G	c.(3397-3399)tAt>tGt	p.Y1133C	KIF1B_ENST00000377081.1_Missense_Mutation_p.Y1133C|KIF1B_ENST00000263934.6_Missense_Mutation_p.Y1087C			O60333	KIF1B_HUMAN	kinesin family member 1B	1133			Y -> C (in dbSNP:rs2297881). {ECO:0000269|PubMed:18334619}.		anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CTCCCAGAGTATGCAGATATC	0.502													A|||	199	0.0397364	0.0537	0.0389	5008	,	,		22973	0.0585		0.0278	False		,,,				2504	0.0143				p.Y1087C		Atlas-SNP	.											.	KIF1B	242	.	0			c.A3260G						PASS	.	A	CYS/TYR	201,4205	124.1+/-161.4	4,193,2006	154.0	154.0	154.0		3260	5.8	1.0	1	dbSNP_100	154	218,8382	91.9+/-153.9	2,214,4084	yes	missense	KIF1B	NM_015074.3	194	6,407,6090	GG,GA,AA		2.5349,4.562,3.2216	probably-damaging	1087/1771	10397567	419,12587	2203	4300	6503	SO:0001583	missense	23095	exon29			CAGAGTATGCAGA	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.3398A>G	1.37:g.10397567A>G	ENSP00000366290:p.Tyr1133Cys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	183	93	0.508197	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		86	0.039377289377289376	20	0.04065040650406504	14	0.03867403314917127	33	0.057692307692307696	19	0.025065963060686015	A	26.3	4.722350	0.89298	0.04562	0.025349	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.81330	-1.48;-1.48;-1.48	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.58666	0.2138	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999	D;D;D;D;D;D	0.91635	0.999;0.999;0.999;0.998;0.972;0.995	T	0.78892	-0.2025	10	0.72032	D	0.01	.	16.2108	0.82158	1.0:0.0:0.0:0.0	rs2297881;rs52832881;rs56817007;rs2297881	1119;1093;1133;1107;1133;1087	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	C	1133;1087;1133;1133	ENSP00000263934:Y1087C;ENSP00000366290:Y1133C;ENSP00000366284:Y1133C	ENSP00000263934:Y1087C	Y	+	2	0	KIF1B	10320154	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.232000	0.73038	0.533000	0.62120	TAT	A|0.963;G|0.037	0.037	strong		0.502	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067065	79067065	+	Missense_Mutation	SNP	G	G	A	rs201460425		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:79067065G>A	ENST00000388820.4	-	12	1987	c.1777C>T	c.(1777-1779)Cct>Tct	p.P593S	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	593	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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 chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P593S(2)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CGGCCAGCAGGGCAGGCCTGC	0.642																																					p.P593S		Atlas-SNP	.											ADAMTS7,NS,carcinoma,+2,2	ADAMTS7	142	2	2	Substitution - Missense(2)	prostate(2)	c.C1777T						scavenged	.						52.0	59.0	57.0					15																	79067065		2196	4293	6489	SO:0001583	missense	11173	exon12			CAGCAGGGCAGGC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1777C>T	15.37:g.79067065G>A	ENSP00000373472:p.Pro593Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	73	11	0.150685	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.852108	0.32699	.	.	ENSG00000136378	ENST00000388820	T	0.07688	3.17	3.51	3.51	0.40186	.	0.281918	0.33980	N	0.004364	T	0.21062	0.0507	M	0.89715	3.055	0.45554	D	0.998507	B;P	0.52577	0.399;0.954	B;P	0.47470	0.15;0.548	T	0.26710	-1.0095	10	0.30854	T	0.27	.	14.2729	0.66162	0.0:0.0:1.0:0.0	.	593;593	A8MQ00;Q9UKP4	.;ATS7_HUMAN	S	593	ENSP00000373472:P593S	ENSP00000373472:P593S	P	-	1	0	ADAMTS7	76854120	1.000000	0.71417	0.972000	0.41901	0.652000	0.38707	3.564000	0.53791	1.986000	0.57962	0.289000	0.19496	CCT	G|0.999;A|0.001	0.001	weak		0.642	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
CHD8	57680	hgsc.bcm.edu	37	14	21878110	21878110	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:21878110G>A	ENST00000557364.1	-	11	2527	c.2264C>T	c.(2263-2265)cCc>cTc	p.P755L	CHD8_ENST00000399982.2_Missense_Mutation_p.P755L|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Missense_Mutation_p.P476L			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	755	Chromo 2. {ECO:0000255|PROSITE- ProRule:PRU00053}.				ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		ATCCTCATAGGGCAGAGAGCA	0.438																																					p.P755L		Atlas-SNP	.											CHD8_ENST00000430710,colon,carcinoma,-1,2	CHD8	339	2	0			c.C2264T						scavenged	.						103.0	92.0	96.0					14																	21878110		1878	4103	5981	SO:0001583	missense	57680	exon10			TCATAGGGCAGAG	AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.2264C>T	14.37:g.21878110G>A	ENSP00000451601:p.Pro755Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	2	0.0232558	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.512568	0.85389	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	T;T;T	0.75821	-0.97;-0.97;-0.97	4.7	3.81	0.43845	.	0.000000	0.85682	D	0.000000	D	0.85860	0.5795	M	0.86028	2.79	0.80722	D	1	D	0.69078	0.997	D	0.72982	0.979	D	0.87630	0.2515	10	0.72032	D	0.01	-14.3055	12.0273	0.53377	0.0854:0.0:0.9146:0.0	.	476	Q9HCK8-2	.	L	476;755;475;755	ENSP00000406288:P476L;ENSP00000382863:P755L;ENSP00000451601:P755L	ENSP00000262707:P475L	P	-	2	0	CHD8	20947950	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.601000	0.98297	1.342000	0.45619	0.655000	0.94253	CCC	.	.	none		0.438	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
KDM4C	23081	hgsc.bcm.edu	37	9	7103816	7103816	+	Silent	SNP	C	C	T	rs3763651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:7103816C>T	ENST00000381309.3	+	18	3121	c.2556C>T	c.(2554-2556)gaC>gaT	p.D852D	KDM4C_ENST00000428870.2_Silent_p.D539D|KDM4C_ENST00000381306.3_Silent_p.D852D|KDM4C_ENST00000442236.2_Silent_p.D597D|KDM4C_ENST00000536108.1_3'UTR	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	852					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						AGCCTGATGACTGGCCTTATG	0.552													T|||	2865	0.572085	0.621	0.634	5008	,	,		21359	0.7143		0.4225	False		,,,				2504	0.4693				p.D852D		Atlas-SNP	.											.	KDM4C	186	.	0			c.C2556T						PASS	.	T	,	2659,1747	521.1+/-370.4	816,1027,360	162.0	126.0	138.0		2556,2556	-5.4	0.3	9	dbSNP_107	138	3732,4868	617.6+/-396.7	792,2148,1360	no	coding-synonymous,coding-synonymous	KDM4C	NM_001146694.1,NM_015061.3	,	1608,3175,1720	TT,TC,CC		43.3953,39.6505,49.1389	,	852/1048,852/1057	7103816	6391,6615	2203	4300	6503	SO:0001819	synonymous_variant	23081	exon18			TGATGACTGGCCT	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2556C>T	9.37:g.7103816C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Silent	SNP	ENST00000381309.3	37	CCDS6471.1																																																																																			C|0.456;T|0.544	0.544	strong		0.552	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
FMN2	56776	hgsc.bcm.edu	37	1	240370941	240370941	+	Silent	SNP	T	T	C	rs71170718|rs4997329|rs562038978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:240370941T>C	ENST00000319653.9	+	5	3059	c.2829T>C	c.(2827-2829)ccT>ccC	p.P943P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	943	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGGAATACCTCCTCCGCCCC	0.697													C|||	1375	0.274561	0.357	0.1902	5008	,	,		7400	0.3105		0.2286	False		,,,				2504	0.2331				p.P943P		Atlas-SNP	.											FMN2,caecum,carcinoma,0,1	FMN2	451	1	0			c.T2829C						scavenged	.	C		371,3909		68,235,1837	23.0	29.0	27.0		2829	-8.0	0.0	1	dbSNP_113	27	396,8032		78,240,3896	no	coding-synonymous	FMN2	NM_020066.4		146,475,5733	CC,CT,TT		4.6986,8.6682,6.0356		943/1723	240370941	767,11941	2140	4214	6354	SO:0001819	synonymous_variant	56776	exon5			AATACCTCCTCCG	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2829T>C	1.37:g.240370941T>C		Somatic	117	4	0.034188		WXS	Illumina HiSeq	Phase_I	61	17	0.278689	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			T|0.863;C|0.137	0.137	strong		0.697	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
MAML3	55534	hgsc.bcm.edu	37	4	140811081	140811081	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:140811081C>T	ENST00000509479.2	-	2	2365	c.1509G>A	c.(1507-1509)caG>caA	p.Q503Q	MAML3_ENST00000398940.1_Intron|MAML3_ENST00000327122.5_Silent_p.Q347Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgct	0.527																																					p.Q503Q		Atlas-SNP	.											MAML3_ENST00000509479,NS,carcinoma,0,2	MAML3	192	2	0			c.G1509A						scavenged	.						23.0	31.0	29.0					4																	140811081		2165	4290	6455	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1509G>A	4.37:g.140811081C>T		Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	69	4	0.057971	NM_018717		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.	.	none		0.527	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
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 GAIIx	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	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	127	77	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	
NLRP1	22861	hgsc.bcm.edu	37	17	5487164	5487164	+	Silent	SNP	C	C	G	rs884367	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5487164C>G	ENST00000572272.1	-	1	113	c.114G>C	c.(112-114)tcG>tcC	p.S38S	NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000577119.1_Silent_p.S38S|NLRP1_ENST00000354411.3_Silent_p.S38S|NLRP1_ENST00000345221.3_Silent_p.S38S|NLRP1_ENST00000269280.4_Silent_p.S38S|NLRP1_ENST00000262467.5_Silent_p.S38S			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	38	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				GTGTCTCACCCGAAGAGCTCC	0.622													C|||	1418	0.283147	0.0234	0.1902	5008	,	,		17977	0.6587		0.1779	False		,,,				2504	0.4213				p.S38S		Atlas-SNP	.											.	NLRP1	358	.	0			c.G114C						PASS	.	C	,,,,	210,4192		9,192,2000	31.0	26.0	28.0		114,114,114,114,114	-6.5	0.0	17	dbSNP_86	28	1477,7107		137,1203,2952	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	,,,,	146,1395,4952	GG,GC,CC		17.2064,4.7706,12.9909	,,,,	38/1376,38/1430,38/1474,38/1444,38/1400	5487164	1687,11299	2201	4292	6493	SO:0001819	synonymous_variant	22861	exon1			CTCACCCGAAGAG	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.114G>C	17.37:g.5487164C>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Silent	SNP	ENST00000572272.1	37	CCDS42246.1																																																																																			C|0.812;G|0.188	0.188	strong		0.622	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
ZC3H3	23144	hgsc.bcm.edu	37	8	144522388	144522388	+	Missense_Mutation	SNP	A	A	T	rs2272753	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144522388A>T	ENST00000262577.5	-	11	2669	c.2638T>A	c.(2638-2640)Tca>Aca	p.S880T		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	880	Poly-Ser.				mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			ggaggggatgaggaggaggag	0.652													A|||	560	0.111821	0.0363	0.1167	5008	,	,		16934	0.2431		0.1461	False		,,,				2504	0.0399				p.S880T		Atlas-SNP	.											.	ZC3H3	75	.	0			c.T2638A						PASS	.	A	THR/SER	208,4198		8,192,2003	29.0	28.0	29.0		2638	-8.5	0.0	8	dbSNP_100	29	945,7653		118,709,3472	no	missense	ZC3H3	NM_015117.2	58	126,901,5475	TT,TA,AA		10.9909,4.7208,8.8665	possibly-damaging	880/949	144522388	1153,11851	2203	4299	6502	SO:0001583	missense	23144	exon11			GGGATGAGGAGGA	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2638T>A	8.37:g.144522388A>T	ENSP00000262577:p.Ser880Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	273	0.125	24	0.04878048780487805	42	0.11602209944751381	124	0.21678321678321677	83	0.10949868073878628	A	10.21	1.288569	0.23478	0.047208	0.109909	ENSG00000014164	ENST00000262577	T	0.44083	0.93	4.25	-8.5	0.00927	.	2.759650	0.01499	N	0.017425	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.23650	0.089	B	0.18263	0.021	T	0.07927	-1.0747	9	0.11794	T	0.64	2.0487	4.56	0.12156	0.1813:0.3576:0.3664:0.0948	rs2272753	880	Q8IXZ2	ZC3H3_HUMAN	T	880	ENSP00000262577:S880T	ENSP00000262577:S880T	S	-	1	0	ZC3H3	144593531	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-4.369000	0.00245	-2.892000	0.00315	-0.605000	0.04089	TCA	A|0.879;T|0.121	0.121	strong		0.652	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
LEPR	3953	hgsc.bcm.edu	37	1	66036441	66036441	+	Missense_Mutation	SNP	A	A	G	rs1137100	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:66036441A>G	ENST00000349533.6	+	4	511	c.326A>G	c.(325-327)aAg>aGg	p.K109R	LEPR_ENST00000371060.3_Missense_Mutation_p.K109R|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371059.3_Missense_Mutation_p.K109R|LEPR_ENST00000344610.8_Missense_Mutation_p.K109R|LEPR_ENST00000406510.3_5'UTR|snoU13_ENST00000459362.1_RNA|LEPR_ENST00000371058.1_Missense_Mutation_p.K109R	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)		ATTGAAGGAAAGACATTTGTT	0.318													A|||	1604	0.320288	0.1528	0.2378	5008	,	,		18463	0.8046		0.2704	False		,,,				2504	0.1575				p.K109R		Atlas-SNP	.											.	LEPR	284	.	0			c.A326G	GRCh37	CM032948	LEPR	M	rs1137100	PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	762,3644	301.0+/-286.6	58,646,1499	65.0	66.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	326,326,326,326,326,326	4.6	0.9	1	dbSNP_86	65	2273,6327	377.6+/-338.6	304,1665,2331	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	26,26,26,26,26,26	362,2311,3830	GG,GA,AA		26.4302,17.2946,23.3354	benign,benign,benign,benign,benign,benign	109/897,109/959,109/959,109/907,109/897,109/1166	66036441	3035,9971	2203	4300	6503	SO:0001583	missense	3953	exon4			AAGGAAAGACATT	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.326A>G	1.37:g.66036441A>G	ENSP00000330393:p.Lys109Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	19	0.283582	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	841	0.3850732600732601	63	0.12804878048780488	96	0.26519337016574585	464	0.8111888111888111	218	0.287598944591029	A	11.95	1.792657	0.31685	0.172946	0.264302	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.59906	0.27;0.26;0.29;0.23;0.27	5.69	4.55	0.56014	.	0.204186	0.43260	D	0.000583	T	0.50188	0.1601	L	0.53249	1.67	0.09310	P	0.999999999901199	D;B;B;D	0.61697	0.971;0.077;0.204;0.99	P;B;B;P	0.59056	0.725;0.021;0.084;0.851	T	0.50206	-0.8855	9	0.20519	T	0.43	-5.8543	8.8143	0.34987	0.9121:0.0:0.0879:0.0	rs1137100;rs1805092;rs3200841;rs3790430;rs17127718;rs17356583;rs17434225;rs59932898;rs1137100	109;109;109;109	P48357-4;P48357;P48357-2;P48357-3	.;LEPR_HUMAN;.;.	R	109	ENSP00000340884:K109R;ENSP00000330393:K109R;ENSP00000360099:K109R;ENSP00000360098:K109R;ENSP00000360097:K109R	ENSP00000340884:K109R	K	+	2	0	LEPR	65809029	0.986000	0.35501	0.871000	0.34182	0.808000	0.45660	2.343000	0.44001	2.167000	0.68274	0.455000	0.32223	AAG	A|0.705;G|0.295	0.295	strong		0.318	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
COL19A1	1310	hgsc.bcm.edu	37	6	70890224	70890224	+	Silent	SNP	G	G	A	rs2273948	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:70890224G>A	ENST00000322773.4	+	43	2790	c.2688G>A	c.(2686-2688)ggG>ggA	p.G896G	COL19A1_ENST00000393344.1_Silent_p.G518G	NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	896	Collagen-like 9.|Triple-helical region 5 (COL5).				cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GTGCCCCAGGGCCTCCAGGAG	0.473													G|||	418	0.0834665	0.1528	0.0605	5008	,	,		19830	0.1339		0.0209	False		,,,				2504	0.0184				p.G896G		Atlas-SNP	.											.	COL19A1	232	.	0			c.G2688A						PASS	.	G		554,3852	249.3+/-256.8	31,492,1680	123.0	143.0	136.0		2688	-5.5	0.9	6	dbSNP_100	136	147,8453	72.6+/-135.2	2,143,4155	no	coding-synonymous	COL19A1	NM_001858.4		33,635,5835	AA,AG,GG		1.7093,12.5738,5.3898		896/1143	70890224	701,12305	2203	4300	6503	SO:0001819	synonymous_variant	1310	exon43			CCCAGGGCCTCCA		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.2688G>A	6.37:g.70890224G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	148	74	0.5	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Silent	SNP	ENST00000322773.4	37	CCDS4970.1																																																																																			G|0.939;A|0.061	0.061	strong		0.473	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
DISP1	84976	hgsc.bcm.edu	37	1	223178561	223178561	+	Silent	SNP	A	A	C	rs9441941	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:223178561A>C	ENST00000284476.6	+	8	3986	c.3822A>C	c.(3820-3822)ccA>ccC	p.P1274P		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1274					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)	p.P1274P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		GTAGCTGCCCAGATGCCTACA	0.522													A|||	2494	0.498003	0.4153	0.5346	5008	,	,		19766	0.4782		0.6163	False		,,,				2504	0.4826				p.P1274P		Atlas-SNP	.											DISP1,NS,carcinoma,0,1	DISP1	145	1	1	Substitution - coding silent(1)	stomach(1)	c.A3822C						PASS	.	A		1997,2409	559.2+/-380.2	412,1173,618	138.0	127.0	131.0		3822	-9.7	0.0	1	dbSNP_119	131	4960,3640	624.2+/-397.5	1419,2122,759	no	coding-synonymous	DISP1	NM_032890.3		1831,3295,1377	CC,CA,AA		42.3256,45.3246,46.5093		1274/1525	223178561	6957,6049	2203	4300	6503	SO:0001819	synonymous_variant	84976	exon10			CTGCCCAGATGCC	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.3822A>C	1.37:g.223178561A>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Silent	SNP	ENST00000284476.6	37	CCDS1536.1																																																																																			A|0.467;C|0.533	0.533	strong		0.522	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
ABCC1	4363	hgsc.bcm.edu	37	16	16138322	16138322	+	Silent	SNP	T	T	C	rs246221	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:16138322T>C	ENST00000399410.3	+	8	1000	c.825T>C	c.(823-825)gtT>gtC	p.V275V	ABCC1_ENST00000349029.5_Silent_p.V275V|ABCC1_ENST00000345148.5_Silent_p.V275V|ABCC1_ENST00000346370.5_Silent_p.V275V|ABCC1_ENST00000399408.2_Silent_p.V275V|ABCC1_ENST00000351154.5_Silent_p.V275V	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	275					arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	CGGTGAAGGTTGTGTACTCCT	0.582													C|||	2127	0.42472	0.7118	0.3617	5008	,	,		17677	0.4425		0.3171	False		,,,				2504	0.1738				p.V275V		Atlas-SNP	.											.	ABCC1	156	.	0			c.T825C						PASS	.	C	,,,,	2485,1507		792,901,303	63.0	63.0	63.0		825,825,825,825,825	-5.3	0.0	16	dbSNP_79	63	2451,5883		345,1761,2061	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	1137,2662,2364	CC,CT,TT		29.4096,37.7505,40.0454	,,,,	275/1532,275/1473,275/1476,275/1417,275/1467	16138322	4936,7390	1996	4167	6163	SO:0001819	synonymous_variant	4363	exon8			GAAGGTTGTGTAC	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.825T>C	16.37:g.16138322T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			T|0.563;C|0.437	0.437	strong		0.582	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
TLE3	7090	hgsc.bcm.edu	37	15	70345626	70345626	+	Silent	SNP	C	C	T	rs1057865	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:70345626C>T	ENST00000558939.1	-	17	3300	c.1923G>A	c.(1921-1923)acG>acA	p.T641T	TLE3_ENST00000558379.1_Silent_p.T636T|TLE3_ENST00000317509.8_Silent_p.T629T|TLE3_ENST00000559929.1_Silent_p.T651T|TLE3_ENST00000560589.1_Silent_p.T585T|TLE3_ENST00000558201.1_Silent_p.T647T|TLE3_ENST00000560939.1_Silent_p.T643T|TLE3_ENST00000442299.2_Silent_p.T633T|TLE3_ENST00000440567.3_Silent_p.T631T|TLE3_ENST00000557907.1_Silent_p.T633T|TLE3_ENST00000559191.1_Silent_p.T222T|TLE3_ENST00000557997.1_Silent_p.T633T|TLE3_ENST00000451782.2_Silent_p.T638T|TLE3_ENST00000539550.1_Silent_p.T568T|TLE3_ENST00000559048.1_Silent_p.T641T	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	641					Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGGAGCGCACCGTGTTGTCCA	0.607													C|||	1818	0.363019	0.2284	0.4726	5008	,	,		18331	0.256		0.4791	False		,,,				2504	0.4581				p.T641T		Atlas-SNP	.											.	TLE3	104	.	0			c.G1923A						PASS	.	C	,,	1175,3125		187,801,1162	61.0	66.0	65.0		1914,1923,1887	-10.1	0.0	15	dbSNP_86	65	4018,4520		965,2088,1216	no	coding-synonymous,coding-synonymous,coding-synonymous	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	,,	1152,2889,2378	TT,TC,CC		47.0602,27.3256,40.4502	,,	638/770,641/773,629/761	70345626	5193,7645	2150	4269	6419	SO:0001819	synonymous_variant	7090	exon17			GCGCACCGTGTTG	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.1923G>A	15.37:g.70345626C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	150	66	0.44	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Silent	SNP	ENST00000558939.1	37	CCDS45293.1																																																																																			C|0.639;T|0.361	0.361	strong		0.607	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
MUTYH	4595	hgsc.bcm.edu	37	1	45797505	45797505	+	Missense_Mutation	SNP	C	C	G	rs587780083|rs3219489	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:45797505C>G	ENST00000372098.3	-	12	1138	c.1005G>C	c.(1003-1005)caG>caC	p.Q335H	MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000354383.6_Missense_Mutation_p.Q311H|MUTYH_ENST00000450313.1_Missense_Mutation_p.Q338H|MUTYH_ENST00000528332.2_Intron|MUTYH_ENST00000372100.5_Missense_Mutation_p.Q321H|MUTYH_ENST00000372110.3_Missense_Mutation_p.Q325H|MUTYH_ENST00000528013.2_Missense_Mutation_p.Q324H|MUTYH_ENST00000372115.3_Missense_Mutation_p.Q324H|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000456914.2_Missense_Mutation_p.Q310H|MUTYH_ENST00000355498.2_Missense_Mutation_p.Q310H|MUTYH_ENST00000372104.1_Missense_Mutation_p.Q310H|MUTYH_ENST00000448481.1_Missense_Mutation_p.Q321H			Q9UIF7	MUTYH_HUMAN	mutY homolog	335			Q -> H (in dbSNP:rs3219489). {ECO:0000269|PubMed:12606733, ECO:0000269|Ref.4}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					ACAGGTGGCACTGTCCAGTGT	0.642			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis				C|||	1570	0.313498	0.2579	0.4841	5008	,	,		17085	0.3909		0.2445	False		,,,				2504	0.2587				p.Q338H		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.G1014C	GRCh37	CM083726	MUTYH	M	rs3219489	PASS	.	C	HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN	1161,3241		169,823,1209	15.0	18.0	17.0		972,933,930,930,1014,1005	1.3	1.0	1	dbSNP_106	17	2143,6457		256,1631,2413	yes	missense,missense,missense,missense,missense,missense	MUTYH	NM_001048171.1,NM_001048172.1,NM_001048173.1,NM_001048174.1,NM_001128425.1,NM_012222.2	24,24,24,24,24,24	425,2454,3622	GG,GC,CC		24.9186,26.3744,25.4115	benign,benign,benign,benign,benign,benign	324/536,311/523,310/522,310/522,338/550,335/547	45797505	3304,9698	2201	4300	6501	SO:0001583	missense	4595	exon12	Familial Cancer Database	MAP, MYH-associated polyposis	GTGGCACTGTCCA	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.1005G>C	1.37:g.45797505C>G	ENSP00000361170:p.Gln335His	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	37	14	0.378378	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	37	CCDS520.1	696	0.31868131868131866	124	0.25203252032520324	149	0.4116022099447514	240	0.4195804195804196	183	0.24142480211081793	C	2.170	-0.390088	0.04932	0.263744	0.249186	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000525481;ENST00000412971	T;T;T;T;T;T;T;T;T;T;T	0.22945	3.23;3.23;3.23;3.23;3.23;3.22;3.22;3.22;3.22;3.23;1.93	5.66	1.26	0.21427	.	0.475733	0.24445	N	0.038471	T	0.00012	0.0000	M	0.69823	2.125	0.38421	P	0.05381199999999997	B;P;B;P;B;B;B	0.38745	0.343;0.645;0.326;0.645;0.219;0.324;0.219	B;B;B;B;B;B;B	0.34346	0.086;0.124;0.18;0.124;0.087;0.124;0.06	T	0.44360	-0.9333	9	0.42905	T	0.14	-13.6442	2.4732	0.04569	0.1089:0.4092:0.1175:0.3645	rs3219489;rs3811430;rs3219489	338;335;325;335;324;218;311	E5KP25;E5KP26;Q9UIF7-2;Q9UIF7;E5KP27;D3DPZ6;E5KP28	.;.;.;MUTYH_HUMAN;.;.;.	H	310;321;310;311;310;335;325;324;338;321;182;182	ENSP00000361176:Q310H;ENSP00000409718:Q321H;ENSP00000407590:Q310H;ENSP00000346354:Q311H;ENSP00000347685:Q310H;ENSP00000361170:Q335H;ENSP00000361182:Q325H;ENSP00000361187:Q324H;ENSP00000408176:Q338H;ENSP00000361172:Q321H;ENSP00000410263:Q182H	ENSP00000346354:Q311H	Q	-	3	2	MUTYH	45570092	0.034000	0.19679	1.000000	0.80357	0.077000	0.17291	0.051000	0.14141	0.240000	0.21263	-0.140000	0.14226	CAG	C|0.710;G|0.290	0.290	strong		0.642	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222	
UQCC1	55245	hgsc.bcm.edu	37	20	33971914	33971914	+	Missense_Mutation	SNP	C	C	T	rs4911494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:33971914C>T	ENST00000374385.5	-	3	329	c.152G>A	c.(151-153)cGa>cAa	p.R51Q	UQCC1_ENST00000397556.3_Intron|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000374384.2_Missense_Mutation_p.R51Q|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000407996.2_Missense_Mutation_p.R51Q|UQCC1_ENST00000374380.2_Intron|UQCC1_ENST00000542501.1_Missense_Mutation_p.R51Q|UQCC1_ENST00000397554.1_Missense_Mutation_p.R51Q|UQCC1_ENST00000349714.5_Missense_Mutation_p.R51Q|UQCC1_ENST00000374377.5_Intron|UQCC1_ENST00000359226.2_Missense_Mutation_p.R51Q	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	51			R -> Q (in dbSNP:rs4911494). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											ACCACATGCTCGGGACTGGCT	0.433													C|||	2642	0.527556	0.3056	0.7104	5008	,	,		21042	0.7113		0.6203	False		,,,				2504	0.4131				p.R51Q		Atlas-SNP	.											.	UQCC	41	.	0			c.G152A						PASS	.	C	,GLN/ARG,GLN/ARG	1612,2794	497.6+/-363.9	303,1006,894	133.0	111.0	118.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,152,152	-9.2	0.0	20	dbSNP_111	118	5226,3374	641.6+/-399.7	1610,2006,684	yes	intron,missense,missense	UQCC	NM_001184977.1,NM_018244.4,NM_199487.2	,43,43	1913,3012,1578	TT,TC,CC		39.2326,36.5865,47.4243	,benign,benign	,51/300,51/274	33971914	6838,6168	2203	4300	6503	SO:0001583	missense	55245	exon3			CATGCTCGGGACT	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.152G>A	20.37:g.33971914C>T	ENSP00000363506:p.Arg51Gln	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	169	82	0.485207	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	ENST00000374385.5	37	CCDS13252.1	1295	0.592948717948718	154	0.3130081300813008	246	0.6795580110497238	430	0.7517482517482518	465	0.6134564643799473	C	3.625	-0.076667	0.07184	0.365865	0.607674	ENSG00000101019	ENST00000349714;ENST00000359226;ENST00000374384;ENST00000374385;ENST00000407996;ENST00000542501;ENST00000438533;ENST00000397554	T;T;T;T;T;T;T;T	0.45276	1.57;1.55;1.45;1.47;0.9;1.5;1.52;1.41	5.02	-9.24	0.00669	.	1.805390	0.02659	N	0.107256	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B;B;B;B	0.17465	0.006;0.001;0.022;0.0;0.0	B;B;B;B;B	0.09377	0.004;0.001;0.001;0.0;0.0	T	0.36187	-0.9758	9	0.25106	T	0.35	-0.363	1.8464	0.03160	0.2733:0.3467:0.0841:0.2959	rs4911494;rs17331152;rs52824048;rs59962559;rs4911494	51;51;51;51;51	B7Z7J8;B7ZBG3;B1AKV2;B7ZBG4;Q9NVA1	.;.;.;.;UQCC_HUMAN	Q	51;51;51;51;51;51;65;51	ENSP00000335364:R51Q;ENSP00000352161:R51Q;ENSP00000363505:R51Q;ENSP00000363506:R51Q;ENSP00000386064:R51Q;ENSP00000445059:R51Q;ENSP00000398531:R65Q;ENSP00000380686:R51Q	ENSP00000335364:R51Q	R	-	2	0	UQCC	33435328	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.101000	0.10973	-1.403000	0.02053	-1.779000	0.00650	CGA	C|0.456;T|0.544	0.544	strong		0.433	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244	
DOK6	220164	hgsc.bcm.edu	37	18	67365668	67365668	+	Silent	SNP	A	A	G	rs4426448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:67365668A>G	ENST00000382713.5	+	5	628	c.438A>G	c.(436-438)acA>acG	p.T146T	DOK6_ENST00000584435.1_3'UTR	NM_152721.5	NP_689934.2	Q6PKX4	DOK6_HUMAN	docking protein 6	146	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.									central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	20		Colorectal(73;0.083)|Esophageal squamous(42;0.131)				TTATGCCTACACCAAACCTGG	0.408													G|||	2429	0.485024	0.4213	0.3501	5008	,	,		20482	0.7331		0.4692	False		,,,				2504	0.4274				p.T146T		Atlas-SNP	.											.	DOK6	56	.	0			c.A438G						PASS	.	G		1966,2440	620.0+/-393.5	426,1114,663	124.0	109.0	114.0		438	-5.9	0.7	18	dbSNP_111	114	4006,4594	598.3+/-393.9	916,2174,1210	no	coding-synonymous	DOK6	NM_152721.5		1342,3288,1873	GG,GA,AA		46.5814,44.621,45.9173		146/332	67365668	5972,7034	2203	4300	6503	SO:0001819	synonymous_variant	220164	exon5			GCCTACACCAAAC	AK057795	CCDS32841.1	18q22.2	2013-01-10	2005-01-18	2005-01-18		ENSG00000206052		"""Pleckstrin homology (PH) domain containing"""	28301	protein-coding gene	gene with protein product		611402	"""docking protein 5-like"""	DOK5L		15286081	Standard	NM_152721		Approved	MGC20785, HsT3226	uc002lkl.3	Q6PKX4		ENST00000382713.5:c.438A>G	18.37:g.67365668A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_152721	A6NNG3|Q4V9S3|Q8WUZ8|Q96HI2|Q96LU2	Silent	SNP	ENST00000382713.5	37	CCDS32841.1																																																																																			A|0.522;G|0.478	0.478	strong		0.408	DOK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442969.1	NM_152721	
PTPRS	5802	hgsc.bcm.edu	37	19	5210782	5210782	+	Silent	SNP	G	G	A	rs1143698	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5210782G>A	ENST00000587303.1	-	33	5368	c.5269C>T	c.(5269-5271)Ctg>Ttg	p.L1757L	PTPRS_ENST00000588012.1_Silent_p.L1719L|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000372412.4_Silent_p.L1758L|PTPRS_ENST00000262963.6_Silent_p.L1737L|PTPRS_ENST00000348075.2_Silent_p.L1719L|PTPRS_ENST00000357368.4_Silent_p.L1757L|PTPRS_ENST00000592099.1_Silent_p.L1310L|PTPRS_ENST00000353284.2_Silent_p.L1310L			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1757	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.L1757L(1)		NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GTCTCCGCCAGCGGCCCCTGT	0.642													G|||	1678	0.335064	0.5545	0.3516	5008	,	,		18919	0.0992		0.2714	False		,,,				2504	0.3354				p.L1757L		Atlas-SNP	.											PTPRS,NS,carcinoma,0,1	PTPRS	169	1	1	Substitution - coding silent(1)	stomach(1)	c.C5269T						PASS	.	G	,,,	2056,2350	567.1+/-382.1	483,1090,630	76.0	61.0	66.0		5269,3928,5155,3940	2.6	0.9	19	dbSNP_86	66	2348,6252	391.5+/-343.7	314,1720,2266	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	797,2810,2896	AA,AG,GG		27.3023,46.6636,33.8613	,,,	1757/1949,1310/1502,1719/1911,1314/1506	5210782	4404,8602	2203	4300	6503	SO:0001819	synonymous_variant	5802	exon34			CCGCCAGCGGCCC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.5269C>T	19.37:g.5210782G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			G|0.667;A|0.333	0.333	strong		0.642	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
BCL2A1	597	hgsc.bcm.edu	37	15	80263406	80263406	+	Missense_Mutation	SNP	C	C	T	rs1138357	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:80263406C>T	ENST00000267953.3	-	1	382	c.56G>A	c.(55-57)tGc>tAc	p.C19Y	BCL2A1_ENST00000335661.6_Missense_Mutation_p.C19Y	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	19			C -> Y (in dbSNP:rs1138357). {ECO:0000269|Ref.6}.		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)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						CTGTAGGACGCACTGCAGATA	0.463													T|||	1763	0.352037	0.2572	0.2767	5008	,	,		20116	0.5367		0.2565	False		,,,				2504	0.4417				p.C19Y		Atlas-SNP	.											.	BCL2A1	28	.	0			c.G56A						PASS	.	T	TYR/CYS,TYR/CYS	1063,3343	723.6+/-409.4	115,833,1255	93.0	85.0	88.0		56,56	1.9	0.0	15	dbSNP_86	88	2210,6390	710.7+/-405.8	263,1684,2353	yes	missense,missense	BCL2A1	NM_001114735.1,NM_004049.3	194,194	378,2517,3608	TT,TC,CC		25.6977,24.1262,25.1653	benign,benign	19/164,19/176	80263406	3273,9733	2203	4300	6503	SO:0001583	missense	597	exon1			AGGACGCACTGCA		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.56G>A	15.37:g.80263406C>T	ENSP00000267953:p.Cys19Tyr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	733	0.3356227106227106	114	0.23170731707317074	117	0.32320441988950277	311	0.5437062937062938	191	0.2519788918205805	T	0.042	-1.282248	0.01398	0.241262	0.256977	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.16597	2.33;2.33	5.63	1.93	0.25924	.	1.078550	0.07069	N	0.835026	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46456	-0.9190	9	0.02654	T	1	-10.7493	4.1144	0.10074	0.2557:0.1385:0.0:0.6058	rs1138357;rs2070264;rs3202145;rs3743425;rs16971625;rs52797061;rs61411122;rs1138357	19;19	Q86W13;Q16548	.;B2LA1_HUMAN	Y	19	ENSP00000267953:C19Y;ENSP00000335250:C19Y	ENSP00000267953:C19Y	C	-	2	0	BCL2A1	78050461	0.007000	0.16637	0.000000	0.03702	0.002000	0.02628	1.334000	0.33827	-0.156000	0.11079	-1.170000	0.01741	TGC	C|0.708;T|0.292	0.292	strong		0.463	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
COL15A1	1306	hgsc.bcm.edu	37	9	101778265	101778265	+	Missense_Mutation	SNP	G	G	T	rs2297603	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:101778265G>T	ENST00000375001.3	+	11	1934	c.1511G>T	c.(1510-1512)gGt>gTt	p.G504V		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	504	4 X tandem repeats.|Nonhelical region 1 (NC1).		G -> V (in dbSNP:rs2297603).		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)				CAGGGTCCTGGTGATGAAGAA	0.592													G|||	427	0.0852636	0.0053	0.1196	5008	,	,		16779	0.2133		0.0885	False		,,,				2504	0.0337				p.G504V		Atlas-SNP	.											COL15A1,brain,glioma,0,1	COL15A1	211	1	0			c.G1511T						PASS	.	G	VAL/GLY	93,4313	73.6+/-111.7	2,89,2112	66.0	62.0	63.0		1511	-1.9	0.0	9	dbSNP_100	63	929,7671	201.3+/-244.8	48,833,3419	yes	missense	COL15A1	NM_001855.3	109	50,922,5531	TT,TG,GG		10.8023,2.1108,7.8579	probably-damaging	504/1389	101778265	1022,11984	2203	4300	6503	SO:0001583	missense	1306	exon11			GTCCTGGTGATGA	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.1511G>T	9.37:g.101778265G>T	ENSP00000364140:p.Gly504Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	238	0.10897435897435898	8	0.016260162601626018	47	0.1298342541436464	115	0.20104895104895104	68	0.08970976253298153	G	8.560	0.877531	0.17395	0.021108	0.108023	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.89875	-2.58	3.93	-1.87	0.07737	.	15.702500	0.00604	N	0.000385	T	0.00384	0.0012	L	0.50333	1.59	0.80722	P	0.0	B	0.14438	0.01	B	0.10450	0.005	T	0.41645	-0.9497	9	0.66056	D	0.02	.	1.185	0.01853	0.2164:0.343:0.278:0.1626	rs2297603;rs17617726;rs52813576;rs2297603	504	P39059	COFA1_HUMAN	V	504;474	ENSP00000364140:G504V	ENSP00000364140:G504V	G	+	2	0	COL15A1	100818086	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.248000	0.18198	-0.153000	0.11137	0.650000	0.86243	GGT	G|0.909;T|0.091	0.091	strong		0.592	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557489	32557489	+	Missense_Mutation	SNP	A	A	T	rs199514452	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32557489A>T	ENST00000360004.5	-	1	136	c.31T>A	c.(31-33)Tgc>Agc	p.C11S		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	11					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCTGTCATGCAGGAGCCTCCA	0.582										Multiple Myeloma(14;0.17)			A|||	371	0.0740815	0.1225	0.0389	5008	,	,		25825	0.0585		0.0417	False		,,,				2504	0.0828				p.C11S		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	0			c.T31A						scavenged	.						86.0	103.0	97.0					6																	32557489		1511	2709	4220	SO:0001583	missense	3123	exon1			TCATGCAGGAGCC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.31T>A	6.37:g.32557489A>T	ENSP00000353099:p.Cys11Ser	Somatic	127	8	0.0629921		WXS	Illumina HiSeq	Phase_I	233	18	0.0772532	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	11.88	1.772049	0.31320	.	.	ENSG00000196126	ENST00000360004	T	0.00241	8.46	4.68	2.29	0.28610	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.48362	1.52	0.09310	N	1	B	0.20887	0.049	B	0.23419	0.046	T	0.38308	-0.9667	9	0.45353	T	0.12	.	3.8919	0.09122	0.7162:0.0:0.0991:0.1848	.	11	P01911	2B1F_HUMAN	S	11	ENSP00000353099:C11S	ENSP00000353099:C11S	C	-	1	0	HLA-DRB1	32665467	0.021000	0.18746	0.048000	0.18961	0.007000	0.05969	0.788000	0.26872	0.321000	0.23259	-0.530000	0.04314	TGC	A|0.864;T|0.136	0.136	strong		0.582	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
FOXRED2	80020	hgsc.bcm.edu	37	22	36900806	36900806	+	Missense_Mutation	SNP	A	A	G	rs760718	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36900806A>G	ENST00000397224.4	-	3	628	c.535T>C	c.(535-537)Ttt>Ctt	p.F179L	FOXRED2_ENST00000216187.6_Missense_Mutation_p.F179L|FOXRED2_ENST00000397223.4_Missense_Mutation_p.F179L	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	179			F -> L (in dbSNP:rs760718). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.		ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GTGGCTACAAAGAGGACGCTG	0.547													G|||	2276	0.454473	0.444	0.7089	5008	,	,		16227	0.2123		0.668	False		,,,				2504	0.318				p.F179L		Atlas-SNP	.											.	FOXRED2	48	.	0			c.T535C						PASS	.	G	LEU/PHE,LEU/PHE	2071,2335	600.7+/-389.6	495,1081,627	39.0	41.0	40.0		535,535	1.9	0.1	22	dbSNP_86	40	6026,2574	414.6+/-351.5	2121,1784,395	yes	missense,missense	FOXRED2	NM_001102371.1,NM_024955.5	22,22	2616,2865,1022	GG,GA,AA		29.9302,47.0041,37.7441	benign,benign	179/685,179/685	36900806	8097,4909	2203	4300	6503	SO:0001583	missense	80020	exon3			CTACAAAGAGGAC	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.535T>C	22.37:g.36900806A>G	ENSP00000380401:p.Phe179Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Missense_Mutation	SNP	ENST00000397224.4	37	CCDS13929.1	1117	0.5114468864468864	211	0.42886178861788615	258	0.712707182320442	143	0.25	505	0.6662269129287599	G	0.010	-1.750466	0.00669	0.470041	0.700698	ENSG00000100350	ENST00000397224;ENST00000216187;ENST00000397223	T;T;T	0.15487	2.42;2.42;2.42	5.6	1.94	0.25998	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.133572	0.50627	N	0.000111	T	0.00012	0.0000	N	0.05031	-0.125	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.28138	-1.0053	9	0.08381	T	0.77	-11.6756	9.7994	0.40755	0.4442:0.0:0.5558:0.0	rs760718;rs3747165;rs17856490;rs57570352;rs760718	179	Q8IWF2	FXRD2_HUMAN	L	179	ENSP00000380401:F179L;ENSP00000216187:F179L;ENSP00000380400:F179L	ENSP00000216187:F179L	F	-	1	0	FOXRED2	35230752	0.423000	0.25482	0.108000	0.21378	0.005000	0.04900	0.726000	0.25984	0.333000	0.23563	-0.119000	0.15052	TTT	A|0.435;G|0.565	0.565	strong		0.547	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
PRAMEF22	653606	hgsc.bcm.edu	37	1	13036639	13036639	+	Silent	SNP	C	C	A	rs375721952		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:13036639C>A	ENST00000376187.1	+	2	711	c.711C>A	c.(709-711)cgC>cgA	p.R237R	PRAMEF6_ENST00000376192.5_Intron	NM_001100631.1	NP_001094101.1	A3QJZ6	PRA22_HUMAN	PRAME family member 22	237					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)					kidney(1)|large_intestine(2)|lung(1)|skin(1)	5						GGAATCTTCGCAAACTCTTCA	0.478																																					p.R237R		Atlas-SNP	.											PRAMEF22,NS,carcinoma,+2,2	PRAMEF22	13	2	0			c.C711A						scavenged	.						148.0	174.0	165.0					1																	13036639		2201	4297	6498	SO:0001819	synonymous_variant	653606	exon2			TCTTCGCAAACTC			1p36.21	2013-01-17			ENSG00000204508			"""-"""	34393	protein-coding gene	gene with protein product							Standard	NM_001100631		Approved	PRAMEF3L	uc009vnq.1	A3QJZ6	OTTHUMG00000074726	ENST00000376187.1:c.711C>A	1.37:g.13036639C>A		Somatic	1123	9	0.00801425		WXS	Illumina HiSeq	Phase_I	1091	29	0.0265811	NM_001100631	A6NMM3	Silent	SNP	ENST00000376187.1	37	CCDS41256.1																																																																																			.	.	none		0.478	PRAMEF22-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158511.1	NM_001100631	
CAPN9	10753	hgsc.bcm.edu	37	1	230923313	230923313	+	Missense_Mutation	SNP	C	C	T	rs12731961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:230923313C>T	ENST00000271971.2	+	13	1677	c.1564C>T	c.(1564-1566)Cgg>Tgg	p.R522W	CAPN9_ENST00000354537.1_Missense_Mutation_p.R496W|RP11-99J16__A.2_ENST00000452640.1_RNA|RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|CAPN9_ENST00000366666.2_Missense_Mutation_p.R459W	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	522	Domain IV.|EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.		R -> W (in dbSNP:rs12731961). {ECO:0000269|Ref.3}.		digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GGAGGAGCAGCGGTTTCGGGC	0.522													C|||	982	0.196086	0.3207	0.1542	5008	,	,		19755	0.0813		0.1819	False		,,,				2504	0.1902				p.R522W		Atlas-SNP	.											.	CAPN9	116	.	0			c.C1564T						PASS	.	C	TRP/ARG,TRP/ARG	1255,3151	430.1+/-342.5	191,873,1139	118.0	99.0	105.0		1564,1486	3.2	0.4	1	dbSNP_121	105	1661,6939	306.2+/-307.8	158,1345,2797	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	101,101	349,2218,3936	TT,TC,CC		19.314,28.4839,22.4204	possibly-damaging,possibly-damaging	522/691,496/665	230923313	2916,10090	2203	4300	6503	SO:0001583	missense	10753	exon13			GAGCAGCGGTTTC	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1564C>T	1.37:g.230923313C>T	ENSP00000271971:p.Arg522Trp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	381	0.17445054945054944	150	0.3048780487804878	56	0.15469613259668508	35	0.06118881118881119	140	0.18469656992084432	C	8.961	0.970662	0.18659	0.284839	0.19314	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	D;D;D	0.95103	-3.61;-3.61;-3.61	5.17	3.18	0.36537	EF-hand-like domain (1);	0.641175	0.17553	N	0.170097	T	0.00039	0.0001	L	0.34521	1.04	0.80722	P	0.0	P;P;P	0.52061	0.917;0.95;0.917	B;P;B	0.45138	0.28;0.471;0.28	T	0.00000	-1.3148	9	0.72032	D	0.01	.	12.7937	0.57549	0.0:0.6867:0.3133:0.0	rs12731961;rs52797755;rs56556331;rs58840974;rs12731961	459;496;522	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	W	522;496;459	ENSP00000271971:R522W;ENSP00000346538:R496W;ENSP00000355626:R459W	ENSP00000271971:R522W	R	+	1	2	CAPN9	228989936	0.185000	0.23213	0.373000	0.26003	0.052000	0.14988	0.780000	0.26760	1.128000	0.42052	0.655000	0.94253	CGG	C|0.793;T|0.207	0.207	strong		0.522	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
TMEM105	284186	hgsc.bcm.edu	37	17	79287477	79287477	+	Missense_Mutation	SNP	G	G	A	rs9916085	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79287477G>A	ENST00000332900.1	-	3	913	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W		NM_178520.3	NP_848615.1	Q8N8V8	TM105_HUMAN	transmembrane protein 105	122			R -> W (in dbSNP:rs9916085).			integral component of membrane (GO:0016021)				NS(1)|large_intestine(3)|lung(1)|ovary(2)	7	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.0892)			CCTGCACCCCGGCCCCACAGC	0.592													G|||	494	0.0986422	0.292	0.0504	5008	,	,		14401	0.0		0.0586	False		,,,				2504	0.0143				p.R122W		Atlas-SNP	.											.	TMEM105	19	.	0			c.C364T						PASS	.	G	TRP/ARG	1170,3234	405.8+/-333.6	157,856,1189	54.0	58.0	56.0		364	0.1	0.0	17	dbSNP_119	56	421,8179	129.3+/-187.4	17,387,3896	yes	missense	TMEM105	NM_178520.3	101	174,1243,5085	AA,AG,GG		4.8953,26.5668,12.2347	possibly-damaging	122/130	79287477	1591,11413	2202	4300	6502	SO:0001583	missense	284186	exon3			CACCCCGGCCCCA	AK096111	CCDS11781.1	17q25.3	2008-04-21	2008-04-21	2008-04-21		ENSG00000185332			26794	protein-coding gene	gene with protein product							Standard	NM_178520		Approved	FLJ38792	uc002kad.2	Q8N8V8		ENST00000332900.1:c.364C>T	17.37:g.79287477G>A	ENSP00000329795:p.Arg122Trp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_178520		Missense_Mutation	SNP	ENST00000332900.1	37	CCDS11781.1	205	0.09386446886446886	145	0.29471544715447157	13	0.03591160220994475	0	0.0	47	0.06200527704485488	G	9.289	1.050099	0.19827	0.265668	0.048953	ENSG00000185332	ENST00000332900	T	0.56444	0.46	1.16	0.114	0.14639	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.27932	0.194	B	0.09377	0.004	T	0.25433	-1.0132	8	0.87932	D	0	.	3.2835	0.06924	0.306:0.0:0.694:0.0	rs9916085;rs59672127;rs9916085	122	Q8N8V8	TM105_HUMAN	W	122	ENSP00000329795:R122W	ENSP00000329795:R122W	R	-	1	2	TMEM105	76902072	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.069000	0.11542	0.047000	0.15862	0.436000	0.28706	CGG	G|0.882;A|0.118	0.118	strong		0.592	TMEM105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439607.1	NM_178520	
ATP10D	57205	hgsc.bcm.edu	37	4	47525054	47525054	+	Missense_Mutation	SNP	T	T	C	rs7683838	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:47525054T>C	ENST00000273859.3	+	4	780	c.511T>C	c.(511-513)Tgc>Cgc	p.C171R	ATP10D_ENST00000504445.1_Missense_Mutation_p.C171R	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	171			C -> R (in dbSNP:rs7683838).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						CATTGACCGATGCTGGAAAGA	0.333													T|||	465	0.0928514	0.1551	0.1138	5008	,	,		15375	0.004		0.1322	False		,,,				2504	0.045				p.C171R		Atlas-SNP	.											.	ATP10D	168	.	0			c.T511C						PASS	.	T	ARG/CYS	705,3701	295.0+/-283.4	56,593,1554	83.0	76.0	78.0		511	2.2	0.5	4	dbSNP_116	78	1114,7486	231.5+/-265.5	76,962,3262	yes	missense	ATP10D	NM_020453.3	180	132,1555,4816	CC,CT,TT		12.9535,16.0009,13.9859	benign	171/1427	47525054	1819,11187	2203	4300	6503	SO:0001583	missense	57205	exon4			GACCGATGCTGGA	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.511T>C	4.37:g.47525054T>C	ENSP00000273859:p.Cys171Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	231	0.10576923076923077	79	0.16056910569105692	51	0.1408839779005525	4	0.006993006993006993	97	0.1279683377308707	T	3.952	-0.012021	0.07727	0.160009	0.129535	ENSG00000145246	ENST00000273859;ENST00000504445	T;T	0.74526	-0.85;-0.85	5.94	2.25	0.28309	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.173510	0.52532	N	0.000077	T	0.00210	0.0006	N	0.01219	-0.95	0.28006	P	0.9350931	B;B	0.18741	0.03;0.0	B;B	0.18263	0.021;0.002	T	0.03662	-1.1015	9	0.25106	T	0.35	-9.2528	9.2908	0.37786	0.0:0.2759:0.0:0.7241	rs7683838;rs52836286;rs61027912;rs7683838	171;171	Q9P241;Q6PEW3	AT10D_HUMAN;.	R	171	ENSP00000273859:C171R;ENSP00000420909:C171R	ENSP00000273859:C171R	C	+	1	0	ATP10D	47219811	0.658000	0.27402	0.517000	0.27799	0.453000	0.32348	0.973000	0.29422	0.498000	0.27948	0.397000	0.26171	TGC	T|0.869;C|0.131	0.131	strong		0.333	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
KIAA1614	57710	hgsc.bcm.edu	37	1	180905352	180905352	+	Silent	SNP	C	C	T	rs3795505	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:180905352C>T	ENST00000367588.4	+	5	2362	c.2307C>T	c.(2305-2307)agC>agT	p.S769S	KIAA1614_ENST00000367587.1_Silent_p.S390S	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	769										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						TTACAGAAAGCCACGAGTCCC	0.602													C|||	1665	0.332468	0.1536	0.4006	5008	,	,		18104	0.2599		0.4245	False		,,,				2504	0.5061				p.S769S		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C2307T						PASS	.	C		775,3357		80,615,1371	84.0	90.0	88.0		2307	0.8	0.0	1	dbSNP_107	88	3455,4929		703,2049,1440	no	coding-synonymous	KIAA1614	NM_020950.1		783,2664,2811	TT,TC,CC		41.2094,18.7561,33.7967		769/1191	180905352	4230,8286	2066	4192	6258	SO:0001819	synonymous_variant	57710	exon5			AGAAAGCCACGAG	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2307C>T	1.37:g.180905352C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_020950	Q5VZ45|Q9HCF8	Silent	SNP	ENST00000367588.4	37	CCDS41442.1																																																																																			C|0.668;T|0.332	0.332	strong		0.602	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
SLC38A5	92745	hgsc.bcm.edu	37	X	48317386	48317386	+	Missense_Mutation	SNP	A	A	G	rs17281188	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:48317386A>G	ENST00000376876.3	-	16	2195	c.1352T>C	c.(1351-1353)aTg>aCg	p.M451T	SLC38A5_ENST00000317669.5_Missense_Mutation_p.M451T|SLC38A5_ENST00000376875.1_Missense_Mutation_p.M400T|SLC38A5_ENST00000480105.1_5'Flank			Q8WUX1	S38A5_HUMAN	solute carrier family 38, member 5	451			M -> T (in dbSNP:rs17281188). {ECO:0000269|PubMed:11243884}.		amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)			breast(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	19						ACTGACGGCCATGAAGAGGAC	0.592													A|||	321	0.0850331	0.0272	0.1441	3775	,	,		12194	0.0685		0.0517	False		,,,				2504	0.0654				p.M451T		Atlas-SNP	.											.	SLC38A5	98	.	0			c.T1352C						PASS	.	A	THR/MET	124,3707		4,99,17,1527,554	49.0	41.0	44.0		1352	3.9	1.0	X	dbSNP_123	44	500,6218		10,338,142,2078,1724	yes	missense	SLC38A5	NM_033518.2	81	14,437,159,3605,2278	GG,GA,G,AA,A		7.4427,3.2368,5.9153	possibly-damaging	451/473	48317386	624,9925	2201	4292	6493	SO:0001583	missense	92745	exon17			ACGGCCATGAAGA	AF276889	CCDS14293.1	Xp11.23	2013-05-22			ENSG00000017483	ENSG00000017483		"""Solute carriers"""	18070	protein-coding gene	gene with protein product		300649				11243884	Standard	NM_033518		Approved	SN2, JM24	uc010nid.3	Q8WUX1	OTTHUMG00000024117	ENST00000376876.3:c.1352T>C	X.37:g.48317386A>G	ENSP00000366073:p.Met451Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	19	0.174312	NM_033518	B3KT20|B5MDE6|B7WPJ9|Q6PIW9|Q8WYU2|Q96PQ4	Missense_Mutation	SNP	ENST00000376876.3	37	CCDS14293.1	143	0.0861965039180229	14	0.028688524590163935	32	0.09937888198757763	20	0.037037037037037035	28	0.03804347826086957	a	13.51	2.257794	0.39896	0.032368	0.074427	ENSG00000017483	ENST00000376876;ENST00000376875;ENST00000317669	T;T;T	0.02525	4.26;4.26;4.26	5.08	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.00384	0.0012	M	0.90145	3.09	0.09310	P	0.99999108501	D	0.71674	0.998	D	0.73380	0.98	T	0.04140	-1.0974	9	0.35671	T	0.21	.	8.5502	0.33447	0.825:0.0:0.0:0.175	rs17281188;rs61481118;rs17281188	451	Q8WUX1	S38A5_HUMAN	T	451;400;451	ENSP00000366073:M451T;ENSP00000366071:M400T;ENSP00000313740:M451T	ENSP00000313740:M451T	M	-	2	0	SLC38A5	48202330	1.000000	0.71417	0.979000	0.43373	0.376000	0.30014	8.322000	0.90000	0.570000	0.29347	0.425000	0.28330	ATG	A|0.906;0|0.027	.	strong		0.592	SLC38A5-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060724.1	NM_033518	
ZNF154	7710	hgsc.bcm.edu	37	19	58213693	58213693	+	Silent	SNP	C	C	T	rs61730373	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58213693C>T	ENST00000512439.2	-	3	820	c.624G>A	c.(622-624)cgG>cgA	p.R208R	AC003006.7_ENST00000594684.1_Intron|AC003006.7_ENST00000599221.1_Intron|ZNF154_ENST00000426889.1_Silent_p.R208R|ZNF551_ENST00000596085.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	208					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(1)|kidney(1)|large_intestine(7)|lung(3)	12		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;0.0257)		TGTGAACTCTCCGGTGCTGAA	0.443													C|||	645	0.128794	0.1762	0.111	5008	,	,		23680	0.0843		0.1948	False		,,,				2504	0.0552				p.R208R		Atlas-SNP	.											ZNF154,caecum,carcinoma,-1,2	ZNF154	34	2	0			c.G624A						PASS	.	C		717,3663	267.7+/-268.0	70,577,1543	99.0	99.0	99.0		624	2.8	0.0	19	dbSNP_129	99	1420,7160	263.8+/-285.2	116,1188,2986	no	coding-synonymous	ZNF154	NM_001085384.1		186,1765,4529	TT,TC,CC		16.5501,16.3699,16.4892		208/438	58213693	2137,10823	2190	4290	6480	SO:0001819	synonymous_variant	7710	exon3			AACTCTCCGGTGC	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"""Zinc fingers, C2H2-type"", ""-"""	12939	protein-coding gene	gene with protein product		604085	"""zinc finger protein 154 (pHZ-92)"""			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.624G>A	19.37:g.58213693C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	167	83	0.497006	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Silent	SNP	ENST00000512439.2	37	CCDS42639.1																																																																																			C|0.843;T|0.157	0.157	strong		0.443	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2		
COL6A1	1291	hgsc.bcm.edu	37	21	47423507	47423507	+	Silent	SNP	G	G	A	rs71336107|rs1053315	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:47423507G>A	ENST00000361866.3	+	35	2781	c.2667G>A	c.(2665-2667)gcG>gcA	p.A889A	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	889	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)	p.A889A(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		CAGAGCGGGCGTCGCTGCAGT	0.682													G|||	1343	0.268171	0.4077	0.281	5008	,	,		14817	0.1379		0.2734	False		,,,				2504	0.1994				p.A889A		Atlas-SNP	.											COL6A1,NS,carcinoma,0,2	COL6A1	101	2	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2667A						PASS	.	G		1718,2686		346,1026,830	29.0	29.0	29.0		2667	-2.6	0.0	21	dbSNP_86	29	2667,5931		438,1791,2070	no	coding-synonymous	COL6A1	NM_001848.2		784,2817,2900	AA,AG,GG		31.0188,39.01,33.7256		889/1029	47423507	4385,8617	2202	4299	6501	SO:0001819	synonymous_variant	1291	exon35			GCGGGCGTCGCTG	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2667G>A	21.37:g.47423507G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	91	60	0.659341	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Silent	SNP	ENST00000361866.3	37	CCDS13727.1																																																																																			ATC|0.500;GTT|0.500	.	alt		0.682	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
VSTM2B	342865	hgsc.bcm.edu	37	19	30020752	30020752	+	Silent	SNP	C	C	T	rs61731469	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:30020752C>T	ENST00000335523.7	+	4	409	c.324C>T	c.(322-324)atC>atT	p.I108I	CTC-525D6.2_ENST00000579268.1_RNA	NM_001146339.1	NP_001139811.1	A6NLU5	VTM2B_HUMAN	V-set and transmembrane domain containing 2B	108	Ig-like V-type.					integral component of membrane (GO:0016021)				breast(2)	2						GCAATGACATCTCACACCGGC	0.657													C|||	173	0.0345447	0.0809	0.0231	5008	,	,		13706	0.001		0.0219	False		,,,				2504	0.0276				p.I108I		Atlas-SNP	.											.	VSTM2B	15	.	0			c.C324T						PASS	.	C		92,1292		5,82,605	22.0	26.0	25.0		324	3.2	1.0	19	dbSNP_129	25	93,3087		1,91,1498	no	coding-synonymous	VSTM2B	NM_001146339.1		6,173,2103	TT,TC,CC		2.9245,6.6474,4.0535		108/286	30020752	185,4379	692	1590	2282	SO:0001819	synonymous_variant	342865	exon4			TGACATCTCACAC		CCDS46034.1	19q12	2013-01-11			ENSG00000187135	ENSG00000187135		"""Immunoglobulin superfamily / V-set domain containing"""	33595	protein-coding gene	gene with protein product							Standard	NM_001146339		Approved		uc010xrl.1	A6NLU5		ENST00000335523.7:c.324C>T	19.37:g.30020752C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_001146339		Silent	SNP	ENST00000335523.7	37	CCDS46034.1																																																																																			C|0.973;T|0.027	0.027	strong		0.657	VSTM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458601.1	NM_001146339	
PLXNA2	5362	hgsc.bcm.edu	37	1	208390086	208390086	+	Silent	SNP	G	G	C	rs1664227	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:208390086G>C	ENST00000367033.3	-	2	1939	c.1182C>G	c.(1180-1182)acC>acG	p.T394T		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	394	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		TTACCGCCTTGGTGCACTGGA	0.622													G|||	1839	0.367212	0.3623	0.3343	5008	,	,		20651	0.4048		0.3042	False		,,,				2504	0.4233				p.T394T		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C1182G						PASS	.	G		1551,2855	488.5+/-361.2	287,977,939	80.0	74.0	76.0		1182	4.9	1.0	1	dbSNP_89	76	2810,5790	443.7+/-360.5	479,1852,1969	no	coding-synonymous	PLXNA2	NM_025179.3		766,2829,2908	CC,CG,GG		32.6744,35.202,33.5307		394/1895	208390086	4361,8645	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			CGCCTTGGTGCAC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.1182C>G	1.37:g.208390086G>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			G|0.664;C|0.336	0.336	strong		0.622	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
COLCA2	120376	hgsc.bcm.edu	37	11	111179054	111179054	+	Silent	SNP	A	A	G	rs3087587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:111179054A>G	ENST00000398035.2	+	5	1115	c.357A>G	c.(355-357)gcA>gcG	p.A119A	COLCA2_ENST00000526216.1_Silent_p.A119A	NM_001136105.2	NP_001129577.1	A8K830	COLC2_HUMAN	colorectal cancer associated 2	119						cytoplasm (GO:0005737)											CTCTCCAGGCAGCAGAGTACT	0.557													G|||	1806	0.360623	0.0545	0.4841	5008	,	,		18587	0.4345		0.5567	False		,,,				2504	0.409				p.A216A		Atlas-SNP	.											.	C11orf93	10	.	0			c.A648G						PASS	.	G		193,1191		18,157,517	95.0	82.0	86.0		357	-12.3	0.0	11	dbSNP_102	86	1779,1403		495,789,307	no	coding-synonymous	C11orf93	NM_001136105.1		513,946,824	GG,GA,AA		44.0918,13.9451,43.1888		119/155	111179054	1972,2594	692	1591	2283	SO:0001819	synonymous_variant	120376	exon5			CCAGGCAGCAGAG	BC042557	CCDS44728.1, CCDS73378.1	11q23.1	2013-10-11	2013-08-22	2013-08-22	ENSG00000214290	ENSG00000214290			26978	protein-coding gene	gene with protein product	"""cancer susceptibility candidate 13"""	615694	"""chromosome 11 open reading frame 93"""	C11orf93		21071539	Standard	NM_001271457		Approved	CASC13	uc031qea.1	A8K830	OTTHUMG00000166657	ENST00000398035.2:c.357A>G	11.37:g.111179054A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	65	0.77381	NM_001271458	E9PMJ8|Q2TBJ3|V5LD62|V5LDI3|V5LDV1|V5LE09|V5LEU3	Silent	SNP	ENST00000398035.2	37	CCDS44728.1																																																																																			G|0.408;N|0.000	0.408	strong		0.557	COLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390991.1	NM_001136105	
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 GAIIx	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		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	151	70	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	
MYBPC2	4606	hgsc.bcm.edu	37	19	50967640	50967640	+	Missense_Mutation	SNP	G	G	A	rs25667	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50967640G>A	ENST00000357701.5	+	27	3317	c.3266G>A	c.(3265-3267)cGt>cAt	p.R1089H		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	1089	Ig-like C2-type 7.		R -> H (in dbSNP:rs25667).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		ATGGAAATCCGTGAAGATCCC	0.537													G|||	705	0.140775	0.0136	0.2522	5008	,	,		20485	0.126		0.2207	False		,,,				2504	0.1667				p.R1089H		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G3266A						PASS	.	G	HIS/ARG	171,4039		2,167,1936	55.0	59.0	58.0		3266	-0.5	0.0	19	dbSNP_72	58	1622,6868		164,1294,2787	yes	missense	MYBPC2	NM_004533.3	29	166,1461,4723	AA,AG,GG		19.1048,4.0618,14.1181	benign	1089/1142	50967640	1793,10907	2105	4245	6350	SO:0001583	missense	4606	exon27			AAATCCGTGAAGA		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.3266G>A	19.37:g.50967640G>A	ENSP00000350332:p.Arg1089His	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	339	0.15521978021978022	9	0.018292682926829267	88	0.2430939226519337	80	0.13986013986013987	162	0.21372031662269128	g	2.377	-0.342929	0.05243	0.040618	0.191048	ENSG00000086967	ENST00000357701	T	0.68331	-0.32	3.99	-0.521	0.11931	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.234288	0.17079	N	0.187854	T	0.00012	0.0000	N	0.16862	0.45	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.06679	-1.0813	9	0.45353	T	0.12	.	5.3863	0.16220	0.2583:0.1555:0.5862:0.0	rs25667;rs2230840;rs17403009;rs17718746;rs52798518;rs56519860;rs61720718;rs17403009	1089	Q14324	MYPC2_HUMAN	H	1089	ENSP00000350332:R1089H	ENSP00000350332:R1089H	R	+	2	0	MYBPC2	55659452	0.000000	0.05858	0.001000	0.08648	0.385000	0.30292	0.074000	0.14662	0.199000	0.20427	0.457000	0.33378	CGT	A|0.143;C|0.000;G|0.857	0.143	strong		0.537	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999753	45999753	+	Missense_Mutation	SNP	C	C	G	rs464424	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45999753C>G	ENST00000400372.1	-	1	728	c.703G>C	c.(703-705)Gtg>Ctg	p.V235L	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	235	22 X 5 AA repeats of C-C-X(3).		V -> L (in dbSNP:rs464424). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GAGATGGGCACGCAGCAGGCG	0.711													.|||	589	0.117612	0.0923	0.0634	5008	,	,		18363	0.2024		0.0626	False		,,,				2504	0.1595				p.V235L		Atlas-SNP	.											.	KRTAP10-5	43	.	0			c.G703C						PASS	.	C	,LEU/VAL	417,3989	194.7+/-219.5	20,377,1806	51.0	61.0	58.0		,703	1.7	0.0	21	dbSNP_80	58	430,8168	129.5+/-187.6	15,400,3884	no	intron,missense	TSPEAR,KRTAP10-5	NM_144991.2,NM_198694.2	,32	35,777,5690	GG,GC,CC		5.0012,9.4644,6.5134	,probably-damaging	,235/272	45999753	847,12157	2203	4299	6502	SO:0001583	missense	386680	exon1			TGGGCACGCAGCA	AJ566384	CCDS42958.1	21q22.3	2007-10-05			ENSG00000241123	ENSG00000241123		"""Keratin associated proteins"""	22969	protein-coding gene	gene with protein product				KRTAP18-5			Standard	NM_198694		Approved	KAP10.5, KAP18.5	uc002zfl.1	P60370	OTTHUMG00000057638	ENST00000400372.1:c.703G>C	21.37:g.45999753C>G	ENSP00000383223:p.Val235Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	226	0.10347985347985347	40	0.08130081300813008	24	0.06629834254143646	122	0.21328671328671328	40	0.052770448548812667	c	9.845	1.192015	0.21954	0.094644	0.050012	ENSG00000241123	ENST00000400372	T	0.00753	5.74	3.59	1.68	0.24146	.	.	.	.	.	T	0.00012	0.0000	M	0.80616	2.505	0.80722	P	0.0	D	0.56287	0.975	D	0.63597	0.916	T	0.44892	-0.9298	8	0.66056	D	0.02	.	6.6908	0.23169	0.0:0.7117:0.1807:0.1076	rs464424	235	P60370	KR105_HUMAN	L	235	ENSP00000383223:V235L	ENSP00000383223:V235L	V	-	1	0	KRTAP10-5	44824181	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-0.031000	0.12287	0.290000	0.22444	-0.384000	0.06662	GTG	C|0.913;G|0.087	0.087	strong		0.711	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
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 GAIIx	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_ENST00000443171.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA|ZNF341_ENST00000342427.2_Silent_p.H637H	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		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	142	75	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			
WWC1	23286	hgsc.bcm.edu	37	5	167850748	167850748	+	Silent	SNP	A	A	G	rs12054944	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:167850748A>G	ENST00000265293.4	+	11	1987	c.1485A>G	c.(1483-1485)tcA>tcG	p.S495S	WWC1_ENST00000521089.1_Silent_p.S495S	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	495					cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		TCCGGCCCTCAGGCTGCATCA	0.632													G|||	3339	0.666733	0.6657	0.6383	5008	,	,		16221	0.9921		0.4473	False		,,,				2504	0.5787				p.S495S		Atlas-SNP	.											WWC1,NS,carcinoma,0,2	WWC1	98	2	0			c.A1485G						PASS	.	G	,,	2774,1632	500.0+/-364.6	861,1052,290	55.0	57.0	56.0		1485,1485,1485	-10.4	0.2	5	dbSNP_120	56	3727,4873	614.4+/-396.2	815,2097,1388	no	coding-synonymous,coding-synonymous,coding-synonymous	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	,,	1676,3149,1678	GG,GA,AA		43.3372,37.0404,49.9846	,,	495/1120,495/1119,495/1114	167850748	6501,6505	2203	4300	6503	SO:0001819	synonymous_variant	23286	exon11			GCCCTCAGGCTGC	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"""WW, C2 and coiled-coil domain containing"""	29435	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 168"""	610533	"""WW, C2 and coiled-coil domain containing 1"""			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.1485A>G	5.37:g.167850748A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Silent	SNP	ENST00000265293.4	37	CCDS4366.1	1438	0.6584249084249084	329	0.6686991869918699	213	0.5883977900552486	571	0.9982517482517482	325	0.4287598944591029	G	7.670	0.686728	0.14973	0.629596	0.433372	ENSG00000113645	ENST00000393895;ENST00000524228	.	.	.	5.22	-10.4	0.00318	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999049553	.	.	.	.	.	.	T	0.16867	-1.0388	3	.	.	.	.	2.1271	0.03741	0.3239:0.2652:0.0693:0.3416	rs12054944;rs17633374;rs59077503;rs12054944	.	.	.	G	457;272	.	.	R	+	1	2	WWC1	167783326	0.000000	0.05858	0.173000	0.22940	0.734000	0.41952	-4.861000	0.00177	-2.954000	0.00292	-0.119000	0.15052	AGG	A|0.448;G|0.552	0.552	strong		0.632	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
C19orf12	83636	hgsc.bcm.edu	37	19	30193721	30193721	+	Silent	SNP	G	G	A	rs10424582	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:30193721G>A	ENST00000392278.2	-	3	483	c.357C>T	c.(355-357)acC>acT	p.T119T	C19orf12_ENST00000392275.1_5'UTR|C19orf12_ENST00000592153.1_Intron|C19orf12_ENST00000392276.1_Silent_p.T44T|C19orf12_ENST00000323670.9_Silent_p.T108T	NM_001031726.3	NP_001026896.2	Q9NSK7	CS012_HUMAN	chromosome 19 open reading frame 12	119					cell death (GO:0008219)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)						Ovarian(5;0.000567)|Breast(6;0.0203)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0435)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.183)			TGACCAGCGCGGTCAGCTGCA	0.622													G|||	3074	0.613818	0.7905	0.5216	5008	,	,		14590	0.3006		0.7565	False		,,,				2504	0.6166				p.T119T		Atlas-SNP	.											.	C19orf12	16	.	0			c.C357T						PASS	.	G	,	3382,1024	722.0+/-409.2	1304,774,125	49.0	49.0	49.0		357,324	-3.8	0.0	19	dbSNP_119	49	6399,2201	706.1+/-405.5	2389,1621,290	no	coding-synonymous,coding-synonymous	C19orf12	NM_001031726.2,NM_031448.3	,	3693,2395,415	AA,AG,GG		25.593,23.241,24.7962	,	119/153,108/142	30193721	9781,3225	2203	4300	6503	SO:0001819	synonymous_variant	83636	exon3			CAGCGCGGTCAGC	AK057185	CCDS12418.2, CCDS42542.1, CCDS59373.1, CCDS74325.1	19q13.11	2013-07-24			ENSG00000131943	ENSG00000131943			25443	protein-coding gene	gene with protein product	"""neurodegeneration with brain iron accumulation 4"""	614297	"""spastic paraplegia 43 (autosomal recessive)"""	SPG43		21981780, 23857908	Standard	NM_031448		Approved	MGC10922, DKFZP762D096, NBIA4	uc002nsj.3	Q9NSK7	OTTHUMG00000149838	ENST00000392278.2:c.357C>T	19.37:g.30193721G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	137	135	0.985401	NM_001031726	B3KQ16|Q0D2Q0|Q6P4C5|Q9BSL7	Silent	SNP	ENST00000392278.2	37	CCDS42542.1																																																																																			G|0.297;A|0.703	0.703	strong		0.622	C19orf12-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313509.2	NM_031448	
PTPN13	5783	hgsc.bcm.edu	37	4	87622624	87622624	+	Missense_Mutation	SNP	G	G	A	rs61730646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:87622624G>A	ENST00000411767.2	+	7	928	c.865G>A	c.(865-867)Ggc>Agc	p.G289S	PTPN13_ENST00000511467.1_Missense_Mutation_p.G289S|PTPN13_ENST00000436978.1_Missense_Mutation_p.G289S|PTPN13_ENST00000316707.6_Missense_Mutation_p.G289S|PTPN13_ENST00000427191.2_Missense_Mutation_p.G289S			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	289					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		ACCCATCCCTGGCATTGATGT	0.428													G|||	43	0.00858626	0.0	0.0029	5008	,	,		20027	0.0		0.008	False		,,,				2504	0.0337				p.G289S		Atlas-SNP	.											.	PTPN13	203	.	0			c.G865A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY,SER/GLY	9,3737		0,9,1864	58.0	56.0	56.0		865,865,865,865	1.6	0.0	4	dbSNP_129	56	86,8134		0,86,4024	yes	missense,missense,missense,missense	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	56,56,56,56	0,95,5888	AA,AG,GG		1.0462,0.2403,0.7939	benign,benign,benign,benign	289/2467,289/2486,289/2295,289/2491	87622624	95,11871	1873	4110	5983	SO:0001583	missense	5783	exon7			ATCCCTGGCATTG		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.865G>A	4.37:g.87622624G>A	ENSP00000407249:p.Gly289Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	G	7.197	0.592654	0.13875	0.002403	0.010462	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.52	1.62	0.23740	.	0.635267	0.13860	N	0.357728	T	0.10723	0.0262	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.09022	0.002;0.002;0.001;0.002	B;B;B;B	0.13407	0.006;0.007;0.003;0.009	T	0.33727	-0.9857	10	0.06494	T	0.89	.	5.6975	0.17863	0.4274:0.1415:0.4311:0.0	rs61730646	289;289;289;289	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	S	289;289;289;289;289;257	ENSP00000408368:G289S;ENSP00000394794:G289S;ENSP00000322675:G289S;ENSP00000407249:G289S;ENSP00000426626:G289S	ENSP00000322675:G289S	G	+	1	0	PTPN13	87841648	0.007000	0.16637	0.002000	0.10522	0.952000	0.60782	0.673000	0.25203	0.231000	0.21079	0.557000	0.71058	GGC	G|0.995;A|0.005	0.005	strong		0.428	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
ABCD4	5826	hgsc.bcm.edu	37	14	74759006	74759006	+	Missense_Mutation	SNP	C	C	T	rs3742801	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74759006C>T	ENST00000356924.4	-	11	1245	c.1102G>A	c.(1102-1104)Gag>Aag	p.E368K	ABCD4_ENST00000557554.1_Intron|AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000298816.7_Missense_Mutation_p.E264K	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	368			E -> K (in dbSNP:rs3742801). {ECO:0000269|PubMed:12111378, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.6}.		cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		AAGCCCCACTCGCTCTCGCCC	0.572													C|||	1354	0.270367	0.1475	0.2723	5008	,	,		20469	0.247		0.3857	False		,,,				2504	0.3405				p.E368K		Atlas-SNP	.											.	ABCD4	54	.	0			c.G1102A						PASS	.	C	LYS/GLU	868,3538	339.4+/-305.8	83,702,1418	91.0	82.0	85.0		1102	1.5	0.5	14	dbSNP_107	85	3128,5472	476.2+/-369.3	553,2022,1725	yes	missense	ABCD4	NM_005050.3	56	636,2724,3143	TT,TC,CC		36.3721,19.7004,30.7243	benign	368/607	74759006	3996,9010	2203	4300	6503	SO:0001583	missense	5826	exon11			CCCACTCGCTCTC	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.1102G>A	14.37:g.74759006C>T	ENSP00000349396:p.Glu368Lys	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	590	0.27014652014652013	65	0.13211382113821138	104	0.287292817679558	138	0.24125874125874125	283	0.3733509234828496	C	13.35	2.210747	0.39102	0.197004	0.363721	ENSG00000119688	ENST00000356924;ENST00000298816	D;D	0.94376	-3.41;-3.14	5.48	1.48	0.22813	ABC transporter, transmembrane domain, type 1 (1);	0.596993	0.19358	N	0.116227	T	0.00012	0.0000	N	0.08118	0	0.49051	P	2.5799999999998047E-4	B;B;B;B	0.14805	0.011;0.001;0.006;0.002	B;B;B;B	0.11329	0.006;0.001;0.001;0.001	T	0.07195	-1.0785	9	0.08381	T	0.77	.	5.2873	0.15708	0.0:0.4646:0.3032:0.2322	rs3742801;rs17782478;rs17850966;rs52835914;rs56756083;rs3742801	264;264;368;368	F8W7M4;B7Z4V6;A8K5L7;O14678	.;.;.;ABCD4_HUMAN	K	368;264	ENSP00000349396:E368K;ENSP00000298816:E264K	ENSP00000298816:E264K	E	-	1	0	ABCD4	73828759	0.003000	0.15002	0.542000	0.28115	0.947000	0.59692	0.007000	0.13174	0.337000	0.23665	0.655000	0.94253	GAG	C|0.710;T|0.290	0.290	strong		0.572	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
P2RY2	5029	hgsc.bcm.edu	37	11	72946020	72946020	+	Silent	SNP	C	C	T	rs1783596	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:72946020C>T	ENST00000311131.2	+	3	1283	c.816C>T	c.(814-816)cgC>cgT	p.R272R	P2RY2_ENST00000393596.2_Silent_p.R272R|P2RY2_ENST00000393597.2_Silent_p.R272R	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	272					cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	ACTCCTTCCGCTCGCTGGACC	0.627													C|||	2888	0.576677	0.5809	0.6628	5008	,	,		16138	0.619		0.5636	False		,,,				2504	0.4796				p.R272R		Atlas-SNP	.											.	P2RY2	54	.	0			c.C816T						PASS	.	C	,,	2488,1912	626.1+/-394.7	730,1028,442	102.0	92.0	95.0		816,816,816	0.9	1.0	11	dbSNP_89	95	4785,3801	611.5+/-395.8	1349,2087,857	yes	coding-synonymous,coding-synonymous,coding-synonymous	P2RY2	NM_002564.2,NM_176071.1,NM_176072.1	,,	2079,3115,1299	TT,TC,CC		44.2697,43.4545,43.9935	,,	272/378,272/378,272/378	72946020	7273,5713	2200	4293	6493	SO:0001819	synonymous_variant	5029	exon3			CTTCCGCTCGCTG	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.816C>T	11.37:g.72946020C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_176071	B2R9W3|Q96EM8	Silent	SNP	ENST00000311131.2	37	CCDS8219.1																																																																																			C|0.425;T|0.575	0.575	strong		0.627	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
SLC22A25	387601	hgsc.bcm.edu	37	11	62984868	62984868	+	Missense_Mutation	SNP	T	T	C	rs11231409	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:62984868T>C	ENST00000306494.6	-	4	747	c.748A>G	c.(748-750)Agc>Ggc	p.S250G	SLC22A10_ENST00000525620.1_Intron|SLC22A25_ENST00000403374.2_Missense_Mutation_p.S84G|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						AAAGCCAGGCTTCCCAGGGTT	0.443													C|||	2145	0.428315	0.2859	0.451	5008	,	,		21477	0.5288		0.3966	False		,,,				2504	0.5337				p.S250G		Atlas-SNP	.											.	SLC22A25	87	.	0			c.A748G						PASS	.	C	GLY/SER	1399,3003	687.4+/-404.8	208,983,1010	138.0	127.0	131.0		748	0.3	0.0	11	dbSNP_120	131	3259,5337	648.8+/-400.5	642,1975,1681	yes	missense	SLC22A25	NM_199352.3	56	850,2958,2691	CC,CT,TT		37.913,31.781,35.8363	benign	250/548	62984868	4658,8340	2201	4298	6499	SO:0001583	missense	387601	exon4			CCAGGCTTCCCAG	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.748A>G	11.37:g.62984868T>C	ENSP00000307443:p.Ser250Gly	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	894	0.40934065934065933	135	0.27439024390243905	136	0.3756906077348066	333	0.5821678321678322	290	0.38258575197889183	C	0.015	-1.546617	0.00926	0.31781	0.37913	ENSG00000196600	ENST00000306494;ENST00000403374	T;T	0.58060	0.44;0.36	3.49	0.346	0.16017	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.787064	0.10545	N	0.662245	T	0.00012	0.0000	N	0.00019	-2.785	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.002	T	0.45338	-0.9268	9	0.02654	T	1	.	6.9208	0.24387	0.0:0.5361:0.0:0.4639	rs11231409;rs52819103;rs60604366;rs11231409	248;250	A4IF29;Q6T423	.;S22AP_HUMAN	G	250;84	ENSP00000307443:S250G;ENSP00000384208:S84G	ENSP00000307443:S250G	S	-	1	0	SLC22A25	62741444	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.206000	0.17375	-0.224000	0.09928	-0.270000	0.10280	AGC	T|0.610;C|0.390	0.390	strong		0.443	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
KIAA1731	85459	hgsc.bcm.edu	37	11	93402006	93402006	+	Silent	SNP	A	A	G	rs61743303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:93402006A>G	ENST00000325212.6	+	4	504	c.342A>G	c.(340-342)gcA>gcG	p.A114A	KIAA1731_ENST00000411936.1_Silent_p.A114A|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	114						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A114A(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CACAGCGGGCAGCAGAAAGGA	0.313													A|||	667	0.133187	0.0908	0.0749	5008	,	,		17069	0.2718		0.0974	False		,,,				2504	0.1258				p.A114A		Atlas-SNP	.											KIAA1731_ENST00000325212,NS,carcinoma,0,1	KIAA1731	173	1	1	Substitution - coding silent(1)	stomach(1)	c.A342G						scavenged	.	A		130,1254		5,120,567	52.0	43.0	46.0		342	3.0	1.0	11	dbSNP_129	46	272,2908		10,252,1328	no	coding-synonymous	KIAA1731	NM_033395.1		15,372,1895	GG,GA,AA		8.5535,9.3931,8.8081		114/2602	93402006	402,4162	692	1590	2282	SO:0001819	synonymous_variant	85459	exon4			GCGGGCAGCAGAA	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.342A>G	11.37:g.93402006A>G		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	96	74	0.770833	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Silent	SNP	ENST00000325212.6	37	CCDS44708.1																																																																																			A|0.867;G|0.133	0.133	strong		0.313	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
TTN	7273	hgsc.bcm.edu	37	2	179458591	179458591	+	Missense_Mutation	SNP	C	C	T	rs2288569	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179458591C>T	ENST00000591111.1	-	248	53737	c.53513G>A	c.(53512-53514)cGt>cAt	p.R17838H	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R19479H|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R10606H|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R10539H|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R10414H|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R16911H|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17838			R -> H. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGTCCAGGACGGTCTGCAGA	0.388													C|||	1064	0.21246	0.0666	0.1513	5008	,	,		20497	0.4544		0.1402	False		,,,				2504	0.2781				p.R19479H		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,-1,5	TTN	18412	5	0			c.G58436A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	284,3428		10,264,1582	54.0	51.0	52.0		31241,50732,31616,31817	6.2	1.0	2	dbSNP_100	52	1208,6994		91,1026,2984	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	101,1290,4566	TT,TC,CC		14.7281,7.6509,12.5231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	10414/26927,16911/33424,10539/27052,10606/27119	179458591	1492,10422	1856	4101	5957	SO:0001583	missense	7273	exon298			CCAGGACGGTCTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.53513G>A	2.37:g.179458591C>T	ENSP00000465570:p.Arg17838His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		423	0.1936813186813187	30	0.06097560975609756	44	0.12154696132596685	244	0.42657342657342656	105	0.13852242744063326	C	18.43	3.621219	0.66787	0.076509	0.147281	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	6.16	6.16	0.99307	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.85859	2.78	0.09310	P	0.99999999872635	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.20472	-1.0274	8	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	rs2288569;rs52796288;rs59952436;rs2288569	10414;10539;10606;17838	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	16911;10414;10606;10539;10412	ENSP00000343764:R16911H;ENSP00000434586:R10414H;ENSP00000340554:R10606H;ENSP00000352154:R10539H	ENSP00000340554:R10606H	R	-	2	0	TTN	179166837	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.807000	0.86032	2.937000	0.99478	0.650000	0.86243	CGT	C|0.818;T|0.182	0.182	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43545893	43545893	+	Silent	SNP	T	T	C	rs1879581	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43545893T>C	ENST00000430334.3	-	5	1123	c.990A>G	c.(988-990)acA>acG	p.T330T	PLEKHM1_ENST00000421073.2_Silent_p.T241T|RN7SL730P_ENST00000583727.1_RNA	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	330					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					TGGGGATCTCTGTTTCTTGGC	0.537													C|||	412	0.0822684	0.0378	0.1556	5008	,	,		19822	0.001		0.1958	False		,,,				2504	0.0573				p.T330T		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.A990G						PASS	.	C		281,4125	800.6+/-415.6	10,261,1932	140.0	137.0	138.0		990	-5.9	0.0	17	dbSNP_92	138	1646,6954	741.1+/-407.1	155,1336,2809	no	coding-synonymous	PLEKHM1	NM_014798.2		165,1597,4741	CC,CT,TT		19.1395,6.3777,14.8162		330/1057	43545893	1927,11079	2203	4300	6503	SO:0001819	synonymous_variant	9842	exon5			GATCTCTGTTTCT	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.990A>G	17.37:g.43545893T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			T|0.863;C|0.137	0.137	strong		0.537	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
FLNC	2318	hgsc.bcm.edu	37	7	128484816	128484816	+	Silent	SNP	A	A	G	rs3734973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128484816A>G	ENST00000325888.8	+	21	3558	c.3297A>G	c.(3295-3297)gtA>gtG	p.V1099V	FLNC_ENST00000346177.6_Silent_p.V1099V	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1099					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GGCTGACCGTAGAGGGCCCCT	0.637													G|||	1903	0.379992	0.6082	0.2248	5008	,	,		19215	0.4891		0.1551	False		,,,				2504	0.3006				p.V1099V		Atlas-SNP	.											FLNC,caecum,carcinoma,+2,1	FLNC	339	1	0			c.A3297G						PASS	.	G	,	2140,1996		574,992,502	57.0	66.0	63.0		3297,3297	2.7	1.0	7	dbSNP_107	63	1392,7054		94,1204,2925	yes	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	668,2196,3427	GG,GA,AA		16.4812,48.2592,28.0718	,	1099/2693,1099/2726	128484816	3532,9050	2068	4223	6291	SO:0001819	synonymous_variant	2318	exon21			GACCGTAGAGGGC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3297A>G	7.37:g.128484816A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			A|0.663;G|0.337	0.337	strong		0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
MB	4151	hgsc.bcm.edu	37	22	36007075	36007075	+	Silent	SNP	C	C	T	rs7293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36007075C>T	ENST00000397326.2	-	2	372	c.174G>A	c.(172-174)gcG>gcA	p.A58A	MB_ENST00000406324.1_Silent_p.A58A|MB_ENST00000359787.1_Silent_p.A58A|MB_ENST00000397328.1_Silent_p.A58A|MB_ENST00000401702.1_Silent_p.A3A	NM_005368.2	NP_005359.1	P02144	MYG_HUMAN	myoglobin	58					brown fat cell differentiation (GO:0050873)|enucleate erythrocyte differentiation (GO:0043353)|heart development (GO:0007507)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			lung(1)	1						AGTCCTCAGACGCCTTCATCT	0.552													C|||	2659	0.53095	0.4501	0.4712	5008	,	,		21677	0.747		0.4483	False		,,,				2504	0.545				p.A58A	GBM(49;694 1113 16998 18419)|Esophageal Squamous(101;120 1973 10459 37086)	Atlas-SNP	.											MB_ENST00000447607,caecum,carcinoma,0,2	MB	7	2	0			c.G174A						PASS	.	C	,,	1974,2432	556.7+/-379.6	421,1132,650	139.0	110.0	120.0		174,174,174	-11.0	0.0	22	dbSNP_52	120	4016,4584	555.6+/-386.7	954,2108,1238	no	coding-synonymous,coding-synonymous,coding-synonymous	MB	NM_005368.2,NM_203377.1,NM_203378.1	,,	1375,3240,1888	TT,TC,CC		46.6977,44.8025,46.0557	,,	58/155,58/155,58/155	36007075	5990,7016	2203	4300	6503	SO:0001819	synonymous_variant	4151	exon3			CTCAGACGCCTTC		CCDS13917.1	22q13.1	2012-10-02			ENSG00000198125	ENSG00000198125			6915	protein-coding gene	gene with protein product		160000				10591208, 2989088	Standard	NM_005368		Approved	PVALB	uc003anz.3	P02144	OTTHUMG00000150606	ENST00000397326.2:c.174G>A	22.37:g.36007075C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	162	71	0.438272	NM_203377	Q52H51|Q5THY7	Silent	SNP	ENST00000397326.2	37	CCDS13917.1																																																																																			C|0.504;T|0.496	0.496	strong		0.552	MB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319057.2	NM_203377	
CBLB	868	hgsc.bcm.edu	37	3	105389153	105389153	+	Silent	SNP	A	A	G	rs11713094	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:105389153A>G	ENST00000264122.4	-	18	2934	c.2613T>C	c.(2611-2613)ccT>ccC	p.P871P	CBLB_ENST00000407712.1_Silent_p.P86P|CBLB_ENST00000394027.3_Silent_p.P849P	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	871	Pro-rich.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						ACCTTCTAGCAGGAGGCAAAG	0.388			Mis S		AML								G|||	1057	0.211062	0.2231	0.2983	5008	,	,		15888	0.1915		0.2306	False		,,,				2504	0.1329				p.P871P	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.T2613C						PASS	.	G		922,3484	737.6+/-410.9	91,740,1372	131.0	115.0	121.0		2613	2.0	1.0	3	dbSNP_120	121	1789,6811	732.2+/-406.8	201,1387,2712	no	coding-synonymous	CBLB	NM_170662.3		292,2127,4084	GG,GA,AA		20.8023,20.926,20.8442		871/983	105389153	2711,10295	2203	4300	6503	SO:0001819	synonymous_variant	868	exon18			TCTAGCAGGAGGC	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.2613T>C	3.37:g.105389153A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	37	CCDS2948.1																																																																																			A|0.789;G|0.211	0.211	strong		0.388	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
SPZ1	84654	hgsc.bcm.edu	37	5	79616083	79616083	+	Missense_Mutation	SNP	G	G	C	rs1862136	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:79616083G>C	ENST00000296739.4	+	1	294	c.49G>C	c.(49-51)Gtt>Ctt	p.V17L		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	17			V -> L (in dbSNP:rs1862136). {ECO:0000269|PubMed:12778315, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(5)|large_intestine(4)|lung(12)|ovary(1)|skin(2)	26		Lung NSC(167;0.0393)|all_lung(232;0.0428)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;3.43e-47)|Epithelial(54;2.25e-41)|all cancers(79;4.19e-36)		CTCCAAAACCGTTAACCCTAC	0.478													C|||	3966	0.791933	0.8555	0.6729	5008	,	,		18587	0.9395		0.6342	False		,,,				2504	0.8006				p.V17L		Atlas-SNP	.											.	SPZ1	60	.	0			c.G49C						PASS	.	C	LEU/VAL	3209,677		1317,575,51	232.0	233.0	233.0		49	1.2	0.0	5	dbSNP_92	233	5591,2705		1884,1823,441	yes	missense	SPZ1	NM_032567.3	32	3201,2398,492	CC,CG,GG		32.6061,17.4215,27.7623	benign	17/431	79616083	8800,3382	1943	4148	6091	SO:0001583	missense	84654	exon1			AAAACCGTTAACC		CCDS43336.1	5q14.1	2014-06-13				ENSG00000164299			30721	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 148"""					11165476, 12778315, 15226296, 15829580, 15899793	Standard	NM_032567		Approved	NYD-TSP1, FLJ25709, PPP1R148	uc003kgn.3	Q9BXG8		ENST00000296739.4:c.49G>C	5.37:g.79616083G>C	ENSP00000369611:p.Val17Leu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	1695	0.7760989010989011	418	0.8495934959349594	247	0.6823204419889503	543	0.9493006993006993	487	0.6424802110817942	C	0.028	-1.351212	0.01256	0.825785	0.673939	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.47177	0.85;1.45	4.19	1.24	0.21308	.	1.343110	0.04997	N	0.468414	T	0.00012	0.0000	N	0.02960	-0.455	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35201	-0.9798	9	0.02654	T	1	-3.9299	4.1624	0.10291	0.0:0.3905:0.3739:0.2355	rs1862136;rs17261570;rs17846065;rs17859059;rs57321756;rs1862136	17	Q9BXG8	SPZ1_HUMAN	L	17	ENSP00000426530:V17L;ENSP00000369611:V17L	ENSP00000369611:V17L	V	+	1	0	SPZ1	79651839	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.295000	0.08298	0.011000	0.14865	-1.481000	0.00988	GTT	G|0.244;C|0.756	0.756	strong		0.478	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567	
DNAH6	1768	hgsc.bcm.edu	37	2	84924823	84924823	+	Missense_Mutation	SNP	T	T	C	rs78190897	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:84924823T>C	ENST00000237449.6	+	46	7657	c.7649T>C	c.(7648-7650)gTa>gCa	p.V2550A	DNAH6_ENST00000398278.2_Missense_Mutation_p.V2501A|DNAH6_ENST00000389394.3_Missense_Mutation_p.V2550A|DNAH6_ENST00000602588.1_Missense_Mutation_p.V522A			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2550	AAA 4. {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(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GCAAAAGAAGTAGGAATTTCT	0.398													T|||	585	0.116813	0.1067	0.1715	5008	,	,		17291	0.0893		0.1382	False		,,,				2504	0.0982				p.V2550A		Atlas-SNP	.											.	DNAH6	194	.	0			c.T7649C						PASS	.	T	ALA/VAL	175,1209		12,151,529	121.0	116.0	118.0		7649	-10.6	0.0	2	dbSNP_131	118	528,2654		42,444,1105	yes	missense	DNAH6	NM_001370.1	64	54,595,1634	CC,CT,TT		16.5933,12.6445,15.3964	benign	2550/4159	84924823	703,3863	692	1591	2283	SO:0001583	missense	1768	exon47			AAGAAGTAGGAAT	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7649T>C	2.37:g.84924823T>C	ENSP00000237449:p.Val2550Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	35	25	0.714286	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	266	0.12179487179487179	43	0.08739837398373984	58	0.16022099447513813	51	0.08916083916083917	114	0.1503957783641161	T	5.764	0.325432	0.10900	0.126445	0.165933	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.42131	0.98;0.98;0.98	5.67	-10.6	0.00265	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	.	.	.	.	T	0.00039	0.0001	N	0.00034	-2.565	0.48696	P	3.1000000000003247E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.48536	-0.9027	8	0.06494	T	0.89	.	23.5218	0.99983	0.0:0.7727:0.0:0.2273	.	2550;2501	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	A	2550;2501;2550	ENSP00000374045:V2550A;ENSP00000381326:V2501A;ENSP00000237449:V2550A	ENSP00000237449:V2550A	V	+	2	0	DNAH6	84778334	0.000000	0.05858	0.012000	0.15200	0.814000	0.46013	-1.615000	0.02055	-2.303000	0.00656	-0.425000	0.05940	GTA	T|0.868;C|0.132	0.132	strong		0.398	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
SLC13A4	26266	hgsc.bcm.edu	37	7	135406176	135406176	+	Silent	SNP	A	A	G	rs4596594	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:135406176A>G	ENST00000354042.4	-	2	884	c.195T>C	c.(193-195)ctT>ctC	p.L65L		NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	65					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						AGAACGGGTAAAGGAAGGCCG	0.617													G|||	2255	0.45028	0.5091	0.3184	5008	,	,		19216	0.4435		0.4553	False		,,,				2504	0.4663				p.L65L		Atlas-SNP	.											SLC13A4,rectum,carcinoma,0,1	SLC13A4	56	1	0			c.T195C						PASS	.	G		2277,2129	577.0+/-384.4	599,1079,525	51.0	44.0	46.0		195	3.4	1.0	7	dbSNP_111	46	3942,4658	601.1+/-394.3	917,2108,1275	no	coding-synonymous	SLC13A4	NM_012450.2		1516,3187,1800	GG,GA,AA		45.8372,48.3205,47.8164		65/627	135406176	6219,6787	2203	4300	6503	SO:0001819	synonymous_variant	26266	exon2			CGGGTAAAGGAAG	AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.195T>C	7.37:g.135406176A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	138	73	0.528986	NM_012450	A4D1Q4|Q8N631	Silent	SNP	ENST00000354042.4	37	CCDS5840.1																																																																																			A|0.531;G|0.469	0.469	strong		0.617	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1	NM_012450	
HPS1	3257	hgsc.bcm.edu	37	10	100190920	100190920	+	Silent	SNP	G	G	A	rs1801287	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:100190920G>A	ENST00000325103.6	-	7	869	c.636C>T	c.(634-636)ctC>ctT	p.L212L	HPS1_ENST00000361490.4_Silent_p.L212L|HPS1_ENST00000467246.1_5'UTR|HPS1_ENST00000338546.5_Silent_p.L212L|MIR4685_ENST00000578185.1_RNA	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	212					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TGGAGTGCACGAGCAGGAAGG	0.622									Hermansky-Pudlak syndrome				G|||	1417	0.282947	0.1369	0.2911	5008	,	,		20397	0.3442		0.2952	False		,,,				2504	0.3988				p.L212L		Atlas-SNP	.											HPS1,NS,carcinoma,0,1	HPS1	65	1	0			c.C636T						PASS	.	G	,	592,3814	258.9+/-262.7	45,502,1656	64.0	56.0	59.0		636,636	-10.6	0.2	10	dbSNP_89	59	2515,6085	408.7+/-349.6	385,1745,2170	no	coding-synonymous,coding-synonymous	HPS1	NM_000195.3,NM_182639.2	,	430,2247,3826	AA,AG,GG		29.2442,13.4362,23.889	,	212/701,212/325	100190920	3107,9899	2203	4300	6503	SO:0001819	synonymous_variant	3257	exon7	Familial Cancer Database	HPS, HPS1-8	GTGCACGAGCAGG	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.636C>T	10.37:g.100190920G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1	601	0.2751831501831502	68	0.13821138211382114	104	0.287292817679558	202	0.3531468531468531	227	0.2994722955145119	G	7.097	0.573403	0.13623	0.134362	0.292442	ENSG00000107521	ENST00000414009	.	.	.	5.3	-10.6	0.00265	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999561151	.	.	.	.	.	.	T	0.12218	-1.0556	3	.	.	.	.	8.2338	0.31614	0.3875:0.4577:0.0859:0.0689	rs1801287;rs17535258;rs1801287	.	.	.	C	80	.	.	R	-	1	0	HPS1	100180910	0.000000	0.05858	0.235000	0.24058	0.788000	0.44548	-1.746000	0.01829	-2.442000	0.00549	-2.005000	0.00442	CGT	G|0.745;A|0.255	0.255	strong		0.622	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
TSPAN2	10100	hgsc.bcm.edu	37	1	115604798	115604798	+	Silent	SNP	C	C	T	rs10776795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:115604798C>T	ENST00000369516.2	-	3	259	c.228G>A	c.(226-228)ggG>ggA	p.G76G	TSPAN2_ENST00000369515.2_Silent_p.G76G|TSPAN2_ENST00000369514.2_Silent_p.G76G	NM_005725.4	NP_005716.2	O60636	TSN2_HUMAN	tetraspanin 2	76					astrocyte development (GO:0014002)|axon development (GO:0061564)|brain development (GO:0007420)|inflammatory response (GO:0006954)|microglia development (GO:0014005)|myelination (GO:0042552)|oligodendrocyte differentiation (GO:0048709)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)				central_nervous_system(1)|large_intestine(4)|lung(3)|pancreas(1)|prostate(1)	10	Lung SC(450;0.211)	all_cancers(81;2.9e-07)|all_epithelial(167;1.42e-06)|all_lung(203;6.72e-06)|Lung NSC(69;1.13e-05)|Acute lymphoblastic leukemia(138;0.191)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|all cancers(265;0.159)|Epithelial(280;0.179)		CTCCGCAGCACCCGAAGAACC	0.627													C|||	1603	0.320088	0.3018	0.3343	5008	,	,		12891	0.4921		0.3012	False		,,,				2504	0.1769				p.G76G		Atlas-SNP	.											TSPAN2,NS,carcinoma,0,1	TSPAN2	37	1	0			c.G228A						PASS	.	C		1292,3114		199,894,1110	54.0	47.0	49.0		228	-4.3	1.0	1	dbSNP_120	49	2512,6082		378,1756,2163	no	coding-synonymous	TSPAN2	NM_005725.4		577,2650,3273	TT,TC,CC		29.2297,29.3236,29.2615		76/222	115604798	3804,9196	2203	4297	6500	SO:0001819	synonymous_variant	10100	exon3			GCAGCACCCGAAG	AF054839	CCDS881.1	1p13.1	2013-02-14			ENSG00000134198	ENSG00000134198		"""Tetraspanins"""	20659	protein-coding gene	gene with protein product		613133				9714763, 11739647	Standard	NM_005725		Approved	TSPAN-2, TSN2, FLJ12082	uc001eft.3	O60636	OTTHUMG00000011878	ENST00000369516.2:c.228G>A	1.37:g.115604798C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	240	113	0.470833	NM_005725	D6PTH4|Q5TET2|Q8WU05	Silent	SNP	ENST00000369516.2	37	CCDS881.1																																																																																			C|0.686;T|0.314	0.314	strong		0.627	TSPAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032828.1	NM_005725	
AASDH	132949	hgsc.bcm.edu	37	4	57204777	57204777	+	Missense_Mutation	SNP	A	A	C	rs8340	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57204777A>C	ENST00000205214.6	-	15	3268	c.3088T>G	c.(3088-3090)Tac>Gac	p.Y1030D	AASDH_ENST00000434343.2_Missense_Mutation_p.Y545D|AASDH_ENST00000602986.1_3'UTR|AASDH_ENST00000451613.1_3'UTR|AASDH_ENST00000513376.1_Missense_Mutation_p.Y930D	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	1030			Y -> D (in dbSNP:rs8340). {ECO:0000269|PubMed:15865210}.		fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)	p.Y1030D(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CTGCCATTGTAGTTATGGAAA	0.413													A|||	1130	0.225639	0.2231	0.379	5008	,	,		18086	0.2153		0.1302	False		,,,				2504	0.229				p.Y1030D		Atlas-SNP	.											AASDH,NS,carcinoma,0,1	AASDH	101	1	1	Substitution - Missense(1)	stomach(1)	c.T3088G						PASS	.	A	ASP/TYR	950,3456	360.6+/-315.3	103,744,1356	93.0	89.0	91.0		3088	2.3	0.0	4	dbSNP_52	91	1096,7504	228.2+/-263.3	69,958,3273	yes	missense	AASDH	NM_181806.2	160	172,1702,4629	CC,CA,AA		12.7442,21.5615,15.7312	benign	1030/1099	57204777	2046,10960	2203	4300	6503	SO:0001583	missense	132949	exon15			CATTGTAGTTATG	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.3088T>G	4.37:g.57204777A>C	ENSP00000205214:p.Tyr1030Asp	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	223	116	0.520179	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	434	0.1987179487179487	100	0.2032520325203252	118	0.3259668508287293	117	0.20454545454545456	99	0.13060686015831136	A	3.749	-0.051936	0.07362	0.215615	0.127442	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343	T;T;T	0.29142	1.58;1.58;1.58	5.9	2.31	0.28768	Quinonprotein alcohol dehydrogenase-like (2);	0.892392	0.10130	N	0.712160	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46345	-0.9198	9	0.27785	T	0.31	4.1894	6.8594	0.24058	0.2768:0.1237:0.5996:0.0	rs8340;rs3193307;rs3733325;rs60987677;rs8340	1030	Q4L235	ACSF4_HUMAN	D	1030;930;545	ENSP00000205214:Y1030D;ENSP00000423760:Y930D;ENSP00000392158:Y545D	ENSP00000205214:Y1030D	Y	-	1	0	AASDH	56899534	0.098000	0.21812	0.000000	0.03702	0.103000	0.19146	1.387000	0.34430	0.125000	0.18397	-0.248000	0.11899	TAC	C|0.176;N|0.000	0.176	strong		0.413	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
ANO7	50636	hgsc.bcm.edu	37	2	242163538	242163538	+	Silent	SNP	G	G	A	rs115620538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242163538G>A	ENST00000274979.8	+	25	2875	c.2772G>A	c.(2770-2772)acG>acA	p.T924T		NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	924					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						CACCCTTCACGGTTCCCAAGG	0.652													G|||	48	0.00958466	0.0	0.0072	5008	,	,		17554	0.0		0.0398	False		,,,				2504	0.0031				p.T924T		Atlas-SNP	.											.	ANO7	136	.	0			c.G2772A						PASS	.	G		49,4357	50.2+/-85.5	0,49,2154	66.0	56.0	59.0		2772	-0.2	0.0	2	dbSNP_132	59	367,8233	121.7+/-180.7	15,337,3948	no	coding-synonymous	ANO7	NM_001001891.3		15,386,6102	AA,AG,GG		4.2674,1.1121,3.1985		924/934	242163538	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	50636	exon25			CTTCACGGTTCCC	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.2772G>A	2.37:g.242163538G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			G|0.974;A|0.026	0.026	strong		0.652	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
MED16	10025	hgsc.bcm.edu	37	19	871222	871222	+	Silent	SNP	G	G	A	rs8100258	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:871222G>A	ENST00000589119.1	-	12	2129	c.2130C>T	c.(2128-2130)gaC>gaT	p.D710D	MED16_ENST00000269814.4_Missense_Mutation_p.T646M|MED16_ENST00000312090.6_Silent_p.D729D|MED16_ENST00000325464.1_Silent_p.D710D|MED16_ENST00000395808.3_Silent_p.D710D|MED16_ENST00000606828.1_5'Flank			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	710					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|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)		CCAGCGCCTCGTCCGGCTCGC	0.706													g|||	640	0.127796	0.084	0.1225	5008	,	,		13479	0.0089		0.2505	False		,,,				2504	0.1871				p.D710D		Atlas-SNP	.											.	MED16	61	.	0			c.C2130T						PASS	.			508,3672		53,402,1635	9.0	9.0	9.0		2130	-5.0	0.1	19	dbSNP_116	9	1957,6373		272,1413,2480	no	coding-synonymous	MED16	NM_005481.2		325,1815,4115	AA,AG,GG		23.4934,12.1531,19.7042		710/878	871222	2465,10045	2090	4165	6255	SO:0001819	synonymous_variant	10025	exon13			CGCCTCGTCCGGC	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.2130C>T	19.37:g.871222G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1	302	0.1382783882783883	51	0.10365853658536585	55	0.15193370165745856	7	0.012237762237762238	189	0.24934036939313983	g	9.363	1.068497	0.20067	0.121531	0.234934	ENSG00000175221	ENST00000269814	.	.	.	4.13	-5.03	0.02973	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.44500	P	0.002557999999999949	B	0.14438	0.01	B	0.15052	0.012	T	0.21759	-1.0236	6	0.39692	T	0.17	-22.4712	11.7769	0.51991	0.7109:0.0:0.2891:0.0	rs8100258	646	Q9Y2X0-4	.	M	646	.	ENSP00000269814:T646M	T	-	2	0	MED16	822222	0.003000	0.15002	0.126000	0.21872	0.229000	0.25112	-1.383000	0.02544	-0.752000	0.04728	-0.244000	0.11960	ACG	G|0.860;A|0.140	0.140	strong		0.706	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
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 GAIIx	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		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	80	33	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	
KDF1	126695	hgsc.bcm.edu	37	1	27278553	27278553	+	Missense_Mutation	SNP	G	G	A	rs3010109	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:27278553G>A	ENST00000320567.5	-	2	407	c.319C>T	c.(319-321)Cgg>Tgg	p.R107W		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		107	Cys-rich.		R -> W (in dbSNP:rs3010109).		developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CTGCATCCCCGCACACAGGCT	0.672													G|||	470	0.0938498	0.0068	0.085	5008	,	,		14326	0.0288		0.173	False		,,,				2504	0.2035				p.R107W		Atlas-SNP	.											.	C1orf172	38	.	0			c.C319T						PASS	.	G	TRP/ARG	138,4262		1,136,2063	15.0	19.0	18.0		319	4.9	1.0	1	dbSNP_101	18	1527,7067		125,1277,2895	yes	missense	C1orf172	NM_152365.2	101	126,1413,4958	AA,AG,GG		17.7682,3.1364,12.8136	possibly-damaging	107/399	27278553	1665,11329	2200	4297	6497	SO:0001583	missense	126695	exon2			ATCCCCGCACACA																												ENST00000320567.5:c.319C>T	1.37:g.27278553G>A	ENSP00000319179:p.Arg107Trp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_152365	Q5QP32|Q8N0S7	Missense_Mutation	SNP	ENST00000320567.5	37	CCDS293.1	229	0.10485347985347986	21	0.042682926829268296	40	0.11049723756906077	25	0.043706293706293704	143	0.18865435356200527	G	18.11	3.549805	0.65311	0.031364	0.177682	ENSG00000175707	ENST00000320567	T	0.28255	1.62	4.92	4.92	0.64577	.	0.566641	0.18788	N	0.131151	T	0.00039	0.0001	N	0.24115	0.695	0.34882	P	0.255348	D	0.59767	0.986	B	0.39876	0.312	T	0.10660	-1.0620	9	0.62326	D	0.03	.	13.491	0.61395	0.0:0.0:1.0:0.0	rs3010109;rs3010109	107	Q8NAX2	CA172_HUMAN	W	107	ENSP00000319179:R107W	ENSP00000319179:R107W	R	-	1	2	C1orf172	27151140	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.282000	0.51693	2.547000	0.85894	0.557000	0.71058	CGG	G|0.894;A|0.106	0.106	strong		0.672	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1		
TUBA3E	112714	hgsc.bcm.edu	37	2	130952038	130952038	+	Splice_Site	SNP	G	G	A	rs13000721	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:130952038G>A	ENST00000312988.7	-	4	477	c.377C>T	c.(376-378)gCg>gTg	p.A126V		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	126			A -> V (in dbSNP:rs13000721).		microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A126V(7)		endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GCACAGATCCGCCTGAGAGAA	0.577																																					p.A126V		Atlas-SNP	.											TUBA3E,NS,carcinoma,0,8	TUBA3E	73	8	7	Substitution - Missense(7)	kidney(7)	c.C377T						scavenged	.						31.0	26.0	28.0					2																	130952038		2195	4267	6462	SO:0001630	splice_region_variant	112714	exon4			AGATCCGCCTGAG	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.376-1C>T	2.37:g.130952038G>A		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	102	16	0.156863	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	729	0.33379120879120877	99	0.20121951219512196	146	0.40331491712707185	247	0.4318181818181818	237	0.31266490765171506	g	9.044	0.990487	0.18966	.	.	ENSG00000152086	ENST00000312988	T	0.66638	-0.22	2.71	1.82	0.25136	Tubulin/FtsZ, GTPase domain (4);	0.305164	0.22723	U	0.056440	T	0.00012	0.0000	L	0.54323	1.7	0.23023	P	0.9984105	B	0.33299	0.407	B	0.40659	0.336	T	0.37663	-0.9696	9	0.87932	D	0	.	7.5288	0.27671	0.1401:0.0:0.8599:0.0	rs13000721;rs52833426;rs13000721	126	Q6PEY2	TBA3E_HUMAN	V	126	ENSP00000318197:A126V	ENSP00000318197:A126V	A	-	2	0	TUBA3E	130668508	1.000000	0.71417	0.941000	0.38009	0.623000	0.37688	6.296000	0.72751	0.488000	0.27723	0.449000	0.29647	GCG	G|0.676;A|0.324	0.324	strong		0.577	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	Missense_Mutation
ENTHD2	146705	hgsc.bcm.edu	37	17	79205736	79205736	+	Silent	SNP	G	G	A	rs11655759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79205736G>A	ENST00000300714.3	-	8	669	c.612C>T	c.(610-612)agC>agT	p.S204S	AC027601.1_ENST00000575922.1_RNA|ENTHD2_ENST00000374769.2_Silent_p.S120S|AC027601.1_ENST00000569559.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	204	Ser-rich.					cytoplasmic vesicle (GO:0031410)											TGCTCAGGTCGCTGTTCTGGG	0.662													G|||	872	0.174121	0.1014	0.2493	5008	,	,		16639	0.0536		0.3857	False		,,,				2504	0.1258				p.S204S		Atlas-SNP	.											.	.	.	.	0			c.C612T						PASS	.	G		661,3745	279.0+/-274.6	55,551,1597	60.0	67.0	65.0		612	-8.4	0.0	17	dbSNP_120	65	3298,5302	487.1+/-372.0	653,1992,1655	no	coding-synonymous	C17orf56	NM_144679.2		708,2543,3252	AA,AG,GG		38.3488,15.0023,30.4398		204/526	79205736	3959,9047	2203	4300	6503	SO:0001819	synonymous_variant	146705	exon8			CAGGTCGCTGTTC	AK056090	CCDS11779.1	17q25.3	2012-07-18	2012-07-18	2012-07-18	ENSG00000167302	ENSG00000167302			26458	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 56"""	C17orf56			Standard	NM_144679		Approved	FLJ31528	uc002jzu.2	Q96N21	OTTHUMG00000177866	ENST00000300714.3:c.612C>T	17.37:g.79205736G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_144679	Q6ZQU0|Q6ZSQ9	Silent	SNP	ENST00000300714.3	37	CCDS11779.1																																																																																			G|0.729;A|0.271	0.271	strong		0.662	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679	
SERHL2	253190	hgsc.bcm.edu	37	22	42970004	42970004	+	Silent	SNP	G	G	C	rs147451679	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:42970004G>C	ENST00000327678.5	+	12	990	c.888G>C	c.(886-888)gtG>gtC	p.V296V	RRP7B_ENST00000357802.2_RNA|SERHL2_ENST00000407614.4_Silent_p.V116V|SERHL2_ENST00000335879.5_Silent_p.V232V|SERHL2_ENST00000340239.4_3'UTR	NM_014509.3	NP_055324.2	Q9NQF3	SERHL_HUMAN	serine hydrolase-like 2	169							hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|lung(3)|skin(1)|stomach(1)	8						CCCAGCACGTGGCCAGTATCA	0.577																																					p.V296V		Atlas-SNP	.											SERHL2,NS,carcinoma,0,3	SERHL2	23	3	0			c.G888C						scavenged	.						132.0	116.0	121.0					22																	42970004		2203	4299	6502	SO:0001819	synonymous_variant	253190	exon12			GCACGTGGCCAGT		CCDS14037.1, CCDS63498.1	22q13	2005-08-09			ENSG00000183569	ENSG00000183569			29446	protein-coding gene	gene with protein product							Standard	NM_014509		Approved		uc003bcr.3	Q9H4I8	OTTHUMG00000150892	ENST00000327678.5:c.888G>C	22.37:g.42970004G>C		Somatic	382	0	0		WXS	Illumina HiSeq	Phase_I	436	57	0.130734	NM_014509	Q5JZ95|Q9UH21	Silent	SNP	ENST00000327678.5	37	CCDS14037.1																																																																																			G|0.998;C|0.002	0.002	strong		0.577	SERHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320454.1	NM_014509	
PCDHB10	56126	hgsc.bcm.edu	37	5	140572668	140572668	+	Silent	SNP	C	C	T	rs597064	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140572668C>T	ENST00000239446.4	+	1	727	c.543C>T	c.(541-543)aaC>aaT	p.N181N		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	181	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCATATTAACATTAGTGGCG	0.478													t|||	2440	0.48722	0.5083	0.5432	5008	,	,		18344	0.5685		0.4076	False		,,,				2504	0.4172				p.N181N		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C543T						PASS	.	A		2071,2335	578.4+/-384.7	491,1089,623	129.0	151.0	144.0		543	-2.5	0.0	5	dbSNP_83	144	3527,5073	626.0+/-397.8	760,2007,1533	no	coding-synonymous	PCDHB10	NM_018930.3		1251,3096,2156	TT,TC,CC		41.0116,47.0041,43.0417		181/801	140572668	5598,7408	2203	4300	6503	SO:0001819	synonymous_variant	56126	exon1			TATTAACATTAGT	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.543C>T	5.37:g.140572668C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	86	33	0.383721	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.561;T|0.439	0.439	strong		0.478	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
PTBP1	5725	hgsc.bcm.edu	37	19	804396	804396	+	Silent	SNP	C	C	T	rs3180287	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:804396C>T	ENST00000349038.4	+	5	466	c.393C>T	c.(391-393)tcC>tcT	p.S131S	PTBP1_ENST00000356948.6_Silent_p.S131S|PTBP1_ENST00000394601.4_Silent_p.S131S|PTBP1_ENST00000350092.4_Intron|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	131	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		TCCAGTTCTCCAACCACAAGG	0.662													C|||	807	0.161142	0.1331	0.268	5008	,	,		14794	0.0228		0.1451	False		,,,				2504	0.2822				p.S131S		Atlas-SNP	.											.	PTBP1	43	.	0			c.C393T						PASS	.	C	,,,	571,3833	251.8+/-258.4	46,479,1677	65.0	56.0	59.0		393,393,393,	1.1	1.0	19	dbSNP_105	59	1274,7326	251.1+/-277.7	86,1102,3112	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	132,1581,4789	TT,TC,CC		14.814,12.9655,14.1879	,,,	131/558,131/551,131/532,	804396	1845,11159	2202	4300	6502	SO:0001819	synonymous_variant	5725	exon5			GTTCTCCAACCAC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.393C>T	19.37:g.804396C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.862;G|0.000;T|0.138	0.138	strong		0.662	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
PCDHGA2	56113	hgsc.bcm.edu	37	5	140720954	140720954	+	Missense_Mutation	SNP	T	T	C	rs66823521	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140720954T>C	ENST00000394576.2	+	1	2416	c.2416T>C	c.(2416-2418)Ttt>Ctt	p.F806L	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_5'Flank	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	806					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAAGAAACGTTTTCTCAGGT	0.393													t|||	223	0.0445288	0.0076	0.085	5008	,	,		21252	0.001		0.1292	False		,,,				2504	0.0235				p.F806L		Atlas-SNP	.											PCDHG_cluster,NS,carcinoma,-2,2	PCDHGA2	205	2	0			c.T2416C						PASS	.	T	,LEU/PHE,LEU/PHE	119,4283		1,117,2083	60.0	64.0	63.0		,2416,2416	-0.9	0.0	5	dbSNP_130	63	1136,7464		65,1006,3229	yes	intron,missense,missense	PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_032009.1	,22,22	66,1123,5312	CC,CT,TT		13.2093,2.7033,9.6524	,,	,806/933,806/824	140720954	1255,11747	2201	4300	6501	SO:0001583	missense	56113	exon1			GAAACGTTTTCTC	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.2416T>C	5.37:g.140720954T>C	ENSP00000378077:p.Phe806Leu	Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	221	98	0.443439	NM_018915	Q52LL6|Q9Y5D5	Missense_Mutation	SNP	ENST00000394576.2	37	CCDS47289.1	123	0.05631868131868132	4	0.008130081300813009	29	0.08011049723756906	0	0.0	90	0.11873350923482849	.	0.234	-1.018508	0.02078	0.027033	0.132093	ENSG00000081853	ENST00000394576	T	0.42900	0.96	3.35	-0.876	0.10624	.	1.381570	0.05478	N	0.554274	T	0.00109	0.0003	N	0.00666	-1.275	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.12863	-1.0531	9	0.06099	T	0.92	.	1.4049	0.02279	0.2755:0.0896:0.1576:0.4774	.	806;806	Q9Y5H1-2;Q9Y5H1	.;PCDG2_HUMAN	L	806	ENSP00000378077:F806L	ENSP00000378077:F806L	F	+	1	0	PCDHGA2	140701138	0.003000	0.15002	0.004000	0.12327	0.030000	0.12068	0.938000	0.28965	-0.250000	0.09555	0.402000	0.26972	TTT	T|0.910;C|0.090	0.090	strong		0.393	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
PARP1	142	hgsc.bcm.edu	37	1	226589958	226589958	+	Silent	SNP	G	G	A	rs1805404	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226589958G>A	ENST00000366794.5	-	2	386	c.243C>T	c.(241-243)gaC>gaT	p.D81D	PARP1_ENST00000366792.1_Silent_p.D81D|PARP1_ENST00000366790.3_Silent_p.D81D|PARP1_ENST00000366791.5_Silent_p.D81D	NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	81					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CTTTCTGCTGGTCATCCCACC	0.587								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					G|||	1093	0.218251	0.115	0.3573	5008	,	,		18540	0.4365		0.1541	False		,,,				2504	0.1002				p.D81D		Atlas-SNP	.											PARP1,colon,carcinoma,-1,1	PARP1	100	1	0			c.C243T						PASS	.	G		553,3853	250.3+/-257.4	37,479,1687	102.0	88.0	93.0		243	3.3	1.0	1	dbSNP_92	93	1368,7232	267.2+/-287.2	124,1120,3056	no	coding-synonymous	PARP1	NM_001618.3		161,1599,4743	AA,AG,GG		15.907,12.5511,14.7701		81/1015	226589958	1921,11085	2203	4300	6503	SO:0001819	synonymous_variant	142	exon2			CTGCTGGTCATCC	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.243C>T	1.37:g.226589958G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_001618	B1ANJ4|Q8IUZ9	Silent	SNP	ENST00000366794.5	37	CCDS1554.1																																																																																			G|0.811;A|0.189	0.189	strong		0.587	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
PMPCA	23203	hgsc.bcm.edu	37	9	139311471	139311471	+	Silent	SNP	C	C	T	rs3812581	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139311471C>T	ENST00000371717.3	+	7	711	c.702C>T	c.(700-702)aaC>aaT	p.N234N	PMPCA_ENST00000399219.3_Silent_p.N103N|PMPCA_ENST00000462616.1_3'UTR	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	234					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		CAAAGATCAACCGAGAGGTGC	0.587													C|||	983	0.196286	0.0598	0.3069	5008	,	,		18840	0.1637		0.2744	False		,,,				2504	0.2556				p.N234N		Atlas-SNP	.											.	PMPCA	29	.	0			c.C702T						PASS	.	C		418,3988	202.1+/-225.0	25,368,1810	77.0	54.0	62.0		702	-7.9	0.0	9	dbSNP_107	62	2431,6169	402.3+/-347.4	328,1775,2197	no	coding-synonymous	PMPCA	NM_015160.1		353,2143,4007	TT,TC,CC		28.2674,9.4871,21.9053		234/526	139311471	2849,10157	2203	4300	6503	SO:0001819	synonymous_variant	23203	exon7			GATCAACCGAGAG	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"""inositol polyphosphate-5-phosphatase, 72 kD"""	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.702C>T	9.37:g.139311471C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	112	62	0.553571	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371717.3	37	CCDS35180.1																																																																																			C|0.785;T|0.215	0.215	strong		0.587	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160	
C5orf60	285679	hgsc.bcm.edu	37	5	179071947	179071947	+	Silent	SNP	A	A	G	rs4645306	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:179071947A>G	ENST00000448248.2	-	1	100	c.75T>C	c.(73-75)atT>atC	p.I25I	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	25						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						GCTCTGTACCAATAACACTGT	0.517																																					p.I25I		Atlas-SNP	.											.	C5orf60	24	.	0			c.T75C						PASS	.						72.0	71.0	71.0					5																	179071947		692	1591	2283	SO:0001819	synonymous_variant	285679	exon1			TGTACCAATAACA	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.75T>C	5.37:g.179071947A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	202	64	0.316832	NM_001142306	A1L488|B7ZM52|B7ZM53	Silent	SNP	ENST00000448248.2	37	CCDS47353.1																																																																																			A|0.743;G|0.257	0.257	strong		0.517	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
NPY5R	4889	hgsc.bcm.edu	37	4	164272703	164272703	+	Silent	SNP	G	G	A	rs11946004	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:164272703G>A	ENST00000515560.1	+	4	2800	c.1278G>A	c.(1276-1278)ggG>ggA	p.G426G	NPY5R_ENST00000506953.1_Silent_p.G426G|NPY5R_ENST00000338566.3_Silent_p.G426G			Q15761	NPY5R_HUMAN	neuropeptide Y receptor Y5	426					cardiac left ventricle morphogenesis (GO:0003214)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of ovulation cycle rhythm (GO:0060112)|negative regulation of apoptotic process (GO:0043066)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuropeptide signaling pathway (GO:0007218)|outflow tract morphogenesis (GO:0003151)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of smooth muscle cell proliferation (GO:0048661)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)|pancreatic polypeptide receptor activity (GO:0001602)|peptide YY receptor activity (GO:0001601)			NS(2)|biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(4)|lung(26)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_hematologic(180;0.166)	Prostate(90;0.109)				TTCTATATGGGTTTCTTAATA	0.338													A|||	414	0.0826677	0.0787	0.0706	5008	,	,		16007	0.0546		0.1083	False		,,,				2504	0.0992				p.G426G	Melanoma(139;1287 1774 9781 19750 25599)	Atlas-SNP	.											.	NPY5R	101	.	0			c.G1278A						PASS	.	A		342,4062	780.8+/-414.5	12,318,1872	87.0	89.0	88.0		1278	-9.9	0.1	4	dbSNP_120	88	991,7609	767.7+/-407.6	43,905,3352	no	coding-synonymous	NPY5R	NM_006174.2		55,1223,5224	AA,AG,GG		11.5233,7.7657,10.2507		426/446	164272703	1333,11671	2202	4300	6502	SO:0001819	synonymous_variant	4889	exon4			ATATGGGTTTCTT	BC042416	CCDS3804.1	4q31-q32	2012-08-08				ENSG00000164129		"""GPCR / Class A : Neuropeptide receptors : Y"""	7958	protein-coding gene	gene with protein product		602001				8700207, 9417917	Standard	NM_006174		Approved	NPYR5	uc003iqn.3	Q15761		ENST00000515560.1:c.1278G>A	4.37:g.164272703G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_006174	Q6GTR7|Q92916	Silent	SNP	ENST00000515560.1	37	CCDS3804.1																																																																																			G|0.899;A|0.101	0.101	strong		0.338	NPY5R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364633.1	NM_006174	
ASPM	259266	hgsc.bcm.edu	37	1	197070442	197070442	+	Missense_Mutation	SNP	G	G	T	rs3762271	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:197070442G>T	ENST00000367409.4	-	18	8195	c.7939C>A	c.(7939-7941)Ctt>Att	p.L2647I	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2647	IQ 28. {ECO:0000255|PROSITE- ProRule:PRU00116}.		L -> I (in dbSNP:rs3762271). {ECO:0000269|PubMed:14574646, ECO:0000269|PubMed:18204051}.		developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						GTTGCTCTAAGGTGGAGATAA	0.363													G|||	1073	0.214257	0.0431	0.2277	5008	,	,		18268	0.1637		0.4105	False		,,,				2504	0.2863				p.L2647I		Atlas-SNP	.											.	ASPM	444	.	0			c.C7939A						PASS	.	G	,ILE/LEU	460,3942	214.5+/-233.7	27,406,1768	66.0	60.0	62.0		,7939	-1.3	0.0	1	dbSNP_107	62	3737,4859	528.1+/-381.3	816,2105,1377	yes	intron,missense	ASPM	NM_001206846.1,NM_018136.4	,5	843,2511,3145	TT,TG,GG		43.4737,10.4498,32.2896	,possibly-damaging	,2647/3478	197070442	4197,8801	2201	4298	6499	SO:0001583	missense	259266	exon18			CTCTAAGGTGGAG	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.7939C>A	1.37:g.197070442G>T	ENSP00000356379:p.Leu2647Ile	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	536	0.2454212454212454	20	0.04065040650406504	101	0.27900552486187846	98	0.17132867132867133	317	0.4182058047493404	G	6.569	0.473256	0.12461	0.104498	0.434737	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.74315	-0.83	4.72	-1.27	0.09347	.	0.800098	0.11415	N	0.566379	T	0.00012	0.0000	L	0.59436	1.845	0.35493	P	0.20087	D;D	0.63046	0.989;0.992	D;P	0.74348	0.983;0.88	T	0.30297	-0.9983	9	0.40728	T	0.16	.	9.5274	0.39173	0.4285:0.0:0.5715:0.0	rs3762271;rs52822679;rs60619702;rs3762271	633;2647	E7EQ84;Q8IZT6	.;ASPM_HUMAN	I	2647;633	ENSP00000356379:L2647I	ENSP00000356376:L633I	L	-	1	0	ASPM	195337065	0.237000	0.23815	0.003000	0.11579	0.172000	0.22775	0.277000	0.18734	-0.167000	0.10871	0.557000	0.71058	CTT	G|0.722;T|0.278	0.278	strong		0.363	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
RBM19	9904	hgsc.bcm.edu	37	12	114374887	114374887	+	Missense_Mutation	SNP	T	T	C	rs2290787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:114374887T>C	ENST00000545145.2	-	16	2071	c.1993A>G	c.(1993-1995)Aca>Gca	p.T665A	RBM19_ENST00000392561.3_Missense_Mutation_p.T665A|RBM19_ENST00000261741.5_Missense_Mutation_p.T665A|RP11-780K2.1_ENST00000550206.1_RNA	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	665			T -> A (in dbSNP:rs2290787). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.T665A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TGTGGGGCTGTGCTGGAGAAG	0.527													C|||	579	0.115615	0.0514	0.0418	5008	,	,		17578	0.1885		0.1103	False		,,,				2504	0.1851				p.T665A		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1993G						PASS	.	C	ALA/THR,ALA/THR,ALA/THR	194,4212		13,168,2022	130.0	129.0	129.0		1993,1993,1993	-7.4	0.1	12	dbSNP_100	129	875,7725		37,801,3462	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	58,58,58	50,969,5484	CC,CT,TT		10.1744,4.4031,8.2193	benign,benign,benign	665/961,665/961,665/961	114374887	1069,11937	2203	4300	6503	SO:0001583	missense	9904	exon16			GGGCTGTGCTGGA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1993A>G	12.37:g.114374887T>C	ENSP00000442053:p.Thr665Ala	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	158	84	0.531646	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	C	7.721	0.697212	0.15106	0.044031	0.101744	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05081	3.5;3.5;3.5	4.5	-7.42	0.01388	Nucleotide-binding, alpha-beta plait (1);	0.638273	0.16199	N	0.225012	T	0.00073	0.0002	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28522	-1.0041	10	0.07990	T	0.79	0.174	2.1166	0.03715	0.1533:0.1255:0.303:0.4182	rs2290787;rs17856103;rs17856172	665	Q9Y4C8	RBM19_HUMAN	A	665	ENSP00000442053:T665A;ENSP00000376344:T665A;ENSP00000261741:T665A	ENSP00000261741:T665A	T	-	1	0	RBM19	112859270	0.076000	0.21285	0.052000	0.19188	0.226000	0.24999	-0.181000	0.09740	-2.257000	0.00695	-1.557000	0.00889	ACA	A|0.076;C|0.019;T|0.905	0.019	strong		0.527	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
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 GAIIx	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	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	22	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	
SYCE1	93426	hgsc.bcm.edu	37	10	135368590	135368590	+	Missense_Mutation	SNP	T	T	C	rs3737031	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135368590T>C	ENST00000343131.5	-	13	1066	c.962A>G	c.(961-963)cAc>cGc	p.H321R	SYCE1_ENST00000432597.2_Intron|SYCE1_ENST00000368517.3_Intron|SPRN_ENST00000541506.1_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	321				H -> R (in Ref. 5; AAH34821). {ECO:0000305}.	synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.H321R(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		CCCTGCTTGGTGTGCAGCTCC	0.552													t|||	775	0.154752	0.0454	0.1715	5008	,	,		20610	0.2698		0.1093	False		,,,				2504	0.2188				p.H321R		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,1	SYCE1	81	1	1	Substitution - Missense(1)	stomach(1)	c.A962G						PASS	.	A	,ARG/HIS,	76,1308		3,70,619	167.0	139.0	147.0		,962,	-0.0	0.0	10	dbSNP_107	147	282,2900		10,262,1319	yes	intron,missense,intron	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	,29,	13,332,1938	CC,CT,TT		8.8624,5.4913,7.8406	,benign,	,321/352,	135368590	358,4208	692	1591	2283	SO:0001583	missense	93426	exon13			GCTTGGTGTGCAG	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.962A>G	10.37:g.135368590T>C	ENSP00000341282:p.His321Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_001143764	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	329	0.15064102564102563	24	0.04878048780487805	62	0.1712707182320442	153	0.2674825174825175	90	0.11873350923482849	t	5.594	0.294345	0.10567	0.054913	0.088624	ENSG00000171772	ENST00000343131	T	0.08634	3.07	3.84	-0.0272	0.13927	.	2.080430	0.01972	N	0.044198	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.11235	0.004	B	0.10450	0.005	T	0.46373	-0.9196	9	0.46703	T	0.11	4.5253	1.2555	0.01990	0.1808:0.104:0.1877:0.5274	rs3737031;rs17846112;rs17859115;rs52813729;rs3737031	321	Q8N0S2	SYCE1_HUMAN	R	321	ENSP00000341282:H321R	ENSP00000341282:H321R	H	-	2	0	SYCE1	135218580	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.269000	0.18589	-0.003000	0.14444	-0.364000	0.07487	CAC	T|0.856;C|0.144	0.144	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
GCNT4	51301	hgsc.bcm.edu	37	5	74324902	74324902	+	Missense_Mutation	SNP	C	C	T	rs4704166	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:74324902C>T	ENST00000322348.4	-	1	1822	c.961G>A	c.(961-963)Gtt>Att	p.V321I		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	321			V -> I (in dbSNP:rs4704166).|V -> L (in dbSNP:rs4704166).		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.V321I(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		AAGTCTTGAACGATGGAGTTG	0.413													N|||	1837	0.366813	0.5295	0.3501	5008	,	,		19819	0.251		0.2982	False		,,,				2504	0.3487				p.V321I		Atlas-SNP	.											GCNT4,NS,carcinoma,0,1	GCNT4	46	1	1	Substitution - Missense(1)	stomach(1)	c.G961A						PASS	.	C	ILE/VAL	2190,2216		550,1090,563	44.0	49.0	47.0		961	0.5	0.0	5	dbSNP_111	47	2324,6276		326,1672,2302	yes	missense	GCNT4	NM_016591.2	29	876,2762,2865	TT,TC,CC		27.0233,49.7049,34.7071	benign	321/454	74324902	4514,8492	2203	4300	6503	SO:0001583	missense	51301	exon1			CTTGAACGATGGA	AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	17973	protein-coding gene	gene with protein product	"""core 2 beta-1,6-N-acetylglucosaminyltransferase 3"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"""		"""glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.961G>A	5.37:g.74324902C>T	ENSP00000317027:p.Val321Ile	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_016591		Missense_Mutation	SNP	ENST00000322348.4	37	CCDS4026.1	747	0.34203296703296704	254	0.516260162601626	117	0.32320441988950277	144	0.2517482517482518	232	0.30606860158311344	.	0.003	-2.484083	0.00163	0.497049	0.270233	ENSG00000176928	ENST00000322348	T	0.11604	2.76	6.06	0.501	0.16925	.	0.638082	0.16922	N	0.194024	T	0.00012	0.0000	N	0.25380	0.74	0.80722	P	0.0	B	0.24882	0.113	B	0.18263	0.021	T	0.35400	-0.9790	9	0.10111	T	0.7	-10.7629	14.9541	0.71098	0.1089:0.8098:0.0:0.0813	rs4704166;rs52805526;rs56892962;rs4704166	321	Q9P109	GCNT4_HUMAN	I	321	ENSP00000317027:V321I	ENSP00000317027:V321I	V	-	1	0	GCNT4	74360658	0.384000	0.25164	0.000000	0.03702	0.004000	0.04260	2.610000	0.46325	-0.207000	0.10187	-1.159000	0.01794	GTT	C|0.657;G|0.000;T|0.343	0.343	strong		0.413	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591	
TRIM69	140691	hgsc.bcm.edu	37	15	45047402	45047402	+	Missense_Mutation	SNP	A	A	G	rs17588988	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:45047402A>G	ENST00000559390.1	+	3	1239	c.311A>G	c.(310-312)aAg>aGg	p.K104R	TRIM69_ENST00000338264.4_Intron|TRIM69_ENST00000560442.1_Intron|TRIM69_ENST00000558173.1_5'UTR|TRIM69_ENST00000329464.4_Missense_Mutation_p.K104R|TRIM69_ENST00000561043.1_Intron|TRIM69_ENST00000558329.1_Intron			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	104	Necessary for nuclear localization. {ECO:0000250}.		K -> R (in dbSNP:rs17588988).		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		GAGAAGATTAAGAAGTTACCC	0.438													A|||	255	0.0509185	0.0968	0.0432	5008	,	,		22016	0.006		0.0567	False		,,,				2504	0.0348				p.K104R	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											.	TRIM69	47	.	0			c.A311G						PASS	.	A	,ARG/LYS	366,4030	187.1+/-213.8	23,320,1855	115.0	102.0	106.0		,311	4.0	1.0	15	dbSNP_123	106	508,8088	142.5+/-198.7	16,476,3806	yes	intron,missense	TRIM69	NM_080745.3,NM_182985.3	,26	39,796,5661	GG,GA,AA		5.9097,8.3258,6.7272	,benign	,104/501	45047402	874,12118	2198	4298	6496	SO:0001583	missense	140691	exon2			AGATTAAGAAGTT	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	17857	protein-coding gene	gene with protein product			"""ring finger protein 36"", ""tripartite motif-containing 69"""	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.311A>G	15.37:g.45047402A>G	ENSP00000453177:p.Lys104Arg	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	96	72	0.75	NM_182985	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Missense_Mutation	SNP	ENST00000559390.1	37	CCDS32220.1	115	0.052655677655677656	46	0.09349593495934959	20	0.055248618784530384	1	0.0017482517482517483	48	0.0633245382585752	A	12.00	1.806778	0.31961	0.083258	0.059097	ENSG00000185880	ENST00000329464	T	0.16897	2.31	5.17	4.04	0.47022	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.53938	D	0.000059	T	0.00300	0.0009	N	0.24115	0.695	0.24382	N	0.994781	P	0.36438	0.553	B	0.32149	0.141	T	0.27971	-1.0058	10	0.07644	T	0.81	.	7.0985	0.25323	0.9002:0.0:0.0998:0.0	rs17588988;rs58042584;rs17588988	104	Q86WT6	TRI69_HUMAN	R	104	ENSP00000332284:K104R	ENSP00000332284:K104R	K	+	2	0	TRIM69	42834694	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	2.265000	0.43311	2.089000	0.63090	0.455000	0.32223	AAG	A|0.936;G|0.064	0.064	strong		0.438	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		
NAMPT	10135	hgsc.bcm.edu	37	7	105903904	105903904	+	Silent	SNP	T	T	C	rs2302559	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:105903904T>C	ENST00000222553.3	-	7	1210	c.903A>G	c.(901-903)tcA>tcG	p.S301S	NAMPT_ENST00000354289.4_Silent_p.S301S	NM_005746.2	NP_005737.1	P43490	NAMPT_HUMAN	nicotinamide phosphoribosyltransferase	301					cell-cell signaling (GO:0007267)|circadian regulation of gene expression (GO:0032922)|NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|nicotinamide metabolic process (GO:0006769)|positive regulation of cell proliferation (GO:0008284)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|nicotinamide phosphoribosyltransferase activity (GO:0047280)|nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14						GTGTACTTCTTGATACTATTA	0.353													C|||	3530	0.704872	0.5696	0.7752	5008	,	,		19586	0.9008		0.6759	False		,,,				2504	0.6656				p.S301S		Atlas-SNP	.											.	NAMPT	37	.	0			c.A903G						PASS	.	C		2490,1916	526.5+/-371.9	730,1030,443	100.0	89.0	92.0		903	-1.9	1.0	7	dbSNP_100	92	5374,3222	471.5+/-368.1	1689,1996,613	no	coding-synonymous	NAMPT	NM_005746.2		2419,3026,1056	CC,CT,TT		37.4826,43.4862,39.517		301/492	105903904	7864,5138	2203	4298	6501	SO:0001819	synonymous_variant	10135	exon7			ACTTCTTGATACT	U02020	CCDS5737.1	7q22.3	2012-10-02	2008-03-27	2008-03-27	ENSG00000105835	ENSG00000105835			30092	protein-coding gene	gene with protein product	"""visfatin"""	608764	"""pre-B-cell colony enhancing factor 1"""	PBEF1		8289818	Standard	NM_005746		Approved	PBEF	uc003vdq.3	P43490	OTTHUMG00000140388	ENST00000222553.3:c.903A>G	7.37:g.105903904T>C		Somatic	325	1	0.00307692		WXS	Illumina HiSeq	Phase_I	257	257	1	NM_005746	A4D0Q9|A4D0R0|Q3KQV0|Q8WW95	Silent	SNP	ENST00000222553.3	37	CCDS5737.1																																																																																			T|0.374;C|0.626	0.626	strong		0.353	NAMPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277146.1	NM_182790	
PGAP1	80055	hgsc.bcm.edu	37	2	197712710	197712710	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:197712710T>G	ENST00000354764.4	-	21	2027	c.1913A>C	c.(1912-1914)aAa>aCa	p.K638T	PGAP1_ENST00000409475.1_3'UTR	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	638					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						AGGATCAACTTTGTATGGTTT	0.284																																					p.K638T		Atlas-SNP	.											PGAP1,caecum,carcinoma,-1,3	PGAP1	84	3	0			c.A1913C						PASS	.						115.0	114.0	114.0					2																	197712710		2202	4296	6498	SO:0001583	missense	80055	exon21			TCAACTTTGTATG		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.1913A>C	2.37:g.197712710T>G	ENSP00000346809:p.Lys638Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	T	19.60	3.858494	0.71834	.	.	ENSG00000197121	ENST00000422382;ENST00000354764	.	.	.	4.09	4.09	0.47781	.	0.000000	0.85682	D	0.000000	T	0.62405	0.2425	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.56511	-0.7967	9	0.15499	T	0.54	-11.6922	13.2227	0.59896	0.0:0.0:0.0:1.0	.	638	Q75T13	PGAP1_HUMAN	T	418;638	.	ENSP00000346809:K638T	K	-	2	0	PGAP1	197420955	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.807000	0.47955	1.707000	0.51288	0.533000	0.62120	AAA	.	.	none		0.284	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
FUT3	2525	hgsc.bcm.edu	37	19	5843784	5843784	+	Missense_Mutation	SNP	A	A	T	rs3894326	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5843784A>T	ENST00000303225.6	-	3	1701	c.1067T>A	c.(1066-1068)aTa>aAa	p.I356K	FUT3_ENST00000589918.1_Missense_Mutation_p.I356K|FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000458379.2_Missense_Mutation_p.I356K|FUT3_ENST00000589620.1_Missense_Mutation_p.I356K	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	356			I -> K (in Le(-); less than 10% reduction in activity; dbSNP:rs3894326). {ECO:0000269|PubMed:7961897, ECO:0000269|PubMed:8063716, ECO:0000269|PubMed:8801770}.		cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						CCAAGCCGCTATGCTGCGCAC	0.642													A|||	482	0.096246	0.0408	0.0504	5008	,	,		17784	0.1478		0.0726	False		,,,				2504	0.1748				p.I356K	Esophageal Squamous(82;745 1728 24593 44831)	Atlas-SNP	.											.	FUT3	30	.	0			c.T1067A	GRCh37	CM940793	FUT3	M	rs3894326	PASS	.	A	LYS/ILE,LYS/ILE,LYS/ILE,LYS/ILE	148,4258	102.1+/-140.7	2,144,2057	58.0	62.0	61.0		1067,1067,1067,1067	2.2	0.2	19	dbSNP_108	61	622,7978	159.1+/-212.4	22,578,3700	no	missense,missense,missense,missense	FUT3	NM_000149.3,NM_001097639.1,NM_001097640.1,NM_001097641.1	102,102,102,102	24,722,5757	TT,TA,AA		7.2326,3.3591,5.9203	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	356/362,356/362,356/362,356/362	5843784	770,12236	2203	4300	6503	SO:0001583	missense	2525	exon3			GCCGCTATGCTGC		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.1067T>A	19.37:g.5843784A>T	ENSP00000305603:p.Ile356Lys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	138	0.06318681318681318	23	0.046747967479674794	13	0.03591160220994475	43	0.07517482517482517	59	0.07783641160949868	A	18.27	3.586525	0.66105	0.033591	0.072326	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.26373	1.74;1.74	2.2	2.2	0.27929	.	1.042650	0.07702	U	0.940582	T	0.05960	0.0155	M	0.91818	3.245	0.42393	D	0.992534	D;P;P;P	0.57899	0.981;0.953;0.953;0.953	D;P;P;P	0.65773	0.938;0.864;0.864;0.864	T	0.17592	-1.0364	10	0.72032	D	0.01	.	8.2938	0.31973	1.0:0.0:0.0:0.0	rs3894326	356;356;356;356	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	K	356	ENSP00000305603:I356K;ENSP00000416443:I356K	ENSP00000305603:I356K	I	-	2	0	FUT3	5794784	0.004000	0.15560	0.214000	0.23707	0.450000	0.32258	1.993000	0.40747	0.959000	0.37980	0.163000	0.16589	ATA	A|0.935;T|0.065	0.065	strong		0.642	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149	
METTL21A	151194	hgsc.bcm.edu	37	2	208477852	208477852	+	Missense_Mutation	SNP	G	G	A	rs2551949	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:208477852G>A	ENST00000411432.1	-	4	791	c.575C>T	c.(574-576)aCt>aTt	p.T192I	METTL21A_ENST00000448007.2_Missense_Mutation_p.T192I|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000272839.3_Missense_Mutation_p.T210I|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000406927.2_Missense_Mutation_p.T192I|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000426075.1_Missense_Mutation_p.T192I|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000442521.1_Missense_Mutation_p.T192I|METTL21A_ENST00000432416.1_Intron	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	192			T -> I (in dbSNP:rs2551949). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						CTTTCTCACAGTAAATTGCCT	0.388													G|||	4528	0.904153	0.8646	0.879	5008	,	,		21589	0.998		0.831	False		,,,				2504	0.954				p.T192I		Atlas-SNP	.											.	METTL21A	24	.	0			c.C575T						PASS	.	G	ILE/THR,ILE/THR	3826,580	771.5+/-413.8	1661,504,38	154.0	154.0	154.0		575,575	2.9	1.0	2	dbSNP_100	154	7025,1575	744.2+/-407.2	2855,1315,130	yes	missense,missense	METTL21A	NM_001127395.1,NM_145280.4	89,89	4516,1819,168	AA,AG,GG		18.314,13.1639,16.5693	possibly-damaging,possibly-damaging	192/219,192/219	208477852	10851,2155	2203	4300	6503	SO:0001583	missense	151194	exon4			CTCACAGTAAATT	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 557b"", ""heat shock protein 70kDa lysine (K) methyltransferase"""	615257	"""family with sequence similarity 119, member A"""	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.575C>T	2.37:g.208477852G>A	ENSP00000415115:p.Thr192Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	121	55	0.454545	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Missense_Mutation	SNP	ENST00000411432.1	37	CCDS2376.1	1943	0.8896520146520146	435	0.8841463414634146	311	0.8591160220994475	572	1.0	625	0.8245382585751979	G	9.518	1.107586	0.20714	0.868361	0.81686	ENSG00000144401	ENST00000411432;ENST00000448007;ENST00000272839;ENST00000406927;ENST00000426075;ENST00000442521	T;T;T;T;T;T	0.16196	2.36;2.36;2.36;2.36;2.36;2.36	4.76	2.88	0.33553	.	0.688774	0.15486	N	0.259817	T	0.00012	0.0000	L	0.46157	1.445	0.33695	P	0.38621300000000003	B	0.20671	0.047	B	0.17979	0.02	T	0.31308	-0.9948	9	0.44086	T	0.13	-7.5229	11.4516	0.50156	0.0:0.1366:0.7213:0.1421	rs2551949;rs17846056;rs17859049;rs59049071;rs2551949	192	Q8WXB1	MT21A_HUMAN	I	192;192;210;192;192;192	ENSP00000415115:T192I;ENSP00000407622:T192I;ENSP00000272839:T210I;ENSP00000385481:T192I;ENSP00000403317:T192I;ENSP00000392062:T192I	ENSP00000272839:T210I	T	-	2	0	METTL21A	208186097	0.999000	0.42202	0.993000	0.49108	0.945000	0.59286	3.042000	0.49815	0.678000	0.31325	0.561000	0.74099	ACT	G|0.142;A|0.858	0.858	strong		0.388	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280	
ZNF407	55628	hgsc.bcm.edu	37	18	72344509	72344509	+	Missense_Mutation	SNP	G	G	A	rs7227263	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72344509G>A	ENST00000299687.5	+	1	1534	c.1534G>A	c.(1534-1536)Ggg>Agg	p.G512R	ZNF407_ENST00000577538.1_Missense_Mutation_p.G512R|ZNF407_ENST00000309902.6_Missense_Mutation_p.G512R|ZNF407_ENST00000582337.1_Missense_Mutation_p.G512R	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	512			G -> R (in dbSNP:rs7227263).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		TCCGGACTCCGGGCTGCATTC	0.562													G|||	339	0.0676917	0.112	0.0663	5008	,	,		18648	0.001		0.1064	False		,,,				2504	0.0378				p.G512R		Atlas-SNP	.											.	ZNF407	231	.	0			c.G1534A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	404,3640		17,370,1635	85.0	93.0	90.0		1534,1534,1534	-9.6	0.0	18	dbSNP_116	90	1156,7212		87,982,3115	yes	missense,missense,missense	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	125,125,125	104,1352,4750	AA,AG,GG		13.8145,9.9901,12.5685	benign,benign,benign	512/1816,512/1661,512/2249	72344509	1560,10852	2022	4184	6206	SO:0001583	missense	55628	exon1			GACTCCGGGCTGC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1534G>A	18.37:g.72344509G>A	ENSP00000299687:p.Gly512Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Missense_Mutation	SNP	ENST00000299687.5	37	CCDS45885.1	173	0.07921245421245421	59	0.11991869918699187	26	0.0718232044198895	0	0.0	88	0.11609498680738786	G	8.956	0.969380	0.18659	0.099901	0.138145	ENSG00000215421	ENST00000299687;ENST00000309902	T;T	0.08984	3.03;3.44	5.78	-9.59	0.00556	.	0.000000	0.18108	U	0.151444	T	0.00039	0.0001	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.01281	0.0;0.0;0.0	T	0.40059	-0.9583	9	0.27785	T	0.31	.	5.3187	0.15870	0.1757:0.2898:0.4351:0.0994	rs7227263;rs57563446;rs7227263	512;512;512	Q9C0G0-3;Q9C0G0-2;Q9C0G0	.;.;ZN407_HUMAN	R	512	ENSP00000299687:G512R;ENSP00000310359:G512R	ENSP00000299687:G512R	G	+	1	0	ZNF407	70473497	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.751000	0.04803	-0.515000	0.06479	-0.806000	0.03193	GGG	G|0.910;A|0.090	0.090	strong		0.562	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
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 GAIIx	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	PLXNB3_ENST00000538776.1_Silent_p.E1493E|SRPK3_ENST00000370104.1_5'Flank|SRPK3_ENST00000393786.3_5'Flank|SRPK3_ENST00000370108.3_5'Flank|SRPK3_ENST00000370100.1_5'Flank|SRPK3_ENST00000370101.3_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		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	47	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		
SENP7	57337	hgsc.bcm.edu	37	3	101177848	101177848	+	Missense_Mutation	SNP	T	T	G	rs6809436|rs386663936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:101177848T>G	ENST00000394095.2	-	4	288	c.235A>C	c.(235-237)Aaa>Caa	p.K79Q	SENP7_ENST00000314261.7_Missense_Mutation_p.K79Q|SENP7_ENST00000348610.3_Missense_Mutation_p.K46Q|SENP7_ENST00000394091.1_Missense_Mutation_p.K46Q|SENP7_ENST00000394094.2_Missense_Mutation_p.K79Q|SENP7_ENST00000358203.3_Missense_Mutation_p.K46Q|Y_RNA_ENST00000364684.1_RNA	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	79			K -> Q (in dbSNP:rs6809436).			intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						ATATGTTTTTTATTTTTATGG	0.338													T|||	357	0.0712859	0.146	0.0591	5008	,	,		16527	0.0		0.0845	False		,,,				2504	0.0389				p.K79Q		Atlas-SNP	.											.	SENP7	170	.	0			c.A235C						PASS	.	T	GLN/LYS,GLN/LYS	625,3781	269.8+/-269.2	50,525,1628	222.0	215.0	218.0		235,235	2.3	0.1	3	dbSNP_116	218	701,7899	173.2+/-223.7	20,661,3619	yes	missense,missense	SENP7	NM_001077203.1,NM_020654.3	53,53	70,1186,5247	GG,GT,TT		8.1512,14.1852,10.1953	benign,benign	79/986,79/1051	101177848	1326,11680	2203	4300	6503	SO:0001583	missense	57337	exon4			GTTTTTTATTTTT		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.235A>C	3.37:g.101177848T>G	ENSP00000377655:p.Lys79Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	120	73	0.608333	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	161	0.07371794871794872	80	0.16260162601626016	21	0.058011049723756904	0	0.0	60	0.079155672823219	T	13.43	2.234760	0.39498	0.141852	0.081512	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.41758	1.97;1.97;0.99;1.84;1.84;1.98	4.78	2.28	0.28536	.	0.250311	0.27495	N	0.019104	T	0.00109	0.0003	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B	0.30281	0.033;0.033;0.275;0.019	B;B;B;B	0.28232	0.022;0.022;0.087;0.01	T	0.08973	-1.0696	9	0.72032	D	0.01	-0.4982	9.0229	0.36211	0.0:0.0:0.3622:0.6378	rs6809436;rs52800936;rs57603507;rs6809436	46;79;46;79	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	Q	79;79;79;46;46;46	ENSP00000377655:K79Q;ENSP00000377654:K79Q;ENSP00000313624:K79Q;ENSP00000377651:K46Q;ENSP00000350936:K46Q;ENSP00000342159:K46Q	ENSP00000313624:K79Q	K	-	1	0	SENP7	102660538	1.000000	0.71417	0.051000	0.19133	0.487000	0.33371	1.220000	0.32491	0.290000	0.22444	0.533000	0.62120	AAA	T|0.902;G|0.098	0.098	strong		0.338	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
RNF19B	127544	hgsc.bcm.edu	37	1	33402515	33402515	+	Silent	SNP	C	C	T	rs35462688	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:33402515C>T	ENST00000373456.7	-	9	2090	c.2091G>A	c.(2089-2091)tcG>tcA	p.S697S	RNF19B_ENST00000356990.5_3'UTR|RNF19B_ENST00000235150.4_Silent_p.S696S	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	697					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CTCTGGGGGTCGAGGGGCAGG	0.592													C|||	274	0.0547125	0.0121	0.1571	5008	,	,		16454	0.0		0.0765	False		,,,				2504	0.0736				p.S697S		Atlas-SNP	.											.	RNF19B	43	.	0			c.G2091A						PASS	.	C	,	110,4296	85.8+/-124.5	0,110,2093	84.0	89.0	87.0		,2091	-10.3	0.1	1	dbSNP_126	87	595,8005	158.3+/-211.8	13,569,3718	yes	utr-3,coding-synonymous	RNF19B	NM_001127361.1,NM_153341.2	,	13,679,5811	TT,TC,CC		6.9186,2.4966,5.4206	,	,697/733	33402515	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	127544	exon9			GGGGGTCGAGGGG	AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"""RING-type (C3HC4) zinc fingers"""	26886	protein-coding gene	gene with protein product		610872	"""IBR domain containing 3"""	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.2091G>A	1.37:g.33402515C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	79	46	0.582278	NM_153341	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Silent	SNP	ENST00000373456.7	37	CCDS372.2																																																																																			C|0.947;T|0.053	0.053	strong		0.592	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341	
FAM86A	196483	hgsc.bcm.edu	37	16	5145474	5145474	+	Silent	SNP	C	C	T	rs7192650	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:5145474C>T	ENST00000427587.4	-	2	206	c.138G>A	c.(136-138)ctG>ctA	p.L46L	FAM86A_ENST00000458008.4_Silent_p.L46L|FAM86A_ENST00000587133.1_Silent_p.L46L	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	46						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						TATCCCGCAGCAGCTCAGAAT	0.488													C|||	541	0.108027	0.034	0.2032	5008	,	,		19172	0.1161		0.1889	False		,,,				2504	0.0491				p.L46L		Atlas-SNP	.											.	FAM86A	32	.	0			c.G138A						PASS	.	C	,	252,4142	141.1+/-176.5	9,234,1954	68.0	71.0	70.0		138,138	4.1	1.0	16	dbSNP_116	70	1546,7046	273.0+/-290.4	151,1244,2901	no	coding-synonymous,coding-synonymous	FAM86A	NM_201400.2,NM_201598.2	,	160,1478,4855	TT,TC,CC		17.9935,5.7351,13.8457	,	46/331,46/297	5145474	1798,11188	2197	4296	6493	SO:0001819	synonymous_variant	196483	exon2			CCGCAGCAGCTCA	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.138G>A	16.37:g.5145474C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	112	110	0.982143	NM_201400	D3DUF0|Q96S85	Silent	SNP	ENST00000427587.4	37	CCDS10529.1																																																																																			C|0.858;T|0.142	0.142	strong		0.488	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400	
DND1	373863	hgsc.bcm.edu	37	5	140052320	140052320	+	Missense_Mutation	SNP	T	T	C	rs201446376	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140052320T>C	ENST00000542735.1	-	3	357	c.314A>G	c.(313-315)tAc>tGc	p.Y105C		NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	105	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTCGAGCTGTAGCGGGCATA	0.687																																					p.Y105C		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	0			c.A314G						scavenged	.						9.0	11.0	10.0					5																	140052320		2177	4273	6450	SO:0001583	missense	373863	exon3			GAGCTGTAGCGGG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.314A>G	5.37:g.140052320T>C	ENSP00000445366:p.Tyr105Cys	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	13	5	0.384615	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.009699	0.54361	.	.	ENSG00000256453	ENST00000542735	T	0.21191	2.02	5.71	5.71	0.89125	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000005	T	0.60573	0.2279	H	0.97365	3.99	0.58432	D	0.999997	D	0.57899	0.981	D	0.63033	0.91	T	0.76116	-0.3077	10	0.87932	D	0	-15.4633	15.6328	0.76926	0.0:0.0:0.0:1.0	.	105	Q8IYX4	DND1_HUMAN	C	105	ENSP00000445366:Y105C	ENSP00000445366:Y105C	Y	-	2	0	DND1	140032504	1.000000	0.71417	1.000000	0.80357	0.203000	0.24098	7.940000	0.87693	2.180000	0.69256	0.377000	0.23210	TAC	T|0.983;C|0.016	0.016	strong		0.687	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
GPSM1	26086	hgsc.bcm.edu	37	9	139235526	139235526	+	Intron	SNP	C	C	A	rs59873903	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139235526C>A	ENST00000440944.1	+	9	1427				GPSM1_ENST00000392945.3_Nonsense_Mutation_p.S428*	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GGGGTGGGATCGAGGCCAGGC	0.662													A|||	1118	0.223243	0.2753	0.1571	5008	,	,		14386	0.2996		0.164	False		,,,				2504	0.182				p.S428X		Atlas-SNP	.											.	GPSM1	50	.	0			c.C1283A						PASS	.						17.0	23.0	21.0					9																	139235526		691	1586	2277	SO:0001627	intron_variant	26086	exon9			TGGGATCGAGGCC	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1207+76C>A	9.37:g.139235526C>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Nonsense_Mutation	SNP	ENST00000440944.1	37	CCDS48055.1	491	0.22481684981684982	164	0.3333333333333333	56	0.15469613259668508	154	0.2692307692307692	117	0.15435356200527706	A	18.32	3.597275	0.66332	.	.	ENSG00000160360	ENST00000392945	.	.	.	1.75	-1.33	0.09172	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	4.7584	0.13095	0.2621:0.5622:0.1757:0.0	rs59873903	.	.	.	X	428	.	ENSP00000376674:S428X	S	+	2	0	GPSM1	138355347	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.274000	0.02820	-0.996000	0.03455	-0.525000	0.04345	TCG	C|0.774;A|0.226	0.226	strong		0.662	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597	
EVC	2121	hgsc.bcm.edu	37	4	5754579	5754579	+	Missense_Mutation	SNP	C	C	T	rs28483498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:5754579C>T	ENST00000264956.6	+	9	1299	c.1115C>T	c.(1114-1116)aCg>aTg	p.T372M	EVC_ENST00000509451.1_Missense_Mutation_p.T372M|EVC_ENST00000382674.2_Missense_Mutation_p.T372M	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	372			T -> M (in dbSNP:rs28483498).		cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				CTGGAGAGGACGATGGGGCGG	0.577													C|||	136	0.0271565	0.0038	0.0331	5008	,	,		18301	0.0		0.0825	False		,,,				2504	0.0256				p.T372M		Atlas-SNP	.											.	EVC	90	.	0			c.C1115T						PASS	.	C	MET/THR	89,4317	73.6+/-111.7	0,89,2114	72.0	69.0	70.0		1115	3.8	0.0	4	dbSNP_125	70	772,7828	181.6+/-230.3	35,702,3563	yes	missense	EVC	NM_153717.2	81	35,791,5677	TT,TC,CC		8.9767,2.02,6.62	probably-damaging	372/993	5754579	861,12145	2203	4300	6503	SO:0001583	missense	2121	exon9			AGAGGACGATGGG	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.1115C>T	4.37:g.5754579C>T	ENSP00000264956:p.Thr372Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	102	72	0.705882	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	82	0.037545787545787544	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	65	0.08575197889182058	C	11.32	1.604900	0.28623	0.0202	0.089767	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.54866	0.55;0.55;0.63	5.56	3.81	0.43845	.	0.252857	0.35495	N	0.003166	T	0.02649	0.0080	L	0.52364	1.645	0.49915	P	1.6799999999994597E-4	D	0.55172	0.97	P	0.47915	0.561	T	0.31251	-0.9950	9	0.33141	T	0.24	.	7.9481	0.29998	0.0:0.7442:0.0:0.2558	rs28483498;rs28483498	372	P57679	EVC_HUMAN	M	372	ENSP00000264956:T372M;ENSP00000372120:T372M;ENSP00000426774:T372M	ENSP00000264956:T372M	T	+	2	0	EVC	5805480	0.025000	0.19082	0.026000	0.17262	0.525000	0.34531	1.078000	0.30754	1.347000	0.45714	0.561000	0.74099	ACG	C|0.947;T|0.053	0.053	strong		0.577	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
CAPRIN2	65981	hgsc.bcm.edu	37	12	30906358	30906358	+	Missense_Mutation	SNP	G	G	A	rs17688567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:30906358G>A	ENST00000395805.2	-	1	887	c.340C>T	c.(340-342)Cct>Tct	p.P114S	CAPRIN2_ENST00000417045.1_Missense_Mutation_p.P114S|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.P114S|CAPRIN2_ENST00000308433.5_5'UTR|RP11-77I22.2_ENST00000500076.2_lincRNA|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.P114S	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)					GCTTGGGAAGGAGATGCAGCA	0.453											OREG0021723	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	188	0.0375399	0.0045	0.072	5008	,	,		19878	0.003		0.0746	False		,,,				2504	0.0552				p.P114S		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.C340T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	51,4355	50.2+/-85.5	0,51,2152	113.0	114.0	114.0		340,340,340,340	4.3	1.0	12	dbSNP_123	114	631,7969	161.7+/-214.6	26,579,3695	yes	missense,missense,missense,missense	CAPRIN2	NM_001002259.1,NM_001206856.1,NM_023925.3,NM_032156.3	74,74,74,74	26,630,5847	AA,AG,GG		7.3372,1.1575,5.2437	probably-damaging,probably-damaging,probably-damaging,probably-damaging	114/1128,114/906,114/1078,114/961	30906358	682,12324	2203	4300	6503	SO:0001583	missense	65981	exon1			GGGAAGGAGATGC	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.340C>T	12.37:g.30906358G>A	ENSP00000379150:p.Pro114Ser	Somatic	125	0	0	820	WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_023925		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	87	0.03983516483516483	4	0.008130081300813009	27	0.07458563535911603	3	0.005244755244755245	53	0.06992084432717678	G	12.29	1.894903	0.33442	0.011575	0.073372	ENSG00000110888	ENST00000298892;ENST00000395805;ENST00000251071;ENST00000417045;ENST00000537108;ENST00000542550;ENST00000540436;ENST00000540584	T;T;T;T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88;1.88;1.88;1.88	5.38	4.29	0.51040	.	0.308243	0.31123	N	0.008213	T	0.00936	0.0031	N	0.11560	0.145	0.80722	D	1	B;B;B;B	0.25850	0.017;0.136;0.022;0.008	B;B;B;B	0.24006	0.021;0.05;0.01;0.011	T	0.12708	-1.0537	10	0.39692	T	0.17	-12.0212	10.657	0.45680	0.0802:0.0:0.7846:0.1352	rs17688567;rs52800765;rs17688567	114;114;114;114	Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2	.;.;CAPR2_HUMAN;.	S	114;114;114;114;33;33;33;33	ENSP00000298892:P114S;ENSP00000379150:P114S;ENSP00000251071:P114S;ENSP00000391479:P114S;ENSP00000438010:P33S;ENSP00000443353:P33S;ENSP00000442295:P33S;ENSP00000441005:P33S	ENSP00000251071:P114S	P	-	1	0	CAPRIN2	30797625	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.359000	0.44142	2.520000	0.84964	0.655000	0.94253	CCT	G|0.953;A|0.047	0.047	strong		0.453	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925	
GTF2H3	2967	hgsc.bcm.edu	37	12	124144395	124144395	+	Silent	SNP	A	A	G	rs1051793	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:124144395A>G	ENST00000543341.2	+	11	769	c.738A>G	c.(736-738)ccA>ccG	p.P246P	GTF2H3_ENST00000228955.7_Silent_p.P205P	NM_001271867.1|NM_001516.3	NP_001258796.1|NP_001507.2	Q13889	TF2H3_HUMAN	general transcription factor IIH, polypeptide 3, 34kDa	246					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|gene expression (GO:0010467)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|translation (GO:0006412)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.1e-05)|Epithelial(86;0.000388)|all cancers(50;0.00362)		TCCCACCCCCAGTTCATGTTG	0.383								Nucleotide excision repair (NER)					A|||	1758	0.351038	0.6135	0.304	5008	,	,		18537	0.0615		0.3817	False		,,,				2504	0.2965				p.P246P	Melanoma(176;111 2022 3038 14733 36962)	Atlas-SNP	.											.	GTF2H3	20	.	0			c.A738G						PASS	.	A		2599,1807	640.4+/-397.3	781,1037,385	124.0	115.0	118.0		738	-7.4	0.0	12	dbSNP_86	118	3479,5121	509.8+/-377.4	699,2081,1520	no	coding-synonymous	GTF2H3	NM_001516.3		1480,3118,1905	GG,GA,AA		40.4535,41.0123,46.7323		246/309	124144395	6078,6928	2203	4300	6503	SO:0001819	synonymous_variant	2967	exon11			ACCCCCAGTTCAT	Z30093	CCDS9252.1, CCDS61275.1, CCDS73544.1	12q24.31	2012-11-05	2002-08-29		ENSG00000111358	ENSG00000111358		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	4657	protein-coding gene	gene with protein product		601750	"""general transcription factor IIH, polypeptide 3 (34kD subunit)"""			8194529	Standard	NM_001516		Approved	BTF2, TFIIH, P34	uc001ufo.2	Q13889	OTTHUMG00000168697	ENST00000543341.2:c.738A>G	12.37:g.124144395A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	159	69	0.433962	NM_001516	B2R819|B4DNZ6|Q7L0G0|Q96AT7	Silent	SNP	ENST00000543341.2	37	CCDS9252.1																																																																																			A|0.577;G|0.423	0.423	strong		0.383	GTF2H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400641.2	NM_001516	
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 GAIIx	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	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	223	64	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 GAIIx	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_ENST00000431317.2_Silent_p.A817A|ARID4A_ENST00000395168.3_Silent_p.A817A|ARID4A_ENST00000348476.3_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		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	16	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 GAIIx	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_ENST00000469376.1_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000366554.2_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	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	47	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	
EPX	8288	hgsc.bcm.edu	37	17	56272390	56272390	+	Silent	SNP	A	A	G	rs2240815	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:56272390A>G	ENST00000225371.5	+	6	770	c.660A>G	c.(658-660)cgA>cgG	p.R220R		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	220					defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	ACCGTGGCCGAGCCCTCATGT	0.607													G|||	2511	0.501398	0.8495	0.2968	5008	,	,		18384	0.244		0.4354	False		,,,				2504	0.5092				p.R220R		Atlas-SNP	.											.	EPX	95	.	0			c.A660G						PASS	.	G		3430,976	365.6+/-317.5	1339,752,112	63.0	59.0	60.0		660	2.2	0.0	17	dbSNP_98	60	3795,4805	613.5+/-396.1	842,2111,1347	no	coding-synonymous	EPX	NM_000502.4		2181,2863,1459	GG,GA,AA		44.1279,22.1516,44.4487		220/716	56272390	7225,5781	2203	4300	6503	SO:0001819	synonymous_variant	8288	exon6			TGGCCGAGCCCTC	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.660A>G	17.37:g.56272390A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_000502	Q4TVP3	Silent	SNP	ENST00000225371.5	37	CCDS11602.1																																																																																			A|0.474;G|0.526	0.526	strong		0.607	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
MPHOSPH6	10200	hgsc.bcm.edu	37	16	82203768	82203768	+	Silent	SNP	G	G	T	rs2303261	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:82203768G>T	ENST00000258169.4	-	1	63	c.13C>A	c.(13-15)Cga>Aga	p.R5R	CTD-2588J6.2_ENST00000563841.1_lincRNA|MPHOSPH6_ENST00000569021.1_Silent_p.R5R|MPHOSPH6_ENST00000563504.1_5'UTR|MPHOSPH6_ENST00000567729.1_5'UTR	NM_005792.2	NP_005783.2	Q99547	MPH6_HUMAN	M-phase phosphoprotein 6	5					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(3)	5						CTTGTCTTTCGCTCGGCCGCC	0.692													G|||	3218	0.642572	0.4054	0.8112	5008	,	,		11750	0.7649		0.7475	False		,,,				2504	0.6094				p.R5R		Atlas-SNP	.											MPHOSPH6,rectum,carcinoma,0,1	MPHOSPH6	16	1	0			c.C13A						PASS	.	G		2089,2305		521,1047,629	27.0	19.0	22.0		13	1.4	0.3	16	dbSNP_100	22	6264,2328		2340,1584,372	no	coding-synonymous	MPHOSPH6	NM_005792.2		2861,2631,1001	TT,TG,GG		27.095,47.5421,35.6769		5/161	82203768	8353,4633	2197	4296	6493	SO:0001819	synonymous_variant	10200	exon1			TCTTTCGCTCGGC	X98263	CCDS10937.1	16q23.3	2008-03-03			ENSG00000135698	ENSG00000135698			7214	protein-coding gene	gene with protein product		605500				8885239	Standard	NM_005792		Approved	MPP6	uc002fgw.3	Q99547	OTTHUMG00000137632	ENST00000258169.4:c.13C>A	16.37:g.82203768G>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	51	19	0.372549	NM_005792	B2RAF0	Silent	SNP	ENST00000258169.4	37	CCDS10937.1																																																																																			G|0.367;T|0.633	0.633	strong		0.692	MPHOSPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269058.1	NM_005792	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362104	105362104	+	Silent	SNP	G	G	A	rs111908946|rs11191741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:105362104G>A	ENST00000369774.4	-	15	3147	c.2871C>T	c.(2869-2871)ttC>ttT	p.F957F	SH3PXD2A_ENST00000355946.2_Silent_p.F929F|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000538130.1_Silent_p.F792F|SH3PXD2A_ENST00000540321.1_Silent_p.F824F			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	957					superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		AGGTCTTGCCGAAGCCCCCGG	0.642													G|||	1618	0.323083	0.1067	0.3559	5008	,	,		18050	0.3502		0.3519	False		,,,				2504	0.5348				p.F929F		Atlas-SNP	.											SH3PXD2A,NS,neuroblastoma,0,1	SH3PXD2A	90	1	0			c.C2787T						scavenged	.	G		686,3720	284.9+/-277.9	56,574,1573	58.0	54.0	55.0		2787	1.1	0.5	10	dbSNP_120	55	3046,5554	457.7+/-364.4	553,1940,1807	no	coding-synonymous	SH3PXD2A	NM_014631.2		609,2514,3380	AA,AG,GG		35.4186,15.5697,28.6944		929/1106	105362104	3732,9274	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			CTTGCCGAAGCCC	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.2871C>T	10.37:g.105362104G>A		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		605	0.27701465201465203	61	0.12398373983739837	122	0.3370165745856354	163	0.28496503496503495	259	0.341688654353562	G	0.009	-1.848781	0.00563	0.155697	0.354186	ENSG00000107957	ENST00000420222	.	.	.	5.02	1.13	0.20643	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999883335	.	.	.	.	.	.	T	0.39099	-0.9630	3	.	.	.	-29.7996	8.6238	0.33877	0.544:0.0:0.456:0.0	rs11191741;rs17339506;rs11191741	.	.	.	W	884	.	.	R	-	1	2	SH3PXD2A	105352094	0.074000	0.21230	0.499000	0.27577	0.147000	0.21601	0.484000	0.22308	-0.041000	0.13558	-0.969000	0.02612	CGG	G|0.718;A|0.282	0.282	strong		0.642	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
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 GAIIx	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_ENST00000303745.7_5'Flank|ATRNL1_ENST00000423111.2_5'UTR	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	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	107	24	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	
LRRC55	219527	hgsc.bcm.edu	37	11	56949691	56949691	+	Missense_Mutation	SNP	G	G	A	rs12364102	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:56949691G>A	ENST00000497933.1	+	1	471	c.324G>A	c.(322-324)atG>atA	p.M108I		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	78					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						ACCTGCCAATGGACACCCGAA	0.612													G|||	333	0.0664936	0.0144	0.0879	5008	,	,		18285	0.0714		0.1113	False		,,,				2504	0.0706				p.M108I		Atlas-SNP	.											.	LRRC55	52	.	0			c.G324A						PASS	.	G	ILE/MET	136,4266	97.1+/-135.8	2,132,2067	59.0	63.0	62.0		324	4.9	0.9	11	dbSNP_120	62	1052,7540	222.2+/-259.3	75,902,3319	yes	missense	LRRC55	NM_001005210.2	10	77,1034,5386	AA,AG,GG		12.2439,3.0895,9.1427	benign	108/342	56949691	1188,11806	2201	4296	6497	SO:0001583	missense	219527	exon1			GCCAATGGACACC		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.324G>A	11.37:g.56949691G>A	ENSP00000419542:p.Met108Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_001005210	A7E2U7|B2RN81	Missense_Mutation	SNP	ENST00000497933.1	37	CCDS31539.1	162	0.07417582417582418	11	0.022357723577235773	35	0.09668508287292818	42	0.07342657342657342	74	0.09762532981530343	G	15.67	2.901736	0.52227	0.030895	0.122439	ENSG00000183908	ENST00000497933	T	0.41065	1.01	5.8	4.89	0.63831	Leucine-rich repeat-containing N-terminal (1);	0.575233	0.18019	N	0.154310	T	0.00271	0.0008	N	0.01668	-0.77	0.23386	P	0.99778324	B	0.09022	0.002	B	0.09377	0.004	T	0.04053	-1.0981	9	0.46703	T	0.11	.	13.5959	0.61988	0.0752:0.0:0.9248:0.0	rs12364102;rs52808242;rs56765576;rs12364102	78	Q6ZSA7	LRC55_HUMAN	I	108	ENSP00000419542:M108I	ENSP00000419542:M108I	M	+	3	0	LRRC55	56706267	1.000000	0.71417	0.894000	0.35097	0.759000	0.43091	4.049000	0.57397	1.455000	0.47813	0.655000	0.94253	ATG	G|0.920;A|0.080	0.080	strong		0.612	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
TPX2	22974	hgsc.bcm.edu	37	20	30354417	30354417	+	Silent	SNP	G	G	A	rs13044019	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:30354417G>A	ENST00000300403.6	+	5	816	c.288G>A	c.(286-288)ccG>ccA	p.P96P	TPX2_ENST00000340513.4_Silent_p.P96P	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	96					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			AATCCATTCCGTCAAATGCTT	0.443													G|||	66	0.0131789	0.0023	0.0274	5008	,	,		15382	0.0		0.0378	False		,,,				2504	0.0061				p.P96P		Atlas-SNP	.											.	TPX2	61	.	0			c.G288A						PASS	.	G		35,4371	40.0+/-72.8	1,33,2169	135.0	131.0	132.0		288	-0.5	0.0	20	dbSNP_121	132	350,8250	118.6+/-178.1	11,328,3961	no	coding-synonymous	TPX2	NM_012112.4		12,361,6130	AA,AG,GG		4.0698,0.7944,2.9602		96/748	30354417	385,12621	2203	4300	6503	SO:0001819	synonymous_variant	22974	exon5			CATTCCGTCAAAT	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.288G>A	20.37:g.30354417G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Silent	SNP	ENST00000300403.6	37	CCDS13190.1																																																																																			G|0.974;A|0.026	0.026	strong		0.443	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
APPL1	26060	hgsc.bcm.edu	37	3	57303684	57303684	+	Missense_Mutation	SNP	A	A	G	rs11544593	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:57303684A>G	ENST00000288266.3	+	22	2246	c.2099A>G	c.(2098-2100)gAa>gGa	p.E700G	ASB14_ENST00000487349.1_Intron|ASB14_ENST00000389601.3_Intron	NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	700			E -> G (in dbSNP:rs11544593).		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		GATTTGGGAGAAGGAGGAAAG	0.443													A|||	364	0.0726837	0.0068	0.1282	5008	,	,		17962	0.004		0.159	False		,,,				2504	0.1043				p.E700G		Atlas-SNP	.											.	APPL1	59	.	0			c.A2099G						PASS	.	A	,GLY/GLU,	191,4215	121.7+/-159.2	3,185,2015	153.0	147.0	149.0		,2099,	5.7	1.0	3	dbSNP_120	149	1470,7130	279.9+/-294.2	132,1206,2962	yes	intron,missense,intron	APPL1,ASB14	NM_001142733.2,NM_012096.2,NM_130387.5	,98,	135,1391,4977	GG,GA,AA		17.093,4.335,12.771	,benign,	,700/710,	57303684	1661,11345	2203	4300	6503	SO:0001583	missense	26060	exon22			TGGGAGAAGGAGG	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"""Pleckstrin homology (PH) domain containing"""	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.2099A>G	3.37:g.57303684A>G	ENSP00000288266:p.Glu700Gly	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_012096	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	191	0.08745421245421245	8	0.016260162601626018	54	0.14917127071823205	2	0.0034965034965034965	127	0.16754617414248021	A	11.55	1.671067	0.29693	0.04335	0.17093	ENSG00000157500	ENST00000288266	T	0.12361	2.69	5.65	5.65	0.86999	.	0.113216	0.64402	D	0.000012	T	0.00039	0.0001	L	0.29908	0.895	0.09310	P	1.0	P	0.34522	0.455	B	0.30105	0.111	T	0.36841	-0.9731	9	0.49607	T	0.09	.	16.1611	0.81712	1.0:0.0:0.0:0.0	rs11544593;rs61231163;rs11544593	700	Q9UKG1	DP13A_HUMAN	G	700	ENSP00000288266:E700G	ENSP00000288266:E700G	E	+	2	0	APPL1	57278724	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.689000	0.91265	2.272000	0.75746	0.460000	0.39030	GAA	A|0.892;G|0.108	0.108	strong		0.443	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	
ARHGEF18	23370	hgsc.bcm.edu	37	19	7524846	7524846	+	Silent	SNP	C	C	T	rs2287914	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:7524846C>T	ENST00000359920.6	+	10	2107	c.1854C>T	c.(1852-1854)gtC>gtT	p.V618V	CTD-2207O23.3_ENST00000593531.1_Missense_Mutation_p.S576L|ARHGEF18_ENST00000319670.9_Silent_p.V460V	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	618					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				GGAAGGTGGTCGAGGCCCGCG	0.657													C|||	938	0.1873	0.1876	0.2233	5008	,	,		18370	0.12		0.2485	False		,,,				2504	0.1677				p.V618V		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.C1854T						PASS	.	C	,	809,3575		79,651,1462	25.0	19.0	21.0		1854,1380	-9.7	0.0	19	dbSNP_100	21	1859,6729		207,1445,2642	no	coding-synonymous,coding-synonymous	ARHGEF18	NM_001130955.1,NM_015318.3	,	286,2096,4104	TT,TC,CC		21.6465,18.4535,20.5674	,	618/1174,460/1016	7524846	2668,10304	2192	4294	6486	SO:0001819	synonymous_variant	23370	exon10			GGTGGTCGAGGCC	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.1854C>T	19.37:g.7524846C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	66	23	0.348485	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	ENST00000359920.6	37	CCDS45946.1																																																																																			C|0.797;T|0.203	0.203	strong		0.657	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
HRH2	3274	hgsc.bcm.edu	37	5	175110779	175110779	+	Silent	SNP	G	G	A	rs1800689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:175110779G>A	ENST00000231683.2	+	1	2316	c.543G>A	c.(541-543)gtG>gtA	p.V181V	HRH2_ENST00000377291.2_Silent_p.V181V	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2	181					digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	TCAATGAAGTGTACGGGCTGG	0.552													G|||	200	0.0399361	0.003	0.036	5008	,	,		20836	0.0456		0.0746	False		,,,				2504	0.0511				p.V181V		Atlas-SNP	.											.	HRH2	108	.	0			c.G543A						PASS	.	G	,	63,4343	57.4+/-93.9	1,61,2141	89.0	75.0	80.0		543,543	-1.7	0.3	5	dbSNP_89	80	548,8052	151.8+/-206.5	17,514,3769	no	coding-synonymous,coding-synonymous	HRH2	NM_001131055.1,NM_022304.2	,	18,575,5910	AA,AG,GG		6.3721,1.4299,4.6978	,	181/398,181/360	175110779	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	3274	exon2			TGAAGTGTACGGG		CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"""GPCR / Class A : Histamine receptors"""	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660	ENST00000231683.2:c.543G>A	5.37:g.175110779G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	NM_001131055	B5BUP7|Q14464|Q7Z5R9	Silent	SNP	ENST00000231683.2	37	CCDS4395.1																																																																																			G|0.952;A|0.048	0.048	strong		0.552	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1		
MCPH1	79648	hgsc.bcm.edu	37	8	6303025	6303025	+	Silent	SNP	G	G	A	rs2584	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:6303025G>A	ENST00000344683.5	+	8	1858	c.1782G>A	c.(1780-1782)acG>acA	p.T594T	MCPH1_ENST00000522905.1_Silent_p.T546T|MCPH1_ENST00000519480.1_Silent_p.T594T	NM_024596.3	NP_078872	Q8NEM0	MCPH1_HUMAN	microcephalin 1	594					cerebral cortex development (GO:0021987)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)	identical protein binding (GO:0042802)		AGPAT5/MCPH1(2)	central_nervous_system(1)|large_intestine(4)|skin(1)	6		Hepatocellular(245;0.0663)		Colorectal(4;0.0505)		ACATGGAGACGTCTACAGAAG	0.423													G|||	662	0.132188	0.0174	0.245	5008	,	,		20565	0.0268		0.338	False		,,,				2504	0.1043				p.T594T	Colon(95;1448 1467 8277 34473 35819)	Atlas-SNP	.											MCPH1,caecum,carcinoma,+1,1	MCPH1	65	1	0			c.G1782A						PASS	.	G	,,	248,3494		9,230,1632	61.0	55.0	57.0		1782,1638,1782	-9.1	0.0	8	dbSNP_36	57	2706,5502		452,1802,1850	no	coding-synonymous,coding-synonymous,coding-synonymous	MCPH1	NM_001172574.1,NM_001172575.1,NM_024596.3	,,	461,2032,3482	AA,AG,GG		32.9678,6.6275,24.7197	,,	594/611,546/563,594/836	6303025	2954,8996	1871	4104	5975	SO:0001819	synonymous_variant	79648	exon8			GGAGACGTCTACA	AK022909	CCDS43689.1, CCDS55190.1, CCDS55191.1	8p23.1	2012-11-26	2007-11-26		ENSG00000147316	ENSG00000147316			6954	protein-coding gene	gene with protein product	"""BRCT-repeat inhibitor of TERT expression 1"""	607117	"""microcephaly, primary autosomal recessive 1"""			9683597, 17925396	Standard	NM_024596		Approved	FLJ12847, BRIT1	uc003wqi.3	Q8NEM0	OTTHUMG00000163618	ENST00000344683.5:c.1782G>A	8.37:g.6303025G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	141	76	0.539007	NM_001172574	B4DWW2|E9PGU5|E9PH63|Q66GU1|Q9H9C7	Silent	SNP	ENST00000344683.5	37	CCDS43689.1																																																																																			G|0.814;A|0.186	0.186	strong		0.423	MCPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374532.2	NM_024596	
TM4SF20	79853	hgsc.bcm.edu	37	2	228243905	228243905	+	Missense_Mutation	SNP	G	G	A	rs7574414	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:228243905G>A	ENST00000304568.3	-	1	117	c.80C>T	c.(79-81)gCg>gTg	p.A27V		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	27			A -> V (in dbSNP:rs7574414). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A27V(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		TAGAGGTATCGCATTGAGAAC	0.483													G|||	530	0.105831	0.0068	0.0807	5008	,	,		19698	0.1935		0.1511	False		,,,				2504	0.1207				p.A27V		Atlas-SNP	.											TM4SF20,NS,carcinoma,0,1	TM4SF20	24	1	1	Substitution - Missense(1)	stomach(1)	c.C80T						PASS	.	G	VAL/ALA	115,4291	87.8+/-126.4	0,115,2088	127.0	125.0	126.0		80	1.8	0.0	2	dbSNP_116	126	1209,7391	244.2+/-273.5	81,1047,3172	yes	missense	TM4SF20	NM_024795.3	64	81,1162,5260	AA,AG,GG		14.0581,2.6101,10.1799	benign	27/230	228243905	1324,11682	2203	4300	6503	SO:0001583	missense	79853	exon1			GGTATCGCATTGA	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.80C>T	2.37:g.228243905G>A	ENSP00000303028:p.Ala27Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	CCDS2466.1	275	0.1259157509157509	4	0.008130081300813009	32	0.08839779005524862	114	0.1993006993006993	125	0.16490765171503957	G	3.354	-0.131890	0.06753	0.026101	0.140581	ENSG00000168955	ENST00000304568	T	0.26518	1.73	5.77	1.78	0.24846	.	0.883848	0.09827	N	0.750664	T	0.00012	0.0000	L	0.41356	1.27	0.80722	P	0.0	D	0.53462	0.96	B	0.37047	0.24	T	0.10917	-1.0609	9	0.06891	T	0.86	-3.7897	5.2601	0.15567	0.1976:0.3385:0.4638:0.0	rs7574414;rs7574414	27	Q53R12	T4S20_HUMAN	V	27	ENSP00000303028:A27V	ENSP00000303028:A27V	A	-	2	0	TM4SF20	227952149	0.000000	0.05858	0.034000	0.17996	0.029000	0.11900	0.089000	0.15002	0.711000	0.32018	0.591000	0.81541	GCG	G|0.889;A|0.111	0.111	strong		0.483	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795	
USP40	55230	hgsc.bcm.edu	37	2	234386134	234386134	+	Silent	SNP	A	A	G	rs2971863	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:234386134A>G	ENST00000427112.2	-	31	3647	c.3612T>C	c.(3610-3612)caT>caC	p.H1204H	USP40_ENST00000251722.6_Silent_p.H1204H|USP40_ENST00000450966.1_Silent_p.H1216H			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1204					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		TGCTCTGCTCATGGAGGGCTT	0.582													G|||	1283	0.25619	0.5053	0.1542	5008	,	,		18552	0.1438		0.2455	False		,,,				2504	0.1186				p.H1216H		Atlas-SNP	.											.	USP40	174	.	0			c.T3648C						PASS	.	G		1725,2407		364,997,705	53.0	59.0	57.0		3648	-5.2	0.0	2	dbSNP_101	57	1772,6656		190,1392,2632	no	coding-synonymous	USP40	NM_018218.2		554,2389,3337	GG,GA,AA		21.0252,41.7473,27.8424		1216/1248	234386134	3497,9063	2066	4214	6280	SO:0001819	synonymous_variant	55230	exon31			CTGCTCATGGAGG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3612T>C	2.37:g.234386134A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_018218	Q6NX38|Q70EL0	Silent	SNP	ENST00000427112.2	37	CCDS46547.1																																																																																			A|0.746;G|0.254	0.254	strong		0.582	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
DNAJB9	4189	hgsc.bcm.edu	37	7	108212353	108212353	+	Silent	SNP	G	G	A	rs1043615	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:108212353G>A	ENST00000249356.3	+	2	729	c.183G>A	c.(181-183)ccG>ccA	p.P61P	DNAJB9_ENST00000465725.1_3'UTR|THAP5_ENST00000313516.5_5'Flank|THAP5_ENST00000493722.1_5'Flank|THAP5_ENST00000415914.3_5'Flank|THAP5_ENST00000438865.1_5'Flank	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	61	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						ATAAGAGCCCGGATGCTGAAG	0.413													G|||	2396	0.478435	0.2648	0.5836	5008	,	,		15419	0.6369		0.497	False		,,,				2504	0.5102				p.P61P		Atlas-SNP	.											.	DNAJB9	25	.	0			c.G183A						PASS	.	G		1313,3093	439.4+/-345.7	214,885,1104	75.0	82.0	80.0		183	-1.5	1.0	7	dbSNP_86	80	4526,4074	591.3+/-392.8	1181,2164,955	yes	coding-synonymous	DNAJB9	NM_012328.2		1395,3049,2059	AA,AG,GG		47.3721,29.8003,44.8947		61/224	108212353	5839,7167	2203	4300	6503	SO:0001819	synonymous_variant	4189	exon2			GAGCCCGGATGCT	AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"""Heat shock proteins / DNAJ (HSP40)"""	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.183G>A	7.37:g.108212353G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_012328		Silent	SNP	ENST00000249356.3	37	CCDS5752.1																																																																																			G|0.543;A|0.457	0.457	strong		0.413	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1		
C9orf50	375759	hgsc.bcm.edu	37	9	132377900	132377900	+	Missense_Mutation	SNP	C	C	T	rs918165	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:132377900C>T	ENST00000372478.4	-	4	944	c.743G>A	c.(742-744)aGg>aAg	p.R248K	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	248			R -> K (in dbSNP:rs918165).							central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				AGCCTTGAGCCTGGGGACCTG	0.687													N|||	2788	0.556709	0.711	0.5216	5008	,	,		17511	0.498		0.4513	False		,,,				2504	0.5419				p.R248K		Atlas-SNP	.											.	C9orf50	25	.	0			c.G743A						PASS	.		LYS/ARG	2947,1459		975,997,231	51.0	50.0	50.0		743	-0.7	0.0	9	dbSNP_86	50	3357,5243		648,2061,1591	yes	missense	C9orf50	NM_199350.3	26	1623,3058,1822	TT,TC,CC		39.0349,33.1139,48.4699	benign	248/432	132377900	6304,6702	2203	4300	6503	SO:0001583	missense	375759	exon4			TTGAGCCTGGGGA	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.743G>A	9.37:g.132377900C>T	ENSP00000361556:p.Arg248Lys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	40	38	0.95	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	1162	0.532051282051282	356	0.7235772357723578	184	0.5082872928176796	288	0.5034965034965035	334	0.44063324538258575	N	0.201	-1.044468	0.01997	0.668861	0.390349	ENSG00000179058	ENST00000372478	T	0.15139	2.45	3.1	-0.718	0.11205	.	1.402030	0.05197	N	0.504289	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36962	-0.9726	9	0.06099	T	0.92	-0.0034	3.8899	0.09114	0.0:0.3712:0.2074:0.4215	rs918165;rs17507612;rs59121984	248	Q5SZB4	CI050_HUMAN	K	248	ENSP00000361556:R248K	ENSP00000361556:R248K	R	-	2	0	C9orf50	131417721	0.002000	0.14202	0.001000	0.08648	0.040000	0.13550	-0.826000	0.04429	-0.455000	0.07054	-0.867000	0.03001	AGG	C|0.491;T|0.509	0.509	strong		0.687	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350	
MYOM2	9172	hgsc.bcm.edu	37	8	2021421	2021421	+	Missense_Mutation	SNP	G	G	T	rs2272720	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:2021421G>T	ENST00000262113.4	+	10	1102	c.961G>T	c.(961-963)Gtg>Ttg	p.V321L	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	321	Ig-like C2-type 2.		V -> L (in dbSNP:rs2272720). {ECO:0000269|PubMed:7505783}.		muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TCTTTCAGACGTGCTGTTGAA	0.562													G|||	1402	0.279952	0.0257	0.379	5008	,	,		19795	0.3601		0.4046	False		,,,				2504	0.3425				p.V321L		Atlas-SNP	.											.	MYOM2	251	.	0			c.G961T						PASS	.	G	LEU/VAL	419,3987	205.2+/-227.1	16,387,1800	94.0	84.0	87.0		961	4.6	0.7	8	dbSNP_100	87	3691,4909	528.5+/-381.4	816,2059,1425	yes	missense	MYOM2	NM_003970.2	32	832,2446,3225	TT,TG,GG		42.9186,9.5098,31.6008	benign	321/1466	2021421	4110,8896	2203	4300	6503	SO:0001583	missense	9172	exon10			TCAGACGTGCTGT		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.961G>T	8.37:g.2021421G>T	ENSP00000262113:p.Val321Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	676	0.30952380952380953	13	0.026422764227642278	148	0.4088397790055249	207	0.3618881118881119	308	0.40633245382585753	G	8.677	0.904279	0.17760	0.095098	0.429186	ENSG00000036448	ENST00000262113	T	0.66815	-0.23	4.63	4.63	0.57726	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.323580	0.29342	N	0.012422	T	0.00012	0.0000	L	0.42686	1.345	0.09310	P	1.0	B	0.12013	0.005	B	0.17098	0.017	T	0.33828	-0.9853	9	0.20519	T	0.43	.	17.4931	0.87710	0.0:0.0:1.0:0.0	rs2272720;rs59193087;rs2272720	321	P54296	MYOM2_HUMAN	L	321	ENSP00000262113:V321L	ENSP00000262113:V321L	V	+	1	0	MYOM2	2008828	1.000000	0.71417	0.666000	0.29783	0.015000	0.08874	5.607000	0.67648	2.093000	0.63338	0.655000	0.94253	GTG	G|0.687;T|0.313	0.313	strong		0.562	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
MUC16	94025	hgsc.bcm.edu	37	19	9046876	9046876	+	Missense_Mutation	SNP	G	G	T	rs4804378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9046876G>T	ENST00000397910.4	-	5	34958	c.34755C>A	c.(34753-34755)agC>agA	p.S11585R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11587	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAACCGTTGTGCTGGTTTCTG	0.522													G|||	927	0.185104	0.062	0.2752	5008	,	,		23096	0.3363		0.167	False		,,,				2504	0.1503				p.S11585R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C34755A						PASS	.		ARG/SER	303,3659		15,273,1693	137.0	134.0	135.0		34755	-0.2	0.0	19	dbSNP_111	135	1507,6803		139,1229,2787	yes	missense	MUC16	NM_024690.2	110	154,1502,4480	TT,TG,GG		18.1348,7.6477,14.749	benign	11585/14508	9046876	1810,10462	1981	4155	6136	SO:0001583	missense	94025	exon5			CGTTGTGCTGGTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34755C>A	19.37:g.9046876G>T	ENSP00000381008:p.Ser11585Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	464	0.21245421245421245	34	0.06910569105691057	91	0.2513812154696133	213	0.3723776223776224	126	0.1662269129287599	g	4.341	0.062787	0.08388	0.076477	0.181348	ENSG00000181143	ENST00000397910	T	0.03181	4.02	2.29	-0.244	0.13031	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	.	.	.	B	0.30889	0.299	B	0.24394	0.053	T	0.45659	-0.9246	8	0.87932	D	0	.	4.6081	0.12387	0.0:0.1924:0.3015:0.506	rs4804378;rs52826356;rs57949188;rs4804378	11585	B5ME49	.	R	11585	ENSP00000381008:S11585R	ENSP00000381008:S11585R	S	-	3	2	MUC16	8907876	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.329000	0.02677	-0.010000	0.14271	0.197000	0.17608	AGC	G|0.807;T|0.193	0.193	strong		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NOX3	50508	hgsc.bcm.edu	37	6	155775980	155775980	+	Silent	SNP	G	G	T	rs12195525	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:155775980G>T	ENST00000159060.2	-	3	322	c.220C>A	c.(220-222)Cga>Aga	p.R74R		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	74	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		ATAAGGTTTCGACTGACAGGT	0.368													G|||	644	0.128594	0.1067	0.2291	5008	,	,		17917	0.1171		0.1044	False		,,,				2504	0.1237				p.R74R		Atlas-SNP	.											NOX3,rectum,carcinoma,+1,1	NOX3	93	1	0			c.C220A						PASS	.	G		472,3934	216.1+/-234.9	30,412,1761	65.0	65.0	65.0		220	5.9	1.0	6	dbSNP_120	65	965,7635	208.9+/-250.2	57,851,3392	no	coding-synonymous	NOX3	NM_015718.2		87,1263,5153	TT,TG,GG		11.2209,10.7127,11.0487		74/569	155775980	1437,11569	2203	4300	6503	SO:0001819	synonymous_variant	50508	exon3			GGTTTCGACTGAC	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.220C>A	6.37:g.155775980G>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	37	CCDS5250.1																																																																																			G|0.886;T|0.114	0.114	strong		0.368	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
ARMC4	55130	hgsc.bcm.edu	37	10	28257853	28257853	+	Splice_Site	SNP	G	G	C	rs57067036	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:28257853G>C	ENST00000305242.5	-	9	1329	c.1237C>G	c.(1237-1239)Cgg>Ggg	p.R413G	ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000537576.1_Splice_Site_p.R105G|ARMC4_ENST00000545014.1_Intron|ARMC4_ENST00000239715.3_Splice_Site_p.R270G	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	413					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.R413G(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						GAAACATACCGAAGTAATTGT	0.453													G|||	402	0.0802716	0.1082	0.1037	5008	,	,		17999	0.0099		0.0845	False		,,,				2504	0.0941				p.R413G		Atlas-SNP	.											ARMC4,rectum,NS,0,1	ARMC4	177	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1237G						scavenged	.						4.0	3.0	3.0					10																	28257853		1476	3114	4590	SO:0001630	splice_region_variant	55130	exon9			CATACCGAAGTAA	AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1238+1C>G	10.37:g.28257853G>C		Somatic	601	116	0.193012		WXS	Illumina HiSeq	Phase_I	756	374	0.494709	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	G	1.710	-0.499285	0.04291	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	3.89	2.01	0.26516	.	1.074070	0.07060	N	0.833582	T	0.32645	0.0836	L	0.54323	1.7	0.09310	N	1	B	0.23650	0.089	B	0.20184	0.028	T	0.29761	-1.0001	10	0.42905	T	0.14	-2.5181	5.8125	0.18473	0.1073:0.1956:0.6971:0.0	.	413	Q5T2S8	ARMC4_HUMAN	G	105;413;105;307;270	ENSP00000443208:R105G;ENSP00000306410:R413G;ENSP00000398155:R307G;ENSP00000239715:R270G	ENSP00000239715:R270G	R	-	1	2	ARMC4	28297859	0.264000	0.24093	0.040000	0.18447	0.005000	0.04900	0.581000	0.23819	0.598000	0.29829	-0.232000	0.12228	CGG	G|0.500;C|0.500	0.500	strong		0.453	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	Missense_Mutation
FCGBP	8857	hgsc.bcm.edu	37	19	40368520	40368520	+	Silent	SNP	G	G	C	rs36079378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40368520G>C	ENST00000221347.6	-	28	12835	c.12828C>G	c.(12826-12828)ggC>ggG	p.G4276G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4276	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.G4276G(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGAAGCCAGGGCCCTCGTACT	0.652													G|||	2378	0.47484	0.5643	0.3026	5008	,	,		15152	0.5853		0.3698	False		,,,				2504	0.4703				p.G4276G		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - coding silent(1)	stomach(1)	c.C12828G						scavenged	.						49.0	51.0	51.0					19																	40368520		2203	4295	6498	SO:0001819	synonymous_variant	8857	exon28			GCCAGGGCCCTCG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12828C>G	19.37:g.40368520G>C		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	189	73	0.386243	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.500;C|0.500	0.500	strong		0.652	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
BOD1	91272	hgsc.bcm.edu	37	5	173036257	173036257	+	Silent	SNP	A	A	G	rs77014290	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:173036257A>G	ENST00000311086.4	-	3	766	c.543T>C	c.(541-543)tcT>tcC	p.S181S	BOD1_ENST00000480951.1_Intron|BOD1_ENST00000471339.1_5'Flank|BOD1_ENST00000285908.5_Intron	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	181					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)		p.S181S(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						AAGTGTCCTGAGATGGAGCTG	0.512																																					p.S181S		Atlas-SNP	.											BOD1,NS,carcinoma,0,1	BOD1	15	1	1	Substitution - coding silent(1)	lung(1)	c.T543C						PASS	.						92.0	91.0	91.0					5																	173036257		2203	4300	6503	SO:0001819	synonymous_variant	91272	exon3			GTCCTGAGATGGA	AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"""biorientation defective 1"""		"""family with sequence similarity 44, member B"""	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.543T>C	5.37:g.173036257A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	140	25	0.178571	NM_138369	B4DXH8|Q9BTW1	Silent	SNP	ENST00000311086.4	37	CCDS4389.1	.	.	.	.	.	.	.	.	.	.	A	10.16	1.274704	0.23307	.	.	ENSG00000145919	ENST00000477985	.	.	.	5.86	2.54	0.30619	.	0.220881	0.48767	D	0.000172	T	0.46580	0.1400	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40701	-0.9549	6	0.39692	T	0.17	-11.0788	1.6489	0.02767	0.2536:0.1527:0.4384:0.1553	.	.	.	.	P	114	.	ENSP00000420005:S114P	S	-	1	0	BOD1	172968863	0.999000	0.42202	0.962000	0.40283	0.898000	0.52572	0.891000	0.28309	0.806000	0.34183	-0.177000	0.13119	TCA	A|0.981;G|0.019	0.019	strong		0.512	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369	
DCTN5	84516	hgsc.bcm.edu	37	16	23677006	23677006	+	Silent	SNP	A	A	G	rs35586	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:23677006A>G	ENST00000300087.2	+	5	559	c.408A>G	c.(406-408)ccA>ccG	p.P136P	DCTN5_ENST00000568589.1_Silent_p.P136P|DCTN5_ENST00000563998.1_Silent_p.P136P	NM_001199743.1|NM_032486.3	NP_001186672.1|NP_115875.1	Q9BTE1	DCTN5_HUMAN	dynactin 5 (p25)	136					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)				endometrium(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(48;0.0156)		TATTACCTCCAGAAACTGTGG	0.393													A|||	1170	0.233626	0.1021	0.1758	5008	,	,		18063	0.4355		0.2117	False		,,,				2504	0.2669				p.P136P		Atlas-SNP	.											.	DCTN5	21	.	0			c.A408G						PASS	.	A	,	516,3878	235.8+/-248.2	34,448,1715	94.0	87.0	89.0		408,408	-1.1	1.0	16	dbSNP_76	89	1738,6862	315.7+/-312.4	172,1394,2734	no	coding-synonymous,coding-synonymous	DCTN5	NM_001199743.1,NM_032486.3	,	206,1842,4449	GG,GA,AA		20.2093,11.7433,17.3465	,	136/153,136/183	23677006	2254,10740	2197	4300	6497	SO:0001819	synonymous_variant	84516	exon5			ACCTCCAGAAACT		CCDS10615.1, CCDS58435.1, CCDS58436.1	16p12.1	2008-02-05			ENSG00000166847	ENSG00000166847			24594	protein-coding gene	gene with protein product		612962				10525537, 15043994	Standard	NM_032486		Approved	MGC3248, p25	uc002dly.2	Q9BTE1	OTTHUMG00000131610	ENST00000300087.2:c.408A>G	16.37:g.23677006A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_032486	A8K9X8|H3BN51|H3BQA4	Silent	SNP	ENST00000300087.2	37	CCDS10615.1																																																																																			A|0.799;G|0.201	0.201	strong		0.393	DCTN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254497.1	NM_032486	
PNPLA5	150379	hgsc.bcm.edu	37	22	44282276	44282276	+	Missense_Mutation	SNP	A	A	G	rs739231	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44282276A>G	ENST00000597664.1	-	6	985	c.856T>C	c.(856-858)Tgg>Cgg	p.W286R	PNPLA5_ENST00000381198.2_Missense_Mutation_p.W172R|PNPLA5_ENST00000593866.1_Missense_Mutation_p.W172R|PNPLA5_ENST00000216177.4_Missense_Mutation_p.W286R			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	286			W -> R (in dbSNP:rs739231). {ECO:0000269|PubMed:14702039}.		lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CCCCCCTTCCAGCGTTGGTCA	0.587													G|||	2516	0.502396	0.2436	0.4597	5008	,	,		18495	0.9048		0.3748	False		,,,				2504	0.5992				p.W286R		Atlas-SNP	.											.	PNPLA5	46	.	0			c.T856C						PASS	.	G	ARG/TRP,ARG/TRP	1175,3231	711.3+/-408.0	165,845,1193	96.0	82.0	87.0		514,856	-2.7	0.0	22	dbSNP_86	87	3209,5391	652.7+/-401.0	585,2039,1676	yes	missense,missense	PNPLA5	NM_001177675.1,NM_138814.3	101,101	750,2884,2869	GG,GA,AA		37.314,26.6682,33.7075	benign,benign	172/316,286/430	44282276	4384,8622	2203	4300	6503	SO:0001583	missense	150379	exon6			CCTTCCAGCGTTG	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.856T>C	22.37:g.44282276A>G	ENSP00000471069:p.Trp286Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	37		1066	0.4880952380952381	113	0.22967479674796748	157	0.43370165745856354	508	0.8881118881118881	288	0.37994722955145116	G	2.853	-0.237927	0.05944	0.266682	0.37314	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.39406	1.56;1.08;1.8	4.2	-2.74	0.05932	.	1.460160	0.04604	N	0.399060	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.25537	-1.0129	9	0.15499	T	0.54	-1.3098	1.9577	0.03379	0.183:0.4234:0.2208:0.1728	rs739231;rs5764378;rs17493115;rs52834315;rs60718837;rs739231	194;172;286	E9PGS4;Q7Z6Z6-2;Q7Z6Z6	.;.;PLPL5_HUMAN	R	286;172;194	ENSP00000216177:W286R;ENSP00000370595:W172R;ENSP00000405732:W194R	ENSP00000216177:W286R	W	-	1	0	PNPLA5	42613609	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.878000	0.04192	-0.705000	0.05035	-1.288000	0.01363	TGG	A|0.572;G|0.428	0.428	strong		0.587	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
ULK4	54986	hgsc.bcm.edu	37	3	41756986	41756986	+	Missense_Mutation	SNP	A	A	T	rs61744385	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:41756986A>T	ENST00000301831.4	-	24	2992	c.2530T>A	c.(2530-2532)Ttg>Atg	p.L844M		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	844					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GGGAGACACAACTTCAGCTGT	0.433													T|||	1330	0.265575	0.5348	0.1628	5008	,	,		17195	0.1478		0.1839	False		,,,				2504	0.18				p.L844M		Atlas-SNP	.											.	ULK4	150	.	0			c.T2530A						PASS	.	T	MET/LEU	1828,2100		435,958,571	104.0	106.0	105.0		2530	-1.8	0.1	3	dbSNP_129	105	1425,6891		128,1169,2861	yes	missense	ULK4	NM_017886.2	15	563,2127,3432	TT,TA,AA		17.1356,46.5377,26.5681	benign	844/1276	41756986	3253,8991	1964	4158	6122	SO:0001583	missense	54986	exon24			GACACAACTTCAG	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2530T>A	3.37:g.41756986A>T	ENSP00000301831:p.Leu844Met	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	550	0.2518315018315018	262	0.532520325203252	57	0.1574585635359116	86	0.15034965034965034	145	0.19129287598944592	T	2.271	-0.366965	0.05069	0.465377	0.171356	ENSG00000168038	ENST00000301831	T	0.52526	0.66	5.72	-1.82	0.07857	Armadillo-type fold (1);	0.393302	0.27513	N	0.019027	T	0.00012	0.0000	N	0.01109	-1.01	0.36343	P	0.14037200000000005	B	0.06786	0.001	B	0.08055	0.003	T	0.41645	-0.9497	9	0.16896	T	0.51	.	4.4795	0.11760	0.2034:0.0585:0.4211:0.317	rs61744385	844	Q96C45	ULK4_HUMAN	M	844	ENSP00000301831:L844M	ENSP00000301831:L844M	L	-	1	2	ULK4	41731990	0.258000	0.24033	0.069000	0.20011	0.931000	0.56810	0.121000	0.15667	-0.930000	0.03752	-1.147000	0.01851	TTG	A|0.770;T|0.230	0.230	strong		0.433	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
SETD6	79918	hgsc.bcm.edu	37	16	58550484	58550484	+	Silent	SNP	G	G	A	rs3743567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:58550484G>A	ENST00000219315.4	+	4	629	c.579G>A	c.(577-579)ctG>ctA	p.L193L	SETD6_ENST00000310682.2_Silent_p.L169L|SETD6_ENST00000418480.1_3'UTR|SETD6_ENST00000394266.4_Intron			Q8TBK2	SETD6_HUMAN	SET domain containing 6	193	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						CCATCGTGCTGCCCTTCATGG	0.617													G|||	691	0.137979	0.0953	0.1182	5008	,	,		16684	0.1796		0.0795	False		,,,				2504	0.227				p.L193L		Atlas-SNP	.											.	SETD6	27	.	0			c.G579A						PASS	.	G	,	401,3995	199.8+/-223.2	17,367,1814	104.0	109.0	107.0		579,507	2.3	1.0	16	dbSNP_107	107	825,7775	190.7+/-237.1	39,747,3514	no	coding-synonymous,coding-synonymous	SETD6	NM_001160305.1,NM_024860.2	,	56,1114,5328	AA,AG,GG		9.593,9.1219,9.4337	,	193/474,169/450	58550484	1226,11770	2198	4300	6498	SO:0001819	synonymous_variant	79918	exon4			CGTGCTGCCCTTC	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.579G>A	16.37:g.58550484G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001160305	A8K380|B5ME38|Q9H787	Silent	SNP	ENST00000219315.4	37	CCDS54013.1																																																																																			G|0.896;A|0.104	0.104	strong		0.617	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860	
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 GAIIx	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_ENST00000382892.2_Missense_Mutation_p.E914K|WHSC1_ENST00000382891.5_Missense_Mutation_p.E914K|WHSC1_ENST00000508803.1_Missense_Mutation_p.E914K|WHSC1_ENST00000482415.2_3'UTR|WHSC1_ENST00000382888.3_Missense_Mutation_p.E262K	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	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	93	4	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	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340836	55340836	+	Missense_Mutation	SNP	A	A	G	rs45551936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55340836A>G	ENST00000391728.4	+	7	1054	c.1021A>G	c.(1021-1023)Att>Gtt	p.I341V	KIR3DL1_ENST00000358178.4_Missense_Mutation_p.I246V|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.I324V|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.I341V|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.I324V	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	341					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ACACCTGCACATTCTGATTGG	0.448													a|||	880	0.175719	0.1626	0.1729	5008	,	,		16245	0.1141		0.2992	False		,,,				2504	0.1319				p.I341V		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.A1021G						PASS	.	G	VAL/ILE	529,3819		169,191,1814	273.0	207.0	230.0		1021	-1.5	0.0	19	dbSNP_127	230	1118,7184		477,164,3510	no	missense	KIR3DL1	NM_013289.2	29	646,355,5324	GG,GA,AA		13.4666,12.1665,13.0198		341/445	55340836	1647,11003	2174	4151	6325	SO:0001583	missense	3811	exon7			CTGCACATTCTGA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1021A>G	19.37:g.55340836A>G	ENSP00000375608:p.Ile341Val	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	334	0.15293040293040294	56	0.11382113821138211	54	0.14917127071823205	57	0.09965034965034965	167	0.22031662269129287	-	0.001	-2.987940	0.00046	0.121665	0.134666	ENSG00000167633	ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T	0.00463	7.25;7.36;7.25;7.36;7.33	0.743	-1.49	0.08718	.	.	.	.	.	T	0.00012	0.0000	N	0.00879	-1.12	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.15435	-1.0437	8	0.02654	T	1	.	5.4332	0.16464	0.6495:0.0:0.3505:0.0	rs45551936	324;246;341	Q15702;Q14946;P43629	.;.;KI3L1_HUMAN	V	341;324;319;341;324;246	ENSP00000443350:I341V;ENSP00000442355:I324V;ENSP00000375608:I341V;ENSP00000326868:I324V;ENSP00000350901:I246V	ENSP00000326868:I324V	I	+	1	0	KIR3DL1	60032648	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.466000	0.02355	-1.524000	0.01764	-1.160000	0.01791	ATT	A|0.847;G|0.153	0.153	strong		0.448	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
OR52E4	390081	hgsc.bcm.edu	37	11	5906203	5906203	+	Missense_Mutation	SNP	T	T	G	rs11823828	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5906203T>G	ENST00000316987.2	+	1	703	c.681T>G	c.(679-681)ttT>ttG	p.F227L		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	227			F -> L (in dbSNP:rs11823828).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAGCTGTTTTTCGCCTTCCCT	0.383													T|||	1792	0.357827	0.3207	0.402	5008	,	,		21849	0.3641		0.4085	False		,,,				2504	0.318				p.F227L		Atlas-SNP	.											.	OR52E4	65	.	0			c.T681G						PASS	.	T	LEU/PHE	1495,2907	476.3+/-357.6	259,977,965	302.0	259.0	273.0		681	0.4	0.2	11	dbSNP_120	273	3625,4967	522.6+/-380.1	780,2065,1451	yes	missense	OR52E4	NM_001005165.1	22	1039,3042,2416	GG,GT,TT		42.1904,33.9618,39.4028	benign	227/313	5906203	5120,7874	2201	4296	6497	SO:0001583	missense	390081	exon1			TGTTTTTCGCCTT	AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"""GPCR / Class A : Olfactory receptors"""	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.681T>G	11.37:g.5906203T>G	ENSP00000321426:p.Phe227Leu	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	234	112	0.478632	NM_001005165	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	828	0.3791208791208791	154	0.3130081300813008	153	0.42265193370165743	204	0.35664335664335667	317	0.4182058047493404	T	11.25	1.582573	0.28180	0.339618	0.421904	ENSG00000180974	ENST00000316987	T	0.00013	9.26	5.15	0.395	0.16304	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000087	T	0.00012	0.0000	L	0.28054	0.825	0.80722	P	0.0	B	0.19331	0.035	B	0.29785	0.107	T	0.13710	-1.0499	9	0.38643	T	0.18	.	5.2374	0.15454	0.0:0.2102:0.4221:0.3677	rs11823828;rs59269559	227	Q8NGH9	O52E4_HUMAN	L	227	ENSP00000321426:F227L	ENSP00000321426:F227L	F	+	3	2	OR52E4	5862779	0.000000	0.05858	0.241000	0.24154	0.768000	0.43524	-0.301000	0.08232	0.202000	0.20498	0.523000	0.50628	TTT	T|0.612;G|0.388	0.388	strong		0.383	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165	
SEMA5B	54437	hgsc.bcm.edu	37	3	122646828	122646828	+	Missense_Mutation	SNP	A	A	G	rs2276774	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:122646828A>G	ENST00000357599.3	-	8	1045	c.659T>C	c.(658-660)aTt>aCt	p.I220T	SEMA5B_ENST00000451055.2_Missense_Mutation_p.I274T|AC078794.1_ENST00000408284.1_RNA|SEMA5B_ENST00000195173.4_Missense_Mutation_p.I220T	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	220	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		I -> T (in dbSNP:rs2276774). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GATCTTCTCAATAGTCCGGCT	0.582													a|||	682	0.136182	0.1846	0.1744	5008	,	,		18987	0.0595		0.1392	False		,,,				2504	0.1196				p.I274T		Atlas-SNP	.											.	SEMA5B	303	.	0			c.T821C						PASS	.		THR/ILE	684,3722	289.2+/-280.3	57,570,1576	76.0	75.0	75.0		659	5.6	0.1	3	dbSNP_100	75	1301,7299	257.2+/-281.3	89,1123,3088	yes	missense	SEMA5B	NM_001031702.2	89	146,1693,4664	GG,GA,AA		15.1279,15.5243,15.2622	possibly-damaging	220/1152	122646828	1985,11021	2203	4300	6503	SO:0001583	missense	54437	exon8			TTCTCAATAGTCC	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.659T>C	3.37:g.122646828A>G	ENSP00000350215:p.Ile220Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	282	0.12912087912087913	90	0.18292682926829268	60	0.16574585635359115	32	0.055944055944055944	100	0.13192612137203166	a	11.03	1.520285	0.27211	0.155243	0.151279	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.10382	2.88;2.88;2.88;2.88	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.347111	0.32687	N	0.005776	T	0.00012	0.0000	N	0.12502	0.225	0.36606	P	0.12503699999999995	B;B;B	0.22851	0.062;0.076;0.076	B;B;B	0.32022	0.085;0.139;0.139	T	0.51687	-0.8674	9	0.21014	T	0.42	.	13.7366	0.62821	1.0:0.0:0.0:0.0	rs2276774;rs52822678;rs59346924;rs2276774	162;220;220	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	T	220;220;162;274;220	ENSP00000350215:I220T;ENSP00000195173:I220T;ENSP00000389588:I274T;ENSP00000377208:I220T	ENSP00000195173:I220T	I	-	2	0	SEMA5B	124129518	0.992000	0.36948	0.056000	0.19401	0.862000	0.49288	6.819000	0.75262	2.368000	0.80403	0.529000	0.55759	ATT	A|0.858;G|0.142	0.142	strong		0.582	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
GRIN2B	2904	hgsc.bcm.edu	37	12	13764774	13764774	+	Silent	SNP	G	G	A	rs1805482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:13764774G>A	ENST00000609686.1	-	8	1874	c.1665C>T	c.(1663-1665)agC>agT	p.S555S		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	555					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ATACGTCAGCGCTGAATGGCT	0.453													g|||	952	0.190096	0.1536	0.3718	5008	,	,		21319	0.0089		0.33	False		,,,				2504	0.1534				p.S555S		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C1665T						PASS	.	A		769,3637	313.6+/-293.2	76,617,1510	120.0	105.0	110.0		1665	-8.0	0.5	12	dbSNP_92	110	2874,5726	451.1+/-362.6	484,1906,1910	no	coding-synonymous	GRIN2B	NM_000834.3		560,2523,3420	AA,AG,GG		33.4186,17.4535,28.0101		555/1485	13764774	3643,9363	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon8			GTCAGCGCTGAAT		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.1665C>T	12.37:g.13764774G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.753;A|0.247	0.247	strong		0.453	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
CAMKV	79012	hgsc.bcm.edu	37	3	49899795	49899795	+	Silent	SNP	G	G	A	rs3796386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49899795G>A	ENST00000477224.1	-	2	505	c.27C>T	c.(25-27)ggC>ggT	p.G9G	CAMKV_ENST00000466940.1_Silent_p.G9G|CAMKV_ENST00000467248.1_5'UTR|RN7SL217P_ENST00000584520.1_RNA|CAMKV_ENST00000296471.7_Silent_p.G9G|CAMKV_ENST00000498324.1_5'UTR|CAMKV_ENST00000463537.1_Silent_p.G9G|CAMKV_ENST00000488336.1_Silent_p.G9G			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	9						cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		TCTTCTTGTCGCCCAGAGTCA	0.552													G|||	1397	0.278954	0.3631	0.3141	5008	,	,		20204	0.124		0.4145	False		,,,				2504	0.1605				p.G9G		Atlas-SNP	.											.	CAMKV	84	.	0			c.C27T						PASS	.	G		1597,2809	496.4+/-363.5	294,1009,900	123.0	109.0	114.0		27	-9.8	0.8	3	dbSNP_107	114	3600,5000	521.0+/-379.8	724,2152,1424	no	coding-synonymous	CAMKV	NM_024046.3		1018,3161,2324	AA,AG,GG		41.8605,36.246,39.9585		9/502	49899795	5197,7809	2203	4300	6503	SO:0001819	synonymous_variant	79012	exon2			CTTGTCGCCCAGA	BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.27C>T	3.37:g.49899795G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	140	135	0.964286	NM_024046	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Silent	SNP	ENST00000477224.1	37	CCDS33762.1																																																																																			G|0.650;A|0.350	0.350	strong		0.552	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046	
DCANP1	140947	hgsc.bcm.edu	37	5	134782576	134782576	+	Missense_Mutation	SNP	T	T	G	rs1031844	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134782576T>G	ENST00000503143.2	-	1	462	c.223A>C	c.(223-225)Acc>Ccc	p.T75P	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		75			T -> P (in dbSNP:rs1031844).			nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCTGGCAAGGTTTTGTTCCTC	0.602													G|||	3232	0.645367	0.9319	0.5533	5008	,	,		17614	0.5635		0.5159	False		,,,				2504	0.5409				p.T75P		Atlas-SNP	.											C5orf20,middle_lobe,carcinoma,+2,1	C5orf20	16	1	0			c.A223C						scavenged	.	G	PRO/THR	3789,617		1645,499,59	29.0	32.0	31.0		223	2.3	0.0	5	dbSNP_86	31	3962,4638		908,2146,1246	yes	missense	C5orf20	NM_130848.2	38	2553,2645,1305	GG,GT,TT		46.0698,14.0036,40.4044	benign	75/245	134782576	7751,5255	2203	4300	6503	SO:0001583	missense	140947	exon1			GCAAGGTTTTGTT																												ENST00000503143.2:c.223A>C	5.37:g.134782576T>G	ENSP00000421871:p.Thr75Pro	Somatic	69	2	0.0289855		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	1332	0.6098901098901099	452	0.9186991869918699	184	0.5082872928176796	316	0.5524475524475524	380	0.5013192612137203	G	5.763	0.325211	0.10900	0.859964	0.460698	ENSG00000251380	ENST00000503143	T	0.37915	1.17	3.15	2.27	0.28462	.	.	.	.	.	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	0.12708	-1.0537	8	0.87932	D	0	.	3.8201	0.08832	0.1305:0.0:0.6301:0.2394	rs1031844;rs17676671;rs1031844	75	Q8TF63	DCNP1_HUMAN	P	75	ENSP00000421871:T75P	ENSP00000421871:T75P	T	-	1	0	C5orf20	134810475	0.001000	0.12720	0.008000	0.14137	0.004000	0.04260	-0.268000	0.08607	0.366000	0.24427	-0.323000	0.08544	ACC	T|0.370;G|0.630	0.630	strong		0.602	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
CCHCR1	54535	hgsc.bcm.edu	37	6	31122482	31122482	+	Missense_Mutation	SNP	G	G	A	rs130076	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31122482G>A	ENST00000376266.5	-	4	447	c.325C>T	c.(325-327)Cgg>Tgg	p.R109W	CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396263.2_Missense_Mutation_p.R109W|CCHCR1_ENST00000396268.3_Missense_Mutation_p.R198W|CCHCR1_ENST00000451521.2_Missense_Mutation_p.R162W	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	109			R -> W (in allele HCR*WWCC; associated with psoriasis; dbSNP:rs130076). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CGCAGGAGCCGGACCTCCTCC	0.677													G|||	618	0.123403	0.1293	0.0893	5008	,	,		17008	0.0387		0.1899	False		,,,				2504	0.1585				p.R198W		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C592T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	474,2540		39,396,1072	33.0	40.0	37.0		484,592,325	5.3	0.4	6	dbSNP_78	37	1138,4280		126,886,1697	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	101,101,101	165,1282,2769	AA,AG,GG		21.0041,15.7266,19.1176	benign,benign,benign	162/836,198/872,109/783	31122482	1612,6820	1507	2709	4216	SO:0001583	missense	54535	exon4			GGAGCCGGACCTC	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.325C>T	6.37:g.31122482G>A	ENSP00000365442:p.Arg109Trp	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	55	0.820895	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	282	0.12912087912087913	72	0.14634146341463414	30	0.08287292817679558	26	0.045454545454545456	154	0.20316622691292877	G	15.13	2.740934	0.49151	0.157266	0.210041	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521;ENST00000448141;ENST00000508683;ENST00000448162;ENST00000513222;ENST00000503420;ENST00000515274;ENST00000507751;ENST00000455279;ENST00000412245;ENST00000503934;ENST00000426967;ENST00000502557;ENST00000507829	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.05580	3.42;3.42;3.42;3.42;3.42;3.42;3.42;3.42;3.42;3.42;3.42;3.42;3.42;3.42;3.42	5.33	5.33	0.75918	.	0.604741	0.14765	N	0.299748	T	0.04724	0.0128	M	0.63428	1.95	0.50313	P	1.36000000000025E-4	B;B;B;B;B	0.24043	0.005;0.002;0.011;0.096;0.017	B;B;B;B;B	0.19946	0.002;0.001;0.002;0.027;0.007	T	0.08269	-1.0730	9	0.52906	T	0.07	-27.6133	14.5639	0.68162	0.0:0.0:1.0:0.0	rs130076;rs3173362;rs52823584;rs59574448;rs130076	109;109;109;162;198	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	W	198;109;109;109;162;73;73;109;83;73;109;109;109;135;109;207;109;109	ENSP00000379566:R198W;ENSP00000365442:R109W;ENSP00000379561:R109W;ENSP00000401039:R162W;ENSP00000414323:R73W;ENSP00000421393:R73W;ENSP00000390027:R109W;ENSP00000425682:R83W;ENSP00000421992:R73W;ENSP00000420941:R109W;ENSP00000398715:R109W;ENSP00000425595:R109W;ENSP00000402432:R207W;ENSP00000425377:R109W;ENSP00000420911:R109W	ENSP00000365442:R109W	R	-	1	2	CCHCR1	31230461	0.211000	0.23529	0.356000	0.25785	0.419000	0.31324	1.616000	0.36933	2.510000	0.84645	0.638000	0.83543	CGG	G|0.828;A|0.172	0.172	strong		0.677	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
VWA3B	200403	hgsc.bcm.edu	37	2	98853173	98853173	+	Missense_Mutation	SNP	G	G	A	rs11889349	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:98853173G>A	ENST00000477737.1	+	19	2857	c.2653G>A	c.(2653-2655)Gtg>Atg	p.V885M		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	885			V -> M (in dbSNP:rs11889349). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.							NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						CAAGCATGTCGTGTCTAAGGT	0.468													g|||	3326	0.664137	0.621	0.4914	5008	,	,		19928	0.7976		0.5447	False		,,,				2504	0.8303				p.V885M		Atlas-SNP	.											.	VWA3B	138	.	0			c.G2653A						PASS	.	G	MET/VAL	2459,1561		749,961,300	138.0	143.0	141.0		2653	0.9	0.0	2	dbSNP_120	141	4564,3812		1250,2064,874	yes	missense	VWA3B	NM_144992.4	21	1999,3025,1174	AA,AG,GG		45.511,38.8308,43.3446	benign	885/1295	98853173	7023,5373	2010	4188	6198	SO:0001583	missense	200403	exon19			CATGTCGTGTCTA	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2653G>A	2.37:g.98853173G>A	ENSP00000417955:p.Val885Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	1320|1320	0.6043956043956044|0.6043956043956044	307|307	0.6239837398373984|0.6239837398373984	181|181	0.5|0.5	440|440	0.7692307692307693|0.7692307692307693	392|392	0.5171503957783641|0.5171503957783641	g|g	0.687|0.687	-0.795959|-0.795959	0.02862|0.02862	0.611692|0.611692	0.54489|0.54489	ENSG00000168658|ENSG00000168658	ENST00000473149|ENST00000477737	.|T	.|0.07327	.|3.2	4.93|4.93	0.946|0.946	0.19549|0.19549	.|.	.|1.329060	.|0.05295	.|N	.|0.521921	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	P|P	0.0|0.0	.|B;B;P;B	.|0.44139	.|0.029;0.099;0.827;0.056	.|B;B;B;B	.|0.33750	.|0.009;0.02;0.169;0.021	T|T	0.29058|0.29058	-1.0024|-1.0024	4|9	.|0.35671	.|T	.|0.21	.|.	4.4952|4.4952	0.11833|0.11833	0.157:0.1227:0.5949:0.1255|0.157:0.1227:0.5949:0.1255	rs11889349;rs52803499;rs61365735;rs11889349|rs11889349;rs52803499;rs61365735;rs11889349	.|277;885;885;885	.|Q502W6-5;Q502W6;Q502W6-8;Q502W6-6	.|.;VWA3B_HUMAN;.;.	H|M	295|885	.|ENSP00000417955:V885M	.|ENSP00000417955:V885M	R|V	+|+	2|1	0|0	VWA3B|VWA3B	98219605|98219605	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.030000|0.030000	0.12068|0.12068	0.250000|0.250000	0.18235|0.18235	-0.049000|-0.049000	0.13379|0.13379	-1.458000|-1.458000	0.01028|0.01028	CGT|GTG	G|0.380;A|0.620	0.620	strong		0.468	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
MXRA5	25878	hgsc.bcm.edu	37	X	3235724	3235724	+	Missense_Mutation	SNP	C	C	T	rs1635242	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3235724C>T	ENST00000217939.6	-	6	6152	c.5998G>A	c.(5998-6000)Ggc>Agc	p.G2000S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2000	Ig-like C2-type 4.		G -> S (in dbSNP:rs1635242). {ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GTGATGCGGCCCTCCACGGGG	0.602													C|||	2623	0.694834	0.5386	0.5043	3775	,	,		14459	0.5595		0.5258	False		,,,				2504	0.4785				p.G2000S		Atlas-SNP	.											.	MXRA5	815	.	0			c.G5998A						PASS	.	C	SER/GLY	2674,1161		783,702,406,147,165	46.0	43.0	44.0		5998	3.5	0.7	X	dbSNP_89	44	4341,2387		1020,1108,1193,300,679	yes	missense	MXRA5	NM_015419.3	56	1803,1810,1599,447,844	TT,TC,T,CC,C		35.4786,30.2738,33.5889	benign	2000/2829	3235724	7015,3548	2203	4300	6503	SO:0001583	missense	25878	exon6			TGCGGCCCTCCAC	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5998G>A	X.37:g.3235724C>T	ENSP00000217939:p.Gly2000Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	1154	0.6955997588908981	184	0.5679012345679012	127	0.4810606060606061	206	0.5885714285714285	272	0.5271317829457365	c	6.436	0.448618	0.12223	0.697262	0.645214	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.78126	-1.15	3.55	3.55	0.40652	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.239206	0.20393	U	0.093219	T	0.00012	0.0000	L	0.38649	1.16	0.36763	P	0.11658199999999996	B	0.25048	0.117	B	0.33454	0.164	T	0.46498	-0.9187	9	0.14656	T	0.56	.	6.6556	0.22986	0.0:0.7548:0.0:0.2452	rs1635242;rs52807899;rs58318664;rs1635242	2000	Q9NR99	MXRA5_HUMAN	S	2000	ENSP00000217939:G2000S	ENSP00000217939:G2000S	G	-	1	0	MXRA5	3245724	0.005000	0.15991	0.677000	0.29947	0.217000	0.24651	0.838000	0.27572	1.399000	0.46721	0.544000	0.68410	GGC	C|0.319;T|0.681	0.681	strong		0.602	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
LTF	4057	hgsc.bcm.edu	37	3	46490474	46490474	+	Silent	SNP	G	G	A	rs2230894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46490474G>A	ENST00000231751.4	-	9	1387	c.1092C>T	c.(1090-1092)gtC>gtT	p.V364V	LTF_ENST00000426532.2_Silent_p.V320V|LTF_ENST00000417439.1_Silent_p.V364V	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	364	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		CACACCACACGACCCGCGCAC	0.662													G|||	1080	0.215655	0.1959	0.2651	5008	,	,		15887	0.2034		0.162	False		,,,				2504	0.2751				p.V364V		Atlas-SNP	.											.	LTF	98	.	0			c.C1092T						PASS	.	G	,	846,3558	314.1+/-293.5	79,688,1435	35.0	31.0	33.0		960,1092	-2.8	0.0	3	dbSNP_98	33	1342,7250	248.2+/-276.0	114,1114,3068	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	193,1802,4503	AA,AG,GG		15.6192,19.2098,16.8359	,	320/667,364/711	46490474	2188,10808	2202	4296	6498	SO:0001819	synonymous_variant	4057	exon9			CCACACGACCCGC		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1092C>T	3.37:g.46490474G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			G|0.814;A|0.186	0.186	strong		0.662	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
EPHX1	2052	hgsc.bcm.edu	37	1	226027659	226027659	+	Silent	SNP	C	C	T	rs2292568	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226027659C>T	ENST00000366837.4	+	6	1048	c.852C>T	c.(850-852)ccC>ccT	p.P284P	EPHX1_ENST00000272167.5_Silent_p.P284P|RP11-285F7.2_ENST00000424332.1_RNA	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	284					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TGCTGTACCCCGTCAAGGAGA	0.557													C|||	378	0.0754792	0.0227	0.0749	5008	,	,		18608	0.1538		0.0487	False		,,,				2504	0.0941				p.P284P		Atlas-SNP	.											.	EPHX1	57	.	0			c.C852T						PASS	.	C	,	106,4300	84.4+/-122.9	0,106,2097	169.0	147.0	154.0		852,852	-3.3	0.0	1	dbSNP_100	154	350,8250	118.3+/-177.8	3,344,3953	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	3,450,6050	TT,TC,CC		4.0698,2.4058,3.5061	,	284/456,284/456	226027659	456,12550	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon6			GTACCCCGTCAAG	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.852C>T	1.37:g.226027659C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	59	0.42446	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			C|0.950;N|0.001	.	strong		0.557	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
AQP7	364	hgsc.bcm.edu	37	9	33395103	33395103	+	Silent	SNP	G	G	A	rs148012859		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33395103G>A	ENST00000539936.1	-	3	355	c.117C>T	c.(115-117)gcC>gcT	p.A39A	AQP7_ENST00000377425.4_Intron|AQP7_ENST00000541274.1_5'UTR|AQP7_ENST00000537089.1_5'UTR			O14520	AQP7_HUMAN	aquaporin 7	39					excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)	p.A39A(1)		NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TCATGAACTCGGCCAGGAACT	0.582																																					p.A39A		Atlas-SNP	.											AQP7,NS,carcinoma,0,1	AQP7	58	1	1	Substitution - coding silent(1)	prostate(1)	c.C117T						scavenged	.						126.0	85.0	99.0					9																	33395103		2203	4300	6503	SO:0001819	synonymous_variant	364	exon3			GAACTCGGCCAGG	AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000539936.1:c.117C>T	9.37:g.33395103G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	168	4	0.0238095	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Silent	SNP	ENST00000539936.1	37																																																																																				A|0.002;G|0.998;T|0.000	0.002	strong		0.582	AQP7-203	KNOWN	basic	protein_coding	protein_coding		NM_001170	
DHRS7C	201140	hgsc.bcm.edu	37	17	9676134	9676134	+	Missense_Mutation	SNP	G	G	A	rs2280490	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:9676134G>A	ENST00000330255.5	-	5	692	c.680C>T	c.(679-681)tCg>tTg	p.S227L	DHRS7C_ENST00000571134.1_Missense_Mutation_p.S226L	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	227			S -> L (in dbSNP:rs2280490).		regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						CACGTGGTACGACCGGATGAA	0.582													G|||	447	0.0892572	0.0741	0.062	5008	,	,		18957	0.0992		0.1054	False		,,,				2504	0.1022				p.S227L		Atlas-SNP	.											.	DHRS7C	34	.	0			c.C680T						PASS	.	G	LEU/SER,LEU/SER	399,3997	174.1+/-203.8	24,351,1823	73.0	81.0	78.0		680,677	4.7	0.3	17	dbSNP_100	78	909,7683	196.8+/-241.6	49,811,3436	yes	missense,missense	DHRS7C	NM_001220493.1,NM_001105571.2	145,145	73,1162,5259	AA,AG,GG		10.5796,9.0764,10.0708	benign,benign	227/313,226/312	9676134	1308,11680	2198	4296	6494	SO:0001583	missense	201140	exon5			TGGTACGACCGGA		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	32423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 32C, member 2"""					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.680C>T	17.37:g.9676134G>A	ENSP00000327975:p.Ser227Leu	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	23	22	0.956522	NM_001220493	B7ZW74|B9EJH3	Missense_Mutation	SNP	ENST00000330255.5	37	CCDS56020.1	212	0.09706959706959707	50	0.1016260162601626	19	0.052486187845303865	60	0.1048951048951049	83	0.10949868073878628	G	10.84	1.462937	0.26248	0.090764	0.105796	ENSG00000184544	ENST00000330255	T	0.54866	0.55	4.68	4.68	0.58851	NAD(P)-binding domain (1);	0.490245	0.21837	N	0.068386	T	0.00875	0.0029	L	0.40543	1.245	0.27351	P	0.956257	B;P	0.38110	0.226;0.618	B;B	0.20184	0.028;0.023	T	0.35400	-0.9790	9	0.87932	D	0	.	16.5323	0.84364	0.0:0.0:1.0:0.0	rs2280490;rs17207682;rs56923642;rs2280490	227;223	A6NNS2;B9EJH3	DRS7C_HUMAN;.	L	227	ENSP00000327975:S227L	ENSP00000327975:S227L	S	-	2	0	DHRS7C	9616859	1.000000	0.71417	0.317000	0.25265	0.045000	0.14185	7.355000	0.79434	2.429000	0.82318	0.655000	0.94253	TCG	G|0.907;A|0.093	0.093	strong		0.582	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37451586	37451586	+	Missense_Mutation	SNP	G	G	A	rs12766884|rs373828826	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:37451586G>A	ENST00000602533.1	+	16	1841	c.1742G>A	c.(1741-1743)gGg>gAg	p.G581E	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.G581E|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.G581E			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	637					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						GAGCCTCCGGGGAAGCCATCT	0.323													.|||	222	0.0443291	0.0265	0.0389	5008	,	,		17622	0.0536		0.0577	False		,,,				2504	0.0491				p.G581E		Atlas-SNP	.											ANKRD30A,right_upper_lobe,carcinoma,+1,3	ANKRD30A	448	3	0			c.G1742A						PASS	.	A	GLU/GLY	50,3592		2,46,1773	184.0	151.0	161.0		1742	0.7	0.2	10	dbSNP_121	161	206,7946		13,180,3883	no	missense	ANKRD30A	NM_052997.2	98	15,226,5656	AA,AG,GG		2.527,1.3729,2.1706	possibly-damaging	581/1342	37451586	256,11538	1821	4076	5897	SO:0001583	missense	91074	exon16			CTCCGGGGAAGCC	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.1742G>A	10.37:g.37451586G>A	ENSP00000473551:p.Gly581Glu	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	202	78	0.386139	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		61	0.027930402930402932	7	0.014227642276422764	15	0.04143646408839779	13	0.022727272727272728	26	0.03430079155672823	.	0.003	-2.510139	0.00153	0.013729	0.02527	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.06294	3.32;3.32	0.731	0.731	0.18277	.	.	.	.	.	T	0.00440	0.0014	N	0.02011	-0.69	0.09310	N	1	B	0.25667	0.131	B	0.19666	0.026	T	0.41875	-0.9484	9	0.02654	T	1	.	2.9801	0.05951	0.6804:0.0:0.3196:0.0	rs12766884;rs12766884	637	Q9BXX3	AN30A_HUMAN	E	581	ENSP00000354432:G581E;ENSP00000363792:G581E	ENSP00000354432:G581E	G	+	2	0	ANKRD30A	37491592	0.496000	0.26059	0.185000	0.23176	0.078000	0.17371	0.519000	0.22862	-0.217000	0.10033	-2.047000	0.00414	GGG	G|0.968;A|0.032	0.032	strong		0.323	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
SP140	11262	hgsc.bcm.edu	37	2	231149097	231149097	+	Missense_Mutation	SNP	T	T	C	rs4972945	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:231149097T>C	ENST00000392045.3	+	16	1649	c.1535T>C	c.(1534-1536)aTg>aCg	p.M512T	SP140_ENST00000420434.3_Missense_Mutation_p.M485T|SP140_ENST00000350136.5_Missense_Mutation_p.M381T|SP140_ENST00000417495.3_Missense_Mutation_p.M398T|SP140_ENST00000343805.6_Missense_Mutation_p.M452T|SP140_ENST00000486687.2_Missense_Mutation_p.M436T	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	512			M -> T (in dbSNP:rs4972945).		defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		AGAATGAGAATGAGAAGGCAG	0.383													T|||	384	0.0766773	0.0076	0.1095	5008	,	,		19523	0.1052		0.1272	False		,,,				2504	0.0654				p.M512T		Atlas-SNP	.											.	SP140	121	.	0			c.T1535C						PASS	.	T	THR/MET	83,3701		0,83,1809	105.0	115.0	112.0		1535	-5.8	0.0	2	dbSNP_111	112	993,7223		69,855,3184	yes	missense	SP140	NM_007237.4	81	69,938,4993	CC,CT,TT		12.0862,2.1934,8.9667	benign	512/868	231149097	1076,10924	1892	4108	6000	SO:0001583	missense	11262	exon16			TGAGAATGAGAAG	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"""Zinc fingers, PHD-type"""	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.1535T>C	2.37:g.231149097T>C	ENSP00000375899:p.Met512Thr	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	156	92	0.589744	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	193	0.08836996336996338	7	0.014227642276422764	39	0.10773480662983426	58	0.10139860139860139	89	0.11741424802110818	T	2.324	-0.354881	0.05138	0.021934	0.120862	ENSG00000079263	ENST00000486687;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T;T	0.55760	0.71;0.98;0.77;0.5;0.79	2.91	-5.82	0.02333	.	.	.	.	.	T	0.00271	0.0008	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B	0.12013	0.0;0.0;0.0;0.005	B;B;B;B	0.09377	0.001;0.0;0.001;0.004	T	0.07121	-1.0789	8	0.29301	T	0.29	0.4595	1.4524	0.02378	0.1897:0.3793:0.1736:0.2575	rs4972945;rs12466261;rs16826973;rs52790583;rs4972945	485;398;452;512	E7EUR5;E7ESH9;E9PFJ6;Q13342	.;.;.;LY10_HUMAN	T	436;381;512;398;452;485	ENSP00000440107:M436T;ENSP00000345846:M381T;ENSP00000375899:M512T;ENSP00000342096:M452T;ENSP00000398210:M485T	ENSP00000342096:M452T	M	+	2	0	SP140	230857341	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.118000	0.01325	-1.695000	0.01423	-1.658000	0.00752	ATG	T|0.878;C|0.122	0.122	strong		0.383	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907496	12907496	+	Missense_Mutation	SNP	T	T	C	rs138700801	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907496T>C	ENST00000317869.6	-	2	872	c.647A>G	c.(646-648)aAa>aGa	p.K216R		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	216						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						CTTAGCATTTTTCACCTCTAC	0.443																																					p.K216R		Atlas-SNP	.											.	HNRNPCL1	68	.	0			c.A647G						PASS	.	T	ARG/LYS	51,4353		1,49,2152	94.0	100.0	98.0		647	-2.2	0.0	1	dbSNP_134	98	189,8389		5,179,4105	no	missense	HNRNPCL1	NM_001013631.1	26	6,228,6257	CC,CT,TT		2.2033,1.158,1.8487	possibly-damaging	216/294	12907496	240,12742	2202	4289	6491	SO:0001583	missense	343069	exon2			GCATTTTTCACCT	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.647A>G	1.37:g.12907496T>C	ENSP00000365370:p.Lys216Arg	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	244	58	0.237705	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	163	0.07463369963369963	4	0.008130081300813009	8	0.022099447513812154	120	0.2097902097902098	31	0.040897097625329816	.	0.016	-1.521686	0.00967	0.01158	0.022033	ENSG00000179172	ENST00000317869	T	0.11277	2.79	1.09	-2.18	0.07037	.	0.121261	0.28273	U	0.015960	T	0.00012	0.0000	L	0.56769	1.78	0.09310	N	1	B	0.29835	0.258	B	0.24006	0.05	T	0.38436	-0.9661	10	0.37606	T	0.19	.	2.209	0.03943	0.2712:0.0:0.2744:0.4544	.	216	O60812	HNRCL_HUMAN	R	216	ENSP00000365370:K216R	ENSP00000365370:K216R	K	-	2	0	HNRNPCL1	12830083	0.171000	0.23029	0.002000	0.10522	0.014000	0.08584	0.510000	0.22723	-2.022000	0.00938	-1.851000	0.00568	AAA	.	.	weak		0.443	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
IL33	90865	hgsc.bcm.edu	37	9	6253571	6253571	+	Silent	SNP	C	C	T	rs10975519	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6253571C>T	ENST00000381434.3	+	5	502	c.489C>T	c.(487-489)taC>taT	p.Y163Y	IL33_ENST00000456383.2_Silent_p.Y121Y|IL33_ENST00000417746.2_Silent_p.Y37Y	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	163					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)			breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		TACTGAGTTACTATGAGTCTC	0.373													C|||	2029	0.405152	0.4175	0.4524	5008	,	,		16658	0.4375		0.3231	False		,,,				2504	0.4059				p.Y163Y		Atlas-SNP	.											.	IL33	27	.	0			c.C489T						PASS	.	C	,,	1678,2728	511.2+/-367.7	313,1052,838	139.0	133.0	135.0		363,111,489	2.5	0.0	9	dbSNP_120	135	2602,5998	421.7+/-353.8	423,1756,2121	no	coding-synonymous,coding-synonymous,coding-synonymous	IL33	NM_001199640.1,NM_001199641.1,NM_033439.3	,,	736,2808,2959	TT,TC,CC		30.2558,38.0844,32.9079	,,	121/229,37/145,163/271	6253571	4280,8726	2203	4300	6503	SO:0001819	synonymous_variant	90865	exon6			GAGTTACTATGAG	AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.489C>T	9.37:g.6253571C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_033439	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Silent	SNP	ENST00000381434.3	37	CCDS6468.1																																																																																			C|0.633;T|0.367	0.367	strong		0.373	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439	
SMG6	23293	hgsc.bcm.edu	37	17	2091765	2091765	+	Missense_Mutation	SNP	C	C	T	rs903160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2091765C>T	ENST00000263073.6	-	11	2964	c.2914G>A	c.(2914-2916)Gca>Aca	p.A972T	SMG6_ENST00000354901.4_Missense_Mutation_p.A64T|SMG6_ENST00000544865.1_Missense_Mutation_p.A941T|SMG6_ENST00000536871.2_Missense_Mutation_p.A64T	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	972			A -> T (in dbSNP:rs903160).		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CCCAGAGCTGCGGCTTGTTCC	0.587													C|||	2022	0.403754	0.5499	0.3012	5008	,	,		20170	0.3264		0.3091	False		,,,				2504	0.456				p.A972T	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G2914A						PASS	.	C	THR/ALA,THR/ALA	2166,2240	583.1+/-385.7	532,1102,569	63.0	57.0	59.0		2821,2914	2.5	1.0	17	dbSNP_86	59	2644,5956	426.6+/-355.3	424,1796,2080	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	58,58	956,2898,2649	TT,TC,CC		30.7442,49.1602,36.9829	benign,benign	941/1389,972/1420	2091765	4810,8196	2203	4300	6503	SO:0001583	missense	23293	exon11			GAGCTGCGGCTTG	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.2914G>A	17.37:g.2091765C>T	ENSP00000263073:p.Ala972Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	775	0.35485347985347987	268	0.5447154471544715	109	0.3011049723756906	158	0.2762237762237762	240	0.316622691292876	C	13.05	2.122399	0.37436	0.491602	0.307442	ENSG00000070366	ENST00000263073;ENST00000544865;ENST00000536871	T;T;T	0.28069	1.63;1.63;1.63	4.64	2.5	0.30297	.	0.140304	0.46145	D	0.000318	T	0.00012	0.0000	N	0.02539	-0.55	0.34659	P	0.277548	B	0.02656	0.0	B	0.04013	0.001	T	0.46076	-0.9217	9	0.23891	T	0.37	-5.3127	4.3033	0.10935	0.0:0.5427:0.0:0.4573	rs903160;rs52800764;rs56856254;rs903160	972	Q86US8	EST1A_HUMAN	T	972;941;64	ENSP00000263073:A972T;ENSP00000443920:A941T;ENSP00000440283:A64T	ENSP00000263073:A972T	A	-	1	0	SMG6	2038515	0.996000	0.38824	0.997000	0.53966	0.992000	0.81027	1.791000	0.38744	1.176000	0.42840	0.561000	0.74099	GCA	C|0.626;T|0.374	0.374	strong		0.587	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
ERCC6	2074	hgsc.bcm.edu	37	10	50667105	50667105	+	Missense_Mutation	SNP	T	T	C	rs2228529	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50667105T>C	ENST00000355832.5	-	21	4316	c.4238A>G	c.(4237-4239)cAg>cGg	p.Q1413R	ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000542458.1_Missense_Mutation_p.Q783R	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1413	Ubiquitin-binding domain (UBD).		Q -> R (in dbSNP:rs2228529). {ECO:0000269|PubMed:9443879, ECO:0000269|Ref.3}.		activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AGAAGCTTCCTGCAGGTGCCC	0.557								Direct reversal of damage;Nucleotide excision repair (NER)					T|||	896	0.178914	0.1248	0.2089	5008	,	,		16314	0.0437		0.2078	False		,,,				2504	0.3405				p.P1413R		Atlas-SNP	.											ERCC6,NS,carcinoma,0,1	ERCC6	162	1	0			c.C4238G						scavenged	.	T	ARG/GLN	596,3810	259.5+/-263.1	58,480,1665	101.0	97.0	98.0		4238	-4.9	0.0	10	dbSNP_98	98	1864,6736	332.7+/-320.2	196,1472,2632	yes	missense	ERCC6	NM_000124.2	43	254,1952,4297	CC,CT,TT		21.6744,13.527,18.9143	benign	1413/1494	50667105	2460,10546	2203	4300	6503	SO:0001583	missense	2074	exon21			GCTTCCTGCAGGT	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.4238A>G	10.37:g.50667105T>C	ENSP00000348089:p.Gln1413Arg	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	107	61	0.570093	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	340	0.15567765567765568	61	0.12398373983739837	82	0.2265193370165746	30	0.05244755244755245	167	0.22031662269129287	T	10.54	1.379579	0.24944	0.13527	0.216744	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.82619	-1.63;-1.38	5.5	-4.93	0.03066	.	.	.	.	.	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B	0.25521	0.128	B	0.16722	0.016	T	0.02015	-1.1229	8	0.15952	T	0.53	1.3308	9.0549	0.36399	0.1418:0.0:0.3427:0.5155	rs2228529;rs17775071;rs52790262;rs61459256;rs2228529	1413	Q03468	ERCC6_HUMAN	R	1413;790;783	ENSP00000348089:Q1413R;ENSP00000445134:Q783R	ENSP00000348089:Q1413R	Q	-	2	0	ERCC6	50337111	0.000000	0.05858	0.000000	0.03702	0.342000	0.28953	0.101000	0.15251	-0.673000	0.05259	-0.316000	0.08728	CAG	T|0.826;C|0.173	0.173	strong		0.557	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
MROH9	80133	hgsc.bcm.edu	37	1	170934394	170934394	+	Missense_Mutation	SNP	T	T	C	rs16863872	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:170934394T>C	ENST00000367758.3	+	7	577	c.478T>C	c.(478-480)Tac>Cac	p.Y160H	MROH9_ENST00000367759.4_Missense_Mutation_p.Y160H	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	160			Y -> H (in dbSNP:rs16863872).														AGTCAGAAAATACGTAAGTCA	0.398													T|||	179	0.0357428	0.0015	0.0476	5008	,	,		19974	0.0		0.0825	False		,,,				2504	0.0624				p.Y160H		Atlas-SNP	.											C1orf129_ENST00000367759,NS,carcinoma,-2,2	.	.	2	0			c.T478C						PASS	.	T	HIS/TYR,HIS/TYR	61,3761		0,61,1850	120.0	113.0	115.0		478,478	-3.0	0.0	1	dbSNP_123	115	692,7570		28,636,3467	yes	missense,missense	C1orf129	NM_001163629.1,NM_025063.2	83,83	28,697,5317	CC,CT,TT		8.3757,1.596,6.2314	benign,benign	160/862,160/574	170934394	753,11331	1911	4131	6042	SO:0001583	missense	80133	exon7			AGAAAATACGTAA	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.478T>C	1.37:g.170934394T>C	ENSP00000356732:p.Tyr160His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	83	0.038003663003663	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	60	0.079155672823219	T	3.376	-0.127423	0.06753	0.01596	0.083757	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.66099	-0.19;2.54	5.6	-2.97	0.05530	.	0.627172	0.15160	N	0.277198	T	0.24699	0.0599	L	0.60455	1.87	0.80722	P	0.0	B;B	0.21071	0.051;0.023	B;B	0.21917	0.037;0.016	T	0.05068	-1.0908	9	0.17369	T	0.5	-2.7243	1.7889	0.03047	0.133:0.3193:0.1372:0.4104	rs16863872;rs52808266;rs56468374;rs16863872	160;160	F5GWX6;Q5TGP6	.;CA129_HUMAN	H	160	ENSP00000356733:Y160H;ENSP00000356732:Y160H	ENSP00000356732:Y160H	Y	+	1	0	C1orf129	169201018	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.653000	0.05360	-0.153000	0.11137	-1.162000	0.01777	TAC	T|0.955;C|0.045	0.045	strong		0.398	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
GAB4	128954	hgsc.bcm.edu	37	22	17469026	17469026	+	Silent	SNP	G	G	A	rs5992604	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:17469026G>A	ENST00000400588.1	-	3	617	c.510C>T	c.(508-510)caC>caT	p.H170H	GAB4_ENST00000523144.1_Intron	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	170										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				AGCAGAGGCCGTGACTGGCTG	0.562													g|||	2125	0.424321	0.382	0.4611	5008	,	,		18368	0.4008		0.3966	False		,,,				2504	0.5082				p.H170H		Atlas-SNP	.											.	GAB4	95	.	0			c.C510T						PASS	.	-		1707,2563		370,967,798	45.0	57.0	53.0		510	-1.9	0.0	22	dbSNP_114	53	3592,4942		786,2020,1461	no	coding-synonymous	GAB4	NM_001037814.1		1156,2987,2259	AA,AG,GG		42.0905,39.9766,41.3855		170/575	17469026	5299,7505	2135	4267	6402	SO:0001819	synonymous_variant	128954	exon3			GAGGCCGTGACTG	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.510C>T	22.37:g.17469026G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			G|0.617;A|0.383	0.383	strong		0.562	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
DTHD1	401124	hgsc.bcm.edu	37	4	36310049	36310049	+	Missense_Mutation	SNP	C	C	T	rs12507599	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:36310049C>T	ENST00000456874.2	+	6	1712	c.1654C>T	c.(1654-1656)Cgt>Tgt	p.R552C	RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000507598.1_Missense_Mutation_p.R592C|DTHD1_ENST00000357504.3_Missense_Mutation_p.R387C	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	552			R -> C (in dbSNP:rs12507599). {ECO:0000269|PubMed:15489334}.		signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						AGAGCCATCTCGTCATTTCCA	0.373													C|||	1571	0.313698	0.2526	0.3141	5008	,	,		18858	0.369		0.2416	False		,,,				2504	0.4131				p.R552C		Atlas-SNP	.											.	DTHD1	63	.	0			c.C1654T						PASS	.	C	CYS/ARG,CYS/ARG	340,1044		32,276,384	77.0	67.0	70.0		1159,1654	2.0	0.0	4	dbSNP_120	70	823,2359		102,619,870	yes	missense,missense	DTHD1	NM_001136536.3,NM_001170700.1	180,180	134,895,1254	TT,TC,CC		25.8642,24.5665,25.4709	benign,benign	387/617,552/782	36310049	1163,3403	692	1591	2283	SO:0001583	missense	401124	exon6			CCATCTCGTCATT	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1654C>T	4.37:g.36310049C>T	ENSP00000401597:p.Arg552Cys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_001170700	B2RXK4|B4E2N7	Missense_Mutation	SNP	ENST00000456874.2	37	CCDS54754.1	594	0.27197802197802196	118	0.23983739837398374	119	0.3287292817679558	179	0.3129370629370629	178	0.23482849604221637	C	2.482	-0.319388	0.05386	0.245665	0.258642	ENSG00000197057	ENST00000357504;ENST00000507598;ENST00000456874	T;T;T	0.79141	-1.24;-1.24;-1.24	4.8	2.05	0.26809	.	0.666605	0.15021	N	0.284984	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.08889	-1.0700	9	0.49607	T	0.09	-2.7289	3.213	0.06689	0.1457:0.5709:0.1328:0.1506	rs12507599;rs56422944;rs12507599	387	Q6ZMT9-2	.	C	387;592;552	ENSP00000350103:R387C;ENSP00000424426:R592C;ENSP00000401597:R552C	ENSP00000350103:R387C	R	+	1	0	DTHD1	35986444	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.404000	0.20999	0.306000	0.22856	-0.137000	0.14449	CGT	C|0.725;T|0.275	0.275	strong		0.373	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
DUSP27	92235	hgsc.bcm.edu	37	1	167097567	167097567	+	Missense_Mutation	SNP	G	G	A	rs61748784	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:167097567G>A	ENST00000361200.2	+	6	3365	c.3199G>A	c.(3199-3201)Gac>Aac	p.D1067N	DUSP27_ENST00000443333.1_Missense_Mutation_p.D1067N|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.D1067N			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	1067					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CAGGTCCAGGGACTGGGAAGA	0.547													G|||	264	0.0527157	0.0061	0.0965	5008	,	,		18346	0.001		0.1441	False		,,,				2504	0.044				p.D1067N		Atlas-SNP	.											.	DUSP27	235	.	0			c.G3199A						PASS	.	G	ASN/ASP	111,4295	82.4+/-120.9	2,107,2094	35.0	38.0	37.0		3199	4.4	1.0	1	dbSNP_129	37	1192,7408	235.1+/-267.8	88,1016,3196	yes	missense	DUSP27	NM_001080426.1	23	90,1123,5290	AA,AG,GG		13.8605,2.5193,10.0185	probably-damaging	1067/1159	167097567	1303,11703	2203	4300	6503	SO:0001583	missense	92235	exon5			TCCAGGGACTGGG	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.3199G>A	1.37:g.167097567G>A	ENSP00000354483:p.Asp1067Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	149	0.06822344322344322	4	0.008130081300813009	46	0.1270718232044199	0	0.0	99	0.13060686015831136	G	5.526	0.281911	0.10458	0.025193	0.138605	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03413	3.94;3.94;3.94	5.29	4.38	0.52667	.	0.117062	0.38272	N	0.001750	T	0.02012	0.0063	M	0.63428	1.95	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.23404	-1.0189	9	0.59425	D	0.04	-28.1394	8.7774	0.34769	0.086:0.2759:0.6381:0.0	rs61748784	1067	Q5VZP5	DUS27_HUMAN	N	1067	ENSP00000354483:D1067N;ENSP00000271385:D1067N;ENSP00000404874:D1067N	ENSP00000271385:D1067N	D	+	1	0	DUSP27	165364191	0.191000	0.23288	0.973000	0.42090	0.084000	0.17831	0.856000	0.27818	1.223000	0.43536	0.549000	0.68633	GAC	G|0.904;A|0.096	0.096	strong		0.547	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
CCL14	6358	hgsc.bcm.edu	37	17	34313612	34313612	+	Missense_Mutation	SNP	G	G	A	rs75238886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:34313612G>A	ENST00000394509.4	-	1	182	c.74C>T	c.(73-75)tCc>tTc	p.S25F	CTB-186H2.3_ENST00000593057.1_Intron|CCL14_ENST00000536149.1_Missense_Mutation_p.S25F|CCL14_ENST00000480944.2_5'UTR|CCL14_ENST00000586216.1_Missense_Mutation_p.S25F|CCL14_ENST00000435911.2_Missense_Mutation_p.S25F|CCL15-CCL14_ENST00000481427.2_3'UTR|CTB-186H2.3_ENST00000591669.1_Missense_Mutation_p.E20K			Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14	25					cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)	extracellular space (GO:0005615)				large_intestine(1)|lung(6)	7		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTCACGTGAGGAGGATTCAGT	0.562													G|||	128	0.0255591	0.0197	0.0144	5008	,	,		16475	0.0466		0.0368	False		,,,				2504	0.0082				p.S25F		Atlas-SNP	.											.	CCL14	22	.	0			c.C74T						PASS	.	G	PHE/SER,PHE/SER	103,4303	81.9+/-120.4	1,101,2101	203.0	145.0	164.0		74,74	1.5	0.0	17	dbSNP_132	164	253,8347	99.9+/-161.4	0,253,4047	yes	missense,missense	CCL14	NM_032962.4,NM_032963.3	155,155	1,354,6148	AA,AG,GG		2.9419,2.3377,2.7372	probably-damaging,probably-damaging	25/110,25/94	34313612	356,12650	2203	4300	6503	SO:0001583	missense	6358	exon1			CGTGAGGAGGATT	Z49270	CCDS32624.1, CCDS45652.1	17q11.2	2014-04-10	2002-08-22	2002-08-23	ENSG00000213494	ENSG00000276409		"""Chemokine ligands"", ""Endogenous ligands"""	10612	protein-coding gene	gene with protein product		601392	"""small inducible cytokine subfamily A (Cys-Cys), member 14"""	SCYA14		8661057	Standard	NM_032963		Approved	HCC-1, HCC-3, NCC-2, SCYL2, CKb1, MCIF	uc010wcq.1	Q16627	OTTHUMG00000188403	ENST00000394509.4:c.74C>T	17.37:g.34313612G>A	ENSP00000378017:p.Ser25Phe	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_032962	E1P649|E1P650|Q13954	Missense_Mutation	SNP	ENST00000394509.4	37	CCDS32624.1	65	0.02976190476190476	10	0.02032520325203252	6	0.016574585635359115	19	0.033216783216783216	30	0.0395778364116095	G	13.77	2.335048	0.41398	0.023377	0.029419	ENSG00000213494	ENST00000394509;ENST00000536149;ENST00000435911	T;T;T	0.03831	4.14;3.79;3.79	4.74	1.52	0.23074	Chemokine interleukin-8-like domain (1);	0.920382	0.09005	U	0.862372	T	0.02119	0.0066	.	.	.	0.09310	N	1	D;D	0.57571	0.965;0.98	P;P	0.55303	0.598;0.773	T	0.34750	-0.9816	9	0.42905	T	0.14	.	7.2842	0.26328	0.0:0.1675:0.4863:0.3462	.	25;25	Q16627;Q16627-2	CCL14_HUMAN;.	F	25	ENSP00000378017:S25F;ENSP00000441771:S25F;ENSP00000409197:S25F	ENSP00000378017:S25F	S	-	2	0	CCL14	31337725	0.012000	0.17670	0.000000	0.03702	0.004000	0.04260	1.387000	0.34430	0.180000	0.19960	-0.302000	0.09304	TCC	G|0.973;A|0.027	0.027	strong		0.562	CCL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272892.2	NM_032962	
CCR3	1232	hgsc.bcm.edu	37	3	46306700	46306700	+	Silent	SNP	T	T	C	rs4987053	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46306700T>C	ENST00000357422.2	+	4	594	c.51T>C	c.(49-51)taT>taC	p.Y17Y	CCR3_ENST00000395940.2_Silent_p.Y17Y|CCR3_ENST00000541018.1_Silent_p.Y17Y|CCR3_ENST00000395942.2_Silent_p.Y17Y|CCR3_ENST00000545097.1_Silent_p.Y38Y			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	17					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell proliferation (GO:0001938)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|chemokine receptor activity (GO:0004950)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(3)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(193;0.00119)|KIRC - Kidney renal clear cell carcinoma(197;0.0183)|Kidney(197;0.0216)		CATCCTACTATGATGACGTGG	0.488													T|||	578	0.115415	0.1573	0.0692	5008	,	,		20484	0.0337		0.0805	False		,,,				2504	0.2117				p.Y38Y		Atlas-SNP	.											.	CCR3	52	.	0			c.T114C						PASS	.	T	,,,	548,3858	249.0+/-256.6	37,474,1692	106.0	101.0	103.0		105,51,114,51	0.7	0.0	3	dbSNP_111	103	613,7987	160.7+/-213.8	22,569,3709	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CCR3	NM_001164680.1,NM_001837.3,NM_178328.1,NM_178329.2	,,,	59,1043,5401	CC,CT,TT		7.1279,12.4376,8.9266	,,,	35/374,17/356,38/377,17/356	46306700	1161,11845	2203	4300	6503	SO:0001819	synonymous_variant	1232	exon3			CTACTATGATGAC	AF247361	CCDS2738.1, CCDS54574.1	3p21.3	2012-08-08			ENSG00000183625	ENSG00000183625		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1604	protein-coding gene	gene with protein product		601268		CMKBR3			Standard	NM_178328		Approved	CC-CKR-3, CKR3, CD193	uc003cpk.2	P51677	OTTHUMG00000133484	ENST00000357422.2:c.51T>C	3.37:g.46306700T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	194	94	0.484536	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Silent	SNP	ENST00000357422.2	37	CCDS2738.1																																																																																			T|0.903;C|0.097	0.097	strong		0.488	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2		
MLF1	4291	hgsc.bcm.edu	37	3	158320703	158320703	+	Missense_Mutation	SNP	C	C	A	rs15967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:158320703C>A	ENST00000355893.5	+	6	814	c.676C>A	c.(676-678)Cct>Act	p.P226T	MLF1_ENST00000392822.3_Missense_Mutation_p.P257T|MLF1_ENST00000469452.1_Missense_Mutation_p.P158T|MLF1_ENST00000497004.1_3'UTR|MLF1_ENST00000478894.2_Missense_Mutation_p.P216T|MLF1_ENST00000471745.1_Missense_Mutation_p.P216T|MLF1_ENST00000359117.5_Missense_Mutation_p.P201T|MLF1_ENST00000482628.1_Missense_Mutation_p.P201T|MLF1_ENST00000484955.1_Missense_Mutation_p.P201T	NM_022443.4	NP_071888.1	P58340	MLF1_HUMAN	myeloid leukemia factor 1	226			P -> T (in dbSNP:rs15967).		cell cycle arrest (GO:0007050)|myeloid progenitor cell differentiation (GO:0002318)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)			large_intestine(3)	3		Melanoma(1037;0.000458)|Prostate(884;0.0235)|all_neural(597;0.0299)	Lung(72;0.00199)|LUSC - Lung squamous cell carcinoma(72;0.00256)			CCATGAGAATCCTGGCTCCCG	0.353			T	NPM1	AML								C|||	1644	0.328275	0.2595	0.3357	5008	,	,		18285	0.3264		0.3797	False		,,,				2504	0.365				p.P257T		Atlas-SNP	.		Dom	yes		3	3q25.1	4291	myeloid leukemia factor 1		L	.	MLF1	62	.	0			c.C769A						PASS	.	C	THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO	1172,3234	411.5+/-335.8	153,866,1184	100.0	95.0	96.0		601,601,769,472,646,676	-1.1	0.0	3	dbSNP_130	96	3341,5259	497.9+/-374.6	659,2023,1618	yes	missense,missense,missense,missense,missense,missense	MLF1	NM_001130156.2,NM_001130157.2,NM_001195432.1,NM_001195433.1,NM_001195434.1,NM_022443.4	38,38,38,38,38,38	812,2889,2802	AA,AC,CC		38.8488,26.6001,34.6994	benign,benign,benign,benign,benign,benign	201/244,201/244,257/300,158/201,216/259,226/269	158320703	4513,8493	2203	4300	6503	SO:0001583	missense	4291	exon8			GAGAATCCTGGCT	L49054	CCDS3182.1, CCDS46945.1, CCDS56286.1, CCDS56287.1, CCDS56288.1	3q25	2008-07-18			ENSG00000178053	ENSG00000178053			7125	protein-coding gene	gene with protein product	"""myeloid leukemia factor 1 variant 1"", ""myeloid leukemia factor 1 variant 2"", ""myeloid leukemia factor 1 variant 3"""	601402				8570204	Standard	NM_022443		Approved		uc003fcb.3	P58340	OTTHUMG00000158775	ENST00000355893.5:c.676C>A	3.37:g.158320703C>A	ENSP00000348157:p.Pro226Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001195432	E9PEU9|Q2TLE3|Q2TLE5|Q8N8F8|Q96MH1	Missense_Mutation	SNP	ENST00000355893.5	37	CCDS3182.1	748	0.3424908424908425	137	0.2784552845528455	130	0.35911602209944754	185	0.32342657342657344	296	0.39050131926121373	C	5.747	0.322256	0.10900	0.266001	0.388488	ENSG00000178053	ENST00000491767;ENST00000355893;ENST00000484955;ENST00000359117;ENST00000498592;ENST00000471745;ENST00000469452;ENST00000482628;ENST00000478894;ENST00000392822	T;T;T;T;T;T;T;T;T;T	0.44881	0.94;0.95;0.95;0.95;0.94;0.94;0.93;0.95;0.94;0.91	5.86	-1.14	0.09741	.	1.745900	0.02981	N	0.145676	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.27450	0.085;0.179;0.085	B;B;B	0.24974	0.026;0.057;0.026	T	0.31166	-0.9953	9	0.13108	T	0.6	1.0188	6.349	0.21365	0.0:0.3453:0.2373:0.4173	rs15967;rs1051384;rs3191775;rs17297392;rs17356837;rs17629834;rs52826737;rs61720717;rs17629834	158;257;226	Q2TLE5;Q8N8F8;P58340	.;.;MLF1_HUMAN	T	152;226;201;201;181;216;158;201;216;257	ENSP00000420410:P152T;ENSP00000348157:P226T;ENSP00000417835:P201T;ENSP00000352025:P201T;ENSP00000419636:P181T;ENSP00000420134:P216T;ENSP00000418595:P158T;ENSP00000417141:P201T;ENSP00000417777:P216T;ENSP00000376568:P257T	ENSP00000348157:P226T	P	+	1	0	MLF1	159803397	0.001000	0.12720	0.003000	0.11579	0.006000	0.05464	-0.079000	0.11357	-0.098000	0.12285	-0.482000	0.04802	CCT	T|0.055;G|0.123	.	strong		0.353	MLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352164.3	NM_022443	
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 GAIIx	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_ENST00000402174.1_Missense_Mutation_p.D450N|ZNRF3_ENST00000332811.4_Missense_Mutation_p.D450N|ZNRF3_ENST00000406323.3_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	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	86	27	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	
FGFBP3	143282	hgsc.bcm.edu	37	10	93668110	93668110	+	Missense_Mutation	SNP	T	T	A	rs1107947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:93668110T>A	ENST00000311575.5	-	2	780	c.617A>T	c.(616-618)gAg>gTg	p.E206V	RP11-402D21.2_ENST00000610263.1_RNA	NM_152429.4	NP_689642.3	Q8TAT2	FGFP3_HUMAN	fibroblast growth factor binding protein 3	206			E -> V (in dbSNP:rs1107947). {ECO:0000269|PubMed:16303743}.		positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of vascular permeability (GO:0043117)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	fibroblast growth factor binding (GO:0017134)|heparin binding (GO:0008201)			large_intestine(1)|prostate(1)	2		Colorectal(252;0.162)				CCTCTTGCCCTCGTTGGTCTT	0.721													T|||	671	0.133986	0.1135	0.1657	5008	,	,		12827	0.0208		0.2505	False		,,,				2504	0.136				p.E206V		Atlas-SNP	.											.	FGFBP3	6	.	0			c.A617T						PASS	.	T	VAL/GLU	623,3783	268.0+/-268.2	48,527,1628	62.0	67.0	65.0		617	-3.7	0.0	10	dbSNP_86	65	2201,6399	373.7+/-337.1	283,1635,2382	yes	missense	FGFBP3	NM_152429.4	121	331,2162,4010	AA,AT,TT		25.593,14.1398,21.7131	benign	206/259	93668110	2824,10182	2203	4300	6503	SO:0001583	missense	143282	exon2			TTGCCCTCGTTGG	AK075410	CCDS7418.1	10q23.33	2006-12-14	2006-12-14	2006-12-14	ENSG00000174721	ENSG00000174721			23428	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 13"""	C10orf13			Standard	NM_152429		Approved	MGC39320	uc001khq.4	Q8TAT2	OTTHUMG00000018751	ENST00000311575.5:c.617A>T	10.37:g.93668110T>A	ENSP00000339067:p.Glu206Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_152429	B2RD68|Q8NBN0	Missense_Mutation	SNP	ENST00000311575.5	37	CCDS7418.1	332	0.152014652014652	68	0.13821138211382114	63	0.17403314917127072	11	0.019230769230769232	190	0.25065963060686014	T	11.08	1.534716	0.27475	0.141398	0.25593	ENSG00000174721	ENST00000311575	T	0.15372	2.43	3.98	-3.7	0.04437	.	8.943870	0.00604	N	0.000383	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.16722	0.016	T	0.39418	-0.9615	9	0.36615	T	0.2	0.0545	8.5613	0.33511	0.0:0.391:0.4381:0.1709	rs1107947;rs1107947	206	Q8TAT2	FGFP3_HUMAN	V	206	ENSP00000339067:E206V	ENSP00000339067:E206V	E	-	2	0	FGFBP3	93658090	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-2.098000	0.01347	-0.953000	0.03645	-0.414000	0.06135	GAG	T|0.805;A|0.195	0.195	strong		0.721	FGFBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049379.1	NM_152429	
PNRC1	10957	hgsc.bcm.edu	37	6	89793894	89793894	+	Silent	SNP	G	G	C	rs1130809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:89793894G>C	ENST00000336032.3	+	2	1080	c.963G>C	c.(961-963)acG>acC	p.T321T	PNRC1_ENST00000369472.1_Silent_p.T136T|PNRC1_ENST00000354922.3_Silent_p.T136T	NM_006813.2	NP_006804.1	Q12796	PNRC1_HUMAN	proline-rich nuclear receptor coactivator 1	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(3)	6		all_cancers(76;3.64e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00527)		BRCA - Breast invasive adenocarcinoma(108;0.102)		ACTTAAAAACGCTCCTCAAAG	0.398										Multiple Myeloma(7;0.094)			G|||	1747	0.348842	0.2443	0.4006	5008	,	,		16481	0.6696		0.167	False		,,,				2504	0.3098				p.T321T		Atlas-SNP	.											.	PNRC1	17	.	0			c.G963C						PASS	.	G		989,3417	357.6+/-314.0	117,755,1331	58.0	57.0	57.0		963	3.4	1.0	6	dbSNP_86	57	1363,7235	255.9+/-280.6	110,1143,3046	no	coding-synonymous	PNRC1	NM_006813.2		227,1898,4377	CC,CG,GG		15.8525,22.4467,18.0867		321/328	89793894	2352,10652	2203	4299	6502	SO:0001819	synonymous_variant	10957	exon2			AAAAACGCTCCTC	U03105	CCDS5018.1	6q16.1	2008-02-05	2003-09-25	2003-09-26	ENSG00000146278	ENSG00000146278			17278	protein-coding gene	gene with protein product		606714	"""proline rich 2"""	PROL2		7578250	Standard	NM_006813		Approved	B4-2, PRR2	uc003pmv.3	Q12796	OTTHUMG00000015191	ENST00000336032.3:c.963G>C	6.37:g.89793894G>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	102	46	0.45098	NM_006813	B2R6Q0|E1P515|Q5T7J6|Q7Z5N0	Silent	SNP	ENST00000336032.3	37	CCDS5018.1																																																																																			G|0.746;C|0.254	0.254	strong		0.398	PNRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041471.1	NM_006813	
INTS1	26173	hgsc.bcm.edu	37	7	1538614	1538614	+	Silent	SNP	G	G	A	rs2289035	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:1538614G>A	ENST00000404767.3	-	8	1219	c.1134C>T	c.(1132-1134)ccC>ccT	p.P378P	INTS1_ENST00000493531.1_5'Flank|INTS1_ENST00000389470.4_Silent_p.P506P	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	378					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		cccgcACCTTGGGGTTCTGCA	0.716													G|||	2437	0.486621	0.4402	0.3761	5008	,	,		4515	0.7123		0.4483	False		,,,				2504	0.4346				p.P378P		Atlas-SNP	.											.	INTS1	145	.	0			c.C1134T						PASS	.			1228,2098		284,660,719	6.0	7.0	7.0		1134	1.7	1.0	7	dbSNP_100	7	2736,4670		590,1556,1557	no	coding-synonymous	INTS1	NM_001080453.2		874,2216,2276	AA,AG,GG		36.943,36.9212,36.9363		378/2191	1538614	3964,6768	1663	3703	5366	SO:0001819	synonymous_variant	26173	exon8			CACCTTGGGGTTC	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1134C>T	7.37:g.1538614G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	35	25	0.714286	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			G|0.492;A|0.508	0.508	strong		0.716	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
OBSCN	84033	hgsc.bcm.edu	37	1	228471379	228471379	+	Silent	SNP	G	G	C	rs56168609	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228471379G>C	ENST00000422127.1	+	33	8957	c.8913G>C	c.(8911-8913)cgG>cgC	p.R2971R	OBSCN_ENST00000284548.11_Silent_p.R2971R|OBSCN_ENST00000359599.6_Silent_p.R1818R|OBSCN_ENST00000366709.4_Silent_p.R90R|OBSCN_ENST00000366707.4_Silent_p.R90R|OBSCN_ENST00000570156.2_Silent_p.R3400R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2971	Ig-like 29.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGACCCTGCGGCTCACCATCA	0.677													g|||	1153	0.230232	0.1989	0.3242	5008	,	,		17988	0.1528		0.3499	False		,,,				2504	0.1626				p.R3400R		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,+1,4	OBSCN	2142	4	0			c.G10200C						PASS	.		,	1049,3203		133,783,1210	36.0	44.0	41.0		8913,8913	0.3	0.1	1	dbSNP_129	41	3121,5357		597,1927,1715	yes	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	730,2710,2925	CC,CG,GG		36.8129,24.6707,32.7573	,	2971/7969,2971/6621	228471379	4170,8560	2126	4239	6365	SO:0001819	synonymous_variant	84033	exon38			CCTGCGGCTCACC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.8913G>C	1.37:g.228471379G>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.721;C|0.279	0.279	strong		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
GSDMC	56169	hgsc.bcm.edu	37	8	130760850	130760850	+	Missense_Mutation	SNP	A	A	G	rs4144738	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:130760850A>G	ENST00000276708.4	-	14	2305	c.1424T>C	c.(1423-1425)aTg>aCg	p.M475T		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	475			M -> T (in dbSNP:rs4144738). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)		p.M475T(1)		autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						ATCCAGCTCCATCCTAAGGCC	0.587													A|||	3542	0.707268	0.9402	0.6427	5008	,	,		20453	0.744		0.4702	False		,,,				2504	0.6442				p.M475T		Atlas-SNP	.											GSDMC,NS,carcinoma,0,1	GSDMC	71	1	1	Substitution - Missense(1)	stomach(1)	c.T1424C						PASS	.	A	THR/MET	3853,553	776.1+/-414.1	1694,465,44	107.0	98.0	101.0		1424	4.7	0.0	8	dbSNP_110	101	3920,4680	547.3+/-385.1	909,2102,1289	yes	missense	GSDMC	NM_031415.2	81	2603,2567,1333	GG,GA,AA		45.5814,12.5511,40.2353	possibly-damaging	475/509	130760850	7773,5233	2203	4300	6503	SO:0001583	missense	56169	exon14			AGCTCCATCCTAA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.1424T>C	8.37:g.130760850A>G	ENSP00000276708:p.Met475Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	109	41	0.376147	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	37	CCDS6360.1	1444	0.6611721611721612	456	0.926829268292683	226	0.6243093922651933	411	0.7185314685314685	351	0.4630606860158311	A	15.34	2.805191	0.50315	0.874489	0.455814	ENSG00000147697	ENST00000276708	T	0.24350	1.86	4.72	4.72	0.59763	.	0.534882	0.19047	N	0.124142	T	0.00012	0.0000	M	0.63843	1.955	0.80722	P	0.0	D	0.69078	0.997	D	0.65233	0.933	T	0.02081	-1.1217	9	0.87932	D	0	.	10.5105	0.44860	1.0:0.0:0.0:0.0	rs4144738;rs17855854;rs52804384;rs61422280;rs4144738	475	Q9BYG8	GSDMC_HUMAN	T	475	ENSP00000276708:M475T	ENSP00000276708:M475T	M	-	2	0	GSDMC	130830032	0.005000	0.15991	0.005000	0.12908	0.172000	0.22775	2.231000	0.43009	1.997000	0.58415	0.477000	0.44152	ATG	A|0.363;G|0.637	0.637	strong		0.587	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
SEMA6C	10500	hgsc.bcm.edu	37	1	151110832	151110832	+	Silent	SNP	G	G	A	rs72708441	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:151110832G>A	ENST00000341697.3	-	8	2198	c.507C>T	c.(505-507)tgC>tgT	p.C169C				Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	169	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CATCAAAGGGGCATCGAGCCT	0.577													G|||	132	0.0263578	0.0038	0.049	5008	,	,		19961	0.0		0.0805	False		,,,				2504	0.0123				p.C169C		Atlas-SNP	.											.	SEMA6C	70	.	0			c.C507T						PASS	.	G	,,	73,4333	65.3+/-102.7	0,73,2130	85.0	84.0	85.0		507,507,507	3.9	1.0	1	dbSNP_130	85	712,7888	173.0+/-223.6	27,658,3615	no	coding-synonymous,coding-synonymous,coding-synonymous	SEMA6C	NM_001178061.1,NM_001178062.1,NM_030913.4	,,	27,731,5745	AA,AG,GG		8.2791,1.6568,6.0357	,,	169/963,169/923,169/931	151110832	785,12221	2203	4300	6503	SO:0001819	synonymous_variant	10500	exon8			AAAGGGGCATCGA	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"""Semaphorins"""	10740	protein-coding gene	gene with protein product	"""m-Sema Y2"""	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.507C>T	1.37:g.151110832G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Silent	SNP	ENST00000341697.3	37	CCDS984.1																																																																																			G|0.947;A|0.053	0.053	strong		0.577	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913	
TBCD	6904	hgsc.bcm.edu	37	17	80887244	80887244	+	Silent	SNP	T	T	C	rs1127986	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:80887244T>C	ENST00000355528.4	+	32	2989	c.2859T>C	c.(2857-2859)gaT>gaC	p.D953D	TBCD_ENST00000539345.2_Silent_p.D953D	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	953					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			GCAGGTCCGATGTGGCCTCCG	0.657													C|||	1207	0.241014	0.2496	0.2406	5008	,	,		16468	0.1796		0.2893	False		,,,				2504	0.2434				p.D953D		Atlas-SNP	.											.	TBCD	94	.	0			c.T2859C						PASS	.	C		969,3357		113,743,1307	56.0	64.0	61.0		2859	-4.5	0.0	17	dbSNP_86	61	2121,6365		268,1585,2390	no	coding-synonymous	TBCD	NM_005993.4		381,2328,3697	CC,CT,TT		24.9941,22.3994,24.118		953/1193	80887244	3090,9722	2163	4243	6406	SO:0001819	synonymous_variant	6904	exon32			GTCCGATGTGGCC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.2859T>C	17.37:g.80887244T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	37	CCDS45818.1																																																																																			T|0.751;C|0.249	0.249	strong		0.657	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
SLC45A1	50651	hgsc.bcm.edu	37	1	8390384	8390384	+	Silent	SNP	G	G	C	rs56125713	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:8390384G>C	ENST00000471889.1	+	5	1216	c.831G>C	c.(829-831)ctG>ctC	p.L277L	SLC45A1_ENST00000289877.8_Silent_p.L277L|Y_RNA_ENST00000516445.1_RNA|SLC45A1_ENST00000377479.2_Silent_p.L311L			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	277					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CGGTCACCCTGAGCGTCACCA	0.652													G|||	683	0.136382	0.0416	0.1225	5008	,	,		13280	0.0575		0.1759	False		,,,				2504	0.3149				p.L277L		Atlas-SNP	.											.	SLC45A1	85	.	0			c.G831C						PASS	.	G		279,4127	154.4+/-187.8	5,269,1929	61.0	62.0	62.0		831	3.5	1.0	1	dbSNP_129	62	1507,7093	284.0+/-296.4	136,1235,2929	no	coding-synonymous	SLC45A1	NM_001080397.1		141,1504,4858	CC,CG,GG		17.5233,6.3323,13.7321		277/749	8390384	1786,11220	2203	4300	6503	SO:0001819	synonymous_variant	50651	exon4			CACCCTGAGCGTC	AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"""Solute carriers"""	17939	protein-coding gene	gene with protein product	"""H+/sugar symporter"""	605763	"""deleted in neuroblastoma 5"""	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.831G>C	1.37:g.8390384G>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_001080397	Q5VY46|Q5VY49	Silent	SNP	ENST00000471889.1	37	CCDS30577.1																																																																																			G|0.867;C|0.133	0.133	strong		0.652	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5		
HSPA9	3313	hgsc.bcm.edu	37	5	137892170	137892170	+	Silent	SNP	G	G	A	rs10117	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:137892170G>A	ENST00000297185.3	-	16	2058	c.1933C>T	c.(1933-1935)Ctg>Ttg	p.L645L	SNORD63_ENST00000411005.1_RNA|HSPA9_ENST00000501917.2_Intron	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	645					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AACAGCTTCAGTGATGCCTGC	0.433													A|||	3234	0.645767	0.8207	0.3761	5008	,	,		19306	0.7907		0.4364	False		,,,				2504	0.6667				p.L645L		Atlas-SNP	.											.	HSPA9	49	.	0			c.C1933T						PASS	.	A		3248,1158	408.9+/-334.8	1193,862,148	193.0	189.0	190.0		1933	-3.8	0.8	5	dbSNP_52	190	3437,5163	637.7+/-399.3	681,2075,1544	no	coding-synonymous	HSPA9	NM_004134.6		1874,2937,1692	AA,AG,GG		39.9651,26.2823,48.6006		645/680	137892170	6685,6321	2203	4300	6503	SO:0001819	synonymous_variant	3313	exon16			GCTTCAGTGATGC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"""Heat shock proteins / HSP70"""	5244	protein-coding gene	gene with protein product		600548	"""heat shock 70kDa protein 9B (mortalin-2)"""	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.1933C>T	5.37:g.137892170G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Silent	SNP	ENST00000297185.3	37	CCDS4208.1																																																																																			G|0.442;A|0.558	0.558	strong		0.433	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
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 GAIIx	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_ENST00000446842.2_Silent_p.S215S|DST_ENST00000370769.4_Silent_p.S541S|DST_ENST00000370788.2_Silent_p.S541S|DST_ENST00000421834.2_Silent_p.S541S|DST_ENST00000370754.5_Silent_p.S719S|DST_ENST00000370765.6_Silent_p.S215S|DST_ENST00000312431.6_Silent_p.S541S|DST_ENST00000244364.6_Silent_p.S215S|DST_ENST00000518935.1_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		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	132	70	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	
MARCH4	57574	hgsc.bcm.edu	37	2	217148417	217148417	+	Silent	SNP	C	C	A	rs876771	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:217148417C>A	ENST00000273067.4	-	2	2318	c.552G>T	c.(550-552)tcG>tcT	p.S184S		NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	184						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		TGCACTTGACCGAGCCATCAC	0.607													C|||	2183	0.435903	0.3147	0.4308	5008	,	,		20032	0.4345		0.493	False		,,,				2504	0.546				p.S184S		Atlas-SNP	.											.	MARCH4	50	.	0			c.G552T						PASS	.	C		1453,2953	469.0+/-355.3	243,967,993	61.0	54.0	56.0		552	-8.5	0.5	2	dbSNP_86	56	4144,4456	565.2+/-388.4	976,2192,1132	no	coding-synonymous	MARCH4	NM_020814.2		1219,3159,2125	AA,AC,CC		48.186,32.9778,43.034		184/411	217148417	5597,7409	2203	4300	6503	SO:0001819	synonymous_variant	57574	exon2			CTTGACCGAGCCA	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	29269	protein-coding gene	gene with protein product		608208	"""membrane-associated ring finger (C3HC4) 4"""			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.552G>T	2.37:g.217148417C>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	68	42	0.617647	NM_020814	Q4KMN7|Q86WR8	Silent	SNP	ENST00000273067.4	37	CCDS33376.1																																																																																			C|0.576;A|0.424	0.424	strong		0.607	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814	
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 GAIIx	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	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	279	197	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	
ADAM19	8728	hgsc.bcm.edu	37	5	156936364	156936364	+	Missense_Mutation	SNP	T	T	C	rs1422795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:156936364T>C	ENST00000517905.1	-	9	894	c.850A>G	c.(850-852)Agt>Ggt	p.S284G	ADAM19_ENST00000257527.4_Missense_Mutation_p.S284G|ADAM19_ENST00000430702.2_Missense_Mutation_p.S17G|ADAM19_ENST00000394020.1_Missense_Mutation_p.S286G			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	284	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CGCCTCCAACTGAGAAAGGAC	0.483													T|||	2076	0.414537	0.6392	0.4438	5008	,	,		18036	0.126		0.3569	False		,,,				2504	0.4468				p.S284G		Atlas-SNP	.											.	ADAM19	216	.	0			c.A850G						PASS	.	T	GLY/SER	2552,1854	633.0+/-395.9	739,1074,390	101.0	96.0	98.0		850	1.3	0.5	5	dbSNP_88	98	3024,5576	465.5+/-366.5	521,1982,1797	yes	missense	ADAM19	NM_033274.3	56	1260,3056,2187	CC,CT,TT		35.1628,42.079,42.8725	possibly-damaging	284/919	156936364	5576,7430	2203	4300	6503	SO:0001583	missense	8728	exon9			TCCAACTGAGAAA	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.850A>G	5.37:g.156936364T>C	ENSP00000428654:p.Ser284Gly	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		826	0.3782051282051282	315	0.6402439024390244	158	0.43646408839779005	82	0.14335664335664336	271	0.3575197889182058	T	13.02	2.112287	0.37242	0.57921	0.351628	ENSG00000135074	ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.39	1.33	0.21861	.	0.504141	0.21542	N	0.072867	T	0.00012	0.0000	L	0.42581	1.335	0.33665	P	0.38981600000000005	P;P	0.47545	0.897;0.682	B;B	0.39217	0.294;0.079	T	0.47018	-0.9149	9	0.33141	T	0.24	.	0.4223	0.00458	0.3419:0.1668:0.1317:0.3596	rs1422795;rs60215604;rs1422795	284;17	Q9H013-2;E9PD32	.;.	G	17;284;286;284	ENSP00000414088:S17G;ENSP00000257527:S284G;ENSP00000377588:S286G;ENSP00000428654:S284G	ENSP00000257527:S284G	S	-	1	0	ADAM19	156868942	0.000000	0.05858	0.470000	0.27216	0.961000	0.63080	0.027000	0.13621	0.411000	0.25702	0.533000	0.62120	AGT	T|0.592;C|0.408	0.408	strong		0.483	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
CDCA7L	55536	hgsc.bcm.edu	37	7	21956405	21956405	+	Silent	SNP	G	G	A	rs1128250	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:21956405G>A	ENST00000406877.3	-	2	411	c.132C>T	c.(130-132)tgC>tgT	p.C44C	CDCA7L_ENST00000373934.4_Silent_p.C44C|CDCA7L_ENST00000465490.1_5'UTR|CDCA7L_ENST00000356195.5_Silent_p.C10C	NM_018719.4	NP_061189.2	Q96GN5	CDA7L_HUMAN	cell division cycle associated 7-like	44					positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	29						CAAAACTATCGCAGCTCTCCT	0.468													G|||	1548	0.309105	0.1074	0.4179	5008	,	,		17366	0.5784		0.1779	False		,,,				2504	0.362				p.C44C		Atlas-SNP	.											CDCA7L,caecum,carcinoma,0,1	CDCA7L	56	1	0			c.C132T						PASS	.	G	,,	581,3825	258.6+/-262.5	35,511,1657	173.0	164.0	167.0		30,132,132	-9.0	0.5	7	dbSNP_86	167	1598,7002	297.5+/-303.5	156,1286,2858	no	coding-synonymous,coding-synonymous,coding-synonymous	CDCA7L	NM_001127370.2,NM_001127371.2,NM_018719.4	,,	191,1797,4515	AA,AG,GG		18.5814,13.1866,16.7538	,,	10/421,44/409,44/455	21956405	2179,10827	2203	4300	6503	SO:0001819	synonymous_variant	55536	exon2			ACTATCGCAGCTC		CCDS5374.1, CCDS47558.1, CCDS47559.1	7p15.3	2007-04-27			ENSG00000164649	ENSG00000164649			30777	protein-coding gene	gene with protein product		609685				16829576	Standard	NM_018719		Approved	RAM2, R1, JPO2	uc010kuk.3	Q96GN5	OTTHUMG00000128429	ENST00000406877.3:c.132C>T	7.37:g.21956405G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	49	8	0.163265	NM_018719	A4D141|A6NF50|B3KTR5|B4DUT3|C9K0Y1|Q6PIL4|Q86YT0|Q8IXN5|Q96C70|Q9H9A2|Q9NPV2	Silent	SNP	ENST00000406877.3	37	CCDS5374.1																																																																																			G|0.773;A|0.227	0.227	strong		0.468	CDCA7L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250218.4	NM_018719	
MTHFR	4524	hgsc.bcm.edu	37	1	11863057	11863057	+	Silent	SNP	G	G	A	rs2066470	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11863057G>A	ENST00000376592.1	-	1	245	c.117C>T	c.(115-117)ccC>ccT	p.P39P	MTHFR_ENST00000376585.1_Silent_p.P80P|MTHFR_ENST00000376583.3_Silent_p.P80P|MTHFR_ENST00000376590.3_Silent_p.P39P			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	39					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	CATGCCGCTCGGGGTCCAGGC	0.592													G|||	509	0.101637	0.0719	0.0548	5008	,	,		18607	0.123		0.0984	False		,,,				2504	0.1564				p.P39P		Atlas-SNP	.											.	MTHFR	65	.	0			c.C117T						PASS	.	G		345,4061	180.1+/-208.5	15,315,1873	60.0	57.0	58.0		117	-11.3	0.0	1	dbSNP_94	58	822,7778	190.8+/-237.2	41,740,3519	no	coding-synonymous	MTHFR	NM_005957.4		56,1055,5392	AA,AG,GG		9.5581,7.8302,8.9728		39/657	11863057	1167,11839	2203	4300	6503	SO:0001819	synonymous_variant	4524	exon2			CCGCTCGGGGTCC	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.117C>T	1.37:g.11863057G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Silent	SNP	ENST00000376592.1	37	CCDS137.1																																																																																			G|0.910;A|0.090	0.090	strong		0.592	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
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 GAIIx	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		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	79	29	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	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377853	138377853	+	Silent	SNP	A	A	G	rs2004074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138377853A>G	ENST00000356818.2	+	4	2046	c.1497A>G	c.(1495-1497)gtA>gtG	p.V499V	PPP1R26_ENST00000605286.1_Silent_p.V499V|PPP1R26_ENST00000605660.1_Silent_p.V499V|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Silent_p.V499V|PPP1R26_ENST00000401470.3_Silent_p.V499V	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	499					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CGGCCCCTGTAGAGGGCAGTG	0.612													G|||	2141	0.427516	0.3275	0.4971	5008	,	,		18876	0.6577		0.2107	False		,,,				2504	0.499				p.V499V		Atlas-SNP	.											KIAA0649,colon,carcinoma,0,1	.	.	1	0			c.A1497G						scavenged	.	G		1266,3140	686.0+/-404.6	174,918,1111	48.0	48.0	48.0		1497	2.8	0.0	9	dbSNP_92	48	1799,6801	719.5+/-406.3	193,1413,2694	no	coding-synonymous	KIAA0649	NM_014811.3		367,2331,3805	GG,GA,AA		20.9186,28.7335,23.566		499/1210	138377853	3065,9941	2203	4300	6503	SO:0001819	synonymous_variant	9858	exon4			CCCTGTAGAGGGC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1497A>G	9.37:g.138377853A>G		Somatic	44	1	0.0227273		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			A|0.691;G|0.309	0.309	strong		0.612	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
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 GAIIx	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|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_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		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	72	31	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	
MAP7D2	256714	hgsc.bcm.edu	37	X	20071046	20071046	+	Missense_Mutation	SNP	T	T	C	rs34519770	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:20071046T>C	ENST00000379651.3	-	5	563	c.545A>G	c.(544-546)aAt>aGt	p.N182S	MAP7D2_ENST00000543767.1_Missense_Mutation_p.N75S|MAP7D2_ENST00000443379.3_Intron|MAP7D2_ENST00000452324.3_Missense_Mutation_p.N138S|MAP7D2_ENST00000379643.5_Missense_Mutation_p.N182S	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	182			N -> S (in dbSNP:rs34519770). {ECO:0000269|PubMed:15489334}.		microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						CAGGCGTTTATTCATGGGAGG	0.438													C|||	1357	0.35947	0.7005	0.196	3775	,	,		17451	0.0248		0.1899	False		,,,				2504	0.0808				p.N182S		Atlas-SNP	.											.	MAP7D2	165	.	0			c.A545G						PASS	.	C	,SER/ASN,SER/ASN,SER/ASN	3197,638		1131,453,482,48,89	244.0	193.0	210.0		,545,413,545	2.9	1.0	X	dbSNP_126	210	1806,4922		164,948,530,1316,1342	yes	intron,missense,missense,missense	MAP7D2	NM_001168466.1,NM_152780.3,NM_001168467.1,NM_001168465.1	,46,46,46	1295,1401,1012,1364,1431	CC,CT,C,TT,T		26.843,16.6362,47.3634	,benign,benign,benign	,182/733,138/681,182/774	20071046	5003,5560	2203	4300	6503	SO:0001583	missense	256714	exon5			CGTTTATTCATGG	BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.545A>G	X.37:g.20071046T>C	ENSP00000368972:p.Asn182Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	156	115	0.737179	NM_152780	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	580	0.34960819770946355	238	0.8380281690140845	60	0.18404907975460122	7	0.012455516014234875	100	0.1510574018126888	C	4.736	0.136847	0.09032	0.833638	0.26843	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000452324;ENST00000330274	T;T;T;T	0.03496	4.06;4.06;3.91;4.06	5.64	2.93	0.34026	.	0.061993	0.64402	N	0.000003	T	0.00012	0.0000	N	0.01761	-0.735	0.58432	P	4.000000000004E-6	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.12156	0.001;0.001;0.007;0.0;0.001	T	0.28004	-1.0057	9	0.02654	T	1	-4.5167	9.4993	0.39008	0.0:0.6418:0.0:0.3582	rs34519770;rs61426853;rs34519770	138;182;215;182;75	C9JYW0;Q96T17-2;B5ME62;Q96T17;F5GYC2	.;.;.;MA7D2_HUMAN;.	S	182;182;75;138;215	ENSP00000368972:N182S;ENSP00000368964:N182S;ENSP00000440691:N75S;ENSP00000413301:N138S	ENSP00000332677:N215S	N	-	2	0	MAP7D2	19980967	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	0.953000	0.29162	-0.033000	0.13736	-0.170000	0.13304	AAT	T|0.544;C|0.456	0.456	strong		0.438	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780	
TBX4	9496	hgsc.bcm.edu	37	17	59560685	59560685	+	Silent	SNP	C	C	T	rs2270150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:59560685C>T	ENST00000240335.1	+	8	1491	c.1446C>T	c.(1444-1446)gtC>gtT	p.V482V	TBX4_ENST00000589449.1_3'UTR|TBX4_ENST00000393853.4_Silent_p.V483V	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	482					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						AGTCTCAGGTCCGAGAGCGGG	0.622													C|||	521	0.104034	0.1188	0.1052	5008	,	,		17375	0.0268		0.1402	False		,,,				2504	0.1258				p.V482V		Atlas-SNP	.											.	TBX4	69	.	0			c.C1446T						PASS	.	C		571,3835	255.2+/-260.5	45,481,1677	59.0	61.0	61.0		1446	4.3	1.0	17	dbSNP_100	61	1184,7416	240.7+/-271.3	92,1000,3208	no	coding-synonymous	TBX4	NM_018488.2		137,1481,4885	TT,TC,CC		13.7674,12.9596,13.4938		482/546	59560685	1755,11251	2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			TCAGGTCCGAGAG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1446C>T	17.37:g.59560685C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			C|0.880;T|0.120	0.120	strong		0.622	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
TMEM51	55092	hgsc.bcm.edu	37	1	15541607	15541607	+	Silent	SNP	T	T	C	rs3820065	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:15541607T>C	ENST00000428417.1	+	2	470	c.24T>C	c.(22-24)aaT>aaC	p.N8N	TMEM51_ENST00000376008.2_Silent_p.N8N|TMEM51_ENST00000434578.2_Silent_p.N8N|TMEM51_ENST00000400796.3_Silent_p.N8N|TMEM51_ENST00000376014.3_Silent_p.N8N	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	8						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		CCAAGGCCAATGGCTCGCACT	0.577													C|||	797	0.159145	0.0764	0.1556	5008	,	,		19408	0.3294		0.162	False		,,,				2504	0.0951				p.N8N		Atlas-SNP	.											.	TMEM51	28	.	0			c.T24C						PASS	.	C	,,,	361,4045	775.5+/-414.1	18,325,1860	65.0	69.0	68.0		24,24,24,24	-0.3	1.0	1	dbSNP_107	68	1451,7149	733.4+/-406.9	125,1201,2974	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TMEM51	NM_001136216.1,NM_001136217.1,NM_001136218.1,NM_018022.2	,,,	143,1526,4834	CC,CT,TT		16.8721,8.1934,13.932	,,,	8/254,8/254,8/254,8/254	15541607	1812,11194	2203	4300	6503	SO:0001819	synonymous_variant	55092	exon2			GGCCAATGGCTCG	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 72"""	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.24T>C	1.37:g.15541607T>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_018022	A8K819	Silent	SNP	ENST00000428417.1	37	CCDS154.1																																																																																			T|0.843;C|0.157	0.157	strong		0.577	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022	
DSP	1832	hgsc.bcm.edu	37	6	7584617	7584617	+	Silent	SNP	C	C	T	rs2076300	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:7584617C>T	ENST00000379802.3	+	24	7463	c.7122C>T	c.(7120-7122)acC>acT	p.T2374T	DSP_ENST00000418664.2_Silent_p.T1775T	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2374	4.5 X 38 AA tandem repeats (Domain B).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.T2374T(1)		biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGATCGCAACCGGGGGGATCA	0.448													C|||	1060	0.211661	0.1369	0.2421	5008	,	,		21083	0.0744		0.3797	False		,,,				2504	0.2597				p.T2374T		Atlas-SNP	.											DSP,NS,carcinoma,0,1	DSP	306	1	1	Substitution - coding silent(1)	stomach(1)	c.C7122T						PASS	.	C	,	758,3648	308.0+/-290.3	71,616,1516	71.0	72.0	72.0		5325,7122	-11.2	0.1	6	dbSNP_96	72	3173,5427	480.6+/-370.4	595,1983,1722	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	666,2599,3238	TT,TC,CC		36.8953,17.2038,30.2245	,	1775/2273,2374/2872	7584617	3931,9075	2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			CGCAACCGGGGGG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.7122C>T	6.37:g.7584617C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	14	0.162791	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			C|0.732;T|0.268	0.268	strong		0.448	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
MRGPRD	116512	hgsc.bcm.edu	37	11	68748003	68748003	+	Silent	SNP	T	T	C	rs34847539	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:68748003T>C	ENST00000309106.3	-	1	452	c.453A>G	c.(451-453)acA>acG	p.T151T		NM_198923.2	NP_944605.2	Q8TDS7	MRGRD_HUMAN	MAS-related GPR, member D	151						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)	22			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GGAGACAGAGTGTCCACAGCA	0.572													C|||	3151	0.629193	0.8154	0.7983	5008	,	,		21728	0.4871		0.6412	False		,,,				2504	0.3916				p.T151T		Atlas-SNP	.											.	MRGPRD	53	.	0			c.A453G						PASS	.	C		3560,840	331.5+/-302.0	1448,664,88	64.0	56.0	59.0		453	-9.5	0.0	11	dbSNP_126	59	5360,3228	485.9+/-371.7	1680,2000,614	no	coding-synonymous	MRGPRD	NM_198923.2		3128,2664,702	CC,CT,TT		37.5873,19.0909,31.3212		151/322	68748003	8920,4068	2200	4294	6494	SO:0001819	synonymous_variant	116512	exon1			ACAGAGTGTCCAC	AB083627	CCDS31625.1	11q13.3	2012-08-21			ENSG00000172938	ENSG00000172938		"""GPCR / Class A : Orphans"""	29626	protein-coding gene	gene with protein product		607231				11551509, 12909716	Standard	NM_198923		Approved	mrgD	uc010rqf.2	Q8TDS7	OTTHUMG00000167896	ENST00000309106.3:c.453A>G	11.37:g.68748003T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	54	0.981818	NM_198923	Q8NGK7	Silent	SNP	ENST00000309106.3	37	CCDS31625.1																																																																																			T|0.325;C|0.675	0.675	strong		0.572	MRGPRD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396874.1	NM_198923	
ADD1	118	hgsc.bcm.edu	37	4	2906707	2906707	+	Missense_Mutation	SNP	G	G	T	rs4961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:2906707G>T	ENST00000398129.1	+	9	1398	c.1378G>T	c.(1378-1380)Ggg>Tgg	p.G460W	ADD1_ENST00000398123.2_Missense_Mutation_p.G460W|ADD1_ENST00000503455.2_Missense_Mutation_p.G460W|ADD1_ENST00000398125.1_Missense_Mutation_p.G460W|ADD1_ENST00000355842.3_Missense_Mutation_p.G460W|ADD1_ENST00000446856.1_Missense_Mutation_p.G460W|ADD1_ENST00000513328.2_Missense_Mutation_p.G460W|ADD1_ENST00000264758.7_Missense_Mutation_p.G460W			P35611	ADDA_HUMAN	adducin 1 (alpha)	460			G -> W (in dbSNP:rs4961). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:9674650}.		actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TTCCGAGGAAGGGCAGAATGG	0.557													G|||	1044	0.208466	0.0492	0.1744	5008	,	,		21712	0.4524		0.2048	False		,,,				2504	0.2004				p.G460W	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.G1378T	GRCh37	CM021240	ADD1	M	rs4961	PASS	.	G	TRP/GLY,TRP/GLY,TRP/GLY,TRP/GLY	377,4029	190.5+/-216.4	20,337,1846	99.0	82.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1378,1378,1378,1378	5.6	1.0	4	dbSNP_52	88	1678,6922	308.9+/-309.1	161,1356,2783	yes	missense,missense,missense,missense	ADD1	NM_001119.4,NM_014189.3,NM_014190.3,NM_176801.2	184,184,184,184	181,1693,4629	TT,TG,GG		19.5116,8.5565,15.8004	probably-damaging,probably-damaging,probably-damaging,probably-damaging	460/738,460/769,460/632,460/663	2906707	2055,10951	2203	4300	6503	SO:0001583	missense	118	exon10			GAGGAAGGGCAGA	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.1378G>T	4.37:g.2906707G>T	ENSP00000381197:p.Gly460Trp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	103	38	0.368932	NM_014190	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	37	CCDS43205.1	543|543	0.24862637362637363|0.24862637362637363	23|23	0.046747967479674794|0.046747967479674794	66|66	0.18232044198895028|0.18232044198895028	288|288	0.5034965034965035|0.5034965034965035	166|166	0.21899736147757257|0.21899736147757257	G|G	20.8|20.8	4.049487|4.049487	0.75846|0.75846	0.085565|0.085565	0.195116|0.195116	ENSG00000087274|ENSG00000087274	ENST00000264758;ENST00000446856;ENST00000398125;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129|ENST00000514940	T;T;T;T;T;T;T;T|.	0.20738|.	2.05;2.05;2.05;2.05;2.05;2.05;2.05;2.05|.	5.55|5.55	5.55|5.55	0.83447|0.83447	.|.	0.048142|.	0.85682|.	D|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.64404|0.64404	1.975|1.975	0.09310|0.09310	P|P	0.9999999881077|0.9999999881077	D;D;D;D;D;D|.	0.89917|.	0.997;1.0;0.999;0.998;1.0;0.997|.	D;D;D;D;D;D|.	0.97110|.	0.972;1.0;0.986;0.97;1.0;0.972|.	T|T	0.42310|0.42310	-0.9459|-0.9459	9|4	0.66056|.	D|.	0.02|.	-32.0883|-32.0883	19.4964|19.4964	0.95075|0.95075	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs4961;rs52823896;rs61347248;rs4961|rs4961;rs52823896;rs61347248;rs4961	460;460;460;460;460;460|.	B4DI79;Q86XM2;P35611;P35611-3;P35611-2;A2A3N8|.	.;.;ADDA_HUMAN;.;.;.|.	W|N	460|165	ENSP00000264758:G460W;ENSP00000399828:G460W;ENSP00000381193:G460W;ENSP00000421907:G460W;ENSP00000423024:G460W;ENSP00000348100:G460W;ENSP00000381191:G460W;ENSP00000381197:G460W|.	ENSP00000264758:G460W|.	G|K	+|+	1|3	0|2	ADD1|ADD1	2876505|2876505	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.784000|0.784000	0.44337|0.44337	6.521000|6.521000	0.73778|0.73778	2.610000|2.610000	0.88304|0.88304	0.655000|0.655000	0.94253|0.94253	GGG|AAG	G|0.800;T|0.200	0.200	strong		0.557	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189	
C9orf66	157983	hgsc.bcm.edu	37	9	214864	214864	+	Missense_Mutation	SNP	C	C	T	rs2236547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:214864C>T	ENST00000382387.2	-	1	1029	c.533G>A	c.(532-534)cGg>cAg	p.R178Q	DOCK8_ENST00000432829.2_5'Flank|DOCK8_ENST00000453981.1_5'Flank	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	178			R -> Q (in dbSNP:rs2236547).							central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CAGCGCCGACCGACAGACGAG	0.692													T|||	1630	0.325479	0.326	0.3213	5008	,	,		11784	0.4117		0.2048	False		,,,				2504	0.363				p.R178Q		Atlas-SNP	.											C9orf66,rectum,carcinoma,0,1	C9orf66	16	1	0			c.G533A						PASS	.	T	GLN/ARG	1030,2672		136,758,957	20.0	17.0	18.0		533	3.5	0.4	9	dbSNP_98	18	1388,6106		127,1134,2486	yes	missense	C9orf66	NM_152569.2	43	263,1892,3443	TT,TC,CC		18.5215,27.8228,21.597	benign	178/296	214864	2418,8778	1851	3747	5598	SO:0001583	missense	157983	exon1			GCCGACCGACAGA	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.533G>A	9.37:g.214864C>T	ENSP00000371824:p.Arg178Gln	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_152569	Q96NB0	Missense_Mutation	SNP	ENST00000382387.2	37	CCDS6439.1	646	0.2957875457875458	174	0.35365853658536583	101	0.27900552486187846	211	0.3688811188811189	160	0.21108179419525067	.	9.102	1.004339	0.19199	0.278228	0.185215	ENSG00000183784	ENST00000382387	T	0.21031	2.03	4.63	3.46	0.39613	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999999980934	B	0.02656	0.0	B	0.01281	0.0	T	0.45862	-0.9232	8	0.87932	D	0	.	4.0571	0.09821	0.18:0.1005:0.0:0.7195	rs2236547;rs2236547	178	Q5T8R8	CI066_HUMAN	Q	178	ENSP00000371824:R178Q	ENSP00000371824:R178Q	R	-	2	0	C9orf66	204864	0.139000	0.22563	0.407000	0.26434	0.054000	0.15201	0.094000	0.15107	0.146000	0.19002	-0.524000	0.04348	CGG	C|0.737;T|0.263	0.263	strong		0.692	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569	
TEP1	7011	hgsc.bcm.edu	37	14	20852029	20852029	+	Missense_Mutation	SNP	A	A	G	rs1760904	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20852029A>G	ENST00000262715.5	-	25	3623	c.3583T>C	c.(3583-3585)Tca>Cca	p.S1195P	TEP1_ENST00000556935.1_Missense_Mutation_p.S1087P|TEP1_ENST00000545983.1_5'Flank	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1195	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		S -> P (in dbSNP:rs1760904). {ECO:0000269|PubMed:9020079}.		RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		AAGACTAATGATGCCACCTTG	0.537													G|||	3462	0.691294	0.9644	0.6196	5008	,	,		21215	0.6181		0.4732	False		,,,				2504	0.6728				p.S1195P		Atlas-SNP	.											.	TEP1	224	.	0			c.T3583C						PASS	.	G	PRO/SER	3918,488	218.7+/-236.7	1749,420,34	40.0	46.0	44.0		3583	4.8	0.5	14	dbSNP_89	44	4060,4540	582.2+/-391.4	941,2178,1181	yes	missense	TEP1	NM_007110.4	74	2690,2598,1215	GG,GA,AA		47.2093,11.0758,38.6591	benign	1195/2628	20852029	7978,5028	2203	4300	6503	SO:0001583	missense	7011	exon25			CTAATGATGCCAC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.3583T>C	14.37:g.20852029A>G	ENSP00000262715:p.Ser1195Pro	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	1384	0.6336996336996337	466	0.9471544715447154	211	0.5828729281767956	348	0.6083916083916084	359	0.4736147757255937	G	1.256	-0.617162	0.03663	0.889242	0.472093	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.78816	-1.21;-1.21	5.84	4.77	0.60923	NACHT nucleoside triphosphatase (1);	0.196582	0.44902	N	0.000417	T	0.00012	0.0000	N	0.02011	-0.69	0.44798	P	0.0021980000000000333	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38001	-0.9681	9	0.08599	T	0.76	-18.4575	9.2287	0.37423	0.1878:0.0:0.8122:0.0	rs1760904;rs2228038;rs17211362;rs52790546;rs60595270;rs1760904	1087;545;1195	G3V5X7;G3V2A4;Q99973	.;.;TEP1_HUMAN	P	1195;1195;1087	ENSP00000262715:S1195P;ENSP00000452574:S1087P	ENSP00000262715:S1195P	S	-	1	0	TEP1	19921869	0.410000	0.25376	0.493000	0.27502	0.915000	0.54546	0.938000	0.28965	1.489000	0.48450	-0.119000	0.15052	TCA	A|0.367;G|0.633	0.633	strong		0.537	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
MAPKAP1	79109	hgsc.bcm.edu	37	9	128246786	128246786	+	Silent	SNP	G	G	A	rs2070113	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:128246786G>A	ENST00000373498.1	-	8	1211	c.1143C>T	c.(1141-1143)caC>caT	p.H381H	MAPKAP1_ENST00000350766.3_Silent_p.H345H|MAPKAP1_ENST00000373511.2_Intron|MAPKAP1_ENST00000265960.3_Silent_p.H381H|MAPKAP1_ENST00000373497.5_Silent_p.H94H|MAPKAP1_ENST00000394063.1_Silent_p.H189H|MAPKAP1_ENST00000373503.3_Silent_p.H189H			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	381					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						ACTTGTAATGGTGGCTGCTAA	0.483													G|||	820	0.163738	0.0272	0.1643	5008	,	,		19569	0.2421		0.2256	False		,,,				2504	0.2035				p.H381H		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.C1143T						PASS	.	G	,,,,	288,4118	159.6+/-192.1	13,262,1928	273.0	210.0	231.0		1143,,567,567,1035	5.3	1.0	9	dbSNP_96	231	2030,6570	353.9+/-329.3	231,1568,2501	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	MAPKAP1	NM_001006617.1,NM_001006619.1,NM_001006620.1,NM_001006621.1,NM_024117.3	,,,,	244,1830,4429	AA,AG,GG		23.6047,6.5365,17.8225	,,,,	381/523,,189/331,189/331,345/487	128246786	2318,10688	2203	4300	6503	SO:0001819	synonymous_variant	79109	exon9			GTAATGGTGGCTG	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"""stress-activated protein kinase-interacting 1"""	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.1143C>T	9.37:g.128246786G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	199	97	0.487437	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Silent	SNP	ENST00000373498.1	37	CCDS35140.1																																																																																			G|0.819;T|0.001	.	strong		0.483	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1		
SLC17A4	10050	hgsc.bcm.edu	37	6	25776949	25776949	+	Missense_Mutation	SNP	G	G	A	rs11754288	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:25776949G>A	ENST00000377905.4	+	9	1233	c.1114G>A	c.(1114-1116)Gcc>Acc	p.A372T	SLC17A4_ENST00000439485.2_Missense_Mutation_p.A142T|SLC17A4_ENST00000397076.2_Missense_Mutation_p.A142T	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	372			A -> T (in dbSNP:rs11754288). {ECO:0000269|PubMed:15489334}.		phosphate ion transmembrane transport (GO:0035435)|phosphate-containing compound metabolic process (GO:0006796)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	sodium:phosphate symporter activity (GO:0005436)			breast(4)|endometrium(1)|kidney(4)|large_intestine(3)|lung(21)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						ACTCTTCACTGCCATTGGTAA	0.488													G|||	1302	0.259984	0.053	0.2781	5008	,	,		19704	0.1726		0.4205	False		,,,				2504	0.4519				p.A372T		Atlas-SNP	.											.	SLC17A4	79	.	0			c.G1114A						PASS	.	G	THR/ALA	490,3916	228.8+/-243.5	37,416,1750	151.0	133.0	139.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1114	-2.3	0.0	6	dbSNP_120	139	3781,4819	535.5+/-382.8	825,2131,1344	yes	missense	SLC17A4	NM_005495.2	58	862,2547,3094	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	43.9651,11.1212,32.8387	benign	372/498	25776949	4271,8735	2203	4300	6503	SO:0001583	missense	10050	exon9			TTCACTGCCATTG	AB020527	CCDS4564.1, CCDS75411.1	6p22.2	2013-07-18	2013-07-18		ENSG00000146039	ENSG00000146039		"""Solute carriers"""	10932	protein-coding gene	gene with protein product		604216	"""solute carrier family 17 (sodium phosphate), member 4"""			10319585	Standard	NM_005495		Approved	KIAA2138	uc003nfe.3	Q9Y2C5	OTTHUMG00000014410	ENST00000377905.4:c.1114G>A	6.37:g.25776949G>A	ENSP00000367137:p.Ala372Thr	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	194	43	0.221649	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	37	CCDS4564.1	527	0.2413003663003663	19	0.03861788617886179	107	0.2955801104972376	86	0.15034965034965034	315	0.4155672823218997	G	18.40	3.615050	0.66672	0.111212	0.439651	ENSG00000146039	ENST00000377905;ENST00000439485;ENST00000397076	T;T;T	0.62364	0.31;0.03;0.05	5.63	-2.34	0.06704	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.404392	0.21229	N	0.078008	T	0.15739	0.0379	N	0.11255	0.115	0.80722	P	0.0	B;B;B	0.27416	0.103;0.178;0.003	B;B;B	0.32928	0.038;0.155;0.023	T	0.10291	-1.0636	9	0.24483	T	0.36	.	4.0818	0.09929	0.2924:0.0:0.3584:0.3493	rs11754288;rs52807624;rs60432554;rs11754288	142;142;372	E7EPE8;E7EU17;Q9Y2C5	.;.;S17A4_HUMAN	T	372;142;142	ENSP00000367137:A372T;ENSP00000391345:A142T;ENSP00000380266:A142T	ENSP00000367137:A372T	A	+	1	0	SLC17A4	25884928	0.000000	0.05858	0.001000	0.08648	0.998000	0.95712	0.261000	0.18442	-0.335000	0.08451	0.655000	0.94253	GCC	G|0.711;A|0.289	0.289	strong		0.488	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1		
PIK3C2G	5288	hgsc.bcm.edu	37	12	18499636	18499636	+	Silent	SNP	C	C	T	rs17847788	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:18499636C>T	ENST00000266497.5	+	10	1529	c.1491C>T	c.(1489-1491)taC>taT	p.Y497Y	PIK3C2G_ENST00000538779.1_Silent_p.Y497Y|PIK3C2G_ENST00000535651.1_Silent_p.Y497Y|PIK3C2G_ENST00000433979.1_Silent_p.Y497Y			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	497	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.Y497Y(1)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TCAATGTCTACTGTAACAGCT	0.423													T|||	700	0.139776	0.1664	0.2493	5008	,	,		17634	0.1786		0.0915	False		,,,				2504	0.0358				p.Y497Y		Atlas-SNP	.											PIK3C2G_ENST00000433979,brain,glioma,0,3	PIK3C2G	315	3	1	Substitution - coding silent(1)	stomach(1)	c.C1491T						PASS	.	T		640,3218		46,548,1335	175.0	176.0	176.0		1491	-3.3	0.0	12	dbSNP_123	176	544,7712		12,520,3596	no	coding-synonymous	PIK3C2G	NM_004570.4		58,1068,4931	TT,TC,CC		6.5891,16.5889,9.7738		497/1446	18499636	1184,10930	1929	4128	6057	SO:0001819	synonymous_variant	5288	exon11			TGTCTACTGTAAC	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1491C>T	12.37:g.18499636C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	109	39	0.357798	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			C|0.869;T|0.131	0.131	strong		0.423	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
MBL2	4153	hgsc.bcm.edu	37	10	54531242	54531242	+	Missense_Mutation	SNP	G	G	A	rs5030737	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:54531242G>A	ENST00000373968.3	-	1	218	c.154C>T	c.(154-156)Cgt>Tgt	p.R52C		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	52	Collagen-like.		R -> C (in 0.05% of European and African populations; dbSNP:rs5030737). {ECO:0000269|PubMed:10447262, ECO:0000269|PubMed:15994813, ECO:0000269|PubMed:9743385}.		acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						GTGCCATCACGCCCATCTTTG	0.532													G|||	136	0.0271565	0.0015	0.0331	5008	,	,		19493	0.001		0.0596	False		,,,				2504	0.0511				p.R52C		Atlas-SNP	.											.	MBL2	55	.	0			c.C154T	GRCh37	CM960957	MBL2	M	rs5030737	PASS	.	G	CYS/ARG	52,4354	52.3+/-87.9	0,52,2151	132.0	119.0	123.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	154	3.1	0.9	10	dbSNP_113	123	596,8004	158.0+/-211.6	22,552,3726	yes	missense	MBL2	NM_000242.2	180	22,604,5877	AA,AG,GG		6.9302,1.1802,4.9823	probably-damaging	52/249	54531242	648,12358	2203	4300	6503	SO:0001583	missense	4153	exon1			CATCACGCCCATC	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"""Collectins"""	6922	protein-coding gene	gene with protein product		154545	"""mannose-binding lectin (protein C) 2, soluble (opsonic defect)"""	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.154C>T	10.37:g.54531242G>A	ENSP00000363079:p.Arg52Cys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Missense_Mutation	SNP	ENST00000373968.3	37	CCDS7247.1	62	0.028388278388278388	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	50	0.06596306068601583	G	17.29	3.352757	0.61293	0.011802	0.069302	ENSG00000165471	ENST00000373968	D	0.93307	-3.2	3.99	3.07	0.35406	.	0.247365	0.25161	N	0.032677	T	0.78704	0.4325	M	0.92691	3.335	0.42641	A	0.993411	D	0.89917	1.0	D	0.72338	0.977	D	0.84502	0.0617	9	0.72032	D	0.01	-3.3749	9.1124	0.36737	0.0:0.0:0.7818:0.2182	rs5030737;rs5030737	52	P11226	MBL2_HUMAN	C	52	ENSP00000363079:R52C	ENSP00000363079:R52C	R	-	1	0	MBL2	54201248	0.017000	0.18338	0.910000	0.35882	0.950000	0.60333	1.121000	0.31283	1.263000	0.44181	0.655000	0.94253	CGT	G|0.957;A|0.043	0.043	strong		0.532	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242	
WDR31	114987	hgsc.bcm.edu	37	9	116082647	116082647	+	Missense_Mutation	SNP	C	C	G	rs41307479	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:116082647C>G	ENST00000374193.4	-	9	1016	c.770G>C	c.(769-771)tGt>tCt	p.C257S	WDR31_ENST00000374195.3_Missense_Mutation_p.C132S|WDR31_ENST00000341761.4_Missense_Mutation_p.C256S|WDR31_ENST00000461942.1_5'UTR	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	257										NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						CGTGGCTTCACAGCCTTCTCC	0.512													C|||	510	0.101837	0.0098	0.0922	5008	,	,		20961	0.0456		0.1879	False		,,,				2504	0.2025				p.C257S		Atlas-SNP	.											.	WDR31	23	.	0			c.G770C						PASS	.	C	SER/CYS,SER/CYS	203,4203	124.5+/-161.8	6,191,2006	117.0	102.0	107.0		770,767	5.8	1.0	9	dbSNP_127	107	1797,6803	326.3+/-317.3	191,1415,2694	yes	missense,missense	WDR31	NM_001012361.2,NM_145241.3	112,112	197,1606,4700	GG,GC,CC		20.8953,4.6074,15.3775	possibly-damaging,possibly-damaging	257/368,256/367	116082647	2000,11006	2203	4300	6503	SO:0001583	missense	114987	exon9			GCTTCACAGCCTT	BC012352	CCDS6792.1, CCDS35110.1	9q33.1	2013-01-09			ENSG00000148225	ENSG00000148225		"""WD repeat domain containing"""	21421	protein-coding gene	gene with protein product	"""similar to spermatid WD-repeat protein"""						Standard	NM_145241		Approved	FLJ35921	uc004bhb.3	Q8NA23	OTTHUMG00000020525	ENST00000374193.4:c.770G>C	9.37:g.116082647C>G	ENSP00000363308:p.Cys257Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_001012361	Q5W0T9|Q96EG8	Missense_Mutation	SNP	ENST00000374193.4	37	CCDS35110.1	221	0.10119047619047619	4	0.008130081300813009	42	0.11602209944751381	23	0.04020979020979021	152	0.20052770448548812	C	21.9	4.210103	0.79240	0.046074	0.208953	ENSG00000148225	ENST00000374193;ENST00000374195;ENST00000341761	T;T;T	0.05717	3.4;3.4;3.4	5.84	5.84	0.93424	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	T	0.00012	0.0000	M	0.81802	2.56	0.09310	P	0.99999999398653	P;P	0.51537	0.91;0.946	P;P	0.51453	0.469;0.67	T	0.45542	-0.9254	9	0.09338	T	0.73	-9.5655	16.2152	0.82206	0.0:0.8673:0.1327:0.0	rs41307479;rs61732662	257;256	Q8NA23;Q8NA23-2	WDR31_HUMAN;.	S	257;132;256	ENSP00000363308:C257S;ENSP00000363310:C132S;ENSP00000345027:C256S	ENSP00000345027:C256S	C	-	2	0	WDR31	115122468	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.162000	0.64942	2.762000	0.94881	0.551000	0.68910	TGT	C|0.850;G|0.150	0.150	strong		0.512	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053734.2	NM_145241	
MYOM1	8736	hgsc.bcm.edu	37	18	3176063	3176063	+	Silent	SNP	C	C	T	rs2230162	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:3176063C>T	ENST00000356443.4	-	6	1332	c.999G>A	c.(997-999)ggG>ggA	p.G333G	MYOM1_ENST00000261606.7_Silent_p.G333G|MYOM1_ENST00000400569.3_Silent_p.G333G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	333	Ig-like C2-type 1.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GAGTGTGCATCCCATATCGAC	0.423													T|||	1368	0.273163	0.2436	0.2161	5008	,	,		22191	0.2659		0.3062	False		,,,				2504	0.3272				p.G333G		Atlas-SNP	.											.	MYOM1	192	.	0			c.G999A						PASS	.	T	,	1005,2911		130,745,1083	106.0	104.0	104.0		999,999	4.7	1.0	18	dbSNP_98	104	2585,5711		409,1767,1972	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	539,2512,3055	TT,TC,CC		31.1596,25.6639,29.3973	,	333/1686,333/1590	3176063	3590,8622	1958	4148	6106	SO:0001819	synonymous_variant	8736	exon6			GTGCATCCCATAT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.999G>A	18.37:g.3176063C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			T|0.164;G|0.282	0.164	strong		0.423	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
KRT72	140807	hgsc.bcm.edu	37	12	52986187	52986187	+	Missense_Mutation	SNP	T	T	C	rs12833456	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52986187T>C	ENST00000537672.2	-	4	801	c.791A>G	c.(790-792)tAt>tGt	p.Y264C	KRT72_ENST00000354310.4_Missense_Mutation_p.Y264C|KRT72_ENST00000293745.2_Missense_Mutation_p.Y264C|KRT72_ENST00000398066.3_Missense_Mutation_p.Y76C	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	264	Coil 1B.|Rod.		Y -> C (in dbSNP:rs12833456). {ECO:0000269|PubMed:14702039}.			extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		TACCCCTTCATAAAGGCACTT	0.498													T|||	1867	0.372804	0.1914	0.2406	5008	,	,		19422	0.5675		0.3638	False		,,,				2504	0.5204				p.Y264C		Atlas-SNP	.											.	KRT72	70	.	0			c.A791G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	1138,3268	405.3+/-333.4	156,826,1221	97.0	87.0	91.0		791,791,791	3.7	1.0	12	dbSNP_121	91	3281,5319	491.9+/-373.2	598,2085,1617	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	194,194,194	754,2911,2838	CC,CT,TT		38.1512,25.8284,33.9766	benign,benign,benign	264/512,264/470,264/512	52986187	4419,8587	2203	4300	6503	SO:0001583	missense	140807	exon4			CCTTCATAAAGGC	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.791A>G	12.37:g.52986187T>C	ENSP00000441160:p.Tyr264Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	785	0.35943223443223443	104	0.21138211382113822	83	0.2292817679558011	308	0.5384615384615384	290	0.38258575197889183	T	13.46	2.243523	0.39697	0.258284	0.381512	ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066	D;D;D;D	0.90261	-2.64;-2.64;-2.64;-2.64	4.85	3.67	0.42095	Filament (1);	0.439409	0.19225	N	0.119562	T	0.00012	0.0000	H	0.95187	3.635	0.40029	P	0.024499999999999966	B	0.15473	0.013	B	0.29077	0.098	T	0.18085	-1.0348	9	0.72032	D	0.01	.	11.0777	0.48040	0.1435:0.0:0.0:0.8565	rs12833456;rs52803577;rs58274768;rs12833456	264	Q14CN4	K2C72_HUMAN	C	264;264;264;76	ENSP00000441160:Y264C;ENSP00000293745:Y264C;ENSP00000346269:Y264C;ENSP00000446151:Y76C	ENSP00000293745:Y264C	Y	-	2	0	KRT72	51272454	0.053000	0.20554	0.979000	0.43373	0.908000	0.53690	0.153000	0.16323	0.914000	0.36822	0.482000	0.46254	TAT	C|0.351;N|0.000	0.351	strong		0.498	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
NME8	51314	hgsc.bcm.edu	37	7	37936530	37936530	+	Silent	SNP	T	T	C	rs3213975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:37936530T>C	ENST00000199447.4	+	17	1975	c.1603T>C	c.(1603-1605)Ttg>Ctg	p.L535L	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Silent_p.L535L	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	535	NDK 3.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)										ATGGAGACGATTGATGGGCCC	0.463													T|||	1034	0.20647	0.1672	0.2017	5008	,	,		16821	0.2292		0.2396	False		,,,				2504	0.2055				p.L535L		Atlas-SNP	.											.	.	.	.	0			c.T1603C						PASS	.	T		907,3499	348.2+/-309.8	94,719,1390	116.0	111.0	113.0		1603	-4.0	0.8	7	dbSNP_106	113	2077,6523	359.8+/-331.7	256,1565,2479	no	coding-synonymous	TXNDC3	NM_016616.4		350,2284,3869	CC,CT,TT		24.1512,20.5856,22.9433		535/589	37936530	2984,10022	2203	4300	6503	SO:0001819	synonymous_variant	51314	exon17			AGACGATTGATGG	AF202051	CCDS5452.1	7p15.2	2012-05-18	2012-05-18	2012-05-18	ENSG00000086288	ENSG00000086288			16473	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 2"""	607421	"""thioredoxin domain containing 3 (spermatozoa)"""	TXNDC3		11737268, 11768308, 19852809	Standard	NM_016616		Approved	CILD6, SPTRX2, NM23-H8	uc003tfn.3	Q8N427	OTTHUMG00000023716	ENST00000199447.4:c.1603T>C	7.37:g.37936530T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	61	42	0.688525	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	37	CCDS5452.1																																																																																			T|0.770;C|0.230	0.230	strong		0.463	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
DHDH	27294	hgsc.bcm.edu	37	19	49442933	49442933	+	Silent	SNP	T	T	C	rs2270939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49442933T>C	ENST00000221403.2	+	4	634	c.594T>C	c.(592-594)tcT>tcC	p.S198S	DHDH_ENST00000523250.1_Intron|DHDH_ENST00000522614.1_Silent_p.S198S	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	198					carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		AGAAGATTTCTGTCGTGGGAA	0.537													C|||	2269	0.453075	0.6982	0.2954	5008	,	,		18321	0.5675		0.2058	False		,,,				2504	0.3701				p.S198S		Atlas-SNP	.											.	DHDH	35	.	0			c.T594C						PASS	.	C		2781,1625	500.0+/-364.6	899,983,321	103.0	106.0	105.0		594	-9.9	0.0	19	dbSNP_100	105	1492,7108	749.0+/-407.4	130,1232,2938	no	coding-synonymous	DHDH	NM_014475.3		1029,2215,3259	CC,CT,TT		17.3488,36.8815,32.8541		198/335	49442933	4273,8733	2203	4300	6503	SO:0001819	synonymous_variant	27294	exon4			GATTTCTGTCGTG	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.594T>C	19.37:g.49442933T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	41	23	0.560976	NM_014475		Silent	SNP	ENST00000221403.2	37	CCDS12741.1																																																																																			T|0.623;C|0.377	0.377	strong		0.537	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
MAP3K6	9064	hgsc.bcm.edu	37	1	27687466	27687466	+	Missense_Mutation	SNP	G	G	T	rs35659744	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:27687466G>T	ENST00000493901.1	-	15	2105	c.1866C>A	c.(1864-1866)aaC>aaA	p.N622K	MAP3K6_ENST00000357582.2_Missense_Mutation_p.N622K|MAP3K6_ENST00000374040.3_Missense_Mutation_p.N614K	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	622			N -> K (in dbSNP:rs35659744). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		TGGAATCCGGGTTCGTCACCC	0.716													G|||	611	0.122005	0.0182	0.1571	5008	,	,		14370	0.0823		0.2684	False		,,,				2504	0.1278				p.N622K		Atlas-SNP	.											MAP3K6_ENST00000493901,brain,glioma,0,16	MAP3K6	134	16	0			c.C1866A						PASS	.	G	LYS/ASN	243,4005		10,223,1891	11.0	15.0	14.0		1866	-0.3	0.6	1	dbSNP_126	14	2513,5979		407,1699,2140	yes	missense	MAP3K6	NM_004672.3	94	417,1922,4031	TT,TG,GG		29.5926,5.7203,21.6327	benign	622/1289	27687466	2756,9984	2124	4246	6370	SO:0001583	missense	9064	exon14			ATCCGGGTTCGTC	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.1866C>A	1.37:g.27687466G>T	ENSP00000419591:p.Asn622Lys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	53	33	0.622642	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	324|324	0.14835164835164835|0.14835164835164835	7|7	0.014227642276422764|0.014227642276422764	60|60	0.16574585635359115|0.16574585635359115	57|57	0.09965034965034965|0.09965034965034965	200|200	0.2638522427440633|0.2638522427440633	G|G	11.29|11.29	1.595660|1.595660	0.28445|0.28445	0.057203|0.057203	0.295926|0.295926	ENSG00000142733|ENSG00000142733	ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582|ENST00000472410	T;T;T|.	0.65549|.	-0.16;-0.16;-0.16|.	5.2|5.2	-0.342|-0.342	0.12635|0.12635	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.10296|.	0.003;0.001|.	B;B|.	0.09377|.	0.004;0.002|.	T|T	0.35025|0.35025	-0.9805|-0.9805	8|4	0.41790|.	T|.	0.15|.	.|.	4.454|4.454	0.11635|0.11635	0.4176:0.2041:0.3783:0.0|0.4176:0.2041:0.3783:0.0	rs35659744;rs35659744|rs35659744;rs35659744	614;622|.	O95382-3;O95382|.	.;M3K6_HUMAN|.	K|N	614;622;345;622|346	ENSP00000363152:N614K;ENSP00000419591:N622K;ENSP00000350195:N622K|.	ENSP00000350195:N622K|.	N|T	-|-	3|2	2|0	MAP3K6|MAP3K6	27560053|27560053	0.001000|0.001000	0.12720|0.12720	0.648000|0.648000	0.29521|0.29521	0.791000|0.791000	0.44710|0.44710	0.029000|0.029000	0.13666|0.13666	0.246000|0.246000	0.21394|0.21394	-0.345000|-0.345000	0.07892|0.07892	AAC|ACC	G|0.846;T|0.154	0.154	strong		0.716	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
STARD13	90627	hgsc.bcm.edu	37	13	33704065	33704065	+	Missense_Mutation	SNP	T	T	C	rs3742321	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:33704065T>C	ENST00000336934.5	-	5	865	c.749A>G	c.(748-750)aAg>aGg	p.K250R	STARD13_ENST00000399365.3_Missense_Mutation_p.K132R|STARD13_ENST00000255486.4_Missense_Mutation_p.K242R	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	250			K -> R (in dbSNP:rs3742321).		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		CCTCGTGGGCTTCTCATTCTT	0.607													T|||	1082	0.216054	0.1059	0.3343	5008	,	,		18298	0.2123		0.2087	False		,,,				2504	0.2924				p.K250R		Atlas-SNP	.											.	STARD13	100	.	0			c.A749G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	575,3831	252.7+/-259.0	38,499,1666	66.0	65.0	66.0		395,749,725	4.4	0.9	13	dbSNP_107	66	1839,6761	327.9+/-318.0	224,1391,2685	yes	missense,missense,missense	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	26,26,26	262,1890,4351	CC,CT,TT		21.3837,13.0504,18.5607	benign,benign,benign	132/996,250/1114,242/1106	33704065	2414,10592	2203	4300	6503	SO:0001583	missense	90627	exon5			GTGGGCTTCTCAT	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.749A>G	13.37:g.33704065T>C	ENSP00000338785:p.Lys250Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	33	12	0.363636	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	452	0.20695970695970695	53	0.10772357723577236	101	0.27900552486187846	127	0.22202797202797203	171	0.22559366754617413	T	15.87	2.959655	0.53400	0.130504	0.213837	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934;ENST00000399364	T;T;T	0.08984	3.03;3.05;3.06	5.58	4.41	0.53225	.	0.133219	0.64402	D	0.000002	T	0.00012	0.0000	L	0.53671	1.685	0.09310	P	1.0	B;B;B;B	0.23128	0.036;0.074;0.044;0.08	B;B;B;B	0.31547	0.029;0.072;0.023;0.132	T	0.39354	-0.9618	9	0.59425	D	0.04	.	10.9262	0.47191	0.0:0.0731:0.0:0.9269	rs3742321;rs52804043;rs57344551;rs3742321	242;215;250;242	Q9Y3M8-5;Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;.;STA13_HUMAN;.	R	132;242;250;242	ENSP00000382300:K132R;ENSP00000255486:K242R;ENSP00000338785:K250R	ENSP00000255486:K242R	K	-	2	0	STARD13	32602065	1.000000	0.71417	0.928000	0.36995	0.943000	0.58893	3.287000	0.51732	2.125000	0.65367	0.460000	0.39030	AAG	T|0.811;C|0.189	0.189	strong		0.607	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
CES3	23491	hgsc.bcm.edu	37	16	66997756	66997756	+	Missense_Mutation	SNP	T	T	C	rs71647892	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:66997756T>C	ENST00000303334.4	+	4	549	c.478T>C	c.(478-480)Tac>Cac	p.Y160H	RP11-361L15.4_ENST00000566869.1_RNA|CES3_ENST00000394037.1_Missense_Mutation_p.Y160H	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	160			Y -> H (in dbSNP:rs71647892). {ECO:0000269|Ref.4}.			endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		TGCCACCTCCTACGATGGATC	0.597													t|||	19	0.00379393	0.0008	0.0058	5008	,	,		19782	0.0		0.0119	False		,,,				2504	0.002				p.Y160H		Atlas-SNP	.											.	CES3	56	.	0			c.T478C						PASS	.	T	HIS/TYR,HIS/TYR	13,4387	20.2+/-43.8	0,13,2187	137.0	119.0	125.0		478,478	1.0	0.0	16	dbSNP_130	125	88,8512	50.2+/-110.2	3,82,4215	yes	missense,missense	CES3	NM_001185177.1,NM_024922.5	83,83	3,95,6402	CC,CT,TT		1.0233,0.2955,0.7769	benign,benign	160/569,160/572	66997756	101,12899	2200	4300	6500	SO:0001583	missense	23491	exon4			ACCTCCTACGATG	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"""Carboxylesterases"""	1865	protein-coding gene	gene with protein product	"""esterase 31"", ""brain carboxylesterase BR3"""	605279	"""carboxylesterase 3 (brain)"""			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.478T>C	16.37:g.66997756T>C	ENSP00000304782:p.Tyr160His	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_024922	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Missense_Mutation	SNP	ENST00000303334.4	37	CCDS10826.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	11.27	1.590632	0.28357	0.002955	0.010233	ENSG00000172828	ENST00000303334;ENST00000394037	T;T	0.10763	2.84;2.84	4.15	0.972	0.19704	Carboxylesterase, type B (1);	0.741477	0.11078	N	0.602150	T	0.12135	0.0295	M	0.67625	2.065	0.25586	N	0.986746	P	0.35226	0.491	B	0.43728	0.429	T	0.21690	-1.0238	10	0.51188	T	0.08	.	7.0781	0.25215	0.0:0.4276:0.0:0.5724	.	160	Q6UWW8	EST3_HUMAN	H	160	ENSP00000304782:Y160H;ENSP00000377602:Y160H	ENSP00000304782:Y160H	Y	+	1	0	CES3	65555257	0.001000	0.12720	0.004000	0.12327	0.045000	0.14185	0.600000	0.24104	0.108000	0.17862	0.496000	0.49642	TAC	T|0.993;C|0.007	0.007	strong		0.597	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922	
LRP1B	53353	hgsc.bcm.edu	37	2	141259376	141259376	+	Silent	SNP	G	G	A	rs35164907	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:141259376G>A	ENST00000389484.3	-	55	9701	c.8730C>T	c.(8728-8730)tgC>tgT	p.C2910C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2910	LDL-receptor class A 20. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CCTTATTGTCGCAAAGACCTC	0.383										TSP Lung(27;0.18)			G|||	632	0.126198	0.0613	0.1167	5008	,	,		13824	0.0198		0.2465	False		,,,				2504	0.2065				p.C2910C	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C8730T						PASS	.	G		381,4025	192.3+/-217.7	15,351,1837	80.0	78.0	79.0		8730	3.4	1.0	2	dbSNP_126	79	2307,6293	386.9+/-342.0	309,1689,2302	no	coding-synonymous	LRP1B	NM_018557.2		324,2040,4139	AA,AG,GG		26.8256,8.6473,20.6674		2910/4600	141259376	2688,10318	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon55			ATTGTCGCAAAGA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8730C>T	2.37:g.141259376G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	40	0.784314	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.818;A|0.182	0.182	strong		0.383	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
CAND2	23066	hgsc.bcm.edu	37	3	12859004	12859004	+	Missense_Mutation	SNP	A	A	C	rs3732678	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:12859004A>C	ENST00000456430.2	+	10	2614	c.2573A>C	c.(2572-2574)cAc>cCc	p.H858P	CAND2_ENST00000295989.5_Missense_Mutation_p.H765P	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	858			H -> P (in dbSNP:rs3732678). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGGCCAGGCCACCAGCGGGAG	0.672													C|||	2866	0.572284	0.9713	0.4755	5008	,	,		18610	0.2897		0.6382	False		,,,				2504	0.3252				p.H858P	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.A2573C						PASS	.	C	PRO/HIS,PRO/HIS	3695,385		1677,341,22	42.0	52.0	49.0		2573,2294	3.9	1.0	3	dbSNP_107	49	5012,3388		1488,2036,676	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	77,77	3165,2377,698	CC,CA,AA		40.3333,9.4363,30.2324	benign,benign	858/1237,765/1120	12859004	8707,3773	2040	4200	6240	SO:0001583	missense	23066	exon10			CAGGCCACCAGCG		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.2573A>C	3.37:g.12859004A>C	ENSP00000387641:p.His858Pro	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1251	0.5728021978021978	464	0.943089430894309	168	0.46408839779005523	148	0.25874125874125875	471	0.6213720316622692	C	6.595	0.478073	0.12521	0.905637	0.596667	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.64618	-0.11;-0.11	4.83	3.88	0.44766	Armadillo-like helical (1);Armadillo-type fold (1);	0.556756	0.16689	N	0.203605	T	0.00012	0.0000	N	0.01576	-0.805	0.09310	P	0.99999999053269	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31971	-0.9924	9	0.29301	T	0.29	-12.7469	10.5248	0.44941	0.4804:0.5196:0.0:0.0	rs3732678;rs57480491	858;765	O75155;O75155-2	CAND2_HUMAN;.	P	765;858	ENSP00000295989:H765P;ENSP00000387641:H858P	ENSP00000295989:H765P	H	+	2	0	CAND2	12834004	0.991000	0.36638	1.000000	0.80357	0.980000	0.70556	2.850000	0.48294	1.150000	0.42419	-0.217000	0.12591	CAC	A|0.402;C|0.597;G|0.000	0.597	strong		0.672	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
SERPINA3	12	hgsc.bcm.edu	37	14	95081081	95081081	+	Silent	SNP	A	A	G	rs17826465	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:95081081A>G	ENST00000467132.1	+	2	1451	c.303A>G	c.(301-303)aaA>aaG	p.K101K	SERPINA3_ENST00000393078.3_Silent_p.K101K|SERPINA3_ENST00000482740.1_5'Flank|SERPINA3_ENST00000393080.4_Silent_p.K101K|RP11-986E7.7_ENST00000553947.1_3'UTR			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	101				K -> R (in Ref. 5; BAD92297). {ECO:0000305}.	acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		AGATTCTCAAAGGCCTCAAGT	0.552													A|||	224	0.0447284	0.0068	0.0648	5008	,	,		19293	0.004		0.1064	False		,,,				2504	0.0603				p.K101K		Atlas-SNP	.											.	SERPINA3	78	.	0			c.A303G						PASS	.	A		111,4295	84.4+/-122.9	3,105,2095	68.0	69.0	69.0		303	-0.0	0.3	14	dbSNP_123	69	959,7641	206.8+/-248.7	54,851,3395	no	coding-synonymous	SERPINA3	NM_001085.4		57,956,5490	GG,GA,AA		11.1512,2.5193,8.227		101/424	95081081	1070,11936	2203	4300	6503	SO:0001819	synonymous_variant	12	exon2			TCTCAAAGGCCTC	K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"""Serine (or cysteine) peptidase inhibitors"""	16	protein-coding gene	gene with protein product		107280	"""alpha-1-antichymotrypsin"", ""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"""	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.303A>G	14.37:g.95081081A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Silent	SNP	ENST00000467132.1	37	CCDS32150.1																																																																																			A|0.935;G|0.065	0.065	strong		0.552	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085	
IRAK2	3656	hgsc.bcm.edu	37	3	10264480	10264480	+	Missense_Mutation	SNP	C	C	G	rs3844283	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:10264480C>G	ENST00000256458.4	+	9	1264	c.1174C>G	c.(1174-1176)Ctg>Gtg	p.L392V		NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2	392	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> V (in dbSNP:rs3844283). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein phosphorylation (GO:0006468)|regulation of cytokine-mediated signaling pathway (GO:0001959)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)			breast(4)|large_intestine(8)|lung(11)|prostate(1)|stomach(1)	25						GGTGGGGCAGCTGACAAAGCG	0.537													C|||	1443	0.288139	0.2126	0.464	5008	,	,		19517	0.1339		0.4185	False		,,,				2504	0.2904				p.L392V		Atlas-SNP	.											IRAK2_ENST00000256458,caecum,carcinoma,-1,2	IRAK2	113	2	0			c.C1174G						PASS	.	C	VAL/LEU	1026,3380	379.2+/-323.2	115,796,1292	108.0	106.0	107.0		1174	5.1	1.0	3	dbSNP_108	107	3605,4995	521.0+/-379.8	768,2069,1463	yes	missense	IRAK2	NM_001570.3	32	883,2865,2755	GG,GC,CC		41.9186,23.2864,35.6066	probably-damaging	392/626	10264480	4631,8375	2203	4300	6503	SO:0001583	missense	3656	exon9			GGGCAGCTGACAA	AF026273	CCDS33697.1	3p25.2	2008-08-18			ENSG00000134070	ENSG00000134070			6113	protein-coding gene	gene with protein product		603304				9374458	Standard	XR_245126		Approved		uc003bve.1	O43187	OTTHUMG00000155358	ENST00000256458.4:c.1174C>G	3.37:g.10264480C>G	ENSP00000256458:p.Leu392Val	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_001570	B4DQZ6|Q08AG6|Q5K546	Missense_Mutation	SNP	ENST00000256458.4	37	CCDS33697.1	663	0.30357142857142855	90	0.18292682926829268	158	0.43646408839779005	84	0.14685314685314685	331	0.4366754617414248	C	19.36	3.812335	0.70912	0.232864	0.419186	ENSG00000134070	ENST00000256458	T	0.34667	1.35	5.14	5.14	0.70334	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.38436	N	0.001683	T	0.00012	0.0000	L	0.56199	1.76	0.19300	P	0.9999795581	D	0.89917	1.0	D	0.87578	0.998	T	0.46610	-0.9179	9	0.62326	D	0.03	-15.6131	14.105	0.65083	0.0:1.0:0.0:0.0	rs3844283;rs52790097;rs57169457;rs3844283	392	O43187	IRAK2_HUMAN	V	392	ENSP00000256458:L392V	ENSP00000256458:L392V	L	+	1	2	IRAK2	10239480	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	1.933000	0.40153	2.369000	0.80426	0.655000	0.94253	CTG	C|0.667;G|0.333	0.333	strong		0.537	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		
ZNF275	10838	hgsc.bcm.edu	37	X	152610985	152610985	+	Silent	SNP	T	T	C	rs3213466	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:152610985T>C	ENST00000421401.3	+	3	216	c.39T>C	c.(37-39)ccT>ccC	p.P13P	ZNF275_ENST00000370249.2_5'UTR|ZNF275_ENST00000440091.1_Silent_p.P43P|ZNF275_ENST00000370251.3_Silent_p.P13P			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	13					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(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CAGGCGTTCCTGTTTTAAATC	0.517													T|||	1776	0.470464	0.503	0.317	3775	,	,		15111	0.4286		0.2386	False		,,,				2504	0.2239				p.P13P		Atlas-SNP	.											.	ZNF275	44	.	0			c.T39C						PASS	.	T		2064,1512		536,655,337,312,233	81.0	79.0	80.0		39	2.3	0.9	X	dbSNP_106	80	2017,4563		244,971,558,1166,1260	no	coding-synonymous	ZNF275	NM_001080485.3		780,1626,895,1478,1493	CC,CT,C,TT,T		30.6535,42.2819,40.1831		13/330	152610985	4081,6075	2073	4199	6272	SO:0001819	synonymous_variant	10838	exon3			CGTTCCTGTTTTA	BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"""Zinc fingers, C2H2-type"", ""-"""	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.39T>C	X.37:g.152610985T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	NM_001080485	A6NE92	Silent	SNP	ENST00000421401.3	37																																																																																				0|0.006;C|0.479	0.479	strong		0.517	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485	
PRRC2B	84726	hgsc.bcm.edu	37	9	134350323	134350323	+	Missense_Mutation	SNP	C	C	G	rs10736851	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:134350323C>G	ENST00000357304.4	+	15	2862	c.2807C>G	c.(2806-2808)aCc>aGc	p.T936S	PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	936				T -> S (in Ref. 5; CAH18678). {ECO:0000305}.			poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						ACGGGCAGGACCCGGAGGTCG	0.607													C|||	3854	0.769569	0.5257	0.7478	5008	,	,		14629	0.9395		0.7654	False		,,,				2504	0.9438				p.T936S		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C2807G						PASS	.	C	SER/THR	2237,1529		655,927,301	14.0	16.0	16.0		2807	4.7	1.0	9	dbSNP_120	16	6630,1582		2687,1256,163	yes	missense	PRRC2B	NM_013318.3	58	3342,2183,464	GG,GC,CC		19.2645,40.6001,25.9726	possibly-damaging	936/2230	134350323	8867,3111	1883	4106	5989	SO:0001583	missense	84726	exon15			GCAGGACCCGGAG	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.2807C>G	9.37:g.134350323C>G	ENSP00000349856:p.Thr936Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	1661	0.7605311355311355	264	0.5365853658536586	280	0.7734806629834254	535	0.9353146853146853	582	0.7678100263852242	C	12.51	1.960869	0.34565	0.593999	0.807355	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.09817	2.94	5.61	4.69	0.59074	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	1.0	B	0.21071	0.051	B	0.12837	0.008	T	0.19647	-1.0299	7	.	.	.	.	13.9405	0.64052	0.0:0.7099:0.2901:0.0	rs10736851;rs10736851	936	Q5JSZ5	PRC2B_HUMAN	S	936;232	ENSP00000349856:T936S	.	T	+	2	0	PRRC2B	133340144	0.957000	0.32711	1.000000	0.80357	0.754000	0.42855	1.269000	0.33074	1.321000	0.45227	0.655000	0.94253	ACC	C|0.230;G|0.770	0.770	strong		0.607	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
NEB	4703	hgsc.bcm.edu	37	2	152420361	152420361	+	Silent	SNP	C	C	T	rs145252235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:152420361C>T	ENST00000172853.10	-	90	13599	c.13452G>A	c.(13450-13452)aaG>aaA	p.K4484K	NEB_ENST00000397345.3_Silent_p.K6185K|NEB_ENST00000603639.1_Silent_p.K6185K|NEB_ENST00000409198.1_Silent_p.K4484K|NEB_ENST00000604864.1_Silent_p.K6185K|NEB_ENST00000427231.2_Silent_p.K6185K			P20929	NEBU_HUMAN	nebulin	4484					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		GATCAGCATGCTTGGCTCCAA	0.498													C|||	30	0.00599042	0.0	0.013	5008	,	,		1556	0.0		0.0099	False		,,,				2504	0.0112				p.K6185K		Atlas-SNP	.											.	NEB	1697	.	0			c.G18555A						PASS	.	C	,,	6,3968		0,6,1981	82.0	82.0	82.0		18555,18555,13452	4.8	1.0	2	dbSNP_134	82	151,8203		1,149,4027	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	1,155,6008	TT,TC,CC		1.8075,0.151,1.2735	,,	6185/8526,6185/8526,4484/6670	152420361	157,12171	1987	4177	6164	SO:0001819	synonymous_variant	4703	exon118			AGCATGCTTGGCT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.13452G>A	2.37:g.152420361C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	23	0.310811	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				C|0.989;T|0.011	0.011	strong		0.498	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
KANSL1	284058	hgsc.bcm.edu	37	17	44108906	44108906	+	Missense_Mutation	SNP	A	A	G	rs34579536	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44108906A>G	ENST00000262419.6	-	15	3724	c.3254T>C	c.(3253-3255)aTt>aCt	p.I1085T	KANSL1_ENST00000575318.1_Missense_Mutation_p.I1021T|KANSL1_ENST00000432791.1_Missense_Mutation_p.I1085T|KANSL1_ENST00000393476.3_Missense_Mutation_p.I379T|KANSL1_ENST00000574590.1_Missense_Mutation_p.I1085T|KANSL1_ENST00000572904.1_Missense_Mutation_p.I1085T	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1085	Sufficient for interaction with KAT8.		I -> T (in dbSNP:rs34579536).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GAGGGGGACAATGGGAGGCGA	0.627													G|||	432	0.086262	0.0151	0.1571	5008	,	,		15744	0.001		0.2406	False		,,,				2504	0.0613				p.I1085T		Atlas-SNP	.											KIAA1267,colon,carcinoma,0,1	.	.	1	0			c.T3254C						PASS	.	G	THR/ILE,THR/ILE,THR/ILE	203,4203	780.9+/-414.5	6,191,2006	29.0	26.0	27.0		3251,3254,3254	2.3	0.0	17	dbSNP_126	27	1914,6686	697.4+/-404.9	220,1474,2606	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	89,89,89	226,1665,4612	GG,GA,AA		22.2558,4.6074,16.2771	benign,benign,benign	1084/1105,1085/1106,1085/1106	44108906	2117,10889	2203	4300	6503	SO:0001583	missense	284058	exon15			GGGACAATGGGAG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.3254T>C	17.37:g.44108906A>G	ENSP00000262419:p.Ile1085Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	3.452	-0.111802	0.06881	0.046074	0.222558	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.25085	2.63;2.63;1.82	5.72	2.34	0.29019	.	1.538450	0.03719	N	0.251449	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37979	-0.9682	9	0.12766	T	0.61	3.041	9.2051	0.37285	0.7644:0.0:0.2356:0.0	rs34579536	416;1085	Q7Z3B3-2;Q7Z3B3	.;K1267_HUMAN	T	1085;1085;379	ENSP00000262419:I1085T;ENSP00000387393:I1085T;ENSP00000377117:I379T	ENSP00000262419:I1085T	I	-	2	0	KIAA1267	41464753	0.000000	0.05858	0.001000	0.08648	0.426000	0.31534	0.910000	0.28571	-0.087000	0.12528	-1.163000	0.01768	ATT	A|0.860;G|0.140	0.140	strong		0.627	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
DYTN	391475	hgsc.bcm.edu	37	2	207572133	207572133	+	Silent	SNP	A	A	C	rs67248530	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:207572133A>C	ENST00000452335.2	-	3	305	c.189T>G	c.(187-189)tcT>tcG	p.S63S	DYTN_ENST00000477734.1_5'Flank	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	63						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GGAGTGCCTGAGAAAGTTGCT	0.532													A|||	287	0.0573083	0.0499	0.1873	5008	,	,		17270	0.0		0.0676	False		,,,				2504	0.0235				p.S63S		Atlas-SNP	.											.	DYTN	168	.	0			c.T189G						PASS	.	A		180,3632		8,164,1734	62.0	60.0	61.0		189	-8.9	0.0	2	dbSNP_130	61	573,7689		22,529,3580	no	coding-synonymous	DYTN	NM_001093730.1		30,693,5314	CC,CA,AA		6.9354,4.7219,6.2365		63/579	207572133	753,11321	1906	4131	6037	SO:0001819	synonymous_variant	391475	exon3			TGCCTGAGAAAGT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.189T>G	2.37:g.207572133A>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	170	82	0.482353	NM_001093730		Silent	SNP	ENST00000452335.2	37	CCDS46502.1																																																																																			A|0.951;C|0.049	0.049	strong		0.532	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
PRG4	10216	hgsc.bcm.edu	37	1	186276661	186276661	+	Missense_Mutation	SNP	A	A	G	rs61831150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186276661A>G	ENST00000445192.2	+	7	1855	c.1810A>G	c.(1810-1812)Act>Gct	p.T604A	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367485.4_Missense_Mutation_p.T511A|PRG4_ENST00000367486.3_Missense_Mutation_p.T561A|PRG4_ENST00000367483.4_Missense_Mutation_p.T563A	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	604	59 X 8 AA repeats of K-X-P-X-P-T-T-X.			T -> A (in Ref. 1; AAB09089). {ECO:0000305}.	cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TGCACCCACCACTCCCAAAGA	0.657													-|||	1149	0.229433	0.1415	0.4078	5008	,	,		8224	0.125		0.33	False		,,,				2504	0.226				p.T604A		Atlas-SNP	.											PRG4,brain,glioma,0,1	PRG4	259	1	0			c.A1810G						scavenged	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR	826,3580	322.6+/-297.7	75,676,1452	77.0	74.0	75.0		1810,1408,1531,1687	-7.0	0.0	1	dbSNP_129	75	3037,5563	461.6+/-365.5	537,1963,1800	no	missense,missense,missense,missense	PRG4	NM_005807.3,NM_001127710.1,NM_001127709.1,NM_001127708.1	58,58,58,58	612,2639,3252	GG,GA,AA		35.314,18.7472,29.7017	benign,benign,benign,benign	604/1405,470/1271,511/1312,563/1364	186276661	3863,9143	2203	4300	6503	SO:0001583	missense	10216	exon7			CCCACCACTCCCA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1810A>G	1.37:g.186276661A>G	ENSP00000399679:p.Thr604Ala	Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	57	48	0.842105	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	533	0.24404761904761904	57	0.11585365853658537	143	0.39502762430939226	73	0.12762237762237763	260	0.34300791556728233	A	6.871	0.530050	0.13127	0.187472	0.35314	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05996	3.36;3.45;3.39;3.46	3.74	-6.98	0.01611	.	0.224316	0.21263	U	0.077456	T	0.00012	0.0000	L	0.55990	1.75	0.80722	P	0.0	B;B;B;B	0.17268	0.021;0.021;0.012;0.021	B;B;B;B	0.11329	0.006;0.006;0.003;0.006	T	0.46596	-0.9180	8	.	.	.	.	2.0325	0.03532	0.2526:0.1179:0.3962:0.2333	rs61831150	470;511;604;563	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	A	561;470;563;511;604	ENSP00000356456:T561A;ENSP00000356453:T563A;ENSP00000356455:T511A;ENSP00000399679:T604A	.	T	+	1	0	PRG4	184543284	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.345000	0.19979	-1.252000	0.02491	-0.486000	0.04755	ACT	A|0.713;G|0.287	0.287	strong		0.657	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
PRICKLE4	29964	hgsc.bcm.edu	37	6	41754576	41754576	+	Silent	SNP	C	C	T	rs9381093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41754576C>T	ENST00000394260.1	+	5	744	c.744C>T	c.(742-744)ctC>ctT	p.L248L	TOMM6_ENST00000398884.3_5'Flank|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000458694.1_Silent_p.L288L|PRICKLE4_ENST00000394263.1_Silent_p.L288L			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	248				L -> LL (in Ref. 5; AAI10460). {ECO:0000305}.		nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GAACACTCCTCGCTGCTGCCG	0.637											OREG0017435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2812	0.561502	0.3419	0.6945	5008	,	,		13973	0.8304		0.7535	False		,,,				2504	0.2894				p.L288L		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.C864T						PASS	.						76.0	74.0	74.0					6																	41754576		2201	4300	6501	SO:0001819	synonymous_variant	29964	exon8			ACTCCTCGCTGCT	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.744C>T	6.37:g.41754576C>T		Somatic	45	0	0	903	WXS	Illumina HiSeq	Phase_I	51	42	0.823529	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Silent	SNP	ENST00000394260.1	37																																																																																				C|0.588;T|0.412	0.412	strong		0.637	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
TMEM2	23670	hgsc.bcm.edu	37	9	74355028	74355028	+	Silent	SNP	A	A	G	rs25690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:74355028A>G	ENST00000377044.4	-	5	1694	c.1155T>C	c.(1153-1155)acT>acC	p.T385T	TMEM2_ENST00000377066.5_Silent_p.T385T	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	385					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GGCCATCCACAGTATAAAATT	0.408													G|||	407	0.08127	0.0393	0.0476	5008	,	,		15182	0.0198		0.0815	False		,,,				2504	0.2249				p.T385T		Atlas-SNP	.											.	TMEM2	112	.	0			c.T1155C						PASS	.	G	,	174,4232	810.7+/-416.0	6,162,2035	114.0	110.0	111.0		1155,1155	-4.1	0.3	9	dbSNP_72	111	722,7878	786.7+/-407.6	31,660,3609	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	37,822,5644	GG,GA,AA		8.3953,3.9492,6.8891	,	385/1321,385/1384	74355028	896,12110	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon5			ATCCACAGTATAA		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1155T>C	9.37:g.74355028A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			A|0.936;G|0.064	0.064	strong		0.408	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
CFHR1	3078	hgsc.bcm.edu	37	1	196799691	196799691	+	Silent	SNP	G	G	A	rs12406079	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196799691G>A	ENST00000320493.5	+	5	757	c.669G>A	c.(667-669)ccG>ccA	p.P223P	CFHR2_ENST00000367421.3_Intron|CFHR1_ENST00000367424.4_Silent_p.P164P	NM_002113.2	NP_002104.2	Q03591	FHR1_HUMAN	complement factor H-related 1	223	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|kidney(1)|large_intestine(2)|lung(7)	11						CTTCATTCCCGTTGTCAGTAT	0.408													-|||	477	0.0952476	0.053	0.0836	5008	,	,		12673	0.123		0.163	False		,,,				2504	0.0624				p.P223P		Atlas-SNP	.											.	CFHR1	47	.	0			c.G669A						PASS	.	G		296,3416		91,114,1651	72.0	85.0	81.0		669	-0.2	0.0	1	dbSNP_120	81	1259,6987		278,703,3142	no	coding-synonymous	CFHR1	NM_002113.2		369,817,4793	AA,AG,GG		15.268,7.9741,13.0038		223/331	196799691	1555,10403	1856	4123	5979	SO:0001819	synonymous_variant	3078	exon5			ATTCCCGTTGTCA	M65292	CCDS1386.1	1q32	2014-09-17	2004-08-09	2006-02-28	ENSG00000244414	ENSG00000244414		"""Complement system"""	4888	protein-coding gene	gene with protein product		134371	"""H factor (complement)-like 1"", ""complement factor H-related 1 pseudogene"", ""H factor (complement)-like 2"""	HFL1, CFHL1, CFHR1P, HFL2, CFHL1P		1711047, 1826708	Standard	NM_002113		Approved	H36-1, FHR1, CFHL, H36-2		Q03591	OTTHUMG00000036276	ENST00000320493.5:c.669G>A	1.37:g.196799691G>A		Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	337	127	0.376855	NM_002113	A8K465|Q3B774|Q9UJ17	Silent	SNP	ENST00000320493.5	37	CCDS1386.1																																																																																			G|0.878;A|0.122	0.122	strong		0.408	CFHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088251.2	NM_002113	
SGCA	6442	hgsc.bcm.edu	37	17	48247689	48247689	+	Silent	SNP	C	C	T	rs1801191	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48247689C>T	ENST00000262018.3	+	7	969	c.933C>T	c.(931-933)gtC>gtT	p.V311V	SGCA_ENST00000513942.1_Intron|SGCA_ENST00000344627.6_Intron|HILS1_ENST00000504307.1_RNA|SGCA_ENST00000543315.1_Intron	NM_000023.2	NP_000014.1	Q16586	SGCA_HUMAN	sarcoglycan, alpha (50kDa dystrophin-associated glycoprotein)	311					muscle contraction (GO:0006936)|muscle organ development (GO:0007517)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(2)|skin(1)	14						TGGCCTATGTCATGTGCTGCC	0.632													C|||	394	0.0786741	0.236	0.0288	5008	,	,		20676	0.0079		0.0457	False		,,,				2504	0.0082				p.V311V		Atlas-SNP	.											.	SGCA	35	.	0			c.C933T						PASS	.	C	,	874,3532	341.8+/-306.9	85,704,1414	98.0	86.0	90.0		933,	2.7	0.9	17	dbSNP_89	90	358,8242	120.2+/-179.5	5,348,3947	no	coding-synonymous,intron	SGCA	NM_000023.2,NM_001135697.1	,	90,1052,5361	TT,TC,CC		4.1628,19.8366,9.4726	,	311/388,	48247689	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	6442	exon7			CTATGTCATGTGC	L34355	CCDS32679.1, CCDS45729.1	17q21	2014-09-17	2002-08-29		ENSG00000108823	ENSG00000108823			10805	protein-coding gene	gene with protein product	"""50kD DAG"", ""Sarcoglycan, alpha (50kD dystrophin-associated glycoprotein; adhalin)"", ""adhalin (limb girdle muscular dystrophy 2D)"""	600119	"""sarcoglycan, alpha (50kD dystrophin-associated glycoprotein)"""	ADL		7937874	Standard	NM_000023		Approved	SCARMD1, LGMD2D, adhalin, DMDA2, A2	uc002iqi.3	Q16586	OTTHUMG00000162024	ENST00000262018.3:c.933C>T	17.37:g.48247689C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_000023	A6NEB8|A8K3K7|Q13710|Q13712	Silent	SNP	ENST00000262018.3	37	CCDS32679.1	149	0.06822344322344322	98	0.1991869918699187	9	0.024861878453038673	8	0.013986013986013986	34	0.044854881266490766	C	10.64	1.407907	0.25378	0.198366	0.041628	ENSG00000108823	ENST00000504073	.	.	.	5.8	2.68	0.31781	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06625	-1.0816	3	.	.	.	-14.6598	9.1601	0.37016	0.0:0.6906:0.0:0.3094	rs1801191;rs1801191	.	.	.	Y	84	.	.	H	+	1	0	SGCA	45602688	1.000000	0.71417	0.897000	0.35233	0.977000	0.68977	1.725000	0.38074	0.349000	0.23975	-0.136000	0.14681	CAT	C|0.911;T|0.089	0.089	strong		0.632	SGCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366841.1	NM_000023	
TBC1D16	125058	hgsc.bcm.edu	37	17	77984141	77984141	+	Silent	SNP	C	C	T	rs35922784	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77984141C>T	ENST00000310924.2	-	3	712	c.597G>A	c.(595-597)ggG>ggA	p.G199G		NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	199							Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			GCGGCTCCCGCCCCTCCTCGG	0.667													C|||	1271	0.253794	0.2791	0.1931	5008	,	,		16029	0.2312		0.2803	False		,,,				2504	0.2587				p.G199G	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.G597A						PASS	.	C		1163,3239		160,843,1198	31.0	34.0	33.0		597	-0.7	0.0	17	dbSNP_126	33	2348,6248		316,1716,2266	no	coding-synonymous	TBC1D16	NM_019020.2		476,2559,3464	TT,TC,CC		27.315,26.4198,27.0118		199/768	77984141	3511,9487	2201	4298	6499	SO:0001819	synonymous_variant	125058	exon3			CTCCCGCCCCTCC	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.597G>A	17.37:g.77984141C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	37	CCDS11766.1																																																																																			C|0.729;T|0.271	0.271	strong		0.667	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020	
GK2	2712	hgsc.bcm.edu	37	4	80329343	80329343	+	Silent	SNP	T	T	C	rs6837906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:80329343T>C	ENST00000358842.3	-	1	29	c.12A>G	c.(10-12)ccA>ccG	p.P4P		NM_033214.2	NP_149991.2	Q01415	GALK2_HUMAN	glycerol kinase 2	0					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			autonomic_ganglia(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	39						CTGCTGTCTTTGGGGCTGCCA	0.607													C|||	1452	0.289936	0.1233	0.3127	5008	,	,		14511	0.4593		0.1491	False		,,,				2504	0.4693				p.P4P		Atlas-SNP	.											.	GK2	102	.	0			c.A12G						PASS	.	C		632,3772		58,516,1628	22.0	23.0	23.0		12	-6.6	0.0	4	dbSNP_116	23	1359,7241		102,1155,3043	no	coding-synonymous	GK2	NM_033214.2		160,1671,4671	CC,CT,TT		15.8023,14.3506,15.3107		4/554	80329343	1991,11013	2202	4300	6502	SO:0001819	synonymous_variant	2712	exon1			TGTCTTTGGGGCT	BC029820	CCDS3585.1	4q13	2008-02-05	2002-10-03	2002-10-04	ENSG00000196475	ENSG00000196475		"""Glycerol kinases"""	4291	protein-coding gene	gene with protein product		600148	"""glycerol kinase pseudogene 2"""	GKP2		7987308	Standard	NM_033214		Approved	GKTA	uc003hlu.3	Q14410	OTTHUMG00000130199	ENST00000358842.3:c.12A>G	4.37:g.80329343T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	33	20	0.606061	NM_033214	Q7Z4Q4	Silent	SNP	ENST00000358842.3	37	CCDS3585.1																																																																																			T|0.803;C|0.197	0.197	strong		0.607	GK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252517.2	NM_033214	
SNAPC4	6621	hgsc.bcm.edu	37	9	139272502	139272502	+	Silent	SNP	T	T	C	rs3812565	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139272502T>C	ENST00000298532.2	-	21	4145	c.3777A>G	c.(3775-3777)ctA>ctG	p.L1259L		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		CAGGCTGGGGTAGGGGCGGCT	0.746													N|||	1642	0.327875	0.2935	0.5648	5008	,	,		12956	0.1885		0.3549	False		,,,				2504	0.3221				p.L1259L		Atlas-SNP	.											SNAPC4,caecum,carcinoma,0,1	SNAPC4	82	1	0			c.A3777G						scavenged	.			899,2601		168,563,1019	4.0	5.0	4.0		3777	-2.4	0.0	9	dbSNP_107	4	2448,4658		514,1420,1619	no	coding-synonymous	SNAPC4	NM_003086.2		682,1983,2638	CC,CT,TT		34.4498,25.6857,31.5576		1259/1470	139272502	3347,7259	1750	3553	5303	SO:0001819	synonymous_variant	6621	exon21			CTGGGGTAGGGGC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.3777A>G	9.37:g.139272502T>C		Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	24	8	0.333333	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			T|0.670;C|0.330	0.330	strong		0.746	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
KBTBD12	166348	hgsc.bcm.edu	37	3	127642814	127642814	+	Missense_Mutation	SNP	G	G	C	rs61268888	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:127642814G>C	ENST00000405109.1	+	2	1377	c.910G>C	c.(910-912)Gta>Cta	p.V304L	KBTBD12_ENST00000405256.1_Missense_Mutation_p.V304L|KBTBD12_ENST00000407609.3_Intron|KBTBD12_ENST00000343941.4_Intron			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	304										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						TTATGATCCTGTATCACGGAA	0.413													G|||	957	0.191094	0.1664	0.085	5008	,	,		17625	0.2331		0.1233	False		,,,				2504	0.3262				p.V304L		Atlas-SNP	.											.	KBTBD12	41	.	0			c.G910C						PASS	.	G	LEU/VAL	649,3191		49,551,1320	134.0	128.0	130.0		910	-1.1	0.0	3	dbSNP_129	130	1054,7168		63,928,3120	yes	missense	KBTBD12	NM_207335.2	32	112,1479,4440	CC,CG,GG		12.8193,16.901,14.1187	benign	304/624	127642814	1703,10359	1920	4111	6031	SO:0001583	missense	166348	exon1			GATCCTGTATCAC		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"""BTB/POZ domain containing"""	25731	protein-coding gene	gene with protein product			"""kelch domain containing 6"""	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.910G>C	3.37:g.127642814G>C	ENSP00000385957:p.Val304Leu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	148	59	0.398649	NM_207335	B5MCC6|Q6ZRK1	Missense_Mutation	SNP	ENST00000405109.1	37	CCDS33848.2	343	0.15705128205128205	89	0.18089430894308944	36	0.09944751381215469	122	0.21328671328671328	96	0.1266490765171504	G	2.653	-0.281515	0.05642	0.16901	0.128193	ENSG00000187715	ENST00000405109;ENST00000405256	T;T	0.66099	-0.19;-0.19	5.47	-1.1	0.09872	Kelch-type beta propeller (1);	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09058	-1.0692	8	0.33141	T	0.24	.	2.4812	0.04587	0.1929:0.1041:0.4764:0.2266	rs61268888;rs61734842	304	Q3ZCT8	KBTBC_HUMAN	L	304	ENSP00000385957:V304L;ENSP00000385879:V304L	ENSP00000385957:V304L	V	+	1	0	KBTBD12	129125504	0.000000	0.05858	0.000000	0.03702	0.971000	0.66376	0.528000	0.23002	0.062000	0.16340	-0.224000	0.12420	GTA	G|0.846;C|0.154	0.154	strong		0.413	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335	
FAM186A	121006	hgsc.bcm.edu	37	12	50727811	50727811	+	Missense_Mutation	SNP	C	C	T	rs6580742	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:50727811C>T	ENST00000327337.5	-	5	6578	c.6579G>A	c.(6577-6579)atG>atA	p.M2193I	FAM186A_ENST00000543096.1_Missense_Mutation_p.M204I|FAM186A_ENST00000543111.1_Missense_Mutation_p.M2193I	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2193			M -> I (in dbSNP:rs6580742).														GTCTGCTCAGCATCATGTGGA	0.423													C|||	340	0.0678914	0.0113	0.1066	5008	,	,		21742	0.001		0.163	False		,,,				2504	0.0879				p.M2193I	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.G6579A						PASS	.	C	ILE/MET	41,1343		1,39,652	277.0	224.0	240.0		6579	3.5	1.0	12	dbSNP_116	240	527,2655		58,411,1122	yes	missense	FAM186A	NM_001145475.1	10	59,450,1774	TT,TC,CC		16.5619,2.9624,12.4398	possibly-damaging	2193/2352	50727811	568,3998	692	1591	2283	SO:0001583	missense	121006	exon5			GCTCAGCATCATG		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6579G>A	12.37:g.50727811C>T	ENSP00000329995:p.Met2193Ile	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	204	106	0.519608	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	169	0.07738095238095238	7	0.014227642276422764	40	0.11049723756906077	2	0.0034965034965034965	120	0.158311345646438	C	9.768	1.171981	0.21704	0.029624	0.165619	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.31247	1.5;1.5;1.5	4.39	3.51	0.40186	.	.	.	.	.	T	0.00144	0.0004	L	0.36672	1.1	0.41050	P	0.014708000000000054	D;D	0.71674	0.998;0.982	D;P	0.69479	0.964;0.873	T	0.05750	-1.0866	8	0.72032	D	0.01	.	8.5972	0.33723	0.0:0.8973:0.0:0.1027	rs6580742;rs17413065;rs52828310;rs58453917;rs6580742	2193;2193	F5GYN0;A6NE01	.;F186A_HUMAN	I	2193;204;2193	ENSP00000441337:M2193I;ENSP00000443703:M204I;ENSP00000329995:M2193I	ENSP00000329995:M2193I	M	-	3	0	FAM186A	49014078	0.996000	0.38824	0.981000	0.43875	0.046000	0.14306	0.791000	0.26915	1.448000	0.47680	-0.150000	0.13652	ATG	C|0.920;T|0.080	0.080	strong		0.423	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
FBP1	2203	hgsc.bcm.edu	37	9	97369151	97369151	+	Silent	SNP	G	G	A	rs1042144|rs386736436	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:97369151G>A	ENST00000375326.4	-	5	847	c.651C>T	c.(649-651)gcC>gcT	p.A217A	FBP1_ENST00000415431.1_Silent_p.A217A	NM_000507.3	NP_000498.2	P09467	F16P1_HUMAN	fructose-1,6-bisphosphatase 1	217					carbohydrate metabolic process (GO:0005975)|cellular response to drug (GO:0035690)|cellular response to magnesium ion (GO:0071286)|dephosphorylation (GO:0016311)|fructose 6-phosphate metabolic process (GO:0006002)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|negative regulation of cell growth (GO:0030308)|negative regulation of glycolytic process (GO:0045820)|negative regulation of Ras protein signal transduction (GO:0046580)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	AMP binding (GO:0016208)|fructose 1,6-bisphosphate 1-phosphatase activity (GO:0042132)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|monosaccharide binding (GO:0048029)			kidney(1)|liver(1)|lung(1)	3		Acute lymphoblastic leukemia(62;0.136)			Adenosine monophosphate(DB00131)	CAAAGTCCCTGGCGTAGCCCT	0.522													G|||	1765	0.352436	0.2716	0.2046	5008	,	,		20345	0.5496		0.3499	False		,,,				2504	0.3661				p.A217A	Ovarian(142;590 2466 25593 44496)	Atlas-SNP	.											.	FBP1	13	.	0			c.C651T						PASS	.	G	,	1229,3177	426.4+/-341.1	164,901,1138	120.0	109.0	113.0		651,651	3.6	1.0	9	dbSNP_86	113	2822,5778	445.1+/-360.9	456,1910,1934	no	coding-synonymous,coding-synonymous	FBP1	NM_000507.3,NM_001127628.1	,	620,2811,3072	AA,AG,GG		32.814,27.8938,31.1472	,	217/339,217/339	97369151	4051,8955	2203	4300	6503	SO:0001819	synonymous_variant	2203	exon5			GTCCCTGGCGTAG	M19922	CCDS6712.1	9q22.3	2012-08-13			ENSG00000165140	ENSG00000165140	3.1.3.11		3606	protein-coding gene	gene with protein product		611570		FBP		8387495	Standard	NM_000507		Approved		uc004auw.4	P09467	OTTHUMG00000020268	ENST00000375326.4:c.651C>T	9.37:g.97369151G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_000507	O75571|Q53F94|Q96E46	Silent	SNP	ENST00000375326.4	37	CCDS6712.1																																																																																			T|0.000;G|0.682;A|0.318	0.318	strong		0.522	FBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053187.1	NM_000507	
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 GAIIx	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_ENST00000514446.1_RNA|CTC-321K16.1_ENST00000509372.1_RNA|CXCL14_ENST00000512158.1_Missense_Mutation_p.A5V	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	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	23	7	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	
CLIC5	53405	hgsc.bcm.edu	37	6	46047458	46047458	+	Silent	SNP	C	C	T	rs3734207	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:46047458C>T	ENST00000185206.6	-	1	674	c.522G>A	c.(520-522)gaG>gaA	p.E174E		NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	174					auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						AGAGGTAAATCTCAGGGTTCA	0.453													C|||	983	0.196286	0.0303	0.1196	5008	,	,		23723	0.3343		0.174	False		,,,				2504	0.3558				p.E174E		Atlas-SNP	.											.	CLIC5	48	.	0			c.G522A						PASS	.						75.0	70.0	71.0					6																	46047458		692	1591	2283	SO:0001819	synonymous_variant	53405	exon1			GTAAATCTCAGGG	AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"""Ion channels / Chloride channels : Intracellular"""	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.522G>A	6.37:g.46047458C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_001114086	B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Silent	SNP	ENST00000185206.6	37	CCDS47438.1																																																																																			C|0.815;T|0.185	0.185	strong		0.453	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1		
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 GAIIx	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	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	29	9	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	
GDPD4	220032	hgsc.bcm.edu	37	11	76954833	76954833	+	Missense_Mutation	SNP	G	G	A	rs11237146	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:76954833G>A	ENST00000376217.2	-	12	1397	c.1147C>T	c.(1147-1149)Cat>Tat	p.H383Y	GDPD4_ENST00000315938.4_Missense_Mutation_p.H383Y			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	383	GP-PDE.		H -> Y (in dbSNP:rs11237146).		glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						CGGCCCACATGCTGAAAACCA	0.408													G|||	1213	0.242212	0.0257	0.1873	5008	,	,		15839	0.256		0.3608	False		,,,				2504	0.4376				p.H383Y		Atlas-SNP	.											.	GDPD4	49	.	0			c.C1147T						PASS	.	G	TYR/HIS	361,4039	183.3+/-210.9	23,315,1862	97.0	92.0	93.0		1147	3.3	0.9	11	dbSNP_120	93	2937,5647	459.0+/-364.8	484,1969,1839	yes	missense	GDPD4	NM_182833.1	83	507,2284,3701	AA,AG,GG		34.2148,8.2045,25.4005	possibly-damaging	383/521	76954833	3298,9686	2200	4292	6492	SO:0001583	missense	220032	exon12			CCACATGCTGAAA	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1147C>T	11.37:g.76954833G>A	ENSP00000365390:p.His383Tyr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	78	11	0.141026	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	37		475	0.2174908424908425	13	0.026422764227642278	74	0.20441988950276244	130	0.22727272727272727	258	0.3403693931398417	G	14.59	2.581875	0.46006	0.082045	0.342148	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.10960	2.82;2.82	4.27	3.34	0.38264	.	0.431410	0.27433	N	0.019382	T	0.00012	0.0000	M	0.62723	1.935	0.36466	P	0.13304899999999997	P	0.52316	0.952	P	0.47075	0.536	T	0.51196	-0.8736	9	0.36615	T	0.2	-1.6698	10.9709	0.47438	0.0:0.0:0.8135:0.1865	rs11237146;rs17824232;rs58856218;rs11237146	383	Q6W3E5-2	.	Y	383	ENSP00000365390:H383Y;ENSP00000320815:H383Y	ENSP00000320815:H383Y	H	-	1	0	GDPD4	76632481	1.000000	0.71417	0.883000	0.34634	0.439000	0.31926	3.107000	0.50329	1.112000	0.41740	0.655000	0.94253	CAT	G|0.770;A|0.229	0.229	strong		0.408	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
HBS1L	10767	hgsc.bcm.edu	37	6	135323873	135323873	+	Splice_Site	SNP	C	C	T	rs34860737	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:135323873C>T	ENST00000367837.5	-	5	744	c.538G>A	c.(538-540)Gga>Aga	p.G180R	HBS1L_ENST00000527578.1_Splice_Site_p.G16R|HBS1L_ENST00000367826.2_Splice_Site_p.G138R|HBS1L_ENST00000415177.2_Splice_Site_p.G115R|HBS1L_ENST00000314674.3_3'UTR|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Splice_Site_p.G16R	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	180					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		AAGTCTTACCCAGGCACTTCA	0.423																																					p.G180R		Atlas-SNP	.											HBS1L,NS,carcinoma,+1,1	HBS1L	75	1	0			c.G538A						scavenged	.	C	ARG/GLY,ARG/GLY	7,4399	12.9+/-30.5	0,7,2196	106.0	94.0	98.0		412,538	3.5	1.0	6	dbSNP_126	98	0,8600		0,0,4300	yes	missense-near-splice,missense-near-splice	HBS1L	NM_001145158.1,NM_006620.3	125,125	0,7,6496	TT,TC,CC		0.0,0.1589,0.0538	benign,benign	138/643,180/685	135323873	7,12999	2203	4300	6503	SO:0001630	splice_region_variant	10767	exon5			CTTACCCAGGCAC	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.539+1G>A	6.37:g.135323873C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	111	2	0.018018	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	37	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165651	0.38217	0.001589	0.0	ENSG00000112339	ENST00000367837;ENST00000527578;ENST00000415177;ENST00000367826;ENST00000367824;ENST00000533274;ENST00000529641;ENST00000527507	T;T;T;T;T;T	0.63580	-0.05;-0.05;0.02;-0.03;-0.05;-0.04	6.17	3.49	0.39957	.	0.278615	0.45126	N	0.000390	T	0.32466	0.0830	L	0.51422	1.61	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.008;0.004	T	0.15206	-1.0445	10	0.31617	T	0.26	-9.6599	5.6006	0.17351	0.1344:0.5968:0.0:0.2688	rs34860737	138;180	Q9Y450-4;Q9Y450	.;HBS1L_HUMAN	R	180;16;115;138;16;50;16;16	ENSP00000356811:G180R;ENSP00000436256:G16R;ENSP00000389826:G115R;ENSP00000356800:G138R;ENSP00000356798:G16R;ENSP00000434533:G50R	ENSP00000356798:G16R	G	-	1	0	HBS1L	135365566	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	1.479000	0.35453	0.505000	0.28104	-0.140000	0.14226	GGA	C|0.999;T|0.001	0.001	strong		0.423	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		Missense_Mutation
DNLZ	728489	hgsc.bcm.edu	37	9	139256541	139256541	+	Missense_Mutation	SNP	C	C	T	rs3812554	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139256541C>T	ENST00000371738.3	-	3	534	c.460G>A	c.(460-462)Gcc>Acc	p.A154T	CARD9_ENST00000460290.1_5'Flank|DNLZ_ENST00000371739.3_Missense_Mutation_p.G107D	NM_001080849.1	NP_001074318.1	Q5SXM8	DNLZ_HUMAN	DNL-type zinc finger	154						mitochondrion (GO:0005739)	zinc ion binding (GO:0008270)			central_nervous_system(1)|prostate(1)	2		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.42e-06)|Epithelial(140;3.3e-06)		GATGTGGGGGCCCCTGCAGCC	0.687													C|||	383	0.0764776	0.0098	0.1023	5008	,	,		12898	0.125		0.0855	False		,,,				2504	0.089				p.A154T		Atlas-SNP	.											.	DNLZ	8	.	0			c.G460A						PASS	.	C	THR/ALA	90,4290		1,88,2101	14.0	20.0	18.0		460	-4.1	0.0	9	dbSNP_107	18	849,7719		42,765,3477	yes	missense	DNLZ	NM_001080849.1	58	43,853,5578	TT,TC,CC		9.909,2.0548,7.2521	benign	154/179	139256541	939,12009	2190	4284	6474	SO:0001583	missense	728489	exon3			TGGGGGCCCCTGC	AL592301	CCDS35179.1	9q34.3	2013-01-10	2007-12-18	2007-12-18	ENSG00000213221	ENSG00000213221		"""Zinc fingers"""	33879	protein-coding gene	gene with protein product	"""translocase of inner mitochondrial membrane 15 homolog (yeast)"", ""HSP70 escort protein"""		"""chromosome 9 open reading frame 151"""	C9orf151		21530495, 22162012	Standard	NM_001080849		Approved	RP11-413M3.2, ZIM17, bA413M3.2, TIMM15, HEP	uc004chf.2	Q5SXM8	OTTHUMG00000020931	ENST00000371738.3:c.460G>A	9.37:g.139256541C>T	ENSP00000360803:p.Ala154Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_001080849	B2RUX5|B9EJE1	Missense_Mutation	SNP	ENST00000371738.3	37	CCDS35179.1	174|174	0.07967032967032966|0.07967032967032966	7|7	0.014227642276422764|0.014227642276422764	29|29	0.08011049723756906|0.08011049723756906	66|66	0.11538461538461539|0.11538461538461539	72|72	0.09498680738786279|0.09498680738786279	C|C	3.261|3.261	-0.151203|-0.151203	0.06585|0.06585	0.020548|0.020548	0.09909|0.09909	ENSG00000213221|ENSG00000213221	ENST00000371738|ENST00000371739	T|.	0.31247|.	1.5|.	4.15|4.15	-4.11|-4.11	0.03928|0.03928	Zinc finger, DNL-type (1);|.	3.109900|.	0.02185|.	N|.	0.060816|.	T|T	0.00241|0.00241	0.0007|0.0007	N|N	0.12182|0.12182	0.205|0.205	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.18053|0.18053	-1.0349|-1.0349	9|5	0.13470|0.87932	T|D	0.59|0	0.2915|0.2915	2.7886|2.7886	0.05381|0.05381	0.2039:0.4347:0.2125:0.1489|0.2039:0.4347:0.2125:0.1489	rs3812554|rs3812554	154|.	Q5SXM8|.	DNLZ_HUMAN|.	T|D	154|107	ENSP00000360803:A154T|.	ENSP00000360803:A154T|ENSP00000360804:G107D	A|G	-|-	1|2	0|0	DNLZ|DNLZ	138376362|138376362	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-0.303000|-0.303000	0.08210|0.08210	-1.441000|-1.441000	0.01958|0.01958	-1.579000|-1.579000	0.00862|0.00862	GCC|GGC	C|0.926;T|0.074	0.074	strong		0.687	DNLZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055075.2	NM_001080849	
INPP4B	8821	hgsc.bcm.edu	37	4	143235865	143235865	+	Splice_Site	SNP	C	C	G	rs3756122	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:143235865C>G	ENST00000513000.1	-	9	856	c.423G>C	c.(421-423)ggG>ggC	p.G141G	INPP4B_ENST00000308502.4_Splice_Site_p.G141G|INPP4B_ENST00000509777.1_Splice_Site_p.G141G|INPP4B_ENST00000508116.1_Splice_Site_p.G141G|INPP4B_ENST00000262992.4_Splice_Site_p.G141G	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	141	C2.				cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					AAACACTTACCCCAACTTCTG	0.418													C|||	999	0.199481	0.0061	0.2032	5008	,	,		19179	0.4623		0.1252	False		,,,				2504	0.2638				p.G141G		Atlas-SNP	.											.	INPP4B	132	.	0			c.G423C						PASS	.	C	,	124,4282	93.0+/-131.7	2,120,2081	125.0	128.0	127.0		423,423	5.1	1.0	4	dbSNP_107	127	1026,7574	219.0+/-257.2	56,914,3330	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	INPP4B	NM_001101669.1,NM_003866.2	,	58,1034,5411	GG,GC,CC		11.9302,2.8143,8.8421	,	141/925,141/925	143235865	1150,11856	2203	4300	6503	SO:0001630	splice_region_variant	8821	exon9			ACTTACCCCAACT	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.423+1G>C	4.37:g.143235865C>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			C|0.877;G|0.123	0.123	strong		0.418	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	Silent
CDHR2	54825	hgsc.bcm.edu	37	5	175998246	175998246	+	Silent	SNP	T	T	C	rs17078320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:175998246T>C	ENST00000510636.1	+	6	622	c.348T>C	c.(346-348)gaT>gaC	p.D116D	CDHR2_ENST00000506348.1_Silent_p.D116D|CDHR2_ENST00000261944.5_Silent_p.D116D	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	116	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						TTGTGGAAGATAGAAACGACA	0.512													C|||	1606	0.320687	0.3026	0.2262	5008	,	,		15205	0.4841		0.2157	False		,,,				2504	0.3517				p.D116D		Atlas-SNP	.											.	CDHR2	152	.	0			c.T348C						PASS	.	C	,	1295,3111	698.0+/-406.3	175,945,1083	99.0	82.0	88.0		348,348	2.4	1.0	5	dbSNP_123	88	1693,6907	737.6+/-407.0	154,1385,2761	no	coding-synonymous,coding-synonymous	CDHR2	NM_001171976.1,NM_017675.4	,	329,2330,3844	CC,CT,TT		19.686,29.3917,22.974	,	116/1311,116/1311	175998246	2988,10018	2203	4300	6503	SO:0001819	synonymous_variant	54825	exon6			GGAAGATAGAAAC	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.348T>C	5.37:g.175998246T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_017675	A1L3U4|A6NC80|Q9NXP8	Silent	SNP	ENST00000510636.1	37	CCDS34297.1																																																																																			T|0.732;C|0.268	0.268	strong		0.512	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
ADCY8	114	hgsc.bcm.edu	37	8	132002770	132002770	+	Silent	SNP	G	G	A	rs2228950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:132002770G>A	ENST00000286355.5	-	2	3071	c.979C>T	c.(979-981)Cta>Tta	p.L327L	ADCY8_ENST00000377928.3_Silent_p.L327L	NM_001115.2	NP_001106.1	P40145	ADCY8_HUMAN	adenylate cyclase 8 (brain)	327					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(21)|lung(67)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(5)|urinary_tract(2)	134	Esophageal squamous(12;0.00693)|Ovarian(258;0.00707)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000538)			CACATGAATAGCACTGCCTGG	0.448										HNSCC(32;0.087)			A|||	1554	0.310304	0.6921	0.2291	5008	,	,		19148	0.0774		0.168	False		,,,				2504	0.2382				p.L327L		Atlas-SNP	.											.	ADCY8	291	.	0			c.C979T						PASS	.	A		2766,1640	502.9+/-365.4	890,986,327	110.0	119.0	116.0		979	-1.1	0.0	8	dbSNP_121	116	1399,7201	753.6+/-407.5	116,1167,3017	no	coding-synonymous	ADCY8	NM_001115.2		1006,2153,3344	AA,AG,GG		16.2674,37.222,32.0237		327/1252	132002770	4165,8841	2203	4300	6503	SO:0001819	synonymous_variant	114	exon2			TGAATAGCACTGC	Z35309	CCDS6363.1	8q24	2013-02-04			ENSG00000155897	ENSG00000155897	4.6.1.1	"""Adenylate cyclases"""	239	protein-coding gene	gene with protein product		103070		ADCY3		8076676	Standard	NM_001115		Approved	HBAC1, AC8	uc003ytd.4	P40145	OTTHUMG00000164756	ENST00000286355.5:c.979C>T	8.37:g.132002770G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_001115		Silent	SNP	ENST00000286355.5	37	CCDS6363.1																																																																																			G|0.701;A|0.299	0.299	strong		0.448	ADCY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380080.1		
TMEM214	54867	hgsc.bcm.edu	37	2	27260469	27260469	+	Missense_Mutation	SNP	G	G	A	rs1124649	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27260469G>A	ENST00000238788.9	+	9	1113	c.1051G>A	c.(1051-1053)Gtg>Atg	p.V351M	TMEM214_ENST00000404032.3_Missense_Mutation_p.V306M	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	351			V -> M (in dbSNP:rs1124649).		apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CCGACTGAAAGTGCTGGCATT	0.542													G|||	1518	0.303115	0.4478	0.4006	5008	,	,		18858	0.0655		0.3091	False		,,,				2504	0.2771				p.V351M		Atlas-SNP	.											.	TMEM214	41	.	0			c.G1051A						PASS	.	G	MET/VAL,MET/VAL	1640,2310		333,974,668	111.0	116.0	115.0		916,1051	5.7	1.0	2	dbSNP_86	115	2550,5770		395,1760,2005	yes	missense,missense	TMEM214	NM_001083590.1,NM_017727.4	21,21	728,2734,2673	AA,AG,GG		30.649,41.519,34.1483	probably-damaging,probably-damaging	306/645,351/690	27260469	4190,8080	1975	4160	6135	SO:0001583	missense	54867	exon9			CTGAAAGTGCTGG		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.1051G>A	2.37:g.27260469G>A	ENSP00000238788:p.Val351Met	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	37	CCDS42664.1	605	0.27701465201465203	208	0.42276422764227645	141	0.38950276243093923	33	0.057692307692307696	223	0.2941952506596306	G	19.92	3.915582	0.73098	0.41519	0.30649	ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397	T;T	0.55588	0.51;0.51	5.69	5.69	0.88448	.	0.057286	0.64402	D	0.000001	T	0.00012	0.0000	M	0.74258	2.255	0.09310	P	0.999999747868	D;D	0.89917	1.0;0.998	D;D	0.81914	0.995;0.991	T	0.20874	-1.0262	9	0.52906	T	0.07	-21.5626	17.5913	0.87997	0.0:0.0:1.0:0.0	rs1124649;rs17529988;rs60677582;rs1124649	306;351	Q6NUQ4-2;Q6NUQ4	.;TM214_HUMAN	M	351;306;91	ENSP00000238788:V351M;ENSP00000384417:V306M	ENSP00000238788:V351M	V	+	1	0	TMEM214	27113973	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.222000	0.95196	2.700000	0.92200	0.561000	0.74099	GTG	G|0.713;A|0.287	0.287	strong		0.542	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727	
P2RX7	5027	hgsc.bcm.edu	37	12	121622304	121622304	+	Missense_Mutation	SNP	A	A	C	rs3751143	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121622304A>C	ENST00000546057.1	+	13	1630	c.1487A>C	c.(1486-1488)gAg>gCg	p.E496A	P2RX7_ENST00000535250.1_Missense_Mutation_p.E406A|P2RX7_ENST00000328963.5_Missense_Mutation_p.E326A|P2RX7_ENST00000541446.1_Missense_Mutation_p.E207A|P2RX7_ENST00000443520.3_3'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	496			E -> A (polymorphism that results in a loss of function; dbSNP:rs3751143). {ECO:0000269|PubMed:11150303, ECO:0000269|PubMed:15489334}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGCCTGGAGGAGCTGTGCTGC	0.607													A|||	1039	0.207468	0.0847	0.1916	5008	,	,		16659	0.2669		0.2087	False		,,,				2504	0.3221				p.E496A		Atlas-SNP	.											.	P2RX7	53	.	0			c.A1487C	GRCh37	CM021316	P2RX7	M	rs3751143	PASS	.	A	ALA/GLU	396,4010	194.7+/-219.5	19,358,1826	41.0	40.0	40.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1487	5.2	1.0	12	dbSNP_107	40	1590,7010	294.4+/-301.9	151,1288,2861	yes	missense	P2RX7	NM_002562.5	107	170,1646,4687	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	18.4884,8.9877,15.2699	probably-damaging	496/596	121622304	1986,11020	2203	4300	6503	SO:0001583	missense	5027	exon13			TGGAGGAGCTGTG	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1487A>C	12.37:g.121622304A>C	ENSP00000442349:p.Glu496Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	49	27	0.55102	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	421	0.19276556776556777	43	0.08739837398373984	77	0.212707182320442	146	0.25524475524475526	155	0.20448548812664907	A	25.1	4.606826	0.87157	0.089877	0.184884	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.05580	4.32;3.93;4.1;3.42	5.21	5.21	0.72293	.	0.000000	0.45867	D	0.000340	T	0.00012	0.0000	M	0.80982	2.52	0.27905	P	0.9388482	D;D;D;D	0.71674	0.986;0.998;0.986;0.991	P;D;P;P	0.81914	0.84;0.995;0.84;0.831	T	0.13710	-1.0499	9	0.87932	D	0	-30.5986	12.4464	0.55653	1.0:0.0:0.0:0.0	rs3751143;rs17850236;rs58839176;rs3751143	326;207;406;496	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	A	496;326;406;207	ENSP00000442349:E496A;ENSP00000330696:E326A;ENSP00000442572:E406A;ENSP00000437471:E207A	ENSP00000330696:E326A	E	+	2	0	P2RX7	120106687	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.490000	0.73645	1.967000	0.57214	0.482000	0.46254	GAG	A|0.826;C|0.174	0.174	strong		0.607	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
ZNF462	58499	hgsc.bcm.edu	37	9	109689859	109689859	+	Silent	SNP	T	T	C	rs3814540	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:109689859T>C	ENST00000277225.5	+	3	3955	c.3666T>C	c.(3664-3666)aaT>aaC	p.N1222N	ZNF462_ENST00000457913.1_Silent_p.N1222N|ZNF462_ENST00000441147.2_Silent_p.N67N			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1222					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						TCAAGGCCAATGCAGATGTGA	0.517													C|||	2598	0.51877	0.7095	0.4481	5008	,	,		15956	0.4802		0.3936	False		,,,				2504	0.4796				p.N1222N		Atlas-SNP	.											.	ZNF462	322	.	0			c.T3666C						PASS	.	C		2798,1608	496.7+/-363.6	890,1018,295	233.0	233.0	233.0		3666	-6.8	0.1	9	dbSNP_107	233	3112,5488	658.0+/-401.5	536,2040,1724	no	coding-synonymous	ZNF462	NM_021224.4		1426,3058,2019	CC,CT,TT		36.186,36.4957,45.4406		1222/2507	109689859	5910,7096	2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			GGCCAATGCAGAT	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.3666T>C	9.37:g.109689859T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			T|0.525;C|0.475	0.475	strong		0.517	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
CCDC157	550631	hgsc.bcm.edu	37	22	30772686	30772686	+	Silent	SNP	C	C	T	rs2286442	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30772686C>T	ENST00000405659.1	+	12	2920	c.2211C>T	c.(2209-2211)ggC>ggT	p.G737G	CCDC157_ENST00000338306.3_Silent_p.G737G|RP1-130H16.16_ENST00000332468.4_RNA			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	737										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						TGTCACCTGGCCGGGGACAGG	0.647													C|||	640	0.127796	0.0287	0.219	5008	,	,		16862	0.1895		0.1133	False		,,,				2504	0.1483				p.G737G		Atlas-SNP	.											.	CCDC157	86	.	0			c.C2211T						PASS	.	C		219,4185		9,201,1992	28.0	29.0	29.0		2211	2.6	0.0	22	dbSNP_100	29	914,7680		41,832,3424	no	coding-synonymous	CCDC157	NM_001017437.2		50,1033,5416	TT,TC,CC		10.6353,4.9728,8.7167		737/753	30772686	1133,11865	2202	4297	6499	SO:0001819	synonymous_variant	550631	exon12			ACCTGGCCGGGGA	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.2211C>T	22.37:g.30772686C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	32	0.355556	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			C|0.898;T|0.102	0.102	strong		0.647	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
ZNF462	58499	hgsc.bcm.edu	37	9	109773145	109773145	+	Missense_Mutation	SNP	A	A	T	rs10217192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:109773145A>T	ENST00000277225.5	+	13	7644	c.7355A>T	c.(7354-7356)cAc>cTc	p.H2452L	ZNF462_ENST00000542028.1_Missense_Mutation_p.H409L|RP11-508N12.2_ENST00000439901.1_RNA|ZNF462_ENST00000457913.1_Missense_Mutation_p.H2512L|ZNF462_ENST00000441147.2_Missense_Mutation_p.H1358L			Q96JM2	ZN462_HUMAN	zinc finger protein 462	2452			H -> L (in dbSNP:rs10217192).		chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GAAGAAATCCACCCAAAAGAG	0.383													A|||	416	0.0830671	0.1513	0.0908	5008	,	,		17008	0.001		0.0924	False		,,,				2504	0.0603				p.H2452L		Atlas-SNP	.											.	ZNF462	322	.	0			c.A7355T						PASS	.	A	LEU/HIS	740,3666	302.7+/-287.5	51,638,1514	75.0	71.0	72.0		7355	3.6	0.7	9	dbSNP_119	72	1003,7597	213.4+/-253.3	45,913,3342	yes	missense	ZNF462	NM_021224.4	99	96,1551,4856	TT,TA,AA		11.6628,16.7953,13.4015	benign	2452/2507	109773145	1743,11263	2203	4300	6503	SO:0001583	missense	58499	exon13			AAATCCACCCAAA	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.7355A>T	9.37:g.109773145A>T	ENSP00000277225:p.His2452Leu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	189	0.08653846153846154	72	0.14634146341463414	40	0.11049723756906077	1	0.0017482517482517483	76	0.10026385224274406	A	12.46	1.943832	0.34283	0.167953	0.116628	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147;ENST00000542028	T;T;T;T;T	0.14766	3.5;3.98;4.08;4.09;2.48	5.91	3.57	0.40892	.	0.377447	0.28742	N	0.014297	T	0.00039	0.0001	L	0.40543	1.245	0.34390	P	0.305955	P;B	0.38370	0.628;0.0	B;B	0.32677	0.15;0.0	T	0.40979	-0.9534	9	0.24483	T	0.36	.	7.5798	0.27959	0.8053:0.0:0.0676:0.1271	rs10217192;rs10217192	2512;2452	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	L	2452;2512;1395;1358;409	ENSP00000277225:H2452L;ENSP00000414570:H2512L;ENSP00000363818:H1395L;ENSP00000397306:H1358L;ENSP00000439771:H409L	ENSP00000277225:H2452L	H	+	2	0	ZNF462	108812966	0.663000	0.27448	0.687000	0.30102	0.478000	0.33099	2.633000	0.46519	1.031000	0.39867	0.533000	0.62120	CAC	A|0.879;T|0.121	0.121	strong		0.383	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
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 GAIIx	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_ENST00000545763.1_Missense_Mutation_p.M501V|MGA_ENST00000568630.1_3'UTR|MGA_ENST00000389936.4_Missense_Mutation_p.M501V|MGA_ENST00000566586.1_Missense_Mutation_p.M501V|MGA_ENST00000219905.7_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	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	40	28	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	
TLR8	51311	hgsc.bcm.edu	37	X	12937804	12937804	+	Silent	SNP	C	C	T	rs5744080	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:12937804C>T	ENST00000218032.6	+	2	732	c.645C>T	c.(643-645)caC>caT	p.H215H	TLR8_ENST00000311912.5_Silent_p.H233H	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	215					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.H233H(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CTCTTTCACACGTGCCACCCA	0.363													c|||	2556	0.677086	0.6157	0.513	3775	,	,		13833	0.6121		0.2843	False		,,,				2504	0.4939				p.H215H		Atlas-SNP	.											.	TLR8	134	.	1	Substitution - coding silent(1)	stomach(1)	c.C645T						PASS	.	T		2877,958		918,610,431,104,140	65.0	70.0	69.0		645	-4.9	0.0	X	dbSNP_114	69	2640,4087		388,1130,734,910,1137	no	coding-synonymous	TLR8	NM_138636.4		1306,1740,1165,1014,1277	TT,TC,T,CC,C		39.2448,24.9804,47.7656		215/1042	12937804	5517,5045	2203	4299	6502	SO:0001819	synonymous_variant	51311	exon2			TTCACACGTGCCA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.645C>T	X.37:g.12937804C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	103	71	0.68932	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																			C|0.402;0|0.003	.	strong		0.363	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
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 GAIIx	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_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_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	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	105	41	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	
PCDHB11	56125	hgsc.bcm.edu	37	5	140579367	140579367	+	Missense_Mutation	SNP	G	G	A	rs917535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140579367G>A	ENST00000354757.3	+	1	20	c.20G>A	c.(19-21)cGc>cAc	p.R7H	PCDHB11_ENST00000536699.1_5'UTR	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	7			R -> H (in dbSNP:rs917535).		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)			CAAGGGACACGCACTCAGCAG	0.502													G|||	319	0.0636981	0.2012	0.0461	5008	,	,		20878	0.0		0.0169	False		,,,				2504	0.0041				p.R7H		Atlas-SNP	.											PCDHB11,NS,carcinoma,+1,1	PCDHB11	162	1	0			c.G20A						PASS	.	G	HIS/ARG	786,3620	317.7+/-295.3	79,628,1496	87.0	82.0	84.0		20	-1.6	0.0	5	dbSNP_86	84	151,8449	73.5+/-136.2	0,151,4149	yes	missense	PCDHB11	NM_018931.2	29	79,779,5645	AA,AG,GG		1.7558,17.8393,7.2044	benign	7/798	140579367	937,12069	2203	4300	6503	SO:0001583	missense	56125	exon1			GGACACGCACTCA	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.20G>A	5.37:g.140579367G>A	ENSP00000346802:p.Arg7His	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	132	0.06043956043956044	101	0.20528455284552846	18	0.049723756906077346	0	0.0	13	0.017150395778364115	G	9.526	1.109447	0.20714	0.178393	0.017558	ENSG00000197479	ENST00000354757	T	0.52057	0.68	2.69	-1.64	0.08318	.	.	.	.	.	T	0.00039	0.0001	L	0.56124	1.755	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.20773	-1.0265	8	0.21540	T	0.41	.	8.2191	0.31530	0.7595:0.0:0.2405:0.0	rs917535;rs52792734;rs917535	7	Q9Y5F2	PCDBB_HUMAN	H	7	ENSP00000346802:R7H	ENSP00000346802:R7H	R	+	2	0	PCDHB11	140559551	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.282000	0.08445	-0.293000	0.08986	0.460000	0.39030	CGC	G|0.931;A|0.069	0.069	strong		0.502	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
RBMXL3	139804	hgsc.bcm.edu	37	X	114425923	114425923	+	Missense_Mutation	SNP	C	C	A	rs142223554		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:114425923C>A	ENST00000424776.3	+	1	1961	c.1919C>A	c.(1918-1920)gCc>gAc	p.A640D	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	640	Gly-rich.			A -> D (in Ref. 1; AK097568). {ECO:0000305}.			nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						TCCCTTGATGCCAACAGTGGA	0.657													C|||	220	0.0582781	0.0038	0.0533	3775	,	,		14344	0.002		0.1123	False		,,,				2504	0.0644				p.A640D		Atlas-SNP	.											.	RBMXL3	83	.	0			c.C1919A						PASS	.	C	ASP/ALA,	34,1175		1,25,7,491,168	52.0	53.0	53.0		1919,		0.0	X	dbSNP_134	53	391,2000		18,215,140,567,651	no	missense,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	126,	19,240,147,1058,819	AA,AC,A,CC,C		16.353,2.8122,11.8056	possibly-damaging,	640/1068,	114425923	425,3175	692	1591	2283	SO:0001583	missense	139804	exon1			TTGATGCCAACAG	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.1919C>A	X.37:g.114425923C>A	ENSP00000417451:p.Ala640Asp	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	130	30	0.230769	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	37	CCDS55478.1	117	0.0705244122965642	3	0.006122448979591836	20	0.056179775280898875	2	0.0034965034965034965	53	0.07703488372093023	C	9.422	1.083366	0.20309	0.028122	0.16353	ENSG00000175718	ENST00000424776	T	0.05717	3.4	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.52842	0.956	B	0.39465	0.3	T	0.50118	-0.8865	6	0.87932	D	0	.	.	.	.	.	640	Q8N7X1	RMXL3_HUMAN	D	640	ENSP00000417451:A640D	ENSP00000417451:A640D	A	+	2	0	RBMXL3	114332179	0.002000	0.14202	0.004000	0.12327	0.004000	0.04260	0.148000	0.16224	0.108000	0.17862	0.110000	0.15639	GCC	C|0.930;A|0.070	0.070	strong		0.657	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
FAM214A	56204	hgsc.bcm.edu	37	15	52901284	52901284	+	Silent	SNP	T	T	C	rs58018557|rs386783993	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:52901284T>C	ENST00000261844.7	-	6	1979	c.1827A>G	c.(1825-1827)tcA>tcG	p.S609S	FAM214A_ENST00000546305.2_Silent_p.S616S	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	609																	TTGAGGAAGTTGATAAACTAG	0.338													C|||	2472	0.49361	0.6233	0.317	5008	,	,		17171	0.8869		0.17	False		,,,				2504	0.3712				p.S609S		Atlas-SNP	.											.	.	.	.	0			c.A1827G						PASS	.	C		1897,1773		487,923,425	110.0	118.0	115.0		1827	-0.1	0.0	15	dbSNP_129	115	1271,6885		119,1033,2926	no	coding-synonymous	KIAA1370	NM_019600.2		606,1956,3351	CC,CT,TT		15.5836,48.3106,26.7884		609/1077	52901284	3168,8658	1835	4078	5913	SO:0001819	synonymous_variant	56204	exon6			GGAAGTTGATAAA	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.1827A>G	15.37:g.52901284T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			T|0.652;C|0.348	0.348	strong		0.338	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
OR2T2	401992	hgsc.bcm.edu	37	1	248616408	248616408	+	Missense_Mutation	SNP	C	C	T	rs67700848	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248616408C>T	ENST00000342927.3	+	1	332	c.310C>T	c.(310-312)Ctc>Ttc	p.L104F		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	104						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(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	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)			TCAGATCTTCCTCTACCTGAC	0.532																																					p.L104F		Atlas-SNP	.											OR2T2,NS,carcinoma,-2,1	OR2T2	73	1	0			c.C310T						PASS	.						300.0	329.0	320.0					1																	248616408		2203	4300	6503	SO:0001583	missense	401992	exon1			ATCTTCCTCTACC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.310C>T	1.37:g.248616408C>T	ENSP00000343062:p.Leu104Phe	Somatic	822	0	0		WXS	Illumina HiSeq	Phase_I	667	137	0.205397	NM_001004136	B2RNM1|B9EH01	Missense_Mutation	SNP	ENST00000342927.3	37	CCDS31116.1	.	.	.	.	.	.	.	.	.	.	c	0.006	-2.038068	0.00402	.	.	ENSG00000196240	ENST00000342927	T	0.00495	6.99	3.59	-0.635	0.11512	GPCR, rhodopsin-like superfamily (1);	0.681714	0.12783	N	0.439555	T	0.00210	0.0006	N	0.04768	-0.165	0.80722	P	0.0	B	0.13594	0.008	B	0.14023	0.01	T	0.23904	-1.0175	9	0.02654	T	1	.	8.1475	0.31121	0.0:0.3677:0.0:0.6323	.	104	Q6IF00	OR2T2_HUMAN	F	104	ENSP00000343062:L104F	ENSP00000343062:L104F	L	+	1	0	OR2T2	246683031	0.000000	0.05858	0.036000	0.18154	0.224000	0.24922	-0.885000	0.04161	-0.046000	0.13446	0.298000	0.19748	CTC	C|0.875;T|0.125	0.125	strong		0.532	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
ARSG	22901	hgsc.bcm.edu	37	17	66364749	66364749	+	Silent	SNP	T	T	C	rs1558877	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:66364749T>C	ENST00000448504.2	+	7	1561	c.765T>C	c.(763-765)ccT>ccC	p.P255P	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Silent_p.P91P	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	255					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)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGCCCTTACCTGTGACTCAGC	0.597													C|||	2561	0.511382	0.6581	0.6167	5008	,	,		18488	0.2708		0.506	False		,,,				2504	0.4918				p.P255P		Atlas-SNP	.											.	ARSG	55	.	0			c.T765C						PASS	.	C		2810,1596	494.5+/-363.0	918,974,311	92.0	90.0	91.0		765	0.5	0.0	17	dbSNP_88	91	4478,4122	563.6+/-388.2	1176,2126,998	no	coding-synonymous	ARSG	NM_014960.3		2094,3100,1309	CC,CT,TT		47.9302,36.2233,43.9643		255/526	66364749	7288,5718	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon7			CTTACCTGTGACT	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.765T>C	17.37:g.66364749T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			T|0.481;C|0.519	0.519	strong		0.597	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
HOXC9	3225	hgsc.bcm.edu	37	12	54394497	54394497	+	Silent	SNP	C	C	T	rs2241820	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:54394497C>T	ENST00000303450.4	+	1	595	c.525C>T	c.(523-525)gcC>gcT	p.A175A	HOXC9_ENST00000504557.1_Intron|HOXC-AS1_ENST00000505700.1_RNA|HOXC-AS1_ENST00000512427.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron|HOXC9_ENST00000508190.1_Silent_p.A175A	NM_006897.1	NP_008828.1	P31274	HXC9_HUMAN	homeobox C9	175					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(3)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14						AGGAGAAGGCCGACCTGGACC	0.692													C|||	2895	0.578075	0.4667	0.5346	5008	,	,		12030	0.7609		0.6014	False		,,,				2504	0.547				p.A175A		Atlas-SNP	.											.	HOXC9	25	.	0			c.C525T						PASS	.	C		1809,1381		539,731,325	6.0	7.0	7.0		525	1.1	1.0	12	dbSNP_98	7	4221,2551		1360,1501,525	no	coding-synonymous	HOXC9	NM_006897.1		1899,2232,850	TT,TC,CC		37.6698,43.2915,39.47		175/261	54394497	6030,3932	1595	3386	4981	SO:0001819	synonymous_variant	3225	exon1			GAAGGCCGACCTG		CCDS8869.1	12q13.13	2011-06-20	2005-12-22			ENSG00000180806		"""Homeoboxes / ANTP class : HOXL subclass"""	5130	protein-coding gene	gene with protein product		142971	"""homeo box C9"""	HOX3, HOX3B		1973146	Standard	NM_006897		Approved		uc001seq.3	P31274		ENST00000303450.4:c.525C>T	12.37:g.54394497C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	15	5	0.333333	NM_006897	B2RCN7|Q9H1I0	Silent	SNP	ENST00000303450.4	37	CCDS8869.1																																																																																			C|0.388;T|0.612	0.612	strong		0.692	HOXC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358958.1		
KLK12	43849	hgsc.bcm.edu	37	19	51535130	51535130	+	Splice_Site	SNP	A	A	G	rs3745540	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51535130A>G	ENST00000525263.1	-	3	577		c.e3+1		CTC-518B2.9_ENST00000594910.1_RNA|KLK12_ENST00000250352.11_Intron|KLK12_ENST00000250351.4_Splice_Site|KLK12_ENST00000319590.4_Splice_Site|KLK12_ENST00000529888.1_Intron			Q9UKR0	KLK12_HUMAN	kallikrein-related peptidase 12						proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	12		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00399)		TGGGCCCCTTACTCCGTGGGT	0.617													A|||	2675	0.534145	0.357	0.5591	5008	,	,		13289	0.6369		0.5656	False		,,,				2504	0.6176				.		Atlas-SNP	.											KLK12,NS,carcinoma,0,2	KLK12	30	2	0			c.457+2T>C	GRCh37	CS042543	KLK12	S	rs3745540	scavenged	.	A	,,	1660,2740		316,1028,856	87.0	97.0	94.0		,,	4.3	1.0	19	dbSNP_107	94	5049,3543		1514,2021,761	yes	splice-5,splice-5,intron	KLK12	NM_019598.2,NM_145894.1,NM_145895.1	,,	1830,3049,1617	GG,GA,AA		41.236,37.7273,48.3605	,,	,,	51535130	6709,6283	2200	4296	6496	SO:0001630	splice_region_variant	43849	exon5			CCCCTTACTCCGT		CCDS12820.1, CCDS12821.1, CCDS54298.1	19q13.33	2008-02-05	2006-10-27		ENSG00000186474	ENSG00000186474		"""Kallikreins"""	6360	protein-coding gene	gene with protein product		605539	"""kallikrein 12"""			16800724, 16800723	Standard	NM_019598		Approved	KLK-L5	uc002pvh.1	Q9UKR0	OTTHUMG00000165806	ENST00000525263.1:c.457+1T>C	19.37:g.51535130A>G		Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	74	24	0.324324	NM_145894	Q9UKR1|Q9UKR2	Splice_Site	SNP	ENST00000525263.1	37	CCDS12821.1	1141	0.5224358974358975	168	0.34146341463414637	208	0.574585635359116	350	0.6118881118881119	415	0.5474934036939314	A	11.67	1.708772	0.30322	0.377273	0.58764	ENSG00000186474	ENST00000525263;ENST00000319590;ENST00000250351	.	.	.	4.27	4.27	0.50696	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9845	0.41832	1.0:0.0:0.0:0.0	rs3745540;rs3926726;rs17715045;rs61507153;rs3745540	.	.	.	.	-1	.	.	.	-	.	.	KLK12	56226942	0.780000	0.28664	1.000000	0.80357	0.355000	0.29361	0.937000	0.28951	1.949000	0.56562	0.528000	0.53228	.	A|0.476;G|0.524	0.524	strong		0.617	KLK12-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386288.1	NM_019598	Intron
CACNG6	59285	hgsc.bcm.edu	37	19	54515415	54515415	+	Missense_Mutation	SNP	G	G	C	rs12980121	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54515415G>C	ENST00000252729.2	+	4	1345	c.755G>C	c.(754-756)tGt>tCt	p.C252S	CACNG6_ENST00000352529.1_Missense_Mutation_p.C181S|CACNG6_ENST00000346968.2_Missense_Mutation_p.C206S	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	252			C -> S (in dbSNP:rs12980121).		calcium ion transport (GO:0006816)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)		GGGTCCCTCTGTCCCAAGCGG	0.647													G|||	137	0.0273562	0.0023	0.0677	5008	,	,		9032	0.0		0.0686	False		,,,				2504	0.0184				p.C252S		Atlas-SNP	.											.	CACNG6	42	.	0			c.G755C						PASS	.	G	SER/CYS,SER/CYS,SER/CYS	47,4343		1,45,2149	42.0	47.0	46.0		542,755,617	3.9	0.8	19	dbSNP_121	46	461,8103		6,449,3827	yes	missense,missense,missense	CACNG6	NM_031897.2,NM_145814.1,NM_145815.1	112,112,112	7,494,5976	CC,CG,GG		5.383,1.0706,3.9216	probably-damaging,probably-damaging,probably-damaging	181/190,252/261,206/215	54515415	508,12446	2195	4282	6477	SO:0001583	missense	59285	exon4			CCCTCTGTCCCAA	AF288386	CCDS12870.1, CCDS12871.1	19q13.4	2008-05-02			ENSG00000130433	ENSG00000130433		"""Calcium channel subunits"""	13625	protein-coding gene	gene with protein product		606898				11170751	Standard	NM_145814		Approved		uc002qct.3	Q9BXT2	OTTHUMG00000064907	ENST00000252729.2:c.755G>C	19.37:g.54515415G>C	ENSP00000252729:p.Cys252Ser	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_145814		Missense_Mutation	SNP	ENST00000252729.2	37	CCDS12870.1	80	0.03663003663003663	1	0.0020325203252032522	30	0.08287292817679558	0	0.0	49	0.06464379947229551	G	15.44	2.834518	0.50951	0.010706	0.05383	ENSG00000130433	ENST00000252729;ENST00000352529;ENST00000346968	T;T;T	0.30981	1.54;1.51;1.51	3.89	3.89	0.44902	.	0.264330	0.34046	N	0.004315	T	0.04227	0.0117	M	0.64170	1.965	0.24928	N	0.991938	D;D;D	0.67145	0.989;0.996;0.981	D;D;D	0.77557	0.985;0.99;0.966	T	0.00171	-1.1960	10	0.66056	D	0.02	-7.1757	11.7327	0.51746	0.0:0.0:1.0:0.0	rs12980121	181;206;252	A6NP74;A6NFR2;Q9BXT2	.;.;CCG6_HUMAN	S	252;181;206	ENSP00000252729:C252S;ENSP00000319135:C181S;ENSP00000319097:C206S	ENSP00000252729:C252S	C	+	2	0	CACNG6	59207227	1.000000	0.71417	0.763000	0.31416	0.403000	0.30841	4.155000	0.58131	2.491000	0.84063	0.650000	0.86243	TGT	G|0.953;C|0.047	0.047	strong		0.647	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1		
NPBWR1	2831	hgsc.bcm.edu	37	8	53852871	53852871	+	Missense_Mutation	SNP	A	A	T	rs33977775	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:53852871A>T	ENST00000331251.3	+	1	1881	c.404A>T	c.(403-405)tAc>tTc	p.Y135F		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	135			Y -> F (in dbSNP:rs33977775).		G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GCCGACCGCTACCTGGTGGTG	0.667													A|||	436	0.0870607	0.0038	0.085	5008	,	,		16505	0.12		0.1302	False		,,,				2504	0.1227				p.Y135F		Atlas-SNP	.											.	NPBWR1	38	.	0			c.A404T						PASS	.	A	PHE/TYR	131,4271		3,125,2073	28.0	29.0	29.0		404	5.1	1.0	8	dbSNP_126	29	1016,7574		60,896,3339	yes	missense	NPBWR1	NM_005285.3	22	63,1021,5412	TT,TA,AA		11.8277,2.9759,8.8285	probably-damaging	135/329	53852871	1147,11845	2201	4295	6496	SO:0001583	missense	2831	exon1			ACCGCTACCTGGT	BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4522	protein-coding gene	gene with protein product		600730	"""G protein-coupled receptor 7"""	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.404A>T	8.37:g.53852871A>T	ENSP00000330284:p.Tyr135Phe	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_005285	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	205	0.09386446886446886	5	0.01016260162601626	34	0.09392265193370165	70	0.12237762237762238	96	0.1266490765171504	A	27.3	4.816662	0.90790	0.029759	0.118277	ENSG00000183729	ENST00000331251	D	0.87029	-2.2	5.06	5.06	0.68205	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000144	T	0.16385	0.0394	M	0.78801	2.425	0.21416	P	0.999690328	D	0.89917	1.0	D	0.91635	0.999	T	0.61232	-0.7104	9	0.87932	D	0	.	14.9709	0.71232	1.0:0.0:0.0:0.0	rs33977775	135	P48145	NPBW1_HUMAN	F	135	ENSP00000330284:Y135F	ENSP00000330284:Y135F	Y	+	2	0	NPBWR1	54015424	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.875000	0.75551	2.120000	0.65058	0.533000	0.62120	TAC	A|0.907;T|0.093	0.093	strong		0.667	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285	
INPP4A	3631	hgsc.bcm.edu	37	2	99172244	99172244	+	Missense_Mutation	SNP	A	A	G	rs2278206	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:99172244A>G	ENST00000523221.1	+	15	1810	c.1810A>G	c.(1810-1812)Act>Gct	p.T604A	INPP4A_ENST00000074304.5_Missense_Mutation_p.T604A|INPP4A_ENST00000545415.1_Intron|INPP4A_ENST00000409851.3_Missense_Mutation_p.T599A|INPP4A_ENST00000409540.3_Intron|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409016.4_Intron			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	604			T -> A (in dbSNP:rs2278206).		inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						CATGCCCTCCACTGCATGCCA	0.552													G|||	1424	0.284345	0.2375	0.3069	5008	,	,		21373	0.3155		0.2654	False		,,,				2504	0.319				p.T604A		Atlas-SNP	.											.	INPP4A	205	.	0			c.A1810G	GRCh37	CM084964	INPP4A	M	rs2278206	PASS	.	G	ALA/THR,ALA/THR,,	351,1033		51,249,392	205.0	209.0	207.0		1810,1795,,	2.4	0.3	2	dbSNP_100	207	805,2377		104,597,890	yes	missense,missense,intron,intron	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	58,58,,	155,846,1282	GG,GA,AA		25.2986,25.3613,25.3176	benign,benign,,	604/978,599/973,,	99172244	1156,3410	692	1591	2283	SO:0001583	missense	3631	exon17			CCCTCCACTGCAT	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.1810A>G	2.37:g.99172244A>G	ENSP00000427722:p.Thr604Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	29	18	0.62069	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Missense_Mutation	SNP	ENST00000523221.1	37	CCDS46369.1	601	0.2751831501831502	127	0.258130081300813	110	0.30386740331491713	171	0.29895104895104896	193	0.2546174142480211	G	1.804	-0.476376	0.04414	0.253613	0.252986	ENSG00000040933	ENST00000409851;ENST00000074304;ENST00000523221	T;T;T	0.15718	2.4;2.4;2.4	5.14	2.4	0.29515	.	0.498696	0.19604	N	0.110315	T	0.00012	0.0000	N	0.08118	0	0.24989	P	0.99154762	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47623	-0.9103	8	.	.	.	-1.1761	1.3523	0.02175	0.3134:0.1264:0.4149:0.1452	rs2278206;rs60846330;rs2278206	604;599	Q96PE3;Q96PE3-3	INP4A_HUMAN;.	A	599;604;604	ENSP00000386777:T599A;ENSP00000074304:T604A;ENSP00000427722:T604A	.	T	+	1	0	INPP4A	98538676	0.004000	0.15560	0.339000	0.25562	0.915000	0.54546	0.194000	0.17135	0.092000	0.17331	-1.653000	0.00756	ACT	A|0.729;G|0.271	0.271	strong		0.552	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
SLC5A12	159963	hgsc.bcm.edu	37	11	26692742	26692742	+	Silent	SNP	G	G	A	rs7128823	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:26692742G>A	ENST00000396005.3	-	15	2073	c.1764C>T	c.(1762-1764)aaC>aaT	p.N588N		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	588					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						TTCTGAGTCCGTTCTGTAAGA	0.433													G|||	1584	0.316294	0.2776	0.2219	5008	,	,		18340	0.4722		0.3151	False		,,,				2504	0.2761				p.N588N		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C1764T						PASS	.	G		999,2821		127,745,1038	214.0	204.0	207.0		1764	-1.2	1.0	11	dbSNP_116	207	2233,5981		322,1589,2196	no	coding-synonymous	SLC5A12	NM_178498.3		449,2334,3234	AA,AG,GG		27.1853,26.1518,26.8572		588/619	26692742	3232,8802	1910	4107	6017	SO:0001819	synonymous_variant	159963	exon15			GAGTCCGTTCTGT	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"""Solute carriers"""	28750	protein-coding gene	gene with protein product		612455	"""solute carrier family 5 (sodium/glucose cotransporter), member 12"""			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1764C>T	11.37:g.26692742G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	171	80	0.467836	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			G|0.686;A|0.314	0.314	strong		0.433	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
GBF1	8729	hgsc.bcm.edu	37	10	104140350	104140350	+	Missense_Mutation	SNP	G	G	A	rs11191274	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:104140350G>A	ENST00000369983.3	+	38	5337	c.5077G>A	c.(5077-5079)Ggc>Agc	p.G1693S		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	1693			G -> S (in dbSNP:rs11191274).		COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		ACGGGGAGGCGGCCCCTCGGC	0.577													G|||	259	0.0517173	0.003	0.0749	5008	,	,		20003	0.0456		0.1213	False		,,,				2504	0.0358				p.G1693S		Atlas-SNP	.											.	GBF1	142	.	0			c.G5077A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	107,4299	82.4+/-120.9	3,101,2099	242.0	265.0	257.0		5068,5065,5077	-3.7	0.0	10	dbSNP_120	257	1117,7483	232.1+/-265.8	62,993,3245	yes	missense,missense,missense	GBF1	NM_001199378.1,NM_001199379.1,NM_004193.2	56,56,56	65,1094,5344	AA,AG,GG		12.9884,2.4285,9.411	probably-damaging,probably-damaging,probably-damaging	1690/1857,1689/1856,1693/1860	104140350	1224,11782	2203	4300	6503	SO:0001583	missense	8729	exon38			GGAGGCGGCCCCT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.5077G>A	10.37:g.104140350G>A	ENSP00000359000:p.Gly1693Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_004193	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	152	0.0695970695970696	2	0.0040650406504065045	32	0.08839779005524862	23	0.04020979020979021	95	0.12532981530343007	G	0.008	-1.878389	0.00537	0.024285	0.129884	ENSG00000107862	ENST00000369983	T	0.08634	3.07	5.91	-3.65	0.04502	.	0.390538	0.32147	N	0.006510	T	0.00039	0.0001	L	0.40543	1.245	0.58432	P	4.000000000004E-6	P;P;B	0.40107	0.703;0.703;0.01	B;B;B	0.30401	0.115;0.115;0.008	T	0.48525	-0.9028	9	0.08837	T	0.75	-0.1049	8.0024	0.30304	0.3925:0.1192:0.4883:0.0	rs11191274;rs52831419;rs59539666;rs11191274	1689;1689;1693	Q149P1;Q149P0;Q92538	.;.;GBF1_HUMAN	S	1693	ENSP00000359000:G1693S	ENSP00000359000:G1693S	G	+	1	0	GBF1	104130340	0.000000	0.05858	0.031000	0.17742	0.082000	0.17680	-0.664000	0.05292	-0.640000	0.05495	-1.058000	0.02302	GGC	G|0.918;A|0.082	0.082	strong		0.577	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
ATHL1	80162	hgsc.bcm.edu	37	11	293188	293188	+	Silent	SNP	T	T	C	rs12801980	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:293188T>C	ENST00000409548.2	+	8	1411	c.1296T>C	c.(1294-1296)caT>caC	p.H432H	ATHL1_ENST00000409479.1_Silent_p.H459H|ATHL1_ENST00000409655.1_Silent_p.H255H	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	432					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		ACGAGTACCATTCAGGGGTCA	0.602													t|||	2007	0.400759	0.3585	0.3718	5008	,	,		14854	0.3998		0.3668	False		,,,				2504	0.5143				p.H432H		Atlas-SNP	.											.	ATHL1	88	.	0			c.T1296C						PASS	.	T		1434,2972	466.4+/-354.5	245,944,1014	236.0	205.0	216.0		1296	-4.6	0.0	11	dbSNP_121	216	2969,5631	461.2+/-365.4	510,1949,1841	no	coding-synonymous	ATHL1	NM_025092.4		755,2893,2855	CC,CT,TT		34.5233,32.5465,33.8536		432/738	293188	4403,8603	2203	4300	6503	SO:0001819	synonymous_variant	80162	exon8			GTACCATTCAGGG	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.1296T>C	11.37:g.293188T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			C|0.344;N|0.000	0.344	strong		0.602	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
CORT	1325	hgsc.bcm.edu	37	1	10511544	10511544	+	Silent	SNP	C	C	T	rs628462	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10511544C>T	ENST00000377049.3	+	2	715	c.210C>T	c.(208-210)gcC>gcT	p.A70A	APITD1_ENST00000602787.1_Silent_p.A129A|APITD1-CORT_ENST00000400900.2_Silent_p.A129A|CORT_ENST00000320498.4_Silent_p.A120A|APITD1-CORT_ENST00000465026.1_3'UTR|APITD1_ENST00000602296.1_3'UTR|APITD1-CORT_ENST00000470413.2_3'UTR	NM_001302.4	NP_001293.3	O00230	CORT_HUMAN	cortistatin	70					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)	G-protein coupled receptor binding (GO:0001664)|neuropeptide hormone activity (GO:0005184)			breast(1)|endometrium(1)|stomach(1)	3	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0487)		GAGAGGAAGCCCGGGAGGTGG	0.627													C|||	1440	0.28754	0.0212	0.3112	5008	,	,		14123	0.4871		0.3907	False		,,,				2504	0.319				p.A129A		Atlas-SNP	.											CORT,colon,carcinoma,0,2	.	.	2	0			c.C387T						PASS	.	C	,,	351,4051		21,309,1871	24.0	30.0	28.0		210,387,	-2.3	0.0	1	dbSNP_83	28	3414,5182		682,2050,1566	no	coding-synonymous,coding-synonymous,utr-3	CORT,APITD1-CORT	NM_001302.4,NM_198544.3,NM_199006.2	,,	703,2359,3437	TT,TC,CC		39.7161,7.9736,28.966	,,	70/106,129/165,	10511544	3765,9233	2201	4298	6499	SO:0001819	synonymous_variant	100526739	exon5			GGAAGCCCGGGAG	AF013252	CCDS117.1, CCDS117.2	1p36.22	2013-02-25			ENSG00000241563	ENSG00000241563		"""Endogenous ligands"""	2257	protein-coding gene	gene with protein product	"""prepro-cortistatin"""	602784				9205124	Standard	NM_001302		Approved	MGC32686		O00230	OTTHUMG00000001906	ENST00000377049.3:c.210C>T	1.37:g.10511544C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	168	165	0.982143	NM_198544	Q5T6G0|Q6UX11	Silent	SNP	ENST00000377049.3	37	CCDS117.2																																																																																			C|0.685;T|0.315	0.315	strong		0.627	CORT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005410.3	NM_001302	
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 GAIIx	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	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	107	30	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	
MUC16	94025	hgsc.bcm.edu	37	19	9086819	9086819	+	Silent	SNP	G	G	A	rs1823056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9086819G>A	ENST00000397910.4	-	1	5199	c.4996C>T	c.(4996-4998)Ctg>Ttg	p.L1666L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1666	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTTCTTTCCAGTGCCATGTTT	0.512													G|||	952	0.190096	0.0711	0.2709	5008	,	,		22140	0.3036		0.172	False		,,,				2504	0.1953				p.L1666L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C4996T						PASS	.	G		282,3728		5,272,1728	109.0	105.0	106.0		4996	-1.9	0.0	19	dbSNP_92	106	1490,6868		127,1236,2816	no	coding-synonymous	MUC16	NM_024690.2		132,1508,4544	AA,AG,GG		17.8272,7.0324,14.3273		1666/14508	9086819	1772,10596	2005	4179	6184	SO:0001819	synonymous_variant	94025	exon1			TTTCCAGTGCCAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4996C>T	19.37:g.9086819G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	131	63	0.480916	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.811;A|0.189	0.189	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MUC13	56667	hgsc.bcm.edu	37	3	124627024	124627024	+	Missense_Mutation	SNP	T	T	G	rs1127233	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:124627024T>G	ENST00000311075.3	-	11	1544	c.1506A>C	c.(1504-1506)agA>agC	p.R502S		NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	503					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						TGCTGCTGTGTCTTGAATAGG	0.537													G|||	1149	0.229433	0.2791	0.2305	5008	,	,		15039	0.0913		0.2525	False		,,,				2504	0.2802				p.R502S		Atlas-SNP	.											MUC13,colon,carcinoma,0,1	MUC13	57	1	0			c.A1506C						PASS	.	G	SER/ARG	1279,3127	699.4+/-406.5	180,919,1104	121.0	103.0	109.0		1506	1.0	0.0	3	dbSNP_86	109	2172,6428	712.1+/-405.9	288,1596,2416	yes	missense	MUC13	NM_033049.3	110	468,2515,3520	GG,GT,TT		25.2558,29.0286,26.5339	benign	502/512	124627024	3451,9555	2203	4300	6503	SO:0001583	missense	56667	exon11			GCTGTGTCTTGAA	AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"""Mucins"""	7511	protein-coding gene	gene with protein product		612181	"""down-regulated in colon cancer 1"", ""mucin 13, epithelial transmembrane"""	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.1506A>C	3.37:g.124627024T>G	ENSP00000312235:p.Arg502Ser	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_033049	Q6UWD9|Q9NXT5	Missense_Mutation	SNP	ENST00000311075.3	37		478	0.21886446886446886	146	0.2967479674796748	83	0.2292817679558011	55	0.09615384615384616	194	0.2559366754617414	G	0.015	-1.547314	0.00926	0.290286	0.252558	ENSG00000173702	ENST00000311075	T	0.13657	2.57	3.76	0.97	0.19692	.	0.615052	0.13704	N	0.368629	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	9	0.02654	T	1	-4.9076	1.2406	0.01962	0.1995:0.1722:0.451:0.1773	rs1127233;rs3182885;rs17352196;rs17512232;rs52804026;rs58180561;rs1127233	502	Q9H3R2	MUC13_HUMAN	S	502	ENSP00000312235:R502S	ENSP00000312235:R502S	R	-	3	2	MUC13	126109714	0.002000	0.14202	0.008000	0.14137	0.001000	0.01503	0.232000	0.17891	-0.032000	0.13758	-1.959000	0.00480	AGA	T|0.752;G|0.248	0.248	strong		0.537	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049	
RSRP1	57035	hgsc.bcm.edu	37	1	25570081	25570081	+	Missense_Mutation	SNP	T	T	C	rs1043879	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:25570081T>C	ENST00000243189.7	-	4	992	c.716A>G	c.(715-717)gAa>gGa	p.E239G	C1orf63_ENST00000417642.2_Missense_Mutation_p.E240G	NM_020317.3	NP_064713.3	Q9BUV0	RSRP1_HUMAN		239			E -> G (in dbSNP:rs1043879). {ECO:0000269|PubMed:15489334}.							breast(1)|large_intestine(1)|lung(4)|pancreas(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.9e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000333)|BRCA - Breast invasive adenocarcinoma(304;0.000443)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000932)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGTAGGTTTTTCATTGGGATT	0.353													T|||	540	0.107827	0.0129	0.2089	5008	,	,		17228	0.0327		0.2724	False		,,,				2504	0.0726				p.E239G		Atlas-SNP	.											.	C1orf63	17	.	0			c.A716G						PASS	.	T	GLY/GLU	237,4169	138.8+/-174.5	11,215,1977	228.0	204.0	212.0	http://www.ncbi.nlm.nih.gov/pubmed?term	716	4.0	0.2	1	dbSNP_86	212	2306,6294	388.1+/-342.4	314,1678,2308	yes	missense	C1orf63	NM_020317.3	98	325,1893,4285	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	26.814,5.379,19.5525	probably-damaging	239/291	25570081	2543,10463	2203	4300	6503	SO:0001583	missense	57035	exon4			GGTTTTTCATTGG																												ENST00000243189.7:c.716A>G	1.37:g.25570081T>C	ENSP00000243189:p.Glu239Gly	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	188	79	0.420213	NM_020317	A8K917|Q49AA4|Q5TH71|Q9GZP6	Missense_Mutation	SNP	ENST00000243189.7	37	CCDS260.1	316	0.1446886446886447	10	0.02032520325203252	76	0.20994475138121546	13	0.022727272727272728	217	0.2862796833773087	T	8.815	0.936144	0.18206	0.05379	0.26814	ENSG00000117616	ENST00000243189;ENST00000417642	T;T	0.34472	1.36;1.41	5.1	3.97	0.46021	.	0.551981	0.14928	N	0.290259	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.999999853191	B	0.23540	0.087	B	0.25759	0.063	T	0.17653	-1.0362	9	0.59425	D	0.04	-3.633	8.5213	0.33277	0.0:0.0886:0.0:0.9114	rs1043879;rs17844932;rs17857662;rs17859787;rs57469912;rs1043879	239	Q9BUV0	CA063_HUMAN	G	239;240	ENSP00000243189:E239G;ENSP00000411631:E240G	ENSP00000243189:E239G	E	-	2	0	C1orf63	25442668	1.000000	0.71417	0.182000	0.23118	0.052000	0.14988	1.995000	0.40767	0.969000	0.38237	0.477000	0.44152	GAA	T|0.831;C|0.169	0.169	strong		0.353	C1orf63-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101966.2		
ZNF180	7733	hgsc.bcm.edu	37	19	44981375	44981375	+	Silent	SNP	T	T	C	rs954314	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:44981375T>C	ENST00000221327.4	-	5	1604	c.1323A>G	c.(1321-1323)caA>caG	p.Q441Q	ZNF180_ENST00000391956.4_Silent_p.Q416Q|ZNF180_ENST00000592529.1_Silent_p.Q414Q|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	441					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)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				ACTTTCCACATTGATTGCATT	0.393													T|||	804	0.160543	0.1513	0.1729	5008	,	,		19777	0.002		0.338	False		,,,				2504	0.1452				p.Q441Q	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											ZNF180,caecum,carcinoma,0,1	ZNF180	103	1	0			c.A1323G						PASS	.	T		872,3534	333.6+/-303.0	88,696,1419	75.0	77.0	76.0		1323	-5.9	0.9	19	dbSNP_86	76	2776,5824	439.2+/-359.1	460,1856,1984	no	coding-synonymous	ZNF180	NM_013256.3		548,2552,3403	CC,CT,TT		32.2791,19.7912,28.0486		441/693	44981375	3648,9358	2203	4300	6503	SO:0001819	synonymous_variant	7733	exon5			TCCACATTGATTG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1323A>G	19.37:g.44981375T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																			T|0.760;C|0.240	0.240	strong		0.393	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
ZNF770	54989	hgsc.bcm.edu	37	15	35273620	35273620	+	Silent	SNP	C	C	T	rs4923849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:35273620C>T	ENST00000356321.4	-	3	2360	c.2016G>A	c.(2014-2016)caG>caA	p.Q672Q		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	672					regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		AGTGAGTAAGCTGATGTCTCT	0.428													T|||	2350	0.469249	0.879	0.4611	5008	,	,		18734	0.376		0.2684	False		,,,				2504	0.2239				p.Q672Q		Atlas-SNP	.											.	ZNF770	64	.	0			c.G2016A						PASS	.	T		3489,911	348.0+/-309.7	1379,731,90	68.0	62.0	64.0		2016	0.8	1.0	15	dbSNP_111	64	2446,6150	695.3+/-404.8	347,1752,2199	no	coding-synonymous	ZNF770	NM_014106.3		1726,2483,2289	TT,TC,CC		28.4551,20.7045,45.6679		672/692	35273620	5935,7061	2200	4298	6498	SO:0001819	synonymous_variant	54989	exon3			AGTAAGCTGATGT	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"""Zinc fingers, C2H2-type"""	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.2016G>A	15.37:g.35273620C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_014106	Q6ZMZ6|Q9NWV2	Silent	SNP	ENST00000356321.4	37	CCDS10042.1																																																																																			C|0.523;T|0.477	0.477	strong		0.428	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106	
THBS1	7057	hgsc.bcm.edu	37	15	39880358	39880358	+	Silent	SNP	C	C	T	rs2228261	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:39880358C>T	ENST00000260356.5	+	9	1575	c.1410C>T	c.(1408-1410)aaC>aaT	p.N470N		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	470	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.N470N(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CCCAGATGAACGGGAAACCCT	0.597													C|||	1336	0.266773	0.4493	0.1383	5008	,	,		20241	0.2897		0.1312	False		,,,				2504	0.227				p.N470N		Atlas-SNP	.											THBS1,NS,carcinoma,0,1	THBS1	106	1	1	Substitution - coding silent(1)	stomach(1)	c.C1410T						PASS	.	C		1702,2698	513.4+/-368.3	331,1040,829	83.0	78.0	80.0		1410	-12.0	0.0	15	dbSNP_98	80	1130,7464	232.5+/-266.1	64,1002,3231	no	coding-synonymous	THBS1	NM_003246.2		395,2042,4060	TT,TC,CC		13.1487,38.6818,21.7947		470/1171	39880358	2832,10162	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon9			GATGAACGGGAAA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1410C>T	15.37:g.39880358C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.766;T|0.234	0.234	strong		0.597	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
ZNF804A	91752	hgsc.bcm.edu	37	2	185801597	185801597	+	Missense_Mutation	SNP	A	A	G	rs61739290	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:185801597A>G	ENST00000302277.6	+	4	2068	c.1474A>G	c.(1474-1476)Att>Gtt	p.I492V		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	492				I -> V (in Ref. 3; AAI50199). {ECO:0000305}.			metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						GCAGGAAGACATTTGCATGGG	0.353													A|||	177	0.0353435	0.0159	0.0331	5008	,	,		17924	0.0159		0.0666	False		,,,				2504	0.0511				p.I492V		Atlas-SNP	.											.	ZNF804A	322	.	0			c.A1474G						PASS	.	A	VAL/ILE	114,4290	81.4+/-119.9	1,112,2089	107.0	112.0	110.0		1474	-5.0	0.0	2	dbSNP_129	110	669,7931	164.9+/-217.2	32,605,3663	yes	missense	ZNF804A	NM_194250.1	29	33,717,5752	GG,GA,AA		7.7791,2.5886,6.0212	benign	492/1210	185801597	783,12221	2202	4300	6502	SO:0001583	missense	91752	exon4			GAAGACATTTGCA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1474A>G	2.37:g.185801597A>G	ENSP00000303252:p.Ile492Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	161	78	0.484472	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	72	0.03296703296703297	3	0.006097560975609756	12	0.03314917127071823	9	0.015734265734265736	48	0.0633245382585752	A	0.014	-1.592774	0.00864	0.025886	0.077791	ENSG00000170396	ENST00000302277	T	0.05258	3.47	5.68	-5.03	0.02973	.	0.939879	0.08892	N	0.878526	T	0.00241	0.0007	L	0.50333	1.59	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.48269	-0.9050	10	0.02654	T	1	-1.6129	0.4618	0.00518	0.2968:0.1227:0.2084:0.372	rs61739290	492	Q7Z570	Z804A_HUMAN	V	492	ENSP00000303252:I492V	ENSP00000303252:I492V	I	+	1	0	ZNF804A	185509842	0.001000	0.12720	0.000000	0.03702	0.008000	0.06430	-0.074000	0.11450	-0.307000	0.08804	0.528000	0.53228	ATT	A|0.947;G|0.053	0.053	strong		0.353	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
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 GAIIx	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		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	56	22	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	
OXNAD1	92106	hgsc.bcm.edu	37	3	16312564	16312564	+	Silent	SNP	C	C	T	rs842259	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:16312564C>T	ENST00000285083.5	+	3	570	c.105C>T	c.(103-105)caC>caT	p.H35H	OXNAD1_ENST00000605932.1_Silent_p.H35H|OXNAD1_ENST00000606098.1_Silent_p.H35H|OXNAD1_ENST00000544043.1_Silent_p.H53H|OXNAD1_ENST00000435829.2_Silent_p.H53H	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	35						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						CTTTGCGCCACCTTACTCTAA	0.483													C|||	2107	0.420727	0.2617	0.4654	5008	,	,		17886	0.4752		0.4324	False		,,,				2504	0.5358				p.H35H		Atlas-SNP	.											OXNAD1,rectum,carcinoma,0,1	OXNAD1	31	1	0			c.C105T						PASS	.	C		1361,3045	450.8+/-349.5	221,919,1063	157.0	146.0	150.0		105	3.0	0.5	3	dbSNP_86	150	3655,4945	526.1+/-380.9	787,2081,1432	no	coding-synonymous	OXNAD1	NM_138381.3		1008,3000,2495	TT,TC,CC		42.5,30.8897,38.5668		35/313	16312564	5016,7990	2203	4300	6503	SO:0001819	synonymous_variant	92106	exon3			GCGCCACCTTACT	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.105C>T	3.37:g.16312564C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_138381	Q2HYC7|Q59FA4	Silent	SNP	ENST00000285083.5	37	CCDS2630.1																																																																																			C|0.609;T|0.391	0.391	strong		0.483	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
ITGAD	3681	hgsc.bcm.edu	37	16	31429879	31429879	+	Missense_Mutation	SNP	T	T	C	rs150615624		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31429879T>C	ENST00000389202.2	+	23	2823	c.2774T>C	c.(2773-2775)aTc>aCc	p.I925T		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	925					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						TACACCATGATCAGCAGGTGC	0.557													t|||	1	0.000199681	0.0	0.0	5008	,	,		19037	0.0		0.001	False		,,,				2504	0.0				p.I925T		Atlas-SNP	.											.	ITGAD	154	.	0			c.T2774C						PASS	.	T	THR/ILE	1,4393	2.1+/-5.4	0,1,2196	124.0	115.0	118.0		2774	2.7	0.9	16	dbSNP_134	118	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ITGAD	NM_005353.2	89	0,4,6493	CC,CT,TT		0.0349,0.0228,0.0308	probably-damaging	925/1162	31429879	4,12990	2197	4300	6497	SO:0001583	missense	3681	exon23			CCATGATCAGCAG	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.2774T>C	16.37:g.31429879T>C	ENSP00000373854:p.Ile925Thr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	13.70	2.314842	0.40996	2.28E-4	3.49E-4	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.54071	0.59	5.06	2.74	0.32292	Integrin alpha-2 (1);	.	.	.	.	T	0.64316	0.2587	M	0.67953	2.075	0.31359	N	0.681608	D;D	0.63880	0.993;0.993	D;D	0.65987	0.94;0.94	T	0.62964	-0.6742	9	0.27082	T	0.32	.	9.3287	0.38008	0.0:0.0:0.3834:0.6166	.	941;925	Q59H14;Q13349	.;ITAD_HUMAN	T	941;925	ENSP00000373854:I925T	ENSP00000373854:I925T	I	+	2	0	ITGAD	31337380	0.835000	0.29415	0.912000	0.35992	0.438000	0.31896	1.936000	0.40183	0.244000	0.21351	0.533000	0.62120	ATC	T|1.000;C|0.000	0.000	strong		0.557	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
CDRT1	374286	hgsc.bcm.edu	37	17	15510988	15510988	+	Missense_Mutation	SNP	T	T	C	rs62070402	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:15510988T>C	ENST00000395906.3	-	6	1131	c.1132A>G	c.(1132-1134)Aac>Gac	p.N378D	RP11-385D13.1_ENST00000455584.2_Missense_Mutation_p.N688D	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	378										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		GTCCACAGGTTGTACTCATTC	0.483													T|||	1466	0.292732	0.264	0.2767	5008	,	,		20919	0.4514		0.1511	False		,,,				2504	0.3252				p.N378D		Atlas-SNP	.											.	CDRT1	83	.	0			c.A1132G						PASS	.	T	ASP/ASN	1076,3330	382.5+/-324.5	143,790,1270	80.0	76.0	78.0		1132	2.7	1.0	17	dbSNP_129	78	1443,7153	270.4+/-288.9	125,1193,2980	no	missense	CDRT1	NM_006382.3	23	268,1983,4250	CC,CT,TT		16.7869,24.4212,19.3739	possibly-damaging	378/753	15510988	2519,10483	2203	4298	6501	SO:0001583	missense	374286	exon6			ACAGGTTGTACTC	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1132A>G	17.37:g.15510988T>C	ENSP00000379242:p.Asn378Asp	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	T	13.75	2.328938	0.41197	0.244212	0.167869	ENSG00000251537	ENST00000261644;ENST00000395906	T	0.21734	1.99	4.99	2.69	0.31865	F-box domain, Skp2-like (1);	0.557353	0.14804	U	0.297455	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	0.9999999699041	P;B	0.42827	0.791;0.421	B;B	0.32677	0.15;0.107	T	0.30297	-0.9983	9	0.35671	T	0.21	.	5.8404	0.18630	0.0:0.0906:0.1708:0.7386	rs62070402	378;702	O95170;Q59EB2	CDRT1_HUMAN;.	D	408;378	ENSP00000379242:N378D	ENSP00000261644:N408D	N	-	1	0	RP11-385D13.1	15451713	0.998000	0.40836	0.993000	0.49108	0.814000	0.46013	1.550000	0.36223	0.824000	0.34613	0.459000	0.35465	AAC	T|0.810;C|0.190	0.190	strong		0.483	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
MRPL22	29093	hgsc.bcm.edu	37	5	154320820	154320820	+	Silent	SNP	C	C	T	rs115393757	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:154320820C>T	ENST00000523037.1	+	2	113	c.72C>T	c.(70-72)gcC>gcT	p.A24A	MRPL22_ENST00000265229.8_5'UTR|MRPL22_ENST00000522038.1_Silent_p.A24A|MRPL22_ENST00000439747.3_Silent_p.A50A	NM_014180.3	NP_054899.2	Q9NWU5	RM22_HUMAN	mitochondrial ribosomal protein L22	24					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GGAAGCTGGCCTTGGGGTGAG	0.532													C|||	13	0.00259585	0.0	0.0043	5008	,	,		16788	0.0		0.0099	False		,,,				2504	0.0				p.A24A		Atlas-SNP	.											.	MRPL22	18	.	0			c.C72T						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	105.0	106.0	106.0		,72	-0.2	0.0	5	dbSNP_132	106	86,8514	49.4+/-109.1	0,86,4214	no	utr-5,coding-synonymous	MRPL22	NM_001014990.2,NM_014180.3	,	0,88,6415	TT,TC,CC		1.0,0.0454,0.6766	,	,24/207	154320820	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	29093	exon2			GCTGGCCTTGGGG	AB051622	CCDS4331.1, CCDS43391.1	5q33.2	2012-09-13			ENSG00000082515	ENSG00000082515		"""Mitochondrial ribosomal proteins / large subunits"""	14480	protein-coding gene	gene with protein product		611835					Standard	NM_014180		Approved	MRP-L25, RPML25, HSPC158	uc003lvy.4	Q9NWU5	OTTHUMG00000130190	ENST00000523037.1:c.72C>T	5.37:g.154320820C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	125	76	0.608	NM_014180	A6NGJ8|Q5H9Q1|Q96Q51|Q9P006	Silent	SNP	ENST00000523037.1	37	CCDS4331.1																																																																																			C|0.995;T|0.005	0.005	strong		0.532	MRPL22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252508.2		
EYS	346007	hgsc.bcm.edu	37	6	66044927	66044927	+	Missense_Mutation	SNP	T	T	C	rs61753610	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:66044927T>C	ENST00000370621.3	-	11	2238	c.1712A>G	c.(1711-1713)cAa>cGa	p.Q571R	EYS_ENST00000370618.3_Missense_Mutation_p.Q571R|EYS_ENST00000342421.5_Missense_Mutation_p.Q571R|EYS_ENST00000503581.1_Missense_Mutation_p.Q571R|EYS_ENST00000370616.2_Missense_Mutation_p.Q571R|EYS_ENST00000393380.2_Missense_Mutation_p.Q571R			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	571	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.		Q -> R (in dbSNP:rs61753610). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CTCATTTTCTTGATCATCAGT	0.348													T|||	622	0.124201	0.0083	0.1902	5008	,	,		17073	0.121		0.17	False		,,,				2504	0.1902				p.Q571R		Atlas-SNP	.											.	EYS	527	.	0			c.A1712G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN	148,4258	101.6+/-140.2	0,148,2055	177.0	162.0	167.0		1712,1712,1712	2.2	0.0	6	dbSNP_129	167	1485,7115	282.1+/-295.4	143,1199,2958	yes	missense,missense,missense	EYS	NM_198283.1,NM_001142801.1,NM_001142800.1	43,43,43	143,1347,5013	CC,CT,TT		17.2674,3.3591,12.5557	benign,benign,benign	571/595,571/620,571/3145	66044927	1633,11373	2203	4300	6503	SO:0001583	missense	346007	exon11			TTTTCTTGATCAT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1712A>G	6.37:g.66044927T>C	ENSP00000359655:p.Gln571Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		263	0.12042124542124542	6	0.012195121951219513	63	0.17403314917127072	66	0.11538461538461539	128	0.16886543535620052	t	8.268	0.812815	0.16537	0.033591	0.172674	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616;ENST00000393380;ENST00000342421;ENST00000370618	T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99	3.47	2.23	0.28157	.	.	.	.	.	T	0.02533	0.0077	N	0.08118	0	0.80722	P	0.0	B;B;B	0.32829	0.218;0.386;0.267	B;B;B	0.28139	0.058;0.086;0.039	T	0.47086	-0.9144	8	0.19147	T	0.46	.	6.7297	0.23377	0.0:0.0:0.2425:0.7575	rs61753610	571;571;571	Q5T1H1-1;Q5T1H1-2;Q5SZM4	.;.;.	R	571	ENSP00000424243:Q571R;ENSP00000359655:Q571R;ENSP00000359650:Q571R;ENSP00000377042:Q571R;ENSP00000341818:Q571R;ENSP00000359652:Q571R	ENSP00000341818:Q571R	Q	-	2	0	EYS	66101648	0.995000	0.38212	0.008000	0.14137	0.032000	0.12392	1.502000	0.35704	0.326000	0.23384	0.402000	0.26972	CAA	T|0.875;C|0.125	0.125	strong		0.348	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
OBSCN	84033	hgsc.bcm.edu	37	1	228526011	228526011	+	Silent	SNP	C	C	T	rs11577699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228526011C>T	ENST00000422127.1	+	68	17066	c.17022C>T	c.(17020-17022)gcC>gcT	p.A5674A	OBSCN_ENST00000284548.11_Silent_p.A5674A|OBSCN_ENST00000366709.4_Silent_p.A2793A|OBSCN_ENST00000366707.4_Silent_p.A3308A|OBSCN_ENST00000570156.2_Silent_p.A6631A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5674					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGTGGGGGGCCGCTGAGGCCC	0.642													C|||	589	0.117612	0.1006	0.1916	5008	,	,		16460	0.1091		0.1372	False		,,,				2504	0.0767				p.A6631A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19893T						PASS	.	C	,	525,3273		33,459,1407	20.0	26.0	24.0		17022,17022	-2.2	0.0	1	dbSNP_120	24	1296,6918		99,1098,2910	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	132,1557,4317	TT,TC,CC		15.7779,13.8231,15.1598	,	5674/7969,5674/6621	228526011	1821,10191	1899	4107	6006	SO:0001819	synonymous_variant	84033	exon79			GGGGGCCGCTGAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17022C>T	1.37:g.228526011C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	273	0.125	40	0.08130081300813008	71	0.19613259668508287	54	0.0944055944055944	108	0.1424802110817942	C	4.625	0.116119	0.08831	0.138231	0.157779	ENSG00000154358	ENST00000441106	.	.	.	4.59	-2.15	0.07102	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.53688	P	2.4000000000024002E-5	.	.	.	.	.	.	T	0.24083	-1.0170	3	.	.	.	.	5.2594	0.15565	0.3755:0.2927:0.0:0.3318	rs11577699	.	.	.	C	290	.	.	R	+	1	0	OBSCN	226592634	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.668000	0.05268	-1.045000	0.03250	-1.579000	0.00862	CGC	C|0.879;T|0.121	0.121	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MAGEB4	4115	hgsc.bcm.edu	37	X	30261158	30261158	+	Silent	SNP	G	G	C	rs2856733	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:30261158G>C	ENST00000378982.2	+	1	1102	c.906G>C	c.(904-906)ctG>ctC	p.L302L	MAGEB1_ENST00000397550.1_5'Flank|MAGEB1_ENST00000378981.3_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	302	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						ACTTCCCACTGCTTTATGAAG	0.517													C|||	3042	0.805828	0.6815	0.6744	3775	,	,		13022	0.4276		0.6829	False		,,,				2504	0.5675				p.L302L		Atlas-SNP	.											.	MAGEB4	75	.	0			c.G906C						PASS	.	C		3431,402		1305,305,516,21,55	63.0	62.0	62.0		906	1.3	0.0	X	dbSNP_100	62	6035,693		1961,444,1669,23,203	no	coding-synonymous	MAGEB4	NM_002367.3		3266,749,2185,44,258	CC,CG,C,GG,G		10.3002,10.4879,10.3683		302/347	30261158	9466,1095	2202	4300	6502	SO:0001819	synonymous_variant	4115	exon1			CCCACTGCTTTAT		CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"""melanoma-associated antigen B4"", ""cancer/testis antigen family 3, member 6"""	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.906G>C	X.37:g.30261158G>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_002367	B2R9G0|Q6FHH4|Q8IZ00	Silent	SNP	ENST00000378982.2	37	CCDS14221.1																																																																																			0|0.003;C|0.849	0.849	strong		0.517	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367	
GRM1	2911	hgsc.bcm.edu	37	6	146755842	146755842	+	Silent	SNP	C	C	A	rs9373491	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:146755842C>A	ENST00000282753.1	+	8	3730	c.3495C>A	c.(3493-3495)ccC>ccA	p.P1165P	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000361719.2_Silent_p.P1165P|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000492807.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1165	Ser-rich.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CCAGCTCCCCCGTGTCCGAGT	0.652													C|||	2968	0.592652	0.6997	0.4726	5008	,	,		16897	0.5466		0.5457	False		,,,				2504	0.6288				p.P1165P		Atlas-SNP	.											.	GRM1	419	.	0			c.C3495A						PASS	.	C	,	2995,1405		1028,939,233	39.0	41.0	41.0		3495,	-11.3	0.5	6	dbSNP_119	41	4574,4024		1255,2064,980	no	coding-synonymous,utr-3	GRM1	NM_000838.3,NM_001114329.1	,	2283,3003,1213	AA,AC,CC		46.8016,31.9318,41.768	,	1165/1195,	146755842	7569,5429	2200	4299	6499	SO:0001819	synonymous_variant	2911	exon9			CTCCCCCGTGTCC	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3495C>A	6.37:g.146755842C>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																			C|0.428;A|0.572	0.572	strong		0.652	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
CEACAM20	125931	hgsc.bcm.edu	37	19	45017249	45017249	+	RNA	SNP	T	T	C	rs1465723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:45017249T>C	ENST00000454753.1	-	0	1687							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				ATTTCTGATGTAGAGAAAATA	0.602											OREG0025538	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	584	0.116613	0.0613	0.1383	5008	,	,		14648	0.0645		0.2376	False		,,,				2504	0.1053				p.Y470C		Atlas-SNP	.											.	CEACAM20	31	.	0			c.A1409G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	322,3624		11,300,1662	72.0	70.0	70.0		1409,1130,1130,1409	1.6	0.0	19	dbSNP_88	70	1766,6564		206,1354,2605	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	194,194,194,194	217,1654,4267	CC,CT,TT		21.2005,8.1602,17.0088	benign,benign,benign,benign	470/597,377/492,377/504,470/585	45017249	2088,10188	1973	4165	6138			125931	exon7			CTGATGTAGAGAA	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45017249T>C		Somatic	71	0	0	928	WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				T|0.864;C|0.136	0.136	strong		0.602	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
DNAH2	146754	hgsc.bcm.edu	37	17	7680159	7680159	+	Silent	SNP	G	G	A	rs62059684	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7680159G>A	ENST00000572933.1	+	32	6470	c.5010G>A	c.(5008-5010)gcG>gcA	p.A1670A	DNAH2_ENST00000389173.2_Silent_p.A1670A			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	1670	Stem. {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(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TGCTGACAGCGAAGGAGCGGG	0.572													G|||	603	0.120407	0.0113	0.2046	5008	,	,		18971	0.0		0.3579	False		,,,				2504	0.0879				p.A1670A		Atlas-SNP	.											.	DNAH2	498	.	0			c.G5010A						PASS	.	G		288,4118	158.1+/-190.9	11,266,1926	69.0	55.0	60.0		5010	-3.8	0.9	17	dbSNP_129	60	2942,5658	456.2+/-364.0	477,1988,1835	no	coding-synonymous	DNAH2	NM_020877.2		488,2254,3761	AA,AG,GG		34.2093,6.5365,24.8347		1670/4428	7680159	3230,9776	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon31			GACAGCGAAGGAG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.5010G>A	17.37:g.7680159G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			G|0.764;A|0.236	0.236	strong		0.572	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
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 GAIIx	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_ENST00000370470.1_Silent_p.V6V|FMR1_ENST00000218200.8_Silent_p.V6V|FMR1_ENST00000439526.2_Silent_p.V6V|FMR1-AS1_ENST00000598667.1_RNA|FMR1-AS1_ENST00000596112.1_RNA|FMR1_ENST00000370477.1_Silent_p.V6V|FMR1-AS1_ENST00000594922.1_RNA|FMR1_ENST00000370471.3_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		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	123	27	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	
ABCC4	10257	hgsc.bcm.edu	37	13	95858978	95858978	+	Silent	SNP	T	T	C	rs2274405	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:95858978T>C	ENST00000376887.4	-	8	1083	c.969A>G	c.(967-969)tcA>tcG	p.S323S	ABCC4_ENST00000412704.1_Silent_p.S323S|ABCC4_ENST00000536256.1_Silent_p.S248S|ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000431522.1_Silent_p.S323S	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	323	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	p.S323S(1)		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)	CACTGAAAAATGAAGCCAAAT	0.478													T|||	3135	0.625998	0.7247	0.5375	5008	,	,		21850	0.5337		0.6282	False		,,,				2504	0.6483				p.S323S		Atlas-SNP	.											ABCC4_ENST00000376887,NS,carcinoma,0,1	ABCC4	248	1	1	Substitution - coding silent(1)	stomach(1)	c.A969G						PASS	.	T	,	3031,1375	689.7+/-405.2	1039,953,211	169.0	161.0	164.0		969,969	-11.2	0.2	13	dbSNP_100	164	5606,2994	666.1+/-402.3	1807,1992,501	no	coding-synonymous,coding-synonymous	ABCC4	NM_001105515.1,NM_005845.3	,	2846,2945,712	CC,CT,TT		34.814,31.2074,33.5922	,	323/860,323/1326	95858978	8637,4369	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon8			GAAAAATGAAGCC	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.969A>G	13.37:g.95858978T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			T|0.367;C|0.633	0.633	strong		0.478	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
NPAP1	23742	hgsc.bcm.edu	37	15	24923390	24923390	+	Silent	SNP	C	C	T	rs60574723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:24923390C>T	ENST00000329468.2	+	1	2850	c.2376C>T	c.(2374-2376)ttC>ttT	p.F792F		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	792					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCCATGATTTCCTGAGCCTTC	0.537													T|||	2160	0.43131	0.5401	0.3357	5008	,	,		18696	0.4742		0.3539	False		,,,				2504	0.3875				p.F792F		Atlas-SNP	.											.	.	.	.	0			c.C2376T						PASS	.	T		2239,2167		572,1095,536	127.0	138.0	134.0		2376	-1.7	0.0	15	dbSNP_129	134	2873,5727		468,1937,1895	no	coding-synonymous	C15orf2	NM_018958.2		1040,3032,2431	TT,TC,CC		33.407,49.1829,39.3049		792/1157	24923390	5112,7894	2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			TGATTTCCTGAGC	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2376C>T	15.37:g.24923390C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_018958		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			C|0.605;T|0.395	0.395	strong		0.537	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
TAPBPL	55080	hgsc.bcm.edu	37	12	6562810	6562810	+	Missense_Mutation	SNP	A	A	G	rs2532500	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6562810A>G	ENST00000266556.7	+	3	658	c.493A>G	c.(493-495)Acc>Gcc	p.T165A	CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000545700.1_3'UTR|TAPBPL_ENST00000544021.1_Missense_Mutation_p.T88A|CD27-AS1_ENST00000399492.2_RNA	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	165			T -> A (in dbSNP:rs2532500). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						TCCCAGGGTCACCAAGAATGA	0.562													G|||	3442	0.6873	0.6225	0.5591	5008	,	,		18556	0.7887		0.675	False		,,,				2504	0.774				p.T165A		Atlas-SNP	.											.	TAPBPL	21	.	0			c.A493G						PASS	.	G	ALA/THR	2585,1821	530.6+/-373.0	761,1063,379	42.0	38.0	40.0		493	1.7	0.0	12	dbSNP_100	40	5954,2646	425.6+/-355.0	2063,1828,409	yes	missense	TAPBPL	NM_018009.4	58	2824,2891,788	GG,GA,AA		30.7674,41.33,34.3457	benign	165/469	6562810	8539,4467	2203	4300	6503	SO:0001583	missense	55080	exon3			AGGGTCACCAAGA	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.493A>G	12.37:g.6562810A>G	ENSP00000266556:p.Thr165Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	1471	0.6735347985347986	289	0.5873983739837398	212	0.585635359116022	456	0.7972027972027972	514	0.6781002638522428	G	0.004	-2.258664	0.00265	0.5867	0.692326	ENSG00000139192	ENST00000544021;ENST00000266556	T;T	0.41400	1.0;3.22	4.56	1.68	0.24146	.	0.758504	0.12774	N	0.440315	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39272	-0.9622	9	0.02654	T	1	0.0054	7.4195	0.27063	0.3832:0.0:0.6168:0.0	rs2532500;rs17856477;rs52817156;rs59900259;rs2532500	165	Q9BX59	TPSNR_HUMAN	A	88;165	ENSP00000445341:T88A;ENSP00000266556:T165A	ENSP00000266556:T165A	T	+	1	0	TAPBPL	6433071	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.518000	0.22847	0.079000	0.16929	-0.855000	0.03028	ACC	A|0.344;G|0.656	0.656	strong		0.562	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
CLDN8	9073	hgsc.bcm.edu	37	21	31587793	31587793	+	Missense_Mutation	SNP	A	A	G	rs686364	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31587793A>G	ENST00000399899.1	-	1	598	c.451T>C	c.(451-453)Tca>Cca	p.S151P	CLDN8_ENST00000286809.1_Missense_Mutation_p.S151P	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	151			S -> P (in dbSNP:rs686364). {ECO:0000269|Ref.3}.		calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						TTCACTATTGAGTTATAGAAA	0.498													G|||	2097	0.41873	0.7216	0.2651	5008	,	,		19712	0.4484		0.2773	False		,,,				2504	0.2331				p.S151P		Atlas-SNP	.											.	CLDN8	40	.	0			c.T451C						PASS	.	G	PRO/SER	2900,1506	480.4+/-358.8	947,1006,250	72.0	72.0	72.0		451	4.0	1.0	21	dbSNP_83	72	2098,6502	717.1+/-406.1	271,1556,2473	yes	missense	CLDN8	NM_199328.2	74	1218,2562,2723	GG,GA,AA		24.3953,34.1807,38.4284	benign	151/226	31587793	4998,8008	2203	4300	6503	SO:0001583	missense	9073	exon1			CTATTGAGTTATA	AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"""Claudins"""	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.451T>C	21.37:g.31587793A>G	ENSP00000382783:p.Ser151Pro	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_199328	D3DSE3|Q53EX7	Missense_Mutation	SNP	ENST00000399899.1	37	CCDS13587.1	883	0.4043040293040293	340	0.6910569105691057	102	0.281767955801105	242	0.4230769230769231	199	0.262532981530343	G	0.021	-1.429690	0.01117	0.658193	0.243953	ENSG00000156284	ENST00000399899;ENST00000286809;ENST00000536721	D;D	0.88741	-2.42;-2.42	4.84	3.96	0.45880	.	0.056944	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00014	-2.91	0.46113	P	0.0011250000000000426	B	0.02656	0.0	B	0.01281	0.0	T	0.48445	-0.9035	9	0.02654	T	1	.	11.4472	0.50131	0.1492:0.0:0.8508:0.0	rs686364;rs3746849;rs52794641;rs56681626;rs686364	151	P56748	CLD8_HUMAN	P	151	ENSP00000382783:S151P;ENSP00000286809:S151P	ENSP00000286809:S151P	S	-	1	0	CLDN8	30509664	1.000000	0.71417	0.983000	0.44433	0.029000	0.11900	7.728000	0.84847	0.776000	0.33473	-0.790000	0.03334	TCA	T|0.003;G|0.402	0.402	strong		0.498	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328	
PANK4	55229	hgsc.bcm.edu	37	1	2441358	2441358	+	Missense_Mutation	SNP	T	T	C	rs2494620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:2441358T>C	ENST00000378466.3	-	18	2063	c.2051A>G	c.(2050-2052)cAg>cGg	p.Q684R	PANK4_ENST00000435556.3_Missense_Mutation_p.Q645R	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	684			Q -> R (in dbSNP:rs2494620). {ECO:0000269|Ref.2}.		coenzyme A biosynthetic process (GO:0015937)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)	p.Q684R(1)		breast(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	23	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.54e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-23)|GBM - Glioblastoma multiforme(42;2.81e-08)|Colorectal(212;4.25e-05)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(365;0.00445)|KIRC - Kidney renal clear cell carcinoma(229;0.00549)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.201)		CCTCTCTTCCTGGAGCGCAGA	0.657													C|||	2313	0.461861	0.7148	0.3444	5008	,	,		17094	0.4702		0.2127	False		,,,				2504	0.4509				p.Q684R		Atlas-SNP	.											PANK4,NS,lymphoid_neoplasm,0,2	PANK4	64	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A2051G						PASS	.	C	ARG/GLN	2888,1508	461.7+/-353.0	962,964,272	46.0	55.0	52.0		2051	-0.2	0.0	1	dbSNP_100	52	1916,6676	711.8+/-405.9	210,1496,2590	yes	missense	PANK4	NM_018216.1	43	1172,2460,2862	CC,CT,TT		22.2998,34.3039,36.988	benign	684/774	2441358	4804,8184	2198	4296	6494	SO:0001583	missense	55229	exon18			TCTTCCTGGAGCG	AK001644	CCDS42.1	1p36.32	2008-02-05			ENSG00000157881	ENSG00000157881			19366	protein-coding gene	gene with protein product		606162				11479594	Standard	XR_241034		Approved	FLJ10782	uc001ajm.1	Q9NVE7	OTTHUMG00000000791	ENST00000378466.3:c.2051A>G	1.37:g.2441358T>C	ENSP00000367727:p.Gln684Arg	Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	852	0.3901098901098901	341	0.693089430894309	114	0.3149171270718232	242	0.4230769230769231	155	0.20448548812664907	C	4.722	0.134313	0.09032	0.656961	0.222998	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.06371	3.31;3.31	5.03	-0.23	0.13090	Domain of unknown function DUF89 (2);	0.544208	0.20048	N	0.100373	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.10613	-1.0622	9	0.10902	T	0.67	-0.009	10.247	0.43347	0.0:0.5005:0.0:0.4995	rs2494620;rs11541160;rs58437041;rs2494620	645;684	E9PHT6;Q9NVE7	.;PANK4_HUMAN	R	684;645	ENSP00000367727:Q684R;ENSP00000421433:Q645R	ENSP00000367727:Q684R	Q	-	2	0	PANK4	2431218	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.488000	0.02308	-0.299000	0.08909	-0.994000	0.02522	CAG	T|0.615;C|0.385	0.385	strong		0.657	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1		
TAPBPL	55080	hgsc.bcm.edu	37	12	6562753	6562753	+	Missense_Mutation	SNP	A	A	G	rs2532501	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6562753A>G	ENST00000266556.7	+	3	601	c.436A>G	c.(436-438)Atg>Gtg	p.M146V	CD27-AS1_ENST00000545339.1_RNA|TAPBPL_ENST00000545700.1_3'UTR|TAPBPL_ENST00000544021.1_Missense_Mutation_p.M69V|CD27-AS1_ENST00000399492.2_RNA	NM_018009.4	NP_060479.3	Q9BX59	TPSNR_HUMAN	TAP binding protein-like	146			M -> V (in dbSNP:rs2532501). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002590)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)			endometrium(2)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	6						CATGGCCAACATGCAGGTCTC	0.557													G|||	3444	0.6877	0.6225	0.5591	5008	,	,		19669	0.7887		0.675	False		,,,				2504	0.7761				p.M146V		Atlas-SNP	.											.	TAPBPL	21	.	0			c.A436G						PASS	.	G	VAL/MET	2584,1822	532.5+/-373.5	761,1062,380	73.0	60.0	64.0		436	-4.2	0.5	12	dbSNP_100	64	5954,2646	427.0+/-355.5	2063,1828,409	yes	missense	TAPBPL	NM_018009.4	21	2824,2890,789	GG,GA,AA		30.7674,41.3527,34.3534	benign	146/469	6562753	8538,4468	2203	4300	6503	SO:0001583	missense	55080	exon3			GCCAACATGCAGG	AK001005	CCDS8546.1	12p13.31	2013-01-11						"""Immunoglobulin superfamily / C1-set domain containing"""	30683	protein-coding gene	gene with protein product		607081				11920573	Standard	NM_018009		Approved	TAPBP-R, FLJ10143, TAPBPR	uc001qog.4	Q9BX59		ENST00000266556.7:c.436A>G	12.37:g.6562753A>G	ENSP00000266556:p.Met146Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_018009	Q9NWB8	Missense_Mutation	SNP	ENST00000266556.7	37	CCDS8546.1	1470	0.6730769230769231	289	0.5873983739837398	212	0.585635359116022	456	0.7972027972027972	513	0.6767810026385225	G	0.005	-2.123095	0.00346	0.586473	0.692326	ENSG00000139192	ENST00000544021;ENST00000266556	T;T	0.38887	1.11;3.28	4.84	-4.16	0.03869	.	0.613513	0.17283	N	0.179917	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28870	-1.0030	9	0.02654	T	1	-1.8542	3.2083	0.06674	0.5406:0.1216:0.2146:0.1233	rs2532501;rs17856476;rs52837454;rs58275029;rs2532501	146	Q9BX59	TPSNR_HUMAN	V	69;146	ENSP00000445341:M69V;ENSP00000266556:M146V	ENSP00000266556:M146V	M	+	1	0	TAPBPL	6433014	0.001000	0.12720	0.460000	0.27093	0.279000	0.26890	-0.360000	0.07622	-0.859000	0.04105	-1.291000	0.01355	ATG	A|0.341;G|0.659	0.659	strong		0.557	TAPBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399263.1	NM_018009	
ABCD1	215	hgsc.bcm.edu	37	X	153005605	153005605	+	Silent	SNP	G	G	A	rs41314153	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153005605G>A	ENST00000218104.3	+	6	1947	c.1548G>A	c.(1546-1548)ctG>ctA	p.L516L	U52111.14_ENST00000434284.1_RNA	NM_000033.3	NP_000024.2	P33897	ABCD1_HUMAN	ATP-binding cassette, sub-family D (ALD), member 1	516	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		L -> P (in ALD). {ECO:0000269|PubMed:21889498}.		alpha-linolenic acid metabolic process (GO:0036109)|ATP catabolic process (GO:0006200)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|linoleic acid metabolic process (GO:0043651)|long-chain fatty acid catabolic process (GO:0042758)|peroxisomal long-chain fatty acid import (GO:0015910)|peroxisomal membrane transport (GO:0015919)|peroxisome organization (GO:0007031)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid catabolic process (GO:0042760)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|peroxisomal fatty-acyl-CoA transporter activity (GO:0005325)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|urinary_tract(2)	18	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGAGCTCCCTGTTCCGGATCC	0.647													G|||	323	0.0855629	0.0371	0.0504	3775	,	,		13590	0.0407		0.0835	False		,,,				2504	0.1166				p.L516L		Atlas-SNP	.											.	ABCD1	59	.	0			c.G1548A						PASS	.	G		192,3643		4,153,31,1475,540	100.0	89.0	93.0		1548	3.1	1.0	X	dbSNP_127	93	729,5999		21,499,188,1908,1684	no	coding-synonymous	ABCD1	NM_000033.3		25,652,219,3383,2224	AA,AG,A,GG,G		10.8353,5.0065,8.7191		516/746	153005605	921,9642	2203	4300	6503	SO:0001819	synonymous_variant	215	exon6			CTCCCTGTTCCGG	Z21876	CCDS14728.1	Xq28	2012-03-14			ENSG00000101986	ENSG00000101986		"""ATP binding cassette transporters / subfamily D"""	61	protein-coding gene	gene with protein product		300371		ALD		8441467, 6795626	Standard	NM_000033		Approved	AMN, ALDP, adrenoleukodystrophy	uc004fif.2	P33897	OTTHUMG00000024215	ENST00000218104.3:c.1548G>A	X.37:g.153005605G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	16	0.216216	NM_000033	Q6GTZ2	Silent	SNP	ENST00000218104.3	37	CCDS14728.1	119	0.07172995780590717	13	0.027196652719665274	7	0.019886363636363636	13	0.023214285714285715	50	0.06925207756232687	G	6.084	0.383792	0.11524	0.050065	0.108353	ENSG00000101986	ENST00000443684	.	.	.	4.93	3.09	0.35607	.	.	.	.	.	T	0.01320	0.0043	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.16928	-1.0386	3	.	.	.	-13.6588	8.638	0.33959	0.0:0.1622:0.6662:0.1716	rs41314153	.	.	.	Y	184	.	.	C	+	2	0	ABCD1	152658799	0.986000	0.35501	0.958000	0.39756	0.644000	0.38419	0.074000	0.14662	0.461000	0.27071	0.429000	0.28392	TGT	G|0.916;A|0.084	0.084	strong		0.647	ABCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061041.1	NM_000033	
ACSM5	54988	hgsc.bcm.edu	37	16	20441020	20441020	+	Missense_Mutation	SNP	G	G	A	rs12932087	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20441020G>A	ENST00000331849.4	+	8	1169	c.1022G>A	c.(1021-1023)aGg>aAg	p.R341K		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	341					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						CAGAGCCTGAGGCACTGTCTG	0.557													G|||	537	0.107228	0.0628	0.1066	5008	,	,		17883	0.1835		0.0537	False		,,,				2504	0.1442				p.R341K		Atlas-SNP	.											.	ACSM5	101	.	0			c.G1022A						PASS	.	G	LYS/ARG	311,4095	161.8+/-193.9	9,293,1901	101.0	101.0	101.0		1022	2.4	1.0	16	dbSNP_121	101	616,7984	156.9+/-210.6	19,578,3703	yes	missense	ACSM5	NM_017888.2	26	28,871,5604	AA,AG,GG		7.1628,7.0586,7.1275	benign	341/580	20441020	927,12079	2203	4300	6503	SO:0001583	missense	54988	exon8			GCCTGAGGCACTG		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1022G>A	16.37:g.20441020G>A	ENSP00000327916:p.Arg341Lys	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	233	0.10668498168498168	30	0.06097560975609756	40	0.11049723756906077	117	0.20454545454545456	46	0.06068601583113457	G	10.02	1.234993	0.22626	0.070586	0.071628	ENSG00000183549	ENST00000331849	T	0.49432	0.78	4.4	2.43	0.29744	AMP-dependent synthetase/ligase (1);	0.461000	0.19441	N	0.114166	T	0.00039	0.0001	L	0.28608	0.87	0.48901	P	2.7200000000005E-4	B	0.02656	0.0	B	0.09377	0.004	T	0.18650	-1.0330	9	0.13853	T	0.58	-6.2474	6.6372	0.22889	0.3838:0.0:0.6162:0.0	rs12932087	341	Q6NUN0	ACSM5_HUMAN	K	341	ENSP00000327916:R341K	ENSP00000327916:R341K	R	+	2	0	ACSM5	20348521	0.000000	0.05858	0.983000	0.44433	0.731000	0.41821	-0.019000	0.12546	0.413000	0.25759	0.551000	0.68910	AGG	G|0.913;A|0.087	0.087	strong		0.557	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
MDM2	4193	hgsc.bcm.edu	37	12	69233215	69233215	+	Silent	SNP	A	A	G	rs769412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:69233215A>G	ENST00000350057.5	+	9	987	c.987A>G	c.(985-987)gaA>gaG	p.E329E	MDM2_ENST00000393410.1_Silent_p.E106E|MDM2_ENST00000356290.4_Silent_p.E184E|MDM2_ENST00000258149.5_Silent_p.E299E|MDM2_ENST00000299252.4_Silent_p.E184E|MDM2_ENST00000258148.7_Silent_p.E305E|MDM2_ENST00000545204.1_Intron|MDM2_ENST00000360430.2_Silent_p.E159E|MDM2_ENST00000478070.1_3'UTR|MDM2_ENST00000393412.3_Silent_p.E81E|MDM2_ENST00000517852.1_Intron|RP11-611O2.5_ENST00000553141.1_RNA|MDM2_ENST00000393413.3_Silent_p.E81E|MDM2_ENST00000540827.1_Silent_p.E159E|MDM2_ENST00000428863.2_Silent_p.E133E|MDM2_ENST00000462284.1_Silent_p.E360E|MDM2_ENST00000544561.1_Intron|MDM2_ENST00000348801.2_Silent_p.E128E			Q00987	MDM2_HUMAN	MDM2 proto-oncogene, E3 ubiquitin protein ligase	354	Necessary for interaction with USP2.|Region II.				cellular response to acid chemical (GO:0071229)|cellular response to alkaloid (GO:0071312)|cellular response to antibiotic (GO:0071236)|cellular response to estrogen stimulus (GO:0071391)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to UV-C (GO:0071494)|cellular response to vitamin B1 (GO:0071301)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of protein localization (GO:0045184)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein processing (GO:0010955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-lysine modification (GO:0018205)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein export from nucleus (GO:0046827)|protein complex assembly (GO:0006461)|protein destabilization (GO:0031648)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of protein catabolic process (GO:0042176)|response to antibiotic (GO:0046677)|response to carbohydrate (GO:0009743)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ether (GO:0045472)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to morphine (GO:0043278)|synaptic transmission (GO:0007268)|traversing start control point of mitotic cell cycle (GO:0007089)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(8)|prostate(1)|urinary_tract(1)	19	all_cancers(1;8.46e-121)|all_epithelial(5;3.21e-36)|Lung NSC(4;2.16e-33)|all_lung(4;3.03e-31)|Glioma(1;1.9e-09)|Breast(13;1.59e-06)|all_neural(1;1.03e-05)|Melanoma(1;0.0171)|Renal(347;0.0684)		all cancers(2;8.67e-65)|GBM - Glioblastoma multiforme(2;8.89e-62)|BRCA - Breast invasive adenocarcinoma(5;2.43e-08)|Lung(24;1.5e-05)|LUAD - Lung adenocarcinoma(15;8.5e-05)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			CACAAGCTGAAGAGGGCTTTG	0.388			A		"""sarcoma, glioma, colorectal, other"""								A|||	391	0.0780751	0.1505	0.072	5008	,	,		20089	0.0179		0.0676	False		,,,				2504	0.0573				p.E360E		Atlas-SNP	.		Dom	yes		12	12q15	4193	Mdm2 p53 binding protein homolog		"""M, O, E, L"""	.	MDM2	92	.	0			c.A1080G						PASS	.	A		453,3245		29,395,1425	102.0	96.0	98.0		1080	1.7	0.7	12	dbSNP_86	98	485,7673		16,453,3610	no	coding-synonymous	MDM2	NM_002392.3		45,848,5035	GG,GA,AA		5.9451,12.2499,7.9116		360/498	69233215	938,10918	1849	4079	5928	SO:0001819	synonymous_variant	4193	exon11			AGCTGAAGAGGGC		CCDS8986.2, CCDS61189.1	12q13-q14	2014-06-26	2014-06-26		ENSG00000135679	ENSG00000135679			6973	protein-coding gene	gene with protein product		164785	"""mouse double minute 2, human homolog of; p53-binding protein"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)"", ""Mdm2 p53 binding protein homolog (mouse)"""			1614537, 16905769	Standard	NM_002392		Approved	HDM2, MGC5370	uc001sui.4	Q00987	OTTHUMG00000142827	ENST00000350057.5:c.987A>G	12.37:g.69233215A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_002392	A6NL51|A8K2S6|Q13226|Q13297|Q13298|Q13299|Q13300|Q13301|Q53XW0|Q71TW9|Q8WYJ1|Q8WYJ2|Q9UGI3|Q9UMT8	Silent	SNP	ENST00000350057.5	37																																																																																				A|0.927;G|0.073	0.073	strong		0.388	MDM2-033	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000402665.1	NM_006880	
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 GAIIx	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_ENST00000389562.2_Silent_p.D2150D|EP400_ENST00000332482.4_Silent_p.D2114D			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		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	43	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	
SLC4A2	6522	hgsc.bcm.edu	37	7	150761314	150761314	+	Missense_Mutation	SNP	G	G	A	rs2303929	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150761314G>A	ENST00000485713.1	+	3	1117	c.77G>A	c.(76-78)gGg>gAg	p.G26E	SLC4A2_ENST00000461735.1_Missense_Mutation_p.G12E|SLC4A2_ENST00000413384.2_Missense_Mutation_p.G26E|SLC4A2_ENST00000310317.5_Intron|SLC4A2_ENST00000392826.2_Missense_Mutation_p.G17E	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	26	Pro-rich.		G -> E (in dbSNP:rs2303929). {ECO:0000269|Ref.2}.		anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTGGGCCCTGGGACGCCTGGG	0.617													G|||	1191	0.237819	0.1089	0.4424	5008	,	,		12118	0.2877		0.2425	False		,,,				2504	0.2106				p.G26E		Atlas-SNP	.											SLC4A2,NS,carcinoma,0,1	SLC4A2	98	1	0			c.G77A						PASS	.	G	GLU/GLY,GLU/GLY,GLU/GLY,GLU/GLY	588,3818	259.5+/-263.1	40,508,1655	59.0	54.0	56.0		77,50,35,77	-0.4	0.0	7	dbSNP_100	56	1943,6657	341.8+/-324.2	220,1503,2577	yes	missense,missense,missense,missense	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	98,98,98,98	260,2011,4232	AA,AG,GG		22.593,13.3454,19.4602	probably-damaging,probably-damaging,probably-damaging,probably-damaging	26/1242,17/1233,12/1228,26/1242	150761314	2531,10475	2203	4300	6503	SO:0001583	missense	6522	exon3			GCCCTGGGACGCC		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.77G>A	7.37:g.150761314G>A	ENSP00000419412:p.Gly26Glu	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	597	0.2733516483516483	62	0.12601626016260162	146	0.40331491712707185	184	0.32167832167832167	205	0.2704485488126649	g	4.728	0.135334	0.09032	0.133454	0.22593	ENSG00000164889	ENST00000483786;ENST00000485713;ENST00000413384;ENST00000490898;ENST00000482950;ENST00000463414;ENST00000488420;ENST00000392826;ENST00000461735	T;T;T;T;T;T;T;T;T	0.75050	0.87;-0.9;-0.9;1.46;0.88;0.88;0.65;-0.86;-0.88	4.28	-0.421	0.12332	.	0.696201	0.13322	N	0.396634	T	0.00012	0.0000	L	0.46157	1.445	0.58432	P	2.9999999999752447E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.29181	-1.0020	9	0.05833	T	0.94	.	1.1008	0.01683	0.1913:0.3358:0.2677:0.2053	rs2303929;rs60575044;rs2303929	17;12;26	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	E	26;26;26;26;26;26;26;17;12	ENSP00000417808:G26E;ENSP00000419412:G26E;ENSP00000405600:G26E;ENSP00000418114:G26E;ENSP00000419379:G26E;ENSP00000418584:G26E;ENSP00000417221:G26E;ENSP00000376571:G17E;ENSP00000419164:G12E	ENSP00000376571:G17E	G	+	2	0	SLC4A2	150392247	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	0.002000	0.13061	-0.328000	0.08539	-0.394000	0.06481	GGG	G|0.779;A|0.221	0.221	strong		0.617	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
OR8B8	26493	hgsc.bcm.edu	37	11	124310622	124310622	+	Silent	SNP	A	A	G	rs4296049	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124310622A>G	ENST00000328064.2	-	1	432	c.360T>C	c.(358-360)taT>taC	p.Y120Y		NM_012378.1	NP_036510.1	Q15620	OR8B8_HUMAN	olfactory receptor, family 8, subfamily B, member 8	120					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)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		CATAGCGGTCATACGCCATTG	0.473													A|||	1244	0.248403	0.0303	0.33	5008	,	,		23587	0.5317		0.2644	False		,,,				2504	0.1769				p.Y120Y		Atlas-SNP	.											.	OR8B8	76	.	0			c.T360C						PASS	.	A		300,4102	164.0+/-195.7	8,284,1909	93.0	86.0	88.0		360	1.2	0.9	11	dbSNP_111	88	2499,6099	410.5+/-350.2	360,1779,2160	no	coding-synonymous	OR8B8	NM_012378.1		368,2063,4069	GG,GA,AA		29.0649,6.8151,21.5308		120/312	124310622	2799,10201	2201	4299	6500	SO:0001819	synonymous_variant	26493	exon1			GCGGTCATACGCC	AF238488	CCDS8446.1	11q24.2	2012-08-09			ENSG00000197125	ENSG00000197125		"""GPCR / Class A : Olfactory receptors"""	8477	protein-coding gene	gene with protein product						9119360	Standard	NM_012378		Approved	TPCR85	uc010sal.2	Q15620	OTTHUMG00000165917	ENST00000328064.2:c.360T>C	11.37:g.124310622A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	64	16	0.25	NM_012378	A1L446|Q96RC8	Silent	SNP	ENST00000328064.2	37	CCDS8446.1																																																																																			A|0.756;G|0.244	0.244	strong		0.473	OR8B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387056.1	NM_012378	
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 GAIIx	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_ENST00000559710.1_Silent_p.V260V|TCF12_ENST00000438423.2_Silent_p.V650V|TCF12_ENST00000452095.2_Silent_p.V646V|TCF12_ENST00000543579.1_Silent_p.V480V|TCF12_ENST00000537840.1_Silent_p.V390V|TCF12_ENST00000559703.1_Silent_p.V283V|TCF12_ENST00000343827.3_Silent_p.V456V|TCF12_ENST00000333725.5_Silent_p.V650V|TCF12_ENST00000557843.1_Silent_p.V626V	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		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	121	61	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 GAIIx	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	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	94	22	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	
UPF1	5976	hgsc.bcm.edu	37	19	18943156	18943156	+	Silent	SNP	G	G	A	rs80065570	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:18943156G>A	ENST00000599848.1	+	1	347	c.138G>A	c.(136-138)acG>acA	p.T46T	UPF1_ENST00000262803.5_Silent_p.T46T			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	46	Sufficient for interaction with RENT2.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						AGACGCAGAcgccccccggcg	0.751													G|||	193	0.0385383	0.0121	0.0259	5008	,	,		4992	0.1081		0.0417	False		,,,				2504	0.0082				p.T46T		Atlas-SNP	.											.	UPF1	88	.	0			c.G138A						PASS	.	G		66,4336		0,66,2135	20.0	23.0	22.0		138	1.6	1.0	19	dbSNP_131	22	312,8284		7,298,3993	no	coding-synonymous	UPF1	NM_002911.3		7,364,6128	AA,AG,GG		3.6296,1.4993,2.9081		46/1119	18943156	378,12620	2201	4298	6499	SO:0001819	synonymous_variant	5976	exon1			GCAGACGCCCCCC	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.138G>A	19.37:g.18943156G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_002911	O00239|O43343|Q86Z25|Q92842	Silent	SNP	ENST00000599848.1	37																																																																																				G|0.966;A|0.034	0.034	strong		0.751	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911	
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 GAIIx	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	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	44	17	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	
PRDM9	56979	hgsc.bcm.edu	37	5	23527637	23527637	+	Missense_Mutation	SNP	A	A	C	rs61051796		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:23527637A>C	ENST00000296682.3	+	11	2622	c.2440A>C	c.(2440-2442)Agc>Cgc	p.S814R		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	814					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)	p.S814R(1)		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						GCGGGGCTTTAGCAATAAGTC	0.567										HNSCC(3;0.000094)																											p.S814R		Atlas-SNP	.											PRDM9,extremity,malignant_melanoma,0,1	PRDM9	344	1	1	Substitution - Missense(1)	skin(1)	c.A2440C						scavenged	.	A	ARG/SER	17,4251		0,17,2117	35.0	47.0	43.0		2440	3.0	0.7	5	dbSNP_129	43	3,8531		0,3,4264	no	missense	PRDM9	NM_020227.2	110	0,20,6381	CC,CA,AA		0.0352,0.3983,0.1562	possibly-damaging	814/895	23527637	20,12782	2134	4267	6401	SO:0001583	missense	56979	exon11			GGCTTTAGCAATA	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.2440A>C	5.37:g.23527637A>C	ENSP00000296682:p.Ser814Arg	Somatic	67	2	0.0298507		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	A	1.621	-0.521388	0.04171	0.003983	3.52E-4	ENSG00000164256	ENST00000296682	T	0.37411	1.2	3.02	3.02	0.34903	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22282	0.0537	L	0.28504	0.86	0.09310	N	0.999998	P	0.42908	0.793	B	0.37304	0.246	T	0.06110	-1.0845	9	0.33940	T	0.23	.	5.6652	0.17690	0.7579:0.0:0.0:0.2421	rs61051796	814	Q9NQV7	PRDM9_HUMAN	R	814	ENSP00000296682:S814R	ENSP00000296682:S814R	S	+	1	0	PRDM9	23563394	0.000000	0.05858	0.690000	0.30148	0.013000	0.08279	-0.284000	0.08422	1.653000	0.50694	0.386000	0.25728	AGC	A|0.999;C|0.001	0.001	weak		0.567	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
XRCC1	7515	hgsc.bcm.edu	37	19	44057574	44057574	+	Missense_Mutation	SNP	G	G	A	rs1799782	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:44057574G>A	ENST00000262887.5	-	6	1127	c.580C>T	c.(580-582)Cgg>Tgg	p.R194W	L34079.3_ENST00000597119.1_RNA|XRCC1_ENST00000543982.1_Missense_Mutation_p.R163W			P18887	XRCC1_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 1	194			R -> W (in dbSNP:rs1799782). {ECO:0000269|PubMed:9485007, ECO:0000269|Ref.2}.		base-excision repair (GO:0006284)|DNA repair (GO:0006281)|hippocampus development (GO:0021766)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to organic substance (GO:0010033)|single strand break repair (GO:0000012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)			breast(2)|endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Prostate(69;0.0153)				TTGTTGATCCGGCTGAAGAAG	0.597								Other BER factors					G|||	620	0.123802	0.0719	0.1167	5008	,	,		18638	0.2817		0.0517	False		,,,				2504	0.1104				p.R194W		Atlas-SNP	.											.	XRCC1	47	.	0			c.C580T	GRCh37	CM033678	XRCC1	M	rs1799782	PASS	.	G	TRP/ARG	247,4159	144.2+/-179.2	7,233,1963	81.0	76.0	78.0		580	1.0	1.0	19	dbSNP_89	78	555,8045	151.9+/-206.6	16,523,3761	yes	missense	XRCC1	NM_006297.2	101	23,756,5724	AA,AG,GG		6.4535,5.606,6.1664	probably-damaging	194/634	44057574	802,12204	2203	4300	6503	SO:0001583	missense	7515	exon6			TGATCCGGCTGAA	M36089	CCDS12624.1	19q13.2	2014-09-17				ENSG00000073050			12828	protein-coding gene	gene with protein product		194360		RCC		2247054	Standard	NM_006297		Approved		uc002owt.2	P18887		ENST00000262887.5:c.580C>T	19.37:g.44057574G>A	ENSP00000262887:p.Arg194Trp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_006297	Q6IBS4|Q9HCB1	Missense_Mutation	SNP	ENST00000262887.5	37	CCDS12624.1	283	0.1295787545787546	36	0.07317073170731707	38	0.10497237569060773	165	0.28846153846153844	44	0.05804749340369393	G	19.83	3.900060	0.72754	0.05606	0.064535	ENSG00000073050	ENST00000458471;ENST00000262887;ENST00000543982;ENST00000538738	T;T	0.03772	3.83;3.81	4.73	1.03	0.20045	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.72894	2.215	0.19575	P	0.9999696885	P;D	0.89917	0.912;1.0	P;P	0.62184	0.574;0.899	T	0.39961	-0.9588	9	0.45353	T	0.12	-6.33	6.6426	0.22917	0.0899:0.0:0.599:0.3111	rs1799782;rs2229674;rs3213359;rs3826914;rs11553655	163;194	F5H8D7;P18887	.;XRCC1_HUMAN	W	208;194;163;194	ENSP00000262887:R194W;ENSP00000443671:R163W	ENSP00000262887:R194W	R	-	1	2	XRCC1	48749414	1.000000	0.71417	0.986000	0.45419	0.972000	0.66771	1.506000	0.35747	0.645000	0.30675	0.655000	0.94253	CGG	G|0.905;A|0.095	0.095	strong		0.597	XRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463194.1	NM_006297	
CNNM4	26504	hgsc.bcm.edu	37	2	97465384	97465384	+	Splice_Site	SNP	C	C	T	rs41286594	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:97465384C>T	ENST00000377075.2	+	5	2045	c.1947C>T	c.(1945-1947)tcC>tcT	p.S649S	CNNM4_ENST00000496186.1_3'UTR|CNNM4_ENST00000540067.1_Splice_Site_p.S136S|MIR3127_ENST00000583925.1_RNA	NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	649					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						CGGTCCCCTCCGGTGAGTTGT	0.607													C|||	61	0.0121805	0.0015	0.0331	5008	,	,		18913	0.0		0.0219	False		,,,				2504	0.0143				p.S649S		Atlas-SNP	.											.	CNNM4	48	.	0			c.C1947T						PASS	.	C		21,4315		0,21,2147	79.0	67.0	71.0		1947	-8.3	0.0	2	dbSNP_127	71	159,8191		4,151,4020	yes	coding-synonymous-near-splice	CNNM4	NM_020184.3		4,172,6167	TT,TC,CC		1.9042,0.4843,1.4189		649/776	97465384	180,12506	2168	4175	6343	SO:0001630	splice_region_variant	26504	exon5			CCCCTCCGGTGAG	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"""cyclin M4"""	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1948+1C>T	2.37:g.97465384C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	151	81	0.536424	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Silent	SNP	ENST00000377075.2	37	CCDS2024.2																																																																																			C|0.986;T|0.014	0.014	strong		0.607	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184	Silent
TOPBP1	11073	hgsc.bcm.edu	37	3	133341988	133341988	+	Missense_Mutation	SNP	T	T	C	rs10935070	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:133341988T>C	ENST00000260810.5	-	19	3256	c.3125A>G	c.(3124-3126)aAt>aGt	p.N1042S		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1042			N -> S (in dbSNP:rs10935070).		cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						CTCTTTATTATTGGTGGCCAT	0.289								Other conserved DNA damage response genes					T|||	941	0.187899	0.0106	0.2997	5008	,	,		17163	0.0258		0.3588	False		,,,				2504	0.3395				p.N1042S	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.A3125G						PASS	.	T	SER/ASN	212,3394		4,204,1595	40.0	37.0	38.0		3125	-9.4	0.0	3	dbSNP_120	38	2657,5461		434,1789,1836	yes	missense	TOPBP1	NM_007027.3	46	438,1993,3431	CC,CT,TT		32.7297,5.8791,24.4712	benign	1042/1523	133341988	2869,8855	1803	4059	5862	SO:0001583	missense	11073	exon19			TTATTATTGGTGG	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.3125A>G	3.37:g.133341988T>C	ENSP00000260810:p.Asn1042Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	389	0.17811355311355312	6	0.012195121951219513	94	0.2596685082872928	18	0.03146853146853147	271	0.3575197889182058	T	2.223	-0.377961	0.05000	0.058791	0.327297	ENSG00000163781	ENST00000260810	T	0.11385	2.78	5.82	-9.36	0.00629	.	1.012260	0.07897	N	0.972048	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46652	-0.9176	9	0.07813	T	0.8	.	20.6666	0.99681	0.0:0.0977:0.0:0.9023	rs10935070;rs17301444;rs52791815;rs61344352;rs10935070	955;1042	A0AV47;Q92547	.;TOPB1_HUMAN	S	1042	ENSP00000260810:N1042S	ENSP00000260810:N1042S	N	-	2	0	TOPBP1	134824678	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.948000	0.00679	-2.029000	0.00930	-0.250000	0.11733	AAT	T|0.819;C|0.181	0.181	strong		0.289	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
ABCC11	85320	hgsc.bcm.edu	37	16	48226479	48226479	+	Silent	SNP	C	C	T	rs12443685	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:48226479C>T	ENST00000394747.1	-	19	3007	c.2658G>A	c.(2656-2658)aaG>aaA	p.K886K	ABCC11_ENST00000353782.5_Silent_p.K886K|ABCC11_ENST00000394748.1_Silent_p.K886K|ABCC11_ENST00000537808.1_3'UTR|ABCC11_ENST00000356608.2_Silent_p.K886K	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	886	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TCCTCGTGACCTTGGTGAAAA	0.582													C|||	683	0.136382	0.0998	0.3184	5008	,	,		15331	0.0298		0.162	False		,,,				2504	0.1401				p.K886K		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2658A						PASS	.	C	,,	481,3921	228.5+/-243.3	29,423,1749	113.0	102.0	106.0		2658,2658,2658	2.0	0.4	16	dbSNP_120	106	1446,7154	276.5+/-292.4	124,1198,2978	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	153,1621,4727	TT,TC,CC		16.814,10.9269,14.8208	,,	886/1383,886/1383,886/1345	48226479	1927,11075	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon19			CGTGACCTTGGTG	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2658G>A	16.37:g.48226479C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			C|0.860;T|0.140	0.140	strong		0.582	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
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 GAIIx	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	RP11-187O7.3_ENST00000554926.1_lincRNA|ESRRB_ENST00000380887.2_Missense_Mutation_p.F456L|ESRRB_ENST00000261532.7_3'UTR	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	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	50	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		
AKAP7	9465	hgsc.bcm.edu	37	6	131520655	131520655	+	Missense_Mutation	SNP	G	G	A	rs1190788	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:131520655G>A	ENST00000431975.2	+	6	742	c.644G>A	c.(643-645)aGt>aAt	p.S215N	AKAP7_ENST00000263050.3_5'Flank|AKAP7_ENST00000541650.1_Missense_Mutation_p.S214N|AKAP7_ENST00000368123.4_Missense_Mutation_p.S193N|AKAP7_ENST00000537868.1_5'Flank	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	215			S -> N (in dbSNP:rs1190788).			cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		GAGAGCAGAAGTTTTAAACCT	0.393													G|||	969	0.19349	0.1407	0.2262	5008	,	,		21588	0.0536		0.3479	False		,,,				2504	0.227				p.S215N		Atlas-SNP	.											.	AKAP7	61	.	0			c.G644A						PASS	.	G	ASN/SER	801,3605	321.0+/-296.9	66,669,1468	139.0	120.0	126.0		644	0.2	0.1	6	dbSNP_87	126	3047,5553	470.0+/-367.7	533,1981,1786	yes	missense	AKAP7	NM_016377.3	46	599,2650,3254	AA,AG,GG		35.4302,18.1798,29.5863	benign	215/349	131520655	3848,9158	2203	4300	6503	SO:0001583	missense	9465	exon6			GCAGAAGTTTTAA	AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"""A-kinase anchor proteins"""	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.644G>A	6.37:g.131520655G>A	ENSP00000405252:p.Ser215Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_016377	B4DUC3|Q9HCZ8	Missense_Mutation	SNP	ENST00000431975.2	37	CCDS5142.2	433	0.19826007326007325	84	0.17073170731707318	94	0.2596685082872928	10	0.017482517482517484	245	0.3232189973614776	G	13.52	2.260534	0.39995	0.181798	0.354302	ENSG00000118507	ENST00000431975;ENST00000541650;ENST00000368123	T;T;T	0.42513	0.97;0.97;0.97	5.36	0.182	0.15077	RNA ligase/cyclic nucleotide phosphodiesterase (1);Protein kinase A anchor protein, nuclear localisation signal domain (1);	0.691962	0.14573	N	0.311309	T	0.12732	0.0309	L	0.54323	1.7	0.50632	P	1.1099999999997223E-4	P;P	0.44344	0.646;0.833	B;B	0.36666	0.23;0.229	T	0.11867	-1.0570	9	0.21540	T	0.41	-10.0413	5.3228	0.15891	0.0822:0.4471:0.3407:0.13	rs1190788;rs1729536;rs17788100;rs58901183;rs1190788	214;215	F5GXD1;Q9P0M2	.;AKA7G_HUMAN	N	215;214;193	ENSP00000405252:S215N;ENSP00000441048:S214N;ENSP00000357105:S193N	ENSP00000357105:S193N	S	+	2	0	AKAP7	131562348	1.000000	0.71417	0.109000	0.21407	0.983000	0.72400	0.811000	0.27198	-0.190000	0.10465	0.655000	0.94253	AGT	G|0.752;A|0.248	0.248	strong		0.393	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842	
STYK1	55359	hgsc.bcm.edu	37	12	10782115	10782115	+	Missense_Mutation	SNP	T	T	C	rs3759259	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:10782115T>C	ENST00000075503.3	-	6	1130	c.610A>G	c.(610-612)Agc>Ggc	p.S204G		NM_018423.2	NP_060893.2	Q6J9G0	STYK1_HUMAN	serine/threonine/tyrosine kinase 1	204	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> G (in dbSNP:rs3759259). {ECO:0000269|PubMed:12841579, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.6}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	26						CAGAGAAAGCTGAGCAGGTCC	0.527										HNSCC(73;0.22)			T|||	2998	0.598642	0.3457	0.7032	5008	,	,		17885	0.7917		0.6431	False		,,,				2504	0.6217				p.S204G		Atlas-SNP	.											.	STYK1	55	.	0			c.A610G						PASS	.	T	GLY/SER	1674,2732	508.3+/-366.9	336,1002,865	55.0	45.0	49.0		610	5.6	1.0	12	dbSNP_107	49	5065,3535	631.7+/-398.5	1486,2093,721	yes	missense	STYK1	NM_018423.2	56	1822,3095,1586	CC,CT,TT		41.1047,37.9936,48.1855	benign	204/423	10782115	6739,6267	2203	4300	6503	SO:0001583	missense	55359	exon6			GAAAGCTGAGCAG	AF251059	CCDS8629.1	12p13.2	2005-01-21							18889	protein-coding gene	gene with protein product		611433				12841579	Standard	NM_018423		Approved	SuRTK106, DKFZp761P1010, NOK	uc001qys.2	Q6J9G0		ENST00000075503.3:c.610A>G	12.37:g.10782115T>C	ENSP00000075503:p.Ser204Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_018423	B2R9T2|Q52LR3|Q9BXY2|Q9NSH1	Missense_Mutation	SNP	ENST00000075503.3	37	CCDS8629.1	1351	0.6185897435897436	173	0.3516260162601626	241	0.6657458563535912	451	0.7884615384615384	486	0.6411609498680739	T	10.93	1.490929	0.26774	0.379936	0.588953	ENSG00000060140	ENST00000075503	T	0.69806	-0.43	5.58	5.58	0.84498	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.427798	0.26369	N	0.024770	T	0.00012	0.0000	N	0.13371	0.34	0.46279	P	0.0010379999999999834	B	0.06786	0.001	B	0.14023	0.01	T	0.40701	-0.9549	9	0.62326	D	0.03	-8.2332	10.0973	0.42482	0.0:0.0:0.1684:0.8316	rs3759259;rs17809572;rs58022630;rs3759259	204	Q6J9G0	STYK1_HUMAN	G	204	ENSP00000075503:S204G	ENSP00000075503:S204G	S	-	1	0	STYK1	10673382	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.496000	0.53288	2.244000	0.73946	0.533000	0.62120	AGC	T|0.438;C|0.562	0.562	strong		0.527	STYK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399622.1	NM_018423	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12908005	12908005	+	Silent	SNP	G	G	A	rs141516126	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12908005G>A	ENST00000317869.6	-	2	363	c.138C>T	c.(136-138)tgC>tgT	p.C46C		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	46	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.					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						TATGAACAGAGCAGCCCGCAA	0.478																																					p.C46C		Atlas-SNP	.											.	HNRNPCL1	68	.	0			c.C138T						PASS	.	G		3,4403	2.1+/-5.4	0,3,2200	108.0	105.0	106.0		138	-0.1	0.1	1	dbSNP_134	106	35,8561	14.0+/-48.4	0,35,4263	no	coding-synonymous	HNRNPCL1	NM_001013631.1		0,38,6463	AA,AG,GG		0.4072,0.0681,0.2923		46/294	12908005	38,12964	2203	4298	6501	SO:0001819	synonymous_variant	343069	exon2			AACAGAGCAGCCC	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.138C>T	1.37:g.12908005G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	220	34	0.154545	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	37	CCDS30591.1																																																																																			G|0.999;A|0.001	0.001	strong		0.478	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
AZU1	566	hgsc.bcm.edu	37	19	830854	830854	+	Silent	SNP	T	T	C	rs595844	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:830854T>C	ENST00000233997.2	+	4	528	c.507T>C	c.(505-507)ttT>ttC	p.F169F		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	169	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		TTCCCAGGTTTGTCAACGTGA	0.662													t|||	3340	0.666933	0.941	0.6398	5008	,	,		14888	0.495		0.5497	False		,,,				2504	0.6135				p.F169F		Atlas-SNP	.											AZU1,NS,carcinoma,0,1	AZU1	31	1	0			c.T507C						PASS	.	T		3866,540	769.9+/-413.7	1698,470,35	41.0	40.0	40.0		507	-3.0	0.0	19	dbSNP_83	40	4598,4002	595.3+/-393.4	1242,2114,944	no	coding-synonymous	AZU1	NM_001700.3		2940,2584,979	CC,CT,TT		46.5349,12.256,34.9223		169/252	830854	8464,4542	2203	4300	6503	SO:0001819	synonymous_variant	566	exon4			CAGGTTTGTCAAC	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.507T>C	19.37:g.830854T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			T|0.360;C|0.640	0.640	strong		0.662	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
OR51G1	79324	hgsc.bcm.edu	37	11	4945236	4945236	+	Missense_Mutation	SNP	T	T	C	rs35666095	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:4945236T>C	ENST00000321961.2	-	1	401	c.334A>G	c.(334-336)Atg>Gtg	p.M112V	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	112						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)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGACTCCATTGAAGACAAG	0.507													C|||	385	0.076877	0.0613	0.1527	5008	,	,		22605	0.0089		0.1083	False		,,,				2504	0.0818				p.M112V		Atlas-SNP	.											.	OR51G1	74	.	0			c.A334G						PASS	.	C	VAL/MET	276,4126	801.0+/-415.6	3,270,1928	100.0	93.0	95.0		334	-0.0	0.1	11	dbSNP_126	95	930,7666	776.4+/-407.7	61,808,3429	yes	missense	OR51G1	NM_001005237.1	21	64,1078,5357	CC,CT,TT		10.819,6.2699,9.2784	benign	112/322	4945236	1206,11792	2201	4298	6499	SO:0001583	missense	79324	exon1			ACTCCATTGAAGA	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.334A>G	11.37:g.4945236T>C	ENSP00000322546:p.Met112Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	171	0.0782967032967033	34	0.06910569105691057	30	0.08287292817679558	5	0.008741258741258742	102	0.1345646437994723	C	0.005	-2.188683	0.00305	0.062699	0.10819	ENSG00000176879	ENST00000321961	T	0.02812	4.15	4.2	-0.00795	0.14007	GPCR, rhodopsin-like superfamily (1);	0.206562	0.23916	N	0.043292	T	0.00039	0.0001	L	0.47190	1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43621	-0.9380	9	0.30078	T	0.28	.	1.644	0.02758	0.1365:0.3161:0.1337:0.4136	rs35666095	112	Q8NGK1	O51G1_HUMAN	V	112	ENSP00000322546:M112V	ENSP00000322546:M112V	M	-	1	0	OR51G1	4901812	0.000000	0.05858	0.095000	0.20976	0.034000	0.12701	-1.074000	0.03427	-0.143000	0.11334	-0.996000	0.02517	ATG	T|0.912;C|0.088	0.088	strong		0.507	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
DHRS1	115817	hgsc.bcm.edu	37	14	24760808	24760808	+	Silent	SNP	C	C	T	rs1131941	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24760808C>T	ENST00000288111.7	-	7	954	c.678G>A	c.(676-678)gcG>gcA	p.A226A	DHRS1_ENST00000559088.1_5'UTR|DHRS1_ENST00000396813.1_Silent_p.A226A	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	226						endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6				GBM - Glioblastoma multiforme(265;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(311;0.0442)		CTGTGGTTTCCGCAGATGAGA	0.498													C|||	746	0.148962	0.1513	0.3473	5008	,	,		22102	0.004		0.1869	False		,,,				2504	0.1155				p.A226A		Atlas-SNP	.											.	DHRS1	21	.	0			c.G678A						PASS	.	C	,	728,3678	301.0+/-286.6	62,604,1537	196.0	192.0	193.0		678,678	-7.2	0.0	14	dbSNP_86	193	1783,6817	322.1+/-315.4	189,1405,2706	no	coding-synonymous,coding-synonymous	DHRS1	NM_001136050.2,NM_138452.2	,	251,2009,4243	TT,TC,CC		20.7326,16.5229,19.3065	,	226/314,226/314	24760808	2511,10495	2203	4300	6503	SO:0001819	synonymous_variant	115817	exon7			GGTTTCCGCAGAT	AK058159	CCDS9623.1	14q11.2	2011-09-14			ENSG00000157379	ENSG00000157379	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16445	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 19C, member 1"""	610410				12153138, 19027726	Standard	NM_138452		Approved	FLJ25430, MGC20204, SDR19C1	uc001wok.3	Q96LJ7	OTTHUMG00000029333	ENST00000288111.7:c.678G>A	14.37:g.24760808C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Silent	SNP	ENST00000288111.7	37	CCDS9623.1																																																																																			C|0.827;T|0.173	0.173	strong		0.498	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452	
PCNXL3	399909	hgsc.bcm.edu	37	11	65384727	65384727	+	Silent	SNP	C	C	T	rs12790427	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:65384727C>T	ENST00000355703.3	+	3	887	c.348C>T	c.(346-348)ccC>ccT	p.P116P		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	116						integral component of membrane (GO:0016021)		p.P116P(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CCAGGGACCCCGGAGTGGAGA	0.542													C|||	1482	0.295927	0.2648	0.4236	5008	,	,		20205	0.4226		0.1968	False		,,,				2504	0.2188				p.P116P		Atlas-SNP	.											PCNXL3_ENST00000355703,NS,carcinoma,0,1	PCNXL3	140	1	1	Substitution - coding silent(1)	stomach(1)	c.C348T						PASS	.	C		958,3066		117,724,1171	35.0	38.0	37.0		348	-4.4	1.0	11	dbSNP_121	37	1638,6686		156,1326,2680	no	coding-synonymous	PCNXL3	NM_032223.2		273,2050,3851	TT,TC,CC		19.678,23.8072,21.0236		116/2035	65384727	2596,9752	2012	4162	6174	SO:0001819	synonymous_variant	399909	exon3			GGACCCCGGAGTG	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.348C>T	11.37:g.65384727C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	27	0.321429	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			C|0.719;T|0.281	0.281	strong		0.542	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
MYH11	4629	hgsc.bcm.edu	37	16	15814717	15814717	+	Silent	SNP	C	C	T	rs11648119	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:15814717C>T	ENST00000300036.5	-	33	4879	c.4770G>A	c.(4768-4770)aaG>aaA	p.K1590K	MYH11_ENST00000396324.3_Silent_p.K1597K|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000452625.2_Silent_p.K1597K|MYH11_ENST00000576790.2_Silent_p.K1590K|NDE1_ENST00000396355.1_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1590					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GTTGCCTCCTCTTCTCCTCAT	0.602			T	CBFB	AML								C|||	24	0.00479233	0.0023	0.0072	5008	,	,		16875	0.0		0.0139	False		,,,				2504	0.002				p.K1597K		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G4791A						PASS	.	C	,,,,,	16,4378	23.3+/-48.9	0,16,2181	85.0	76.0	79.0		4791,4791,,4770,,4770	2.9	0.5	16	dbSNP_120	79	177,8423	80.4+/-143.0	3,171,4126	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	3,187,6307	TT,TC,CC		2.0581,0.3641,1.4853	,,,,,	1597/1946,1597/1980,,1590/1973,,1590/1939	15814717	193,12801	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon34			CCTCCTCTTCTCC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.4770G>A	16.37:g.15814717C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			C|0.989;T|0.011	0.011	strong		0.602	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
NRG3	10718	hgsc.bcm.edu	37	10	84745040	84745040	+	Silent	SNP	A	A	G	rs17101196	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:84745040A>G	ENST00000404547.1	+	10	1842	c.1842A>G	c.(1840-1842)ccA>ccG	p.P614P	NRG3_ENST00000545131.1_Silent_p.P240P|NRG3_ENST00000556918.1_Silent_p.P420P|NRG3_ENST00000537893.1_Silent_p.P240P|NRG3_ENST00000372141.2_Silent_p.P590P|NRG3_ENST00000404576.2_Silent_p.P394P|NRG3_ENST00000372142.2_Silent_p.P393P			P56975	NRG3_HUMAN	neuregulin 3	614					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		TGCAAATGCCAGGGATTTCTG	0.473													A|||	477	0.0952476	0.1732	0.1571	5008	,	,		19753	0.0109		0.0567	False		,,,				2504	0.0726				p.P590P		Atlas-SNP	.											.	NRG3	301	.	0			c.A1770G						PASS	.	A	,,	686,3720	289.5+/-280.5	58,570,1575	97.0	98.0	98.0		1770,1767,1179	4.8	1.0	10	dbSNP_123	98	502,8098	144.8+/-200.6	15,472,3813	no	coding-synonymous,coding-synonymous,coding-synonymous	NRG3	NM_001010848.3,NM_001165972.1,NM_001165973.1	,,	73,1042,5388	GG,GA,AA		5.8372,15.5697,9.1342	,,	590/697,589/696,393/500	84745040	1188,11818	2203	4300	6503	SO:0001819	synonymous_variant	10718	exon9			AATGCCAGGGATT	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1842A>G	10.37:g.84745040A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	50	0.632911	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Silent	SNP	ENST00000404547.1	37	CCDS31233.1																																																																																			A|0.911;G|0.089	0.089	strong		0.473	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
LEFTY1	10637	hgsc.bcm.edu	37	1	226076669	226076669	+	Missense_Mutation	SNP	C	C	T	rs41310561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226076669C>T	ENST00000272134.5	-	1	177	c.98G>A	c.(97-99)cGg>cAg	p.R33Q	RP4-559A3.7_ENST00000432920.2_Intron|LEFTY1_ENST00000492457.1_Intron	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	33					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					CTGCAGCTGCCGCAGCAGGCT	0.706													C|||	328	0.0654952	0.0008	0.0735	5008	,	,		15639	0.1458		0.0497	False		,,,				2504	0.0808				p.R33Q		Atlas-SNP	.											LEFTY1,NS,carcinoma,0,1	LEFTY1	30	1	0			c.G98A						PASS	.	C	GLN/ARG	29,4257		0,29,2114	11.0	12.0	12.0		98	-5.9	0.7	1	dbSNP_127	12	348,8060		8,332,3864	no	missense	LEFTY1	NM_020997.3	43	8,361,5978	TT,TC,CC		4.1389,0.6766,2.9699	benign	33/367	226076669	377,12317	2143	4204	6347	SO:0001583	missense	10637	exon1			AGCTGCCGCAGCA	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"""left-right determination, factor B"""	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.98G>A	1.37:g.226076669C>T	ENSP00000272134:p.Arg33Gln	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	56	34	0.607143	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	145	0.06639194139194139	0	0.0	20	0.055248618784530384	85	0.1486013986013986	40	0.052770448548812667	c	0.016	-1.515749	0.00975	0.006766	0.041389	ENSG00000243709	ENST00000272134	T	0.65916	-0.18	4.18	-5.9	0.02275	Transforming growth factor-beta, N-terminal (1);	0.596957	0.18283	N	0.145963	T	0.00109	0.0003	N	0.00972	-1.085	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.13072	-1.0523	9	0.06236	T	0.91	.	12.5504	0.56223	0.0:0.5422:0.0:0.4578	rs41310561;rs61995950	33;33	B2R7U0;O75610	.;LFTY1_HUMAN	Q	33	ENSP00000272134:R33Q	ENSP00000272134:R33Q	R	-	2	0	LEFTY1	224143292	0.011000	0.17503	0.705000	0.30386	0.126000	0.20510	-0.619000	0.05572	-1.087000	0.03081	-2.087000	0.00375	CGG	C|0.955;T|0.045	0.045	strong		0.706	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
TMEM232	642987	hgsc.bcm.edu	37	5	109973902	109973902	+	Silent	SNP	T	T	G	rs1422495	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:109973902T>G	ENST00000455884.2	-	5	548	c.498A>C	c.(496-498)gcA>gcC	p.A166A	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Silent_p.A166A			C9JQI7	TM232_HUMAN	transmembrane protein 232	166						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						AACATACCTTTGCTAGCTTTA	0.303													T|||	434	0.0866613	0.0756	0.1153	5008	,	,		14761	0.0903		0.0895	False		,,,				2504	0.0746				p.A166A		Atlas-SNP	.											.	TMEM232	57	.	0			c.A498C						PASS	.	T		109,1275		3,103,586	76.0	63.0	67.0		498	0.9	0.3	5	dbSNP_88	67	276,2906		14,248,1329	no	coding-synonymous	TMEM232	NM_001039763.3		17,351,1915	GG,GT,TT		8.6738,7.8757,8.4319		166/658	109973902	385,4181	692	1591	2283	SO:0001819	synonymous_variant	642987	exon5			TACCTTTGCTAGC	AK125070	CCDS47253.1, CCDS47253.2	5q22.1	2014-02-12	2009-10-02		ENSG00000186952	ENSG00000186952			37270	protein-coding gene	gene with protein product							Standard	NM_001039763		Approved	FLJ43080	uc011cvh.2	C9JQI7	OTTHUMG00000163297	ENST00000455884.2:c.498A>C	5.37:g.109973902T>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_001039763	B4DKF4	Silent	SNP	ENST00000455884.2	37	CCDS47253.2																																																																																			T|0.910;G|0.090	0.090	strong		0.303	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
CCDC176	80127	hgsc.bcm.edu	37	14	74523949	74523949	+	Silent	SNP	G	G	A	rs3742808	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74523949G>A	ENST00000394009.3	+	11	1689	c.1566G>A	c.(1564-1566)caG>caA	p.Q522Q	ALDH6A1_ENST00000553458.1_3'UTR|CCDC176_ENST00000553773.1_Silent_p.Q247Q|AC005484.5_ENST00000492026.1_RNA|CCDC176_ENST00000492247.2_Silent_p.Q66Q	NM_025057.2	NP_079333.2	Q8ND07	BBOF1_HUMAN	coiled-coil domain containing 176	522					motile cilium assembly (GO:0044458)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)											AAGAACCTCAGGAGTCTGACA	0.398													A|||	1505	0.300519	0.3555	0.1801	5008	,	,		20419	0.2381		0.1909	False		,,,				2504	0.4888				p.Q522Q		Atlas-SNP	.											.	.	.	.	0			c.G1566A						PASS	.	A		1483,2923	676.6+/-403.3	263,957,983	63.0	61.0	62.0		1566	-2.0	0.0	14	dbSNP_107	62	1616,6984	741.2+/-407.1	147,1322,2831	no	coding-synonymous	C14orf45	NM_025057.2		410,2279,3814	AA,AG,GG		18.7907,33.6586,23.8275		522/530	74523949	3099,9907	2203	4300	6503	SO:0001819	synonymous_variant	80127	exon11			ACCTCAGGAGTCT	BI457605	CCDS32119.2	14q24.3	2013-01-04	2012-09-25	2012-09-25	ENSG00000119636	ENSG00000119636			19855	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 45"""	C14orf45			Standard	NM_025057		Approved		uc010tup.2	Q8ND07	OTTHUMG00000152786	ENST00000394009.3:c.1566G>A	14.37:g.74523949G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_025057	Q0P604|Q9H5P8	Silent	SNP	ENST00000394009.3	37	CCDS32119.2																																																																																			G|0.755;A|0.245	0.245	strong		0.398	CCDC176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327863.1	NM_025057	
PRRC2A	7916	hgsc.bcm.edu	37	6	31603770	31603770	+	Silent	SNP	A	A	G	rs11229	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31603770A>G	ENST00000376033.2	+	25	5802	c.5568A>G	c.(5566-5568)caA>caG	p.Q1856Q	PRRC2A_ENST00000376007.4_Silent_p.Q1856Q	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1856						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						TGGACTCTCAATTACATCCAA	0.512													A|||	668	0.133387	0.2126	0.0793	5008	,	,		13510	0.0714		0.1461	False		,,,				2504	0.1155				p.Q1856Q		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A5568G						PASS	.	A	,	880,3526	343.1+/-307.5	85,710,1408	67.0	60.0	63.0		5568,5568	0.3	1.0	6	dbSNP_52	63	1542,7058	289.6+/-299.4	146,1250,2904	yes	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	231,1960,4312	GG,GA,AA		17.9302,19.9728,18.6222	,	1856/2158,1856/2158	31603770	2422,10584	2203	4300	6503	SO:0001819	synonymous_variant	7916	exon25			CTCTCAATTACAT	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.5568A>G	6.37:g.31603770A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	92	0.821429	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	286	0.13095238095238096	112	0.22764227642276422	30	0.08287292817679558	33	0.057692307692307696	111	0.14643799472295516	A	7.453	0.642991	0.14451	0.199728	0.179302	ENSG00000204469	ENST00000424184;ENST00000435052	.	.	.	5.24	0.33	0.15929	.	.	.	.	.	T	0.32255	0.0823	.	.	.	0.09310	P	0.9999999855904	.	.	.	.	.	.	T	0.20438	-1.0275	4	0.87932	D	0	-4.865	7.5454	0.27764	0.2257:0.1228:0.6515:0.0	rs11229;rs1046090;rs3173343;rs9267522;rs17354367;rs17398279;rs52803694;rs61060019;rs9267522	.	.	.	V	1850;1839	.	ENSP00000407986:I1850V	I	+	1	0	PRRC2A	31711749	0.999000	0.42202	0.987000	0.45799	0.746000	0.42486	0.221000	0.17680	-0.122000	0.11766	-1.811000	0.00612	ATT	A|0.841;G|0.159	0.159	strong		0.512	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
FAM170B	170370	hgsc.bcm.edu	37	10	50339925	50339925	+	Silent	SNP	G	G	A	rs12765281	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50339925G>A	ENST00000311787.5	-	2	674	c.585C>T	c.(583-585)gaC>gaT	p.D195D	FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	195										central_nervous_system(1)|endometrium(1)|skin(1)	3						TGACCAGCCAGTCCGGCGGCT	0.687													G|||	1228	0.245208	0.118	0.3444	5008	,	,		15830	0.3075		0.2684	False		,,,				2504	0.2587				p.D195D		Atlas-SNP	.											.	FAM170B	20	.	0			c.C585T						PASS	.						7.0	11.0	10.0					10																	50339925		684	1579	2263	SO:0001819	synonymous_variant	170370	exon2			CAGCCAGTCCGGC		CCDS53536.1	10q11.23	2008-11-06	2008-06-12	2008-06-12	ENSG00000172538	ENSG00000172538			19736	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 73"""	C10orf73			Standard	NM_001164484		Approved	Em:AC084727.4	uc001jhj.3	A6NMN3	OTTHUMG00000018187	ENST00000311787.5:c.585C>T	10.37:g.50339925G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_001164484	Q86WY6|Q8N6K8	Silent	SNP	ENST00000311787.5	37	CCDS53536.1																																																																																			G|0.768;A|0.232	0.232	strong		0.687	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
ZNF366	167465	hgsc.bcm.edu	37	5	71739602	71739602	+	Missense_Mutation	SNP	G	G	C	rs13188519	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:71739602G>C	ENST00000318442.5	-	5	2706	c.2216C>G	c.(2215-2217)gCa>gGa	p.A739G	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	739	Interaction with CTBP1.|Interaction with NRIP1.		A -> G (in dbSNP:rs13188519).		negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		TAAAAGCACTGCTTGTTTTTC	0.388													G|||	363	0.072484	0.0605	0.0389	5008	,	,		18997	0.0714		0.0964	False		,,,				2504	0.089				p.A739G		Atlas-SNP	.											.	ZNF366	108	.	0			c.C2216G						PASS	.	G	GLY/ALA	259,4117		4,251,1933	46.0	52.0	50.0		2216	5.9	1.0	5	dbSNP_121	50	927,7669		45,837,3416	yes	missense	ZNF366	NM_152625.1	60	49,1088,5349	CC,CG,GG		10.7841,5.9186,9.1428	benign	739/745	71739602	1186,11786	2188	4298	6486	SO:0001583	missense	167465	exon5			AGCACTGCTTGTT	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.2216C>G	5.37:g.71739602G>C	ENSP00000313158:p.Ala739Gly	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	92	25	0.271739	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	140	0.0641025641025641	30	0.06097560975609756	13	0.03591160220994475	20	0.03496503496503497	77	0.10158311345646438	G	16.77	3.215688	0.58452	0.059186	0.107841	ENSG00000178175	ENST00000318442	T	0.10288	2.89	5.87	5.87	0.94306	.	0.171581	0.41605	D	0.000860	T	0.00210	0.0006	L	0.29908	0.895	0.33098	D	0.538779	P	0.36282	0.546	B	0.32149	0.141	T	0.05386	-1.0888	10	0.59425	D	0.04	-6.1181	16.1124	0.81273	0.0:0.0:0.8657:0.1343	rs13188519;rs52832178;rs13188519	739	Q8N895	ZN366_HUMAN	G	739	ENSP00000313158:A739G	ENSP00000313158:A739G	A	-	2	0	ZNF366	71775358	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.660000	0.61511	2.941000	0.99782	0.655000	0.94253	GCA	G|0.916;C|0.084	0.084	strong		0.388	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
RBM12B	389677	hgsc.bcm.edu	37	8	94746049	94746049	+	Missense_Mutation	SNP	T	T	G	rs16916188	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:94746049T>G	ENST00000399300.2	-	3	2803	c.2590A>C	c.(2590-2592)Aat>Cat	p.N864H	RBM12B_ENST00000517700.1_Missense_Mutation_p.N744H|RBM12B_ENST00000520961.1_Intron|RP11-10N23.4_ENST00000517998.1_RNA	NM_203390.2	NP_976324.2	Q8IXT5	RB12B_HUMAN	RNA binding motif protein 12B	864			N -> H (in dbSNP:rs16916188).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	30	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.0168)			GGTCTAAAATTGTCAGGAAGT	0.507													T|||	224	0.0447284	0.0401	0.0591	5008	,	,		13910	0.0268		0.0358	False		,,,				2504	0.0685				p.N864H		Atlas-SNP	.											.	RBM12B	78	.	0			c.A2590C						PASS	.	T	HIS/ASN	137,3501		0,137,1682	88.0	91.0	90.0		2590	-2.4	0.0	8	dbSNP_123	90	366,7790		4,358,3716	yes	missense	RBM12B	NM_203390.2	68	4,495,5398	GG,GT,TT		4.4875,3.7658,4.2649	possibly-damaging	864/1002	94746049	503,11291	1819	4078	5897	SO:0001583	missense	389677	exon3			TAAAATTGTCAGG		CCDS43755.1	8q22	2014-05-20			ENSG00000183808	ENSG00000183808		"""RNA binding motif (RRM) containing"""	32310	protein-coding gene	gene with protein product							Standard	NM_203390		Approved		uc003yfz.3	Q8IXT5	OTTHUMG00000164317	ENST00000399300.2:c.2590A>C	8.37:g.94746049T>G	ENSP00000382239:p.Asn864His	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	32	11	0.34375	NM_203390	A8MYB5	Missense_Mutation	SNP	ENST00000399300.2	37	CCDS43755.1	77	0.035256410256410256	12	0.024390243902439025	21	0.058011049723756904	16	0.027972027972027972	28	0.036939313984168866	T	12.89	2.073478	0.36566	0.037658	0.044875	ENSG00000183808	ENST00000399300;ENST00000517700	T;T	0.06849	3.25;3.25	5.95	-2.4	0.06583	.	.	.	.	.	T	0.00524	0.0017	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.40459	-0.9562	9	0.49607	T	0.09	2.4636	6.1738	0.20433	0.0:0.3041:0.3746:0.3212	rs16916188;rs16916188	864	Q8IXT5	RB12B_HUMAN	H	864;744	ENSP00000382239:N864H;ENSP00000427729:N744H	ENSP00000382239:N864H	N	-	1	0	RBM12B	94815225	.	.	0.000000	0.03702	0.991000	0.79684	.	.	-0.381000	0.07882	0.460000	0.39030	AAT	T|0.964;G|0.036	0.036	strong		0.507	RBM12B-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383603.1	NM_203390	
AGXT2	64902	hgsc.bcm.edu	37	5	35039437	35039437	+	Silent	SNP	A	A	G	rs2279651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:35039437A>G	ENST00000231420.6	-	3	554	c.354T>C	c.(352-354)caT>caC	p.H118H		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	118					cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|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)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	ACGGGTGGCAATGGCCAACAC	0.438													G|||	1999	0.399161	0.4289	0.4121	5008	,	,		19911	0.2331		0.5815	False		,,,				2504	0.3333				p.H118H		Atlas-SNP	.											.	AGXT2	89	.	0			c.T354C						PASS	.	G		1854,2552	627.9+/-395.0	376,1102,725	95.0	102.0	99.0		354	3.5	1.0	5	dbSNP_100	99	5161,3439	506.2+/-376.5	1560,2041,699	no	coding-synonymous	AGXT2	NM_031900.3		1936,3143,1424	GG,GA,AA		39.9884,42.079,46.0634		118/515	35039437	7015,5991	2203	4300	6503	SO:0001819	synonymous_variant	64902	exon3			GTGGCAATGGCCA	AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"""beta-alanine-pyruvate aminotransferase"", ""beta-ALAAT II"""	612471	"""alanine-glyoxylate aminotransferase 2"""			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.354T>C	5.37:g.35039437A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	193	88	0.455959	NM_031900	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Silent	SNP	ENST00000231420.6	37	CCDS3908.1																																																																																			A|0.516;G|0.484	0.484	strong		0.438	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900	
CPS1	1373	hgsc.bcm.edu	37	2	211540507	211540507	+	Missense_Mutation	SNP	C	C	A	rs1047891	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:211540507C>A	ENST00000233072.5	+	36	4413	c.4217C>A	c.(4216-4218)aCc>aAc	p.T1406N	CPS1_ENST00000451903.2_Missense_Mutation_p.T955N|CPS1_ENST00000430249.2_Missense_Mutation_p.T1412N	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1406			T -> N (associated with PHN susceptibility; 30-40% higher activity; also highly associated with hepatocellular carcinoma (HCC) progression; dbSNP:rs1047891). {ECO:0000269|PubMed:11407344, ECO:0000269|PubMed:12853138, ECO:0000269|PubMed:12955727, ECO:0000269|PubMed:1840546, ECO:0000269|PubMed:20520828, ECO:0000269|PubMed:21767969, ECO:0000269|PubMed:24237036}.		anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GTCCCTGCCACCCCAGTGGCA	0.443													C|||	1445	0.288538	0.3684	0.3429	5008	,	,		16610	0.1389		0.3012	False		,,,				2504	0.2832				p.T1412N		Atlas-SNP	.											.	CPS1	485	.	0			c.C4235A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR	1605,2801	497.2+/-363.8	305,995,903	68.0	68.0	68.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4235,2864,4217	5.2	1.0	2	dbSNP_86	68	2676,5924	428.0+/-355.8	422,1832,2046	yes	missense,missense,missense	CPS1	NM_001122633.2,NM_001122634.2,NM_001875.4	65,65,65	727,2827,2949	AA,AC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	31.1163,36.4276,32.9156	benign,benign,benign	1412/1507,955/1050,1406/1501	211540507	4281,8725	2203	4300	6503	SO:0001583	missense	1373	exon37			CTGCCACCCCAGT	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.4217C>A	2.37:g.211540507C>A	ENSP00000233072:p.Thr1406Asn	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	586	0.2683150183150183	154	0.3130081300813008	122	0.3370165745856354	81	0.14160839160839161	229	0.3021108179419525	C	14.03	2.413514	0.42817	0.364276	0.311163	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.82984	-1.67;-1.67;-1.67	6.08	5.2	0.72013	Methylglyoxal synthase-like domain (4);	0.301714	0.35124	N	0.003423	T	0.00012	0.0000	L	0.48877	1.53	0.37459	P	0.08485100000000001	B;B	0.14012	0.009;0.009	B;B	0.19391	0.025;0.025	T	0.08371	-1.0725	9	0.32370	T	0.25	-11.1012	9.5512	0.39310	0.1496:0.7771:0.0:0.0732	rs1047891;rs2229587;rs3187890;rs7422339;rs52831019;rs7422339	1416;1406	Q59HF8;P31327	.;CPSM_HUMAN	N	1412;1414;1406;955	ENSP00000402608:T1412N;ENSP00000233072:T1406N;ENSP00000406136:T955N	ENSP00000233072:T1406N	T	+	2	0	CPS1	211248752	0.977000	0.34250	1.000000	0.80357	0.981000	0.71138	1.756000	0.38390	1.580000	0.49851	0.591000	0.81541	ACC	C|0.699;A|0.301	0.301	strong		0.443	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
WHAMM	123720	hgsc.bcm.edu	37	15	83481880	83481880	+	Missense_Mutation	SNP	A	A	G	rs35270670	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:83481880A>G	ENST00000286760.4	+	2	734	c.635A>G	c.(634-636)aAc>aGc	p.N212S		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	212	Mediates association with membranes. {ECO:0000269|PubMed:18614018}.		N -> S (in dbSNP:rs35270670).		actin filament organization (GO:0007015)|actin filament reorganization (GO:0090527)|ER to Golgi vesicle-mediated transport (GO:0006888)|focal adhesion assembly (GO:0048041)|lamellipodium assembly (GO:0030032)|membrane tubulation (GO:0097320)|positive regulation of actin nucleation (GO:0051127)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|Golgi membrane (GO:0000139)	Arp2/3 complex binding (GO:0071933)|GTP-Rho binding (GO:0017049)|microtubule binding (GO:0008017)			endometrium(6)|large_intestine(5)|lung(1)|prostate(1)	13						GGAAAAGCCAACACCATGGTA	0.388													A|||	531	0.10603	0.0772	0.1225	5008	,	,		16852	0.0		0.2346	False		,,,				2504	0.1104				p.N212S		Atlas-SNP	.											.	WHAMM	63	.	0			c.A635G						PASS	.	A	SER/ASN	405,3375		18,369,1503	92.0	79.0	83.0		635	3.3	1.0	15	dbSNP_126	83	1861,6379		226,1409,2485	no	missense	WHAMM	NM_001080435.1	46	244,1778,3988	GG,GA,AA		22.585,10.7143,18.8519	benign	212/810	83481880	2266,9754	1890	4120	6010	SO:0001583	missense	123720	exon2			AAGCCAACACCAT	AK126887	CCDS45333.1	15q25.2	2009-02-18	2009-02-18	2009-02-18	ENSG00000156232	ENSG00000156232			30493	protein-coding gene	gene with protein product		612393	"""WAS protein homology region 2 domain containing 1"""	WHDC1		11853319, 18226259, 18614018, 18812086	Standard	XM_005272422		Approved	KIAA1971	uc002bje.3	Q8TF30		ENST00000286760.4:c.635A>G	15.37:g.83481880A>G	ENSP00000286760:p.Asn212Ser	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	235	109	0.46383	NM_001080435	Q8N1J9	Missense_Mutation	SNP	ENST00000286760.4	37	CCDS45333.1	270	0.12362637362637363	34	0.06910569105691057	51	0.1408839779005525	0	0.0	185	0.24406332453825857	A	12.39	1.922534	0.33908	0.107143	0.22585	ENSG00000156232	ENST00000286760;ENST00000234505	T	0.07216	3.21	4.42	3.3	0.37823	.	0.203652	0.49916	D	0.000135	T	0.00012	0.0000	L	0.57536	1.79	0.35267	P	0.219928	P	0.47910	0.902	B	0.36608	0.229	T	0.47535	-0.9110	9	0.42905	T	0.14	.	8.7226	0.34449	0.9099:0.0:0.0901:0.0	rs35270670;rs61732381	212	Q8TF30	WHAMM_HUMAN	S	212	ENSP00000286760:N212S	ENSP00000234505:N212S	N	+	2	0	WHAMM	81278934	1.000000	0.71417	0.991000	0.47740	0.645000	0.38454	3.869000	0.56062	0.754000	0.32968	0.533000	0.62120	AAC	A|0.847;G|0.153	0.153	strong		0.388	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1		
POLR3A	11128	hgsc.bcm.edu	37	10	79769647	79769647	+	Missense_Mutation	SNP	C	C	A	rs34588967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:79769647C>A	ENST00000372371.3	-	13	1882	c.1745G>T	c.(1744-1746)cGc>cTc	p.R582L		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	582			R -> L (in dbSNP:rs34588967).		defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			CGGTGGGAGGCGAACTTTAAT	0.483													C|||	17	0.00339457	0.0008	0.0101	5008	,	,		20588	0.0		0.0089	False		,,,				2504	0.0				p.R582L		Atlas-SNP	.											POLR3A,NS,carcinoma,-1,2	POLR3A	104	2	0			c.G1745T						scavenged	.	C	LEU/ARG	11,4395	19.1+/-41.9	0,11,2192	123.0	112.0	116.0		1745	3.9	1.0	10	dbSNP_126	116	142,8458	70.3+/-132.9	0,142,4158	yes	missense	POLR3A	NM_007055.3	102	0,153,6350	AA,AC,CC		1.6512,0.2497,1.1764	benign	582/1391	79769647	153,12853	2203	4300	6503	SO:0001583	missense	11128	exon13			GGGAGGCGAACTT	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"""RNA polymerase subunits"""	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.1745G>T	10.37:g.79769647C>A	ENSP00000361446:p.Arg582Leu	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	144	63	0.4375	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	16.88	3.244567	0.59103	0.002497	0.016512	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.74947	-0.89	5.72	3.88	0.44766	RNA polymerase Rpb1, domain 3 (1);	0.163679	0.56097	D	0.000023	T	0.42675	0.1213	N	0.20881	0.62	0.48830	D	0.999718	B	0.26602	0.154	B	0.28139	0.086	T	0.40289	-0.9571	9	.	.	.	-12.3618	10.576	0.45227	0.0:0.7932:0.0:0.2068	rs34588967	582	O14802	RPC1_HUMAN	L	582	ENSP00000361446:R582L	.	R	-	2	0	POLR3A	79439653	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	2.431000	0.44775	0.782000	0.33613	0.655000	0.94253	CGC	A|0.005;C|0.990;T|0.006	0.005	strong		0.483	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055	
COL4A3BP	10087	hgsc.bcm.edu	37	5	74681773	74681773	+	Silent	SNP	T	T	C	rs698912	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:74681773T>C	ENST00000405807.4	-	13	1792	c.1371A>G	c.(1369-1371)gaA>gaG	p.E457E	COL4A3BP_ENST00000380494.5_Silent_p.E585E|COL4A3BP_ENST00000508692.1_5'Flank|COL4A3BP_ENST00000261415.7_Silent_p.E431E	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	457	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)	p.E457E(1)		breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		AATTGCAGACTTCATGTCCTG	0.328													t|||	1451	0.289736	0.2655	0.1715	5008	,	,		15831	0.3313		0.2197	False		,,,				2504	0.4356				p.E585E		Atlas-SNP	.											COL4A3BP,NS,carcinoma,0,1	COL4A3BP	72	1	1	Substitution - coding silent(1)	stomach(1)	c.A1755G						PASS	.	T	,,	1142,3262	398.8+/-331.0	149,844,1209	65.0	58.0	61.0		1755,1371,1293	1.4	1.0	5	dbSNP_86	61	1805,6791	318.7+/-313.8	192,1421,2685	no	coding-synonymous,coding-synonymous,coding-synonymous	COL4A3BP	NM_001130105.1,NM_005713.2,NM_031361.2	,,	341,2265,3894	CC,CT,TT		20.9981,25.931,22.6692	,,	585/753,457/625,431/599	74681773	2947,10053	2202	4298	6500	SO:0001819	synonymous_variant	10087	exon14			GCAGACTTCATGT	AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"""StAR-related lipid transfer (START) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2205	protein-coding gene	gene with protein product	"""ceramide transporter"", ""StAR-related lipid transfer (START) domain containing 11"""	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1371A>G	5.37:g.74681773T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Silent	SNP	ENST00000405807.4	37	CCDS4028.1																																																																																			T|0.743;C|0.257	0.257	strong		0.328	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713	
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 GAIIx	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_ENST00000409098.1_5'Flank|MIR5001_ENST00000580185.1_RNA|EIF4E2_ENST00000409495.1_5'Flank|EIF4E2_ENST00000409514.1_5'Flank|EIF4E2_ENST00000409322.1_5'Flank|EIF4E2_ENST00000409167.3_5'Flank|EIF4E2_ENST00000409394.1_5'Flank|EIF4E2_ENST00000258416.3_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	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	20	9	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	
COL6A3	1293	hgsc.bcm.edu	37	2	238243292	238243292	+	Missense_Mutation	SNP	G	G	A	rs1131296	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238243292G>A	ENST00000295550.4	-	41	9658	c.9206C>T	c.(9205-9207)aCc>aTc	p.T3069I	COL6A3_ENST00000472056.1_Missense_Mutation_p.T2462I|COL6A3_ENST00000353578.4_Missense_Mutation_p.T2863I|COL6A3_ENST00000346358.4_Missense_Mutation_p.T2869I|COL6A3_ENST00000347401.3_Missense_Mutation_p.T2868I|COL6A3_ENST00000409809.1_Missense_Mutation_p.T2863I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	3069	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region.		T -> I (in dbSNP:rs1131296). {ECO:0000269|PubMed:17886299}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TCCGTGGTAGGTGGCTCTGAC	0.502													G|||	1734	0.346246	0.2504	0.3256	5008	,	,		18933	0.4802		0.4036	False		,,,				2504	0.2935				p.T3069I		Atlas-SNP	.											.	COL6A3	608	.	0			c.C9206T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	1256,3150	430.6+/-342.6	191,874,1138	71.0	60.0	63.0		8588,7385,9206	-1.1	0.2	2	dbSNP_86	63	3456,5144	507.7+/-376.9	696,2064,1540	yes	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	89,89,89	887,2938,2678	AA,AG,GG		40.186,28.5066,36.2294	benign,benign,benign	2863/2972,2462/2571,3069/3178	238243292	4712,8294	2203	4300	6503	SO:0001583	missense	1293	exon41			TGGTAGGTGGCTC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.9206C>T	2.37:g.238243292G>A	ENSP00000295550:p.Thr3069Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	826	0.3782051282051282	127	0.258130081300813	121	0.3342541436464088	284	0.4965034965034965	294	0.38786279683377306	G	11.26	1.586755	0.28268	0.285066	0.40186	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58	5.43	-1.13	0.09775	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.851480	0.10078	N	0.718837	T	0.00012	0.0000	N	0.14661	0.345	0.42095	P	0.008685999999999972	B;B;B	0.10296	0.002;0.003;0.002	B;B;B	0.11329	0.003;0.006;0.003	T	0.48703	-0.9012	9	0.25751	T	0.34	.	9.5989	0.39591	0.4842:0.0:0.5158:0.0	rs1131296;rs2270670;rs3088291;rs3191076;rs11547644;rs17352867;rs59730490;rs1131296	2462;2863;3069	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	I	3069;2868;2863;2462;2863;2869	ENSP00000295550:T3069I;ENSP00000315609:T2868I;ENSP00000315873:T2863I;ENSP00000418285:T2462I;ENSP00000386844:T2863I;ENSP00000295546:T2869I	ENSP00000295550:T3069I	T	-	2	0	COL6A3	237908031	0.913000	0.31002	0.164000	0.22755	0.986000	0.74619	0.603000	0.24149	-0.602000	0.05775	0.557000	0.71058	ACC	G|0.635;A|0.365	0.365	strong		0.502	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
PODXL	5420	hgsc.bcm.edu	37	7	131193739	131193739	+	Missense_Mutation	SNP	C	C	T	rs3212298	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:131193739C>T	ENST00000378555.3	-	5	1319	c.1072G>A	c.(1072-1074)Gtc>Atc	p.V358I	PODXL_ENST00000537928.1_Intron|PODXL_ENST00000322985.9_Missense_Mutation_p.V326I|PODXL_ENST00000465001.1_5'Flank|PODXL_ENST00000541194.1_Missense_Mutation_p.V360I			O00592	PODXL_HUMAN	podocalyxin-like	358			V -> I (in dbSNP:rs3212298). {ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					AGGTTCAGGACGAGCTGCTTC	0.522													c|||	391	0.0780751	0.0151	0.0216	5008	,	,		17804	0.1974		0.0557	False		,,,				2504	0.1033				p.V358I		Atlas-SNP	.											PODXL,NS,malignant_melanoma,+2,2	PODXL	53	2	0			c.G1072A						PASS	.	T	ILE/VAL,ILE/VAL	78,4328	67.6+/-105.2	0,78,2125	202.0	143.0	163.0		1072,976	-7.7	0.0	7	dbSNP_105	163	406,8194	129.2+/-187.3	11,384,3905	yes	missense,missense	PODXL	NM_001018111.2,NM_005397.3	29,29	11,462,6030	TT,TC,CC		4.7209,1.7703,3.7214	benign,benign	358/559,326/527	131193739	484,12522	2203	4300	6503	SO:0001583	missense	5420	exon5			TCAGGACGAGCTG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.1072G>A	7.37:g.131193739C>T	ENSP00000367817:p.Val358Ile	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	394	175	0.444162	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	200	0.09157509157509157	15	0.03048780487804878	13	0.03591160220994475	131	0.229020979020979	41	0.05408970976253298	c	0.012	-1.650881	0.00785	0.017703	0.047209	ENSG00000128567	ENST00000541194;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T	0.20738	2.05;2.05;2.05	3.85	-7.7	0.01259	.	1.568090	0.03777	N	0.260675	T	0.00012	0.0000	N	0.00677	-1.265	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.13176	-1.0519	9	0.02654	T	1	-15.9701	9.2846	0.37749	0.1012:0.6313:0.1024:0.1652	rs3212298;rs52792894;rs59241478;rs3212298	326;358	O00592-2;O00592	.;PODXL_HUMAN	I	360;316;358;326	ENSP00000440518:V360I;ENSP00000367817:V358I;ENSP00000319782:V326I	ENSP00000319782:V326I	V	-	1	0	PODXL	130844279	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-3.882000	0.00343	-3.316000	0.00189	-2.940000	0.00087	GTC	C|0.940;T|0.060	0.060	strong		0.522	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
PCNT	5116	hgsc.bcm.edu	37	21	47856053	47856053	+	Silent	SNP	C	C	T	rs61735826	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:47856053C>T	ENST00000359568.5	+	39	9095	c.8988C>T	c.(8986-8988)gcC>gcT	p.A2996A	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2996	Interaction with NEK2.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CCAGCCAGGCCGTGGACAGGT	0.701													C|||	55	0.0109824	0.0008	0.0202	5008	,	,		13256	0.0		0.0278	False		,,,				2504	0.0123				p.A2996A		Atlas-SNP	.											.	PCNT	283	.	0			c.C8988T						PASS	.	C		29,4259		0,29,2115	20.0	19.0	19.0		8988	-11.2	0.0	21	dbSNP_129	19	327,8073		6,315,3879	no	coding-synonymous	PCNT	NM_006031.5		6,344,5994	TT,TC,CC		3.8929,0.6763,2.8058		2996/3337	47856053	356,12332	2144	4200	6344	SO:0001819	synonymous_variant	5116	exon39			CCAGGCCGTGGAC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.8988C>T	21.37:g.47856053C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.974;T|0.026	0.026	strong		0.701	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
ZNF91	7644	hgsc.bcm.edu	37	19	23542697	23542697	+	Silent	SNP	G	G	C	rs1821845	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:23542697G>C	ENST00000300619.7	-	4	3289	c.3084C>G	c.(3082-3084)ggC>ggG	p.G1028G	ZNF91_ENST00000397082.2_Silent_p.G996G|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1028					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TAAAAGCTTTGCCACATTCTT	0.378													G|||	2175	0.434305	0.3956	0.5101	5008	,	,		21416	0.1855		0.6193	False		,,,				2504	0.499				p.G1028G		Atlas-SNP	.											.	ZNF91	349	.	0			c.C3084G						PASS	.	G		1866,2524	481.4+/-359.1	413,1040,742	82.0	84.0	84.0		3084	-2.9	0.4	19	dbSNP_92	84	5189,3399	621.4+/-397.2	1564,2061,669	no	coding-synonymous	ZNF91	NM_003430.2		1977,3101,1411	CC,CG,GG		39.5785,42.5057,45.6388		1028/1192	23542697	7055,5923	2195	4294	6489	SO:0001819	synonymous_variant	7644	exon4			AGCTTTGCCACAT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.3084C>G	19.37:g.23542697G>C		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			G|0.505;C|0.495	0.495	strong		0.378	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
RSPH10B	222967	hgsc.bcm.edu	37	7	6005323	6005323	+	Missense_Mutation	SNP	C	C	T	rs200962894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6005323C>T	ENST00000405415.1	-	3	661	c.275G>A	c.(274-276)cGt>cAt	p.R92H	RSPH10B_ENST00000404406.1_Missense_Mutation_p.R92H|RSPH10B_ENST00000337579.3_Missense_Mutation_p.R92H|RSPH10B_ENST00000441023.2_Missense_Mutation_p.R92H|RSPH10B_ENST00000535104.1_5'Flank			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	92										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		ATACAGCCCACGAACCTTTTC	0.438													C|||	294	0.0587061	0.0166	0.121	5008	,	,		13170	0.0149		0.1362	False		,,,				2504	0.0368				p.R92H		Atlas-SNP	.											RSPH10B,NS,carcinoma,0,2	RSPH10B	28	2	0			c.G275A						scavenged	.						4.0	4.0	4.0					7																	6005323		1653	3655	5308	SO:0001583	missense	222967	exon4			AGCCCACGAACCT		CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026			27362	protein-coding gene	gene with protein product						16507594	Standard	NM_173565		Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.275G>A	7.37:g.6005323C>T	ENSP00000385443:p.Arg92His	Somatic	1034	0	0		WXS	Illumina HiSeq	Phase_I	1248	514	0.411859	NM_173565	A6NMW7|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000405415.1	37	CCDS34598.1	104	0.047619047619047616	9	0.018292682926829267	29	0.08011049723756906	2	0.0034965034965034965	64	0.08443271767810026	C	4.777	0.144454	0.09134	.	.	ENSG00000155026	ENST00000405415;ENST00000404406;ENST00000337579;ENST00000441023	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.73	0.597	0.17504	.	0.588391	0.17861	N	0.159518	T	0.01156	0.0038	N	0.21508	0.67	0.09310	N	1	B	0.26876	0.162	B	0.24394	0.053	T	0.05903	-1.0857	10	0.42905	T	0.14	.	5.1232	0.14871	0.0:0.4291:0.1466:0.4243	.	92	P0C881	R10B1_HUMAN	H	92	ENSP00000385443:R92H;ENSP00000384097:R92H;ENSP00000338556:R92H;ENSP00000400988:R92H	ENSP00000338556:R92H	R	-	2	0	RSPH10B	5971849	0.011000	0.17503	0.159000	0.22649	0.202000	0.24057	0.078000	0.14761	0.040000	0.15660	0.561000	0.74099	CGT	C|0.950;T|0.050	0.050	strong		0.438	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325465.2	NM_173565	
ZNF331	55422	hgsc.bcm.edu	37	19	54080067	54080067	+	Missense_Mutation	SNP	T	T	C	rs61744130	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54080067T>C	ENST00000253144.9	+	7	1586	c.253T>C	c.(253-255)Tgt>Cgt	p.C85R	ZNF331_ENST00000449416.1_Missense_Mutation_p.C85R|ZNF331_ENST00000513999.1_Missense_Mutation_p.C85R|ZNF331_ENST00000411977.2_Missense_Mutation_p.C85R|ZNF331_ENST00000511593.2_Missense_Mutation_p.C85R|ZNF331_ENST00000512387.1_Missense_Mutation_p.C85R|ZNF331_ENST00000511154.1_Missense_Mutation_p.C85R|ZNF331_ENST00000513265.1_Missense_Mutation_p.C85R	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	85					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)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		TAACTGGATATGTGAAGGTAC	0.408			T	?	follicular thyroid adenoma								T|||	320	0.0638978	0.0038	0.0303	5008	,	,		18385	0.0833		0.0596	False		,,,				2504	0.1534				p.C85R		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	.	ZNF331	66	.	0			c.T253C						PASS	.	T	ARG/CYS,ARG/CYS,ARG/CYS	34,4372	39.2+/-71.8	0,34,2169	75.0	77.0	76.0		253,253,253	-0.5	0.0	19	dbSNP_129	76	485,8115	140.5+/-197.0	9,467,3824	yes	missense,missense,missense	ZNF331	NM_001079906.1,NM_001079907.1,NM_018555.5	180,180,180	9,501,5993	CC,CT,TT		5.6395,0.7717,3.9905	possibly-damaging,possibly-damaging,possibly-damaging	85/464,85/464,85/464	54080067	519,12487	2203	4300	6503	SO:0001583	missense	55422	exon5			TGGATATGTGAAG	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"""Zinc fingers, C2H2-type"", ""-"""	15489	protein-coding gene	gene with protein product	"""rearranged in thyroid adenomas"""	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.253T>C	19.37:g.54080067T>C	ENSP00000253144:p.Cys85Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_001253801	Q96GJ4	Missense_Mutation	SNP	ENST00000253144.9	37	CCDS33102.1	107	0.04899267399267399	3	0.006097560975609756	13	0.03591160220994475	56	0.0979020979020979	35	0.04617414248021108	T	3.843	-0.033402	0.07543	0.007717	0.056395	ENSG00000130844	ENST00000253144;ENST00000511593;ENST00000449416;ENST00000514374;ENST00000411977;ENST00000511154;ENST00000509047;ENST00000513999;ENST00000512387;ENST00000511567;ENST00000514022;ENST00000505949;ENST00000513265;ENST00000502616	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.08984	3.23;3.23;3.23;4.99;3.23;3.23;4.71;3.23;3.23;5.04;3.3;3.03;4.98;4.82	3.55	-0.507	0.11985	.	0.236034	0.22113	N	0.064457	T	0.00178	0.0005	L	0.54323	1.7	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.33445	-0.9868	9	0.24483	T	0.36	.	1.1413	0.01766	0.1787:0.1205:0.184:0.5168	rs61744130	85	Q9NQX6	ZN331_HUMAN	R	85	ENSP00000253144:C85R;ENSP00000427439:C85R;ENSP00000393817:C85R;ENSP00000424835:C85R;ENSP00000393336:C85R;ENSP00000421014:C85R;ENSP00000423263:C85R;ENSP00000423156:C85R;ENSP00000421728:C85R;ENSP00000426127:C85R;ENSP00000422471:C85R;ENSP00000427532:C85R;ENSP00000426458:C85R;ENSP00000422586:C85R	ENSP00000253144:C85R	C	+	1	0	ZNF331	58771879	0.000000	0.05858	0.013000	0.15412	0.097000	0.18754	-1.283000	0.02796	-0.235000	0.09767	0.383000	0.25322	TGT	T|0.955;C|0.045	0.045	strong		0.408	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555	
ALDH9A1	223	hgsc.bcm.edu	37	1	165667781	165667781	+	Silent	SNP	T	T	G	rs12408101	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:165667781T>G	ENST00000354775.4	-	1	319	c.15A>C	c.(13-15)gcA>gcC	p.A5A	ALDH9A1_ENST00000461664.1_5'Flank|RP11-466F5.6_ENST00000400982.2_RNA|ALDH9A1_ENST00000538148.1_5'Flank	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	0					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)					CGGCCAGGCCTGCTCGGAGAA	0.721													T|||	594	0.11861	0.0779	0.2176	5008	,	,		11031	0.004		0.2584	False		,,,				2504	0.0777				p.A5A	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											ALDH9A1_ENST00000354775,NS,carcinoma,0,1	ALDH9A1	75	1	0			c.A15C						scavenged	.	T		400,3912		27,346,1783	9.0	13.0	12.0		15	-6.6	0.0	1	dbSNP_120	12	2056,6430		227,1602,2414	yes	coding-synonymous	ALDH9A1	NM_000696.3		254,1948,4197	GG,GT,TT		24.2281,9.2764,19.1905		5/519	165667781	2456,10342	2156	4243	6399	SO:0001819	synonymous_variant	223	exon1			CAGGCCTGCTCGG	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.15A>C	1.37:g.165667781T>G		Somatic	62	1	0.016129		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Silent	SNP	ENST00000354775.4	37	CCDS1250.2																																																																																			T|0.850;G|0.150	0.150	strong		0.721	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
CYP4Z1	199974	hgsc.bcm.edu	37	1	47571902	47571902	+	Silent	SNP	C	C	T	rs4926802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47571902C>T	ENST00000334194.3	+	9	1173	c.1170C>T	c.(1168-1170)atC>atT	p.I390I	CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	390						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						ACAAACCCATCACCTTTCCAG	0.443													T|||	2953	0.589657	0.5121	0.4683	5008	,	,		17743	0.9563		0.34	False		,,,				2504	0.6595				p.I390I		Atlas-SNP	.											.	CYP4Z1	43	.	0			c.C1170T						PASS	.	T		2180,2226	582.0+/-385.5	552,1076,575	95.0	88.0	91.0		1170	-6.5	0.4	1	dbSNP_111	91	2807,5793	670.8+/-402.8	419,1969,1912	no	coding-synonymous	CYP4Z1	NM_178134.2		971,3045,2487	TT,TC,CC		32.6395,49.478,38.3438		390/506	47571902	4987,8019	2203	4300	6503	SO:0001819	synonymous_variant	199974	exon9			ACCCATCACCTTT	AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"""Cytochrome P450s"""	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.1170C>T	1.37:g.47571902C>T		Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	284	111	0.390845	NM_178134	Q5VVE4	Silent	SNP	ENST00000334194.3	37	CCDS545.1																																																																																			.	.	weak		0.443	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134	
PLXNA2	5362	hgsc.bcm.edu	37	1	208391085	208391085	+	Silent	SNP	G	G	A	rs12120681	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:208391085G>A	ENST00000367033.3	-	2	940	c.183C>T	c.(181-183)gcC>gcT	p.A61A		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	61	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CCACATAGACGGCCCCCGTCC	0.582													G|||	413	0.0824681	0.0129	0.1412	5008	,	,		18311	0.0159		0.159	False		,,,				2504	0.1247				p.A61A		Atlas-SNP	.											PLXNA2,colon,carcinoma,-1,1	PLXNA2	178	1	0			c.C183T						PASS	.	G		197,4209	122.9+/-160.3	6,185,2012	105.0	101.0	102.0		183	-11.7	0.1	1	dbSNP_120	102	1434,7166	275.4+/-291.8	120,1194,2986	no	coding-synonymous	PLXNA2	NM_025179.3		126,1379,4998	AA,AG,GG		16.6744,4.4712,12.5404		61/1895	208391085	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon2			ATAGACGGCCCCC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.183C>T	1.37:g.208391085G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	171	90	0.526316	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			G|0.894;A|0.106	0.106	strong		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
PCDHB7	56129	hgsc.bcm.edu	37	5	140552585	140552585	+	Missense_Mutation	SNP	G	G	C	rs28470552	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140552585G>C	ENST00000231137.3	+	1	343	c.169G>C	c.(169-171)Ggg>Cgg	p.G57R		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	57	Cadherin 1. {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(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTTAGGGGTAGGGGAACTGAG	0.488													G|||	320	0.0638978	0.202	0.0461	5008	,	,		17212	0.0		0.0169	False		,,,				2504	0.0041				p.G57R		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G169C						PASS	.	G	ARG/GLY	783,3623	316.9+/-294.8	78,627,1498	83.0	86.0	85.0		169	4.6	0.3	5	dbSNP_125	85	154,8446	74.5+/-137.1	0,154,4146	yes	missense	PCDHB7	NM_018940.2	125	78,781,5644	CC,CG,GG		1.7907,17.7712,7.2044	benign	57/794	140552585	937,12069	2203	4300	6503	SO:0001583	missense	56129	exon1			GGGGTAGGGGAAC	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.169G>C	5.37:g.140552585G>C	ENSP00000231137:p.Gly57Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	133	0.060897435897435896	102	0.2073170731707317	18	0.049723756906077346	0	0.0	13	0.017150395778364115	G	1.972	-0.436342	0.04636	0.177712	0.017907	ENSG00000113212	ENST00000231137	T	0.26660	1.72	4.55	4.55	0.56014	Cadherin, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.25992	0.78	0.80722	P	0.0	B	0.12630	0.006	B	0.21151	0.033	T	0.13845	-1.0494	8	0.05721	T	0.95	.	17.2648	0.87083	0.0:0.0:1.0:0.0	rs28470552	57	Q9Y5E2	PCDB7_HUMAN	R	57	ENSP00000231137:G57R	ENSP00000231137:G57R	G	+	1	0	PCDHB7	140532769	0.000000	0.05858	0.253000	0.24343	0.233000	0.25261	0.046000	0.14035	2.212000	0.71576	0.655000	0.94253	GGG	G|0.929;C|0.071	0.071	strong		0.488	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
POM121L12	285877	hgsc.bcm.edu	37	7	53103946	53103946	+	Silent	SNP	G	G	C	rs12113170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:53103946G>C	ENST00000408890.4	+	1	598	c.582G>C	c.(580-582)ggG>ggC	p.G194G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	194										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GGTTCGACGGGCCGTTGTGGT	0.682													G|||	1647	0.328874	0.1725	0.4308	5008	,	,		12550	0.3026		0.4871	False		,,,				2504	0.3323				p.G194G		Atlas-SNP	.											.	POM121L12	146	.	0			c.G582C						PASS	.	G		802,3142		90,622,1260	48.0	55.0	53.0		582	-4.4	0.0	7	dbSNP_120	53	4189,4093		1054,2081,1006	no	coding-synonymous	POM121L12	NM_182595.3		1144,2703,2266	CC,CG,GG		49.4204,20.3347,40.8228		194/297	53103946	4991,7235	1972	4141	6113	SO:0001819	synonymous_variant	285877	exon1			CGACGGGCCGTTG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.582G>C	7.37:g.53103946G>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.631;C|0.369	0.369	strong		0.682	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
TGS1	96764	hgsc.bcm.edu	37	8	56723557	56723557	+	Missense_Mutation	SNP	T	T	G	rs7823773	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:56723557T>G	ENST00000260129.5	+	11	2738	c.2261T>G	c.(2260-2262)tTt>tGt	p.F754C		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	754	Sufficient for catalytic activity.		F -> C (in dbSNP:rs7823773).		7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CTGGCTTCTTTTTTAAAGGCT	0.453													G|||	720	0.14377	0.2784	0.121	5008	,	,		15559	0.0099		0.1103	False		,,,				2504	0.1503				p.F754C	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.T2261G						PASS	.	G	CYS/PHE	1144,3262	715.1+/-408.4	159,826,1218	182.0	182.0	182.0		2261	-8.0	0.0	8	dbSNP_116	182	925,7675	776.8+/-407.7	48,829,3423	yes	missense	TGS1	NM_024831.6	205	207,1655,4641	GG,GT,TT		10.7558,25.9646,15.908	benign	754/854	56723557	2069,10937	2203	4300	6503	SO:0001583	missense	96764	exon11			CTTCTTTTTTAAA	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.2261T>G	8.37:g.56723557T>G	ENSP00000260129:p.Phe754Cys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	281	0.12866300366300365	153	0.31097560975609756	43	0.11878453038674033	0	0.0	85	0.11213720316622691	G	11.16	1.557800	0.27827	0.259646	0.107558	ENSG00000137574	ENST00000260129	T	0.43294	0.95	5.47	-7.97	0.01139	.	0.692844	0.14897	N	0.292059	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21690	-1.0238	9	0.51188	T	0.08	4.4542	5.7511	0.18148	0.3023:0.1505:0.4721:0.075	rs7823773;rs52793536;rs7823773	754	Q96RS0	TGS1_HUMAN	C	754	ENSP00000260129:F754C	ENSP00000260129:F754C	F	+	2	0	TGS1	56886111	0.000000	0.05858	0.000000	0.03702	0.929000	0.56500	0.021000	0.13489	-2.030000	0.00929	-0.121000	0.15023	TTT	T|0.844;G|0.156	0.156	strong		0.453	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
NUP210	23225	hgsc.bcm.edu	37	3	13383540	13383540	+	Silent	SNP	A	A	G	rs2271504	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:13383540A>G	ENST00000254508.5	-	22	3130	c.3048T>C	c.(3046-3048)ttT>ttC	p.F1016F	NUP210_ENST00000485755.1_5'Flank	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1016					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TCAGGTCCATAAAGGGGAAGT	0.557													G|||	2888	0.576677	0.9017	0.4467	5008	,	,		20666	0.4008		0.5457	False		,,,				2504	0.4427				p.F1016F		Atlas-SNP	.											.	NUP210	182	.	0			c.T3048C						PASS	.	G		3685,721	298.1+/-285.1	1538,609,56	106.0	105.0	106.0		3048	2.9	1.0	3	dbSNP_100	106	4859,3741	533.1+/-382.3	1373,2113,814	no	coding-synonymous	NUP210	NM_024923.2		2911,2722,870	GG,GA,AA		43.5,16.364,34.3072		1016/1888	13383540	8544,4462	2203	4300	6503	SO:0001819	synonymous_variant	23225	exon22			GTCCATAAAGGGG	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.3048T>C	3.37:g.13383540A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1																																																																																			A|0.369;G|0.631	0.631	strong		0.557	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
IKBKAP	8518	hgsc.bcm.edu	37	9	111663754	111663754	+	Silent	SNP	G	G	A	rs2230791	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:111663754G>A	ENST00000374647.5	-	18	2272	c.1965C>T	c.(1963-1965)acC>acT	p.T655T	IKBKAP_ENST00000537196.1_Silent_p.T306T	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	655					chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						TATGGGAATGGGTTGTCAACA	0.403													G|||	393	0.0784744	0.1755	0.0346	5008	,	,		18415	0.0		0.0885	False		,,,				2504	0.0491				p.T655T		Atlas-SNP	.											.	IKBKAP	122	.	0			c.C1965T						PASS	.	G		664,3742	281.4+/-275.9	50,564,1589	94.0	82.0	86.0		1965	3.1	1.0	9	dbSNP_98	86	685,7915	170.9+/-221.9	28,629,3643	no	coding-synonymous	IKBKAP	NM_003640.3		78,1193,5232	AA,AG,GG		7.9651,15.0704,10.3721		655/1333	111663754	1349,11657	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon18			GGAATGGGTTGTC	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.1965C>T	9.37:g.111663754G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	98	32	0.326531	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			G|0.775;T|0.018	.	strong		0.403	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
PRIMA1	145270	hgsc.bcm.edu	37	14	94245652	94245652	+	Silent	SNP	C	C	T	rs4900195	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94245652C>T	ENST00000393140.1	-	3	201	c.99G>A	c.(97-99)acG>acA	p.T33T	PRIMA1_ENST00000393143.1_Silent_p.T33T|PRIMA1_ENST00000316227.3_Silent_p.T33T	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	33					establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202)				endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		GCTCACCATGCGTCACCTGTA	0.647													C|||	1818	0.363019	0.3949	0.3573	5008	,	,		9432	0.2302		0.4692	False		,,,				2504	0.3517				p.T33T		Atlas-SNP	.											PRIMA1,rectum,carcinoma,0,1	PRIMA1	21	1	0			c.G99A						PASS	.	C		1764,2638		367,1030,804	40.0	34.0	36.0		99	-8.8	0.2	14	dbSNP_111	36	4098,4500		978,2142,1179	no	coding-synonymous	PRIMA1	NM_178013.3		1345,3172,1983	TT,TC,CC		47.6622,40.0727,45.0923		33/154	94245652	5862,7138	2201	4299	6500	SO:0001819	synonymous_variant	145270	exon3			ACCATGCGTCACC		CCDS9912.1	14q32.13	2008-08-29			ENSG00000175785	ENSG00000175785			18319	protein-coding gene	gene with protein product	"""membrane anchor of acetylcholinesterase"""	613851				11804574	Standard	NM_178013		Approved	PRIMA	uc001ybw.1	Q86XR5	OTTHUMG00000141313	ENST00000393140.1:c.99G>A	14.37:g.94245652C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	29	28	0.965517	NM_178013	Q86XR6	Silent	SNP	ENST00000393140.1	37	CCDS9912.1																																																																																			C|0.579;T|0.421	0.421	strong		0.647	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013	
CLSTN3	9746	hgsc.bcm.edu	37	12	7288432	7288432	+	Missense_Mutation	SNP	A	A	G	rs7302230	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:7288432A>G	ENST00000266546.6	+	5	1075	c.625A>G	c.(625-627)Agt>Ggt	p.S209G	CLSTN3_ENST00000537408.1_Missense_Mutation_p.S221G	NM_014718.3	NP_055533.2	Q9BQT9	CSTN3_HUMAN	calsyntenin 3	209	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> G (in dbSNP:rs7302230).		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(7)|prostate(1)|skin(1)	33						GCTGCAGTACAGTGGTGAGAG	0.542													A|||	92	0.0183706	0.0129	0.0274	5008	,	,		-128	0.0		0.0487	False		,,,				2504	0.0072				p.S209G		Atlas-SNP	.											.	CLSTN3	84	.	0			c.A625G						PASS	.	A	GLY/SER	81,4325	70.9+/-108.8	0,81,2122	127.0	115.0	120.0		625	4.9	1.0	12	dbSNP_116	120	493,8107	142.0+/-198.3	14,465,3821	yes	missense	CLSTN3	NM_014718.3	56	14,546,5943	GG,GA,AA		5.7326,1.8384,4.4133	benign	209/957	7288432	574,12432	2203	4300	6503	SO:0001583	missense	9746	exon5			CAGTACAGTGGTG	AB018269	CCDS8575.1	12p13.31	2011-07-01			ENSG00000139182	ENSG00000139182		"""Cadherins / Cadherin-related"""	18371	protein-coding gene	gene with protein product	"""cadherin-related family member 14"""	611324				12498782	Standard	NM_014718		Approved	CSTN3, KIAA0726, CDHR14	uc001qsr.3	Q9BQT9	OTTHUMG00000168167	ENST00000266546.6:c.625A>G	12.37:g.7288432A>G	ENSP00000266546:p.Ser209Gly	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_014718	D3DUT6|O94831|Q2T9J5|Q5UE57	Missense_Mutation	SNP	ENST00000266546.6	37	CCDS8575.1	54	0.024725274725274724	3	0.006097560975609756	12	0.03314917127071823	0	0.0	39	0.051451187335092345	A	9.377	1.071908	0.20147	0.018384	0.057326	ENSG00000139182	ENST00000266546;ENST00000537408	T;T	0.61627	0.09;0.09	4.89	4.89	0.63831	Cadherin (5);Cadherin-like (1);	0.128222	0.64402	D	0.000001	T	0.04048	0.0113	N	0.02802	-0.49	0.47698	D	0.999499	B;B	0.25667	0.131;0.0	B;B	0.19946	0.027;0.004	T	0.03981	-1.0987	10	0.21540	T	0.41	-19.9128	14.68	0.69009	1.0:0.0:0.0:0.0	rs7302230;rs17727152;rs52802010;rs60504550;rs7302230	221;209	Q5UE57;Q9BQT9	.;CSTN3_HUMAN	G	209;221	ENSP00000266546:S209G;ENSP00000440679:S221G	ENSP00000266546:S209G	S	+	1	0	CLSTN3	7179699	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	4.915000	0.63355	2.053000	0.61076	0.379000	0.24179	AGT	A|0.964;G|0.036	0.036	strong		0.542	CLSTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398560.2	NM_014718	
CAMTA2	23125	hgsc.bcm.edu	37	17	4875628	4875628	+	Missense_Mutation	SNP	A	A	G	rs16942615	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4875628A>G	ENST00000348066.3	-	16	2830	c.2707T>C	c.(2707-2709)Tcc>Ccc	p.S903P	CAMTA2_ENST00000572543.1_Missense_Mutation_p.S908P|CAMTA2_ENST00000361571.5_Missense_Mutation_p.S902P|CAMTA2_ENST00000381311.5_Missense_Mutation_p.S905P|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000358183.4_Missense_Mutation_p.S903P|CAMTA2_ENST00000414043.3_Missense_Mutation_p.S926P	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	903			S -> P (in dbSNP:rs16942615). {ECO:0000269|PubMed:10048485, ECO:0000269|PubMed:17974005}.		cardiac muscle hypertrophy in response to stress (GO:0014898)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						GGCCCCTTGGAGTTGGTAGCC	0.617													A|||	457	0.091254	0.1316	0.1326	5008	,	,		16538	0.0486		0.0835	False		,,,				2504	0.0593				p.S926P		Atlas-SNP	.											.	CAMTA2	93	.	0			c.T2776C						PASS	.	A	PRO/SER,PRO/SER,PRO/SER,PRO/SER	521,3885	219.7+/-237.4	33,455,1715	53.0	56.0	55.0		2713,2776,2704,2707	0.4	0.9	17	dbSNP_123	55	639,7961	157.9+/-211.5	28,583,3689	yes	missense,missense,missense,missense	CAMTA2	NM_001171166.1,NM_001171167.1,NM_001171168.1,NM_015099.3	74,74,74,74	61,1038,5404	GG,GA,AA		7.4302,11.8248,8.919	benign,benign,benign,benign	905/1198,926/1242,902/1202,903/1203	4875628	1160,11846	2203	4300	6503	SO:0001583	missense	23125	exon16			CCTTGGAGTTGGT	AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.2707T>C	17.37:g.4875628A>G	ENSP00000321813:p.Ser903Pro	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Missense_Mutation	SNP	ENST00000348066.3	37	CCDS11063.1	178	0.0815018315018315	52	0.10569105691056911	38	0.10497237569060773	28	0.04895104895104895	60	0.079155672823219	A	4.219	0.039495	0.08148	0.118248	0.074302	ENSG00000108509	ENST00000414043;ENST00000381311;ENST00000361571;ENST00000358183;ENST00000348066	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.88	0.446	0.16602	.	0.613098	0.16082	N	0.230460	T	0.00271	0.0008	N	0.04508	-0.205	0.32188	P	0.579502	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.22034	-1.0228	9	0.07325	T	0.83	-0.052	7.9089	0.29778	0.4473:0.0:0.5527:0.0	rs16942615;rs60587346;rs16942615	879;926;905;903;902	B7ZM30;E7EWU5;O94983-3;O94983;O94983-4	.;.;.;CMTA2_HUMAN;.	P	926;905;902;903;903	ENSP00000412886:S926P;ENSP00000370712:S905P;ENSP00000354828:S902P;ENSP00000350910:S903P;ENSP00000321813:S903P	ENSP00000321813:S903P	S	-	1	0	CAMTA2	4816352	0.519000	0.26242	0.934000	0.37439	0.010000	0.07245	-0.137000	0.10389	-0.104000	0.12154	-0.462000	0.05337	TCC	A|0.914;G|0.086	0.086	strong		0.617	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
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 GAIIx	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	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	29	16	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	
RPS20	6224	hgsc.bcm.edu	37	8	56985814	56985814	+	Silent	SNP	T	T	C	rs1050403	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:56985814T>C	ENST00000521262.1	-	4	448	c.195A>G	c.(193-195)acA>acG	p.T65T	RPS20_ENST00000519606.1_Missense_Mutation_p.K41E|RPS20_ENST00000520490.1_5'UTR|RPS20_ENST00000524349.1_Silent_p.T10T|RPS20_ENST00000520627.1_Silent_p.T10T|RPS20_ENST00000523936.1_3'UTR|RPS20_ENST00000009589.3_Silent_p.T65T|CTA-397H3.3_ENST00000521403.1_RNA|SNORD54_ENST00000459159.1_RNA|RPS20_ENST00000519807.1_Silent_p.T65T			P60866	RS20_HUMAN	ribosomal protein S20	65					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)						all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.155)	Epithelial(17;0.00117)|all cancers(17;0.00879)			GAGTTTTTCTTGTAGTGATTC	0.373													T|||	446	0.0890575	0.0234	0.1571	5008	,	,		21606	0.002		0.2266	False		,,,				2504	0.0777				p.T65T		Atlas-SNP	.											.	RPS20	16	.	0			c.A195G						PASS	.	T	,	201,3951		4,193,1879	83.0	87.0	86.0		195,195	-10.2	0.8	8	dbSNP_86	86	1752,6150		194,1364,2393	no	coding-synonymous,coding-synonymous	RPS20	NM_001023.3,NM_001146227.1	,	198,1557,4272	CC,CT,TT		22.1716,4.841,16.2021	,	65/120,65/143	56985814	1953,10101	2076	3951	6027	SO:0001819	synonymous_variant	6224	exon4			TTTTCTTGTAGTG	L06498	CCDS6163.1, CCDS55231.1	8q12.1	2011-04-05				ENSG00000008988		"""S ribosomal proteins"""	10405	protein-coding gene	gene with protein product		603682				9582194, 8479924	Standard	NM_001023		Approved	S20	uc003xsm.2	P60866		ENST00000521262.1:c.195A>G	8.37:g.56985814T>C		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_001146227	B2R4F4|B4DW28|P17075|Q5M8S9	Silent	SNP	ENST00000521262.1	37		241	0.11034798534798534	13	0.026422764227642278	69	0.19060773480662985	0	0.0	159	0.20976253298153033	T	11.86	1.764707	0.31228	0.04841	0.221716	ENSG00000008988	ENST00000519606	.	.	.	5.1	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.25984	-1.0116	4	0.87932	D	0	-25.2257	3.7165	0.08439	0.0927:0.2245:0.3814:0.3015	rs2976047;rs2976047	.	.	.	E	41	.	ENSP00000429333:K41E	K	-	1	0	RPS20	57148368	0.016000	0.18221	0.787000	0.31911	0.702000	0.40608	-0.858000	0.04281	-1.780000	0.01279	0.482000	0.46254	AAG	T|0.863;C|0.137	0.137	strong		0.373	RPS20-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378166.1	NM_001023	
LEFTY1	10637	hgsc.bcm.edu	37	1	226074563	226074563	+	Missense_Mutation	SNP	T	T	G	rs360057	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226074563T>G	ENST00000272134.5	-	4	1044	c.965A>C	c.(964-966)gAc>gCc	p.D322A	RP4-559A3.7_ENST00000432920.2_3'UTR|LEFTY1_ENST00000492457.1_5'Flank	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	322			D -> A (in dbSNP:rs360057).		cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					GGGCAGCGAGTCAGTCTCCGA	0.652													t|||	1276	0.254792	0.1407	0.3415	5008	,	,		16775	0.2073		0.3946	False		,,,				2504	0.2526				p.D322A		Atlas-SNP	.											LEFTY1,colon,carcinoma,0,1	LEFTY1	30	1	0			c.A965C						PASS	.	T	ALA/ASP	817,3589	308.8+/-290.8	69,679,1455	40.0	36.0	37.0		965	2.1	0.0	1	dbSNP_79	37	3097,5503	450.7+/-362.5	545,2007,1748	yes	missense	LEFTY1	NM_020997.3	126	614,2686,3203	GG,GT,TT		36.0116,18.5429,30.0938	benign	322/367	226074563	3914,9092	2203	4300	6503	SO:0001583	missense	10637	exon4			AGCGAGTCAGTCT	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"""left-right determination, factor B"""	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.965A>C	1.37:g.226074563T>G	ENSP00000272134:p.Asp322Ala	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	160	84	0.525	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	638	0.29212454212454214	76	0.15447154471544716	131	0.36187845303867405	122	0.21328671328671328	309	0.4076517150395778	t	0.011	-1.720453	0.00700	0.185429	0.360116	ENSG00000243709	ENST00000272134	T	0.70282	-0.47	4.14	2.09	0.27110	Transforming growth factor-beta, C-terminal (2);	0.418705	0.28146	N	0.016436	T	0.00012	0.0000	N	0.00554	-1.385	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.38714	-0.9648	9	0.21540	T	0.41	.	9.6529	0.39908	0.0:0.1533:0.6867:0.1599	rs360057	322	O75610	LFTY1_HUMAN	A	322	ENSP00000272134:D322A	ENSP00000272134:D322A	D	-	2	0	LEFTY1	224141186	1.000000	0.71417	0.011000	0.14972	0.063000	0.16089	5.788000	0.69020	0.753000	0.32945	-0.672000	0.03802	GAC	T|0.711;G|0.289	0.289	strong		0.652	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
SDHA	6389	hgsc.bcm.edu	37	5	256455	256455	+	Missense_Mutation	SNP	C	C	G	rs1126697		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:256455C>G	ENST00000264932.6	+	15	2030	c.1915C>G	c.(1915-1917)Ctg>Gtg	p.L639V	SDHA_ENST00000504309.1_Missense_Mutation_p.L558V|SDHA_ENST00000510361.1_Missense_Mutation_p.L591V|SDHA_ENST00000507522.1_Intron	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	639					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	CAAGGTCACTCTGGAATATAG	0.418									Familial Paragangliomas																												p.L639V		Atlas-SNP	.											SDHA,NS,adenocarcinoma,0,1	SDHA	80	1	0			c.C1915G						scavenged	.						92.0	103.0	99.0					5																	256455		2203	4300	6503	SO:0001583	missense	6389	exon15	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	GTCACTCTGGAAT	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1915C>G	5.37:g.256455C>G	ENSP00000264932:p.Leu639Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	2	0.0238095	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	4.275|4.275	0.050102|0.050102	0.08243|0.08243	.|.	.|.	ENSG00000073578|ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361|ENST00000515815	D;D;D|.	0.82344|.	-1.6;-1.6;-1.6|.	4.12|4.12	-1.06|-1.06	0.10002|0.10002	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (1);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);|.	0.000000|.	0.64402|.	U|.	0.000014|.	T|T	0.53899|0.53899	0.1825|0.1825	L|L	0.50333|0.50333	1.59|1.59	0.50467|0.50467	D|D	0.999871|0.999871	B;B;D;B|.	0.57257|.	0.432;0.049;0.979;0.072|.	B;B;D;B|.	0.71414|.	0.344;0.085;0.973;0.063|.	T|T	0.47799|0.47799	-0.9089|-0.9089	10|5	0.72032|.	D|.	0.01|.	.|.	7.982|7.982	0.30190|0.30190	0.0:0.2524:0.0:0.7476|0.0:0.2524:0.0:0.7476	rs1126697;rs3181866;rs17414511|rs1126697;rs3181866;rs17414511	591;233;558;639|.	E9PBJ5;B3KYA5;D6RFM5;P31040|.	.;.;.;DHSA_HUMAN|.	V|C	639;494;558;591|121	ENSP00000264932:L639V;ENSP00000426514:L558V;ENSP00000427703:L591V|.	ENSP00000264932:L639V|.	L|S	+|+	1|2	2|0	SDHA|SDHA	309455|309455	0.152000|0.152000	0.22762|0.22762	0.492000|0.492000	0.27490|0.27490	0.237000|0.237000	0.25408|0.25408	0.546000|0.546000	0.23284|0.23284	-0.096000|-0.096000	0.12329|0.12329	-0.680000|-0.680000	0.03767|0.03767	CTG|TCT	C|0.998;G|0.002	0.002	weak		0.418	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
NBPF3	84224	hgsc.bcm.edu	37	1	21808159	21808159	+	Silent	SNP	G	G	A	rs71512991	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:21808159G>A	ENST00000318249.5	+	13	1853	c.1503G>A	c.(1501-1503)tcG>tcA	p.S501S	NBPF3_ENST00000342104.5_Silent_p.S489S|NBPF3_ENST00000318220.6_Silent_p.S445S|NBPF3_ENST00000454000.2_Silent_p.S431S	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	501	NBPF 4. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GATGGTATTCGACTCCTTTCA	0.478													.|||	2339	0.467053	0.3192	0.4827	5008	,	,		23166	0.4871		0.495	False		,,,				2504	0.6063				p.P501P		Atlas-SNP	.											NBPF3,NS,carcinoma,+1,1	NBPF3	55	1	0			c.A1503A						scavenged	.						36.0	41.0	39.0					1																	21808159		2182	4262	6444	SO:0001819	synonymous_variant	84224	exon13			GTATTCGACTCCT	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.1503G>A	1.37:g.21808159G>A		Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	165	94	0.569697	NM_032264	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Silent	SNP	ENST00000318249.5	37	CCDS216.1																																																																																			G|0.500;A|0.500	0.500	weak		0.478	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
EMILIN3	90187	hgsc.bcm.edu	37	20	39990614	39990614	+	Missense_Mutation	SNP	C	C	T	rs2235592	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:39990614C>T	ENST00000332312.3	-	4	1787	c.1595G>A	c.(1594-1596)aGc>aAc	p.S532N		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	532			S -> N (in dbSNP:rs2235592). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				TGCCACGAGGCTGTCCAGGAT	0.647													T|||	1418	0.283147	0.3139	0.3012	5008	,	,		18066	0.4772		0.2127	False		,,,				2504	0.1012				p.S532N		Atlas-SNP	.											.	EMILIN3	63	.	0			c.G1595A						PASS	.	T	ASN/SER	1419,2987	678.0+/-403.5	227,965,1011	58.0	59.0	58.0		1595	0.3	1.0	20	dbSNP_98	58	1628,6970	736.7+/-407.0	165,1298,2836	yes	missense	EMILIN3	NM_052846.1	46	392,2263,3847	TT,TC,CC		18.9346,32.2061,23.4313	benign	532/767	39990614	3047,9957	2203	4299	6502	SO:0001583	missense	90187	exon4			ACGAGGCTGTCCA	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1595G>A	20.37:g.39990614C>T	ENSP00000332806:p.Ser532Asn	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Missense_Mutation	SNP	ENST00000332312.3	37	CCDS13316.1	687	0.31456043956043955	143	0.29065040650406504	99	0.27348066298342544	274	0.479020979020979	171	0.22559366754617413	T	0.015	-1.566276	0.00903	0.322061	0.189346	ENSG00000183798	ENST00000332312	T	0.13778	2.56	4.56	0.312	0.15837	.	0.972341	0.08500	N	0.936658	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44892	-0.9298	8	.	.	.	-6.6365	2.2658	0.04078	0.1108:0.2638:0.3711:0.2543	rs2235592	532	Q9NT22	EMIL3_HUMAN	N	532	ENSP00000332806:S532N	.	S	-	2	0	EMILIN3	39424028	0.054000	0.20591	0.964000	0.40570	0.647000	0.38526	-0.098000	0.11024	-0.055000	0.13244	-0.361000	0.07541	AGC	C|0.743;T|0.257	0.257	strong		0.647	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
PLXNA4	91584	hgsc.bcm.edu	37	7	132192949	132192949	+	Silent	SNP	T	T	C	rs156962	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:132192949T>C	ENST00000359827.3	-	2	1466	c.504A>G	c.(502-504)tcA>tcG	p.S168S	PLXNA4_ENST00000378539.5_Silent_p.S168S|PLXNA4_ENST00000423507.2_Silent_p.S168S|PLXNA4_ENST00000321063.4_Silent_p.S168S			Q9HCM2	PLXA4_HUMAN	plexin A4	168	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.S168S(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CTCCAAAGACTGAGCCGCTCT	0.542													C|||	1970	0.393371	0.5159	0.3588	5008	,	,		19381	0.2718		0.3917	False		,,,				2504	0.3793				p.S168S		Atlas-SNP	.											PLXNA4_ENST00000359827,NS,carcinoma,0,2	PLXNA4	873	2	2	Substitution - coding silent(2)	stomach(2)	c.A504G						PASS	.	C	,,	2117,2289	600.1+/-389.4	512,1093,598	110.0	98.0	102.0		504,504,504	-10.5	0.1	7	dbSNP_79	102	3346,5254	642.8+/-399.9	639,2068,1593	no	coding-synonymous,coding-synonymous,coding-synonymous	PLXNA4	NM_001105543.1,NM_020911.1,NM_181775.3	,,	1151,3161,2191	CC,CT,TT		38.907,48.0481,42.0037	,,	168/493,168/1895,168/523	132192949	5463,7543	2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			AAAGACTGAGCCG	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.504A>G	7.37:g.132192949T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			T|0.598;C|0.402	0.402	strong		0.542	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
C2CD3	26005	hgsc.bcm.edu	37	11	73785326	73785326	+	Silent	SNP	T	T	C	rs4453265	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:73785326T>C	ENST00000334126.7	-	24	5149	c.4923A>G	c.(4921-4923)gtA>gtG	p.V1641V	C2CD3_ENST00000313663.7_Silent_p.V1641V			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1641	C2 2.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TTGCTCTTTCTACTAGGATGC	0.532													T|||	2259	0.451078	0.4312	0.4798	5008	,	,		20957	0.4425		0.4692	False		,,,				2504	0.4479				p.V1641V		Atlas-SNP	.											.	C2CD3	288	.	0			c.A4923G						PASS	.	T		1833,2567	534.0+/-373.9	369,1095,736	106.0	89.0	95.0		4923	1.6	1.0	11	dbSNP_111	95	4033,4553	555.8+/-386.7	982,2069,1242	yes	coding-synonymous	C2CD3	NM_015531.4		1351,3164,1978	CC,CT,TT		46.9718,41.6591,45.1717		1641/1964	73785326	5866,7120	2200	4293	6493	SO:0001819	synonymous_variant	26005	exon24			TCTTTCTACTAGG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4923A>G	11.37:g.73785326T>C		Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Silent	SNP	ENST00000334126.7	37																																																																																				T|0.543;C|0.457	0.457	strong		0.532	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
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 GAIIx	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		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	38	3	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		
SAMD10	140700	hgsc.bcm.edu	37	20	62607160	62607160	+	Silent	SNP	C	C	T	rs817343	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62607160C>T	ENST00000369886.3	-	4	645	c.471G>A	c.(469-471)gcG>gcA	p.A157A	SAMD10_ENST00000498830.1_5'UTR|ZNF512B_ENST00000217130.3_Intron|ZNF512B_ENST00000450537.1_Intron	NM_080621.4	NP_542188.1	Q9BYL1	SAM10_HUMAN	sterile alpha motif domain containing 10	157	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	7	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GCAGCTTCTCCGCATTCAGCC	0.682													C|||	1301	0.259784	0.469	0.17	5008	,	,		18212	0.0456		0.1769	False		,,,				2504	0.3466				p.A157A		Atlas-SNP	.											SAMD10,rectum,carcinoma,0,2	SAMD10	16	2	0			c.G471A						PASS	.	C		1825,2553		410,1005,774	15.0	18.0	17.0		471	-6.0	0.8	20	dbSNP_86	17	1455,7105		123,1209,2948	no	coding-synonymous	SAMD10	NM_080621.4		533,2214,3722	TT,TC,CC		16.9977,41.6857,25.3517		157/203	62607160	3280,9658	2189	4280	6469	SO:0001819	synonymous_variant	140700	exon4			CTTCTCCGCATTC		CCDS13549.1	20q13.33	2013-01-10	2004-07-15	2004-07-16	ENSG00000130590	ENSG00000130590		"""Sterile alpha motif (SAM) domain containing"""	16129	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 136"""	C20orf136			Standard	NM_080621		Approved		uc002yhm.2	Q9BYL1	OTTHUMG00000033011	ENST00000369886.3:c.471G>A	20.37:g.62607160C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	39	15	0.384615	NM_080621		Silent	SNP	ENST00000369886.3	37	CCDS13549.1																																																																																			C|0.770;T|0.230	0.230	strong		0.682	SAMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080255.1	NM_080621	
AZU1	566	hgsc.bcm.edu	37	19	830820	830820	+	Missense_Mutation	SNP	G	G	A	rs28626600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:830820G>A	ENST00000233997.2	+	4	494	c.473G>A	c.(472-474)cGc>cAc	p.R158H		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	158	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		GGGAGCCAGCGCAGTGGGGGG	0.657													G|||	285	0.0569089	0.0045	0.0576	5008	,	,		15019	0.0079		0.1223	False		,,,				2504	0.1104				p.R158H		Atlas-SNP	.											AZU1,rectum,carcinoma,0,2	AZU1	31	2	0			c.G473A						PASS	.	G	HIS/ARG	73,4331	58.7+/-95.3	1,71,2130	29.0	28.0	29.0		473	-0.8	0.0	19	dbSNP_125	29	869,7731	189.1+/-236.0	48,773,3479	yes	missense	AZU1	NM_001700.3	29	49,844,5609	AA,AG,GG		10.1047,1.6576,7.2439	probably-damaging	158/252	830820	942,12062	2202	4300	6502	SO:0001583	missense	566	exon4			GCCAGCGCAGTGG	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.473G>A	19.37:g.830820G>A	ENSP00000233997:p.Arg158His	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	26	16	0.615385	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Missense_Mutation	SNP	ENST00000233997.2	37	CCDS12044.1	124	0.056776556776556776	2	0.0040650406504065045	26	0.0718232044198895	3	0.005244755244755245	93	0.12269129287598944	G	10.53	1.374773	0.24857	0.016576	0.101047	ENSG00000172232	ENST00000334630;ENST00000233997	D	0.88896	-2.44	1.51	-0.763	0.11030	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.04048	0.0113	N	0.16307	0.4	0.09310	N	1	D	0.65815	0.995	B	0.43950	0.437	T	0.40850	-0.9541	9	0.42905	T	0.14	.	3.9576	0.09396	0.4496:0.0:0.5504:0.0	rs28626600	158	P20160	CAP7_HUMAN	H	172;158	ENSP00000233997:R158H	ENSP00000233997:R158H	R	+	2	0	AZU1	781820	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.143000	0.16115	-0.178000	0.10672	-0.258000	0.10820	CGC	G|0.933;A|0.067	0.067	strong		0.657	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
LRP1B	53353	hgsc.bcm.edu	37	2	141457985	141457985	+	Silent	SNP	T	T	A	rs13431727	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:141457985T>A	ENST00000389484.3	-	41	7604	c.6633A>T	c.(6631-6633)ccA>ccT	p.P2211P		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2211					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATGGCCTTATTGGGGAATTTA	0.348										TSP Lung(27;0.18)			T|||	1227	0.245008	0.4607	0.1873	5008	,	,		17336	0.0933		0.1392	False		,,,				2504	0.2597				p.P2211P	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A6633T						PASS	.	T		1721,2685	513.2+/-368.3	339,1043,821	119.0	127.0	125.0		6633	2.0	1.0	2	dbSNP_121	125	1388,7212	267.6+/-287.4	119,1150,3031	no	coding-synonymous	LRP1B	NM_018557.2		458,2193,3852	AA,AT,TT		16.1395,39.0604,23.9044		2211/4600	141457985	3109,9897	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon41			CCTTATTGGGGAA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.6633A>T	2.37:g.141457985T>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	57	17	0.298246	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			T|0.782;A|0.218	0.218	strong		0.348	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
LRRC43	254050	hgsc.bcm.edu	37	12	122674780	122674780	+	Missense_Mutation	SNP	C	C	A	rs11060094	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:122674780C>A	ENST00000339777.4	+	5	794	c.766C>A	c.(766-768)Cag>Aag	p.Q256K	LRRC43_ENST00000425921.1_Missense_Mutation_p.Q71K	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	256			Q -> K (in dbSNP:rs11060094). {ECO:0000269|PubMed:14702039}.							NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		CCTGGTGCTGCAGGGAAACCC	0.637													C|||	671	0.133986	0.0953	0.2666	5008	,	,		20331	0.0357		0.2038	False		,,,				2504	0.1217				p.Q256K		Atlas-SNP	.											.	LRRC43	105	.	0			c.C766A						PASS	.	C	LYS/GLN,LYS/GLN	436,3902		20,396,1753	91.0	103.0	99.0		766,211	4.9	1.0	12	dbSNP_120	99	1763,6753		199,1365,2694	yes	missense,missense	LRRC43	NM_001098519.1,NM_152759.4	53,53	219,1761,4447	AA,AC,CC		20.7022,10.0507,17.1075	benign,benign	256/657,71/472	122674780	2199,10655	2169	4258	6427	SO:0001583	missense	254050	exon5			GTGCTGCAGGGAA	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.766C>A	12.37:g.122674780C>A	ENSP00000344233:p.Gln256Lys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	147	77	0.52381	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	303	0.13873626373626374	49	0.09959349593495935	98	0.27071823204419887	15	0.026223776223776224	141	0.18601583113456466	C	22.3	4.268532	0.80469	0.100507	0.207022	ENSG00000158113	ENST00000537729;ENST00000339777;ENST00000289014;ENST00000425921	T;T;T	0.23348	1.91;1.91;1.91	4.95	4.95	0.65309	.	0.068949	0.64402	D	0.000017	T	0.00012	0.0000	M	0.63208	1.945	0.26746	P	0.9702966	D	0.58268	0.982	D	0.70227	0.968	T	0.01294	-1.1393	9	0.48119	T	0.1	-55.8197	17.807	0.88604	0.0:1.0:0.0:0.0	rs11060094;rs57783714;rs11060094	256	Q8N309	LRC43_HUMAN	K	71;256;127;71	ENSP00000438751:Q71K;ENSP00000344233:Q256K;ENSP00000416628:Q71K	ENSP00000289014:Q127K	Q	+	1	0	LRRC43	121240733	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.532000	0.60608	2.309000	0.77851	0.561000	0.74099	CAG	C|0.865;A|0.135	0.135	strong		0.637	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
TLR8	51311	hgsc.bcm.edu	37	X	12939112	12939112	+	Silent	SNP	G	G	C	rs2407992	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:12939112G>C	ENST00000218032.6	+	2	2040	c.1953G>C	c.(1951-1953)ctG>ctC	p.L651L	TLR8_ENST00000311912.5_Silent_p.L669L	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	651					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TTAATAGGCTGAAGCACATCC	0.368													C|||	2729	0.722914	0.7239	0.5231	3775	,	,		15448	0.6151		0.2893	False		,,,				2504	0.5092				p.L651L		Atlas-SNP	.											.	TLR8	134	.	0			c.G1953C						PASS	.	C		3387,448		1275,330,507,27,64	58.0	60.0	59.0		1953	-6.9	0.0	X	dbSNP_100	59	2654,4072		392,1133,737,903,1133	no	coding-synonymous	TLR8	NM_138636.4		1667,1463,1244,930,1197	CC,CG,C,GG,G		39.4588,11.6819,42.799		651/1042	12939112	6041,4520	2203	4298	6501	SO:0001819	synonymous_variant	51311	exon2			TAGGCTGAAGCAC	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1953G>C	X.37:g.12939112G>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	116	86	0.741379	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																			0|0.007;C|0.613	0.613	strong		0.368	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
LINC00283	100874057	hgsc.bcm.edu	37	13	103397583	103397583	+	RNA	SNP	C	C	G	rs9582626	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103397583C>G	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		TTTAACAATGCCTCCTGTTTC	0.388													C|||	3479	0.694688	0.5424	0.7493	5008	,	,		21547	0.5923		0.826	False		,,,				2504	0.8323				p.A1822P		Atlas-SNP	.											.	.	.	.	0			c.G5464C						PASS	.	C	PRO/ALA	774,610		217,340,135	117.0	102.0	107.0		5464	-0.5	0.0	13	dbSNP_119	107	2544,638		1024,496,71	yes	missense	CCDC168	NM_001146197.1	27	1241,836,206	GG,GC,CC		20.0503,44.0751,27.3325		1822/7082	103397583	3318,1248	692	1591	2283			643677	exon4			ACAATGCCTCCTG			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103397583C>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.319;G|0.681	0.681	strong		0.388	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
PKD1L2	114780	hgsc.bcm.edu	37	16	81253759	81253759	+	RNA	SNP	A	A	G	rs9924371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:81253759A>G	ENST00000525539.1	-	0	216				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGCAGAAACCACTGGGTGCCT	0.572													G|||	2677	0.534545	0.5983	0.562	5008	,	,		22265	0.4405		0.6511	False		,,,				2504	0.4059				p.W73R		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T217C						PASS	.	G	ARG/TRP,ARG/TRP	2615,1463		849,917,273	103.0	101.0	101.0		217,217	-0.1	0.0	16	dbSNP_119	101	5314,3088		1668,1978,555	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	101,101	2517,2895,828	GG,GA,AA		36.7532,35.8754,36.4663	benign,benign	73/992,73/2460	81253759	7929,4551	2039	4201	6240			114780	exon1			GAAACCACTGGGT	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81253759A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	103	57	0.553398	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1248	0.5714285714285714	298	0.6056910569105691	225	0.6215469613259669	233	0.40734265734265734	492	0.6490765171503958	G	0.003	-2.430925	0.00184	0.641246	0.632468	ENSG00000166473	ENST00000337114	T	0.16597	2.33	4.17	-0.109	0.13584	C-type lectin fold (1);C-type lectin (3);	0.543965	0.16764	N	0.200499	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34329	-0.9833	8	0.15499	T	0.54	0.6019	0.212	0.00157	0.2358:0.2029:0.2363:0.3249	rs9924371;rs58449243;rs9924371	73;73	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	R	73	ENSP00000337397:W73R	ENSP00000337397:W73R	W	-	1	0	PKD1L2	79811260	0.984000	0.35163	0.022000	0.16811	0.214000	0.24535	0.397000	0.20883	-0.436000	0.07254	-0.930000	0.02707	TGG	A|0.425;G|0.575	0.575	strong		0.572	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
LAMC3	10319	hgsc.bcm.edu	37	9	133914570	133914570	+	Silent	SNP	G	G	A	rs2293518	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:133914570G>A	ENST00000361069.4	+	6	1351	c.1218G>A	c.(1216-1218)acG>acA	p.T406T	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	406	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GCAAGCCCACGGTGACTGGCT	0.647													T|||	776	0.154952	0.1104	0.2061	5008	,	,		19185	0.1399		0.2445	False		,,,				2504	0.1022				p.T406T		Atlas-SNP	.											LAMC3,NS,adenoma,0,1	LAMC3	167	1	0			c.G1218A						PASS	.	T		505,3901		30,445,1728	65.0	59.0	61.0		1218	-10.2	0.0	9	dbSNP_100	61	2181,6419		277,1627,2396	no	coding-synonymous	LAMC3	NM_006059.3		307,2072,4124	AA,AG,GG		25.3605,11.4616,20.652		406/1576	133914570	2686,10320	2203	4300	6503	SO:0001819	synonymous_variant	10319	exon6			GCCCACGGTGACT	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.1218G>A	9.37:g.133914570G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			G|0.809;A|0.191	0.191	strong		0.647	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
CYP1B1	1545	hgsc.bcm.edu	37	2	38298139	38298139	+	Missense_Mutation	SNP	T	T	C	rs1800440	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:38298139T>C	ENST00000260630.3	-	3	1759	c.1358A>G	c.(1357-1359)aAc>aGc	p.N453S	CYP1B1_ENST00000494864.1_5'UTR|CYP1B1_ENST00000407341.1_Missense_Mutation_p.N453S	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	453			N -> S (in allele CYP1B1*4; dbSNP:rs1800440). {ECO:0000269|PubMed:10655546, ECO:0000269|PubMed:11854439, ECO:0000269|PubMed:12036985, ECO:0000269|PubMed:12525557, ECO:0000269|PubMed:14635112, ECO:0000269|PubMed:15342693, ECO:0000269|PubMed:15475877, ECO:0000269|PubMed:16688110, ECO:0000269|PubMed:9823305, ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|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)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	CAGGTCCTTGTTGATGAGGCC	0.473													T|||	499	0.0996406	0.0068	0.1311	5008	,	,		20848	0.005		0.1958	False		,,,				2504	0.2014				p.N453S		Atlas-SNP	.											CYP1B1,colon,carcinoma,0,3	CYP1B1	39	3	0			c.A1358G	GRCh37	CM994676	CYP1B1	M	rs1800440	PASS	.	T	SER/ASN	147,4259	103.4+/-141.9	4,139,2060	82.0	77.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1358	5.9	0.9	2	dbSNP_89	78	1608,6992	298.6+/-304.0	143,1322,2835	yes	missense	CYP1B1	NM_000104.3	46	147,1461,4895	CC,CT,TT		18.6977,3.3364,13.4938	possibly-damaging	453/544	38298139	1755,11251	2203	4300	6503	SO:0001583	missense	1545	exon3			TCCTTGTTGATGA	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.1358A>G	2.37:g.38298139T>C	ENSP00000260630:p.Asn453Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_000104	Q5TZW8|Q93089|Q9H316	Missense_Mutation	SNP	ENST00000260630.3	37	CCDS1793.1	216	0.0989010989010989	3	0.006097560975609756	58	0.16022099447513813	4	0.006993006993006993	151	0.19920844327176782	T	18.56	3.651256	0.67472	0.033364	0.186977	ENSG00000138061	ENST00000260630;ENST00000407341	T;T	0.66638	-0.22;-0.22	5.95	5.95	0.96441	.	0.172254	0.64402	D	0.000008	T	0.00144	0.0004	L	0.55103	1.725	0.20403	P	0.9999085855	P	0.37466	0.596	B	0.39660	0.306	T	0.08411	-1.0723	9	0.59425	D	0.04	.	14.3758	0.66874	0.0:0.0:0.0:1.0	rs1800440;rs4134586;rs4986886;rs17405302;rs56879535;rs1800440	453	Q53TK1	.	S	453	ENSP00000260630:N453S;ENSP00000384972:N453S	ENSP00000260630:N453S	N	-	2	0	CYP1B1	38151643	1.000000	0.71417	0.934000	0.37439	0.897000	0.52465	6.035000	0.70940	2.279000	0.76181	0.533000	0.62120	AAC	T|0.882;C|0.118	0.118	strong		0.473	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163831	73163831	+	Silent	SNP	C	C	T	rs2931423	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:73163831C>T	ENST00000426542.2	+	18	2303	c.2283C>T	c.(2281-2283)ggC>ggT	p.G761G	ARHGEF28_ENST00000296799.4_Silent_p.G448G|ARHGEF28_ENST00000287898.5_Silent_p.G761G|ARHGEF28_ENST00000545377.1_Silent_p.G761G|ARHGEF28_ENST00000437974.1_Silent_p.G761G|ARHGEF28_ENST00000296794.6_Silent_p.G761G|ARHGEF28_ENST00000513042.2_Silent_p.G761G			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	761					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GTGTTCCAGGCACCACCTTGG	0.537													C|||	1115	0.222644	0.177	0.3631	5008	,	,		20460	0.1389		0.3012	False		,,,				2504	0.1902				p.G761G		Atlas-SNP	.											.	.	.	.	0			c.C2283T						PASS	.	C	,	795,3125		85,625,1250	100.0	95.0	97.0		2283,2283	-1.7	0.1	5	dbSNP_101	97	2594,5698		409,1776,1961	no	coding-synonymous,coding-synonymous	RGNEF	NM_001080479.2,NM_001177693.1	,	494,2401,3211	TT,TC,CC		31.2832,20.2806,27.7514	,	761/1732,761/1706	73163831	3389,8823	1960	4146	6106	SO:0001819	synonymous_variant	64283	exon19			TCCAGGCACCACC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2283C>T	5.37:g.73163831C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			C|0.759;T|0.241	0.241	strong		0.537	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
PCDHB1	29930	hgsc.bcm.edu	37	5	140433038	140433038	+	Silent	SNP	C	C	T	rs2233594	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140433038C>T	ENST00000306549.3	+	1	2060	c.1983C>T	c.(1981-1983)atC>atT	p.I661I		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	661	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)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|liver(1)|lung(13)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	53			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CACTCAACATCCTGCTGGTAG	0.448													C|||	28	0.00559105	0.0008	0.0173	5008	,	,		20814	0.0		0.0139	False		,,,				2504	0.001				p.I661I		Atlas-SNP	.											.	PCDHB1	148	.	0			c.C1983T						PASS	.	C		18,4388	26.2+/-53.5	0,18,2185	146.0	141.0	143.0		1983	-0.1	1.0	5	dbSNP_98	143	153,8447	73.2+/-135.9	0,153,4147	no	coding-synonymous	PCDHB1	NM_013340.2		0,171,6332	TT,TC,CC		1.7791,0.4085,1.3148		661/819	140433038	171,12835	2203	4300	6503	SO:0001819	synonymous_variant	29930	exon1			CAACATCCTGCTG	AF152488	CCDS4243.1	5q31	2010-01-26			ENSG00000171815	ENSG00000171815		"""Cadherins / Protocadherins : Clustered"""	8680	other	protocadherin		606327				10380929	Standard	NM_013340		Approved	PCDH-BETA1	uc003lik.1	Q9Y5F3	OTTHUMG00000129627	ENST00000306549.3:c.1983C>T	5.37:g.140433038C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	NM_013340	Q2M257	Silent	SNP	ENST00000306549.3	37	CCDS4243.1																																																																																			C|0.987;T|0.013	0.013	strong		0.448	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340	
CLEC4F	165530	hgsc.bcm.edu	37	2	71044211	71044211	+	Missense_Mutation	SNP	C	C	T	rs2075221	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71044211C>T	ENST00000272367.2	-	4	378	c.302G>A	c.(301-303)cGa>cAa	p.R101Q	CLEC4F_ENST00000426626.1_Missense_Mutation_p.R101Q	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	101			R -> Q (in dbSNP:rs2075221).		endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						GATAAGCTCTCGCATTTCTGC	0.488													C|||	1655	0.330471	0.028	0.402	5008	,	,		21486	0.5248		0.3817	False		,,,				2504	0.4356				p.R101Q	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											CLEC4F,caecum,carcinoma,-1,1	CLEC4F	95	1	0			c.G302A						scavenged	.	C	GLN/ARG	423,3983	204.5+/-226.7	30,363,1810	58.0	53.0	55.0		302	3.9	0.0	2	dbSNP_96	55	3155,5445	479.6+/-370.2	611,1933,1756	yes	missense	CLEC4F	NM_173535.2	43	641,2296,3566	TT,TC,CC		36.686,9.6005,27.5104	benign	101/590	71044211	3578,9428	2203	4300	6503	SO:0001583	missense	165530	exon4			AGCTCTCGCATTT	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.302G>A	2.37:g.71044211C>T	ENSP00000272367:p.Arg101Gln	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	36	22	0.611111	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	768	0.3516483516483517	15	0.03048780487804878	123	0.3397790055248619	343	0.5996503496503497	287	0.3786279683377309	C	1.674	-0.508202	0.04231	0.096005	0.36686	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.01397	5.0;4.94	5.04	3.88	0.44766	.	0.366890	0.20087	N	0.099533	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.18935	-1.0321	9	0.02654	T	1	.	7.7138	0.28692	0.0:0.0975:0.0:0.9025	rs2075221;rs52820023;rs57574782;rs2075221	101;101	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	Q	101	ENSP00000272367:R101Q;ENSP00000390581:R101Q	ENSP00000272367:R101Q	R	-	2	0	CLEC4F	70897719	0.678000	0.27586	0.026000	0.17262	0.084000	0.17831	0.690000	0.25451	0.878000	0.35920	-0.483000	0.04790	CGA	C|0.692;T|0.308	0.308	strong		0.488	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
ZNF860	344787	hgsc.bcm.edu	37	3	32031615	32031615	+	Missense_Mutation	SNP	A	A	C	rs13064905	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:32031615A>C	ENST00000360311.4	+	2	1593	c.1044A>C	c.(1042-1044)gaA>gaC	p.E348D		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	348					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(3)|lung(4)|ovary(1)	8						AGGTTTGTGAAAAGGCTTTCA	0.393													C|||	2356	0.470447	0.7988	0.3602	5008	,	,		21648	0.4524		0.1968	False		,,,				2504	0.4049				p.E348D		Atlas-SNP	.											.	ZNF860	96	.	0			c.A1044C						PASS	.						45.0	47.0	46.0					3																	32031615		692	1591	2283	SO:0001583	missense	344787	exon2			TTGTGAAAAGGCT	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1044A>C	3.37:g.32031615A>C	ENSP00000373274:p.Glu348Asp	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	126	124	0.984127	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	911	0.41712454212454214	385	0.782520325203252	126	0.34806629834254144	248	0.43356643356643354	152	0.20052770448548812	C	3.265	-0.150374	0.06585	.	.	ENSG00000197385	ENST00000360311	T	0.01185	5.21	0.345	0.345	0.16011	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04148	-0.265	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02411	-1.1163	7	.	.	.	.	2.5267	0.04693	0.3212:0.3574:0.3213:0.0	rs13064905;rs61529855;rs13064905	348	A6NHJ4	ZN860_HUMAN	D	348	ENSP00000373274:E348D	.	E	+	3	2	ZNF860	32006619	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-1.684000	0.01932	-0.518000	0.06452	-0.525000	0.04345	GAA	A|0.614;C|0.386	0.386	strong		0.393	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
ANXA1	301	hgsc.bcm.edu	37	9	75775235	75775235	+	Silent	SNP	A	A	G	rs1050305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:75775235A>G	ENST00000376911.1	+	4	1209	c.327A>G	c.(325-327)ttA>ttG	p.L109L	ANXA1_ENST00000257497.6_Silent_p.L109L			P04083	ANXA1_HUMAN	annexin A1	109					alpha-beta T cell differentiation (GO:0046632)|arachidonic acid secretion (GO:0050482)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to hydrogen peroxide (GO:0070301)|endocrine pancreas development (GO:0031018)|estrous cycle phase (GO:0060206)|gliogenesis (GO:0042063)|hepatocyte differentiation (GO:0070365)|inflammatory response (GO:0006954)|insulin secretion (GO:0030073)|keratinocyte differentiation (GO:0030216)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of apoptotic process (GO:0043066)|negative regulation of catalytic activity (GO:0043086)|negative regulation of interleukin-8 secretion (GO:2000483)|neutrophil clearance (GO:0097350)|neutrophil homeostasis (GO:0001780)|peptide cross-linking (GO:0018149)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of neutrophil apoptotic process (GO:0033031)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of vesicle fusion (GO:0031340)|regulation of cell proliferation (GO:0042127)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to interleukin-1 (GO:0070555)|response to peptide hormone (GO:0043434)|response to X-ray (GO:0010165)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cilium (GO:0005929)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|phospholipase A2 inhibitor activity (GO:0019834)|phospholipid binding (GO:0005543)|protein binding, bridging (GO:0030674)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(5)	8		all_epithelial(88;2.54e-11)		OV - Ovarian serous cystadenocarcinoma(323;2.82e-06)|GBM - Glioblastoma multiforme(74;0.0325)	Amcinonide(DB00288)|Dexamethasone(DB01234)|Hydrocortisone(DB00741)	AGGTTGTTTTAGCTCTGCTAA	0.423													A|||	751	0.14996	0.23	0.0951	5008	,	,		16826	0.1458		0.0974	False		,,,				2504	0.1391				p.L109L		Atlas-SNP	.											.	ANXA1	27	.	0			c.A327G						PASS	.	A		968,3438	367.8+/-318.4	111,746,1346	115.0	117.0	116.0		327	2.8	0.1	9	dbSNP_86	116	704,7896	174.3+/-224.6	29,646,3625	no	coding-synonymous	ANXA1	NM_000700.1		140,1392,4971	GG,GA,AA		8.186,21.97,12.8556		109/347	75775235	1672,11334	2203	4300	6503	SO:0001819	synonymous_variant	301	exon5			TGTTTTAGCTCTG	X05908	CCDS6645.1	9q21.13	2013-02-25			ENSG00000135046	ENSG00000135046		"""Annexins"", ""Endogenous ligands"""	533	protein-coding gene	gene with protein product		151690		ANX1, LPC1		2936963	Standard	NM_000700		Approved		uc004ajf.1	P04083	OTTHUMG00000020016	ENST00000376911.1:c.327A>G	9.37:g.75775235A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_000700		Silent	SNP	ENST00000376911.1	37	CCDS6645.1																																																																																			A|0.863;G|0.137	0.137	strong		0.423	ANXA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052665.1	NM_000700	
ASAH1	427	hgsc.bcm.edu	37	8	17930772	17930772	+	Intron	SNP	C	C	T	rs3753115	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17930772C>T	ENST00000262097.6	-	3	437				ASAH1_ENST00000314146.10_Missense_Mutation_p.V63I|ASAH1_ENST00000520051.1_Intron|ASAH1_ENST00000520781.1_Intron|ASAH1_ENST00000381733.4_Intron|ASAH1_ENST00000417108.2_Intron	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1						cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		CACCTTATAACAGCAGGGAAG	0.328													T|||	2071	0.413538	0.2504	0.5735	5008	,	,		19990	0.3532		0.4771	False		,,,				2504	0.5174				p.V63I		Atlas-SNP	.											.	ASAH1	71	.	0			c.G187A						PASS	.	T	ILE/VAL,,	880,2254		138,604,825	60.0	44.0	49.0		187,,	-1.6	0.0	8	dbSNP_107	49	3484,3676		840,1804,936	yes	missense,intron,intron	ASAH1	NM_001127505.1,NM_004315.4,NM_177924.3	29,,	978,2408,1761	TT,TC,CC		48.6592,28.0791,42.3936	,,	63/390,,	17930772	4364,5930	1567	3580	5147	SO:0001627	intron_variant	427	exon3			TTATAACAGCAGG	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"""N-acylsphingosine amidohydrolase (acid ceramidase)"""	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.126-1873G>A	8.37:g.17930772C>T		Somatic	408	1	0.00245098		WXS	Illumina HiSeq	Phase_I	187	184	0.983957	NM_001127505	E9PDS0|Q6W898|Q96AS2	Missense_Mutation	SNP	ENST00000262097.6	37	CCDS6006.1	920	0.42124542124542125	148	0.3008130081300813	219	0.6049723756906077	200	0.34965034965034963	353	0.4656992084432718	T	2.153	-0.394073	0.04899	0.280791	0.486592	ENSG00000104763	ENST00000314146	T	0.70869	-0.52	3.6	-1.63	0.08345	.	.	.	.	.	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	0.44877	-0.9299	8	0.19590	T	0.45	.	2.3428	0.04264	0.1861:0.4184:0.2471:0.1484	rs3753115;rs58952721;rs3753115	63	E9PDS0	.	I	63	ENSP00000326970:V63I	ENSP00000326970:V63I	V	-	1	0	ASAH1	17975052	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.047000	0.03521	-0.675000	0.05246	-2.597000	0.00163	GTT	C|0.584;T|0.416	0.416	strong		0.328	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
EPHB3	2049	hgsc.bcm.edu	37	3	184289152	184289152	+	Silent	SNP	A	A	G	rs13069661	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:184289152A>G	ENST00000330394.2	+	2	617	c.165A>G	c.(163-165)acA>acG	p.T55T	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	55	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TGGCGTGGACATCTCATCCAG	0.527													A|||	1059	0.211462	0.1415	0.111	5008	,	,		19852	0.3264		0.2217	False		,,,				2504	0.2485				p.T55T		Atlas-SNP	.											EPHB3,NS,adenoma,0,1	EPHB3	114	1	0			c.A165G						PASS	.	A		690,3716	289.2+/-280.3	57,576,1570	181.0	169.0	173.0		165	-0.7	1.0	3	dbSNP_121	173	1752,6848	318.0+/-313.5	152,1448,2700	no	coding-synonymous	EPHB3	NM_004443.3		209,2024,4270	GG,GA,AA		20.3721,15.6605,18.7759		55/999	184289152	2442,10564	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon2			GTGGACATCTCAT	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.165A>G	3.37:g.184289152A>G		Somatic	328	1	0.00304878		WXS	Illumina HiSeq	Phase_I	302	128	0.423841	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			A|0.802;G|0.198	0.198	strong		0.527	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
PCDHB6	56130	hgsc.bcm.edu	37	5	140531215	140531215	+	Silent	SNP	C	C	G	rs246706	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140531215C>G	ENST00000231136.1	+	1	1377	c.1377C>G	c.(1375-1377)cgC>cgG	p.R459R	PCDHB6_ENST00000543635.1_Silent_p.R323R	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	459	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)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGTTCGTCCGCGAGAACAACA	0.617													C|||	432	0.086262	0.2867	0.0591	5008	,	,		16170	0.0		0.0119	False		,,,				2504	0.0				p.R459R		Atlas-SNP	.											PCDHB6,caecum,carcinoma,+2,2	PCDHB6	161	2	0			c.C1377G						scavenged	.	C		986,3418	354.4+/-312.6	134,718,1350	75.0	85.0	82.0		1377	-4.9	0.1	5	dbSNP_79	82	122,8470	61.3+/-123.2	0,122,4174	no	coding-synonymous	PCDHB6	NM_018939.2		134,840,5524	GG,GC,CC		1.4199,22.3887,8.5257		459/795	140531215	1108,11888	2202	4296	6498	SO:0001819	synonymous_variant	56130	exon1			CGTCCGCGAGAAC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1377C>G	5.37:g.140531215C>G		Somatic	60	1	0.0166667		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																			C|0.800;G|0.200	0.200	strong		0.617	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
GEMIN4	50628	hgsc.bcm.edu	37	17	648157	648157	+	Silent	SNP	G	G	A	rs1045481	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:648157G>A	ENST00000319004.5	-	2	3244	c.3126C>T	c.(3124-3126)atC>atT	p.I1042I	GEMIN4_ENST00000576778.1_Silent_p.I1031I	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	1042					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CTTCAGGGCCGATGCCCTCAG	0.572													G|||	794	0.158546	0.0545	0.1772	5008	,	,		19937	0.122		0.2455	False		,,,				2504	0.2342				p.I1042I		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C3126T						PASS	.	G		363,3619		17,329,1645	45.0	44.0	44.0		3126	-2.2	1.0	17	dbSNP_86	44	2088,6240		281,1526,2357	no	coding-synonymous	GEMIN4	NM_015721.2		298,1855,4002	AA,AG,GG		25.072,9.116,19.9106		1042/1059	648157	2451,9859	1991	4164	6155	SO:0001819	synonymous_variant	50628	exon2			AGGGCCGATGCCC	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.3126C>T	17.37:g.648157G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			G|0.829;A|0.172	0.172	strong		0.572	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
SEC24D	9871	hgsc.bcm.edu	37	4	119736607	119736607	+	Splice_Site	SNP	C	C	T	rs114611353	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:119736607C>T	ENST00000280551.6	-	5	910	c.672G>A	c.(670-672)caG>caA	p.Q224Q	SEC24D_ENST00000379735.5_Splice_Site_p.Q224Q|SEC24D_ENST00000419654.2_5'UTR			O94855	SC24D_HUMAN	SEC24 family member D	224	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						CCGCCTTACCCTGCTGCGGAG	0.552													C|||	94	0.01877	0.0113	0.0231	5008	,	,		19077	0.001		0.0547	False		,,,				2504	0.0072				p.Q224Q		Atlas-SNP	.											.	SEC24D	96	.	0			c.G672A						PASS	.	C		104,4302	78.3+/-116.7	0,104,2099	67.0	65.0	66.0		672	-3.5	1.0	4	dbSNP_132	66	519,8081	137.5+/-194.4	12,495,3793	yes	coding-synonymous-near-splice	SEC24D	NM_014822.2		12,599,5892	TT,TC,CC		6.0349,2.3604,4.7901		224/1033	119736607	623,12383	2203	4300	6503	SO:0001630	splice_region_variant	9871	exon5			CTTACCCTGCTGC	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.673+1G>A	4.37:g.119736607C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			C|0.960;T|0.040	0.040	strong		0.552	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		Silent
VSIG4	11326	hgsc.bcm.edu	37	X	65244971	65244971	+	Splice_Site	SNP	C	C	T	rs17315645	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:65244971C>T	ENST00000374737.4	-	6	944	c.836G>A	c.(835-837)gGa>gAa	p.G279E	VSIG4_ENST00000455586.2_Splice_Site_p.G279E|VSIG4_ENST00000412866.2_Splice_Site_p.G185E	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	279			G -> E (in dbSNP:rs17315645).		complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGGCTCTTTCCTAGAGGGTA	0.418													C|||	70	0.018543	0.0	0.0029	3775	,	,		15530	0.0		0.0249	False		,,,				2504	0.044				p.G279E		Atlas-SNP	.											.	VSIG4	54	.	0			c.G836A						PASS	.	C	GLU/GLY,GLU/GLY,GLU/GLY,GLU/GLY	18,3817		0,16,2,1616,569	96.0	71.0	80.0		554,836,554,836	2.5	0.1	X	dbSNP_123	80	199,6529		3,143,50,2282,1822	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	VSIG4	NM_001100431.1,NM_001184830.1,NM_001184831.1,NM_007268.2	98,98,98,98	3,159,52,3898,2391	TT,TC,T,CC,C		2.9578,0.4694,2.0543	probably-damaging,probably-damaging,probably-damaging,probably-damaging	185/306,279/322,185/228,279/400	65244971	217,10346	2203	4300	6503	SO:0001630	splice_region_variant	11326	exon6			CTCTTTCCTAGAG	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.836-1G>A	X.37:g.65244971C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	108	30	0.277778	NM_001257403	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	29	0.017480409885473176	0	0.0	2	0.0055248618784530384	0	0.0	24	0.032	C	8.554	0.876160	0.17395	0.004694	0.029578	ENSG00000155659	ENST00000374737;ENST00000455586;ENST00000412866	T;T;T	0.45668	1.54;1.34;0.89	4.29	2.53	0.30540	.	0.118469	0.37955	N	0.001872	T	0.32194	0.0821	M	0.72894	2.215	0.80722	P	0.0	D;D;D;D;D	0.89917	1.0;0.986;1.0;1.0;0.997	D;P;D;D;P	0.97110	0.998;0.791;0.998;1.0;0.861	T	0.57797	-0.7749	9	0.51188	T	0.08	.	6.0134	0.19588	0.0:0.7601:0.0:0.2399	rs17315645;rs52799472;rs17315645	185;279;269;185;279	C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279	.;.;.;.;VSIG4_HUMAN	E	279;279;185	ENSP00000363869:G279E;ENSP00000411581:G279E;ENSP00000394143:G185E	ENSP00000363869:G279E	G	-	2	0	VSIG4	65161696	0.065000	0.20965	0.052000	0.19188	0.002000	0.02628	0.387000	0.20718	0.313000	0.23062	-0.881000	0.02953	GGA	C|0.964;0|0.016	.	strong		0.418	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268	Missense_Mutation
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 GAIIx	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		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	47	23	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	
KIF26A	26153	hgsc.bcm.edu	37	14	104643721	104643721	+	Silent	SNP	C	C	A	rs2487301	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:104643721C>A	ENST00000423312.2	+	12	4596	c.4596C>A	c.(4594-4596)gcC>gcA	p.A1532A	KIF26A_ENST00000315264.7_Silent_p.A1393A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1532					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GCCCTGTGGCCGGTCCCAGAG	0.731													C|||	2298	0.458866	0.7383	0.2911	5008	,	,		13223	0.372		0.3419	False		,,,				2504	0.41				p.A1532A		Atlas-SNP	.											.	KIF26A	84	.	0			c.C4596A						PASS	.	C		2061,1315		665,731,292	4.0	6.0	5.0		4596	-7.6	0.0	14	dbSNP_100	5	2447,5087		528,1391,1848	no	coding-synonymous	KIF26A	NM_015656.1		1193,2122,2140	AA,AC,CC		32.4794,38.9514,41.3199		1532/1883	104643721	4508,6402	1688	3767	5455	SO:0001819	synonymous_variant	26153	exon12			TGTGGCCGGTCCC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.4596C>A	14.37:g.104643721C>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			C|0.566;A|0.434	0.434	strong		0.731	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
TSNARE1	203062	hgsc.bcm.edu	37	8	143425354	143425354	+	Missense_Mutation	SNP	C	C	T	rs79460462	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143425354C>T	ENST00000307180.3	-	4	835	c.718G>A	c.(718-720)Gag>Aag	p.E240K	TSNARE1_ENST00000524325.1_Missense_Mutation_p.E240K|TSNARE1_ENST00000520166.1_Missense_Mutation_p.E240K|TSNARE1_ENST00000519651.1_Intron	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	240					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CTGAAGCCCTCGGAGGGCAGG	0.677													C|||	169	0.033746	0.0477	0.0216	5008	,	,		9843	0.0397		0.0189	False		,,,				2504	0.0327				p.E240K		Atlas-SNP	.											.	TSNARE1	59	.	0			c.G718A						PASS	.	C	LYS/GLU	157,4117		3,151,1983	18.0	17.0	18.0		718	2.0	0.0	8	dbSNP_131	18	161,8227		0,161,4033	yes	missense	TSNARE1	NM_145003.3	56	3,312,6016	TT,TC,CC		1.9194,3.6734,2.5115	benign	240/514	143425354	318,12344	2137	4194	6331	SO:0001583	missense	203062	exon4			AGCCCTCGGAGGG			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.718G>A	8.37:g.143425354C>T	ENSP00000303437:p.Glu240Lys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	60	0.027472527472527472	21	0.042682926829268296	6	0.016574585635359115	21	0.03671328671328671	12	0.0158311345646438	C	12.64	1.999038	0.35226	0.036734	0.019194	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166	T;T;T	0.14144	2.54;2.53;2.54	3.91	1.99	0.26369	.	0.500084	0.14530	U	0.313909	T	0.01905	0.0060	L	0.51422	1.61	0.09310	N	1	P;P;P	0.36438	0.553;0.553;0.553	B;B;B	0.23018	0.043;0.043;0.043	T	0.25676	-1.0125	10	0.46703	T	0.11	-1.9197	4.6953	0.12800	0.2139:0.6667:0.0:0.1194	.	240;240;240	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	K	240	ENSP00000428763:E240K;ENSP00000303437:E240K;ENSP00000427770:E240K	ENSP00000303437:E240K	E	-	1	0	TSNARE1	143423261	0.002000	0.14202	0.007000	0.13788	0.186000	0.23388	0.500000	0.22562	0.210000	0.20664	0.603000	0.83216	GAG	C|0.973;T|0.027	0.027	strong		0.677	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
DMXL1	1657	hgsc.bcm.edu	37	5	118513876	118513876	+	Missense_Mutation	SNP	G	G	A	rs79460759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:118513876G>A	ENST00000311085.8	+	28	7152	c.7072G>A	c.(7072-7074)Gct>Act	p.A2358T	DMXL1_ENST00000539542.1_Missense_Mutation_p.A2358T	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2358										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		AATGTGGTCTGCTGTGTTTGG	0.403													G|||	151	0.0301518	0.0038	0.0317	5008	,	,		14358	0.0109		0.0606	False		,,,				2504	0.0532				p.A2358T		Atlas-SNP	.											.	DMXL1	268	.	0			c.G7072A						PASS	.	G	THR/ALA	54,4350	54.2+/-90.2	1,52,2149	109.0	102.0	105.0		7072	5.7	1.0	5	dbSNP_131	105	522,8078	146.5+/-202.0	14,494,3792	yes	missense	DMXL1	NM_005509.4	58	15,546,5941	AA,AG,GG		6.0698,1.2262,4.4294	benign	2358/3028	118513876	576,12428	2202	4300	6502	SO:0001583	missense	1657	exon28			TGGTCTGCTGTGT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.7072G>A	5.37:g.118513876G>A	ENSP00000309690:p.Ala2358Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	112	48	0.428571	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	64	0.029304029304029304	3	0.006097560975609756	13	0.03591160220994475	5	0.008741258741258742	43	0.05672823218997362	G	11.43	1.637933	0.29157	0.012262	0.060698	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.09723	2.95;2.95	5.72	5.72	0.89469	.	0.195984	0.56097	D	0.000039	T	0.00936	0.0031	L	0.39397	1.21	0.49213	D	0.999764	P;B	0.38395	0.629;0.077	B;B	0.29942	0.109;0.021	T	0.40572	-0.9556	10	0.12103	T	0.63	-18.6291	19.8965	0.96963	0.0:0.0:1.0:0.0	.	2358;2358	F5H269;Q9Y485	.;DMXL1_HUMAN	T	2358	ENSP00000309690:A2358T;ENSP00000439479:A2358T	ENSP00000309690:A2358T	A	+	1	0	DMXL1	118541775	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.876000	0.69667	2.717000	0.92951	0.655000	0.94253	GCT	G|0.958;A|0.042	0.042	strong		0.403	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
ZNF596	169270	hgsc.bcm.edu	37	8	195254	195254	+	Missense_Mutation	SNP	C	C	A	rs2074718	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:195254C>A	ENST00000398612.1	+	6	790	c.407C>A	c.(406-408)aCg>aAg	p.T136K	ZNF596_ENST00000308811.4_Missense_Mutation_p.T136K|ZNF596_ENST00000320552.2_Missense_Mutation_p.T66K	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	136			T -> K (in dbSNP:rs2074718).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(5)	14		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)		TACATGAGAACGAAACACTTT	0.343													.|||	901	0.179912	0.3411	0.0519	5008	,	,		21221	0.2063		0.0805	False		,,,				2504	0.1278				p.T136K		Atlas-SNP	.											.	ZNF596	34	.	0			c.C407A						PASS	.	A	LYS/THR,LYS/THR,LYS/THR	1444,2962		252,940,1011	80.0	81.0	81.0		407,407,407	2.5	0.3	8	dbSNP_96	81	655,7945		16,623,3661	yes	missense,missense,missense	ZNF596	NM_001042415.1,NM_001042416.1,NM_173539.2	78,78,78	268,1563,4672	AA,AC,CC		7.6163,32.7735,16.1387	benign,benign,benign	136/505,136/505,136/505	195254	2099,10907	2203	4300	6503	SO:0001583	missense	169270	exon6			TGAGAACGAAACA	BC026190	CCDS5951.2	8p23.3	2013-01-08			ENSG00000172748	ENSG00000172748		"""Zinc fingers, C2H2-type"", ""-"""	27268	protein-coding gene	gene with protein product						12477932	Standard	NM_001287256		Approved		uc003wot.3	Q8TC21	OTTHUMG00000086931	ENST00000398612.1:c.407C>A	8.37:g.195254C>A	ENSP00000381613:p.Thr136Lys	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	125	67	0.536	NM_173539	B2R8P4|O95015|Q8N9X0	Missense_Mutation	SNP	ENST00000398612.1	37	CCDS5951.2	382	0.1749084249084249	167	0.3394308943089431	21	0.058011049723756904	129	0.22552447552447552	65	0.08575197889182058	.	2.992	-0.207879	0.06180	0.327735	0.076163	ENSG00000172748	ENST00000521145;ENST00000308811;ENST00000320552;ENST00000398612	T;T;T;T	0.60040	2.5;0.22;3.52;0.22	2.49	2.49	0.30216	.	.	.	.	.	T	0.00012	0.0000	N	0.00462	-1.47	0.54753	P	1.6000000000016E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.32188	-0.9916	8	0.52906	T	0.07	.	7.1816	0.25776	0.7719:0.2281:0.0:0.0	rs2074718;rs52814433;rs2074718	136	Q8TC21	ZN596_HUMAN	K	136;136;66;136	ENSP00000429671:T136K;ENSP00000310033:T136K;ENSP00000318719:T66K;ENSP00000381613:T136K	ENSP00000310033:T136K	T	+	2	0	ZNF596	185254	0.413000	0.25400	0.269000	0.24586	0.009000	0.06853	2.238000	0.43070	0.388000	0.25054	-0.335000	0.08231	ACG	C|0.837;A|0.163	0.163	strong		0.343	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539	
TARM1	441864	hgsc.bcm.edu	37	19	54573301	54573301	+	Missense_Mutation	SNP	G	G	A	rs77768804	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54573301G>A	ENST00000432826.1	-	5	796	c.772C>T	c.(772-774)Cgg>Tgg	p.R258W	TARM1_ENST00000446034.2_Missense_Mutation_p.R266W	NM_001135686.1	NP_001129158.2	B6A8C7	TARM1_HUMAN	T cell-interacting, activating receptor on myeloid cells 1	258			R -> W (in dbSNP:rs77768804).			integral component of membrane (GO:0016021)		p.R258W(1)|p.R258R(1)		endometrium(1)|stomach(2)	3						GACACATTCCGGCTGTACCAG	0.547													G|||	174	0.0347444	0.0015	0.111	5008	,	,		17070	0.0258		0.0626	False		,,,				2504	0.0061				p.R258W		Atlas-SNP	.											TARM1,NS,carcinoma,0,2	TARM1	10	2	2	Substitution - Missense(1)|Substitution - coding silent(1)	stomach(1)|endometrium(1)	c.C772T						scavenged	.	G	TRP/ARG	18,1366		0,18,674	76.0	74.0	74.0		772	-0.5	0.0	19	dbSNP_132	74	198,2984		8,182,1401	yes	missense	TARM1	NM_001135686.1	101	8,200,2075	AA,AG,GG		6.2225,1.3006,4.7306	possibly-damaging	258/272	54573301	216,4350	692	1591	2283	SO:0001583	missense	441864	exon5			CATTCCGGCTGTA		CCDS46173.1	19q13.42	2013-01-29			ENSG00000248385	ENSG00000248385		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	37250	protein-coding gene	gene with protein product							Standard	XM_005258952		Approved		uc010yei.1	B6A8C7		ENST00000432826.1:c.772C>T	19.37:g.54573301G>A	ENSP00000439454:p.Arg258Trp	Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	60	23	0.383333	NM_001135686	B4DWY4	Missense_Mutation	SNP	ENST00000432826.1	37	CCDS46173.1	109	0.04990842490842491	2	0.0040650406504065045	37	0.10220994475138122	16	0.027972027972027972	54	0.0712401055408971	G	13.14	2.146839	0.37923	0.013006	0.062225	ENSG00000248385	ENST00000432826;ENST00000446034	T;T	0.00532	6.88;6.75	2.98	-0.497	0.12023	.	.	.	.	.	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	D	0.59357	0.985	P	0.51055	0.657	T	0.52997	-0.8500	8	0.49607	T	0.09	.	1.4352	0.02342	0.1334:0.2292:0.4235:0.2139	.	258	B6A8C7	TARM1_HUMAN	W	258;266	ENSP00000439454:R258W;ENSP00000441055:R266W	ENSP00000439454:R258W	R	-	1	2	TARM1	59265113	0.018000	0.18449	0.001000	0.08648	0.002000	0.02628	0.811000	0.27198	0.005000	0.14708	-0.302000	0.09304	CGG	G|0.950;A|0.050	0.050	strong		0.547	TARM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465679.1	NM_001135686	
LILRB4	11006	hgsc.bcm.edu	37	19	55175740	55175740	+	Silent	SNP	C	C	T	rs3745871	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55175740C>T	ENST00000391736.1	+	6	774	c.459C>T	c.(457-459)ttC>ttT	p.F153F	LILRB4_ENST00000391733.3_Silent_p.F153F|LILRB4_ENST00000270452.2_Silent_p.F153F|LILRB4_ENST00000430952.2_Silent_p.F153F|LILRB4_ENST00000391734.3_Silent_p.F153F	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	153	Ig-like C2-type 2.				immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGGACACTTTCCTTCTGATCA	0.572													C|||	1997	0.398762	0.3048	0.4179	5008	,	,		20496	0.5804		0.3817	False		,,,				2504	0.3425				p.F153F		Atlas-SNP	.											.	LILRB4	86	.	0			c.C459T						PASS	.	C	,	1448,2958	468.3+/-355.1	233,982,988	103.0	92.0	96.0		459,459	-1.3	0.0	19	dbSNP_107	96	3157,5443	482.1+/-370.8	594,1969,1737	no	coding-synonymous,coding-synonymous	LILRB4	NM_001081438.1,NM_006847.3	,	827,2951,2725	TT,TC,CC		36.7093,32.8643,35.4067	,	153/448,153/449	55175740	4605,8401	2203	4300	6503	SO:0001819	synonymous_variant	11006	exon4			CACTTTCCTTCTG	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.459C>T	19.37:g.55175740C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	96	37	0.385417	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Silent	SNP	ENST00000391736.1	37	CCDS12902.1																																																																																			C|0.609;N|0.000	.	strong		0.572	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
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 GAIIx	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_ENST00000419828.1_Intron|GNB2_ENST00000393926.1_Silent_p.N16N|GNB2_ENST00000424361.1_Intron|GNB2_ENST00000393924.1_Silent_p.N16N|GNB2_ENST00000427895.1_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		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	98	10	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	
CLCN1	1180	hgsc.bcm.edu	37	7	143042837	143042837	+	Silent	SNP	C	C	T	rs2272251	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143042837C>T	ENST00000343257.2	+	17	2241	c.2154C>T	c.(2152-2154)gaC>gaT	p.D718D		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	718					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|neuronal action potential propagation (GO:0019227)|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)|sarcolemma (GO:0042383)	adenyl nucleotide binding (GO:0030554)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(4)|central_nervous_system(1)|endometrium(1)|large_intestine(11)|lung(26)|ovary(3)|prostate(2)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	58	Melanoma(164;0.205)					AGGACGAAGACCTCTCTGGCA	0.677											OREG0018402	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2395	0.478235	0.3593	0.585	5008	,	,		13451	0.6141		0.4592	False		,,,				2504	0.4427				p.D718D		Atlas-SNP	.											CLCN1,NS,carcinoma,0,1	CLCN1	141	1	0			c.C2154T						PASS	.	C		1498,2778		328,842,968	7.0	8.0	8.0		2154	-1.8	0.1	7	dbSNP_100	8	3583,4875		839,1905,1485	no	coding-synonymous	CLCN1	NM_000083.2		1167,2747,2453	TT,TC,CC		42.3623,35.0327,39.9011		718/989	143042837	5081,7653	2138	4229	6367	SO:0001819	synonymous_variant	1180	exon17			CGAAGACCTCTCT	Z25884	CCDS5881.1	7q12	2012-09-26	2012-02-23		ENSG00000188037	ENSG00000188037		"""Ion channels / Chloride channels : Voltage-sensitive"""	2019	protein-coding gene	gene with protein product	"""Thomsen disease, autosomal dominant"""	118425	"""chloride channel 1, skeletal muscle"""			1379744	Standard	NM_000083		Approved	CLC1, ClC-1	uc003wcr.1	P35523	OTTHUMG00000152695	ENST00000343257.2:c.2154C>T	7.37:g.143042837C>T		Somatic	43	0	0	1676	WXS	Illumina HiSeq	Phase_I	45	26	0.577778	NM_000083	A4D2H5|Q2M202	Silent	SNP	ENST00000343257.2	37	CCDS5881.1																																																																																			C|0.502;T|0.498	0.498	strong		0.677	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083	
IRF2BP2	359948	hgsc.bcm.edu	37	1	234744250	234744250	+	Silent	SNP	G	G	A	rs8722	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:234744250G>A	ENST00000366609.3	-	1	1021	c.991C>T	c.(991-993)Ctg>Ttg	p.L331L	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000491430.1_5'Flank|IRF2BP2_ENST00000366610.3_Silent_p.L331L	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	331					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11	Ovarian(103;0.0303)	all_cancers(173;0.0236)|Prostate(94;0.0115)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)|Epithelial(3;6.2e-05)			CCTGCAGTCAGGGCCGGCTCC	0.642													G|||	680	0.135783	0.0129	0.1398	5008	,	,		14867	0.2034		0.2455	False		,,,				2504	0.1166				p.L331L		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.C991T						PASS	.	G	,	199,4203		5,189,2007	22.0	21.0	22.0		991,991	4.8	1.0	1	dbSNP_52	22	1983,6617		240,1503,2557	no	coding-synonymous,coding-synonymous	IRF2BP2	NM_001077397.1,NM_182972.2	,	245,1692,4564	AA,AG,GG		23.0581,4.5207,16.782	,	331/572,331/588	234744250	2182,10820	2201	4300	6501	SO:0001819	synonymous_variant	359948	exon1			CAGTCAGGGCCGG	AY278023	CCDS1602.1, CCDS41475.1	1q42.3	2008-02-05			ENSG00000168264	ENSG00000168264			21729	protein-coding gene	gene with protein product		615332				12799427	Standard	NM_182972		Approved	IRF-2BP2	uc001hwg.3	Q7Z5L9	OTTHUMG00000037981	ENST00000366609.3:c.991C>T	1.37:g.234744250G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Silent	SNP	ENST00000366609.3	37	CCDS1602.1																																																																																			G|0.834;A|0.166	0.166	strong		0.642	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972	
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 GAIIx	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	FAM65B_ENST00000540914.1_Silent_p.N559N|FAM65B_ENST00000538035.1_Silent_p.N588N|FAM65B_ENST00000473070.1_5'UTR|FAM65B_ENST00000510784.2_Silent_p.N593N|FAM65B_ENST00000378023.4_Silent_p.N559N|AL512428.1_ENST00000583229.1_RNA	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		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	87	68	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		
TNRC6B	23112	hgsc.bcm.edu	37	22	40552119	40552119	+	Splice_Site	SNP	G	G	A	rs9611280	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:40552119G>A	ENST00000301923.9	+	4	348	c.46G>A	c.(46-48)Gtg>Atg	p.V16M	TNRC6B_ENST00000402203.1_Splice_Site_p.V16M	NM_001024843.1	NP_001020014.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	0	Interaction with argonaute proteins.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						GCCTTTGCAGGTGGAACAGGA	0.493													G|||	173	0.0345447	0.0068	0.0476	5008	,	,		21118	0.0		0.0934	False		,,,				2504	0.0378				p.V16M		Atlas-SNP	.											TNRC6B_ENST00000301923,lymph_node,lymphoid_neoplasm,0,1	TNRC6B	195	1	0			c.G46A						PASS	.	G	MET/VAL	78,4016		1,76,1970	67.0	67.0	67.0		46	3.4	1.0	22	dbSNP_119	67	875,7515		39,797,3359	yes	missense-near-splice	TNRC6B	NM_001024843.1	21	40,873,5329	AA,AG,GG		10.4291,1.9052,7.6338		16/1030	40552119	953,11531	2047	4195	6242	SO:0001630	splice_region_variant	23112	exon4			TTGCAGGTGGAAC	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"""Trinucleotide (CAG) repeat containing"""	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000301923.9:c.46-1G>A	22.37:g.40552119G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_001024843	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Missense_Mutation	SNP	ENST00000301923.9	37	CCDS46712.1	105	0.04807692307692308	5	0.01016260162601626	21	0.058011049723756904	0	0.0	79	0.10422163588390501	G	14.63	2.593253	0.46214	0.019052	0.104291	ENSG00000100354	ENST00000441751;ENST00000301923;ENST00000402203	T;T	0.36878	1.23;1.23	5.52	3.44	0.39384	.	0.812716	0.09400	U	0.807347	T	0.00552	0.0018	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13737	-1.0498	8	.	.	.	.	5.8592	0.18736	0.3051:0.0:0.6949:0.0	rs9611280;rs52808489;rs61442552;rs9611280	16	Q9UPQ9-2	.	M	16	ENSP00000306759:V16M;ENSP00000384795:V16M	.	V	+	1	0	TNRC6B	38882065	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.007000	0.49536	1.340000	0.45581	0.650000	0.86243	GTG	G|0.943;A|0.057	0.057	strong		0.493	TNRC6B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321393.1		Missense_Mutation
NLRP3	114548	hgsc.bcm.edu	37	1	247588053	247588053	+	Silent	SNP	C	C	T	rs34298354	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247588053C>T	ENST00000336119.3	+	3	2054	c.1308C>T	c.(1306-1308)tcC>tcT	p.S436S	NLRP3_ENST00000348069.2_Silent_p.S436S|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391828.3_Silent_p.S436S|NLRP3_ENST00000366496.2_Silent_p.S436S|NLRP3_ENST00000366497.2_Silent_p.S436S|NLRP3_ENST00000391827.2_Silent_p.S436S	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	436	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CCCAGACATCCAAGACCACCA	0.612													C|||	329	0.0656949	0.0053	0.062	5008	,	,		19956	0.0685		0.1143	False		,,,				2504	0.0971				p.S436S		Atlas-SNP	.											NLRP3,NS,carcinoma,+1,1	NLRP3	286	1	0			c.C1308T						PASS	.	C	,,,,	106,4300	81.9+/-120.4	1,104,2098	97.0	80.0	86.0		1308,1308,1308,1308,1308	1.3	1.0	1	dbSNP_126	86	1051,7549	223.1+/-260.0	59,933,3308	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	,,,,	60,1037,5406	TT,TC,CC		12.2209,2.4058,8.8959	,,,,	436/1037,436/980,436/980,436/1037,436/923	247588053	1157,11849	2203	4300	6503	SO:0001819	synonymous_variant	114548	exon3			GACATCCAAGACC	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1308C>T	1.37:g.247588053C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	CCDS1632.1																																																																																			C|0.912;T|0.088	0.088	strong		0.612	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
MAGED1	9500	hgsc.bcm.edu	37	X	51644748	51644748	+	Silent	SNP	C	C	A	rs3199687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:51644748C>A	ENST00000375722.1	+	12	2311	c.2059C>A	c.(2059-2061)Cgg>Agg	p.R687R	MAGED1_ENST00000375772.3_Silent_p.R687R|MAGED1_ENST00000494718.1_3'UTR|MAGED1_ENST00000375695.2_Silent_p.R743R|MAGED1_ENST00000326587.7_Silent_p.R687R			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1	687					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					GGCCGAAGCCCGGGCTGAAGC	0.577										Multiple Myeloma(10;0.10)			C|||	341	0.0903311	0.0371	0.0605	3775	,	,		13146	0.0258		0.1382	False		,,,				2504	0.0869				p.R743R		Atlas-SNP	.											.	MAGED1	84	.	0			c.C2227A						PASS	.	C	,,	227,3608		12,168,35,1452,536	58.0	52.0	54.0		2059,2227,2059	3.2	1.0	X	dbSNP_105	54	1305,5423		98,764,345,1566,1527	no	coding-synonymous,coding-synonymous,coding-synonymous	MAGED1	NM_001005332.1,NM_001005333.1,NM_006986.3	,,	110,932,380,3018,2063	AA,AC,A,CC,C		19.3966,5.9192,14.5035	,,	687/779,743/835,687/779	51644748	1532,9031	2203	4300	6503	SO:0001819	synonymous_variant	9500	exon13			GAAGCCCGGGCTG	AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.2059C>A	X.37:g.51644748C>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	110	27	0.245455	NM_001005333	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Silent	SNP	ENST00000375722.1	37	CCDS14337.1																																																																																			C|0.875;A|0.125	0.125	strong		0.577	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332	
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 GAIIx	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		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	51	21	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		
DPH3	285381	hgsc.bcm.edu	37	3	16305674	16305674	+	Silent	SNP	C	C	G	rs14080	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:16305674C>G	ENST00000488423.1	-	2	266	c.171G>C	c.(169-171)gtG>gtC	p.V57V	OXNAD1_ENST00000605932.1_5'Flank|OXNAD1_ENST00000606098.1_5'Flank|OXNAD1_ENST00000285083.5_5'Flank|DPH3_ENST00000285082.4_5'UTR|DPH3_ENST00000383775.4_Intron|OXNAD1_ENST00000435829.2_5'Flank	NM_206831.2	NP_996662.1	Q96FX2	DPH3_HUMAN	diphthamide biosynthesis 3	57					negative regulation of protein secretion (GO:0050709)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of binding (GO:0051099)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			large_intestine(2)	2						TGTCATAAATCACTTTTATAA	0.418													C|||	2172	0.433706	0.3079	0.4712	5008	,	,		17298	0.4762		0.4324	False		,,,				2504	0.5348				p.V57V		Atlas-SNP	.											DPH3,NS,adenoma,0,1	DPH3	7	1	0			c.G171C						PASS	.	C	,	1546,2860	483.5+/-359.7	274,998,931	107.0	99.0	102.0		,171	3.8	1.0	3	dbSNP_52	102	3648,4952	520.9+/-379.8	782,2084,1434	no	intron,coding-synonymous	DPH3	NM_001047434.2,NM_206831.2	,	1056,3082,2365	GG,GC,CC		42.4186,35.0885,39.9354	,	,57/83	16305674	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	285381	exon2			ATAAATCACTTTT	BC010181	CCDS2629.1, CCDS43058.1	3p25.1	2013-06-19	2013-06-19	2006-10-25	ENSG00000154813	ENSG00000154813			27717	protein-coding gene	gene with protein product	"""DPH3A, KTI11 homolog A (S. cerevisiae)"""	608959	"""zinc finger, CSL-type containing 2"", ""DPH3 homolog (KTI11, S. cerevisiae)"", ""DPH3, KTI11 homolog (S. cerevisiae)"""	ZCSL2		14527407, 14980502, 15485916, 16648478	Standard	NM_001047434		Approved	DESR1, DELGIP1, MGC20197, KTI11, DELGIP, DPH3A	uc003cau.3	Q96FX2	OTTHUMG00000129866	ENST00000488423.1:c.171G>C	3.37:g.16305674C>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_206831		Silent	SNP	ENST00000488423.1	37	CCDS2629.1																																																																																			C|0.590;G|0.410	0.410	strong		0.418	DPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252108.2	NM_206831	
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 GAIIx	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_ENST00000397394.2_Silent_p.P192P|LARGE_ENST00000437602.2_Silent_p.P192P|LARGE_ENST00000402320.1_Silent_p.P192P|LARGE_ENST00000337431.2_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		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	104	67	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	
SFT2D1	113402	hgsc.bcm.edu	37	6	166739646	166739646	+	Missense_Mutation	SNP	T	T	C	rs11551053	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:166739646T>C	ENST00000361731.3	-	5	434	c.325A>G	c.(325-327)Ata>Gta	p.I109V	SFT2D1_ENST00000487841.1_5'UTR	NM_145169.1	NP_660152.1			SFT2 domain containing 1									p.I109V(1)		NS(1)|central_nervous_system(1)|large_intestine(3)|upper_aerodigestive_tract(1)	6		Breast(66;0.000148)|Prostate(117;0.109)|Ovarian(120;0.199)		OV - Ovarian serous cystadenocarcinoma(33;2.63e-19)|BRCA - Breast invasive adenocarcinoma(81;4.92e-06)|GBM - Glioblastoma multiforme(31;4.58e-05)		AGGGTAAATATGAAACACAAC	0.413													C|||	557	0.111222	0.0356	0.0793	5008	,	,		18011	0.3313		0.0398	False		,,,				2504	0.0828				p.I109V		Atlas-SNP	.											SFT2D1,colon,carcinoma,+1,2	SFT2D1	12	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.A325G						PASS	.	C	VAL/ILE	147,4259	812.6+/-416.1	1,145,2057	82.0	78.0	79.0		325	-1.3	0.0	6	dbSNP_120	79	304,8296	805.6+/-407.3	5,294,4001	yes	missense	SFT2D1	NM_145169.1	29	6,439,6058	CC,CT,TT		3.5349,3.3364,3.4676	benign	109/160	166739646	451,12555	2203	4300	6503	SO:0001583	missense	113402	exon5			TAAATATGAAACA	AF041429	CCDS5292.1	6q27	2008-02-05	2005-07-25	2005-07-25	ENSG00000198818	ENSG00000198818			21102	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 83"""	C6orf83			Standard	NM_145169		Approved	MGC19825, pRGR1	uc003qux.3	Q8WV19	OTTHUMG00000016001	ENST00000361731.3:c.325A>G	6.37:g.166739646T>C	ENSP00000354590:p.Ile109Val	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_145169		Missense_Mutation	SNP	ENST00000361731.3	37	CCDS5292.1	278	0.12728937728937728	19	0.03861788617886179	26	0.0718232044198895	199	0.3479020979020979	34	0.044854881266490766	C	0	-2.803354	0.00075	0.033364	0.035349	ENSG00000198818	ENST00000361731	T	0.58652	0.32	4.98	-1.34	0.09143	.	0.690574	0.13904	N	0.354704	T	0.07458	0.0188	N	0.03209	-0.39	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.25012	-1.0144	9	0.02654	T	1	-6.1183	5.4909	0.16774	0.1304:0.4651:0.0:0.4045	rs11551053;rs36102427;rs60635309	109	Q8WV19	SFT2A_HUMAN	V	109	ENSP00000354590:I109V	ENSP00000354590:I109V	I	-	1	0	SFT2D1	166659636	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.557000	0.02166	-0.259000	0.09432	-1.008000	0.02478	ATA	T|0.932;C|0.068	0.068	strong		0.413	SFT2D1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043061.2	NM_145169	
SACS	26278	hgsc.bcm.edu	37	13	23909162	23909162	+	Silent	SNP	A	A	G	rs9552929	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:23909162A>G	ENST00000382292.3	-	9	9126	c.8853T>C	c.(8851-8853)gtT>gtC	p.V2951V	SACS_ENST00000382298.3_Silent_p.V2951V|SACS_ENST00000402364.1_Silent_p.V2201V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2951					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGTCCTTTACAACATGAATAG	0.353													A|||	1298	0.259185	0.056	0.3617	5008	,	,		20798	0.3145		0.2783	False		,,,				2504	0.3845				p.V2951V		Atlas-SNP	.											.	SACS	871	.	0			c.T8853C						PASS	.	A		427,3979	207.8+/-229.1	21,385,1797	98.0	99.0	99.0		8853	-11.3	0.6	13	dbSNP_119	99	2236,6364	378.4+/-338.9	292,1652,2356	no	coding-synonymous	SACS	NM_014363.4		313,2037,4153	GG,GA,AA		26.0,9.6913,20.4752		2951/4580	23909162	2663,10343	2203	4300	6503	SO:0001819	synonymous_variant	26278	exon10			CTTTACAACATGA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8853T>C	13.37:g.23909162A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	54	19	0.351852	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			A|0.767;G|0.233	0.233	strong		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
MAP4K4	9448	hgsc.bcm.edu	37	2	102472459	102472459	+	Silent	SNP	A	A	G	rs1139583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:102472459A>G	ENST00000347699.4	+	13	1254	c.1254A>G	c.(1252-1254)gaA>gaG	p.E418E	MAP4K4_ENST00000350198.4_Silent_p.E418E|MAP4K4_ENST00000425019.1_Silent_p.E418E|MAP4K4_ENST00000413150.2_Silent_p.E418E|MAP4K4_ENST00000350878.4_Silent_p.E398E|MAP4K4_ENST00000456652.1_Silent_p.E271E|MAP4K4_ENST00000302217.5_Silent_p.E271E|MAP4K4_ENST00000324219.4_Silent_p.E418E	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	418					intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						gagagcgggaagctagaaggc	0.463													A|||	660	0.131789	0.1051	0.0879	5008	,	,		20227	0.0982		0.1789	False		,,,				2504	0.1851				p.E418E		Atlas-SNP	.											.	MAP4K4	111	.	0			c.A1254G						PASS	.	A	,,,,	260,1932		18,224,854	127.0	169.0	155.0		1254,1254,1254,1254,1254	-2.0	0.3	2	dbSNP_86	155	684,3626		53,578,1524	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAP4K4	NM_001242559.1,NM_001242560.1,NM_004834.4,NM_145686.3,NM_145687.3	,,,,	71,802,2378	GG,GA,AA		15.8701,11.8613,14.5186	,,,,	418/1240,418/1236,418/1166,418/1274,418/1213	102472459	944,5558	1096	2155	3251	SO:0001819	synonymous_variant	9448	exon13			GCGGGAAGCTAGA	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.1254A>G	2.37:g.102472459A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_004834	O75172|Q9NST7	Silent	SNP	ENST00000347699.4	37	CCDS56130.1	248	0.11355311355311355	40	0.08130081300813008	34	0.09392265193370165	41	0.07167832167832168	133	0.17546174142480211	A	9.181	1.023658	0.19433	0.118613	0.158701	ENSG00000071054	ENST00000421882	.	.	.	4.29	-1.97	0.07503	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.35830	P	0.17476999999999998	.	.	.	.	.	.	T	0.22382	-1.0218	3	.	.	.	.	8.4533	0.32884	0.5261:0.0:0.4739:0.0	rs1139583;rs2074745;rs11556523;rs17802230;rs57286746;rs1139583	.	.	.	G	158	.	.	S	+	1	0	MAP4K4	101838891	0.999000	0.42202	0.305000	0.25099	0.972000	0.66771	0.324000	0.19610	-0.219000	0.10003	0.377000	0.23210	AGC	A|0.881;G|0.119	0.119	strong		0.463	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
SERTAD4	56256	hgsc.bcm.edu	37	1	210411429	210411429	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:210411429C>T	ENST00000367012.3	+	2	354	c.124C>T	c.(124-126)Cca>Tca	p.P42S	SERTAD4_ENST00000490620.1_3'UTR	NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	42						nucleus (GO:0005634)		p.P42T(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		CCCCCCAGGGCCAGCACAAGC	0.627																																					p.P42S		Atlas-SNP	.											SERTAD4,NS,carcinoma,0,1	SERTAD4	53	1	1	Substitution - Missense(1)	lung(1)	c.C124T						scavenged	.						70.0	71.0	71.0					1																	210411429		2203	4300	6503	SO:0001583	missense	56256	exon2			CCAGGGCCAGCAC	BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.124C>T	1.37:g.210411429C>T	ENSP00000355979:p.Pro42Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	168	3	0.0178571	NM_019605	B2RD32	Missense_Mutation	SNP	ENST00000367012.3	37	CCDS1494.1	.	.	.	.	.	.	.	.	.	.	C	14.69	2.610065	0.46527	.	.	ENSG00000082497	ENST00000367012	.	.	.	5.37	4.45	0.53987	.	0.204142	0.34700	N	0.003760	T	0.26593	0.0650	N	0.24115	0.695	0.23221	N	0.99809	B	0.09022	0.002	B	0.06405	0.002	T	0.13335	-1.0513	9	0.33940	T	0.23	-8.2722	7.9726	0.30136	0.0:0.6072:0.311:0.0819	.	42	Q9NUC0	SRTD4_HUMAN	S	42	.	ENSP00000355979:P42S	P	+	1	0	SERTAD4	208478052	0.998000	0.40836	0.997000	0.53966	0.929000	0.56500	3.498000	0.53302	1.240000	0.43803	0.655000	0.94253	CCA	.	.	none		0.627	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605	
NEB	4703	hgsc.bcm.edu	37	2	152422087	152422087	+	Silent	SNP	A	A	G	rs2288211	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:152422087A>G	ENST00000172853.10	-	88	13338	c.13191T>C	c.(13189-13191)taT>taC	p.Y4397Y	NEB_ENST00000397345.3_Silent_p.Y6098Y|NEB_ENST00000603639.1_Silent_p.Y6098Y|NEB_ENST00000409198.1_Silent_p.Y4397Y|NEB_ENST00000604864.1_Silent_p.Y6098Y|NEB_ENST00000427231.2_Silent_p.Y6098Y			P20929	NEBU_HUMAN	nebulin	4397					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.Y4397Y(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TAAAGTTAGGATAGTTTTCAA	0.388													A|||	1121	0.223842	0.0363	0.3761	5008	,	,		19432	0.3036		0.328	False		,,,				2504	0.18				p.Y6098Y		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	1	Substitution - coding silent(1)	stomach(1)	c.T18294C						PASS	.	A	,,	314,3372		8,298,1537	70.0	63.0	65.0		18294,18294,13191	1.2	1.0	2	dbSNP_100	65	2380,5802		349,1682,2060	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	357,1980,3597	GG,GA,AA		29.0882,8.5187,22.6997	,,	6098/8526,6098/8526,4397/6670	152422087	2694,9174	1843	4091	5934	SO:0001819	synonymous_variant	4703	exon116			GTTAGGATAGTTT	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.13191T>C	2.37:g.152422087A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	132	33	0.25	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				A|0.732;G|0.268	0.268	strong		0.388	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
SHBG	6462	hgsc.bcm.edu	37	17	7536527	7536527	+	Missense_Mutation	SNP	G	G	A	rs6259	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7536527G>A	ENST00000380450.4	+	8	1097	c.1066G>A	c.(1066-1068)Gac>Aac	p.D356N	SHBG_ENST00000416273.3_Silent_p.K286K|SHBG_ENST00000572262.1_Missense_Mutation_p.D244N|SHBG_ENST00000570547.1_Missense_Mutation_p.D183N|SHBG_ENST00000574539.1_Silent_p.K228K|SHBG_ENST00000575314.1_Missense_Mutation_p.D298N|SHBG_ENST00000575903.1_Missense_Mutation_p.D338N|SHBG_ENST00000572182.1_Silent_p.K75K|SHBG_ENST00000340624.5_Silent_p.K228K|SHBG_ENST00000576478.1_Missense_Mutation_p.D129N|SHBG_ENST00000576728.1_Silent_p.K174K|SHBG_ENST00000441599.2_Missense_Mutation_p.D241N	NM_001040.3	NP_001031.2	P04278	SHBG_HUMAN	sex hormone-binding globulin	356	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		D -> N (polymorphism that generates a N- glycosylation site; dbSNP:rs6259). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:1400872, ECO:0000269|PubMed:7714097}.		primary spermatocyte growth (GO:0007285)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	androgen binding (GO:0005497)	p.0?(1)|p.?(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_cancers(10;0.0867)		READ - Rectum adenocarcinoma(115;0.168)	Danazol(DB01406)|Drostanolone(DB00858)|Estradiol(DB00783)|Estropipate(DB04574)|Fluoxymesterone(DB01185)|Hydrocortisone(DB00741)|Methyltestosterone(DB06710)|Mitotane(DB00648)|Norethindrone(DB00717)|Spironolactone(DB00421)|Testosterone(DB00624)|transdermal testosterone gel(DB05275)	TCTAGGAGAAGACTCTTCCAC	0.522											OREG0024140	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	327	0.0652955	0.0091	0.0605	5008	,	,		18617	0.1161		0.1024	False		,,,				2504	0.0542				p.D356N		Atlas-SNP	.											.	SHBG	21	.	2	Unknown(1)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)|bone(1)	c.G1066A	GRCh37	CM994728	SHBG	M	rs6259	PASS	.	G	ASN/ASP,ASN/ASP,,ASN/ASP	158,4248	108.2+/-146.6	4,150,2049	188.0	153.0	165.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1066,1012,858,721	-0.6	0.3	17	dbSNP_52	165	1044,7556	222.4+/-259.5	83,878,3339	yes	missense,missense,coding-synonymous,missense	SHBG	NM_001040.3,NM_001146279.1,NM_001146280.1,NM_001146281.1	23,23,,23	87,1028,5388	AA,AG,GG		12.1395,3.586,9.2419	benign,benign,,benign	356/403,338/385,286/294,241/288	7536527	1202,11804	2203	4300	6503	SO:0001583	missense	6462	exon8			GGAGAAGACTCTT		CCDS11117.1, CCDS54082.1, CCDS54083.1, CCDS58513.1, CCDS73961.1, CCDS73962.1	17p13.1	2013-09-19			ENSG00000129214	ENSG00000129214			10839	protein-coding gene	gene with protein product	"""androgen binding protein"""	182205				2587256	Standard	NM_001146279		Approved	ABP, TEBG, MGC126834, MGC138391	uc002gie.2	P04278	OTTHUMG00000108153	ENST00000380450.4:c.1066G>A	17.37:g.7536527G>A	ENSP00000369816:p.Asp356Asn	Somatic	68	0	0	642	WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_001040	B0FWH4|E9PGW1|F5H5Z8|I3L1N7|P14689|Q16616|Q3MIL0|Q6ISD2	Missense_Mutation	SNP	ENST00000380450.4	37	CCDS11117.1	190	0.08699633699633699	6	0.012195121951219513	21	0.058011049723756904	82	0.14335664335664336	81	0.10686015831134564	G	9.751	1.167367	0.21621	0.03586	0.121395	ENSG00000129214	ENST00000441599;ENST00000380450	D;T	0.82167	-1.58;-1.24	5.08	-0.55	0.11825	Concanavalin A-like lectin/glucanase (1);	0.983616	0.08333	N	0.961970	T	0.01189	0.0039	L	0.29908	0.895	0.52099	P	5.8000000000002494E-5	B;B;B;B	0.12630	0.001;0.002;0.0;0.006	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	T	0.11179	-1.0598	9	0.17369	T	0.5	0.0196	9.1399	0.36897	0.4956:0.0:0.5044:0.0	rs6259;rs4134762;rs52829242;rs57418591;rs6259	160;241;214;356	B0FWH6;E9PGW1;B0FWH4;P04278	.;.;.;SHBG_HUMAN	N	241;356	ENSP00000393426:D241N;ENSP00000369816:D356N	ENSP00000369816:D356N	D	+	1	0	SHBG	7477252	0.000000	0.05858	0.251000	0.24312	0.231000	0.25187	0.070000	0.14573	0.007000	0.14760	-0.253000	0.11424	GAC	G|0.910;A|0.090	0.090	strong		0.522	SHBG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226957.2	NM_001040	
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815681	23815681	+	Silent	SNP	G	G	A	rs17574213	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:23815681G>A	ENST00000264867.2	-	8	1544	c.1425C>T	c.(1423-1425)gaC>gaT	p.D475D	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	475	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				CTGCTTCGTCGTCAAAAACAG	0.468													G|||	117	0.0233626	0.0174	0.0403	5008	,	,		19749	0.0		0.0497	False		,,,				2504	0.0164				p.D475D	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.C1425T						PASS	.	G		138,4268	98.9+/-137.6	3,132,2068	116.0	104.0	108.0		1425	0.9	1.0	4	dbSNP_123	108	580,8020	155.4+/-209.4	21,538,3741	no	coding-synonymous	PPARGC1A	NM_013261.3		24,670,5809	AA,AG,GG		6.7442,3.1321,5.5205		475/799	23815681	718,12288	2203	4300	6503	SO:0001819	synonymous_variant	10891	exon8			TTCGTCGTCAAAA	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.1425C>T	4.37:g.23815681G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	37	CCDS3429.1																																																																																			G|0.955;A|0.045	0.045	strong		0.468	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
CDR1	1038	hgsc.bcm.edu	37	X	139866477	139866477	+	Missense_Mutation	SNP	T	T	C	rs41299075	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:139866477T>C	ENST00000370532.2	-	1	246	c.55A>G	c.(55-57)Ata>Gta	p.I19V		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	19	23 X 6 AA approximate repeats.									breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				AACAAAGGTATGTCTTCCAAC	0.418													t|||	362	0.095894	0.121	0.0403	3775	,	,		16678	0.0079		0.0646	False		,,,				2504	0.1033				p.I19V		Atlas-SNP	.											.	CDR1	58	.	0			c.A55G						PASS	.	C	VAL/ILE	468,3367		21,355,71,1256,500	182.0	172.0	176.0		55	-6.9	0.0	X	dbSNP_127	176	612,6116		23,389,177,2016,1695	yes	missense	CDR1	NM_004065.2	29	44,744,248,3272,2195	CC,CT,C,TT,T		9.0963,12.2034,10.2244	benign	19/263	139866477	1080,9483	2203	4300	6503	SO:0001583	missense	1038	exon1			AAGGTATGTCTTC		CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"""Cerebellar degeneration-related protein-1 (34kD)"""	302650	"""cerebellar degeneration-related protein (34kD)"""	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.55A>G	X.37:g.139866477T>C	ENSP00000359563:p.Ile19Val	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	226	162	0.716814	NM_004065	Q5JXH6	Missense_Mutation	SNP	ENST00000370532.2	37	CCDS14670.1	117	0.0705244122965642	30	0.06437768240343347	9	0.025714285714285714	5	0.008802816901408451	32	0.04456824512534819	t	0.005	-2.163025	0.00318	0.122034	0.090963	ENSG00000184258	ENST00000370532	T	0.28069	1.63	3.45	-6.9	0.01655	.	.	.	.	.	T	0.00144	0.0004	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26677	-1.0096	7	.	.	.	.	10.1854	0.42995	0.0:0.1082:0.2802:0.6115	rs41299075	19	P51861	CDR1_HUMAN	V	19	ENSP00000359563:I19V	.	I	-	1	0	CDR1	139694143	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-11.934000	0.00002	-3.884000	0.00095	-2.193000	0.00311	ATA	T|0.901;C|0.099	0.099	strong		0.418	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065	
CDC27	996	hgsc.bcm.edu	37	17	45214604	45214604	+	Missense_Mutation	SNP	A	A	T	rs75661039		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:45214604A>T	ENST00000066544.3	-	14	1920	c.1827T>A	c.(1825-1827)caT>caA	p.H609Q	CDC27_ENST00000531206.1_Missense_Mutation_p.H615Q|CDC27_ENST00000527547.1_Missense_Mutation_p.H608Q|CDC27_ENST00000446365.2_Missense_Mutation_p.H548Q	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	609					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AGACAAACTCATGCCCTAATA	0.368																																					p.H615Q		Atlas-SNP	.											.	CDC27	337	.	0			c.T1845A						PASS	.																																			SO:0001583	missense	996	exon14			AAACTCATGCCCT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1827T>A	17.37:g.45214604A>T	ENSP00000066544:p.His609Gln	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	20	4	0.2	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.387750	0.82902	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.58358	0.34;0.34;0.34;0.34	5.81	-1.66	0.08265	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.72374	0.3452	M	0.90019	3.08	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.999;0.999;0.998	D;D;D;D	0.74348	0.983;0.971;0.979;0.976	T	0.74090	-0.3777	10	0.87932	D	0	-29.2384	11.9196	0.52785	0.494:0.0:0.506:0.0	.	548;608;615;609	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	Q	609;615;548;608	ENSP00000066544:H609Q;ENSP00000434614:H615Q;ENSP00000392802:H548Q;ENSP00000437339:H608Q	ENSP00000066544:H609Q	H	-	3	2	CDC27	42569603	0.800000	0.28916	0.974000	0.42286	0.997000	0.91878	0.088000	0.14979	-0.648000	0.05437	0.477000	0.44152	CAT	A|0.993;T|0.007	0.007	weak		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
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 GAIIx	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		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	41	17	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	
DGKH	160851	hgsc.bcm.edu	37	13	42729441	42729441	+	Silent	SNP	C	C	T	rs3208827	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:42729441C>T	ENST00000337343.4	+	4	420	c.399C>T	c.(397-399)ttC>ttT	p.F133F	DGKH_ENST00000536612.1_5'UTR|DGKH_ENST00000540693.1_Silent_p.F133F|DGKH_ENST00000379274.2_5'UTR|DGKH_ENST00000538674.1_5'UTR|DGKH_ENST00000261491.5_Silent_p.F133F|DGKH_ENST00000498255.2_3'UTR	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	133	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TCACTCCATTCAGAAGGCTAA	0.403													C|||	258	0.0515176	0.0159	0.0476	5008	,	,		19636	0.0179		0.0994	False		,,,				2504	0.0879				p.F133F		Atlas-SNP	.											.	DGKH	106	.	0			c.C399T						PASS	.	C	,,,,	111,4295	87.3+/-125.9	1,109,2093	148.0	144.0	145.0		399,,,399,399	3.0	1.0	13	dbSNP_126	145	932,7668	206.5+/-248.5	51,830,3419	no	coding-synonymous,utr-5,utr-5,coding-synonymous,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	52,939,5512	TT,TC,CC		10.8372,2.5193,8.0194	,,,,	133/1165,,,133/1165,133/1221	42729441	1043,11963	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon5			TCCATTCAGAAGG	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.399C>T	13.37:g.42729441C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	248	73	0.294355	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			C|0.928;T|0.072	0.072	strong		0.403	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
FRG2B	441581	hgsc.bcm.edu	37	10	135440203	135440203	+	Missense_Mutation	SNP	A	A	T	rs200661929	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135440203A>T	ENST00000425520.1	-	1	96	c.44T>A	c.(43-45)aTc>aAc	p.I15N	FRG2B_ENST00000443774.1_Missense_Mutation_p.I15N	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	15						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		GGAGCACTGGATGGAGGAGCA	0.507													.|||	867	0.173123	0.1437	0.1254	5008	,	,		19912	0.2411		0.0885	False		,,,				2504	0.2638				p.I15N		Atlas-SNP	.											FRG2B,NS,haematopoietic_neoplasm,0,1	FRG2B	47	1	0			c.T44A						scavenged	.	A	ASN/ILE	303,4103		0,303,1900	227.0	254.0	245.0		44	0.1	0.0	10		245	380,8220		0,380,3920	no	missense	FRG2B	NM_001080998.1	149	0,683,5820	TT,TA,AA		4.4186,6.877,5.2514	benign	15/279	135440203	683,12323	2203	4300	6503	SO:0001583	missense	441581	exon1			CACTGGATGGAGG	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.44T>A	10.37:g.135440203A>T	ENSP00000401310:p.Ile15Asn	Somatic	633	0	0		WXS	Illumina HiSeq	Phase_I	687	138	0.200873	NM_001080998	Q5VSQ1	Missense_Mutation	SNP	ENST00000425520.1	37	CCDS44502.1	.	.	.	.	.	.	.	.	.	.	.	3.902	-0.021862	0.07634	0.06877	0.044186	ENSG00000225899	ENST00000443774;ENST00000425520	T;T	0.44881	0.91;0.91	0.109	0.109	0.14578	.	2.975530	0.01571	N	0.020585	T	0.01905	0.0060	N	0.14661	0.345	0.09310	N	1	B	0.31859	0.343	B	0.24155	0.051	T	0.14227	-1.0480	9	0.87932	D	0	1.8074	.	.	.	.	15	Q96QU4	FRG2B_HUMAN	N	15	ENSP00000408343:I15N;ENSP00000401310:I15N	ENSP00000401310:I15N	I	-	2	0	FRG2B	135290193	0.957000	0.32711	0.030000	0.17652	0.030000	0.12068	0.803000	0.27083	0.156000	0.19299	0.155000	0.16302	ATC	A|0.986;T|0.014	0.014	strong		0.507	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
GET4	51608	hgsc.bcm.edu	37	7	930689	930689	+	Silent	SNP	C	C	T	rs13171	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:930689C>T	ENST00000265857.3	+	5	685	c.591C>T	c.(589-591)gcC>gcT	p.A197A	GET4_ENST00000407192.1_Silent_p.A144A	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	197					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TGTTCGTGGCCCAGGCCGTGC	0.617													C|||	1007	0.201078	0.0862	0.2435	5008	,	,		17773	0.2669		0.1879	False		,,,				2504	0.272				p.A197A		Atlas-SNP	.											GET4,NS,carcinoma,0,1	GET4	17	1	0			c.C591T						PASS	.	C		437,3969	207.5+/-228.8	23,391,1789	110.0	88.0	95.0		591	-2.1	1.0	7	dbSNP_52	95	1435,7165	275.4+/-291.8	116,1203,2981	no	coding-synonymous	GET4	NM_015949.2		139,1594,4770	TT,TC,CC		16.686,9.9183,14.3934		197/328	930689	1872,11134	2203	4300	6503	SO:0001819	synonymous_variant	51608	exon5			CGTGGCCCAGGCC	AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"""CGI-20 protein"", ""conserved edge protein"", ""transmembrane domain recognition complex, 35kDa"""	612056	"""chromosome 7 open reading frame 20"""	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.591C>T	7.37:g.930689C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	291	156	0.536082	NM_015949	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Silent	SNP	ENST00000265857.3	37	CCDS5317.1																																																																																			C|0.831;T|0.169	0.169	strong		0.617	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949	
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 GAIIx	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		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	57	31	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	
KDM2B	84678	hgsc.bcm.edu	37	12	121881848	121881848	+	Silent	SNP	G	G	A	rs10849885	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121881848G>A	ENST00000377071.4	-	16	2490	c.2418C>T	c.(2416-2418)taC>taT	p.Y806Y	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Silent_p.Y775Y|KDM2B_ENST00000542973.1_Silent_p.Y174Y	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	806					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						GGGGCTTCTCGTATTTCCGCT	0.657											OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1617	0.322883	0.1543	0.3919	5008	,	,		14673	0.4435		0.3956	False		,,,				2504	0.3027				p.Y806Y		Atlas-SNP	.											KDM2B_ENST00000377071,NS,carcinoma,0,2	KDM2B	218	2	0			c.C2418T						PASS	.	G	,	724,3338		72,580,1379	68.0	75.0	73.0		2325,2418	-9.6	0.3	12	dbSNP_120	73	3095,5229		576,1943,1643	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	648,2523,3022	AA,AG,GG		37.1816,17.8237,30.8332	,	775/1266,806/1337	121881848	3819,8567	2031	4162	6193	SO:0001819	synonymous_variant	84678	exon16			CTTCTCGTATTTC	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2418C>T	12.37:g.121881848G>A		Somatic	59	0	0	1514	WXS	Illumina HiSeq	Phase_I	82	48	0.585366	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.666;A|0.334	0.334	strong		0.657	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
KCNH2	3757	hgsc.bcm.edu	37	7	150649603	150649603	+	Silent	SNP	G	G	A	rs740952	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150649603G>A	ENST00000262186.5	-	6	1868	c.1467C>T	c.(1465-1467)atC>atT	p.I489I	KCNH2_ENST00000430723.3_Silent_p.I489I|KCNH2_ENST00000392968.2_Silent_p.I393I|KCNH2_ENST00000330883.4_Silent_p.I149I	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	489					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	AGTGGACGGCGATGCGGCCGG	0.592													G|||	1716	0.342652	0.2632	0.3372	5008	,	,		19711	0.6131		0.2127	False		,,,				2504	0.3088				p.I489I	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.C1467T						PASS	.	G	,,,	1158,3248	409.1+/-334.9	154,850,1199	129.0	112.0	118.0		1467,447,1467,447	-1.3	1.0	7	dbSNP_86	118	1836,6764	329.6+/-318.8	201,1434,2665	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNH2	NM_000238.3,NM_001204798.1,NM_172056.2,NM_172057.2	,,,	355,2284,3864	AA,AG,GG		21.3488,26.2823,23.0201	,,,	489/1160,149/549,489/889,149/820	150649603	2994,10012	2203	4300	6503	SO:0001819	synonymous_variant	3757	exon6			GACGGCGATGCGG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1467C>T	7.37:g.150649603G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	37	CCDS5910.1																																																																																			A|0.278;G|0.722;T|0.000	0.278	strong		0.592	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
FAT2	2196	hgsc.bcm.edu	37	5	150901630	150901630	+	Silent	SNP	G	G	T	rs3734049	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150901630G>T	ENST00000261800.5	-	18	10536	c.10524C>A	c.(10522-10524)atC>atA	p.I3508I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3508	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGAGGGGAGGGATGCCACTGT	0.572													G|||	488	0.0974441	0.0083	0.1585	5008	,	,		20709	0.126		0.1948	False		,,,				2504	0.045				p.I3508I		Atlas-SNP	.											.	FAT2	465	.	0			c.C10524A						PASS	.	G		161,4245	104.3+/-142.8	5,151,2047	39.0	34.0	35.0		10524	2.3	0.5	5	dbSNP_107	35	1819,6781	314.2+/-311.7	203,1413,2684	no	coding-synonymous	FAT2	NM_001447.2		208,1564,4731	TT,TG,GG		21.1512,3.6541,15.2237		3508/4350	150901630	1980,11026	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon18			GGGAGGGATGCCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10524C>A	5.37:g.150901630G>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	25	7	0.28	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	290	0.13278388278388278	6	0.012195121951219513	65	0.17955801104972377	82	0.14335664335664336	137	0.18073878627968337	G	6.259	0.415816	0.11870	0.036541	0.211512	ENSG00000086570	ENST00000520200	.	.	.	5.14	2.28	0.28536	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.18053	-1.0349	3	.	.	.	.	4.0795	0.09919	0.1445:0.1277:0.5961:0.1316	rs3734049;rs59902096;rs3734049	.	.	.	T	367	.	.	P	-	1	0	FAT2	150881823	0.930000	0.31532	0.496000	0.27539	0.869000	0.49853	1.367000	0.34204	0.652000	0.30806	0.563000	0.77884	CCC	G|0.872;T|0.128	0.128	strong		0.572	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
KAL1	3730	hgsc.bcm.edu	37	X	8504833	8504833	+	Missense_Mutation	SNP	C	C	T	rs808119	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:8504833C>T	ENST00000262648.3	-	11	1749	c.1600G>A	c.(1600-1602)Gtt>Att	p.V534I	KAL1_ENST00000481896.1_5'UTR	NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	534			V -> I (in dbSNP:rs808119). {ECO:0000269|PubMed:11297579, ECO:0000269|PubMed:15001591, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17223984, ECO:0000269|PubMed:1913827, ECO:0000269|PubMed:1922361, ECO:0000269|PubMed:8504298, ECO:0000269|PubMed:8989261, ECO:0000269|PubMed:9589672, ECO:0000269|Ref.5}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						AGGCAGCCAACAGGCTTGTGG	0.507													C|||	1843	0.488212	0.2458	0.3487	3775	,	,		14377	0.506		0.5089	False		,,,				2504	0.2597				p.V534I		Atlas-SNP	.											.	KAL1	78	.	0			c.G1600A						PASS	.	C	ILE/VAL	1441,2394		233,766,209,633,362	78.0	59.0	65.0		1600	-4.1	0.0	X	dbSNP_86	65	4512,2216		1099,1062,1252,267,620	no	missense	KAL1	NM_000216.2	29	1332,1828,1461,900,982	TT,TC,T,CC,C		32.937,37.575,43.6429	benign	534/681	8504833	5953,4610	2203	4300	6503	SO:0001583	missense	3730	exon11			AGCCAACAGGCTT		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1600G>A	X.37:g.8504833C>T	ENSP00000262648:p.Val534Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	37	CCDS14130.1	913	0.5503315250150693	72	0.17391304347826086	79	0.3015267175572519	194	0.5418994413407822	247	0.4862204724409449	C	0.004	-2.328820	0.00229	0.37575	0.67063	ENSG00000011201	ENST00000262648	T	0.73363	-0.74	3.89	-4.09	0.03951	.	0.740248	0.12185	N	0.491758	T	0.00012	0.0000	N	0.03238	-0.38	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.27938	-1.0059	9	0.02654	T	1	-1.3626	7.395	0.26931	0.1398:0.1336:0.0:0.7266	rs808119;rs56908549	534	P23352	KALM_HUMAN	I	534	ENSP00000262648:V534I	ENSP00000262648:V534I	V	-	1	0	KAL1	8464833	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	-0.458000	0.06737	-1.055000	0.03209	-0.198000	0.12761	GTT	C|0.447;T|0.553	0.553	strong		0.507	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
FYCO1	79443	hgsc.bcm.edu	37	3	46007825	46007825	+	Missense_Mutation	SNP	T	T	C	rs71622515|rs13059238	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46007825T>C	ENST00000296137.2	-	8	3206	c.3001A>G	c.(3001-3003)Aac>Gac	p.N1001D	FYCO1_ENST00000535325.1_Missense_Mutation_p.N1001D	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1001			N -> D (in dbSNP:rs13059238).		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)		TTGAGGGTGTTGAGCTCCTGG	0.617													C|||	548	0.109425	0.0189	0.0634	5008	,	,		19562	0.004		0.1233	False		,,,				2504	0.3589				p.N1001D		Atlas-SNP	.											.	FYCO1	115	.	0			c.A3001G						PASS	.	C	ASP/ASN	40,4366	819.4+/-416.4	1,38,2164	95.0	82.0	86.0		3001	2.3	0.2	3	dbSNP_121	86	35,8565	809.3+/-407.2	5,25,4270	no	missense	FYCO1	NM_024513.2	23	6,63,6434	CC,CT,TT		0.407,0.9079,0.5767	benign	1001/1479	46007825	75,12931	2203	4300	6503	SO:0001583	missense	79443	exon8			GGGTGTTGAGCTC	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.3001A>G	3.37:g.46007825T>C	ENSP00000296137:p.Asn1001Asp	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	161	64	0.397516	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	136	0.06227106227106227	10	0.02032520325203252	21	0.058011049723756904	0	0.0	105	0.13852242744063326	C	0.383	-0.927848	0.02377	0.009079	0.00407	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.79554	-1.28;-1.28	5.49	2.29	0.28610	.	0.437095	0.25572	N	0.029755	T	0.00468	0.0015	N	0.02916	-0.46	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04781	-1.0927	9	0.06625	T	0.88	-17.5834	4.0771	0.09909	0.2588:0.4452:0.0:0.296	rs13059238;rs13059238	1001;1001	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	D	1001	ENSP00000296137:N1001D;ENSP00000441178:N1001D	ENSP00000296137:N1001D	N	-	1	0	FYCO1	45982829	0.017000	0.18338	0.216000	0.23742	0.995000	0.86356	0.889000	0.28282	0.260000	0.21731	-0.119000	0.15052	AAC	T|0.928;C|0.072	0.072	strong		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
CD19	930	hgsc.bcm.edu	37	16	28944700	28944700	+	Silent	SNP	G	G	T	rs35979293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28944700G>T	ENST00000324662.3	+	4	749	c.705G>T	c.(703-705)ccG>ccT	p.P235P	CD19_ENST00000538922.1_Silent_p.P235P|CD19_ENST00000567541.1_Silent_p.P235P			P15391	CD19_HUMAN	CD19 molecule	235	Ig-like C2-type 2.				B cell receptor signaling pathway (GO:0050853)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(4)|urinary_tract(1)	29						ACGATCGCCCGGCCAGAGATA	0.587													G|||	937	0.187101	0.0711	0.2406	5008	,	,		17615	0.1726		0.3976	False		,,,				2504	0.1043				p.P235P		Atlas-SNP	.											.	CD19	65	.	0			c.G705T						PASS	.	G	,	509,3885	233.3+/-246.5	21,467,1709	67.0	65.0	66.0		705,705	-8.5	0.0	16	dbSNP_126	66	3069,5531	470.9+/-367.9	541,1987,1772	no	coding-synonymous,coding-synonymous	CD19	NM_001178098.1,NM_001770.5	,	562,2454,3481	TT,TG,GG		35.686,11.584,27.5358	,	235/558,235/557	28944700	3578,9416	2197	4300	6497	SO:0001819	synonymous_variant	930	exon4			TCGCCCGGCCAGA		CCDS10644.1, CCDS53998.1	16p11.2	2014-09-17	2006-03-28		ENSG00000177455	ENSG00000177455		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1633	protein-coding gene	gene with protein product		107265	"""CD19 antigen"""				Standard	NM_001770		Approved		uc010byo.2	P15391	OTTHUMG00000097049	ENST00000324662.3:c.705G>T	16.37:g.28944700G>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_001178098	A0N0P9|F5H635|Q96S68|Q9BRD6	Silent	SNP	ENST00000324662.3	37	CCDS10644.1																																																																																			G|0.736;T|0.264	0.264	strong		0.587	CD19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214152.2		
OSBPL7	114881	hgsc.bcm.edu	37	17	45890707	45890707	+	Silent	SNP	C	C	T	rs2301690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:45890707C>T	ENST00000007414.3	-	16	1853	c.1662G>A	c.(1660-1662)aaG>aaA	p.K554K	OSBPL7_ENST00000392507.3_Silent_p.K554K	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	554					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						GGTTGAAGGGCTTGCAGCCGG	0.622													c|||	795	0.158746	0.0643	0.2233	5008	,	,		19047	0.0139		0.3569	False		,,,				2504	0.1861				p.K554K		Atlas-SNP	.											.	OSBPL7	65	.	0			c.G1662A						PASS	.			480,3926	224.6+/-240.7	22,436,1745	65.0	64.0	64.0		1662	1.4	1.0	17	dbSNP_100	64	3302,5298	494.0+/-373.7	653,1996,1651	no	coding-synonymous	OSBPL7	NM_145798.2		675,2432,3396	TT,TC,CC		38.3953,10.8942,29.0789		554/843	45890707	3782,9224	2203	4300	6503	SO:0001819	synonymous_variant	114881	exon16			GAAGGGCTTGCAG	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.1662G>A	17.37:g.45890707C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																			C|0.759;T|0.241	0.241	strong		0.622	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
ZNF460	10794	hgsc.bcm.edu	37	19	57802911	57802911	+	Silent	SNP	G	G	A	rs36032958	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57802911G>A	ENST00000360338.3	+	3	1324	c.1002G>A	c.(1000-1002)agG>agA	p.R334R	ZNF460_ENST00000537645.1_Silent_p.R293R	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	334					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)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CTGGGGAGAGGCCCTTTAAGT	0.502													g|||	142	0.0283546	0.0023	0.049	5008	,	,		21455	0.0		0.0875	False		,,,				2504	0.0174				p.R334R		Atlas-SNP	.											.	ZNF460	59	.	0			c.G1002A						PASS	.	G		64,4342	59.3+/-96.0	0,64,2139	88.0	79.0	82.0		1002	1.8	0.5	19	dbSNP_126	82	643,7957	164.3+/-216.7	24,595,3681	no	coding-synonymous	ZNF460	NM_006635.3		24,659,5820	AA,AG,GG		7.4767,1.4526,5.436		334/563	57802911	707,12299	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			GGAGAGGCCCTTT	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.1002G>A	19.37:g.57802911G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			G|0.947;A|0.053	0.053	strong		0.502	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
KY	339855	hgsc.bcm.edu	37	3	134322814	134322814	+	Silent	SNP	G	G	C	rs2293294	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:134322814G>C	ENST00000423778.2	-	11	1654	c.1593C>G	c.(1591-1593)ggC>ggG	p.G531G	KY_ENST00000503669.1_3'UTR|KY_ENST00000508956.1_Silent_p.G510G	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	531					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)	p.G531G(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGGCAAACTTGCCTGCATGGG	0.527													G|||	1482	0.295927	0.413	0.2349	5008	,	,		20559	0.1101		0.33	False		,,,				2504	0.3374				p.G531G		Atlas-SNP	.											KY_ENST00000423778,NS,carcinoma,0,1	KY	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C1593G						scavenged	.	G		1556,2496		331,894,801	79.0	81.0	80.0		1593	3.8	1.0	3	dbSNP_100	80	2993,5407		564,1865,1771	no	coding-synonymous	KY	NM_178554.4		895,2759,2572	CC,CG,GG		35.631,38.4008,36.5323		531/662	134322814	4549,7903	2026	4200	6226	SO:0001819	synonymous_variant	339855	exon11			AAACTTGCCTGCA	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1593C>G	3.37:g.134322814G>C		Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			G|0.694;C|0.306	0.306	strong		0.527	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
ATP13A4	84239	hgsc.bcm.edu	37	3	193210768	193210768	+	Silent	SNP	A	A	G	rs2130407	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193210768A>G	ENST00000342695.4	-	5	793	c.471T>C	c.(469-471)ctT>ctC	p.L157L	ATP13A4_ENST00000392443.3_Silent_p.L157L|ATP13A4_ENST00000295548.3_Silent_p.L157L	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	157						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)		TGGCAGAACTAAGCCAGTCTT	0.318													G|||	2641	0.527356	0.6573	0.5029	5008	,	,		16069	0.5476		0.4036	False		,,,				2504	0.4755				p.L157L		Atlas-SNP	.											.	ATP13A4	154	.	0			c.T471C						PASS	.	G		2708,1698	511.9+/-367.9	814,1080,309	134.0	129.0	131.0		471	1.5	1.0	3	dbSNP_96	131	3530,5068	629.8+/-398.3	746,2038,1515	no	coding-synonymous	ATP13A4	NM_032279.2		1560,3118,1824	GG,GA,AA		41.0561,38.5384,47.9699		157/1197	193210768	6238,6766	2203	4299	6502	SO:0001819	synonymous_variant	84239	exon5			AGAACTAAGCCAG	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.471T>C	3.37:g.193210768A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	48	0.571429	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			A|0.508;G|0.492	0.492	strong		0.318	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
ZNF792	126375	hgsc.bcm.edu	37	19	35449409	35449409	+	Silent	SNP	G	G	A	rs2651081	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35449409G>A	ENST00000404801.1	-	4	1736	c.1350C>T	c.(1348-1350)caC>caT	p.H450H	ZNF792_ENST00000605484.1_Silent_p.H383H	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	450					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H371H(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CACCACACCCGTGAGGCCGCT	0.502													G|||	1639	0.327276	0.4841	0.1859	5008	,	,		21139	0.2034		0.329	False		,,,				2504	0.3415				p.H450H	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											FLJ38451,NS,carcinoma,0,1	ZNF792	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C1350T						PASS	.	G		1953,2453	554.8+/-379.1	408,1137,658	117.0	115.0	116.0		1350	-0.8	0.0	19	dbSNP_100	116	2546,6054	416.0+/-352.0	383,1780,2137	no	coding-synonymous	ZNF792	NM_175872.4		791,2917,2795	AA,AG,GG		29.6047,44.3259,34.5917		450/633	35449409	4499,8507	2203	4300	6503	SO:0001819	synonymous_variant	126375	exon4			ACACCCGTGAGGC	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.1350C>T	19.37:g.35449409G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Silent	SNP	ENST00000404801.1	37	CCDS12440.2																																																																																			G|0.659;A|0.341	0.341	strong		0.502	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
PRICKLE4	29964	hgsc.bcm.edu	37	6	41753084	41753084	+	Silent	SNP	C	C	T	rs9394831	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41753084C>T	ENST00000394260.1	+	3	268	c.268C>T	c.(268-270)Ctg>Ttg	p.L90L	PRICKLE4_ENST00000394259.1_Silent_p.L90L|TOMM6_ENST00000398884.3_5'Flank|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000463606.1_3'UTR|PRICKLE4_ENST00000359201.5_Silent_p.L130L|PRICKLE4_ENST00000458694.1_Silent_p.L130L|PRICKLE4_ENST00000394263.1_Silent_p.L130L			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	90	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GTGTAGGGAGCTGCTGAAGCC	0.612													C|||	815	0.16274	0.0159	0.1297	5008	,	,		18817	0.3016		0.2525	False		,,,				2504	0.1493				p.L130L		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.C388T						PASS	.	C		242,4164	141.5+/-176.9	12,218,1973	44.0	42.0	43.0		388	2.7	0.8	6	dbSNP_119	43	2210,6390	375.2+/-337.7	315,1580,2405	no	coding-synonymous	PRICKLE4	NM_013397.5		327,1798,4378	TT,TC,CC		25.6977,5.4925,18.8528		130/385	41753084	2452,10554	2203	4300	6503	SO:0001819	synonymous_variant	29964	exon6			AGGGAGCTGCTGA	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.268C>T	6.37:g.41753084C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	52	0.787879	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Silent	SNP	ENST00000394260.1	37																																																																																				C|0.821;T|0.179	0.179	strong		0.612	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
PIWIL4	143689	hgsc.bcm.edu	37	11	94326765	94326765	+	Missense_Mutation	SNP	G	G	C	rs57607909	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:94326765G>C	ENST00000299001.6	+	9	1319	c.1108G>C	c.(1108-1110)Gct>Cct	p.A370P	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	370	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.		A -> P (in dbSNP:rs57607909). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CAACAGTGAGGCTCAGCTCGC	0.438													G|||	1151	0.229832	0.3071	0.1686	5008	,	,		18030	0.2649		0.2286	False		,,,				2504	0.1339				p.A370P		Atlas-SNP	.											.	PIWIL4	70	.	0			c.G1108C						PASS	.	G	PRO/ALA	1234,3168	426.6+/-341.2	163,908,1130	149.0	148.0	148.0		1108	-1.1	0.0	11	dbSNP_129	148	1922,6674	340.9+/-323.8	225,1472,2601	yes	missense	PIWIL4	NM_152431.2	27	388,2380,3731	CC,CG,GG		22.3592,28.0327,24.2807	benign	370/853	94326765	3156,9842	2201	4298	6499	SO:0001583	missense	143689	exon9			AGTGAGGCTCAGC	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1108G>C	11.37:g.94326765G>C	ENSP00000299001:p.Ala370Pro	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	104	18	0.173077	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	509	0.23305860805860806	135	0.27439024390243905	69	0.19060773480662985	136	0.23776223776223776	169	0.22295514511873352	G	0.011	-1.692544	0.00731	0.280327	0.223592	ENSG00000134627	ENST00000299001	T	0.09073	3.02	4.77	-1.1	0.09872	Argonaute/Dicer protein, PAZ (4);	0.585427	0.15970	N	0.235824	T	0.00012	0.0000	N	0.13043	0.29	0.54753	P	1.8999999999991246E-5	B	0.02656	0.0	B	0.09377	0.004	T	0.46830	-0.9163	9	0.30078	T	0.28	-0.0363	13.5706	0.61845	0.0775:0.6422:0.2803:0.0	rs57607909	370	Q7Z3Z4	PIWL4_HUMAN	P	370	ENSP00000299001:A370P	ENSP00000299001:A370P	A	+	1	0	PIWIL4	93966413	0.488000	0.25996	0.005000	0.12908	0.009000	0.06853	0.106000	0.15354	-0.073000	0.12842	-0.379000	0.06801	GCT	G|0.768;C|0.232	0.232	strong		0.438	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
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 GAIIx	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	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	91	27	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	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59500116	59500116	+	Missense_Mutation	SNP	T	T	C	rs3825937	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:59500116T>C	ENST00000307144.4	+	1	1075	c.977T>C	c.(976-978)aTt>aCt	p.I326T	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	326			I -> T (in dbSNP:rs3825937). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						TCCACCATAATTAAGGGCCTC	0.393													T|||	1998	0.398962	0.2496	0.3934	5008	,	,		19264	0.5694		0.2734	False		,,,				2504	0.5583				p.I326T		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.T977C						PASS	.	T	,THR/ILE	1144,3238	380.4+/-323.7	168,808,1215	80.0	86.0	84.0		,977	1.5	1.0	15	dbSNP_107	84	2385,6191	388.1+/-342.4	328,1729,2231	no	intron,missense	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,89	496,2537,3446	CC,CT,TT		27.8102,26.1068,27.2341	,benign	,326/382	59500116	3529,9429	2191	4288	6479	SO:0001583	missense	92483	exon1			CCATAATTAAGGG	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.977T>C	15.37:g.59500116T>C	ENSP00000302393:p.Ile326Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	37	CCDS10171.1	793	0.3630952380952381	120	0.24390243902439024	126	0.34806629834254144	340	0.5944055944055944	207	0.27308707124010556	T	18.32	3.597035	0.66332	0.261068	0.278102	ENSG00000171989	ENST00000307144	T	0.63255	-0.03	1.47	1.47	0.22746	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.099877	0.42964	U	0.000632	T	0.00012	0.0000	M	0.71581	2.175	0.37666	P	0.07706800000000003	B	0.22414	0.069	P	0.46320	0.512	T	0.48570	-0.9024	9	0.54805	T	0.06	.	4.9571	0.14048	0.0:0.0:0.0:1.0	rs3825937;rs17856652;rs59074481;rs3825937	326	Q9BYZ2	LDH6B_HUMAN	T	326	ENSP00000302393:I326T	ENSP00000302393:I326T	I	+	2	0	LDHAL6B	57287408	0.999000	0.42202	0.963000	0.40424	0.968000	0.65278	4.730000	0.62015	0.654000	0.30846	0.254000	0.18369	ATT	T|0.679;C|0.321	0.321	strong		0.393	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
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 GAIIx	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*	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	196	95	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		
SMOC1	64093	hgsc.bcm.edu	37	14	70418881	70418881	+	Silent	SNP	G	G	A	rs3742909	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:70418881G>A	ENST00000381280.4	+	2	379	c.126G>A	c.(124-126)caG>caA	p.Q42Q	SMOC1_ENST00000361956.3_Silent_p.Q42Q|SMOC1_ENST00000555917.1_3'UTR	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	42	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GTGACCCACAGTGCAACCTCC	0.507													G|||	1087	0.217053	0.0076	0.3718	5008	,	,		20143	0.375		0.2634	False		,,,				2504	0.18				p.Q42Q		Atlas-SNP	.											.	SMOC1	61	.	0			c.G126A						PASS	.	G	,	272,4134	153.7+/-187.2	12,248,1943	126.0	116.0	120.0		126,126	4.5	1.0	14	dbSNP_107	120	2163,6437	372.1+/-336.5	259,1645,2396	no	coding-synonymous,coding-synonymous	SMOC1	NM_001034852.2,NM_022137.5	,	271,1893,4339	AA,AG,GG		25.1512,6.1734,18.7221	,	42/436,42/435	70418881	2435,10571	2203	4300	6503	SO:0001819	synonymous_variant	64093	exon2			CCCACAGTGCAAC	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.126G>A	14.37:g.70418881G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	73	71	0.972603	NM_001034852	A8K1S3|B2R7P5|Q96F78	Silent	SNP	ENST00000381280.4	37	CCDS9798.1																																																																																			G|0.784;A|0.216	0.216	strong		0.507	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1		
PDHB	5162	hgsc.bcm.edu	37	3	58416535	58416535	+	Silent	SNP	C	C	T	rs1126551	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:58416535C>T	ENST00000302746.6	-	6	480	c.438G>A	c.(436-438)ggG>ggA	p.G146G	PDHB_ENST00000485460.1_Intron|PDHB_ENST00000474765.1_Silent_p.G128G|RP11-802O23.3_ENST00000607214.1_RNA	NM_000925.3|NM_001173468.1	NP_000916.2|NP_001166939.1	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta	146					acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	9				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	Pyruvic acid(DB00119)	CACCATTGGGCCCTCTGAAGA	0.532													c|||	1025	0.204673	0.2133	0.2839	5008	,	,		15206	0.001		0.3757	False		,,,				2504	0.1708				p.G146G		Atlas-SNP	.											PDHB,NS,carcinoma,0,1	PDHB	19	1	0			c.G438A						PASS	.	T	,	127,4279		55,17,2131	87.0	88.0	88.0		438,	-5.5	0.8	3	dbSNP_86	88	732,7868		282,168,3850	no	coding-synonymous,intron	PDHB	NM_000925.3,NM_001173468.1	,	337,185,5981	TT,TC,CC		8.5116,2.8824,6.6046	,	146/360,	58416535	859,12147	2203	4300	6503	SO:0001819	synonymous_variant	5162	exon6			ATTGGGCCCTCTG		CCDS2890.1, CCDS54602.1	3p21.1-p14.2	1995-12-20			ENSG00000168291	ENSG00000168291	1.2.4.1		8808	protein-coding gene	gene with protein product		179060					Standard	NR_033384		Approved		uc003dkf.4	P11177	OTTHUMG00000159157	ENST00000302746.6:c.438G>A	3.37:g.58416535C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_000925	B2R7L0|B4DDD7|Q6FH45|Q9BQ27|Q9UFK3	Silent	SNP	ENST00000302746.6	37	CCDS2890.1																																																																																			C|0.695;T|0.305	0.305	strong		0.532	PDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353558.1		
STKLD1	169436	hgsc.bcm.edu	37	9	136268038	136268038	+	Silent	SNP	C	C	T	rs3124748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136268038C>T	ENST00000371957.3	+	14	1478	c.1371C>T	c.(1369-1371)aaC>aaT	p.N457N	C9orf96_ENST00000371955.1_Intron	NM_153710.3	NP_714921.4	Q8NE28	STKL1_HUMAN		457							ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(2)|stomach(2)	25				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		AGCTGCAGAACGCTGGGCTGC	0.647													C|||	2221	0.44349	0.3926	0.4928	5008	,	,		18663	0.4643		0.4334	False		,,,				2504	0.4663				p.N457N		Atlas-SNP	.											.	C9orf96	77	.	0			c.C1371T						PASS	.	C		1773,2625		368,1037,794	34.0	31.0	32.0		1371	-1.3	0.1	9	dbSNP_103	32	3808,4786		858,2092,1347	no	coding-synonymous	C9orf96	NM_153710.3		1226,3129,2141	TT,TC,CC		44.31,40.3138,42.9572		457/681	136268038	5581,7411	2199	4297	6496	SO:0001819	synonymous_variant	169436	exon14			GCAGAACGCTGGG																												ENST00000371957.3:c.1371C>T	9.37:g.136268038C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_153710	Q5T8U8|Q6ZMP6|Q6ZMQ5	Silent	SNP	ENST00000371957.3	37	CCDS35169.1																																																																																			C|0.588;T|0.412	0.412	strong		0.647	C9orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054855.1		
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 GAIIx	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	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	189	45	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		
FAM83A	84985	hgsc.bcm.edu	37	8	124206324	124206324	+	Missense_Mutation	SNP	G	G	A	rs7813708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124206324G>A	ENST00000518448.1	+	4	2723	c.709G>A	c.(709-711)Gct>Act	p.A237T	FAM83A_ENST00000276699.6_Missense_Mutation_p.A237T|FAM83A_ENST00000318462.6_Missense_Mutation_p.A237T|FAM83A_ENST00000522648.1_Missense_Mutation_p.A181T|FAM83A_ENST00000536633.1_Missense_Mutation_p.A237T|FAM83A_ENST00000546351.1_Missense_Mutation_p.A181T			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	237			A -> T (in dbSNP:rs7813708). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			CAGGAAATTCGCTGGCCAAAT	0.478													G|||	784	0.15655	0.0219	0.1988	5008	,	,		21893	0.2133		0.2008	False		,,,				2504	0.2045				p.A237T		Atlas-SNP	.											.	FAM83A	64	.	0			c.G709A						PASS	.	G	THR/ALA,THR/ALA	254,4152	148.0+/-182.4	7,240,1956	139.0	117.0	125.0		709,709	1.2	0.3	8	dbSNP_116	125	1791,6809	324.7+/-316.6	191,1409,2700	yes	missense,missense	FAM83A	NM_032899.4,NM_207006.1	58,58	198,1649,4656	AA,AG,GG		20.8256,5.7649,15.7235	benign,benign	237/435,237/368	124206324	2045,10961	2203	4300	6503	SO:0001583	missense	84985	exon3			AAATTCGCTGGCC	BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.709G>A	8.37:g.124206324G>A	ENSP00000428876:p.Ala237Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	79	28	0.35443	NM_032899	Q71HL2|Q8N7I1|Q96I47	Missense_Mutation	SNP	ENST00000518448.1	37	CCDS6340.1	389	0.17811355311355312	14	0.028455284552845527	70	0.19337016574585636	150	0.26223776223776224	155	0.20448548812664907	G	7.351	0.622953	0.14193	0.057649	0.208256	ENSG00000147689	ENST00000518448;ENST00000546351;ENST00000536633;ENST00000318462;ENST00000522648;ENST00000276699	T;T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83;2.83	5.62	1.17	0.20885	.	0.346115	0.30455	N	0.009597	T	0.00012	0.0000	N	0.17082	0.46	0.48632	P	3.1800000000004047E-4	B;B;B	0.31209	0.313;0.066;0.048	B;B;B	0.22601	0.03;0.009;0.04	T	0.41215	-0.9521	9	0.02654	T	1	-15.2663	14.8562	0.70338	0.0:0.0:0.4168:0.5832	rs7813708;rs13279798;rs17377444;rs17845132;rs17857935;rs52838187;rs59588076;rs7813708	181;237;237	Q86UY5-2;Q86UY5-3;Q86UY5	.;.;FA83A_HUMAN	T	237;181;237;237;181;237	ENSP00000428876:A237T;ENSP00000440565:A181T;ENSP00000445218:A237T;ENSP00000323034:A237T;ENSP00000427979:A181T;ENSP00000276699:A237T	ENSP00000276699:A237T	A	+	1	0	FAM83A	124275505	0.211000	0.23529	0.302000	0.25058	0.914000	0.54420	1.323000	0.33701	0.273000	0.22049	0.555000	0.69702	GCT	G|0.835;A|0.165	0.165	strong		0.478	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1	NM_032899	
PITRM1	10531	hgsc.bcm.edu	37	10	3191830	3191830	+	Missense_Mutation	SNP	G	G	C	rs41305673	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:3191830G>C	ENST00000224949.4	-	16	1888	c.1854C>G	c.(1852-1854)ttC>ttG	p.F618L	PITRM1_ENST00000464395.1_5'Flank|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380994.1_Missense_Mutation_p.F176L|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.F618L|PITRM1_ENST00000451104.2_Missense_Mutation_p.F586L			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	618					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						GGACGCTGCAGAAGAGGGGCA	0.512													G|||	104	0.0207668	0.003	0.0231	5008	,	,		15520	0.001		0.0447	False		,,,				2504	0.0389				p.F618L		Atlas-SNP	.											.	PITRM1	109	.	0			c.C1854G						PASS	.	G	LEU/PHE,LEU/PHE,LEU/PHE	33,4045		0,33,2006	184.0	187.0	186.0		1854,1758,1854	2.5	1.0	10	dbSNP_127	186	420,7972		9,402,3785	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	22,22,22	9,435,5791	CC,CG,GG		5.0048,0.8092,3.6327	probably-damaging,probably-damaging,probably-damaging	618/1039,586/940,618/1038	3191830	453,12017	2039	4196	6235	SO:0001583	missense	10531	exon16			GCTGCAGAAGAGG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.1854C>G	10.37:g.3191830G>C	ENSP00000224949:p.Phe618Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	41	0.018772893772893772	0	0.0	12	0.03314917127071823	0	0.0	29	0.03825857519788918	g	17.36	3.369327	0.61624	0.008092	0.050048	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.41	2.49	0.30216	Peptidase M16C associated (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.21921	0.0528	M	0.90309	3.105	0.50171	D	0.99985	P;P;D;D;D	0.76494	0.463;0.93;0.999;0.999;0.999	B;D;D;D;D	0.78314	0.241;0.951;0.991;0.991;0.991	T	0.43065	-0.9414	10	0.40728	T	0.16	.	9.6562	0.39928	0.4061:0.0:0.5939:0.0	rs41305673	611;586;618;618;611	E9PDX6;E7ES23;C9JSL2;Q5JRX3;B4DH07	.;.;.;PREP_HUMAN;.	L	618;611;618;176;586	ENSP00000224949:F618L;ENSP00000370377:F618L;ENSP00000370382:F176L;ENSP00000401201:F586L	ENSP00000224949:F618L	F	-	3	2	PITRM1	3181830	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	3.323000	0.52014	0.250000	0.21479	0.555000	0.69702	TTC	G|0.972;C|0.028	0.028	strong		0.512	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
SLC4A1	6521	hgsc.bcm.edu	37	17	42335135	42335135	+	Silent	SNP	C	C	T	rs5017	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:42335135C>T	ENST00000262418.6	-	12	1478	c.1323G>A	c.(1321-1323)ctG>ctA	p.L441L	AC003043.1_ENST00000597382.1_5'Flank|SLC4A1_ENST00000471005.1_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	441	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CAGTGGAGATCAGCAGCTCCG	0.587													C|||	115	0.0229633	0.003	0.0375	5008	,	,		19938	0.001		0.0676	False		,,,				2504	0.0164				p.L441L		Atlas-SNP	.											.	SLC4A1	104	.	0			c.G1323A						PASS	.	C		77,4329	68.7+/-106.4	2,73,2128	84.0	76.0	79.0		1323	3.6	1.0	17	dbSNP_52	79	714,7886	174.9+/-225.1	32,650,3618	no	coding-synonymous	SLC4A1	NM_000342.3		34,723,5746	TT,TC,CC		8.3023,1.7476,6.0818		441/912	42335135	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	6521	exon12			GGAGATCAGCAGC		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.1323G>A	17.37:g.42335135C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	62	0.553571	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Silent	SNP	ENST00000262418.6	37	CCDS11481.1																																																																																			C|0.948;T|0.052	0.052	strong		0.587	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629129	32629129	+	Missense_Mutation	SNP	T	T	C	rs1130432	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32629129T>C	ENST00000399084.1	-	5	945	c.767A>G	c.(766-768)cAg>cGg	p.Q256R	HLA-DQB1_ENST00000399079.3_Intron|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.Q256R|HLA-DQB1-AS1_ENST00000419852.1_RNA|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.Q256R			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	256			Q -> R (in allele DQB1*05:01, allele DQB1*05:02 and allele DQB1*05:03; dbSNP:rs1130432).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	CTCACCTTTCTGACTCCTTTG	0.557									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1335	0.266573	0.2723	0.1902	5008	,	,		12932	0.3204		0.2445	False		,,,				2504	0.2802				p.Q256R	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.A767G						PASS	.	T	ARG/GLN	946,3042		238,470,1286	28.0	25.0	26.0		767	3.6	0.9	6	dbSNP_86	26	1711,6421		446,819,2801	yes	missense	HLA-DQB1	NM_002123.4	43	684,1289,4087	CC,CT,TT		21.0403,23.7212,21.9224	benign	256/262	32629129	2657,9463	1994	4066	6060	SO:0001583	missense	3119	exon4	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CCTTTCTGACTCC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.767A>G	6.37:g.32629129T>C	ENSP00000382034:p.Gln256Arg	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	417	0.19093406593406592	113	0.22967479674796748	63	0.17403314917127072	86	0.15034965034965034	155	0.20448548812664907	.	13.83	2.354500	0.41700	0.237212	0.210403	ENSG00000179344	ENST00000374943;ENST00000434651;ENST00000399084	T;T;T	0.00637	6.13;6.05;6.05	4.75	3.6	0.41247	.	0.567063	0.16716	N	0.202474	T	0.00384	0.0012	L	0.54965	1.715	0.39169	P	0.03744599999999998	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.10450	0.003;0.004;0.005	T	0.39702	-0.9601	9	0.87932	D	0	.	7.8247	0.29307	0.0:0.1:0.0:0.9	rs1130432;rs3189265;rs9273619;rs9273620;rs12722395;rs35107830	221;256;256	A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.	R	256	ENSP00000364080:Q256R;ENSP00000407332:Q256R;ENSP00000382034:Q256R	ENSP00000364080:Q256R	Q	-	2	0	HLA-DQB1	32737107	0.999000	0.42202	0.933000	0.37362	0.910000	0.53928	1.001000	0.29783	1.776000	0.52262	0.528000	0.53228	CAG	T|0.827;C|0.173	0.173	strong		0.557	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
BACH2	60468	hgsc.bcm.edu	37	6	90660319	90660319	+	Silent	SNP	T	T	C	rs9451298	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90660319T>C	ENST00000257749.4	-	7	2213	c.1506A>G	c.(1504-1506)gtA>gtG	p.V502V	BACH2_ENST00000343122.3_Silent_p.V502V|BACH2_ENST00000537989.1_Silent_p.V502V|RP3-512E2.2_ENST00000413986.1_RNA|RP3-512E2.2_ENST00000445838.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	502						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.V502V(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		CTTTGATTGGTACCGGGCAGC	0.662													C|||	1555	0.310503	0.4251	0.1931	5008	,	,		17279	0.2361		0.2773	False		,,,				2504	0.3497				p.V502V		Atlas-SNP	.											BACH2_ENST00000257749,NS,carcinoma,0,3	BACH2	224	3	1	Substitution - coding silent(1)	stomach(1)	c.A1506G						PASS	.	C	,	1636,2770	644.3+/-398.0	306,1024,873	51.0	59.0	56.0		1506,1506	5.3	1.0	6	dbSNP_119	56	2434,6166	683.4+/-403.9	355,1724,2221	no	coding-synonymous,coding-synonymous	BACH2	NM_001170794.1,NM_021813.2	,	661,2748,3094	CC,CT,TT		28.3023,37.1312,31.2932	,	502/842,502/842	90660319	4070,8936	2203	4300	6503	SO:0001819	synonymous_variant	60468	exon5			GATTGGTACCGGG	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1506A>G	6.37:g.90660319T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	37	CCDS5026.1																																																																																			T|0.695;C|0.305	0.305	strong		0.662	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2396556	2396556	+	Silent	SNP	C	C	T	rs7252886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:2396556C>T	ENST00000332578.3	+	2	162	c.162C>T	c.(160-162)ggC>ggT	p.G54G	TMPRSS9_ENST00000592650.1_3'UTR	NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	54					plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		CTACACAGGGCTTCCACGTGG	0.697													C|||	2157	0.430711	0.5696	0.464	5008	,	,		15889	0.504		0.2306	False		,,,				2504	0.3497				p.G54G		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C162T						PASS	.	C		2330,2076		614,1102,487	30.0	26.0	27.0		162	-3.4	0.4	19	dbSNP_116	27	2123,6477		274,1575,2451	no	coding-synonymous	TMPRSS9	NM_182973.1		888,2677,2938	TT,TC,CC		24.686,47.1176,34.238		54/1060	2396556	4453,8553	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon2			ACAGGGCTTCCAC	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.162C>T	19.37:g.2396556C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.631;T|0.369	0.369	strong		0.697	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
INPP5E	56623	hgsc.bcm.edu	37	9	139327439	139327439	+	Silent	SNP	A	A	G	rs10781542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139327439A>G	ENST00000371712.3	-	5	1650	c.1248T>C	c.(1246-1248)acT>acC	p.T416T		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		AGAGGAAGGAAGTGCCAAAAA	0.582													G|||	1895	0.378395	0.3896	0.6196	5008	,	,		17746	0.1935		0.4145	False		,,,				2504	0.3456				p.T416T		Atlas-SNP	.											.	INPP5E	18	.	0			c.T1248C						PASS	.	G		1747,2657	636.1+/-396.5	345,1057,800	189.0	168.0	175.0		1248	3.7	1.0	9	dbSNP_120	175	3922,4676	602.2+/-394.5	875,2172,1252	no	coding-synonymous	INPP5E	NM_019892.4		1220,3229,2052	GG,GA,AA		45.6153,39.6685,43.601		416/645	139327439	5669,7333	2202	4299	6501	SO:0001819	synonymous_variant	56623	exon5			GAAGGAAGTGCCA	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1248T>C	9.37:g.139327439A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			A|0.597;G|0.403	0.403	strong		0.582	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
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 GAIIx	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_ENST00000593191.1_5'Flank|ECSIT_ENST00000417981.2_Silent_p.R211R|ECSIT_ENST00000591352.1_5'Flank|ECSIT_ENST00000591104.1_3'UTR|ZNF653_ENST00000293771.5_5'Flank|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000252440.7_3'UTR|ECSIT_ENST00000588998.1_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		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	44	26	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	
SAGE1	55511	hgsc.bcm.edu	37	X	134994054	134994054	+	Silent	SNP	G	G	A	rs4829584	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:134994054G>A	ENST00000370709.3	+	17	2463	c.2463G>A	c.(2461-2463)aaG>aaA	p.K821K	SAGE1_ENST00000535938.1_Silent_p.K821K|SAGE1_ENST00000537770.1_Silent_p.K445K|SAGE1_ENST00000324447.3_Silent_p.K821K			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	821						nucleus (GO:0005634)		p.I823fs*5(1)		breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CCATGGCAAAGAAAATTAATG	0.373													g|||	373	0.0988079	0.0265	0.121	3775	,	,		15260	0.0615		0.1531	False		,,,				2504	0.0389				p.K821K		Atlas-SNP	.											.	SAGE1	160	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.G2463A						PASS	.	G		174,3661		3,146,22,1483,549	54.0	52.0	52.0		2463	-0.5	0.0	X	dbSNP_111	52	1251,5476		92,737,330,1599,1541	no	coding-synonymous	SAGE1	NM_018666.2		95,883,352,3082,2090	AA,AG,A,GG,G		18.5967,4.5372,13.4918		821/905	134994054	1425,9137	2203	4299	6502	SO:0001819	synonymous_variant	55511	exon18			GGCAAAGAAAATT	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.2463G>A	X.37:g.134994054G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	85	14	0.164706	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			0|0.004;A|0.130	0.130	strong		0.373	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
CNDP2	55748	hgsc.bcm.edu	37	18	72178161	72178161	+	Silent	SNP	T	T	C	rs2278159	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72178161T>C	ENST00000324262.4	+	6	886	c.570T>C	c.(568-570)taT>taC	p.Y190Y	CNDP2_ENST00000579847.1_Silent_p.Y190Y|CNDP2_ENST00000324301.8_Silent_p.Y106Y	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	190					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.Y190Y(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		ATGTGGACTATGTCTGCATTT	0.507													T|||	1013	0.202276	0.0779	0.3026	5008	,	,		23053	0.2986		0.162	False		,,,				2504	0.2413				p.Y190Y		Atlas-SNP	.											CNDP2,NS,carcinoma,0,1	CNDP2	55	1	1	Substitution - coding silent(1)	stomach(1)	c.T570C						PASS	.	T	,	493,3913	230.4+/-244.6	34,425,1744	146.0	127.0	134.0		318,570	1.8	0.9	18	dbSNP_100	134	1634,6966	303.4+/-306.4	133,1368,2799	no	coding-synonymous,coding-synonymous	CNDP2	NM_001168499.1,NM_018235.2	,	167,1793,4543	CC,CT,TT		19.0,11.1893,16.354	,	106/392,190/476	72178161	2127,10879	2203	4300	6503	SO:0001819	synonymous_variant	55748	exon6			GGACTATGTCTGC	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.570T>C	18.37:g.72178161T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Silent	SNP	ENST00000324262.4	37	CCDS12006.1																																																																																			T|0.825;C|0.175	0.175	strong		0.507	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
NUP62CL	54830	hgsc.bcm.edu	37	X	106396402	106396402	+	Splice_Site	SNP	A	A	G	rs1298577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:106396402A>G	ENST00000372466.4	-	7	781	c.530T>C	c.(529-531)aTc>aCc	p.I177T	NUP62CL_ENST00000372461.3_3'UTR	NM_017681.2	NP_060151.2	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	177			I -> T (in dbSNP:rs1298577). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		protein transport (GO:0015031)	nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			lung(4)	4						AGTTACTTACATCTCCACATG	0.438													G|||	1812	0.48	0.6566	0.3213	3775	,	,		14275	0.3333		0.1521	False		,,,				2504	0.2372				p.I177T		Atlas-SNP	.											.	NUP62CL	10	.	0			c.T530C						PASS	.	G	THR/ILE	2886,949		925,604,432,103,139	194.0	212.0	206.0		530	-4.0	0.0	X	dbSNP_87	206	1226,5502		66,739,355,1623,1517	yes	missense-near-splice	NUP62CL	NM_017681.2	89	991,1343,787,1726,1656	GG,GA,G,AA,A		18.2224,24.7458,38.9283	benign	177/185	106396402	4112,6451	2203	4300	6503	SO:0001630	splice_region_variant	54830	exon7			ACTTACATCTCCA	AK000137	CCDS14527.1	Xq22.3	2008-02-05			ENSG00000198088	ENSG00000198088			25960	protein-coding gene	gene with protein product						12477932	Standard	NM_017681		Approved	FLJ20130	uc004ena.3	Q9H1M0	OTTHUMG00000022159	ENST00000372466.4:c.530+1T>C	X.37:g.106396402A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	174	40	0.229885	NM_017681	D3DUX4|Q8WVL6|Q9NXP2	Missense_Mutation	SNP	ENST00000372466.4	37	CCDS14527.1	738	0.4448462929475588	217	0.7138157894736842	67	0.23591549295774647	137	0.315668202764977	77	0.11290322580645161	G	1.065	-0.671578	0.03403	0.752542	0.182224	ENSG00000198088	ENST00000372466;ENST00000372465	T	0.48836	0.8	5.44	-4.01	0.04045	Nucleoporin, NSP1-like, C-terminal (1);	0.153986	0.56097	N	0.000021	T	0.00012	0.0000	N	0.01505	-0.83	0.09310	P	0.9999999999999784	B	0.02656	0.0	B	0.01281	0.0	T	0.27872	-1.0061	8	.	.	.	0.0386	9.0347	0.36280	0.6223:0.1049:0.2727:0.0	rs1298577;rs52826101;rs61274773;rs1298577	177	Q9H1M0	N62CL_HUMAN	T	177	ENSP00000361544:I177T	.	I	-	2	0	NUP62CL	106283058	1.000000	0.71417	0.001000	0.08648	0.038000	0.13279	1.926000	0.40084	-2.277000	0.00677	-0.396000	0.06452	ATC;ATT	A|0.540;0|0.011	.	strong		0.438	NUP62CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057828.1	NM_017681	Missense_Mutation
DLEC1	9940	hgsc.bcm.edu	37	3	38081031	38081031	+	Silent	SNP	A	A	T	rs7616776	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:38081031A>T	ENST00000308059.6	+	1	336	c.315A>T	c.(313-315)tcA>tcT	p.S105S	DLEC1_ENST00000346219.3_Silent_p.S105S|DLEC1_ENST00000452631.2_Silent_p.S105S					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		ACTTGTACTCAGCCGAGGTCA	0.632													g|||	1715	0.342452	0.2927	0.3429	5008	,	,		19111	0.5546		0.3032	False		,,,				2504	0.2311				p.S105S		Atlas-SNP	.											DLEC1_ENST00000346219,NS,carcinoma,0,2	DLEC1	278	2	0			c.A315T						PASS	.	G	,	1240,2908		182,876,1016	55.0	59.0	58.0		315,315	-6.2	0.0	3	dbSNP_116	58	2475,5941		387,1701,2120	no	coding-synonymous,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	569,2577,3136	TT,TA,AA		29.4083,29.8939,29.5686	,	105/1756,105/1779	38081031	3715,8849	2074	4208	6282	SO:0001819	synonymous_variant	9940	exon1			GTACTCAGCCGAG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.315A>T	3.37:g.38081031A>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_007337		Silent	SNP	ENST00000308059.6	37	CCDS2672.2																																																																																			A|0.652;T|0.348	0.348	strong		0.632	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
NPTXR	23467	hgsc.bcm.edu	37	22	39222652	39222652	+	Silent	SNP	G	G	A	rs5757299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39222652G>A	ENST00000333039.2	-	3	1074	c.951C>T	c.(949-951)taC>taT	p.Y317Y		NM_014293.3	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	317	Pentaxin.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			central_nervous_system(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	Melanoma(58;0.04)					CGGTGAATGCGTAGAGCTCGG	0.627													G|||	2305	0.460264	0.4107	0.2824	5008	,	,		18082	0.7589		0.3847	False		,,,				2504	0.4233				p.Y317Y	Pancreas(139;2521 3281 36965)	Atlas-SNP	.											.	NPTXR	34	.	0			c.C951T						PASS	.	G		1671,2735	509.3+/-367.2	325,1021,857	93.0	82.0	85.0		951	3.6	1.0	22	dbSNP_114	85	3442,5158	506.1+/-376.5	696,2050,1554	no	coding-synonymous	NPTXR	NM_014293.3		1021,3071,2411	AA,AG,GG		40.0233,37.9256,39.3126		317/501	39222652	5113,7893	2203	4300	6503	SO:0001819	synonymous_variant	23467	exon3			GAATGCGTAGAGC	AF052163	CCDS33647.1	22q13.1	2007-01-25			ENSG00000221890	ENSG00000221890			7954	protein-coding gene	gene with protein product		609474				16497176	Standard	NM_014293		Approved		uc003awk.3	O95502	OTTHUMG00000150458	ENST00000333039.2:c.951C>T	22.37:g.39222652G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_014293		Silent	SNP	ENST00000333039.2	37	CCDS33647.1																																																																																			G|0.577;A|0.423	0.423	strong		0.627	NPTXR-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318194.2	NM_014293	
SEC16B	89866	hgsc.bcm.edu	37	1	177929940	177929940	+	Silent	SNP	G	G	A	rs7413442	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:177929940G>A	ENST00000308284.6	-	7	1011	c.922C>T	c.(922-924)Ctg>Ttg	p.L308L	SEC16B_ENST00000464631.2_Silent_p.L309L|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	308					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						ATGCTGTGCAGTTCAACAAGG	0.542													G|||	1392	0.277955	0.5719	0.2003	5008	,	,		19999	0.1944		0.1819	False		,,,				2504	0.1207				p.L308L		Atlas-SNP	.											.	SEC16B	92	.	0			c.C922T						PASS	.	G		2005,2213		490,1025,594	42.0	46.0	45.0		922	-0.2	0.9	1	dbSNP_116	45	1459,7027		128,1203,2912	no	coding-synonymous	SEC16B	NM_033127.2		618,2228,3506	AA,AG,GG		17.193,47.5344,27.267		308/1061	177929940	3464,9240	2109	4243	6352	SO:0001819	synonymous_variant	89866	exon7			TGTGCAGTTCAAC	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.922C>T	1.37:g.177929940G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			G|0.727;A|0.273	0.273	strong		0.542	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
OBSCN	84033	hgsc.bcm.edu	37	1	228407260	228407260	+	Intron	SNP	G	G	A	rs1771484	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228407260G>A	ENST00000422127.1	+	8	2697				OBSCN_ENST00000570156.2_Silent_p.E963E|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000284548.11_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACAGCTGTGAGGCCAGGGGAC	0.642													G|||	1388	0.277157	0.3147	0.3487	5008	,	,		19787	0.1746		0.3588	False		,,,				2504	0.1973				p.E963E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2889A						PASS	.																																			SO:0001627	intron_variant	84033	exon9			CTGTGAGGCCAGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2653+2271G>A	1.37:g.228407260G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.718;A|0.282	0.282	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ARHGAP24	83478	hgsc.bcm.edu	37	4	86915923	86915923	+	Silent	SNP	G	G	A	rs11547776	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:86915923G>A	ENST00000395184.1	+	9	1582	c.1116G>A	c.(1114-1116)agG>agA	p.R372R	ARHGAP24_ENST00000264343.4_Silent_p.R279R|ARHGAP24_ENST00000395183.2_Silent_p.R277R	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	372					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)	p.R279R(1)		breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		GCCCTAGTAGGCAGTGCTCCT	0.498													G|||	1275	0.254593	0.1036	0.2882	5008	,	,		19491	0.3135		0.2227	False		,,,				2504	0.407				p.R372R		Atlas-SNP	.											ARHGAP24,NS,carcinoma,0,1	ARHGAP24	116	1	1	Substitution - coding silent(1)	stomach(1)	c.G1116A						PASS	.	G	,,	628,3778	271.3+/-270.1	52,524,1627	156.0	156.0	156.0		1116,831,837	-3.0	0.0	4	dbSNP_120	156	1905,6695	337.6+/-322.4	230,1445,2625	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP24	NM_001025616.2,NM_001042669.1,NM_031305.2	,,	282,1969,4252	AA,AG,GG		22.1512,14.2533,19.4756	,,	372/749,277/654,279/656	86915923	2533,10473	2203	4300	6503	SO:0001819	synonymous_variant	83478	exon9			TAGTAGGCAGTGC	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1116G>A	4.37:g.86915923G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	37	CCDS34025.1																																																																																			G|0.791;A|0.209	0.209	strong		0.498	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
MTUS1	57509	hgsc.bcm.edu	37	8	17612323	17612323	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17612323C>T	ENST00000262102.6	-	2	1218	c.994G>A	c.(994-996)Gaa>Aaa	p.E332K	MTUS1_ENST00000381869.3_Missense_Mutation_p.E332K|MTUS1_ENST00000381862.3_Missense_Mutation_p.E332K|MTUS1_ENST00000519263.1_Missense_Mutation_p.E332K	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	332					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)		TGGCCCATTTCCTTGTGCCTG	0.423																																					p.E332K		Atlas-SNP	.											MTUS1,lower_third,carcinoma,0,1	MTUS1	144	1	0			c.G994A						scavenged	.						158.0	150.0	152.0					8																	17612323		1901	4130	6031	SO:0001583	missense	57509	exon2			CCATTTCCTTGTG	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.994G>A	8.37:g.17612323C>T	ENSP00000262102:p.Glu332Lys	Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	160	2	0.0125	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.183008	0.78677	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.30714	2.42;2.48;2.42;1.52	4.28	4.28	0.50868	.	0.265678	0.29745	N	0.011316	T	0.44329	0.1288	L	0.32530	0.975	0.39068	D	0.960664	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.46289	-0.9202	10	0.87932	D	0	-23.3776	14.679	0.69004	0.0:1.0:0.0:0.0	.	332;332;332	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	K	332	ENSP00000371293:E332K;ENSP00000262102:E332K;ENSP00000430167:E332K;ENSP00000371286:E332K	ENSP00000262102:E332K	E	-	1	0	MTUS1	17656603	0.984000	0.35163	1.000000	0.80357	0.980000	0.70556	1.396000	0.34531	2.697000	0.92050	0.655000	0.94253	GAA	.	.	none		0.423	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
FAM86A	196483	hgsc.bcm.edu	37	16	5140561	5140561	+	Silent	SNP	C	C	T	rs9673770	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:5140561C>T	ENST00000427587.4	-	5	416	c.348G>A	c.(346-348)tcG>tcA	p.S116S	FAM86A_ENST00000458008.4_Silent_p.S82S|FAM86A_ENST00000587133.1_Silent_p.S55S	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	116						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						CCGAGCCTCCCGAGGGCTGCA	0.582													c|||	459	0.0916534	0.0242	0.17	5008	,	,		20650	0.128		0.1402	False		,,,				2504	0.0399				p.S116S		Atlas-SNP	.											FAM86A,NS,carcinoma,0,1	FAM86A	32	1	0			c.G348A						PASS	.	C	,	138,4256	98.5+/-137.1	3,132,2062	62.0	63.0	63.0		348,246	-10.0	0.0	16	dbSNP_119	63	1084,7516	225.2+/-261.4	74,936,3290	no	coding-synonymous,coding-synonymous	FAM86A	NM_201400.2,NM_201598.2	,	77,1068,5352	TT,TC,CC		12.6047,3.1406,9.4043	,	116/331,82/297	5140561	1222,11772	2197	4300	6497	SO:0001819	synonymous_variant	196483	exon5			GCCTCCCGAGGGC	BC010084	CCDS10529.1, CCDS10530.1, CCDS73823.1	16p13.3	2012-11-07			ENSG00000118894	ENSG00000118894			32221	protein-coding gene	gene with protein product		615263					Standard	NM_201400		Approved	SB153, MGC19636	uc002cyo.2	Q96G04	OTTHUMG00000129527	ENST00000427587.4:c.348G>A	16.37:g.5140561C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	80	50	0.625	NM_201400	D3DUF0|Q96S85	Silent	SNP	ENST00000427587.4	37	CCDS10529.1																																																																																			C|0.896;T|0.104	0.104	strong		0.582	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919240	51919240	+	Silent	SNP	C	C	T	rs79484306	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51919240C>T	ENST00000339313.5	-	5	1052	c.936G>A	c.(934-936)ggG>ggA	p.G312G	SIGLEC10_ENST00000439889.2_Silent_p.G254G|SIGLEC10_ENST00000436984.2_Silent_p.G264G|SIGLEC10_ENST00000353836.5_Silent_p.G312G|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000432469.2_Silent_p.G229G|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.G312G|SIGLEC10_ENST00000441969.3_Silent_p.G254G|CTD-2616J11.2_ENST00000532688.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	312	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CAGCCTTCACCCCGGGCAGCT	0.672																																					p.G312G		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,-2,2	SIGLEC10	112	2	0			c.G936A						PASS	.						37.0	42.0	40.0					19																	51919240		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			CTTCACCCCGGGC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.936G>A	19.37:g.51919240C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	154	39	0.253247	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			C|0.910;T|0.090	0.090	strong		0.672	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ARL16	339231	hgsc.bcm.edu	37	17	79650828	79650828	+	Missense_Mutation	SNP	T	T	G	rs8066889	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79650828T>G	ENST00000397498.4	-	1	126	c.28A>C	c.(28-30)Agc>Cgc	p.S10R	ARL16_ENST00000576135.1_5'Flank|ARL16_ENST00000570561.1_5'Flank|ARL16_ENST00000573392.1_5'Flank|ARL16_ENST00000574938.1_5'Flank|HGS_ENST00000329138.4_5'Flank	NM_001040025.1	NP_001035114.1	Q0P5N6	ARL16_HUMAN	ADP-ribosylation factor-like 16	10			S -> R (in dbSNP:rs8066889).		small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			central_nervous_system(1)|endometrium(1)|lung(4)|skin(1)	7	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GCGCCGCGGCTCAAGGCCCGC	0.632													G|||	1243	0.248203	0.3578	0.1556	5008	,	,		12437	0.2292		0.2604	False		,,,				2504	0.1728				p.S10R		Atlas-SNP	.											.	ARL16	14	.	0			c.A28C						PASS	.	G	ARG/SER	1280,2528		237,806,861	14.0	17.0	16.0		28	0.8	0.0	17	dbSNP_116	16	1807,6371		212,1383,2494	yes	missense	ARL16	NM_001040025.1	110	449,2189,3355	GG,GT,TT		22.0959,33.6134,25.755	benign	10/198	79650828	3087,8899	1904	4089	5993	SO:0001583	missense	339231	exon1			CGCGGCTCAAGGC		CCDS45813.1	17q25.3	2014-05-09				ENSG00000214087		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	27902	protein-coding gene	gene with protein product						12477932	Standard	NM_001040025		Approved		uc002kbf.3	Q0P5N6		ENST00000397498.4:c.28A>C	17.37:g.79650828T>G	ENSP00000380635:p.Ser10Arg	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	26	5	0.192308	NM_001040025		Missense_Mutation	SNP	ENST00000397498.4	37	CCDS45813.1	573	0.2623626373626374	193	0.39227642276422764	62	0.1712707182320442	135	0.23601398601398602	183	0.24142480211081793	G	10.73	1.431804	0.25813	0.336134	0.220959	ENSG00000214087	ENST00000397498	T	0.70749	-0.51	4.35	0.805	0.18703	.	0.727362	0.09205	U	0.834153	T	0.00012	0.0000	L	0.34521	1.04	0.51012	P	9.199999999998099E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.26224	-1.0109	9	0.72032	D	0.01	.	8.4458	0.32841	0.0:0.133:0.4606:0.4064	rs8066889;rs59418595;rs8066889	10	Q0P5N6	ARL16_HUMAN	R	10	ENSP00000380635:S10R	ENSP00000380635:S10R	S	-	1	0	ARL16	77261233	0.004000	0.15560	0.003000	0.11579	0.002000	0.02628	0.878000	0.28126	0.263000	0.21812	-0.121000	0.15023	AGC	T|0.736;G|0.264	0.264	strong		0.632	ARL16-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440514.1	XM_290777	
CILP2	148113	hgsc.bcm.edu	37	19	19654189	19654189	+	Silent	SNP	G	G	A	rs45556231	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:19654189G>A	ENST00000291495.5	+	7	1195	c.1110G>A	c.(1108-1110)tcG>tcA	p.S370S	CILP2_ENST00000586018.1_Silent_p.S376S	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	370	Ig-like C2-type.					extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.S370S(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCGTGCGCTCGGGCACTGCCC	0.647													G|||	593	0.118411	0.1634	0.1167	5008	,	,		14555	0.0		0.166	False		,,,				2504	0.1319				p.S370S		Atlas-SNP	.											CILP2,NS,carcinoma,0,1	CILP2	84	1	1	Substitution - coding silent(1)	prostate(1)	c.G1110A						PASS	.	G		716,3690		51,614,1538	43.0	43.0	43.0		1110	-8.9	0.0	19	dbSNP_127	43	1420,7178		113,1194,2992	no	coding-synonymous	CILP2	NM_153221.2		164,1808,4530	AA,AG,GG		16.5155,16.2506,16.4257		370/1157	19654189	2136,10868	2203	4299	6502	SO:0001819	synonymous_variant	148113	exon7			GCGCTCGGGCACT	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1110G>A	19.37:g.19654189G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	145	55	0.37931	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			G|0.842;A|0.158	0.158	strong		0.647	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552537	43552537	+	Silent	SNP	G	G	A	rs71238846	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43552537G>A	ENST00000430334.3	-	4	985	c.852C>T	c.(850-852)tgC>tgT	p.C284C	PLEKHM1_ENST00000421073.2_Silent_p.C195C	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	284					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					TGGGCTCCTCGCAATGGTCTG	0.572													G|||	412	0.0822684	0.0378	0.1556	5008	,	,		18814	0.001		0.1958	False		,,,				2504	0.0573				p.C284C		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.C852T						PASS	.	G		281,4125	157.0+/-190.0	10,261,1932	50.0	47.0	48.0		852	0.9	0.5	17	dbSNP_130	48	1648,6952	303.6+/-306.5	155,1338,2807	no	coding-synonymous	PLEKHM1	NM_014798.2		165,1599,4739	AA,AG,GG		19.1628,6.3777,14.8316		284/1057	43552537	1929,11077	2203	4300	6503	SO:0001819	synonymous_variant	9842	exon4			CTCCTCGCAATGG	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.852C>T	17.37:g.43552537G>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	127	122	0.96063	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			G|0.865;A|0.135	0.135	strong		0.572	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
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 GAIIx	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_ENST00000395211.2_Missense_Mutation_p.M247L|TMOD1_ENST00000375175.1_Missense_Mutation_p.M120L	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	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	97	50	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	
KIF3B	9371	hgsc.bcm.edu	37	20	30915461	30915461	+	Silent	SNP	T	T	C	rs1129012	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:30915461T>C	ENST00000375712.3	+	7	2132	c.1965T>C	c.(1963-1965)taT>taC	p.Y655Y	KIF3B_ENST00000418717.2_Silent_p.Y281Y	NM_004798.3	NP_004789.1	O15066	KIF3B_HUMAN	kinesin family member 3B	655	Globular.				anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytoskeleton-dependent intracellular transport (GO:0030705)|determination of left/right symmetry (GO:0007368)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic spindle organization (GO:0007052)|plus-end-directed vesicle transport along microtubule (GO:0072383)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|plus-end kinesin complex (GO:0005873)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|Rho GTPase binding (GO:0017048)	p.Y655Y(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(5)|lung(9)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AGGCCCGATATAGGGTGAGAA	0.468													T|||	1011	0.201877	0.3313	0.1441	5008	,	,		17700	0.2222		0.1859	False		,,,				2504	0.0634				p.Y655Y		Atlas-SNP	.											KIF3B,NS,carcinoma,0,1	KIF3B	75	1	1	Substitution - coding silent(1)	stomach(1)	c.T1965C						PASS	.	T		1346,3060	448.3+/-348.6	204,938,1061	93.0	81.0	85.0		1965	-4.2	0.4	20	dbSNP_86	85	1471,7129	281.7+/-295.2	136,1199,2965	no	coding-synonymous	KIF3B	NM_004798.3		340,2137,4026	CC,CT,TT		17.1047,30.5493,21.6592		655/748	30915461	2817,10189	2203	4300	6503	SO:0001819	synonymous_variant	9371	exon7			CCGATATAGGGTG	AB002357	CCDS13200.1	20q11.21	2012-08-01			ENSG00000101350	ENSG00000101350		"""Kinesins"""	6320	protein-coding gene	gene with protein product		603754				9205841	Standard	NM_004798		Approved	KIAA0359, FLA8, KLP-11	uc002wxq.3	O15066	OTTHUMG00000032214	ENST00000375712.3:c.1965T>C	20.37:g.30915461T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_004798	B2RMP4|B4DSR5|E1P5M5	Silent	SNP	ENST00000375712.3	37	CCDS13200.1																																																																																			A|0.000;C|0.216;G|0.000;T|0.784	0.216	strong		0.468	KIF3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078619.1	NM_004798	
CEP83	51134	hgsc.bcm.edu	37	12	94761701	94761701	+	Silent	SNP	T	T	C	rs12426243	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:94761701T>C	ENST00000397809.5	-	11	1761	c.1212A>G	c.(1210-1212)agA>agG	p.R404R	CCDC41_ENST00000397807.2_Silent_p.R371R|CCDC41_ENST00000549352.1_5'Flank|CCDC41_ENST00000339839.5_Silent_p.R404R	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		396					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						AATCTGCTAATCTGTTCTCGA	0.353													T|||	396	0.0790735	0.0492	0.1311	5008	,	,		17366	0.0595		0.1183	False		,,,				2504	0.0624				p.R404R		Atlas-SNP	.											.	CCDC41	59	.	0			c.A1212G						PASS	.	T	,	181,3509		4,173,1668	147.0	128.0	134.0		1212,1212	5.8	1.0	12	dbSNP_120	134	930,7258		57,816,3221	no	coding-synonymous,coding-synonymous	CCDC41	NM_001042399.1,NM_016122.2	,	61,989,4889	CC,CT,TT		11.3581,4.9051,9.3534	,	404/702,404/702	94761701	1111,10767	1845	4094	5939	SO:0001819	synonymous_variant	51134	exon11			TGCTAATCTGTTC																												ENST00000397809.5:c.1212A>G	12.37:g.94761701T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_016122	A4FVB1|Q08AP1	Silent	SNP	ENST00000397809.5	37	CCDS41820.1																																																																																			T|0.891;C|0.109	0.109	strong		0.353	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3		
LAT	27040	hgsc.bcm.edu	37	16	28996225	28996225	+	5'Flank	SNP	T	T	C	rs41301797	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28996225T>C	ENST00000360872.5	+	0	0				LAT_ENST00000354453.4_5'Flank|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000566177.1_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000395461.3_Silent_p.L15L			O43561	LAT_HUMAN	linker for activation of T cells						blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				TGTCCCCGTCTTGGGGGGGGC	0.721													T|||	17	0.00339457	0.0	0.0014	5008	,	,		11049	0.0		0.0159	False		,,,				2504	0.0				p.L15L		Atlas-SNP	.											.	LAT	22	.	0			c.T43C						PASS	.						6.0	8.0	7.0					16																	28996225		689	1585	2274	SO:0001631	upstream_gene_variant	27040	exon1			CCCGTCTTGGGGG	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"""linker for activation of T cells, transmembrane adaptor"""	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761		16.37:g.28996225T>C	Exception_encountered	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	33	14	0.424242	NM_001014989	B7WPI0|C7C5T6|G5E9K3|O43919	Silent	SNP	ENST00000360872.5	37	CCDS10647.1																																																																																			T|0.500;C|0.500	0.500	weak		0.721	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2		
PIP4K2A	5305	hgsc.bcm.edu	37	10	22839628	22839628	+	Missense_Mutation	SNP	T	T	C	rs2230469	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:22839628T>C	ENST00000376573.4	-	7	980	c.752A>G	c.(751-753)aAc>aGc	p.N251S	PIP4K2A_ENST00000323883.7_Missense_Mutation_p.N111S|PIP4K2A_ENST00000545335.1_Missense_Mutation_p.N192S	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	251	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.		N -> S (in dbSNP:rs10828317). {ECO:0000269|PubMed:7639683}.		megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						GACCTTCTTGTTGTTGTCATC	0.363											OREG0020068	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1063	0.21226	0.0696	0.134	5008	,	,		18073	0.3839		0.3131	False		,,,				2504	0.18				p.N251S		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.A752G	GRCh37	CM068312	PIP4K2A	M	rs10828317	PASS	.	T	SER/ASN	456,3948	217.4+/-235.8	29,398,1775	180.0	175.0	177.0		752	6.1	1.0	10	dbSNP_120	177	2740,5860	437.2+/-358.5	451,1838,2011	yes	missense	PIP4K2A	NM_005028.4	46	480,2236,3786	CC,CT,TT		31.8605,10.3542,24.5771	benign	251/407	22839628	3196,9808	2202	4300	6502	SO:0001583	missense	5305	exon7			TTCTTGTTGTTGT	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"""phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"""	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.752A>G	10.37:g.22839628T>C	ENSP00000365757:p.Asn251Ser	Somatic	124	0	0	759	WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Missense_Mutation	SNP	ENST00000376573.4	37	CCDS7141.1	564	0.25824175824175827	38	0.07723577235772358	44	0.12154696132596685	232	0.40559440559440557	250	0.32981530343007914	T	9.613	1.131741	0.21041	0.103542	0.318605	ENSG00000150867	ENST00000376573;ENST00000323883;ENST00000545335	T;T;T	0.34275	1.37;1.37;1.37	6.07	6.07	0.98685	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.042713	0.85682	D	0.000000	T	0.00012	0.0000	N	0.11673	0.155	0.09310	P	0.999999748043	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.004	T	0.45760	-0.9239	9	0.15066	T	0.55	-58.1863	16.6277	0.84984	0.0:0.0:0.0:1.0	rs10828317;rs52795826;rs59726485;rs10828317	111;251	B4DH09;P48426	.;PI42A_HUMAN	S	251;111;192	ENSP00000365757:N251S;ENSP00000326294:N111S;ENSP00000442098:N192S	ENSP00000326294:N111S	N	-	2	0	PIP4K2A	22879634	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.912000	0.69948	2.330000	0.79161	0.528000	0.53228	AAC	T|0.753;C|0.247	0.247	strong		0.363	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	
CSMD3	114788	hgsc.bcm.edu	37	8	113364696	113364696	+	Silent	SNP	A	A	G	rs11778209	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:113364696A>G	ENST00000297405.5	-	39	6448	c.6204T>C	c.(6202-6204)taT>taC	p.Y2068Y	CSMD3_ENST00000343508.3_Silent_p.Y2028Y|CSMD3_ENST00000352409.3_Silent_p.Y1998Y|CSMD3_ENST00000455883.2_Silent_p.Y1964Y	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2068	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CTCCAACCATATATCTGTCTC	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	1253	0.2502	0.0673	0.3156	5008	,	,		16747	0.3938		0.2435	False		,,,				2504	0.3098				p.Y2068Y		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,-1,2	CSMD3	2325	2	0			c.T6204C						PASS	.	A	,,	373,4033	191.6+/-217.2	21,331,1851	111.0	103.0	106.0		5892,6204,6084	-7.8	0.8	8	dbSNP_120	106	1916,6682	339.2+/-323.1	218,1480,2601	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	239,1811,4452	GG,GA,AA		22.2843,8.4657,17.6023	,,	1964/3539,2068/3708,2028/3668	113364696	2289,10715	2203	4299	6502	SO:0001819	synonymous_variant	114788	exon39			AACCATATATCTG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6204T>C	8.37:g.113364696A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	137	63	0.459854	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.790;G|0.210	0.210	strong		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
HOXC10	3226	hgsc.bcm.edu	37	12	54379670	54379670	+	Silent	SNP	C	C	T	rs4564384	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:54379670C>T	ENST00000303460.4	+	1	701	c.627C>T	c.(625-627)ccC>ccT	p.P209P	HOXC-AS3_ENST00000514702.1_RNA|HOXC-AS3_ENST00000509870.1_RNA|RP11-834C11.12_ENST00000513209.1_Silent_p.P14P|HOXC-AS3_ENST00000513165.1_RNA|HOXC-AS3_ENST00000567780.1_RNA	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	209					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						GCCAGACCCCCAGCCCCAATG	0.642													C|||	371	0.0740815	0.0174	0.1095	5008	,	,		14760	0.0893		0.0855	False		,,,				2504	0.0982				p.P209P		Atlas-SNP	.											.	HOXC10	42	.	0			c.C627T						PASS	.	C		132,4274		1,130,2072	26.0	31.0	29.0		627	-1.4	1.0	12	dbSNP_111	29	714,7884		27,660,3612	no	coding-synonymous	HOXC10	NM_017409.3		28,790,5684	TT,TC,CC		8.3043,2.9959,6.5057		209/343	54379670	846,12158	2203	4299	6502	SO:0001819	synonymous_variant	3226	exon1			GACCCCCAGCCCC		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"""Homeoboxes / ANTP class : HOXL subclass"""	5122	protein-coding gene	gene with protein product		605560	"""homeo box C10"""	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.627C>T	12.37:g.54379670C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	81	31	0.382716	NM_017409	O15219|O15220|Q9BVD5	Silent	SNP	ENST00000303460.4	37	CCDS8868.1																																																																																			T|0.070;G|0.000;C|0.929	0.070	strong		0.642	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2		
MADCAM1	8174	hgsc.bcm.edu	37	19	498524	498524	+	Silent	SNP	A	A	G	rs2302217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:498524A>G	ENST00000215637.3	+	3	412	c.366A>G	c.(364-366)ccA>ccG	p.P122P	AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000346144.4_Silent_p.P122P|MADCAM1_ENST00000587541.1_Intron|MADCAM1_ENST00000382683.4_Silent_p.P27P	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	122	Ig-like 2.				aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-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)		CCGTCTCCCCAGCAGCCCTGG	0.706													G|||	3173	0.633586	0.826	0.438	5008	,	,		12677	0.753		0.4563	False		,,,				2504	0.5716				p.P122P		Atlas-SNP	.											MADCAM1,NS,carcinoma,0,1	MADCAM1	29	1	0			c.A366G						scavenged	.	G	,	3385,1019		1317,751,134	24.0	32.0	29.0		366,366	-8.3	0.0	19	dbSNP_100	29	3942,4656		931,2080,1288	no	coding-synonymous,coding-synonymous	MADCAM1	NM_130760.2,NM_130762.2	,	2248,2831,1422	GG,GA,AA		45.8479,23.1381,43.6471	,	122/383,122/296	498524	7327,5675	2202	4299	6501	SO:0001819	synonymous_variant	8174	exon3			CTCCCCAGCAGCC	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.366A>G	19.37:g.498524A>G		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Silent	SNP	ENST00000215637.3	37	CCDS12028.1																																																																																			A|0.429;G|0.571	0.571	strong		0.706	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
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 GAIIx	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	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	38	9	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:84547771A>C	ENST00000585776.1	-	0	1039				SPATA31D4_ENST00000341875.4_RNA|RP11-383M4.2_ENST00000427387.1_lincRNA																							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		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_001145197		Missense_Mutation	SNP	ENST00000585776.1	37																																																																																				.	.	none		0.448	RP11-383M4.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000453562.1		
TMPRSS5	80975	hgsc.bcm.edu	37	11	113570385	113570385	+	Missense_Mutation	SNP	C	C	T	rs11601425	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:113570385C>T	ENST00000299882.5	-	3	285	c.137G>A	c.(136-138)cGa>cAa	p.R46Q	TMPRSS5_ENST00000536856.1_Intron|TMPRSS5_ENST00000538955.1_Missense_Mutation_p.R2Q|TMPRSS5_ENST00000545579.1_Missense_Mutation_p.R37Q|TMPRSS5_ENST00000544476.1_Missense_Mutation_p.R2Q|TMPRSS5_ENST00000544634.1_Missense_Mutation_p.R46Q|TMPRSS5_ENST00000540540.1_Intron	NM_030770.2	NP_110397.2	Q9H3S3	TMPS5_HUMAN	transmembrane protease, serine 5	46			R -> Q (in dbSNP:rs11601425). {ECO:0000269|PubMed:17918732}.		proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	peptidase activity (GO:0008233)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	10		all_cancers(61;2.71e-16)|all_epithelial(67;1e-09)|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)|Prostate(24;0.0421)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.75e-06)|Epithelial(105;6.34e-05)|all cancers(92;0.000502)		ACAGCCACGTCGCATGGAACG	0.632													c|||	210	0.0419329	0.0061	0.0764	5008	,	,		16592	0.001		0.0905	False		,,,				2504	0.0583				p.R46Q		Atlas-SNP	.											.	TMPRSS5	69	.	0			c.G137A						PASS	.		GLN/ARG	93,4151		2,89,2031	18.0	25.0	23.0		137	3.1	0.4	11	dbSNP_120	23	919,7551		52,815,3368	yes	missense	TMPRSS5	NM_030770.2	43	54,904,5399	TT,TC,CC		10.8501,2.1913,7.9597	benign	46/458	113570385	1012,11702	2122	4235	6357	SO:0001583	missense	80975	exon3			CCACGTCGCATGG	AB028140	CCDS44735.1, CCDS73390.1, CCDS73391.1, CCDS73392.1, CCDS73393.1	11q	2010-04-13	2008-07-31		ENSG00000166682	ENSG00000166682		"""Serine peptidases / Transmembrane"""	14908	protein-coding gene	gene with protein product	"""spinesin"""	606751					Standard	NM_030770		Approved	MGC141886, MGC148044	uc001poc.4	Q9H3S3	OTTHUMG00000168186	ENST00000299882.5:c.137G>A	11.37:g.113570385C>T	ENSP00000299882:p.Arg46Gln	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	215	31	0.144186	NM_030770		Missense_Mutation	SNP	ENST00000299882.5	37	CCDS44735.1	107	0.04899267399267399	6	0.012195121951219513	27	0.07458563535911603	0	0.0	74	0.09762532981530343	c	16.55	3.155673	0.57259	0.021913	0.108501	ENSG00000166682	ENST00000299882;ENST00000545579;ENST00000538955;ENST00000544634;ENST00000544476	D;D;D;D;D	0.88896	-2.44;-2.44;-2.37;-2.42;-2.43	4.02	3.09	0.35607	.	0.350692	0.23859	N	0.043867	T	0.05273	0.0140	N	0.17082	0.46	0.20489	N	0.999895	B;B;B	0.31318	0.201;0.319;0.005	B;B;B	0.17433	0.012;0.018;0.002	T	0.15292	-1.0442	10	0.38643	T	0.18	.	6.9714	0.24650	0.0:0.8679:0.0:0.1321	rs11601425;rs17533506;rs52821493;rs11601425	46;37;46	F5GYA3;F5GX83;Q9H3S3	.;.;TMPS5_HUMAN	Q	46;37;2;46;2	ENSP00000299882:R46Q;ENSP00000441104:R37Q;ENSP00000445528:R2Q;ENSP00000440783:R46Q;ENSP00000445930:R2Q	ENSP00000299882:R46Q	R	-	2	0	TMPRSS5	113075595	0.000000	0.05858	0.354000	0.25760	0.035000	0.12851	-0.348000	0.07740	1.001000	0.39076	0.450000	0.29827	CGA	C|0.946;T|0.054	0.054	strong		0.632	TMPRSS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398652.1	NM_030770	
CD276	80381	hgsc.bcm.edu	37	15	74001993	74001993	+	Silent	SNP	T	T	C	rs11552770	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:74001993T>C	ENST00000318443.5	+	8	1811	c.1509T>C	c.(1507-1509)gcT>gcC	p.A503A	CD276_ENST00000537340.2_Silent_p.A357A|CD276_ENST00000318424.5_Silent_p.A285A|CD276_ENST00000561213.1_Silent_p.A503A|CD276_ENST00000564751.1_Silent_p.A285A	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	503					cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						TTGCAGGAGCTGAGGACCAGG	0.522													T|||	1004	0.200479	0.4289	0.1023	5008	,	,		19244	0.1349		0.0964	False		,,,				2504	0.136				p.A503A		Atlas-SNP	.											.	CD276	29	.	0			c.T1509C						PASS	.	T	,	1706,2690	514.4+/-368.6	354,998,846	97.0	105.0	102.0		1509,855	-8.1	0.6	15	dbSNP_120	102	840,7754	193.4+/-239.1	33,774,3490	no	coding-synonymous,coding-synonymous	CD276	NM_001024736.1,NM_025240.2	,	387,1772,4336	CC,CT,TT		9.7743,38.808,19.5997	,	503/535,285/317	74001993	2546,10444	2198	4297	6495	SO:0001819	synonymous_variant	80381	exon8			AGGAGCTGAGGAC	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.1509T>C	15.37:g.74001993T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Silent	SNP	ENST00000318443.5	37	CCDS32288.1																																																																																			T|0.807;C|0.193	0.193	strong		0.522	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
PDIA5	10954	hgsc.bcm.edu	37	3	122880191	122880191	+	Silent	SNP	T	T	C	rs8935	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:122880191T>C	ENST00000316218.7	+	16	1463	c.1368T>C	c.(1366-1368)tgT>tgC	p.C456C	PDIA5_ENST00000467157.1_3'UTR	NM_006810.3	NP_006801.1	Q14554	PDIA5_HUMAN	protein disulfide isomerase family A, member 5	456	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	oxidoreductase activity (GO:0016491)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	21				GBM - Glioblastoma multiforme(114;0.0427)		CTGTTGACTGTGTCAAAGACA	0.537													T|||	1412	0.281949	0.1195	0.281	5008	,	,		19701	0.4613		0.328	False		,,,				2504	0.2699				p.C456C		Atlas-SNP	.											.	PDIA5	66	.	0			c.T1368C						PASS	.	T		748,3658	306.3+/-289.4	72,604,1527	101.0	89.0	93.0		1368	-3.0	0.9	3	dbSNP_52	93	2632,5968	425.7+/-355.0	412,1808,2080	no	coding-synonymous	PDIA5	NM_006810.3		484,2412,3607	CC,CT,TT		30.6047,16.9768,25.988		456/520	122880191	3380,9626	2203	4300	6503	SO:0001819	synonymous_variant	10954	exon16			TGACTGTGTCAAA	AK054963	CCDS3020.1	3q21.1	2009-11-20	2005-06-29		ENSG00000065485	ENSG00000065485	5.3.4.1	"""Protein disulfide isomerases"""	24811	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 5"""			7556671	Standard	NM_006810		Approved	PDIR, FLJ30401	uc003egc.2	Q14554	OTTHUMG00000159558	ENST00000316218.7:c.1368T>C	3.37:g.122880191T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_006810	D3DN95|Q9BV43	Silent	SNP	ENST00000316218.7	37	CCDS3020.1																																																																																			C|0.276;T|0.724	0.276	strong		0.537	PDIA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356192.1	NM_006810	
WDR66	144406	hgsc.bcm.edu	37	12	122369762	122369762	+	Silent	SNP	C	C	T	rs7313748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:122369762C>T	ENST00000288912.4	+	4	1712	c.858C>T	c.(856-858)aaC>aaT	p.N286N	WDR66_ENST00000397454.2_Silent_p.N286N	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	286							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TCATCTACAACGTGTTCAGGA	0.438													C|||	1400	0.279553	0.0204	0.3602	5008	,	,		21400	0.4821		0.3131	False		,,,				2504	0.3292				p.N286N	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C858T						PASS	.	C	,	228,3760		10,208,1776	162.0	148.0	152.0		858,858	-1.1	0.1	12	dbSNP_116	152	2499,5849		383,1733,2058	no	coding-synonymous,coding-synonymous	WDR66	NM_001178003.1,NM_144668.5	,	393,1941,3834	TT,TC,CC		29.9353,5.7172,22.106	,	286/942,286/1150	122369762	2727,9609	1994	4174	6168	SO:0001819	synonymous_variant	144406	exon4			CTACAACGTGTTC	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.858C>T	12.37:g.122369762C>T		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	227	111	0.488987	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	37	CCDS41853.1																																																																																			C|0.713;T|0.287	0.287	strong		0.438	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
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 GAIIx	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	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	173	9	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	
P2RY11	5032	hgsc.bcm.edu	37	19	10224548	10224548	+	Missense_Mutation	SNP	G	G	A	rs3745601	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10224548G>A	ENST00000321826.4	+	2	443	c.259G>A	c.(259-261)Gcc>Acc	p.A87T	PPAN_ENST00000556468.1_Missense_Mutation_p.A507T|PPAN-P2RY11_ENST00000428358.1_3'UTR|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.A507T	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	87			A -> T (in dbSNP:rs3745601).		activation of adenylate cyclase activity (GO:0007190)|adenosine receptor signaling pathway (GO:0001973)|calcium-mediated signaling (GO:0019722)|cellular response to ATP (GO:0071318)|defense response (GO:0006952)|G-protein coupled receptor signaling pathway (GO:0007186)|neuronal signal transduction (GO:0023041)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|neurotransmitter receptor activity (GO:0030594)|receptor activity (GO:0004872)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)	16			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			CCCGCTGGCCGCCTACCTCTA	0.677											OREG0025230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	914	0.182508	0.1142	0.1585	5008	,	,		16337	0.3304		0.1083	False		,,,				2504	0.2157				p.A507T		Atlas-SNP	.											.	PPAN-P2RY11	81	.	0			c.G1519A						PASS	.	G	THR/ALA,THR/ALA,	479,3927	221.3+/-238.5	19,441,1743	31.0	29.0	30.0		1519,259,	3.5	1.0	19	dbSNP_107	30	978,7620	209.8+/-250.9	58,862,3379	yes	missense,missense,utr-3	P2RY11,PPAN-P2RY11	NM_001040664.2,NM_002566.4,NM_001198690.1	58,58,	77,1303,5122	AA,AG,GG		11.3747,10.8715,11.2042	probably-damaging,probably-damaging,	507/795,87/375,	10224548	1457,11547	2203	4299	6502	SO:0001583	missense	692312	exon13			CTGGCCGCCTACC	AF030335	CCDS12226.1	19p13.2	2012-08-08			ENSG00000244165	ENSG00000244165		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8540	protein-coding gene	gene with protein product		602697				9405388	Standard	NM_002566		Approved	P2Y11		Q96G91	OTTHUMG00000150166	ENST00000321826.4:c.259G>A	19.37:g.10224548G>A	ENSP00000323872:p.Ala87Thr	Somatic	64	0	0	663	WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_001040664	B2R8X9|O43190|Q9BYU4|Q9H170	Missense_Mutation	SNP	ENST00000321826.4	37	CCDS12226.1	390	0.17857142857142858	62	0.12601626016260162	53	0.1464088397790055	193	0.3374125874125874	82	0.10817941952506596	G	16.86	3.239499	0.58995	0.108715	0.113747	ENSG00000243207;ENSG00000130810;ENSG00000244165	ENST00000393796;ENST00000556468;ENST00000321826	T;T;T	0.37915	1.17;1.17;1.17	4.62	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.824795	0.10482	U	0.669521	T	0.00012	0.0000	L	0.46670	1.46	0.43179	P	0.005009999999999959	D	0.63046	0.992	P	0.55965	0.788	T	0.36286	-0.9754	9	0.22706	T	0.39	.	11.8118	0.52188	0.0:0.0:0.7753:0.2247	rs3745601;rs59821413;rs3745601	87	Q96G91	P2Y11_HUMAN	T	507;507;87	ENSP00000377385:A507T;ENSP00000450710:A507T;ENSP00000323872:A87T	ENSP00000323872:A87T	A	+	1	0	PPAN;P2RY11;PPAN-P2RY11	10085548	0.000000	0.05858	0.997000	0.53966	0.348000	0.29142	-0.044000	0.12023	2.411000	0.81874	0.561000	0.74099	GCC	G|0.855;A|0.145	0.145	strong		0.677	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
RCN3	57333	hgsc.bcm.edu	37	19	50045878	50045878	+	Missense_Mutation	SNP	C	C	T	rs34654230	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50045878C>T	ENST00000270645.3	+	6	1195	c.748C>T	c.(748-750)Cgg>Tgg	p.R250W		NM_020650.2	NP_065701.2	Q96D15	RCN3_HUMAN	reticulocalbin 3, EF-hand calcium binding domain	250	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.		R -> W (in dbSNP:rs34654230).			endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0159)		GCAGCAGTTCCGGGACTTCCG	0.677													C|||	493	0.0984425	0.1899	0.0735	5008	,	,		14291	0.0258		0.0835	False		,,,				2504	0.0828				p.R250W		Atlas-SNP	.											RCN3,NS,carcinoma,0,1	RCN3	28	1	0			c.C748T						PASS	.	C	TRP/ARG	780,3622		61,658,1482	34.0	36.0	35.0		748	5.2	1.0	19	dbSNP_126	35	652,7948		21,610,3669	yes	missense	RCN3	NM_020650.2	101	82,1268,5151	TT,TC,CC		7.5814,17.7192,11.0137	probably-damaging	250/329	50045878	1432,11570	2201	4300	6501	SO:0001583	missense	57333	exon6			CAGTTCCGGGACT	AY195859	CCDS12771.1	19q13.33	2013-01-10				ENSG00000142552		"""EF-hand domain containing"""	21145	protein-coding gene	gene with protein product							Standard	NM_020650		Approved	RLP49	uc002poj.3	Q96D15		ENST00000270645.3:c.748C>T	19.37:g.50045878C>T	ENSP00000270645:p.Arg250Trp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_020650	Q9HBZ8	Missense_Mutation	SNP	ENST00000270645.3	37	CCDS12771.1	200	0.09157509157509157	98	0.1991869918699187	24	0.06629834254143646	18	0.03146853146853147	60	0.079155672823219	C	20.6	4.016193	0.75161	0.177192	0.075814	ENSG00000142552	ENST00000270645	T	0.54279	0.58	5.16	5.16	0.70880	EF-hand-like domain (1);	0.238060	0.37012	N	0.002299	T	0.00073	0.0002	L	0.54323	1.7	0.33592	P	0.39876199999999995	D	0.63880	0.993	B	0.40534	0.332	T	0.23655	-1.0182	9	0.66056	D	0.02	-27.0776	7.5588	0.27839	0.0:0.7425:0.169:0.0885	rs34654230;rs58180887	250	Q96D15	RCN3_HUMAN	W	250	ENSP00000270645:R250W	ENSP00000270645:R250W	R	+	1	2	RCN3	54737690	0.065000	0.20965	1.000000	0.80357	0.864000	0.49448	0.501000	0.22578	2.421000	0.82119	0.650000	0.86243	CGG	C|0.891;G|0.000;T|0.108	0.108	strong		0.677	RCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465261.1	NM_020650	
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 GAIIx	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		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	7	5	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 GAIIx	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		Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	295	17	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		
IBA57	200205	hgsc.bcm.edu	37	1	228362682	228362682	+	Missense_Mutation	SNP	G	G	A	rs2298014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228362682G>A	ENST00000366711.3	+	2	633	c.631G>A	c.(631-633)Ggc>Agc	p.G211S	IBA57_ENST00000546123.1_Missense_Mutation_p.G18S|IBA57_ENST00000484749.1_3'UTR	NM_001010867.2	NP_001010867.1	Q5T440	CAF17_HUMAN	IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)	211			G -> S (in dbSNP:rs2298014).		glycine catabolic process (GO:0006546)|heme biosynthetic process (GO:0006783)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|prostate(1)	11						GGTGCCCGGGGGCCGGCTCGG	0.687													G|||	786	0.156949	0.0371	0.2666	5008	,	,		15317	0.0546		0.329	False		,,,				2504	0.1697				p.G211S		Atlas-SNP	.											.	IBA57	22	.	0			c.G631A						PASS	.	G	SER/GLY	373,4015		17,339,1838	16.0	21.0	20.0		631	1.7	0.0	1	dbSNP_100	20	2959,5621		527,1905,1858	yes	missense	IBA57	NM_001010867.2	56	544,2244,3696	AA,AG,GG		34.4872,8.5005,25.694	benign	211/357	228362682	3332,9636	2194	4290	6484	SO:0001583	missense	200205	exon2			CCCGGGGGCCGGC	AK022796	CCDS31046.1	1q42.13	2011-03-11	2011-03-11	2011-03-11	ENSG00000181873	ENSG00000181873			27302	protein-coding gene	gene with protein product	"""iron-sulfur cluster assembly factor for biotin synthase- and aconitase-like mitochondrial proteins, with a mass of 57kDa"""	615316	"""chromosome 1 open reading frame 69"""	C1orf69			Standard	NM_001010867		Approved	FLJ12734	uc001hsl.4	Q5T440	OTTHUMG00000039769	ENST00000366711.3:c.631G>A	1.37:g.228362682G>A	ENSP00000355672:p.Gly211Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_001010867		Missense_Mutation	SNP	ENST00000366711.3	37	CCDS31046.1	402	0.18406593406593408	16	0.032520325203252036	105	0.2900552486187845	32	0.055944055944055944	249	0.32849604221635886	G	9.295	1.051708	0.19827	0.085005	0.344872	ENSG00000181873	ENST00000366711;ENST00000546123	T;T	0.74632	-0.86;0.99	4.89	1.69	0.24217	Glycine cleavage T-protein, N-terminal (1);	0.415911	0.28119	N	0.016538	T	0.00012	0.0000	L	0.41824	1.3	0.80722	P	0.0	B	0.10296	0.003	B	0.12156	0.007	T	0.12863	-1.0531	9	0.07325	T	0.83	-8.7236	3.9045	0.09176	0.2665:0.0:0.5435:0.19	rs2298014	211	Q5T440	CAF17_HUMAN	S	211;18	ENSP00000355672:G211S;ENSP00000437347:G18S	ENSP00000355672:G211S	G	+	1	0	IBA57	226429305	0.003000	0.15002	0.000000	0.03702	0.010000	0.07245	0.534000	0.23098	0.622000	0.30249	0.655000	0.94253	GGC	G|0.783;A|0.217	0.217	strong		0.687	IBA57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095980.1	NM_001010867	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75415677	75415677	+	Missense_Mutation	SNP	C	C	T	rs60632610	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:75415677C>T	ENST00000394810.2	-	1	153	c.4G>A	c.(4-6)Ggt>Agt	p.G2S	RP11-464F9.21_ENST00000606726.1_RNA|RP11-464F9.21_ENST00000607450.1_RNA	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	2						cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					TCCTCAGCACCCATCGCTCAG	0.622													c|||	825	0.164736	0.2012	0.1182	5008	,	,		11156	0.1577		0.1372	False		,,,				2504	0.184				p.G2S		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.G4A						PASS	.	C	SER/GLY	265,1119		26,213,453	65.0	73.0	70.0		4	4.5	1.0	10	dbSNP_129	70	507,2675		41,425,1125	yes	missense	SYNPO2L	NM_001114133.1	56	67,638,1578	TT,TC,CC		15.9334,19.1474,16.9076	probably-damaging	2/978	75415677	772,3794	692	1591	2283	SO:0001583	missense	79933	exon1			CAGCACCCATCGC	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.4G>A	10.37:g.75415677C>T	ENSP00000378289:p.Gly2Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	340	0.15567765567765568	99	0.20121951219512196	41	0.1132596685082873	96	0.16783216783216784	104	0.13720316622691292	C	28.5	4.924089	0.92319	0.191474	0.159334	ENSG00000166317	ENST00000372872;ENST00000394810	T;T	0.48836	0.8;1.34	4.53	4.53	0.55603	.	0.166827	0.40144	U	0.001165	T	0.00109	0.0003	L	0.54323	1.7	0.23186	P	0.99815486	D	0.69078	0.997	P	0.60789	0.879	T	0.03534	-1.1027	9	0.62326	D	0.03	-4.7819	12.8341	0.57763	0.0:1.0:0.0:0.0	rs60632610	2	Q9H987	SYP2L_HUMAN	S	2	ENSP00000361963:G2S;ENSP00000378289:G2S	ENSP00000361963:G2S	G	-	1	0	SYNPO2L	75085683	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.517000	0.60503	2.080000	0.62538	0.543000	0.68304	GGT	C|0.845;G|0.000;T|0.155	0.155	strong		0.622	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
MUC6	4588	hgsc.bcm.edu	37	11	1018316	1018316	+	Silent	SNP	G	G	A	rs201954368		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1018316G>A	ENST00000421673.2	-	31	4535	c.4485C>T	c.(4483-4485)tcC>tcT	p.S1495S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1495	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|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;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGTGTGGGTGGACCCTGTGG	0.572																																					p.S1495S		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,4	MUC6	408	4	0			c.C4485T						scavenged	.						280.0	289.0	286.0					11																	1018316		2189	4268	6457	SO:0001819	synonymous_variant	4588	exon31			GTGGGTGGACCCT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4485C>T	11.37:g.1018316G>A		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	268	7	0.0261194	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	weak		0.572	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
DOCK1	1793	hgsc.bcm.edu	37	10	129242515	129242515	+	Silent	SNP	G	G	A	rs11371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:129242515G>A	ENST00000280333.6	+	50	5431	c.5322G>A	c.(5320-5322)agG>agA	p.R1774R		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1774					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TTACACCAAGGGCCAAGCTCA	0.572													G|||	1690	0.33746	0.2133	0.2824	5008	,	,		19267	0.4653		0.3658	False		,,,				2504	0.3834				p.R1774R		Atlas-SNP	.											.	DOCK1	188	.	0			c.G5322A						PASS	.	G		911,3281		108,695,1293	85.0	96.0	92.0		5277	1.9	0.8	10	dbSNP_52	92	3176,5248		615,1946,1651	no	coding-synonymous	DOCK1	NM_001380.3		723,2641,2944	AA,AG,GG		37.7018,21.7319,32.3954		1759/1851	129242515	4087,8529	2096	4212	6308	SO:0001819	synonymous_variant	1793	exon50			ACCAAGGGCCAAG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5322G>A	10.37:g.129242515G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				G|0.667;A|0.333	0.333	strong		0.572	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
RAB11B	9230	hgsc.bcm.edu	37	19	8468337	8468337	+	Silent	SNP	C	C	T	rs2230876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8468337C>T	ENST00000328024.6	+	5	770	c.552C>T	c.(550-552)cgC>cgT	p.R184R		NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	184				R -> C (in Ref. 6; CAG46492). {ECO:0000305}.	cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(1)|ovary(1)	4						TCGCAGACCGCGCTGCCCACG	0.652													C|||	1653	0.330072	0.2632	0.219	5008	,	,		15294	0.5188		0.2873	False		,,,				2504	0.3487				p.R184R		Atlas-SNP	.											.	RAB11B	15	.	0			c.C552T						PASS	.	C		1104,3302	397.2+/-330.3	144,816,1243	137.0	110.0	119.0		552	-5.4	0.0	19	dbSNP_98	119	2468,6132	407.7+/-349.2	355,1758,2187	no	coding-synonymous	RAB11B	NM_004218.3		499,2574,3430	TT,TC,CC		28.6977,25.0567,27.4642		184/219	8468337	3572,9434	2203	4300	6503	SO:0001819	synonymous_variant	9230	exon5			AGACCGCGCTGCC	X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"""RAB, member RAS oncogene"""	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.552C>T	19.37:g.8468337C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_004218	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Silent	SNP	ENST00000328024.6	37	CCDS12201.1																																																																																			C|0.701;A|0.004	.	strong		0.652	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218	
CBX2	84733	hgsc.bcm.edu	37	17	77758484	77758484	+	Silent	SNP	G	G	A	rs3751956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77758484G>A	ENST00000310942.4	+	5	1346	c.1242G>A	c.(1240-1242)ctG>ctA	p.L414L		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	414					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GTGAGAAGCTGGCTTCCAGAG	0.677													G|||	1024	0.204473	0.0287	0.2334	5008	,	,		3668	0.1806		0.4443	False		,,,				2504	0.1994				p.L414L		Atlas-SNP	.											CBX2,NS,carcinoma,0,2	CBX2	50	2	0			c.G1242A						PASS	.	G		388,4014		16,356,1829	17.0	19.0	19.0		1242	3.1	0.8	17	dbSNP_107	19	3567,5033		731,2105,1464	no	coding-synonymous	CBX2	NM_005189.2		747,2461,3293	AA,AG,GG		41.4767,8.8142,30.4184		414/533	77758484	3955,9047	2201	4300	6501	SO:0001819	synonymous_variant	84733	exon5			GAAGCTGGCTTCC	BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.1242G>A	17.37:g.77758484G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_005189	Q0VDA5|Q9BTB1	Silent	SNP	ENST00000310942.4	37	CCDS32757.1																																																																																			G|0.744;A|0.256	0.256	strong		0.677	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
H2AFY2	55506	hgsc.bcm.edu	37	10	71851653	71851653	+	Silent	SNP	G	G	A	rs116804623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:71851653G>A	ENST00000373255.4	+	4	684	c.420G>A	c.(418-420)acG>acA	p.T140T		NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	140	Lys-rich.				brain development (GO:0007420)|chromatin modification (GO:0016568)|dosage compensation (GO:0007549)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901837)|nucleosome assembly (GO:0006334)	Barr body (GO:0001740)|extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|transcription regulatory region DNA binding (GO:0044212)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(4)|skin(1)	15						GGAAGGCCACGTCAGGCAAGA	0.597													G|||	34	0.00678914	0.0008	0.0115	5008	,	,		16194	0.0		0.0209	False		,,,				2504	0.0041				p.T140T		Atlas-SNP	.											.	H2AFY2	30	.	0			c.G420A						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	72.0	67.0	68.0		420	-6.4	0.5	10	dbSNP_132	68	169,8431	77.2+/-139.8	4,161,4135	no	coding-synonymous	H2AFY2	NM_018649.2		4,176,6323	AA,AG,GG		1.9651,0.3404,1.4147		140/373	71851653	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	55506	exon4			GGCCACGTCAGGC	AF336304	CCDS7296.1	10q22.1	2011-01-27			ENSG00000099284	ENSG00000099284		"""Histones / Replication-independent"""	14453	protein-coding gene	gene with protein product						11331621, 11262398	Standard	NM_018649		Approved	macroH2A2	uc001jqm.3	Q9P0M6	OTTHUMG00000018396	ENST00000373255.4:c.420G>A	10.37:g.71851653G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_018649	Q5SQT2	Silent	SNP	ENST00000373255.4	37	CCDS7296.1																																																																																			G|0.988;A|0.012	0.012	strong		0.597	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649	
TLE1	7088	hgsc.bcm.edu	37	9	84205860	84205860	+	Silent	SNP	G	G	A	rs8782	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:84205860G>A	ENST00000376499.3	-	16	2753	c.1689C>T	c.(1687-1689)acC>acT	p.T563T		NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	563					multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						TGATGCGCGGGGTTGGAGCCG	0.597													G|||	871	0.173922	0.1475	0.2075	5008	,	,		16820	0.0387		0.333	False		,,,				2504	0.1616				p.T563T	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											.	TLE1	81	.	0			c.C1689T						PASS	.	G		749,3657	305.5+/-289.0	56,637,1510	66.0	67.0	66.0		1689	2.6	1.0	9	dbSNP_52	66	2977,5623	459.7+/-365.0	501,1975,1824	no	coding-synonymous	TLE1	NM_005077.3		557,2612,3334	AA,AG,GG		34.6163,16.9995,28.6483		563/771	84205860	3726,9280	2203	4300	6503	SO:0001819	synonymous_variant	7088	exon16			GCGCGGGGTTGGA		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"""WD repeat domain containing"""	11837	protein-coding gene	gene with protein product	"""enhancer of split groucho 1"""	600189	"""transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"""			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.1689C>T	9.37:g.84205860G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_005077	A8K495|Q5T3G4|Q969V9	Silent	SNP	ENST00000376499.3	37	CCDS6661.1																																																																																			G|0.736;A|0.264	0.264	strong		0.597	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077	
ZNF530	348327	hgsc.bcm.edu	37	19	58117083	58117083	+	Missense_Mutation	SNP	A	A	G	rs9677004	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58117083A>G	ENST00000332854.6	+	3	410	c.190A>G	c.(190-192)Acg>Gcg	p.T64A	ZNF530_ENST00000597864.1_Intron	NM_020880.3	NP_065931.3	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	64	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		T -> A (in dbSNP:rs9677004). {ECO:0000269|PubMed:10819331}.		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(6)|skin(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AGATGAGGGGACGCCTTCTGC	0.463													G|||	1490	0.297524	0.4932	0.2133	5008	,	,		18988	0.3244		0.173	False		,,,				2504	0.1933				p.T64A		Atlas-SNP	.											.	ZNF530	71	.	0			c.A190G						PASS	.	G	ALA/THR	1945,2461	602.3+/-389.9	437,1071,695	65.0	67.0	67.0		190	-3.4	0.0	19	dbSNP_119	67	1428,7172	738.6+/-407.1	117,1194,2989	yes	missense	ZNF530	NM_020880.3	58	554,2265,3684	GG,GA,AA		16.6047,44.1443,25.9342	benign	64/600	58117083	3373,9633	2203	4300	6503	SO:0001583	missense	348327	exon3			GAGGGGACGCCTT	AK096831	CCDS12955.1	19q13.43	2013-01-08				ENSG00000183647		"""Zinc fingers, C2H2-type"", ""-"""	29297	protein-coding gene	gene with protein product						10819331	Standard	NM_020880		Approved	KIAA1508	uc002qpk.2	Q6P9A1		ENST00000332854.6:c.190A>G	19.37:g.58117083A>G	ENSP00000332861:p.Thr64Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_020880	O43340|Q9P220	Missense_Mutation	SNP	ENST00000332854.6	37	CCDS12955.1	631	0.2889194139194139	246	0.5	75	0.20718232044198895	182	0.3181818181818182	128	0.16886543535620052	G	0.006	-2.095964	0.00364	0.441443	0.166047	ENSG00000183647	ENST00000332854	T	0.05025	3.51	1.83	-3.39	0.04868	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.13098	0.295	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41645	-0.9497	8	0.05351	T	0.99	.	5.137	0.14939	0.6324:0.0:0.2014:0.1662	rs9677004;rs52811543;rs57193532;rs9677004	64	Q6P9A1	ZN530_HUMAN	A	64	ENSP00000332861:T64A	ENSP00000332861:T64A	T	+	1	0	ZNF530	62808895	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.373000	0.07494	-1.446000	0.01945	-0.971000	0.02607	ACG	A|0.716;G|0.284	0.284	strong		0.463	ZNF530-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466797.1	NM_020880	
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 GAIIx	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	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	143	22	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	
OR8G5	219865	hgsc.bcm.edu	37	11	124135662	124135662	+	Missense_Mutation	SNP	A	A	G	rs2512166	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124135662A>G	ENST00000524943.2	+	1	940	c.940A>G	c.(940-942)Act>Gct	p.T314A	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	314						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|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;0.0523)		TGTGTTTTATACTATTGTTGT	0.473													A|||	503	0.100439	0.0174	0.1585	5008	,	,		19370	0.13		0.1441	False		,,,				2504	0.0961				p.T314A	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.A940G						PASS	.	A	ALA/THR	161,3897		4,153,1872	83.0	82.0	82.0		940	3.0	0.0	11	dbSNP_100	82	1323,7117		96,1131,2993	no	missense	OR8G5	NM_001005198.1	58	100,1284,4865	GG,GA,AA		15.6754,3.9675,11.8739		314/347	124135662	1484,11014	2029	4220	6249	SO:0001583	missense	219865	exon1			TTTTATACTATTG	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.940A>G	11.37:g.124135662A>G	ENSP00000477014:p.Thr314Ala	Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	228	186	0.815789	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				A|0.887;G|0.113	0.113	strong		0.473	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
LRRC41	10489	hgsc.bcm.edu	37	1	46746164	46746164	+	Missense_Mutation	SNP	C	C	T	rs11542623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46746164C>T	ENST00000343304.6	-	6	2110	c.1825G>A	c.(1825-1827)Gtt>Att	p.V609I	LRRC41_ENST00000472710.1_5'UTR	NM_006369.4	NP_006360.3	Q15345	LRC41_HUMAN	leucine rich repeat containing 41	609			V -> I (in dbSNP:rs11542623). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		protein ubiquitination (GO:0016567)	membrane (GO:0016020)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					GCCTTCAGAACGGAGCACAGC	0.557													C|||	931	0.185903	0.0265	0.1167	5008	,	,		18916	0.2758		0.1392	False		,,,				2504	0.4059				p.V609I		Atlas-SNP	.											.	LRRC41	74	.	0			c.G1825A						PASS	.	C	ILE/VAL	191,4215	121.7+/-159.2	3,185,2015	83.0	94.0	90.0		1825	4.9	1.0	1	dbSNP_120	90	1050,7550	221.9+/-259.1	60,930,3310	yes	missense	LRRC41	NM_006369.4	29	63,1115,5325	TT,TC,CC		12.2093,4.335,9.5417	possibly-damaging	609/813	46746164	1241,11765	2203	4300	6503	SO:0001583	missense	10489	exon6			TCAGAACGGAGCA	AK024051	CCDS533.1	1p34.1	2008-02-05			ENSG00000132128	ENSG00000132128			16917	protein-coding gene	gene with protein product						11384984	Standard	XM_005270376		Approved	MUF1	uc001cpn.3	Q15345	OTTHUMG00000007810	ENST00000343304.6:c.1825G>A	1.37:g.46746164C>T	ENSP00000343298:p.Val609Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	121	64	0.528926	NM_006369	A8K5G8|Q3MJ96|Q5TDF5|Q71RA8|Q9BSM0	Missense_Mutation	SNP	ENST00000343304.6	37	CCDS533.1	319	0.14606227106227107	10	0.02032520325203252	47	0.1298342541436464	168	0.2937062937062937	94	0.12401055408970976	C	17.77	3.470831	0.63625	0.04335	0.122093	ENSG00000132128	ENST00000343304	T	0.52754	0.65	5.81	4.9	0.64082	.	0.084454	0.49305	N	0.000143	T	0.00012	0.0000	N	0.24115	0.695	0.34601	P	0.28349199999999997	B;B	0.26041	0.14;0.066	B;B	0.22880	0.042;0.008	T	0.17048	-1.0382	9	0.49607	T	0.09	-2.4736	14.6845	0.69040	0.0:0.9307:0.0:0.0693	rs11542623;rs52792268;rs11542623	609;609	Q15345-3;Q15345	.;LRC41_HUMAN	I	609	ENSP00000343298:V609I	ENSP00000343298:V609I	V	-	1	0	LRRC41	46518751	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	5.114000	0.64648	1.469000	0.48083	0.644000	0.83932	GTT	C|0.869;A|0.002	.	strong		0.557	LRRC41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021438.1	NM_006369	
MGAT1	4245	hgsc.bcm.edu	37	5	180218668	180218668	+	Missense_Mutation	SNP	A	A	G	rs634501	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180218668A>G	ENST00000446023.2	-	3	2054	c.1304T>C	c.(1303-1305)cTg>cCg	p.L435P	MGAT1_ENST00000333055.3_Missense_Mutation_p.L435P|MGAT1_ENST00000393340.3_Missense_Mutation_p.L435P|MGAT1_ENST00000307826.4_Missense_Mutation_p.L435P|MGAT1_ENST00000427865.2_Missense_Mutation_p.L435P	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	435			L -> P (in dbSNP:rs634501). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1827260, ECO:0000269|Ref.4}.		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTCCCACGTCAGTGGGGGCGC	0.622													G|||	3671	0.733027	0.879	0.5576	5008	,	,		15523	0.5526		0.7455	False		,,,				2504	0.8333				p.L435P		Atlas-SNP	.											MGAT1,NS,carcinoma,0,1	MGAT1	48	1	0			c.T1304C						PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	3693,713	279.9+/-275.1	1556,581,66	38.0	41.0	40.0		1304,1304,1304,1304,1304	3.8	0.7	5	dbSNP_83	40	6294,2306	363.1+/-333.0	2306,1682,312	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	98,98,98,98,98	3862,2263,378	GG,GA,AA		26.814,16.1825,23.2124	benign,benign,benign,benign,benign	435/446,435/446,435/446,435/446,435/446	180218668	9987,3019	2203	4300	6503	SO:0001583	missense	4245	exon3			CACGTCAGTGGGG	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.1304T>C	5.37:g.180218668A>G	ENSP00000404718:p.Leu435Pro	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	1352	0.6190476190476191	356	0.7235772357723578	195	0.5386740331491713	293	0.5122377622377622	508	0.6701846965699209	G	0.413	-0.912114	0.02415	0.838175	0.73186	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	4.96	3.79	0.43588	.	0.498752	0.20868	N	0.084227	T	0.00012	0.0000	N	0.00926	-1.1	0.43347	P	0.0045960000000000445	B	0.02656	0.0	B	0.08055	0.003	T	0.41088	-0.9528	9	0.30854	T	0.27	-3.7269	7.0726	0.25187	0.1439:0.0:0.1564:0.6997	rs634501;rs17856087;rs60466398;rs634501	435	P26572	MGAT1_HUMAN	P	435;435;435;435;292;435	ENSP00000332073:L435P;ENSP00000311888:L435P;ENSP00000404718:L435P;ENSP00000377010:L435P;ENSP00000402838:L435P	ENSP00000311888:L435P	L	-	2	0	MGAT1	180151274	0.001000	0.12720	0.654000	0.29608	0.025000	0.11179	0.597000	0.24059	0.470000	0.27294	-1.059000	0.02297	CTG	A|0.273;G|0.727	0.727	strong		0.622	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
KIAA0753	9851	hgsc.bcm.edu	37	17	6515454	6515454	+	Missense_Mutation	SNP	C	C	T	rs386794940|rs2289643	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6515454C>T	ENST00000361413.3	-	8	1688	c.1330G>A	c.(1330-1332)Gat>Aat	p.D444N	KIAA0753_ENST00000572370.1_Missense_Mutation_p.D145N|KIAA0753_ENST00000589033.1_Intron|KIAA0753_ENST00000542606.1_Missense_Mutation_p.D145N	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	444			D -> N (in dbSNP:rs2289643). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.D444N(1)		endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		AGCTCCGTATCGGGCTGATAC	0.398													C|||	2686	0.536342	0.3275	0.621	5008	,	,		20370	0.7103		0.5149	False		,,,				2504	0.6012				p.D444N		Atlas-SNP	.											KIAA0753,NS,carcinoma,0,1	KIAA0753	63	1	1	Substitution - Missense(1)	prostate(1)	c.G1330A						PASS	.	C	ASN/ASP	1366,2330		252,862,734	94.0	93.0	93.0		1330	3.4	0.0	17	dbSNP_100	93	4397,3793		1174,2049,872	yes	missense	KIAA0753	NM_014804.2	23	1426,2911,1606	TT,TC,CC		46.3126,36.9589,48.4856	benign	444/968	6515454	5763,6123	1848	4095	5943	SO:0001583	missense	9851	exon8			CCGTATCGGGCTG		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1330G>A	17.37:g.6515454C>T	ENSP00000355250:p.Asp444Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	1171	0.5361721611721612	184	0.37398373983739835	225	0.6215469613259669	391	0.6835664335664335	371	0.4894459102902375	C	8.089	0.774006	0.16051	0.369589	0.536874	ENSG00000198920	ENST00000361413;ENST00000542606	T;T	0.08896	3.04;3.04	4.33	3.36	0.38483	.	1.505420	0.03377	N	0.199827	T	0.00012	0.0000	L	0.51422	1.61	0.50813	P	1.0699999999996823E-4	B	0.18013	0.025	B	0.10450	0.005	T	0.41980	-0.9478	9	0.21540	T	0.41	0.075	8.2745	0.31864	0.0:0.8936:0.0:0.1064	rs2289643;rs17731526;rs52837019;rs59901755;rs2289643	444	Q2KHM9	K0753_HUMAN	N	444;145	ENSP00000355250:D444N;ENSP00000444634:D145N	ENSP00000355250:D444N	D	-	1	0	KIAA0753	6456178	0.245000	0.23899	0.040000	0.18447	0.004000	0.04260	1.423000	0.34837	1.434000	0.47414	0.591000	0.81541	GAT	C|0.456;T|0.544	0.544	strong		0.398	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
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 GAIIx	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	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	29	15	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		
SNAPC4	6621	hgsc.bcm.edu	37	9	139279173	139279173	+	Splice_Site	SNP	G	G	A	rs10781510	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139279173G>A	ENST00000298532.2	-	13	1787	c.1419C>T	c.(1417-1419)gtC>gtT	p.V473V		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GCAACTTACCGACACCATATT	0.353													A|||	1831	0.365615	0.2557	0.5692	5008	,	,		19230	0.3165		0.3867	False		,,,				2504	0.3988				p.V473V		Atlas-SNP	.											.	SNAPC4	82	.	0			c.C1419T						PASS	.	A		1233,3173	700.6+/-406.6	169,895,1139	114.0	112.0	113.0		1419	-10.0	0.0	9	dbSNP_120	113	3521,5077	630.5+/-398.4	714,2093,1492	yes	coding-synonymous-near-splice	SNAPC4	NM_003086.2		883,2988,2631	AA,AG,GG		40.9514,27.9846,36.558		473/1470	139279173	4754,8250	2203	4299	6502	SO:0001630	splice_region_variant	6621	exon13			CTTACCGACACCA	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.1420+1C>T	9.37:g.139279173G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			G|0.640;A|0.360	0.360	strong		0.353	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	Silent
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 GAIIx	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_ENST00000354233.3_Silent_p.T239T|HCFC1_ENST00000369984.4_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		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	48	10	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	
ERN2	10595	hgsc.bcm.edu	37	16	23722280	23722280	+	Silent	SNP	G	G	A	rs56342512	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:23722280G>A	ENST00000457008.2	-	2	191	c.153C>T	c.(151-153)caC>caT	p.H51H	ERN2_ENST00000256797.4_Silent_p.H99H|CTD-2385L22.1_ENST00000563611.1_RNA					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		TGCTTAGTGCGTGGAGACTTC	0.567													G|||	135	0.0269569	0.003	0.0303	5008	,	,		21481	0.001		0.0765	False		,,,				2504	0.0327				p.H99H		Atlas-SNP	.											.	ERN2	131	.	0			c.C297T						PASS	.	G		98,4296	78.8+/-117.2	1,96,2100	139.0	124.0	129.0		297	-8.8	0.2	16	dbSNP_129	129	730,7870	177.5+/-227.1	43,644,3613	no	coding-synonymous	ERN2	NM_033266.3		44,740,5713	AA,AG,GG		8.4884,2.2303,6.3722		99/975	23722280	828,12166	2197	4300	6497	SO:0001819	synonymous_variant	10595	exon2			TAGTGCGTGGAGA	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"""ER to nucleus signalling 2"""			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.153C>T	16.37:g.23722280G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_033266		Silent	SNP	ENST00000457008.2	37																																																																																				G|0.944;A|0.056	0.056	strong		0.567	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1		
MXRA5	25878	hgsc.bcm.edu	37	X	3241256	3241256	+	Missense_Mutation	SNP	T	T	C	rs5983119	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3241256T>C	ENST00000217939.6	-	5	2624	c.2470A>G	c.(2470-2472)Att>Gtt	p.I824V		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	824			I -> V (in dbSNP:rs5983119). {ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GGGGGAGAAATAGCAGGAAAA	0.488													C|||	2831	0.749934	0.6853	0.5216	3775	,	,		14207	0.5595		0.5288	False		,,,				2504	0.4775				p.I824V		Atlas-SNP	.											.	MXRA5	815	.	0			c.A2470G						PASS	.	C	VAL/ILE	3360,475		1270,329,491,33,80	128.0	127.0	128.0		2470	0.1	0.0	X	dbSNP_114	128	4339,2389		1019,1109,1192,300,680	yes	missense	MXRA5	NM_015419.3	29	2289,1438,1683,333,760	CC,CT,C,TT,T		35.5083,12.3859,27.1135	benign	824/2829	3241256	7699,2864	2203	4300	6503	SO:0001583	missense	25878	exon5			GAGAAATAGCAGG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2470A>G	X.37:g.3241256T>C	ENSP00000217939:p.Ile824Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	1233	0.7432188065099458	236	0.8251748251748252	131	0.5077519379844961	206	0.5885714285714285	272	0.5291828793774319	c	0.011	-1.733413	0.00687	0.876141	0.644917	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.61274	0.12	3.63	0.0923	0.14472	.	1.970240	0.02957	N	0.142505	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	0.41893	-0.9483	9	0.02654	T	1	.	2.6272	0.04933	0.1281:0.4316:0.2503:0.1899	rs5983119;rs6420602;rs17259953;rs52798373;rs58224949;rs5983119	824	Q9NR99	MXRA5_HUMAN	V	824	ENSP00000217939:I824V	ENSP00000217939:I824V	I	-	1	0	MXRA5	3251256	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.202000	0.17295	0.025000	0.15241	-0.252000	0.11476	ATT	0|0.003;C|0.749	0.749	strong		0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
MTMR11	10903	hgsc.bcm.edu	37	1	149908108	149908108	+	Silent	SNP	A	A	G	rs386547202|rs1868992	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:149908108A>G	ENST00000439741.2	-	2	331	c.81T>C	c.(79-81)aaT>aaC	p.N27N	MTMR11_ENST00000361405.6_Silent_p.N27N|MTMR11_ENST00000406732.3_5'UTR|MTMR11_ENST00000492824.1_5'UTR|MTMR11_ENST00000369140.3_5'UTR	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	27							phosphatase activity (GO:0016791)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			CCGGCATCCTATTTTCCTGGA	0.557													G|||	2087	0.416733	0.6914	0.3991	5008	,	,		18119	0.3571		0.2594	False		,,,				2504	0.2812				p.N27N		Atlas-SNP	.											.	MTMR11	136	.	0			c.T81C						PASS	.	G	,	2708,1698	513.9+/-368.5	837,1034,332	90.0	92.0	91.0		81,	-0.8	0.0	1	dbSNP_92	91	2236,6364	709.0+/-405.7	320,1596,2384	no	coding-synonymous,utr-5	MTMR11	NM_001145862.1,NM_181873.3	,	1157,2630,2716	GG,GA,AA		26.0,38.5384,38.0132	,	27/710,	149908108	4944,8062	2203	4300	6503	SO:0001819	synonymous_variant	10903	exon2			CATCCTATTTTCC	AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	24307	protein-coding gene	gene with protein product	"""cisplatin resistance associated"""					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.81T>C	1.37:g.149908108A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	68	0.985507	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Silent	SNP	ENST00000439741.2	37	CCDS53360.1																																																																																			A|0.617;G|0.382	0.382	strong		0.557	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873	
MARC2	54996	hgsc.bcm.edu	37	1	220928334	220928334	+	Silent	SNP	A	A	G	rs12048193	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:220928334A>G	ENST00000366913.3	+	2	516	c.318A>G	c.(316-318)cgA>cgG	p.R106R	MARC2_ENST00000359316.2_Silent_p.R106R	NM_017898.3	NP_060368.2	Q969Z3	MARC2_HUMAN	mitochondrial amidoxime reducing component 2	106					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										TCACTGCCCGACAGGAGCCTC	0.517													G|||	111	0.0221645	0.003	0.0014	5008	,	,		19076	0.0585		0.0099	False		,,,				2504	0.0378				p.R106R		Atlas-SNP	.											MOSC2,NS,carcinoma,+2,1	.	.	1	0			c.A318G						PASS	.	G		15,4391	824.9+/-416.5	0,15,2188	179.0	173.0	175.0		318	0.0	1.0	1	dbSNP_120	175	47,8553	817.2+/-406.9	0,47,4253	no	coding-synonymous	MOSC2	NM_017898.3		0,62,6441	GG,GA,AA		0.5465,0.3404,0.4767		106/336	220928334	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	54996	exon2			TGCCCGACAGGAG		CCDS1525.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000117791	ENSG00000117791			26064	protein-coding gene	gene with protein product		614127	"""MOCO sulphurase C-terminal domain containing 2"""	MOSC2		11886751	Standard	NM_017898		Approved	FLJ20605	uc001hmq.3	Q969Z3	OTTHUMG00000037354	ENST00000366913.3:c.318A>G	1.37:g.220928334A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_017898	B2D0R5|D3DTB3|Q0JSK7|Q5VT67|Q5VXC7|Q7L317|Q9H066|Q9NWU0	Silent	SNP	ENST00000366913.3	37	CCDS1525.1																																																																																			A|0.989;G|0.011	0.011	strong		0.517	MARC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090911.1	NM_017898	
C9orf156	51531	hgsc.bcm.edu	37	9	100684757	100684757	+	Missense_Mutation	SNP	A	A	G	rs3183927	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:100684757A>G	ENST00000375119.3	-	1	95	c.19T>C	c.(19-21)Tcg>Ccg	p.S7P	C9orf156_ENST00000478126.1_5'Flank	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	7			S -> P (in dbSNP:rs3183927). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				CGAGGCCCCGACTCCTCCAAG	0.642											OREG0019350	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	1327	0.264976	0.1952	0.3401	5008	,	,		16189	0.2113		0.4115	False		,,,				2504	0.2106				p.S7P		Atlas-SNP	.											C9orf156,NS,carcinoma,0,1	C9orf156	35	1	0			c.T19C						PASS	.	T	PRO/SER	952,3440		112,728,1356	27.0	25.0	25.0		19	-5.1	0.0	9	dbSNP_105	25	2990,5584		552,1886,1849	yes	missense	C9orf156	NM_016481.3	74	664,2614,3205	GG,GA,AA		34.8729,21.6758,30.4026	benign	7/442	100684757	3942,9024	2196	4287	6483	SO:0001583	missense	51531	exon1			GCCCCGACTCCTC	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"""Nef (lentivirus myristoylated factor) associated protein 1"""						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.19T>C	9.37:g.100684757A>G	ENSP00000364260:p.Ser7Pro	Somatic	40	0	0	1353	WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	37	CCDS6730.1	645	0.29532967032967034	93	0.18902439024390244	125	0.3453038674033149	123	0.21503496503496503	304	0.40105540897097625	g	8.662	0.900725	0.17686	0.216758	0.348729	ENSG00000136932	ENST00000375119;ENST00000375117;ENST00000455506	T;T;T	0.48522	1.93;0.88;0.81	4.3	-5.1	0.02911	.	1.101020	0.07041	N	0.830090	T	0.00012	0.0000	N	0.04508	-0.205	0.38558	P	0.05037899999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.38045	-0.9679	9	0.12103	T	0.63	5.6295	2.8986	0.05698	0.4873:0.2426:0.1632:0.1069	rs3183927;rs3802476;rs17347008;rs17844969;rs17857712;rs61307628;rs3183927	7	Q9BU70	NAP1_HUMAN	P	7;6;5	ENSP00000364260:S7P;ENSP00000364258:S6P;ENSP00000408473:S5P	ENSP00000364258:S6P	S	-	1	0	C9orf156	99724578	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.407000	0.02488	-1.408000	0.02040	-2.020000	0.00432	TCG	A|0.729;G|0.271	0.271	strong		0.642	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
OR4D6	219983	hgsc.bcm.edu	37	11	59225221	59225221	+	Missense_Mutation	SNP	T	T	C	rs1453541	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:59225221T>C	ENST00000300127.2	+	1	811	c.788T>C	c.(787-789)aTg>aCg	p.M263T		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	263			M -> T (in dbSNP:rs1453541).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						CGGCCCTTCATGACGCTGCCC	0.527													C|||	1329	0.265375	0.3245	0.2695	5008	,	,		20460	0.1845		0.2972	False		,,,				2504	0.2331				p.M263T		Atlas-SNP	.											OR4D6,NS,carcinoma,-1,2	OR4D6	65	2	0			c.T788C						PASS	.	T	THR/MET	1469,2933	679.3+/-403.7	238,993,970	114.0	109.0	111.0		788	-2.7	0.0	11	dbSNP_88	111	2714,5876	681.6+/-403.7	417,1880,1998	yes	missense	OR4D6	NM_001004708.1	81	655,2873,2968	CC,CT,TT		31.5949,33.3712,32.1967	benign	263/315	59225221	4183,8809	2201	4295	6496	SO:0001583	missense	219983	exon1			CCTTCATGACGCT	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.788T>C	11.37:g.59225221T>C	ENSP00000300127:p.Met263Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	623	0.28525641025641024	159	0.3231707317073171	109	0.3011049723756906	119	0.20804195804195805	236	0.3113456464379947	C	0.001	-3.142940	0.00029	0.333712	0.315949	ENSG00000166884	ENST00000300127	T	0.00054	8.8	6.01	-2.74	0.05932	GPCR, rhodopsin-like superfamily (1);	0.805216	0.11028	N	0.607551	T	0.00012	0.0000	N	0.00055	-2.37	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37126	-0.9719	9	0.02654	T	1	-1.5571	4.6597	0.12636	0.0933:0.5045:0.0917:0.3105	rs1453541;rs17500443;rs59250564;rs1453541	263	Q8NGJ1	OR4D6_HUMAN	T	263	ENSP00000300127:M263T	ENSP00000300127:M263T	M	+	2	0	OR4D6	58981797	0.000000	0.05858	0.001000	0.08648	0.089000	0.18198	-0.221000	0.09202	-0.898000	0.03906	-1.990000	0.00449	ATG	T|0.689;C|0.311	0.311	strong		0.527	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
FCRLB	127943	hgsc.bcm.edu	37	1	161693199	161693199	+	Missense_Mutation	SNP	C	C	T	rs35002732	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161693199C>T	ENST00000367948.2	+	5	310	c.95C>T	c.(94-96)aCc>aTc	p.T32I	FCRLB_ENST00000367946.3_Missense_Mutation_p.T32I|FCRLB_ENST00000367945.1_Missense_Mutation_p.T25I|FCRLB_ENST00000336830.5_Missense_Mutation_p.T32I|FCRLB_ENST00000392158.1_Missense_Mutation_p.T32I|FCRLB_ENST00000367944.3_Missense_Mutation_p.T25I			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	32	Ig-like C2-type 1.				negative regulation of immune response (GO:0050777)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|skin(1)	17	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CCACCTTGGACCACCATCTTC	0.557													C|||	52	0.0103834	0.0	0.0259	5008	,	,		15806	0.0		0.0278	False		,,,				2504	0.0061				p.T32I		Atlas-SNP	.											.	FCRLB	35	.	0			c.C95T						PASS	.	C	ILE/THR	46,4360	48.9+/-83.8	0,46,2157	126.0	126.0	126.0		95	5.8	1.0	1	dbSNP_126	126	318,8282	112.1+/-172.3	6,306,3988	yes	missense	FCRLB	NM_001002901.2	89	6,352,6145	TT,TC,CC		3.6977,1.044,2.7987	probably-damaging	32/427	161693199	364,12642	2203	4300	6503	SO:0001583	missense	127943	exon3			CTTGGACCACCAT	AY670683	CCDS30927.1, CCDS72962.1, CCDS72963.1, CCDS72964.1, CCDS72965.1	1q23.3	2013-01-11	2006-09-26	2006-09-26	ENSG00000162746	ENSG00000162746		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26431	protein-coding gene	gene with protein product		609251	"""Fc receptor-like and mucin-like 2"""	FCRLM2		15676285	Standard	NM_001288829		Approved	FLJ31052, FCRL2, FREB-2, FCRLY	uc001gbi.3	Q6BAA4	OTTHUMG00000133629	ENST00000367948.2:c.95C>T	1.37:g.161693199C>T	ENSP00000356925:p.Thr32Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Missense_Mutation	SNP	ENST00000367948.2	37	CCDS30927.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	C	17.72	3.460228	0.63401	0.01044	0.036977	ENSG00000162746	ENST00000367948;ENST00000367946;ENST00000367945;ENST00000336830;ENST00000367944;ENST00000392158	T;T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;2.51;2.51	5.76	5.76	0.90799	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000042	T	0.16085	0.0387	L	0.38692	1.165	0.39018	D	0.959681	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.982;0.999;0.998;0.999;0.998	T	0.08086	-1.0739	10	0.15499	T	0.54	.	15.4858	0.75564	0.0:1.0:0.0:0.0	rs35002732;rs61801181	25;25;32;32;32	Q6BAA4-3;Q6BAA4-5;Q6BAA4-2;Q6BAA4-4;Q6BAA4	.;.;.;.;FCRLB_HUMAN	I	32;32;25;32;25;32	ENSP00000356925:T32I;ENSP00000356923:T32I;ENSP00000356922:T25I;ENSP00000338598:T32I;ENSP00000356921:T25I;ENSP00000375999:T32I	ENSP00000338598:T32I	T	+	2	0	FCRLB	159959823	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	2.307000	0.43682	2.706000	0.92434	0.655000	0.94253	ACC	C|0.976;T|0.024	0.024	strong		0.557	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378	
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 GAIIx	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_ENST00000372917.4_Missense_Mutation_p.G119D|TRERF1_ENST00000340840.2_Missense_Mutation_p.G119D|TRERF1_ENST00000354325.2_Missense_Mutation_p.G119D|TRERF1_ENST00000541110.1_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	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	90	19	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	
SCO2	9997	hgsc.bcm.edu	37	22	50962259	50962259	+	Silent	SNP	G	G	A	rs131811	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50962259G>A	ENST00000543927.1	-	2	788	c.582C>T	c.(580-582)tcC>tcT	p.S194S	SCO2_ENST00000252785.3_Silent_p.S194S|SCO2_ENST00000535425.1_Silent_p.S194S|CTA-384D8.36_ENST00000608319.1_RNA|SCO2_ENST00000395693.3_Silent_p.S194S	NM_001169109.1	NP_001162580.1	O43819	SCO2_HUMAN	SCO2 cytochrome c oxidase assembly protein	194	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|eye development (GO:0001654)|in utero embryonic development (GO:0001701)|muscle system process (GO:0003012)|oxidation-reduction process (GO:0055114)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			endometrium(1)|lung(1)	2		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCTGTTTGGTGGAGCCGGTCA	0.587													G|||	129	0.0257588	0.003	0.0533	5008	,	,		19707	0.001		0.0815	False		,,,				2504	0.0051				p.S194S		Atlas-SNP	.											.	SCO2	38	.	0			c.C582T						PASS	.	G	,,,,,	72,4334	65.3+/-102.7	0,72,2131	119.0	104.0	109.0		582,582,582,,582,	-7.8	0.0	22	dbSNP_78	109	604,7996	159.4+/-212.7	22,560,3718	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous,utr-3	SCO2,NCAPH2	NM_001169109.1,NM_001169110.1,NM_001169111.1,NM_001185011.1,NM_005138.2,NM_152299.3	,,,,,	22,632,5849	AA,AG,GG		7.0233,1.6341,5.1976	,,,,,	194/267,194/267,194/267,,194/267,	50962259	676,12330	2203	4300	6503	SO:0001819	synonymous_variant	9997	exon2			TTTGGTGGAGCCG	AL021683	CCDS14095.1	22q13.33	2014-01-30	2012-10-15		ENSG00000130489	ENSG00000130489		"""Mitochondrial respiratory chain complex assembly factors"""	10604	protein-coding gene	gene with protein product		604272	"""SCO (cytochrome oxidase deficient, yeast) homolog 2"", ""SCO cytochrome oxidase deficient homolog 2 (yeast)"", ""myopia 6"""	MYP6		10218584, 16091356, 23643385	Standard	NM_005138		Approved	SCO1L	uc003bma.3	O43819	OTTHUMG00000150251	ENST00000543927.1:c.582C>T	22.37:g.50962259G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_001169111	Q3T1B5|Q9UK87	Silent	SNP	ENST00000543927.1	37	CCDS14095.1																																																																																			G|0.958;A|0.042	0.042	strong		0.587	SCO2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317091.1	NM_005138	
SLC39A4	55630	hgsc.bcm.edu	37	8	145642111	145642111	+	Silent	SNP	C	C	G	rs13251676	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145642111C>G	ENST00000301305.3	-	1	168	c.63G>C	c.(61-63)acG>acC	p.T21T	SLC39A4_ENST00000276833.5_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	21					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GCGGGGACGCCGTCGCCGTCA	0.667													C|||	110	0.0219649	0.0015	0.0245	5008	,	,		14299	0.0		0.0785	False		,,,				2504	0.0123				p.T21T		Atlas-SNP	.											.	SLC39A4	54	.	0			c.G63C						PASS	.	C		61,4325	54.2+/-90.2	0,61,2132	45.0	43.0	44.0		63	-4.1	0.0	8	dbSNP_121	44	575,8019	147.7+/-203.1	23,529,3745	no	coding-synonymous	SLC39A4	NM_130849.2		23,590,5877	GG,GC,CC		6.6907,1.3908,4.8998		21/648	145642111	636,12344	2193	4297	6490	SO:0001819	synonymous_variant	55630	exon1			GGACGCCGTCGCC	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.63G>C	8.37:g.145642111C>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	172	99	0.575581	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Silent	SNP	ENST00000301305.3	37	CCDS6424.1																																																																																			C|0.962;G|0.038	0.038	strong		0.667	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
DNAJC7	7266	hgsc.bcm.edu	37	17	40142302	40142302	+	Silent	SNP	T	T	C	rs1127182	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40142302T>C	ENST00000457167.4	-	6	815	c.579A>G	c.(577-579)ccA>ccG	p.P193P	DNAJC7_ENST00000316603.7_Silent_p.P137P|DNAJC7_ENST00000426588.3_Silent_p.P137P	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	193					chaperone cofactor-dependent protein refolding (GO:0070389)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	heat shock protein binding (GO:0031072)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)	9		all_cancers(22;0.00273)|Breast(137;0.00104)|all_epithelial(22;0.0305)				ACTGTGCTTCTGGATAACGAC	0.498													T|||	660	0.131789	0.2224	0.0447	5008	,	,		19879	0.124		0.0726	False		,,,				2504	0.1401				p.P193P	Colon(63;618 1117 8600 10857 19751)	Atlas-SNP	.											.	DNAJC7	51	.	0			c.A579G						PASS	.	T	,	722,3230		60,602,1314	60.0	57.0	58.0		411,579	-2.8	1.0	17	dbSNP_86	58	540,7764		12,516,3624	no	coding-synonymous,coding-synonymous	DNAJC7	NM_001144766.2,NM_003315.3	,	72,1118,4938	CC,CT,TT		6.5029,18.2692,10.297	,	137/439,193/495	40142302	1262,10994	1976	4152	6128	SO:0001819	synonymous_variant	7266	exon6			TGCTTCTGGATAA	U46571	CCDS45677.1, CCDS45678.1	17q11.2	2013-01-10				ENSG00000168259		"""Heat shock proteins / DNAJ (HSP40)"", ""Tetratricopeptide (TTC) repeat domain containing"""	12392	protein-coding gene	gene with protein product		601964		TTC2		8836031, 11147971	Standard	NR_029431		Approved	TPR2	uc002hyo.3	Q99615		ENST00000457167.4:c.579A>G	17.37:g.40142302T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	98	54	0.55102	NM_003315	Q7Z784	Silent	SNP	ENST00000457167.4	37	CCDS45677.1																																																																																			T|0.894;C|0.106	0.106	strong		0.498	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453366.2		
LILRB4	11006	hgsc.bcm.edu	37	19	55179145	55179145	+	Missense_Mutation	SNP	A	A	T	rs61738946	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55179145A>T	ENST00000391736.1	+	13	1416	c.1101A>T	c.(1099-1101)agA>agT	p.R367S	LILRB4_ENST00000391733.3_Missense_Mutation_p.R368S|LILRB4_ENST00000270452.2_Missense_Mutation_p.R367S|LILRB4_ENST00000430952.2_Missense_Mutation_p.R366S|LILRB4_ENST00000391734.3_Intron	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	367					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		AACACTCCAGACCTAGGAGAG	0.567																																					p.R367S		Atlas-SNP	.											LILRB4,NS,carcinoma,+2,1	LILRB4	86	1	0			c.A1101T						scavenged	.						116.0	118.0	117.0					19																	55179145		2203	4300	6503	SO:0001583	missense	11006	exon11			CTCCAGACCTAGG	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1101A>T	19.37:g.55179145A>T	ENSP00000375616:p.Arg367Ser	Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	252	13	0.0515873	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	23	0.010531135531135532	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	6.892	0.534167	0.13188	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391733;ENST00000434286	T;T;T;T;T	0.00505	6.93;6.93;7.0;6.94;6.93	1.73	1.73	0.24493	.	.	.	.	.	T	0.00144	0.0004	L	0.41710	1.295	0.09310	N	1	B;B;B;B	0.23490	0.002;0.086;0.086;0.043	B;B;B;B	0.12837	0.0;0.008;0.008;0.007	T	0.40627	-0.9553	9	0.27785	T	0.31	.	5.5252	0.16955	1.0:0.0:0.0:0.0	rs61738946	366;368;366;367	C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	S	367;367;366;368;366	ENSP00000375616:R367S;ENSP00000270452:R367S;ENSP00000408995:R366S;ENSP00000375613:R368S;ENSP00000401962:R366S	ENSP00000270452:R367S	R	+	3	2	LILRB4	59870957	0.002000	0.14202	0.018000	0.16275	0.021000	0.10359	0.274000	0.18680	1.054000	0.40438	0.459000	0.35465	AGA	A|0.990;T|0.010	0.010	strong		0.567	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
ACP1	52	hgsc.bcm.edu	37	2	272203	272203	+	Intron	SNP	C	C	T	rs11553746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:272203C>T	ENST00000272065.5	+	3	324				ACP1_ENST00000272067.6_Silent_p.D43D|ACP1_ENST00000439645.2_Silent_p.D43D|ACP1_ENST00000405233.1_Missense_Mutation_p.T53I|ACP1_ENST00000484464.1_Intron|ACP1_ENST00000407983.3_Missense_Mutation_p.T95I	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble							cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	GGGTCATTGACAGCGGTGCTG	0.542													C|||	1219	0.243411	0.1286	0.232	5008	,	,		16562	0.249		0.334	False		,,,				2504	0.3078				p.T95I		Atlas-SNP	.											ACP1_ENST00000272067,NS,carcinoma,+1,1	ACP1	42	1	0			c.C284T						PASS	.	C	ILE/THR,,	749,3657	306.3+/-289.4	63,623,1517	185.0	149.0	161.0		284,,129	5.9	1.0	2	dbSNP_120	161	2963,5637	459.5+/-364.9	486,1991,1823	yes	missense,intron,coding-synonymous	ACP1	NM_001040649.2,NM_004300.3,NM_007099.3	89,,	549,2614,3340	TT,TC,CC		34.4535,16.9995,28.5407	,,	95/113,,43/159	272203	3712,9294	2203	4300	6503	SO:0001627	intron_variant	52	exon3			CATTGACAGCGGT	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"""Protein tyrosine phosphatases / Class II Cys-based PTPs"""	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.231+53C>T	2.37:g.272203C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	180	93	0.516667	NM_001040649	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Missense_Mutation	SNP	ENST00000272065.5	37	CCDS1639.1	520	0.23809523809523808	56	0.11382113821138211	86	0.23756906077348067	126	0.2202797202797203	252	0.3324538258575198	C	17.56	3.419926	0.62622	0.169995	0.344535	ENSG00000143727	ENST00000407983;ENST00000405233;ENST00000449425	T;T	0.47528	0.91;0.84	5.87	5.87	0.94306	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.28039	P	0.9338388	D	0.76494	0.999	D	0.83275	0.996	T	0.01697	-1.1293	7	0.44086	T	0.13	-21.5954	17.6971	0.88285	0.0:1.0:0.0:0.0	rs11553746	95	B5MCC7	.	I	95;53;53	ENSP00000385404:T95I;ENSP00000384307:T53I	ENSP00000384307:T53I	T	+	2	0	ACP1	262203	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.667000	0.68067	2.779000	0.95612	0.655000	0.94253	ACA	C|0.738;T|0.262	0.262	strong		0.542	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3		
CCDC81	60494	hgsc.bcm.edu	37	11	86123464	86123464	+	Silent	SNP	T	T	C	rs11234644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:86123464T>C	ENST00000445632.2	+	11	1526	c.1254T>C	c.(1252-1254)ccT>ccC	p.P418P	CCDC81_ENST00000278487.3_Silent_p.P153P|CCDC81_ENST00000354755.1_Silent_p.P328P|CCDC81_ENST00000528728.1_Silent_p.P153P	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	418										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				CACTCAGTCCTGCGCTTAATG	0.373													T|||	91	0.0181709	0.003	0.0231	5008	,	,		20403	0.0		0.0646	False		,,,				2504	0.0061				p.P418P		Atlas-SNP	.											CCDC81,colon,carcinoma,+1,1	CCDC81	89	1	0			c.T1254C						PASS	.	T	,	50,4354	51.6+/-87.1	0,50,2152	116.0	115.0	115.0		1254,984	1.7	1.0	11	dbSNP_120	115	552,8046	151.3+/-206.1	22,508,3769	no	coding-synonymous,coding-synonymous	CCDC81	NM_001156474.1,NM_021827.4	,	22,558,5921	CC,CT,TT		6.4201,1.1353,4.6301	,	418/653,328/563	86123464	602,12400	2202	4299	6501	SO:0001819	synonymous_variant	60494	exon11			CAGTCCTGCGCTT	AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.1254T>C	11.37:g.86123464T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	117	95	0.811966	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Silent	SNP	ENST00000445632.2	37	CCDS53691.1																																																																																			T|0.954;C|0.046	0.046	strong		0.373	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827	
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 GAIIx	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	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	15	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		
DPY19L2	283417	hgsc.bcm.edu	37	12	63954304	63954304	+	Silent	SNP	T	T	C	rs1054891	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:63954304T>C	ENST00000324472.4	-	22	2448	c.2265A>G	c.(2263-2265)ttA>ttG	p.L755L	DPY19L2_ENST00000413230.2_Silent_p.L202L	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	755					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		AGTTAACCTTTAATACTCTGT	0.418													N|||	2174	0.434105	0.7057	0.4568	5008	,	,		16369	0.2857		0.4245	False		,,,				2504	0.2137				p.L755L		Atlas-SNP	.											DPY19L2,colon,carcinoma,0,1	DPY19L2	97	1	0			c.A2265G						PASS	.	C		2776,1630	500.0+/-364.6	884,1008,311	85.0	80.0	82.0		2265	-1.3	0.3	12	dbSNP_86	82	3491,5109	633.6+/-398.7	694,2103,1503	no	coding-synonymous	DPY19L2	NM_173812.4		1578,3111,1814	CC,CT,TT		40.593,36.995,48.1855		755/759	63954304	6267,6739	2203	4300	6503	SO:0001819	synonymous_variant	283417	exon22			AACCTTTAATACT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.2265A>G	12.37:g.63954304T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Silent	SNP	ENST00000324472.4	37	CCDS31851.1																																																																																			T|0.532;C|0.468	0.468	strong		0.418	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
PRR18	285800	hgsc.bcm.edu	37	6	166721224	166721224	+	Missense_Mutation	SNP	C	C	G	rs7757150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:166721224C>G	ENST00000322583.3	-	1	647	c.407G>C	c.(406-408)tGc>tCc	p.C136S		NM_175922.3	NP_787118.2	Q8N4B5	PRR18_HUMAN	proline rich 18	136			C -> S (in dbSNP:rs7757150). {ECO:0000269|PubMed:15489334}.							haematopoietic_and_lymphoid_tissue(2)|lung(1)	3		Breast(66;2.35e-05)|Ovarian(120;0.0606)|Prostate(117;0.0959)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-19)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;7.96e-05)		GAGATTCAGGCAGAAGCGCGC	0.726													G|||	4014	0.801518	0.8676	0.621	5008	,	,		6220	0.9206		0.7475	False		,,,				2504	0.773				p.C136S		Atlas-SNP	.											.	PRR18	4	.	0			c.G407C						PASS	.	G	SER/CYS	3548,596		1530,488,54	7.0	9.0	9.0		407	2.5	0.9	6	dbSNP_116	9	6181,2029		2352,1477,276	yes	missense	PRR18	NM_175922.3	112	3882,1965,330	GG,GC,CC		24.7138,14.3822,21.2482	benign	136/296	166721224	9729,2625	2072	4105	6177	SO:0001583	missense	285800	exon1			TTCAGGCAGAAGC	BC034775	CCDS5291.1	6q27	2009-01-27	2009-01-27						28574	protein-coding gene	gene with protein product			"""proline rich region 18"""			12477932	Standard	NM_175922		Approved	MGC35308	uc003quw.1	Q8N4B5		ENST00000322583.3:c.407G>C	6.37:g.166721224C>G	ENSP00000319590:p.Cys136Ser	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_175922		Missense_Mutation	SNP	ENST00000322583.3	37	CCDS5291.1	1743	0.7980769230769231	432	0.8780487804878049	224	0.6187845303867403	526	0.9195804195804196	561	0.7401055408970977	G	0.326	-0.958761	0.02267	0.856178	0.752862	ENSG00000176381	ENST00000322583	T	0.32515	1.45	2.49	2.49	0.30216	.	0.566584	0.12731	N	0.443833	T	0.02267	0.0070	N	0.01352	-0.895	0.48696	P	3.009999999999957E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.46541	-0.9184	9	0.02654	T	1	.	8.7463	0.34589	0.0:0.2366:0.7634:0.0	rs7757150;rs17857022	136	Q8N4B5	PRR18_HUMAN	S	136	ENSP00000319590:C136S	ENSP00000319590:C136S	C	-	2	0	PRR18	166641214	0.001000	0.12720	0.891000	0.34965	0.217000	0.24651	-0.220000	0.09215	0.247000	0.21414	-0.335000	0.08231	TGC	C|0.208;G|0.792	0.792	strong		0.726	PRR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392563.3	NM_175922	
TNFRSF19	55504	hgsc.bcm.edu	37	13	24242166	24242166	+	Missense_Mutation	SNP	C	C	T	rs35041805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:24242166C>T	ENST00000382258.4	+	8	988	c.784C>T	c.(784-786)Ccc>Tcc	p.P262S	TNFRSF19_ENST00000382263.3_Missense_Mutation_p.P262S|TNFRSF19_ENST00000403372.2_Missense_Mutation_p.P130S|TNFRSF19_ENST00000248484.4_Missense_Mutation_p.P262S	NM_018647.3	NP_061117.2	Q9NS68	TNR19_HUMAN	tumor necrosis factor receptor superfamily, member 19	262					apoptotic process (GO:0006915)|hair follicle development (GO:0001942)|JNK cascade (GO:0007254)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)	tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	22		all_cancers(29;3.4e-22)|all_epithelial(30;8.75e-19)|all_lung(29;5.09e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00193)|Epithelial(112;0.0137)|OV - Ovarian serous cystadenocarcinoma(117;0.0465)|GBM - Glioblastoma multiforme(144;0.184)|Lung(94;0.19)		GGCCTGCAGCCCCAACCCGGC	0.562													C|||	88	0.0175719	0.0393	0.0216	5008	,	,		15996	0.0		0.0179	False		,,,				2504	0.0031				p.P262S		Atlas-SNP	.											.	TNFRSF19	52	.	0			c.C784T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	155,4251	103.0+/-141.5	5,145,2053	54.0	48.0	50.0		784,388,784,784	-11.2	0.0	13	dbSNP_126	50	132,8468	63.5+/-125.6	2,128,4170	yes	missense,missense,missense,missense	TNFRSF19	NM_001204458.1,NM_001204459.1,NM_018647.3,NM_148957.3	74,74,74,74	7,273,6223	TT,TC,CC		1.5349,3.5179,2.2067	benign,benign,benign,benign	262/418,130/286,262/424,262/418	24242166	287,12719	2203	4300	6503	SO:0001583	missense	55504	exon8			TGCAGCCCCAACC	AB040434	CCDS9301.1, CCDS9302.1, CCDS55893.1	13q12.11-q12.3	2008-07-18			ENSG00000127863	ENSG00000127863		"""Tumor necrosis factor receptor superfamily"""	11915	protein-coding gene	gene with protein product	"""toxicity and JNK inducer"""	606122				10764796, 10809768	Standard	NM_018647		Approved	TAJ-alpha, TROY, TAJ, TRADE	uc001uov.2	Q9NS68	OTTHUMG00000016568	ENST00000382258.4:c.784C>T	13.37:g.24242166C>T	ENSP00000371693:p.Pro262Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_018647	A8KA09|A8KA26|B1AM40|B1AM41|B4E2I6|Q9BXZ9|Q9BY00|Q9NZV2	Missense_Mutation	SNP	ENST00000382258.4	37	CCDS9302.1	40	0.018315018315018316	27	0.054878048780487805	5	0.013812154696132596	0	0.0	8	0.010554089709762533	C	1.414	-0.574621	0.03882	0.035179	0.015349	ENSG00000127863	ENST00000248484;ENST00000403372;ENST00000382258;ENST00000382263	T;T;T;T	0.75477	-0.94;1.64;-0.94;-0.94	5.6	-11.2	0.00127	.	1.541490	0.03240	N	0.180303	T	0.07593	0.0191	N	0.02011	-0.69	0.09310	N	0.999999	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.10870	-1.0611	10	0.07482	T	0.82	1.7599	4.075	0.09899	0.1155:0.3711:0.3077:0.2057	rs35041805	130;262;262	B4E2I6;Q9NS68;Q9NS68-2	.;TNR19_HUMAN;.	S	262;130;262;262	ENSP00000248484:P262S;ENSP00000385408:P130S;ENSP00000371693:P262S;ENSP00000371698:P262S	ENSP00000248484:P262S	P	+	1	0	TNFRSF19	23140166	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-2.593000	0.00897	-4.787000	0.00032	-0.868000	0.02995	CCC	C|0.981;T|0.019	0.019	strong		0.562	TNFRSF19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044156.2	NM_018647	
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 GAIIx	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_ENST00000564448.1_Silent_p.A35A|CNGB1_ENST00000311183.4_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		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	46	20	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	
HN1	51155	hgsc.bcm.edu	37	17	73144665	73144665	+	Missense_Mutation	SNP	C	C	A	rs117208625	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73144665C>A	ENST00000409753.3	-	2	443	c.158G>T	c.(157-159)gGg>gTg	p.G53V	Y_RNA_ENST00000516233.1_RNA|HN1_ENST00000405458.3_Missense_Mutation_p.G7V|HN1_ENST00000465454.1_5'UTR|HN1_ENST00000392566.2_Missense_Mutation_p.G7V|HN1_ENST00000581874.1_Missense_Mutation_p.G53V|RP11-649A18.4_ENST00000579554.1_RNA|HN1_ENST00000470924.1_Missense_Mutation_p.G7V|HN1_ENST00000482348.1_Missense_Mutation_p.G7V|HN1_ENST00000476258.1_Missense_Mutation_p.G7V|HN1_ENST00000481647.1_Missense_Mutation_p.G7V|HN1_ENST00000356033.4_Missense_Mutation_p.G53V	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	53					developmental process (GO:0032502)	nucleus (GO:0005634)			HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					TTCAGGTGTCCCAAAGATATT	0.463													C|||	6	0.00119808	0.0	0.0	5008	,	,		19039	0.0		0.006	False		,,,				2504	0.0				p.G53V		Atlas-SNP	.											.	HN1	17	.	0			c.G158T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY	1,4405	2.1+/-5.4	0,1,2202	121.0	104.0	110.0		158,20,158	4.8	1.0	17	dbSNP_132	110	35,8565	24.0+/-70.4	0,35,4265	yes	missense,missense,missense	HN1	NM_001002032.1,NM_001002033.1,NM_016185.2	109,109,109	0,36,6467	AA,AC,CC		0.407,0.0227,0.2768	probably-damaging,probably-damaging,probably-damaging	53/182,7/109,53/155	73144665	36,12970	2203	4300	6503	SO:0001583	missense	51155	exon2			GGTGTCCCAAAGA	AF086910	CCDS32729.1, CCDS45771.1, CCDS45772.1	17q25.1	2013-09-20			ENSG00000189159	ENSG00000189159			14569	protein-coding gene	gene with protein product	"""androgen-regulated protein 2"""					15094197	Standard	NM_001002032		Approved	ARM2, HN1A	uc002jnb.1	Q9UK76	OTTHUMG00000154521	ENST00000409753.3:c.158G>T	17.37:g.73144665C>A	ENSP00000387059:p.Gly53Val	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	233	113	0.484979	NM_016185	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	37	CCDS45771.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	18.98	3.737406	0.69304	2.27E-4	0.00407	ENSG00000189159	ENST00000405458;ENST00000409753;ENST00000356033;ENST00000409135;ENST00000392566	.	.	.	4.76	4.76	0.60689	.	0.057328	0.64402	D	0.000001	T	0.79375	0.4435	M	0.76170	2.325	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.996	D;D;D	0.97110	0.962;1.0;0.944	T	0.82261	-0.0545	9	0.87932	D	0	-23.3811	17.5543	0.87886	0.0:1.0:0.0:0.0	.	53;53;53	B8ZZT7;Q9UK76-2;Q9UK76	.;.;HN1_HUMAN	V	7;53;53;53;7	.	ENSP00000348316:G53V	G	-	2	0	HN1	70656260	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	4.826000	0.62715	2.475000	0.83589	0.563000	0.77884	GGG	C|0.998;A|0.002	0.002	strong		0.463	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032	
MUC2	4583	hgsc.bcm.edu	37	11	1081757	1081757	+	Missense_Mutation	SNP	G	G	C	rs57737240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1081757G>C	ENST00000441003.2	+	13	1712	c.1685G>C	c.(1684-1686)aGc>aCc	p.S562T	MUC2_ENST00000359061.5_Missense_Mutation_p.S562T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	562	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	GCACAGTCAAGCTGCCATGAC	0.647													G|||	1838	0.367013	0.4266	0.366	5008	,	,		18028	0.3889		0.2197	False		,,,				2504	0.4162				p.S562T		Atlas-SNP	.											.	MUC2	614	.	0			c.G1685C						PASS	.	G	THR/SER	1613,2501		331,951,775	36.0	41.0	39.0		1685	-0.0	0.0	11	dbSNP_129	39	1711,6651		188,1335,2658	yes	missense	MUC2	NM_002457.2	58	519,2286,3433	CC,CG,GG		20.4616,39.2076,26.6432	benign	562/2813	1081757	3324,9152	2057	4181	6238	SO:0001583	missense	4583	exon13			AGTCAAGCTGCCA	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.1685G>C	11.37:g.1081757G>C	ENSP00000415183:p.Ser562Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	121	118	0.975207	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		690	0.3159340659340659	188	0.3821138211382114	110	0.30386740331491713	230	0.4020979020979021	162	0.21372031662269128	G	0.576	-0.839120	0.02692	0.392076	0.204616	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12984	2.67;2.63	3.06	-0.0447	0.13854	.	0.845665	0.10123	U	0.713130	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.25169	0.119	B	0.30716	0.119	T	0.45145	-0.9281	8	0.02654	T	1	.	6.6078	0.22735	0.1934:0.4181:0.3885:0.0	rs57737240;rs61732123	562	E7EUV1	.	T	562	ENSP00000415183:S562T;ENSP00000351956:S562T	ENSP00000351956:S562T	S	+	2	0	MUC2	1071757	0.003000	0.15002	0.031000	0.17742	0.321000	0.28281	0.085000	0.14912	-0.239000	0.09710	-0.258000	0.10820	AGC	G|0.707;C|0.293	0.293	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
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 GAIIx	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	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	160	77	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	
PDCD11	22984	hgsc.bcm.edu	37	10	105194086	105194086	+	Missense_Mutation	SNP	C	C	T	rs2986014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:105194086C>T	ENST00000369797.3	+	24	3740	c.3646C>T	c.(3646-3648)Ctc>Ttc	p.L1216F		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1216	S1 motif 10. {ECO:0000255|PROSITE- ProRule:PRU00180}.		L -> F (in dbSNP:rs2986014). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8724849}.		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)		CTCCAAGACCCTCTTATGTCT	0.552													T|||	2396	0.478435	0.4803	0.402	5008	,	,		16763	0.4236		0.4235	False		,,,				2504	0.6431				p.L1216F		Atlas-SNP	.											.	PDCD11	160	.	0			c.C3646T						PASS	.	T	PHE/LEU	1975,2431	618.4+/-393.2	414,1147,642	94.0	96.0	96.0		3646	5.2	1.0	10	dbSNP_101	96	3395,5205	639.6+/-399.5	654,2087,1559	yes	missense	PDCD11	NM_014976.1	22	1068,3234,2201	TT,TC,CC		39.4767,44.8252,41.2886	benign	1216/1872	105194086	5370,7636	2203	4300	6503	SO:0001583	missense	22984	exon24			AAGACCCTCTTAT	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.3646C>T	10.37:g.105194086C>T	ENSP00000358812:p.Leu1216Phe	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	926	0.423992673992674	230	0.46747967479674796	138	0.3812154696132597	243	0.42482517482517484	315	0.4155672823218997	T	0.710	-0.787661	0.02884	0.448252	0.394767	ENSG00000148843	ENST00000369797	T	0.17691	2.26	5.23	5.23	0.72850	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);RNA-binding domain, S1 (1);Ribosomal protein S1, RNA-binding domain (1);	0.333692	0.35555	N	0.003121	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45454	-0.9260	9	0.09843	T	0.71	-12.7858	5.2262	0.15396	0.1666:0.0853:0.0:0.7481	rs2986014;rs3765527;rs11558730;rs52819868;rs57673953;rs2986014	1216	Q14690	RRP5_HUMAN	F	1216	ENSP00000358812:L1216F	ENSP00000358812:L1216F	L	+	1	0	PDCD11	105184076	0.302000	0.24454	1.000000	0.80357	0.439000	0.31926	0.859000	0.27858	0.947000	0.37659	-0.361000	0.07541	CTC	C|0.578;T|0.422	0.422	strong		0.552	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
SLC16A6	9120	hgsc.bcm.edu	37	17	66267691	66267691	+	Missense_Mutation	SNP	A	A	T	rs7222013	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:66267691A>T	ENST00000327268.4	-	6	774	c.610T>A	c.(610-612)Ttt>Att	p.F204I	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Missense_Mutation_p.F204I	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	204			F -> I (in dbSNP:rs7222013). {ECO:0000269|PubMed:9425115}.		monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	CCTCTGATAAAGATGGGTCTG	0.473													T|||	1901	0.379593	0.6853	0.3746	5008	,	,		18980	0.247		0.1928	False		,,,				2504	0.2986				p.F204I		Atlas-SNP	.											.	SLC16A6	56	.	0			c.T610A						PASS	.	T	ILE/PHE,ILE/PHE,	2758,1648	505.9+/-366.3	868,1022,313	116.0	112.0	113.0		610,610,	-0.5	0.0	17	dbSNP_116	113	2012,6588	722.1+/-406.4	239,1534,2527	yes	missense,missense,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	21,21,	1107,2556,2840	TT,TA,AA		23.3953,37.4035,36.6754	benign,benign,	204/524,204/524,	66267691	4770,8236	2203	4300	6503	SO:0001583	missense	9120	exon6			TGATAAAGATGGG	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.610T>A	17.37:g.66267691A>T	ENSP00000319991:p.Phe204Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	127	60	0.472441	NM_001174166	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	37	CCDS11675.1	725	0.33195970695970695	326	0.6626016260162602	133	0.3674033149171271	137	0.2395104895104895	129	0.17018469656992086	T	0.008	-1.881272	0.00532	0.625965	0.233953	ENSG00000108932	ENST00000327268	T	0.03889	3.77	4.33	-0.528	0.11905	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.619301	0.16867	N	0.196264	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08493	-1.0719	9	0.33141	T	0.24	.	6.1866	0.20500	0.1265:0.4151:0.0:0.4584	rs7222013;rs7222013	204	O15403	MOT7_HUMAN	I	204	ENSP00000319991:F204I	ENSP00000319991:F204I	F	-	1	0	SLC16A6	63779286	0.000000	0.05858	0.000000	0.03702	0.133000	0.20885	-2.006000	0.01459	-0.690000	0.05142	-0.514000	0.04452	TTT	A|0.636;T|0.364	0.364	strong		0.473	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
ESF1	51575	hgsc.bcm.edu	37	20	13695607	13695607	+	Missense_Mutation	SNP	T	T	G	rs34414644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:13695607T>G	ENST00000202816.1	-	14	2577	c.2470A>C	c.(2470-2472)Att>Ctt	p.I824L		NM_001276380.1|NM_016649.3	NP_001263309.1|NP_057733.2	Q9H501	ESF1_HUMAN	ESF1, nucleolar pre-rRNA processing protein, homolog (S. cerevisiae)	824	Lys-rich.		I -> L (in dbSNP:rs34414644).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|skin(1)|stomach(1)	31						GCAGGATCAATGGACTTCCTT	0.358													T|||	368	0.0734824	0.0045	0.1455	5008	,	,		15043	0.0694		0.1123	False		,,,				2504	0.0798				p.I824L		Atlas-SNP	.											.	ESF1	77	.	0			c.A2470C						PASS	.	T	LEU/ILE	125,4281	92.5+/-131.2	1,123,2079	165.0	151.0	156.0		2470	4.9	1.0	20	dbSNP_126	156	1074,7526	225.1+/-261.3	75,924,3301	yes	missense	ESF1	NM_016649.3	5	76,1047,5380	GG,GT,TT		12.4884,2.837,9.2188	benign	824/852	13695607	1199,11807	2203	4300	6503	SO:0001583	missense	51575	exon14			GATCAATGGACTT		CCDS13117.1	20p12.1	2007-02-12	2006-11-13	2006-11-13	ENSG00000089048	ENSG00000089048			15898	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 6"""	C20orf6			Standard	NM_016649		Approved	bA526K24.1	uc002wok.2	Q9H501	OTTHUMG00000031906	ENST00000202816.1:c.2470A>C	20.37:g.13695607T>G	ENSP00000202816:p.Ile824Leu	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	162	83	0.512346	NM_001276380	Q86X92|Q9H9Q5|Q9HA35|Q9NX93|Q9P1S6	Missense_Mutation	SNP	ENST00000202816.1	37	CCDS13117.1	169	0.07738095238095238	4	0.008130081300813009	48	0.13259668508287292	30	0.05244755244755245	87	0.11477572559366754	T	10.73	1.432380	0.25813	0.02837	0.124884	ENSG00000089048	ENST00000202816	T	0.52526	0.66	6.05	4.95	0.65309	.	0.307141	0.34067	N	0.004282	T	0.00384	0.0012	L	0.44542	1.39	0.42677	P	0.006461999999999968	B	0.06786	0.001	B	0.06405	0.002	T	0.09618	-1.0666	9	0.27785	T	0.31	0.0172	7.6251	0.28208	0.1258:0.0675:0.0:0.8067	rs34414644	824	Q9H501	ESF1_HUMAN	L	824	ENSP00000202816:I824L	ENSP00000202816:I824L	I	-	1	0	ESF1	13643607	0.823000	0.29233	0.997000	0.53966	0.986000	0.74619	2.142000	0.42177	1.123000	0.41961	0.528000	0.53228	ATT	T|0.915;G|0.085	0.085	strong		0.358	ESF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078049.1	NM_016649	
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 GAIIx	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_ENST00000473875.1_Intron|C1orf101_ENST00000366533.4_Silent_p.S265S|C1orf101_ENST00000366531.3_Silent_p.S114S	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		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	194	86	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	
LINC00283	100874057	hgsc.bcm.edu	37	13	103396716	103396716	+	RNA	SNP	C	C	G	rs6491708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103396716C>G	ENST00000430111.1	+	0	1089									long intergenic non-protein coding RNA 283																		GCAGTTTTCTCAGAAATAGAA	0.373													C|||	3479	0.694688	0.5424	0.7493	5008	,	,		19636	0.5913		0.827	False		,,,				2504	0.8323				p.E2111Q		Atlas-SNP	.											.	.	.	.	0			c.G6331C						PASS	.	C	GLN/GLU	773,611		217,339,136	69.0	55.0	59.0		6331	0.4	0.0	13	dbSNP_116	59	2544,636		1024,496,70	yes	missense	CCDC168	NM_001146197.1	29	1241,835,206	GG,GC,CC		20.0,44.1474,27.3225		2111/7082	103396716	3317,1247	692	1590	2282			643677	exon4			TTTTCTCAGAAAT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103396716C>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.327;G|0.673	0.673	strong		0.373	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
KIAA0556	23247	hgsc.bcm.edu	37	16	27692835	27692835	+	Silent	SNP	G	G	A	rs12923861	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:27692835G>A	ENST00000261588.4	+	8	943	c.924G>A	c.(922-924)caG>caA	p.Q308Q	KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000564893.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	308						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TCCCAGACCAGGAGAGGATGT	0.587													G|||	531	0.10603	0.1528	0.1902	5008	,	,		19008	0.001		0.1541	False		,,,				2504	0.0419				p.Q308Q		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G924A						PASS	.	G		658,3736	279.0+/-274.6	48,562,1587	114.0	121.0	119.0		924	1.8	1.0	16	dbSNP_121	119	1281,7319	252.8+/-278.7	90,1101,3109	no	coding-synonymous	KIAA0556	NM_015202.2		138,1663,4696	AA,AG,GG		14.8953,14.975,14.9223		308/1619	27692835	1939,11055	2197	4300	6497	SO:0001819	synonymous_variant	23247	exon8			AGACCAGGAGAGG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.924G>A	16.37:g.27692835G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																			G|0.863;A|0.137	0.137	strong		0.587	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
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 GAIIx	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	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	126	65	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	
CYP4A22	284541	hgsc.bcm.edu	37	1	47611598	47611598	+	Missense_Mutation	SNP	T	T	C	rs2405599	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47611598T>C	ENST00000371891.3	+	10	1314	c.1283T>C	c.(1282-1284)cTa>cCa	p.L428P	CYP4A22_ENST00000294337.3_Missense_Mutation_p.L428P|CYP4A22_ENST00000371890.3_Missense_Mutation_p.L330P|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000485117.1_3'UTR	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	428			L -> P (in allele CYP4A22*6, allele CYP4A22*9, allele CYP4A22*10, allele CYP4A22*12, allele CYP4A22*13 and allele CYP4A22*15; dbSNP:rs2405599). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGGCCCAACCTAGAGGTATGT	0.512													C|||	1882	0.375799	0.2239	0.2896	5008	,	,		21691	0.6141		0.2237	False		,,,				2504	0.5532				p.L428P	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.T1283C						PASS	.	C	PRO/LEU	1117,3289		132,853,1218	290.0	284.0	286.0		1283	0.6	0.7	1	dbSNP_100	286	1931,6669		221,1489,2590	no	missense	CYP4A22	NM_001010969.2	98	353,2342,3808	CC,CT,TT		22.4535,25.3518,23.4353	benign	428/520	47611598	3048,9958	2203	4300	6503	SO:0001583	missense	284541	exon10			CCAACCTAGAGGT		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.1283T>C	1.37:g.47611598T>C	ENSP00000360958:p.Leu428Pro	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	190	92	0.484211	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	683	0.31272893772893773	97	0.19715447154471544	91	0.2513812154696133	335	0.5856643356643356	160	0.21108179419525067	N	0.023	-1.394920	0.01175	0.253518	0.224535	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.27890	1.64;1.64;1.64	1.59	0.642	0.17765	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00001	-3.695	0.30109	P	0.806743	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.0	T	0.44221	-0.9342	9	0.02654	T	1	.	5.7987	0.18401	0.0:0.6711:0.0:0.3289	rs2405599;rs59295354	330;428	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	P	330;428;428	ENSP00000360957:L330P;ENSP00000360958:L428P;ENSP00000294337:L428P	ENSP00000294337:L428P	L	+	2	0	CYP4A22	47384185	1.000000	0.71417	0.722000	0.30670	0.190000	0.23558	3.694000	0.54742	-0.120000	0.11809	-1.033000	0.02402	CTA	T|0.740;C|0.260	0.260	strong		0.512	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43915893	43915893	+	Missense_Mutation	SNP	G	G	C	rs62538181|rs200215881		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:43915893G>C	ENST00000377564.3	+	23	4134	c.3741G>C	c.(3739-3741)atG>atC	p.M1247I		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	1247					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						CTGCTGTCATGGGAGGTAACA	0.433																																					p.M1247I		Atlas-SNP	.											CNTNAP3B,NS,carcinoma,0,4	CNTNAP3B	37	4	0			c.G3741C						scavenged	.																																			SO:0001583	missense	728577	exon23			TGTCATGGGAGGT	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.3741G>C	9.37:g.43915893G>C	ENSP00000366787:p.Met1247Ile	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	138	11	0.0797101	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.	.	.	.	.	.	.	.	.	.	C	1.267	-0.614036	0.03690	.	.	ENSG00000154529	ENST00000377564;ENST00000377555	T	0.23552	1.9	2.87	-2.82	0.05787	.	.	.	.	.	T	0.03053	0.0090	N	0.00018	-2.82	0.09310	P	0.9999999999977237	B	0.02656	0.0	B	0.01281	0.0	T	0.44267	-0.9339	8	0.11794	T	0.64	.	7.2283	0.26028	0.0:0.1691:0.1448:0.6861	.	161	E9PBG0	.	I	1247;161	ENSP00000366787:M1247I	ENSP00000366778:M161I	M	+	3	0	CNTNAP3B	43855889	0.990000	0.36364	0.901000	0.35422	0.347000	0.29111	0.022000	0.13511	-1.052000	0.03222	-2.091000	0.00372	ATG	.	.	weak		0.433	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
BTNL8	79908	hgsc.bcm.edu	37	5	180377470	180377470	+	Missense_Mutation	SNP	G	G	A	rs113820381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180377470G>A	ENST00000340184.4	+	8	1635	c.1429G>A	c.(1429-1431)Gca>Aca	p.A477T	BTNL8_ENST00000511704.1_Missense_Mutation_p.A361T|BTNL8_ENST00000508408.1_3'UTR|BTNL8_ENST00000231229.4_3'UTR|BTNL8_ENST00000505126.1_Missense_Mutation_p.A270T|BTNL8_ENST00000400707.3_Missense_Mutation_p.A352T|BTNL8_ENST00000533815.2_Missense_Mutation_p.A293T	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	477			A -> T (in dbSNP:rs113820381). {ECO:0000269|PubMed:15489334}.		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGGGCCTCTGCAATCCCAGA	0.507													a|||	1213	0.242212	0.556	0.1153	5008	,	,		16171	0.1171		0.1143	False		,,,				2504	0.1687				p.A477T		Atlas-SNP	.											.	BTNL8	114	.	0			c.G1429A						PASS	.	A	THR/ALA,THR/ALA,,THR/ALA,THR/ALA,	1953,1869		598,757,556	83.0	71.0	75.0		1429,1081,,1054,877,	-2.0	0.0	5	dbSNP_132	75	1063,6535		289,485,3025	yes	missense,missense,utr-3,missense,missense,utr-3	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	58,58,,58,58,	887,1242,3581	AA,AG,GG		13.9905,48.9011,26.4098	benign,benign,,benign,benign,	477/501,361/385,,352/376,293/317,	180377470	3016,8404	1911	3799	5710	SO:0001583	missense	79908	exon8			GCCTCTGCAATCC	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.1429G>A	5.37:g.180377470G>A	ENSP00000342197:p.Ala477Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001040462	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	498	0.22802197802197802	291	0.5914634146341463	50	0.13812154696132597	64	0.11188811188811189	93	0.12269129287598944	A	0.009	-1.822179	0.00589	0.510989	0.139905	ENSG00000113303	ENST00000340184;ENST00000400707;ENST00000511704;ENST00000505126;ENST00000533815	T;T;T;T;T	0.60171	1.35;0.66;0.64;0.21;0.25	0.981	-1.96	0.07525	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43507	-0.9387	8	0.13853	T	0.58	.	6.7613	0.23542	0.5773:0.0:0.4227:0.0	.	352;361;477	E9PG07;E9PEF6;Q6UX41	.;.;BTNL8_HUMAN	T	477;352;361;270;293	ENSP00000342197:A477T;ENSP00000383543:A352T;ENSP00000425207:A361T;ENSP00000427441:A270T;ENSP00000435098:A293T	ENSP00000342197:A477T	A	+	1	0	BTNL8	180310076	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.136000	0.15974	-2.423000	0.00562	-2.245000	0.00285	GCA	G|0.772;A|0.228	0.228	strong		0.507	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
HFM1	164045	hgsc.bcm.edu	37	1	91782031	91782031	+	Missense_Mutation	SNP	T	T	C	rs11584478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:91782031T>C	ENST00000370425.3	-	26	2913	c.2815A>G	c.(2815-2817)Ata>Gta	p.I939V	HFM1_ENST00000370424.3_Missense_Mutation_p.I618V|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Missense_Mutation_p.I171V	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	939	SEC63.		I -> V (in dbSNP:rs11584478).		resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		GACAATGTTATACCTGTGGAA	0.239													T|||	626	0.125	0.1233	0.1571	5008	,	,		12671	0.005		0.2346	False		,,,				2504	0.1155				p.I939V		Atlas-SNP	.											.	HFM1	188	.	0			c.A2815G						PASS	.	T	VAL/ILE	616,3788	261.9+/-264.6	38,540,1624	73.0	76.0	75.0		2815	1.3	1.0	1	dbSNP_120	75	2199,6389	372.1+/-336.5	275,1649,2370	yes	missense	HFM1	NM_001017975.3	29	313,2189,3994	CC,CT,TT		25.6055,13.9873,21.6672	benign	939/1436	91782031	2815,10177	2202	4294	6496	SO:0001583	missense	164045	exon26			ATGTTATACCTGT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2815A>G	1.37:g.91782031T>C	ENSP00000359454:p.Ile939Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	96	55	0.572917	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	294	0.1346153846153846	53	0.10772357723577236	63	0.17403314917127072	2	0.0034965034965034965	176	0.23218997361477572	T	4.108	0.018200	0.07959	0.139873	0.256055	ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	T;T;T	0.60040	0.22;0.22;0.22	5.07	1.31	0.21738	Sec63 domain (2);	0.276343	0.34906	N	0.003594	T	0.11707	0.0285	N	0.04203	-0.255	0.37949	P	0.06741399999999997	B;B;B	0.14012	0.001;0.009;0.009	B;B;B	0.15484	0.007;0.013;0.013	T	0.14755	-1.0461	9	0.20519	T	0.43	.	6.864	0.24082	0.0:0.6073:0.0:0.3927	rs11584478;rs17556195;rs52804592;rs59939430;rs11584478	618;150;939	A6NGI5;B1B0B5;A2PYH4	.;.;HFM1_HUMAN	V	939;171;618;623	ENSP00000359454:I939V;ENSP00000294696:I171V;ENSP00000359453:I618V	ENSP00000294696:I171V	I	-	1	0	HFM1	91554619	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.352000	0.44080	0.254000	0.21573	0.455000	0.32223	ATA	T|0.824;C|0.176	0.176	strong		0.239	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
ZWILCH	55055	hgsc.bcm.edu	37	15	66821250	66821250	+	Missense_Mutation	SNP	A	A	G	rs11071896	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:66821250A>G	ENST00000307897.5	+	11	1410	c.1030A>G	c.(1030-1032)Agt>Ggt	p.S344G	ZWILCH_ENST00000535141.2_Missense_Mutation_p.S230G|ZWILCH_ENST00000446801.2_Missense_Mutation_p.S230G|ZWILCH_ENST00000565627.1_Missense_Mutation_p.S230G	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	344			S -> G (in dbSNP:rs11071896).		mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(1)|lung(6)|ovary(1)	18						CAAAGTTCGGAGTGATCTTGA	0.378													A|||	910	0.181709	0.0325	0.1585	5008	,	,		18579	0.1825		0.2535	False		,,,				2504	0.3252				p.S344G		Atlas-SNP	.											.	ZWILCH	46	.	0			c.A1030G						PASS	.	A	GLY/SER	321,4081	173.7+/-203.5	12,297,1892	121.0	110.0	113.0		1030	3.2	0.0	15	dbSNP_120	113	2191,6407	373.7+/-337.1	267,1657,2375	yes	missense	ZWILCH	NM_017975.3	56	279,1954,4267	GG,GA,AA		25.4827,7.2921,19.3231	benign	344/592	66821250	2512,10488	2201	4299	6500	SO:0001583	missense	55055	exon11			GTTCGGAGTGATC	AK023175	CCDS10219.1, CCDS73746.1	15q22.31	2013-01-17	2012-12-13		ENSG00000174442	ENSG00000174442			25468	protein-coding gene	gene with protein product		609984	"""Zwilch, kinetochore associated, homolog (Drosophila)"""			12686595	Standard	NM_017975		Approved	FLJ10036, KNTC1AP	uc002aqb.3	Q9H900	OTTHUMG00000133194	ENST00000307897.5:c.1030A>G	15.37:g.66821250A>G	ENSP00000311429:p.Ser344Gly	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	148	65	0.439189	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	37	CCDS10219.1	348	0.15934065934065933	8	0.016260162601626018	75	0.20718232044198895	75	0.13111888111888112	190	0.25065963060686014	A	8.607	0.888157	0.17540	0.072921	0.254827	ENSG00000174442	ENST00000307897;ENST00000446801;ENST00000535141	T;T;T	0.38887	1.11;1.11;1.11	5.26	3.19	0.36642	.	0.149273	0.64402	N	0.000011	T	0.00012	0.0000	N	0.00082	-2.215	0.40739	P	0.01719000000000004	B	0.02656	0.0	B	0.01281	0.0	T	0.36261	-0.9755	9	0.02654	T	1	-4.1282	8.9379	0.35711	0.0848:0.0:0.7718:0.1434	rs11071896;rs52805664;rs59123612;rs11071896	344	Q9H900	ZWILC_HUMAN	G	344;230;230	ENSP00000311429:S344G;ENSP00000402217:S230G;ENSP00000437749:S230G	ENSP00000311429:S344G	S	+	1	0	ZWILCH	64608304	1.000000	0.71417	0.029000	0.17559	0.464000	0.32679	4.667000	0.61561	0.566000	0.29273	0.374000	0.22700	AGT	A|0.818;G|0.182	0.182	strong		0.378	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975	
KLHL35	283212	hgsc.bcm.edu	37	11	75133765	75133765	+	Silent	SNP	G	G	A	rs11539810	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:75133765G>A	ENST00000539798.1	-	6	1610	c.1611C>T	c.(1609-1611)ggC>ggT	p.G537G	KLHL35_ENST00000376292.4_Silent_p.G317G	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	537								p.G537G(1)		lung(2)|stomach(1)	3						CATCCCGCCCGCCAAGGATGT	0.592													G|||	544	0.108626	0.034	0.0432	5008	,	,		20945	0.1885		0.0656	False		,,,				2504	0.2178				p.G537G	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											KLHL35,NS,carcinoma,0,1	KLHL35	15	1	1	Substitution - coding silent(1)	stomach(1)	c.C1611T						PASS	.	G		145,3883		0,145,1869	103.0	104.0	104.0		1611	-10.7	0.6	11	dbSNP_120	104	568,7822		24,520,3651	yes	coding-synonymous	KLHL35	NM_001039548.2		24,665,5520	AA,AG,GG		6.77,3.5998,5.7417		537/584	75133765	713,11705	2014	4195	6209	SO:0001819	synonymous_variant	283212	exon6			CCGCCCGCCAAGG		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"""Kelch-like"", ""BTB/POZ domain containing"""	26597	protein-coding gene	gene with protein product			"""kelch-like 35 (Drosophila)"""				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.1611C>T	11.37:g.75133765G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	62	6	0.0967742	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Silent	SNP	ENST00000539798.1	37	CCDS44685.2																																																																																			G|0.910;A|0.090	0.090	strong		0.592	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847050	100847050	+	Silent	SNP	A	A	G	rs569270	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:100847050A>G	ENST00000298815.8	+	20	2121	c.2118A>G	c.(2116-2118)tcA>tcG	p.S706S	ARHGAP42_ENST00000524892.2_Silent_p.S672S	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	706	Ser-rich.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						GTGTTGCTTCAGTCACTAGCC	0.478													G|||	2805	0.560104	0.2027	0.6009	5008	,	,		21556	0.997		0.4344	False		,,,				2504	0.6933				p.S706S		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A2118G						PASS	.	G		423,961		64,295,333	73.0	55.0	61.0		2118	-11.4	0.0	11	dbSNP_83	61	1402,1780		313,776,502	no	coding-synonymous	ARHGAP42	NM_152432.2		377,1071,835	GG,GA,AA		44.0603,30.5636,39.9693		706/875	100847050	1825,2741	692	1591	2283	SO:0001819	synonymous_variant	143872	exon20			TGCTTCAGTCACT			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2118A>G	11.37:g.100847050A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.479;G|0.521	0.521	strong		0.478	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
PHLDB1	23187	hgsc.bcm.edu	37	11	118514625	118514625	+	Silent	SNP	C	C	T	rs11216938	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:118514625C>T	ENST00000361417.2	+	15	3396	c.2985C>T	c.(2983-2985)agC>agT	p.S995S	PHLDB1_ENST00000527898.1_Silent_p.S31S|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000356063.5_Silent_p.S948S|PHLDB1_ENST00000524713.1_Silent_p.S138S	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	995										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		ccCAGCTCAGCGTGGCTACCC	0.692													C|||	1104	0.220447	0.1082	0.2118	5008	,	,		13682	0.2302		0.2157	False		,,,				2504	0.3732				p.S995S		Atlas-SNP	.											PHLDB1,rectum,carcinoma,0,1	PHLDB1	103	1	0			c.C2985T						PASS	.	C	,,	533,3867	223.3+/-239.8	32,469,1699	25.0	29.0	28.0		2985,2844,2985	-1.7	1.0	11	dbSNP_120	28	1851,6737	307.6+/-308.5	197,1457,2640	no	coding-synonymous,coding-synonymous,coding-synonymous	PHLDB1	NM_001144758.1,NM_001144759.1,NM_015157.2	,,	229,1926,4339	TT,TC,CC		21.5533,12.1136,18.3554	,,	995/1378,948/1320,995/1378	118514625	2384,10604	2200	4294	6494	SO:0001819	synonymous_variant	23187	exon14			GCTCAGCGTGGCT		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.2985C>T	11.37:g.118514625C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	81	71	0.876543	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	37	CCDS8401.1																																																																																			C|0.822;T|0.178	0.178	strong		0.692	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157	
ABCC12	94160	hgsc.bcm.edu	37	16	48122582	48122582	+	Missense_Mutation	SNP	G	G	A	rs7193955	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:48122582G>A	ENST00000311303.3	-	24	3694	c.3349C>T	c.(3349-3351)Cgt>Tgt	p.R1117C	ABCC12_ENST00000532355.1_5'Flank|ABCC12_ENST00000448542.1_3'UTR|ABCC12_ENST00000416054.1_3'UTR	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	1117			R -> C (in dbSNP:rs7193955). {ECO:0000269|PubMed:11483364}.			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				ATCTCCCCACGGCTGGGCCAG	0.512													G|||	2961	0.591254	0.1112	0.5331	5008	,	,		18261	0.8889		0.7873	False		,,,				2504	0.773				p.R1117C		Atlas-SNP	.											ABCC12,colon,carcinoma,0,1	ABCC12	190	1	0			c.C3349T						PASS	.	G	CYS/ARG	1020,3382	375.4+/-321.6	124,772,1305	90.0	78.0	82.0		3349	2.7	0.5	16	dbSNP_116	82	6730,1870	729.2+/-406.7	2660,1410,230	yes	missense	ABCC12	NM_033226.2	180	2784,2182,1535	AA,AG,GG		21.7442,23.1713,40.3938	benign	1117/1360	48122582	7750,5252	2201	4300	6501	SO:0001583	missense	94160	exon24			CCCCACGGCTGGG	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.3349C>T	16.37:g.48122582G>A	ENSP00000311030:p.Arg1117Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	1384	0.6336996336996337	69	0.1402439024390244	197	0.5441988950276243	512	0.8951048951048951	606	0.7994722955145118	G	7.927	0.739832	0.15642	0.231713	0.782558	ENSG00000140798	ENST00000311303	D	0.90844	-2.74	5.87	2.67	0.31697	.	0.634955	0.17864	N	0.159431	T	0.00012	0.0000	L	0.60904	1.88	0.80722	P	0.0	B	0.11235	0.004	B	0.11329	0.006	T	0.34925	-0.9809	9	0.56958	D	0.05	.	3.9511	0.09369	0.0766:0.2455:0.4345:0.2434	rs7193955;rs52806630;rs60981757;rs7193955	1117	Q96J65	MRP9_HUMAN	C	1117	ENSP00000311030:R1117C	ENSP00000311030:R1117C	R	-	1	0	ABCC12	46680083	0.000000	0.05858	0.535000	0.28026	0.087000	0.18053	0.035000	0.13797	0.781000	0.33589	-0.150000	0.13652	CGT	G|0.395;A|0.605	0.605	strong		0.512	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
AFAP1	60312	hgsc.bcm.edu	37	4	7783163	7783163	+	Intron	SNP	G	G	A	rs28542374	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:7783163G>A	ENST00000360265.4	-	12	1765				AFAP1_ENST00000358461.2_Intron|AFAP1-AS1_ENST00000608442.1_RNA|AFAP1_ENST00000420658.1_Silent_p.S574S|AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000382543.3_Silent_p.S574S			Q8N556	AFAP1_HUMAN	actin filament associated protein 1							cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						CAGACTGAGCGGAGGCAGGGT	0.537													G|||	3132	0.625399	0.4448	0.7176	5008	,	,		18997	0.8036		0.6382	False		,,,				2504	0.6074				p.S574S		Atlas-SNP	.											.	AFAP1	93	.	0			c.C1722T						PASS	.	G	,	654,730		153,348,191	107.0	104.0	105.0		1722,	-0.0	0.0	4	dbSNP_125	105	2084,1098		682,720,189	no	coding-synonymous,intron	AFAP1	NM_001134647.1,NM_198595.2	,	835,1068,380	AA,AG,GG		34.5066,47.2543,40.035	,	574/815,	7783163	2738,1828	692	1591	2283	SO:0001627	intron_variant	60312	exon13			CTGAGCGGAGGCA	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1531-2560C>T	4.37:g.7783163G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			G|0.356;A|0.644	0.644	strong		0.537	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
AGXT	189	hgsc.bcm.edu	37	2	241813453	241813453	+	Silent	SNP	G	G	A	rs33958047	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:241813453G>A	ENST00000307503.3	+	6	1041	c.654G>A	c.(652-654)tcG>tcA	p.S218S		NM_000030.2	NP_000021.1	P21549	SPYA_HUMAN	alanine-glyoxylate aminotransferase	218			S -> L (in HP1). {ECO:0000269|PubMed:15963748}.		cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process (GO:0042853)|L-cysteine catabolic process (GO:0019448)|oxalic acid secretion (GO:0046724)|pyruvate biosynthetic process (GO:0042866)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alanine-glyoxylate transaminase activity (GO:0008453)|amino acid binding (GO:0016597)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|receptor binding (GO:0005102)|serine-pyruvate transaminase activity (GO:0004760)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)	18		all_epithelial(40;1.61e-15)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)	Glycine(DB00145)|L-Alanine(DB00160)|L-Serine(DB00133)	CAGGGACCTCGCTCATCTCCT	0.642													g|||	767	0.153155	0.2118	0.0778	5008	,	,		18207	0.1895		0.1074	False		,,,				2504	0.137				p.S218S		Atlas-SNP	.											.	AGXT	50	.	0			c.G654A						PASS	.	G		895,3511	346.9+/-309.2	94,707,1402	90.0	80.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	654	-8.2	0.0	2	dbSNP_126	84	818,7782	189.4+/-236.2	49,720,3531	no	coding-synonymous	AGXT	NM_000030.2		143,1427,4933	AA,AG,GG		9.5116,20.3132,13.1708		218/393	241813453	1713,11293	2203	4300	6503	SO:0001819	synonymous_variant	189	exon6			GACCTCGCTCATC	D13368	CCDS2543.1	2q37.3	2008-02-05	2007-04-13		ENSG00000172482	ENSG00000172482	2.6.1.44, 2.6.1.51		341	protein-coding gene	gene with protein product	"""oxalosis I"", ""primary hyperoxaluria type 1"", ""L-alanine: glyoxylate aminotransferase 1"", ""serine:pyruvate aminotransferase"", ""glycolicaciduria"""	604285		SPAT		2039493, 2045108	Standard	NM_000030		Approved	AGXT1, PH1, AGT, SPT, AGT1	uc002waa.4	P21549	OTTHUMG00000133354	ENST00000307503.3:c.654G>A	2.37:g.241813453G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_000030	Q53QU6	Silent	SNP	ENST00000307503.3	37	CCDS2543.1																																																																																			G|0.866;A|0.134	0.134	strong		0.642	AGXT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257186.1	NM_000030	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549362	32549362	+	Silent	SNP	G	G	A	rs199704140	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32549362G>A	ENST00000360004.5	-	3	729	c.624C>T	c.(622-624)agC>agT	p.S208S		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	208	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GGCTTGTCACGCTTGGGTGCT	0.532										Multiple Myeloma(14;0.17)			G|||	507	0.101238	0.0885	0.1427	5008	,	,		16004	0.0506		0.1531	False		,,,				2504	0.0879				p.S208S		Atlas-SNP	.											HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	1	0			c.C624T						scavenged	.						125.0	112.0	117.0					6																	32549362		1504	2686	4190	SO:0001819	synonymous_variant	3123	exon3			TGTCACGCTTGGG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.624C>T	6.37:g.32549362G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	153	6	0.0392157	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.410;A|0.590	0.590	strong		0.532	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
CAPN7	23473	hgsc.bcm.edu	37	3	15276541	15276541	+	Silent	SNP	A	A	G	rs17539942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:15276541A>G	ENST00000253693.2	+	12	1549	c.1296A>G	c.(1294-1296)aaA>aaG	p.K432K	Y_RNA_ENST00000516276.1_RNA	NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	432	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						GATTTCACAAAGGAGATGTCC	0.383													A|||	256	0.0511182	0.0091	0.0908	5008	,	,		17069	0.0		0.1034	False		,,,				2504	0.0787				p.K432K		Atlas-SNP	.											.	CAPN7	63	.	0			c.A1296G						PASS	.	A		128,4278	84.4+/-122.9	3,122,2078	83.0	84.0	83.0		1296	4.5	1.0	3	dbSNP_123	83	917,7683	187.3+/-234.6	53,811,3436	no	coding-synonymous	CAPN7	NM_014296.2		56,933,5514	GG,GA,AA		10.6628,2.9051,8.0348		432/814	15276541	1045,11961	2203	4300	6503	SO:0001819	synonymous_variant	23473	exon12			TCACAAAGGAGAT	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"""calpain like protease"", ""homolog of Aspergillus Nidulans PALB"""	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.1296A>G	3.37:g.15276541A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_014296		Silent	SNP	ENST00000253693.2	37	CCDS2624.1	122	0.055860805860805864	6	0.012195121951219513	40	0.11049723756906077	0	0.0	76	0.10026385224274406	A	9.571	1.121003	0.20877	0.029051	0.106628	ENSG00000131375	ENST00000415565	.	.	.	5.69	4.53	0.55603	.	.	.	.	.	T	0.01558	0.0050	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.28808	-1.0032	3	.	.	.	-22.6379	9.6499	0.39890	0.8554:0.0:0.1446:0.0	rs17539942;rs17539942	.	.	.	G	170	.	.	R	+	1	2	CAPN7	15251545	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.407000	0.34657	0.975000	0.38392	0.528000	0.53228	AGG	A|0.924;G|0.076	0.076	strong		0.383	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296	
FAM71F2	346653	hgsc.bcm.edu	37	7	128317658	128317658	+	Missense_Mutation	SNP	C	C	T	rs6467210	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128317658C>T	ENST00000480462.1	+	3	512	c.406C>T	c.(406-408)Cgg>Tgg	p.R136W	FAM71F2_ENST00000477515.1_Intron|FAM71F2_ENST00000460349.1_3'UTR|FAM71F2_ENST00000378704.3_Missense_Mutation_p.R127W			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	136			R -> W (in dbSNP:rs6467210). {ECO:0000269|PubMed:15489334}.							NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						AATCTACGACCGGCTCCAGCG	0.478													C|||	1657	0.330871	0.1778	0.3098	5008	,	,		15344	0.5615		0.2913	False		,,,				2504	0.3558				p.R136W		Atlas-SNP	.											.	FAM71F2	19	.	0			c.C406T						PASS	.	C	TRP/ARG,TRP/ARG	743,3129		75,593,1268	33.0	35.0	34.0		406,379	3.6	0.7	7	dbSNP_116	34	2451,5835		378,1695,2070	yes	missense,missense	FAM71F2	NM_001012454.3,NM_001128926.1	101,101	453,2288,3338	TT,TC,CC		29.58,19.189,26.2708	probably-damaging,probably-damaging	136/310,127/301	128317658	3194,8964	1936	4143	6079	SO:0001583	missense	346653	exon3			TACGACCGGCTCC	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member B"""	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.406C>T	7.37:g.128317658C>T	ENSP00000420140:p.Arg136Trp	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	709	0.32463369963369965	99	0.20121951219512196	101	0.27900552486187846	296	0.5174825174825175	213	0.28100263852242746	C	14.79	2.640013	0.47153	0.19189	0.2958	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.6	3.58	0.41010	.	0.319242	0.23017	N	0.052892	T	0.00012	0.0000	L	0.47716	1.5	0.38219	P	0.05929300000000004	D;D	0.76494	0.998;0.999	P;P	0.60345	0.799;0.873	T	0.46992	-0.9151	9	0.52906	T	0.07	-11.1258	10.036	0.42129	0.446:0.554:0.0:0.0	rs6467210;rs17169437;rs6467210	127;136	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	W	127;136;127;127	ENSP00000418907:R127W;ENSP00000420140:R136W;ENSP00000367976:R127W;ENSP00000401654:R127W	ENSP00000367976:R127W	R	+	1	2	FAM71F2	128104894	0.171000	0.23029	0.727000	0.30756	0.340000	0.28889	0.272000	0.18644	1.316000	0.45131	0.650000	0.86243	CGG	C|0.674;T|0.326	0.326	strong		0.478	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
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 GAIIx	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		Somatic	33	0	0	1593	WXS	Illumina HiSeq	Phase_I	28	10	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 GAIIx	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_ENST00000438828.2_Missense_Mutation_p.E647K|WDR12_ENST00000477723.1_Intron|CARF_ENST00000428585.1_Missense_Mutation_p.E571K|CARF_ENST00000545262.1_Missense_Mutation_p.E571K|CARF_ENST00000320443.8_Missense_Mutation_p.E647K|CARF_ENST00000545253.1_Missense_Mutation_p.E559K|CARF_ENST00000414439.1_Missense_Mutation_p.E545K	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	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	170	52	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	
CCT3	7203	hgsc.bcm.edu	37	1	156290656	156290656	+	Missense_Mutation	SNP	T	T	C	rs11548200	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156290656T>C	ENST00000295688.3	-	7	863	c.583A>G	c.(583-585)Ata>Gta	p.I195V	CCT3_ENST00000368261.3_Missense_Mutation_p.I150V|CCT3_ENST00000472765.2_Missense_Mutation_p.I150V|CCT3_ENST00000368259.2_Missense_Mutation_p.I157V	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	195					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					TATTTTTTTATGTCAATCTCT	0.398													T|||	104	0.0207668	0.0015	0.0403	5008	,	,		23838	0.002		0.0537	False		,,,				2504	0.0184				p.I195V		Atlas-SNP	.											.	CCT3	61	.	0			c.A583G						PASS	.	T	VAL/ILE,VAL/ILE	58,4348	56.8+/-93.2	0,58,2145	253.0	243.0	246.0		469,583	5.9	1.0	1	dbSNP_120	246	493,8107	142.0+/-198.3	19,455,3826	yes	missense,missense	CCT3	NM_001008800.2,NM_005998.4	29,29	19,513,5971	CC,CT,TT		5.7326,1.3164,4.2365	possibly-damaging,possibly-damaging	157/508,195/546	156290656	551,12455	2203	4300	6503	SO:0001583	missense	7203	exon7			TTTTTATGTCAAT	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"""Heat Shock Proteins / Chaperonins"""	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.583A>G	1.37:g.156290656T>C	ENSP00000295688:p.Ile195Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	148	69	0.466216	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	37	CCDS1140.2	65	0.02976190476190476	0	0.0	18	0.049723756906077346	1	0.0017482517482517483	46	0.06068601583113457	T	22.1	4.250744	0.80135	0.013164	0.057326	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765;ENST00000413555;ENST00000496684;ENST00000533194;ENST00000446905	T;T;T;T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;-1.04;-1.04;-1.04;0.4	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.80539	0.4642	L	0.49571	1.57	0.58432	D	0.999994	B;D;B	0.63880	0.078;0.993;0.153	B;D;B	0.85130	0.019;0.997;0.111	T	0.81320	-0.0986	10	0.44086	T	0.13	-18.4868	12.7903	0.57530	0.0:0.0:0.0:1.0	rs11548200	157;194;195	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	V	195;157;150;150;219;194;116;181	ENSP00000295688:I195V;ENSP00000357242:I157V;ENSP00000357244:I150V;ENSP00000431543:I150V;ENSP00000413308:I219V;ENSP00000434232:I194V;ENSP00000434481:I116V;ENSP00000388799:I181V	ENSP00000295688:I195V	I	-	1	0	CCT3	154557280	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	7.697000	0.84279	2.274000	0.75844	0.519000	0.50382	ATA	T|0.961;C|0.039	0.039	strong		0.398	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998	
TMEM17	200728	hgsc.bcm.edu	37	2	62733189	62733189	+	Missense_Mutation	SNP	C	C	T	rs17854454	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:62733189C>T	ENST00000335390.5	-	1	287	c.76G>A	c.(76-78)Ggt>Agt	p.G26S		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	26			G -> S (in dbSNP:rs17854454). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GACTCTGGACCGGTCCGATTG	0.647													C|||	773	0.154353	0.0492	0.134	5008	,	,		12335	0.2302		0.1541	False		,,,				2504	0.2331				p.G26S		Atlas-SNP	.											.	TMEM17	19	.	0			c.G76A						PASS	.	C	SER/GLY	287,4119	151.4+/-185.3	11,265,1927	35.0	36.0	36.0		76	3.9	1.0	2	dbSNP_123	36	1491,7109	271.9+/-289.8	137,1217,2946	yes	missense	TMEM17	NM_198276.2	56	148,1482,4873	TT,TC,CC		17.3372,6.5138,13.6706	benign	26/199	62733189	1778,11228	2203	4300	6503	SO:0001583	missense	200728	exon1			CTGGACCGGTCCG		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.76G>A	2.37:g.62733189C>T	ENSP00000335094:p.Gly26Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	37	CCDS1871.1	344	0.1575091575091575	29	0.05894308943089431	52	0.143646408839779	141	0.2465034965034965	122	0.16094986807387862	C	8.752	0.921567	0.17982	0.065138	0.173372	ENSG00000186889	ENST00000335390	T	0.42513	0.97	4.82	3.92	0.45320	.	0.476121	0.23926	N	0.043188	T	0.00012	0.0000	L	0.27053	0.805	0.30744	P	0.745851	B	0.24368	0.102	B	0.15052	0.012	T	0.13229	-1.0517	9	0.08599	T	0.76	-3.2417	10.6935	0.45886	0.0:0.9078:0.0:0.0922	rs17854454	26	Q86X19	TMM17_HUMAN	S	26	ENSP00000335094:G26S	ENSP00000335094:G26S	G	-	1	0	TMEM17	62586693	1.000000	0.71417	0.991000	0.47740	0.022000	0.10575	2.764000	0.47613	2.525000	0.85131	0.456000	0.33151	GGT	C|0.865;T|0.135	0.135	strong		0.647	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18649057	18649057	+	Missense_Mutation	SNP	C	C	T	rs12312266	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:18649057C>T	ENST00000266497.5	+	19	2770	c.2732C>T	c.(2731-2733)cCg>cTg	p.P911L	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.P952L|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.P911L			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	911			P -> L (in dbSNP:rs12312266). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9878262, ECO:0000269|Ref.3}.		chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				AATGCTAATCCGATGGGCAAA	0.323													C|||	1875	0.374401	0.5008	0.366	5008	,	,		18017	0.3046		0.2425	False		,,,				2504	0.4172				p.P911L		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.C2732T						PASS	.	C	LEU/PRO	1621,2027		369,883,572	103.0	89.0	94.0		2732	4.4	1.0	12	dbSNP_120	94	1837,6305		236,1365,2470	yes	missense	PIK3C2G	NM_004570.4	98	605,2248,3042	TT,TC,CC		22.562,44.4353,29.3299	probably-damaging	911/1446	18649057	3458,8332	1824	4071	5895	SO:0001583	missense	5288	exon20			CTAATCCGATGGG	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.2732C>T	12.37:g.18649057C>T	ENSP00000266497:p.Pro911Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	703	0.3218864468864469	218	0.44308943089430897	129	0.356353591160221	178	0.3111888111888112	178	0.23482849604221637	C	24.1	4.498890	0.85069	0.444353	0.22562	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	D;D;D	0.81908	-1.55;-1.55;-1.55	4.37	4.37	0.52481	Protein kinase-like domain (1);	0.071120	0.56097	D	0.000035	T	0.00012	0.0000	M	0.78456	2.415	0.09310	P	0.99999999684936	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.94	T	0.00768	-1.1574	9	0.59425	D	0.04	-16.2062	16.7234	0.85416	0.0:1.0:0.0:0.0	rs12312266;rs17847799;rs52825188;rs58825824;rs12312266	952;911	F5H369;O75747	.;P3C2G_HUMAN	L	911;911;952	ENSP00000404845:P911L;ENSP00000266497:P911L;ENSP00000445381:P952L	ENSP00000266497:P911L	P	+	2	0	PIK3C2G	18540324	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.384000	0.66225	2.724000	0.93272	0.650000	0.86243	CCG	C|0.665;N|0.000	.	strong		0.323	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
GNL1	2794	hgsc.bcm.edu	37	6	30521137	30521137	+	Silent	SNP	G	G	A	rs2074505	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30521137G>A	ENST00000376621.3	-	6	1768	c.798C>T	c.(796-798)gaC>gaT	p.D266D		NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	266	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						CACTACTAGGGTCCTGTGGGG	0.557													G|||	3311	0.661142	0.6641	0.5605	5008	,	,		19592	0.621		0.667	False		,,,				2504	0.7638				p.D266D		Atlas-SNP	.											.	GNL1	47	.	0			c.C798T						PASS	.	G		2009,1013		680,649,182	122.0	141.0	134.0		798	2.6	1.0	6	dbSNP_96	134	3581,1837		1206,1169,334	no	coding-synonymous	GNL1	NM_005275.3		1886,1818,516	AA,AG,GG		33.9055,33.5208,33.7678		266/608	30521137	5590,2850	1511	2709	4220	SO:0001819	synonymous_variant	2794	exon6			ACTAGGGTCCTGT		CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590			4413	protein-coding gene	gene with protein product		143024				8180467	Standard	NM_005275		Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.798C>T	6.37:g.30521137G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_005275	B0S838|Q96CT5	Silent	SNP	ENST00000376621.3	37	CCDS4680.1																																																																																			G|0.335;A|0.665	0.665	strong		0.557	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076241.2		
C12orf60	144608	hgsc.bcm.edu	37	12	14976553	14976553	+	Silent	SNP	G	G	C	rs17761825	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:14976553G>C	ENST00000330828.2	+	2	888	c.684G>C	c.(682-684)gcG>gcC	p.A228A	C12orf60_ENST00000527783.1_Intron	NM_175874.3	NP_787070.2	Q5U649	CL060_HUMAN	chromosome 12 open reading frame 60	228										breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	9						TCCAAAAAGCGATAAAGACTA	0.363													C|||	526	0.105032	0.0545	0.1945	5008	,	,		18187	0.0317		0.1879	False		,,,				2504	0.1002				p.A228A		Atlas-SNP	.											.	C12orf60	31	.	0			c.G684C						PASS	.	C		289,4097		10,269,1914	40.0	40.0	40.0		684	2.5	0.0	12	dbSNP_123	40	1675,6909		169,1337,2786	no	coding-synonymous	C12orf60	NM_175874.3		179,1606,4700	CC,CG,GG		19.513,6.5891,15.1426		228/246	14976553	1964,11006	2193	4292	6485	SO:0001819	synonymous_variant	144608	exon2			AAAAGCGATAAAG	BC038836	CCDS8667.1	12p12.3	2012-08-16			ENSG00000182993	ENSG00000182993			28726	protein-coding gene	gene with protein product						12477932	Standard	NM_175874		Approved	MGC47869	uc001rcj.4	Q5U649	OTTHUMG00000167473	ENST00000330828.2:c.684G>C	12.37:g.14976553G>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_175874	A8K1M7|Q5XKK8|Q8IXY2	Silent	SNP	ENST00000330828.2	37	CCDS8667.1																																																																																			G|0.853;C|0.147	0.147	strong		0.363	C12orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394735.1	NM_175874	
TRIM23	373	hgsc.bcm.edu	37	5	64905256	64905256	+	Silent	SNP	T	T	C	rs17240173	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:64905256T>C	ENST00000231524.9	-	6	1229	c.858A>G	c.(856-858)tcA>tcG	p.S286S	TRIM23_ENST00000274327.7_Silent_p.S286S|TRIM23_ENST00000381018.3_Silent_p.S286S|TRIM23_ENST00000508808.1_5'UTR	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	286					GTP catabolic process (GO:0006184)|positive regulation of catalytic activity (GO:0043085)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	28		Lung NSC(167;3.24e-06)|Prostate(74;0.0138)|Breast(144;0.0433)|Ovarian(174;0.0545)|Colorectal(97;0.234)		Lung(70;0.00473)		CTCGAATACATGACCGGGCAT	0.323													T|||	29	0.00579073	0.0023	0.0144	5008	,	,		20315	0.0		0.0149	False		,,,				2504	0.001				p.S286S		Atlas-SNP	.											.	TRIM23	73	.	0			c.A858G						PASS	.	T	,,	14,4392	20.2+/-43.8	0,14,2189	76.0	70.0	72.0		858,858,858	-2.5	1.0	5	dbSNP_123	72	148,8452	72.3+/-134.9	0,148,4152	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM23	NM_001656.3,NM_033227.2,NM_033228.2	,,	0,162,6341	CC,CT,TT		1.7209,0.3177,1.2456	,,	286/575,286/570,286/547	64905256	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	373	exon6			AATACATGACCGG	L04510	CCDS3986.1, CCDS3987.1, CCDS43322.1	5q12.3	2013-01-09	2011-01-25	2004-06-04	ENSG00000113595	ENSG00000113595		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	660	protein-coding gene	gene with protein product		601747	"""ADP-ribosylation factor domain protein 1, 64kDa"", ""tripartite motif-containing 23"""	ARFD1		8473324	Standard	NM_001656		Approved	ARD1, RNF46	uc003jty.3	P36406	OTTHUMG00000097802	ENST00000231524.9:c.858A>G	5.37:g.64905256T>C		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	230	112	0.486957	NM_033228	Q9BZY4|Q9BZY5	Silent	SNP	ENST00000231524.9	37	CCDS3987.1																																																																																			T|0.990;C|0.010	0.010	strong		0.323	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656	
LMTK2	22853	hgsc.bcm.edu	37	7	97822115	97822115	+	Missense_Mutation	SNP	T	T	A	rs11765552	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:97822115T>A	ENST00000297293.5	+	11	2631	c.2338T>A	c.(2338-2340)Ttg>Atg	p.L780M		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	780			L -> M (in dbSNP:rs11765552). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:17344846}.		early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					TAAGCCAGGCTTGTCTTTGTT	0.428													T|||	1121	0.223842	0.0356	0.3156	5008	,	,		19913	0.1528		0.5119	False		,,,				2504	0.1902				p.L780M		Atlas-SNP	.											.	LMTK2	228	.	0			c.T2338A						PASS	.	T	MET/LEU	551,3855	247.2+/-255.5	34,483,1686	119.0	124.0	122.0		2338	-0.9	0.0	7	dbSNP_120	122	4710,3890	607.9+/-395.3	1300,2110,890	yes	missense	LMTK2	NM_014916.3	15	1334,2593,2576	AA,AT,TT		45.2326,12.5057,40.4506	benign	780/1504	97822115	5261,7745	2203	4300	6503	SO:0001583	missense	22853	exon11			CCAGGCTTGTCTT	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.2338T>A	7.37:g.97822115T>A	ENSP00000297293:p.Leu780Met	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_014916	A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	613	0.2806776556776557	21	0.042682926829268296	120	0.3314917127071823	81	0.14160839160839161	391	0.5158311345646438	T	12.80	2.047819	0.36085	0.125057	0.547674	ENSG00000164715	ENST00000297293	T	0.78126	-1.15	5.66	-0.876	0.10624	.	1.102820	0.06652	N	0.762926	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.41748	0.761	B	0.35413	0.202	T	0.31052	-0.9957	9	0.33940	T	0.23	.	6.0057	0.19544	0.0:0.2644:0.1255:0.6101	rs11765552;rs17527184;rs11765552	780	Q8IWU2	LMTK2_HUMAN	M	780	ENSP00000297293:L780M	ENSP00000297293:L780M	L	+	1	2	LMTK2	97660051	0.002000	0.14202	0.000000	0.03702	0.033000	0.12548	1.132000	0.31418	-0.292000	0.08999	0.533000	0.62120	TTG	T|0.639;A|0.361	0.361	strong		0.428	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
MUC6	4588	hgsc.bcm.edu	37	11	1016889	1016889	+	Missense_Mutation	SNP	G	G	A	rs373231068		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1016889G>A	ENST00000421673.2	-	31	5962	c.5912C>T	c.(5911-5913)cCa>cTa	p.P1971L		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1971	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|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;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCTGTAGGTGGGGAGTGTGT	0.587																																					p.P1971L		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	0			c.C5912T						scavenged	.						1041.0	1055.0	1050.0					11																	1016889		2203	4298	6501	SO:0001583	missense	4588	exon31			GTAGGTGGGGAGT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5912C>T	11.37:g.1016889G>A	ENSP00000406861:p.Pro1971Leu	Somatic	412	0	0		WXS	Illumina HiSeq	Phase_I	556	21	0.0377698	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.862334	0.32884	.	.	ENSG00000184956	ENST00000421673	T	0.18016	2.24	3.08	0.802	0.18686	.	.	.	.	.	T	0.12220	0.0297	L	0.47716	1.5	0.09310	N	1	B	0.23650	0.089	B	0.16722	0.016	T	0.36744	-0.9735	9	0.13108	T	0.6	.	6.4541	0.21920	0.0:0.2122:0.5938:0.194	.	1971	Q6W4X9	MUC6_HUMAN	L	1971	ENSP00000406861:P1971L	ENSP00000406861:P1971L	P	-	2	0	MUC6	1006889	0.003000	0.15002	0.002000	0.10522	0.377000	0.30045	1.212000	0.32394	0.602000	0.29896	0.306000	0.20318	CCA	.	.	weak		0.587	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
NES	10763	hgsc.bcm.edu	37	1	156639753	156639753	+	Silent	SNP	G	G	A	rs11582300	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156639753G>A	ENST00000368223.3	-	4	4359	c.4227C>T	c.(4225-4227)tcC>tcT	p.S1409S		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1409	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CAAACCCATCGGACTCCCCAT	0.647													G|||	3097	0.618411	0.385	0.6787	5008	,	,		15954	0.8611		0.6312	False		,,,				2504	0.6278				p.S1409S		Atlas-SNP	.											.	NES	196	.	0			c.C4227T						PASS	.	G		1758,2648		355,1048,800	22.0	24.0	23.0		4227	0.8	1.0	1	dbSNP_120	23	5323,3269		1696,1931,669	no	coding-synonymous	NES	NM_006617.1		2051,2979,1469	AA,AG,GG		38.047,39.9001,45.5224		1409/1622	156639753	7081,5917	2203	4296	6499	SO:0001819	synonymous_variant	10763	exon4			CCCATCGGACTCC	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.4227C>T	1.37:g.156639753G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	178	88	0.494382	NM_006617	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	37	CCDS1151.1																																																																																			G|0.413;A|0.587	0.587	strong		0.647	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
RGSL1	353299	hgsc.bcm.edu	37	1	182443014	182443014	+	Missense_Mutation	SNP	G	G	C	rs647224	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:182443014G>C	ENST00000294854.8	+	6	788	c.768G>C	c.(766-768)tgG>tgC	p.W256C	RGSL1_ENST00000542961.1_Missense_Mutation_p.W291C	NM_001137669.1	NP_001131141.1	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1	256			W -> C (in dbSNP:rs647224).		termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)		p.W291C(1)		central_nervous_system(2)|skin(4)	6						GGAAGATGTGGCAATTGGTAG	0.493													G|||	617	0.123203	0.1089	0.1412	5008	,	,		23260	0.246		0.0567	False		,,,				2504	0.0716				p.W256C	Ovarian(71;11 616 11292 12944 18021 32289 33994 41738 46526)	Atlas-SNP	.											RGSL2,NS,carcinoma,0,1	RGSL1	111	1	1	Substitution - Missense(1)	stomach(1)	c.G768C						PASS	.	G	CYS/TRP	148,1236		10,128,554	156.0	145.0	148.0		768	5.1	1.0	1	dbSNP_83	148	170,3012		7,156,1428	yes	missense	RGSL1	NM_001137669.1	215	17,284,1982	CC,CG,GG		5.3426,10.6936,6.9645	probably-damaging	256/1077	182443014	318,4248	692	1591	2283	SO:0001583	missense	353299	exon6			GATGTGGCAATTG	AF510428	CCDS58049.1	1q25	2013-04-02	2007-08-14		ENSG00000121446	ENSG00000121446			18636	protein-coding gene	gene with protein product		611012	"""regulator of G-protein signalling like 1"", ""regulator of G-protein signaling like 2"", ""regulator of G-protein signalling like 2"""	RGSL2		12801632	Standard	NM_001137669		Approved		uc009wxw.3	A5PLK6	OTTHUMG00000035217	ENST00000294854.8:c.768G>C	1.37:g.182443014G>C	ENSP00000457748:p.Trp256Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	128	55	0.429688	NM_001137669	A2A2Z0|A6PVM2|A6PVM3|Q0VAJ4|Q0VAJ5|Q6ZRL0|Q86UV0|Q9H084	Missense_Mutation	SNP	ENST00000294854.8	37	CCDS58049.1																																																																																			G|0.871;C|0.129	0.129	strong		0.493	RGSL1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320710.3	NM_181572	
PNPLA5	150379	hgsc.bcm.edu	37	22	44282307	44282307	+	Silent	SNP	G	G	A	rs739232	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44282307G>A	ENST00000597664.1	-	6	954	c.825C>T	c.(823-825)gaC>gaT	p.D275D	PNPLA5_ENST00000381198.2_Silent_p.D161D|PNPLA5_ENST00000593866.1_Silent_p.D161D|PNPLA5_ENST00000216177.4_Silent_p.D275D			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	275					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CCCAGTTTCCGTCAGCCGGGG	0.572													A|||	2486	0.496406	0.2224	0.4568	5008	,	,		18935	0.9048		0.3748	False		,,,				2504	0.5992				p.D275D		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C825T						PASS	.	A	,	1099,3307	720.0+/-409.0	142,815,1246	85.0	77.0	80.0		483,825	-4.8	0.0	22	dbSNP_86	80	3208,5392	652.5+/-400.9	585,2038,1677	no	coding-synonymous,coding-synonymous	PNPLA5	NM_001177675.1,NM_138814.3	,	727,2853,2923	AA,AG,GG		37.3023,24.9433,33.1155	,	161/316,275/430	44282307	4307,8699	2203	4300	6503	SO:0001819	synonymous_variant	150379	exon6			GTTTCCGTCAGCC	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.825C>T	22.37:g.44282307G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Silent	SNP	ENST00000597664.1	37																																																																																				G|0.598;A|0.402	0.402	strong		0.572	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
IVL	3713	hgsc.bcm.edu	37	1	152882981	152882981	+	Silent	SNP	A	A	T	rs62637699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152882981A>T	ENST00000368764.3	+	2	772	c.708A>T	c.(706-708)ccA>ccT	p.P236P	IVL_ENST00000392667.2_Silent_p.P90P			P07476	INVO_HUMAN	involucrin	236	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		P -> S (in dbSNP:rs17855670). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2873896}.		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)			tggagctcccacagcagcagg	0.677																																					p.P236P		Atlas-SNP	.											IVL,colon,carcinoma,+2,2	IVL	100	2	0			c.A708T						PASS	.						3.0	4.0	3.0					1																	152882981		1601	3431	5032	SO:0001819	synonymous_variant	3713	exon2			GCTCCCACAGCAG	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.708A>T	1.37:g.152882981A>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	55	11	0.2	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			A|0.696;T|0.304	0.304	strong		0.677	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
CR1L	1379	hgsc.bcm.edu	37	1	207857254	207857254	+	Missense_Mutation	SNP	A	A	G	rs3085	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207857254A>G	ENST00000508064.2	+	4	475	c.415A>G	c.(415-417)Atc>Gtc	p.I139V	CR1L_ENST00000530905.1_3'UTR	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	139	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> V (in dbSNP:rs3085).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CACATGCATCATCTCAGGCAA	0.358													N|||	807	0.161142	0.0189	0.0648	5008	,	,		20001	0.3601		0.1083	False		,,,				2504	0.271				p.I139V		Atlas-SNP	.											.	CR1L	97	.	0			c.A415G						PASS	.	A	VAL/ILE	141,3869		1,139,1865	175.0	168.0	170.0		415	-4.0	0.0	1	dbSNP_36	170	951,7415		55,841,3287	yes	missense	CR1L	NM_175710.1	29	56,980,5152	GG,GA,AA		11.3674,3.5162,8.8235	benign	139/570	207857254	1092,11284	2005	4183	6188	SO:0001583	missense	1379	exon4			TGCATCATCTCAG	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.415A>G	1.37:g.207857254A>G	ENSP00000421736:p.Ile139Val	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	323	0.1478937728937729	13	0.026422764227642278	21	0.058011049723756904	203	0.3548951048951049	86	0.11345646437994723	A	9.486	1.099475	0.20552	0.035162	0.113674	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.23552	1.9	2.81	-3.99	0.04069	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.39020	1.185	0.80722	P	0.0	B	0.12013	0.005	B	0.26094	0.066	T	0.48864	-0.8997	8	0.21540	T	0.41	.	5.6438	0.17579	0.276:0.5862:0.1378:0.0	rs3085;rs52799932;rs3085	139	Q2VPA4	CR1L_HUMAN	V	139	ENSP00000421736:I139V	ENSP00000434864:I83V	I	+	1	0	CR1L	205923877	0.000000	0.05858	0.002000	0.10522	0.436000	0.31835	-2.954000	0.00676	-0.487000	0.06735	0.338000	0.21704	ATC	A|0.852;G|0.148	0.148	strong		0.358	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
TMEM261	90871	hgsc.bcm.edu	37	9	7799653	7799653	+	Missense_Mutation	SNP	G	G	T	rs1127430	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:7799653G>T	ENST00000358227.4	-	1	414	c.82C>A	c.(82-84)Ccc>Acc	p.P28T	TMEM261_ENST00000484082.1_Intron	NM_033428.1	NP_219500.1	Q96GE9	TM261_HUMAN	transmembrane protein 261	28			P -> T (in dbSNP:rs1127430).			integral component of membrane (GO:0016021)											GTAGCTGGGGGCGCAGGTTTG	0.662													g|||	1874	0.374201	0.264	0.5375	5008	,	,		9632	0.371		0.3926	False		,,,				2504	0.3916				p.P28T		Atlas-SNP	.											.	C9orf123	7	.	0			c.C82A						PASS	.	G	THR/PRO	1224,3182		178,868,1157	22.0	26.0	25.0		82	3.5	0.0	9	dbSNP_86	25	3382,5218		663,2056,1581	no	missense	C9orf123	NM_033428.1	38	841,2924,2738	TT,TG,GG		39.3256,27.7803,35.4144	probably-damaging	28/113	7799653	4606,8400	2203	4300	6503	SO:0001583	missense	90871	exon1			CTGGGGGCGCAGG	BC009510	CCDS34989.1	9p24.1	2014-02-21	2013-09-11	2013-09-11	ENSG00000137038	ENSG00000137038			30536	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 123"""	C9orf123		21666724	Standard	NM_033428		Approved	MGC4730	uc003zkj.3	Q96GE9	OTTHUMG00000019539	ENST00000358227.4:c.82C>A	9.37:g.7799653G>T	ENSP00000350961:p.Pro28Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	26	0.962963	NM_033428	A8K9B7|Q5T6Y9|Q9NT74	Missense_Mutation	SNP	ENST00000358227.4	37	CCDS34989.1	819	0.375	137	0.2784552845528455	198	0.5469613259668509	197	0.34440559440559443	287	0.3786279683377309	g	17.75	3.467238	0.63625	0.277803	0.393256	ENSG00000137038	ENST00000358227	T	0.52526	0.66	5.34	3.45	0.39498	.	0.309163	0.24041	N	0.042086	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	P;P	0.46512	0.717;0.879	B;P	0.45639	0.243;0.488	T	0.48547	-0.9026	9	0.72032	D	0.01	-4.188	8.6511	0.34035	0.0:0.166:0.6616:0.1724	rs1127430;rs3183396	28;28	Q96GE9-2;Q96GE9	.;CI123_HUMAN	T	28	ENSP00000350961:P28T	ENSP00000350961:P28T	P	-	1	0	C9orf123	7789653	0.000000	0.05858	0.003000	0.11579	0.139000	0.21198	-0.242000	0.08928	0.773000	0.33404	0.645000	0.84053	CCC	G|0.647;T|0.353	0.353	strong		0.662	TMEM261-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051705.1	NM_033428	
ALG8	79053	hgsc.bcm.edu	37	11	77825320	77825320	+	Missense_Mutation	SNP	T	T	C	rs665278	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77825320T>C	ENST00000299626.5	-	6	736	c.665A>G	c.(664-666)aAt>aGt	p.N222S	ALG8_ENST00000532552.2_Intron|ALG8_ENST00000376156.3_Missense_Mutation_p.N222S	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	222			N -> S (in dbSNP:rs665278). {ECO:0000269|PubMed:11124703, ECO:0000269|PubMed:15235028}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|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)			NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			GCCTGGTTTATTTGCAGTGAA	0.383													T|||	733	0.146366	0.0439	0.2003	5008	,	,		20019	0.0942		0.2286	False		,,,				2504	0.2157				p.N222S		Atlas-SNP	.											.	ALG8	54	.	0			c.A665G						PASS	.	T	SER/ASN,SER/ASN	325,4075	170.1+/-200.6	7,311,1882	88.0	83.0	84.0		665,665	1.6	1.0	11	dbSNP_83	84	1967,6617	344.4+/-325.3	229,1509,2554	yes	missense,missense	ALG8	NM_001007027.2,NM_024079.4	46,46	236,1820,4436	CC,CT,TT		22.9147,7.3864,17.6525	benign,benign	222/468,222/527	77825320	2292,10692	2200	4292	6492	SO:0001583	missense	79053	exon6			GGTTTATTTGCAG	AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	608103	"""asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.665A>G	11.37:g.77825320T>C	ENSP00000299626:p.Asn222Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	89	16	0.179775	NM_024079	A6NDW6|O60860	Missense_Mutation	SNP	ENST00000299626.5	37	CCDS8258.1	332|332	0.152014652014652|0.152014652014652	22|22	0.044715447154471545|0.044715447154471545	77|77	0.212707182320442|0.212707182320442	58|58	0.10139860139860139|0.10139860139860139	175|175	0.23087071240105542|0.23087071240105542	T|T	2.710|2.710	-0.269072|-0.269072	0.05716|0.05716	0.073864|0.073864	0.229147|0.229147	ENSG00000159063|ENSG00000159063	ENST00000532306;ENST00000529139|ENST00000299626;ENST00000376156;ENST00000532440;ENST00000525755;ENST00000530454;ENST00000525870;ENST00000527099	.|D;D;D;D;D;D;D	.|0.83419	.|-1.72;-1.72;-1.72;-1.72;-1.72;-1.72;-1.72	5.43|5.43	1.56|1.56	0.23342|0.23342	.|.	.|0.537635	.|0.21930	.|N	.|0.067028	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.33485|0.33485	1.01|1.01	0.35199|0.35199	P|P	0.225893|0.225893	.|B;B;B	.|0.06786	.|0.0;0.0;0.001	.|B;B;B	.|0.09377	.|0.004;0.002;0.004	T|T	0.03784|0.03784	-1.1004|-1.1004	4|9	.|0.06099	.|T	.|0.92	-2.1437|-2.1437	5.0202|5.0202	0.14358|0.14358	0.1276:0.2353:0.0:0.637|0.1276:0.2353:0.0:0.637	rs665278;rs3197648;rs52799833;rs56532042;rs57243244;rs665278|rs665278;rs3197648;rs52799833;rs56532042;rs57243244;rs665278	.|222;222;222	.|B3KQL8;Q9BVK2;A6NDW6	.|.;ALG8_HUMAN;.	V|S	96;67|222;222;40;171;223;134;134	.|ENSP00000299626:N222S;ENSP00000365326:N222S;ENSP00000433429:N40S;ENSP00000435467:N171S;ENSP00000434660:N223S;ENSP00000435417:N134S;ENSP00000436064:N134S	.|ENSP00000299626:N222S	I|N	-|-	1|2	0|0	ALG8|ALG8	77502968|77502968	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.989000|0.989000	0.77384|0.77384	0.541000|0.541000	0.23207|0.23207	0.064000|0.064000	0.16427|0.16427	0.383000|0.383000	0.25322|0.25322	ATA|AAT	T|0.842;C|0.158	0.158	strong		0.383	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079	
C9orf84	158401	hgsc.bcm.edu	37	9	114484783	114484783	+	Silent	SNP	A	A	G	rs12352352	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:114484783A>G	ENST00000318737.4	-	13	1973	c.1845T>C	c.(1843-1845)ccT>ccC	p.P615P	C9orf84_ENST00000394779.3_Silent_p.P576P|C9orf84_ENST00000394777.4_Silent_p.P576P|C9orf84_ENST00000374287.3_Silent_p.P615P	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	615										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						AATTAGCAGTAGGGAGGGTAC	0.403													A|||	719	0.14357	0.1422	0.196	5008	,	,		15905	0.0278		0.2286	False		,,,				2504	0.1401				p.P615P		Atlas-SNP	.											.	C9orf84	207	.	0			c.T1845C						PASS	.	A	,	770,3636	312.5+/-292.6	67,636,1500	109.0	106.0	107.0		1728,1845	3.3	0.6	9	dbSNP_120	107	1995,6605	348.2+/-326.9	228,1539,2533	no	coding-synonymous,coding-synonymous	C9orf84	NM_001080551.1,NM_173521.3	,	295,2175,4033	GG,GA,AA		23.1977,17.4762,21.2594	,	576/1406,615/1445	114484783	2765,10241	2203	4300	6503	SO:0001819	synonymous_variant	158401	exon13			AGCAGTAGGGAGG	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.1845T>C	9.37:g.114484783A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	37	CCDS6781.3																																																																																			A|0.817;G|0.183	0.183	strong		0.403	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157224	26157224	+	Silent	SNP	G	G	A	rs147799648	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26157224G>A	ENST00000304218.3	+	1	666	c.606G>A	c.(604-606)aaG>aaA	p.K202K	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	202					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						CTAAACCAAAGACCGCCAAGC	0.532													G|||	6	0.00119808	0.0023	0.0	5008	,	,		14995	0.0		0.002	False		,,,				2504	0.001				p.K202K		Atlas-SNP	.											HIST1H1E,NS,lymphoid_neoplasm,+2,1	HIST1H1E	69	1	0			c.G606A						scavenged	.	G		0,4402		0,0,2201	32.0	33.0	33.0		606	1.7	0.1	6	dbSNP_134	33	6,8592		0,6,4293	no	coding-synonymous	HIST1H1E	NM_005321.2		0,6,6494	AA,AG,GG		0.0698,0.0,0.0462		202/220	26157224	6,12994	2201	4299	6500	SO:0001819	synonymous_variant	3008	exon1			ACCAAAGACCGCC	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.606G>A	6.37:g.26157224G>A		Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	74	7	0.0945946	NM_005321	Q4VB25	Silent	SNP	ENST00000304218.3	37	CCDS4586.1																																																																																			G|0.999;A|0.001	0.001	strong		0.532	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
ENTPD7	57089	hgsc.bcm.edu	37	10	101451194	101451194	+	Silent	SNP	A	A	C	rs72832512	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101451194A>C	ENST00000370489.4	+	8	940	c.762A>C	c.(760-762)gtA>gtC	p.V254V		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	254						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		GAAGGACAGTAGGGATACTGG	0.428													A|||	80	0.0159744	0.0023	0.013	5008	,	,		16832	0.001		0.0338	False		,,,				2504	0.0337				p.V254V		Atlas-SNP	.											.	ENTPD7	44	.	0			c.A762C						PASS	.	A		25,4381	31.7+/-61.6	0,25,2178	111.0	102.0	105.0		762	-0.1	1.0	10	dbSNP_130	105	314,8286	111.8+/-172.0	6,302,3992	no	coding-synonymous	ENTPD7	NM_020354.3		6,327,6170	CC,CA,AA		3.6512,0.5674,2.6065		254/605	101451194	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	57089	exon8			GACAGTAGGGATA	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.762A>C	10.37:g.101451194A>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_020354	B2RB83|B3KP21|D3DR64	Silent	SNP	ENST00000370489.4	37	CCDS7480.1																																																																																			A|0.978;C|0.022	0.022	strong		0.428	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
NDUFAF2	91942	hgsc.bcm.edu	37	5	60241142	60241142	+	Silent	SNP	G	G	A	rs158921	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:60241142G>A	ENST00000296597.5	+	1	187	c.60G>A	c.(58-60)aaG>aaA	p.K20K	ERCC8_ENST00000543101.1_5'Flank|ERCC8_ENST00000265038.5_5'Flank|NDUFAF2_ENST00000511107.1_Silent_p.K20K|ERCC8_ENST00000426742.2_5'Flank	NM_174889.4	NP_777549.1	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 2	20					negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)	mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|ovary(1)	6		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				GGGAAGTGAAGGAGCACGTGG	0.597													G|||	3470	0.692891	0.6074	0.6974	5008	,	,		18298	0.9484		0.5696	False		,,,				2504	0.6687				p.K20K		Atlas-SNP	.											.	NDUFAF2	10	.	0			c.G60A						PASS	.						77.0	65.0	69.0					5																	60241142		2203	4298	6501	SO:0001819	synonymous_variant	91942	exon1			AGTGAAGGAGCAC	AB183433	CCDS3979.1	5q12.1	2012-10-12	2012-05-08	2008-02-15	ENSG00000164182	ENSG00000164182		"""Mitochondrial respiratory chain complex assembly factors"""	28086	protein-coding gene	gene with protein product	"""Myc-induced mitochondrial protein"""	609653	"""NDUFA12-like"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 2"""	NDUFA12L		15774466, 16200211, 17383918	Standard	NM_174889		Approved	B17.2L, MMTN, mimitin	uc003jsp.4	Q8N183	OTTHUMG00000131221	ENST00000296597.5:c.60G>A	5.37:g.60241142G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	136	103	0.757353	NM_174889	A8K5I1	Silent	SNP	ENST00000296597.5	37	CCDS3979.1																																																																																			.	.	weak		0.597	NDUFAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253965.1	NM_174889	
SMG6	23293	hgsc.bcm.edu	37	17	2203025	2203025	+	Missense_Mutation	SNP	T	T	G	rs1885987	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2203025T>G	ENST00000263073.6	-	2	1072	c.1022A>C	c.(1021-1023)aAc>aCc	p.N341T	SMG6_ENST00000544865.1_Missense_Mutation_p.N310T	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	341	Interaction with telomeric DNA.		N -> T (in dbSNP:rs1885987). {ECO:0000269|PubMed:12676087, ECO:0000269|PubMed:9872452}.		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTTAGCACTGTTTTTCTGCTC	0.473													T|||	1149	0.229433	0.0469	0.438	5008	,	,		19830	0.1716		0.3827	False		,,,				2504	0.2301				p.N341T	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											SMG6,NS,carcinoma,+1,1	SMG6	97	1	0			c.A1022C						PASS	.	T	THR/ASN,THR/ASN	414,3992	201.5+/-224.5	24,366,1813	132.0	115.0	121.0		929,1022	2.3	1.0	17	dbSNP_92	121	3325,5275	492.6+/-373.4	640,2045,1615	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	65,65	664,2411,3428	GG,GT,TT		38.6628,9.3963,28.7483	benign,benign	310/1389,341/1420	2203025	3739,9267	2203	4300	6503	SO:0001583	missense	23293	exon2			GCACTGTTTTTCT	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.1022A>C	17.37:g.2203025T>G	ENSP00000263073:p.Asn341Thr	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	247	124	0.502024	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	569	0.26053113553113555	30	0.06097560975609756	162	0.44751381215469616	99	0.17307692307692307	278	0.36675461741424803	T	8.744	0.919722	0.17982	0.093963	0.386628	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.07908	3.15;3.15	5.35	2.3	0.28687	.	0.902977	0.09887	N	0.742929	T	0.00012	0.0000	N	0.08118	0	0.46279	P	0.0010320000000000329	B	0.06786	0.001	B	0.09377	0.004	T	0.43426	-0.9392	9	0.21540	T	0.41	-2.6793	10.1357	0.42706	0.0:0.7847:0.0:0.2153	rs1885987;rs56772408;rs1885987	341	Q86US8	EST1A_HUMAN	T	341;310	ENSP00000263073:N341T;ENSP00000443920:N310T	ENSP00000263073:N341T	N	-	2	0	SMG6	2149775	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.302000	0.51849	0.252000	0.21531	-0.146000	0.13790	AAC	T|0.736;G|0.264	0.264	strong		0.473	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
PRX	57716	hgsc.bcm.edu	37	19	40901496	40901496	+	Missense_Mutation	SNP	T	T	C	rs268673	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40901496T>C	ENST00000324001.7	-	7	3033	c.2763A>G	c.(2761-2763)atA>atG	p.I921M	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	921			I -> M (in dbSNP:rs268673). {ECO:0000269|PubMed:11133365}.		axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CTTTTGTCTCTATCATCTCCA	0.577													C|||	1486	0.296725	0.3071	0.3833	5008	,	,		18355	0.1885		0.3767	False		,,,				2504	0.2505				p.I921M		Atlas-SNP	.											.	PRX	151	.	0			c.A2763G						PASS	.	C	,MET/ILE	1428,2978	683.5+/-404.3	254,920,1029	75.0	86.0	82.0		,2763	-5.4	0.0	19	dbSNP_79	82	3336,5264	642.8+/-399.9	633,2070,1597	yes	utr-3,missense	PRX	NM_020956.2,NM_181882.2	,10	887,2990,2626	CC,CT,TT		38.7907,32.4103,36.6292	,benign	,921/1462	40901496	4764,8242	2203	4300	6503	SO:0001583	missense	57716	exon7			TGTCTCTATCATC	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.2763A>G	19.37:g.40901496T>C	ENSP00000326018:p.Ile921Met	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_181882	Q9BXL9|Q9HCF2	Missense_Mutation	SNP	ENST00000324001.7	37	CCDS33028.1	683	0.31272893772893773	153	0.31097560975609756	158	0.43646408839779005	93	0.16258741258741258	279	0.36807387862796836	C	1.471	-0.559849	0.03967	0.324103	0.387907	ENSG00000105227	ENST00000324001;ENST00000341562	T	0.03094	4.05	5.2	-5.36	0.02689	.	2.289120	0.01899	N	0.039096	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.9999999999480482	B	0.02656	0.0	B	0.01281	0.0	T	0.46428	-0.9192	9	0.29301	T	0.29	7.6947	8.8913	0.35434	0.1258:0.2674:0.0:0.6068	rs268673;rs60675249;rs268673	921	Q9BXM0	PRAX_HUMAN	M	921	ENSP00000326018:I921M	ENSP00000326018:I921M	I	-	3	3	PRX	45593336	0.000000	0.05858	0.003000	0.11579	0.076000	0.17211	-2.763000	0.00784	-0.939000	0.03709	-0.215000	0.12644	ATA	T|0.669;C|0.331	0.331	strong		0.577	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
DNAH12	201625	hgsc.bcm.edu	37	3	57414097	57414097	+	Missense_Mutation	SNP	T	T	A	rs17793014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:57414097T>A	ENST00000351747.2	-	35	5442	c.5262A>T	c.(5260-5262)aaA>aaT	p.K1754N		NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	1754			K -> N (in dbSNP:rs17793014).		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(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GAGGCACATATTTAAAATAAT	0.259													T|||	1189	0.23742	0.1157	0.2651	5008	,	,		17345	0.0853		0.4423	False		,,,				2504	0.3282				p.K1754N		Atlas-SNP	.											.	DNAH12	182	.	0			c.A5262T						PASS	.						10.0	10.0	10.0					3																	57414097		692	1562	2254	SO:0001583	missense	201625	exon35			CACATATTTAAAA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.5262A>T	3.37:g.57414097T>A	ENSP00000295937:p.Lys1754Asn	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		581	0.266025641025641	77	0.1565040650406504	110	0.30386740331491713	42	0.07342657342657342	352	0.46437994722955145	T	3.072	-0.190912	0.06299	.	.	ENSG00000174844	ENST00000351747	T	0.20738	2.05	3.21	-2.61	0.06171	.	.	.	.	.	T	0.00012	0.0000	N	0.20986	0.625	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.48811	-0.9002	8	0.23302	T	0.38	.	3.1973	0.06637	0.1889:0.3487:0.0:0.4624	rs17793014;rs17793014	1754	Q6ZR08	DYH12_HUMAN	N	1754	ENSP00000295937:K1754N	ENSP00000295937:K1754N	K	-	3	2	DNAH12	57389137	0.145000	0.22656	0.001000	0.08648	0.019000	0.09904	0.906000	0.28517	-0.524000	0.06400	-1.542000	0.00909	AAA	T|0.739;A|0.261	0.261	strong		0.259	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
DCAF16	54876	hgsc.bcm.edu	37	4	17805379	17805379	+	Missense_Mutation	SNP	G	G	A	rs7690457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:17805379G>A	ENST00000382247.1	-	3	1446	c.386C>T	c.(385-387)aCa>aTa	p.T129I	DCAF16_ENST00000536863.1_Missense_Mutation_p.T129I|DCAF16_ENST00000507768.1_5'Flank	NM_017741.3	NP_060211.3	Q9NXF7	DCA16_HUMAN	DDB1 and CUL4 associated factor 16	129			T -> I (in dbSNP:rs7690457).		protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				cervix(1)|endometrium(1)|lung(2)|ovary(1)	5						GCTGGGACTTGTAAGAGGCTT	0.507													G|||	580	0.115815	0.2648	0.0259	5008	,	,		17963	0.1002		0.0249	False		,,,				2504	0.0879				p.T129I		Atlas-SNP	.											.	DCAF16	19	.	0			c.C386T						PASS	.	G	ILE/THR	978,3428	366.6+/-317.9	109,760,1334	145.0	154.0	151.0		386	-7.8	0.0	4	dbSNP_116	151	251,8349	99.3+/-160.8	1,249,4050	yes	missense	DCAF16	NM_017741.3	89	110,1009,5384	AA,AG,GG		2.9186,22.197,9.4495	benign	129/217	17805379	1229,11777	2203	4300	6503	SO:0001583	missense	54876	exon3			GGACTTGTAAGAG	AK000287	CCDS3423.1	4p15.32	2009-07-17	2009-07-17	2009-07-17	ENSG00000163257	ENSG00000163257		"""DDB1 and CUL4 associated factors"""	25987	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 30"""	C4orf30		12477932	Standard	XM_005248169		Approved	FLJ20280	uc003gpn.3	Q9NXF7	OTTHUMG00000128536	ENST00000382247.1:c.386C>T	4.37:g.17805379G>A	ENSP00000371682:p.Thr129Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	155	67	0.432258	NM_017741	B3KPB7	Missense_Mutation	SNP	ENST00000382247.1	37	CCDS3423.1	228	0.1043956043956044	140	0.2845528455284553	10	0.027624309392265192	57	0.09965034965034965	21	0.027704485488126648	G	10.28	1.307852	0.23821	0.22197	0.029186	ENSG00000163257	ENST00000382247;ENST00000536863	T;T	0.32272	1.46;1.46	3.91	-7.81	0.01210	.	.	.	.	.	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	0.38607	-0.9653	8	0.87932	D	0	5.3752	1.8409	0.03150	0.4934:0.1097:0.1651:0.2318	rs7690457;rs52827649;rs57652056;rs7690457	129	Q9NXF7	DCA16_HUMAN	I	129	ENSP00000371682:T129I;ENSP00000445736:T129I	ENSP00000371682:T129I	T	-	2	0	DCAF16	17414477	0.063000	0.20901	0.001000	0.08648	0.903000	0.53119	-1.319000	0.02702	-2.132000	0.00814	-0.367000	0.07326	ACA	G|0.893;A|0.107	0.107	strong		0.507	DCAF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250371.1	NM_017741	
MMP8	4317	hgsc.bcm.edu	37	11	102593248	102593248	+	Missense_Mutation	SNP	T	T	C	rs1940475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102593248T>C	ENST00000236826.3	-	2	357	c.259A>G	c.(259-261)Aaa>Gaa	p.K87E		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	87			K -> E (in dbSNP:rs1940475). {ECO:0000269|Ref.2}.		collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	CGAGGCTTTTTCATCATGTCC	0.453													T|||	3005	0.60004	0.7095	0.5173	5008	,	,		21446	0.5685		0.5467	False		,,,				2504	0.5982				p.K87E		Atlas-SNP	.											MMP8,face,malignant_melanoma,+2,1	MMP8	68	1	0			c.A259G						PASS	.	T	GLU/LYS	2849,1557	669.7+/-402.2	919,1011,273	166.0	158.0	161.0		259	-6.1	0.0	11	dbSNP_92	161	4348,4250	579.6+/-390.9	1099,2150,1050	yes	missense	MMP8	NM_002424.2	56	2018,3161,1323	CC,CT,TT		49.4301,35.3382,44.6555	benign	87/468	102593248	7197,5807	2203	4299	6502	SO:0001583	missense	4317	exon2			GCTTTTTCATCAT	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.259A>G	11.37:g.102593248T>C	ENSP00000236826:p.Lys87Glu	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	310	308	0.993548	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	1288|1288	0.5897435897435898|0.5897435897435898	355|355	0.7215447154471545|0.7215447154471545	195|195	0.5386740331491713|0.5386740331491713	340|340	0.5944055944055944|0.5944055944055944	398|398	0.525065963060686|0.525065963060686	T|T	14.71|14.71	2.615422|2.615422	0.46631|0.46631	0.646618|0.646618	0.505699|0.505699	ENSG00000118113|ENSG00000118113	ENST00000438475|ENST00000236826;ENST00000544383;ENST00000534942	.|T	.|0.30714	.|1.52	5.73|5.73	-6.06|-6.06	0.02165|0.02165	.|Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1);	.|1.456970	.|0.04177	.|N	.|0.325809	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43701|0.43701	1.375|1.375	0.53688|0.53688	P|P	2.4000000000024002E-5|2.4000000000024002E-5	.|B;B	.|0.14438	.|0.001;0.01	.|B;B	.|0.17098	.|0.017;0.009	T|T	0.40664|0.40664	-0.9551|-0.9551	4|9	.|0.40728	.|T	.|0.16	.|.	12.0951|12.0951	0.53750|0.53750	0.0:0.2066:0.0998:0.6936|0.0:0.2066:0.0998:0.6936	rs1940475;rs52827903;rs59499834;rs1940475|rs1940475;rs52827903;rs59499834;rs1940475	.|22;87	.|F5GXB5;P22894	.|.;MMP8_HUMAN	G|E	62|87;64;22	.|ENSP00000236826:K87E	.|ENSP00000236826:K87E	E|K	-|-	2|1	0|0	MMP8|MMP8	102098458|102098458	0.003000|0.003000	0.15002|0.15002	0.001000|0.001000	0.08648|0.08648	0.763000|0.763000	0.43281|0.43281	-0.023000|-0.023000	0.12456|0.12456	-1.123000|-1.123000	0.02940|0.02940	-0.242000|-0.242000	0.12053|0.12053	GAA|AAA	T|0.417;C|0.583	0.583	strong		0.453	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
KRT14	3861	hgsc.bcm.edu	37	17	39742894	39742894	+	Silent	SNP	G	G	A	rs3826551	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39742894G>A	ENST00000167586.6	-	1	279	c.193C>T	c.(193-195)Ctg>Ttg	p.L65L		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	65	Head.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)	p.L65L(2)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				CCGCCCCCCAGCCCGCAGGCT	0.692													G|||	3409	0.680711	0.4788	0.7248	5008	,	,		13759	0.9425		0.5855	False		,,,				2504	0.7505				p.L65L		Atlas-SNP	.											KRT14,NS,carcinoma,0,3	KRT14	65	3	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(1)|prostate(1)	c.C193T						PASS	.	G		2041,2323		501,1039,642	23.0	29.0	27.0		193	-6.8	0.5	17	dbSNP_107	27	4639,3895		1302,2035,930	no	coding-synonymous	KRT14	NM_000526.4		1803,3074,1572	AA,AG,GG		45.641,46.769,48.209		65/473	39742894	6680,6218	2182	4267	6449	SO:0001819	synonymous_variant	3861	exon1			CCCCCAGCCCGCA	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.193C>T	17.37:g.39742894G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	30	20	0.666667	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Silent	SNP	ENST00000167586.6	37	CCDS11400.1																																																																																			G|0.454;A|0.546	0.546	strong		0.692	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
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 GAIIx	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_ENST00000522826.1_Missense_Mutation_p.R853H|ENPP2_ENST00000427067.2_Missense_Mutation_p.R849H|ENPP2_ENST00000522167.1_Missense_Mutation_p.R463H|ENPP2_ENST00000259486.6_Missense_Mutation_p.R880H	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	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	5	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		
OBSCN	84033	hgsc.bcm.edu	37	1	228486404	228486404	+	Intron	SNP	C	C	T	rs56021350	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228486404C>T	ENST00000422127.1	+	43	11703				OBSCN_ENST00000284548.11_Intron|OBSCN_ENST00000359599.6_3'UTR|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000366707.4_Missense_Mutation_p.T1089M|OBSCN_ENST00000570156.2_Missense_Mutation_p.T4399M	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACCTCGGCCACGCTCACTGTC	0.547													C|||	831	0.165935	0.1982	0.2378	5008	,	,		21966	0.1518		0.1581	False		,,,				2504	0.0941				p.T4399M		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	0			c.C13196T						scavenged	.	C	,	402,1350		37,328,511	99.0	84.0	89.0		,	-4.7	0.0	1	dbSNP_129	89	712,3270		62,588,1341	no	intron,intron	OBSCN	NM_001098623.1,NM_052843.2	,	99,916,1852	TT,TC,CC		17.8805,22.9452,19.428	,	,	228486404	1114,4620	876	1991	2867	SO:0001627	intron_variant	84033	exon49			CGGCCACGCTCAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11659+3660C>T	1.37:g.228486404C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	12	4	0.333333	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	380	0.17399267399267399	86	0.17479674796747968	85	0.23480662983425415	87	0.1520979020979021	122	0.16094986807387862	C	8.711	0.911956	0.17907	0.229452	0.178805	ENSG00000154358	ENST00000366707	T	0.68903	-0.36	4.68	-4.67	0.03319	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.24119	-1.0169	5	0.33940	T	0.23	.	12.6558	0.56786	0.0:0.3898:0.0:0.6102	rs56021350;rs61825284	.	.	.	M	1089	ENSP00000355668:T1089M	ENSP00000355668:T1089M	T	+	2	0	OBSCN	226553027	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.459000	0.01000	-1.387000	0.02095	-0.254000	0.11334	ACG	C|0.825;T|0.175	0.175	strong		0.547	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
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 GAIIx	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	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	211	108	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	
FOXQ1	94234	hgsc.bcm.edu	37	6	1313470	1313470	+	Silent	SNP	C	C	T	rs4435985	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:1313470C>T	ENST00000296839.2	+	1	796	c.531C>T	c.(529-531)ttC>ttT	p.F177F		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	177					hair follicle morphogenesis (GO:0031069)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|urinary_tract(1)	2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)		ACGACTGCTTCGTCAAGGTGC	0.622													C|||	956	0.190895	0.1241	0.1167	5008	,	,		7348	0.2986		0.2048	False		,,,				2504	0.2086				p.F177F		Atlas-SNP	.											FOXQ1,NS,carcinoma,0,1	FOXQ1	8	1	0			c.C531T						PASS	.	C		619,3785		37,545,1620	43.0	45.0	44.0		531	3.8	1.0	6	dbSNP_111	44	1699,6897		159,1381,2758	no	coding-synonymous	FOXQ1	NM_033260.3		196,1926,4378	TT,TC,CC		19.765,14.0554,17.8308		177/404	1313470	2318,10682	2202	4298	6500	SO:0001819	synonymous_variant	94234	exon1			CTGCTTCGTCAAG	AF153341	CCDS4471.1	6p25	2008-02-05			ENSG00000164379	ENSG00000164379		"""Forkhead boxes"""	20951	protein-coding gene	gene with protein product		612788				11747606, 12011061	Standard	NM_033260		Approved	HFH1	uc003mtl.4	Q9C009	OTTHUMG00000016160	ENST00000296839.2:c.531C>T	6.37:g.1313470C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	111	16	0.144144	NM_033260	Q9NS06	Silent	SNP	ENST00000296839.2	37	CCDS4471.1																																																																																			C|0.811;T|0.189	0.189	strong		0.622	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	NM_033260	
SRRM4	84530	hgsc.bcm.edu	37	12	119588962	119588962	+	Missense_Mutation	SNP	G	G	A	rs2723880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:119588962G>A	ENST00000267260.4	+	10	1605	c.1217G>A	c.(1216-1218)cGa>cAa	p.R406Q		NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	406	Ser-rich.		R -> Q (in dbSNP:rs2723880).		cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CACTCGTCCCGATCCCCAAAT	0.567													G|||	1228	0.245208	0.1641	0.3804	5008	,	,		18490	0.1468		0.3966	False		,,,				2504	0.2045				p.R406Q		Atlas-SNP	.											.	SRRM4	131	.	0			c.G1217A						PASS	.	G	GLN/ARG	689,3221		60,569,1326	78.0	82.0	81.0		1217	2.6	1.0	12	dbSNP_100	81	3203,5087		615,1973,1557	yes	missense	SRRM4	NM_194286.3	43	675,2542,2883	AA,AG,GG		38.6369,17.6215,31.9016	possibly-damaging	406/612	119588962	3892,8308	1955	4145	6100	SO:0001583	missense	84530	exon10			CGTCCCGATCCCC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.1217G>A	12.37:g.119588962G>A	ENSP00000267260:p.Arg406Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	41	0.61194	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	602	0.27564102564102566	74	0.15040650406504066	139	0.3839779005524862	80	0.13986013986013987	309	0.4076517150395778	G	22.3	4.265032	0.80358	0.176215	0.386369	ENSG00000139767	ENST00000267260	T	0.25250	1.81	5.58	2.63	0.31362	.	0.488214	0.18593	N	0.136681	T	0.00012	0.0000	L	0.40543	1.245	0.49798	P	1.7500000000003624E-4	B	0.24132	0.098	B	0.12837	0.008	T	0.47169	-0.9138	8	.	.	.	-0.6904	3.8042	0.08770	0.1511:0.1305:0.5842:0.1342	rs2723880;rs52812470;rs59964857;rs2723880	406	A7MD48	SRRM4_HUMAN	Q	406	ENSP00000267260:R406Q	.	R	+	2	0	SRRM4	118073345	0.270000	0.24152	0.970000	0.41538	0.964000	0.63967	0.685000	0.25378	1.489000	0.48450	0.655000	0.94253	CGA	G|0.714;A|0.286	0.286	strong		0.567	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
PCK1	5105	hgsc.bcm.edu	37	20	56137798	56137798	+	Silent	SNP	G	G	A	rs1062600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:56137798G>A	ENST00000319441.4	+	4	617	c.453G>A	c.(451-453)tcG>tcA	p.S151S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Silent_p.S19S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	151					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CGCTGGGCTCGCCTCTGTCAA	0.607													G|||	1478	0.295128	0.3101	0.3141	5008	,	,		17801	0.0308		0.4732	False		,,,				2504	0.3507				p.S151S		Atlas-SNP	.											.	PCK1	95	.	0			c.G453A						PASS	.	G		1415,2991	464.0+/-353.7	204,1007,992	65.0	53.0	57.0		453	-10.3	0.2	20	dbSNP_86	57	3953,4647	548.9+/-385.4	894,2165,1241	no	coding-synonymous	PCK1	NM_002591.3		1098,3172,2233	AA,AG,GG		45.9651,32.1153,41.2733		151/623	56137798	5368,7638	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon4			GGGCTCGCCTCTG		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.453G>A	20.37:g.56137798G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			G|0.633;A|0.367	0.367	strong		0.607	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
MRC2	9902	hgsc.bcm.edu	37	17	60769803	60769803	+	Silent	SNP	A	A	G	rs3826537	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:60769803A>G	ENST00000303375.5	+	30	4833	c.4431A>G	c.(4429-4431)caA>caG	p.Q1477Q	MRC2_ENST00000446119.2_Silent_p.Q343Q	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1477					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						TGAATGAGCAACAAGAATAGA	0.657													G|||	1675	0.334465	0.1944	0.4193	5008	,	,		16751	0.3135		0.4085	False		,,,				2504	0.409				p.Q1477Q		Atlas-SNP	.											.	MRC2	126	.	0			c.A4431G						PASS	.	G		941,3379		128,685,1347	16.0	19.0	18.0		4431	4.2	1.0	17	dbSNP_107	18	3396,5086		759,1878,1604	no	coding-synonymous	MRC2	NM_006039.3		887,2563,2951	GG,GA,AA		40.0377,21.7824,33.8775		1477/1480	60769803	4337,8465	2160	4241	6401	SO:0001819	synonymous_variant	9902	exon30			TGAGCAACAAGAA	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.4431A>G	17.37:g.60769803A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	37	CCDS11634.1																																																																																			A|0.680;G|0.320	0.320	strong		0.657	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
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 GAIIx	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_ENST00000497989.1_Missense_Mutation_p.K394R|INTS6_ENST00000398119.2_Missense_Mutation_p.K559R|INTS6_ENST00000463928.1_Intron	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	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	87	26	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	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121513561	121513561	+	Missense_Mutation	SNP	T	T	G	rs740965	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:121513561T>G	ENST00000393386.2	+	1	419	c.8T>G	c.(7-9)aTc>aGc	p.I3S	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.I3S	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	3			I -> S (in dbSNP:rs740965).		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						GAAATGCGAATCCTAAAGCGT	0.567													T|||	815	0.16274	0.0136	0.2305	5008	,	,		13339	0.3026		0.1243	False		,,,				2504	0.2117				p.I3S		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T8G						PASS	.	T	SER/ILE,SER/ILE,SER/ILE	192,4214	121.3+/-158.8	3,186,2014	98.0	92.0	94.0		8,8,8	-2.7	0.0	7	dbSNP_86	94	1317,7283	260.9+/-283.5	104,1109,3087	yes	missense,missense,missense	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	142,142,142	107,1295,5101	GG,GT,TT		15.314,4.3577,11.6023	probably-damaging,probably-damaging,probably-damaging	3/1456,3/1449,3/2316	121513561	1509,11497	2203	4300	6503	SO:0001583	missense	5803	exon1			TGCGAATCCTAAA	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.8T>G	7.37:g.121513561T>G	ENSP00000377047:p.Ile3Ser	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	351	0.16071428571428573	11	0.022357723577235773	74	0.20441988950276244	179	0.3129370629370629	87	0.11477572559366754	T	12.81	2.049157	0.36181	0.043577	0.15314	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.52983	0.65;0.64	4.27	-2.66	0.06077	.	2.658710	0.02120	N	0.055569	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.17038	0.008;0.02	B;B	0.15052	0.005;0.012	T	0.32241	-0.9914	9	0.87932	D	0	.	4.6046	0.12371	0.1552:0.3918:0.0:0.453	rs740965;rs1050503;rs3190831;rs740965	3;3	C9JFM0;P23471	.;PTPRZ_HUMAN	S	3	ENSP00000377047:I3S;ENSP00000410000:I3S	ENSP00000377047:I3S	I	+	2	0	PTPRZ1	121300797	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.488000	0.22371	-0.449000	0.07117	-0.516000	0.04426	ATC	T|0.868;G|0.132	0.132	strong		0.567	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
HTT	3064	hgsc.bcm.edu	37	4	3234980	3234980	+	Missense_Mutation	SNP	G	G	A	rs362272	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:3234980G>A	ENST00000355072.5	+	61	8501	c.8356G>A	c.(8356-8358)Gtc>Atc	p.V2786I	HTT_ENST00000513806.1_Intron	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2786			V -> I (in dbSNP:rs362272). {ECO:0000269|PubMed:7903579}.		anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CCTGCACGGCGTCCTCTATGT	0.642													G|||	1053	0.210264	0.0106	0.2867	5008	,	,		19312	0.3185		0.3091	False		,,,				2504	0.2127				p.V2786I		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	1	0			c.G8356A						PASS	.	G	ILE/VAL	285,3955		18,249,1853	94.0	107.0	103.0		8356	-4.2	0.0	4	dbSNP_79	103	2508,5958		359,1790,2084	yes	missense	HTT	NM_002111.6	29	377,2039,3937	AA,AG,GG		29.6244,6.7217,21.9817	benign	2786/3143	3234980	2793,9913	2120	4233	6353	SO:0001583	missense	3064	exon61			CACGGCGTCCTCT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.8356G>A	4.37:g.3234980G>A	ENSP00000347184:p.Val2786Ile	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	107	34	0.317757	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	539	0.2467948717948718	6	0.012195121951219513	110	0.30386740331491713	179	0.3129370629370629	244	0.32189973614775724	G	5.633	0.301421	0.10678	0.067217	0.296244	ENSG00000197386	ENST00000355072	T	0.65549	-0.16	5.08	-4.25	0.03766	.	0.893841	0.09733	N	0.762867	T	0.00012	0.0000	N	0.10874	0.06	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.26815	-1.0092	9	0.06365	T	0.9	.	12.9961	0.58648	0.6315:0.0:0.3685:0.0	rs362272;rs2229986;rs59711124;rs362272	2786	P42858	HD_HUMAN	I	2786	ENSP00000347184:V2786I	ENSP00000347184:V2786I	V	+	1	0	HTT	3204778	0.646000	0.27295	0.006000	0.13384	0.820000	0.46376	1.389000	0.34453	-0.795000	0.04462	-0.487000	0.04747	GTC	G|0.759;T|0.008	.	strong		0.642	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18195348	18195348	+	Missense_Mutation	SNP	C	C	T	rs11024532	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18195348C>T	ENST00000314254.3	+	1	965	c.545C>T	c.(544-546)gCg>gTg	p.A182V	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	182			A -> V (in dbSNP:rs11024532). {ECO:0000269|PubMed:11850634, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						ATCCCAGTCGCGTGGCTGATT	0.512													C|||	636	0.126997	0.0461	0.1441	5008	,	,		20406	0.0347		0.2644	False		,,,				2504	0.1779				p.A182V		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.C545T						PASS	.	C	VAL/ALA	389,4009	193.6+/-218.7	12,365,1822	210.0	199.0	203.0		545	-0.4	0.0	11	dbSNP_120	203	2493,6093	409.6+/-349.9	390,1713,2190	yes	missense	MRGPRX4	NM_054032.3	64	402,2078,4012	TT,TC,CC		29.0356,8.8449,22.1965	benign	182/323	18195348	2882,10102	2199	4293	6492	SO:0001583	missense	117196	exon1			CAGTCGCGTGGCT	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.545C>T	11.37:g.18195348C>T	ENSP00000314042:p.Ala182Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Missense_Mutation	SNP	ENST00000314254.3	37	CCDS7831.1	307	0.14056776556776557	28	0.056910569105691054	61	0.1685082872928177	17	0.02972027972027972	201	0.26517150395778366	C	10.12	1.263710	0.23136	0.088449	0.290356	ENSG00000179817	ENST00000314254	T	0.33865	1.39	2.85	-0.447	0.12234	GPCR, rhodopsin-like superfamily (1);	1.195330	0.05937	N	0.636357	T	0.00012	0.0000	L	0.28740	0.885	0.80722	P	0.0	B	0.24963	0.115	B	0.28385	0.089	T	0.37888	-0.9686	9	0.30854	T	0.27	.	3.211	0.06682	0.0:0.4219:0.2751:0.303	rs11024532;rs52828189;rs58386901;rs11024532	182	Q96LA9	MRGX4_HUMAN	V	182	ENSP00000314042:A182V	ENSP00000314042:A182V	A	+	2	0	MRGPRX4	18151924	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.465000	0.06680	0.074000	0.16767	-0.573000	0.04149	GCG	C|0.817;T|0.183	0.183	strong		0.512	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
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 GAIIx	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_ENST00000435683.2_Missense_Mutation_p.R1315C|ABCA7_ENST00000433129.1_Missense_Mutation_p.R1453C	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	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	39	20	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	
OR2T29	343563	hgsc.bcm.edu	37	1	248722624	248722624	+	Missense_Mutation	SNP	C	C	T	rs200919674	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248722624C>T	ENST00000328570.3	-	1	173	c.169G>A	c.(169-171)Gcc>Acc	p.A57T	RP11-438F14.3_ENST00000438623.1_RNA	NM_001004694.2	NP_001004694.2	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T, member 29	57						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|lung(4)	5	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)			TGGAGGTGGGCGTCACAGTGT	0.483													.|||	1468	0.293131	0.3578	0.2277	5008	,	,		22185	0.3462		0.2217	False		,,,				2504	0.271				p.A57T		Atlas-SNP	.											.	OR2T29	8	.	0			c.G169A						PASS	.						9.0	6.0	7.0					1																	248722624		2006	3595	5601	SO:0001583	missense	343563	exon1			GGTGGGCGTCACA		CCDS55695.1	1q44	2012-08-09			ENSG00000182783	ENSG00000182783		"""GPCR / Class A : Olfactory receptors"""	31253	protein-coding gene	gene with protein product							Standard	NM_001004694		Approved		uc001ieo.2	Q8NH02	OTTHUMG00000040382	ENST00000328570.3:c.169G>A	1.37:g.248722624C>T	ENSP00000331774:p.Ala57Thr	Somatic	480	0	0		WXS	Illumina HiSeq	Phase_I	482	89	0.184647	NM_001004694		Missense_Mutation	SNP	ENST00000328570.3	37	CCDS55695.1	.	.	.	.	.	.	.	.	.	.	c	0.005	-2.123857	0.00346	.	.	ENSG00000182783	ENST00000328570	T	0.00438	7.42	2.73	-4.97	0.03029	GPCR, rhodopsin-like superfamily (1);	1.038830	0.07667	N	0.934741	T	0.00144	0.0004	N	0.05351	-0.065	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.23726	-1.0180	9	0.07325	T	0.83	.	5.7058	0.17907	0.0:0.25:0.1673:0.5827	.	57	Q8NH02	O2T29_HUMAN	T	57	ENSP00000331774:A57T	ENSP00000331774:A57T	A	-	1	0	OR2T29	246789247	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-3.088000	0.00610	-0.784000	0.04528	-2.687000	0.00140	GCC	C|0.250;T|0.750	0.750	weak		0.483	OR2T29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097132.1	NM_001004694	
FAT2	2196	hgsc.bcm.edu	37	5	150905398	150905398	+	Silent	SNP	C	C	T	rs3734051	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150905398C>T	ENST00000261800.5	-	17	10449	c.10437G>A	c.(10435-10437)ccG>ccA	p.P3479P		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3479	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCCATCCATCCGGGGTCACTC	0.577													C|||	872	0.174121	0.2005	0.196	5008	,	,		19464	0.1319		0.2624	False		,,,				2504	0.0757				p.P3479P		Atlas-SNP	.											FAT2,colon,carcinoma,-1,2	FAT2	465	2	0			c.G10437A						PASS	.	C		900,3506	345.7+/-308.6	90,720,1393	81.0	74.0	76.0		10437	-4.5	1.0	5	dbSNP_107	76	2263,6337	383.8+/-340.9	313,1637,2350	no	coding-synonymous	FAT2	NM_001447.2		403,2357,3743	TT,TC,CC		26.314,20.4267,24.3195		3479/4350	150905398	3163,9843	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon17			TCCATCCGGGGTC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10437G>A	5.37:g.150905398C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	477	0.2184065934065934	115	0.23373983739837398	82	0.2265193370165746	87	0.1520979020979021	193	0.2546174142480211	C	9.298	1.052233	0.19827	0.204267	0.26314	ENSG00000086570	ENST00000520200	.	.	.	5.11	-4.53	0.03462	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998391	.	.	.	.	.	.	T	0.38950	-0.9637	3	.	.	.	.	4.0147	0.09639	0.3573:0.2731:0.0:0.3695	rs3734051;rs17404132;rs56590107;rs60495232;rs3734051	.	.	.	R	338	.	.	G	-	1	0	FAT2	150885591	0.296000	0.24398	0.993000	0.49108	0.831000	0.47069	-0.350000	0.07721	-0.238000	0.09724	-1.028000	0.02416	GGA	C|0.776;N|0.000	.	strong		0.577	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
OR1S2	219958	hgsc.bcm.edu	37	11	57970760	57970760	+	Missense_Mutation	SNP	C	C	T	rs200054918		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57970760C>T	ENST00000302592.6	-	1	893	c.894G>A	c.(892-894)atG>atA	p.M298I		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M298I(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGAAGGGGTTCATCATGGGTG	0.468																																					p.M298I		Atlas-SNP	.											OR1S2,NS,carcinoma,0,3	OR1S2	119	3	1	Substitution - Missense(1)	endometrium(1)	c.G894A						scavenged	.						160.0	152.0	155.0					11																	57970760		2201	4296	6497	SO:0001583	missense	219958	exon1			GGGGTTCATCATG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.894G>A	11.37:g.57970760C>T	ENSP00000305469:p.Met298Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	91	7	0.0769231	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.903545	0.33628	.	.	ENSG00000197887	ENST00000302592	T	0.34072	1.38	4.75	1.8	0.24995	GPCR, rhodopsin-like superfamily (1);	1.116300	0.06795	N	0.787733	T	0.30386	0.0763	L	0.33137	0.985	0.26469	N	0.975316	B	0.02656	0.0	B	0.06405	0.002	T	0.34378	-0.9831	10	0.72032	D	0.01	.	10.1183	0.42605	0.0:0.7564:0.0:0.2436	.	298	Q8NGQ3	OR1S2_HUMAN	I	298	ENSP00000305469:M298I	ENSP00000305469:M298I	M	-	3	0	OR1S2	57727336	0.014000	0.17966	0.995000	0.50966	0.993000	0.82548	-0.853000	0.04303	0.694000	0.31654	0.655000	0.94253	ATG	.	.	weak		0.468	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
ANGPTL5	253935	hgsc.bcm.edu	37	11	101765654	101765654	+	Missense_Mutation	SNP	G	G	A	rs77315074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:101765654G>A	ENST00000334289.3	-	8	1398	c.803C>T	c.(802-804)aCg>aTg	p.T268M		NM_178127.4	NP_835228.2	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5	268	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(2)|skin(3)	29		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)		BRCA - Breast invasive adenocarcinoma(274;0.0328)		AAAAAATCTCGTTTCATCCTC	0.313													G|||	106	0.0211661	0.0333	0.0101	5008	,	,		14880	0.006		0.0258	False		,,,				2504	0.0235				p.T268M		Atlas-SNP	.											ANGPTL5,NS,carcinoma,+1,1	ANGPTL5	60	1	0			c.C803T						PASS	.	G	MET/THR	131,4273	92.5+/-131.2	2,127,2073	86.0	88.0	87.0		803	5.4	1.0	11	dbSNP_132	87	262,8334	100.3+/-161.8	2,258,4038	yes	missense	ANGPTL5	NM_178127.4	81	4,385,6111	AA,AG,GG		3.0479,2.9746,3.0231	probably-damaging	268/389	101765654	393,12607	2202	4298	6500	SO:0001583	missense	253935	exon8			AATCTCGTTTCAT	BC049170	CCDS8312.1	11q22.2	2013-02-06				ENSG00000187151		"""Fibrinogen C domain containing"""	19705	protein-coding gene	gene with protein product		607666				12624729	Standard	NM_178127		Approved		uc001pgl.3	Q86XS5		ENST00000334289.3:c.803C>T	11.37:g.101765654G>A	ENSP00000335255:p.Thr268Met	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	161	138	0.857143	NM_178127	A8K658|Q86VR9	Missense_Mutation	SNP	ENST00000334289.3	37	CCDS8312.1	37	0.01694139194139194	5	0.01016260162601626	6	0.016574585635359115	5	0.008741258741258742	21	0.027704485488126648	G	17.78	3.473334	0.63737	0.029746	0.030479	ENSG00000187151	ENST00000334289	D	0.81821	-1.54	5.38	5.38	0.77491	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.203205	0.51477	D	0.000092	T	0.60261	0.2255	L	0.54965	1.715	0.36017	D	0.838453	D	0.54601	0.967	P	0.49332	0.607	T	0.78239	-0.2281	10	0.49607	T	0.09	.	9.1891	0.37189	0.0764:0.1473:0.7763:0.0	.	268	Q86XS5	ANGL5_HUMAN	M	268	ENSP00000335255:T268M	ENSP00000335255:T268M	T	-	2	0	ANGPTL5	101270864	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.037000	0.41174	2.504000	0.84457	0.650000	0.86243	ACG	G|0.973;A|0.027	0.027	strong		0.313	ANGPTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394138.1	NM_178127	
STT3A	3703	hgsc.bcm.edu	37	11	125482982	125482982	+	Silent	SNP	T	T	C	rs34079079	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:125482982T>C	ENST00000529196.1	+	14	1670	c.1464T>C	c.(1462-1464)atT>atC	p.I488I	STT3A_ENST00000531491.1_Silent_p.I396I|STT3A_ENST00000392708.4_Silent_p.I488I			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	488					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|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)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		CTCCGTCCATTGTACTATCTG	0.468													T|||	58	0.0115815	0.003	0.0259	5008	,	,		17622	0.0		0.0338	False		,,,				2504	0.002				p.I488I		Atlas-SNP	.											.	STT3A	52	.	0			c.T1464C						PASS	.	T		27,4375	34.3+/-65.2	0,27,2174	209.0	190.0	197.0		1464	-1.8	1.0	11	dbSNP_126	197	243,8355	98.4+/-159.9	1,241,4057	no	coding-synonymous	STT3A	NM_152713.3		1,268,6231	CC,CT,TT		2.8262,0.6134,2.0769		488/706	125482982	270,12730	2201	4299	6500	SO:0001819	synonymous_variant	3703	exon13			GTCCATTGTACTA	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.1464T>C	11.37:g.125482982T>C		Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	333	282	0.846847	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Silent	SNP	ENST00000529196.1	37	CCDS8458.1																																																																																			T|0.980;C|0.020	0.020	strong		0.468	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
MURC	347273	hgsc.bcm.edu	37	9	103348634	103348634	+	Silent	SNP	G	G	A	rs2780956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:103348634G>A	ENST00000307584.5	+	2	1061	c.996G>A	c.(994-996)agG>agA	p.R332R		NM_001018116.1	NP_001018126.1	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	332					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Z disc (GO:0030018)				endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)	16		Acute lymphoblastic leukemia(62;0.0461)				ATGAAGGAAGGGAAATCCCCA	0.483													G|||	1469	0.293331	0.2405	0.4784	5008	,	,		15010	0.0804		0.4254	False		,,,				2504	0.317				p.R332R		Atlas-SNP	.											.	MURC	43	.	0			c.G996A						PASS	.	G		1353,3053	445.9+/-347.8	209,935,1059	48.0	51.0	50.0		996	3.4	0.2	9	dbSNP_100	50	3583,5017	516.7+/-378.9	729,2125,1446	no	coding-synonymous	MURC	NM_001018116.1		938,3060,2505	AA,AG,GG		41.6628,30.7081,37.9517		332/365	103348634	4936,8070	2203	4300	6503	SO:0001819	synonymous_variant	347273	exon2			AGGAAGGGAAATC	BC090888	CCDS35083.1	9q31.1	2014-09-17			ENSG00000170681	ENSG00000170681			33742	protein-coding gene	gene with protein product	"""muscle-restricted coiled-coil protein"""					18508909, 18332105	Standard	NM_001018116		Approved	cavin-4, CAVIN4	uc004bba.3	Q5BKX8	OTTHUMG00000020368	ENST00000307584.5:c.996G>A	9.37:g.103348634G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_001018116	B1PRL3|B4DT88	Silent	SNP	ENST00000307584.5	37	CCDS35083.1																																																																																			G|0.649;A|0.351	0.351	strong		0.483	MURC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053419.2	NM_001018116	
USP15	9958	hgsc.bcm.edu	37	12	62785663	62785663	+	Silent	SNP	T	T	C	rs11174457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:62785663T>C	ENST00000280377.5	+	17	2359	c.2301T>C	c.(2299-2301)gcT>gcC	p.A767A	USP15_ENST00000353364.3_Silent_p.A738A|USP15_ENST00000393654.3_Silent_p.A742A	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	767	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		AAAATGCTGCTGAGGTAAGTC	0.318													T|||	302	0.0603035	0.0635	0.0836	5008	,	,		15367	0.006		0.0875	False		,,,				2504	0.0675				p.A767A	Melanoma(181;615 2041 39364 49691 50001)	Atlas-SNP	.											USP15,NS,carcinoma,0,1	USP15	105	1	0			c.T2301C						PASS	.	T		249,4153	138.8+/-174.5	6,237,1958	65.0	63.0	63.0		2214	0.4	1.0	12	dbSNP_120	63	707,7877	169.3+/-220.7	33,641,3618	no	coding-synonymous	USP15	NM_006313.1		39,878,5576	CC,CT,TT		8.2363,5.6565,7.3618		738/953	62785663	956,12030	2201	4292	6493	SO:0001819	synonymous_variant	9958	exon17			TGCTGCTGAGGTA	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.2301T>C	12.37:g.62785663T>C		Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	200	90	0.45	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Silent	SNP	ENST00000280377.5	37	CCDS58251.1																																																																																			T|0.933;C|0.067	0.067	strong		0.318	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
PKD1	5310	hgsc.bcm.edu	37	16	2162839	2162839	+	Silent	SNP	T	T	C	rs2099534	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:2162839T>C	ENST00000262304.4	-	13	3319	c.3111A>G	c.(3109-3111)ctA>ctG	p.L1037L	PKD1_ENST00000423118.1_Silent_p.L1037L|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1037	PKD 5. {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						CCGTCAGTGCTAGCGTGGCAT	0.652													c|||	100	0.0199681	0.003	0.036	5008	,	,		10955	0.002		0.0676	False		,,,				2504	0.001				p.L1037L		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	1	0			c.A3111G						PASS	.	C	,	38,4356	813.1+/-416.1	1,36,2160	89.0	84.0	86.0		3111,3111	4.0	0.0	16	dbSNP_96	86	499,8101	791.7+/-407.5	14,471,3815	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	15,507,5975	CC,CT,TT		5.8023,0.8648,4.1327	,	1037/4303,1037/4304	2162839	537,12457	2197	4300	6497	SO:0001819	synonymous_variant	5310	exon13			CAGTGCTAGCGTG	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.3111A>G	16.37:g.2162839T>C		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			T|0.971;C|0.029	0.029	strong		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
NSRP1	84081	hgsc.bcm.edu	37	17	28505174	28505174	+	Missense_Mutation	SNP	A	A	C	rs11544945	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:28505174A>C	ENST00000247026.5	+	4	320	c.257A>C	c.(256-258)aAg>aCg	p.K86T	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	86			K -> T (in dbSNP:rs11544945).		developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						CAGAAAAAAAAGGAGGAAAAT	0.333													A|||	106	0.0211661	0.0038	0.036	5008	,	,		18096	0.001		0.0666	False		,,,				2504	0.0082				p.K86T		Atlas-SNP	.											.	NSRP1	49	.	0			c.A257C						PASS	.	A	THR/LYS	51,4355	50.9+/-86.3	0,51,2152	75.0	77.0	76.0		257	3.9	1.0	17	dbSNP_120	76	489,8105	138.9+/-195.6	16,457,3824	yes	missense	NSRP1	NM_032141.2	78	16,508,5976	CC,CA,AA		5.69,1.1575,4.1538	probably-damaging	86/559	28505174	540,12460	2203	4297	6500	SO:0001583	missense	84081	exon4			AAAAAAAGGAGGA	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"""coiled-coil domain containing 55"""	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.257A>C	17.37:g.28505174A>C	ENSP00000247026:p.Lys86Thr	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	224	99	0.441964	NM_032141	Q6FI71	Missense_Mutation	SNP	ENST00000247026.5	37	CCDS11255.1	63	0.028846153846153848	5	0.01016260162601626	15	0.04143646408839779	1	0.0017482517482517483	42	0.055408970976253295	A	18.91	3.723239	0.68959	0.011575	0.0569	ENSG00000126653	ENST00000247026;ENST00000540900;ENST00000394826	T	0.47869	0.83	5.0	3.9	0.45041	Domain of unknown function DUF2040 (1);	0.140240	0.64402	D	0.000005	T	0.12305	0.0299	L	0.42529	1.33	0.80722	D	1	D	0.63046	0.992	D	0.65773	0.938	T	0.15122	-1.0448	10	0.66056	D	0.02	-10.4035	9.4935	0.38974	0.9127:0.0:0.0873:0.0	rs11544945;rs12951415;rs11544945	86	Q9H0G5	NSRP1_HUMAN	T	86;17;32	ENSP00000247026:K86T	ENSP00000247026:K86T	K	+	2	0	NSRP1	25529300	1.000000	0.71417	0.993000	0.49108	0.983000	0.72400	3.209000	0.51122	0.829000	0.34733	0.533000	0.62120	AAG	A|0.966;C|0.034	0.034	strong		0.333	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141	
TULP3	7289	hgsc.bcm.edu	37	12	3046802	3046802	+	Silent	SNP	A	A	G	rs33973716	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:3046802A>G	ENST00000448120.2	+	9	981	c.930A>G	c.(928-930)acA>acG	p.T310T	TULP3_ENST00000397132.2_Silent_p.T310T	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	310					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			TCCAGGAAACAAACGTACTTG	0.378													a|||	1108	0.221246	0.2163	0.1801	5008	,	,		18091	0.2083		0.2048	False		,,,				2504	0.2873				p.T310T		Atlas-SNP	.											.	TULP3	45	.	0			c.A930G						PASS	.		,	899,3505	341.8+/-306.9	91,717,1394	48.0	44.0	45.0		930,930	-1.2	1.0	12	dbSNP_126	45	1784,6816	319.9+/-314.4	168,1448,2684	no	coding-synonymous,coding-synonymous	TULP3	NM_001160408.1,NM_003324.4	,	259,2165,4078	GG,GA,AA		20.7442,20.4133,20.6321	,	310/502,310/443	3046802	2683,10321	2202	4300	6502	SO:0001819	synonymous_variant	7289	exon9			GGAAACAAACGTA	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.930A>G	12.37:g.3046802A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	142	77	0.542253	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Silent	SNP	ENST00000448120.2	37	CCDS8519.1																																																																																			A|0.796;G|0.204	0.204	strong		0.378	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
NSUN4	387338	hgsc.bcm.edu	37	1	46810670	46810670	+	Silent	SNP	T	T	C	rs17361763	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46810670T>C	ENST00000474844.1	+	2	941	c.291T>C	c.(289-291)gaT>gaC	p.D97D	NSUN4_ENST00000537428.1_Silent_p.D48D|NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000536062.1_Silent_p.D48D	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	97					rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					GTGCCAAGGATTTTGTGAATG	0.547													C|||	660	0.131789	0.1331	0.147	5008	,	,		21008	0.0179		0.2724	False		,,,				2504	0.092				p.D97D		Atlas-SNP	.											.	NSUN4	26	.	0			c.T291C						PASS	.	C		673,3733	763.6+/-413.2	58,557,1588	117.0	105.0	109.0		291	2.2	1.0	1	dbSNP_123	109	2493,6107	695.1+/-404.8	360,1773,2167	no	coding-synonymous	NSUN4	NM_199044.2		418,2330,3755	CC,CT,TT		28.9884,15.2746,24.3426		97/385	46810670	3166,9840	2203	4300	6503	SO:0001819	synonymous_variant	387338	exon2			CAAGGATTTTGTG	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"""NOP2/Sun domain containing"""	31802	protein-coding gene	gene with protein product	"""sperm head and tail associated protein"""	615394	"""NOL1/NOP2/Sun domain family 4"", ""NOL1/NOP2/Sun domain family, member 4"""				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.291T>C	1.37:g.46810670T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	111	44	0.396396	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Silent	SNP	ENST00000474844.1	37	CCDS534.1																																																																																			T|0.802;C|0.198	0.198	strong		0.547	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
SLC35D3	340146	hgsc.bcm.edu	37	6	137245534	137245534	+	Missense_Mutation	SNP	G	G	C	rs150994900	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:137245534G>C	ENST00000331858.4	+	2	1116	c.951G>C	c.(949-951)caG>caC	p.Q317H		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	317					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		TGGAGGCCCAGCCTCGGGGAG	0.612													G|||	27	0.00539137	0.003	0.0144	5008	,	,		18737	0.0		0.0119	False		,,,				2504	0.001				p.Q317H		Atlas-SNP	.											.	SLC35D3	33	.	0			c.G951C						PASS	.	G	HIS/GLN	20,4386	24.3+/-50.5	0,20,2183	35.0	38.0	37.0		951	3.1	0.9	6	dbSNP_134	37	252,8348	96.6+/-158.3	6,240,4054	yes	missense	SLC35D3	NM_001008783.1	24	6,260,6237	CC,CG,GG		2.9302,0.4539,2.0913	benign	317/417	137245534	272,12734	2203	4300	6503	SO:0001583	missense	340146	exon2			GGCCCAGCCTCGG		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"""Solute carriers"""	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.951G>C	6.37:g.137245534G>C	ENSP00000333591:p.Gln317His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	37	CCDS34544.1	13	0.005952380952380952	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	0.754	-0.771583	0.02951	0.004539	0.029302	ENSG00000182747	ENST00000331858	T	0.56776	0.44	6.06	3.14	0.36123	.	0.639469	0.15100	N	0.280557	T	0.12135	0.0295	N	0.08118	0	0.21841	N	0.999512	B	0.24368	0.102	B	0.24541	0.054	T	0.24512	-1.0158	10	0.31617	T	0.26	-7.7485	7.32	0.26521	0.3119:0.1297:0.5584:0.0	.	317	Q5M8T2	S35D3_HUMAN	H	317	ENSP00000333591:Q317H	ENSP00000333591:Q317H	Q	+	3	2	SLC35D3	137287227	0.789000	0.28775	0.873000	0.34254	0.151000	0.21798	1.094000	0.30951	0.462000	0.27095	-0.797000	0.03246	CAG	G|0.983;C|0.017	0.017	strong		0.612	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017	
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 GAIIx	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		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	105	53	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 GAIIx	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	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	14	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	
OR13C2	392376	hgsc.bcm.edu	37	9	107367841	107367841	+	Missense_Mutation	SNP	A	A	T	rs10991326	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107367841A>T	ENST00000542196.1	-	1	110	c.68T>A	c.(67-69)cTt>cAt	p.L23H		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	23						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(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GAGTAACTCAAGTCTTGGGTG	0.408													A|||	1868	0.373003	0.4342	0.2161	5008	,	,		20515	0.5645		0.1789	False		,,,				2504	0.4039				p.L23H		Atlas-SNP	.											OR13C2,NS,carcinoma,-1,1	OR13C2	46	1	0			c.T68A						PASS	.						31.0	35.0	33.0					9																	107367841		2181	4289	6470	SO:0001583	missense	392376	exon1			AACTCAAGTCTTG		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.68T>A	9.37:g.107367841A>T	ENSP00000438815:p.Leu23His	Somatic	351	1	0.002849		WXS	Illumina HiSeq	Phase_I	359	133	0.370474	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	708	0.3241758241758242	184	0.37398373983739835	74	0.20441988950276244	319	0.5576923076923077	131	0.17282321899736147	A	10.73	1.431549	0.25813	.	.	ENSG00000257019	ENST00000542196	T	0.03413	3.94	3.39	3.39	0.38822	.	0.000000	0.33477	U	0.004878	T	0.00012	0.0000	M	0.78456	2.415	0.80722	P	0.0	D	0.76494	0.999	D	0.63033	0.91	T	0.36866	-0.9730	9	0.87932	D	0	.	9.8158	0.40851	1.0:0.0:0.0:0.0	rs10991326;rs60657466	23	Q8NGS9	O13C2_HUMAN	H	23	ENSP00000438815:L23H	ENSP00000438815:L23H	L	-	2	0	OR13C2	106407662	0.001000	0.12720	0.022000	0.16811	0.190000	0.23558	1.352000	0.34033	1.409000	0.46915	0.379000	0.24179	CTT	A|0.026;T|0.974	0.974	strong		0.408	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
LAMA5	3911	hgsc.bcm.edu	37	20	60913127	60913127	+	Silent	SNP	A	A	G	rs8124907	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60913127A>G	ENST00000252999.3	-	14	1902	c.1836T>C	c.(1834-1836)gcT>gcC	p.A612A		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	612	Laminin EGF-like 6. {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)			AATGAGGTCCAGCAAACTCAG	0.652													G|||	1177	0.235024	0.3427	0.1686	5008	,	,		19473	0.2054		0.2455	False		,,,				2504	0.1564				p.A612A		Atlas-SNP	.											LAMA5,NS,carcinoma,0,3	LAMA5	268	3	0			c.T1836C						PASS	.	G		1436,2966	650.5+/-399.1	230,976,995	38.0	37.0	37.0		1836	-10.1	0.0	20	dbSNP_116	37	1971,6617	699.9+/-405.1	236,1499,2559	no	coding-synonymous	LAMA5	NM_005560.3		466,2475,3554	GG,GA,AA		22.9506,32.6215,26.2279		612/3696	60913127	3407,9583	2201	4294	6495	SO:0001819	synonymous_variant	3911	exon14			AGGTCCAGCAAAC	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.1836T>C	20.37:g.60913127A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	119	41	0.344538	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			A|0.749;G|0.251	0.251	strong		0.652	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
PKD1L1	168507	hgsc.bcm.edu	37	7	47921682	47921682	+	Splice_Site	SNP	A	A	T	rs10951936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:47921682A>T	ENST00000289672.2	-	20	3317	c.3267T>A	c.(3265-3267)gcT>gcA	p.A1089A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1089	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TGGTGTCCTTAGCTAGGAAGA	0.443													T|||	1238	0.247204	0.1914	0.3674	5008	,	,		16918	0.2242		0.334	False		,,,				2504	0.1718				p.A1089A		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T3267A						PASS	.	T		923,3483	738.5+/-411.0	102,719,1382	56.0	50.0	52.0		3267	-0.8	0.0	7	dbSNP_120	52	2847,5753	673.7+/-403.0	457,1933,1910	yes	coding-synonymous-near-splice	PKD1L1	NM_138295.3		559,2652,3292	TT,TA,AA		33.1047,20.9487,28.9866		1089/2850	47921682	3770,9236	2203	4300	6503	SO:0001630	splice_region_variant	168507	exon20			GTCCTTAGCTAGG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.3266-1T>A	7.37:g.47921682A>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	60	23	0.383333	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			A|0.721;T|0.279	0.279	strong		0.443	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	Silent
ZCWPW2	152098	hgsc.bcm.edu	37	3	28533658	28533658	+	Silent	SNP	G	G	A	rs13100556	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:28533658G>A	ENST00000383768.2	+	6	839	c.651G>A	c.(649-651)aaG>aaA	p.K217K	ZCWPW2_ENST00000421010.1_Silent_p.K217K			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	217							zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						CACTGGTCAAGAAAAGGGTAA	0.269													G|||	1282	0.25599	0.0938	0.2291	5008	,	,		14198	0.4653		0.161	False		,,,				2504	0.3763				p.K217K		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.G651A						PASS	.	G		428,3978	183.3+/-210.9	22,384,1797	46.0	45.0	45.0		651	3.8	1.0	3	dbSNP_121	45	1372,7226	242.6+/-272.5	111,1150,3038	no	coding-synonymous	ZCWPW2	NM_001040432.1		133,1534,4835	AA,AG,GG		15.9572,9.714,13.8419		217/357	28533658	1800,11204	2203	4299	6502	SO:0001819	synonymous_variant	152098	exon5			GGTCAAGAAAAGG	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.651G>A	3.37:g.28533658G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	195	68	0.348718	NM_001040432		Silent	SNP	ENST00000383768.2	37	CCDS33723.1	502	0.22985347985347984	44	0.08943089430894309	78	0.2154696132596685	258	0.45104895104895104	122	0.16094986807387862	G	0.944	-0.708672	0.03230	0.09714	0.159572	ENSG00000206559	ENST00000419130	.	.	.	4.72	3.84	0.44239	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999524966	.	.	.	.	.	.	T	0.48758	-0.9007	3	.	.	.	-9.0178	8.7367	0.34532	0.106:0.0:0.894:0.0	rs13100556;rs13100556	.	.	.	K	102	.	.	E	+	1	0	ZCWPW2	28508662	1.000000	0.71417	1.000000	0.80357	0.216000	0.24613	1.240000	0.32731	1.108000	0.41662	0.650000	0.86243	GAA	G|0.823;A|0.176	0.176	strong		0.269	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384	
MUC21	394263	hgsc.bcm.edu	37	6	30954873	30954873	+	Silent	SNP	G	G	A	rs1625781	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30954873G>A	ENST00000376296.3	+	2	1162	c.921G>A	c.(919-921)acG>acA	p.T307T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	307	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						AGTCCAGTACGACCTCCAGTG	0.597													g|||	707	0.141174	0.1059	0.2594	5008	,	,		21191	0.0427		0.2386	False		,,,				2504	0.1063				p.T307T		Atlas-SNP	.											.	MUC21	98	.	0			c.G921A						PASS	.	G		688,3718	289.2+/-280.3	41,606,1556	166.0	160.0	162.0		921	-8.6	0.0	6	dbSNP_89	162	2411,6189	400.9+/-346.9	330,1751,2219	no	coding-synonymous	MUC21	NM_001010909.2		371,2357,3775	AA,AG,GG		28.0349,15.6151,23.8275		307/567	30954873	3099,9907	2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			CAGTACGACCTCC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.921G>A	6.37:g.30954873G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	59	43	0.728814	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			G|0.774;A|0.226	0.226	strong		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
ANO7	50636	hgsc.bcm.edu	37	2	242141719	242141719	+	Splice_Site	SNP	C	C	T	rs2074840	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242141719C>T	ENST00000274979.8	+	8	988	c.885C>T	c.(883-885)gaC>gaT	p.D295D	ANO7_ENST00000402430.3_Splice_Site_p.D294D	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	295					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						CCCTGCATGACGTGAGCTCGG	0.657													C|||	2077	0.414736	0.4796	0.5086	5008	,	,		17915	0.0794		0.6829	False		,,,				2504	0.3303				p.D295D		Atlas-SNP	.											ANO7,NS,carcinoma,+2,1	ANO7	136	1	0			c.C885T						PASS	.	C		2330,2076	601.1+/-389.6	642,1046,515	51.0	49.0	50.0		885	-7.5	0.0	2	dbSNP_96	50	5930,2670	682.1+/-403.8	2039,1852,409	yes	coding-synonymous-near-splice	ANO7	NM_001001891.3		2681,2898,924	TT,TC,CC		31.0465,47.1176,36.4909		295/934	242141719	8260,4746	2203	4300	6503	SO:0001630	splice_region_variant	50636	exon8			GCATGACGTGAGC	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.885+1C>T	2.37:g.242141719C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			C|0.452;T|0.548	0.548	strong		0.657	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	Silent
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1017974C>G	ENST00000421673.2	-	31	4877	c.4827G>C	c.(4825-4827)caG>caC	p.Q1609H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1609	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.Q1609H(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|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;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAAGTGTGGTCTGAGGGTGTG	0.547																																					p.Q1609H		Atlas-SNP	.											MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	large_intestine(2)	c.G4827C						scavenged	.						473.0	441.0	452.0					11																	1017974		2186	4282	6468	SO:0001583	missense	4588	exon31			TGTGGTCTGAGGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4827G>C	11.37:g.1017974C>G	ENSP00000406861:p.Gln1609His	Somatic	268	3	0.011194		WXS	Illumina HiSeq	Phase_I	346	11	0.0317919	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	5.277	0.236564	0.10023	.	.	ENSG00000184956	ENST00000421673	T	0.35421	1.31	2.39	0.333	0.15943	.	.	.	.	.	T	0.26702	0.0653	L	0.52011	1.625	0.09310	N	1	B	0.25486	0.127	B	0.27715	0.082	T	0.28681	-1.0036	9	0.22109	T	0.4	.	3.4702	0.07565	0.0:0.5042:0.2173:0.2785	.	1609	Q6W4X9	MUC6_HUMAN	H	1609	ENSP00000406861:Q1609H	ENSP00000406861:Q1609H	Q	-	3	2	MUC6	1007974	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-2.394000	0.01054	-0.057000	0.13199	-0.710000	0.03640	CAG	.	.	weak		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
PTX4	390667	hgsc.bcm.edu	37	16	1538464	1538464	+	Intron	SNP	C	C	T	rs2745103	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1538464C>T	ENST00000447419.2	-	1	167				PTX4_ENST00000440447.2_Intron|PTX4_ENST00000293922.1_Missense_Mutation_p.G2E			Q96A99	PTX4_HUMAN	pentraxin 4, long							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GTTTCCACTCCCCATGACACT	0.652													C|||	1291	0.257788	0.1316	0.1945	5008	,	,		15785	0.497		0.2416	False		,,,				2504	0.2434				p.G2E		Atlas-SNP	.											.	PTX4	46	.	0			c.G5A						PASS	.	C	GLU/GLY	591,3807	258.6+/-262.5	37,517,1645	64.0	54.0	57.0		5	0.9	0.0	16	dbSNP_100	57	2187,6413	367.0+/-334.5	254,1679,2367	yes	missense	PTX4	NM_001013658.1	98	291,2196,4012	TT,TC,CC		25.4302,13.4379,21.3725	benign	2/474	1538464	2778,10220	2199	4300	6499	SO:0001627	intron_variant	390667	exon1			CCACTCCCCATGA		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.141+305G>A	16.37:g.1538464C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	147	62	0.421769	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		632	0.2893772893772894	57	0.11585365853658537	67	0.1850828729281768	309	0.5402097902097902	199	0.262532981530343	C	5.219	0.226002	0.09916	0.134379	0.254302	ENSG00000251692	ENST00000293922	T	0.07444	3.19	2.87	0.856	0.19019	.	1820.570000	0.00166	N	0.000000	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.27498	0.18	B	0.26310	0.068	T	0.46992	-0.9151	8	0.87932	D	0	.	4.118	0.10092	0.0:0.6175:0.2436:0.1389	rs2745103;rs58765039;rs2745103	2	Q96A99-2	.	E	2	ENSP00000293922:G2E	ENSP00000293922:G2E	G	-	2	0	PTX4	1478465	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	0.239000	0.18023	0.260000	0.21731	0.563000	0.77884	GGG	C|0.758;T|0.242	0.242	strong		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
C1QTNF1	114897	hgsc.bcm.edu	37	17	77043894	77043894	+	Silent	SNP	C	C	T	rs35435268	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77043894C>T	ENST00000339142.2	+	5	1125	c.570C>T	c.(568-570)ccC>ccT	p.P190P	C1QTNF1_ENST00000583904.1_Silent_p.P190P|C1QTNF1_ENST00000580474.1_Silent_p.P190P|C1QTNF1_ENST00000392445.2_Silent_p.P190P|C1QTNF1_ENST00000581774.1_Silent_p.P190P|C1QTNF1_ENST00000582625.1_3'UTR|C1QTNF1_ENST00000579760.1_Silent_p.P190P|C1QTNF1_ENST00000311661.4_Silent_p.P108P|C1QTNF1_ENST00000580454.1_Silent_p.P190P|C1QTNF1_ENST00000578229.1_Silent_p.P108P|C1QTNF1_ENST00000354124.3_Silent_p.P200P	NM_198593.3	NP_940995.1	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	190	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase B signaling (GO:0051897)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|regulation of glucose metabolic process (GO:0010906)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(2)	14			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)			GCTACGTGCCCGGCCTCTACT	0.537													C|||	80	0.0159744	0.0189	0.0317	5008	,	,		20138	0.0		0.0298	False		,,,				2504	0.0031				p.P190P		Atlas-SNP	.											.	C1QTNF1	62	.	0			c.C570T						PASS	.	C	,,	74,4332	65.8+/-103.3	1,72,2130	171.0	154.0	159.0		570,570,324	-6.8	1.0	17	dbSNP_126	159	191,8409	85.0+/-147.5	2,187,4111	no	coding-synonymous,coding-synonymous,coding-synonymous	C1QTNF1	NM_030968.2,NM_198593.2,NM_198594.1	,,	3,259,6241	TT,TC,CC		2.2209,1.6795,2.0375	,,	190/282,190/282,108/200	77043894	265,12741	2203	4300	6503	SO:0001819	synonymous_variant	114897	exon4			CGTGCCCGGCCTC	AF329840	CCDS11761.1, CCDS11762.1	17q25	2012-07-02			ENSG00000173918	ENSG00000173918			14324	protein-coding gene	gene with protein product	"""G protein coupled receptor interacting protein"""	610365				12409230	Standard	NM_198593		Approved	CTRP1, ZSIG37, GIP, FLJ90694	uc002jwp.4	Q9BXJ1	OTTHUMG00000177533	ENST00000339142.2:c.570C>T	17.37:g.77043894C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	30	0.275229	NM_030968	Q6ZMH6|Q96NF2|Q9GZR4	Silent	SNP	ENST00000339142.2	37	CCDS11761.1																																																																																			C|0.979;T|0.021	0.021	strong		0.537	C1QTNF1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437388.2	NM_030968	
CST1	1469	hgsc.bcm.edu	37	20	23731412	23731412	+	Missense_Mutation	SNP	G	G	A	rs2070856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:23731412G>A	ENST00000304749.2	-	1	162	c.92C>T	c.(91-93)cCg>cTg	p.P31L	CST1_ENST00000398402.1_Missense_Mutation_p.P31L	NM_001898.2	NP_001889.2	P01037	CYTN_HUMAN	cystatin SN	31			P -> L (in dbSNP:rs2070856).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			kidney(1)|large_intestine(1)|lung(8)|ovary(1)|stomach(1)|urinary_tract(1)	13	Lung NSC(19;0.0676)|all_lung(19;0.148)					GATGCCACCCGGGATTATCCT	0.567													.|||	891	0.177915	0.2315	0.0937	5008	,	,		14900	0.0764		0.1113	False		,,,				2504	0.3384				p.P31L		Atlas-SNP	.											.	CST1	37	.	0			c.C92T						PASS	.	G	LEU/PRO	908,3498	352.1+/-311.5	88,732,1383	117.0	101.0	107.0		92	-2.9	0.0	20	dbSNP_96	107	1157,7443	237.9+/-269.6	75,1007,3218	yes	missense	CST1	NM_001898.2	98	163,1739,4601	AA,AG,GG		13.4535,20.6083,15.8773	benign	31/142	23731412	2065,10941	2203	4300	6503	SO:0001583	missense	1469	exon1			CCACCCGGGATTA	M19169	CCDS13160.1	20p11.2	2008-04-15			ENSG00000170373	ENSG00000170373			2473	protein-coding gene	gene with protein product		123855					Standard	NM_001898		Approved		uc002wtp.3	P01037	OTTHUMG00000032085	ENST00000304749.2:c.92C>T	20.37:g.23731412G>A	ENSP00000305731:p.Pro31Leu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	133	74	0.556391	NM_001898	Q96LE6|Q9UCQ6	Missense_Mutation	SNP	ENST00000304749.2	37	CCDS13160.1	285	0.1304945054945055	117	0.23780487804878048	41	0.1132596685082873	44	0.07692307692307693	83	0.10949868073878628	G	2.600	-0.293234	0.05568	0.206083	0.134535	ENSG00000170373	ENST00000304749;ENST00000398402	T;T	0.12672	2.66;2.66	1.45	-2.91	0.05631	Proteinase inhibitor I25, cystatin (1);	0.902916	0.09313	N	0.819400	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.42716	-0.9435	9	0.06236	T	0.91	.	5.9667	0.19328	0.6797:0.0:0.3203:0.0	rs2070856;rs2234831;rs58967935;rs2070856	31	P01037	CYTN_HUMAN	L	31	ENSP00000305731:P31L;ENSP00000381439:P31L	ENSP00000305731:P31L	P	-	2	0	CST1	23679412	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.296000	0.19083	-1.070000	0.03149	-1.207000	0.01640	CCG	G|0.847;A|0.153	0.153	strong		0.567	CST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078351.2	NM_001898	
USP8	9101	hgsc.bcm.edu	37	15	50769520	50769520	+	Missense_Mutation	SNP	G	G	A	rs61733869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:50769520G>A	ENST00000396444.3	+	10	1380	c.1042G>A	c.(1042-1044)Gct>Act	p.A348T	USP8_ENST00000425032.3_Missense_Mutation_p.A271T|USP8_ENST00000433963.1_Missense_Mutation_p.A348T|USP8_ENST00000307179.4_Missense_Mutation_p.A348T	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	348					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TTCTAAACCTGCTGCCCAGAC	0.353													G|||	59	0.0117812	0.0023	0.0245	5008	,	,		16343	0.0		0.0358	False		,,,				2504	0.0031				p.A348T		Atlas-SNP	.											.	USP8	90	.	0			c.G1042A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	46,4346	46.7+/-81.2	0,46,2150	48.0	50.0	50.0		1042,1042,1042	-9.4	0.1	15	dbSNP_129	50	373,8215	123.2+/-182.1	9,355,3930	yes	missense,missense,missense	USP8	NM_001128610.1,NM_001128611.1,NM_005154.3	58,58,58	9,401,6080	AA,AG,GG		4.3433,1.0474,3.228	benign,benign,benign	348/1119,348/1119,348/1119	50769520	419,12561	2196	4294	6490	SO:0001583	missense	9101	exon10			AAACCTGCTGCCC	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.1042G>A	15.37:g.50769520G>A	ENSP00000379721:p.Ala348Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	37	CCDS10137.1	42	0.019230769230769232	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	32	0.04221635883905013	G	0.879	-0.729342	0.03135	0.010474	0.043433	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.17370	2.28;2.28;2.28;2.29	4.72	-9.45	0.00600	.	1.505420	0.03406	N	0.204125	T	0.01730	0.0055	N	0.22421	0.69	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.17167	-1.0378	10	0.11485	T	0.65	0.0554	7.2057	0.25905	0.4933:0.2568:0.2499:0.0	rs61733869	271;348;348	B4DKA8;P40818;A8K8N5	.;UBP8_HUMAN;.	T	348;348;348;271	ENSP00000379721:A348T;ENSP00000405537:A348T;ENSP00000302239:A348T;ENSP00000412682:A271T	ENSP00000302239:A348T	A	+	1	0	USP8	48556812	0.306000	0.24490	0.093000	0.20910	0.259000	0.26198	-0.155000	0.10115	-2.533000	0.00490	-0.444000	0.05651	GCT	G|0.971;A|0.029	0.029	strong		0.353	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154	
ENTPD6	955	hgsc.bcm.edu	37	20	25193949	25193949	+	Silent	SNP	G	G	A	rs2076561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:25193949G>A	ENST00000376652.4	+	5	667	c.504G>A	c.(502-504)ccG>ccA	p.P168P	ENTPD6_ENST00000354989.5_Silent_p.P151P|ENTPD6_ENST00000433259.2_Silent_p.P168P|ENTPD6_ENST00000360031.2_Silent_p.P167P|Y_RNA_ENST00000365544.1_RNA			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	168					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						AGGACATTCCGTTCGACTTCT	0.547													G|||	1553	0.310104	0.0983	0.2262	5008	,	,		20740	0.5913		0.3459	False		,,,				2504	0.3292				p.P168P		Atlas-SNP	.											ENTPD6,face,carcinoma,+2,1	ENTPD6	57	1	0			c.G504A						PASS	.	G	,	619,3787	269.2+/-268.9	42,535,1626	169.0	127.0	141.0		453,504	-11.6	0.0	20	dbSNP_96	141	2765,5835	439.7+/-359.3	431,1903,1966	no	coding-synonymous,coding-synonymous	ENTPD6	NM_001114089.1,NM_001247.2	,	473,2438,3592	AA,AG,GG		32.1512,14.049,26.0188	,	151/468,168/485	25193949	3384,9622	2203	4300	6503	SO:0001819	synonymous_variant	955	exon5			CATTCCGTTCGAC	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.504G>A	20.37:g.25193949G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Silent	SNP	ENST00000376652.4	37	CCDS13170.1	755	0.3456959706959707	59	0.11991869918699187	92	0.2541436464088398	346	0.6048951048951049	258	0.3403693931398417	G	0.470	-0.885057	0.02511	0.14049	0.321512	ENSG00000197586	ENST00000433417;ENST00000447877	.	.	.	5.79	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999861442	.	.	.	.	.	.	T	0.26608	-1.0098	3	.	.	.	-1.1705	1.9584	0.03381	0.1245:0.3117:0.2786:0.2853	rs2076561;rs17250460;rs58880188;rs2076561	.	.	.	H	89;61	.	.	R	+	2	0	ENTPD6	25141949	0.000000	0.05858	0.008000	0.14137	0.056000	0.15407	-2.000000	0.01466	-3.712000	0.00117	-2.589000	0.00165	CGT	G|0.708;A|0.292	0.292	strong		0.547	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
NSUN4	387338	hgsc.bcm.edu	37	1	46806550	46806550	+	Missense_Mutation	SNP	C	C	T	rs41293277	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46806550C>T	ENST00000474844.1	+	1	702	c.52C>T	c.(52-54)Ctc>Ttc	p.L18F	NSUN4_ENST00000537428.1_5'Flank|NSUN4_ENST00000536062.1_5'UTR	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	18					rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					GCGTGTGGACCTCGCGACGGT	0.602											OREG0013456	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	637	0.127196	0.115	0.147	5008	,	,		15523	0.0179		0.2773	False		,,,				2504	0.0879				p.L18F		Atlas-SNP	.											.	NSUN4	26	.	0			c.C52T						PASS	.	T	PHE/LEU	604,3800	755.8+/-412.6	55,494,1653	29.0	30.0	30.0		52	2.9	0.1	1	dbSNP_127	30	2510,6088	680.6+/-403.7	367,1776,2156	yes	missense	NSUN4	NM_199044.2	22	422,2270,3809	TT,TC,CC		29.1928,13.7148,23.9502	benign	18/385	46806550	3114,9888	2202	4299	6501	SO:0001583	missense	387338	exon1			GTGGACCTCGCGA	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"""NOP2/Sun domain containing"""	31802	protein-coding gene	gene with protein product	"""sperm head and tail associated protein"""	615394	"""NOL1/NOP2/Sun domain family 4"", ""NOL1/NOP2/Sun domain family, member 4"""				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.52C>T	1.37:g.46806550C>T	ENSP00000419740:p.Leu18Phe	Somatic	94	0	0	942	WXS	Illumina HiSeq	Phase_I	79	29	0.367089	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	37	CCDS534.1	338	0.15476190476190477	59	0.11991869918699187	60	0.16574585635359115	11	0.019230769230769232	208	0.27440633245382584	T	5.578	0.291507	0.10567	0.137148	0.291928	ENSG00000117481	ENST00000474844	T	0.15017	2.46	4.09	2.93	0.34026	.	0.748109	0.13086	N	0.414936	T	0.00012	0.0000	N	0.08118	0	0.51767	P	6.700000000003925E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.46289	-0.9202	9	0.08179	T	0.78	-0.8149	4.8239	0.13407	0.0:0.4319:0.0:0.5681	rs41293277	18	Q96CB9	NSUN4_HUMAN	F	18	ENSP00000419740:L18F	ENSP00000419740:L18F	L	+	1	0	NSUN4	46579137	0.005000	0.15991	0.105000	0.21289	0.096000	0.18686	0.284000	0.18864	0.630000	0.30394	-0.490000	0.04691	CTC	C|0.790;T|0.210	0.210	strong		0.602	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
FAM71F1	84691	hgsc.bcm.edu	37	7	128358891	128358891	+	Silent	SNP	C	C	A	rs745229|rs397954408	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128358891C>A	ENST00000315184.5	+	3	494	c.441C>A	c.(439-441)ctC>ctA	p.L147L	FAM71F1_ENST00000469348.1_Intron|FAM71F1_ENST00000485070.1_Intron	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	147										NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						TCAGGATTCTCCCATTGAGGT	0.473													C|||	1008	0.201278	0.2209	0.1571	5008	,	,		21880	0.1042		0.2366	False		,,,				2504	0.2699				p.L147L		Atlas-SNP	.											.	FAM71F1	42	.	0			c.C441A						PASS	.	C		877,3529	342.0+/-307.0	85,707,1411	263.0	240.0	248.0		441	2.8	1.0	7	dbSNP_86	248	1989,6611	349.1+/-327.3	209,1571,2520	no	coding-synonymous	FAM71F1	NM_032599.2		294,2278,3931	AA,AC,CC		23.1279,19.9047,22.036		147/345	128358891	2866,10140	2203	4300	6503	SO:0001819	synonymous_variant	84691	exon3			GATTCTCCCATTG	AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248			30704	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member A"""	FAM137A		12477932	Standard	XM_005250645		Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000315184.5:c.441C>A	7.37:g.128358891C>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_032599	Q8IY75|Q8NA48	Silent	SNP	ENST00000315184.5	37	CCDS5804.1																																																																																			C|0.797;A|0.203	0.203	strong		0.473	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	NM_032599	
FLNC	2318	hgsc.bcm.edu	37	7	128477547	128477547	+	Silent	SNP	T	T	C	rs2291561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128477547T>C	ENST00000325888.8	+	4	1056	c.795T>C	c.(793-795)ggT>ggC	p.G265G	FLNC_ENST00000346177.6_Silent_p.G265G	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	265					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCAAACCTGGTGCCCCTGTTC	0.597													C|||	606	0.121006	0.1218	0.062	5008	,	,		14951	0.121		0.1093	False		,,,				2504	0.1738				p.G265G		Atlas-SNP	.											FLNC,NS,carcinoma,0,1	FLNC	339	1	0			c.T795C						PASS	.	C	,	529,3827	714.4+/-408.4	36,457,1685	133.0	144.0	141.0		795,795	-5.9	0.9	7	dbSNP_100	141	952,7638	757.3+/-407.5	49,854,3392	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	85,1311,5077	CC,CT,TT		11.0827,12.1442,11.4398	,	265/2693,265/2726	128477547	1481,11465	2178	4295	6473	SO:0001819	synonymous_variant	2318	exon4			ACCTGGTGCCCCT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.795T>C	7.37:g.128477547T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			T|0.881;C|0.119	0.119	strong		0.597	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
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 GAIIx	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_ENST00000550629.1_5'Flank|SCAF11_ENST00000465950.1_Missense_Mutation_p.R532H|SCAF11_ENST00000549162.1_Missense_Mutation_p.R655H|SCAF11_ENST00000419565.2_Missense_Mutation_p.R847H	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	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	147	72	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	
NOL11	25926	hgsc.bcm.edu	37	17	65739627	65739627	+	Silent	SNP	A	A	G	rs10127	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:65739627A>G	ENST00000253247.4	+	17	2083	c.1968A>G	c.(1966-1968)gcA>gcG	p.A656A	NOL11_ENST00000535137.1_Silent_p.A474A|SNORA38B_ENST00000363524.1_RNA	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	656					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			TTCTGGATGCAAATTTTACTG	0.303													A|||	2441	0.48742	0.3623	0.6196	5008	,	,		14755	0.5069		0.5249	False		,,,				2504	0.5041				p.A656A		Atlas-SNP	.											.	NOL11	48	.	0			c.A1968G						PASS	.	A		1796,2610	525.1+/-371.5	347,1102,754	82.0	86.0	85.0		1968	-0.0	1.0	17	dbSNP_52	85	4700,3888	603.0+/-394.6	1286,2128,880	no	coding-synonymous	NOL11	NM_015462.3		1633,3230,1634	GG,GA,AA		45.2725,40.7626,49.9923		656/720	65739627	6496,6498	2203	4294	6497	SO:0001819	synonymous_variant	25926	exon17			GGATGCAAATTTT	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1968A>G	17.37:g.65739627A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	186	186	1	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Silent	SNP	ENST00000253247.4	37	CCDS11671.1																																																																																			A|0.511;G|0.489	0.489	strong		0.303	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462	
SLC36A3	285641	hgsc.bcm.edu	37	5	150666933	150666933	+	Silent	SNP	C	C	A	rs375396	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150666933C>A	ENST00000335230.3	-	6	993	c.582G>T	c.(580-582)ctG>ctT	p.L194L	SLC36A3_ENST00000377713.3_Silent_p.L235L	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	194						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCAGGATTATCAGCATGTAGA	0.527													C|||	1267	0.252995	0.1997	0.1455	5008	,	,		20331	0.4474		0.1809	False		,,,				2504	0.2751				p.L235L		Atlas-SNP	.											.	SLC36A3	54	.	0			c.G705T						PASS	.	C	,	822,3584	327.5+/-300.1	85,652,1466	168.0	156.0	160.0		705,582	-2.0	0.1	5	dbSNP_80	160	1566,7034	294.0+/-301.7	149,1268,2883	no	coding-synonymous,coding-synonymous	SLC36A3	NM_001145017.1,NM_181774.3	,	234,1920,4349	AA,AC,CC		18.2093,18.6564,18.3608	,	235/512,194/471	150666933	2388,10618	2203	4300	6503	SO:0001819	synonymous_variant	285641	exon7			GATTATCAGCATG	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"""Solute carriers"""	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.582G>T	5.37:g.150666933C>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Silent	SNP	ENST00000335230.3	37	CCDS4314.1																																																																																			C|0.776;A|0.224	0.224	strong		0.527	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
CCHCR1	54535	hgsc.bcm.edu	37	6	31116502	31116502	+	Missense_Mutation	SNP	C	C	T	rs2027937	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31116502C>T	ENST00000376266.5	-	9	1221	c.1099G>A	c.(1099-1101)Gcc>Acc	p.A367T	CCHCR1_ENST00000480060.1_5'Flank|CCHCR1_ENST00000396263.2_Missense_Mutation_p.A367T|CCHCR1_ENST00000396268.3_Missense_Mutation_p.A456T|CCHCR1_ENST00000451521.2_Missense_Mutation_p.A420T	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	367			A -> T (in dbSNP:rs2027937). {ECO:0000269|PubMed:11348465}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						TGGAGTGAGGCCACCTGGGGG	0.587													C|||	364	0.0726837	0.0378	0.1023	5008	,	,		12329	0.0417		0.0795	False		,,,				2504	0.1237				p.A456T		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1366A						PASS	.		THR/ALA,THR/ALA,THR/ALA	157,2863		5,147,1358	59.0	62.0	61.0		1258,1366,1099	3.6	1.0	6	dbSNP_94	61	393,5025		21,351,2337	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	58,58,58	26,498,3695	TT,TC,CC		7.2536,5.1987,6.5181	possibly-damaging,possibly-damaging,possibly-damaging	420/836,456/872,367/783	31116502	550,7888	1510	2709	4219	SO:0001583	missense	54535	exon9			GTGAGGCCACCTG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1099G>A	6.37:g.31116502C>T	ENSP00000365442:p.Ala367Thr	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	5	0.0724638	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	119	0.05448717948717949	16	0.032520325203252036	33	0.09116022099447514	13	0.022727272727272728	57	0.07519788918205805	c	12.40	1.925236	0.34002	0.051987	0.072536	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.06294	3.32;3.32;3.32;3.32	4.53	3.64	0.41730	.	0.575934	0.16282	N	0.221286	T	0.09335	0.0230	M	0.72118	2.19	0.27472	N	0.952833	D;P;D;D;D	0.89917	0.957;0.536;1.0;1.0;1.0	P;B;D;D;D	0.91635	0.86;0.396;0.999;0.99;0.998	T	0.15407	-1.0438	10	0.14656	T	0.56	-4.0548	11.9413	0.52903	0.0:0.9041:0.0:0.0959	rs2027937;rs11540821;rs17840018;rs2027937	367;367;367;420;456	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	T	456;367;367;367;420	ENSP00000379566:A456T;ENSP00000365442:A367T;ENSP00000379561:A367T;ENSP00000401039:A420T	ENSP00000365442:A367T	A	-	1	0	CCHCR1	31224481	0.997000	0.39634	0.968000	0.41197	0.002000	0.02628	1.327000	0.33746	0.460000	0.27045	-1.263000	0.01449	GCC	C|0.937;T|0.063	0.063	strong		0.587	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
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 GAIIx	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_ENST00000417961.1_Silent_p.S519S|SLC9A8_ENST00000541138.1_Silent_p.S203S|SLC9A8_ENST00000539601.1_Silent_p.S284S|SLC9A8_ENST00000490250.1_3'UTR			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		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	105	55	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	
CSMD2	114784	hgsc.bcm.edu	37	1	34071525	34071525	+	Intron	SNP	C	C	T	rs376790279|rs1874045	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:34071525C>T	ENST00000373380.1	-	21	3183				CSMD2_ENST00000373381.4_Intron|CSMD2_ENST00000373388.2_Intron|CSMD2_ENST00000373377.1_Intron			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGAGTTGGTTCTTTCCAACTC	0.478													C|||	2596	0.518371	0.323	0.6787	5008	,	,		21656	0.5516		0.5755	False		,,,				2504	0.5757				p.R2096K		Atlas-SNP	.											CSMD2,brain,glioma,0,1	CSMD2	946	1	0			c.G6287A						scavenged	.	C	LYS/ARG	1744,2662	520.1+/-370.2	344,1056,803	66.0	65.0	65.0		6287	3.0	0.0	1	dbSNP_92	65	4953,3647	623.0+/-397.4	1436,2081,783	yes	missense	CSMD2	NM_052896.3	26	1780,3137,1586	TT,TC,CC		42.407,39.5824,48.5084		2096/3488	34071525	6697,6309	2203	4300	6503	SO:0001627	intron_variant	114784	exon42			TTGGTTCTTTCCA	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.2963-455G>A	1.37:g.34071525C>T		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373380.1	37																																																																																				C|0.479;T|0.521	0.521	strong		0.478	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	
OTOR	56914	hgsc.bcm.edu	37	20	16729138	16729138	+	Missense_Mutation	SNP	T	T	C	rs6135876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:16729138T>C	ENST00000246081.2	+	1	136	c.92T>C	c.(91-93)cTc>cCc	p.L31P		NM_020157.2	NP_064542.1	Q9NRC9	OTOR_HUMAN	otoraplin	31			L -> P (in dbSNP:rs6135876). {ECO:0000269|Ref.6}.		cartilage condensation (GO:0001502)|sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(1)|liver(4)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	10						TCCAAGAAGCTCTGTGCAGAT	0.363													T|||	974	0.194489	0.0545	0.1239	5008	,	,		18794	0.3165		0.16	False		,,,				2504	0.3436				p.L31P		Atlas-SNP	.											.	OTOR	22	.	0			c.T92C						PASS	.	T	PRO/LEU	345,4061	179.0+/-207.6	12,321,1870	216.0	215.0	215.0		92	5.9	1.0	20	dbSNP_114	215	1503,7097	285.8+/-297.4	142,1219,2939	yes	missense	OTOR	NM_020157.2	98	154,1540,4809	CC,CT,TT		17.4767,7.8302,14.2088	probably-damaging	31/129	16729138	1848,11158	2203	4300	6503	SO:0001583	missense	56914	exon1			AGAAGCTCTGTGC	AF233261	CCDS13124.1	20p12.1-p11.23	2005-11-14			ENSG00000125879	ENSG00000125879			8517	protein-coding gene	gene with protein product		606067				10873378	Standard	NM_020157		Approved	MIAL, MIAL1, FDP	uc002wpj.3	Q9NRC9	OTTHUMG00000031931	ENST00000246081.2:c.92T>C	20.37:g.16729138T>C	ENSP00000246081:p.Leu31Pro	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_020157	D3DW22|Q3MIU6	Missense_Mutation	SNP	ENST00000246081.2	37	CCDS13124.1	381	0.17445054945054944	31	0.06300813008130081	53	0.1464088397790055	172	0.3006993006993007	125	0.16490765171503957	T	20.9	4.074316	0.76415	0.078302	0.174767	ENSG00000125879	ENST00000246081	D	0.83506	-1.73	5.93	5.93	0.95920	Src homology-3 domain (1);	0.145914	0.49916	D	0.000140	T	0.00039	0.0001	L	0.43152	1.355	0.09310	P	0.999999999207977	D	0.76494	0.999	D	0.67231	0.95	T	0.00054	-1.2181	9	0.72032	D	0.01	-13.0638	14.9654	0.71188	0.0:0.0:0.0:1.0	rs6135876;rs52799694;rs58763389;rs6135876	31	Q9NRC9	OTOR_HUMAN	P	31	ENSP00000246081:L31P	ENSP00000246081:L31P	L	+	2	0	OTOR	16677138	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.835000	0.69368	2.281000	0.76405	0.533000	0.62120	CTC	T|0.844;C|0.156	0.156	strong		0.363	OTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078108.2		
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 GAIIx	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_ENST00000475231.1_Silent_p.T2004T|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	148	34	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	
FANCI	55215	hgsc.bcm.edu	37	15	89838318	89838318	+	Missense_Mutation	SNP	A	A	T	rs35875311	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89838318A>T	ENST00000310775.7	+	24	2715	c.2629A>T	c.(2629-2631)Ata>Tta	p.I877L	FANCI_ENST00000300027.8_Intron	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	877				I -> L (in Ref. 6; BAB47423). {ECO:0000305}.	cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CCTCTGTGACATAACTCGGTA	0.478								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				A|||	298	0.0595048	0.0038	0.072	5008	,	,		19029	0.0595		0.0924	False		,,,				2504	0.092				p.I877L		Atlas-SNP	.											.	FANCI	129	.	0			c.A2629T						PASS	.	A	LEU/ILE,	29,1349		1,27,661	117.0	105.0	108.0		2629,	6.0	1.0	15	dbSNP_126	108	349,2831		17,315,1258	yes	missense,intron	FANCI	NM_001113378.1,NM_018193.2	5,	18,342,1919	TT,TA,AA		10.9748,2.1045,8.2931	benign,	877/1329,	89838318	378,4180	689	1590	2279	SO:0001583	missense	55215	exon24	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGTGACATAACTC	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.2629A>T	15.37:g.89838318A>T	ENSP00000310842:p.Ile877Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	140	0.0641025641025641	2	0.0040650406504065045	25	0.06906077348066299	37	0.06468531468531469	76	0.10026385224274406	A	19.13	3.766935	0.69878	0.021045	0.109748	ENSG00000140525	ENST00000310775	T	0.73897	-0.79	5.98	5.98	0.97165	.	0.101413	0.36409	U	0.002613	T	0.03348	0.0097	L	0.48362	1.52	0.80722	D	1	B	0.22604	0.072	B	0.25140	0.058	T	0.36578	-0.9742	10	0.13108	T	0.6	-2.4301	16.4696	0.84102	1.0:0.0:0.0:0.0	rs35875311	877	Q9NVI1	FANCI_HUMAN	L	877	ENSP00000310842:I877L	ENSP00000310842:I877L	I	+	1	0	FANCI	87639322	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.129000	0.57957	2.289000	0.77006	0.482000	0.46254	ATA	A|0.931;T|0.069	0.069	strong		0.478	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
ZNF446	55663	hgsc.bcm.edu	37	19	58991900	58991900	+	Missense_Mutation	SNP	G	G	A	rs882610	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58991900G>A	ENST00000594369.1	+	7	1541	c.1160G>A	c.(1159-1161)cGc>cAc	p.R387H	ZNF446_ENST00000335841.4_3'UTR|ZNF446_ENST00000596341.1_Missense_Mutation_p.R336H	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	387			R -> H (in dbSNP:rs882610).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CACCCCCGACGCTCACTCACA	0.662													G|||	1423	0.284145	0.4349	0.1772	5008	,	,		15898	0.2619		0.2535	False		,,,				2504	0.2106				p.R387H		Atlas-SNP	.											ZNF446,NS,carcinoma,+1,1	ZNF446	22	1	0			c.G1160A						PASS	.	G	HIS/ARG	1827,2579		381,1065,757	23.0	27.0	25.0		1160	2.0	0.0	19	dbSNP_86	25	2383,6213		332,1719,2247	yes	missense	ZNF446	NM_017908.2	29	713,2784,3004	AA,AG,GG		27.7222,41.4662,32.3796	benign	387/451	58991900	4210,8792	2203	4298	6501	SO:0001583	missense	55663	exon7			CCCGACGCTCACT		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.1160G>A	19.37:g.58991900G>A	ENSP00000472802:p.Arg387His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	78	27	0.346154	NM_017908		Missense_Mutation	SNP	ENST00000594369.1	37	CCDS12982.1	634	0.2902930402930403	217	0.4410569105691057	73	0.20165745856353592	142	0.24825174825174826	202	0.26649076517150394	G	5.166	0.216171	0.09810	0.414662	0.277222	ENSG00000083838	ENST00000335841;ENST00000540481;ENST00000391694	.	.	.	3.05	2.0	0.26442	.	0.739778	0.11129	N	0.596567	T	0.00012	0.0000	L	0.61036	1.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	8	0.66056	D	0.02	-9.4638	6.2625	0.20907	0.1125:0.0:0.7073:0.1802	rs882610;rs57562390;rs882610	387	Q9NWS9	ZN446_HUMAN	H	387;387;284	.	ENSP00000336565:R387H	R	+	2	0	ZNF446	63683712	0.018000	0.18449	0.000000	0.03702	0.000000	0.00434	1.172000	0.31908	0.327000	0.23409	-1.164000	0.01763	CGC	G|0.697;A|0.303	0.303	strong		0.662	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	
DSPP	1834	hgsc.bcm.edu	37	4	88537268	88537268	+	Missense_Mutation	SNP	G	G	A	rs62651555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88537268G>A	ENST00000282478.7	+	4	3487	c.3454G>A	c.(3454-3456)Gac>Aac	p.D1152N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1152N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1152	Asp/Ser-rich.			D -> N (in Ref. 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		tgaaagcagcgacagcagtga	0.557													G|||	745	0.148762	0.0144	0.3372	5008	,	,		27589	0.1776		0.2147	False		,,,				2504	0.0992				p.D1152N		Atlas-SNP	.											.	DSPP	174	.	0			c.G3454A						PASS	.	G	ASN/ASP	162,3000		5,152,1424	46.0	60.0	55.0		3454	1.5	0.4	4	dbSNP_134	55	1296,4426		118,1060,1683	no	missense	DSPP	NM_014208.3	23	123,1212,3107	AA,AG,GG		22.6494,5.1233,16.4115	probably-damaging	1152/1302	88537268	1458,7426	1581	2861	4442	SO:0001583	missense	1834	exon5			AGCAGCGACAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3454G>A	4.37:g.88537268G>A	ENSP00000282478:p.Asp1152Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	121	49	0.404959	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	G	2.285	-0.363699	0.05103	0.051233	0.226494	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.90444	-2.67;-2.67	1.52	1.52	0.23074	.	0.483859	0.15263	N	0.271667	T	0.00271	0.0008	L	0.29908	0.895	0.52501	P	4.199999999998649E-5	D	0.89917	1.0	D	0.74348	0.983	T	0.09640	-1.0665	9	0.44086	T	0.13	.	6.5429	0.22390	0.0:0.0:1.0:0.0	rs62651555	1152	Q9NZW4	DSPP_HUMAN	N	1152	ENSP00000382213:D1152N;ENSP00000282478:D1152N	ENSP00000282478:D1152N	D	+	1	0	DSPP	88756292	0.924000	0.31332	0.365000	0.25901	0.010000	0.07245	1.465000	0.35299	1.179000	0.42884	0.298000	0.19748	GAC	.	.	weak		0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
COX10	1352	hgsc.bcm.edu	37	17	13972955	13972955	+	Silent	SNP	C	C	T	rs8076787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:13972955C>T	ENST00000261643.3	+	1	110	c.33C>T	c.(31-33)cgC>cgT	p.R11R	COX10_ENST00000429152.2_Silent_p.R11R|COX10-AS1_ENST00000602743.1_RNA|COX10_ENST00000537334.1_5'UTR|COX10_ENST00000536205.1_5'UTR|COX10-AS1_ENST00000602539.1_RNA|COX10-AS1_ENST00000449363.1_RNA	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	11					aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TCTCCTCACGCCTCCTGACAG	0.627													C|||	166	0.033147	0.0045	0.036	5008	,	,		16178	0.0288		0.0666	False		,,,				2504	0.0399				p.R11R		Atlas-SNP	.											.	COX10	36	.	0			c.C33T						PASS	.	C		49,4357	50.9+/-86.3	1,47,2155	54.0	47.0	49.0		33	4.3	1.0	17	dbSNP_116	49	579,8021	153.3+/-207.7	25,529,3746	no	coding-synonymous	COX10	NM_001303.3		26,576,5901	TT,TC,CC		6.7326,1.1121,4.8285		11/444	13972955	628,12378	2203	4300	6503	SO:0001819	synonymous_variant	1352	exon1			CTCACGCCTCCTG	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"""Mitochondrial respiratory chain complex assembly factors"""	2260	protein-coding gene	gene with protein product	"""heme A: farnesyltransferase"", ""protoheme IX farnesyltransferase, mitochondrial"", ""heme O synthase"""	602125	"""COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)"", ""COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"""			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.33C>T	17.37:g.13972955C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Silent	SNP	ENST00000261643.3	37	CCDS11166.1																																																																																			C|0.957;T|0.043	0.043	strong		0.627	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
MYO15A	51168	hgsc.bcm.edu	37	17	18057167	18057167	+	Missense_Mutation	SNP	A	A	T	rs712270	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18057167A>T	ENST00000205890.5	+	43	8383	c.8045A>T	c.(8044-8046)tAc>tTc	p.Y2682F	MYO15A_ENST00000418233.3_De_novo_Start_OutOfFrame|MYO15A_ENST00000585180.1_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2682	Tail.		Y -> F (in dbSNP:rs712270).		inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CCCAACTTCTACGGCTATCAG	0.667													A|||	1066	0.212859	0.1732	0.2968	5008	,	,		8448	0.0704		0.3907	False		,,,				2504	0.1708				p.Y2682F		Atlas-SNP	.											MYO15A,NS,carcinoma,0,1	MYO15A	268	1	0			c.A8045T						PASS	.	A	PHE/TYR	861,2937		86,689,1124	44.0	45.0	45.0		8045	5.1	0.5	17	dbSNP_86	45	3348,4886		696,1956,1465	yes	missense	MYO15A	NM_016239.3	22	782,2645,2589	TT,TA,AA		40.6607,22.6698,34.9817	probably-damaging	2682/3531	18057167	4209,7823	1899	4117	6016	SO:0001583	missense	51168	exon42			ACTTCTACGGCTA	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8045A>T	17.37:g.18057167A>T	ENSP00000205890:p.Tyr2682Phe	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	192	82	0.427083	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	538	0.24633699633699635	84	0.17073170731707318	107	0.2955801104972376	42	0.07342657342657342	305	0.4023746701846966	A	17.13	3.311675	0.60414	0.226698	0.406607	ENSG00000091536	ENST00000205890	D	0.87571	-2.27	5.07	5.07	0.68467	.	.	.	.	.	T	0.00012	0.0000	L	0.33485	1.01	0.09310	P	1.0	D	0.76494	0.999	D	0.63283	0.913	T	0.22452	-1.0216	8	0.19147	T	0.46	.	8.7972	0.34887	0.9117:0.0:0.0883:0.0	rs712270;rs1671919;rs52825480;rs57683381;rs712270	2682	Q9UKN7	MYO15_HUMAN	F	2682	ENSP00000205890:Y2682F	ENSP00000205890:Y2682F	Y	+	2	0	MYO15A	17997892	1.000000	0.71417	0.513000	0.27749	0.804000	0.45430	5.142000	0.64820	1.915000	0.55452	0.460000	0.39030	TAC	A|0.723;T|0.277	0.277	strong		0.667	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
CCDC137	339230	hgsc.bcm.edu	37	17	79634774	79634774	+	Missense_Mutation	SNP	A	A	T	rs61742303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79634774A>T	ENST00000329214.8	+	2	553	c.150A>T	c.(148-150)aaA>aaT	p.K50N	OXLD1_ENST00000573786.1_5'Flank|OXLD1_ENST00000374741.3_5'Flank|OXLD1_ENST00000571503.1_5'Flank	NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	50							poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			AGAAGAAGAAAGTGAACTGCA	0.493													A|||	537	0.107228	0.1467	0.0951	5008	,	,		17005	0.002		0.1928	False		,,,				2504	0.0828				p.K50N		Atlas-SNP	.											.	CCDC137	27	.	0			c.A150T						PASS	.	A	ASN/LYS	722,3022		70,582,1220	58.0	62.0	61.0		150	0.8	1.0	17	dbSNP_129	61	1370,6838		127,1116,2861	yes	missense	CCDC137	NM_199287.2	94	197,1698,4081	TT,TA,AA		16.691,19.2842,17.5033	probably-damaging	50/290	79634774	2092,9860	1872	4104	5976	SO:0001583	missense	339230	exon2			GAAGAAAGTGAAC	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.150A>T	17.37:g.79634774A>T	ENSP00000329360:p.Lys50Asn	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	15	6	0.4	NM_199287		Missense_Mutation	SNP	ENST00000329214.8	37	CCDS42400.1	244	0.11172161172161173	72	0.14634146341463414	41	0.1132596685082873	0	0.0	131	0.17282321899736147	A	17.85	3.491233	0.64074	0.192842	0.16691	ENSG00000185298	ENST00000329214	D	0.90788	-2.73	4.26	0.759	0.18438	.	0.625364	0.15478	N	0.260244	T	0.01353	0.0044	M	0.78637	2.42	0.31061	P	0.714183	D	0.58268	0.982	P	0.54924	0.764	T	0.41179	-0.9523	9	0.72032	D	0.01	0.0104	7.9003	0.29731	0.6186:0.0:0.3814:0.0	rs61742303	50	Q6PK04	CC137_HUMAN	N	50	ENSP00000329360:K50N	ENSP00000329360:K50N	K	+	3	2	CCDC137	77245179	0.956000	0.32656	0.997000	0.53966	0.879000	0.50718	0.792000	0.26929	0.221000	0.20879	0.460000	0.39030	AAA	A|0.867;T|0.133	0.133	strong		0.493	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
CASQ2	845	hgsc.bcm.edu	37	1	116243877	116243877	+	Silent	SNP	G	G	A	rs7413162|rs397516641	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:116243877G>A	ENST00000261448.5	-	11	1424	c.1185C>T	c.(1183-1185)gaC>gaT	p.D395D	CASQ2_ENST00000456138.2_Silent_p.D324D	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	395	Asp/Glu-rich (acidic).				cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-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)		catcatcatcgtcatcactgt	0.398													A|||	2132	0.425719	0.4599	0.464	5008	,	,		23773	0.3224		0.4135	False		,,,				2504	0.4714				p.D395D		Atlas-SNP	.											.	CASQ2	54	.	0			c.C1185T						PASS	.	A		1973,2433	619.6+/-393.4	458,1057,688	231.0	197.0	208.0		1185	-9.6	0.5	1	dbSNP_116	208	3073,5527	660.2+/-401.7	565,1943,1792	no	coding-synonymous	CASQ2	NM_001232.3		1023,3000,2480	AA,AG,GG		35.7326,44.7798,38.7975		395/400	116243877	5046,7960	2203	4300	6503	SO:0001819	synonymous_variant	845	exon11			ATCATCGTCATCA	BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"""Protein disulfide isomerases"""	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.1185C>T	1.37:g.116243877G>A		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	222	100	0.45045	NM_001232	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Silent	SNP	ENST00000261448.5	37	CCDS884.1																																																																																			G|0.586;A|0.414	0.414	strong		0.398	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232	
TTLL1	25809	hgsc.bcm.edu	37	22	43455531	43455531	+	Silent	SNP	C	C	T	rs1132079	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:43455531C>T	ENST00000266254.7	-	8	990	c.750G>A	c.(748-750)gaG>gaA	p.E250E	TTLL1_ENST00000331018.7_Silent_p.E250E	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	250	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		GGTTGTAGTCCTCCTGGTGAC	0.617													C|||	742	0.148163	0.0772	0.2363	5008	,	,		16638	0.001		0.2793	False		,,,				2504	0.1984				p.E250E		Atlas-SNP	.											.	TTLL1	41	.	0			c.G750A						PASS	.	C		475,3931	219.4+/-237.2	30,415,1758	95.0	67.0	76.0		750	-3.2	1.0	22	dbSNP_86	76	2551,6049	405.5+/-348.5	379,1793,2128	no	coding-synonymous	TTLL1	NM_012263.4		409,2208,3886	TT,TC,CC		29.6628,10.7808,23.2662		250/424	43455531	3026,9980	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon8			GTAGTCCTCCTGG	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.750G>A	22.37:g.43455531C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	360	0.16483516483516483	45	0.09146341463414634	99	0.27348066298342544	3	0.005244755244755245	213	0.28100263852242746	C	7.209	0.595020	0.13875	0.107808	0.296628	ENSG00000100271	ENST00000495814	.	.	.	5.16	-3.19	0.05171	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41324	-0.9515	3	.	.	.	.	1.3538	0.02178	0.4502:0.1905:0.1963:0.163	rs1132079;rs3192571;rs4822258;rs17417670;rs17506442;rs4822258	.	.	.	K	176	.	.	R	-	2	0	TTLL1	41785475	0.921000	0.31238	0.992000	0.48379	0.575000	0.36095	0.074000	0.14662	-0.301000	0.08882	-1.823000	0.00598	AGG	T|0.177;G|0.153	0.177	strong		0.617	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	
LRRK2	120892	hgsc.bcm.edu	37	12	40713873	40713873	+	Silent	SNP	A	A	G	rs11176013	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:40713873A>G	ENST00000298910.7	+	34	4969	c.4911A>G	c.(4909-4911)aaA>aaG	p.K1637K		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1637					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.K1637K(1)|p.K1649K(1)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				TTCTTTCAAAAAAAAGGAAAT	0.358											OREG0003827	type=REGULATORY REGION|Gene=LOC486608|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	2933	0.585663	0.587	0.6052	5008	,	,		14667	0.501		0.5427	False		,,,				2504	0.7014				p.K1637K		Atlas-SNP	.											LRRK2_ENST00000298910,rectum,carcinoma,0,2	LRRK2	763	2	2	Substitution - coding silent(2)	large_intestine(2)	c.A4911G						PASS	.	G		2529,1869	498.4+/-364.1	744,1041,414	54.0	64.0	60.0		4911	5.5	1.0	12	dbSNP_120	60	4638,3954	529.1+/-381.5	1240,2158,898	no	coding-synonymous	LRRK2	NM_198578.3		1984,3199,1312	GG,GA,AA		46.0196,42.4966,44.8268		1637/2528	40713873	7167,5823	2199	4296	6495	SO:0001819	synonymous_variant	120892	exon34			TTCAAAAAAAAGG	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4911A>G	12.37:g.40713873A>G		Somatic	82	0	0	895	WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																			A|0.453;G|0.547	0.547	strong		0.358	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
RP1L1	94137	hgsc.bcm.edu	37	8	10474042	10474042	+	Missense_Mutation	SNP	T	T	G	rs4388421	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:10474042T>G	ENST00000382483.3	-	3	888	c.665A>C	c.(664-666)cAt>cCt	p.H222P		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	222	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.		H -> P (in dbSNP:rs4388421).		cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GAAGGCCTCATGCCCGGCACA	0.582													T|||	1085	0.216653	0.1573	0.2392	5008	,	,		17626	0.4573		0.1382	False		,,,				2504	0.1135				p.H222P		Atlas-SNP	.											RP1L1,NS,carcinoma,-1,1	RP1L1	453	1	0			c.A665C						PASS	.	T	PRO/HIS	618,3232		56,506,1363	47.0	49.0	49.0		665	3.2	0.0	8	dbSNP_111	49	1268,7008		106,1056,2976	yes	missense	RP1L1	NM_178857.5	77	162,1562,4339	GG,GT,TT		15.3214,16.0519,15.5534	possibly-damaging	222/2401	10474042	1886,10240	1925	4138	6063	SO:0001583	missense	94137	exon3			GCCTCATGCCCGG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.665A>C	8.37:g.10474042T>G	ENSP00000371923:p.His222Pro	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	542	0.24816849816849818	81	0.16463414634146342	88	0.2430939226519337	271	0.4737762237762238	102	0.1345646437994723	T	10.43	1.348313	0.24426	0.160519	0.153214	ENSG00000183638	ENST00000382483	D	0.92048	-2.96	4.42	3.24	0.37175	.	1.072000	0.07446	N	0.898278	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D	0.56035	0.974	P	0.54026	0.74	T	0.13980	-1.0489	9	0.48119	T	0.1	-2.2994	3.2303	0.06746	0.2065:0.113:0.0:0.6805	rs4388421;rs4388421	222	A6NKC6	.	P	222	ENSP00000371923:H222P	ENSP00000371923:H222P	H	-	2	0	RP1L1	10511452	0.944000	0.32072	0.003000	0.11579	0.151000	0.21798	3.784000	0.55416	0.716000	0.32124	0.379000	0.24179	CAT	T|0.771;G|0.229	0.229	strong		0.582	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
FCN2	2220	hgsc.bcm.edu	37	9	137779091	137779091	+	Missense_Mutation	SNP	G	G	T	rs7851696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:137779091G>T	ENST00000291744.6	+	8	782	c.772G>T	c.(772-774)Gct>Tct	p.A258S	FCN2_ENST00000350339.2_Missense_Mutation_p.A220S	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	258	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		A -> S (in dbSNP:rs7851696).		complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		CGGAAATTGTGCTGTGATGTT	0.493													G|||	780	0.155751	0.2095	0.121	5008	,	,		22332	0.1895		0.1044	False		,,,				2504	0.1258				p.A258S		Atlas-SNP	.											.	FCN2	55	.	0			c.G772T	GRCh37	CM051923	FCN2	M	rs7851696	PASS	.	G	SER/ALA,SER/ALA	850,3556	335.7+/-304.0	86,678,1439	168.0	148.0	155.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	772,658	4.1	0.1	9	dbSNP_116	155	919,7681	204.1+/-246.9	48,823,3429	yes	missense,missense	FCN2	NM_004108.2,NM_015837.2	99,99	134,1501,4868	TT,TG,GG		10.686,19.2919,13.6014	probably-damaging,probably-damaging	258/314,220/276	137779091	1769,11237	2203	4300	6503	SO:0001583	missense	2220	exon8			AATTGTGCTGTGA	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.772G>T	9.37:g.137779091G>T	ENSP00000291744:p.Ala258Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	326	0.14926739926739926	94	0.1910569105691057	50	0.13812154696132597	102	0.17832167832167833	80	0.10554089709762533	G	21.6	4.173027	0.78452	0.192919	0.10686	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.79352	-1.26;-1.26	4.05	4.05	0.47172	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.41938	D	0.000783	T	0.00695	0.0023	M	0.87328	2.875	0.09310	P	0.999999198096	P;P	0.51537	0.946;0.865	P;P	0.59889	0.865;0.839	T	0.18967	-1.0320	9	0.87932	D	0	.	13.7007	0.62606	0.0:0.0:1.0:0.0	rs7851696;rs17549200;rs57217091;rs7851696	220;258	Q15485-2;Q15485	.;FCN2_HUMAN	S	220;258	ENSP00000291741:A220S;ENSP00000291744:A258S	ENSP00000291744:A258S	A	+	1	0	FCN2	136918912	1.000000	0.71417	0.077000	0.20336	0.008000	0.06430	6.062000	0.71155	1.791000	0.52520	0.563000	0.77884	GCT	G|0.858;T|0.142	0.142	strong		0.493	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
RPRD1B	58490	hgsc.bcm.edu	37	20	36668874	36668874	+	Silent	SNP	G	G	A	rs2273353	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:36668874G>A	ENST00000373433.4	+	2	591	c.189G>A	c.(187-189)gcG>gcA	p.A63A		NM_021215.3	NP_067038.1	Q9NQG5	RPR1B_HUMAN	regulation of nuclear pre-mRNA domain containing 1B	63	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.				dephosphorylation of RNA polymerase II C-terminal domain (GO:0070940)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle process (GO:0010564)|transcription, DNA-templated (GO:0006351)	DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nucleus (GO:0005634)	RNA polymerase II core binding (GO:0000993)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)	12						TGTATTTAGCGAATGATGTCA	0.323													G|||	1456	0.290735	0.4962	0.134	5008	,	,		18769	0.2163		0.164	False		,,,				2504	0.3313				p.A63A		Atlas-SNP	.											RPRD1B,NS,carcinoma,+1,2	RPRD1B	25	2	0			c.G189A						PASS	.	G		1909,2495	546.1+/-377.0	425,1059,718	153.0	149.0	150.0		189	-10.3	0.4	20	dbSNP_100	150	1413,7187	269.8+/-288.6	113,1187,3000	no	coding-synonymous	RPRD1B	NM_021215.3		538,2246,3718	AA,AG,GG		16.4302,43.347,25.546		63/327	36668874	3322,9682	2202	4300	6502	SO:0001819	synonymous_variant	58490	exon2			TTTAGCGAATGAT	AL109823	CCDS13301.1	20q11.21-q12	2012-02-09	2008-08-15	2008-07-28	ENSG00000101413	ENSG00000101413			16209	protein-coding gene	gene with protein product		614694	"""chromosome 20 open reading frame 77"""	C20orf77		22231121	Standard	NM_021215		Approved	dJ1057B20.2, DKFZp434P0735, CREPT, FLJ44520, NET60	uc002xho.4	Q9NQG5	OTTHUMG00000032434	ENST00000373433.4:c.189G>A	20.37:g.36668874G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	47	0.451923	NM_021215	Q1WDE7|Q6PKF4	Silent	SNP	ENST00000373433.4	37	CCDS13301.1																																																																																			G|0.747;A|0.253	0.253	strong		0.323	RPRD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079142.2	NM_021215	
TSC22D2	9819	hgsc.bcm.edu	37	3	150128994	150128994	+	Silent	SNP	T	T	G	rs34647320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:150128994T>G	ENST00000361875.3	+	1	2873	c.1857T>G	c.(1855-1857)ccT>ccG	p.P619P	TSC22D2_ENST00000361136.2_Silent_p.P619P	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	619					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TGAAGCCGCCTGTTGCAGATT	0.468													T|||	413	0.0824681	0.0386	0.0879	5008	,	,		18932	0.0317		0.172	False		,,,				2504	0.0982				p.P619P		Atlas-SNP	.											.	TSC22D2	42	.	0			c.T1857G						PASS	.	T		314,4092	166.9+/-198.0	10,294,1899	85.0	94.0	91.0		1857	1.2	1.0	3	dbSNP_126	91	1717,6883	311.8+/-310.5	165,1387,2748	no	coding-synonymous	TSC22D2	NM_014779.2		175,1681,4647	GG,GT,TT		19.9651,7.1266,15.6159		619/781	150128994	2031,10975	2203	4300	6503	SO:0001819	synonymous_variant	9819	exon1			GCCGCCTGTTGCA	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.1857T>G	3.37:g.150128994T>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	115	67	0.582609	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Silent	SNP	ENST00000361875.3	37	CCDS3149.1	203|203	0.09294871794871795|0.09294871794871795	15|15	0.03048780487804878|0.03048780487804878	33|33	0.09116022099447514|0.09116022099447514	29|29	0.050699300699300696|0.050699300699300696	126|126	0.1662269129287599|0.1662269129287599	T|T	8.025|8.025	0.760446|0.760446	0.15914|0.15914	0.071266|0.071266	0.199651|0.199651	ENSG00000196428|ENSG00000196428	ENST00000466814|ENST00000480589	.|.	.|.	.|.	5.05|5.05	1.23|1.23	0.21249|0.21249	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999991805|0.9999999999991805	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18967|0.18967	-1.0320|-1.0320	3|3	.|.	.|.	.|.	.|.	3.3184|3.3184	0.07041|0.07041	0.1903:0.3818:0.0:0.4278|0.1903:0.3818:0.0:0.4278	rs34647320|rs34647320	.|.	.|.	.|.	G|R	67|80	.|.	.|.	C|L	+|+	1|2	0|0	TSC22D2|TSC22D2	151611684|151611684	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	0.378000|0.378000	0.20569|0.20569	0.244000|0.244000	0.21351|0.21351	0.374000|0.374000	0.22700|0.22700	TGT|CTG	T|0.866;G|0.134;A|0.000	0.134	strong		0.468	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
SRCIN1	80725	hgsc.bcm.edu	37	17	36708225	36708225	+	Missense_Mutation	SNP	C	C	T	rs118010851	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:36708225C>T	ENST00000264659.7	-	14	2848	c.2624G>A	c.(2623-2625)aGc>aAc	p.S875N	SRCIN1_ENST00000578925.1_Missense_Mutation_p.S909N|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	747	Pro-rich.				exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)			endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						AGCTGGCCCGCTCAGCTCATG	0.602													C|||	61	0.0121805	0.0008	0.013	5008	,	,		16191	0.0		0.0288	False		,,,				2504	0.0225				p.S875N		Atlas-SNP	.											.	SRCIN1	66	.	0			c.G2624A						PASS	.	C	ASN/SER	25,3815		0,25,1895	37.0	42.0	40.0		2624	3.7	0.5	17	dbSNP_132	40	299,7925		2,295,3815	yes	missense	SRCIN1	NM_025248.2	46	2,320,5710	TT,TC,CC		3.6357,0.651,2.6857	benign	875/1184	36708225	324,11740	1920	4112	6032	SO:0001583	missense	80725	exon14			GGCCCGCTCAGCT		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"""p130Cas-associated protein"", ""SNAP-25-interacting protein"""	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.2624G>A	17.37:g.36708225C>T	ENSP00000264659:p.Ser875Asn	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	37	CCDS45660.1	29	0.013278388278388278	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	22	0.029023746701846966	C	9.671	1.146677	0.21288	0.00651	0.036357	ENSG00000017373	ENST00000264659;ENST00000542707;ENST00000398579	T	0.46451	0.87	4.69	3.7	0.42460	.	0.381315	0.32416	N	0.006122	T	0.09335	0.0230	L	0.39898	1.24	0.29106	N	0.881164	P;B;B;B	0.38767	0.646;0.302;0.302;0.145	B;B;B;B	0.39152	0.292;0.167;0.167;0.109	T	0.08066	-1.0740	10	0.52906	T	0.07	-6.3177	8.3265	0.32160	0.0:0.7517:0.1608:0.0875	.	181;747;747;875	Q9C0H9-4;Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;.;SRCN1_HUMAN;.	N	875;656;729	ENSP00000264659:S875N	ENSP00000264659:S875N	S	-	2	0	SRCIN1	33961751	0.925000	0.31364	0.502000	0.27614	0.156000	0.22039	3.364000	0.52328	1.300000	0.44818	0.561000	0.74099	AGC	C|0.982;T|0.018	0.018	strong		0.602	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	
MMRN1	22915	hgsc.bcm.edu	37	4	90816294	90816294	+	Missense_Mutation	SNP	A	A	G	rs1442138	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:90816294A>G	ENST00000394980.1	+	2	491	c.172A>G	c.(172-174)Act>Gct	p.T58A	MMRN1_ENST00000264790.2_Missense_Mutation_p.T58A|MMRN1_ENST00000394981.1_Missense_Mutation_p.T58A			Q13201	MMRN1_HUMAN	multimerin 1	58			T -> A (in dbSNP:rs1442138).		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		ACTGCCAACCACTCGGGTCAT	0.458													A|||	366	0.0730831	0.174	0.0461	5008	,	,		19127	0.0		0.0596	False		,,,				2504	0.045				p.T58A		Atlas-SNP	.											.	MMRN1	174	.	0			c.A172G						PASS	.	A	ALA/THR	638,3768	275.2+/-272.4	46,546,1611	64.0	69.0	67.0		172	-8.0	0.0	4	dbSNP_88	67	487,8113	141.2+/-197.6	21,445,3834	yes	missense	MMRN1	NM_007351.2	58	67,991,5445	GG,GA,AA		5.6628,14.4803,8.6499	benign	58/1229	90816294	1125,11881	2203	4300	6503	SO:0001583	missense	22915	exon1			CCAACCACTCGGG	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.172A>G	4.37:g.90816294A>G	ENSP00000378431:p.Thr58Ala	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	150	0.06868131868131869	86	0.17479674796747968	18	0.049723756906077346	0	0.0	46	0.06068601583113457	A	0.191	-1.053694	0.01965	0.144803	0.056628	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000394981	T;T;T	0.80393	0.0;0.0;-1.37	4.01	-8.03	0.01114	.	1.363460	0.04858	N	0.443517	T	0.00241	0.0007	N	0.14661	0.345	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.003	T	0.04178	-1.0971	9	0.19147	T	0.46	.	2.6911	0.05121	0.1636:0.4534:0.1598:0.2232	rs1442138;rs58378963;rs1442138	58;58	Q13201-2;Q13201	.;MMRN1_HUMAN	A	58	ENSP00000378431:T58A;ENSP00000264790:T58A;ENSP00000378432:T58A	ENSP00000264790:T58A	T	+	1	0	MMRN1	91035317	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-0.632000	0.05489	-2.072000	0.00879	0.460000	0.39030	ACT	A|0.914;G|0.086	0.086	strong		0.458	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351	
RIC1	57589	hgsc.bcm.edu	37	9	5747390	5747390	+	Missense_Mutation	SNP	C	C	A	rs41280731	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:5747390C>A	ENST00000414202.2	+	12	1528	c.1337C>A	c.(1336-1338)tCt>tAt	p.S446Y	KIAA1432_ENST00000381532.2_Missense_Mutation_p.S367Y|KIAA1432_ENST00000251879.6_Missense_Mutation_p.S446Y|KIAA1432_ENST00000449720.2_Missense_Mutation_p.S367Y|KIAA1432_ENST00000418622.3_Missense_Mutation_p.S367Y	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		CCCAGGAGTTCTTCAACACAC	0.478													C|||	15	0.00299521	0.0	0.0	5008	,	,		18779	0.0		0.0139	False		,,,				2504	0.001				p.S446Y		Atlas-SNP	.											.	KIAA1432	97	.	0			c.C1337A						PASS	.	C	TYR/SER,TYR/SER,TYR/SER	8,4398	14.3+/-33.2	0,8,2195	130.0	121.0	124.0		1337,1337,1337	6.1	0.7	9	dbSNP_127	124	110,8490	59.5+/-121.1	1,108,4191	yes	missense,missense,missense	KIAA1432	NM_001135920.2,NM_001206557.1,NM_020829.3	144,144,144	1,116,6386	AA,AC,CC		1.2791,0.1816,0.9073	benign,benign,benign	446/1166,446/1387,446/1424	5747390	118,12888	2203	4300	6503	SO:0001583	missense	57589	exon12			GGAGTTCTTCAAC																												ENST00000414202.2:c.1337C>A	9.37:g.5747390C>A	ENSP00000416696:p.Ser446Tyr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	120	73	0.608333	NM_001206557		Missense_Mutation	SNP	ENST00000414202.2	37	CCDS34982.2	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	16.11|16.11	3.029174|3.029174	0.54790|0.54790	0.001816|0.001816	0.012791|0.012791	ENSG00000107036|ENSG00000107036	ENST00000545641|ENST00000251879;ENST00000414202;ENST00000381532;ENST00000418622;ENST00000449720	.|T;T;T;T;T	.|0.41758	.|0.99;0.99;0.99;0.99;0.99	6.05|6.05	6.05|6.05	0.98169|0.98169	.|.	.|0.379769	.|0.26820	.|N	.|0.022324	T|T	0.24812|0.24812	0.0602|0.0602	N|N	0.12182|0.12182	0.205|0.205	0.23991|0.23991	N|N	0.996244|0.996244	.|P;P;P	.|0.48016	.|0.845;0.845;0.904	.|B;B;P	.|0.44946	.|0.275;0.272;0.465	T|T	0.20605|0.20605	-1.0270|-1.0270	5|10	.|0.49607	.|T	.|0.09	-15.5896|-15.5896	15.6722|15.6722	0.77286|0.77286	0.0:0.8635:0.1365:0.0|0.0:0.8635:0.1365:0.0	rs41280731|rs41280731	.|367;446;446	.|B7ZM67;Q4ADV7;G5E932	.|.;RIC1_HUMAN;.	L|Y	374|446;446;367;367;367	.|ENSP00000251879:S446Y;ENSP00000416696:S446Y;ENSP00000370943:S367Y;ENSP00000402240:S367Y;ENSP00000398823:S367Y	.|ENSP00000251879:S446Y	F|S	+|+	3|2	2|0	KIAA1432|KIAA1432	5737390|5737390	0.347000|0.347000	0.24853|0.24853	0.719000|0.719000	0.30619|0.30619	0.960000|0.960000	0.62799|0.62799	1.811000|1.811000	0.38942|0.38942	2.878000|2.878000	0.98634|0.98634	0.650000|0.650000	0.86243|0.86243	TTC|TCT	C|0.992;A|0.008	0.008	strong		0.478	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3		
MASTL	84930	hgsc.bcm.edu	37	10	27459746	27459746	+	Missense_Mutation	SNP	C	C	G	rs3802526	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27459746C>G	ENST00000375940.4	+	8	1915	c.1858C>G	c.(1858-1860)Cca>Gca	p.P620A	MASTL_ENST00000375946.4_Missense_Mutation_p.P620A|MASTL_ENST00000477034.1_3'UTR|MASTL_ENST00000342386.6_Missense_Mutation_p.P620A			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	620	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> A (in dbSNP:rs3802526). {ECO:0000269|PubMed:17344846}.		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						AAAGACCTCACCAAAAGGTGT	0.398													C|||	553	0.110423	0.0825	0.0432	5008	,	,		19224	0.1528		0.0646	False		,,,				2504	0.1994				p.P620A		Atlas-SNP	.											.	MASTL	81	.	0			c.C1858G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	361,4045	185.3+/-212.5	15,331,1857	47.0	46.0	46.0		1858,1858,1858	4.3	0.1	10	dbSNP_107	46	449,8151	134.9+/-192.2	10,429,3861	yes	missense,missense,missense	MASTL	NM_001172303.1,NM_001172304.1,NM_032844.3	27,27,27	25,760,5718	GG,GC,CC		5.2209,8.1934,6.2279	benign,benign,benign	620/880,620/841,620/879	27459746	810,12196	2203	4300	6503	SO:0001583	missense	84930	exon8			ACCTCACCAAAAG	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.1858C>G	10.37:g.27459746C>G	ENSP00000365107:p.Pro620Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	210	0.09615384615384616	30	0.06097560975609756	18	0.049723756906077346	116	0.20279720279720279	46	0.06068601583113457	C	4.898	0.166844	0.09339	0.081934	0.052209	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.21031	2.03;2.03;2.03	5.28	4.32	0.51571	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.498560	0.23151	N	0.051360	T	0.00039	0.0001	L	0.60455	1.87	0.58432	P	4.000000000004E-6	B;B;B	0.30605	0.152;0.116;0.287	B;B;B	0.31101	0.116;0.053;0.124	T	0.25398	-1.0133	9	0.18276	T	0.48	-1.2401	14.7985	0.69894	0.0:0.8555:0.1445:0.0	rs3802526;rs52826430;rs3802526	620;620;620	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	A	620	ENSP00000365113:P620A;ENSP00000343446:P620A;ENSP00000365107:P620A	ENSP00000343446:P620A	P	+	1	0	MASTL	27499752	0.000000	0.05858	0.135000	0.22099	0.068000	0.16541	0.314000	0.19432	2.617000	0.88574	0.591000	0.81541	CCA	C|0.921;G|0.079	0.079	strong		0.398	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
LRRC56	115399	hgsc.bcm.edu	37	11	554018	554018	+	Silent	SNP	G	G	A	rs112033363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:554018G>A	ENST00000270115.7	+	14	1871	c.1371G>A	c.(1369-1371)agG>agA	p.R457R		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	457										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-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;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCACCCAAGGCCACGAGATT	0.667													G|||	275	0.0549121	0.0507	0.049	5008	,	,		16806	0.0466		0.0656	False		,,,				2504	0.0624				p.R457R		Atlas-SNP	.											.	LRRC56	23	.	0			c.G1371A						PASS	.	G		274,4132	149.2+/-183.4	10,254,1939	94.0	96.0	95.0		1371	2.0	0.0	11	dbSNP_132	95	530,8068	144.8+/-200.6	21,488,3790	no	coding-synonymous	LRRC56	NM_198075.3		31,742,5729	AA,AG,GG		6.1642,6.2188,6.1827		457/543	554018	804,12200	2203	4299	6502	SO:0001819	synonymous_variant	115399	exon14			CCCAAGGCCACGA		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.1371G>A	11.37:g.554018G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_198075	Q8N3Q4	Silent	SNP	ENST00000270115.7	37	CCDS7700.1																																																																																			G|0.939;A|0.061	0.061	strong		0.667	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
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 GAIIx	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_ENST00000541063.1_Silent_p.L102L|HIRA_ENST00000464189.1_5'Flank|HIRA_ENST00000546308.1_Silent_p.L102L|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		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	49	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	
HLCS	3141	hgsc.bcm.edu	37	21	38308911	38308911	+	Silent	SNP	G	G	A	rs1065758	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:38308911G>A	ENST00000399120.1	-	5	2064	c.834C>T	c.(832-834)agC>agT	p.S278S	HLCS_ENST00000336648.4_Silent_p.S278S	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	278					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	GCTTCACCTCGCTCTGGTCAG	0.592													G|||	357	0.0712859	0.031	0.0821	5008	,	,		19451	0.0417		0.172	False		,,,				2504	0.045				p.S278S		Atlas-SNP	.											.	HLCS	64	.	0			c.C834T						PASS	.	G	,,	242,4164	142.3+/-177.5	7,228,1968	78.0	74.0	75.0		834,834,834	-9.0	0.0	21	dbSNP_86	75	1407,7193	271.7+/-289.7	125,1157,3018	yes	coding-synonymous,coding-synonymous,coding-synonymous	HLCS	NM_000411.6,NM_001242784.1,NM_001242785.1	,,	132,1385,4986	AA,AG,GG		16.3605,5.4925,12.6788	,,	278/727,278/727,278/727	38308911	1649,11357	2203	4300	6503	SO:0001819	synonymous_variant	3141	exon5			CACCTCGCTCTGG		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"""holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)"", ""holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"""			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.834C>T	21.37:g.38308911G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	125	76	0.608	NM_000411	B2RAH1|D3DSG6|Q99451	Silent	SNP	ENST00000399120.1	37	CCDS13647.1																																																																																			G|0.893;A|0.107	0.107	strong		0.592	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2		
NFATC1	4772	hgsc.bcm.edu	37	18	77227476	77227476	+	Silent	SNP	A	A	G	rs25656	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:77227476A>G	ENST00000427363.2	+	8	1986	c.1986A>G	c.(1984-1986)ccA>ccG	p.P662P	NFATC1_ENST00000591814.1_Silent_p.P662P|NFATC1_ENST00000329101.4_Silent_p.P649P|NFATC1_ENST00000253506.5_Silent_p.P662P|NFATC1_ENST00000545796.1_Silent_p.P190P|NFATC1_ENST00000318065.5_Silent_p.P649P|NFATC1_ENST00000586434.1_Silent_p.P649P|NFATC1_ENST00000592223.1_Silent_p.P649P|NFATC1_ENST00000397790.2_Silent_p.P190P|NFATC1_ENST00000587635.1_Missense_Mutation_p.H634R|NFATC1_ENST00000542384.1_Silent_p.P662P			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	662					calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	AGATCCCGCCATTTCGGAATC	0.587													G|||	2028	0.404952	0.6717	0.379	5008	,	,		15486	0.374		0.2972	False		,,,				2504	0.2055				p.P662P	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.A1986G						PASS	.	G	,,,,	2671,1735	518.3+/-369.7	803,1065,335	99.0	76.0	84.0		1986,1947,570,1947,1986	-9.4	0.2	18	dbSNP_116	84	2780,5820	677.6+/-403.4	453,1874,1973	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	,,,,	1256,2939,2308	GG,GA,AA		32.3256,39.3781,41.9114	,,,,	662/826,649/931,190/354,649/813,662/717	77227476	5451,7555	2203	4300	6503	SO:0001819	synonymous_variant	4772	exon8			CCCGCCATTTCGG	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1986A>G	18.37:g.77227476A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Silent	SNP	ENST00000427363.2	37																																																																																				A|0.576;G|0.424	0.424	strong		0.587	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33624430	33624430	+	Silent	SNP	A	A	G	rs61748198	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:33624430A>G	ENST00000504830.1	-	14	2384	c.2049T>C	c.(2047-2049)gaT>gaC	p.D683D	ADAMTS12_ENST00000352040.3_Intron|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	683	Cys-rich.				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						TGGCATTGGAATCGATCTCAT	0.527										HNSCC(64;0.19)			A|||	805	0.160743	0.1445	0.1066	5008	,	,		19584	0.2669		0.0736	False		,,,				2504	0.2014				p.D683D		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.T2049C						PASS	.	A		549,3857	246.5+/-255.1	36,477,1690	105.0	78.0	87.0		2049	-0.8	0.7	5	dbSNP_129	87	672,7928	168.8+/-220.3	25,622,3653	no	coding-synonymous	ADAMTS12	NM_030955.2		61,1099,5343	GG,GA,AA		7.814,12.4603,9.388		683/1595	33624430	1221,11785	2203	4300	6503	SO:0001819	synonymous_variant	81792	exon14			ATTGGAATCGATC	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.2049T>C	5.37:g.33624430A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	253	101	0.399209	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																			A|0.893;G|0.107	0.107	strong		0.527	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
GRXCR1	389207	hgsc.bcm.edu	37	4	42895423	42895423	+	Missense_Mutation	SNP	C	C	T	rs57655409	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:42895423C>T	ENST00000399770.2	+	1	140	c.140C>T	c.(139-141)gCc>gTc	p.A47V	RN7SKP82_ENST00000516786.1_RNA	NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	47					auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						TCTGAATGTGCCAGTATCTGT	0.507													C|||	826	0.164936	0.0454	0.1988	5008	,	,		20993	0.3125		0.0398	False		,,,				2504	0.2791				p.A47V		Atlas-SNP	.											.	GRXCR1	78	.	0			c.C140T						PASS	.	C	VAL/ALA	213,3753		8,197,1778	181.0	183.0	182.0		140	5.7	1.0	4	dbSNP_129	182	488,7872		14,460,3706	yes	missense	GRXCR1	NM_001080476.2	64	22,657,5484	TT,TC,CC		5.8373,5.3707,5.6872	benign	47/291	42895423	701,11625	1983	4180	6163	SO:0001583	missense	389207	exon1			AATGTGCCAGTAT		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 88"""	613283	"""deafness, autosomal recessive 25"""	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.140C>T	4.37:g.42895423C>T	ENSP00000382670:p.Ala47Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	37	CCDS43225.1	333	0.15247252747252749	24	0.04878048780487805	71	0.19613259668508287	208	0.36363636363636365	30	0.0395778364116095	C	15.37	2.813216	0.50527	0.053707	0.058373	ENSG00000215203	ENST00000399770	T	0.33865	1.39	5.68	5.68	0.88126	.	0.146939	0.46442	U	0.000300	T	0.00012	0.0000	L	0.29908	0.895	0.30981	P	0.7224999999999999	B	0.22800	0.075	B	0.19946	0.027	T	0.43458	-0.9390	9	0.27785	T	0.31	-4.1182	18.7897	0.91968	0.0:1.0:0.0:0.0	rs57655409	47	A8MXD5	GRCR1_HUMAN	V	47	ENSP00000382670:A47V	ENSP00000382670:A47V	A	+	2	0	GRXCR1	42590180	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	5.685000	0.68204	2.683000	0.91414	0.650000	0.86243	GCC	C|0.877;T|0.123	0.123	strong		0.507	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476	
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 GAIIx	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	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	39	9	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 GAIIx	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	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	170	84	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	
URGCP	55665	hgsc.bcm.edu	37	7	43916727	43916727	+	Missense_Mutation	SNP	T	T	G	rs2232108	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:43916727T>G	ENST00000453200.1	-	6	2828	c.2335A>C	c.(2335-2337)Atg>Ctg	p.M779L	URGCP_ENST00000336086.6_Missense_Mutation_p.M736L|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000443736.1_Missense_Mutation_p.M736L|URGCP_ENST00000447717.3_Missense_Mutation_p.M736L|URGCP_ENST00000223341.7_Missense_Mutation_p.M736L|URGCP_ENST00000402306.3_Missense_Mutation_p.M770L|URGCP_ENST00000497914.1_5'UTR			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	779	VLIG-type G.		M -> L (in dbSNP:rs2232108). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CTCAGTCCCATGAGCAGAGTG	0.527													T|||	2559	0.510982	0.3933	0.5231	5008	,	,		20920	0.5764		0.4602	False		,,,				2504	0.6462				p.M779L		Atlas-SNP	.											.	URGCP	170	.	0			c.A2335C						PASS	.	T	LEU/MET,LEU/MET,,LEU/MET	1544,2518		301,942,788	79.0	78.0	79.0		2335,2206,,2308	3.0	1.0	7	dbSNP_98	79	3973,4427		962,2049,1189	yes	missense,missense,intron,missense	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	15,15,,15	1263,2991,1977	GG,GT,TT		47.2976,38.0108,44.2706	benign,benign,,benign	779/932,736/889,,770/923	43916727	5517,6945	2031	4200	6231	SO:0001583	missense	55665	exon6			GTCCCATGAGCAG		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2335A>C	7.37:g.43916727T>G	ENSP00000396918:p.Met779Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	49	15	0.306122	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Missense_Mutation	SNP	ENST00000453200.1	37	CCDS47578.1	1042	0.47710622710622713	185	0.37601626016260165	191	0.5276243093922652	308	0.5384615384615384	358	0.47229551451187335	T	14.29	2.491278	0.44249	0.380108	0.472976	ENSG00000106608	ENST00000223341;ENST00000336086;ENST00000402306;ENST00000443736;ENST00000453200;ENST00000447717	T;T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27;0.27	5.41	3.0	0.34707	.	0.351075	0.32719	N	0.005730	T	0.00012	0.0000	L	0.44542	1.39	0.42695	P	0.006406000000000023	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.42120	-0.9470	9	0.62326	D	0.03	-45.4448	3.0295	0.06102	0.1831:0.1741:0.0:0.6428	rs2232108;rs3735264;rs11551793;rs17654527;rs52829585;rs58683263;rs2232108	770;779	Q8TCY9-2;Q8TCY9	.;URGCP_HUMAN	L	736;736;770;736;779;736	ENSP00000223341:M736L;ENSP00000336872:M736L;ENSP00000384955:M770L;ENSP00000392136:M736L;ENSP00000396918:M779L;ENSP00000402803:M736L	ENSP00000223341:M736L	M	-	1	0	URGCP	43883252	0.219000	0.23619	0.979000	0.43373	0.991000	0.79684	0.607000	0.24209	0.854000	0.35336	0.482000	0.46254	ATG	T|0.515;G|0.485	0.485	strong		0.527	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
IFT74	80173	hgsc.bcm.edu	37	9	27009100	27009100	+	Missense_Mutation	SNP	T	T	C	rs17694549	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:27009100T>C	ENST00000443698.1	+	9	841	c.670T>C	c.(670-672)Ttt>Ctt	p.F224L	IFT74_ENST00000433700.1_Missense_Mutation_p.F224L|IFT74_ENST00000429045.2_Missense_Mutation_p.F224L|IFT74_ENST00000380062.5_Missense_Mutation_p.F224L	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	224			F -> L (in dbSNP:rs17694549). {ECO:0000269|PubMed:14702039}.		cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|keratinocyte development (GO:0003334)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|nucleus (GO:0005634)	beta-tubulin binding (GO:0048487)|chromatin binding (GO:0003682)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		AAATATGTCTTTTGAAAACCA	0.343													C|||	371	0.0740815	0.1006	0.0346	5008	,	,		17761	0.0278		0.0547	False		,,,				2504	0.1339				p.F224L		Atlas-SNP	.											.	IFT74	46	.	0			c.T670C						PASS	.	C	LEU/PHE,LEU/PHE,LEU/PHE,LEU/PHE	387,3299		21,345,1477	94.0	90.0	91.0		670,670,670,670	3.8	1.0	9	dbSNP_123	91	460,7720		12,436,3642	yes	missense,missense,missense,missense	IFT74	NM_001099222.1,NM_001099223.1,NM_001099224.1,NM_025103.2	22,22,22,22	33,781,5119	CC,CT,TT		5.6235,10.4992,7.138	benign,benign,benign,benign	224/601,224/601,224/373,224/601	27009100	847,11019	1843	4090	5933	SO:0001583	missense	80173	exon9			ATGTCTTTTGAAA	AK023707	CCDS43793.1, CCDS47955.1	9p21.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000096872	ENSG00000096872		"""Intraflagellar transport homologs"""	21424	protein-coding gene	gene with protein product	"""capillary morphogenesis protein 1"""	608040	"""coiled-coil domain containing 2"", ""intraflagellar transport 74 homolog (Chlamydomonas)"""	CCDC2		11683410	Standard	NM_001099223		Approved	CMG1, CMG-1, FLJ22621	uc003zqg.4	Q96LB3	OTTHUMG00000021028	ENST00000443698.1:c.670T>C	9.37:g.27009100T>C	ENSP00000404122:p.Phe224Leu	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	164	61	0.371951	NM_001099222	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Missense_Mutation	SNP	ENST00000443698.1	37	CCDS43793.1	105	0.04807692307692308	29	0.05894308943089431	16	0.04419889502762431	14	0.024475524475524476	46	0.06068601583113457	C	14.10	2.434757	0.43224	0.104992	0.056235	ENSG00000096872	ENST00000433700;ENST00000443698;ENST00000380062;ENST00000544022;ENST00000429045	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.67	3.79	0.43588	.	0.612906	0.17074	N	0.188042	T	0.00384	0.0012	N	0.14661	0.345	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.25328	-1.0135	10	0.27082	T	0.32	-0.0904	2.8142	0.05451	0.1324:0.4752:0.2402:0.1522	rs17694549;rs52818293;rs17694549	224;224	Q96LB3;Q96LB3-2	IFT74_HUMAN;.	L	224	ENSP00000389224:F224L;ENSP00000404122:F224L;ENSP00000369402:F224L;ENSP00000393907:F224L	ENSP00000369402:F224L	F	+	1	0	IFT74	26999100	0.345000	0.24835	0.994000	0.49952	0.951000	0.60555	0.362000	0.20284	0.326000	0.23384	-0.227000	0.12334	TTT	T|0.943;C|0.057	0.057	strong		0.343	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103	
WDFY4	57705	hgsc.bcm.edu	37	10	50022040	50022040	+	Silent	SNP	G	G	A	rs41283275	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50022040G>A	ENST00000325239.5	+	30	5280	c.5253G>A	c.(5251-5253)agG>agA	p.R1751R	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1751						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						TCCTGCAGAGGCACCACCAGG	0.582													G|||	749	0.149561	0.2322	0.1484	5008	,	,		19475	0.1022		0.1213	False		,,,				2504	0.1166				p.R1751R		Atlas-SNP	.											.	WDFY4	205	.	0			c.G5253A						PASS	.	G		318,1066		31,256,405	36.0	40.0	39.0		5253	-4.1	0.0	10	dbSNP_127	39	342,2840		19,304,1268	no	coding-synonymous	WDFY4	NM_020945.1		50,560,1673	AA,AG,GG		10.748,22.9769,14.4547		1751/3185	50022040	660,3906	692	1591	2283	SO:0001819	synonymous_variant	57705	exon31			GCAGAGGCACCAC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5253G>A	10.37:g.50022040G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	17	7	0.411765	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	313	0.1433150183150183	105	0.21341463414634146	48	0.13259668508287292	68	0.11888111888111888	92	0.12137203166226913	G	5.144	0.212184	0.09757	0.229769	0.10748	ENSG00000128815	ENST00000312002;ENST00000374161	.	.	.	5.83	-4.12	0.03916	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.30698	P	0.750638	.	.	.	.	.	.	T	0.34104	-0.9842	3	.	.	.	.	2.7652	0.05318	0.5275:0.1495:0.21:0.1131	rs41283275;rs61838867	.	.	.	T	842;298	.	.	A	+	1	0	WDFY4	49692046	0.590000	0.26815	0.009000	0.14445	0.628000	0.37860	-0.339000	0.07832	-0.628000	0.05582	-0.964000	0.02622	GCA	G|0.855;A|0.145	0.145	strong		0.582	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
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 GAIIx	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_ENST00000402325.1_Missense_Mutation_p.R472W|CCDC178_ENST00000579947.1_Missense_Mutation_p.R472W|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000583930.1_Missense_Mutation_p.R472W|CCDC178_ENST00000300227.8_Missense_Mutation_p.R472W|CCDC178_ENST00000403303.1_Missense_Mutation_p.R472W|CCDC178_ENST00000406524.2_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	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	54	22	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	
MUC16	94025	hgsc.bcm.edu	37	19	9049149	9049149	+	Missense_Mutation	SNP	G	G	A	rs12461007	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9049149G>A	ENST00000397910.4	-	5	32685	c.32482C>T	c.(32482-32484)Cct>Tct	p.P10828S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10830	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCTGTGCAGGATGCGTGACC	0.483													G|||	997	0.199081	0.1982	0.2695	5008	,	,		23097	0.0258		0.2813	False		,,,				2504	0.2444				p.P10828S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C32482T						PASS	.		SER/PRO	750,3182		72,606,1288	172.0	156.0	161.0		32482	-6.0	0.0	19	dbSNP_120	161	2519,5795		401,1717,2039	yes	missense	MUC16	NM_024690.2	74	473,2323,3327	AA,AG,GG		30.2983,19.0743,26.6944	benign	10828/14508	9049149	3269,8977	1966	4157	6123	SO:0001583	missense	94025	exon5			GTGCAGGATGCGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32482C>T	19.37:g.9049149G>A	ENSP00000381008:p.Pro10828Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	150	68	0.453333	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	426	0.19505494505494506	103	0.20934959349593496	95	0.26243093922651933	11	0.019230769230769232	217	0.2862796833773087	g	5.293	0.239478	0.10023	0.190743	0.302983	ENSG00000181143	ENST00000397910	T	0.03124	4.04	3.0	-5.99	0.02213	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.20052	0.041	B	0.15870	0.014	T	0.50466	-0.8825	8	0.87932	D	0	.	6.055	0.19807	0.3575:0.1554:0.487:0.0	rs12461007;rs52811941;rs61073913;rs12461007	10828	B5ME49	.	S	10828	ENSP00000381008:P10828S	ENSP00000381008:P10828S	P	-	1	0	MUC16	8910149	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	-0.091000	0.11146	-1.512000	0.01791	-0.633000	0.03987	CCT	G|0.783;A|0.217	0.217	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
OTUD7B	56957	hgsc.bcm.edu	37	1	149943157	149943157	+	Silent	SNP	G	G	A	rs77015846	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:149943157G>A	ENST00000369135.4	-	3	402	c.108C>T	c.(106-108)gcC>gcT	p.A36A	OTUD7B_ENST00000479905.1_5'UTR	NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	36					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CACTGAGGGCGGCATTCACAT	0.468													G|||	132	0.0263578	0.0083	0.0346	5008	,	,		18494	0.001		0.0875	False		,,,				2504	0.0082				p.A36A		Atlas-SNP	.											.	OTUD7B	76	.	0			c.C108T						PASS	.	G		76,3836		0,76,1880	107.0	107.0	107.0		108	-10.4	0.0	1	dbSNP_132	107	606,7694		30,546,3574	no	coding-synonymous	OTUD7B	NM_020205.2		30,622,5454	AA,AG,GG		7.3012,1.9427,5.5847		36/844	149943157	682,11530	1956	4150	6106	SO:0001819	synonymous_variant	56957	exon3			GAGGGCGGCATTC	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"""OTU domain containing"""	16683	protein-coding gene	gene with protein product		611748	"""zinc finger, A20 domain containing 1"", ""OTU domain containing 7B"""	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.108C>T	1.37:g.149943157G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	64	18	0.28125	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Silent	SNP	ENST00000369135.4	37	CCDS41389.1																																																																																			G|0.947;A|0.053	0.053	strong		0.468	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205	
AKNA	80709	hgsc.bcm.edu	37	9	117110046	117110046	+	Missense_Mutation	SNP	C	C	T	rs3748178	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:117110046C>T	ENST00000307564.4	-	16	3517	c.3356G>A	c.(3355-3357)cGg>cAg	p.R1119Q	AKNA_ENST00000223791.3_Missense_Mutation_p.R579Q|AKNA_ENST00000492875.1_5'Flank|AKNA_ENST00000374088.3_Missense_Mutation_p.R1119Q|AKNA_ENST00000374075.5_Missense_Mutation_p.R1038Q|AKNA_ENST00000374079.4_Missense_Mutation_p.R64Q	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1119			R -> Q (in dbSNP:rs3748178). {ECO:0000269|PubMed:14702039}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|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)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GTCTGCTGGCCGGCCGCGGGT	0.662													C|||	533	0.10643	0.0106	0.1427	5008	,	,		13674	0.0685		0.2624	False		,,,				2504	0.089				p.R1119Q		Atlas-SNP	.											.	AKNA	119	.	0			c.G3356A						PASS	.	C	GLN/ARG	179,3903		8,163,1870	7.0	8.0	8.0		3356	1.0	0.0	9	dbSNP_107	8	1759,6341		177,1405,2468	yes	missense	AKNA	NM_030767.4	43	185,1568,4338	TT,TC,CC		21.716,4.3851,15.9087	probably-damaging	1119/1440	117110046	1938,10244	2041	4050	6091	SO:0001583	missense	80709	exon16			GCTGGCCGGCCGC	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3356G>A	9.37:g.117110046C>T	ENSP00000303769:p.Arg1119Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	46	35	0.76087	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	300	0.13736263736263737	8	0.016260162601626018	62	0.1712707182320442	31	0.05419580419580419	199	0.262532981530343	C	18.55	3.649336	0.67358	0.043851	0.21716	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000320310;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.24350	2.37;1.86;2.37;2.13;2.36	5.01	0.963	0.19649	.	0.323271	0.22341	N	0.061322	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;P	0.36874	0.436;0.572	B;B	0.29267	0.027;0.1	T	0.24621	-1.0155	9	0.62326	D	0.03	-11.2927	4.2153	0.10531	0.0:0.5399:0.1702:0.2899	rs3748178;rs17230383;rs3748178	1119;1038	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	Q	1119;64;131;1119;579;1038	ENSP00000303769:R1119Q;ENSP00000363192:R64Q;ENSP00000363201:R1119Q;ENSP00000223791:R579Q;ENSP00000363188:R1038Q	ENSP00000223791:R579Q	R	-	2	0	AKNA	116149867	0.004000	0.15560	0.001000	0.08648	0.013000	0.08279	0.196000	0.17176	0.084000	0.17077	0.655000	0.94253	CGG	C|0.891;T|0.109	0.109	strong		0.662	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
ZSCAN30	100101467	hgsc.bcm.edu	37	18	32844056	32844056	+	Silent	SNP	G	G	T	rs75902053	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:32844056G>T	ENST00000420878.3	-	3	716	c.261C>A	c.(259-261)atC>atA	p.I87I	ZSCAN30_ENST00000601405.1_Intron|ZNF397_ENST00000589420.1_Intron|ZSCAN30_ENST00000589178.1_Silent_p.I87I|ZSCAN30_ENST00000592278.1_Silent_p.I87I|ZSCAN30_ENST00000383091.2_Silent_p.I87I|ZSCAN30_ENST00000333206.5_Silent_p.I87I	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	87	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				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)			large_intestine(5)|lung(3)|urinary_tract(1)	9						GCAGCTCCAGGATCTGCTCCT	0.592													G|||	123	0.0245607	0.003	0.0274	5008	,	,		17331	0.0		0.0845	False		,,,				2504	0.0153				p.I87I		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.C261A						PASS	.	G	,	53,3083		1,51,1516	57.0	56.0	56.0		261,261	0.5	1.0	18	dbSNP_132	56	557,6607		25,507,3050	no	coding-synonymous,coding-synonymous	ZSCAN30	NM_001112734.2,NM_001166012.1	,	26,558,4566	TT,TG,GG		7.775,1.6901,5.9223	,	87/495,87/495	32844056	610,9690	1568	3582	5150	SO:0001819	synonymous_variant	100101467	exon3			CTCCAGGATCTGC	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"""-"", ""Zinc fingers, C2H2-type"""	33517	protein-coding gene	gene with protein product			"""zinc finger protein 397 opposite strand"", ""ZNF397 opposite strand"""	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.261C>A	18.37:g.32844056G>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Silent	SNP	ENST00000420878.3	37	CCDS42427.1																																																																																			G|0.958;T|0.042	0.042	strong		0.592	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734	
OLFML1	283298	hgsc.bcm.edu	37	11	7530985	7530985	+	Missense_Mutation	SNP	G	G	A	rs12803046	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7530985G>A	ENST00000329293.3	+	3	1169	c.775G>A	c.(775-777)Gca>Aca	p.A259T	CTD-2516F10.2_ENST00000530201.1_RNA|OLFML1_ENST00000530135.1_Missense_Mutation_p.A259T|OLFML1_ENST00000528758.1_3'UTR	NM_198474.3	NP_940876.2	Q6UWY5	OLFL1_HUMAN	olfactomedin-like 1	259	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.		A -> T (in dbSNP:rs12803046).			extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(3)|prostate(2)	24				Epithelial(150;6.96e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GGTAGGCCGAGCATTGGTTTA	0.498													G|||	56	0.0111821	0.0045	0.0115	5008	,	,		19850	0.0		0.0338	False		,,,				2504	0.0082				p.A259T		Atlas-SNP	.											.	OLFML1	54	.	0			c.G775A						PASS	.	G	THR/ALA	24,4378	30.8+/-60.4	0,24,2177	54.0	50.0	52.0		775	3.1	1.0	11	dbSNP_121	52	284,8308	105.8+/-166.7	3,278,4015	yes	missense	OLFML1	NM_198474.3	58	3,302,6192	AA,AG,GG		3.3054,0.5452,2.3703	benign	259/403	7530985	308,12686	2201	4296	6497	SO:0001583	missense	283298	exon3			GGCCGAGCATTGG	AY358591	CCDS7779.1	11p15	2008-02-05			ENSG00000183801	ENSG00000183801			24473	protein-coding gene	gene with protein product							Standard	NM_198474		Approved	UNQ564	uc001mfi.3	Q6UWY5	OTTHUMG00000165527	ENST00000329293.3:c.775G>A	11.37:g.7530985G>A	ENSP00000332511:p.Ala259Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_198474	B4DP03|Q569G4	Missense_Mutation	SNP	ENST00000329293.3	37	CCDS7779.1	34	0.015567765567765568	4	0.008130081300813009	3	0.008287292817679558	0	0.0	27	0.03562005277044855	G	8.164	0.790177	0.16258	0.005452	0.033054	ENSG00000183801	ENST00000530135;ENST00000329293	D;D	0.88509	-2.39;-2.39	5.13	3.06	0.35304	Olfactomedin-like (3);	0.427236	0.24070	N	0.041837	T	0.36303	0.0962	N	0.02192	-0.645	0.52099	D	0.999949	B;B	0.13145	0.003;0.007	B;B	0.10450	0.005;0.005	T	0.51458	-0.8703	10	0.24483	T	0.36	.	3.3144	0.07027	0.1863:0.0:0.5398:0.2738	rs12803046;rs12803046	123;259	B4DN61;Q6UWY5	.;OLFL1_HUMAN	T	259	ENSP00000433455:A259T;ENSP00000332511:A259T	ENSP00000332511:A259T	A	+	1	0	OLFML1	7487561	0.940000	0.31905	0.974000	0.42286	0.709000	0.40893	1.756000	0.38390	1.325000	0.45301	0.563000	0.77884	GCA	G|0.977;A|0.023	0.023	strong		0.498	OLFML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384656.1	NM_198474	
RTKN2	219790	hgsc.bcm.edu	37	10	63964653	63964653	+	Silent	SNP	C	C	T	rs41274060	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:63964653C>T	ENST00000373789.3	-	10	1245	c.1149G>A	c.(1147-1149)aaG>aaA	p.K383K	RTKN2_ENST00000395265.1_Silent_p.K404K|RTKN2_ENST00000315289.2_Silent_p.K185K	NM_145307.2	NP_660350.2	Q8IZC4	RTKN2_HUMAN	rhotekin 2	383	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(12;0.0297)|all_hematologic(501;0.215)					CTTCCATCCACTTCTGAAGAT	0.358													C|||	704	0.140575	0.295	0.1066	5008	,	,		17023	0.005		0.16	False		,,,				2504	0.0757				p.K383K		Atlas-SNP	.											.	RTKN2	68	.	0			c.G1149A						PASS	.	C		1173,3233	412.4+/-336.1	170,833,1200	77.0	79.0	78.0		1149	0.4	1.0	10	dbSNP_127	78	1355,7245	264.9+/-285.8	114,1127,3059	no	coding-synonymous	RTKN2	NM_145307.2		284,1960,4259	TT,TC,CC		15.7558,26.6228,19.4372		383/610	63964653	2528,10478	2203	4300	6503	SO:0001819	synonymous_variant	219790	exon10			CATCCACTTCTGA	BC025765	CCDS7263.1, CCDS73140.1	10q21.3	2013-01-10	2007-12-14	2007-12-14	ENSG00000182010	ENSG00000182010		"""Pleckstrin homology (PH) domain containing"""	19364	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family K member 1"""	PLEKHK1		15504364	Standard	NM_001282941		Approved	Em:AC024597.2, bA531F24.1, FLJ39352	uc001jlw.3	Q8IZC4	OTTHUMG00000018299	ENST00000373789.3:c.1149G>A	10.37:g.63964653C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_145307	Q3ZCR1|Q68DZ6|Q8N8K1|Q8TAV2	Silent	SNP	ENST00000373789.3	37	CCDS7263.1																																																																																			C|0.821;T|0.179	0.179	strong		0.358	RTKN2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091618.1	NM_145307	
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 GAIIx	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_ENST00000543719.1_Missense_Mutation_p.S360I|CCAR1_ENST00000535016.1_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	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	109	55	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	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45479055	45479055	+	Silent	SNP	C	C	T	rs2838475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45479055C>T	ENST00000291574.4	+	6	925	c.750C>T	c.(748-750)gaC>gaT	p.D250D	TRAPPC10_ENST00000380221.3_Silent_p.D250D	NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	250					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						ACGAACTGGACGCCCTCTTCT	0.507													C|||	275	0.0549121	0.0129	0.0576	5008	,	,		16057	0.0506		0.1093	False		,,,				2504	0.0583				p.D250D		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.C750T						PASS	.	C		113,4293	86.8+/-125.4	3,107,2093	72.0	59.0	63.0		750	1.0	1.0	21	dbSNP_100	63	905,7695	201.3+/-244.8	60,785,3455	no	coding-synonymous	TRAPPC10	NM_003274.4		63,892,5548	TT,TC,CC		10.5233,2.5647,7.8272		250/1260	45479055	1018,11988	2203	4300	6503	SO:0001819	synonymous_variant	7109	exon6			ACTGGACGCCCTC	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.750C>T	21.37:g.45479055C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																			C|0.929;T|0.071	0.071	strong		0.507	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
HPN	3249	hgsc.bcm.edu	37	19	35550878	35550878	+	Silent	SNP	C	C	T	rs45512696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35550878C>T	ENST00000262626.2	+	6	1216	c.391C>T	c.(391-393)Ctg>Ttg	p.L131L	HPN_ENST00000597419.1_Intron|HPN_ENST00000392226.1_Silent_p.L131L|HPN-AS1_ENST00000392227.2_RNA|HPN_ENST00000600675.1_3'UTR	NM_182983.2	NP_892028.1	P05981	HEPS_HUMAN	hepsin	131	SRCR.				basement membrane disassembly (GO:0034769)|cholesterol homeostasis (GO:0042632)|cochlea morphogenesis (GO:0090103)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|epithelium development (GO:0060429)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pilomotor reflex (GO:0097195)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|positive regulation of gene expression (GO:0010628)|positive regulation of hepatocyte proliferation (GO:2000347)|positive regulation of plasminogen activation (GO:0010756)|positive regulation of thyroid hormone generation (GO:2000611)|potassium ion transmembrane transport (GO:0071805)|proteolysis (GO:0006508)|regulation of cell shape (GO:0008360)|response to thyroid hormone (GO:0097066)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	19	all_lung(56;5.38e-08)|Lung NSC(56;8.61e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Coagulation factor VIIa(DB00036)	CACCCAGAGGCTGCTGGAGGT	0.667													C|||	323	0.0644968	0.0045	0.072	5008	,	,		13357	0.0109		0.162	False		,,,				2504	0.0951				p.L131L		Atlas-SNP	.											.	HPN	45	.	0			c.C391T						PASS	.	C	,	163,4241	101.2+/-139.8	6,151,2045	29.0	31.0	30.0		391,391	3.0	1.0	19	dbSNP_127	30	1379,7221	255.5+/-280.4	113,1153,3034	no	coding-synonymous,coding-synonymous	HPN	NM_002151.2,NM_182983.2	,	119,1304,5079	TT,TC,CC		16.0349,3.7012,11.8579	,	131/418,131/418	35550878	1542,11462	2202	4300	6502	SO:0001819	synonymous_variant	3249	exon6			CAGAGGCTGCTGG		CCDS32993.1	19q13.12	2013-04-25	2008-12-08		ENSG00000105707	ENSG00000105707		"""Serine peptidases / Transmembrane"""	5155	protein-coding gene	gene with protein product	"""transmembrane protease, serine 1"""	142440				2835076	Standard	NM_182983		Approved	TMPRSS1	uc002nxq.2	P05981	OTTHUMG00000182474	ENST00000262626.2:c.391C>T	19.37:g.35550878C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	29	0.386667	NM_182983	B2RDS4	Silent	SNP	ENST00000262626.2	37	CCDS32993.1																																																																																			C|0.904;T|0.096	0.096	strong		0.667	HPN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461573.1	NM_002151	
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 GAIIx	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_ENST00000370909.2_Intron|LRRIQ3_ENST00000370911.3_Silent_p.Y140Y|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		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	83	26	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 GAIIx	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	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	20	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	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921333	12921333	+	Missense_Mutation	SNP	G	G	A	rs56145411	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12921333G>A	ENST00000240189.2	+	4	1211	c.1124G>A	c.(1123-1125)tGc>tAc	p.C375Y		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	375			C -> R (in dbSNP:rs17039307).		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)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCTGAGCTGCTGCTCCCAG	0.562													.|||	1359	0.271366	0.3858	0.1844	5008	,	,		27344	0.2857		0.2157	False		,,,				2504	0.2209				p.C375Y		Atlas-SNP	.											PRAMEF2,NS,carcinoma,+1,1	PRAMEF2	85	1	0			c.G1124A						PASS	.						111.0	118.0	116.0					1																	12921333		2201	4294	6495	SO:0001583	missense	65122	exon4			TGAGCTGCTGCTC		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.1124G>A	1.37:g.12921333G>A	ENSP00000240189:p.Cys375Tyr	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	272	41	0.150735	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	357	0.16346153846153846	115	0.23373983739837398	63	0.17403314917127072	80	0.13986013986013987	99	0.13060686015831136	g	3.142	-0.176022	0.06380	.	.	ENSG00000120952	ENST00000240189	T	0.09163	3.01	0.824	-0.682	0.11339	.	1.330770	0.04798	N	0.433017	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	1.999999999946489E-6	B	0.09022	0.002	B	0.29440	0.102	T	0.47114	-0.9142	9	0.72032	D	0.01	.	5.1225	0.14867	0.5904:0.0:0.4096:0.0	rs56145411	375	O60811	PRAM2_HUMAN	Y	375	ENSP00000240189:C375Y	ENSP00000240189:C375Y	C	+	2	0	PRAMEF2	12843920	0.000000	0.05858	0.596000	0.28811	0.002000	0.02628	-0.801000	0.04550	-2.179000	0.00767	-2.900000	0.00093	TGC	G|0.837;A|0.163	0.163	strong		0.562	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
SMC5	23137	hgsc.bcm.edu	37	9	72897440	72897440	+	Missense_Mutation	SNP	T	T	C	rs1180117	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:72897440T>C	ENST00000361138.5	+	7	980	c.922T>C	c.(922-924)Tgt>Cgt	p.C308R		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	308			C -> R (in dbSNP:rs1180117). {ECO:0000269|PubMed:11408570, ECO:0000269|PubMed:15489334}.		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						TCCTGTAACATGTCGAATTGA	0.353													C|||	1232	0.246006	0.2655	0.1542	5008	,	,		17121	0.2659		0.1928	False		,,,				2504	0.319				p.C308R		Atlas-SNP	.											.	SMC5	96	.	0			c.T922C						PASS	.	C	ARG/CYS	1071,3335	722.2+/-409.3	126,819,1258	93.0	90.0	91.0		922	2.6	0.0	9	dbSNP_87	91	1730,6870	736.5+/-407.0	180,1370,2750	yes	missense	SMC5	NM_015110.3	180	306,2189,4008	CC,CT,TT		20.1163,24.3078,21.5362	benign	308/1102	72897440	2801,10205	2203	4300	6503	SO:0001583	missense	23137	exon7			GTAACATGTCGAA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.922T>C	9.37:g.72897440T>C	ENSP00000354957:p.Cys308Arg	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	181	93	0.513812	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	491	0.22481684981684982	142	0.2886178861788618	56	0.15469613259668508	146	0.25524475524475526	147	0.19393139841688653	C	0.018	-1.486534	0.01018	0.243078	0.201163	ENSG00000198887	ENST00000361138	T	0.15952	2.38	5.61	2.61	0.31194	RecF/RecN/SMC (1);	0.675701	0.15131	N	0.278842	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46735	-0.9170	9	0.14252	T	0.57	1.4368	3.2463	0.06798	0.3592:0.4049:0.1067:0.1292	rs1180117;rs57413829;rs1180117	308	Q8IY18	SMC5_HUMAN	R	308	ENSP00000354957:C308R	ENSP00000354957:C308R	C	+	1	0	SMC5	72087260	0.000000	0.05858	0.000000	0.03702	0.626000	0.37791	0.328000	0.19681	0.076000	0.16826	-0.128000	0.14901	TGT	T|0.778;C|0.222	0.222	strong		0.353	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
SH3GLB2	56904	hgsc.bcm.edu	37	9	131771505	131771505	+	Silent	SNP	C	C	T	rs1129098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131771505C>T	ENST00000372564.3	-	10	1105	c.960G>A	c.(958-960)ccG>ccA	p.P320P	SH3GLB2_ENST00000372559.1_Silent_p.P320P|SH3GLB2_ENST00000372554.4_Silent_p.P329P|SH3GLB2_ENST00000417224.1_Silent_p.P325P|SH3GLB2_ENST00000416629.1_Silent_p.P299P	NM_020145.2	NP_064530.1	Q9NR46	SHLB2_HUMAN	SH3-domain GRB2-like endophilin B2	320						cytoplasm (GO:0005737)				NS(1)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)	12						AGGCCTCCCCCGGAGGGGCCA	0.697													C|||	1281	0.255791	0.0885	0.3991	5008	,	,		13246	0.1696		0.4135	False		,,,				2504	0.3067				p.P320P		Atlas-SNP	.											.	SH3GLB2	32	.	0			c.G960A						PASS	.	C		514,3880		35,444,1718	12.0	14.0	13.0		960	-9.2	0.0	9	dbSNP_86	13	3084,5506		580,1924,1791	no	coding-synonymous	SH3GLB2	NM_020145.2		615,2368,3509	TT,TC,CC		35.9022,11.6978,27.711		320/396	131771505	3598,9386	2197	4295	6492	SO:0001819	synonymous_variant	56904	exon10			CTCCCCCGGAGGG	AF257319	CCDS6916.1, CCDS69680.1	9q34	2008-02-05	2001-12-04		ENSG00000148341	ENSG00000148341			10834	protein-coding gene	gene with protein product		609288	"""SH3-domain, GRB2-like, endophilin B2"""			11161816	Standard	NM_020145		Approved	KIAA1848	uc004bwv.3	Q9NR46	OTTHUMG00000020769	ENST00000372564.3:c.960G>A	9.37:g.131771505C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_020145	A6NC47|A8MPS4|Q8WY61|Q96JH9	Silent	SNP	ENST00000372564.3	37	CCDS6916.1																																																																																			C|0.726;T|0.274	0.274	strong		0.697	SH3GLB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054535.2		
MINOS1	440574	hgsc.bcm.edu	37	1	19950062	19950062	+	Silent	SNP	T	T	C	rs1737428	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19950062T>C	ENST00000322753.6	+	3	263	c.207T>C	c.(205-207)caT>caC	p.H69H	MINOS1-NBL1_ENST00000602662.1_Intron|MINOS1_ENST00000486890.1_3'UTR	NM_001032363.3|NM_001204082.1|NM_001204083.1	NP_001027535.1|NP_001191011.1|NP_001191012.1	Q5TGZ0	MIC10_HUMAN	mitochondrial inner membrane organizing system 1	69						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)											ATCTTCTACATGGAAAATATG	0.383													C|||	1731	0.345647	0.705	0.2032	5008	,	,		19847	0.1419		0.2346	False		,,,				2504	0.2853				p.H69H		Atlas-SNP	.											.	.	.	.	0			c.T207C						PASS	.	C	,,,,	2865,1541	484.9+/-360.2	929,1007,267	119.0	116.0	117.0		207,159,207,,	0.9	1.0	1	dbSNP_89	117	1739,6861	736.3+/-407.0	208,1323,2769	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron	MINOS1,C1orf151-NBL1	NM_001032363.3,NM_001204082.1,NM_001204083.1,NM_001204088.1,NM_001204089.1	,,,,	1137,2330,3036	CC,CT,TT		20.2209,34.975,35.399	,,,,	69/79,53/63,69/141,,	19950062	4604,8402	2203	4300	6503	SO:0001819	synonymous_variant	440574	exon3			TCTACATGGAAAA	AK094318	CCDS30620.1, CCDS72719.1	1p36.13	2013-10-11	2011-10-04	2011-10-04	ENSG00000173436	ENSG00000173436			32068	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 151"""	C1orf151		21944719	Standard	NM_001032363		Approved	RP5-1056L3.2, FLJ36999, MIO10	uc021ohu.1	Q5TGZ0	OTTHUMG00000002712	ENST00000322753.6:c.207T>C	1.37:g.19950062T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_001032363	Q96G68	Silent	SNP	ENST00000322753.6	37	CCDS30620.1																																																																																			T|0.661;C|0.339	0.339	strong		0.383	MINOS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007697.2	NM_001032363	
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 GAIIx	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		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	141	63	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		
SLC22A25	387601	hgsc.bcm.edu	37	11	62931484	62931484	+	Missense_Mutation	SNP	T	T	C	rs6591771	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:62931484T>C	ENST00000306494.6	-	9	1455	c.1456A>G	c.(1456-1458)Atg>Gtg	p.M486V	SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						AGGATCATCATGAGGGAAGCC	0.473													C|||	2720	0.543131	0.6377	0.5	5008	,	,		19828	0.5337		0.4473	False		,,,				2504	0.5542				p.M486V		Atlas-SNP	.											.	SLC22A25	87	.	0			c.A1456G						PASS	.	C	VAL/MET	2736,1666	507.6+/-366.7	847,1042,312	145.0	156.0	152.0		1456	-9.1	0.0	11	dbSNP_116	152	3752,4844	616.4+/-396.5	824,2104,1370	yes	missense	SLC22A25	NM_199352.3	21	1671,3146,1682	CC,CT,TT		43.6482,37.8464,49.9154	benign	486/548	62931484	6488,6510	2201	4298	6499	SO:0001583	missense	387601	exon9			TCATCATGAGGGA	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.1456A>G	11.37:g.62931484T>C	ENSP00000307443:p.Met486Val	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	179	84	0.469274	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	1108	0.5073260073260073	296	0.6016260162601627	150	0.4143646408839779	334	0.583916083916084	328	0.43271767810026385	C	0.016	-1.521232	0.00967	0.621536	0.436482	ENSG00000196600	ENST00000306494	T	0.55234	0.53	4.56	-9.12	0.00707	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.731034	0.12480	N	0.465234	T	0.00012	0.0000	N	0.00483	-1.445	0.53005	P	3.500000000000725E-5	B	0.06786	0.001	B	0.06405	0.002	T	0.19778	-1.0295	9	0.08381	T	0.77	.	3.3572	0.07173	0.1046:0.2737:0.3903:0.2314	rs6591771;rs17646973;rs57023289;rs6591771	486	Q6T423	S22AP_HUMAN	V	486	ENSP00000307443:M486V	ENSP00000307443:M486V	M	-	1	0	SLC22A25	62688060	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.285000	0.01153	-4.095000	0.00074	-3.042000	0.00070	ATG	T|0.486;C|0.514	0.514	strong		0.473	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
NSUN5	55695	hgsc.bcm.edu	37	7	72717933	72717933	+	Silent	SNP	C	C	T	rs11544043	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:72717933C>T	ENST00000252594.6	-	8	1050	c.1035G>A	c.(1033-1035)gcG>gcA	p.A345A	NSUN5_ENST00000310326.8_Silent_p.A345A|NSUN5_ENST00000438747.2_Silent_p.A345A|NSUN5_ENST00000428206.1_Silent_p.A307A			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	345					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				GGAAAGTGAGCGCGTGGCACA	0.662													.|||	1253	0.2502	0.2595	0.3228	5008	,	,		16894	0.2381		0.2197	False		,,,				2504	0.2301				p.A345A		Atlas-SNP	.											NSUN5_ENST00000438747,NS,carcinoma,0,2	NSUN5	47	2	0			c.G1035A						PASS	.	C	,,,	1103,3303		141,821,1241	36.0	39.0	38.0		1035,921,1035,1035	-4.2	0.0	7	dbSNP_120	38	2086,6512		247,1592,2460	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	,,,	388,2413,3701	TT,TC,CC		24.2615,25.034,24.5232	,,,	345/471,307/392,345/430,345/467	72717933	3189,9815	2203	4299	6502	SO:0001819	synonymous_variant	55695	exon8			AGTGAGCGCGTGG	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.1035G>A	7.37:g.72717933C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	129	69	0.534884	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Silent	SNP	ENST00000252594.6	37	CCDS5547.1																																																																																			C|0.714;T|0.286	0.286	strong		0.662	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
MUC16	94025	hgsc.bcm.edu	37	19	9056930	9056930	+	Silent	SNP	T	T	G	rs918535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9056930T>G	ENST00000397910.4	-	3	30719	c.30516A>C	c.(30514-30516)acA>acC	p.T10172T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10174	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGGACATGTTTGTCTTCCTAA	0.443													g|||	1218	0.243211	0.3525	0.2867	5008	,	,		22488	0.0258		0.2833	False		,,,				2504	0.2474				p.T10172T		Atlas-SNP	.											.	MUC16	4315	.	0			c.A30516C						PASS	.	G		1268,2662		217,834,914	122.0	121.0	121.0		30516	-6.6	0.0	19	dbSNP_86	121	2525,5781		402,1721,2030	no	coding-synonymous	MUC16	NM_024690.2		619,2555,2944	GG,GT,TT		30.3997,32.2646,30.9987		10172/14508	9056930	3793,8443	1965	4153	6118	SO:0001819	synonymous_variant	94025	exon3			CATGTTTGTCTTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30516A>C	19.37:g.9056930T>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.739;G|0.261	0.261	strong		0.443	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF417	147687	hgsc.bcm.edu	37	19	58420699	58420699	+	Missense_Mutation	SNP	C	C	A	rs3745133	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58420699C>A	ENST00000312026.5	-	3	1111	c.947G>T	c.(946-948)cGt>cTt	p.R316L	ZNF417_ENST00000595559.1_Missense_Mutation_p.R315L|CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000536263.1_Missense_Mutation_p.R117L	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	316				R -> L (in Ref. 3; AAH25783). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R316L(1)		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)		AGTGTGAACACGCTGATGGCT	0.458													C|||	1690	0.33746	0.4153	0.2911	5008	,	,		25205	0.2817		0.3499	False		,,,				2504	0.3098				p.R316L		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - Missense(1)	stomach(1)	c.G947T						PASS	.						167.0	147.0	154.0					19																	58420699		2203	4300	6503	SO:0001583	missense	147687	exon3			TGAACACGCTGAT	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.947G>T	19.37:g.58420699C>A	ENSP00000311319:p.Arg316Leu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	645	0.29532967032967034	167	0.3394308943089431	107	0.2955801104972376	118	0.2062937062937063	253	0.3337730870712401	.	8.577	0.881369	0.17467	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.25085	1.82;1.82	2.15	-2.01	0.07410	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.60012	1.86	0.80722	P	0.0	P	0.38335	0.627	B	0.36922	0.236	T	0.32981	-0.9886	8	0.66056	D	0.02	.	7.8865	0.29653	0.0:0.6777:0.0:0.3223	rs3745133;rs17856732	316	Q8TAU3	ZN417_HUMAN	L	316;117	ENSP00000311319:R316L;ENSP00000442760:R117L	ENSP00000311319:R316L	R	-	2	0	ZNF417	63112511	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-2.414000	0.01037	-0.691000	0.05135	-1.050000	0.02344	CGT	C|0.500;A|0.500	0.500	weak		0.458	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
ATP5O	539	hgsc.bcm.edu	37	21	35284683	35284683	+	Silent	SNP	A	A	G	rs78234759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:35284683A>G	ENST00000290299.2	-	3	324	c.108T>C	c.(106-108)ggT>ggC	p.G36G	ATP5O_ENST00000496044.1_5'UTR|AP000304.12_ENST00000429238.1_5'Flank	NM_001697.2	NP_001688.1	P48047	ATPO_HUMAN	ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit	36					ATP biosynthetic process (GO:0006754)|ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|transmembrane transporter activity (GO:0022857)|transporter activity (GO:0005215)			large_intestine(2)|lung(1)|ovary(1)|urinary_tract(1)	5						GACCTTCAATACCGTATACCT	0.373													A|||	153	0.0305511	0.0038	0.0418	5008	,	,		16725	0.002		0.0636	False		,,,				2504	0.0542				p.G36G		Atlas-SNP	.											.	ATP5O	9	.	0			c.T108C						PASS	.	A		43,4363	46.7+/-81.2	0,43,2160	90.0	86.0	87.0		108	-1.2	0.0	21	dbSNP_131	87	447,8153	136.4+/-193.5	11,425,3864	no	coding-synonymous	ATP5O	NM_001697.2		11,468,6024	GG,GA,AA		5.1977,0.9759,3.7675		36/214	35284683	490,12516	2203	4300	6503	SO:0001819	synonymous_variant	539	exon3			TTCAATACCGTAT	AF088071	CCDS13634.1	21q22	2012-10-12	2008-07-31		ENSG00000241837	ENSG00000241837	3.6.3.14	"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	850	protein-coding gene	gene with protein product	"""oligomycin sensitivity conferring protein"""	600828				7490082	Standard	NM_001697		Approved	OSCP, ATPO		P48047	OTTHUMG00000065186	ENST00000290299.2:c.108T>C	21.37:g.35284683A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	75	19	0.253333	NM_001697	B2R4E2|Q5U042|Q6IBI2	Silent	SNP	ENST00000290299.2	37	CCDS13634.1																																																																																			A|0.962;G|0.038;T|0.000	0.038	strong		0.373	ATP5O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139907.1	NM_001697	
GATA6	2627	hgsc.bcm.edu	37	18	19762986	19762986	+	Silent	SNP	A	A	G	rs146949786	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:19762986A>G	ENST00000269216.3	+	6	1879	c.1602A>G	c.(1600-1602)acA>acG	p.T534T	GATA6_ENST00000581694.1_Silent_p.T534T|RNU6-702P_ENST00000364982.1_RNA	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	534					blood coagulation (GO:0007596)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cellular response to BMP stimulus (GO:0071773)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to hypoxia (GO:0071456)|Clara cell differentiation (GO:0060486)|endodermal cell fate determination (GO:0007493)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|liver development (GO:0001889)|lung saccule development (GO:0060430)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta1 production (GO:0032911)|negative regulation of transforming growth factor beta2 production (GO:0032912)|organ formation (GO:0048645)|outflow tract septum morphogenesis (GO:0003148)|pancreatic A cell differentiation (GO:0003310)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to growth factor (GO:0070848)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)|tube morphogenesis (GO:0035239)|type B pancreatic cell differentiation (GO:0003309)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	18	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			CCCCCACAACACAACCTACAG	0.388													A|||	6	0.00119808	0.0008	0.0029	5008	,	,		15699	0.0		0.003	False		,,,				2504	0.0				p.T534T	Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)	Atlas-SNP	.											.	GATA6	35	.	0			c.A1602G						PASS	.	A		6,4400	9.9+/-24.2	0,6,2197	107.0	95.0	99.0		1602	-0.3	1.0	18	dbSNP_134	99	47,8553	32.3+/-84.9	0,47,4253	no	coding-synonymous	GATA6	NM_005257.3		0,53,6450	GG,GA,AA		0.5465,0.1362,0.4075		534/596	19762986	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	2627	exon6			CACAACACAACCT	U66075	CCDS11872.1	18q11-q12	2013-01-25	2001-11-28		ENSG00000141448	ENSG00000141448		"""GATA zinc finger domain containing"""	4174	protein-coding gene	gene with protein product		601656	"""GATA-binding protein 6"""			8975704	Standard	XM_005258248		Approved		uc002ktt.2	Q92908	OTTHUMG00000131767	ENST00000269216.3:c.1602A>G	18.37:g.19762986A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_005257	B0YJ17|P78327	Silent	SNP	ENST00000269216.3	37	CCDS11872.1																																																																																			A|0.996;G|0.004	0.004	strong		0.388	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257	
WDR24	84219	hgsc.bcm.edu	37	16	737269	737269	+	Silent	SNP	C	C	T	rs17850290	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:737269C>T	ENST00000248142.6	-	7	1196	c.1197G>A	c.(1195-1197)acG>acA	p.T399T	JMJD8_ENST00000609261.1_5'Flank|JMJD8_ENST00000454700.1_5'Flank|WDR24_ENST00000293883.4_Silent_p.T269T|LA16c-313D11.12_ENST00000566927.1_RNA|JMJD8_ENST00000293882.4_5'Flank|JMJD8_ENST00000562824.1_5'Flank|JMJD8_ENST00000412368.2_5'Flank|JMJD8_ENST00000562111.1_5'Flank			Q96S15	WDR24_HUMAN	WD repeat domain 24	399										breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(3)	19		Hepatocellular(780;0.0218)				TCATGGAGCACGTGGCCAGGT	0.622													C|||	438	0.0874601	0.0053	0.0706	5008	,	,		16745	0.002		0.1461	False		,,,				2504	0.2382				p.T269T		Atlas-SNP	.											.	WDR24	111	.	0			c.G807A						PASS	.	C		146,4252	98.5+/-137.1	4,138,2057	40.0	42.0	41.0		807	-8.6	0.2	16	dbSNP_123	41	1397,7199	264.6+/-285.7	106,1185,3007	no	coding-synonymous	WDR24	NM_032259.2		110,1323,5064	TT,TC,CC		16.2517,3.3197,11.8747		269/791	737269	1543,11451	2199	4298	6497	SO:0001819	synonymous_variant	84219	exon3			GGAGCACGTGGCC	AL136863	CCDS10420.1	16p13.3	2013-01-09			ENSG00000127580	ENSG00000127580		"""WD repeat domain containing"""	20852	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 21"""	C16orf21		11230166	Standard	NM_032259		Approved	DKFZp434F054, JFP7	uc002ciz.1	Q96S15	OTTHUMG00000090421	ENST00000248142.6:c.1197G>A	16.37:g.737269C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	46	44	0.956522	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Silent	SNP	ENST00000248142.6	37																																																																																				C|0.902;T|0.098	0.098	strong		0.622	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259	
HEATR5B	54497	hgsc.bcm.edu	37	2	37230728	37230728	+	Silent	SNP	T	T	C	rs1007823	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:37230728T>C	ENST00000233099.5	-	31	5102	c.5007A>G	c.(5005-5007)gtA>gtG	p.V1669V	HEATR5B_ENST00000354531.2_Silent_p.V1669V	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1669						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)		p.V1669V(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				GAGCAGCTCTTACTATCTGTT	0.368													T|||	904	0.180511	0.0061	0.1614	5008	,	,		15078	0.5278		0.0855	False		,,,				2504	0.1697				p.V1669V		Atlas-SNP	.											HEATR5B,NS,carcinoma,0,1	HEATR5B	185	1	1	Substitution - coding silent(1)	stomach(1)	c.A5007G						PASS	.	T		92,4314	74.7+/-112.8	1,90,2112	85.0	85.0	85.0		5007	-3.6	1.0	2	dbSNP_86	85	663,7937	168.6+/-220.1	29,605,3666	no	coding-synonymous	HEATR5B	NM_019024.1		30,695,5778	CC,CT,TT		7.7093,2.0881,5.805		1669/2072	37230728	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	54497	exon31			AGCTCTTACTATC	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.5007A>G	2.37:g.37230728T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			C|0.124;T|0.876	0.124	strong		0.368	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
MEIOB	254528	hgsc.bcm.edu	37	16	1894912	1894912	+	Silent	SNP	C	C	T	rs9806826	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1894912C>T	ENST00000397344.3	-	10	1025	c.831G>A	c.(829-831)acG>acA	p.T277T	MEIOB_ENST00000470044.1_Silent_p.T70T|LA16c-429E7.1_ENST00000570247.1_RNA|MEIOB_ENST00000452149.2_Silent_p.T277T|MEIOB_ENST00000412554.2_Silent_p.T277T|MEIOB_ENST00000325962.3_Silent_p.T277T	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	277					double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										CCAGAACATTCGTTTCTTTAT	0.279													T|||	1854	0.370208	0.3548	0.3242	5008	,	,		17509	0.4246		0.3141	False		,,,				2504	0.4254				p.T277T		Atlas-SNP	.											C16orf73_ENST00000412554,NS,carcinoma,-1,2	.	.	2	0			c.G831A						scavenged	.	T	,	1467,2921	665.6+/-401.6	242,983,969	50.0	51.0	50.0		831,831	0.8	0.0	16	dbSNP_119	50	2459,6107	685.3+/-404.0	374,1711,2198	no	coding-synonymous,coding-synonymous	C16orf73	NM_001163560.2,NM_152764.2	,	616,2694,3167	TT,TC,CC		28.7065,33.4321,30.3072	,	277/472,277/443	1894912	3926,9028	2194	4283	6477	SO:0001819	synonymous_variant	254528	exon10			AACATTCGTTTCT	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.831G>A	16.37:g.1894912C>T		Somatic	212	3	0.0141509		WXS	Illumina HiSeq	Phase_I	153	82	0.535948	NM_001163560	B1AK39|C9J0S1|Q96RY0	Silent	SNP	ENST00000397344.3	37	CCDS10449.2																																																																																			C|0.681;T|0.319	0.319	strong		0.279	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
SVEP1	79987	hgsc.bcm.edu	37	9	113276356	113276356	+	Missense_Mutation	SNP	C	C	G	rs3818764	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:113276356C>G	ENST00000401783.2	-	4	1331	c.995G>C	c.(994-996)gGc>gCc	p.G332A	SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374461.1_Missense_Mutation_p.G309A|SVEP1_ENST00000374469.1_Missense_Mutation_p.G309A|SVEP1_ENST00000302728.8_Missense_Mutation_p.G332A	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	332			G -> A (in dbSNP:rs3818764). {ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TCCTGGTGAGCCTTCAGGTTT	0.502													C|||	723	0.144369	0.034	0.2666	5008	,	,		18784	0.1081		0.2008	False		,,,				2504	0.1861				p.G332A		Atlas-SNP	.											.	SVEP1	326	.	0			c.G995C						PASS	.	C	ALA/GLY	223,3805		7,209,1798	69.0	68.0	68.0		995	3.6	0.7	9	dbSNP_107	68	1658,6708		180,1298,2705	yes	missense	SVEP1	NM_153366.3	60	187,1507,4503	GG,GC,CC		19.8183,5.5362,15.1767	benign	332/3572	113276356	1881,10513	2014	4183	6197	SO:0001583	missense	79987	exon4			GGTGAGCCTTCAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.995G>C	9.37:g.113276356C>G	ENSP00000384917:p.Gly332Ala	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	161	81	0.503106	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	326	0.14926739926739926	28	0.056910569105691054	96	0.26519337016574585	63	0.11013986013986014	139	0.18337730870712401	C	12.03	1.814249	0.32053	0.055362	0.198183	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.58	3.61	0.41365	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.163234	0.53938	N	0.000055	T	0.00012	0.0000	N	0.04746	-0.17	0.40684	P	0.017664000000000013	B;B;B;B	0.22276	0.067;0.067;0.004;0.031	B;B;B;B	0.25291	0.044;0.059;0.026;0.026	T	0.47394	-0.9121	9	0.15066	T	0.55	.	16.1518	0.81626	0.0:0.6854:0.3146:0.0	rs3818764;rs17806854;rs52807409;rs3818764	332;332;332;332	E9PBN8;Q4LDE5;B3KV07;Q4LDE5-2	.;SVEP1_HUMAN;.;.	A	332;309;332;309	ENSP00000384917:G332A;ENSP00000363593:G309A;ENSP00000304118:G332A;ENSP00000363585:G309A	ENSP00000304118:G332A	G	-	2	0	SVEP1	112316177	0.904000	0.30761	0.656000	0.29637	0.908000	0.53690	1.705000	0.37867	0.678000	0.31325	0.650000	0.86243	GGC	C|0.847;G|0.153	0.153	strong		0.502	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
DDX55	57696	hgsc.bcm.edu	37	12	124104686	124104686	+	Silent	SNP	G	G	A	rs3204541	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:124104686G>A	ENST00000238146.4	+	14	1852	c.1802G>A	c.(1801-1803)tGa>tAa	p.*601*	DDX55_ENST00000421670.3_Silent_p.*208*|DDX55_ENST00000538744.1_Silent_p.*570*	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	0						membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		GATGACTGCTGATTCCAGTGC	0.418													G|||	1263	0.252196	0.4463	0.2205	5008	,	,		19827	0.0159		0.2654	False		,,,				2504	0.2423				p.X601X		Atlas-SNP	.											.	DDX55	51	.	0			c.G1802A						PASS	.	G		1828,2578	531.5+/-373.2	384,1060,759	75.0	75.0	75.0		1802	5.5	1.0	12	dbSNP_105	75	2376,6224	393.5+/-344.4	341,1694,2265	no	coding-synonymous	DDX55	NM_020936.1		725,2754,3024	AA,AG,GG		27.6279,41.4889,32.3235		601/601	124104686	4204,8802	2203	4300	6503	SO:0001819	synonymous_variant	57696	exon14			ACTGCTGATTCCA	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.1802G>A	12.37:g.124104686G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Silent	SNP	ENST00000238146.4	37	CCDS9251.1																																																																																			G|0.707;A|0.293	0.293	strong		0.418	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
FMN2	56776	hgsc.bcm.edu	37	1	240370952	240370952	+	Missense_Mutation	SNP	C	C	T	rs201741828	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:240370952C>T	ENST00000319653.9	+	5	3070	c.2840C>T	c.(2839-2841)cCt>cTt	p.P947L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	947	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCTCCGCCCCCTCTACCCGGA	0.692																																					p.P947L		Atlas-SNP	.											FMN2,NS,carcinoma,+1,2	FMN2	451	2	0			c.C2840T						PASS	.						25.0	30.0	29.0					1																	240370952		2201	4295	6496	SO:0001583	missense	56776	exon5			CGCCCCCTCTACC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2840C>T	1.37:g.240370952C>T	ENSP00000318884:p.Pro947Leu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	52	6	0.115385	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	C	10.92	1.486864	0.26686	.	.	ENSG00000155816	ENST00000319653	T	0.57436	0.4	4.22	3.31	0.37934	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.64843	0.2635	M	0.78456	2.415	0.80722	D	1	D	0.60575	0.988	P	0.59761	0.863	T	0.65421	-0.6172	8	.	.	.	.	7.9072	0.29769	0.0:0.7888:0.0:0.2112	.	947	Q9NZ56	FMN2_HUMAN	L	947	ENSP00000318884:P947L	.	P	+	2	0	FMN2	238437575	0.192000	0.23301	0.105000	0.21289	0.009000	0.06853	1.683000	0.37638	1.135000	0.42183	-0.361000	0.07541	CCT	C|0.986;G|0.000;T|0.014	0.014	strong		0.692	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
MTTP	4547	hgsc.bcm.edu	37	4	100510859	100510859	+	Silent	SNP	T	T	C	rs991811	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100510859T>C	ENST00000265517.5	+	4	656	c.453T>C	c.(451-453)ggT>ggC	p.G151G	MTTP_ENST00000457717.1_Silent_p.G151G|MTTP_ENST00000511045.1_Silent_p.G178G			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	151	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	TCAAGAGAGGTCTGGCTAGCC	0.393													C|||	2726	0.544329	0.8238	0.3084	5008	,	,		17575	0.6706		0.3141	False		,,,				2504	0.4407				p.G151G		Atlas-SNP	.											.	MTTP	127	.	0			c.T453C						PASS	.	C		3279,1127	400.1+/-331.5	1220,839,144	83.0	88.0	86.0		453	1.4	1.0	4	dbSNP_86	86	3129,5471	656.9+/-401.4	597,1935,1768	no	coding-synonymous	MTTP	NM_000253.2		1817,2774,1912	CC,CT,TT		36.3837,25.5788,49.2696		151/895	100510859	6408,6598	2203	4300	6503	SO:0001819	synonymous_variant	4547	exon5			GAGAGGTCTGGCT		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.453T>C	4.37:g.100510859T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_000253	A8K428|Q08AM4|Q6P5T3	Silent	SNP	ENST00000265517.5	37	CCDS3651.1																																																																																			T|0.472;C|0.528	0.528	strong		0.393	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
MMP8	4317	hgsc.bcm.edu	37	11	102595492	102595492	+	Missense_Mutation	SNP	G	G	A	rs3765620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102595492G>A	ENST00000236826.3	-	1	193	c.95C>T	c.(94-96)aCt>aTt	p.T32I		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	32			T -> I (in dbSNP:rs3765620). {ECO:0000269|PubMed:2159879, ECO:0000269|Ref.2}.		collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	TACCTGAACAGTTTTTGTATT	0.363													A|||	3277	0.654353	0.8147	0.5605	5008	,	,		19429	0.5774		0.5885	False		,,,				2504	0.6513				p.T32I		Atlas-SNP	.											.	MMP8	68	.	0			c.C95T						PASS	.	A	ILE/THR	3309,1097	393.7+/-329.0	1232,845,126	126.0	149.0	142.0		95	1.0	0.0	11	dbSNP_107	142	4788,3810	538.7+/-383.5	1326,2136,837	yes	missense	MMP8	NM_002424.2	89	2558,2981,963	AA,AG,GG		44.3126,24.8979,37.7345	benign	32/468	102595492	8097,4907	2203	4299	6502	SO:0001583	missense	4317	exon1			TGAACAGTTTTTG	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.95C>T	11.37:g.102595492G>A	ENSP00000236826:p.Thr32Ile	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	198	198	1	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	1384	0.6336996336996337	399	0.8109756097560976	213	0.5883977900552486	343	0.5996503496503497	429	0.5659630606860159	A	10.71	1.428057	0.25726	0.751021	0.556874	ENSG00000118113	ENST00000236826	T	0.35789	1.29	5.09	0.964	0.19655	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	1.716080	0.03198	N	0.174354	T	0.00012	0.0000	N	0.03029	-0.43	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42699	-0.9436	9	0.31617	T	0.26	.	8.3601	0.32353	0.5761:0.0:0.4239:0.0	rs3765620;rs52832345;rs59665335;rs3765620	32	P22894	MMP8_HUMAN	I	32	ENSP00000236826:T32I	ENSP00000236826:T32I	T	-	2	0	MMP8	102100702	0.010000	0.17322	0.001000	0.08648	0.006000	0.05464	0.819000	0.27308	-0.276000	0.09206	-0.269000	0.10298	ACT	G|0.357;A|0.643	0.643	strong		0.363	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
BTN3A1	11119	hgsc.bcm.edu	37	6	26413744	26413744	+	Missense_Mutation	SNP	C	C	A	rs4712990	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26413744C>A	ENST00000289361.6	+	10	1734	c.1366C>A	c.(1366-1368)Ccc>Acc	p.P456T	BTN3A1_ENST00000414912.2_Missense_Mutation_p.P404T	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	456	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		P -> T (in dbSNP:rs4712990). {ECO:0000269|PubMed:15489334}.		activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						ACTTCCTAAGCCCCCTAAGAA	0.468													C|||	530	0.105831	0.1089	0.1455	5008	,	,		19003	0.0288		0.1163	False		,,,				2504	0.1421				p.P456T		Atlas-SNP	.											.	BTN3A1	80	.	0			c.C1366A						PASS	.	C	THR/PRO,,THR/PRO,	560,3846		31,498,1674	129.0	129.0	129.0		1210,,1366,	1.4	0.0	6	dbSNP_111	129	1048,7552		70,908,3322	yes	missense,utr-3,missense,utr-3	BTN3A1	NM_001145008.1,NM_001145009.1,NM_007048.5,NM_194441.2	38,,38,	101,1406,4996	AA,AC,CC		12.186,12.7099,12.3635	benign,,benign,	404/462,,456/514,	26413744	1608,11398	2203	4300	6503	SO:0001583	missense	11119	exon10			CCTAAGCCCCCTA	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.1366C>A	6.37:g.26413744C>A	ENSP00000289361:p.Pro456Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	15	0.15	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	37	CCDS4608.1	220	0.10073260073260074	64	0.13008130081300814	55	0.15193370165745856	12	0.02097902097902098	89	0.11741424802110818	.	7.732	0.699391	0.15106	0.127099	0.12186	ENSG00000026950	ENST00000289361;ENST00000414912	T;T	0.68624	-0.34;-0.34	2.31	1.4	0.22301	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.57359	0.2048	M	0.81239	2.535	0.80722	P	0.0	P;P	0.48016	0.631;0.904	B;P	0.48598	0.406;0.583	T	0.54456	-0.8291	8	0.52906	T	0.07	.	6.8441	0.23979	0.0:0.7198:0.0:0.2802	rs4712990;rs17538334;rs58345406;rs4712990	404;456	E9PGB4;O00481	.;BT3A1_HUMAN	T	456;404	ENSP00000289361:P456T;ENSP00000406667:P404T	ENSP00000289361:P456T	P	+	1	0	BTN3A1	26521723	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.345000	0.02637	0.087000	0.17167	-0.921000	0.02739	CCC	C|0.883;A|0.117	0.117	strong		0.468	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3		
MGAM	8972	hgsc.bcm.edu	37	7	141759274	141759274	+	Silent	SNP	T	T	C	rs2960758	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:141759274T>C	ENST00000549489.2	+	32	3917	c.3822T>C	c.(3820-3822)gaT>gaC	p.D1274D	MGAM_ENST00000475668.2_Silent_p.D1274D	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1274	Glucoamylase.				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)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCCCGCAGGATGTGCAGTACT	0.562													N|||	1101	0.219848	0.1785	0.3862	5008	,	,		18252	0.0099		0.3777	False		,,,				2504	0.2117				p.D1274D		Atlas-SNP	.											.	MGAM	767	.	0			c.T3822C						PASS	.						33.0	29.0	31.0					7																	141759274		2002	4150	6152	SO:0001819	synonymous_variant	8972	exon32			GCAGGATGTGCAG	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.3822T>C	7.37:g.141759274T>C		Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	151	37	0.245033	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			C|1.000;|0.000	1.000	weak		0.562	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
OBSL1	23363	hgsc.bcm.edu	37	2	220422905	220422905	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:220422905C>T	ENST00000404537.1	-	10	3559		c.e10+1		RP11-256I23.2_ENST00000597192.1_RNA|OBSL1_ENST00000265318.4_Intron|OBSL1_ENST00000265317.5_Splice_Site|OBSL1_ENST00000373876.1_Splice_Site|OBSL1_ENST00000603926.1_Splice_Site	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1						cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GGAGCACCCACCAGCCAGGAT	0.627																																					.		Atlas-SNP	.											.	OBSL1	120	.	0			c.3502+1G>A						PASS	.						33.0	40.0	38.0					2																	220422905		2099	4227	6326	SO:0001630	splice_region_variant	23363	exon11			CACCCACCAGCCA	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.3502+1G>A	2.37:g.220422905C>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	170	87	0.511765	NM_015311	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Splice_Site	SNP	ENST00000404537.1	37	CCDS46520.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.882422	0.51908	.	.	ENSG00000124006	ENST00000404537;ENST00000373876;ENST00000265317;ENST00000456147	.	.	.	4.47	4.47	0.54385	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.3271	0.87252	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	OBSL1	220131149	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	7.190000	0.77755	2.322000	0.78497	0.313000	0.20887	.	.	.	none		0.627	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		Intron
C1orf27	54953	hgsc.bcm.edu	37	1	186363119	186363119	+	Missense_Mutation	SNP	C	C	G	rs12084264	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186363119C>G	ENST00000287859.6	+	9	877	c.752C>G	c.(751-753)tCt>tGt	p.S251C	C1orf27_ENST00000367470.3_Intron|C1orf27_ENST00000419367.3_Missense_Mutation_p.S219C|C1orf27_ENST00000432021.3_Intron	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	251			S -> C (in dbSNP:rs12084264). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						ACTAGTCATTCTTTTGATGTC	0.279													C|||	1164	0.232428	0.149	0.4078	5008	,	,		14393	0.127		0.335	False		,,,				2504	0.2239				p.S251C		Atlas-SNP	.											C1orf27_ENST00000287859,NS,carcinoma,0,2	C1orf27	41	2	0			c.C752G						PASS	.	C	,CYS/SER,CYS/SER	581,2775		48,485,1145	27.0	24.0	25.0		,656,752	3.4	0.9	1	dbSNP_120	25	2399,5149		385,1629,1760	yes	intron,missense,missense	C1orf27	NM_001164245.1,NM_001164246.1,NM_017847.5	,112,112	433,2114,2905	GG,GC,CC		31.7833,17.3123,27.3294	,benign,benign	,219/423,251/455	186363119	2980,7924	1678	3774	5452	SO:0001583	missense	54953	exon9			GTCATTCTTTTGA	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"""transactivated by recombinant transforming growth factor beta"""	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.752C>G	1.37:g.186363119C>G	ENSP00000287859:p.Ser251Cys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	189	188	0.994709	NM_017847	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	557	0.25503663003663	65	0.13211382113821138	148	0.4088397790055249	77	0.1346153846153846	267	0.35224274406332456	C	15.80	2.939210	0.52972	0.173123	0.317833	ENSG00000157181	ENST00000419367;ENST00000432021;ENST00000287859	T;T	0.46451	0.87;0.87	5.34	3.43	0.39272	.	0.556512	0.18307	N	0.145224	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	0.99999999387866	D;B	0.57899	0.981;0.0	P;B	0.53062	0.717;0.003	T	0.43702	-0.9375	9	0.37606	T	0.19	-3.9611	6.5884	0.22634	0.0:0.5515:0.3334:0.1151	rs12084264;rs17521893;rs12084264	219;251	E9PFR7;Q5SWX8	.;ODR4_HUMAN	C	219;251;251	ENSP00000395084:S219C;ENSP00000287859:S251C	ENSP00000287859:S251C	S	+	2	0	C1orf27	184629742	0.008000	0.16893	0.940000	0.37924	0.976000	0.68499	0.050000	0.14120	0.605000	0.29947	-0.300000	0.09419	TCT	C|0.756;G|0.244	0.244	strong		0.279	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847	
LRP1B	53353	hgsc.bcm.edu	37	2	141032088	141032088	+	Silent	SNP	C	C	T	rs1386356	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:141032088C>T	ENST00000389484.3	-	85	14018	c.13047G>A	c.(13045-13047)acG>acA	p.T4349T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4349	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTTCATAGCGCGTTGGACAGA	0.423										TSP Lung(27;0.18)			T|||	2435	0.486222	0.1558	0.5735	5008	,	,		15952	0.6508		0.665	False		,,,				2504	0.5174				p.T4349T	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G13047A						PASS	.	T		1129,3277	716.0+/-408.5	140,849,1214	178.0	143.0	155.0		13047	-2.2	1.0	2	dbSNP_88	155	5790,2810	443.8+/-360.5	1954,1882,464	no	coding-synonymous	LRP1B	NM_018557.2		2094,2731,1678	TT,TC,CC		32.6744,25.6241,46.8015		4349/4600	141032088	6919,6087	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon85			ATAGCGCGTTGGA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.13047G>A	2.37:g.141032088C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	84	55	0.654762	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1	1188	0.5439560439560439	92	0.18699186991869918	206	0.569060773480663	385	0.6730769230769231	505	0.6662269129287599	T	9.384	1.073697	0.20147	0.256241	0.673256	ENSG00000168702	ENST00000437977;ENST00000442974	.	.	.	5.36	-2.23	0.06930	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21553	P	0.999642195	.	.	.	.	.	.	T	0.40156	-0.9578	3	.	.	.	.	1.7664	0.03003	0.1132:0.2733:0.208:0.4055	rs1386356;rs3748866;rs1386356	.	.	.	H	581;81	.	.	R	-	2	0	LRP1B	140748558	0.956000	0.32656	0.993000	0.49108	0.991000	0.79684	0.285000	0.18883	-0.237000	0.09739	-0.254000	0.11334	CGC	C|0.462;T|0.538	0.538	strong		0.423	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
TLE2	7089	hgsc.bcm.edu	37	19	2997897	2997897	+	Silent	SNP	G	G	A	rs11150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:2997897G>A	ENST00000262953.6	-	20	2443	c.2181C>T	c.(2179-2181)atC>atT	p.I727I	TLE2_ENST00000586422.1_Intron|TLE2_ENST00000590536.1_Silent_p.I728I|TLE2_ENST00000455444.2_Silent_p.I605I|TLE2_ENST00000443826.3_Silent_p.I605I|TLE2_ENST00000447365.2_Silent_p.I394I|TLE2_ENST00000591529.1_3'UTR	NM_003260.4	NP_003251.2	Q04725	TLE2_HUMAN	transducin-like enhancer of split 2	727					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	13				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)		AGCCTGTCACGATGTATTTGT	0.542													G|||	871	0.173922	0.1218	0.2709	5008	,	,		19507	0.248		0.1561	False		,,,				2504	0.1176				p.I727I		Atlas-SNP	.											.	TLE2	35	.	0			c.C2181T						PASS	.	G	,,	493,3583		40,413,1585	82.0	82.0	82.0		,1815,2181	2.0	1.0	19	dbSNP_52	82	1189,7167		80,1029,3069	no	utr-3,coding-synonymous,coding-synonymous	TLE2	NM_001144761.1,NM_001144762.1,NM_003260.4	,,	120,1442,4654	AA,AG,GG		14.2293,12.0952,13.5296	,,	,605/622,727/744	2997897	1682,10750	2038	4178	6216	SO:0001819	synonymous_variant	7089	exon20			TGTCACGATGTAT	M99436	CCDS45911.1, CCDS45912.1, CCDS45913.1, CCDS74255.1	19p13.3	2014-03-07	2014-03-07					"""WD repeat domain containing"""	11838	protein-coding gene	gene with protein product	"""enhancer of split groucho 2"""	601041	"""transducin-like enhancer of split 2, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)"""			8808280	Standard	NM_003260		Approved	ESG2, GRG2, ESG, FLJ41188	uc002lww.3	Q04725		ENST00000262953.6:c.2181C>T	19.37:g.2997897G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_003260	B4DE03|E9PEV7|F8WCH2|Q8WVY0|Q9Y6S0	Silent	SNP	ENST00000262953.6	37	CCDS45911.1																																																																																			G|0.801;A|0.199	0.199	strong		0.542	TLE2-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452194.2	NM_003260	
RBAK	57786	hgsc.bcm.edu	37	7	5096958	5096958	+	Silent	SNP	T	T	C	rs11975068	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:5096958T>C	ENST00000353796.3	+	4	372	c.48T>C	c.(46-48)gaT>gaC	p.D16D	RBAK_ENST00000396912.1_Silent_p.D16D|RBAK-RBAKDN_ENST00000407184.1_Silent_p.D16D|RBAK-RBAKDN_ENST00000396904.2_Silent_p.D16D	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	16	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription, DNA-templated (GO:0045892)|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)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TGGCTGTGGATTTCACCCAGG	0.473													T|||	1279	0.255391	0.1687	0.2277	5008	,	,		11943	0.379		0.2724	False		,,,				2504	0.2474				p.D16D		Atlas-SNP	.											RBAK_ENST00000396912,NS,carcinoma,0,1	.	.	1	0			c.T48C						PASS	.	T	,,	808,3598	322.9+/-297.8	75,658,1470	110.0	115.0	113.0		48,48,48	1.9	0.9	7	dbSNP_120	113	2200,6400	374.2+/-337.3	261,1678,2361	no	coding-synonymous,coding-synonymous,coding-synonymous	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	,,	336,2336,3831	CC,CT,TT		25.5814,18.3386,23.1278	,,	16/715,16/114,16/715	5096958	3008,9998	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGTGGATTTCACC	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.48T>C	7.37:g.5096958T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	189	117	0.619048	NM_001204513	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	ENST00000353796.3	37	CCDS5337.1																																																																																			T|0.756;C|0.244	0.244	strong		0.473	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
TAF4B	6875	hgsc.bcm.edu	37	18	23866349	23866349	+	Silent	SNP	G	G	A	rs3744961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:23866349G>A	ENST00000269142.5	+	7	2474	c.1476G>A	c.(1474-1476)ggG>ggA	p.G492G	TAF4B_ENST00000400466.2_Silent_p.G492G|TAF4B_ENST00000578121.1_Silent_p.G492G	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	492				SAGTTSD -> FCWDHIC (in Ref. 2; CAA70499). {ECO:0000305}.	gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CTTCTGCTGGGACCACATCTG	0.493													G|||	589	0.117612	0.1528	0.121	5008	,	,		17159	0.1121		0.1083	False		,,,				2504	0.0828				p.G492G		Atlas-SNP	.											.	TAF4B	71	.	0			c.G1476A						PASS	.	G		564,3156		36,492,1332	88.0	82.0	84.0		1476	0.8	1.0	18	dbSNP_107	84	883,7347		49,785,3281	no	coding-synonymous	TAF4B	NM_005640.1		85,1277,4613	AA,AG,GG		10.729,15.1613,12.1088		492/863	23866349	1447,10503	1860	4115	5975	SO:0001819	synonymous_variant	6875	exon7			TGCTGGGACCACA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.1476G>A	18.37:g.23866349G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	CCDS42421.1	265	0.12133699633699634	73	0.1483739837398374	46	0.1270718232044199	57	0.09965034965034965	89	0.11741424802110818	G	5.134	0.210342	0.09757	0.151613	0.10729	ENSG00000141384	ENST00000418698	.	.	.	5.28	0.775	0.18527	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999698558	.	.	.	.	.	.	T	0.25257	-1.0137	4	0.17369	T	0.5	6.4391	2.3266	0.04224	0.1916:0.1519:0.5012:0.1553	rs3744961;rs52827702;rs56906477;rs3744961	.	.	.	N	492	.	ENSP00000389365:D492N	D	+	1	0	TAF4B	22120347	0.990000	0.36364	1.000000	0.80357	0.624000	0.37722	0.500000	0.22562	0.220000	0.20860	-0.319000	0.08680	GAC	G|0.879;A|0.121	0.121	strong		0.493	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
EXD3	54932	hgsc.bcm.edu	37	9	140243844	140243844	+	Missense_Mutation	SNP	C	C	T	rs28545754	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:140243844C>T	ENST00000340951.4	-	15	1829	c.1634G>A	c.(1633-1635)tGc>tAc	p.C545Y	EXD3_ENST00000342129.4_Missense_Mutation_p.C225Y	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0								p.C545Y(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CTGCTCCTCGCAGAGCGGCCT	0.706													c|||	2902	0.579473	0.2625	0.4135	5008	,	,		14487	0.8403		0.6054	False		,,,				2504	0.8303				p.C545Y		Atlas-SNP	.											EXD3,NS,carcinoma,0,1	EXD3	86	1	1	Substitution - Missense(1)	prostate(1)	c.G1634A						PASS	.		TYR/CYS	1363,2813		229,905,954	19.0	25.0	23.0		1634	1.9	0.0	9	dbSNP_125	23	5357,3063		1742,1873,595	yes	missense	EXD3	NM_017820.3	194	1971,2778,1549	TT,TC,CC		36.3777,32.6389,46.6497	benign	545/877	140243844	6720,5876	2088	4210	6298	SO:0001583	missense	54932	exon15			TCCTCGCAGAGCG		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.1634G>A	9.37:g.140243844C>T	ENSP00000340474:p.Cys545Tyr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	1239	0.5673076923076923	133	0.2703252032520325	158	0.43646408839779005	478	0.8356643356643356	470	0.6200527704485488	c	7.090	0.571880	0.13623	0.326389	0.636223	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.62105	0.05;0.05	3.8	1.9	0.25705	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	0.563354	0.16772	U	0.200172	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.23937	0.094;0.092	B;B	0.16289	0.012;0.015	T	0.42310	-0.9459	9	0.02654	T	1	.	5.7863	0.18334	0.1926:0.6981:0.0:0.1092	rs28545754	225;545	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	Y	225;545	ENSP00000343705:C225Y;ENSP00000340474:C545Y	ENSP00000340474:C545Y	C	-	2	0	EXD3	139363665	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.764000	0.26532	0.121000	0.18284	-0.560000	0.04181	TGC	C|0.432;T|0.568	0.568	strong		0.706	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086488	46086488	+	Missense_Mutation	SNP	C	C	T	rs75799438	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46086488C>T	ENST00000360770.3	-	1	356	c.316G>A	c.(316-318)Gtg>Atg	p.V106M	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	106	23 X 5 AA approximate repeats.					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						CTCACAGGCACGCACAGGGAG	0.652													C|||	140	0.0279553	0.0219	0.0389	5008	,	,		19632	0.001		0.0626	False		,,,				2504	0.0204				p.V106M		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.G316A						PASS	.	C	,MET/VAL	92,4246		0,92,2077	60.0	69.0	66.0		,316	-6.2	0.0	21	dbSNP_131	66	413,8099		12,389,3855	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,21	12,481,5932	TT,TC,CC		4.852,2.1208,3.93	,possibly-damaging	,106/147	46086488	505,12345	2169	4256	6425	SO:0001583	missense	353323	exon1			CAGGCACGCACAG	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.316G>A	21.37:g.46086488C>T	ENSP00000354001:p.Val106Met	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	185	67	0.362162	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	69	0.03159340659340659	10	0.02032520325203252	13	0.03591160220994475	1	0.0017482517482517483	45	0.059366754617414245	c	14.28	2.489659	0.44249	0.021208	0.04852	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.03272	3.99	3.77	-6.15	0.02105	.	.	.	.	.	T	0.00356	0.0011	L	0.54323	1.7	0.09310	N	1	P	0.35348	0.496	B	0.26969	0.075	T	0.32508	-0.9904	9	0.48119	T	0.1	.	3.7118	0.08423	0.2285:0.3345:0.35:0.0869	.	106	P59991	KR122_HUMAN	M	106;56	ENSP00000354001:V106M	ENSP00000354001:V106M	V	-	1	0	KRTAP12-2	44910916	0.994000	0.37717	0.000000	0.03702	0.089000	0.18198	0.137000	0.15995	-0.762000	0.04664	0.407000	0.27541	GTG	C|0.963;T|0.037	0.037	strong		0.652	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
PRKAR1B	5575	hgsc.bcm.edu	37	7	590199	590199	+	Silent	SNP	A	A	G	rs11545042	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:590199A>G	ENST00000406797.1	-	11	1188	c.1014T>C	c.(1012-1014)acT>acC	p.T338T	PRKAR1B_ENST00000537384.1_Silent_p.T338T|PRKAR1B_ENST00000360274.4_Silent_p.T338T|AC147651.2_ENST00000517177.1_RNA|PRKAR1B_ENST00000403562.1_Silent_p.T338T|PRKAR1B_ENST00000544935.1_Silent_p.T338T	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	338					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		GGGCCACGACAGTGGCCGCCC	0.672													.|||	795	0.158746	0.2322	0.1124	5008	,	,		11673	0.2391		0.1123	False		,,,				2504	0.0573				p.T338T		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.T1014C						PASS	.	G	,,,,,	885,3459		93,699,1380	21.0	20.0	20.0		1014,1014,1014,1014,1014,1014	-2.0	1.0	7	dbSNP_120	20	967,7557		46,875,3341	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKAR1B	NM_001164758.1,NM_001164759.1,NM_001164760.1,NM_001164761.1,NM_001164762.1,NM_002735.2	,,,,,	139,1574,4721	GG,GA,AA		11.3444,20.3729,14.3923	,,,,,	338/382,338/382,338/382,338/382,338/382,338/382	590199	1852,11016	2172	4262	6434	SO:0001819	synonymous_variant	5575	exon11			CACGACAGTGGCC	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.1014T>C	7.37:g.590199A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	37	CCDS34579.1	379	0.17353479853479853	126	0.25609756097560976	44	0.12154696132596685	130	0.22727272727272727	79	0.10422163588390501	a	3.749	-0.051904	0.07362	0.203729	0.113444	ENSG00000188191	ENST00000400758	.	.	.	4.65	-1.96	0.07525	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999987	.	.	.	.	.	.	T	0.26780	-1.0093	3	.	.	.	-1.4289	8.2013	0.31426	0.5175:0.2625:0.2199:0.0	rs11545042;rs28722665	.	.	.	P	199	.	.	L	-	2	0	PRKAR1B	556725	0.000000	0.05858	0.964000	0.40570	0.529000	0.34654	-2.186000	0.01251	-0.857000	0.04115	-2.296000	0.00263	CTG	A|0.826;G|0.174	0.174	strong		0.672	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1		
PLEKHA8	84725	hgsc.bcm.edu	37	7	30113706	30113706	+	Silent	SNP	A	A	G	rs11977829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:30113706A>G	ENST00000449726.1	+	13	1670	c.1320A>G	c.(1318-1320)acA>acG	p.T440T	PLEKHA8_ENST00000258679.7_Intron|AC007285.7_ENST00000433088.1_RNA|PLEKHA8_ENST00000396257.2_Silent_p.T440T|PLEKHA8_ENST00000396259.1_Intron	NM_001197027.1	NP_001183956.1	Q96JA3	PKHA8_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 8	440	Glycolipid transfer protein homology domain.				ER to Golgi ceramide transport (GO:0035621)|lipid transport (GO:0006869)|protein transport (GO:0015031)	membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ceramide binding (GO:0097001)|glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)|phosphatidylinositol-4-phosphate binding (GO:0070273)			breast(4)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)	17						ATGGTAAAACATTGCGGCAAC	0.378													G|||	1244	0.248403	0.4228	0.2378	5008	,	,		18953	0.1141		0.2396	False		,,,				2504	0.1677				p.T440T		Atlas-SNP	.											PLEKHA8_ENST00000449726,NS,carcinoma,0,2	PLEKHA8	68	2	0			c.A1320G						PASS	.	G	,,	722,1030		155,412,309	72.0	68.0	69.0		1320,1320,	-11.5	0.0	7	dbSNP_120	69	942,3040		107,728,1156	no	coding-synonymous,coding-synonymous,intron	PLEKHA8	NM_001197026.1,NM_001197027.1,NM_032639.3	,,	262,1140,1465	GG,GA,AA		23.6565,41.21,29.0199	,,	440/520,440/460,	30113706	1664,4070	876	1991	2867	SO:0001819	synonymous_variant	84725	exon13			TAAAACATTGCGG	BC053990	CCDS5424.1, CCDS56473.1, CCDS75574.1	7p21-p11.2	2013-01-10			ENSG00000106086	ENSG00000106086		"""Pleckstrin homology (PH) domain containing"""	30037	protein-coding gene	gene with protein product		608639				11001876	Standard	NM_001197027		Approved	FAPP2, MGC3358	uc003taq.3	Q96JA3	OTTHUMG00000097751	ENST00000449726.1:c.1320A>G	7.37:g.30113706A>G		Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	201	45	0.223881	NM_001197027	B4DH00|Q7Z5V8|Q9BU78|Q9H274|Q9H8Z7	Silent	SNP	ENST00000449726.1	37	CCDS56473.1																																																																																			A|0.748;G|0.252	0.252	strong		0.378	PLEKHA8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032639	
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 GAIIx	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_ENST00000447989.2_Silent_p.T118T|ALDH7A1_ENST00000553117.1_Silent_p.T91T|ALDH7A1_ENST00000413020.1_5'UTR	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		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	96	51	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	
ZNF100	163227	hgsc.bcm.edu	37	19	21948570	21948570	+	Missense_Mutation	SNP	T	T	C	rs12974842	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:21948570T>C	ENST00000358296.6	-	2	220	c.22A>G	c.(22-24)Atg>Gtg	p.M8V	ZNF100_ENST00000596452.1_5'UTR	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	8			M -> V (in dbSNP:rs12974842).		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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						AGAGGACACATTCCATACCTC	0.468													T|||	362	0.0722843	0.0045	0.0432	5008	,	,		16637	0.0546		0.0586	False		,,,				2504	0.2168				p.M8V		Atlas-SNP	.											.	ZNF100	62	.	0			c.A22G						PASS	.	T	VAL/MET	73,4297	63.5+/-100.7	2,69,2114	78.0	84.0	82.0		22	-0.9	0.0	19	dbSNP_121	82	649,7949	164.3+/-216.7	26,597,3676	yes	missense	ZNF100	NM_173531.3	21	28,666,5790	CC,CT,TT		7.5483,1.6705,5.5676	benign	8/543	21948570	722,12246	2185	4299	6484	SO:0001583	missense	163227	exon2			GACACATTCCATA	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"""Zinc fingers, C2H2-type"", ""-"""	12880	protein-coding gene	gene with protein product		603982	"""zinc finger protein 100 (Y1)"""			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.22A>G	19.37:g.21948570T>C	ENSP00000351042:p.Met8Val	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	28	21	0.75	NM_173531	Q7M4M0	Missense_Mutation	SNP	ENST00000358296.6	37	CCDS42538.1	89	0.04075091575091575	2	0.0040650406504065045	21	0.058011049723756904	23	0.04020979020979021	43	0.05672823218997362	T	0.001	-3.439773	0.00012	0.016705	0.075483	ENSG00000197020	ENST00000358296	T	0.04275	3.66	0.461	-0.922	0.10468	.	.	.	.	.	T	0.00144	0.0004	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46707	-0.9172	8	0.11182	T	0.66	.	.	.	.	rs12974842;rs17686398;rs12974842	8	Q8IYN0	ZN100_HUMAN	V	8	ENSP00000351042:M8V	ENSP00000351042:M8V	M	-	1	0	ZNF100	21740410	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	-1.890000	0.01613	-0.591000	0.05859	-0.782000	0.03352	ATG	T|0.950;C|0.050	0.050	strong		0.468	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
HSPA6	3310	hgsc.bcm.edu	37	1	161496134	161496134	+	Missense_Mutation	SNP	C	C	G	rs753856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161496134C>G	ENST00000309758.4	+	1	2099	c.1686C>G	c.(1684-1686)gaC>gaG	p.D562E	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	562			D -> E (in dbSNP:rs753856). {ECO:0000269|Ref.2}.		ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCCTTAGGGACAAGATTCCCG	0.547													C|||	617	0.123203	0.0265	0.1268	5008	,	,		20455	0.2837		0.1143	False		,,,				2504	0.0951				p.D562E		Atlas-SNP	.											.	HSPA6	53	.	0			c.C1686G						PASS	.	C	GLU/ASP	168,4238		2,164,2037	26.0	26.0	26.0		1686	1.6	0.8	1	dbSNP_86	26	889,7709		46,797,3456	no	missense	HSPA6	NM_002155.3	45	48,961,5493	GG,GC,CC		10.3396,3.813,8.1283	benign	562/644	161496134	1057,11947	2203	4299	6502	SO:0001583	missense	3310	exon1			TAGGGACAAGATT		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.1686C>G	1.37:g.161496134C>G	ENSP00000310219:p.Asp562Glu	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	138	54	0.391304	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	302	0.1382783882783883	19	0.03861788617886179	39	0.10773480662983426	153	0.2674825174825175	91	0.12005277044854881	.	13.45	2.240135	0.39598	0.03813	0.103396	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.15139	2.45	3.6	1.6	0.23607	.	0.237482	0.21074	U	0.080613	T	0.08088	0.0202	L	0.35542	1.07	0.44539	P	0.0025079999999999547	B	0.29115	0.233	P	0.45099	0.469	T	0.25745	-1.0123	9	0.51188	T	0.08	.	5.4576	0.16600	0.1978:0.6893:0.0:0.113	rs753856;rs52815568;rs753856	562	P17066	HSP76_HUMAN	E	562;538	ENSP00000310219:D562E	ENSP00000310219:D562E	D	+	3	2	HSPA6	159762758	0.158000	0.22850	0.770000	0.31555	0.633000	0.38033	0.049000	0.14099	0.167000	0.19631	0.591000	0.81541	GAC	C|0.914;G|0.086	0.086	strong		0.547	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
CTNS	1497	hgsc.bcm.edu	37	17	3559823	3559823	+	Silent	SNP	G	G	A	rs1800528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3559823G>A	ENST00000046640.3	+	8	1097	c.504G>A	c.(502-504)acG>acA	p.T168T	CTNS_ENST00000414524.2_Silent_p.T21T|CTNS_ENST00000441220.2_Silent_p.T60T|RP11-235E17.6_ENST00000575741.1_RNA|CTNS_ENST00000381870.3_Silent_p.T168T	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	168	PQ-loop 1.				adult walking behavior (GO:0007628)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|cellular amino acid metabolic process (GO:0006520)|cognition (GO:0050890)|glutathione metabolic process (GO:0006749)|grooming behavior (GO:0007625)|L-cystine transport (GO:0015811)|lens development in camera-type eye (GO:0002088)|long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	L-cystine transmembrane transporter activity (GO:0015184)			NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	TGAACCTGACGGGCTTCGTGG	0.607													G|||	754	0.150559	0.0151	0.1945	5008	,	,		10888	0.2063		0.2147	False		,,,				2504	0.1789				p.T168T		Atlas-SNP	.											.	CTNS	42	.	0			c.G504A						PASS	.	G	,	206,4200	123.7+/-161.0	3,200,2000	151.0	103.0	119.0		504,504	-7.0	0.0	17	dbSNP_89	119	1561,7039	290.1+/-299.6	150,1261,2889	no	coding-synonymous,coding-synonymous	CTNS	NM_001031681.2,NM_004937.2	,	153,1461,4889	AA,AG,GG		18.1512,4.6754,13.586	,	168/401,168/368	3559823	1767,11239	2203	4300	6503	SO:0001819	synonymous_variant	1497	exon8			CCTGACGGGCTTC	AJ222967	CCDS11031.1, CCDS32530.1	17p13	2011-06-07	2011-06-07		ENSG00000040531	ENSG00000040531			2518	protein-coding gene	gene with protein product		606272	"""cystinosis, nephropathic"""			9537412, 15128704	Standard	NM_004937		Approved	CTNS-LSB, PQLC4	uc002fwa.3	O60931	OTTHUMG00000090693	ENST00000046640.3:c.504G>A	17.37:g.3559823G>A		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	295	290	0.983051	NM_001031681	D3DTJ5|Q8IZ01|Q9UNK6	Silent	SNP	ENST00000046640.3	37	CCDS11031.1																																																																																			G|0.853;A|0.147	0.147	strong		0.607	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937	
FBN3	84467	hgsc.bcm.edu	37	19	8197958	8197958	+	Missense_Mutation	SNP	C	C	T	rs36124795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8197958C>T	ENST00000600128.1	-	14	2038	c.1624G>A	c.(1624-1626)Gtc>Atc	p.V542I	FBN3_ENST00000601739.1_Missense_Mutation_p.V542I|FBN3_ENST00000270509.2_Missense_Mutation_p.V542I			Q75N90	FBN3_HUMAN	fibrillin 3	542	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		V -> I (in dbSNP:rs36124795).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						ACGCCGTTGACGCACATGGTG	0.642													c|||	102	0.0203674	0.0038	0.0303	5008	,	,		18448	0.0		0.0477	False		,,,				2504	0.0286				p.V542I		Atlas-SNP	.											.	FBN3	300	.	0			c.G1624A						PASS	.		ILE/VAL	48,4352		1,46,2153	60.0	37.0	45.0		1624	-5.5	0.0	19	dbSNP_126	45	466,8128		16,434,3847	yes	missense	FBN3	NM_032447.3	29	17,480,6000	TT,TC,CC		5.4224,1.0909,3.9557	benign	542/2810	8197958	514,12480	2200	4297	6497	SO:0001583	missense	84467	exon13			CGTTGACGCACAT		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.1624G>A	19.37:g.8197958C>T	ENSP00000470498:p.Val542Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	50	0.022893772893772892	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	36	0.047493403693931395	c	5.340	0.248083	0.10130	0.010909	0.054224	ENSG00000142449	ENST00000270509	D	0.91996	-2.95	2.76	-5.52	0.02560	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.368768	0.24957	U	0.034242	T	0.45316	0.1336	N	0.20530	0.585	0.09310	N	0.999996	B	0.20671	0.047	B	0.15052	0.012	T	0.56208	-0.8017	10	0.37606	T	0.19	.	7.8839	0.29637	0.0:0.3335:0.3639:0.3026	rs36124795	542	Q75N90	FBN3_HUMAN	I	542	ENSP00000270509:V542I	ENSP00000270509:V542I	V	-	1	0	FBN3	8103958	1.000000	0.71417	0.002000	0.10522	0.002000	0.02628	1.371000	0.34250	-2.152000	0.00794	-1.497000	0.00963	GTC	C|0.972;T|0.028	0.028	strong		0.642	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
PPP1R17	10842	hgsc.bcm.edu	37	7	31746837	31746837	+	Silent	SNP	C	C	T	rs2072409	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:31746837C>T	ENST00000342032.3	+	5	1036	c.408C>T	c.(406-408)gaC>gaT	p.D136D	PPP1R17_ENST00000409146.3_Silent_p.D85D|PPP1R17_ENST00000498609.1_3'UTR	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	136					central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)	p.D136D(1)									TGCTCAGGGACGAGAGACCCA	0.418													C|||	590	0.117812	0.0431	0.0994	5008	,	,		21741	0.2361		0.1252	False		,,,				2504	0.1022				p.D136D		Atlas-SNP	.											C7orf16,colon,carcinoma,0,4	.	.	4	1	Substitution - coding silent(1)	stomach(1)	c.C408T						PASS	.	C	,	232,4174	137.3+/-173.1	5,222,1976	132.0	115.0	121.0		255,408	-8.4	0.3	7	dbSNP_96	121	1109,7491	230.7+/-264.9	79,951,3270	no	coding-synonymous,coding-synonymous	C7orf16	NM_001145123.2,NM_006658.4	,	84,1173,5246	TT,TC,CC		12.8953,5.2655,10.3106	,	85/105,136/156	31746837	1341,11665	2203	4300	6503	SO:0001819	synonymous_variant	10842	exon5			CAGGGACGAGAGA	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16973	protein-coding gene	gene with protein product	"""G-substrate"""	604088	"""chromosome 7 open reading frame 16"""	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.408C>T	7.37:g.31746837C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	70	15	0.214286	NM_006658	B4DE58|Q9UDQ0	Silent	SNP	ENST00000342032.3	37	CCDS5436.1																																																																																			C|0.890;T|0.110	0.110	strong		0.418	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658	
AMELX	265	hgsc.bcm.edu	37	X	11316742	11316742	+	Silent	SNP	C	C	T	rs2106416	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:11316742C>T	ENST00000380714.3	+	5	287	c.219C>T	c.(217-219)caC>caT	p.H73H	ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000380736.1_Intron|AMELX_ENST00000380712.3_Silent_p.H87H|AMELX_ENST00000348912.4_Silent_p.H57H|ARHGAP6_ENST00000380732.3_Intron|ARHGAP6_ENST00000337414.4_Intron|ARHGAP6_ENST00000413512.3_Intron	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	73					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						CCCAACAGCACCCCCCGACTC	0.597													C|||	622	0.164768	0.2133	0.0865	3775	,	,		11178	0.0149		0.168	False		,,,				2504	0.0982				p.H87H		Atlas-SNP	.											.	AMELX	31	.	0			c.C261T						PASS	.	C	,,,,	1114,2721		134,679,167,819,404	140.0	121.0	128.0		219,,,261,171	-3.8	0.9	X	dbSNP_96	128	1475,5253		94,850,437,1484,1435	no	coding-synonymous,intron,intron,coding-synonymous,coding-synonymous	AMELX,ARHGAP6	NM_001142.2,NM_006125.2,NM_013427.2,NM_182680.1,NM_182681.1	,,,,	228,1529,604,2303,1839	TT,TC,T,CC,C		21.9233,29.0482,24.5101	,,,,	73/192,,,87/206,57/176	11316742	2589,7974	2203	4300	6503	SO:0001819	synonymous_variant	265	exon6			ACAGCACCCCCCG		CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"""amelogenesis imperfecta 1"""	300391	"""amelogenin (X chromosome, amelogenesis imperfecta 1)"""	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.219C>T	X.37:g.11316742C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	62	47	0.758065	NM_182680	Q96NW6|Q9UCA7	Silent	SNP	ENST00000380714.3	37	CCDS14144.1																																																																																			C|0.765;T|0.235	0.235	strong		0.597	AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142	
UPK3BL	100134938	hgsc.bcm.edu	37	7	102279601	102279601	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:102279601G>T	ENST00000340457.8	-	4	580	c.531C>A	c.(529-531)acC>acA	p.T177T	POLR2J2_ENST00000476151.1_3'UTR|POLR2J2_ENST00000591000.1_3'UTR|RP11-514P8.6_ENST00000519541.1_Silent_p.T177T	NM_001114403.2	NP_001107875.1	B0FP48	UPK3L_HUMAN	uroplakin 3B-like	177						integral component of membrane (GO:0016021)		p.T177T(2)		kidney(2)|stomach(1)	3						TGGACCACTTGGTTTCAGCCA	0.622																																					p.T177T		Atlas-SNP	.											UPK3BL,NS,carcinoma,0,2	UPK3BL	6	2	2	Substitution - coding silent(2)	kidney(2)	c.C531A						scavenged	.						126.0	79.0	93.0					7																	102279601		691	1582	2273	SO:0001819	synonymous_variant	100134938	exon4			CCACTTGGTTTCA	EU341824	CCDS47675.1	7q22.1	2014-02-12	2010-03-03		ENSG00000267368	ENSG00000267368			37278	protein-coding gene	gene with protein product	"""uroplakin-like protein"""						Standard	NM_001114403		Approved	UPLP		B0FP48	OTTHUMG00000165036	ENST00000340457.8:c.531C>A	7.37:g.102279601G>T		Somatic	469	0	0		WXS	Illumina HiSeq	Phase_I	420	39	0.0928571	NM_001114403		Silent	SNP	ENST00000340457.8	37	CCDS47675.1																																																																																			G|0.500;T|0.500	0.500	weak		0.622	UPK3BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381510.1	NM_001114403	
NUAK2	81788	hgsc.bcm.edu	37	1	205272722	205272722	+	Silent	SNP	C	C	T	rs41264877	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205272722C>T	ENST00000367157.3	-	7	1869	c.1743G>A	c.(1741-1743)gaG>gaA	p.E581E		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			AGGGGGGCTCCTCAAGCCCCG	0.642													C|||	52	0.0103834	0.0008	0.0159	5008	,	,		15516	0.0		0.0298	False		,,,				2504	0.0102				p.E581E		Atlas-SNP	.											.	NUAK2	107	.	0			c.G1743A						PASS	.	C		32,4372		0,32,2170	30.0	36.0	34.0		1743	1.6	0.6	1	dbSNP_127	34	389,8207		9,371,3918	no	coding-synonymous	NUAK2	NM_030952.1		9,403,6088	TT,TC,CC		4.5254,0.7266,3.2385		581/629	205272722	421,12579	2202	4298	6500	SO:0001819	synonymous_variant	81788	exon7			GGGCTCCTCAAGC	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1743G>A	1.37:g.205272722C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_030952		Silent	SNP	ENST00000367157.3	37	CCDS1453.1																																																																																			C|0.974;T|0.026	0.026	strong		0.642	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
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 GAIIx	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_ENST00000306176.1_Missense_Mutation_p.L84M|ZPLD1_ENST00000466937.1_Missense_Mutation_p.L68M			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	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	118	44	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	
CYP2B6	1555	hgsc.bcm.edu	37	19	41512841	41512841	+	Missense_Mutation	SNP	G	G	T	rs3745274	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41512841G>T	ENST00000324071.4	+	4	523	c.516G>T	c.(514-516)caG>caT	p.Q172H	CYP2B6_ENST00000598834.1_3'UTR|CYP2B6_ENST00000593831.1_Intron|CYP2B6_ENST00000330446.5_Intron	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	172			Q -> H (in allele CYP2B6*6, allele CYP2B6*7, allele CYP2B6*9 and allele CYP2B6*13; dbSNP:rs3745274). {ECO:0000269|PubMed:11243870, ECO:0000269|PubMed:11470993, ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:14551287, ECO:0000269|PubMed:15469410, ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		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)	TCCTCTTCCAGTCCATTACCG	0.507													g|||	1581	0.315695	0.3744	0.3732	5008	,	,		19726	0.2153		0.2356	False		,,,				2504	0.3814				p.Q172H		Atlas-SNP	.											.	CYP2B6	79	.	0			c.G516T	GRCh37	CS080663	CYP2B6	S	rs3745274	PASS	.	G	HIS/GLN	1629,2777		311,1007,885	87.0	77.0	81.0		516	-9.0	0.0	19	dbSNP_107	81	2148,6452		267,1614,2419	yes	missense	CYP2B6	NM_000767.4	24	578,2621,3304	TT,TG,GG		24.9767,36.9723,29.0404	benign	172/492	41512841	3777,9229	2203	4300	6503	SO:0001583	missense	1555	exon4			CTTCCAGTCCATT	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.516G>T	19.37:g.41512841G>T	ENSP00000324648:p.Gln172His	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	37	CCDS12570.1	583	0.26694139194139194	174	0.35365853658536583	131	0.36187845303867405	102	0.17832167832167833	176	0.23218997361477572	.	7.755	0.704176	0.15172	0.369723	0.249767	ENSG00000197408	ENST00000324071	T	0.69561	-0.41	4.48	-8.96	0.00761	.	0.221834	0.44285	N	0.000465	T	0.00012	0.0000	N	0.17838	0.53	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.18493	-1.0335	9	0.45353	T	0.12	.	1.071	0.01621	0.199:0.1663:0.3402:0.2946	rs3745274;rs57685583;rs3745274	172	P20813	CP2B6_HUMAN	H	172	ENSP00000324648:Q172H	ENSP00000324648:Q172H	Q	+	3	2	CYP2B6	46204681	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.320000	0.02700	-1.641000	0.01523	-1.412000	0.01120	CAG	.	.	weak		0.507	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767	
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1812972	1812972	+	Silent	SNP	G	G	C	rs2294616	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1812972G>C	ENST00000250894.4	+	16	2017	c.1860G>C	c.(1858-1860)tcG>tcC	p.S620S	MAPK8IP3_ENST00000356010.5_Silent_p.S614S	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	620					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						GCCCGATCTCGGCAGGCAGCC	0.657													G|||	754	0.150559	0.0371	0.0965	5008	,	,		16664	0.2698		0.1441	False		,,,				2504	0.226				p.S620S		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.G1860C						PASS	.	G	,	172,3746		1,170,1788	53.0	62.0	59.0		1842,1860	-9.4	0.1	16	dbSNP_100	59	1053,7275		65,923,3176	no	coding-synonymous,coding-synonymous	MAPK8IP3	NM_001040439.1,NM_015133.3	,	66,1093,4964	CC,CG,GG		12.6441,4.39,10.0033	,	614/1331,620/1337	1812972	1225,11021	1959	4164	6123	SO:0001819	synonymous_variant	23162	exon16			GATCTCGGCAGGC	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.1860G>C	16.37:g.1812972G>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	136	55	0.404412	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	37	CCDS10442.2																																																																																			G|0.835;C|0.165	0.165	strong		0.657	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
MAGEB3	4114	hgsc.bcm.edu	37	X	30254361	30254361	+	Missense_Mutation	SNP	G	G	A	rs2071308	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:30254361G>A	ENST00000361644.2	+	5	1057	c.320G>A	c.(319-321)cGc>cAc	p.R107H		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	107			R -> H (in dbSNP:rs2071308). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9441743}.					p.R107H(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						GTGCAGTCTCGCACAGACCCT	0.393													G|||	1761	0.46649	0.2474	0.3746	3775	,	,		15649	0.4008		0.3648	False		,,,				2504	0.4121				p.R107H		Atlas-SNP	.											.	MAGEB3	54	.	1	Substitution - Missense(1)	prostate(1)	c.G320A						PASS	.	G	HIS/ARG	1296,2537		173,752,198,706,373	53.0	46.0	48.0		320	-8.2	0.0	X	dbSNP_96	48	3005,3723		470,1214,851,744,1021	yes	missense	MAGEB3	NM_002365.4	29	643,1966,1049,1450,1394	AA,AG,A,GG,G		44.6641,33.8116,40.7253	benign	107/347	30254361	4301,6260	2202	4300	6502	SO:0001583	missense	4114	exon5			AGTCTCGCACAGA	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.320G>A	X.37:g.30254361G>A	ENSP00000355198:p.Arg107His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	77	51	0.662338	NM_002365	A0AVE4|B3KQ52|O75861	Missense_Mutation	SNP	ENST00000361644.2	37	CCDS14220.1	778	0.4689572031344183	91	0.21064814814814814	97	0.3592592592592593	142	0.355	200	0.3412969283276451	G	0.013	-1.639962	0.00799	0.338116	0.446641	ENSG00000198798	ENST00000378986;ENST00000361644	T;T	0.01804	4.63;4.63	4.1	-8.21	0.01041	.	1.050360	0.07707	U	0.941400	T	0.00012	0.0000	N	0.21324	0.655	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44590	-0.9318	9	0.13108	T	0.6	.	14.2771	0.66187	0.0972:0.4816:0.4211:0.0	rs2071308;rs2071308	107	O15480	MAGB3_HUMAN	H	107	ENSP00000368271:R107H;ENSP00000355198:R107H	ENSP00000355198:R107H	R	+	2	0	MAGEB3	30164282	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.470000	0.00460	-6.183000	0.00006	-1.991000	0.00449	CGC	G|0.569;A|0.431	0.431	strong		0.393	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365	
PPP1R1A	5502	hgsc.bcm.edu	37	12	54974803	54974803	+	Silent	SNP	C	C	T	rs8407	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:54974803C>T	ENST00000257905.8	-	6	605	c.435G>A	c.(433-435)gaG>gaA	p.E145E	PPP1R1A_ENST00000547431.1_Missense_Mutation_p.R72K	NM_006741.3	NP_006732	Q13522	PPR1A_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1A	145	Interaction with PPP1R15A.				glycogen metabolic process (GO:0005977)|negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein serine/threonine phosphatase inhibitor activity (GO:0004865)			lung(2)	2						TACTGCCTCTCTCGTGAGTTT	0.542													C|||	829	0.165535	0.0348	0.2666	5008	,	,		17061	0.0595		0.3012	False		,,,				2504	0.2403				p.E145E		Atlas-SNP	.											PPP1R1A_ENST00000257905,NS,carcinoma,-2,2	PPP1R1A	18	2	0			c.G435A						PASS	.	C		284,3490		5,274,1608	203.0	190.0	194.0		435	4.9	1.0	12	dbSNP_52	194	2522,5724		381,1760,1982	no	coding-synonymous	PPP1R1A	NM_006741.3		386,2034,3590	TT,TC,CC		30.5845,7.5252,23.3444		145/172	54974803	2806,9214	1887	4123	6010	SO:0001819	synonymous_variant	5502	exon6			GCCTCTCTCGTGA	U48707	CCDS44912.1	12q13.2	2012-04-17			ENSG00000135447	ENSG00000135447	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9286	protein-coding gene	gene with protein product		613246				8611507	Standard	NM_006741		Approved		uc001sgg.2	Q13522	OTTHUMG00000169934	ENST00000257905.8:c.435G>A	12.37:g.54974803C>T		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	264	140	0.530303	NM_006741	Q6IB01|Q8TBJ2|Q8WWV2	Silent	SNP	ENST00000257905.8	37	CCDS44912.1	381	0.17445054945054944	20	0.04065040650406504	94	0.2596685082872928	39	0.06818181818181818	228	0.3007915567282322	C	5.450	0.268099	0.10349	0.075252	0.305845	ENSG00000135447	ENST00000379690;ENST00000553113	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.04053	-1.0981	4	0.02654	T	1	.	14.0661	0.64831	0.0:1.0:0.0:0.0	rs8407;rs867623;rs1050103;rs3190383;rs17795135;rs17845698;rs17858640;rs8407	.	.	.	K	72;64	.	ENSP00000369012:R72K	R	-	2	0	PPP1R1A	53261070	0.985000	0.35326	0.963000	0.40424	0.460000	0.32559	3.445000	0.52921	2.458000	0.83093	0.655000	0.94253	AGA	C|0.825;T|0.175	0.175	strong		0.542	PPP1R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406604.1	NM_006741	
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 GAIIx	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	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	68	27	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		
PARD3B	117583	hgsc.bcm.edu	37	2	206364737	206364737	+	Silent	SNP	T	T	C	rs10197347	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:206364737T>C	ENST00000406610.2	+	21	3369	c.3162T>C	c.(3160-3162)tcT>tcC	p.S1054S	PARD3B_ENST00000349953.3_Silent_p.S953S|PARD3B_ENST00000488622.1_3'UTR|PARD3B_ENST00000351153.1_Silent_p.S985S|PARD3B_ENST00000358768.2_Silent_p.S992S	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	1054					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		CAAGGCCATCTGAGTATGACC	0.438													T|||	2246	0.448482	0.3601	0.5692	5008	,	,		21928	0.4871		0.4115	False		,,,				2504	0.4806				p.S992S		Atlas-SNP	.											.	PARD3B	314	.	0			c.T2976C						PASS	.	T	,,	1436,2416		266,904,756	216.0	198.0	203.0		2955,2976,2859	2.5	1.0	2	dbSNP_119	203	3152,5096		639,1874,1611	yes	coding-synonymous,coding-synonymous,coding-synonymous	PARD3B	NM_057177.6,NM_152526.5,NM_205863.3	,,	905,2778,2367	CC,CT,TT		38.2153,37.2793,37.9174	,,	985/1137,992/1144,953/1105	206364737	4588,7512	1926	4124	6050	SO:0001819	synonymous_variant	117583	exon20			GCCATCTGAGTAT	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.3162T>C	2.37:g.206364737T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_152526	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				T|0.587;C|0.413	0.413	strong		0.438	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
ZNF814	730051	hgsc.bcm.edu	37	19	58386284	58386284	+	Silent	SNP	T	T	C	rs201805246	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58386284T>C	ENST00000435989.2	-	3	708	c.474A>G	c.(472-474)gcA>gcG	p.A158A	ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	158				A -> V (in Ref. 1; BAH13293). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TACACCTCTTTGCAAACAACG	0.493																																					p.A158A		Atlas-SNP	.											ZNF814,NS,carcinoma,0,1	ZNF814	93	1	0			c.A474G						scavenged	.						158.0	116.0	128.0					19																	58386284		692	1587	2279	SO:0001819	synonymous_variant	730051	exon3			CCTCTTTGCAAAC		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.474A>G	19.37:g.58386284T>C		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	240	61	0.254167	NM_001144989	A6NF35	Silent	SNP	ENST00000435989.2	37	CCDS46212.1																																																																																			.	.	alt		0.493	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
SLC10A1	6554	hgsc.bcm.edu	37	14	70263648	70263648	+	Silent	SNP	C	C	T	rs4646285	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:70263648C>T	ENST00000216540.4	-	1	358	c.225G>A	c.(223-225)acG>acA	p.T75T		NM_003049.3	NP_003040.1	Q14973	NTCP_HUMAN	solute carrier family 10 (sodium/bile acid cotransporter), member 1	75					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)	14				all cancers(60;0.00228)|BRCA - Breast invasive adenocarcinoma(234;0.0137)|OV - Ovarian serous cystadenocarcinoma(108;0.0226)	Bumetanide(DB00887)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Ethinyl Estradiol(DB00977)|Indomethacin(DB00328)|Liothyronine(DB00279)|Liotrix(DB01583)|Pitavastatin(DB08860)|Probenecid(DB01032)|Progesterone(DB00396)|Testosterone(DB00624)|Ursodeoxycholic acid(DB01586)	GCACAAAGGCCGTGAGGGGCA	0.567													C|||	500	0.0998403	0.0083	0.134	5008	,	,		22636	0.1726		0.0855	False		,,,				2504	0.1391				p.T75T		Atlas-SNP	.											.	SLC10A1	32	.	0			c.G225A						PASS	.	C		122,4284	91.6+/-130.3	0,122,2081	94.0	77.0	83.0		225	-10.0	0.6	14	dbSNP_111	83	745,7855	179.0+/-228.3	37,671,3592	no	coding-synonymous	SLC10A1	NM_003049.3		37,793,5673	TT,TC,CC		8.6628,2.769,6.6662		75/350	70263648	867,12139	2203	4300	6503	SO:0001819	synonymous_variant	6554	exon1			AAAGGCCGTGAGG	L21893	CCDS9797.1	14q24.2	2013-07-18	2013-07-18		ENSG00000100652	ENSG00000100652		"""Solute carriers"""	10905	protein-coding gene	gene with protein product		182396				8132774	Standard	NM_003049		Approved	NTCP	uc001xlr.2	Q14973	OTTHUMG00000171236	ENST00000216540.4:c.225G>A	14.37:g.70263648C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_003049	B9EGB6|Q2TU29	Silent	SNP	ENST00000216540.4	37	CCDS9797.1																																																																																			C|0.920;T|0.080	0.080	strong		0.567	SLC10A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412464.1		
B4GALNT3	283358	hgsc.bcm.edu	37	12	662838	662838	+	Silent	SNP	T	T	C	rs1056008	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:662838T>C	ENST00000266383.5	+	14	1762	c.1749T>C	c.(1747-1749)ccT>ccC	p.P583P		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	583					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)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			CTCAGGCCCCTGGAAGGGGCT	0.652													C|||	1424	0.284345	0.3805	0.1945	5008	,	,		17522	0.1974		0.2942	False		,,,				2504	0.2975				p.P583P		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.T1749C						PASS	.	C		1649,2757		302,1045,856	32.0	34.0	33.0		1749	-0.4	0.0	12	dbSNP_86	33	2267,6327		310,1647,2340	no	coding-synonymous	B4GALNT3	NM_173593.3		612,2692,3196	CC,CT,TT		26.3789,37.4262,30.1231		583/999	662838	3916,9084	2203	4297	6500	SO:0001819	synonymous_variant	283358	exon14			GGCCCCTGGAAGG	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1749T>C	12.37:g.662838T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	37	CCDS8504.1																																																																																			.	.	weak		0.652	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
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 GAIIx	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	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	54	28	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	
PLXNA2	5362	hgsc.bcm.edu	37	1	208391254	208391254	+	Missense_Mutation	SNP	C	C	T	rs2782948	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:208391254C>T	ENST00000367033.3	-	2	771	c.14G>A	c.(13-15)cGg>cAg	p.R5Q		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	5			R -> Q (in dbSNP:rs2782948). {ECO:0000269|PubMed:12975309}.		axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.R5Q(1)		NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGGCCAGGGCCGCCTCTGTTC	0.667													C|||	1826	0.364617	0.3601	0.3314	5008	,	,		14354	0.4018		0.3022	False		,,,				2504	0.4202				p.R5Q		Atlas-SNP	.											PLXNA2,NS,carcinoma,0,1	PLXNA2	178	1	1	Substitution - Missense(1)	prostate(1)	c.G14A						PASS	.	C	GLN/ARG	1475,2785		301,873,956	14.0	18.0	17.0		14	5.5	1.0	1	dbSNP_100	17	2702,5660		522,1658,2001	yes	missense	PLXNA2	NM_025179.3	43	823,2531,2957	TT,TC,CC		32.3128,34.6244,33.093	probably-damaging	5/1895	208391254	4177,8445	2130	4181	6311	SO:0001583	missense	5362	exon2			CAGGGCCGCCTCT	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.14G>A	1.37:g.208391254C>T	ENSP00000356000:p.Arg5Gln	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	787	0.36034798534798534	172	0.34959349593495936	127	0.35082872928176795	261	0.4562937062937063	227	0.2994722955145119	C	12.54	1.969753	0.34754	0.346244	0.323128	ENSG00000076356	ENST00000367033	T	0.00902	5.56	5.5	5.5	0.81552	.	1.704600	0.03240	N	0.180311	T	0.00012	0.0000	N	0.19112	0.55	0.36191	P	0.14992899999999998	P;B	0.46706	0.883;0.029	B;B	0.34038	0.174;0.011	T	0.48570	-0.9024	9	0.66056	D	0.02	.	13.6821	0.62491	0.0:0.9266:0.0:0.0734	rs2782948;rs3748736;rs2782948	59;5	O75051-2;O75051	.;PLXA2_HUMAN	Q	5	ENSP00000356000:R5Q	ENSP00000356000:R5Q	R	-	2	0	PLXNA2	206457877	0.994000	0.37717	0.985000	0.45067	0.023000	0.10783	0.519000	0.22862	2.588000	0.87417	0.650000	0.86243	CGG	C|0.660;T|0.340	0.340	strong		0.667	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
MUC4	4585	hgsc.bcm.edu	37	3	195508478	195508478	+	Missense_Mutation	SNP	G	G	C	rs76305071	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195508478G>C	ENST00000463781.3	-	2	10432	c.9973C>G	c.(9973-9975)Cac>Gac	p.H3325D	MUC4_ENST00000475231.1_Missense_Mutation_p.H3325D|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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)	p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		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)		GGGGTGGCGTGACCTGTGGAT	0.582													.|||	36	0.0071885	0.025	0.0043	5008	,	,		11084	0.0		0.0	False		,,,				2504	0.0				p.H3325D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,3	MUC4	1505	3	1	Deletion - In frame(1)	stomach(1)	c.C9973G						scavenged	.						16.0	16.0	16.0					3																	195508478		681	1566	2247	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.9973C>G	3.37:g.195508478G>C	ENSP00000417498:p.His3325Asp	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	2	0.030303	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	2.541	-0.306191	0.05458	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26957	1.7;1.7	1.03	-0.504	0.11997	.	.	.	.	.	T	0.11110	0.0271	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33854	-0.9852	7	.	.	.	.	2.6532	0.05004	0.0:0.4387:0.3046:0.2566	.	3197	E7ESK3	.	D	3325	ENSP00000417498:H3325D;ENSP00000420243:H3325D	.	H	-	1	0	MUC4	196993257	0.129000	0.22400	0.000000	0.03702	0.009000	0.06853	0.657000	0.24963	-2.022000	0.00938	-1.954000	0.00483	CAC	G|0.990;C|0.010	0.010	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
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 GAIIx	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_ENST00000467303.1_5'Flank|KIAA0226_ENST00000389665.5_Silent_p.S387S|KIAA0226_ENST00000449205.1_Silent_p.S387S|KIAA0226_ENST00000273582.5_Silent_p.S327S	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		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	132	63	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	
MNDA	4332	hgsc.bcm.edu	37	1	158813819	158813819	+	Silent	SNP	A	A	G	rs857870	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158813819A>G	ENST00000368141.4	+	4	738	c.477A>G	c.(475-477)ccA>ccG	p.P159P		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	159					B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					GTAAGCCCCCAGGTCCCTCAG	0.463													a|||	2645	0.528155	0.3071	0.5447	5008	,	,		17925	0.6954		0.5825	False		,,,				2504	0.5869				p.P159P		Atlas-SNP	.											.	MNDA	147	.	0			c.A477G						PASS	.	A		1628,2778	501.3+/-365.0	294,1040,869	215.0	181.0	192.0		477	-2.4	0.0	1	dbSNP_86	192	4936,3664	623.4+/-397.5	1404,2128,768	no	coding-synonymous	MNDA	NM_002432.1		1698,3168,1637	GG,GA,AA		42.6047,36.9496,49.531		159/408	158813819	6564,6442	2203	4300	6503	SO:0001819	synonymous_variant	4332	exon4			GCCCCCAGGTCCC	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.477A>G	1.37:g.158813819A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_002432		Silent	SNP	ENST00000368141.4	37	CCDS1177.1																																																																																			A|0.493;G|0.507	0.507	strong		0.463	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432	
TBC1D10C	374403	hgsc.bcm.edu	37	11	67171736	67171736	+	Silent	SNP	C	C	T	rs2514256	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67171736C>T	ENST00000542590.1	+	1	77	c.63C>T	c.(61-63)tcC>tcT	p.S21S	PPP1CA_ENST00000376745.4_5'Flank|TBC1D10C_ENST00000312390.5_Silent_p.S21S|PPP1CA_ENST00000358239.4_5'Flank|PPP1CA_ENST00000532446.1_5'Flank|PPP1CA_ENST00000312989.7_5'Flank|TBC1D10C_ENST00000526387.1_Silent_p.S21S			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	21					retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			ACTCCAGCTCCTTGGGGTCCG	0.667													T|||	1762	0.351837	0.8283	0.4049	5008	,	,		15412	0.2589		0.0785	False		,,,				2504	0.047				p.S21S		Atlas-SNP	.											TBC1D10C,NS,carcinoma,0,1	TBC1D10C	42	1	0			c.C63T						PASS	.	T		2948,1446		1011,926,260	17.0	19.0	18.0		63	-4.5	0.5	11	dbSNP_100	18	633,7937		24,585,3676	no	coding-synonymous	TBC1D10C	NM_198517.2		1035,1511,3936	TT,TC,CC		7.3862,32.9085,27.6226		21/447	67171736	3581,9383	2197	4285	6482	SO:0001819	synonymous_variant	374403	exon2			CAGCTCCTTGGGG	BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.63C>T	11.37:g.67171736C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	13	0.158537	NM_001256508	G3V1D6	Silent	SNP	ENST00000542590.1	37	CCDS8162.1																																																																																			C|0.683;T|0.317	0.317	strong		0.667	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395492.2	NM_198517	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058968	79058968	+	Silent	SNP	T	T	C	rs112827102	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:79058968T>C	ENST00000388820.4	-	19	3495	c.3285A>G	c.(3283-3285)acA>acG	p.T1095T	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1095					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 chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GTGGTGGGGGTGTCCGGTCCC	0.622													t|||	553	0.110423	0.0477	0.0562	5008	,	,		13778	0.2063		0.0855	False		,,,				2504	0.1605				p.T1095T		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.A3285G						PASS	.	C		153,4213		5,143,2035	16.0	23.0	21.0		3285	-7.3	0.0	15	dbSNP_132	21	545,8023		18,509,3757	no	coding-synonymous	ADAMTS7	NM_014272.3		23,652,5792	CC,CT,TT		6.3609,3.5044,5.3966		1095/1687	79058968	698,12236	2183	4284	6467	SO:0001819	synonymous_variant	11173	exon19			TGGGGGTGTCCGG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3285A>G	15.37:g.79058968T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			T|0.935;C|0.065	0.065	strong		0.622	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
ITIH2	3698	hgsc.bcm.edu	37	10	7759595	7759595	+	Silent	SNP	C	C	T	rs7072478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:7759595C>T	ENST00000358415.4	+	6	640	c.474C>T	c.(472-474)agC>agT	p.S158S	ITIH2_ENST00000379587.4_Silent_p.S147S|ITIH2_ENST00000480387.1_3'UTR	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	158	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.S158S(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TTAGGAGCAGCGCTCTTGATA	0.488													C|||	1037	0.207069	0.2201	0.2781	5008	,	,		21172	0.2202		0.172	False		,,,				2504	0.1616				p.S158S		Atlas-SNP	.											ITIH2,NS,carcinoma,0,1	ITIH2	144	1	1	Substitution - coding silent(1)	stomach(1)	c.C474T						PASS	.	C		994,3412	370.3+/-319.5	113,768,1322	163.0	174.0	171.0		474	-8.4	0.0	10	dbSNP_116	171	1200,7400	243.3+/-273.0	84,1032,3184	no	coding-synonymous	ITIH2	NM_002216.2		197,1800,4506	TT,TC,CC		13.9535,22.5601,16.8691		158/947	7759595	2194,10812	2203	4300	6503	SO:0001819	synonymous_variant	3698	exon6			GAGCAGCGCTCTT	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.474C>T	10.37:g.7759595C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																			C|0.819;T|0.181	0.181	strong		0.488	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
PLA2G2A	5320	hgsc.bcm.edu	37	1	20304926	20304926	+	Silent	SNP	G	G	A	rs4744	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:20304926G>A	ENST00000375111.3	-	4	403	c.132C>T	c.(130-132)taC>taT	p.Y44Y	PLA2G2A_ENST00000496748.1_5'UTR|PLA2G2A_ENST00000400520.3_Silent_p.Y44Y	NM_000300.3|NM_001161727.1	NP_000291.1|NP_001155199.1	P14555	PA2GA_HUMAN	phospholipase A2, group IIA (platelets, synovial fluid)	44					defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of epithelial cell proliferation (GO:0050680)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidic acid metabolic process (GO:0046473)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|small molecule metabolic process (GO:0044281)|somatic stem cell maintenance (GO:0035019)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|phospholipase A2 activity (GO:0004623)|phospholipid binding (GO:0005543)	p.Y44Y(1)		central_nervous_system(1)|lung(6)|prostate(1)|stomach(1)	9		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Diclofenac(DB00586)|Ginkgo biloba(DB01381)|Indomethacin(DB00328)|Suramin(DB04786)	AGTGGCAGCCGTAGAAGCCAT	0.572													G|||	530	0.105831	0.0968	0.1052	5008	,	,		16112	0.0268		0.2078	False		,,,				2504	0.0951				p.Y44Y		Atlas-SNP	.											PLA2G2A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PLA2G2A	14	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C132T						PASS	.	G	,,,	436,3970		31,374,1798	35.0	40.0	39.0		132,132,132,132	-3.7	0.0	1	dbSNP_52	39	1798,6798		198,1402,2698	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLA2G2A	NM_000300.3,NM_001161727.1,NM_001161728.1,NM_001161729.1	,,,	229,1776,4496	AA,AG,GG		20.9167,9.8956,17.182	,,,	44/145,44/145,44/145,44/145	20304926	2234,10768	2203	4298	6501	SO:0001819	synonymous_variant	5320	exon3			GCAGCCGTAGAAG	BC005919	CCDS201.1	1p35	2008-09-19			ENSG00000188257	ENSG00000188257	3.1.1.4		9031	protein-coding gene	gene with protein product		172411		PLA2B, PLA2L		8838795	Standard	NM_000300		Approved		uc010odb.2	P14555	OTTHUMG00000002699	ENST00000375111.3:c.132C>T	1.37:g.20304926G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_001161729	A8K5I7|Q6DN24|Q6IBD9|Q9UCD2	Silent	SNP	ENST00000375111.3	37	CCDS201.1																																																																																			G|0.860;A|0.140	0.140	strong		0.572	PLA2G2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007675.1	NM_000300	
FMN2	56776	hgsc.bcm.edu	37	1	240371426	240371426	+	Missense_Mutation	SNP	T	T	C	rs200640213	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:240371426T>C	ENST00000319653.9	+	5	3544	c.3314T>C	c.(3313-3315)gTg>gCg	p.V1105A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1105	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CTACCCGGAGTGGGCATACCT	0.736													-|||	349	0.0696885	0.0605	0.049	5008	,	,		2970	0.0724		0.0974	False		,,,				2504	0.0654				p.V1105A		Atlas-SNP	.											FMN2,rectum,carcinoma,0,1	FMN2	451	1	0			c.T3314C						scavenged	.	C	ALA/VAL	89,4025		0,89,1968	8.0	11.0	10.0		3314	-4.6	0.0	1		10	380,7864		4,372,3746	no	missense	FMN2	NM_020066.4	64	4,461,5714	CC,CT,TT		4.6094,2.1633,3.7951	benign	1105/1723	240371426	469,11889	2057	4122	6179	SO:0001583	missense	56776	exon5			CCGGAGTGGGCAT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3314T>C	1.37:g.240371426T>C	ENSP00000318884:p.Val1105Ala	Somatic	50	4	0.08		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	t	6.825	0.521456	0.13005	0.021633	0.046094	ENSG00000155816	ENST00000319653	T	0.54071	0.59	3.44	-4.56	0.03431	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (2);	2.607690	0.02057	N	0.050513	T	0.04363	0.0120	N	0.04335	-0.225	0.09310	N	1	B	0.23650	0.089	B	0.25614	0.062	T	0.03576	-1.1023	9	.	.	.	.	4.0237	0.09677	0.2447:0.3179:0.0:0.4374	.	1105	Q9NZ56	FMN2_HUMAN	A	1105	ENSP00000318884:V1105A	.	V	+	2	0	FMN2	238438049	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.925000	0.01564	-1.108000	0.03000	-2.277000	0.00273	GTG	T|0.940;C|0.060	0.060	strong		0.736	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
KIAA1211	57482	hgsc.bcm.edu	37	4	57182758	57182758	+	Silent	SNP	C	C	T	rs28559894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57182758C>T	ENST00000504228.1	+	6	3195	c.3090C>T	c.(3088-3090)gaC>gaT	p.D1030D	KIAA1211_ENST00000541073.1_Silent_p.D1023D|KIAA1211_ENST00000264229.6_Silent_p.D1030D			Q6ZU35	K1211_HUMAN	KIAA1211	1030										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AGAAGAGGGACGAGGAGGAAG	0.627													C|||	1128	0.22524	0.1407	0.2233	5008	,	,		12589	0.254		0.341	False		,,,				2504	0.1922				p.D1030D		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	0			c.C3090T						PASS	.	C		672,3328		52,568,1380	18.0	21.0	20.0		3090	-6.2	0.0	4	dbSNP_125	20	2858,5480		498,1862,1809	no	coding-synonymous	KIAA1211	NM_020722.1		550,2430,3189	TT,TC,CC		34.2768,16.8,28.6108		1030/1234	57182758	3530,8808	2000	4169	6169	SO:0001819	synonymous_variant	57482	exon8			GAGGGACGAGGAG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.3090C>T	4.37:g.57182758C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			C|0.728;T|0.272	0.272	strong		0.627	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
P2RY2	5029	hgsc.bcm.edu	37	11	72946204	72946204	+	Missense_Mutation	SNP	C	C	T	rs1626154	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:72946204C>T	ENST00000311131.2	+	3	1467	c.1000C>T	c.(1000-1002)Cgc>Tgc	p.R334C	P2RY2_ENST00000393596.2_Missense_Mutation_p.R334C|P2RY2_ENST00000393597.2_Missense_Mutation_p.R334C	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	334			R -> C (in dbSNP:rs1626154). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.6}.		cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CCCGGCTCGCCGCAGGCTGGG	0.652													C|||	457	0.091254	0.0212	0.1571	5008	,	,		14819	0.0506		0.2087	False		,,,				2504	0.0603				p.R334C		Atlas-SNP	.											.	P2RY2	54	.	0			c.C1000T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	178,4220		6,166,2027	29.0	34.0	32.0		1000,1000,1000	3.4	0.9	11	dbSNP_89	32	1595,6989		152,1291,2849	yes	missense,missense,missense	P2RY2	NM_002564.2,NM_176071.1,NM_176072.1	180,180,180	158,1457,4876	TT,TC,CC		18.5811,4.0473,13.6574	probably-damaging,probably-damaging,probably-damaging	334/378,334/378,334/378	72946204	1773,11209	2199	4292	6491	SO:0001583	missense	5029	exon3			GCTCGCCGCAGGC	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.1000C>T	11.37:g.72946204C>T	ENSP00000310305:p.Arg334Cys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	39	0.735849	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	263	0.12042124542124542	16	0.032520325203252036	62	0.1712707182320442	34	0.05944055944055944	151	0.19920844327176782	C	10.24	1.296099	0.23650	0.040473	0.185811	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.26660	1.72;1.72;1.72	4.44	3.44	0.39384	.	1.660570	0.03269	N	0.184484	T	0.00012	0.0000	N	0.08118	0	0.27732	P	0.9447875	D	0.61697	0.99	B	0.43809	0.432	T	0.19031	-1.0318	9	0.59425	D	0.04	.	9.8209	0.40883	0.0:0.7905:0.2095:0.0	rs1626154;rs1626154	334	P41231	P2RY2_HUMAN	C	334	ENSP00000377222:R334C;ENSP00000310305:R334C;ENSP00000377221:R334C	ENSP00000310305:R334C	R	+	1	0	P2RY2	72623852	0.012000	0.17670	0.929000	0.37066	0.293000	0.27360	1.895000	0.39778	2.196000	0.70406	0.561000	0.74099	CGC	C|0.873;T|0.127	0.127	strong		0.652	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
ACVR1	90	hgsc.bcm.edu	37	2	158636910	158636910	+	Silent	SNP	G	G	A	rs2227861	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:158636910G>A	ENST00000263640.3	-	4	699	c.270C>T	c.(268-270)gcC>gcT	p.A90A	ACVR1_ENST00000487456.1_5'UTR|ACVR1_ENST00000434821.1_Silent_p.A90A|ACVR1_ENST00000409283.2_Silent_p.A90A|ACVR1_ENST00000410057.2_Silent_p.A90A	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	90					activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	AGCACTCCACGGCTTGGCCAG	0.537													G|||	3260	0.650958	0.1838	0.7666	5008	,	,		19153	0.9067		0.7793	False		,,,				2504	0.8047				p.A90A		Atlas-SNP	.											.	ACVR1	52	.	0			c.C270T						PASS	.	G	,	1220,3186	422.3+/-339.7	178,864,1161	64.0	67.0	66.0		270,270	-7.7	0.8	2	dbSNP_98	66	6645,1955	723.8+/-406.5	2563,1519,218	no	coding-synonymous,coding-synonymous	ACVR1	NM_001105.4,NM_001111067.2	,	2741,2383,1379	AA,AG,GG		22.7326,27.6895,39.5279	,	90/510,90/510	158636910	7865,5141	2203	4300	6503	SO:0001819	synonymous_variant	90	exon4			CTCCACGGCTTGG		CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.270C>T	2.37:g.158636910G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001105		Silent	SNP	ENST00000263640.3	37	CCDS2206.1																																																																																			G|0.366;A|0.634	0.634	strong		0.537	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105	
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 GAIIx	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	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	172	80	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	
OR6M1	390261	hgsc.bcm.edu	37	11	123676231	123676231	+	Missense_Mutation	SNP	G	G	T	rs4936845	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:123676231G>T	ENST00000309154.2	-	1	864	c.827C>A	c.(826-828)aCa>aAa	p.T276K		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	276			T -> K (in dbSNP:rs4936845).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(2)|skin(5)|urinary_tract(1)	29		Breast(109;0.0109)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.028)		GGTCACCACTGTGATGAGGAC	0.478													G|||	1219	0.243411	0.1029	0.317	5008	,	,		17328	0.2946		0.2853	False		,,,				2504	0.2853				p.T276K		Atlas-SNP	.											OR6M1,colon,carcinoma,0,1	OR6M1	60	1	0			c.C827A						PASS	.	G	LYS/THR	540,3864	243.4+/-253.1	44,452,1706	127.0	120.0	122.0		827	3.5	0.3	11	dbSNP_111	122	2568,6030	420.5+/-353.4	389,1790,2120	yes	missense	OR6M1	NM_001005325.1	78	433,2242,3826	TT,TG,GG		29.8674,12.2616,23.904	possibly-damaging	276/314	123676231	3108,9894	2202	4299	6501	SO:0001583	missense	390261	exon1			ACCACTGTGATGA	AB065762	CCDS31696.1	11q24.1	2012-08-09			ENSG00000196099	ENSG00000196099		"""GPCR / Class A : Olfactory receptors"""	14711	protein-coding gene	gene with protein product							Standard	NM_001005325		Approved		uc010rzz.2	Q8NGM8	OTTHUMG00000166012	ENST00000309154.2:c.827C>A	11.37:g.123676231G>T	ENSP00000311038:p.Thr276Lys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	144	119	0.826389	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	526	0.24084249084249085	54	0.10975609756097561	94	0.2596685082872928	161	0.28146853146853146	217	0.2862796833773087	G	13.48	2.251267	0.39797	0.122616	0.298674	ENSG00000196099	ENST00000309154	T	0.00265	8.39	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34200	U	0.004164	T	0.00012	0.0000	M	0.92970	3.365	0.80722	P	0.0	P	0.41188	0.741	P	0.53809	0.735	T	0.04153	-1.0973	9	0.87932	D	0	.	6.5789	0.22583	0.1324:0.0:0.8676:0.0	rs4936845;rs52810786;rs56873896;rs4936845	276	Q8NGM8	OR6M1_HUMAN	K	276	ENSP00000311038:T276K	ENSP00000311038:T276K	T	-	2	0	OR6M1	123181441	0.010000	0.17322	0.295000	0.24960	0.731000	0.41821	1.794000	0.38774	1.754000	0.51921	0.655000	0.94253	ACA	G|0.763;T|0.237	0.237	strong		0.478	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325	
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 GAIIx	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		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	54	10	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 GAIIx	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		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	22	12	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	
NUP88	4927	hgsc.bcm.edu	37	17	5289580	5289580	+	Silent	SNP	A	A	G	rs11209	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5289580A>G	ENST00000573584.1	-	17	2681	c.2172T>C	c.(2170-2172)caT>caC	p.H724H	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	724					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						TTTCCCTTATATGTTCACCCC	0.358													G|||	2887	0.576478	0.5061	0.4308	5008	,	,		17870	0.8244		0.4165	False		,,,				2504	0.684				p.H724H		Atlas-SNP	.											.	NUP88	47	.	0			c.T2172C						PASS	.	G		2220,2186	586.2+/-386.4	558,1104,541	224.0	208.0	214.0		2172	4.0	1.0	17	dbSNP_52	214	3248,5352	649.5+/-400.6	606,2036,1658	no	coding-synonymous	NUP88	NM_002532.4		1164,3140,2199	GG,GA,AA		37.7674,49.6142,42.0421		724/742	5289580	5468,7538	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon17			CCTTATATGTTCA	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.2172T>C	17.37:g.5289580A>G		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	155	87	0.56129	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			A|0.526;G|0.474	0.474	strong		0.358	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
TENM2	57451	hgsc.bcm.edu	37	5	167474474	167474474	+	Missense_Mutation	SNP	A	A	G	rs114898031	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:167474474A>G	ENST00000518659.1	+	6	1268	c.1229A>G	c.(1228-1230)gAt>gGt	p.D410G	TENM2_ENST00000545108.1_Missense_Mutation_p.D410G|TENM2_ENST00000403607.2_Missense_Mutation_p.D243G|TENM2_ENST00000520394.1_Intron|TENM2_ENST00000519204.1_Missense_Mutation_p.D289G	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	410					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										CAGCCTGCAGATGGGCACACC	0.463											OREG0017008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	26	0.00519169	0.0008	0.0101	5008	,	,		20998	0.0		0.0159	False		,,,				2504	0.002				p.D410G		Atlas-SNP	.											ODZ2_ENST00000519204,NS,carcinoma,0,3	.	.	3	0			c.A1229G						PASS	.	A	GLY/ASP	7,1377		0,7,685	106.0	88.0	93.0		1229	5.7	1.0	5	dbSNP_132	93	77,3105		1,75,1515	yes	missense	ODZ2	NM_001122679.1	94	1,82,2200	GG,GA,AA		2.4199,0.5058,1.8397	possibly-damaging	410/2766	167474474	84,4482	692	1591	2283	SO:0001583	missense	57451	exon6			CTGCAGATGGGCA	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.1229A>G	5.37:g.167474474A>G	ENSP00000429430:p.Asp410Gly	Somatic	179	0	0	1862	WXS	Illumina HiSeq	Phase_I	171	78	0.45614	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	A	16.21	3.058451	0.55325	0.005058	0.024199	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000403607	D;D;D;D	0.89415	-2.04;-2.03;-2.14;-2.51	5.67	5.67	0.87782	.	0.175663	0.46442	D	0.000281	T	0.79076	0.4385	L	0.34521	1.04	0.48236	D	0.999615	P;P	0.48640	0.858;0.913	B;P	0.47044	0.334;0.535	D	0.85154	0.0988	10	0.72032	D	0.01	.	15.5819	0.76448	1.0:0.0:0.0:0.0	.	410;289	Q9NT68;G3V106	TEN2_HUMAN;.	G	410;410;289;243	ENSP00000429430:D410G;ENSP00000438635:D410G;ENSP00000428964:D289G;ENSP00000384905:D243G	ENSP00000384905:D243G	D	+	2	0	ODZ2	167407052	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.131000	0.71670	2.164000	0.68074	0.533000	0.62120	GAT	A|0.990;G|0.010	0.010	strong		0.463	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
TIMP3	7078	hgsc.bcm.edu	37	22	33253280	33253280	+	Silent	SNP	T	T	C	rs9862	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:33253280T>C	ENST00000266085.6	+	3	550	c.249T>C	c.(247-249)caT>caC	p.H83H	SYN3_ENST00000358763.2_Intron|SYN3_ENST00000332840.5_Intron	NM_000362.4	NP_000353.1	P35625	TIMP3_HUMAN	TIMP metallopeptidase inhibitor 3	83	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				cellular response to organic substance (GO:0071310)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(2)|large_intestine(3)|lung(1)|urinary_tract(1)	7						AGTACATCCATACGGAAGCTT	0.507													C|||	3260	0.650958	0.8835	0.696	5008	,	,		20747	0.6121		0.4821	False		,,,				2504	0.5184				p.H83H		Atlas-SNP	.											.	TIMP3	31	.	0			c.T249C						PASS	.	C	,,,	3637,769	312.7+/-292.7	1499,639,65	159.0	130.0	140.0		249,,,	5.6	1.0	22	dbSNP_52	140	4332,4268	575.9+/-390.3	1095,2142,1063	no	coding-synonymous,intron,intron,intron	TIMP3,SYN3	NM_000362.4,NM_001135774.1,NM_003490.3,NM_133633.2	,,,	2594,2781,1128	CC,CT,TT		49.6279,17.4535,38.7283	,,,	83/212,,,	33253280	7969,5037	2203	4300	6503	SO:0001819	synonymous_variant	7078	exon3			CATCCATACGGAA		CCDS13911.1	22q12.3	2013-01-08	2008-07-31		ENSG00000100234	ENSG00000100234			11822	protein-coding gene	gene with protein product		188826	"""tissue inhibitor of metalloproteinase 3 (Sorsby fundus dystrophy, pseudoinflammatory)"""	SFD		8188246, 12652295	Standard	NM_000362		Approved		uc003anb.3	P35625	OTTHUMG00000030784	ENST00000266085.6:c.249T>C	22.37:g.33253280T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	183	181	0.989071	NM_000362	B2RBY9|Q5THV4|Q9UC74|Q9UGS2	Silent	SNP	ENST00000266085.6	37	CCDS13911.1																																																																																			T|0.372;C|0.628	0.628	strong		0.507	TIMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075672.2	NM_000362	
OR10G8	219869	hgsc.bcm.edu	37	11	123901175	123901175	+	Silent	SNP	C	C	A	rs11825515	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:123901175C>A	ENST00000431524.1	+	1	879	c.846C>A	c.(844-846)ctC>ctA	p.L282L		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L282L(1)		breast(1)|endometrium(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		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;0.0521)		CGCCCCTTCTCAACCCTGTTG	0.498													C|||	367	0.0732827	0.1286	0.0202	5008	,	,		19804	0.0734		0.0308	False		,,,				2504	0.0798				p.L282L		Atlas-SNP	.											OR10G8,middle_lobe,carcinoma,+1,2	OR10G8	132	2	1	Substitution - coding silent(1)	stomach(1)	c.C846A						PASS	.	C		536,3866	243.1+/-252.9	31,474,1696	121.0	116.0	118.0		846	-0.1	0.9	11	dbSNP_120	118	267,8331	102.3+/-163.5	4,259,4036	no	coding-synonymous	OR10G8	NM_001004464.1		35,733,5732	AA,AC,CC		3.1054,12.1763,6.1769		282/312	123901175	803,12197	2201	4299	6500	SO:0001819	synonymous_variant	219869	exon1			CCTTCTCAACCCT	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"""GPCR / Class A : Olfactory receptors"""	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.846C>A	11.37:g.123901175C>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	156	120	0.769231	NM_001004464	B2RNJ3|Q6IEV2	Silent	SNP	ENST00000431524.1	37	CCDS31704.1																																																																																			A|0.066;C|0.934;T|0.000	0.066	strong		0.498	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
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 GAIIx	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		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	62	33	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	
ZNF646	9726	hgsc.bcm.edu	37	16	31088347	31088347	+	Silent	SNP	G	G	A	rs749671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31088347G>A	ENST00000394979.2	+	1	1125	c.702G>A	c.(700-702)gaG>gaA	p.E234E	ZNF646_ENST00000300850.5_Silent_p.E234E|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000300849.4_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	234					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						CTCCTGCTGAGGAGGAGCGGC	0.597													G|||	1770	0.353435	0.0545	0.4035	5008	,	,		18624	0.8849		0.3817	False		,,,				2504	0.1452				p.E234E		Atlas-SNP	.											.	ZNF646	133	.	0			c.G702A						PASS	.	G		504,3890	230.1+/-244.4	33,438,1726	50.0	51.0	51.0		702	4.8	1.0	16	dbSNP_86	51	3413,5187	500.9+/-375.3	670,2073,1557	no	coding-synonymous	ZNF646	NM_014699.3		703,2511,3283	AA,AG,GG		39.686,11.4702,30.1447		234/1833	31088347	3917,9077	2197	4300	6497	SO:0001819	synonymous_variant	9726	exon2			TGCTGAGGAGGAG	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.702G>A	16.37:g.31088347G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	22	0.354839	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																				G|0.646;A|0.354	0.354	strong		0.597	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
TTLL1	25809	hgsc.bcm.edu	37	22	43459846	43459846	+	Silent	SNP	G	G	A	rs1052160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:43459846G>A	ENST00000266254.7	-	7	960	c.720C>T	c.(718-720)ctC>ctT	p.L240L	TTLL1_ENST00000331018.7_Silent_p.L240L	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	240	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		CGACGTTGGTGAGATGAACGA	0.512													G|||	744	0.148562	0.0779	0.2392	5008	,	,		20003	0.001		0.2803	False		,,,				2504	0.1963				p.L240L		Atlas-SNP	.											.	TTLL1	41	.	0			c.C720T						PASS	.	G		475,3931	223.3+/-239.8	30,415,1758	231.0	200.0	211.0		720	3.9	1.0	22	dbSNP_86	211	2560,6040	416.4+/-352.1	385,1790,2125	no	coding-synonymous	TTLL1	NM_012263.4		415,2205,3883	AA,AG,GG		29.7674,10.7808,23.3354		240/424	43459846	3035,9971	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon7			GTTGGTGAGATGA	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.720C>T	22.37:g.43459846G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	363	0.1662087912087912	46	0.09349593495934959	100	0.27624309392265195	3	0.005244755244755245	214	0.28232189973614774	G	10.34	1.322681	0.23994	0.107808	0.297674	ENSG00000100271	ENST00000495814	.	.	.	5.98	3.89	0.44902	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33471	-0.9867	3	.	.	.	.	4.3768	0.11274	0.2554:0.0:0.5867:0.158	rs1052160;rs3192570;rs17417663;rs1052160	.	.	.	L	166	.	.	S	-	2	0	TTLL1	41789790	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	1.410000	0.34691	0.845000	0.35118	0.591000	0.81541	TCA	G|0.794;A|0.206	0.206	strong		0.512	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	
OR13C2	392376	hgsc.bcm.edu	37	9	107367612	107367612	+	Silent	SNP	C	C	T	rs55706329	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107367612C>T	ENST00000542196.1	-	1	339	c.297G>A	c.(295-297)gtG>gtA	p.V99V		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	99						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(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GGAACATCTGCACTGCACAGC	0.517													C|||	1853	0.370008	0.4962	0.2089	5008	,	,		23529	0.5129		0.175	False		,,,				2504	0.3671				p.V99V		Atlas-SNP	.											.	OR13C2	46	.	0			c.G297A						PASS	.	C		2203,2203		462,1279,462	141.0	129.0	133.0		297	-7.1	0.0	9	dbSNP_129	133	1617,6983		132,1353,2815	no	coding-synonymous	OR13C2	NM_001004481.1		594,2632,3277	TT,TC,CC		18.8023,50.0,29.3711		99/319	107367612	3820,9186	2203	4300	6503	SO:0001819	synonymous_variant	392376	exon1			CATCTGCACTGCA		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.297G>A	9.37:g.107367612C>T		Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	356	150	0.421348	NM_001004481	B9EGV8|Q6IF54	Silent	SNP	ENST00000542196.1	37	CCDS35092.1																																																																																			C|0.652;T|0.348	0.348	strong		0.517	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
TEC	7006	hgsc.bcm.edu	37	4	48172266	48172266	+	Splice_Site	SNP	G	G	A	rs2271173	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:48172266G>A	ENST00000381501.3	-	5	610	c.453C>T	c.(451-453)agC>agT	p.S151S		NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	151					B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						AATACTTACTGCTCTCAAAAA	0.313													A|||	2608	0.520767	0.3381	0.4942	5008	,	,		18392	0.8929		0.3579	False		,,,				2504	0.5706				p.S151S		Atlas-SNP	.											.	TEC	81	.	0			c.C453T						PASS	.	A		1474,2926	667.6+/-401.9	247,980,973	64.0	72.0	70.0		453	1.8	1.0	4	dbSNP_100	70	2955,5629	660.9+/-401.8	531,1893,1868	yes	coding-synonymous-near-splice	TEC	NM_003215.2		778,2873,2841	AA,AG,GG		34.4245,33.5,34.1112		151/632	48172266	4429,8555	2200	4292	6492	SO:0001630	splice_region_variant	7006	exon5			CTTACTGCTCTCA	D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.454+1C>T	4.37:g.48172266G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	173	73	0.421965	NM_003215	B7ZKZ6|Q3MIS5	Silent	SNP	ENST00000381501.3	37	CCDS3481.1																																																																																			G|0.583;A|0.417	0.417	strong		0.313	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3		Silent
FAM161A	84140	hgsc.bcm.edu	37	2	62069358	62069358	+	Missense_Mutation	SNP	T	T	C	rs11125895	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:62069358T>C	ENST00000405894.3	-	2	422	c.321A>G	c.(319-321)atA>atG	p.I107M	FAM161A_ENST00000404929.1_Missense_Mutation_p.I107M	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	107			I -> M (in dbSNP:rs11125895). {ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						CCATAGTTTCTATGTGGGCAG	0.388													T|||	802	0.160144	0.1104	0.1787	5008	,	,		19735	0.1508		0.173	False		,,,				2504	0.2106				p.I107M		Atlas-SNP	.											.	FAM161A	200	.	0			c.A321G						PASS	.	T	MET/ILE,MET/ILE	466,3200		23,420,1390	93.0	85.0	88.0		321,321	1.7	0.3	2	dbSNP_120	88	1522,6640		153,1216,2712	yes	missense,missense	FAM161A	NM_001201543.1,NM_032180.2	10,10	176,1636,4102	CC,CT,TT		18.6474,12.7114,16.8076	benign,benign	107/717,107/661	62069358	1988,9840	1833	4081	5914	SO:0001583	missense	84140	exon2			AGTTTCTATGTGG		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.321A>G	2.37:g.62069358T>C	ENSP00000385893:p.Ile107Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	332	0.152014652014652	44	0.08943089430894309	78	0.2154696132596685	85	0.1486013986013986	125	0.16490765171503957	T	10.85	1.468017	0.26335	0.127114	0.186474	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.66099	-0.19;-0.19	5.95	1.73	0.24493	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.53688	P	2.199999999996649E-5	B;B	0.16396	0.008;0.017	B;B	0.10450	0.002;0.005	T	0.10268	-1.0637	8	0.30854	T	0.27	-6.3985	7.8459	0.29424	0.0:0.5917:0.0:0.4083	rs11125895;rs17573015;rs52802415;rs59431884;rs11125895	107;107	Q3B820;Q3B820-3	F161A_HUMAN;.	M	107	ENSP00000385158:I107M;ENSP00000385893:I107M	ENSP00000385158:I107M	I	-	3	3	FAM161A	61922862	0.996000	0.38824	0.261000	0.24466	0.960000	0.62799	1.338000	0.33873	0.020000	0.15106	0.533000	0.62120	ATA	T|0.833;C|0.167	0.167	strong		0.388	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
DLEC1	9940	hgsc.bcm.edu	37	3	38080952	38080952	+	Missense_Mutation	SNP	T	T	G	rs7625806	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:38080952T>G	ENST00000308059.6	+	1	257	c.236T>G	c.(235-237)cTg>cGg	p.L79R	DLEC1_ENST00000346219.3_Missense_Mutation_p.L79R|DLEC1_ENST00000452631.2_Missense_Mutation_p.L79R					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		GAGCCTCAGCTGCTTCGTCTG	0.652													G|||	2258	0.450879	0.5658	0.4092	5008	,	,		18071	0.6062		0.3429	False		,,,				2504	0.2761				p.L79R		Atlas-SNP	.											DLEC1_ENST00000346219,NS,carcinoma,0,2	DLEC1	278	2	0			c.T236G						PASS	.	G	ARG/LEU,ARG/LEU	2107,1909		567,973,468	35.0	40.0	39.0		236,236	0.3	0.0	3	dbSNP_116	39	2839,5501		509,1821,1840	yes	missense,missense	DLEC1	NM_007335.2,NM_007337.2	102,102	1076,2794,2308	GG,GT,TT		34.0408,47.5349,40.0291	probably-damaging,probably-damaging	79/1756,79/1779	38080952	4946,7410	2008	4170	6178	SO:0001583	missense	9940	exon1			CTCAGCTGCTTCG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.236T>G	3.37:g.38080952T>G	ENSP00000308597:p.Leu79Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	38	15	0.394737	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	988	0.4523809523809524	267	0.5426829268292683	142	0.39226519337016574	328	0.5734265734265734	251	0.3311345646437995	G	10.55	1.381461	0.24944	0.524651	0.340408	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.06528	3.32;3.29;3.54	5.47	0.309	0.15820	.	0.942952	0.08797	N	0.892317	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B;B	0.12630	0.006;0.006;0.006	B;B;B	0.17098	0.017;0.017;0.017	T	0.34725	-0.9817	9	0.30078	T	0.28	0.0241	2.3534	0.04290	0.1262:0.1483:0.132:0.5935	rs7625806;rs60689091;rs7625806	79;79;79	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	R	79	ENSP00000308597:L79R;ENSP00000315914:L79R;ENSP00000410427:L79R	ENSP00000308597:L79R	L	+	2	0	DLEC1	38055956	0.383000	0.25156	0.028000	0.17463	0.050000	0.14768	0.147000	0.16202	-0.457000	0.07033	-1.717000	0.00709	CTG	T|0.555;G|0.445	0.445	strong		0.652	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
MDN1	23195	hgsc.bcm.edu	37	6	90418331	90418331	+	Silent	SNP	A	A	G	rs55729223	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90418331A>G	ENST00000369393.3	-	51	7897	c.7782T>C	c.(7780-7782)ccT>ccC	p.P2594P	MDN1_ENST00000428876.1_Silent_p.P2594P			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2594					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GGGGATCCAGAGGGATCACAA	0.403													A|||	579	0.115615	0.1021	0.0793	5008	,	,		19905	0.0079		0.1879	False		,,,				2504	0.1963				p.P2594P		Atlas-SNP	.											.	MDN1	478	.	0			c.T7782C						PASS	.	A		405,4001	195.3+/-220.0	16,373,1814	159.0	166.0	164.0		7782	-0.2	0.0	6	dbSNP_129	164	1575,7025	290.1+/-299.6	142,1291,2867	no	coding-synonymous	MDN1	NM_014611.1		158,1664,4681	GG,GA,AA		18.314,9.192,15.2237		2594/5597	90418331	1980,11026	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon51			ATCCAGAGGGATC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.7782T>C	6.37:g.90418331A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			A|0.858;G|0.142	0.142	strong		0.403	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
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 GAIIx	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	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	17	5	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	
OR51B6	390058	hgsc.bcm.edu	37	11	5372881	5372881	+	Silent	SNP	G	G	A	rs77135024	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5372881G>A	ENST00000380219.1	+	1	144	c.144G>A	c.(142-144)agG>agA	p.R48R	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	48					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)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCTCATCAGGAATGATCATA	0.473													G|||	529	0.105631	0.0303	0.1614	5008	,	,		22613	0.0754		0.1541	False		,,,				2504	0.1493				p.R48R		Atlas-SNP	.											OR51B6,NS,carcinoma,+1,1	OR51B6	53	1	0			c.G144A						PASS	.	G		241,4161	141.1+/-176.5	4,233,1964	167.0	135.0	146.0		144	1.6	0.9	11	dbSNP_131	146	1309,7285	259.1+/-282.5	119,1071,3107	no	coding-synonymous	OR51B6	NM_001004750.1		123,1304,5071	AA,AG,GG		15.2316,5.4748,11.9267		48/313	5372881	1550,11446	2201	4297	6498	SO:0001819	synonymous_variant	390058	exon1			CATCAGGAATGAT		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.144G>A	11.37:g.5372881G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	175	68	0.388571	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			G|0.877;A|0.123	0.123	strong		0.473	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
TTYH2	94015	hgsc.bcm.edu	37	17	72240168	72240168	+	Missense_Mutation	SNP	G	G	A	rs35682745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72240168G>A	ENST00000269346.4	+	6	858	c.784G>A	c.(784-786)Gct>Act	p.A262T	TTYH2_ENST00000529107.1_Missense_Mutation_p.A241T|TTYH2_ENST00000534346.1_3'UTR	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	262			A -> T (in dbSNP:rs35682745). {ECO:0000269|PubMed:15489334}.			chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						ATCCCTGGCCGCTGATGGCTC	0.652													G|||	545	0.108826	0.0847	0.1556	5008	,	,		13730	0.0486		0.1511	False		,,,				2504	0.1268				p.A262T		Atlas-SNP	.											TTYH2,colon,carcinoma,-1,1	TTYH2	63	1	0			c.G784A						PASS	.	G	THR/ALA	513,3893	232.0+/-245.7	34,445,1724	69.0	64.0	66.0		784	3.2	0.0	17	dbSNP_126	66	1327,7273	260.6+/-283.4	108,1111,3081	yes	missense	TTYH2	NM_032646.5	58	142,1556,4805	AA,AG,GG		15.4302,11.6432,14.1473	benign	262/535	72240168	1840,11166	2203	4300	6503	SO:0001583	missense	94015	exon6			CTGGCCGCTGATG		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.784G>A	17.37:g.72240168G>A	ENSP00000269346:p.Ala262Thr	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	32	10	0.3125	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	230	0.10531135531135531	39	0.07926829268292683	50	0.13812154696132597	25	0.043706293706293704	116	0.15303430079155672	G	15.05	2.716813	0.48622	0.116432	0.154302	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.12255	2.7;2.7	5.21	3.16	0.36331	.	0.292448	0.37261	N	0.002167	T	0.00109	0.0003	M	0.78223	2.4	0.20489	P	0.999897314	B;B	0.17667	0.023;0.009	B;B	0.15484	0.01;0.013	T	0.04153	-1.0973	9	0.46703	T	0.11	-4.1565	8.8593	0.35247	0.1856:0.0:0.8144:0.0	rs35682745;rs62065674	241;262	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	T	262;241	ENSP00000269346:A262T;ENSP00000433089:A241T	ENSP00000269346:A262T	A	+	1	0	TTYH2	69751763	0.860000	0.29831	0.028000	0.17463	0.195000	0.23768	4.109000	0.57824	0.536000	0.28733	-0.493000	0.04662	GCT	G|0.877;A|0.123	0.123	strong		0.652	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
ERCC5	2073	hgsc.bcm.edu	37	13	103514870	103514870	+	Silent	SNP	C	C	T	rs149867583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103514870C>T	ENST00000355739.4	+	8	2794	c.1371C>T	c.(1369-1371)caC>caT	p.H457H	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.R883C|ERCC5_ENST00000375954.1_5'Flank	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	457					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CAGAGGAGCACGTAGCCAGCA	0.478			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.H911H		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	ERCC5,NS,carcinoma,+2,1	.	.	1	0			c.C2733T						scavenged	.						76.0	69.0	72.0					13																	103514870		2203	4300	6503	SO:0001819	synonymous_variant	0	exon16	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGAGCACGTAGCC	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.1371C>T	13.37:g.103514870C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	96	2	0.0208333	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			C|1.000;T|0.000	0.000	strong		0.478	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
KRT36	8689	hgsc.bcm.edu	37	17	39643340	39643340	+	Missense_Mutation	SNP	T	T	G	rs11657323	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39643340T>G	ENST00000328119.6	-	6	1069	c.1070A>C	c.(1069-1071)aAc>aCc	p.N357T	KRT36_ENST00000393986.2_Missense_Mutation_p.N307T	NM_003771.4	NP_003762.1	O76013	KRT36_HUMAN	keratin 36	357	Coil 2.|Rod.		N -> T (in dbSNP:rs11657323).		regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of epidermis (GO:0030280)			breast(2)|cervix(1)|kidney(2)|large_intestine(3)|lung(8)|skin(1)	17		Breast(137;0.000286)				GGCCTCCACGTTGCTGATCAG	0.622													T|||	712	0.142173	0.1755	0.1239	5008	,	,		20036	0.004		0.2316	False		,,,				2504	0.1605				p.N357T		Atlas-SNP	.											.	KRT36	52	.	0			c.A1070C						PASS	.	T	THR/ASN	747,3659	305.5+/-289.0	53,641,1509	89.0	89.0	89.0		1070	3.8	0.0	17	dbSNP_120	89	1861,6739	331.1+/-319.5	212,1437,2651	no	missense	KRT36	NM_003771.4	65	265,2078,4160	GG,GT,TT		21.6395,16.9542,20.0523	benign	357/468	39643340	2608,10398	2203	4300	6503	SO:0001583	missense	8689	exon6			TCCACGTTGCTGA	Y16792	CCDS11395.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000126337	ENSG00000126337		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6454	protein-coding gene	gene with protein product		604540	"""keratin, hair, acidic, 6"""	KRTHA6		9756910, 16831889	Standard	XM_005257762		Approved		uc002hwt.3	O76013	OTTHUMG00000133431	ENST00000328119.6:c.1070A>C	17.37:g.39643340T>G	ENSP00000329165:p.Asn357Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_003771	Q86XG4	Missense_Mutation	SNP	ENST00000328119.6	37	CCDS11395.1	330	0.1510989010989011	92	0.18699186991869918	52	0.143646408839779	1	0.0017482517482517483	185	0.24406332453825857	T	14.29	2.491425	0.44249	0.169542	0.216395	ENSG00000126337	ENST00000393986;ENST00000328119	D;D	0.88818	-2.43;-2.43	6.07	3.84	0.44239	Filament (1);	0.000000	0.53938	D	0.000047	T	0.00178	0.0005	M	0.65975	2.015	0.80722	P	0.0	B	0.30584	0.286	B	0.42692	0.395	T	0.33777	-0.9855	9	0.66056	D	0.02	.	5.6032	0.17365	0.0:0.2203:0.1759:0.6038	rs11657323;rs11657323	357	O76013	KRT36_HUMAN	T	307;357	ENSP00000377555:N307T;ENSP00000329165:N357T	ENSP00000329165:N357T	N	-	2	0	KRT36	36896866	0.000000	0.05858	0.023000	0.16930	0.956000	0.61745	-0.770000	0.04705	0.520000	0.28426	0.533000	0.62120	AAC	T|0.822;G|0.178	0.178	strong		0.622	KRT36-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259508.1	NM_003771	
SLC9C1	285335	hgsc.bcm.edu	37	3	111962851	111962851	+	Missense_Mutation	SNP	T	T	C	rs6768523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111962851T>C	ENST00000305815.5	-	11	1522	c.1270A>G	c.(1270-1272)Act>Gct	p.T424A	SLC9C1_ENST00000487372.1_Missense_Mutation_p.T376A	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	424			T -> A (in dbSNP:rs6768523). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CCTAGTATAGTAACTGCCACT	0.313													T|||	1627	0.32488	0.3427	0.3963	5008	,	,		17034	0.3304		0.2376	False		,,,				2504	0.3344				p.T424A		Atlas-SNP	.											.	.	.	.	0			c.A1270G						PASS	.	T	ALA/THR	1465,2941	465.1+/-354.1	249,967,987	69.0	74.0	72.0		1270	4.0	0.9	3	dbSNP_116	72	2328,6272	387.2+/-342.1	320,1688,2292	yes	missense	SLC9A10	NM_183061.1	58	569,2655,3279	CC,CT,TT		27.0698,33.2501,29.1635	benign	424/1178	111962851	3793,9213	2203	4300	6503	SO:0001583	missense	285335	exon11			GTATAGTAACTGC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.1270A>G	3.37:g.111962851T>C	ENSP00000306627:p.Thr424Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	112	44	0.392857	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	669	0.30631868131868134	167	0.3394308943089431	134	0.3701657458563536	183	0.31993006993006995	185	0.24406332453825857	T	2.635	-0.285462	0.05605	0.332501	0.270698	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.76709	-1.04;-1.04	5.11	3.96	0.45880	.	1.027890	0.07726	N	0.944446	T	0.00012	0.0000	L	0.40543	1.245	0.38456	P	0.052908999999999984	B;P	0.34462	0.202;0.454	B;B	0.38755	0.281;0.192	T	0.09250	-1.0683	9	0.30078	T	0.28	-7.0031	7.6407	0.28292	0.0:0.0978:0.0:0.9022	rs6768523;rs52800559;rs56653457;rs6768523	376;424	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	A	424;376	ENSP00000306627:T424A;ENSP00000420688:T376A	ENSP00000306627:T424A	T	-	1	0	SLC9A10	113445541	0.185000	0.23213	0.936000	0.37596	0.290000	0.27261	0.071000	0.14594	0.896000	0.36366	0.352000	0.21897	ACT	T|0.708;C|0.292	0.292	strong		0.313	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
ODF4	146852	hgsc.bcm.edu	37	17	8243469	8243469	+	Missense_Mutation	SNP	T	T	C	rs12943505	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:8243469T>C	ENST00000328248.2	+	1	288	c.100T>C	c.(100-102)Tgg>Cgg	p.W34R	ODF4_ENST00000584943.1_Missense_Mutation_p.W34R|RP11-849F2.4_ENST00000585275.1_lincRNA	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	34			W -> R (in dbSNP:rs12943505). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)				endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						GGAGGCAGGATGGGGCACAGG	0.572													T|||	897	0.179113	0.0151	0.3963	5008	,	,		18988	0.0675		0.3469	False		,,,				2504	0.1892				p.W34R		Atlas-SNP	.											.	ODF4	23	.	0			c.T100C						PASS	.	T	ARG/TRP	261,4145	148.4+/-182.8	6,249,1948	85.0	80.0	82.0		100	-2.7	0.0	17	dbSNP_121	82	2589,6011	418.0+/-352.6	410,1769,2121	yes	missense	ODF4	NM_153007.4	101	416,2018,4069	CC,CT,TT		30.1047,5.9237,21.913	benign	34/258	8243469	2850,10156	2203	4300	6503	SO:0001583	missense	146852	exon1			GCAGGATGGGGCA	AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"""cancer/testis antigen 136"""	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.100T>C	17.37:g.8243469T>C	ENSP00000331086:p.Trp34Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	70	27	0.385714	NM_153007	Q8J021	Missense_Mutation	SNP	ENST00000328248.2	37	CCDS11140.1	455	0.20833333333333334	10	0.02032520325203252	136	0.3756906077348066	46	0.08041958041958042	263	0.3469656992084433	T	4.163	0.028769	0.08054	0.059237	0.301047	ENSG00000184650	ENST00000328248	T	0.27557	1.66	3.68	-2.74	0.05932	.	2.012190	0.02669	N	0.108369	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.14438	0.01	B	0.17098	0.017	T	0.36187	-0.9758	9	0.07175	T	0.84	3.2504	5.4871	0.16755	0.0:0.4853:0.1835:0.3312	rs12943505;rs12943505	34	Q2M2E3	ODFP4_HUMAN	R	34	ENSP00000331086:W34R	ENSP00000331086:W34R	W	+	1	0	ODF4	8184194	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.952000	0.01528	-0.593000	0.05844	0.533000	0.62120	TGG	T|0.790;C|0.210	0.210	strong		0.572	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1		
XIRP2	129446	hgsc.bcm.edu	37	2	168103701	168103701	+	Silent	SNP	A	A	G	rs16853313	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:168103701A>G	ENST00000409195.1	+	9	5888	c.5799A>G	c.(5797-5799)caA>caG	p.Q1933Q	XIRP2_ENST00000409273.1_Silent_p.Q1711Q|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000295237.9_Silent_p.Q1933Q|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1758					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAGAAGCACAAAGAAGTTTCA	0.373													A|||	409	0.0816693	0.0787	0.0735	5008	,	,		19987	0.119		0.0408	False		,,,				2504	0.0951				p.Q1933Q		Atlas-SNP	.											.	XIRP2	914	.	0			c.A5799G						PASS	.	A	,,,,	273,3399		10,253,1573	49.0	46.0	47.0		,,5133,,5799	-2.6	0.0	2	dbSNP_123	47	350,7840		6,338,3751	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	16,591,5324	GG,GA,AA		4.2735,7.4346,5.2521	,,,,	,,1711/3328,,1933/3550	168103701	623,11239	1836	4095	5931	SO:0001819	synonymous_variant	129446	exon9			AGCACAAAGAAGT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5799A>G	2.37:g.168103701A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			A|0.928;G|0.072	0.072	strong		0.373	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
TTC23	64927	hgsc.bcm.edu	37	15	99715352	99715352	+	Silent	SNP	A	A	G	rs2602016	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:99715352A>G	ENST00000394132.2	-	10	1585	c.768T>C	c.(766-768)ctT>ctC	p.L256L	TTC23_ENST00000558613.1_Silent_p.L256L|TTC23_ENST00000262074.4_Silent_p.L256L|TTC23_ENST00000394135.3_Silent_p.L256L|TTC23_ENST00000394129.2_Silent_p.L256L|TTC23_ENST00000394130.1_Silent_p.L256L|TTC23_ENST00000394136.1_Silent_p.L256L|TTC23_ENST00000558663.1_Silent_p.L256L			Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	256										endometrium(2)|large_intestine(3)|lung(9)|urinary_tract(2)	16	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)			TCAGGATGATAAGATGTGCCT	0.512													G|||	4286	0.855831	0.9569	0.7795	5008	,	,		20885	0.9415		0.7913	False		,,,				2504	0.7515				p.L256L		Atlas-SNP	.											.	TTC23	33	.	0			c.T768C						PASS	.	G	,,,,,,	4079,315	168.7+/-199.5	1896,287,14	81.0	66.0	71.0		768,768,768,768,768,768,768	3.2	0.1	15	dbSNP_100	71	6515,2079	359.6+/-331.6	2475,1565,257	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTC23	NM_001040655.1,NM_001040656.1,NM_001040657.1,NM_001040658.1,NM_001040659.1,NM_001040660.1,NM_022905.4	,,,,,,	4371,1852,271	GG,GA,AA		24.1913,7.1689,18.4324	,,,,,,	256/448,256/448,256/448,256/448,256/448,256/448,256/448	99715352	10594,2394	2197	4297	6494	SO:0001819	synonymous_variant	64927	exon8			GATGATAAGATGT		CCDS10379.2	15q26.3	2013-01-11			ENSG00000103852	ENSG00000103852		"""Tetratricopeptide (TTC) repeat domain containing"""	25730	protein-coding gene	gene with protein product						12477932	Standard	NM_001288615		Approved	FLJ12572, HCC-8	uc002bux.3	Q5W5X9	OTTHUMG00000147344	ENST00000394132.2:c.768T>C	15.37:g.99715352A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_001040657	A8K6M5|Q53HK0|Q96BC9|Q9H8W9|Q9H9S7	Silent	SNP	ENST00000394132.2	37	CCDS10379.2																																																																																			A|0.168;G|0.832	0.832	strong		0.512	TTC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303953.2	NM_022905	
LRIT3	345193	hgsc.bcm.edu	37	4	110772711	110772711	+	Silent	SNP	C	C	T	rs17040904	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:110772711C>T	ENST00000594814.1	+	2	168	c.168C>T	c.(166-168)ccC>ccT	p.P56P	LRIT3_ENST00000379920.3_Silent_p.P11P|LRIT3_ENST00000327908.3_5'UTR	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	56					regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		CGAACCTCCCCGTGGACACTG	0.493													C|||	111	0.0221645	0.0008	0.049	5008	,	,		18825	0.0		0.0437	False		,,,				2504	0.0327				p.P56P		Atlas-SNP	.											.	LRIT3	107	.	0			c.C168T						PASS	.	C		9,1375		0,9,683	79.0	73.0	75.0		33	-10.6	0.0	4	dbSNP_123	75	158,3024		1,156,1434	no	coding-synonymous	LRIT3	NM_198506.2		1,165,2117	TT,TC,CC		4.9654,0.6503,3.6575		11/635	110772711	167,4399	692	1591	2283	SO:0001819	synonymous_variant	345193	exon2			CCTCCCCGTGGAC	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.168C>T	4.37:g.110772711C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	37	CCDS3688.3																																																																																			C|0.972;T|0.028	0.028	strong		0.493	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
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 GAIIx	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_ENST00000396175.1_Missense_Mutation_p.P545S|TRAK1_ENST00000487159.1_3'UTR|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	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	24	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	
EP400	57634	hgsc.bcm.edu	37	12	132547090	132547090	+	Silent	SNP	A	A	G	rs7974276	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132547090A>G	ENST00000333577.4	+	48	8395	c.8286A>G	c.(8284-8286)caA>caG	p.Q2762Q	EP400_ENST00000389561.2_Silent_p.Q2726Q|EP400_ENST00000330386.6_Silent_p.Q2645Q|EP400_ENST00000389562.2_Silent_p.Q2725Q|EP400_ENST00000332482.4_Silent_p.Q2689Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2762	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				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)		agcagcagcaacaacagcagc	0.557													G|||	1450	0.289537	0.6316	0.1671	5008	,	,		15386	0.1865		0.1322	False		,,,				2504	0.182				p.Q2726Q		Atlas-SNP	.											EP400,colon,carcinoma,0,3	EP400	370	3	0			c.A8178G						scavenged	.						26.0	30.0	29.0					12																	132547090		2181	4250	6431	SO:0001819	synonymous_variant	57634	exon47			GCAGCAACAACAG	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.8286A>G	12.37:g.132547090A>G		Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	85	32	0.376471	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				A|0.794;G|0.206	0.206	strong		0.557	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
CYP4A22	284541	hgsc.bcm.edu	37	1	47607785	47607785	+	Missense_Mutation	SNP	G	G	A	rs2056900	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47607785G>A	ENST00000371891.3	+	4	419	c.388G>A	c.(388-390)Ggc>Agc	p.G130S	CYP4A22_ENST00000294337.3_Missense_Mutation_p.G130S|CYP4A22_ENST00000371890.3_Missense_Mutation_p.G130S|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000485117.1_3'UTR	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	130			G -> S (in allele CYP4A22*4, allele CYP4A22*10, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs2056900). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTTAGGGTACGGCTTGCTCCT	0.537													G|||	1684	0.336262	0.2073	0.232	5008	,	,		22904	0.5546		0.1928	False		,,,				2504	0.5072				p.G130S	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.G388A						PASS	.	G	SER/GLY	1005,3401	374.2+/-321.1	104,797,1302	100.0	83.0	89.0		388	0.7	0.1	1	dbSNP_94	89	1733,6867	316.6+/-312.8	183,1367,2750	yes	missense	CYP4A22	NM_001010969.2	56	287,2164,4052	AA,AG,GG		20.1512,22.8098,21.0518	probably-damaging	130/520	47607785	2738,10268	2203	4300	6503	SO:0001583	missense	284541	exon4			GGGTACGGCTTGC		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.388G>A	1.37:g.47607785G>A	ENSP00000360958:p.Gly130Ser	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	640	0.29304029304029305	98	0.1991869918699187	86	0.23756906077348067	315	0.5506993006993007	141	0.18601583113456466	g	18.98	3.738385	0.69304	0.228098	0.201512	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.72394	-0.65;-0.65;-0.65	1.7	0.679	0.17975	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.87328	2.875	0.22811	P	0.99870156	P;D	0.69078	0.935;0.997	B;P	0.61722	0.38;0.893	T	0.45716	-0.9242	9	0.72032	D	0.01	.	8.2754	0.31868	0.1313:0.0:0.8687:0.0	rs2056900;rs52794745;rs2056900	130;130	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	S	130	ENSP00000360957:G130S;ENSP00000360958:G130S;ENSP00000294337:G130S	ENSP00000294337:G130S	G	+	1	0	CYP4A22	47380372	1.000000	0.71417	0.118000	0.21660	0.682000	0.39822	3.218000	0.51192	0.034000	0.15491	0.195000	0.17529	GGC	G|0.768;A|0.232	0.232	strong		0.537	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
SLC6A5	9152	hgsc.bcm.edu	37	11	20648380	20648380	+	Missense_Mutation	SNP	G	G	A	rs1805091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:20648380G>A	ENST00000525748.1	+	8	1660	c.1387G>A	c.(1387-1389)Gat>Aat	p.D463N		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	463			D -> N (in dbSNP:rs1805091). {ECO:0000269|PubMed:10606742}.		glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	GAAACTCACGGATGCCACGGT	0.552													G|||	815	0.16274	0.1165	0.1787	5008	,	,		16566	0.0883		0.2505	False		,,,				2504	0.2004				p.D463N		Atlas-SNP	.											SLC6A5,caecum,carcinoma,0,1	SLC6A5	151	1	0			c.G1387A						PASS	.	G	ASN/ASP	551,3855	247.5+/-255.7	35,481,1687	108.0	102.0	104.0		1387	6.0	1.0	11	dbSNP_89	104	2470,6130	406.1+/-348.7	352,1766,2182	yes	missense	SLC6A5	NM_004211.3	23	387,2247,3869	AA,AG,GG		28.7209,12.5057,23.2277	possibly-damaging	463/798	20648380	3021,9985	2203	4300	6503	SO:0001583	missense	9152	exon8			CTCACGGATGCCA	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1387G>A	11.37:g.20648380G>A	ENSP00000434364:p.Asp463Asn	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	395	0.18086080586080586	82	0.16666666666666666	75	0.20718232044198895	52	0.09090909090909091	186	0.24538258575197888	G	21.1	4.096148	0.76870	0.125057	0.287209	ENSG00000165970	ENST00000525748	T	0.74526	-0.85	6.04	6.04	0.98038	.	0.087926	0.85682	D	0.000000	T	0.00012	0.0000	L	0.35288	1.05	0.09310	P	0.9999999999330931	B	0.23937	0.094	B	0.32393	0.145	T	0.01743	-1.1283	9	0.38643	T	0.18	.	20.1743	0.98175	0.0:0.0:1.0:0.0	rs1805091;rs3740871;rs45629968;rs52834191;rs59290674;rs1805091	463	Q9Y345	SC6A5_HUMAN	N	463	ENSP00000434364:D463N	ENSP00000434364:D463N	D	+	1	0	SLC6A5	20604956	1.000000	0.71417	0.993000	0.49108	0.966000	0.64601	9.869000	0.99810	2.873000	0.98535	0.561000	0.74099	GAT	G|0.790;A|0.210	0.210	strong		0.552	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
VPS13C	54832	hgsc.bcm.edu	37	15	62172907	62172907	+	Silent	SNP	T	T	C	rs12901055	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62172907T>C	ENST00000261517.5	-	73	9976	c.9903A>G	c.(9901-9903)caA>caG	p.Q3301Q	VPS13C_ENST00000558919.1_5'UTR|VPS13C_ENST00000395896.4_Silent_p.Q3301Q|VPS13C_ENST00000395898.3_Silent_p.Q3258Q|VPS13C_ENST00000249837.3_Silent_p.Q3258Q	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.Q3301Q(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CAATATCTTGTTGGATTAACT	0.269													T|||	236	0.0471246	0.0182	0.0418	5008	,	,		13894	0.0397		0.0755	False		,,,				2504	0.0685				p.Q3301Q		Atlas-SNP	.											VPS13C_ENST00000395896,NS,carcinoma,-2,3	VPS13C	506	3	1	Substitution - coding silent(1)	stomach(1)	c.A9903G						PASS	.	T	,,,	117,4275	82.9+/-121.4	1,115,2080	42.0	42.0	42.0		9903,9774,9774,9903	-3.3	0.9	15	dbSNP_121	42	681,7893	162.5+/-215.2	31,619,3637	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	,,,	32,734,5717	CC,CT,TT		7.9426,2.6639,6.1546	,,,	3301/3629,3258/3711,3258/3586,3301/3754	62172907	798,12168	2196	4287	6483	SO:0001819	synonymous_variant	54832	exon73			ATCTTGTTGGATT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.9903A>G	15.37:g.62172907T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_020821		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																			T|0.946;C|0.054	0.054	strong		0.269	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
VARS2	57176	hgsc.bcm.edu	37	6	30893941	30893941	+	Missense_Mutation	SNP	G	G	A	rs4678	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30893941G>A	ENST00000321897.5	+	29	3778	c.3146G>A	c.(3145-3147)cGg>cAg	p.R1049Q	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000542001.1_Missense_Mutation_p.R909Q|VARS2_ENST00000541562.1_Missense_Mutation_p.R1079Q|VARS2_ENST00000416670.2_Missense_Mutation_p.R1049Q			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	1049			R -> Q (in dbSNP:rs4678). {ECO:0000269|PubMed:11572484, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TCTCACCTCCGGCAGCTGATG	0.557													G|||	453	0.0904553	0.0968	0.0663	5008	,	,		19166	0.0258		0.1551	False		,,,				2504	0.0992				p.R1079Q		Atlas-SNP	.											.	VARS2	60	.	0			c.G3236A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	367,2653		15,337,1158	53.0	57.0	56.0		2726,3236,3146	-8.5	0.1	6	dbSNP_52	56	1047,4367		94,859,1754	yes	missense,missense,missense	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	43,43,43	109,1196,2912	AA,AG,GG		19.3388,12.1523,16.7655	benign,benign,benign	909/924,1079/1094,1049/1064	30893941	1414,7020	1510	2707	4217	SO:0001583	missense	57176	exon30			ACCTCCGGCAGCT	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.3146G>A	6.37:g.30893941G>A	ENSP00000316092:p.Arg1049Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	170	135	0.794118	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	246	0.11263736263736264	71	0.1443089430894309	27	0.07458563535911603	20	0.03496503496503497	128	0.16886543535620052	G	4.681	0.126566	0.08931	0.121523	0.193388	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.8	-8.54	0.00912	.	1.356270	0.04712	N	0.417762	T	0.02929	0.0087	N	0.11845	0.185	0.80722	P	0.0	B;B;B;B	0.22983	0.078;0.0;0.0;0.0	B;B;B;B	0.16722	0.016;0.0;0.001;0.0	T	0.14699	-1.0463	9	0.02654	T	1	-4.8705	8.5559	0.33480	0.3693:0.0:0.5217:0.109	rs4678;rs1043490;rs3173376;rs6929532;rs16898111;rs17189642;rs52796175;rs56648004;rs60218550;rs4678	487;1047;1079;1049	Q5ST30-2;B7ZL25;F5GXJ0;Q5ST30	.;.;.;SYVM_HUMAN	Q	1049;1049;909;1079	ENSP00000316092:R1049Q;ENSP00000394802:R1049Q;ENSP00000438200:R909Q;ENSP00000441000:R1079Q	ENSP00000316092:R1049Q	R	+	2	0	VARS2	31001920	0.057000	0.20700	0.058000	0.19502	0.721000	0.41392	-1.020000	0.03618	-1.624000	0.01556	-0.150000	0.13652	CGG	G|0.856;A|0.144	0.144	strong		0.557	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
SF3B6	51639	hgsc.bcm.edu	37	2	24290671	24290671	+	Silent	SNP	G	G	A	rs61742149	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:24290671G>A	ENST00000233468.4	-	4	552	c.339C>T	c.(337-339)ctC>ctT	p.L113L		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)					ATTTCTCCTTGAGAAGCTTCA	0.373													G|||	172	0.034345	0.0038	0.062	5008	,	,		18007	0.001		0.0895	False		,,,				2504	0.0337				p.L113L		Atlas-SNP	.											.	SF3B14	6	.	0			c.C339T						PASS	.	G		88,4316	72.5+/-110.5	1,86,2115	263.0	255.0	257.0		339	3.4	1.0	2	dbSNP_129	257	928,7672	204.8+/-247.4	52,824,3424	no	coding-synonymous	SF3B14	NM_016047.3		53,910,5539	AA,AG,GG		10.7907,1.9982,7.813		113/126	24290671	1016,11988	2202	4300	6502	SO:0001819	synonymous_variant	0	exon4			CTCCTTGAGAAGC																												ENST00000233468.4:c.339C>T	2.37:g.24290671G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	155	66	0.425806	NM_016047		Silent	SNP	ENST00000233468.4	37	CCDS1707.1																																																																																			G|0.930;A|0.070	0.070	strong		0.373	SF3B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246826.1		
PCK1	5105	hgsc.bcm.edu	37	20	56137807	56137807	+	Silent	SNP	A	A	G	rs1042523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:56137807A>G	ENST00000319441.4	+	4	626	c.462A>G	c.(460-462)tcA>tcG	p.S154S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Silent_p.S22S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	154					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			CGCCTCTGTCAAAGATCGGCA	0.622													G|||	1569	0.313299	0.3222	0.3357	5008	,	,		17654	0.0308		0.5229	False		,,,				2504	0.3609				p.S154S		Atlas-SNP	.											.	PCK1	95	.	0			c.A462G						PASS	.	G		1506,2900	673.0+/-402.7	230,1046,927	67.0	55.0	59.0		462	-6.0	0.5	20	dbSNP_86	59	4342,4258	573.2+/-389.8	1084,2174,1042	no	coding-synonymous	PCK1	NM_002591.3		1314,3220,1969	GG,GA,AA		49.5116,34.1807,44.9639		154/623	56137807	5848,7158	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon4			TCTGTCAAAGATC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.462A>G	20.37:g.56137807A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			A|0.601;G|0.399	0.399	strong		0.622	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
EPHA2	1969	hgsc.bcm.edu	37	1	16464673	16464673	+	Silent	SNP	G	G	A	rs2230597	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:16464673G>A	ENST00000358432.5	-	5	1141	c.987C>T	c.(985-987)ccC>ccT	p.P329P		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	329	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		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;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	GTGGGGCGGAGGGGGGTCCTG	0.662													G|||	1750	0.349441	0.3396	0.4294	5008	,	,		18391	0.1458		0.4215	False		,,,				2504	0.4417				p.P329P		Atlas-SNP	.											.	EPHA2	102	.	0			c.C987T						PASS	.	G		1588,2816		299,990,913	21.0	21.0	21.0		987	1.9	1.0	1	dbSNP_98	21	3467,5131		711,2045,1543	no	coding-synonymous	EPHA2	NM_004431.3		1010,3035,2456	AA,AG,GG		40.3233,36.0581,38.8786		329/977	16464673	5055,7947	2202	4299	6501	SO:0001819	synonymous_variant	1969	exon5			GGCGGAGGGGGGT	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.987C>T	1.37:g.16464673G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			G|0.649;A|0.351	0.351	strong		0.662	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
FRMD7	90167	hgsc.bcm.edu	37	X	131212512	131212512	+	Silent	SNP	A	A	G	rs5977623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:131212512A>G	ENST00000298542.4	-	12	1708	c.1533T>C	c.(1531-1533)atT>atC	p.I511I	FRMD7_ENST00000464296.1_Silent_p.I496I|FRMD7_ENST00000370879.1_Silent_p.I391I	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	511					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.I511I(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					CCTCTGCTCTAATTGGGGACC	0.488													G|||	984	0.260662	0.3578	0.0821	3775	,	,		13740	0.0843		0.2276	False		,,,				2504	0.1431				p.I511I		Atlas-SNP	.											.	FRMD7	69	.	1	Substitution - coding silent(1)	prostate(1)	c.T1533C						PASS	.	G		1689,2146		313,807,256,512,315	139.0	136.0	137.0		1533	1.1	0.4	X	dbSNP_114	137	2072,4656		243,1011,575,1174,1297	no	coding-synonymous	FRMD7	NM_194277.2		556,1818,831,1686,1612	GG,GA,G,AA,A		30.7967,44.0417,35.6054		511/715	131212512	3761,6802	2203	4300	6503	SO:0001819	synonymous_variant	90167	exon12			TGCTCTAATTGGG	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1533T>C	X.37:g.131212512A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	107	73	0.682243	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	37	CCDS35397.1																																																																																			A|0.670;0|0.003	.	strong		0.488	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
SPRR1B	6699	hgsc.bcm.edu	37	1	153004853	153004853	+	Missense_Mutation	SNP	C	C	T	rs3795382	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153004853C>T	ENST00000307098.4	+	2	97	c.32C>T	c.(31-33)aCc>aTc	p.T11I	SPRR1B_ENST00000392661.3_Missense_Mutation_p.T11I	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	11	2 X 12 AA approximate repeats.		T -> I (in dbSNP:rs3795382). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3133554, ECO:0000269|PubMed:8388378, ECO:0000269|Ref.4}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CAGCCTTGCACCCCACCCCCT	0.552													T|||	2474	0.49401	0.4402	0.4251	5008	,	,		16011	0.5913		0.5099	False		,,,				2504	0.499				p.T11I		Atlas-SNP	.											SPRR1B,head_neck,carcinoma,0,1	SPRR1B	18	1	0			c.C32T						PASS	.	T	ILE/THR	2068,2338	570.8+/-382.9	482,1104,617	142.0	138.0	139.0		32	-0.1	0.0	1	dbSNP_107	139	4392,4208	584.4+/-391.7	1128,2136,1036	no	missense	SPRR1B	NM_003125.2	89	1610,3240,1653	TT,TC,CC		48.9302,46.936,49.6694	benign	11/90	153004853	6460,6546	2203	4300	6503	SO:0001583	missense	6699	exon2			CTTGCACCCCACC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.32C>T	1.37:g.153004853C>T	ENSP00000306461:p.Thr11Ile	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	139	59	0.42446	NM_003125	B2R5H7|P22529|P22530|Q5T524	Missense_Mutation	SNP	ENST00000307098.4	37	CCDS30863.1	1134	0.5192307692307693	228	0.4634146341463415	167	0.4613259668508287	355	0.6206293706293706	384	0.5065963060686016	c	1.477	-0.558376	0.03967	0.46936	0.510698	ENSG00000169469	ENST00000307098;ENST00000392661	T;T	0.14391	2.62;2.51	3.98	-0.059	0.13795	.	.	.	.	.	T	0.02418	0.0074	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47560	-0.9108	7	0.23891	T	0.37	-0.0032	8.0665	0.30663	0.0:0.5816:0.0:0.4184	rs3795382;rs17846538;rs17859612;rs17884771;rs52805231	11	P22528	SPR1B_HUMAN	I	11	ENSP00000306461:T11I;ENSP00000376429:T11I	ENSP00000306461:T11I	T	+	2	0	SPRR1B	151271477	0.005000	0.15991	0.000000	0.03702	0.408000	0.30992	-0.240000	0.08952	-0.338000	0.08413	-1.551000	0.00897	ACC	C|0.497;T|0.503	0.503	strong		0.552	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
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 GAIIx	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_ENST00000371910.1_5'Flank|ADAMTS13_ENST00000356589.2_Intron|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000355699.2_Intron|ADAMTS13_ENST00000485925.1_Intron	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	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	35	19	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	
AIFM1	9131	hgsc.bcm.edu	37	X	129283520	129283520	+	Silent	SNP	A	A	G	rs1139851	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:129283520A>G	ENST00000287295.3	-	3	503	c.273T>C	c.(271-273)gaT>gaC	p.D91D	AIFM1_ENST00000319908.3_Silent_p.D87D|AIFM1_ENST00000535724.1_Silent_p.D4D|AIFM1_ENST00000346424.2_Intron	NM_001130847.3|NM_004208.3	NP_001124319.1|NP_004199.1	O95831	AIFM1_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 1	91					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cell redox homeostasis (GO:0045454)|chromosome condensation (GO:0030261)|DNA catabolic process (GO:0006308)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitochondrial respiratory chain complex I assembly (GO:0032981)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic DNA fragmentation (GO:1902510)	cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|FAD binding (GO:0071949)|NAD(P)H oxidase activity (GO:0016174)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(4)|prostate(2)|urinary_tract(1)	30					Flavin adenine dinucleotide(DB03147)	ATCTTTTTTCATCCTCTTTCA	0.383													G|||	1854	0.491126	0.5825	0.3588	3775	,	,		13492	0.1438		0.3171	False		,,,				2504	0.3793				p.D91D		Atlas-SNP	.											.	AIFM1	75	.	0			c.T273C						PASS	.	G	,,,	2712,1121		833,639,407,159,164	208.0	184.0	192.0		273,273,261,	3.7	0.1	X	dbSNP_86	192	2672,4056		387,1157,741,884,1131	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	AIFM1	NM_001130847.3,NM_004208.3,NM_145812.2,NM_145813.2	,,,	1220,1796,1148,1043,1295	GG,GA,G,AA,A		39.7146,29.246,49.02	,,,	91/325,91/614,87/610,	129283520	5384,5177	2202	4300	6502	SO:0001819	synonymous_variant	9131	exon3			TTTTTCATCCTCT	AF100928	CCDS14618.1, CCDS14619.1, CCDS48167.1	Xq26.1	2014-01-30	2006-11-16	2006-11-16	ENSG00000156709	ENSG00000156709			8768	protein-coding gene	gene with protein product		300169	"""programmed cell death 8 (apoptosis-inducing factor)"", ""neuropathy, axonal, motor-sensory with deafness and mental retardation (Cowchock syndrome)"""	PDCD8, NAMSD		9989411, 23217327	Standard	NM_004208		Approved	AIF, CMTX4	uc004evg.3	O95831	OTTHUMG00000022392	ENST00000287295.3:c.273T>C	X.37:g.129283520A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_001130847	A4QPB4|B1ALN1|B2RB08|D3DTE9|Q1L6K4|Q1L6K6|Q2QKE4|Q5JUZ7|Q6I9X6|Q9Y3I3|Q9Y3I4	Silent	SNP	ENST00000287295.3	37	CCDS14618.1																																																																																			0|0.004;G|0.504	0.504	strong		0.383	AIFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058247.2		
MTUS1	57509	hgsc.bcm.edu	37	8	17612639	17612639	+	Silent	SNP	T	T	C	rs209568	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17612639T>C	ENST00000262102.6	-	2	902	c.678A>G	c.(676-678)gaA>gaG	p.E226E	MTUS1_ENST00000381869.3_Silent_p.E226E|MTUS1_ENST00000381862.3_Silent_p.E226E|MTUS1_ENST00000519263.1_Silent_p.E226E	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	226					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)		TTTCAAAGCTTTCTCTATCAT	0.403													T|||	1476	0.294728	0.0741	0.2046	5008	,	,		22798	0.4464		0.2237	False		,,,				2504	0.5736				p.E226E		Atlas-SNP	.											.	MTUS1	144	.	0			c.A678G						PASS	.	T	,	339,3455		13,313,1571	192.0	165.0	173.0		678,678	-0.6	0.0	8	dbSNP_79	173	1672,6566		175,1322,2622	no	coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2	,	188,1635,4193	CC,CT,TT		20.2962,8.9352,16.7138	,	226/1271,226/1217	17612639	2011,10021	1897	4119	6016	SO:0001819	synonymous_variant	57509	exon2			AAAGCTTTCTCTA	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.678A>G	8.37:g.17612639T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			T|0.758;C|0.242	0.242	strong		0.403	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
CD6	923	hgsc.bcm.edu	37	11	60785463	60785463	+	Silent	SNP	C	C	T	rs12417503	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:60785463C>T	ENST00000313421.7	+	11	2001	c.1815C>T	c.(1813-1815)gcC>gcT	p.A605A	CD6_ENST00000352009.5_Silent_p.A573A|CD6_ENST00000452451.2_Silent_p.A564A|CD6_ENST00000346437.4_Silent_p.A532A|CD6_ENST00000344028.5_Silent_p.A573A	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	605					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						TGGAGCTGGCCGGCACCCAGC	0.587													C|||	446	0.0890575	0.0832	0.1239	5008	,	,		16155	0.001		0.1958	False		,,,				2504	0.0532				p.A605A	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											CD6_ENST00000313421,NS,carcinoma,+2,2	CD6	122	2	0			c.C1815T						scavenged	.	C		425,3973		19,387,1793	41.0	46.0	44.0		1815	-4.3	0.5	11	dbSNP_120	44	1430,7150		125,1180,2985	no	coding-synonymous	CD6	NM_006725.3		144,1567,4778	TT,TC,CC		16.6667,9.6635,14.2934		605/669	60785463	1855,11123	2199	4290	6489	SO:0001819	synonymous_variant	923	exon11			GCTGGCCGGCACC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1815C>T	11.37:g.60785463C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	27	9	0.333333	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	37	CCDS7999.1																																																																																			C|0.875;T|0.125	0.125	strong		0.587	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
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 GAIIx	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	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	50	21	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	
WDR93	56964	hgsc.bcm.edu	37	15	90245253	90245253	+	Silent	SNP	C	C	T	rs4316730	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90245253C>T	ENST00000268130.7	+	2	377	c.276C>T	c.(274-276)acC>acT	p.T92T	WDR93_ENST00000558000.1_Silent_p.T92T|RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000560294.1_Silent_p.T92T	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	92					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TCCAGCCCACCGTCTACCCTC	0.483													C|||	1986	0.396565	0.5234	0.3631	5008	,	,		19440	0.2063		0.4026	False		,,,				2504	0.4387				p.T92T		Atlas-SNP	.											.	WDR93	63	.	0			c.C276T						PASS	.	C		2200,2200	588.5+/-386.9	559,1082,559	51.0	55.0	53.0		276	-3.0	0.0	15	dbSNP_111	53	3847,4751	540.1+/-383.7	846,2155,1298	yes	coding-synonymous	WDR93	NM_020212.1		1405,3237,1857	TT,TC,CC		44.743,50.0,46.5225		92/687	90245253	6047,6951	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon2			GCCCACCGTCTAC		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.276C>T	15.37:g.90245253C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			C|0.564;T|0.436	0.436	strong		0.483	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
TP53RK	112858	hgsc.bcm.edu	37	20	45315786	45315786	+	3'UTR	SNP	C	C	T	rs34983477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:45315786C>T	ENST00000372102.3	-	0	398				RP1-28H20.3_ENST00000606362.1_lincRNA			Q96S44	PRPK_HUMAN	TP53 regulating kinase						lipopolysaccharide biosynthetic process (GO:0009103)|protein phosphorylation (GO:0006468)|tRNA processing (GO:0008033)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|large_intestine(1)|lung(4)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				AATATAATCTCGAACAGTCAC	0.423													C|||	113	0.0225639	0.0023	0.0778	5008	,	,		18111	0.0		0.0398	False		,,,				2504	0.0164				p.R123Q		Atlas-SNP	.											.	TP53RK	13	.	0			c.G368A						PASS	.	C	GLN/ARG	43,4361	41.6+/-74.8	1,41,2160	145.0	166.0	159.0		368	4.4	1.0	20	dbSNP_126	159	365,8235	119.7+/-179.0	7,351,3942	yes	missense	TP53RK	NM_033550.3	43	8,392,6102	TT,TC,CC		4.2442,0.9764,3.1375	possibly-damaging	123/254	45315786	408,12596	2202	4300	6502	SO:0001624	3_prime_UTR_variant	112858	exon2			TAATCTCGAACAG		CCDS13401.1	20q13.2	2014-05-14	2004-05-10	2004-05-12	ENSG00000172315	ENSG00000172315			16197	protein-coding gene	gene with protein product		608679	"""chromosome 20 open reading frame 64"""	C20orf64		11546806, 12914926	Standard	NM_033550		Approved	dJ101A2.2, prpk, Nori-2p, BUD32	uc002xsk.3	Q96S44	OTTHUMG00000085887	ENST00000372102.3:c.*7G>A	20.37:g.45315786C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_033550	B3KU44|Q3T977|Q5JZ01|Q6NZ60|Q96FM7|Q9NQE6	Missense_Mutation	SNP	ENST00000372102.3	37		61	0.027930402930402932	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	34	0.044854881266490766	C	13.33	2.206229	0.39003	0.009764	0.042442	ENSG00000172315	ENST00000372114	T	0.21361	2.01	5.38	4.43	0.53597	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.060711	0.64402	D	0.000002	T	0.01421	0.0046	L	0.48218	1.51	0.80722	D	1	P	0.44521	0.837	B	0.42188	0.379	T	0.01202	-1.1420	10	0.39692	T	0.17	-6.2701	10.0951	0.42471	0.0:0.7799:0.141:0.0791	rs34983477;rs62214396	123	Q96S44	PRPK_HUMAN	Q	123	ENSP00000361186:R123Q	ENSP00000361186:R123Q	R	-	2	0	TP53RK	44749193	1.000000	0.71417	0.999000	0.59377	0.228000	0.25075	5.855000	0.69510	1.482000	0.48325	-0.175000	0.13238	CGA	C|0.969;T|0.031	0.031	strong		0.423	TP53RK-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000193688.1	NM_033550	
PHTF2	57157	hgsc.bcm.edu	37	7	77531113	77531113	+	Silent	SNP	T	T	C	rs78163487	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:77531113T>C	ENST00000248550.7	+	6	397	c.321T>C	c.(319-321)ccT>ccC	p.P107P	PHTF2_ENST00000422959.2_Silent_p.P73P|PHTF2_ENST00000450574.1_Silent_p.P73P|PHTF2_ENST00000275575.7_Silent_p.P69P|PHTF2_ENST00000415251.2_Silent_p.P69P|PHTF2_ENST00000416283.2_Silent_p.P73P|PHTF2_ENST00000307305.8_Silent_p.P69P|PHTF2_ENST00000424760.1_Silent_p.P69P			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	107					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	19						CTGAAAGTCCTTGGACTTCTC	0.353													T|||	697	0.139177	0.2194	0.0965	5008	,	,		14071	0.0952		0.0527	False		,,,				2504	0.1953				p.P73P		Atlas-SNP	.											.	PHTF2	104	.	0			c.T219C						PASS	.	T	,,,,	675,2963		66,543,1210	76.0	70.0	72.0		219,207,219,207,207	-4.0	1.0	7	dbSNP_132	72	474,7684		16,442,3621	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PHTF2	NM_001127357.1,NM_001127358.1,NM_001127359.1,NM_001127360.1,NM_020432.4	,,,,	82,985,4831	CC,CT,TT		5.8102,18.5542,9.7406	,,,,	73/752,69/748,73/357,69/353,69/748	77531113	1149,10647	1819	4079	5898	SO:0001819	synonymous_variant	57157	exon5			AAGTCCTTGGACT	AL136883	CCDS47621.1, CCDS47622.1, CCDS47623.1, CCDS47624.1	7q11.23-q21	2008-02-01			ENSG00000006576	ENSG00000006576			13411	protein-coding gene	gene with protein product						10729229	Standard	NM_020432		Approved	DKFZp434D166	uc003ugq.4	Q8N3S3	OTTHUMG00000155557	ENST00000248550.7:c.321T>C	7.37:g.77531113T>C		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	199	102	0.512563	NM_001127359	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Silent	SNP	ENST00000248550.7	37																																																																																				T|0.903;C|0.097	0.097	strong		0.353	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432	
OR4M1	441670	hgsc.bcm.edu	37	14	20249176	20249176	+	Missense_Mutation	SNP	G	G	A	rs2815960	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20249176G>A	ENST00000315957.4	+	1	776	c.695G>A	c.(694-696)gGt>gAt	p.G232D		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	232			G -> D (in dbSNP:rs2815960).			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)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCAGGCTCAGGTGAGAATACC	0.463																																					p.G232D		Atlas-SNP	.											.	OR4M1	104	.	0			c.G695A						PASS	.		ASP/GLY	584,3822		18,548,1637	353.0	300.0	318.0		695	3.5	1.0	14	dbSNP_100	318	2769,5831		267,2235,1798	yes	missense	OR4M1	NM_001005500.1	94	285,2783,3435	AA,AG,GG		32.1977,13.2547,25.7804	benign	232/314	20249176	3353,9653	2203	4300	6503	SO:0001583	missense	441670	exon1			GCTCAGGTGAGAA		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"""GPCR / Class A : Olfactory receptors"""	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.695G>A	14.37:g.20249176G>A	ENSP00000319654:p.Gly232Asp	Somatic	556	0	0		WXS	Illumina HiSeq	Phase_I	634	123	0.194006	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	CCDS32021.1	595	0.2724358974358974	42	0.08536585365853659	120	0.3314917127071823	163	0.28496503496503495	270	0.3562005277044855	.	10.89	1.478364	0.26511	0.132547	0.321977	ENSG00000176299	ENST00000315957	T	0.00293	8.26	4.42	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.392518	0.21951	N	0.066723	T	0.00012	0.0000	N	0.08118	0	0.37415	P	0.08660699999999999	B	0.02656	0.0	B	0.08055	0.003	T	0.16571	-1.0398	9	0.72032	D	0.01	-1.8975	7.0717	0.25181	0.2025:0.0:0.7975:0.0	rs2815960;rs52830018	232	Q8NGD0	OR4M1_HUMAN	D	232	ENSP00000319654:G232D	ENSP00000319654:G232D	G	+	2	0	OR4M1	19319016	0.000000	0.05858	1.000000	0.80357	0.744000	0.42396	0.118000	0.15605	1.225000	0.43566	0.506000	0.49869	GGT	G|0.739;A|0.261	0.261	strong		0.463	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1		
NOP9	161424	hgsc.bcm.edu	37	14	24769663	24769663	+	Silent	SNP	T	T	G	rs11158632	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24769663T>G	ENST00000267425.3	+	2	390	c.297T>G	c.(295-297)gcT>gcG	p.A99A	NOP9_ENST00000396802.3_Silent_p.A99A|DHRS1_ENST00000396813.1_5'Flank|DHRS1_ENST00000288111.7_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	99							poly(A) RNA binding (GO:0044822)										AGGCCCTAGCTTTGTCCACGA	0.478													T|||	753	0.150359	0.1581	0.3473	5008	,	,		19252	0.004		0.1849	False		,,,				2504	0.1155				p.A99A		Atlas-SNP	.											.	.	.	.	0			c.T297G						PASS	.	T		736,3670	303.2+/-287.8	63,610,1530	102.0	88.0	93.0		297	-0.8	1.0	14	dbSNP_120	93	1780,6820	321.5+/-315.1	189,1402,2709	no	coding-synonymous	C14orf21	NM_174913.1		252,2012,4239	GG,GT,TT		20.6977,16.7045,19.3449		99/637	24769663	2516,10490	2203	4300	6503	SO:0001819	synonymous_variant	161424	exon2			CCTAGCTTTGTCC		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.297T>G	14.37:g.24769663T>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	36	0.423529	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			T|0.838;G|0.162	0.162	strong		0.478	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
MARC2	54996	hgsc.bcm.edu	37	1	220955168	220955168	+	Silent	SNP	A	A	G	rs12030434	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:220955168A>G	ENST00000366913.3	+	7	1131	c.933A>G	c.(931-933)ccA>ccG	p.P311P	MARC2_ENST00000359316.2_Intron|MARC2_ENST00000472447.1_3'UTR	NM_017898.3	NP_060368.2	Q969Z3	MARC2_HUMAN	mitochondrial amidoxime reducing component 2	311	MOSC. {ECO:0000255|PROSITE- ProRule:PRU00670}.				detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										AGTTGTCTCCACTTTTTGGGA	0.413													G|||	156	0.0311502	0.0439	0.0043	5008	,	,		17276	0.0526		0.0099	False		,,,				2504	0.0327				p.P311P		Atlas-SNP	.											.	.	.	.	0			c.A933G						PASS	.	G		146,4260	812.9+/-416.1	2,142,2059	192.0	192.0	192.0		933	-4.5	0.8	1	dbSNP_120	192	52,8548	817.0+/-406.9	0,52,4248	no	coding-synonymous	MOSC2	NM_017898.3		2,194,6307	GG,GA,AA		0.6047,3.3137,1.5224		311/336	220955168	198,12808	2203	4300	6503	SO:0001819	synonymous_variant	54996	exon7			GTCTCCACTTTTT		CCDS1525.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000117791	ENSG00000117791			26064	protein-coding gene	gene with protein product		614127	"""MOCO sulphurase C-terminal domain containing 2"""	MOSC2		11886751	Standard	NM_017898		Approved	FLJ20605	uc001hmq.3	Q969Z3	OTTHUMG00000037354	ENST00000366913.3:c.933A>G	1.37:g.220955168A>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_017898	B2D0R5|D3DTB3|Q0JSK7|Q5VT67|Q5VXC7|Q7L317|Q9H066|Q9NWU0	Silent	SNP	ENST00000366913.3	37	CCDS1525.1																																																																																			A|0.974;G|0.026	0.026	strong		0.413	MARC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090911.1	NM_017898	
HDC	3067	hgsc.bcm.edu	37	15	50534832	50534832	+	Silent	SNP	A	A	G	rs1549521	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:50534832A>G	ENST00000267845.3	-	12	2016	c.1614T>C	c.(1612-1614)aaT>aaC	p.N538N	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Silent_p.N505N	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		GATGGAGGCCATTTTCCCTTT	0.552													G|||	705	0.140775	0.4138	0.0317	5008	,	,		18759	0.1071		0.0219	False		,,,				2504	0.0061				p.N538N	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											HDC,NS,carcinoma,-2,1	HDC	86	1	0			c.T1614C						PASS	.	G		1506,2886	673.2+/-402.8	266,974,956	74.0	73.0	73.0		1614	-3.9	0.0	15	dbSNP_88	73	244,8346	808.2+/-407.2	2,240,4053	no	coding-synonymous	HDC	NM_002112.3		268,1214,5009	GG,GA,AA		2.8405,34.2896,13.4802		538/663	50534832	1750,11232	2196	4295	6491	SO:0001819	synonymous_variant	3067	exon12			GAGGCCATTTTCC		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1614T>C	15.37:g.50534832A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	86	33	0.383721	NM_002112		Silent	SNP	ENST00000267845.3	37	CCDS10134.1																																																																																			A|0.862;G|0.138	0.138	strong		0.552	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
ZNF318	24149	hgsc.bcm.edu	37	6	43305520	43305520	+	Silent	SNP	C	C	T	rs35650765	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:43305520C>T	ENST00000361428.2	-	10	6293	c.6216G>A	c.(6214-6216)ccG>ccA	p.P2072P	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	2072					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)			GAGAATCTAACGGAAACCCAG	0.443													C|||	94	0.01877	0.003	0.0202	5008	,	,		20560	0.0129		0.0487	False		,,,				2504	0.0143				p.P2072P		Atlas-SNP	.											ZNF318,colon,carcinoma,0,1	ZNF318	175	1	0			c.G6216A						PASS	.	C		40,4366	44.6+/-78.6	0,40,2163	80.0	76.0	78.0		6216	-11.7	0.2	6	dbSNP_126	78	413,8187	130.0+/-188.0	10,393,3897	no	coding-synonymous	ZNF318	NM_014345.2		10,433,6060	TT,TC,CC		4.8023,0.9079,3.483		2072/2280	43305520	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	24149	exon10			ATCTAACGGAAAC	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.6216G>A	6.37:g.43305520C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	142	72	0.507042	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Silent	SNP	ENST00000361428.2	37	CCDS4895.2																																																																																			C|0.970;T|0.030	0.030	strong		0.443	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345	
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 GAIIx	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	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	27	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	
ORC3	23595	hgsc.bcm.edu	37	6	88362943	88362943	+	Silent	SNP	C	C	T	rs2307393	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:88362943C>T	ENST00000392844.3	+	14	1540	c.1492C>T	c.(1492-1494)Ctg>Ttg	p.L498L	ORC3_ENST00000257789.4_Silent_p.L498L|ORC3_ENST00000546266.1_Silent_p.L355L|ORC3_ENST00000417380.2_3'UTR	NM_012381.3|NM_181837.2	NP_036513.2|NP_862820.1	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3	498					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|neural precursor cell proliferation (GO:0061351)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA replication origin binding (GO:0003688)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	28						AGAGGAGTTCCTGGCCCAGTT	0.408													C|||	235	0.0469249	0.0953	0.0504	5008	,	,		17284	0.0099		0.0467	False		,,,				2504	0.0174				p.L498L		Atlas-SNP	.											.	ORC3	51	.	0			c.C1492T						PASS	.	C	,,	421,3985	203.8+/-226.2	21,379,1803	94.0	89.0	91.0		1063,1492,1492	4.8	1.0	6	dbSNP_100	91	395,8205	125.5+/-184.1	8,379,3913	no	coding-synonymous,coding-synonymous,coding-synonymous	ORC3	NM_001197259.1,NM_012381.3,NM_181837.2	,,	29,758,5716	TT,TC,CC		4.593,9.5552,6.274	,,	355/569,498/712,498/713	88362943	816,12190	2203	4300	6503	SO:0001819	synonymous_variant	23595	exon14			GAGTTCCTGGCCC	AF093535	CCDS5012.1, CCDS43486.1, CCDS56440.1	6q	2010-10-12	2010-10-12	2010-10-12	ENSG00000135336	ENSG00000135336			8489	protein-coding gene	gene with protein product		604972	"""origin recognition complex, subunit 3 (yeast homolog)-like"", ""origin recognition complex, subunit 3-like (yeast)"", ""origin recognition complex, subunit 3 honolog (yeast)"""	ORC3L		9829972, 10402192	Standard	NM_181837		Approved	IMAGE50150, LATHEO	uc003pmg.3	Q9UBD5	OTTHUMG00000015179	ENST00000392844.3:c.1492C>T	6.37:g.88362943C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_181837	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	Silent	SNP	ENST00000392844.3	37	CCDS43486.1																																																																																			C|0.945;T|0.055	0.055	strong		0.408	ORC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041452.2		
OR13C5	138799	hgsc.bcm.edu	37	9	107360826	107360826	+	Missense_Mutation	SNP	A	A	G	rs1851725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107360826A>G	ENST00000374779.2	-	1	962	c.869T>C	c.(868-870)aTg>aCg	p.M290T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	290			M -> T (in dbSNP:rs1851725).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AGGATTCATCATGGGAGTCAT	0.373													G|||	2184	0.436102	0.6475	0.2277	5008	,	,		20206	0.5754		0.1789	False		,,,				2504	0.4192				p.M290T		Atlas-SNP	.											.	OR13C5	60	.	0			c.T869C						PASS	.	G	THR/MET	2577,1829	532.5+/-373.5	762,1053,388	112.0	114.0	113.0		869	-0.1	0.0	9	dbSNP_92	113	1669,6931	739.5+/-407.1	183,1303,2814	yes	missense	OR13C5	NM_001004482.1	81	945,2356,3202	GG,GA,AA		19.407,41.5116,32.6465	benign	290/319	107360826	4246,8760	2203	4300	6503	SO:0001583	missense	138799	exon1			TTCATCATGGGAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.869T>C	9.37:g.107360826A>G	ENSP00000363911:p.Met290Thr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	839	0.3841575091575092	297	0.6036585365853658	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	G	9.506	1.104528	0.20632	0.584884	0.19407	ENSG00000255800	ENST00000374779	T	0.37411	1.2	4.03	-0.0854	0.13686	GPCR, rhodopsin-like superfamily (1);	0.153284	0.29660	N	0.011536	T	0.00012	0.0000	M	0.80508	2.5	0.49687	P	1.8499999999999073E-4	B	0.17268	0.021	B	0.20577	0.03	T	0.34675	-0.9819	9	0.45353	T	0.12	.	4.7671	0.13137	0.6686:0.0:0.191:0.1404	rs1851725;rs58161788;rs1851725	290	Q8NGS8	O13C5_HUMAN	T	290	ENSP00000363911:M290T	ENSP00000363911:M290T	M	-	2	0	OR13C5	106400647	0.002000	0.14202	0.005000	0.12908	0.202000	0.24057	1.919000	0.40015	-0.437000	0.07243	-2.339000	0.00246	ATG	A|0.634;G|0.366	0.366	strong		0.373	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
CD69	969	hgsc.bcm.edu	37	12	9906179	9906179	+	Silent	SNP	G	G	A	rs11052883	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9906179G>A	ENST00000228434.3	-	5	578	c.498C>T	c.(496-498)aaC>aaT	p.N166N		NM_001781.2	NP_001772.1	Q07108	CD69_HUMAN	CD69 molecule	166	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular response to drug (GO:0035690)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10						ACCCTGTAACGTTGAACCTGT	0.358													G|||	63	0.0125799	0.0015	0.0303	5008	,	,		18994	0.0		0.0348	False		,,,				2504	0.0051				p.N166N		Atlas-SNP	.											CD69,NS,carcinoma,-1,1	CD69	23	1	0			c.C498T						PASS	.	G		41,4365	43.8+/-77.6	0,41,2162	43.0	43.0	43.0		498	5.1	0.8	12	dbSNP_120	43	414,8186	129.7+/-187.7	8,398,3894	yes	coding-synonymous	CD69	NM_001781.2		8,439,6056	AA,AG,GG		4.814,0.9305,3.4984		166/200	9906179	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	969	exon5			TGTAACGTTGAAC	Z22576	CCDS8604.1	12p13	2011-08-30	2006-03-28		ENSG00000110848	ENSG00000110848		"""C-type lectin domain containing"", ""CD molecules"""	1694	protein-coding gene	gene with protein product		107273	"""CD69 antigen (p60, early T-cell activation antigen)"""			1612643	Standard	NM_001781		Approved	CLEC2C	uc001qwk.3	Q07108	OTTHUMG00000168481	ENST00000228434.3:c.498C>T	12.37:g.9906179G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_001781		Silent	SNP	ENST00000228434.3	37	CCDS8604.1																																																																																			G|0.970;A|0.030	0.030	strong		0.358	CD69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399876.1		
SIRPG	55423	hgsc.bcm.edu	37	20	1629906	1629906	+	Silent	SNP	C	C	T	rs6079967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:1629906C>T	ENST00000303415.3	-	2	286	c.222G>A	c.(220-222)cgG>cgA	p.R74R	SIRPG_ENST00000216927.4_Silent_p.R74R|RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000344103.4_Silent_p.R74R|SIRPG_ENST00000381583.2_Silent_p.R74R|SIRPG_ENST00000381580.1_Silent_p.R41R	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	74	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.R74R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						AGATTAATTCCCGGCCTGGTC	0.507													t|||	1761	0.351637	0.3064	0.5058	5008	,	,		19787	0.2708		0.4394	False		,,,				2504	0.2965				p.R74R		Atlas-SNP	.											SIRPG,right_upper_lobe,carcinoma,-1,2	SIRPG	61	2	1	Substitution - coding silent(1)	stomach(1)	c.G222A						PASS	.	T	,,	1457,2949		248,961,994	182.0	165.0	171.0		222,222,222	-0.1	0.0	20	dbSNP_114	171	3939,4661		906,2127,1267	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	1154,3088,2261	TT,TC,CC		45.8023,33.0685,41.4885	,,	74/277,74/388,74/171	1629906	5396,7610	2203	4300	6503	SO:0001819	synonymous_variant	55423	exon2			TAATTCCCGGCCT	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.222G>A	20.37:g.1629906C>T		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	286	284	0.993007	NM_001039508	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			C|0.593;T|0.407	0.407	strong		0.507	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
SLC5A9	200010	hgsc.bcm.edu	37	1	48708250	48708250	+	Missense_Mutation	SNP	C	C	T	rs78427303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:48708250C>T	ENST00000438567.2	+	13	1851	c.1799C>T	c.(1798-1800)gCg>gTg	p.A600V	SLC5A9_ENST00000533824.1_Missense_Mutation_p.A621V|SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000236495.5_Missense_Mutation_p.A625V	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	600					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						GGAGGTGGAGCGGCAGAGAAC	0.647													c|||	164	0.0327476	0.0045	0.0533	5008	,	,		15556	0.001		0.0915	False		,,,				2504	0.0286				p.A625V		Atlas-SNP	.											.	SLC5A9	82	.	0			c.C1874T						PASS	.	C	VAL/ALA,VAL/ALA	81,4325	70.3+/-108.2	1,79,2123	30.0	34.0	33.0		1799,1874	-9.3	0.0	1	dbSNP_132	33	797,7803	182.5+/-230.9	42,713,3545	yes	missense,missense	SLC5A9	NM_001011547.2,NM_001135181.1	64,64	43,792,5668	TT,TC,CC		9.2674,1.8384,6.7507	benign,benign	600/682,625/707	48708250	878,12128	2203	4300	6503	SO:0001583	missense	200010	exon14			GTGGAGCGGCAGA	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.1799C>T	1.37:g.48708250C>T	ENSP00000401730:p.Ala600Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	50	0.588235	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	103	0.04716117216117216	3	0.006097560975609756	27	0.07458563535911603	1	0.0017482517482517483	72	0.09498680738786279	c	5.018	0.189038	0.09547	0.018384	0.092674	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	T;T;T	0.64085	-0.08;-0.08;-0.08	4.65	-9.29	0.00653	.	0.957662	0.08646	N	0.914845	T	0.01061	0.0035	N	0.11698	0.16	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.04915	-1.0918	9	0.19147	T	0.46	.	0.2848	0.00250	0.2517:0.283:0.1836:0.2817	.	621;600;625	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	V	621;600;625	ENSP00000431900:A621V;ENSP00000401730:A600V;ENSP00000236495:A625V	ENSP00000236495:A625V	A	+	2	0	SLC5A9	48480837	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.855000	0.00729	-3.616000	0.00131	-3.307000	0.00045	GCG	C|0.939;T|0.061	0.061	strong		0.647	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
ATP8B2	57198	hgsc.bcm.edu	37	1	154303976	154303976	+	Silent	SNP	T	T	C	rs6702754	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:154303976T>C	ENST00000368489.3	+	6	459	c.459T>C	c.(457-459)aaT>aaC	p.N153N	ATP8B2_ENST00000426445.1_3'UTR|ATP8B2_ENST00000341822.2_Silent_p.N139N|ATP8B2_ENST00000368487.3_Silent_p.N120N	NM_020452.3	NP_065185.1	P98198	AT8B2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 2	139					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)		IL6R/ATP8B2(2)	breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			TGCTGATCAATGGAATGTGAG	0.522													T|||	1459	0.291334	0.3396	0.2363	5008	,	,		18588	0.2103		0.3181	False		,,,				2504	0.3211				p.N153N		Atlas-SNP	.											.	ATP8B2	158	.	0			c.T459C						PASS	.	T	,	1361,3045	454.5+/-350.7	210,941,1052	92.0	91.0	92.0		360,459	3.2	1.0	1	dbSNP_116	92	2539,6061	414.5+/-351.5	396,1747,2157	no	coding-synonymous,coding-synonymous	ATP8B2	NM_001005855.1,NM_020452.3	,	606,2688,3209	CC,CT,TT		29.5233,30.8897,29.9862	,	120/388,153/1224	154303976	3900,9106	2203	4300	6503	SO:0001819	synonymous_variant	57198	exon6			GATCAATGGAATG	AB032963	CCDS1066.1, CCDS41405.1	1q21.3	2012-03-09	2012-03-09		ENSG00000143515	ENSG00000143515		"""ATPases / P-type"""	13534	protein-coding gene	gene with protein product		605867	"""ATPase, class I, type 8B, member 2"""			10574461, 11015572	Standard	NM_020452		Approved	ATPID, KIAA1137	uc001fex.3	P98198	OTTHUMG00000035979	ENST00000368489.3:c.459T>C	1.37:g.154303976T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_020452	B4E3P4|Q6NT69|Q7Z486|Q96I43|Q96NQ7	Silent	SNP	ENST00000368489.3	37	CCDS1066.1																																																																																			T|0.700;C|0.300	0.300	strong		0.522	ATP8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087658.2	NM_020452	
C3orf52	79669	hgsc.bcm.edu	37	3	111821747	111821747	+	Missense_Mutation	SNP	A	A	G	rs16859190	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111821747A>G	ENST00000264848.5	+	3	390	c.331A>G	c.(331-333)Atc>Gtc	p.I111V	C3orf52_ENST00000430855.1_Missense_Mutation_p.I111V|C3orf52_ENST00000431717.2_Missense_Mutation_p.I111V	NM_024616.2	NP_078892	Q5BVD1	TTMP_HUMAN	chromosome 3 open reading frame 52	111			I -> V (in dbSNP:rs16859190).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						AACATTCTTCATCATGCTGAA	0.363													G|||	618	0.123403	0.2799	0.0591	5008	,	,		19051	0.0605		0.0368	False		,,,				2504	0.1115				p.I111V		Atlas-SNP	.											.	C3orf52	28	.	0			c.A331G						PASS	.	G	VAL/ILE,VAL/ILE	831,2907		83,665,1121	75.0	69.0	71.0		331,331	2.6	0.2	3	dbSNP_123	71	250,7962		3,244,3859	yes	missense,missense	C3orf52	NM_001171747.1,NM_024616.2	29,29	86,909,4980	GG,GA,AA		3.0443,22.2311,9.046	benign,benign	111/251,111/218	111821747	1081,10869	1869	4106	5975	SO:0001583	missense	79669	exon3			TTCTTCATCATGC	AY830714	CCDS46887.1, CCDS54620.1	3q13.2	2006-01-30			ENSG00000114529	ENSG00000114529			26255	protein-coding gene	gene with protein product	"""TPA induced trans-membrane protein"""	611956				15737651	Standard	NM_024616		Approved	FLJ23186, TTMP	uc011bhs.2	Q5BVD1	OTTHUMG00000159230	ENST00000264848.5:c.331A>G	3.37:g.111821747A>G	ENSP00000264848:p.Ile111Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	151	71	0.470199	NM_001171747	B4DNV2|B4E0Z2|Q96AJ4|Q9H5Q1	Missense_Mutation	SNP	ENST00000264848.5	37	CCDS46887.1	225|225	0.10302197802197802|0.10302197802197802	142|142	0.2886178861788618|0.2886178861788618	23|23	0.06353591160220995|0.06353591160220995	34|34	0.05944055944055944|0.05944055944055944	26|26	0.03430079155672823|0.03430079155672823	G|G	0.004|0.004	-2.336876|-2.336876	0.00224|0.00224	0.222311|0.222311	0.030443|0.030443	ENSG00000114529|ENSG00000114529	ENST00000484828|ENST00000430855;ENST00000431717;ENST00000264848	.|T;T;T	.|0.09445	.|2.98;2.98;2.98	5.66|5.66	2.6|2.6	0.31112|0.31112	.|.	.|0.242891	.|0.33040	.|N	.|0.005345	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01576|0.01576	-0.805|-0.805	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.001;0.001;0.001	T|T	0.45440|0.45440	-0.9261|-0.9261	4|9	.|0.02654	.|T	.|1	-31.071|-31.071	3.6032|3.6032	0.08032|0.08032	0.4011:0.1919:0.407:0.0|0.4011:0.1919:0.407:0.0	rs16859190;rs52821979;rs16859190|rs16859190;rs52821979;rs16859190	.|111;111;111	.|Q5BVD1-2;Q5BVD1-3;Q5BVD1	.|.;.;TTMP_HUMAN	R|V	101|111	.|ENSP00000390333:I111V;ENSP00000399392:I111V;ENSP00000264848:I111V	.|ENSP00000264848:I111V	H|I	+|+	2|1	0|0	C3orf52|C3orf52	113304437|113304437	0.000000|0.000000	0.05858|0.05858	0.168000|0.168000	0.22838|0.22838	0.051000|0.051000	0.14879|0.14879	-0.301000|-0.301000	0.08232|0.08232	-0.028000|-0.028000	0.13850|0.13850	-0.684000|-0.684000	0.03749|0.03749	CAT|ATC	A|0.895;G|0.105	0.105	strong		0.363	C3orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353961.1	NM_024616	
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 GAIIx	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_ENST00000475231.1_Missense_Mutation_p.P4098A|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	26	19	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	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68024134	68024134	+	Splice_Site	SNP	A	A	T	rs3825723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:68024134A>T	ENST00000329153.5	+	4	470	c.338A>T	c.(337-339)cAg>cTg	p.Q113L		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	113			Q -> L (in dbSNP:rs3825723).			cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CTGGAGAAGCAGGTAAGGGCT	0.567													A|||	790	0.157748	0.0484	0.1383	5008	,	,		19248	0.2937		0.1491	False		,,,				2504	0.1881				p.Q113L		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.A338T						PASS	.	A	LEU/GLN	269,3779		9,251,1764	60.0	61.0	61.0		338	5.4	1.0	14	dbSNP_107	61	1227,7161		93,1041,3060	yes	missense-near-splice	PLEKHH1	NM_020715.2	113	102,1292,4824	TT,TA,AA		14.628,6.6453,12.0296	possibly-damaging	113/1365	68024134	1496,10940	2024	4194	6218	SO:0001630	splice_region_variant	57475	exon4			AGAAGCAGGTAAG	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.339+1A>T	14.37:g.68024134A>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	366	0.16758241758241757	30	0.06097560975609756	47	0.1298342541436464	172	0.3006993006993007	117	0.15435356200527706	A	24.6	4.550030	0.86127	0.066453	0.14628	ENSG00000054690	ENST00000329153	T	0.32753	1.44	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.73962	2.25	0.09310	P	1.0	D	0.76494	0.999	D	0.78314	0.991	T	0.15037	-1.0451	9	0.36615	T	0.2	.	13.0709	0.59061	1.0:0.0:0.0:0.0	rs3825723;rs52813401;rs3825723	113	Q9ULM0	PKHH1_HUMAN	L	113	ENSP00000330278:Q113L	ENSP00000330278:Q113L	Q	+	2	0	PLEKHH1	67093887	1.000000	0.71417	1.000000	0.80357	0.893000	0.52053	7.541000	0.82084	2.279000	0.76181	0.459000	0.35465	CAG	A|0.828;T|0.172	0.172	strong		0.567	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	Missense_Mutation
ELMOD3	84173	hgsc.bcm.edu	37	2	85617913	85617913	+	Missense_Mutation	SNP	G	G	T	rs17850709	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85617913G>T	ENST00000409890.2	+	14	1641	c.974G>T	c.(973-975)cGg>cTg	p.R325L	ELMOD3_ENST00000315658.7_3'UTR|ELMOD3_ENST00000409344.3_Missense_Mutation_p.R325L|ELMOD3_ENST00000409013.3_Missense_Mutation_p.R325L|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000393852.4_Missense_Mutation_p.R325L			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	325				R -> L (in Ref. 6; AAH10991). {ECO:0000305}.	phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						AAGAGCCCACGGCGGCTGCTC	0.582													G|||	214	0.0427316	0.0439	0.0432	5008	,	,		18444	0.006		0.0656	False		,,,				2504	0.0552				p.R325L		Atlas-SNP	.											ELMOD3_ENST00000409890,NS,carcinoma,0,1	ELMOD3	53	1	0			c.G974T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG,	64,1320		2,60,630	16.0	21.0	20.0		974,974,974,	1.3	0.0	2	dbSNP_123	20	239,2943		9,221,1361	yes	missense,missense,missense,utr-3	ELMOD3	NM_001135021.1,NM_001135022.1,NM_001135023.1,NM_032213.4	102,102,102,	11,281,1991	TT,TG,GG		7.511,4.6243,6.636	,,,	325/382,325/382,325/382,	85617913	303,4263	692	1591	2283	SO:0001583	missense	84173	exon14			GCCCACGGCGGCT	AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"""RNA binding motif (RRM) containing"""	26158	protein-coding gene	gene with protein product		615427	"""RNA binding motif protein 29"", ""RNA binding motif and ELMO/CED-12 domain 1"", ""deafness, autosomal recessive 88"""	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.974G>T	2.37:g.85617913G>T	ENSP00000386304:p.Arg325Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	68	46	0.676471	NM_001135022	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Missense_Mutation	SNP	ENST00000409890.2	37	CCDS46352.1	80	0.03663003663003663	15	0.03048780487804878	16	0.04419889502762431	5	0.008741258741258742	44	0.05804749340369393	G	14.96	2.692566	0.48202	0.046243	0.07511	ENSG00000115459	ENST00000409013;ENST00000409890;ENST00000409344;ENST00000393852	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.65	1.28	0.21552	.	.	.	.	.	T	0.01156	0.0038	L	0.44542	1.39	0.09310	N	1	B	0.14805	0.011	B	0.08055	0.003	T	0.11275	-1.0594	9	0.41790	T	0.15	.	6.4947	0.22136	0.4557:0.0:0.5443:0.0	rs17850709;rs17850709	325	Q96FG2	ELMD3_HUMAN	L	325	ENSP00000387139:R325L;ENSP00000386304:R325L;ENSP00000386248:R325L;ENSP00000377434:R325L	ENSP00000377434:R325L	R	+	2	0	ELMOD3	85471424	0.616000	0.27035	0.017000	0.16124	0.894000	0.52154	0.831000	0.27476	0.326000	0.23384	0.655000	0.94253	CGG	G|0.962;T|0.038	0.038	strong		0.582	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213	
COL18A1	80781	hgsc.bcm.edu	37	21	46876083	46876083	+	Silent	SNP	A	A	G	rs2236451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46876083A>G	ENST00000359759.4	+	1	660	c.639A>G	c.(637-639)ccA>ccG	p.P213P	COL18A1_ENST00000355480.5_Silent_p.P213P|COL18A1_ENST00000400337.2_Intron			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	213					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		TGCCACCACCATCTTCAGGTA	0.697													G|||	1881	0.375599	0.5673	0.2997	5008	,	,		14080	0.3284		0.326	False		,,,				2504	0.2699				p.P213P		Atlas-SNP	.											.	COL18A1	129	.	0			c.A639G						PASS	.	G	,	2040,2022		519,1002,510	27.0	35.0	32.0		639,	-6.4	0.0	21	dbSNP_98	32	2719,5647		469,1781,1933	no	coding-synonymous,intron	COL18A1	NM_030582.3,NM_130445.2	,	988,2783,2443	GG,GA,AA		32.5006,49.7784,38.2926	,	213/1520,	46876083	4759,7669	2031	4183	6214	SO:0001819	synonymous_variant	80781	exon1			ACCACCATCTTCA		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.639A>G	21.37:g.46876083A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	109	39	0.357798	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				A|0.628;G|0.372	0.372	strong		0.697	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
ELN	2006	hgsc.bcm.edu	37	7	73470714	73470714	+	Missense_Mutation	SNP	G	G	A	rs2071307	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:73470714G>A	ENST00000252034.7	+	20	1663	c.1264G>A	c.(1264-1266)Ggt>Agt	p.G422S	ELN_ENST00000358929.4_Missense_Mutation_p.G422S|ELN_ENST00000429192.1_Missense_Mutation_p.G427S|ELN_ENST00000380553.4_Missense_Mutation_p.G305S|ELN_ENST00000380575.4_Missense_Mutation_p.G412S|ELN_ENST00000380562.4_Missense_Mutation_p.G422S|ELN_ENST00000380584.4_Missense_Mutation_p.G408S|ELN_ENST00000380576.5_Missense_Mutation_p.G422S|ELN_ENST00000320399.6_Missense_Mutation_p.G422S|ELN_ENST00000357036.5_Missense_Mutation_p.G427S|ELN_ENST00000320492.7_Intron|ELN_ENST00000414324.1_Missense_Mutation_p.G417S|ELN_ENST00000445912.1_Missense_Mutation_p.G422S|ELN_ENST00000458204.1_Missense_Mutation_p.G412S	NM_000501.2|NM_001278915.1	NP_000492.2|NP_001265844.1	P15502	ELN_HUMAN	elastin	0	Ala-rich.		G -> S (in dbSNP:rs2071307). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2831431, ECO:0000269|PubMed:3039501, ECO:0000269|PubMed:3171221, ECO:0000269|PubMed:8689688, ECO:0000269|PubMed:9215670}.		blood circulation (GO:0008015)|blood vessel remodeling (GO:0001974)|cell proliferation (GO:0008283)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|organ morphogenesis (GO:0009887)|regulation of actin filament polymerization (GO:0030833)|respiratory gaseous exchange (GO:0007585)|skeletal muscle tissue development (GO:0007519)|stress fiber assembly (GO:0043149)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|extracellular matrix constituent conferring elasticity (GO:0030023)|extracellular matrix structural constituent (GO:0005201)	p.G422S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(4)|pancreas(2)|prostate(1)|skin(2)|stomach(1)	32		Lung NSC(55;0.159)				AGGTGTCCCTGGTGTCGGAGG	0.617			T	PAX5	B-ALL		"""Supravalvular Aortic Stenosis, Cutis laxa , Williams-Beuren Syndrome"""						A|||	1104	0.220447	0.1339	0.2464	5008	,	,		15486	0.1081		0.4205	False		,,,				2504	0.229				p.G427S		Atlas-SNP	.		Dom	yes		7	7q11.23	2006	elastin	yes	L	ELN,NS,carcinoma,0,1	ELN	81	1	1	Substitution - Missense(1)	stomach(1)	c.G1279A						PASS	.	A	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	779,3627	753.3+/-412.4	72,635,1496	110.0	108.0	108.0		1264,1279,1279,1234,1264	1.2	0.0	7	dbSNP_96	108	3551,5049	630.5+/-398.4	728,2095,1477	yes	missense,missense,missense,missense,missense	ELN	NM_001081755.1,NM_001081754.1,NM_001081753.1,NM_001081752.1,NM_000501.2	56,56,56,56,56	800,2730,2973	AA,AG,GG		41.2907,17.6804,33.2923	benign,benign,benign,benign,benign	422/706,427/712,427/693,412/678,422/725	73470714	4330,8676	2203	4300	6503	SO:0001583	missense	2006	exon20			GTCCCTGGTGTCG		CCDS5562.2, CCDS43598.1, CCDS43599.1, CCDS47611.1, CCDS47612.1, CCDS64673.1, CCDS64674.1, CCDS64675.1, CCDS64676.1, CCDS64677.1, CCDS64678.1, CCDS75616.1, CCDS75617.1	7q11.1-q21.1	2008-08-01	2008-08-01		ENSG00000049540	ENSG00000049540			3327	protein-coding gene	gene with protein product	"""tropoelastin"", ""supravalvular aortic stenosis"", ""Williams-Beuren syndrome"""	130160				8096434	Standard	NM_001278939		Approved	WBS, WS, SVAS	uc003tzn.3	P15502	OTTHUMG00000150229	ENST00000252034.7:c.1264G>A	7.37:g.73470714G>A	ENSP00000252034:p.Gly422Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_001081753	B3KTS6|O15336|O15337|Q14233|Q14234|Q14235|Q14238|Q6P0L4|Q6ZWJ6|Q75MU5|Q7Z316|Q7Z3F5|Q9UMF5	Missense_Mutation	SNP	ENST00000252034.7	37	CCDS5562.2	559	0.25595238095238093	74	0.15040650406504066	108	0.2983425414364641	78	0.13636363636363635	299	0.3944591029023747	A	10.41	1.343509	0.24339	0.176804	0.412907	ENSG00000049540	ENST00000445912;ENST00000252034;ENST00000358929;ENST00000414324;ENST00000380562;ENST00000380575;ENST00000380584;ENST00000458204;ENST00000357036;ENST00000429192;ENST00000442462;ENST00000380553;ENST00000380576;ENST00000320399	T;T;T;T;T;T;T;T;T;T;T;T;T	0.58652	1.13;1.16;0.32;1.18;1.14;1.25;1.38;1.14;1.11;1.27;1.31;1.28;1.16	2.18	1.2	0.21068	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B;B;B	0.15141	0.012;0.012;0.012;0.012;0.007;0.012;0.012;0.012;0.012;0.012;0.012;0.012	B;B;B;B;B;B;B;B;B;B;B;B	0.06405	0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002;0.002	T	0.36237	-0.9756	7	0.49607	T	0.09	.	7.3905	0.26907	0.1691:0.0:0.8309:0.0	rs2071307;rs11567855;rs17855987;rs58147333;rs2071307	422;391;417;412;422;412;427;427;422;305;408;422	E7ENM0;E9PBM4;G3V0G6;E7EN65;P15502-1;P15502-7;P15502-12;P15502-5;P15502-13;P15502-11;P15502-8;P15502-2	.;.;.;.;.;.;.;.;.;.;.;.	S	422;422;422;417;422;412;408;412;427;427;391;305;422;422	ENSP00000389857:G422S;ENSP00000252034:G422S;ENSP00000351807:G422S;ENSP00000392575:G417S;ENSP00000369936:G422S;ENSP00000369949:G412S;ENSP00000369958:G408S;ENSP00000403162:G412S;ENSP00000349540:G427S;ENSP00000391129:G427S;ENSP00000369926:G305S;ENSP00000369950:G422S;ENSP00000313565:G422S	ENSP00000252034:G422S	G	+	1	0	ELN	73108650	0.111000	0.22076	0.002000	0.10522	0.002000	0.02628	0.532000	0.23067	-0.267000	0.09325	-1.446000	0.01064	GGT	G|0.704;A|0.296	0.296	strong		0.617	ELN-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316913.1	NM_000501	
WDR43	23160	hgsc.bcm.edu	37	2	29135468	29135468	+	Silent	SNP	C	C	G	rs6715296	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:29135468C>G	ENST00000407426.3	+	4	554	c.498C>G	c.(496-498)ggC>ggG	p.G166G	SNORD92_ENST00000585078.1_RNA	NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	166						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					AATGGAAAGGCGACAATAGCA	0.373													C|||	3502	0.699281	0.5166	0.7622	5008	,	,		18134	0.8591		0.7048	False		,,,				2504	0.7311				p.G166G		Atlas-SNP	.											.	WDR43	38	.	0			c.C498G						PASS	.	C		2125,1609		595,935,337	134.0	124.0	127.0		498	-2.6	1.0	2	dbSNP_116	127	5907,2289		2134,1639,325	no	coding-synonymous	WDR43	NM_015131.1		2729,2574,662	GG,GC,CC		27.9283,43.0905,32.6739		166/678	29135468	8032,3898	1867	4098	5965	SO:0001819	synonymous_variant	23160	exon4			GAAAGGCGACAAT	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"""WD repeat domain containing"""	28945	protein-coding gene	gene with protein product	"""UTP5, small subunit (SSU) processome component, homolog (yeast)"""					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.498C>G	2.37:g.29135468C>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	220	116	0.527273	NM_015131	Q15395|Q92577	Silent	SNP	ENST00000407426.3	37	CCDS46251.1																																																																																			C|0.293;G|0.707	0.707	strong		0.373	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089	
CCDC94	55702	hgsc.bcm.edu	37	19	4251069	4251069	+	Silent	SNP	T	T	C	rs1045750	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4251069T>C	ENST00000262962.7	+	3	239	c.171T>C	c.(169-171)aaT>aaC	p.N57N		NM_018074.4	NP_060544.2	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94	57								p.N57N(1)		NS(1)|endometrium(1)|lung(2)|ovary(1)|stomach(2)	7				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)		AGAAATTCAATGCTCGGAAGG	0.567													C|||	2385	0.476238	0.7262	0.2795	5008	,	,		18805	0.4464		0.3022	False		,,,				2504	0.4877				p.N57N		Atlas-SNP	.											CCDC94,NS,carcinoma,0,1	CCDC94	28	1	1	Substitution - coding silent(1)	stomach(1)	c.T171C						PASS	.	C		2936,1470	472.4+/-356.4	974,988,241	124.0	121.0	122.0		171	-2.0	0.5	19	dbSNP_86	122	2458,6142	697.2+/-404.9	374,1710,2216	no	coding-synonymous	CCDC94	NM_018074.4		1348,2698,2457	CC,CT,TT		28.5814,33.3636,41.4732		57/324	4251069	5394,7612	2203	4300	6503	SO:0001819	synonymous_variant	55702	exon3			ATTCAATGCTCGG	AK001236	CCDS12124.1	19p13.3	2008-02-05				ENSG00000105248			25518	protein-coding gene	gene with protein product						12477932	Standard	NM_018074		Approved	FLJ10374	uc002lzv.4	Q9BW85		ENST00000262962.7:c.171T>C	19.37:g.4251069T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_018074	O75270|Q9H862|Q9NW16	Silent	SNP	ENST00000262962.7	37	CCDS12124.1																																																																																			T|0.563;C|0.437	0.437	strong		0.567	CCDC94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458007.2	NM_018074	
OTUD3	23252	hgsc.bcm.edu	37	1	20233086	20233086	+	Missense_Mutation	SNP	G	G	A	rs10916668	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:20233086G>A	ENST00000375120.3	+	7	998	c.997G>A	c.(997-999)Gca>Aca	p.A333T		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	333			A -> T (in dbSNP:rs10916668).		protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAAACAAAGCAAATAAAAA	0.478													G|||	252	0.0503195	0.0091	0.1182	5008	,	,		19749	0.0208		0.0567	False		,,,				2504	0.0818				p.A333T		Atlas-SNP	.											OTUD3,NS,carcinoma,-2,1	OTUD3	25	1	0			c.G997A						PASS	.	G	THR/ALA	62,3844		1,60,1892	85.0	85.0	85.0		997	3.7	1.0	1	dbSNP_120	85	514,7752		14,486,3633	yes	missense	OTUD3	NM_015207.1	58	15,546,5525	AA,AG,GG		6.2182,1.5873,4.7322	benign	333/399	20233086	576,11596	1953	4133	6086	SO:0001583	missense	23252	exon7			AACAAAGCAAATA	AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"""OTU domain containing"""	29038	protein-coding gene	gene with protein product		611758	"""OTU domain containing 3"""			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.997G>A	1.37:g.20233086G>A	ENSP00000364261:p.Ala333Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	106	58	0.54717	NM_015207	O75047	Missense_Mutation	SNP	ENST00000375120.3	37	CCDS41279.1	116	0.05311355311355311	4	0.008130081300813009	43	0.11878453038674033	18	0.03146853146853147	51	0.06728232189973615	G	13.74	2.328108	0.41197	0.015873	0.062182	ENSG00000169914	ENST00000375120	T	0.23147	1.92	5.88	3.67	0.42095	.	0.163049	0.53938	D	0.000057	T	0.00241	0.0007	L	0.31752	0.955	0.44048	D	0.996788	B	0.11235	0.004	B	0.10450	0.005	T	0.20672	-1.0268	10	0.19590	T	0.45	.	10.0034	0.41942	0.0855:0.1437:0.7708:0.0	rs10916668;rs52818455;rs57768647;rs10916668	333	Q5T2D3	OTUD3_HUMAN	T	333	ENSP00000364261:A333T	ENSP00000364261:A333T	A	+	1	0	OTUD3	20105673	1.000000	0.71417	0.991000	0.47740	0.704000	0.40688	1.730000	0.38125	1.482000	0.48325	0.650000	0.86243	GCA	G|0.948;A|0.052	0.052	strong		0.478	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1		
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407290	75407290	+	Missense_Mutation	SNP	G	G	A	rs3812629	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:75407290G>A	ENST00000394810.2	-	4	2269	c.2120C>T	c.(2119-2121)cCt>cTt	p.P707L	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.P483L	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	707	Pro-rich.		P -> L (in dbSNP:rs3812629).			cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					AGCCATTGGAGGGGGGGTCTT	0.607													G|||	855	0.170727	0.2073	0.111	5008	,	,		13642	0.1845		0.1332	False		,,,				2504	0.1881				p.P707L		Atlas-SNP	.											SYNPO2L_ENST00000394810,brain,glioma,0,4	SYNPO2L	118	4	0			c.C2120T						PASS	.	G	LEU/PRO,LEU/PRO	848,3558		80,688,1435	57.0	69.0	65.0		2120,1448	4.6	0.9	10	dbSNP_107	65	1281,7319		95,1091,3114	yes	missense,missense	SYNPO2L	NM_001114133.1,NM_024875.3	98,98	175,1779,4549	AA,AG,GG		14.8953,19.2465,16.3694	probably-damaging,probably-damaging	707/978,483/754	75407290	2129,10877	2203	4300	6503	SO:0001583	missense	79933	exon4			ATTGGAGGGGGGG	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.2120C>T	10.37:g.75407290G>A	ENSP00000378289:p.Pro707Leu	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	353	0.16163003663003664	92	0.18699186991869918	40	0.11049723756906077	118	0.2062937062937063	103	0.1358839050131926	G	15.22	2.768581	0.49680	0.192465	0.148953	ENSG00000166317	ENST00000372873;ENST00000394810	T;T	0.24538	1.85;2.15	4.59	4.59	0.56863	.	0.000000	0.46442	D	0.000284	T	0.00039	0.0001	L	0.40543	1.245	0.23138	P	0.99823654	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.02668	-1.1126	9	0.48119	T	0.1	-10.9221	13.0916	0.59169	0.0:0.0:1.0:0.0	rs3812629;rs52807846;rs3812629	707;483	Q9H987;Q9H987-2	SYP2L_HUMAN;.	L	483;707	ENSP00000361964:P483L;ENSP00000378289:P707L	ENSP00000361964:P483L	P	-	2	0	SYNPO2L	75077296	1.000000	0.71417	0.949000	0.38748	0.519000	0.34347	4.478000	0.60230	2.529000	0.85273	0.561000	0.74099	CCT	G|0.841;A|0.159	0.159	strong		0.607	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
NLRC5	84166	hgsc.bcm.edu	37	16	57101373	57101373	+	Missense_Mutation	SNP	A	A	G	rs7185320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57101373A>G	ENST00000262510.6	+	35	4622	c.4397A>G	c.(4396-4398)cAg>cGg	p.Q1466R	NLRC5_ENST00000539144.1_Missense_Mutation_p.Q1437R|NLRC5_ENST00000308149.7_Missense_Mutation_p.Q1437R|NLRC5_ENST00000436936.1_Missense_Mutation_p.Q1466R	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1466			Q -> R (in dbSNP:rs7185320).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GCCAGGCTGCAGCAGCTCAGG	0.592													A|||	448	0.0894569	0.1445	0.0893	5008	,	,		19321	0.1181		0.0646	False		,,,				2504	0.0112				p.Q1466R		Atlas-SNP	.											.	NLRC5	186	.	0			c.A4397G						PASS	.	A	ARG/GLN	549,3847	245.6+/-254.5	33,483,1682	95.0	90.0	92.0		4397	-7.1	0.9	16	dbSNP_116	92	445,8155	134.1+/-191.5	15,415,3870	yes	missense	NLRC5	NM_032206.3	43	48,898,5552	GG,GA,AA		5.1744,12.4886,7.6485	benign	1466/1867	57101373	994,12002	2198	4300	6498	SO:0001583	missense	84166	exon34			GGCTGCAGCAGCT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.4397A>G	16.37:g.57101373A>G	ENSP00000262510:p.Gln1466Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	212	0.09706959706959707	55	0.11178861788617886	30	0.08287292817679558	80	0.13986013986013987	47	0.06200527704485488	A	8.371	0.835258	0.16820	0.124886	0.051744	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	T;T;T;T	0.52057	2.41;2.41;0.68;2.41	4.84	-7.14	0.01527	.	1.182760	0.06591	N	0.752071	T	0.00178	0.0005	N	0.05306	-0.075	0.58432	P	8.000000000008E-6	B	0.12630	0.006	B	0.09377	0.004	T	0.27806	-1.0063	9	0.12766	T	0.61	.	15.6136	0.76748	0.8566:0.0:0.1434:0.0	rs7185320;rs7185320	1466	Q86WI3	NLRC5_HUMAN	R	1466;1437;1466;1437	ENSP00000262510:Q1466R;ENSP00000308886:Q1437R;ENSP00000389739:Q1466R;ENSP00000441727:Q1437R	ENSP00000262510:Q1466R	Q	+	2	0	NLRC5	55658874	0.118000	0.22208	0.865000	0.33974	0.681000	0.39784	-1.372000	0.02570	-1.318000	0.02289	-0.395000	0.06472	CAG	A|0.917;G|0.083	0.083	strong		0.592	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
FAM71F2	346653	hgsc.bcm.edu	37	7	128315791	128315791	+	Silent	SNP	C	C	G	rs61738927	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128315791C>G	ENST00000480462.1	+	2	349	c.243C>G	c.(241-243)gtC>gtG	p.V81V	FAM71F2_ENST00000460349.1_3'UTR|FAM71F2_ENST00000378704.3_Silent_p.V72V|FAM71F2_ENST00000477515.1_Silent_p.V81V			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	81										NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						TCCTCGGGGTCACCTCCTCGG	0.597													.|||	1680	0.335463	0.1959	0.3098	5008	,	,		13009	0.5615		0.2903	False		,,,				2504	0.3558				p.V81V		Atlas-SNP	.											.	FAM71F2	19	.	0			c.C243G						PASS	.	G	,	814,3120		87,640,1240	49.0	51.0	50.0		243,216	1.7	1.0	7	dbSNP_129	50	2477,5833		382,1713,2060	no	coding-synonymous,coding-synonymous	FAM71F2	NM_001012454.3,NM_001128926.1	,	469,2353,3300	GG,GC,CC		29.8075,20.6914,26.8785	,	81/310,72/301	128315791	3291,8953	1967	4155	6122	SO:0001819	synonymous_variant	346653	exon2			CGGGGTCACCTCC	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member B"""	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.243C>G	7.37:g.128315791C>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Silent	SNP	ENST00000480462.1	37	CCDS47701.1																																																																																			C|0.679;G|0.321	0.321	strong		0.597	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
CEP120	153241	hgsc.bcm.edu	37	5	122727026	122727026	+	Silent	SNP	G	G	A	rs6876883	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:122727026G>A	ENST00000306467.5	-	7	1120	c.816C>T	c.(814-816)caC>caT	p.H272H	CEP120_ENST00000328236.5_Silent_p.H272H|CEP120_ENST00000395431.2_Silent_p.H272H|CEP120_ENST00000306481.6_Silent_p.H246H			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	272					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						CACAGCAGAGGTGAATCTAAT	0.368													G|||	2310	0.461262	0.4697	0.4207	5008	,	,		18490	0.506		0.4483	False		,,,				2504	0.4458				p.H272H		Atlas-SNP	.											.	CEP120	72	.	0			c.C816T						PASS	.	G	,	1716,1972		408,900,536	84.0	82.0	82.0		738,816	1.8	1.0	5	dbSNP_116	82	3513,4675		747,2019,1328	no	coding-synonymous,coding-synonymous	CEP120	NM_001166226.1,NM_153223.3	,	1155,2919,1864	AA,AG,GG		42.9043,46.5293,44.03	,	246/961,272/987	122727026	5229,6647	1844	4094	5938	SO:0001819	synonymous_variant	153241	exon8			GCAGAGGTGAATC	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.816C>T	5.37:g.122727026G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Silent	SNP	ENST00000306467.5	37	CCDS4134.2																																																																																			G|0.531;A|0.469	0.469	strong		0.368	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
SPTA1	6708	hgsc.bcm.edu	37	1	158592935	158592935	+	Silent	SNP	G	G	A	rs3753068	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158592935G>A	ENST00000368147.4	-	43	6138	c.5958C>T	c.(5956-5958)ccC>ccT	p.P1986P		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1986					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.P1986P(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAGTGATCTCGGGAAGTCTCT	0.498													G|||	1555	0.310503	0.4387	0.2478	5008	,	,		17157	0.2044		0.3091	False		,,,				2504	0.2924				p.P1986P		Atlas-SNP	.											SPTA1,mouth,carcinoma,0,1	SPTA1	720	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C5958T						PASS	.	G		1561,2283		303,955,664	290.0	291.0	291.0		5958	-9.6	0.0	1	dbSNP_107	291	2386,5880		341,1704,2088	no	coding-synonymous	SPTA1	NM_003126.2		644,2659,2752	AA,AG,GG		28.8652,40.6087,32.5929		1986/2420	158592935	3947,8163	1922	4133	6055	SO:0001819	synonymous_variant	6708	exon43			GATCTCGGGAAGT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5958C>T	1.37:g.158592935G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	209	107	0.511962	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.680;A|0.320	0.320	strong		0.498	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
EGF	1950	hgsc.bcm.edu	37	4	110882051	110882051	+	Silent	SNP	T	T	C	rs11568937	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:110882051T>C	ENST00000265171.5	+	7	1540	c.1095T>C	c.(1093-1095)caT>caC	p.H365H	EGF_ENST00000509793.1_Silent_p.H323H|EGF_ENST00000503392.1_Silent_p.H365H	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	365	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	TTTGGAATCATGGCTGTACTC	0.388													T|||	83	0.0165735	0.0008	0.0216	5008	,	,		19320	0.001		0.0328	False		,,,				2504	0.0337				p.H365H		Atlas-SNP	.											.	EGF	113	.	0			c.T1095C						PASS	.	T	,,	40,4366	43.8+/-77.6	0,40,2163	281.0	244.0	256.0		1095,969,1095	1.0	1.0	4	dbSNP_120	256	296,8304	108.8+/-169.4	5,286,4009	no	coding-synonymous,coding-synonymous,coding-synonymous	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	,,	5,326,6172	CC,CT,TT		3.4419,0.9079,2.5834	,,	365/1167,323/1166,365/1208	110882051	336,12670	2203	4300	6503	SO:0001819	synonymous_variant	1950	exon7			GAATCATGGCTGT	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.1095T>C	4.37:g.110882051T>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	159	67	0.421384	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Silent	SNP	ENST00000265171.5	37	CCDS3689.1																																																																																			T|0.978;C|0.022	0.022	strong		0.388	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		
UPK1A	11045	hgsc.bcm.edu	37	19	36168914	36168914	+	Missense_Mutation	SNP	T	T	C	rs2285421	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36168914T>C	ENST00000222275.2	+	7	770	c.770T>C	c.(769-771)aTg>aCg	p.M257T	UPK1A_ENST00000379013.2_3'UTR	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	257			M -> T (in dbSNP:rs2285421). {ECO:0000269|PubMed:15489334}.		epithelial cell differentiation (GO:0030855)|protein oligomerization (GO:0051259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	monosaccharide binding (GO:0048029)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(2)|stomach(2)	9	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TTCTACACCATGCTCTGAGGG	0.647													C|||	3299	0.658746	0.8359	0.5029	5008	,	,		14729	0.6161		0.5	False		,,,				2504	0.7372				p.M257T		Atlas-SNP	.											.	UPK1A	23	.	0			c.T770C						PASS	.	C	THR/MET	3461,943	337.3+/-304.8	1355,751,96	47.0	49.0	48.0		770	0.5	0.1	19	dbSNP_100	48	4165,4435	555.1+/-386.6	982,2201,1117	yes	missense	UPK1A	NM_007000.2	81	2337,2952,1213	CC,CT,TT		48.4302,21.4124,41.3565	benign	257/259	36168914	7626,5378	2202	4300	6502	SO:0001583	missense	11045	exon7			ACACCATGCTCTG	AF085807	CCDS12470.1, CCDS62640.1	19q13.1	2013-02-14			ENSG00000105668	ENSG00000105668		"""Tetraspanins"""	12577	protein-coding gene	gene with protein product		611557				9846985, 10404304	Standard	NM_007000		Approved	TSPAN21	uc002oaw.3	O00322	OTTHUMG00000048115	ENST00000222275.2:c.770T>C	19.37:g.36168914T>C	ENSP00000222275:p.Met257Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_007000	Q3KNU5|Q3KNU6	Missense_Mutation	SNP	ENST00000222275.2	37	CCDS12470.1	1339	0.6130952380952381	401	0.8150406504065041	188	0.5193370165745856	361	0.6311188811188811	389	0.5131926121372031	C	7.118	0.577334	0.13686	0.785876	0.484302	ENSG00000105668	ENST00000222275	T	0.05025	3.51	5.22	0.485	0.16830	.	.	.	.	.	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	0.11470	-1.0586	8	0.09843	T	0.71	.	4.7632	0.13118	0.1406:0.4845:0.0:0.3749	rs2285421;rs17652127;rs52810906;rs58866560;rs2285421	257	O00322	UPK1A_HUMAN	T	257	ENSP00000222275:M257T	ENSP00000222275:M257T	M	+	2	0	UPK1A	40860754	0.015000	0.18098	0.101000	0.21167	0.255000	0.26057	-0.031000	0.12287	0.085000	0.17107	-0.929000	0.02709	ATG	T|0.391;C|0.609	0.609	strong		0.647	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3		
TPRX1	284355	hgsc.bcm.edu	37	19	48305357	48305357	+	Missense_Mutation	SNP	G	G	A	rs77144450	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48305357G>A	ENST00000322175.3	-	2	1066	c.911C>T	c.(910-912)cCg>cTg	p.P304L	TPRX1_ENST00000535759.1_Missense_Mutation_p.P401L|TPRX1_ENST00000543508.1_Missense_Mutation_p.P294L	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	304	Gly-rich.			P -> L (in Ref. 1; BAC05130). {ECO:0000305}.		nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		gcctAAAATCGGGGCTAGGCC	0.657													G|||	296	0.0591054	0.0008	0.0317	5008	,	,		15558	0.13		0.0408	False		,,,				2504	0.1033				p.P304L	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.C911T						PASS	.	G	LEU/PRO	42,4364	42.3+/-75.8	0,42,2161	25.0	26.0	25.0		911	0.9	0.0	19	dbSNP_131	25	402,8198	123.1+/-182.0	12,378,3910	yes	missense	TPRX1	NM_198479.2	98	12,420,6071	AA,AG,GG		4.6744,0.9532,3.4138	probably-damaging	304/412	48305357	444,12562	2203	4300	6503	SO:0001583	missense	284355	exon2			AAAATCGGGGCTA		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.911C>T	19.37:g.48305357G>A	ENSP00000323455:p.Pro304Leu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	107	0.04899267399267399	0	0.0	14	0.03867403314917127	63	0.11013986013986014	30	0.0395778364116095	g	11.96	1.794615	0.31777	0.009532	0.046744	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	D;D	0.93712	-1.97;-3.27	0.938	0.938	0.19500	.	.	.	.	.	T	0.06371	0.0164	N	0.08118	0	0.80722	P	0.0	P	0.50272	0.933	B	0.26969	0.075	T	0.59537	-0.7436	8	0.59425	D	0.04	.	5.2106	0.15314	0.0:0.0:1.0:0.0	.	304	Q8N7U7	TPRX1_HUMAN	L	304;401;294	ENSP00000323455:P304L;ENSP00000438832:P401L	ENSP00000323455:P304L	P	-	2	0	TPRX1	52997169	0.007000	0.16637	0.001000	0.08648	0.003000	0.03518	0.975000	0.29449	0.811000	0.34303	0.491000	0.48974	CCG	G|0.965;A|0.035	0.035	strong		0.657	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
WNK1	65125	hgsc.bcm.edu	37	12	993930	993930	+	Silent	SNP	C	C	T	rs7300444	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:993930C>T	ENST00000315939.6	+	19	4603	c.3960C>T	c.(3958-3960)aaC>aaT	p.N1320N	WNK1_ENST00000535572.1_Silent_p.N1073N|WNK1_ENST00000530271.2_Silent_p.N1818N|WNK1_ENST00000537687.1_Silent_p.N1580N|WNK1_ENST00000340908.4_Silent_p.N913N	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1320					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)			AAGGACCCAACACAGCACCTC	0.483													T|||	1998	0.398962	0.2685	0.428	5008	,	,		20670	0.5377		0.4404	False		,,,				2504	0.3691				p.N1580N	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C4740T						PASS	.	T	,,,	1307,3099	698.6+/-406.4	187,933,1083	130.0	113.0	119.0		4740,3219,3960,4716	-1.8	0.1	12	dbSNP_116	119	3787,4813	614.3+/-396.2	847,2093,1360	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	,,,	1034,3026,2443	TT,TC,CC		44.0349,29.6641,39.1665	,,,	1580/2643,1073/2135,1320/2383,1572/2635	993930	5094,7912	2203	4300	6503	SO:0001819	synonymous_variant	65125	exon19			ACCCAACACAGCA	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.3960C>T	12.37:g.993930C>T		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	193	192	0.994819	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			C|0.597;T|0.403	0.403	strong		0.483	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
TMCO6	55374	hgsc.bcm.edu	37	5	140021482	140021482	+	Silent	SNP	C	C	T	rs11554680	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140021482C>T	ENST00000394671.3	+	4	443	c.342C>T	c.(340-342)gtC>gtT	p.V114V	TMCO6_ENST00000252100.6_Silent_p.V114V|TMCO6_ENST00000537378.1_Intron|TMCO6_ENST00000511410.1_3'UTR|NDUFA2_ENST00000510680.1_Intron	NM_018502.3	NP_060972.3	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	114					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|urinary_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGACCCTGGTCGGGCTCCTGA	0.637													C|||	1194	0.238419	0.1891	0.2248	5008	,	,		18076	0.2966		0.2455	False		,,,				2504	0.2474				p.V114V		Atlas-SNP	.											TMCO6,NS,carcinoma,+1,1	TMCO6	30	1	0			c.C342T						PASS	.	C		708,3390		72,564,1413	34.0	38.0	37.0		342	-8.4	0.9	5	dbSNP_120	37	2006,6370		247,1512,2429	no	coding-synonymous	TMCO6	NM_018502.3		319,2076,3842	TT,TC,CC		23.9494,17.2767,21.7573		114/494	140021482	2714,9760	2049	4188	6237	SO:0001819	synonymous_variant	55374	exon4			CCTGGTCGGGCTC	BC001910	CCDS4233.2, CCDS75320.1	5q31.3	2008-11-06			ENSG00000113119	ENSG00000113119			28814	protein-coding gene	gene with protein product						12477932	Standard	XM_005268476		Approved	FLJ39769, PRO1580	uc003lgl.3	Q96DC7	OTTHUMG00000129497	ENST00000394671.3:c.342C>T	5.37:g.140021482C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_018502	Q9BUU0|Q9P198	Silent	SNP	ENST00000394671.3	37	CCDS4233.2																																																																																			C|0.757;T|0.243	0.243	strong		0.637	TMCO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251666.2	NM_018502	
MEF2D	4209	hgsc.bcm.edu	37	1	156450740	156450740	+	Silent	SNP	G	G	A	rs1925950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156450740G>A	ENST00000348159.4	-	4	762	c.282C>T	c.(280-282)aaC>aaT	p.N94N	MEF2D_ENST00000340875.5_Intron|MEF2D_ENST00000464356.2_Intron|MEF2D_ENST00000368240.2_Silent_p.N94N|MEF2D_ENST00000353795.3_Intron|MEF2D_ENST00000360595.3_Silent_p.N94N	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	94					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGTCGCAGCCGTTGAAGCCCT	0.672											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2866	0.572284	0.2368	0.5951	5008	,	,		14671	0.756		0.673	False		,,,				2504	0.7168				p.N94N		Atlas-SNP	.											.	MEF2D	43	.	0			c.C282T						PASS	.	G		1385,3021	437.0+/-344.8	237,911,1055	79.0	88.0	85.0		282	-1.4	1.0	1	dbSNP_92	85	5655,2941	642.9+/-399.9	1854,1947,497	no	coding-synonymous	MEF2D	NM_005920.2		2091,2858,1552	AA,AG,GG		34.2136,31.4344,45.8545		94/522	156450740	7040,5962	2203	4298	6501	SO:0001819	synonymous_variant	4209	exon4			GCAGCCGTTGAAG	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.282C>T	1.37:g.156450740G>A		Somatic	103	0	0	1778	WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	37	CCDS1143.1																																																																																			G|0.452;A|0.548	0.548	strong		0.672	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
TMF1	7110	hgsc.bcm.edu	37	3	69082708	69082708	+	Missense_Mutation	SNP	C	C	G	rs1532918	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:69082708C>G	ENST00000398559.2	-	10	2608	c.2392G>C	c.(2392-2394)Gat>Cat	p.D798H	TMF1_ENST00000543976.1_Missense_Mutation_p.D801H|CTD-2013N24.2_ENST00000598783.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000599467.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000596274.1_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000597366.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	798			D -> H (in dbSNP:rs1532918).		acrosome assembly (GO:0001675)|cellular response to organic cyclic compound (GO:0071407)|defense response to bacterium (GO:0042742)|Leydig cell differentiation (GO:0033327)|luteinizing hormone secretion (GO:0032275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|positive regulation of cytokine production (GO:0001819)|positive regulation of testosterone secretion (GO:2000845)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of transcription, DNA-templated (GO:0006355)|sperm motility (GO:0030317)|spermatid nucleus differentiation (GO:0007289)|transcription from RNA polymerase II promoter (GO:0006366)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription cofactor activity (GO:0003712)			cervix(1)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Lung NSC(201;0.0193)|Prostate(884;0.174)		BRCA - Breast invasive adenocarcinoma(55;4.48e-05)|Epithelial(33;0.000274)|LUSC - Lung squamous cell carcinoma(21;0.0123)|KIRC - Kidney renal clear cell carcinoma(39;0.211)|Kidney(39;0.247)		CCAAGCCTATCAGAAAGATTC	0.363													C|||	285	0.0569089	0.0113	0.0764	5008	,	,		15443	0.001		0.1521	False		,,,				2504	0.0644				p.D798H		Atlas-SNP	.											.	TMF1	77	.	0			c.G2392C						PASS	.	C	HIS/ASP	86,3560		1,84,1738	118.0	112.0	114.0		2392	5.8	1.0	3	dbSNP_88	114	1213,6943		97,1019,2962	yes	missense	TMF1	NM_007114.2	81	98,1103,4700	GG,GC,CC		14.8725,2.3587,11.0066	probably-damaging	798/1094	69082708	1299,10503	1823	4078	5901	SO:0001583	missense	7110	exon10			GCCTATCAGAAAG		CCDS43105.1	3p21-p12	2009-02-11			ENSG00000144747	ENSG00000144747			11870	protein-coding gene	gene with protein product		601126				1409643	Standard	NM_007114		Approved	ARA160, TMF	uc003dnn.3	P82094	OTTHUMG00000158771	ENST00000398559.2:c.2392G>C	3.37:g.69082708C>G	ENSP00000381567:p.Asp798His	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	37	CCDS43105.1	156	0.07142857142857142	6	0.012195121951219513	30	0.08287292817679558	0	0.0	120	0.158311345646438	C	27.0	4.790972	0.90367	0.023587	0.148725	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248	T;T	0.19394	2.15;2.15	5.83	5.83	0.93111	.	0.134289	0.64402	D	0.000003	T	0.00241	0.0007	L	0.60455	1.87	0.09310	P	0.999999999219925	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.979	T	0.00002	-1.2649	9	0.72032	D	0.01	-14.6947	20.1338	0.98010	0.0:1.0:0.0:0.0	rs1532918;rs11557641;rs17330362;rs52791053;rs56563580;rs1532918	801;798	P82094-2;P82094	.;TMF1_HUMAN	H	798;801;714	ENSP00000381567:D798H;ENSP00000438706:D801H	ENSP00000348582:D714H	D	-	1	0	TMF1	69165398	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.786000	0.85741	2.770000	0.95276	0.655000	0.94253	GAT	C|0.912;G|0.088	0.088	strong		0.363	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114	
CENPI	2491	hgsc.bcm.edu	37	X	100395663	100395663	+	Silent	SNP	G	G	T	rs2273380	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:100395663G>T	ENST00000372927.1	+	15	1756	c.1479G>T	c.(1477-1479)gtG>gtT	p.V493V	CENPI_ENST00000218507.5_Silent_p.V493V|CENPI_ENST00000423383.1_Silent_p.V493V|CENPI_ENST00000372926.1_Silent_p.V493V	NM_006733.2	NP_006724.2	Q92674	CENPI_HUMAN	centromere protein I	493					CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)|sex differentiation (GO:0007548)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(19)|prostate(1)|skin(2)	30						AGTGTAGTGTGCTTCAGAGTC	0.393													T|||	1238	0.327947	0.3472	0.2061	3775	,	,		14673	0.1994		0.1769	False		,,,				2504	0.2628				p.V493V		Atlas-SNP	.											.	CENPI	70	.	0			c.G1479T						PASS	.	T		1584,2251		266,800,252,566,319	224.0	211.0	215.0		1479	4.3	1.0	X	dbSNP_100	215	1659,5069		146,913,454,1369,1418	no	coding-synonymous	CENPI	NM_006733.2		412,1713,706,1935,1737	TT,TG,T,GG,G		24.6581,41.3038,30.7015		493/757	100395663	3243,7320	2203	4300	6503	SO:0001819	synonymous_variant	2491	exon15			TAGTGTGCTTCAG	X97249	CCDS14479.1	Xq22.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000102384	ENSG00000102384			3968	protein-coding gene	gene with protein product		300065	"""FSH primary response (LRPR1, rat) homolog 1"", ""FSH primary response (LRPR1 homolog, rat) 1"""	FSHPRH1		16622420	Standard	NM_006733		Approved	LRPR1, CENP-I, Mis6	uc004egx.3	Q92674	OTTHUMG00000022018	ENST00000372927.1:c.1479G>T	X.37:g.100395663G>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	134	39	0.291045	NM_006733	Q5JWZ9|Q96ED0	Silent	SNP	ENST00000372927.1	37	CCDS14479.1																																																																																			G|0.697;0|0.002	.	strong		0.393	CENPI-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057519.1	NM_006733	
ESR1	2099	hgsc.bcm.edu	37	6	152129077	152129077	+	Silent	SNP	T	T	C	rs2077647	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152129077T>C	ENST00000206249.3	+	1	392	c.30T>C	c.(28-30)tcT>tcC	p.S10S	ESR1_ENST00000406599.1_Silent_p.S10S|ESR1_ENST00000440973.1_Silent_p.S10S|ESR1_ENST00000338799.5_Silent_p.S10S|ESR1_ENST00000456483.2_Silent_p.S10S|ESR1_ENST00000427531.2_5'Flank|ESR1_ENST00000443427.1_Silent_p.S10S	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	10	Modulating (transactivation AF-1); mediates interaction with MACROD1.				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)	CCAAAGCATCTGGGATGGCCC	0.667													C|||	2336	0.466454	0.5212	0.4654	5008	,	,		14556	0.378		0.4414	False		,,,				2504	0.5102				p.S10S		Atlas-SNP	.											.	ESR1	94	.	0			c.T30C						PASS	.	C	,,,	2127,2279	583.6+/-385.9	519,1089,595	35.0	33.0	34.0		30,30,30,30	-6.6	0.0	6	dbSNP_96	34	4101,4499	579.7+/-390.9	1006,2089,1205	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR1	NM_000125.3,NM_001122740.1,NM_001122741.1,NM_001122742.1	,,,	1525,3178,1800	CC,CT,TT		47.686,48.2751,47.8856	,,,	10/596,10/596,10/596,10/596	152129077	6228,6778	2203	4300	6503	SO:0001819	synonymous_variant	2099	exon1			AGCATCTGGGATG	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.30T>C	6.37:g.152129077T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1																																																																																			T|0.538;C|0.462	0.462	strong		0.667	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
PXK	54899	hgsc.bcm.edu	37	3	58395863	58395863	+	Missense_Mutation	SNP	A	A	G	rs56384862	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:58395863A>G	ENST00000356151.2	+	16	1551	c.1442A>G	c.(1441-1443)aAg>aGg	p.K481R	PXK_ENST00000479241.1_Missense_Mutation_p.K464R|PXK_ENST00000484288.1_Missense_Mutation_p.K481R|PXK_ENST00000536660.1_Missense_Mutation_p.K344R|PXK_ENST00000383716.3_Missense_Mutation_p.K448R|PXK_ENST00000463280.1_Missense_Mutation_p.K448R|PXK_ENST00000302779.5_Missense_Mutation_p.K464R|PXK_ENST00000383715.4_Missense_Mutation_p.K464R	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		CATTCAGCGAAGTACAGCAAC	0.428													A|||	888	0.177316	0.1112	0.2767	5008	,	,		18559	0.001		0.3777	False		,,,				2504	0.1718				p.K481R		Atlas-SNP	.											PXK_ENST00000356151,NS,carcinoma,0,1	PXK	89	1	0			c.A1442G						PASS	.	A	ARG/LYS	580,3826	256.7+/-261.4	39,502,1662	88.0	82.0	84.0		1442	5.9	1.0	3	dbSNP_129	84	3205,5395	483.2+/-371.1	614,1977,1709	yes	missense	PXK	NM_017771.3	26	653,2479,3371	GG,GA,AA		37.2674,13.1639,29.102	benign	481/579	58395863	3785,9221	2203	4300	6503	SO:0001583	missense	54899	exon16			CAGCGAAGTACAG	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.1442A>G	3.37:g.58395863A>G	ENSP00000348472:p.Lys481Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	NM_017771		Missense_Mutation	SNP	ENST00000356151.2	37	CCDS2889.1	445|445	0.20375457875457875|0.20375457875457875	65|65	0.13211382113821138|0.13211382113821138	107|107	0.2955801104972376|0.2955801104972376	0|0	0.0|0.0	273|273	0.36015831134564646|0.36015831134564646	A|A	14.95|14.95	2.689584|2.689584	0.48097|0.48097	0.131639|0.131639	0.372674|0.372674	ENSG00000168297|ENSG00000168297	ENST00000356151;ENST00000302779;ENST00000383716;ENST00000463280;ENST00000383715;ENST00000484288;ENST00000479241;ENST00000536660;ENST00000493474|ENST00000479134;ENST00000495557	T;T;T;T;T;T;T;T;T|.	0.57752|.	1.94;1.94;1.94;1.49;1.49;1.49;1.46;2.14;0.38|.	5.9|5.9	5.9|5.9	0.94986|0.94986	Protein kinase, catalytic domain (1);|.	0.291482|.	0.37623|.	N|.	0.002018|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.41236|0.41236	1.265|1.265	0.24800|0.24800	P|P	0.9927006|0.9927006	B;B;B;B;B|.	0.24618|.	0.107;0.001;0.001;0.003;0.0|.	B;B;B;B;B|.	0.18263|.	0.021;0.003;0.001;0.003;0.003|.	T|T	0.35649|0.35649	-0.9780|-0.9780	9|4	0.33141|.	T|.	0.24|.	-8.3281|-8.3281	14.9448|14.9448	0.71023|0.71023	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs56384862;rs62258125|rs56384862;rs62258125	448;448;481;464;481|.	E9PD56;Q7Z7A4-6;Q7Z7A4;Q7Z7A4-4;Q7Z7A4-2|.	.;.;PXK_HUMAN;.;.|.	R|G	481;464;448;448;464;481;464;344;17|236;53	ENSP00000348472:K481R;ENSP00000305045:K464R;ENSP00000373222:K448R;ENSP00000417903:K448R;ENSP00000373221:K464R;ENSP00000417915:K481R;ENSP00000419049:K464R;ENSP00000438356:K344R;ENSP00000418836:K17R|.	ENSP00000305045:K464R|.	K|S	+|+	2|1	0|0	PXK|PXK	58370903|58370903	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.963000|0.963000	0.63663|0.63663	4.760000|4.760000	0.62235|0.62235	2.268000|2.268000	0.75426|0.75426	0.519000|0.519000	0.50382|0.50382	AAG|AGT	A|0.717;G|0.283	0.283	strong		0.428	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771	
ZNF385C	201181	hgsc.bcm.edu	37	17	40189830	40189830	+	Silent	SNP	C	C	T	rs60110245	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40189830C>T	ENST00000436535.3	-	2	324	c.324G>A	c.(322-324)ccG>ccA	p.P108P	CTD-2132N18.2_ENST00000587304.1_RNA|CTD-2132N18.4_ENST00000602842.1_RNA			Q66K41	Z385C_HUMAN	zinc finger protein 385C	27						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				TGAAGTCCAGCGGGGGCTGCA	0.706													C|||	459	0.0916534	0.2103	0.0562	5008	,	,		12615	0.0268		0.0934	False		,,,				2504	0.0215				p.P29P		Atlas-SNP	.											.	ZNF385C	7	.	0			c.G87A						PASS	.																																			SO:0001819	synonymous_variant	201181	exon2			GTCCAGCGGGGGC	BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595			33722	protein-coding gene	gene with protein product							Standard	NM_001242704		Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.324G>A	17.37:g.40189830C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_001242704	Q4G0J1	Silent	SNP	ENST00000436535.3	37																																																																																				C|0.898;T|0.102	0.102	strong		0.706	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000347740.3	NM_001013624	
RPP38	10557	hgsc.bcm.edu	37	10	15145948	15145948	+	Missense_Mutation	SNP	T	T	C	rs10242	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:15145948T>C	ENST00000378197.4	+	3	1149	c.635T>C	c.(634-636)aTt>aCt	p.I212T	RPP38_ENST00000378202.5_Missense_Mutation_p.I212T|NMT2_ENST00000466201.1_Intron|RPP38_ENST00000451677.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	212			I -> T (in dbSNP:rs10242).		RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)	8						CAAGACAGAATTGAAGATTCT	0.438													T|||	73	0.0145767	0.0038	0.0245	5008	,	,		19247	0.0		0.0427	False		,,,				2504	0.0082				p.I212T	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.T635C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE	21,4385	27.2+/-55.0	0,21,2182	66.0	69.0	68.0		635,635,635	-5.2	0.0	10	dbSNP_52	68	247,8353	98.6+/-160.1	3,241,4056	yes	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	89,89,89	3,262,6238	CC,CT,TT		2.8721,0.4766,2.0606	benign,benign,benign	212/284,212/284,212/284	15145948	268,12738	2203	4300	6503	SO:0001583	missense	10557	exon2			ACAGAATTGAAGA	U77664	CCDS7108.1	10p13	2012-05-21			ENSG00000152464	ENSG00000152464			30329	protein-coding gene	gene with protein product		606116				9037013, 9630247	Standard	NM_183005		Approved		uc001inx.5	P78345	OTTHUMG00000017728	ENST00000378197.4:c.635T>C	10.37:g.15145948T>C	ENSP00000367439:p.Ile212Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	37	CCDS7108.1	49	0.022435897435897436	5	0.01016260162601626	12	0.03314917127071823	0	0.0	32	0.04221635883905013	T	0.006	-2.026492	0.00414	0.004766	0.028721	ENSG00000152464	ENST00000378203;ENST00000378202;ENST00000378197	T;T;T	0.08546	3.08;3.08;3.08	5.35	-5.15	0.02866	.	0.941611	0.08925	N	0.873875	T	0.00440	0.0014	N	0.00289	-1.7	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	10	0.02654	T	1	-0.5777	15.1003	0.72269	0.0:0.5549:0.0:0.4451	rs10242;rs61037821;rs10242	212	P78345	RPP38_HUMAN	T	212	ENSP00000367445:I212T;ENSP00000367444:I212T;ENSP00000367439:I212T	ENSP00000367439:I212T	I	+	2	0	RPP38	15185954	0.000000	0.05858	0.000000	0.03702	0.263000	0.26337	-0.010000	0.12743	-0.767000	0.04633	-0.936000	0.02699	ATT	T|0.978;C|0.022	0.022	strong		0.438	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
RYR1	6261	hgsc.bcm.edu	37	19	38994910	38994910	+	Silent	SNP	G	G	A	rs2229144	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38994910G>A	ENST00000359596.3	+	50	7977	c.7977G>A	c.(7975-7977)acG>acA	p.T2659T	RYR1_ENST00000360985.3_Silent_p.T2659T|RYR1_ENST00000355481.4_Silent_p.T2659T			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2659	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.T2659T(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GCCTACCCACGGGCTGGGCCA	0.587													A|||	2065	0.41234	0.5182	0.3689	5008	,	,		17530	0.3532		0.2982	False		,,,				2504	0.4785				p.T2659T		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	1	1	Substitution - coding silent(1)	stomach(1)	c.G7977A						PASS	.	A	,	2016,2390	613.2+/-392.1	457,1102,644	75.0	63.0	67.0		7977,7977	-7.9	0.3	19	dbSNP_98	67	2140,6460	715.0+/-406.0	286,1568,2446	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	743,2670,3090	AA,AG,GG		24.8837,45.7558,31.9545	,	2659/5039,2659/5034	38994910	4156,8850	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon50			ACCCACGGGCTGG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.7977G>A	19.37:g.38994910G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			G|0.657;A|0.343	0.343	strong		0.587	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
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 GAIIx	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_ENST00000391773.1_Silent_p.L323L|NLRP12_ENST00000391775.3_Silent_p.L323L|NLRP12_ENST00000391772.1_Silent_p.L323L|NLRP12_ENST00000351894.4_Silent_p.L323L|NLRP12_ENST00000354278.3_Silent_p.L323L|NLRP12_ENST00000535162.1_Silent_p.L323L|NLRP12_ENST00000345770.5_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		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	27	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	
ADAMTS4	9507	hgsc.bcm.edu	37	1	161168189	161168189	+	Missense_Mutation	SNP	C	C	T	rs34448954	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161168189C>T	ENST00000367996.5	-	1	657	c.229G>A	c.(229-231)Gcc>Acc	p.A77T	ADAMTS4_ENST00000478394.1_5'Flank|ADAMTS4_ENST00000367995.3_Missense_Mutation_p.A77T|NDUFS2_ENST00000367993.3_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	77			A -> T (in dbSNP:rs34448954). {ECO:0000269|PubMed:9734811}.		defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	CTGGCAGGGGCGCCCGAGCCA	0.677													C|||	257	0.0513179	0.0068	0.0418	5008	,	,		15569	0.0099		0.1113	False		,,,				2504	0.0992				p.A77T		Atlas-SNP	.											ADAMTS4_ENST00000367996,rectum,carcinoma,0,2	ADAMTS4	171	2	0			c.G229A						PASS	.	C	THR/ALA	82,4276		4,74,2101	12.0	12.0	12.0		229	-6.9	0.0	1	dbSNP_126	12	831,7711		48,735,3488	yes	missense	ADAMTS4	NM_005099.4	58	52,809,5589	TT,TC,CC		9.7284,1.8816,7.0775	benign	77/838	161168189	913,11987	2179	4271	6450	SO:0001583	missense	9507	exon1			CAGGGGCGCCCGA	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.229G>A	1.37:g.161168189C>T	ENSP00000356975:p.Ala77Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	117	0.05357142857142857	7	0.014227642276422764	17	0.04696132596685083	6	0.01048951048951049	87	0.11477572559366754	C	11.17	1.560306	0.27827	0.018816	0.097284	ENSG00000158859	ENST00000367996;ENST00000367995	T;T	0.07021	3.23;3.23	5.48	-6.94	0.01633	Peptidase M12B, propeptide (1);	1.266050	0.05430	N	0.545706	T	0.00936	0.0031	N	0.08118	0	0.09310	N	0.999995	B;B	0.22346	0.004;0.068	B;B	0.27887	0.003;0.084	T	0.47018	-0.9149	10	0.28530	T	0.3	.	2.4191	0.04444	0.4451:0.2678:0.082:0.2051	rs34448954	77;77	Q5VTW1;O75173	.;ATS4_HUMAN	T	77	ENSP00000356975:A77T;ENSP00000356974:A77T	ENSP00000356974:A77T	A	-	1	0	ADAMTS4	159434813	0.000000	0.05858	0.000000	0.03702	0.828000	0.46876	-1.501000	0.02281	-0.961000	0.03609	0.491000	0.48974	GCC	C|0.946;T|0.054	0.054	strong		0.677	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099	
LY6D	8581	hgsc.bcm.edu	37	8	143867905	143867905	+	Missense_Mutation	SNP	C	C	T	rs2572925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143867905C>T	ENST00000301263.4	-	1	103	c.28G>A	c.(28-30)Gcc>Acc	p.A10T	LY6D_ENST00000518434.1_5'UTR|RP11-706C16.8_ENST00000510610.2_RNA	NM_003695.2	NP_003686.1	Q14210	LY6D_HUMAN	lymphocyte antigen 6 complex, locus D	10			A -> T (in dbSNP:rs2572925). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9366413}.		cell adhesion (GO:0007155)|lymphocyte differentiation (GO:0030098)|response to stilbenoid (GO:0035634)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|membrane (GO:0016020)|plasma membrane (GO:0005886)				large_intestine(1)|lung(3)|prostate(1)	5	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					ACAGCCAGGGCTGCAAGGAGC	0.662													C|||	1812	0.361821	0.4841	0.4049	5008	,	,		226	0.1865		0.3996	False		,,,				2504	0.3078				p.A10T		Atlas-SNP	.											.	LY6D	10	.	0			c.G28A						PASS	.	C	THR/ALA	1754,2194		417,920,637	16.0	14.0	15.0		28	-0.7	0.0	8	dbSNP_100	15	2774,4930		553,1668,1631	yes	missense	LY6D	NM_003695.2	58	970,2588,2268	TT,TC,CC		36.0073,44.4276,38.8603	possibly-damaging	10/129	143867905	4528,7124	1974	3852	5826	SO:0001583	missense	8581	exon1			CCAGGGCTGCAAG	U66837	CCDS6390.1	8q24	2004-07-06			ENSG00000167656	ENSG00000167656			13348	protein-coding gene	gene with protein product		606204				7790363, 9551972	Standard	NM_003695		Approved	E48	uc003yxf.1	Q14210	OTTHUMG00000164693	ENST00000301263.4:c.28G>A	8.37:g.143867905C>T	ENSP00000301263:p.Ala10Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	117	60	0.512821	NM_003695	B2R5F1|D3DWJ0|O43783|Q6GTV9|Q8TBD4|Q92933	Missense_Mutation	SNP	ENST00000301263.4	37	CCDS6390.1	784	0.358974358974359	235	0.47764227642276424	130	0.35911602209944754	129	0.22552447552447552	290	0.38258575197889183	c	7.205	0.594206	0.13875	0.444276	0.360073	ENSG00000167656	ENST00000301263	T	0.26518	1.73	3.32	-0.69	0.11309	.	2.614030	0.02032	N	0.048634	T	0.00012	0.0000	M	0.65498	2.005	0.80722	P	0.0	P	0.37525	0.598	B	0.34301	0.179	T	0.44205	-0.9343	9	0.30078	T	0.28	-8.6153	8.2882	0.31941	0.0:0.5788:0.0:0.4212	rs2572925;rs11553465;rs17852948;rs57621469;rs2572925	10	Q14210	LY6D_HUMAN	T	10	ENSP00000301263:A10T	ENSP00000301263:A10T	A	-	1	0	LY6D	143864907	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.314000	0.01125	-0.442000	0.07190	-1.688000	0.00730	GCC	C|0.637;T|0.363	0.363	strong		0.662	LY6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379774.1	NM_003695	
CCDC13	152206	hgsc.bcm.edu	37	3	42787469	42787469	+	Silent	SNP	A	A	G	rs2240859	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42787469A>G	ENST00000310232.6	-	7	854	c.771T>C	c.(769-771)tcT>tcC	p.S257S	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	257										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TCCCTGGCGAAGATAGGAGCT	0.512													G|||	2511	0.501398	0.5439	0.402	5008	,	,		18576	0.4534		0.4592	False		,,,				2504	0.6074				p.S257S		Atlas-SNP	.											.	CCDC13	71	.	0			c.T771C						PASS	.	G		2397,2009	561.2+/-380.7	650,1097,456	93.0	90.0	91.0		771	2.1	0.9	3	dbSNP_98	91	3943,4657	602.8+/-394.6	898,2147,1255	yes	coding-synonymous	CCDC13	NM_144719.3		1548,3244,1711	GG,GA,AA		45.8488,45.5969,48.7467		257/716	42787469	6340,6666	2203	4300	6503	SO:0001819	synonymous_variant	152206	exon7			TGGCGAAGATAGG	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.771T>C	3.37:g.42787469A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_144719		Silent	SNP	ENST00000310232.6	37	CCDS2705.1																																																																																			A|0.512;G|0.488	0.488	strong		0.512	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
RSPH4A	345895	hgsc.bcm.edu	37	6	116938232	116938232	+	Missense_Mutation	SNP	C	C	G	rs13213314	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:116938232C>G	ENST00000229554.5	+	1	583	c.446C>G	c.(445-447)aCc>aGc	p.T149S	RSPH4A_ENST00000368581.4_Missense_Mutation_p.T149S|RSPH4A_ENST00000368580.4_Missense_Mutation_p.T149S	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	149			T -> S (in dbSNP:rs13213314).		axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						GAAGGAAACACCTTTCAACAG	0.453									Kartagener syndrome				C|||	186	0.0371406	0.0091	0.049	5008	,	,		21180	0.0		0.1292	False		,,,				2504	0.0102				p.T149S		Atlas-SNP	.											.	RSPH4A	54	.	0			c.C446G						PASS	.	C	SER/THR,SER/THR	118,4288	88.2+/-126.9	3,112,2088	127.0	126.0	126.0		446,446	2.8	0.0	6	dbSNP_121	126	1056,7544	223.1+/-260.0	58,940,3302	yes	missense,missense	RSPH4A	NM_001010892.2,NM_001161664.1	58,58	61,1052,5390	GG,GC,CC		12.2791,2.6782,9.0266	benign,benign	149/717,149/601	116938232	1174,11832	2203	4300	6503	SO:0001583	missense	345895	exon1	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GAAACACCTTTCA		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"""radial spokehead-like 3"""	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.446C>G	6.37:g.116938232C>G	ENSP00000229554:p.Thr149Ser	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	156	60	0.384615	NM_001161664	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	128	0.05860805860805861	9	0.018292682926829267	19	0.052486187845303865	0	0.0	100	0.13192612137203166	C	6.816	0.519696	0.13005	0.026782	0.122791	ENSG00000111834	ENST00000368581;ENST00000229554;ENST00000368580	T;T;T	0.64438	-0.1;1.54;1.51	5.53	2.84	0.33178	.	1.282210	0.05002	N	0.469321	T	0.23572	0.0570	L	0.27053	0.805	0.80722	P	0.0	B;B	0.11235	0.004;0.001	B;B	0.10450	0.005;0.002	T	0.06570	-1.0819	9	0.14656	T	0.56	0.5597	5.8791	0.18846	0.0:0.6759:0.1572:0.167	rs13213314;rs52838245;rs13213314	149;149	Q5TD94-3;Q5TD94	.;RSH4A_HUMAN	S	149	ENSP00000357570:T149S;ENSP00000229554:T149S;ENSP00000357569:T149S	ENSP00000229554:T149S	T	+	2	0	RSPH4A	117044925	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.850000	0.04317	0.465000	0.27167	-0.121000	0.15023	ACC	C|0.925;G|0.075	0.075	strong		0.453	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	
GALR3	8484	hgsc.bcm.edu	37	22	38221141	38221141	+	Silent	SNP	C	C	T	rs117618411	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:38221141C>T	ENST00000249041.2	+	2	796	c.771C>T	c.(769-771)tgC>tgT	p.C257C		NM_003614.1	NP_003605.1	O60755	GALR3_HUMAN	galanin receptor 3	257					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|learning or memory (GO:0007611)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|peptide hormone binding (GO:0017046)			endometrium(1)|liver(2)|lung(1)	4	Melanoma(58;0.045)					TCATCCTGTGCTTCTGGTACG	0.736													C|||	60	0.0119808	0.0008	0.0159	5008	,	,		5587	0.0		0.0457	False		,,,				2504	0.002				p.C257C		Atlas-SNP	.											.	GALR3	12	.	0			c.C771T						PASS	.	C		27,3731		0,27,1852	12.0	10.0	11.0		771	2.8	1.0	22	dbSNP_132	11	244,7004		7,230,3387	no	coding-synonymous	GALR3	NM_003614.1		7,257,5239	TT,TC,CC		3.3664,0.7185,2.4623		257/369	38221141	271,10735	1879	3624	5503	SO:0001819	synonymous_variant	8484	exon2			CCTGTGCTTCTGG	AF073799	CCDS13958.1	22q113.1	2012-08-08			ENSG00000128310	ENSG00000128310		"""GPCR / Class A : Galanin receptors"""	4134	protein-coding gene	gene with protein product		603692				9722565, 9832121	Standard	NM_003614		Approved		uc003aub.1	O60755	OTTHUMG00000150658	ENST00000249041.2:c.771C>T	22.37:g.38221141C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_003614	Q53YJ4	Silent	SNP	ENST00000249041.2	37	CCDS13958.1																																																																																			C|0.975;T|0.025	0.025	strong		0.736	GALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319452.1		
SNRNP70	6625	hgsc.bcm.edu	37	19	49611319	49611319	+	Silent	SNP	C	C	T	rs1058882	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49611319C>T	ENST00000598441.1	+	10	1157	c.933C>T	c.(931-933)ggC>ggT	p.G311G	SNRNP70_ENST00000221448.5_Silent_p.G302G			P08621	RU17_HUMAN	small nuclear ribonucleoprotein 70kDa (U1)	311	Poly-Gly.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	12						AGCTGCGTGGCGGCGGTGGCG	0.751													C|||	836	0.166933	0.0537	0.1499	5008	,	,		10446	0.0575		0.2962	False		,,,				2504	0.3119				p.G311G		Atlas-SNP	.											SNRNP70,NS,carcinoma,0,1	SNRNP70	30	1	0			c.C933T						PASS	.	C		302,3788		22,258,1765	6.0	10.0	9.0		933	-7.3	0.0	19	dbSNP_86	9	2319,5669		375,1569,2050	no	coding-synonymous	SNRNP70	NM_003089.4		397,1827,3815	TT,TC,CC		29.031,7.3839,21.7006		311/438	49611319	2621,9457	2045	3994	6039	SO:0001819	synonymous_variant	6625	exon10			GCGTGGCGGCGGT		CCDS12756.1, CCDS74417.1	19q13.3	2013-02-12	2008-10-29	2008-10-29		ENSG00000104852		"""RNA binding motif (RRM) containing"""	11150	protein-coding gene	gene with protein product		180740	"""small nuclear ribonucleoprotein 70kDa (RNP antigen)"""	RNPU1Z, RPU1, SNRP70			Standard	XM_005259177		Approved	U1-70K, Snp1	uc021uxh.1	P08621		ENST00000598441.1:c.933C>T	19.37:g.49611319C>T		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_003089	B3KUA3|P78493|P78494|Q15364|Q15686|Q15687|Q15689|Q99377|Q9UE45|Q9UE46|Q9UE47|Q9UE48|Q9UFQ6	Silent	SNP	ENST00000598441.1	37	CCDS12756.1																																																																																			C|0.830;T|0.170	0.170	strong		0.751	SNRNP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466266.1	NM_003089	
CCNG2	901	hgsc.bcm.edu	37	4	78079772	78079772	+	Silent	SNP	G	G	A	rs4150052	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:78079772G>A	ENST00000316355.5	+	2	443	c.87G>A	c.(85-87)gaG>gaA	p.E29E	CCNG2_ENST00000502280.1_Silent_p.E29E|CCNG2_ENST00000509972.1_Silent_p.E29E|CCNG2_ENST00000354403.5_Silent_p.E29E|CCNG2_ENST00000497512.1_3'UTR|CCNG2_ENST00000395640.1_Silent_p.E29E	NM_004354.2	NP_004345.1	Q16589	CCNG2_HUMAN	cyclin G2	29					cell cycle checkpoint (GO:0000075)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						AACAAGAAGAGAGATTCCAAC	0.498													G|||	360	0.071885	0.1195	0.0447	5008	,	,		16828	0.0357		0.0716	False		,,,				2504	0.0644				p.E29E		Atlas-SNP	.											.	CCNG2	27	.	0			c.G87A						PASS	.	G		510,3896	234.2+/-247.1	26,458,1719	112.0	112.0	112.0		87	4.7	1.0	4	dbSNP_110	112	701,7899	173.9+/-224.3	25,651,3624	no	coding-synonymous	CCNG2	NM_004354.2		51,1109,5343	AA,AG,GG		8.1512,11.5751,9.3111		29/345	78079772	1211,11795	2203	4300	6503	SO:0001819	synonymous_variant	901	exon2			AGAAGAGAGATTC	BC032518	CCDS3581.1	4q21.22	2009-05-07			ENSG00000138764	ENSG00000138764			1593	protein-coding gene	gene with protein product		603203				8806701	Standard	NM_004354		Approved		uc003hkq.4	Q16589	OTTHUMG00000130100	ENST00000316355.5:c.87G>A	4.37:g.78079772G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_004354	B4DF25|Q6FGA7|Q6FGC6	Silent	SNP	ENST00000316355.5	37	CCDS3581.1																																																																																			G|0.914;A|0.086	0.086	strong		0.498	CCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252404.3	NM_004354	
NKX2-6	137814	hgsc.bcm.edu	37	8	23563908	23563908	+	Silent	SNP	A	A	G	rs61732911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:23563908A>G	ENST00000325017.3	-	1	203	c.204T>C	c.(202-204)gaT>gaC	p.D68D	NKX2-6_ENST00000418222.1_5'UTR|RP11-175E9.1_ENST00000523874.1_RNA	NM_001136271.2	NP_001129743.2	A6NCS4	NKX26_HUMAN	NK2 homeobox 6	68					atrial cardiac muscle cell development (GO:0055014)|cell differentiation (GO:0030154)|digestive tract development (GO:0048565)|embryonic heart tube development (GO:0035050)|hypothalamus development (GO:0021854)|negative regulation of apoptotic process (GO:0043066)|pericardium development (GO:0060039)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCTCCGAACCATCCAGCTTTC	0.617													G|||	835	0.166733	0.0666	0.2003	5008	,	,		13859	0.2044		0.2048	False		,,,				2504	0.2004				p.D68D		Atlas-SNP	.											.	NKX2-6	6	.	0			c.T204C						PASS	.	G		124,1260		6,112,574	29.0	33.0	32.0			-10.3	0.0	8	dbSNP_129	32	652,2530		60,532,999	no	utr-5	NKX2-6	NM_001136271.2		66,644,1573	GG,GA,AA		20.4903,8.9595,16.9952			23563908	776,3790	692	1591	2283	SO:0001819	synonymous_variant	137814	exon1			CGAACCATCCAGC	CN272646		8p21.2	2012-03-09	2011-06-01			ENSG00000180053		"""Homeoboxes / ANTP class : NKL subclass"""	32940	protein-coding gene	gene with protein product	"""tinman paralog (Drosophila)"""	611770	"""NK2 transcription factor related, locus 6 (Drosophila)"""			15649947	Standard	NM_001136271		Approved	CSX2, NKX4-2	uc011kzy.3	A6NCS4		ENST00000325017.3:c.204T>C	8.37:g.23563908A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	22	0.4	NM_001136271		Silent	SNP	ENST00000325017.3	37																																																																																				A|0.816;G|0.184	0.184	strong		0.617	NKX2-6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376057.4	NM_001136271	
SNX18	112574	hgsc.bcm.edu	37	5	53815240	53815240	+	Silent	SNP	G	G	C	rs61739378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:53815240G>C	ENST00000326277.3	+	1	1648	c.1458G>C	c.(1456-1458)tcG>tcC	p.S486S	SNX18_ENST00000381410.4_Silent_p.S486S|SNX18_ENST00000343017.6_Silent_p.S486S	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	486	BAR.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.S486S(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				AGGCCTTCTCGGTGGGCCTGA	0.632													g|||	1618	0.323083	0.2398	0.3545	5008	,	,		19334	0.4831		0.2286	False		,,,				2504	0.3456				p.S486S		Atlas-SNP	.											SNX18,NS,carcinoma,0,1	SNX18	102	1	1	Substitution - coding silent(1)	stomach(1)	c.G1458C						PASS	.	G	,,	1028,3378	380.2+/-323.6	125,778,1300	45.0	44.0	44.0		1458,1458,1458	-7.7	0.0	5	dbSNP_129	44	2144,6456	367.0+/-334.5	285,1574,2441	yes	coding-synonymous,coding-synonymous,coding-synonymous	SNX18	NM_001102575.1,NM_001145427.1,NM_052870.2	,,	410,2352,3741	CC,CG,GG		24.9302,23.3318,24.3887	,,	486/625,486/592,486/629	53815240	3172,9834	2203	4300	6503	SO:0001819	synonymous_variant	112574	exon1			CTTCTCGGTGGGC	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.1458G>C	5.37:g.53815240G>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	42	12	0.285714	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Silent	SNP	ENST00000326277.3	37	CCDS3962.1																																																																																			G|0.741;C|0.259	0.259	strong		0.632	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
PHYHD1	254295	hgsc.bcm.edu	37	9	131689361	131689361	+	Silent	SNP	G	G	A	rs751340	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131689361G>A	ENST00000372592.3	+	4	1011	c.78G>A	c.(76-78)gcG>gcA	p.A26A	PHYHD1_ENST00000421063.2_Silent_p.A26A|PHYHD1_ENST00000353176.5_Silent_p.A26A|PHYHD1_ENST00000308941.5_Silent_p.A26A	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	26							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.A26A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						TCTTGTCTGCGGAAGAGTGTG	0.542													A|||	1852	0.369808	0.4228	0.4294	5008	,	,		20654	0.2371		0.4105	False		,,,				2504	0.3507				p.A26A		Atlas-SNP	.											PHYHD1,caecum,carcinoma,+1,2	PHYHD1	29	2	1	Substitution - coding silent(1)	stomach(1)	c.G78A						PASS	.	A	,,	1846,2560	634.6+/-396.2	366,1114,723	212.0	175.0	187.0		78,78,78	-9.8	0.0	9	dbSNP_86	187	3252,5348	649.9+/-400.7	632,1988,1680	no	coding-synonymous,coding-synonymous,coding-synonymous	PHYHD1	NM_001100876.1,NM_001100877.1,NM_174933.3	,,	998,3102,2403	AA,AG,GG		37.814,41.8974,39.1973	,,	26/292,26/271,26/298	131689361	5098,7908	2203	4300	6503	SO:0001819	synonymous_variant	254295	exon2			GTCTGCGGAAGAG	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.78G>A	9.37:g.131689361G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_001100877	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Silent	SNP	ENST00000372592.3	37	CCDS43885.1																																																																																			G|0.615;A|0.385	0.385	strong		0.542	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933	
C1orf127	148345	hgsc.bcm.edu	37	1	11008341	11008341	+	Silent	SNP	G	G	A	rs10864483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11008341G>A	ENST00000377008.4	-	11	1796	c.1350C>T	c.(1348-1350)tgC>tgT	p.C450C	C1orf127_ENST00000377004.4_Silent_p.C617C			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	450										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)		CCGTTCCAGAGCACGTTTCCT	0.657													G|||	890	0.177716	0.3699	0.1254	5008	,	,		16984	0.2093		0.0557	False		,,,				2504	0.0481				p.C617C		Atlas-SNP	.											.	C1orf127	134	.	0			c.C1851T						PASS	.	G		1463,2943	459.2+/-352.2	244,975,984	59.0	68.0	65.0		1851	-0.2	0.0	1	dbSNP_120	65	364,8236	120.1+/-179.3	7,350,3943	no	coding-synonymous	C1orf127	NM_001170754.1		251,1325,4927	AA,AG,GG		4.2326,33.2047,14.0474		617/824	11008341	1827,11179	2203	4300	6503	SO:0001819	synonymous_variant	148345	exon12			TCCAGAGCACGTT	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.1350C>T	1.37:g.11008341G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		381	0.17445054945054944	180	0.36585365853658536	41	0.1132596685082873	115	0.20104895104895104	45	0.059366754617414245	G	3.870	-0.028045	0.07589	0.332047	0.042326	ENSG00000175262	ENST00000418570;ENST00000520253	.	.	.	3.9	-0.204	0.13200	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44375	-0.9332	3	.	.	.	-0.1999	1.0939	0.01669	0.2064:0.1773:0.4339:0.1824	rs10864483;rs10864483	.	.	.	V	452;569	.	.	A	-	2	0	C1orf127	10930928	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.046000	0.11983	-0.020000	0.14032	0.491000	0.48974	GCT	G|0.844;A|0.156	0.156	strong		0.657	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
TLR8	51311	hgsc.bcm.edu	37	X	12939412	12939412	+	Silent	SNP	C	C	A	rs3747414	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:12939412C>A	ENST00000218032.6	+	2	2340	c.2253C>A	c.(2251-2253)atC>atA	p.I751I	TLR8_ENST00000311912.5_Silent_p.I769I	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	751					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.I769I(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	TAAAAACAATCAACAAATCCG	0.423													C|||	2048	0.542517	0.289	0.4712	3775	,	,		15702	0.6131		0.2416	False		,,,				2504	0.4888				p.I751I		Atlas-SNP	.											.	TLR8	134	.	1	Substitution - coding silent(1)	stomach(1)	c.C2253A						PASS	.	C		1450,2385		241,759,209,632,362	102.0	93.0	96.0		2253	4.0	0.1	X	dbSNP_107	96	2320,4408		289,1095,647,1044,1225	no	coding-synonymous	TLR8	NM_138636.4		530,1854,856,1676,1587	AA,AC,A,CC,C		34.4828,37.8096,35.6906		751/1042	12939412	3770,6793	2203	4300	6503	SO:0001819	synonymous_variant	51311	exon2			AACAATCAACAAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.2253C>A	X.37:g.12939412C>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	51	0.68	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Silent	SNP	ENST00000218032.6	37	CCDS14152.1																																																																																			0|0.006;A|0.430	0.430	strong		0.423	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	
NAT8	9027	hgsc.bcm.edu	37	2	73868328	73868328	+	Missense_Mutation	SNP	A	A	G	rs13538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73868328A>G	ENST00000272425.3	-	2	577	c.428T>C	c.(427-429)tTt>tCt	p.F143S		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)											breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						ACTGTCCACAAAGAGATGAAA	0.562													.|||	1350	0.269569	0.6172	0.2622	5008	,	,		19442	0.005		0.2097	False		,,,				2504	0.1391				p.F143S		Atlas-SNP	.											.	NAT8	26	.	0			c.T428C						PASS	.	A	SER/PHE	2321,2085	605.2+/-390.5	620,1081,502	73.0	76.0	75.0	http://www.ncbi.nlm.nih.gov/pubmed?term	428	-7.7	0.0	2	dbSNP_52	75	1917,6683	339.4+/-323.1	206,1505,2589	no	missense	NAT8	NM_003960.3	155	826,2586,3091	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	22.2907,47.3218,32.585	benign	143/228	73868328	4238,8768	2203	4300	6503	SO:0001583	missense	9027	exon2			TCCACAAAGAGAT	AB013094	CCDS1926.1	2p13.2	2012-03-20	2008-09-24		ENSG00000144035	ENSG00000144035			18069	protein-coding gene	gene with protein product		606716	"""N-acetyltransferase 8"""			11397015, 9852678, 19011241	Standard	NM_003960		Approved	Hcml1, TSC501, GLA, ATase2	uc002sji.1	Q9UHE5	OTTHUMG00000129818	ENST00000272425.3:c.428T>C	2.37:g.73868328A>G	ENSP00000272425:p.Phe143Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	64	45	0.703125	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	37	CCDS1926.1	548	0.2509157509157509	302	0.6138211382113821	81	0.22375690607734808	4	0.006993006993006993	161	0.21240105540897097	a	0.010	-1.771572	0.00645	0.526782	0.222907	ENSG00000144035	ENST00000272425	T	0.22539	1.95	3.86	-7.73	0.01245	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.610629	0.17818	N	0.160960	T	0.00012	0.0000	N	0.02960	-0.455	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26018	-1.0115	9	0.09084	T	0.74	-0.7893	3.5914	0.07990	0.4:0.2826:0.2389:0.0785	rs13538;rs3174952;rs17009281;rs13538	143	Q9UHE5	NAT8_HUMAN	S	143	ENSP00000272425:F143S	ENSP00000272425:F143S	F	-	2	0	NAT8	73721836	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.187000	0.16998	-2.616000	0.00442	-3.803000	0.00020	TTT	A|0.708;G|0.292	0.292	strong		0.562	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960	
COL16A1	1307	hgsc.bcm.edu	37	1	32138045	32138045	+	Missense_Mutation	SNP	G	G	A	rs2228553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:32138045G>A	ENST00000373672.3	-	47	3593	c.3077C>T	c.(3076-3078)cCg>cTg	p.P1026L	COL16A1_ENST00000271069.6_Missense_Mutation_p.P1026L	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1026	Collagen-like 6.|Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		TGGCAATCCCGGAGGACCAGG	0.607													G|||	23	0.00459265	0.0023	0.0029	5008	,	,		18688	0.0		0.0179	False		,,,				2504	0.0				p.P1026L	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.C3077T						PASS	.	G	LEU/PRO	11,4011		1,9,2001	80.0	88.0	85.0		3077	3.5	0.8	1	dbSNP_98	85	156,8172		3,150,4011	yes	missense	COL16A1	NM_001856.3	98	4,159,6012	AA,AG,GG		1.8732,0.2735,1.3522	probably-damaging	1026/1605	32138045	167,12183	2011	4164	6175	SO:0001583	missense	1307	exon47			AATCCCGGAGGAC	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3077C>T	1.37:g.32138045G>A	ENSP00000362776:p.Pro1026Leu	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	37	CCDS41297.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	G	15.28	2.786123	0.49997	0.002735	0.018732	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000458715	D;D;D	0.96685	-4.09;-4.09;-2.89	4.45	3.52	0.40303	.	0.288831	0.32488	N	0.006024	D	0.91613	0.7350	M	0.81497	2.545	0.50813	D	0.999896	P;P	0.50272	0.933;0.918	B;B	0.42625	0.393;0.273	D	0.90640	0.4574	10	0.66056	D	0.02	.	9.8202	0.40878	0.0:0.0:0.7947:0.2053	rs2228553;rs2228553	1026;1026	Q07092;Q07092-2	COGA1_HUMAN;.	L	1026;1026;231	ENSP00000362776:P1026L;ENSP00000271069:P1026L;ENSP00000411457:P231L	ENSP00000271069:P1026L	P	-	2	0	COL16A1	31910632	0.999000	0.42202	0.814000	0.32528	0.952000	0.60782	3.693000	0.54735	1.206000	0.43276	0.561000	0.74099	CCG	G|0.990;A|0.010	0.010	strong		0.607	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
MECOM	2122	hgsc.bcm.edu	37	3	168810874	168810874	+	Silent	SNP	C	C	T	rs17466625	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:168810874C>T	ENST00000464456.1	-	12	3645	c.2445G>A	c.(2443-2445)tcG>tcA	p.S815S	MECOM_ENST00000460814.1_Silent_p.S815S|MECOM_ENST00000468789.1_Silent_p.S824S|MECOM_ENST00000392736.3_Silent_p.S824S|MECOM_ENST00000494292.1_Silent_p.S1003S|MECOM_ENST00000264674.3_Silent_p.S889S|MECOM_ENST00000472280.1_Silent_p.S825S|MECOM_ENST00000433243.2_Silent_p.S825S	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CAGAATGAGGCGACGATGTTG	0.393													C|||	455	0.0908546	0.0159	0.1037	5008	,	,		18533	0.0694		0.2008	False		,,,				2504	0.092				p.S1012S		Atlas-SNP	.											.	MECOM	216	.	0			c.G3036A						PASS	.	C	,,,,,,	206,4200	127.8+/-164.7	5,196,2002	111.0	100.0	104.0		2667,2472,2448,2445,2472,3036,2472	-1.1	1.0	3	dbSNP_123	104	1750,6850	317.2+/-313.1	180,1390,2730	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MECOM	NM_001105077.3,NM_001105078.3,NM_001163999.1,NM_001164000.1,NM_001205194.1,NM_004991.3,NM_005241.3	,,,,,,	185,1586,4732	TT,TC,CC		20.3488,4.6754,15.0392	,,,,,,	889/1117,824/1052,816/1044,815/1043,824/1052,1012/1240,824/1052	168810874	1956,11050	2203	4300	6503	SO:0001819	synonymous_variant	2122	exon14			ATGAGGCGACGAT	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.2445G>A	3.37:g.168810874C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_004991	Q13466|Q6FH90	Silent	SNP	ENST00000464456.1	37	CCDS54669.1																																																																																			C|0.871;T|0.129	0.129	strong		0.393	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
MUC2	4583	hgsc.bcm.edu	37	11	1104123	1104123	+	Silent	SNP	C	C	T	rs12270802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1104123C>T	ENST00000441003.2	+	49	8341	c.8314C>T	c.(8314-8316)Ctg>Ttg	p.L2772L		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5134					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)		p.L2772L(1)		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)	TGAGGTGGTCCTGAGCTGCCC	0.672													C|||	778	0.155351	0.4039	0.072	5008	,	,		14321	0.0357		0.0934	False		,,,				2504	0.0654				p.L2768L		Atlas-SNP	.											MUC2_ENST00000441003,NS,lymphoid_neoplasm,0,1	MUC2	614	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C8302T						PASS	.	C		1294,2806		202,890,958	14.0	20.0	18.0		8299	1.6	0.0	11	dbSNP_120	18	690,7674		27,636,3519	no	coding-synonymous	MUC2	NM_002457.2		229,1526,4477	TT,TC,CC		8.2496,31.561,15.9178		2767/2813	1104123	1984,10480	2050	4182	6232	SO:0001819	synonymous_variant	4583	exon50			GTGGTCCTGAGCT	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.8314C>T	11.37:g.1104123C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.894;T|0.106	0.106	strong		0.672	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ABCG8	64241	hgsc.bcm.edu	37	2	44102302	44102302	+	Silent	SNP	G	G	A	rs145756111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44102302G>A	ENST00000272286.2	+	11	1596	c.1506G>A	c.(1504-1506)ccG>ccA	p.P502P		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	502	ABC transmembrane type-2.				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)	GGGAGCTTCCGGAGCACTGTG	0.552													G|||	9	0.00179712	0.0008	0.0	5008	,	,		19553	0.0		0.004	False		,,,				2504	0.0041				p.P502P		Atlas-SNP	.											ABCG8,NS,carcinoma,0,2	ABCG8	98	2	0			c.G1506A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	78.0	75.0	76.0		1506	-9.2	0.1	2	dbSNP_134	76	53,8547	34.3+/-88.2	0,53,4247	no	coding-synonymous	ABCG8	NM_022437.2		0,55,6448	AA,AG,GG		0.6163,0.0454,0.4229		502/674	44102302	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	64241	exon11			GCTTCCGGAGCAC	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.1506G>A	2.37:g.44102302G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	37	CCDS1815.1																																																																																			G|0.995;A|0.005	0.005	strong		0.552	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
PLXNB3	5365	hgsc.bcm.edu	37	X	153042419	153042419	+	Silent	SNP	G	G	A	rs34966902	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153042419G>A	ENST00000361971.5	+	29	5025	c.4911G>A	c.(4909-4911)agG>agA	p.R1637R	PLXNB3_ENST00000538776.1_Silent_p.R1290R|PLXNB3_ENST00000538966.1_Silent_p.R1660R|SRPK3_ENST00000489426.1_5'UTR	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1637					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)					TGGCCCAGAGGTGCCCCTTGG	0.657													G|||	1516	0.401589	0.3707	0.3026	3775	,	,		8007	0.128		0.501	False		,,,				2504	0.1871				p.R1660R		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G4980A						PASS	.	G	,	1987,1832		458,781,290,389,273	35.0	33.0	34.0		4980,4911	3.1	0.6	X	dbSNP_126	34	4446,2273		1089,1048,1220,290,645	no	coding-synonymous,coding-synonymous	PLXNB3	NM_001163257.1,NM_005393.2	,	1547,1829,1510,679,918	AA,AG,A,GG,G		33.8294,47.9707,38.9543	,	1660/1933,1637/1910	153042419	6433,4105	2191	4292	6483	SO:0001819	synonymous_variant	5365	exon30			CCAGAGGTGCCCC	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.4911G>A	X.37:g.153042419G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	86	84	0.976744	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Silent	SNP	ENST00000361971.5	37	CCDS14729.1	774	0.4665461121157324	138	0.359375	81	0.2892857142857143	48	0.09302325581395349	265	0.5115830115830116	G	2.424	-0.332388	0.05314	0.520293	0.661706	ENSG00000198753	ENST00000455214	.	.	.	4.92	3.14	0.36123	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999955812	.	.	.	.	.	.	T	0.40175	-0.9577	3	.	.	.	.	4.3884	0.11328	0.0:0.5533:0.1703:0.2764	rs34966902	.	.	.	M	141	.	.	V	+	1	0	PLXNB3	152695613	0.974000	0.33945	0.624000	0.29186	0.156000	0.22039	0.190000	0.17057	0.434000	0.26340	-0.311000	0.09066	GTG	G|0.439;A|0.561	0.561	strong		0.657	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
BCKDK	10295	hgsc.bcm.edu	37	16	31121793	31121793	+	Silent	SNP	G	G	A	rs14235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31121793G>A	ENST00000394951.1	+	8	1238	c.615G>A	c.(613-615)acG>acA	p.T205T	AC135050.1_ENST00000517000.2_RNA|BCKDK_ENST00000287507.3_Silent_p.T205T|BCKDK_ENST00000219794.6_Silent_p.T205T|BCKDK_ENST00000394950.3_Silent_p.T205T			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	205	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|stomach(1)	2						TGTTGGCCACGCATCACCTGG	0.567													G|||	1799	0.359225	0.0893	0.3833	5008	,	,		18067	0.8849		0.3817	False		,,,				2504	0.1421				p.T205T		Atlas-SNP	.											BCKDK_ENST00000394951,rectum,carcinoma,0,2	BCKDK	52	2	0			c.G615A						PASS	.	G	,	592,3802	255.8+/-260.9	44,504,1649	62.0	63.0	63.0		615,615	-9.0	0.9	16	dbSNP_52	63	3344,5256	492.2+/-373.3	638,2068,1594	no	coding-synonymous,coding-synonymous	BCKDK	NM_001122957.1,NM_005881.2	,	682,2572,3243	AA,AG,GG		38.8837,13.4729,30.2909	,	205/366,205/413	31121793	3936,9058	2197	4300	6497	SO:0001819	synonymous_variant	10295	exon7			GGCCACGCATCAC	AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.615G>A	16.37:g.31121793G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_005881	A8MY43|Q6FGL4|Q96G95|Q96IN5	Silent	SNP	ENST00000394951.1	37	CCDS10705.1																																																																																			G|0.642;A|0.358	0.358	strong		0.567	BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881	
GRHL3	57822	hgsc.bcm.edu	37	1	24690764	24690764	+	Missense_Mutation	SNP	T	T	A	rs545809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:24690764T>A	ENST00000350501.5	+	16	1911	c.1784T>A	c.(1783-1785)aTg>aAg	p.M595K	STPG1_ENST00000337248.4_Intron|STPG1_ENST00000440416.1_Intron|STPG1_ENST00000468303.1_Intron|STPG1_ENST00000003583.8_Intron|STPG1_ENST00000374409.1_Intron	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	595					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GTGAGGaacatgggttttgga	0.537													T|||	1497	0.298922	0.2247	0.2305	5008	,	,		15454	0.4127		0.2734	False		,,,				2504	0.3569				p.M595K		Atlas-SNP	.											.	GRHL3	69	.	0			c.T1784A						PASS	.																																			SO:0001583	missense	57822	exon16			GGAACATGGGTTT	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.1784T>A	1.37:g.24690764T>A	ENSP00000288955:p.Met595Lys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_198174	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	647	0.29624542124542125	114	0.23170731707317074	90	0.24861878453038674	246	0.43006993006993005	197	0.2598944591029024	T	12.15	1.851371	0.32699	.	.	ENSG00000158055	ENST00000350501	T	0.09817	2.94	3.18	-1.22	0.09494	.	1.427050	0.03899	N	0.279931	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	.	.	.	.	.	.	T	0.44112	-0.9349	7	0.87932	D	0	-0.5292	0.3876	0.00405	0.2209:0.1397:0.2261:0.4132	rs545809;rs545809	.	.	.	K	595	ENSP00000288955:M595K	ENSP00000288955:M595K	M	+	2	0	GRHL3	24563351	0.000000	0.05858	0.002000	0.10522	0.400000	0.30750	-0.344000	0.07780	0.006000	0.14734	0.260000	0.18958	ATG	A|0.304;N|0.003	0.304	strong		0.537	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
CD276	80381	hgsc.bcm.edu	37	15	73994806	73994806	+	Missense_Mutation	SNP	C	C	T	rs7173448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:73994806C>T	ENST00000318443.5	+	3	592	c.290C>T	c.(289-291)cCg>cTg	p.P97L	CD276_ENST00000537340.2_5'UTR|CD276_ENST00000318424.5_Missense_Mutation_p.P97L|CD276_ENST00000561213.1_Missense_Mutation_p.P97L|CD276_ENST00000564751.1_Missense_Mutation_p.P97L	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	97	Ig-like V-type 1.		P -> L (in dbSNP:rs7173448).		cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GCCCTCTTCCCGGACCTGCTG	0.642													C|||	1003	0.20028	0.4281	0.1023	5008	,	,		18941	0.1349		0.0964	False		,,,				2504	0.136				p.P97L		Atlas-SNP	.											.	CD276	29	.	0			c.C290T						PASS	.	C	LEU/PRO,LEU/PRO	1699,2697	501.8+/-365.1	353,993,852	48.0	42.0	44.0		290,290	-0.2	0.8	15	dbSNP_116	44	834,7760	190.6+/-237.0	33,768,3496	no	missense,missense	CD276	NM_001024736.1,NM_025240.2	98,98	386,1761,4348	TT,TC,CC		9.7044,38.6488,19.4996	possibly-damaging,possibly-damaging	97/535,97/317	73994806	2533,10457	2198	4297	6495	SO:0001583	missense	80381	exon3			TCTTCCCGGACCT	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.290C>T	15.37:g.73994806C>T	ENSP00000320084:p.Pro97Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_025240	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	394	0.1804029304029304	207	0.42073170731707316	41	0.1132596685082873	73	0.12762237762237763	73	0.09630606860158311	C	1.420	-0.573026	0.03882	0.386488	0.097044	ENSG00000103855	ENST00000318424;ENST00000318443;ENST00000379823;ENST00000543481	T;T	0.65732	-0.17;-0.17	2.9	-0.162	0.13367	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.20685	0.6	0.35681	P	0.18593800000000005	B;B;B;B	0.21905	0.0;0.062;0.001;0.001	B;B;B;B	0.15870	0.0;0.014;0.001;0.001	T	0.37033	-0.9723	8	0.59425	D	0.04	.	3.4963	0.07655	0.2715:0.4051:0.0:0.3233	rs7173448	43;97;97;97	B4DK26;Q5ZPR3-2;Q5ZPR3;Q5ZPR3-4	.;.;CD276_HUMAN;.	L	97	ENSP00000320058:P97L;ENSP00000320084:P97L	ENSP00000320058:P97L	P	+	2	0	CD276	71781859	0.099000	0.21834	0.785000	0.31869	0.261000	0.26267	0.663000	0.25053	-0.033000	0.13736	-1.206000	0.01644	CCG	C|0.813;T|0.187	0.187	strong		0.642	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
RNF213	57674	hgsc.bcm.edu	37	17	78319136	78319136	+	Missense_Mutation	SNP	G	G	A	rs9674961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78319136G>A	ENST00000582970.1	+	29	7144	c.7001G>A	c.(7000-7002)aGt>aAt	p.S2334N	RNF213_ENST00000336301.6_Missense_Mutation_p.S407N|RNF213_ENST00000508628.2_Missense_Mutation_p.S2383N	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2334					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S407N(2)|p.S2383N(2)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GATGCCATCAGTCACTTGACT	0.522													A|||	2797	0.558506	0.6528	0.4337	5008	,	,		20475	0.376		0.6879	False		,,,				2504	0.5746				p.S2334N		Atlas-SNP	.											RNF213_ENST00000411702,colon,carcinoma,0,6	RNF213	766	6	4	Substitution - Missense(4)	large_intestine(2)|stomach(2)	c.G7001A						PASS	.	A	ASN/SER	2876,1530	485.5+/-360.3	950,976,277	124.0	114.0	117.0		7148	0.9	0.0	17	dbSNP_119	117	5714,2886	452.3+/-362.9	1909,1896,495	yes	missense	RNF213	NM_020914.4	46	2859,2872,772	AA,AG,GG		33.5581,34.7254,33.9536	benign	2383/5257	78319136	8590,4416	2203	4300	6503	SO:0001583	missense	57674	exon29			CCATCAGTCACTT	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.7001G>A	17.37:g.78319136G>A	ENSP00000464087:p.Ser2334Asn	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	1244	0.5695970695970696	326	0.6626016260162602	173	0.47790055248618785	212	0.3706293706293706	533	0.7031662269129287	A	3.858	-0.030522	0.07543	0.652746	0.664419	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.21734	1.99	5.84	0.943	0.19531	.	0.670270	0.15010	N	0.285649	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35025	-0.9805	9	0.07644	T	0.81	.	11.2868	0.49226	0.6123:0.0:0.3877:0.0	rs9674961;rs52799145;rs61333363;rs9674961	407	Q63HN8	RN213_HUMAN	N	2334;2383;407	ENSP00000338218:S407N	ENSP00000338218:S407N	S	+	2	0	RNF213	75933731	0.098000	0.21812	0.000000	0.03702	0.002000	0.02628	2.159000	0.42339	-0.073000	0.12842	-0.982000	0.02568	AGT	G|0.368;A|0.632	0.632	strong		0.522	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
OR4M1	441670	hgsc.bcm.edu	37	14	20248828	20248828	+	Missense_Mutation	SNP	C	C	T	rs2635535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20248828C>T	ENST00000315957.4	+	1	428	c.347C>T	c.(346-348)aCa>aTa	p.T116I		NM_001005500.1	NP_001005500.1	Q8NGD0	OR4M1_HUMAN	olfactory receptor, family 4, subfamily M, member 1	116			T -> I (in dbSNP:rs2635535).			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)|large_intestine(4)|lung(32)|prostate(1)|skin(2)	42	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTCTTGCTCACAGTGATGGCC	0.493													.|||	1274	0.254393	0.0847	0.3242	5008	,	,		27958	0.2937		0.3439	False		,,,				2504	0.3016				p.T116I		Atlas-SNP	.											.	OR4M1	104	.	0			c.C347T						PASS	.		ILE/THR	587,3819		18,551,1634	237.0	249.0	245.0		347	3.4	1.0	14	dbSNP_100	245	2790,5810		266,2258,1776	no	missense	OR4M1	NM_001005500.1	89	284,2809,3410	TT,TC,CC		32.4419,13.3227,25.9649	possibly-damaging	116/314	20248828	3377,9629	2203	4300	6503	SO:0001583	missense	441670	exon1			TGCTCACAGTGAT		CCDS32021.1	14q11.2	2013-09-23			ENSG00000176299	ENSG00000176299		"""GPCR / Class A : Olfactory receptors"""	14735	protein-coding gene	gene with protein product							Standard	NM_001005500		Approved		uc010tku.2	Q8NGD0	OTTHUMG00000170599	ENST00000315957.4:c.347C>T	14.37:g.20248828C>T	ENSP00000319654:p.Thr116Ile	Somatic	464	0	0		WXS	Illumina HiSeq	Phase_I	538	104	0.193309	NM_001005500	B9EH18|Q6IFA3	Missense_Mutation	SNP	ENST00000315957.4	37	CCDS32021.1	599	0.2742673992673993	40	0.08130081300813008	115	0.31767955801104975	169	0.29545454545454547	275	0.3627968337730871	.	11.72	1.723491	0.30593	0.133227	0.324419	ENSG00000176299	ENST00000315957	T	0.00380	7.64	4.33	3.43	0.39272	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000124	T	0.00012	0.0000	L	0.38649	1.16	0.36142	P	0.15317000000000003	B	0.18741	0.03	B	0.15052	0.012	T	0.03148	-1.1067	9	0.08599	T	0.76	-7.5579	9.9477	0.41621	0.0:0.8968:0.0:0.1032	rs2635535;rs52798113	116	Q8NGD0	OR4M1_HUMAN	I	116	ENSP00000319654:T116I	ENSP00000319654:T116I	T	+	2	0	OR4M1	19318668	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	1.306000	0.33505	2.407000	0.81776	0.506000	0.49869	ACA	C|0.736;T|0.264	0.264	strong		0.493	OR4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409770.1		
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 GAIIx	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_ENST00000595559.1_Silent_p.C409C|CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000536263.1_Silent_p.C211C	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		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	25	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	
FAM71F1	84691	hgsc.bcm.edu	37	7	128363287	128363287	+	Missense_Mutation	SNP	G	G	A	rs6971091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128363287G>A	ENST00000315184.5	+	4	777	c.724G>A	c.(724-726)Gag>Aag	p.E242K	FAM71F1_ENST00000469348.1_3'UTR|FAM71F1_ENST00000485070.1_Missense_Mutation_p.E143K	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	242			E -> K (in dbSNP:rs6971091).							NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						CCAGCCCAGCGAGAGTCTCAT	0.453													G|||	799	0.159545	0.0598	0.1628	5008	,	,		18826	0.1052		0.2336	False		,,,				2504	0.272				p.E242K		Atlas-SNP	.											.	FAM71F1	42	.	0			c.G724A						PASS	.	G	LYS/GLU	351,4055	181.2+/-209.3	12,327,1864	118.0	121.0	120.0		724	5.2	1.0	7	dbSNP_116	120	1973,6627	347.0+/-326.4	209,1555,2536	yes	missense	FAM71F1	NM_032599.2	56	221,1882,4400	AA,AG,GG		22.9419,7.9664,17.8687	benign	242/345	128363287	2324,10682	2203	4300	6503	SO:0001583	missense	84691	exon4			CCCAGCGAGAGTC	AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248			30704	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member A"""	FAM137A		12477932	Standard	XM_005250645		Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000315184.5:c.724G>A	7.37:g.128363287G>A	ENSP00000326652:p.Glu242Lys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_032599	Q8IY75|Q8NA48	Missense_Mutation	SNP	ENST00000315184.5	37	CCDS5804.1	334	0.15293040293040294	33	0.06707317073170732	53	0.1464088397790055	67	0.11713286713286714	181	0.23878627968337732	G	19.03	3.748148	0.69533	0.079664	0.229419	ENSG00000135248	ENST00000485070;ENST00000315184;ENST00000466842	T;T;T	0.33865	1.39;2.87;1.61	5.2	5.2	0.72013	.	0.104089	0.42964	D	0.000627	T	0.00039	0.0001	M	0.68952	2.095	0.26570	P	0.9735895	D;D;P;P;D	0.71674	0.996;0.998;0.954;0.923;0.978	P;P;B;B;P	0.61658	0.541;0.892;0.374;0.207;0.469	T	0.01149	-1.1436	9	0.36615	T	0.2	-11.422	14.4309	0.67249	0.0:0.0:1.0:0.0	rs6971091;rs52795285;rs57035392;rs6971091	134;242;242;242;143	B4DY15;F8WC62;Q96KD3-2;Q96KD3;Q8NA48	.;.;.;F71F1_HUMAN;.	K	143;242;98	ENSP00000418192:E143K;ENSP00000326652:E242K;ENSP00000417930:E98K	ENSP00000326652:E242K	E	+	1	0	FAM71F1	128150523	0.997000	0.39634	0.986000	0.45419	0.944000	0.59088	4.046000	0.57376	2.868000	0.98415	0.555000	0.69702	GAG	G|0.836;A|0.164	0.164	strong		0.453	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	NM_032599	
GLYATL1	92292	hgsc.bcm.edu	37	11	58722296	58722296	+	Silent	SNP	A	A	G	rs140293060	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:58722296A>G	ENST00000317391.4	+	6	580	c.240A>G	c.(238-240)aaA>aaG	p.K80K	RP11-142C4.6_ENST00000533954.1_RNA|GLYATL1_ENST00000300079.5_Silent_p.K111K	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	80						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	TGTTCTCCAAAGAGCCTCAAA	0.378													A|||	9	0.00179712	0.0008	0.0058	5008	,	,		18733	0.0		0.004	False		,,,				2504	0.0				p.K111K		Atlas-SNP	.											.	GLYATL1	89	.	0			c.A333G						PASS	.	A	,,	5,4397		0,5,2196	93.0	88.0	90.0		240,240,333	-3.0	0.0	11	dbSNP_134	90	39,8551		0,39,4256	no	coding-synonymous,coding-synonymous,coding-synonymous	GLYATL1	NM_001220494.1,NM_001220496.1,NM_080661.3	,,	0,44,6452	GG,GA,AA		0.454,0.1136,0.3387	,,	80/303,80/303,111/334	58722296	44,12948	2201	4295	6496	SO:0001819	synonymous_variant	92292	exon5			CTCCAAAGAGCCT	AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.240A>G	11.37:g.58722296A>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	194	91	0.469072	NM_080661	A6NDT0|Q7Z510|Q8NAW8	Silent	SNP	ENST00000317391.4	37	CCDS55768.1																																																																																			A|0.997;G|0.003	0.003	strong		0.378	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661	
OR10AD1	121275	hgsc.bcm.edu	37	12	48597053	48597053	+	Missense_Mutation	SNP	A	A	G	rs17122812	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48597053A>G	ENST00000310248.2	-	1	117	c.23T>C	c.(22-24)gTg>gCg	p.V8A		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	8			V -> A (in dbSNP:rs17122812).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						AAATTCCGTCACTATGCTGCC	0.517													A|||	705	0.140775	0.0628	0.1643	5008	,	,		22063	0.1935		0.2107	False		,,,				2504	0.1033				p.V8A		Atlas-SNP	.											OR10AD1,NS,carcinoma,0,1	OR10AD1	24	1	0			c.T23C						PASS	.	A	ALA/VAL	348,4058	176.9+/-206.0	10,328,1865	50.0	47.0	48.0		23	3.9	0.3	12	dbSNP_123	48	1853,6747	323.2+/-315.9	196,1461,2643	yes	missense	OR10AD1	NM_001004134.1	64	206,1789,4508	GG,GA,AA		21.5465,7.8983,16.923	benign	8/318	48597053	2201,10805	2203	4300	6503	SO:0001583	missense	121275	exon1			TCCGTCACTATGC		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.23T>C	12.37:g.48597053A>G	ENSP00000308689:p.Val8Ala	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	372	0.17032967032967034	34	0.06910569105691057	66	0.18232044198895028	121	0.21153846153846154	151	0.19920844327176782	A	7.785	0.710317	0.15239	0.078983	0.215465	ENSG00000172640	ENST00000310248	T	0.00892	5.57	5.07	3.93	0.45458	.	0.599767	0.12846	N	0.434418	T	0.00012	0.0000	M	0.68317	2.08	0.43381	P	0.0045199999999999685	B	0.31077	0.307	B	0.31946	0.138	T	0.40478	-0.9561	9	0.56958	D	0.05	-15.4666	7.5959	0.28048	0.9023:0.0:0.0977:0.0	rs17122812;rs17122812	8	Q8NGE0	O10AD_HUMAN	A	8	ENSP00000308689:V8A	ENSP00000308689:V8A	V	-	2	0	OR10AD1	46883320	0.038000	0.19896	0.286000	0.24833	0.014000	0.08584	3.127000	0.50484	0.894000	0.36317	0.460000	0.39030	GTG	A|0.830;G|0.170	0.170	strong		0.517	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
TMC2	117532	hgsc.bcm.edu	37	20	2539387	2539387	+	Missense_Mutation	SNP	G	G	A	rs6050063	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:2539387G>A	ENST00000358864.1	+	3	383	c.368G>A	c.(367-369)aGg>aAg	p.R123K		NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	123	Arg/Asp/Glu/Lys-rich (highly charged).		R -> K (in dbSNP:rs6050063). {ECO:0000269|PubMed:11850618}.		detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						ATTCCGAGGAGGGAGGAGAAG	0.637													a|||	3277	0.654353	0.7398	0.634	5008	,	,		16289	0.5466		0.6203	False		,,,				2504	0.6994				p.R123K		Atlas-SNP	.											.	TMC2	121	.	0			c.G368A						PASS	.	-	LYS/ARG	3182,1220		1154,874,173	22.0	23.0	23.0		368		0.9	20	dbSNP_114	23	5362,3236		1685,1992,622	yes	missense	TMC2	NM_080751.2	26	2839,2866,795	AA,AG,GG		37.6367,27.7147,34.2769	benign	123/907	2539387	8544,4456	2201	4299	6500	SO:0001583	missense	117532	exon3			CGAGGAGGGAGGA	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.368G>A	20.37:g.2539387G>A	ENSP00000351732:p.Arg123Lys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	1388	0.6355311355311355	368	0.7479674796747967	239	0.6602209944751382	288	0.5034965034965035	493	0.6503957783641161	a	0.020	-1.437675	0.01098	0.722853	0.623633	ENSG00000149488	ENST00000358864	T	0.48522	0.81	.	.	.	.	0.174385	0.48286	N	0.000188	T	0.00012	0.0000	N	0.00146	-1.995	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21348	-1.0248	7	0.06891	T	0.86	-20.9672	.	.	.	rs6050063;rs57765410;rs6050063	123;123	Q8TDI7-3;Q8TDI7	.;TMC2_HUMAN	K	123	ENSP00000351732:R123K	ENSP00000351732:R123K	R	+	2	0	TMC2	2487387	1.000000	0.71417	0.924000	0.36721	0.018000	0.09664	2.139000	0.42149	-1.413000	0.02027	-1.375000	0.01183	AGG	G|0.349;A|0.651	0.651	strong		0.637	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
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 GAIIx	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_ENST00000431842.2_Intron|FAM208A_ENST00000355628.5_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	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	67	36	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	
DMP1	1758	hgsc.bcm.edu	37	4	88584160	88584160	+	Silent	SNP	G	G	A	rs2615497	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88584160G>A	ENST00000339673.6	+	6	1329	c.1230G>A	c.(1228-1230)gaG>gaA	p.E410E	RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA|DMP1_ENST00000282479.7_Silent_p.E394E|RP11-742B18.1_ENST00000506480.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	410					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		AATCCAGTGAGAGCCTCAACT	0.567													G|||	1609	0.321286	0.4652	0.2061	5008	,	,		20365	0.2589		0.2366	False		,,,				2504	0.3599				p.E410E		Atlas-SNP	.											DMP1,caecum,carcinoma,0,1	DMP1	72	1	0			c.G1230A						PASS	.	G	,	1752,2654	521.9+/-370.6	343,1066,794	77.0	82.0	80.0		1182,1230	3.4	0.9	4	dbSNP_100	80	1930,6670	340.7+/-323.7	209,1512,2579	no	coding-synonymous,coding-synonymous	DMP1	NM_001079911.2,NM_004407.3	,	552,2578,3373	AA,AG,GG		22.4419,39.764,28.31	,	394/498,410/514	88584160	3682,9324	2203	4300	6503	SO:0001819	synonymous_variant	1758	exon6			CAGTGAGAGCCTC	U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"""dentin matrix acidic phosphoprotein"""			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.1230G>A	4.37:g.88584160G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_004407	A1L4L3|O43265	Silent	SNP	ENST00000339673.6	37	CCDS3623.1																																																																																			G|0.715;A|0.285	0.285	strong		0.567	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1		
OR2L3	391192	hgsc.bcm.edu	37	1	248224754	248224754	+	Silent	SNP	T	T	C	rs55893924	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248224754T>C	ENST00000359959.3	+	1	771	c.771T>C	c.(769-771)acT>acC	p.T257T	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	257						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)			TTGTCTACACTTATCTACGTC	0.488													N|||	1555	0.310503	0.7398	0.1326	5008	,	,		20515	0.254		0.1481	False		,,,				2504	0.0818				p.T257T		Atlas-SNP	.											.	OR2L3	97	.	0			c.T771C						PASS	.	C	,	2706,1700	500.3+/-364.7	826,1054,323	121.0	115.0	117.0		771,	-4.0	0.0	1	dbSNP_129	117	1145,7449	760.4+/-407.6	69,1007,3221	no	coding-synonymous,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	,	895,2061,3544	CC,CT,TT		13.3232,38.5837,29.6231	,	257/313,	248224754	3851,9149	2203	4297	6500	SO:0001819	synonymous_variant	391192	exon1			CTACACTTATCTA	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.771T>C	1.37:g.248224754T>C		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	165	91	0.551515	NM_001004687	B9EH44	Silent	SNP	ENST00000359959.3	37	CCDS31104.1																																																																																			.	.	weak		0.488	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
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 GAIIx	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_ENST00000590798.1_Silent_p.S44S|ZNF763_ENST00000591944.1_Silent_p.S93S|ZNF763_ENST00000592625.1_Silent_p.S24S|ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000538752.1_Silent_p.S44S|ZNF763_ENST00000343949.5_Silent_p.S27S			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		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	96	9	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	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51917735	51917735	+	Silent	SNP	G	G	A	rs1974821	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51917735G>A	ENST00000339313.5	-	9	1766	c.1650C>T	c.(1648-1650)aaC>aaT	p.N550N	SIGLEC10_ENST00000439889.2_Silent_p.N492N|SIGLEC10_ENST00000436984.2_Silent_p.N407N|SIGLEC10_ENST00000353836.5_Silent_p.N455N|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Silent_p.N365N|SIGLEC10_ENST00000432469.2_Silent_p.N372N|SIGLEC10_ENST00000442846.3_Silent_p.N307N|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.N550N|SIGLEC10_ENST00000441969.3_Silent_p.N397N|CTD-2616J11.2_ENST00000532688.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	550					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.N492N(1)|p.N550N(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		GAAACGCTCCGTTGGAGAATG	0.587													g|||	1142	0.228035	0.3404	0.1816	5008	,	,		18581	0.2113		0.1451	False		,,,				2504	0.2117				p.N550N		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,0,2	SIGLEC10	112	2	2	Substitution - coding silent(2)	stomach(2)	c.C1650T						scavenged	.	G	,,,,,,	1407,2999		211,985,1007	99.0	88.0	92.0		1476,1365,1221,1191,1116,921,1650	-9.1	0.0	19	dbSNP_92	92	1207,7393		84,1039,3177	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	,,,,,,	295,2024,4184	AA,AG,GG		14.0349,31.9337,20.0984	,,,,,,	492/640,455/603,407/555,397/545,372/520,307/455,550/698	51917735	2614,10392	2203	4300	6503	SO:0001819	synonymous_variant	89790	exon9			CGCTCCGTTGGAG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.1650C>T	19.37:g.51917735G>A		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			G|0.795;A|0.205	0.205	strong		0.587	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
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 GAIIx	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	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	203	93	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		
ADAM15	8751	hgsc.bcm.edu	37	1	155026871	155026871	+	Silent	SNP	G	G	T	rs11548311	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:155026871G>T	ENST00000356955.2	+	6	602	c.501G>T	c.(499-501)tcG>tcT	p.S167S	ADAM15_ENST00000447332.3_Silent_p.S151S|ADAM15_ENST00000355956.2_Silent_p.S167S|ADAM15_ENST00000449910.2_Silent_p.S167S|ADAM15_ENST00000531455.1_Silent_p.S177S|ADAM15_ENST00000271836.6_Silent_p.S167S|ADAM15_ENST00000368412.3_Silent_p.S167S|ADAM15_ENST00000368410.2_Intron|ADAM15_ENST00000360674.4_Silent_p.S167S|ADAM15_ENST00000368413.1_Intron|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000359280.4_Silent_p.S167S	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	167					angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CCATTATTTCGCGAATCCAAG	0.582													G|||	401	0.0800719	0.1172	0.0576	5008	,	,		14300	0.003		0.1451	False		,,,				2504	0.0583				p.S177S		Atlas-SNP	.											ADAM15,NS,carcinoma,0,1	ADAM15	92	1	0			c.G531T						PASS	.	G	,,,,,	503,3903	226.9+/-242.2	34,435,1734	53.0	59.0	57.0		501,501,501,501,501,501	1.7	0.7	1	dbSNP_120	57	1110,7490	225.9+/-261.8	69,972,3259	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADAM15	NM_003815.3,NM_207191.1,NM_207194.1,NM_207195.1,NM_207196.1,NM_207197.1	,,,,,	103,1407,4993	TT,TG,GG		12.907,11.4163,12.402	,,,,,	167/815,167/773,167/840,167/839,167/863,167/864	155026871	1613,11393	2203	4300	6503	SO:0001819	synonymous_variant	8751	exon6			TATTTCGCGAATC	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"""ADAM metallopeptidase domain containing"""	193	protein-coding gene	gene with protein product	"""metargidin"""	605548	"""a disintegrin and metalloproteinase domain 15 (metargidin)"""			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.501G>T	1.37:g.155026871G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	76	27	0.355263	NM_001261464	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Silent	SNP	ENST00000356955.2	37	CCDS1087.1																																																																																			G|0.889;T|0.111	0.111	strong		0.582	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	
OR2L3	391192	hgsc.bcm.edu	37	1	248224578	248224578	+	Missense_Mutation	SNP	T	T	C	rs60743763	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248224578T>C	ENST00000359959.3	+	1	595	c.595T>C	c.(595-597)Ttt>Ctt	p.F199L	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	199						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)			GGGCACAGTGTTTTTGAGCAC	0.488													t|||	389	0.0776757	0.1324	0.0288	5008	,	,		24690	0.119		0.0626	False		,,,				2504	0.0112				p.F199L		Atlas-SNP	.											OR2L3,NS,carcinoma,-1,1	OR2L3	97	1	0			c.T595C						scavenged	.						179.0	198.0	191.0					1																	248224578		2189	4300	6489	SO:0001583	missense	391192	exon1			ACAGTGTTTTTGA	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.595T>C	1.37:g.248224578T>C	ENSP00000353044:p.Phe199Leu	Somatic	357	0	0		WXS	Illumina HiSeq	Phase_I	228	12	0.0526316	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	145	0.06639194139194139	38	0.07723577235772358	9	0.024861878453038673	67	0.11713286713286714	31	0.040897097625329816	T	7.648	0.682293	0.14907	.	.	ENSG00000198128	ENST00000359959	T	0.00042	8.84	2.05	0.915	0.19366	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33732	U	0.004607	T	0.00012	0.0000	N	0.13043	0.29	0.09310	N	1	P	0.49447	0.924	P	0.56088	0.791	T	0.44667	-0.9313	10	0.51188	T	0.08	.	0.1554	0.00097	0.2252:0.2557:0.23:0.2891	rs60743763	199	Q8NG85	OR2L3_HUMAN	L	199	ENSP00000353044:F199L	ENSP00000353044:F199L	F	+	1	0	OR2L3	246291201	0.000000	0.05858	0.068000	0.19968	0.037000	0.13140	-2.920000	0.00694	0.928000	0.37168	0.379000	0.24179	TTT	T|0.933;C|0.067	0.067	strong		0.488	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
COL6A1	1291	hgsc.bcm.edu	37	21	47423389	47423389	+	Missense_Mutation	SNP	G	G	A	rs1053312	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:47423389G>A	ENST00000361866.3	+	35	2663	c.2549G>A	c.(2548-2550)cGc>cAc	p.R850H	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	850	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		R -> H (in dbSNP:rs1053312). {ECO:0000269|PubMed:15689448}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		ACCACCAAGCGCTTCGCCAAG	0.706													G|||	1353	0.270168	0.4198	0.281	5008	,	,		14974	0.1339		0.2724	False		,,,				2504	0.1984				p.R850H		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2549A						PASS	.	G	HIS/ARG	1739,2625		376,987,819	16.0	19.0	18.0		2549	0.7	1.0	21	dbSNP_86	18	2627,5865		454,1719,2073	yes	missense	COL6A1	NM_001848.2	29	830,2706,2892	AA,AG,GG		30.935,39.8488,33.9608	probably-damaging	850/1029	47423389	4366,8490	2182	4246	6428	SO:0001583	missense	1291	exon35			CCAAGCGCTTCGC	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2549G>A	21.37:g.47423389G>A	ENSP00000355180:p.Arg850His	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	607	0.27793040293040294	208	0.42276422764227645	107	0.2955801104972376	87	0.1520979020979021	205	0.2704485488126649	G	19.07	3.755932	0.69648	0.398488	0.30935	ENSG00000142156	ENST00000361866	D	0.83673	-1.75	4.84	0.709	0.18150	von Willebrand factor, type A (3);	0.771200	0.12213	N	0.489117	T	0.00012	0.0000	N	0.14661	0.345	0.43868	P	0.003523000000000054	B	0.09022	0.002	B	0.06405	0.002	T	0.21415	-1.0246	9	0.41790	T	0.15	-7.3617	3.4558	0.07515	0.2694:0.0:0.4037:0.3269	rs1053312;rs3193825;rs17845675;rs17858614;rs59583777;rs1053312	850	P12109	CO6A1_HUMAN	H	850	ENSP00000355180:R850H	ENSP00000355180:R850H	R	+	2	0	COL6A1	46247817	0.006000	0.16342	0.992000	0.48379	0.989000	0.77384	-0.001000	0.12947	0.063000	0.16370	0.530000	0.56133	CGC	G|0.703;A|0.297	0.297	strong		0.706	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
BARX1	56033	hgsc.bcm.edu	37	9	96714491	96714491	+	Silent	SNP	C	C	G	rs11793856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:96714491C>G	ENST00000253968.6	-	4	945	c.720G>C	c.(718-720)ccG>ccC	p.P240P	BARX1_ENST00000401724.1_Silent_p.P86P	NM_021570.3	NP_067545.3	Q9HBU1	BARX1_HUMAN	BARX homeobox 1	240					anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|digestive system development (GO:0055123)|epithelial cell differentiation (GO:0030855)|negative regulation of Wnt signaling pathway (GO:0030178)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)	1						GCACCTCCGCCGGTTTCTCTG	0.677													C|||	1021	0.203874	0.1815	0.317	5008	,	,		12492	0.0933		0.2823	False		,,,				2504	0.1871				p.P240P		Atlas-SNP	.											.	BARX1	9	.	0			c.G720C						PASS	.	C		890,3516	322.6+/-297.7	93,704,1406	32.0	30.0	31.0		720	-1.7	0.7	9	dbSNP_120	31	2381,6219	372.9+/-336.8	339,1703,2258	no	coding-synonymous	BARX1	NM_021570.3		432,2407,3664	GG,GC,CC		27.686,20.1997,25.1499		240/255	96714491	3271,9735	2203	4300	6503	SO:0001819	synonymous_variant	56033	exon4			CTCCGCCGGTTTC		CCDS35070.2	9q22.32	2011-06-20	2007-07-09		ENSG00000131668	ENSG00000131668		"""Homeoboxes / ANTP class : NKL subclass"""	955	protein-coding gene	gene with protein product		603260	"""BarH-like homeobox 1"""				Standard	NM_021570		Approved		uc010mrh.3	Q9HBU1	OTTHUMG00000020255	ENST00000253968.6:c.720G>C	9.37:g.96714491C>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_021570	Q6P2R4|Q96GH8	Silent	SNP	ENST00000253968.6	37	CCDS35070.2																																																																																			C|0.773;G|0.227	0.227	strong		0.677	BARX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053164.4		
ZNF577	84765	hgsc.bcm.edu	37	19	52376507	52376507	+	Missense_Mutation	SNP	T	T	C	rs2288868	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52376507T>C	ENST00000301399.5	-	7	1101	c.736A>G	c.(736-738)Aaa>Gaa	p.K246E	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000451628.2_Missense_Mutation_p.K187E|ZNF577_ENST00000420592.1_Missense_Mutation_p.K187E|ZNF577_ENST00000485702.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	246			K -> E (in dbSNP:rs2288868). {ECO:0000269|PubMed:15489334}.		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)		TTTCCGCATTTGCTGCATCTG	0.498													C|||	2537	0.506589	0.6808	0.4553	5008	,	,		20982	0.3026		0.3897	False		,,,				2504	0.638				p.K246E		Atlas-SNP	.											.	ZNF577	63	.	0			c.A736G						PASS	.	C	GLU/LYS,GLU/LYS	2801,1605		911,979,313	71.0	66.0	68.0		559,736	0.9	0.0	19	dbSNP_100	68	3326,5274		637,2052,1611	yes	missense,missense	ZNF577	NM_001135590.1,NM_032679.2	56,56	1548,3031,1924	CC,CT,TT		38.6744,36.4276,47.109	benign,benign	187/427,246/486	52376507	6127,6879	2203	4300	6503	SO:0001583	missense	84765	exon7			CGCATTTGCTGCA	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.736A>G	19.37:g.52376507T>C	ENSP00000301399:p.Lys246Glu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	37	CCDS12842.2	989	0.45283882783882784	335	0.6808943089430894	175	0.48342541436464087	177	0.3094405594405594	302	0.39841688654353563	.	0.004	-2.338582	0.00224	0.635724	0.386744	ENSG00000161551	ENST00000301399;ENST00000420592;ENST00000451628;ENST00000458390	T;T;T;T	0.07444	3.19;3.19;3.19;3.19	3.1	0.885	0.19188	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00991	-1.07	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33445	-0.9868	8	0.02654	T	1	.	7.5218	0.27633	0.0:0.6874:0.0:0.3126	rs2288868;rs17856122;rs52818789;rs60409315;rs2288868	246;187	Q9BSK1;Q9BSK1-2	ZN577_HUMAN;.	E	246;187;187;246	ENSP00000301399:K246E;ENSP00000413476:K187E;ENSP00000389652:K187E;ENSP00000404509:K246E	ENSP00000301399:K246E	K	-	1	0	ZNF577	57068319	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.289000	0.08365	-0.108000	0.12066	-0.119000	0.15052	AAA	T|0.520;C|0.480	0.480	strong		0.498	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
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 GAIIx	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	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	202	151	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	
TMEM86A	144110	hgsc.bcm.edu	37	11	18728650	18728650	+	IGR	SNP	T	T	C	rs2289965	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18728650T>C	ENST00000280734.2	+	0	3595				IGSF22_ENST00000510673.1_5'Flank|IGSF22_ENST00000513874.1_Missense_Mutation_p.I1131V|RP11-1081L13.4_ENST00000527285.1_RNA	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A							integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						TTCATGATGATGTAGTGAGCC	0.582													C|||	947	0.189097	0.0166	0.3429	5008	,	,		20413	0.1339		0.3976	False		,,,				2504	0.1554				p.I1131V		Atlas-SNP	.											.	IGSF22	211	.	0			c.A3391G						PASS	.	C	VAL/ILE	104,1280		8,88,596	176.0	140.0	151.0		3391	2.5	0.3	11	dbSNP_100	151	1267,1915		245,777,569	yes	missense	IGSF22	NM_173588.3	29	253,865,1165	CC,CT,TT		39.8177,7.5145,30.0263	benign	1131/1327	18728650	1371,3195	692	1591	2283	SO:0001628	intergenic_variant	283284	exon21			TGATGATGTAGTG	BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4			11.37:g.18728650T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_173588	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	511	0.23397435897435898	13	0.026422764227642278	133	0.3674033149171271	68	0.11888111888111888	297	0.391820580474934	C	8.429	0.848099	0.17034	0.075145	0.398177	ENSG00000179057	ENST00000513874	T	0.56444	0.46	3.57	2.53	0.30540	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	8	0.08179	T	0.78	.	4.9575	0.14050	0.0:0.612:0.1654:0.2226	rs2289965;rs17400035;rs52807214;rs60072054;rs2289965	1131	D6RGV7	.	V	1131	ENSP00000421191:I1131V	ENSP00000421191:I1131V	I	-	1	0	IGSF22	18685226	0.000000	0.05858	0.252000	0.24328	0.490000	0.33462	-0.206000	0.09398	0.218000	0.20820	-0.213000	0.12676	ATC	T|0.800;C|0.200	0.200	strong		0.582	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
TCHP	84260	hgsc.bcm.edu	37	12	110341933	110341933	+	Missense_Mutation	SNP	A	A	G	rs10774978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:110341933A>G	ENST00000312777.5	+	3	594	c.380A>G	c.(379-381)aAa>aGa	p.K127R	TCHP_ENST00000405876.4_Missense_Mutation_p.K127R	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						AAATCAGCCAAAGAAGAGCAG	0.562													G|||	1562	0.311901	0.674	0.1844	5008	,	,		19945	0.1438		0.1769	False		,,,				2504	0.2249				p.K127R		Atlas-SNP	.											.	TCHP	45	.	0			c.A380G						PASS	.	G	ARG/LYS,ARG/LYS	2603,1787		779,1045,371	50.0	45.0	47.0		380,380	3.3	1.0	12	dbSNP_120	47	1357,7219		108,1141,3039	yes	missense,missense	TCHP	NM_001143852.1,NM_032300.4	26,26	887,2186,3410	GG,GA,AA		15.8232,40.7062,30.5414	benign,benign	127/499,127/499	110341933	3960,9006	2195	4288	6483	SO:0001583	missense	84260	exon3			CAGCCAAAGAAGA	AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.380A>G	12.37:g.110341933A>G	ENSP00000324404:p.Lys127Arg	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	554	0.25366300366300365	301	0.6117886178861789	70	0.19337016574585636	54	0.0944055944055944	129	0.17018469656992086	G	0.176	-1.067266	0.01934	0.592938	0.158232	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.33865	2.2;2.2;1.39	5.21	3.3	0.37823	.	0.117657	0.56097	N	0.000036	T	0.00012	0.0000	N	0.00230	-1.795	0.09310	P	0.9999999999948324	B	0.02656	0.0	B	0.01281	0.0	T	0.47736	-0.9094	9	0.02654	T	1	-0.1723	8.7459	0.34587	0.2659:0.0:0.7341:0.0	rs10774978;rs61441019;rs10774978	127	Q9BT92	TCHP_HUMAN	R	127	ENSP00000384520:K127R;ENSP00000324404:K127R;ENSP00000441835:K127R	ENSP00000324404:K127R	K	+	2	0	TCHP	108826316	0.826000	0.29277	0.968000	0.41197	0.210000	0.24377	1.397000	0.34543	0.268000	0.21939	-1.101000	0.02118	AAA	A|0.700;G|0.300	0.300	strong		0.562	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
FCHO1	23149	hgsc.bcm.edu	37	19	17886940	17886940	+	Silent	SNP	G	G	A	rs2287854	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17886940G>A	ENST00000596536.1	+	16	1435	c.1152G>A	c.(1150-1152)gcG>gcA	p.A384A	FCHO1_ENST00000600676.1_Silent_p.A384A|FCHO1_ENST00000594202.1_Silent_p.A384A|FCHO1_ENST00000597512.1_Silent_p.A391A|FCHO1_ENST00000539407.1_Silent_p.A384A|FCHO1_ENST00000596951.1_Silent_p.A384A|FCHO1_ENST00000389133.4_Silent_p.A384A|FCHO1_ENST00000252771.7_Silent_p.A384A|FCHO1_ENST00000595033.1_Silent_p.A334A	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	384	Mediates interaction with the adaptor protein complex AP-2.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						GGGCCACCGCGGGCAGCCTCA	0.667													G|||	2874	0.573882	0.5696	0.536	5008	,	,		15073	0.7778		0.4006	False		,,,				2504	0.5746				p.A384A		Atlas-SNP	.											.	FCHO1	69	.	0			c.G1152A						PASS	.	G	,,,	2423,1983	613.9+/-392.3	666,1091,446	88.0	74.0	79.0		1152,1152,1002,1152	-9.3	0.0	19	dbSNP_100	79	3520,5080	509.4+/-377.3	747,2026,1527	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCHO1	NM_001161357.1,NM_001161358.1,NM_001161359.1,NM_015122.2	,,,	1413,3117,1973	AA,AG,GG		40.9302,45.0068,45.6943	,,,	384/892,384/890,334/840,384/890	17886940	5943,7063	2203	4300	6503	SO:0001819	synonymous_variant	23149	exon15			CACCGCGGGCAGC	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.1152G>A	19.37:g.17886940G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Silent	SNP	ENST00000596536.1	37	CCDS32955.1																																																																																			G|0.500;A|0.500	0.500	strong		0.667	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122	
RBMXL2	27288	hgsc.bcm.edu	37	11	7110363	7110363	+	Silent	SNP	G	G	A	rs4758158	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7110363G>A	ENST00000306904.5	+	1	199	c.12G>A	c.(10-12)gcG>gcA	p.A4A		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	4						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TGGTTGAAGCGGATCGCCCGG	0.652													G|||	1589	0.317292	0.1437	0.2954	5008	,	,		11303	0.4385		0.3648	False		,,,				2504	0.3937				p.A4A		Atlas-SNP	.											.	RBMXL2	47	.	0			c.G12A						PASS	.	G		670,3732	274.9+/-272.2	61,548,1592	30.0	33.0	32.0		12	-5.6	0.4	11	dbSNP_111	32	2890,5702	447.9+/-361.7	513,1864,1919	no	coding-synonymous	RBMXL2	NM_014469.4		574,2412,3511	AA,AG,GG		33.6359,15.2204,27.3973		4/393	7110363	3560,9434	2201	4296	6497	SO:0001819	synonymous_variant	27288	exon1			TGAAGCGGATCGC	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"""RNA binding motif (RRM) containing"""	17886	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G T"""	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.12G>A	11.37:g.7110363G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	124	65	0.524194	NM_014469	Q6PEZ2|Q9NQU0	Silent	SNP	ENST00000306904.5	37	CCDS7777.1																																																																																			G|0.709;A|0.291	0.291	strong		0.652	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469	
RABEP1	9135	hgsc.bcm.edu	37	17	5284719	5284719	+	Silent	SNP	T	T	C	rs1065482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5284719T>C	ENST00000546142.2	+	17	2593	c.2406T>C	c.(2404-2406)aaT>aaC	p.N802N	RABEP1_ENST00000262477.6_Silent_p.N802N|RABEP1_ENST00000408982.2_Silent_p.N769N|RABEP1_ENST00000537505.1_Silent_p.N759N|RABEP1_ENST00000341923.6_Silent_p.N769N|NUP88_ENST00000573169.1_Intron			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	802					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						AAGAGAAGAATAAAGCTCAGA	0.393													C|||	2765	0.552117	0.3964	0.4251	5008	,	,		21936	0.8254		0.4394	False		,,,				2504	0.6871				p.N802N		Atlas-SNP	.											.	RABEP1	59	.	0			c.T2406C						PASS	.	C	,	1531,2177		327,877,650	86.0	85.0	85.0		2307,2406	1.4	1.0	17	dbSNP_86	85	3199,4993		619,1961,1516	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	946,2838,2166	CC,CT,TT		39.0503,41.2891,39.7479	,	769/830,802/863	5284719	4730,7170	1854	4096	5950	SO:0001819	synonymous_variant	9135	exon17			GAAGAATAAAGCT	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2406T>C	17.37:g.5284719T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			T|0.500;C|0.500	0.500	strong		0.393	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
LIMK2	3985	hgsc.bcm.edu	37	22	31621792	31621792	+	Missense_Mutation	SNP	G	G	A	rs5997917	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:31621792G>A	ENST00000331728.4	+	2	217	c.103G>A	c.(103-105)Ggc>Agc	p.G35S	LIMK2_ENST00000444929.2_Missense_Mutation_p.G35S|LIMK2_ENST00000406516.1_Intron|RNU6-1128P_ENST00000362825.1_RNA	NM_005569.3	NP_005560.1	P53671	LIMK2_HUMAN	LIM domain kinase 2	35	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.		G -> S (in dbSNP:rs5997917). {ECO:0000269|PubMed:17344846}.		phosphorylation (GO:0016310)|spermatogenesis (GO:0007283)	cis-Golgi network (GO:0005801)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			endometrium(7)|kidney(3)|large_intestine(6)|lung(6)|ovary(2)|prostate(4)|skin(1)	29						AACCTGGCACGGCTCTTGCTT	0.507													G|||	1137	0.227037	0.5159	0.2522	5008	,	,		19778	0.0198		0.1292	False		,,,				2504	0.1329				p.G35S		Atlas-SNP	.											.	LIMK2	101	.	0			c.G103A						PASS	.	G	SER/GLY	2146,2260	575.3+/-384.0	531,1084,588	150.0	113.0	126.0		103	0.8	0.8	22	dbSNP_114	126	987,7613	213.1+/-253.2	58,871,3371	yes	missense	LIMK2	NM_005569.3	56	589,1955,3959	AA,AG,GG		11.4767,48.7063,24.0889	benign	35/639	31621792	3133,9873	2203	4300	6503	SO:0001583	missense	3985	exon2			TGGCACGGCTCTT	D45906	CCDS13891.1, CCDS13892.1, CCDS33637.1	22q12	2005-01-21			ENSG00000182541	ENSG00000182541			6614	protein-coding gene	gene with protein product		601988				8537403, 10591208	Standard	NM_005569		Approved		uc003akh.3	P53671	OTTHUMG00000151251	ENST00000331728.4:c.103G>A	22.37:g.31621792G>A	ENSP00000332687:p.Gly35Ser	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	197	84	0.426396	NM_005569	A8K6H5|Q7KZ80|Q7L3H5|Q96E10|Q99464|Q9UFU0	Missense_Mutation	SNP	ENST00000331728.4	37	CCDS13891.1	446	0.2042124542124542	252	0.5121951219512195	84	0.23204419889502761	9	0.015734265734265736	101	0.13324538258575197	G	1.054	-0.675097	0.03378	0.487063	0.114767	ENSG00000182541	ENST00000444929;ENST00000331728	T;D	0.86769	-0.66;-2.17	5.66	0.799	0.18667	Zinc finger, LIM-type (5);	.	.	.	.	T	0.00012	0.0000	N	0.00765	-1.205	0.52099	P	5.500000000002725E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.25676	-1.0125	8	0.02654	T	1	.	4.6983	0.12815	0.5177:0.3083:0.174:0.0	rs5997917;rs8140730;rs52802182;rs57331916;rs5997917	35;35	E7EUC1;P53671	.;LIMK2_HUMAN	S	35	ENSP00000409522:G35S;ENSP00000332687:G35S	ENSP00000332687:G35S	G	+	1	0	LIMK2	29951792	0.000000	0.05858	0.817000	0.32601	0.072000	0.16883	0.089000	0.15002	-0.193000	0.10415	-0.379000	0.06801	GGC	G|0.774;A|0.226	0.226	strong		0.507	LIMK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321911.1	NM_016733	
RSAD1	55316	hgsc.bcm.edu	37	17	48559559	48559559	+	Silent	SNP	A	A	G	rs7210579	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48559559A>G	ENST00000258955.2	+	4	667	c.582A>G	c.(580-582)gtA>gtG	p.V194V		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	194					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)			GCGTGTCTGTAGACTTGATGC	0.667											OREG0024567	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1429	0.285343	0.4909	0.2723	5008	,	,		13876	0.0804		0.2594	False		,,,				2504	0.2546				p.V194V		Atlas-SNP	.											RSAD1,colon,carcinoma,0,1	RSAD1	36	1	0			c.A582G						PASS	.	G		1952,2454	593.0+/-387.9	460,1032,711	34.0	39.0	37.0		582	3.4	1.0	17	dbSNP_116	37	2150,6448	680.1+/-403.6	296,1558,2445	no	coding-synonymous	RSAD1	NM_018346.1		756,2590,3156	GG,GA,AA		25.0058,44.3032,31.5441		194/443	48559559	4102,8902	2203	4299	6502	SO:0001819	synonymous_variant	55316	exon4			GTCTGTAGACTTG	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.582A>G	17.37:g.48559559A>G		Somatic	90	0	0	955	WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Silent	SNP	ENST00000258955.2	37	CCDS11569.1																																																																																			A|0.693;G|0.307	0.307	strong		0.667	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346	
CTCFL	140690	hgsc.bcm.edu	37	20	56090807	56090807	+	Silent	SNP	A	A	G	rs6025601	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:56090807A>G	ENST00000608263.1	-	5	1804	c.1143T>C	c.(1141-1143)gaT>gaC	p.D381D	CTCFL_ENST00000371196.2_Silent_p.D381D|CTCFL_ENST00000608425.1_Silent_p.D381D|CTCFL_ENST00000243914.3_Silent_p.D381D|CTCFL_ENST00000539382.1_Silent_p.D176D|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000422869.2_Silent_p.D381D|CTCFL_ENST00000433949.3_Silent_p.D176D|CTCFL_ENST00000423479.3_Silent_p.D381D|CTCFL_ENST00000608903.1_Silent_p.D119D|CTCFL_ENST00000502686.2_Silent_p.D119D|CTCFL_ENST00000429804.3_Silent_p.D381D|CTCFL_ENST00000608440.1_Silent_p.D381D|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000609232.1_Silent_p.D381D	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	381					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|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 (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GCTTGTAGGTATCTCTGCTGG	0.473													G|||	1645	0.328474	0.4092	0.33	5008	,	,		18536	0.369		0.2097	False		,,,				2504	0.2986				p.D381D		Atlas-SNP	.											CTCFL,bladder,carcinoma,-2,2	CTCFL	97	2	0			c.T1143C						scavenged	.	G		1579,2827	666.5+/-401.7	259,1061,883	176.0	166.0	170.0		1143	2.9	1.0	20	dbSNP_114	170	1675,6925	739.7+/-407.1	172,1331,2797	no	coding-synonymous	CTCFL	NM_080618.2		431,2392,3680	GG,GA,AA		19.4767,35.8375,25.0192		381/664	56090807	3254,9752	2203	4300	6503	SO:0001819	synonymous_variant	140690	exon5			GTAGGTATCTCTG		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1143T>C	20.37:g.56090807A>G		Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Silent	SNP	ENST00000608263.1	37	CCDS13459.1																																																																																			A|0.717;G|0.283	0.283	strong		0.473	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
NDST3	9348	hgsc.bcm.edu	37	4	119158345	119158345	+	Silent	SNP	C	C	T	rs138955155	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:119158345C>T	ENST00000296499.5	+	10	2491	c.2088C>T	c.(2086-2088)gaC>gaT	p.D696D		NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	696	Heparan sulfate N-sulfotransferase 3.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	54						TTCTCATTGACCCTTCAGACC	0.433													C|||	39	0.00778754	0.0008	0.0072	5008	,	,		15903	0.0		0.0149	False		,,,				2504	0.0184				p.D696D		Atlas-SNP	.											.	NDST3	107	.	0			c.C2088T						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	84.0	78.0	80.0		2088	4.2	1.0	4	dbSNP_134	80	109,8491	58.7+/-120.3	0,109,4191	no	coding-synonymous	NDST3	NM_004784.2		0,117,6386	TT,TC,CC		1.2674,0.1816,0.8996		696/874	119158345	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	9348	exon10			CATTGACCCTTCA	AF074924	CCDS3708.1	4q26	2008-08-04			ENSG00000164100	ENSG00000164100		"""Sulfotransferases, membrane-bound"""	7682	protein-coding gene	gene with protein product		603950				9915799	Standard	NM_004784		Approved	HSST3	uc003ibx.3	O95803	OTTHUMG00000132959	ENST00000296499.5:c.2088C>T	4.37:g.119158345C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Silent	SNP	ENST00000296499.5	37	CCDS3708.1																																																																																			C|0.990;T|0.010	0.010	strong		0.433	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784	
LINC00283	100874057	hgsc.bcm.edu	37	13	103400083	103400083	+	RNA	SNP	G	G	A	rs1026158	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103400083G>A	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		GTCTATCTGTGCTTTGCTTCA	0.423													G|||	2430	0.485224	0.1331	0.6513	5008	,	,		19922	0.4702		0.674	False		,,,				2504	0.6646				p.S988S		Atlas-SNP	.											.	.	.	.	0			c.C2964T						PASS	.	G		325,1059		49,227,416	192.0	157.0	168.0		2964	1.5	0.0	13	dbSNP_86	168	2093,1089		697,699,195	no	coding-synonymous	CCDC168	NM_001146197.1		746,926,611	AA,AG,GG		34.2238,23.4827,47.0434		988/7082	103400083	2418,2148	692	1591	2283			643677	exon4			ATCTGTGCTTTGC			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103400083G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	140	104	0.742857	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				G|0.544;A|0.456	0.456	strong		0.423	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
SERPINB10	5273	hgsc.bcm.edu	37	18	61600384	61600384	+	Missense_Mutation	SNP	C	C	T	rs963075	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61600384C>T	ENST00000238508.3	+	7	795	c.736C>T	c.(736-738)Cgt>Tgt	p.R246C		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	246			R -> C (in dbSNP:rs963075).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				CTACAAAAGCCGTGACCTCAG	0.413													C|||	2367	0.472644	0.7731	0.4193	5008	,	,		19382	0.4623		0.2942	False		,,,				2504	0.2986				p.R246C		Atlas-SNP	.											SERPINB10,colon,carcinoma,0,1	SERPINB10	53	1	0			c.C736T						PASS	.	C	CYS/ARG	3064,1342	693.0+/-405.6	1057,950,196	123.0	137.0	132.0		736	0.7	0.0	18	dbSNP_86	132	2224,6376	377.7+/-338.6	310,1604,2386	yes	missense	SERPINB10	NM_005024.1	180	1367,2554,2582	TT,TC,CC		25.8605,30.4585,40.6582		246/398	61600384	5288,7718	2203	4300	6503	SO:0001583	missense	5273	exon6			AAAAGCCGTGACC	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.736C>T	18.37:g.61600384C>T	ENSP00000238508:p.Arg246Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	959	0.4391025641025641	357	0.725609756097561	144	0.39779005524861877	243	0.42482517482517484	215	0.2836411609498681	C	6.757	0.508440	0.12883	0.695415	0.258605	ENSG00000242550	ENST00000238508	D	0.83250	-1.7	5.95	0.68	0.17980	Serpin domain (3);	0.740672	0.13840	N	0.359069	T	0.00012	0.0000	M	0.78916	2.43	0.80722	P	0.0	B	0.22346	0.068	B	0.15484	0.013	T	0.41574	-0.9501	9	0.52906	T	0.07	.	1.2349	0.01951	0.2737:0.303:0.2636:0.1597	rs963075;rs58118394;rs963075	246	P48595	SPB10_HUMAN	C	246	ENSP00000238508:R246C	ENSP00000238508:R246C	R	+	1	0	SERPINB10	59751364	0.000000	0.05858	0.018000	0.16275	0.041000	0.13682	-0.160000	0.10041	0.380000	0.24823	0.655000	0.94253	CGT	C|0.570;T|0.430	0.430	strong		0.413	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
PCF11	51585	hgsc.bcm.edu	37	11	82875359	82875359	+	Silent	SNP	G	G	A	rs7130527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:82875359G>A	ENST00000298281.4	+	4	1070	c.618G>A	c.(616-618)caG>caA	p.Q206Q		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	206					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TAATAAGGCAGCAGTTACTGG	0.428													A|||	519	0.103634	0.1641	0.0663	5008	,	,		15411	0.0496		0.0805	False		,,,				2504	0.1278				p.Q206Q		Atlas-SNP	.											.	PCF11	220	.	0			c.G618A						PASS	.	A		547,3157		44,459,1349	58.0	52.0	54.0		618	-2.9	1.0	11	dbSNP_116	54	702,7482		27,648,3417	no	coding-synonymous	PCF11	NM_015885.3		71,1107,4766	AA,AG,GG		8.5777,14.7678,10.5064		206/1556	82875359	1249,10639	1852	4092	5944	SO:0001819	synonymous_variant	51585	exon4			AAGGCAGCAGTTA	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.618G>A	11.37:g.82875359G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	11	0.141026	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			G|0.905;A|0.095	0.095	strong		0.428	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
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 GAIIx	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*	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	144	74	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		
MYOM3	127294	hgsc.bcm.edu	37	1	24421950	24421950	+	Missense_Mutation	SNP	C	C	G	rs4319261	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:24421950C>G	ENST00000374434.3	-	8	934	c.772G>C	c.(772-774)Gat>Cat	p.D258H	MYOM3_ENST00000330966.7_Missense_Mutation_p.D259H|MYOM3_ENST00000329601.7_Missense_Mutation_p.D258H|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	258			D -> H (in dbSNP:rs4319261). {ECO:0000269|PubMed:17974005}.			M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		ATCTCTGAATCGAAGCCAGCA	0.507													C|||	2056	0.410543	0.5416	0.3386	5008	,	,		18793	0.377		0.497	False		,,,				2504	0.2301				p.D258H		Atlas-SNP	.											.	MYOM3	131	.	0			c.G772C						PASS	.	C	HIS/ASP	1877,1889		489,899,495	110.0	113.0	112.0		772	5.8	1.0	1	dbSNP_111	112	3907,4327		929,2049,1139	yes	missense	MYOM3	NM_152372.3	81	1418,2948,1634	GG,GC,CC		47.4496,49.8407,48.2	benign	258/1438	24421950	5784,6216	1883	4117	6000	SO:0001583	missense	127294	exon8			CTGAATCGAAGCC	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.772G>C	1.37:g.24421950C>G	ENSP00000363557:p.Asp258His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	1004	0.4597069597069597	275	0.5589430894308943	136	0.3756906077348066	200	0.34965034965034963	393	0.5184696569920845	C	8.135	0.783923	0.16189	0.498407	0.474496	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.58358	0.38;0.39;0.34	5.81	5.81	0.92471	.	0.367568	0.32918	N	0.005498	T	0.00012	0.0000	N	0.20530	0.585	0.24931	P	0.99191579	B;D	0.76494	0.235;0.999	B;P	0.60117	0.097;0.869	T	0.48547	-0.9026	9	0.24483	T	0.36	.	17.0405	0.86488	0.0:1.0:0.0:0.0	rs4319261;rs4319261	258;258	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	H	258;259;258	ENSP00000363557:D258H;ENSP00000332670:D259H;ENSP00000328415:D258H	ENSP00000328415:D258H	D	-	1	0	MYOM3	24294537	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	4.329000	0.59260	2.764000	0.94973	0.558000	0.71614	GAT	C|0.542;G|0.458	0.458	strong		0.507	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
POGK	57645	hgsc.bcm.edu	37	1	166818566	166818566	+	Silent	SNP	A	A	G	rs2075946	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:166818566A>G	ENST00000367875.1	+	5	1110	c.750A>G	c.(748-750)gcA>gcG	p.A250A	POGK_ENST00000537173.1_Silent_p.A132A|POGK_ENST00000536514.1_Silent_p.A165A|POGK_ENST00000367876.4_Silent_p.A250A			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	250	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	22						TGCGGCGGGCATTCCGAGGCC	0.577													A|||	1386	0.276757	0.152	0.17	5008	,	,		19070	0.5565		0.162	False		,,,				2504	0.3507				p.A250A	GBM(76;192 1530 30153 48742)	Atlas-SNP	.											.	POGK	54	.	0			c.A750G						PASS	.	A		769,3637	285.5+/-278.2	61,647,1495	38.0	41.0	40.0		750	-11.0	0.0	1	dbSNP_96	40	1593,7007	271.9+/-289.8	144,1305,2851	no	coding-synonymous	POGK	NM_017542.3		205,1952,4346	GG,GA,AA		18.5233,17.4535,18.1608		250/610	166818566	2362,10644	2203	4300	6503	SO:0001819	synonymous_variant	57645	exon5			GCGGGCATTCCGA	AB040946	CCDS1254.1	1q23.2	2013-01-08			ENSG00000143157	ENSG00000143157		"""-"""	18800	protein-coding gene	gene with protein product	"""KRAB box domain containing 2"""						Standard	NM_017542		Approved	KIAA15131, LST003, BASS2, KRBOX2	uc001gdt.1	Q9P215	OTTHUMG00000034325	ENST00000367875.1:c.750A>G	1.37:g.166818566A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_017542	Q5TIJ1|Q8TE07	Silent	SNP	ENST00000367875.1	37	CCDS1254.1																																																																																			A|0.786;G|0.214	0.214	strong		0.577	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542	
SMCR8	140775	hgsc.bcm.edu	37	17	18221134	18221134	+	Silent	SNP	C	C	T	rs1563631	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18221134C>T	ENST00000406438.3	+	1	2511	c.2031C>T	c.(2029-2031)taC>taT	p.Y677Y	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	677						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CCACCAGCTACGTGAGCAGTG	0.577													C|||	895	0.178714	0.1611	0.2421	5008	,	,		20625	0.0605		0.3062	False		,,,				2504	0.1483				p.Y677Y		Atlas-SNP	.											SMCR8,colon,carcinoma,0,1	SMCR8	62	1	0			c.C2031T						PASS	.	C		922,3484	355.1+/-312.9	87,748,1368	77.0	75.0	76.0		2031	-9.4	0.0	17	dbSNP_88	76	2597,6003	423.1+/-354.3	382,1833,2085	yes	coding-synonymous	SMCR8	NM_144775.2		469,2581,3453	TT,TC,CC		30.1977,20.926,27.0567		677/938	18221134	3519,9487	2203	4300	6503	SO:0001819	synonymous_variant	140775	exon1			CAGCTACGTGAGC	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.2031C>T	17.37:g.18221134C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			C|0.770;T|0.230	0.230	strong		0.577	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
GP2	2813	hgsc.bcm.edu	37	16	20335325	20335325	+	Silent	SNP	G	G	A	rs12930599	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20335325G>A	ENST00000381362.4	-	3	424	c.348C>T	c.(346-348)gaC>gaT	p.D116D	GP2_ENST00000381360.5_Intron|GP2_ENST00000573897.1_5'Flank|GP2_ENST00000341642.5_Intron|GP2_ENST00000302555.5_Silent_p.D116D	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	116					antigen transcytosis by M cells in mucosal-associated lymphoid tissue (GO:0002412)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(25)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48						ACATGGGAGCGTCTGTCTGGC	0.572													G|||	414	0.0826677	0.0068	0.1772	5008	,	,		18878	0.0089		0.2256	False		,,,				2504	0.047				p.D116D		Atlas-SNP	.											.	GP2	122	.	0			c.C348T						PASS	.	G	,,,	205,4201	124.5+/-161.8	3,199,2001	98.0	77.0	84.0		348,,,348	-10.0	0.0	16	dbSNP_121	84	1890,6710	335.5+/-321.5	201,1488,2611	no	coding-synonymous,intron,intron,coding-synonymous	GP2	NM_001007240.1,NM_001007241.1,NM_001007242.1,NM_001502.2	,,,	204,1687,4612	AA,AG,GG		21.9767,4.6527,16.108	,,,	116/538,,,116/535	20335325	2095,10911	2203	4300	6503	SO:0001819	synonymous_variant	2813	exon3			GGGAGCGTCTGTC	U36221	CCDS10582.2, CCDS42128.1, CCDS45432.1, CCDS45433.1	16p12.3	2008-02-05			ENSG00000169347	ENSG00000169347			4441	protein-coding gene	gene with protein product		602977				9605860	Standard	XM_005255259		Approved		uc002dgw.3	P55259	OTTHUMG00000131489	ENST00000381362.4:c.348C>T	16.37:g.20335325G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_001007240	A6NFM9|A6NJA8|Q13338|Q9UIF1	Silent	SNP	ENST00000381362.4	37	CCDS42128.1																																																																																			G|0.865;A|0.135	0.135	strong		0.572	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295	
CRMP1	1400	hgsc.bcm.edu	37	4	5830296	5830296	+	Missense_Mutation	SNP	C	C	T	rs34611001	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:5830296C>T	ENST00000397890.2	-	12	1595	c.1381G>A	c.(1381-1383)Gtc>Atc	p.V461I	CRMP1_ENST00000512574.1_Missense_Mutation_p.V459I|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Missense_Mutation_p.V575I|EVC_ENST00000382674.2_3'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	461			V -> I (in dbSNP:rs34611001).		axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|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)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CCCTTGTTGACGTTGATGTTT	0.567													C|||	65	0.0129792	0.0008	0.0231	5008	,	,		19907	0.0218		0.0229	False		,,,				2504	0.0031				p.V575I		Atlas-SNP	.											.	CRMP1	118	.	0			c.G1723A						PASS	.	C	ILE/VAL,ILE/VAL	18,4388	25.3+/-52.1	0,18,2185	162.0	111.0	129.0		1723,1381	4.3	0.0	4	dbSNP_126	129	217,8383	91.1+/-153.3	1,215,4084	yes	missense,missense	CRMP1	NM_001014809.1,NM_001313.3	29,29	1,233,6269	TT,TC,CC		2.5233,0.4085,1.8069	probably-damaging,probably-damaging	575/687,461/573	5830296	235,12771	2203	4300	6503	SO:0001583	missense	1400	exon12			TGTTGACGTTGAT	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1381G>A	4.37:g.5830296C>T	ENSP00000380987:p.Val461Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	110	41	0.372727	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Missense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	37	0.01694139194139194	0	0.0	7	0.019337016574585635	10	0.017482517482517484	20	0.026385224274406333	C	11.74	1.727991	0.30593	0.004085	0.025233	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	T;T;T	0.74209	-0.82;-0.82;-0.82	4.33	4.33	0.51752	Metal-dependent hydrolase, composite domain (1);	0.066261	0.64402	D	0.000012	T	0.47002	0.1422	M	0.75150	2.29	0.46798	D	0.9992	B;P;B;P	0.42993	0.055;0.618;0.106;0.797	B;B;B;B	0.29077	0.014;0.057;0.021;0.098	T	0.72814	-0.4179	10	0.87932	D	0	-45.9591	15.9993	0.80280	0.0:1.0:0.0:0.0	rs34611001	575;459;461;398	A0EJG6;E9PD68;Q14194;B3KT07	.;.;DPYL1_HUMAN;.	I	575;461;461;459	ENSP00000321606:V575I;ENSP00000380987:V461I;ENSP00000425742:V459I	ENSP00000321606:V575I	V	-	1	0	CRMP1	5881197	0.988000	0.35896	0.044000	0.18714	0.050000	0.14768	3.630000	0.54273	2.245000	0.73994	0.561000	0.74099	GTC	C|0.984;T|0.016	0.016	strong		0.567	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
MTCL1	23255	hgsc.bcm.edu	37	18	8825096	8825096	+	Silent	SNP	G	G	A	rs113084211	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:8825096G>A	ENST00000306329.11	+	13	4545	c.4545G>A	c.(4543-4545)ccG>ccA	p.P1515P	SOGA2_ENST00000400050.3_Silent_p.P1155P|SOGA2_ENST00000306285.7_Silent_p.P521P|SOGA2_ENST00000517570.1_Silent_p.P1155P|SOGA2_ENST00000359865.3_Silent_p.P1196P|SOGA2_ENST00000518815.1_Silent_p.P521P																							TACACAGCCCGCCTGCCGTGC	0.672													G|||	20	0.00399361	0.0008	0.0029	5008	,	,		18045	0.0		0.0139	False		,,,				2504	0.0031				p.P1196P		Atlas-SNP	.											.	.	.	.	0			c.G3588A						PASS	.	G		20,4358		0,20,2169	44.0	37.0	39.0		3588	-7.8	0.1	18	dbSNP_132	39	180,8386		1,178,4104	no	coding-synonymous	CCDC165	NM_015210.3		1,198,6273	AA,AG,GG		2.1013,0.4568,1.5451		1196/1587	8825096	200,12744	2189	4283	6472	SO:0001819	synonymous_variant	23255	exon15			CAGCCCGCCTGCC																												ENST00000306329.11:c.4545G>A	18.37:g.8825096G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	99	34	0.343434	NM_015210		Silent	SNP	ENST00000306329.11	37																																																																																				G|0.987;A|0.013	0.013	strong		0.672	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
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 GAIIx	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		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	112	40	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	
PINX1	54984	hgsc.bcm.edu	37	8	10623138	10623138	+	Missense_Mutation	SNP	T	T	A	rs1078543	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:10623138T>A	ENST00000314787.3	-	7	879	c.760A>T	c.(760-762)Agc>Tgc	p.S254C	PINX1_ENST00000426190.2_3'UTR|SOX7_ENST00000553390.1_Intron|PINX1_ENST00000519088.1_3'UTR|CTD-2135J3.3_ENST00000506149.2_RNA|CTD-2135J3.3_ENST00000519568.1_RNA|SOX7_ENST00000554914.1_Intron	NM_017884.4	NP_060354.4	Q96BK5	PINX1_HUMAN	PIN2/TERF1 interacting, telomerase inhibitor 1	254	Telomerase inhibitory domain (TID).		S -> C (in dbSNP:rs1078543). {ECO:0000269|PubMed:11701125}.		mitotic metaphase plate congression (GO:0007080)|negative regulation of cell proliferation (GO:0008285)|negative regulation of telomerase activity (GO:0051974)|regulation of telomerase activity (GO:0051972)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|spindle (GO:0005819)	telomerase inhibitor activity (GO:0010521)|telomeric RNA binding (GO:0070034)			kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)		GCTGGCGCGCTCTTCTTCTTG	0.632													T|||	943	0.188299	0.438	0.1124	5008	,	,		14708	0.0288		0.1372	False		,,,				2504	0.1217				p.S254C		Atlas-SNP	.											PINX1,NS,carcinoma,+2,1	PINX1	38	1	0			c.A760T						PASS	.	T	CYS/SER	1441,2431		260,921,755	47.0	52.0	50.0		760	4.1	0.5	8	dbSNP_86	50	1075,7201		51,973,3114	yes	missense	PINX1	NM_017884.4	112	311,1894,3869	AA,AT,TT		12.9894,37.2159,20.7112		254/329	10623138	2516,9632	1936	4138	6074	SO:0001583	missense	54984	exon7			GCGCGCTCTTCTT	AF418553	CCDS47801.1, CCDS64825.1	8p23	2013-01-28				ENSG00000254093		"""G patch domain containing"""	30046	protein-coding gene	gene with protein product	"""PIN2 interacting protein 1"", ""liver-related putative tumor suppressor"""	606505				11003615, 11701125	Standard	NM_001284356		Approved	PinX1, LPTL, LPTS, FLJ20565, MGC8850		Q96BK5		ENST00000314787.3:c.760A>T	8.37:g.10623138T>A	ENSP00000318966:p.Ser254Cys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_017884	B2R9B1|Q548A5|Q6QWG9|Q7Z7J8|Q96QD7|Q9HBU7|Q9NWW2	Missense_Mutation	SNP	ENST00000314787.3	37	CCDS47801.1	368	0.1684981684981685	208	0.42276422764227645	39	0.10773480662983426	20	0.03496503496503497	101	0.13324538258575197	T	11.99	1.803132	0.31869	0.372159	0.129894	ENSG00000254093	ENST00000314787	T	0.18960	2.18	5.27	4.13	0.48395	.	0.753612	0.12935	N	0.427064	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.999999999540518	P	0.48640	0.913	B	0.43103	0.408	T	0.48317	-0.9046	9	0.49607	T	0.09	.	7.5449	0.27761	0.0:0.094:0.0:0.906	rs1078543;rs2280046;rs1078543	254	Q96BK5	PINX1_HUMAN	C	254	ENSP00000318966:S254C	ENSP00000318966:S254C	S	-	1	0	PINX1	10660548	0.030000	0.19436	0.489000	0.27452	0.075000	0.17131	0.167000	0.16602	1.033000	0.39918	0.533000	0.62120	AGC	T|0.831;A|0.169	0.169	strong		0.632	PINX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375683.1	NM_017884	
OR6B1	135946	hgsc.bcm.edu	37	7	143701884	143701884	+	Silent	SNP	C	C	T	rs728275	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143701884C>T	ENST00000408922.2	+	1	863	c.795C>T	c.(793-795)gcC>gcT	p.A265A		NM_001005281.1	NP_001005281.1	O95007	OR6B1_HUMAN	olfactory receptor, family 6, subfamily B, member 1	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(3)|large_intestine(3)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	27	Melanoma(164;0.0783)					TTATCCATGCCTTCAACATGA	0.428													C|||	1939	0.387181	0.3381	0.5461	5008	,	,		23941	0.5823		0.3201	False		,,,				2504	0.2086				p.A265A		Atlas-SNP	.											.	OR6B1	60	.	0			c.C795T						PASS	.	C		1274,2644		199,876,884	138.0	129.0	132.0		795	2.4	1.0	7	dbSNP_86	132	2979,5325		542,1895,1715	no	coding-synonymous	OR6B1	NM_001005281.1		741,2771,2599	TT,TC,CC		35.8743,32.5166,34.7979		265/312	143701884	4253,7969	1959	4152	6111	SO:0001819	synonymous_variant	135946	exon1			CCATGCCTTCAAC		CCDS43667.1	7q33-q35	2012-08-09			ENSG00000221813	ENSG00000221813		"""GPCR / Class A : Olfactory receptors"""	8354	protein-coding gene	gene with protein product							Standard	NM_001005281		Approved	OR7-3	uc003wdt.1	O95007	OTTHUMG00000157765	ENST00000408922.2:c.795C>T	7.37:g.143701884C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001005281	A4D2G2|B9EH47|Q6IFP6|Q96R38	Silent	SNP	ENST00000408922.2	37	CCDS43667.1																																																																																			C|0.586;T|0.414	0.414	strong		0.428	OR6B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349566.1		
HMCN1	83872	hgsc.bcm.edu	37	1	186026474	186026474	+	Missense_Mutation	SNP	T	T	C	rs12129650	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186026474T>C	ENST00000271588.4	+	46	7482	c.7253T>C	c.(7252-7254)aTa>aCa	p.I2418T	HMCN1_ENST00000367492.2_Missense_Mutation_p.I2418T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2418	Ig-like C2-type 22.		I -> T (in dbSNP:rs12129650). {ECO:0000269|PubMed:14570714, ECO:0000269|Ref.1}.		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						CTGCCTTCCATAACCTGGTTC	0.413													T|||	2654	0.529952	0.5393	0.6124	5008	,	,		15388	0.5675		0.496	False		,,,				2504	0.455				p.I2418T		Atlas-SNP	.											.	HMCN1	797	.	0			c.T7253C						PASS	.	T	THR/ILE	2446,1960	619.5+/-393.4	686,1074,443	115.0	115.0	115.0		7253	4.7	0.9	1	dbSNP_120	115	4387,4213	583.2+/-391.5	1138,2111,1051	yes	missense	HMCN1	NM_031935.2	89	1824,3185,1494	CC,CT,TT		48.9884,44.4848,47.4627	benign	2418/5636	186026474	6833,6173	2203	4300	6503	SO:0001583	missense	83872	exon46			CTTCCATAACCTG	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.7253T>C	1.37:g.186026474T>C	ENSP00000271588:p.Ile2418Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1198	0.5485347985347986	254	0.516260162601626	216	0.5966850828729282	341	0.5961538461538461	387	0.5105540897097626	T	18.19	3.569521	0.65765	0.555152	0.510116	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.72282	-0.64;-0.64	5.8	4.67	0.58626	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.183947	0.56097	N	0.000027	T	0.00012	0.0000	M	0.85542	2.76	0.20307	P	0.9999161177	P	0.48998	0.918	B	0.44315	0.446	T	0.47674	-0.9099	9	0.56958	D	0.05	.	11.7655	0.51928	0.0:0.0685:0.0:0.9315	rs12129650;rs52819931;rs57046032;rs12129650	2418	Q96RW7	HMCN1_HUMAN	T	2418	ENSP00000271588:I2418T;ENSP00000356462:I2418T	ENSP00000271588:I2418T	I	+	2	0	HMCN1	184293097	1.000000	0.71417	0.907000	0.35723	0.830000	0.47004	5.743000	0.68655	1.020000	0.39573	-0.263000	0.10527	ATA	C|0.538;N|0.000	0.538	strong		0.413	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
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 GAIIx	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		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	60	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	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45502844	45502844	+	Missense_Mutation	SNP	T	T	G	rs915877	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45502844T>G	ENST00000291574.4	+	14	2074	c.1899T>G	c.(1897-1899)atT>atG	p.I633M		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	633			I -> M (in dbSNP:rs915877). {ECO:0000269|PubMed:9370297}.		sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						ACTTCAGCATTGAGAAAAACA	0.517													T|||	245	0.0489217	0.0825	0.0389	5008	,	,		21901	0.0		0.0626	False		,,,				2504	0.047				p.I633M		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.T1899G						PASS	.	T	MET/ILE	377,4029	193.3+/-218.5	15,347,1841	168.0	149.0	156.0		1899	-10.8	0.2	21	dbSNP_86	156	531,8069	148.6+/-203.8	20,491,3789	yes	missense	TRAPPC10	NM_003274.4	10	35,838,5630	GG,GT,TT		6.1744,8.5565,6.9814	possibly-damaging	633/1260	45502844	908,12098	2203	4300	6503	SO:0001583	missense	7109	exon14			CAGCATTGAGAAA	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.1899T>G	21.37:g.45502844T>G	ENSP00000291574:p.Ile633Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	153	97	0.633987	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	98	0.04487179487179487	35	0.07113821138211382	13	0.03591160220994475	0	0.0	50	0.06596306068601583	T	15.27	2.783165	0.49891	0.085565	0.061744	ENSG00000160218	ENST00000291574	T	0.46451	0.87	5.58	-10.8	0.00216	.	0.351400	0.30667	N	0.009139	T	0.00496	0.0016	N	0.14661	0.345	0.31699	N	0.640884	P	0.42735	0.788	B	0.35971	0.215	T	0.38023	-0.9680	10	0.46703	T	0.11	.	7.8181	0.29271	0.084:0.0992:0.1674:0.6494	rs915877;rs17178647;rs52822086;rs915877	633	P48553	TPC10_HUMAN	M	633	ENSP00000291574:I633M	ENSP00000291574:I633M	I	+	3	3	TRAPPC10	44327272	0.046000	0.20272	0.230000	0.23976	0.954000	0.61252	-0.971000	0.03806	-2.204000	0.00743	-1.151000	0.01829	ATT	T|0.954;G|0.046	0.046	strong		0.517	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
PAPPA	5069	hgsc.bcm.edu	37	9	119158814	119158814	+	Silent	SNP	T	T	C	rs8456	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:119158814T>C	ENST00000328252.3	+	22	5172	c.4803T>C	c.(4801-4803)gaT>gaC	p.D1601D	PAPPA_ENST00000483254.1_3'UTR|AL137024.1_ENST00000401363.1_RNA|PAPPA_ENST00000534838.1_Silent_p.D639D	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1601					cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						TGTCCTGTGATCTACAAGGTG	0.527													C|||	3367	0.672324	0.5703	0.7349	5008	,	,		19633	0.6438		0.6938	False		,,,				2504	0.773				p.D1601D		Atlas-SNP	.											.	PAPPA	243	.	0			c.T4803C						PASS	.	C		2559,1847	537.8+/-374.8	732,1095,376	202.0	176.0	185.0		4803	4.7	1.0	9	dbSNP_120	185	6106,2494	410.2+/-350.1	2157,1792,351	no	coding-synonymous	PAPPA	NM_002581.3		2889,2887,727	CC,CT,TT		29.0,41.9201,33.3769		1601/1628	119158814	8665,4341	2203	4300	6503	SO:0001819	synonymous_variant	5069	exon22			CTGTGATCTACAA		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.4803T>C	9.37:g.119158814T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																			C|0.669;N|0.001	0.669	strong		0.527	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
CFLAR	8837	hgsc.bcm.edu	37	2	202006096	202006096	+	Intron	SNP	G	G	A	rs10190751	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:202006096G>A	ENST00000309955.3	+	5	1121				CFLAR_ENST00000341582.6_Intron|CFLAR_ENST00000341222.6_Splice_Site|CFLAR_ENST00000342795.5_Intron|CFLAR_ENST00000457277.1_Intron|CFLAR-AS1_ENST00000594911.1_RNA|CFLAR_ENST00000443227.1_Intron|CFLAR_ENST00000340870.5_Intron|CFLAR-AS1_ENST00000598453.1_RNA|CFLAR_ENST00000440180.1_Splice_Site|CFLAR_ENST00000355558.4_Intron|CFLAR-AS1_ENST00000474886.2_RNA|CFLAR_ENST00000423241.2_Intron|CFLAR_ENST00000479953.2_Intron|RNU7-45P_ENST00000459460.1_RNA|CFLAR-AS1_ENST00000415011.2_RNA	NM_001202515.1|NM_003879.5	NP_001189444.1|NP_003870.4	O15519	CFLAR_HUMAN	CASP8 and FADD-like apoptosis regulator						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of myoblast fusion (GO:1901740)|positive regulation of catalytic activity (GO:0043085)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of necroptotic process (GO:0060544)|regulation of satellite cell proliferation (GO:0014842)|skeletal muscle atrophy (GO:0014732)|skeletal muscle tissue development (GO:0007519)|skeletal muscle tissue regeneration (GO:0043403)|skeletal myofibril assembly (GO:0014866)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|ripoptosome (GO:0097342)	cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|enzyme activator activity (GO:0008047)|protease binding (GO:0002020)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|stomach(1)	13						ctcttctacagatgataacac	0.338													A|||	1084	0.216454	0.4622	0.147	5008	,	,		18717	0.0516		0.2147	False		,,,				2504	0.1053				.	Pancreas(16;548 657 22190 32864 42338)	Atlas-SNP	.											.	CFLAR	37	.	0			c.607-1G>A						PASS	.	A	,,,,,,,	1221,1891		265,691,600	115.0	94.0	100.0		,,,,,,,	-4.6	0.0	2	dbSNP_119	100	1377,5755		145,1087,2334	yes	intron,splice-3,intron,intron,intron,intron,intron,intron	CFLAR	NM_001127183.2,NM_001127184.2,NM_001202515.1,NM_001202516.1,NM_001202517.1,NM_001202518.1,NM_001202519.1,NM_003879.5	,,,,,,,	410,1778,2934	AA,AG,GG		19.3073,39.2352,25.3612	,,,,,,,	,,,,,,,	202006096	2598,7646	1556	3566	5122	SO:0001627	intron_variant	8837	exon6			TCTACAGATGATA	AF005774	CCDS2337.1, CCDS46487.1, CCDS56157.1, CCDS56158.1, CCDS59436.1	2q33-q34	2014-01-30			ENSG00000003402	ENSG00000003402		"""Endogenous ligands"""	1876	protein-coding gene	gene with protein product		603599		CASP8AP1		9208847, 9217161	Standard	NM_003879		Approved	CASH, Casper, CLARP, FLAME, FLIP, I-FLICE, MRIT, c-FLIP	uc002uxb.4	O15519	OTTHUMG00000132819	ENST00000309955.3:c.606+934G>A	2.37:g.202006096G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	121	49	0.404959	NM_001127184	B4DJE0|B7Z9F9|O14673|O14674|O14675|O15137|O15138|O15356|O15510|O43618|O43619|O43620|O60458|O60459|Q53TS6|Q54AF1|Q96TE4|Q9UEW1	Splice_Site	SNP	ENST00000309955.3	37	CCDS2337.1																																																																																			G|0.764;A|0.236	0.236	strong		0.338	CFLAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256276.3	NM_003879	
PMPCA	23203	hgsc.bcm.edu	37	9	139306467	139306467	+	Silent	SNP	C	C	T	rs10870144	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139306467C>T	ENST00000371717.3	+	2	99	c.90C>T	c.(88-90)taC>taT	p.Y30Y	SDCCAG3_ENST00000371725.3_5'Flank|PMPCA_ENST00000371720.1_Silent_p.Y30Y|PMPCA_ENST00000399219.3_5'UTR|SDCCAG3_ENST00000298537.7_5'Flank|SDCCAG3_ENST00000357365.3_5'Flank	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	30					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|urinary_tract(1)	14		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;9.3e-06)|Epithelial(140;1.15e-05)		CTCCTGCGTACAGACGGTTTA	0.488													C|||	696	0.138978	0.0333	0.2651	5008	,	,		19777	0.1419		0.1581	False		,,,				2504	0.1697				p.Y30Y		Atlas-SNP	.											.	PMPCA	29	.	0			c.C90T						PASS	.	C		232,4174	138.0+/-173.8	6,220,1977	139.0	117.0	125.0		90	4.5	0.4	9	dbSNP_120	125	1496,7104	281.7+/-295.2	132,1232,2936	no	coding-synonymous	PMPCA	NM_015160.1		138,1452,4913	TT,TC,CC		17.3953,5.2655,13.2862		30/526	139306467	1728,11278	2203	4300	6503	SO:0001819	synonymous_variant	23203	exon2			TGCGTACAGACGG	D21064	CCDS35180.1, CCDS65192.1	9q34.3	2008-02-05	2003-06-13	2003-06-20	ENSG00000165688	ENSG00000165688			18667	protein-coding gene	gene with protein product		613036	"""inositol polyphosphate-5-phosphatase, 72 kD"""	INPP5E		8590280, 7788527	Standard	NM_015160		Approved	KIAA0123, Alpha-MPP	uc004chl.3	Q10713	OTTHUMG00000020926	ENST00000371717.3:c.90C>T	9.37:g.139306467C>T		Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	305	161	0.527869	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371717.3	37	CCDS35180.1																																																																																			C|0.870;T|0.130	0.130	strong		0.488	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160	
RSPH1	89765	hgsc.bcm.edu	37	21	43905830	43905830	+	Silent	SNP	G	G	A	rs117797631	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43905830G>A	ENST00000291536.3	-	5	617	c.450C>T	c.(448-450)gcC>gcT	p.A150A	RSPH1_ENST00000398352.3_Silent_p.A112A	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	150					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)				large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						GAATGAGCTCGGCCGTGCCCT	0.512													G|||	10	0.00199681	0.0008	0.0	5008	,	,		21262	0.0		0.0089	False		,,,				2504	0.0				p.A150A	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											.	RSPH1	36	.	0			c.C450T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	162.0	138.0	146.0		450	-2.7	0.9	21	dbSNP_132	146	96,8504	54.0+/-114.7	1,94,4205	no	coding-synonymous	RSPH1	NM_080860.2		1,100,6402	AA,AG,GG		1.1163,0.1362,0.7843		150/310	43905830	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	89765	exon5			GAGCTCGGCCGTG	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"""meichroacidin"""	609314	"""testis specific A2 homolog (mouse)"""	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.450C>T	21.37:g.43905830G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	170	76	0.447059	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Silent	SNP	ENST00000291536.3	37	CCDS13688.1																																																																																			G|0.992;A|0.008	0.008	strong		0.512	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		
PM20D1	148811	hgsc.bcm.edu	37	1	205817018	205817018	+	Missense_Mutation	SNP	T	T	C	rs11540015	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205817018T>C	ENST00000367136.4	-	2	295	c.251A>G	c.(250-252)cAt>cGt	p.H84R	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	84				H -> R (in Ref. 3; AAH39170). {ECO:0000305}.	negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			CTGACCTTTATGAATGTATTT	0.433													T|||	779	0.155551	0.0545	0.062	5008	,	,		19451	0.3978		0.0964	False		,,,				2504	0.1697				p.H84R		Atlas-SNP	.											.	PM20D1	56	.	0			c.A251G						PASS	.	T	ARG/HIS	252,4150	129.4+/-166.1	4,244,1953	45.0	40.0	42.0		251	-9.7	0.0	1	dbSNP_134	42	617,7939	152.8+/-207.3	8,601,3669	no	missense	PM20D1	NM_152491.4	29	12,845,5622	CC,CT,TT		7.2113,5.7247,6.7063	benign	84/503	205817018	869,12089	2201	4278	6479	SO:0001583	missense	148811	exon2			CCTTTATGAATGT		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.251A>G	1.37:g.205817018T>C	ENSP00000356104:p.His84Arg	Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	324	134	0.41358	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	352	0.16117216117216118	24	0.04878048780487805	23	0.06353591160220995	232	0.40559440559440557	73	0.09630606860158311	T	0.087	-1.173601	0.01646	0.057247	0.072113	ENSG00000162877	ENST00000367136	T	0.06933	3.24	4.86	-9.72	0.00515	.	0.648666	0.16780	N	0.199831	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44802	-0.9304	9	0.12766	T	0.61	.	10.3431	0.43891	0.0:0.3064:0.0951:0.5986	rs11540015	84	Q6GTS8	P20D1_HUMAN	R	84	ENSP00000356104:H84R	ENSP00000356104:H84R	H	-	2	0	PM20D1	204083641	0.000000	0.05858	0.006000	0.13384	0.284000	0.27059	-2.964000	0.00671	-1.525000	0.01762	-0.337000	0.08149	CAT	.	.	weak		0.433	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
LCP1	3936	hgsc.bcm.edu	37	13	46705068	46705068	+	Silent	SNP	C	C	A	rs11558762	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:46705068C>A	ENST00000398576.2	-	18	2020	c.1632G>T	c.(1630-1632)ccG>ccT	p.P544P	LCP1_ENST00000323076.2_Silent_p.P544P|LCP1_ENST00000435666.2_Silent_p.P113P			P13796	PLSL_HUMAN	lymphocyte cytosolic protein 1 (L-plastin)	544	Actin-binding 2.|CH 4. {ECO:0000255|PROSITE- ProRule:PRU00044}.		P -> A (in dbSNP:rs17067725).		actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|organ regeneration (GO:0031100)|protein kinase A signaling (GO:0010737)|regulation of intracellular protein transport (GO:0033157)|T cell activation involved in immune response (GO:0002286)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			breast(2)|kidney(1)|large_intestine(6)|lung(18)|ovary(4)|prostate(2)|skin(1)	34		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		TACTAATCTTCGGGTCCTATG	0.443			T	BCL6	NHL								C|||	319	0.0636981	0.0098	0.0951	5008	,	,		18693	0.0268		0.173	False		,,,				2504	0.0399				p.P544P		Atlas-SNP	.		Dom	yes		13	13q14.1-q14.3	3936	lymphocyte cytosolic protein 1 (L-plastin)		L	.	LCP1	69	.	0			c.G1632T						PASS	.	C		194,4212	123.7+/-161.0	3,188,2012	164.0	151.0	155.0		1632	-10.7	0.1	13	dbSNP_120	155	1752,6848	318.4+/-313.7	186,1380,2734	no	coding-synonymous	LCP1	NM_002298.4		189,1568,4746	AA,AC,CC		20.3721,4.4031,14.9623		544/628	46705068	1946,11060	2203	4300	6503	SO:0001819	synonymous_variant	3936	exon15			AATCTTCGGGTCC	M22300	CCDS9403.1	13q14.3	2013-01-10			ENSG00000136167	ENSG00000136167		"""EF-hand domain containing"""	6528	protein-coding gene	gene with protein product	"""plastin 2"""	153430				2111166	Standard	NM_002298		Approved	PLS2, CP64, L-PLASTIN, LC64P	uc001vba.4	P13796	OTTHUMG00000016864	ENST00000398576.2:c.1632G>T	13.37:g.46705068C>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	145	83	0.572414	NM_002298	B2R613|B4DUA0|Q5TBN4	Silent	SNP	ENST00000398576.2	37	CCDS9403.1																																																																																			T|0.011;G|0.182	.	strong		0.443	LCP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044800.3	NM_002298	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518286	161518286	+	Missense_Mutation	SNP	C	C	T	rs200727785		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161518286C>T	ENST00000436743.1	-	4	398	c.244G>A	c.(244-246)Gac>Aac	p.D82N	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000367969.3_Missense_Mutation_p.D118N|FCGR3A_ENST00000443193.1_Missense_Mutation_p.D117N|FCGR3A_ENST00000540048.1_Missense_Mutation_p.D82N	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	82	Ig-like C2-type 1.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CCACTGTCGTCGACTGTGGCA	0.547																																					p.D118N		Atlas-SNP	.											FCGR3A,colon,carcinoma,+2,1	FCGR3A	38	1	0			c.G352A						scavenged	.						282.0	257.0	266.0					1																	161518286		2203	4300	6503	SO:0001583	missense	2214	exon3			TGTCGTCGACTGT	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.244G>A	1.37:g.161518286C>T	ENSP00000416607:p.Asp82Asn	Somatic	497	0	0		WXS	Illumina HiSeq	Phase_I	359	37	0.103064	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	.	.	.	.	.	.	.	.	.	.	T	0.254	-1.004529	0.02112	.	.	ENSG00000203747	ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048;ENST00000442336	T;T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7;2.7	4.42	-8.84	0.00803	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.472120	0.04313	N	0.349334	T	0.01061	0.0035	N	0.11756	0.17	0.09310	A	2.22055e-13	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30937	-0.9961	9	0.02654	T	1	.	6.7583	0.23526	0.0842:0.2147:0.084:0.6171	.	82;117	P08637;E9PG94	FCG3A_HUMAN;.	N	118;117;82;82;82;81	ENSP00000356946:D118N;ENSP00000392047:D117N;ENSP00000416607:D82N;ENSP00000356944:D82N;ENSP00000444971:D82N;ENSP00000396567:D81N	ENSP00000356944:D82N	D	-	1	0	FCGR3A	159784910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.472000	0.00459	-3.122000	0.00238	-3.646000	0.00026	GAC	C|0.667;T|0.333	0.333	strong		0.547	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
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 GAIIx	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	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	28	20	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	
HSPA2	3306	hgsc.bcm.edu	37	14	65008251	65008251	+	Silent	SNP	C	C	T	rs1063391	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:65008251C>T	ENST00000394709.1	+	2	760	c.684C>T	c.(682-684)gaC>gaT	p.D228D	RP11-973N13.4_ENST00000554918.1_RNA|HSPA2_ENST00000247207.6_Silent_p.D228D|HSPA2_ENST00000554883.1_3'UTR			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	228					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CGGCCGGCGACACCCACCTGG	0.602													C|||	3268	0.652556	0.3956	0.696	5008	,	,		18230	0.8601		0.6819	False		,,,				2504	0.7249				p.D228D	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											HSPA2,right_upper_lobe,carcinoma,+1,1	HSPA2	83	1	0			c.C684T						PASS	.	C		1935,2471	548.2+/-377.5	446,1043,714	62.0	66.0	65.0		684	3.4	1.0	14	dbSNP_86	65	5877,2723	679.6+/-403.6	2002,1873,425	no	coding-synonymous	HSPA2	NM_021979.3		2448,2916,1139	TT,TC,CC		31.6628,43.9174,39.9354		228/640	65008251	7812,5194	2203	4300	6503	SO:0001819	synonymous_variant	3306	exon1			CGGCGACACCCAC	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"""Heat shock proteins / HSP70"""	5235	protein-coding gene	gene with protein product		140560	"""heat shock 70kD protein 2"""				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.684C>T	14.37:g.65008251C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_021979	Q15508|Q53XM3|Q9UE78	Silent	SNP	ENST00000394709.1	37	CCDS9766.1																																																																																			C|0.368;T|0.632	0.632	strong		0.602	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1		
SLC5A12	159963	hgsc.bcm.edu	37	11	26692733	26692733	+	Silent	SNP	T	T	C	rs7114378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:26692733T>C	ENST00000396005.3	-	15	2082	c.1773A>G	c.(1771-1773)agA>agG	p.R591R		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	591					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						GGCTTTCTCTTCTGAGTCCGT	0.433													C|||	1593	0.318091	0.2844	0.2219	5008	,	,		18514	0.4732		0.3141	False		,,,				2504	0.2761				p.R591R		Atlas-SNP	.											.	SLC5A12	134	.	0			c.A1773G						PASS	.	C		1007,2845		129,749,1048	237.0	227.0	230.0		1773	0.4	0.0	11	dbSNP_116	230	2229,5993		322,1585,2204	no	coding-synonymous	SLC5A12	NM_178498.3		451,2334,3252	CC,CT,TT		27.1102,26.1423,26.8014		591/619	26692733	3236,8838	1926	4111	6037	SO:0001819	synonymous_variant	159963	exon15			TTCTCTTCTGAGT	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"""Solute carriers"""	28750	protein-coding gene	gene with protein product		612455	"""solute carrier family 5 (sodium/glucose cotransporter), member 12"""			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1773A>G	11.37:g.26692733T>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	180	86	0.477778	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			T|0.681;C|0.319	0.319	strong		0.433	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
TUBD1	51174	hgsc.bcm.edu	37	17	57963537	57963537	+	Missense_Mutation	SNP	A	A	G	rs1292053	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:57963537A>G	ENST00000592426.1	-	2	227	c.227T>C	c.(226-228)aTg>aCg	p.M76T	TUBD1_ENST00000325752.3_Missense_Mutation_p.M76T|TUBD1_ENST00000394239.3_Missense_Mutation_p.M76T|TUBD1_ENST00000539018.1_Intron|TUBD1_ENST00000376094.4_Missense_Mutation_p.M76T|TUBD1_ENST00000591611.1_5'UTR|TUBD1_ENST00000346141.6_Intron|TUBD1_ENST00000340993.6_Missense_Mutation_p.M76T			Q9UJT1	TBD_HUMAN	tubulin, delta 1	76			M -> T (in dbSNP:rs1292053). {ECO:0000269|PubMed:10620804, ECO:0000269|PubMed:15081367}.		cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|protein polymerization (GO:0051258)|spermatogenesis (GO:0007283)	centriole (GO:0005814)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.M76T(1)		NS(2)|breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(2)	21	all_cancers(5;3.18e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;9.34e-13)|all cancers(12;1.91e-11)		Vinblastine(DB00570)	CTTTGACAGCATTTGATTGAT	0.418													G|||	2410	0.48123	0.5204	0.4597	5008	,	,		17567	0.5754		0.4175	False		,,,				2504	0.4121				p.M76T		Atlas-SNP	.											TUBD1,NS,carcinoma,0,1	TUBD1	38	1	1	Substitution - Missense(1)	stomach(1)	c.T227C						PASS	.	G	THR/MET,THR/MET,THR/MET,,,THR/MET	2123,2283	599.7+/-389.3	520,1083,600	99.0	96.0	97.0		227,227,227,,,227	4.1	0.7	17	dbSNP_87	97	3751,4849	617.5+/-396.7	846,2059,1395	yes	missense,missense,missense,utr-5,intron,missense	TUBD1	NM_001193609.1,NM_001193610.1,NM_001193611.1,NM_001193612.1,NM_001193613.1,NM_016261.3	81,81,81,,,81	1366,3142,1995	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	43.6163,48.1843,45.1638	benign,benign,benign,,,benign	76/399,76/397,76/352,,,76/454	57963537	5874,7132	2203	4300	6503	SO:0001583	missense	51174	exon3			GACAGCATTTGAT	AF201333	CCDS11620.1, CCDS54151.1, CCDS54152.1, CCDS54153.1, CCDS54154.1	17q23.1	2007-03-16						"""Tubulins"""	16811	protein-coding gene	gene with protein product		607344				10620804	Standard	NM_016261		Approved	FLJ12709, TUBD	uc002ixw.2	Q9UJT1		ENST00000592426.1:c.227T>C	17.37:g.57963537A>G	ENSP00000468518:p.Met76Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_016261	B4DPT8|B4DW01|D3DU02|E9PCA7|E9PCQ8|Q5KU36|Q9BWG9|Q9H7Z8	Missense_Mutation	SNP	ENST00000592426.1	37	CCDS11620.1	1077	0.49313186813186816	261	0.5304878048780488	159	0.43922651933701656	342	0.5979020979020979	315	0.4155672823218997	G	2.326	-0.354555	0.05138	0.481843	0.436163	ENSG00000108423	ENST00000325752;ENST00000340993;ENST00000394239;ENST00000376094	T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47	6.08	4.1	0.47936	Tubulin/FtsZ, GTPase domain (4);	0.183702	0.64402	N	0.000019	T	0.00012	0.0000	N	0.00960	-1.095	0.52099	P	5.299999999996974E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.45425	-0.9262	9	0.11485	T	0.65	-1.7956	11.3011	0.49306	0.1943:0.0:0.8057:0.0	rs1292053;rs59005131;rs1292053	76;76;76;76	E9PCA7;E9PCQ8;Q9UJT1-2;Q9UJT1	.;.;.;TBD_HUMAN	T	76	ENSP00000320797:M76T;ENSP00000342399:M76T;ENSP00000377785:M76T;ENSP00000365262:M76T	ENSP00000320797:M76T	M	-	2	0	TUBD1	55318319	1.000000	0.71417	0.705000	0.30386	0.931000	0.56810	4.164000	0.58190	0.476000	0.27440	-0.119000	0.15052	ATG	A|0.522;G|0.478	0.478	strong		0.418	TUBD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448815.1	NM_016261	
ZNF521	25925	hgsc.bcm.edu	37	18	22807046	22807046	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:22807046G>A	ENST00000361524.3	-	4	984	c.836C>T	c.(835-837)gCg>gTg	p.A279V	ZNF521_ENST00000538137.2_Missense_Mutation_p.A279V|ZNF521_ENST00000584787.1_Missense_Mutation_p.A59V|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	279					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CTGGAGGGCCGCTCGGTCCTC	0.557			T	PAX5	ALL																																p.A279V		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,bladder,carcinoma,0,1	ZNF521	269	1	0			c.C836T						scavenged	.						102.0	95.0	97.0					18																	22807046		2203	4300	6503	SO:0001583	missense	25925	exon4			AGGGCCGCTCGGT	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.836C>T	18.37:g.22807046G>A	ENSP00000354794:p.Ala279Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	2	0.016	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	G	13.63	2.295102	0.40594	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.09630	2.96;2.98	6.02	6.02	0.97574	.	0.110174	0.64402	D	0.000007	T	0.15869	0.0382	L	0.38175	1.15	0.46203	D	0.998926	P	0.46706	0.883	P	0.45138	0.471	T	0.00141	-1.1998	10	0.87932	D	0	-24.0898	20.5407	0.99260	0.0:0.0:1.0:0.0	.	279	Q96K83	ZN521_HUMAN	V	279;313;279	ENSP00000354794:A279V;ENSP00000382352:A279V	ENSP00000354794:A279V	A	-	2	0	ZNF521	21061044	1.000000	0.71417	0.379000	0.26080	0.989000	0.77384	9.199000	0.95003	2.865000	0.98341	0.655000	0.94253	GCG	.	.	none		0.557	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
IGFALS	3483	hgsc.bcm.edu	37	16	1838037	1838037	+	IGR	SNP	C	C	G	rs2272977	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1838037C>G	ENST00000215539.3	-	0	2116				NUBP2_ENST00000568706.1_Silent_p.T54T|NUBP2_ENST00000262302.9_Silent_p.T195T|NUBP2_ENST00000565987.1_Silent_p.T135T|NUBP2_ENST00000565134.1_Silent_p.T195T|NUBP2_ENST00000543305.1_Silent_p.T54T			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit						cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						GCGGCTTCACCTGCCCACACT	0.667													C|||	560	0.111821	0.0726	0.0937	5008	,	,		15605	0.1657		0.1233	False		,,,				2504	0.1104				p.T195T		Atlas-SNP	.											NUBP2,NS,carcinoma,0,1	NUBP2	25	1	0			c.C585G						PASS	.	C		289,4107	157.4+/-190.3	8,273,1917	77.0	76.0	76.0		585	2.2	0.8	16	dbSNP_100	76	1009,7591	215.9+/-255.1	65,879,3356	no	coding-synonymous	NUBP2	NM_012225.2		73,1152,5273	GG,GC,CC		11.7326,6.5742,9.9877		195/272	1838037	1298,11698	2198	4300	6498	SO:0001628	intergenic_variant	10101	exon5			CTTCACCTGCCCA	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638		16.37:g.1838037C>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_012225	B4DZY8|E9PGU3	Silent	SNP	ENST00000215539.3	37	CCDS10446.1																																																																																			C|0.891;G|0.109	0.109	strong		0.667	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
FMO2	2327	hgsc.bcm.edu	37	1	171168585	171168585	+	Silent	SNP	A	A	G	rs2020861|rs386636736	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171168585A>G	ENST00000209929.7	+	5	743	c.585A>G	c.(583-585)tcA>tcG	p.S195S	FMO2_ENST00000529935.1_Intron|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000441535.1_Silent_p.S195S|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	195					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.S195S(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGGGAAACTCAGGCTCAGATA	0.488													G|||	2951	0.589257	0.7209	0.6167	5008	,	,		19431	0.6032		0.3877	False		,,,				2504	0.5849				p.S195S		Atlas-SNP	.											FMO2,NS,carcinoma,0,2	FMO2	66	2	1	Substitution - coding silent(1)	stomach(1)	c.A585G						PASS	.	G		2951,1455	468.5+/-355.1	983,985,235	135.0	140.0	139.0		585	-12.3	0.0	1	dbSNP_98	139	3589,5011	627.2+/-397.9	765,2059,1476	no	coding-synonymous	FMO2	NM_001460.2		1748,3044,1711	GG,GA,AA		41.7326,33.0232,49.7155		195/472	171168585	6540,6466	2203	4300	6503	SO:0001819	synonymous_variant	2327	exon5			AAACTCAGGCTCA	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.585A>G	1.37:g.171168585A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	37	CCDS1293.1																																																																																			A|0.536;G|0.464	0.464	strong		0.488	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
CSAG1	158511	hgsc.bcm.edu	37	X	151909156	151909156	+	Missense_Mutation	SNP	A	A	G	rs2515848	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:151909156A>G	ENST00000370287.3	+	5	513	c.185A>G	c.(184-186)aAa>aGa	p.K62R	CSAG1_ENST00000452779.2_Missense_Mutation_p.K62R|CSAG1_ENST00000370291.2_3'UTR	NM_153478.1	NP_705611.1	Q6PB30	CSAG1_HUMAN	chondrosarcoma associated gene 1	62			K -> R (in dbSNP:rs2515848). {ECO:0000269|PubMed:12039054, ECO:0000269|PubMed:15489334}.							central_nervous_system(1)|kidney(1)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Acute lymphoblastic leukemia(192;6.56e-05)					AGACAACCCAAAAGGGAAAAG	0.517													.|||	2176	0.576424	0.5749	0.5778	3775	,	,		12287	0.2688		0.4344	False		,,,				2504	0.3139				p.K62R		Atlas-SNP	.											.	CSAG1	27	.	0			c.A185G						PASS	.	G	ARG/LYS,ARG/LYS	2793,1042		861,660,411,111,160	93.0	96.0	95.0		185,185	0.8	0.0	X	dbSNP_100	95	3934,2794		804,1204,1122,420,750	yes	missense,missense	CSAG1	NM_153478.1,NM_001102576.1	26,26	1665,1864,1533,531,910	GG,GA,G,AA,A		41.5279,27.1708,36.3154	benign,benign	62/79,62/79	151909156	6727,3836	2203	4300	6503	SO:0001583	missense	158511	exon5			AACCCAAAAGGGA	AF268419	CCDS76047.1	Xq28	2009-08-07			ENSG00000198930	ENSG00000198930			24294	protein-coding gene	gene with protein product	"""cancer/testis antigen family 24, member 1"""					12039054	Standard	XM_006724810		Approved	CSAGE, CT24.1	uc004fgf.3	Q6PB30	OTTHUMG00000022648	ENST00000370287.3:c.185A>G	X.37:g.151909156A>G	ENSP00000359310:p.Lys62Arg	Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	404	285	0.705446	NM_153478	A6NE22	Missense_Mutation	SNP	ENST00000370287.3	37	CCDS14711.1	960	0.5786618444846293	199	0.6257861635220126	146	0.6403508771929824	89	0.18619246861924685	226	0.4035714285714286	G	1.239	-0.621960	0.03636	0.728292	0.584721	ENSG00000198930	ENST00000370287;ENST00000452779	T;T	0.34667	1.35;1.35	0.837	0.837	0.18896	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26467	-1.0102	6	0.32370	T	0.25	.	.	.	.	rs2515848;rs17855711;rs52837255;rs2515848	62	Q6PB30	CSAG1_HUMAN	R	62	ENSP00000359310:K62R;ENSP00000396520:K62R	ENSP00000359310:K62R	K	+	2	0	CSAG1	151659812	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.195000	0.17155	-0.098000	0.12285	-1.150000	0.01838	AAA	A|0.382;G|0.618	0.618	strong		0.517	CSAG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058760.2	NM_153479	
MUC2	4583	hgsc.bcm.edu	37	11	1092954	1092954	+	Splice_Site	SNP	G	G	A	rs56352686		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1092954G>A	ENST00000359061.5	+	30	4776	c.4776G>A	c.(4774-4776)acG>acA	p.T1592T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000441003.2_Silent_p.T1591T			Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				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)	ccaccactacggtgaccccaa	0.627																																					p.T1591T		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,0,4	MUC2	614	4	0			c.G4773A						scavenged	.						52.0	85.0	74.0					11																	1092954		1812	3296	5108	SO:0001630	splice_region_variant	4583	exon30			CACTACGGTGACC	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	ENST00000359061.5:c.4776+1G>A	11.37:g.1092954G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	2	0.0555556	NM_002457	Q14878	Silent	SNP	ENST00000359061.5	37																																																																																				.	.	none		0.627	MUC2-202	KNOWN	basic	protein_coding	protein_coding		NM_002457	Silent
ERI2	112479	hgsc.bcm.edu	37	16	20809283	20809283	+	Silent	SNP	C	C	A	rs11648835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20809283C>A	ENST00000357967.4	-	9	1881	c.1839G>T	c.(1837-1839)ccG>ccT	p.P613P	ERI2_ENST00000563117.1_Silent_p.P520P|ERI2_ENST00000564349.1_Silent_p.P520P|ERI2_ENST00000569729.1_3'UTR|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000389345.5_Silent_p.P348P	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	613							exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						TTCCATGGTTCGGTCCATTAT	0.393													C|||	1025	0.204673	0.3064	0.1023	5008	,	,		18283	0.2212		0.1262	False		,,,				2504	0.2035				p.P613P		Atlas-SNP	.											.	ERI2	50	.	0			c.G1839T						PASS	.	C	,	377,1007		53,271,368	110.0	88.0	95.0		1839,	-2.5	1.0	16	dbSNP_120	95	450,2732		33,384,1174	no	coding-synonymous,intron	ERI2	NM_001142725.1,NM_080663.2	,	86,655,1542	AA,AC,CC		14.142,27.2399,18.1121	,	613/692,	20809283	827,3739	692	1591	2283	SO:0001819	synonymous_variant	112479	exon9			ATGGTTCGGTCCA	BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678		"""Enhanced RNAi three prime mRNA exonucleases"""	30541	protein-coding gene	gene with protein product	"""enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans)"", ""exoribonuclease 2"", ""zinc finger, GRF-type containing 5"""		"""exonuclease domain containing 1"""	EXOD1		10819331	Standard	NM_080663		Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000357967.4:c.1839G>T	16.37:g.20809283C>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	157	87	0.55414	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Silent	SNP	ENST00000357967.4	37	CCDS45436.1																																																																																			C|0.817;A|0.183	0.183	strong		0.393	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663	
TENM1	10178	hgsc.bcm.edu	37	X	123540315	123540315	+	Silent	SNP	G	G	T	rs960869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:123540315G>T	ENST00000371130.3	-	25	5049	c.4986C>A	c.(4984-4986)acC>acA	p.T1662T	TENM1_ENST00000422452.2_Silent_p.T1669T|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1662					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)										ACGTTGCATTGGTCAGGTGTC	0.483													G|||	1436	0.380397	0.2973	0.3069	3775	,	,		13411	0.2708		0.3241	False		,,,				2504	0.2362				p.T1669T		Atlas-SNP	.											.	.	.	.	0			c.C5007A						PASS	.	G	,,	1524,2311		260,779,225,593,346	136.0	120.0	126.0		5007,5004,4986	4.7	1.0	X	dbSNP_86	126	2837,3891		421,1206,789,801,1083	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	681,1985,1014,1394,1429	TT,TG,T,GG,G		42.1671,39.7392,41.2856	,,	1669/2733,1668/2732,1662/2726	123540315	4361,6202	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon26			TGCATTGGTCAGG	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.4986C>A	X.37:g.123540315G>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	71	23	0.323944	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			G|0.579;0|0.024	.	strong		0.483	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
ZFYVE1	53349	hgsc.bcm.edu	37	14	73465003	73465003	+	Silent	SNP	A	A	G	rs997667	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:73465003A>G	ENST00000556143.1	-	3	1224	c.504T>C	c.(502-504)ttT>ttC	p.F168F	ZFYVE1_ENST00000553891.1_Silent_p.F168F|ZFYVE1_ENST00000318876.5_Silent_p.F168F	NM_001281735.1|NM_021260.2	NP_001268664.1|NP_067083.1	Q9HBF4	ZFYV1_HUMAN	zinc finger, FYVE domain containing 1	168					negative regulation of phosphatase activity (GO:0010923)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|ER-mitochondrion membrane contact site (GO:0044233)|Golgi stack (GO:0005795)|perinuclear region of cytoplasm (GO:0048471)|pre-autophagosomal structure (GO:0000407)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(17)|ovary(1)|prostate(2)|skin(1)	35		all_lung(585;1.33e-09)		OV - Ovarian serous cystadenocarcinoma(108;1.6e-46)|BRCA - Breast invasive adenocarcinoma(234;0.00349)		ATTTTCTAATAAAGTCTTCTT	0.353													G|||	1444	0.288339	0.23	0.2233	5008	,	,		15127	0.3542		0.3628	False		,,,				2504	0.2689				p.F168F		Atlas-SNP	.											.	ZFYVE1	67	.	0			c.T504C						PASS	.	G		1112,3248		150,812,1218	34.0	34.0	34.0		504	-0.9	1.0	14	dbSNP_86	34	2916,5610		509,1898,1856	yes	coding-synonymous	ZFYVE1	NM_021260.2		659,2710,3074	GG,GA,AA		34.2013,25.5046,31.2587		168/778	73465003	4028,8858	2180	4263	6443	SO:0001819	synonymous_variant	53349	exon3			TCTAATAAAGTCT	AF251025	CCDS9811.1, CCDS41969.1, CCDS61498.1	14q24.2	2014-06-13	2003-02-28	2003-03-07		ENSG00000165861		"""Zinc fingers, FYVE domain containing"""	13180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 172"""	605471	"""zinc finger protein, subfamily 2A (FYVE domain containing), 1"""	ZNFN2A1		11024279, 11256955	Standard	NM_021260		Approved	DFCP1, KIAA1589, TAFF1, PPP1R172	uc001xnm.3	Q9HBF4		ENST00000556143.1:c.504T>C	14.37:g.73465003A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_021260	J3KNL9|Q8WYX7|Q96K57|Q9BXP9|Q9HCI3	Silent	SNP	ENST00000556143.1	37	CCDS9811.1																																																																																			A|0.678;G|0.322	0.322	strong		0.353	ZFYVE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413172.1	NM_021260	
TRPM5	29850	hgsc.bcm.edu	37	11	2438963	2438963	+	Missense_Mutation	SNP	C	C	A	rs34350821	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:2438963C>A	ENST00000155858.6	-	7	1011	c.1003G>T	c.(1003-1005)Gtg>Ttg	p.V335L	TRPM5_ENST00000452833.1_Missense_Mutation_p.V337L|TRPM5_ENST00000533060.1_Missense_Mutation_p.V335L|TRPM5_ENST00000528453.1_Missense_Mutation_p.V335L	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		TCACCTTTCACCAGCGCCTTC	0.622													C|||	197	0.0393371	0.0061	0.0692	5008	,	,		11783	0.0		0.1292	False		,,,				2504	0.0112				p.V335L	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1003T						PASS	.	C	LEU/VAL	92,4294		2,88,2103	24.0	24.0	24.0		1003	2.1	0.9	11	dbSNP_126	24	1026,7564		65,896,3334	yes	missense	TRPM5	NM_014555.3	32	67,984,5437	AA,AC,CC		11.9441,2.0976,8.6159	probably-damaging	335/1166	2438963	1118,11858	2193	4295	6488	SO:0001583	missense	29850	exon7			CTTTCACCAGCGC	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.1003G>T	11.37:g.2438963C>A	ENSP00000155858:p.Val335Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	119	68	0.571429	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	136	0.06227106227106227	10	0.02032520325203252	30	0.08287292817679558	0	0.0	96	0.1266490765171504	C	14.99	2.699987	0.48307	0.020976	0.119441	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0	4.05	2.09	0.27110	.	0.000000	0.64402	D	0.000004	T	0.00784	0.0026	N	0.13168	0.305	0.27006	P	0.9647967	D;D;D	0.89917	1.0;1.0;0.98	D;D;P	0.87578	0.998;0.998;0.873	T	0.25710	-1.0124	9	0.09084	T	0.74	-27.6599	6.3181	0.21202	0.1805:0.722:0.0:0.0975	rs34350821	335;337;335	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	L	329;335;337;335;335;335	ENSP00000434383:V329L;ENSP00000155858:V335L;ENSP00000387965:V337L;ENSP00000434121:V335L;ENSP00000436809:V335L	ENSP00000155858:V335L	V	-	1	0	TRPM5	2395539	0.996000	0.38824	0.932000	0.37286	0.882000	0.50991	1.974000	0.40559	0.271000	0.22005	0.313000	0.20887	GTG	C|0.925;A|0.075	0.075	strong		0.622	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
DDX51	317781	hgsc.bcm.edu	37	12	132625960	132625960	+	Silent	SNP	G	G	A	rs34067942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132625960G>A	ENST00000397333.3	-	8	1148	c.1110C>T	c.(1108-1110)atC>atT	p.I370I		NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	370	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		CAGCCTCGTCGATAATCTGCA	0.697													G|||	192	0.0383387	0.0265	0.0821	5008	,	,		15501	0.0218		0.0368	False		,,,				2504	0.0419				p.I370I		Atlas-SNP	.											.	DDX51	33	.	0			c.C1110T						PASS	.	G		112,3846		3,106,1870	56.0	68.0	64.0		1110	-9.9	0.0	12	dbSNP_126	64	282,8020		7,268,3876	no	coding-synonymous	DDX51	NM_175066.3		10,374,5746	AA,AG,GG		3.3968,2.8297,3.2137		370/667	132625960	394,11866	1979	4151	6130	SO:0001819	synonymous_variant	317781	exon8			CTCGTCGATAATC	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.1110C>T	12.37:g.132625960G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Silent	SNP	ENST00000397333.3	37	CCDS41865.1																																																																																			G|0.961;A|0.039	0.039	strong		0.697	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
MSH5	4439	hgsc.bcm.edu	37	6	31727897	31727897	+	Silent	SNP	C	C	T	rs3115672	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31727897C>T	ENST00000375755.3	+	19	2002	c.1716C>T	c.(1714-1716)acC>acT	p.T572T	MSH5_ENST00000375750.3_Silent_p.T572T|MSH5_ENST00000375742.3_Silent_p.T589T|MSH5_ENST00000375740.3_Silent_p.T589T|MSH5_ENST00000375703.3_Silent_p.T572T|MSH5_ENST00000395853.1_Silent_p.T246T|SAPCD1_ENST00000415669.2_5'Flank|MSH5_ENST00000431848.2_Silent_p.T271T|MSH5_ENST00000534153.4_Silent_p.T589T|MSH5-SAPCD1_ENST00000493662.2_Silent_p.T589T|SAPCD1_ENST00000425424.1_5'Flank	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	572					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						GTGCCCGAACCTTTGTGCCCA	0.532								Direct reversal of damage;Mismatch excision repair (MMR)					C|||	169	0.033746	0.0567	0.0274	5008	,	,		21313	0.0		0.0746	False		,,,				2504	0.0				p.T589T		Atlas-SNP	.											MSH5_ENST00000375742,bladder,carcinoma,+1,2	MSH5	108	2	0			c.C1767T						PASS	.	C	,,,	299,4107	162.5+/-194.5	8,283,1912	109.0	110.0	109.0		1716,1767,1716,1716	0.1	1.0	6	dbSNP_103	109	932,7668	205.5+/-247.9	55,822,3423	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MSH5	NM_002441.4,NM_025259.5,NM_172165.3,NM_172166.3	,,,	63,1105,5335	TT,TC,CC		10.8372,6.7862,9.4649	,,,	572/835,589/823,572/836,572/835	31727897	1231,11775	2203	4300	6503	SO:0001819	synonymous_variant	4439	exon19			CCGAACCTTTGTG	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.1716C>T	6.37:g.31727897C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	66	0.868421	NM_025259	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Silent	SNP	ENST00000375755.3	37	CCDS4720.1																																																																																			C|0.923;T|0.077	0.077	strong		0.532	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
WDR35	57539	hgsc.bcm.edu	37	2	20131079	20131079	+	Missense_Mutation	SNP	T	T	C	rs1191778	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:20131079T>C	ENST00000345530.3	-	25	3063	c.2948A>G	c.(2947-2949)gAa>gGa	p.E983G	WDR35_ENST00000416055.2_Missense_Mutation_p.E456G|WDR35_ENST00000281405.4_Missense_Mutation_p.E972G	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	983			E -> G (in dbSNP:rs1191778). {ECO:0000269|PubMed:14702039}.		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)				breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCATCTGTTCATGGTATTG	0.358													T|||	1164	0.232428	0.1097	0.3588	5008	,	,		16337	0.1171		0.4443	False		,,,				2504	0.2096				p.E983G		Atlas-SNP	.											WDR35,NS,carcinoma,-1,1	WDR35	92	1	0			c.A2948G						scavenged	.	T	GLY/GLU,GLY/GLU	709,3697	293.8+/-282.8	52,605,1546	166.0	159.0	161.0		2948,2915	4.8	0.0	2	dbSNP_87	161	3463,5137	508.0+/-377.0	689,2085,1526	yes	missense,missense	WDR35	NM_001006657.1,NM_020779.3	98,98	741,2690,3072	CC,CT,TT		40.2674,16.0917,32.0775	benign,benign	983/1182,972/1171	20131079	4172,8834	2203	4300	6503	SO:0001583	missense	57539	exon25			ATCTGTTCATGGT	AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.2948A>G	2.37:g.20131079T>C	ENSP00000314444:p.Glu983Gly	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	611	0.27976190476190477	53	0.10772357723577236	139	0.3839779005524862	87	0.1520979020979021	332	0.43799472295514513	T	12.10	1.837657	0.32513	0.160917	0.402674	ENSG00000118965	ENST00000345530;ENST00000281405;ENST00000416055	T;T;T	0.74526	-0.23;-0.23;-0.85	4.82	4.82	0.62117	.	0.210756	0.48767	D	0.000173	T	0.00012	0.0000	M	0.76002	2.32	0.40456	P	0.01980599999999999	B;B;P	0.42692	0.348;0.073;0.787	B;B;P	0.46758	0.156;0.066;0.526	T	0.17806	-1.0357	9	0.54805	T	0.06	-18.7985	13.8697	0.63610	0.0:0.0:0.0:1.0	rs1191778;rs1658525;rs52827575;rs61210615;rs1191778	972;983;456	Q9P2L0-2;Q9P2L0;B3KR94	.;WDR35_HUMAN;.	G	983;972;456	ENSP00000314444:E983G;ENSP00000281405:E972G;ENSP00000399159:E456G	ENSP00000281405:E972G	E	-	2	0	WDR35	19994560	0.992000	0.36948	0.019000	0.16419	0.680000	0.39746	3.878000	0.56130	1.933000	0.56026	0.482000	0.46254	GAA	T|0.710;C|0.290	0.290	strong		0.358	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
FAM184B	27146	hgsc.bcm.edu	37	4	17635336	17635336	+	Missense_Mutation	SNP	G	G	A	rs61741403	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:17635336G>A	ENST00000265018.3	-	17	3277	c.3065C>T	c.(3064-3066)tCt>tTt	p.S1022F	MED28_ENST00000237380.7_3'UTR	NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	1022										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						TGCATCTGTAGACTGGTTGGG	0.512													G|||	50	0.00998403	0.003	0.0173	5008	,	,		16527	0.0		0.0288	False		,,,				2504	0.0051				p.S1022F		Atlas-SNP	.											.	FAM184B	38	.	0			c.C3065T						PASS	.	G	PHE/SER	3,1381		0,3,689	88.0	83.0	84.0		3065	3.7	0.0	4	dbSNP_129	84	128,3054		0,128,1463	yes	missense	FAM184B	NM_015688.1	155	0,131,2152	AA,AG,GG		4.0226,0.2168,2.869	probably-damaging	1022/1061	17635336	131,4435	692	1591	2283	SO:0001583	missense	27146	exon17			TCTGTAGACTGGT		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.3065C>T	4.37:g.17635336G>A	ENSP00000265018:p.Ser1022Phe	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_015688		Missense_Mutation	SNP	ENST00000265018.3	37	CCDS47033.1	34	0.015567765567765568	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	25	0.032981530343007916	G	11.82	1.752653	0.31046	0.002168	0.040226	ENSG00000047662	ENST00000265018	T	0.34072	1.38	5.43	3.68	0.42216	.	0.700610	0.13870	N	0.357090	T	0.07007	0.0178	L	0.44542	1.39	0.09310	N	1	P	0.44380	0.834	B	0.34242	0.178	T	0.02581	-1.1138	10	0.59425	D	0.04	2.9877	9.7468	0.40451	0.153:0.0:0.847:0.0	rs61741403	1022	Q9ULE4	F184B_HUMAN	F	1022	ENSP00000265018:S1022F	ENSP00000265018:S1022F	S	-	2	0	FAM184B	17244434	0.032000	0.19561	0.002000	0.10522	0.385000	0.30292	2.170000	0.42443	0.756000	0.33013	0.655000	0.94253	TCT	G|0.979;A|0.021	0.021	strong		0.512	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
HSPG2	3339	hgsc.bcm.edu	37	1	22179451	22179451	+	Silent	SNP	C	C	T	rs34443576	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22179451C>T	ENST00000374695.3	-	51	6631	c.6552G>A	c.(6550-6552)acG>acA	p.T2184T	HSPG2_ENST00000430507.1_Silent_p.T130T	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2184	Ig-like C2-type 7.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCTTGTGCCACGTGACCTGGG	0.711													C|||	173	0.0345447	0.0015	0.0245	5008	,	,		15210	0.0		0.0487	False		,,,				2504	0.1074				p.T2184T		Atlas-SNP	.											.	HSPG2	311	.	0			c.G6552A						PASS	.	C		42,4362	46.0+/-80.4	0,42,2160	41.0	43.0	42.0		6552	-11.9	0.0	1	dbSNP_126	42	488,8108	137.9+/-194.8	16,456,3826	no	coding-synonymous	HSPG2	NM_005529.5		16,498,5986	TT,TC,CC		5.6771,0.9537,4.0769		2184/4392	22179451	530,12470	2202	4298	6500	SO:0001819	synonymous_variant	3339	exon51			GTGCCACGTGACC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6552G>A	1.37:g.22179451C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	64	38	0.59375	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			C|0.965;T|0.035	0.035	strong		0.711	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
CEP78	84131	hgsc.bcm.edu	37	9	80879149	80879149	+	Silent	SNP	C	C	T	rs1057650	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:80879149C>T	ENST00000424347.2	+	13	1831	c.1542C>T	c.(1540-1542)atC>atT	p.I514I	CEP78_ENST00000415759.2_Silent_p.I515I|CEP78_ENST00000376598.2_Silent_p.I514I|CEP78_ENST00000376597.4_Silent_p.I515I|CEP78_ENST00000277082.5_Silent_p.I514I			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	514					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)		p.I514I(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						CAAATATGATCCTGGATGATG	0.373													C|||	424	0.0846645	0.1399	0.0778	5008	,	,		15567	0.0109		0.0835	False		,,,				2504	0.092				p.I515I		Atlas-SNP	.											CEP78,NS,carcinoma,0,1	CEP78	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C1545T						PASS	.	C	,	482,3220		27,428,1396	107.0	100.0	102.0		1545,1545	2.3	1.0	9	dbSNP_86	102	693,7485		26,641,3422	no	coding-synonymous,coding-synonymous	CEP78	NM_001098802.1,NM_032171.1	,	53,1069,4818	TT,TC,CC		8.474,13.02,9.8906	,	515/723,515/707	80879149	1175,10705	1851	4089	5940	SO:0001819	synonymous_variant	84131	exon13			TATGATCCTGGAT	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 81"""	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.1542C>T	9.37:g.80879149C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Silent	SNP	ENST00000424347.2	37																																																																																				C|0.921;T|0.079	0.079	strong		0.373	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991	
ACSM1	116285	hgsc.bcm.edu	37	16	20648702	20648702	+	Silent	SNP	G	G	A	rs151328	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20648702G>A	ENST00000307493.4	-	8	1255	c.1188C>T	c.(1186-1188)taC>taT	p.Y396Y	ACSM1_ENST00000520010.1_Silent_p.Y396Y|ACSM1_ENST00000219151.4_Silent_p.Y15Y	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	396					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						CCTGGACGTCGTAGGGTGGAG	0.542													G|||	1737	0.346845	0.5416	0.1916	5008	,	,		20252	0.3512		0.1799	False		,,,				2504	0.3609				p.Y396Y		Atlas-SNP	.											.	ACSM1	118	.	0			c.C1188T						PASS	.	G		2177,2225	586.1+/-386.4	540,1097,564	126.0	117.0	120.0		1188	-9.1	0.0	16	dbSNP_79	120	1726,6874	315.1+/-312.1	176,1374,2750	no	coding-synonymous	ACSM1	NM_052956.2		716,2471,3314	AA,AG,GG		20.0698,49.4548,30.0185		396/578	20648702	3903,9099	2201	4300	6501	SO:0001819	synonymous_variant	116285	exon8			GACGTCGTAGGGT	AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1188C>T	16.37:g.20648702G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_052956	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	37	CCDS10587.1	674	0.3086080586080586	255	0.5182926829268293	73	0.20165745856353592	196	0.34265734265734266	150	0.19788918205804748	G	0.019	-1.451414	0.01080	0.494548	0.200698	ENSG00000166743	ENST00000524149	.	.	.	5.07	-9.12	0.00707	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.01920	-1.1247	3	.	.	.	.	17.3287	0.87257	0.8454:0.0:0.1546:0.0	rs151328;rs1262366;rs16970472;rs61455665;rs151328	.	.	.	M	102	.	.	T	-	2	0	ACSM1	20556203	0.000000	0.05858	0.015000	0.15790	0.014000	0.08584	-2.456000	0.01002	-1.806000	0.01237	-0.192000	0.12808	ACG	G|0.685;A|0.315	0.315	strong		0.542	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	
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 GAIIx	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		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	89	52	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 GAIIx	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		Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	392	16	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
CPXCR1	53336	hgsc.bcm.edu	37	X	88009170	88009170	+	Missense_Mutation	SNP	G	G	C	rs41307393	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:88009170G>C	ENST00000276127.4	+	3	1014	c.755G>C	c.(754-756)gGt>gCt	p.G252A	CPXCR1_ENST00000373111.1_Missense_Mutation_p.G252A	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	252							metal ion binding (GO:0046872)	p.G252D(1)		NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						AATATAAAAGGTTTTGTGGAT	0.333													G|||	14	0.00370861	0.0008	0.0014	3775	,	,		12774	0.0		0.0119	False		,,,				2504	0.0				p.G252A		Atlas-SNP	.											.	CPXCR1	83	.	1	Substitution - Missense(1)	large_intestine(1)	c.G755C						PASS	.	G	ALA/GLY,ALA/GLY	4,3830		0,4,0,1628,570	31.0	29.0	30.0		755,755	-1.3	0.0	X	dbSNP_127	30	92,6629		0,68,24,2359,1843	yes	missense,missense	CPXCR1	NM_001184771.1,NM_033048.5	60,60	0,72,24,3987,2413	CC,CG,C,GG,G		1.3688,0.1043,0.9095	probably-damaging,probably-damaging	252/302,252/302	88009170	96,10459	2202	4294	6496	SO:0001583	missense	53336	exon3			TAAAAGGTTTTGT	AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"""cancer/testis antigen 77"""					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.755G>C	X.37:g.88009170G>C	ENSP00000276127:p.Gly252Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	35	0.3125	NM_001184771	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	37	CCDS14458.1	10	0.006027727546714889	1	0.0020325203252032522	0	0.0	0	0.0	10	0.013227513227513227	G	0.260	-1.000008	0.02128	0.001043	0.013688	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.22336	1.96;1.96	3.43	-1.32	0.09201	.	1.642850	0.03711	N	0.250142	T	0.06690	0.0171	N	0.12182	0.205	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.19063	-1.0317	9	.	.	.	-0.039	0.3507	0.00348	0.1885:0.2811:0.1995:0.3309	rs41307393	252	Q8N123	CPXCR_HUMAN	A	252	ENSP00000276127:G252A;ENSP00000362203:G252A	.	G	+	2	0	CPXCR1	87895826	0.002000	0.14202	0.003000	0.11579	0.014000	0.08584	-1.610000	0.02064	-0.419000	0.07439	-0.223000	0.12442	GGT	G|0.994;C|0.006	0.006	strong		0.333	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048	
TCF19	6941	hgsc.bcm.edu	37	6	31129310	31129310	+	Missense_Mutation	SNP	C	C	T	rs7750641	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31129310C>T	ENST00000376257.3	+	3	1079	c.325C>T	c.(325-327)Ccc>Tcc	p.P109S	TCF19_ENST00000376255.4_Missense_Mutation_p.P109S|TCF19_ENST00000496421.1_3'UTR	NM_007109.2	NP_009040.2	Q9Y242	TCF19_HUMAN	transcription factor 19	109			P -> S (in dbSNP:rs7750641). {ECO:0000269|PubMed:14574404}.		cell proliferation (GO:0008283)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						CCCTGAAGGGCCCCCAGGAAC	0.542													C|||	119	0.023762	0.0091	0.0303	5008	,	,		16616	0.0		0.0855	False		,,,				2504	0.0				p.P109S		Atlas-SNP	.											TCF19,colon,carcinoma,0,1	TCF19	16	1	0			c.C325T						PASS	.	C	SER/PRO,SER/PRO	67,2239		1,65,1087	87.0	93.0	91.0		325,325	-1.2	0.4	6	dbSNP_116	91	592,4420		37,518,1951	yes	missense,missense	TCF19	NM_001077511.1,NM_007109.2	74,74	38,583,3038	TT,TC,CC		11.8117,2.9055,9.0052	benign,benign	109/346,109/346	31129310	659,6659	1153	2506	3659	SO:0001583	missense	6941	exon3			GAAGGGCCCCCAG	U25826	CCDS43446.1	6p21.3	2013-01-28	2009-02-05		ENSG00000137310	ENSG00000137310		"""Zinc fingers, PHD-type"""	11629	protein-coding gene	gene with protein product		600912				1868030, 8595903	Standard	NM_001077511		Approved	SC1	uc003nss.3	Q9Y242	OTTHUMG00000031274	ENST00000376257.3:c.325C>T	6.37:g.31129310C>T	ENSP00000365433:p.Pro109Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	111	85	0.765766	NM_001077511	A6NCT8|B0UY11|Q0EFA8|Q13176|Q15967|Q5SQ89|Q5STD6|Q5STF5|Q9BUM2|Q9UBH7	Missense_Mutation	SNP	ENST00000376257.3	37	CCDS43446.1	84	0.038461538461538464	7	0.014227642276422764	10	0.027624309392265192	0	0.0	67	0.08839050131926121	C	11.15	1.554187	0.27739	0.029055	0.118117	ENSG00000137310	ENST00000376257;ENST00000376255;ENST00000542218	T;T;T	0.22134	2.05;2.05;1.97	5.71	-1.19	0.09585	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	0.729507	0.13820	N	0.360476	T	0.05914	0.0154	L	0.56769	1.78	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35475	-0.9787	10	0.33940	T	0.23	-23.8533	4.3142	0.10984	0.21:0.3167:0.3941:0.0793	rs7750641;rs9263793;rs57999952;rs7750641	109	Q9Y242	TCF19_HUMAN	S	109;109;29	ENSP00000365433:P109S;ENSP00000365431:P109S;ENSP00000439397:P29S	ENSP00000365431:P109S	P	+	1	0	TCF19	31237289	0.018000	0.18449	0.445000	0.26908	0.921000	0.55340	-0.156000	0.10100	-0.211000	0.10124	0.549000	0.68633	CCC	C|0.947;T|0.053	0.053	strong		0.542	TCF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076595.2	NM_007109	
ANKRD33	341405	hgsc.bcm.edu	37	12	52284620	52284620	+	Missense_Mutation	SNP	C	C	T	rs117498175	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52284620C>T	ENST00000340970.4	+	5	886	c.515C>T	c.(514-516)cCg>cTg	p.P172L	ANKRD33_ENST00000538991.1_Missense_Mutation_p.P103L|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000301190.6_Missense_Mutation_p.P297L			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	172					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		CCCTTTGCCCCGTCTCCTCAG	0.667													C|||	58	0.0115815	0.0015	0.0115	5008	,	,		13112	0.0		0.0368	False		,,,				2504	0.0112				p.P297L		Atlas-SNP	.											.	ANKRD33	33	.	0			c.C890T						PASS	.	C	LEU/PRO,LEU/PRO	40,4366	43.8+/-77.6	0,40,2163	37.0	30.0	32.0		515,890	0.7	0.7	12	dbSNP_132	32	318,8282	107.4+/-168.2	5,308,3987	yes	missense,missense	ANKRD33	NM_001130015.1,NM_182608.3	98,98	5,348,6150	TT,TC,CC		3.6977,0.9079,2.7526	benign,benign	172/273,297/453	52284620	358,12648	2203	4300	6503	SO:0001583	missense	341405	exon5			TTGCCCCGTCTCC		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"""Ankyrin repeat domain containing"""	13788	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 7"""	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.515C>T	12.37:g.52284620C>T	ENSP00000344690:p.Pro172Leu	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	29	0.013278388278388278	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	26	0.03430079155672823	C	2.251	-0.371659	0.05034	0.009079	0.036977	ENSG00000167612	ENST00000301190;ENST00000538991;ENST00000340970	T;T;T	0.21543	2.14;2.0;2.38	4.7	0.712	0.18167	.	0.168210	0.26489	U	0.024086	T	0.01287	0.0042	N	0.02011	-0.69	0.27223	N	0.95961	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32745	-0.9895	10	0.26408	T	0.33	-1.5256	6.2069	0.20608	0.5345:0.311:0.0:0.1544	.	172;103;297	Q7Z3H0;Q0VAA8;Q7Z3H0-2	ANR33_HUMAN;.;.	L	297;103;172	ENSP00000301190:P297L;ENSP00000443722:P103L;ENSP00000344690:P172L	ENSP00000301190:P297L	P	+	2	0	ANKRD33	50570887	0.001000	0.12720	0.694000	0.30210	0.269000	0.26545	0.014000	0.13333	0.045000	0.15804	-1.550000	0.00899	CCG	C|0.978;T|0.022	0.022	strong		0.667	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
OR2A12	346525	hgsc.bcm.edu	37	7	143792991	143792991	+	Missense_Mutation	SNP	G	G	A	rs34947817	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143792991G>A	ENST00000408949.2	+	1	851	c.791G>A	c.(790-792)aGc>aAc	p.S264N		NM_001004135.1	NP_001004135.1	Q8NGT7	O2A12_HUMAN	olfactory receptor, family 2, subfamily A, member 12	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)	25	Melanoma(164;0.0783)					CCCAAGTCAAGCCATTCTCAA	0.537													.|||	572	0.114217	0.2368	0.1182	5008	,	,		18290	0.0		0.165	False		,,,				2504	0.0112				p.S264N		Atlas-SNP	.											OR2A12,colon,carcinoma,+1,4	OR2A12	56	4	0			c.G791A						scavenged	.	G	ASN/SER	913,2905		115,683,1111	172.0	166.0	168.0		791	1.4	0.1	7	dbSNP_126	168	1653,6627		156,1341,2643	yes	missense	OR2A12	NM_001004135.1	46	271,2024,3754	AA,AG,GG		19.9638,23.913,21.2101	benign	264/311	143792991	2566,9532	1909	4140	6049	SO:0001583	missense	346525	exon1			AGTCAAGCCATTC		CCDS43670.1	7q35	2013-09-20	2002-11-13	2002-11-13	ENSG00000221858	ENSG00000221858		"""GPCR / Class A : Olfactory receptors"""	15082	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 12 pseudogene"""	OR2A12P			Standard	NM_001004135		Approved		uc011kty.2	Q8NGT7	OTTHUMG00000157996	ENST00000408949.2:c.791G>A	7.37:g.143792991G>A	ENSP00000386174:p.Ser264Asn	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_001004135	Q6IF43	Missense_Mutation	SNP	ENST00000408949.2	37	CCDS43670.1	279	0.12774725274725274	114	0.23170731707317074	46	0.1270718232044199	0	0.0	119	0.15699208443271767	G	2.634	-0.285607	0.05605	0.23913	0.199638	ENSG00000221858	ENST00000408949	T	0.81247	-1.47	4.33	1.4	0.22301	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.43598	1.365	0.80722	P	0.0	B	0.06786	0.001	B	0.12837	0.008	T	0.03202	-1.1061	8	0.23891	T	0.37	0.4492	5.1407	0.14957	0.2059:0.1727:0.6214:0.0	rs34947817;rs61730068;rs34947817	264	Q8NGT7	O2A12_HUMAN	N	264	ENSP00000386174:S264N	ENSP00000386174:S264N	S	+	2	0	OR2A12	143423924	0.000000	0.05858	0.055000	0.19348	0.277000	0.26821	-2.583000	0.00904	0.089000	0.17243	0.505000	0.49811	AGC	G|0.844;A|0.156	0.156	strong		0.537	OR2A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349969.1		
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 GAIIx	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_ENST00000523126.1_5'Flank|ITGB2_ENST00000397854.3_Silent_p.L11L|ITGB2_ENST00000397857.1_Silent_p.L11L|ITGB2_ENST00000397846.3_Silent_p.L11L|ITGB2_ENST00000355153.4_Silent_p.L11L|ITGB2_ENST00000302347.5_Silent_p.L11L|ITGB2_ENST00000397852.1_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		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	74	28	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	
DSG4	147409	hgsc.bcm.edu	37	18	28956904	28956904	+	Silent	SNP	C	C	T	rs36101975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:28956904C>T	ENST00000308128.4	+	1	165	c.30C>T	c.(28-30)tgC>tgT	p.C10C	RP11-534N16.1_ENST00000581452.1_RNA|DSG4_ENST00000359747.4_Silent_p.C10C|RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	10					anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.C10C(1)		NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			GAAACATTTGCCTTTTGATCA	0.428													C|||	609	0.121605	0.121	0.0821	5008	,	,		19221	0.1081		0.1382	False		,,,				2504	0.1472				p.C10C		Atlas-SNP	.											DSG4,NS,carcinoma,0,1	DSG4	343	1	1	Substitution - coding silent(1)	stomach(1)	c.C30T						scavenged	.	C	,	603,3803	262.5+/-264.9	43,517,1643	109.0	93.0	99.0		30,30	1.9	0.9	18	dbSNP_126	99	1234,7366	247.9+/-275.8	79,1076,3145	yes	coding-synonymous,coding-synonymous	DSG4	NM_001134453.1,NM_177986.3	,	122,1593,4788	TT,TC,CC		14.3488,13.6859,14.1243	,	10/1060,10/1041	28956904	1837,11169	2203	4300	6503	SO:0001819	synonymous_variant	147409	exon1			CATTTGCCTTTTG	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.30C>T	18.37:g.28956904C>T		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	37	CCDS11897.1																																																																																			C|0.858;T|0.142	0.142	strong		0.428	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25268368	25268368	+	Silent	SNP	A	A	G	rs4787310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:25268368A>G	ENST00000328086.7	-	1	884	c.81T>C	c.(79-81)ccT>ccC	p.P27P		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	27					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.P27P(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		ATGCCCACTCAGGGTCCTTTT	0.557											OREG0023690	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2309	0.461062	0.6346	0.4481	5008	,	,		19215	0.4722		0.338	False		,,,				2504	0.3507				p.P27P		Atlas-SNP	.											ZKSCAN2,NS,carcinoma,0,1	ZKSCAN2	90	1	1	Substitution - coding silent(1)	stomach(1)	c.T81C						PASS	.	G		2596,1798	516.7+/-369.2	775,1046,376	73.0	79.0	77.0		81	2.0	0.9	16	dbSNP_111	77	3045,5555	655.5+/-401.3	540,1965,1795	no	coding-synonymous	ZKSCAN2	NM_001012981.4		1315,3011,2171	GG,GA,AA		35.407,40.9194,43.4123		27/968	25268368	5641,7353	2197	4300	6497	SO:0001819	synonymous_variant	342357	exon1			CCACTCAGGGTCC	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.81T>C	16.37:g.25268368A>G		Somatic	80	0	0	777	WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_001012981	A1L3B4|Q6ZN77	Silent	SNP	ENST00000328086.7	37	CCDS32410.1																																																																																			A|0.562;G|0.438	0.438	strong		0.557	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
DGKH	160851	hgsc.bcm.edu	37	13	42764564	42764564	+	Silent	SNP	C	C	G	rs7324235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:42764564C>G	ENST00000337343.4	+	16	1959	c.1938C>G	c.(1936-1938)ccC>ccG	p.P646P	DGKH_ENST00000536612.1_Silent_p.P510P|DGKH_ENST00000540693.1_Silent_p.P646P|DGKH_ENST00000379274.2_Silent_p.P510P|DGKH_ENST00000538674.1_Silent_p.P401P|DGKH_ENST00000261491.5_Silent_p.P646P|DGKH_ENST00000498255.2_3'UTR	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	646					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		CAGTTCACCCCTGTGAACCAG	0.388													C|||	871	0.173922	0.0643	0.2666	5008	,	,		15383	0.0942		0.2624	False		,,,				2504	0.2474				p.P646P		Atlas-SNP	.											DGKH,caecum,carcinoma,0,1	DGKH	106	1	0			c.C1938G						PASS	.	C	,,,,	445,3961	216.1+/-234.9	22,401,1780	121.0	117.0	119.0		1938,1530,1530,1938,1938	-2.6	0.1	13	dbSNP_116	119	2332,6268	390.9+/-343.5	335,1662,2303	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	357,2063,4083	GG,GC,CC		27.1163,10.0999,21.3517	,,,,	646/1165,510/1101,510/1085,646/1165,646/1221	42764564	2777,10229	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon17			TCACCCCTGTGAA	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.1938C>G	13.37:g.42764564C>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	94	27	0.287234	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			C|0.796;G|0.204	0.204	strong		0.388	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
MXRA5	25878	hgsc.bcm.edu	37	X	3238167	3238167	+	Silent	SNP	T	T	G	rs1635245	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3238167T>G	ENST00000217939.6	-	5	5713	c.5559A>C	c.(5557-5559)ccA>ccC	p.P1853P		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1853	Ig-like C2-type 3.					extracellular vesicular exosome (GO:0070062)		p.P1853P(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TGAGGATTTGTGGCTTTTCCC	0.517													G|||	1777	0.470728	0.3169	0.4006	3775	,	,		11504	0.2728		0.4583	False		,,,				2504	0.3517				p.P1853P		Atlas-SNP	.											.	MXRA5	815	.	1	Substitution - coding silent(1)	stomach(1)	c.A5559C						PASS	.	G		1614,2221		275,813,251,544,320	98.0	85.0	89.0		5559	0.4	0.1	X	dbSNP_89	89	3839,2889		793,1187,1066,448,806	no	coding-synonymous	MXRA5	NM_015419.3		1068,2000,1317,992,1126	GG,GT,G,TT,T		42.94,42.086,48.3764		1853/2829	3238167	5453,5110	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			GATTTGTGGCTTT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5559A>C	X.37:g.3238167T>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			T|0.500;G|0.500	0.500	strong		0.517	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
CEP44	80817	hgsc.bcm.edu	37	4	175237408	175237408	+	Silent	SNP	T	T	C	rs1553669	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:175237408T>C	ENST00000503780.1	+	10	1467	c.1053T>C	c.(1051-1053)acT>acC	p.T351T	CEP44_ENST00000296519.4_Silent_p.T351T|CEP44_ENST00000457424.2_Silent_p.T351T|CEP44_ENST00000426172.1_Silent_p.T351T	NM_001040157.2	NP_001035247.1	Q9C0F1	CEP44_HUMAN	centrosomal protein 44kDa	351						centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|spindle pole (GO:0000922)		p.T351T(1)		endometrium(2)|large_intestine(4)|lung(5)|stomach(1)	12						GAGCCTCTACTGTTAATTACT	0.388													C|||	3438	0.686502	0.702	0.5605	5008	,	,		15790	0.744		0.7366	False		,,,				2504	0.6442				p.T351T		Atlas-SNP	.											CEP44,NS,carcinoma,0,1	CEP44	35	1	1	Substitution - coding silent(1)	stomach(1)	c.T1053C						PASS	.	C	,	3083,1323	443.9+/-347.2	1075,933,195	122.0	133.0	129.0		1053,1053	-2.6	0.0	4	dbSNP_88	129	6277,2323	389.4+/-342.9	2301,1675,324	no	coding-synonymous,coding-synonymous	CEP44	NM_001040157.2,NM_001145314.1	,	3376,2608,519	CC,CT,TT		27.0116,30.0272,28.0332	,	351/391,351/400	175237408	9360,3646	2203	4300	6503	SO:0001819	synonymous_variant	80817	exon10			CTCTACTGTTAAT	AB051499	CCDS34106.1, CCDS47163.1	4q34	2014-02-20	2011-05-06	2011-05-06	ENSG00000164118	ENSG00000164118			29356	protein-coding gene	gene with protein product			"""KIAA1712"""	KIAA1712		21399614	Standard	NM_001040157		Approved		uc010iro.2	Q9C0F1	OTTHUMG00000160752	ENST00000503780.1:c.1053T>C	4.37:g.175237408T>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_001040157	A8K8W9|A8MW11|B3KT53|D3DP42|Q8IXZ4	Silent	SNP	ENST00000503780.1	37	CCDS34106.1																																																																																			T|0.287;C|0.713	0.713	strong		0.388	CEP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362109.2	NM_030633	
PVRL4	81607	hgsc.bcm.edu	37	1	161049509	161049509	+	Missense_Mutation	SNP	G	G	T	rs35434391	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161049509G>T	ENST00000368012.3	-	2	612	c.310C>A	c.(310-312)Cca>Aca	p.P104T		NM_030916.2	NP_112178.2	Q96NY8	PVRL4_HUMAN	poliovirus receptor-related 4	104	Ig-like V-type 1.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|urinary_tract(1)	20	all_cancers(52;8.9e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00165)			GGGTTGCGTGGGGGCGGCGGC	0.692													G|||	193	0.0385383	0.0038	0.0476	5008	,	,		15751	0.0		0.1342	False		,,,				2504	0.0204				p.P104T	NSCLC(76;1160 1387 14476 16172 29359)	Atlas-SNP	.											.	PVRL4	48	.	0			c.C310A						PASS	.	G	THR/PRO	86,4254		1,84,2085	19.0	21.0	20.0		310	5.5	0.3	1	dbSNP_126	20	873,7639		53,767,3436	yes	missense	PVRL4	NM_030916.2	38	54,851,5521	TT,TG,GG		10.2561,1.9816,7.4619	probably-damaging	104/511	161049509	959,11893	2170	4256	6426	SO:0001583	missense	81607	exon2			TGCGTGGGGGCGG	AF426163	CCDS1216.1	1q22-q23.2	2013-01-14			ENSG00000143217	ENSG00000143217		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19688	protein-coding gene	gene with protein product		609607				11544254	Standard	NM_030916		Approved	nectin-4, PRR4, LNIR	uc001fxo.2	Q96NY8	OTTHUMG00000031475	ENST00000368012.3:c.310C>A	1.37:g.161049509G>T	ENSP00000356991:p.Pro104Thr	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_030916	B4DQW3|Q96K15	Missense_Mutation	SNP	ENST00000368012.3	37	CCDS1216.1	133	0.060897435897435896	3	0.006097560975609756	24	0.06629834254143646	0	0.0	106	0.13984168865435356	G	17.62	3.435258	0.62955	0.019816	0.102561	ENSG00000143217	ENST00000368012	T	0.27104	1.69	5.51	5.51	0.81932	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000015	T	0.31888	0.0811	L	0.39633	1.23	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01420	-1.1359	10	0.27082	T	0.32	.	16.9215	0.86165	0.0:0.0:1.0:0.0	rs35434391	104	Q96NY8	PVRL4_HUMAN	T	104	ENSP00000356991:P104T	ENSP00000356991:P104T	P	-	1	0	PVRL4	159316133	0.983000	0.35010	0.253000	0.24343	0.508000	0.34012	2.543000	0.45752	2.574000	0.86865	0.650000	0.86243	CCA	G|0.929;T|0.071	0.071	strong		0.692	PVRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077074.1	NM_030916	
PYGB	5834	hgsc.bcm.edu	37	20	25260931	25260931	+	Silent	SNP	A	A	G	rs2227890	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:25260931A>G	ENST00000216962.4	+	10	1232	c.1122A>G	c.(1120-1122)gcA>gcG	p.A374A		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	374					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						AGACCTGTGCATACACCAACC	0.537													G|||	2690	0.537141	0.4523	0.3473	5008	,	,		21077	0.9107		0.4334	False		,,,				2504	0.5082				p.A374A		Atlas-SNP	.											PYGB,NS,carcinoma,0,1	PYGB	84	1	0			c.A1122G						PASS	.	G		1903,2503	628.7+/-395.1	401,1101,701	136.0	122.0	126.0		1122	-7.7	0.6	20	dbSNP_98	126	3754,4846	616.5+/-396.5	813,2128,1359	no	coding-synonymous	PYGB	NM_002862.3		1214,3229,2060	GG,GA,AA		43.6512,43.1911,43.4953		374/844	25260931	5657,7349	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon10			CTGTGCATACACC		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.1122A>G	20.37:g.25260931A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	146	79	0.541096	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			A|0.513;G|0.487	0.487	strong		0.537	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
SAMM50	25813	hgsc.bcm.edu	37	22	44386281	44386281	+	Silent	SNP	C	C	T	rs7587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44386281C>T	ENST00000350028.4	+	14	1516	c.1359C>T	c.(1357-1359)ggC>ggT	p.G453G	SAMM50_ENST00000396202.3_Silent_p.G243G	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	453					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)				endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TACAGACAGGCGACAGGTACG	0.478													C|||	1116	0.222843	0.1604	0.1657	5008	,	,		17728	0.3621		0.2068	False		,,,				2504	0.2209				p.G453G		Atlas-SNP	.											.	SAMM50	30	.	0			c.C1359T						PASS	.	C		754,3652	307.2+/-289.9	67,620,1516	138.0	104.0	115.0		1359	-9.7	0.0	22	dbSNP_52	115	1906,6694	338.2+/-322.6	219,1468,2613	no	coding-synonymous	SAMM50	NM_015380.4		286,2088,4129	TT,TC,CC		22.1628,17.113,20.4521		453/470	44386281	2660,10346	2203	4300	6503	SO:0001819	synonymous_variant	25813	exon14			GACAGGCGACAGG	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.1359C>T	22.37:g.44386281C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Silent	SNP	ENST00000350028.4	37	CCDS14055.1																																																																																			T|0.178;G|0.125	0.178	strong		0.478	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
BPI	671	hgsc.bcm.edu	37	20	36939052	36939052	+	Silent	SNP	G	G	C	rs5743507	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:36939052G>C	ENST00000262865.4	+	4	635	c.546G>C	c.(544-546)gtG>gtC	p.V182V	CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	182					defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				AGAGCAAAGTGGGGTATGGAC	0.557													g|||	279	0.0557109	0.0061	0.1513	5008	,	,		20228	0.002		0.1193	False		,,,				2504	0.045				p.V182V		Atlas-SNP	.											BPI,caecum,carcinoma,0,1	BPI	67	1	0			c.G546C						PASS	.			90,4316	72.5+/-110.5	1,88,2114	107.0	87.0	94.0		546	2.6	1.0	20	dbSNP_114	94	1001,7599	215.6+/-254.9	61,879,3360	no	coding-synonymous	BPI	NM_001725.2		62,967,5474	CC,CG,GG		11.6395,2.0427,8.3884		182/488	36939052	1091,11915	2203	4300	6503	SO:0001819	synonymous_variant	671	exon4			CAAAGTGGGGTAT	J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"""BPI fold containing"""	1095	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 1"""	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.546G>C	20.37:g.36939052G>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Silent	SNP	ENST00000262865.4	37	CCDS13303.1																																																																																			G|0.928;C|0.072	0.072	strong		0.557	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	
FAM107A	11170	hgsc.bcm.edu	37	3	58552950	58552950	+	Silent	SNP	C	C	T	rs1139701	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:58552950C>T	ENST00000394481.1	-	4	870	c.312G>A	c.(310-312)caG>caA	p.Q104Q	FAM107A_ENST00000447756.2_Silent_p.Q132Q|FAM107A_ENST00000360997.2_Silent_p.Q104Q|FAM107A_ENST00000464064.1_Silent_p.Q104Q|FAM107A_ENST00000474531.1_Silent_p.Q135Q	NM_001282713.1|NM_007177.2	NP_001269642.1|NP_009108.1	O95990	F107A_HUMAN	family with sequence similarity 107, member A	104					regulation of cell growth (GO:0001558)	neuron projection (GO:0043005)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)		TCAGCCTCTGCTGCCGTCTCA	0.627													C|||	87	0.0173722	0.0015	0.0288	5008	,	,		20130	0.001		0.0527	False		,,,				2504	0.0112				p.Q104Q		Atlas-SNP	.											.	FAM107A	33	.	0			c.G312A						PASS	.	C	,	49,4357	50.9+/-86.3	1,47,2155	47.0	39.0	42.0		312,312	3.2	1.0	3	dbSNP_132	42	404,8196	126.0+/-184.5	6,392,3902	no	coding-synonymous,coding-synonymous	FAM107A	NM_001076778.1,NM_007177.2	,	7,439,6057	TT,TC,CC		4.6977,1.1121,3.483	,	104/145,104/145	58552950	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	11170	exon3			CCTCTGCTGCCGT	AF089854	CCDS2892.1, CCDS63672.1, CCDS63673.1	3p14.2	2006-02-03			ENSG00000168309	ENSG00000168309			30827	protein-coding gene	gene with protein product		608295				10564580, 10702698	Standard	XM_005264835		Approved	DRR1, TU3A	uc003dkn.3	O95990	OTTHUMG00000159159	ENST00000394481.1:c.312G>A	3.37:g.58552950C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	154	82	0.532468	NM_001076778	B3KNQ4|B7ZAY5|J3KR61|Q96NH4	Silent	SNP	ENST00000394481.1	37	CCDS2892.1																																																																																			C|0.964;T|0.036	0.036	strong		0.627	FAM107A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353585.1	NM_007177	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651643	1651643	+	Silent	SNP	C	C	T	rs576867883|rs4752771|rs71025765		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1651643C>T	ENST00000399676.2	+	1	611	c.573C>T	c.(571-573)ccC>ccT	p.P191P		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	191	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.Y182_P191delYCCQSSCCKP(1)		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)		GCTGTAAGCCCTACTGCTGCC	0.602																																					p.P191P		Atlas-SNP	.											KRTAP5-5,NS,carcinoma,0,1	KRTAP5-5	86	1	1	Deletion - In frame(1)	urinary_tract(1)	c.C573T						scavenged	.						67.0	68.0	68.0					11																	1651643		2201	4297	6498	SO:0001819	synonymous_variant	439915	exon1			TAAGCCCTACTGC	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.573C>T	11.37:g.1651643C>T		Somatic	55	3	0.0545455		WXS	Illumina HiSeq	Phase_I	44	8	0.181818	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			C|0.691;T|0.309	0.309	strong		0.602	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
GRM1	2911	hgsc.bcm.edu	37	6	146755560	146755560	+	Silent	SNP	T	T	G	rs1047006	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:146755560T>G	ENST00000282753.1	+	8	3448	c.3213T>G	c.(3211-3213)ccT>ccG	p.P1071P	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000361719.2_Silent_p.P1071P|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000492807.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1071	Gln/Pro-rich.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CCCCGCCACCTCCGCAGCACC	0.682													t|||	998	0.199281	0.0499	0.2925	5008	,	,		14141	0.0843		0.4165	False		,,,				2504	0.2301				p.P1071P		Atlas-SNP	.											GRM1,colon,carcinoma,0,2	GRM1	419	2	0			c.T3213G						PASS	.	T	,	492,3896		30,432,1732	28.0	33.0	31.0		3213,	-11.4	0.0	6	dbSNP_86	31	3341,5243		672,1997,1623	no	coding-synonymous,utr-3	GRM1	NM_000838.3,NM_001114329.1	,	702,2429,3355	GG,GT,TT		38.9212,11.2124,29.5483	,	1071/1195,	146755560	3833,9139	2194	4292	6486	SO:0001819	synonymous_variant	2911	exon9			GCCACCTCCGCAG	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3213T>G	6.37:g.146755560T>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	37	11	0.297297	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																			T|0.746;G|0.254	0.254	strong		0.682	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
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 GAIIx	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_ENST00000296306.7_Silent_p.S241S|PIGG_ENST00000504346.1_Silent_p.S241S|PIGG_ENST00000383028.4_Silent_p.S197S|PIGG_ENST00000310340.5_Silent_p.S330S|PIGG_ENST00000503111.1_Silent_p.S241S|PIGG_ENST00000536264.1_Silent_p.S208S|PIGG_ENST00000509768.1_Silent_p.S241S	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		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	80	27	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 GAIIx	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		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	22	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	
F13A1	2162	hgsc.bcm.edu	37	6	6174866	6174866	+	Missense_Mutation	SNP	G	G	A	rs5982	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:6174866G>A	ENST00000264870.3	-	12	1959	c.1694C>T	c.(1693-1695)cCg>cTg	p.P565L		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	565			P -> L (in allele F13A*1A, allele F13A*2A and allele F13*(2)A; dbSNP:rs5982). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:2901091, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.P565L(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TTCTGCCTTCGGGACCCCGGT	0.522													G|||	1204	0.240415	0.1452	0.1009	5008	,	,		18278	0.3581		0.2107	False		,,,				2504	0.3773				p.P565L		Atlas-SNP	.											F13A1,NS,malignant_melanoma,-1,2	F13A1	135	2	1	Substitution - Missense(1)	breast(1)	c.C1694T						PASS	.	G	LEU/PRO	697,3709	292.4+/-282.0	58,581,1564	300.0	255.0	271.0		1694	5.8	0.2	6	dbSNP_52	271	1807,6793	325.6+/-317.0	205,1397,2698	yes	missense	F13A1	NM_000129.3	98	263,1978,4262	AA,AG,GG		21.0116,15.8193,19.2527	benign	565/733	6174866	2504,10502	2203	4300	6503	SO:0001583	missense	2162	exon12			GCCTTCGGGACCC	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1694C>T	6.37:g.6174866G>A	ENSP00000264870:p.Pro565Leu	Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	264	222	0.840909	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	467	0.21382783882783882	82	0.16666666666666666	45	0.12430939226519337	176	0.3076923076923077	164	0.21635883905013192	G	0.427	-0.905523	0.02453	0.158193	0.210116	ENSG00000124491	ENST00000264870;ENST00000441301	T	0.63744	-0.06	5.78	5.78	0.91487	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.568490	0.18516	N	0.138901	T	0.16557	0.0398	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.10296	0.001;0.003	B;B	0.06405	0.001;0.002	T	0.06752	-1.0809	9	0.09084	T	0.74	.	12.3343	0.55058	0.0763:0.0:0.9237:0.0	rs5982;rs3191129;rs3818482;rs17375117;rs57528694;rs5982	502;565	F5H080;P00488	.;F13A_HUMAN	L	565;502	ENSP00000264870:P565L	ENSP00000264870:P565L	P	-	2	0	F13A1	6119865	0.586000	0.26782	0.164000	0.22755	0.127000	0.20565	2.506000	0.45433	2.726000	0.93360	0.643000	0.83706	CCG	G|0.798;A|0.202	0.202	strong		0.522	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
PFKM	5213	hgsc.bcm.edu	37	12	48527186	48527186	+	Silent	SNP	C	C	T	rs1049392	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48527186C>T	ENST00000312352.7	+	6	555	c.516C>T	c.(514-516)acC>acT	p.T172T	PFKM_ENST00000551804.1_Silent_p.T172T|PFKM_ENST00000395233.2_Silent_p.T172T|PFKM_ENST00000359794.5_Silent_p.T172T|PFKM_ENST00000340802.6_Silent_p.T243T|PFKM_ENST00000547587.1_Silent_p.T172T	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	172	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						TCTGTGGCACCGATATGACCA	0.512													C|||	941	0.187899	0.3396	0.111	5008	,	,		20414	0.1399		0.1382	False		,,,				2504	0.138				p.T243T		Atlas-SNP	.											.	PFKM	117	.	0			c.C729T						PASS	.	C	,,,	1405,3001	462.6+/-353.3	222,961,1020	182.0	145.0	157.0		516,729,516,516	-6.2	1.0	12	dbSNP_86	157	1160,7440	236.1+/-268.4	64,1032,3204	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PFKM	NM_000289.5,NM_001166686.1,NM_001166687.1,NM_001166688.1	,,,	286,1993,4224	TT,TC,CC		13.4884,31.8883,19.7217	,,,	172/781,243/852,172/781,172/781	48527186	2565,10441	2203	4300	6503	SO:0001819	synonymous_variant	5213	exon8			TGGCACCGATATG	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 122"""	610681	"""phosphofructokinase, polypeptide X"""	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.516C>T	12.37:g.48527186C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	248	123	0.495968	NM_001166686	J3KNX3|Q16814|Q16815|Q6ZTT1	Silent	SNP	ENST00000312352.7	37	CCDS8760.1																																																																																			C|0.804;T|0.196	0.196	strong		0.512	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289	
DOCK10	55619	hgsc.bcm.edu	37	2	225672460	225672460	+	Silent	SNP	G	G	A	rs12328236	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:225672460G>A	ENST00000258390.7	-	33	3694	c.3627C>T	c.(3625-3627)taC>taT	p.Y1209Y	DOCK10_ENST00000409592.3_Silent_p.Y1203Y	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1209					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		GGAGCATGCCGTACAGGGGCA	0.403													G|||	826	0.164936	0.4251	0.0749	5008	,	,		19288	0.0248		0.1103	False		,,,				2504	0.0777				p.Y1209Y		Atlas-SNP	.											DOCK10,colon,carcinoma,0,1	DOCK10	308	1	0			c.C3627T						PASS	.	G		1411,2291		262,887,702	55.0	52.0	53.0		3627	-0.3	1.0	2	dbSNP_120	53	842,7334		39,764,3285	no	coding-synonymous	DOCK10	NM_014689.2		301,1651,3987	AA,AG,GG		10.2984,38.1145,18.9678		1209/2187	225672460	2253,9625	1851	4088	5939	SO:0001819	synonymous_variant	55619	exon33			CATGCCGTACAGG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3627C>T	2.37:g.225672460G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1	333	0.15247252747252749	205	0.4166666666666667	29	0.08011049723756906	16	0.027972027972027972	83	0.10949868073878628	G	5.256	0.232714	0.09969	0.381145	0.102984	ENSG00000135905	ENST00000422684	.	.	.	5.27	-0.308	0.12773	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46331	-0.9199	3	.	.	.	.	9.1186	0.36773	0.6983:0.0:0.3017:0.0	rs12328236;rs58012372;rs12328236	.	.	.	M	100	.	.	T	-	2	0	DOCK10	225380704	1.000000	0.71417	0.996000	0.52242	0.729000	0.41735	1.345000	0.33953	-0.159000	0.11021	-0.982000	0.02568	ACG	G|0.827;A|0.173	0.173	strong		0.403	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
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 GAIIx	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		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	71	18	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	
YTHDF1	54915	hgsc.bcm.edu	37	20	61834092	61834092	+	Silent	SNP	G	G	A	rs41282994	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61834092G>A	ENST00000370339.3	-	4	1541	c.1200C>T	c.(1198-1200)gaC>gaT	p.D400D	YTHDF1_ENST00000370333.4_Silent_p.D350D|YTHDF1_ENST00000370334.4_Intron	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	400	YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.						N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						GGTGGATGTCGTCCTCAGAGT	0.542													G|||	281	0.0561102	0.0038	0.0648	5008	,	,		18268	0.001		0.1153	False		,,,				2504	0.1166				p.D400D		Atlas-SNP	.											.	YTHDF1	66	.	0			c.C1200T						PASS	.	G		93,4313	76.2+/-114.5	2,89,2112	99.0	87.0	91.0		1200	-7.2	0.1	20	dbSNP_127	91	886,7714	199.4+/-243.5	43,800,3457	no	coding-synonymous	YTHDF1	NM_017798.3		45,889,5569	AA,AG,GG		10.3023,2.1108,7.5273		400/560	61834092	979,12027	2203	4300	6503	SO:0001819	synonymous_variant	54915	exon4			GATGTCGTCCTCA	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"""YTH domain family 1"""	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.1200C>T	20.37:g.61834092G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Silent	SNP	ENST00000370339.3	37	CCDS13511.1																																																																																			G|0.930;A|0.070	0.070	strong		0.542	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798	
VOPP1	81552	hgsc.bcm.edu	37	7	55540707	55540707	+	Silent	SNP	G	G	A	rs815957	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:55540707G>A	ENST00000285279.5	-	5	560	c.360C>T	c.(358-360)acC>acT	p.T120T	VOPP1_ENST00000454227.1_Silent_p.T57T|VOPP1_ENST00000427700.1_Silent_p.T118T|VOPP1_ENST00000545390.1_Silent_p.T117T|VOPP1_ENST00000428648.1_Silent_p.T53T|VOPP1_ENST00000453256.1_Silent_p.T53T|VOPP1_ENST00000433959.1_Silent_p.T111T|VOPP1_ENST00000418904.1_Silent_p.T103T|VOPP1_ENST00000428097.1_Silent_p.T53T	NM_001284282.1|NM_030796.3	NP_001271211.1|NP_110423.3	Q96AW1	VOPP1_HUMAN	vesicular, overexpressed in cancer, prosurvival protein 1	120	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|integral component of organelle membrane (GO:0031301)	signal transducer activity (GO:0004871)			endometrium(1)|lung(4)	5						CTCCTGGGTCGGTGTAATAGG	0.617													G|||	1708	0.341054	0.1422	0.5317	5008	,	,		16359	0.5109		0.2982	False		,,,				2504	0.3436				p.T120T		Atlas-SNP	.											.	VOPP1	14	.	0			c.C360T						PASS	.	G		742,3018		81,580,1219	32.0	37.0	36.0		360	-11.4	0.0	7	dbSNP_86	36	2441,5755		372,1697,2029	no	coding-synonymous	VOPP1	NM_030796.3		453,2277,3248	AA,AG,GG		29.7828,19.734,26.6226		120/173	55540707	3183,8773	1880	4098	5978	SO:0001819	synonymous_variant	81552	exon5			TGGGTCGGTGTAA		CCDS47588.1, CCDS64654.1, CCDS64656.1	7p11.2	2010-06-22			ENSG00000154978	ENSG00000154978			34518	protein-coding gene	gene with protein product	"""Glioblastoma-amplified secreted protein"", ""EGFR-coamplified and overexpressed protein"""	611915				15735698	Standard	NM_030796		Approved	ECop, GASP, FLJ20532, DKFZp564K0822	uc003tqs.3	Q96AW1	OTTHUMG00000156124	ENST00000285279.5:c.360C>T	7.37:g.55540707G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	196	186	0.94898	NM_030796	B0AZU1|B2RAT4|B3KS72|C9JWR3|Q6FIE3|Q8NBN8|Q96RE5|Q9H0W4	Silent	SNP	ENST00000285279.5	37	CCDS47588.1																																																																																			G|0.651;A|0.348	0.348	strong		0.617	VOPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343074.1	NM_030796	
GJD2	57369	hgsc.bcm.edu	37	15	35045276	35045276	+	Silent	SNP	G	G	A	rs35174018	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:35045276G>A	ENST00000290374.4	-	2	845	c.369C>T	c.(367-369)tcC>tcT	p.S123S	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	123					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		GACCTCCTATGGACTCAGGGG	0.557													G|||	312	0.0623003	0.062	0.0476	5008	,	,		18758	0.0873		0.0626	False		,,,				2504	0.047				p.S123S		Atlas-SNP	.											.	GJD2	49	.	0			c.C369T						PASS	.	G		278,4124		3,272,1926	75.0	82.0	80.0		369	-2.3	1.0	15	dbSNP_126	80	645,7951		27,591,3680	no	coding-synonymous	GJD2	NM_020660.1		30,863,5606	AA,AG,GG		7.5035,6.3153,7.1011		123/322	35045276	923,12075	2201	4298	6499	SO:0001819	synonymous_variant	57369	exon2			TCCTATGGACTCA	AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.369C>T	15.37:g.35045276G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	174	85	0.488506	NM_020660	Q2M241|Q9P2R0	Silent	SNP	ENST00000290374.4	37	CCDS10040.1																																																																																			G|0.933;A|0.067	0.067	strong		0.557	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2		
TMEM17	200728	hgsc.bcm.edu	37	2	62733253	62733253	+	Silent	SNP	C	C	T	rs11676567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:62733253C>T	ENST00000335390.5	-	1	223	c.12G>A	c.(10-12)ccG>ccA	p.P4P		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	4					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GCACCGGATCCGGCAGCTCCA	0.672													C|||	2167	0.432708	0.4433	0.4568	5008	,	,		13268	0.5248		0.3569	False		,,,				2504	0.3845				p.P4P		Atlas-SNP	.											TMEM17,NS,carcinoma,0,1	TMEM17	19	1	0			c.G12A						PASS	.	C		1912,2494		431,1050,722	23.0	25.0	25.0		12	-1.9	1.0	2	dbSNP_120	25	3217,5383		619,1979,1702	no	coding-synonymous	TMEM17	NM_198276.2		1050,3029,2424	TT,TC,CC		37.407,43.3954,39.4356		4/199	62733253	5129,7877	2203	4300	6503	SO:0001819	synonymous_variant	200728	exon1			CGGATCCGGCAGC		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.12G>A	2.37:g.62733253C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_198276	Q53QP7|Q53R98	Silent	SNP	ENST00000335390.5	37	CCDS1871.1																																																																																			C|0.598;T|0.402	0.402	strong		0.672	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
MUC6	4588	hgsc.bcm.edu	37	11	1017566	1017566	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1017566G>A	ENST00000421673.2	-	31	5285	c.5235C>T	c.(5233-5235)acC>acT	p.T1745T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1745	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|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;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGATGTAGAGGTTTTGGCCG	0.547																																					p.T1745T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,-2,2	MUC6	408	2	0			c.C5235T						scavenged	.						769.0	740.0	750.0					11																	1017566		2199	4287	6486	SO:0001819	synonymous_variant	4588	exon31			TGTAGAGGTTTTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5235C>T	11.37:g.1017566G>A		Somatic	338	7	0.0207101		WXS	Illumina HiSeq	Phase_I	477	20	0.0419287	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	none		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929392	2929392	+	Silent	SNP	G	G	A	rs55904912	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2929392G>A	ENST00000254695.8	+	20	1932	c.1842G>A	c.(1840-1842)ccG>ccA	p.P614P	RAP1GAP2_ENST00000542807.1_Silent_p.P614P|RAP1GAP2_ENST00000366401.4_Silent_p.P599P|RAP1GAP2_ENST00000540393.2_Silent_p.P595P	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	614	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.P614P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CCAGCTCTCCGGAAATCTGCC	0.577													G|||	2146	0.428514	0.2451	0.4986	5008	,	,		16508	0.5466		0.4066	False		,,,				2504	0.5276				p.P614P		Atlas-SNP	.											RAP1GAP2_ENST00000254695,NS,carcinoma,0,2	RAP1GAP2	90	2	1	Substitution - coding silent(1)	stomach(1)	c.G1842A						PASS	.	G	,	1082,2966		152,778,1094	45.0	48.0	47.0		1797,1842	-7.4	1.0	17	dbSNP_129	47	3415,4945		687,2041,1452	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	839,2819,2546	AA,AG,GG		40.8493,26.7292,36.2427	,	599/716,614/731	2929392	4497,7911	2024	4180	6204	SO:0001819	synonymous_variant	23108	exon20			CTCTCCGGAAATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1842G>A	17.37:g.2929392G>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	204	89	0.436274	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			G|0.579;A|0.421	0.421	strong		0.577	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
CLCN6	1185	hgsc.bcm.edu	37	1	11897082	11897082	+	Silent	SNP	C	C	T	rs41275500	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11897082C>T	ENST00000346436.6	+	19	2059	c.2007C>T	c.(2005-2007)ggC>ggT	p.G669G	CLCN6_ENST00000312413.6_3'UTR|CLCN6_ENST00000376496.3_Silent_p.G669G|CLCN6_ENST00000376487.3_Silent_p.G647G	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	669					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CCCGGGCTGGCGAGCAGCGCA	0.582													C|||	325	0.0648962	0.0242	0.0461	5008	,	,		18861	0.122		0.0338	False		,,,				2504	0.1063				p.G669G		Atlas-SNP	.											.	CLCN6	77	.	0			c.C2007T						PASS	.	C		132,4274	95.3+/-134.0	2,128,2073	62.0	60.0	60.0		2007	-9.2	0.0	1	dbSNP_127	60	400,8200	127.7+/-186.0	6,388,3906	no	coding-synonymous	CLCN6	NM_001286.2		8,516,5979	TT,TC,CC		4.6512,2.9959,4.0904		669/870	11897082	532,12474	2203	4300	6503	SO:0001819	synonymous_variant	1185	exon19			GGCTGGCGAGCAG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.2007C>T	1.37:g.11897082C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																			C|0.954;T|0.046	0.046	strong		0.582	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
ATP13A2	23400	hgsc.bcm.edu	37	1	17314942	17314942	+	Silent	SNP	G	G	A	rs9435662	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17314942G>A	ENST00000326735.8	-	24	2670	c.2637C>T	c.(2635-2637)ggC>ggT	p.G879G	ATP13A2_ENST00000341676.5_Silent_p.G835G|ATP13A2_ENST00000452699.1_Silent_p.G874G|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	879					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGTCATTGGCGCCGTCTCCGC	0.617													G|||	1696	0.338658	0.1369	0.4568	5008	,	,		14687	0.2599		0.508	False		,,,				2504	0.4346				p.G879G		Atlas-SNP	.											.	ATP13A2	85	.	0			c.C2637T						PASS	.	G	,,	912,3494	352.3+/-311.7	101,710,1392	85.0	84.0	84.0		2622,2505,2637	-7.5	0.6	1	dbSNP_119	84	4491,4109	590.3+/-392.7	1154,2183,963	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	1255,2893,2355	AA,AG,GG		47.7791,20.699,41.5424	,,	874/1176,835/1159,879/1181	17314942	5403,7603	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon24			ATTGGCGCCGTCT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2637C>T	1.37:g.17314942G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	124	69	0.556452	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			G|0.606;A|0.394	0.394	strong		0.617	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
NUCB1	4924	hgsc.bcm.edu	37	19	49407660	49407660	+	Silent	SNP	G	G	A	rs1058483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49407660G>A	ENST00000405315.4	+	3	526	c.192G>A	c.(190-192)acG>acA	p.T64T	NUCB1_ENST00000485798.1_Intron|NUCB1_ENST00000407032.1_Silent_p.T64T|NUCB1_ENST00000263273.5_Silent_p.T64T	NM_006184.5	NP_006175.2	Q02818	NUCB1_HUMAN	nucleobindin 1	64						endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			cervix(1)|endometrium(4)|large_intestine(4)|lung(8)	17		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;8.64e-05)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000171)|all cancers(93;0.000333)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0244)		TACTGGAGACGGATGGGCATT	0.627													g|||	274	0.0547125	0.0076	0.062	5008	,	,		13827	0.001		0.1441	False		,,,				2504	0.0767				p.T64T		Atlas-SNP	.											NUCB1,NS,carcinoma,+1,1	NUCB1	44	1	0			c.G192A						PASS	.			135,4271	95.7+/-134.4	5,125,2073	90.0	67.0	75.0		192	-8.5	0.2	19	dbSNP_86	75	1442,7158	276.4+/-292.3	112,1218,2970	no	coding-synonymous	NUCB1	NM_006184.5		117,1343,5043	AA,AG,GG		16.7674,3.064,12.1252		64/462	49407660	1577,11429	2203	4300	6503	SO:0001819	synonymous_variant	4924	exon3			GGAGACGGATGGG	BC002356	CCDS12740.1	19q13.33	2013-01-10			ENSG00000104805	ENSG00000104805		"""EF-hand domain containing"""	8043	protein-coding gene	gene with protein product		601323				8661046	Standard	NM_006184		Approved	NUC, Calnuc	uc002plb.4	Q02818	OTTHUMG00000152514	ENST00000405315.4:c.192G>A	19.37:g.49407660G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_006184	B2RD64|Q15838|Q7Z4J7|Q9BUR1	Silent	SNP	ENST00000405315.4	37	CCDS12740.1	140	0.0641025641025641	7	0.014227642276422764	25	0.06906077348066299	1	0.0017482517482517483	107	0.14116094986807387	g	0.400	-0.918842	0.02396	0.03064	0.167674	ENSG00000104805	ENST00000424608	.	.	.	4.27	-8.54	0.00912	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.999999382115	.	.	.	.	.	.	T	0.11227	-1.0596	3	.	.	.	.	8.5909	0.33686	0.2339:0.0:0.5512:0.2149	rs1058483;rs3199107;rs17272721;rs1058483	.	.	.	Q	64	.	.	R	+	2	0	NUCB1	54099472	0.000000	0.05858	0.239000	0.24122	0.026000	0.11368	-6.299000	0.00071	-1.883000	0.01120	-0.849000	0.03036	CGG	G|0.903;A|0.097	0.097	strong		0.627	NUCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326545.2	NM_006184	
ZHX3	23051	hgsc.bcm.edu	37	20	39832628	39832628	+	Missense_Mutation	SNP	T	T	C	rs17265513	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:39832628T>C	ENST00000309060.3	-	4	1344	c.929A>G	c.(928-930)aAt>aGt	p.N310S	ZHX3_ENST00000560361.1_Missense_Mutation_p.N310S|ZHX3_ENST00000540170.1_Missense_Mutation_p.N310S|ZHX3_ENST00000432768.2_Missense_Mutation_p.N310S|ZHX3_ENST00000544979.2_Missense_Mutation_p.N310S|ZHX3_ENST00000557816.1_Intron|ZHX3_ENST00000558993.1_Intron|ZHX3_ENST00000559234.1_Missense_Mutation_p.N310S			Q9H4I2	ZHX3_HUMAN	zinc fingers and homeoboxes 3	310	Required for homodimerization and interaction with NFYA.|Required for repressor activity.		N -> S (in dbSNP:rs17265513).		cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoblast differentiation (GO:0045669)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(5)|large_intestine(8)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		Myeloproliferative disorder(115;0.00425)				CATGGCTGCATTGTACGTTGG	0.557													T|||	295	0.0589058	0.0113	0.0706	5008	,	,		20230	0.001		0.1948	False		,,,				2504	0.0348				p.N310S		Atlas-SNP	.											.	ZHX3	78	.	0			c.A929G						PASS	.	T	SER/ASN	175,4231	114.6+/-152.6	8,159,2036	104.0	95.0	98.0		929	4.8	0.8	20	dbSNP_123	98	1612,6988	299.4+/-304.4	162,1288,2850	yes	missense	ZHX3	NM_015035.3	46	170,1447,4886	CC,CT,TT		18.7442,3.9719,13.7398	probably-damaging	310/957	39832628	1787,11219	2203	4300	6503	SO:0001583	missense	23051	exon3			GCTGCATTGTACG	AB007855	CCDS13315.1	20q12	2012-03-09	2004-01-29	2004-01-30	ENSG00000174306	ENSG00000174306		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	15935	protein-coding gene	gene with protein product		609598	"""triple homeobox 1"""	TIX1		9455477	Standard	XM_005260343		Approved	KIAA0395	uc002xjs.1	Q9H4I2	OTTHUMG00000032481	ENST00000309060.3:c.929A>G	20.37:g.39832628T>C	ENSP00000312222:p.Asn310Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_015035	E1P5W5|F5H820|O43145|Q6NUJ7	Missense_Mutation	SNP	ENST00000309060.3	37	CCDS13315.1	194	0.08882783882783883	4	0.008130081300813009	34	0.09392265193370165	1	0.0017482517482517483	155	0.20448548812664907	T	15.34	2.803175	0.50315	0.039719	0.187442	ENSG00000174306	ENST00000309060;ENST00000373263;ENST00000540170;ENST00000544979;ENST00000373262;ENST00000432768	T;T;T;T;T	0.41758	0.99;2.4;2.4;2.16;0.99	5.88	4.79	0.61399	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.044464	0.85682	D	0.000000	T	0.00109	0.0003	M	0.79926	2.475	0.22500	P	0.999041207	D;D;D	0.58268	0.974;0.974;0.982	P;P;P	0.58970	0.829;0.78;0.849	T	0.04165	-1.0972	9	0.36615	T	0.2	-25.1632	11.8515	0.52413	0.0:0.068:0.0:0.932	rs17265513;rs17265513	310;310;310	A8K8Q0;Q9H4I2;F5H820	.;ZHX3_HUMAN;.	S	310;310;310;310;88;310	ENSP00000312222:N310S;ENSP00000362360:N310S;ENSP00000442290:N310S;ENSP00000443783:N310S;ENSP00000415498:N310S	ENSP00000312222:N310S	N	-	2	0	ZHX3	39266042	1.000000	0.71417	0.817000	0.32601	0.778000	0.44026	4.110000	0.57831	1.055000	0.40461	0.533000	0.62120	AAT	T|0.891;C|0.109	0.109	strong		0.557	ZHX3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079262.3	NM_015035	
TRIM22	10346	hgsc.bcm.edu	37	11	5718517	5718517	+	Missense_Mutation	SNP	G	G	A	rs7935564	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5718517G>A	ENST00000379965.3	+	3	740	c.463G>A	c.(463-465)Gat>Aat	p.D155N	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	155			D -> N (in dbSNP:rs7935564). {ECO:0000269|PubMed:15489334}.		defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		GATAAAGGAGGATCAAGAGGC	0.463											OREG0003730	type=REGULATORY REGION|Gene=TRIM22|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	2289	0.457069	0.4728	0.4928	5008	,	,		18237	0.1766		0.6372	False		,,,				2504	0.5143				p.D155N	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.G463A						PASS	.	G	ASN/ASP,ASN/ASP	1890,1908		463,964,472	46.0	50.0	48.0		463,463	-4.5	0.0	11	dbSNP_116	48	4965,3357		1482,2001,678	yes	missense,missense	TRIM22	NM_001199573.1,NM_006074.4	23,23	1945,2965,1150	AA,AG,GG		40.3389,49.763,43.4406	benign,benign	155/495,155/499	5718517	6855,5265	1899	4161	6060	SO:0001583	missense	10346	exon3			AAGGAGGATCAAG	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16379	protein-coding gene	gene with protein product		606559	"""tripartite motif-containing 22"""			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.463G>A	11.37:g.5718517G>A	ENSP00000369299:p.Asp155Asn	Somatic	75	0	0	628	WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_001199573	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	994	0.4551282051282051	233	0.4735772357723577	179	0.494475138121547	104	0.18181818181818182	478	0.6306068601583114	G	13.40	2.227061	0.39399	0.49763	0.596611	ENSG00000132274	ENST00000379965;ENST00000425490;ENST00000414641	T;T;T	0.71103	-0.08;-0.36;-0.54	4.07	-4.48	0.03515	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.26147	0.143;0.139	B;B	0.28011	0.085;0.03	T	0.44329	-0.9335	8	0.72032	D	0.01	.	2.2631	0.04072	0.3158:0.3428:0.2409:0.1004	rs7935564;rs52804308;rs60125811;rs7935564	155;155	Q8IYM9-2;Q8IYM9	.;TRI22_HUMAN	N	155	ENSP00000369299:D155N;ENSP00000400417:D155N;ENSP00000396849:D155N	ENSP00000369299:D155N	D	+	1	0	TRIM22	5675093	0.000000	0.05858	0.000000	0.03702	0.218000	0.24690	-2.582000	0.00905	-0.659000	0.05359	0.313000	0.20887	GAT	G|0.528;A|0.472	0.472	strong		0.463	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
TRIM26	7726	hgsc.bcm.edu	37	6	30166266	30166266	+	Silent	SNP	C	C	T	rs2523721	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30166266C>T	ENST00000454678.2	-	5	910	c.474G>A	c.(472-474)agG>agA	p.R158R	TRIM26_ENST00000453195.1_Silent_p.R158R|TRIM26_ENST00000487829.1_5'Flank|TRIM26_ENST00000437089.1_Silent_p.R158R	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	158					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						TGTCTCTGTCCCTCCTTAGGG	0.562													T|||	1153	0.230232	0.4017	0.1585	5008	,	,		20227	0.1081		0.1829	False		,,,				2504	0.2239				p.R158R		Atlas-SNP	.											.	TRIM26	74	.	0			c.G474A						PASS	.	T	,	1011,2011		166,679,666	133.0	141.0	138.0		474,474	2.2	1.0	6	dbSNP_100	138	1083,4335		116,851,1742	yes	coding-synonymous,coding-synonymous	TRIM26	NM_001242783.1,NM_003449.4	,	282,1530,2408	TT,TC,CC		19.9889,33.4547,24.8104	,	158/540,158/540	30166266	2094,6346	1511	2709	4220	SO:0001819	synonymous_variant	7726	exon4			TCTGTCCCTCCTT	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.474G>A	6.37:g.30166266C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	47	0.734375	NM_001242783	A6NG96|Q5SRL2	Silent	SNP	ENST00000454678.2	37	CCDS4678.1																																																																																			C|0.765;T|0.235	0.235	strong		0.562	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	
KRT14	3861	hgsc.bcm.edu	37	17	39742898	39742898	+	Silent	SNP	G	G	A	rs11551758|rs386797102	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39742898G>A	ENST00000167586.6	-	1	275	c.189C>T	c.(187-189)tgC>tgT	p.C63C		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	63	Head.		C -> Y (in dbSNP:rs6503640). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2580298, ECO:0000269|Ref.3}.		aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)	p.C63C(4)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				CCCCCAGCCCGCAGGCTCCCC	0.687													G|||	3409	0.680711	0.4788	0.7248	5008	,	,		13333	0.9425		0.5855	False		,,,				2504	0.7505				p.C63C		Atlas-SNP	.											KRT14,NS,carcinoma,0,4	KRT14	65	4	4	Substitution - coding silent(4)	prostate(3)|haematopoietic_and_lymphoid_tissue(1)	c.C189T						PASS	.						23.0	29.0	27.0					17																	39742898		2180	4266	6446	SO:0001819	synonymous_variant	3861	exon1			CAGCCCGCAGGCT	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.189C>T	17.37:g.39742898G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	26	17	0.653846	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Silent	SNP	ENST00000167586.6	37	CCDS11400.1																																																																																			G|0.461;A|0.539	0.539	strong		0.687	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
RP1L1	94137	hgsc.bcm.edu	37	8	10480679	10480679	+	Silent	SNP	C	C	T	rs80059299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:10480679C>T	ENST00000382483.3	-	2	256	c.33G>A	c.(31-33)ccG>ccA	p.P11P	RP1L1_ENST00000329335.3_5'UTR	NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	11					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CACGGTGGCTCGGGGCCTGGG	0.642													c|||	74	0.0147764	0.0	0.0173	5008	,	,		15577	0.001		0.0268	False		,,,				2504	0.0348				p.P11P		Atlas-SNP	.											.	RP1L1	453	.	0			c.G33A						PASS	.			21,3907		0,21,1943	30.0	33.0	32.0		33	-8.4	0.0	8	dbSNP_132	32	169,8091		1,167,3962	no	coding-synonymous	RP1L1	NM_178857.5		1,188,5905	TT,TC,CC		2.046,0.5346,1.5589		11/2401	10480679	190,11998	1964	4130	6094	SO:0001819	synonymous_variant	94137	exon2			GTGGCTCGGGGCC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.33G>A	8.37:g.10480679C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.987;T|0.013	0.013	strong		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
MYH4	4622	hgsc.bcm.edu	37	17	10355371	10355371	+	Missense_Mutation	SNP	C	C	T	rs11651295	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:10355371C>T	ENST00000255381.2	-	27	3735	c.3625G>A	c.(3625-3627)Gag>Aag	p.E1209K	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1209			E -> K (in dbSNP:rs11651295). {ECO:0000269|PubMed:10388558}.		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TCAATCTGCTCCCCAAGCTCA	0.542													C|||	2544	0.507987	0.3011	0.4841	5008	,	,		18293	0.8631		0.334	False		,,,				2504	0.6176				p.E1209K		Atlas-SNP	.											.	MYH4	349	.	0			c.G3625A						PASS	.	C	LYS/GLU	1391,3015	458.6+/-352.0	222,947,1034	105.0	85.0	92.0		3625	5.5	1.0	17	dbSNP_120	92	3130,5470	476.6+/-369.4	595,1940,1765	yes	missense	MYH4	NM_017533.2	56	817,2887,2799	TT,TC,CC		36.3953,31.5706,34.7609	probably-damaging	1209/1940	10355371	4521,8485	2203	4300	6503	SO:0001583	missense	4622	exon27			TCTGCTCCCCAAG		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.3625G>A	17.37:g.10355371C>T	ENSP00000255381:p.Glu1209Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	1069	0.48946886446886445	147	0.29878048780487804	170	0.4696132596685083	498	0.8706293706293706	254	0.33509234828496043	C	34	5.299995	0.95574	0.315706	0.363953	ENSG00000141048	ENST00000255381	T	0.80480	-1.38	5.51	5.51	0.81932	Myosin tail (1);	0.000000	0.37577	U	0.002023	T	0.00012	0.0000	H	0.94847	3.59	0.09310	P	0.999999800477	D	0.58970	0.984	D	0.63113	0.911	T	0.48525	-0.9028	9	0.87932	D	0	.	19.7768	0.96398	0.0:1.0:0.0:0.0	rs11651295;rs52799277;rs58579935;rs11651295	1209	Q9Y623	MYH4_HUMAN	K	1209	ENSP00000255381:E1209K	ENSP00000255381:E1209K	E	-	1	0	MYH4	10296096	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	7.722000	0.84778	2.745000	0.94114	0.655000	0.94253	GAG	C|0.616;T|0.384	0.384	strong		0.542	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
TMEM132A	54972	hgsc.bcm.edu	37	11	60699230	60699230	+	Silent	SNP	G	G	A	rs2285733	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:60699230G>A	ENST00000453848.2	+	6	1244	c.1086G>A	c.(1084-1086)gcG>gcA	p.A362A	TMEM132A_ENST00000005286.4_Silent_p.A363A			Q24JP5	T132A_HUMAN	transmembrane protein 132A	362						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						GGGGCGTAGCGGTCACTCGCC	0.577													G|||	360	0.071885	0.0083	0.0735	5008	,	,		18888	0.1905		0.0129	False		,,,				2504	0.0951				p.A363A		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G1089A						PASS	.	G	,	27,4379	33.5+/-64.1	0,27,2176	117.0	112.0	114.0		1089,1086	-9.6	0.5	11	dbSNP_100	114	116,8482	61.3+/-123.2	0,116,4183	no	coding-synonymous,coding-synonymous	TMEM132A	NM_017870.3,NM_178031.2	,	0,143,6359	AA,AG,GG		1.3492,0.6128,1.0997	,	363/1025,362/1024	60699230	143,12861	2203	4299	6502	SO:0001819	synonymous_variant	54972	exon6			CGTAGCGGTCACT	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.1086G>A	11.37:g.60699230G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Silent	SNP	ENST00000453848.2	37	CCDS44618.1	157	0.07188644688644688	9	0.018292682926829267	28	0.07734806629834254	110	0.19230769230769232	10	0.013192612137203167	G	9.739	1.164255	0.21538	0.006128	0.013492	ENSG00000006118	ENST00000536409	.	.	.	4.79	-9.58	0.00559	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.32797	P	0.500393	.	.	.	.	.	.	T	0.11518	-1.0584	3	.	.	.	.	4.3243	0.11032	0.6008:0.1537:0.0913:0.1542	rs2285733;rs17845984;rs17858966	.	.	.	S	2	.	.	G	+	1	0	TMEM132A	60455806	0.000000	0.05858	0.455000	0.27031	0.957000	0.61999	-5.697000	0.00104	-2.300000	0.00658	0.455000	0.32223	GGT	G|0.973;A|0.027	0.027	strong		0.577	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
MARCH8	220972	hgsc.bcm.edu	37	10	45953767	45953767	+	Missense_Mutation	SNP	A	A	G	rs7908745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:45953767A>G	ENST00000319836.3	-	7	1545	c.796T>C	c.(796-798)Tat>Cat	p.Y266H	MARCH8_ENST00000395769.2_Missense_Mutation_p.Y266H|MARCH8_ENST00000453424.2_Missense_Mutation_p.Y548H|MARCH8_ENST00000395771.3_Missense_Mutation_p.Y266H|MARCH8_ENST00000476962.1_5'UTR	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	266			Y -> H (in dbSNP:rs7908745). {ECO:0000269|PubMed:15489334}.		immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						CAGATTCCATATCCATGTTTA	0.378													G|||	1517	0.302915	0.3328	0.3703	5008	,	,		18414	0.1706		0.3529	False		,,,				2504	0.2996				p.Y266H	NSCLC(102;658 1594 2173 16344 34808)	Atlas-SNP	.											.	MARCH8	29	.	0			c.T796C						PASS	.	G	HIS/TYR,HIS/TYR,HIS/TYR	1554,2852	669.9+/-402.2	280,994,929	118.0	119.0	118.0		796,796,796	0.5	0.0	10	dbSNP_116	118	2615,5985	688.1+/-404.3	406,1803,2091	yes	missense,missense,missense	MARCH8	NM_145021.4,NM_001002266.1,NM_001002265.1	83,83,83	686,2797,3020	GG,GA,AA		30.407,35.2701,32.0544	benign,benign,benign	266/292,266/292,266/292	45953767	4169,8837	2203	4300	6503	SO:0001583	missense	220972	exon7			TTCCATATCCATG	AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	23356	protein-coding gene	gene with protein product		613335	"""c-mir, cellular modulator of immune recognition"", ""membrane-associated ring finger (C3HC4) 8"""	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.796T>C	10.37:g.45953767A>G	ENSP00000317087:p.Tyr266His	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_001002266	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Missense_Mutation	SNP	ENST00000319836.3	37	CCDS7213.1	674|674	0.3086080586080586|0.3086080586080586	172|172	0.34959349593495936|0.34959349593495936	128|128	0.35359116022099446|0.35359116022099446	105|105	0.18356643356643357|0.18356643356643357	269|269	0.3548812664907652|0.3548812664907652	G|G	6.703|6.703	0.498336|0.498336	0.12762|0.12762	0.352701|0.352701	0.30407|0.30407	ENSG00000165406|ENSG00000165406	ENST00000453424|ENST00000395771;ENST00000319836;ENST00000395769	.|T;T;T	.|0.11063	.|2.81;2.81;2.81	5.67|5.67	0.455|0.455	0.16649|0.16649	.|.	.|2.502220	.|0.01143	.|N	.|0.006245	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.46775|0.46775	-0.9167|-0.9167	4|9	.|0.14252	.|T	.|0.57	-13.9368|-13.9368	5.5414|5.5414	0.17039|0.17039	0.2911:0.2462:0.4628:0.0|0.2911:0.2462:0.4628:0.0	rs7908745;rs17856729;rs52802616;rs56558105;rs58961986;rs7908745|rs7908745;rs17856729;rs52802616;rs56558105;rs58961986;rs7908745	.|266;430	.|Q5T0T0;Q5JQ16	.|MARH8_HUMAN;.	T|H	430|266	.|ENSP00000379118:Y266H;ENSP00000317087:Y266H;ENSP00000379116:Y266H	.|ENSP00000317087:Y266H	I|Y	-|-	2|1	0|0	MARCH8|MARCH8	45273773|45273773	0.987000|0.987000	0.35691|0.35691	0.004000|0.004000	0.12327|0.12327	0.945000|0.945000	0.59286|0.59286	2.648000|2.648000	0.46647|0.46647	-0.157000|-0.157000	0.11059|0.11059	-0.119000|-0.119000	0.15052|0.15052	ATA|TAT	A|0.697;G|0.303	0.303	strong		0.378	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021	
HSPA4	3308	hgsc.bcm.edu	37	5	132437531	132437531	+	Silent	SNP	C	C	T	rs1131809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:132437531C>T	ENST00000304858.2	+	17	2407	c.2118C>T	c.(2116-2118)atC>atT	p.I706I		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	706					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGAAACAGATCCAACAGTATA	0.289													C|||	837	0.167133	0.1664	0.1066	5008	,	,		18023	0.0913		0.2316	False		,,,				2504	0.2229				p.I706I	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.C2118T						PASS	.	C		738,3668	300.1+/-286.2	67,604,1532	65.0	63.0	64.0		2118	1.3	1.0	5	dbSNP_86	64	2017,6583	347.9+/-326.8	228,1561,2511	no	coding-synonymous	HSPA4	NM_002154.3		295,2165,4043	TT,TC,CC		23.4535,16.7499,21.1825		706/841	132437531	2755,10251	2203	4300	6503	SO:0001819	synonymous_variant	3308	exon17			ACAGATCCAACAG	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"""Heat shock proteins / HSP70"""	5237	protein-coding gene	gene with protein product	"""hsp70 RY"""	601113	"""heat shock 70kD protein 4"""			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.2118C>T	5.37:g.132437531C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_002154	O95756|Q2TAL4|Q9BUK9	Silent	SNP	ENST00000304858.2	37	CCDS4166.1																																																																																			C|0.802;T|0.198	0.198	strong		0.289	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431	
ATP2A3	489	hgsc.bcm.edu	37	17	3844787	3844787	+	Silent	SNP	C	C	G	rs1800912	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3844787C>G	ENST00000352011.3	-	13	1761	c.1707G>C	c.(1705-1707)gcG>gcC	p.A569A	ATP2A3_ENST00000397043.3_Silent_p.A569A|ATP2A3_ENST00000359983.3_Silent_p.A569A|ATP2A3_ENST00000397035.3_Silent_p.A569A|ATP2A3_ENST00000397041.3_Silent_p.A569A|ATP2A3_ENST00000309890.7_Silent_p.A569A|ATP2A3_ENST00000397039.1_5'UTR			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	569					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		TCCTTGGGGGCGCGTCCCGGG	0.652													c|||	741	0.147963	0.1589	0.2637	5008	,	,		17537	0.004		0.2515	False		,,,				2504	0.093				p.A569A	GBM(32;29 774 15719 37967)	Atlas-SNP	.											ATP2A3,NS,carcinoma,-2,1	ATP2A3	148	1	0			c.G1707C						PASS	.		,,,,,,	776,3630	305.8+/-289.2	74,628,1501	86.0	85.0	85.0		1707,1707,1707,1707,1707,1707,1707	-7.3	0.0	17	dbSNP_89	85	2122,6478	357.5+/-330.8	286,1550,2464	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	360,2178,3965	GG,GC,CC		24.6744,17.6123,22.282	,,,,,,	569/1000,569/1053,569/1045,569/1044,569/1030,569/999,569/1030	3844787	2898,10108	2203	4300	6503	SO:0001819	synonymous_variant	489	exon13			TGGGGGCGCGTCC		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1707G>C	17.37:g.3844787C>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			C|0.787;G|0.213	0.213	strong		0.652	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
SETD6	79918	hgsc.bcm.edu	37	16	58552921	58552921	+	Silent	SNP	G	G	A	rs3607	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:58552921G>A	ENST00000219315.4	+	8	1460	c.1410G>A	c.(1408-1410)gaG>gaA	p.E470E	SETD6_ENST00000310682.2_Silent_p.E446E|SETD6_ENST00000394266.4_Silent_p.E401E			Q8TBK2	SETD6_HUMAN	SET domain containing 6	470					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						AGTTGTTGGAGCTGACAAGTT	0.398													A|||	3854	0.769569	0.8026	0.7104	5008	,	,		23078	0.9544		0.5616	False		,,,				2504	0.7904				p.E470E		Atlas-SNP	.											.	SETD6	27	.	0			c.G1410A						PASS	.	A	,	3326,1070	388.6+/-327.0	1268,790,140	69.0	69.0	69.0		1410,1338	3.2	0.3	16	dbSNP_36	69	4723,3877	543.7+/-384.5	1309,2105,886	no	coding-synonymous,coding-synonymous	SETD6	NM_001160305.1,NM_024860.2	,	2577,2895,1026	AA,AG,GG		45.0814,24.3403,38.0656	,	470/474,446/450	58552921	8049,4947	2198	4300	6498	SO:0001819	synonymous_variant	79918	exon8			GTTGGAGCTGACA	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.1410G>A	16.37:g.58552921G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_001160305	A8K380|B5ME38|Q9H787	Silent	SNP	ENST00000219315.4	37	CCDS54013.1																																																																																			G|0.344;A|0.656	0.656	strong		0.398	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860	
MED8	112950	hgsc.bcm.edu	37	1	43851797	43851797	+	Silent	SNP	G	G	A	rs11541153	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:43851797G>A	ENST00000372457.4	-	6	637	c.594C>T	c.(592-594)ggC>ggT	p.G198G	MED8_ENST00000372455.4_Silent_p.G109G|MED8_ENST00000290663.6_Silent_p.G198G|RP1-92O14.6_ENST00000436713.1_RNA	NM_001001653.2|NM_201542.3	NP_001001653.1|NP_963836.2	Q96G25	MED8_HUMAN	mediator complex subunit 8	198					gene expression (GO:0010467)|protein ubiquitination (GO:0016567)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	9	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GACCACTGCTGCCTGAAGGTC	0.572													G|||	113	0.0225639	0.0023	0.0331	5008	,	,		19276	0.001		0.0537	False		,,,				2504	0.0327				p.G198G		Atlas-SNP	.											.	MED8	38	.	0			c.C594T						PASS	.	G	,	69,4337	63.5+/-100.7	0,69,2134	137.0	135.0	135.0		594,594	0.7	1.0	1	dbSNP_120	135	564,8036	153.6+/-207.9	27,510,3763	no	coding-synonymous,coding-synonymous	MED8	NM_052877.3,NM_201542.3	,	27,579,5897	AA,AG,GG		6.5581,1.566,4.867	,	198/302,198/269	43851797	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	112950	exon6			ACTGCTGCCTGAA	AF521562, BC010543	CCDS486.2, CCDS487.2, CCDS60108.1	1p34.1	2008-02-05	2007-07-30		ENSG00000159479	ENSG00000159479			19971	protein-coding gene	gene with protein product		607956	"""mediator of RNA polymerase II transcription, subunit 8 homolog (S. cerevisiae)"""			12149480, 9671713	Standard	NM_052877		Approved	MGC17544, MGC19641, ARC32	uc001cje.2	Q96G25	OTTHUMG00000007421	ENST00000372457.4:c.594C>T	1.37:g.43851797G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_201542	A9IZ91|A9IZ92|Q5JUY8|Q96FQ4	Silent	SNP	ENST00000372457.4	37	CCDS487.2																																																																																			G|0.958;A|0.042	0.042	strong		0.572	MED8-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318959.1	NM_052877	
KPRP	448834	hgsc.bcm.edu	37	1	152732106	152732106	+	Missense_Mutation	SNP	A	A	T	rs17612167	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152732106A>T	ENST00000606109.1	+	1	70	c.42A>T	c.(40-42)caA>caT	p.Q14H	KPRP_ENST00000368773.1_Missense_Mutation_p.Q14H			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	14	Gln-rich.		Q -> H (in dbSNP:rs17612167).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCCGCTCCAACAGTGCTGCG	0.582													A|||	887	0.177117	0.0106	0.1441	5008	,	,		20191	0.2262		0.2256	False		,,,				2504	0.3252				p.Q14H		Atlas-SNP	.											.	KPRP	152	.	0			c.A42T						PASS	.	A	HIS/GLN	191,4215	122.1+/-159.5	6,179,2018	78.0	77.0	77.0		42	-0.2	0.9	1	dbSNP_123	77	1997,6603	350.0+/-327.7	243,1511,2546	yes	missense	KPRP	NM_001025231.1	24	249,1690,4564	TT,TA,AA		23.2209,4.335,16.823	benign	14/580	152732106	2188,10818	2203	4300	6503	SO:0001583	missense	448834	exon2			GCTCCAACAGTGC	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.42A>T	1.37:g.152732106A>T	ENSP00000475216:p.Gln14His	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	346	0.15842490842490842	8	0.016260162601626018	49	0.13535911602209943	109	0.19055944055944055	180	0.23746701846965698	A	13.87	2.367214	0.41902	0.04335	0.232209	ENSG00000203786	ENST00000368773	T	0.12147	2.71	5.54	-0.206	0.13193	.	0.316889	0.23211	N	0.050675	T	0.02230	0.0069	N	0.08118	0	0.50313	P	1.32000000000021E-4	P	0.39624	0.681	B	0.38056	0.264	T	0.45279	-0.9272	9	0.66056	D	0.02	.	8.3266	0.32160	0.4162:0.355:0.2288:0.0	rs17612167;rs17612167	14	Q5T749	KPRP_HUMAN	H	14	ENSP00000357762:Q14H	ENSP00000357762:Q14H	Q	+	3	2	KPRP	150998730	0.759000	0.28416	0.917000	0.36280	0.694000	0.40290	-0.281000	0.08456	0.066000	0.16515	-0.250000	0.11733	CAA	A|0.835;T|0.165	0.165	strong		0.582	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
FCGR2A	2212	hgsc.bcm.edu	37	1	161487863	161487863	+	Silent	SNP	C	C	T	rs143182858	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161487863C>T	ENST00000271450.6	+	7	917	c.879C>T	c.(877-879)ccC>ccT	p.P293P	FCGR2A_ENST00000367972.4_Silent_p.P292P|RP11-25K21.6_ENST00000537821.2_RNA|FCGR2A_ENST00000486608.1_3'UTR	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	293					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTCTGAACCCCAGGGCACCTA	0.453													C|||	607	0.121206	0.0242	0.1239	5008	,	,		19315	0.2758		0.1183	False		,,,				2504	0.0941				p.P293P		Atlas-SNP	.											.	FCGR2A	38	.	0			c.C879T						PASS	.	C	,	150,4256		2,146,2055	69.0	72.0	71.0		879,876	0.6	0.0	1	dbSNP_134	71	982,7612		48,886,3363	no	coding-synonymous,coding-synonymous	FCGR2A	NM_001136219.1,NM_021642.3	,	50,1032,5418	TT,TC,CC		11.4266,3.4044,8.7077	,	293/318,292/317	161487863	1132,11868	2203	4297	6500	SO:0001819	synonymous_variant	2212	exon7			GAACCCCAGGGCA	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3616	protein-coding gene	gene with protein product	"""Immunoglobulin G Fc receptor II"""	146790	"""Fc fragment of IgG, low affinity IIa, receptor for (CD32)"""	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.879C>T	1.37:g.161487863C>T		Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	226	102	0.451327	NM_001136219	Q8WUN1|Q8WW64	Silent	SNP	ENST00000271450.6	37	CCDS44264.1																																																																																			C|0.901;T|0.099	0.099	strong		0.453	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642	
RAPGEF5	9771	hgsc.bcm.edu	37	7	22202117	22202117	+	Silent	SNP	G	G	A	rs12592	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:22202117G>A	ENST00000401957.2	-	3	664	c.417C>T	c.(415-417)gaC>gaT	p.D139D	RAPGEF5_ENST00000344041.6_Silent_p.D289D			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5	139	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						TACGCGGAACGTCTGAGTTTT	0.343													A|||	2976	0.594249	0.6815	0.438	5008	,	,		19331	0.6062		0.5557	False		,,,				2504	0.6145				p.D289D		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.C867T						PASS	.	A		2428,1258		802,824,217	75.0	74.0	74.0		867	-0.1	1.0	7	dbSNP_52	74	4501,3669		1249,2003,833	no	coding-synonymous	RAPGEF5	NM_012294.3		2051,2827,1050	AA,AG,GG		44.9082,34.1291,41.557		289/731	22202117	6929,4927	1843	4085	5928	SO:0001819	synonymous_variant	9771	exon13			CGGAACGTCTGAG	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"""M-Ras-regulated GEF"""	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525	ENST00000401957.2:c.417C>T	7.37:g.22202117G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_012294	A4D140|Q8IXU5	Silent	SNP	ENST00000401957.2	37																																																																																				G|0.404;A|0.596	0.596	strong		0.343	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294	
CCT6A	908	hgsc.bcm.edu	37	7	56126360	56126360	+	Silent	SNP	T	T	C	rs2230197	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:56126360T>C	ENST00000275603.4	+	8	1152	c.933T>C	c.(931-933)gtT>gtC	p.V311V	CCT6A_ENST00000335503.3_Silent_p.V266V|CCT6A_ENST00000540286.1_Silent_p.V280V|SNORA15_ENST00000384439.1_RNA	NM_001762.3	NP_001753.1	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A (zeta 1)	311					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|cervix(2)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	15	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			AAGGCATAGTTGCTCTGCGCA	0.328													C|||	3216	0.642173	0.5961	0.6614	5008	,	,		16443	0.7103		0.6789	False		,,,				2504	0.5828				p.V311V		Atlas-SNP	.											.	CCT6A	44	.	0			c.T933C						PASS	.	C	,	2658,1748	515.2+/-368.8	814,1030,359	63.0	66.0	65.0		798,933	-4.2	0.8	7	dbSNP_98	65	6012,2588	419.8+/-353.2	2099,1814,387	no	coding-synonymous,coding-synonymous	CCT6A	NM_001009186.1,NM_001762.3	,	2913,2844,746	CC,CT,TT		30.093,39.6732,33.3385	,	266/487,311/532	56126360	8670,4336	2203	4300	6503	SO:0001819	synonymous_variant	908	exon8			CATAGTTGCTCTG	M94083	CCDS5523.1, CCDS34640.1	7p11.2	2011-09-02			ENSG00000146731	ENSG00000146731		"""Heat Shock Proteins / Chaperonins"""	1620	protein-coding gene	gene with protein product		104613		CCT6		1352881, 8034610	Standard	NM_001762		Approved	TTCP20, TCPZ, Cctz, HTR3, TCP20	uc003trl.1	P40227	OTTHUMG00000022842	ENST00000275603.4:c.933T>C	7.37:g.56126360T>C		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_001762	A6NCD2|Q3KP28|Q75LP4|Q96S46	Silent	SNP	ENST00000275603.4	37	CCDS5523.1																																																																																			T|0.335;C|0.665	0.665	strong		0.328	CCT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251526.2	NM_001762	
KBTBD13	390594	hgsc.bcm.edu	37	15	65369395	65369395	+	Missense_Mutation	SNP	C	C	T	rs2919358	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:65369395C>T	ENST00000432196.2	+	1	242	c.242C>T	c.(241-243)gCc>gTc	p.A81V	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	81					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						CTGCTGCAGGCCGTGGAGTGC	0.736													C|||	2613	0.521765	0.6036	0.5447	5008	,	,		9840	0.7312		0.3887	False		,,,				2504	0.316				p.A81V		Atlas-SNP	.											.	KBTBD13	9	.	0			c.C242T						PASS	.	C	VAL/ALA	1463,1441		405,653,394	2.0	3.0	2.0		242	4.6	1.0	15	dbSNP_101	2	2172,4110		500,1172,1469	no	missense	KBTBD13	NM_001101362.2	64	905,1825,1863	TT,TC,CC		34.575,49.6212,39.5711	possibly-damaging	81/459	65369395	3635,5551	1452	3141	4593	SO:0001583	missense	390594	exon1			TGCAGGCCGTGGA		CCDS45281.1	15q22.31	2014-09-17			ENSG00000234438	ENSG00000234438		"""BTB/POZ domain containing"""	37227	protein-coding gene	gene with protein product	"""nemaline myopathy type 6"""	613727				21109227, 22542517	Standard	NM_001101362		Approved	hCG_1645727, NEM6	uc010uis.2	C9JR72		ENST00000432196.2:c.242C>T	15.37:g.65369395C>T	ENSP00000388723:p.Ala81Val	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_001101362		Missense_Mutation	SNP	ENST00000432196.2	37	CCDS45281.1	1197	0.5480769230769231	302	0.6138211382113821	191	0.5276243093922652	410	0.7167832167832168	294	0.38786279683377306	C	20.9	4.061996	0.76187	0.503788	0.34575	ENSG00000234438	ENST00000432196	T	0.67865	-0.29	4.6	4.6	0.57074	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	.	.	.	.	T	0.00012	0.0000	N	0.21324	0.655	0.22629	P	0.99891774	P	0.47034	0.889	P	0.50896	0.653	T	0.37753	-0.9692	8	0.26408	T	0.33	.	17.2241	0.86964	0.0:1.0:0.0:0.0	rs2919358	81	C9JR72	KBTBD_HUMAN	V	81	ENSP00000388723:A81V	ENSP00000388723:A81V	A	+	2	0	KBTBD13	63156448	1.000000	0.71417	0.996000	0.52242	0.931000	0.56810	7.251000	0.78297	2.390000	0.81377	0.650000	0.86243	GCC	C|0.451;T|0.549	0.549	strong		0.736	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362	
LRRC75A	388341	hgsc.bcm.edu	37	17	16347325	16347325	+	Missense_Mutation	SNP	T	T	C	rs61745139	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:16347325T>C	ENST00000409083.3	-	3	658	c.496A>G	c.(496-498)Aga>Gga	p.R166G	C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000475953.1_RNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000391079.1_RNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000580770.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|FAM211A_ENST00000470794.1_Silent_p.V204V|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000582911.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA	NM_207387.3	NP_997270.2														lung(1)	1						CCACGCTGTCTACCTGCTCCC	0.647													T|||	241	0.048123	0.0083	0.0562	5008	,	,		18322	0.0		0.1203	False		,,,				2504	0.0716				p.R166G		Atlas-SNP	.											FAM211A_ENST00000470794,NS,carcinoma,0,3	FAM211A	21	3	0			c.A496G						PASS	.	T	,GLY/ARG	119,4287	87.3+/-125.9	3,113,2087	58.0	48.0	51.0		612,496	3.4	1.0	17	dbSNP_129	51	1153,7447	234.3+/-267.3	70,1013,3217	yes	coding-synonymous,missense	C17orf76	NM_001113567.1,NM_207387.2	,125	73,1126,5304	CC,CT,TT		13.407,2.7009,9.7801	,	204/345,166/213	16347325	1272,11734	2203	4300	6503	SO:0001583	missense	388341	exon3			GCTGTCTACCTGC																												ENST00000409083.3:c.496A>G	17.37:g.16347325T>C	ENSP00000386504:p.Arg166Gly	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_207387		Missense_Mutation	SNP	ENST00000409083.3	37	CCDS11178.2	130	0.05952380952380952	15	0.03048780487804878	22	0.06077348066298342	0	0.0	93	0.12269129287598944	T	14.35	2.510037	0.44660	0.027009	0.13407	ENSG00000181350	ENST00000409083	.	.	.	5.34	3.36	0.38483	.	1.464120	0.03657	N	0.242032	T	0.00496	0.0016	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10337	-1.0634	7	0.87932	D	0	.	10.0548	0.42239	0.0:0.8345:0.0:0.1655	.	166	Q8NAA5-2	.	G	166	.	ENSP00000386504:R166G	R	-	1	2	C17orf76	16288050	0.982000	0.34865	1.000000	0.80357	0.980000	0.70556	0.185000	0.16958	0.772000	0.33382	-0.232000	0.12228	AGA	T|0.918;C|0.082	0.082	strong		0.647	FAM211A-001	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130461.2		
SLCO1C1	53919	hgsc.bcm.edu	37	12	20903757	20903757	+	Intron	SNP	T	T	C	rs10841611	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:20903757T>C	ENST00000266509.2	+	14	2284				SLCO1C1_ENST00000545604.1_Silent_p.H649H|SLCO1C1_ENST00000540354.1_Intron|SLCO1C1_ENST00000545102.1_Silent_p.H531H|SLCO1C1_ENST00000381552.1_Silent_p.H649H	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1						sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.H649H(1)		NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	CCGCATCTCATTGCTACAGCA	0.378													C|||	2391	0.477436	0.1952	0.5735	5008	,	,		16607	0.5913		0.504	False		,,,				2504	0.6462				p.H649H		Atlas-SNP	.											.	SLCO1C1	216	.	1	Substitution - coding silent(1)	kidney(1)	c.T1947C						PASS	.	C	,,,	1072,3334	722.3+/-409.3	137,798,1268	115.0	105.0	108.0		1593,,1947,	0.4	0.0	12	dbSNP_120	108	4722,3878	544.0+/-384.5	1285,2152,863	no	coding-synonymous,intron,coding-synonymous,intron	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	,,,	1422,2950,2131	CC,CT,TT		45.093,24.3305,44.5487	,,,	531/613,,649/731,	20903757	5794,7212	2203	4300	6503	SO:0001627	intron_variant	53919	exon15			ATCTCATTGCTAC	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1916+31T>C	12.37:g.20903757T>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	120	65	0.541667	NM_001145946	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Silent	SNP	ENST00000266509.2	37	CCDS8683.1																																																																																			T|0.496;C|0.504	0.504	strong		0.378	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
DEAF1	10522	hgsc.bcm.edu	37	11	654043	654043	+	Silent	SNP	G	G	A	rs10902188	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:654043G>A	ENST00000382409.3	-	11	1996	c.1512C>T	c.(1510-1512)tgC>tgT	p.C504C	DEAF1_ENST00000525904.1_5'UTR|DEAF1_ENST00000338675.6_Silent_p.C429C	NM_021008.2	NP_066288.2	O75398	DEAF1_HUMAN	DEAF1 transcription factor	504					anatomical structure morphogenesis (GO:0009653)|embryonic skeletal system development (GO:0048706)|germ cell development (GO:0007281)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mammary gland epithelial cell proliferation (GO:0033599)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;1.76e-27)|Epithelial(43;8.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.55e-21)|BRCA - Breast invasive adenocarcinoma(625;4.83e-05)|Lung(200;0.0259)|LUSC - Lung squamous cell carcinoma(625;0.075)		CGCAGTTAACGCAGGACTGCT	0.627													G|||	518	0.103435	0.0552	0.1729	5008	,	,		14599	0.1528		0.0815	False		,,,				2504	0.091				p.C504C		Atlas-SNP	.											.	DEAF1	47	.	0			c.C1512T						PASS	.	G		249,4157	143.8+/-178.8	14,221,1968	115.0	87.0	96.0		1512	-2.0	1.0	11	dbSNP_120	96	712,7888	174.0+/-224.4	29,654,3617	no	coding-synonymous	DEAF1	NM_021008.2		43,875,5585	AA,AG,GG		8.2791,5.6514,7.3889		504/566	654043	961,12045	2203	4300	6503	SO:0001819	synonymous_variant	10522	exon11			GTTAACGCAGGAC	AF049460	CCDS31327.1	11p15.5	2013-01-10	2013-01-10		ENSG00000177030	ENSG00000177030		"""Zinc fingers, MYND-type"""	14677	protein-coding gene	gene with protein product		602635	"""deformed epidermal autoregulatory factor 1 (Drosophila)"""			9773984	Standard	XR_428838		Approved	NUDR, SPN, ZMYND5	uc001lqq.1	O75398	OTTHUMG00000165363	ENST00000382409.3:c.1512C>T	11.37:g.654043G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	37	21	0.567568	NM_021008	A8K1F8|A8K5R8|C7T5V5|O15152|O75399|O75510|O75511|O75512|O75513|Q9UET1	Silent	SNP	ENST00000382409.3	37	CCDS31327.1																																																																																			G|0.911;A|0.089	0.089	strong		0.627	DEAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383614.3	NM_021008	
MGAT5B	146664	hgsc.bcm.edu	37	17	74928758	74928758	+	Silent	SNP	C	C	T	rs79286496	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74928758C>T	ENST00000569840.2	+	11	1897	c.1323C>T	c.(1321-1323)ttC>ttT	p.F441F	MGAT5B_ENST00000428789.2_Silent_p.F452F|MGAT5B_ENST00000301618.4_Silent_p.F441F	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	441					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCATGGGCTTCGTGTCCGAGG	0.622													C|||	1054	0.210463	0.1135	0.1441	5008	,	,		14629	0.3631		0.1909	False		,,,				2504	0.2515				p.F452F		Atlas-SNP	.											.	MGAT5B	98	.	0			c.C1356T						PASS	.	C	,,	550,3856	246.8+/-255.3	35,480,1688	103.0	89.0	94.0		1323,1323,1356	3.0	1.0	17	dbSNP_131	94	1457,7143	279.5+/-294.0	127,1203,2970	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	162,1683,4658	TT,TC,CC		16.9419,12.483,15.4313	,,	441/793,441/791,452/802	74928758	2007,10999	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon10			GGGCTTCGTGTCC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1323C>T	17.37:g.74928758C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	135	73	0.540741	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			C|0.825;T|0.175	0.175	strong		0.622	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
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 GAIIx	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		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	52	22	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		
HLX	3142	hgsc.bcm.edu	37	1	221057662	221057662	+	Silent	SNP	G	G	A	rs3738182	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:221057662G>A	ENST00000366903.6	+	4	2584	c.1083G>A	c.(1081-1083)gaG>gaA	p.E361E	HLX_ENST00000549319.1_Silent_p.E147E	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	361					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)			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)		CGGATGGCGAGCAGGACGAGA	0.667													G|||	936	0.186901	0.2572	0.1801	5008	,	,		11857	0.0942		0.1779	False		,,,				2504	0.2014				p.E361E		Atlas-SNP	.											.	HLX	67	.	0			c.G1083A						PASS	.	G		1007,3399	342.5+/-307.2	124,759,1320	34.0	35.0	35.0		1083	-2.2	0.0	1	dbSNP_107	35	1707,6893	294.6+/-302.0	151,1405,2744	no	coding-synonymous	HLX	NM_021958.3		275,2164,4064	AA,AG,GG		19.8488,22.8552,20.8673		361/489	221057662	2714,10292	2203	4300	6503	SO:0001819	synonymous_variant	3142	exon4			TGGCGAGCAGGAC	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.1083G>A	1.37:g.221057662G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	135	64	0.474074	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Silent	SNP	ENST00000366903.6	37	CCDS1527.1																																																																																			G|0.810;A|0.190	0.190	strong		0.667	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495725C>G	ENST00000237305.7	-	2	165		c.e2-1		SGK1_ENST00000413996.3_Splice_Site|SGK1_ENST00000367857.5_Missense_Mutation_p.A16P|SGK1_ENST00000475719.2_Splice_Site|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367858.5_Splice_Site|SGK1_ENST00000528577.1_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		Somatic	67	0	0	1611	WXS	Illumina HiSeq	Phase_I	41	11	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
COL2A1	1280	hgsc.bcm.edu	37	12	48376291	48376291	+	Silent	SNP	G	G	A	rs2276454	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48376291G>A	ENST00000380518.3	-	34	2459	c.2295C>T	c.(2293-2295)ggC>ggT	p.G765G	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Silent_p.G696G	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	765	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)	TTACCCTGTCGCCTTTGGGCC	0.617													G|||	2152	0.429712	0.3563	0.3501	5008	,	,		18562	0.5556		0.3926	False		,,,				2504	0.4939				p.G765G		Atlas-SNP	.											.	COL2A1	368	.	0			c.C2295T						PASS	.	G	,	1535,2871	483.5+/-359.7	261,1013,929	41.0	40.0	40.0		2295,2088	1.9	1.0	12	dbSNP_100	40	3496,5104	507.9+/-376.9	679,2138,1483	no	coding-synonymous,coding-synonymous	COL2A1	NM_001844.4,NM_033150.2	,	940,3151,2412	AA,AG,GG		40.6512,34.8389,38.6821	,	765/1488,696/1419	48376291	5031,7975	2203	4300	6503	SO:0001819	synonymous_variant	1280	exon34			CCTGTCGCCTTTG	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.2295C>T	12.37:g.48376291G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	74	71	0.959459	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|0.590;A|0.410	0.410	strong		0.617	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
KRT74	121391	hgsc.bcm.edu	37	12	52966428	52966428	+	Missense_Mutation	SNP	G	G	C	rs11170177	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52966428G>C	ENST00000305620.2	-	2	542	c.495C>G	c.(493-495)aaC>aaG	p.N165K	KRT74_ENST00000549343.1_Missense_Mutation_p.N165K	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	165	Coil 1A.|Rod.		N -> K (in dbSNP:rs11170177).		intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)			kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		CTAGAACCTGGTTCTGCTGCT	0.552													G|||	489	0.0976438	0.0053	0.0259	5008	,	,		21114	0.3175		0.0517	False		,,,				2504	0.0941				p.N165K		Atlas-SNP	.											.	KRT74	67	.	0			c.C495G						PASS	.	G	LYS/ASN	60,4346	58.1+/-94.6	1,58,2144	98.0	89.0	92.0		495	3.8	1.0	12	dbSNP_120	92	472,8128	139.0+/-195.8	12,448,3840	yes	missense	KRT74	NM_175053.3	94	13,506,5984	CC,CG,GG		5.4884,1.3618,4.0904	probably-damaging	165/530	52966428	532,12474	2203	4300	6503	SO:0001583	missense	121391	exon2			AACCTGGTTCTGC	BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.495C>G	12.37:g.52966428G>C	ENSP00000307240:p.Asn165Lys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_175053	B5MD61|Q86Y45	Missense_Mutation	SNP	ENST00000305620.2	37	CCDS8832.1	227	0.10393772893772894	1	0.0020325203252032522	8	0.022099447513812154	172	0.3006993006993007	46	0.06068601583113457	G	22.6	4.306532	0.81247	0.013618	0.054884	ENSG00000170484	ENST00000549343;ENST00000305620	D;D	0.97959	-4.63;-4.63	4.71	3.82	0.43975	Filament (1);	0.000000	0.38663	N	0.001605	T	0.00468	0.0015	H	0.99783	4.775	0.20873	P	0.999830008	D	0.89917	1.0	D	0.97110	1.0	T	0.00000	-1.8587	9	0.87932	D	0	.	13.466	0.61254	0.0771:0.0:0.9229:0.0	rs11170177	165	Q7RTS7	K2C74_HUMAN	K	165	ENSP00000447447:N165K;ENSP00000307240:N165K	ENSP00000307240:N165K	N	-	3	2	KRT74	51252695	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.695000	0.74593	1.297000	0.44761	0.650000	0.86243	AAC	G|0.933;C|0.067	0.067	strong		0.552	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053	
IGSF3	3321	hgsc.bcm.edu	37	1	117158745	117158745	+	Missense_Mutation	SNP	A	A	C	rs373093989		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117158745A>C	ENST00000369486.3	-	3	1143	c.378T>G	c.(376-378)gaT>gaG	p.D126E	IGSF3_ENST00000318837.6_Missense_Mutation_p.D126E|IGSF3_ENST00000369483.1_Missense_Mutation_p.D126E	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	126	Ig-like C2-type 1.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.D126E(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		AGTATTGCTTATCAGTGCTGG	0.498																																					p.D126E		Atlas-SNP	.											IGSF3,extremity,malignant_melanoma,0,1	IGSF3	294	1	1	Substitution - Missense(1)	skin(1)	c.T378G						scavenged	.						61.0	55.0	57.0					1																	117158745		2203	4300	6503	SO:0001583	missense	3321	exon3			TTGCTTATCAGTG	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.378T>G	1.37:g.117158745A>C	ENSP00000358498:p.Asp126Glu	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	263	13	0.0494297	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	8.319	0.823848	0.16678	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.65364	-0.15;-0.15;-0.15	4.63	-8.69	0.00855	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.109427	0.64402	N	0.000011	T	0.34250	0.0891	M	0.69523	2.12	0.30895	N	0.729963	B;B	0.10296	0.003;0.002	B;B	0.20384	0.015;0.029	T	0.06481	-1.0824	10	0.66056	D	0.02	-9.8434	10.4193	0.44341	0.1981:0.2275:0.5744:0.0	.	126;126	O75054;A6NJZ6	IGSF3_HUMAN;.	E	126	ENSP00000358498:D126E;ENSP00000358495:D126E;ENSP00000321184:D126E	ENSP00000321184:D126E	D	-	3	2	IGSF3	116960268	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-2.110000	0.01334	-1.801000	0.01245	0.454000	0.30748	GAT	.	.	none		0.498	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
ZNF7	7553	hgsc.bcm.edu	37	8	146068322	146068322	+	Silent	SNP	C	C	T	rs9004	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:146068322C>T	ENST00000528372.1	+	5	2070	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y	ZNF7_ENST00000525266.1_Intron|ZNF7_ENST00000446747.2_Silent_p.Y621Y|ZNF7_ENST00000325217.5_Intron|ZNF7_ENST00000544249.1_Silent_p.Y514Y|ZNF7_ENST00000325241.6_Silent_p.Y610Y			P17097	ZNF7_HUMAN	zinc finger protein 7	610					multicellular organismal development (GO:0007275)|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(1)|large_intestine(7)|lung(6)|ovary(5)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)	Breast(495;0.0812)|Ovarian(118;0.0822)|Acute lymphoblastic leukemia(644;0.143)	Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)	GBM - Glioblastoma multiforme(99;2.11e-07)		AGTGGTTTTACGAATATGGGA	0.448													C|||	1544	0.308307	0.2345	0.2262	5008	,	,		18618	0.3204		0.3052	False		,,,				2504	0.4571				p.Y610Y		Atlas-SNP	.											.	ZNF7	62	.	0			c.C1830T						PASS	.	C		1094,3312	395.8+/-329.8	144,806,1253	71.0	75.0	73.0		1830	-4.3	0.3	8	dbSNP_52	73	2751,5849	434.7+/-357.8	404,1943,1953	no	coding-synonymous	ZNF7	NM_003416.2		548,2749,3206	TT,TC,CC		31.9884,24.8298,29.5633		610/687	146068322	3845,9161	2203	4300	6503	SO:0001819	synonymous_variant	7553	exon5			GTTTTACGAATAT	AB209619	CCDS6435.1, CCDS64996.1, CCDS64998.1, CCDS64999.1	8q24	2013-01-08	2006-05-09		ENSG00000147789	ENSG00000147789		"""Zinc fingers, C2H2-type"", ""-"""	13139	protein-coding gene	gene with protein product		194531	"""zinc finger protein 7 (KOX 4, clone HF.16)"""			2106481, 1946370	Standard	NM_003416		Approved	KOX4, HF.16	uc003zeg.4	P17097	OTTHUMG00000165200	ENST00000528372.1:c.1830C>T	8.37:g.146068322C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_003416	B4DT08|D3DWN6|P17015|Q8N8Y4	Silent	SNP	ENST00000528372.1	37	CCDS6435.1																																																																																			C|0.716;T|0.284	0.284	strong		0.448	ZNF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382660.1	NM_003416	
OTOGL	283310	hgsc.bcm.edu	37	12	80761411	80761411	+	Missense_Mutation	SNP	G	G	T	rs11114416	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:80761411G>T	ENST00000547103.1	+	53	6345	c.6339G>T	c.(6337-6339)ttG>ttT	p.L2113F	OTOGL_ENST00000546620.1_Missense_Mutation_p.L144F|OTOGL_ENST00000458043.2_Missense_Mutation_p.L2125F			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2113					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TAAAGTATTTGGAAGAAGACT	0.323													G|||	851	0.169928	0.1846	0.2075	5008	,	,		14825	0.0417		0.1819	False		,,,				2504	0.2434				p.L2125F		Atlas-SNP	.											C12orf64,NS,carcinoma,-1,1	OTOGL	235	1	0			c.G6375T						PASS	.	G	PHE/LEU	807,3593		72,663,1465	68.0	65.0	66.0		6375	2.7	1.0	12	dbSNP_120	66	1648,6936		165,1318,2809	yes	missense	OTOGL	NM_173591.3	22	237,1981,4274	TT,TG,GG		19.1985,18.3409,18.9079	benign	2125/2345	80761411	2455,10529	2200	4292	6492	SO:0001583	missense	283310	exon53			GTATTTGGAAGAA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6339G>T	12.37:g.80761411G>T	ENSP00000447211:p.Leu2113Phe	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		323|323	0.1478937728937729|0.1478937728937729	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	26|26	0.045454545454545456|0.045454545454545456	136|136	0.17941952506596306|0.17941952506596306	G|G	7.587|7.587	0.670053|0.670053	0.14776|0.14776	0.183409|0.183409	0.191985|0.191985	ENSG00000165899|ENSG00000165899	ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182|ENST00000298820	T;T;T;T|.	0.45276|.	2.32;2.32;2.23;0.9|.	5.53|5.53	2.66|2.66	0.31614|0.31614	.|.	0.498844|.	0.17868|.	N|.	0.159272|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.41027|0.41027	1.25|1.25	0.38267|0.38267	P|P	0.057950999999999975|0.057950999999999975	B|.	0.13594|.	0.008|.	B|.	0.16722|.	0.016|.	T|T	0.08889|0.08889	-1.0700|-1.0700	9|4	0.10636|.	T|.	0.68|.	.|.	9.0285|9.0285	0.36245|0.36245	0.1297:0.0:0.7494:0.1209|0.1297:0.0:0.7494:0.1209	rs11114416;rs52818722;rs11114416|rs11114416;rs52818722;rs11114416	490|.	Q3ZCN5|.	OTOGL_HUMAN|.	F|L	2113;2125;144;142|533	ENSP00000447211:L2113F;ENSP00000400895:L2125F;ENSP00000449094:L144F;ENSP00000449641:L142F|.	ENSP00000400895:L2125F|.	L|W	+|+	3|2	2|0	OTOGL|OTOGL	79285542|79285542	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.341000|0.341000	0.28922|0.28922	1.200000|1.200000	0.32247|0.32247	0.354000|0.354000	0.24105|0.24105	-0.198000|-0.198000	0.12761|0.12761	TTG|TGG	G|0.827;T|0.173	0.173	strong		0.323	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
TMEM99	147184	hgsc.bcm.edu	37	17	38991032	38991032	+	Silent	SNP	T	T	A	rs6694	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38991032T>A	ENST00000301665.3	+	3	568	c.264T>A	c.(262-264)ggT>ggA	p.G88G		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	88						integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				GTGCTTGCGGTCATCGGTTGA	0.458													A|||	2920	0.583067	0.6846	0.4539	5008	,	,		20037	0.4494		0.6064	False		,,,				2504	0.6513				p.G88G		Atlas-SNP	.											.	TMEM99	21	.	0			c.T264A						PASS	.	A	,,	2612,1240		891,830,205	223.0	221.0	221.0		264,264,264	-0.5	0.0	17	dbSNP_52	221	4948,3342		1454,2040,651	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	,,	2345,2870,856	AA,AT,TT		40.3136,32.1911,37.7368	,,	88/259,88/259,88/259	38991032	7560,4582	1926	4145	6071	SO:0001819	synonymous_variant	147184	exon3			TTGCGGTCATCGG	AK097454	CCDS42319.1	17q21.2	2008-11-06			ENSG00000167920	ENSG00000167920			28305	protein-coding gene	gene with protein product						12477932	Standard	NM_001195386		Approved	MGC21518	uc021txc.1	Q8N816	OTTHUMG00000133579	ENST00000301665.3:c.264T>A	17.37:g.38991032T>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	179	178	0.994413	NM_001195386	B4DQ34|Q96BP9	Silent	SNP	ENST00000301665.3	37	CCDS42319.1																																																																																			T|0.426;A|0.574	0.574	strong		0.458	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
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 GAIIx	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		Somatic	114	0	0	1652	WXS	Illumina HiSeq	Phase_I	112	59	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	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629161	32629161	+	Silent	SNP	A	A	G	rs1130430	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32629161A>G	ENST00000399084.1	-	5	913	c.735T>C	c.(733-735)ctT>ctC	p.L245L	HLA-DQB1_ENST00000399079.3_Intron|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000374943.4_Silent_p.L245L|HLA-DQB1-AS1_ENST00000419852.1_RNA|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.L245L			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	245					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GGCCCAGCCCAAGGAAGATCA	0.557									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	2632	0.525559	0.4039	0.6441	5008	,	,		12337	0.5625		0.495	False		,,,				2504	0.5992				p.L245L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	0			c.T735C						scavenged	.						35.0	31.0	32.0					6																	32629161		1941	3850	5791	SO:0001819	synonymous_variant	3119	exon4	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CAGCCCAAGGAAG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.735T>C	6.37:g.32629161A>G		Somatic	5	5	1		WXS	Illumina HiSeq	Phase_I	45	19	0.422222	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			A|0.389;G|0.611	0.611	strong		0.557	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
C5orf52	100190949	hgsc.bcm.edu	37	5	157098756	157098756	+	Missense_Mutation	SNP	G	G	T	rs11740603	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:157098756G>T	ENST00000409999.3	+	1	196	c.134G>T	c.(133-135)cGc>cTc	p.R45L	SOX30_ENST00000519442.1_5'Flank	NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	45										endometrium(2)|lung(1)	3						CTCGGCCGCCGCCCAGAAATC	0.697													.|||	838	0.167332	0.2943	0.1326	5008	,	,		12484	0.0734		0.1581	False		,,,				2504	0.1268				p.R45L		Atlas-SNP	.											.	C5orf52	17	.	0			c.G134T						PASS	.						7.0	12.0	10.0					5																	157098756		682	1560	2242	SO:0001583	missense	100190949	exon1			GCCGCCGCCCAGA	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.134G>T	5.37:g.157098756G>T	ENSP00000387027:p.Arg45Leu	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	NM_001145132		Missense_Mutation	SNP	ENST00000409999.3	37	CCDS47329.1	367	0.16804029304029305	142	0.2886178861788618	56	0.15469613259668508	49	0.08566433566433566	120	0.158311345646438	G	12.96	2.095218	0.36952	.	.	ENSG00000187658	ENST00000409999	.	.	.	0.946	0.946	0.19549	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P	0.47841	0.901	P	0.45276	0.475	T	0.34079	-0.9843	7	0.49607	T	0.09	-2.3101	5.1825	0.15167	0.0:0.0:1.0:0.0	rs11740603;rs58072612;rs11740603	45	A6NGY3	CE052_HUMAN	L	45	.	ENSP00000387027:R45L	R	+	2	0	C5orf52	157031334	0.005000	0.15991	0.005000	0.12908	0.012000	0.07955	-0.028000	0.12350	0.780000	0.33566	0.313000	0.20887	CGC	G|0.814;T|0.186	0.186	strong		0.697	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
CCDC146	57639	hgsc.bcm.edu	37	7	76871113	76871113	+	Silent	SNP	A	A	G	rs17230060	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:76871113A>G	ENST00000285871.4	+	4	472	c.345A>G	c.(343-345)gcA>gcG	p.A115A	CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	115								p.A115A(1)		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)				TTCCAGAAGCATTCTCCACGG	0.403													A|||	353	0.0704872	0.0068	0.072	5008	,	,		19981	0.0516		0.163	False		,,,				2504	0.0798				p.A115A		Atlas-SNP	.											CCDC146,NS,carcinoma,0,1	CCDC146	87	1	1	Substitution - coding silent(1)	stomach(1)	c.A345G						PASS	.	A		140,4266	100.7+/-139.4	2,136,2065	112.0	111.0	112.0		345	-11.4	0.0	7	dbSNP_123	112	1373,7227	267.4+/-287.2	114,1145,3041	no	coding-synonymous	CCDC146	NM_020879.2		116,1281,5106	GG,GA,AA		15.9651,3.1775,11.6331		115/956	76871113	1513,11493	2203	4300	6503	SO:0001819	synonymous_variant	57639	exon4			AGAAGCATTCTCC	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.345A>G	7.37:g.76871113A>G		Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	242	93	0.384298	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	37	CCDS34671.1																																																																																			A|0.896;G|0.104	0.104	strong		0.403	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
PLCG2	5336	hgsc.bcm.edu	37	16	81819768	81819768	+	Silent	SNP	T	T	C	rs1143685	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:81819768T>C	ENST00000359376.3	+	2	388	c.174T>C	c.(172-174)gcT>gcC	p.A58A		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	58	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						GCAAGACCGCTGACAAGATCG	0.632													T|||	3672	0.733227	0.6422	0.7277	5008	,	,		16454	0.8591		0.6859	False		,,,				2504	0.7791				p.A58A		Atlas-SNP	.											PLCG2_ENST00000359376,NS,carcinoma,+2,2	PLCG2	276	2	0			c.T174C						PASS	.	T		2627,1547		840,947,300	39.0	47.0	44.0		174	-6.6	0.8	16	dbSNP_111	44	5775,2629		1991,1793,418	no	coding-synonymous	PLCG2	NM_002661.3		2831,2740,718	CC,CT,TT		31.2827,37.0628,33.2008		58/1266	81819768	8402,4176	2087	4202	6289	SO:0001819	synonymous_variant	5336	exon2			GACCGCTGACAAG		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.174T>C	16.37:g.81819768T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			T|0.273;C|0.727	0.727	strong		0.632	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
DNAH8	1769	hgsc.bcm.edu	37	6	38746176	38746176	+	Missense_Mutation	SNP	G	G	A	rs61748601	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:38746176G>A	ENST00000359357.3	+	12	1578	c.1324G>A	c.(1324-1326)Gca>Aca	p.A442T	DNAH8_ENST00000441566.1_Missense_Mutation_p.A442T|DNAH8_ENST00000449981.2_Missense_Mutation_p.A659T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	442					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						ACAAATACAGGCATTTATGAA	0.308													G|||	427	0.0852636	0.053	0.2334	5008	,	,		15929	0.0198		0.1362	False		,,,				2504	0.0389				p.A659T		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G1975A						PASS	.	G	THR/ALA	287,4119	151.8+/-185.6	8,271,1924	57.0	62.0	60.0		1975	3.5	1.0	6	dbSNP_129	60	1305,7291	252.5+/-278.5	94,1117,3087	yes	missense	DNAH8	NM_001206927.1	58	102,1388,5011	AA,AG,GG		15.1815,6.5138,12.2443	benign	659/4708	38746176	1592,11410	2203	4298	6501	SO:0001583	missense	1769	exon14			ATACAGGCATTTA	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.1324G>A	6.37:g.38746176G>A	ENSP00000352312:p.Ala442Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	64	41	0.640625	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		231	0.10576923076923077	31	0.06300813008130081	78	0.2154696132596685	14	0.024475524475524476	108	0.1424802110817942	G	5.727	0.318627	0.10845	0.065138	0.151815	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.55760	0.5;0.5;0.5	5.38	3.55	0.40652	Dynein heavy chain, domain-1 (1);	0.218905	0.36234	N	0.002710	T	0.06735	0.0172	N	0.01656	-0.775	0.27748	P	0.944242	B	0.02656	0.0	B	0.10450	0.005	T	0.27706	-1.0066	9	0.11182	T	0.66	.	4.7673	0.13139	0.1818:0.0:0.6235:0.1947	rs61748601	442	Q96JB1	DYH8_HUMAN	T	647;647;442;442	ENSP00000333363:A647T;ENSP00000352312:A442T;ENSP00000402294:A442T	ENSP00000333363:A647T	A	+	1	0	DNAH8	38854154	0.503000	0.26115	0.999000	0.59377	0.891000	0.51852	0.659000	0.24994	1.222000	0.43521	-0.274000	0.10170	GCA	G|0.880;A|0.120	0.120	strong		0.308	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
SSTR4	6754	hgsc.bcm.edu	37	20	23017082	23017082	+	Missense_Mutation	SNP	T	T	C	rs2567608	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:23017082T>C	ENST00000255008.3	+	1	1026	c.962T>C	c.(961-963)tTc>tCc	p.F321S	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	321			F -> S (in dbSNP:rs2567608). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8483934, ECO:0000269|PubMed:8512564, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					TTCCGCCGATTCTTCCAGCGG	0.577													C|||	2602	0.519569	0.5303	0.4726	5008	,	,		18159	0.5466		0.4304	False		,,,				2504	0.6022				p.F321S	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,colon,carcinoma,0,1	SSTR4	83	1	0			c.T962C						PASS	.	C	SER/PHE	2237,2157	530.0+/-372.8	585,1067,545	73.0	79.0	77.0		962	3.7	0.2	20	dbSNP_100	77	3917,4683	587.0+/-392.1	925,2067,1308	yes	missense	SSTR4	NM_001052.2	155	1510,3134,1853	CC,CT,TT		45.5465,49.0897,47.3603	benign	321/389	23017082	6154,6840	2197	4300	6497	SO:0001583	missense	6754	exon1			GCCGATTCTTCCA		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.962T>C	20.37:g.23017082T>C	ENSP00000255008:p.Phe321Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	1113	0.5096153846153846	272	0.5528455284552846	177	0.4889502762430939	343	0.5996503496503497	321	0.4234828496042216	C	0.006	-2.097028	0.00360	0.509103	0.455465	ENSG00000132671	ENST00000255008	T	0.35973	1.28	3.65	3.65	0.41850	.	0.000000	0.64402	N	0.000016	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47195	-0.9136	9	0.02654	T	1	.	9.9983	0.41913	0.0:0.8974:0.0:0.1026	rs2567608;rs3746729;rs60934281;rs2567608	321	P31391	SSR4_HUMAN	S	321	ENSP00000255008:F321S	ENSP00000255008:F321S	F	+	2	0	SSTR4	22965082	0.010000	0.17322	0.154000	0.22540	0.215000	0.24574	1.591000	0.36665	0.739000	0.32628	-0.119000	0.15052	TTC	T|0.474;C|0.526	0.526	strong		0.577	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
GPR133	283383	hgsc.bcm.edu	37	12	131590404	131590404	+	Silent	SNP	G	G	A	rs4759544	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:131590404G>A	ENST00000261654.5	+	17	2440	c.1881G>A	c.(1879-1881)ccG>ccA	p.P627P	GPR133_ENST00000543617.1_Silent_p.P146P|GPR133_ENST00000376682.4_Silent_p.P313P|GPR133_ENST00000535015.1_Silent_p.P659P	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	627					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(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GCCTCGAGCCGGGCACGGTGA	0.617													G|||	1030	0.205671	0.028	0.1859	5008	,	,		20228	0.1935		0.2922	False		,,,				2504	0.3834				p.P627P		Atlas-SNP	.											.	GPR133	136	.	0			c.G1881A						PASS	.	G		328,4078	165.8+/-197.2	15,298,1890	113.0	75.0	88.0		1881	-2.0	1.0	12	dbSNP_111	88	2488,6112	393.7+/-344.5	382,1724,2194	no	coding-synonymous	GPR133	NM_198827.3		397,2022,4084	AA,AG,GG		28.9302,7.4444,21.6515		627/875	131590404	2816,10190	2203	4300	6503	SO:0001819	synonymous_variant	283383	exon17			CGAGCCGGGCACG	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.1881G>A	12.37:g.131590404G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Silent	SNP	ENST00000261654.5	37	CCDS9272.1																																																																																			G|0.798;A|0.202	0.202	strong		0.617	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
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 GAIIx	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_ENST00000368956.2_Intron|DMBT1_ENST00000368955.3_Silent_p.L525L|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000344338.3_Silent_p.L525L|DMBT1_ENST00000330163.4_Intron			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		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	49	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	
TLE3	7090	hgsc.bcm.edu	37	15	70346923	70346923	+	Silent	SNP	C	C	T	rs2228178	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:70346923C>T	ENST00000558939.1	-	16	3066	c.1689G>A	c.(1687-1689)tcG>tcA	p.S563S	TLE3_ENST00000558379.1_Silent_p.S558S|TLE3_ENST00000317509.8_Silent_p.S551S|TLE3_ENST00000559929.1_Silent_p.S573S|TLE3_ENST00000560589.1_Silent_p.S507S|TLE3_ENST00000558201.1_Silent_p.S569S|TLE3_ENST00000560939.1_Silent_p.S565S|TLE3_ENST00000442299.2_Silent_p.S555S|TLE3_ENST00000440567.3_Silent_p.S553S|TLE3_ENST00000557907.1_Silent_p.S555S|TLE3_ENST00000559191.1_Silent_p.S144S|TLE3_ENST00000557997.1_Silent_p.S555S|TLE3_ENST00000451782.2_Silent_p.S560S|TLE3_ENST00000539550.1_Silent_p.S490S|TLE3_ENST00000559048.1_Silent_p.S563S	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	563					Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GGGGCGTGGGCGAGGCCAGGT	0.657													C|||	1816	0.36262	0.2284	0.4726	5008	,	,		18079	0.255		0.4781	False		,,,				2504	0.4581				p.S563S		Atlas-SNP	.											TLE3,bladder,carcinoma,-1,1	TLE3	104	1	0			c.G1689A						PASS	.	C	,,	1199,3183		179,841,1171	30.0	35.0	33.0		1680,1689,1653	-9.1	0.7	15	dbSNP_98	33	4037,4549		969,2099,1225	no	coding-synonymous,coding-synonymous,coding-synonymous	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	,,	1148,2940,2396	TT,TC,CC		47.0184,27.3619,40.3763	,,	560/770,563/773,551/761	70346923	5236,7732	2191	4293	6484	SO:0001819	synonymous_variant	7090	exon16			CGTGGGCGAGGCC	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.1689G>A	15.37:g.70346923C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Silent	SNP	ENST00000558939.1	37	CCDS45293.1																																																																																			C|0.629;T|0.371	0.371	strong		0.657	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
MBP	4155	hgsc.bcm.edu	37	18	74701984	74701984	+	Silent	SNP	G	G	A	rs470797	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:74701984G>A	ENST00000397869.3	-	2	256	c.210C>T	c.(208-210)taC>taT	p.Y70Y	MBP_ENST00000527041.1_Silent_p.Y70Y|MBP_ENST00000359645.3_Silent_p.Y96Y|MBP_ENST00000354542.4_Intron|MBP_ENST00000580402.1_Silent_p.Y203Y|MBP_ENST00000578193.1_Silent_p.Y70Y|MBP_ENST00000382582.3_Silent_p.Y96Y|MBP_ENST00000355994.2_Silent_p.Y203Y|MBP_ENST00000397866.4_Silent_p.Y70Y|MBP_ENST00000528160.1_Intron|MBP_ENST00000397865.5_Silent_p.Y70Y|MBP_ENST00000397875.3_Silent_p.Y70Y|MBP_ENST00000526111.1_Silent_p.Y48Y|MBP_ENST00000579129.1_Silent_p.Y203Y			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)	p.Y203Y(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	GCAGGGAGCCGTAGTGAGCAG	0.567													G|||	1166	0.232827	0.2368	0.1916	5008	,	,		17334	0.3204		0.1372	False		,,,				2504	0.2648				p.Y203Y	NSCLC(17;72 1131 19392)	Atlas-SNP	.											MBP,colon,carcinoma,0,2	MBP	45	2	1	Substitution - coding silent(1)	stomach(1)	c.C609T						PASS	.	G	,,,,	909,3497	349.3+/-310.3	98,713,1392	135.0	122.0	126.0		288,210,210,609,288	-5.9	1.0	18	dbSNP_83	126	1322,7278	259.9+/-283.0	102,1118,3080	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MBP	NM_001025081.1,NM_001025090.1,NM_001025092.1,NM_001025101.1,NM_002385.2	,,,,	200,1831,4472	AA,AG,GG		15.3721,20.631,17.1536	,,,,	96/198,70/172,70/161,203/305,96/187	74701984	2231,10775	2203	4300	6503	SO:0001819	synonymous_variant	4155	exon5			GGAGCCGTAGTGA		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.210C>T	18.37:g.74701984G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001025101	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000397869.3	37																																																																																				A|0.185;C|0.000;G|0.815;T|0.000	0.185	strong		0.567	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081	
ABCC4	10257	hgsc.bcm.edu	37	13	95859035	95859035	+	Splice_Site	SNP	C	C	A	rs2274407	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:95859035C>A	ENST00000376887.4	-	8	1026	c.912G>T	c.(910-912)aaG>aaT	p.K304N	ABCC4_ENST00000412704.1_Splice_Site_p.K304N|ABCC4_ENST00000536256.1_Splice_Site_p.K229N|ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000431522.1_Splice_Site_p.K304N	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	304	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		K -> N (transport properties comparable to wild-type; dbSNP:rs2274407).		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)	AAATCTCCTTCCTGAAAGAGA	0.433													C|||	754	0.150559	0.2095	0.062	5008	,	,		20958	0.1845		0.0805	False		,,,				2504	0.1708				p.K304N		Atlas-SNP	.											.	ABCC4	248	.	0			c.G912T						PASS	.	C	ASN/LYS,ASN/LYS	754,3652	302.1+/-287.2	72,610,1521	115.0	120.0	118.0		912,912	1.7	1.0	13	dbSNP_100	118	606,7994	159.8+/-213.0	17,572,3711	yes	missense-near-splice,missense-near-splice	ABCC4	NM_001105515.1,NM_005845.3	94,94	89,1182,5232	AA,AC,CC		7.0465,17.113,10.4567	benign,benign	304/860,304/1326	95859035	1360,11646	2203	4300	6503	SO:0001630	splice_region_variant	10257	exon8			CTCCTTCCTGAAA	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.912-1G>T	13.37:g.95859035C>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Missense_Mutation	SNP	ENST00000376887.4	37	CCDS9474.1	303	0.13873626373626374	109	0.22154471544715448	26	0.0718232044198895	114	0.1993006993006993	54	0.0712401055408971	C	9.111	1.006660	0.19199	0.17113	0.070465	ENSG00000125257	ENST00000412704;ENST00000376887;ENST00000536256;ENST00000431522	D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45	5.59	1.73	0.24493	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.271788	0.46758	D	0.000265	T	0.00300	0.0009	M	0.62723	1.935	0.22737	P	0.99879784	B;B;B;B;B	0.33940	0.016;0.433;0.214;0.254;0.086	B;B;B;B;B	0.41946	0.11;0.371;0.119;0.371;0.201	T	0.10567	-1.0624	9	0.48119	T	0.1	.	9.9661	0.41725	0.0:0.64:0.0:0.36	rs2274407;rs52813831;rs58221897;rs2274407	229;304;304;304;304	B7Z3Q7;A8K2Q2;O15439-2;Q8IVZ4;O15439	.;.;.;.;MRP4_HUMAN	N	304;304;229;304	ENSP00000388657:K304N;ENSP00000366084:K304N;ENSP00000442024:K229N;ENSP00000398562:K304N	ENSP00000366084:K304N	K	-	3	2	ABCC4	94657036	1.000000	0.71417	0.998000	0.56505	0.082000	0.17680	0.983000	0.29552	0.639000	0.30564	-0.345000	0.07892	AAG	A|0.118;C|0.882	0.118	strong		0.433	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	Missense_Mutation
VCAN	1462	hgsc.bcm.edu	37	5	82833391	82833391	+	Silent	SNP	A	A	G	rs16900528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:82833391A>G	ENST00000265077.3	+	8	5134	c.4569A>G	c.(4567-4569)acA>acG	p.T1523T	VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Silent_p.T536T|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1523	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|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 organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AATCAGTCACAGAGAGAGATA	0.443													A|||	288	0.057508	0.0098	0.036	5008	,	,		21611	0.0685		0.0825	False		,,,				2504	0.1002				p.T1523T		Atlas-SNP	.											.	VCAN	498	.	0			c.A4569G						PASS	.	A	,,,	109,4297	84.8+/-123.5	0,109,2094	77.0	75.0	75.0		,1608,,4569	-3.3	0.0	5	dbSNP_123	75	697,7903	171.4+/-222.4	26,645,3629	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	26,754,5723	GG,GA,AA		8.1047,2.4739,6.1971	,,,	,536/2410,,1523/3397	82833391	806,12200	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			AGTCACAGAGAGA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4569A>G	5.37:g.82833391A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			A|0.942;G|0.058	0.058	strong		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
PDGFA	5154	hgsc.bcm.edu	37	7	552046	552046	+	Silent	SNP	A	A	G	rs1129401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:552046A>G	ENST00000354513.5	-	3	599	c.207T>C	c.(205-207)caT>caC	p.H69H	PDGFA_ENST00000426681.2_5'Flank|PDGFA_ENST00000402802.3_Silent_p.H69H	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	69					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		GCTTAGTGGCATGGACCCCGT	0.652													G|||	1244	0.248403	0.1271	0.2133	5008	,	,		16261	0.3234		0.2535	False		,,,				2504	0.3548				p.H69H		Atlas-SNP	.											.	PDGFA	34	.	0			c.T207C						PASS	.	G	,	710,3696	759.4+/-412.9	58,594,1551	65.0	62.0	63.0		207,207	-6.8	0.0	7	dbSNP_86	63	2246,6346	707.6+/-405.6	300,1646,2350	no	coding-synonymous,coding-synonymous	PDGFA	NM_002607.5,NM_033023.4	,	358,2240,3901	GG,GA,AA		26.1406,16.1144,22.742	,	69/212,69/197	552046	2956,10042	2203	4296	6499	SO:0001819	synonymous_variant	5154	exon3			AGTGGCATGGACC		CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"""PDGF A-chain"", ""platelet-derived growth factor alpha chain"""	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.207T>C	7.37:g.552046A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_002607	B5BU73	Silent	SNP	ENST00000354513.5	37	CCDS34578.1	536	0.2454212454212454	59	0.11991869918699187	84	0.23204419889502761	199	0.3479020979020979	194	0.2559366754617414	G	0.412	-0.912876	0.02415	0.161144	0.261406	ENSG00000197461	ENST00000400761	.	.	.	5.03	-6.84	0.01687	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.06197	-1.0840	3	.	.	.	-5.3505	17.1287	0.86721	0.6784:0.0:0.3216:0.0	rs1129401;rs1800816;rs2228457;rs3187241;rs17415666;rs61732882	.	.	.	R	76	.	.	C	-	1	0	PDGFA	518572	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.539000	0.06113	-1.968000	0.01006	-0.374000	0.07098	TGC	A|0.769;G|0.231	0.231	strong		0.652	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1		
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047925	46047925	+	Silent	SNP	G	G	T	rs9979457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46047925G>T	ENST00000397911.3	+	1	886	c.837G>T	c.(835-837)ccG>ccT	p.P279P	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	279						keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GCTCCCGCCCGGCCTGCTACA	0.692													G|||	3169	0.632788	0.5212	0.6715	5008	,	,		17780	0.6627		0.7107	False		,,,				2504	0.6452				p.P279P		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.G837T						PASS	.	G	,	2373,1995		667,1039,478	60.0	74.0	70.0		,837	-5.6	0.0	21	dbSNP_119	70	5797,2777		1967,1863,457	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	2634,2902,935	TT,TG,GG		32.3886,45.6731,36.8722	,	,279/293	46047925	8170,4772	2184	4287	6471	SO:0001819	synonymous_variant	386676	exon1			CCGCCCGGCCTGC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.837G>T	21.37:g.46047925G>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			G|0.347;T|0.653	0.653	strong		0.692	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
WNK2	65268	hgsc.bcm.edu	37	9	95993215	95993215	+	Silent	SNP	C	C	T	rs34976687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:95993215C>T	ENST00000297954.4	+	3	900	c.900C>T	c.(898-900)agC>agT	p.S300S	WNK2_ENST00000349097.3_5'UTR|WNK2_ENST00000395475.2_Silent_p.S286S|WNK2_ENST00000427277.2_5'UTR|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395477.2_Silent_p.S300S	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	300	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						TTCTCCGCAGCTGGTGCCGGC	0.592													C|||	142	0.0283546	0.0015	0.1081	5008	,	,		18339	0.0		0.0586	False		,,,				2504	0.0061				p.S300S		Atlas-SNP	.											.	WNK2	277	.	0			c.C900T						PASS	.	C		71,4335	64.1+/-101.4	0,71,2132	86.0	75.0	79.0		900	4.6	1.0	9	dbSNP_126	79	609,7991	159.5+/-212.8	31,547,3722	no	coding-synonymous	WNK2	NM_006648.3		31,618,5854	TT,TC,CC		7.0814,1.6114,5.2284		300/2218	95993215	680,12326	2203	4300	6503	SO:0001819	synonymous_variant	65268	exon3			CCGCAGCTGGTGC	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.900C>T	9.37:g.95993215C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	47	0.594937	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		81	0.03708791208791209	1	0.0020325203252032522	36	0.09944751381215469	0	0.0	44	0.05804749340369393	C	10.61	1.397401	0.25205	0.016114	0.070814	ENSG00000165238	ENST00000432730	.	.	.	5.52	4.62	0.57501	.	.	.	.	.	T	0.03053	0.0090	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01643	-1.1305	4	.	.	.	.	8.8405	0.35140	0.0:0.7609:0.0:0.2391	rs34976687;rs62618691	.	.	.	V	296	.	.	A	+	2	0	WNK2	95033036	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.847000	0.27696	1.333000	0.45449	0.655000	0.94253	GCT	C|0.953;T|0.047	0.047	strong		0.592	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
OR4L1	122742	hgsc.bcm.edu	37	14	20529043	20529043	+	Silent	SNP	C	C	G	rs1959628	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20529043C>G	ENST00000315683.1	+	1	840	c.840C>G	c.(838-840)ccC>ccG	p.P280P		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	280						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TTATCACACCCTTACTGAATC	0.353													C|||	2146	0.428514	0.3623	0.3934	5008	,	,		18716	0.5357		0.3221	False		,,,				2504	0.5419				p.P280P		Atlas-SNP	.											.	OR4L1	98	.	0			c.C840G						PASS	.	C		1587,2819		285,1017,901	78.0	80.0	79.0		840	-2.2	1.0	14	dbSNP_92	79	2776,5824		486,1804,2010	no	coding-synonymous	OR4L1	NM_001004717.1		771,2821,2911	GG,GC,CC		32.2791,36.0191,33.5461		280/313	20529043	4363,8643	2203	4300	6503	SO:0001819	synonymous_variant	122742	exon1			CACACCCTTACTG		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.840C>G	14.37:g.20529043C>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_001004717	Q6IEZ5	Silent	SNP	ENST00000315683.1	37	CCDS32029.1																																																																																			C|0.638;G|0.362	0.362	strong		0.353	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
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 GAIIx	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		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	48	25	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	
CCDC27	148870	hgsc.bcm.edu	37	1	3669201	3669201	+	Silent	SNP	A	A	G	rs10797410	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3669201A>G	ENST00000294600.2	+	1	240	c.156A>G	c.(154-156)ccA>ccG	p.P52P		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	52										breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		AGGCCAGCCCATCTCAGAGGC	0.607													a|||	2549	0.508986	0.8389	0.4452	5008	,	,		17754	0.2897		0.3996	False		,,,				2504	0.4468				p.P52P		Atlas-SNP	.											.	CCDC27	79	.	0			c.A156G						PASS	.	A		3279,1127	717.7+/-408.7	1241,797,165	134.0	115.0	121.0		156	-6.7	0.0	1	dbSNP_120	121	3194,5406	484.1+/-371.3	596,2002,1702	no	coding-synonymous	CCDC27	NM_152492.2		1837,2799,1867	GG,GA,AA		37.1395,25.5788,49.7693		52/657	3669201	6473,6533	2203	4300	6503	SO:0001819	synonymous_variant	148870	exon1			CAGCCCATCTCAG		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.156A>G	1.37:g.3669201A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	99	35	0.353535	NM_152492	Q5TBV3|Q96M50	Silent	SNP	ENST00000294600.2	37	CCDS50.1																																																																																			A|0.502;G|0.498	0.498	strong		0.607	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
PCLO	27445	hgsc.bcm.edu	37	7	82785097	82785097	+	Missense_Mutation	SNP	T	T	C	rs61741659	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:82785097T>C	ENST00000333891.9	-	2	1197	c.860A>G	c.(859-861)gAc>gGc	p.D287G	PCLO_ENST00000423517.2_Missense_Mutation_p.D287G	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCTTACTATGTCTGCCTGTTT	0.507													T|||	768	0.153355	0.1225	0.147	5008	,	,		18860	0.0675		0.2664	False		,,,				2504	0.1718				p.D287G		Atlas-SNP	.											.	PCLO	1506	.	0			c.A860G						PASS	.	T	GLY/ASP,GLY/ASP	525,3621		39,447,1587	121.0	110.0	114.0		860,860	4.1	0.7	7	dbSNP_129	114	1914,6508		223,1468,2520	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	94,94	262,1915,4107	CC,CT,TT		22.7262,12.6628,19.4064	benign,benign	287/5143,287/4936	82785097	2439,10129	2073	4211	6284	SO:0001583	missense	27445	exon2			ACTATGTCTGCCT	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.860A>G	7.37:g.82785097T>C	ENSP00000334319:p.Asp287Gly	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	147	68	0.462585	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	368	0.1684981684981685	69	0.1402439024390244	57	0.1574585635359116	47	0.08216783216783216	195	0.25725593667546176	T	8.676	0.903995	0.17760	0.126628	0.227262	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.20463	2.07;2.08	5.26	4.08	0.47627	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B;B	0.17268	0.021;0.021	B;B	0.15484	0.013;0.013	T	0.26849	-1.0091	8	0.87932	D	0	.	9.6854	0.40096	0.0:0.081:0.0:0.919	.	287;287	Q9Y6V0-5;Q9Y6V0-6	.;.	G	287	ENSP00000334319:D287G;ENSP00000388393:D287G	ENSP00000334319:D287G	D	-	2	0	PCLO	82623033	0.990000	0.36364	0.696000	0.30242	0.886000	0.51366	2.445000	0.44899	0.819000	0.34492	0.533000	0.62120	GAC	T|0.813;C|0.187	0.187	strong		0.507	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
C14orf159	80017	hgsc.bcm.edu	37	14	91636532	91636532	+	Splice_Site	SNP	C	C	T	rs4900072	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:91636532C>T	ENST00000523771.1	+	5	1044		c.e5+2		C14orf159_ENST00000523816.1_Splice_Site|C14orf159_ENST00000522322.1_Splice_Site|C14orf159_ENST00000518868.1_Missense_Mutation_p.A148V|C14orf159_ENST00000412671.2_Missense_Mutation_p.A148V|C14orf159_ENST00000256324.10_Missense_Mutation_p.A148V|C14orf159_ENST00000521077.2_Missense_Mutation_p.A148V|C14orf159_ENST00000525393.2_Splice_Site_p.A19V|C14orf159_ENST00000428926.2_Splice_Site|C14orf159_ENST00000520328.1_Splice_Site			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159							mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CACAGCCAGGCGGGTGCATAC	0.592													C|||	837	0.167133	0.1036	0.2262	5008	,	,		18191	0.0585		0.3241	False		,,,				2504	0.1616				p.A148V		Atlas-SNP	.											.	C14orf159	57	.	0			c.C443T						PASS	.	C	,,VAL/ALA,,	711,3695	290.7+/-281.1	62,587,1554	37.0	37.0	37.0		,,443,,	-5.0	0.0	14	dbSNP_111	37	2897,5703	447.4+/-361.5	493,1911,1896	yes	splice-5,splice-5,missense,splice-5,splice-5	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,64,,	555,2498,3450	TT,TC,CC		33.686,16.1371,27.741	,,,,	,,148/622,,	91636532	3608,9398	2203	4300	6503	SO:0001630	splice_region_variant	80017	exon5			GCCAGGCGGGTGC	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.441+2C>T	14.37:g.91636532C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	29	17	0.586207	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	425|425	0.1945970695970696|0.1945970695970696	51|51	0.10365853658536585|0.10365853658536585	88|88	0.2430939226519337|0.2430939226519337	36|36	0.06293706293706294|0.06293706293706294	250|250	0.32981530343007914|0.32981530343007914	C|C	1.312|1.312	-0.601802|-0.601802	0.03744|0.03744	0.161371|0.161371	0.33686|0.33686	ENSG00000133943|ENSG00000133943	ENST00000520328;ENST00000523816;ENST00000428926;ENST00000522322;ENST00000523771|ENST00000521334;ENST00000256324;ENST00000522170;ENST00000519950;ENST00000521077;ENST00000518868;ENST00000517518;ENST00000525393;ENST00000523894;ENST00000412671	.|T;T;T;T;T;T;T;T;T;T	.|0.49432	.|1.55;1.55;1.55;1.55;1.55;1.55;1.55;0.78;1.55;1.55	4.65|4.65	-5.0|-5.0	0.03001|0.03001	.|.	.|1.370970	.|0.04809	.|N	.|0.434989	.|T	.|0.00012	.|0.0000	N|N	0.01242|0.01242	-0.935|-0.935	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.34226	.|0.443;0.022;0.004;0.004	.|B;B;B;B	.|0.36666	.|0.23;0.004;0.002;0.002	.|T	.|0.05937	.|-1.0855	.|9	.|0.02654	.|T	.|1	.|.	2.8008|2.8008	0.05414|0.05414	0.1309:0.1886:0.1299:0.5506|0.1309:0.1886:0.1299:0.5506	rs4900072;rs4900072|rs4900072;rs4900072	.|19;148;148;148	.|Q8NB88;B3KVU6;Q7Z3D6-2;Q7Z3D6-3	.|.;.;.;.	.|V	-1|148;148;148;148;148;148;148;19;148;148	.|ENSP00000430022:A148V;ENSP00000256324:A148V;ENSP00000430666:A148V;ENSP00000428296:A148V;ENSP00000430137:A148V;ENSP00000428263:A148V;ENSP00000428652:A148V;ENSP00000435459:A19V;ENSP00000429459:A148V;ENSP00000404196:A148V	.|ENSP00000256324:A148V	.|A	+|+	.|2	.|0	C14orf159|C14orf159	90706285|90706285	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.014000|0.014000	0.08584|0.08584	-0.492000|-0.492000	0.06467|0.06467	-0.830000|-0.830000	0.04262|0.04262	-0.258000|-0.258000	0.10820|0.10820	.|GCG	C|0.773;T|0.227	0.227	strong		0.592	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	Intron
DNLZ	728489	hgsc.bcm.edu	37	9	139256495	139256495	+	Missense_Mutation	SNP	G	G	T	rs3812553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139256495G>T	ENST00000371738.3	-	3	580	c.506C>A	c.(505-507)cCc>cAc	p.P169H	CARD9_ENST00000460290.1_5'Flank|DNLZ_ENST00000371739.3_3'UTR	NM_001080849.1	NP_001074318.1	Q5SXM8	DNLZ_HUMAN	DNL-type zinc finger	169			P -> H (in dbSNP:rs3812553).			mitochondrion (GO:0005739)	zinc ion binding (GO:0008270)			central_nervous_system(1)|prostate(1)	2		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.42e-06)|Epithelial(140;3.3e-06)		AGGGCTGGGGGGACCCTCATC	0.692													G|||	312	0.0623003	0.0469	0.0072	5008	,	,		14130	0.131		0.0368	False		,,,				2504	0.0777				p.P169H		Atlas-SNP	.											.	DNLZ	8	.	0			c.C506A						PASS	.	G	HIS/PRO	152,4224		5,142,2041	16.0	20.0	18.0		506	2.6	0.0	9	dbSNP_107	18	252,8320		3,246,4037	yes	missense	DNLZ	NM_001080849.1	77	8,388,6078	TT,TG,GG		2.9398,3.4735,3.1202	possibly-damaging	169/179	139256495	404,12544	2188	4286	6474	SO:0001583	missense	728489	exon3			CTGGGGGGACCCT	AL592301	CCDS35179.1	9q34.3	2013-01-10	2007-12-18	2007-12-18	ENSG00000213221	ENSG00000213221		"""Zinc fingers"""	33879	protein-coding gene	gene with protein product	"""translocase of inner mitochondrial membrane 15 homolog (yeast)"", ""HSP70 escort protein"""		"""chromosome 9 open reading frame 151"""	C9orf151		21530495, 22162012	Standard	NM_001080849		Approved	RP11-413M3.2, ZIM17, bA413M3.2, TIMM15, HEP	uc004chf.2	Q5SXM8	OTTHUMG00000020931	ENST00000371738.3:c.506C>A	9.37:g.139256495G>T	ENSP00000360803:p.Pro169His	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_001080849	B2RUX5|B9EJE1	Missense_Mutation	SNP	ENST00000371738.3	37	CCDS35179.1	112	0.05128205128205128	24	0.04878048780487805	5	0.013812154696132596	57	0.09965034965034965	26	0.03430079155672823	G	14.80	2.642921	0.47153	0.034735	0.029398	ENSG00000213221	ENST00000371738	T	0.31247	1.5	3.49	2.59	0.31030	.	0.961104	0.08490	U	0.938175	T	0.01029	0.0034	L	0.27053	0.805	0.28821	P	0.897688	D	0.67145	0.996	P	0.57371	0.819	T	0.13229	-1.0517	9	0.45353	T	0.12	-5.9998	10.1435	0.42749	0.1045:0.0:0.8955:0.0	rs3812553	169	Q5SXM8	DNLZ_HUMAN	H	169	ENSP00000360803:P169H	ENSP00000360803:P169H	P	-	2	0	DNLZ	138376316	0.000000	0.05858	0.008000	0.14137	0.003000	0.03518	0.393000	0.20817	1.037000	0.40024	0.491000	0.48974	CCC	G|0.956;T|0.044	0.044	strong		0.692	DNLZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055075.2	NM_001080849	
NCOR1	9611	hgsc.bcm.edu	37	17	15950400	15950400	+	Missense_Mutation	SNP	C	C	T	rs61753149	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:15950400C>T	ENST00000268712.3	-	42	6801	c.6544G>A	c.(6544-6546)Gcc>Acc	p.A2182T	NCOR1_ENST00000395857.3_Missense_Mutation_p.A766T|NCOR1_ENST00000395851.1_Missense_Mutation_p.A2079T	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	2182	Interaction with C1D. {ECO:0000250}.				CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		GGTGAGCGGGCATCATTCCTG	0.408													C|||	11	0.00219649	0.0	0.0029	5008	,	,		20819	0.0		0.008	False		,,,				2504	0.001				p.A2182T		Atlas-SNP	.											.	NCOR1	240	.	0			c.G6544A						PASS	.	C	THR/ALA,THR/ALA	11,4395	19.1+/-41.9	0,11,2192	174.0	158.0	163.0		6235,6544	4.5	1.0	17	dbSNP_129	163	104,8496	57.2+/-118.5	0,104,4196	yes	missense,missense	NCOR1	NM_001190440.1,NM_006311.3	58,58	0,115,6388	TT,TC,CC		1.2093,0.2497,0.8842	benign,benign	2079/2338,2182/2441	15950400	115,12891	2203	4300	6503	SO:0001583	missense	9611	exon42			AGCGGGCATCATT	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.6544G>A	17.37:g.15950400C>T	ENSP00000268712:p.Ala2182Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_006311	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	14.24	2.477573	0.44044	0.002497	0.012093	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395857	T;T;T	0.43688	0.94;1.53;0.94	5.61	4.53	0.55603	.	0.051849	0.85682	D	0.000000	T	0.18676	0.0448	N	0.08118	0	0.26712	N	0.970959	B;B;B;B;B;B	0.20780	0.002;0.001;0.0;0.048;0.001;0.001	B;B;B;B;B;B	0.21546	0.005;0.003;0.001;0.035;0.007;0.009	T	0.19418	-1.0306	10	0.87932	D	0	-3.7798	12.1852	0.54234	0.8557:0.1443:0.0:0.0	rs61753149	992;2086;2182;2079;702;196	B4DZ48;E7EVK1;O75376;O75376-2;Q86YY1;Q86YY2	.;.;NCOR1_HUMAN;.;.;.	T	2182;2079;2086;766	ENSP00000268712:A2182T;ENSP00000379192:A2079T;ENSP00000379198:A766T	ENSP00000268712:A2182T	A	-	1	0	NCOR1	15891125	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	6.885000	0.75606	0.962000	0.38057	-0.376000	0.06991	GCC	C|0.993;T|0.007	0.007	strong		0.408	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
RNF43	54894	hgsc.bcm.edu	37	17	56492800	56492800	+	Missense_Mutation	SNP	T	T	C	rs3744093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:56492800T>C	ENST00000584437.1	-	1	2094	c.139A>G	c.(139-141)Att>Gtt	p.I47V	RNF43_ENST00000500597.2_Missense_Mutation_p.I47V|RNF43_ENST00000583753.1_Missense_Mutation_p.I47V|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Intron|RNF43_ENST00000407977.2_Missense_Mutation_p.I47V|RNF43_ENST00000577716.1_Missense_Mutation_p.I47V|RNF43_ENST00000580014.1_5'Flank			Q68DV7	RNF43_HUMAN	ring finger protein 43	47			I -> V (in dbSNP:rs3744093). {ECO:0000269|PubMed:14702039}.		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACTCTGATAATAGCTTTCTGT	0.517													T|||	1872	0.373802	0.1694	0.5317	5008	,	,		17973	0.5258		0.3718	False		,,,				2504	0.3834				p.I47V		Atlas-SNP	.											.	RNF43	157	.	0			c.A139G						PASS	.	T	VAL/ILE	958,3448	362.1+/-316.0	116,726,1361	100.0	92.0	95.0		139	3.2	1.0	17	dbSNP_107	95	3312,5288	494.7+/-373.9	638,2036,1626	yes	missense	RNF43	NM_017763.4	29	754,2762,2987	CC,CT,TT		38.5116,21.7431,32.831	benign	47/784	56492800	4270,8736	2203	4300	6503	SO:0001583	missense	54894	exon2			TGATAATAGCTTT		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.139A>G	17.37:g.56492800T>C	ENSP00000463069:p.Ile47Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	855	0.3914835164835165	94	0.1910569105691057	184	0.5082872928176796	298	0.5209790209790209	279	0.36807387862796836	T	9.051	0.992132	0.18966	0.217431	0.385116	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.09350	3.24;2.99	5.49	3.19	0.36642	.	0.436978	0.21813	N	0.068731	T	0.00012	0.0000	N	0.14661	0.345	0.42420	P	0.007365999999999984	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.40924	-0.9537	9	0.17832	T	0.49	-11.177	6.2359	0.20762	0.0:0.1484:0.1361:0.7155	rs3744093;rs52822933;rs58301389;rs3744093	47;47	Q68DV7-2;Q68DV7	.;RNF43_HUMAN	V	47	ENSP00000385328:I47V;ENSP00000441969:I47V	ENSP00000385328:I47V	I	-	1	0	RNF43	53847799	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	1.086000	0.30853	0.973000	0.38340	0.533000	0.62120	ATT	T|0.651;C|0.349	0.349	strong		0.517	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84488636	84488636	+	Missense_Mutation	SNP	A	A	G	rs4483821	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:84488636A>G	ENST00000286744.5	+	6	661	c.437A>G	c.(436-438)cAt>cGt	p.H146R	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.H146R	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	146			H -> R (in dbSNP:rs4483821). {ECO:0000269|PubMed:15489334}.			proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			TATCAGGGGCATTACTATGAA	0.527													G|||	3402	0.679313	0.8306	0.549	5008	,	,		18661	0.8085		0.4742	False		,,,				2504	0.6452				p.H146R		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.A437G						PASS	.	G	ARG/HIS	3358,1048	382.5+/-324.5	1291,776,136	95.0	76.0	82.0		437	-3.4	0.0	15	dbSNP_111	82	3958,4642	601.5+/-394.4	947,2064,1289	yes	missense	ADAMTSL3	NM_207517.2	29	2238,2840,1425	GG,GA,AA		46.0233,23.7857,43.749	benign	146/1692	84488636	7316,5690	2203	4300	6503	SO:0001583	missense	57188	exon6			AGGGGCATTACTA	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.437A>G	15.37:g.84488636A>G	ENSP00000286744:p.His146Arg	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	1435	0.657051282051282	412	0.8373983739837398	192	0.5303867403314917	464	0.8111888111888111	367	0.4841688654353562	G	0.192	-1.052018	0.01981	0.762143	0.460233	ENSG00000156218	ENST00000286744	T	0.03212	4.01	5.26	-3.36	0.04913	.	1.142310	0.06302	N	0.701085	T	0.00012	0.0000	N	0.05574	-0.02	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.19647	-1.0299	9	0.15952	T	0.53	.	15.3716	0.74570	0.8582:0.0:0.1418:0.0	rs4483821;rs12914935;rs52797666;rs58219167;rs4483821	146;146	P82987-2;P82987	.;ATL3_HUMAN	R	146	ENSP00000286744:H146R	ENSP00000286744:H146R	H	+	2	0	ADAMTSL3	82279640	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	0.350000	0.20079	-0.823000	0.04301	-1.663000	0.00750	CAT	A|0.386;G|0.614	0.614	strong		0.527	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
RSPO3	84870	hgsc.bcm.edu	37	6	127476516	127476516	+	Silent	SNP	G	G	A	rs1892172	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:127476516G>A	ENST00000356698.4	+	4	1156	c.567G>A	c.(565-567)ctG>ctA	p.L189L	RSPO3_ENST00000368317.3_Silent_p.L189L	NM_032784.3	NP_116173.2	Q9BXY4	RSPO3_HUMAN	R-spondin 3	189	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)	extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)		PTPRK/RSPO3(10)	breast(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(8)|skin(1)	17				GBM - Glioblastoma multiforme(226;0.0555)		AGGGTAACCTGTGTCCCCCAA	0.438													g|||	2668	0.532748	0.5983	0.5231	5008	,	,		20533	0.494		0.5	False		,,,				2504	0.5245				p.L189L		Atlas-SNP	.											RSPO3,rectum,carcinoma,0,1	RSPO3	32	1	0			c.G567A						PASS	.	A		2614,1792	641.7+/-397.5	789,1036,378	110.0	99.0	103.0		567	4.6	1.0	6	dbSNP_92	103	4583,4017	597.8+/-393.8	1220,2143,937	yes	coding-synonymous	RSPO3	NM_032784.3		2009,3179,1315	AA,AG,GG		46.7093,40.6718,44.664		189/273	127476516	7197,5809	2203	4300	6503	SO:0001819	synonymous_variant	84870	exon4			TAACCTGTGTCCC	BC022367	CCDS5135.1	6q22.33	2013-02-28	2011-06-29	2005-08-08	ENSG00000146374	ENSG00000146374		"""Endogenous ligands"""	20866	protein-coding gene	gene with protein product		610574	"""thrombospondin, type I, domain containing 2"", ""R-spondin 3 homolog (Xenopus laevis)"""	THSD2		10842357, 15469841	Standard	NM_032784		Approved	FLJ14440	uc003qar.3	Q9BXY4	OTTHUMG00000015521	ENST00000356698.4:c.567G>A	6.37:g.127476516G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	142	68	0.478873	NM_032784	B2RC27|Q5VTV4|Q96K87	Silent	SNP	ENST00000356698.4	37	CCDS5135.1																																																																																			G|0.455;A|0.545	0.545	strong		0.438	RSPO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042111.1	NM_032784	
ALDH3B2	222	hgsc.bcm.edu	37	11	67430698	67430698	+	Silent	SNP	G	G	A	rs3741172	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67430698G>A	ENST00000349015.3	-	10	1584	c.1146C>T	c.(1144-1146)tgC>tgT	p.C382C	ALDH3B2_ENST00000530069.1_Silent_p.C382C	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	382					alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						ACAGGAGGGTGCAGCTCTGGG	0.592													G|||	347	0.0692891	0.0567	0.0576	5008	,	,		18255	0.0903		0.1123	False		,,,				2504	0.0286				p.C382C		Atlas-SNP	.											.	ALDH3B2	46	.	0			c.C1146T						PASS	.	G	,	278,4122	155.9+/-189.0	15,248,1937	90.0	92.0	91.0		1146,1146	1.9	0.8	11	dbSNP_107	91	854,7734	195.1+/-240.3	38,778,3478	no	coding-synonymous,coding-synonymous	ALDH3B2	NM_000695.3,NM_001031615.1	,	53,1026,5415	AA,AG,GG		9.9441,6.3182,8.7157	,	382/386,382/386	67430698	1132,11856	2200	4294	6494	SO:0001819	synonymous_variant	222	exon10			GAGGGTGCAGCTC	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"""Aldehyde dehydrogenases"""	411	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 8"", ""acetaldehyde dehydrogenase 8"""	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.1146C>T	11.37:g.67430698G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	59	0.855072	NM_001031615	Q53Y98|Q8NAL5|Q96IB2	Silent	SNP	ENST00000349015.3	37	CCDS31622.1	165	0.07554945054945054	23	0.046747967479674794	27	0.07458563535911603	35	0.06118881118881119	80	0.10554089709762533	G	9.767	1.171533	0.21704	0.063182	0.099441	ENSG00000132746	ENST00000531248	.	.	.	3.75	1.86	0.25419	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.13124	-1.0521	3	.	.	.	.	7.8688	0.29554	0.2:0.0:0.8:0.0	rs3741172;rs17850238;rs57258945	.	.	.	V	111	.	.	A	-	2	0	ALDH3B2	67187274	1.000000	0.71417	0.797000	0.32132	0.042000	0.13812	1.648000	0.37271	0.386000	0.24997	-0.339000	0.08088	GCA	G|0.917;A|0.083	0.083	strong		0.592	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695	
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44004010	44004010	+	Missense_Mutation	SNP	T	T	C	rs2288709	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44004010T>C	ENST00000260605.8	+	2	198	c.98T>C	c.(97-99)tTt>tCt	p.F33S	DYNC2LI1_ENST00000406852.3_Missense_Mutation_p.F33S|DYNC2LI1_ENST00000489222.2_Intron|DYNC2LI1_ENST00000443170.3_5'UTR|DYNC2LI1_ENST00000605786.1_Missense_Mutation_p.F33S|DYNC2LI1_ENST00000398823.2_Missense_Mutation_p.F33S	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1	33			F -> S (in dbSNP:rs2288709). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.3}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GCAGAAAAATTTGTTTTCTTC	0.328													C|||	2570	0.513179	0.8933	0.4942	5008	,	,		14614	0.1696		0.3479	False		,,,				2504	0.5368				p.F33S		Atlas-SNP	.											.	DYNC2LI1	46	.	0			c.T98C						PASS	.	C	SER/PHE,SER/PHE,SER/PHE	3602,804	322.1+/-297.4	1473,656,74	115.0	127.0	123.0		98,98,98	5.4	1.0	2	dbSNP_100	123	3138,5462	656.7+/-401.4	579,1980,1741	yes	missense,missense,missense	DYNC2LI1	NM_001193464.1,NM_015522.3,NM_016008.3	155,155,155	2052,2636,1815	CC,CT,TT		36.4884,18.2478,48.1778	benign,benign,benign	33/353,33/202,33/352	44004010	6740,6266	2203	4300	6503	SO:0001583	missense	51626	exon2			AAAAATTTGTTTT		CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"""Cytoplasmic dyneins"""	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.98T>C	2.37:g.44004010T>C	ENSP00000260605:p.Phe33Ser	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_016008	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Missense_Mutation	SNP	ENST00000260605.8	37	CCDS1813.1	982	0.44963369963369965	439	0.8922764227642277	183	0.505524861878453	100	0.17482517482517482	260	0.34300791556728233	C	9.980	1.227764	0.22542	0.817522	0.364884	ENSG00000138036	ENST00000260605;ENST00000406852;ENST00000398823	T;T;T	0.28666	1.6;1.6;1.6	5.41	5.41	0.78517	.	0.054487	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00392	-1.555	0.09310	P	1.0	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.002;0.001	B;B;B;B;B	0.06405	0.0;0.0;0.0;0.002;0.002	T	0.32851	-0.9891	9	0.07030	T	0.85	-6.1844	12.3708	0.55254	0.0:0.9213:0.0:0.0787	rs2288709;rs17414745;rs52800670;rs61513437;rs2288709	33;33;33;33;33	Q8TCX1-2;Q8TCX1;Q8TCX1-3;Q8TCX1-5;Q8TCX1-4	.;DC2L1_HUMAN;.;.;.	S	33	ENSP00000260605:F33S;ENSP00000385738:F33S;ENSP00000381804:F33S	ENSP00000260605:F33S	F	+	2	0	DYNC2LI1	43857514	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.034000	0.49751	1.306000	0.44926	-0.119000	0.15052	TTT	T|0.516;C|0.483	0.483	strong		0.328	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008	
IGFLR1	79713	hgsc.bcm.edu	37	19	36230767	36230767	+	Missense_Mutation	SNP	A	A	G	rs34562867	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36230767A>G	ENST00000592537.1	-	4	665	c.565T>C	c.(565-567)Tgg>Cgg	p.W189R	AD000671.6_ENST00000589807.1_3'UTR|IGFLR1_ENST00000588992.1_Intron|IGFLR1_ENST00000246532.1_Missense_Mutation_p.W189R|IGFLR1_ENST00000592889.1_Intron|KMT2B_ENST00000607650.1_RNA|IGFLR1_ENST00000587101.1_5'UTR|IGFLR1_ENST00000344990.3_Intron			Q9H665	IGFR1_HUMAN	IGF-like family receptor 1	189			W -> R (in dbSNP:rs34562867).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(3)|large_intestine(1)|lung(8)|prostate(1)	15						TCCTTGGGCCAGCAGAGATGC	0.617													a|||	512	0.102236	0.087	0.1037	5008	,	,		17881	0.0883		0.1163	False		,,,				2504	0.1217				p.W189R		Atlas-SNP	.											.	IGFLR1	28	.	0			c.T565C						PASS	.	G	ARG/TRP	382,4024	192.3+/-217.7	11,360,1832	84.0	85.0	85.0		565	-6.9	0.0	19	dbSNP_126	85	808,7792	188.0+/-235.1	32,744,3524	yes	missense	IGFLR1	NM_024660.2	101	43,1104,5356	GG,GA,AA		9.3953,8.67,9.1496	benign	189/356	36230767	1190,11816	2203	4300	6503	SO:0001583	missense	79713	exon4			TGGGCCAGCAGAG	AK026226	CCDS12472.1	19q13.12	2012-10-02	2011-04-04	2011-04-04	ENSG00000126246	ENSG00000126246			23620	protein-coding gene	gene with protein product		614143	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 4"", ""transmembrane protein 149"""	U2AF1L4, TMEM149		21454693	Standard	NM_024660		Approved	FLJ22573	uc002obd.4	Q9H665		ENST00000592537.1:c.565T>C	19.37:g.36230767A>G	ENSP00000466181:p.Trp189Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_024660	Q8N5X0	Missense_Mutation	SNP	ENST00000592537.1	37	CCDS12472.1	222	0.10164835164835165	48	0.0975609756097561	37	0.10220994475138122	48	0.08391608391608392	89	0.11741424802110818	a	1.272	-0.612700	0.03690	0.0867	0.093953	ENSG00000126246	ENST00000246532	T	0.43688	0.94	4.86	-6.94	0.01633	.	1.644740	0.03371	N	0.198957	T	0.00210	0.0006	N	0.03115	-0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07501	-1.0769	9	0.06365	T	0.9	0.0469	3.4203	0.07391	0.5219:0.1111:0.2544:0.1126	rs34562867;rs61644838	189	Q9H665	IGFR1_HUMAN	R	189	ENSP00000246532:W189R	ENSP00000246532:W189R	W	-	1	0	IGFLR1	40922607	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.954000	0.03873	-1.998000	0.00968	-2.826000	0.00107	TGG	T|0.000;G|0.091;A|0.909	0.091	strong		0.617	IGFLR1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459077.1	NM_024660	
CCDC27	148870	hgsc.bcm.edu	37	1	3679775	3679775	+	Missense_Mutation	SNP	C	C	T	rs10910024	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3679775C>T	ENST00000294600.2	+	7	1142	c.1058C>T	c.(1057-1059)aCg>aTg	p.T353M		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	353	Glu-rich.		T -> M (in dbSNP:rs10910024). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		GTGGAGGACACGGGTGCCTGG	0.667													C|||	744	0.148562	0.1074	0.2738	5008	,	,		16229	0.003		0.2435	False		,,,				2504	0.1677				p.T353M		Atlas-SNP	.											.	CCDC27	79	.	0			c.C1058T						PASS	.	C	MET/THR	547,3823		32,483,1670	57.0	57.0	57.0		1058	-5.1	0.0	1	dbSNP_120	57	2072,6486		256,1560,2463	yes	missense	CCDC27	NM_152492.2	81	288,2043,4133	TT,TC,CC		24.2113,12.5172,20.2584	probably-damaging	353/657	3679775	2619,10309	2185	4279	6464	SO:0001583	missense	148870	exon7			AGGACACGGGTGC		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.1058C>T	1.37:g.3679775C>T	ENSP00000294600:p.Thr353Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	323	0.1478937728937729	48	0.0975609756097561	87	0.24033149171270718	0	0.0	188	0.24802110817941952	C	5.949	0.359090	0.11239	0.125172	0.242113	ENSG00000162592	ENST00000294600	T	0.18960	2.18	2.93	-5.07	0.02938	.	3.906960	0.00575	N	0.000301	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.19583	0.037	B	0.12156	0.007	T	0.28267	-1.0049	9	0.41790	T	0.15	.	1.2646	0.02008	0.1856:0.2133:0.1286:0.4725	rs10910024;rs57282654;rs10910024	353	Q2M243	CCD27_HUMAN	M	353	ENSP00000294600:T353M	ENSP00000294600:T353M	T	+	2	0	CCDC27	3669635	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.171000	0.00281	-1.283000	0.02393	-1.406000	0.01132	ACG	C|0.836;T|0.164	0.164	strong		0.667	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
RBMXL1	494115	hgsc.bcm.edu	37	1	89448608	89448608	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:89448608G>A	ENST00000321792.5	-	2	1329	c.902C>T	c.(901-903)cCg>cTg	p.P301L	RBMXL1_ENST00000399794.2_Missense_Mutation_p.P301L|CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'Flank|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	301	Ser-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										ATAAGATGGCGGGGGCCCTCG	0.483																																					p.P301L		Atlas-SNP	.											CCBL2,caecum,carcinoma,+1,1	.	.	1	0			c.C902T						scavenged	.						172.0	172.0	172.0					1																	89448608		2203	4300	6503	SO:0001583	missense	494115	exon3			GATGGCGGGGGCC	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.902C>T	1.37:g.89448608G>A	ENSP00000318415:p.Pro301Leu	Somatic	203	5	0.0246305		WXS	Illumina HiSeq	Phase_I	168	10	0.0595238	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022446	0.35701	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.78126	-1.15;-1.15	1.41	0.0579	0.14325	.	0.060058	0.64402	D	0.000002	T	0.52629	0.1746	M	0.66939	2.045	0.46725	D	0.999174	B	0.34255	0.445	B	0.20577	0.03	T	0.56341	-0.7995	10	0.52906	T	0.07	-2.8526	6.2127	0.20638	0.0:0.0:0.7093:0.2907	.	301	Q96E39	RBMXL_HUMAN	L	301	ENSP00000318415:P301L;ENSP00000446099:P301L	ENSP00000318415:P301L	P	-	2	0	RBMXL1	89221196	1.000000	0.71417	0.993000	0.49108	0.967000	0.64934	6.229000	0.72294	0.760000	0.33108	0.306000	0.20318	CCG	.	.	none		0.483	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
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 GAIIx	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_ENST00000455274.1_Intron|TTLL3_ENST00000426895.4_Nonsense_Mutation_p.R704*|ARPC4-TTLL3_ENST00000397256.1_Intron|TTLL3_ENST00000430793.1_Nonsense_Mutation_p.R349*|TTLL3_ENST00000427853.3_Intron|TTLL3_ENST00000397241.1_Intron|TTLL3_ENST00000383827.1_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*	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	61	37	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	
CEACAM19	56971	hgsc.bcm.edu	37	19	45176028	45176028	+	Silent	SNP	C	C	T	rs35695969	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:45176028C>T	ENST00000403660.3	+	2	426	c.216C>T	c.(214-216)taC>taT	p.Y72Y	CTB-171A8.1_ENST00000590796.1_RNA|CEACAM19_ENST00000480278.1_3'UTR|CEACAM19_ENST00000358777.4_Silent_p.Y72Y			Q7Z692	CEA19_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 19	72						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	11	Lung NSC(12;0.00308)|all_lung(12;0.00806)	Prostate(69;0.0376)				AGGAGACGTACGGAGGCACGA	0.572																																					p.Y72Y		Atlas-SNP	.											.	CEACAM19	27	.	0			c.C216T						PASS	.	T	,	121,4285	815.2+/-416.2	3,115,2085	130.0	85.0	101.0		216,216	-2.2	0.0	19	dbSNP_126	101	469,8131	798.2+/-407.4	10,449,3841	no	coding-synonymous,coding-synonymous	CEACAM19	NM_001127893.1,NM_020219.3	,	13,564,5926	TT,TC,CC		5.4535,2.7463,4.5364	,	72/300,72/301	45176028	590,12416	2203	4300	6503	SO:0001819	synonymous_variant	56971	exon2			GACGTACGGAGGC	AF406955	CCDS12641.1, CCDS46108.1	19q13.31	2013-01-11			ENSG00000186567	ENSG00000186567		"""Immunoglobulin superfamily / V-set domain containing"""	31951	protein-coding gene	gene with protein product		606691					Standard	NM_020219		Approved	CEAL1	uc002ozo.4	Q7Z692	OTTHUMG00000151528	ENST00000403660.3:c.216C>T	19.37:g.45176028C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	130	62	0.476923	NM_001127893	Q5XJ15|Q7Z693	Silent	SNP	ENST00000403660.3	37	CCDS12641.1																																																																																			C|0.959;T|0.041	0.041	strong		0.572	CEACAM19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323022.1	NM_020219	
ZNF587B	100293516	hgsc.bcm.edu	37	19	58352806	58352806	+	Missense_Mutation	SNP	T	T	C	rs35313547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58352806T>C	ENST00000442832.4	+	3	998	c.764T>C	c.(763-765)gTt>gCt	p.V255A	ZNF587B_ENST00000594901.1_Missense_Mutation_p.V255A|ZNF587B_ENST00000316462.4_Intron|CTD-2583A14.10_ENST00000598031.1_Intron	NM_001204818.1	NP_001191747.1	E7ETH6	Z587B_HUMAN	zinc finger protein 587B	255					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AGCAAATATGTTAGCTTCAGT	0.388													.|||	662	0.132188	0.0151	0.1398	5008	,	,		22065	0.1925		0.173	False		,,,				2504	0.181				p.V255A		Atlas-SNP	.											.	.	.	.	0			c.T764C						PASS	.																																			SO:0001583	missense	100293516	exon3			AATATGTTAGCTT	AK299091	CCDS56109.1	19q13.43	2013-01-08				ENSG00000269343		"""Zinc fingers, C2H2-type"", ""-"""	37142	protein-coding gene	gene with protein product							Standard	NM_001204818		Approved		uc021vcp.1	E7ETH6		ENST00000442832.4:c.764T>C	19.37:g.58352806T>C	ENSP00000392410:p.Val255Ala	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	59	25	0.423729	NM_001204818	B4DR41	Missense_Mutation	SNP	ENST00000442832.4	37	CCDS56109.1	285	0.1304945054945055	8	0.016260162601626018	46	0.1270718232044199	98	0.17132867132867133	133	0.17546174142480211	.	0.015	-1.569397	0.00895	.	.	ENSG00000198466	ENST00000442832	T	0.14391	2.51	2.01	-4.03	0.04021	.	.	.	.	.	T	0.00012	0.0000	N	0.03294	-0.36	.	.	.	B;B	0.18461	0.0;0.028	B;B	0.09377	0.001;0.004	T	0.37337	-0.9710	7	.	.	.	.	0.2177	0.00164	0.2831:0.1557:0.2683:0.2929	rs35313547;rs61733716	255;204	E7ETH6;Q92967	.;.	A	255	ENSP00000392410:V255A	.	V	+	2	0	ZNF587	63044618	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.768000	0.01794	-2.618000	0.00441	-1.004000	0.02495	GTT	T|0.866;C|0.134	0.134	strong		0.388	ZNF587B-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466834.2	NM_001204818	
STH	246744	hgsc.bcm.edu	37	17	44076665	44076665	+	Missense_Mutation	SNP	A	A	G	rs62063857	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44076665A>G	ENST00000537309.1	+	1	50	c.20A>G	c.(19-21)cAa>cGa	p.Q7R	MAPT_ENST00000334239.8_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000415613.2_Intron|MAPT_ENST00000574436.1_Intron	NM_001007532.2	NP_001007533.1	Q8IWL8	STH_HUMAN	saitohin	7			Q -> R (in dbSNP:rs62063857). {ECO:0000269|PubMed:12032355, ECO:0000269|PubMed:12402275, ECO:0000269|PubMed:12913211}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						ggtggaggccaagtctcatgc	0.532													G|||	439	0.0876597	0.0204	0.1571	5008	,	,		18794	0.001		0.2406	False		,,,				2504	0.0613				p.Q7R		Atlas-SNP	.											STH,rectum,carcinoma,+1,1	STH	14	1	0			c.A20G	GRCh37	CM032397	STH	M	rs62063857	PASS	.	G	ARG/GLN,,,,,,,,	187,3759		7,173,1793	50.0	49.0	49.0		20,,,,,,,,	-0.9	0.0	17	dbSNP_129	49	1836,6500		201,1434,2533	yes	missense,intron,intron,intron,intron,intron,intron,intron,intron	MAPT,STH	NM_001007532.2,NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	43,,,,,,,,	208,1607,4326	GG,GA,AA		22.025,4.739,16.4713	benign,,,,,,,,	7/129,,,,,,,,	44076665	2023,10259	1973	4168	6141	SO:0001583	missense	246744	exon1			GAGGCCAAGTCTC	AA325304	CCDS54136.1	17q21.1	2008-01-22				ENSG00000256762			18839	protein-coding gene	gene with protein product	"""microtubule-associated protein tau (MAPT) intronic transcript"""	607067				12032355, 16186110	Standard	NM_001007532		Approved	MAPTIT	uc002ijy.2	Q8IWL8		ENST00000537309.1:c.20A>G	17.37:g.44076665A>G	ENSP00000443168:p.Gln7Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_001007532	A1L3X7	Missense_Mutation	SNP	ENST00000537309.1	37	CCDS54136.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	0.974	-0.699349	0.03279	0.04739	0.22025	ENSG00000256762	ENST00000537309	T	0.51817	0.69	1.27	-0.939	0.10408	.	.	.	.	.	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	0.17471	-1.0368	8	0.87932	D	0	.	5.2426	0.15479	0.5798:0.0:0.4202:0.0	rs62063857	7	Q8IWL8	STH_HUMAN	R	7	ENSP00000443168:Q7R	ENSP00000443168:Q7R	Q	+	2	0	STH	41432502	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.093000	0.01353	-0.835000	0.04234	-1.668000	0.00747	CAA	A|0.159;C|0.093	.	strong		0.532	STH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400444.1		
ANO3	63982	hgsc.bcm.edu	37	11	26621117	26621117	+	Silent	SNP	A	A	C	rs11604868	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:26621117A>C	ENST00000256737.3	+	17	2544	c.1692A>C	c.(1690-1692)gcA>gcC	p.A564A	ANO3_ENST00000525139.1_Silent_p.A548A|ANO3_ENST00000537978.1_Silent_p.A548A|ANO3_ENST00000531568.1_Silent_p.A418A	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	564					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						TGATCACTGCAGTGTTTGGAG	0.388													A|||	816	0.162939	0.0794	0.1268	5008	,	,		18447	0.3224		0.2058	False		,,,				2504	0.093				p.A564A		Atlas-SNP	.											.	ANO3	145	.	0			c.A1692C						PASS	.	A		387,4019	193.0+/-218.2	18,351,1834	306.0	266.0	280.0		1692	-2.6	1.0	11	dbSNP_120	280	1528,7070	289.3+/-299.2	127,1274,2898	no	coding-synonymous	ANO3	NM_031418.2		145,1625,4732	CC,CA,AA		17.7716,8.7835,14.7262		564/982	26621117	1915,11089	2203	4299	6502	SO:0001819	synonymous_variant	63982	exon17			CACTGCAGTGTTT	AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	14004	protein-coding gene	gene with protein product	"""transmembrane protein 16C (eight membrane-spanning domains)"""	610110	"""chromosome 11 open reading frame 25"", ""transmembrane protein 16C"""	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1692A>C	11.37:g.26621117A>C		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	197	80	0.406091	NM_031418	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																			A|0.835;C|0.165	0.165	strong		0.388	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418	
KIF16B	55614	hgsc.bcm.edu	37	20	16359650	16359650	+	Silent	SNP	C	C	T	rs8116503	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:16359650C>T	ENST00000354981.2	-	19	3154	c.2997G>A	c.(2995-2997)aaG>aaA	p.K999K	KIF16B_ENST00000355755.3_Silent_p.K999K|KIF16B_ENST00000408042.1_Silent_p.K999K|KIF16B_ENST00000378003.2_Silent_p.K225K	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	999	Glu-rich.		K -> N (in dbSNP:rs8116503).		ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CTCTCTGCTGCTTCTCTCTGG	0.542													C|||	915	0.182708	0.2912	0.1383	5008	,	,		19268	0.0565		0.2038	False		,,,				2504	0.1759				p.K999K		Atlas-SNP	.											.	KIF16B	305	.	0			c.G2997A						PASS	.	C	,,	1392,3014	457.1+/-351.5	219,954,1030	102.0	107.0	105.0		2997,2997,2997	4.6	1.0	20	dbSNP_116	105	1662,6938	305.3+/-307.4	155,1352,2793	no	coding-synonymous,coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	,,	374,2306,3823	TT,TC,CC		19.3256,31.5933,23.4815	,,	999/1267,999/1393,999/1318	16359650	3054,9952	2203	4300	6503	SO:0001819	synonymous_variant	55614	exon19			CTGCTGCTTCTCT	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.2997G>A	20.37:g.16359650C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	170	80	0.470588	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			C|0.793;T|0.207	0.207	strong		0.542	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
GPC5	2262	hgsc.bcm.edu	37	13	92345579	92345579	+	Missense_Mutation	SNP	C	C	T	rs553717	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:92345579C>T	ENST00000377067.3	+	3	836	c.464C>T	c.(463-465)gCg>gTg	p.A155V		NM_004466.4	NP_004457.1	P78333	GPC5_HUMAN	glypican 5	155			A -> V (in dbSNP:rs553717).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|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)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(4)|endometrium(6)|kidney(4)|large_intestine(7)|lung(34)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69	all_cancers(3;1.43e-07)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)	Lung NSC(4;0.00454)				TTATTTGGTGCGGATGTTAAT	0.443													C|||	986	0.196885	0.1936	0.1513	5008	,	,		18441	0.2897		0.1481	False		,,,				2504	0.1881				p.A155V		Atlas-SNP	.											GPC5,NS,carcinoma,-1,1	GPC5	140	1	0			c.C464T						PASS	.	C	VAL/ALA	822,3584	328.5+/-300.6	67,688,1448	153.0	156.0	155.0		464	4.2	0.8	13	dbSNP_83	155	970,7630	211.4+/-252.0	45,880,3375	yes	missense	GPC5	NM_004466.4	64	112,1568,4823	TT,TC,CC		11.2791,18.6564,13.7783	benign	155/573	92345579	1792,11214	2203	4300	6503	SO:0001583	missense	2262	exon3			TTGGTGCGGATGT	AF001462	CCDS9468.1	13q32	2011-08-01			ENSG00000179399	ENSG00000179399		"""Proteoglycans / Cell Surface : Glypicans"""	4453	protein-coding gene	gene with protein product	"""glypican proteoglycan 5"""	602446				9070915, 20304703, 19556317, 15057823	Standard	NM_004466		Approved		uc010tif.2	P78333	OTTHUMG00000017200	ENST00000377067.3:c.464C>T	13.37:g.92345579C>T	ENSP00000366267:p.Ala155Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	223	126	0.565022	NM_004466	B2R726|O60436|Q9BX27	Missense_Mutation	SNP	ENST00000377067.3	37	CCDS9468.1	379	0.17353479853479853	78	0.15853658536585366	44	0.12154696132596685	165	0.28846153846153844	92	0.12137203166226913	C	14.72	2.620512	0.46736	0.186564	0.112791	ENSG00000179399	ENST00000377067	T	0.54071	0.59	5.07	4.19	0.49359	.	0.330872	0.32518	N	0.005993	T	0.00012	0.0000	L	0.46157	1.445	0.27994	P	0.9355561	B	0.15473	0.013	B	0.15870	0.014	T	0.09862	-1.0655	9	0.59425	D	0.04	.	11.2088	0.48786	0.0:0.9046:0.0:0.0954	rs553717;rs52808980;rs57920264;rs553717	155	P78333	GPC5_HUMAN	V	155	ENSP00000366267:A155V	ENSP00000366267:A155V	A	+	2	0	GPC5	91143580	0.601000	0.26907	0.790000	0.31976	0.620000	0.37586	2.728000	0.47319	1.044000	0.40200	0.467000	0.42956	GCG	C|0.842;T|0.158	0.158	strong		0.443	GPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045454.1	NM_004466	
MRPL10	124995	hgsc.bcm.edu	37	17	45904420	45904420	+	Missense_Mutation	SNP	C	C	T	rs11538868	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:45904420C>T	ENST00000351111.2	-	3	378	c.373G>A	c.(373-375)Gtc>Atc	p.V125I	MRPL10_ENST00000290208.7_Missense_Mutation_p.V135I|MRPL10_ENST00000414011.1_Missense_Mutation_p.V135I	NM_145255.3	NP_660298.2	Q7Z7H8	RM10_HUMAN	mitochondrial ribosomal protein L10	125			V -> I (in dbSNP:rs16948568). {ECO:0000269|PubMed:15489334}.		ribosome biogenesis (GO:0042254)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(3)|large_intestine(1)|lung(3)|ovary(1)	8						TTGGGGAAGACCTTCATCAGG	0.577													C|||	795	0.158746	0.0696	0.2161	5008	,	,		20754	0.0139		0.3549	False		,,,				2504	0.1861				p.V135I		Atlas-SNP	.											.	MRPL10	24	.	0			c.G403A						PASS	.	C	ILE/VAL,ILE/VAL	493,3913	228.8+/-243.5	22,449,1732	83.0	71.0	76.0		373,403	-0.1	1.0	17	dbSNP_120	76	3273,5327	491.8+/-373.2	642,1989,1669	yes	missense,missense	MRPL10	NM_145255.3,NM_148887.2	29,29	664,2438,3401	TT,TC,CC		38.0581,11.1893,28.9559	benign,benign	125/262,135/272	45904420	3766,9240	2203	4300	6503	SO:0001583	missense	124995	exon4			GGAAGACCTTCAT	AB051618	CCDS11516.1, CCDS11517.1	17q21.3	2012-09-13			ENSG00000159111	ENSG00000159111		"""Mitochondrial ribosomal proteins / large subunits"""	14055	protein-coding gene	gene with protein product	"""39S ribosomal protein L10, mitochondrial"""	611825				11551941	Standard	NM_148887		Approved	RPML8, MRP-L8, L10MT, MRP-L10, MRPL8, MGC17973	uc002ily.3	Q7Z7H8	OTTHUMG00000156302	ENST00000351111.2:c.373G>A	17.37:g.45904420C>T	ENSP00000324100:p.Val125Ile	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_148887	A6NGJ4|Q96B80|Q96Q55	Missense_Mutation	SNP	ENST00000351111.2	37	CCDS11516.1	425	0.1945970695970696	45	0.09146341463414634	95	0.26243093922651933	7	0.012237762237762238	278	0.36675461741424803	C	10.70	1.425026	0.25639	0.111893	0.380581	ENSG00000159111	ENST00000351111;ENST00000290208;ENST00000414011	T;T;T	0.53857	0.6;0.6;0.6	5.62	-0.131	0.13494	.	0.482175	0.23941	N	0.043052	T	0.00012	0.0000	N	0.21448	0.665	0.48511	P	3.3799999999994945E-4	B;B	0.15930	0.002;0.015	B;B	0.18561	0.015;0.022	T	0.37820	-0.9689	9	0.42905	T	0.14	-2.0015	1.9376	0.03340	0.127:0.3325:0.1243:0.4161	rs16948568;rs17700922;rs17851354;rs52817339;rs16948568	125;135	Q7Z7H8;A6NGJ4	RM10_HUMAN;.	I	125;135;135	ENSP00000324100:V125I;ENSP00000290208:V135I;ENSP00000395870:V135I	ENSP00000290208:V135I	V	-	1	0	MRPL10	43259419	0.779000	0.28652	0.971000	0.41717	0.804000	0.45430	0.048000	0.14078	-0.216000	0.10048	-0.367000	0.07326	GTC	C|0.761;T|0.239	0.239	strong		0.577	MRPL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343764.1	NM_145255	
ABCC2	1244	hgsc.bcm.edu	37	10	101563815	101563815	+	Missense_Mutation	SNP	G	G	A	rs2273697	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101563815G>A	ENST00000370449.4	+	10	1362	c.1249G>A	c.(1249-1251)Gtt>Att	p.V417I		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	417	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		V -> I (in dbSNP:rs2273697). {ECO:0000269|PubMed:11266082, ECO:0000269|PubMed:11477083}.		cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	GGAGTACACCGTTGGAGAAAC	0.463													G|||	934	0.186502	0.1891	0.1585	5008	,	,		23541	0.0962		0.2038	False		,,,				2504	0.2781				p.V417I		Atlas-SNP	.											ABCC2,NS,adenoma,0,1	ABCC2	160	1	0			c.G1249A	GRCh37	CM067967	ABCC2	M	rs2273697	PASS	.		ILE/VAL	824,3582	325.9+/-299.3	81,662,1460	184.0	151.0	162.0		1249	-10.3	0.1	10	dbSNP_100	162	1675,6925	307.6+/-308.5	174,1327,2799	yes	missense	ABCC2	NM_000392.3	29	255,1989,4259	AA,AG,GG		19.4767,18.7018,19.2142	benign	417/1546	101563815	2499,10507	2203	4300	6503	SO:0001583	missense	1244	exon10			TACACCGTTGGAG	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.1249G>A	10.37:g.101563815G>A	ENSP00000359478:p.Val417Ile	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	204	121	0.593137	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	379	0.17353479853479853	98	0.1991869918699187	57	0.1574585635359116	73	0.12762237762237763	151	0.19920844327176782	G	12.32	1.903578	0.33628	0.187018	0.194767	ENSG00000023839	ENST00000370449	D	0.90955	-2.76	5.48	-10.3	0.00346	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.601291	0.17938	N	0.156921	T	0.00300	0.0009	N	0.17474	0.49	0.25643	P	0.9861835	B	0.13594	0.008	B	0.20955	0.032	T	0.04153	-1.0973	9	0.41790	T	0.15	-1.4461	20.1781	0.98191	0.3045:0.0:0.6955:0.0	rs2273697;rs17216184;rs60620335;rs2273697	417	Q92887	MRP2_HUMAN	I	417	ENSP00000359478:V417I	ENSP00000359478:V417I	V	+	1	0	ABCC2	101553805	0.000000	0.05858	0.132000	0.22025	0.617000	0.37484	-0.363000	0.07593	-1.996000	0.00970	-1.022000	0.02435	GTT	A|0.183;C|0.005	0.183	strong		0.463	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
GPR149	344758	hgsc.bcm.edu	37	3	154146922	154146922	+	Silent	SNP	A	A	G	rs34792862	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:154146922A>G	ENST00000389740.2	-	1	582	c.483T>C	c.(481-483)agT>agC	p.S161S		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	161					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AGAGCAGCAGACTGGCTGCCC	0.642													A|||	814	0.16254	0.112	0.1974	5008	,	,		14601	0.246		0.1392	False		,,,				2504	0.1442				p.S161S		Atlas-SNP	.											.	GPR149	134	.	0			c.T483C						PASS	.	A		464,3572		20,424,1574	22.0	27.0	25.0		483	-2.7	0.9	3	dbSNP_126	25	1177,7171		88,1001,3085	no	coding-synonymous	GPR149	NM_001038705.1		108,1425,4659	GG,GA,AA		14.0992,11.4965,13.251		161/732	154146922	1641,10743	2018	4174	6192	SO:0001819	synonymous_variant	344758	exon1			CAGCAGACTGGCT	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.483T>C	3.37:g.154146922A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_001038705		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																			A|0.841;G|0.159	0.159	strong		0.642	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
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 GAIIx	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		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	157	43	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	
TMEM173	340061	hgsc.bcm.edu	37	5	138856982	138856982	+	Missense_Mutation	SNP	C	C	T	rs7380824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:138856982C>T	ENST00000330794.4	-	7	1211	c.878G>A	c.(877-879)cGg>cAg	p.R293Q	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	293	c-di-GMP-binding domain (CBD).		R -> Q (in dbSNP:rs7380824).		activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTCAAGTGTCCGGCAGAAGAG	0.562													C|||	1377	0.27496	0.2708	0.2882	5008	,	,		19161	0.4048		0.1531	False		,,,				2504	0.2628				p.R293Q		Atlas-SNP	.											.	TMEM173	19	.	0			c.G878A						PASS	.	C	GLN/ARG	1172,3234	412.6+/-336.2	151,870,1182	92.0	85.0	87.0		878	5.5	1.0	5	dbSNP_116	87	1214,7386	245.1+/-274.1	90,1034,3176	yes	missense	TMEM173	NM_198282.2	43	241,1904,4358	TT,TC,CC		14.1163,26.6001,18.3454	probably-damaging	293/380	138856982	2386,10620	2203	4300	6503	SO:0001583	missense	340061	exon7			AGTGTCCGGCAGA		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.878G>A	5.37:g.138856982C>T	ENSP00000331288:p.Arg293Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	581	0.266025641025641	138	0.2804878048780488	92	0.2541436464088398	237	0.4143356643356643	114	0.1503957783641161	C	32	5.158298	0.94686	0.266001	0.141163	ENSG00000184584	ENST00000330794	T	0.26518	1.73	5.53	5.53	0.82687	.	0.062472	0.64402	D	0.000011	T	0.00012	0.0000	M	0.78049	2.395	0.09310	P	0.99999547022	D	0.89917	1.0	D	0.91635	0.999	T	0.26780	-1.0093	9	0.87932	D	0	-29.0556	19.0483	0.93030	0.0:1.0:0.0:0.0	rs7380824;rs59604760;rs7380824	293	Q86WV6	TM173_HUMAN	Q	293	ENSP00000331288:R293Q	ENSP00000331288:R293Q	R	-	2	0	TMEM173	138837166	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	3.440000	0.52886	2.617000	0.88574	0.561000	0.74099	CGG	C|0.780;T|0.220	0.220	strong		0.562	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
CCDC50	152137	hgsc.bcm.edu	37	3	191093310	191093310	+	Intron	SNP	A	A	G	rs4677728	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:191093310A>G	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Missense_Mutation_p.K303R	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		GAGCACAGAAAAAGGAGACAC	0.532													A|||	2515	0.502196	0.7247	0.4697	5008	,	,		19772	0.4702		0.4105	False		,,,				2504	0.3517				p.K303R		Atlas-SNP	.											.	CCDC50	39	.	0			c.A908G						PASS	.	A	,ARG/LYS	2953,1451	656.2+/-400.0	986,981,235	56.0	57.0	57.0		,908	2.3	1.0	3	dbSNP_111	57	3398,5202	475.0+/-369.0	675,2048,1577	yes	intron,missense	CCDC50	NM_174908.3,NM_178335.2	,26	1661,3029,1812	GG,GA,AA		39.5116,32.9473,48.8388	,benign	,303/483	191093310	6351,6653	2202	4300	6502	SO:0001627	intron_variant	152137	exon6			ACAGAAAAAGGAG	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4638A>G	3.37:g.191093310A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	37	CCDS33913.1	1090	0.4990842490842491	356	0.7235772357723578	165	0.4558011049723757	254	0.44405594405594406	315	0.4155672823218997	A	6.952	0.545436	0.13312	0.670527	0.395116	ENSG00000152492	ENST00000392456	T	0.29655	1.56	5.96	2.32	0.28847	.	0.536798	0.19013	N	0.125006	T	0.00012	0.0000	.	.	.	0.48452	P	3.4199999999995345E-4	B	0.24721	0.11	B	0.19391	0.025	T	0.41520	-0.9504	8	0.02654	T	1	.	7.3769	0.26833	0.752:0.0:0.248:0.0	rs4677728;rs52807307;rs57021632;rs4677728	303	Q8IVM0-2	.	R	303	ENSP00000376250:K303R	ENSP00000376250:K303R	K	+	2	0	CCDC50	192576004	0.999000	0.42202	0.992000	0.48379	0.922000	0.55478	1.352000	0.34033	0.168000	0.19655	0.533000	0.62120	AAA	A|0.502;G|0.498	0.498	strong		0.532	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
WDR55	54853	hgsc.bcm.edu	37	5	140048544	140048544	+	Missense_Mutation	SNP	C	C	T	rs2286394	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140048544C>T	ENST00000358337.5	+	5	866	c.629C>T	c.(628-630)tCt>tTt	p.S210F	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	210			S -> F (in dbSNP:rs2286394).		rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAACCTCAGTCTGGGGACCTG	0.542													C|||	1004	0.200479	0.0545	0.2161	5008	,	,		19980	0.3016		0.2396	False		,,,				2504	0.2423				p.S210F		Atlas-SNP	.											.	WDR55	27	.	0			c.C629T						PASS	.	C	PHE/SER	336,4070	177.3+/-206.3	11,314,1878	81.0	76.0	77.0		629	3.5	1.0	5	dbSNP_100	77	2014,6586	353.0+/-328.9	241,1532,2527	yes	missense	WDR55	NM_017706.4	155	252,1846,4405	TT,TC,CC		23.4186,7.626,18.0686	possibly-damaging	210/384	140048544	2350,10656	2203	4300	6503	SO:0001583	missense	54853	exon5			CTCAGTCTGGGGA	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"""WD repeat domain containing"""	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.629C>T	5.37:g.140048544C>T	ENSP00000351100:p.Ser210Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_017706	Q9NXK4	Missense_Mutation	SNP	ENST00000358337.5	37	CCDS4235.1	470	0.21520146520146521	34	0.06910569105691057	87	0.24033149171270718	162	0.28321678321678323	187	0.24670184696569922	C	16.24	3.066190	0.55539	0.07626	0.234186	ENSG00000120314	ENST00000358337	T	0.31510	1.49	5.44	3.55	0.40652	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.415951	0.22830	N	0.055103	T	0.00012	0.0000	L	0.44542	1.39	0.31277	P	0.691004	D;D	0.60575	0.967;0.988	P;P	0.54664	0.689;0.758	T	0.22695	-1.0209	9	0.72032	D	0.01	-9.5498	5.3458	0.16008	0.1201:0.5804:0.2139:0.0856	rs2286394;rs60780836;rs2286394	49;210	G3V1J0;Q9H6Y2	.;WDR55_HUMAN	F	210	ENSP00000351100:S210F	ENSP00000351100:S210F	S	+	2	0	WDR55	140028728	0.955000	0.32602	0.999000	0.59377	0.865000	0.49528	0.943000	0.29030	1.290000	0.44636	0.467000	0.42956	TCT	C|0.806;T|0.194	0.194	strong		0.542	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706	
DPYSL3	1809	hgsc.bcm.edu	37	5	146780273	146780273	+	Silent	SNP	G	G	A	rs10515587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:146780273G>A	ENST00000398514.3	-	10	1463	c.1092C>T	c.(1090-1092)gtC>gtT	p.V364V	CTB-108O6.2_ENST00000607270.1_RNA|DPYSL3_ENST00000343218.5_Silent_p.V478V|DPYSL3_ENST00000534907.1_Intron	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	364					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)			breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTCCCAGATGACAGACATCC	0.572													G|||	819	0.163538	0.3147	0.1744	5008	,	,		20096	0.0		0.1541	False		,,,				2504	0.1299				p.V478V		Atlas-SNP	.											DPYSL3,NS,carcinoma,-1,1	DPYSL3	58	1	0			c.C1434T						scavenged	.	G	,	1300,3106	418.3+/-338.2	207,886,1110	114.0	119.0	117.0		1434,1092	4.7	1.0	5	dbSNP_119	117	1337,7263	256.2+/-280.8	94,1149,3057	no	coding-synonymous,coding-synonymous	DPYSL3	NM_001197294.1,NM_001387.2	,	301,2035,4167	AA,AG,GG		15.5465,29.5052,20.2753	,	478/685,364/571	146780273	2637,10369	2203	4300	6503	SO:0001819	synonymous_variant	1809	exon10			CCAGATGACAGAC	D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.1092C>T	5.37:g.146780273G>A		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_001197294	B3SXQ8|Q93012	Silent	SNP	ENST00000398514.3	37	CCDS43381.1	349	0.15979853479853479	172	0.34959349593495936	60	0.16574585635359115	0	0.0	117	0.15435356200527706	G	9.539	1.112781	0.20795	0.295052	0.155465	ENSG00000113657	ENST00000520473	.	.	.	5.53	4.66	0.58398	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.43621	-0.9380	3	.	.	.	-14.7881	6.6299	0.22851	0.1472:0.0:0.7074:0.1454	rs10515587;rs60929588;rs10515587	.	.	.	Y	63	.	.	H	-	1	0	DPYSL3	146760466	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.402000	0.52608	1.475000	0.48197	0.650000	0.86243	CAT	G|0.890;A|0.110	0.110	strong		0.572	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387	
MXRA5	25878	hgsc.bcm.edu	37	X	3238733	3238733	+	Missense_Mutation	SNP	G	G	A	rs1974522	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3238733G>A	ENST00000217939.6	-	5	5147	c.4993C>T	c.(4993-4995)Cca>Tca	p.P1665S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1665			P -> S (in dbSNP:rs1974522).			extracellular vesicular exosome (GO:0070062)		p.P1665S(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GATAATCTTGGAGTTGTAAAC	0.423													G|||	1629	0.431523	0.2118	0.3905	3775	,	,		16126	0.2728		0.4573	False		,,,				2504	0.3507				p.P1665S		Atlas-SNP	.											.	MXRA5	815	.	2	Substitution - Missense(2)	stomach(2)	c.C4993T						PASS	.	G	SER/PRO	1167,2668		139,714,175,779,396	166.0	158.0	161.0		4993	2.3	0.0	X	dbSNP_92	161	3839,2889		793,1187,1066,448,806	yes	missense	MXRA5	NM_015419.3	74	932,1901,1241,1227,1202	AA,AG,A,GG,G		42.94,30.4302,47.3918	probably-damaging	1665/2829	3238733	5006,5557	2203	4300	6503	SO:0001583	missense	25878	exon5			ATCTTGGAGTTGT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.4993C>T	X.37:g.3238733G>A	ENSP00000217939:p.Pro1665Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	743	0.4478601567209162	70	0.16203703703703703	89	0.31338028169014087	105	0.23863636363636365	240	0.43636363636363634	g	9.833	1.188977	0.21954	0.304302	0.5706	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.63096	-0.02	3.2	2.3	0.28687	.	0.184807	0.26149	U	0.026059	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.39809	0.689	B	0.31547	0.132	T	0.46965	-0.9153	9	0.51188	T	0.08	.	11.4118	0.49929	0.0:0.0:0.8176:0.1824	rs1974522;rs3752335;rs17335205;rs57959586;rs1974522	1665	Q9NR99	MXRA5_HUMAN	S	1665	ENSP00000217939:P1665S	ENSP00000217939:P1665S	P	-	1	0	MXRA5	3248733	0.091000	0.21658	0.004000	0.12327	0.040000	0.13550	1.291000	0.33330	0.345000	0.23873	0.431000	0.28591	CCA	0|0.015;A|0.441;C|0.000;G|0.544;N|0.000	0.441	strong		0.423	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
PSG1	5669	hgsc.bcm.edu	37	19	43383680	43383680	+	Silent	SNP	G	G	T	rs1141653	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43383680G>T	ENST00000436291.2	-	1	170	c.54C>A	c.(52-54)ctC>ctA	p.L18L	PSG1_ENST00000312439.6_Silent_p.L18L|PSG1_ENST00000403380.3_Silent_p.L18L|PSG1_ENST00000595124.1_Silent_p.L18L|PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000244296.2_Silent_p.L18L|PSG1_ENST00000595356.1_Silent_p.L18L	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	18					female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				CTGTGAGCAGGAGCCCCTTCC	0.552													.|||	1633	0.326078	0.4614	0.2046	5008	,	,		18648	0.4167		0.1014	False		,,,				2504	0.3671				p.L18L		Atlas-SNP	.											.	PSG1	196	.	0			c.C54A						PASS	.	G	,,	1275,1745		292,691,527	157.0	140.0	146.0		54,54,54	0.4	0.1	19	dbSNP_86	146	576,4838		45,486,2176	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	,,	337,1177,2703	TT,TG,GG		10.6391,42.2185,21.9469	,,	18/420,18/418,18/427	43383680	1851,6583	1510	2707	4217	SO:0001819	synonymous_variant	5669	exon1			GAGCAGGAGCCCC		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.54C>A	19.37:g.43383680G>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	37	CCDS54275.1																																																																																			G|0.775;T|0.225	0.225	strong		0.552	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
CEMIP	57214	hgsc.bcm.edu	37	15	81212521	81212521	+	Silent	SNP	T	T	C	rs2271160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:81212521T>C	ENST00000394685.3	+	15	2303	c.1884T>C	c.(1882-1884)tgT>tgC	p.C628C	RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Silent_p.C628C|KIAA1199_ENST00000220244.3_Silent_p.C628C			Q8WUJ3	CEMIP_HUMAN		628					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)	p.C628C(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TTGACCACTGTCTTGGCCTCC	0.557													T|||	885	0.176717	0.1399	0.1354	5008	,	,		20777	0.2669		0.1342	False		,,,				2504	0.2065				p.C628C		Atlas-SNP	.											KIAA1199,NS,carcinoma,0,1	KIAA1199	118	1	1	Substitution - coding silent(1)	stomach(1)	c.T1884C						PASS	.	T		610,3796	268.3+/-268.4	41,528,1634	188.0	126.0	147.0		1884	-3.3	0.7	15	dbSNP_100	147	1181,7419	240.6+/-271.2	86,1009,3205	no	coding-synonymous	KIAA1199	NM_018689.1		127,1537,4839	CC,CT,TT		13.7326,13.8448,13.7706		628/1362	81212521	1791,11215	2203	4300	6503	SO:0001819	synonymous_variant	57214	exon14			CCACTGTCTTGGC																												ENST00000394685.3:c.1884T>C	15.37:g.81212521T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			T|0.844;C|0.156	0.156	strong		0.557	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
ZNF638	27332	hgsc.bcm.edu	37	2	71633275	71633275	+	Silent	SNP	T	T	C	rs3732233	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71633275T>C	ENST00000409544.1	+	19	3648	c.3018T>C	c.(3016-3018)atT>atC	p.I1006I	ZNF638_ENST00000355812.3_Silent_p.I1006I|ZNF638_ENST00000409407.1_5'Flank|ZNF638_ENST00000264447.4_Silent_p.I1006I	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1006					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TAGATACAATTTATGATCGAT	0.343													T|||	2065	0.41234	0.1649	0.6398	5008	,	,		18894	0.2927		0.5517	False		,,,				2504	0.5654				p.I1006I		Atlas-SNP	.											.	ZNF638	179	.	0			c.T3018C						PASS	.	T	,	1029,3377	377.8+/-322.6	108,813,1282	162.0	150.0	154.0		3018,3018	2.0	0.4	2	dbSNP_107	154	4972,3628	625.2+/-397.7	1432,2108,760	no	coding-synonymous,coding-synonymous	ZNF638	NM_001014972.1,NM_014497.3	,	1540,2921,2042	CC,CT,TT		42.186,23.3545,46.1402	,	1006/1979,1006/1979	71633275	6001,7005	2203	4300	6503	SO:0001819	synonymous_variant	27332	exon19			TACAATTTATGAT	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3018T>C	2.37:g.71633275T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	37	CCDS1917.1																																																																																			T|0.560;C|0.440	0.440	strong		0.343	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
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 GAIIx	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_ENST00000412512.2_Intron|KCNC4_ENST00000438661.2_Silent_p.G426G|KCNC4_ENST00000413138.3_Silent_p.G426G	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		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	81	42	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	
C9orf84	158401	hgsc.bcm.edu	37	9	114468966	114468966	+	Missense_Mutation	SNP	A	A	C	rs7036568	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:114468966A>C	ENST00000318737.4	-	18	2555	c.2427T>G	c.(2425-2427)aaT>aaG	p.N809K	C9orf84_ENST00000394779.3_Missense_Mutation_p.N770K|C9orf84_ENST00000394777.4_Missense_Mutation_p.N735K|C9orf84_ENST00000374287.3_Missense_Mutation_p.N809K	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	809			N -> K (in dbSNP:rs7036568).							breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						CAAATGAGAAATTACTCCAGG	0.358													C|||	1089	0.217452	0.3275	0.2205	5008	,	,		16153	0.0476		0.2475	False		,,,				2504	0.2106				p.N809K		Atlas-SNP	.											C9orf84_ENST00000374287,colon,carcinoma,0,2	C9orf84	207	2	0			c.T2427G						PASS	.	C	LYS/ASN,LYS/ASN	1478,2928	675.8+/-403.1	246,986,971	143.0	159.0	153.0		2310,2427	-3.9	0.1	9	dbSNP_116	153	2164,6434	712.1+/-405.9	264,1636,2399	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	94,94	510,2622,3370	CC,CA,AA		25.1686,33.5452,28.0068	benign,benign	770/1406,809/1445	114468966	3642,9362	2203	4299	6502	SO:0001583	missense	158401	exon18			TGAGAAATTACTC	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.2427T>G	9.37:g.114468966A>C	ENSP00000322108:p.Asn809Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	469	0.21474358974358973	168	0.34146341463414637	78	0.2154696132596685	33	0.057692307692307696	190	0.25065963060686014	C	0.082	-1.181676	0.01633	0.335452	0.251686	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.04156	3.69;3.7;3.7;3.7	4.84	-3.94	0.04130	.	1.009520	0.07955	N	0.981503	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.45877	-0.9231	9	0.02654	T	1	-0.0067	2.5329	0.04707	0.3654:0.196:0.3348:0.1039	rs7036568;rs57781556;rs7036568	735;809;770	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	K	770;735;423;809;809	ENSP00000378259:N770K;ENSP00000378257:N735K;ENSP00000363405:N809K;ENSP00000322108:N809K	ENSP00000322108:N809K	N	-	3	2	C9orf84	113508787	0.001000	0.12720	0.098000	0.21074	0.807000	0.45602	-0.190000	0.09615	-0.675000	0.05246	-1.740000	0.00687	AAT	A|0.750;C|0.250	0.250	strong		0.358	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
ADCK4	79934	hgsc.bcm.edu	37	19	41209477	41209477	+	Silent	SNP	C	C	T	rs11538385	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41209477C>T	ENST00000324464.3	-	9	1069	c.768G>A	c.(766-768)gcG>gcA	p.A256A	ADCK4_ENST00000243583.6_Silent_p.A215A|ADCK4_ENST00000450541.1_Silent_p.A215A	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	256	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			TCTTGAGTACCGCCAGCAGGT	0.622													C|||	1149	0.229433	0.084	0.196	5008	,	,		17506	0.2361		0.3032	False		,,,				2504	0.3671				p.A256A		Atlas-SNP	.											ADCK4_ENST00000324464,colon,carcinoma,-1,6	ADCK4	92	6	0			c.G768A						scavenged	.	C	,	543,3863	240.9+/-251.5	35,473,1695	55.0	57.0	56.0		645,768	-10.1	0.5	19	dbSNP_120	56	2474,6126	404.1+/-348.0	353,1768,2179	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	388,2241,3874	TT,TC,CC		28.7674,12.3241,23.197	,	215/504,256/545	41209477	3017,9989	2203	4300	6503	SO:0001819	synonymous_variant	79934	exon9			GAGTACCGCCAGC	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.768G>A	19.37:g.41209477C>T		Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_024876	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			C|0.773;T|0.227	0.227	strong		0.622	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
HCLS1	3059	hgsc.bcm.edu	37	3	121351338	121351338	+	Missense_Mutation	SNP	C	C	T	rs2070180	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:121351338C>T	ENST00000314583.3	-	12	1172	c.1081G>A	c.(1081-1083)Gaa>Aaa	p.E361K	HCLS1_ENST00000473883.1_5'UTR|HCLS1_ENST00000428394.2_Missense_Mutation_p.E324K	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	361			E -> K (in dbSNP:rs2070180).		actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		ggctcTGCTTCGTACACTGGC	0.592													C|||	733	0.146366	0.1271	0.1398	5008	,	,		13576	0.0913		0.2813	False		,,,				2504	0.0951				p.E361K		Atlas-SNP	.											.	HCLS1	78	.	0			c.G1081A						PASS	.	C	LYS/GLU	662,3744	280.2+/-275.2	49,564,1590	113.0	108.0	109.0		1081	4.1	0.9	3	dbSNP_96	109	2464,6136	404.2+/-348.1	369,1726,2205	yes	missense	HCLS1	NM_005335.4	56	418,2290,3795	TT,TC,CC		28.6512,15.025,24.0351	benign	361/487	121351338	3126,9880	2203	4300	6503	SO:0001583	missense	3059	exon12			CTGCTTCGTACAC		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.1081G>A	3.37:g.121351338C>T	ENSP00000320176:p.Glu361Lys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Missense_Mutation	SNP	ENST00000314583.3	37	CCDS3003.1	373	0.1707875457875458	63	0.12804878048780488	49	0.13535911602209943	54	0.0944055944055944	207	0.27308707124010556	C	9.453	1.090966	0.20471	0.15025	0.286512	ENSG00000180353	ENST00000314583;ENST00000428394	T;T	0.21031	2.03;2.03	5.06	4.14	0.48551	.	1.220880	0.05550	N	0.567392	T	0.00012	0.0000	L	0.46157	1.445	0.40396	P	0.02041000000000004	P;P	0.49635	0.926;0.926	B;B	0.31946	0.138;0.138	T	0.31447	-0.9943	9	0.37606	T	0.19	-27.1314	11.5842	0.50908	0.0:0.8212:0.1788:0.0	rs2070180;rs3184687;rs57559761;rs2070180	324;361	E7EVW7;P14317	.;HCLS1_HUMAN	K	361;324	ENSP00000320176:E361K;ENSP00000387645:E324K	ENSP00000320176:E361K	E	-	1	0	HCLS1	122834028	0.998000	0.40836	0.919000	0.36401	0.042000	0.13812	1.511000	0.35801	2.638000	0.89438	0.655000	0.94253	GAA	C|0.798;T|0.202	0.202	strong		0.592	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	
ST14	6768	hgsc.bcm.edu	37	11	130068491	130068491	+	Silent	SNP	G	G	C	rs11827924	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:130068491G>C	ENST00000278742.5	+	14	2077	c.1659G>C	c.(1657-1659)ggG>ggC	p.G553G		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	553	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	GTGGGGACGGGTCCGACGAGG	0.657													g|||	589	0.117612	0.1029	0.0749	5008	,	,		13855	0.1974		0.1133	False		,,,				2504	0.09				p.G553G		Atlas-SNP	.											ST14,NS,malignant_melanoma,+1,1	ST14	82	1	0			c.G1659C						PASS	.			480,3922	222.0+/-238.9	26,428,1747	46.0	47.0	47.0		1659	-3.3	0.6	11	dbSNP_120	47	1206,7388	241.7+/-271.9	85,1036,3176	no	coding-synonymous	ST14	NM_021978.3		111,1464,4923	CC,CG,GG		14.033,10.9041,12.9732		553/856	130068491	1686,11310	2201	4297	6498	SO:0001819	synonymous_variant	6768	exon14			GGACGGGTCCGAC	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.1659G>C	11.37:g.130068491G>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	168	37	0.220238	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	CCDS8487.1																																																																																			G|0.868;C|0.132	0.132	strong		0.657	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
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 GAIIx	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		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	151	85	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	
KCNS1	3787	hgsc.bcm.edu	37	20	43723627	43723627	+	Missense_Mutation	SNP	T	T	C	rs734784	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:43723627T>C	ENST00000306117.1	-	5	1861	c.1465A>G	c.(1465-1467)Att>Gtt	p.I489V	KCNS1_ENST00000537075.1_Missense_Mutation_p.I489V	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	489			I -> V (in dbSNP:rs734784). {ECO:0000269|PubMed:15489334}.		potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)	p.I489V(1)		endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				ACCCCATCAATGCTGCTCAGC	0.577													C|||	2036	0.40655	0.6203	0.3833	5008	,	,		19952	0.2143		0.4642	False		,,,				2504	0.273				p.I489V		Atlas-SNP	.											KCNS1,NS,carcinoma,0,1	KCNS1	30	1	1	Substitution - Missense(1)	stomach(1)	c.A1465G						PASS	.	C	VAL/ILE	2490,1916	548.7+/-377.6	685,1120,398	115.0	120.0	118.0		1465	0.3	0.0	20	dbSNP_86	118	3866,4734	608.4+/-395.4	855,2156,1289	yes	missense	KCNS1	NM_002251.3	29	1540,3276,1687	CC,CT,TT		44.9535,43.4862,48.8698	benign	489/527	43723627	6356,6650	2203	4300	6503	SO:0001583	missense	3787	exon5			CATCAATGCTGCT	AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.1465A>G	20.37:g.43723627T>C	ENSP00000307694:p.Ile489Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	64	35	0.546875	NM_002251	A2RUL9|B7ZM31|O43652|Q6DJU6	Missense_Mutation	SNP	ENST00000306117.1	37	CCDS13342.1	867	0.39697802197802196	290	0.5894308943089431	132	0.36464088397790057	105	0.18356643356643357	340	0.44854881266490765	C	1.535	-0.543409	0.04053	0.565138	0.449535	ENSG00000124134	ENST00000306117;ENST00000537075	D;D	0.96073	-3.9;-3.9	5.57	0.293	0.15742	.	0.706306	0.12780	N	0.439721	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23476	-1.0187	9	0.02654	T	1	.	6.1247	0.20172	0.0:0.4232:0.1263:0.4505	rs734784;rs52800490;rs56536526;rs56916043;rs734784	489	Q96KK3	KCNS1_HUMAN	V	489	ENSP00000307694:I489V;ENSP00000445595:I489V	ENSP00000307694:I489V	I	-	1	0	KCNS1	43157041	0.000000	0.05858	0.005000	0.12908	0.307000	0.27823	-0.710000	0.05024	-0.404000	0.07610	-0.974000	0.02594	ATT	T|0.555;C|0.445	0.445	strong		0.577	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080507.3	NM_002251	
SPHKAP	80309	hgsc.bcm.edu	37	2	228886457	228886457	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:228886457C>T	ENST00000392056.3	-	6	713	c.667G>A	c.(667-669)Gag>Aag	p.E223K	SPHKAP_ENST00000344657.5_Missense_Mutation_p.E223K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	223						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.E223K(2)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCGCTTTCCTCCTCCAAGTGC	0.448																																					p.E223K		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,malignant_melanoma,0,2	SPHKAP	750	2	2	Substitution - Missense(2)	NS(2)	c.G667A						scavenged	.						96.0	96.0	96.0					2																	228886457		2203	4300	6503	SO:0001583	missense	80309	exon6			TTTCCTCCTCCAA		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.667G>A	2.37:g.228886457C>T	ENSP00000375909:p.Glu223Lys	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	143	4	0.027972	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.795945	0.90453	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.23147	1.92;1.94	5.79	5.79	0.91817	.	0.203379	0.51477	D	0.000098	T	0.51329	0.1668	M	0.71581	2.175	0.58432	D	0.999996	D;D	0.67145	0.995;0.996	P;D	0.65140	0.738;0.932	T	0.50816	-0.8783	10	0.87932	D	0	.	19.0195	0.92908	0.0:1.0:0.0:0.0	.	223;223	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	K	223	ENSP00000375909:E223K;ENSP00000339886:E223K	ENSP00000339886:E223K	E	-	1	0	SPHKAP	228594701	1.000000	0.71417	1.000000	0.80357	0.601000	0.36947	7.194000	0.77789	2.746000	0.94184	0.655000	0.94253	GAG	.	.	none		0.448	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
SERPINB6	5269	hgsc.bcm.edu	37	6	2955802	2955802	+	Missense_Mutation	SNP	T	T	C	rs2295769	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:2955802T>C	ENST00000380520.1	-	2	2262	c.268A>G	c.(268-270)Atg>Gtg	p.M90V	SERPINB6_ENST00000335686.5_Missense_Mutation_p.M90V|SERPINB6_ENST00000380539.1_Missense_Mutation_p.M90V|SERPINB6_ENST00000380546.3_Missense_Mutation_p.M90V|SERPINB6_ENST00000380529.1_Missense_Mutation_p.M90V|SERPINB6_ENST00000380524.1_Missense_Mutation_p.M90V			P35237	SPB6_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 6	90			M -> V (in dbSNP:rs2295769). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:8136380, ECO:0000269|PubMed:8415716}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|stomach(1)|upper_aerodigestive_tract(2)	17	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Drotrecogin alfa(DB00055)	CTGTTGGCCATCCTAAGCAAG	0.473													T|||	1066	0.212859	0.0295	0.2464	5008	,	,		18368	0.2728		0.2992	False		,,,				2504	0.2863				p.M109V		Atlas-SNP	.											.	SERPINB6	31	.	0			c.A325G						PASS	.	T	VAL/MET,VAL/MET	291,4115	158.5+/-191.2	13,265,1925	84.0	82.0	82.0		268,268	3.8	0.0	6	dbSNP_100	82	2574,6026	418.3+/-352.7	364,1846,2090	yes	missense,missense	SERPINB6	NM_001195291.1,NM_004568.5	21,21	377,2111,4015	CC,CT,TT		29.9302,6.6046,22.0283	benign,benign	90/377,90/377	2955802	2865,10141	2203	4300	6503	SO:0001583	missense	5269	exon3			TGGCCATCCTAAG	Z22658	CCDS4479.1, CCDS75386.1, CCDS75387.1	6p25.2	2014-02-18	2005-08-18		ENSG00000124570	ENSG00000124570		"""Serine (or cysteine) peptidase inhibitors"""	8950	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase"""	173321	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 6"", ""deafness, autosomal recessive 91"""	PI6, DFNB91		8415716, 9858835, 20451170, 24172014	Standard	NM_004568		Approved	PTI, CAP	uc031smo.1	P35237	OTTHUMG00000016170	ENST00000380520.1:c.268A>G	6.37:g.2955802T>C	ENSP00000369891:p.Met90Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	67	51	0.761194	NM_001271823	B2RBA8|Q59F97|Q5TD06|Q7Z2Y7|Q96J44|Q9UDI7	Missense_Mutation	SNP	ENST00000380520.1	37	CCDS4479.1	524	0.23992673992673993	17	0.034552845528455285	87	0.24033149171270718	178	0.3111888111888112	242	0.31926121372031663	T	1.306	-0.603400	0.03744	0.066046	0.299302	ENSG00000124570	ENST00000380524;ENST00000380520;ENST00000335686;ENST00000380529;ENST00000380539;ENST00000380546;ENST00000440670	D;D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79;-1.79	4.97	3.8	0.43715	Serpin domain (3);	0.484707	0.24251	N	0.040170	T	0.38081	0.1027	N	0.04768	-0.165	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.10291	-1.0636	9	0.02654	T	1	.	9.206	0.37289	0.0:0.0889:0.0:0.9111	rs2295769;rs17233203;rs17856048;rs52804912;rs61064774;rs2295769	90	P35237	SPB6_HUMAN	V	90	ENSP00000369896:M90V;ENSP00000369891:M90V;ENSP00000338358:M90V;ENSP00000369901:M90V;ENSP00000369912:M90V;ENSP00000369919:M90V	ENSP00000338358:M90V	M	-	1	0	SERPINB6	2900801	0.032000	0.19561	0.002000	0.10522	0.284000	0.27059	2.224000	0.42945	0.984000	0.38629	0.459000	0.35465	ATG	C|0.227;N|0.000	0.227	strong		0.473	SERPINB6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043422.1		
C1orf85	112770	hgsc.bcm.edu	37	1	156263940	156263940	+	Missense_Mutation	SNP	T	T	C	rs10908495	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156263940T>C	ENST00000362007.1	-	4	693	c.667A>G	c.(667-669)Att>Gtt	p.I223V	C1orf85_ENST00000482579.1_5'Flank	NM_001256604.1|NM_001256609.1|NM_144580.2	NP_001243533.1|NP_001243538.1|NP_653181.1	Q8WWB7	NCUG1_HUMAN	chromosome 1 open reading frame 85	223			I -> V (in dbSNP:rs10908495). {ECO:0000269|PubMed:15489334}.		intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(2)|skin(3)	14	Hepatocellular(266;0.158)					GAGGCTCCAATCAGGGCCACC	0.627													C|||	1034	0.20647	0.0923	0.2795	5008	,	,		18007	0.2272		0.2694	False		,,,				2504	0.2229				p.I223V		Atlas-SNP	.											.	C1orf85	41	.	0			c.A667G						PASS	.	C	VAL/ILE	544,3862	774.6+/-414.0	33,478,1692	57.0	58.0	58.0		667	2.5	0.9	1	dbSNP_120	58	2522,6078	693.0+/-404.6	385,1752,2163	yes	missense	C1orf85	NM_144580.1	29	418,2230,3855	CC,CT,TT		29.3256,12.3468,23.5737	benign	223/407	156263940	3066,9940	2203	4300	6503	SO:0001583	missense	112770	exon4			CTCCAATCAGGGC	BC011575	CCDS1139.1, CCDS72947.1, CCDS72948.1, CCDS72949.1	1q22	2014-08-07			ENSG00000198715	ENSG00000198715			29436	protein-coding gene	gene with protein product	"""kidney lysosomal membrane protein"""					12975309, 18021396, 19489740	Standard	NM_144580		Approved	MGC31963, NCU-G1	uc001foh.4	Q8WWB7	OTTHUMG00000019789	ENST00000362007.1:c.667A>G	1.37:g.156263940T>C	ENSP00000354553:p.Ile223Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_001256608	A6NH16|B4DJN4|Q5SZX4|Q6UX96|Q8IV07|Q96F65	Missense_Mutation	SNP	ENST00000362007.1	37	CCDS1139.1	468	0.21428571428571427	46	0.09349593495934959	82	0.2265193370165746	135	0.23601398601398602	205	0.2704485488126649	C	0.703	-0.790072	0.02884	0.123468	0.293256	ENSG00000198715	ENST00000362007;ENST00000368264	T;T	0.20598	2.06;2.06	5.53	2.5	0.30297	.	0.633137	0.15407	N	0.263993	T	0.01124	0.0037	N	0.00246	-1.78	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47275	-0.9130	9	0.14656	T	0.56	-15.783	6.1842	0.20488	0.2601:0.5935:0.0:0.1463	rs10908495;rs59165206;rs10908495	142;223	Q8WWB7-2;Q8WWB7	.;NCUG1_HUMAN	V	223;137	ENSP00000354553:I223V;ENSP00000357247:I137V	ENSP00000354553:I223V	I	-	1	0	C1orf85	154530564	0.004000	0.15560	0.917000	0.36280	0.600000	0.36913	-0.073000	0.11468	0.301000	0.22738	-0.355000	0.07637	ATT	T|0.785;C|0.215	0.215	strong		0.627	C1orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052108.1	NM_144580	
RNF43	54894	hgsc.bcm.edu	37	17	56448297	56448297	+	Missense_Mutation	SNP	C	C	T	rs2257205	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:56448297C>T	ENST00000584437.1	-	2	2305	c.350G>A	c.(349-351)cGc>cAc	p.R117H	RNF43_ENST00000577625.1_5'UTR|RNF43_ENST00000500597.2_Intron|RNF43_ENST00000583753.1_Intron|RNF43_ENST00000581868.1_5'UTR|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000407977.2_Missense_Mutation_p.R117H|RNF43_ENST00000577716.1_Missense_Mutation_p.R117H			Q68DV7	RNF43_HUMAN	ring finger protein 43	117			R -> H (in dbSNP:rs2257205).		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CAGGCAGGGGCGGGGGGCCCG	0.602													C|||	1133	0.226238	0.1831	0.1009	5008	,	,		15835	0.373		0.1163	False		,,,				2504	0.3354				p.R117H		Atlas-SNP	.											.	RNF43	157	.	0			c.G350A						PASS	.	C	HIS/ARG	816,3590	315.5+/-294.2	78,660,1465	53.0	49.0	51.0	http://www.ncbi.nlm.nih.gov/pubmed?term	350	5.4	1.0	17	dbSNP_100	51	936,7664	201.1+/-244.7	56,824,3420	yes	missense	RNF43	NM_017763.4	29	134,1484,4885	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	10.8837,18.5202,13.4707	probably-damaging	117/784	56448297	1752,11254	2203	4300	6503	SO:0001583	missense	54894	exon3			CAGGGGCGGGGGG		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.350G>A	17.37:g.56448297C>T	ENSP00000463069:p.Arg117His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	418	0.19139194139194138	90	0.18292682926829268	39	0.10773480662983426	198	0.34615384615384615	91	0.12005277044854881	C	19.62	3.862560	0.71949	0.185202	0.108837	ENSG00000108375	ENST00000407977	T	0.44881	0.91	5.45	5.45	0.79879	.	0.368624	0.26753	N	0.022674	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.9999999999999997	D	0.89917	1.0	P	0.62435	0.902	T	0.34976	-0.9807	9	0.87932	D	0	-4.475	7.9904	0.30237	0.0:0.8262:0.0:0.1738	rs2257205;rs59777215;rs2257205	117	Q68DV7	RNF43_HUMAN	H	117	ENSP00000385328:R117H	ENSP00000385328:R117H	R	-	2	0	RNF43	53803296	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.818000	0.48041	2.555000	0.86185	0.655000	0.94253	CGC	C|0.838;T|0.162	0.162	strong		0.602	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
COX18	285521	hgsc.bcm.edu	37	4	73930552	73930552	+	Silent	SNP	G	G	A	rs3762883	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:73930552G>A	ENST00000295890.4	-	4	754	c.663C>T	c.(661-663)ccC>ccT	p.P221P	COX18_ENST00000507544.2_Silent_p.P222P	NM_173827.2	NP_776188.1	Q8N8Q8	COX18_HUMAN	COX18 cytochrome C oxidase assembly factor	221					protein insertion into mitochondrial membrane (GO:0051204)|protein transport (GO:0015031)|respiratory chain complex IV assembly (GO:0008535)	integral component of mitochondrial inner membrane (GO:0031305)	protein transporter activity (GO:0008565)			large_intestine(4)|lung(2)	6	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAGTGGAGTCGGGTGCAGTGA	0.383													c|||	1710	0.341454	0.1891	0.2983	5008	,	,		17295	0.3879		0.4563	False		,,,				2504	0.4121				p.P221P		Atlas-SNP	.											.	COX18	20	.	0			c.C663T						PASS	.	T		1055,3351		146,763,1294	77.0	76.0	77.0		663	0.5	0.3	4	dbSNP_107	77	3677,4923		774,2129,1397	no	coding-synonymous	COX18	NM_173827.2		920,2892,2691	AA,AG,GG		42.7558,23.9446,36.3832		221/334	73930552	4732,8274	2203	4300	6503	SO:0001819	synonymous_variant	285521	exon4			GGAGTCGGGTGCA	AY957564	CCDS3554.1, CCDS75139.1	4q13.3	2013-06-12	2013-06-12		ENSG00000163626	ENSG00000163626		"""Mitochondrial respiratory chain complex assembly factors"""	26801	protein-coding gene	gene with protein product		610428	"""COX18 cytochrome c oxidase assembly homolog (S. cerevisiae)"", ""cytochrome c oxidase assembly homolog 18 (yeast)"""			16212937, 16911509	Standard	XM_005265679		Approved	FLJ38991	uc003hgm.1	Q8N8Q8	OTTHUMG00000129917	ENST00000295890.4:c.663C>T	4.37:g.73930552G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	153	80	0.522876	NM_173827	Q2PB66|Q2PB67|Q2PB68|Q49B97|Q6IPP9	Silent	SNP	ENST00000295890.4	37	CCDS3554.1																																																																																			G|0.650;C|0.000;A|0.350	0.350	strong		0.383	COX18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252169.2	NM_173827	
OR13J1	392309	hgsc.bcm.edu	37	9	35870225	35870225	+	Silent	SNP	G	G	A	rs72727089	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:35870225G>A	ENST00000377981.2	-	1	236	c.174C>T	c.(172-174)ccC>ccT	p.P58P		NM_001004487.1	NP_001004487.1	Q8NGT2	O13J1_HUMAN	olfactory receptor, family 13, subfamily J, member 1	58						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_epithelial(49;0.169)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00494)|STAD - Stomach adenocarcinoma(86;0.194)			AGAAGTACACGGGCGTGTGCA	0.582													G|||	890	0.177716	0.0272	0.2608	5008	,	,		22168	0.0804		0.3091	False		,,,				2504	0.2873				p.P58P		Atlas-SNP	.											.	OR13J1	37	.	0			c.C174T						PASS	.	G		330,4076	173.4+/-203.2	12,306,1885	119.0	105.0	110.0		174	4.8	1.0	9	dbSNP_130	110	2665,5935	428.6+/-355.9	411,1843,2046	no	coding-synonymous	OR13J1	NM_001004487.1		423,2149,3931	AA,AG,GG		30.9884,7.4898,23.0278		58/313	35870225	2995,10011	2203	4300	6503	SO:0001819	synonymous_variant	392309	exon1			GTACACGGGCGTG		CCDS35011.1	9p13.3	2013-09-24			ENSG00000168828	ENSG00000168828		"""GPCR / Class A : Olfactory receptors"""	15108	protein-coding gene	gene with protein product							Standard	NM_001004487		Approved		uc011lph.2	Q8NGT2	OTTHUMG00000019879	ENST00000377981.2:c.174C>T	9.37:g.35870225G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	103	58	0.563107	NM_001004487	B2RN66|Q6IF20|Q96R40	Silent	SNP	ENST00000377981.2	37	CCDS35011.1																																																																																			G|0.779;A|0.221	0.221	strong		0.582	OR13J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052381.1		
TET2	54790	hgsc.bcm.edu	37	4	106196951	106196951	+	Missense_Mutation	SNP	A	A	G	rs2454206	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106196951A>G	ENST00000540549.1	+	11	6144	c.5284A>G	c.(5284-5286)Ata>Gta	p.I1762V	TET2_ENST00000513237.1_Missense_Mutation_p.I1783V|TET2_ENST00000380013.4_Missense_Mutation_p.I1762V|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1762			I -> V (in dbSNP:rs2454206). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19483684}.		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.I1762fs*3(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)		ACCTTCTCACATAATCCATAA	0.458			"""Mis N, F"""		MDS								A|||	1154	0.230431	0.0658	0.2795	5008	,	,		23352	0.1895		0.3718	False		,,,				2504	0.3149				p.I1762V		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.A5284G						PASS	.	A	VAL/ILE	124,1260		11,102,579	19.0	16.0	17.0		5284	-10.3	0.0	4	dbSNP_100	17	1188,1994		223,742,626	yes	missense	TET2	NM_001127208.2	29	234,844,1205	GG,GA,AA		37.335,8.9595,28.7341	benign	1762/2003	106196951	1312,3254	692	1591	2283	SO:0001583	missense	54790	exon11			TCTCACATAATCC	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.5284A>G	4.37:g.106196951A>G	ENSP00000442788:p.Ile1762Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	31	0.607843	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	526	0.24084249084249085	33	0.06707317073170732	92	0.2541436464088398	107	0.18706293706293706	294	0.38786279683377306	A	8.920	0.960733	0.18583	0.089595	0.37335	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.01963	4.53;4.53;4.53	5.16	-10.3	0.00346	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.58432	P	1.0000000000287557E-6	B;B	0.15141	0.001;0.012	B;B	0.19666	0.001;0.026	T	0.48340	-0.9044	8	0.13853	T	0.58	0.7576	3.9686	0.09443	0.1159:0.4443:0.2131:0.2267	rs2454206;rs52829850;rs58031039;rs2454206	1783;1762	E7EQS8;Q6N021	.;TET2_HUMAN	V	1762;1783;1762	ENSP00000442788:I1762V;ENSP00000425443:I1783V;ENSP00000369351:I1762V	ENSP00000369351:I1762V	I	+	1	0	TET2	106416400	0.000000	0.05858	0.000000	0.03702	0.738000	0.42128	-0.301000	0.08232	-1.622000	0.01560	-0.456000	0.05471	ATA	A|0.768;G|0.232	0.232	strong		0.458	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
FCGR3A	2214	hgsc.bcm.edu	37	1	161599693	161599693	+	Intron	SNP	T	T	C	rs448740	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161599693T>C	ENST00000540048.1	-	2	94				FCGR2B_ENST00000403078.3_Intron|FCGR2B_ENST00000367962.4_Intron|FCGR2B_ENST00000428605.2_Intron|FCGR3B_ENST00000367964.2_Missense_Mutation_p.N65S|FCGR2B_ENST00000367960.5_Intron|FCGR3B_ENST00000294800.3_Missense_Mutation_p.N65S|FCGR3B_ENST00000531221.1_Missense_Mutation_p.N101S			P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)						Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TGAGATGAGGTTCTCATTGTG	0.537													C|||	2669	0.532947	0.5628	0.4827	5008	,	,		9553	0.3383		0.664	False		,,,				2504	0.5941				p.N101S		Atlas-SNP	.											.	FCGR3B	35	.	0			c.A302G						PASS	.						70.0	67.0	68.0					1																	161599693		2161	4291	6452	SO:0001627	intron_variant	2215	exon3			ATGAGGTTCTCAT	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000540048.1:c.61+464A>G	1.37:g.161599693T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	101	96	0.950495	NM_001244753	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000540048.1	37		.	.	.	.	.	.	.	.	.	.	C	0.077	-1.191278	0.01607	.	.	ENSG00000162747	ENST00000367964;ENST00000294800;ENST00000531221;ENST00000534776	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	2.79	-2.58	0.06228	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.45542	-0.9254	5	0.05833	T	0.94	.	5.2778	0.15659	0.0:0.2748:0.481:0.2442	.	.	.	.	S	65;65;101;48	ENSP00000356941:N65S;ENSP00000294800:N65S;ENSP00000433642:N101S;ENSP00000437084:N48S	ENSP00000294800:N65S	N	-	2	0	FCGR3B	159866317	0.000000	0.05858	0.000000	0.03702	0.202000	0.24057	-4.948000	0.00167	-0.657000	0.05373	-0.631000	0.03989	AAC	T|0.338;C|0.662	0.662	strong		0.537	FCGR3A-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_000569	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084048	31084048	+	Intron	SNP	A	A	G	rs3094216	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31084048A>G	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Silent_p.C448C|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						ACTTGCTGCCACAAGGCTGAA	0.617													A|||	940	0.1877	0.2065	0.1527	5008	,	,		18491	0.1637		0.1879	False		,,,				2504	0.2117				p.C448C		Atlas-SNP	.											.	CDSN	48	.	0			c.T1344C						PASS	.	A	,	996,3410	370.3+/-319.5	95,806,1302	40.0	41.0	40.0		1344,	-3.1	1.0	6	dbSNP_103	40	1931,6669	339.9+/-323.4	227,1477,2596	yes	coding-synonymous,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	,	322,2283,3898	GG,GA,AA		22.4535,22.6055,22.505	,	448/530,	31084048	2927,10079	2203	4300	6503	SO:0001627	intron_variant	1041	exon2			GCTGCCACAAGGC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+1380A>G	6.37:g.31084048A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	107	83	0.775701	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																			A|0.790;G|0.210	0.210	strong		0.617	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
KCNJ15	3772	hgsc.bcm.edu	37	21	39671476	39671476	+	Missense_Mutation	SNP	G	G	A	rs2230033	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:39671476G>A	ENST00000328656.4	+	4	596	c.293G>A	c.(292-294)gGt>gAt	p.G98D	KCNJ15_ENST00000398930.1_Missense_Mutation_p.G98D|KCNJ15_ENST00000398932.1_Missense_Mutation_p.G98D|KCNJ15_ENST00000398934.1_Missense_Mutation_p.G98D|KCNJ15_ENST00000398938.2_Missense_Mutation_p.G98D	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	98			G -> D (in dbSNP:rs2230033). {ECO:0000269|PubMed:8995301, ECO:0000269|Ref.3}.		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)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	TTAGAACCCGGTGAGCCCATT	0.483													G|||	1446	0.288738	0.0363	0.4625	5008	,	,		20529	0.253		0.497	False		,,,				2504	0.3292				p.L98X		Atlas-SNP	.											KCNJ15,colon,carcinoma,+1,1	KCNJ15	43	1	0			c.T293A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY	533,3873	244.7+/-253.9	32,469,1702	118.0	117.0	117.0		293,293,293	4.2	0.0	21	dbSNP_98	117	4707,3893	606.8+/-395.1	1302,2103,895	yes	missense,missense,missense	KCNJ15	NM_002243.3,NM_170736.1,NM_170737.1	94,94,94	1334,2572,2597	AA,AG,GG		45.2674,12.0971,40.2891	benign,benign,benign	98/376,98/376,98/376	39671476	5240,7766	2203	4300	6503	SO:0001583	missense	3772	exon3			AACCCGGTGAGCC	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.293G>A	21.37:g.39671476G>A	ENSP00000331698:p.Gly98Asp	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	173	62	0.358382	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Nonsense_Mutation	SNP	ENST00000328656.4	37	CCDS13656.1	727	0.33287545787545786	25	0.0508130081300813	167	0.4613259668508287	159	0.27797202797202797	376	0.49604221635883905	G	0.011	-1.728508	0.00694	0.120971	0.547326	ENSG00000157551	ENST00000328656;ENST00000398928;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934;ENST00000398927;ENST00000419868	D;D;D;D;D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27;-3.27	5.13	4.22	0.49857	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.593826	0.15252	U	0.272284	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B	0.23891	0.093	B	0.27380	0.079	T	0.42865	-0.9426	8	.	.	.	.	2.9987	0.06007	0.1131:0.1737:0.5343:0.1789	rs2230033;rs3746877;rs61521838;rs2230033	98	Q99712	IRK15_HUMAN	D	98	ENSP00000331698:G98D;ENSP00000381902:G98D;ENSP00000381911:G98D;ENSP00000381905:G98D;ENSP00000414487:G98D;ENSP00000381904:G98D;ENSP00000381907:G98D;ENSP00000381901:G98D;ENSP00000400849:G98D	.	G	+	2	0	KCNJ15	38593346	0.001000	0.12720	0.005000	0.12908	0.019000	0.09904	1.174000	0.31932	1.249000	0.43950	0.655000	0.94253	GGT	G|0.642;A|0.358	0.358	strong		0.483	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
NPY	4852	hgsc.bcm.edu	37	7	24325009	24325009	+	Silent	SNP	G	G	A	rs5573	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:24325009G>A	ENST00000407573.1	+	3	440	c.150G>A	c.(148-150)tcG>tcA	p.S50S	NPY_ENST00000242152.2_Silent_p.S50S|NPY_ENST00000405982.1_Silent_p.S50S			P01303	NPY_HUMAN	neuropeptide Y	50					adult feeding behavior (GO:0008343)|behavior (GO:0007610)|blood circulation (GO:0008015)|calcium ion transport (GO:0006816)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|positive regulation of appetite (GO:0032100)|regulation of blood pressure (GO:0008217)|synaptic transmission (GO:0007268)	cell (GO:0005623)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			breast(1)|kidney(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	9						GATACTACTCGGCGCTGCGAC	0.677													G|||	2574	0.513978	0.3555	0.6643	5008	,	,		16319	0.6379		0.507	False		,,,				2504	0.501				p.S50S		Atlas-SNP	.											NPY,colon,carcinoma,0,1	NPY	25	1	0			c.G150A						PASS	.	G		1644,2762	501.0+/-364.9	315,1014,874	75.0	55.0	62.0		150	-8.2	0.4	7	dbSNP_52	62	4301,4299	574.9+/-390.1	1052,2197,1051	no	coding-synonymous	NPY	NM_000905.3		1367,3211,1925	AA,AG,GG		49.9884,37.3128,45.7097		50/98	24325009	5945,7061	2203	4300	6503	SO:0001819	synonymous_variant	4852	exon2			CTACTCGGCGCTG	K01911	CCDS5387.1	7p15.3	2013-02-26			ENSG00000122585	ENSG00000122585		"""Endogenous ligands"""	7955	protein-coding gene	gene with protein product	"""prepro-neuropeptide Y"""	162640					Standard	NM_000905		Approved	PYY4	uc003sww.2	P01303	OTTHUMG00000022973	ENST00000407573.1:c.150G>A	7.37:g.24325009G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	37	11	0.297297	NM_000905		Silent	SNP	ENST00000407573.1	37	CCDS5387.1																																																																																			A|0.483;C|0.000;G|0.517;T|0.000	0.483	strong		0.677	NPY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326748.1	NM_000905	
VWA3B	200403	hgsc.bcm.edu	37	2	98709684	98709684	+	Silent	SNP	T	T	C	rs298917	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:98709684T>C	ENST00000477737.1	+	2	333	c.129T>C	c.(127-129)caT>caC	p.H43H	VWA3B_ENST00000451075.2_5'UTR|VWA3B_ENST00000435344.1_Silent_p.H43H	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	43										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TTCAACTGCATGGGCTTAAGA	0.458													T|||	535	0.106829	0.0877	0.1427	5008	,	,		17580	0.0407		0.1938	False		,,,				2504	0.0859				p.H43H		Atlas-SNP	.											.	VWA3B	138	.	0			c.T129C						PASS	.	T		380,3546		24,332,1607	126.0	117.0	120.0		129	-1.3	0.9	2	dbSNP_79	120	1680,6646		174,1332,2657	no	coding-synonymous	VWA3B	NM_144992.4		198,1664,4264	CC,CT,TT		20.1778,9.6791,16.8136		43/1295	98709684	2060,10192	1963	4163	6126	SO:0001819	synonymous_variant	200403	exon2			ACTGCATGGGCTT	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.129T>C	2.37:g.98709684T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	182	92	0.505495	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	37	CCDS42718.1																																																																																			T|0.871;C|0.129	0.129	strong		0.458	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
ALG1	56052	hgsc.bcm.edu	37	16	5128857	5128857	+	Silent	SNP	G	G	C	rs12921879	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:5128857G>C	ENST00000262374.5	+	7	871	c.840G>C	c.(838-840)ctG>ctC	p.L280L	ALG1_ENST00000544428.1_Silent_p.L169L|ALG1_ENST00000588623.1_Silent_p.L169L	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	280					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				CAGCCCTGCTGGTCAGCAGCA	0.677													G|||	151	0.0301518	0.0439	0.0461	5008	,	,		15833	0.0		0.0517	False		,,,				2504	0.0092				p.L280L		Atlas-SNP	.											.	ALG1	35	.	0			c.G840C						PASS	.	G		217,4167		3,211,1978	19.0	19.0	19.0		840	4.3	1.0	16	dbSNP_121	19	492,8090		10,472,3809	no	coding-synonymous	ALG1	NM_019109.4		13,683,5787	CC,CG,GG		5.7329,4.9498,5.4681		280/465	5128857	709,12257	2192	4291	6483	SO:0001819	synonymous_variant	56052	exon7			CCTGCTGGTCAGC	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.840G>C	16.37:g.5128857G>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	161	60	0.372671	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Silent	SNP	ENST00000262374.5	37	CCDS10528.1																																																																																			G|0.949;C|0.051	0.051	strong		0.677	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
CARD9	64170	hgsc.bcm.edu	37	9	139270876	139270876	+	5'Flank	SNP	G	G	A	rs3812561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139270876G>A	ENST00000371732.5	-	0	0				CARD9_ENST00000371734.3_5'Flank|SNAPC4_ENST00000298532.2_Missense_Mutation_p.P1448S|CARD9_ENST00000315908.7_5'Flank	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9						defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		AGGTCGTCAGGGTCATTAGAA	0.607													G|||	336	0.0670927	0.059	0.0101	5008	,	,		20839	0.1349		0.0378	False		,,,				2504	0.0787				p.P1448S		Atlas-SNP	.											.	SNAPC4	82	.	0			c.C4342T						PASS	.	G	SER/PRO	222,4184	134.1+/-170.4	10,202,1991	148.0	141.0	144.0		4342	1.8	0.0	9	dbSNP_107	144	270,8330	104.2+/-165.2	2,266,4032	yes	missense	SNAPC4	NM_003086.2	74	12,468,6023	AA,AG,GG		3.1395,5.0386,3.7829	benign	1448/1470	139270876	492,12514	2203	4300	6503	SO:0001631	upstream_gene_variant	6621	exon22			CGTCAGGGTCATT	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925		9.37:g.139270876G>A	Exception_encountered	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_003086	Q5SXM5|Q5SXM6|Q9H854	Missense_Mutation	SNP	ENST00000371732.5	37	CCDS6997.1	128	0.05860805860805861	35	0.07113821138211382	6	0.016574585635359115	59	0.10314685314685315	28	0.036939313984168866	G	0.444	-0.897316	0.02472	0.050386	0.031395	ENSG00000165684	ENST00000298532	T	0.19532	2.14	3.69	1.84	0.25277	.	2.601350	0.02054	N	0.050278	T	0.00328	0.0010	N	0.08118	0	0.80722	P	0.0	B	0.17268	0.021	B	0.15052	0.012	T	0.20672	-1.0268	9	0.48119	T	0.1	.	5.7239	0.18002	0.2536:0.0:0.7464:0.0	rs3812561;rs58033950;rs3812561	1448	Q5SXM2	SNPC4_HUMAN	S	1448	ENSP00000298532:P1448S	ENSP00000298532:P1448S	P	-	1	0	SNAPC4	138390697	0.012000	0.17670	0.002000	0.10522	0.003000	0.03518	-0.673000	0.05239	0.262000	0.21774	0.511000	0.50034	CCT	G|0.949;A|0.051	0.051	strong		0.607	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
ICAM3	3385	hgsc.bcm.edu	37	19	10449358	10449358	+	Splice_Site	SNP	T	T	C	rs7258015	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10449358T>C	ENST00000160262.5	-	2	551	c.343A>G	c.(343-345)Agg>Ggg	p.R115G	ICAM3_ENST00000589261.1_Splice_Site_p.R38G	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	115			R -> G (in dbSNP:rs7258015). {ECO:0000269|PubMed:1448174, ECO:0000269|PubMed:8459213}.		extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			GTCGACTCACTGTACACGGTG	0.547													T|||	896	0.178914	0.1392	0.1744	5008	,	,		19949	0.1141		0.2356	False		,,,				2504	0.2444				p.R115G		Atlas-SNP	.											ICAM3,colon,carcinoma,0,1	ICAM3	29	1	0			c.A343G						scavenged	.	T	GLY/ARG	745,3661	304.1+/-288.3	56,633,1514	76.0	59.0	65.0		343	-11.5	0.0	19	dbSNP_116	65	1967,6633	344.9+/-325.5	238,1491,2571	yes	missense-near-splice	ICAM3	NM_002162.3	125	294,2124,4085	CC,CT,TT		22.8721,16.9088,20.8519	benign	115/548	10449358	2712,10294	2203	4300	6503	SO:0001630	splice_region_variant	3385	exon2			ACTCACTGTACAC		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.343+1A>G	19.37:g.10449358T>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_002162	Q6PD68	Missense_Mutation	SNP	ENST00000160262.5	37	CCDS12235.1	382	0.1749084249084249	58	0.11788617886178862	69	0.19060773480662985	70	0.12237762237762238	185	0.24406332453825857	T	12.32	1.901485	0.33535	0.169088	0.228721	ENSG00000076662	ENST00000160262	T	0.24350	1.86	5.75	-11.5	0.00074	Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal (1);Intercellular adhesion molecule, N-terminal (1);Immunoglobulin-like fold (1);	0.854576	0.10072	N	0.719602	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.20739	-1.0266	8	.	.	.	-3.8943	6.787	0.23679	0.0633:0.391:0.1209:0.4248	rs7258015;rs58067369;rs7258015	38;115	B7Z6W6;P32942	.;ICAM3_HUMAN	G	115	ENSP00000160262:R115G	.	R	-	1	2	ICAM3	10310358	0.022000	0.18835	0.001000	0.08648	0.172000	0.22775	-2.406000	0.01044	-2.000000	0.00965	-0.213000	0.12676	AGG	T|0.809;C|0.191	0.191	strong		0.547	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		Missense_Mutation
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 GAIIx	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	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	57	6	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 GAIIx	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		Somatic	385	0	0		WXS	Illumina HiSeq	Phase_I	290	206	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	
GRID2IP	392862	hgsc.bcm.edu	37	7	6591008	6591008	+	Silent	SNP	C	C	T	rs73059373	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6591008C>T	ENST00000457091.2	-	1	59	c.60G>A	c.(58-60)cgG>cgA	p.R20R		NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	20	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.		R -> Q (in dbSNP:rs11761490).		long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						AGCCACCTAGCCGGAAGCCAA	0.652													C|||	778	0.155351	0.3812	0.1081	5008	,	,		11775	0.0526		0.0736	False		,,,				2504	0.0736				p.R20R		Atlas-SNP	.											GRID2IP_ENST00000457091,NS,carcinoma,0,2	GRID2IP	82	2	0			c.G60A						PASS	.						7.0	9.0	9.0					7																	6591008		687	1585	2272	SO:0001819	synonymous_variant	392862	exon1			ACCTAGCCGGAAG		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.60G>A	7.37:g.6591008C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	29	19	0.655172	NM_001145118		Silent	SNP	ENST00000457091.2	37	CCDS47537.1																																																																																			C|0.859;T|0.141	0.141	strong		0.652	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
PIDD1	55367	hgsc.bcm.edu	37	11	802379	802379	+	Missense_Mutation	SNP	T	T	C	rs10902221	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:802379T>C	ENST00000347755.5	-	6	1133	c.992A>G	c.(991-993)cAa>cGa	p.Q331R	PIDD_ENST00000411829.2_Missense_Mutation_p.Q331R|PIDD_ENST00000534649.1_5'Flank	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					TGAGCAGCCTTGAGGGGTCAC	0.637													C|||	1761	0.351637	0.2927	0.6354	5008	,	,		15748	0.2748		0.494	False		,,,				2504	0.1626				p.Q331R		Atlas-SNP	.											PIDD_ENST00000347755,NS,carcinoma,-1,1	PIDD	76	1	0			c.A992G						scavenged	.	C	ARG/GLN,ARG/GLN	1396,3008		217,962,1023	32.0	39.0	36.0		992,992	-3.7	0.4	11	dbSNP_120	36	4394,4200		1144,2106,1047	yes	missense,missense	PIDD	NM_145886.3,NM_145887.3	43,43	1361,3068,2070	CC,CT,TT		48.8713,31.6985,44.5453	benign,benign	331/911,331/894	802379	5790,7208	2202	4297	6499	SO:0001583	missense	55367	exon6			CAGCCTTGAGGGG																												ENST00000347755.5:c.992A>G	11.37:g.802379T>C	ENSP00000337797:p.Gln331Arg	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_145887		Missense_Mutation	SNP	ENST00000347755.5	37	CCDS7716.1	940	0.43040293040293043	150	0.3048780487804878	221	0.6104972375690608	185	0.32342657342657344	384	0.5065963060686016	C	3.101	-0.184843	0.06340	0.316985	0.511287	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.37915	1.26;1.17	4.02	-3.74	0.04385	ZU5 (1);	0.887930	0.09591	N	0.781494	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.40440	-0.9563	9	0.02654	T	1	.	8.8035	0.34923	0.1025:0.1046:0.0:0.7929	rs10902221;rs57449058;rs10902221	331;185;331	Q9HB75;Q9HB75-3;Q9HB75-2	PIDD_HUMAN;.;.	R	331	ENSP00000416801:Q331R;ENSP00000337797:Q331R	ENSP00000337797:Q331R	Q	-	2	0	PIDD	792379	0.024000	0.19004	0.422000	0.26621	0.170000	0.22686	-0.263000	0.08670	-1.566000	0.01673	-0.974000	0.02594	CAA	T|0.588;C|0.412	0.412	strong		0.637	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551915	32551915	+	Missense_Mutation	SNP	A	A	G	rs17424145	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32551915A>G	ENST00000360004.5	-	2	446	c.341T>C	c.(340-342)gTt>gCt	p.V114A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	114	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCTCTCCACAACCCCGTAGTT	0.647										Multiple Myeloma(14;0.17)			A|||	326	0.0650958	0.0794	0.0836	5008	,	,		5592	0.1012		0.0408	False		,,,				2504	0.0204				p.V114A		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.T341C						PASS	.	A	ALA/VAL	334,3970		47,240,1865	33.0	32.0	32.0		341	-0.8	0.0	6	dbSNP_123	32	312,8198		34,244,3977	no	missense	HLA-DRB1	NM_002124.3	64	81,484,5842	GG,GA,AA		3.6663,7.7602,5.0414		114/267	32551915	646,12168	2152	4255	6407	SO:0001583	missense	3123	exon2			TCCACAACCCCGT	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.341T>C	6.37:g.32551915A>G	ENSP00000353099:p.Val114Ala	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	13	6	0.461538	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	146	0.06684981684981685	44	0.08943089430894309	29	0.08011049723756906	45	0.07867132867132867	28	0.036939313984168866	.	9.369	1.070111	0.20147	0.077602	0.036663	ENSG00000196126	ENST00000360004	T	0.00358	7.88	3.45	-0.756	0.11057	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	4.550560	0.00559	N	0.000280	T	0.00109	0.0003	M	0.64260	1.97	0.80722	P	0.0	B	0.02656	0.0	B	0.11329	0.006	T	0.41034	-0.9531	9	0.56958	D	0.05	.	5.2529	0.15532	0.554:0.3441:0.1018:0.0	rs17424145;rs17882525;rs34778461	114	P01911	2B1F_HUMAN	A	114	ENSP00000353099:V114A	ENSP00000353099:V114A	V	-	2	0	HLA-DRB1	32659893	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.239000	0.08965	-0.211000	0.10124	-1.021000	0.02439	GTT	A|0.941;G|0.059	0.059	strong		0.647	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ZNF280D	54816	hgsc.bcm.edu	37	15	56959028	56959028	+	Missense_Mutation	SNP	C	C	T	rs28620278	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:56959028C>T	ENST00000267807.7	-	15	1918	c.1702G>A	c.(1702-1704)Gtc>Atc	p.V568I	ZNF280D_ENST00000396245.1_Missense_Mutation_p.V272I|ZNF280D_ENST00000559237.1_Missense_Mutation_p.V555I|ZNF280D_ENST00000559000.1_Missense_Mutation_p.V555I	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	568			V -> I (in dbSNP:rs28620278). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		TTGGATTTGACTGTATTAGGT	0.333													T|||	2640	0.527157	0.7141	0.6225	5008	,	,		15602	0.3829		0.4066	False		,,,				2504	0.4796				p.V568I		Atlas-SNP	.											.	ZNF280D	82	.	0			c.G1702A						PASS	.	T	ILE/VAL,ILE/VAL	2803,1581	486.2+/-360.5	917,969,306	139.0	145.0	143.0		1663,1702	-0.9	0.0	15	dbSNP_125	143	3481,5103	631.5+/-398.5	697,2087,1508	yes	missense,missense	ZNF280D	NM_001002843.1,NM_017661.2	29,29	1614,3056,1814	TT,TC,CC		40.5522,36.063,48.4577	benign,benign	555/967,568/980	56959028	6284,6684	2192	4292	6484	SO:0001583	missense	54816	exon15			ATTTGACTGTATT	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.1702G>A	15.37:g.56959028C>T	ENSP00000267807:p.Val568Ile	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	229	95	0.414847	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Missense_Mutation	SNP	ENST00000267807.7	37	CCDS32245.1	1099	0.5032051282051282	370	0.7520325203252033	214	0.5911602209944752	225	0.39335664335664333	290	0.38258575197889183	T	1.441	-0.567698	0.03910	0.63937	0.405522	ENSG00000137871	ENST00000267807;ENST00000455329;ENST00000396245	T;T	0.03004	4.08;4.5	4.58	-0.931	0.10438	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.05305	-1.0893	8	0.17832	T	0.49	0.0847	6.768	0.23579	0.0:0.4082:0.1329:0.459	rs28620278;rs28620278	568	Q6N043	Z280D_HUMAN	I	568;555;272	ENSP00000267807:V568I;ENSP00000379545:V272I	ENSP00000267807:V568I	V	-	1	0	ZNF280D	54746320	0.059000	0.20769	0.018000	0.16275	0.511000	0.34104	-0.286000	0.08399	-0.282000	0.09128	-0.332000	0.08345	GTC	C|0.495;T|0.505	0.505	strong		0.333	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
MAVS	57506	hgsc.bcm.edu	37	20	3844929	3844929	+	Missense_Mutation	SNP	C	C	T	rs45437096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3844929C>T	ENST00000428216.2	+	6	780	c.652C>T	c.(652-654)Cgt>Tgt	p.R218C	MAVS_ENST00000416600.2_Missense_Mutation_p.R77C|MAVS_ENST00000358134.6_3'UTR	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	218					activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CACACCATCCCGTGGGCCTGT	0.602													C|||	263	0.052516	0.0106	0.0893	5008	,	,		18036	0.0		0.159	False		,,,				2504	0.0276				p.R218C		Atlas-SNP	.											.	MAVS	34	.	0			c.C652T						PASS	.	C	CYS/ARG,CYS/ARG	169,4237	111.6+/-149.8	6,157,2040	91.0	91.0	91.0		229,652	0.3	0.0	20	dbSNP_127	91	1418,7182	272.7+/-290.2	110,1198,2992	yes	missense,missense	MAVS	NM_001206491.1,NM_020746.4	180,180	116,1355,5032	TT,TC,CC		16.4884,3.8357,12.2021	benign,benign	77/400,218/541	3844929	1587,11419	2203	4300	6503	SO:0001583	missense	57506	exon6			CCATCCCGTGGGC	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"""virus-induced signaling adaptor"", ""IFN-B promoter stimulator 1"", ""CARD adaptor inducing IFN-beta"""	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.652C>T	20.37:g.3844929C>T	ENSP00000401980:p.Arg218Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	37	CCDS33437.1	163	0.07463369963369963	5	0.01016260162601626	38	0.10497237569060773	0	0.0	120	0.158311345646438	C	15.29	2.789708	0.50102	0.038357	0.164884	ENSG00000088888	ENST00000416600;ENST00000428216	T;T	0.34072	1.38;2.34	4.72	0.349	0.16032	.	1.472750	0.03891	N	0.278641	T	0.00109	0.0003	L	0.42245	1.32	0.80722	P	0.0	B	0.15930	0.015	B	0.12837	0.008	T	0.10965	-1.0607	9	0.34782	T	0.22	2.0676	4.4764	0.11746	0.0:0.5479:0.163:0.2891	rs45437096;rs62210536	218	Q7Z434	MAVS_HUMAN	C	77;218	ENSP00000413749:R77C;ENSP00000401980:R218C	ENSP00000413749:R77C	R	+	1	0	MAVS	3792929	0.000000	0.05858	0.012000	0.15200	0.954000	0.61252	-0.940000	0.03929	0.018000	0.15052	0.650000	0.86243	CGT	C|0.888;T|0.112	0.112	strong		0.602	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746	
C17orf102	400591	hgsc.bcm.edu	37	17	32906008	32906008	+	Missense_Mutation	SNP	C	C	G	rs58529418	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:32906008C>G	ENST00000357754.1	-	1	380	c.292G>C	c.(292-294)Ggg>Cgg	p.G98R	TMEM132E_ENST00000321639.5_5'Flank	NM_207454.2	NP_997337.2	A2RUQ5	CQ102_HUMAN	chromosome 17 open reading frame 102	98			G -> R (in dbSNP:rs58529418). {ECO:0000269|PubMed:14702039}.							central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(3)|ovary(1)	9						CCAGAGCCCCCGCGGCCCGAG	0.672													C|||	752	0.15016	0.1074	0.0994	5008	,	,		14420	0.2361		0.0895	False		,,,				2504	0.2178				p.G98R		Atlas-SNP	.											.	C17orf102	24	.	0			c.G292C						PASS	.	C	ARG/GLY	337,3381		14,309,1536	44.0	51.0	49.0		292	-1.7	0.0	17	dbSNP_129	49	600,7576		27,546,3515	yes	missense	C17orf102	NM_207454.2	125	41,855,5051	GG,GC,CC		7.3386,9.064,7.8779	possibly-damaging	98/168	32906008	937,10957	1859	4088	5947	SO:0001583	missense	400591	exon1			AGCCCCCGCGGCC		CCDS42297.1	17q12	2009-02-11			ENSG00000197322	ENSG00000197322			34412	protein-coding gene	gene with protein product							Standard	NM_207454		Approved	FLJ44815	uc002hie.1	A2RUQ5	OTTHUMG00000156883	ENST00000357754.1:c.292G>C	17.37:g.32906008C>G	ENSP00000350392:p.Gly98Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	39	13	0.333333	NM_207454	A5PKX0|Q6ZTB3	Missense_Mutation	SNP	ENST00000357754.1	37	CCDS42297.1	301	0.13782051282051283	53	0.10772357723577236	34	0.09392265193370165	147	0.256993006993007	67	0.08839050131926121	C	11.00	1.511180	0.27036	0.09064	0.073386	ENSG00000197322	ENST00000357754	T	0.46819	0.86	3.59	-1.73	0.08081	.	1.147840	0.06879	N	0.802091	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.36125	0.538	B	0.40199	0.322	T	0.18524	-1.0334	9	0.87932	D	0	.	6.4711	0.22009	0.5276:0.31:0.1624:0.0	rs58529418	98	A2RUQ5	CQ102_HUMAN	R	98	ENSP00000350392:G98R	ENSP00000350392:G98R	G	-	1	0	C17orf102	29930121	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.000000	0.03693	-0.401000	0.07644	-0.165000	0.13383	GGG	C|0.876;G|0.124	0.124	strong		0.672	C17orf102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346435.1	NM_207454	
ZNF860	344787	hgsc.bcm.edu	37	3	32031622	32031622	+	Missense_Mutation	SNP	T	T	C	rs13087612	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:32031622T>C	ENST00000360311.4	+	2	1600	c.1051T>C	c.(1051-1053)Ttc>Ctc	p.F351L		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	351					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(3)|lung(4)|ovary(1)	8						TGAAAAGGCTTTCAGGCGTGA	0.398													T|||	2329	0.465056	0.7799	0.3573	5008	,	,		21477	0.4524		0.1968	False		,,,				2504	0.4049				p.F351L		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,2	ZNF860	96	2	0			c.T1051C						PASS	.	T	LEU/PHE	897,487		298,301,93	48.0	49.0	49.0		1051	0.3	0.0	3	dbSNP_121	49	608,2574		57,494,1040	yes	missense	ZNF860	NM_001137674.2	22	355,795,1133	CC,CT,TT		19.1075,35.1879,32.961	probably-damaging	351/633	32031622	1505,3061	692	1591	2283	SO:0001583	missense	344787	exon2			AAGGCTTTCAGGC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1051T>C	3.37:g.32031622T>C	ENSP00000373274:p.Phe351Leu	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	131	128	0.977099	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	899	0.4116300366300366	373	0.758130081300813	125	0.3453038674033149	248	0.43356643356643354	153	0.20184696569920843	T	14.79	2.640073	0.47153	0.648121	0.191075	ENSG00000197385	ENST00000360311	T	0.46063	0.88	0.345	0.345	0.16011	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.90977	3.165	0.58432	P	5.999999999950489E-6	D	0.63880	0.993	D	0.68192	0.956	T	0.39683	-0.9602	7	.	.	.	.	4.9959	0.14240	0.0:2.0E-4:0.0:0.9998	rs13087612;rs59979195;rs13087612	351	A6NHJ4	ZN860_HUMAN	L	351	ENSP00000373274:F351L	.	F	+	1	0	ZNF860	32006626	0.979000	0.34478	0.003000	0.11579	0.003000	0.03518	5.394000	0.66285	0.332000	0.23536	0.323000	0.21402	TTC	T|0.621;C|0.379	0.379	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
PDE1C	5137	hgsc.bcm.edu	37	7	32209459	32209459	+	Silent	SNP	C	C	T	rs977626	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:32209459C>T	ENST00000396193.1	-	3	839	c.246G>A	c.(244-246)gaG>gaA	p.E82E		NM_001191058.1	NP_001177987.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	0					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CAGCTAGGATCTCCTCTGGGG	0.493													T|||	2755	0.55012	0.5484	0.3127	5008	,	,		20371	0.7579		0.3767	False		,,,				2504	0.6851				p.E82E		Atlas-SNP	.											.	PDE1C	465	.	0			c.G246A						PASS	.	T		913,839		232,449,195	153.0	132.0	138.0		246	0.9	1.0	7	dbSNP_86	138	1519,2463		298,923,770	no	coding-synonymous	PDE1C	NM_001191058.1		530,1372,965	TT,TC,CC		38.1467,47.8881,42.4137		82/770	32209459	2432,3302	876	1991	2867	SO:0001819	synonymous_variant	5137	exon3			TAGGATCTCCTCT	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396193.1:c.246G>A	7.37:g.32209459C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	84	19	0.22619	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396193.1	37	CCDS55100.1																																																																																			C|0.476;N|0.002	.	strong		0.493	PDE1C-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215075.1		
GTF3C2	2976	hgsc.bcm.edu	37	2	27550967	27550967	+	Silent	SNP	A	A	G	rs1049817	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27550967A>G	ENST00000359541.2	-	17	2775	c.2346T>C	c.(2344-2346)ccT>ccC	p.P782P	MPV17_ENST00000357186.6_5'Flank|GTF3C2_ENST00000264720.3_Silent_p.P782P			Q8WUA4	TF3C2_HUMAN	general transcription factor IIIC, polypeptide 2, beta 110kDa	782					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	nucleoplasm (GO:0005654)|transcription factor TFIIIC complex (GO:0000127)				central_nervous_system(4)|endometrium(6)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	38	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCGAGCCTTAGGAGGGTTGG	0.468													G|||	2255	0.45028	0.7413	0.4755	5008	,	,		18593	0.1647		0.3807	False		,,,				2504	0.4049				p.H782H		Atlas-SNP	.											.	GTF3C2	73	.	0			c.T2346C						PASS	.	G	,	2978,1428	463.4+/-353.5	1030,918,255	104.0	98.0	100.0		2346,2346	2.3	1.0	2	dbSNP_86	100	3344,5256	643.3+/-399.9	633,2078,1589	yes	coding-synonymous,coding-synonymous	GTF3C2	NM_001035521.1,NM_001521.2	,	1663,2996,1844	GG,GA,AA		38.8837,32.4103,48.6083	,	782/912,782/912	27550967	6322,6684	2203	4300	6503	SO:0001819	synonymous_variant	2976	exon18			AGCCTTAGGAGGG	D13636	CCDS1749.1	2p23.3	2013-01-10	2002-08-29		ENSG00000115207	ENSG00000115207		"""General transcription factors"", ""WD repeat domain containing"""	4665	protein-coding gene	gene with protein product		604883	"""general transcription factor IIIC, polypeptide 2 (beta subunit, 110kD)"""			7729686	Standard	NM_001521		Approved	KIAA0011, TFIIIC110	uc002rjw.2	Q8WUA4	OTTHUMG00000097785	ENST00000359541.2:c.2346T>C	2.37:g.27550967A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_001521	D6W557|Q16632|Q9BWI7	Silent	SNP	ENST00000359541.2	37	CCDS1749.1	886|886	0.4056776556776557|0.4056776556776557	363|363	0.7378048780487805|0.7378048780487805	151|151	0.4171270718232044|0.4171270718232044	76|76	0.13286713286713286|0.13286713286713286	296|296	0.39050131926121373|0.39050131926121373	G|G	7.681|7.681	0.689087|0.689087	0.14973|0.14973	0.675897|0.675897	0.388837|0.388837	ENSG00000115207|ENSG00000115207	ENST00000454704;ENST00000415683|ENST00000457098	.|.	.|.	.|.	5.16|5.16	2.32|2.32	0.28847|0.28847	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999992096|0.9999999999992096	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.28713|.	-1.0035|.	3|.	.|.	.|.	.|.	-12.1842|-12.1842	4.5341|4.5341	0.12020|0.12020	0.2565:0.0:0.5912:0.1522|0.2565:0.0:0.5912:0.1522	rs1049817;rs1124771;rs3189992;rs17006023;rs56842809;rs1049817|rs1049817;rs1124771;rs3189992;rs17006023;rs56842809;rs1049817	.|.	.|.	.|.	P|Q	291;205|76	.|.	.|.	L|X	-|-	2|1	0|0	GTF3C2|GTF3C2	27404471|27404471	0.305000|0.305000	0.24481|0.24481	0.999000|0.999000	0.59377|0.59377	0.961000|0.961000	0.63080|0.63080	-0.432000|-0.432000	0.06956|0.06956	0.197000|0.197000	0.20387|0.20387	-0.119000|-0.119000	0.15052|0.15052	CTA|TAA	A|0.544;G|0.456	0.456	strong		0.468	GTF3C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215028.2		
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 GAIIx	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_ENST00000405885.2_Missense_Mutation_p.N28T|IRF1_ENST00000463784.1_Intron	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	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	48	19	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	
PRSS3	5646	hgsc.bcm.edu	37	9	33796673	33796673	+	Missense_Mutation	SNP	G	G	A	rs76740888		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33796673G>A	ENST00000361005.5	+	2	244	c.244G>A	c.(244-246)Gtt>Att	p.V82I	PRSS3_ENST00000429677.3_Missense_Mutation_p.V18I|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000342836.4_Missense_Mutation_p.V39I|PRSS3_ENST00000379405.3_Missense_Mutation_p.V25I	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	82	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)			TGACAAGATTGTTGGGGGCTA	0.557																																					p.V82I		Atlas-SNP	.											.	PRSS3	79	.	0			c.G244A						PASS	.						190.0	179.0	183.0					9																	33796673		2203	4300	6503	SO:0001583	missense	5646	exon2			AAGATTGTTGGGG		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.244G>A	9.37:g.33796673G>A	ENSP00000354280:p.Val82Ile	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	116	16	0.137931	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	37	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	G	0.331	-0.956310	0.02267	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	D;D;D;D;D	0.93906	-2.54;-2.54;-3.31;-2.54;-3.31	3.21	1.32	0.21799	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.057900	0.64402	D	0.000002	D	0.88529	0.6461	L	0.41573	1.285	0.37860	D	0.929704	B;B;B	0.30542	0.122;0.266;0.284	B;B;B	0.40101	0.184;0.319;0.127	T	0.77464	-0.2578	10	0.11182	T	0.66	.	6.4881	0.22099	0.3388:0.0:0.6612:0.0	.	25;82;39	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	I	82;37;39;18;25	ENSP00000354280:V82I;ENSP00000401249:V37I;ENSP00000340889:V39I;ENSP00000401828:V18I;ENSP00000368715:V25I	ENSP00000340889:V39I	V	+	1	0	PRSS3	33786673	0.998000	0.40836	0.673000	0.29887	0.001000	0.01503	2.615000	0.46368	0.048000	0.15891	-2.635000	0.00153	GTT	.	.	weak		0.557	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
CDHR1	92211	hgsc.bcm.edu	37	10	85978939	85978939	+	IGR	SNP	G	G	A	rs4244947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:85978939G>A	ENST00000372117.3	+	0	5428				CDHR1_ENST00000332904.3_Silent_p.L715L	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1						cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						gCCAGGGTCTGTTCTTGCATC	0.398													A|||	2775	0.554113	0.8185	0.5331	5008	,	,		18287	0.4107		0.4632	False		,,,				2504	0.453				p.L715L		Atlas-SNP	.											.	CDHR1	122	.	0			c.G2145A						PASS	.																																			SO:0001628	intergenic_variant	92211	exon17			GGGTCTGTTCTTG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634		10.37:g.85978939G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	74	46	0.621622	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			G|0.460;A|0.540	0.540	strong		0.398	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
FSIP1	161835	hgsc.bcm.edu	37	15	40005772	40005772	+	Missense_Mutation	SNP	C	C	T	rs937961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:40005772C>T	ENST00000350221.3	-	10	1270	c.1061G>A	c.(1060-1062)cGt>cAt	p.R354H		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	354			R -> H (in dbSNP:rs937961). {ECO:0000269|Ref.3}.							NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TTCACCATCACGGTCAGGTTT	0.408													C|||	474	0.0946486	0.202	0.0576	5008	,	,		16276	0.002		0.1024	False		,,,				2504	0.0634				p.R354H		Atlas-SNP	.											.	FSIP1	53	.	0			c.G1061A						PASS	.	C	HIS/ARG	896,3510	346.7+/-309.1	98,700,1405	160.0	156.0	157.0		1061	-3.6	0.0	15	dbSNP_86	157	924,7676	204.1+/-246.9	39,846,3415	yes	missense	FSIP1	NM_152597.4	29	137,1546,4820	TT,TC,CC		10.7442,20.3359,13.9935	benign	354/582	40005772	1820,11186	2203	4300	6503	SO:0001583	missense	161835	exon10			CCATCACGGTCAG	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1061G>A	15.37:g.40005772C>T	ENSP00000280236:p.Arg354His	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	216	0.0989010989010989	110	0.22357723577235772	24	0.06629834254143646	1	0.0017482517482517483	81	0.10686015831134564	C	3.084	-0.188366	0.06299	0.203359	0.107442	ENSG00000150667	ENST00000350221	T	0.21932	1.98	4.22	-3.64	0.04515	.	1.005130	0.08016	N	0.991281	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	0.44050	-0.9353	8	.	.	.	0.6025	1.2779	0.02034	0.2823:0.2888:0.2841:0.1448	rs937961;rs17855663;rs52819744;rs58344936;rs937961	354	Q8NA03	FSIP1_HUMAN	H	354	ENSP00000280236:R354H	.	R	-	2	0	FSIP1	37793064	0.015000	0.18098	0.000000	0.03702	0.012000	0.07955	1.188000	0.32102	-0.731000	0.04862	-0.364000	0.07487	CGT	C|0.882;T|0.118	0.118	strong		0.408	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
PRRC2A	7916	hgsc.bcm.edu	37	6	31604591	31604591	+	Missense_Mutation	SNP	C	C	T	rs10885	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31604591C>T	ENST00000376033.2	+	28	6250	c.6016C>T	c.(6016-6018)Ccc>Tcc	p.P2006S	PRRC2A_ENST00000376007.4_Missense_Mutation_p.P2006S	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	2006	3 X 50 AA type C repeats.		P -> S (in dbSNP:rs10885). {ECO:0000269|PubMed:14574404}.			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						TGCCCCACCTCCCCTTTCTCT	0.622													C|||	668	0.133387	0.2126	0.0793	5008	,	,		15995	0.0714		0.1461	False		,,,				2504	0.1155				p.P2006S		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C6016T						PASS	.	C	SER/PRO,SER/PRO	590,2424		59,472,976	132.0	170.0	156.0		6016,6016	5.3	1.0	6	dbSNP_52	156	955,4459		93,769,1845	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	74,74	152,1241,2821	TT,TC,CC		17.6395,19.5753,18.3318	probably-damaging,probably-damaging	2006/2158,2006/2158	31604591	1545,6883	1507	2707	4214	SO:0001583	missense	7916	exon28			CCACCTCCCCTTT	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.6016C>T	6.37:g.31604591C>T	ENSP00000365201:p.Pro2006Ser	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	61	40	0.655738	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	286	0.13095238095238096	112	0.22764227642276422	30	0.08287292817679558	33	0.057692307692307696	111	0.14643799472295516	C	12.65	2.002477	0.35320	0.195753	0.176395	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01767	4.65;4.65	5.28	5.28	0.74379	.	0.000000	0.56097	D	0.000029	T	0.02156	0.0067	N	0.19112	0.55	0.26717	P	0.9708672	D	0.55172	0.97	P	0.57244	0.816	T	0.64266	-0.6448	9	0.87932	D	0	-9.7066	17.8506	0.88746	0.0:1.0:0.0:0.0	rs10885;rs1046121;rs3173341;rs3817660;rs17207260;rs17342597;rs17354298;rs10885	2006	P48634	PRC2A_HUMAN	S	1998;1987;2006;2006;1231	ENSP00000365175:P2006S;ENSP00000365201:P2006S	ENSP00000365175:P2006S	P	+	1	0	PRRC2A	31712570	0.553000	0.26513	0.968000	0.41197	0.994000	0.84299	3.080000	0.50112	2.747000	0.94245	0.643000	0.83706	CCC	C|0.836;T|0.164	0.164	strong		0.622	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
PPA2	27068	hgsc.bcm.edu	37	4	106395181	106395181	+	Silent	SNP	G	G	A	rs4699179	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106395181G>A	ENST00000341695.5	-	1	57	c.27C>T	c.(25-27)cgC>cgT	p.R9R	PPA2_ENST00000432483.2_Silent_p.R9R|PPA2_ENST00000380004.2_Silent_p.R9R|PPA2_ENST00000348706.5_Silent_p.R9R|PPA2_ENST00000357415.4_Silent_p.R9R|PPA2_ENST00000354147.3_Silent_p.R9R|PPA2_ENST00000310267.7_5'Flank|PPA2_ENST00000509426.1_5'UTR	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	9					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		GGGCACCCGTGCGCAGCAGCC	0.741											OREG0016281	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	406	0.0810703	0.0129	0.1628	5008	,	,		11677	0.001		0.2167	False		,,,				2504	0.0583				p.R9R		Atlas-SNP	.											.	PPA2	23	.	0			c.C27T						PASS	.	G	,,,	181,3919		7,167,1876	6.0	9.0	8.0		27,27,27,27	2.1	0.0	4	dbSNP_111	8	1774,6384		207,1360,2512	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPA2	NM_006903.4,NM_176866.2,NM_176867.3,NM_176869.2	,,,	214,1527,4388	AA,AG,GG		21.7455,4.4146,15.9488	,,,	9/306,9/233,9/169,9/335	106395181	1955,10303	2050	4079	6129	SO:0001819	synonymous_variant	27068	exon1			ACCCGTGCGCAGC		CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.27C>T	4.37:g.106395181G>A		Somatic	11	0	0	1396	WXS	Illumina HiSeq	Phase_I	23	23	1	NM_176866	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Silent	SNP	ENST00000341695.5	37	CCDS3667.1	240	0.10989010989010989	12	0.024390243902439025	47	0.1298342541436464	1	0.0017482517482517483	180	0.23746701846965698	G	1.531	-0.544344	0.04024	0.044146	0.217455	ENSG00000138777	ENST00000508518	.	.	.	2.93	2.09	0.27110	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.099999999995774E-5	.	.	.	.	.	.	T	0.17440	-1.0369	3	.	.	.	-4.9447	5.9932	0.19478	0.1442:0.0:0.8558:0.0	rs4699179;rs17508567	.	.	.	V	6	.	.	A	-	2	0	PPA2	106614630	0.669000	0.27502	0.010000	0.14722	0.017000	0.09413	0.839000	0.27586	0.817000	0.34445	0.557000	0.71058	GCA	G|0.892;A|0.108	0.108	strong		0.741	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869	
HDAC10	83933	hgsc.bcm.edu	37	22	50687178	50687178	+	Silent	SNP	C	C	T	rs41283469	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50687178C>T	ENST00000216271.5	-	10	1171	c.819G>A	c.(817-819)ggG>ggA	p.G273G	MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000448072.1_Intron|HDAC10_ENST00000349505.4_Silent_p.G253G|HDAC10_ENST00000498366.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	273	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCTGCATTTGCCCCTGGAACC	0.687													C|||	188	0.0375399	0.0008	0.0317	5008	,	,		17267	0.0833		0.0288	False		,,,				2504	0.0532				p.G273G		Atlas-SNP	.											HDAC10,NS,carcinoma,-1,1	HDAC10	29	1	0			c.G819A						PASS	.	C	,	16,4350		0,16,2167	34.0	36.0	36.0		759,819	-0.0	1.0	22	dbSNP_127	36	190,8394		1,188,4103	no	coding-synonymous,coding-synonymous	HDAC10	NM_001159286.1,NM_032019.5	,	1,204,6270	TT,TC,CC		2.2134,0.3665,1.5907	,	253/650,273/670	50687178	206,12744	2183	4292	6475	SO:0001819	synonymous_variant	83933	exon10			CATTTGCCCCTGG	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.819G>A	22.37:g.50687178C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Silent	SNP	ENST00000216271.5	37	CCDS14088.1																																																																																			C|0.974;T|0.026	0.026	strong		0.687	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	
HLA-C	3107	hgsc.bcm.edu	37	6	31239518	31239518	+	Silent	SNP	C	C	T	rs1050420	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31239518C>T	ENST00000376228.5	-	2	215	c.201G>A	c.(199-201)ccG>ccA	p.P67P	HLA-C_ENST00000383329.3_Silent_p.P67P	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	67	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GCTCCCCTCTCGGACTCGCGG	0.701													t|||	2230	0.445288	0.5363	0.513	5008	,	,		12078	0.2808		0.4314	False		,,,				2504	0.4581				p.P67P		Atlas-SNP	.											.	HLA-C	92	.	0			c.G201A						PASS	.	T		1449,1571		354,741,415	38.0	40.0	39.0		201	-0.2	0.0	6	dbSNP_86	39	2233,3179		465,1303,938	no	coding-synonymous	HLA-C	NM_002117.5		819,2044,1353	TT,TC,CC		41.2602,47.9801,43.667		67/367	31239518	3682,4750	1510	2706	4216	SO:0001819	synonymous_variant	3107	exon2			CCCTCTCGGACTC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.201G>A	6.37:g.31239518C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	136	22	0.161765	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	910	0.4166666666666667	245	0.49796747967479676	195	0.5386740331491713	155	0.270979020979021	315	0.4155672823218997	-	6.921	0.539543	0.13250	0.479801	0.412602	ENSG00000204525	ENST00000415537	.	.	.	2.81	-0.177	0.13307	.	.	.	.	.	T	0.11793	0.0287	.	.	.	0.51233	P	8.699999999994823E-5	.	.	.	.	.	.	T	0.24476	-1.0159	3	.	.	.	.	3.289	0.06942	0.0:0.5067:0.2214:0.2719	rs1050420;rs2308551;rs3173347;rs16868214;rs17849592	.	.	.	K	67	.	.	E	-	1	0	HLA-C	31347497	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-0.011000	0.12721	-0.051000	0.13334	-0.679000	0.03777	GAG	C|0.581;T|0.419	0.419	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
GET4	51608	hgsc.bcm.edu	37	7	925717	925717	+	Silent	SNP	G	G	A	rs11543222	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:925717G>A	ENST00000265857.3	+	2	274	c.180G>A	c.(178-180)acG>acA	p.T60T	GET4_ENST00000407192.1_Silent_p.T7T|RP11-449P15.2_ENST00000609998.1_RNA	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	60					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						GCAAGCACACGGAGGCCCGGG	0.642													G|||	470	0.0938498	0.0983	0.1772	5008	,	,		14263	0.001		0.1501	False		,,,				2504	0.0665				p.T60T		Atlas-SNP	.											.	GET4	17	.	0			c.G180A						PASS	.	G		415,3991	201.5+/-224.5	22,371,1810	102.0	86.0	92.0		180	-10.1	0.0	7	dbSNP_120	92	1263,7335	251.5+/-278.0	93,1077,3129	no	coding-synonymous	GET4	NM_015949.2		115,1448,4939	AA,AG,GG		14.6895,9.419,12.9037		60/328	925717	1678,11326	2203	4299	6502	SO:0001819	synonymous_variant	51608	exon2			GCACACGGAGGCC	AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"""CGI-20 protein"", ""conserved edge protein"", ""transmembrane domain recognition complex, 35kDa"""	612056	"""chromosome 7 open reading frame 20"""	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.180G>A	7.37:g.925717G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	29	0.295918	NM_015949	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Silent	SNP	ENST00000265857.3	37	CCDS5317.1																																																																																			G|0.878;A|0.122	0.122	strong		0.642	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949	
LAMC2	3918	hgsc.bcm.edu	37	1	183201970	183201970	+	Missense_Mutation	SNP	G	G	C	rs2296303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:183201970G>C	ENST00000264144.4	+	14	2263	c.2198G>C	c.(2197-2199)aGt>aCt	p.S733T	LAMC2_ENST00000493293.1_Missense_Mutation_p.S733T	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	733	Domain II and I.		S -> T (in dbSNP:rs2296303).		cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						CTGGCAGAAAGTGAAGCTTCC	0.483													G|||	726	0.144968	0.2186	0.1556	5008	,	,		21932	0.1468		0.1024	False		,,,				2504	0.0798				p.S733T		Atlas-SNP	.											.	LAMC2	113	.	0			c.G2198C						PASS	.	G	THR/SER,THR/SER	997,3409	368.3+/-318.6	131,735,1337	71.0	72.0	72.0		2198,2198	1.7	0.0	1	dbSNP_100	72	1107,7493	228.9+/-263.8	66,975,3259	yes	missense,missense	LAMC2	NM_005562.2,NM_018891.2	58,58	197,1710,4596	CC,CG,GG		12.8721,22.6282,16.1771	benign,benign	733/1194,733/1112	183201970	2104,10902	2203	4300	6503	SO:0001583	missense	3918	exon14			CAGAAAGTGAAGC	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2198G>C	1.37:g.183201970G>C	ENSP00000264144:p.Ser733Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	335	0.1533882783882784	110	0.22357723577235772	54	0.14917127071823205	90	0.15734265734265734	81	0.10686015831134564	G	6.469	0.454627	0.12283	0.226282	0.128721	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.16743	2.47;2.32	5.67	1.73	0.24493	.	0.170371	0.53938	D	0.000055	T	0.00012	0.0000	M	0.67953	2.075	0.38090	P	0.06306900000000004	B;B;B	0.29432	0.104;0.244;0.167	B;B;B	0.33750	0.081;0.125;0.169	T	0.34054	-0.9844	9	0.22109	T	0.4	.	6.3536	0.21389	0.2164:0.1312:0.6524:0.0	rs2296303;rs60229317	733;733;733	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	T	733	ENSP00000432063:S733T;ENSP00000264144:S733T	ENSP00000264144:S733T	S	+	2	0	LAMC2	181468593	0.348000	0.24861	0.002000	0.10522	0.005000	0.04900	1.207000	0.32333	0.063000	0.16370	-0.143000	0.13931	AGT	G|0.841;C|0.159	0.159	strong		0.483	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
CDH23	64072	hgsc.bcm.edu	37	10	73537978	73537978	+	Silent	SNP	C	C	T	rs10762480	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73537978C>T	ENST00000224721.6	+	39	5120	c.5115C>T	c.(5113-5115)taC>taT	p.Y1705Y		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1700	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						AGCTGGACTACGAGATCAGCC	0.602													C|||	898	0.179313	0.1755	0.1556	5008	,	,		20598	0.2004		0.2097	False		,,,				2504	0.1483				p.Y1700Y		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	0			c.C5100T						PASS	.	C		781,3459		70,641,1409	70.0	77.0	75.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5100	-5.9	0.9	10	dbSNP_120	75	1660,6786		168,1324,2731	no	coding-synonymous	CDH23	NM_022124.5		238,1965,4140	TT,TC,CC		19.6543,18.4198,19.2417		1700/3355	73537978	2441,10245	2120	4223	6343	SO:0001819	synonymous_variant	64072	exon38			GGACTACGAGATC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.5115C>T	10.37:g.73537978C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.824;T|0.176	0.176	strong		0.602	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
HSPG2	3339	hgsc.bcm.edu	37	1	22168845	22168845	+	Missense_Mutation	SNP	A	A	T	rs2229489	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22168845A>T	ENST00000374695.3	-	68	9018	c.8939T>A	c.(8938-8940)cTc>cAc	p.L2980H		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2980	Ig-like C2-type 15.		L -> H (in dbSNP:rs2229489). {ECO:0000269|PubMed:1730768}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	AGGGGAGACGAGGTGGAGCCG	0.632													T|||	172	0.034345	0.0015	0.0245	5008	,	,		16319	0.0		0.0487	False		,,,				2504	0.1063				p.L2980H		Atlas-SNP	.											HSPG2,NS,carcinoma,0,1	HSPG2	311	1	0			c.T8939A						PASS	.	T	HIS/LEU	40,4366	789.4+/-415.0	0,40,2163	26.0	24.0	25.0		8939	4.9	0.7	1	dbSNP_98	25	479,8121	769.3+/-407.6	15,449,3836	yes	missense	HSPG2	NM_005529.5	99	15,489,5999	TT,TA,AA		5.5698,0.9079,3.9905	benign	2980/4392	22168845	519,12487	2203	4300	6503	SO:0001583	missense	3339	exon68			GAGACGAGGTGGA	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8939T>A	1.37:g.22168845A>T	ENSP00000363827:p.Leu2980His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	49	0.022435897435897436	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	36	0.047493403693931395	T	0.164	-1.078225	0.01903	0.009079	0.055698	ENSG00000142798	ENST00000374695	T	0.40476	1.03	4.95	4.95	0.65309	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.650396	0.12701	N	0.446358	T	0.01592	0.0051	N	0.00960	-1.095	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.17561	-1.0365	10	0.18710	T	0.47	.	10.1342	0.42697	0.15:0.0:0.0:0.85	rs2229489	920;2980	Q59EG0;P98160	.;PGBM_HUMAN	H	2980	ENSP00000363827:L2980H	ENSP00000363827:L2980H	L	-	2	0	HSPG2	22041432	0.939000	0.31865	0.745000	0.31077	0.077000	0.17291	1.886000	0.39688	0.730000	0.32425	-0.527000	0.04329	CTC	A|0.957;T|0.043	0.043	strong		0.632	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
SNX8	29886	hgsc.bcm.edu	37	7	2290522	2290522	+	IGR	SNP	C	C	T	rs1799832	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:2290522C>T	ENST00000222990.3	-	0	4727				NUDT1_ENST00000397048.1_Silent_p.D142D|NUDT1_ENST00000343985.4_Silent_p.D142D|NUDT1_ENST00000397046.1_Silent_p.D119D|NUDT1_ENST00000487426.1_3'UTR|NUDT1_ENST00000356714.1_Silent_p.D119D|NUDT1_ENST00000397049.1_Silent_p.D142D|NUDT1_ENST00000339737.2_Silent_p.D119D	NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8						early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)	early endosome membrane (GO:0031901)	identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			breast(2)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(2)|skin(3)	26		Ovarian(82;0.11)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0853)|OV - Ovarian serous cystadenocarcinoma(56;3.79e-14)		TGTGGCCCGACGACAGCTACT	0.552													C|||	746	0.148962	0.0968	0.2061	5008	,	,		16718	0.0625		0.2087	False		,,,				2504	0.2065				p.D142D		Atlas-SNP	.											.	NUDT1	22	.	0			c.C426T						PASS	.	C	,,,,,,	510,3896	237.1+/-249.0	36,438,1729	172.0	178.0	176.0		357,357,426,357,426,357,426	-9.6	0.1	7	dbSNP_89	176	1624,6976	303.0+/-306.2	154,1316,2830	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NUDT1	NM_002452.3,NM_198948.1,NM_198949.1,NM_198950.1,NM_198952.1,NM_198953.1,NM_198954.1	,,,,,,	190,1754,4559	TT,TC,CC		18.8837,11.5751,16.4078	,,,,,,	119/157,119/157,142/180,119/157,142/180,119/157,142/180	2290522	2134,10872	2203	4300	6503	SO:0001628	intergenic_variant	4521	exon5			GCCCGACGACAGC	AF121858	CCDS5331.1	7p22.3	2010-08-05			ENSG00000106266	ENSG00000106266		"""Sorting nexins"""	14972	protein-coding gene	gene with protein product		614905					Standard	NM_013321		Approved	Mvp1	uc003slw.3	Q9Y5X2	OTTHUMG00000151512		7.37:g.2290522C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	91	52	0.571429	NM_198949	A4D207|Q96I67	Silent	SNP	ENST00000222990.3	37	CCDS5331.1																																																																																			C|0.841;T|0.159	0.159	strong		0.552	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2		
PLEKHG7	440107	hgsc.bcm.edu	37	12	93139348	93139348	+	Missense_Mutation	SNP	A	A	G	rs17790310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:93139348A>G	ENST00000344636.3	+	5	480	c.296A>G	c.(295-297)gAc>gGc	p.D99G	PLEKHG7_ENST00000549856.1_Missense_Mutation_p.D99G	NM_001004330.2	NP_001004330.1	Q6ZR37	PKHG7_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 7	99	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		D -> G (in dbSNP:rs17790310).				Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)	17						CAGAGAGATGACTTTGGAATT	0.378													A|||	89	0.0177716	0.0023	0.0274	5008	,	,		18766	0.0		0.0447	False		,,,				2504	0.0225				p.D99G		Atlas-SNP	.											.	PLEKHG7	38	.	0			c.A296G						PASS	.	A	GLY/ASP	54,4352	52.3+/-87.9	0,54,2149	105.0	102.0	103.0		296	5.2	0.9	12	dbSNP_123	103	503,8097	143.7+/-199.7	17,469,3814	yes	missense	PLEKHG7	NM_001004330.2	94	17,523,5963	GG,GA,AA		5.8488,1.2256,4.2826	probably-damaging	99/380	93139348	557,12449	2203	4300	6503	SO:0001583	missense	440107	exon5			GAGATGACTTTGG	AK128530	CCDS31873.1	12q22	2013-01-11				ENSG00000187510		"""Pleckstrin homology (PH) domain containing"""	33829	protein-coding gene	gene with protein product							Standard	NM_001004330		Approved	FLJ46688	uc001tcj.2	Q6ZR37		ENST00000344636.3:c.296A>G	12.37:g.93139348A>G	ENSP00000344961:p.Asp99Gly	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_001004330	B2RNR7	Missense_Mutation	SNP	ENST00000344636.3	37	CCDS31873.1	43	0.019688644688644688	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	27	0.03562005277044855	A	21.9	4.215419	0.79352	0.012256	0.058488	ENSG00000187510	ENST00000344636	T	0.64085	-0.08	5.21	5.21	0.72293	Dbl homology (DH) domain (4);	0.209202	0.50627	D	0.000115	T	0.30792	0.0776	M	0.72894	2.215	0.58432	D	0.999999	D	0.89917	1.0	D	0.79784	0.993	T	0.59101	-0.7517	10	0.25106	T	0.35	-8.9033	15.0379	0.71764	1.0:0.0:0.0:0.0	rs17790310;rs17790310	99	Q6ZR37	PKHG7_HUMAN	G	99	ENSP00000344961:D99G	ENSP00000344961:D99G	D	+	2	0	PLEKHG7	91663479	1.000000	0.71417	0.910000	0.35882	0.897000	0.52465	8.162000	0.89657	2.087000	0.62958	0.528000	0.53228	GAC	A|0.966;G|0.034	0.034	strong		0.378	PLEKHG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407288.1	NM_001004330	
CCDC27	148870	hgsc.bcm.edu	37	1	3677933	3677933	+	Missense_Mutation	SNP	T	T	C	rs1181883	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3677933T>C	ENST00000294600.2	+	5	884	c.800T>C	c.(799-801)aTg>aCg	p.M267T		NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	267			M -> T (in dbSNP:rs1181883). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		GCCCTGAAGATGCAGCTGAAA	0.577													C|||	2384	0.476038	0.6944	0.4683	5008	,	,		18850	0.2788		0.4354	False		,,,				2504	0.4315				p.M267T		Atlas-SNP	.											.	CCDC27	79	.	0			c.T800C						PASS	.	C	THR/MET	2721,1685	508.9+/-367.1	851,1019,333	80.0	77.0	78.0		800	-1.3	0.3	1	dbSNP_87	78	3371,5229	641.1+/-399.7	666,2039,1595	yes	missense	CCDC27	NM_152492.2	81	1517,3058,1928	CC,CT,TT		39.1977,38.2433,46.8399	benign	267/657	3677933	6092,6914	2203	4300	6503	SO:0001583	missense	148870	exon5			TGAAGATGCAGCT		CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	ENST00000294600.2:c.800T>C	1.37:g.3677933T>C	ENSP00000294600:p.Met267Thr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	152	67	0.440789	NM_152492	Q5TBV3|Q96M50	Missense_Mutation	SNP	ENST00000294600.2	37	CCDS50.1	994	0.4551282051282051	356	0.7235772357723578	164	0.4530386740331492	148	0.25874125874125875	326	0.43007915567282323	C	0.025	-1.378822	0.01204	0.617567	0.391977	ENSG00000162592	ENST00000294600	T	0.16897	2.31	3.75	-1.31	0.09230	.	0.477568	0.17824	N	0.160777	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	0.24870	-1.0148	9	0.17832	T	0.49	-30.5079	0.0397	0.00008	0.2978:0.1762:0.2037:0.3224	rs1181883;rs17371673;rs52791836;rs58427864;rs1181883	267	Q2M243	CCD27_HUMAN	T	267	ENSP00000294600:M267T	ENSP00000294600:M267T	M	+	2	0	CCDC27	3667793	0.039000	0.19947	0.345000	0.25642	0.018000	0.09664	-0.489000	0.06490	-0.433000	0.07286	-3.293000	0.00046	ATG	T|0.530;C|0.470	0.470	strong		0.577	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
SH3BP2	6452	hgsc.bcm.edu	37	4	2831383	2831383	+	Silent	SNP	T	T	G	rs231399	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:2831383T>G	ENST00000356331.5	+	8	1011	c.750T>G	c.(748-750)gcT>gcG	p.A250A	SH3BP2_ENST00000511747.1_Silent_p.A250A|SH3BP2_ENST00000452765.2_Silent_p.A250A|SH3BP2_ENST00000435136.2_Silent_p.A250A|SH3BP2_ENST00000503393.2_Silent_p.A307A|SH3BP2_ENST00000515183.1_3'UTR|SH3BP2_ENST00000442312.2_Silent_p.A278A	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	250					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)	p.A250A(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		TTGGCCTGGCTGCTGAGGACT	0.677									Cherubism				T|||	2335	0.466254	0.3533	0.5245	5008	,	,		10753	0.4712		0.4851	False		,,,				2504	0.5532				p.A307A		Atlas-SNP	.											SH3BP2,NS,carcinoma,0,1	SH3BP2	43	1	1	Substitution - coding silent(1)	prostate(1)	c.T921G						PASS	.	T	,,,	1649,2757	491.7+/-362.2	285,1079,839	39.0	44.0	42.0		750,834,921,750	-9.2	0.0	4	dbSNP_79	42	4260,4340	561.2+/-387.7	1083,2094,1123	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	1368,3173,1962	GG,GT,TT		49.5349,37.4262,45.4329	,,,	250/562,278/590,307/619,250/562	2831383	5909,7097	2203	4300	6503	SO:0001819	synonymous_variant	6452	exon8	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CCTGGCTGCTGAG	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	10825	protein-coding gene	gene with protein product		602104	"""Cherubism"""			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.750T>G	4.37:g.2831383T>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			T|0.554;G|0.446	0.446	strong		0.677	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
METTL13	51603	hgsc.bcm.edu	37	1	171755182	171755182	+	Missense_Mutation	SNP	G	G	A	rs2232819	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171755182G>A	ENST00000361735.3	+	3	1343	c.1077G>A	c.(1075-1077)atG>atA	p.M359I	METTL13_ENST00000458517.1_Missense_Mutation_p.M358I|METTL13_ENST00000362019.3_Missense_Mutation_p.M273I|METTL13_ENST00000367737.5_Missense_Mutation_p.M203I	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	359			M -> I (in dbSNP:rs2232819).				methyltransferase activity (GO:0008168)	p.M359I(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						CTAGAGTCATGGAGCTGGCCC	0.562													G|||	526	0.105032	0.0212	0.1138	5008	,	,		19889	0.1329		0.1968	False		,,,				2504	0.089				p.M359I		Atlas-SNP	.											METTL13,NS,carcinoma,0,1	METTL13	67	1	1	Substitution - Missense(1)	stomach(1)	c.G1077A						PASS	.	G	ILE/MET,ILE/MET,ILE/MET	207,4199	126.1+/-163.2	6,195,2002	48.0	41.0	44.0		609,819,1077	5.4	1.0	1	dbSNP_98	44	1677,6923	302.0+/-305.7	166,1345,2789	yes	missense,missense,missense	METTL13	NM_001007239.1,NM_014955.2,NM_015935.4	10,10,10	172,1540,4791	AA,AG,GG		19.5,4.6981,14.4856	possibly-damaging,possibly-damaging,possibly-damaging	203/544,273/614,359/700	171755182	1884,11122	2203	4300	6503	SO:0001583	missense	51603	exon3			AGTCATGGAGCTG	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1077G>A	1.37:g.171755182G>A	ENSP00000354920:p.Met359Ile	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	64	0.587156	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	37	CCDS1299.1	288	0.13186813186813187	13	0.026422764227642278	43	0.11878453038674033	74	0.12937062937062938	158	0.20844327176781002	G	16.43	3.120562	0.56613	0.046981	0.195	ENSG00000010165	ENST00000458517;ENST00000362019;ENST00000367737;ENST00000361735	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.36	5.36	0.76844	.	0.372977	0.34603	N	0.003825	T	0.35740	0.0942	L	0.54323	1.7	0.18873	P	0.999982305	B;P;P	0.44090	0.376;0.826;0.722	B;P;B	0.45712	0.164;0.491;0.231	T	0.07966	-1.0745	9	0.32370	T	0.25	-9.2721	18.0318	0.89286	0.0:0.0:1.0:0.0	rs2232819;rs2232819	358;203;359	B4E2X3;Q8N6R0-1;Q8N6R0	.;.;MTL13_HUMAN	I	358;273;203;359	ENSP00000401955:M358I;ENSP00000355393:M273I;ENSP00000356711:M203I;ENSP00000354920:M359I	ENSP00000354920:M359I	M	+	3	0	METTL13	170021805	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	9.463000	0.97652	2.793000	0.96121	0.561000	0.74099	ATG	G|0.869;A|0.131	0.131	strong		0.562	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
ITPKB	3707	hgsc.bcm.edu	37	1	226923264	226923264	+	Silent	SNP	G	G	A	rs708775	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226923264G>A	ENST00000272117.3	-	1	1895	c.1896C>T	c.(1894-1896)gcC>gcT	p.A632A	ITPKB_ENST00000429204.1_Silent_p.A632A|ITPKB_ENST00000366784.1_Silent_p.A632A			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	632					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)	p.A632A(1)		central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				TATGCAGGAAGGCTGAGTTGG	0.547													G|||	1410	0.28155	0.2428	0.317	5008	,	,		20089	0.2639		0.3141	False		,,,				2504	0.2935				p.A632A	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	1	Substitution - coding silent(1)	stomach(1)	c.C1896T						PASS	.	G		1123,3283	401.5+/-332.0	133,857,1213	130.0	123.0	125.0		1896	2.8	1.0	1	dbSNP_86	125	2530,6070	413.4+/-351.1	390,1750,2160	yes	coding-synonymous	ITPKB	NM_002221.3		523,2607,3373	AA,AG,GG		29.4186,25.488,28.087		632/947	226923264	3653,9353	2203	4300	6503	SO:0001819	synonymous_variant	3707	exon2			CAGGAAGGCTGAG	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1896C>T	1.37:g.226923264G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	142	65	0.457746	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																			G|0.716;A|0.284	0.284	strong		0.547	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
CRMP1	1400	hgsc.bcm.edu	37	4	5830393	5830393	+	Silent	SNP	C	C	T	rs61746000	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:5830393C>T	ENST00000397890.2	-	12	1498	c.1284G>A	c.(1282-1284)gcG>gcA	p.A428A	CRMP1_ENST00000512574.1_Silent_p.A426A|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Silent_p.A542A|EVC_ENST00000382674.2_3'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	428					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|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)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TGTACTCCACCGCCTGCACCA	0.502													T|||	434	0.0866613	0.2655	0.049	5008	,	,		18664	0.0218		0.0239	False		,,,				2504	0.0031				p.A542A		Atlas-SNP	.											CRMP1,NS,carcinoma,-1,1	CRMP1	118	1	0			c.G1626A						PASS	.	T	,	1009,3397	730.1+/-410.1	112,785,1306	105.0	72.0	83.0		1626,1284	-8.9	0.0	4	dbSNP_129	83	237,8363	808.7+/-407.2	1,235,4064	no	coding-synonymous,coding-synonymous	CRMP1	NM_001014809.1,NM_001313.3	,	113,1020,5370	TT,TC,CC		2.7558,22.9006,9.5802	,	542/687,428/573	5830393	1246,11760	2203	4300	6503	SO:0001819	synonymous_variant	1400	exon12			CTCCACCGCCTGC	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1284G>A	4.37:g.5830393C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																			C|0.918;T|0.082	0.082	strong		0.502	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
FAM135A	57579	hgsc.bcm.edu	37	6	71238105	71238105	+	Missense_Mutation	SNP	A	A	G	rs2747701	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:71238105A>G	ENST00000418814.2	+	16	4339	c.3725A>G	c.(3724-3726)gAt>gGt	p.D1242G	FAM135A_ENST00000370479.3_Missense_Mutation_p.D1029G|FAM135A_ENST00000505769.1_Missense_Mutation_p.D822G|FAM135A_ENST00000505868.1_Missense_Mutation_p.D1242G|FAM135A_ENST00000457062.2_Missense_Mutation_p.D1029G|FAM135A_ENST00000361499.3_Missense_Mutation_p.D1046G	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1242			D -> G (in dbSNP:rs2747701). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16192744}.							breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						GAAGAAGAGGATGGTTCTGAA	0.403													A|||	1699	0.339257	0.0189	0.2507	5008	,	,		16392	0.5427		0.4761	False		,,,				2504	0.4847				p.D1242G		Atlas-SNP	.											.	FAM135A	181	.	0			c.A3725G						PASS	.	A	GLY/ASP,GLY/ASP,GLY/ASP	381,4025	192.3+/-217.7	13,355,1835	215.0	183.0	194.0		3137,3725,3086	3.8	0.7	6	dbSNP_100	194	4138,4462	564.9+/-388.4	1003,2132,1165	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	94,94,94	1016,2487,3000	GG,GA,AA		48.1163,8.6473,34.7455	benign,benign,benign	1046/1320,1242/1516,1029/1303	71238105	4519,8487	2203	4300	6503	SO:0001583	missense	57579	exon14			AAGAGGATGGTTC	AK000183	CCDS34481.1, CCDS47448.1, CCDS55028.1	6q13	2008-10-30	2007-05-11	2007-05-11	ENSG00000082269	ENSG00000082269			21084	protein-coding gene	gene with protein product			"""KIAA1411"""	KIAA1411		10718198	Standard	NM_001105531		Approved	FLJ20176	uc003pfj.3	Q9P2D6	OTTHUMG00000014991	ENST00000418814.2:c.3725A>G	6.37:g.71238105A>G	ENSP00000410768:p.Asp1242Gly	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	779	0.3566849816849817	12	0.024390243902439025	98	0.27071823204419887	305	0.5332167832167832	364	0.48021108179419525	A	12.22	1.872457	0.33069	0.086473	0.481163	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.24538	2.16;2.16;1.85;2.16;2.16;2.15	4.92	3.77	0.43336	.	0.230845	0.51477	N	0.000093	T	0.14874	0.0359	M	0.67953	2.075	0.09310	P	0.99999351703	B;B;B;B;B	0.31040	0.305;0.11;0.067;0.076;0.11	B;B;B;B;B	0.33042	0.109;0.157;0.075;0.047;0.157	T	0.04053	-1.0981	9	0.59425	D	0.04	.	10.304	0.43670	0.9221:0.0:0.0779:0.0	rs2747701;rs3736753;rs60825985;rs2747701	822;1242;1242;1046;1029	D6RCC7;Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;.;F135A_HUMAN;.;.	G	1242;1029;822;1029;1046;1242	ENSP00000410768:D1242G;ENSP00000359510:D1029G;ENSP00000423785:D822G;ENSP00000409201:D1029G;ENSP00000354913:D1046G;ENSP00000423307:D1242G	ENSP00000354913:D1046G	D	+	2	0	FAM135A	71294826	1.000000	0.71417	0.723000	0.30687	0.305000	0.27757	6.153000	0.71819	0.843000	0.35070	0.482000	0.46254	GAT	A|0.647;G|0.353	0.353	strong		0.403	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
KRT28	162605	hgsc.bcm.edu	37	17	38955991	38955991	+	Missense_Mutation	SNP	C	C	T	rs7209228	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38955991C>T	ENST00000306658.7	-	1	220	c.155G>A	c.(154-156)gGc>gAc	p.G52D		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				ACTGCCCAAGCCCCCTCCCAA	0.567													C|||	521	0.104034	0.1256	0.1124	5008	,	,		17892	0.004		0.1829	False		,,,				2504	0.091				p.G52D	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.G155A						PASS	.	C	ASP/GLY	496,3910	230.7+/-244.8	31,434,1738	71.0	75.0	74.0		155	3.5	0.8	17	dbSNP_116	74	1518,7082	286.9+/-297.9	131,1256,2913	yes	missense	KRT28	NM_181535.3	94	162,1690,4651	TT,TC,CC		17.6512,11.2574,15.4852	benign	52/465	38955991	2014,10992	2203	4300	6503	SO:0001583	missense	162605	exon1			CCCAAGCCCCCTC	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30842	protein-coding gene	gene with protein product			"""keratin 25D"""	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.155G>A	17.37:g.38955991C>T	ENSP00000305263:p.Gly52Asp	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_181535		Missense_Mutation	SNP	ENST00000306658.7	37	CCDS11376.1	239	0.10943223443223443	65	0.13211382113821138	47	0.1298342541436464	0	0.0	127	0.16754617414248021	C	14.98	2.696528	0.48202	0.112574	0.176512	ENSG00000173908	ENST00000306658	D	0.88354	-2.37	5.52	3.47	0.39725	.	0.453405	0.18702	N	0.133542	T	0.00580	0.0019	L	0.29908	0.895	0.41216	P	0.01352500000000001	P	0.43477	0.808	B	0.34590	0.186	T	0.24154	-1.0168	9	0.45353	T	0.12	.	14.9934	0.71412	0.0:0.7198:0.2802:0.0	rs7209228;rs52810060;rs59201813;rs7209228	52	Q7Z3Y7	K1C28_HUMAN	D	52	ENSP00000305263:G52D	ENSP00000305263:G52D	G	-	2	0	KRT28	36209517	0.015000	0.18098	0.846000	0.33378	0.886000	0.51366	2.612000	0.46343	0.765000	0.33221	0.650000	0.86243	GGC	C|0.859;T|0.141	0.141	strong		0.567	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
ADCY1	107	hgsc.bcm.edu	37	7	45753324	45753324	+	Silent	SNP	G	G	A	rs2293106	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:45753324G>A	ENST00000297323.7	+	20	3112	c.3090G>A	c.(3088-3090)agG>agA	p.R1030R		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	1030	Interaction with calmodulin. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TGCTGAGAAGGTGCCCCTACC	0.532													G|||	837	0.167133	0.32	0.1167	5008	,	,		20093	0.121		0.173	False		,,,				2504	0.0378				p.R1030R		Atlas-SNP	.											.	ADCY1	187	.	0			c.G3090A						PASS	.	G		1341,3065	447.5+/-348.4	212,917,1074	84.0	79.0	81.0		3090	2.8	0.0	7	dbSNP_100	81	1443,7157	277.1+/-292.7	125,1193,2982	no	coding-synonymous	ADCY1	NM_021116.2		337,2110,4056	AA,AG,GG		16.7791,30.4358,21.4055		1030/1120	45753324	2784,10222	2203	4300	6503	SO:0001819	synonymous_variant	107	exon20			GAGAAGGTGCCCC	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"""Adenylate cyclases"""	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.3090G>A	7.37:g.45753324G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	36	26	0.722222	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	37	CCDS34631.1																																																																																			G|0.797;A|0.203	0.203	strong		0.532	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116	
FAM186B	84070	hgsc.bcm.edu	37	12	49993678	49993678	+	Missense_Mutation	SNP	C	C	T	rs52824916	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49993678C>T	ENST00000257894.2	-	4	1906	c.1745G>A	c.(1744-1746)cGg>cAg	p.R582Q	PRPF40B_ENST00000508736.1_3'UTR|FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.R492Q	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	582						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AGATTGGGTCCGGCTTGGGGC	0.577													C|||	567	0.113219	0.2012	0.0922	5008	,	,		18406	0.0823		0.0885	False		,,,				2504	0.0665				p.R582Q		Atlas-SNP	.											.	FAM186B	72	.	0			c.G1745A						PASS	.	C	GLN/ARG	765,3641	313.0+/-292.9	62,641,1500	92.0	83.0	86.0		1745	1.5	0.0	12	dbSNP_128	86	721,7879	175.8+/-225.7	30,661,3609	yes	missense	FAM186B	NM_032130.2	43	92,1302,5109	TT,TC,CC		8.3837,17.3627,11.4255	possibly-damaging	582/894	49993678	1486,11520	2203	4300	6503	SO:0001583	missense	84070	exon4			TGGGTCCGGCTTG	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 25"""	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.1745G>A	12.37:g.49993678C>T	ENSP00000257894:p.Arg582Gln	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_032130	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	250	0.11446886446886446	103	0.20934959349593496	44	0.12154696132596685	35	0.06118881118881119	68	0.08970976253298153	C	10.34	1.324055	0.24080	0.173627	0.083837	ENSG00000135436	ENST00000544141;ENST00000532262;ENST00000257894	T;T;T	0.13089	2.63;2.62;2.85	4.33	1.51	0.23008	.	0.417675	0.17762	N	0.162860	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B;B	0.31318	0.319;0.168	B;B	0.25405	0.06;0.048	T	0.30327	-0.9982	8	.	.	.	-12.2787	6.0347	0.19699	0.0:0.6777:0.0:0.3223	rs52824916	492;582	B4DZ15;Q8IYM0	.;F186B_HUMAN	Q	492;195;582	ENSP00000438569:R492Q;ENSP00000436995:R195Q;ENSP00000257894:R582Q	.	R	-	2	0	FAM186B	48279945	0.000000	0.05858	0.026000	0.17262	0.074000	0.17049	0.139000	0.16036	0.577000	0.29470	0.563000	0.77884	CGG	C|0.886;T|0.114	0.114	strong		0.577	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130	
OR5P2	120065	hgsc.bcm.edu	37	11	7818190	7818190	+	Silent	SNP	C	C	T	rs73406607	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7818190C>T	ENST00000329434.2	-	1	330	c.300G>A	c.(298-300)gcG>gcA	p.A100A	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CAAAGAAAGCCGCTGAACCAA	0.483													C|||	1185	0.236621	0.348	0.2911	5008	,	,		18298	0.128		0.2763	False		,,,				2504	0.1186				p.A100A		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	0			c.G300A						PASS	.	C		1370,2838		401,568,1135	98.0	116.0	110.0		300	-7.1	0.0	11	dbSNP_130	110	2424,6160		392,1640,2260	no	coding-synonymous	OR5P2	NM_153444.1		793,2208,3395	TT,TC,CC		28.2386,32.557,29.6592		100/323	7818190	3794,8998	2104	4292	6396	SO:0001819	synonymous_variant	120065	exon1			GAAAGCCGCTGAA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.300G>A	11.37:g.7818190C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			C|0.738;T|0.262	0.262	strong		0.483	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
POLRMT	5442	hgsc.bcm.edu	37	19	621063	621063	+	Silent	SNP	A	A	G	rs76890343	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:621063A>G	ENST00000588649.2	-	10	2719	c.2635T>C	c.(2635-2637)Ttg>Ctg	p.L879L	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	879	Mediates interaction with TEFM.				gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		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)		CCTACCGTCAAGGGTTGGTCC	0.756													A|||	1109	0.221446	0.1823	0.1499	5008	,	,		4907	0.249		0.172	False		,,,				2504	0.3476				p.L879L		Atlas-SNP	.											.	POLRMT	91	.	0			c.T2635C						PASS	.	A		667,3715		53,561,1577	17.0	20.0	19.0		2635	0.9	0.9	19	dbSNP_131	19	1367,7215		124,1119,3048	no	coding-synonymous	POLRMT	NM_005035.3		177,1680,4625	GG,GA,AA		15.9287,15.2214,15.6896		879/1231	621063	2034,10930	2191	4291	6482	SO:0001819	synonymous_variant	5442	exon10			CCGTCAAGGGTTG		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.2635T>C	19.37:g.621063A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			A|0.839;G|0.161	0.161	strong		0.756	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
TMEM150B	284417	hgsc.bcm.edu	37	19	55824332	55824332	+	Missense_Mutation	SNP	T	T	G	rs7246479	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55824332T>G	ENST00000326652.4	-	8	779	c.597A>C	c.(595-597)ttA>ttC	p.L199F	TMEM150B_ENST00000438693.1_Missense_Mutation_p.L199F|CTD-2105E13.14_ENST00000596786.1_RNA	NM_001282011.1	NP_001268940.1	A6NC51	T150B_HUMAN	transmembrane protein 150B	199			L -> F (in dbSNP:rs7246479). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)	3						AGTCAACGGCTAAGAGACCGA	0.687													G|||	2933	0.585663	0.9758	0.5504	5008	,	,		15517	0.1845		0.507	False		,,,				2504	0.5777				p.L199F		Atlas-SNP	.											TMEM150B,NS,carcinoma,0,2	TMEM150B	19	2	0			c.A597C						PASS	.	G	PHE/LEU	3912,418		1776,360,29	33.0	40.0	38.0	http://omim.org/entry/612884	597	-9.1	0.0	19	dbSNP_116	38	4404,4134		1169,2066,1034	yes	missense	TMEM150B	NM_001085488.1	22	2945,2426,1063	GG,GT,TT		48.4188,9.6536,35.3746	benign	199/234	55824332	8316,4552	2165	4269	6434	SO:0001583	missense	284417	exon8			AACGGCTAAGAGA	BC020862	CCDS42629.1	19q13.42	2009-06-12	2009-06-12	2009-06-12		ENSG00000180061			34415	protein-coding gene	gene with protein product			"""transmembrane protein 224"""	TMEM224			Standard	XM_005258812		Approved		uc010esw.1	A6NC51		ENST00000326652.4:c.597A>C	19.37:g.55824332T>G	ENSP00000320757:p.Leu199Phe	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	130	65	0.5	NM_001085488	B7ZW71	Missense_Mutation	SNP	ENST00000326652.4	37	CCDS42629.1	1163	0.5325091575091575	476	0.967479674796748	209	0.5773480662983426	97	0.16958041958041958	381	0.5026385224274407	.	0.004	-2.287974	0.00248	0.903464	0.515812	ENSG00000180061	ENST00000326652;ENST00000438693	T;T	0.38722	1.12;1.12	4.55	-9.11	0.00711	.	0.338095	0.29100	N	0.013156	T	0.00012	0.0000	N	0.00885	-1.115	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.49244	-0.8960	9	0.02654	T	1	-5.6985	2.8377	0.05520	0.3262:0.4128:0.106:0.155	rs7246479;rs17667776;rs59720218;rs7246479	199	A6NC51	T150B_HUMAN	F	199	ENSP00000320757:L199F;ENSP00000412658:L199F	ENSP00000320757:L199F	L	-	3	2	TMEM150B	60516144	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-4.614000	0.00208	-3.831000	0.00101	-1.592000	0.00843	TTA	T|0.444;G|0.556	0.556	strong		0.687	TMEM150B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452685.1	NM_001085488	
MYH11	4629	hgsc.bcm.edu	37	16	15839034	15839034	+	Silent	SNP	G	G	A	rs587781048|rs1050113	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:15839034G>A	ENST00000300036.5	-	20	2581	c.2472C>T	c.(2470-2472)gcC>gcT	p.A824A	MYH11_ENST00000396324.3_Silent_p.A831A|MYH11_ENST00000452625.2_Silent_p.A831A|MYH11_ENST00000576790.2_Silent_p.A824A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	824					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGAGGTAGGCGGCGCAGTTCC	0.627			T	CBFB	AML								G|||	1270	0.253594	0.1112	0.2695	5008	,	,		18020	0.3542		0.339	False		,,,				2504	0.2434				p.A831A		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	MYH11_ENST00000396324,NS,carcinoma,-2,4	MYH11	520	4	0			c.C2493T						PASS	.	G	,,,	651,3743	279.9+/-275.1	53,545,1599	82.0	80.0	81.0		2493,2493,2472,2472	-9.6	0.3	16	dbSNP_86	81	2769,5831	440.5+/-359.5	471,1827,2002	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	524,2372,3601	AA,AG,GG		32.1977,14.8157,26.3198	,,,	831/1946,831/1980,824/1973,824/1939	15839034	3420,9574	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon21			GTAGGCGGCGCAG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.2472C>T	16.37:g.15839034G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	28	0.595745	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			T|0.000;G|0.726;C|0.000;A|0.274	0.274	strong		0.627	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
KLHL38	340359	hgsc.bcm.edu	37	8	124663895	124663895	+	Silent	SNP	G	G	A	rs16898689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124663895G>A	ENST00000325995.7	-	1	1295	c.1272C>T	c.(1270-1272)ccC>ccT	p.P424P	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	424										breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						CAGCGACTGCGGGGTGGAGCA	0.552													G|||	916	0.182907	0.2284	0.1311	5008	,	,		21736	0.2202		0.0686	False		,,,				2504	0.2372				p.P424P		Atlas-SNP	.											.	KLHL38	81	.	0			c.C1272T						PASS	.	G		754,3296		80,594,1351	94.0	93.0	94.0		1272	-0.5	1.0	8	dbSNP_123	94	568,7802		21,526,3638	no	coding-synonymous	KLHL38	NM_001081675.2		101,1120,4989	AA,AG,GG		6.7861,18.6173,10.6441		424/582	124663895	1322,11098	2025	4185	6210	SO:0001819	synonymous_variant	340359	exon1			GACTGCGGGGTGG		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1272C>T	8.37:g.124663895G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_001081675	A0PK12	Silent	SNP	ENST00000325995.7	37	CCDS43766.1																																																																																			G|0.857;A|0.143	0.143	strong		0.552	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
SPPL2C	162540	hgsc.bcm.edu	37	17	43923683	43923683	+	Missense_Mutation	SNP	A	A	G	rs12185268	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43923683A>G	ENST00000329196.5	+	1	1428	c.1411A>G	c.(1411-1413)Atc>Gtc	p.I471V	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	471			I -> V (in dbSNP:rs12185268).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CTCCCGTCAGATCTACTTCGT	0.582													G|||	432	0.086262	0.0151	0.1585	5008	,	,		22310	0.001		0.2396	False		,,,				2504	0.0613				p.I471V		Atlas-SNP	.											.	.	.	.	0			c.A1411G						PASS	.	G	VAL/ILE	203,4203	807.6+/-415.9	5,193,2005	134.0	101.0	112.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1411	0.8	0.3	17	dbSNP_120	112	1928,6672	726.4+/-406.6	221,1486,2593	yes	missense	IMP5	NM_175882.2	29	226,1679,4598	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	22.4186,4.6074,16.3847	benign	471/685	43923683	2131,10875	2203	4300	6503	SO:0001583	missense	162540	exon1			CGTCAGATCTACT		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1411A>G	17.37:g.43923683A>G	ENSP00000332488:p.Ile471Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	0	-2.736907	0.00088	0.046074	0.224186	ENSG00000185294	ENST00000329196	T	0.17213	2.29	5.2	0.828	0.18841	.	0.406531	0.17861	N	0.159532	T	0.00012	0.0000	N	0.00869	-1.13	0.58432	P	8.000000000008E-6	B	0.11235	0.004	B	0.15484	0.013	T	0.41431	-0.9509	9	0.02654	T	1	-17.3089	4.7545	0.13077	0.3353:0.3144:0.3503:0.0	rs12185268;rs17763723;rs60640757;rs12185268	471	Q8IUH8	IMP5_HUMAN	V	471	ENSP00000332488:I471V	ENSP00000332488:I471V	I	+	1	0	AC217771.1	41279463	0.049000	0.20398	0.302000	0.25058	0.000000	0.00434	0.337000	0.19841	-0.152000	0.11156	-0.971000	0.02607	ATC	A|0.853;G|0.147	0.147	strong		0.582	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
ARSG	22901	hgsc.bcm.edu	37	17	66364804	66364804	+	Missense_Mutation	SNP	T	T	C	rs1558878	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:66364804T>C	ENST00000448504.2	+	7	1616	c.820T>C	c.(820-822)Tgg>Cgg	p.W274R	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Missense_Mutation_p.W110R	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	274			W -> R (in dbSNP:rs1558878).		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)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGCAGGGCTCTGGGAGATGGA	0.542													C|||	1800	0.359425	0.3185	0.4424	5008	,	,		21144	0.2351		0.4831	False		,,,				2504	0.3569				p.W274R		Atlas-SNP	.											.	ARSG	55	.	0			c.T820C						PASS	.	C	ARG/TRP	1524,2882	673.2+/-402.8	268,988,947	117.0	109.0	112.0		820	4.3	0.4	17	dbSNP_88	112	4276,4324	579.7+/-390.9	1066,2144,1090	yes	missense	ARSG	NM_014960.3	101	1334,3132,2037	CC,CT,TT		49.7209,34.5892,44.5948	benign	274/526	66364804	5800,7206	2203	4300	6503	SO:0001583	missense	22901	exon7			GGGCTCTGGGAGA	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.820T>C	17.37:g.66364804T>C	ENSP00000407193:p.Trp274Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	37	CCDS11676.1	807	0.3695054945054945	146	0.2967479674796748	153	0.42265193370165743	144	0.2517482517482518	364	0.48021108179419525	C	0.021	-1.427426	0.01117	0.345892	0.497209	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.26	4.28	0.50868	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.780131	0.12215	N	0.488911	T	0.00012	0.0000	N	0.00325	-1.645	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47142	-0.9140	8	0.15499	T	0.54	.	5.0112	0.14313	0.25:0.5859:0.0:0.1641	rs1558878;rs3744299;rs52799630;rs61503778;rs1558878	274	Q96EG1	ARSG_HUMAN	R	274;173	.	ENSP00000407193:W173R	W	+	1	0	ARSG	63876399	0.021000	0.18746	0.385000	0.26158	0.028000	0.11728	0.486000	0.22340	1.467000	0.48044	-0.119000	0.15052	TGG	T|0.602;C|0.398	0.398	strong		0.542	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
CAMTA1	23261	hgsc.bcm.edu	37	1	7723588	7723588	+	Silent	SNP	C	C	T	rs3737906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:7723588C>T	ENST00000303635.7	+	9	1188	c.981C>T	c.(979-981)aaC>aaT	p.N327N	CAMTA1_ENST00000439411.2_Silent_p.N327N	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	327					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		AGAAGAGGAACGGCAAGGTGG	0.652			T	WWTR1	epitheliod hemangioendothelioma								C|||	298	0.0595048	0.0061	0.0735	5008	,	,		18971	0.0198		0.1431	False		,,,				2504	0.0767				p.N327N		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.C981T						PASS	.	C		135,4271	98.0+/-136.7	1,133,2069	97.0	94.0	95.0		981	-1.3	1.0	1	dbSNP_107	95	1224,7376	246.9+/-275.2	97,1030,3173	no	coding-synonymous	CAMTA1	NM_015215.2		98,1163,5242	TT,TC,CC		14.2326,3.064,10.449		327/1674	7723588	1359,11647	2203	4300	6503	SO:0001819	synonymous_variant	23261	exon9			GAGGAACGGCAAG	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.981C>T	1.37:g.7723588C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	37	CCDS30576.1																																																																																			C|0.901;T|0.099	0.099	strong		0.652	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
WDR93	56964	hgsc.bcm.edu	37	15	90246336	90246336	+	Silent	SNP	A	A	G	rs16974175	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90246336A>G	ENST00000268130.7	+	3	560	c.459A>G	c.(457-459)ttA>ttG	p.L153L	WDR93_ENST00000558000.1_Silent_p.L153L|RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000560294.1_Silent_p.L153L	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	153					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CCACAGATTTAGGGAATGAAA	0.388													G|||	1964	0.392173	0.5061	0.3631	5008	,	,		20249	0.2063		0.4016	False		,,,				2504	0.4407				p.L153L		Atlas-SNP	.											.	WDR93	63	.	0			c.A459G						PASS	.	G		2142,2258	594.6+/-388.3	529,1084,587	187.0	183.0	185.0		459	0.2	1.0	15	dbSNP_123	185	3848,4750	609.9+/-395.6	846,2156,1297	no	coding-synonymous	WDR93	NM_020212.1		1375,3240,1884	GG,GA,AA		44.7546,48.6818,46.084		153/687	90246336	5990,7008	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon3			AGATTTAGGGAAT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.459A>G	15.37:g.90246336A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			A|0.575;G|0.425	0.425	strong		0.388	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
TMEM63A	9725	hgsc.bcm.edu	37	1	226046974	226046974	+	Silent	SNP	T	T	C	rs2292561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226046974T>C	ENST00000366835.3	-	15	1569	c.1299A>G	c.(1297-1299)ctA>ctG	p.L433L	TMEM63A_ENST00000474478.1_5'Flank	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	433					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					TCAGGAAAAATAGCCCCAGGA	0.542													C|||	548	0.109425	0.1452	0.0965	5008	,	,		17585	0.1577		0.0497	False		,,,				2504	0.0818				p.L433L		Atlas-SNP	.											.	TMEM63A	75	.	0			c.A1299G						PASS	.	C		628,3778	767.6+/-413.5	44,540,1619	131.0	118.0	122.0		1299	-4.3	0.9	1	dbSNP_100	122	354,8246	803.7+/-407.3	3,348,3949	no	coding-synonymous	TMEM63A	NM_014698.2		47,888,5568	CC,CT,TT		4.1163,14.2533,7.5504		433/808	226046974	982,12024	2203	4300	6503	SO:0001819	synonymous_variant	9725	exon15			GAAAAATAGCCCC		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.1299A>G	1.37:g.226046974T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	193	91	0.471503	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			T|0.916;C|0.084	0.084	strong		0.542	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
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 GAIIx	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		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	106	49	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	
MAPT	4137	hgsc.bcm.edu	37	17	44073889	44073889	+	Silent	SNP	A	A	G	rs1052553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44073889A>G	ENST00000571987.1	+	9	1632	c.1632A>G	c.(1630-1632)gcA>gcG	p.A544A	MAPT_ENST00000334239.8_Silent_p.A169A|MAPT_ENST00000535772.1_Silent_p.A227A|MAPT_ENST00000347967.5_Silent_p.A133A|MAPT_ENST00000351559.5_Silent_p.A227A|MAPT_ENST00000344290.5_Silent_p.A562A|MAPT_ENST00000420682.2_Silent_p.A198A|MAPT_ENST00000340799.5_Silent_p.A198A|MAPT_ENST00000446361.3_Silent_p.A169A|MAPT_ENST00000262410.5_Silent_p.A544A|MAPT_ENST00000570299.1_3'UTR|STH_ENST00000537309.1_5'Flank|MAPT_ENST00000576518.1_Silent_p.A158A|MAPT_ENST00000431008.3_Silent_p.A227A|MAPT_ENST00000415613.2_Silent_p.A562A|MAPT_ENST00000574436.1_Silent_p.A227A			P10636	TAU_HUMAN	microtubule-associated protein tau	544					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	AGAAGGTGGCAGTGGTCCGTA	0.682													G|||	442	0.0882588	0.0219	0.1571	5008	,	,		11254	0.001		0.2416	False		,,,				2504	0.0613				p.A562A		Atlas-SNP	.											MAPT_ENST00000344290,NS,carcinoma,0,2	MAPT	135	2	0			c.A1686G						PASS	.	G	,,,,,,,	231,4175	776.6+/-414.2	6,219,1978	24.0	25.0	24.0		1686,594,594,681,681,507,1632,507	-11.2	0.4	17	dbSNP_86	24	1901,6699	699.3+/-405.1	215,1471,2614	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,	221,1690,4592	GG,GA,AA		22.1047,5.2429,16.3924	,,,,,,,	562/777,198/413,198/382,227/411,227/442,169/384,544/759,169/353	44073889	2132,10874	2203	4300	6503	SO:0001819	synonymous_variant	4137	exon11			GGTGGCAGTGGTC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1632A>G	17.37:g.44073889A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			A|0.865;G|0.135	0.135	strong		0.682	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
PHYHD1	254295	hgsc.bcm.edu	37	9	131702891	131702891	+	Silent	SNP	A	A	G	rs2273866	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131702891A>G	ENST00000372592.3	+	11	1533	c.600A>G	c.(598-600)agA>agG	p.R200R	PHYHD1_ENST00000421063.2_Silent_p.R179R|PHYHD1_ENST00000487504.1_3'UTR|PHYHD1_ENST00000353176.5_Silent_p.R179R|RP11-101E3.5_ENST00000482796.1_5'Flank|PHYHD1_ENST00000308941.5_Missense_Mutation_p.E193G	NM_001100876.1	NP_001094346.1	Q5SRE7	PHYD1_HUMAN	phytanoyl-CoA dioxygenase domain containing 1	200							dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)	p.E193G(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(1)|stomach(3)	10						GTGTGTCAAGAAGGATGGTCC	0.607													A|||	1760	0.351438	0.3555	0.4251	5008	,	,		18832	0.2381		0.4095	False		,,,				2504	0.3507				p.E193G		Atlas-SNP	.											PHYHD1,NS,carcinoma,0,1	PHYHD1	29	1	1	Substitution - Missense(1)	stomach(1)	c.A578G						PASS	.	A	,,GLY/GLU	1558,2848	490.6+/-361.9	254,1050,899	108.0	100.0	103.0		600,537,578	-1.5	0.9	9	dbSNP_100	103	3247,5353	488.0+/-372.2	631,1985,1684	yes	coding-synonymous,coding-synonymous,missense	PHYHD1	NM_001100876.1,NM_001100877.1,NM_174933.3	,,98	885,3035,2583	GG,GA,AA		37.7558,35.3609,36.9445	,,	200/292,179/271,193/298	131702891	4805,8201	2203	4300	6503	SO:0001819	synonymous_variant	254295	exon10			GTCAAGAAGGATG	BC051300	CCDS6914.1, CCDS43885.1, CCDS43886.1	9q34.13	2010-08-13			ENSG00000175287	ENSG00000175287			23396	protein-coding gene	gene with protein product						12477932	Standard	NM_174933		Approved	MGC16638	uc004bwp.2	Q5SRE7	OTTHUMG00000020764	ENST00000372592.3:c.600A>G	9.37:g.131702891A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	54	34	0.62963	NM_174933	A6PWN9|A6PWP0|B3KT57|B4E3X8|Q5SRE9|Q5SRF0|Q7Z623|Q7Z7P9|Q96GM4	Missense_Mutation	SNP	ENST00000372592.3	37	CCDS43885.1	790	0.3617216117216117	198	0.4024390243902439	149	0.4116022099447514	130	0.22727272727272727	313	0.4129287598944591	A	14.23	2.473911	0.43942	0.353609	0.377558	ENSG00000175287	ENST00000308941	.	.	.	4.78	-1.45	0.08828	.	2.450790	0.02210	N	0.063064	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999990798	B	0.06786	0.001	B	0.08055	0.003	T	0.39143	-0.9628	7	0.22109	T	0.4	0.7128	8.2316	0.31601	0.2791:0.1426:0.5782:0.0	rs2273866;rs17452324;rs17455259;rs17485374;rs17850494;rs52819401;rs56896723;rs2273866	193	Q5SRE7-3	.	G	193	.	ENSP00000309515:E193G	E	+	2	0	PHYHD1	130742712	0.920000	0.31207	0.901000	0.35422	0.949000	0.60115	-0.020000	0.12525	-0.043000	0.13513	0.454000	0.30748	GAA	A|0.643;G|0.357	0.357	strong		0.607	PHYHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054506.2	NM_174933	
SYNJ2	8871	hgsc.bcm.edu	37	6	158517308	158517308	+	Missense_Mutation	SNP	A	A	G	rs2502601	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:158517308A>G	ENST00000355585.4	+	27	4478	c.4403A>G	c.(4402-4404)gAa>gGa	p.E1468G	SYNJ2_ENST00000367112.1_Missense_Mutation_p.E553G|SYNJ2_ENST00000367122.2_Missense_Mutation_p.E1423G	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1468			E -> G (in dbSNP:rs2502601). {ECO:0000269|PubMed:15489334}.		phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		CCAGATCATGAACACAAAACC	0.522													A|||	2741	0.547324	0.612	0.3573	5008	,	,		19391	0.5694		0.5119	False		,,,				2504	0.6084				p.E1468G		Atlas-SNP	.											SYNJ2,colon,carcinoma,0,1	SYNJ2	111	1	0			c.A4403G						PASS	.	A	GLY/GLU,GLY/GLU	2563,1843	609.5+/-391.4	733,1097,373	36.0	40.0	39.0		3692,4403	0.1	0.0	6	dbSNP_100	39	4379,4221	556.6+/-386.9	1112,2155,1033	yes	missense,missense	SYNJ2	NM_001178088.1,NM_003898.3	98,98	1845,3252,1406	GG,GA,AA		49.0814,41.8293,46.6246	benign,benign	1231/1260,1468/1497	158517308	6942,6064	2203	4300	6503	SO:0001583	missense	8871	exon27			ATCATGAACACAA	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.4403A>G	6.37:g.158517308A>G	ENSP00000347792:p.Glu1468Gly	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	55	54	0.981818	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	1147	0.5251831501831502	308	0.6260162601626016	139	0.3839779005524862	304	0.5314685314685315	396	0.5224274406332454	A	8.806	0.934158	0.18206	0.581707	0.509186	ENSG00000078269	ENST00000367122;ENST00000355585;ENST00000367112	D;D;T	0.92199	-2.96;-2.99;1.03	5.06	0.0796	0.14417	.	1.323870	0.04980	N	0.465520	T	0.59307	0.2184	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.54669	-0.8259	9	0.10902	T	0.67	.	5.0449	0.14479	0.4384:0.148:0.4136:0.0	rs2502601;rs17568135;rs17854277;rs56616670;rs56887519;rs2502601	863;1468	B4DLC4;O15056	.;SYNJ2_HUMAN	G	1423;1468;553	ENSP00000356089:E1423G;ENSP00000347792:E1468G;ENSP00000356079:E553G	ENSP00000347792:E1468G	E	+	2	0	SYNJ2	158437296	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.017000	0.12590	-0.029000	0.13827	-0.242000	0.12053	GAA	A|0.464;G|0.536	0.536	strong		0.522	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2		
C9orf152	401546	hgsc.bcm.edu	37	9	112963702	112963702	+	Silent	SNP	G	G	A	rs4978888	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:112963702G>A	ENST00000400613.4	-	2	855	c.246C>T	c.(244-246)aaC>aaT	p.N82N	C9orf152_ENST00000473442.1_Intron	NM_001012993.2	NP_001013011.2	Q5JTZ5	CI152_HUMAN	chromosome 9 open reading frame 152	82										NS(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						TTCTCTCCTTGTTAATCCAAA	0.567													G|||	1092	0.218051	0.3517	0.1744	5008	,	,		20932	0.126		0.167	False		,,,				2504	0.2157				p.N82N		Atlas-SNP	.											.	C9orf152	20	.	0			c.C246T						PASS	.	G		1352,3054	446.1+/-347.9	215,922,1066	67.0	66.0	67.0		246	2.7	1.0	9	dbSNP_111	67	1309,7291	255.0+/-280.0	102,1105,3093	no	coding-synonymous	C9orf152	NM_001012993.2		317,2027,4159	AA,AG,GG		15.2209,30.6854,20.4598		82/240	112963702	2661,10345	2203	4300	6503	SO:0001819	synonymous_variant	401546	exon2			CTCCTTGTTAATC	BX648620	CCDS35102.2	9q31.3	2012-04-03			ENSG00000188959	ENSG00000188959			31455	protein-coding gene	gene with protein product							Standard	NM_001012993		Approved	bA470J20.2	uc011lwk.2	Q5JTZ5	OTTHUMG00000020478	ENST00000400613.4:c.246C>T	9.37:g.112963702G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_001012993	A8MWT6	Silent	SNP	ENST00000400613.4	37	CCDS35102.2																																																																																			G|0.786;A|0.214	0.214	strong		0.567	C9orf152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053602.2	NM_001012993	
LOXHD1	125336	hgsc.bcm.edu	37	18	44181227	44181227	+	Missense_Mutation	SNP	C	C	T	rs10163657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44181227C>T	ENST00000398722.4	-	1	252	c.253G>A	c.(253-255)Gtc>Atc	p.V85I	LOXHD1_ENST00000441551.2_Missense_Mutation_p.V363I|LOXHD1_ENST00000536736.1_Missense_Mutation_p.V363I			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	85	PLAT 1. {ECO:0000255|PROSITE- ProRule:PRU00152}.		V -> I (in dbSNP:rs10163657).		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						CCATGCCCGACGGAGACCCGA	0.587													T|||	214	0.0427316	0.0113	0.049	5008	,	,		16573	0.0347		0.0885	False		,,,				2504	0.0419				p.V363I		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G1087A						PASS	.	T	ILE/VAL	25,1359		1,23,668	36.0	35.0	35.0		1087	5.6	1.0	18	dbSNP_119	35	287,2895		15,257,1319	yes	missense	LOXHD1	NM_144612.6	29	16,280,1987	TT,TC,CC		9.0195,1.8064,6.8331	benign	363/2212	44181227	312,4254	692	1591	2283	SO:0001583	missense	125336	exon8			GCCCGACGGAGAC	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.253G>A	18.37:g.44181227C>T	ENSP00000381707:p.Val85Ile	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		117|117	0.05357142857142857|0.05357142857142857	9|9	0.018292682926829267|0.018292682926829267	22|22	0.06077348066298342|0.06077348066298342	23|23	0.04020979020979021|0.04020979020979021	63|63	0.08311345646437995|0.08311345646437995	T|T	16.42|16.42	3.118123|3.118123	0.56505|0.56505	0.018064|0.018064	0.090195|0.090195	ENSG00000167210|ENSG00000167210	ENST00000441551|ENST00000398722;ENST00000536736;ENST00000335730	T|T;T	0.63580|0.60920	-0.05|0.15;0.15	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	.|0.000000	.|0.85682	.|N	.|0.000000	T|T	0.00875|0.00875	0.0029|0.0029	N|N	0.01289|0.01289	-0.905|-0.905	0.80722|0.80722	D|D	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.08166|0.08166	-1.0735|-1.0735	6|10	.|0.02654	.|T	.|1	.|.	11.5812|11.5812	0.50891|0.50891	0.0:0.0699:0.0:0.9301|0.0:0.0699:0.0:0.9301	rs10163657;rs52829357;rs61505174;rs10163657|rs10163657;rs52829357;rs61505174;rs10163657	.|363;85	.|F5GZB4;Q8IVV2-2	.|.;.	H|I	343|85;363;85	ENSP00000387621:R343H|ENSP00000381707:V85I;ENSP00000444586:V363I	.|ENSP00000338222:V85I	R|V	-|-	2|1	0|0	LOXHD1|LOXHD1	42435225|42435225	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.985000|0.985000	0.73830|0.73830	5.156000|5.156000	0.64905|0.64905	0.950000|0.950000	0.37743|0.37743	-0.361000|-0.361000	0.07541|0.07541	CGT|GTC	C|0.945;T|0.055	0.055	strong		0.587	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
BRINP1	1620	hgsc.bcm.edu	37	9	122001000	122001000	+	Silent	SNP	G	G	A	rs2274157	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:122001000G>A	ENST00000265922.3	-	5	1079	c.618C>T	c.(616-618)agC>agT	p.S206S	BRINP1_ENST00000373964.2_Silent_p.S206S	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	206	MACPF.				cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)		p.S206S(1)									GATTGTCATAGCTGTTACAGC	0.502													G|||	2214	0.442093	0.1664	0.4726	5008	,	,		19411	0.6736		0.4523	False		,,,				2504	0.544				p.S206S		Atlas-SNP	.											DBC1,NS,carcinoma,0,1	DBC1	194	1	1	Substitution - coding silent(1)	stomach(1)	c.C618T						PASS	.	G		900,3506	349.3+/-310.3	95,710,1398	129.0	93.0	105.0		618	5.9	1.0	9	dbSNP_100	105	3669,4931	526.4+/-380.9	780,2109,1411	no	coding-synonymous	DBC1	NM_014618.2		875,2819,2809	AA,AG,GG		42.6628,20.4267,35.1299		206/762	122001000	4569,8437	2203	4300	6503	SO:0001819	synonymous_variant	1620	exon5			GTCATAGCTGTTA	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.618C>T	9.37:g.122001000G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																			A|0.392;C|0.004	0.392	strong		0.502	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
IFNGR2	3460	hgsc.bcm.edu	37	21	34787312	34787312	+	Missense_Mutation	SNP	A	A	G	rs9808753	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:34787312A>G	ENST00000290219.6	+	2	839	c.191A>G	c.(190-192)cAa>cGa	p.Q64R	IFNGR2_ENST00000381995.1_Missense_Mutation_p.Q83R|IFNGR2_ENST00000405436.1_5'UTR	NM_005534.3	NP_005525.2	P38484	INGR2_HUMAN	interferon gamma receptor 2 (interferon gamma transducer 1)	64	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		Q -> R (in dbSNP:rs9808753). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8124716}.		cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	interferon-gamma receptor activity (GO:0004906)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|urinary_tract(1)	13					Interferon gamma-1b(DB00033)	GTTGTCTACCAAGTGCAGTTT	0.577													G|||	1362	0.271965	0.2489	0.196	5008	,	,		17759	0.4296		0.1431	False		,,,				2504	0.3272				p.Q64R		Atlas-SNP	.											.	IFNGR2	30	.	0			c.A191G						PASS	.	G	ARG/GLN	991,3415	731.6+/-410.3	106,779,1318	123.0	129.0	127.0		191	-1.3	0.1	21	dbSNP_119	127	1183,7417	764.3+/-407.6	89,1005,3206	yes	missense	IFNGR2	NM_005534.3	43	195,1784,4524	GG,GA,AA		13.7558,22.4921,16.7154	benign	64/338	34787312	2174,10832	2203	4300	6503	SO:0001583	missense	3460	exon2			TCTACCAAGTGCA		CCDS33544.1	21q22.1	2014-09-17			ENSG00000159128	ENSG00000159128		"""Interferons"", ""Fibronectin type III domain containing"""	5440	protein-coding gene	gene with protein product		147569		IFNGT1		3136170	Standard	NM_005534		Approved	AF-1	uc002yrp.4	P38484	OTTHUMG00000065188	ENST00000290219.6:c.191A>G	21.37:g.34787312A>G	ENSP00000290219:p.Gln64Arg	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	118	32	0.271186	NM_005534	Q9BTL5	Missense_Mutation	SNP	ENST00000290219.6	37	CCDS33544.1	562	0.2573260073260073	109	0.22154471544715448	80	0.22099447513812154	255	0.4458041958041958	118	0.15567282321899736	G	0.005	-2.136795	0.00335	0.224921	0.137558	ENSG00000159128	ENST00000290219;ENST00000381995	T;T	0.73258	-0.73;-0.73	5.39	-1.31	0.09230	Fibronectin, type III (2);Immunoglobulin-like fold (1);	1.344440	0.05212	N	0.507005	T	0.00012	0.0000	N	0.21617	0.685	0.54753	P	1.399999999995849E-5	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.29549	-1.0008	8	.	.	.	-7.6724	7.2739	0.26273	0.6569:0.142:0.2011:0.0	rs9808753;rs17879493;rs52804646;rs61332453;rs9808753	83;64	E7EUY1;P38484	.;INGR2_HUMAN	R	64;83	ENSP00000290219:Q64R;ENSP00000371425:Q83R	.	Q	+	2	0	IFNGR2	33709182	0.198000	0.23374	0.107000	0.21349	0.006000	0.05464	0.163000	0.16520	-0.769000	0.04620	-1.557000	0.00889	CAA	A|0.793;G|0.207	0.207	strong		0.577	IFNGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139916.1		
OR13D1	286365	hgsc.bcm.edu	37	9	107456933	107456933	+	Silent	SNP	C	C	T	rs12347076	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107456933C>T	ENST00000318763.5	+	1	274	c.231C>T	c.(229-231)ctC>ctT	p.L77L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	77						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						ATAGCCTCCTCATTATCATCA	0.448													C|||	1354	0.270367	0.1657	0.183	5008	,	,		20502	0.4821		0.1909	False		,,,				2504	0.3374				p.L77L		Atlas-SNP	.											.	OR13D1	42	.	0			c.C231T						PASS	.	C		789,3617	319.1+/-295.9	75,639,1489	208.0	208.0	208.0		231	0.3	0.2	9	dbSNP_120	208	1824,6776	328.2+/-318.2	224,1376,2700	no	coding-synonymous	OR13D1	NM_001004484.1		299,2015,4189	TT,TC,CC		21.2093,17.9074,20.0907		77/347	107456933	2613,10393	2203	4300	6503	SO:0001819	synonymous_variant	286365	exon1			CCTCCTCATTATC		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"""GPCR / Class A : Olfactory receptors"""	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.231C>T	9.37:g.107456933C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_001004484	B9EIS1|Q6IFL1	Silent	SNP	ENST00000318763.5	37	CCDS35094.1																																																																																			C|0.771;T|0.229	0.229	strong		0.448	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
LZTS2	84445	hgsc.bcm.edu	37	10	102766574	102766574	+	Silent	SNP	A	A	G	rs807024|rs386747052	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:102766574A>G	ENST00000370220.1	+	4	4722	c.1659A>G	c.(1657-1659)gcA>gcG	p.A553A	LZTS2_ENST00000370223.3_Silent_p.A553A					leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		TCCTCCTGGCAGAGAGTGATG	0.697													A|||	1840	0.367412	0.385	0.3271	5008	,	,		14091	0.5387		0.2346	False		,,,				2504	0.3323				p.A553A	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											LZTS2,colon,carcinoma,+1,1	LZTS2	57	1	0			c.A1659G						PASS	.	A		1461,2925		264,933,996	10.0	12.0	12.0		1659	-10.8	0.2	10	dbSNP_86	12	2083,6487		279,1525,2481	no	coding-synonymous	LZTS2	NM_032429.2		543,2458,3477	GG,GA,AA		24.3057,33.3105,27.3541		553/670	102766574	3544,9412	2193	4285	6478	SO:0001819	synonymous_variant	84445	exon5			CCTGGCAGAGAGT	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914	ENST00000370220.1:c.1659A>G	10.37:g.102766574A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	39	29	0.74359	NM_032429		Silent	SNP	ENST00000370220.1	37	CCDS7507.1																																																																																			A|0.651;G|0.349	0.349	strong		0.697	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743	
ENPP3	5169	hgsc.bcm.edu	37	6	132068060	132068060	+	Silent	SNP	A	A	G	rs145544747	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:132068060A>G	ENST00000414305.1	+	26	2920	c.2592A>G	c.(2590-2592)ctA>ctG	p.L864L	ENPP3_ENST00000358229.5_3'UTR|ENPP3_ENST00000357639.3_Silent_p.L864L			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	864	Nuclease.				immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		TTTTGCAACTAAAGACATATT	0.333													A|||	18	0.00359425	0.0023	0.0043	5008	,	,		13242	0.0		0.0119	False		,,,				2504	0.0				p.L864L		Atlas-SNP	.											.	ENPP3	117	.	0			c.A2592G						PASS	.	A		11,4395	17.9+/-39.9	0,11,2192	48.0	51.0	50.0		2592	-4.4	0.8	6	dbSNP_134	50	94,8506	50.6+/-110.7	0,94,4206	no	coding-synonymous	ENPP3	NM_005021.3		0,105,6398	GG,GA,AA		1.093,0.2497,0.8073		864/876	132068060	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	5169	exon25			GCAACTAAAGACA	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2592A>G	6.37:g.132068060A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_005021	Q5JTL3	Silent	SNP	ENST00000414305.1	37	CCDS5148.1																																																																																			A|0.994;G|0.006	0.006	strong		0.333	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		
FAM71F2	346653	hgsc.bcm.edu	37	7	128323034	128323034	+	Missense_Mutation	SNP	A	A	G	rs1109552	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128323034A>G	ENST00000480462.1	+	5	857	c.751A>G	c.(751-753)Att>Gtt	p.I251V	FAM71F2_ENST00000378704.3_Missense_Mutation_p.I242V|FAM71F2_ENST00000477515.1_Silent_p.P167P			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	251			I -> V (in dbSNP:rs1109552). {ECO:0000269|PubMed:15489334}.							NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						TGACACTGCCATTGAAATAGA	0.408													A|||	1661	0.331669	0.1778	0.3127	5008	,	,		19982	0.5635		0.2913	False		,,,				2504	0.3558				p.I251V		Atlas-SNP	.											.	FAM71F2	19	.	0			c.A751G						PASS	.	A	VAL/ILE,VAL/ILE	725,3011		75,575,1218	48.0	46.0	46.0		751,724	3.5	0.3	7	dbSNP_86	46	2449,5769		381,1687,2041	yes	missense,missense	FAM71F2	NM_001012454.3,NM_001128926.1	29,29	456,2262,3259	GG,GA,AA		29.8004,19.4058,26.5518	benign,benign	251/310,242/301	128323034	3174,8780	1868	4109	5977	SO:0001583	missense	346653	exon5			ACTGCCATTGAAA	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member B"""	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.751A>G	7.37:g.128323034A>G	ENSP00000420140:p.Ile251Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	711	0.32554945054945056	99	0.20121951219512196	103	0.2845303867403315	296	0.5174825174825175	213	0.28100263852242746	A	5.828	0.337080	0.11013	0.194058	0.298004	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001	T;T;T;T	0.06608	3.28;3.29;3.28;3.28	3.55	3.55	0.40652	.	0.835352	0.10227	N	0.700121	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.24368	0.102;0.062	B;B	0.22152	0.038;0.017	T	0.37709	-0.9694	9	0.02654	T	1	-9.2246	8.8344	0.35104	1.0:0.0:0.0:0.0	rs1109552;rs1133338;rs3178347;rs3195043;rs7458430;rs11536596;rs17133086;rs17418578;rs17846395;rs17859437;rs56738675;rs1109552	242;251	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	V	242;251;242;242	ENSP00000418907:I242V;ENSP00000420140:I251V;ENSP00000367976:I242V;ENSP00000401654:I242V	ENSP00000367976:I242V	I	+	1	0	FAM71F2	128110270	0.002000	0.14202	0.286000	0.24833	0.327000	0.28475	0.794000	0.26958	1.875000	0.54330	0.456000	0.33151	ATT	A|0.674;G|0.326	0.326	strong		0.408	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
SACS	26278	hgsc.bcm.edu	37	13	23905711	23905711	+	Silent	SNP	A	A	G	rs2737699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:23905711A>G	ENST00000382292.3	-	9	12577	c.12304T>C	c.(12304-12306)Ttg>Ctg	p.L4102L	SACS_ENST00000382298.3_Silent_p.L4102L|SACS_ENST00000402364.1_Silent_p.L3352L			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4102					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GTCATTGCCAATGCTAACAGG	0.343													A|||	1294	0.258387	0.053	0.3617	5008	,	,		22100	0.3145		0.2783	False		,,,				2504	0.3845				p.L4102L		Atlas-SNP	.											.	SACS	871	.	0			c.T12304C						PASS	.	A		426,3980	206.8+/-228.3	21,384,1798	94.0	90.0	91.0		12304	0.2	0.1	13	dbSNP_100	91	2234,6364	375.8+/-337.9	291,1652,2356	no	coding-synonymous	SACS	NM_014363.4		312,2036,4154	GG,GA,AA		25.9828,9.6686,20.4552		4102/4580	23905711	2660,10344	2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			TTGCCAATGCTAA	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.12304T>C	13.37:g.23905711A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	109	66	0.605505	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			G|0.232;N|0.000	0.232	strong		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
GAREM	64762	hgsc.bcm.edu	37	18	29867504	29867504	+	Silent	SNP	T	T	C	rs16962977	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:29867504T>C	ENST00000269209.6	-	4	1059	c.1056A>G	c.(1054-1056)gaA>gaG	p.E352E	GAREM_ENST00000578619.1_5'Flank|RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000399218.4_Silent_p.E352E			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	352					cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										TCTTGCATTCTTCATTCCAGT	0.562													C|||	487	0.0972444	0.2716	0.0476	5008	,	,		20431	0.0397		0.0388	False		,,,				2504	0.0164				p.E352E		Atlas-SNP	.											.	.	.	.	0			c.A1056G						PASS	.	C	,	1067,3339	721.0+/-409.1	122,823,1258	89.0	93.0	91.0		1056,1056	1.5	1.0	18	dbSNP_123	91	190,8410	810.1+/-407.1	0,190,4110	no	coding-synonymous,coding-synonymous	FAM59A	NM_001242409.1,NM_022751.2	,	122,1013,5368	CC,CT,TT		2.2093,24.217,9.6648	,	352/877,352/876	29867504	1257,11749	2203	4300	6503	SO:0001819	synonymous_variant	64762	exon4			GCATTCTTCATTC	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.1056A>G	18.37:g.29867504T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																			T|0.907;C|0.093	0.093	strong		0.562	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751	
ZFP64	55734	hgsc.bcm.edu	37	20	50803444	50803444	+	Silent	SNP	C	C	T	rs36027430	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:50803444C>T	ENST00000216923.4	-	2	562	c.213G>A	c.(211-213)tcG>tcA	p.S71S	ZFP64_ENST00000346617.4_Silent_p.S71S|ZFP64_ENST00000371515.4_Silent_p.S69S|ZFP64_ENST00000361387.2_Silent_p.S71S|ZFP64_ENST00000371518.2_Silent_p.S71S	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	71					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(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						CTGTTTCCTCCGATACAAACT	0.577													C|||	842	0.168131	0.3154	0.1643	5008	,	,		16761	0.1736		0.0706	False		,,,				2504	0.0665				p.S71S		Atlas-SNP	.											.	ZFP64	240	.	0			c.G213A						PASS	.	C	,,,	1206,3200	419.3+/-338.6	170,866,1167	138.0	121.0	127.0		213,213,207,213	-11.2	0.0	20	dbSNP_126	127	493,8107	142.3+/-198.5	8,477,3815	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	,,,	178,1343,4982	TT,TC,CC		5.7326,27.3718,13.0632	,,,	71/682,71/628,69/680,71/646	50803444	1699,11307	2203	4300	6503	SO:0001819	synonymous_variant	55734	exon2			TTCCTCCGATACA	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.213G>A	20.37:g.50803444C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			C|0.865;T|0.135	0.135	strong		0.577	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
LILRB5	10990	hgsc.bcm.edu	37	19	54754778	54754778	+	Missense_Mutation	SNP	G	G	A	rs150660840	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54754778G>A	ENST00000316219.5	-	13	1752	c.1645C>T	c.(1645-1647)Ccc>Tcc	p.P549S	LILRB5_ENST00000449561.2_Missense_Mutation_p.P550S|CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000450632.1_Silent_p.P619P|LILRB5_ENST00000345866.6_Missense_Mutation_p.P450S	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	549					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACATCCTGGGGGGCTTCAGAT	0.632																																					p.P550S		Atlas-SNP	.											LILRB5,NS,carcinoid-endocrine_tumour,+1,1	LILRB5	176	1	0			c.C1648T						scavenged	.	G	SER/PRO,SER/PRO,SER/PRO	50,4356	36.8+/-68.6	2,46,2155	38.0	43.0	42.0		1648,1348,1645	0.3	0.0	19	dbSNP_134	42	5,8587	3.7+/-12.6	0,5,4291	no	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	74,74,74	2,51,6446	AA,AG,GG		0.0582,1.1348,0.4231	benign,benign,benign	550/592,450/492,549/591	54754778	55,12943	2203	4296	6499	SO:0001583	missense	10990	exon13			CCTGGGGGGCTTC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1645C>T	19.37:g.54754778G>A	ENSP00000320390:p.Pro549Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	151	6	0.0397351	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559321	0.27827	0.011348	5.82E-4	ENSG00000105609	ENST00000316219;ENST00000449561;ENST00000345866	T;T;T	0.00543	6.77;6.74;6.68	2.75	0.32	0.15878	.	.	.	.	.	T	0.00496	0.0016	M	0.72894	2.215	0.09310	N	0.999999	B;B;P	0.43169	0.235;0.041;0.8	B;B;B	0.41036	0.202;0.054;0.346	T	0.46596	-0.9180	9	0.59425	D	0.04	.	3.188	0.06607	0.1533:0.0:0.5888:0.2579	.	450;550;549	O75023-2;O75023-3;O75023	.;.;LIRB5_HUMAN	S	549;550;450	ENSP00000320390:P549S;ENSP00000406478:P550S;ENSP00000263430:P450S	ENSP00000320390:P549S	P	-	1	0	LILRB5	59446590	0.000000	0.05858	0.034000	0.17996	0.619000	0.37552	-0.640000	0.05440	0.033000	0.15463	0.585000	0.79938	CCC	G|0.994;A|0.006	0.006	strong		0.632	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
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 GAIIx	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		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	80	37	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		
RYR1	6261	hgsc.bcm.edu	37	19	38990345	38990345	+	Silent	SNP	C	C	T	rs2229147	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38990345C>T	ENST00000359596.3	+	44	7098	c.7098C>T	c.(7096-7098)ccC>ccT	p.P2366P	RYR1_ENST00000360985.3_Silent_p.P2366P|RYR1_ENST00000355481.4_Silent_p.P2366P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2366	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GCTTCGGACCCGCCCTGCGGG	0.687													C|||	610	0.121805	0.2042	0.0937	5008	,	,		13215	0.13		0.0815	False		,,,				2504	0.0634				p.P2366P		Atlas-SNP	.											.	RYR1	708	.	0			c.C7098T						PASS	.	C	,	728,3674	279.6+/-274.9	61,606,1534	34.0	30.0	31.0		7098,7098	-8.0	0.8	19	dbSNP_98	31	491,8105	135.9+/-193.0	15,461,3822	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	76,1067,5356	TT,TC,CC		5.712,16.5379,9.3784	,	2366/5039,2366/5034	38990345	1219,11779	2201	4298	6499	SO:0001819	synonymous_variant	6261	exon44			CGGACCCGCCCTG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.7098C>T	19.37:g.38990345C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	27	20	0.740741	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.893;T|0.107	0.107	strong		0.687	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
CAND2	23066	hgsc.bcm.edu	37	3	12858028	12858028	+	Missense_Mutation	SNP	T	T	C	rs3732675	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:12858028T>C	ENST00000456430.2	+	10	1638	c.1597T>C	c.(1597-1599)Tct>Cct	p.S533P	CAND2_ENST00000295989.5_Missense_Mutation_p.S440P	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	533			S -> P (in dbSNP:rs3732675).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TGTGGCTGACTCTTTCTACAA	0.637													C|||	3025	0.604034	0.9584	0.4914	5008	,	,		18601	0.4365		0.6243	False		,,,				2504	0.3569				p.S533P	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,NS,carcinoma,0,2	CAND2	138	2	0			c.T1597C						PASS	.	C	PRO/SER,PRO/SER	3700,460		1648,404,28	39.0	44.0	43.0		1597,1318	4.2	1.0	3	dbSNP_107	43	4931,3475		1439,2053,711	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	74,74	3087,2457,739	CC,CT,TT		41.3395,11.0577,31.3147	benign,benign	533/1237,440/1120	12858028	8631,3935	2080	4203	6283	SO:0001583	missense	23066	exon10			GCTGACTCTTTCT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1597T>C	3.37:g.12858028T>C	ENSP00000387641:p.Ser533Pro	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1331	0.6094322344322345	468	0.9512195121951219	173	0.47790055248618785	226	0.3951048951048951	464	0.6121372031662269	C	1.795	-0.478506	0.04414	0.889423	0.586605	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.63744	-0.06;-0.06	5.12	4.25	0.50352	Armadillo-like helical (1);Armadillo-type fold (1);	0.204228	0.42682	N	0.000667	T	0.00012	0.0000	N	0.01086	-1.025	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42103	-0.9471	9	0.02654	T	1	-27.0988	7.3268	0.26560	0.0:0.7304:0.0:0.2696	rs3732675;rs17825071;rs60814914;rs3732675	533;440	O75155;O75155-2	CAND2_HUMAN;.	P	440;533	ENSP00000295989:S440P;ENSP00000387641:S533P	ENSP00000295989:S440P	S	+	1	0	CAND2	12833028	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	1.701000	0.37825	0.577000	0.29470	-0.215000	0.12644	TCT	C|0.609;G|0.000;T|0.391	0.609	strong		0.637	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
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 GAIIx	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	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	41	25	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		
EPHX2	2053	hgsc.bcm.edu	37	8	27358505	27358505	+	Missense_Mutation	SNP	A	A	G	rs41507953	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27358505A>G	ENST00000521400.1	+	2	594	c.164A>G	c.(163-165)aAa>aGa	p.K55R	EPHX2_ENST00000520666.1_3'UTR|EPHX2_ENST00000518379.1_Missense_Mutation_p.K55R|EPHX2_ENST00000380476.3_Missense_Mutation_p.K2R|EPHX2_ENST00000521780.1_Intron|EPHX2_ENST00000517536.1_Missense_Mutation_p.K55R	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	55	Phosphatase.		K -> R (decreased phosphatase activity; no effect on epoxyde hydrolase activity; dbSNP:rs41507953). {ECO:0000269|Ref.6}.		arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		CGGCTTATGAAAGGAGAGATC	0.527													G|||	504	0.100639	0.2201	0.0836	5008	,	,		18406	0.001		0.0865	False		,,,				2504	0.0685				p.K55R		Atlas-SNP	.											.	EPHX2	57	.	0			c.A164G	GRCh37	CM033767	EPHX2	M	rs41507953	PASS	.	G	ARG/LYS	959,3447	734.1+/-410.5	114,731,1358	103.0	97.0	99.0		164	-5.8	0.0	8	dbSNP_127	99	895,7705	778.4+/-407.7	47,801,3452	yes	missense	EPHX2	NM_001979.4	26	161,1532,4810	GG,GA,AA		10.407,21.7658,14.255	benign	55/556	27358505	1854,11152	2203	4300	6503	SO:0001583	missense	2053	exon2			TTATGAAAGGAGA	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.164A>G	8.37:g.27358505A>G	ENSP00000430269:p.Lys55Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Missense_Mutation	SNP	ENST00000521400.1	37	CCDS6060.1	220|220	0.10073260073260074|0.10073260073260074	121|121	0.2459349593495935|0.2459349593495935	30|30	0.08287292817679558|0.08287292817679558	1|1	0.0017482517482517483|0.0017482517482517483	68|68	0.08970976253298153|0.08970976253298153	G|G	0.069|0.069	-1.206660|-1.206660	0.01568|0.01568	0.217658|0.217658	0.10407|0.10407	ENSG00000120915|ENSG00000120915	ENST00000521684|ENST00000521400;ENST00000518328;ENST00000517536;ENST00000380476;ENST00000415449;ENST00000518379	T|T;T;T;T;T	0.09538|0.09073	2.97|3.02;3.02;3.02;3.02;3.02	4.33|4.33	-5.81|-5.81	0.02340|0.02340	.|Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.650048|0.650048	0.15154|0.15154	N|N	0.277528|0.277528	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01729|0.01729	-0.75|-0.75	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.10450	.|0.002;0.005;0.001	T|T	0.18304|0.18304	-1.0341|-1.0341	7|9	0.59425|0.02654	D|T	0.04|1	-3.2011|-3.2011	7.5338|7.5338	0.27697|0.27697	0.6253:0.2288:0.146:0.0|0.6253:0.2288:0.146:0.0	rs41507953;rs56620636;rs57378862;rs62504273;rs41507953|rs41507953;rs56620636;rs57378862;rs62504273;rs41507953	.|55;55;55	.|E5RFU2;E7ETW9;P34913	.|.;.;HYES_HUMAN	E|R	55|55;55;55;2;55;55	ENSP00000428191:K55E|ENSP00000430269:K55R;ENSP00000430779:K55R;ENSP00000428875:K55R;ENSP00000369843:K2R;ENSP00000427956:K55R	ENSP00000428191:K55E|ENSP00000369843:K2R	K|K	+|+	1|2	0|0	EPHX2|EPHX2	27414422|27414422	0.085000|0.085000	0.21516|0.21516	0.023000|0.023000	0.16930|0.16930	0.464000|0.464000	0.32679|0.32679	-1.570000|-1.570000	0.02140|0.02140	-1.722000|-1.722000	0.01377|0.01377	-0.349000|-0.349000	0.07799|0.07799	AAG|AAA	A|0.878;G|0.122	0.122	strong		0.527	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
SEPT4	5414	hgsc.bcm.edu	37	17	56598439	56598439	+	Silent	SNP	T	T	C	rs1057068	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:56598439T>C	ENST00000317268.3	-	10	1373	c.1197A>G	c.(1195-1197)acA>acG	p.T399T	SEPT4_ENST00000393086.1_Silent_p.T380T|SEPT4_ENST00000317256.6_Silent_p.T380T|SEPT4_ENST00000580844.1_Silent_p.T300T|SEPT4_ENST00000583114.1_Silent_p.T252T|SEPT4_ENST00000426861.1_3'UTR|SEPT4_ENST00000457347.2_Silent_p.T414T|SEPT4_ENST00000412945.3_Silent_p.T391T|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000579371.1_Silent_p.T300T	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	399	Septin-type G.				apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GTGTCTCCCGTGTCACATCCT	0.547											OREG0024614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2007	0.400759	0.2693	0.5778	5008	,	,		21447	0.5188		0.3708	False		,,,				2504	0.362				p.T414T		Atlas-SNP	.											.	SEPT4	48	.	0			c.A1242G						PASS	.	C	,,,	1323,3083	697.1+/-406.2	204,915,1084	182.0	158.0	166.0		1173,1197,,1140	-11.0	0.0	17	dbSNP_86	166	3292,5308	647.1+/-400.3	650,1992,1658	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous	SEPT4	NM_001198713.1,NM_004574.3,NM_080415.2,NM_080416.2	,,,	854,2907,2742	CC,CT,TT		38.2791,30.0272,35.4836	,,,	391/471,399/479,,380/460	56598439	4615,8391	2203	4300	6503	SO:0001819	synonymous_variant	5414	exon11			CTCCCGTGTCACA	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"""Septins"""	9165	protein-coding gene	gene with protein product	"""bradeoin"", ""septin-M"""	603696	"""peanut-like 2 (Drosophila)"""	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.1197A>G	17.37:g.56598439T>C		Somatic	207	0	0	1016	WXS	Illumina HiSeq	Phase_I	176	83	0.471591	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Silent	SNP	ENST00000317268.3	37	CCDS11610.1																																																																																			T|0.629;C|0.371	0.371	strong		0.547	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	
TMEM2	23670	hgsc.bcm.edu	37	9	74354983	74354983	+	Silent	SNP	A	A	G	rs25691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:74354983A>G	ENST00000377044.4	-	5	1739	c.1200T>C	c.(1198-1200)atT>atC	p.I400I	TMEM2_ENST00000377066.5_Silent_p.I400I	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	400					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GCCTACCTTCAATCCATTCAC	0.368													G|||	407	0.08127	0.0393	0.0476	5008	,	,		17161	0.0198		0.0815	False		,,,				2504	0.2249				p.I400I		Atlas-SNP	.											.	TMEM2	112	.	0			c.T1200C						PASS	.	G	,	173,4233	810.4+/-416.0	6,161,2036	100.0	98.0	99.0		1200,1200	-1.6	0.9	9	dbSNP_72	99	722,7878	786.7+/-407.6	31,660,3609	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	37,821,5645	GG,GA,AA		8.3953,3.9265,6.8814	,	400/1321,400/1384	74354983	895,12111	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon5			ACCTTCAATCCAT		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1200T>C	9.37:g.74354983A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			A|0.937;G|0.063	0.063	strong		0.368	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
UBXN2B	137886	hgsc.bcm.edu	37	8	59329438	59329438	+	Silent	SNP	A	A	G	rs13277646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:59329438A>G	ENST00000399598.2	+	2	236	c.114A>G	c.(112-114)gaA>gaG	p.E38E	UBXN2B_ENST00000522978.1_3'UTR	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	38						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						ATGAAGATGAAGTGAAGTGCA	0.378													A|||	1292	0.257987	0.1369	0.513	5008	,	,		15223	0.2411		0.2853	False		,,,				2504	0.2301				p.E38E		Atlas-SNP	.											.	UBXN2B	36	.	0			c.A114G						PASS	.	A		695,3061		64,567,1247	97.0	88.0	91.0		114	5.6	1.0	8	dbSNP_121	91	2352,5842		344,1664,2089	no	coding-synonymous	UBXN2B	NM_001077619.1		408,2231,3336	GG,GA,AA		28.7039,18.5037,25.4979		38/332	59329438	3047,8903	1878	4097	5975	SO:0001819	synonymous_variant	137886	exon2			AGATGAAGTGAAG	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"""UBX domain containing"""	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.114A>G	8.37:g.59329438A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001077619	B3KWZ3	Silent	SNP	ENST00000399598.2	37	CCDS43741.1																																																																																			A|0.746;G|0.254	0.254	strong		0.378	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	
SDCCAG3	10807	hgsc.bcm.edu	37	9	139301960	139301960	+	Silent	SNP	G	G	A	rs3812580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139301960G>A	ENST00000357365.3	-	5	585	c.456C>T	c.(454-456)acC>acT	p.T152T	SDCCAG3_ENST00000461693.1_5'Flank|SDCCAG3_ENST00000371725.3_Silent_p.T79T|SDCCAG3_ENST00000298537.7_Silent_p.T129T	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	152						cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		CATACCCGCCGGTTTGGGAGG	0.527													G|||	445	0.0888578	0.1362	0.0159	5008	,	,		14991	0.1369		0.0378	False		,,,				2504	0.0798				p.T152T		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.C456T						PASS	.	G	,,	390,3332		21,348,1492	24.0	29.0	27.0		456,237,387	-5.9	0.0	9	dbSNP_107	27	240,7948		1,238,3855	no	coding-synonymous,coding-synonymous,coding-synonymous	SDCCAG3	NM_001039707.1,NM_001039708.1,NM_006643.3	,,	22,586,5347	AA,AG,GG		2.9311,10.4782,5.2897	,,	152/436,79/363,129/413	139301960	630,11280	1861	4094	5955	SO:0001819	synonymous_variant	10807	exon5			CCCGCCGGTTTGG	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.456C>T	9.37:g.139301960G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Silent	SNP	ENST00000357365.3	37	CCDS43904.1																																																																																			G|0.918;A|0.082	0.082	strong		0.527	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	
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 GAIIx	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_ENST00000483972.1_Intron|LTB_ENST00000446745.2_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	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	84	46	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		
PDE6C	5146	hgsc.bcm.edu	37	10	95372734	95372734	+	Silent	SNP	G	G	A	rs1131978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:95372734G>A	ENST00000371447.3	+	1	390	c.252G>A	c.(250-252)ctG>ctA	p.L84L		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	84	GAF 1.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	ACAGGGCCCTGCAGAGGCTGG	0.662													G|||	823	0.164337	0.2421	0.1643	5008	,	,		18058	0.1131		0.167	False		,,,				2504	0.1094				p.L84L		Atlas-SNP	.											.	PDE6C	97	.	0			c.G252A						PASS	.	G		1058,3348	379.7+/-323.4	136,786,1281	31.0	33.0	32.0		252	4.3	1.0	10	dbSNP_86	32	1472,7128	277.4+/-292.8	135,1202,2963	no	coding-synonymous	PDE6C	NM_006204.3		271,1988,4244	AA,AG,GG		17.1163,24.0127,19.4526		84/859	95372734	2530,10476	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon1			GGCCCTGCAGAGG	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.252G>A	10.37:g.95372734G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			A|0.180;G|0.820;T|0.000	0.180	strong		0.662	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
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 GAIIx	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	C12orf79_ENST00000551563.2_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|RP11-796E2.4_ENST00000499685.2_RNA	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	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	151	48	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:35733116C>T	ENST00000314888.9	-	0	0				TLN1_ENST00000540444.1_5'Flank|CREB3_ENST00000353704.2_Missense_Mutation_p.R85W|CREB3_ENST00000486056.1_3'UTR	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	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	250	135	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	
STX17	55014	hgsc.bcm.edu	37	9	102677589	102677589	+	Missense_Mutation	SNP	T	T	C	rs41305451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:102677589T>C	ENST00000259400.6	+	2	204	c.68T>C	c.(67-69)aTa>aCa	p.I23T	RP11-60I3.4_ENST00000524512.1_RNA|STX17_ENST00000525640.1_Missense_Mutation_p.I23T|STX17_ENST00000534052.1_Missense_Mutation_p.I23T	NM_017919.2	NP_060389.2	P56962	STX17_HUMAN	syntaxin 17	23					autophagic vacuole fusion (GO:0000046)|endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111)|ER to Golgi vesicle-mediated transport (GO:0006888)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|protein localization to pre-autophagosomal structure (GO:0034497)	autophagic vacuole membrane (GO:0000421)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle (GO:0030134)|ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|smooth endoplasmic reticulum membrane (GO:0030868)|SNARE complex (GO:0031201)	protein phosphatase binding (GO:0019903)|SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				TTCATTAAGATAGTAATCCCA	0.363													T|||	153	0.0305511	0.0038	0.036	5008	,	,		16231	0.001		0.0924	False		,,,				2504	0.0297				p.I23T		Atlas-SNP	.											.	STX17	17	.	0			c.T68C						PASS	.	T	THR/ILE	63,4343	59.3+/-96.0	1,61,2141	99.0	102.0	101.0		68	5.3	1.0	9	dbSNP_127	101	770,7830	182.2+/-230.7	35,700,3565	yes	missense	STX17	NM_017919.2	89	36,761,5706	CC,CT,TT		8.9535,1.4299,6.4047	benign	23/303	102677589	833,12173	2203	4300	6503	SO:0001583	missense	55014	exon2			TTAAGATAGTAAT	AL834371	CCDS6745.1	9q31.1	2008-02-05			ENSG00000136874	ENSG00000136874			11432	protein-coding gene	gene with protein product		604204				9852078	Standard	NM_017919		Approved	FLJ20651	uc004bal.4	P56962	OTTHUMG00000020359	ENST00000259400.6:c.68T>C	9.37:g.102677589T>C	ENSP00000259400:p.Ile23Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_017919	Q4VXC2	Missense_Mutation	SNP	ENST00000259400.6	37	CCDS6745.1	94	0.04304029304029304	4	0.008130081300813009	13	0.03591160220994475	1	0.0017482517482517483	76	0.10026385224274406	T	16.64	3.180517	0.57800	0.014299	0.089535	ENSG00000136874	ENST00000259400;ENST00000531035;ENST00000525640;ENST00000534052;ENST00000526607	T;T;T	0.21734	1.99;1.99;1.99	5.32	5.32	0.75619	t-SNARE (1);	0.108846	0.64402	D	0.000007	T	0.00356	0.0011	N	0.19112	0.55	0.35359	D	0.78806	B;P	0.38504	0.309;0.634	B;B	0.34242	0.039;0.178	T	0.17653	-1.0362	10	0.66056	D	0.02	-5.6625	12.974	0.58527	0.0:0.0:0.0:1.0	rs41305451	23;23	P56962;B4DJ69	STX17_HUMAN;.	T	23	ENSP00000259400:I23T;ENSP00000435981:I23T;ENSP00000433484:I23T	ENSP00000259400:I23T	I	+	2	0	STX17	101717410	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.766000	0.68843	2.150000	0.67090	0.533000	0.62120	ATA	T|0.945;C|0.055	0.055	strong		0.363	STX17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053398.3	NM_017919	
TENM2	57451	hgsc.bcm.edu	37	5	167674472	167674472	+	Silent	SNP	G	G	A	rs17070023	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:167674472G>A	ENST00000518659.1	+	27	6567	c.6528G>A	c.(6526-6528)acG>acA	p.T2176T	TENM2_ENST00000545108.1_Silent_p.T2175T|TENM2_ENST00000403607.2_Silent_p.T2000T|TENM2_ENST00000520394.1_Silent_p.T1937T|TENM2_ENST00000519204.1_Silent_p.T2055T	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2176					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										ACTGGATGACGGTGCAATATG	0.547													G|||	532	0.10623	0.1815	0.0634	5008	,	,		21125	0.004		0.0825	False		,,,				2504	0.1646				p.T2167T		Atlas-SNP	.											ODZ2_ENST00000519204,NS,carcinoma,+1,6	.	.	6	0			c.G6501A						PASS	.	G		616,3524		45,526,1499	108.0	103.0	105.0		6501	-11.0	0.2	5	dbSNP_123	105	764,7646		32,700,3473	no	coding-synonymous	ODZ2	NM_001122679.1		77,1226,4972	AA,AG,GG		9.0844,14.8792,10.996		2167/2766	167674472	1380,11170	2070	4205	6275	SO:0001819	synonymous_variant	57451	exon27			GATGACGGTGCAA	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.6528G>A	5.37:g.167674472G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				G|0.910;A|0.090	0.090	strong		0.547	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
GNG2	54331	hgsc.bcm.edu	37	14	52433339	52433339	+	Silent	SNP	C	C	T	rs61740049	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:52433339C>T	ENST00000335281.4	+	3	556	c.150C>T	c.(148-150)ctC>ctT	p.L50L	GNG2_ENST00000553299.1_3'UTR|GNG2_ENST00000556752.1_Silent_p.L50L|GNG2_ENST00000557376.1_Silent_p.L89L|GNG2_ENST00000553432.1_Silent_p.L81L|GNG2_ENST00000554736.1_Silent_p.L50L|RP11-463J10.3_ENST00000553603.1_RNA|GNG2_ENST00000555472.1_Silent_p.L50L|GNG2_ENST00000556766.1_Silent_p.L50L	NM_001243774.1	NP_001230703.1	P59768	GBG2_HUMAN	guanine nucleotide binding protein (G protein), gamma 2	50					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|platelet activation (GO:0030168)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|signal transducer activity (GO:0004871)			lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	5	all_epithelial(31;0.0659)|Breast(41;0.0684)				Halothane(DB01159)	AAGACCCCCTCCTGACCCCTG	0.527													c|||	98	0.0195687	0.0098	0.0058	5008	,	,		17862	0.0298		0.003	False		,,,				2504	0.0491				p.L50L		Atlas-SNP	.											.	GNG2	12	.	0			c.C150T						PASS	.	C		53,4353	52.9+/-88.7	0,53,2150	106.0	110.0	109.0		150	-2.0	1.0	14	dbSNP_129	109	26,8574	17.9+/-57.8	0,26,4274	no	coding-synonymous	GNG2	NM_053064.4		0,79,6424	TT,TC,CC		0.3023,1.2029,0.6074		50/72	52433339	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	54331	exon4			CCCCCTCCTGACC	AK001024	CCDS32082.1	14q21	2008-07-28				ENSG00000186469			4404	protein-coding gene	gene with protein product		606981				10833460	Standard	NM_053064		Approved		uc001wzj.3	P59768		ENST00000335281.4:c.150C>T	14.37:g.52433339C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_053064	Q5JPE2|Q6P9A9	Silent	SNP	ENST00000335281.4	37	CCDS32082.1																																																																																			C|0.993;T|0.007	0.007	strong		0.527	GNG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411585.1		
HELZ2	85441	hgsc.bcm.edu	37	20	62196253	62196253	+	Missense_Mutation	SNP	C	C	A	rs310631	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62196253C>A	ENST00000467148.1	-	8	3991	c.3922G>T	c.(3922-3924)Gtg>Ttg	p.V1308L	HELZ2_ENST00000427522.2_Missense_Mutation_p.V739L	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1308			V -> L (in dbSNP:rs310631).		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)										GACGGGGGCACCCTCAAGCTG	0.672													C|||	1825	0.364417	0.4644	0.3876	5008	,	,		16343	0.1587		0.4105	False		,,,				2504	0.3773				p.V1308L		Atlas-SNP	.											.	.	.	.	0			c.G3922T						PASS	.	C	LEU/VAL,LEU/VAL	1927,2469		437,1053,708	29.0	33.0	32.0		3922,2215	-3.4	0.0	20	dbSNP_79	32	3663,4927		785,2093,1417	yes	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	32,32	1222,3146,2125	AA,AC,CC		42.6426,43.8353,43.0464	benign,benign	1308/2650,739/2081	62196253	5590,7396	2198	4295	6493	SO:0001583	missense	85441	exon9			GGGGCACCCTCAA	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.3922G>T	20.37:g.62196253C>A	ENSP00000417401:p.Val1308Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	781	0.3576007326007326	247	0.5020325203252033	131	0.36187845303867405	100	0.17482517482517482	303	0.3997361477572559	C	0.479	-0.880862	0.02530	0.438353	0.426426	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.28666	1.6;1.6	4.13	-3.42	0.04825	.	5.775600	0.00166	N	0.000004	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.23591	0.011;0.088	B;B	0.23419	0.014;0.046	T	0.44298	-0.9337	9	0.41790	T	0.15	0.0044	4.6608	0.12641	0.0:0.3327:0.2889:0.3783	rs310631;rs311512;rs3827024;rs57773129;rs310631	1308;739	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	L	739;1308	ENSP00000393257:V739L;ENSP00000417401:V1308L	ENSP00000393257:V739L	V	-	1	0	RP4-697K14.7	61666697	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-1.448000	0.02394	-0.528000	0.06366	-0.662000	0.03851	GTG	T|0.004;G|0.003	.	strong		0.672	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
CCDC88B	283234	hgsc.bcm.edu	37	11	64110668	64110668	+	Silent	SNP	G	G	A	rs574835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64110668G>A	ENST00000356786.5	+	11	1124	c.1080G>A	c.(1078-1080)tcG>tcA	p.S360S	CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	360						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGGTGCTCTCGGGGGTGCTGG	0.697													A|||	1126	0.22484	0.0855	0.3703	5008	,	,		10601	0.1657		0.3658	False		,,,				2504	0.226				p.S360S		Atlas-SNP	.											.	CCDC88B	89	.	0			c.G1080A						PASS	.	A		471,3691		29,413,1639	9.0	8.0	8.0		1080	-8.7	0.0	11	dbSNP_83	8	2492,5608		402,1688,1960	no	coding-synonymous	CCDC88B	NM_032251.5		431,2101,3599	AA,AG,GG		30.7654,11.3167,24.1641		360/1477	64110668	2963,9299	2081	4050	6131	SO:0001819	synonymous_variant	283234	exon11			GCTCTCGGGGGTG	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1080G>A	11.37:g.64110668G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.738;A|0.262	0.262	strong		0.697	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
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 GAIIx	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	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	135	32	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 GAIIx	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_ENST00000395003.1_Silent_p.D366D|PHF15_ENST00000282605.4_Silent_p.D366D|PHF15_ENST00000361895.2_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		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	84	43	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 GAIIx	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_ENST00000379224.5_Missense_Mutation_p.G47R|ISG20_ENST00000560741.1_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	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	16	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	
STK10	6793	hgsc.bcm.edu	37	5	171533629	171533629	+	Silent	SNP	A	A	G	rs2306963	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:171533629A>G	ENST00000176763.5	-	6	1126	c.783T>C	c.(781-783)tcT>tcC	p.S261S		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTCACCACTTAGAGGGCGTGA	0.662													A|||	3801	0.758986	0.677	0.768	5008	,	,		13410	0.8542		0.7435	False		,,,				2504	0.7812				p.S261S		Atlas-SNP	.											.	STK10	100	.	0			c.T783C						PASS	.	A		3019,1387	682.9+/-404.2	1056,907,240	62.0	58.0	59.0		783	-5.2	0.2	5	dbSNP_100	59	6124,2476	694.2+/-404.7	2177,1770,353	no	coding-synonymous	STK10	NM_005990.3		3233,2677,593	GG,GA,AA		28.7907,31.4798,29.7017		261/969	171533629	9143,3863	2203	4300	6503	SO:0001819	synonymous_variant	6793	exon6			CCACTTAGAGGGC	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.783T>C	5.37:g.171533629A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	37	CCDS34290.1																																																																																			A|0.272;G|0.728	0.728	strong		0.662	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
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 GAIIx	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_ENST00000406859.3_Silent_p.G35G|NRXN1_ENST00000405472.3_Silent_p.G35G|NRXN1_ENST00000405581.1_Silent_p.G35G|NRXN1_ENST00000401669.2_Silent_p.G35G|NRXN1_ENST00000404971.1_Silent_p.G35G|NRXN1_ENST00000402717.3_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		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	22	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		
SPRR2F	6705	hgsc.bcm.edu	37	1	153085152	153085152	+	Missense_Mutation	SNP	C	C	T	rs151137674	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153085152C>T	ENST00000468739.1	-	2	118	c.58G>A	c.(58-60)Gcg>Acg	p.A20T	SPRR2B_ENST00000368752.4_Intron	NM_001014450.1	NP_001014450.1	Q96RM1	SPR2F_HUMAN	small proline-rich protein 2F	20					epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	4	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CACTTTGGCGCGGGGCACACA	0.572													t|||	76	0.0151757	0.0182	0.0231	5008	,	,		16303	0.001		0.0338	False		,,,				2504	0.001				p.A20T		Atlas-SNP	.											SPRR2F,caecum,carcinoma,+2,1	SPRR2F	12	1	0			c.G58A						scavenged	.	T	THR/ALA	56,4350	819.2+/-416.3	0,56,2147	106.0	94.0	98.0		58	-3.5	0.0	1	dbSNP_134	98	105,8489	809.3+/-407.2	1,103,4193	no	missense	SPRR2F	NM_001014450.1	58	1,159,6340	TT,TC,CC		1.2218,1.271,1.2385	benign	20/73	153085152	161,12839	2203	4297	6500	SO:0001583	missense	6705	exon2			TTGGCGCGGGGCA	AF333956	CCDS30867.1	1q21-q22	2008-02-05			ENSG00000244094	ENSG00000244094			11266	protein-coding gene	gene with protein product						8325635, 11279051	Standard	NM_001014450		Approved		uc001fbi.3	Q96RM1	OTTHUMG00000014398	ENST00000468739.1:c.58G>A	1.37:g.153085152C>T	ENSP00000418193:p.Ala20Thr	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	8	0.125	NM_001014450	Q5T9T3	Missense_Mutation	SNP	ENST00000468739.1	37	CCDS30867.1	25	0.011446886446886446	8	0.016260162601626018	3	0.008287292817679558	1	0.0017482517482517483	13	0.017150395778364115	T	2.586	-0.296265	0.05532	0.01271	0.012218	ENSG00000244094	ENST00000468739	T	0.26810	1.71	2.66	-3.46	0.04767	.	0.891598	0.09133	N	0.844110	T	0.05640	0.0148	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40327	-0.9569	9	0.87932	D	0	.	5.6027	0.17363	0.0:0.4524:0.2541:0.2935	.	20	Q96RM1	SPR2F_HUMAN	T	20	ENSP00000418193:A20T	ENSP00000418193:A20T	A	-	1	0	SPRR2F	151351776	0.006000	0.16342	0.006000	0.13384	0.150000	0.21749	-0.639000	0.05446	-1.375000	0.02129	-0.848000	0.03037	GCG	.	.	weak		0.572	SPRR2F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040056.1		
SPAG1	6674	hgsc.bcm.edu	37	8	101253184	101253184	+	Silent	SNP	G	G	A	rs1788190	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:101253184G>A	ENST00000388798.2	+	19	2906	c.2715G>A	c.(2713-2715)tcG>tcA	p.S905S	SPAG1_ENST00000251809.3_Silent_p.S905S	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	905					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		AGGACCTTTCGGACACACCAA	0.343													G|||	1498	0.299121	0.028	0.3991	5008	,	,		10641	0.5149		0.3688	False		,,,				2504	0.3006				p.S905S		Atlas-SNP	.											.	SPAG1	80	.	0			c.G2715A						PASS	.	G	,	376,4030	189.9+/-215.9	13,350,1840	78.0	78.0	78.0		2715,2715	-2.2	0.0	8	dbSNP_89	78	3163,5437	479.7+/-370.2	579,2005,1716	no	coding-synonymous,coding-synonymous	SPAG1	NM_003114.4,NM_172218.2	,	592,2355,3556	AA,AG,GG		36.7791,8.5338,27.2105	,	905/927,905/927	101253184	3539,9467	2203	4300	6503	SO:0001819	synonymous_variant	6674	exon19			CCTTTCGGACACA	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.2715G>A	8.37:g.101253184G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Silent	SNP	ENST00000388798.2	37	CCDS34930.1																																																																																			G|0.707;A|0.293	0.293	strong		0.343	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
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 GAIIx	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_ENST00000423908.2_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000537233.2_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000539968.1_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		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	24	15	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	
HAPLN1	1404	hgsc.bcm.edu	37	5	82940273	82940273	+	Silent	SNP	C	C	G	rs2242128	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:82940273C>G	ENST00000274341.4	-	4	1534	c.684G>C	c.(682-684)ggG>ggC	p.G228G		NM_001884.3	NP_001875.1	P10915	HPLN1_HUMAN	hyaluronan and proteoglycan link protein 1	228	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|liver(1)|lung(15)|ovary(1)|prostate(1)|skin(1)	34		Lung NSC(167;0.0484)|all_lung(232;0.0522)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;7.82e-42)|Epithelial(54;5.88e-35)|all cancers(79;1.14e-29)	Hyaluronan(DB08818)	CTGTGTTCTGCCCCCCACAGG	0.512													G|||	3697	0.738219	0.8699	0.7565	5008	,	,		16974	0.5813		0.7187	False		,,,				2504	0.729				p.G228G		Atlas-SNP	.											.	HAPLN1	79	.	0			c.G684C						PASS	.	G		3752,654	262.8+/-265.1	1606,540,57	53.0	60.0	57.0		684	1.5	1.0	5	dbSNP_98	57	5852,2748	422.5+/-354.0	1998,1856,446	no	coding-synonymous	HAPLN1	NM_001884.3		3604,2396,503	GG,GC,CC		31.9535,14.8434,26.1572		228/355	82940273	9604,3402	2203	4300	6503	SO:0001819	synonymous_variant	1404	exon4			GTTCTGCCCCCCA		CCDS4061.1	5q14.3	2013-01-11	2004-03-16	2004-03-17	ENSG00000145681	ENSG00000145681		"""Immunoglobulin superfamily / V-set domain containing"""	2380	protein-coding gene	gene with protein product	"""Cartilage link protein"", ""hyaluronan and proteoglycan link protein 1"""	115435	"""cartilage linking protein 1"""	CRTL1		2286376, 2320422	Standard	NM_001884		Approved		uc003kin.3	P10915	OTTHUMG00000119045	ENST00000274341.4:c.684G>C	5.37:g.82940273C>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_001884	B2R9A9	Silent	SNP	ENST00000274341.4	37	CCDS4061.1																																																																																			C|0.272;G|0.728	0.728	strong		0.512	HAPLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239256.2	NM_001884	
PTK2B	2185	hgsc.bcm.edu	37	8	27293865	27293865	+	Splice_Site	SNP	C	C	T	rs7005936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27293865C>T	ENST00000397501.1	+	20	2149	c.1341C>T	c.(1339-1341)caC>caT	p.H447H	PTK2B_ENST00000544172.1_Splice_Site_p.H447H|PTK2B_ENST00000517339.1_Splice_Site_p.H447H|PTK2B_ENST00000338238.4_Splice_Site_p.H447H|PTK2B_ENST00000420218.2_Splice_Site_p.H447H|PTK2B_ENST00000397497.4_Splice_Site_p.H193H|PTK2B_ENST00000346049.5_Splice_Site_p.H447H	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	447	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|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 cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	ACACAAATCACGTGAGTTCTA	0.498													C|||	1854	0.370208	0.4607	0.3804	5008	,	,		21147	0.1954		0.3867	False		,,,				2504	0.4039				p.H447H		Atlas-SNP	.											PTK2B_ENST00000544172,brain,glioma,0,6	PTK2B	304	6	0			c.C1341T						PASS	.	C	,,,	1959,2447	554.2+/-379.0	444,1071,688	250.0	227.0	235.0		1341,1341,1341,1341	-0.6	1.0	8	dbSNP_116	235	3396,5204	502.2+/-375.6	689,2018,1593	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	1133,3089,2281	TT,TC,CC		39.4884,44.4621,41.1733	,,,	447/1010,447/1010,447/968,447/1010	27293865	5355,7651	2203	4300	6503	SO:0001630	splice_region_variant	2185	exon20			AAATCACGTGAGT	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.1341+1C>T	8.37:g.27293865C>T		Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	236	124	0.525424	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			C|0.638;T|0.362	0.362	strong		0.498	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	Silent
MOV10	4343	hgsc.bcm.edu	37	1	113236681	113236681	+	Silent	SNP	C	C	T	rs3748656	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:113236681C>T	ENST00000413052.2	+	8	1572	c.1182C>T	c.(1180-1182)ggC>ggT	p.G394G	MOV10_ENST00000369645.1_Silent_p.G394G|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000357443.2_Silent_p.G394G|MOV10_ENST00000369644.1_Silent_p.G338G|MOV10_ENST00000468624.1_3'UTR	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	394					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		TGCTACGGGGCGACCACCTGT	0.582													C|||	1426	0.284744	0.1672	0.2911	5008	,	,		17209	0.5427		0.2346	False		,,,				2504	0.2249				p.G394G		Atlas-SNP	.											MOV10,NS,carcinoma,+1,1	MOV10	74	1	0			c.C1182T						PASS	.	C	,	805,3601	321.3+/-297.0	83,639,1481	104.0	95.0	98.0		1182,1182	-10.5	0.4	1	dbSNP_107	98	1768,6832	321.1+/-314.9	181,1406,2713	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	264,2045,4194	TT,TC,CC		20.5581,18.2705,19.7832	,	394/1004,394/1004	113236681	2573,10433	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon8			ACGGGGCGACCAC	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1182C>T	1.37:g.113236681C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			C|0.752;T|0.248	0.248	strong		0.582	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
KIAA1804	84451	hgsc.bcm.edu	37	1	233514975	233514975	+	Missense_Mutation	SNP	G	G	T	rs3795374	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:233514975G>T	ENST00000366624.3	+	9	2484	c.2223G>T	c.(2221-2223)gaG>gaT	p.E741D	MLK4_ENST00000366622.1_Missense_Mutation_p.E187D	NM_032435.2	NP_115811.2												p.E741D(1)									ACCTCAGAGAGCTTCATAAAG	0.547													G|||	1385	0.276558	0.2405	0.3444	5008	,	,		19126	0.3442		0.173	False		,,,				2504	0.3139				p.E741D		Atlas-SNP	.											KIAA1804,NS,carcinoma,0,1	KIAA1804	129	1	1	Substitution - Missense(1)	stomach(1)	c.G2223T						scavenged	.	G	ASP/GLU	996,3410	372.7+/-320.5	105,786,1312	69.0	76.0	73.0		2223	1.7	0.4	1	dbSNP_107	73	1571,7029	294.2+/-301.7	146,1279,2875	yes	missense	KIAA1804	NM_032435.2	45	251,2065,4187	TT,TG,GG		18.2674,22.6055,19.737	benign	741/1037	233514975	2567,10439	2203	4300	6503	SO:0001583	missense	0	exon9			CAGAGAGCTTCAT																												ENST00000366624.3:c.2223G>T	1.37:g.233514975G>T	ENSP00000355583:p.Glu741Asp	Somatic	39	1	0.025641		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	552	0.25274725274725274	130	0.26422764227642276	98	0.27071823204419887	195	0.3409090909090909	129	0.17018469656992086	G	13.04	2.117899	0.37339	0.226055	0.182674	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.35421	1.31;1.31	4.85	1.71	0.24356	.	0.065665	0.64402	D	0.000013	T	0.00012	0.0000	L	0.43923	1.385	0.32265	P	0.569661	D;B	0.69078	0.997;0.165	D;B	0.71870	0.975;0.066	T	0.27054	-1.0085	9	0.62326	D	0.03	.	8.5793	0.33619	0.3511:0.0:0.6489:0.0	rs3795374;rs52794079;rs3795374	188;741	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	D	741;187	ENSP00000355583:E741D;ENSP00000355581:E187D	ENSP00000355581:E187D	E	+	3	2	RP5-862P8.2	231581598	1.000000	0.71417	0.413000	0.26509	0.507000	0.33981	1.010000	0.29898	0.627000	0.30340	0.650000	0.86243	GAG	G|0.774;T|0.226	0.226	strong		0.547	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
TM7SF3	51768	hgsc.bcm.edu	37	12	27143508	27143508	+	Missense_Mutation	SNP	G	G	A	rs10771314	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27143508G>A	ENST00000343028.4	-	6	968	c.743C>T	c.(742-744)cCg>cTg	p.P248L	TM7SF3_ENST00000542667.1_Intron	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	248			P -> L (in dbSNP:rs10771314).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	18	Colorectal(261;0.0847)					ACCTTGTCCCGGGAGGGAGGA	0.428													G|||	244	0.048722	0.0144	0.0807	5008	,	,		19155	0.0595		0.0775	False		,,,				2504	0.0317				p.P248L		Atlas-SNP	.											.	TM7SF3	41	.	0			c.C743T						PASS	.	G	LEU/PRO	125,4281	93.4+/-132.2	1,123,2079	122.0	110.0	114.0		743	-1.8	0.0	12	dbSNP_120	114	879,7721	198.5+/-242.8	44,791,3465	yes	missense	TM7SF3	NM_016551.2	98	45,914,5544	AA,AG,GG		10.2209,2.837,7.7195	benign	248/571	27143508	1004,12002	2203	4300	6503	SO:0001583	missense	51768	exon6			TGTCCCGGGAGGG	AB032470	CCDS8710.1	12q11-q12	2012-08-10			ENSG00000064115	ENSG00000064115			23049	protein-coding gene	gene with protein product		605181				10828615	Standard	NM_016551		Approved		uc010sjl.2	Q9NS93	OTTHUMG00000169243	ENST00000343028.4:c.743C>T	12.37:g.27143508G>A	ENSP00000342322:p.Pro248Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	37	CCDS8710.1	130|130	0.05952380952380952|0.05952380952380952	4|4	0.008130081300813009|0.008130081300813009	27|27	0.07458563535911603|0.07458563535911603	41|41	0.07167832167832168|0.07167832167832168	58|58	0.07651715039577836|0.07651715039577836	G|G	11.88|11.88	1.769765|1.769765	0.31320|0.31320	0.02837|0.02837	0.102209|0.102209	ENSG00000064115|ENSG00000064115	ENST00000343028;ENST00000543655;ENST00000535819|ENST00000545303	T;T;T|.	0.45668|.	1.42;0.89;0.89|.	5.0|5.0	-1.78|-1.78	0.07957|0.07957	.|.	0.288766|.	0.38897|.	N|.	0.001531|.	T|T	0.02047|0.02047	0.0064|0.0064	L|L	0.42245|0.42245	1.32|1.32	0.58432|0.58432	D|D	0.999996|0.999996	B|.	0.32653|.	0.379|.	B|.	0.17979|.	0.02|.	T|T	0.05209|0.05209	-1.0899|-1.0899	10|5	0.35671|.	T|.	0.21|.	7.0E-4|7.0E-4	9.1426|9.1426	0.36912|0.36912	0.0849:0.1585:0.6733:0.0832|0.0849:0.1585:0.6733:0.0832	rs10771314;rs52837696;rs60050366;rs10771314|rs10771314;rs52837696;rs60050366;rs10771314	248|.	Q9NS93|.	TM7S3_HUMAN|.	L|W	248;39;39|29	ENSP00000342322:P248L;ENSP00000441924:P39L;ENSP00000445156:P39L|.	ENSP00000342322:P248L|.	P|R	-|-	2|1	0|2	TM7SF3|TM7SF3	27034775|27034775	0.993000|0.993000	0.37304|0.37304	0.026000|0.026000	0.17262|0.17262	0.878000|0.878000	0.50629|0.50629	1.827000|1.827000	0.39102|0.39102	-0.105000|-0.105000	0.12132|0.12132	-0.237000|-0.237000	0.12165|0.12165	CCG|CGG	G|0.933;A|0.067	0.067	strong		0.428	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551	
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 GAIIx	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_ENST00000356000.3_Intron|RTN3_ENST00000540798.1_Silent_p.D241D|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000339997.4_Silent_p.D334D|RTN3_ENST00000354497.4_Intron|RTN3_ENST00000537981.1_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		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	21	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 GAIIx	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_ENST00000367897.1_Missense_Mutation_p.K153N|PBX1_ENST00000560641.1_Missense_Mutation_p.K48N|PBX1_ENST00000401534.1_Missense_Mutation_p.K153N|PBX1_ENST00000540246.1_Missense_Mutation_p.K48N|PBX1_ENST00000540236.1_Missense_Mutation_p.K153N|PBX1_ENST00000559240.1_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	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	13	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	
OR10H5	284433	hgsc.bcm.edu	37	19	15905639	15905639	+	Silent	SNP	C	C	T	rs3746151	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15905639C>T	ENST00000308940.8	+	1	879	c.781C>T	c.(781-783)Ctg>Ttg	p.L261L		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						CGTCATTTACCTGAAGCCCAA	0.567													.|||	764	0.152556	0.1422	0.1153	5008	,	,		17530	0.122		0.161	False		,,,				2504	0.2157				p.L261L		Atlas-SNP	.											.	OR10H5	49	.	0			c.C781T						PASS	.	C		680,3726		54,572,1577	108.0	86.0	94.0		781	3.9	1.0	19	dbSNP_107	94	1549,7051		150,1249,2901	no	coding-synonymous	OR10H5	NM_001004466.1		204,1821,4478	TT,TC,CC		18.0116,15.4335,17.1382		261/316	15905639	2229,10777	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			ATTTACCTGAAGC	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.781C>T	19.37:g.15905639C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			C|0.841;T|0.159	0.159	strong		0.567	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
KIAA1614	57710	hgsc.bcm.edu	37	1	180905694	180905694	+	Silent	SNP	C	C	T	rs3795503	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:180905694C>T	ENST00000367588.4	+	5	2704	c.2649C>T	c.(2647-2649)aaC>aaT	p.N883N	KIAA1614_ENST00000367587.1_Silent_p.N504N	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	883										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						ACTGCAACAACAGCGCACCTC	0.697													C|||	1446	0.288738	0.1316	0.2738	5008	,	,		16039	0.495		0.3012	False		,,,				2504	0.2863				p.N883N		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C2649T						PASS	.	C		667,3347		63,541,1403	27.0	33.0	31.0		2649	2.4	0.0	1	dbSNP_107	31	2521,5791		392,1737,2027	no	coding-synonymous	KIAA1614	NM_020950.1		455,2278,3430	TT,TC,CC		30.3296,16.6168,25.864		883/1191	180905694	3188,9138	2007	4156	6163	SO:0001819	synonymous_variant	57710	exon5			CAACAACAGCGCA	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2649C>T	1.37:g.180905694C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_020950	Q5VZ45|Q9HCF8	Silent	SNP	ENST00000367588.4	37	CCDS41442.1																																																																																			C|0.696;T|0.304	0.304	strong		0.697	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
PREX2	80243	hgsc.bcm.edu	37	8	69017584	69017584	+	Intron	SNP	G	G	T	rs35559159	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:69017584G>T	ENST00000288368.4	+	24	2992				PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2						adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TTAGCAGAGAGGGCCCCTGTC	0.522													G|||	24	0.00479233	0.0015	0.0072	5008	,	,		16544	0.0		0.0129	False		,,,				2504	0.0041				p.R976M		Atlas-SNP	.											.	PREX2	614	.	0			c.G2927T						PASS	.	G	,MET/ARG	18,4388	25.3+/-52.1	0,18,2185	56.0	46.0	49.0		,2927	1.0	0.0	8	dbSNP_126	49	149,8451	69.7+/-132.2	1,147,4152	yes	intron,missense	PREX2	NM_024870.2,NM_025170.4	,91	1,165,6337	TT,TG,GG		1.7326,0.4085,1.284	,	,976/980	69017584	167,12839	2203	4300	6503	SO:0001627	intron_variant	80243	exon24			CAGAGAGGGCCCC	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2716-2760G>T	8.37:g.69017584G>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	92	52	0.565217	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	14	0.00641025641025641	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	10	0.013192612137203167	G	5.420	0.262698	0.10294	0.004085	0.017326	ENSG00000046889	ENST00000354677	.	.	.	2.14	0.986	0.19784	.	.	.	.	.	T	0.14485	0.0350	.	.	.	0.09310	N	1	B	0.25105	0.118	B	0.19391	0.025	T	0.21484	-1.0244	7	0.87932	D	0	.	3.2591	0.06843	0.7143:0.0:0.2857:0.0	rs35559159	976	Q70Z35-3	.	M	976	.	ENSP00000346707:R976M	R	+	2	0	PREX2	69180138	0.019000	0.18553	0.006000	0.13384	0.127000	0.20565	0.486000	0.22340	0.269000	0.21961	0.508000	0.49915	AGG	G|0.990;T|0.010	0.010	strong		0.522	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
CCDC34	91057	hgsc.bcm.edu	37	11	27362359	27362359	+	Missense_Mutation	SNP	T	T	G	rs17244028	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:27362359T>G	ENST00000328697.6	-	5	1464	c.791A>C	c.(790-792)gAa>gCa	p.E264A	CCDC34_ENST00000529615.1_5'UTR	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	264			E -> A (in dbSNP:rs17244028). {ECO:0000269|Ref.6}.							endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						CTCCTGTATTTCAGCTTGCTG	0.338													T|||	808	0.161342	0.056	0.2637	5008	,	,		16669	0.0734		0.34	False		,,,				2504	0.138				p.E264A		Atlas-SNP	.											.	CCDC34	48	.	0			c.A791C						PASS	.	T	ALA/GLU	479,3925	223.3+/-239.8	26,427,1749	155.0	144.0	148.0		791	5.9	1.0	11	dbSNP_123	148	3029,5569	467.1+/-367.0	545,1939,1815	yes	missense	CCDC34	NM_030771.1	107	571,2366,3564	GG,GT,TT		35.2291,10.8765,26.9805	probably-damaging	264/374	27362359	3508,9494	2202	4299	6501	SO:0001583	missense	91057	exon5			TGTATTTCAGCTT	AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.791A>C	11.37:g.27362359T>G	ENSP00000330240:p.Glu264Ala	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	203	203	1	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	Missense_Mutation	SNP	ENST00000328697.6	37	CCDS31448.1	433	0.19826007326007325	33	0.06707317073170732	100	0.27624309392265195	40	0.06993006993006994	260	0.34300791556728233	T	13.88	2.367807	0.42003	0.108765	0.352291	ENSG00000109881	ENST00000328697	T	0.25250	1.81	5.92	5.92	0.95590	.	0.067529	0.56097	D	0.000022	T	0.00012	0.0000	L	0.49455	1.56	0.09310	P	1.0	D	0.52996	0.957	P	0.59595	0.86	T	0.44697	-0.9311	9	0.48119	T	0.1	-10.9812	11.2236	0.48871	0.0:0.0:0.1532:0.8468	rs17244028;rs52822831;rs17244028	264	Q96HJ3	CCD34_HUMAN	A	264	ENSP00000330240:E264A	ENSP00000330240:E264A	E	-	2	0	CCDC34	27318935	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.873000	0.56093	2.266000	0.75297	0.533000	0.62120	GAA	T|0.772;G|0.228	0.228	strong		0.338	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771	
RPTOR	57521	hgsc.bcm.edu	37	17	78865546	78865546	+	Silent	SNP	T	T	C	rs2289764	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78865546T>C	ENST00000306801.3	+	18	2372	c.2010T>C	c.(2008-2010)ctT>ctC	p.L670L	RPTOR_ENST00000544334.2_Silent_p.L512L|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	670					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						TGAGTCATCTTGTGGTTCAGT	0.517													C|||	1910	0.38139	0.7057	0.2435	5008	,	,		17130	0.2262		0.2247	False		,,,				2504	0.362				p.L670L		Atlas-SNP	.											.	RPTOR	122	.	0			c.T2010C						PASS	.	C	,	2806,1600	496.5+/-363.6	894,1018,291	182.0	158.0	166.0		1536,2010	-9.4	0.0	17	dbSNP_100	166	2029,6571	720.4+/-406.3	254,1521,2525	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	1148,2539,2816	CC,CT,TT		23.593,36.3141,37.1751	,	512/1178,670/1336	78865546	4835,8171	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon18			TCATCTTGTGGTT		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.2010T>C	17.37:g.78865546T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			T|0.634;C|0.366	0.366	strong		0.517	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
OBSCN	84033	hgsc.bcm.edu	37	1	228525008	228525008	+	Missense_Mutation	SNP	G	G	A	rs3795809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228525008G>A	ENST00000422127.1	+	66	16768	c.16724G>A	c.(16723-16725)cGc>cAc	p.R5575H	OBSCN_ENST00000284548.11_Missense_Mutation_p.R5575H|OBSCN_ENST00000366709.4_Missense_Mutation_p.R2694H|OBSCN_ENST00000366707.4_Missense_Mutation_p.R3209H|OBSCN_ENST00000570156.2_Missense_Mutation_p.R6532H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5575			R -> H (in dbSNP:rs3795809).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCATCCCCCCGCCATGGCCGA	0.647													G|||	384	0.0766773	0.0189	0.1744	5008	,	,		18983	0.0556		0.1252	False		,,,				2504	0.0573				p.R6532H		Atlas-SNP	.											OBSCN_ENST00000570156,caecum,carcinoma,0,3	OBSCN	2142	3	0			c.G19595A						PASS	.	G	HIS/ARG,HIS/ARG	146,3960		1,144,1908	24.0	32.0	29.0		16724,16724	4.4	0.9	1	dbSNP_107	29	1133,7223		70,993,3115	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	29,29	71,1137,5023	AA,AG,GG		13.5591,3.5558,10.2632	possibly-damaging,possibly-damaging	5575/7969,5575/6621	228525008	1279,11183	2053	4178	6231	SO:0001583	missense	84033	exon77			CCCCCCGCCATGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.16724G>A	1.37:g.228525008G>A	ENSP00000409493:p.Arg5575His	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	164	65	0.396341	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	204	0.09340659340659341	8	0.016260162601626018	65	0.17955801104972377	32	0.055944055944055944	99	0.13060686015831136	G	17.96	3.516358	0.64634	0.035558	0.135591	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.35421	1.31;1.31;1.31;1.31	4.37	4.37	0.52481	.	0.164006	0.40554	N	0.001072	T	0.00073	0.0002	L	0.44542	1.39	0.26854	P	0.9681028	B;P	0.36249	0.123;0.545	B;B	0.23852	0.032;0.049	T	0.12372	-1.0550	9	0.41790	T	0.15	.	17.4671	0.87635	0.0:0.0:1.0:0.0	rs3795809;rs59686075;rs3795809	5575;5575	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	H	5575;5575;3209;2694	ENSP00000284548:R5575H;ENSP00000409493:R5575H;ENSP00000355668:R3209H;ENSP00000355670:R2694H	ENSP00000284548:R5575H	R	+	2	0	OBSCN	226591631	1.000000	0.71417	0.858000	0.33744	0.006000	0.05464	6.878000	0.75567	2.437000	0.82529	0.655000	0.94253	CGC	G|0.913;A|0.087	0.087	strong		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
EXPH5	23086	hgsc.bcm.edu	37	11	108381247	108381247	+	Missense_Mutation	SNP	C	C	T	rs2640779	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:108381247C>T	ENST00000265843.4	-	6	5097	c.4987G>A	c.(4987-4989)Gga>Aga	p.G1663R	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000428840.1_Missense_Mutation_p.G1587R|EXPH5_ENST00000525344.1_Missense_Mutation_p.G1656R|EXPH5_ENST00000443411.1_Missense_Mutation_p.G1475R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1663			G -> R (in dbSNP:rs2640779). {ECO:0000269|PubMed:12062444, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)	p.G1663R(1)		breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		ACATGCTTTCCGTTCTCACTC	0.478													C|||	1434	0.286342	0.028	0.3689	5008	,	,		21940	0.6419		0.2465	False		,,,				2504	0.2515				p.G1663R		Atlas-SNP	.											EXPH5,NS,adenoma,0,2	EXPH5	193	2	1	Substitution - Missense(1)	stomach(1)	c.G4987A						PASS	.	C	ARG/GLY	276,4126	155.9+/-189.0	4,268,1929	207.0	200.0	202.0		4987	3.4	0.0	11	dbSNP_100	202	2037,6559	355.4+/-329.9	265,1507,2526	yes	missense	EXPH5	NM_015065.2	125	269,1775,4455	TT,TC,CC		23.6971,6.2699,17.795	possibly-damaging	1663/1990	108381247	2313,10685	2201	4298	6499	SO:0001583	missense	23086	exon6			GCTTTCCGTTCTC		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4987G>A	11.37:g.108381247C>T	ENSP00000265843:p.Gly1663Arg	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	196	33	0.168367	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	708	0.3241758241758242	18	0.036585365853658534	115	0.31767955801104975	373	0.6520979020979021	202	0.26649076517150394	C	11.38	1.622865	0.28889	0.062699	0.236971	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312	T;T;T;T;T	0.02787	4.38;4.31;4.16;4.38;4.23	4.36	3.44	0.39384	.	0.571316	0.16944	N	0.193156	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B	0.20887	0.049	B	0.17098	0.017	T	0.02860	-1.1101	9	0.17369	T	0.5	-0.3997	11.0934	0.48130	0.0:0.9131:0.0:0.0869	rs2640779;rs3802835;rs52819961;rs60165688;rs2640779	1663	Q8NEV8	EXPH5_HUMAN	R	1663;1587;1475;1656;1587	ENSP00000265843:G1663R;ENSP00000391966:G1587R;ENSP00000411390:G1475R;ENSP00000432546:G1656R;ENSP00000432683:G1587R	ENSP00000265843:G1663R	G	-	1	0	EXPH5	107886457	0.005000	0.15991	0.004000	0.12327	0.012000	0.07955	1.616000	0.36933	1.178000	0.42870	0.650000	0.86243	GGA	C|0.760;T|0.240	0.240	strong		0.478	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
PADI2	11240	hgsc.bcm.edu	37	1	17419024	17419024	+	Silent	SNP	G	G	A	rs11203297	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17419024G>A	ENST00000375486.4	-	6	597	c.534C>T	c.(532-534)ctC>ctT	p.L178L	PADI2_ENST00000444885.2_Intron|PADI2_ENST00000375481.1_Silent_p.L178L	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	178					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	ACATGTCCTTGAGATCTGAGG	0.493													G|||	1409	0.28135	0.0877	0.3631	5008	,	,		19329	0.5099		0.1869	False		,,,				2504	0.3466				p.L178L		Atlas-SNP	.											PADI2,NS,carcinoma,-2,1	PADI2	72	1	0			c.C534T						PASS	.	G		506,3900	233.3+/-246.5	26,454,1723	63.0	59.0	60.0		534	1.3	1.0	1	dbSNP_120	60	1678,6922	309.2+/-309.3	160,1358,2782	no	coding-synonymous	PADI2	NM_007365.2		186,1812,4505	AA,AG,GG		19.5116,11.4843,16.7922		178/666	17419024	2184,10822	2203	4300	6503	SO:0001819	synonymous_variant	11240	exon6			GTCCTTGAGATCT	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.534C>T	1.37:g.17419024G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	CCDS177.1																																																																																			G|0.800;A|0.200	0.200	strong		0.493	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
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 GAIIx	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_ENST00000544197.1_Missense_Mutation_p.D99H|HAVCR1_ENST00000523175.1_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	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	133	71	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		
PCDH19	57526	hgsc.bcm.edu	37	X	99662459	99662459	+	Silent	SNP	G	G	A	rs56277715		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:99662459G>A	ENST00000373034.4	-	1	2812	c.1137C>T	c.(1135-1137)ggC>ggT	p.G379G	PCDH19_ENST00000255531.7_Silent_p.G379G|PCDH19_ENST00000420881.2_Silent_p.G379G	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	379	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(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						GTCCATTGAGGCCTGAGTCGC	0.597													G|||	17	0.00450331	0.0	0.0058	3775	,	,		15258	0.0		0.0129	False		,,,				2504	0.0				p.G379G		Atlas-SNP	.											.	PCDH19	269	.	0			c.C1137T						PASS	.	G	,,	7,3802		0,5,2,1614,569	67.0	67.0	67.0		1137,1137,1137	-2.4	1.0	X	dbSNP_129	67	110,6584		0,79,31,2341,1823	no	coding-synonymous,coding-synonymous,coding-synonymous	PCDH19	NM_001105243.1,NM_001184880.1,NM_020766.2	,,	0,84,33,3955,2392	AA,AG,A,GG,G		1.6433,0.1838,1.114	,,	379/1102,379/1149,379/1101	99662459	117,10386	2190	4274	6464	SO:0001819	synonymous_variant	57526	exon1			ATTGAGGCCTGAG	AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.1137C>T	X.37:g.99662459G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	NM_001184880	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Silent	SNP	ENST00000373034.4	37	CCDS55462.1																																																																																			G|0.993;A|0.007	0.007	strong		0.597	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766	
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 GAIIx	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	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	133	24	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	
CASP5	838	hgsc.bcm.edu	37	11	104869708	104869708	+	Missense_Mutation	SNP	G	G	C	rs523104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:104869708G>C	ENST00000260315.3	-	7	999	c.1000C>G	c.(1000-1002)Ctc>Gtc	p.L334V	CASP5_ENST00000531367.1_Missense_Mutation_p.L192V|CASP5_ENST00000418434.1_Missense_Mutation_p.L192V|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000526056.1_Missense_Mutation_p.L347V|CASP5_ENST00000393141.2_Missense_Mutation_p.L347V|CASP5_ENST00000444749.2_Missense_Mutation_p.L276V			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	334			L -> V (in dbSNP:rs523104). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16893518, ECO:0000269|PubMed:7797592, ECO:0000269|Ref.7}.		apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		GAAGAGATGAGTGCCAAGGAT	0.418													C|||	2650	0.529153	0.4644	0.4035	5008	,	,		18397	0.7728		0.4732	False		,,,				2504	0.5123				p.L347V		Atlas-SNP	.											CASP5_ENST00000393141,NS,carcinoma,0,2	CASP5	213	2	0			c.C1039G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	1952,2452	620.7+/-393.6	423,1106,673	117.0	103.0	108.0		826,574,1039,1000	-4.7	0.0	11	dbSNP_83	108	3947,4651	603.5+/-394.7	906,2135,1258	yes	missense,missense,missense,missense	CASP5	NM_001136109.1,NM_001136110.1,NM_001136112.1,NM_004347.3	32,32,32,32	1329,3241,1931	CC,CG,GG		45.906,44.3233,45.3699	benign,benign,benign,benign	276/377,192/293,347/448,334/435	104869708	5899,7103	2202	4299	6501	SO:0001583	missense	838	exon7			AGATGAGTGCCAA		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"""Caspases"""	1506	protein-coding gene	gene with protein product		602665	"""caspase 5, apoptosis-related cysteine protease"""			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.1000C>G	11.37:g.104869708G>C	ENSP00000260315:p.Leu334Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	139	15	0.107914	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	37	CCDS8328.2	1145	0.5242673992673993	225	0.4573170731707317	150	0.4143646408839779	430	0.7517482517482518	340	0.44854881266490765	C	1.710	-0.499303	0.04291	0.443233	0.45906	ENSG00000137757	ENST00000393141;ENST00000418434;ENST00000260315;ENST00000444749;ENST00000526056;ENST00000531367	T;T;T;T;T;T	0.03181	4.02;4.02;4.02;4.02;4.02;4.02	4.19	-4.68	0.03309	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);	1.643900	0.03386	N	0.201138	T	0.00012	0.0000	N	0.00500	-1.43	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	0.29427	-1.0012	9	0.16420	T	0.52	.	1.7822	0.03034	0.1254:0.187:0.3485:0.3391	rs523104;rs3824929;rs17222987;rs52796995;rs61281764;rs523104	192;276;334;347	P51878-3;P51878-2;P51878;P51878-5	.;.;CASP5_HUMAN;.	V	347;192;334;276;347;192	ENSP00000376849:L347V;ENSP00000398130:L192V;ENSP00000260315:L334V;ENSP00000388365:L276V;ENSP00000436877:L347V;ENSP00000434471:L192V	ENSP00000260315:L334V	L	-	1	0	CASP5	104374918	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.448000	0.06820	-1.532000	0.01747	-0.968000	0.02614	CTC	G|0.508;C|0.492	0.492	strong		0.418	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	
HOXC4	3221	hgsc.bcm.edu	37	12	54448106	54448106	+	Missense_Mutation	SNP	A	A	G	rs75256744	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:54448106A>G	ENST00000430889.2	+	1	446	c.400A>G	c.(400-402)Ata>Gta	p.I134V	HOXC4_ENST00000609810.1_Missense_Mutation_p.I134V|HOXC4_ENST00000303406.4_Missense_Mutation_p.I134V	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	134					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						CAAGCAACCCATAGTCTACCC	0.647													A|||	554	0.110623	0.0174	0.0908	5008	,	,		8955	0.0337		0.1769	False		,,,				2504	0.2618				p.I134V		Atlas-SNP	.											.	HOXC4	29	.	0			c.A400G						PASS	.	A	VAL/ILE,VAL/ILE	184,4222		6,172,2025	25.0	25.0	25.0		400,400	4.3	1.0	12	dbSNP_131	25	1507,7091		132,1243,2924	yes	missense,missense	HOXC4	NM_014620.4,NM_153633.2	29,29	138,1415,4949	GG,GA,AA		17.5273,4.1761,13.0037	benign,benign	134/265,134/265	54448106	1691,11313	2203	4299	6502	SO:0001583	missense	3221	exon3			CAACCCATAGTCT		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"""Homeoboxes / ANTP class : HOXL subclass"""	5126	protein-coding gene	gene with protein product		142974	"""homeo box C4"""	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.400A>G	12.37:g.54448106A>G	ENSP00000399808:p.Ile134Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_014620		Missense_Mutation	SNP	ENST00000430889.2	37	CCDS8873.1	217	0.09935897435897435	24	0.04878048780487805	38	0.10497237569060773	19	0.033216783216783216	136	0.17941952506596306	A	0.226	-1.024613	0.02061	0.041761	0.175273	ENSG00000198353	ENST00000303406;ENST00000430889	D;D	0.88354	-2.37;-2.37	4.26	4.26	0.50523	.	0.062472	0.64402	D	0.000007	T	0.00210	0.0006	N	0.00258	-1.755	0.26297	P	0.9780349	B	0.06786	0.001	B	0.08055	0.003	T	0.42032	-0.9475	9	0.02654	T	1	.	12.7918	0.57539	1.0:0.0:0.0:0.0	.	134	P09017	HXC4_HUMAN	V	134	ENSP00000305973:I134V;ENSP00000399808:I134V	ENSP00000305973:I134V	I	+	1	0	HOXC4	52734373	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.533000	0.45667	1.918000	0.55548	0.379000	0.24179	ATA	A|0.880;G|0.120	0.120	strong		0.647	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1		
C9orf156	51531	hgsc.bcm.edu	37	9	100675816	100675816	+	Silent	SNP	A	A	G	rs1127703	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:100675816A>G	ENST00000375119.3	-	3	352	c.276T>C	c.(274-276)aaT>aaC	p.N92N	Y_RNA_ENST00000364960.1_RNA|C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	92	TsaA-like. {ECO:0000255|PROSITE- ProRule:PRU01003}.				viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				TCAAATGACCATTTTTGTGAA	0.398													A|||	852	0.170128	0.1717	0.1931	5008	,	,		18939	0.1498		0.2654	False		,,,				2504	0.0746				p.N92N		Atlas-SNP	.											.	C9orf156	35	.	0			c.T276C						PASS	.	A		799,3607	322.3+/-297.6	76,647,1480	79.0	75.0	76.0		276	3.1	1.0	9	dbSNP_86	76	2240,6360	379.5+/-339.3	301,1638,2361	no	coding-synonymous	C9orf156	NM_016481.3		377,2285,3841	GG,GA,AA		26.0465,18.1344,23.3661		92/442	100675816	3039,9967	2203	4300	6503	SO:0001819	synonymous_variant	51531	exon3			ATGACCATTTTTG	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"""Nef (lentivirus myristoylated factor) associated protein 1"""						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.276T>C	9.37:g.100675816A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Silent	SNP	ENST00000375119.3	37	CCDS6730.1																																																																																			A|0.790;G|0.210	0.210	strong		0.398	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
CDH11	1009	hgsc.bcm.edu	37	16	65025718	65025718	+	Missense_Mutation	SNP	G	G	A	rs35195	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:65025718G>A	ENST00000268603.4	-	6	1379	c.764C>T	c.(763-765)aCg>aTg	p.T255M	CDH11_ENST00000394156.3_Missense_Mutation_p.T255M|CDH11_ENST00000566827.1_Missense_Mutation_p.T129M	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	255	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> M (in dbSNP:rs35195).		adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CAGTGTGATCGTCACTTTGGT	0.537			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			G|||	909	0.18151	0.0234	0.2075	5008	,	,		18677	0.2044		0.331	False		,,,				2504	0.1994				p.T255M		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	CDH11,NS,carcinoma,+1,1	CDH11	260	1	0			c.C764T						PASS	.	G	MET/THR	321,4085	170.9+/-201.2	12,297,1894	344.0	230.0	269.0		764	4.6	1.0	16	dbSNP_76	269	3062,5538	471.8+/-368.2	536,1990,1774	yes	missense	CDH11	NM_001797.2	81	548,2287,3668	AA,AG,GG		35.6047,7.2855,26.0111	probably-damaging	255/797	65025718	3383,9623	2203	4300	6503	SO:0001583	missense	1009	exon6			GTGATCGTCACTT	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.764C>T	16.37:g.65025718G>A	ENSP00000268603:p.Thr255Met	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	484	0.2216117216117216	14	0.028455284552845527	92	0.2541436464088398	133	0.23251748251748253	245	0.3232189973614776	G	19.20	3.782474	0.70222	0.072855	0.356047	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.03468	3.92;3.92	5.54	4.59	0.56863	Cadherin (5);Cadherin-like (1);	0.145674	0.64402	N	0.000008	T	0.00012	0.0000	M	0.72576	2.205	0.21675	P	0.999594887	D;D	0.67145	0.986;0.996	B;P	0.60886	0.219;0.88	T	0.48885	-0.8995	9	0.72032	D	0.01	.	13.2834	0.60228	0.076:0.0:0.924:0.0	rs35195;rs966262;rs1200180;rs2229572;rs17851050;rs52827080;rs57188221;rs35195	255;255	P55287-2;P55287	.;CAD11_HUMAN	M	255;255;238	ENSP00000268603:T255M;ENSP00000377711:T255M	ENSP00000268603:T255M	T	-	2	0	CDH11	63583219	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.388000	0.52509	1.344000	0.45657	0.650000	0.86243	ACG	G|0.763;A|0.237	0.237	strong		0.537	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
PNMAL1	55228	hgsc.bcm.edu	37	19	46974233	46974233	+	Silent	SNP	G	G	A	rs3826851	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46974233G>A	ENST00000313683.10	-	2	365	c.60C>T	c.(58-60)gaC>gaT	p.D20D	PNMAL1_ENST00000602246.1_Silent_p.D20D|PNMAL1_ENST00000438932.2_Silent_p.D20D	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	20										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		acctgtggatgtccacttcca	0.532													G|||	1073	0.214257	0.2534	0.1988	5008	,	,		18007	0.1806		0.2475	False		,,,				2504	0.1728				p.D20D		Atlas-SNP	.											.	PNMAL1	87	.	0			c.C60T						PASS	.	G	,	1267,3139	432.6+/-343.3	183,901,1119	93.0	86.0	88.0		60,60	0.6	1.0	19	dbSNP_107	88	2077,6523	361.4+/-332.3	273,1531,2496	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	456,2432,3615	AA,AG,GG		24.1512,28.7562,25.7112	,	20/379,20/440	46974233	3344,9662	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			GTGGATGTCCACT	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.60C>T	19.37:g.46974233G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			A|0.247;C|0.000;G|0.753	0.247	strong		0.532	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
TFEB	7942	hgsc.bcm.edu	37	6	41652514	41652514	+	Silent	SNP	C	C	T	rs2073158	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41652514C>T	ENST00000230323.4	-	10	1555	c.1254G>A	c.(1252-1254)gcG>gcA	p.A418A	AL035588.1_ENST00000597468.1_5'Flank|TFEB_ENST00000420312.1_Silent_p.A333A|TFEB_ENST00000373033.1_Silent_p.A418A|TFEB_ENST00000358871.2_Silent_p.A432A|TFEB_ENST00000403298.4_Silent_p.A418A	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB	418					autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			CATGCCCCGGCGCCAGGGGTT	0.647			T	ALPHA	renal (childhood epithelioid)								C|||	989	0.197484	0.0749	0.183	5008	,	,		14273	0.3194		0.1998	False		,,,				2504	0.2454				p.A432A		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"""E,M"""	TFEB,NS,carcinoma,-1,1	TFEB	37	1	0			c.G1296A						PASS	.	C	,	385,4019	183.6+/-211.2	14,357,1831	34.0	36.0	35.0		1254,1254	4.3	1.0	6	dbSNP_96	35	1681,6919	294.2+/-301.7	175,1331,2794	no	coding-synonymous,coding-synonymous	TFEB	NM_001167827.1,NM_007162.2	,	189,1688,4625	TT,TC,CC		19.5465,8.7421,15.8874	,	418/477,418/477	41652514	2066,10938	2202	4300	6502	SO:0001819	synonymous_variant	7942	exon9			CCCCGGCGCCAGG	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"""Basic helix-loop-helix proteins"""	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.1254G>A	6.37:g.41652514C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	135	28	0.207407	NM_001167827	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Silent	SNP	ENST00000230323.4	37	CCDS4858.1																																																																																			C|0.832;T|0.168	0.168	strong		0.647	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		
EPHX2	2053	hgsc.bcm.edu	37	8	27394366	27394366	+	Silent	SNP	C	C	T	rs13439459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27394366C>T	ENST00000521400.1	+	13	1666	c.1236C>T	c.(1234-1236)agC>agT	p.S412S	EPHX2_ENST00000518379.1_Silent_p.S380S|EPHX2_ENST00000380476.3_Silent_p.S359S|EPHX2_ENST00000521780.1_Silent_p.S346S|EPHX2_ENST00000517536.1_Silent_p.S229S	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	412	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		TCAGAGCAAGCGATGAGGTGA	0.527													C|||	314	0.0626997	0.084	0.0807	5008	,	,		15715	0.001		0.0845	False		,,,				2504	0.0624				p.S412S		Atlas-SNP	.											.	EPHX2	57	.	0			c.C1236T						PASS	.	C		359,4047	184.7+/-212.0	17,325,1861	63.0	65.0	64.0		1236	0.1	0.0	8	dbSNP_121	64	874,7726	197.8+/-242.3	44,786,3470	no	coding-synonymous	EPHX2	NM_001979.4		61,1111,5331	TT,TC,CC		10.1628,8.148,9.4802		412/556	27394366	1233,11773	2203	4300	6503	SO:0001819	synonymous_variant	2053	exon13			AGCAAGCGATGAG	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1236C>T	8.37:g.27394366C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	52	0.55914	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1																																																																																			C|0.918;T|0.082	0.082	strong		0.527	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
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 GAIIx	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	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	94	7	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	
LAMB2	3913	hgsc.bcm.edu	37	3	49162583	49162583	+	Missense_Mutation	SNP	C	C	T	rs35713889	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49162583C>T	ENST00000418109.1	-	21	2904	c.2740G>A	c.(2740-2742)Ggg>Agg	p.G914R	LAMB2_ENST00000464891.1_5'UTR|LAMB2_ENST00000305544.4_Missense_Mutation_p.G914R	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	914	Laminin EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00460}.			G -> R (in Ref. 1; CAA92279). {ECO:0000305}.	astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CGTGGGTCCCCGTGGAAACCA	0.607													C|||	153	0.0305511	0.0461	0.0389	5008	,	,		17245	0.0139		0.0338	False		,,,				2504	0.0174				p.G914R		Atlas-SNP	.											.	LAMB2	156	.	0			c.G2740A						PASS	.	C	ARG/GLY	169,4237	106.5+/-144.9	5,159,2039	42.0	38.0	40.0		2740	6.0	1.0	3	dbSNP_126	40	367,8233	117.4+/-177.0	5,357,3938	yes	missense	LAMB2	NM_002292.3	125	10,516,5977	TT,TC,CC		4.2674,3.8357,4.1212	probably-damaging	914/1799	49162583	536,12470	2203	4300	6503	SO:0001583	missense	3913	exon20			GGTCCCCGTGGAA		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.2740G>A	3.37:g.49162583C>T	ENSP00000388325:p.Gly914Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	67	0.030677655677655676	21	0.042682926829268296	17	0.04696132596685083	1	0.0017482517482517483	28	0.036939313984168866	C	25.0	4.596618	0.86953	0.038357	0.042674	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.66460	-0.21;-0.21	5.98	5.98	0.97165	EGF-like, laminin (4);	0.000000	0.85682	D	0.000000	T	0.42200	0.1192	L	0.42529	1.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.65755	-0.6091	10	0.52906	T	0.07	.	20.4561	0.99145	0.0:1.0:0.0:0.0	rs35713889;rs35713889	914	P55268	LAMB2_HUMAN	R	914	ENSP00000388325:G914R;ENSP00000307156:G914R	ENSP00000307156:G914R	G	-	1	0	LAMB2	49137587	1.000000	0.71417	0.967000	0.41034	0.708000	0.40852	7.693000	0.84214	2.847000	0.97988	0.591000	0.81541	GGG	C|0.959;T|0.041	0.041	strong		0.607	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
CWH43	80157	hgsc.bcm.edu	37	4	48988450	48988450	+	Missense_Mutation	SNP	C	C	A	rs3747690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:48988450C>A	ENST00000226432.4	+	1	187	c.4C>A	c.(4-6)Ccc>Acc	p.P2T	CWH43_ENST00000513409.1_5'Flank	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	2			P -> T (in dbSNP:rs3747690). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		GPI anchor biosynthetic process (GO:0006506)	integral component of membrane (GO:0016021)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(26)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43						CGCGGCGATGCCCTCGCTGTG	0.726													C|||	1478	0.295128	0.1256	0.5043	5008	,	,		13727	0.1825		0.492	False		,,,				2504	0.2894				p.P2T		Atlas-SNP	.											.	CWH43	101	.	0			c.C4A						PASS	.	C	THR/PRO	732,3534		80,572,1481	12.0	14.0	13.0		4	-1.0	0.0	4	dbSNP_107	13	3702,4622		933,1836,1393	yes	missense	CWH43	NM_025087.2	38	1013,2408,2874	AA,AC,CC		44.4738,17.1589,35.2184	benign	2/700	48988450	4434,8156	2133	4162	6295	SO:0001583	missense	80157	exon1			GCGATGCCCTCGC		CCDS3486.1, CCDS68697.1	4p12-p11	2010-09-21			ENSG00000109182	ENSG00000109182			26133	protein-coding gene	gene with protein product						17714445, 17761529	Standard	NM_025087		Approved	FLJ21511, CWH43-C	uc003gyv.3	Q9H720	OTTHUMG00000128627	ENST00000226432.4:c.4C>A	4.37:g.48988450C>A	ENSP00000226432:p.Pro2Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_025087	B2RPD7	Missense_Mutation	SNP	ENST00000226432.4	37	CCDS3486.1	747	0.34203296703296704	71	0.1443089430894309	199	0.5497237569060773	104	0.18181818181818182	373	0.4920844327176781	C	7.217	0.596628	0.13875	0.171589	0.444738	ENSG00000109182	ENST00000226432	T	0.28895	1.59	3.07	-1.03	0.10102	.	1.378150	0.04887	N	0.448797	T	0.00012	0.0000	N	0.08118	0	0.22034	P	0.999408227	B	0.02656	0.0	B	0.01281	0.0	T	0.46569	-0.9182	8	.	.	.	.	1.7701	0.03010	0.1493:0.3689:0.2929:0.189	rs3747690;rs17676219;rs3747690	2	Q9H720	PG2IP_HUMAN	T	2	ENSP00000226432:P2T	.	P	+	1	0	CWH43	48683207	0.000000	0.05858	0.008000	0.14137	0.009000	0.06853	-1.223000	0.02962	-0.280000	0.09154	-0.300000	0.09419	CCC	C|0.691;A|0.309	0.309	strong		0.726	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087	
NLRP11	204801	hgsc.bcm.edu	37	19	56329334	56329334	+	Silent	SNP	G	G	C	rs8113630	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56329334G>C	ENST00000589093.1	-	2	300	c.207C>G	c.(205-207)ctC>ctG	p.L69L	NLRP11_ENST00000592953.1_Intron|NLRP11_ENST00000589824.2_Silent_p.L69L|NLRP11_ENST00000360133.3_Silent_p.L69L|NLRP11_ENST00000443188.1_Silent_p.L69L			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	69	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		ATATGCTGAAGAGCATATTCC	0.428													G|||	410	0.081869	0.1959	0.0504	5008	,	,		19709	0.0		0.0596	False		,,,				2504	0.0573				p.L69L		Atlas-SNP	.											.	NLRP11	139	.	0			c.C207G						PASS	.	G		774,3632	314.9+/-293.9	64,646,1493	148.0	135.0	139.0		207	-5.4	0.0	19	dbSNP_116	139	626,7974	162.2+/-214.9	27,572,3701	no	coding-synonymous	NLRP11	NM_145007.3		91,1218,5194	CC,CG,GG		7.2791,17.567,10.7643		69/1034	56329334	1400,11606	2203	4300	6503	SO:0001819	synonymous_variant	204801	exon4			GCTGAAGAGCATA	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.207C>G	19.37:g.56329334G>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	148	66	0.445946	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	37	CCDS12935.1																																																																																			G|0.900;C|0.100	0.100	strong		0.428	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
FBXW10	10517	hgsc.bcm.edu	37	17	18682505	18682505	+	Missense_Mutation	SNP	T	T	C	rs1024657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18682505T>C	ENST00000395665.4	+	14	3274	c.3053T>C	c.(3052-3054)gTc>gCc	p.V1018A	TVP23B_ENST00000307767.8_5'Flank|FBXW10_ENST00000301938.4_Missense_Mutation_p.V965A|TVP23B_ENST00000476139.1_5'Flank|TVP23B_ENST00000574226.1_5'Flank|FBXW10_ENST00000395667.1_Missense_Mutation_p.V1017A|FBXW10_ENST00000308799.4_Missense_Mutation_p.V1027A			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	1018								p.V1017A(1)		NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						CCAGGAAAAGTCAGCAAAGCT	0.488													N|||	744	0.148562	0.1846	0.2147	5008	,	,		13486	0.0903		0.2018	False		,,,				2504	0.0583				p.V1018A		Atlas-SNP	.											FBXW10,NS,carcinoma,0,2	FBXW10	82	2	1	Substitution - Missense(1)	prostate(1)	c.T3053C						scavenged	.						42.0	40.0	41.0					17																	18682505		1906	3581	5487	SO:0001583	missense	10517	exon14			GAAAAGTCAGCAA	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.3053T>C	17.37:g.18682505T>C	ENSP00000379025:p.Val1018Ala	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	195	5	0.025641	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	498	0.22802197802197802	92	0.18699186991869918	107	0.2955801104972376	65	0.11363636363636363	234	0.3087071240105541	C	0.015	-1.557317	0.00910	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	3.38	2.36	0.29203	.	0.000000	0.31936	N	0.006834	T	0.00012	0.0000	N	0.00128	-2.045	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.24693	-1.0153	9	0.02654	T	1	.	4.0906	0.09968	0.4063:0.4743:0.0:0.1194	.	965;1027;1018;1017	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	A	1017;1027;965;1018	ENSP00000379026:V1017A;ENSP00000310382:V1027A;ENSP00000306937:V965A;ENSP00000379025:V1018A	ENSP00000306937:V965A	V	+	2	0	FBXW10	18623230	0.407000	0.25352	0.286000	0.24833	0.737000	0.42083	0.661000	0.25023	0.116000	0.18110	-0.473000	0.04963	GTC	T|0.778;C|0.222	0.222	strong		0.488	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855898	12855898	+	Missense_Mutation	SNP	C	C	T	rs76032448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12855898C>T	ENST00000332296.7	+	4	1281	c.1178C>T	c.(1177-1179)gCc>gTc	p.A393V	PRAMEF1_ENST00000400814.3_Missense_Mutation_p.A148V	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	393					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)					cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TCTATTGACGCCCTGAAGGAC	0.552																																					p.A393V		Atlas-SNP	.											PRAMEF1,NS,carcinoma,+1,2	PRAMEF1	78	2	0			c.C1178T						scavenged	.	C	VAL/ALA	18,4386		0,18,2184	62.0	56.0	58.0		1178	-0.6	0.0	1	dbSNP_131	58	95,8497		0,95,4201	no	missense	PRAMEF1	NM_023013.2	64	0,113,6385	TT,TC,CC		1.1057,0.4087,0.8695	possibly-damaging	393/475	12855898	113,12883	2202	4296	6498	SO:0001583	missense	65121	exon4			TTGACGCCCTGAA	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.1178C>T	1.37:g.12855898C>T	ENSP00000332134:p.Ala393Val	Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	233	59	0.253219	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	0.839	-0.742620	0.03088	0.004087	0.011057	ENSG00000116721	ENST00000332296;ENST00000400814	T;T	0.08720	3.06;3.06	1.56	-0.547	0.11836	.	2.443230	0.01567	N	0.020432	T	0.03220	0.0094	N	0.13043	0.29	0.09310	N	1	B	0.25809	0.135	B	0.29942	0.109	T	0.29488	-1.0010	10	0.02654	T	1	.	4.967	0.14096	0.0:0.703:0.0:0.297	.	393	O95521	PRAM1_HUMAN	V	393;148	ENSP00000332134:A393V;ENSP00000383616:A148V	ENSP00000332134:A393V	A	+	2	0	PRAMEF1	12778485	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.937000	0.01547	-0.161000	0.10983	0.205000	0.17691	GCC	C|0.986;T|0.014	0.014	strong		0.552	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
CELSR2	1952	hgsc.bcm.edu	37	1	109810544	109810544	+	Silent	SNP	C	C	A	rs2281894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109810544C>A	ENST00000271332.3	+	17	6241	c.6180C>A	c.(6178-6180)cgC>cgA	p.R2060R		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2060					cerebrospinal fluid secretion (GO:0033326)|cilium assembly (GO:0042384)|cilium movement (GO:0003341)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neural plate anterior/posterior regionalization (GO:0021999)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of cell-cell adhesion (GO:0022407)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|ventricular system development (GO:0021591)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(27)|ovary(5)|prostate(1)|skin(3)|urinary_tract(2)	82		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0296)|Lung(183;0.067)|COAD - Colon adenocarcinoma(174;0.114)|Epithelial(280;0.193)|all cancers(265;0.219)		TGCTCCTGCGCAACGCCACGC	0.677													C|||	1131	0.225839	0.0537	0.2205	5008	,	,		18633	0.4206		0.1928	False		,,,				2504	0.2955				p.R2060R	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											.	CELSR2	228	.	0			c.C6180A						PASS	.	C		313,4093	152.9+/-186.6	17,279,1907	29.0	29.0	29.0		6180	0.1	1.0	1	dbSNP_100	29	1603,6997	272.4+/-290.1	169,1265,2866	no	coding-synonymous	CELSR2	NM_001408.2		186,1544,4773	AA,AC,CC		18.6395,7.1039,14.7317		2060/2924	109810544	1916,11090	2203	4300	6503	SO:0001819	synonymous_variant	1952	exon17			CCTGCGCAACGCC	D87469	CCDS796.1	1p13.3	2014-08-08	2013-02-18		ENSG00000143126	ENSG00000143126		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3231	protein-coding gene	gene with protein product		604265	"""cadherin, EGF LAG seven-pass G-type receptor 2, flamingo (Drosophila) homolog"""	EGFL2		9693030, 10907856	Standard	NM_001408		Approved	KIAA0279, MEGF3, Flamingo1, CDHF10	uc001dxa.4	Q9HCU4	OTTHUMG00000012003	ENST00000271332.3:c.6180C>A	1.37:g.109810544C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	125	68	0.544	NM_001408	Q5T2Y7|Q92566	Silent	SNP	ENST00000271332.3	37	CCDS796.1																																																																																			C|0.824;A|0.176	0.176	strong		0.677	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408	
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 GAIIx	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		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	47	28	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	
DOCK10	55619	hgsc.bcm.edu	37	2	225709926	225709926	+	Silent	SNP	A	A	G	rs7577271	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:225709926A>G	ENST00000258390.7	-	21	2542	c.2475T>C	c.(2473-2475)agT>agC	p.S825S	DOCK10_ENST00000409592.3_Silent_p.S819S	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	825	DHR-1.				regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		ATACCTTTCCACTTGCAGAAT	0.348													G|||	904	0.180511	0.4818	0.0764	5008	,	,		20059	0.0218		0.1133	False		,,,				2504	0.0798				p.S825S		Atlas-SNP	.											.	DOCK10	308	.	0			c.T2475C						PASS	.	G		1559,2147		325,909,619	72.0	65.0	67.0		2475	-1.3	1.0	2	dbSNP_116	67	840,7360		42,756,3302	no	coding-synonymous	DOCK10	NM_014689.2		367,1665,3921	GG,GA,AA		10.2439,42.0669,20.1495		825/2187	225709926	2399,9507	1853	4100	5953	SO:0001819	synonymous_variant	55619	exon21			CTTTCCACTTGCA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.2475T>C	2.37:g.225709926A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																			A|0.820;G|0.180	0.180	strong		0.348	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
EGFLAM	133584	hgsc.bcm.edu	37	5	38370537	38370537	+	Missense_Mutation	SNP	T	T	C	rs1465567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:38370537T>C	ENST00000354891.3	+	6	1031	c.685T>C	c.(685-687)Tgg>Cgg	p.W229R	EGFLAM_ENST00000322350.5_Missense_Mutation_p.W229R	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	229	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		W -> R (in dbSNP:rs1465567).		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)	p.W229R(1)		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)					CCCCCGCAGCTGGCCCAGTGA	0.567													T|||	1288	0.257188	0.4372	0.1354	5008	,	,		17182	0.1796		0.2038	False		,,,				2504	0.2352				p.W229R	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											EGFLAM,NS,carcinoma,0,1	EGFLAM	302	1	1	Substitution - Missense(1)	stomach(1)	c.T685C						PASS	.	T	ARG/TRP,ARG/TRP	1746,2660	520.6+/-370.3	349,1048,806	43.0	42.0	42.0		685,685	-2.0	0.0	5	dbSNP_88	42	1663,6937	305.6+/-307.5	175,1313,2812	yes	missense,missense	EGFLAM	NM_001205301.1,NM_152403.3	101,101	524,2361,3618	CC,CT,TT		19.3372,39.6278,26.211	benign,benign	229/1018,229/1010	38370537	3409,9597	2203	4300	6503	SO:0001583	missense	133584	exon6			CGCAGCTGGCCCA	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.685T>C	5.37:g.38370537T>C	ENSP00000346964:p.Trp229Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	565	0.2586996336996337	239	0.48577235772357724	58	0.16022099447513813	118	0.2062937062937063	150	0.19788918205804748	T	7.093	0.572574	0.13623	0.396278	0.193372	ENSG00000164318	ENST00000354891;ENST00000322350	T;T	0.52057	0.68;0.68	5.82	-2.02	0.07388	Fibronectin, type III (2);Immunoglobulin-like fold (1);	2.059790	0.01504	N	0.017616	T	0.00012	0.0000	N	0.01761	-0.735	0.53688	P	2.6999999999999247E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35847	-0.9772	9	0.06625	T	0.88	-0.0747	5.516	0.16906	0.0841:0.6017:0.2313:0.083	rs1465567;rs1465567	229;229	Q63HQ2;Q63HQ2-2	EGFLA_HUMAN;.	R	229	ENSP00000346964:W229R;ENSP00000313084:W229R	ENSP00000313084:W229R	W	+	1	0	EGFLAM	38406294	0.000000	0.05858	0.016000	0.15963	0.941000	0.58515	-0.353000	0.07691	-0.389000	0.07786	-0.379000	0.06801	TGG	T|0.741;C|0.259	0.259	strong		0.567	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
NRG3	10718	hgsc.bcm.edu	37	10	84745256	84745256	+	Silent	SNP	C	C	T	rs2295933	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:84745256C>T	ENST00000404547.1	+	10	2058	c.2058C>T	c.(2056-2058)agC>agT	p.S686S	NRG3_ENST00000545131.1_Silent_p.S312S|NRG3_ENST00000556918.1_Silent_p.S492S|NRG3_ENST00000537893.1_Silent_p.S312S|NRG3_ENST00000372141.2_Silent_p.S662S|NRG3_ENST00000404576.2_Silent_p.S466S|NRG3_ENST00000372142.2_Silent_p.S465S			P56975	NRG3_HUMAN	neuregulin 3	686					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		ACAGTGCAAGCGAAAACACAG	0.483													C|||	2352	0.469649	0.4236	0.4438	5008	,	,		17216	0.6637		0.3439	False		,,,				2504	0.4796				p.S662S		Atlas-SNP	.											.	NRG3	301	.	0			c.C1986T						PASS	.	C	,,	1867,2539	538.7+/-375.1	389,1089,725	80.0	73.0	75.0		1986,1983,1395	0.6	1.0	10	dbSNP_100	75	2565,6035	418.3+/-352.7	386,1793,2121	no	coding-synonymous,coding-synonymous,coding-synonymous	NRG3	NM_001010848.3,NM_001165972.1,NM_001165973.1	,,	775,2882,2846	TT,TC,CC		29.8256,42.374,34.0766	,,	662/697,661/696,465/500	84745256	4432,8574	2203	4300	6503	SO:0001819	synonymous_variant	10718	exon9			TGCAAGCGAAAAC	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.2058C>T	10.37:g.84745256C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Silent	SNP	ENST00000404547.1	37	CCDS31233.1																																																																																			C|0.606;T|0.394	0.394	strong		0.483	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17914122	17914122	+	Missense_Mutation	SNP	G	G	A	rs35497285	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17914122G>A	ENST00000361221.3	+	3	364	c.205G>A	c.(205-207)Gac>Aac	p.D69N	ARHGEF10L_ENST00000434513.1_Missense_Mutation_p.D69N|ARHGEF10L_ENST00000375420.3_5'Flank|ARHGEF10L_ENST00000375415.1_Missense_Mutation_p.D69N|ARHGEF10L_ENST00000452522.1_Missense_Mutation_p.D69N	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	69			D -> N (in dbSNP:rs35497285).			cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		GATCCACTTGGACTCCATCCC	0.587													G|||	464	0.0926518	0.0038	0.1225	5008	,	,		17367	0.2044		0.0835	False		,,,				2504	0.0859				p.D69N		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.G205A						PASS	.	G	ASN/ASP,ASN/ASP	79,4327	69.2+/-107.0	1,77,2125	130.0	142.0	138.0		205,205	5.3	0.4	1	dbSNP_126	138	727,7873	177.5+/-227.1	44,639,3617	yes	missense,missense	ARHGEF10L	NM_001011722.2,NM_018125.3	23,23	45,716,5742	AA,AG,GG		8.4535,1.793,6.1971	benign,benign	69/1241,69/1280	17914122	806,12200	2203	4300	6503	SO:0001583	missense	55160	exon3			CACTTGGACTCCA	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.205G>A	1.37:g.17914122G>A	ENSP00000355060:p.Asp69Asn	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	32	9	0.28125	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Missense_Mutation	SNP	ENST00000361221.3	37	CCDS182.1	221	0.10119047619047619	1	0.0020325203252032522	44	0.12154696132596685	115	0.20104895104895104	61	0.08047493403693931	G	19.11	3.764533	0.69878	0.01793	0.084535	ENSG00000074964	ENST00000361221;ENST00000452522;ENST00000434513;ENST00000375415	T;T;T;T	0.61274	0.3;0.3;0.12;0.3	5.3	5.3	0.74995	.	0.181464	0.37348	N	0.002128	T	0.00109	0.0003	L	0.27053	0.805	0.09310	P	0.9999999999970101	D;D;D;D	0.69078	0.996;0.969;0.969;0.997	P;P;P;D	0.73380	0.889;0.829;0.766;0.98	T	0.01720	-1.1288	9	0.16420	T	0.52	-37.9281	14.7973	0.69886	0.0:0.0:1.0:0.0	rs35497285;rs61749342	69;69;69;69	Q9HCE6-5;Q9HCE6-3;Q9HCE6-2;Q9HCE6	.;.;.;ARGAL_HUMAN	N	69	ENSP00000355060:D69N;ENSP00000399401:D69N;ENSP00000394621:D69N;ENSP00000364564:D69N	ENSP00000355060:D69N	D	+	1	0	ARHGEF10L	17786709	0.334000	0.24739	0.387000	0.26183	0.004000	0.04260	2.057000	0.41365	2.649000	0.89929	0.561000	0.74099	GAC	G|0.929;A|0.071	0.071	strong		0.587	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
MROH2B	133558	hgsc.bcm.edu	37	5	40998235	40998235	+	Silent	SNP	C	C	T	rs722575	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:40998235C>T	ENST00000399564.4	-	42	5127	c.4677G>A	c.(4675-4677)ccG>ccA	p.P1559P	MROH2B_ENST00000506092.2_Silent_p.P1114P	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1559								p.P1559P(1)									CACTAATACACGGATCTTGAC	0.483													C|||	1635	0.326478	0.295	0.3646	5008	,	,		21196	0.2956		0.3936	False		,,,				2504	0.3047				p.P1559P		Atlas-SNP	.											HEATR7B2,NS,carcinoma,-2,2	.	.	2	1	Substitution - coding silent(1)	stomach(1)	c.G4677A						PASS	.	C		1182,2674		181,820,927	181.0	169.0	172.0		4677	-0.2	1.0	5	dbSNP_86	172	3323,4985		669,1985,1500	no	coding-synonymous	HEATR7B2	NM_173489.4		850,2805,2427	TT,TC,CC		39.9976,30.6535,37.0355		1559/1586	40998235	4505,7659	1928	4154	6082	SO:0001819	synonymous_variant	133558	exon42			AATACACGGATCT		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.4677G>A	5.37:g.40998235C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	78	32	0.410256	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	ENST00000399564.4	37	CCDS47202.1																																																																																			C|0.702;T|0.298	0.298	strong		0.483	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
CTAGE1	64693	hgsc.bcm.edu	37	18	19996805	19996805	+	5'Flank	SNP	T	T	C	rs12961009	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:19996805T>C	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.I324V			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					AGATTTTTAATATGCTCTGTA	0.313													T|||	78	0.0155751	0.0015	0.0245	5008	,	,		18989	0.001		0.0497	False		,,,				2504	0.0082				p.I324V		Atlas-SNP	.											.	CTAGE1	146	.	0			c.A970G						PASS	.	T	VAL/ILE	43,4211		0,43,2084	34.0	38.0	37.0		970	0.7	0.0	18	dbSNP_121	37	371,8155		6,359,3898	no	missense	CTAGE1	NM_172241.2	29	6,402,5982	CC,CT,TT		4.3514,1.0108,3.2394	benign	324/746	19996805	414,12366	2127	4263	6390	SO:0001631	upstream_gene_variant	64693	exon1			TTTTAATATGCTC	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 1"", ""cutaneous T-cell lymphoma-associated antigen 2"", ""cancer/testis antigen family 21, member 1"", ""cancer/testis antigen family 21, member 2"""	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19996805T>C	Exception_encountered	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	97	62	0.639175	NM_172241	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	37		45	0.020604395604395604	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	34	0.044854881266490766	T	6.941	0.543343	0.13250	0.010108	0.043514	ENSG00000212710	ENST00000391403	T	0.37584	1.19	0.741	0.741	0.18336	.	.	.	.	.	T	0.10252	0.0251	M	0.77486	2.375	0.09310	N	1	B	0.33940	0.433	B	0.35470	0.203	T	0.15838	-1.0423	8	.	.	.	.	3.7843	0.08694	0.0:0.0:0.0:1.0	rs12961009	324	Q96RT6	CTGE2_HUMAN	V	324	ENSP00000375220:I324V	.	I	-	1	0	CTAGE1	18250803	1.000000	0.71417	0.034000	0.17996	0.294000	0.27393	2.665000	0.46791	0.560000	0.29169	0.369000	0.22263	ATT	T|0.976;C|0.024	0.024	strong		0.313	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241	
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 GAIIx	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	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	110	31	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	
IL32	9235	hgsc.bcm.edu	37	16	3119304	3119304	+	Missense_Mutation	SNP	A	A	G	rs398100042|rs2981599		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3119304A>G	ENST00000534507.1	+	6	864	c.653A>G	c.(652-654)gAc>gGc	p.D218G	IL32_ENST00000396887.3_Missense_Mutation_p.D115G|IL32_ENST00000549213.1_Missense_Mutation_p.D115G|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000552356.1_Missense_Mutation_p.D152G|IL32_ENST00000526464.2_Missense_Mutation_p.D172G|IL32_ENST00000551513.1_Missense_Mutation_p.D209G|IL32_ENST00000530538.2_Missense_Mutation_p.D172G|IL32_ENST00000008180.9_Missense_Mutation_p.D152G|IL32_ENST00000533097.2_Missense_Mutation_p.D172G|IL32_ENST00000440815.3_Missense_Mutation_p.D172G|IL32_ENST00000325568.5_Missense_Mutation_p.D172G|IL32_ENST00000525643.2_Missense_Mutation_p.D172G|IL32_ENST00000552664.1_Missense_Mutation_p.D172G|IL32_ENST00000396890.2_Missense_Mutation_p.D218G|IL32_ENST00000548652.1_Missense_Mutation_p.D163G|IL32_ENST00000528163.2_Missense_Mutation_p.D172G|IL32_ENST00000529550.1_Missense_Mutation_p.D172G|IL32_ENST00000529699.1_Missense_Mutation_p.D152G|IL32_ENST00000382213.3_Missense_Mutation_p.D163G|IL32_ENST00000548246.1_Missense_Mutation_p.D132G|IL32_ENST00000444393.3_Missense_Mutation_p.D172G|IL32_ENST00000552936.1_Missense_Mutation_p.D196G|IL32_ENST00000548476.1_Missense_Mutation_p.D218G|IL32_ENST00000530890.1_Missense_Mutation_p.D152G|IL32_ENST00000551122.1_Missense_Mutation_p.D115G|IL32_ENST00000531965.1_Missense_Mutation_p.D162G			P24001	IL32_HUMAN	interleukin 32	218					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CCACGGGGGGACAAGGAGGAG	0.577																																					p.D172G		Atlas-SNP	.											IL32,NS,carcinoma,+1,2	IL32	32	2	0			c.A515G						scavenged	.						91.0	117.0	108.0					16																	3119304		2197	4300	6497	SO:0001583	missense	9235	exon7			GGGGGGACAAGGA	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.653A>G	16.37:g.3119304A>G	ENSP00000431775:p.Asp218Gly	Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	157	66	0.420382	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Missense_Mutation	SNP	ENST00000534507.1	37		.	.	.	.	.	.	.	.	.	.	G	0.809	-0.752764	0.03041	.	.	ENSG00000008517	ENST00000325568;ENST00000534507;ENST00000531965;ENST00000396887;ENST00000529699;ENST00000526464;ENST00000440815;ENST00000529550;ENST00000551122;ENST00000525643;ENST00000548807;ENST00000528163;ENST00000530890;ENST00000444393;ENST00000533097;ENST00000008180;ENST00000396890;ENST00000548652;ENST00000530538;ENST00000549213;ENST00000552936;ENST00000548476;ENST00000552664;ENST00000552356;ENST00000551513;ENST00000382213;ENST00000548246	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.56776	0.45;0.46;0.45;0.44;0.45;0.45;0.45;0.45;0.44;0.45;0.46;0.45;0.45;0.45;0.45;0.45;0.46;0.45;0.45;0.44;0.46;0.46;0.45;0.45;0.46;0.45;0.45	1.26	-2.53	0.06326	.	.	.	.	.	T	0.24736	0.0600	N	0.14661	0.345	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001;0.0;0.0	T	0.14839	-1.0458	9	0.15952	T	0.53	.	0.7126	0.00926	0.1695:0.1865:0.3513:0.2928	rs2981599	132;152;163;152;218;172;115	B8Q191;C6GKH1;A6NNM0;A8MPX0;P24001;P24001-2;P24001-4	.;.;.;.;IL32_HUMAN;.;.	G	172;218;162;115;152;172;172;172;115;172;218;172;152;172;172;152;218;163;172;115;196;218;172;152;209;163;132	ENSP00000324742:D172G;ENSP00000431775:D218G;ENSP00000433177:D162G;ENSP00000380096:D115G;ENSP00000436937:D152G;ENSP00000450364:D172G;ENSP00000405063:D172G;ENSP00000437020:D172G;ENSP00000447496:D115G;ENSP00000432218:D172G;ENSP00000448354:D218G;ENSP00000432850:D172G;ENSP00000433747:D152G;ENSP00000411958:D172G;ENSP00000432917:D172G;ENSP00000008180:D152G;ENSP00000380099:D218G;ENSP00000446624:D163G;ENSP00000436929:D172G;ENSP00000447812:D115G;ENSP00000447033:D196G;ENSP00000449483:D218G;ENSP00000448683:D172G;ENSP00000446978:D152G;ENSP00000449147:D209G;ENSP00000371648:D163G;ENSP00000447979:D132G	ENSP00000008180:D152G	D	+	2	0	IL32	3059305	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.447000	0.02396	-1.773000	0.01290	-0.245000	0.11935	GAC	.	.	weak		0.577	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
RNF123	63891	hgsc.bcm.edu	37	3	49728870	49728870	+	Missense_Mutation	SNP	A	A	G	rs145883512	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49728870A>G	ENST00000327697.6	+	3	239	c.95A>G	c.(94-96)gAg>gGg	p.E32G	RNF123_ENST00000432042.1_Intron|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_5'Flank|MST1_ENST00000449682.2_5'Flank|MST1_ENST00000545762.1_5'Flank	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	32					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)		ATTGTGCAGGAGAAGCTGCTG	0.587													A|||	11	0.00219649	0.0008	0.0043	5008	,	,		24235	0.0		0.007	False		,,,				2504	0.0				p.E32G		Atlas-SNP	.											.	RNF123	100	.	0			c.A95G						PASS	.	A	GLY/GLU	4,4402	6.2+/-15.9	0,4,2199	39.0	36.0	37.0		95	5.1	1.0	3	dbSNP_134	37	67,8533	35.3+/-89.8	0,67,4233	yes	missense	RNF123	NM_022064.2	98	0,71,6432	GG,GA,AA		0.7791,0.0908,0.5459	benign	32/1315	49728870	71,12935	2203	4300	6503	SO:0001583	missense	63891	exon3			TGCAGGAGAAGCT	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.95A>G	3.37:g.49728870A>G	ENSP00000328287:p.Glu32Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	16.06	3.015403	0.54468	9.08E-4	0.007791	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000454491	T;T	0.74209	-0.82;0.69	5.14	5.14	0.70334	.	0.338915	0.28977	N	0.013527	T	0.54159	0.1841	L	0.32530	0.975	0.80722	D	1	B	0.22800	0.075	B	0.19946	0.027	T	0.60414	-0.7268	10	0.72032	D	0.01	-20.9173	7.9952	0.30265	0.9073:0.0:0.0927:0.0	.	32	Q5XPI4	RN123_HUMAN	G	32	ENSP00000328287:E32G;ENSP00000408490:E32G	ENSP00000328287:E32G	E	+	2	0	RNF123	49703874	1.000000	0.71417	0.981000	0.43875	0.959000	0.62525	6.125000	0.71627	2.070000	0.61991	0.482000	0.46254	GAG	A|0.995;G|0.005	0.005	strong		0.587	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
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 GAIIx	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_ENST00000413996.3_Silent_p.N86N|SGK1_ENST00000367857.5_Silent_p.N62N|SGK1_ENST00000475719.2_Silent_p.N72N|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367858.5_Silent_p.N167N|SGK1_ENST00000528577.1_Silent_p.N100N	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		Somatic	76	1	0.0131579		WXS	Illumina HiSeq	Phase_I	61	12	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		
CADPS2	93664	hgsc.bcm.edu	37	7	122078414	122078414	+	Silent	SNP	T	T	G	rs2074589	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:122078414T>G	ENST00000449022.2	-	17	2476	c.2457A>C	c.(2455-2457)acA>acC	p.T819T	CADPS2_ENST00000334010.7_Silent_p.T820T|RP5-1101C3.1_ENST00000592542.1_RNA|CADPS2_ENST00000412584.2_Silent_p.T816T|CADPS2_ENST00000313070.7_Silent_p.T816T	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	819	Interaction with DRD2.				cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						TGGCATATTCTGTGAGTCTAG	0.418													T|||	1423	0.284145	0.1346	0.3761	5008	,	,		18938	0.3889		0.2982	False		,,,				2504	0.2986				p.T819T		Atlas-SNP	.											.	CADPS2	116	.	0			c.A2457C						PASS	.	T	,,	560,3312		46,468,1422	106.0	99.0	101.0		2448,2457,2457	5.7	1.0	7	dbSNP_96	101	2585,5717		415,1755,1981	no	coding-synonymous,coding-synonymous,coding-synonymous	CADPS2	NM_001009571.3,NM_001167940.1,NM_017954.10	,,	461,2223,3403	GG,GT,TT		31.1371,14.4628,25.8337	,,	816/1256,819/1301,819/1297	122078414	3145,9029	1936	4151	6087	SO:0001819	synonymous_variant	93664	exon17			ATATTCTGTGAGT		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"""Pleckstrin homology (PH) domain containing"""	16018	protein-coding gene	gene with protein product		609978	"""Ca++-dependent activator protein for secretion 2"""				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.2457A>C	7.37:g.122078414T>G		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	157	78	0.496815	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Silent	SNP	ENST00000449022.2	37	CCDS55158.1	653	0.298992673992674	61	0.12398373983739837	134	0.3701657458563536	244	0.42657342657342656	214	0.28232189973614774	T	7.004	0.555450	0.13436	0.144628	0.311371	ENSG00000081803	ENST00000462699	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.50890	-0.8774	3	.	.	.	-19.2451	11.1223	0.48298	0.1378:0.0:0.0:0.8622	rs2074589;rs56567509;rs57701012;rs2074589	.	.	.	P	6	.	.	Q	-	2	0	CADPS2	121865650	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.420000	0.34804	2.172000	0.68678	0.533000	0.62120	CAG	T|0.713;G|0.287	0.287	strong		0.418	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21943820	21943820	+	Silent	SNP	G	G	A	rs2275360	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:21943820G>A	ENST00000374765.4	-	7	470	c.270C>T	c.(268-270)taC>taT	p.Y90Y	RAP1GAP_ENST00000542643.2_Silent_p.Y90Y|RAP1GAP_ENST00000374757.3_5'UTR|RAP1GAP_ENST00000374763.2_Silent_p.Y90Y|RAP1GAP_ENST00000374761.2_Silent_p.Y121Y|RAP1GAP_ENST00000290101.4_Silent_p.Y154Y	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	90					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		AGTGCTTCCGGTAGATGCGGG	0.647													G|||	1633	0.326078	0.1884	0.5072	5008	,	,		18458	0.5298		0.2495	False		,,,				2504	0.2526				p.Y154Y		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C462T						PASS	.	G	,,	832,3566		79,674,1446	109.0	88.0	95.0		270,462,270	3.7	1.0	1	dbSNP_100	95	2224,6360		280,1664,2348	no	coding-synonymous,coding-synonymous,coding-synonymous	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	359,2338,3794	AA,AG,GG		25.9087,18.9177,23.5403	,,	90/682,154/728,90/664	21943820	3056,9926	2199	4292	6491	SO:0001819	synonymous_variant	5909	exon7			CTTCCGGTAGATG	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.270C>T	1.37:g.21943820G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			G|0.715;A|0.285	0.285	strong		0.647	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
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 GAIIx	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	FAM65B_ENST00000538035.1_Missense_Mutation_p.S633R|FAM65B_ENST00000473070.1_5'Flank|AL512428.1_ENST00000583229.1_RNA	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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	38	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		
FOXM1	2305	hgsc.bcm.edu	37	12	2968169	2968169	+	Missense_Mutation	SNP	A	A	G	rs3742076	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:2968169A>G	ENST00000359843.3	-	9	1995	c.1927T>C	c.(1927-1929)Tcc>Ccc	p.S643P	AC005841.1_ENST00000382678.3_5'Flank|Y_RNA_ENST00000410561.1_RNA|FOXM1_ENST00000361953.3_Missense_Mutation_p.S628P|FOXM1_ENST00000342628.2_Missense_Mutation_p.S681P|ITFG2_ENST00000545509.1_Intron	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	643			S -> P (in dbSNP:rs3742076). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|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 double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			GCACCCTGGGAGGTTTGTACT	0.612													G|||	1541	0.307708	0.5817	0.2723	5008	,	,		16895	0.2341		0.164	False		,,,				2504	0.1861				p.S681P		Atlas-SNP	.											FOXM1,NS,carcinoma,0,2	FOXM1	62	2	0			c.T2041C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER	2044,2360		575,894,733	50.0	60.0	57.0		1927,2041,1882	3.4	0.0	12	dbSNP_107	57	1186,7414		106,974,3220	yes	missense,missense,missense	FOXM1	NM_021953.3,NM_202002.2,NM_202003.2	74,74,74	681,1868,3953	GG,GA,AA		13.7907,46.4124,24.8385	benign,benign,benign	643/764,681/802,628/749	2968169	3230,9774	2202	4300	6502	SO:0001583	missense	2305	exon10			CCTGGGAGGTTTG	Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"""Forkhead boxes"""	3818	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 2"""	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.1927T>C	12.37:g.2968169A>G	ENSP00000352901:p.Ser643Pro	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	25	6	0.24	NM_202002	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Missense_Mutation	SNP	ENST00000359843.3	37	CCDS8515.1	630	0.28846153846153844	274	0.556910569105691	97	0.26795580110497236	148	0.25874125874125875	111	0.14643799472295516	G	0.017	-1.501525	0.01001	0.464124	0.137907	ENSG00000111206	ENST00000342628;ENST00000361953;ENST00000359843	D;D;D	0.91068	-2.71;-2.78;-2.7	4.29	3.4	0.38934	.	0.061535	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00092	-2.175	0.44323	P	0.002797999999999967	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.42275	-0.9461	9	0.06236	T	0.91	.	9.7095	0.40236	0.1686:0.0:0.8314:0.0	rs3742076;rs17856176;rs17856193;rs59442255;rs3742076	627;643;628;643;681	A8K591;Q53Y49;Q08050-2;Q08050;Q08050-3	.;.;.;FOXM1_HUMAN;.	P	681;628;643	ENSP00000342307:S681P;ENSP00000354492:S628P;ENSP00000352901:S643P	ENSP00000342307:S681P	S	-	1	0	FOXM1	2838430	1.000000	0.71417	0.020000	0.16555	0.116000	0.19942	3.722000	0.54948	0.579000	0.29504	-0.215000	0.12644	TCC	A|0.714;G|0.286	0.286	strong		0.612	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953	
WLS	79971	hgsc.bcm.edu	37	1	68614320	68614320	+	Silent	SNP	G	G	A	rs17130529	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:68614320G>A	ENST00000262348.4	-	7	1249	c.996C>T	c.(994-996)atC>atT	p.I332I	WLS_ENST00000354777.2_Silent_p.I330I|WLS_ENST00000540432.1_Silent_p.I332I|GNG12-AS1_ENST00000413628.1_RNA|WLS_ENST00000370976.3_Silent_p.I241I|WLS_ENST00000491811.1_5'UTR|GNG12-AS1_ENST00000420587.1_RNA	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	332					anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						AATACCCTGCGATGTGGTTCC	0.507													A|||	301	0.0601038	0.0847	0.0461	5008	,	,		21430	0.0625		0.0477	False		,,,				2504	0.047				p.I332I		Atlas-SNP	.											.	WLS	97	.	0			c.C996T						PASS	.	A	,,	377,4029	791.7+/-415.1	18,341,1844	137.0	91.0	106.0		990,723,996	-3.5	0.9	1	dbSNP_123	106	380,8220	802.1+/-407.4	6,368,3926	yes	coding-synonymous,coding-synonymous,coding-synonymous	WLS	NM_001002292.3,NM_001193334.1,NM_024911.6	,,	24,709,5770	AA,AG,GG		4.4186,8.5565,5.8204	,,	330/544,241/451,332/542	68614320	757,12249	2203	4300	6503	SO:0001819	synonymous_variant	79971	exon7			CCCTGCGATGTGG	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"""wntless homolog"""	611514	"""chromosome 1 open reading frame 139"", ""G protein-coupled receptor 177"", ""wntless homolog (Drosophila)"""	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.996C>T	1.37:g.68614320G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Silent	SNP	ENST00000262348.4	37	CCDS642.1																																																																																			G|0.937;A|0.063	0.063	strong		0.507	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911	
SUCO	51430	hgsc.bcm.edu	37	1	172547465	172547465	+	Silent	SNP	A	A	G	rs2285664	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:172547465A>G	ENST00000263688.3	+	14	1587	c.1368A>G	c.(1366-1368)gaA>gaG	p.E456E	SUCO_ENST00000367723.4_Silent_p.E607E|SUCO_ENST00000610051.1_Silent_p.E419E|SUCO_ENST00000608151.1_Silent_p.E608E	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	456					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											TGGTGGAAGAATATGAAGAAA	0.358													A|||	1273	0.254193	0.2368	0.2089	5008	,	,		17330	0.2024		0.2296	False		,,,				2504	0.3885				p.E456E		Atlas-SNP	.											.	.	.	.	0			c.A1368G						PASS	.	A	,	1025,3381	378.3+/-322.8	111,803,1289	132.0	124.0	127.0		1368,1236	5.4	1.0	1	dbSNP_100	127	2069,6531	359.0+/-331.4	229,1611,2460	no	coding-synonymous,coding-synonymous	C1orf9	NM_014283.3,NM_016227.2	,	340,2414,3749	GG,GA,AA		24.0581,23.2637,23.789	,	456/1255,412/1211	172547465	3094,9912	2203	4300	6503	SO:0001819	synonymous_variant	51430	exon14			GGAAGAATATGAA	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1368A>G	1.37:g.172547465A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Silent	SNP	ENST00000263688.3	37	CCDS1303.1																																																																																			A|0.770;G|0.230	0.230	strong		0.358	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
RSU1	6251	hgsc.bcm.edu	37	10	16796919	16796919	+	Silent	SNP	C	C	A	rs1049632	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:16796919C>A	ENST00000377921.3	-	4	652	c.351G>T	c.(349-351)acG>acT	p.T117T	RSU1_ENST00000345264.5_Silent_p.T117T|RSU1_ENST00000602389.1_Silent_p.T64T|RSU1_ENST00000464074.2_5'UTR			Q15404	RSU1_HUMAN	Ras suppressor protein 1	117					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		AGTTGTTGTACGTCAAGTCCA	0.448													A|||	2090	0.417332	0.736	0.2911	5008	,	,		15063	0.4028		0.2624	False		,,,				2504	0.2505				p.T117T		Atlas-SNP	.											.	RSU1	31	.	0			c.G351T						PASS	.	A	,	2881,1525	481.9+/-359.3	945,991,267	84.0	93.0	90.0		351,192	2.8	1.0	10	dbSNP_86	90	2149,6451	714.3+/-406.0	268,1613,2419	no	coding-synonymous,coding-synonymous	RSU1	NM_012425.3,NM_152724.2	,	1213,2604,2686	AA,AC,CC		24.9884,34.6119,38.6745	,	117/278,64/225	16796919	5030,7976	2203	4300	6503	SO:0001819	synonymous_variant	6251	exon5			GTTGTACGTCAAG	AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.351G>T	10.37:g.16796919C>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_012425	A8KA46|D3DRU3|Q6FI17	Silent	SNP	ENST00000377921.3	37	CCDS7112.1																																																																																			C|0.598;A|0.402	0.402	strong		0.448	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724	
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 GAIIx	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	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	70	13	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	
CX3CR1	1524	hgsc.bcm.edu	37	3	39307162	39307162	+	Missense_Mutation	SNP	G	G	A	rs3732378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:39307162G>A	ENST00000541347.1	-	2	1078	c.839C>T	c.(838-840)aCg>aTg	p.T280M	CX3CR1_ENST00000542107.1_Missense_Mutation_p.T280M|CX3CR1_ENST00000399220.2_Missense_Mutation_p.T280M|CX3CR1_ENST00000358309.3_Missense_Mutation_p.T312M	NM_001171171.1	NP_001164642.1	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	280			T -> M (common polymorphism in Caucasian population; associated with higher risk of developing ARMD12; chemotaxis of monocytes of individuals with homozygous Met-280 and Ile-249 genotypes is impaired in the presence of bound CX3CR1 protein; dbSNP:rs3732378). {ECO:0000269|PubMed:10731151, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15208270, ECO:0000269|Ref.6}.		cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cerebral cortex cell migration (GO:0021795)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|macrophage chemotaxis (GO:0048246)|microglial cell activation involved in immune response (GO:0002282)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|response to wounding (GO:0009611)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|neuronal cell body membrane (GO:0032809)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-X3-C chemokine receptor activity (GO:0016495)|chemokine receptor activity (GO:0004950)			endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		AAATGCAACCGTCTCAGTCAC	0.468													G|||	428	0.0854633	0.0083	0.1556	5008	,	,		22185	0.0288		0.172	False		,,,				2504	0.1094				p.T312M		Atlas-SNP	.											CX3CR1_ENST00000358309,NS,adenocarcinoma,+1,4	CX3CR1	91	4	0			c.C935T	GRCh37	CM000505	CX3CR1	M	rs3732378	PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	126,3788		2,122,1833	138.0	136.0	137.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	839,839,935,839	4.0	0.7	3	dbSNP_107	137	1432,6886		124,1184,2851	yes	missense,missense,missense,missense	CX3CR1	NM_001171171.1,NM_001171172.1,NM_001171174.1,NM_001337.3	81,81,81,81	126,1306,4684	AA,AG,GG		17.2157,3.2192,12.7371	probably-damaging,probably-damaging,probably-damaging,probably-damaging	280/356,280/356,312/388,280/356	39307162	1558,10674	1957	4159	6116	SO:0001583	missense	1524	exon2			GCAACCGTCTCAG	BC028078	CCDS43069.1, CCDS54571.1	3p21.3	2012-08-08	2002-08-22		ENSG00000168329	ENSG00000168329		"""GPCR / Class A : Chemokine receptors : C-X-3-C motif"""	2558	protein-coding gene	gene with protein product		601470	"""chemokine (C-X3-C) receptor 1"""	GPR13, CMKBRL1		9726990, 7646814	Standard	NM_001171171		Approved	CMKDR1, V28, CCRL1	uc021wwc.1	P49238	OTTHUMG00000156249	ENST00000541347.1:c.839C>T	3.37:g.39307162G>A	ENSP00000439140:p.Thr280Met	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	124	44	0.354839	NM_001171174	A0N0N6|B2R5Z4|J3KP17	Missense_Mutation	SNP	ENST00000541347.1	37	CCDS43069.1	211	0.09661172161172162	6	0.012195121951219513	57	0.1574585635359116	19	0.033216783216783216	129	0.17018469656992086	G	11.03	1.519699	0.27211	0.032192	0.172157	ENSG00000168329	ENST00000399220;ENST00000538756;ENST00000358309;ENST00000541347;ENST00000542107	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.77	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.227311	0.45361	N	0.000375	T	0.00300	0.0009	M	0.80028	2.48	0.42331	P	0.007707000000000019	P	0.42248	0.774	B	0.28139	0.086	T	0.29027	-1.0025	9	0.59425	D	0.04	.	6.1781	0.20455	0.155:0.0:0.6947:0.1503	rs3732378;rs17792900;rs52789411;rs60081475;rs3732378	280	P49238	CX3C1_HUMAN	M	280;288;312;280;280	ENSP00000382166:T280M;ENSP00000351059:T312M;ENSP00000439140:T280M;ENSP00000444928:T280M	ENSP00000351059:T312M	T	-	2	0	CX3CR1	39282166	0.922000	0.31269	0.681000	0.30009	0.221000	0.24807	1.916000	0.39986	0.790000	0.33803	0.655000	0.94253	ACG	A|0.101;C|0.011	0.101	strong		0.468	CX3CR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343613.1	NM_001337	
STPG2	285555	hgsc.bcm.edu	37	4	99027137	99027137	+	Silent	SNP	T	T	C	rs2865979	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:99027137T>C	ENST00000295268.3	-	5	668	c.579A>G	c.(577-579)ctA>ctG	p.L193L		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	193																	TTATTTCATATAGTCGTGGGA	0.274													T|||	1880	0.375399	0.4425	0.2882	5008	,	,		15184	0.2758		0.4026	False		,,,				2504	0.4213				p.L193L		Atlas-SNP	.											.	.	.	.	0			c.A579G						PASS	.	T		1962,2436	542.8+/-376.1	451,1060,688	85.0	88.0	87.0		579	1.1	0.9	4	dbSNP_101	87	3402,5194	491.9+/-373.2	692,2018,1588	no	coding-synonymous	C4orf37	NM_174952.2		1143,3078,2276	CC,CT,TT		39.5765,44.6112,41.2806		193/460	99027137	5364,7630	2199	4298	6497	SO:0001819	synonymous_variant	285555	exon5			TTCATATAGTCGT	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.579A>G	4.37:g.99027137T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	114	47	0.412281	NM_174952		Silent	SNP	ENST00000295268.3	37	CCDS3645.1																																																																																			T|0.607;C|0.393	0.393	strong		0.274	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
TCOF1	6949	hgsc.bcm.edu	37	5	149772280	149772280	+	Missense_Mutation	SNP	C	C	G	rs1136103	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149772280C>G	ENST00000504761.2	+	22	3527	c.3527C>G	c.(3526-3528)cCc>cGc	p.P1176R	TCOF1_ENST00000377797.3_Missense_Mutation_p.P1177R|TCOF1_ENST00000513346.1_Missense_Mutation_p.P1176R|TCOF1_ENST00000451292.1_Missense_Mutation_p.P1213R|TCOF1_ENST00000445265.2_Missense_Mutation_p.P1100R|TCOF1_ENST00000439160.2_Missense_Mutation_p.P1139R|TCOF1_ENST00000323668.7_Missense_Mutation_p.P1099R			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	1176			P -> R (in dbSNP:rs1136103).		skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGTCCCACCCCCTCCAGGACA	0.642													C|||	408	0.0814696	0.0076	0.1282	5008	,	,		17532	0.001		0.2396	False		,,,				2504	0.0685				p.P1176R		Atlas-SNP	.											.	TCOF1	154	.	0			c.C3527G						PASS	.	C	ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO	201,4205	124.9+/-162.1	5,191,2007	51.0	47.0	48.0		3296,3527,3416,3299,3413	2.6	0.0	5	dbSNP_86	48	2018,6582	347.8+/-326.7	215,1588,2497	yes	missense,missense,missense,missense,missense	TCOF1	NM_000356.3,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	103,103,103,103,103	220,1779,4504	GG,GC,CC		23.4651,4.562,17.0614	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	1099/1412,1176/1489,1139/1452,1100/1413,1138/1451	149772280	2219,10787	2203	4300	6503	SO:0001583	missense	6949	exon22			CCACCCCCTCCAG		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.3527C>G	5.37:g.149772280C>G	ENSP00000421655:p.Pro1176Arg	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	236	0.10805860805860806	7	0.014227642276422764	42	0.11602209944751381	0	0.0	187	0.24670184696569922	C	17.94	3.512605	0.64522	0.04562	0.234651	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42;0.42;0.42;0.42	5.28	2.57	0.30868	.	0.629309	0.13283	N	0.399585	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	D;P;D;D;P	0.69078	0.971;0.95;0.971;0.997;0.95	P;P;P;P;P	0.60886	0.839;0.776;0.839;0.88;0.776	T	0.07986	-1.0744	9	0.56958	D	0.05	-0.2445	7.322	0.26533	0.0:0.7321:0.0:0.2679	rs1136103;rs3199234;rs17420522;rs52811168	1139;1099;1138;1176;1100	Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8	.;.;.;TCOF_HUMAN;.	R	1213;1177;1100;1099;1139;1138;1176;1176	ENSP00000400939:P1213R;ENSP00000367028:P1177R;ENSP00000409944:P1100R;ENSP00000325223:P1099R;ENSP00000406888:P1139R;ENSP00000390717:P1138R;ENSP00000421655:P1176R;ENSP00000427484:P1176R	ENSP00000325223:P1099R	P	+	2	0	TCOF1	149752473	0.001000	0.12720	0.000000	0.03702	0.647000	0.38526	0.723000	0.25939	0.246000	0.21394	0.561000	0.74099	CCC	C|0.855;G|0.145	0.145	strong		0.642	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
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 GAIIx	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_ENST00000361908.3_Silent_p.P29P|OPA1_ENST00000361715.2_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		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	158	8	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	
FBXO25	26260	hgsc.bcm.edu	37	8	363192	363192	+	Missense_Mutation	SNP	G	G	A	rs10090550	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:363192G>A	ENST00000276326.5	+	2	232	c.113G>A	c.(112-114)cGt>cAt	p.R38H	FBXO25_ENST00000350302.3_Missense_Mutation_p.R38H|FBXO25_ENST00000382824.1_De_novo_Start_OutOfFrame|FBXO25_ENST00000352684.2_De_novo_Start_OutOfFrame	NM_183421.1	NP_904357.1	Q8TCJ0	FBX25_HUMAN	F-box protein 25	38	Interaction with beta-actin.		R -> H (in dbSNP:rs10090550). {ECO:0000269|PubMed:15489334}.		protein ubiquitination (GO:0016567)	nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	10		Ovarian(12;0.00965)|Colorectal(14;0.0815)|Myeloproliferative disorder(644;0.116)|all_neural(12;0.122)		Epithelial(5;3.14e-14)|OV - Ovarian serous cystadenocarcinoma(5;1.56e-07)|BRCA - Breast invasive adenocarcinoma(11;1.88e-06)		GAGAATAACCGTTGTAACATC	0.433													A|||	2844	0.567891	0.9531	0.415	5008	,	,		13937	0.4127		0.3917	False		,,,				2504	0.4969				p.R38H		Atlas-SNP	.											.	FBXO25	25	.	0			c.G113A						PASS	.	A	,HIS/ARG,HIS/ARG	3776,630		1634,508,61	100.0	143.0	128.0		,113,113	1.0	0.0	8	dbSNP_119	128	3173,5427		618,1937,1745	no	utr-5,missense,missense	FBXO25	NM_012173.3,NM_183420.1,NM_183421.1	,29,29	2252,2445,1806	AA,AG,GG		36.8953,14.2987,46.5708	,benign,benign	,38/359,38/368	363192	6949,6057	2203	4300	6503	SO:0001583	missense	26260	exon2			ATAACCGTTGTAA	AF174605	CCDS5952.1, CCDS5953.1, CCDS5954.1	8p23.3	2007-03-30	2004-06-15		ENSG00000147364	ENSG00000147364		"""F-boxes /  ""other"""""	13596	protein-coding gene	gene with protein product		609098	"""F-box only protein 25"""			10531035, 10531037	Standard	NM_012173		Approved	FBX25	uc003wox.3	Q8TCJ0	OTTHUMG00000090341	ENST00000276326.5:c.113G>A	8.37:g.363192G>A	ENSP00000276326:p.Arg38His	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	136	56	0.411765	NM_183420	Q6PJ83|Q7Z4V4|Q9UKB8	Missense_Mutation	SNP	ENST00000276326.5	37	CCDS5953.1	1081	0.49496336996337	447	0.9085365853658537	146	0.40331491712707185	233	0.40734265734265734	255	0.33641160949868076	.	13.69	2.313914	0.40996	0.857013	0.368953	ENSG00000147364	ENST00000518240;ENST00000350302;ENST00000276326;ENST00000447233	T;T;T	0.17054	2.3;2.3;2.3	3.6	1.04	0.20106	.	0.614649	0.16439	N	0.214398	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.11717	-1.0576	9	0.15499	T	0.54	-20.4951	3.2558	0.06831	0.5396:0.2137:0.2467:0.0	rs10090550;rs17857381;rs58860314	38;38	Q8TCJ0-2;Q8TCJ0	.;FBX25_HUMAN	H	38	ENSP00000428872:R38H;ENSP00000342077:R38H;ENSP00000276326:R38H	ENSP00000276326:R38H	R	+	2	0	FBXO25	353192	0.006000	0.16342	0.002000	0.10522	0.929000	0.56500	0.496000	0.22499	-0.009000	0.14296	-0.945000	0.02674	CGT	G|0.481;A|0.519	0.519	strong		0.433	FBXO25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206710.2	NM_012173	
MAPT	4137	hgsc.bcm.edu	37	17	44061023	44061023	+	Missense_Mutation	SNP	G	G	A	rs62063786	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44061023G>A	ENST00000571987.1	+	5	853	c.853G>A	c.(853-855)Gac>Aac	p.D285N	MAPT_ENST00000334239.8_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.D285N|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.D285N|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.D285N|MAPT_ENST00000574436.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	285			D -> N (risk factor for PSNP1; dbSNP:rs62063786). {ECO:0000269|PubMed:10534245, ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	CTCAGAGCCCGACGGGCCCAG	0.622													G|||	439	0.0876597	0.0204	0.1571	5008	,	,		15639	0.001		0.2406	False		,,,				2504	0.0613				p.D285N		Atlas-SNP	.											.	MAPT	135	.	0			c.G853A						PASS	.	G	ASN/ASP,,,,,,ASN/ASP,	228,4178	130.6+/-167.2	8,212,1983	39.0	44.0	42.0		853,,,,,,853,	-3.2	0.0	17	dbSNP_129	42	1928,6672	327.6+/-317.9	221,1486,2593	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	23,,,,,,23,	229,1698,4576	AA,AG,GG		22.4186,5.1748,16.577	benign,,,,,,benign,	285/777,,,,,,285/759,	44061023	2156,10850	2203	4300	6503	SO:0001583	missense	4137	exon6			GAGCCCGACGGGC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.853G>A	17.37:g.44061023G>A	ENSP00000458742:p.Asp285Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	97	95	0.979381	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	13.42	2.230841	0.39399	0.051748	0.224186	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.12147	2.72;2.71;2.72	4.94	-3.22	0.05125	.	2.226750	0.01871	N	0.037217	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B;B	0.26363	0.117;0.147	B;B	0.21546	0.035;0.023	T	0.37731	-0.9693	9	0.28530	T	0.3	4.184	6.1584	0.20350	0.5145:0.1459:0.3396:0.0	rs62063786	285;285	P10636-9;P10636	.;TAU_HUMAN	N	285	ENSP00000340820:D285N;ENSP00000262410:D285N;ENSP00000410838:D285N	ENSP00000262410:D285N	D	+	1	0	MAPT	41416860	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.030000	0.13688	-0.440000	0.07211	0.561000	0.74099	GAC	A|0.118;C|0.246	0.118	strong		0.622	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
THAP9	79725	hgsc.bcm.edu	37	4	83838262	83838262	+	Missense_Mutation	SNP	G	G	T	rs897945	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:83838262G>T	ENST00000302236.5	+	5	948	c.897G>T	c.(895-897)ttG>ttT	p.L299F	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	299			L -> F (in dbSNP:rs897945). {ECO:0000269|PubMed:14702039}.		DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				GTCACAGTTTGCAGGGGTTTA	0.413													G|||	1629	0.32528	0.0651	0.6484	5008	,	,		20952	0.2004		0.5507	False		,,,				2504	0.3446				p.L299F		Atlas-SNP	.											THAP9,colon,carcinoma,+2,1	THAP9	65	1	0			c.G897T						PASS	.	G	PHE/LEU	666,3740	282.2+/-276.4	68,530,1605	136.0	127.0	130.0		897	2.8	1.0	4	dbSNP_86	130	4799,3801	613.2+/-396.1	1359,2081,860	yes	missense	THAP9	NM_024672.4	22	1427,2611,2465	TT,TG,GG		44.1977,15.1158,42.0191	probably-damaging	299/904	83838262	5465,7541	2203	4300	6503	SO:0001583	missense	79725	exon5			CAGTTTGCAGGGG	AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"""THAP (C2CH-type zinc finger) domain containing"""	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.897G>T	4.37:g.83838262G>T	ENSP00000305533:p.Leu299Phe	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_024672	B3KRE2|Q59AC9	Missense_Mutation	SNP	ENST00000302236.5	37	CCDS3598.1	801	0.36675824175824173	32	0.06504065040650407	220	0.6077348066298343	124	0.21678321678321677	425	0.5606860158311345	G	7.015	0.557611	0.13436	0.151158	0.558023	ENSG00000168152	ENST00000302236;ENST00000536314	T	0.46063	0.88	3.7	2.85	0.33270	.	1.365610	0.05330	N	0.528170	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.999999999612521	P	0.48162	0.906	B	0.38378	0.272	T	0.41251	-0.9519	9	0.20519	T	0.43	-2.6801	9.1917	0.37204	0.104:0.0:0.896:0.0	rs897945;rs17354399;rs52815233;rs59971666;rs897945	299	Q9H5L6	THAP9_HUMAN	F	299	ENSP00000305533:L299F	ENSP00000305533:L299F	L	+	3	2	THAP9	84057286	0.829000	0.29322	0.999000	0.59377	0.224000	0.24922	0.295000	0.19065	1.141000	0.42275	0.650000	0.86243	TTG	G|0.624;T|0.375	0.375	strong		0.413	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672	
DUSP27	92235	hgsc.bcm.edu	37	1	167095163	167095163	+	Missense_Mutation	SNP	G	G	C	rs267745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:167095163G>C	ENST00000361200.2	+	6	961	c.795G>C	c.(793-795)gaG>gaC	p.E265D	DUSP27_ENST00000443333.1_Missense_Mutation_p.E265D|DUSP27_ENST00000485151.1_3'UTR|DUSP27_ENST00000271385.5_Missense_Mutation_p.E265D			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	265			E -> D (in dbSNP:rs267745). {ECO:0000269|PubMed:15489334}.		protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						ACCCCAATGAGGGCTTCCTGA	0.587													C|||	3215	0.641973	0.888	0.4597	5008	,	,		19822	0.872		0.4751	False		,,,				2504	0.3732				p.E265D		Atlas-SNP	.											.	DUSP27	235	.	0			c.G795C						PASS	.	C	ASP/GLU	3677,729	302.1+/-287.2	1536,605,62	77.0	76.0	76.0		795	-4.6	0.8	1	dbSNP_79	76	4153,4447	588.8+/-392.4	1003,2147,1150	yes	missense	DUSP27	NM_001080426.1	45	2539,2752,1212	CC,CG,GG		48.2907,16.5456,39.797	benign	265/1159	167095163	7830,5176	2203	4300	6503	SO:0001583	missense	92235	exon5			CAATGAGGGCTTC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.795G>C	1.37:g.167095163G>C	ENSP00000354483:p.Glu265Asp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	40	0.634921	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	1439	0.6588827838827839	417	0.8475609756097561	181	0.5	508	0.8881118881118881	333	0.4393139841688654	C	2.612	-0.290557	0.05568	0.834544	0.482907	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	D;D;D	0.85484	-1.99;-1.99;-1.99	5.55	-4.59	0.03400	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.312145	0.34802	N	0.003677	T	0.30386	0.0763	N	0.04787	-0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.34428	-0.9829	9	0.02654	T	1	-28.9626	2.8034	0.05421	0.1828:0.2921:0.0838:0.4413	rs267745;rs12734908;rs52812145;rs61430367;rs267745	265	Q5VZP5	DUS27_HUMAN	D	265	ENSP00000354483:E265D;ENSP00000271385:E265D;ENSP00000404874:E265D	ENSP00000271385:E265D	E	+	3	2	DUSP27	165361787	0.000000	0.05858	0.815000	0.32552	0.967000	0.64934	-2.213000	0.01224	-0.793000	0.04475	-0.756000	0.03474	GAG	G|0.373;C|0.627	0.627	strong		0.587	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
RYR2	6262	hgsc.bcm.edu	37	1	237841390	237841390	+	Missense_Mutation	SNP	A	A	G	rs34967813	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:237841390A>G	ENST00000366574.2	+	61	9190	c.8873A>G	c.(8872-8874)cAa>cGa	p.Q2958R	RYR2_ENST00000609119.1_Intron|RYR2_ENST00000542537.1_Missense_Mutation_p.Q2942R|RYR2_ENST00000360064.6_Missense_Mutation_p.Q2956R	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2958			Q -> R (in dbSNP:rs34967813). {ECO:0000269|PubMed:11157710}.		BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			CCTTATGAACAAGAAATCAAG	0.358													A|||	497	0.0992412	0.0113	0.1988	5008	,	,		19250	0.0		0.2942	False		,,,				2504	0.0491				p.Q2958R		Atlas-SNP	.											.	RYR2	1273	.	0			c.A8873G						PASS	.	A	ARG/GLN	199,3583		7,185,1699	109.0	106.0	107.0		8873	5.7	1.0	1	dbSNP_126	107	2499,5717		379,1741,1988	yes	missense	RYR2	NM_001035.2	43	386,1926,3687	GG,GA,AA		30.4163,5.2618,22.4871	possibly-damaging	2958/4968	237841390	2698,9300	1891	4108	5999	SO:0001583	missense	6262	exon61			ATGAACAAGAAAT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.8873A>G	1.37:g.237841390A>G	ENSP00000355533:p.Gln2958Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	100	40	0.4	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	313	0.1433150183150183	10	0.02032520325203252	77	0.212707182320442	0	0.0	226	0.29815303430079154	A	17.35	3.367905	0.61513	0.052618	0.304163	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	T;D;D	0.96745	-0.29;-4.08;-4.11	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000013	T	0.00039	0.0001	L	0.38649	1.16	0.09310	P	1.0	B	0.30605	0.287	B	0.20955	0.032	T	0.04708	-1.0932	9	0.21014	T	0.42	.	10.2872	0.43575	0.9266:0.0:0.0734:0.0	rs34967813	2958	Q92736	RYR2_HUMAN	R	2958;2956;2942	ENSP00000355533:Q2958R;ENSP00000353174:Q2956R;ENSP00000443798:Q2942R	ENSP00000353174:Q2956R	Q	+	2	0	RYR2	235908013	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.168000	0.77570	2.164000	0.68074	0.482000	0.46254	CAA	A|0.827;G|0.173	0.173	strong		0.358	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
GPR112	139378	hgsc.bcm.edu	37	X	135430803	135430803	+	Silent	SNP	C	C	G	rs111880833	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135430803C>G	ENST00000394143.1	+	6	5229	c.4938C>G	c.(4936-4938)ctC>ctG	p.L1646L	GPR112_ENST00000394141.1_Silent_p.L1441L|GPR112_ENST00000370652.1_Silent_p.L1646L|GPR112_ENST00000287534.4_Silent_p.L1583L|GPR112_ENST00000412101.1_Silent_p.L1441L	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1646					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(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CGACCTTTCTCTCTCCAACAG	0.463													c|||	41	0.0108609	0.0008	0.0086	3775	,	,		14588	0.001		0.0169	False		,,,				2504	0.0164				p.L1646L		Atlas-SNP	.											.	GPR112	459	.	0			c.C4938G						PASS	.			21,3814		0,18,3,1614,568	144.0	139.0	141.0		4938	0.3	0.0	X	dbSNP_132	141	229,6499		5,160,59,2263,1813	no	coding-synonymous	GPR112	NM_153834.3		5,178,62,3877,2381	GG,GC,G,CC,C		3.4037,0.5476,2.3668		1646/3081	135430803	250,10313	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			CTTTCTCTCTCCA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4938C>G	X.37:g.135430803C>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	106	28	0.264151	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			C|0.978;G|0.022	0.022	strong		0.463	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
OR13F1	138805	hgsc.bcm.edu	37	9	107267244	107267244	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107267244G>A	ENST00000334726.2	+	1	790	c.701G>A	c.(700-702)cGa>cAa	p.R234Q		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	234						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						GTGGAAGGTCGAAGTAAAGCC	0.483																																					p.R234Q		Atlas-SNP	.											OR13F1,rectum,carcinoma,+1,2	OR13F1	75	2	0			c.G701A						scavenged	.						200.0	181.0	188.0					9																	107267244		2203	4300	6503	SO:0001583	missense	138805	exon1			AAGGTCGAAGTAA		CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"""GPCR / Class A : Olfactory receptors"""	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.701G>A	9.37:g.107267244G>A	ENSP00000334452:p.Arg234Gln	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	114	2	0.0175439	NM_001004485	Q6IF50	Missense_Mutation	SNP	ENST00000334726.2	37	CCDS35087.1	.	.	.	.	.	.	.	.	.	.	G	8.227	0.803894	0.16467	.	.	ENSG00000186881	ENST00000334726	T	0.00311	8.15	4.3	-0.948	0.10379	GPCR, rhodopsin-like superfamily (1);	0.340853	0.20123	N	0.098743	T	0.00210	0.0006	M	0.64630	1.985	0.19300	N	0.999979	P	0.36660	0.564	B	0.32393	0.145	T	0.41662	-0.9496	10	0.46703	T	0.11	.	8.9094	0.35543	0.4514:0.0:0.5486:0.0	.	234	Q8NGS4	O13F1_HUMAN	Q	234	ENSP00000334452:R234Q	ENSP00000334452:R234Q	R	+	2	0	OR13F1	106307065	0.001000	0.12720	0.062000	0.19696	0.212000	0.24457	0.202000	0.17295	-0.166000	0.10890	-0.122000	0.15005	CGA	.	.	none		0.483	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1		
SERHL2	253190	hgsc.bcm.edu	37	22	42970032	42970032	+	Missense_Mutation	SNP	T	T	C	rs137055	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:42970032T>C	ENST00000327678.5	+	12	1018	c.916T>C	c.(916-918)Tgc>Cgc	p.C306R	RRP7B_ENST00000357802.2_RNA|SERHL2_ENST00000407614.4_Missense_Mutation_p.C126R|SERHL2_ENST00000335879.5_Missense_Mutation_p.C242R|SERHL2_ENST00000340239.4_3'UTR	NM_014509.3	NP_055324.2	Q9NQF3	SERHL_HUMAN	serine hydrolase-like 2	0							hydrolase activity (GO:0016787)	p.C306R(1)		breast(1)|endometrium(2)|lung(3)|skin(1)|stomach(1)	8						CTTCTTACAGTGCACACACAT	0.562													.|||	1865	0.372404	0.5265	0.1801	5008	,	,		21842	0.7093		0.1004	False		,,,				2504	0.2331				p.C306R		Atlas-SNP	.											SERHL2,NS,carcinoma,0,1	SERHL2	23	1	1	Substitution - Missense(1)	stomach(1)	c.T916C						scavenged	.	T	ARG/CYS	2011,2395	612.7+/-392.0	424,1163,616	139.0	119.0	126.0		916	-0.9	0.0	22	dbSNP_78	126	816,7782	781.9+/-407.6	45,726,3528	no	missense	SERHL2	NM_014509.3	180	469,1889,4144	CC,CT,TT		9.4906,45.6423,21.7395	benign	306/315	42970032	2827,10177	2203	4299	6502	SO:0001583	missense	253190	exon12			TTACAGTGCACAC		CCDS14037.1, CCDS63498.1	22q13	2005-08-09			ENSG00000183569	ENSG00000183569			29446	protein-coding gene	gene with protein product							Standard	NM_014509		Approved		uc003bcr.3	Q9H4I8	OTTHUMG00000150892	ENST00000327678.5:c.916T>C	22.37:g.42970032T>C	ENSP00000331376:p.Cys306Arg	Somatic	345	2	0.0057971		WXS	Illumina HiSeq	Phase_I	374	157	0.419786	NM_014509	Q5JZ95|Q9UH21	Missense_Mutation	SNP	ENST00000327678.5	37	CCDS14037.1	795	0.364010989010989	270	0.5487804878048781	66	0.18232044198895028	384	0.6713286713286714	75	0.09894459102902374	C	5.546	0.285594	0.10513	0.456423	0.094906	ENSG00000183569	ENST00000327678;ENST00000356720;ENST00000407614;ENST00000335879	T;T;T	0.41400	2.86;1.0;1.04	4.05	-0.864	0.10666	.	1.070450	0.07397	N	0.890154	T	0.00012	0.0000	N	0.00661	-1.28	0.52099	P	5.999999999994898E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41928	-0.9481	9	0.17369	T	0.5	.	1.1602	0.01804	0.3199:0.3417:0.1963:0.1421	rs137055;rs3201029;rs3747190;rs60116198;rs137055	242;306	Q9H4I8-2;Q9H4I8	.;SEHL2_HUMAN	R	306;126;126;242	ENSP00000331376:C306R;ENSP00000385691:C126R;ENSP00000336578:C242R	ENSP00000331376:C306R	C	+	1	0	SERHL2	41299976	0.000000	0.05858	0.006000	0.13384	0.009000	0.06853	-1.099000	0.03343	-0.094000	0.12374	-2.546000	0.00178	TGC	.	.	weak		0.562	SERHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320454.1	NM_014509	
SLC5A9	200010	hgsc.bcm.edu	37	1	48708228	48708228	+	Nonsense_Mutation	SNP	G	G	T	rs850763	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:48708228G>T	ENST00000438567.2	+	13	1829	c.1777G>T	c.(1777-1779)Gag>Tag	p.E593*	SLC5A9_ENST00000533824.1_Nonsense_Mutation_p.E614*|SLC5A9_ENST00000471020.1_3'UTR|SLC5A9_ENST00000236495.5_Nonsense_Mutation_p.E618*	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	593					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						GCCAGCCGGGGAGTGCCCTGC	0.652													G|||	570	0.113818	0.1142	0.1037	5008	,	,		15774	0.0109		0.1581	False		,,,				2504	0.181				p.E618X		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G1852T						PASS	.	G	stop/GLU,stop/GLU	589,3817	250.6+/-257.6	41,507,1655	37.0	41.0	39.0		1777,1852	2.6	0.0	1	dbSNP_86	39	1337,7263	257.5+/-281.5	99,1139,3062	yes	stop-gained,stop-gained	SLC5A9	NM_001011547.2,NM_001135181.1	,	140,1646,4717	TT,TG,GG		15.5465,13.3681,14.8085	,	593/682,618/707	48708228	1926,11080	2203	4300	6503	SO:0001587	stop_gained	200010	exon14			GCCGGGGAGTGCC	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.1777G>T	1.37:g.48708228G>T	ENSP00000401730:p.Glu593*	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	101	35	0.346535	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Nonsense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	230	0.10531135531135531	66	0.13414634146341464	41	0.1132596685082873	3	0.005244755244755245	120	0.158311345646438	G	18.33	3.601378	0.66445	0.133681	0.155465	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	.	.	.	4.65	2.61	0.31194	.	1.755070	0.02799	N	0.123016	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	9.5686	0.39414	0.0:0.154:0.6906:0.1554	rs850763;rs17371426;rs850763	.	.	.	X	614;593;618	.	ENSP00000236495:E618X	E	+	1	0	SLC5A9	48480815	0.004000	0.15560	0.000000	0.03702	0.002000	0.02628	1.339000	0.33885	0.491000	0.27793	-0.795000	0.03280	GAG	G|0.867;T|0.133	0.133	strong		0.652	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
PITPNA	5306	hgsc.bcm.edu	37	17	1456318	1456318	+	Silent	SNP	G	G	A	rs2230463	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1456318G>A	ENST00000313486.7	-	3	432	c.177C>T	c.(175-177)caC>caT	p.H59H	PITPNA_ENST00000539476.1_Silent_p.H59H	NM_006224.3	NP_006215.1	Q00169	PIPNA_HUMAN	phosphatidylinositol transfer protein, alpha	59					axon guidance (GO:0007411)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)|phosphatidylcholine transporter activity (GO:0008525)|phosphatidylinositol transporter activity (GO:0008526)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				UCEC - Uterine corpus endometrioid carcinoma (25;0.0845)		GGTAGATCTTGTGTGTGTACT	0.512													G|||	194	0.038738	0.0189	0.0418	5008	,	,		16861	0.0069		0.0954	False		,,,				2504	0.0378				p.H59H		Atlas-SNP	.											.	PITPNA	14	.	0			c.C177T						PASS	.	G		120,4058		2,116,1971	176.0	178.0	178.0		177	6.2	1.0	17	dbSNP_98	178	892,7546		47,798,3374	yes	coding-synonymous	PITPNA	NM_006224.3		49,914,5345	AA,AG,GG		10.5712,2.8722,8.0216		59/271	1456318	1012,11604	2089	4219	6308	SO:0001819	synonymous_variant	5306	exon3			GATCTTGTGTGTG	M73704	CCDS45563.1	17p13.3	2012-06-29	2003-05-09	2004-09-03	ENSG00000174238	ENSG00000174238			9001	protein-coding gene	gene with protein product		600174	"""phosphotidylinositol transfer protein"""	PITPN		8255295	Standard	NM_006224		Approved	VIB1A	uc021tnf.1	Q00169	OTTHUMG00000177779	ENST00000313486.7:c.177C>T	17.37:g.1456318G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_006224		Silent	SNP	ENST00000313486.7	37	CCDS45563.1																																																																																			G|0.940;C|0.000;A|0.060	0.060	strong		0.512	PITPNA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438927.3		
KIAA1211	57482	hgsc.bcm.edu	37	4	57181995	57181995	+	Missense_Mutation	SNP	C	C	T	rs3796547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57181995C>T	ENST00000504228.1	+	6	2432	c.2327C>T	c.(2326-2328)tCg>tTg	p.S776L	KIAA1211_ENST00000541073.1_Missense_Mutation_p.S769L|KIAA1211_ENST00000264229.6_Missense_Mutation_p.S776L			Q6ZU35	K1211_HUMAN	KIAA1211	776			S -> L (in dbSNP:rs3796547). {ECO:0000269|PubMed:14702039}.					p.S776L(1)		endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CCGGAGAAGTCGGAGATGCAC	0.597													C|||	1212	0.242013	0.1997	0.2334	5008	,	,		14559	0.254		0.34	False		,,,				2504	0.1922				p.S776L		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	1	Substitution - Missense(1)	stomach(1)	c.C2327T						PASS	.	C	LEU/SER	878,3072		96,686,1193	62.0	76.0	72.0		2327	-5.8	0.0	4	dbSNP_107	72	2849,5455		497,1855,1800	yes	missense	KIAA1211	NM_020722.1	145	593,2541,2993	TT,TC,CC		34.3088,22.2278,30.4146	benign	776/1234	57181995	3727,8527	1975	4152	6127	SO:0001583	missense	57482	exon8			AGAAGTCGGAGAT	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.2327C>T	4.37:g.57181995C>T	ENSP00000423366:p.Ser776Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	575	0.2632783882783883	84	0.17073170731707318	92	0.2541436464088398	144	0.2517482517482518	255	0.33641160949868076	C	10.70	1.425095	0.25639	0.222278	0.343088	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.10668	2.85;2.85;2.85	4.79	-5.82	0.02333	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.20887	0.049;0.049	B;B	0.12156	0.007;0.007	T	0.48670	-0.9015	8	0.10111	T	0.7	0.6006	10.3039	0.43670	0.0975:0.5901:0.0:0.3124	rs3796547;rs17490484;rs58264499;rs3796547	769;776	F5H1N7;Q6ZU35	.;K1211_HUMAN	L	776;776;769;686	ENSP00000264229:S776L;ENSP00000423366:S776L;ENSP00000444006:S769L	ENSP00000264229:S776L	S	+	2	0	KIAA1211	56876752	0.000000	0.05858	0.000000	0.03702	0.197000	0.23852	-0.293000	0.08320	-1.173000	0.02758	-0.367000	0.07326	TCG	C|0.728;T|0.272	0.272	strong		0.597	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
PMFBP1	83449	hgsc.bcm.edu	37	16	72184629	72184629	+	Missense_Mutation	SNP	C	C	T	rs217180	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:72184629C>T	ENST00000237353.10	-	5	775	c.514G>A	c.(514-516)Gcc>Acc	p.A172T	PMFBP1_ENST00000537465.1_Missense_Mutation_p.A172T|PMFBP1_ENST00000355636.6_Missense_Mutation_p.A27T	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	172			A -> T (in dbSNP:rs217180).			cytoplasm (GO:0005737)				NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	45		Ovarian(137;0.179)				TCTAGAGAGGCGATCTTGTCC	0.507													C|||	430	0.0858626	0.003	0.1326	5008	,	,		19868	0.1736		0.0875	False		,,,				2504	0.0726				p.A172T		Atlas-SNP	.											.	PMFBP1	101	.	0			c.G514A						PASS	.	C	THR/ALA,THR/ALA	92,4304	75.7+/-113.9	1,90,2107	119.0	111.0	114.0		79,514	-4.6	0.0	16	dbSNP_79	114	731,7869	177.6+/-227.2	31,669,3600	yes	missense,missense	PMFBP1	NM_001160213.1,NM_031293.2	58,58	32,759,5707	TT,TC,CC		8.5,2.0928,6.3327	benign,benign	27/883,172/1008	72184629	823,12173	2198	4300	6498	SO:0001583	missense	83449	exon5			GAGAGGCGATCTT	AF239683	CCDS32483.1	16q23.1	2008-08-04			ENSG00000118557	ENSG00000118557			17728	protein-coding gene	gene with protein product						11468771	Standard	NM_031293		Approved		uc002fcd.3	Q8TBY8	OTTHUMG00000167827	ENST00000237353.10:c.514G>A	16.37:g.72184629C>T	ENSP00000237353:p.Ala172Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	35	0.411765	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Missense_Mutation	SNP	ENST00000237353.10	37	CCDS32483.1	216	0.0989010989010989	3	0.006097560975609756	46	0.1270718232044199	99	0.17307692307692307	68	0.08970976253298153	C	14.35	2.509389	0.44660	0.020928	0.085	ENSG00000118557	ENST00000537465;ENST00000237353;ENST00000355636	T;T;T	0.78003	-1.14;-1.14;2.77	6.17	-4.61	0.03380	.	1.378430	0.04711	N	0.417677	T	0.00178	0.0005	N	0.14661	0.345	0.80722	P	0.0	P;P;P	0.42039	0.769;0.642;0.769	B;B;B	0.25614	0.062;0.062;0.062	T	0.09378	-1.0677	9	0.14656	T	0.56	0.0471	1.8798	0.03225	0.1193:0.2169:0.3507:0.313	rs217180;rs17667549;rs57451652;rs217180	172;172;172	Q8TBY8;Q8TBY8-2;G3V1Q7	PMFBP_HUMAN;.;.	T	172;172;27	ENSP00000443817:A172T;ENSP00000237353:A172T;ENSP00000347854:A27T	ENSP00000237353:A172T	A	-	1	0	PMFBP1	70742130	0.000000	0.05858	0.009000	0.14445	0.823000	0.46562	-2.843000	0.00736	-0.318000	0.08665	0.655000	0.94253	GCC	C|0.923;T|0.077	0.077	strong		0.507	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293	
OR2F2	135948	hgsc.bcm.edu	37	7	143633157	143633157	+	Missense_Mutation	SNP	T	T	C	rs13235235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143633157T>C	ENST00000408955.2	+	1	899	c.832T>C	c.(832-834)Tat>Cat	p.Y278H		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	278			Y -> H (in dbSNP:rs13235235).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					CTCTGTCTTCTATGCCATTGT	0.478													T|||	829	0.165535	0.3464	0.1657	5008	,	,		21510	0.002		0.2028	False		,,,				2504	0.0511				p.Y278H		Atlas-SNP	.											.	OR2F2	63	.	0			c.T832C						PASS	.	T	HIS/TYR	1462,2926	434.7+/-344.0	237,988,969	96.0	98.0	98.0		832	3.6	0.6	7	dbSNP_121	98	1923,6675	330.9+/-319.4	205,1513,2581	yes	missense	OR2F2	NM_001004685.1	83	442,2501,3550	CC,CT,TT		22.3657,33.3181,26.0665	probably-damaging	278/318	143633157	3385,9601	2194	4299	6493	SO:0001583	missense	135948	exon1			GTCTTCTATGCCA		CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"""GPCR / Class A : Olfactory receptors"""	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.832T>C	7.37:g.143633157T>C	ENSP00000386222:p.Tyr278His	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_001004685	A4D2G0|Q6IFP8	Missense_Mutation	SNP	ENST00000408955.2	37	CCDS43666.1	371	0.16987179487179488	159	0.3231707317073171	68	0.1878453038674033	0	0.0	144	0.18997361477572558	T	9.646	1.140355	0.21205	0.333181	0.223657	ENSG00000221910	ENST00000408955	T	0.00321	8.11	3.57	3.57	0.40892	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43919	D	0.000515	T	0.00012	0.0000	M	0.91196	3.185	0.39213	P	0.03664500000000004	D	0.89917	1.0	D	0.91635	0.999	T	0.41980	-0.9478	9	0.87932	D	0	-21.8475	10.4204	0.44346	0.0:0.0:0.0:1.0	rs13235235;rs17164452;rs52806957;rs13235235	278	O95006	OR2F2_HUMAN	H	278	ENSP00000386222:Y278H	ENSP00000386222:Y278H	Y	+	1	0	OR2F2	143264090	0.970000	0.33590	0.616000	0.29078	0.088000	0.18126	4.377000	0.59562	1.626000	0.50381	0.402000	0.26972	TAT	T|0.805;C|0.195	0.195	strong		0.478	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1		
STK40	83931	hgsc.bcm.edu	37	1	36807481	36807481	+	Missense_Mutation	SNP	C	C	T	rs3795498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:36807481C>T	ENST00000373129.3	-	12	1589	c.1183G>A	c.(1183-1185)Gcc>Acc	p.A395T	STK40_ENST00000359297.2_3'UTR|STK40_ENST00000373132.3_Missense_Mutation_p.A395T|STK40_ENST00000373130.3_Missense_Mutation_p.A400T	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	395			A -> T (in dbSNP:rs3795498). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A395T(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				CAGCTCCGGGCGTCATGGATG	0.637													C|||	897	0.179113	0.1672	0.1369	5008	,	,		18658	0.1429		0.2336	False		,,,				2504	0.2065				p.A395T		Atlas-SNP	.											SgK495,NS,lymphoid_neoplasm,0,2	STK40	53	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G1183A						PASS	.	C	THR/ALA	858,3548	336.0+/-304.2	89,680,1434	52.0	51.0	51.0		1183	5.1	1.0	1	dbSNP_107	51	2177,6423	371.6+/-336.3	290,1597,2413	yes	missense	STK40	NM_032017.1	58	379,2277,3847	TT,TC,CC		25.314,19.4734,23.3354	benign	395/436	36807481	3035,9971	2203	4300	6503	SO:0001583	missense	83931	exon12			TCCGGGCGTCATG	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.1183G>A	1.37:g.36807481C>T	ENSP00000362221:p.Ala395Thr	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Missense_Mutation	SNP	ENST00000373129.3	37	CCDS407.1	376	0.17216117216117216	77	0.1565040650406504	55	0.15193370165745856	71	0.12412587412587413	173	0.22823218997361477	C	18.13	3.554608	0.65425	0.194734	0.25314	ENSG00000196182	ENST00000373129;ENST00000373130;ENST00000373132	T;T;T	0.63096	-0.02;-0.02;-0.02	5.11	5.11	0.69529	.	0.104349	0.64402	D	0.000003	T	0.00012	0.0000	N	0.14661	0.345	0.21147	P	0.999770197	B;B	0.19935	0.04;0.024	B;B	0.10450	0.005;0.002	T	0.03202	-1.1061	9	0.32370	T	0.25	-13.8877	17.5055	0.87743	0.0:1.0:0.0:0.0	rs3795498;rs17856244;rs57485791;rs3795498	400;395	Q8N2I9-4;Q8N2I9	.;STK40_HUMAN	T	395;400;395	ENSP00000362221:A395T;ENSP00000362222:A400T;ENSP00000362224:A395T	ENSP00000362221:A395T	A	-	1	0	STK40	36580068	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	5.664000	0.68045	2.370000	0.80446	0.514000	0.50259	GCC	C|0.795;T|0.205	0.205	strong		0.637	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017	
F7	2155	hgsc.bcm.edu	37	13	113770068	113770068	+	Silent	SNP	C	C	T	rs6042	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:113770068C>T	ENST00000375581.3	+	6	560	c.525C>T	c.(523-525)caC>caT	p.H175H	F7_ENST00000541084.1_Silent_p.H106H|F7_ENST00000346342.3_Silent_p.H153H	NM_000131.4	NP_000122.1	P08709	FA7_HUMAN	coagulation factor VII (serum prothrombin conversion accelerator)	175	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|cellular protein metabolic process (GO:0044267)|circadian rhythm (GO:0007623)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell migration (GO:0030335)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to growth hormone (GO:0060416)|response to vitamin K (GO:0032571)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	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)	all_cancers(25;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)	GTCGGTGCCACGAGGGGTACT	0.617													C|||	729	0.145567	0.1346	0.1282	5008	,	,		19696	0.0446		0.1213	False		,,,				2504	0.3016				p.H175H		Atlas-SNP	.											F7,NS,carcinoma,0,1	F7	49	1	0			c.C525T						PASS	.	C	,	590,3816	257.0+/-261.6	43,504,1656	64.0	54.0	57.0		525,459	-3.2	0.4	13	dbSNP_52	57	1008,7592	215.7+/-255.0	62,884,3354	no	coding-synonymous,coding-synonymous	F7	NM_000131.3,NM_019616.2	,	105,1388,5010	TT,TC,CC		11.7209,13.3908,12.2866	,	175/467,153/445	113770068	1598,11408	2203	4300	6503	SO:0001819	synonymous_variant	2155	exon6			GTGCCACGAGGGG		CCDS9528.1, CCDS9529.1, CCDS73602.1	13q34	2014-02-03			ENSG00000057593	ENSG00000057593	3.4.21.21		3544	protein-coding gene	gene with protein product	"""eptacog alfa"", ""FVII coagulation protein"", ""factor VII"""	613878				3264725, 2511201	Standard	NM_000131		Approved		uc001vsv.4	P08709	OTTHUMG00000017373	ENST00000375581.3:c.525C>T	13.37:g.113770068C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	64	50	0.78125	NM_000131	B0YJC8|Q14339|Q5JVF1|Q5JVF2|Q9UD52|Q9UD53|Q9UD54	Silent	SNP	ENST00000375581.3	37	CCDS9528.1																																																																																			C|0.876;T|0.124	0.124	strong		0.617	F7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045838.4	NM_000131	
INADL	10207	hgsc.bcm.edu	37	1	62253483	62253483	+	Missense_Mutation	SNP	G	G	A	rs3762321	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:62253483G>A	ENST00000371158.2	+	8	1021	c.907G>A	c.(907-909)Gga>Aga	p.G303R	INADL_ENST00000316485.6_Missense_Mutation_p.G303R	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	303	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.		G -> R (in dbSNP:rs3762321).		cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AAACGTGCAGGGAATGACCAG	0.448													G|||	588	0.117412	0.0068	0.1326	5008	,	,		19692	0.1567		0.1014	False		,,,				2504	0.2321				p.G303R		Atlas-SNP	.											.	INADL	179	.	0			c.G907A						PASS	.	G	ARG/GLY	110,4296	85.8+/-124.5	5,100,2098	101.0	86.0	91.0		907	5.1	1.0	1	dbSNP_107	91	758,7842	181.6+/-230.3	36,686,3578	yes	missense	INADL	NM_176877.2	125	41,786,5676	AA,AG,GG		8.814,2.4966,6.6738	probably-damaging	303/1802	62253483	868,12138	2203	4300	6503	SO:0001583	missense	10207	exon8			GTGCAGGGAATGA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.907G>A	1.37:g.62253483G>A	ENSP00000360200:p.Gly303Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	56	20	0.357143	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	234	0.10714285714285714	7	0.014227642276422764	56	0.15469613259668508	92	0.16083916083916083	79	0.10422163588390501	G	23.9	4.470729	0.84533	0.024966	0.08814	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.23348	1.91;1.91	5.07	5.07	0.68467	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000003	T	0.00328	0.0010	M	0.82630	2.6	0.09310	P	1.0	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.00193	-1.1934	9	0.59425	D	0.04	.	18.6436	0.91404	0.0:0.0:1.0:0.0	rs3762321;rs52824294;rs57304909;rs3762321	303;303;303	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	R	303	ENSP00000360200:G303R;ENSP00000326199:G303R	ENSP00000255202:G303R	G	+	1	0	INADL	62026071	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	8.279000	0.89901	2.636000	0.89361	0.467000	0.42956	GGA	G|0.916;A|0.084	0.084	strong		0.448	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
RPS6KB2	6199	hgsc.bcm.edu	37	11	67202156	67202156	+	Missense_Mutation	SNP	C	C	T	rs13859	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67202156C>T	ENST00000312629.5	+	14	1304	c.1259C>T	c.(1258-1260)gCc>gTc	p.A420V	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	420	Pro-rich.		A -> V (in dbSNP:rs13859). {ECO:0000269|PubMed:10490847, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9804755, ECO:0000269|PubMed:9878560}.		epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			AGCCCCCGGGCCCCCGTCAGG	0.657													C|||	2438	0.486821	0.8079	0.5692	5008	,	,		17451	0.3264		0.4225	False		,,,				2504	0.226				p.A420V		Atlas-SNP	.											RPS6KB2_ENST00000312629,NS,carcinoma,0,2	RPS6KB2	92	2	0			c.C1259T						PASS	.	C	VAL/ALA	2835,1023		1045,745,139	12.0	13.0	13.0		1259	4.4	1.0	11	dbSNP_52	13	3510,4694		792,1926,1384	yes	missense	RPS6KB2	NM_003952.2	64	1837,2671,1523	TT,TC,CC		42.784,26.5163,47.3968	benign	420/483	67202156	6345,5717	1929	4102	6031	SO:0001583	missense	6199	exon14			CCCGGGCCCCCGT	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.1259C>T	11.37:g.67202156C>T	ENSP00000308413:p.Ala420Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Missense_Mutation	SNP	ENST00000312629.5	37	CCDS41677.1	1093	0.5004578754578755	381	0.774390243902439	195	0.5386740331491713	182	0.3181818181818182	335	0.4419525065963061	C	14.64	2.596768	0.46318	0.734837	0.42784	ENSG00000175634	ENST00000312629	T	0.68331	-0.32	4.45	4.45	0.53987	.	0.068776	0.56097	D	0.000031	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	B	0.10296	0.003	B	0.13407	0.009	T	0.39210	-0.9625	9	0.51188	T	0.08	.	15.058	0.71930	0.0:1.0:0.0:0.0	rs13859;rs1132410;rs1790751;rs3178163;rs3193142;rs11558387;rs17296783	420	Q9UBS0	KS6B2_HUMAN	V	420	ENSP00000308413:A420V	ENSP00000308413:A420V	A	+	2	0	RPS6KB2	66958732	1.000000	0.71417	0.998000	0.56505	0.220000	0.24768	6.850000	0.75420	2.300000	0.77407	0.462000	0.41574	GCC	C|0.515;T|0.485	0.485	strong		0.657	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	
ZIM2	23619	hgsc.bcm.edu	37	19	57293394	57293394	+	Silent	SNP	A	A	G	rs2286751	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57293394A>G	ENST00000391708.3	-	10	1115	c.573T>C	c.(571-573)agT>agC	p.S191S	ZIM2_ENST00000593711.1_Silent_p.S191S|AC006115.3_ENST00000595954.1_RNA|ZIM2_ENST00000221722.5_Silent_p.S191S|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000599935.1_Silent_p.S191S|ZIM2_ENST00000601070.1_Silent_p.S191S|AC006115.3_ENST00000597946.1_RNA	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	191	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		CACTAAGGGAACTAAGTTCCT	0.502													G|||	3742	0.747204	0.6846	0.8026	5008	,	,		19828	0.6627		0.7624	False		,,,				2504	0.864				p.S191S		Atlas-SNP	.											.	ZIM2	511	.	0			c.T573C						PASS	.	G	,,	3136,1270	433.3+/-343.5	1100,936,167	158.0	143.0	148.0		573,573,573	1.8	0.0	19	dbSNP_100	148	6865,1735	317.9+/-313.4	2729,1407,164	no	coding-synonymous,coding-synonymous,coding-synonymous	ZIM2	NM_001146326.1,NM_001146327.1,NM_015363.4	,,	3829,2343,331	GG,GA,AA		20.1744,28.8243,23.1047	,,	191/528,191/528,191/528	57293394	10001,3005	2203	4300	6503	SO:0001819	synonymous_variant	23619	exon9			AAGGGAACTAAGT	AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"""Zinc fingers, C2H2-type"""	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.573T>C	19.37:g.57293394A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_015363	Q2M3K1	Silent	SNP	ENST00000391708.3	37	CCDS33123.1																																																																																			A|0.252;G|0.748	0.748	strong		0.502	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2		
CAPG	822	hgsc.bcm.edu	37	2	85622059	85622059	+	Missense_Mutation	SNP	T	T	C	rs6886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85622059T>C	ENST00000409921.1	-	10	1025	c.959A>G	c.(958-960)cAt>cGt	p.H320R	CAPG_ENST00000263867.4_Missense_Mutation_p.H335R|CAPG_ENST00000483659.1_5'Flank|CAPG_ENST00000409670.1_Missense_Mutation_p.H335R|CAPG_ENST00000409724.1_Missense_Mutation_p.H335R			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						GGGACTCTCATGGCCCTGAGG	0.602													C|||	2930	0.585064	0.7489	0.3977	5008	,	,		19490	0.504		0.6551	False		,,,				2504	0.5082				p.H335R		Atlas-SNP	.											.	CAPG	32	.	0			c.A1004G						PASS	.	C	ARG/HIS	3228,1178	413.0+/-336.3	1184,860,159	56.0	54.0	55.0		1004	3.9	0.9	2	dbSNP_52	55	5543,3057	469.4+/-367.6	1807,1929,564	yes	missense	CAPG	NM_001747.2	29	2991,2789,723	CC,CT,TT		35.5465,26.7363,32.5619	benign	335/349	85622059	8771,4235	2203	4300	6503	SO:0001583	missense	822	exon10			CTCTCATGGCCCT	M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"""macrophage capping protein"""	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.959A>G	2.37:g.85622059T>C	ENSP00000387063:p.His320Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	126	91	0.722222	NM_001256139	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000409921.1	37	CCDS58715.1	1340	0.6135531135531136	389	0.790650406504065	159	0.43922651933701656	287	0.5017482517482518	505	0.6662269129287599	C	11.37	1.618331	0.28801	0.732637	0.644535	ENSG00000042493	ENST00000542681;ENST00000263867;ENST00000453973;ENST00000409921;ENST00000409670;ENST00000409724	T;T;T;T;T	0.52983	0.64;0.64;0.64;0.64;0.64	5.69	3.9	0.45041	Gelsolin domain (1);	0.200680	0.41823	N	0.000809	T	0.00012	0.0000	N	0.03967	-0.31	0.53688	P	2.1000000000048757E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27571	-1.0070	9	0.26408	T	0.33	.	8.0924	0.30807	0.0:0.7496:0.0:0.2504	rs6886;rs1131551;rs2271627;rs3191581;rs3209744;rs17294682;rs17764992;rs17856020;rs17856462;rs57062873;rs6886	320;335	B8ZZS7;P40121	.;CAPG_HUMAN	R	314;335;90;320;335;335	ENSP00000263867:H335R;ENSP00000397381:H90R;ENSP00000387063:H320R;ENSP00000386315:H335R;ENSP00000386965:H335R	ENSP00000263867:H335R	H	-	2	0	CAPG	85475570	0.947000	0.32204	0.876000	0.34364	0.961000	0.63080	2.004000	0.40854	0.368000	0.24481	-0.733000	0.03571	CAT	T|0.353;C|0.647	0.647	strong		0.602	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747	
PRC1	9055	hgsc.bcm.edu	37	15	91525048	91525048	+	Missense_Mutation	SNP	C	C	G	rs142416384	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:91525048C>G	ENST00000361188.5	-	4	1642	c.431G>C	c.(430-432)aGt>aCt	p.S144T	PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000442656.2_Missense_Mutation_p.S103T|PRC1_ENST00000361919.3_Missense_Mutation_p.S144T|PRC1_ENST00000394249.3_Missense_Mutation_p.S144T|PRC1_ENST00000556129.1_5'Flank					protein regulator of cytokinesis 1											endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					CACTGAGGCACTGTCAATATC	0.423													C|||	105	0.0209665	0.0	0.0029	5008	,	,		22971	0.002		0.0219	False		,,,				2504	0.0808				p.S144T		Atlas-SNP	.											.	PRC1	51	.	0			c.G431C						PASS	.	C	THR/SER,THR/SER,THR/SER	8,4388	14.3+/-33.2	0,8,2190	142.0	124.0	130.0		431,431,431	3.3	0.0	15	dbSNP_134	130	84,8512	48.5+/-108.0	1,82,4215	yes	missense,missense,missense	PRC1	NM_003981.2,NM_199413.1,NM_199414.1	58,58,58	1,90,6405	GG,GC,CC		0.9772,0.182,0.7081	benign,benign,benign	144/621,144/607,144/567	91525048	92,12900	2198	4298	6496	SO:0001583	missense	9055	exon4			GAGGCACTGTCAA	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"""anaphase spindle elongation 1 homolog (S. cerevisiae)"""	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.431G>C	15.37:g.91525048C>G	ENSP00000354679:p.Ser144Thr	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	186	92	0.494624	NM_199413		Missense_Mutation	SNP	ENST00000361188.5	37	CCDS45352.1	17	0.007783882783882784	0	0.0	1	0.0027624309392265192	0	0.0	16	0.021108179419525065	C	0.031	-1.332586	0.01298	0.00182	0.009772	ENSG00000198901	ENST00000394249;ENST00000361919;ENST00000361188;ENST00000442656	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.26	3.28	0.37604	.	0.670270	0.16679	N	0.204011	T	0.07818	0.0196	N	0.25201	0.72	0.09310	N	1	P;B;B;B;B	0.39424	0.673;0.02;0.022;0.022;0.027	B;B;B;B;B	0.37550	0.253;0.015;0.015;0.015;0.026	T	0.06588	-1.0818	10	0.15952	T	0.53	.	4.4701	0.11708	0.1531:0.595:0.1487:0.1032	.	92;103;144;144;144	B4E238;O43663-3;F8W9B5;O43663-2;O43663	.;.;.;.;PRC1_HUMAN	T	144;144;144;103	ENSP00000377793:S144T;ENSP00000354618:S144T;ENSP00000354679:S144T;ENSP00000409549:S103T	ENSP00000354679:S144T	S	-	2	0	PRC1	89326052	0.000000	0.05858	0.028000	0.17463	0.029000	0.11900	0.024000	0.13555	1.445000	0.47624	0.655000	0.94253	AGT	C|0.992;G|0.008	0.008	strong		0.423	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981	
ZNF667	63934	hgsc.bcm.edu	37	19	56953585	56953585	+	Missense_Mutation	SNP	T	T	C	rs3760849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56953585T>C	ENST00000504904.3	-	7	1498	c.779A>G	c.(778-780)aAa>aGa	p.K260R	ZNF667_ENST00000292069.6_Missense_Mutation_p.K260R|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Missense_Mutation_p.K388R			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	260			K -> R (in dbSNP:rs3760849).		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)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		ATTGAAGGCTTTTCCGCACTT	0.363													T|||	3181	0.635184	0.5295	0.6254	5008	,	,		18644	0.874		0.5169	False		,,,				2504	0.6605				p.K260R		Atlas-SNP	.											.	ZNF667	95	.	0			c.A779G						PASS	.	T	ARG/LYS	2289,2117	588.3+/-386.9	605,1079,519	93.0	97.0	96.0		779	2.9	0.0	19	dbSNP_107	96	4490,4110	589.1+/-392.5	1159,2172,969	yes	missense	ZNF667	NM_022103.3	26	1764,3251,1488	CC,CT,TT		47.7907,48.0481,47.8779	probably-damaging	260/611	56953585	6779,6227	2203	4300	6503	SO:0001583	missense	63934	exon5			AAGGCTTTTCCGC		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.779A>G	19.37:g.56953585T>C	ENSP00000439402:p.Lys260Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Missense_Mutation	SNP	ENST00000504904.3	37	CCDS12944.1	1376	0.63003663003663	277	0.5630081300813008	209	0.5773480662983426	490	0.8566433566433567	400	0.5277044854881267	T	8.125	0.781707	0.16120	0.519519	0.522093	ENSG00000198046	ENST00000342634;ENST00000504904;ENST00000292069;ENST00000452518	T;T;T	0.58060	0.36;0.36;0.36	5.05	2.87	0.33458	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.144445	0.32244	N	0.006374	T	0.00012	0.0000	L	0.59436	1.845	0.40445	P	0.01992000000000005	B;B	0.33477	0.413;0.12	B;B	0.36186	0.219;0.105	T	0.10291	-1.0636	9	0.66056	D	0.02	-11.761	6.3787	0.21521	0.0:0.0857:0.1586:0.7557	rs3760849;rs52832752;rs58796129;rs3760849	388;260	E7EPS0;Q5HYK9	.;ZN667_HUMAN	R	388;260;260;42	ENSP00000344699:K388R;ENSP00000439402:K260R;ENSP00000292069:K260R	ENSP00000292069:K260R	K	-	2	0	ZNF667	61645397	0.604000	0.26932	0.028000	0.17463	0.004000	0.04260	3.228000	0.51270	0.346000	0.23899	0.482000	0.46254	AAA	T|0.426;C|0.574	0.574	strong		0.363	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
F7	2155	hgsc.bcm.edu	37	13	113773159	113773159	+	Missense_Mutation	SNP	G	G	A	rs6046	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:113773159G>A	ENST00000375581.3	+	9	1273	c.1238G>A	c.(1237-1239)cGg>cAg	p.R413Q	F7_ENST00000541084.1_Missense_Mutation_p.R344Q|F7_ENST00000346342.3_Missense_Mutation_p.R391Q	NM_000131.4	NP_000122.1	P08709	FA7_HUMAN	coagulation factor VII (serum prothrombin conversion accelerator)	413	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> G (in FA7D). {ECO:0000269|PubMed:18976247}.|R -> Q (may be associated with decreased susceptibility to myocardial infarction; dbSNP:rs6046). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10984565, ECO:0000269|PubMed:16292673, ECO:0000269|PubMed:8043443, ECO:0000269|PubMed:8844208, ECO:0000269|Ref.6}.		blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|cellular protein metabolic process (GO:0044267)|circadian rhythm (GO:0007623)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell migration (GO:0030335)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to growth hormone (GO:0060416)|response to vitamin K (GO:0032571)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	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)	all_cancers(25;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)	ACCCACTACCGGGGCACGTGG	0.627													G|||	693	0.138379	0.1172	0.1225	5008	,	,		15937	0.0466		0.1113	False		,,,				2504	0.3006				p.R413Q		Atlas-SNP	.											.	F7	49	.	0			c.G1238A	GRCh37	CM074160|CM940396	F7	M	rs6046	PASS	.	G	GLN/ARG,GLN/ARG	516,3886	218.7+/-236.7	32,452,1717	27.0	28.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1238,1172	-4.6	0.0	13	dbSNP_52	28	914,7684	192.4+/-238.4	56,802,3441	yes	missense,missense	F7	NM_000131.3,NM_019616.2	43,43	88,1254,5158	AA,AG,GG		10.6304,11.7219,11.0	benign,benign	413/467,391/445	113773159	1430,11570	2201	4299	6500	SO:0001583	missense	2155	exon9			ACTACCGGGGCAC		CCDS9528.1, CCDS9529.1, CCDS73602.1	13q34	2014-02-03			ENSG00000057593	ENSG00000057593	3.4.21.21		3544	protein-coding gene	gene with protein product	"""eptacog alfa"", ""FVII coagulation protein"", ""factor VII"""	613878				3264725, 2511201	Standard	NM_000131		Approved		uc001vsv.4	P08709	OTTHUMG00000017373	ENST00000375581.3:c.1238G>A	13.37:g.113773159G>A	ENSP00000364731:p.Arg413Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	85	61	0.717647	NM_000131	B0YJC8|Q14339|Q5JVF1|Q5JVF2|Q9UD52|Q9UD53|Q9UD54	Missense_Mutation	SNP	ENST00000375581.3	37	CCDS9528.1	206	0.09432234432234432	55	0.11178861788617886	42	0.11602209944751381	30	0.05244755244755245	79	0.10422163588390501	G	7.007	0.556041	0.13436	0.117219	0.106304	ENSG00000057593	ENST00000346342;ENST00000541084;ENST00000375581	D;D;D	0.81579	-1.51;-1.51;-1.51	4.11	-4.6	0.03390	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.744753	0.11868	N	0.521729	T	0.01592	0.0051	L	0.35854	1.095	0.80722	P	0.0	B;B;B	0.30889	0.092;0.254;0.299	B;B;B	0.14578	0.011;0.005;0.008	T	0.03017	-1.1082	9	0.40728	T	0.16	.	5.9568	0.19277	0.5017:0.0:0.3766:0.1217	rs6046;rs532977;rs36209568;rs6046	344;391;413	F5H8B0;P08709-2;P08709	.;.;FA7_HUMAN	Q	391;344;413	ENSP00000329546:R391Q;ENSP00000442051:R344Q;ENSP00000364731:R413Q	ENSP00000329546:R391Q	R	+	2	0	F7	112821160	0.036000	0.19791	0.003000	0.11579	0.015000	0.08874	0.104000	0.15313	-1.032000	0.03304	-0.518000	0.04402	CGG	T|0.001;G|0.877;C|0.007;A|0.115	0.115	strong		0.627	F7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045838.4	NM_000131	
LAMC2	3918	hgsc.bcm.edu	37	1	183184616	183184616	+	Silent	SNP	C	C	T	rs2274980	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:183184616C>T	ENST00000264144.4	+	3	362	c.297C>T	c.(295-297)tcC>tcT	p.S99S	LAMC2_ENST00000493293.1_Silent_p.S99S	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	99	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						GTGACAACTCCGGACGGTGCA	0.517													C|||	1571	0.313698	0.4024	0.317	5008	,	,		20715	0.3333		0.1571	False		,,,				2504	0.3323				p.S99S		Atlas-SNP	.											LAMC2,NS,carcinoma,+1,1	LAMC2	113	1	0			c.C297T						PASS	.	C	,	1682,2724	509.4+/-367.2	348,986,869	105.0	93.0	97.0		297,297	-1.6	0.6	1	dbSNP_100	97	1519,7081	286.9+/-297.9	130,1259,2911	no	coding-synonymous,coding-synonymous	LAMC2	NM_005562.2,NM_018891.2	,	478,2245,3780	TT,TC,CC		17.6628,38.1752,24.6117	,	99/1194,99/1112	183184616	3201,9805	2203	4300	6503	SO:0001819	synonymous_variant	3918	exon3			CAACTCCGGACGG	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.297C>T	1.37:g.183184616C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	37	CCDS1352.1																																																																																			C|0.732;T|0.268	0.268	strong		0.517	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
PCF11	51585	hgsc.bcm.edu	37	11	82880341	82880341	+	Silent	SNP	G	G	A	rs12284052	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:82880341G>A	ENST00000298281.4	+	8	3416	c.2964G>A	c.(2962-2964)caG>caA	p.Q988Q		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	988	Gly-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						CACATGGTCAGCCAGGGGTTG	0.517													A|||	1226	0.244808	0.6657	0.1167	5008	,	,		20858	0.0496		0.0835	False		,,,				2504	0.1339				p.Q988Q		Atlas-SNP	.											.	PCF11	220	.	0			c.G2964A						PASS	.	A		2068,1764		558,952,406	90.0	92.0	91.0		2964	-1.0	1.0	11	dbSNP_120	91	727,7533		29,669,3432	no	coding-synonymous	PCF11	NM_015885.3		587,1621,3838	AA,AG,GG		8.8015,46.0334,23.1145		988/1556	82880341	2795,9297	1916	4130	6046	SO:0001819	synonymous_variant	51585	exon8			TGGTCAGCCAGGG	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.2964G>A	11.37:g.82880341G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	193	33	0.170984	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			G|0.783;A|0.217	0.217	strong		0.517	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
SGK223	157285	hgsc.bcm.edu	37	8	8234192	8234192	+	Missense_Mutation	SNP	G	G	C	rs4840953	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:8234192G>C	ENST00000520004.1	-	3	1991	c.1727C>G	c.(1726-1728)tCt>tGt	p.S576C	SGK223_ENST00000330777.4_Missense_Mutation_p.S576C			Q86YV5	SG223_HUMAN		578							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCTGCCGCCAGAGCTCCCATC	0.652													G|||	2276	0.454473	0.3918	0.4323	5008	,	,		16373	0.6409		0.3022	False		,,,				2504	0.5194				p.S576C	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1727G						PASS	.	G	CYS/SER	1306,2738		222,862,938	21.0	25.0	24.0		1727	1.9	0.0	8	dbSNP_111	24	2304,5992		322,1660,2166	yes	missense	SGK223	NM_001080826.1	112	544,2522,3104	CC,CG,GG		27.7724,32.2948,29.2545	benign	576/1403	8234192	3610,8730	2022	4148	6170	SO:0001583	missense	0	exon2			CCGCCAGAGCTCC																												ENST00000520004.1:c.1727C>G	8.37:g.8234192G>C	ENSP00000428054:p.Ser576Cys	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	950	0.434981684981685	201	0.40853658536585363	142	0.39226519337016574	389	0.6800699300699301	218	0.287598944591029	G	10.25	1.297067	0.23650	0.322948	0.277724	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59083	0.29;0.29	4.92	1.93	0.25924	.	2.545670	0.01254	N	0.008962	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.47169	-0.9138	9	0.38643	T	0.18	.	4.1097	0.10053	0.0811:0.2388:0.4682:0.212	rs4840953;rs52796687;rs59893685;rs4840953	576	Q86YV5	SG223_HUMAN	C	576	ENSP00000330930:S576C;ENSP00000428054:S576C	ENSP00000330930:S576C	S	-	2	0	AC068353.1	8271602	0.000000	0.05858	0.016000	0.15963	0.045000	0.14185	0.024000	0.13555	1.199000	0.43173	0.655000	0.94253	TCT	G|0.602;C|0.398	0.398	strong		0.652	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
VWF	7450	hgsc.bcm.edu	37	12	6153514	6153514	+	Silent	SNP	A	A	G	rs1063857	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6153514A>G	ENST00000261405.5	-	18	2639	c.2385T>C	c.(2383-2385)taT>taC	p.Y795Y		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	795	E1.|TIL 3.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	ACTCCAGGTCATAGTTCTGGC	0.607													G|||	1685	0.336462	0.6377	0.2406	5008	,	,		20371	0.0913		0.3678	False		,,,				2504	0.2178				p.Y795Y		Atlas-SNP	.											.	VWF	338	.	0			c.T2385C						PASS	.	G		2503,1903	545.1+/-376.7	701,1101,401	114.0	96.0	102.0		2385	-5.5	0.8	12	dbSNP_86	102	3075,5525	660.4+/-401.8	547,1981,1772	no	coding-synonymous	VWF	NM_000552.3		1248,3082,2173	GG,GA,AA		35.7558,43.1911,42.8879		795/2814	6153514	5578,7428	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon18			CAGGTCATAGTTC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2385T>C	12.37:g.6153514A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			A|0.615;G|0.385	0.385	strong		0.607	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
GATA5	140628	hgsc.bcm.edu	37	20	61048549	61048549	+	Silent	SNP	G	G	A	rs41305803	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61048549G>A	ENST00000252997.2	-	3	670	c.609C>T	c.(607-609)gaC>gaT	p.D203D		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	203					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			GGCCGGTGCCGTCTCGGCGCC	0.647													G|||	1944	0.388179	0.4501	0.438	5008	,	,		12093	0.3403		0.4404	False		,,,				2504	0.2648				p.D203D		Atlas-SNP	.											.	GATA5	22	.	0			c.C609T						PASS	.	G		1860,2530		391,1078,726	44.0	37.0	39.0		609	-3.5	0.2	20	dbSNP_127	39	3733,4861		818,2097,1382	no	coding-synonymous	GATA5	NM_080473.4		1209,3175,2108	AA,AG,GG		43.4373,42.369,43.0761		203/398	61048549	5593,7391	2195	4297	6492	SO:0001819	synonymous_variant	140628	exon3			GGTGCCGTCTCGG	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"""GATA zinc finger domain containing"""	15802	protein-coding gene	gene with protein product		611496	"""GATA-binding protein 5"""			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.609C>T	20.37:g.61048549G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	138	71	0.514493	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			G|0.568;A|0.432	0.432	strong		0.647	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473	
PCF11	51585	hgsc.bcm.edu	37	11	82879825	82879825	+	Silent	SNP	G	G	A	rs75717911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:82879825G>A	ENST00000298281.4	+	8	2900	c.2448G>A	c.(2446-2448)ggG>ggA	p.G816G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	816	Gly-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TAGGAGGTGGGTGTCCTTTGA	0.562													G|||	19	0.00379393	0.0	0.0	5008	,	,		18518	0.0		0.0129	False		,,,				2504	0.0061				p.G816G		Atlas-SNP	.											.	PCF11	220	.	0			c.G2448A						PASS	.	G		5,3839		0,5,1917	60.0	63.0	62.0		2448	-1.9	1.0	11	dbSNP_133	62	102,8136		0,102,4017	no	coding-synonymous	PCF11	NM_015885.3		0,107,5934	AA,AG,GG		1.2382,0.1301,0.8856		816/1556	82879825	107,11975	1922	4119	6041	SO:0001819	synonymous_variant	51585	exon8			AGGTGGGTGTCCT	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.2448G>A	11.37:g.82879825G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	134	113	0.843284	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			G|0.995;A|0.005	0.005	strong		0.562	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
RYR1	6261	hgsc.bcm.edu	37	19	38993547	38993547	+	Silent	SNP	C	C	T	rs2229142	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38993547C>T	ENST00000359596.3	+	49	7863	c.7863C>T	c.(7861-7863)caC>caT	p.H2621H	RYR1_ENST00000360985.3_Silent_p.H2621H|RYR1_ENST00000355481.4_Silent_p.H2621H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2621	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.H2621H(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGCTGCAGCACCTGTTGCGCC	0.622													C|||	1191	0.237819	0.2163	0.1902	5008	,	,		13091	0.3095		0.16	False		,,,				2504	0.3067				p.H2621H		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	1	1	Substitution - coding silent(1)	stomach(1)	c.C7863T						PASS	.	C	,	834,3572	331.0+/-301.8	81,672,1450	118.0	81.0	94.0		7863,7863	3.0	1.0	19	dbSNP_98	94	1219,7381	244.6+/-273.7	100,1019,3181	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	181,1691,4631	TT,TC,CC		14.1744,18.9287,15.785	,	2621/5039,2621/5034	38993547	2053,10953	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon49			GCAGCACCTGTTG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.7863C>T	19.37:g.38993547C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.834;T|0.166	0.166	strong		0.622	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
C2CD3	26005	hgsc.bcm.edu	37	11	73796917	73796917	+	Missense_Mutation	SNP	C	C	T	rs826058	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:73796917C>T	ENST00000334126.7	-	21	3882	c.3656G>A	c.(3655-3657)cGg>cAg	p.R1219Q	C2CD3_ENST00000313663.7_Missense_Mutation_p.R1219Q			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1219	C2 1.		R -> Q (in dbSNP:rs826058). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1}.		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					AGCGGGTTCCCGTTCAGCCAA	0.493													T|||	1754	0.35024	0.5741	0.4135	5008	,	,		20841	0.1577		0.3091	False		,,,				2504	0.2434				p.R1219Q		Atlas-SNP	.											C2CD3_ENST00000334126,NS,adenoma,0,2	C2CD3	288	2	0			c.G3656A						PASS	.	T	GLN/ARG	2227,2173	585.0+/-386.2	561,1105,534	50.0	47.0	48.0		3656	4.7	1.0	11	dbSNP_86	48	2640,5946	685.7+/-404.1	410,1820,2063	yes	missense	C2CD3	NM_015531.4	43	971,2925,2597	TT,TC,CC		30.7477,49.3864,37.4788	benign	1219/1964	73796917	4867,8119	2200	4293	6493	SO:0001583	missense	26005	exon21			GGTTCCCGTTCAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3656G>A	11.37:g.73796917C>T	ENSP00000334379:p.Arg1219Gln	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	84	68	0.809524	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		772	0.3534798534798535	291	0.5914634146341463	138	0.3812154696132597	97	0.16958041958041958	246	0.3245382585751979	T	2.369	-0.344862	0.05208	0.506136	0.307477	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.12147	3.16;3.15;2.71	5.8	4.66	0.58398	.	0.243070	0.42053	N	0.000770	T	0.00012	0.0000	N	0.00308	-1.67	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.35025	-0.9805	8	.	.	.	-2.6174	7.8745	0.29586	0.1231:0.0674:0.0:0.8096	rs826058;rs1278706;rs17244733;rs58708907;rs826058	1219	Q4AC94-1	.	Q	1219;1219;1219;27	ENSP00000334379:R1219Q;ENSP00000323339:R1219Q;ENSP00000388750:R27Q	.	R	-	2	0	C2CD3	73474565	1.000000	0.71417	1.000000	0.80357	0.253000	0.25986	2.328000	0.43867	0.447000	0.26695	-0.254000	0.11334	CGG	C|0.635;T|0.365	0.365	strong		0.493	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
FAM214A	56204	hgsc.bcm.edu	37	15	52901283	52901283	+	Missense_Mutation	SNP	T	T	C	rs61731670|rs386783993	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:52901283T>C	ENST00000261844.7	-	6	1980	c.1828A>G	c.(1828-1830)Act>Gct	p.T610A	FAM214A_ENST00000546305.2_Missense_Mutation_p.T617A	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	610				T -> A (in Ref. 2; BAF85606/BAG57301 and 5; AAI09129). {ECO:0000305}.													ATTGAGGAAGTTGATAAACTA	0.333													T|||	2157	0.430711	0.4402	0.2968	5008	,	,		17056	0.8482		0.167	False		,,,				2504	0.3538				p.T610A		Atlas-SNP	.											.	.	.	.	0			c.A1828G						PASS	.	T	ALA/THR	1334,2336		232,870,733	112.0	119.0	117.0		1828	2.1	0.0	15	dbSNP_129	117	1230,6926		116,998,2964	yes	missense	KIAA1370	NM_019600.2	58	348,1868,3697	CC,CT,TT		15.0809,36.3488,21.681	benign	610/1077	52901283	2564,9262	1835	4078	5913	SO:0001583	missense	56204	exon6			AGGAAGTTGATAA	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.1828A>G	15.37:g.52901283T>C	ENSP00000261844:p.Thr610Ala	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	72	25	0.347222	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	760	0.34798534798534797	156	0.3170731707317073	86	0.23756906077348067	424	0.7412587412587412	94	0.12401055408970976	T	1.003	-0.690316	0.03303	0.363488	0.150809	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T	0.30448	1.53;1.53	5.92	2.07	0.26955	.	0.209202	0.49916	N	0.000136	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.14023	0.01;0.004	T	0.20174	-1.0283	9	0.29301	T	0.29	.	5.2861	0.15702	0.1281:0.1543:0.0:0.7176	rs61731670	617;610	F5H8G0;Q32MH5	.;K1370_HUMAN	A	610;610;609;617	ENSP00000261844:T610A;ENSP00000443598:T617A	ENSP00000261844:T610A	T	-	1	0	KIAA1370	50688575	0.807000	0.29009	0.042000	0.18584	0.040000	0.13550	1.242000	0.32755	0.452000	0.26830	0.533000	0.62120	ACT	T|0.697;C|0.303	0.303	strong		0.333	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
FKRP	79147	hgsc.bcm.edu	37	19	47258842	47258842	+	Silent	SNP	C	C	T	rs2287717	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47258842C>T	ENST00000318584.5	+	4	432	c.135C>T	c.(133-135)gcC>gcT	p.A45A	FKRP_ENST00000391909.3_Silent_p.A45A|FKRP_ENST00000600646.1_Intron	NM_001039885.2|NM_024301.4	NP_001034974.1|NP_077277.1	Q9H9S5	FKRP_HUMAN	fukutin related protein	45					glycoprotein biosynthetic process (GO:0009101)|protein processing (GO:0016485)	dystrophin-associated glycoprotein complex (GO:0016010)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)	transferase activity (GO:0016740)			NS(1)|large_intestine(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)		CCTCTGCTGCCGGCCCCCGTG	0.667													C|||	752	0.15016	0.1664	0.1311	5008	,	,		13153	0.1319		0.1431	False		,,,				2504	0.1677				p.A45A		Atlas-SNP	.											.	FKRP	16	.	0			c.C135T						PASS	.	C	,	625,3773		46,533,1620	22.0	21.0	21.0		135,135	-5.0	0.0	19	dbSNP_100	21	1218,7374		91,1036,3169	no	coding-synonymous,coding-synonymous	FKRP	NM_001039885.2,NM_024301.4	,	137,1569,4789	TT,TC,CC		14.176,14.211,14.1878	,	45/496,45/496	47258842	1843,11147	2199	4296	6495	SO:0001819	synonymous_variant	79147	exon4			TGCTGCCGGCCCC	AJ314847	CCDS12691.1	19q13.32	2014-09-17			ENSG00000181027	ENSG00000181027			17997	protein-coding gene	gene with protein product		606596				11592034, 11741828	Standard	NM_024301		Approved	LGMD2I, MDC1C	uc002pfp.2	Q9H9S5		ENST00000318584.5:c.135C>T	19.37:g.47258842C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_024301	A8K5G7	Silent	SNP	ENST00000318584.5	37	CCDS12691.1																																																																																			C|0.859;T|0.141	0.141	strong		0.667	FKRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465473.1	NM_024301	
C10orf71	118461	hgsc.bcm.edu	37	10	50534862	50534862	+	Silent	SNP	T	T	C	rs12411843	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50534862T>C	ENST00000374144.3	+	3	4560	c.4272T>C	c.(4270-4272)gaT>gaC	p.D1424D	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1424										endometrium(1)	1						TCTCCACTGATGACCTAGAGG	0.602													C|||	1521	0.303714	0.1316	0.3818	5008	,	,		14631	0.4127		0.333	False		,,,				2504	0.3384				p.D1424D		Atlas-SNP	.											.	C10orf71	179	.	0			c.T4272C						PASS	.	C	,	239,1145		19,201,472	29.0	33.0	32.0		4272,	-6.5	0.0	10	dbSNP_120	32	1018,2164		162,694,735	no	coding-synonymous,intron	C10orf71	NM_001135196.1,NM_199459.3	,	181,895,1207	CC,CT,TT		31.9925,17.2688,27.5296	,	1424/1436,	50534862	1257,3309	692	1591	2283	SO:0001819	synonymous_variant	118461	exon3			CACTGATGACCTA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.4272T>C	10.37:g.50534862T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			T|0.690;C|0.310	0.310	strong		0.602	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
EFNA3	1944	hgsc.bcm.edu	37	1	155058663	155058663	+	Missense_Mutation	SNP	G	G	A	rs17723260	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:155058663G>A	ENST00000368408.3	+	4	638	c.568G>A	c.(568-570)Gtg>Atg	p.V190M	EFNA3_ENST00000556931.1_Missense_Mutation_p.V185M|EFNA3_ENST00000505139.1_Missense_Mutation_p.V185M|EFNA3_ENST00000418360.2_Intron|EFNA3_ENST00000498667.1_3'UTR	NM_004952.4	NP_004943.1	P52797	EFNA3_HUMAN	ephrin-A3	190			V -> M (in dbSNP:rs17723260).		axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		all cancers(21;5.67e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000284)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGGCCCCAATGTGAAGATCAA	0.687											OREG0013850	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	381	0.0760783	0.0234	0.0994	5008	,	,		13282	0.0109		0.1342	False		,,,				2504	0.138				p.V190M		Atlas-SNP	.											EFNA3,colon,carcinoma,0,1	EFNA3	15	1	0			c.G568A						PASS	.	G	MET/VAL	172,4234	109.9+/-148.2	1,170,2032	44.0	43.0	43.0		568	4.5	1.0	1	dbSNP_123	43	1202,7396	238.8+/-270.1	82,1038,3179	yes	missense	EFNA3	NM_004952.4	21	83,1208,5211	AA,AG,GG		13.98,3.9038,10.566	possibly-damaging	190/239	155058663	1374,11630	2203	4299	6502	SO:0001583	missense	1944	exon4			CCCAATGTGAAGA	BC017722	CCDS1090.1	1q21-q22	2011-03-09			ENSG00000143590	ENSG00000143590		"""Ephrins"""	3223	protein-coding gene	gene with protein product		601381		EPLG3		8660976	Standard	NM_004952		Approved	LERK3, Ehk1-L	uc001fhf.3	P52797	OTTHUMG00000035313	ENST00000368408.3:c.568G>A	1.37:g.155058663G>A	ENSP00000357393:p.Val190Met	Somatic	215	0	0	220	WXS	Illumina HiSeq	Phase_I	226	113	0.5	NM_004952	B7ZAD3|D3DV85|Q0VGC9|Q5SR70	Missense_Mutation	SNP	ENST00000368408.3	37	CCDS1090.1	165	0.07554945054945054	12	0.024390243902439025	45	0.12430939226519337	3	0.005244755244755245	105	0.13852242744063326	G	16.17	3.046837	0.55110	0.039038	0.1398	ENSG00000143590;ENSG00000143590;ENSG00000251246	ENST00000556931;ENST00000368408;ENST00000505139	D;D;D	0.94897	-3.55;-3.53;-3.55	4.51	4.51	0.55191	.	0.000000	0.33534	N	0.004810	D	0.89326	0.6683	N	0.14661	0.345	0.09310	P	1.0	P;P	0.51351	0.944;0.936	P;P	0.51355	0.667;0.578	D	0.90589	0.4535	9	0.45353	T	0.12	-13.0846	15.1743	0.72899	0.0:0.0:1.0:0.0	rs17723260;rs17723260	185;190	B4DXG7;P52797	.;EFNA3_HUMAN	M	185;190;185	ENSP00000450814:V185M;ENSP00000357393:V190M;ENSP00000426741:V185M	ENSP00000357393:V190M	V	+	1	0	RP11-540D14.8;EFNA3	153325287	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.093000	0.50217	2.525000	0.85131	0.456000	0.33151	GTG	G|0.911;A|0.089	0.089	strong		0.687	EFNA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085429.1	NM_004952	
OR2L3	391192	hgsc.bcm.edu	37	1	248224099	248224099	+	Missense_Mutation	SNP	T	T	C	rs6666048	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248224099T>C	ENST00000359959.3	+	1	116	c.116T>C	c.(115-117)aTt>aCt	p.I39T	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	39			I -> T (in dbSNP:rs6666048).			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)			ATGGCTCTAATTGGAAACCTA	0.393													t|||	943	0.188299	0.298	0.098	5008	,	,		20570	0.254		0.1461	False		,,,				2504	0.0798				p.I39T		Atlas-SNP	.											.	OR2L3	97	.	0			c.T116C						PASS	.	T	THR/ILE,	1206,3200		158,890,1155	249.0	246.0	247.0		116,	0.7	0.0	1	dbSNP_116	247	1186,7408		90,1006,3201	no	missense,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	89,	248,1896,4356	CC,CT,TT		13.8003,27.3718,18.4	benign,	39/313,	248224099	2392,10608	2203	4297	6500	SO:0001583	missense	391192	exon1			CTCTAATTGGAAA	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.116T>C	1.37:g.248224099T>C	ENSP00000353044:p.Ile39Thr	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	271	108	0.398524	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	465	0.2129120879120879	147	0.29878048780487804	37	0.10220994475138122	172	0.3006993006993007	109	0.1437994722955145	.	0	-2.828662	0.00070	0.273718	0.138003	ENSG00000198128	ENST00000359959	T	0.00472	7.19	2.05	0.726	0.18248	.	.	.	.	.	T	0.00012	0.0000	N	0.04805	-0.155	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.00341	-1.1804	8	0.12430	T	0.62	.	7.3385	0.26623	0.0:0.0:0.2246:0.7754	rs6666048;rs59835396	39	Q8NG85	OR2L3_HUMAN	T	39	ENSP00000353044:I39T	ENSP00000353044:I39T	I	+	2	0	OR2L3	246290722	0.000000	0.05858	0.006000	0.13384	0.016000	0.09150	0.425000	0.21346	0.023000	0.15187	0.379000	0.24179	ATT	.	.	weak		0.393	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
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 GAIIx	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_ENST00000376929.3_Silent_p.I340I|SQSTM1_ENST00000510187.1_Missense_Mutation_p.S341L|SQSTM1_ENST00000402874.3_Silent_p.I340I|C5orf45_ENST00000403396.2_3'UTR|C5orf45_ENST00000523267.1_5'Flank	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		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	70	30	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 GAIIx	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_ENST00000545534.2_Silent_p.T315T|MYO1C_ENST00000438665.2_Silent_p.T320T|MYO1C_ENST00000359786.5_Silent_p.T339T|MYO1C_ENST00000573198.1_5'UTR|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		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	123	57	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		
SDHA	6389	hgsc.bcm.edu	37	5	236617	236617	+	Silent	SNP	G	G	T	rs200223188	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:236617G>T	ENST00000264932.6	+	10	1450	c.1335G>T	c.(1333-1335)tcG>tcT	p.S445S	SDHA_ENST00000504309.1_Silent_p.S445S|SDHA_ENST00000510361.1_Silent_p.S397S	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	445					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)	p.S445S(1)		NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	CCTGTGCCTCGGTACATGGTG	0.597									Familial Paragangliomas				G|||	2	0.000399361	0.0015	0.0	5008	,	,		17972	0.0		0.0	False		,,,				2504	0.0				p.S445S		Atlas-SNP	.											SDHA,NS,carcinoma,0,1	SDHA	80	1	1	Substitution - coding silent(1)	breast(1)	c.G1335T						scavenged	.						73.0	67.0	69.0					5																	236617		2203	4300	6503	SO:0001819	synonymous_variant	6389	exon10	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	TGCCTCGGTACAT	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1335G>T	5.37:g.236617G>T		Somatic	215	3	0.0139535		WXS	Illumina HiSeq	Phase_I	236	7	0.029661	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			A|0.002;G|0.988;T|0.011	0.011	strong		0.597	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
HTATSF1	27336	hgsc.bcm.edu	37	X	135593629	135593629	+	Silent	SNP	C	C	T	rs3027849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135593629C>T	ENST00000218364.4	+	9	1899	c.1725C>T	c.(1723-1725)gaC>gaT	p.D575D	HTATSF1_ENST00000535601.1_Silent_p.D575D	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	575	Asp/Glu-rich (acidic).|Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					AAGATTTGGACGAGGAAGGTT	0.393													C|||	326	0.0863576	0.0053	0.2032	3775	,	,		15204	0.0258		0.1143	False		,,,				2504	0.0378				p.D575D		Atlas-SNP	.											.	HTATSF1	66	.	0			c.C1725T						PASS	.	C	,	77,3757		0,68,9,1564,561	51.0	55.0	54.0		1725,1725	-8.6	0.0	X	dbSNP_102	54	899,5827		50,555,244,1823,1626	no	coding-synonymous,coding-synonymous	HTATSF1	NM_001163280.1,NM_014500.4	,	50,623,253,3387,2187	TT,TC,T,CC,C		13.366,2.0083,9.2424	,	575/756,575/756	135593629	976,9584	2202	4298	6500	SO:0001819	synonymous_variant	27336	exon10			TTTGGACGAGGAA	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.1725C>T	X.37:g.135593629C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	31	20	0.645161	NM_001163280	D3DWG9|Q59G06|Q99730	Silent	SNP	ENST00000218364.4	37	CCDS14657.1																																																																																			C|0.902;0|0.017	.	strong		0.393	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500	
TTC21A	199223	hgsc.bcm.edu	37	3	39152345	39152345	+	Missense_Mutation	SNP	G	G	A	rs1112438	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:39152345G>A	ENST00000431162.2	+	4	406	c.272G>A	c.(271-273)cGa>cAa	p.R91Q	TTC21A_ENST00000301819.6_Missense_Mutation_p.R91Q|TTC21A_ENST00000440121.1_Missense_Mutation_p.R91Q|GORASP1_ENST00000319283.3_5'Flank			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	91			R -> Q (in dbSNP:rs1112438).							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TTTACAGACCGAGAAGCAATT	0.542													G|||	1741	0.347644	0.5681	0.2911	5008	,	,		22574	0.252		0.2714	False		,,,				2504	0.2669				p.R91Q		Atlas-SNP	.											TTC21A,caecum,carcinoma,0,1	TTC21A	96	1	0			c.G272A						PASS	.	G	GLN/ARG,GLN/ARG	1928,1994		483,962,516	59.0	61.0	60.0		272,272	0.6	0.8	3	dbSNP_86	60	2377,5959		360,1657,2151	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	43,43	843,2619,2667	AA,AG,GG		28.5149,49.1586,35.1199	benign,benign	91/1273,91/1321	39152345	4305,7953	1961	4168	6129	SO:0001583	missense	199223	exon4			CAGACCGAGAAGC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.272G>A	3.37:g.39152345G>A	ENSP00000398211:p.Arg91Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	121	47	0.38843	NM_001105513	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	733	0.3356227106227106	264	0.5365853658536586	111	0.30662983425414364	154	0.2692307692307692	204	0.2691292875989446	G	15.81	2.943055	0.53079	0.491586	0.285149	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.63096	0.34;0.34;-0.02	5.74	0.555	0.17247	Tetratricopeptide-like helical (1);	1.254700	0.05507	N	0.559506	T	0.00012	0.0000	L	0.45137	1.4	0.80722	P	0.0	B;B;B;B;B	0.27416	0.178;0.068;0.116;0.07;0.068	B;B;B;B;B	0.17433	0.018;0.008;0.008;0.003;0.008	T	0.42050	-0.9474	9	0.25106	T	0.35	3.0433	2.0891	0.03652	0.2241:0.2337:0.4224:0.1198	rs1112438;rs4557093;rs17855762;rs52803003;rs59061178;rs1112438	91;91;91;91;91	Q8NDW8-6;Q8NDW8-5;Q8NDW8-7;Q8NDW8;F5H6V8	.;.;.;TT21A_HUMAN;.	Q	91	ENSP00000301819:R91Q;ENSP00000398211:R91Q;ENSP00000410882:R91Q	ENSP00000301819:R91Q	R	+	2	0	TTC21A	39127349	0.349000	0.24870	0.838000	0.33150	0.989000	0.77384	0.487000	0.22356	-0.189000	0.10482	0.655000	0.94253	CGA	G|0.662;A|0.338	0.338	strong		0.542	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
RCN3	57333	hgsc.bcm.edu	37	19	50046437	50046437	+	Silent	SNP	C	C	T	rs1129459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50046437C>T	ENST00000270645.3	+	7	1401	c.954C>T	c.(952-954)ggC>ggT	p.G318G		NM_020650.2	NP_065701.2	Q96D15	RCN3_HUMAN	reticulocalbin 3, EF-hand calcium binding domain	318						endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0159)		CCAACTATGGCGAGGACCTGA	0.632													C|||	496	0.0990415	0.1906	0.0735	5008	,	,		15228	0.0258		0.0835	False		,,,				2504	0.0849				p.G318G		Atlas-SNP	.											.	RCN3	28	.	0			c.C954T						PASS	.	C		776,3630	313.8+/-293.3	60,656,1487	72.0	55.0	61.0		954	-3.5	0.9	19	dbSNP_86	61	662,7938	166.2+/-218.2	23,616,3661	no	coding-synonymous	RCN3	NM_020650.2		83,1272,5148	TT,TC,CC		7.6977,17.6123,11.0564		318/329	50046437	1438,11568	2203	4300	6503	SO:0001819	synonymous_variant	57333	exon7			CTATGGCGAGGAC	AY195859	CCDS12771.1	19q13.33	2013-01-10				ENSG00000142552		"""EF-hand domain containing"""	21145	protein-coding gene	gene with protein product							Standard	NM_020650		Approved	RLP49	uc002poj.3	Q96D15		ENST00000270645.3:c.954C>T	19.37:g.50046437C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_020650	Q9HBZ8	Silent	SNP	ENST00000270645.3	37	CCDS12771.1																																																																																			C|0.895;T|0.105	0.105	strong		0.632	RCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465261.1	NM_020650	
DHX58	79132	hgsc.bcm.edu	37	17	40257163	40257163	+	Missense_Mutation	SNP	T	T	C	rs2074158	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40257163T>C	ENST00000251642.3	-	10	1496	c.1274A>G	c.(1273-1275)cAg>cGg	p.Q425R		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	425	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		Q -> R (in dbSNP:rs2074158).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TTGGAACTTCTGGATCACTTC	0.587													T|||	1787	0.356829	0.8139	0.1772	5008	,	,		19401	0.1875		0.1779	False		,,,				2504	0.2249				p.Q425R		Atlas-SNP	.											.	DHX58	39	.	0			c.A1274G						PASS	.	T	ARG/GLN	3120,1286	697.8+/-406.3	1122,876,205	58.0	49.0	52.0		1274	-4.2	0.6	17	dbSNP_96	52	1453,7147	277.5+/-292.9	135,1183,2982	yes	missense	DHX58	NM_024119.2	43	1257,2059,3187	CC,CT,TT		16.8953,29.1875,35.1607	benign	425/679	40257163	4573,8433	2203	4300	6503	SO:0001583	missense	79132	exon10			AACTTCTGGATCA	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"""RNA helicase LGP2"""	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.1274A>G	17.37:g.40257163T>C	ENSP00000251642:p.Gln425Arg	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_024119	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	37	CCDS11416.1	666	0.30494505494505497	382	0.7764227642276422	64	0.17679558011049723	85	0.1486013986013986	135	0.17810026385224276	T	0.014	-1.586724	0.00872	0.708125	0.168953	ENSG00000108771	ENST00000251642;ENST00000423748	T	0.74737	-0.87	4.87	-4.24	0.03777	Helicase, C-terminal (3);	0.603639	0.17818	N	0.160968	T	0.00012	0.0000	N	0.02368	-0.58	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.43475	-0.9389	9	0.14252	T	0.57	.	14.4174	0.67160	0.0:0.1363:0.0:0.8637	rs2074158;rs60447450;rs2074158	418;425	B7Z455;Q96C10	.;DHX58_HUMAN	R	425;388	ENSP00000251642:Q425R	ENSP00000251642:Q425R	Q	-	2	0	DHX58	37510689	0.001000	0.12720	0.638000	0.29380	0.143000	0.21401	-0.256000	0.08757	-0.564000	0.06070	-1.342000	0.01247	CAG	T|0.647;C|0.353	0.353	strong		0.587	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119	
GNL1	2794	hgsc.bcm.edu	37	6	30515043	30515043	+	Silent	SNP	T	T	C	rs3130247	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30515043T>C	ENST00000376621.3	-	10	2257	c.1287A>G	c.(1285-1287)gcA>gcG	p.A429A		NM_005275.3	NP_005266.2	P36915	GNL1_HUMAN	guanine nucleotide binding protein-like 1	429					cellular response to DNA damage stimulus (GO:0006974)|GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)|signal transduction (GO:0007165)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			cervix(2)|endometrium(4)|large_intestine(1)|lung(10)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	25						GGTAGATCCCTGCCAGAACCT	0.597													T|||	110	0.0219649	0.0121	0.0216	5008	,	,		19418	0.0		0.0785	False		,,,				2504	0.0				p.A429A		Atlas-SNP	.											.	GNL1	47	.	0			c.A1287G						PASS	.	T		103,2919		1,101,1409	195.0	185.0	189.0		1287	-10.0	0.3	6	dbSNP_103	189	578,4840		35,508,2166	yes	coding-synonymous	GNL1	NM_005275.3		36,609,3575	CC,CT,TT		10.6681,3.4083,8.0687		429/608	30515043	681,7759	1511	2709	4220	SO:0001819	synonymous_variant	2794	exon10			GATCCCTGCCAGA		CCDS4680.1	6p21.3	2010-02-17			ENSG00000204590	ENSG00000204590			4413	protein-coding gene	gene with protein product		143024				8180467	Standard	NM_005275		Approved	HSR1	uc003nqh.3	P36915	OTTHUMG00000031137	ENST00000376621.3:c.1287A>G	6.37:g.30515043T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	76	0.844444	NM_005275	B0S838|Q96CT5	Silent	SNP	ENST00000376621.3	37	CCDS4680.1																																																																																			T|0.939;C|0.061	0.061	strong		0.597	GNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076241.2		
FGFBP2	83888	hgsc.bcm.edu	37	4	15964485	15964485	+	Missense_Mutation	SNP	G	G	A	rs758329	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:15964485G>A	ENST00000259989.6	-	1	374	c.268C>T	c.(268-270)Cct>Tct	p.P90S	FGFBP2_ENST00000509331.1_Intron	NM_031950.3	NP_114156.1	Q9BYJ0	FGFP2_HUMAN	fibroblast growth factor binding protein 2	90			P -> S (in dbSNP:rs758329).			extracellular region (GO:0005576)				central_nervous_system(1)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	9						TTCCAGTAAGGTTTGGGGTCA	0.632													G|||	1689	0.33726	0.2194	0.2954	5008	,	,		20479	0.501		0.4722	False		,,,				2504	0.2188				p.P90S		Atlas-SNP	.											FGFBP2,colon,carcinoma,0,2	FGFBP2	22	2	0			c.C268T						PASS	.	G	SER/PRO	1068,3338	388.2+/-326.8	136,796,1271	54.0	54.0	54.0		268	1.1	0.2	4	dbSNP_86	54	3973,4627	549.9+/-385.6	947,2079,1274	yes	missense	FGFBP2	NM_031950.3	74	1083,2875,2545	AA,AG,GG		46.1977,24.2397,38.759	benign	90/224	15964485	5041,7965	2203	4300	6503	SO:0001583	missense	83888	exon1			AGTAAGGTTTGGG	AB021123	CCDS3419.1	4p15.32	2008-07-16			ENSG00000137441	ENSG00000137441			29451	protein-coding gene	gene with protein product	"""killer-specific secretory protein of 37 kDa"""	607713				11342666, 12322897	Standard	NM_031950		Approved	KSP37	uc003gon.3	Q9BYJ0	OTTHUMG00000128513	ENST00000259989.6:c.268C>T	4.37:g.15964485G>A	ENSP00000259989:p.Pro90Ser	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	9	5	0.555556	NM_031950		Missense_Mutation	SNP	ENST00000259989.6	37	CCDS3419.1	915	0.41895604395604397	121	0.2459349593495935	112	0.30939226519337015	307	0.5367132867132867	375	0.4947229551451187	G	0.169	-1.073128	0.01918	0.242397	0.461977	ENSG00000137441	ENST00000259989	T	0.12672	2.66	2.98	1.08	0.20341	.	0.651924	0.13462	U	0.386030	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.25441	0.126	B	0.22880	0.042	T	0.37009	-0.9724	9	0.21014	T	0.42	0.3963	5.9323	0.19146	0.0:0.1584:0.3635:0.4782	rs758329;rs17709603;rs758329	90	Q9BYJ0	FGFP2_HUMAN	S	90	ENSP00000259989:P90S	ENSP00000259989:P90S	P	-	1	0	FGFBP2	15573583	0.917000	0.31117	0.160000	0.22671	0.187000	0.23431	0.703000	0.25646	-0.187000	0.10516	-1.067000	0.02272	CCT	G|0.606;A|0.394	0.394	strong		0.632	FGFBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250324.1	NM_031950	
CABP5	56344	hgsc.bcm.edu	37	19	48543923	48543923	+	Silent	SNP	C	C	A	rs12982629	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48543923C>A	ENST00000293255.2	-	3	307	c.177G>T	c.(175-177)acG>acT	p.T59T		NM_019855.4	NP_062829.1	Q9NP86	CABP5_HUMAN	calcium binding protein 5	59	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				signal transduction (GO:0007165)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	11		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		TGTAACCCATCGTCCTCATGA	0.522													c|||	710	0.141773	0.0825	0.2248	5008	,	,		19329	0.0099		0.2724	False		,,,				2504	0.1646				p.T59T		Atlas-SNP	.											.	CABP5	28	.	0			c.G177T						PASS	.	C		548,3858	247.5+/-255.7	31,486,1686	123.0	101.0	108.0		177	-8.8	0.2	19	dbSNP_121	108	2440,6160	404.0+/-348.0	353,1734,2213	no	coding-synonymous	CABP5	NM_019855.4		384,2220,3899	AA,AC,CC		28.3721,12.4376,22.974		59/174	48543923	2988,10018	2203	4300	6503	SO:0001819	synonymous_variant	56344	exon3			ACCCATCGTCCTC	AF169159	CCDS12709.1	19q13.33	2014-08-12			ENSG00000105507	ENSG00000105507		"""EF-hand domain containing"""	13714	protein-coding gene	gene with protein product		607315	"""calcium binding protein 3"""	CABP3		10625670	Standard	NM_019855		Approved	CaBP3	uc002phu.2	Q9NP86	OTTHUMG00000183139	ENST00000293255.2:c.177G>T	19.37:g.48543923C>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_019855	A0AUY4	Silent	SNP	ENST00000293255.2	37	CCDS12709.1																																																																																			C|0.798;A|0.202	0.202	strong		0.522	CABP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465212.1	NM_019855	
CNGB1	1258	hgsc.bcm.edu	37	16	57950057	57950057	+	Silent	SNP	G	G	A	rs376270	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57950057G>A	ENST00000251102.8	-	22	2253	c.2193C>T	c.(2191-2193)aaC>aaT	p.N731N	CNGB1_ENST00000564448.1_Silent_p.N725N	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	731			N -> K (in dbSNP:rs376270).		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						ACTTCAGGTAGTTATTTCGCA	0.522													G|||	1813	0.362021	0.1808	0.3372	5008	,	,		19169	0.5486		0.3191	False		,,,				2504	0.4765				p.N731N	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.C2193T						PASS	.	G		722,3178		56,610,1284	135.0	133.0	134.0		2193	-0.2	0.7	16	dbSNP_80	134	2856,5418		495,1866,1776	no	coding-synonymous	CNGB1	NM_001297.4		551,2476,3060	AA,AG,GG		34.5178,18.5128,29.3905		731/1252	57950057	3578,8596	1950	4137	6087	SO:0001819	synonymous_variant	1258	exon22			CAGGTAGTTATTT	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.2193C>T	16.37:g.57950057G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																			A|0.342;C|0.004;G|0.647;N|0.000;T|0.007	0.342	strong		0.522	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
DZANK1	55184	hgsc.bcm.edu	37	20	18445963	18445963	+	Silent	SNP	A	A	G	rs6035051	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:18445963A>G	ENST00000358866.6	-	1	62	c.40T>C	c.(40-42)Tta>Cta	p.L14L	DZANK1_ENST00000262547.5_Silent_p.L14L|POLR3F_ENST00000377603.4_5'Flank|DZANK1_ENST00000329494.5_Silent_p.L14L|DZANK1_ENST00000357236.4_5'UTR			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	14							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						GGCACTCGTAATGGTATGATC	0.353													G|||	2893	0.577676	0.6157	0.572	5008	,	,		15653	0.6101		0.5567	False		,,,				2504	0.5184				p.L14L		Atlas-SNP	.											DZANK1,caecum,carcinoma,+1,1	DZANK1	65	1	0			c.T40C						PASS	.	G		2283,1531		693,897,317	97.0	89.0	92.0		40	2.1	1.0	20	dbSNP_114	92	4686,3560		1323,2040,760	no	coding-synonymous	DZANK1	NM_001099407.1		2016,2937,1077	GG,GA,AA		43.1724,40.1416,42.2139		14/753	18445963	6969,5091	1907	4123	6030	SO:0001819	synonymous_variant	55184	exon2			CTCGTAATGGTAT	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"""Ankyrin repeat domain containing"""	15858	protein-coding gene	gene with protein product	"""ankyrin repeat domain 64"""		"""chromosome 20 open reading frame 12"""	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.40T>C	20.37:g.18445963A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Silent	SNP	ENST00000358866.6	37	CCDS46582.1																																																																																			A|0.419;G|0.581	0.581	strong		0.353	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407	
BTN3A1	11119	hgsc.bcm.edu	37	6	26405835	26405835	+	Missense_Mutation	SNP	G	G	A	rs56161420	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26405835G>A	ENST00000289361.6	+	2	412	c.44G>A	c.(43-45)cGt>cAt	p.R15H	BTN3A1_ENST00000414912.2_Missense_Mutation_p.R15H|BTN3A1_ENST00000476549.2_Missense_Mutation_p.R15H|BTN3A1_ENST00000425234.2_Missense_Mutation_p.R15H	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	15			R -> H (in dbSNP:rs56161420). {ECO:0000269|PubMed:14702039}.		activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						CTCAACTTTCGTGTCTGCCTC	0.473													G|||	720	0.14377	0.1619	0.1643	5008	,	,		20713	0.0308		0.165	False		,,,				2504	0.1994				p.R15H		Atlas-SNP	.											BTN3A1_ENST00000476549,NS,carcinoma,0,4	BTN3A1	80	4	0			c.G44A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	787,3619		66,655,1482	241.0	185.0	204.0		44,44,44,44	-3.2	0.0	6	dbSNP_129	204	1477,7123		126,1225,2949	yes	missense,missense,missense,missense	BTN3A1	NM_001145008.1,NM_001145009.1,NM_007048.5,NM_194441.2	29,29,29,29	192,1880,4431	AA,AG,GG		17.1744,17.862,17.4074	benign,benign,benign,benign	15/462,15/379,15/514,15/353	26405835	2264,10742	2203	4300	6503	SO:0001583	missense	11119	exon2			ACTTTCGTGTCTG	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.44G>A	6.37:g.26405835G>A	ENSP00000289361:p.Arg15His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	155	36	0.232258	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	37	CCDS4608.1	291	0.13324175824175824	94	0.1910569105691057	60	0.16574585635359115	12	0.02097902097902098	125	0.16490765171503957	.	4.425	0.078648	0.08533	0.17862	0.171744	ENSG00000026950	ENST00000476549;ENST00000289361;ENST00000450085;ENST00000425234;ENST00000427334;ENST00000506698;ENST00000414912	T;T;T;T;T;T;T	0.46451	3.98;1.21;3.42;3.96;0.95;2.55;0.87	1.58	-3.16	0.05217	.	.	.	.	.	T	0.03011	0.0089	N	0.00621	-1.32	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.36841	-0.9731	8	0.39692	T	0.17	.	2.4136	0.04430	0.2889:0.0:0.2541:0.457	rs56161420	15;15;15;15	E9PGB4;O00481-3;O00481-2;O00481	.;.;.;BT3A1_HUMAN	H	15	ENSP00000420010:R15H;ENSP00000289361:R15H;ENSP00000394937:R15H;ENSP00000396684:R15H;ENSP00000399393:R15H;ENSP00000427013:R15H;ENSP00000406667:R15H	ENSP00000289361:R15H	R	+	2	0	BTN3A1	26513814	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.000000	0.12993	-0.905000	0.03871	-1.935000	0.00506	CGT	G|0.835;A|0.165	0.165	strong		0.473	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3		
FKBP15	23307	hgsc.bcm.edu	37	9	115968797	115968797	+	Missense_Mutation	SNP	C	C	T	rs1133618	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:115968797C>T	ENST00000238256.3	-	4	433	c.316G>A	c.(316-318)Gcc>Acc	p.A106T	FKBP15_ENST00000493847.1_5'UTR	NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	106	Important for function in growth cone organization. {ECO:0000250}.		A -> T (in dbSNP:rs1133618).		endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						ACCTCTCTGGCTGTGTGGTTC	0.423													C|||	952	0.190096	0.3298	0.2161	5008	,	,		17470	0.0228		0.2078	False		,,,				2504	0.137				p.A106T		Atlas-SNP	.											.	FKBP15	128	.	0			c.G316A						PASS	.	C	THR/ALA	1052,2738		152,748,995	116.0	112.0	113.0		316	2.8	1.0	9	dbSNP_86	113	1576,6668		170,1236,2716	yes	missense	FKBP15	NM_015258.1	58	322,1984,3711	TT,TC,CC		19.1169,27.7573,21.8381	benign	106/1220	115968797	2628,9406	1895	4122	6017	SO:0001583	missense	23307	exon4			CTCTGGCTGTGTG	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.316G>A	9.37:g.115968797C>T	ENSP00000238256:p.Ala106Thr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	403	0.18452380952380953	150	0.3048780487804878	76	0.20994475138121546	13	0.022727272727272728	164	0.21635883905013192	C	5.870	0.344614	0.11126	0.277573	0.191169	ENSG00000119321	ENST00000446284;ENST00000238256;ENST00000414250	T;T;T	0.42513	0.97;0.97;0.97	5.71	2.84	0.33178	.	.	.	.	.	T	0.00012	0.0000	N	0.11789	0.175	0.41464	P	0.011938000000000004	B;B;B	0.12630	0.006;0.002;0.004	B;B;B	0.16289	0.015;0.003;0.007	T	0.40232	-0.9574	8	0.10377	T	0.69	-1.6684	6.3222	0.21225	0.1488:0.6889:0.0:0.1623	rs1133618;rs3195502;rs11558693;rs52819213;rs56950186;rs1133618	106;106;106	Q5T1M5-2;Q5T1M5-3;Q5T1M5	.;.;FKB15_HUMAN	T	131;106;131	ENSP00000416158:A131T;ENSP00000238256:A106T;ENSP00000415733:A131T	ENSP00000238256:A106T	A	-	1	0	FKBP15	115008618	0.899000	0.30636	0.999000	0.59377	0.993000	0.82548	1.143000	0.31553	0.329000	0.23460	0.563000	0.77884	GCC	C|0.805;T|0.195	0.195	strong		0.423	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
COMMD5	28991	hgsc.bcm.edu	37	8	146076708	146076708	+	Missense_Mutation	SNP	C	C	T	rs1209879	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:146076708C>T	ENST00000305103.3	-	2	268	c.16G>A	c.(16-18)Gct>Act	p.A6T	ZNF250_ENST00000543949.1_3'UTR|AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000402718.3_Missense_Mutation_p.A6T|COMMD5_ENST00000450361.2_Missense_Mutation_p.A6T	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	6			A -> T (in dbSNP:rs1209879). {ECO:0000269|PubMed:10931946}.			nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			GGAGTTGCAGCCCCCACAGCA	0.592													C|||	1344	0.268371	0.0446	0.232	5008	,	,		19951	0.3254		0.3419	False		,,,				2504	0.4622				p.A6T		Atlas-SNP	.											.	COMMD5	18	.	0			c.G16A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	447,3959	212.8+/-232.6	26,395,1782	64.0	67.0	66.0		16,16,16	1.5	0.0	8	dbSNP_87	66	3126,5474	464.3+/-366.2	524,2078,1698	yes	missense,missense,missense	COMMD5	NM_001081003.1,NM_001081004.1,NM_014066.3	58,58,58	550,2473,3480	TT,TC,CC		36.3488,10.1453,27.4719	benign,benign,benign	6/225,6/225,6/225	146076708	3573,9433	2203	4300	6503	SO:0001583	missense	28991	exon2			TTGCAGCCCCCAC	AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.16G>A	8.37:g.146076708C>T	ENSP00000304544:p.Ala6Thr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	NM_001081004	D3DWN7|Q9NVN6|Q9UHX5	Missense_Mutation	SNP	ENST00000305103.3	37	CCDS6436.1	531	0.24313186813186813	26	0.052845528455284556	93	0.2569060773480663	148	0.25874125874125875	264	0.3482849604221636	C	9.609	1.130698	0.21041	0.101453	0.363488	ENSG00000170619	ENST00000402718;ENST00000450361;ENST00000305103;ENST00000529143;ENST00000533270	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	4.48	1.48	0.22813	.	1.416370	0.04663	N	0.409266	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	1.0000000000287557E-6	B	0.24186	0.099	B	0.19391	0.025	T	0.41770	-0.9490	9	0.18276	T	0.48	3.0506	7.9519	0.30019	0.1709:0.4976:0.3316:0.0	rs1209879;rs1622745;rs3199266;rs17816149;rs52798652;rs58731279;rs1209879	6	Q9GZQ3	COMD5_HUMAN	T	6	ENSP00000385793:A6T;ENSP00000394331:A6T;ENSP00000304544:A6T;ENSP00000435552:A6T;ENSP00000433758:A6T	ENSP00000304544:A6T	A	-	1	0	COMMD5	146047512	0.003000	0.15002	0.001000	0.08648	0.300000	0.27592	-0.806000	0.04525	0.062000	0.16340	0.557000	0.71058	GCT	T|0.254;G|0.001	0.254	strong		0.592	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066	
METTL12	751071	hgsc.bcm.edu	37	11	62434173	62434173	+	Missense_Mutation	SNP	G	G	A	rs11231181	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:62434173G>A	ENST00000532971.1	+	3	630	c.373G>A	c.(373-375)Ggc>Agc	p.G125S	SNORA57_ENST00000383870.1_RNA|RP11-831H9.11_ENST00000528405.1_5'Flank|C11orf48_ENST00000525675.1_5'Flank|C11orf48_ENST00000532208.1_Intron|METTL12_ENST00000398922.2_3'UTR|C11orf48_ENST00000524958.1_5'Flank|C11orf48_ENST00000354588.3_Intron|C11orf48_ENST00000431002.2_Intron	NM_001043229.1	NP_001036694.1	A8MUP2	MET12_HUMAN	methyltransferase like 12	125			G -> S (in dbSNP:rs11231181).			mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	6						GGGTGGCCCAGGCCAAACACC	0.592													G|||	748	0.149361	0.0756	0.2161	5008	,	,		17989	0.0526		0.2604	False		,,,				2504	0.1871				p.G125S		Atlas-SNP	.											.	METTL12	11	.	0			c.G373A						PASS	.	G	SER/GLY,	467,3523		31,405,1559	42.0	46.0	45.0		373,	1.7	0.2	11	dbSNP_120	45	2405,5925		366,1673,2126	yes	missense,intron	C11orf48,METTL12	NM_001043229.1,NM_024099.3	56,	397,2078,3685	AA,AG,GG		28.8715,11.7043,23.3117	benign,	125/241,	62434173	2872,9448	1995	4165	6160	SO:0001583	missense	751071	exon3			GGCCCAGGCCAAA	BC041359	CCDS41657.1	11q12.3	2013-09-30			ENSG00000214756	ENSG00000214756			33113	protein-coding gene	gene with protein product							Standard	NM_001043229		Approved	U99HG	uc001nuh.3	A8MUP2	OTTHUMG00000167545	ENST00000532971.1:c.373G>A	11.37:g.62434173G>A	ENSP00000431287:p.Gly125Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_001043229	B7Z4C1	Missense_Mutation	SNP	ENST00000532971.1	37	CCDS41657.1	371	0.16987179487179488	41	0.08333333333333333	95	0.26243093922651933	36	0.06293706293706294	199	0.262532981530343	G	9.658	1.143349	0.21205	0.117043	0.288715	ENSG00000214756	ENST00000532971	T	0.42513	0.97	4.87	1.72	0.24424	Methyltransferase type 11 (1);	1.077670	0.07388	U	0.888510	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.13145	0.007	B	0.15052	0.012	T	0.34179	-0.9839	9	0.38643	T	0.18	-25.8093	3.6963	0.08365	0.2209:0.0:0.5822:0.1969	rs11231181;rs11231181	125	A8MUP2	MTL12_HUMAN	S	125	ENSP00000431287:G125S	ENSP00000431287:G125S	G	+	1	0	METTL12	62190749	0.001000	0.12720	0.161000	0.22692	0.358000	0.29455	0.978000	0.29488	0.258000	0.21686	-0.355000	0.07637	GGC	G|0.803;A|0.197	0.197	strong		0.592	METTL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394990.1	NM_001043229	
NDC80	10403	hgsc.bcm.edu	37	18	2616457	2616457	+	Missense_Mutation	SNP	G	G	C	rs9051	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:2616457G>C	ENST00000261597.4	+	17	1995	c.1813G>C	c.(1813-1815)Gct>Cct	p.A605P		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	605	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.		A -> P (in dbSNP:rs1983346).		attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GGAGCAGATTGCTAAAGTTGA	0.259													G|||	919	0.183506	0.1241	0.1354	5008	,	,		16739	0.125		0.2286	False		,,,				2504	0.3119				p.A605P		Atlas-SNP	.											.	NDC80	62	.	0			c.G1813C						PASS	.	G	PRO/ALA	664,3738	254.6+/-260.1	53,558,1590	44.0	47.0	46.0		1813	1.3	1.0	18	dbSNP_92	46	2000,6572	333.7+/-320.7	235,1530,2521	yes	missense	NDC80	NM_006101.2	27	288,2088,4111	CC,CG,GG		23.3318,15.0841,20.5334	benign	605/643	2616457	2664,10310	2201	4286	6487	SO:0001583	missense	10403	exon17			CAGATTGCTAAAG	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1813G>C	18.37:g.2616457G>C	ENSP00000261597:p.Ala605Pro	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	169	84	0.497041	NM_006101	Q6PJX2	Missense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	383	0.17536630036630035	66	0.13414634146341464	61	0.1685082872928177	70	0.12237762237762238	186	0.24538258575197888	G	9.867	1.197860	0.22037	0.150841	0.233318	ENSG00000080986	ENST00000261597	T	0.48522	0.81	5.32	1.29	0.21616	.	1.211720	0.05314	N	0.525294	T	0.00012	0.0000	N	0.08118	0	0.49051	P	2.550000000000052E-4	B	0.26876	0.162	B	0.25614	0.062	T	0.20472	-1.0274	9	0.31617	T	0.26	-0.0998	5.5394	0.17030	0.24:0.247:0.513:0.0	rs9051	605	O14777	NDC80_HUMAN	P	605	ENSP00000261597:A605P	ENSP00000261597:A605P	A	+	1	0	NDC80	2606457	0.018000	0.18449	0.985000	0.45067	0.503000	0.33858	-0.152000	0.10159	0.332000	0.23536	0.555000	0.69702	GCT	G|0.806;C|0.194	0.194	strong		0.259	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
MARVELD3	91862	hgsc.bcm.edu	37	16	71660310	71660310	+	Missense_Mutation	SNP	G	G	A	rs4788821	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:71660310G>A	ENST00000268485.3	+	1	222	c.178G>A	c.(178-180)Gag>Aag	p.E60K	RP11-432I5.2_ENST00000562763.1_RNA|MARVELD3_ENST00000565261.1_Missense_Mutation_p.E60K|MARVELD3_ENST00000299952.4_Missense_Mutation_p.E60K|MARVELD3_ENST00000567566.1_Missense_Mutation_p.E60K|MARVELD3_ENST00000567501.1_5'Flank	NM_052858.4	NP_443090.4	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	60	Arg-rich.		E -> K (in dbSNP:rs4788821). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				CCGGGACCCGGAGAGAGACCA	0.731													G|||	2072	0.413738	0.2451	0.5231	5008	,	,		11452	0.7421		0.325	False		,,,				2504	0.317				p.E60K		Atlas-SNP	.											.	MARVELD3	63	.	0			c.G178A						PASS	.	G	LYS/GLU,LYS/GLU	875,2933		104,667,1133	33.0	51.0	45.0		178,178	1.2	0.0	16	dbSNP_111	45	2199,5223		322,1555,1834	yes	missense,missense	MARVELD3	NM_052858.3,NM_001017967.2	56,56	426,2222,2967	AA,AG,GG		29.6281,22.9779,27.3731	benign,benign	60/402,60/411	71660310	3074,8156	1904	3711	5615	SO:0001583	missense	91862	exon1			GACCCGGAGAGAG	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"""MARVEL (membrane-associating) domain containing 3"""	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000268485.3:c.178G>A	16.37:g.71660310G>A	ENSP00000268485:p.Glu60Lys	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_001017967	A8K820|H3BQM5|Q96MJ4	Missense_Mutation	SNP	ENST00000268485.3	37	CCDS10904.1	936	0.42857142857142855	120	0.24390243902439024	164	0.4530386740331492	414	0.7237762237762237	238	0.31398416886543534	G	12.99	2.104181	0.37145	0.229779	0.296281	ENSG00000140832	ENST00000268485;ENST00000299952	T;T	0.56444	0.46;0.46	2.15	1.17	0.20885	.	3.055740	0.01243	U	0.008678	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.9999999999985243	B;B	0.30889	0.159;0.299	B;B	0.17098	0.017;0.017	T	0.43605	-0.9381	9	0.18276	T	0.48	.	6.0428	0.19744	0.1747:0.0:0.8253:0.0	rs4788821;rs17262334;rs17845037;rs17856380;rs17856423;rs17857810;rs52819161;rs59320056;rs4788821	60;60	Q96A59-2;Q96A59	.;MALD3_HUMAN	K	60	ENSP00000268485:E60K;ENSP00000299952:E60K	ENSP00000268485:E60K	E	+	1	0	MARVELD3	70217811	0.017000	0.18338	0.002000	0.10522	0.013000	0.08279	1.980000	0.40618	0.129000	0.18514	0.298000	0.19748	GAG	G|0.561;A|0.439	0.439	strong		0.731	MARVELD3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268991.2	NM_052858	
PAPL	390928	hgsc.bcm.edu	37	19	39589189	39589189	+	Silent	SNP	C	C	T	rs55878600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39589189C>T	ENST00000331256.5	+	3	487	c.213C>T	c.(211-213)ccC>ccT	p.P71P	PAPL_ENST00000594229.1_Silent_p.P71P	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		71						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										GGCCCCTGCCCCTCCGCGCCC	0.647													c|||	1149	0.229433	0.0348	0.2709	5008	,	,		13054	0.4077		0.2306	False		,,,				2504	0.2781				p.P71P		Atlas-SNP	.											.	.	.	.	0			c.C213T						PASS	.	C		372,4034	187.4+/-214.1	14,344,1845	36.0	34.0	35.0		213	-0.2	0.3	19	dbSNP_129	35	2109,6491	351.2+/-328.2	258,1593,2449	no	coding-synonymous	PAPL	NM_001004318.2		272,1937,4294	TT,TC,CC		24.5233,8.443,19.0758		71/439	39589189	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			CCTGCCCCTCCGC																												ENST00000331256.5:c.213C>T	19.37:g.39589189C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	12	0.428571	NM_001004318	B2RN68	Silent	SNP	ENST00000331256.5	37	CCDS33018.1																																																																																			C|0.796;T|0.204	0.204	strong		0.647	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
CEL	1056	hgsc.bcm.edu	37	9	135947034	135947034	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135947034G>C	ENST00000372080.4	+	11	2170	c.2154G>C	c.(2152-2154)ccG>ccC	p.P718P	CEL_ENST00000351304.7_Silent_p.P649P	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	715	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				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)		CCCCCGTGCCGCCCACGGGTG	0.761																																					p.P718P		Atlas-SNP	.											CEL,NS,carcinoma,+2,2	CEL	71	2	0			c.G2154C						scavenged	.						7.0	9.0	8.0					9																	135947034		1675	3862	5537	SO:0001819	synonymous_variant	1056	exon11			CGTGCCGCCCACG	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.2154G>C	9.37:g.135947034G>C		Somatic	27	3	0.111111		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Silent	SNP	ENST00000372080.4	37	CCDS43896.1																																																																																			.	.	none		0.761	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
KCNS3	3790	hgsc.bcm.edu	37	2	18113508	18113508	+	Silent	SNP	G	G	A	rs3747516	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:18113508G>A	ENST00000403915.1	+	3	1684	c.1233G>A	c.(1231-1233)aaG>aaA	p.K411K	KCNS3_ENST00000304101.4_Silent_p.K411K|KCNS3_ENST00000465292.1_Intron	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	411					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AGTTTTCCAAGTACTACCAGA	0.478													G|||	1788	0.357029	0.3343	0.3833	5008	,	,		24317	0.4702		0.164	False		,,,				2504	0.4509				p.K411K		Atlas-SNP	.											.	KCNS3	85	.	0			c.G1233A						PASS	.	G		1266,3140	433.3+/-343.5	188,890,1125	191.0	169.0	176.0		1233	4.1	1.0	2	dbSNP_107	176	1359,7241	266.1+/-286.5	91,1177,3032	no	coding-synonymous	KCNS3	NM_002252.3		279,2067,4157	AA,AG,GG		15.8023,28.7335,20.183		411/492	18113508	2625,10381	2203	4300	6503	SO:0001819	synonymous_variant	3790	exon3			TTCCAAGTACTAC	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.1233G>A	2.37:g.18113508G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	40	0.425532	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Silent	SNP	ENST00000403915.1	37	CCDS1692.1																																																																																			G|0.744;A|0.256	0.256	strong		0.478	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252	
OR1S1	219959	hgsc.bcm.edu	37	11	57982896	57982896	+	Missense_Mutation	SNP	G	G	T	rs2903566	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57982896G>T	ENST00000309433.6	+	1	680	c.680G>T	c.(679-681)aGc>aTc	p.S227I		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	227			S -> I (in dbSNP:rs2903566).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTTACACTCAGCTTCTTTTCC	0.448													T|||	2616	0.522364	0.2814	0.5418	5008	,	,		21979	0.8036		0.4225	False		,,,				2504	0.6472				p.S227I		Atlas-SNP	.											.	OR1S1	139	.	0			c.G680T						PASS	.	T	ILE/SER	1299,3103	697.4+/-406.2	195,909,1097	157.0	124.0	135.0		680	2.1	0.1	11	dbSNP_101	135	3641,4949	623.4+/-397.5	784,2073,1438	yes	missense	OR1S1	NM_001004458.1	142	979,2982,2535	TT,TG,GG		42.3865,29.5093,38.0234	benign	227/326	57982896	4940,8052	2201	4295	6496	SO:0001583	missense	219959	exon1			CACTCAGCTTCTT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.680G>T	11.37:g.57982896G>T	ENSP00000311688:p.Ser227Ile	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1080	0.4945054945054945	146	0.2967479674796748	186	0.5138121546961326	433	0.756993006993007	315	0.4155672823218997	T	0.003	-2.561584	0.00136	0.295093	0.423865	ENSG00000172774	ENST00000309433	T	0.00010	9.43	3.23	2.08	0.27032	GPCR, rhodopsin-like superfamily (1);	0.128568	0.34828	N	0.003657	T	0.00012	0.0000	N	0.00008	-3.13	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46569	-0.9182	9	0.02654	T	1	.	4.0934	0.09980	0.0:0.3043:0.1798:0.516	rs2903566;rs17463613;rs52823244;rs2903566	227	Q8NH92	OR1S1_HUMAN	I	227	ENSP00000311688:S227I	ENSP00000311688:S227I	S	+	2	0	OR1S1	57739472	0.027000	0.19231	0.078000	0.20375	0.442000	0.32017	1.851000	0.39338	-0.026000	0.13895	-0.527000	0.04329	AGC	G|0.565;T|0.435	0.435	strong		0.448	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
KLK3	354	hgsc.bcm.edu	37	19	51361315	51361315	+	Silent	SNP	C	C	T	rs12946	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51361315C>T	ENST00000326003.2	+	3	278	c.237C>T	c.(235-237)agC>agT	p.S79S	KLK3_ENST00000595952.1_Intron|KLK3_ENST00000593997.1_Silent_p.S79S|KLK3_ENST00000360617.3_Silent_p.S79S|KLK3_ENST00000597483.1_Intron	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		GTCGGCACAGCCTGTTTCATC	0.542													C|||	438	0.0874601	0.0764	0.1009	5008	,	,		21521	0.0685		0.1272	False		,,,				2504	0.0716				p.S79S	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.C237T						PASS	.	C	,,	371,4035	187.4+/-214.1	14,343,1846	69.0	59.0	62.0		237,,237	2.3	0.0	19	dbSNP_52	62	1085,7515	225.9+/-261.8	64,957,3279	yes	coding-synonymous,intron,coding-synonymous	KLK3	NM_001030047.1,NM_001030048.1,NM_001648.2	,,	78,1300,5125	TT,TC,CC		12.6163,8.4203,11.1948	,,	79/239,,79/262	51361315	1456,11550	2203	4300	6503	SO:0001819	synonymous_variant	354	exon3			GCACAGCCTGTTT	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.237C>T	19.37:g.51361315C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_001030047	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			C|0.890;T|0.110	0.110	strong		0.542	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
SPATA17	128153	hgsc.bcm.edu	37	1	217915324	217915324	+	Silent	SNP	C	C	T	rs34347452	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:217915324C>T	ENST00000366933.4	+	6	458	c.403C>T	c.(403-405)Ctg>Ttg	p.L135L		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	135						cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		CAGGAAGGCACTGGAGGAGTT	0.383													C|||	632	0.126198	0.0817	0.0951	5008	,	,		21411	0.1419		0.174	False		,,,				2504	0.1431				p.L135L		Atlas-SNP	.											.	SPATA17	59	.	0			c.C403T						PASS	.	C		464,3942	220.4+/-237.8	18,428,1757	99.0	93.0	95.0		403	2.8	0.7	1	dbSNP_126	95	1306,7294	258.1+/-281.9	109,1088,3103	no	coding-synonymous	SPATA17	NM_138796.2		127,1516,4860	TT,TC,CC		15.186,10.5311,13.6091		135/362	217915324	1770,11236	2203	4300	6503	SO:0001819	synonymous_variant	128153	exon6			AAGGCACTGGAGG	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"""IQ motif containing H"""	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.403C>T	1.37:g.217915324C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			C|0.870;T|0.130	0.130	strong		0.383	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
MEP1B	4225	hgsc.bcm.edu	37	18	29797921	29797921	+	Missense_Mutation	SNP	C	C	T	rs616114	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:29797921C>T	ENST00000269202.6	+	14	2131	c.2084C>T	c.(2083-2085)cCg>cTg	p.P695L	MEP1B_ENST00000581447.1_Missense_Mutation_p.P695L	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	695			P -> L (in dbSNP:rs616114). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9288916}.		digestion (GO:0007586)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						AATTTGACTCCGCAAAATGTA	0.393													C|||	1782	0.355831	0.4251	0.2882	5008	,	,		22256	0.255		0.3648	False		,,,				2504	0.4049				p.P695L		Atlas-SNP	.											.	MEP1B	54	.	0			c.C2084T	GRCh37	CM065309	MEP1B	M	rs616114	PASS	.	C	LEU/PRO	1534,2324		321,892,716	103.0	101.0	101.0		2084	0.4	0.0	18	dbSNP_83	101	3220,5040		638,1944,1548	yes	missense	MEP1B	NM_005925.2	98	959,2836,2264	TT,TC,CC		38.9831,39.7615,39.2309	benign	695/702	29797921	4754,7364	1929	4130	6059	SO:0001583	missense	4225	exon14			TGACTCCGCAAAA	X81333	CCDS45846.1	18q12.2-q12.3	2003-12-17				ENSG00000141434	3.4.24.18		7020	protein-coding gene	gene with protein product		600389				7774936	Standard	NM_005925		Approved		uc002kxj.4	Q16820		ENST00000269202.6:c.2084C>T	18.37:g.29797921C>T	ENSP00000269202:p.Pro695Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	778	0.35622710622710624	225	0.4573170731707317	109	0.3011049723756906	160	0.27972027972027974	284	0.37467018469656993	C	0.016	-1.529447	0.00951	0.397615	0.389831	ENSG00000141434	ENST00000269202	T	0.17854	2.25	5.68	0.414	0.16406	.	2.205680	0.01512	N	0.017988	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45512	-0.9256	9	0.02654	T	1	5.6145	9.8349	0.40963	0.0:0.3279:0.0:0.6721	rs616114;rs17663247;rs616114	695	Q16820	MEP1B_HUMAN	L	695	ENSP00000269202:P695L	ENSP00000269202:P695L	P	+	2	0	MEP1B	28051919	0.005000	0.15991	0.004000	0.12327	0.028000	0.11728	0.916000	0.28651	-0.149000	0.11215	-0.600000	0.04104	CCG	C|0.631;T|0.368	0.368	strong		0.393	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925	
ALMS1	7840	hgsc.bcm.edu	37	2	73651967	73651967	+	Missense_Mutation	SNP	C	C	T	rs3813227	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73651967C>T	ENST00000264448.6	+	5	1285	c.1174C>T	c.(1174-1176)Cgt>Tgt	p.R392C	ALMS1_ENST00000409009.1_Missense_Mutation_p.R350C|ALMS1_ENST00000377715.1_Missense_Mutation_p.R392C	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	392					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						TGATGCTGCTCGTTCATATGG	0.358													T|||	1821	0.363618	0.8782	0.3919	5008	,	,		21829	0.0089		0.2266	False		,,,				2504	0.1544				p.R392C		Atlas-SNP	.											.	ALMS1	384	.	0			c.C1174T						PASS	.	T	CYS/ARG	2778,990		1038,702,144	78.0	73.0	75.0		1174	0.2	0.0	2	dbSNP_107	75	1953,6271		220,1513,2379	yes	missense	ALMS1	NM_015120.4	180	1258,2215,2523	TT,TC,CC		23.7476,26.2739,39.4513	benign	392/4168	73651967	4731,7261	1884	4112	5996	SO:0001583	missense	7840	exon5			GCTGCTCGTTCAT	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.1174C>T	2.37:g.73651967C>T	ENSP00000264448:p.Arg392Cys	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	130	80	0.615385	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	739	0.3383699633699634	427	0.8678861788617886	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	T	0.187	-1.056607	0.01965	0.737261	0.237476	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.16073	3.26;3.26;2.37	4.17	0.185	0.15096	.	0.550399	0.15361	N	0.266386	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28202	-1.0051	9	0.02654	T	1	.	1.7727	0.03015	0.1619:0.0947:0.335:0.4083	rs3813227;rs17349398;rs17848877;rs52832700;rs58256220;rs3813227	350;392	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	C	350;392;392	ENSP00000386627:R350C;ENSP00000264448:R392C;ENSP00000366944:R392C	ENSP00000264448:R392C	R	+	1	0	ALMS1	73505475	0.383000	0.25156	0.009000	0.14445	0.009000	0.06853	0.260000	0.18424	-0.200000	0.10300	-0.381000	0.06696	CGT	C|0.661;T|0.339	0.339	strong		0.358	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33572347	33572347	+	Missense_Mutation	SNP	T	T	C	rs7853994	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33572347T>C	ENST00000290943.6	+	16	3121	c.3025T>C	c.(3025-3027)Ttt>Ctt	p.F1009L		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	1009										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						TCCTATCTACTTTCTTCTCTA	0.323													.|||	972	0.194089	0.1679	0.2104	5008	,	,		16850	0.2103		0.2048	False		,,,				2504	0.1902				p.F1008L		Atlas-SNP	.											ANKRD18B,NS,carcinoma,0,1	ANKRD18B	46	1	0			c.T3022C						scavenged	.																																			SO:0001583	missense	441459	exon16			ATCTACTTTCTTC			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.3025T>C	9.37:g.33572347T>C	ENSP00000290943:p.Phe1009Leu	Somatic	159	1	0.00628931		WXS	Illumina HiSeq	Phase_I	210	110	0.52381	NM_001244752		Missense_Mutation	SNP	ENST00000290943.6	37		467	0.21382783882783882	102	0.2073170731707317	84	0.23204419889502761	125	0.21853146853146854	156	0.20580474934036938	T	11.80	1.746056	0.30955	.	.	ENSG00000230453	ENST00000290943	T	0.26223	1.75	1.46	-2.27	0.06846	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.30974	P	0.7227589999999999	.	.	.	.	.	.	T	0.40850	-0.9541	5	0.08837	T	0.75	.	5.3397	0.15976	0.0:0.3931:0.0:0.6069	rs7853994;rs17503365;rs52813410;rs7853994	.	.	.	L	1009	ENSP00000290943:F1009L	ENSP00000290943:F1009L	F	+	1	0	ANKRD18B	33562347	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.197000	0.09518	-0.749000	0.04747	0.248000	0.18094	TTT	T|0.791;C|0.209	0.209	strong		0.323	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
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 GAIIx	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		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	116	53	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	
RBBP6	5930	hgsc.bcm.edu	37	16	24583406	24583406	+	Silent	SNP	A	A	G	rs7593	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:24583406A>G	ENST00000319715.4	+	18	5451	c.5019A>G	c.(5017-5019)gcA>gcG	p.A1673A	RBBP6_ENST00000348022.2_Silent_p.A1639A|RBBP6_ENST00000381039.3_Silent_p.A833A	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1673					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		TGGAGAAAGCAAAAGAGAGCC	0.458													G|||	1559	0.311302	0.3464	0.3343	5008	,	,		18720	0.0893		0.4095	False		,,,				2504	0.3753				p.A1673A		Atlas-SNP	.											.	RBBP6	158	.	0			c.A5019G						PASS	.	G	,	1613,2781	658.3+/-400.4	291,1031,875	59.0	67.0	64.0		5019,4917	-4.5	0.9	16	dbSNP_52	64	3431,5169	632.8+/-398.7	689,2053,1558	no	coding-synonymous,coding-synonymous	RBBP6	NM_006910.4,NM_018703.3	,	980,3084,2433	GG,GA,AA		39.8953,36.7091,38.8179	,	1673/1793,1639/1759	24583406	5044,7950	2197	4300	6497	SO:0001819	synonymous_variant	5930	exon18			GAAAGCAAAAGAG		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.5019A>G	16.37:g.24583406A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	ENST00000319715.4	37	CCDS10621.1																																																																																			A|0.650;G|0.350	0.350	strong		0.458	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
WBSCR28	135886	hgsc.bcm.edu	37	7	73279361	73279361	+	Silent	SNP	C	C	T	rs61742124	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:73279361C>T	ENST00000320531.2	+	2	147	c.111C>T	c.(109-111)ctC>ctT	p.L37L		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	37						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				ATTTCCTGCTCCTCAAGATCA	0.582													C|||	1049	0.209465	0.3268	0.219	5008	,	,		16536	0.0784		0.2028	False		,,,				2504	0.1861				p.L37L		Atlas-SNP	.											.	WBSCR28	24	.	0			c.C111T						PASS	.	C		1004,2802		144,716,1043	263.0	271.0	269.0		111	-6.3	0.8	7	dbSNP_129	269	1622,6604		168,1286,2659	no	coding-synonymous	WBSCR28	NM_182504.3		312,2002,3702	TT,TC,CC		19.718,26.3794,21.8251		37/266	73279361	2626,9406	1903	4113	6016	SO:0001819	synonymous_variant	135886	exon2			CCTGCTCCTCAAG	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.111C>T	7.37:g.73279361C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_182504	Q6UE04|Q8NHP4	Silent	SNP	ENST00000320531.2	37	CCDS43597.1																																																																																			C|0.789;T|0.211	0.211	strong		0.582	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
LEPR	3953	hgsc.bcm.edu	37	1	66058513	66058513	+	Missense_Mutation	SNP	A	A	G	rs1137101	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:66058513A>G	ENST00000349533.6	+	6	853	c.668A>G	c.(667-669)cAg>cGg	p.Q223R	LEPR_ENST00000371060.3_Missense_Mutation_p.Q223R|LEPR_ENST00000462765.1_3'UTR|LEPR_ENST00000371059.3_Missense_Mutation_p.Q223R|LEPR_ENST00000344610.8_Missense_Mutation_p.Q223R|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000371058.1_Missense_Mutation_p.Q223R	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)		GTAATTTTCCAGTCACCTCTA	0.363													A|||	2926	0.584265	0.5923	0.4366	5008	,	,		18691	0.869		0.4692	False		,,,				2504	0.5031				p.Q223R		Atlas-SNP	.											.	LEPR	284	.	0			c.A668G	GRCh37	CM010905	LEPR	M	rs1137101	PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	2471,1935	623.5+/-394.1	694,1083,426	97.0	95.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	668,668,668,668,668,668	3.7	1.0	1	dbSNP_86	95	3906,4694	544.9+/-384.7	901,2104,1295	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	43,43,43,43,43,43	1595,3187,1721	GG,GA,AA		45.4186,43.9174,49.0312	benign,benign,benign,benign,benign,benign	223/897,223/959,223/959,223/907,223/897,223/1166	66058513	6377,6629	2203	4300	6503	SO:0001583	missense	3953	exon6			TTTTCCAGTCACC	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.668A>G	1.37:g.66058513A>G	ENSP00000330393:p.Gln223Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	118	45	0.381356	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	1287	0.5892857142857143	265	0.5386178861788617	153	0.42265193370165743	496	0.8671328671328671	373	0.4920844327176781	A	13.55	2.271131	0.40194	0.560826	0.454186	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.54675	0.57;0.56;0.58;0.56;0.57	5.96	3.66	0.41972	.	0.550372	0.19543	N	0.111741	T	0.20740	0.0499	L	0.42245	1.32	0.09310	P	0.999999999633346	B;B;P	0.44195	0.282;0.404;0.828	B;B;B	0.36845	0.081;0.109;0.234	T	0.03566	-1.1024	9	0.21540	T	0.41	-0.1619	9.2279	0.37418	0.7896:0.0:0.2104:0.0	rs1137101;rs1805093;rs2229418;rs3200842;rs9282885;rs12131454;rs17356624;rs52820808;rs59347832;rs1137101	223;223;223	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	R	223	ENSP00000340884:Q223R;ENSP00000330393:Q223R;ENSP00000360099:Q223R;ENSP00000360098:Q223R;ENSP00000360097:Q223R	ENSP00000340884:Q223R	Q	+	2	0	LEPR	65831101	1.000000	0.71417	0.999000	0.59377	0.899000	0.52679	2.850000	0.48294	0.513000	0.28278	0.528000	0.53228	CAG	A|0.463;G|0.537	0.537	strong		0.363	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
LAMA4	3910	hgsc.bcm.edu	37	6	112522852	112522852	+	Missense_Mutation	SNP	G	G	A	rs11757455	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:112522852G>A	ENST00000230538.7	-	5	857	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W	LAMA4_ENST00000389463.4_Missense_Mutation_p.R154W|LAMA4_ENST00000424408.2_Missense_Mutation_p.R154W|LAMA4_ENST00000522006.1_Missense_Mutation_p.R154W|LAMA4_ENST00000524032.1_5'UTR	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	154	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.		R -> W (in dbSNP:rs11757455).		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)		CAAATGCACCGAACAGCTCCA	0.368													G|||	155	0.0309505	0.0015	0.0303	5008	,	,		19937	0.0		0.0596	False		,,,				2504	0.0736				p.R154W		Atlas-SNP	.											.	LAMA4	227	.	0			c.C460T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	53,4353	54.2+/-90.2	0,53,2150	256.0	270.0	265.0		460,460,460	4.2	1.0	6	dbSNP_120	265	558,8042	152.2+/-206.8	18,522,3760	yes	missense,missense,missense	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	101,101,101	18,575,5910	AA,AG,GG		6.4884,1.2029,4.6978	probably-damaging,probably-damaging,probably-damaging	154/1824,154/1817,154/1817	112522852	611,12395	2203	4300	6503	SO:0001583	missense	3910	exon5			TGCACCGAACAGC		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.460C>T	6.37:g.112522852G>A	ENSP00000230538:p.Arg154Trp	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	63	0.028846153846153848	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	50	0.06596306068601583	G	21.8	4.197126	0.79015	0.012029	0.064884	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408;ENST00000454881;ENST00000521398;ENST00000542588;ENST00000368639	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06	6.07	4.2	0.49525	EGF-like, laminin (3);	0.000000	0.85682	D	0.000000	T	0.72566	0.3476	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71656	0.974;0.936	T	0.78309	-0.2254	10	0.87932	D	0	.	14.0564	0.64772	0.0:0.0:0.7267:0.2733	rs11757455;rs52801464;rs11757455	154;154	Q16363;Q16363-2	LAMA4_HUMAN;.	W	154	ENSP00000230538:R154W;ENSP00000429488:R154W;ENSP00000374114:R154W;ENSP00000416470:R154W;ENSP00000430336:R154W	ENSP00000230538:R154W	R	-	1	2	LAMA4	112629545	0.992000	0.36948	1.000000	0.80357	0.988000	0.76386	2.346000	0.44027	1.526000	0.49068	0.655000	0.94253	CGG	G|0.961;A|0.039	0.039	strong		0.368	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
STARD13	90627	hgsc.bcm.edu	37	13	33700374	33700374	+	Silent	SNP	T	T	G	rs1980781	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:33700374T>G	ENST00000336934.5	-	7	2042	c.1926A>C	c.(1924-1926)tcA>tcC	p.S642S	STARD13_ENST00000399365.3_Silent_p.S524S|STARD13_ENST00000255486.4_Silent_p.S634S	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	642					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		ACTTTGGAACTGACCTAGAAT	0.512													T|||	1229	0.245407	0.2042	0.3372	5008	,	,		19407	0.2123		0.2107	False		,,,				2504	0.3057				p.S642S		Atlas-SNP	.											.	STARD13	100	.	0			c.A1926C						PASS	.	T	,,	958,3448	361.6+/-315.8	93,772,1338	135.0	133.0	134.0		1572,1926,1902	-2.2	1.0	13	dbSNP_92	134	1865,6735	333.7+/-320.7	230,1405,2665	no	coding-synonymous,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	323,2177,4003	GG,GT,TT		21.686,21.7431,21.7054	,,	524/996,642/1114,634/1106	33700374	2823,10183	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon7			TGGAACTGACCTA	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.1926A>C	13.37:g.33700374T>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			T|0.780;G|0.220	0.220	strong		0.512	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
IGSF22	283284	hgsc.bcm.edu	37	11	18743180	18743180	+	Missense_Mutation	SNP	C	C	G	rs10832975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18743180C>G	ENST00000513874.1	-	4	419	c.280G>C	c.(280-282)Gcc>Ccc	p.A94P	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	94	Ig-like 1.		A -> P (in dbSNP:rs10832975).							NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TGGGGTTTGGCGTTCCCCTGC	0.587											OREG0020822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1803	0.360024	0.171	0.5187	5008	,	,		17972	0.3224		0.3897	False		,,,				2504	0.5112				p.A94P		Atlas-SNP	.											IGSF22_ENST00000513874,NS,carcinoma,0,2	IGSF22	211	2	0			c.G280C						scavenged	.	G	PRO/ALA	865,3119		102,661,1229	103.0	104.0	104.0		280	4.4	1.0	11	dbSNP_120	104	3270,5036		665,1940,1548	yes	missense	IGSF22	NM_173588.3	27	767,2601,2777	GG,GC,CC		39.3691,21.7118,33.6452	benign	94/1327	18743180	4135,8155	1992	4153	6145	SO:0001583	missense	283284	exon4			GTTTGGCGTTCCC	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.280G>C	11.37:g.18743180C>G	ENSP00000421191:p.Ala94Pro	Somatic	105	2	0.0190476	90	WXS	Illumina HiSeq	Phase_I	111	111	1	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	767	0.35119047619047616	92	0.18699186991869918	186	0.5138121546961326	179	0.3129370629370629	310	0.40897097625329815	G	7.324	0.617487	0.14129	0.217118	0.393691	ENSG00000179057	ENST00000513874	T	0.57907	0.37	5.33	4.39	0.52855	.	0.256726	0.20434	N	0.092411	T	0.00012	0.0000	N	0.00025	-2.68	0.52501	P	4.700000000001925E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.49303	-0.8954	9	0.02654	T	1	.	13.1751	0.59621	0.0:0.3071:0.6929:0.0	rs10832975;rs52802422;rs56874939;rs10832975	94	D6RGV7	.	P	94	ENSP00000421191:A94P	ENSP00000322422:A94P	A	-	1	0	IGSF22	18699756	1.000000	0.71417	0.995000	0.50966	0.868000	0.49771	5.417000	0.66423	0.606000	0.29965	-0.120000	0.15030	GCC	C|0.636;G|0.364	0.364	strong		0.587	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
EVA1A	84141	hgsc.bcm.edu	37	2	75720372	75720372	+	Missense_Mutation	SNP	C	C	T	rs11126472	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:75720372C>T	ENST00000233712.1	-	4	886	c.449G>A	c.(448-450)cGc>cAc	p.R150H	EVA1A_ENST00000490746.1_Intron|EVA1A_ENST00000393913.3_Missense_Mutation_p.R150H|EVA1A_ENST00000410071.1_Missense_Mutation_p.R150H|EVA1A_ENST00000410113.1_Missense_Mutation_p.R150H|EVA1A_ENST00000410010.1_Missense_Mutation_p.R138H	NM_032181.2	NP_115557.1	Q9H8M9	EVA1A_HUMAN	eva-1 homolog A (C. elegans)	150			R -> H (in dbSNP:rs11126472).		apoptotic process (GO:0006915)|autophagy (GO:0006914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|plasma membrane (GO:0005886)											CTAATAGTAGCGATTCAGGCT	0.637													C|||	221	0.0441294	0.0764	0.036	5008	,	,		16379	0.001		0.0547	False		,,,				2504	0.0399				p.R150H		Atlas-SNP	.											.	.	.	.	0			c.G449A						PASS	.	C	HIS/ARG,HIS/ARG	281,4111		9,263,1924	68.0	78.0	74.0		449,449	4.8	1.0	2	dbSNP_120	74	437,8141		12,413,3864	yes	missense,missense	FAM176A	NM_001135032.1,NM_032181.2	29,29	21,676,5788	TT,TC,CC		5.0944,6.398,5.5359	probably-damaging,probably-damaging	150/153,150/153	75720372	718,12252	2196	4289	6485	SO:0001583	missense	84141	exon4			TAGTAGCGATTCA	BC016157	CCDS1959.1	2p12	2012-11-05	2012-11-05	2012-11-05	ENSG00000115363	ENSG00000115363			25816	protein-coding gene	gene with protein product			"""transmembrane protein 166"", ""family with sequence similarity 176, member A"""	TMEM166, FAM176A		12477932	Standard	NM_001135032		Approved	FLJ13391	uc002sni.2	Q9H8M9	OTTHUMG00000129991	ENST00000233712.1:c.449G>A	2.37:g.75720372C>T	ENSP00000233712:p.Arg150His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	58	10	0.172414	NM_032181	D6W5J3|Q9HC41	Missense_Mutation	SNP	ENST00000233712.1	37	CCDS1959.1	87	0.03983516483516483	34	0.06910569105691057	14	0.03867403314917127	0	0.0	39	0.051451187335092345	C	26.4	4.732446	0.89482	0.06398	0.050944	ENSG00000115363	ENST00000393913;ENST00000233712;ENST00000410113;ENST00000410010;ENST00000410071	T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.68	4.79	4.79	0.61399	.	0.047760	0.85682	D	0.000000	T	0.15825	0.0381	M	0.78223	2.4	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.47761	-0.9092	10	0.41790	T	0.15	-6.97	16.1387	0.81509	0.0:1.0:0.0:0.0	rs11126472;rs52794573;rs59993973;rs11126472	150	Q9H8M9	F176A_HUMAN	H	150;150;150;138;150	ENSP00000377490:R150H;ENSP00000233712:R150H;ENSP00000386435:R150H;ENSP00000386835:R138H;ENSP00000386930:R150H	ENSP00000233712:R150H	R	-	2	0	FAM176A	75573880	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.663000	0.83820	2.573000	0.86826	0.655000	0.94253	CGC	C|0.948;T|0.052	0.052	strong		0.637	EVA1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328707.1	NM_032181	
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 GAIIx	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_ENST00000423061.1_Missense_Mutation_p.S7435G|SYNE1_ENST00000265368.4_Missense_Mutation_p.S7506G|SYNE1_ENST00000448038.1_Missense_Mutation_p.S7435G|SYNE1_ENST00000356820.4_Missense_Mutation_p.S2030G|SYNE1_ENST00000341594.5_Missense_Mutation_p.S7118G	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	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	34	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	
ZBTB21	49854	hgsc.bcm.edu	37	21	43412705	43412705	+	Silent	SNP	A	A	G	rs61751943	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43412705A>G	ENST00000310826.5	-	3	1683	c.1500T>C	c.(1498-1500)aaT>aaC	p.N500N	ZBTB21_ENST00000398505.3_Silent_p.N500N|ZBTB21_ENST00000398511.3_Silent_p.N500N|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398499.1_Silent_p.N500N	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	500					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										ACCCGTGCTCATTCACCTTTA	0.433													A|||	142	0.0283546	0.0023	0.0346	5008	,	,		19551	0.0		0.1034	False		,,,				2504	0.0112				p.N500N		Atlas-SNP	.											.	.	.	.	0			c.T1500C						PASS	.	A	,,	107,4299	83.9+/-122.4	1,105,2097	107.0	107.0	107.0		1500,1500,1500	-6.6	0.0	21	dbSNP_129	107	916,7684	204.0+/-246.8	52,812,3436	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF295	NM_001098402.1,NM_001098403.1,NM_020727.4	,,	53,917,5533	GG,GA,AA		10.6512,2.4285,7.8656	,,	500/1067,500/866,500/1067	43412705	1023,11983	2203	4300	6503	SO:0001819	synonymous_variant	49854	exon3			GTGCTCATTCACC	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.1500T>C	21.37:g.43412705A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	105	42	0.4	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Silent	SNP	ENST00000310826.5	37	CCDS13678.1																																																																																			A|0.931;G|0.069	0.069	strong		0.433	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
SEH1L	81929	hgsc.bcm.edu	37	18	12984144	12984144	+	Missense_Mutation	SNP	C	C	A	rs6505776	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:12984144C>A	ENST00000262124.11	+	8	1152	c.1025C>A	c.(1024-1026)aCt>aAt	p.T342N	SEH1L_ENST00000399892.2_Missense_Mutation_p.T342N|RP11-773H22.4_ENST00000588211.1_RNA|SEH1L_ENST00000592582.1_3'UTR	NM_031216.3	NP_112493.2	Q96EE3	SEH1_HUMAN	SEH1-like (S. cerevisiae)	342			T -> N (in dbSNP:rs6505776). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|carbohydrate metabolic process (GO:0005975)|cytokine production involved in inflammatory response (GO:0002534)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore organization (GO:0006999)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						CTAGGTTCAACTATTCCAAGT	0.408													A|||	3917	0.782149	0.9788	0.6441	5008	,	,		18285	0.8105		0.6203	False		,,,				2504	0.7515				p.T342N		Atlas-SNP	.											.	SEH1L	33	.	0			c.C1025A						PASS	.	A	ASN/THR,ASN/THR	4059,347	177.3+/-206.3	1870,319,14	104.0	114.0	111.0		1025,1025	1.0	0.9	18	dbSNP_116	111	5337,3261	488.5+/-372.4	1661,2015,623	yes	missense,missense	SEH1L	NM_001013437.1,NM_031216.3	65,65	3531,2334,637	AA,AC,CC		37.9274,7.8756,27.7453	benign,benign	342/422,342/361	12984144	9396,3608	2203	4299	6502	SO:0001583	missense	81929	exon8			GTTCAACTATTCC	BC012430	CCDS32791.1, CCDS45832.1	18p11.21	2013-01-10				ENSG00000085415		"""WD repeat domain containing"""	30379	protein-coding gene	gene with protein product	"""sec13 like protein"", ""nucleoporin Seh1"""	609263				12196509, 14517296	Standard	XM_005258152		Approved	SEH1A, SEH1B, Seh1, SEC13L	uc002krq.3	Q96EE3		ENST00000262124.11:c.1025C>A	18.37:g.12984144C>A	ENSP00000262124:p.Thr342Asn	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_001013437	A8K5B1|Q8NFU6|Q96MH3|Q9C069	Missense_Mutation	SNP	ENST00000262124.11	37	CCDS45832.1	1647	0.7541208791208791	476	0.967479674796748	237	0.6546961325966851	462	0.8076923076923077	472	0.6226912928759895	A	3.658	-0.070133	0.07228	0.921244	0.620726	ENSG00000085415	ENST00000399892;ENST00000262124	T;T	0.68765	-0.29;-0.35	6.04	1.0	0.19881	.	0.378371	0.31884	N	0.006907	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	4.000000000004E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32134	-0.9918	9	0.10377	T	0.69	-10.2768	7.0792	0.25221	0.3928:0.3408:0.2663:0.0	rs6505776;rs52825360;rs58418692;rs6505776	342;342	Q96EE3;Q96EE3-1	SEH1_HUMAN;.	N	342	ENSP00000382779:T342N;ENSP00000262124:T342N	ENSP00000262124:T342N	T	+	2	0	SEH1L	12974144	1.000000	0.71417	0.929000	0.37066	0.983000	0.72400	1.686000	0.37669	-0.279000	0.09167	-0.362000	0.07510	ACT	C|0.252;A|0.748	0.748	strong		0.408	SEH1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458254.1	NM_031216	
TANC1	85461	hgsc.bcm.edu	37	2	159954175	159954175	+	Missense_Mutation	SNP	C	C	T	rs34588551	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:159954175C>T	ENST00000263635.6	+	4	325	c.88C>T	c.(88-90)Cca>Tca	p.P30S	TANC1_ENST00000454300.1_Missense_Mutation_p.P30S	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	30			P -> S (in dbSNP:rs34588551).		dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						AGAGACTTCTCCAGTCCTGCA	0.458													C|||	683	0.136382	0.0295	0.2493	5008	,	,		18486	0.003		0.3469	False		,,,				2504	0.1217				p.P30S		Atlas-SNP	.											.	TANC1	157	.	0			c.C88T						PASS	.	C	SER/PRO,SER/PRO	309,3621		8,293,1664	119.0	113.0	115.0		88,88	0.7	0.0	2	dbSNP_126	115	2993,5307		533,1927,1690	yes	missense,missense	TANC1	NM_001145909.1,NM_033394.2	74,74	541,2220,3354	TT,TC,CC		36.0602,7.8626,26.9992	benign,benign	30/1391,30/1862	159954175	3302,8928	1965	4150	6115	SO:0001583	missense	85461	exon4			ACTTCTCCAGTCC	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.88C>T	2.37:g.159954175C>T	ENSP00000263635:p.Pro30Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	63	18	0.285714	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	386	0.17673992673992675	20	0.04065040650406504	112	0.30939226519337015	1	0.0017482517482517483	253	0.3337730870712401	C	7.078	0.569622	0.13560	0.078626	0.360602	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.68624	-0.34;-0.32	5.76	0.726	0.18248	.	0.550760	0.16234	N	0.223445	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.0	B;B	0.16289	0.015;0.0	T	0.33007	-0.9885	9	0.27082	T	0.32	.	2.2854	0.04124	0.124:0.4056:0.2705:0.2	rs34588551	30;30	Q9C0D5-2;Q9C0D5	.;TANC1_HUMAN	S	30	ENSP00000396339:P30S;ENSP00000263635:P30S	ENSP00000263635:P30S	P	+	1	0	TANC1	159662421	0.001000	0.12720	0.003000	0.11579	0.987000	0.75469	0.420000	0.21263	0.127000	0.18452	0.655000	0.94253	CCA	C|0.753;T|0.247	0.247	strong		0.458	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
PIWIL4	143689	hgsc.bcm.edu	37	11	94337220	94337220	+	Silent	SNP	C	C	T	rs593690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:94337220C>T	ENST00000299001.6	+	13	1847	c.1636C>T	c.(1636-1638)Ctg>Ttg	p.L546L	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	546	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				TGATGTTCAGCTGGTAAGTAC	0.318													T|||	2933	0.585663	0.9085	0.4524	5008	,	,		14671	0.502		0.4145	False		,,,				2504	0.5061				p.L546L		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C1636T						PASS	.	T		3586,810	313.0+/-292.9	1473,640,85	89.0	90.0	90.0		1636	-0.6	1.0	11	dbSNP_83	90	3446,5146	623.1+/-397.4	706,2034,1556	no	coding-synonymous	PIWIL4	NM_152431.2		2179,2674,1641	TT,TC,CC		40.1071,18.4258,45.8577		546/853	94337220	7032,5956	2198	4296	6494	SO:0001819	synonymous_variant	143689	exon13			GTTCAGCTGGTAA	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.1636C>T	11.37:g.94337220C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	17	0.193182	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			C|0.455;T|0.545	0.545	strong		0.318	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
KCNH2	3757	hgsc.bcm.edu	37	7	150649531	150649531	+	Silent	SNP	G	G	A	rs1805120	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150649531G>A	ENST00000262186.5	-	6	1940	c.1539C>T	c.(1537-1539)ttC>ttT	p.F513F	KCNH2_ENST00000430723.3_Silent_p.F513F|KCNH2_ENST00000392968.2_Silent_p.F417F|KCNH2_ENST00000330883.4_Silent_p.F173F	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	513					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	AGCCAGAGCCGAAGATGAGCA	0.647													G|||	1711	0.341653	0.2511	0.3357	5008	,	,		18979	0.622		0.2127	False		,,,				2504	0.3119				p.F513F	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.C1539T						PASS	.	G	,,,	1110,3296	395.6+/-329.7	146,818,1239	67.0	58.0	61.0		1539,519,1539,519	-9.4	0.8	7	dbSNP_89	61	1834,6766	328.4+/-318.3	202,1430,2668	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNH2	NM_000238.3,NM_001204798.1,NM_172056.2,NM_172057.2	,,,	348,2248,3907	AA,AG,GG		21.3256,25.1929,22.6357	,,,	513/1160,173/549,513/889,173/820	150649531	2944,10062	2203	4300	6503	SO:0001819	synonymous_variant	3757	exon6			AGAGCCGAAGATG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1539C>T	7.37:g.150649531G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	37	CCDS5910.1																																																																																			G|0.708;A|0.292	0.292	strong		0.647	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
CMPK2	129607	hgsc.bcm.edu	37	2	6990020	6990020	+	Silent	SNP	C	C	T	rs10495545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:6990020C>T	ENST00000256722.5	-	5	1310	c.1311G>A	c.(1309-1311)acG>acA	p.T437T	CMPK2_ENST00000478738.1_5'UTR|CMPK2_ENST00000458098.1_Intron	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	437					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					GGCTTAATACCGTCTGCAGGA	0.483													C|||	518	0.103435	0.0197	0.1023	5008	,	,		18490	0.2669		0.1153	False		,,,				2504	0.0368				p.T437T		Atlas-SNP	.											.	CMPK2	30	.	0			c.G1311A						PASS	.	C		120,3700		0,120,1790	113.0	113.0	113.0		1311	-3.6	0.0	2	dbSNP_119	113	897,7333		53,791,3271	no	coding-synonymous	CMPK2	NM_207315.2		53,911,5061	TT,TC,CC		10.8991,3.1414,8.4398		437/450	6990020	1017,11033	1910	4115	6025	SO:0001819	synonymous_variant	129607	exon5			TAATACCGTCTGC		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"""cytidylate kinase 2"""	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.1311G>A	2.37:g.6990020C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	21	0.344262	NM_207315	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Silent	SNP	ENST00000256722.5	37	CCDS42648.1																																																																																			C|0.876;N|0.001	.	strong		0.483	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315	
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 GAIIx	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_ENST00000566203.2_RNA|MMP24-AS1_ENST00000456350.1_RNA|RP4-614O4.11_ENST00000444717.1_RNA|MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000453892.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000433764.1_RNA|MMP24-AS1_ENST00000438751.1_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		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	4	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	
RASGRF1	5923	hgsc.bcm.edu	37	15	79277511	79277511	+	Silent	SNP	A	A	G	rs2230518	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:79277511A>G	ENST00000419573.3	-	24	3574	c.3300T>C	c.(3298-3300)aaT>aaC	p.N1100N	RP11-16K12.1_ENST00000316148.4_RNA|RASGRF1_ENST00000394745.3_Silent_p.N316N|RASGRF1_ENST00000558480.2_Silent_p.N1084N|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1100	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TGATGTCCTCATTGCGGATGA	0.473													G|||	1411	0.281749	0.4697	0.1945	5008	,	,		20696	0.1865		0.2644	False		,,,				2504	0.2055				p.N1100N		Atlas-SNP	.											.	RASGRF1	168	.	0			c.T3300C						PASS	.	G	,,	1782,2610	640.9+/-397.4	346,1090,760	138.0	118.0	125.0		3252,3300,948	-7.9	0.5	15	dbSNP_98	125	2295,6291	704.9+/-405.4	301,1693,2299	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRF1	NM_001145648.1,NM_002891.4,NM_153815.2	,,	647,2783,3059	GG,GA,AA		26.7296,40.5738,31.4147	,,	1084/1258,1100/1274,316/490	79277511	4077,8901	2196	4293	6489	SO:0001819	synonymous_variant	5923	exon24			GTCCTCATTGCGG	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3300T>C	15.37:g.79277511A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	106	46	0.433962	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																			T|0.132;G|0.239;C|0.053;N|0.000;A|0.576	0.239	strong		0.473	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
POM121L12	285877	hgsc.bcm.edu	37	7	53103571	53103571	+	Silent	SNP	G	G	A	rs11238248	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:53103571G>A	ENST00000408890.4	+	1	223	c.207G>A	c.(205-207)ggG>ggA	p.G69G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	69										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						TCCAGTGGGGGCGCCCGGTGC	0.706													g|||	1646	0.328674	0.1725	0.4308	5008	,	,		11528	0.3026		0.4861	False		,,,				2504	0.3323				p.G69G		Atlas-SNP	.											.	POM121L12	146	.	0			c.G207A						PASS	.	A		812,3026		96,620,1203	23.0	28.0	26.0		207	-1.0	0.0	7	dbSNP_120	26	4179,4089		1058,2063,1013	no	coding-synonymous	POM121L12	NM_182595.3		1154,2683,2216	AA,AG,GG		49.4557,21.1569,41.2275		69/297	53103571	4991,7115	1919	4134	6053	SO:0001819	synonymous_variant	285877	exon1			GTGGGGGCGCCCG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.207G>A	7.37:g.53103571G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	23	22	0.956522	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			G|0.585;A|0.415	0.415	strong		0.706	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
HHIPL2	79802	hgsc.bcm.edu	37	1	222713503	222713503	+	Silent	SNP	C	C	G	rs3748664	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:222713503C>G	ENST00000343410.6	-	4	1357	c.1299G>C	c.(1297-1299)acG>acC	p.T433T		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	433					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		GGCCCTGGCGCGTGATGGGGT	0.567													C|||	1881	0.375599	0.3434	0.5058	5008	,	,		17111	0.5089		0.2604	False		,,,				2504	0.3078				p.T433T		Atlas-SNP	.											HHIPL2,colon,carcinoma,0,1	HHIPL2	122	1	0			c.G1299C						PASS	.	C		1446,2960	466.2+/-354.4	222,1002,979	70.0	70.0	70.0		1299	-11.0	0.0	1	dbSNP_107	70	2505,6095	408.3+/-349.4	366,1773,2161	no	coding-synonymous	HHIPL2	NM_024746.3		588,2775,3140	GG,GC,CC		29.1279,32.8189,30.3783		433/725	222713503	3951,9055	2203	4300	6503	SO:0001819	synonymous_variant	79802	exon4			CTGGCGCGTGATG	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1299G>C	1.37:g.222713503C>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																			C|0.679;G|0.321	0.321	strong		0.567	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
OR2T12	127064	hgsc.bcm.edu	37	1	248458051	248458051	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248458051G>C	ENST00000317996.1	-	1	829	c.830C>G	c.(829-831)aCt>aGt	p.T277S		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	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;0.0201)			GGTGAACATAGTATAGAAGGC	0.473																																					p.T277S		Atlas-SNP	.											OR2T12,NS,carcinoma,0,1	OR2T12	113	1	0			c.C830G						scavenged	.						154.0	152.0	153.0					1																	248458051		2203	4300	6503	SO:0001583	missense	127064	exon1			AACATAGTATAGA	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.830C>G	1.37:g.248458051G>C	ENSP00000324583:p.Thr277Ser	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	267	5	0.0187266	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	9.675	1.147786	0.21288	.	.	ENSG00000177201	ENST00000317996	T	0.00211	8.54	1.71	0.648	0.17801	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34178	U	0.004198	T	0.00210	0.0006	L	0.54323	1.7	0.09310	N	1	P	0.39551	0.678	P	0.44696	0.458	T	0.37244	-0.9714	10	0.54805	T	0.06	.	5.3804	0.16187	0.1421:0.2024:0.6554:0.0	.	277	Q8NG77	O2T12_HUMAN	S	277	ENSP00000324583:T277S	ENSP00000324583:T277S	T	-	2	0	OR2T12	246524674	0.000000	0.05858	0.004000	0.12327	0.003000	0.03518	0.249000	0.18216	0.754000	0.32968	0.418000	0.28097	ACT	.	.	none		0.473	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
SOCS6	9306	hgsc.bcm.edu	37	18	67992684	67992684	+	Silent	SNP	C	C	T	rs1047657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:67992684C>T	ENST00000397942.3	+	2	1096	c.780C>T	c.(778-780)cgC>cgT	p.R260R	SOCS6_ENST00000582322.1_Silent_p.R260R	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	260					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				TGGGAGGGCGCGCTTTCCCCG	0.552													C|||	384	0.0766773	0.0825	0.1455	5008	,	,		19163	0.0238		0.1044	False		,,,				2504	0.046				p.R260R	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											SOCS6,NS,carcinoma,+2,2	SOCS6	54	2	0			c.C780T						PASS	.	C		462,3944	219.1+/-236.9	24,414,1765	111.0	92.0	98.0		780	2.3	0.0	18	dbSNP_86	98	905,7695	201.8+/-245.2	53,799,3448	no	coding-synonymous	SOCS6	NM_004232.3		77,1213,5213	TT,TC,CC		10.5233,10.4857,10.5105		260/536	67992684	1367,11639	2203	4300	6503	SO:0001819	synonymous_variant	9306	exon2			AGGGCGCGCTTTC	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16833	protein-coding gene	gene with protein product		605118	"""suppressor of cytokine signaling 4"""	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.780C>T	18.37:g.67992684C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	200	92	0.46	NM_004232	Q8WUM3	Silent	SNP	ENST00000397942.3	37	CCDS11998.1																																																																																			C|0.900;T|0.100	0.100	strong		0.552	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2		
H2BFM	286436	hgsc.bcm.edu	37	X	103294760	103294760	+	Nonsense_Mutation	SNP	C	C	T	rs2301384	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:103294760C>T	ENST00000355016.3	+	1	245	c.217C>T	c.(217-219)Cag>Tag	p.Q73*	H2BFM_ENST00000243297.5_Nonsense_Mutation_p.Q176*	NM_001164416.1	NP_001157888.1	P0C1H6	H2BFM_HUMAN	H2B histone family, member M	73						nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|lung(1)|ovary(1)	3						GCAGGTTCACCAGGGCCTCAG	0.632													.|||	1157	0.30649	0.0272	0.1902	3775	,	,		13564	0.2986		0.3211	False		,,,				2504	0.3732				p.Q73X		Atlas-SNP	.											.	H2BFM	25	.	0			c.C217T						PASS	.	C	stop/GLN	78,1131		4,56,14,457,161	33.0	36.0	35.0		217	-5.1	0.0	X	dbSNP_100	35	1054,1337		163,388,340,249,451	yes	stop-gained	H2BFM	NM_001164416.1		167,444,354,706,612	TT,TC,T,CC,C		44.082,6.4516,31.4444		73/155	103294760	1132,2468	692	1591	2283	SO:0001587	stop_gained	286436	exon1			GTTCACCAGGGCC	AK093522	CCDS55468.1	Xq22.2	2011-01-27			ENSG00000101812	ENSG00000101812		"""Histones / Replication-independent"""	27867	protein-coding gene	gene with protein product							Standard	NM_001164416		Approved		uc004els.2	P0C1H6	OTTHUMG00000022122	ENST00000355016.3:c.217C>T	X.37:g.103294760C>T	ENSP00000347119:p.Gln73*	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	114	74	0.649123	NM_001164416	A6NP82	Nonsense_Mutation	SNP	ENST00000355016.3	37	CCDS55468.1	542	0.32670283303194697	13	0.026970954356846474	56	0.1891891891891892	122	0.26991150442477874	179	0.2934426229508197	.	14.19	2.462579	0.43736	0.064516	0.44082	ENSG00000101812	ENST00000243297;ENST00000355016	.	.	.	2.54	-5.08	0.02929	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999982547	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	2.3382	0.04252	0.135:0.2701:0.3961:0.1989	rs2301384	.	.	.	X	176;73	.	ENSP00000243297:Q176X	Q	+	1	0	H2BFM	103181416	0.834000	0.29399	0.000000	0.03702	0.002000	0.02628	0.930000	0.28858	-2.587000	0.00458	-0.389000	0.06534	CAG	C|0.676;T|0.324	0.324	strong		0.632	H2BFM-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057758.2	XM_210048	
C4orf17	84103	hgsc.bcm.edu	37	4	100443720	100443720	+	Missense_Mutation	SNP	G	G	A	rs13143848	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100443720G>A	ENST00000326581.4	+	3	553	c.191G>A	c.(190-192)gGa>gAa	p.G64E	C4orf17_ENST00000514652.1_Missense_Mutation_p.G64E|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	64			G -> E (in dbSNP:rs13143848). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.					p.G64E(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		ACATTGTGGGGAGTTGGCCAG	0.428													G|||	1574	0.314297	0.3449	0.219	5008	,	,		18112	0.2361		0.2992	False		,,,				2504	0.4366				p.G64E		Atlas-SNP	.											C4orf17,NS,carcinoma,0,1	C4orf17	42	1	1	Substitution - Missense(1)	prostate(1)	c.G191A						PASS	.	G	GLU/GLY	1479,2927	475.7+/-357.4	239,1001,963	178.0	155.0	163.0		191	1.2	0.0	4	dbSNP_121	163	2649,5951	425.6+/-355.0	408,1833,2059	yes	missense	C4orf17	NM_032149.2	98	647,2834,3022	AA,AG,GG		30.8023,33.5679,31.7392	probably-damaging	64/360	100443720	4128,8878	2203	4300	6503	SO:0001583	missense	84103	exon3			TGTGGGGAGTTGG	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.191G>A	4.37:g.100443720G>A	ENSP00000322582:p.Gly64Glu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	565	0.2586996336996337	172	0.34959349593495936	84	0.23204419889502761	91	0.1590909090909091	218	0.287598944591029	G	7.485	0.649475	0.14516	0.335679	0.308023	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.16743	2.33;2.32	5.18	1.2	0.21068	.	1.209900	0.05571	N	0.571058	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.28850	0.225	B	0.27380	0.079	T	0.44847	-0.9301	9	0.15066	T	0.55	1.6219	3.2821	0.06918	0.3038:0.0:0.5128:0.1834	rs13143848;rs58148455;rs13143848	64	Q53FE4	CD017_HUMAN	E	64	ENSP00000322582:G64E;ENSP00000427663:G64E	ENSP00000322582:G64E	G	+	2	0	C4orf17	100662743	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.097000	0.15168	0.332000	0.23536	0.585000	0.79938	GGA	G|0.699;A|0.301	0.301	strong		0.428	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
IQGAP3	128239	hgsc.bcm.edu	37	1	156526387	156526387	+	Missense_Mutation	SNP	C	C	G	rs11264498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156526387C>G	ENST00000361170.2	-	12	1238	c.1228G>C	c.(1228-1230)Gtg>Ctg	p.V410L		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	410			V -> L (in dbSNP:rs11264498).		activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ACAGGGTACACTGGAGGCAGC	0.602													C|||	1894	0.378195	0.1407	0.5519	5008	,	,		17223	0.4286		0.6272	False		,,,				2504	0.2679				p.V410L		Atlas-SNP	.											.	IQGAP3	146	.	0			c.G1228C						PASS	.	C	LEU/VAL	1045,3361	383.5+/-324.9	126,793,1284	55.0	46.0	49.0		1228	5.5	1.0	1	dbSNP_120	49	5490,3110	655.3+/-401.2	1773,1944,583	yes	missense	IQGAP3	NM_178229.4	32	1899,2737,1867	GG,GC,CC		36.1628,23.7177,49.754	probably-damaging	410/1632	156526387	6535,6471	2203	4300	6503	SO:0001583	missense	128239	exon12			GGTACACTGGAGG	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.1228G>C	1.37:g.156526387C>G	ENSP00000354451:p.Val410Leu	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	1032	0.4725274725274725	82	0.16666666666666666	207	0.5718232044198895	262	0.458041958041958	481	0.6345646437994723	C	23.0	4.361937	0.82353	0.237177	0.638372	ENSG00000183856	ENST00000361170	T	0.13089	2.62	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	T	0.26991	0.0661	L	0.58354	1.805	0.09310	P	0.9999999329442	D	0.64830	0.994	D	0.70716	0.97	T	0.01004	-1.1484	9	0.72032	D	0.01	-21.1507	18.0563	0.89365	0.0:1.0:0.0:0.0	rs11264498;rs17391967;rs52823677;rs57058839;rs11264498	410	Q86VI3	IQGA3_HUMAN	L	410	ENSP00000354451:V410L	ENSP00000354451:V410L	V	-	1	0	IQGAP3	154793011	1.000000	0.71417	0.988000	0.46212	0.445000	0.32107	5.769000	0.68865	2.589000	0.87451	0.491000	0.48974	GTG	C|0.513;G|0.487	0.487	strong		0.602	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289329	98289329	+	Silent	SNP	G	G	A	rs34070970	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:98289329G>A	ENST00000322128.3	-	1	847	c.744C>T	c.(742-744)atC>atT	p.I248I		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	248					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					AGAAGCCCGGGATATTTTGGA	0.542													G|||	132	0.0263578	0.0295	0.0331	5008	,	,		16980	0.001		0.0567	False		,,,				2504	0.0123				p.I248I		Atlas-SNP	.											.	TSPYL5	48	.	0			c.C744T						PASS	.	G		138,4268	96.7+/-135.4	0,138,2065	52.0	58.0	56.0		744	-0.6	0.2	8	dbSNP_126	56	569,8031	150.6+/-205.5	16,537,3747	no	coding-synonymous	TSPYL5	NM_033512.2		16,675,5812	AA,AG,GG		6.6163,3.1321,5.436		248/418	98289329	707,12299	2203	4300	6503	SO:0001819	synonymous_variant	85453	exon1			GCCCGGGATATTT	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.744C>T	8.37:g.98289329G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	34	23	0.676471	NM_033512	B3KRF0|Q9C0B3	Silent	SNP	ENST00000322128.3	37	CCDS34927.1																																																																																			G|0.953;A|0.047	0.047	strong		0.542	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
ACTG1	71	hgsc.bcm.edu	37	17	79478007	79478007	+	Silent	SNP	G	G	A	rs1135989	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79478007G>A	ENST00000575842.1	-	4	1356	c.930C>T	c.(928-930)gcC>gcT	p.A310A	ACTG1_ENST00000331925.2_Silent_p.A310A|ACTG1_ENST00000573283.1_Silent_p.A310A|ACTG1_ENST00000575087.1_Silent_p.A310A|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	310					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)			GCATCCTGTCGGCAATGCCCG	0.612													g|||	928	0.185304	0.1505	0.2522	5008	,	,		20969	0.005		0.3966	False		,,,				2504	0.1534				p.A310A		Atlas-SNP	.											.	ACTG1	55	.	0			c.C930T						PASS	.	G	,	852,3554	331.0+/-301.8	89,674,1440	67.0	64.0	65.0		930,930	-6.6	0.6	17	dbSNP_86	65	3263,5337	483.9+/-371.3	603,2057,1640	no	coding-synonymous,coding-synonymous	ACTG1	NM_001199954.1,NM_001614.3	,	692,2731,3080	AA,AG,GG		37.9419,19.3373,31.6392	,	310/376,310/376	79478007	4115,8891	2203	4300	6503	SO:0001819	synonymous_variant	71	exon5			CCTGTCGGCAATG		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.930C>T	17.37:g.79478007G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Silent	SNP	ENST00000575842.1	37	CCDS11782.1																																																																																			G|0.711;A|0.289	0.289	strong		0.612	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614	
LINC00283	100874057	hgsc.bcm.edu	37	13	103397387	103397387	+	RNA	SNP	T	T	G	rs7339187	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103397387T>G	ENST00000430111.1	+	0	1760									long intergenic non-protein coding RNA 283																		TGTGCCATTTTGGGTCTGGAG	0.393													T|||	329	0.0656949	0.1271	0.0144	5008	,	,		21811	0.1042		0.0268	False		,,,				2504	0.0194				p.Q1887P		Atlas-SNP	.											.	.	.	.	0			c.A5660C						PASS	.	T	PRO/GLN	145,1239		9,127,556	199.0	149.0	164.0		5660	1.1	0.0	13	dbSNP_116	164	68,3112		2,64,1524	yes	missense	CCDC168	NM_001146197.1	76	11,191,2080	GG,GT,TT		2.1384,10.4769,4.667		1887/7082	103397387	213,4351	692	1590	2282			643677	exon4			CCATTTTGGGTCT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103397387T>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				T|0.916;G|0.084	0.084	strong		0.393	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
PCBP3	54039	hgsc.bcm.edu	37	21	47329352	47329352	+	Silent	SNP	T	T	C	rs2277812	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:47329352T>C	ENST00000400314.1	+	8	761	c.423T>C	c.(421-423)tgT>tgC	p.C141C	PCBP3_ENST00000400309.1_Silent_p.C141C|PCBP3_ENST00000400304.1_Silent_p.C109C|PCBP3_ENST00000400310.1_Silent_p.C141C|PCBP3_ENST00000400308.1_Silent_p.C141C|PCBP3_ENST00000449640.1_Silent_p.C141C			P57721	PCBP3_HUMAN	poly(rC) binding protein 3	141	KH 2. {ECO:0000255|PROSITE- ProRule:PRU00117}.				mRNA metabolic process (GO:0016071)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(3)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17	all_hematologic(128;0.24)			Colorectal(79;0.0411)|READ - Rectum adenocarcinoma(84;0.0649)		CCAGCCAGTGTGGGTCCCTGA	0.627													C|||	4414	0.88139	0.9531	0.8098	5008	,	,		14211	0.997		0.7068	False		,,,				2504	0.8957				p.C141C		Atlas-SNP	.											.	PCBP3	82	.	0			c.T423C						PASS	.	C	,	3831,301		1777,277,12	47.0	55.0	53.0		423,423	-8.4	0.1	21	dbSNP_100	53	5860,2590		2044,1772,409	no	coding-synonymous,coding-synonymous	PCBP3	NM_001130141.1,NM_020528.2	,	3821,2049,421	CC,CT,TT		30.6509,7.2846,22.9773	,	141/346,141/372	47329352	9691,2891	2066	4225	6291	SO:0001819	synonymous_variant	54039	exon6			CCAGTGTGGGTCC	AF176329	CCDS42974.2, CCDS46652.1	21q22.3	2013-07-16	2001-11-28		ENSG00000183570	ENSG00000183570			8651	protein-coding gene	gene with protein product		608502	"""poly(rC)-binding protein 3"""			10936052	Standard	NM_020528		Approved		uc002zhq.2	P57721	OTTHUMG00000090399	ENST00000400314.1:c.423T>C	21.37:g.47329352T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	81	79	0.975309	NM_001130141	A8MPS2|A8MQ26|B7WNN9|B7WPC1|Q8N9K6|Q96EP6	Silent	SNP	ENST00000400314.1	37	CCDS42974.2																																																																																			T|0.204;C|0.796	0.796	strong		0.627	PCBP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206808.2		
DNHD1	144132	hgsc.bcm.edu	37	11	6541225	6541225	+	Missense_Mutation	SNP	C	C	G	rs11603869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6541225C>G	ENST00000527990.2	+	7	1678	c.1678C>G	c.(1678-1680)Cag>Gag	p.Q560E	DNHD1_ENST00000354685.3_Missense_Mutation_p.Q560E|DNHD1_ENST00000254579.6_Missense_Mutation_p.Q560E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	560			Q -> E (in dbSNP:rs11603869).		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)		TCTCTCATCACAGCTGGTCTT	0.488													C|||	714	0.142572	0.1233	0.1628	5008	,	,		20440	0.0327		0.1909	False		,,,				2504	0.2178				p.Q560E		Atlas-SNP	.											.	DNHD1	198	.	0			c.C1678G						PASS	.	C	GLU/GLN,GLU/GLN	545,3857	247.2+/-255.5	36,473,1692	161.0	149.0	153.0		1678,1678	3.6	0.2	11	dbSNP_120	153	1840,6752	328.8+/-318.4	201,1438,2657	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	29,29	237,1911,4349	GG,GC,CC		21.4153,12.3807,18.3546	possibly-damaging,possibly-damaging	560/4754,560/598	6541225	2385,10609	2201	4296	6497	SO:0001583	missense	144132	exon8			TCATCACAGCTGG	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.1678C>G	11.37:g.6541225C>G	ENSP00000436180:p.Gln560Glu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	56	21	0.375	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	291	0.13324175824175824	65	0.13211382113821138	52	0.143646408839779	25	0.043706293706293704	149	0.19656992084432717	C	10.69	1.420306	0.25552	0.123807	0.214153	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.25579	1.79;2.79;1.79	5.7	3.63	0.41609	.	0.813344	0.10962	N	0.614855	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B;B	0.32467	0.001;0.372	B;B	0.27796	0.002;0.083	T	0.13019	-1.0525	9	0.02654	T	1	.	9.8502	0.41053	0.1636:0.695:0.1414:0.0	rs11603869;rs11603869	560;560	Q96M86;Q96M86-4	DNHD1_HUMAN;.	E	560	ENSP00000254579:Q560E;ENSP00000346716:Q560E;ENSP00000436180:Q560E	ENSP00000254579:Q560E	Q	+	1	0	DNHD1	6497801	0.348000	0.24861	0.198000	0.23420	0.556000	0.35491	1.531000	0.36018	1.401000	0.46761	0.561000	0.74099	CAG	C|0.836;G|0.164	0.164	strong		0.488	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
CERK	64781	hgsc.bcm.edu	37	22	47116905	47116905	+	Silent	SNP	G	G	A	rs12166204	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:47116905G>A	ENST00000216264.8	-	2	262	c.150C>T	c.(148-150)tgC>tgT	p.C50C	CERK_ENST00000541677.1_5'UTR	NM_022766.5	NP_073603.2	Q8TCT0	CERK1_HUMAN	ceramide kinase	50	Required for binding to sulfatide and phosphoinositides.				ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lipid phosphorylation (GO:0046834)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ceramide kinase activity (GO:0001729)|diacylglycerol kinase activity (GO:0004143)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)			cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	20		Breast(42;0.00571)|Ovarian(80;0.00965)|all_neural(38;0.0416)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CAGGCACAGAGCAGGCATCTG	0.448													G|||	450	0.0898562	0.1664	0.0663	5008	,	,		16415	0.0397		0.0964	False		,,,				2504	0.0481				p.C50C		Atlas-SNP	.											.	CERK	40	.	0			c.C150T						PASS	.	G		680,3726	288.7+/-280.0	64,552,1587	163.0	149.0	153.0		150	2.7	1.0	22	dbSNP_120	153	958,7642	209.8+/-250.9	60,838,3402	no	coding-synonymous	CERK	NM_022766.5		124,1390,4989	AA,AG,GG		11.1395,15.4335,12.5942		50/538	47116905	1638,11368	2203	4300	6503	SO:0001819	synonymous_variant	64781	exon2			CACAGAGCAGGCA	AB079066	CCDS14077.1	22q13.31	2008-06-10			ENSG00000100422	ENSG00000100422			19256	protein-coding gene	gene with protein product		610307				11956206, 11258795	Standard	NM_022766		Approved	hCERK, FLJ23239, dA59H18.3, DKFZp434E0211, FLJ21430, KIAA1646, LK4, dA59H18.2	uc003bia.3	Q8TCT0	OTTHUMG00000150395	ENST00000216264.8:c.150C>T	22.37:g.47116905G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_022766	A0JNT4|A8K611|Q6NX59|Q9BYB3|Q9UGE5	Silent	SNP	ENST00000216264.8	37	CCDS14077.1																																																																																			G|0.891;A|0.109	0.109	strong		0.448	CERK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317924.2	NM_022766	
OCA2	4948	hgsc.bcm.edu	37	15	28211921	28211921	+	Silent	SNP	G	G	A	rs1800411	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:28211921G>A	ENST00000354638.3	-	15	1706	c.1551C>T	c.(1549-1551)tgC>tgT	p.C517C	OCA2_ENST00000353809.5_Silent_p.C493C|OCA2_ENST00000382996.2_Silent_p.C517C	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	517					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		GGAGAACAAGGCAAATCCCAA	0.493									Oculocutaneous Albinism				G|||	1823	0.364018	0.2383	0.4712	5008	,	,		20394	0.1558		0.6779	False		,,,				2504	0.3497				p.C517C		Atlas-SNP	.											OCA2,NS,carcinoma,-2,1	OCA2	173	1	0			c.C1551T						PASS	.	G		1302,3104	439.8+/-345.8	203,896,1104	111.0	90.0	97.0		1551	4.2	0.9	15	dbSNP_89	97	6073,2527	692.7+/-404.6	2144,1785,371	no	coding-synonymous	OCA2	NM_000275.2		2347,2681,1475	AA,AG,GG		29.3837,29.5506,43.2954		517/839	28211921	7375,5631	2203	4300	6503	SO:0001819	synonymous_variant	4948	exon15	Familial Cancer Database		AACAAGGCAAATC		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.1551C>T	15.37:g.28211921G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																			G|0.543;A|0.457	0.457	strong		0.493	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
SPTLC3	55304	hgsc.bcm.edu	37	20	13071816	13071816	+	Silent	SNP	C	C	T	rs6109692	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:13071816C>T	ENST00000399002.2	+	5	967	c.693C>T	c.(691-693)ttC>ttT	p.F231F	SPTLC3_ENST00000378194.4_Silent_p.F231F	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	231					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						GGATGGGATTCGCAACTAACT	0.413													C|||	371	0.0740815	0.0567	0.0836	5008	,	,		20998	0.0694		0.1054	False		,,,				2504	0.0634				p.F231F		Atlas-SNP	.											.	SPTLC3	78	.	0			c.C693T						PASS	.	C		250,3606		4,242,1682	140.0	140.0	140.0		693	0.8	1.0	20	dbSNP_114	140	888,7366		44,800,3283	no	coding-synonymous	SPTLC3	NM_018327.2		48,1042,4965	TT,TC,CC		10.7584,6.4834,9.3972		231/553	13071816	1138,10972	1928	4127	6055	SO:0001819	synonymous_variant	55304	exon5			GGGATTCGCAACT	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.693C>T	20.37:g.13071816C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	157	87	0.55414	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Silent	SNP	ENST00000399002.2	37	CCDS13115.2																																																																																			C|0.913;T|0.087	0.087	strong		0.413	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
CCDC66	285331	hgsc.bcm.edu	37	3	56628031	56628031	+	Missense_Mutation	SNP	G	G	A	rs7637449	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:56628031G>A	ENST00000394672.3	+	10	1449	c.1379G>A	c.(1378-1380)cGa>cAa	p.R460Q	CCDC66_ENST00000326595.7_Missense_Mutation_p.R426Q|CCDC66_ENST00000436465.2_Missense_Mutation_p.R460Q	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	460			R -> Q (in dbSNP:rs7637449). {ECO:0000269|PubMed:15489334}.		post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		CGAGACAGACGACGACAAAAA	0.378													G|||	1077	0.215056	0.0741	0.2839	5008	,	,		20188	0.0486		0.5388	False		,,,				2504	0.1953				p.R460Q		Atlas-SNP	.											.	CCDC66	145	.	0			c.G1379A						PASS	.	G	GLN/ARG,GLN/ARG	678,3728	287.2+/-279.2	66,546,1591	181.0	169.0	173.0		1277,1379	5.8	0.9	3	dbSNP_116	173	4621,3979	600.5+/-394.2	1241,2139,920	yes	missense,missense	CCDC66	NM_001012506.4,NM_001141947.1	43,43	1307,2685,2511	AA,AG,GG		46.2674,15.3881,40.7427	probably-damaging,probably-damaging	426/915,460/949	56628031	5299,7707	2203	4300	6503	SO:0001583	missense	285331	exon10			ACAGACGACGACA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1379G>A	3.37:g.56628031G>A	ENSP00000378167:p.Arg460Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	617	0.2825091575091575	42	0.08536585365853659	118	0.3259668508287293	34	0.05944055944055944	423	0.558047493403694	G	29.8	5.038495	0.93630	0.153881	0.537326	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.51521	-0.8695	9	0.72032	D	0.01	-9.6521	17.8518	0.88748	0.0:0.0:1.0:0.0	rs7637449;rs52797312;rs58163850;rs7637449	460	A2RUB6	CCD66_HUMAN	Q	416;460;426;460	ENSP00000401451:R416Q;ENSP00000378167:R460Q;ENSP00000326050:R426Q;ENSP00000404320:R460Q	ENSP00000326050:R426Q	R	+	2	0	CCDC66	56603071	0.998000	0.40836	0.875000	0.34327	0.968000	0.65278	4.880000	0.63107	2.739000	0.93911	0.585000	0.79938	CGA	G|0.660;A|0.340	0.340	strong		0.378	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
TACC2	10579	hgsc.bcm.edu	37	10	123847355	123847355	+	Silent	SNP	G	G	A	rs10788237	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123847355G>A	ENST00000369005.1	+	4	5680	c.5340G>A	c.(5338-5340)ggG>ggA	p.G1780G	TACC2_ENST00000334433.3_Silent_p.G1780G|TACC2_ENST00000515603.1_Silent_p.G1780G|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Silent_p.G1780G|TACC2_ENST00000515273.1_Silent_p.G1780G	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1780					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				AGCAGCCAGGGCCTGAGCGCC	0.642													G|||	1005	0.200679	0.2867	0.1844	5008	,	,		17167	0.1002		0.2187	False		,,,				2504	0.181				p.G1780G		Atlas-SNP	.											TACC2,colon,carcinoma,0,1	TACC2	271	1	0			c.G5340A						PASS	.	G	,	1413,2993	444.9+/-347.5	226,961,1016	35.0	35.0	35.0		,5340	0.6	0.0	10	dbSNP_120	35	1963,6637	330.1+/-319.0	223,1517,2560	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	449,2478,3576	AA,AG,GG		22.8256,32.0699,25.9573	,	,1780/2949	123847355	3376,9630	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			GCCAGGGCCTGAG	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.5340G>A	10.37:g.123847355G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			G|0.767;A|0.233	0.233	strong		0.642	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
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 GAIIx	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_ENST00000315144.10_Missense_Mutation_p.S9Y|FLAD1_ENST00000368433.1_Missense_Mutation_p.S106Y|FLAD1_ENST00000368432.1_Missense_Mutation_p.S9Y|FLAD1_ENST00000368431.3_5'UTR|FLAD1_ENST00000487371.1_3'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	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	103	31	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	
COL13A1	1305	hgsc.bcm.edu	37	10	71678058	71678058	+	Silent	SNP	C	C	G	rs2274181	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:71678058C>G	ENST00000398978.3	+	19	1506	c.1014C>G	c.(1012-1014)gcC>gcG	p.A338A	COL13A1_ENST00000357811.3_Silent_p.A316A|COL13A1_ENST00000520133.1_Silent_p.A287A|COL13A1_ENST00000398966.3_Silent_p.A316A|COL13A1_ENST00000398964.3_Silent_p.A309A|COL13A1_ENST00000398969.3_Silent_p.A281A|COL13A1_ENST00000522165.1_Silent_p.A319A|COL13A1_ENST00000356340.3_Silent_p.A338A|COL13A1_ENST00000520267.1_Silent_p.A281A|COL13A1_ENST00000354547.3_Silent_p.A316A|COL13A1_ENST00000517713.1_Silent_p.A316A|COL13A1_ENST00000398974.3_Silent_p.A326A|COL13A1_ENST00000398968.3_Silent_p.A319A|COL13A1_ENST00000398972.3_Silent_p.A338A|COL13A1_ENST00000398971.3_Silent_p.A338A|COL13A1_ENST00000398973.3_Silent_p.A338A	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						CCGGAATTGCCGTGGCTGGGA	0.597													C|||	1072	0.214058	0.0083	0.2752	5008	,	,		16449	0.2946		0.2217	False		,,,				2504	0.3579				p.A338A		Atlas-SNP	.											COL13A1_ENST00000398978,NS,carcinoma,+2,2	COL13A1	133	2	0			c.C1014G						PASS	.	C	,,,,,	169,3591		8,153,1719	47.0	50.0	49.0		1014,843,957,948,948,861	-8.5	0.0	10	dbSNP_100	49	1913,6315		216,1481,2417	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL13A1	NM_001130103.1,NM_080798.3,NM_080800.3,NM_080801.3,NM_080802.3,NM_080805.3	,,,,,	224,1634,4136	GG,GC,CC		23.2499,4.4947,17.3674	,,,,,	338/718,281/646,319/687,316/696,316/669,287/611	71678058	2082,9906	1880	4114	5994	SO:0001819	synonymous_variant	1305	exon19			AATTGCCGTGGCT	AJ293624	CCDS44419.1, CCDS44423.1, CCDS44424.1, CCDS44425.1, CCDS44427.1, CCDS44428.1, CCDS44423.2, CCDS44424.2, CCDS44425.2, CCDS44427.2, CCDS44428.2	10q22	2013-01-16			ENSG00000197467	ENSG00000197467		"""Collagens"""	2190	protein-coding gene	gene with protein product		120350					Standard	NM_001130103		Approved		uc001jql.3	Q5TAT6	OTTHUMG00000018394	ENST00000398978.3:c.1014C>G	10.37:g.71678058C>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	34	13	0.382353	NM_001130103		Silent	SNP	ENST00000398978.3	37	CCDS44419.1																																																																																			C|0.804;G|0.196	0.196	strong		0.597	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203	
TRPV1	7442	hgsc.bcm.edu	37	17	3495374	3495374	+	Missense_Mutation	SNP	G	G	A	rs222749	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3495374G>A	ENST00000571088.1	-	2	484	c.271C>T	c.(271-273)Ccc>Tcc	p.P91S	TRPV1_ENST00000399756.4_Missense_Mutation_p.P91S|TRPV1_ENST00000399759.3_Missense_Mutation_p.P91S|TRPV1_ENST00000174621.6_Silent_p.A65A|TRPV1_ENST00000425167.2_Missense_Mutation_p.P91S|SHPK_ENST00000572705.1_Missense_Mutation_p.P91S|TRPV1_ENST00000310522.5_Missense_Mutation_p.P91S|TRPV1_ENST00000576351.1_Missense_Mutation_p.P91S	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	91			P -> S (in dbSNP:rs222749). {ECO:0000269|PubMed:11243859}.		calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	GCACCGGTGGGGCCGTCTCCT	0.642													G|||	480	0.0958466	0.0023	0.1066	5008	,	,		17208	0.2401		0.0616	False		,,,				2504	0.1012				p.P91S	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.C271T	GRCh37	CM077646	TRPV1	M	rs222749	PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	39,4003		0,39,1982	24.0	28.0	27.0		271,271,271,271	3.7	0.8	17	dbSNP_79	27	412,7934		13,386,3774	yes	missense,missense,missense,missense	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	74,74,74,74	13,425,5756	AA,AG,GG		4.9365,0.9649,3.6406	benign,benign,benign,benign	91/840,91/840,91/840,91/840	3495374	451,11937	2021	4173	6194	SO:0001583	missense	7442	exon2			CGGTGGGGCCGTC	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.271C>T	17.37:g.3495374G>A	ENSP00000461007:p.Pro91Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	37	CCDS45576.1	221	0.10119047619047619	2	0.0040650406504065045	35	0.09668508287292818	138	0.24125874125874125	46	0.06068601583113457	G	10.56	1.384333	0.25031	0.009649	0.049365	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000425167;ENST00000310522	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	4.75	3.69	0.42338	.	2.105880	0.01827	N	0.034453	T	0.00012	0.0000	L	0.41236	1.265	0.09310	P	0.9999999999998447	B;B;P	0.35328	0.179;0.323;0.495	B;B;B	0.27170	0.052;0.05;0.077	T	0.06232	-1.0838	9	0.38643	T	0.18	-12.6473	9.5064	0.39048	0.0:0.0:0.7898:0.2102	rs222749;rs224544;rs16953225;rs222749	91;91;91	Q8NER1;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.	S	91	ENSP00000382661:P91S;ENSP00000382659:P91S;ENSP00000409627:P91S;ENSP00000311692:P91S	ENSP00000311692:P91S	P	-	1	0	TRPV1	3442123	0.044000	0.20184	0.807000	0.32361	0.235000	0.25334	0.442000	0.21628	2.583000	0.87209	0.650000	0.86243	CCC	G|0.903;A|0.097	0.097	strong		0.642	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
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 GAIIx	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_ENST00000383675.2_Missense_Mutation_p.S420P|C3orf17_ENST00000393857.2_Missense_Mutation_p.S354P	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	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	116	65	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	
C15orf41	84529	hgsc.bcm.edu	37	15	36946303	36946303	+	Missense_Mutation	SNP	C	C	G	rs3784678	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:36946303C>G	ENST00000566621.1	+	4	467	c.217C>G	c.(217-219)Ctg>Gtg	p.L73V	C15orf41_ENST00000437989.2_Missense_Mutation_p.L73V|C15orf41_ENST00000338183.4_5'UTR|C15orf41_ENST00000562877.1_5'UTR|C15orf41_ENST00000567389.1_5'UTR|RP11-16L14.2_ENST00000565366.1_RNA|C15orf41_ENST00000569302.1_Missense_Mutation_p.L73V	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	73			L -> V (in dbSNP:rs3784678).							kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		all_epithelial(112;3.06e-10)|Lung NSC(122;6.48e-08)|all_lung(180;8.31e-07)|Melanoma(134;0.222)		all cancers(64;1.76e-19)|GBM - Glioblastoma multiforme(113;5.03e-07)|BRCA - Breast invasive adenocarcinoma(123;0.11)		GTCTAGGTACCTGAATGGAGT	0.448													C|||	2489	0.497005	0.3782	0.3818	5008	,	,		18193	0.6815		0.4423	False		,,,				2504	0.6053				p.L73V		Atlas-SNP	.											.	C15orf41	24	.	0			c.C217G						PASS	.	C	VAL/LEU,	1239,1893		241,757,568	96.0	85.0	89.0		217,	5.5	1.0	15	dbSNP_107	89	3286,3870		758,1770,1050	yes	missense,utr-5	C15orf41	NM_001130010.1,NM_032499.4	32,	999,2527,1618	GG,GC,CC		45.9195,39.5594,43.9833	possibly-damaging,	73/282,	36946303	4525,5763	1566	3578	5144	SO:0001583	missense	84529	exon4			AGGTACCTGAATG	BC006254	CCDS45215.1, CCDS45216.1	15q14	2012-05-31			ENSG00000186073	ENSG00000186073			26929	protein-coding gene	gene with protein product		615626					Standard	XM_005254719		Approved	HH114, MGC11326, FLJ22851	uc001zje.4	Q9Y2V0	OTTHUMG00000172659	ENST00000566621.1:c.217C>G	15.37:g.36946303C>G	ENSP00000455397:p.Leu73Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_001130010	B2RD87	Missense_Mutation	SNP	ENST00000566621.1	37	CCDS45215.1	1078	0.4935897435897436	206	0.4186991869918699	137	0.3784530386740331	380	0.6643356643356644	355	0.4683377308707124	C	15.37	2.813509	0.50527	0.395594	0.459195	ENSG00000186073	ENST00000437989	T	0.47177	0.85	5.5	5.5	0.81552	.	.	.	.	.	T	0.00012	0.0000	L	0.46741	1.465	0.09310	P	1.0	P	0.46512	0.879	P	0.46076	0.503	T	0.47289	-0.9129	8	0.40728	T	0.16	-2.9736	12.8542	0.57876	0.0:0.9263:0.0:0.0737	rs3784678;rs17657081;rs60628223;rs3784678	73	Q9Y2V0	CO041_HUMAN	V	73	ENSP00000401362:L73V	ENSP00000401362:L73V	L	+	1	2	C15orf41	34733595	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.645000	0.54389	2.854000	0.98071	0.655000	0.94253	CTG	C|0.492;G|0.508	0.508	strong		0.448	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499	
TTLL12	23170	hgsc.bcm.edu	37	22	43576904	43576904	+	Silent	SNP	G	G	A	rs2071723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:43576904G>A	ENST00000216129.6	-	3	453	c.390C>T	c.(388-390)caC>caT	p.H130H		NM_015140.3	NP_055955.1	Q14166	TTL12_HUMAN	tubulin tyrosine ligase-like family, member 12	130					cellular protein modification process (GO:0006464)					central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)	13		Ovarian(80;0.221)|Glioma(61;0.222)				GCTGGCGCGCGTGCTCCACAC	0.662													G|||	1641	0.327676	0.2383	0.3905	5008	,	,		17213	0.3165		0.4105	False		,,,				2504	0.3303				p.H130H		Atlas-SNP	.											TTLL12,NS,carcinoma,0,1	TTLL12	50	1	0			c.C390T						scavenged	.	G		1081,3325	377.5+/-322.5	126,829,1248	47.0	42.0	44.0		390	-10.7	0.4	22	dbSNP_96	44	3465,5131	494.2+/-373.8	718,2029,1551	no	coding-synonymous	TTLL12	NM_015140.3		844,2858,2799	AA,AG,GG		40.3094,24.5347,34.9639		130/645	43576904	4546,8456	2203	4298	6501	SO:0001819	synonymous_variant	23170	exon3			GCGCGCGTGCTCC	D63487	CCDS14047.1	22q13.31	2013-02-14	2006-02-02		ENSG00000100304	ENSG00000100304		"""Tubulin tyrosine ligase-like family"""	28974	protein-coding gene	gene with protein product						15890843	Standard	NM_015140		Approved	KIAA0153	uc003bdp.3	Q14166	OTTHUMG00000150682	ENST00000216129.6:c.390C>T	22.37:g.43576904G>A		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_015140	Q20WK5|Q9UGU3	Silent	SNP	ENST00000216129.6	37	CCDS14047.1																																																																																			A|0.339;C|0.000;G|0.661	0.339	strong		0.662	TTLL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319611.1	NM_015140	
TNFRSF25	8718	hgsc.bcm.edu	37	1	6524688	6524688	+	Silent	SNP	T	T	C	rs3170675	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:6524688T>C	ENST00000356876.3	-	4	474	c.387A>G	c.(385-387)caA>caG	p.Q129Q	TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000377782.3_Silent_p.Q129Q|TNFRSF25_ENST00000351748.3_Intron|TNFRSF25_ENST00000351959.5_Silent_p.Q129Q|TNFRSF25_ENST00000348333.3_Silent_p.Q84Q	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	129					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		TGCTGACACATTGGCTGACCT	0.632													t|||	101	0.0201677	0.003	0.0317	5008	,	,		17533	0.0		0.0726	False		,,,				2504	0.002				p.Q129Q		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.A387G						PASS	.	T	,,,,,	44,4362	46.7+/-81.2	0,44,2159	65.0	66.0	66.0		387,387,387,387,252,	-11.0	0.0	1	dbSNP_105	66	445,8155	134.7+/-192.1	20,405,3875	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	TNFRSF25	NM_001039664.1,NM_003790.2,NM_148965.1,NM_148966.1,NM_148967.1,NM_148970.1	,,,,,	20,449,6034	CC,CT,TT		5.1744,0.9986,3.7598	,,,,,	129/182,129/418,129/427,129/381,84/373,	6524688	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	8718	exon4			GACACATTGGCTG	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"""Tumor necrosis factor receptor superfamily"""	11910	protein-coding gene	gene with protein product		603366	"""tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"""	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.387A>G	1.37:g.6524688T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	46	0.605263	NM_148966	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Silent	SNP	ENST00000356876.3	37	CCDS71.1																																																																																			T|0.965;C|0.035	0.035	strong		0.632	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965	
CTSB	1508	hgsc.bcm.edu	37	8	11710888	11710888	+	Missense_Mutation	SNP	G	G	C	rs12338	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11710888G>C	ENST00000353047.6	-	2	329	c.76C>G	c.(76-78)Ctg>Gtg	p.L26V	CTSB_ENST00000531089.1_Missense_Mutation_p.L26V|CTSB_ENST00000415599.2_Missense_Mutation_p.L26V|CTSB_ENST00000453527.2_Missense_Mutation_p.L26V|CTSB_ENST00000530640.2_Missense_Mutation_p.L26V|CTSB_ENST00000434271.1_Missense_Mutation_p.L26V|CTSB_ENST00000345125.3_Missense_Mutation_p.L26V|CTSB_ENST00000533455.1_Missense_Mutation_p.L26V|CTSB_ENST00000525076.1_5'UTR|CTSB_ENST00000534510.1_Missense_Mutation_p.L26V	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	26			L -> V (in dbSNP:rs12338). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3463996}.		cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		TCATCCGACAGGGGATGGAAA	0.597													G|||	1983	0.395966	0.3298	0.3905	5008	,	,		20207	0.5149		0.3827	False		,,,				2504	0.3804				p.L26V		Atlas-SNP	.											.	CTSB	24	.	0			c.C76G	GRCh37	CM066015	CTSB	M	rs12338	PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	1491,2915	476.4+/-357.6	249,993,961	126.0	99.0	108.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	76,76,76,76,76	2.4	0.2	8	dbSNP_52	108	3222,5378	485.5+/-371.6	593,2036,1671	yes	missense,missense,missense,missense,missense	CTSB	NM_001908.3,NM_147780.2,NM_147781.2,NM_147782.2,NM_147783.2	32,32,32,32,32	842,3029,2632	CC,CG,GG		37.4651,33.8402,36.2371	benign,benign,benign,benign,benign	26/340,26/340,26/340,26/340,26/340	11710888	4713,8293	2203	4300	6503	SO:0001583	missense	1508	exon4			CCGACAGGGGATG	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"""Cathepsins"""	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.76C>G	8.37:g.11710888G>C	ENSP00000345672:p.Leu26Val	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	28	0.608696	NM_147780	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	884	0.40476190476190477	163	0.3313008130081301	139	0.3839779005524862	285	0.4982517482517482	297	0.391820580474934	G	13.16	2.154838	0.38021	0.338402	0.374651	ENSG00000164733	ENST00000434271;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000415599;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000534636;ENST00000533572;ENST00000530296;ENST00000526195;ENST00000527243;ENST00000534149;ENST00000526645;ENST00000530573;ENST00000505496;ENST00000524500;ENST00000531502;ENST00000527215;ENST00000532656;ENST00000534382;ENST00000528965;ENST00000524654	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.77489	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-1.1	5.16	2.39	0.29439	Peptidase C1A, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.95151	3.63	0.21064	P	0.999794298	B	0.14438	0.01	B	0.17098	0.017	T	0.28364	-1.0046	9	0.72032	D	0.01	.	4.8161	0.13367	0.233:0.0:0.617:0.15	rs12338;rs17572;rs1059863;rs1122181;rs3200720;rs4292649;rs17855419;rs52795645;rs12338	26	P07858	CATB_HUMAN	V	26	ENSP00000415889:L26V;ENSP00000345672:L26V;ENSP00000435105:L26V;ENSP00000433215:L26V;ENSP00000409917:L26V;ENSP00000411254:L26V;ENSP00000342070:L26V;ENSP00000432244:L26V;ENSP00000434217:L26V;ENSP00000436159:L26V;ENSP00000433995:L26V;ENSP00000435074:L26V;ENSP00000436627:L26V;ENSP00000434725:L26V;ENSP00000436122:L26V;ENSP00000431518:L26V;ENSP00000435650:L26V;ENSP00000436074:L26V;ENSP00000435886:L26V;ENSP00000431143:L26V;ENSP00000435260:L26V;ENSP00000433929:L26V;ENSP00000432077:L26V	ENSP00000342070:L26V	L	-	1	2	CTSB	11748297	0.941000	0.31946	0.212000	0.23672	0.642000	0.38348	1.474000	0.35398	0.192000	0.20272	0.462000	0.41574	CTG	G|0.625;C|0.375	0.375	strong		0.597	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48525507	48525507	+	Missense_Mutation	SNP	G	G	A	rs2303690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48525507G>A	ENST00000339841.2	+	6	773	c.595G>A	c.(595-597)Gaa>Aaa	p.E199K	ELSPBP1_ENST00000597519.1_Missense_Mutation_p.E51K	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	199	Fibronectin type-II 4. {ECO:0000255|PROSITE-ProRule:PRU00479}.		E -> K (in dbSNP:rs2303690). {ECO:0000269|PubMed:11144225, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		CTGCACTAACGAAGGATCAAA	0.458													a|||	3432	0.685304	0.6672	0.719	5008	,	,		21670	0.8671		0.5696	False		,,,				2504	0.6176				p.E199K		Atlas-SNP	.											ELSPBP1,NS,adenoma,0,1	ELSPBP1	29	1	0			c.G595A						PASS	.	A	LYS/GLU	2699,1707	514.5+/-368.7	854,991,358	172.0	160.0	164.0		595	1.5	0.0	19	dbSNP_100	164	4879,3721	530.3+/-381.8	1393,2093,814	yes	missense	ELSPBP1	NM_022142.4	56	2247,3084,1172	AA,AG,GG		43.2674,38.7426,41.7346	benign	199/224	48525507	7578,5428	2203	4300	6503	SO:0001583	missense	64100	exon6			ACTAACGAAGGAT	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.595G>A	19.37:g.48525507G>A	ENSP00000340660:p.Glu199Lys	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	160	81	0.50625	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	1512	0.6923076923076923	325	0.6605691056910569	242	0.6685082872928176	497	0.8688811188811189	448	0.5910290237467019	A	1.554	-0.538579	0.04053	0.612574	0.567326	ENSG00000169393	ENST00000339841	T	0.52295	0.67	3.66	1.54	0.23209	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.248846	0.28031	N	0.016863	T	0.00012	0.0000	N	0.20401	0.57	0.80722	P	0.0	B	0.14805	0.011	B	0.15870	0.014	T	0.44651	-0.9314	9	0.02654	T	1	.	3.8049	0.08773	0.4456:0.2051:0.3493:0.0	rs2303690;rs17845467;rs17858345;rs59769918;rs2303690	199	Q96BH3	ESPB1_HUMAN	K	199	ENSP00000340660:E199K	ENSP00000340660:E199K	E	+	1	0	ELSPBP1	53217319	0.439000	0.25610	0.044000	0.18714	0.012000	0.07955	0.521000	0.22893	0.108000	0.17862	-0.308000	0.09152	GAA	G|0.365;A|0.635	0.635	strong		0.458	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
KCNA1	3736	hgsc.bcm.edu	37	12	5021984	5021984	+	Silent	SNP	T	T	A	rs4766309	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:5021984T>A	ENST00000382545.3	+	2	2547	c.1440T>A	c.(1438-1440)acT>acA	p.T480T	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	480					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	ATTGCACCACTGCTAACCAAA	0.398													A|||	4109	0.820487	0.8903	0.7493	5008	,	,		20478	0.9623		0.6928	False		,,,				2504	0.7618				p.T480T		Atlas-SNP	.											.	KCNA1	112	.	0			c.T1440A						PASS	.	A		3772,634	273.4+/-271.3	1621,530,52	139.0	138.0	139.0		1440	2.9	1.0	12	dbSNP_111	139	5885,2715	434.8+/-357.8	2006,1873,421	no	coding-synonymous	KCNA1	NM_000217.2		3627,2403,473	AA,AT,TT		31.5698,14.3895,25.7497		480/496	5021984	9657,3349	2203	4300	6503	SO:0001819	synonymous_variant	3736	exon2			CACCACTGCTAAC	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.1440T>A	12.37:g.5021984T>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_000217	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	37	CCDS8535.1																																																																																			T|0.233;A|0.767	0.767	strong		0.398	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
OR2T34	127068	hgsc.bcm.edu	37	1	248737319	248737319	+	Missense_Mutation	SNP	G	G	A	rs77940099	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248737319G>A	ENST00000328782.2	-	1	761	c.740C>T	c.(739-741)tCc>tTc	p.S247F		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S247F(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	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)			CATGTGGGAGGAGCAGGTGGC	0.562																																					p.S247F		Atlas-SNP	.											OR2T34,NS,carcinoma,0,1	OR2T34	72	1	1	Substitution - Missense(1)	stomach(1)	c.C740T						scavenged	.	G	PHE/SER	1234,3114		180,874,1120	90.0	101.0	98.0		740	1.1	1.0	1	dbSNP_131	98	912,7688		3,906,3391	no	missense	OR2T34	NM_001001821.1	155	183,1780,4511	AA,AG,GG		10.6047,28.3809,16.574	possibly-damaging	247/319	248737319	2146,10802	2174	4300	6474	SO:0001583	missense	127068	exon1			TGGGAGGAGCAGG	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.740C>T	1.37:g.248737319G>A	ENSP00000330904:p.Ser247Phe	Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	314	87	0.27707	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	342	0.1565934065934066	151	0.30691056910569103	49	0.13535911602209943	54	0.0944055944055944	88	0.11609498680738786	.	10.47	1.358825	0.24598	0.283809	0.106047	ENSG00000183310	ENST00000328782	T	0.37058	1.22	2.22	1.14	0.20703	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.92169	3.28	0.49299	P	2.2599999999994846E-4	D	0.56287	0.975	P	0.61940	0.896	T	0.04467	-1.0949	8	0.72032	D	0.01	.	4.6375	0.12531	0.1478:0.4341:0.418:0.0	.	247	Q8NGX1	O2T34_HUMAN	F	247	ENSP00000330904:S247F	ENSP00000330904:S247F	S	-	2	0	OR2T34	246803942	0.000000	0.05858	0.989000	0.46669	0.333000	0.28666	-0.317000	0.08060	1.083000	0.41159	0.123000	0.15791	TCC	G|0.841;A|0.159	0.159	strong		0.562	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
ABCG8	64241	hgsc.bcm.edu	37	2	44104925	44104925	+	Missense_Mutation	SNP	T	T	C	rs6544718	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44104925T>C	ENST00000272286.2	+	13	1985	c.1895T>C	c.(1894-1896)gTc>gCc	p.V632A		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	632	ABC transmembrane type-2.		V -> A (in dbSNP:rs6544718). {ECO:0000269|PubMed:11452359, ECO:0000269|PubMed:11668628}.		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)	ATCCTCAGTGTCATGGAGCTG	0.532											OREG0014582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	4622	0.922923	0.9887	0.8559	5008	,	,		20192	1.0		0.8042	False		,,,				2504	0.9243				p.V632A		Atlas-SNP	.											.	ABCG8	98	.	0			c.T1895C	GRCh37	CM067333	ABCG8	M	rs6544718	PASS	.	C	ALA/VAL	4174,232	136.1+/-172.1	1980,214,9	162.0	126.0	138.0		1895	0.1	0.0	2	dbSNP_116	138	6715,1885	336.0+/-321.7	2651,1413,236	yes	missense	ABCG8	NM_022437.2	64	4631,1627,245	CC,CT,TT		21.9186,5.2655,16.2771	benign	632/674	44104925	10889,2117	2203	4300	6503	SO:0001583	missense	64241	exon13			TCAGTGTCATGGA	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.1895T>C	2.37:g.44104925T>C	ENSP00000272286:p.Val632Ala	Somatic	139	1	0.00719424	921	WXS	Illumina HiSeq	Phase_I	164	161	0.981707	NM_022437	Q53QN8	Missense_Mutation	SNP	ENST00000272286.2	37	CCDS1815.1	1952	0.8937728937728938	483	0.9817073170731707	299	0.8259668508287292	572	1.0	598	0.7889182058047494	C	0.801	-0.755503	0.03019	0.947345	0.780814	ENSG00000143921	ENST00000272286	T	0.15372	2.43	5.48	0.0541	0.14309	.	1.230800	0.05487	N	0.555832	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27331	-1.0077	9	0.06236	T	0.91	.	5.3432	0.15994	0.4315:0.298:0.21:0.0606	rs6544718;rs52825019;rs56853199;rs6544718	631;632	Q9H221-2;Q9H221	.;ABCG8_HUMAN	A	632	ENSP00000272286:V632A	ENSP00000272286:V632A	V	+	2	0	ABCG8	43958429	0.000000	0.05858	0.010000	0.14722	0.101000	0.19017	0.137000	0.15995	-0.225000	0.09913	-0.119000	0.15052	GTC	C|0.867;T|0.133	0.867	strong		0.532	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
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 GAIIx	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_ENST00000369461.3_Missense_Mutation_p.G379E|TRIM45_ENST00000369464.3_Missense_Mutation_p.G418E	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	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	73	40	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	
KIAA1804	84451	hgsc.bcm.edu	37	1	233515071	233515071	+	Silent	SNP	C	C	T	rs963982	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:233515071C>T	ENST00000366624.3	+	9	2580	c.2319C>T	c.(2317-2319)agC>agT	p.S773S	MLK4_ENST00000366622.1_Silent_p.S219S	NM_032435.2	NP_115811.2																					CCCGCAGAAGCGCCAGTCCTC	0.592													C|||	1386	0.276757	0.2413	0.3444	5008	,	,		17877	0.3433		0.174	False		,,,				2504	0.3139				p.S773S		Atlas-SNP	.											.	KIAA1804	129	.	0			c.C2319T						PASS	.	C		994,3412	371.5+/-320.0	105,784,1314	58.0	64.0	62.0		2319	-8.0	0.0	1	dbSNP_86	62	1572,7028	293.9+/-301.6	147,1278,2875	no	coding-synonymous	KIAA1804	NM_032435.2		252,2062,4189	TT,TC,CC		18.2791,22.5601,19.7294		773/1037	233515071	2566,10440	2203	4300	6503	SO:0001819	synonymous_variant	0	exon9			CAGAAGCGCCAGT																												ENST00000366624.3:c.2319C>T	1.37:g.233515071C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	59	21	0.355932	NM_032435		Silent	SNP	ENST00000366624.3	37	CCDS1598.1																																																																																			C|0.775;T|0.225	0.225	strong		0.592	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
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 GAIIx	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	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	69	33	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		
MOB3C	148932	hgsc.bcm.edu	37	1	47080741	47080741	+	Intron	SNP	C	C	T	rs12029680	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47080741C>T	ENST00000319928.3	-	1	181				MOB3C_ENST00000477318.1_Intron|MOB3C_ENST00000271139.8_Missense_Mutation_p.R3H|MKNK1_ENST00000545730.1_Intron|MOB3C_ENST00000371940.1_5'UTR	NM_201403.2	NP_958805.1	Q70IA8	MOB3C_HUMAN	MOB kinase activator 3C								metal ion binding (GO:0046872)										GAGATTTCTGCGCTTCATTTG	0.517													C|||	1674	0.334265	0.5272	0.3516	5008	,	,		15350	0.246		0.2684	False		,,,				2504	0.2198				p.R3H		Atlas-SNP	.											.	MOB3C	1	.	0			c.G8A						PASS	.	C	HIS/ARG,	2141,2265	580.9+/-385.2	522,1097,584	67.0	67.0	67.0		8,	-6.2	0.0	1	dbSNP_120	67	2178,6422	371.8+/-336.4	255,1668,2377	yes	missense,intron	MOB3C	NM_145279.4,NM_201403.2	29,	777,2765,2961	TT,TC,CC		25.3256,48.5928,33.2078	,	3/269,	47080741	4319,8687	2203	4300	6503	SO:0001627	intron_variant	148932	exon1			TTTCTGCGCTTCA	AK091808	CCDS539.1, CCDS540.1	1p34.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000142961	ENSG00000142961		"""MOB kinase activators"""	29800	protein-coding gene	gene with protein product			"""MOB1, Mps One Binder kinase activator-like 2C (yeast)"""	MOBKL2C		12477932	Standard	NM_145279		Approved	MOB1E	uc001cqe.4	Q70IA8	OTTHUMG00000007989	ENST00000319928.3:c.49+1641G>A	1.37:g.47080741C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	123	40	0.325203	NM_145279	D3DQ22|Q0VA98|Q5TC10|Q5TC11|Q8NAZ2|Q8NF28	Missense_Mutation	SNP	ENST00000319928.3	37	CCDS540.1	717	0.3282967032967033	248	0.5040650406504065	134	0.3701657458563536	146	0.25524475524475526	189	0.24934036939313983	C	9.051	0.992086	0.18966	0.485928	0.253256	ENSG00000142961	ENST00000271139	.	.	.	3.12	-6.24	0.02046	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.22977	-1.0201	4	0.87932	D	0	.	9.3601	0.38190	0.0:0.1714:0.1148:0.7139	rs12029680;rs52809751;rs60956522;rs12029680	.	.	.	H	3	.	ENSP00000271139:R3H	R	-	2	0	MOBKL2C	46853328	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.176000	0.00571	-2.577000	0.00464	-0.743000	0.03520	CGC	C|0.666;T|0.334	0.334	strong		0.517	MOB3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145279	
SLC4A4	8671	hgsc.bcm.edu	37	4	72433545	72433545	+	3'UTR	SNP	A	A	C	rs1062677	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:72433545A>C	ENST00000264485.5	+	0	3434				SLC4A4_ENST00000351898.6_3'UTR|SLC4A4_ENST00000425175.1_Missense_Mutation_p.I1074L|SLC4A4_ENST00000340595.3_3'UTR	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4						bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	TCAAATTAGAATAGAACTTGA	0.338													A|||	860	0.171725	0.0998	0.3487	5008	,	,		17638	0.1181		0.1849	False		,,,				2504	0.1851				p.I1074L		Atlas-SNP	.											.	SLC4A4	269	.	0			c.A3220C						PASS	.	A	,LEU/ILE,	393,2721		31,331,1195	75.0	66.0	69.0		,3220,	4.4	1.0	4	dbSNP_86	69	1332,5804		132,1068,2368	yes	utr-3,missense,utr-3	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	,5,	163,1399,3563	CC,CA,AA		18.6659,12.6204,16.8293	,benign,	,1074/1095,	72433545	1725,8525	1557	3568	5125	SO:0001624	3_prime_UTR_variant	8671	exon25			ATTAGAATAGAAC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.*77A>C	4.37:g.72433545A>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	166	86	0.518072	NM_001134742	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	346	0.15842490842490842	56	0.11382113821138211	107	0.2955801104972376	54	0.0944055944055944	129	0.17018469656992086	A	13.89	2.371522	0.42003	0.126204	0.186659	ENSG00000080493	ENST00000425175	T	0.78816	-1.21	5.62	4.42	0.53409	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.41340	P	0.012705999999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.05209	-1.0899	8	0.66056	D	0.02	.	13.1225	0.59336	0.8661:0.1339:0.0:0.0	rs1062677;rs1453454;rs3203670;rs17400075;rs59241443;rs1062677	1074	A5JJ20	.	L	1074	ENSP00000393557:I1074L	ENSP00000393557:I1074L	I	+	1	0	SLC4A4	72652409	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.445000	0.52921	1.053000	0.40415	0.477000	0.44152	ATA	A|0.847;C|0.153	0.153	strong		0.338	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
DKKL1	27120	hgsc.bcm.edu	37	19	49878196	49878196	+	Missense_Mutation	SNP	G	G	A	rs2288481	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49878196G>A	ENST00000221498.2	+	5	1045	c.640G>A	c.(640-642)Gaa>Aaa	p.E214K	DKKL1_ENST00000594268.1_Missense_Mutation_p.E72K|AC010524.2_ENST00000599433.1_RNA	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	214			E -> K (in dbSNP:rs2288481).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		GGACGTCCTAGAAGAGGGGAC	0.662													G|||	1294	0.258387	0.1952	0.2003	5008	,	,		17220	0.3264		0.2068	False		,,,				2504	0.3681				p.E214K		Atlas-SNP	.											.	DKKL1	23	.	0			c.G640A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	887,3519	314.7+/-293.7	95,697,1411	33.0	35.0	34.0		547,415,640	3.1	0.0	19	dbSNP_100	34	1979,6621	320.3+/-314.5	240,1499,2561	yes	missense,missense,missense	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	56,56,56	335,2196,3972	AA,AG,GG		23.0116,20.1316,22.036	possibly-damaging,possibly-damaging,possibly-damaging	183/212,139/168,214/243	49878196	2866,10140	2203	4300	6503	SO:0001583	missense	27120	exon5			GTCCTAGAAGAGG	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.640G>A	19.37:g.49878196G>A	ENSP00000221498:p.Glu214Lys	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	490	0.22435897435897437	83	0.16869918699186992	73	0.20165745856353592	179	0.3129370629370629	155	0.20448548812664907	G	14.07	2.424616	0.43020	0.201316	0.230116	ENSG00000104901	ENST00000221498	T	0.14266	2.52	4.15	3.09	0.35607	.	0.449220	0.18957	N	0.126514	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P	0.36909	0.573	B	0.36666	0.23	T	0.47235	-0.9133	9	0.87932	D	0	-7.7924	10.0305	0.42099	0.0:0.2047:0.7953:0.0	rs2288481;rs3195289;rs61144855;rs2288481	214	Q9UK85	DKKL1_HUMAN	K	214	ENSP00000221498:E214K	ENSP00000221498:E214K	E	+	1	0	DKKL1	54570008	0.014000	0.17966	0.007000	0.13788	0.009000	0.06853	0.384000	0.20668	1.320000	0.45209	0.655000	0.94253	GAA	G|0.767;A|0.233	0.233	strong		0.662	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	
RBM19	9904	hgsc.bcm.edu	37	12	114377835	114377835	+	Missense_Mutation	SNP	A	A	G	rs2290788	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:114377835A>G	ENST00000545145.2	-	15	1946	c.1868T>C	c.(1867-1869)aTc>aCc	p.I623T	RBM19_ENST00000392561.3_Missense_Mutation_p.I623T|RBM19_ENST00000261741.5_Missense_Mutation_p.I623T|RP11-780K2.1_ENST00000550206.1_RNA	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	623	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.		I -> T (in dbSNP:rs2290788). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GATGGCAGTGATTCCGCCCTC	0.642													A|||	965	0.192692	0.3245	0.0735	5008	,	,		16454	0.1885		0.1133	False		,,,				2504	0.1851				p.I623T		Atlas-SNP	.											.	RBM19	117	.	0			c.T1868C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE	1342,3064	436.1+/-344.5	224,894,1085	54.0	60.0	58.0		1868,1868,1868	3.1	0.7	12	dbSNP_100	58	888,7712	196.3+/-241.3	39,810,3451	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	89,89,89	263,1704,4536	GG,GA,AA		10.3256,30.4585,17.1459	benign,benign,benign	623/961,623/961,623/961	114377835	2230,10776	2203	4300	6503	SO:0001583	missense	9904	exon15			GCAGTGATTCCGC	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1868T>C	12.37:g.114377835A>G	ENSP00000442053:p.Ile623Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	19	0.306452	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	351	0.16071428571428573	137	0.2784552845528455	26	0.0718232044198895	102	0.17832167832167833	86	0.11345646437994723	A	12.45	1.941992	0.34283	0.304585	0.103256	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.06608	3.28;3.28;3.28	4.3	3.08	0.35506	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.262265	0.37219	N	0.002186	T	0.00012	0.0000	N	0.10645	0.015	0.21915	P	0.999477564	B	0.20261	0.043	B	0.36808	0.233	T	0.44390	-0.9331	9	0.02654	T	1	-12.7717	10.0478	0.42197	0.8499:0.0:0.0:0.1501	rs2290788;rs17849835;rs17857860;rs2290788	623	Q9Y4C8	RBM19_HUMAN	T	623	ENSP00000442053:I623T;ENSP00000376344:I623T;ENSP00000261741:I623T	ENSP00000261741:I623T	I	-	2	0	RBM19	112862218	1.000000	0.71417	0.693000	0.30195	0.561000	0.35649	8.500000	0.90498	1.600000	0.50102	0.459000	0.35465	ATC	A|0.832;G|0.168	0.168	strong		0.642	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
YAE1D1	57002	hgsc.bcm.edu	37	7	39610177	39610177	+	Missense_Mutation	SNP	A	A	G	rs6947660	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:39610177A>G	ENST00000223273.2	+	2	245	c.202A>G	c.(202-204)Aaa>Gaa	p.K68E	YAE1D1_ENST00000432096.2_Missense_Mutation_p.K68E|YAE1D1_ENST00000448268.1_Missense_Mutation_p.K68E|YAE1D1_ENST00000469737.1_3'UTR	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	68			K -> E (in dbSNP:rs6947660).														AGGTTATAAGAAAGGTGCAGA	0.368													G|||	776	0.154952	0.298	0.072	5008	,	,		18998	0.1131		0.0984	False		,,,				2504	0.1217				p.K68E		Atlas-SNP	.											.	YAE1D1	2	.	0			c.A202G						PASS	.	G	GLU/LYS	1035,3371	726.8+/-409.8	126,783,1294	133.0	136.0	135.0		202	4.1	1.0	7	dbSNP_116	135	806,7794	782.6+/-407.6	30,746,3524	yes	missense	C7orf36	NM_020192.3	56	156,1529,4818	GG,GA,AA		9.3721,23.4907,14.155	benign	68/227	39610177	1841,11165	2203	4300	6503	SO:0001583	missense	57002	exon2			TATAAGAAAGGTG	AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 36"""	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.202A>G	7.37:g.39610177A>G	ENSP00000223273:p.Lys68Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_020192	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Missense_Mutation	SNP	ENST00000223273.2	37	CCDS5459.1	339	0.15521978021978022	163	0.3313008130081301	27	0.07458563535911603	79	0.1381118881118881	70	0.09234828496042216	G	5.662	0.306799	0.10733	0.234907	0.093721	ENSG00000241127	ENST00000223273;ENST00000448268;ENST00000432096	T;T;T	0.38401	1.14;1.14;1.14	6.02	4.12	0.48240	Essential protein Yae1, N-terminal (1);	0.212623	0.48286	N	0.000186	T	0.00012	0.0000	N	0.00146	-1.995	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40813	-0.9543	9	0.02654	T	1	-8.7331	8.356	0.32331	0.1451:0.1927:0.6622:0.0	rs6947660;rs10486684;rs59204652;rs6947660	68	Q9NRH1	CG036_HUMAN	E	68	ENSP00000223273:K68E;ENSP00000400511:K68E;ENSP00000395777:K68E	ENSP00000223273:K68E	K	+	1	0	C7orf36	39576702	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	1.236000	0.32683	0.897000	0.36392	-0.790000	0.03334	AAA	A|0.858;G|0.142	0.142	strong		0.368	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250586.1	NM_020192	
TEC	7006	hgsc.bcm.edu	37	4	48147309	48147309	+	Silent	SNP	T	T	C	rs17574371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:48147309T>C	ENST00000381501.3	-	14	1414	c.1257A>G	c.(1255-1257)aaA>aaG	p.K419K	TEC_ENST00000511471.2_5'UTR	NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	419	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell receptor signaling pathway (GO:0050853)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of platelet activation (GO:0010543)|tissue regeneration (GO:0042246)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)	31						GGTGTGTCAGTTTCCTGGGAA	0.408													T|||	957	0.191094	0.1785	0.3228	5008	,	,		20119	0.0169		0.3748	False		,,,				2504	0.1053				p.K419K		Atlas-SNP	.											.	TEC	81	.	0			c.A1257G						PASS	.	T		947,3459	359.6+/-314.9	112,723,1368	72.0	70.0	71.0		1257	-2.6	1.0	4	dbSNP_123	71	3367,5233	500.3+/-375.2	686,1995,1619	no	coding-synonymous	TEC	NM_003215.2		798,2718,2987	CC,CT,TT		39.1512,21.4934,33.1693		419/632	48147309	4314,8692	2203	4300	6503	SO:0001819	synonymous_variant	7006	exon14			TGTCAGTTTCCTG	D29767	CCDS3481.1	4p12	2013-02-14			ENSG00000135605	ENSG00000135605		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	11719	protein-coding gene	gene with protein product		600583				7934162	Standard	NM_003215		Approved	PSCTK4	uc003gxz.3	P42680	OTTHUMG00000128623	ENST00000381501.3:c.1257A>G	4.37:g.48147309T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_003215	B7ZKZ6|Q3MIS5	Silent	SNP	ENST00000381501.3	37	CCDS3481.1																																																																																			T|0.704;C|0.296	0.296	strong		0.408	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3		
REST	5978	hgsc.bcm.edu	37	4	57798189	57798189	+	Silent	SNP	G	G	A	rs2227901	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57798189G>A	ENST00000309042.7	+	4	3479	c.3165G>A	c.(3163-3165)gcG>gcA	p.A1055A		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	1055	Interaction with RCOR1.				cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAGTCAAAGCGGCTAAGGGAG	0.433													G|||	1270	0.253594	0.2595	0.2161	5008	,	,		20278	0.3661		0.1849	False		,,,				2504	0.227				p.A1055A		Atlas-SNP	.											.	REST	104	.	0			c.G3165A						PASS	.	G	,	1041,3365	384.9+/-325.5	111,819,1273	80.0	77.0	78.0		3165,3165	1.1	0.0	4	dbSNP_98	78	1641,6959	303.6+/-306.5	143,1355,2802	no	coding-synonymous,coding-synonymous	REST	NM_001193508.1,NM_005612.4	,	254,2174,4075	AA,AG,GG		19.0814,23.6269,20.6213	,	1055/1098,1055/1098	57798189	2682,10324	2203	4300	6503	SO:0001819	synonymous_variant	5978	exon4			CAAAGCGGCTAAG	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.3165G>A	4.37:g.57798189G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Silent	SNP	ENST00000309042.7	37	CCDS3509.1																																																																																			G|0.791;A|0.209	0.209	strong		0.433	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
CD101	9398	hgsc.bcm.edu	37	1	117560929	117560929	+	Silent	SNP	C	C	A	rs3736907	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117560929C>A	ENST00000256652.4	+	6	1822	c.1764C>A	c.(1762-1764)atC>atA	p.I588I	CD101_ENST00000369470.1_Silent_p.I588I	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	588	Ig-like C2-type 5.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GCTCTCACATCTTCCACCAGC	0.507													C|||	1050	0.209665	0.0129	0.3876	5008	,	,		18282	0.2054		0.2326	False		,,,				2504	0.3303				p.I588I		Atlas-SNP	.											.	CD101	95	.	0			c.C1764A						PASS	.	C		240,4166	140.4+/-175.9	10,220,1973	136.0	104.0	115.0		1764	3.2	0.0	1	dbSNP_107	115	2046,6554	355.9+/-330.1	240,1566,2494	no	coding-synonymous	CD101	NM_004258.3		250,1786,4467	AA,AC,CC		23.7907,5.4471,17.5765		588/1022	117560929	2286,10720	2203	4300	6503	SO:0001819	synonymous_variant	9398	exon6			TCACATCTTCCAC	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1764C>A	1.37:g.117560929C>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_001256109	Q15856	Silent	SNP	ENST00000256652.4	37	CCDS891.1																																																																																			C|0.812;N|0.000	.	strong		0.507	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
SPATA13	221178	hgsc.bcm.edu	37	13	24797169	24797169	+	Intron	SNP	G	G	A	rs369711697	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:24797169G>A	ENST00000382095.4	+	2	185				RP11-307N16.6_ENST00000382141.4_Silent_p.S34S|SPATA13_ENST00000382108.3_Silent_p.S34S|SPATA13_ENST00000424834.2_Silent_p.S34S	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		GTGCAGGCTCGGACCTGAAAG	0.662													.|||	6	0.00119808	0.0015	0.0	5008	,	,		16081	0.001		0.0	False		,,,				2504	0.0031				p.S34S		Atlas-SNP	.											SPATA13_ENST00000382108,NS,carcinoma,+1,2	SPATA13	92	2	0			c.G102A						PASS	.	G	,	2,1382		0,2,690	76.0	84.0	81.0		102,	-10.0	0.0	13		81	1,3181		0,1,1590	no	coding-synonymous,intron	SPATA13	NM_001166271.1,NM_153023.2	,	0,3,2280	AA,AG,GG		0.0314,0.1445,0.0657	,	34/1278,	24797169	3,4563	692	1591	2283	SO:0001627	intron_variant	221178	exon2			AGGCTCGGACCTG	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-222-26446G>A	13.37:g.24797169G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	37	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	G	5.270	0.235296	0.09969	0.001445	3.14E-4	ENSG00000182957	ENST00000424834	.	.	.	5.0	-9.99	0.00435	.	.	.	.	.	T	0.23210	0.0561	.	.	.	0.09310	N	0.999992	.	.	.	.	.	.	T	0.10989	-1.0606	4	.	.	.	.	6.5302	0.22322	0.1278:0.3672:0.4109:0.094	.	.	.	.	R	72	.	.	G	+	1	0	SPATA13	23695169	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.709000	0.01890	-4.349000	0.00055	-1.518000	0.00936	GGA	.	.	weak		0.662	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
MCEE	84693	hgsc.bcm.edu	37	2	71351487	71351487	+	Missense_Mutation	SNP	G	G	A	rs11541017	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71351487G>A	ENST00000244217.5	-	2	244	c.227C>T	c.(226-228)gCg>gTg	p.A76V	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	76			A -> V (in dbSNP:rs11541017).		cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						AAGAGGGACCGCTTCACTTAC	0.473													g|||	914	0.182508	0.0318	0.2695	5008	,	,		15349	0.0446		0.3956	False		,,,				2504	0.2474				p.A76V		Atlas-SNP	.											MCEE,colon,carcinoma,0,2	MCEE	19	2	0			c.C227T						PASS	.	A	VAL/ALA	357,4049	183.3+/-210.9	17,323,1863	104.0	106.0	105.0		227	-4.1	0.0	2	dbSNP_120	105	3202,5398	484.1+/-371.3	627,1948,1725	yes	missense	MCEE	NM_032601.3	64	644,2271,3588	AA,AG,GG		37.2326,8.1026,27.3643	benign	76/177	71351487	3559,9447	2203	4300	6503	SO:0001583	missense	84693	exon2			GGGACCGCTTCAC	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"""glyoxalase domain containing 2"""	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.227C>T	2.37:g.71351487G>A	ENSP00000244217:p.Ala76Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_032601	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	450	0.20604395604395603	15	0.03048780487804878	109	0.3011049723756906	26	0.045454545454545456	300	0.39577836411609496	g	9.982	1.228432	0.22542	0.081026	0.372326	ENSG00000124370	ENST00000244217	T	0.62639	0.01	5.39	-4.05	0.03998	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.856358	0.10314	N	0.689564	T	0.00012	0.0000	N	0.13299	0.325	0.80722	P	0.0	B	0.15930	0.015	B	0.08055	0.003	T	0.37150	-0.9718	9	0.18710	T	0.47	-16.0397	7.0962	0.25311	0.4702:0.0:0.4227:0.107	rs11541017;rs59298445;rs11541017	76	Q96PE7	MCEE_HUMAN	V	76	ENSP00000244217:A76V	ENSP00000244217:A76V	A	-	2	0	MCEE	71204995	0.000000	0.05858	0.000000	0.03702	0.597000	0.36814	-0.150000	0.10189	-1.116000	0.02969	-0.127000	0.14921	GCG	G|0.753;A|0.247	0.247	strong		0.473	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73163965	73163965	+	Missense_Mutation	SNP	C	C	A	rs2973558	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:73163965C>A	ENST00000426542.2	+	19	2358	c.2338C>A	c.(2338-2340)Cat>Aat	p.H780N	ARHGEF28_ENST00000296799.4_Missense_Mutation_p.H467N|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.H780N|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.H780N|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.H780N|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.H780N|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.H780N			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	780			H -> N (in dbSNP:rs2973558).		central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										TGAGAGTGACCATAACAGCTG	0.502													A|||	1115	0.222644	0.177	0.3631	5008	,	,		18281	0.1389		0.3012	False		,,,				2504	0.1902				p.H780N		Atlas-SNP	.											.	.	.	.	0			c.C2338A						PASS	.	A	ASN/HIS,ASN/HIS	792,3138		87,618,1260	56.0	55.0	55.0		2338,2338	-0.6	0.0	5	dbSNP_101	55	2584,5732		406,1772,1980	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	68,68	493,2390,3240	AA,AC,CC		31.0726,20.1527,27.5682	benign,benign	780/1732,780/1706	73163965	3376,8870	1965	4158	6123	SO:0001583	missense	64283	exon20			AGTGACCATAACA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.2338C>A	5.37:g.73163965C>A	ENSP00000412175:p.His780Asn	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	528	0.24175824175824176	92	0.18699186991869918	122	0.3370165745856354	78	0.13636363636363635	236	0.3113456464379947	A	10.03	1.238640	0.22711	0.201527	0.310726	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.09073	3.27;3.27;3.27;3.02;3.27;3.27;3.11	5.27	-0.557	0.11800	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.09022	0.001;0.001;0.001;0.002	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47724	-0.9095	8	0.32370	T	0.25	.	9.0502	0.36372	0.4623:0.0982:0.4395:0.0	rs2973558;rs52798984;rs57008739;rs2973558	467;780;780;780	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	N	780;780;780;780;780;780;467	ENSP00000296794:H780N;ENSP00000441913:H780N;ENSP00000441436:H780N;ENSP00000287898:H780N;ENSP00000411459:H780N;ENSP00000412175:H780N;ENSP00000296799:H467N	ENSP00000287898:H780N	H	+	1	0	RP11-428C6.1	73199721	0.000000	0.05858	0.044000	0.18714	0.936000	0.57629	-0.252000	0.08806	-0.418000	0.07450	-0.539000	0.04255	CAT	C|0.764;A|0.236	0.236	strong		0.502	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
SPANXD	64648	hgsc.bcm.edu	37	X	140785739	140785739	+	Missense_Mutation	SNP	A	A	C	rs149295712		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:140785739A>C	ENST00000370515.3	-	2	510	c.177T>G	c.(175-177)ttT>ttG	p.F59L		NM_032417.2|NM_145665.1	NP_115793.1|NP_663698.1	Q9BXN6	SPNXD_HUMAN	SPANX family, member D	59						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	Acute lymphoblastic leukemia(192;7.65e-05)					ATGTTCTTTTAAAGTTCCTCC	0.483																																					p.F59L		Atlas-SNP	.											.	.	.	.	0			c.T177G						PASS	.						232.0	182.0	199.0					X																	140785739		2202	4287	6489	SO:0001583	missense	171489	exon2			TCTTTTAAAGTTC	AJ457791	CCDS14675.1	Xq27.2	2014-06-19			ENSG00000196406	ENSG00000196406			14332	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 4"""	300670, 300671	"""SPANX family, member E"""	SPANXE			Standard	NM_032417		Approved	CT11.4		Q9BXN6	OTTHUMG00000022563	ENST00000370515.3:c.177T>G	X.37:g.140785739A>C	ENSP00000359546:p.Phe59Leu	Somatic	371	0	0		WXS	Illumina HiSeq	Phase_I	576	76	0.131944	NM_145665	Q5JWI1	Missense_Mutation	SNP	ENST00000370515.3	37	CCDS14675.1	.	.	.	.	.	.	.	.	.	.	N	6.679	0.493851	0.12702	.	.	ENSG00000196406	ENST00000370515	T	0.05925	3.37	.	.	.	.	.	.	.	.	T	0.03915	0.0110	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.44682	-0.9312	6	0.26408	T	0.33	.	.	.	.	rs1059179;rs2933669;rs3176112;rs17845058;rs17857837;rs17859694	59	Q9BXN6	SPNXD_HUMAN	L	59	ENSP00000359546:F59L	ENSP00000359546:F59L	F	-	3	2	SPANXD	140613405	0.008000	0.16893	0.009000	0.14445	0.008000	0.06430	0.072000	0.14617	0.358000	0.24211	0.058000	0.15282	TTT	.	.	weak		0.483	SPANXD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058598.1		
PREX1	57580	hgsc.bcm.edu	37	20	47261017	47261017	+	Silent	SNP	T	T	C	rs6066802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47261017T>C	ENST00000371941.3	-	27	3553	c.3531A>G	c.(3529-3531)cgA>cgG	p.R1177R	PREX1_ENST00000496915.1_5'Flank|PREX1_ENST00000396220.1_Silent_p.R1177R	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1177					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1177R(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GGACCGAGTCTCGATTGCTGT	0.592													C|||	1605	0.320487	0.2118	0.3559	5008	,	,		17511	0.369		0.2624	False		,,,				2504	0.4519				p.R1177R		Atlas-SNP	.											PREX1,NS,carcinoma,0,1	PREX1	441	1	1	Substitution - coding silent(1)	stomach(1)	c.A3531G						PASS	.	C		973,3433	733.1+/-410.4	100,773,1330	95.0	76.0	82.0		3531	1.5	1.0	20	dbSNP_114	82	2242,6358	707.8+/-405.6	289,1664,2347	no	coding-synonymous	PREX1	NM_020820.3		389,2437,3677	CC,CT,TT		26.0698,22.0835,24.7194		1177/1660	47261017	3215,9791	2203	4300	6503	SO:0001819	synonymous_variant	57580	exon27			CGAGTCTCGATTG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.3531A>G	20.37:g.47261017T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			T|0.728;C|0.272	0.272	strong		0.592	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
STAB1	23166	hgsc.bcm.edu	37	3	52537109	52537109	+	Silent	SNP	G	G	A	rs112337417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:52537109G>A	ENST00000321725.6	+	7	754	c.678G>A	c.(676-678)caG>caA	p.Q226Q		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	226	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076, 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)		ACACACAGCAGGGCAGTGAAT	0.662													G|||	89	0.0177716	0.003	0.0303	5008	,	,		17859	0.0		0.0567	False		,,,				2504	0.0072				p.Q226Q		Atlas-SNP	.											.	STAB1	178	.	0			c.G678A						PASS	.	G		46,4336		0,46,2145	13.0	15.0	14.0		678	1.1	0.0	3	dbSNP_132	14	408,8172		7,394,3889	no	coding-synonymous	STAB1	NM_015136.2		7,440,6034	AA,AG,GG		4.7552,1.0497,3.5025		226/2571	52537109	454,12508	2191	4290	6481	SO:0001819	synonymous_variant	23166	exon7			ACAGCAGGGCAGT	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.678G>A	3.37:g.52537109G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																			G|0.970;A|0.030	0.030	strong		0.662	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
UBN1	29855	hgsc.bcm.edu	37	16	4930100	4930100	+	Silent	SNP	C	C	T	rs1876359	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4930100C>T	ENST00000396658.4	+	17	4075	c.3372C>T	c.(3370-3372)caC>caT	p.H1124H	UBN1_ENST00000262376.6_Silent_p.H1124H|UBN1_ENST00000545171.1_Silent_p.H1094H|UBN1_ENST00000590769.1_Silent_p.H1094H	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	1124					chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of phosphatase activity (GO:0010923)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(6)|kidney(4)|large_intestine(10)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38						CTCAGCTTCACGGGAAAGGGC	0.488													C|||	1901	0.379593	0.2852	0.4582	5008	,	,		21591	0.3343		0.3767	False		,,,				2504	0.501				p.H1124H		Atlas-SNP	.											.	UBN1	88	.	0			c.C3372T						PASS	.	C	,	1305,3089	442.0+/-346.6	167,971,1059	132.0	129.0	130.0		3372,3372	-3.0	1.0	16	dbSNP_92	130	3073,5527	470.7+/-367.9	547,1979,1774	no	coding-synonymous,coding-synonymous	UBN1	NM_001079514.1,NM_016936.3	,	714,2950,2833	TT,TC,CC		35.7326,29.6996,33.6925	,	1124/1135,1124/1135	4930100	4378,8616	2197	4300	6497	SO:0001819	synonymous_variant	29855	exon18			GCTTCACGGGAAA	AF108460	CCDS10525.1, CCDS73822.1	16p13.3	2010-11-09			ENSG00000118900	ENSG00000118900			12506	protein-coding gene	gene with protein product		609771				10725330	Standard	XM_005255277		Approved		uc002cyb.3	Q9NPG3	OTTHUMG00000129531	ENST00000396658.4:c.3372C>T	16.37:g.4930100C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	113	58	0.513274	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Silent	SNP	ENST00000396658.4	37	CCDS10525.1																																																																																			C|0.650;T|0.350	0.350	strong		0.488	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936	
ORC4	5000	hgsc.bcm.edu	37	2	148716428	148716428	+	Missense_Mutation	SNP	T	T	C	rs2307394	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:148716428T>C	ENST00000392857.5	-	5	340	c.233A>G	c.(232-234)aAt>aGt	p.N78S	ORC4_ENST00000392858.1_Missense_Mutation_p.N78S|ORC4_ENST00000536575.1_5'UTR|ORC4_ENST00000542387.1_Intron|ORC4_ENST00000264169.2_Missense_Mutation_p.N78S|ORC4_ENST00000535373.1_Missense_Mutation_p.N78S|ORC4_ENST00000540442.1_Missense_Mutation_p.N4S	NM_001190879.2|NM_001190882.2|NM_002552.4|NM_181741.3	NP_001177808.1|NP_001177811.1|NP_002543.2|NP_859525.1	O43929	ORC4_HUMAN	origin recognition complex, subunit 4	78			N -> S (in dbSNP:rs2307394). {ECO:0000269|PubMed:9353276, ECO:0000269|Ref.2, ECO:0000269|Ref.3, ECO:0000269|Ref.7}.		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	14						CAAAGCATGATTTATTAACTA	0.259													T|||	1782	0.355831	0.2859	0.4611	5008	,	,		14669	0.4762		0.325	False		,,,				2504	0.2832				p.N78S		Atlas-SNP	.											.	ORC4	40	.	0			c.A233G						PASS	.	T	SER/ASN,,SER/ASN,SER/ASN,SER/ASN,SER/ASN	1354,3032		218,918,1057	47.0	45.0	46.0		233,,11,233,233,233	5.5	1.0	2	dbSNP_100	46	2678,5882		415,1848,2017	yes	missense,utr-5,missense,missense,missense,missense	ORC4	NM_001190879.2,NM_001190881.2,NM_001190882.2,NM_002552.4,NM_181741.3,NM_181742.3	46,,46,46,46,46	633,2766,3074	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	31.285,30.871,31.1448	benign,,benign,benign,benign,benign	78/437,,4/363,78/437,78/437,78/437	148716428	4032,8914	2193	4280	6473	SO:0001583	missense	5000	exon5			GCATGATTTATTA	AF022108	CCDS2187.1, CCDS54404.1, CCDS54405.1	2q22-q23	2010-10-12	2010-10-12	2010-10-12	ENSG00000115947	ENSG00000115947		"""ATPases / AAA-type"""	8490	protein-coding gene	gene with protein product		603056	"""origin recognition complex, subunit 4 (yeast homolog)-like"", ""origin recognition complex, subunit 4-like (yeast)"", ""origin recognition complex, subunit 4-like (S. cerevisiae)"", ""origin recognition complex, subunit 4 homolog (S. cerevisiae)"""	ORC4L		9353276, 9691185	Standard	NM_181742		Approved	HsORC4, Orc4p	uc002twk.3	O43929	OTTHUMG00000131849	ENST00000392857.5:c.233A>G	2.37:g.148716428T>C	ENSP00000376597:p.Asn78Ser	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_002552	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	848	0.3882783882783883	148	0.3008130081300813	161	0.4447513812154696	277	0.48426573426573427	262	0.34564643799472294	T	13.60	2.286415	0.40494	0.30871	0.31285	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000540442;ENST00000392857;ENST00000416719;ENST00000457954;ENST00000440042	T;T;T;T;T;T;T;T	0.72615	0.45;0.45;0.45;-0.67;0.45;0.45;0.45;0.45	5.48	5.48	0.80851	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.490109	0.25768	N	0.028426	T	0.00012	0.0000	L	0.31476	0.935	0.09310	P	0.9999999999997147	B;B;B	0.23249	0.082;0.021;0.021	B;B;B	0.21151	0.033;0.009;0.021	T	0.41124	-0.9526	9	0.19147	T	0.46	-18.291	9.1469	0.36939	0.0:0.0831:0.0:0.9169	rs2307394;rs3768682;rs17225472;rs59475490;rs2307394	78;78;78	B7Z2M4;A8K7H4;O43929	.;.;ORC4_HUMAN	S	78;78;78;4;78;78;78;78	ENSP00000264169:N78S;ENSP00000441953:N78S;ENSP00000376598:N78S;ENSP00000438326:N4S;ENSP00000376597:N78S;ENSP00000413939:N78S;ENSP00000391484:N78S;ENSP00000403105:N78S	ENSP00000264169:N78S	N	-	2	0	ORC4	148432898	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.450000	0.44943	2.069000	0.61940	0.477000	0.44152	AAT	T|0.653;C|0.346	0.346	strong		0.259	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742	
SHPK	23729	hgsc.bcm.edu	37	17	3526637	3526637	+	Missense_Mutation	SNP	C	C	T	rs150857	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3526637C>T	ENST00000225519.3	-	4	745	c.643G>A	c.(643-645)Gag>Aag	p.E215K		NM_013276.2	NP_037408	Q9UHJ6	SHPK_HUMAN	sedoheptulokinase	215			E -> K (in dbSNP:rs150857). {ECO:0000269|PubMed:10673275}.		carbohydrate metabolic process (GO:0005975)|cellular response to interleukin-13 (GO:0035963)|cellular response to interleukin-4 (GO:0071353)|cellular response to lipopolysaccharide (GO:0071222)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|phosphorylation (GO:0016310)|regulation of inflammatory response (GO:0050727)|regulation of macrophage activation (GO:0043030)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|sedoheptulokinase activity (GO:0050277)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				COAD - Colon adenocarcinoma(5;0.0828)		ACTCACGTCTCTACGTTCCAG	0.562													C|||	1387	0.276957	0.4962	0.1744	5008	,	,		21811	0.2361		0.1113	False		,,,				2504	0.2658				p.E215K		Atlas-SNP	.											.	SHPK	34	.	0			c.G643A						PASS	.	C	LYS/GLU	1912,2494	547.3+/-377.3	430,1052,721	145.0	128.0	134.0		643	4.1	0.6	17	dbSNP_79	134	832,7768	191.4+/-237.6	54,724,3522	yes	missense	SHPK	NM_013276.2	56	484,1776,4243	TT,TC,CC		9.6744,43.3954,21.098	benign	215/479	3526637	2744,10262	2203	4300	6503	SO:0001583	missense	23729	exon4			ACGTCTCTACGTT	AF163573	CCDS11030.1	17p13	2008-02-08	2008-02-08	2008-02-08	ENSG00000197417	ENSG00000197417	2.7.1.14		1492	protein-coding gene	gene with protein product		605060	"""carbohydrate kinase-like"""	CARKL		10673275, 18186520	Standard	NM_013276		Approved	SHK	uc002fvz.1	Q9UHJ6	OTTHUMG00000090694	ENST00000225519.3:c.643G>A	17.37:g.3526637C>T	ENSP00000225519:p.Glu215Lys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_013276	B2R640|Q8WUH3	Missense_Mutation	SNP	ENST00000225519.3	37	CCDS11030.1	516	0.23626373626373626	253	0.5142276422764228	56	0.15469613259668508	121	0.21153846153846154	86	0.11345646437994723	C	12.44	1.937870	0.34189	0.433954	0.096744	ENSG00000197417	ENST00000225519	T	0.50277	0.75	5.15	4.12	0.48240	Carbohydrate kinase, FGGY, N-terminal (1);	0.397595	0.29093	N	0.013174	T	0.00012	0.0000	L	0.56280	1.765	0.35463	P	0.203353	B	0.30511	0.282	B	0.37198	0.243	T	0.51260	-0.8728	9	0.52906	T	0.07	.	15.4768	0.75489	0.0:0.8617:0.1383:0.0	rs150857;rs16953310;rs56508810;rs58041020;rs150857	215	Q9UHJ6	SHPK_HUMAN	K	215	ENSP00000225519:E215K	ENSP00000225519:E215K	E	-	1	0	SHPK	3473386	0.946000	0.32159	0.638000	0.29380	0.026000	0.11368	2.415000	0.44635	2.562000	0.86427	0.561000	0.74099	GAG	C|0.763;T|0.237	0.237	strong		0.562	SHPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207378.2		
OBSCN	84033	hgsc.bcm.edu	37	1	228504591	228504591	+	Missense_Mutation	SNP	C	C	A	rs61825301	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228504591C>A	ENST00000422127.1	+	51	13511	c.13467C>A	c.(13465-13467)caC>caA	p.H4489Q	OBSCN_ENST00000284548.11_Missense_Mutation_p.H4489Q|OBSCN_ENST00000366709.4_Missense_Mutation_p.H1608Q|OBSCN_ENST00000366707.4_Missense_Mutation_p.H2123Q|OBSCN_ENST00000570156.2_Missense_Mutation_p.H5446Q	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4489	Ig-like 46.			H -> Q (in Ref. 1; CAC44768). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCAGTCACCACGCCCTACTGC	0.716													c|||	728	0.145367	0.121	0.2349	5008	,	,		14096	0.1518		0.159	False		,,,				2504	0.0941				p.H5446Q		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C16338A						PASS	.		GLN/HIS,GLN/HIS	675,3615		55,565,1525	9.0	14.0	12.0		13467,13467	0.2	0.1	1	dbSNP_129	12	1406,7004		118,1170,2917	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	24,24	173,1735,4442	AA,AC,CC		16.7182,15.7343,16.3858	probably-damaging,probably-damaging	4489/7969,4489/6621	228504591	2081,10619	2145	4205	6350	SO:0001583	missense	84033	exon62			TCACCACGCCCTA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13467C>A	1.37:g.228504591C>A	ENSP00000409493:p.His4489Gln	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	346	0.15842490842490842	50	0.1016260162601626	86	0.23756906077348067	87	0.1520979020979021	123	0.16226912928759896	c	12.44	1.937450	0.34189	0.157343	0.167182	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.76968	-1.06;-1.06;0.09;0.6	5.41	0.187	0.15109	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.149471	0.46758	D	0.000266	T	0.00073	0.0002	L	0.59967	1.855	0.49130	P	2.4400000000002198E-4	D;D	0.76494	0.998;0.999	P;D	0.64042	0.835;0.921	T	0.16158	-1.0412	9	0.29301	T	0.29	.	9.7878	0.40686	0.0:0.5739:0.0:0.4261	rs61825301	4489;4489	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	Q	4489;4489;2123;1608	ENSP00000284548:H4489Q;ENSP00000409493:H4489Q;ENSP00000355668:H2123Q;ENSP00000355670:H1608Q	ENSP00000284548:H4489Q	H	+	3	2	OBSCN	226571214	0.000000	0.05858	0.074000	0.20217	0.153000	0.21895	-0.722000	0.04958	-0.223000	0.09943	0.550000	0.68814	CAC	C|0.841;A|0.159	0.159	strong		0.716	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CRYBA1	1411	hgsc.bcm.edu	37	17	27580756	27580756	+	Silent	SNP	C	C	T	rs1047790	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27580756C>T	ENST00000225387.3	+	5	457	c.456C>T	c.(454-456)ggC>ggT	p.G152G		NM_005208.4	NP_005199.2	P05813	CRBA1_HUMAN	crystallin, beta A1	152	Beta/gamma crystallin 'Greek key' 3. {ECO:0000255|PROSITE-ProRule:PRU00028}.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			AAGCCATGGGCTGGTTCAACA	0.453													T|||	1456	0.290735	0.3578	0.1916	5008	,	,		17909	0.3244		0.173	False		,,,				2504	0.3569				p.G152G		Atlas-SNP	.											.	CRYBA1	15	.	0			c.C456T						PASS	.	T		1462,2944	680.2+/-403.8	236,990,977	83.0	82.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	456	-4.9	0.8	17	dbSNP_86	82	1403,7197	753.3+/-407.4	104,1195,3001	no	coding-synonymous	CRYBA1	NM_005208.4		340,2185,3978	TT,TC,CC		16.314,33.182,22.0283		152/216	27580756	2865,10141	2203	4300	6503	SO:0001819	synonymous_variant	1411	exon5			CATGGGCTGGTTC		CCDS11249.1	17q11.2-q12	2008-07-18			ENSG00000108255	ENSG00000108255			2394	protein-coding gene	gene with protein product	"""eye lens structural protein"""	123610		CRYB1		3745196, 3770741	Standard	NM_005208		Approved		uc002hdw.3	P05813	OTTHUMG00000132729	ENST00000225387.3:c.456C>T	17.37:g.27580756C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_005208	Q13633|Q14CM9	Silent	SNP	ENST00000225387.3	37	CCDS11249.1																																																																																			C|0.756;T|0.244	0.244	strong		0.453	CRYBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256071.2	NM_005208	
TEX101	83639	hgsc.bcm.edu	37	19	43920612	43920612	+	Missense_Mutation	SNP	G	G	T	rs35033974	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43920612G>T	ENST00000598265.1	+	4	462	c.296G>T	c.(295-297)gGc>gTc	p.G99V	TEX101_ENST00000601707.1_3'UTR|TEX101_ENST00000602198.1_Missense_Mutation_p.G117V|TEX101_ENST00000253435.7_Missense_Mutation_p.G117V	NM_001130011.1	NP_001123483.1	Q9BY14	TX101_HUMAN	testis expressed 101	99			G -> V (in dbSNP:rs35033974).			acrosomal membrane (GO:0002080)|anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				large_intestine(1)|lung(12)|ovary(1)|skin(1)	15		Prostate(69;0.0199)				TCACCTCCCGGCCTGATCGTG	0.522													G|||	205	0.0409345	0.0038	0.0576	5008	,	,		20632	0.0		0.1362	False		,,,				2504	0.0235				p.G117V		Atlas-SNP	.											.	TEX101	28	.	0			c.G350T						PASS	.	G	VAL/GLY,VAL/GLY	106,4300	81.9+/-120.4	4,98,2101	213.0	197.0	202.0		296,350	3.2	0.0	19	dbSNP_126	202	1063,7537	223.3+/-260.1	71,921,3308	yes	missense,missense	TEX101	NM_001130011.1,NM_031451.4	109,109	75,1019,5409	TT,TG,GG		12.3605,2.4058,8.9882	probably-damaging,probably-damaging	99/250,117/268	43920612	1169,11837	2203	4300	6503	SO:0001583	missense	83639	exon7			CTCCCGGCCTGAT	AF241268	CCDS12619.1, CCDS59393.1	19q13.31	2013-06-06	2007-03-13			ENSG00000131126			30722	protein-coding gene	gene with protein product	"""cancer/testis antigen 131"", ""spermatogenesis associated 44"""	612665	"""testis expressed sequence 101"""			16388701, 16516155	Standard	NM_031451		Approved	MGC4766, SGRG, CT131, SPATA44	uc010xwo.2	Q9BY14		ENST00000598265.1:c.296G>T	19.37:g.43920612G>T	ENSP00000472769:p.Gly99Val	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_031451	Q7L5R2|Q9BPY7	Missense_Mutation	SNP	ENST00000598265.1	37	CCDS59393.1	119	0.05448717948717949	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	92	0.12137203166226913	G	14.15	2.449093	0.43531	0.024058	0.123605	ENSG00000131126	ENST00000253435;ENST00000407156	T	0.60171	0.21	4.26	3.23	0.37069	.	0.318038	0.26879	N	0.022036	T	0.02888	0.0086	M	0.81497	2.545	0.49687	P	1.8700000000004824E-4	D;D	0.89917	0.999;1.0	D;D	0.77004	0.974;0.989	T	0.54801	-0.8239	9	0.87932	D	0	-6.9895	7.8289	0.29332	0.1107:0.0:0.8893:0.0	rs35033974;rs35033974	99;117	Q9BY14;Q9BY14-2	TX101_HUMAN;.	V	117;112	ENSP00000253435:G117V	ENSP00000253435:G117V	G	+	2	0	TEX101	48612452	0.117000	0.22190	0.017000	0.16124	0.019000	0.09904	1.777000	0.38604	1.390000	0.46547	0.561000	0.74099	GGC	G|0.921;T|0.079	0.079	strong		0.522	TEX101-004	KNOWN	non_canonical_other|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000463176.1	NM_031451	
CFAP97	57587	hgsc.bcm.edu	37	4	186097045	186097045	+	Silent	SNP	C	C	T	rs6855305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:186097045C>T	ENST00000458385.2	-	3	1334	c.1215G>A	c.(1213-1215)ccG>ccA	p.P405P	KIAA1430_ENST00000502992.1_5'UTR|KIAA1430_ENST00000296775.6_Silent_p.P405P|KIAA1430_ENST00000514798.1_Silent_p.P405P	NM_020827.1	NP_065878.1	Q9P2B7	K1430_HUMAN		405										endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1)	11		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		TTTTGCTTCCCGGCTTTTCCG	0.448													T|||	2532	0.505591	0.6573	0.464	5008	,	,		16644	0.3998		0.505	False		,,,				2504	0.4397				p.P405P		Atlas-SNP	.											.	KIAA1430	55	.	0			c.G1215A						PASS	.	T		2252,1430		694,864,283	143.0	134.0	136.0		1215	0.6	1.0	4	dbSNP_116	136	3818,4346		893,2032,1157	no	coding-synonymous	KIAA1430	NM_020827.1		1587,2896,1440	TT,TC,CC		46.7663,38.8376,48.7591		405/533	186097045	6070,5776	1841	4082	5923	SO:0001819	synonymous_variant	57587	exon3			GCTTCCCGGCTTT																												ENST00000458385.2:c.1215G>A	4.37:g.186097045C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	157	78	0.496815	NM_020827	B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45	Silent	SNP	ENST00000458385.2	37	CCDS47168.1																																																																																			C|0.502;N|0.000	.	strong		0.448	KIAA1430-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360717.2		
RMDN2	151393	hgsc.bcm.edu	37	2	38178406	38178406	+	Intron	SNP	A	A	G	rs4670799	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:38178406A>G	ENST00000406384.1	+	2	646				RMDN2-AS1_ENST00000414365.2_RNA|RMDN2_ENST00000234195.3_Silent_p.R16R|RMDN2_ENST00000402091.3_Silent_p.R16R|RMDN2_ENST00000417700.2_Intron|RMDN2_ENST00000354545.2_Intron|RMDN2_ENST00000407257.1_Silent_p.R16R	NM_001170792.1	NP_001164263.1	Q96LZ7	RMD2_HUMAN	regulator of microtubule dynamics 2							cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)											GCTTCCAACGATGTTCTCCAG	0.458													A|||	1644	0.328275	0.2247	0.3804	5008	,	,		19531	0.0883		0.4553	False		,,,				2504	0.5481				p.R16R		Atlas-SNP	.											.	.	.	.	0			c.A48G						PASS	.	A	,,,	1215,3191	422.8+/-339.9	167,881,1155	73.0	71.0	72.0		,,,48	0.3	0.0	2	dbSNP_111	72	4127,4471	562.5+/-388.0	991,2145,1163	no	intron,intron,intron,coding-synonymous	FAM82A1	NM_001170791.1,NM_001170792.1,NM_001170793.1,NM_144713.3	,,,	1158,3026,2318	GG,GA,AA		47.9995,27.576,41.0797	,,,	,,,16/574	38178406	5342,7662	2203	4299	6502	SO:0001627	intron_variant	151393	exon2			CCAACGATGTTCT	AK057516	CCDS1792.1, CCDS54351.1, CCDS54352.1	2p22.2	2013-01-11	2013-01-11	2013-01-11	ENSG00000115841	ENSG00000115841			26567	protein-coding gene	gene with protein product		611872	"""family with sequence similarity 82, member A1"""	FAM82A, FAM82A1		12477932	Standard	XM_005264161		Approved	FLJ32954, RMD2	uc002rqn.2	Q96LZ7	OTTHUMG00000128487	ENST00000406384.1:c.452+21534A>G	2.37:g.38178406A>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_144713	A9UMZ7|A9UN00|Q4ZG33|Q6UXN4|Q8N657|Q8N9A2|Q8NCV6|Q8NHM0	Silent	SNP	ENST00000406384.1	37	CCDS54351.1																																																																																			A|0.638;G|0.362	0.362	strong		0.458	RMDN2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325577.1	NM_144713	
FAM69C	125704	hgsc.bcm.edu	37	18	72103782	72103782	+	Missense_Mutation	SNP	T	T	C	rs2278154	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72103782T>C	ENST00000343998.6	-	4	1222	c.1214A>G	c.(1213-1215)cAa>cGa	p.Q405R	FAM69C_ENST00000400291.2_Missense_Mutation_p.Q106R	NM_001044369.2	NP_001037834.2	Q0P6D2	FA69C_HUMAN	family with sequence similarity 69, member C	405						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|ovary(2)	5						TTGGAGGAGTTGGCGAAGCTT	0.582													C|||	1678	0.335064	0.3419	0.2997	5008	,	,		13728	0.2589		0.3797	False		,,,				2504	0.3834				p.Q405R		Atlas-SNP	.											.	FAM69C	45	.	0			c.A1214G						PASS	.	C	ARG/GLN	1222,2620		199,824,898	32.0	35.0	34.0		1214	4.1	0.0	18	dbSNP_100	34	3165,5081		615,1935,1573	yes	missense	FAM69C	NM_001044369.2	43	814,2759,2471	CC,CT,TT		38.3822,31.8064,36.2922	benign	405/420	72103782	4387,7701	1921	4123	6044	SO:0001583	missense	125704	exon4			AGGAGTTGGCGAA	BC019628	CCDS42445.2	18q22.3	2012-08-03	2009-07-23	2009-07-23	ENSG00000187773	ENSG00000187773			31729	protein-coding gene	gene with protein product		614544	"""chromosome 18 open reading frame 51"""	C18orf51		21334309	Standard	NM_001044369		Approved		uc002llk.3	Q0P6D2	OTTHUMG00000156984	ENST00000343998.6:c.1214A>G	18.37:g.72103782T>C	ENSP00000344331:p.Gln405Arg	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_001044369		Missense_Mutation	SNP	ENST00000343998.6	37	CCDS42445.2	724	0.3315018315018315	174	0.35365853658536583	115	0.31767955801104975	152	0.26573426573426573	283	0.3733509234828496	C	1.680	-0.506740	0.04231	0.318064	0.383822	ENSG00000187773	ENST00000400291;ENST00000343998	.	.	.	4.95	4.08	0.47627	.	0.507764	0.20656	N	0.088114	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42344	-0.9457	8	0.12766	T	0.61	-9.8332	8.5284	0.33319	0.0:0.6981:0.0:0.3019	rs2278154;rs56640189;rs2278154	405	Q0P6D2	FA69C_HUMAN	R	106;405	.	ENSP00000344331:Q405R	Q	-	2	0	FAM69C	70254762	0.003000	0.15002	0.021000	0.16686	0.285000	0.27093	1.315000	0.33608	0.639000	0.30564	-0.220000	0.12472	CAA	T|0.666;C|0.334	0.334	strong		0.582	FAM69C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346971.2	XM_058931	
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 GAIIx	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		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	86	10	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		
ERLIN1	10613	hgsc.bcm.edu	37	10	101912064	101912064	+	Missense_Mutation	SNP	T	T	C	rs2862954	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101912064T>C	ENST00000421367.2	-	11	3578	c.871A>G	c.(871-873)Att>Gtt	p.I291V	ERLIN1_ENST00000407654.3_Missense_Mutation_p.I291V	NM_001100626.1|NM_006459.3	NP_001094096.1|NP_006450.2	O75477	ERLN1_HUMAN	ER lipid raft associated 1	289					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|protein complex (GO:0043234)							Colorectal(252;0.234)		Epithelial(162;3.85e-10)|all cancers(201;3.25e-08)		TTAGAAGCAATGGCCTGGTAC	0.438													T|||	940	0.1877	0.0295	0.2997	5008	,	,		21899	0.0665		0.4811	False		,,,				2504	0.1452				p.I291V		Atlas-SNP	.											.	.	.	.	0			c.A871G						PASS	.	T	VAL/ILE,VAL/ILE	460,3946	220.7+/-238.1	29,402,1772	112.0	110.0	111.0		871,871	4.4	1.0	10	dbSNP_101	111	4044,4556	558.7+/-387.3	949,2146,1205	yes	missense,missense	ERLIN1	NM_001100626.1,NM_006459.3	29,29	978,2548,2977	CC,CT,TT		47.0233,10.4403,34.6302	benign,benign	291/349,291/349	101912064	4504,8502	2203	4300	6503	SO:0001583	missense	10613	exon11			AAGCAATGGCCTG	AF064093	CCDS7487.2	10q24.31	2014-03-03	2007-01-26	2007-01-26	ENSG00000107566	ENSG00000107566			16947	protein-coding gene	gene with protein product	"""Band_7 23-211 Keo4 (Interim) similar to C.elegans protein C42C1.9"""	611604	"""chromosome 10 open reading frame 69"", ""SPFH domain family, member 1"""	C10orf69, SPFH1		11118313, 16835267, 24482476	Standard	NM_006459		Approved	KE04, Erlin-1, SPG62	uc001kqo.4	O75477	OTTHUMG00000018900	ENST00000421367.2:c.871A>G	10.37:g.101912064T>C	ENSP00000410964:p.Ile291Val	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	199	91	0.457286	NM_006459	B0QZ42|Q53HV0	Missense_Mutation	SNP	ENST00000421367.2	37	CCDS7487.2	540	0.24725274725274726	15	0.03048780487804878	135	0.3729281767955801	39	0.06818181818181818	351	0.4630606860158311	T	14.97	2.695080	0.48202	0.104403	0.470233	ENSG00000107566	ENST00000421367;ENST00000407654;ENST00000370410	T;T	0.66638	-0.22;-0.22	5.49	4.36	0.52297	.	0.175745	0.46442	U	0.000283	T	0.00012	0.0000	L	0.31157	0.91	0.09310	P	0.99999600384	B;B	0.13594	0.008;0.004	B;B	0.18263	0.021;0.015	T	0.41610	-0.9499	9	0.37606	T	0.19	-9.2173	9.7803	0.40645	0.0:0.0821:0.0:0.9179	rs2862954;rs17728805;rs59558087;rs2862954	289;291	O75477;D3DR65	ERLN1_HUMAN;.	V	291;291;207	ENSP00000410964:I291V;ENSP00000384900:I291V	ENSP00000359438:I207V	I	-	1	0	ERLIN1	101902054	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.751000	0.68720	1.037000	0.40024	0.459000	0.35465	ATT	A|0.005;C|0.270	0.270	strong		0.438	ERLIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049840.2	NM_006459	
SYNC	81493	hgsc.bcm.edu	37	1	33160644	33160644	+	Missense_Mutation	SNP	T	T	G	rs3795424	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:33160644T>G	ENST00000409190.3	-	2	1513	c.1055A>C	c.(1054-1056)gAg>gCg	p.E352A	SYNC_ENST00000373484.3_Missense_Mutation_p.E352A	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	352	Coil 2.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TTCTTTCCTCTCTAGGAGCCG	0.587													T|||	322	0.0642971	0.003	0.1772	5008	,	,		17450	0.1062		0.0298	False		,,,				2504	0.0593				p.E352A		Atlas-SNP	.											.	SYNC	36	.	0			c.A1055C						PASS	.	T	ALA/GLU,ALA/GLU	48,4358	48.9+/-83.8	0,48,2155	60.0	61.0	61.0		1055,1055	3.9	1.0	1	dbSNP_107	61	303,8297	109.4+/-169.9	6,291,4003	yes	missense,missense	SYNC	NM_001161708.1,NM_030786.2	107,107	6,339,6158	GG,GT,TT		3.5233,1.0894,2.6988	probably-damaging,probably-damaging	352/477,352/483	33160644	351,12655	2203	4300	6503	SO:0001583	missense	81493	exon2			TTCCTCTCTAGGA	AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"""Intermediate filaments type III"""	28897	protein-coding gene	gene with protein product		611750	"""syncoilin, intermediate filament 1"""	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.1055A>C	1.37:g.33160644T>G	ENSP00000386439:p.Glu352Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_001161708	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	37	CCDS367.2	134	0.06135531135531135	2	0.0040650406504065045	50	0.13812154696132597	62	0.10839160839160839	20	0.026385224274406333	T	19.57	3.851650	0.71719	0.010894	0.035233	ENSG00000162520	ENST00000373484;ENST00000409190	D;D	0.89050	-2.46;-2.46	3.86	3.86	0.44501	Filament (1);	0.059863	0.64402	D	0.000002	T	0.06096	0.0158	N	0.19112	0.55	0.29714	P	0.839156	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.997	T	0.64045	-0.6499	9	0.66056	D	0.02	-13.686	12.2986	0.54862	0.0:0.0:0.0:1.0	rs3795424;rs52821720;rs60813832;rs3795424	352;352	Q9H7C4-2;Q9H7C4	.;SYNCI_HUMAN	A	352	ENSP00000362583:E352A;ENSP00000386439:E352A	ENSP00000362583:E352A	E	-	2	0	SYNC	32933231	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.340000	0.52143	1.769000	0.52152	0.402000	0.26972	GAG	T|0.959;G|0.041	0.041	strong		0.587	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786	
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 GAIIx	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	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	115	59	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	
TAS2R50	259296	hgsc.bcm.edu	37	12	11138852	11138852	+	Missense_Mutation	SNP	C	C	T	rs1376251	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11138852C>T	ENST00000506868.1	-	1	659	c.608G>A	c.(607-609)tGt>tAt	p.C203Y	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	203			C -> Y (in dbSNP:rs1376251). {ECO:0000269|PubMed:12379855}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)	17						GAGATGTTTACACAGAGAACA	0.413													C|||	2055	0.410343	0.056	0.3775	5008	,	,		20640	0.755		0.3579	False		,,,				2504	0.6115				p.C203Y		Atlas-SNP	.											.	TAS2R50	37	.	0			c.G608A	GRCh37	CM053427	TAS2R50	M	rs1376251	PASS	.	C	TYR/CYS	420,3986	204.8+/-226.9	20,380,1803	140.0	132.0	135.0		608	1.2	0.1	12	dbSNP_88	135	2878,5722	451.3+/-362.6	495,1888,1917	yes	missense	TAS2R50	NM_176890.2	194	515,2268,3720	TT,TC,CC		33.4651,9.5325,25.3575	benign	203/300	11138852	3298,9708	2203	4300	6503	SO:0001583	missense	259296	exon1			TGTTTACACAGAG	AF494235	CCDS8638.1	12p13.2	2012-08-22			ENSG00000212126	ENSG00000212126		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18882	protein-coding gene	gene with protein product		609627				12379855, 12584440, 16175505	Standard	NM_176890		Approved	T2R51	uc001qzl.2	P59544	OTTHUMG00000162719	ENST00000506868.1:c.608G>A	12.37:g.11138852C>T	ENSP00000424040:p.Cys203Tyr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_176890	P59545|Q2M255|Q645Y0	Missense_Mutation	SNP	ENST00000506868.1	37	CCDS8638.1	868	0.3974358974358974	26	0.052845528455284556	150	0.4143646408839779	426	0.7447552447552448	266	0.35092348284960423	C	7.954	0.745525	0.15710	0.095325	0.334651	ENSG00000212126	ENST00000506868	T	0.36520	1.25	2.19	1.22	0.21188	.	0.531082	0.16393	U	0.216373	T	0.00012	0.0000	M	0.86028	2.79	0.58432	P	1.0000000000287557E-6	B	0.19583	0.037	B	0.27608	0.081	T	0.26985	-1.0087	9	0.27785	T	0.31	.	7.5054	0.27542	0.2586:0.7414:0.0:0.0	rs1376251;rs52810970;rs57200136;rs1376251	203	P59544	T2R50_HUMAN	Y	203	ENSP00000424040:C203Y	ENSP00000424040:C203Y	C	-	2	0	TAS2R50	11030119	0.336000	0.24757	0.078000	0.20375	0.492000	0.33523	1.588000	0.36633	0.217000	0.20800	0.313000	0.20887	TGT	C|0.687;A|0.002	.	strong		0.413	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890	
CCDC50	152137	hgsc.bcm.edu	37	3	191075902	191075902	+	Silent	SNP	C	C	T	rs11542549	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:191075902C>T	ENST00000392455.3	+	3	826	c.228C>T	c.(226-228)cgC>cgT	p.R76R	CCDC50_ENST00000392456.3_Silent_p.R76R	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	76						cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		TCCAGAAGCGCTACAAAGACC	0.552													C|||	1339	0.267372	0.2322	0.3156	5008	,	,		17820	0.2579		0.332	False		,,,				2504	0.2239				p.R76R		Atlas-SNP	.											.	CCDC50	39	.	0			c.C228T						PASS	.	C	,	1123,3283	398.3+/-330.8	143,837,1223	105.0	103.0	103.0		228,228	4.4	1.0	3	dbSNP_120	103	2734,5866	435.2+/-358.0	439,1856,2005	no	coding-synonymous,coding-synonymous	CCDC50	NM_174908.3,NM_178335.2	,	582,2693,3228	TT,TC,CC		31.7907,25.488,29.6555	,	76/307,76/483	191075902	3857,9149	2203	4300	6503	SO:0001819	synonymous_variant	152137	exon3			GAAGCGCTACAAA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.228C>T	3.37:g.191075902C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_174908	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																			C|0.584;A|0.042	.	strong		0.552	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
SOCS5	9655	hgsc.bcm.edu	37	2	46986416	46986416	+	Silent	SNP	A	A	G	rs6738426	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:46986416A>G	ENST00000306503.5	+	2	919	c.747A>G	c.(745-747)acA>acG	p.T249T	SOCS5_ENST00000394861.2_Silent_p.T249T	NM_014011.4	NP_054730.1	O75159	SOCS5_HUMAN	suppressor of cytokine signaling 5	249					cell growth (GO:0016049)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|JAK-STAT cascade (GO:0007259)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of signal transduction (GO:0009968)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)		receptor tyrosine kinase binding (GO:0030971)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(9)|ovary(2)	22		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	LUSC - Lung squamous cell carcinoma(58;0.114)			TTTTTGATACATTTGATCCAT	0.428													A|||	1094	0.21845	0.1172	0.389	5008	,	,		21133	0.0853		0.339	False		,,,				2504	0.2474				p.T249T		Atlas-SNP	.											.	SOCS5	62	.	0			c.A747G						PASS	.	A	,	672,3734	265.0+/-266.4	52,568,1583	50.0	51.0	51.0		747,747	-3.0	1.0	2	dbSNP_116	51	3281,5315	453.3+/-363.2	627,2027,1644	no	coding-synonymous,coding-synonymous	SOCS5	NM_014011.4,NM_144949.2	,	679,2595,3227	GG,GA,AA		38.1689,15.2519,30.403	,	249/537,249/537	46986416	3953,9049	2203	4298	6501	SO:0001819	synonymous_variant	9655	exon2			TGATACATTTGAT	AB014571	CCDS1830.1	2p21	2013-02-14			ENSG00000171150	ENSG00000171150		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16852	protein-coding gene	gene with protein product		607094				9734811, 11230166	Standard	NM_014011		Approved	KIAA0671, SOCS-5, CIS6, CISH6, Cish5	uc002rvf.3	O75159	OTTHUMG00000128852	ENST00000306503.5:c.747A>G	2.37:g.46986416A>G		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	217	101	0.465438	NM_144949	Q53SD4|Q8IYZ4	Silent	SNP	ENST00000306503.5	37	CCDS1830.1																																																																																			A|0.715;G|0.285	0.285	strong		0.428	SOCS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250791.2		
ETV3L	440695	hgsc.bcm.edu	37	1	157067699	157067699	+	Missense_Mutation	SNP	T	T	C	rs61736984	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:157067699T>C	ENST00000454449.2	-	4	852	c.568A>G	c.(568-570)Acc>Gcc	p.T190A		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	190					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				TCCCCAGAGGTCTCTGGTGGC	0.632													C|||	186	0.0371406	0.1157	0.013	5008	,	,		17934	0.0		0.008	False		,,,				2504	0.0164				p.T190A		Atlas-SNP	.											.	ETV3L	73	.	0			c.A568G						PASS	.	C	ALA/THR	475,3931	782.0+/-414.5	21,433,1749	80.0	81.0	81.0		568	2.6	0.1	1	dbSNP_129	81	82,8518	815.1+/-407.0	1,80,4219	yes	missense	ETV3L	NM_001004341.2	58	22,513,5968	CC,CT,TT		0.9535,10.7808,4.2826	benign	190/362	157067699	557,12449	2203	4300	6503	SO:0001583	missense	440695	exon4			CAGAGGTCTCTGG	AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"""ets variant gene 3-like"""				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.568A>G	1.37:g.157067699T>C	ENSP00000430271:p.Thr190Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	34	0.641509	NM_001004341		Missense_Mutation	SNP	ENST00000454449.2	37	CCDS30893.1	72	0.03296703296703297	59	0.11991869918699187	8	0.022099447513812154	0	0.0	5	0.006596306068601583	C	0.003	-2.467713	0.00169	0.107808	0.009535	ENSG00000253831	ENST00000454449	T	0.07800	3.16	3.51	2.6	0.31112	.	.	.	.	.	T	0.00637	0.0021	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46978	-0.9152	8	0.07990	T	0.79	.	5.7157	0.17958	0.0:0.7525:0.0:0.2475	.	190	Q6ZN32	ETV3L_HUMAN	A	190	ENSP00000430271:T190A	ENSP00000430271:T190A	T	-	1	0	ETV3L	155334323	0.000000	0.05858	0.070000	0.20053	0.050000	0.14768	-0.453000	0.06778	0.488000	0.27723	-0.222000	0.12452	ACC	T|0.957;C|0.043	0.043	strong		0.632	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341	
AGBL1	123624	hgsc.bcm.edu	37	15	86838497	86838497	+	Silent	SNP	C	C	T	rs9630451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:86838497C>T	ENST00000441037.2	+	16	2189	c.2094C>T	c.(2092-2094)gaC>gaT	p.D698D	AGBL1-AS1_ENST00000564487.1_RNA|AGBL1-AS1_ENST00000566878.1_RNA|AGBL1_ENST00000421325.2_Silent_p.D698D|AGBL1_ENST00000389298.3_Silent_p.D429D	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	698					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						CTCATCTTGACATCCTGGAAA	0.423													C|||	894	0.178514	0.4546	0.0519	5008	,	,		20602	0.1567		0.0447	False		,,,				2504	0.0552				p.D698D		Atlas-SNP	.											.	AGBL1	151	.	0			c.C2094T						PASS	.	C		1501,2289		306,889,700	52.0	53.0	53.0		2094	-1.9	0.0	15	dbSNP_119	53	313,7919		5,303,3808	no	coding-synonymous	AGBL1	NM_152336.2		311,1192,4508	TT,TC,CC		3.8022,39.6042,15.089		698/1067	86838497	1814,10208	1895	4116	6011	SO:0001819	synonymous_variant	123624	exon16			TCTTGACATCCTG	AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2094C>T	15.37:g.86838497C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	54	39	0.722222	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			C|0.819;T|0.181	0.181	strong		0.423	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
CNGA4	1262	hgsc.bcm.edu	37	11	6262715	6262715	+	Silent	SNP	G	G	A	rs7129498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6262715G>A	ENST00000379936.2	+	5	1087	c.972G>A	c.(970-972)caG>caA	p.Q324Q	CNGA4_ENST00000533426.1_Silent_p.Q93Q	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	324					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCATCTTACAGCACTTGCCTG	0.552													G|||	1062	0.212061	0.4546	0.1599	5008	,	,		21775	0.0407		0.163	False		,,,				2504	0.1483				p.Q324Q		Atlas-SNP	.											.	CNGA4	96	.	0			c.G972A						PASS	.	G		1736,2666	518.6+/-369.8	334,1068,799	99.0	93.0	95.0		972	1.2	1.0	11	dbSNP_116	95	1513,7079	287.0+/-298.0	125,1263,2908	no	coding-synonymous	CNGA4	NM_001037329.3		459,2331,3707	AA,AG,GG		17.6094,39.4366,25.0038		324/576	6262715	3249,9745	2201	4296	6497	SO:0001819	synonymous_variant	1262	exon5			CTTACAGCACTTG	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2152	protein-coding gene	gene with protein product		609472	"""cyclic nucleotide gated channel beta 2"""	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.972G>A	11.37:g.6262715G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	86	49	0.569767	NM_001037329		Silent	SNP	ENST00000379936.2	37	CCDS31408.1																																																																																			G|0.774;A|0.226	0.226	strong		0.552	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	
PDE4DIP	9659	hgsc.bcm.edu	37	1	145021150	145021150	+	Missense_Mutation	SNP	T	T	C	rs11538401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145021150T>C	ENST00000530740.1	-	2	289	c.251A>G	c.(250-252)gAt>gGt	p.D84G	RP11-326G21.1_ENST00000610119.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.D84G|PDE4DIP_ENST00000478649.2_Missense_Mutation_p.D13G|PDE4DIP_ENST00000493130.2_Missense_Mutation_p.D13G|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.D84G|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.D13G			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.D84G(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTCCCCATCATCCTCTGCAAA	0.448			T	PDGFRB	MPD																																p.D84G		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369348,NS,carcinoma,0,1	PDE4DIP	817	1	1	Substitution - Missense(1)	kidney(1)	c.A251G						scavenged	.	T	GLY/ASP,GLY/ASP	50,4356	36.8+/-68.6	0,50,2153	210.0	192.0	198.0		38,251	4.3	1.0	1	dbSNP_131	198	41,8559	16.0+/-53.3	0,41,4259	yes	missense,missense	PDE4DIP	NM_001198832.1,NM_022359.5	94,94	0,91,6412	CC,CT,TT		0.4767,1.1348,0.6997	,	13/2241,84/311	145021150	91,12915	2203	4300	6503	SO:0001583	missense	9659	exon2			CCATCATCCTCTG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.251A>G	1.37:g.145021150T>C	ENSP00000435654:p.Asp84Gly	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	216	28	0.12963	NM_022359	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000530740.1	37		.	.	.	.	.	.	.	.	.	.	T	15.15	2.746559	0.49257	0.011348	0.004767	ENSG00000178104	ENST00000313382;ENST00000530740;ENST00000369359;ENST00000532801;ENST00000530078;ENST00000369348;ENST00000531369;ENST00000493130;ENST00000478649	T;T;T;T;T;T	0.58940	3.99;3.96;3.94;0.3;2.45;1.35	4.33	4.33	0.51752	.	.	.	.	.	T	0.40094	0.1103	L	0.27053	0.805	0.80722	D	1	P;P;P	0.46784	0.877;0.884;0.884	P;P;P	0.49829	0.623;0.516;0.516	T	0.47774	-0.9091	9	0.72032	D	0.01	.	9.8293	0.40932	0.0:0.0:0.0:1.0	.	13;84;13	Q5VU43-3;E9PJ64;E9PQH9	.;.;.	G	13;84;84;13;13;84;14;13;13	ENSP00000327209:D13G;ENSP00000435654:D84G;ENSP00000358366:D84G;ENSP00000436751:D13G;ENSP00000358354:D84G;ENSP00000435616:D14G	ENSP00000327209:D13G	D	-	2	0	PDE4DIP	143732507	1.000000	0.71417	0.997000	0.53966	0.973000	0.67179	3.601000	0.54059	1.820000	0.53075	0.533000	0.62120	GAT	T|0.979;C|0.021	0.021	strong		0.448	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359	
SERPINA9	327657	hgsc.bcm.edu	37	14	94933640	94933640	+	Missense_Mutation	SNP	A	A	T	rs28583900	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94933640A>T	ENST00000380365.3	-	3	786	c.708T>A	c.(706-708)caT>caA	p.H236Q	SERPINA9_ENST00000448305.2_Missense_Mutation_p.H156Q|SERPINA9_ENST00000337425.5_Missense_Mutation_p.H254Q|SERPINA9_ENST00000424550.2_Missense_Mutation_p.H105Q|SERPINA9_ENST00000539349.1_5'Flank|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000546329.1_Missense_Mutation_p.H218Q|SERPINA9_ENST00000298845.7_Missense_Mutation_p.H154Q			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	236			H -> Q (in dbSNP:rs28583900). {ECO:0000269|PubMed:12975309}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TCATGGGGACATGCACAGTGA	0.507													A|||	1615	0.322484	0.146	0.3847	5008	,	,		21179	0.4643		0.3101	False		,,,				2504	0.3834				p.H254Q		Atlas-SNP	.											.	SERPINA9	105	.	0			c.T762A						PASS	.	A	GLN/HIS,GLN/HIS	638,3366		54,530,1418	73.0	71.0	72.0		462,762	-6.9	0.0	14	dbSNP_125	72	2511,5847		374,1763,2042	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	24,24	428,2293,3460	TT,TA,AA		30.0431,15.9341,25.4732	benign,benign	154/336,254/436	94933640	3149,9213	2002	4179	6181	SO:0001583	missense	327657	exon3			GGGGACATGCACA	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.708T>A	14.37:g.94933640A>T	ENSP00000369723:p.His236Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		721	0.3301282051282051	79	0.16056910569105692	127	0.35082872928176795	275	0.4807692307692308	240	0.316622691292876	A	1.410	-0.575794	0.03882	0.159341	0.300431	ENSG00000170054	ENST00000448305;ENST00000298845;ENST00000424550;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68;-1.68	3.89	-6.94	0.01633	Serpin domain (3);	1.031920	0.07716	N	0.942849	T	0.00012	0.0000	N	0.00890	-1.11	0.58432	P	4.000000000004E-6	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.0;0.002	B;B;B;B;B	0.12156	0.004;0.0;0.003;0.0;0.007	T	0.21348	-1.0248	9	0.12766	T	0.61	.	1.5507	0.02574	0.5155:0.1089:0.2329:0.1427	rs28583900	218;236;156;254;154	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7;Q86WD7-2	.;SPA9_HUMAN;.;.;.	Q	156;154;105;254;236;218	ENSP00000414092:H156Q;ENSP00000298845:H154Q;ENSP00000409012:H105Q;ENSP00000337133:H254Q;ENSP00000369723:H236Q;ENSP00000445476:H218Q	ENSP00000298845:H154Q	H	-	3	2	SERPINA9	94003393	0.005000	0.15991	0.002000	0.10522	0.028000	0.11728	-0.058000	0.11750	-1.227000	0.02571	-0.464000	0.05259	CAT	A|0.681;T|0.319	0.319	strong		0.507	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178634672	178634672	+	Missense_Mutation	SNP	C	C	T	rs398829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178634672C>T	ENST00000251582.7	-	4	834	c.733G>A	c.(733-735)Gtc>Atc	p.V245I	ADAMTS2_ENST00000274609.5_Missense_Mutation_p.V245I	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	245			V -> I (in dbSNP:rs398829).		collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		TCCTCTAGGACGCCCAGGGCG	0.657													C|||	2163	0.431909	0.4054	0.2565	5008	,	,		15058	0.6349		0.2763	False		,,,				2504	0.5429				p.V245I		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.G733A						PASS	.	C	ILE/VAL,ILE/VAL	1674,2732	508.4+/-367.0	314,1046,843	90.0	78.0	82.0		733,733	1.2	0.4	5	dbSNP_80	82	2555,6045	415.5+/-351.8	378,1799,2123	yes	missense,missense	ADAMTS2	NM_014244.4,NM_021599.2	29,29	692,2845,2966	TT,TC,CC		29.7093,37.9936,32.5158	benign,benign	245/1212,245/567	178634672	4229,8777	2203	4300	6503	SO:0001583	missense	9509	exon4			CTAGGACGCCCAG	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.733G>A	5.37:g.178634672C>T	ENSP00000251582:p.Val245Ile	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	62	40	0.645161	NM_021599		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	867	0.39697802197802196	198	0.4024390243902439	99	0.27348066298342544	368	0.6433566433566433	202	0.26649076517150394	C	3.478	-0.106590	0.06924	0.379936	0.297093	ENSG00000087116	ENST00000251582;ENST00000274609	T;T	0.59772	0.28;0.24	5.34	1.18	0.20946	.	0.836897	0.09859	N	0.746428	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.001	T	0.46925	-0.9156	9	0.18276	T	0.48	.	6.6881	0.23156	0.0:0.5061:0.1613:0.3326	rs398829;rs3733917;rs61577946;rs398829	245;245	O95450-2;O95450	.;ATS2_HUMAN	I	245	ENSP00000251582:V245I;ENSP00000274609:V245I	ENSP00000251582:V245I	V	-	1	0	ADAMTS2	178567278	0.000000	0.05858	0.426000	0.26672	0.034000	0.12701	-0.564000	0.05936	0.250000	0.21479	0.561000	0.74099	GTC	C|0.635;T|0.365	0.365	strong		0.657	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
C9orf84	158401	hgsc.bcm.edu	37	9	114476748	114476748	+	Missense_Mutation	SNP	T	T	A	rs11791445	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:114476748T>A	ENST00000318737.4	-	15	2328	c.2200A>T	c.(2200-2202)Atg>Ttg	p.M734L	C9orf84_ENST00000394779.3_Missense_Mutation_p.M695L|C9orf84_ENST00000394777.4_Missense_Mutation_p.M660L|C9orf84_ENST00000374287.3_Missense_Mutation_p.M734L	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	734			M -> L (in dbSNP:rs11791445).							breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TGACTTTGCATCCAACTTAGT	0.338													T|||	718	0.143371	0.1422	0.196	5008	,	,		18121	0.0268		0.2286	False		,,,				2504	0.1401				p.M734L		Atlas-SNP	.											C9orf84_ENST00000374287,NS,adenoma,0,2	C9orf84	207	2	0			c.A2200T						PASS	.	T	LEU/MET,LEU/MET	769,3635	311.9+/-292.3	67,635,1500	186.0	171.0	176.0		2083,2200	2.9	1.0	9	dbSNP_120	176	1991,6609	348.2+/-326.9	227,1537,2536	yes	missense,missense	C9orf84	NM_001080551.1,NM_173521.3	15,15	294,2172,4036	AA,AT,TT		23.1512,17.4614,21.2242	benign,benign	695/1406,734/1445	114476748	2760,10244	2202	4300	6502	SO:0001583	missense	158401	exon15			TTTGCATCCAACT	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.2200A>T	9.37:g.114476748T>A	ENSP00000322108:p.Met734Leu	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	171	74	0.432749	NM_173521	A2A2V3|Q2M1H8|Q96M73	Missense_Mutation	SNP	ENST00000318737.4	37	CCDS6781.3	331	0.15155677655677655	72	0.14634146341463414	69	0.19060773480662985	15	0.026223776223776224	175	0.23087071240105542	T	12.51	1.959296	0.34565	0.174614	0.231512	ENSG00000165181	ENST00000394779;ENST00000394777;ENST00000394778;ENST00000374287;ENST00000318737	T;T;T;T	0.03860	3.78;3.78;3.79;3.79	5.63	2.93	0.34026	.	0.269718	0.28006	N	0.016970	T	0.00012	0.0000	N	0.12746	0.255	0.44129	P	0.003082000000000029	B;B;B	0.18461	0.028;0.028;0.028	B;B;B	0.16722	0.016;0.016;0.016	T	0.49244	-0.8960	9	0.23891	T	0.37	-7.6893	7.4418	0.27187	0.0:0.1267:0.1384:0.7349	rs11791445;rs17271275;rs11791445	660;734;695	A6PVK7;Q5VXU9;A2A2V3	.;CI084_HUMAN;.	L	695;660;348;734;734	ENSP00000378259:M695L;ENSP00000378257:M660L;ENSP00000363405:M734L;ENSP00000322108:M734L	ENSP00000322108:M734L	M	-	1	0	C9orf84	113516569	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.577000	0.23758	0.955000	0.37878	0.533000	0.62120	ATG	T|0.809;A|0.191	0.191	strong		0.338	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
PGM2	55276	hgsc.bcm.edu	37	4	37857342	37857342	+	Silent	SNP	G	G	C	rs11554509	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:37857342G>C	ENST00000381967.4	+	13	1816	c.1716G>C	c.(1714-1716)ctG>ctC	p.L572L	PGM2_ENST00000537241.1_Silent_p.L412L	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	572					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						ATGCAGAGCTGTGTGCCCCAC	0.493													G|||	862	0.172125	0.323	0.1167	5008	,	,		16436	0.1091		0.1471	False		,,,				2504	0.0982				p.L572L		Atlas-SNP	.											.	PGM2	45	.	0			c.G1716C						PASS	.	G		1271,3135	434.9+/-344.1	192,887,1124	98.0	90.0	93.0		1716	3.0	1.0	4	dbSNP_120	93	1189,7411	241.8+/-272.0	92,1005,3203	no	coding-synonymous	PGM2	NM_018290.3		284,1892,4327	CC,CG,GG		13.8256,28.847,18.9143		572/613	37857342	2460,10546	2203	4300	6503	SO:0001819	synonymous_variant	55276	exon13			AGAGCTGTGTGCC	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.1716G>C	4.37:g.37857342G>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	122	48	0.393443	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	37	CCDS3443.1																																																																																			G|0.826;C|0.174	0.174	strong		0.493	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290	
ICAM3	3385	hgsc.bcm.edu	37	19	10444603	10444603	+	Missense_Mutation	SNP	C	C	G	rs2230399	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10444603C>G	ENST00000160262.5	-	7	1782	c.1574G>C	c.(1573-1575)aGc>aCc	p.S525T	ICAM3_ENST00000589261.1_Missense_Mutation_p.S448T|RAVER1_ENST00000293677.6_5'Flank	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	525			S -> T (in dbSNP:rs2230399).		extracellular matrix organization (GO:0030198)|regulation of immune response (GO:0050776)|single organismal cell-cell adhesion (GO:0016337)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	13			OV - Ovarian serous cystadenocarcinoma(20;6.13e-09)|Epithelial(33;9.69e-06)|all cancers(31;2.05e-05)			CAGATAGGTGCTCTCCTCCCT	0.582													C|||	494	0.0986422	0.2383	0.0346	5008	,	,		14915	0.003		0.0755	False		,,,				2504	0.0777				p.S525T		Atlas-SNP	.											ICAM3,NS,adenoma,0,1	ICAM3	29	1	0			c.G1574C						PASS	.	C	THR/SER	880,3526	344.1+/-307.9	82,716,1405	194.0	163.0	174.0		1574	1.0	0.0	19	dbSNP_98	174	726,7874	177.2+/-226.9	26,674,3600	yes	missense	ICAM3	NM_002162.3	58	108,1390,5005	GG,GC,CC		8.4419,19.9728,12.3481	possibly-damaging	525/548	10444603	1606,11400	2203	4300	6503	SO:0001583	missense	3385	exon7			TAGGTGCTCTCCT		CCDS12235.1	19p13.3-p13.2	2013-01-11				ENSG00000076662		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5346	protein-coding gene	gene with protein product		146631				1448174	Standard	NM_002162		Approved	CDW50, ICAM-R, CD50	uc002mob.2	P32942		ENST00000160262.5:c.1574G>C	19.37:g.10444603C>G	ENSP00000160262:p.Ser525Thr	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	229	98	0.427948	NM_002162	Q6PD68	Missense_Mutation	SNP	ENST00000160262.5	37	CCDS12235.1	195	0.08928571428571429	124	0.25203252032520324	15	0.04143646408839779	1	0.0017482517482517483	55	0.07255936675461741	C	11.53	1.667187	0.29604	0.199728	0.084419	ENSG00000076662	ENST00000160262	T	0.02606	4.23	4.39	0.959	0.19624	.	1.288390	0.05251	N	0.513919	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P	0.39480	0.675	B	0.28553	0.091	T	0.48833	-0.9000	9	0.34782	T	0.22	-4.6196	4.6192	0.12442	0.0:0.6156:0.1808:0.2037	rs2230399;rs2230399	525	P32942	ICAM3_HUMAN	T	525	ENSP00000160262:S525T	ENSP00000160262:S525T	S	-	2	0	ICAM3	10305603	0.001000	0.12720	0.001000	0.08648	0.009000	0.06853	-0.193000	0.09573	0.197000	0.20387	-0.291000	0.09656	AGC	C|0.889;G|0.111	0.111	strong		0.582	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		
DND1	373863	hgsc.bcm.edu	37	5	140052331	140052331	+	Silent	SNP	G	G	T	rs200268202	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140052331G>T	ENST00000542735.1	-	3	346	c.303C>A	c.(301-303)gcC>gcA	p.A101A		NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	101	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)	p.A101A(1)		central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCGGGCATAGGCGAAGCCGC	0.687																																					p.A101A		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	1	Substitution - coding silent(1)	prostate(1)	c.C303A						scavenged	.						10.0	13.0	12.0					5																	140052331		2186	4289	6475	SO:0001819	synonymous_variant	373863	exon3			GGCATAGGCGAAG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.303C>A	5.37:g.140052331G>T		Somatic	15	1	0.0666667		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			G|0.952;T|0.047	0.047	strong		0.687	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
RNF207	388591	hgsc.bcm.edu	37	1	6279370	6279370	+	Missense_Mutation	SNP	G	G	C	rs846111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:6279370G>C	ENST00000377939.4	+	18	1935	c.1808G>C	c.(1807-1809)gGc>gCc	p.G603A	RNF207_ENST00000483336.1_3'UTR|ICMT_ENST00000495791.1_5'Flank|RNF207_ENST00000377948.2_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	603			G -> A (in dbSNP:rs846111). {ECO:0000269|PubMed:19305409}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		GCTCCGAACGGCCTCTCAGAA	0.498													G|||	864	0.172524	0.0227	0.1758	5008	,	,		16230	0.1756		0.2604	False		,,,				2504	0.2791				p.G603A		Atlas-SNP	.											RNF207,caecum,carcinoma,0,2	RNF207	45	2	0			c.G1808C						PASS	.	G	ALA/GLY	219,3517		9,201,1658	54.0	56.0	55.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1808	1.0	0.0	1	dbSNP_86	55	2163,6045		285,1593,2226	yes	missense	RNF207	NM_207396.2	60	294,1794,3884	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	26.3523,5.8619,19.9431	benign	603/635	6279370	2382,9562	1868	4104	5972	SO:0001583	missense	388591	exon18			CGAACGGCCTCTC	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1808G>C	1.37:g.6279370G>C	ENSP00000367173:p.Gly603Ala	Somatic	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	207	115	0.555556	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	380	0.17399267399267399	13	0.026422764227642278	70	0.19337016574585636	101	0.17657342657342656	196	0.25857519788918204	G	7.864	0.726640	0.15439	0.058619	0.263523	ENSG00000158286	ENST00000377939	T	0.15952	2.38	5.33	1.01	0.19927	.	0.326684	0.20268	U	0.095722	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.45264	-0.9273	9	0.13470	T	0.59	-0.5354	1.7254	0.02921	0.1818:0.1635:0.4863:0.1684	rs846111;rs3765570;rs17437807;rs846111	603	Q6ZRF8	RN207_HUMAN	A	603	ENSP00000367173:G603A	ENSP00000367173:G603A	G	+	2	0	RNF207	6201957	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.127000	0.10547	0.314000	0.23086	-0.140000	0.14226	GGC	G|0.803;C|0.197	0.197	strong		0.498	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
CD97	976	hgsc.bcm.edu	37	19	14512489	14512489	+	Missense_Mutation	SNP	G	G	A	rs2230748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:14512489G>A	ENST00000242786.5	+	11	1180	c.1100G>A	c.(1099-1101)cGg>cAg	p.R367Q	CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000357355.3_Missense_Mutation_p.R318Q|CD97_ENST00000358600.3_Missense_Mutation_p.R274Q	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	367			R -> Q (in dbSNP:rs2230748).		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						ATCCAGGAGCGGGGGGACAAG	0.637													g|||	1084	0.216454	0.0764	0.1499	5008	,	,		18239	0.4593		0.1054	False		,,,				2504	0.317				p.R367Q		Atlas-SNP	.											.	CD97	86	.	0			c.G1100A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	375,4031	189.9+/-215.9	15,345,1843	63.0	52.0	55.0		953,821,1100	-2.5	0.0	19	dbSNP_98	55	1132,7468	232.5+/-266.1	84,964,3252	no	missense,missense,missense	CD97	NM_001025160.2,NM_001784.4,NM_078481.3	43,43,43	99,1309,5095	AA,AG,GG		13.1628,8.5111,11.587	benign,benign,benign	318/787,274/743,367/836	14512489	1507,11499	2203	4300	6503	SO:0001583	missense	976	exon11			AGGAGCGGGGGGA		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	1711	protein-coding gene	gene with protein product	"""leukocyte antigen CD97"", ""seven-span transmembrane protein"", ""seven-transmembrane, heterodimeric receptor associated with inflammation"", ""seven transmembrane helix receptor"""	601211	"""CD97 antigen"""			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.1100G>A	19.37:g.14512489G>A	ENSP00000242786:p.Arg367Gln	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	37	CCDS32929.1	429	0.19642857142857142	43	0.08739837398373984	62	0.1712707182320442	244	0.42657342657342656	80	0.10554089709762533	G	1.460	-0.562593	0.03939	0.085111	0.131628	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	T;T;T	0.70045	-0.45;-0.37;0.01	5.29	-2.53	0.06326	.	.	.	.	.	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.27536	-1.0071	8	0.02654	T	1	.	7.4003	0.26960	0.2883:0.5487:0.163:0.0	rs2230748;rs2252171;rs52805742;rs60220444;rs2230748	274;318;367	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	Q	367;318;274;317	ENSP00000242786:R367Q;ENSP00000349918:R318Q;ENSP00000351413:R274Q	ENSP00000242786:R367Q	R	+	2	0	CD97	14373489	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.727000	0.00807	-0.574000	0.05990	-1.786000	0.00637	CGG	G|0.848;A|0.152	0.152	strong		0.637	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481	
ZNF668	79759	hgsc.bcm.edu	37	16	31075175	31075175	+	Silent	SNP	G	G	A	rs2303223	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31075175G>A	ENST00000538906.1	-	2	1390	c.606C>T	c.(604-606)ggC>ggT	p.G202G	ZNF668_ENST00000539836.3_Silent_p.G225G|AC135050.5_ENST00000568708.1_RNA|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000394983.2_Silent_p.G202G|ZNF668_ENST00000300849.4_Silent_p.G202G|ZNF668_ENST00000535577.1_Silent_p.G202G|ZNF668_ENST00000426488.2_Silent_p.G225G	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	202					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(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CATAGGCTTTGCCGCAACGCT	0.672													G|||	1732	0.345847	0.0174	0.4092	5008	,	,		18553	0.8859		0.3877	False		,,,				2504	0.1452				p.G225G	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											ZNF668,NS,carcinoma,-2,1	ZNF668	121	1	0			c.C675T						PASS	.	G	,,,	390,3998		24,342,1828	16.0	16.0	16.0		606,675,606,606	0.6	1.0	16	dbSNP_100	16	3446,5152		692,2062,1545	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	716,2404,3373	AA,AG,GG		40.0791,8.8879,29.5395	,,,	202/620,225/643,202/620,202/620	31075175	3836,9150	2194	4299	6493	SO:0001819	synonymous_variant	79759	exon3			GGCTTTGCCGCAA		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.606C>T	16.37:g.31075175G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																			G|0.657;A|0.343	0.343	strong		0.672	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
ZNF417	147687	hgsc.bcm.edu	37	19	58421128	58421128	+	Missense_Mutation	SNP	C	C	T	rs201944488	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58421128C>T	ENST00000312026.5	-	3	682	c.518G>A	c.(517-519)cGc>cAc	p.R173H	ZNF417_ENST00000595559.1_Missense_Mutation_p.R172H|CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000536263.1_5'UTR	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	173				R -> H (in Ref. 3; AAH25783). {ECO:0000305}.	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)		CCCAAACTCGCGGAAGACAAA	0.478													c|||	1646	0.328674	0.2496	0.3069	5008	,	,		19752	0.3631		0.3708	False		,,,				2504	0.3722				p.R173H		Atlas-SNP	.											ZNF417,NS,carcinoma,+1,1	ZNF417	44	1	0			c.G518A						scavenged	.	C	HIS/ARG	938,2814		296,346,1234	50.0	52.0	51.0		518	-3.3	0.0	19	dbSNP_134	51	3014,4976		1034,946,2015	no	missense	ZNF417	NM_152475.2	29	1330,1292,3249	TT,TC,CC		37.7222,25.0,33.657	benign	173/576	58421128	3952,7790	1876	3995	5871	SO:0001583	missense	147687	exon3			AACTCGCGGAAGA	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.518G>A	19.37:g.58421128C>T	ENSP00000311319:p.Arg173His	Somatic	325	2	0.00615385		WXS	Illumina HiSeq	Phase_I	518	211	0.407336	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	554	0.25366300366300365	111	0.22560975609756098	90	0.24861878453038674	138	0.24125874125874125	215	0.2836411609498681	.	0.284	-0.984691	0.02180	0.25	0.377222	ENSG00000173480	ENST00000312026	T	0.06294	3.32	1.86	-3.31	0.04988	.	.	.	.	.	T	0.00012	0.0000	N	0.16201	0.385	0.53688	P	2.999999999997449E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47086	-0.9144	8	0.41790	T	0.15	.	7.2829	0.26322	0.0:0.4727:0.0:0.5273	.	173;173	F5H0M9;Q8TAU3	.;ZN417_HUMAN	H	173	ENSP00000311319:R173H	ENSP00000311319:R173H	R	-	2	0	ZNF417	63112940	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.558000	0.05978	-0.695000	0.05105	-2.164000	0.00325	CGC	C|0.500;T|0.500	0.500	weak		0.478	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
SBF1	6305	hgsc.bcm.edu	37	22	50898026	50898026	+	Silent	SNP	G	G	A	rs58335489	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50898026G>A	ENST00000390679.3	-	27	3745	c.3561C>T	c.(3559-3561)taC>taT	p.Y1187Y	SBF1_ENST00000348911.6_Silent_p.Y1188Y|SBF1_ENST00000380817.3_Silent_p.Y1187Y|SBF1_ENST00000476293.1_5'Flank			O95248	MTMR5_HUMAN	SET binding factor 1	1187	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)		GGTTCTGGCGGTAGCAGCGGG	0.682													G|||	949	0.189497	0.0272	0.2507	5008	,	,		16077	0.4524		0.0666	False		,,,				2504	0.2209				p.Y1187Y		Atlas-SNP	.											.	SBF1	211	.	0			c.C3561T						PASS	.	G		143,4147		0,143,2002	18.0	21.0	20.0		3561	2.5	1.0	22	dbSNP_129	20	573,7889		18,537,3676	no	coding-synonymous	SBF1	NM_002972.2		18,680,5678	AA,AG,GG		6.7714,3.3333,5.6148		1187/1894	50898026	716,12036	2145	4231	6376	SO:0001819	synonymous_variant	6305	exon27			CTGGCGGTAGCAG	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.3561C>T	22.37:g.50898026G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				G|0.848;A|0.152	0.152	strong		0.682	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
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 GAIIx	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*	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	20	7	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		
DNMT3A	1788	hgsc.bcm.edu	37	2	25469502	25469502	+	Silent	SNP	C	C	T	rs2276598	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:25469502C>T	ENST00000264709.3	-	10	1603	c.1266G>A	c.(1264-1266)ctG>ctA	p.L422L	DNMT3A_ENST00000402667.1_Silent_p.L199L|DNMT3A_ENST00000380746.4_Silent_p.L233L|DNMT3A_ENST00000474887.1_5'Flank|DNMT3A_ENST00000321117.5_Silent_p.L422L	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	422					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGGTGGCTCCAGGCCCTTAG	0.622			"""Mis, F, N, S"""		AML								c|||	1121	0.223842	0.3162	0.1556	5008	,	,		18289	0.3204		0.1541	False		,,,				2504	0.1196				p.L422L		Atlas-SNP	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.G1266A						PASS	.	T	,,	1301,3097		189,923,1087	37.0	38.0	38.0		1266,699,1266	2.4	1.0	2	dbSNP_100	38	1355,7207		110,1135,3036	no	coding-synonymous,coding-synonymous,coding-synonymous	DNMT3A	NM_022552.3,NM_153759.2,NM_175629.1	,,	299,2058,4123	TT,TC,CC		15.8257,29.5816,20.4938	,,	422/913,233/724,422/913	25469502	2656,10304	2199	4281	6480	SO:0001819	synonymous_variant	1788	exon10			TGGCTCCAGGCCC		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1266G>A	2.37:g.25469502C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_175629	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Silent	SNP	ENST00000264709.3	37	CCDS33157.1																																																																																			C|0.792;T|0.208	0.208	strong		0.622	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	
MDC1	9656	hgsc.bcm.edu	37	6	30680916	30680916	+	Missense_Mutation	SNP	C	C	T	rs9262152	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30680916C>T	ENST00000376406.3	-	5	1450	c.803G>A	c.(802-804)aGg>aAg	p.R268K	MDC1_ENST00000494654.1_5'Flank|MDC1_ENST00000376405.2_Missense_Mutation_p.R268K|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	268	Required for nuclear localization (NLS1).		R -> K (in dbSNP:rs9262152). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:17974005}.		DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						ATCATTGTCCCTCTCCTTCAC	0.512								Other conserved DNA damage response genes					C|||	534	0.106629	0.0091	0.1412	5008	,	,		20215	0.0556		0.1789	False		,,,				2504	0.1922				p.R268K		Atlas-SNP	.											.	MDC1	218	.	0			c.G803A						PASS	.	C	LYS/ARG	96,2926		4,88,1419	136.0	124.0	128.0		803	-2.1	0.0	6	dbSNP_118	128	857,4561		72,713,1924	yes	missense	MDC1	NM_014641.2	26	76,801,3343	TT,TC,CC		15.8176,3.1767,11.2915	benign	268/2090	30680916	953,7487	1511	2709	4220	SO:0001583	missense	9656	exon5			TTGTCCCTCTCCT	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.803G>A	6.37:g.30680916C>T	ENSP00000365588:p.Arg268Lys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	177	31	0.175141	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	234	0.10714285714285714	9	0.018292682926829267	46	0.1270718232044199	41	0.07167832167832168	138	0.1820580474934037	C	1.495	-0.553583	0.03996	0.031767	0.158176	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.02280	4.36;4.37	4.59	-2.14	0.07123	.	0.689133	0.12094	N	0.500150	T	0.00328	0.0010	N	0.20401	0.57	0.80722	P	0.0	B;B;B	0.20550	0.046;0.017;0.001	B;B;B	0.17722	0.019;0.011;0.001	T	0.44112	-0.9349	9	0.06891	T	0.86	1.8205	1.2461	0.01973	0.1313:0.3147:0.183:0.3711	rs9262152;rs59033148;rs9262152	268;140;268	Q14676-2;B4DYH4;Q14676	.;.;MDC1_HUMAN	K	268;268;268;140	ENSP00000365588:R268K;ENSP00000365587:R268K	ENSP00000365587:R268K	R	-	2	0	MDC1	30788895	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.735000	0.04888	-0.391000	0.07763	0.655000	0.94253	AGG	C|0.897;T|0.103	0.103	strong		0.512	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907385	12907385	+	Missense_Mutation	SNP	G	G	A	rs150590256		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907385G>A	ENST00000317869.6	-	2	983	c.758C>T	c.(757-759)cCa>cTa	p.P253L		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	253						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						ATCATCCAGTGGGTCCCCCTC	0.507																																					p.P253L		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	0			c.C758T						scavenged	.						104.0	106.0	105.0					1																	12907385		2202	4295	6497	SO:0001583	missense	343069	exon2			TCCAGTGGGTCCC	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.758C>T	1.37:g.12907385G>A	ENSP00000365370:p.Pro253Leu	Somatic	132	12	0.0909091		WXS	Illumina HiSeq	Phase_I	213	8	0.0375587	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.105909	0.00356	.	.	ENSG00000179172	ENST00000317869	T	0.08008	3.14	0.848	-1.58	0.08479	.	0.359505	0.22097	N	0.064662	T	0.01287	0.0042	N	0.00074	-2.255	0.23930	N	0.996434	B	0.02656	0.0	B	0.01281	0.0	T	0.47032	-0.9148	10	0.45353	T	0.12	.	4.3013	0.10925	0.7598:0.0:0.2402:0.0	.	253	O60812	HNRCL_HUMAN	L	253	ENSP00000365370:P253L	ENSP00000365370:P253L	P	-	2	0	HNRNPCL1	12829972	1.000000	0.71417	0.049000	0.19019	0.006000	0.05464	1.770000	0.38532	-0.163000	0.10946	-0.755000	0.03482	CCA	.	.	weak		0.507	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
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 GAIIx	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_ENST00000438926.2_Silent_p.F223F|SLC12A3_ENST00000566786.1_Silent_p.F222F|SLC12A3_ENST00000262502.5_Silent_p.F222F			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		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	4	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		
RRP12	23223	hgsc.bcm.edu	37	10	99125949	99125949	+	Missense_Mutation	SNP	C	C	T	rs2275580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:99125949C>T	ENST00000370992.4	-	29	3544	c.3433G>A	c.(3433-3435)Ggc>Agc	p.G1145S	RRP12_ENST00000414986.1_Missense_Mutation_p.G1084S|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000315563.6_Missense_Mutation_p.G1045S|RRP12_ENST00000536831.1_Missense_Mutation_p.G863S	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1145			G -> S (in dbSNP:rs2275580). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.			integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		ACCTTGAAGCCGTGGTCCTTC	0.627													C|||	1983	0.395966	0.1271	0.562	5008	,	,		16365	0.3968		0.5934	False		,,,				2504	0.4376				p.G1145S		Atlas-SNP	.											.	RRP12	97	.	0			c.G3433A						PASS	.	C	SER/GLY,SER/GLY	928,3478	354.1+/-312.5	110,708,1385	125.0	99.0	108.0		3250,3433	4.3	1.0	10	dbSNP_100	108	5136,3464	635.4+/-399.0	1550,2036,714	yes	missense,missense	RRP12	NM_001145114.1,NM_015179.3	56,56	1660,2744,2099	TT,TC,CC		40.2791,21.0622,46.6246	possibly-damaging,possibly-damaging	1084/1237,1145/1298	99125949	6064,6942	2203	4300	6503	SO:0001583	missense	23223	exon29			TGAAGCCGTGGTC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3433G>A	10.37:g.99125949C>T	ENSP00000360031:p.Gly1145Ser	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	970	0.4441391941391941	59	0.11991869918699187	208	0.574585635359116	248	0.43356643356643354	455	0.600263852242744	C	19.39	3.819004	0.71028	0.210622	0.597209	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.31510	1.49;1.49;1.5;1.49	5.19	4.28	0.50868	.	0.094109	0.64402	D	0.000001	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.9999928566	D;B;P;P	0.62365	0.991;0.383;0.719;0.943	B;B;B;B	0.41510	0.359;0.114;0.164;0.178	T	0.44620	-0.9316	9	0.16420	T	0.52	-25.5986	12.1406	0.53996	0.0:0.9174:0.0:0.0826	rs2275580;rs17850958;rs60383842;rs2275580	1084;1045;863;1145	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	S	1145;1045;1084;863	ENSP00000360031:G1145S;ENSP00000324315:G1045S;ENSP00000414863:G1084S;ENSP00000446184:G863S	ENSP00000324315:G1045S	G	-	1	0	RRP12	99115939	1.000000	0.71417	0.980000	0.43619	0.974000	0.67602	5.615000	0.67702	2.422000	0.82143	0.555000	0.69702	GGC	C|0.553;T|0.447	0.447	strong		0.627	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
ZNF366	167465	hgsc.bcm.edu	37	5	71757267	71757267	+	Silent	SNP	C	C	T	rs78980395	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:71757267C>T	ENST00000318442.5	-	2	547	c.57G>A	c.(55-57)gtG>gtA	p.V19V		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	19					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		GGGTCTTCTTCACAGCCAAGT	0.502													C|||	244	0.048722	0.0401	0.0231	5008	,	,		16693	0.0546		0.0298	False		,,,				2504	0.092				p.V19V		Atlas-SNP	.											.	ZNF366	108	.	0			c.G57A						PASS	.						65.0	62.0	63.0					5																	71757267		2203	4300	6503	SO:0001819	synonymous_variant	167465	exon2			CTTCTTCACAGCC	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.57G>A	5.37:g.71757267C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_152625	Q5HYI9|Q7RTV4	Silent	SNP	ENST00000318442.5	37	CCDS4015.1																																																																																			C|0.950;T|0.050	0.050	strong		0.502	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
PTPRN2	5799	hgsc.bcm.edu	37	7	157396697	157396697	+	Silent	SNP	G	G	A	rs17853260	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:157396697G>A	ENST00000389418.4	-	16	2424	c.2415C>T	c.(2413-2415)ccC>ccT	p.P805P	PTPRN2_ENST00000389416.4_Silent_p.P788P|PTPRN2_ENST00000389413.3_Silent_p.P776P|PTPRN2_ENST00000409483.1_Silent_p.P767P|PTPRN2_ENST00000404321.2_Silent_p.P828P	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	805	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CACTTACGATGGGGCTAGCGT	0.622													G|||	599	0.119609	0.0129	0.1628	5008	,	,		18666	0.006		0.334	False		,,,				2504	0.1299				p.P805P		Atlas-SNP	.											PTPRN2,NS,carcinoma,0,1	PTPRN2	243	1	0			c.C2415T						PASS	.		,,	300,4106	163.6+/-195.4	10,280,1913	112.0	85.0	94.0		2415,2364,2328	4.4	1.0	7	dbSNP_123	94	2910,5690	454.6+/-363.5	514,1882,1904	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	524,2162,3817	AA,AG,GG		33.8372,6.8089,24.6809	,,	805/1016,788/999,776/987	157396697	3210,9796	2203	4300	6503	SO:0001819	synonymous_variant	5799	exon16			TACGATGGGGCTA	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2415C>T	7.37:g.157396697G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	100	37	0.37	NM_002847	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.779;A|0.221	0.221	strong		0.622	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
VSIG10	54621	hgsc.bcm.edu	37	12	118520170	118520170	+	Silent	SNP	G	G	A	rs7488309	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:118520170G>A	ENST00000359236.5	-	3	702	c.426C>T	c.(424-426)taC>taT	p.Y142Y	VSIG10_ENST00000536905.1_5'UTR	NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	142	Ig-like C2-type 2.					integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						CCCTGGCTGCGTAGAGGGTGC	0.607													G|||	2320	0.463259	0.4705	0.5908	5008	,	,		15185	0.5903		0.4115	False		,,,				2504	0.2853				p.Y142Y		Atlas-SNP	.											VSIG10,colon,carcinoma,0,1	VSIG10	41	1	0			c.C426T						PASS	.	G		1665,2219		373,919,650	66.0	72.0	70.0		426	-4.7	0.0	12	dbSNP_116	70	3382,4882		685,2012,1435	no	coding-synonymous	VSIG10	NM_019086.5		1058,2931,2085	AA,AG,GG		40.9245,42.8682,41.5459		142/541	118520170	5047,7101	1942	4132	6074	SO:0001819	synonymous_variant	54621	exon3			GGCTGCGTAGAGG		CCDS44992.1	12q24.23	2013-01-29			ENSG00000176834	ENSG00000176834		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26078	protein-coding gene	gene with protein product						12477932	Standard	NM_019086		Approved		uc001tws.3	Q8N0Z9		ENST00000359236.5:c.426C>T	12.37:g.118520170G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_019086	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																			G|0.506;A|0.494	0.494	strong		0.607	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
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 GAIIx	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_ENST00000373023.2_Silent_p.I638I|INPP5B_ENST00000373024.3_Silent_p.I558I|INPP5B_ENST00000373027.1_Silent_p.I394I|INPP5B_ENST00000458109.2_3'UTR			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		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	92	37	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	
C2orf49	79074	hgsc.bcm.edu	37	2	105954140	105954140	+	Silent	SNP	G	G	A	rs55772482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:105954140G>A	ENST00000258457.2	+	1	325	c.96G>A	c.(94-96)gaG>gaA	p.E32E	C2orf49_ENST00000410049.1_Silent_p.E32E|RP11-332H14.2_ENST00000610036.1_lincRNA|C2orf49_ENST00000437250.2_Silent_p.E70E			Q9BVC5	ASHWN_HUMAN	chromosome 2 open reading frame 49	32					embryonic morphogenesis (GO:0048598)	tRNA-splicing ligase complex (GO:0072669)				endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6						TCACTCTGGAGCAGGTTGGGC	0.677													G|||	277	0.0553115	0.0076	0.1138	5008	,	,		5061	0.0238		0.1193	False		,,,				2504	0.045				p.E32E		Atlas-SNP	.											C2orf49,NS,carcinoma,+2,1	C2orf49	19	1	0			c.G96A						PASS	.	G		117,4279		1,115,2082	12.0	13.0	13.0		96	5.5	1.0	2	dbSNP_129	13	1114,7448		68,978,3235	no	coding-synonymous	C2orf49	NM_024093.1		69,1093,5317	AA,AG,GG		13.011,2.6615,9.4999		32/233	105954140	1231,11727	2198	4281	6479	SO:0001819	synonymous_variant	79074	exon1			TCTGGAGCAGGTT	BC001310	CCDS2068.1, CCDS74550.1	2q12.2	2009-04-22			ENSG00000135974	ENSG00000135974			28772	protein-coding gene	gene with protein product	"""ashwin"""					12477932	Standard	NM_001286537		Approved	MGC5509, asw	uc002tcs.1	Q9BVC5	OTTHUMG00000130808	ENST00000258457.2:c.96G>A	2.37:g.105954140G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_024093	B3KXN3|B4E2G9	Silent	SNP	ENST00000258457.2	37	CCDS2068.1																																																																																			G|0.927;A|0.073	0.073	strong		0.677	C2orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253353.2	NM_024093	
TMEM63C	57156	hgsc.bcm.edu	37	14	77708804	77708804	+	Silent	SNP	C	C	T	rs61731611	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:77708804C>T	ENST00000298351.4	+	14	1323	c.1179C>T	c.(1177-1179)gaC>gaT	p.D393D		NM_020431.2	NP_065164.2	Q9P1W3	CSC1_HUMAN	transmembrane protein 63C	393					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)	integral component of membrane (GO:0016021)	calcium activated cation channel activity (GO:0005227)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(1)	23			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0342)		ACCCCAAAGACATTATTTGGT	0.542													C|||	733	0.146366	0.0106	0.1902	5008	,	,		19087	0.1042		0.2555	False		,,,				2504	0.2301				p.D393D		Atlas-SNP	.											.	TMEM63C	77	.	0			c.C1179T						PASS	.	C		190,3786		4,182,1802	178.0	173.0	175.0		1179	4.1	1.0	14	dbSNP_129	175	2000,6328		234,1532,2398	no	coding-synonymous	TMEM63C	NM_020431.2		238,1714,4200	TT,TC,CC		24.0154,4.7787,17.7991		393/807	77708804	2190,10114	1988	4164	6152	SO:0001819	synonymous_variant	57156	exon14			CAAAGACATTATT		CCDS45141.1	14q24.3	2014-05-30	2005-07-25	2005-07-25	ENSG00000165548	ENSG00000165548			23787	protein-coding gene	gene with protein product	"""calcium permeable stress-gated cation channel 1 homolog (Arabidopsis)"""		"""chromosome 14 open reading frame 171"""	C14orf171		24503647	Standard	NM_020431		Approved	DKFZp434P0111, CSC1, hsCSC1	uc001xtf.2	Q9P1W3	OTTHUMG00000171557	ENST00000298351.4:c.1179C>T	14.37:g.77708804C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	107	35	0.327103	NM_020431	B2RN22|B3KWJ5|Q86TS3|Q86TS4|Q9NSQ4|Q9P1W1	Silent	SNP	ENST00000298351.4	37	CCDS45141.1																																																																																			C|0.813;T|0.187	0.187	strong		0.542	TMEM63C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414193.1		
SH3YL1	26751	hgsc.bcm.edu	37	2	224919	224919	+	Splice_Site	SNP	A	A	G	rs2290911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:224919A>G	ENST00000405430.1	-	11	1159	c.783T>C	c.(781-783)agT>agC	p.S261S	SH3YL1_ENST00000403712.2_Intron|SH3YL1_ENST00000356150.5_Splice_Site_p.S261S|SH3YL1_ENST00000403657.1_Intron|SH3YL1_ENST00000468321.1_5'UTR|SH3YL1_ENST00000403658.1_Intron|SH3YL1_ENST00000415006.2_Splice_Site_p.S165S			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	261					phosphatidylinositol biosynthetic process (GO:0006661)|regulation of ruffle assembly (GO:1900027)	ruffle membrane (GO:0032587)	phosphatase binding (GO:0019902)|phosphatidylinositol binding (GO:0035091)			large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.034)		all cancers(51;0.000647)|Epithelial(75;0.0043)|OV - Ovarian serous cystadenocarcinoma(76;0.00871)|GBM - Glioblastoma multiforme(21;0.148)		CATTTCTGTTACCTGCCAAAA	0.323													A|||	1280	0.255591	0.1747	0.2291	5008	,	,		17201	0.248		0.331	False		,,,				2504	0.3139				p.S261S		Atlas-SNP	.											.	SH3YL1	49	.	0			c.T783C						PASS	.	A	,	733,2907		71,591,1158	119.0	111.0	114.0		,783	2.6	0.7	2	dbSNP_100	114	2797,5365		459,1879,1743	yes	intron,coding-synonymous-near-splice	SH3YL1	NM_001159597.1,NM_015677.2	,	530,2470,2901	GG,GA,AA		34.2686,20.1374,29.9102	,	,261/343	224919	3530,8272	1820	4081	5901	SO:0001630	splice_region_variant	26751	exon9			TCTGTTACCTGCC		CCDS42646.1, CCDS42646.2, CCDS54332.1, CCDS62841.1	2p25.3	2013-10-18	2013-10-18		ENSG00000035115	ENSG00000035115			29546	protein-coding gene	gene with protein product			"""SH3 domain containing, Ysc84-like 1 (S. cerevisiae)"""			21624956	Standard	NM_001282687		Approved	Ray, DKFZP586F1318	uc002qvx.3	Q96HL8	OTTHUMG00000151359	ENST00000405430.1:c.782-1T>C	2.37:g.224919A>G		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	243	119	0.489712	NM_015677	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Silent	SNP	ENST00000405430.1	37																																																																																				A|0.752;G|0.248	0.248	strong		0.323	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677	Silent
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 GAIIx	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		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	55	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	
TELO2	9894	hgsc.bcm.edu	37	16	1559838	1559838	+	Silent	SNP	T	T	C	rs3180228	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1559838T>C	ENST00000262319.6	+	21	2694	c.2415T>C	c.(2413-2415)gcT>gcC	p.A805A		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	805					regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				CAGACGTGGCTGAGAAAGACC	0.622													C|||	2112	0.421725	0.6876	0.2147	5008	,	,		17239	0.4226		0.2455	False		,,,				2504	0.3896				p.A805A		Atlas-SNP	.											.	TELO2	44	.	0			c.T2415C						PASS	.	C		2721,1669	487.3+/-360.9	840,1041,314	46.0	46.0	46.0		2415	-10.7	0.1	16	dbSNP_105	46	2218,6380	689.4+/-404.4	282,1654,2363	no	coding-synonymous	TELO2	NM_016111.3		1122,2695,2677	CC,CT,TT		25.7967,38.0182,38.0274		805/838	1559838	4939,8049	2195	4299	6494	SO:0001819	synonymous_variant	9894	exon21			CGTGGCTGAGAAA	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.2415T>C	16.37:g.1559838T>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Silent	SNP	ENST00000262319.6	37	CCDS32363.1																																																																																			T|0.598;C|0.402	0.402	strong		0.622	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
UBE2J1	51465	hgsc.bcm.edu	37	6	90039670	90039670	+	Missense_Mutation	SNP	G	G	C	rs10502	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90039670G>C	ENST00000435041.2	-	8	963	c.685C>G	c.(685-687)Ctc>Gtc	p.L229V		NM_016021.2	NP_057105.2	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	229			L -> V (in dbSNP:rs10502). {ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6, ECO:0000269|Ref.8}.		ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(11)|stomach(1)	18		all_cancers(76;1.65e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;2.5e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0139)		GAATTCTGGAGTCCGTACTAG	0.433													C|||	3417	0.682308	0.8918	0.4856	5008	,	,		17126	0.7391		0.3648	False		,,,				2504	0.8067				p.L229V		Atlas-SNP	.											.	UBE2J1	28	.	0			c.C685G						PASS	.	C	VAL/LEU	3576,830	326.7+/-299.7	1446,684,73	88.0	93.0	91.0		685	2.7	0.0	6	dbSNP_52	91	3251,5349	649.3+/-400.6	634,1983,1683	yes	missense	UBE2J1	NM_016021.2	32	2080,2667,1756	CC,CG,GG		37.8023,18.8379,47.5088	benign	229/319	90039670	6827,6179	2203	4300	6503	SO:0001583	missense	51465	exon8			TCTGGAGTCCGTA	AJ245898	CCDS5021.1	6q15	2014-01-28	2012-06-08		ENSG00000198833	ENSG00000198833		"""Ubiquitin-conjugating enzymes E2"""	17598	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2, J1 (UBC6 homolog, yeast)"""			10708578	Standard	NM_016021		Approved	HSPC153, CGI-76, NCUBE1, UBC6	uc003pnc.3	Q9Y385	OTTHUMG00000016337	ENST00000435041.2:c.685C>G	6.37:g.90039670G>C	ENSP00000451261:p.Leu229Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_016021	A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10	Missense_Mutation	SNP	ENST00000435041.2	37	CCDS5021.1	1289	0.5902014652014652	434	0.8821138211382114	172	0.47513812154696133	406	0.7097902097902098	277	0.3654353562005277	C	0.012	-1.667752	0.00765	0.811621	0.378023	ENSG00000198833	ENST00000435041;ENST00000536477	T	0.62232	0.04	5.87	2.74	0.32292	.	1.177030	0.05953	N	0.639136	T	0.17746	0.0426	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09079	-1.0691	9	0.29301	T	0.29	-16.7701	4.3479	0.11141	0.1088:0.5818:0.1061:0.2033	rs10502;rs1137338;rs1804991;rs3201092;rs3777513;rs11557089;rs17295734;rs17354187;rs17742143;rs17845403;rs17858261;rs52799914;rs61042761;rs10502	229	Q9Y385	UB2J1_HUMAN	V	229;214	ENSP00000451261:L229V	ENSP00000354684:L229V	L	-	1	0	UBE2J1	90096389	0.000000	0.05858	0.023000	0.16930	0.034000	0.12701	-0.938000	0.03938	0.407000	0.25591	-0.120000	0.15030	CTC	G|0.396;C|0.604	0.604	strong		0.433	UBE2J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043742.2	NM_016021	
DEPDC5	9681	hgsc.bcm.edu	37	22	32217539	32217539	+	Missense_Mutation	SNP	C	C	T	rs16989528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:32217539C>T	ENST00000382112.3	+	22	1992	c.1922C>T	c.(1921-1923)gCg>gTg	p.A641V	DEPDC5_ENST00000536766.1_Intron|DEPDC5_ENST00000382105.2_Intron|DEPDC5_ENST00000400249.2_Missense_Mutation_p.A641V|DEPDC5_ENST00000382111.2_Missense_Mutation_p.A641V|DEPDC5_ENST00000400246.1_Missense_Mutation_p.A641V|DEPDC5_ENST00000400248.2_Missense_Mutation_p.A641V|DEPDC5_ENST00000266091.3_Missense_Mutation_p.A641V|DEPDC5_ENST00000535622.1_Intron	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	641			A -> V (in dbSNP:rs16989528).		intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						CAGAATATGGCGGAGCTACAA	0.547													C|||	164	0.0327476	0.003	0.0173	5008	,	,		19700	0.0228		0.0408	False		,,,				2504	0.0859				p.A641V		Atlas-SNP	.											.	DEPDC5	266	.	0			c.C1922T						PASS	.	C	VAL/ALA,VAL/ALA,,VAL/ALA	22,4046		0,22,2012	139.0	146.0	144.0		1922,1922,,1922	0.4	1.0	22	dbSNP_123	144	247,8113		3,241,3936	yes	missense,missense,intron,missense	DEPDC5	NM_001136029.2,NM_001242896.1,NM_001242897.1,NM_014662.3	64,64,,64	3,263,5948	TT,TC,CC		2.9545,0.5408,2.1645	benign,benign,,benign	641/1595,641/1604,,641/1573	32217539	269,12159	2034	4180	6214	SO:0001583	missense	9681	exon22			ATATGGCGGAGCT	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.1922C>T	22.37:g.32217539C>T	ENSP00000371546:p.Ala641Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001136029	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	67	0.030677655677655676	5	0.01016260162601626	10	0.027624309392265192	18	0.03146853146853147	34	0.044854881266490766	C	15.45	2.837225	0.50951	0.005408	0.029545	ENSG00000100150	ENST00000266091;ENST00000400249;ENST00000400246;ENST00000382112;ENST00000382111;ENST00000400248	T;T;T;T;T;T	0.22945	1.94;1.95;1.93;1.95;1.93;1.95	6.01	0.383	0.16239	.	0.216429	0.47455	N	0.000238	T	0.03739	0.0106	L	0.35723	1.085	0.80722	D	1	B;B;B;B	0.21821	0.046;0.061;0.009;0.036	B;B;B;B	0.16722	0.01;0.016;0.003;0.007	T	0.11941	-1.0567	10	0.23891	T	0.37	.	10.0513	0.42216	0.0:0.6722:0.0:0.3278	rs16989528;rs16989528	641;641;641;641	B9EGN9;O75140-4;A8MPX9;O75140	.;.;.;DEPD5_HUMAN	V	641	ENSP00000266091:A641V;ENSP00000383108:A641V;ENSP00000383105:A641V;ENSP00000371546:A641V;ENSP00000371545:A641V;ENSP00000383107:A641V	ENSP00000266091:A641V	A	+	2	0	DEPDC5	30547539	0.927000	0.31430	0.983000	0.44433	0.976000	0.68499	1.050000	0.30404	0.158000	0.19367	0.655000	0.94253	GCG	C|0.967;T|0.033	0.033	strong		0.547	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
UPK1A	11045	hgsc.bcm.edu	37	19	36159368	36159368	+	Missense_Mutation	SNP	T	T	G	rs2267586	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36159368T>G	ENST00000222275.2	+	2	97	c.97T>G	c.(97-99)Tcc>Gcc	p.S33A	UPK1A_ENST00000379013.2_Missense_Mutation_p.S33A|UPK1A-AS1_ENST00000443196.1_RNA	NM_007000.2	NP_008931.1	O00322	UPK1A_HUMAN	uroplakin 1A	33			S -> A (in dbSNP:rs2267586).		epithelial cell differentiation (GO:0030855)|protein oligomerization (GO:0051259)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	monosaccharide binding (GO:0048029)|protein homodimerization activity (GO:0042803)	p.S33A(1)		breast(1)|large_intestine(4)|lung(2)|stomach(2)	9	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTCAGGCCTGTCCCTGTTTGC	0.597													G|||	602	0.120208	0.0598	0.1023	5008	,	,		18777	0.2312		0.1163	False		,,,				2504	0.1043				p.S33A		Atlas-SNP	.											UPK1A,NS,carcinoma,0,1	UPK1A	23	1	1	Substitution - Missense(1)	stomach(1)	c.T97G						scavenged	.	G	ALA/SER	310,4096	798.0+/-415.4	3,304,1896	110.0	80.0	91.0		97	5.3	1.0	19	dbSNP_100	91	787,7813	783.5+/-407.6	35,717,3548	no	missense	UPK1A	NM_007000.2	99	38,1021,5444	GG,GT,TT		9.1512,7.0359,8.4346	possibly-damaging	33/259	36159368	1097,11909	2203	4300	6503	SO:0001583	missense	11045	exon2			GGCCTGTCCCTGT	AF085807	CCDS12470.1, CCDS62640.1	19q13.1	2013-02-14			ENSG00000105668	ENSG00000105668		"""Tetraspanins"""	12577	protein-coding gene	gene with protein product		611557				9846985, 10404304	Standard	NM_007000		Approved	TSPAN21	uc002oaw.3	O00322	OTTHUMG00000048115	ENST00000222275.2:c.97T>G	19.37:g.36159368T>G	ENSP00000222275:p.Ser33Ala	Somatic	89	2	0.0224719		WXS	Illumina HiSeq	Phase_I	90	53	0.588889	NM_007000	Q3KNU5|Q3KNU6	Missense_Mutation	SNP	ENST00000222275.2	37	CCDS12470.1	310	0.14194139194139194	36	0.07317073170731707	36	0.09944751381215469	148	0.25874125874125875	90	0.11873350923482849	G	15.38	2.816433	0.50527	0.070359	0.091512	ENSG00000105668	ENST00000222275;ENST00000379013	T;T	0.76709	-1.04;-1.04	5.33	5.33	0.75918	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00159	-1.955	0.54753	P	1.7000000000044757E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15809	-1.0424	9	0.02654	T	1	.	13.6535	0.62325	0.0:0.0:0.8438:0.1562	rs2267586;rs59655407;rs2267586	33;33	O00322-2;O00322	.;UPK1A_HUMAN	A	33	ENSP00000222275:S33A;ENSP00000368298:S33A	ENSP00000222275:S33A	S	+	1	0	UPK1A	40851208	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	4.266000	0.58871	1.402000	0.46780	-0.217000	0.12591	TCC	T|0.893;G|0.107	0.107	strong		0.597	UPK1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109486.3		
OR2F2	135948	hgsc.bcm.edu	37	7	143632833	143632833	+	Missense_Mutation	SNP	A	A	G	rs13229174	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143632833A>G	ENST00000408955.2	+	1	575	c.508A>G	c.(508-510)Act>Gct	p.T170A		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, member 2	170			T -> A (in dbSNP:rs13229174).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(19)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	32	Melanoma(164;0.0903)					GCCCATGTGCACTAACAAGTT	0.522													A|||	511	0.102037	0.1596	0.1239	5008	,	,		21740	0.001		0.167	False		,,,				2504	0.046				p.T170A		Atlas-SNP	.											.	OR2F2	63	.	0			c.A508G						PASS	.	A	ALA/THR	725,3681	300.1+/-286.2	55,615,1533	165.0	145.0	152.0		508	2.3	0.1	7	dbSNP_121	152	1704,6896	312.1+/-310.7	162,1380,2758	yes	missense	OR2F2	NM_001004685.1	58	217,1995,4291	GG,GA,AA		19.814,16.4548,18.676	benign	170/318	143632833	2429,10577	2203	4300	6503	SO:0001583	missense	135948	exon1			ATGTGCACTAACA		CCDS43666.1	7q33-q35	2012-08-09			ENSG00000221910	ENSG00000221910		"""GPCR / Class A : Olfactory receptors"""	8247	protein-coding gene	gene with protein product							Standard	NM_001004685		Approved	OR7-1	uc011ktv.2	O95006	OTTHUMG00000157768	ENST00000408955.2:c.508A>G	7.37:g.143632833A>G	ENSP00000386222:p.Thr170Ala	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	181	104	0.574586	NM_001004685	A4D2G0|Q6IFP8	Missense_Mutation	SNP	ENST00000408955.2	37	CCDS43666.1	247	0.1130952380952381	78	0.15853658536585366	50	0.13812154696132597	0	0.0	119	0.15699208443271767	A	5.995	0.367465	0.11352	0.164548	0.19814	ENSG00000221910	ENST00000408955	T	0.37058	1.22	3.49	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.602412	0.14920	N	0.290681	T	0.00012	0.0000	N	0.02345	-0.59	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.22173	-1.0224	9	0.72032	D	0.01	-0.0686	2.9661	0.05908	0.6654:0.0:0.1192:0.2154	rs13229174;rs52797869;rs13229174	170	O95006	OR2F2_HUMAN	A	170	ENSP00000386222:T170A	ENSP00000386222:T170A	T	+	1	0	OR2F2	143263766	0.000000	0.05858	0.093000	0.20910	0.482000	0.33219	0.187000	0.16998	0.494000	0.27859	0.402000	0.26972	ACT	A|0.871;G|0.129	0.129	strong		0.522	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1		
ANKLE2	23141	hgsc.bcm.edu	37	12	133306503	133306503	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:133306503A>G	ENST00000357997.5	-	11	2334	c.2245T>C	c.(2245-2247)Tcc>Ccc	p.S749P	ANKLE2_ENST00000539605.1_Missense_Mutation_p.S687P|ANKLE2_ENST00000542657.1_Missense_Mutation_p.S104P|ANKLE2_ENST00000542282.1_Missense_Mutation_p.S104P|ANKLE2_ENST00000542374.1_Intron	NM_015114.1	NP_055929.1	Q86XL3	ANKL2_HUMAN	ankyrin repeat and LEM domain containing 2	749					mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|negative regulation of phosphorylation (GO:0042326)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of catalytic activity (GO:0050790)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	protein phosphatase 2A binding (GO:0051721)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(2)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(20)|ovary(1)|urinary_tract(2)	45	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.3e-08)|Epithelial(86;1.56e-07)|all cancers(50;4.94e-06)		GGTGTCTTGGAAACGCTACGT	0.453																																					p.S749P		Atlas-SNP	.											ANKLE2,NS,carcinoma,+1,1	ANKLE2	76	1	0			c.T2245C						scavenged	.						150.0	147.0	148.0					12																	133306503		1946	4132	6078	SO:0001583	missense	23141	exon11			TCTTGGAAACGCT	AB014592	CCDS41869.1	12q24.33	2013-01-11	2008-03-25	2008-03-25	ENSG00000176915	ENSG00000176915		"""Ankyrin repeat domain containing"""	29101	protein-coding gene	gene with protein product	"""LEM domain containing 7"""		"""KIAA0692"""	KIAA0692		9734811	Standard	XM_005266159		Approved	LEMD7, Lem4	uc001ukx.2	Q86XL3	OTTHUMG00000168046	ENST00000357997.5:c.2245T>C	12.37:g.133306503A>G	ENSP00000350686:p.Ser749Pro	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	223	5	0.0224215	NM_015114	A8KAG3|B3KN97|B3KSF8|O75176|Q6P6A5|Q8TAZ9|Q96DH4	Missense_Mutation	SNP	ENST00000357997.5	37	CCDS41869.1	.	.	.	.	.	.	.	.	.	.	A	8.095	0.775371	0.16051	.	.	ENSG00000176915	ENST00000539605;ENST00000357997;ENST00000542282;ENST00000542657;ENST00000538766	T;T;T;T;T	0.48836	1.82;1.82;0.8;0.8;0.8	5.64	1.78	0.24846	.	1.224630	0.05489	N	0.556351	T	0.39517	0.1081	L	0.54323	1.7	0.09310	N	0.999999	P	0.44006	0.824	B	0.36719	0.231	T	0.24693	-1.0153	10	0.35671	T	0.21	-1.3451	4.9923	0.14220	0.7138:0.0:0.1514:0.1348	.	749	Q86XL3	ANKL2_HUMAN	P	687;749;104;104;104	ENSP00000446268:S687P;ENSP00000350686:S749P;ENSP00000437807:S104P;ENSP00000438551:S104P;ENSP00000445760:S104P	ENSP00000350686:S749P	S	-	1	0	ANKLE2	131816576	0.000000	0.05858	0.008000	0.14137	0.016000	0.09150	-0.091000	0.11146	0.108000	0.17862	0.524000	0.50904	TCC	.	.	none		0.453	ANKLE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397712.1		
CDHR3	222256	hgsc.bcm.edu	37	7	105662690	105662690	+	Silent	SNP	T	T	C	rs10258293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:105662690T>C	ENST00000317716.9	+	14	1952	c.1872T>C	c.(1870-1872)aaT>aaC	p.N624N	CDHR3_ENST00000478080.1_Silent_p.N536N|CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000542731.1_Silent_p.N624N|CDHR3_ENST00000343407.5_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	624	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)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						CTGGTTCCAATGTCACACGCC	0.428													t|||	879	0.175519	0.2186	0.1311	5008	,	,		23774	0.0813		0.2018	False		,,,				2504	0.2188				p.N624N		Atlas-SNP	.											.	CDHR3	153	.	0			c.T1872C						PASS	.	T		846,3206		81,684,1261	185.0	172.0	176.0		1872	-6.0	0.0	7	dbSNP_119	176	1404,6972		132,1140,2916	no	coding-synonymous	CDHR3	NM_152750.4		213,1824,4177	CC,CT,TT		16.7622,20.8786,18.1043		624/886	105662690	2250,10178	2026	4188	6214	SO:0001819	synonymous_variant	222256	exon14			TTCCAATGTCACA	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1872T>C	7.37:g.105662690T>C		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	252	122	0.484127	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1	347	0.15888278388278387	98	0.1991869918699187	58	0.16022099447513813	40	0.06993006993006994	151	0.19920844327176782	C	5.913	0.352602	0.11182	0.208786	0.167622	ENSG00000128536	ENST00000468477	.	.	.	5.23	-5.99	0.02213	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.99999885036	.	.	.	.	.	.	T	0.33394	-0.9870	3	.	.	.	-18.1293	18.9616	0.92679	0.0:0.252:0.0:0.748	rs10258293;rs56524808;rs10258293	.	.	.	T	93	.	.	M	+	2	0	CDHR3	105449926	0.000000	0.05858	0.002000	0.10522	0.787000	0.44495	-1.882000	0.01624	-1.794000	0.01256	-0.699000	0.03677	ATG	T|0.839;C|0.161	0.161	strong		0.428	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
SPTBN1	6711	hgsc.bcm.edu	37	2	54886347	54886347	+	Silent	SNP	G	G	A	rs1052820	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54886347G>A	ENST00000356805.4	+	31	6581	c.6300G>A	c.(6298-6300)ccG>ccA	p.P2100P	AC093110.3_ENST00000456363.1_RNA|SPTBN1_ENST00000333896.5_Silent_p.P2087P	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	2100					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)	p.P2100P(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGAGGCGGCCGCCTTCTCCCG	0.572													G|||	1393	0.278155	0.1498	0.3617	5008	,	,		15704	0.2877		0.3469	False		,,,				2504	0.3119				p.P2100P		Atlas-SNP	.											SPTBN1,NS,carcinoma,0,1	SPTBN1	378	1	1	Substitution - coding silent(1)	stomach(1)	c.G6300A						PASS	.	G	,	818,3588	324.5+/-298.6	80,658,1465	115.0	139.0	131.0		6300,6261	-2.9	1.0	2	dbSNP_86	131	2771,5829	440.9+/-359.6	415,1941,1944	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	495,2599,3409	AA,AG,GG		32.2209,18.5656,27.595	,	2100/2365,2087/2156	54886347	3589,9417	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon31			GCGGCCGCCTTCT		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.6300G>A	2.37:g.54886347G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			G|0.724;A|0.276	0.276	strong		0.572	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
DHRS7C	201140	hgsc.bcm.edu	37	17	9676148	9676148	+	Silent	SNP	C	C	T	rs2280489	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:9676148C>T	ENST00000330255.5	-	5	678	c.666G>A	c.(664-666)ccG>ccA	p.P222P	DHRS7C_ENST00000571134.1_Silent_p.P221P	NM_001105571.2|NM_001220493.1	NP_001099041.1|NP_001207422.1	A6NNS2	DRS7C_HUMAN	dehydrogenase/reductase (SDR family) member 7C	222					regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	extracellular region (GO:0005576)|longitudinal sarcoplasmic reticulum (GO:0014801)|sarcoplasmic reticulum membrane (GO:0033017)	retinol dehydrogenase activity (GO:0004745)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	15						GGATGAAAGTCGGGCTCACGG	0.582													C|||	502	0.10024	0.112	0.0692	5008	,	,		19224	0.0992		0.1054	False		,,,				2504	0.1022				p.P222P		Atlas-SNP	.											.	DHRS7C	34	.	0			c.G666A						PASS	.	C	,	512,3890	208.5+/-229.5	40,432,1729	75.0	82.0	80.0		663,666	-9.1	0.0	17	dbSNP_100	80	912,7686	198.0+/-242.5	48,816,3435	no	coding-synonymous,coding-synonymous	DHRS7C	NM_001105571.2,NM_001220493.1	,	88,1248,5164	TT,TC,CC		10.6071,11.6311,10.9538	,	221/312,222/313	9676148	1424,11576	2201	4299	6500	SO:0001819	synonymous_variant	201140	exon5			GAAAGTCGGGCTC		CCDS56020.1, CCDS58517.1	17p13.1	2011-09-20				ENSG00000184544		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	32423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 32C, member 2"""					19027726	Standard	NM_001105571		Approved	SDR32C2	uc010vvb.2	A6NNS2		ENST00000330255.5:c.666G>A	17.37:g.9676148C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	24	23	0.958333	NM_001220493	B7ZW74|B9EJH3	Silent	SNP	ENST00000330255.5	37	CCDS56020.1																																																																																			T|0.103;C|0.897	0.103	strong		0.582	DHRS7C-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439863.1	XM_113912	
OR56A1	120796	hgsc.bcm.edu	37	11	6048056	6048056	+	Silent	SNP	T	T	C	rs11040335	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6048056T>C	ENST00000316650.5	-	1	915	c.879A>G	c.(877-879)gcA>gcG	p.A293A		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, member 1	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAGGGTTCAATGCAGGAGGAA	0.458													.|||	1352	0.269968	0.2572	0.3689	5008	,	,		23031	0.0516		0.3966	False		,,,				2504	0.3119				p.A293A		Atlas-SNP	.											.	OR56A1	73	.	0			c.A879G						PASS	.	T		1183,3219	416.7+/-337.7	150,883,1168	109.0	100.0	103.0		879	1.2	0.9	11	dbSNP_120	103	3187,5405	482.3+/-370.9	596,1995,1705	no	coding-synonymous	OR56A1	NM_001001917.2		746,2878,2873	CC,CT,TT		37.0926,26.8741,33.6309		293/319	6048056	4370,8624	2201	4296	6497	SO:0001819	synonymous_variant	120796	exon1			GTTCAATGCAGGA	AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"""GPCR / Class A : Olfactory receptors"""	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.879A>G	11.37:g.6048056T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001001917	B2RNI2|Q6IFL0	Silent	SNP	ENST00000316650.5	37	CCDS31405.1																																																																																			T|0.695;C|0.305	0.305	strong		0.458	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917	
LTF	4057	hgsc.bcm.edu	37	3	46488854	46488854	+	Silent	SNP	T	T	C	rs2239692	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46488854T>C	ENST00000231751.4	-	10	1543	c.1248A>G	c.(1246-1248)ggA>ggG	p.G416G	LTF_ENST00000426532.2_Silent_p.G372G|LTF_ENST00000417439.1_Silent_p.G414G	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	416	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		TGTACACATATCCTCCATCCA	0.502													T|||	920	0.183706	0.1982	0.1138	5008	,	,		21975	0.1984		0.1183	False		,,,				2504	0.2658				p.G416G		Atlas-SNP	.											.	LTF	98	.	0			c.A1248G						PASS	.	T	,	828,3578	328.3+/-300.5	80,668,1455	260.0	215.0	230.0		1116,1248	-0.8	0.1	3	dbSNP_98	230	979,7613	212.1+/-252.5	54,871,3371	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	134,1539,4826	CC,CT,TT		11.3943,18.7926,13.9021	,	372/667,416/711	46488854	1807,11191	2203	4296	6499	SO:0001819	synonymous_variant	4057	exon10			CACATATCCTCCA		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1248A>G	3.37:g.46488854T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			T|0.845;C|0.155	0.155	strong		0.502	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
MFRP	83552	hgsc.bcm.edu	37	11	119216279	119216279	+	Silent	SNP	G	G	A	rs36015759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119216279G>A	ENST00000530681.1	-	5	636	c.492C>T	c.(490-492)taC>taT	p.Y164Y	MFRP_ENST00000360167.4_Silent_p.Y164Y|MFRP_ENST00000529147.1_5'UTR|C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000555262.1_Silent_p.Y164Y|MFRP_ENST00000449574.2_Silent_p.Y164Y	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	164	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		TGTTGGGGGGGTAAGGGTCTG	0.572													G|||	1009	0.201478	0.2489	0.1657	5008	,	,		18533	0.2024		0.2028	False		,,,				2504	0.1605				p.Y164Y		Atlas-SNP	.											.	MFRP	63	.	0			c.C492T						PASS	.	G	,	1038,3360	379.7+/-323.4	135,768,1296	50.0	49.0	49.0		,492	2.1	1.0	11	dbSNP_126	49	1885,6705	332.8+/-320.3	210,1465,2620	no	utr-5,coding-synonymous	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,	345,2233,3916	AA,AG,GG		21.9441,23.6016,22.5054	,	,164/580	119216279	2923,10065	2199	4295	6494	SO:0001819	synonymous_variant	83552	exon5			GGGGGGGTAAGGG	AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"""membrane-type frizzled-related protein"", ""complement C1q tumor necrosis factor-related protein 5 precursor variant 1"""	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.492C>T	11.37:g.119216279G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	58	10	0.172414	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Silent	SNP	ENST00000530681.1	37	CCDS8421.1																																																																																			G|0.781;A|0.219	0.219	strong		0.572	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433	
ZNF419	79744	hgsc.bcm.edu	37	19	58002964	58002964	+	Splice_Site	SNP	G	G	C	rs1135692	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58002964G>C	ENST00000221735.7	+	3	384	c.198G>C	c.(196-198)ctG>ctC	p.L66L	ZNF419_ENST00000354197.4_Splice_Site_p.L54L|ZNF419_ENST00000442920.2_Splice_Site_p.L53L|ZNF419_ENST00000426954.2_Splice_Site_p.L54L|ZNF419_ENST00000424930.2_Splice_Site_p.L67L|AC003005.4_ENST00000601674.1_Splice_Site_p.L53L|ZNF419_ENST00000518999.1_Splice_Site_p.L67L|ZNF419_ENST00000415379.2_Splice_Site_p.L53L|ZNF419_ENST00000520540.1_Splice_Site_p.L54L|ZNF419_ENST00000347466.6_Splice_Site_p.L67L			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		TGGCCTCTCTGGGTAAGGTTC	0.542													G|||	1310	0.261581	0.2761	0.2608	5008	,	,		20364	0.1181		0.3638	False		,,,				2504	0.2853				p.L67L		Atlas-SNP	.											.	ZNF419	134	.	0			c.G201C						PASS	.	G	,,,,,,	1262,3144	428.7+/-342.0	179,904,1120	67.0	69.0	69.0		201,162,159,201,162,159,198	-0.9	0.2	19	dbSNP_116	69	3010,5588	464.4+/-366.2	498,2014,1787	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	,,,,,,	677,2918,2907	CC,CG,GG		35.0081,28.6428,32.8514	,,,,,,	67/512,54/499,53/498,67/479,54/466,53/465,66/511	58002964	4272,8732	2203	4299	6502	SO:0001630	splice_region_variant	79744	exon3			CTCTCTGGGTAAG	AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.199+1G>C	19.37:g.58002964G>C		Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	128	123	0.960938	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																			G|0.730;C|0.270	0.270	strong		0.542	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	Silent
SLC25A29	123096	hgsc.bcm.edu	37	14	100759046	100759046	+	Silent	SNP	C	C	A	rs3825555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:100759046C>A	ENST00000359232.3	-	4	786	c.486G>T	c.(484-486)acG>acT	p.T162T	SLC25A29_ENST00000554912.1_Silent_p.T96T|RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000556505.1_Silent_p.T96T|SLC25A29_ENST00000539621.1_Silent_p.T96T|AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000392908.3_3'UTR|SLC25A29_ENST00000555927.1_Silent_p.T96T	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	162						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	acyl carnitine transmembrane transporter activity (GO:0015227)			NS(1)|endometrium(1)|ovary(1)	3		Melanoma(154;0.152)			L-Carnitine(DB00583)	CGAAGCTGGGCGTCTCACGCA	0.682													C|||	2656	0.530351	0.3865	0.6081	5008	,	,		13189	0.7083		0.5676	False		,,,				2504	0.4479				p.T162T		Atlas-SNP	.											SLC25A29,NS,carcinoma,0,1	SLC25A29	14	1	0			c.G486T						PASS	.	C		1913,2477		431,1051,713	29.0	19.0	22.0		486	1.1	1.0	14	dbSNP_107	22	4870,3718		1397,2076,821	no	coding-synonymous	SLC25A29	NM_001039355.1		1828,3127,1534	AA,AC,CC		43.293,43.5763,47.7346		162/304	100759046	6783,6195	2195	4294	6489	SO:0001819	synonymous_variant	123096	exon4			GCTGGGCGTCTCA	AK095532	CCDS32156.1	14q32.2	2013-05-22	2012-03-29	2004-01-21	ENSG00000197119	ENSG00000197119		"""Solute carriers"""	20116	protein-coding gene	gene with protein product		615064	"""chromosome 14 open reading frame 69"", ""solute carrier family 25, member 29"""	C14orf69			Standard	XM_005267343		Approved	FLJ38975	uc010twx.2	Q8N8R3	OTTHUMG00000171569	ENST00000359232.3:c.486G>T	14.37:g.100759046C>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_001039355	A3KMR5|Q541V0	Silent	SNP	ENST00000359232.3	37	CCDS32156.1																																																																																			C|0.465;A|0.535	0.535	strong		0.682	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3		
IFT172	26160	hgsc.bcm.edu	37	2	27676287	27676287	+	Silent	SNP	A	A	T	rs56076827	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27676287A>T	ENST00000260570.3	-	35	4018	c.3915T>A	c.(3913-3915)tcT>tcA	p.S1305S		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	1305					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					CGCTGTTTCCAGAGTCTCGCA	0.592													A|||	1771	0.353634	0.3722	0.4539	5008	,	,		19253	0.1667		0.3678	False		,,,				2504	0.4356				p.S1305S		Atlas-SNP	.											.	IFT172	119	.	0			c.T3915A						PASS	.	A		1612,2794	498.6+/-364.2	309,994,900	80.0	77.0	78.0		3915	-10.5	0.0	2	dbSNP_129	78	3276,5324	491.8+/-373.2	614,2048,1638	no	coding-synonymous	IFT172	NM_015662.1		923,3042,2538	TT,TA,AA		38.093,36.5865,37.5827		1305/1750	27676287	4888,8118	2203	4300	6503	SO:0001819	synonymous_variant	26160	exon35			GTTTCCAGAGTCT	AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.3915T>A	2.37:g.27676287A>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Silent	SNP	ENST00000260570.3	37	CCDS1755.1	674	0.3086080586080586	166	0.33739837398373984	143	0.39502762430939226	79	0.1381118881118881	286	0.37730870712401055	A	10.62	1.401574	0.25291	0.365865	0.38093	ENSG00000138002	ENST00000443889	.	.	.	5.26	-10.5	0.00291	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.41104	P	0.014307999999999987	.	.	.	.	.	.	T	0.33420	-0.9869	3	.	.	.	-1.0E-4	1.3346	0.02142	0.1981:0.2238:0.3303:0.2478	rs56076827;rs61741148	.	.	.	R	174	.	.	W	-	1	0	IFT172	27529791	0.037000	0.19845	0.001000	0.08648	0.137000	0.21094	-0.796000	0.04575	-2.461000	0.00536	0.260000	0.18958	TGG	A|0.641;T|0.359	0.359	strong		0.592	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	
RHBDD3	25807	hgsc.bcm.edu	37	22	29659960	29659960	+	Silent	SNP	C	C	T	rs879580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:29659960C>T	ENST00000216085.7	-	4	820	c.396G>A	c.(394-396)gaG>gaA	p.E132E	CTA-984G1.5_ENST00000433125.1_RNA	NM_012265.1	NP_036397.1	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	132					liver development (GO:0001889)|MAPK cascade (GO:0000165)|negative regulation of natural killer cell activation (GO:0032815)|positive regulation of protein catabolic process (GO:0045732)|regulation of acute inflammatory response (GO:0002673)|regulation of protein secretion (GO:0050708)|response to xenobiotic stimulus (GO:0009410)	integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			lung(1)|ovary(1)	2						GGCGGTGTCCCTCCCCAGCCA	0.687													c|||	1197	0.239018	0.1225	0.3818	5008	,	,		17495	0.2837		0.1561	False		,,,				2504	0.3344				p.E132E		Atlas-SNP	.											.	RHBDD3	17	.	0			c.G396A						PASS	.			536,3720		42,452,1634	18.0	17.0	17.0		396	4.2	0.4	22	dbSNP_86	17	1215,7155		76,1063,3046	no	coding-synonymous	RHBDD3	NM_012265.1		118,1515,4680	TT,TC,CC		14.5161,12.594,13.8682		132/387	29659960	1751,10875	2128	4185	6313	SO:0001819	synonymous_variant	25807	exon4			GTGTCCCTCCCCA	AL050346	CCDS13850.1	22q12.2	2006-02-22	2006-02-22	2006-02-22	ENSG00000100263	ENSG00000100263			1308	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 3"""	C22orf3		10591208, 15105437	Standard	NM_012265		Approved	PTAG	uc003aeq.1	Q9Y3P4	OTTHUMG00000151032	ENST00000216085.7:c.396G>A	22.37:g.29659960C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_012265	Q6I9X3|Q9UGQ7	Silent	SNP	ENST00000216085.7	37	CCDS13850.1																																																																																			C|0.814;T|0.186	0.186	strong		0.687	RHBDD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321085.1	NM_012265	
PTBP1	5725	hgsc.bcm.edu	37	19	804642	804642	+	Silent	SNP	C	C	T	rs3170451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:804642C>T	ENST00000349038.4	+	6	619	c.546C>T	c.(544-546)ccC>ccT	p.P182P	PTBP1_ENST00000356948.6_Silent_p.P182P|PTBP1_ENST00000394601.4_Silent_p.P182P|PTBP1_ENST00000350092.4_Intron|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	182					alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		GGCAGAGCCCCGTGCTCAGGA	0.682													C|||	806	0.160942	0.1331	0.2666	5008	,	,		14242	0.0228		0.1451	False		,,,				2504	0.2822				p.P182P		Atlas-SNP	.											PTBP1,NS,carcinoma,0,1	PTBP1	43	1	0			c.C546T						scavenged	.	C	,,,	571,3835	245.3+/-254.3	46,479,1678	60.0	58.0	59.0		546,546,546,	-9.6	0.0	19	dbSNP_105	59	1273,7327	247.4+/-275.4	85,1103,3112	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	131,1582,4790	TT,TC,CC		14.8023,12.9596,14.1781	,,,	182/558,182/551,182/532,	804642	1844,11162	2203	4300	6503	SO:0001819	synonymous_variant	5725	exon6			GAGCCCCGTGCTC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.546C>T	19.37:g.804642C>T		Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.860;T|0.140	0.140	strong		0.682	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
CRYBA1	1411	hgsc.bcm.edu	37	17	27576202	27576202	+	Missense_Mutation	SNP	C	C	T	rs142631461	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27576202C>T	ENST00000225387.3	+	2	75	c.74C>T	c.(73-75)cCg>cTg	p.P25L		NM_005208.4	NP_005199.2	P05813	CRBA1_HUMAN	crystallin, beta A1	25	N-terminal arm.				lens development in camera-type eye (GO:0002088)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	structural constituent of eye lens (GO:0005212)			breast(1)|large_intestine(2)|lung(1)|prostate(1)	5			BRCA - Breast invasive adenocarcinoma(11;3.3e-05)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			AACCCTACGCCGGGGTCCCTG	0.622													C|||	34	0.00678914	0.0008	0.0101	5008	,	,		19306	0.0		0.0249	False		,,,				2504	0.001				p.P25L		Atlas-SNP	.											.	CRYBA1	15	.	0			c.C74T						PASS	.	C	LEU/PRO	30,4376	35.2+/-66.4	0,30,2173	95.0	82.0	86.0		74	3.7	0.9	17	dbSNP_134	86	232,8368	95.0+/-156.8	5,222,4073	yes	missense	CRYBA1	NM_005208.4	98	5,252,6246	TT,TC,CC		2.6977,0.6809,2.0145	benign	25/216	27576202	262,12744	2203	4300	6503	SO:0001583	missense	1411	exon2			CTACGCCGGGGTC		CCDS11249.1	17q11.2-q12	2008-07-18			ENSG00000108255	ENSG00000108255			2394	protein-coding gene	gene with protein product	"""eye lens structural protein"""	123610		CRYB1		3745196, 3770741	Standard	NM_005208		Approved		uc002hdw.3	P05813	OTTHUMG00000132729	ENST00000225387.3:c.74C>T	17.37:g.27576202C>T	ENSP00000225387:p.Pro25Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	53	34	0.641509	NM_005208	Q13633|Q14CM9	Missense_Mutation	SNP	ENST00000225387.3	37	CCDS11249.1	25	0.011446886446886446	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	19	0.025065963060686015	C	11.89	1.773686	0.31411	0.006809	0.026977	ENSG00000108255	ENST00000225387	T	0.75589	-0.95	5.72	3.69	0.42338	.	0.496591	0.23928	N	0.043173	T	0.30198	0.0757	N	0.08118	0	0.53688	D	0.999971	B	0.30851	0.297	B	0.13407	0.009	T	0.32929	-0.9888	10	0.48119	T	0.1	.	16.6741	0.85274	0.3326:0.6674:0.0:0.0	.	25	P05813	CRBA1_HUMAN	L	25	ENSP00000225387:P25L	ENSP00000225387:P25L	P	+	2	0	CRYBA1	24600328	0.985000	0.35326	0.901000	0.35422	0.913000	0.54294	2.694000	0.47035	0.328000	0.23435	-1.466000	0.01016	CCG	C|0.983;T|0.017	0.017	strong		0.622	CRYBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256071.2	NM_005208	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49379182	49379182	+	Silent	SNP	G	G	C	rs386810065|rs527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49379182G>C	ENST00000200453.5	+	3	2246	c.1977G>C	c.(1975-1977)tcG>tcC	p.S659S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	659					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CTTCCCGCTCGTCTGCTGCTG	0.567													G|||	1786	0.356629	0.5764	0.2896	5008	,	,		16609	0.1984		0.2803	False		,,,				2504	0.3487				p.S659S		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1977C						PASS	.	G		2273,2133	583.2+/-385.8	569,1135,499	70.0	72.0	71.0		1977	-3.2	0.0	19	dbSNP_36	71	2469,6131	396.7+/-345.5	354,1761,2185	no	coding-synonymous	PPP1R15A	NM_014330.3		923,2896,2684	CC,CG,GG		28.7093,48.4113,36.4601		659/675	49379182	4742,8264	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon3			CCGCTCGTCTGCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1977G>C	19.37:g.49379182G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			G|0.646;C|0.354	0.354	strong		0.567	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
ACSF3	197322	hgsc.bcm.edu	37	16	89199651	89199651	+	Silent	SNP	G	G	A	rs12447947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89199651G>A	ENST00000317447.4	+	8	1724	c.1347G>A	c.(1345-1347)ctG>ctA	p.L449L	ACSF3_ENST00000406948.3_Silent_p.L449L|ACSF3_ENST00000378345.4_Silent_p.L184L	NM_001127214.2|NM_001243279.1|NM_001284316.1|NM_174917.3	NP_001120686.1|NP_001230208.1|NP_001271245.1|NP_777577.2	Q4G176	ACSF3_HUMAN	acyl-CoA synthetase family member 3	449					fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|malonate catabolic process (GO:0090410)	mitochondrion (GO:0005739)	acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)|malonyl-CoA synthetase activity (GO:0090409)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(9)|prostate(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(80;0.0281)		CATTCACCCTGGATGGCTGGT	0.557													G|||	728	0.145367	0.0295	0.2608	5008	,	,		18812	0.0109		0.3608	False		,,,				2504	0.137				p.L449L		Atlas-SNP	.											.	ACSF3	40	.	0			c.G1347A						PASS	.	G	,	320,4076	170.9+/-201.2	16,288,1894	61.0	61.0	61.0		1347,1347	-9.6	0.0	16	dbSNP_120	61	3095,5505	472.3+/-368.3	573,1949,1778	no	coding-synonymous,coding-synonymous	ACSF3	NM_001127214.2,NM_174917.3	,	589,2237,3672	AA,AG,GG		35.9884,7.2793,26.2773	,	449/577,449/577	89199651	3415,9581	2198	4300	6498	SO:0001819	synonymous_variant	197322	exon8			CACCCTGGATGGC	AK075499	CCDS10974.1, CCDS73926.1	16q24.3	2013-01-15			ENSG00000176715	ENSG00000176715		"""Acyl-CoA synthetase family"""	27288	protein-coding gene	gene with protein product	"""malonyl-CoA synthetase"""	614245				17762044, 21846720	Standard	XM_005256293		Approved		uc010cig.2	Q4G176	OTTHUMG00000138044	ENST00000317447.4:c.1347G>A	16.37:g.89199651G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_174917	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	Silent	SNP	ENST00000317447.4	37	CCDS10974.1																																																																																			G|0.746;A|0.254	0.254	strong		0.557	ACSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269919.1	NM_174917	
ATF1	466	hgsc.bcm.edu	37	12	51203371	51203371	+	Splice_Site	SNP	C	C	T	rs1129406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:51203371C>T	ENST00000262053.3	+	4	349	c.327C>T	c.(325-327)taC>taT	p.Y109Y	ATF1_ENST00000539132.1_Intron	NM_005171.4	NP_005162.1	P18846	ATF1_HUMAN	activating transcription factor 1	109					cellular protein complex assembly (GO:0043623)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to cobalt ion (GO:0032025)|response to organic cyclic compound (GO:0014070)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/ATF1(347)|FUS/ATF1(4)	breast(1)|large_intestine(1)|ovary(2)	4					Pseudoephedrine(DB00852)	GCGGACAGTACAGTATGTATA	0.403			T	"""EWSR1, FUS"""	"""malignant melanoma of soft parts , angiomatoid fibrous histiocytoma """								C|||	1970	0.393371	0.5658	0.281	5008	,	,		15388	0.2619		0.3877	False		,,,				2504	0.3814				p.Y109Y		Atlas-SNP	.		Dom	yes		12	12q13	466	activating transcription factor 1		"""E, M"""	.	ATF1	32	.	0			c.C327T						PASS	.	C		2333,2073	605.6+/-390.6	601,1131,471	60.0	61.0	61.0		327	3.8	1.0	12	dbSNP_86	61	3479,5121	510.8+/-377.6	716,2047,1537	yes	coding-synonymous-near-splice	ATF1	NM_005171.4		1317,3178,2008	TT,TC,CC		40.4535,47.0495,44.6871		109/272	51203371	5812,7194	2203	4300	6503	SO:0001630	splice_region_variant	466	exon4			ACAGTACAGTATG	BC029619	CCDS8803.1	12q13	2014-05-13			ENSG00000123268	ENSG00000123268		"""basic leucine zipper proteins"""	783	protein-coding gene	gene with protein product		123803				8401579	Standard	NM_005171		Approved	TREB36	uc001rww.4	P18846		ENST00000262053.3:c.328+1C>T	12.37:g.51203371C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_005171	B4DRF9|P25168|Q9H4A8	Silent	SNP	ENST00000262053.3	37	CCDS8803.1																																																																																			C|0.586;T|0.414	0.414	strong		0.403	ATF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404285.1	NM_005171	Silent
AHCTF1	25909	hgsc.bcm.edu	37	1	247021085	247021085	+	Silent	SNP	G	G	C	rs41308162	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247021085G>C	ENST00000391829.2	-	30	4287	c.4164C>G	c.(4162-4164)ctC>ctG	p.L1388L	AHCTF1_ENST00000366508.1_Silent_p.L1423L|AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000326225.3_Silent_p.L1397L			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1388	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			CTGCAACTAAGAGATCCTTTG	0.343													G|||	913	0.182308	0.4728	0.0821	5008	,	,		17161	0.0079		0.0875	False		,,,				2504	0.138				p.L1397L	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											AHCTF1,NS,carcinoma,0,1	AHCTF1	187	1	0			c.C4191G						PASS	.	G		1838,2568	522.5+/-370.8	388,1062,753	61.0	62.0	62.0		4191	2.3	0.0	1	dbSNP_127	62	738,7862	178.5+/-227.8	32,674,3594	no	coding-synonymous	AHCTF1	NM_015446.4		420,1736,4347	CC,CG,GG		8.5814,41.7158,19.8062		1397/2276	247021085	2576,10430	2203	4300	6503	SO:0001819	synonymous_variant	25909	exon30			AACTAAGAGATCC		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.4164C>G	1.37:g.247021085G>C		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	237	234	0.987342	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				G|0.826;C|0.174	0.174	strong		0.343	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
MUC16	94025	hgsc.bcm.edu	37	19	9047305	9047305	+	Silent	SNP	G	G	A	rs10415818	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9047305G>A	ENST00000397910.4	-	5	34529	c.34326C>T	c.(34324-34326)caC>caT	p.H11442H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11444	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGAACTTGTGTGTGTCTCAG	0.478													G|||	918	0.183307	0.177	0.1945	5008	,	,		23374	0.0258		0.2823	False		,,,				2504	0.2444				p.H11442H		Atlas-SNP	.											.	MUC16	4315	.	0			c.C34326T						PASS	.			696,3340		57,582,1379	187.0	188.0	187.0		34326	-6.2	0.0	19	dbSNP_119	187	2515,5805		401,1713,2046	no	coding-synonymous	MUC16	NM_024690.2		458,2295,3425	AA,AG,GG		30.2284,17.2448,25.9874		11442/14508	9047305	3211,9145	2018	4160	6178	SO:0001819	synonymous_variant	94025	exon5			ACTTGTGTGTGTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34326C>T	19.37:g.9047305G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	45	0.608108	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.797;A|0.203	0.203	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NPTXR	23467	hgsc.bcm.edu	37	22	39222598	39222598	+	Silent	SNP	G	G	A	rs56034166	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39222598G>A	ENST00000333039.2	-	3	1128	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G		NM_014293.3	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	335	Pentaxin.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			central_nervous_system(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	Melanoma(58;0.04)					AGAAGGGGGTGCCCTGGCCGG	0.637													G|||	61	0.0121805	0.0	0.0259	5008	,	,		16716	0.002		0.0268	False		,,,				2504	0.0143				p.G335G	Pancreas(139;2521 3281 36965)	Atlas-SNP	.											.	NPTXR	34	.	0			c.C1005T						PASS	.	G		27,4379	33.5+/-64.1	0,27,2176	69.0	66.0	67.0		1005	3.6	1.0	22	dbSNP_129	67	296,8304	107.6+/-168.3	5,286,4009	no	coding-synonymous	NPTXR	NM_014293.3		5,313,6185	AA,AG,GG		3.4419,0.6128,2.4835		335/501	39222598	323,12683	2203	4300	6503	SO:0001819	synonymous_variant	23467	exon3			GGGGGTGCCCTGG	AF052163	CCDS33647.1	22q13.1	2007-01-25			ENSG00000221890	ENSG00000221890			7954	protein-coding gene	gene with protein product		609474				16497176	Standard	NM_014293		Approved		uc003awk.3	O95502	OTTHUMG00000150458	ENST00000333039.2:c.1005C>T	22.37:g.39222598G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_014293		Silent	SNP	ENST00000333039.2	37	CCDS33647.1																																																																																			G|0.979;A|0.021	0.021	strong		0.637	NPTXR-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318194.2	NM_014293	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84706461	84706461	+	Missense_Mutation	SNP	C	C	T	rs950169	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:84706461C>T	ENST00000286744.5	+	30	5203	c.4979C>T	c.(4978-4980)aCa>aTa	p.T1660I	ADAMTSL3_ENST00000567476.1_Intron	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1660	PLAC. {ECO:0000255|PROSITE- ProRule:PRU00233}.		T -> I (in dbSNP:rs950169).			proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			GGAGACTGCACAGACACAACT	0.338													C|||	646	0.128994	0.0113	0.1787	5008	,	,		19381	0.0536		0.2734	False		,,,				2504	0.182				p.T1660I		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C4979T						PASS	.	C	ILE/THR	210,4196	129.0+/-165.8	6,198,1999	118.0	112.0	114.0		4979	-0.0	0.7	15	dbSNP_86	114	2323,6275	390.3+/-343.2	313,1697,2289	yes	missense	ADAMTSL3	NM_207517.2	89	319,1895,4288	TT,TC,CC		27.0179,4.7662,19.4786	benign	1660/1692	84706461	2533,10471	2203	4299	6502	SO:0001583	missense	57188	exon30			ACTGCACAGACAC	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.4979C>T	15.37:g.84706461C>T	ENSP00000286744:p.Thr1660Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	62	22	0.354839	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	326	0.14926739926739926	8	0.016260162601626018	72	0.19889502762430938	31	0.05419580419580419	215	0.2836411609498681	C	12.18	1.861131	0.32884	0.047662	0.270179	ENSG00000156218	ENST00000286744	T	0.44083	0.93	4.92	-0.0221	0.13948	PLAC (2);	1.471100	0.04514	N	0.383369	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.999999831154	B	0.02656	0.0	B	0.04013	0.001	T	0.27157	-1.0082	9	0.45353	T	0.12	.	3.8634	0.09005	0.3118:0.3571:0.0:0.3311	rs950169;rs17371948;rs52790868;rs58129969;rs950169	1660	P82987	ATL3_HUMAN	I	1660	ENSP00000286744:T1660I	ENSP00000286744:T1660I	T	+	2	0	ADAMTSL3	82497465	1.000000	0.71417	0.731000	0.30826	0.988000	0.76386	2.507000	0.45442	0.071000	0.16664	0.591000	0.81541	ACA	T|0.150;G|0.006	0.150	strong		0.338	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
ZBTB42	100128927	hgsc.bcm.edu	37	14	105267934	105267934	+	Missense_Mutation	SNP	G	G	A	rs34284721	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105267934G>A	ENST00000342537.7	+	1	685	c.400G>A	c.(400-402)Gca>Aca	p.A134T	ZBTB42_ENST00000555360.1_Missense_Mutation_p.A134T	NM_001137601.1	NP_001131073.1	B2RXF5	ZBT42_HUMAN	zinc finger and BTB domain containing 42	134	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TGCCCCTGGGGCAGAACCTGC	0.657													G|||	213	0.0425319	0.003	0.0706	5008	,	,		16804	0.0		0.1133	False		,,,				2504	0.047				p.A134T		Atlas-SNP	.											.	ZBTB42	10	.	0			c.G400A						PASS	.	G	THR/ALA	29,1353		2,25,664	21.0	25.0	24.0		400	-2.4	0.0	14	dbSNP_126	24	376,2802		19,338,1232	yes	missense	ZBTB42	NM_001137601.1	58	21,363,1896	AA,AG,GG		11.8313,2.0984,8.8816	benign	134/423	105267934	405,4155	691	1589	2280	SO:0001583	missense	100128927	exon2			CCTGGGGCAGAAC	AX721091	CCDS45174.1	14q32.33	2013-01-09				ENSG00000179627		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	32550	protein-coding gene	gene with protein product		613915					Standard	NM_001137601		Approved	ZNF925	uc001ypp.3	B2RXF5		ENST00000342537.7:c.400G>A	14.37:g.105267934G>A	ENSP00000409107:p.Ala134Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	115	63	0.547826	NM_001137601	B7ZW21	Missense_Mutation	SNP	ENST00000342537.7	37	CCDS45174.1	121	0.0554029304029304	2	0.0040650406504065045	33	0.09116022099447514	0	0.0	86	0.11345646437994723	G	0.669	-0.802607	0.02841	0.020984	0.118313	ENSG00000179627	ENST00000555360;ENST00000342537	T;T	0.12361	2.69;2.69	3.09	-2.4	0.06583	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.44528	-0.9322	8	0.17369	T	0.5	.	1.9749	0.03414	0.2171:0.142:0.4775:0.1634	rs34284721	134	B2RXF5	ZBT42_HUMAN	T	134	ENSP00000450673:A134T;ENSP00000409107:A134T	ENSP00000409107:A134T	A	+	1	0	ZBTB42	104338979	0.021000	0.18746	0.003000	0.11579	0.002000	0.02628	1.115000	0.31209	-0.266000	0.09339	-0.379000	0.06801	GCA	G|0.930;A|0.070	0.070	strong		0.657	ZBTB42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410372.1		
RNF26	79102	hgsc.bcm.edu	37	11	119206375	119206375	+	Silent	SNP	G	G	A	rs2511841	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119206375G>A	ENST00000311413.4	+	1	1139	c.543G>A	c.(541-543)acG>acA	p.T181T	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	181						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(1)	12		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;3.8e-05)		GGAGGATGACGGACGTAGTGG	0.602													G|||	3634	0.725639	0.7421	0.7349	5008	,	,		21354	0.6607		0.659	False		,,,				2504	0.8323				p.T181T		Atlas-SNP	.											.	RNF26	23	.	0			c.G543A						PASS	.	G		3125,1273	699.9+/-406.5	1128,869,202	107.0	92.0	97.0		543	-9.2	0.1	11	dbSNP_100	97	5815,2775	678.3+/-403.5	1977,1861,457	yes	coding-synonymous	RNF26	NM_032015.3		3105,2730,659	AA,AG,GG		32.305,28.945,31.1672		181/434	119206375	8940,4048	2199	4295	6494	SO:0001819	synonymous_variant	79102	exon1			GATGACGGACGTA	AB055622	CCDS8419.1	11q23	2008-07-21				ENSG00000173456		"""RING-type (C3HC4) zinc fingers"""	14646	protein-coding gene	gene with protein product	"""ring finger protein with leucine zipper"""	606130				11352657	Standard	NM_032015		Approved	MGC2642	uc001pwh.3	Q9BY78		ENST00000311413.4:c.543G>A	11.37:g.119206375G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	196	196	1	NM_032015	Q542Y8	Silent	SNP	ENST00000311413.4	37	CCDS8419.1																																																																																			G|0.315;A|0.685	0.685	strong		0.602	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015	
CHPF2	54480	hgsc.bcm.edu	37	7	150934975	150934975	+	Silent	SNP	C	C	G	rs2487154	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150934975C>G	ENST00000035307.2	+	4	3040	c.1527C>G	c.(1525-1527)gcC>gcG	p.A509A	RP4-548D19.3_ENST00000607902.1_RNA|CHPF2_ENST00000495645.1_Silent_p.A501A|MIR671_ENST00000390183.1_RNA	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	509					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						TCCTCGAGGCCTTTGCAGCCA	0.602													C|||	2171	0.433506	0.2685	0.4164	5008	,	,		17374	0.7153		0.4503	False		,,,				2504	0.3609				p.A509A		Atlas-SNP	.											.	CHPF2	52	.	0			c.C1527G						PASS	.	C		1305,3099		204,897,1101	34.0	33.0	33.0		1527	5.0	1.0	7	dbSNP_100	33	3510,5088		712,2086,1501	no	coding-synonymous	CHPF2	NM_019015.1		916,2983,2602	GG,GC,CC		40.8234,29.6322,37.0328		509/773	150934975	4815,8187	2202	4299	6501	SO:0001819	synonymous_variant	54480	exon4			CGAGGCCTTTGCA	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.1527C>G	7.37:g.150934975C>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Silent	SNP	ENST00000035307.2	37	CCDS34779.1																																																																																			C|0.595;G|0.405	0.405	strong		0.602	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
ASAH1	427	hgsc.bcm.edu	37	8	17928811	17928811	+	Missense_Mutation	SNP	C	C	T	rs1071645	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17928811C>T	ENST00000262097.6	-	3	525	c.214G>A	c.(214-216)Gtg>Atg	p.V72M	ASAH1_ENST00000314146.10_Missense_Mutation_p.V95M|ASAH1_ENST00000520051.1_5'Flank|ASAH1_ENST00000520781.1_Missense_Mutation_p.V72M|ASAH1_ENST00000381733.4_Missense_Mutation_p.V88M|ASAH1_ENST00000417108.2_Missense_Mutation_p.V7M	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	72			V -> M (in dbSNP:rs1071645). {ECO:0000269|PubMed:10993717, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8955159, ECO:0000269|Ref.2}.		cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		TAGCATACCACTGGTGCCTTG	0.303													T|||	2106	0.420527	0.2504	0.5735	5008	,	,		15607	0.373		0.4761	False		,,,				2504	0.5337				p.V95M		Atlas-SNP	.											.	ASAH1	71	.	0			c.G283A						PASS	.	T	MET/VAL,MET/VAL,MET/VAL	1275,3131	685.6+/-404.6	194,887,1122	164.0	132.0	143.0		283,262,214	-3.3	0.0	8	dbSNP_86	143	4243,4357	564.2+/-388.3	1031,2181,1088	yes	missense,missense,missense	ASAH1	NM_001127505.1,NM_004315.4,NM_177924.3	21,21,21	1225,3068,2210	TT,TC,CC		49.3372,28.9378,42.4266	benign,benign,benign	95/390,88/412,72/396	17928811	5518,7488	2203	4300	6503	SO:0001583	missense	427	exon4			ATACCACTGGTGC	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"""N-acylsphingosine amidohydrolase (acid ceramidase)"""	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.214G>A	8.37:g.17928811C>T	ENSP00000262097:p.Val72Met	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001127505	E9PDS0|Q6W898|Q96AS2	Missense_Mutation	SNP	ENST00000262097.6	37	CCDS6006.1	925	0.42353479853479853	147	0.29878048780487804	219	0.6049723756906077	204	0.35664335664335667	355	0.4683377308707124	T	8.835	0.940822	0.18281	0.289378	0.493372	ENSG00000104763	ENST00000262097;ENST00000381733;ENST00000520781;ENST00000417108;ENST00000314146	T;T;T;T;T	0.52057	0.79;0.79;0.79;0.79;0.68	5.1	-3.27	0.05048	.	1.506130	0.03689	N	0.246842	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.09377	0.0;0.003;0.004;0.004	T	0.41556	-0.9502	9	0.35671	T	0.21	-4.7588	6.9396	0.24486	0.2468:0.5673:0.1013:0.0846	rs1071645;rs1804720;rs3190053;rs3190062;rs11538151;rs12544854;rs17416573;rs17845496;rs17858382;rs52809253;rs60844591;rs12544854	95;88;72;72	E9PDS0;Q13510-2;E7EMM4;Q13510	.;.;.;ASAH1_HUMAN	M	72;88;72;7;95	ENSP00000262097:V72M;ENSP00000371152:V88M;ENSP00000427751:V72M;ENSP00000394125:V7M;ENSP00000326970:V95M	ENSP00000262097:V72M	V	-	1	0	ASAH1	17973091	0.212000	0.23540	0.000000	0.03702	0.002000	0.02628	0.402000	0.20965	-1.107000	0.03004	-2.194000	0.00310	GTG	T|0.339;G|0.122	0.339	strong		0.303	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
MORC4	79710	hgsc.bcm.edu	37	X	106200202	106200202	+	Missense_Mutation	SNP	G	G	A	rs6622126	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:106200202G>A	ENST00000355610.4	-	12	1692	c.1418C>T	c.(1417-1419)aCt>aTt	p.T473I	MORC4_ENST00000535534.1_Missense_Mutation_p.T221I|MORC4_ENST00000255495.7_Missense_Mutation_p.T473I	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	473			T -> I (in dbSNP:rs6622126). {ECO:0000269|PubMed:14702039}.			nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						GTCTTCATCAGTGAGTTCTTG	0.423													A|||	2837	0.751523	0.6589	0.5764	3775	,	,		13471	0.7063		0.3161	False		,,,				2504	0.5481				p.T473I		Atlas-SNP	.											.	MORC4	155	.	0			c.C1418T						PASS	.	A	ILE/THR,ILE/THR	3119,716		1090,486,453,56,118	176.0	158.0	164.0		1418,1418	-3.7	0.1	X	dbSNP_116	164	2890,3838		441,1207,801,780,1071	yes	missense,missense	MORC4	NM_001085354.2,NM_024657.4	89,89	1531,1693,1254,836,1189	AA,AG,A,GG,G		42.9548,18.6701,43.1128	benign,benign	473/901,473/938	106200202	6009,4554	2203	4300	6503	SO:0001583	missense	79710	exon12			TCATCAGTGAGTT	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.1418C>T	X.37:g.106200202G>A	ENSP00000347821:p.Thr473Ile	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	128	36	0.28125	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	1173	0.7070524412296564	220	0.7692307692307693	127	0.5521739130434783	274	0.9013157894736842	168	0.28187919463087246	A	0.004	-2.304218	0.00240	0.813299	0.429548	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.30714	2.74;1.52;2.74	5.17	-3.74	0.04385	.	1.099420	0.06827	N	0.793253	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.26710	-1.0095	9	0.37606	T	0.19	0.0119	0.387	0.00404	0.2206:0.2629:0.2562:0.2603	rs6622126;rs60963505;rs6622126	221;473;473	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	I	473;221;473	ENSP00000347821:T473I;ENSP00000440359:T221I;ENSP00000255495:T473I	ENSP00000255495:T473I	T	-	2	0	MORC4	106086858	0.027000	0.19231	0.097000	0.21041	0.165000	0.22458	-0.704000	0.05058	-0.938000	0.03714	-3.323000	0.00044	ACT	0|0.012;A|0.648	0.648	strong		0.423	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
FIGNL1	63979	hgsc.bcm.edu	37	7	50514577	50514577	+	Missense_Mutation	SNP	C	C	T	rs10235371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:50514577C>T	ENST00000419119.1	-	2	1962	c.409G>A	c.(409-411)Gtg>Atg	p.V137M	FIGNL1_ENST00000395556.2_Missense_Mutation_p.V137M|FIGNL1_ENST00000435566.1_3'UTR|FIGNL1_ENST00000433017.1_Missense_Mutation_p.V137M|FIGNL1_ENST00000356889.4_Missense_Mutation_p.V137M			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	137			V -> M (in dbSNP:rs10235371). {ECO:0000269|PubMed:15489334}.		ATP metabolic process (GO:0046034)|cellular response to ionizing radiation (GO:0071479)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|regulation of cell cycle (GO:0051726)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	29	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;3.73e-08)|all_hematologic(4;7.51e-06)				TGGATTACCACTGATGCAAGA	0.383													C|||	316	0.063099	0.0446	0.0836	5008	,	,		21357	0.0377		0.1153	False		,,,				2504	0.046				p.V137M		Atlas-SNP	.											.	FIGNL1	73	.	0			c.G409A						PASS	.	C	MET/VAL,MET/VAL	206,4200	126.6+/-163.6	5,196,2002	104.0	104.0	104.0		409,409	-4.6	0.0	7	dbSNP_119	104	895,7705	200.3+/-244.1	50,795,3455	yes	missense,missense	FIGNL1	NM_001042762.1,NM_022116.3	21,21	55,991,5457	TT,TC,CC		10.407,4.6754,8.4653	possibly-damaging,possibly-damaging	137/675,137/675	50514577	1101,11905	2203	4300	6503	SO:0001583	missense	63979	exon4			TTACCACTGATGC	AK023142	CCDS5510.1	7p12.2	2010-04-21			ENSG00000132436	ENSG00000132436		"""ATPases / AAA-type"""	13286	protein-coding gene	gene with protein product		615383					Standard	XM_005271783		Approved		uc003tpc.3	Q6PIW4	OTTHUMG00000022866	ENST00000419119.1:c.409G>A	7.37:g.50514577C>T	ENSP00000410811:p.Val137Met	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	63	42	0.666667	NM_001042762	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	37	CCDS5510.1	159	0.07280219780219781	32	0.06504065040650407	29	0.08011049723756906	23	0.04020979020979021	75	0.09894459102902374	C	11.45	1.642477	0.29246	0.046754	0.10407	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.49	-4.56	0.03431	.	0.659654	0.14095	N	0.341751	T	0.00384	0.0012	L	0.50333	1.59	0.58432	P	5.000000000032756E-6	B	0.34103	0.437	B	0.30401	0.115	T	0.05053	-1.0909	9	0.46703	T	0.11	-4.6804	10.0545	0.42237	0.0:0.3473:0.4724:0.1803	rs10235371;rs52821479;rs10235371	137	Q6PIW4	FIGL1_HUMAN	M	137	ENSP00000349356:V137M;ENSP00000378924:V137M;ENSP00000399997:V137M;ENSP00000410811:V137M	ENSP00000349356:V137M	V	-	1	0	FIGNL1	50482071	0.001000	0.12720	0.000000	0.03702	0.877000	0.50540	0.561000	0.23515	-0.842000	0.04195	-0.344000	0.07964	GTG	C|0.920;T|0.080	0.080	strong		0.383	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762	
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 GAIIx	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_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_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*	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	41	19	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	
THUMPD3	25917	hgsc.bcm.edu	37	3	9425911	9425911	+	Silent	SNP	G	G	A	rs1129170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9425911G>A	ENST00000345094.3	+	9	1585	c.1251G>A	c.(1249-1251)aaG>aaA	p.K417K	THUMPD3_ENST00000515662.2_Silent_p.K417K|SETD5-AS1_ENST00000519043.1_RNA|SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000452837.2_Silent_p.K417K|SETD5-AS1_ENST00000523354.1_RNA|SETD5-AS1_ENST00000521609.1_RNA|SETD5-AS1_ENST00000520629.1_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	417						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		GATCCAAGAAGAGAAACTGGA	0.423													g|||	3027	0.604433	0.5371	0.5821	5008	,	,		18542	0.5655		0.5915	False		,,,				2504	0.7648				p.K417K		Atlas-SNP	.											.	THUMPD3	46	.	0			c.G1251A						PASS	.		,	2407,1999	615.1+/-392.5	664,1079,460	192.0	207.0	202.0		1251,1251	1.9	1.0	3	dbSNP_86	202	5096,3504	631.9+/-398.5	1504,2088,708	no	coding-synonymous,coding-synonymous	THUMPD3	NM_001114092.1,NM_015453.2	,	2168,3167,1168	AA,AG,GG		40.7442,45.37,42.3112	,	417/508,417/508	9425911	7503,5503	2203	4300	6503	SO:0001819	synonymous_variant	25917	exon9			CAAGAAGAGAAAC	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.1251G>A	3.37:g.9425911G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Silent	SNP	ENST00000345094.3	37	CCDS2573.1	1234	0.565018315018315	262	0.532520325203252	206	0.569060773480663	327	0.5716783216783217	439	0.579155672823219	G	9.581	1.123543	0.20959	0.5463	0.592558	ENSG00000134077	ENST00000416603	.	.	.	5.66	1.89	0.25635	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48725	-0.9010	3	.	.	.	-22.952	8.9034	0.35507	0.4144:0.0:0.5856:0.0	rs1129170;rs2251595;rs3177482;rs3186764;rs17171661;rs17849508;rs60440721	.	.	.	K	188	.	.	E	+	1	0	THUMPD3	9400911	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.283000	0.33237	0.773000	0.33404	-0.143000	0.13931	GAG	G|0.425;A|0.575	0.575	strong		0.423	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453	
MPHOSPH6	10200	hgsc.bcm.edu	37	16	82203742	82203742	+	Silent	SNP	T	T	C	rs1134847	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:82203742T>C	ENST00000258169.4	-	1	89	c.39A>G	c.(37-39)ctA>ctG	p.L13L	CTD-2588J6.2_ENST00000563841.1_lincRNA|MPHOSPH6_ENST00000569021.1_Silent_p.L13L|MPHOSPH6_ENST00000563504.1_5'UTR|MPHOSPH6_ENST00000567729.1_5'UTR	NM_005792.2	NP_005783.2	Q99547	MPH6_HUMAN	M-phase phosphoprotein 6	13					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(1)|large_intestine(1)|lung(3)	5						TCATGCGCAGTAGATTCTTGG	0.711													C|||	3218	0.642572	0.4054	0.8127	5008	,	,		13310	0.7649		0.7465	False		,,,				2504	0.6094				p.L13L		Atlas-SNP	.											MPHOSPH6,rectum,carcinoma,0,1	MPHOSPH6	16	1	0			c.A39G						PASS	.	C		2116,2282		524,1068,607	32.0	24.0	27.0		39	2.6	1.0	16	dbSNP_86	27	6335,2261		2348,1639,311	no	coding-synonymous	MPHOSPH6	NM_005792.2		2872,2707,918	CC,CT,TT		26.3029,48.1128,34.9623		13/161	82203742	8451,4543	2199	4298	6497	SO:0001819	synonymous_variant	10200	exon1			GCGCAGTAGATTC	X98263	CCDS10937.1	16q23.3	2008-03-03			ENSG00000135698	ENSG00000135698			7214	protein-coding gene	gene with protein product		605500				8885239	Standard	NM_005792		Approved	MPP6	uc002fgw.3	Q99547	OTTHUMG00000137632	ENST00000258169.4:c.39A>G	16.37:g.82203742T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_005792	B2RAF0	Silent	SNP	ENST00000258169.4	37	CCDS10937.1																																																																																			T|0.362;G|0.000;C|0.638;A|0.000	0.638	strong		0.711	MPHOSPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269058.1	NM_005792	
MYO1C	4641	hgsc.bcm.edu	37	17	1387472	1387472	+	Silent	SNP	C	C	T	rs11538156	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1387472C>T	ENST00000575158.1	-	2	272	c.96G>A	c.(94-96)ctG>ctA	p.L32L	MYO1C_ENST00000545534.2_Silent_p.L43L|MYO1C_ENST00000438665.2_Silent_p.L48L|MYO1C_ENST00000359786.5_Silent_p.L67L|MYO1C_ENST00000573198.1_5'Flank|MYO1C_ENST00000361007.2_Silent_p.L32L			Q12965	MYO1E_HUMAN	myosin IC	39	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)		ATCGCCGCCGCAGGTTCTCGA	0.627													C|||	332	0.0662939	0.0552	0.0562	5008	,	,		14022	0.0169		0.1322	False		,,,				2504	0.0716				p.L67L		Atlas-SNP	.											.	MYO1C	57	.	0			c.G201A						PASS	.	C	,,	333,4073	175.5+/-204.9	14,305,1884	49.0	46.0	47.0		201,144,96	2.5	1.0	17	dbSNP_120	47	1355,7245	264.3+/-285.5	106,1143,3051	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	120,1448,4935	TT,TC,CC		15.7558,7.5579,12.9786	,,	67/1064,48/1045,32/1029	1387472	1688,11318	2203	4300	6503	SO:0001819	synonymous_variant	4641	exon2			CCGCCGCAGGTTC	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.96G>A	17.37:g.1387472C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			T|0.112;G|0.000;C|0.888	0.112	strong		0.627	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
KIF19	124602	hgsc.bcm.edu	37	17	72350362	72350362	+	Silent	SNP	G	G	A	rs72852235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72350362G>A	ENST00000389916.4	+	18	2508	c.2370G>A	c.(2368-2370)tcG>tcA	p.S790S	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	790					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GGCGGCGCTCGCGGGCCCTGG	0.682													G|||	1277	0.254992	0.1051	0.3012	5008	,	,		14395	0.3452		0.2803	False		,,,				2504	0.3057				p.S790S		Atlas-SNP	.											KIF19,NS,carcinoma,0,1	KIF19	102	1	0			c.G2370A						PASS	.	G		461,3551		32,397,1577	35.0	46.0	42.0		2370	-10.1	0.3	17	dbSNP_130	42	2350,5960		329,1692,2134	no	coding-synonymous	KIF19	NM_153209.3		361,2089,3711	AA,AG,GG		28.2792,11.4905,22.8129		790/999	72350362	2811,9511	2006	4155	6161	SO:0001819	synonymous_variant	124602	exon18			GCGCTCGCGGGCC	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2370G>A	17.37:g.72350362G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			G|0.736;A|0.264	0.264	strong		0.682	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
MAP3K1	4214	hgsc.bcm.edu	37	5	56168712	56168712	+	Silent	SNP	C	C	T	rs2229882	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:56168712C>T	ENST00000399503.3	+	9	1566	c.1566C>T	c.(1564-1566)acC>acT	p.T522T		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	522					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)		AGCAGCAAACCGTACAGCAGC	0.413													C|||	223	0.0445288	0.031	0.062	5008	,	,		16426	0.0625		0.0487	False		,,,				2504	0.0276				p.T522T		Atlas-SNP	.											.	MAP3K1	355	.	0			c.C1566T						PASS	.	C		113,3647		1,111,1768	78.0	75.0	76.0		1566	0.2	0.0	5	dbSNP_98	76	454,7760		16,422,3669	no	coding-synonymous	MAP3K1	NM_005921.1		17,533,5437	TT,TC,CC		5.5271,3.0053,4.7353		522/1513	56168712	567,11407	1880	4107	5987	SO:0001819	synonymous_variant	4214	exon9			GCAAACCGTACAG	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.1566C>T	5.37:g.56168712C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_005921		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			C|0.953;T|0.047	0.047	strong		0.413	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
ABHD15	116236	hgsc.bcm.edu	37	17	27889986	27889986	+	Missense_Mutation	SNP	T	T	C	rs542939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27889986T>C	ENST00000307201.4	-	2	1170	c.1000A>G	c.(1000-1002)Acc>Gcc	p.T334A	RP11-68I3.2_ENST00000581474.1_RNA	NM_198147.2	NP_937790.2	Q6UXT9	ABH15_HUMAN	abhydrolase domain containing 15	334			T -> A (in dbSNP:rs542939). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	10						TCCCAGTAGGTATCCCAGCTG	0.602													T|||	3846	0.767971	0.8109	0.6585	5008	,	,		18388	0.8998		0.6531	False		,,,				2504	0.7699				p.T334A		Atlas-SNP	.											.	ABHD15	18	.	0			c.A1000G						PASS	.	T	ALA/THR	3388,1018	725.8+/-409.7	1293,802,108	68.0	62.0	64.0		1000	2.6	1.0	17	dbSNP_83	64	5642,2958	666.5+/-402.4	1840,1962,498	yes	missense	ABHD15	NM_198147.2	58	3133,2764,606	CC,CT,TT		34.3953,23.1049,30.5705	benign	334/469	27889986	9030,3976	2203	4300	6503	SO:0001583	missense	116236	exon2			AGTAGGTATCCCA	AK056717	CCDS32602.1	17q11.2	2009-11-20			ENSG00000168792	ENSG00000168792		"""Abhydrolase domain containing"""	26971	protein-coding gene	gene with protein product						12975309	Standard	NM_198147		Approved		uc002hed.2	Q6UXT9		ENST00000307201.4:c.1000A>G	17.37:g.27889986T>C	ENSP00000302657:p.Thr334Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	76	0.987013	NM_198147	Q96EC5	Missense_Mutation	SNP	ENST00000307201.4	37	CCDS32602.1	1665	0.7623626373626373	395	0.8028455284552846	243	0.6712707182320442	520	0.9090909090909091	507	0.6688654353562006	T	9.089	1.001241	0.19121	0.768951	0.656047	ENSG00000168792	ENST00000307201	T	0.10763	2.84	5.92	2.57	0.30868	.	0.492803	0.21005	N	0.081795	T	0.00012	0.0000	N	0.02916	-0.46	0.44539	P	0.0025020000000000042	B	0.19935	0.04	B	0.20184	0.028	T	0.09952	-1.0651	9	0.23891	T	0.37	-10.5565	7.8137	0.29247	0.0:0.3108:0.0:0.6892	rs542939;rs3809794;rs52828212;rs59993345;rs542939	334	Q6UXT9	ABH15_HUMAN	A	334	ENSP00000302657:T334A	ENSP00000302657:T334A	T	-	1	0	ABHD15	24914112	0.040000	0.19996	0.994000	0.49952	0.997000	0.91878	0.092000	0.15066	0.510000	0.28216	0.533000	0.62120	ACC	T|0.268;C|0.732	0.732	strong		0.602	ABHD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447796.2	NM_198147	
OR5B17	219965	hgsc.bcm.edu	37	11	58125620	58125620	+	Missense_Mutation	SNP	T	T	C	rs4127353	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:58125620T>C	ENST00000357377.3	-	1	922	c.923A>G	c.(922-924)tAt>tGt	p.Y308C		NM_001005489.1	NP_001005489.1	Q8NGF7	OR5BH_HUMAN	olfactory receptor, family 5, subfamily B, member 17	308			Y -> C (in dbSNP:rs4127353).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATCTAGAGAATATTTTGCCTT	0.328													c|||	3660	0.730831	0.7307	0.7334	5008	,	,		20467	0.8562		0.6312	False		,,,				2504	0.7025				p.Y308C		Atlas-SNP	.											OR5B17,NS,adenoma,0,1	OR5B17	64	1	0			c.A923G						PASS	.	C	CYS/TYR	3240,1162	410.2+/-335.3	1188,864,149	93.0	92.0	92.0		923	-5.2	0.0	11	dbSNP_108	92	5449,3141	474.9+/-369.0	1717,2015,563	yes	missense	OR5B17	NM_001005489.1	194	2905,2879,712	CC,CT,TT		36.5658,26.3971,33.1204	benign	308/315	58125620	8689,4303	2201	4295	6496	SO:0001583	missense	219965	exon1			AGAGAATATTTTG	AB065849	CCDS31548.1	11q12.1	2012-08-09			ENSG00000197786	ENSG00000197786		"""GPCR / Class A : Olfactory receptors"""	15267	protein-coding gene	gene with protein product				OR5B20P			Standard	NM_001005489		Approved		uc010rke.2	Q8NGF7	OTTHUMG00000167465	ENST00000357377.3:c.923A>G	11.37:g.58125620T>C	ENSP00000349945:p.Tyr308Cys	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_001005489	Q6IEX1	Missense_Mutation	SNP	ENST00000357377.3	37	CCDS31548.1	1560	0.7142857142857143	332	0.6747967479674797	273	0.7541436464088398	477	0.833916083916084	478	0.6306068601583114	c	5.148	0.212877	0.09757	0.736029	0.634342	ENSG00000197786	ENST00000357377	T	0.00363	7.83	2.58	-5.15	0.02866	.	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.36480	-0.9746	8	0.34782	T	0.22	15.9981	0.2523	0.00207	0.2327:0.1805:0.2112:0.3757	rs4127353;rs56431252;rs4127353	308	Q8NGF7	OR5BH_HUMAN	C	308	ENSP00000349945:Y308C	ENSP00000349945:Y308C	Y	-	2	0	OR5B17	57882196	0.000000	0.05858	0.000000	0.03702	0.278000	0.26855	-2.791000	0.00767	-2.914000	0.00307	-0.741000	0.03529	TAT	T|0.312;C|0.688	0.688	strong		0.328	OR5B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394708.2	NM_001005489	
CCDC168	643677	hgsc.bcm.edu	37	13	103386940	103386940	+	Silent	SNP	C	C	T	rs367699341	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103386940C>T	ENST00000322527.2	-	1	2219	c.2220G>A	c.(2218-2220)gaG>gaA	p.E740E		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	740																	TTTGGTTCCTCTCTTCTTTTT	0.388													C|||	3	0.000599042	0.0023	0.0	5008	,	,		21382	0.0		0.0	False		,,,				2504	0.0				p.E5369E		Atlas-SNP	.											.	.	.	.	0			c.G16107A						PASS	.	C		6,1378		0,6,686	242.0	172.0	193.0		16107	-3.6	0.0	13		193	0,3182		0,0,1591	no	coding-synonymous	CCDC168	NM_001146197.1		0,6,2277	TT,TC,CC		0.0,0.4335,0.1314		5369/7082	103386940	6,4560	692	1591	2283	SO:0001819	synonymous_variant	643677	exon4			GTTCCTCTCTTCT		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.2220G>A	13.37:g.103386940C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	93	30	0.322581	NM_001146197	Q8N800	Silent	SNP	ENST00000322527.2	37																																																																																				.	.	weak		0.388	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
LINC00283	100874057	hgsc.bcm.edu	37	13	103392562	103392562	+	RNA	SNP	C	C	A	rs12585626	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103392562C>A	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		CTGATGATTTCATTCCTTTTG	0.333													C|||	371	0.0740815	0.1573	0.0159	5008	,	,		21018	0.1052		0.0268	False		,,,				2504	0.0194				p.M3495I		Atlas-SNP	.											.	.	.	.	0			c.G10485T						PASS	.	C	ILE/MET	187,1197		14,159,519	72.0	58.0	62.0		10485	0.3	0.0	13	dbSNP_120	62	68,3112		2,64,1524	yes	missense	CCDC168	NM_001146197.1	10	16,223,2043	AA,AC,CC		2.1384,13.5116,5.5872		3495/7082	103392562	255,4309	692	1590	2282			643677	exon4			TGATTTCATTCCT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103392562C>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	34	9	0.264706	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.905;A|0.095	0.095	strong		0.333	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
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 GAIIx	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_ENST00000423025.2_5'Flank|DCST1_ENST00000295542.1_5'Flank|DCST2_ENST00000295536.5_Missense_Mutation_p.V233M|DCST1_ENST00000368419.2_5'Flank|DCST1_ENST00000392480.1_5'Flank	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	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	165	78	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:56966040T>C	ENST00000370706.4	+	3	430				ZNF451_ENST00000370708.4_Silent_p.L276L|ZNF451_ENST00000370702.1_Intron|ZNF451_ENST00000357489.3_Intron|ZNF451_ENST00000491832.2_Intron	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		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	28	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 GAIIx	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	RP11-498C9.12_ENST00000580897.1_RNA|MAFG_ENST00000392366.3_Silent_p.A135A	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		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	12	7	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	
AIRE	326	hgsc.bcm.edu	37	21	45709906	45709906	+	Missense_Mutation	SNP	C	C	G	rs1800520	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45709906C>G	ENST00000291582.5	+	7	961	c.834C>G	c.(832-834)agC>agG	p.S278R	AIRE_ENST00000329347.4_5'Flank|AIRE_ENST00000355347.4_5'Flank	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	278	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.		S -> R (in dbSNP:rs1800520). {ECO:0000269|PubMed:11524731, ECO:0000269|PubMed:12625412, ECO:0000269|PubMed:9717837}.		humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		AGCAGGGCAGCGTTCCCGCCC	0.687									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				G|||	1143	0.228235	0.3064	0.1268	5008	,	,		13697	0.3462		0.0835	False		,,,				2504	0.2219				p.S278R		Atlas-SNP	.											.	AIRE	61	.	0			c.C834G	GRCh37	CM025479	AIRE	M	rs1800520	PASS	.	G	ARG/SER	1240,3126		193,854,1136	19.0	21.0	21.0		834	1.6	0.0	21	dbSNP_89	21	787,7809		40,707,3551	yes	missense	AIRE	NM_000383.2	110	233,1561,4687	GG,GC,CC		9.1554,28.4013,15.638	benign	278/546	45709906	2027,10935	2183	4298	6481	SO:0001583	missense	326	exon7	Familial Cancer Database	APECED	GGGCAGCGTTCCC	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.834C>G	21.37:g.45709906C>G	ENSP00000291582:p.Ser278Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	151	84	0.556291	NM_000383	B2RP50|O43922|O43932|O75745	Missense_Mutation	SNP	ENST00000291582.5	37	CCDS13706.1	500	0.22893772893772893	162	0.32926829268292684	51	0.1408839779005525	219	0.38286713286713286	68	0.08970976253298153	G	0.147	-1.095963	0.01843	0.284013	0.091554	ENSG00000160224	ENST00000291582	D	0.94613	-3.47	3.44	1.58	0.23477	SAND domain (1);Zinc finger, FYVE/PHD-type (1);	0.275715	0.25842	N	0.027957	T	0.00012	0.0000	N	0.00707	-1.245	0.50171	P	1.48000000000037E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.32824	-0.9892	9	0.14656	T	0.56	-26.7239	3.2424	0.06786	0.2576:0.2275:0.5149:0.0	rs1800520	278	O43918	AIRE_HUMAN	R	278	ENSP00000291582:S278R	ENSP00000291582:S278R	S	+	3	2	AIRE	44534334	0.001000	0.12720	0.036000	0.18154	0.008000	0.06430	-0.271000	0.08572	0.258000	0.21686	-0.647000	0.03941	AGC	C|0.804;G|0.196	0.196	strong		0.687	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
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 GAIIx	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_ENST00000329971.3_Missense_Mutation_p.Q682L|R3HDM1_ENST00000410054.1_Missense_Mutation_p.Q756L|R3HDM1_ENST00000409606.1_Missense_Mutation_p.Q812L|R3HDM1_ENST00000409478.1_Missense_Mutation_p.Q683L	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	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	206	87	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	
AOC1	26	hgsc.bcm.edu	37	7	150555915	150555915	+	Silent	SNP	A	A	G	rs10893	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150555915A>G	ENST00000493429.1	+	5	2219	c.1635A>G	c.(1633-1635)ccA>ccG	p.P545P	AOC1_ENST00000467291.1_Silent_p.P545P|AOC1_ENST00000360937.4_Silent_p.P545P|AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000416793.2_Silent_p.P545P			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	545					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	CCTGGAGCCCAAGACACCGCG	0.562													G|||	2299	0.459065	0.5643	0.3977	5008	,	,		18858	0.4792		0.2734	False		,,,				2504	0.5307				p.P545P		Atlas-SNP	.											.	ABP1	92	.	0			c.A1635G						PASS	.	G		1898,2130		462,974,578	39.0	44.0	42.0		1635	-10.8	0.0	7	dbSNP_52	42	2525,5833		408,1709,2062	no	coding-synonymous	ABP1	NM_001091.2		870,2683,2640	GG,GA,AA		30.2106,47.1202,35.7097		545/752	150555915	4423,7963	2014	4179	6193	SO:0001819	synonymous_variant	26	exon3			GAGCCCAAGACAC	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1635A>G	7.37:g.150555915A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	41	0.386792	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																			A|0.571;G|0.429	0.429	strong		0.562	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
AMPD1	270	hgsc.bcm.edu	37	1	115231254	115231254	+	Missense_Mutation	SNP	G	G	A	rs61752479	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:115231254G>A	ENST00000520113.2	-	3	257	c.242C>T	c.(241-243)cCg>cTg	p.P81L	AMPD1_ENST00000353928.6_Missense_Mutation_p.P48L|AMPD1_ENST00000369538.3_Missense_Mutation_p.P77L			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	81			P -> L (polymorphism; activity comparable to wild-type; dbSNP:rs61752479). {ECO:0000269|PubMed:1631143}.		IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-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)	Adenosine monophosphate(DB00131)	ATGAGAAATCGGACAGATCTC	0.473													G|||	195	0.0389377	0.0045	0.0634	5008	,	,		20447	0.001		0.1233	False		,,,				2504	0.0204				p.P81L		Atlas-SNP	.											AMPD1_ENST00000520113,NS,carcinoma,0,2	AMPD1	223	2	0			c.C242T	GRCh37	CM920026	AMPD1	M	rs61752479	PASS	.	G	LEU/PRO,LEU/PRO	103,4303	82.4+/-120.9	2,99,2102	147.0	140.0	142.0		242,230	5.6	1.0	1	dbSNP_129	142	1144,7456	236.7+/-268.8	90,964,3246	yes	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	98,98	92,1063,5348	AA,AG,GG		13.3023,2.3377,9.5879	probably-damaging,probably-damaging	81/781,77/777	115231254	1247,11759	2203	4300	6503	SO:0001583	missense	270	exon3			GAAATCGGACAGA	M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	3.5.4.6		468	protein-coding gene	gene with protein product	"""AMPD isoform M"", ""skeletal muscle AMPD"""	102770	"""adenosine monophosphate deaminase 1 (isoform M)"""			1400401	Standard	NM_001172626		Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000520113.2:c.242C>T	1.37:g.115231254G>A	ENSP00000430075:p.Pro81Leu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	188	97	0.515957	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	119	0.05448717948717949	3	0.006097560975609756	31	0.0856353591160221	0	0.0	85	0.11213720316622691	G	19.67	3.871817	0.72180	0.023377	0.133023	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	T;T;T	0.63744	-0.06;-0.06;-0.06	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.70859	0.3272	L	0.43152	1.355	0.09310	P	0.9999999999943356	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.72354	-0.4319	9	0.87932	D	0	-11.3019	20.0247	0.97519	0.0:0.0:1.0:0.0	rs61752479	77;48	Q5TF02;P23109	.;AMPD1_HUMAN	L	81;77;48	ENSP00000430075:P81L;ENSP00000358551:P77L;ENSP00000316520:P48L	ENSP00000316520:P48L	P	-	2	0	AMPD1	115032777	1.000000	0.71417	1.000000	0.80357	0.172000	0.22775	9.232000	0.95325	2.804000	0.96469	0.655000	0.94253	CCG	G|0.913;A|0.087	0.087	strong		0.473	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4		
NMT1	4836	hgsc.bcm.edu	37	17	43171154	43171154	+	Silent	SNP	C	C	T	rs1132898	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43171154C>T	ENST00000592782.1	+	5	618	c.487C>T	c.(487-489)Ctg>Ttg	p.L163L	NMT1_ENST00000590114.1_3'UTR|NMT1_ENST00000258960.2_Silent_p.L163L			P30419	NMT1_HUMAN	N-myristoyltransferase 1	163					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				TGCTTTGGACCTGGGCGATCG	0.592													C|||	997	0.199081	0.3616	0.134	5008	,	,		16891	0.0367		0.1769	False		,,,				2504	0.2157				p.L163L		Atlas-SNP	.											.	NMT1	31	.	0			c.C487T						PASS	.	C		1432,2974	464.5+/-353.9	247,938,1018	79.0	65.0	70.0		487	4.1	1.0	17	dbSNP_86	70	1747,6853	316.3+/-312.7	170,1407,2723	no	coding-synonymous	NMT1	NM_021079.3		417,2345,3741	TT,TC,CC		20.314,32.5011,24.4426		163/497	43171154	3179,9827	2203	4300	6503	SO:0001819	synonymous_variant	4836	exon4			TTGGACCTGGGCG		CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"""alternative, short form NMT-S"", ""myristoyl-CoA:protein N-myristoyltransferase"", ""long form, NMT-L"""	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.487C>T	17.37:g.43171154C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_021079	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1																																																																																			C|0.785;G|0.000;T|0.215	0.215	strong		0.592	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
FCGBP	8857	hgsc.bcm.edu	37	19	40389657	40389657	+	Missense_Mutation	SNP	T	T	G	rs3746010|rs148187888		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40389657T>G	ENST00000221347.6	-	18	8532	c.8525A>C	c.(8524-8526)aAc>aCc	p.N2842T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2842	Cys-rich.			N -> T (in Ref. 1; BAA19526). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)		p.N2842T(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			agcACCTTTGTTGACGCAGCT	0.637																																					p.N2842T		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	large_intestine(1)	c.A8525C						scavenged	.						47.0	40.0	42.0					19																	40389657		2103	3809	5912	SO:0001583	missense	8857	exon18			CCTTTGTTGACGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8525A>C	19.37:g.40389657T>G	ENSP00000221347:p.Asn2842Thr	Somatic	430	7	0.0162791		WXS	Illumina HiSeq	Phase_I	226	19	0.0840708	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	t	0.013	-1.641107	0.00799	.	.	ENSG00000090920	ENST00000221347	T	0.19938	2.11	2.94	-3.79	0.04320	von Willebrand factor, type C (1);	0.689783	0.12210	N	0.489415	T	0.04952	0.0133	N	0.01219	-0.95	0.09310	N	1	B	0.19935	0.04	B	0.18871	0.023	T	0.41179	-0.9523	10	0.13108	T	0.6	.	6.0306	0.19679	0.0:0.1722:0.2977:0.5301	.	2842	Q9Y6R7	FCGBP_HUMAN	T	2842	ENSP00000221347:N2842T	ENSP00000221347:N2842T	N	-	2	0	FCGBP	45081497	0.511000	0.26179	0.068000	0.19968	0.025000	0.11179	-0.344000	0.07780	-0.736000	0.04831	-0.708000	0.03648	AAC	T|0.250;G|0.750	0.750	weak		0.637	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PADI3	51702	hgsc.bcm.edu	37	1	17601165	17601165	+	Silent	SNP	C	C	T	rs11585357	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17601165C>T	ENST00000375460.3	+	11	1231	c.1191C>T	c.(1189-1191)cgC>cgT	p.R397R		NM_016233.2	NP_057317.2	Q9ULW8	PADI3_HUMAN	peptidyl arginine deiminase, type III	397					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|liver(2)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;1.17e-05)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	GGGAACCACGCGACAGGTCTG	0.597											OREG0013148	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	304	0.0607029	0.0121	0.0994	5008	,	,		17565	0.001		0.1759	False		,,,				2504	0.0419				p.R397R		Atlas-SNP	.											PADI3,colon,carcinoma,+2,1	PADI3	81	1	0			c.C1191T						PASS	.	C		130,4276	94.4+/-133.1	1,128,2074	65.0	63.0	64.0		1191	-6.9	0.0	1	dbSNP_120	64	1309,7291	259.0+/-282.4	106,1097,3097	no	coding-synonymous	PADI3	NM_016233.2		107,1225,5171	TT,TC,CC		15.2209,2.9505,11.0641		397/665	17601165	1439,11567	2203	4300	6503	SO:0001819	synonymous_variant	51702	exon11			ACCACGCGACAGG	AB026831	CCDS179.1	1p36.13	2008-02-05			ENSG00000142619	ENSG00000142619	3.5.3.15	"""Peptidyl arginine deiminases"""	18337	protein-coding gene	gene with protein product		606755				11069618	Standard	NM_016233		Approved	PDI3	uc001bai.3	Q9ULW8	OTTHUMG00000002373	ENST00000375460.3:c.1191C>T	1.37:g.17601165C>T		Somatic	82	0	0	719	WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_016233	Q58EY7|Q70SX5	Silent	SNP	ENST00000375460.3	37	CCDS179.1																																																																																			C|0.902;T|0.098	0.098	strong		0.597	PADI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006805.1		
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 GAIIx	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_ENST00000522444.1_Silent_p.F133F|FGL1_ENST00000381840.2_Silent_p.F133F|FGL1_ENST00000398054.1_Silent_p.F133F|FGL1_ENST00000518650.1_Silent_p.F133F|FGL1_ENST00000381841.2_Silent_p.F133F|FGL1_ENST00000427924.1_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		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	102	45	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	
PDGFC	56034	hgsc.bcm.edu	37	4	157684248	157684248	+	Silent	SNP	T	T	C	rs3815861	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:157684248T>C	ENST00000502773.1	-	6	1522	c.1032A>G	c.(1030-1032)ggA>ggG	p.G344G	PDGFC_ENST00000422544.2_Silent_p.G281G|PDGFC_ENST00000542208.1_Silent_p.G189G|PDGFC_ENST00000504672.1_5'UTR|PDGFC_ENST00000541126.1_Silent_p.G181G	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	344					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cellular response to amino acid stimulus (GO:0071230)|central nervous system development (GO:0007417)|organ morphogenesis (GO:0009887)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)	p.G344G(1)		central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(180;0.24)	Renal(120;0.0458)		KIRC - Kidney renal clear cell carcinoma(143;0.08)|Kidney(143;0.0977)|COAD - Colon adenocarcinoma(41;0.212)		GCGGCTATCCTCCTGTGCTCC	0.542													T|||	1176	0.234824	0.2307	0.1686	5008	,	,		16765	0.1716		0.165	False		,,,				2504	0.4243				p.G344G		Atlas-SNP	.											PDGFC,NS,carcinoma,0,1	PDGFC	46	1	1	Substitution - coding silent(1)	prostate(1)	c.A1032G						scavenged	.	T		870,3536	337.6+/-304.9	98,674,1431	125.0	94.0	105.0		1032	-2.2	0.9	4	dbSNP_107	105	1329,7271	261.0+/-283.6	113,1103,3084	no	coding-synonymous	PDGFC	NM_016205.2		211,1777,4515	CC,CT,TT		15.4535,19.7458,16.9076		344/346	157684248	2199,10807	2203	4300	6503	SO:0001819	synonymous_variant	56034	exon6			CTATCCTCCTGTG	AF091434	CCDS3795.1	4q32	2008-02-05			ENSG00000145431	ENSG00000145431			8801	protein-coding gene	gene with protein product		608452				10858496, 10858548	Standard	NM_016205		Approved	SCDGF, fallotein	uc003iph.2	Q9NRA1	OTTHUMG00000161803	ENST00000502773.1:c.1032A>G	4.37:g.157684248T>C		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_016205	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Silent	SNP	ENST00000502773.1	37	CCDS3795.1																																																																																			A|0.000;C|0.171;T|0.829	0.171	strong		0.542	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1		
MUC16	94025	hgsc.bcm.edu	37	19	9069792	9069792	+	Missense_Mutation	SNP	G	G	A	rs1862458	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9069792G>A	ENST00000397910.4	-	3	17857	c.17654C>T	c.(17653-17655)tCc>tTc	p.S5885F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5887	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCCTTCCCAGGAAGCTGTGCT	0.502													G|||	1006	0.200879	0.0938	0.2824	5008	,	,		21349	0.3254		0.167	False		,,,				2504	0.1943				p.S5885F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C17654T						PASS	.	G	PHE/SER	403,3541		18,367,1587	175.0	160.0	165.0		17654	1.9	0.0	19	dbSNP_92	165	1510,6798		137,1236,2781	yes	missense	MUC16	NM_024690.2	155	155,1603,4368	AA,AG,GG		18.1753,10.2181,15.6138	probably-damaging	5885/14508	9069792	1913,10339	1972	4154	6126	SO:0001583	missense	94025	exon3			TCCCAGGAAGCTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.17654C>T	19.37:g.9069792G>A	ENSP00000381008:p.Ser5885Phe	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	125	50	0.4	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	479	0.21932234432234432	56	0.11382113821138211	92	0.2541436464088398	205	0.3583916083916084	126	0.1662269129287599	g	4.115	0.019520	0.08006	0.102181	0.181753	ENSG00000181143	ENST00000397910	T	0.24908	1.83	1.87	1.87	0.25490	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	.	.	.	D	0.65815	0.995	D	0.69824	0.966	T	0.38090	-0.9677	8	0.87932	D	0	.	7.2365	0.26072	0.0:0.0:1.0:0.0	rs1862458;rs52791883;rs56970751;rs1862458	5885	B5ME49	.	F	5885	ENSP00000381008:S5885F	ENSP00000381008:S5885F	S	-	2	0	MUC16	8930792	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.065000	0.11617	1.369000	0.46134	0.305000	0.20034	TCC	G|0.798;A|0.202	0.202	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NRP1	8829	hgsc.bcm.edu	37	10	33510768	33510768	+	Silent	SNP	G	G	A	rs2229934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:33510768G>A	ENST00000265371.4	-	9	1686	c.1161C>T	c.(1159-1161)ccC>ccT	p.P387P	NRP1_ENST00000374823.5_Silent_p.P387P|NRP1_ENST00000432372.2_Silent_p.P387P|NRP1_ENST00000395995.1_Silent_p.P387P|NRP1_ENST00000374875.1_Silent_p.P206P|NRP1_ENST00000374822.4_Silent_p.P387P|NRP1_ENST00000374867.2_Silent_p.P387P|NRP1_ENST00000374816.3_Silent_p.P387P|NRP1_ENST00000374821.5_Silent_p.P387P			O14786	NRP1_HUMAN	neuropilin 1	387	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	CAACATCTGTGGGGTTGGTGT	0.408													G|||	1799	0.359225	0.18	0.4337	5008	,	,		17724	0.623		0.2485	False		,,,				2504	0.3906				p.P387P	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											.	NRP1	126	.	0			c.C1161T						PASS	.	G	,,	917,3489	354.4+/-312.6	99,719,1385	140.0	135.0	137.0		1161,1161,1161	3.9	1.0	10	dbSNP_98	137	2285,6315	385.2+/-341.4	302,1681,2317	no	coding-synonymous,coding-synonymous,coding-synonymous	NRP1	NM_001024628.2,NM_001024629.2,NM_003873.5	,,	401,2400,3702	AA,AG,GG		26.5698,20.8125,24.6194	,,	387/645,387/610,387/924	33510768	3202,9804	2203	4300	6503	SO:0001819	synonymous_variant	8829	exon8			ATCTGTGGGGTTG	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.1161C>T	10.37:g.33510768G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	37	CCDS7177.1																																																																																			G|0.724;A|0.276	0.276	strong		0.408	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
RNF123	63891	hgsc.bcm.edu	37	3	49751585	49751585	+	Silent	SNP	C	C	T	rs2291542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49751585C>T	ENST00000327697.6	+	31	3132	c.2988C>T	c.(2986-2988)gaC>gaT	p.D996D	RNF123_ENST00000433785.1_Silent_p.D108D	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	996					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)		AACTTGAGGACGCCAATTTGC	0.597													C|||	1254	0.250399	0.2519	0.2061	5008	,	,		19901	0.1538		0.3091	False		,,,				2504	0.319				p.D996D		Atlas-SNP	.											RNF123,caecum,carcinoma,0,1	RNF123	100	1	0			c.C2988T						PASS	.	C		1113,3293	399.2+/-331.1	143,827,1233	90.0	90.0	90.0		2988	-4.6	0.9	3	dbSNP_100	90	2588,6012	421.6+/-353.8	391,1806,2103	no	coding-synonymous	RNF123	NM_022064.2		534,2633,3336	TT,TC,CC		30.093,25.261,28.4561		996/1315	49751585	3701,9305	2203	4300	6503	SO:0001819	synonymous_variant	63891	exon31			TGAGGACGCCAAT	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.2988C>T	3.37:g.49751585C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	CCDS33758.1																																																																																			C|0.736;T|0.264	0.264	strong		0.597	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
LMBRD2	92255	hgsc.bcm.edu	37	5	36142648	36142648	+	Silent	SNP	A	A	G	rs12658867	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:36142648A>G	ENST00000296603.4	-	3	690	c.228T>C	c.(226-228)aaT>aaC	p.N76N		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	76						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.N76N(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TAATGTTGCTATTCTCAGGAG	0.358													A|||	1137	0.227037	0.0272	0.2493	5008	,	,		15180	0.2192		0.4056	False		,,,				2504	0.3057				p.N76N		Atlas-SNP	.											LMBRD2,NS,carcinoma,0,1	LMBRD2	89	1	1	Substitution - coding silent(1)	prostate(1)	c.T228C						PASS	.	A		406,4000	201.1+/-224.2	19,368,1816	158.0	148.0	151.0		228	-3.7	0.0	5	dbSNP_120	151	3496,5104	511.1+/-377.6	714,2068,1518	no	coding-synonymous	LMBRD2	NM_001007527.1		733,2436,3334	GG,GA,AA		40.6512,9.2147,30.0015		76/696	36142648	3902,9104	2203	4300	6503	SO:0001819	synonymous_variant	92255	exon3			GTTGCTATTCTCA		CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.228T>C	5.37:g.36142648A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_001007527	B3KRB6|Q9NTC7	Silent	SNP	ENST00000296603.4	37	CCDS34145.1																																																																																			A|0.736;G|0.264	0.264	strong		0.358	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527	
OR2L13	284521	hgsc.bcm.edu	37	1	248262731	248262731	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248262731C>T	ENST00000358120.2	+	2	199	c.54C>T	c.(52-54)ccC>ccT	p.P18P	OR2L13_ENST00000366478.2_Silent_p.P18P			Q8N349	OR2LD_HUMAN	olfactory receptor, family 2, subfamily L, member 13	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P18P(2)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(32)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	59	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;0.0132)			GTCTGCTTCCCCCAAATCAAA	0.408																																					p.P18P		Atlas-SNP	.											OR2L13_ENST00000366478,NS,carcinoma,0,2	OR2L13	261	2	2	Substitution - coding silent(2)	lung(2)	c.C54T						scavenged	.						171.0	168.0	169.0					1																	248262731		2203	4300	6503	SO:0001819	synonymous_variant	284521	exon3			GCTTCCCCCAAAT	BC028158	CCDS1637.1	1q44	2012-08-09			ENSG00000196071	ENSG00000196071		"""GPCR / Class A : Olfactory receptors"""	19578	protein-coding gene	gene with protein product				OR2L14			Standard	NM_175911		Approved		uc001ids.3	Q8N349	OTTHUMG00000040446	ENST00000358120.2:c.54C>T	1.37:g.248262731C>T		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	179	2	0.0111732	NM_175911	Q5VUR5	Silent	SNP	ENST00000358120.2	37	CCDS1637.1																																																																																			.	.	none		0.408	OR2L13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097342.1	NM_175911	
DPF1	8193	hgsc.bcm.edu	37	19	38702950	38702950	+	Silent	SNP	G	G	A	rs11547760	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38702950G>A	ENST00000420980.2	-	10	1068	c.1042C>T	c.(1042-1044)Ctg>Ttg	p.L348L	DPF1_ENST00000416611.1_Silent_p.L366L|DPF1_ENST00000456296.1_Silent_p.L356L|DPF1_ENST00000355526.4_Silent_p.L382L|DPF1_ENST00000414789.1_Silent_p.L300L|DPF1_ENST00000412732.1_Silent_p.L300L	NM_004647.2	NP_004638.2	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1	348					apoptotic process (GO:0006915)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GGGGGACTCAGGCAGTACATG	0.657													N|||	338	0.067492	0.0023	0.0994	5008	,	,		3690	0.0437		0.1103	False		,,,				2504	0.1135				p.L382L		Atlas-SNP	.											.	DPF1	54	.	0			c.C1144T						PASS	.	G	,,	73,4223		2,69,2077	11.0	12.0	12.0		1144,898,1042	3.7	1.0	19	dbSNP_120	12	691,7681		17,657,3512	no	coding-synonymous,coding-synonymous,coding-synonymous	DPF1	NM_001135155.1,NM_001135156.1,NM_004647.2	,,	19,726,5589	AA,AG,GG		8.2537,1.6993,6.0309	,,	382/415,300/333,348/381	38702950	764,11904	2148	4186	6334	SO:0001819	synonymous_variant	8193	exon11			GACTCAGGCAGTA	U43843	CCDS33008.2, CCDS46064.1, CCDS46065.1	19q13.12	2013-01-28			ENSG00000011332	ENSG00000011332		"""Zinc fingers, PHD-type"""	20225	protein-coding gene	gene with protein product		601670				8812431	Standard	XM_005259288		Approved	neuro-d4, NEUD4, BAF45b	uc002ohm.3	Q92782	OTTHUMG00000157164	ENST00000420980.2:c.1042C>T	19.37:g.38702950G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001135155	B3KSY8|Q08AJ0	Silent	SNP	ENST00000420980.2	37	CCDS33008.2	143	0.06547619047619048	2	0.0040650406504065045	39	0.10773480662983426	24	0.04195804195804196	78	0.10290237467018469	G	9.165	1.019756	0.19355	0.016993	0.082537	ENSG00000011332	ENST00000355526	.	.	.	3.71	3.71	0.42584	.	.	.	.	.	T	0.01287	0.0042	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.21930	-1.0231	3	.	.	.	-8.7884	8.48	0.33036	0.1108:0.0:0.8892:0.0	rs11547760	.	.	.	L	374	.	.	P	-	2	0	DPF1	43394790	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.718000	0.54919	1.896000	0.54893	0.579000	0.79373	CCT	G|0.929;A|0.071	0.071	strong		0.657	DPF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347721.1		
STK17A	9263	hgsc.bcm.edu	37	7	43647879	43647879	+	Silent	SNP	C	C	T	rs11555026	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:43647879C>T	ENST00000319357.5	+	3	623	c.444C>T	c.(442-444)gaC>gaT	p.D148D	STK17A_ENST00000462448.1_3'UTR	NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	148	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						AAATCTTTGACCAGTGTGTTG	0.373													C|||	456	0.0910543	0.0091	0.1354	5008	,	,		17699	0.0119		0.2167	False		,,,				2504	0.1227				p.D148D		Atlas-SNP	.											.	STK17A	31	.	0			c.C444T						PASS	.	C		173,4233	113.3+/-151.4	5,163,2035	92.0	91.0	92.0		444	2.9	1.0	7	dbSNP_120	92	1816,6784	326.4+/-317.4	194,1428,2678	no	coding-synonymous	STK17A	NM_004760.2		199,1591,4713	TT,TC,CC		21.1163,3.9265,15.2929		148/415	43647879	1989,11017	2203	4300	6503	SO:0001819	synonymous_variant	9263	exon3			CTTTGACCAGTGT	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 1"""	604726	"""serine/threonine kinase 17a (apoptosis-inducing)"""			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.444C>T	7.37:g.43647879C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	63	40	0.634921	NM_004760	A4D1V6|Q8IVC8	Silent	SNP	ENST00000319357.5	37	CCDS5470.1																																																																																			C|0.858;T|0.142	0.142	strong		0.373	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760	
MARC2	54996	hgsc.bcm.edu	37	1	220936372	220936372	+	Missense_Mutation	SNP	G	G	A	rs3795535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:220936372G>A	ENST00000366913.3	+	4	928	c.730G>A	c.(730-732)Ggc>Agc	p.G244S	MARC2_ENST00000359316.2_Missense_Mutation_p.G244S	NM_017898.3	NP_060368.2	Q969Z3	MARC2_HUMAN	mitochondrial amidoxime reducing component 2	244	MOSC. {ECO:0000255|PROSITE- ProRule:PRU00670}.		G -> S (decreased catalytic efficiency toward benzamidoxime; no effect on affinity for benzamidoxime; no effect on binding of the molybdenum cofactor; dbSNP:rs3795535). {ECO:0000269|PubMed:24423752, ECO:0000269|Ref.3}.		detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										TGTGGTGACCGGCTGTGATGC	0.502													G|||	161	0.0321486	0.0393	0.0029	5008	,	,		19743	0.0585		0.0109	False		,,,				2504	0.0378				p.G244S		Atlas-SNP	.											MOSC2,NS,carcinoma,-2,1	.	.	1	0			c.G730A						PASS	.	G	SER/GLY	133,4273	95.3+/-134.0	4,125,2074	134.0	133.0	133.0		730	5.7	1.0	1	dbSNP_107	133	47,8553	30.1+/-81.4	0,47,4253	yes	missense	MOSC2	NM_017898.3	56	4,172,6327	AA,AG,GG		0.5465,3.0186,1.384	probably-damaging	244/336	220936372	180,12826	2203	4300	6503	SO:0001583	missense	54996	exon4			GTGACCGGCTGTG		CCDS1525.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000117791	ENSG00000117791			26064	protein-coding gene	gene with protein product		614127	"""MOCO sulphurase C-terminal domain containing 2"""	MOSC2		11886751	Standard	NM_017898		Approved	FLJ20605	uc001hmq.3	Q969Z3	OTTHUMG00000037354	ENST00000366913.3:c.730G>A	1.37:g.220936372G>A	ENSP00000355880:p.Gly244Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_017898	B2D0R5|D3DTB3|Q0JSK7|Q5VT67|Q5VXC7|Q7L317|Q9H066|Q9NWU0	Missense_Mutation	SNP	ENST00000366913.3	37	CCDS1525.1	74	0.03388278388278388	24	0.04878048780487805	1	0.0027624309392265192	44	0.07692307692307693	5	0.006596306068601583	G	26.2	4.714388	0.89112	0.030186	0.005465	ENSG00000117791	ENST00000359316;ENST00000366913;ENST00000425560	T;T;T	0.56103	0.48;0.48;0.48	5.67	5.67	0.87782	Pyruvate kinase-like, insert domain (1);Molybdenum cofactor sulfurase, C-terminal (2);	0.159474	0.42821	D	0.000642	T	0.18718	0.0449	M	0.90425	3.115	0.45733	D	0.998634	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	T	0.63603	-0.6600	10	0.66056	D	0.02	-28.1595	16.678	0.85284	0.0:0.0:1.0:0.0	rs3795535;rs52794890;rs3795535	244;244	Q969Z3-2;Q969Z3	.;MOSC2_HUMAN	S	244;244;145	ENSP00000352266:G244S;ENSP00000355880:G244S;ENSP00000416442:G145S	ENSP00000352266:G244S	G	+	1	0	MOSC2	219002995	1.000000	0.71417	0.958000	0.39756	0.767000	0.43475	7.414000	0.80117	2.661000	0.90470	0.655000	0.94253	GGC	G|0.977;A|0.023	0.023	strong		0.502	MARC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090911.1	NM_017898	
FREM2	341640	hgsc.bcm.edu	37	13	39264690	39264690	+	Missense_Mutation	SNP	T	T	C	rs2496425	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:39264690T>C	ENST00000280481.7	+	1	3425	c.3209T>C	c.(3208-3210)tTt>tCt	p.F1070S		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1070			F -> S (in dbSNP:rs2496425).		cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CCAGAAATCTTTGTAGGTGAA	0.413													C|||	2410	0.48123	0.8381	0.4496	5008	,	,		21289	0.4177		0.2624	False		,,,				2504	0.3119				p.F1070S		Atlas-SNP	.											FREM2,colon,carcinoma,0,1	FREM2	385	1	0			c.T3209C	GRCh37	CM065186	FREM2	M	rs2496425	PASS	.	C	SER/PHE	3315,1091	395.4+/-329.6	1247,821,135	105.0	106.0	106.0		3209	6.1	1.0	13	dbSNP_100	106	2360,6240	702.8+/-405.3	325,1710,2265	yes	missense	FREM2	NM_207361.4	155	1572,2531,2400	CC,CT,TT		27.4419,24.7617,43.6337	benign	1070/3170	39264690	5675,7331	2203	4300	6503	SO:0001583	missense	341640	exon1			AAATCTTTGTAGG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.3209T>C	13.37:g.39264690T>C	ENSP00000280481:p.Phe1070Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	114	31	0.27193	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	998	0.45695970695970695	403	0.8191056910569106	151	0.4171270718232044	245	0.42832167832167833	199	0.262532981530343	C	0.013	-1.615018	0.00835	0.752383	0.274419	ENSG00000150893	ENST00000280481	T	0.39229	1.09	6.07	6.07	0.98685	.	0.283692	0.41001	N	0.000966	T	0.00012	0.0000	N	0.21545	0.675	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27839	-1.0062	9	0.11794	T	0.64	.	10.1398	0.42728	0.0:0.8123:0.0:0.1877	rs2496425;rs17304515;rs57839593;rs2496425	1070	Q5SZK8	FREM2_HUMAN	S	1070	ENSP00000280481:F1070S	ENSP00000280481:F1070S	F	+	2	0	FREM2	38162690	0.000000	0.05858	0.989000	0.46669	0.624000	0.37722	0.928000	0.28831	1.598000	0.50083	-0.128000	0.14901	TTT	T|0.546;C|0.454	0.454	strong		0.413	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
DTHD1	401124	hgsc.bcm.edu	37	4	36345377	36345377	+	Silent	SNP	G	G	A	rs2270880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:36345377G>A	ENST00000456874.2	+	9	2335	c.2277G>A	c.(2275-2277)gaG>gaA	p.E759E	DTHD1_ENST00000503528.1_3'UTR|RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000507598.1_Silent_p.E799E|DTHD1_ENST00000357504.3_Silent_p.E594E	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	759	Death. {ECO:0000255|PROSITE- ProRule:PRU00064}.				signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						TTGCAGAAGAGCTCAAATTCA	0.458													G|||	541	0.108027	0.0106	0.062	5008	,	,		19226	0.121		0.165	False		,,,				2504	0.2004				p.E759E		Atlas-SNP	.											.	DTHD1	63	.	0			c.G2277A						PASS	.	G	,	62,1322		3,56,633	19.0	17.0	18.0		1782,2277	4.3	1.0	4	dbSNP_100	18	526,2656		43,440,1108	no	coding-synonymous,coding-synonymous	DTHD1	NM_001136536.3,NM_001170700.1	,	46,496,1741	AA,AG,GG		16.5305,4.4798,12.8778	,	594/617,759/782	36345377	588,3978	692	1591	2283	SO:0001819	synonymous_variant	401124	exon9			AGAAGAGCTCAAA	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.2277G>A	4.37:g.36345377G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			G|0.895;A|0.105	0.105	strong		0.458	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
FBXO34	55030	hgsc.bcm.edu	37	14	55818517	55818517	+	Missense_Mutation	SNP	T	T	A	rs1045002	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:55818517T>A	ENST00000313833.4	+	2	1654	c.1409T>A	c.(1408-1410)aTt>aAt	p.I470N	FBXO34_ENST00000440021.1_Missense_Mutation_p.I470N	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	470			I -> N (in dbSNP:rs1045002). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.					p.I470N(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						CAGCCTTCCATTTTAAACTCC	0.423													A|||	1661	0.331669	0.2322	0.3098	5008	,	,		20331	0.3185		0.4245	False		,,,				2504	0.3998				p.I470N		Atlas-SNP	.											FBXO34,NS,carcinoma,0,1	FBXO34	61	1	1	Substitution - Missense(1)	stomach(1)	c.T1409A						PASS	.	A	ASN/ILE,ASN/ILE	1147,3259	713.6+/-408.3	154,839,1210	115.0	112.0	113.0		1409,1409	-0.8	0.0	14	dbSNP_86	113	3621,4979	624.3+/-397.6	780,2061,1459	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	149,149	934,2900,2669	AA,AT,TT		42.1047,26.0327,36.66	benign,benign	470/712,470/712	55818517	4768,8238	2203	4300	6503	SO:0001583	missense	55030	exon2			CTTCCATTTTAAA	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1409T>A	14.37:g.55818517T>A	ENSP00000313159:p.Ile470Asn	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	192	188	0.979167	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	748	0.3424908424908425	118	0.23983739837398374	116	0.32044198895027626	191	0.3339160839160839	323	0.4261213720316623	A	0.013	-1.642727	0.00792	0.260327	0.421047	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.16457	2.34;2.34	5.48	-0.84	0.10755	.	1.461070	0.04686	N	0.413270	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.12837	0.008	T	0.48139	-0.9061	9	0.15499	T	0.54	-0.416	4.9015	0.13777	0.1197:0.4841:0.1548:0.2414	rs1045002;rs3168901;rs3742568;rs17674186;rs60147901;rs1045002	470	Q9NWN3	FBX34_HUMAN	N	470	ENSP00000313159:I470N;ENSP00000394117:I470N	ENSP00000313159:I470N	I	+	2	0	FBXO34	54888270	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.270000	0.08584	-0.639000	0.05502	-1.546000	0.00904	ATT	A|0.366;N|0.000	0.366	strong		0.423	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
PTBP1	5725	hgsc.bcm.edu	37	19	808742	808742	+	Silent	SNP	G	G	T	rs1135908	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:808742G>T	ENST00000349038.4	+	12	1438	c.1365G>T	c.(1363-1365)acG>acT	p.T455T	PTBP1_ENST00000356948.6_Silent_p.T481T|PTBP1_ENST00000394601.4_Silent_p.T474T|PTBP1_ENST00000350092.4_Silent_p.T121T	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	455	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		CCTCGGCCACGCTGCACCTCT	0.662													G|||	799	0.159545	0.1331	0.2651	5008	,	,		9373	0.0218		0.1451	False		,,,				2504	0.2771				p.T481T		Atlas-SNP	.											.	PTBP1	43	.	0			c.G1443T						PASS	.	G	,,,	561,3835		43,475,1680	30.0	29.0	29.0		1443,1422,1365,363	0.0	1.0	19	dbSNP_86	29	1259,7327		83,1093,3117	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	126,1568,4797	TT,TG,GG		14.6634,12.7616,14.0194	,,,	481/558,474/551,455/532,121/198	808742	1820,11162	2198	4293	6491	SO:0001819	synonymous_variant	5725	exon13			GGCCACGCTGCAC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.1365G>T	19.37:g.808742G>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	149	68	0.456376	NM_002819	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			G|0.864;T|0.136	0.136	strong		0.662	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
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 GAIIx	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_ENST00000429473.1_Missense_Mutation_p.E50K|GNGT1_ENST00000455502.1_3'UTR	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	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	39	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	
LPA	4018	hgsc.bcm.edu	37	6	161006172	161006172	+	Missense_Mutation	SNP	T	T	G	rs41272110	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:161006172T>G	ENST00000316300.5	-	26	4239	c.4195A>C	c.(4195-4197)Aca>Cca	p.T1399P	LPA_ENST00000447678.1_Missense_Mutation_p.T1399P			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3907	Kringle 13. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GTGGAGAGTGTGCCTCGATAA	0.463													T|||	298	0.0595048	0.0076	0.0951	5008	,	,		18632	0.0		0.1491	False		,,,				2504	0.0736				p.T1399P		Atlas-SNP	.											.	LPA	237	.	0			c.A4195C	GRCh37	CM995215	LPA	M	rs41272110	PASS	.	T	PRO/THR	122,4260	84.8+/-123.5	3,116,2072	222.0	221.0	222.0		4195	2.4	0.1	6	dbSNP_127	222	1281,7311	249.4+/-276.7	100,1081,3115	yes	missense	LPA	NM_005577.2	38	103,1197,5187	GG,GT,TT		14.9092,2.7841,10.8139	probably-damaging	1399/2041	161006172	1403,11571	2191	4296	6487	SO:0001583	missense	4018	exon27			AGAGTGTGCCTCG	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4195A>C	6.37:g.161006172T>G	ENSP00000321334:p.Thr1399Pro	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	168	0.07692307692307693	6	0.012195121951219513	42	0.11602209944751381	0	0.0	120	0.158311345646438	t	8.813	0.935731	0.18206	0.027841	0.149092	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.65732	-0.17;-0.17	2.41	2.41	0.29592	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.65407	0.2688	M	0.73962	2.25	0.80722	P	0.0	D	0.67145	0.996	D	0.78314	0.991	T	0.64521	-0.6388	8	0.56958	D	0.05	.	6.6034	0.22712	0.0:0.0:0.0:1.0	rs41272110	3907	P08519	APOA_HUMAN	P	1399	ENSP00000321334:T1399P;ENSP00000395608:T1399P	ENSP00000321334:T1399P	T	-	1	0	LPA	160926162	0.668000	0.27493	0.050000	0.19076	0.007000	0.05969	4.669000	0.61575	1.087000	0.41251	0.358000	0.22013	ACA	T|0.898;G|0.102	0.102	strong		0.463	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
OGFR	11054	hgsc.bcm.edu	37	20	61444600	61444600	+	Missense_Mutation	SNP	C	C	A	rs6122313	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61444600C>A	ENST00000290291.6	+	7	1658	c.1633C>A	c.(1633-1635)Cgc>Agc	p.R545S	OGFR_ENST00000370461.1_Missense_Mutation_p.R493S	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	545	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].		R -> S (in dbSNP:rs6122313).		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)	p.R545S(1)		endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CCCAGGCCCCCGCCCAGCAGG	0.741																																					p.R545S		Atlas-SNP	.											OGFR,extremity,malignant_melanoma,0,1	OGFR	63	1	1	Substitution - Missense(1)	skin(1)	c.C1633A						scavenged	.						12.0	18.0	16.0					20																	61444600		2126	4164	6290	SO:0001583	missense	11054	exon7			GGCCCCCGCCCAG	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.1633C>A	20.37:g.61444600C>A	ENSP00000290291:p.Arg545Ser	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	177	0.08104395604395605	9	0.018292682926829267	28	0.07734806629834254	113	0.19755244755244755	27	0.03562005277044855	A	0.017	-1.504049	0.00992	.	.	ENSG00000060491	ENST00000290291;ENST00000370461	T;T	0.54866	0.55;0.55	1.4	-0.396	0.12427	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.19289	-1.0310	8	0.20046	T	0.44	.	3.5878	0.07977	0.2924:0.5063:0.2013:0.0	rs6122313	528;545	Q05BV5;Q9NZT2	.;OGFR_HUMAN	S	545;493	ENSP00000290291:R545S;ENSP00000359491:R493S	ENSP00000290291:R545S	R	+	1	0	OGFR	60915045	0.000000	0.05858	0.001000	0.08648	0.049000	0.14656	-0.544000	0.06077	-0.264000	0.09365	-1.293000	0.01348	CGC	C|0.918;A|0.082	0.082	strong		0.741	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
SETBP1	26040	hgsc.bcm.edu	37	18	42532693	42532693	+	Missense_Mutation	SNP	C	C	A	rs1064204	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:42532693C>A	ENST00000282030.5	+	4	3684	c.3388C>A	c.(3388-3390)Cct>Act	p.P1130T		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1130			P -> T (in dbSNP:rs1064204).			nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		TGACATGCAGCCTTCTCTGAA	0.527									Schinzel-Giedion syndrome				C|||	594	0.11861	0.0182	0.2435	5008	,	,		20858	0.1895		0.1103	False		,,,				2504	0.1012				p.P1130T		Atlas-SNP	.											.	SETBP1	577	.	0			c.C3388A						PASS	.	C	THR/PRO	212,4194	130.2+/-166.9	5,202,1996	109.0	87.0	94.0		3388	4.1	1.0	18	dbSNP_86	94	1030,7570	219.0+/-257.2	57,916,3327	yes	missense	SETBP1	NM_015559.2	38	62,1118,5323	AA,AC,CC		11.9767,4.8116,9.5494	benign	1130/1597	42532693	1242,11764	2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ATGCAGCCTTCTC	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3388C>A	18.37:g.42532693C>A	ENSP00000282030:p.Pro1130Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	289	0.13232600732600733	11	0.022357723577235773	74	0.20441988950276244	120	0.2097902097902098	84	0.11081794195250659	C	5.865	0.343735	0.11126	0.048116	0.119767	ENSG00000152217	ENST00000282030	T	0.69175	-0.38	5.88	4.09	0.47781	.	0.283324	0.36482	N	0.002561	T	0.00039	0.0001	N	0.24115	0.695	0.33516	P	0.40827899999999995	B	0.02656	0.0	B	0.08055	0.003	T	0.05716	-1.0868	9	0.39692	T	0.17	.	2.183	0.03879	0.1765:0.4964:0.1718:0.1553	rs1064204;rs3205204;rs3744826;rs52806906;rs61239753;rs1064204	1130	Q9Y6X0	SETBP_HUMAN	T	1130	ENSP00000282030:P1130T	ENSP00000282030:P1130T	P	+	1	0	SETBP1	40786691	1.000000	0.71417	0.999000	0.59377	0.928000	0.56348	1.873000	0.39558	0.823000	0.34589	0.561000	0.74099	CCT	C|0.892;A|0.108	0.108	strong		0.527	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
UIMC1	51720	hgsc.bcm.edu	37	5	176382995	176382995	+	Missense_Mutation	SNP	G	G	A	rs3733876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176382995G>A	ENST00000377227.4	-	8	1436	c.1304C>T	c.(1303-1305)cCa>cTa	p.P435L	UIMC1_ENST00000506128.1_Missense_Mutation_p.P269L|UIMC1_ENST00000511320.1_Missense_Mutation_p.P435L|UIMC1_ENST00000503273.1_5'UTR|UIMC1_ENST00000377219.2_Missense_Mutation_p.P435L			Q96RL1	UIMC1_HUMAN	ubiquitin interaction motif containing 1	435	Necessary for interaction with NR6A1 C- terminus.		P -> L (common polymorphism not associated with susceptibility to breast cancer; dbSNP:rs3733876). {ECO:0000269|PubMed:18695986}.		double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|histone H2A K63-linked deubiquitination (GO:0070537)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)	BRCA1-A complex (GO:0070531)|nucleus (GO:0005634)	histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)			NS(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(5)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	21	all_cancers(89;7.96e-05)|Renal(175;0.000269)|Lung NSC(126;0.00476)|all_lung(126;0.00806)	Medulloblastoma(196;0.0145)|all_neural(177;0.0325)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGAACTCTCTGGCATAAGGAC	0.378													G|||	514	0.102636	0.0189	0.0879	5008	,	,		20269	0.1944		0.1571	False		,,,				2504	0.0757				p.P435L		Atlas-SNP	.											.	UIMC1	55	.	0			c.C1304T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	192,4214	121.7+/-159.2	4,184,2015	111.0	105.0	107.0		1304,1304,1304	5.5	1.0	5	dbSNP_107	107	1496,7104	284.7+/-296.8	142,1212,2946	yes	missense,missense,missense	UIMC1	NM_001199297.1,NM_001199298.1,NM_016290.4	98,98,98	146,1396,4961	AA,AG,GG		17.3953,4.3577,12.9786	probably-damaging,probably-damaging,probably-damaging	435/720,435/720,435/720	176382995	1688,11318	2203	4300	6503	SO:0001583	missense	51720	exon8			CTCTCTGGCATAA	AF349313	CCDS4408.1	5q35.2	2008-02-05			ENSG00000087206	ENSG00000087206			30298	protein-coding gene	gene with protein product	"""receptor associated protein 80"""	609433				12080054	Standard	NM_001199297		Approved	RAP80	uc021yin.1	Q96RL1	OTTHUMG00000130852	ENST00000377227.4:c.1304C>T	5.37:g.176382995G>A	ENSP00000366434:p.Pro435Leu	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	200	110	0.55	NM_016290	A8MSA1|B3KMZ1|B4E3N2|Q5XKQ1|Q7Z3W7|Q8N5B9|Q9BZR1|Q9BZR5|Q9UHX7	Missense_Mutation	SNP	ENST00000377227.4	37	CCDS4408.1	279	0.12774725274725274	14	0.028455284552845527	38	0.10497237569060773	99	0.17307692307692307	128	0.16886543535620052	G	12.80	2.047947	0.36085	0.043577	0.173953	ENSG00000087206	ENST00000377227;ENST00000377219;ENST00000511320;ENST00000506128;ENST00000377220;ENST00000323774	T;T;T;T	0.13901	2.58;2.58;2.58;2.55	5.53	5.53	0.82687	.	0.106427	0.40818	N	0.001018	T	0.00073	0.0002	L	0.43152	1.355	0.22034	P	0.999408074	D;D;D;D;P	0.89917	0.96;1.0;0.986;0.977;0.928	P;D;P;P;P	0.91635	0.55;0.999;0.775;0.73;0.494	T	0.00657	-1.1623	9	0.59425	D	0.04	.	15.1875	0.73016	0.0:0.1397:0.8603:0.0	rs3733876;rs52809311;rs56465845;rs58246171;rs3733876	435;154;269;65;357	Q96RL1;D6RCF3;C9JR12;Q96RL1-4;Q96RL1-3	UIMC1_HUMAN;.;.;.;.	L	435;435;435;269;357;65	ENSP00000366434:P435L;ENSP00000366425:P435L;ENSP00000421926:P435L;ENSP00000427480:P269L	ENSP00000314909:P65L	P	-	2	0	UIMC1	176315601	1.000000	0.71417	0.990000	0.47175	0.754000	0.42855	2.389000	0.44407	2.775000	0.95449	0.650000	0.86243	CCA	G|0.879;A|0.121	0.121	strong		0.378	UIMC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253422.1	NM_016290	
GABRD	2563	hgsc.bcm.edu	37	1	1960674	1960674	+	Silent	SNP	C	C	T	rs28408173	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1960674C>T	ENST00000378585.4	+	7	899	c.816C>T	c.(814-816)agC>agT	p.S272S		NM_000815.4	NP_000806.2	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	272					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(2)|endometrium(3)|kidney(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCTGGATCAGCCAGGCGGCGG	0.667													C|||	993	0.198283	0.0121	0.2089	5008	,	,		17568	0.4415		0.1143	False		,,,				2504	0.2781				p.S272S		Atlas-SNP	.											.	GABRD	49	.	0			c.C816T						PASS	.	C		141,4239		5,131,2054	53.0	45.0	47.0		816	-3.4	1.0	1	dbSNP_125	47	1123,7427		78,967,3230	no	coding-synonymous	GABRD	NM_000815.4		83,1098,5284	TT,TC,CC		13.1345,3.2192,9.7757		272/453	1960674	1264,11666	2190	4275	6465	SO:0001819	synonymous_variant	2563	exon7			GATCAGCCAGGCG	BC033801	CCDS36.1	1p36.3	2012-06-22			ENSG00000187730	ENSG00000187730		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4084	protein-coding gene	gene with protein product	"""GABA(A) receptor, delta"""	137163				2176788, 10965146	Standard	NM_000815		Approved		uc001aip.2	O14764	OTTHUMG00000041064	ENST00000378585.4:c.816C>T	1.37:g.1960674C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_000815	Q8N4N9	Silent	SNP	ENST00000378585.4	37	CCDS36.1																																																																																			C|0.874;T|0.126	0.126	strong		0.667	GABRD-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098493.1	NM_000815	
TTLL3	26140	hgsc.bcm.edu	37	3	9870857	9870857	+	Silent	SNP	G	G	A	rs2290303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9870857G>A	ENST00000547186.1	+	10	1548	c.1332G>A	c.(1330-1332)caG>caA	p.Q444Q	TTLL3_ENST00000455274.1_Silent_p.Q232Q|TTLL3_ENST00000426895.4_Silent_p.Q587Q|ARPC4-TTLL3_ENST00000397256.1_Silent_p.Q505Q|TTLL3_ENST00000430793.1_Silent_p.Q232Q|TTLL3_ENST00000427853.3_Silent_p.Q232Q|TTLL3_ENST00000466245.1_3'UTR|TTLL3_ENST00000397241.1_Silent_p.Q232Q|TTLL3_ENST00000383827.1_Silent_p.Q232Q	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	444	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				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)					ACACCGTGCAGTGTCGGAAGG	0.592													G|||	1367	0.272963	0.1286	0.3112	5008	,	,		22011	0.1577		0.5746	False		,,,				2504	0.2495				p.Q587Q		Atlas-SNP	.											.	TTLL3	51	.	0			c.G1761A						PASS	.	G	,	794,3612	319.6+/-296.2	81,632,1490	118.0	89.0	99.0		1761,1515	0.7	0.6	3	dbSNP_100	99	4342,4258	579.8+/-391.0	1109,2124,1067	no	coding-synonymous,coding-synonymous	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	,	1190,2756,2557	AA,AG,GG		49.5116,18.0209,39.4895	,	587/916,505/626	9870857	5136,7870	2203	4300	6503	SO:0001819	synonymous_variant	26140	exon10			CGTGCAGTGTCGG		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.1332G>A	3.37:g.9870857G>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Silent	SNP	ENST00000547186.1	37		722	0.3305860805860806	67	0.13617886178861788	126	0.34806629834254144	89	0.1555944055944056	440	0.5804749340369393	G	7.645	0.681788	0.14907	0.180209	0.504884	ENSG00000214021	ENST00000310252	.	.	.	4.93	0.73	0.18271	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27062	P	0.9635391	.	.	.	.	.	.	T	0.47071	-0.9145	3	.	.	.	.	5.6426	0.17572	0.2252:0.0:0.5736:0.2012	rs2290303;rs17319071	.	.	.	M	400	.	.	V	+	1	0	TTLL3	9845857	0.050000	0.20438	0.650000	0.29550	0.977000	0.68977	0.301000	0.19174	0.489000	0.27749	0.563000	0.77884	GTG	G|0.623;A|0.377	0.377	strong		0.592	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
FABP2	2169	hgsc.bcm.edu	37	4	120240238	120240238	+	Silent	SNP	T	T	C	rs1511025	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:120240238T>C	ENST00000274024.3	-	4	644	c.357A>G	c.(355-357)gtA>gtG	p.V119V		NM_000134.3	NP_000125.2	P12104	FABPI_HUMAN	fatty acid binding protein 2, intestinal	119					digestion (GO:0007586)	cytoplasm (GO:0005737)	fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			breast(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	8					Estradiol(DB00783)|Ibuprofen(DB01050)|Sulfinpyrazone(DB01138)	CTCCTTCATATACATAAGTCT	0.299													T|||	1668	0.333067	0.4017	0.33	5008	,	,		11767	0.3948		0.3121	False		,,,				2504	0.2004				p.V119V		Atlas-SNP	.											FABP2,NS,carcinoma,-1,1	FABP2	21	1	0			c.A357G						PASS	.	T		1656,2750	503.4+/-365.5	308,1040,855	107.0	108.0	108.0		357	-10.1	0.0	4	dbSNP_88	108	2817,5775	443.7+/-360.5	465,1887,1944	no	coding-synonymous	FABP2	NM_000134.3		773,2927,2799	CC,CT,TT		32.7863,37.5851,34.413		119/133	120240238	4473,8525	2203	4296	6499	SO:0001819	synonymous_variant	2169	exon4			TTCATATACATAA	J03465	CCDS3712.1	4q28-q31	2013-03-01			ENSG00000145384	ENSG00000145384		"""Fatty acid binding protein family"""	3556	protein-coding gene	gene with protein product		134640					Standard	NM_000134		Approved	I-FABP	uc003icw.3	P12104	OTTHUMG00000132972	ENST00000274024.3:c.357A>G	4.37:g.120240238T>C		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	163	86	0.527607	NM_000134	Q2NKJ1	Silent	SNP	ENST00000274024.3	37	CCDS3712.1																																																																																			T|0.654;C|0.346	0.346	strong		0.299	FABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256531.1	NM_000134	
PRR5L	79899	hgsc.bcm.edu	37	11	36458997	36458997	+	Missense_Mutation	SNP	A	A	G	rs62621409	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:36458997A>G	ENST00000378867.3	+	7	770	c.415A>G	c.(415-417)Acc>Gcc	p.T139A	PRR5L_ENST00000311599.5_Missense_Mutation_p.T113A|PRR5L_ENST00000530639.1_Missense_Mutation_p.T139A|PRR5L_ENST00000527487.1_Missense_Mutation_p.T139A|PRR5L_ENST00000389693.3_3'UTR	NM_024841.4	NP_079117.3	Q6MZQ0	PRR5L_HUMAN	proline rich 5 like	139					negative regulation of protein phosphorylation (GO:0001933)|negative regulation of signal transduction (GO:0009968)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|regulation of fibroblast migration (GO:0010762)|TORC2 signaling (GO:0038203)	mitochondrion (GO:0005739)|TORC2 complex (GO:0031932)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(7)|ovary(1)	19						GACTCTCCCTACCCTGCAGGC	0.517													A|||	94	0.01877	0.0015	0.0202	5008	,	,		20169	0.0		0.0586	False		,,,				2504	0.0194				p.T139A		Atlas-SNP	.											.	PRR5L	35	.	0			c.A415G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR	25,4379	31.7+/-61.6	0,25,2177	225.0	196.0	206.0		415,172,415,415	5.3	1.0	11	dbSNP_129	206	350,8246	118.6+/-178.1	6,338,3954	yes	missense,missense,missense,missense	PRR5L	NM_001160167.1,NM_001160168.1,NM_001160169.1,NM_024841.4	58,58,58,58	6,363,6131	GG,GA,AA		4.0717,0.5677,2.8846	probably-damaging,probably-damaging,probably-damaging,probably-damaging	139/369,58/241,139/206,139/369	36458997	375,12625	2202	4298	6500	SO:0001583	missense	79899	exon7			CTCCCTACCCTGC		CCDS31463.1, CCDS53617.1	11p13-p12	2009-07-09				ENSG00000135362			25878	protein-coding gene	gene with protein product	"""protein observed with Rictor-2"""	611728				17461779	Standard	NM_024841		Approved	FLJ14213, PROTOR-2	uc001mwp.3	Q6MZQ0		ENST00000378867.3:c.415A>G	11.37:g.36458997A>G	ENSP00000368144:p.Thr139Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_024841	A4QN22|E9PKY1|Q96H46|Q9H7V4	Missense_Mutation	SNP	ENST00000378867.3	37	CCDS31463.1	52	0.023809523809523808	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	42	0.055408970976253295	A	21.3	4.134067	0.77662	0.005677	0.040717	ENSG00000135362	ENST00000530639;ENST00000311599;ENST00000378867;ENST00000527487	T;T;T;T	0.76186	1.79;1.94;1.79;-1.0	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.39682	0.1087	L	0.46157	1.445	0.58432	D	0.999997	P;D;P	0.67145	0.857;0.996;0.726	P;D;P	0.77557	0.588;0.99;0.506	T	0.67292	-0.5707	10	0.44086	T	0.13	-32.3272	15.1352	0.72558	1.0:0.0:0.0:0.0	rs62621409	139;58;139	E9PKY1;Q6MZQ0-3;Q6MZQ0	.;.;PRR5L_HUMAN	A	139;113;139;139	ENSP00000435050:T139A;ENSP00000310103:T113A;ENSP00000368144:T139A;ENSP00000435241:T139A	ENSP00000310103:T113A	T	+	1	0	PRR5L	36415573	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.737000	0.68606	2.103000	0.63969	0.533000	0.62120	ACC	A|0.972;G|0.028	0.028	strong		0.517	PRR5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389209.1	NM_024841	
ANKS1B	56899	hgsc.bcm.edu	37	12	99837570	99837570	+	Missense_Mutation	SNP	C	C	T	rs148678454	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:99837570C>T	ENST00000547776.2	-	11	1455	c.1456G>A	c.(1456-1458)Gca>Aca	p.A486T	ANKS1B_ENST00000329257.7_Missense_Mutation_p.A486T|ANKS1B_ENST00000547010.1_Missense_Mutation_p.A66T	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	486						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GTAGTAACTGCTACCTCAGAG	0.378													C|||	40	0.00798722	0.0	0.013	5008	,	,		17405	0.0		0.0298	False		,,,				2504	0.001				p.A486T		Atlas-SNP	.											.	ANKS1B	180	.	0			c.G1456A						PASS	.	C	THR/ALA	14,3718		0,14,1852	158.0	152.0	154.0		1456	5.2	1.0	12	dbSNP_134	154	130,8108		1,128,3990	yes	missense	ANKS1B	NM_152788.4	58	1,142,5842	TT,TC,CC		1.5781,0.3751,1.203	possibly-damaging	486/1249	99837570	144,11826	1866	4119	5985	SO:0001583	missense	56899	exon11			TAACTGCTACCTC	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1456G>A	12.37:g.99837570C>T	ENSP00000449629:p.Ala486Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	28	0.01282051282051282	0	0.0	8	0.022099447513812154	0	0.0	20	0.026385224274406333	C	13.47	2.245771	0.39697	0.003751	0.015781	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000549866	T;T;T;T	0.60424	0.96;0.19;0.96;0.71	6.04	5.15	0.70609	.	0.073833	0.56097	D	0.000034	T	0.37705	0.1013	L	0.36672	1.1	0.80722	D	1	D;D;P	0.60160	0.987;0.98;0.916	P;P;B	0.56823	0.807;0.701;0.409	T	0.51276	-0.8726	9	.	.	.	-12.4757	15.7622	0.78091	0.0:0.8644:0.1356:0.0	.	452;66;486	F8VVQ4;Q7Z6G8-6;Q7Z6G8	.;.;ANS1B_HUMAN	T	486;66;486;65;452	ENSP00000449629:A486T;ENSP00000448512:A66T;ENSP00000331381:A486T;ENSP00000449894:A452T	.	A	-	1	0	ANKS1B	98361701	1.000000	0.71417	1.000000	0.80357	0.746000	0.42486	2.695000	0.47043	1.557000	0.49525	0.563000	0.77884	GCA	C|0.986;T|0.014	0.014	strong		0.378	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
AIPL1	23746	hgsc.bcm.edu	37	17	6330068	6330068	+	Silent	SNP	T	T	C	rs2292546	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6330068T>C	ENST00000381129.3	-	5	731	c.651A>G	c.(649-651)ccA>ccG	p.P217P	AIPL1_ENST00000570466.1_Silent_p.P195P|AIPL1_ENST00000576776.1_Intron|AIPL1_ENST00000576307.1_Silent_p.P157P|AIPL1_ENST00000575265.1_Silent_p.P217P|AIPL1_ENST00000250087.5_Silent_p.P154P|AIPL1_ENST00000571740.1_Silent_p.P209P|AIPL1_ENST00000574506.1_Silent_p.P205P	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	217					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)		GCACCTCCCATGGCTTCTCCT	0.617													C|||	3574	0.713658	0.73	0.745	5008	,	,		15613	0.6716		0.7614	False		,,,				2504	0.6636				p.P217P		Atlas-SNP	.											AIPL1,NS,carcinoma,0,1	AIPL1	34	1	0			c.A651G						PASS	.	C	,,	3182,1224	422.1+/-339.6	1155,872,176	90.0	65.0	73.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	462,471,651	-5.1	0.9	17	dbSNP_100	73	6425,2175	371.5+/-336.3	2386,1653,261	no	coding-synonymous,coding-synonymous,coding-synonymous	AIPL1	NM_001033054.1,NM_001033055.1,NM_014336.3	,,	3541,2525,437	CC,CT,TT		25.2907,27.7803,26.1341	,,	154/322,157/325,217/385	6330068	9607,3399	2203	4300	6503	SO:0001819	synonymous_variant	23746	exon5			CTCCCATGGCTTC	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.651A>G	17.37:g.6330068T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Silent	SNP	ENST00000381129.3	37	CCDS11075.1																																																																																			T|0.262;C|0.738	0.738	strong		0.617	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336	
POLR1A	25885	hgsc.bcm.edu	37	2	86259443	86259443	+	Silent	SNP	C	C	T	rs2276626	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:86259443C>T	ENST00000263857.6	-	29	4602	c.4224G>A	c.(4222-4224)ggG>ggA	p.G1408G	POLR1A_ENST00000409681.1_Silent_p.G1408G			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1408					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)	p.G1408G(1)		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						CATCGGCGTCCCCCTCCTCAG	0.582													C|||	2889	0.576877	0.8283	0.4712	5008	,	,		17574	0.3611		0.5934	False		,,,				2504	0.5174				p.G1408G		Atlas-SNP	.											POLR1A,NS,carcinoma,0,1	POLR1A	137	1	1	Substitution - coding silent(1)	stomach(1)	c.G4224A						PASS	.	C		3443,807		1386,671,68	166.0	180.0	175.0		4224	-0.6	0.9	2	dbSNP_100	175	5431,3037		1742,1947,545	no	coding-synonymous	POLR1A	NM_015425.3		3128,2618,613	TT,TC,CC		35.8644,18.9882,30.2249		1408/1721	86259443	8874,3844	2125	4234	6359	SO:0001819	synonymous_variant	25885	exon29			GGCGTCCCCCTCC	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.4224G>A	2.37:g.86259443C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	74	69	0.932432	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Silent	SNP	ENST00000263857.6	37	CCDS42706.1																																																																																			T|0.595;C|0.405;A|0.000	0.595	strong		0.582	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
MUC5B	727897	hgsc.bcm.edu	37	11	1280238	1280238	+	Missense_Mutation	SNP	G	G	A	rs55856616	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1280238G>A	ENST00000529681.1	+	44	16718	c.16660G>A	c.(16660-16662)Gac>Aac	p.D5554N	MUC5B_ENST00000447027.1_Missense_Mutation_p.D5557N	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5554	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)		GGACACCCAGGACCCAACGGT	0.647													G|||	253	0.0505192	0.0832	0.0403	5008	,	,		16282	0.002		0.0388	False		,,,				2504	0.0757				p.D5554N		Atlas-SNP	.											.	MUC5B	473	.	0			c.G16660A						PASS	.	G	ASN/ASP	329,3565		11,307,1629	42.0	50.0	47.0		16660	1.6	0.0	11	dbSNP_129	47	247,7959		4,239,3860	yes	missense	MUC5B	NM_002458.2	23	15,546,5489	AA,AG,GG		3.01,8.4489,4.7603	benign	5554/5763	1280238	576,11524	1947	4103	6050	SO:0001583	missense	727897	exon44			ACCCAGGACCCAA	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.16660G>A	11.37:g.1280238G>A	ENSP00000436812:p.Asp5554Asn	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	91	0.041666666666666664	41	0.08333333333333333	19	0.052486187845303865	1	0.0017482517482517483	30	0.0395778364116095	G	12.75	2.030419	0.35797	0.084489	0.0301	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000546052;ENST00000406844;ENST00000526859	T;T	0.16743	2.32;2.51	4.8	1.63	0.23807	.	.	.	.	.	T	0.00524	0.0017	L	0.34521	1.04	0.09310	N	1	B;B	0.34349	0.22;0.45	B;B	0.30251	0.113;0.113	T	0.29792	-1.0000	9	0.87932	D	0	.	3.182	0.06588	0.0977:0.1739:0.549:0.1793	rs55856616	5891;5557	A7Y9J9;E9PBJ0	.;.	N	5554;5557;5498;453;5266;99	ENSP00000436812:D5554N;ENSP00000415793:D5557N	ENSP00000343037:D5498N	D	+	1	0	MUC5B	1236814	0.000000	0.05858	0.000000	0.03702	0.320000	0.28249	-0.366000	0.07563	0.550000	0.28991	0.561000	0.74099	GAC	G|0.961;A|0.039	0.039	strong		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TULP3	7289	hgsc.bcm.edu	37	12	3042634	3042634	+	Silent	SNP	C	C	T	rs145294361	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:3042634C>T	ENST00000448120.2	+	7	798	c.747C>T	c.(745-747)taC>taT	p.Y249Y	TULP3_ENST00000397132.2_Silent_p.Y249Y	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	249					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CAGCCAACTACCTTATCTCCA	0.408													C|||	13	0.00259585	0.0	0.0	5008	,	,		17848	0.0		0.0129	False		,,,				2504	0.0				p.Y249Y		Atlas-SNP	.											.	TULP3	45	.	0			c.C747T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	154.0	138.0	143.0		747,747	4.5	1.0	12	dbSNP_134	143	38,8562	25.7+/-73.6	0,38,4262	no	coding-synonymous,coding-synonymous	TULP3	NM_001160408.1,NM_003324.4	,	0,39,6464	TT,TC,CC		0.4419,0.0227,0.2999	,	249/502,249/443	3042634	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	7289	exon7			CAACTACCTTATC	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.747C>T	12.37:g.3042634C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Silent	SNP	ENST00000448120.2	37	CCDS8519.1																																																																																			C|0.996;T|0.004	0.004	strong		0.408	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
LRRC19	64922	hgsc.bcm.edu	37	9	26995787	26995787	+	Missense_Mutation	SNP	G	G	A	rs41272237	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:26995787G>A	ENST00000380055.5	-	5	955	c.845C>T	c.(844-846)aCg>aTg	p.T282M	LRRC19_ENST00000482770.1_5'UTR|IFT74_ENST00000443698.1_Intron|IFT74_ENST00000433700.1_Intron|IFT74_ENST00000429045.2_Intron|IFT74_ENST00000380062.5_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	282						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)	6		all_neural(11;1.81e-09)		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)		AAGTGAAGTCGTCAGTACAGT	0.373													G|||	275	0.0549121	0.0303	0.0317	5008	,	,		17735	0.0288		0.0537	False		,,,				2504	0.1329				p.T282M		Atlas-SNP	.											.	LRRC19	24	.	0			c.C845T						PASS	.	G	,,,MET/THR,	160,4246	108.6+/-147.0	5,150,2048	80.0	73.0	75.0		,,,845,	3.5	0.0	9	dbSNP_127	75	486,8114	142.3+/-198.5	11,464,3825	yes	intron,intron,intron,missense,intron	LRRC19,IFT74	NM_001099222.1,NM_001099223.1,NM_001099224.1,NM_022901.2,NM_025103.2	,,,81,	16,614,5873	AA,AG,GG		5.6512,3.6314,4.9669	,,,benign,	,,,282/371,	26995787	646,12360	2203	4300	6503	SO:0001583	missense	64922	exon5			GAAGTCGTCAGTA	AK024955	CCDS6518.1	9p21.1	2008-02-05			ENSG00000184434	ENSG00000184434			23379	protein-coding gene	gene with protein product							Standard	NM_022901		Approved	FLJ21302	uc003zqh.3	Q9H756	OTTHUMG00000019710	ENST00000380055.5:c.845C>T	9.37:g.26995787G>A	ENSP00000369395:p.Thr282Met	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_022901	A0AV00|B9EG91	Missense_Mutation	SNP	ENST00000380055.5	37	CCDS6518.1	86	0.039377289377289376	9	0.018292682926829267	15	0.04143646408839779	17	0.02972027972027972	45	0.059366754617414245	G	1.352	-0.591147	0.03799	0.036314	0.056512	ENSG00000184434	ENST00000380055	T	0.50548	0.74	4.72	3.5	0.40072	.	1.132640	0.06444	N	0.726486	T	0.02119	0.0066	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07712	-1.0758	10	0.33141	T	0.24	1.5351	7.1144	0.25409	0.7251:0.1893:0.0855:0.0	rs41272237	282	Q9H756	LRC19_HUMAN	M	282	ENSP00000369395:T282M	ENSP00000369395:T282M	T	-	2	0	LRRC19	26985787	0.000000	0.05858	0.013000	0.15412	0.210000	0.24377	0.285000	0.18883	0.934000	0.37316	-0.438000	0.05819	ACG	G|0.949;A|0.051	0.051	strong		0.373	LRRC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051961.2	NM_022901	
TTC21A	199223	hgsc.bcm.edu	37	3	39161464	39161464	+	Missense_Mutation	SNP	G	G	A	rs1274971	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:39161464G>A	ENST00000431162.2	+	8	1011	c.877G>A	c.(877-879)Gaa>Aaa	p.E293K	TTC21A_ENST00000301819.6_Missense_Mutation_p.E293K|TTC21A_ENST00000440121.1_Missense_Mutation_p.E244K			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	293			E -> K (in dbSNP:rs1274971).							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AAGGGAACCCGAAAATCCAAG	0.443													G|||	2282	0.455671	0.8495	0.3429	5008	,	,		18210	0.2738		0.334	False		,,,				2504	0.316				p.E293K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G877A						PASS	.	G	LYS/GLU,LYS/GLU	2790,932		1038,714,109	106.0	114.0	111.0		730,877	3.9	0.9	3	dbSNP_87	111	2786,5410		485,1816,1797	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	56,56	1523,2530,1906	AA,AG,GG		33.9922,25.0403,46.7864	benign,benign	244/1273,293/1321	39161464	5576,6342	1861	4098	5959	SO:0001583	missense	199223	exon8			GAACCCGAAAATC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.877G>A	3.37:g.39161464G>A	ENSP00000398211:p.Glu293Lys	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	147	58	0.394558	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	959	0.4391025641025641	410	0.8333333333333334	133	0.3674033149171271	166	0.2902097902097902	250	0.32981530343007914	G	11.56	1.675769	0.29783	0.749597	0.339922	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.56941	0.43;0.43;2.34	5.67	3.86	0.44501	.	0.701416	0.13630	N	0.373771	T	0.00012	0.0000	N	0.02916	-0.46	0.47094	P	6.859999999999644E-4	B;B;B	0.27498	0.01;0.18;0.113	B;B;B	0.16722	0.004;0.016;0.007	T	0.39781	-0.9597	9	0.02654	T	1	-0.0123	15.4035	0.74861	0.0:0.7314:0.2686:0.0	rs1274971;rs17735053;rs57380373;rs1274971	244;293;293	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	293;285;293;244	ENSP00000301819:E293K;ENSP00000398211:E293K;ENSP00000410882:E244K	ENSP00000301819:E293K	E	+	1	0	TTC21A	39136468	0.956000	0.32656	0.881000	0.34555	0.486000	0.33341	1.922000	0.40045	0.746000	0.32786	-0.147000	0.13772	GAA	G|0.552;A|0.448	0.448	strong		0.443	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
SLC22A5	6584	hgsc.bcm.edu	37	5	131705949	131705949	+	Silent	SNP	T	T	C	rs2631365	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131705949T>C	ENST00000245407.3	+	1	506	c.285T>C	c.(283-285)ctT>ctC	p.L95L	AC034220.3_ENST00000417795.1_RNA|SLC22A5_ENST00000435065.2_Silent_p.L95L|AC034220.3_ENST00000457998.2_RNA	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	95					carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	TCTCGGCGCTTGGGCTGGAGC	0.692											OREG0003451	type=REGULATORY REGION|Gene=BC043424|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2435	0.486222	0.3434	0.3285	5008	,	,		11579	0.6736		0.4165	False		,,,				2504	0.6697				p.L95L		Atlas-SNP	.											.	SLC22A5	34	.	0			c.T285C						PASS	.	C		1347,2899		253,841,1029	9.0	11.0	10.0		285	-0.6	1.0	5	dbSNP_100	10	3097,5365		647,1803,1781	no	coding-synonymous	SLC22A5	NM_003060.3		900,2644,2810	CC,CT,TT		36.5989,31.724,34.9701		95/558	131705949	4444,8264	2123	4231	6354	SO:0001819	synonymous_variant	6584	exon1			GGCGCTTGGGCTG	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"""Solute carriers"""	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.285T>C	5.37:g.131705949T>C		Somatic	83	0	0	1589	WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Silent	SNP	ENST00000245407.3	37	CCDS4154.1																																																																																			T|0.732;C|0.268	0.268	strong		0.692	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	
CEACAM5	1048	hgsc.bcm.edu	37	19	42213772	42213772	+	Missense_Mutation	SNP	A	A	G	rs12971352	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:42213772A>G	ENST00000221992.6	+	2	352	c.238A>G	c.(238-240)Ata>Gta	p.I80V	CEA_ENST00000598976.1_Missense_Mutation_p.I80V|CEACAM5_ENST00000405816.1_Missense_Mutation_p.I80V|CEACAM7_ENST00000599715.1_5'Flank|CEACAM5_ENST00000398599.4_Missense_Mutation_p.I80V	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	80	Ig-like 1.		I -> V (in dbSNP:rs12971352).		homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CCGTCAAATTATAGGATATGT	0.478													a|||	818	0.163339	0.3986	0.1037	5008	,	,		18246	0.0		0.1958	False		,,,				2504	0.0225				p.I80V		Atlas-SNP	.											.	CEACAM5	84	.	0			c.A238G						PASS	.	A	VAL/ILE	1325,3081		310,705,1188	154.0	163.0	160.0		238	-1.3	0.0	19	dbSNP_121	160	1069,7531		115,839,3346	no	missense	CEACAM5	NM_004363.2	29	425,1544,4534	GG,GA,AA		12.4302,30.0726,18.4069	benign	80/703	42213772	2394,10612	2203	4300	6503	SO:0001583	missense	1048	exon2			CAAATTATAGGAT	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.238A>G	19.37:g.42213772A>G	ENSP00000221992:p.Ile80Val	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	175	109	0.622857	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	303|303	0.13873626373626374|0.13873626373626374	131|131	0.266260162601626|0.266260162601626	40|40	0.11049723756906077|0.11049723756906077	0|0	0.0|0.0	132|132	0.1741424802110818|0.1741424802110818	-|-	0.004|0.004	-2.303796|-2.303796	0.00240|0.00240	0.300726|0.300726	0.124302|0.124302	ENSG00000105388|ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181|ENST00000398599	T;T|.	0.66099|.	-0.19;-0.19|.	2.56|2.56	-1.31|-1.31	0.09230|0.09230	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.11724|0.11724	0.165|0.165	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.12013|.	0.005;0.0;0.0|.	B;B;B|.	0.26517|.	0.07;0.005;0.016|.	T|T	0.44697|0.44697	-0.9311|-0.9311	8|4	0.05721|.	T|.	0.95|.	.|.	4.8298|4.8298	0.13434|0.13434	0.1374:0.4321:0.4306:0.0|0.1374:0.4321:0.4306:0.0	rs12971352|rs12971352	80;80;80|.	Q8N4D0;P06731;Q53G30|.	.;CEAM5_HUMAN;.|.	V|C	80|76	ENSP00000221992:I80V;ENSP00000385072:I80V|.	ENSP00000221992:I80V|.	I|Y	+|+	1|2	0|0	CEACAM5|CEACAM5	46905612|46905612	0.001000|0.001000	0.12720|0.12720	0.002000|0.002000	0.10522|0.10522	0.000000|0.000000	0.00434|0.00434	-0.284000|-0.284000	0.08422|0.08422	-0.113000|-0.113000	0.11958|0.11958	-2.226000|-2.226000	0.00293|0.00293	ATA|TAT	A|0.810;G|0.190	0.190	strong		0.478	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
DMGDH	29958	hgsc.bcm.edu	37	5	78328560	78328560	+	Silent	SNP	G	G	A	rs1805072	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:78328560G>A	ENST00000255189.3	-	9	1495	c.1467C>T	c.(1465-1467)ggC>ggT	p.G489G	DMGDH_ENST00000540686.1_Silent_p.G109G|DMGDH_ENST00000380311.4_Silent_p.G288G	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	489					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		GCTGCTCCCAGCCAGCATGGA	0.542													G|||	995	0.198682	0.2398	0.134	5008	,	,		17116	0.1399		0.1988	False		,,,				2504	0.2495				p.G489G		Atlas-SNP	.											.	DMGDH	88	.	0			c.C1467T						PASS	.	G		1005,3401	374.6+/-321.3	101,803,1299	127.0	129.0	129.0		1467	4.6	1.0	5	dbSNP_89	129	1621,6979	300.8+/-305.1	162,1297,2841	no	coding-synonymous	DMGDH	NM_013391.2		263,2100,4140	AA,AG,GG		18.8488,22.8098,20.1907		489/867	78328560	2626,10380	2203	4300	6503	SO:0001819	synonymous_variant	29958	exon9			CTCCCAGCCAGCA	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1467C>T	5.37:g.78328560G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_013391	B2RBN0|B4E1J9	Silent	SNP	ENST00000255189.3	37	CCDS4044.1																																																																																			G|0.796;A|0.204	0.204	strong		0.542	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
IQUB	154865	hgsc.bcm.edu	37	7	123152019	123152019	+	Missense_Mutation	SNP	C	C	T	rs10255061	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:123152019C>T	ENST00000466202.1	-	2	952	c.376G>A	c.(376-378)Gtg>Atg	p.V126M	IQUB_ENST00000324698.6_Missense_Mutation_p.V126M|IQUB_ENST00000488987.1_Intron|IQUB_ENST00000434450.1_Missense_Mutation_p.V126M	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	126			V -> M (in dbSNP:rs10255061). {ECO:0000269|PubMed:15489334}.		cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)		p.V126M(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						GAATCTTCCACTGATTCTTGC	0.353													T|||	1342	0.267971	0.2194	0.2637	5008	,	,		19187	0.369		0.2863	False		,,,				2504	0.2137				p.V126M		Atlas-SNP	.											IQUB,NS,adenoma,0,2	IQUB	117	2	1	Substitution - Missense(1)	stomach(1)	c.G376A						scavenged	.	T	MET/VAL	1048,3356	723.4+/-409.4	131,786,1285	64.0	64.0	64.0		376	-4.5	0.0	7	dbSNP_119	64	2296,6304	703.7+/-405.4	298,1700,2302	yes	missense	IQUB	NM_178827.4	21	429,2486,3587	TT,TC,CC		26.6977,23.7965,25.7152	benign	126/792	123152019	3344,9660	2202	4300	6502	SO:0001583	missense	154865	exon2			CTTCCACTGATTC	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.376G>A	7.37:g.123152019C>T	ENSP00000417769:p.Val126Met	Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	37	CCDS5787.1	634	0.2902930402930403	104	0.21138211382113822	109	0.3011049723756906	202	0.3531468531468531	219	0.28891820580474936	T	7.972	0.749246	0.15710	0.237965	0.266977	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.42513	0.97;0.97;0.97	5.41	-4.47	0.03525	.	1.448530	0.04416	N	0.366878	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.33752	-0.9856	9	0.14252	T	0.57	.	11.0952	0.48141	0.1213:0.676:0.0:0.2027	rs10255061;rs56649278;rs59485939;rs10255061	126;126;126	A1A4Z1;Q8NA54-2;Q8NA54	.;.;IQUB_HUMAN	M	126	ENSP00000417769:V126M;ENSP00000324882:V126M;ENSP00000388498:V126M	ENSP00000324882:V126M	V	-	1	0	IQUB	122939255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.742000	0.01835	-1.087000	0.03081	-0.254000	0.11334	GTG	C|0.741;T|0.259	0.259	strong		0.353	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
NEK10	152110	hgsc.bcm.edu	37	3	27332820	27332820	+	Missense_Mutation	SNP	A	A	G	rs10510592	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:27332820A>G	ENST00000429845.2	-	19	1900	c.1538T>C	c.(1537-1539)tTg>tCg	p.L513S	NEK10_ENST00000357467.2_5'UTR|NEK10_ENST00000341435.5_Missense_Mutation_p.L513S			Q6ZWH5	NEK10_HUMAN	NIMA-related kinase 10	513			L -> S (in dbSNP:rs10510592). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:17974005}.		positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein autophosphorylation (GO:0031954)|protein phosphorylation (GO:0006468)|regulation of cell cycle G2/M phase transition (GO:1902749)|regulation of ERK1 and ERK2 cascade (GO:0070372)	protein kinase complex (GO:1902911)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TATATATTTCAAAGGAGCTTT	0.353													G|||	1059	0.211462	0.1203	0.353	5008	,	,		18497	0.1002		0.2744	False		,,,				2504	0.2843				p.L513S		Atlas-SNP	.											.	NEK10	271	.	0			c.T1538C						PASS	.	G	SER/LEU	528,2608		48,432,1088	145.0	133.0	137.0		1538	2.8	1.0	3	dbSNP_119	137	1932,5232		282,1368,1932	yes	missense	NEK10	NM_199347.2	145	330,1800,3020	GG,GA,AA		26.9682,16.8367,23.8835	benign	513/713	27332820	2460,7840	1568	3582	5150	SO:0001583	missense	152110	exon19			TATTTCAAAGGAG	AK123061, AK057247	CCDS46781.1	3p24.1	2012-11-15	2012-11-15		ENSG00000163491	ENSG00000163491			18592	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)- related kinase 10"""			15289607	Standard	NM_199347		Approved	FLJ32685	uc003cdt.2	Q6ZWH5	OTTHUMG00000130571	ENST00000429845.2:c.1538T>C	3.37:g.27332820A>G	ENSP00000395849:p.Leu513Ser	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	239	119	0.497908	NM_199347	A8MWG1|B9ZVR0|Q45VJ4|Q6ZR11|Q7Z671|Q86XB1|Q96MB3	Missense_Mutation	SNP	ENST00000429845.2	37		465|465	0.2129120879120879|0.2129120879120879	64|64	0.13008130081300814|0.13008130081300814	132|132	0.36464088397790057|0.36464088397790057	58|58	0.10139860139860139|0.10139860139860139	211|211	0.2783641160949868|0.2783641160949868	G|G	0.517|0.517	-0.863737|-0.863737	0.02590|0.02590	0.168367|0.168367	0.269682|0.269682	ENSG00000163491|ENSG00000163491	ENST00000341435;ENST00000396636|ENST00000424275	T|.	0.39787|.	1.06|.	5.55|5.55	2.77|2.77	0.32553|0.32553	Protein kinase-like domain (1);|.	0.444912|.	0.23237|.	N|.	0.050389|.	T|.	0.00012|.	0.0000|.	N|N	0.03084|0.03084	-0.415|-0.415	0.09310|0.09310	P|P	0.99999999496892|0.99999999496892	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|.	0.46638|.	-0.9177|.	9|.	0.05620|.	T|.	0.96|.	.|.	7.4239|7.4239	0.27088|0.27088	0.2038:0.1204:0.6758:0.0|0.2038:0.1204:0.6758:0.0	rs10510592;rs17630275;rs52817784;rs61064099;rs10510592|rs10510592;rs17630275;rs52817784;rs61064099;rs10510592	513|.	Q6ZWH5|.	NEK10_HUMAN|.	S|R	513|46	ENSP00000343847:L513S|.	ENSP00000343847:L513S|.	L|X	-|-	2|1	0|0	NEK10|NEK10	27307824|27307824	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.960000|0.960000	0.62799|0.62799	2.318000|2.318000	0.43779|0.43779	0.039000|0.039000	0.15632|0.15632	-0.784000|-0.784000	0.03344|0.03344	TTG|TGA	A|0.824;G|0.176	0.176	strong		0.353	NEK10-016	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000438156.1	NM_152534	
GIT1	28964	hgsc.bcm.edu	37	17	27904711	27904711	+	Silent	SNP	G	G	A	rs11080105	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27904711G>A	ENST00000225394.3	-	10	1181	c.933C>T	c.(931-933)gcC>gcT	p.A311A	GIT1_ENST00000579937.1_Silent_p.A311A|GIT1_ENST00000581348.1_Silent_p.A320A|GIT1_ENST00000394869.3_Silent_p.A320A|RP11-68I3.2_ENST00000581474.1_RNA	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1	311	ARHGEF6-binding. {ECO:0000250}.|PTK2/FAK1-binding. {ECO:0000250}.				regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)		GGAAGGGCACGGCACTGCGCT	0.642													G|||	1933	0.385982	0.0673	0.3876	5008	,	,		17951	0.6845		0.4284	False		,,,				2504	0.4642				p.A320A	Colon(81;41 1719 20078 35068)	Atlas-SNP	.											.	GIT1	84	.	0			c.C960T						PASS	.	G	,	570,3836	254.6+/-260.1	40,490,1673	116.0	100.0	105.0		960,933	-8.7	0.9	17	dbSNP_120	105	3702,4898	528.6+/-381.4	807,2088,1405	no	coding-synonymous,coding-synonymous	GIT1	NM_001085454.1,NM_014030.3	,	847,2578,3078	AA,AG,GG		43.0465,12.9369,32.8464	,	320/771,311/762	27904711	4272,8734	2203	4300	6503	SO:0001819	synonymous_variant	28964	exon11			GGGCACGGCACTG	AF124490	CCDS11250.1, CCDS42290.1	17p11.2	2013-01-10	2008-09-05		ENSG00000108262	ENSG00000108262		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4272	protein-coding gene	gene with protein product		608434	"""G protein-coupled receptor kinase interactor 1"""			9826657, 10896954	Standard	NM_014030		Approved		uc002heg.2	Q9Y2X7	OTTHUMG00000132730	ENST00000225394.3:c.933C>T	17.37:g.27904711G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_001085454	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Silent	SNP	ENST00000225394.3	37	CCDS11250.1																																																																																			G|0.638;A|0.362	0.362	strong		0.642	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030	
ATXN1	6310	hgsc.bcm.edu	37	6	16327903	16327903	+	Missense_Mutation	SNP	C	C	A	rs3817753		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:16327903C>A	ENST00000244769.4	-	8	1575	c.639G>T	c.(637-639)caG>caT	p.Q213H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q213H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	213	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgctgctgatgct	0.667																																					p.Q213H		Atlas-SNP	.											ATXN1,rectum,carcinoma,0,1	ATXN1	117	1	0			c.G639T						scavenged	.						5.0	8.0	7.0					6																	16327903		1624	3504	5128	SO:0001583	missense	6310	exon7			CTGCTGCTGCTGA	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.639G>T	6.37:g.16327903C>A	ENSP00000244769:p.Gln213His	Somatic	38	3	0.0789474		WXS	Illumina HiSeq	Phase_I	47	6	0.12766	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	221	0.10119047619047619	38	0.07723577235772358	47	0.1298342541436464	89	0.1555944055944056	47	0.06200527704485488	C	4.787	0.146322	0.09134	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.62941	-0.01;-0.01	.	.	.	.	.	.	.	.	T	0.18676	0.0448	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.19582	-1.0301	5	0.45353	T	0.12	.	.	.	.	rs3817753	213	P54253	ATX1_HUMAN	H	213	ENSP00000244769:Q213H;ENSP00000416360:Q213H	ENSP00000244769:Q213H	Q	-	3	2	ATXN1	16435882	0.034000	0.19679	0.018000	0.16275	0.072000	0.16883	0.306000	0.19279	0.000000	0.14550	0.000000	0.15137	CAG	C|0.899;A|0.101	0.101	strong		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131825083C>A	ENST00000245414.4	-	2	346		c.e2+1		IRF1_ENST00000405885.2_Splice_Site|IRF1_ENST00000463784.1_Intron	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		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	49	21	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
SLC4A11	83959	hgsc.bcm.edu	37	20	3214581	3214581	+	Silent	SNP	C	C	T	rs3803956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3214581C>T	ENST00000380056.3	-	5	686	c.639G>A	c.(637-639)tcG>tcA	p.S213S	SLC4A11_ENST00000380059.3_Silent_p.S240S|SLC4A11_ENST00000539553.2_Silent_p.S197S	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	213			S -> L (in CHED2). {ECO:0000269|PubMed:17679935}.|S -> P (in CDPD). {ECO:0000269|PubMed:17220209}.		bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						TGCAGAGCCACGACTGCTGGT	0.627													C|||	833	0.166334	0.2186	0.1254	5008	,	,		17524	0.128		0.1779	False		,,,				2504	0.1524				p.S240S	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G720A						PASS	.	C	,,	933,3473	355.6+/-313.1	107,719,1377	123.0	114.0	117.0		591,720,639	-10.4	0.0	20	dbSNP_107	117	1489,7111	283.3+/-296.1	121,1247,2932	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	228,1966,4309	TT,TC,CC		17.314,21.1757,18.6222	,,	197/876,240/919,213/892	3214581	2422,10584	2203	4300	6503	SO:0001819	synonymous_variant	83959	exon6			GAGCCACGACTGC	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.639G>A	20.37:g.3214581C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																			C|0.820;T|0.180	0.180	strong		0.627	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
MACROD1	28992	hgsc.bcm.edu	37	11	63884474	63884474	+	Intron	SNP	C	C	T	rs3751121	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:63884474C>T	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.S245S	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						ACACCTTCAGCCGCCTACAGA	0.662													C|||	582	0.116214	0.0008	0.1138	5008	,	,		19497	0.4782		0.0179	False		,,,				2504	0.002				p.S245S		Atlas-SNP	.											.	FLRT1	46	.	0			c.C735T						PASS	.	C	,	50,4352	50.2+/-85.5	0,50,2151	30.0	28.0	29.0		735,	4.6	1.0	11	dbSNP_107	29	103,8491	50.6+/-110.7	1,101,4195	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	1,151,6346	TT,TC,CC		1.1985,1.1358,1.1773	,	245/675,	63884474	153,12843	2201	4297	6498	SO:0001627	intron_variant	23769	exon2			CTTCAGCCGCCTA	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34236G>A	11.37:g.63884474C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			C|0.950;T|0.050	0.050	strong		0.662	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
BACE1	23621	hgsc.bcm.edu	37	11	117163824	117163824	+	Silent	SNP	C	C	G	rs638405	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:117163824C>G	ENST00000313005.6	-	5	1246	c.786G>C	c.(784-786)gtG>gtC	p.V262V	BACE1_ENST00000445823.2_Silent_p.V218V|BACE1_ENST00000510630.1_Silent_p.V137V|BACE1_ENST00000513780.1_Silent_p.V237V|BACE1_ENST00000392937.6_Silent_p.V162V|BACE1_ENST00000528053.1_Silent_p.V262V|BACE1_ENST00000428381.2_Silent_p.V193V|BACE1_ENST00000514464.1_5'Flank	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	262					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		GCACAATGATCACCTCATAAT	0.507													C|||	2772	0.553514	0.5363	0.549	5008	,	,		17135	0.6498		0.4076	False		,,,				2504	0.6309				p.V262V		Atlas-SNP	.											.	BACE1	33	.	0			c.G786C						PASS	.	C	,,,,,	2289,2113	601.2+/-389.7	589,1111,501	250.0	238.0	242.0		486,411,786,654,711,579	0.6	1.0	11	dbSNP_83	242	3400,5192	502.6+/-375.7	683,2034,1579	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BACE1	NM_001207048.1,NM_001207049.1,NM_012104.4,NM_138971.3,NM_138972.3,NM_138973.3	,,,,,	1272,3145,2080	GG,GC,CC		39.5717,48.0009,43.7817	,,,,,	162/402,137/377,262/502,218/458,237/477,193/433	117163824	5689,7305	2201	4296	6497	SO:0001819	synonymous_variant	23621	exon5			AATGATCACCTCA	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"""beta-site APP-cleaving enzyme"""	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.786G>C	11.37:g.117163824C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	142	115	0.809859	NM_012104	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Silent	SNP	ENST00000313005.6	37	CCDS8383.1	1119	0.5123626373626373	278	0.5650406504065041	190	0.5248618784530387	354	0.6188811188811189	297	0.391820580474934	C	10.34	1.322171	0.23994	0.519991	0.395717	ENSG00000186318	ENST00000530844;ENST00000504995	.	.	.	6.07	0.58	0.17402	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40553	-0.9557	3	.	.	.	.	1.3856	0.02240	0.1254:0.3307:0.2724:0.2714	rs638405;rs60889749;rs638405	.	.	.	H	132;192	.	.	D	-	1	0	BACE1	116669034	0.957000	0.32711	1.000000	0.80357	0.977000	0.68977	0.011000	0.13264	0.414000	0.25790	-0.768000	0.03414	GAT	C|0.533;G|0.467	0.467	strong		0.507	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
SLC39A3	29985	hgsc.bcm.edu	37	19	2733250	2733250	+	Silent	SNP	C	C	T	rs61736898	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:2733250C>T	ENST00000269740.4	-	3	773	c.444G>A	c.(442-444)gtG>gtA	p.V148V	AC006538.4_ENST00000586572.1_Intron|SLC39A3_ENST00000545664.1_Silent_p.V148V	NM_144564.4	NP_653165.2	Q9BRY0	S39A3_HUMAN	solute carrier family 39 (zinc transporter), member 3	148					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10		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)		CGTGGGGCTCCACGTACAGCG	0.726													C|||	508	0.101438	0.1399	0.0836	5008	,	,		14256	0.0268		0.1471	False		,,,				2504	0.092				p.V148V		Atlas-SNP	.											.	SLC39A3	20	.	0			c.G444A						PASS	.	C		648,3728		47,554,1587	15.0	17.0	17.0		444	-9.3	0.0	19	dbSNP_129	17	1190,7354		79,1032,3161	no	coding-synonymous	SLC39A3	NM_144564.4		126,1586,4748	TT,TC,CC		13.9279,14.808,14.226		148/315	2733250	1838,11082	2188	4272	6460	SO:0001819	synonymous_variant	29985	exon3			GGGCTCCACGTAC	AF052125	CCDS12093.1, CCDS45909.1	19p13.3	2013-05-22			ENSG00000141873	ENSG00000141873		"""Solute carriers"""	17128	protein-coding gene	gene with protein product		612168				10681536	Standard	NM_144564		Approved	ZIP3	uc002lwg.3	Q9BRY0		ENST00000269740.4:c.444G>A	19.37:g.2733250C>T		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_144564	B3KMJ3|Q8WUG1	Silent	SNP	ENST00000269740.4	37	CCDS12093.1																																																																																			C|0.879;T|0.121	0.121	strong		0.726	SLC39A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451354.2		
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 GAIIx	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		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	106	45	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	
NCOA3	8202	hgsc.bcm.edu	37	20	46279839	46279839	+	Silent	SNP	G	G	A	rs147879509|rs2664555|rs397778717|rs3830809		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:46279839G>A	ENST00000371998.3	+	20	3956	c.3765G>A	c.(3763-3765)caG>caA	p.Q1255Q	NCOA3_ENST00000341724.6_Silent_p.Q1181Q|NCOA3_ENST00000372004.3_Silent_p.Q1251Q|NCOA3_ENST00000371997.3_Silent_p.Q1246Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1255	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q1255delQ(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcaacagcagcagcagc	0.557																																					p.Q1255Q		Atlas-SNP	.											NCOA3,rectum,carcinoma,0,1	NCOA3	156	1	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.G3765A						PASS	.						41.0	44.0	43.0					20																	46279839		2202	4300	6502	SO:0001819	synonymous_variant	8202	exon20			GCAACAGCAGCAG	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3765G>A	20.37:g.46279839G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	46	5	0.108696	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			.	.	weak		0.557	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183958706G>A	ENST00000397676.3	-	0	1528				ALG3_ENST00000463495.1_5'Flank|VWA5B2_ENST00000426955.2_Silent_p.V956V|EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Silent_p.V738V|MIR1224_ENST00000408193.1_RNA	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		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	60	15	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	
PREX1	57580	hgsc.bcm.edu	37	20	47269233	47269233	+	Missense_Mutation	SNP	C	C	G	rs41283558	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47269233C>G	ENST00000371941.3	-	21	2380	c.2358G>C	c.(2356-2358)caG>caC	p.Q786H	PREX1_ENST00000396220.1_Missense_Mutation_p.Q786H	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	786			Q -> H (in dbSNP:rs41283558). {ECO:0000269|PubMed:17974005}.		actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GGTAGATCCACTGGTACAGGC	0.652													C|||	749	0.149561	0.0197	0.2118	5008	,	,		15382	0.1468		0.1849	False		,,,				2504	0.2474				p.Q786H		Atlas-SNP	.											PREX1_ENST00000396220,colon,carcinoma,0,2	PREX1	441	2	0			c.G2358C						PASS	.	C	HIS/GLN	250,4156	144.2+/-179.2	10,230,1963	58.0	47.0	51.0		2358	3.6	1.0	20	dbSNP_127	51	1623,6977	299.4+/-304.4	148,1327,2825	yes	missense	PREX1	NM_020820.3	24	158,1557,4788	GG,GC,CC		18.8721,5.6741,14.401	benign	786/1660	47269233	1873,11133	2203	4300	6503	SO:0001583	missense	57580	exon21			GATCCACTGGTAC	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2358G>C	20.37:g.47269233C>G	ENSP00000361009:p.Gln786His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	310	0.14194139194139194	13	0.026422764227642278	81	0.22375690607734808	81	0.14160839160839161	135	0.17810026385224276	C	13.41	2.228164	0.39399	0.056741	0.188721	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.41758	0.99;0.99	4.5	3.56	0.40772	PDZ/DHR/GLGF (1);	0.117523	0.37219	N	0.002182	T	0.00039	0.0001	L	0.50333	1.59	0.21675	P	0.999593756	B;B	0.16603	0.009;0.018	B;B	0.21546	0.019;0.035	T	0.09122	-1.0689	9	0.36615	T	0.2	.	13.9532	0.64131	0.1531:0.8469:0.0:0.0	rs41283558	786;83	Q8TCU6;Q8TCU6-2	PREX1_HUMAN;.	H	786	ENSP00000361009:Q786H;ENSP00000379522:Q786H	ENSP00000361009:Q786H	Q	-	3	2	PREX1	46702640	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	3.347000	0.52200	0.893000	0.36288	-0.224000	0.12420	CAG	C|0.852;G|0.148	0.148	strong		0.652	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
IMMT	10989	hgsc.bcm.edu	37	2	86389119	86389119	+	Silent	SNP	G	G	A	rs370662846		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:86389119G>A	ENST00000410111.3	-	8	1263	c.876C>T	c.(874-876)gcC>gcT	p.A292A	IMMT_ENST00000449247.2_Silent_p.A281A|IMMT_ENST00000254636.5_Silent_p.A193A|IMMT_ENST00000442664.2_Silent_p.A291A|IMMT_ENST00000490238.1_5'UTR|IMMT_ENST00000409051.2_Silent_p.A245A|Y_RNA_ENST00000363371.1_RNA	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	292					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GAAGGGCATCGGCAGCTTCAT	0.453																																					p.A292A		Atlas-SNP	.											IMMT,NS,carcinoma,-1,1	IMMT	65	1	0			c.C876T						scavenged	.	G	,,	0,3826		0,0,1913	50.0	51.0	51.0		873,843,876	-10.3	0.4	2		51	1,8277		0,1,4138	no	coding-synonymous,coding-synonymous,coding-synonymous	IMMT	NM_001100169.1,NM_001100170.1,NM_006839.2	,,	0,1,6051	AA,AG,GG		0.0121,0.0,0.0083	,,	291/758,281/748,292/759	86389119	1,12103	1913	4139	6052	SO:0001819	synonymous_variant	10989	exon8			GGCATCGGCAGCT	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"""mitofilin"", ""mitochondrial inner membrane organizing system 2"""	600378	"""inner membrane protein, mitochondrial (mitofilin)"""			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.876C>T	2.37:g.86389119G>A		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	169	4	0.0236686	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	.	.	.	.	.	.	.	.	.	.	G	9.701	1.154596	0.21371	0.0	1.21E-4	ENSG00000132305	ENST00000419070	.	.	.	5.15	-10.3	0.00346	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.053	7.0947	0.25303	0.6267:0.0737:0.2264:0.0733	.	.	.	.	X	147	.	.	R	-	1	2	IMMT	86242630	0.118000	0.22208	0.378000	0.26068	0.983000	0.72400	-0.920000	0.04013	-2.672000	0.00413	-0.362000	0.07510	CGA	.	.	weak		0.453	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60986019	60986019	+	Missense_Mutation	SNP	A	A	C	rs2236200	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60986019A>C	ENST00000252998.1	-	14	2066	c.1910T>G	c.(1909-1911)cTg>cGg	p.L637R		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	637			L -> R (in dbSNP:rs2236200). {ECO:0000269|PubMed:15489334}.			extracellular space (GO:0005615)		p.L637R(1)									AGTGGCTGTCAGTTTCCTTCT	0.642													A|||	758	0.151358	0.0106	0.1859	5008	,	,		16833	0.2262		0.2505	False		,,,				2504	0.138				p.L637R		Atlas-SNP	.											C20orf151,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T1910G						PASS	.	A	ARG/LEU	231,4175	134.9+/-171.1	6,219,1978	104.0	103.0	103.0		1910	1.3	0.0	20	dbSNP_98	103	2167,6433	369.9+/-335.7	296,1575,2429	yes	missense	C20orf151	NM_080833.2	102	302,1794,4407	CC,CA,AA		25.1977,5.2429,18.4376	probably-damaging	637/665	60986019	2398,10608	2203	4300	6503	SO:0001583	missense	140893	exon14			GCTGTCAGTTTCC	AL121832	CCDS13498.1	20q13.33	2012-10-30	2012-10-30	2012-10-30	ENSG00000130701	ENSG00000130701			16144	protein-coding gene	gene with protein product	"""hypothetical protein LOC140893"""		"""chromosome 20 open reading frame 151"""	C20orf151		11780052	Standard	NM_080833		Approved	dJ908M14.3	uc002ycw.2	Q8NC74	OTTHUMG00000032913	ENST00000252998.1:c.1910T>G	20.37:g.60986019A>C	ENSP00000252998:p.Leu637Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	375	0.1717032967032967	7	0.014227642276422764	71	0.19613259668508287	113	0.19755244755244755	184	0.24274406332453827	A	8.227	0.803891	0.16467	0.052429	0.251977	ENSG00000130701	ENST00000252998	T	0.24908	1.83	2.42	1.32	0.21799	.	0.219840	0.20847	N	0.084581	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	D	0.57899	0.981	P	0.56960	0.81	T	0.22591	-1.0212	9	0.54805	T	0.06	-3.8159	4.1038	0.10026	0.8238:0.0:0.1762:0.0	rs2236200;rs57636275;rs2236200	637	Q8NC74	CT151_HUMAN	R	637	ENSP00000252998:L637R	ENSP00000252998:L637R	L	-	2	0	C20orf151	60419414	0.000000	0.05858	0.006000	0.13384	0.041000	0.13682	0.033000	0.13754	0.374000	0.24650	0.402000	0.26972	CTG	A|0.827;C|0.173	0.173	strong		0.642	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
NEU4	129807	hgsc.bcm.edu	37	2	242757411	242757411	+	Silent	SNP	C	C	T	rs36111671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242757411C>T	ENST00000391969.2	+	5	1203	c.492C>T	c.(490-492)ggC>ggT	p.G164G	NEU4_ENST00000405370.1_Silent_p.G164G|NEU4_ENST00000404257.1_Silent_p.G176G|NEU4_ENST00000325935.6_Silent_p.G177G|NEU4_ENST00000407683.1_Silent_p.G164G	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	164					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CCGGCCACGGCGTGCAGCTGC	0.697													C|||	1083	0.216254	0.118	0.1571	5008	,	,		12056	0.2222		0.2237	False		,,,				2504	0.3773				p.G177G		Atlas-SNP	.											.	NEU4	39	.	0			c.C531T						PASS	.		,,,,	714,3680		71,572,1554	36.0	28.0	31.0		531,492,492,492,528	-2.6	0.5	2	dbSNP_126	31	1901,6693		211,1479,2607	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	282,2051,4161	TT,TC,CC		22.1201,16.2494,20.134	,,,,	177/498,164/485,164/485,164/485,176/497	242757411	2615,10373	2197	4297	6494	SO:0001819	synonymous_variant	129807	exon4			CCACGGCGTGCAG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.492C>T	2.37:g.242757411C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1	405	0.18543956043956045	66	0.13414634146341464	61	0.1685082872928177	102	0.17832167832167833	176	0.23218997361477572	C	15.63	2.889694	0.52014	0.162494	0.221201	ENSG00000204099	ENST00000415936;ENST00000426032	T;T	0.38240	1.15;1.15	4.47	-2.61	0.06171	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.28618	-1.0038	5	0.45353	T	0.12	-24.8925	0.4689	0.00529	0.2954:0.2317:0.2665:0.2065	rs36111671	.	.	.	V	79;91	ENSP00000397167:A79V;ENSP00000406678:A91V	ENSP00000397167:A79V	A	+	2	0	NEU4	242406084	0.855000	0.29742	0.491000	0.27477	0.281000	0.26958	-0.030000	0.12308	-0.497000	0.06641	0.443000	0.29094	GCG	C|0.817;T|0.183	0.183	strong		0.697	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
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 GAIIx	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_ENST00000527020.1_Silent_p.G127G|USH1C_ENST00000005226.7_Silent_p.G127G|USH1C_ENST00000527720.1_Silent_p.G96G	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		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	36	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	
ALS2CR11	151254	hgsc.bcm.edu	37	2	202430584	202430584	+	Missense_Mutation	SNP	G	G	A	rs73991652	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:202430584G>A	ENST00000286195.3	-	9	889	c.845C>T	c.(844-846)aCa>aTa	p.T282I	ALS2CR11_ENST00000439140.1_Missense_Mutation_p.T282I|ALS2CR11_ENST00000439802.1_Missense_Mutation_p.T282I|ALS2CR11_ENST00000450242.1_Missense_Mutation_p.T282I	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	282										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						TGTCTGTGGTGTAATAACTTT	0.393													G|||	219	0.04373	0.0991	0.0476	5008	,	,		14690	0.0		0.0477	False		,,,				2504	0.0072				p.T282I		Atlas-SNP	.											.	ALS2CR11	194	.	0			c.C845T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	342,4064	178.7+/-207.4	15,312,1876	72.0	72.0	72.0		845,845,845,845	-3.5	0.0	2	dbSNP_130	72	463,8137	137.1+/-194.1	14,435,3851	yes	missense,missense,missense,missense	ALS2CR11	NM_001168216.1,NM_001168217.1,NM_001168221.1,NM_152525.5	89,89,89,89	29,747,5727	AA,AG,GG		5.3837,7.7621,6.1895	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	282/396,282/551,282/1821,282/624	202430584	805,12201	2203	4300	6503	SO:0001583	missense	151254	exon9			TGTGGTGTAATAA	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.845C>T	2.37:g.202430584G>A	ENSP00000286195:p.Thr282Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_001168217	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Missense_Mutation	SNP	ENST00000286195.3	37	CCDS2349.1	87	0.03983516483516483	32	0.06504065040650407	16	0.04419889502762431	0	0.0	39	0.051451187335092345	G	0.033	-1.320890	0.01320	0.077621	0.053837	ENSG00000155754	ENST00000286195;ENST00000439802;ENST00000439140;ENST00000450242	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.88	-3.54	0.04653	.	2.050610	0.01917	N	0.040204	T	0.01695	0.0054	N	0.25890	0.77	0.09310	N	1	B;B;B	0.28470	0.018;0.213;0.2	B;B;B	0.25506	0.011;0.029;0.061	T	0.12967	-1.0527	10	0.35671	T	0.21	.	11.585	0.50912	0.2363:0.0:0.6546:0.1091	.	282;282;282	Q53TS8-2;E9PGG4;Q53TS8	.;.;AL2SA_HUMAN	I	282	ENSP00000286195:T282I;ENSP00000400672:T282I;ENSP00000409937:T282I;ENSP00000399016:T282I	ENSP00000286195:T282I	T	-	2	0	ALS2CR11	202138829	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	-0.378000	0.07446	-0.455000	0.07054	-0.302000	0.09304	ACA	G|0.948;A|0.052	0.052	strong		0.393	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525	
MAVS	57506	hgsc.bcm.edu	37	20	3838441	3838441	+	Missense_Mutation	SNP	C	C	G	rs17857295	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3838441C>G	ENST00000428216.2	+	3	405	c.277C>G	c.(277-279)Cag>Gag	p.Q93E	MAVS_ENST00000416600.2_Intron|MAVS_ENST00000358134.6_Missense_Mutation_p.Q93E	NM_020746.4	NP_065797.2	Q7Z434	MAVS_HUMAN	mitochondrial antiviral signaling protein	93			Q -> E (in dbSNP:rs17857295). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16127453, ECO:0000269|PubMed:16153868}.		activation of innate immune response (GO:0002218)|cellular response to exogenous dsRNA (GO:0071360)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of IP-10 production (GO:0071660)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of peroxisome organization (GO:1900063)|RIG-I signaling pathway (GO:0039529)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	CARD domain binding (GO:0050700)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			autonomic_ganglia(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						CTCTGTCTACCAGAGCTACCA	0.632													C|||	1457	0.290935	0.0779	0.2882	5008	,	,		15267	0.5605		0.2833	False		,,,				2504	0.3108				p.Q93E		Atlas-SNP	.											.	MAVS	34	.	0			c.C277G						PASS	.	C	,GLU/GLN	452,3954	217.8+/-236.0	27,398,1778	113.0	87.0	96.0		,277	2.5	0.4	20	dbSNP_123	96	2136,6464	368.6+/-335.1	250,1636,2414	yes	intron,missense	MAVS	NM_001206491.1,NM_020746.4	,29	277,2034,4192	GG,GC,CC		24.8372,10.2587,19.8985	,possibly-damaging	,93/541	3838441	2588,10418	2203	4300	6503	SO:0001583	missense	57506	exon3			GTCTACCAGAGCT	DQ174270	CCDS33437.1, CCDS56176.1	20p13	2009-04-02			ENSG00000088888	ENSG00000088888			29233	protein-coding gene	gene with protein product	"""virus-induced signaling adaptor"", ""IFN-B promoter stimulator 1"", ""CARD adaptor inducing IFN-beta"""	609676				16125763, 16153868	Standard	NM_020746		Approved	VISA, KIAA1271, IPS-1, Cardif	uc002wjw.4	Q7Z434	OTTHUMG00000031765	ENST00000428216.2:c.277C>G	20.37:g.3838441C>G	ENSP00000401980:p.Gln93Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	54	0.62069	NM_020746	A8K6X0|B2BD33|B2BD34|F5H6C8|Q2HWT5|Q3I0Y2|Q5T7I6|Q86VY7|Q9H1H3|Q9H4Y1|Q9H8D3|Q9ULE9	Missense_Mutation	SNP	ENST00000428216.2	37	CCDS33437.1	663	0.30357142857142855	38	0.07723577235772358	96	0.26519337016574585	323	0.5646853146853147	206	0.2717678100263852	C	10.82	1.458798	0.26248	0.102587	0.248372	ENSG00000088888	ENST00000428216;ENST00000358134	T;T	0.12039	2.88;2.72	4.67	2.53	0.30540	.	0.520418	0.17532	N	0.170837	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	P;P;P	0.46784	0.571;0.884;0.759	B;B;B	0.42851	0.37;0.4;0.4	T	0.39583	-0.9607	9	0.31617	T	0.26	-4.6837	6.7646	0.23560	0.2075:0.5973:0.1952:0.0	rs17857295;rs59161240	93;93;93	B2BD34;Q7Z434;Q7Z434-2	.;MAVS_HUMAN;.	E	93	ENSP00000401980:Q93E;ENSP00000350852:Q93E	ENSP00000350852:Q93E	Q	+	1	0	MAVS	3786441	0.000000	0.05858	0.401000	0.26359	0.936000	0.57629	-0.228000	0.09114	1.093000	0.41377	0.609000	0.83330	CAG	C|0.764;G|0.236	0.236	strong		0.632	MAVS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077784.3	NM_020746	
EPG5	57724	hgsc.bcm.edu	37	18	43481075	43481075	+	Missense_Mutation	SNP	G	G	A	rs1893523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:43481075G>A	ENST00000282041.5	-	26	4566	c.4532C>T	c.(4531-4533)gCt>gTt	p.A1511V	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1511			A -> T (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|A -> V (in dbSNP:rs1893523).		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						CGGGTGCAGAGCAAGGGGAGG	0.488													A|||	1604	0.320288	0.4523	0.3329	5008	,	,		20661	0.3046		0.169	False		,,,				2504	0.3047				p.A1511V		Atlas-SNP	.											EPG5,NS,carcinoma,-1,1	EPG5	199	1	0			c.C4532T						PASS	.	A	VAL/ALA	1602,2422		306,990,716	64.0	72.0	69.0		4532	-3.1	0.0	18	dbSNP_92	69	1183,7147		85,1013,3067	yes	missense	EPG5	NM_020964.2	64	391,2003,3783	AA,AG,GG		14.2017,39.8111,22.5433	benign	1511/2580	43481075	2785,9569	2012	4165	6177	SO:0001583	missense	57724	exon26			TGCAGAGCAAGGG	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.4532C>T	18.37:g.43481075G>A	ENSP00000282041:p.Ala1511Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	626	0.2866300366300366	209	0.4247967479674797	113	0.31215469613259667	177	0.3094405594405594	127	0.16754617414248021	A	4.836	0.155387	0.09236	0.398111	0.142017	ENSG00000152223	ENST00000282041;ENST00000308403	T	0.09538	2.97	5.59	-3.12	0.05282	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46048	-0.9219	8	0.24483	T	0.36	0.359	5.9743	0.19369	0.2483:0.1136:0.5183:0.1197	rs1893523;rs3744994;rs52830351;rs61517336;rs1893523	1511	Q9HCE0	EPG5_HUMAN	V	1511;386	ENSP00000282041:A1511V	ENSP00000282041:A1511V	A	-	2	0	EPG5	41735073	0.000000	0.05858	0.005000	0.12908	0.075000	0.17131	0.057000	0.14279	-1.280000	0.02402	-1.204000	0.01649	GCT	G|0.748;A|0.252	0.252	strong		0.488	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
HOXA10	3206	hgsc.bcm.edu	37	7	27211548	27211548	+	Silent	SNP	C	C	T	rs34957925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:27211548C>T	ENST00000283921.4	-	2	1202	c.1203G>A	c.(1201-1203)cgG>cgA	p.R401R	HOXA10_ENST00000521421.1_5'UTR|HOXA-AS4_ENST00000523790.1_RNA|RP1-170O19.20_ENST00000465941.1_Intron|HOXA-AS4_ENST00000519694.1_RNA|HOXA-AS4_ENST00000519935.1_RNA|RP1-170O19.20_ENST00000470747.4_Intron|MIR196B_ENST00000384852.1_RNA|HOXA9_ENST00000497089.1_5'Flank|HOXA10_ENST00000396344.4_Silent_p.R85R	NM_018951.3	NP_061824.3	P31260	HXA10_HUMAN	homeobox A10	401					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|male gonad development (GO:0008584)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|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)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	9						CTGTGAGCTCCCGGATCCGGT	0.512													C|||	63	0.0125799	0.003	0.0216	5008	,	,		15678	0.0		0.0388	False		,,,				2504	0.0051				p.R401R		Atlas-SNP	.											.	HOXA10	55	.	0			c.G1203A						PASS	.	C		29,4377	35.2+/-66.4	0,29,2174	81.0	91.0	88.0		1203	1.8	1.0	7	dbSNP_126	88	336,8264	116.8+/-176.5	10,316,3974	no	coding-synonymous	HOXA10	NM_018951.3		10,345,6148	TT,TC,CC		3.907,0.6582,2.8064		401/411	27211548	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	3206	exon2			GAGCTCCCGGATC		CCDS5410.2	7p15.2	2011-06-20	2005-12-22		ENSG00000253293	ENSG00000253293		"""Homeoboxes / ANTP class : HOXL subclass"""	5100	protein-coding gene	gene with protein product		142957	"""homeo box A10"""	HOX1H, HOX1		1973146, 1358459	Standard	NR_037939		Approved		uc011jzm.2	P31260	OTTHUMG00000023436	ENST00000283921.4:c.1203G>A	7.37:g.27211548C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	123	32	0.260163	NM_018951	O43370|O43605|Q15949|Q504T1	Silent	SNP	ENST00000283921.4	37	CCDS5410.2																																																																																			C|0.959;T|0.041	0.041	strong		0.512	HOXA10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358724.2		
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 GAIIx	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_ENST00000298834.3_Silent_p.L866L|AMBRA1_ENST00000528950.1_Silent_p.L897L|AMBRA1_ENST00000533727.1_Silent_p.L807L|AMBRA1_ENST00000426438.1_Silent_p.L897L|AMBRA1_ENST00000314845.3_Silent_p.L836L|AMBRA1_ENST00000534300.1_Silent_p.L866L			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		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	176	101	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	
TGIF1	7050	hgsc.bcm.edu	37	18	3457607	3457607	+	Missense_Mutation	SNP	C	C	T	rs2229333	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:3457607C>T	ENST00000330513.5	+	3	1178	c.875C>T	c.(874-876)cCg>cTg	p.P292L	TGIF1_ENST00000405385.3_Missense_Mutation_p.P143L|TGIF1_ENST00000407501.2_Missense_Mutation_p.P163L|TGIF1_ENST00000472042.1_Missense_Mutation_p.P143L|TGIF1_ENST00000548489.2_Missense_Mutation_p.P177L|TGIF1_ENST00000345133.5_Missense_Mutation_p.P143L|TGIF1_ENST00000551541.1_Missense_Mutation_p.P143L|TGIF1_ENST00000343820.5_Missense_Mutation_p.P163L|TGIF1_ENST00000400167.2_Missense_Mutation_p.P143L|TGIF1_ENST00000401449.1_Missense_Mutation_p.P143L	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	292			P -> L (in dbSNP:rs2229333).|P -> S (in dbSNP:rs4468717). {ECO:0000269|PubMed:10764806, ECO:0000269|Ref.3}.		determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				CCGTCATCCCCGGGATCAGTT	0.532													C|||	389	0.0776757	0.0061	0.0461	5008	,	,		18746	0.1647		0.0596	False		,,,				2504	0.1258				p.P292L		Atlas-SNP	.											.	TGIF1	41	.	0			c.C875T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	54,4352	52.9+/-88.7	1,52,2150	55.0	51.0	52.0		488,875,530,488,428,428,428,428	4.4	0.5	18	dbSNP_98	52	521,8079	146.8+/-202.3	11,499,3790	no	missense,missense,missense,missense,missense,missense,missense,missense	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_173211.1,NM_174886.1	98,98,98,98,98,98,98,98	12,551,5940	TT,TC,CC		6.0581,1.2256,4.421	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	163/273,292/402,177/287,163/273,143/253,143/253,143/253,143/253	3457607	575,12431	2203	4300	6503	SO:0001583	missense	7050	exon3			CATCCCCGGGATC	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.875C>T	18.37:g.3457607C>T	ENSP00000327959:p.Pro292Leu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	150	77	0.513333	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Missense_Mutation	SNP	ENST00000330513.5	37	CCDS11834.1	134	0.06135531135531135	4	0.008130081300813009	27	0.07458563535911603	62	0.10839160839160839	41	0.05408970976253298	C	8.345	0.829631	0.16749	0.012256	0.060581	ENSG00000177426	ENST00000552383;ENST00000401449;ENST00000548489;ENST00000549780;ENST00000405385;ENST00000343820;ENST00000407501;ENST00000551541;ENST00000345133;ENST00000330513;ENST00000549546;ENST00000400167;ENST00000472042	T;T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.17;0.38;0.28;-0.18;0.38;0.37;0.37;0.38;0.38;0.15;0.39;0.38;0.38	5.26	4.39	0.52855	.	0.000000	0.85682	D	0.000000	T	0.05227	0.0139	M	0.74258	2.255	0.09310	P	0.9999999869808	D;D;D	0.76494	0.999;0.982;0.997	P;P;D	0.63033	0.863;0.535;0.91	T	0.52049	-0.8627	9	0.36615	T	0.2	-21.8135	13.868	0.63600	0.0:0.926:0.0:0.074	rs2229333;rs3750274;rs17647302;rs52799550;rs2229333	292;163;177	Q15583;Q15583-2;F8VZB6	TGIF1_HUMAN;.;.	L	143;143;177;143;143;163;163;143;143;292;143;143;143	ENSP00000449287:P143L;ENSP00000385206:P143L;ENSP00000447747:P177L;ENSP00000448121:P143L;ENSP00000384970:P143L;ENSP00000339631:P163L;ENSP00000384133:P163L;ENSP00000450025:P143L;ENSP00000343969:P143L;ENSP00000327959:P292L;ENSP00000449580:P143L;ENSP00000383031:P143L;ENSP00000449501:P143L	ENSP00000327959:P292L	P	+	2	0	TGIF1	3447607	1.000000	0.71417	0.499000	0.27577	0.499000	0.33736	7.301000	0.78850	1.225000	0.43566	0.467000	0.42956	CCG	C|0.942;G|0.000;T|0.057	0.057	strong		0.532	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
FIBCD1	84929	hgsc.bcm.edu	37	9	133787225	133787225	+	Silent	SNP	A	A	G	rs6597650	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:133787225A>G	ENST00000372338.4	-	5	1142	c.900T>C	c.(898-900)gaT>gaC	p.D300D	FIBCD1_ENST00000253018.4_Silent_p.D142D|FIBCD1_ENST00000448616.1_Silent_p.D300D|FIBCD1_ENST00000372337.2_Silent_p.D142D	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	300	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitin binding (GO:0008061)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|prostate(5)|urinary_tract(1)	12	all_hematologic(7;0.0028)			OV - Ovarian serous cystadenocarcinoma(145;3.52e-05)|Epithelial(140;0.00019)		CTCGGTACGCATCCCAGCCCC	0.672													G|||	3010	0.601038	0.8381	0.5965	5008	,	,		16495	0.6121		0.4046	False		,,,				2504	0.4744				p.D300D		Atlas-SNP	.											.	FIBCD1	34	.	0			c.T900C						PASS	.	G	,	3424,974		1338,748,113	47.0	39.0	42.0		900,900	-2.0	0.7	9	dbSNP_116	42	3425,5175		682,2061,1557	no	coding-synonymous,coding-synonymous	FIBCD1	NM_001145106.1,NM_032843.4	,	2020,2809,1670	GG,GA,AA		39.8256,22.1464,47.3073	,	300/462,300/462	133787225	6849,6149	2199	4300	6499	SO:0001819	synonymous_variant	84929	exon6			GTACGCATCCCAG	AK027716	CCDS6937.1	9q34.2	2013-02-06			ENSG00000130720	ENSG00000130720		"""Fibrinogen C domain containing"""	25922	protein-coding gene	gene with protein product		613357				12975309	Standard	NM_001145106		Approved	FLJ14810	uc004bzz.3	Q8N539	OTTHUMG00000020814	ENST00000372338.4:c.900T>C	9.37:g.133787225A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_001145106	A3KFK0|Q6UXK6|Q96SJ7	Silent	SNP	ENST00000372338.4	37	CCDS6937.1	1262	0.5778388278388278	404	0.8211382113821138	185	0.511049723756906	362	0.6328671328671329	311	0.4102902374670185	G	3.545	-0.092788	0.07053	0.778536	0.398256	ENSG00000130720	ENST00000444139	.	.	.	5.06	-1.98	0.07480	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999850689	.	.	.	.	.	.	T	0.23655	-1.0182	3	.	.	.	.	1.5364	0.02546	0.2048:0.2805:0.3178:0.1969	rs6597650;rs59798032;rs6597650	.	.	.	T	254	.	.	M	-	2	0	FIBCD1	132777046	0.000000	0.05858	0.664000	0.29753	0.275000	0.26752	-1.838000	0.01687	-0.680000	0.05211	-1.535000	0.00915	ATG	A|0.442;G|0.558	0.558	strong		0.672	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843	
UQCRH	7388	hgsc.bcm.edu	37	1	46774783	46774783	+	Missense_Mutation	SNP	A	A	G	rs41292543	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46774783A>G	ENST00000311672.5	+	2	201	c.65A>G	c.(64-66)gAa>gGa	p.E22G	UQCRH_ENST00000486951.1_3'UTR	NM_001089591.1|NM_006004.2	NP_001083060.1|NP_005995.2	P07919	QCR6_HUMAN	ubiquinol-cytochrome c reductase hinge protein	22	Poly-Glu.				aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|protein heterooligomerization (GO:0051291)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	4	Acute lymphoblastic leukemia(166;0.155)					GAGGAAGAGGAAGAGGAGGAA	0.358													A|||	312	0.0623003	0.0038	0.072	5008	,	,		21037	0.0		0.1173	False		,,,				2504	0.1421				p.E22G		Atlas-SNP	.											.	UQCRH	4	.	0			c.A65G						PASS	.	A	GLY/GLU	91,4315	75.7+/-113.9	4,83,2116	153.0	144.0	147.0		65	4.9	1.0	1	dbSNP_127	147	911,7689	201.1+/-244.7	43,825,3432	yes	missense	UQCRH	NM_006004.2	98	47,908,5548	GG,GA,AA		10.593,2.0654,7.7041	probably-damaging	22/92	46774783	1002,12004	2203	4300	6503	SO:0001583	missense	7388	exon2			AAGAGGAAGAGGA	BC001934	CCDS30704.1	1p34.1	2011-07-04			ENSG00000173660	ENSG00000173660	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12590	protein-coding gene	gene with protein product	"""ubiquinol-cytochrome c reductase, complex III subunit VIII"""	613844				2826252	Standard	XM_005271167		Approved	QCR6, UQCR8	uc001cpp.3	P07919	OTTHUMG00000007813	ENST00000311672.5:c.65A>G	1.37:g.46774783A>G	ENSP00000309565:p.Glu22Gly	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_006004	B2R4V9|D3DQ18|Q5TDF6|Q6LDB8|Q9BQ91	Missense_Mutation	SNP	ENST00000311672.5	37	CCDS30704.1	108	0.04945054945054945	4	0.008130081300813009	28	0.07734806629834254	0	0.0	76	0.10026385224274406	A	22.4	4.280810	0.80692	0.020654	0.10593	ENSG00000173660	ENST00000311672	T	0.51325	0.71	4.88	4.88	0.63580	Ubiquinol-cytochrome C reductase hinge domain (2);	0.000000	0.85682	D	0.000000	T	0.01940	0.0061	.	.	.	0.20196	P	0.9999287157	D	0.60160	0.987	P	0.54544	0.755	T	0.42865	-0.9426	8	0.66056	D	0.02	-8.5585	12.2515	0.54601	1.0:0.0:0.0:0.0	rs41292543	22	P07919	QCR6_HUMAN	G	22	ENSP00000309565:E22G	ENSP00000309565:E22G	E	+	2	0	UQCRH	46547370	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.865000	0.62998	2.169000	0.68431	0.528000	0.53228	GAA	A|0.926;G|0.074	0.074	strong		0.358	UQCRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021451.1	NM_006004	
EPHX1	2052	hgsc.bcm.edu	37	1	226019653	226019653	+	Silent	SNP	G	G	A	rs1131873	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226019653G>A	ENST00000366837.4	+	3	553	c.357G>A	c.(355-357)aaG>aaA	p.K119K	EPHX1_ENST00000272167.5_Silent_p.K119K|EPHX1_ENST00000467015.1_3'UTR	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	119					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TCAAGACTAAGATTGAAGGTA	0.438													G|||	957	0.191094	0.1165	0.1484	5008	,	,		23249	0.2867		0.162	False		,,,				2504	0.2536				p.K119K		Atlas-SNP	.											.	EPHX1	57	.	0			c.G357A						PASS	.	G	,	643,3763	275.7+/-272.7	50,543,1610	88.0	80.0	83.0		357,357	3.7	1.0	1	dbSNP_100	83	1236,7364	247.8+/-275.7	82,1072,3146	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	132,1615,4756	AA,AG,GG		14.3721,14.5937,14.4472	,	119/456,119/456	226019653	1879,11127	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon3			GACTAAGATTGAA	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.357G>A	1.37:g.226019653G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			G|0.831;A|0.169	0.169	strong		0.438	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
ULK1	8408	hgsc.bcm.edu	37	12	132401566	132401566	+	Missense_Mutation	SNP	C	C	T	rs11546871	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132401566C>T	ENST00000321867.4	+	21	2492	c.2141C>T	c.(2140-2142)cCg>cTg	p.P714L	ULK1_ENST00000540647.1_5'Flank	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	714			P -> L (in dbSNP:rs11546871). {ECO:0000269|PubMed:17344846}.		autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)	p.P714L(1)		breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		GCCCCGGACCCGGGCAGCACG	0.672													c|||	1020	0.203674	0.0877	0.2651	5008	,	,		9562	0.0377		0.326	False		,,,				2504	0.362				p.P714L		Atlas-SNP	.											ULK1,NS,carcinoma,0,2	ULK1	92	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2141T						PASS	.		LEU/PRO	449,3933	198.7+/-222.5	15,419,1757	32.0	42.0	39.0		2141	4.2	0.3	12	dbSNP_120	39	2658,5922	403.8+/-347.9	403,1852,2035	yes	missense	ULK1	NM_003565.2	98	418,2271,3792	TT,TC,CC		30.979,10.2465,23.9701	benign	714/1051	132401566	3107,9855	2191	4290	6481	SO:0001583	missense	8408	exon21			CGGACCCGGGCAG	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.2141C>T	12.37:g.132401566C>T	ENSP00000324560:p.Pro714Leu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	93	0.547059	NM_003565	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	37	CCDS9274.1	407	0.18635531135531136	44	0.08943089430894309	108	0.2983425414364641	19	0.033216783216783216	236	0.3113456464379947	c	6.883	0.532418	0.13127	0.102465	0.30979	ENSG00000177169	ENST00000321867;ENST00000541761	T;T	0.28454	1.61;1.61	5.06	4.16	0.48862	.	0.806381	0.11335	N	0.574590	T	0.00012	0.0000	N	0.08118	0	0.35606	P	0.19176400000000005	B	0.13145	0.007	B	0.06405	0.002	T	0.41875	-0.9484	9	0.10902	T	0.67	-6.2137	9.0411	0.36319	0.0:0.7578:0.1633:0.079	rs11546871	714	O75385	ULK1_HUMAN	L	714;62	ENSP00000324560:P714L;ENSP00000444298:P62L	ENSP00000324560:P714L	P	+	2	0	ULK1	130967519	0.590000	0.26815	0.345000	0.25642	0.033000	0.12548	2.192000	0.42649	1.226000	0.43582	0.556000	0.70494	CCG	C|0.780;T|0.220	0.220	strong		0.672	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
PCDHB8	56128	hgsc.bcm.edu	37	5	140558580	140558580	+	Missense_Mutation	SNP	C	C	T	rs7700833	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140558580C>T	ENST00000239444.2	+	1	1210	c.965C>T	c.(964-966)gCg>gTg	p.A322V	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	322	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> V (in dbSNP:rs7700833).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AATATCGAGGCGAGAGATGCT	0.403													C|||	310	0.061901	0.202	0.0447	5008	,	,		30648	0.0		0.0119	False		,,,				2504	0.0				p.A322V		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C965T						PASS	.	C	VAL/ALA	772,3634	312.5+/-292.6	78,616,1509	159.0	228.0	204.0		965	4.2	0.2	5	dbSNP_116	204	114,8486	58.7+/-120.3	0,114,4186	yes	missense	PCDHB8	NM_019120.3	64	78,730,5695	TT,TC,CC		1.3256,17.5216,6.8122	probably-damaging	322/802	140558580	886,12120	2203	4300	6503	SO:0001583	missense	56128	exon1			TCGAGGCGAGAGA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.965C>T	5.37:g.140558580C>T	ENSP00000239444:p.Ala322Val	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	297	71	0.239057	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	127	0.05815018315018315	102	0.2073170731707317	17	0.04696132596685083	0	0.0	8	0.010554089709762533	C	13.68	2.308295	0.40895	0.175216	0.013256	ENSG00000120322	ENST00000239444	T	0.73363	-0.74	4.25	4.25	0.50352	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00384	0.0012	M	0.86573	2.825	0.26369	P	0.9769165	D	0.89917	1.0	D	0.79784	0.993	T	0.02015	-1.1229	8	0.87932	D	0	.	16.2711	0.82622	0.0:1.0:0.0:0.0	rs7700833;rs52790631;rs7700833	322	Q9UN66	PCDB8_HUMAN	V	322	ENSP00000239444:A322V	ENSP00000239444:A322V	A	+	2	0	PCDHB8	140538764	1.000000	0.71417	0.192000	0.23308	0.098000	0.18820	7.445000	0.80570	1.911000	0.55334	0.585000	0.79938	GCG	C|0.932;T|0.068	0.068	strong		0.403	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
GYPB	2994	hgsc.bcm.edu	37	4	144922436	144922436	+	Splice_Site	SNP	T	T	G	rs201662569	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:144922436T>G	ENST00000502664.1	-	2	89	c.38A>C	c.(37-39)gAa>gCa	p.E13A	GYPB_ENST00000283126.7_Splice_Site_p.E13A|GYPB_ENST00000510196.2_5'UTR|GYPB_ENST00000429670.2_Splice_Site_p.E13A|RP11-673E1.4_ENST00000506982.1_RNA|GYPB_ENST00000513128.1_Intron	NM_002100.4	NP_002091	P06028	GLPB_HUMAN	glycophorin B (MNS blood group)	13						integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.E13A(1)		breast(1)|large_intestine(2)|skin(1)	4	all_hematologic(180;0.158)					GCTCACAATTTCTGTATAAAA	0.403																																					p.E13A		Atlas-SNP	.											GYPB_ENST00000502664,NS,carcinoma,0,3	GYPB	17	3	1	Substitution - Missense(1)	skin(1)	c.A38C						scavenged	.						76.0	98.0	91.0					4																	144922436		2195	4297	6492	SO:0001630	splice_region_variant	2994	exon2			ACAATTTCTGTAT		CCDS54809.1	4q31.21	2014-09-17	2006-02-23			ENSG00000250361		"""CD molecules"", ""Blood group antigens"""	4703	protein-coding gene	gene with protein product		111740	"""glycophorin B (includes Ss blood group)"", ""glycophorin B (Ss blood group)"""	MNS			Standard	NM_002100		Approved	GPB, SS, CD235b		P06028		ENST00000502664.1:c.38-1A>C	4.37:g.144922436T>G		Somatic	384	2	0.00520833		WXS	Illumina HiSeq	Phase_I	414	68	0.164251	NM_002100	B8Q174|E2QBW7|Q0VAF4|Q58HE9|Q58HF0|Q58HF1|Q9UCH7	Missense_Mutation	SNP	ENST00000502664.1	37	CCDS54809.1	.	.	.	.	.	.	.	.	.	.	T	0.018	-1.468978	0.01053	.	.	ENSG00000250361	ENST00000283126;ENST00000502664;ENST00000429670	T;T;T	0.06849	4.29;4.29;3.25	1.74	-3.49	0.04724	.	.	.	.	.	T	0.04272	0.0118	.	.	.	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.39121	-0.9629	8	0.21540	T	0.41	.	4.8253	0.13412	0.0:0.3816:0.3337:0.2847	.	13	E2QBW7	.	A	13	ENSP00000283126:E13A;ENSP00000427690:E13A;ENSP00000394200:E13A	ENSP00000283126:E13A	E	-	2	0	GYPB	145141886	0.000000	0.05858	0.001000	0.08648	0.084000	0.17831	-2.531000	0.00943	-2.543000	0.00484	-1.616000	0.00795	GAA	.	.	weak		0.403	GYPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364791.1	NM_002100	Missense_Mutation
H1FNT	341567	hgsc.bcm.edu	37	12	48723595	48723595	+	Missense_Mutation	SNP	G	G	A	rs1471997	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48723595G>A	ENST00000335017.1	+	1	833	c.521G>A	c.(520-522)cGg>cAg	p.R174Q		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	174	Arg-rich.		R -> Q (in a Japanese man; dbSNP:rs1471997). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16533358}.		chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						GTGTGGAGACGGAACGCGAGG	0.711													G|||	807	0.161142	0.09	0.2176	5008	,	,		12981	0.2212		0.2137	False		,,,				2504	0.1012				p.R174Q		Atlas-SNP	.											.	H1FNT	30	.	0			c.G521A						PASS	.	G	GLN/ARG	450,3908		19,412,1748	32.0	29.0	30.0		521	-1.3	0.0	12	dbSNP_88	30	1851,6731		199,1453,2639	yes	missense	H1FNT	NM_181788.1	43	218,1865,4387	AA,AG,GG		21.5684,10.3258,17.7821	benign	174/256	48723595	2301,10639	2179	4291	6470	SO:0001583	missense	341567	exon1			GGAGACGGAACGC	AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"""Histones / Replication-independent"""	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.521G>A	12.37:g.48723595G>A	ENSP00000334805:p.Arg174Gln	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	42	27	0.642857	NM_181788	Q147U8|Q5GKZ5|Q7Z694	Missense_Mutation	SNP	ENST00000335017.1	37	CCDS8762.1	403	0.18452380952380953	45	0.09146341463414634	82	0.2265193370165746	121	0.21153846153846154	155	0.20448548812664907	G	12.20	1.866692	0.32977	0.103258	0.215684	ENSG00000187166	ENST00000335017	T	0.18960	2.18	4.18	-1.27	0.09347	.	0.299800	0.18034	N	0.153839	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.18968	0.032	B	0.11329	0.006	T	0.32771	-0.9894	9	0.42905	T	0.14	-0.671	1.7845	0.03038	0.2282:0.2568:0.3824:0.1326	rs1471997;rs52803112;rs57038423;rs1471997	174	Q75WM6	H1FNT_HUMAN	Q	174	ENSP00000334805:R174Q	ENSP00000334805:R174Q	R	+	2	0	H1FNT	47009862	0.007000	0.16637	0.001000	0.08648	0.023000	0.10783	0.557000	0.23454	-0.379000	0.07906	-1.367000	0.01198	CGG	G|0.832;A|0.168	0.168	strong		0.711	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788	
USHBP1	83878	hgsc.bcm.edu	37	19	17361064	17361064	+	Silent	SNP	C	C	T	rs10415471	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17361064C>T	ENST00000252597.3	-	13	2255	c.2082G>A	c.(2080-2082)ccG>ccA	p.P694P	AC010646.3_ENST00000594059.1_Intron|USHBP1_ENST00000431146.2_Silent_p.P630P	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						GCTGGGGAGGCGGGAGGGGAG	0.627													C|||	623	0.124401	0.1868	0.0994	5008	,	,		17027	0.002		0.1759	False		,,,				2504	0.1309				p.P694P		Atlas-SNP	.											.	USHBP1	85	.	0			c.G2082A						PASS	.	C		908,3498	324.8+/-298.8	86,736,1381	26.0	25.0	25.0		2082	-6.7	0.0	19	dbSNP_119	25	1669,6931	287.5+/-298.3	174,1321,2805	no	coding-synonymous	USHBP1	NM_031941.3		260,2057,4186	TT,TC,CC		19.407,20.6083,19.8139		694/704	17361064	2577,10429	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon13			GGGAGGCGGGAGG	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.2082G>A	19.37:g.17361064C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			C|0.828;T|0.172	0.172	strong		0.627	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
SLC37A2	219855	hgsc.bcm.edu	37	11	124947396	124947396	+	Missense_Mutation	SNP	A	A	G	rs55752830	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124947396A>G	ENST00000403796.2	+	4	587	c.286A>G	c.(286-288)Atc>Gtc	p.I96V	SLC37A2_ENST00000298280.5_Missense_Mutation_p.I96V|SLC37A2_ENST00000308074.4_Missense_Mutation_p.I96V|SLC37A2_ENST00000407458.1_Missense_Mutation_p.I96V	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	96			I -> V (in dbSNP:rs55752830).		carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		CGCCTTCCTCATCGCCTATGC	0.527													G|||	1889	0.377196	0.5348	0.3689	5008	,	,		22449	0.1468		0.3757	False		,,,				2504	0.409				p.I96V	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.A286G						PASS	.	G	VAL/ILE,VAL/ILE	2137,2265	597.0+/-388.8	528,1081,592	99.0	90.0	93.0		286,286	3.6	0.8	11	dbSNP_129	93	3034,5564	663.3+/-402.1	532,1970,1797	yes	missense,missense	SLC37A2	NM_001145290.1,NM_198277.2	29,29	1060,3051,2389	GG,GA,AA		35.2873,48.5461,39.7769	benign,benign	96/502,96/506	124947396	5171,7829	2201	4299	6500	SO:0001583	missense	219855	exon4			TTCCTCATCGCCT	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.286A>G	11.37:g.124947396A>G	ENSP00000384407:p.Ile96Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	102	79	0.77451	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	742	0.33974358974358976	244	0.4959349593495935	140	0.3867403314917127	80	0.13986013986013987	278	0.36675461741424803	G	0.151	-1.091165	0.01858	0.485461	0.352873	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000532000;ENST00000308074	T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41	4.5	3.56	0.40772	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00483	-1.445	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.42666	-0.9438	9	0.07325	T	0.83	-19.5978	10.8993	0.47043	0.1591:0.0:0.8409:0.0	rs55752830;rs61753650	96;96	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	V	96;96;96;59;96	ENSP00000384407:I96V;ENSP00000385126:I96V;ENSP00000298280:I96V;ENSP00000432254:I59V;ENSP00000311833:I96V	ENSP00000298280:I96V	I	+	1	0	SLC37A2	124452606	1.000000	0.71417	0.818000	0.32626	0.004000	0.04260	2.952000	0.49097	1.128000	0.42052	-0.227000	0.12334	ATC	A|0.619;G|0.381	0.381	strong		0.527	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
KIF19	124602	hgsc.bcm.edu	37	17	72351406	72351406	+	Silent	SNP	C	C	T	rs2271536	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72351406C>T	ENST00000389916.4	+	20	3090	c.2952C>T	c.(2950-2952)caC>caT	p.H984H		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	984					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCCTGCCCCACGGCACAAGCA	0.652													C|||	1757	0.350839	0.2163	0.3804	5008	,	,		18224	0.4077		0.3598	False		,,,				2504	0.4438				p.H984H		Atlas-SNP	.											.	KIF19	102	.	0			c.C2952T						PASS	.	C		979,2863		131,717,1073	31.0	34.0	33.0		2952	-6.1	0.0	17	dbSNP_100	33	3026,5216		571,1884,1666	yes	coding-synonymous	KIF19	NM_153209.3		702,2601,2739	TT,TC,CC		36.7144,25.4815,33.143		984/999	72351406	4005,8079	1921	4121	6042	SO:0001819	synonymous_variant	124602	exon20			GCCCCACGGCACA	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2952C>T	17.37:g.72351406C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	28	11	0.392857	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			C|0.650;T|0.350	0.350	strong		0.652	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
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 GAIIx	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	TEN1-CDK3_ENST00000567351.1_RNA|EVPL_ENST00000586740.1_Missense_Mutation_p.V1943I	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	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	33	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	
PPA2	27068	hgsc.bcm.edu	37	4	106317429	106317429	+	Missense_Mutation	SNP	C	C	G	rs13787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106317429C>G	ENST00000341695.5	-	9	876	c.846G>C	c.(844-846)aaG>aaC	p.K282N	PPA2_ENST00000432483.2_Missense_Mutation_p.K180N|PPA2_ENST00000380004.2_Missense_Mutation_p.K264N|PPA2_ENST00000348706.5_Missense_Mutation_p.K253N|PPA2_ENST00000357415.4_Missense_Mutation_p.K297N|PPA2_ENST00000354147.3_Missense_Mutation_p.K116N|PPA2_ENST00000509426.1_5'Flank	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	282			K -> N (in dbSNP:rs13787). {ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039}.		diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		CTCCATTACACTTCTTCATAA	0.294													C|||	2167	0.432708	0.0923	0.5086	5008	,	,		17915	0.6766		0.4592	False		,,,				2504	0.5603				p.K282N		Atlas-SNP	.											.	PPA2	23	.	0			c.G846C						PASS	.	C	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	585,3821	251.5+/-258.2	40,505,1658	96.0	91.0	93.0		759,540,348,846	0.1	0.7	4	dbSNP_52	93	3925,4669	539.8+/-383.7	890,2145,1262	yes	missense,missense,missense,missense	PPA2	NM_006903.4,NM_176866.2,NM_176867.3,NM_176869.2	94,94,94,94	930,2650,2920	GG,GC,CC		45.6714,13.2773,34.6923	benign,benign,benign,benign	253/306,180/233,116/169,282/335	106317429	4510,8490	2203	4297	6500	SO:0001583	missense	27068	exon9			ATTACACTTCTTC		CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.846G>C	4.37:g.106317429C>G	ENSP00000343885:p.Lys282Asn	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_176869	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	973	0.44551282051282054	49	0.09959349593495935	163	0.45027624309392267	390	0.6818181818181818	371	0.4894459102902375	C	11.86	1.763782	0.31228	0.132773	0.456714	ENSG00000138777	ENST00000341695;ENST00000348706;ENST00000354147;ENST00000432483;ENST00000357415;ENST00000380004	T;T;T;T;T;T	0.48522	0.81;0.81;0.81;0.81;0.81;0.81	5.93	0.105	0.14535	.	0.217385	0.45867	D	0.000321	T	0.00012	0.0000	M	0.73217	2.22	0.21386	P	0.999704449	P;B;B;B;B	0.36789	0.57;0.344;0.033;0.076;0.038	B;B;B;B;B	0.35240	0.198;0.05;0.049;0.011;0.011	T	0.38993	-0.9635	9	0.42905	T	0.14	-22.2528	6.7286	0.23371	0.1115:0.4337:0.0:0.4549	rs13787;rs1127137;rs3182696;rs11267057;rs11566570;rs17256954;rs17839004;rs13787	116;180;253;264;282	Q9H2U2-4;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.;.;.;.;IPYR2_HUMAN	N	282;253;116;180;297;264	ENSP00000343885:K282N;ENSP00000313061:K253N;ENSP00000340352:K116N;ENSP00000389957:K180N;ENSP00000349996:K297N;ENSP00000369340:K264N	ENSP00000343885:K282N	K	-	3	2	PPA2	106536878	0.000000	0.05858	0.742000	0.31022	0.987000	0.75469	-0.843000	0.04350	-0.083000	0.12618	-0.181000	0.13052	AAG	C|0.611;G|0.389	0.389	strong		0.294	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869	
SLC4A7	9497	hgsc.bcm.edu	37	3	27473066	27473066	+	Silent	SNP	A	A	G	rs13077400	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:27473066A>G	ENST00000295736.5	-	7	916	c.846T>C	c.(844-846)ctT>ctC	p.L282L	SLC4A7_ENST00000446700.1_Silent_p.L274L|SLC4A7_ENST00000454389.1_Silent_p.L291L|SLC4A7_ENST00000428386.1_Intron|SLC4A7_ENST00000435667.2_Intron|SLC4A7_ENST00000425128.2_Silent_p.L274L|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000437179.1_Intron|SLC4A7_ENST00000445684.1_Silent_p.L278L|SLC4A7_ENST00000440156.1_Silent_p.L278L|SLC4A7_ENST00000455077.1_Intron	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	282					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	GAAGATGACCAAGAAGAAGAG	0.522													G|||	823	0.164337	0.1702	0.1772	5008	,	,		17626	0.0575		0.2276	False		,,,				2504	0.1922				p.L282L		Atlas-SNP	.											.	SLC4A7	119	.	0			c.T846C						PASS	.	G		833,3573	747.4+/-411.8	77,679,1447	89.0	97.0	94.0		846	6.0	1.0	3	dbSNP_121	94	2165,6435	713.6+/-406.0	271,1623,2406	no	coding-synonymous	SLC4A7	NM_003615.3		348,2302,3853	GG,GA,AA		25.1744,18.906,23.0509		282/1215	27473066	2998,10008	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon7			ATGACCAAGAAGA	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.846T>C	3.37:g.27473066A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			A|0.800;G|0.200	0.200	strong		0.522	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
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 GAIIx	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_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Splice_Site_p.S338S	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		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	28	12	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
BTN3A2	11118	hgsc.bcm.edu	37	6	26370605	26370605	+	Silent	SNP	T	T	C	rs9379860	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26370605T>C	ENST00000356386.2	+	5	677	c.489T>C	c.(487-489)caT>caC	p.H163H	BTN3A2_ENST00000527422.1_Silent_p.H163H|BTN3A2_ENST00000377708.2_Silent_p.H163H|BTN3A2_ENST00000396934.3_Silent_p.H140H|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000396948.1_Silent_p.H163H|BTN3A2_ENST00000508906.2_Silent_p.H121H	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	163					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						GAGGGATCCATCTGGAGTGCA	0.522													T|||	1755	0.350439	0.4266	0.3098	5008	,	,		18970	0.2232		0.4135	False		,,,				2504	0.3425				p.H163H		Atlas-SNP	.											.	BTN3A2	44	.	0			c.T489C						PASS	.	T	,,,,	1865,2541	540.1+/-375.4	382,1101,720	115.0	102.0	107.0		489,489,420,363,489	-4.6	0.0	6	dbSNP_119	107	3406,5194	503.8+/-376.0	658,2090,1552	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	1040,3191,2272	CC,CT,TT		39.6047,42.3286,40.5274	,,,,	163/335,163/335,140/312,121/293,163/335	26370605	5271,7735	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			GATCCATCTGGAG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.489T>C	6.37:g.26370605T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	23	0.244681	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			T|0.614;C|0.386	0.386	strong		0.522	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
MYPOP	339344	hgsc.bcm.edu	37	19	46394322	46394322	+	Silent	SNP	G	G	A	rs114387602	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46394322G>A	ENST00000322217.5	-	3	845	c.759C>T	c.(757-759)ctC>ctT	p.L253L		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	253	Pro-rich.					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 negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						ctgaggccgagagcgtgggtg	0.721													G|||	445	0.0888578	0.1475	0.085	5008	,	,		3566	0.001		0.1024	False		,,,				2504	0.089				p.L253L		Atlas-SNP	.											.	MYPOP	23	.	0			c.C759T						PASS	.	G		426,3480		26,374,1553	3.0	3.0	3.0		759	1.3	0.1	19	dbSNP_132	3	744,6954		37,670,3142	no	coding-synonymous	MYPOP	NM_001012643.2		63,1044,4695	AA,AG,GG		9.6648,10.9063,10.0827		253/400	46394322	1170,10434	1953	3849	5802	SO:0001819	synonymous_variant	339344	exon3			GGCCGAGAGCGTG	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"""p42 Myb-related transcription factor, partner of profilin"""					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.759C>T	19.37:g.46394322G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_001012643		Silent	SNP	ENST00000322217.5	37	CCDS33055.1																																																																																			G|0.923;A|0.077	0.077	strong		0.721	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643	
PPL	5493	hgsc.bcm.edu	37	16	4935146	4935146	+	Silent	SNP	C	C	T	rs1049206	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4935146C>T	ENST00000345988.2	-	22	3599	c.3510G>A	c.(3508-3510)gtG>gtA	p.V1170V	PPL_ENST00000590782.2_Silent_p.V1168V	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1170					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.V1170V(1)		breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CCTTCTCCTGCACCACCACTT	0.622													C|||	1841	0.367612	0.3359	0.4135	5008	,	,		18711	0.2907		0.3241	False		,,,				2504	0.502				p.V1170V		Atlas-SNP	.											PPL,NS,carcinoma,0,1	PPL	168	1	1	Substitution - coding silent(1)	stomach(1)	c.G3510A						PASS	.	C		1539,2855	487.3+/-360.9	274,991,932	120.0	110.0	113.0		3510	2.1	1.0	16	dbSNP_86	113	2550,6050	414.9+/-351.6	376,1798,2126	no	coding-synonymous	PPL	NM_002705.4		650,2789,3058	TT,TC,CC		29.6512,35.025,31.4684		1170/1757	4935146	4089,8905	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			CTCCTGCACCACC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3510G>A	16.37:g.4935146C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			C|0.673;T|0.327	0.327	strong		0.622	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
GRIN3A	116443	hgsc.bcm.edu	37	9	104433347	104433347	+	Silent	SNP	G	G	A	rs13284303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:104433347G>A	ENST00000361820.3	-	3	1947	c.1347C>T	c.(1345-1347)atC>atT	p.I449I		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	449					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	CTTTTACTCTGATGGAACCAC	0.468													G|||	615	0.122804	0.0068	0.1931	5008	,	,		18256	0.1716		0.167	False		,,,				2504	0.1339				p.I449I		Atlas-SNP	.											.	GRIN3A	186	.	0			c.C1347T						PASS	.	G		153,4253	103.4+/-141.9	6,141,2056	117.0	119.0	118.0		1347	5.8	1.0	9	dbSNP_121	118	1454,7146	276.9+/-292.6	124,1206,2970	no	coding-synonymous	GRIN3A	NM_133445.2		130,1347,5026	AA,AG,GG		16.907,3.4725,12.3558		449/1116	104433347	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			TACTCTGATGGAA		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.1347C>T	9.37:g.104433347G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			G|0.871;A|0.129	0.129	strong		0.468	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
KIAA0556	23247	hgsc.bcm.edu	37	16	27720201	27720201	+	Missense_Mutation	SNP	C	C	T	rs12930355	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:27720201C>T	ENST00000261588.4	+	13	1584	c.1565C>T	c.(1564-1566)aCg>aTg	p.T522M	CTD-2049O4.1_ENST00000568831.1_RNA|CTD-2049O4.1_ENST00000563052.1_RNA|KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000564893.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	522			T -> M (in dbSNP:rs12930355).			extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.T522M(1)		breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						AACACAGCCACGCCTGGGGAG	0.537													C|||	342	0.0682907	0.0189	0.1715	5008	,	,		19377	0.001		0.1551	False		,,,				2504	0.0419				p.T522M		Atlas-SNP	.											KIAA0556_ENST00000261588,caecum,carcinoma,-1,3	KIAA0556	348	3	1	Substitution - Missense(1)	large_intestine(1)	c.C1565T						scavenged	.	C	MET/THR	222,4172	132.9+/-169.3	4,214,1979	69.0	63.0	65.0		1565	-4.6	0.0	16	dbSNP_121	65	1284,7316	255.1+/-280.1	87,1110,3103	yes	missense	KIAA0556	NM_015202.2	81	91,1324,5082	TT,TC,CC		14.9302,5.0523,11.59	benign	522/1619	27720201	1506,11488	2197	4300	6497	SO:0001583	missense	23247	exon13			CAGCCACGCCTGG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.1565C>T	16.37:g.27720201C>T	ENSP00000261588:p.Thr522Met	Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	190	0.08699633699633699	11	0.022357723577235773	56	0.15469613259668508	0	0.0	123	0.16226912928759896	C	3.230	-0.157586	0.06544	0.050523	0.149302	ENSG00000047578	ENST00000261588;ENST00000327217	T	0.13901	2.55	5.49	-4.56	0.03431	.	1.266200	0.04883	N	0.448051	T	0.00039	0.0001	N	0.16478	0.41	0.80722	P	0.0	B;B	0.16166	0.016;0.007	B;B	0.12837	0.008;0.006	T	0.42155	-0.9468	9	0.33940	T	0.23	-5.3447	4.9772	0.14146	0.3099:0.3468:0.0:0.3433	rs12930355;rs12930355	430;522	Q8N803;O60303	.;K0556_HUMAN	M	522;429	ENSP00000261588:T522M	ENSP00000261588:T522M	T	+	2	0	KIAA0556	27627702	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-1.350000	0.02624	-0.536000	0.06298	-0.448000	0.05591	ACG	C|0.898;T|0.102	0.102	strong		0.537	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
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 GAIIx	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|RP11-284F21.7_ENST00000448869.1_RNA|RP11-284F21.10_ENST00000605886.1_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	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	47	22	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	
OASL	8638	hgsc.bcm.edu	37	12	121471337	121471337	+	Silent	SNP	G	G	A	rs3213545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121471337G>A	ENST00000257570.5	-	2	678	c.408C>T	c.(406-408)ctC>ctT	p.L136L	OASL_ENST00000339275.5_Silent_p.L136L	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	136					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGGTGAAGACGAGAGCATCGG	0.602													G|||	1568	0.313099	0.1293	0.2839	5008	,	,		19668	0.4692		0.3072	False		,,,				2504	0.4274				p.L136L	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.C408T						PASS	.	G	,	645,3761	274.6+/-272.0	46,553,1604	120.0	101.0	108.0	http://www.ncbi.nlm.nih.gov/pubmed?term	408,408	-2.8	0.0	12	dbSNP_106	108	2585,6015	421.5+/-353.7	411,1763,2126	no	coding-synonymous,coding-synonymous	OASL	NM_003733.2,NM_198213.1	,	457,2316,3730	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	30.0581,14.6391,24.8347	,	136/515,136/256	121471337	3230,9776	2203	4300	6503	SO:0001819	synonymous_variant	8638	exon2			GAAGACGAGAGCA	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.408C>T	12.37:g.121471337G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	79	77	0.974684	NM_198213	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Silent	SNP	ENST00000257570.5	37	CCDS9211.1																																																																																			G|0.722;A|0.278	0.278	strong		0.602	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733	
INPP5E	56623	hgsc.bcm.edu	37	9	139327034	139327034	+	Silent	SNP	A	A	G	rs10870194	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139327034A>G	ENST00000371712.3	-	6	1686	c.1284T>C	c.(1282-1284)ggT>ggC	p.G428G		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		CCTTCCCGTCACCTGCTGTGG	0.632													G|||	1892	0.377796	0.3911	0.6182	5008	,	,		16010	0.1925		0.4115	False		,,,				2504	0.3456				p.G428G		Atlas-SNP	.											.	INPP5E	18	.	0			c.T1284C						PASS	.	G		1559,2627		308,943,842	52.0	36.0	42.0		1284	-8.3	0.2	9	dbSNP_120	42	3413,4611		789,1835,1388	no	coding-synonymous	INPP5E	NM_019892.4		1097,2778,2230	GG,GA,AA		42.5349,37.2432,40.7207		428/645	139327034	4972,7238	2093	4012	6105	SO:0001819	synonymous_variant	56623	exon6			CCCGTCACCTGCT	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1284T>C	9.37:g.139327034A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	26	12	0.461538	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			A|0.612;G|0.388	0.388	strong		0.632	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
HSPA6	3310	hgsc.bcm.edu	37	1	161495040	161495040	+	Missense_Mutation	SNP	C	C	T	rs63749092	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161495040C>T	ENST00000309758.4	+	1	1005	c.592C>T	c.(592-594)Ctc>Ttc	p.L198F	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	198			L -> F (in dbSNP:rs1079109). {ECO:0000269|Ref.2}.		ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCGCAACGTGCTCATTTTTGA	0.622													c|||	622	0.124201	0.0272	0.1268	5008	,	,		15815	0.2837		0.1183	False		,,,				2504	0.0951				p.L198F		Atlas-SNP	.											.	HSPA6	53	.	0			c.C592T						PASS	.	C	PHE/LEU	175,4231		3,169,2031	39.0	45.0	43.0		592	2.3	0.8	1	dbSNP_129	43	990,7610		57,876,3367	no	missense	HSPA6	NM_002155.3	22	60,1045,5398	TT,TC,CC		11.5116,3.9719,8.9574	probably-damaging	198/644	161495040	1165,11841	2203	4300	6503	SO:0001583	missense	3310	exon1			AACGTGCTCATTT		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.592C>T	1.37:g.161495040C>T	ENSP00000310219:p.Leu198Phe	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	229	99	0.432314	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	307	0.14056776556776557	19	0.03861788617886179	39	0.10773480662983426	154	0.2692307692307692	95	0.12532981530343007	.	15.86	2.957350	0.53400	0.039719	0.115116	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.13538	2.58	3.19	2.27	0.28462	.	0.000000	0.34291	U	0.004084	T	0.34658	0.0905	H	0.97158	3.95	0.21984	P	0.999432756	D	0.89917	1.0	D	0.97110	1.0	T	0.43212	-0.9405	9	0.72032	D	0.01	-29.3593	7.5914	0.28023	0.0:0.8669:0.0:0.1331	rs63749092	198	P17066	HSP76_HUMAN	F	198;174	ENSP00000310219:L198F	ENSP00000310219:L198F	L	+	1	0	HSPA6	159761664	0.999000	0.42202	0.751000	0.31187	0.707000	0.40811	3.892000	0.56235	0.519000	0.28406	0.486000	0.48141	CTC	C|0.897;T|0.103	0.103	strong		0.622	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
CTDP1	9150	hgsc.bcm.edu	37	18	77473127	77473127	+	Missense_Mutation	SNP	C	C	T	rs2279103	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:77473127C>T	ENST00000299543.7	+	7	1166	c.1019C>T	c.(1018-1020)aCg>aTg	p.T340M	CTDP1_ENST00000075430.7_Missense_Mutation_p.T340M	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	340	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.		T -> M (in dbSNP:rs2279103).		exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		GAATCTCAGACGAGAAAGAAA	0.433													C|||	414	0.0826677	0.0045	0.0677	5008	,	,		16222	0.1389		0.169	False		,,,				2504	0.0521				p.T340M		Atlas-SNP	.											.	CTDP1	67	.	0			c.C1019T						PASS	.	C	MET/THR,MET/THR,MET/THR	170,4236	109.5+/-147.8	7,156,2040	54.0	53.0	54.0		662,1019,1019	0.3	0.0	18	dbSNP_100	54	1538,7062	288.6+/-298.9	139,1260,2901	yes	missense,missense,missense	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	81,81,81	146,1416,4941	TT,TC,CC		17.8837,3.8584,13.1324	benign,benign,benign	221/843,340/962,340/868	77473127	1708,11298	2203	4300	6503	SO:0001583	missense	9150	exon7			CTCAGACGAGAAA	AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.1019C>T	18.37:g.77473127C>T	ENSP00000299543:p.Thr340Met	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	89	51	0.573034	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	37	CCDS12017.1	245	0.11217948717948718	7	0.014227642276422764	28	0.07734806629834254	70	0.12237762237762238	140	0.18469656992084432	C	2.918	-0.223925	0.06061	0.038584	0.178837	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.09817	2.97;2.94	4.82	0.332	0.15938	NLI interacting factor (1);	0.670270	0.15369	N	0.265948	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.30114	0.165;0.269;0.103	B;B;B	0.17979	0.013;0.02;0.006	T	0.45877	-0.9231	9	0.40728	T	0.16	-3.9704	3.0092	0.06039	0.2026:0.2918:0.0:0.5055	rs2279103;rs61656723;rs2279103	221;340;340	Q9Y5B0-3;Q9Y5B0-4;Q9Y5B0	.;.;CTDP1_HUMAN	M	340	ENSP00000299543:T340M;ENSP00000075430:T340M	ENSP00000075430:T340M	T	+	2	0	CTDP1	75574115	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.099000	0.15210	0.186000	0.20125	-0.122000	0.15005	ACG	C|0.885;T|0.115	0.115	strong		0.433	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
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 GAIIx	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	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	63	25	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 GAIIx	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_ENST00000265368.4_Missense_Mutation_p.C4021R|SYNE1_ENST00000448038.1_Missense_Mutation_p.C3950R|SYNE1_ENST00000341594.5_Intron	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	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	104	42	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	
TRPM1	4308	hgsc.bcm.edu	37	15	31329944	31329944	+	Silent	SNP	G	G	A	rs12911350	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:31329944G>A	ENST00000256552.6	-	20	2688	c.2541C>T	c.(2539-2541)aaC>aaT	p.N847N	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Silent_p.N825N|TRPM1_ENST00000542188.1_Silent_p.N864N|RP11-348B17.1_ENST00000558755.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		CAATGGGCGCGTTATAGAATT	0.408													g|||	446	0.0890575	0.0983	0.1297	5008	,	,		19983	0.0079		0.1362	False		,,,				2504	0.0828				p.N864N		Atlas-SNP	.											.	TRPM1	183	.	0			c.C2592T						PASS	.	A		435,3371		21,393,1489	166.0	151.0	156.0		2475	-5.7	0.5	15	dbSNP_121	156	1099,7153		75,949,3102	no	coding-synonymous	TRPM1	NM_002420.4		96,1342,4591	AA,AG,GG		13.318,11.4293,12.7218		825/1604	31329944	1534,10524	1903	4126	6029	SO:0001819	synonymous_variant	4308	exon19			GGGCGCGTTATAG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2541C>T	15.37:g.31329944G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			G|0.909;A|0.091	0.091	strong		0.408	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
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 GAIIx	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_ENST00000314740.8_Silent_p.A56A|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000417793.1_Silent_p.A767A|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		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	33	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	
ABCF2	10061	hgsc.bcm.edu	37	7	150916228	150916228	+	Silent	SNP	G	G	A	rs6949587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150916228G>A	ENST00000287844.2	-	8	1048	c.939C>T	c.(937-939)taC>taT	p.Y313Y	ABCF2_ENST00000473874.1_5'UTR|ABCF2_ENST00000222388.2_Silent_p.Y313Y	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	313	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GCGTCTTCACGTACTGATCAT	0.498													G|||	2100	0.419329	0.2095	0.4107	5008	,	,		19404	0.7202		0.4563	False		,,,				2504	0.3609				p.Y313Y		Atlas-SNP	.											.	ABCF2	54	.	0			c.C939T						PASS	.	G	,	992,3414	368.8+/-318.8	111,770,1322	173.0	151.0	158.0		939,939	0.3	1.0	7	dbSNP_116	158	3537,5063	514.7+/-378.4	717,2103,1480	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	828,2873,2802	AA,AG,GG		41.1279,22.5148,34.8224	,	313/635,313/624	150916228	4529,8477	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon8			CTTCACGTACTGA	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"""ATP binding cassette transporters / subfamily F"""	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.939C>T	7.37:g.150916228G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			G|0.611;A|0.389	0.389	strong		0.498	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
RYR1	6261	hgsc.bcm.edu	37	19	39061258	39061258	+	Silent	SNP	C	C	G	rs35959206	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39061258C>G	ENST00000359596.3	+	94	13671	c.13671C>G	c.(13669-13671)tcC>tcG	p.S4557S	RYR1_ENST00000360985.3_Silent_p.S4552S|RYR1_ENST00000355481.4_Silent_p.S4552S			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	4557					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACTACCTGTCCCGGAACTTTT	0.478													C|||	168	0.0335463	0.0106	0.0432	5008	,	,		14556	0.001		0.0755	False		,,,				2504	0.0481				p.S4557S		Atlas-SNP	.											.	RYR1	708	.	0			c.C13671G						PASS	.	C	,	60,4346	58.1+/-94.6	0,60,2143	170.0	168.0	168.0		13671,13656	-4.0	0.9	19	dbSNP_126	168	420,8180	129.2+/-187.3	10,400,3890	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	10,460,6033	GG,GC,CC		4.8837,1.3618,3.6906	,	4557/5039,4552/5034	39061258	480,12526	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon94			CCTGTCCCGGAAC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.13671C>G	19.37:g.39061258C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.960;G|0.040	0.040	strong		0.478	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
HELZ	9931	hgsc.bcm.edu	37	17	65212042	65212042	+	Missense_Mutation	SNP	C	C	T	rs57482031|rs8080100	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:65212042C>T	ENST00000358691.5	-	5	386	c.220G>A	c.(220-222)Gtg>Atg	p.V74M	HELZ_ENST00000580168.1_Missense_Mutation_p.V74M|HELZ_ENST00000580662.1_5'UTR	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	74			V -> M (in dbSNP:rs8080100).			membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TCAGCTTGCACATAATTTTTC	0.284													C|||	981	0.195887	0.2489	0.1614	5008	,	,		19637	0.1994		0.1769	False		,,,				2504	0.1646				p.V74M		Atlas-SNP	.											.	HELZ	160	.	0			c.G220A						PASS	.	C	MET/VAL	851,2751		107,637,1057	58.0	54.0	55.0		220	4.9	1.0	17	dbSNP_116	55	1313,6823		88,1137,2843	yes	missense	HELZ	NM_014877.3	21	195,1774,3900	TT,TC,CC		16.1382,23.6258,18.4358	benign	74/1943	65212042	2164,9574	1801	4068	5869	SO:0001583	missense	9931	exon5			CTTGCACATAATT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.220G>A	17.37:g.65212042C>T	ENSP00000351524:p.Val74Met	Somatic	365	0	0		WXS	Illumina HiSeq	Phase_I	340	141	0.414706	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	408	0.18681318681318682	108	0.21951219512195122	49	0.13535911602209943	112	0.1958041958041958	139	0.18337730870712401	C	14.46	2.543148	0.45280	0.236258	0.161382	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.73897	-0.79;-0.79	4.86	4.86	0.63082	.	0.116901	0.64402	D	0.000010	T	0.00039	0.0001	N	0.08118	0	0.39472	P	0.03226799999999996	B;D	0.57899	0.259;0.981	B;P	0.45195	0.075;0.473	T	0.12192	-1.0557	9	0.49607	T	0.09	-5.7503	18.0445	0.89328	0.0:1.0:0.0:0.0	rs8080100;rs58229173;rs8080100	74;74	F8WBX6;P42694	.;HELZ_HUMAN	M	74	ENSP00000351524:V74M;ENSP00000411144:V74M	ENSP00000351524:V74M	V	-	1	0	HELZ	62642504	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.095000	0.64529	2.260000	0.74910	0.539000	0.68188	GTG	C|0.831;T|0.169	0.169	strong		0.284	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
ALPK1	80216	hgsc.bcm.edu	37	4	113353358	113353358	+	Silent	SNP	G	G	A	rs35129721	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:113353358G>A	ENST00000458497.1	+	11	2934	c.2655G>A	c.(2653-2655)gcG>gcA	p.A885A	ALPK1_ENST00000177648.9_Silent_p.A885A|ALPK1_ENST00000504176.2_Silent_p.A807A	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	885							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GTCAGAGGGCGGAGACCCCCA	0.552													G|||	9	0.00179712	0.0	0.0	5008	,	,		20833	0.001		0.008	False		,,,				2504	0.0				p.A885A		Atlas-SNP	.											ALPK1,caecum,carcinoma,+1,1	ALPK1	125	1	0			c.G2655A						scavenged	.	G	,	6,4400	11.4+/-27.6	0,6,2197	88.0	87.0	88.0		2655,2655	-10.1	0.0	4	dbSNP_126	88	86,8514	49.4+/-109.1	0,86,4214	no	coding-synonymous,coding-synonymous	ALPK1	NM_001102406.1,NM_025144.3	,	0,92,6411	AA,AG,GG		1.0,0.1362,0.7074	,	885/1245,885/1245	113353358	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	80216	exon11			GAGGGCGGAGACC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2655G>A	4.37:g.113353358G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	100	3	0.03	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	37	CCDS3697.1																																																																																			G|0.994;A|0.006	0.006	strong		0.552	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
FDFT1	2222	hgsc.bcm.edu	37	8	11660362	11660362	+	Silent	SNP	T	T	C	rs1047643	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11660362T>C	ENST00000220584.4	+	1	243	c.21T>C	c.(19-21)ctT>ctC	p.L7L	FDFT1_ENST00000528812.1_5'Flank|FDFT1_ENST00000525900.1_Silent_p.L7L|RP11-297N6.4_ENST00000533405.1_5'Flank|FDFT1_ENST00000443614.2_Silent_p.L7L|FDFT1_ENST00000446331.2_3'UTR|FDFT1_ENST00000538689.1_Intron	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	7					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		TGAAATGCCTTGGCCACCCCG	0.677													G|||	876	0.17492	0.3752	0.1254	5008	,	,		13713	0.0079		0.1809	False		,,,				2504	0.1053				p.L7L		Atlas-SNP	.											.	FDFT1	25	.	0			c.T21C						PASS	.	G		1456,2950		217,1022,964	47.0	39.0	41.0		21	2.0	0.8	8	dbSNP_86	41	1320,7278		104,1112,3083	no	coding-synonymous	FDFT1	NM_004462.3		321,2134,4047	CC,CT,TT		15.3524,33.0458,21.3473		7/418	11660362	2776,10228	2203	4299	6502	SO:0001819	synonymous_variant	2222	exon1			ATGCCTTGGCCAC	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.21T>C	8.37:g.11660362T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Silent	SNP	ENST00000220584.4	37	CCDS5985.1																																																																																			T|0.802;C|0.198	0.198	strong		0.677	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
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 GAIIx	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_ENST00000396980.3_5'Flank|HIST1H2BN_ENST00000606613.1_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*	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	50	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	
NPNT	255743	hgsc.bcm.edu	37	4	106859549	106859549	+	Missense_Mutation	SNP	G	G	C	rs35132891	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106859549G>C	ENST00000379987.2	+	5	693	c.477G>C	c.(475-477)caG>caC	p.Q159H	NPNT_ENST00000506666.1_Missense_Mutation_p.Q189H|NPNT_ENST00000305572.8_Missense_Mutation_p.Q159H|NPNT_ENST00000514622.1_Missense_Mutation_p.Q159H|NPNT_ENST00000453617.2_Missense_Mutation_p.Q176H|NPNT_ENST00000427316.2_Missense_Mutation_p.Q189H	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	159	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.		Q -> H (in dbSNP:rs35132891). {ECO:0000269|PubMed:12975309}.		branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		CTGGCCTGCAGCTGGCTCCTG	0.517													G|||	1626	0.324681	0.4607	0.3329	5008	,	,		17415	0.1825		0.334	False		,,,				2504	0.272				p.Q189H		Atlas-SNP	.											.	NPNT	69	.	0			c.G567C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN	1810,2596	530.8+/-373.0	369,1072,762	70.0	66.0	67.0		477,528,567,477,567	3.5	1.0	4	dbSNP_126	67	2797,5803	443.5+/-360.4	457,1883,1960	yes	missense,missense,missense,missense,missense	NPNT	NM_001033047.2,NM_001184690.1,NM_001184691.1,NM_001184692.1,NM_001184693.1	24,24,24,24,24	826,2955,2722	CC,CG,GG		32.5233,41.0803,35.4221	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	159/566,176/583,189/596,159/537,189/567	106859549	4607,8399	2203	4300	6503	SO:0001583	missense	255743	exon6			CCTGCAGCTGGCT		CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.477G>C	4.37:g.106859549G>C	ENSP00000369323:p.Gln159His	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	35	22	0.628571	NM_001184691	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Missense_Mutation	SNP	ENST00000379987.2	37	CCDS34046.1	692|692	0.31684981684981683|0.31684981684981683	212|212	0.43089430894308944|0.43089430894308944	127|127	0.35082872928176795|0.35082872928176795	113|113	0.19755244755244755|0.19755244755244755	240|240	0.316622691292876|0.316622691292876	G|G	17.26|17.26	3.344923|3.344923	0.61073|0.61073	0.410803|0.410803	0.325233|0.325233	ENSG00000168743|ENSG00000168743	ENST00000514837|ENST00000504304;ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000305572;ENST00000506666;ENST00000503451	.|T;D;D;D;D;D;D;D	.|0.87491	.|1.3;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26;-2.26	5.22|5.22	3.49|3.49	0.39957|0.39957	.|Epidermal growth factor-like (1);	.|0.049867	.|0.85682	.|D	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.65975|0.65975	2.015|2.015	0.26849|0.26849	P|P	0.9681974|0.9681974	.|D;B;B;D;B;D;D	.|0.69078	.|0.997;0.112;0.23;0.989;0.23;0.996;0.995	.|D;B;B;D;B;D;D	.|0.66847	.|0.931;0.082;0.082;0.921;0.082;0.93;0.947	T|T	0.01013|0.01013	-1.1481|-1.1481	4|9	.|0.72032	.|D	.|0.01	.|.	8.6958|8.6958	0.34296|0.34296	0.2933:0.0:0.7067:0.0|0.2933:0.0:0.7067:0.0	rs35132891|rs35132891	.|159;189;189;176;206;159;159	.|E9PF04;E9PE64;E9PCQ1;E9PCK8;D6RH31;Q6UXI9-2;Q6UXI9	.|.;.;.;.;.;.;NPNT_HUMAN	P|H	136|55;159;176;189;159;159;189;206	.|ENSP00000426951:Q55H;ENSP00000369323:Q159H;ENSP00000402884:Q176H;ENSP00000389252:Q189H;ENSP00000422044:Q159H;ENSP00000302557:Q159H;ENSP00000422474:Q189H;ENSP00000426146:Q206H	.|ENSP00000302557:Q159H	A|Q	+|+	1|3	0|2	NPNT|NPNT	107078998|107078998	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.935000|0.935000	0.57460|0.57460	3.803000|3.803000	0.55560|0.55560	0.698000|0.698000	0.31739|0.31739	-0.122000|-0.122000	0.15005|0.15005	GCT|CAG	G|0.658;C|0.342	0.342	strong		0.517	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278	
ASGR1	432	hgsc.bcm.edu	37	17	7080316	7080316	+	Silent	SNP	C	C	T	rs55714927	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7080316C>T	ENST00000269299.3	-	4	666	c.267G>A	c.(265-267)aaG>aaA	p.K89K	ASGR1_ENST00000574388.1_Silent_p.K50K|ASGR1_ENST00000380920.4_5'UTR|ASGR1_ENST00000572879.1_5'UTR	NM_001197216.2|NM_001671.4	NP_001184145.1|NP_001662.1	P07306	ASGR1_HUMAN	asialoglycoprotein receptor 1	89					cellular response to extracellular stimulus (GO:0031668)|receptor-mediated endocytosis (GO:0006898)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(1)|urinary_tract(1)	10						TGCTCAAGCCCTTGACCTGGG	0.706													C|||	866	0.172923	0.0469	0.2839	5008	,	,		6394	0.3165		0.1839	False		,,,				2504	0.1053				p.K89K		Atlas-SNP	.											.	ASGR1	20	.	0			c.G267A						PASS	.	C	,	314,4092		8,298,1897	30.0	29.0	29.0		150,267	3.9	0.7	17	dbSNP_129	29	1525,7075		139,1247,2914	no	coding-synonymous,coding-synonymous	ASGR1	NM_001197216.2,NM_001671.4	,	147,1545,4811	TT,TC,CC		17.7326,7.1266,14.1396	,	50/253,89/292	7080316	1839,11167	2203	4300	6503	SO:0001819	synonymous_variant	432	exon4			CAAGCCCTTGACC		CCDS11089.1, CCDS56017.1	17p13-p11	2011-08-30			ENSG00000141505	ENSG00000141505		"""C-type lectin domain containing"""	742	protein-coding gene	gene with protein product		108360					Standard	NM_001671		Approved	CLEC4H1	uc002ges.4	P07306	OTTHUMG00000102159	ENST00000269299.3:c.267G>A	17.37:g.7080316C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	14	0.222222	NM_001671	I3L1X1	Silent	SNP	ENST00000269299.3	37	CCDS11089.1																																																																																			C|0.844;T|0.156	0.156	strong		0.706	ASGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220004.3	NM_001671	
GPSM3	63940	hgsc.bcm.edu	37	6	32159956	32159956	+	Silent	SNP	T	T	C	rs3134605	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32159956T>C	ENST00000375040.3	-	2	506	c.114A>G	c.(112-114)ccA>ccG	p.P38P	GPSM3_ENST00000375043.3_Silent_p.P38P|GPSM3_ENST00000487761.1_Silent_p.P35P|PBX2_ENST00000375050.4_5'Flank	NM_001276501.1	NP_001263430.1	Q9Y4H4	GPSM3_HUMAN	G-protein signaling modulator 3	38	Pro-rich.				regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cytoplasm (GO:0005737)	GDP-dissociation inhibitor activity (GO:0005092)			large_intestine(1)	1						GAGGAGGGGATGGAGGAGCAG	0.627													C|||	1144	0.228435	0.1974	0.1772	5008	,	,		11010	0.2688		0.1918	False		,,,				2504	0.3027				p.P38P		Atlas-SNP	.											GPSM3,colon,carcinoma,0,1	GPSM3	9	1	0			c.A114G						PASS	.	C		812,3594	739.1+/-411.0	76,660,1467	44.0	48.0	47.0		114	-7.0	0.9	6	dbSNP_103	47	1792,6806	727.0+/-406.6	188,1416,2695	yes	coding-synonymous	GPSM3	NM_022107.1		264,2076,4162	CC,CT,TT		20.8421,18.4294,20.0246		38/161	32159956	2604,10400	2203	4299	6502	SO:0001819	synonymous_variant	63940	exon6			AGGGGATGGAGGA	AF155657	CCDS34419.1	6p21.3	2010-06-24	2010-06-24	2004-02-04	ENSG00000213654	ENSG00000213654			13945	protein-coding gene	gene with protein product	"""activator of G-protein signaling 4"""		"""chromosome 6 open reading frame 9"", ""G-protein signalling modulator 3 (AGS3-like, C. elegans)"""	C6orf9		2259622, 15096500	Standard	NM_022107		Approved	NG1, G18, G18.1a, G18.1b, G18.2, AGS4	uc003oaz.3	Q9Y4H4	OTTHUMG00000031244	ENST00000375040.3:c.114A>G	6.37:g.32159956T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	36	0.705882	NM_022107	A2BFJ3	Silent	SNP	ENST00000375040.3	37	CCDS34419.1																																																																																			T|0.814;C|0.186	0.186	strong		0.627	GPSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076509.1	NM_022107	
OR10R2	343406	hgsc.bcm.edu	37	1	158450192	158450192	+	Silent	SNP	C	C	T	rs61741711	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158450192C>T	ENST00000368152.1	+	1	525	c.525C>T	c.(523-525)gcC>gcT	p.A175A	RP11-144L1.4_ENST00000426251.1_RNA|RP11-144L1.4_ENST00000419738.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	175						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(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					GCTTCTTGGCCTCTCTTACAG	0.468													C|||	188	0.0375399	0.0053	0.0562	5008	,	,		20564	0.0		0.0994	False		,,,				2504	0.0429				p.A175A		Atlas-SNP	.											OR10R2,NS,carcinoma,+1,1	OR10R2	81	1	0			c.C525T						PASS	.	C		91,4315	75.2+/-113.4	1,89,2113	124.0	118.0	120.0		525	1.1	0.0	1	dbSNP_129	120	854,7746	194.2+/-239.7	35,784,3481	no	coding-synonymous	OR10R2	NM_001004472.1		36,873,5594	TT,TC,CC		9.9302,2.0654,7.2659		175/336	158450192	945,12061	2203	4300	6503	SO:0001819	synonymous_variant	343406	exon1			CTTGGCCTCTCTT	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"""GPCR / Class A : Olfactory receptors"""	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.525C>T	1.37:g.158450192C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	218	91	0.417431	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Silent	SNP	ENST00000368152.1	37	CCDS30898.1																																																																																			C|0.926;T|0.074	0.074	strong		0.468	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472	
COL12A1	1303	hgsc.bcm.edu	37	6	75848181	75848181	+	Missense_Mutation	SNP	A	A	G	rs240736	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:75848181A>G	ENST00000322507.8	-	29	5522	c.5213T>C	c.(5212-5214)aTt>aCt	p.I1738T	COL12A1_ENST00000416123.2_Missense_Mutation_p.I1738T|COL12A1_ENST00000483888.2_Missense_Mutation_p.I1738T|COL12A1_ENST00000345356.6_Missense_Mutation_p.I574T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	1738	Fibronectin type-III 12. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> T (in dbSNP:rs240736).		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)			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						CTCACTGCCAATCAGGTCATC	0.373													A|||	1327	0.264976	0.3487	0.2911	5008	,	,		19678	0.1548		0.2883	False		,,,				2504	0.2229				p.I1738T		Atlas-SNP	.											.	COL12A1	385	.	0			c.T5213C						PASS	.	A	THR/ILE,THR/ILE	1179,2649		179,821,914	95.0	88.0	90.0		5213,1721	-11.6	0.0	6	dbSNP_79	90	2364,5942		327,1710,2116	yes	missense,missense	COL12A1	NM_004370.5,NM_080645.2	89,89	506,2531,3030	GG,GA,AA		28.4614,30.7994,29.1989	benign,benign	1738/3064,574/1900	75848181	3543,8591	1914	4153	6067	SO:0001583	missense	1303	exon29			CTGCCAATCAGGT	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.5213T>C	6.37:g.75848181A>G	ENSP00000325146:p.Ile1738Thr	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	96	58	0.604167	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	563	0.25778388278388276	169	0.3434959349593496	102	0.281767955801105	86	0.15034965034965034	206	0.2717678100263852	A	6.073	0.381789	0.11524	0.307994	0.284614	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	D;D;D;D	0.86769	-2.13;-2.17;-2.14;-2.11	5.79	-11.6	0.00059	Fibronectin, type III (2);	1.352220	0.04630	N	0.403531	T	0.44138	0.1279	N	0.05306	-0.075	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42103	-0.9471	9	0.12766	T	0.61	.	11.4509	0.50151	0.6276:0.2382:0.1342:0.0	rs240736;rs1758118;rs52807243;rs60846728;rs240736	574;1738	Q99715-2;Q99715	.;COCA1_HUMAN	T	1738;1738;574;1738;1738	ENSP00000325146:I1738T;ENSP00000305147:I574T;ENSP00000412864:I1738T;ENSP00000421216:I1738T	ENSP00000325146:I1738T	I	-	2	0	COL12A1	75904901	0.004000	0.15560	0.002000	0.10522	0.480000	0.33159	0.400000	0.20932	-2.627000	0.00436	-1.074000	0.02243	ATT	A|0.734;G|0.266	0.266	strong		0.373	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511873	99511873	+	Missense_Mutation	SNP	G	G	A	rs2715423	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:99511873G>A	ENST00000378919.6	-	5	630	c.425C>T	c.(424-426)gCg>gTg	p.A142V	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_Missense_Mutation_p.A88V	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	142			A -> V (in dbSNP:rs2715423). {ECO:0000269|PubMed:15489334}.				cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						GATGAGTGCCGCGCAGCCCTT	0.542													G|||	638	0.127396	0.0681	0.183	5008	,	,		19533	0.0794		0.2316	False		,,,				2504	0.1104				p.A142V		Atlas-SNP	.											PGPEP1L,NS,carcinoma,-1,2	PGPEP1L	26	2	0			c.C425T						scavenged	.	G	VAL/ALA,VAL/ALA	370,3622		16,338,1642	27.0	28.0	28.0		425,263	3.2	0.0	15	dbSNP_100	28	2266,6046		309,1648,2199	yes	missense,missense	PGPEP1L	NM_001102612.2,NM_001167902.1	64,64	325,1986,3841	AA,AG,GG		27.2618,9.2685,21.4239	possibly-damaging,possibly-damaging	142/197,88/143	99511873	2636,9668	1996	4156	6152	SO:0001583	missense	145814	exon5			AGTGCCGCGCAGC		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.425C>T	15.37:g.99511873G>A	ENSP00000368199:p.Ala142Val	Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	327	0.14972527472527472	37	0.07520325203252033	72	0.19889502762430938	34	0.05944055944055944	184	0.24274406332453827	G	9.528	1.109957	0.20714	0.092685	0.272618	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.31510	1.49	5.16	3.23	0.37069	.	0.067583	0.56097	D	0.000021	T	0.00012	0.0000	L	0.31157	0.91	0.80722	P	0.0	B	0.26876	0.162	B	0.18561	0.022	T	0.33085	-0.9882	9	0.49607	T	0.09	-16.6381	7.1523	0.25618	0.1471:0.0:0.7136:0.1393	rs2715423;rs60642727;rs2715423	142	A6NFU8	PGPIL_HUMAN	V	142;135	ENSP00000368199:A142V	ENSP00000368199:A142V	A	-	2	0	PGPEP1L	97329396	0.897000	0.30589	0.001000	0.08648	0.002000	0.02628	4.920000	0.63390	0.527000	0.28560	-0.143000	0.13931	GCG	G|0.846;A|0.154	0.154	strong		0.542	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
CSMD1	64478	hgsc.bcm.edu	37	8	2807783	2807783	+	Silent	SNP	G	G	A	rs35043129	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:2807783G>A	ENST00000520002.1	-	68	10842	c.10287C>T	c.(10285-10287)ttC>ttT	p.F3429F	CSMD1_ENST00000400186.3_Silent_p.F3252F|CSMD1_ENST00000542608.1_Silent_p.F3251F|CSMD1_ENST00000602557.1_Silent_p.F3429F|CSMD1_ENST00000537824.1_Silent_p.F3428F|CSMD1_ENST00000602723.1_Silent_p.F3252F			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3429						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)		TGTCATTTTCGAACTTGCTTA	0.428													G|||	776	0.154952	0.2345	0.1311	5008	,	,		18125	0.1319		0.1511	False		,,,				2504	0.092				p.F3428F		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C10284T						PASS	.	G		751,2953		82,587,1183	173.0	172.0	172.0		10284	-0.1	1.0	8	dbSNP_126	172	1018,7164		72,874,3145	no	coding-synonymous	CSMD1	NM_033225.5		154,1461,4328	AA,AG,GG		12.4419,20.2754,14.8831		3428/3565	2807783	1769,10117	1852	4091	5943	SO:0001819	synonymous_variant	64478	exon67			ATTTTCGAACTTG			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.10287C>T	8.37:g.2807783G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		372	0.17032967032967034	132	0.2682926829268293	41	0.1132596685082873	87	0.1520979020979021	112	0.14775725593667546	G	6.388	0.439751	0.12104	0.202754	0.124419	ENSG00000183117	ENST00000335551	.	.	.	5.14	-0.13	0.13498	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999783068	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0882	0.42432	0.6522:0.0:0.3478:0.0	rs35043129;rs56930695	.	.	.	X	2831	.	.	R	-	1	2	CSMD1	2795190	0.999000	0.42202	0.999000	0.59377	0.694000	0.40290	0.880000	0.28159	0.007000	0.14760	-1.062000	0.02293	CGA	G|0.836;A|0.164	0.164	strong		0.428	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
THBS1	7057	hgsc.bcm.edu	37	15	39880277	39880277	+	Silent	SNP	G	G	A	rs35275624	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:39880277G>A	ENST00000260356.5	+	9	1494	c.1329G>A	c.(1327-1329)ccG>ccA	p.P443P		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	443	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		ACTGGTCCCCGTGGTCATCTT	0.522													G|||	181	0.0361422	0.0038	0.0476	5008	,	,		19893	0.002		0.1034	False		,,,				2504	0.0378				p.P443P		Atlas-SNP	.											.	THBS1	106	.	0			c.G1329A						PASS	.	G		108,4292	85.3+/-124.0	1,106,2093	116.0	102.0	107.0		1329	-12.0	0.2	15	dbSNP_126	107	954,7640	207.7+/-249.4	45,864,3388	no	coding-synonymous	THBS1	NM_003246.2		46,970,5481	AA,AG,GG		11.1008,2.4545,8.173		443/1171	39880277	1062,11932	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon9			GTCCCCGTGGTCA		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1329G>A	15.37:g.39880277G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			A|0.072;G|0.928;T|0.000	0.072	strong		0.522	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394613	103394613	+	RNA	SNP	T	T	G	rs9585986	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103394613T>G	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		TGGGAAACTGTTATTCTTTTT	0.368													G|||	3479	0.694688	0.5424	0.7493	5008	,	,		21477	0.5913		0.827	False		,,,				2504	0.8323				p.T2812P		Atlas-SNP	.											.	.	.	.	0			c.A8434C						PASS	.	G	PRO/THR	775,609		217,341,134	179.0	137.0	150.0		8434	2.2	0.0	13	dbSNP_119	150	2544,636		1024,496,70	yes	missense	CCDC168	NM_001146197.1	38	1241,837,204	GG,GT,TT		20.0,44.0029,27.2787		2812/7082	103394613	3319,1245	692	1590	2282			643677	exon4			AAACTGTTATTCT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103394613T>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				T|0.304;G|0.696	0.696	strong		0.368	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
FYCO1	79443	hgsc.bcm.edu	37	3	46009487	46009487	+	Missense_Mutation	SNP	G	G	A	rs33910087	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46009487G>A	ENST00000296137.2	-	8	1544	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C	FYCO1_ENST00000535325.1_Missense_Mutation_p.R447C	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	447			R -> C (in dbSNP:rs33910087).		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)		TTCACCAGGCGCTCCAGGCTG	0.622													G|||	542	0.108227	0.0166	0.0591	5008	,	,		17259	0.005		0.1223	False		,,,				2504	0.3589				p.R447C		Atlas-SNP	.											.	FYCO1	115	.	0			c.C1339T						PASS	.	G	CYS/ARG	136,4270	97.6+/-136.3	1,134,2068	133.0	146.0	142.0		1339	-5.4	0.0	3	dbSNP_126	142	948,7652	208.7+/-250.1	49,850,3401	yes	missense	FYCO1	NM_024513.2	180	50,984,5469	AA,AG,GG		11.0233,3.0867,8.3346	possibly-damaging	447/1479	46009487	1084,11922	2203	4300	6503	SO:0001583	missense	79443	exon8			CCAGGCGCTCCAG	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.1339C>T	3.37:g.46009487G>A	ENSP00000296137:p.Arg447Cys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	135	0.061813186813186816	9	0.018292682926829267	19	0.052486187845303865	0	0.0	107	0.14116094986807387	G	7.220	0.597222	0.13875	0.030867	0.110233	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21543	2.0;2.03	5.14	-5.38	0.02673	.	1.186910	0.05604	N	0.576849	T	0.00109	0.0003	L	0.44542	1.39	0.80722	P	0.0	P;P	0.52463	0.712;0.953	B;B	0.38712	0.216;0.28	T	0.14980	-1.0453	9	0.66056	D	0.02	0.1586	0.9601	0.01393	0.2509:0.3417:0.1553:0.2521	rs33910087	447;447	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	C	447	ENSP00000296137:R447C;ENSP00000441178:R447C	ENSP00000296137:R447C	R	-	1	0	FYCO1	45984491	0.000000	0.05858	0.001000	0.08648	0.201000	0.24016	-0.006000	0.12833	-0.676000	0.05238	-0.345000	0.07892	CGC	G|0.916;A|0.084	0.084	strong		0.622	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
VNN1	8876	hgsc.bcm.edu	37	6	133015271	133015271	+	Missense_Mutation	SNP	T	T	C	rs2272996	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:133015271T>C	ENST00000367928.4	-	3	405	c.392A>G	c.(391-393)aAc>aGc	p.N131S		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	131	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		N -> S (in dbSNP:rs2272996). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		ATAGATAGAGTTGTTCTTGGC	0.433													T|||	1332	0.265974	0.1725	0.1916	5008	,	,		17060	0.3621		0.2972	False		,,,				2504	0.3139				p.N131S		Atlas-SNP	.											.	VNN1	69	.	0			c.A392G						PASS	.	T	SER/ASN	840,3566	331.8+/-302.1	84,672,1447	141.0	128.0	132.0		392	6.1	0.4	6	dbSNP_100	132	2320,6280	388.5+/-342.6	309,1702,2289	yes	missense	VNN1	NM_004666.2	46	393,2374,3736	CC,CT,TT		26.9767,19.0649,24.2965	probably-damaging	131/514	133015271	3160,9846	2203	4300	6503	SO:0001583	missense	8876	exon3			ATAGAGTTGTTCT	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.392A>G	6.37:g.133015271T>C	ENSP00000356905:p.Asn131Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	189	98	0.518519	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	597	0.2733516483516483	91	0.18495934959349594	62	0.1712707182320442	216	0.3776223776223776	228	0.3007915567282322	T	19.74	3.883832	0.72410	0.190649	0.269767	ENSG00000112299	ENST00000367928	D	0.85861	-2.04	6.07	6.07	0.98685	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.064498	0.64402	D	0.000007	D	0.89646	0.6775	M	0.68728	2.09	0.26675	P	0.9716475	D	0.67145	0.996	D	0.72075	0.976	D	0.89228	0.3575	9	0.44086	T	0.13	-24.5999	16.6277	0.84984	0.0:0.0:0.0:1.0	rs2272996;rs60821439;rs2272996	131	O95497	VNN1_HUMAN	S	131	ENSP00000356905:N131S	ENSP00000356905:N131S	N	-	2	0	VNN1	133056964	1.000000	0.71417	0.443000	0.26883	0.833000	0.47200	3.909000	0.56363	2.330000	0.79161	0.528000	0.53228	AAC	T|0.736;C|0.264	0.264	strong		0.433	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
SLC7A1	6541	hgsc.bcm.edu	37	13	30107067	30107067	+	Silent	SNP	G	G	C	rs2277451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:30107067G>C	ENST00000380752.5	-	4	809	c.423C>G	c.(421-423)ggC>ggG	p.G141G		NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	141					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)	p.G141G(1)		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)	CGATGGGTCTGCCTATCAGCT	0.552													G|||	1246	0.248802	0.152	0.2723	5008	,	,		17784	0.6052		0.0517	False		,,,				2504	0.1984				p.G141G		Atlas-SNP	.											SLC7A1,NS,carcinoma,0,1	SLC7A1	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C423G						scavenged	.	G		650,3756	276.0+/-272.9	46,558,1599	85.0	81.0	82.0		423	2.0	1.0	13	dbSNP_100	82	462,8138	137.6+/-194.5	14,434,3852	no	coding-synonymous	SLC7A1	NM_003045.4		60,992,5451	CC,CG,GG		5.3721,14.7526,8.5499		141/630	30107067	1112,11894	2203	4300	6503	SO:0001819	synonymous_variant	6541	exon4			GGGTCTGCCTATC	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.423C>G	13.37:g.30107067G>C		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_003045	Q5JR50	Silent	SNP	ENST00000380752.5	37	CCDS9333.1																																																																																			G|0.860;C|0.140	0.140	strong		0.552	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045	
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 GAIIx	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	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	42	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	
EPHB1	2047	hgsc.bcm.edu	37	3	134670524	134670524	+	Silent	SNP	C	C	T	rs7644369	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:134670524C>T	ENST00000398015.3	+	3	805	c.435C>T	c.(433-435)agC>agT	p.S145S	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	145	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CAGATGAGAGCTTCTCCCAGG	0.498													C|||	2411	0.48143	0.6377	0.5692	5008	,	,		19990	0.2123		0.4394	False		,,,				2504	0.5286				p.S145S		Atlas-SNP	.											.	EPHB1	519	.	0			c.C435T						PASS	.	C		2277,1677		699,879,399	154.0	152.0	153.0		435	4.6	1.0	3	dbSNP_116	153	3757,4657		844,2069,1294	no	coding-synonymous	EPHB1	NM_004441.4		1543,2948,1693	TT,TC,CC		44.6518,42.4127,48.7872		145/985	134670524	6034,6334	1977	4207	6184	SO:0001819	synonymous_variant	2047	exon3			TGAGAGCTTCTCC	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.435C>T	3.37:g.134670524C>T		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	185	181	0.978378	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																			C|0.559;T|0.441	0.441	strong		0.498	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
SCN9A	6335	hgsc.bcm.edu	37	2	167144995	167144995	+	Silent	SNP	T	T	C	rs13402180	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:167144995T>C	ENST00000409435.1	-	9	1265	c.1266A>G	c.(1264-1266)gaA>gaG	p.E422E	SCN9A_ENST00000375387.4_Silent_p.E423E|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.E423E|SCN9A_ENST00000409672.1_Silent_p.E422E			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	422					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTGTTGAAATTCTAATTCTT	0.363													T|||	1775	0.354433	0.357	0.3242	5008	,	,		14756	0.3065		0.4036	False		,,,				2504	0.3712				p.E422E		Atlas-SNP	.											.	SCN9A	296	.	0			c.A1266G						PASS	.	T		1403,2275		281,841,717	143.0	150.0	148.0		1266	4.6	1.0	2	dbSNP_121	148	3184,5004		600,1984,1510	no	coding-synonymous	SCN9A	NM_002977.3		881,2825,2227	CC,CT,TT		38.8862,38.1457,38.6567		422/1978	167144995	4587,7279	1839	4094	5933	SO:0001819	synonymous_variant	6335	exon10			TTGAAATTCTAAT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1266A>G	2.37:g.167144995T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	55	36	0.654545	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			C|0.338;T|0.662	0.338	strong		0.363	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
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 GAIIx	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		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	113	61	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		
TLE6	79816	hgsc.bcm.edu	37	19	2994921	2994921	+	Silent	SNP	G	G	A	rs34551565	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:2994921G>A	ENST00000246112.4	+	17	1839	c.1638G>A	c.(1636-1638)acG>acA	p.T546T	TLE6_ENST00000452088.1_Silent_p.T423T	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	546					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				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)		CTCCAGTCACGTGCTGTGACG	0.622													G|||	1456	0.290735	0.3495	0.3329	5008	,	,		11993	0.3343		0.2266	False		,,,				2504	0.2025				p.T546T		Atlas-SNP	.											.	TLE6	68	.	0			c.G1638A						PASS	.	G	,	1371,3035	427.6+/-341.6	234,903,1066	75.0	48.0	57.0		1638,1269	0.4	0.1	19	dbSNP_126	57	1860,6740	302.9+/-306.2	200,1460,2640	no	coding-synonymous,coding-synonymous	TLE6	NM_001143986.1,NM_024760.2	,	434,2363,3706	AA,AG,GG		21.6279,31.1167,24.8424	,	546/573,423/450	2994921	3231,9775	2203	4300	6503	SO:0001819	synonymous_variant	79816	exon17			AGTCACGTGCTGT	AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"""WD repeat domain containing"""	30788	protein-coding gene	gene with protein product		612399	"""transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"""			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.1638G>A	19.37:g.2994921G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_001143986	J3KMZ1	Silent	SNP	ENST00000246112.4	37	CCDS45910.1																																																																																			G|0.736;A|0.264	0.264	strong		0.622	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760	
CATSPERD	257062	hgsc.bcm.edu	37	19	5772950	5772950	+	Missense_Mutation	SNP	G	G	A	rs61180947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5772950G>A	ENST00000381624.3	+	20	1976	c.1915G>A	c.(1915-1917)Ggg>Agg	p.G639R	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	639					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											AAAGGAATTCGGGGGGCCCTT	0.582													G|||	1150	0.229633	0.0098	0.3905	5008	,	,		16949	0.3839		0.2356	False		,,,				2504	0.2474				p.G639R		Atlas-SNP	.											.	.	.	.	0			c.G1915A						PASS	.	G	ARG/GLY	193,3609		5,183,1713	47.0	51.0	50.0		1915	1.6	0.0	19	dbSNP_129	50	1791,6429		202,1387,2521	yes	missense	TMEM146	NM_152784.3	125	207,1570,4234	AA,AG,GG		21.7883,5.0763,16.5031	probably-damaging	639/799	5772950	1984,10038	1901	4110	6011	SO:0001583	missense	257062	exon20			GAATTCGGGGGGC	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.1915G>A	19.37:g.5772950G>A	ENSP00000371037:p.Gly639Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	579	0.2651098901098901	7	0.014227642276422764	135	0.3729281767955801	244	0.42657342657342656	193	0.2546174142480211	G	9.822	1.186111	0.21870	0.050763	0.217883	ENSG00000174898	ENST00000381624;ENST00000381613	T	0.25085	1.82	2.73	1.63	0.23807	.	1.526280	0.04359	N	0.357052	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	D	0.76494	0.999	P	0.54924	0.764	T	0.36768	-0.9734	9	0.42905	T	0.14	-3.1778	7.393	0.26921	0.0:0.2719:0.7281:0.0	rs61180947	639	Q86XM0	TM146_HUMAN	R	639;308	ENSP00000371037:G639R	ENSP00000371026:G308R	G	+	1	0	TMEM146	5723950	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.637000	0.24659	0.676000	0.31285	0.561000	0.74099	GGG	G|0.749;A|0.251	0.251	strong		0.582	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
C14orf182	283551	hgsc.bcm.edu	37	14	50472405	50472405	+	Missense_Mutation	SNP	G	G	A	rs6572635	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:50472405G>A	ENST00000399206.1	-	1	1833	c.113C>T	c.(112-114)cCg>cTg	p.P38L	C14orf182_ENST00000529902.1_5'UTR	NM_001012706.1	NP_001012724.1	A1A4T8	CN182_HUMAN	chromosome 14 open reading frame 182	38			P -> L (in dbSNP:rs6572635).							large_intestine(2)|urinary_tract(1)	3						AAGACCTCTCGGTTCGTGAAT	0.537													G|||	1481	0.295727	0.3873	0.317	5008	,	,		18805	0.124		0.2773	False		,,,				2504	0.3528				p.P38L		Atlas-SNP	.											C14orf182,bladder,carcinoma,+1,1	C14orf182	8	1	0			c.C113T						PASS	.	G	LEU/PRO	1523,2561		289,945,808	269.0	286.0	281.0		113	1.7	0.0	14	dbSNP_116	281	2240,6136		301,1638,2249	yes	missense	C14orf182	NM_001012706.1	98	590,2583,3057	AA,AG,GG		26.7431,37.2919,30.2006	probably-damaging	38/108	50472405	3763,8697	2042	4188	6230	SO:0001583	missense	283551	exon1			CCTCTCGGTTCGT	AK090420	CCDS41949.1	14q22.1	2009-02-24			ENSG00000214900	ENSG00000214900			27503	protein-coding gene	gene with protein product							Standard	NM_001012706		Approved		uc001wxi.1	A1A4T8		ENST00000399206.1:c.113C>T	14.37:g.50472405G>A	ENSP00000382157:p.Pro38Leu	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	165	82	0.49697	NM_001012706	A8MYX4	Missense_Mutation	SNP	ENST00000399206.1	37	CCDS41949.1	555	0.2541208791208791	165	0.3353658536585366	106	0.292817679558011	79	0.1381118881118881	205	0.2704485488126649	G	10.57	1.385916	0.25031	0.372919	0.267431	ENSG00000214900	ENST00000399206	T	0.62639	0.01	3.63	1.72	0.24424	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.36412	0.552	B	0.28916	0.096	T	0.29427	-1.0012	7	0.87932	D	0	.	4.3609	0.11201	0.1184:0.0:0.6603:0.2213	rs6572635;rs56709337;rs6572635	38	A1A4T8-2	.	L	38	ENSP00000382157:P38L	ENSP00000382157:P38L	P	-	2	0	C14orf182	49542155	0.050000	0.20438	0.004000	0.12327	0.014000	0.08584	0.925000	0.28791	0.492000	0.27815	-0.263000	0.10527	CCG	G|0.739;A|0.261	0.261	strong		0.537	C14orf182-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395717.1	NM_001012706	
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 GAIIx	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_ENST00000422223.2_Silent_p.Y2086Y|FREM1_ENST00000380894.1_Silent_p.Y622Y|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		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	64	32	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	
RBM19	9904	hgsc.bcm.edu	37	12	114383651	114383651	+	Silent	SNP	C	C	T	rs12321179	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:114383651C>T	ENST00000545145.2	-	13	1686	c.1608G>A	c.(1606-1608)aaG>aaA	p.K536K	RBM19_ENST00000392561.3_Silent_p.K536K|RBM19_ENST00000261741.5_Silent_p.K536K	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	536					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.K536K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					ACACTTGACTCTTGGTGGCGT	0.552													C|||	994	0.198482	0.3472	0.0764	5008	,	,		22010	0.1885		0.1133	False		,,,				2504	0.182				p.K536K		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - coding silent(1)	stomach(1)	c.G1608A						PASS	.	C	,,	1440,2966	466.0+/-354.4	254,932,1017	161.0	119.0	133.0		1608,1608,1608	3.8	1.0	12	dbSNP_120	133	887,7713	199.4+/-243.5	39,809,3452	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	293,1741,4469	TT,TC,CC		10.314,32.6827,17.8917	,,	536/961,536/961,536/961	114383651	2327,10679	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon13			TTGACTCTTGGTG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1608G>A	12.37:g.114383651C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			C|0.823;T|0.177	0.177	strong		0.552	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
SPTBN5	51332	hgsc.bcm.edu	37	15	42145936	42145936	+	Missense_Mutation	SNP	G	G	C	rs1197660	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42145936G>C	ENST00000320955.6	-	58	10051	c.9824C>G	c.(9823-9825)gCc>gGc	p.A3275G	RNA5SP393_ENST00000363423.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	3275			A -> G (in dbSNP:rs1197660).		actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CAGTCGGCAGGCCTCCGTCTG	0.672													G|||	1474	0.294329	0.4523	0.2349	5008	,	,		16740	0.0337		0.3489	False		,,,				2504	0.3354				p.A3240G		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C9719G						PASS	.	G	GLY/ALA	1691,2325		388,915,705	24.0	29.0	27.0		9719	2.9	0.1	15	dbSNP_87	27	2801,5507		502,1797,1855	yes	missense	SPTBN5	NM_016642.2	60	890,2712,2560	CC,CG,GG		33.7145,42.1066,36.4492	possibly-damaging	3240/3640	42145936	4492,7832	2008	4154	6162	SO:0001583	missense	51332	exon58			CGGCAGGCCTCCG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.9824C>G	15.37:g.42145936G>C	ENSP00000317790:p.Ala3275Gly	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		575	0.2632783882783883	217	0.4410569105691057	89	0.24585635359116023	14	0.024475524475524476	255	0.33641160949868076	.	14.97	2.695561	0.48202	0.421066	0.337145	ENSG00000137877	ENST00000320955	T	0.34472	1.36	4.74	2.86	0.33363	.	0.298852	0.27117	N	0.020856	T	0.00012	0.0000	M	0.76002	2.32	0.49687	P	1.8300000000004424E-4	P	0.37061	0.58	B	0.38683	0.279	T	0.46162	-0.9211	9	0.22109	T	0.4	.	9.1685	0.37065	0.1688:0.0:0.8312:0.0	rs1197660;rs1197660	3275	Q9NRC6	SPTN5_HUMAN	G	3275	ENSP00000317790:A3275G	ENSP00000317790:A3275G	A	-	2	0	SPTBN5	39933228	0.909000	0.30893	0.146000	0.22360	0.058000	0.15608	2.647000	0.46639	0.542000	0.28846	0.313000	0.20887	GCC	G|0.736;C|0.264	0.264	strong		0.672	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
TM4SF19	116211	hgsc.bcm.edu	37	3	196054439	196054439	+	Missense_Mutation	SNP	T	T	G	rs6785339	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:196054439T>G	ENST00000273695.3	-	2	148	c.23A>C	c.(22-24)cAg>cCg	p.Q8P	TM4SF19_ENST00000442633.1_Missense_Mutation_p.Q8P|TM4SF19-AS1_ENST00000452051.1_RNA|TM4SF19_ENST00000454715.1_Missense_Mutation_p.Q8P|TM4SF19_ENST00000446879.1_Missense_Mutation_p.Q8P	NM_001204897.1|NM_138461.3	NP_001191826.1|NP_612470.2	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	8			Q -> P (in dbSNP:rs6785339). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(5)	12	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		TGAGCTTGCCTGCGTGCAGGG	0.602													G|||	3159	0.630791	0.4402	0.6009	5008	,	,		20050	0.871		0.5726	False		,,,				2504	0.7219				p.Q8P		Atlas-SNP	.											TM4SF19,NS,carcinoma,0,1	TM4SF19	21	1	0			c.A23C						PASS	.	G	PRO/GLN,PRO/GLN,PRO/GLN	2112,2294	599.9+/-389.4	524,1064,615	75.0	64.0	68.0		23,23,23	3.1	0.0	3	dbSNP_116	68	4958,3642	522.3+/-380.1	1419,2120,761	yes	missense,missense,missense	TM4SF19	NM_001204897.1,NM_001204898.1,NM_138461.3	76,76,76	1943,3184,1376	GG,GT,TT		42.3488,47.9346,45.6405	benign,benign,benign	8/243,8/184,8/210	196054439	7070,5936	2203	4300	6503	SO:0001583	missense	116211	exon2			CTTGCCTGCGTGC	BC013113	CCDS3316.1, CCDS56299.1	3q29	2005-08-09			ENSG00000145107	ENSG00000145107			25167	protein-coding gene	gene with protein product						12477932	Standard	NM_138461		Approved		uc021xjs.1	Q96DZ7	OTTHUMG00000155675	ENST00000273695.3:c.23A>C	3.37:g.196054439T>G	ENSP00000273695:p.Gln8Pro	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_001204897	B2RV20|E9PH22|Q336K7	Missense_Mutation	SNP	ENST00000273695.3	37	CCDS3316.1	1407	0.6442307692307693	237	0.4817073170731707	222	0.6132596685082873	504	0.8811188811188811	444	0.5857519788918206	G	10.19	1.282160	0.23392	0.479346	0.576512	ENSG00000145107	ENST00000446879;ENST00000454715;ENST00000273695	T;T;T	0.30714	1.88;1.52;1.53	5.58	3.1	0.35709	.	0.984540	0.08285	N	0.969300	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.23226	-1.0194	9	0.41790	T	0.15	0.2119	3.4069	0.07344	0.654:0.0:0.179:0.167	rs6785339;rs17856417;rs52827973;rs60135622;rs6785339	8;8;8	E9PH22;C9JCD5;Q96DZ7	.;.;T4S19_HUMAN	P	8	ENSP00000395280:Q8P;ENSP00000387728:Q8P;ENSP00000273695:Q8P	ENSP00000273695:Q8P	Q	-	2	0	TM4SF19	197538836	0.029000	0.19370	0.005000	0.12908	0.001000	0.01503	0.670000	0.25157	0.407000	0.25591	-1.094000	0.02160	CAG	T|0.414;G|0.586	0.586	strong		0.602	TM4SF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341174.1	NM_138461	
GRIN3A	116443	hgsc.bcm.edu	37	9	104449294	104449294	+	Silent	SNP	G	G	A	rs33945236	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:104449294G>A	ENST00000361820.3	-	2	1488	c.888C>T	c.(886-888)aaC>aaT	p.N296N		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	296					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	TAGCGGTGATGTTGATGATAG	0.483													G|||	614	0.122604	0.0068	0.1902	5008	,	,		19332	0.1716		0.167	False		,,,				2504	0.135				p.N296N		Atlas-SNP	.											GRIN3A,colon,carcinoma,0,1	GRIN3A	186	1	0			c.C888T						scavenged	.	G		155,4251	104.3+/-142.8	6,143,2054	144.0	128.0	133.0		888	2.7	1.0	9	dbSNP_126	133	1457,7143	277.6+/-293.0	125,1207,2968	no	coding-synonymous	GRIN3A	NM_133445.2		131,1350,5022	AA,AG,GG		16.9419,3.5179,12.3943		296/1116	104449294	1612,11394	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon2			GGTGATGTTGATG		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.888C>T	9.37:g.104449294G>A		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	143	59	0.412587	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			G|0.865;A|0.135	0.135	strong		0.483	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
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 GAIIx	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_ENST00000417045.1_Missense_Mutation_p.P494S|CAPRIN2_ENST00000298892.5_Missense_Mutation_p.P494S|CAPRIN2_ENST00000308433.5_Missense_Mutation_p.P161S|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.P494S|CAPRIN2_ENST00000538387.1_5'UTR	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	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	155	92	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	
BEND3	57673	hgsc.bcm.edu	37	6	107391396	107391396	+	Silent	SNP	G	G	A	rs3814073	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:107391396G>A	ENST00000369042.1	-	4	1189	c.999C>T	c.(997-999)aaC>aaT	p.N333N	BEND3_ENST00000429433.2_Silent_p.N333N			Q5T5X7	BEND3_HUMAN	BEN domain containing 3	333	BEN 1. {ECO:0000255|PROSITE- ProRule:PRU00784}.									central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(7)|lung(10)|ovary(4)|prostate(3)	30						TGAAGAAGTCGTTCAGCTGGG	0.647													g|||	1323	0.264177	0.1104	0.3617	5008	,	,		16213	0.4107		0.2038	False		,,,				2504	0.3139				p.N333N		Atlas-SNP	.											.	BEND3	70	.	0			c.C999T						PASS	.	G		535,3851		36,463,1694	13.0	14.0	13.0		999	0.2	1.0	6	dbSNP_107	13	1555,6997		136,1283,2857	no	coding-synonymous	BEND3	NM_001080450.2		172,1746,4551	AA,AG,GG		18.1829,12.1979,16.154		333/829	107391396	2090,10848	2193	4276	6469	SO:0001819	synonymous_variant	57673	exon5			GAAGTCGTTCAGC	AB046773	CCDS34507.1	6q21	2012-11-22	2008-10-03	2008-10-03	ENSG00000178409	ENSG00000178409		"""BEN domain containing"""	23040	protein-coding gene	gene with protein product			"""KIAA1553"""	KIAA1553			Standard	NM_001080450		Approved		uc003prs.2	Q5T5X7	OTTHUMG00000015308	ENST00000369042.1:c.999C>T	6.37:g.107391396G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_001080450	A2RRH2|Q9HCL9	Silent	SNP	ENST00000369042.1	37	CCDS34507.1																																																																																			G|0.783;A|0.217	0.217	strong		0.647	BEND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041686.1	NM_020913	
MMP3	4314	hgsc.bcm.edu	37	11	102713465	102713465	+	Silent	SNP	A	A	G	rs602128	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102713465A>G	ENST00000299855.5	-	2	544	c.288T>C	c.(286-288)gaT>gaC	p.D96D		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	96					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	AGTGACCAACATCAGGAACTC	0.498													G|||	3098	0.61861	0.5499	0.6643	5008	,	,		16797	0.6667		0.5278	False		,,,				2504	0.7229				p.D96D		Atlas-SNP	.											MMP3,NS,carcinoma,0,1	MMP3	60	1	0			c.T288C						PASS	.	G		2375,2031	563.8+/-381.3	636,1103,464	73.0	66.0	68.0		288	-12.1	0.0	11	dbSNP_83	68	4301,4297	577.9+/-390.6	1066,2169,1064	no	coding-synonymous	MMP3	NM_002422.3		1702,3272,1528	GG,GA,AA		49.9767,46.0962,48.662		96/478	102713465	6676,6328	2203	4299	6502	SO:0001819	synonymous_variant	4314	exon2			ACCAACATCAGGA	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.288T>C	11.37:g.102713465A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Silent	SNP	ENST00000299855.5	37	CCDS8323.1																																																																																			A|0.461;G|0.539	0.539	strong		0.498	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
OR6K3	391114	hgsc.bcm.edu	37	1	158687163	158687163	+	Missense_Mutation	SNP	G	G	A	rs28568406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158687163G>A	ENST00000368146.1	-	1	790	c.791C>T	c.(790-792)cCg>cTg	p.P264L	OR6K3_ENST00000368145.1_Missense_Mutation_p.P248L			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	264			P -> L (in dbSNP:rs28568406). {ECO:0000269|PubMed:14983052}.			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)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					AAAGAATATCGGGAAGACCAT	0.453													A|||	1948	0.388978	0.4773	0.4323	5008	,	,		22981	0.4474		0.3966	False		,,,				2504	0.1708				p.P248L		Atlas-SNP	.											.	OR6K3	101	.	0			c.C743T						PASS	.	A	LEU/PRO	2096,2310	603.5+/-390.1	496,1104,603	131.0	112.0	118.0		743	3.8	0.0	1	dbSNP_125	118	3256,5344	649.7+/-400.6	613,2030,1657	yes	missense	OR6K3	NM_001005327.2	98	1109,3134,2260	AA,AG,GG		37.8605,47.5715,41.1502	benign	248/316	158687163	5352,7654	2203	4300	6503	SO:0001583	missense	391114	exon1			AATATCGGGAAGA	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.791C>T	1.37:g.158687163G>A	ENSP00000357128:p.Pro264Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	85	50	0.588235	NM_001005327	Q5VUV0|Q6IFR5	Missense_Mutation	SNP	ENST00000368146.1	37		913	0.41804029304029305	225	0.4573170731707317	152	0.4198895027624309	238	0.4160839160839161	298	0.39313984168865435	A	1.380	-0.583678	0.03827	0.475715	0.378605	ENSG00000203757	ENST00000368145;ENST00000368146	T;T	0.32988	1.43;1.43	3.77	3.77	0.43336	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01092	0.0036	N	0.00022	-2.74	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.43196	-0.9406	8	0.07325	T	0.83	.	8.466	0.32956	0.9021:0.0:0.0979:0.0	rs28568406;rs52822126;rs57495154	264	Q8NGY3	OR6K3_HUMAN	L	248;264	ENSP00000357127:P248L;ENSP00000357128:P264L	ENSP00000357127:P248L	P	-	2	0	OR6K3	156953787	0.000000	0.05858	0.001000	0.08648	0.446000	0.32137	0.037000	0.13840	0.606000	0.29965	-0.516000	0.04426	CCG	G|0.585;A|0.415	0.415	strong		0.453	OR6K3-201	KNOWN	basic	protein_coding	protein_coding			
LCP2	3937	hgsc.bcm.edu	37	5	169693858	169693858	+	Silent	SNP	G	G	A	rs56262228	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:169693858G>A	ENST00000046794.5	-	10	1341	c.726C>T	c.(724-726)ccC>ccT	p.P242P	LCP2_ENST00000521416.1_Silent_p.P37P	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	242					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		AACGATCTAGGGGAGGTTTCG	0.448													G|||	227	0.0453275	0.0431	0.0432	5008	,	,		19665	0.0308		0.0398	False		,,,				2504	0.0706				p.P242P		Atlas-SNP	.											.	LCP2	133	.	0			c.C726T						PASS	.	G		193,3567		8,177,1695	231.0	228.0	229.0		726	1.4	0.5	5	dbSNP_129	229	363,7835		12,339,3748	no	coding-synonymous	LCP2	NM_005565.3		20,516,5443	AA,AG,GG		4.4279,5.133,4.6496		242/534	169693858	556,11402	1880	4099	5979	SO:0001819	synonymous_variant	3937	exon10			ATCTAGGGGAGGT		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.726C>T	5.37:g.169693858G>A		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	179	84	0.469274	NM_005565	A8KA25|Q53XV4	Silent	SNP	ENST00000046794.5	37	CCDS47339.1																																																																																			G|0.960;A|0.040	0.040	strong		0.448	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
CAD	790	hgsc.bcm.edu	37	2	27460968	27460968	+	Silent	SNP	A	A	G	rs1141313	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27460968A>G	ENST00000403525.1	+	29	4728	c.4584A>G	c.(4582-4584)gcA>gcG	p.A1528A	CAD_ENST00000264705.4_Silent_p.A1591A			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGCTCACGCAGAGCAGCAAA	0.557													G|||	2277	0.454673	0.8374	0.4683	5008	,	,		21934	0.1488		0.2883	False		,,,				2504	0.4141				p.A1591A		Atlas-SNP	.											CAD,NS,carcinoma,+1,1	CAD	199	1	0			c.A4773G						PASS	.	G		3287,1119	398.1+/-330.7	1233,821,149	102.0	95.0	98.0		4773	-9.6	0.5	2	dbSNP_86	98	2564,6036	690.7+/-404.5	377,1810,2113	no	coding-synonymous	CAD	NM_004341.3		1610,2631,2262	GG,GA,AA		29.814,25.3972,44.9869		1591/2226	27460968	5851,7155	2203	4300	6503	SO:0001819	synonymous_variant	790	exon30			TCACGCAGAGCAG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.4584A>G	2.37:g.27460968A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	144	84	0.583333	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37		825	0.37774725274725274	400	0.8130081300813008	152	0.4198895027624309	64	0.11188811188811189	209	0.2757255936675462	G	0.885	-0.727540	0.03158	0.746028	0.29814	ENSG00000084774	ENST00000458503	.	.	.	4.8	-9.6	0.00553	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999980619	.	.	.	.	.	.	T	0.20306	-1.0279	3	.	.	.	-0.1691	2.9165	0.05754	0.3979:0.2642:0.2509:0.0869	rs1141313;rs17855322;rs58779686;rs1141313	.	.	.	R	243	.	.	Q	+	2	0	CAD	27314472	0.000000	0.05858	0.529000	0.27951	0.107000	0.19398	-4.974000	0.00164	-2.338000	0.00627	-1.195000	0.01675	CAG	A|0.568;G|0.432	0.432	strong		0.557	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
DNAH8	1769	hgsc.bcm.edu	37	6	38729511	38729511	+	Missense_Mutation	SNP	T	T	C	rs61748600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:38729511T>C	ENST00000359357.3	+	9	1152	c.898T>C	c.(898-900)Tat>Cat	p.Y300H	DNAH8_ENST00000441566.1_Missense_Mutation_p.Y300H|DNAH8_ENST00000449981.2_Missense_Mutation_p.Y517H			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	300					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						ATGTAAAGCATATATTACTGA	0.264													T|||	420	0.0838658	0.0469	0.2334	5008	,	,		14654	0.0198		0.1372	False		,,,				2504	0.0389				p.Y517H		Atlas-SNP	.											.	DNAH8	1239	.	0			c.T1549C						PASS	.	T	HIS/TYR	279,4127	155.5+/-188.7	8,263,1932	82.0	85.0	84.0		1549	6.0	1.0	6	dbSNP_129	84	1313,7285	257.7+/-281.7	96,1121,3082	yes	missense	DNAH8	NM_001206927.1	83	104,1384,5014	CC,CT,TT		15.271,6.3323,12.2424	benign	517/4708	38729511	1592,11412	2203	4299	6502	SO:0001583	missense	1769	exon11			AAAGCATATATTA	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.898T>C	6.37:g.38729511T>C	ENSP00000352312:p.Tyr300His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	157	129	0.821656	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		226	0.10347985347985347	26	0.052845528455284556	78	0.2154696132596685	14	0.024475524475524476	108	0.1424802110817942	T	21.2	4.114753	0.77210	0.063323	0.15271	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.58210	0.35;0.35;0.35	6.0	6.0	0.97389	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.46870	0.1415	L	0.58428	1.81	0.09310	P	0.99999613319	B	0.33857	0.429	P	0.44772	0.46	T	0.51857	-0.8652	9	0.35671	T	0.21	.	14.0315	0.64617	0.0:0.0:0.0:1.0	rs61748600	300	Q96JB1	DYH8_HUMAN	H	505;505;300;300	ENSP00000333363:Y505H;ENSP00000352312:Y300H;ENSP00000402294:Y300H	ENSP00000333363:Y505H	Y	+	1	0	DNAH8	38837489	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	4.287000	0.59001	2.297000	0.77311	0.519000	0.50382	TAT	T|0.879;C|0.121	0.121	strong		0.264	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
COL16A1	1307	hgsc.bcm.edu	37	1	32127953	32127953	+	Silent	SNP	G	G	A	rs2271928	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:32127953G>A	ENST00000373672.3	-	58	4179	c.3663C>T	c.(3661-3663)gaC>gaT	p.D1221D	RP11-73M7.6_ENST00000609033.1_RNA|RP11-73M7.6_ENST00000591592.1_RNA|RP11-73M7.6_ENST00000588288.1_RNA|COL16A1_ENST00000271069.6_Silent_p.D1221D|RP11-73M7.6_ENST00000608332.1_RNA|RP11-73M7.6_ENST00000609338.1_RNA|RP11-73M7.6_ENST00000585660.1_RNA|RP11-73M7.6_ENST00000589462.1_RNA|RP11-73M7.6_ENST00000609625.1_RNA|RP11-73M7.6_ENST00000445166.1_RNA|RP11-73M7.6_ENST00000607926.1_RNA|RP11-73M7.6_ENST00000609549.1_RNA|RP11-73M7.6_ENST00000585413.1_RNA|RP11-73M7.6_ENST00000608246.1_RNA|RP11-73M7.6_ENST00000609373.1_RNA|RP11-73M7.6_ENST00000591929.1_RNA|RP11-73M7.6_ENST00000608888.1_RNA|RP11-73M7.6_ENST00000610216.1_RNA|RP11-73M7.6_ENST00000610043.1_RNA|RP11-73M7.6_ENST00000587445.1_RNA|RP11-73M7.6_ENST00000593188.1_RNA	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1221	Triple-helical region 2 (COL2) with 2 imperfections.				cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|female pregnancy (GO:0007565)|integrin-mediated signaling pathway (GO:0007229)	collagen type XVI trimer (GO:0005597)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(15)|ovary(8)|prostate(4)	48		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0423)|all_neural(195;0.0837)|Breast(348;0.116)		STAD - Stomach adenocarcinoma(196;0.059)		CAGGCTTGCCGTCCTTCCCAT	0.612													G|||	2363	0.471845	0.5174	0.4741	5008	,	,		14434	0.6369		0.4016	False		,,,				2504	0.3108				p.D1221D	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.C3663T						PASS	.	G		1855,2017		441,973,522	40.0	43.0	42.0		3663	-2.8	1.0	1	dbSNP_100	42	3290,4958		658,1974,1492	no	coding-synonymous	COL16A1	NM_001856.3		1099,2947,2014	AA,AG,GG		39.8885,47.9081,42.4505		1221/1605	32127953	5145,6975	1936	4124	6060	SO:0001819	synonymous_variant	1307	exon58			CTTGCCGTCCTTC	M92642	CCDS41297.1	1p35-p34	2013-01-16			ENSG00000084636	ENSG00000084636		"""Collagens"""	2193	protein-coding gene	gene with protein product		120326				1631157	Standard	NM_001856		Approved		uc001btk.1	Q07092	OTTHUMG00000003883	ENST00000373672.3:c.3663C>T	1.37:g.32127953G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																			G|0.511;A|0.489	0.489	strong		0.612	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856	
TM4SF4	7104	hgsc.bcm.edu	37	3	149192676	149192676	+	Silent	SNP	G	G	A	rs12488126	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:149192676G>A	ENST00000305354.4	+	1	916	c.12G>A	c.(10-12)ggG>ggA	p.G4G		NM_004617.3	NP_004608.1	P48230	T4S4_HUMAN	transmembrane 4 L six family member 4	4					tissue regeneration (GO:0042246)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)|ovary(1)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TGTGCACTGGGGGCTGTGCCA	0.532													G|||	945	0.188698	0.0514	0.3602	5008	,	,		18015	0.0208		0.4066	False		,,,				2504	0.2014				p.G4G		Atlas-SNP	.											.	TM4SF4	27	.	0			c.G12A						PASS	.	G		382,3480		24,334,1573	59.0	62.0	61.0		12	-0.5	0.0	3	dbSNP_120	61	3223,5043		631,1961,1541	no	coding-synonymous	TM4SF4	NM_004617.3		655,2295,3114	AA,AG,GG		38.991,9.8912,29.7246		4/203	149192676	3605,8523	1931	4133	6064	SO:0001819	synonymous_variant	7104	exon1			CACTGGGGGCTGT		CCDS46932.1	3q25	2005-03-21	2005-03-21		ENSG00000169903	ENSG00000169903			11856	protein-coding gene	gene with protein product		606567	"""transmembrane 4 superfamily member 4"""			7665614	Standard	NM_004617		Approved	il-TMP	uc003exd.2	P48230	OTTHUMG00000159619	ENST00000305354.4:c.12G>A	3.37:g.149192676G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_004617	B2RDA4	Silent	SNP	ENST00000305354.4	37	CCDS46932.1																																																																																			G|0.791;A|0.209	0.209	strong		0.532	TM4SF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356528.1		
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 GAIIx	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	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	103	57	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	
CAB39L	81617	hgsc.bcm.edu	37	13	49951142	49951142	+	Silent	SNP	T	T	C	rs8002829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:49951142T>C	ENST00000355854.4	-	3	734	c.237A>G	c.(235-237)ctA>ctG	p.L79L	CAB39L_ENST00000347776.5_Silent_p.L79L|CAB39L_ENST00000410043.1_Silent_p.L79L|CAB39L_ENST00000409308.1_Silent_p.L79L	NM_030925.2	NP_112187.2	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	79					cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(4)|lung(3)|pancreas(1)|stomach(1)	12		Lung NSC(96;2.11e-05)|Breast(56;0.00017)|Prostate(109;0.00314)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.66e-09)|COAD - Colon adenocarcinoma(199;0.226)		TCAGTGTCACTAGCAGGCCAC	0.438													C|||	2483	0.495807	0.7436	0.4784	5008	,	,		15683	0.1448		0.5139	False		,,,				2504	0.5164				p.L79L		Atlas-SNP	.											.	CAB39L	35	.	0			c.A237G						PASS	.	C	,	3193,1213	422.8+/-339.9	1159,875,169	115.0	109.0	111.0		237,237	3.6	1.0	13	dbSNP_116	111	4369,4231	572.1+/-389.6	1136,2097,1067	no	coding-synonymous,coding-synonymous	CAB39L	NM_001079670.1,NM_030925.2	,	2295,2972,1236	CC,CT,TT		49.1977,27.5306,41.8576	,	79/338,79/338	49951142	7562,5444	2203	4300	6503	SO:0001819	synonymous_variant	81617	exon3			TGTCACTAGCAGG	AK022639	CCDS9416.2	13q14.11	2008-02-05			ENSG00000102547	ENSG00000102547			20290	protein-coding gene	gene with protein product		612175					Standard	NM_030925		Approved	bA103J18.3, FLJ12577, MO2L	uc001vcw.3	Q9H9S4	OTTHUMG00000016914	ENST00000355854.4:c.237A>G	13.37:g.49951142T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	160	94	0.5875	NM_030925	Q5TAW6|Q6WG71|Q96FG1|Q9BZ33	Silent	SNP	ENST00000355854.4	37	CCDS9416.2																																																																																			T|0.457;C|0.543	0.543	strong		0.438	CAB39L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044908.3	NM_030925	
ANO4	121601	hgsc.bcm.edu	37	12	101520689	101520689	+	Silent	SNP	A	A	G	rs1055734	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:101520689A>G	ENST00000392977.3	+	27	2919	c.2709A>G	c.(2707-2709)tcA>tcG	p.S903S	ANO4_ENST00000299222.9_Silent_p.S423S|ANO4_ENST00000550015.1_Silent_p.S423S|ANO4_ENST00000392979.3_Silent_p.S868S			Q32M45	ANO4_HUMAN	anoctamin 4	903					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						ACCTCATTTCATATCTGATCC	0.443										HNSCC(74;0.22)			A|||	737	0.147165	0.0968	0.1182	5008	,	,		23218	0.1895		0.1302	False		,,,				2504	0.2096				p.S868S		Atlas-SNP	.											ANO4,NS,carcinoma,+1,1	ANO4	183	1	0			c.A2604G						scavenged	.	A		469,3937	222.6+/-239.4	26,417,1760	100.0	90.0	94.0		2604	-2.5	1.0	12	dbSNP_86	94	1317,7283	259.8+/-282.9	97,1123,3080	no	coding-synonymous	ANO4	NM_178826.3		123,1540,4840	GG,GA,AA		15.314,10.6446,13.7321		868/921	101520689	1786,11220	2203	4300	6503	SO:0001819	synonymous_variant	121601	exon26			CATTTCATATCTG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	23837	protein-coding gene	gene with protein product		610111	"""transmembrane protein 16D"""	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.2709A>G	12.37:g.101520689A>G		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	214	92	0.429907	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	37																																																																																				A|0.860;G|0.140	0.140	strong		0.443	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	
WFIKKN1	117166	hgsc.bcm.edu	37	16	681284	681284	+	Silent	SNP	C	C	T	rs8062289	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:681284C>T	ENST00000319070.2	+	1	353	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	11					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)				CCTGCCGCTCCTGCTCCTCCT	0.741													c|||	1093	0.218251	0.3986	0.0965	5008	,	,		11117	0.0357		0.1859	False		,,,				2504	0.2822				p.L11L		Atlas-SNP	.											WFIKKN1,rectum,carcinoma,0,2	WFIKKN1	30	2	0			c.C31T						scavenged	.			1488,2824		287,914,955	10.0	11.0	11.0		31	0.8	0.0	16	dbSNP_116	11	1579,6943		165,1249,2847	no	coding-synonymous	WFIKKN1	NM_053284.2		452,2163,3802	TT,TC,CC		18.5285,34.5083,23.8975		11/549	681284	3067,9767	2156	4261	6417	SO:0001819	synonymous_variant	117166	exon1			CCGCTCCTGCTCC	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.31C>T	16.37:g.681284C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_053284	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																			C|0.799;T|0.201	0.201	strong		0.741	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284	
ZNF646	9726	hgsc.bcm.edu	37	16	31088625	31088625	+	Missense_Mutation	SNP	A	A	G	rs749670	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31088625A>G	ENST00000394979.2	+	1	1403	c.980A>G	c.(979-981)gAg>gGg	p.E327G	ZNF646_ENST00000300850.5_Missense_Mutation_p.E327G|ZNF668_ENST00000300849.4_5'Flank			O15015	ZN646_HUMAN	zinc finger protein 646	327			E -> G (in dbSNP:rs749670). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		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						CGCTGGGAGGAGAAAGGGATG	0.632													A|||	1731	0.345647	0.0174	0.4092	5008	,	,		17956	0.8849		0.3877	False		,,,				2504	0.1452				p.E327G		Atlas-SNP	.											.	ZNF646	133	.	0			c.A980G						PASS	.	A	GLY/GLU	392,4002	190.5+/-216.4	24,344,1829	46.0	39.0	42.0		980	4.2	1.0	16	dbSNP_86	42	3462,5138	492.6+/-373.4	694,2074,1532	yes	missense	ZNF646	NM_014699.3	98	718,2418,3361	GG,GA,AA		40.2558,8.9213,29.6598	benign	327/1833	31088625	3854,9140	2197	4300	6497	SO:0001583	missense	9726	exon2			GGGAGGAGAAAGG	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.980A>G	16.37:g.31088625A>G	ENSP00000378429:p.Glu327Gly	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		1002	0.45879120879120877	15	0.03048780487804878	158	0.43646408839779005	525	0.9178321678321678	304	0.40105540897097625	A	4.428	0.079178	0.08533	0.089213	0.402558	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.10005	2.92;2.96	5.34	4.18	0.49190	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.45272	P	0.0017249999999999766	B	0.16802	0.019	B	0.12156	0.007	T	0.40213	-0.9575	8	0.11485	T	0.65	-10.072	6.2909	0.21059	0.7526:0.1626:0.0848:0.0	rs749670;rs3751854;rs17853439;rs56886700;rs749670	327	O15015-2	.	G	327	ENSP00000300850:E327G;ENSP00000378429:E327G	ENSP00000300850:E327G	E	+	2	0	ZNF646	30996126	0.005000	0.15991	0.990000	0.47175	0.196000	0.23810	-0.083000	0.11286	2.022000	0.59522	0.533000	0.62120	GAG	A|0.653;G|0.347	0.347	strong		0.632	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
TCP11L1	55346	hgsc.bcm.edu	37	11	33079580	33079580	+	Missense_Mutation	SNP	A	A	G	rs2273549	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:33079580A>G	ENST00000334274.4	+	5	933	c.533A>G	c.(532-534)aAg>aGg	p.K178R	TCP11L1_ENST00000531632.2_Missense_Mutation_p.K178R|TCP11L1_ENST00000530171.1_3'UTR|TCP11L1_ENST00000432887.1_Missense_Mutation_p.K178R|TCP11L1_ENST00000324357.9_5'Flank	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	178			K -> R (in dbSNP:rs2273549). {ECO:0000269|PubMed:15489334}.			microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						GACATTTCCAAGCTGGCAGAA	0.453													A|||	597	0.119209	0.0696	0.1297	5008	,	,		17057	0.122		0.1948	False		,,,				2504	0.0982				p.K178R		Atlas-SNP	.											.	TCP11L1	40	.	0			c.A533G						PASS	.	A	ARG/LYS,ARG/LYS	442,3962	212.2+/-232.1	27,388,1787	94.0	87.0	89.0		533,533	0.7	0.4	11	dbSNP_100	89	1535,7061	288.1+/-298.6	143,1249,2906	yes	missense,missense	TCP11L1	NM_001145541.1,NM_018393.3	26,26	170,1637,4693	GG,GA,AA		17.8571,10.0363,15.2077	benign,benign	178/510,178/510	33079580	1977,11023	2202	4298	6500	SO:0001583	missense	55346	exon5			TTTCCAAGCTGGC	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 1"""				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.533A>G	11.37:g.33079580A>G	ENSP00000335595:p.Lys178Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_001145541	D3DR01|Q8IVX4	Missense_Mutation	SNP	ENST00000334274.4	37	CCDS7882.1	315	0.14423076923076922	43	0.08739837398373984	59	0.16298342541436464	69	0.12062937062937062	144	0.18997361477572558	A	0.721	-0.783462	0.02907	0.100363	0.178571	ENSG00000176148	ENST00000334274;ENST00000531632;ENST00000432887	T;T;T	0.12361	2.69;2.69;2.69	5.53	0.691	0.18045	.	0.410144	0.28847	N	0.013949	T	0.00012	0.0000	N	0.12961	0.28	0.53688	P	2.6999999999999247E-5	B	0.10296	0.003	B	0.16289	0.015	T	0.45026	-0.9289	8	.	.	.	-23.1467	5.6678	0.17704	0.6024:0.1339:0.2637:0.0	rs2273549;rs17343833;rs17846314;rs17859344;rs59182277;rs2273549	178	Q9NUJ3	T11L1_HUMAN	R	178	ENSP00000335595:K178R;ENSP00000433067:K178R;ENSP00000395070:K178R	.	K	+	2	0	TCP11L1	33036156	0.893000	0.30496	0.442000	0.26870	0.199000	0.23934	1.417000	0.34770	0.383000	0.24910	-0.619000	0.04042	AAG	A|0.857;G|0.143	0.143	strong		0.453	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
IL17REL	400935	hgsc.bcm.edu	37	22	50435480	50435480	+	Missense_Mutation	SNP	A	A	G	rs5771069	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50435480A>G	ENST00000389983.2	-	14	1262	c.998T>C	c.(997-999)cTt>cCt	p.L333P	IL17REL_ENST00000341280.5_Missense_Mutation_p.L333P	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	333			L -> P (in dbSNP:rs5771069).							endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GGAAGGCAAAAGCAGGGGCGG	0.637													G|||	3040	0.607029	0.6505	0.4755	5008	,	,		18704	0.5536		0.5209	False		,,,				2504	0.7853				p.L333P		Atlas-SNP	.											.	IL17REL	21	.	0			c.T998C						PASS	.	G	PRO/LEU	2651,1721		832,987,367	34.0	36.0	35.0	http://omim.org/entry/266600|http://www.ncbi.nlm.nih.gov/pubmed?term	998	-4.3	0.0	22	dbSNP_114	35	4311,4279		1079,2153,1063	yes	missense	IL17REL	NM_001001694.2	98	1911,3140,1430	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	49.8137,39.3641,46.2892	benign	333/337	50435480	6962,6000	2186	4295	6481	SO:0001583	missense	400935	exon14			GGCAAAAGCAGGG	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.998T>C	22.37:g.50435480A>G	ENSP00000374633:p.Leu333Pro	Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	251	121	0.482072	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	37	CCDS33679.1	1213	0.5554029304029304	327	0.6646341463414634	177	0.4889502762430939	307	0.5367132867132867	402	0.5303430079155673	G	6.947	0.544605	0.13312	0.606359	0.501863	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.27402	1.67;1.67	2.79	-4.33	0.03677	.	.	.	.	.	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	0.41858	-0.9485	8	0.31617	T	0.26	.	1.356	0.02182	0.1398:0.2964:0.3237:0.2401	rs5771069;rs8135877;rs17780586;rs59525470;rs5771069	333	Q6ZVW7	I17EL_HUMAN	P	333	ENSP00000374633:L333P;ENSP00000342520:L333P	ENSP00000342520:L333P	L	-	2	0	IL17REL	48777607	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-3.930000	0.00332	-1.041000	0.03266	-0.355000	0.07637	CTT	A|0.431;G|0.569	0.569	strong		0.637	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694	
BAZ1A	11177	hgsc.bcm.edu	37	14	35222732	35222732	+	Silent	SNP	C	C	T	rs61754296	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:35222732C>T	ENST00000382422.2	-	26	4980	c.4653G>A	c.(4651-4653)gcG>gcA	p.A1551A	BAZ1A_ENST00000360310.1_Silent_p.A1551A|BAZ1A_ENST00000358716.4_Silent_p.A1519A			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1551					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)	p.A1551A(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		GTGACTTTTTCGCAGCCGGTG	0.388													C|||	546	0.109026	0.0779	0.2738	5008	,	,		17599	0.0387		0.1412	False		,,,				2504	0.0736				p.A1551A		Atlas-SNP	.											BAZ1A,NS,carcinoma,0,2	BAZ1A	128	2	1	Substitution - coding silent(1)	stomach(1)	c.G4653A						PASS	.	C	,	348,4058	181.2+/-209.3	17,314,1872	102.0	91.0	95.0		4653,4557	-3.9	1.0	14	dbSNP_129	95	986,7614	211.8+/-252.3	53,880,3367	no	coding-synonymous,coding-synonymous	BAZ1A	NM_013448.2,NM_182648.1	,	70,1194,5239	TT,TC,CC		11.4651,7.8983,10.2568	,	1551/1557,1519/1525	35222732	1334,11672	2203	4300	6503	SO:0001819	synonymous_variant	11177	exon27			CTTTTTCGCAGCC	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.4653G>A	14.37:g.35222732C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	117	66	0.564103	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1	249	0.11401098901098901	37	0.07520325203252033	80	0.22099447513812154	26	0.045454545454545456	106	0.13984168865435356	c	7.327	0.618179	0.14129	0.078983	0.114651	ENSG00000198604	ENST00000543083	.	.	.	5.59	-3.87	0.04218	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.25916	-1.0118	4	0.17832	T	0.49	.	8.4789	0.33030	0.089:0.1256:0.6173:0.1681	rs61754296	.	.	.	Q	1203	.	ENSP00000445562:R1203Q	R	-	2	0	BAZ1A	34292483	0.926000	0.31397	0.960000	0.40013	0.954000	0.61252	-0.240000	0.08952	-0.984000	0.03507	-0.482000	0.04802	CGA	C|0.895;T|0.105	0.105	strong		0.388	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
SH3D21	79729	hgsc.bcm.edu	37	1	36773405	36773405	+	Silent	SNP	T	T	G	rs35343437	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:36773405T>G	ENST00000426732.2	+	5	408	c.123T>G	c.(121-123)ccT>ccG	p.P41P	SH3D21_ENST00000312808.4_5'UTR|SH3D21_ENST00000505871.1_Silent_p.P46P|SH3D21_ENST00000453908.2_Silent_p.P157P			A4FU49	SH321_HUMAN	SH3 domain containing 21	41						extracellular vesicular exosome (GO:0070062)				endometrium(1)|large_intestine(6)|lung(4)|pancreas(1)	12						CAGTCAGCCCTGGTCCCCAGC	0.582													T|||	2109	0.421126	0.1241	0.562	5008	,	,		19550	0.7192		0.4443	False		,,,				2504	0.3916				p.P157P		Atlas-SNP	.											.	SH3D21	73	.	0			c.T471G						PASS	.	T	,	257,1127		20,217,455	89.0	78.0	81.0		471,138	-2.8	0.0	1	dbSNP_126	81	1567,1615		371,825,395	no	coding-synonymous,coding-synonymous	SH3D21	NM_001162530.1,NM_024676.4	,	391,1042,850	GG,GT,TT		49.2458,18.5694,39.9474	,	157/757,46/646	36773405	1824,2742	692	1591	2283	SO:0001819	synonymous_variant	79729	exon6			CAGCCCTGGTCCC	AK056459	CCDS30674.1, CCDS30674.2	1p34.3	2011-02-21	2011-02-21	2011-02-21	ENSG00000214193	ENSG00000214193			26236	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 113"""	C1orf113		12477932	Standard	NM_024676		Approved	FLJ22938	uc010oia.1	A4FU49	OTTHUMG00000007868	ENST00000426732.2:c.123T>G	1.37:g.36773405T>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_001162530	B4DLI6|D3DPS6|J3KQM5|Q5VTK7|Q86XZ6|Q8N445|Q96DN4|Q9H5W5	Silent	SNP	ENST00000426732.2	37																																																																																				T|0.555;G|0.445	0.445	strong		0.582	SH3D21-202	KNOWN	basic	protein_coding	protein_coding		NM_024676	
MOB3C	148932	hgsc.bcm.edu	37	1	47080679	47080679	+	Intron	SNP	G	G	A	rs6671527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47080679G>A	ENST00000319928.3	-	2	181				MOB3C_ENST00000477318.1_Intron|MOB3C_ENST00000271139.8_Nonsense_Mutation_p.R24*|MKNK1_ENST00000545730.1_Intron|MOB3C_ENST00000371940.1_5'UTR	NM_201403.2	NP_958805.1	Q70IA8	MOB3C_HUMAN	MOB kinase activator 3C								metal ion binding (GO:0046872)										CCGACTCTTCGACTTCTCACC	0.478													A|||	3216	0.642173	0.5643	0.5202	5008	,	,		15802	0.9256		0.4751	False		,,,				2504	0.7137				p.R24X		Atlas-SNP	.											.	MOB3C	1	.	0			c.C70T						PASS	.	A	stop/ARG,	2458,1948	552.3+/-378.5	687,1084,432	82.0	82.0	82.0		70,	2.2	0.0	1	dbSNP_116	82	4029,4571	597.2+/-393.7	943,2143,1214	yes	stop-gained,intron	MOB3C	NM_145279.4,NM_201403.2	,	1630,3227,1646	AA,AG,GG		46.8488,44.2124,49.877	,	24/269,	47080679	6487,6519	2203	4300	6503	SO:0001627	intron_variant	148932	exon1			CTCTTCGACTTCT	AK091808	CCDS539.1, CCDS540.1	1p34.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000142961	ENSG00000142961		"""MOB kinase activators"""	29800	protein-coding gene	gene with protein product			"""MOB1, Mps One Binder kinase activator-like 2C (yeast)"""	MOBKL2C		12477932	Standard	NM_145279		Approved	MOB1E	uc001cqe.4	Q70IA8	OTTHUMG00000007989	ENST00000319928.3:c.50-1636C>T	1.37:g.47080679G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_145279	D3DQ22|Q0VA98|Q5TC10|Q5TC11|Q8NAZ2|Q8NF28	Nonsense_Mutation	SNP	ENST00000319928.3	37	CCDS540.1	1345	0.6158424908424909	270	0.5487804878048781	192	0.5303867403314917	531	0.9283216783216783	352	0.46437994722955145	A	17.44	3.390983	0.62066	0.557876	0.468488	ENSG00000142961	ENST00000271139	.	.	.	3.5	2.2	0.27929	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	5.3107	0.15829	0.6965:0.0:0.3035:0.0	rs6671527;rs59375346;rs6671527	.	.	.	X	24	.	ENSP00000271139:R24X	R	-	1	2	MOBKL2C	46853266	0.000000	0.05858	0.031000	0.17742	0.044000	0.14063	-0.426000	0.07008	0.145000	0.18977	-0.254000	0.11334	CGA	G|0.438;A|0.562	0.562	strong		0.478	MOB3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145279	
ABCD4	5826	hgsc.bcm.edu	37	14	74759059	74759059	+	Missense_Mutation	SNP	G	G	C	rs35073715	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74759059G>C	ENST00000356924.4	-	11	1192	c.1049C>G	c.(1048-1050)aCg>aGg	p.T350R	ABCD4_ENST00000557554.1_Intron|AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000298816.7_Missense_Mutation_p.T246R	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	350			T -> R (in dbSNP:rs35073715).		cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		GTCCAGAAGCGTCTCCCGAAG	0.557													G|||	46	0.0091853	0.0023	0.0173	5008	,	,		20740	0.0		0.0308	False		,,,				2504	0.0				p.T350R		Atlas-SNP	.											.	ABCD4	54	.	0			c.C1049G						PASS	.	G	ARG/THR	29,4377	34.3+/-65.2	0,29,2174	64.0	60.0	61.0		1049	5.6	1.0	14	dbSNP_126	61	226,8374	92.6+/-154.6	3,220,4077	yes	missense	ABCD4	NM_005050.3	71	3,249,6251	CC,CG,GG		2.6279,0.6582,1.9606	benign	350/607	74759059	255,12751	2203	4300	6503	SO:0001583	missense	5826	exon11			AGAAGCGTCTCCC	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.1049C>G	14.37:g.74759059G>C	ENSP00000349396:p.Thr350Arg	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	31	0.014194139194139194	3	0.006097560975609756	7	0.019337016574585635	0	0.0	21	0.027704485488126648	G	12.70	2.016056	0.35606	0.006582	0.026279	ENSG00000119688	ENST00000356924;ENST00000298816;ENST00000537629	D;D	0.94376	-3.41;-3.12	5.63	5.63	0.86233	ABC transporter, transmembrane domain, type 1 (1);	0.455607	0.26875	N	0.022042	T	0.81805	0.4900	M	0.62088	1.915	0.32605	N	0.525399	B;B;B;B	0.24317	0.011;0.015;0.047;0.101	B;B;B;B	0.23852	0.032;0.049;0.014;0.049	D	0.86715	0.1938	10	0.45353	T	0.12	.	12.5402	0.56165	0.0767:0.0:0.9233:0.0	rs35073715	246;246;350;350	F8W7M4;B7Z4V6;A8K5L7;O14678	.;.;.;ABCD4_HUMAN	R	350;246;87	ENSP00000349396:T350R;ENSP00000298816:T246R	ENSP00000298816:T246R	T	-	2	0	ABCD4	73828812	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	3.473000	0.53122	2.797000	0.96272	0.655000	0.94253	ACG	G|0.982;C|0.018	0.018	strong		0.557	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
HTT	3064	hgsc.bcm.edu	37	4	3213832	3213832	+	Silent	SNP	G	G	A	rs362336	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:3213832G>A	ENST00000355072.5	+	48	6736	c.6591G>A	c.(6589-6591)gaG>gaA	p.E2197E		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2197					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TGCCTGCAGAGCCGGCGGCCT	0.493													G|||	1200	0.239617	0.0946	0.2939	5008	,	,		17362	0.3542		0.3151	False		,,,				2504	0.2014				p.E2197E		Atlas-SNP	.											.	HTT	221	.	0			c.G6591A						PASS	.	G		582,3214		47,488,1363	39.0	42.0	41.0		6591	1.0	0.0	4	dbSNP_79	41	2461,5771		346,1769,2001	no	coding-synonymous	HTT	NM_002111.6		393,2257,3364	AA,AG,GG		29.8955,15.3319,25.2993		2197/3143	3213832	3043,8985	1898	4116	6014	SO:0001819	synonymous_variant	3064	exon48			TGCAGAGCCGGCG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.6591G>A	4.37:g.3213832G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			G|0.718;A|0.282	0.282	strong		0.493	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
C5orf52	100190949	hgsc.bcm.edu	37	5	157106968	157106968	+	Silent	SNP	C	C	T	rs6892478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:157106968C>T	ENST00000409999.3	+	3	503	c.441C>T	c.(439-441)agC>agT	p.S147S		NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	147										endometrium(2)|lung(1)	3						CCGTGAACAGCAACCGGTACT	0.498													.|||	828	0.165335	0.2912	0.1326	5008	,	,		18596	0.0734		0.1551	False		,,,				2504	0.1237				p.S147S		Atlas-SNP	.											.	C5orf52	17	.	0			c.C441T						PASS	.	C		348,1036		42,264,386	123.0	120.0	121.0		441	1.0	0.0	5	dbSNP_116	121	439,2743		34,371,1186	no	coding-synonymous	C5orf52	NM_001145132.1		76,635,1572	TT,TC,CC		13.7964,25.1445,17.2361		147/160	157106968	787,3779	692	1591	2283	SO:0001819	synonymous_variant	100190949	exon3			GAACAGCAACCGG	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.441C>T	5.37:g.157106968C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001145132		Silent	SNP	ENST00000409999.3	37	CCDS47329.1																																																																																			C|0.837;G|0.000;T|0.162	0.162	strong		0.498	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
MYOM1	8736	hgsc.bcm.edu	37	18	3173964	3173964	+	Silent	SNP	G	G	A	rs2230163	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:3173964G>A	ENST00000356443.4	-	8	1479	c.1146C>T	c.(1144-1146)caC>caT	p.H382H	MYOM1_ENST00000261606.7_Silent_p.H382H|MYOM1_ENST00000400569.3_Silent_p.H382H	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	382					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AAGCCCCAGCGTGGAAGCGAG	0.408													A|||	1583	0.316094	0.4002	0.2262	5008	,	,		16674	0.2669		0.3062	False		,,,				2504	0.3272				p.H382H		Atlas-SNP	.											.	MYOM1	192	.	0			c.C1146T						PASS	.	A	,	1462,2268		303,856,706	82.0	78.0	79.0		1146,1146	-0.4	0.0	18	dbSNP_98	79	2593,5621		417,1759,1931	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	720,2615,2637	AA,AG,GG		31.5681,39.1957,33.9501	,	382/1686,382/1590	3173964	4055,7889	1865	4107	5972	SO:0001819	synonymous_variant	8736	exon8			CCCAGCGTGGAAG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1146C>T	18.37:g.3173964G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			T|0.130;G|0.427;C|0.268;A|0.175	0.175	strong		0.408	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
SEMA4D	10507	hgsc.bcm.edu	37	9	91978397	91978397	+	Missense_Mutation	SNP	C	C	T	rs13295305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:91978397C>T	ENST00000420987.1	-	19	2584	c.2138G>A	c.(2137-2139)aGg>aAg	p.R713K	SEMA4D_ENST00000339861.4_Missense_Mutation_p.R713K|SEMA4D_ENST00000343780.4_Missense_Mutation_p.R713K|SEMA4D_ENST00000455551.2_Missense_Mutation_p.R713K|SEMA4D_ENST00000469653.1_5'UTR|SEMA4D_ENST00000420101.2_Missense_Mutation_p.R98K	NM_001142287.1	NP_001135759.1	Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	0					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AGCCACAGCCCTCCAGGCAGA	0.627													C|||	788	0.157348	0.025	0.366	5008	,	,		17146	0.2331		0.1203	False		,,,				2504	0.1483				p.R713K		Atlas-SNP	.											.	SEMA4D	81	.	0			c.G2138A						PASS	.	C	LYS/ARG	184,4222	117.5+/-155.4	5,174,2024	59.0	64.0	62.0		2138	0.8	0.5	9	dbSNP_121	62	1147,7453	235.4+/-268.0	84,979,3237	yes	missense	SEMA4D	NM_001142287.1	26	89,1153,5261	TT,TC,CC		13.3372,4.1761,10.2337		713/739	91978397	1331,11675	2203	4300	6503	SO:0001583	missense	10507	exon20			ACAGCCCTCCAGG	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000420987.1:c.2138G>A	9.37:g.91978397C>T	ENSP00000391733:p.Arg713Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	74	32	0.432432	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000420987.1	37	CCDS47991.1	345	0.15796703296703296	21	0.042682926829268296	116	0.32044198895027626	100	0.17482517482517482	108	0.1424802110817942	C	10.11	1.260965	0.23051	0.041761	0.133372	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000420101;ENST00000455551;ENST00000343780	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	4.99	0.793	0.18632	.	0.437294	0.20662	N	0.088017	T	0.00012	0.0000	.	.	.	0.33217	P	0.44578799999999996	B	0.11235	0.004	B	0.12156	0.007	T	0.47446	-0.9117	8	0.13470	T	0.59	.	8.526	0.33304	0.0:0.6353:0.0:0.3647	rs13295305	713	Q92854-2	.	K	713;713;98;713;713	ENSP00000344923:R713K;ENSP00000391733:R713K;ENSP00000411981:R713K;ENSP00000343418:R713K	ENSP00000344923:R713K	R	-	2	0	SEMA4D	91168217	0.113000	0.22115	0.486000	0.27416	0.819000	0.46315	0.259000	0.18405	0.285000	0.22329	0.561000	0.74099	AGG	C|0.880;T|0.120	0.120	strong		0.627	SEMA4D-203	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402418.2	NM_006378	
ALKBH3	221120	hgsc.bcm.edu	37	11	43913604	43913604	+	Silent	SNP	G	G	A	rs16937692	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:43913604G>A	ENST00000302708.4	+	7	795	c.384G>A	c.(382-384)caG>caA	p.Q128Q	ALKBH3_ENST00000532410.1_Intron|ALKBH3_ENST00000378840.4_Intron	NM_139178.3	NP_631917.1	Q96Q83	ALKB3_HUMAN	alkB, alkylation repair homolog 3 (E. coli)	128					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA repair (GO:0006281)|oxidative single-stranded DNA demethylation (GO:0035552)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)			endometrium(2)|kidney(1)|lung(4)|prostate(1)	8					Vitamin C(DB00126)	TAACTTATCAGCAACCAAGAC	0.368								Direct reversal of damage					G|||	303	0.0605032	0.0393	0.2046	5008	,	,		20438	0.0248		0.0268	False		,,,				2504	0.0583				p.Q128Q		Atlas-SNP	.											.	ALKBH3	33	.	0			c.G384A						PASS	.	G		145,4261	102.1+/-140.7	2,141,2060	119.0	109.0	112.0		384	3.0	1.0	11	dbSNP_123	112	264,8336	101.6+/-162.9	5,254,4041	no	coding-synonymous	ALKBH3	NM_139178.3		7,395,6101	AA,AG,GG		3.0698,3.291,3.1447		128/287	43913604	409,12597	2203	4300	6503	SO:0001819	synonymous_variant	221120	exon7			TTATCAGCAACCA	AB042029	CCDS7906.1	11p11.2	2013-10-11			ENSG00000166199	ENSG00000166199		"""Alkylation repair homologs"""	30141	protein-coding gene	gene with protein product		610603				22055184	Standard	NM_139178		Approved	DEPC-1	uc001mxs.2	Q96Q83	OTTHUMG00000166417	ENST00000302708.4:c.384G>A	11.37:g.43913604G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_139178	A6NDJ1|Q3SYI0|Q6NX57|Q96BU8	Silent	SNP	ENST00000302708.4	37	CCDS7906.1																																																																																			G|0.961;A|0.039	0.039	strong		0.368	ALKBH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389693.1	NM_139178	
CCDC88B	283234	hgsc.bcm.edu	37	11	64124515	64124515	+	Silent	SNP	T	T	C	rs612448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64124515T>C	ENST00000356786.5	+	27	4424	c.4380T>C	c.(4378-4380)ccT>ccC	p.P1460P	CCDC88B_ENST00000463837.1_3'UTR|RPS6KA4_ENST00000334205.4_5'Flank|CCDC88B_ENST00000301897.4_Silent_p.P123P|RPS6KA4_ENST00000528057.1_5'Flank|CCDC88B_ENST00000359902.2_Missense_Mutation_p.L565P|RPS6KA4_ENST00000294261.4_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1460						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTCTAGGCCCTGAGGTACAGG	0.632													C|||	1303	0.260184	0.0303	0.4107	5008	,	,		17803	0.1845		0.4334	False		,,,				2504	0.364				p.P1460P		Atlas-SNP	.											CCDC88B_ENST00000359902,NS,carcinoma,-1,1	CCDC88B	89	1	0			c.T4380C						scavenged	.	C		426,3976		23,380,1798	133.0	102.0	112.0		4380	0.6	0.0	11	dbSNP_83	112	3738,4856		794,2150,1353	no	coding-synonymous	CCDC88B	NM_032251.5		817,2530,3151	CC,CT,TT		43.4955,9.6774,32.0406		1460/1477	64124515	4164,8832	2201	4297	6498	SO:0001819	synonymous_variant	283234	exon27			AGGCCCTGAGGTA	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.4380T>C	11.37:g.64124515T>C		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	95	55	0.578947	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2	605	0.27701465201465203	21	0.042682926829268296	141	0.38950276243093923	104	0.18181818181818182	339	0.4472295514511873	N	11.12	1.545644	0.27652	0.096774	0.434955	ENSG00000168071	ENST00000359902	T	0.57907	0.37	3.89	0.573	0.17363	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46652	-0.9176	6	.	.	.	.	3.3622	0.07190	0.0:0.4118:0.2053:0.3829	rs612448;rs58613170;rs612448	549	A6NC98-5	.	P	565	ENSP00000352974:L565P	.	L	+	2	0	CCDC88B	63881091	0.000000	0.05858	0.010000	0.14722	0.161000	0.22273	-0.393000	0.07305	0.007000	0.14760	-0.511000	0.04467	CTG	T|0.706;C|0.294	0.294	strong		0.632	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
RNF175	285533	hgsc.bcm.edu	37	4	154644537	154644537	+	Missense_Mutation	SNP	T	T	C	rs10517577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:154644537T>C	ENST00000347063.4	-	5	847	c.475A>G	c.(475-477)Atg>Gtg	p.M159V	RP11-153M7.5_ENST00000505051.1_RNA|RNF175_ENST00000274068.4_Missense_Mutation_p.M31V|RNF175_ENST00000506505.1_5'UTR	NM_173662.2	NP_775933	Q8N4F7	RN175_HUMAN	ring finger protein 175	159			M -> V (in dbSNP:rs10517577).			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	13	all_hematologic(180;0.093)	Renal(120;0.118)				ATTGTAAACATGATCGCCAAG	0.388													T|||	467	0.0932508	0.0053	0.1628	5008	,	,		16695	0.004		0.2247	False		,,,				2504	0.1196				p.M159V		Atlas-SNP	.											.	RNF175	40	.	0			c.A475G						PASS	.	T	VAL/MET	160,3704		4,152,1776	100.0	86.0	90.0		475	0.7	1.0	4	dbSNP_119	90	1923,6345		194,1535,2405	yes	missense	RNF175	NM_173662.2	21	198,1687,4181	CC,CT,TT		23.2583,4.1408,17.1695	benign	159/329	154644537	2083,10049	1932	4134	6066	SO:0001583	missense	285533	exon5			TAAACATGATCGC	BC034385	CCDS47149.1	4q31.3	2008-02-05			ENSG00000145428	ENSG00000145428		"""RING-type (C3HC4) zinc fingers"""	27735	protein-coding gene	gene with protein product							Standard	NM_173662		Approved	FLJ34190	uc003int.3	Q8N4F7	OTTHUMG00000161557	ENST00000347063.4:c.475A>G	4.37:g.154644537T>C	ENSP00000340979:p.Met159Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	98	62	0.632653	NM_173662	C9JL66|Q8NB61	Missense_Mutation	SNP	ENST00000347063.4	37	CCDS47149.1	245	0.11217948717948718	2	0.0040650406504065045	61	0.1685082872928177	1	0.0017482517482517483	181	0.23878627968337732	T	13.82	2.350213	0.41599	0.041408	0.232583	ENSG00000145428	ENST00000347063;ENST00000274068;ENST00000508248	T;T;T	0.77229	-1.08;-1.08;-1.08	4.34	0.707	0.18139	.	0.198777	0.49916	N	0.000139	T	0.00039	0.0001	L	0.55481	1.735	0.25431	P	0.9881882	P;B	0.36683	0.565;0.002	B;B	0.36335	0.222;0.008	T	0.01894	-1.1252	9	0.30854	T	0.27	-5.8208	7.4098	0.27011	0.0:0.2644:0.0:0.7356	rs10517577;rs17370896;rs52808550;rs57008646;rs10517577	31;159	Q8NB61;Q8N4F7	.;RN175_HUMAN	V	159;31;99	ENSP00000340979:M159V;ENSP00000274068:M31V;ENSP00000427472:M99V	ENSP00000274068:M31V	M	-	1	0	RNF175	154863987	1.000000	0.71417	0.996000	0.52242	0.935000	0.57460	3.291000	0.51764	0.136000	0.18733	0.455000	0.32223	ATG	T|0.917;C|0.083	0.083	strong		0.388	RNF175-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365286.1	NM_173662	
ATP10A	57194	hgsc.bcm.edu	37	15	25926179	25926179	+	Missense_Mutation	SNP	C	C	T	rs2076744	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:25926179C>T	ENST00000356865.6	-	18	3646	c.3535G>A	c.(3535-3537)Gcc>Acc	p.A1179T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1179			A -> T (in dbSNP:rs2076744).		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CTCTGGAAGGCGGCGTCGGCC	0.517													c|||	1413	0.282149	0.4735	0.3516	5008	,	,		19333	0.2599		0.1441	False		,,,				2504	0.1391				p.A1179T		Atlas-SNP	.											ATP10A,colon,carcinoma,0,1	ATP10A	270	1	0			c.G3535A						PASS	.	C	THR/ALA	1839,2567	535.6+/-374.3	379,1081,743	90.0	86.0	87.0		3535	0.3	0.2	15	dbSNP_96	87	1378,7222	268.2+/-287.7	103,1172,3025	yes	missense	ATP10A	NM_024490.3	58	482,2253,3768	TT,TC,CC		16.0233,41.7385,24.7347	benign	1179/1500	25926179	3217,9789	2203	4300	6503	SO:0001583	missense	57194	exon18			GGAAGGCGGCGTC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3535G>A	15.37:g.25926179C>T	ENSP00000349325:p.Ala1179Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	637	0.2916666666666667	239	0.48577235772357724	118	0.3259668508287293	172	0.3006993006993007	108	0.1424802110817942	c	8.127	0.782181	0.16189	0.417385	0.160233	ENSG00000206190	ENST00000356865	T	0.43688	0.94	4.84	0.298	0.15766	.	0.495561	0.22824	N	0.055187	T	0.00012	0.0000	N	0.11255	0.115	0.53005	P	3.399999999997849E-5	P	0.38729	0.644	B	0.28849	0.095	T	0.47355	-0.9124	9	0.48119	T	0.1	-16.3478	1.5902	0.02653	0.2175:0.4237:0.1137:0.2452	rs2076744;rs2076744	1179	O60312	AT10A_HUMAN	T	1179	ENSP00000349325:A1179T	ENSP00000349325:A1179T	A	-	1	0	ATP10A	23477272	0.152000	0.22762	0.210000	0.23637	0.050000	0.14768	0.681000	0.25320	0.111000	0.17947	-1.349000	0.01238	GCC	C|0.734;T|0.266	0.266	strong		0.517	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
AOC3	8639	hgsc.bcm.edu	37	17	41004637	41004637	+	Missense_Mutation	SNP	G	G	A	rs33986943	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:41004637G>A	ENST00000308423.2	+	1	1437	c.1277G>A	c.(1276-1278)cGt>cAt	p.R426H	AOC3_ENST00000591562.1_5'Flank	NM_003734.2	NP_003725.1	Q16853	AOC3_HUMAN	amine oxidase, copper containing 3	426			R -> H (in dbSNP:rs33986943). {ECO:0000269|Ref.6}.		amine metabolic process (GO:0009308)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|response to antibiotic (GO:0046677)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			breast(1)|central_nervous_system(4)|endometrium(4)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|skin(8)	41		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)	Hydralazine(DB01275)|Phenelzine(DB00780)	AAGACAATACGTGATGCCTTT	0.587													G|||	242	0.0483227	0.0091	0.0548	5008	,	,		19023	0.0		0.1123	False		,,,				2504	0.0808				p.R426H	NSCLC(3;192 220 10664 11501 16477)	Atlas-SNP	.											.	AOC3	88	.	0			c.G1277A						PASS	.	G	HIS/ARG	95,4311	77.8+/-116.1	0,95,2108	93.0	83.0	86.0		1277	-3.7	0.0	17	dbSNP_126	86	874,7726	197.3+/-242.0	46,782,3472	yes	missense	AOC3	NM_003734.2	29	46,877,5580	AA,AG,GG		10.1628,2.1562,7.4504	benign	426/764	41004637	969,12037	2203	4300	6503	SO:0001583	missense	8639	exon1			CAATACGTGATGC	AF067406	CCDS11444.1, CCDS62198.1, CCDS74071.1	17q21	2013-05-08	2013-05-08			ENSG00000131471	1.4.3.21		550	protein-coding gene	gene with protein product	"""vascular adhesion protein 1"""	603735				9653080, 8972912	Standard	NM_003734		Approved	VAP1, HPAO, VAP-1	uc002ibv.4	Q16853		ENST00000308423.2:c.1277G>A	17.37:g.41004637G>A	ENSP00000312326:p.Arg426His	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	262	120	0.458015	NM_003734	B2RCI5|K7ESB3|L0L8N9|Q45F94	Missense_Mutation	SNP	ENST00000308423.2	37	CCDS11444.1	120	0.054945054945054944	10	0.02032520325203252	23	0.06353591160220995	0	0.0	87	0.11477572559366754	G	7.371	0.626759	0.14257	0.021562	0.101628	ENSG00000131471	ENST00000308423	T	0.04015	3.73	4.64	-3.71	0.04424	Copper amine oxidase, C-terminal (3);	0.701778	0.14252	N	0.331410	T	0.00073	0.0002	N	0.14661	0.345	0.09310	N	1	B	0.17268	0.021	B	0.09377	0.004	T	0.43212	-0.9405	10	0.41790	T	0.15	.	8.4995	0.33150	0.6385:0.1246:0.2368:0.0	rs33986943;rs33986943	426	Q16853	AOC3_HUMAN	H	426	ENSP00000312326:R426H	ENSP00000312326:R426H	R	+	2	0	AOC3	38258163	0.000000	0.05858	0.000000	0.03702	0.643000	0.38383	-0.172000	0.09868	-0.747000	0.04759	0.591000	0.81541	CGT	G|0.930;A|0.070	0.070	strong		0.587	AOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452444.1	NM_003734	
PDE1C	5137	hgsc.bcm.edu	37	7	32338337	32338337	+	Missense_Mutation	SNP	G	G	A	rs215607	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:32338337G>A	ENST00000396193.1	-	1	604	c.11C>T	c.(10-12)gCc>gTc	p.A4V		NM_001191058.1	NP_001177987.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	0					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CCTGTTGCCGGCGTCCGTCAT	0.677													G|||	3929	0.784545	0.7179	0.853	5008	,	,		12754	0.7917		0.8012	False		,,,				2504	0.8016				p.A4V		Atlas-SNP	.											.	PDE1C	465	.	0			c.C11T						PASS	.	G	VAL/ALA	1243,509		440,363,73	11.0	11.0	11.0		11	4.1	1.0	7	dbSNP_79	11	3053,923		1192,669,127	yes	missense	PDE1C	NM_001191058.1	64	1632,1032,200	AA,AG,GG		23.2143,29.0525,25.0		4/770	32338337	4296,1432	876	1988	2864	SO:0001583	missense	5137	exon1			TTGCCGGCGTCCG	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396193.1:c.11C>T	7.37:g.32338337G>A	ENSP00000379496:p.Ala4Val	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396193.1	37	CCDS55100.1	1724	0.7893772893772893	377	0.766260162601626	302	0.8342541436464088	438	0.7657342657342657	607	0.8007915567282322	G	15.49	2.849002	0.51164	0.709475	0.767857	ENSG00000154678	ENST00000396193	T	0.75938	-0.98	4.05	4.05	0.47172	.	1.067080	0.07452	N	0.899131	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	B	0.15141	0.012	B	0.12837	0.008	T	0.50816	-0.8783	9	0.54805	T	0.06	.	15.136	0.72566	0.0:0.0:1.0:0.0	rs215607;rs10386994;rs56788611;rs215607	4	E9PE92	.	V	4	ENSP00000379496:A4V	ENSP00000379496:A4V	A	-	2	0	PDE1C	32304862	1.000000	0.71417	1.000000	0.80357	0.461000	0.32589	6.649000	0.74364	2.085000	0.62840	0.491000	0.48974	GCC	G|0.214;A|0.786	0.786	strong		0.677	PDE1C-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215075.1		
ZNF682	91120	hgsc.bcm.edu	37	19	20133876	20133876	+	Missense_Mutation	SNP	G	G	A	rs201103446		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:20133876G>A	ENST00000397165.2	-	3	323	c.163C>T	c.(163-165)Cgt>Tgt	p.R55C	ZNF682_ENST00000596019.1_Missense_Mutation_p.R55C|ZNF682_ENST00000397162.1_Missense_Mutation_p.R23C|ZNF682_ENST00000358523.5_Missense_Mutation_p.R23C|ZNF682_ENST00000595736.1_Intron|ZNF682_ENST00000597972.1_Missense_Mutation_p.R61C|ZNF682_ENST00000593468.1_Missense_Mutation_p.R55C	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						TGCTCCAGACGGCTAATCAGT	0.438																																					p.R55C		Atlas-SNP	.											ZNF682,NS,carcinoma,0,2	ZNF682	51	2	0			c.C163T						scavenged	.	A	CYS/ARG,CYS/ARG	0,4118		0,0,2059	124.0	126.0	125.0		67,163	-0.3	0.6	19		125	3,8483		0,3,4240	yes	missense,missense	ZNF682	NM_001077349.1,NM_033196.2	180,180	0,3,6299	AA,AG,GG		0.0354,0.0,0.0238	benign,benign	23/467,55/499	20133876	3,12601	2059	4243	6302	SO:0001583	missense	91120	exon3			CCAGACGGCTAAT	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.163C>T	19.37:g.20133876G>A	ENSP00000380351:p.Arg55Cys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	89	3	0.0337079	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	.	.	.	.	.	.	.	.	.	.	A	0.020	-1.439898	0.01098	0.0	3.54E-4	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000358523	T;T;T	0.00816	5.66;5.66;5.66	0.898	-0.34	0.12643	Krueppel-associated box (3);	.	.	.	.	T	0.00552	0.0018	N	0.12961	0.28	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47129	-0.9141	9	0.02654	T	1	.	4.6047	0.12371	0.3764:0.0:0.6236:0.0	.	55	O95780	ZN682_HUMAN	C	55;23;23	ENSP00000380351:R55C;ENSP00000380348:R23C;ENSP00000351324:R23C	ENSP00000351324:R23C	R	-	1	0	ZNF682	19994876	0.059000	0.20769	0.587000	0.28692	0.593000	0.36681	-0.697000	0.05098	-1.061000	0.03185	-1.115000	0.02055	CGT	.	.	weak		0.438	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
RSF1	51773	hgsc.bcm.edu	37	11	77378388	77378388	+	Silent	SNP	T	T	C	rs4945197	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77378388T>C	ENST00000308488.6	-	16	4202	c.3900A>G	c.(3898-3900)ctA>ctG	p.L1300L	RSF1_ENST00000360355.2_Silent_p.L1269L|RSF1_ENST00000480887.1_Silent_p.L1048L			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1300					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)	p.L1300L(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			CAATCCGGTGTAGCCGTTTGC	0.562													T|||	983	0.196286	0.329	0.2147	5008	,	,		20309	0.1736		0.0984	False		,,,				2504	0.1278				p.L1300L		Atlas-SNP	.											RSF1,NS,carcinoma,0,1	RSF1	105	1	1	Substitution - coding silent(1)	stomach(1)	c.A3900G						PASS	.	T		1335,3065	446.7+/-348.1	204,927,1069	113.0	100.0	105.0		3900	0.0	1.0	11	dbSNP_111	105	831,7753	191.8+/-238.0	36,759,3497	yes	coding-synonymous	RSF1	NM_016578.3		240,1686,4566	CC,CT,TT		9.6808,30.3409,16.6821		1300/1442	77378388	2166,10818	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon16			CCGGTGTAGCCGT	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.3900A>G	11.37:g.77378388T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	93	0.853211	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1																																																																																			T|0.813;C|0.187	0.187	strong		0.562	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
ALG10B	144245	hgsc.bcm.edu	37	12	38715000	38715000	+	Silent	SNP	A	A	G	rs35518352	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:38715000A>G	ENST00000308742.4	+	3	1723	c.1407A>G	c.(1405-1407)caA>caG	p.Q469Q	ALG10B_ENST00000551464.1_Intron|AC117372.1_ENST00000401168.2_RNA	NM_001013620.3	NP_001013642.1	Q5I7T1	AG10B_HUMAN	ALG10B, alpha-1,2-glucosyltransferase	469					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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transferase activity, transferring hexosyl groups (GO:0016758)			breast(2)|kidney(3)|large_intestine(7)|lung(8)|ovary(4)|skin(1)	25	Esophageal squamous(101;0.187)	Lung NSC(34;0.204)|all_lung(34;0.235)				AGGACATTCAAAGGTTTATGT	0.318													A|||	1259	0.251398	0.1377	0.2867	5008	,	,		16352	0.1429		0.4513	False		,,,				2504	0.2863				p.Q469Q		Atlas-SNP	.											ALG10B,colon,carcinoma,0,1	ALG10B	58	1	0			c.A1407G						PASS	.	A		716,3688	278.7+/-274.4	65,586,1551	118.0	120.0	119.0		1407	-0.6	1.0	12	dbSNP_126	119	3877,4717	533.8+/-382.5	859,2159,1279	no	coding-synonymous	ALG10B	NM_001013620.3		924,2745,2830	GG,GA,AA		45.1129,16.2579,35.3362		469/474	38715000	4593,8405	2202	4297	6499	SO:0001819	synonymous_variant	144245	exon3			CATTCAAAGGTTT	AY845858	CCDS31772.1	12q12	2013-03-04	2013-03-04		ENSG00000175548	ENSG00000175548	2.4.1.256		31088	protein-coding gene	gene with protein product	"""potassium channel regulator 1"", ""dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"""		"""asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog B (yeast)"""				Standard	NM_001013620		Approved	KCR1	uc001rln.4	Q5I7T1	OTTHUMG00000169298	ENST00000308742.4:c.1407A>G	12.37:g.38715000A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_001013620	B2RPF4	Silent	SNP	ENST00000308742.4	37	CCDS31772.1																																																																																			A|0.664;G|0.336	0.336	strong		0.318	ALG10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403349.1	NM_001013620	
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 GAIIx	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_ENST00000556859.1_Missense_Mutation_p.Q513E|DACT1_ENST00000541264.2_Missense_Mutation_p.Q513E|DACT1_ENST00000395153.3_Missense_Mutation_p.Q757E			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	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	30	13	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	
BTBD2	55643	hgsc.bcm.edu	37	19	1997363	1997363	+	Silent	SNP	A	A	G	rs1610045	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1997363A>G	ENST00000255608.4	-	2	523	c.507T>C	c.(505-507)gcT>gcC	p.A169A	BTBD2_ENST00000590646.1_5'UTR	NM_017797.3	NP_060267.2	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	169	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.					cytoplasmic mRNA processing body (GO:0000932)				endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	12		Ovarian(11;2.11e-07)|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)		CGAGGAAGGCAGCGGGTTCCA	0.622													A|||	2277	0.454673	0.6074	0.4092	5008	,	,		17550	0.4891		0.329	False		,,,				2504	0.3742				p.A169A		Atlas-SNP	.											.	BTBD2	31	.	0			c.T507C						PASS	.	A		2474,1932	622.6+/-394.0	686,1102,415	155.0	143.0	147.0		507	-3.1	0.9	19	dbSNP_88	147	2774,5826	440.5+/-359.5	437,1900,1963	no	coding-synonymous	BTBD2	NM_017797.3		1123,3002,2378	GG,GA,AA		32.2558,43.8493,40.3506		169/526	1997363	5248,7758	2203	4300	6503	SO:0001819	synonymous_variant	55643	exon2			GAAGGCAGCGGGT	AF355797	CCDS12078.1	19p13.3	2013-10-02			ENSG00000133243	ENSG00000133243		"""BTB/POZ domain containing"""	15504	protein-coding gene	gene with protein product		608531				11179693	Standard	XM_005259593		Approved		uc002lup.1	Q9BX70	OTTHUMG00000180017	ENST00000255608.4:c.507T>C	19.37:g.1997363A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_017797	O60418|O75248|Q4VBZ1|Q6IAC5|Q7Z5W0|Q96SX8|Q9NPS1|Q9NX81	Silent	SNP	ENST00000255608.4	37	CCDS12078.1																																																																																			A|0.571;G|0.429	0.429	strong		0.622	BTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449300.2		
AFF3	3899	hgsc.bcm.edu	37	2	100210642	100210642	+	Missense_Mutation	SNP	T	T	C	rs1047265	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:100210642T>C	ENST00000409236.2	-	13	1593	c.1481A>G	c.(1480-1482)aAt>aGt	p.N494S	AFF3_ENST00000409579.1_Missense_Mutation_p.N519S|AFF3_ENST00000356421.2_Missense_Mutation_p.N519S|AFF3_ENST00000317233.4_Missense_Mutation_p.N494S			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	494			N -> S (in dbSNP:rs1047265).		embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GTAGTACTGATTGCTCTCTGA	0.507													T|||	740	0.147764	0.0877	0.1239	5008	,	,		12796	0.0873		0.2038	False		,,,				2504	0.2505				p.N519S		Atlas-SNP	.											.	AFF3	164	.	0			c.A1556G						PASS	.	T	SER/ASN,SER/ASN	510,3896	231.7+/-245.5	31,448,1724	144.0	162.0	156.0		1556,1481	-11.7	0.0	2	dbSNP_86	156	1745,6855	308.1+/-308.7	165,1415,2720	yes	missense,missense	AFF3	NM_001025108.1,NM_002285.2	46,46	196,1863,4444	CC,CT,TT		20.2907,11.5751,17.3382	benign,benign	519/1252,494/1227	100210642	2255,10751	2203	4300	6503	SO:0001583	missense	3899	exon14			TACTGATTGCTCT	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1481A>G	2.37:g.100210642T>C	ENSP00000387207:p.Asn494Ser	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	37	CCDS42723.1	312	0.14285714285714285	39	0.07926829268292683	52	0.143646408839779	60	0.1048951048951049	161	0.21240105540897097	T	0.604	-0.827843	0.02734	0.115751	0.202907	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01	5.87	-11.7	0.00046	.	1.472120	0.03891	N	0.278719	T	0.00039	0.0001	L	0.33485	1.01	0.80722	P	0.0	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.12837	0.002;0.008;0.001	T	0.01156	-1.1434	9	0.09084	T	0.74	.	8.322	0.32134	0.0762:0.5375:0.2298:0.1565	rs1047265;rs3187296;rs3792127;rs61654541;rs1047265	647;494;519	B7Z4I6;P51826;P51826-2	.;AFF3_HUMAN;.	S	494;519;519;494;494;647;519	ENSP00000317421:N494S;ENSP00000348793:N519S;ENSP00000386834:N519S;ENSP00000387207:N494S	ENSP00000317421:N494S	N	-	2	0	AFF3	99577074	0.000000	0.05858	0.000000	0.03702	0.911000	0.54048	-1.095000	0.03356	-2.514000	0.00502	-0.250000	0.11733	AAT	T|0.848;C|0.152	0.152	strong		0.507	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
C9orf24	84688	hgsc.bcm.edu	37	9	34397545	34397545	+	Silent	SNP	A	A	G	rs11790577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:34397545A>G	ENST00000297623.2	-	1	285	c.87T>C	c.(85-87)taT>taC	p.Y29Y		NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	29					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		GTGGGTCCTTATAGACCTCCT	0.567													A|||	2025	0.404353	0.2844	0.3934	5008	,	,		18772	0.3968		0.5239	False		,,,				2504	0.4591				p.Y29Y		Atlas-SNP	.											.	C9orf24	15	.	0			c.T87C						PASS	.	A		1396,3010	459.0+/-352.1	227,942,1034	185.0	169.0	175.0		87	-2.7	1.0	9	dbSNP_120	175	4473,4127	590.6+/-392.7	1159,2155,986	yes	coding-synonymous	C9orf24	NM_032596.3		1386,3097,2020	GG,GA,AA		47.9884,31.6841,45.1253		29/263	34397545	5869,7137	2203	4300	6503	SO:0001819	synonymous_variant	84688	exon1			GTCCTTATAGACC	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"""ciliated bronchial epithelium 1"", ""spermatid-specific manchette-related protein 1"""					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.87T>C	9.37:g.34397545A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_032596	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Silent	SNP	ENST00000297623.2	37	CCDS6554.1																																																																																			A|0.552;G|0.448	0.448	strong		0.567	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	
COL5A3	50509	hgsc.bcm.edu	37	19	10114759	10114759	+	Silent	SNP	C	C	T	rs76321360	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10114759C>T	ENST00000264828.3	-	5	742	c.657G>A	c.(655-657)cgG>cgA	p.R219R		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	219	Laminin G-like.|Nonhelical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			CGGGGAGGTACCGCTCACAAG	0.607													C|||	92	0.0183706	0.0045	0.036	5008	,	,		18069	0.0		0.0537	False		,,,				2504	0.0072				p.R219R		Atlas-SNP	.											.	COL5A3	243	.	0			c.G657A						PASS	.	C		49,4357	49.6+/-84.7	1,47,2155	109.0	90.0	96.0		657	-3.1	0.0	19	dbSNP_132	96	495,8105	142.5+/-198.7	8,479,3813	no	coding-synonymous	COL5A3	NM_015719.3		9,526,5968	TT,TC,CC		5.7558,1.1121,4.1827		219/1746	10114759	544,12462	2203	4300	6503	SO:0001819	synonymous_variant	50509	exon5			GAGGTACCGCTCA	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.657G>A	19.37:g.10114759C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	64	0.615385	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																			C|0.959;G|0.000;T|0.041	0.041	strong		0.607	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
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 GAIIx	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	NUTM2G_ENST00000354649.3_Intron|HIATL2_ENST00000506067.1_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		Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	360	124	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	
SETBP1	26040	hgsc.bcm.edu	37	18	42532606	42532606	+	Missense_Mutation	SNP	G	G	A	rs3744825	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:42532606G>A	ENST00000282030.5	+	4	3597	c.3301G>A	c.(3301-3303)Gta>Ata	p.V1101I		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	1101			V -> I (in dbSNP:rs3744825). {ECO:0000269|PubMed:11231286, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9455477}.			nucleus (GO:0005634)	DNA binding (GO:0003677)	p.V1047I(1)		NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AAACTCCCACGTAAAGATGTC	0.542									Schinzel-Giedion syndrome				G|||	625	0.1248	0.0356	0.0865	5008	,	,		19030	0.2659		0.1322	False		,,,				2504	0.1196				p.V1101I		Atlas-SNP	.											SETBP1,NS,carcinoma,0,1	SETBP1	577	1	1	Substitution - Missense(1)	stomach(1)	c.G3301A						PASS	.	G	ILE/VAL	252,4154	146.9+/-181.5	3,246,1954	117.0	99.0	105.0		3301	-0.5	0.0	18	dbSNP_107	105	1072,7528	225.2+/-261.4	68,936,3296	yes	missense	SETBP1	NM_015559.2	29	71,1182,5250	AA,AG,GG		12.4651,5.7195,10.1799	benign	1101/1597	42532606	1324,11682	2203	4300	6503	SO:0001583	missense	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	TCCCACGTAAAGA	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.3301G>A	18.37:g.42532606G>A	ENSP00000282030:p.Val1101Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Missense_Mutation	SNP	ENST00000282030.5	37	CCDS11923.2	325	0.1488095238095238	20	0.04065040650406504	32	0.08839779005524862	160	0.27972027972027974	113	0.14907651715039577	G	4.173	0.030690	0.08101	0.057195	0.124651	ENSG00000152217	ENST00000282030	T	0.68479	-0.33	5.88	-0.533	0.11887	.	0.438725	0.24576	N	0.037351	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.21147	0.052	B	0.15870	0.014	T	0.19192	-1.0313	9	0.19147	T	0.46	.	6.3875	0.21569	0.5841:0.1418:0.2741:0.0	rs3744825;rs58638841;rs3744825	1101	Q9Y6X0	SETBP_HUMAN	I	1101	ENSP00000282030:V1101I	ENSP00000282030:V1101I	V	+	1	0	SETBP1	40786604	0.856000	0.29760	0.019000	0.16419	0.927000	0.56198	1.206000	0.32321	-0.157000	0.11059	0.561000	0.74099	GTA	G|0.874;A|0.126	0.126	strong		0.542	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
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 GAIIx	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	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	52	14	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		
ANKRD44	91526	hgsc.bcm.edu	37	2	197872574	197872574	+	Missense_Mutation	SNP	C	C	T	rs61752170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:197872574C>T	ENST00000328737.2	-	20	2087	c.2011G>A	c.(2011-2013)Gta>Ata	p.V671I	ANKRD44_ENST00000282272.8_Missense_Mutation_p.V688I|ANKRD44_ENST00000337207.5_Missense_Mutation_p.V671I|ANKRD44_ENST00000450567.1_Missense_Mutation_p.V671I			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	696										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			ACAGTGTCTACGTTGGCTTCC	0.408													C|||	29	0.00579073	0.0	0.0115	5008	,	,		19535	0.0		0.0159	False		,,,				2504	0.0051				p.V696I		Atlas-SNP	.											.	ANKRD44	281	.	0			c.G2086A						PASS	.	C	ILE/VAL	13,4393	20.2+/-43.8	0,13,2190	176.0	148.0	158.0		2086	4.2	0.9	2	dbSNP_129	158	86,8514	49.4+/-109.1	0,86,4214	yes	missense	ANKRD44	NM_001195144.1	29	0,99,6404	TT,TC,CC		1.0,0.2951,0.7612	benign	696/994	197872574	99,12907	2203	4300	6503	SO:0001583	missense	91526	exon20			TGTCTACGTTGGC	AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.2011G>A	2.37:g.197872574C>T	ENSP00000331516:p.Val671Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	37		17	0.007783882783882784	0	0.0	5	0.013812154696132596	0	0.0	12	0.0158311345646438	C	15.33	2.800946	0.50315	0.002951	0.01	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207	T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18	5.09	4.22	0.49857	.	0.000000	0.85682	D	0.000000	T	0.32496	0.0831	N	0.21194	0.64	0.80722	D	1	B	0.12013	0.005	B	0.12156	0.007	T	0.37502	-0.9703	10	0.54805	T	0.06	.	13.8694	0.63610	0.0:0.9267:0.0:0.0733	rs61752170	714	Q8N8A2-2	.	I	511;688;671;671;671	ENSP00000403415:V511I;ENSP00000282272:V688I;ENSP00000331516:V671I;ENSP00000402420:V671I;ENSP00000338794:V671I	ENSP00000282272:V688I	V	-	1	0	ANKRD44	197580819	1.000000	0.71417	0.871000	0.34182	0.921000	0.55340	3.171000	0.50824	1.386000	0.46466	-0.137000	0.14449	GTA	C|0.991;T|0.009	0.009	strong		0.408	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
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 GAIIx	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	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	43	12	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		
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383027	39383027	+	Missense_Mutation	SNP	G	G	T	rs71371478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39383027G>T	ENST00000377721.3	+	1	128	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.A41S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	41	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)		p.A41S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGCCAGCCCGCCTGCTGTGT	0.637																																					p.A41S		Atlas-SNP	.											KRTAP9-2,extremity,malignant_melanoma,0,1	KRTAP9-2	24	1	1	Substitution - Missense(1)	skin(1)	c.G121T						scavenged	.						59.0	53.0	55.0					17																	39383027		2203	4300	6503	SO:0001583	missense	83899	exon1			CAGCCCGCCTGCT	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.121G>T	17.37:g.39383027G>T	ENSP00000366950:p.Ala41Ser	Somatic	43	2	0.0465116		WXS	Illumina HiSeq	Phase_I	40	11	0.275	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.020245	0.00418	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01192	5.2;5.4	2.86	-2.81	0.05805	.	.	.	.	.	T	0.00328	0.0010	N	0.00368	-1.59	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.02654	T	1	.	5.0512	0.14508	0.3642:0.0:0.0934:0.5425	.	41	Q9BYQ4	KRA92_HUMAN	S	41	ENSP00000366950:A41S;ENSP00000398325:A41S	ENSP00000366950:A41S	A	+	1	0	KRTAP9-2	36636553	0.000000	0.05858	0.088000	0.20740	0.203000	0.24098	-1.973000	0.01500	-1.243000	0.02519	-4.519000	0.00005	GCC	G|0.997;T|0.003	0.003	strong		0.637	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
TNS3	64759	hgsc.bcm.edu	37	7	47343083	47343083	+	Silent	SNP	C	C	T	rs3807589	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:47343083C>T	ENST00000398879.1	-	22	3288	c.2922G>A	c.(2920-2922)gaG>gaA	p.E974E	TNS3_ENST00000355730.3_Silent_p.E734E|TNS3_ENST00000311160.9_Silent_p.E974E			Q68CZ2	TENS3_HUMAN	tensin 3	974					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						TACCGGAGAACTCAGCGCTGA	0.652													C|||	544	0.108626	0.1725	0.0548	5008	,	,		16317	0.0744		0.0716	False		,,,				2504	0.1339				p.E974E		Atlas-SNP	.											.	TNS3	140	.	0			c.G2922A						PASS	.	C		567,3485		35,497,1494	24.0	29.0	28.0		2922	0.3	0.0	7	dbSNP_107	28	595,7773		21,553,3610	no	coding-synonymous	TNS3	NM_022748.11		56,1050,5104	TT,TC,CC		7.1104,13.9931,9.3559		974/1446	47343083	1162,11258	2026	4184	6210	SO:0001819	synonymous_variant	64759	exon22			GGAGAACTCAGCG	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"""SH2 domain containing"""	21616	protein-coding gene	gene with protein product	"""tumor endothelial marker 6"""	606825	"""tensin-like SH2 domain-containing 1"""	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.2922G>A	7.37:g.47343083C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	59	17	0.288136	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Silent	SNP	ENST00000398879.1	37	CCDS5506.2																																																																																			C|0.907;T|0.093	0.093	strong		0.652	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748	
MUC16	94025	hgsc.bcm.edu	37	19	9060059	9060059	+	Missense_Mutation	SNP	A	A	C	rs12977368	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9060059A>C	ENST00000397910.4	-	3	27590	c.27387T>G	c.(27385-27387)gaT>gaG	p.D9129E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9131	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCCATGGCACATCTCCAGGAG	0.483													A|||	897	0.179113	0.1445	0.2061	5008	,	,		23138	0.0099		0.3121	False		,,,				2504	0.2444				p.D9129E		Atlas-SNP	.											.	MUC16	4315	.	0			c.T27387G						PASS	.	A	GLU/ASP	610,3382		40,530,1426	79.0	75.0	76.0		27387	-1.2	0.0	19	dbSNP_121	76	2806,5520		497,1812,1854	yes	missense	MUC16	NM_024690.2	45	537,2342,3280	CC,CA,AA		33.7017,15.2806,27.7318	possibly-damaging	9129/14508	9060059	3416,8902	1996	4163	6159	SO:0001583	missense	94025	exon3			TGGCACATCTCCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.27387T>G	19.37:g.9060059A>C	ENSP00000381008:p.Asp9129Glu	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	390	0.17857142857142858	68	0.13821138211382114	78	0.2154696132596685	5	0.008741258741258742	239	0.3153034300791557	a	6.593	0.477708	0.12521	0.152806	0.337017	ENSG00000181143	ENST00000397910	T	0.23348	1.91	2.34	-1.19	0.09585	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	P	0.41041	0.736	B	0.44224	0.444	T	0.40887	-0.9539	8	0.87932	D	0	.	2.9933	0.05990	0.4644:0.2373:0.2983:0.0	rs12977368;rs12977368	9129	B5ME49	.	E	9129	ENSP00000381008:D9129E	ENSP00000381008:D9129E	D	-	3	2	MUC16	8921059	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-2.522000	0.00950	-0.409000	0.07553	-0.775000	0.03384	GAT	A|0.794;C|0.206	0.206	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FAM66D	100132923	hgsc.bcm.edu	37	8	11990038	11990038	+	RNA	SNP	G	G	A	rs9694759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11990038G>A	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		CTGATCTGTCGGTTTCGTCGA	0.463													-|||	463	0.0924521	0.2489	0.0562	5008	,	,		25300	0.0397		0.0318	False		,,,				2504	0.0235				p.P494L		Atlas-SNP	.											.	.	.	.	0			c.C1481T						PASS	.																																					392197	exon1			TCTGTCGGTTTCG			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11990038G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	153	38	0.248366	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				G|0.911;A|0.089	0.089	strong		0.463	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
ALDH3A1	218	hgsc.bcm.edu	37	17	19646690	19646690	+	Silent	SNP	C	C	T	rs138392076	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:19646690C>T	ENST00000457500.2	-	2	578	c.249G>A	c.(247-249)gcG>gcA	p.A83A	ALDH3A1_ENST00000225740.6_Silent_p.A83A|ALDH3A1_ENST00000444455.1_Silent_p.A83A|ALDH3A1_ENST00000485231.1_5'UTR|ALDH3A1_ENST00000494157.2_Silent_p.A10A|ALDH3A1_ENST00000395555.3_Silent_p.A83A	NM_001135168.1	NP_001128640.1	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3 family, member A1	83					aging (GO:0007568)|cellular aldehyde metabolic process (GO:0006081)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|alcohol dehydrogenase (NADP+) activity (GO:0008106)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)		CGGGCTCATCCGCGGCCCACT	0.587													C|||	3	0.000599042	0.0008	0.0	5008	,	,		18723	0.0		0.002	False		,,,				2504	0.0				p.A83A		Atlas-SNP	.											ALDH3A1,NS,carcinoma,-1,1	ALDH3A1	40	1	0			c.G249A						scavenged	.						132.0	120.0	124.0					17																	19646690		2203	4300	6503	SO:0001819	synonymous_variant	218	exon2			CTCATCCGCGGCC	M74542	CCDS11212.1	17p11.2	2010-05-07	2010-05-07		ENSG00000108602	ENSG00000108602	1.2.1.5	"""Aldehyde dehydrogenases"""	405	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase, dimeric NADP-preferring"""	100660		ALDH3		7774944, 1737758	Standard	NM_000691		Approved		uc010cqu.3	P30838	OTTHUMG00000059469	ENST00000457500.2:c.249G>A	17.37:g.19646690C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	112	3	0.0267857	NM_001135168	A8K828|Q9BT37	Silent	SNP	ENST00000457500.2	37	CCDS11212.1																																																																																			A|0.000;C|1.000;T|0.000	0.000	strong		0.587	ALDH3A1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132265.4	NM_000691	
PROSER2	254427	hgsc.bcm.edu	37	10	11911764	11911764	+	Missense_Mutation	SNP	G	G	A	rs117789748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:11911764G>A	ENST00000277570.5	+	4	821	c.667G>A	c.(667-669)Ggg>Agg	p.G223R	PROSER2-AS1_ENST00000453242.1_RNA|PROSER2-AS1_ENST00000445498.1_RNA|PROSER2_ENST00000379200.1_Missense_Mutation_p.G27R	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	223	Pro-rich.																GGGCCGGCCCGGGGAGTGGAG	0.726													G|||	249	0.0497204	0.0038	0.072	5008	,	,		8094	0.0		0.1024	False		,,,				2504	0.093				p.G223R		Atlas-SNP	.											.	.	.	.	0			c.G667A						PASS	.	G	ARG/GLY	84,4136		2,80,2028	5.0	6.0	5.0		667	4.0	0.0	10	dbSNP_132	5	921,7407		45,831,3288	no	missense	C10orf47	NM_153256.3	125	47,911,5316	AA,AG,GG		11.0591,1.9905,8.0092	probably-damaging	223/436	11911764	1005,11543	2110	4164	6274	SO:0001583	missense	254427	exon4			CGGCCCGGGGAGT	BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426			23728	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 47"", ""proline and serine-rich protein 2"""	C10orf47		12477932	Standard	NM_153256		Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.667G>A	10.37:g.11911764G>A	ENSP00000277570:p.Gly223Arg	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	25	16	0.64	NM_153256	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	Missense_Mutation	SNP	ENST00000277570.5	37	CCDS7085.1	108	0.04945054945054945	3	0.006097560975609756	21	0.058011049723756904	0	0.0	84	0.11081794195250659	G	11.11	1.542229	0.27563	0.019905	0.110591	ENSG00000148426	ENST00000379208;ENST00000277570;ENST00000379202;ENST00000379200	T;T	0.08634	3.07;3.07	5.02	3.99	0.46301	.	0.411883	0.23012	N	0.052942	T	0.00300	0.0009	L	0.42245	1.32	0.80722	P	0.0	D	0.76494	0.999	P	0.62740	0.906	T	0.02925	-1.1093	9	0.87932	D	0	-6.992	7.4733	0.27361	0.2297:0.0:0.7703:0.0	.	223	Q86WR7	CJ047_HUMAN	R	223;223;223;27	ENSP00000277570:G223R;ENSP00000368498:G27R	ENSP00000277570:G223R	G	+	1	0	C10orf47	11951770	0.142000	0.22610	0.011000	0.14972	0.010000	0.07245	2.643000	0.46604	2.308000	0.77769	0.305000	0.20034	GGG	G|0.943;A|0.057	0.057	strong		0.726	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256	
MUC16	94025	hgsc.bcm.edu	37	19	9071834	9071834	+	Silent	SNP	G	G	C	rs17000803	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9071834G>C	ENST00000397910.4	-	3	15815	c.15612C>G	c.(15610-15612)ccC>ccG	p.P5204P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5206	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTGTGTCCGTGGGAAAGCTGG	0.468													G|||	1007	0.201078	0.0946	0.2824	5008	,	,		21218	0.3254		0.167	False		,,,				2504	0.1943				p.P5204P		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	0			c.C15612G						scavenged	.	G		399,3425		18,363,1531	188.0	177.0	180.0		15612	-1.2	0.0	19	dbSNP_123	180	1504,6742		136,1232,2755	no	coding-synonymous	MUC16	NM_024690.2		154,1595,4286	CC,CG,GG		18.2391,10.4341,15.7664		5204/14508	9071834	1903,10167	1912	4123	6035	SO:0001819	synonymous_variant	94025	exon3			GTCCGTGGGAAAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15612C>G	19.37:g.9071834G>C		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.792;C|0.208	0.208	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DNAH3	55567	hgsc.bcm.edu	37	16	20966273	20966273	+	Missense_Mutation	SNP	G	G	A	rs12924551	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20966273G>A	ENST00000261383.3	-	55	10932	c.10933C>T	c.(10933-10935)Cgc>Tgc	p.R3645C	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3645	AAA 6. {ECO:0000250}.		R -> C (in dbSNP:rs12924551).		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)|microtubule motor activity (GO:0003777)	p.R3645S(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		AGGTAGGAGCGCAACAGGTTG	0.493													G|||	439	0.0876597	0.0197	0.0706	5008	,	,		14793	0.1716		0.0746	False		,,,				2504	0.1186				p.R3645C		Atlas-SNP	.											DNAH3_ENST00000261383,NS,carcinoma,+1,4	DNAH3	1142	4	2	Substitution - Missense(2)	upper_aerodigestive_tract(2)	c.C10933T						PASS	.	G	CYS/ARG	122,4280	90.6+/-129.3	3,116,2082	123.0	120.0	121.0		10933	5.4	1.0	16	dbSNP_121	121	715,7885	175.6+/-225.6	28,659,3613	yes	missense	DNAH3	NM_017539.1	180	31,775,5695	AA,AG,GG		8.314,2.7715,6.4375	probably-damaging	3645/4117	20966273	837,12165	2201	4300	6501	SO:0001583	missense	55567	exon55			AGGAGCGCAACAG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.10933C>T	16.37:g.20966273G>A	ENSP00000261383:p.Arg3645Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	131	66	0.503817	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	182	0.08333333333333333	15	0.03048780487804878	19	0.052486187845303865	83	0.1451048951048951	65	0.08575197889182058	G	24.4	4.531842	0.85706	0.027715	0.08314	ENSG00000158486	ENST00000261383	T	0.10960	2.82	5.43	5.43	0.79202	Dynein heavy chain (1);	0.064262	0.64402	D	0.000007	T	0.00356	0.0011	H	0.97315	3.98	0.09310	P	1.0	D	0.89917	1.0	D	0.68943	0.961	T	0.26643	-1.0097	9	0.87932	D	0	.	19.2436	0.93893	0.0:0.0:1.0:0.0	rs12924551;rs52819084;rs12924551	3645	Q8TD57	DYH3_HUMAN	C	3645	ENSP00000261383:R3645C	ENSP00000261383:R3645C	R	-	1	0	DNAH3	20873774	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.870000	0.87175	2.543000	0.85770	0.655000	0.94253	CGC	G|0.926;A|0.074	0.074	strong		0.493	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
RSPH1	89765	hgsc.bcm.edu	37	21	43896143	43896143	+	Missense_Mutation	SNP	C	C	T	rs117385282	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43896143C>T	ENST00000291536.3	-	8	909	c.742G>A	c.(742-744)Ggg>Agg	p.G248R	RSPH1_ENST00000398352.3_Missense_Mutation_p.G210R	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	248					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.G248R(1)		large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						GCCTCCTCCCCGGGTTCTCCT	0.602													C|||	420	0.0838658	0.0076	0.1254	5008	,	,		18028	0.0109		0.171	False		,,,				2504	0.1431				p.G248R	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											RSPH1,NS,carcinoma,0,1	RSPH1	36	1	1	Substitution - Missense(1)	stomach(1)	c.G742A						PASS	.	C	ARG/GLY	159,4247	108.2+/-146.6	2,155,2046	69.0	64.0	66.0		742	-0.7	0.0	21	dbSNP_132	66	1647,6953	304.1+/-306.8	179,1289,2832	yes	missense	RSPH1	NM_080860.2	125	181,1444,4878	TT,TC,CC		19.1512,3.6087,13.8859	benign	248/310	43896143	1806,11200	2203	4300	6503	SO:0001583	missense	89765	exon8			CCTCCCCGGGTTC	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"""meichroacidin"""	609314	"""testis specific A2 homolog (mouse)"""	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.742G>A	21.37:g.43896143C>T	ENSP00000291536:p.Gly248Arg	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	30	0.357143	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Missense_Mutation	SNP	ENST00000291536.3	37	CCDS13688.1	191	0.08745421245421245	5	0.01016260162601626	50	0.13812154696132597	6	0.01048951048951049	130	0.17150395778364116	C	1.930	-0.446146	0.04604	0.036087	0.191512	ENSG00000160188	ENST00000291536;ENST00000398352	T;T	0.60171	0.29;0.21	3.39	-0.712	0.11226	.	0.549173	0.16469	N	0.213079	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.09185	-1.0686	9	0.14252	T	0.57	.	2.8184	0.05464	0.2015:0.4424:0.0:0.356	.	248	Q8WYR4	RSPH1_HUMAN	R	248;210	ENSP00000291536:G248R;ENSP00000381395:G210R	ENSP00000291536:G248R	G	-	1	0	RSPH1	42769212	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.695000	0.05109	-0.152000	0.11156	0.655000	0.94253	GGG	C|0.869;T|0.131	0.131	strong		0.602	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		
ABHD12B	145447	hgsc.bcm.edu	37	14	51368610	51368610	+	Missense_Mutation	SNP	A	A	G	rs28564871|rs386777431	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:51368610A>G	ENST00000337334.2	+	10	859	c.844A>G	c.(844-846)Atc>Gtc	p.I282V	ABHD12B_ENST00000395752.1_Missense_Mutation_p.I175V|ABHD12B_ENST00000353130.1_Missense_Mutation_p.I205V|PYGL_ENST00000532462.1_Intron	NM_001206673.1	NP_001193602.1	Q7Z5M8	AB12B_HUMAN	abhydrolase domain containing 12B	282			I -> V (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.				hydrolase activity (GO:0016787)	p.I205V(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(5)	10	all_epithelial(31;0.00481)|Breast(41;0.148)					AGACAAAATAATCTTTCCTAA	0.313													G|||	1421	0.283746	0.1649	0.3876	5008	,	,		18507	0.4573		0.2028	False		,,,				2504	0.2751				p.I282V		Atlas-SNP	.											ABHD12B_ENST00000337334,colon,carcinoma,-1,5	ABHD12B	53	5	1	Substitution - Missense(1)	breast(1)	c.A844G						PASS	.	G	VAL/ILE,VAL/ILE	673,3733	760.5+/-413.0	54,565,1584	75.0	72.0	73.0		844,613	3.3	1.0	14	dbSNP_125	73	1637,6955	738.4+/-407.1	151,1335,2810	yes	missense,missense	ABHD12B	NM_001206673.1,NM_181814.1	29,29	205,1900,4394	GG,GA,AA		19.0526,15.2746,17.772	benign,benign	282/363,205/286	51368610	2310,10688	2203	4296	6499	SO:0001583	missense	145447	exon10			AAAATAATCTTTC	BG698443	CCDS9702.1, CCDS55916.1	14q21.3	2009-10-09	2007-04-03	2007-04-03	ENSG00000131969	ENSG00000131969		"""Abhydrolase domain containing"""	19837	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 29"""	C14orf29			Standard	NM_181814		Approved	BEM46L3	uc001wys.3	Q7Z5M8	OTTHUMG00000140286	ENST00000337334.2:c.844A>G	14.37:g.51368610A>G	ENSP00000336693:p.Ile282Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	81	49	0.604938	NM_001206673	Q3KNR9|Q3KNS0|Q7Z5M6|Q7Z5M7|Q8N4D2	Missense_Mutation	SNP	ENST00000337334.2	37	CCDS55916.1	657	0.3008241758241758	90	0.18292682926829268	139	0.3839779005524862	268	0.46853146853146854	160	0.21108179419525067	G	6.676	0.493340	0.12702	0.152746	0.190526	ENSG00000131969	ENST00000353130;ENST00000337334;ENST00000395752	T;T;T	0.41065	2.23;1.01;2.27	5.24	3.35	0.38373	.	0.502898	0.21095	N	0.080253	T	0.00012	0.0000	N	0.11789	0.175	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.47611	-0.9104	9	0.09843	T	0.71	-9.4496	5.205	0.15285	0.175:0.0:0.6608:0.1641	rs28564871;rs28564871	282;205	Q7Z5M8;Q7Z5M8-2	AB12B_HUMAN;.	V	205;282;175	ENSP00000343951:I205V;ENSP00000336693:I282V;ENSP00000379101:I175V	ENSP00000336693:I282V	I	+	1	0	ABHD12B	50438360	0.799000	0.28903	0.998000	0.56505	0.960000	0.62799	0.331000	0.19733	0.401000	0.25424	-0.119000	0.15052	ATC	A|0.765;G|0.235	0.235	strong		0.313	ABHD12B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411030.1		
FAM21C	253725	hgsc.bcm.edu	37	10	46254783	46254783	+	Silent	SNP	A	A	G	rs186891138	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:46254783A>G	ENST00000336378.4	+	17	1687	c.1569A>G	c.(1567-1569)aaA>aaG	p.K523K	FAM21C_ENST00000537517.1_Silent_p.K499K|FAM21C_ENST00000359860.4_Silent_p.K467K|FAM21C_ENST00000374362.2_Silent_p.K523K|FAM21C_ENST00000540872.1_Silent_p.K523K	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	523					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CTTACAGCAAAAATCTCAAGC	0.403																																					p.K523K		Atlas-SNP	.											FAM21C,caecum,carcinoma,0,1	FAM21C	68	1	0			c.A1569G						scavenged	.						62.0	73.0	69.0					10																	46254783		1735	3995	5730	SO:0001819	synonymous_variant	253725	exon17			CAGCAAAAATCTC		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.1569A>G	10.37:g.46254783A>G		Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	158	28	0.177215	NM_015262	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Silent	SNP	ENST00000336378.4	37																																																																																				A|0.375;G|0.625	0.625	strong		0.403	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
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 GAIIx	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		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	86	38	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 GAIIx	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_ENST00000529824.2_Missense_Mutation_p.P1496L|TIAM2_ENST00000456144.1_Missense_Mutation_p.P1496L|TIAM2_ENST00000275246.7_Missense_Mutation_p.P392L|TIAM2_ENST00000528391.2_Missense_Mutation_p.P803L|TIAM2_ENST00000318981.5_Missense_Mutation_p.P1467L|TIAM2_ENST00000367174.2_Missense_Mutation_p.P843L|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000456877.2_Missense_Mutation_p.P779L|TIAM2_ENST00000360366.4_Missense_Mutation_p.P1491L			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	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	175	94	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	
CPSF3L	54973	hgsc.bcm.edu	37	1	1247494	1247494	+	Silent	SNP	T	T	C	rs12103	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1247494T>C	ENST00000435064.1	-	16	1723	c.1641A>G	c.(1639-1641)ccA>ccG	p.P547P	CPSF3L_ENST00000545578.1_Silent_p.P518P|CPSF3L_ENST00000419704.1_Silent_p.P446P|CPSF3L_ENST00000540437.1_Silent_p.P553P|CPSF3L_ENST00000421495.2_Silent_p.P289P|CPSF3L_ENST00000450926.2_Silent_p.P525P|CPSF3L_ENST00000462432.1_5'UTR|CPSF3L_ENST00000411962.1_Silent_p.P449P	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	547					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		CAGAGCCGTCTGGGAGGTGCT	0.687													T|||	1599	0.319289	0.0923	0.4424	5008	,	,		12806	0.0188		0.8121	False		,,,				2504	0.3415				p.P553P		Atlas-SNP	.											.	CPSF3L	33	.	0			c.A1659G						PASS	.	T		874,3504		97,680,1412	18.0	16.0	17.0		1641	-7.9	0.3	1	dbSNP_52	17	6892,1654		2820,1252,201	no	coding-synonymous	CPSF3L	NM_017871.4		2917,1932,1613	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	19.3541,19.9635,39.9102		547/601	1247494	7766,5158	2189	4273	6462	SO:0001819	synonymous_variant	54973	exon18			GCCGTCTGGGAGG	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"""integrator complex subunit 11"""	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.1641A>G	1.37:g.1247494T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001256456	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Silent	SNP	ENST00000435064.1	37	CCDS21.1																																																																																			T|0.554;C|0.446	0.446	strong		0.687	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871	
OR2W5	441932	hgsc.bcm.edu	37	1	247654498	247654498	+	RNA	SNP	G	G	A	rs61070846	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247654498G>A	ENST00000522351.1	+	0	129							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)			GGCCTGGACTGGAGAAAATTC	0.488													g|||	647	0.129193	0.1483	0.2176	5008	,	,		18871	0.0288		0.1909	False		,,,				2504	0.0808				p.L23L		Atlas-SNP	.											.	OR2W5	97	.	0			c.G69A						PASS	.	A		647,3759	277.5+/-273.7	41,565,1597	164.0	149.0	154.0		69	-3.0	0.0	1	dbSNP_129	154	1810,6790	326.0+/-317.2	186,1438,2676	no	coding-synonymous	OR2W5	NM_001004698.2		227,2003,4273	AA,AG,GG		21.0465,14.6845,18.8913		23/321	247654498	2457,10549	2203	4300	6503			441932	exon1			TGGACTGGAGAAA			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.247654498G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	182	73	0.401099	NM_001004698	B9EH85	Silent	SNP	ENST00000522351.1	37																																																																																				G|0.820;A|0.180	0.180	strong		0.488	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
PARP16	54956	hgsc.bcm.edu	37	15	65553246	65553246	+	Silent	SNP	C	C	T	rs2304896	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:65553246C>T	ENST00000444347.2	-	3	881	c.465G>A	c.(463-465)gtG>gtA	p.V155V	PARP16_ENST00000261888.6_Silent_p.V270V			Q8N5Y8	PAR16_HUMAN	poly (ADP-ribose) polymerase family, member 16	270	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cell death (GO:0060548)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum tubular network (GO:0071782)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	kinase binding (GO:0019900)|NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|protein serine/threonine kinase activator activity (GO:0043539)			kidney(1)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	9						TCTGTGAATACACCAGGAGGT	0.498													C|||	1155	0.230631	0.2572	0.4049	5008	,	,		19655	0.125		0.2714	False		,,,				2504	0.138				p.V270V	NSCLC(50;885 1163 13509 21242 41978)	Atlas-SNP	.											.	PARP16	23	.	0			c.G810A						PASS	.	C		1145,3257	406.9+/-334.0	150,845,1206	181.0	162.0	169.0		810	1.9	1.0	15	dbSNP_100	169	2567,6031	417.6+/-352.5	374,1819,2106	yes	coding-synonymous	PARP16	NM_017851.4		524,2664,3312	TT,TC,CC		29.8558,26.0109,28.5538		270/324	65553246	3712,9288	2201	4299	6500	SO:0001819	synonymous_variant	54956	exon5			TGAATACACCAGG	AK000516	CCDS10204.1	15q22.2	2010-02-16	2004-08-25	2004-08-25	ENSG00000138617	ENSG00000138617		"""Poly (ADP-ribose) polymerases"""	26040	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 30"""	C15orf30		15273990	Standard	NM_017851		Approved	FLJ20509, FLJ25281, pART15	uc002aoq.3	Q8N5Y8	OTTHUMG00000133138	ENST00000444347.2:c.465G>A	15.37:g.65553246C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_017851	Q6PK64|Q9NX03	Silent	SNP	ENST00000444347.2	37																																																																																				C|0.729;T|0.271	0.271	strong		0.498	PARP16-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000418174.1	NM_017851	
SPRR1A	6698	hgsc.bcm.edu	37	1	152957887	152957887	+	Missense_Mutation	SNP	G	G	A	rs1611764	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152957887G>A	ENST00000368762.1	+	1	181	c.181G>A	c.(181-183)Gtt>Att	p.V61I	SPRR1A_ENST00000307122.2_Missense_Mutation_p.V61I			P35321	SPR1A_HUMAN	small proline-rich protein 1A	61	6 X 8 AA approximate tandem repeats.		V -> I (in dbSNP:rs1611764). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8325635, ECO:0000269|Ref.3}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCAGCCCAAGGTTCCAGAGCC	0.627													G|||	2810	0.561102	0.6278	0.4524	5008	,	,		15250	0.6319		0.5348	False		,,,				2504	0.502				p.V61I		Atlas-SNP	.											.	SPRR1A	17	.	0			c.G181A						PASS	.	G	ILE/VAL,ILE/VAL	2805,1601	660.2+/-400.7	897,1011,295	108.0	105.0	106.0		181,181	3.8	0.3	1	dbSNP_89	106	4674,3926	602.4+/-394.5	1279,2116,905	no	missense,missense	SPRR1A	NM_001199828.1,NM_005987.3	29,29	2176,3127,1200	AA,AG,GG		45.6512,36.3368,42.4958	benign,benign	61/90,61/90	152957887	7479,5527	2203	4300	6503	SO:0001583	missense	6698	exon2			CCCAAGGTTCCAG	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.181G>A	1.37:g.152957887G>A	ENSP00000357751:p.Val61Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	37	CCDS1032.1	1269	0.5810439560439561	319	0.6483739837398373	180	0.4972375690607735	372	0.6503496503496503	398	0.525065963060686	G	12.59	1.983175	0.34942	0.636632	0.543488	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.14766	2.48;2.48	5.64	3.77	0.43336	.	0.874660	0.09328	N	0.817264	T	0.08537	0.0212	.	.	.	0.53688	P	2.5000000000052758E-5	P	0.44195	0.828	P	0.47251	0.542	T	0.21143	-1.0254	8	0.45353	T	0.12	0.414	7.7627	0.28961	0.1845:0.0:0.8155:0.0	rs1611764;rs17881890;rs58884077;rs1611764	61	P35321	SPR1A_HUMAN	I	61	ENSP00000307340:V61I;ENSP00000357751:V61I	ENSP00000307340:V61I	V	+	1	0	SPRR1A	151224511	0.044000	0.20184	0.277000	0.24703	0.039000	0.13416	1.015000	0.29963	1.389000	0.46526	-0.266000	0.10368	GTT	G|0.417;A|0.583	0.583	strong		0.627	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987	
CFHR3	10878	hgsc.bcm.edu	37	1	196759347	196759347	+	Silent	SNP	A	A	T	rs149352569		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196759347A>T	ENST00000367425.4	+	5	878	c.786A>T	c.(784-786)ccA>ccT	p.P262P	CFHR3_ENST00000391985.3_Silent_p.P201P	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	262	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.P262P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						CGGAACCACCAAGATGCATAC	0.363																																					p.P262P		Atlas-SNP	.											CFHR3,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CFHR3	52	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A786T						scavenged	.						29.0	39.0	36.0					1																	196759347		1522	3863	5385	SO:0001819	synonymous_variant	10878	exon5			ACCACCAAGATGC	X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"""Complement system"""	16980	protein-coding gene	gene with protein product	"""complement factor H related 3"""	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.786A>T	1.37:g.196759347A>T		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	222	21	0.0945946	NM_021023	B4DPR0|Q9UJ16	Silent	SNP	ENST00000367425.4	37	CCDS30958.1																																																																																			.	.	weak		0.363	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023	
CCDC137	339230	hgsc.bcm.edu	37	17	79634813	79634813	+	Silent	SNP	T	T	C	rs11546632	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79634813T>C	ENST00000329214.8	+	2	592	c.189T>C	c.(187-189)atT>atC	p.I63I	OXLD1_ENST00000573786.1_5'Flank|OXLD1_ENST00000374741.3_5'Flank|OXLD1_ENST00000571503.1_5'Flank	NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	63							poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			AACAGGAGATTCCTTTCCGGC	0.517													C|||	537	0.107228	0.1467	0.0951	5008	,	,		16061	0.002		0.1928	False		,,,				2504	0.0828				p.I63I		Atlas-SNP	.											.	CCDC137	27	.	0			c.T189C						PASS	.	C		714,3016		71,572,1222	50.0	53.0	52.0		189	-0.3	1.0	17	dbSNP_120	52	1366,6824		126,1114,2855	no	coding-synonymous	CCDC137	NM_199287.2		197,1686,4077	CC,CT,TT		16.6789,19.1421,17.4497		63/290	79634813	2080,9840	1865	4095	5960	SO:0001819	synonymous_variant	339230	exon2			GGAGATTCCTTTC	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.189T>C	17.37:g.79634813T>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	17	7	0.411765	NM_199287		Silent	SNP	ENST00000329214.8	37	CCDS42400.1																																																																																			T|0.868;C|0.132	0.132	strong		0.517	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
CEL	1056	hgsc.bcm.edu	37	9	135947032	135947032	+	Missense_Mutation	SNP	C	C	A	rs201411101		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135947032C>A	ENST00000372080.4	+	11	2168	c.2152C>A	c.(2152-2154)Ccg>Acg	p.P718T	CEL_ENST00000351304.7_Missense_Mutation_p.P649T	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	715	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				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)	p.P718T(1)		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)		CGCCCCCGTGCCGCCCACGGG	0.766																																					p.P718T		Atlas-SNP	.											CEL,NS,carcinoma,0,2	CEL	71	2	1	Substitution - Missense(1)	lung(1)	c.C2152A						scavenged	.						7.0	9.0	8.0					9																	135947032		1666	3839	5505	SO:0001583	missense	1056	exon11			CCCGTGCCGCCCA	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.2152C>A	9.37:g.135947032C>A	ENSP00000361151:p.Pro718Thr	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	c	9.217	1.032353	0.19590	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.71341	-0.35;-0.56	2.24	1.28	0.21552	.	.	.	.	.	T	0.56031	0.1958	L	0.34521	1.04	0.09310	N	1	B	0.29862	0.259	B	0.23018	0.043	T	0.50294	-0.8845	9	0.87932	D	0	.	8.747	0.34591	0.0:0.7634:0.2366:0.0	.	715	P19835	CEL_HUMAN	T	718;649;684	ENSP00000361151:P718T;ENSP00000342217:P649T	ENSP00000304021:P684T	P	+	1	0	CEL	134936853	0.000000	0.05858	0.006000	0.13384	0.004000	0.04260	0.377000	0.20552	0.473000	0.27368	0.306000	0.20318	CCG	.	.	weak		0.766	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
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 GAIIx	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_ENST00000405493.2_Missense_Mutation_p.L258P|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.L300P|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.L258P|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.L300P|RAPGEF3_ENST00000171000.4_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	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	14	5	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	
ABCC2	1244	hgsc.bcm.edu	37	10	101604207	101604207	+	Silent	SNP	C	C	T	rs3740066	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101604207C>T	ENST00000370449.4	+	28	4085	c.3972C>T	c.(3970-3972)atC>atT	p.I1324I		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1324	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.I1324I(1)		NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CTTGTGACATCGGTAGCATGG	0.542													C|||	1443	0.288139	0.2163	0.3415	5008	,	,		20904	0.247		0.3708	False		,,,				2504	0.3047				p.I1324I		Atlas-SNP	.											ABCC2,NS,carcinoma,0,1	ABCC2	160	1	1	Substitution - coding silent(1)	stomach(1)	c.C3972T	GRCh37	CM080009	ABCC2	M	rs3740066	PASS	.			1145,3261	407.3+/-334.2	151,843,1209	144.0	126.0	132.0		3972	0.7	0.8	10	dbSNP_107	132	3193,5407	483.7+/-371.2	605,1983,1712	no	coding-synonymous	ABCC2	NM_000392.3		756,2826,2921	TT,TC,CC		37.1279,25.9873,33.3538		1324/1546	101604207	4338,8668	2203	4300	6503	SO:0001819	synonymous_variant	1244	exon28			TGACATCGGTAGC	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.3972C>T	10.37:g.101604207C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Silent	SNP	ENST00000370449.4	37	CCDS7484.1																																																																																			C|0.678;T|0.322	0.322	strong		0.542	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
SERPINB2	5055	hgsc.bcm.edu	37	18	61570470	61570470	+	Silent	SNP	T	T	G	rs6102	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61570470T>G	ENST00000299502.4	+	8	1259	c.1179T>G	c.(1177-1179)ccT>ccG	p.P393P	SERPINB2_ENST00000457692.1_Silent_p.P393P	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	393					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P393P(1)		NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	CAGATCATCCTTTTCTTTTTC	0.443													T|||	1091	0.217851	0.1747	0.2954	5008	,	,		19162	0.254		0.2058	False		,,,				2504	0.1963				p.P393P		Atlas-SNP	.											SERPINB2,NS,carcinoma,0,1	SERPINB2	63	1	1	Substitution - coding silent(1)	stomach(1)	c.T1179G						PASS	.	T	,	893,3513	345.1+/-308.4	79,735,1389	85.0	90.0	89.0		1179,1179	1.4	1.0	18	dbSNP_52	89	1755,6845	317.2+/-313.1	169,1417,2714	no	coding-synonymous,coding-synonymous	SERPINB2	NM_001143818.1,NM_002575.2	,	248,2152,4103	GG,GT,TT		20.407,20.2678,20.3598	,	393/416,393/416	61570470	2648,10358	2203	4300	6503	SO:0001819	synonymous_variant	5055	exon8			TCATCCTTTTCTT	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.1179T>G	18.37:g.61570470T>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	155	56	0.36129	NM_002575	Q96E96	Silent	SNP	ENST00000299502.4	37	CCDS11989.1																																																																																			T|0.779;G|0.221	0.221	strong		0.443	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
ABCA13	154664	hgsc.bcm.edu	37	7	48312674	48312674	+	Silent	SNP	G	G	A	rs1358066	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48312674G>A	ENST00000435803.1	+	17	3435	c.3411G>A	c.(3409-3411)gtG>gtA	p.V1137V		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1137					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.V1082V(1)|p.V1137V(1)		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						ATGTCAGTGTGTTCAACAAGT	0.343													G|||	2881	0.57528	0.5507	0.5101	5008	,	,		19492	0.7708		0.4632	False		,,,				2504	0.5685				p.V1137V		Atlas-SNP	.											ABCA13_ENST00000435803,NS,carcinoma,0,2	ABCA13	1192	2	2	Substitution - coding silent(2)	stomach(2)	c.G3411A						scavenged	.	G		1847,1833		453,941,446	80.0	77.0	78.0		3411	-5.3	0.0	7	dbSNP_88	78	4016,4160		990,2036,1062	no	coding-synonymous	ABCA13	NM_152701.3		1443,2977,1508	AA,AG,GG		49.1194,49.8098,49.4518		1137/5059	48312674	5863,5993	1840	4088	5928	SO:0001819	synonymous_variant	154664	exon17			CAGTGTGTTCAAC	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.3411G>A	7.37:g.48312674G>A		Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	30	29	0.966667	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			G|0.441;A|0.559	0.559	strong		0.343	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
ALPP	250	hgsc.bcm.edu	37	2	233243981	233243981	+	Missense_Mutation	SNP	A	A	T	rs13026692	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233243981A>T	ENST00000392027.2	+	3	534	c.265A>T	c.(265-267)Ata>Tta	p.I89L	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	89			I -> L (in dbSNP:rs13026692). {ECO:0000269|PubMed:15489334}.		dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		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;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GGGGCCTGAGATACCCCTGGC	0.552													a|||	1947	0.388778	0.2496	0.4611	5008	,	,		19167	0.5377		0.337	False		,,,				2504	0.4254				p.I89L		Atlas-SNP	.											ALPP,NS,carcinoma,0,1	ALPP	53	1	0			c.A265T						PASS	.	A	LEU/ILE	1184,3222		157,870,1176	100.0	100.0	100.0		265	-0.2	0.1	2	dbSNP_121	100	2714,5886		437,1840,2023	yes	missense	ALPP	NM_001632.3	5	594,2710,3199	TT,TA,AA		31.5581,26.8724,29.9708	benign	89/536	233243981	3898,9108	2203	4300	6503	SO:0001583	missense	250	exon3			CCTGAGATACCCC	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.265A>T	2.37:g.233243981A>T	ENSP00000375881:p.Ile89Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	155	73	0.470968	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	817	0.3740842490842491	110	0.22357723577235772	151	0.4171270718232044	301	0.5262237762237763	255	0.33641160949868076	.	11.92	1.781661	0.31502	0.268724	0.315581	ENSG00000163283	ENST00000392027	D	0.95724	-3.79	2.47	-0.159	0.13379	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.285447	0.37809	N	0.001939	T	0.00012	0.0000	N	0.01874	-0.695	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.47433	-0.9118	9	0.66056	D	0.02	.	4.3616	0.11205	0.6235:0.1681:0.2084:0.0	rs13026692;rs57554920;rs13026692	89	P05187	PPB1_HUMAN	L	89	ENSP00000375881:I89L	ENSP00000375881:I89L	I	+	1	0	ALPP	232952225	0.950000	0.32346	0.117000	0.21633	0.049000	0.14656	2.236000	0.43052	-0.152000	0.11156	0.248000	0.18094	ATA	A|0.675;T|0.325	0.325	strong		0.552	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
CA5B	11238	hgsc.bcm.edu	37	X	15800751	15800751	+	Silent	SNP	G	G	A	rs1808	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:15800751G>A	ENST00000318636.3	+	8	1054	c.918G>A	c.(916-918)gcG>gcA	p.A306A	CA5B_ENST00000454127.2_Silent_p.A306A	NM_007220.3	NP_009151.1	Q8WTZ4	CA5BL_HUMAN	carbonic anhydrase VB, mitochondrial	0						mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.A306A(1)		endometrium(1)|kidney(2)|lung(3)|prostate(1)|stomach(2)	9	Hepatocellular(33;0.183)					ATGTACAAGCGAAACCCAAGC	0.433													G|||	1313	0.347815	0.2383	0.3415	3775	,	,		13207	0.2996		0.2505	False		,,,				2504	0.2117				p.A306A		Atlas-SNP	.											.	CA5B	23	.	1	Substitution - coding silent(1)	stomach(1)	c.G918A						PASS	.	G		1072,2763		117,670,168,845,403	95.0	79.0	85.0		918	-8.9	0.0	X	dbSNP_36	85	2276,4452		266,1088,656,1074,1216	no	coding-synonymous	CA5B	NM_007220.3		383,1758,824,1919,1619	AA,AG,A,GG,G		33.8288,27.9531,31.6955		306/318	15800751	3348,7215	2203	4300	6503	SO:0001819	synonymous_variant	11238	exon8			ACAAGCGAAACCC	AB021660	CCDS14171.1	Xp22.1	2008-08-13			ENSG00000169239	ENSG00000169239		"""Carbonic anhydrases"""	1378	protein-coding gene	gene with protein product		300230				10409679	Standard	XM_005274442		Approved		uc004cxe.3	Q9Y2D0	OTTHUMG00000021183	ENST00000318636.3:c.918G>A	X.37:g.15800751G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	103	31	0.300971	NM_007220	A6NEZ4	Silent	SNP	ENST00000318636.3	37	CCDS14171.1																																																																																			G|0.655;0|0.003	.	strong		0.433	CA5B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354933.1	NM_007220	
NLRP2	55655	hgsc.bcm.edu	37	19	55512137	55512137	+	Silent	SNP	C	C	A	rs12768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55512137C>A	ENST00000543010.1	+	13	3203	c.3060C>A	c.(3058-3060)atC>atA	p.I1020I	NLRP2_ENST00000263437.6_Silent_p.I1017I|NLRP2_ENST00000391721.4_Silent_p.I996I|NLRP2_ENST00000537859.1_Silent_p.I998I|NLRP2_ENST00000448584.2_Silent_p.I1020I|NLRP2_ENST00000427260.2_Silent_p.I997I|NLRP2_ENST00000339757.7_Silent_p.I998I|NLRP2_ENST00000538819.1_Silent_p.I996I	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	1020					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GGTTGAAAATCGATGACTTTA	0.388													A|||	2757	0.550519	0.4486	0.6686	5008	,	,		16582	0.6815		0.495	False		,,,				2504	0.5266				p.I1020I		Atlas-SNP	.											.	NLRP2	161	.	0			c.C3060A						PASS	.	A	,,,	2044,2362	610.0+/-391.5	478,1088,637	81.0	78.0	79.0		3060,2994,2991,3060	-6.3	0.0	19	dbSNP_52	79	4569,4031	556.8+/-386.9	1206,2157,937	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	1684,3245,1574	AA,AC,CC		46.8721,46.3913,49.1542	,,,	1020/1063,998/1041,997/1040,1020/1063	55512137	6613,6393	2203	4300	6503	SO:0001819	synonymous_variant	55655	exon13			GAAAATCGATGAC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.3060C>A	19.37:g.55512137C>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			T|0.004;G|0.004	.	strong		0.388	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
SYPL2	284612	hgsc.bcm.edu	37	1	110019439	110019439	+	Missense_Mutation	SNP	A	A	G	rs62623713	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:110019439A>G	ENST00000369872.3	+	4	512	c.296A>G	c.(295-297)gAg>gGg	p.E99G	SYPL2_ENST00000475497.1_3'UTR|SYPL2_ENST00000401021.3_Missense_Mutation_p.E99G	NM_001040709.1	NP_001035799.1	Q5VXT5	SYPL2_HUMAN	synaptophysin-like 2	99	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.			E -> G (in Ref. 2; BAD18604). {ECO:0000305}.	cellular calcium ion homeostasis (GO:0006874)|substantia nigra development (GO:0021762)	integral component of synaptic vesicle membrane (GO:0030285)	transporter activity (GO:0005215)			breast(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	16		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Colorectal(144;0.0129)|Lung(183;0.0436)|READ - Rectum adenocarcinoma(129;0.0698)|Epithelial(280;0.0808)|all cancers(265;0.0869)|LUSC - Lung squamous cell carcinoma(189;0.231)		TGCGATGAAGAGTCCAGCTCC	0.582													A|||	151	0.0301518	0.0144	0.0159	5008	,	,		17314	0.002		0.0547	False		,,,				2504	0.0654				p.E99G		Atlas-SNP	.											SYPL2,NS,carcinoma,-1,1	SYPL2	41	1	0			c.A296G						PASS	.	A	GLY/GLU	109,3975		2,105,1935	84.0	87.0	86.0		296	3.3	0.0	1	dbSNP_129	86	475,7899		12,451,3724	yes	missense	SYPL2	NM_001040709.1	98	14,556,5659	GG,GA,AA		5.6723,2.669,4.6878	possibly-damaging	99/273	110019439	584,11874	2042	4187	6229	SO:0001583	missense	284612	exon4			ATGAAGAGTCCAG	AK131459	CCDS41365.1	1p13.3	2008-02-05			ENSG00000143028	ENSG00000143028			27638	protein-coding gene	gene with protein product	"""mitsugumin-29"""					12975309	Standard	NM_001040709		Approved	Mg29	uc001dxp.3	Q5VXT5	OTTHUMG00000010969	ENST00000369872.3:c.296A>G	1.37:g.110019439A>G	ENSP00000358888:p.Glu99Gly	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_001040709	A8K0E8|A8KAL7|I0IT67|Q6ZMX1	Missense_Mutation	SNP	ENST00000369872.3	37	CCDS41365.1	64	0.029304029304029304	9	0.018292682926829267	8	0.022099447513812154	1	0.0017482517482517483	46	0.06068601583113457	A	6.996	0.553889	0.13374	0.02669	0.056723	ENSG00000143028	ENST00000401021;ENST00000369872	T	0.32515	1.45	5.64	3.32	0.38043	Marvel (1);MARVEL-like domain (1);	1.132410	0.06169	N	0.677290	T	0.04003	0.0112	N	0.03917	-0.325	0.09310	N	1	B;B;B;B	0.12013	0.005;0.0;0.0;0.001	B;B;B;B	0.14578	0.011;0.001;0.001;0.004	T	0.41034	-0.9531	10	0.13853	T	0.58	.	7.1401	0.25552	0.744:0.0:0.256:0.0	rs62623713	99;7;99;99	B4DYR7;Q14DL7;Q5VXT5;Q5VXT5-2	.;.;SYPL2_HUMAN;.	G	99	ENSP00000358888:E99G	ENSP00000358888:E99G	E	+	2	0	SYPL2	109820962	0.021000	0.18746	0.005000	0.12908	0.506000	0.33950	1.418000	0.34782	0.421000	0.25980	0.374000	0.22700	GAG	A|0.962;G|0.038	0.038	strong		0.582	SYPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030191.1	NM_001006603	
KLK3	354	hgsc.bcm.edu	37	19	51359503	51359503	+	Silent	SNP	A	A	G	rs1135766	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51359503A>G	ENST00000326003.2	+	2	95	c.54A>G	c.(52-54)gcA>gcG	p.A18A	KLK3_ENST00000595952.1_Silent_p.A18A|KLK3_ENST00000593997.1_Silent_p.A18A|KLK3_ENST00000360617.3_Silent_p.A18A|KLK3_ENST00000597483.1_Silent_p.A18A	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	18					cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		CAGGTGCTGCACCCCTCATCC	0.592													a|||	1702	0.339856	0.1921	0.4914	5008	,	,		19322	0.4851		0.4195	False		,,,				2504	0.2004				p.A18A	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											KLK3_ENST00000360617,colon,carcinoma,0,2	KLK3	76	2	0			c.A54G						PASS	.	G	,,,	1071,3335	391.4+/-328.1	140,791,1272	96.0	86.0	89.0		54,54,54,54	-4.2	0.0	19	dbSNP_86	89	3585,5015	518.6+/-379.3	765,2055,1480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLK3	NM_001030047.1,NM_001030048.1,NM_001030050.1,NM_001648.2	,,,	905,2846,2752	GG,GA,AA		41.686,24.3078,35.7989	,,,	18/239,18/219,18/70,18/262	51359503	4656,8350	2203	4300	6503	SO:0001819	synonymous_variant	354	exon2			TGCTGCACCCCTC	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.54A>G	19.37:g.51359503A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001030050	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			A|0.599;C|0.019	.	strong		0.592	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
FBXO39	162517	hgsc.bcm.edu	37	17	6683215	6683215	+	Missense_Mutation	SNP	C	C	T	rs4796555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6683215C>T	ENST00000321535.4	+	2	158	c.28C>T	c.(28-30)Ccc>Tcc	p.P10S		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	10			P -> S (in dbSNP:rs4796555).							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						ACTGATCCAGCCCCAAGACCA	0.537													C|||	1626	0.324681	0.2148	0.2896	5008	,	,		20496	0.6151		0.2107	False		,,,				2504	0.316				p.P10S		Atlas-SNP	.											.	FBXO39	50	.	0			c.C28T						PASS	.	C	SER/PRO	958,3448	361.6+/-315.8	107,744,1352	89.0	85.0	86.0		28	2.3	0.9	17	dbSNP_111	86	1879,6721	334.2+/-320.9	213,1453,2634	yes	missense	FBXO39	NM_153230.2	74	320,2197,3986	TT,TC,CC		21.8488,21.7431,21.813	possibly-damaging	10/443	6683215	2837,10169	2203	4300	6503	SO:0001583	missense	162517	exon2			ATCCAGCCCCAAG	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.28C>T	17.37:g.6683215C>T	ENSP00000321386:p.Pro10Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_153230		Missense_Mutation	SNP	ENST00000321535.4	37	CCDS11082.1	740	0.33882783882783885	109	0.22154471544715448	92	0.2541436464088398	380	0.6643356643356644	159	0.20976253298153033	C	12.69	2.013227	0.35511	0.217431	0.218488	ENSG00000177294	ENST00000321535	T	0.54279	0.58	5.56	2.26	0.28386	.	0.525149	0.18834	N	0.129870	T	0.00012	0.0000	L	0.27053	0.805	0.43338	P	0.004612999999999978	B	0.17465	0.022	B	0.14023	0.01	T	0.44221	-0.9342	9	0.10902	T	0.67	-13.5396	4.7906	0.13247	0.1528:0.6137:0.1485:0.085	rs4796555;rs17794696;rs52829409;rs56480343;rs60341795;rs4796555	10	Q8N4B4	FBX39_HUMAN	S	10	ENSP00000321386:P10S	ENSP00000321386:P10S	P	+	1	0	FBXO39	6623939	0.046000	0.20272	0.902000	0.35471	0.970000	0.65996	0.928000	0.28831	0.813000	0.34350	0.561000	0.74099	CCC	C|0.730;N|0.000	.	strong		0.537	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
FBF1	85302	hgsc.bcm.edu	37	17	73922941	73922941	+	Missense_Mutation	SNP	T	T	C	rs2305913	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73922941T>C	ENST00000586717.1	-	9	724	c.451A>G	c.(451-453)Aga>Gga	p.R151G	FBF1_ENST00000389570.4_Missense_Mutation_p.R151G|FBF1_ENST00000319129.5_Missense_Mutation_p.R151G			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	151			R -> G (in dbSNP:rs2305913). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:18838552}.		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)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						AGAAGTCCTCTCAATGGGTCT	0.522													C|||	2265	0.452276	0.8396	0.3213	5008	,	,		20258	0.2202		0.3549	False		,,,				2504	0.3609				p.R151G		Atlas-SNP	.											.	FBF1	48	.	0			c.A451G						PASS	.	C	GLY/ARG	2928,1030		1084,760,135	53.0	51.0	52.0		451	4.3	0.9	17	dbSNP_100	52	2887,5423		518,1851,1786	yes	missense	FBF1	NM_001080542.1	125	1602,2611,1921	CC,CT,TT		34.7413,26.0232,47.3997	benign	151/1134	73922941	5815,6453	1979	4155	6134	SO:0001583	missense	85302	exon9			GTCCTCTCAATGG	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.451A>G	17.37:g.73922941T>C	ENSP00000465132:p.Arg151Gly	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		935	0.4281135531135531	407	0.8272357723577236	130	0.35911602209944754	145	0.2534965034965035	253	0.3337730870712401	C	6.969	0.548733	0.13312	0.739768	0.347413	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.17054	2.3;2.3	5.28	4.31	0.51392	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.09729	-1.0661	8	0.45353	T	0.12	-2.1032	8.3301	0.32180	0.0:0.8185:0.0:0.1815	rs2305913;rs17856694;rs57572964;rs2305913	165;151;151	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	G	151;151;151;164	ENSP00000374221:R151G;ENSP00000324292:R151G	ENSP00000324292:R151G	R	-	1	2	FBF1	71434536	1.000000	0.71417	0.905000	0.35620	0.016000	0.09150	2.331000	0.43894	0.632000	0.30432	-0.119000	0.15052	AGA	T|0.549;C|0.451	0.451	strong		0.522	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
ZFHX3	463	hgsc.bcm.edu	37	16	72993622	72993622	+	Silent	SNP	C	C	T	rs62053190	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:72993622C>T	ENST00000268489.5	-	2	1095	c.423G>A	c.(421-423)gcG>gcA	p.A141A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	141					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CCACAATGTACGCGGAGCCGT	0.667													C|||	219	0.04373	0.0507	0.0317	5008	,	,		13453	0.003		0.0616	False		,,,				2504	0.0665				p.A141A		Atlas-SNP	.											ZFHX3,NS,carcinoma,0,2	ZFHX3	404	2	0			c.G423A						PASS	.	C	,	276,4120	146.9+/-181.5	9,258,1931	35.0	39.0	38.0		,423	-10.2	0.4	16	dbSNP_129	38	604,7996	152.8+/-207.3	25,554,3721	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	34,812,5652	TT,TC,CC		7.0233,6.2784,6.7713	,	,141/3704	72993622	880,12116	2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			AATGTACGCGGAG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.423G>A	16.37:g.72993622C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			C|0.941;T|0.059	0.059	strong		0.667	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
CELA2A	63036	hgsc.bcm.edu	37	1	15789297	15789297	+	Silent	SNP	A	A	C	rs3815787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:15789297A>C	ENST00000359621.4	+	4	322	c.297A>C	c.(295-297)gcA>gcC	p.A99A		NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	99	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)	p.A99A(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						GCTCGCTGGCAGTCAGTGTCT	0.602													C|||	1997	0.398762	0.6762	0.3213	5008	,	,		15780	0.2321		0.3161	False		,,,				2504	0.3354				p.A99A		Atlas-SNP	.											CELA2A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	CELA2A	32	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A297C						PASS	.	C		2681,1725	516.5+/-369.2	827,1027,349	98.0	104.0	102.0		297	-6.5	0.0	1	dbSNP_107	102	2851,5749	673.3+/-403.0	473,1905,1922	no	coding-synonymous	CELA2A	NM_033440.2		1300,2932,2271	CC,CA,AA		33.1512,39.1512,42.5342		99/270	15789297	5532,7474	2203	4300	6503	SO:0001819	synonymous_variant	63036	exon4			GCTGGCAGTCAGT		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"""elastase 2A"""	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.297A>C	1.37:g.15789297A>C		Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_033440	B2R5I4|Q14243	Silent	SNP	ENST00000359621.4	37	CCDS157.1																																																																																			.	.	weak		0.602	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440	
OCEL1	79629	hgsc.bcm.edu	37	19	17337928	17337928	+	Silent	SNP	C	C	T	rs1045201	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17337928C>T	ENST00000215061.4	+	3	416	c.372C>T	c.(370-372)gcC>gcT	p.A124A	OCEL1_ENST00000601576.1_3'UTR|OCEL1_ENST00000601529.1_Silent_p.A124A|OCEL1_ENST00000597836.1_Silent_p.A68A	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	124										central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						TCTCCCAGGCCCTCCTGGGCG	0.612													C|||	397	0.0792732	0.1203	0.0879	5008	,	,		14459	0.001		0.0775	False		,,,				2504	0.1002				p.A124A		Atlas-SNP	.											OCEL1,colon,carcinoma,0,1	OCEL1	20	1	0			c.C372T						PASS	.	C		484,3922	224.6+/-240.7	27,430,1746	68.0	79.0	75.0		372	-5.0	0.0	19	dbSNP_86	75	674,7926	168.3+/-219.8	22,630,3648	no	coding-synonymous	OCEL1	NM_024578.1		49,1060,5394	TT,TC,CC		7.8372,10.985,8.9036		124/265	17337928	1158,11848	2203	4300	6503	SO:0001819	synonymous_variant	79629	exon3			CCAGGCCCTCCTG	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.372C>T	19.37:g.17337928C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	47	17	0.361702	NM_024578		Silent	SNP	ENST00000215061.4	37	CCDS12351.1																																																																																			C|0.914;T|0.086	0.086	strong		0.612	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578	
ULK4	54986	hgsc.bcm.edu	37	3	41756965	41756965	+	Missense_Mutation	SNP	C	C	T	rs61744388	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:41756965C>T	ENST00000301831.4	-	24	3013	c.2551G>A	c.(2551-2553)Gta>Ata	p.V851I		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	851					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGAAGCACTACAGGCATCAGG	0.428													T|||	1330	0.265575	0.5348	0.1628	5008	,	,		17563	0.1478		0.1839	False		,,,				2504	0.18				p.V851I		Atlas-SNP	.											.	ULK4	150	.	0			c.G2551A						PASS	.	T	ILE/VAL	1816,2052		436,944,554	103.0	104.0	104.0		2551	-10.1	0.0	3	dbSNP_129	104	1420,6868		128,1164,2852	yes	missense	ULK4	NM_017886.2	29	564,2108,3406	TT,TC,CC		17.1332,46.9493,26.6206	benign	851/1276	41756965	3236,8920	1934	4144	6078	SO:0001583	missense	54986	exon24			GCACTACAGGCAT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2551G>A	3.37:g.41756965C>T	ENSP00000301831:p.Val851Ile	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	550	0.2518315018315018	262	0.532520325203252	57	0.1574585635359116	86	0.15034965034965034	145	0.19129287598944592	T	8.060	0.767962	0.15983	0.469493	0.171332	ENSG00000168038	ENST00000301831	T	0.62941	-0.01	5.72	-10.1	0.00402	Armadillo-type fold (1);	0.423778	0.22435	N	0.060092	T	0.00012	0.0000	N	0.24115	0.695	0.49915	P	1.6599999999999948E-4	B	0.09022	0.002	B	0.10450	0.005	T	0.36768	-0.9734	9	0.25106	T	0.35	.	25.2475	0.99993	0.0:0.8218:0.0:0.1782	.	851	Q96C45	ULK4_HUMAN	I	851	ENSP00000301831:V851I	ENSP00000301831:V851I	V	-	1	0	ULK4	41731969	0.000000	0.05858	0.000000	0.03702	0.404000	0.30871	-0.947000	0.03901	-2.451000	0.00543	-1.977000	0.00459	GTA	C|0.772;T|0.228	0.228	strong		0.428	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
SNAPC4	6621	hgsc.bcm.edu	37	9	139272058	139272058	+	Silent	SNP	A	A	G	rs10781507	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139272058A>G	ENST00000298532.2	-	21	4589	c.4221T>C	c.(4219-4221)agT>agC	p.S1407S		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa									p.S1407S(1)		biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GTTCCAGCTCACTCAGGAGGT	0.667													G|||	1850	0.369409	0.2579	0.572	5008	,	,		15887	0.3214		0.3956	False		,,,				2504	0.3988				p.S1407S		Atlas-SNP	.											SNAPC4,NS,lymphoid_neoplasm,0,1	SNAPC4	82	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T4221C						PASS	.			1240,3166		172,896,1135	39.0	38.0	39.0		4221	-4.8	0.0	9	dbSNP_120	39	3584,5008		744,2096,1456	no	coding-synonymous	SNAPC4	NM_003086.2		916,2992,2591	GG,GA,AA		41.7132,28.1434,37.1134		1407/1470	139272058	4824,8174	2203	4296	6499	SO:0001819	synonymous_variant	6621	exon21			CAGCTCACTCAGG	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.4221T>C	9.37:g.139272058A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.635;G|0.365	0.365	strong		0.667	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
C10orf120	399814	hgsc.bcm.edu	37	10	124459139	124459139	+	Silent	SNP	T	T	C	rs11813597	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124459139T>C	ENST00000329446.4	-	1	199	c.168A>G	c.(166-168)tcA>tcG	p.S56S		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	56								p.S56S(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				ACCGCAACGGTGAAGCAGAAC	0.478													T|||	2233	0.445887	0.4145	0.33	5008	,	,		19618	0.5327		0.4076	False		,,,				2504	0.5204				p.S56S		Atlas-SNP	.											C10orf120,NS,carcinoma,0,1	C10orf120	55	1	1	Substitution - coding silent(1)	stomach(1)	c.A168G						PASS	.	T		1827,2579	533.7+/-373.8	391,1045,767	99.0	86.0	90.0		168	-1.2	0.0	10	dbSNP_120	90	3560,5040	518.0+/-379.2	740,2080,1480	no	coding-synonymous	C10orf120	NM_001010912.1		1131,3125,2247	CC,CT,TT		41.3953,41.4662,41.4193		56/336	124459139	5387,7619	2203	4300	6503	SO:0001819	synonymous_variant	399814	exon1			CAACGGTGAAGCA		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.168A>G	10.37:g.124459139T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_001010912	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1	966	0.4423076923076923	229	0.4654471544715447	143	0.39502762430939226	290	0.506993006993007	304	0.40105540897097625	T	4.042	0.005438	0.07866	0.414662	0.413953	ENSG00000183559	ENST00000432000	.	.	.	4.28	-1.2	0.09554	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.47959	-0.9076	3	.	.	.	-0.4259	6.7398	0.23428	0.0:0.0978:0.5383:0.3639	rs11813597;rs17649853;rs11813597	.	.	.	R	49	.	.	H	-	2	0	C10orf120	124449129	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.094000	0.11094	-0.300000	0.08895	-0.323000	0.08544	CAC	C|0.427;N|0.000	0.427	strong		0.478	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	
SPAG1	6674	hgsc.bcm.edu	37	8	101252680	101252680	+	Missense_Mutation	SNP	T	T	C	rs6511	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:101252680T>C	ENST00000388798.2	+	18	2521	c.2330T>C	c.(2329-2331)aTg>aCg	p.M777T	SPAG1_ENST00000251809.3_Missense_Mutation_p.M777T	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	777			M -> T (in dbSNP:rs6511). {ECO:0000269|PubMed:11517287}.		axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)	p.M777T(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		GAGGTCTCCATGGGATGCCTT	0.483													C|||	3142	0.627396	0.7179	0.7233	5008	,	,		17979	0.5327		0.6193	False		,,,				2504	0.5429				p.M777T		Atlas-SNP	.											SPAG1,pharynx,carcinoma,-1,2	SPAG1	80	2	1	Substitution - Missense(1)	stomach(1)	c.T2330C						PASS	.	C	THR/MET,THR/MET	3051,1355	438.2+/-345.2	1073,905,225	82.0	90.0	87.0		2330,2330	-3.7	0.0	8	dbSNP_52	87	5241,3359	495.6+/-374.1	1599,2043,658	yes	missense,missense	SPAG1	NM_003114.4,NM_172218.2	81,81	2672,2948,883	CC,CT,TT		39.0581,30.7535,36.2448	benign,benign	777/927,777/927	101252680	8292,4714	2203	4300	6503	SO:0001583	missense	6674	exon18			TCTCCATGGGATG	AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	ENST00000388798.2:c.2330T>C	8.37:g.101252680T>C	ENSP00000373450:p.Met777Thr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_003114	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	Missense_Mutation	SNP	ENST00000388798.2	37	CCDS34930.1	1387	0.63507326007326	353	0.717479674796748	259	0.7154696132596685	294	0.513986013986014	481	0.6345646437994723	C	0.080	-1.186039	0.01620	0.692465	0.609419	ENSG00000104450	ENST00000251809;ENST00000388798	T;T	0.59502	0.26;0.26	5.77	-3.7	0.04437	.	1.659360	0.03303	N	0.189258	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31641	-0.9936	9	0.06494	T	0.89	2.3277	4.5629	0.12168	0.0974:0.2617:0.0968:0.5441	rs6511;rs1631163;rs52789688;rs61672000;rs6511	777	Q07617	SPAG1_HUMAN	T	777	ENSP00000251809:M777T;ENSP00000373450:M777T	ENSP00000251809:M777T	M	+	2	0	SPAG1	101321856	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.164000	0.09983	-1.149000	0.02843	-0.215000	0.12644	ATG	T|0.369;C|0.631	0.631	strong		0.483	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2	NM_172218	
ADCY9	115	hgsc.bcm.edu	37	16	4033436	4033436	+	Missense_Mutation	SNP	T	T	C	rs2230739	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4033436T>C	ENST00000294016.3	-	7	2854	c.2316A>G	c.(2314-2316)atA>atG	p.I772M		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	772			I -> M (in 37.5% of the Asian population, in 30% of the Caucasian population and in 16.3% of the African-American population; reduced adenylyl cyclase activity in response to stimulation of the beta- adregnergic receptor by the agonists Mn(2+), isoproteronol and NaF; increased albuterol-stimulated adenylyl cyclase activity in the presence of corticosteroid; dbSNP:rs2230739). {ECO:0000269|PubMed:12972952, ECO:0000269|PubMed:15879435}.		activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGGAGTTCTTTATGACCTGTG	0.572													T|||	1304	0.260383	0.1172	0.2334	5008	,	,		19237	0.3819		0.341	False		,,,				2504	0.2648				p.I772M		Atlas-SNP	.											ADCY9,NS,carcinoma,0,1	ADCY9	151	1	0			c.A2316G	GRCh37	CM034003	ADCY9	M	rs2230739	PASS	.	T	MET/ILE	649,3745		40,569,1588	71.0	60.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2316	-7.9	0.0	16	dbSNP_98	64	2688,5912		445,1798,2057	yes	missense	ADCY9	NM_001116.3	10	485,2367,3645	CC,CT,TT		31.2558,14.7701,25.6811	benign	772/1354	4033436	3337,9657	2197	4300	6497	SO:0001583	missense	115	exon7			GTTCTTTATGACC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.2316A>G	16.37:g.4033436T>C	ENSP00000294016:p.Ile772Met	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	610	0.2793040293040293	50	0.1016260162601626	91	0.2513812154696133	228	0.3986013986013986	241	0.3179419525065963	T	6.786	0.513906	0.12944	0.147701	0.312558	ENSG00000162104	ENST00000294016	D	0.82433	-1.61	5.94	-7.94	0.01152	.	0.557796	0.20751	N	0.086357	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.11717	-1.0576	9	0.19590	T	0.45	.	11.3789	0.49746	0.0:0.3363:0.4723:0.1914	rs2230739;rs2531981;rs17184038;rs60378382;rs2230739	772	O60503	ADCY9_HUMAN	M	772	ENSP00000294016:I772M	ENSP00000294016:I772M	I	-	3	3	ADCY9	3973437	0.000000	0.05858	0.005000	0.12908	0.081000	0.17604	-1.685000	0.01930	-1.914000	0.01078	-0.429000	0.05907	ATA	T|0.736;C|0.264	0.264	strong		0.572	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
CADM3	57863	hgsc.bcm.edu	37	1	159169641	159169641	+	Silent	SNP	T	T	C	rs862999	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:159169641T>C	ENST00000368125.4	+	8	1210	c.1053T>C	c.(1051-1053)ctT>ctC	p.L351L	CTA-134P22.2_ENST00000415675.2_RNA|CADM3_ENST00000368124.4_Silent_p.L385L|CADM3_ENST00000497636.1_3'UTR|CTA-134P22.2_ENST00000609696.1_RNA	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	351					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|protein localization (GO:0008104)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					TCATCTTCCTTGGCCACTACT	0.572													C|||	4162	0.83107	0.9123	0.7205	5008	,	,		19844	0.9276		0.7425	False		,,,				2504	0.7914				p.L385L		Atlas-SNP	.											.	CADM3	118	.	0			c.T1155C						PASS	.	C	,	3886,520	239.9+/-250.9	1707,472,24	132.0	103.0	113.0		1053,1155	-9.3	0.0	1	dbSNP_86	113	6384,2216	377.0+/-338.4	2374,1636,290	no	coding-synonymous,coding-synonymous	CADM3	NM_001127173.1,NM_021189.3	,	4081,2108,314	CC,CT,TT		25.7674,11.8021,21.0364	,	351/399,385/433	159169641	10270,2736	2203	4300	6503	SO:0001819	synonymous_variant	57863	exon9			CTTCCTTGGCCAC	AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17601	protein-coding gene	gene with protein product	"""nectin-like 1"""	609743	"""immunoglobulin superfamily, member 4B"""	IGSF4B		11536053	Standard	NM_021189		Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.1053T>C	1.37:g.159169641T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_021189	Q8IZQ9|Q9NVJ5|Q9UJP1	Silent	SNP	ENST00000368125.4	37	CCDS44251.1																																																																																			T|0.188;C|0.812	0.812	strong		0.572	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189	
DMKN	93099	hgsc.bcm.edu	37	19	36002393	36002393	+	Missense_Mutation	SNP	C	C	T	rs56743379|rs58579970|rs11667007	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36002393C>T	ENST00000339686.3	-	5	1014	c.838G>A	c.(838-840)Ggc>Agc	p.G280S	DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.G280S|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.G280S|DMKN_ENST00000451297.2_Missense_Mutation_p.G280S|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.G280S|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G280S|DMKN_ENST00000462126.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	280	Gly-rich.		G -> S (in dbSNP:rs11667007). {ECO:0000269|PubMed:17380110}.			extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			ccactgctgccgccactgctg	0.637																																					p.G280S		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.G838A						PASS	.						26.0	20.0	22.0					19																	36002393		2167	4203	6370	SO:0001583	missense	93099	exon5			TGCTGCCGCCACT	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.838G>A	19.37:g.36002393C>T	ENSP00000342012:p.Gly280Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	37	32	0.864865	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	673	0.30815018315018317	210	0.4268292682926829	75	0.20718232044198895	240	0.4195804195804196	148	0.19525065963060687	C	1.811	-0.474606	0.04414	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07;1.07	3.22	-6.45	0.01914	.	1.501560	0.04069	N	0.307709	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P;P;P;P;P	0.45428	0.858;0.858;0.858;0.858;0.749	B;B;B;B;B	0.29942	0.061;0.109;0.109;0.109;0.061	T	0.37244	-0.9714	9	0.07482	T	0.82	5.4478	5.8619	0.18752	0.149:0.2427:0.0:0.6083	rs11667007	280;280;280;280;280	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	280	ENSP00000342012:G280S;ENSP00000394908:G280S;ENSP00000415277:G280S;ENSP00000414743:G280S;ENSP00000388404:G280S;ENSP00000409513:G280S	ENSP00000342012:G280S	G	-	1	0	DMKN	40694233	0.008000	0.16893	0.000000	0.03702	0.008000	0.06430	-0.639000	0.05446	-1.330000	0.02255	-0.291000	0.09656	GGC	C|0.691;T|0.309	0.309	strong		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
FER1L6	654463	hgsc.bcm.edu	37	8	125061895	125061895	+	Silent	SNP	G	G	A	rs4870887	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:125061895G>A	ENST00000522917.1	+	22	2978	c.2772G>A	c.(2770-2772)aaG>aaA	p.K924K	FER1L6_ENST00000399018.1_Silent_p.K924K|FER1L6-AS2_ENST00000601180.1_RNA|FER1L6-AS2_ENST00000520031.1_RNA	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	924						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			CTGTTGTGAAGCTGGCTGACC	0.473													G|||	2409	0.48103	0.5038	0.4452	5008	,	,		18205	0.506		0.492	False		,,,				2504	0.4387				p.K924K		Atlas-SNP	.											FER1L6,colon,carcinoma,+2,2	FER1L6	268	2	0			c.G2772A						PASS	.	G		1806,2076		419,968,554	74.0	80.0	78.0		2772	-0.2	0.4	8	dbSNP_111	78	4147,4161		1063,2021,1070	yes	coding-synonymous	FER1L6	NM_001039112.2		1482,2989,1624	AA,AG,GG		49.9157,46.5224,48.8351		924/1858	125061895	5953,6237	1941	4154	6095	SO:0001819	synonymous_variant	654463	exon22			TGTGAAGCTGGCT	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.2772G>A	8.37:g.125061895G>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	161	83	0.515528	NM_001039112		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																			G|0.501;A|0.498	0.498	strong		0.473	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
AFP	174	hgsc.bcm.edu	37	4	74318177	74318177	+	Silent	SNP	T	T	C	rs35920062	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:74318177T>C	ENST00000395792.2	+	12	1588	c.1488T>C	c.(1486-1488)ggT>ggC	p.G496G	AFP_ENST00000226359.2_Silent_p.G496G	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein	496	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.				ovulation from ovarian follicle (GO:0001542)|progesterone metabolic process (GO:0042448)|SMAD protein signal transduction (GO:0060395)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|urinary_tract(1)	22	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TAAACCCTGGTGTTGGCCAGT	0.453									Alpha-Fetoprotein, Hereditary Persistence of				T|||	128	0.0255591	0.0038	0.0259	5008	,	,		19934	0.0		0.0716	False		,,,				2504	0.0337				p.G496G		Atlas-SNP	.											.	AFP	60	.	0			c.T1488C						PASS	.	T		54,4352	52.9+/-88.7	0,54,2149	137.0	128.0	131.0		1488	-5.2	0.0	4	dbSNP_126	131	549,8051	150.6+/-205.5	24,501,3775	no	coding-synonymous	AFP	NM_001134.1		24,555,5924	CC,CT,TT		6.3837,1.2256,4.6363		496/610	74318177	603,12403	2203	4300	6503	SO:0001819	synonymous_variant	174	exon12	Familial Cancer Database	HPAFP	CCCTGGTGTTGGC	V01514	CCDS3556.1	4q13.3	2012-05-16			ENSG00000081051	ENSG00000081051			317	protein-coding gene	gene with protein product		104150		HPAFP			Standard	NM_001134		Approved	FETA	uc003hgz.1	P02771	OTTHUMG00000130011	ENST00000395792.2:c.1488T>C	4.37:g.74318177T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	187	101	0.540107	NM_001134	B2RBU3	Silent	SNP	ENST00000395792.2	37	CCDS3556.1																																																																																			T|0.955;C|0.045	0.045	strong		0.453	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3		
KANSL1	284058	hgsc.bcm.edu	37	17	44159849	44159849	+	Silent	SNP	T	T	C	rs17576165	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44159849T>C	ENST00000262419.6	-	4	1961	c.1491A>G	c.(1489-1491)ccA>ccG	p.P497P	KANSL1_ENST00000575318.1_Silent_p.P497P|KANSL1_ENST00000432791.1_Silent_p.P497P|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.P497P|KANSL1_ENST00000572904.1_Silent_p.P497P	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	497					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CAGAACTAAGTGGAAGAAATA	0.428													C|||	432	0.086262	0.0151	0.1571	5008	,	,		20419	0.001		0.2406	False		,,,				2504	0.0613				p.P497P		Atlas-SNP	.											.	.	.	.	0			c.A1491G						PASS	.	C	,,	202,4204	807.5+/-415.9	5,192,2006	87.0	86.0	87.0		1491,1491,1491	-0.7	1.0	17	dbSNP_123	87	1928,6672	726.3+/-406.6	220,1488,2592	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	225,1680,4598	CC,CT,TT		22.4186,4.5847,16.3771	,,	497/1105,497/1106,497/1106	44159849	2130,10876	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon4			ACTAAGTGGAAGA	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.1491A>G	17.37:g.44159849T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			T|0.854;C|0.146	0.146	strong		0.428	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
SYNE1	23345	hgsc.bcm.edu	37	6	152660451	152660451	+	Silent	SNP	G	G	A	rs71575926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152660451G>A	ENST00000367255.5	-	75	12877	c.12276C>T	c.(12274-12276)ctC>ctT	p.L4092L	SYNE1_ENST00000423061.1_Silent_p.L4021L|SYNE1_ENST00000265368.4_Silent_p.L4092L|SYNE1_ENST00000448038.1_Silent_p.L4021L|SYNE1_ENST00000341594.5_Silent_p.L3957L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4092					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)		TGGAGCAAAGGAGATCTAGGT	0.413										HNSCC(10;0.0054)			G|||	367	0.0732827	0.0817	0.072	5008	,	,		19444	0.0258		0.1471	False		,,,				2504	0.0358				p.L4092L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C12276T						PASS	.	G	,	380,4026	192.6+/-218.0	22,336,1845	154.0	140.0	145.0		12063,12276	-2.6	1.0	6	dbSNP_130	145	1131,7469	233.3+/-266.6	77,977,3246	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	99,1313,5091	AA,AG,GG		13.1512,8.6246,11.6177	,	4021/8750,4092/8798	152660451	1511,11495	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon75			GCAAAGGAGATCT	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.12276C>T	6.37:g.152660451G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			G|0.895;A|0.105	0.105	strong		0.413	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28338298	28338298	+	Missense_Mutation	SNP	C	C	G	rs457947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:28338298C>G	ENST00000284987.5	-	1	534	c.413G>C	c.(412-414)gGt>gCt	p.G138A		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	138			G -> A (in dbSNP:rs457947). {ECO:0000269|PubMed:10438522, ECO:0000269|PubMed:15489334}.		defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GCGGGGACTACCGTCCACTGT	0.662													C|||	701	0.139976	0.2489	0.17	5008	,	,		14671	0.004		0.1332	False		,,,				2504	0.1186				p.G138A	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G413C						PASS	.	C	ALA/GLY	1025,3381		112,801,1290	28.0	26.0	27.0		413	4.6	1.0	21	dbSNP_80	27	1407,7191		127,1153,3019	yes	missense	ADAMTS5	NM_007038.3	60	239,1954,4309	GG,GC,CC		16.3643,23.2637,18.7019	possibly-damaging	138/931	28338298	2432,10572	2203	4299	6502	SO:0001583	missense	11096	exon1			GGACTACCGTCCA	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.413G>C	21.37:g.28338298C>G	ENSP00000284987:p.Gly138Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	93	53	0.569892	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	294	0.1346153846153846	119	0.241869918699187	62	0.1712707182320442	1	0.0017482517482517483	112	0.14775725593667546	C	10.96	1.499434	0.26861	0.232637	0.163643	ENSG00000154736	ENST00000284987	T	0.09723	2.95	4.57	4.57	0.56435	Peptidase M12B, propeptide (1);	0.163396	0.44097	D	0.000487	T	0.00012	0.0000	L	0.45228	1.405	0.31486	P	0.666612	P	0.47604	0.898	P	0.49192	0.602	T	0.51748	-0.8666	9	0.26408	T	0.33	.	12.9996	0.58667	0.0:0.8377:0.1623:0.0	rs457947	138	Q9UNA0	ATS5_HUMAN	A	138	ENSP00000284987:G138A	ENSP00000284987:G138A	G	-	2	0	ADAMTS5	27260169	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	3.780000	0.55386	2.344000	0.79699	0.563000	0.77884	GGT	C|0.834;G|0.166	0.166	strong		0.662	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
XDH	7498	hgsc.bcm.edu	37	2	31590917	31590917	+	Missense_Mutation	SNP	T	T	C	rs17011368	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:31590917T>C	ENST00000379416.3	-	20	2155	c.2107A>G	c.(2107-2109)Ata>Gta	p.I703V		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	703			I -> V (in dbSNP:rs17011368). {ECO:0000269|Ref.6}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	TTGTTCTTTATAGCATCCTGA	0.428													T|||	260	0.0519169	0.1195	0.0317	5008	,	,		20601	0.004		0.0477	False		,,,				2504	0.0286				p.I703V	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.A2107G	GRCh37	CM080637	XDH	M	rs17011368	PASS	.	T	VAL/ILE	508,3898	235.2+/-247.8	33,442,1728	143.0	135.0	138.0		2107	4.8	1.0	2	dbSNP_123	138	294,8306	107.4+/-168.2	4,286,4010	yes	missense	XDH	NM_000379.3	29	37,728,5738	CC,CT,TT		3.4186,11.5297,6.1664	possibly-damaging	703/1334	31590917	802,12204	2203	4300	6503	SO:0001583	missense	7498	exon20			TCTTTATAGCATC	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.2107A>G	2.37:g.31590917T>C	ENSP00000368727:p.Ile703Val	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	157	79	0.503185	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	37	CCDS1775.1	106	0.048534798534798536	68	0.13821138211382114	12	0.03314917127071823	0	0.0	26	0.03430079155672823	T	16.30	3.084344	0.55861	0.115297	0.034186	ENSG00000158125	ENST00000379416	T	0.39229	1.09	6.02	4.8	0.61643	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.044294	0.85682	D	0.000000	T	0.00356	0.0011	L	0.53561	1.675	0.09310	P	0.99999870301	B	0.15473	0.013	B	0.28638	0.092	T	0.13361	-1.0512	9	0.87932	D	0	.	11.1748	0.48593	0.0:0.0:0.1538:0.8462	rs17011368;rs52829758;rs58778509;rs17011368	703	P47989	XDH_HUMAN	V	703	ENSP00000368727:I703V	ENSP00000368727:I703V	I	-	1	0	XDH	31444421	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	3.383000	0.52471	2.311000	0.77944	0.533000	0.62120	ATA	T|0.942;C|0.058	0.058	strong		0.428	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
GRIK2	2898	hgsc.bcm.edu	37	6	102266322	102266322	+	Silent	SNP	C	C	G	rs34747916	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:102266322C>G	ENST00000421544.1	+	9	1771	c.1281C>G	c.(1279-1281)tcC>tcG	p.S427S	GRIK2_ENST00000369134.4_Silent_p.S378S|GRIK2_ENST00000318991.6_Silent_p.S427S|GRIK2_ENST00000369138.1_Silent_p.S427S|GRIK2_ENST00000369137.3_Silent_p.S427S|GRIK2_ENST00000413795.1_Silent_p.S427S	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	427					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)	TCACAGATTCCTTATCCAATC	0.368													C|||	164	0.0327476	0.0121	0.0504	5008	,	,		19777	0.0268		0.0537	False		,,,				2504	0.0327				p.S427S		Atlas-SNP	.											GRIK2_ENST00000421544,mucosal,malignant_melanoma,+2,3	GRIK2	487	3	0			c.C1281G						PASS	.	C	,,	76,4330	65.8+/-103.3	0,76,2127	220.0	198.0	205.0		1281,1281,1281	1.1	1.0	6	dbSNP_126	205	527,8073	147.7+/-203.1	13,501,3786	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIK2	NM_001166247.1,NM_021956.4,NM_175768.3	,,	13,577,5913	GG,GC,CC		6.1279,1.7249,4.6363	,,	427/893,427/909,427/870	102266322	603,12403	2203	4300	6503	SO:0001819	synonymous_variant	2898	exon9			AGATTCCTTATCC		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.1281C>G	6.37:g.102266322C>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	188	88	0.468085	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Silent	SNP	ENST00000421544.1	37	CCDS5048.1																																																																																			C|0.954;G|0.046	0.046	strong		0.368	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1		
SLC25A10	1468	hgsc.bcm.edu	37	17	79682051	79682051	+	Silent	SNP	C	C	T	rs3204270	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79682051C>T	ENST00000350690.5	+	2	248	c.162C>T	c.(160-162)acC>acT	p.T54T	SLC25A10_ENST00000331531.5_Silent_p.T54T|SLC25A10_ENST00000545862.1_Silent_p.T11T|SLC25A10_ENST00000541223.1_Silent_p.T209T|SLC25A10_ENST00000571730.1_Silent_p.T209T	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	54					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	TGGTGCGTACCGACGGCATCC	0.667													C|||	204	0.0407348	0.0068	0.0548	5008	,	,		19512	0.001		0.1272	False		,,,				2504	0.0286				p.T54T		Atlas-SNP	.											SLC25A10,NS,carcinoma,0,2	SLC25A10	24	2	0			c.C162T						PASS	.	C		100,4296	79.9+/-118.3	2,96,2100	57.0	42.0	47.0		162	-7.7	0.1	17	dbSNP_105	47	887,7711	195.6+/-240.8	44,799,3456	no	coding-synonymous	SLC25A10	NM_012140.3		46,895,5556	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	10.3164,2.2748,7.5958		54/288	79682051	987,12007	2198	4299	6497	SO:0001819	synonymous_variant	1468	exon2			GCGTACCGACGGC		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"""Solute carriers"""	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.162C>T	17.37:g.79682051C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	153	69	0.45098	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Silent	SNP	ENST00000350690.5	37	CCDS11786.1																																																																																			C|0.937;G|0.000;T|0.062	0.062	strong		0.667	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1		
SLC9C1	285335	hgsc.bcm.edu	37	3	111901099	111901099	+	Missense_Mutation	SNP	T	T	C	rs74840030	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111901099T>C	ENST00000305815.5	-	21	2782	c.2530A>G	c.(2530-2532)Atg>Gtg	p.M844V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.M796V	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	844					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										TTTTTGGCCATGATTAACTAA	0.343													T|||	185	0.0369409	0.0045	0.036	5008	,	,		15999	0.002		0.0537	False		,,,				2504	0.1002				p.M844V		Atlas-SNP	.											.	.	.	.	0			c.A2530G						PASS	.	T	VAL/MET	37,4369	41.6+/-74.8	0,37,2166	75.0	83.0	80.0		2530	4.6	1.0	3	dbSNP_132	80	458,8132	135.4+/-192.6	12,434,3849	yes	missense	SLC9A10	NM_183061.1	21	12,471,6015	CC,CT,TT		5.3318,0.8398,3.8089	benign	844/1178	111901099	495,12501	2203	4295	6498	SO:0001583	missense	285335	exon21			TGGCCATGATTAA	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2530A>G	3.37:g.111901099T>C	ENSP00000306627:p.Met844Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	63	0.028846153846153848	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	41	0.05408970976253298	T	8.685	0.906139	0.17760	0.008398	0.053318	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.77750	-1.12;-1.12	5.81	4.59	0.56863	.	0.343378	0.29602	N	0.011697	T	0.29389	0.0732	M	0.64997	1.995	0.25998	N	0.982155	B;B	0.32918	0.39;0.176	B;B	0.37731	0.257;0.037	T	0.58120	-0.7692	10	0.59425	D	0.04	.	9.328	0.38005	0.0:0.0:0.1806:0.8194	.	796;844	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	844;796	ENSP00000306627:M844V;ENSP00000420688:M796V	ENSP00000306627:M844V	M	-	1	0	SLC9A10	113383789	0.888000	0.30383	1.000000	0.80357	0.012000	0.07955	1.327000	0.33746	2.215000	0.71742	0.491000	0.48974	ATG	T|0.962;C|0.038	0.038	strong		0.343	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
MCF2L	23263	hgsc.bcm.edu	37	13	113720476	113720476	+	Silent	SNP	C	C	T	rs2297192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:113720476C>T	ENST00000375608.3	+	9	1021	c.963C>T	c.(961-963)acC>acT	p.T321T	MCF2L_ENST00000535094.2_Silent_p.T291T|MCF2L_ENST00000375604.2_Silent_p.T348T|MCF2L_ENST00000423482.2_Silent_p.T289T|MCF2L_ENST00000375601.3_Silent_p.T295T|MCF2L_ENST00000421756.1_Silent_p.T295T|MCF2L_ENST00000397030.1_Silent_p.T324T|MCF2L_ENST00000434480.2_Silent_p.T297T|MCF2L_ENST00000375597.4_Silent_p.T289T|MCF2L_ENST00000442652.2_Silent_p.T321T			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	321					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	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)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				ACCAGGCCACCGTGCAGAGGT	0.617													C|||	944	0.188498	0.025	0.2478	5008	,	,		18249	0.4573		0.1571	False		,,,				2504	0.1227				p.T291T		Atlas-SNP	.											.	MCF2L	182	.	0			c.C873T						PASS	.	C	,	235,4171	137.3+/-173.1	8,219,1976	86.0	72.0	77.0		873,867	-10.0	0.4	13	dbSNP_100	77	1400,7198	269.3+/-288.3	107,1186,3006	yes	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	115,1405,4982	TT,TC,CC		16.2829,5.3336,12.5731	,	291/1126,289/1124	113720476	1635,11369	2203	4299	6502	SO:0001819	synonymous_variant	23263	exon8			GGCCACCGTGCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.963C>T	13.37:g.113720476C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	28	8	0.285714	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37																																																																																				C|0.846;T|0.154	0.154	strong		0.617	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
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 GAIIx	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_ENST00000540648.1_Missense_Mutation_p.K136R|BTBD8_ENST00000370382.3_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	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	145	66	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 GAIIx	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		Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	396	212	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	
RINL	126432	hgsc.bcm.edu	37	19	39360597	39360597	+	Missense_Mutation	SNP	C	C	T	rs113728915	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39360597C>T	ENST00000591812.1	-	9	1414	c.1328G>A	c.(1327-1329)cGa>cAa	p.R443Q	RINL_ENST00000602238.1_5'Flank|CTC-360G5.6_ENST00000593830.1_RNA|RINL_ENST00000598904.1_Missense_Mutation_p.R329Q|RINL_ENST00000340740.3_Missense_Mutation_p.R329Q			Q6ZS11	RINL_HUMAN	Ras and Rab interactor-like	443	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)	actin cytoskeleton (GO:0015629)|cytoplasmic vesicle (GO:0031410)|ruffle (GO:0001726)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|urinary_tract(2)	17						GTTCTCGCCTCGAGCCAGGCC	0.652											OREG0025454	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	180	0.0359425	0.003	0.0735	5008	,	,		14470	0.0		0.1153	False		,,,				2504	0.0092				p.R443Q		Atlas-SNP	.											RINL,NS,carcinoma,0,1	RINL	32	1	0			c.G1328A						PASS	.	C	GLN/ARG,GLN/ARG	91,4123		3,85,2019	16.0	18.0	17.0		1328,986	-6.5	0.0	19	dbSNP_132	17	896,7562		56,784,3389	yes	missense,missense	RINL	NM_001195833.1,NM_198445.3	43,43	59,869,5408	TT,TC,CC		10.5935,2.1595,7.7888	benign,benign	443/567,329/453	39360597	987,11685	2107	4229	6336	SO:0001583	missense	126432	exon9			TCGCCTCGAGCCA	AK127808	CCDS12522.1, CCDS59386.1	19q13.2	2010-07-13			ENSG00000187994	ENSG00000187994			24795	protein-coding gene	gene with protein product							Standard	NM_001195833		Approved	FLJ45909	uc010xuo.2	Q6ZS11		ENST00000591812.1:c.1328G>A	19.37:g.39360597C>T	ENSP00000467107:p.Arg443Gln	Somatic	45	0	0	885	WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_001195833	B4DPG5	Missense_Mutation	SNP	ENST00000591812.1	37	CCDS59386.1	137	0.06272893772893773	16	0.032520325203252036	32	0.08839779005524862	5	0.008741258741258742	84	0.11081794195250659	C	7.812	0.715927	0.15306	0.021595	0.105935	ENSG00000187994	ENST00000340740;ENST00000536520	T	0.31510	1.49	4.17	-6.5	0.01884	Vacuolar sorting protein 9 (2);	2.320620	0.01291	N	0.010015	T	0.00178	0.0005	N	0.01576	-0.805	0.80722	P	0.0	B;B	0.18741	0.03;0.016	B;B	0.10450	0.005;0.004	T	0.13575	-1.0504	9	0.09843	T	0.71	0.8182	4.5149	0.11930	0.1188:0.2033:0.5128:0.165	.	443;329	B4DPG5;Q6ZS11	.;RINL_HUMAN	Q	329	ENSP00000340369:R329Q	ENSP00000340369:R329Q	R	-	2	0	RINL	44052437	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-2.089000	0.01357	-0.961000	0.03609	-0.448000	0.05591	CGA	C|0.924;T|0.076	0.076	strong		0.652	RINL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460433.1	NM_198445	
ALDH3B2	222	hgsc.bcm.edu	37	11	67432799	67432799	+	Silent	SNP	G	G	A	rs80147122		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67432799G>A	ENST00000349015.3	-	7	1101	c.663C>T	c.(661-663)cgC>cgT	p.R221R	ALDH3B2_ENST00000531881.1_5'Flank|ALDH3B2_ENST00000530069.1_Silent_p.R221R	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	221					alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						CAATGGCCACGCGGCTGCAGC	0.632																																					p.R221R		Atlas-SNP	.											ALDH3B2,NS,haematopoietic_neoplasm,0,2	ALDH3B2	46	2	0			c.C663T						scavenged	.						52.0	59.0	57.0					11																	67432799		2200	4293	6493	SO:0001819	synonymous_variant	222	exon7			GGCCACGCGGCTG	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"""Aldehyde dehydrogenases"""	411	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 8"", ""acetaldehyde dehydrogenase 8"""	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.663C>T	11.37:g.67432799G>A		Somatic	218	2	0.00917431		WXS	Illumina HiSeq	Phase_I	232	5	0.0215517	NM_001031615	Q53Y98|Q8NAL5|Q96IB2	Silent	SNP	ENST00000349015.3	37	CCDS31622.1																																																																																			.	.	strong		0.632	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695	
SAMD12	401474	hgsc.bcm.edu	37	8	119391866	119391866	+	Silent	SNP	G	G	A	rs12171673	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:119391866G>A	ENST00000314727.4	-	4	532	c.396C>T	c.(394-396)caC>caT	p.H132H	SAMD12_ENST00000409003.4_Silent_p.H132H|SAMD12_ENST00000527515.1_5'Flank|AC023590.1_ENST00000430457.1_Intron	NM_207506.2	NP_997389.2	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12	132	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			GTTGTAAGATGTGCTGCCGGA	0.498													G|||	332	0.0662939	0.0295	0.085	5008	,	,		17552	0.001		0.2008	False		,,,				2504	0.0317				p.H132H		Atlas-SNP	.											.	SAMD12	24	.	0			c.C396T						PASS	.	G	,	220,4186	130.6+/-167.2	8,204,1991	156.0	138.0	144.0		396,396	6.2	1.0	8	dbSNP_120	144	1493,7107	283.9+/-296.4	130,1233,2937	no	coding-synonymous,coding-synonymous	SAMD12	NM_001101676.1,NM_207506.2	,	138,1437,4928	AA,AG,GG		17.3605,4.9932,13.1708	,	132/162,132/202	119391866	1713,11293	2203	4300	6503	SO:0001819	synonymous_variant	401474	exon4			TAAGATGTGCTGC	AK096777	CCDS6325.1, CCDS47913.1	8q24.12	2013-01-10			ENSG00000177570	ENSG00000177570		"""Sterile alpha motif (SAM) domain containing"""	31750	protein-coding gene	gene with protein product							Standard	NM_207506		Approved	FLJ39458	uc003yom.2	Q8N8I0	OTTHUMG00000059817	ENST00000314727.4:c.396C>T	8.37:g.119391866G>A		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	246	123	0.5	NM_207506	Q0P502	Silent	SNP	ENST00000314727.4	37	CCDS6325.1	209|209	0.09569597069597069|0.09569597069597069	12|12	0.024390243902439025|0.024390243902439025	35|35	0.09668508287292818|0.09668508287292818	1|1	0.0017482517482517483|0.0017482517482517483	161|161	0.21240105540897097|0.21240105540897097	G|G	10.51|10.51	1.369714|1.369714	0.24771|0.24771	0.049932|0.049932	0.173605|0.173605	ENSG00000177570|ENSG00000177570	ENST00000453675|ENST00000526765	D|.	0.85258|.	-1.96|.	6.17|6.17	6.17|6.17	0.99709|0.99709	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00241|0.00241	0.0007|0.0007	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.00171|0.00171	-1.1960|-1.1960	5|3	.|.	.|.	.|.	-9.19|-9.19	20.8794|20.8794	0.99867|0.99867	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs12171673;rs17682010;rs12171673|rs12171673;rs17682010;rs12171673	.|.	.|.	.|.	Y|I	119|147	ENSP00000402786:H119Y|.	.|.	H|T	-|-	1|2	0|0	SAMD12|SAMD12	119461047|119461047	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	3.768000|3.768000	0.55295|0.55295	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	CAT|ACA	G|0.884;A|0.116	0.116	strong		0.498	SAMD12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132989.3	NM_207506	
F13A1	2162	hgsc.bcm.edu	37	6	6152137	6152137	+	Missense_Mutation	SNP	C	C	G	rs5988	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:6152137C>G	ENST00000264870.3	-	14	2219	c.1954G>C	c.(1954-1956)Gag>Cag	p.E652Q		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	652			Q -> E (in allele F13A*1A and allele F13A*1B; dbSNP:rs5988). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TTGGTAAACTCAACTGTCACA	0.448													C|||	971	0.19389	0.2292	0.2046	5008	,	,		20265	0.0923		0.2406	False		,,,				2504	0.1953				p.E652Q		Atlas-SNP	.											.	F13A1	135	.	0			c.G1954C						PASS	.	C	GLN/GLU	881,3525	343.6+/-307.7	100,681,1422	89.0	80.0	83.0		1954	4.5	1.0	6	dbSNP_52	83	2003,6597	349.8+/-327.6	237,1529,2534	yes	missense	F13A1	NM_000129.3	29	337,2210,3956	GG,GC,CC		23.2907,19.9955,22.1744	benign	652/733	6152137	2884,10122	2203	4300	6503	SO:0001583	missense	2162	exon14			TAAACTCAACTGT	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1954G>C	6.37:g.6152137C>G	ENSP00000264870:p.Glu652Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	13	0.270833	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	412	0.18864468864468864	93	0.18902439024390244	91	0.2513812154696133	60	0.1048951048951049	168	0.22163588390501318	C	15.85	2.954677	0.53293	0.199955	0.232907	ENSG00000124491	ENST00000264870	T	0.68765	-0.35	5.37	4.5	0.54988	.	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	.	.	.	0.20873	P	0.999837872	.	.	.	.	.	.	T	0.49643	-0.8918	6	0.17832	T	0.49	.	13.3365	0.60520	0.1587:0.8413:0.0:0.0	rs5988;rs3191130;rs52826565;rs5988	.	.	.	Q	652	ENSP00000264870:E652Q	ENSP00000264870:E652Q	E	-	1	0	F13A1	6097136	0.999000	0.42202	0.994000	0.49952	0.406000	0.30931	4.372000	0.59530	1.484000	0.48361	0.650000	0.86243	GAG	C|0.786;G|0.214	0.214	strong		0.448	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
IP6K3	117283	hgsc.bcm.edu	37	6	33694659	33694659	+	Silent	SNP	G	G	A	rs34252064	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33694659G>A	ENST00000293756.4	-	4	764	c.438C>T	c.(436-438)tcC>tcT	p.S146S	IP6K3_ENST00000451316.1_Silent_p.S146S	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	146					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						GGTGGGGCTCGGACCTCAGAA	0.647													G|||	453	0.0904553	0.2912	0.0317	5008	,	,		17666	0.001		0.0398	False		,,,				2504	0.0051				p.S146S		Atlas-SNP	.											.	IP6K3	52	.	0			c.C438T						PASS	.	G	,	1010,3396	376.1+/-321.9	114,782,1307	73.0	73.0	73.0		438,438	1.1	1.0	6	dbSNP_126	73	384,8216	125.0+/-183.6	12,360,3928	no	coding-synonymous,coding-synonymous	IP6K3	NM_001142883.1,NM_054111.4	,	126,1142,5235	AA,AG,GG		4.4651,22.9233,10.7181	,	146/411,146/411	33694659	1394,11612	2203	4300	6503	SO:0001819	synonymous_variant	117283	exon5			GGGCTCGGACCTC	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"""inositol hexaphosphate kinase 3"""	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.438C>T	6.37:g.33694659G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	112	18	0.160714	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	37	CCDS34435.1																																																																																			G|0.901;A|0.099	0.099	strong		0.647	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
CD207	50489	hgsc.bcm.edu	37	2	71058835	71058835	+	Missense_Mutation	SNP	A	A	G	rs741326	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71058835A>G	ENST00000410009.3	-	5	878	c.833T>C	c.(832-834)gTg>gCg	p.V278A		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	278	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		V -> A (no effect on mannose-binding ability; dbSNP:rs741326). {ECO:0000269|PubMed:10661407, ECO:0000269|PubMed:16567809}.		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)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						GGCTTACCTCACACTTTGGAC	0.602													G|||	2731	0.545327	0.5219	0.4813	5008	,	,		20392	0.6548		0.4722	False		,,,				2504	0.5849				p.V278A		Atlas-SNP	.											CD207,NS,carcinoma,-1,1	CD207	47	1	0			c.T833C						PASS	.	G	ALA/VAL	1902,2188		453,996,596	106.0	117.0	113.0	http://omim.org/entry/604862	833	-9.6	0.0	2	dbSNP_86	113	3551,4831		776,1999,1416	yes	missense	CD207	NM_015717.3	64	1229,2995,2012	GG,GA,AA		42.3646,46.5037,43.7219	benign	278/329	71058835	5453,7019	2045	4191	6236	SO:0001583	missense	50489	exon5			TACCTCACACTTT	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"""C-type lectin domain containing"", ""CD molecules"""	17935	protein-coding gene	gene with protein product		604862	"""CD207 antigen, langerin"""			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.833T>C	2.37:g.71058835A>G	ENSP00000386378:p.Val278Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	NM_015717		Missense_Mutation	SNP	ENST00000410009.3	37		1177	0.5389194139194139	261	0.5304878048780488	159	0.43922651933701656	396	0.6923076923076923	361	0.4762532981530343	G	0.069	-1.205573	0.01568	0.465037	0.423646	ENSG00000116031	ENST00000410009	T	0.16597	2.33	4.78	-9.57	0.00562	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.732970	0.03032	N	0.152259	T	0.00012	0.0000	N	0.00670	-1.27	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.17369	T	0.5	.	1.3582	0.02186	0.3227:0.1701:0.0961:0.4111	rs741326;rs56623291;rs58272034;rs741326	278	Q9UJ71	CLC4K_HUMAN	A	278	ENSP00000386378:V278A	ENSP00000386378:V278A	V	-	2	0	CD207	70912343	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.932000	0.01554	-2.881000	0.00319	-2.349000	0.00243	GTG	A|0.465;G|0.535	0.535	strong		0.602	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
TMEM150A	129303	hgsc.bcm.edu	37	2	85826721	85826721	+	Silent	SNP	G	G	A	rs11891495	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85826721G>A	ENST00000409668.1	-	6	968	c.501C>T	c.(499-501)acC>acT	p.T167T	TMEM150A_ENST00000306353.3_Silent_p.T114T|TMEM150A_ENST00000334462.5_Silent_p.T167T			Q86TG1	T150A_HUMAN	transmembrane protein 150A	167					catabolic process (GO:0009056)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|lung(1)|skin(1)	7						CCAGCGGGGCGGTGGCCCCTT	0.617													G|||	880	0.175719	0.1369	0.1801	5008	,	,		20935	0.0823		0.2535	False		,,,				2504	0.2413				p.T167T		Atlas-SNP	.											.	TMEM150A	15	.	0			c.C501T						PASS	.	G		645,3761	274.9+/-272.2	42,561,1600	70.0	67.0	68.0		501	-10.2	0.1	2	dbSNP_120	68	2184,6416	372.2+/-336.6	267,1650,2383	no	coding-synonymous	TMEM150A	NM_001031738.2		309,2211,3983	AA,AG,GG		25.3953,14.6391,21.7515		167/272	85826721	2829,10177	2203	4300	6503	SO:0001819	synonymous_variant	129303	exon7			CGGGGCGGTGGCC	AK098152	CCDS33233.1	2p11.2	2009-06-12	2009-06-12	2009-06-12	ENSG00000168890	ENSG00000168890			24677	protein-coding gene	gene with protein product			"""transmembrane protein 150"""	TMEM150		10858565	Standard	NM_001031738		Approved	TM6P1, FLJ90024	uc002spy.2	Q86TG1	OTTHUMG00000130168	ENST00000409668.1:c.501C>T	2.37:g.85826721G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	180	52	0.288889	NM_001031738	A8K764|B7WPQ9|D6W5L2|Q8N2R6	Silent	SNP	ENST00000409668.1	37	CCDS33233.1																																																																																			G|0.810;A|0.190	0.190	strong		0.617	TMEM150A-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329474.1	NM_153342	
SVEP1	79987	hgsc.bcm.edu	37	9	113169126	113169126	+	Silent	SNP	G	G	A	rs2281937	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:113169126G>A	ENST00000401783.2	-	38	9090	c.8754C>T	c.(8752-8754)caC>caT	p.H2918H	SVEP1_ENST00000297826.5_Silent_p.H844H|SVEP1_ENST00000374469.1_Silent_p.H2895H	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2918	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TGTAGCCCTCGTGACAGTGGA	0.537													G|||	1317	0.262979	0.2095	0.3372	5008	,	,		21927	0.0913		0.4344	False		,,,				2504	0.2832				p.H2918H		Atlas-SNP	.											.	SVEP1	326	.	0			c.C8754T						PASS	.	G		991,3139		134,723,1208	126.0	128.0	127.0		8754	-7.0	0.8	9	dbSNP_100	127	3595,4831		768,2059,1386	no	coding-synonymous	SVEP1	NM_153366.3		902,2782,2594	AA,AG,GG		42.6656,23.9952,36.5244		2918/3572	113169126	4586,7970	2065	4213	6278	SO:0001819	synonymous_variant	79987	exon38			GCCCTCGTGACAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8754C>T	9.37:g.113169126G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	53	13	0.245283	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			G|0.723;A|0.277	0.277	strong		0.537	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
RBM19	9904	hgsc.bcm.edu	37	12	114377885	114377885	+	Silent	SNP	G	G	C	rs2290790	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:114377885G>C	ENST00000545145.2	-	15	1896	c.1818C>G	c.(1816-1818)acC>acG	p.T606T	RBM19_ENST00000392561.3_Silent_p.T606T|RBM19_ENST00000261741.5_Silent_p.T606T|RP11-780K2.1_ENST00000550206.1_RNA	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	606	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					AATGGCCGAAGGTCTCCTGCA	0.632													G|||	1099	0.219449	0.0688	0.2565	5008	,	,		17610	0.1756		0.3191	False		,,,				2504	0.3395				p.T606T		Atlas-SNP	.											.	RBM19	117	.	0			c.C1818G						PASS	.	G	,,	469,3937	221.0+/-238.3	31,407,1765	67.0	72.0	70.0		1818,1818,1818	0.1	0.2	12	dbSNP_100	70	2825,5775	441.5+/-359.8	470,1885,1945	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	501,2292,3710	CC,CG,GG		32.8488,10.6446,25.3268	,,	606/961,606/961,606/961	114377885	3294,9712	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon15			GCCGAAGGTCTCC	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1818C>G	12.37:g.114377885G>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	41	0.66129	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.761;C|0.239	0.239	strong		0.632	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
TRIB3	57761	hgsc.bcm.edu	37	20	377226	377226	+	Silent	SNP	C	C	T	rs6115830	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:377226C>T	ENST00000217233.3	+	4	1522	c.969C>T	c.(967-969)gcC>gcT	p.A323A	TRIB3_ENST00000422053.2_Silent_p.A350A	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	323					cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of protein binding (GO:0032092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|regulation of glucose transport (GO:0010827)|regulation of MAP kinase activity (GO:0043405)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|transcription corepressor activity (GO:0003714)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase regulator activity (GO:0055106)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|skin(1)	21		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		TGCCCTTAGCCCCAACCCGAT	0.642													C|||	1984	0.396166	0.4592	0.3199	5008	,	,		18335	0.3125		0.4254	False		,,,				2504	0.4213				p.A323A	Melanoma(101;421 2374 19538)	Atlas-SNP	.											.	TRIB3	50	.	0			c.C969T						PASS	.	C		1999,2397		459,1081,658	53.0	49.0	50.0		969	0.3	0.0	20	dbSNP_114	50	3693,4893		827,2039,1427	no	coding-synonymous	TRIB3	NM_021158.3		1286,3120,2085	TT,TC,CC		43.0119,45.4732,43.8453		323/359	377226	5692,7290	2198	4293	6491	SO:0001819	synonymous_variant	57761	exon4			CTTAGCCCCAACC	AF250311	CCDS12997.1	20p13-p12.2	2013-10-03	2013-10-03	2004-05-04	ENSG00000101255	ENSG00000101255			16228	protein-coding gene	gene with protein product		607898	"""chromosome 20 open reading frame 97"", ""tribbles homolog 3 (Drosophila)"""	C20orf97		12791994, 16715410	Standard	XM_005260773		Approved	dJ1103G7.3, TRB3	uc002wdm.3	Q96RU7	OTTHUMG00000031627	ENST00000217233.3:c.969C>T	20.37:g.377226C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_021158	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Silent	SNP	ENST00000217233.3	37	CCDS12997.1																																																																																			C|0.572;T|0.428	0.428	strong		0.642	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158	
C14orf159	80017	hgsc.bcm.edu	37	14	91636395	91636395	+	Silent	SNP	C	C	T	rs4900071	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:91636395C>T	ENST00000523771.1	+	5	909	c.306C>T	c.(304-306)ggC>ggT	p.G102G	C14orf159_ENST00000523816.1_Silent_p.G102G|C14orf159_ENST00000522322.1_Silent_p.G102G|C14orf159_ENST00000518868.1_Silent_p.G102G|C14orf159_ENST00000412671.2_Silent_p.G102G|C14orf159_ENST00000256324.10_Silent_p.G102G|C14orf159_ENST00000521077.2_Silent_p.G102G|C14orf159_ENST00000525393.2_Intron|C14orf159_ENST00000428926.2_Silent_p.G102G|C14orf159_ENST00000520328.1_Silent_p.G102G			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	102						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CCTGCACCGGCAGCCTGGCTT	0.627													C|||	837	0.167133	0.1036	0.2262	5008	,	,		17755	0.0585		0.3241	False		,,,				2504	0.1616				p.G102G		Atlas-SNP	.											C14orf159,NS,carcinoma,0,1	C14orf159	57	1	0			c.C306T						PASS	.	C	,,,,	711,3695	295.3+/-283.6	62,587,1554	84.0	89.0	87.0		306,306,306,306,306	2.0	0.4	14	dbSNP_111	87	2897,5703	453.6+/-363.3	492,1913,1895	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	554,2500,3449	TT,TC,CC		33.686,16.1371,27.741	,,,,	102/617,102/617,102/622,102/565,102/617	91636395	3608,9398	2203	4300	6503	SO:0001819	synonymous_variant	80017	exon7			CACCGGCAGCCTG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.306C>T	14.37:g.91636395C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	70	45	0.642857	NM_001102366	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1																																																																																			C|0.767;T|0.233	0.233	strong		0.627	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
COX10	1352	hgsc.bcm.edu	37	17	13980058	13980058	+	Missense_Mutation	SNP	A	A	T	rs2230351	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:13980058A>T	ENST00000261643.3	+	3	261	c.184A>T	c.(184-186)Aca>Tca	p.T62S	COX10_ENST00000429152.2_Missense_Mutation_p.T62S|COX10_ENST00000537334.1_Intron|COX10_ENST00000536205.1_5'UTR	NM_001303.3	NP_001294.2	Q12887	COX10_HUMAN	cytochrome c oxidase assembly homolog 10 (yeast)	62			T -> S (in dbSNP:rs2230351).		aerobic respiration (GO:0009060)|cellular respiration (GO:0045333)|heme a biosynthetic process (GO:0006784)|heme biosynthetic process (GO:0006783)|heme O biosynthetic process (GO:0048034)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|mitochondrial fission (GO:0000266)|porphyrin-containing compound metabolic process (GO:0006778)|respiratory chain complex IV assembly (GO:0008535)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	farnesyltranstransferase activity (GO:0004311)|protoheme IX farnesyltransferase activity (GO:0008495)			cervix(1)|endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14		all_lung(20;0.06)|Lung SC(565;0.168)		UCEC - Uterine corpus endometrioid carcinoma (92;0.106)		TTAGTATGTCACACAGCTGAA	0.408													A|||	308	0.0615016	0.0061	0.1153	5008	,	,		16223	0.1032		0.0686	False		,,,				2504	0.0481				p.T62S		Atlas-SNP	.											.	COX10	36	.	0			c.A184T						PASS	.	A	SER/THR	63,4343	56.8+/-93.2	1,61,2141	60.0	57.0	58.0		184	5.3	1.0	17	dbSNP_98	58	586,8014	155.4+/-209.4	25,536,3739	yes	missense	COX10	NM_001303.3	58	26,597,5880	TT,TA,AA		6.814,1.4299,4.99	benign	62/444	13980058	649,12357	2203	4300	6503	SO:0001583	missense	1352	exon3			TATGTCACACAGC	U09466	CCDS11166.1	17p12	2013-05-24	2012-10-15		ENSG00000006695	ENSG00000006695		"""Mitochondrial respiratory chain complex assembly factors"""	2260	protein-coding gene	gene with protein product	"""heme A: farnesyltransferase"", ""protoheme IX farnesyltransferase, mitochondrial"", ""heme O synthase"""	602125	"""COX10 (yeast) homolog, cytochrome c oxidase assembly protein (heme A: farnesyltransferase)"", ""COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase (yeast)"""			9177788, 12928484	Standard	NM_001303		Approved		uc002gof.4	Q12887	OTTHUMG00000058814	ENST00000261643.3:c.184A>T	17.37:g.13980058A>T	ENSP00000261643:p.Thr62Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_001303	B2R6U5|B4DJ50|O15334|Q969F7	Missense_Mutation	SNP	ENST00000261643.3	37	CCDS11166.1	156|156	0.07142857142857142|0.07142857142857142	3|3	0.006097560975609756|0.006097560975609756	33|33	0.09116022099447514|0.09116022099447514	70|70	0.12237762237762238|0.12237762237762238	50|50	0.06596306068601583|0.06596306068601583	A|A	17.14|17.14	3.312828|3.312828	0.60414|0.60414	0.014299|0.014299	0.06814|0.06814	ENSG00000006695|ENSG00000006695	ENST00000429152|ENST00000261643	.|T	.|0.37411	.|1.2	5.33|5.33	5.33|5.33	0.75918|0.75918	.|.	.|0.122077	.|0.53938	.|D	.|0.000048	T|T	0.00608|0.00608	0.0020|0.0020	M|M	0.71581|0.71581	2.175|2.175	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.16396	.|0.017	.|B	.|0.15052	.|0.012	T|T	0.06881|0.06881	-1.0802|-1.0802	4|9	.|0.41790	.|T	.|0.15	-18.9765|-18.9765	14.2362|14.2362	0.65929|0.65929	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs2230351;rs34342426|rs2230351;rs34342426	.|62	.|Q12887	.|COX10_HUMAN	L|S	22|62	.|ENSP00000261643:T62S	.|ENSP00000261643:T62S	H|T	+|+	2|1	0|0	COX10|COX10	13920783|13920783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	6.042000|6.042000	0.70996|0.70996	2.163000|2.163000	0.67991|0.67991	0.529000|0.529000	0.55759|0.55759	CAC|ACA	A|0.940;T|0.060	0.060	strong		0.408	COX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130003.1	NM_001303	
NPPA	4878	hgsc.bcm.edu	37	1	11907648	11907648	+	Missense_Mutation	SNP	C	C	T	rs5063	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11907648C>T	ENST00000376480.3	-	1	192	c.94G>A	c.(94-96)Gtg>Atg	p.V32M	NPPA-AS1_ENST00000446542.1_RNA|NPPA-AS1_ENST00000400892.2_RNA|NPPA_ENST00000376476.1_Intron	NM_006172.3	NP_006163.1	P01160	ANF_HUMAN	natriuretic peptide A	32			V -> M (in dbSNP:rs5063).		cardiac muscle hypertrophy in response to stress (GO:0014898)|cellular response to mechanical stimulus (GO:0071260)|cGMP biosynthetic process (GO:0006182)|female pregnancy (GO:0007565)|gene expression (GO:0010467)|negative regulation of cell growth (GO:0030308)|negative regulation of systemic arterial blood pressure (GO:0003085)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|transcription initiation from RNA polymerase II promoter (GO:0006367)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mast cell granule (GO:0042629)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCGTTGGACACGGCATTGTAC	0.557													C|||	368	0.0734824	0.0613	0.0476	5008	,	,		18211	0.1151		0.0348	False		,,,				2504	0.1053				p.V32M		Atlas-SNP	.											.	NPPA	14	.	0			c.G94A	GRCh37	CM057551	NPPA	M	rs5063	PASS	.	C	MET/VAL	266,4140	152.2+/-185.9	10,246,1947	206.0	188.0	194.0		94	-0.4	0.0	1	dbSNP_52	194	405,8195	128.7+/-186.9	7,391,3902	yes	missense	NPPA	NM_006172.3	21	17,637,5849	TT,TC,CC		4.7093,6.0372,5.1592	benign	32/152	11907648	671,12335	2203	4300	6503	SO:0001583	missense	4878	exon1			TGGACACGGCATT	BC005893	CCDS139.1	1p36.21	2014-09-17	2010-11-09		ENSG00000175206	ENSG00000175206		"""Endogenous ligands"""	7939	protein-coding gene	gene with protein product		108780	"""natriuretic peptide precursor A"""	ANP, PND			Standard	NM_006172		Approved		uc001ati.3	P01160	OTTHUMG00000002388	ENST00000376480.3:c.94G>A	1.37:g.11907648C>T	ENSP00000365663:p.Val32Met	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_006172	Q13766|Q5JZE1	Missense_Mutation	SNP	ENST00000376480.3	37	CCDS139.1	126	0.057692307692307696	28	0.056910569105691054	17	0.04696132596685083	51	0.08916083916083917	30	0.0395778364116095	C	3.799	-0.041992	0.07452	0.060372	0.047093	ENSG00000175206	ENST00000376480	T	0.49720	0.77	5.84	-0.381	0.12485	.	0.724342	0.13309	N	0.397680	T	0.00815	0.0027	L	0.35487	1.065	0.45216	D	0.998226	P	0.42556	0.783	B	0.25140	0.058	T	0.08330	-1.0727	10	0.30854	T	0.27	-9.3274	4.5953	0.12327	0.1413:0.4726:0.0:0.3861	rs5063;rs56762574;rs5063	32	P01160	ANF_HUMAN	M	32	ENSP00000365663:V32M	ENSP00000365663:V32M	V	-	1	0	NPPA	11830235	0.003000	0.15002	0.019000	0.16419	0.282000	0.26991	-0.378000	0.07446	-0.327000	0.08551	-0.424000	0.05967	GTG	C|0.943;T|0.057	0.057	strong		0.557	NPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006852.1	NM_006172	
XRCC6	2547	hgsc.bcm.edu	37	22	42059768	42059768	+	Silent	SNP	G	G	T	rs132788	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:42059768G>T	ENST00000359308.4	+	12	2434	c.1779G>T	c.(1777-1779)ggG>ggT	p.G593G	XRCC6_ENST00000405878.1_Silent_p.G593G|XRCC6_ENST00000402580.3_Silent_p.G552G|XRCC6_ENST00000360079.3_Silent_p.G593G|XRCC6_ENST00000428575.2_Silent_p.G460G|XRCC6_ENST00000405506.1_Silent_p.G543G			P12956	XRCC6_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 6	593	Interaction with DEAF1.|SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				brain development (GO:0007420)|cellular hyperosmotic salinity response (GO:0071475)|cellular response to X-ray (GO:0071481)|DNA duplex unwinding (GO:0032508)|DNA ligation (GO:0006266)|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)|innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neurogenesis (GO:0050769)|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)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytosol (GO:0005829)|Ku70:Ku80 complex (GO:0043564)|membrane (GO:0016020)|nonhomologous end joining complex (GO:0070419)|nuclear telomere cap complex (GO:0000783)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	5'-deoxyribose-5-phosphate lyase activity (GO:0051575)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|telomeric DNA binding (GO:0042162)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	31						TGAAGAGTGGGCTGAAGAAGC	0.622								Non-homologous end-joining					G|||	1047	0.209065	0.034	0.2089	5008	,	,		19059	0.2331		0.3628	False		,,,				2504	0.2628				p.G593G		Atlas-SNP	.											.	XRCC6	64	.	0			c.G1779T						PASS	.	G		405,4001	190.9+/-216.7	25,355,1823	50.0	49.0	50.0		1779	1.6	0.2	22	dbSNP_78	50	3082,5518	449.5+/-362.1	553,1976,1771	no	coding-synonymous	XRCC6	NM_001469.3		578,2331,3594	TT,TG,GG		35.8372,9.192,26.8107		593/610	42059768	3487,9519	2203	4300	6503	SO:0001819	synonymous_variant	2547	exon13			GAGTGGGCTGAAG	J04607	CCDS14021.1, CCDS74870.1, CCDS74871.1	22q13.2	2011-09-12	2008-07-31	2005-05-06	ENSG00000196419	ENSG00000196419			4055	protein-coding gene	gene with protein product	"""Ku autoantigen, 70kDa"""	152690	"""thyroid autoantigen 70kD (Ku antigen)"", ""thyroid autoantigen 70kDa (Ku antigen)"""	G22P1		9200330, 9223317	Standard	NM_001469		Approved	D22S731, D22S671, KU70, ML8	uc003bao.1	P12956	OTTHUMG00000151190	ENST00000359308.4:c.1779G>T	22.37:g.42059768G>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_001469	B1AHC8|Q6FG89|Q9UCQ2|Q9UCQ3	Silent	SNP	ENST00000359308.4	37	CCDS14021.1																																																																																			.	.	weak		0.622	XRCC6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321688.1	NM_001469	
NOP56	10528	hgsc.bcm.edu	37	20	2638882	2638882	+	Missense_Mutation	SNP	T	T	C	rs5856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:2638882T>C	ENST00000329276.5	+	12	2243	c.1727T>C	c.(1726-1728)gTt>gCt	p.V576A	SNORD56_ENST00000413522.1_RNA|NOP56_ENST00000492135.1_3'UTR|SNORD86_ENST00000391196.1_RNA|SNORD57_ENST00000448188.1_RNA|IDH3B_ENST00000488299.1_5'Flank	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	576	Lys-rich.		V -> A (in dbSNP:rs5856).		cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						GAAGAGGCGGTTGGCAAGAGC	0.502													C|||	1890	0.377396	0.6188	0.379	5008	,	,		17055	0.255		0.2664	False		,,,				2504	0.2904				p.V576A		Atlas-SNP	.											.	NOP56	73	.	0			c.T1727C						PASS	.	C	ALA/VAL	2180,2120		590,1000,560	8.0	11.0	10.0		1727	1.2	0.0	20	dbSNP_52	10	2163,6351		332,1499,2426	no	missense	NOP56	NM_006392.3	64	922,2499,2986	CC,CT,TT		25.4052,49.3023,33.8926	benign	576/595	2638882	4343,8471	2150	4257	6407	SO:0001583	missense	10528	exon12			AGGCGGTTGGCAA	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.1727T>C	20.37:g.2638882T>C	ENSP00000370589:p.Val576Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	775	0.35485347985347987	323	0.6565040650406504	127	0.35082872928176795	132	0.23076923076923078	193	0.2546174142480211	C	0.004	-2.265039	0.00259	0.506977	0.254052	ENSG00000101361	ENST00000329276	T	0.56444	0.46	5.27	1.17	0.20885	.	0.164771	0.36268	N	0.002692	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45818	-0.9235	9	0.02654	T	1	-0.1242	8.327	0.32162	0.0:0.5943:0.0:0.4057	rs5856;rs6754;rs3174890;rs59007437	576	O00567	NOP56_HUMAN	A	576	ENSP00000370589:V576A	ENSP00000370589:V576A	V	+	2	0	NOP56	2586882	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.686000	0.05161	-0.128000	0.11641	-1.026000	0.02426	GTT	T|0.673;C|0.327	0.327	strong		0.502	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
TAS2R46	259292	hgsc.bcm.edu	37	12	11214145	11214145	+	Nonsense_Mutation	SNP	C	C	T	rs2708381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11214145C>T	ENST00000533467.1	-	1	748	c.749G>A	c.(748-750)tGg>tAg	p.W250*	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	250					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		CTCAAAACTCCAAACTGACAT	0.428													.|||	1061	0.211861	0.2375	0.2378	5008	,	,		21792	0.1925		0.2068	False		,,,				2504	0.184				p.W250X		Atlas-SNP	.											.	TAS2R46	43	.	0			c.G749A						PASS	.	C	stop/TRP	1007,3399	347.7+/-309.6	120,767,1316	178.0	188.0	185.0		749	-0.0	0.0	12	dbSNP_100	185	1953,6647	341.7+/-324.1	224,1505,2571	no	stop-gained	TAS2R46	NM_176887.2		344,2272,3887	TT,TC,CC		22.7093,22.8552,22.7587		250/310	11214145	2960,10046	2203	4300	6503	SO:0001587	stop_gained	259292	exon1			AAACTCCAAACTG	AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.749G>A	12.37:g.11214145C>T	ENSP00000436450:p.Trp250*	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	194	104	0.536082	NM_176887	P59548|Q645X6	Nonsense_Mutation	SNP	ENST00000533467.1	37	CCDS53748.1	471	0.21565934065934067	104	0.21138211382113822	73	0.20165745856353592	125	0.21853146853146854	169	0.22295514511873352	C	10.07	1.249107	0.22880	0.228552	0.227093	ENSG00000226761	ENST00000533467	.	.	.	2.37	-0.0226	0.13947	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999717726	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.8362	0.29371	0.4251:0.5749:0.0:0.0	rs2708381;rs2708381	.	.	.	X	250	.	ENSP00000436450:W250X	W	-	2	0	TAS2R46	11105412	0.000000	0.05858	0.026000	0.17262	0.008000	0.06430	-0.395000	0.07287	0.309000	0.22966	0.194000	0.17425	TGG	C|0.785;T|0.215	0.215	strong		0.428	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887	
PRC1	9055	hgsc.bcm.edu	37	15	91525197	91525197	+	Silent	SNP	C	C	T	rs2301826	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:91525197C>T	ENST00000361188.5	-	4	1493	c.282G>A	c.(280-282)acG>acA	p.T94T	PRC1-AS1_ENST00000554388.1_RNA|PRC1_ENST00000442656.2_Silent_p.T53T|PRC1_ENST00000361919.3_Silent_p.T94T|PRC1_ENST00000394249.3_Silent_p.T94T|PRC1_ENST00000556129.1_5'Flank					protein regulator of cytokinesis 1											endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					GCAAGATGGTCGTCTCTCCTT	0.418													T|||	2357	0.470647	0.767	0.3271	5008	,	,		22656	0.5109		0.2147	False		,,,				2504	0.3937				p.T94T		Atlas-SNP	.											PRC1,NS,carcinoma,-1,1	PRC1	51	1	0			c.G282A						scavenged	.	T	,,	3004,1392	457.1+/-351.5	1031,942,225	160.0	166.0	164.0		282,282,282	-10.8	0.0	15	dbSNP_100	164	1766,6830	734.0+/-406.9	180,1406,2712	no	coding-synonymous,coding-synonymous,coding-synonymous	PRC1	NM_003981.2,NM_199413.1,NM_199414.1	,,	1211,2348,2937	TT,TC,CC		20.5444,31.6652,36.7149	,,	94/621,94/607,94/567	91525197	4770,8222	2198	4298	6496	SO:0001819	synonymous_variant	9055	exon4			GATGGTCGTCTCT	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"""anaphase spindle elongation 1 homolog (S. cerevisiae)"""	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.282G>A	15.37:g.91525197C>T		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	134	68	0.507463	NM_199413		Silent	SNP	ENST00000361188.5	37	CCDS45352.1																																																																																			C|0.592;T|0.408	0.408	strong		0.418	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981	
ZNF134	7693	hgsc.bcm.edu	37	19	58131576	58131576	+	Missense_Mutation	SNP	T	T	C	rs10414451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58131576T>C	ENST00000396161.5	+	3	399	c.89T>C	c.(88-90)aTt>aCt	p.I30T	ZNF134_ENST00000597975.1_3'UTR	NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	30			I -> T (in dbSNP:rs10414451).		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)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		GAACAGAGCATTTCTATAGCA	0.453													T|||	369	0.0736821	0.056	0.0749	5008	,	,		23618	0.0923		0.1014	False		,,,				2504	0.0491				p.I30T		Atlas-SNP	.											.	ZNF134	34	.	0			c.T89C						PASS	.	T	THR/ILE	237,3917		7,223,1847	98.0	96.0	97.0		89	1.3	0.0	19	dbSNP_119	97	761,7711		30,701,3505	yes	missense	ZNF134	NM_003435.3	89	37,924,5352	CC,CT,TT		8.9825,5.7053,7.9043	benign	30/428	58131576	998,11628	2077	4236	6313	SO:0001583	missense	7693	exon3			AGAGCATTTCTAT	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.89T>C	19.37:g.58131576T>C	ENSP00000379464:p.Ile30Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_003435	Q9Y4B2	Missense_Mutation	SNP	ENST00000396161.5	37	CCDS42638.1	186	0.08516483516483517	29	0.05894308943089431	28	0.07734806629834254	56	0.0979020979020979	73	0.09630606860158311	T	10.31	1.314860	0.23908	0.057053	0.089825	ENSG00000213762	ENST00000418193;ENST00000396161	T	0.07688	3.17	3.56	1.29	0.21616	.	.	.	.	.	T	0.00144	0.0004	N	0.20986	0.625	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.43669	-0.9377	8	0.16420	T	0.52	.	4.1857	0.10397	0.0:0.1269:0.4221:0.451	rs10414451;rs52838341;rs60319932;rs10414451	30	P52741	ZN134_HUMAN	T	97;30	ENSP00000379464:I30T	ENSP00000379464:I30T	I	+	2	0	ZNF134	62823388	0.042000	0.20092	0.001000	0.08648	0.563000	0.35712	0.717000	0.25851	0.207000	0.20607	0.533000	0.62120	ATT	T|0.913;C|0.087	0.087	strong		0.453	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435	
MLPH	79083	hgsc.bcm.edu	37	2	238427251	238427251	+	Missense_Mutation	SNP	G	G	A	rs3751107	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238427251G>A	ENST00000264605.3	+	5	809	c.515G>A	c.(514-516)gGc>gAc	p.G172D	MLPH_ENST00000338530.4_Missense_Mutation_p.G172D|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Missense_Mutation_p.G172D|MLPH_ENST00000409373.1_Missense_Mutation_p.G172D|MLPH_ENST00000410032.1_Missense_Mutation_p.G172D	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	172			G -> D (in dbSNP:rs3751107).		melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		GGAGAACCTGGCTCAGAGGCC	0.582													N|||	895	0.178714	0.3714	0.0994	5008	,	,		18072	0.0843		0.1412	False		,,,				2504	0.1104				p.G172D		Atlas-SNP	.											.	MLPH	41	.	0			c.G515A						PASS	.		ASP/GLY,ASP/GLY	1527,2879		255,1017,931	66.0	72.0	70.0		515,515	1.5	0.0	2	dbSNP_107	70	1458,7142		126,1206,2968	yes	missense,missense	MLPH	NM_001042467.1,NM_024101.5	94,94	381,2223,3899	AA,AG,GG		16.9535,34.6573,22.9509	benign,benign	172/573,172/601	238427251	2985,10021	2203	4300	6503	SO:0001583	missense	79083	exon5			AACCTGGCTCAGA	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.515G>A	2.37:g.238427251G>A	ENSP00000264605:p.Gly172Asp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	120	67	0.558333	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	370	0.16941391941391942	174	0.35365853658536583	38	0.10497237569060773	47	0.08216783216783216	111	0.14643799472295516	N	0	-2.589005	0.00128	0.346573	0.169535	ENSG00000115648	ENST00000410032;ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T;T;T;T;T	0.26067	1.76;2.14;2.12;1.96;1.77	2.65	1.49	0.22878	.	3.191120	0.02093	U	0.053301	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.06405	0.001;0.0;0.001;0.001;0.002;0.001;0.0	T	0.40289	-0.9571	9	0.11485	T	0.65	-12.4387	4.6532	0.12605	0.702:0.0:0.298:0.0	rs3751107;rs52809179;rs60441489;rs3751107	172;56;172;172;172;172;172	B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36;G5E9G5	.;.;.;.;.;MELPH_HUMAN;.	D	172	ENSP00000386338:G172D;ENSP00000264605:G172D;ENSP00000414849:G172D;ENSP00000341845:G172D;ENSP00000386780:G172D	ENSP00000264605:G172D	G	+	2	0	MLPH	238091990	0.001000	0.12720	0.002000	0.10522	0.016000	0.09150	-0.123000	0.10611	0.059000	0.16252	-1.342000	0.01247	GGC	G|0.795;A|0.205	0.205	strong		0.582	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
DDX58	23586	hgsc.bcm.edu	37	9	32526146	32526146	+	Missense_Mutation	SNP	G	G	A	rs10813831	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:32526146G>A	ENST00000379883.2	-	1	176	c.19C>T	c.(19-21)Cgc>Tgc	p.R7C	DDX58_ENST00000545044.1_De_novo_Start_InFrame|DDX58_ENST00000379882.1_Missense_Mutation_p.R7C|DDX58_ENST00000379868.1_De_novo_Start_InFrame	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	7	CARD 1.		R -> C (in dbSNP:rs10813831). {ECO:0000269|PubMed:17974005}.		cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TGCAGGCTGCGTCGCTGCTCG	0.607													G|||	922	0.184105	0.2073	0.1628	5008	,	,		14229	0.1052		0.2773	False		,,,				2504	0.1534				p.R7C		Atlas-SNP	.											.	DDX58	82	.	0			c.C19T						PASS	.	G	CYS/ARG	1018,3388	377.1+/-322.3	122,774,1307	64.0	56.0	59.0		19	-2.1	0.0	9	dbSNP_120	59	2213,6387	375.4+/-337.8	288,1637,2375	yes	missense	DDX58	NM_014314.3	180	410,2411,3682	AA,AG,GG		25.7326,23.1049,24.8424	probably-damaging	7/926	32526146	3231,9775	2203	4300	6503	SO:0001583	missense	23586	exon1			GGCTGCGTCGCTG	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.19C>T	9.37:g.32526146G>A	ENSP00000369213:p.Arg7Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	416	0.19047619047619047	99	0.20121951219512196	70	0.19337016574585636	41	0.07167832167832168	206	0.2717678100263852	G	15.14	2.743956	0.49151	0.231049	0.257326	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000542960	T;T	0.06371	3.4;3.31	4.02	-2.08	0.07254	.	1.305430	0.05512	N	0.560359	T	0.00012	0.0000	L	0.56769	1.78	0.49915	P	1.6099999999996673E-4	D;D	0.71674	0.997;0.998	P;P	0.53861	0.736;0.65	T	0.35773	-0.9775	9	0.87932	D	0	0.1979	8.0968	0.30833	0.0:0.2914:0.1955:0.513	rs10813831;rs17553642;rs52815553;rs59478737;rs10813831	7;7	O95786-2;O95786	.;DDX58_HUMAN	C	7	ENSP00000369212:R7C;ENSP00000369213:R7C	ENSP00000369212:R7C	R	-	1	0	DDX58	32516146	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.144000	0.10280	-0.381000	0.07882	-0.261000	0.10672	CGC	G|0.788;A|0.212	0.212	strong		0.607	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
PRX	57716	hgsc.bcm.edu	37	19	40901604	40901604	+	Silent	SNP	A	A	G	rs268672	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40901604A>G	ENST00000324001.7	-	7	2925	c.2655T>C	c.(2653-2655)ccT>ccC	p.P885P	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	885					axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			CTGCCACCTCAGGGCCCTCCA	0.637													G|||	2664	0.531949	0.8427	0.4784	5008	,	,		17346	0.2401		0.506	False		,,,				2504	0.4775				p.P885P		Atlas-SNP	.											.	PRX	151	.	0			c.T2655C						PASS	.	G	,	3471,935	339.1+/-305.6	1385,701,117	40.0	49.0	46.0		,2655	-7.2	0.0	19	dbSNP_79	46	4451,4149	555.1+/-386.6	1155,2141,1004	no	utr-3,coding-synonymous	PRX	NM_020956.2,NM_181882.2	,	2540,2842,1121	GG,GA,AA		48.2442,21.2211,39.0897	,	,885/1462	40901604	7922,5084	2203	4300	6503	SO:0001819	synonymous_variant	57716	exon7			CACCTCAGGGCCC	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.2655T>C	19.37:g.40901604A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_181882	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	CCDS33028.1																																																																																			A|0.457;G|0.543	0.543	strong		0.637	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956	
POLD4	57804	hgsc.bcm.edu	37	11	67120530	67120530	+	Missense_Mutation	SNP	C	C	G	rs28364240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67120530C>G	ENST00000312419.3	-	2	262	c.116G>C	c.(115-117)cGc>cCc	p.R39P	AP003419.11_ENST00000543494.1_RNA|POLD4_ENST00000539074.1_Missense_Mutation_p.R39P|POLD4_ENST00000529704.1_5'UTR	NM_021173.4	NP_066996.3	Q9HCU8	DPOD4_HUMAN	polymerase (DNA-directed), delta 4, accessory subunit	39			R -> P (in dbSNP:rs28364240). {ECO:0000269|Ref.2}.		base-excision repair (GO:0006284)|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)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(1)|endometrium(1)|lung(1)	3			BRCA - Breast invasive adenocarcinoma(15;3.08e-06)			CTCCTCGTCGCGGGGCTGGGG	0.662													C|||	183	0.0365415	0.0015	0.255	5008	,	,		16205	0.001		0.003	False		,,,				2504	0.0				p.R39P		Atlas-SNP	.											.	POLD4	9	.	0			c.G116C						PASS	.	C	PRO/ARG	8,4388		0,8,2190	24.0	21.0	22.0		116	-2.0	0.5	11	dbSNP_125	22	22,8558		0,22,4268	no	missense	POLD4	NM_021173.3	103	0,30,6458	GG,GC,CC		0.2564,0.182,0.2312	benign	39/108	67120530	30,12946	2198	4290	6488	SO:0001583	missense	57804	exon2			TCGTCGCGGGGCT	AF179890	CCDS8158.1, CCDS58149.1	11q13	2012-05-18	2012-05-18		ENSG00000175482	ENSG00000175482		"""DNA polymerases"""	14106	protein-coding gene	gene with protein product	"""DNA polymerase delta smallest subunit p12"""	611525	"""polymerase (DNA-directed), delta 4"""			10751307	Standard	NM_021173		Approved	p12, POLDS	uc001okm.4	Q9HCU8	OTTHUMG00000167135	ENST00000312419.3:c.116G>C	11.37:g.67120530C>G	ENSP00000311368:p.Arg39Pro	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	74	23	0.310811	NM_021173	F5H506	Missense_Mutation	SNP	ENST00000312419.3	37	CCDS8158.1	74	0.03388278388278388	2	0.0040650406504065045	68	0.1878453038674033	1	0.0017482517482517483	3	0.00395778364116095	C	5.363	0.252299	0.10185	0.00182	0.002564	ENSG00000175482	ENST00000312419;ENST00000539074	T;T	0.31769	1.48;1.48	4.56	-1.95	0.07548	.	1.353330	0.05020	N	0.472606	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29212	-1.0019	9	0.30078	T	0.28	-8.294	0.871	0.01214	0.2825:0.3398:0.2144:0.1633	rs28364240	39;39	Q6NSD7;Q9HCU8	.;DPOD4_HUMAN	P	39	ENSP00000311368:R39P;ENSP00000444780:R39P	ENSP00000311368:R39P	R	-	2	0	POLD4	66877106	0.013000	0.17824	0.515000	0.27774	0.236000	0.25371	-0.486000	0.06513	-0.185000	0.10550	-0.693000	0.03709	CGC	G|0.015;C|0.985;A|0.000	0.015	strong		0.662	POLD4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393336.1	NM_021173	
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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.R45K|SGK1_ENST00000367857.5_Missense_Mutation_p.R21K|SGK1_ENST00000475719.2_Missense_Mutation_p.R31K|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367858.5_Missense_Mutation_p.R126K|SGK1_ENST00000528577.1_Missense_Mutation_p.R59K	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	Somatic	70	0	0	1611	WXS	Illumina HiSeq	Phase_I	40	8	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		
SV2C	22987	hgsc.bcm.edu	37	5	75591710	75591710	+	Missense_Mutation	SNP	C	C	G	rs2270927	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:75591710C>G	ENST00000502798.2	+	9	1887	c.1445C>G	c.(1444-1446)aCt>aGt	p.T482S	SV2C_ENST00000322285.7_Missense_Mutation_p.T482S|RP11-466P24.6_ENST00000502589.1_RNA	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	482			T -> S (in dbSNP:rs2270927).		neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		GCAAATTTCACTATTAACTTT	0.348													G|||	891	0.177915	0.289	0.1599	5008	,	,		20707	0.1657		0.1044	False		,,,				2504	0.1288				p.T482S		Atlas-SNP	.											.	SV2C	97	.	0			c.C1445G						PASS	.	G	SER/THR	949,2731		120,709,1011	112.0	108.0	110.0		1445	0.7	0.9	5	dbSNP_100	110	821,7339		35,751,3294	yes	missense	SV2C	NM_014979.1	58	155,1460,4305	GG,GC,CC		10.0613,25.788,14.9493	benign	482/728	75591710	1770,10070	1840	4080	5920	SO:0001583	missense	22987	exon9			ATTTCACTATTAA	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.1445C>G	5.37:g.75591710C>G	ENSP00000423541:p.Thr482Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	37	CCDS43331.1	386	0.17673992673992675	148	0.3008130081300813	54	0.14917127071823205	107	0.18706293706293706	77	0.10158311345646438	G	11.83	1.756265	0.31137	0.25788	0.100613	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.79352	-0.89;-1.26	5.87	0.657	0.17850	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.292064	0.43416	N	0.000565	T	0.00012	0.0000	M	0.75777	2.31	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.09443	-1.0674	9	0.29301	T	0.29	-9.794	8.7831	0.34802	0.1029:0.5641:0.2338:0.0992	rs2270927;rs17674646;rs52802028;rs2270927	482	Q496J9	SV2C_HUMAN	S	482	ENSP00000423541:T482S;ENSP00000316983:T482S	ENSP00000316983:T482S	T	+	2	0	SV2C	75627466	0.102000	0.21896	0.890000	0.34922	0.985000	0.73830	0.506000	0.22658	-0.032000	0.13758	-0.120000	0.15030	ACT	C|0.830;G|0.170	0.170	strong		0.348	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4		
PARP4	143	hgsc.bcm.edu	37	13	25052393	25052393	+	Missense_Mutation	SNP	G	G	T	rs79107024	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25052393G>T	ENST00000381989.3	-	13	1575	c.1470C>A	c.(1468-1470)caC>caA	p.H490Q		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	490	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.H490Q(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCTCTCCCGGGTGTGAGTACT	0.418																																					p.H490Q		Atlas-SNP	.											.	PARP4	142	.	1	Substitution - Missense(1)	lung(1)	c.C1470A						PASS	.						106.0	86.0	92.0					13																	25052393		2203	4300	6503	SO:0001583	missense	143	exon13			TCCCGGGTGTGAG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1470C>A	13.37:g.25052393G>T	ENSP00000371419:p.His490Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	121	34	0.280992	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	285	0.1304945054945055	99	0.20121951219512196	44	0.12154696132596685	36	0.06293706293706294	106	0.13984168865435356	G	3.333	-0.136204	0.06711	.	.	ENSG00000102699	ENST00000381989	T	0.13420	2.59	3.91	-0.744	0.11101	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.898333	0.09533	N	0.789209	T	0.00012	0.0000	L	0.60067	1.865	0.24090	N	0.995918	B	0.14805	0.011	B	0.13407	0.009	T	0.44314	-0.9336	10	0.16896	T	0.51	-1.9083	3.6715	0.08276	0.2177:0.0:0.3285:0.4537	.	490	Q9UKK3	PARP4_HUMAN	Q	490	ENSP00000371419:H490Q	ENSP00000371419:H490Q	H	-	3	2	PARP4	23950393	0.588000	0.26799	0.018000	0.16275	0.865000	0.49528	-0.111000	0.10807	-0.008000	0.14320	0.644000	0.83932	CAC	G|0.874;T|0.126	0.126	strong		0.418	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
VWA8	23078	hgsc.bcm.edu	37	13	42465713	42465713	+	Missense_Mutation	SNP	C	C	T	rs9562362	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:42465713C>T	ENST00000379310.3	-	5	562	c.494G>A	c.(493-495)cGt>cAt	p.R165H	VWA8_ENST00000281496.6_Missense_Mutation_p.R165H	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	165			R -> H (in dbSNP:rs9562362).			extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										TGTGGCTGCACGAACTGCACA	0.398													C|||	1012	0.202077	0.0151	0.2954	5008	,	,		20968	0.1786		0.3171	False		,,,				2504	0.2945				p.R165H		Atlas-SNP	.											.	.	.	.	0			c.G494A						PASS	.	C	HIS/ARG,HIS/ARG	262,4144	147.3+/-181.8	4,254,1945	77.0	69.0	72.0		494,494	5.7	1.0	13	dbSNP_119	72	2737,5863	436.9+/-358.5	439,1859,2002	yes	missense,missense	KIAA0564	NM_001009814.1,NM_015058.1	29,29	443,2113,3947	TT,TC,CC		31.8256,5.9464,23.0586	probably-damaging,probably-damaging	165/1040,165/1906	42465713	2999,10007	2203	4300	6503	SO:0001583	missense	23078	exon5			GCTGCACGAACTG	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.494G>A	13.37:g.42465713C>T	ENSP00000368612:p.Arg165His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	84	54	0.642857	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	488	0.22344322344322345	10	0.02032520325203252	114	0.3149171270718232	115	0.20104895104895104	249	0.32849604221635886	C	36	5.662997	0.96745	0.059464	0.318256	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	T;T	0.59083	0.29;0.29	5.71	5.71	0.89125	ATPase, dynein-related, AAA domain (1);	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	M	0.92077	3.27	0.09310	P	0.999999999480994	D	0.61080	0.989	P	0.58077	0.832	T	0.00756	-1.1579	9	0.87932	D	0	.	20.2245	0.98337	0.0:1.0:0.0:0.0	rs9562362;rs17534916;rs52826154;rs60454473;rs9562362	165	A3KMH1	K0564_HUMAN	H	69;165;165;165	ENSP00000368612:R165H;ENSP00000281496:R165H	ENSP00000251030:R69H	R	-	2	0	KIAA0564	41363713	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.536000	0.82023	2.861000	0.98227	0.650000	0.86243	CGT	C|0.775;T|0.225	0.225	strong		0.398	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
GGA3	23163	hgsc.bcm.edu	37	17	73237124	73237124	+	Missense_Mutation	SNP	T	T	C	rs146877619	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73237124T>C	ENST00000245541.6	-	11	1177	c.961A>G	c.(961-963)Agt>Ggt	p.S321G	GGA3_ENST00000582717.1_Missense_Mutation_p.S249G|GGA3_ENST00000351904.7_Missense_Mutation_p.S288G|GGA3_ENST00000537686.1_3'UTR|GGA3_ENST00000582486.1_Missense_Mutation_p.S249G|GGA3_ENST00000578348.1_Missense_Mutation_p.S199G|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000538886.1_Missense_Mutation_p.S199G	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	321	Unstructured hinge.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			CCTTGGTTACTGCACTGACTG	0.572											OREG0024730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	3	0.000599042	0.0	0.0	5008	,	,		19748	0.0		0.003	False		,,,				2504	0.0				p.S321G		Atlas-SNP	.											.	GGA3	54	.	0			c.A961G						PASS	.	T	GLY/SER,GLY/SER,GLY/SER,GLY/SER	2,4404	4.2+/-10.8	0,2,2201	124.0	122.0	122.0		745,595,862,961	-2.1	0.0	17	dbSNP_134	122	30,8570	21.0+/-64.5	0,30,4270	yes	missense,missense,missense,missense	GGA3	NM_001172703.1,NM_001172704.1,NM_014001.3,NM_138619.2	56,56,56,56	0,32,6471	CC,CT,TT		0.3488,0.0454,0.246	benign,benign,benign,benign	249/652,199/593,288/691,321/724	73237124	32,12974	2203	4300	6503	SO:0001583	missense	23163	exon11			GGTTACTGCACTG	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.961A>G	17.37:g.73237124T>C	ENSP00000245541:p.Ser321Gly	Somatic	89	0	0	1143	WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_138619	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Missense_Mutation	SNP	ENST00000245541.6	37	CCDS11717.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	5.212	0.224623	0.09916	4.54E-4	0.003488	ENSG00000125447	ENST00000245541;ENST00000351904;ENST00000537584;ENST00000538886	T;T	0.46819	2.19;0.86	4.37	-2.14	0.07123	.	0.449389	0.27567	N	0.018799	T	0.17704	0.0425	N	0.05383	-0.06	0.09310	N	0.999993	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.06250	-1.0837	10	0.25751	T	0.34	-22.5352	1.3881	0.02244	0.1321:0.2348:0.1371:0.496	.	199;288;321	B7Z7E2;Q9NZ52-2;Q9NZ52	.;.;GGA3_HUMAN	G	321;288;249;199	ENSP00000245541:S321G;ENSP00000326575:S288G	ENSP00000245541:S321G	S	-	1	0	GGA3	70748719	0.024000	0.19004	0.000000	0.03702	0.131000	0.20780	1.651000	0.37302	-0.553000	0.06158	0.533000	0.62120	AGT	T|0.998;C|0.002	0.002	strong		0.572	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619	
GABRE	2564	hgsc.bcm.edu	37	X	151138179	151138179	+	Missense_Mutation	SNP	A	A	C	rs1139916	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:151138179A>C	ENST00000370328.3	-	3	357	c.304T>G	c.(304-306)Tcc>Gcc	p.S102A	GABRE_ENST00000393914.3_5'UTR|GABRE_ENST00000370325.1_Missense_Mutation_p.S102A	NM_004961.3	NP_004952.2	P78334	GBRE_HUMAN	gamma-aminobutyric acid (GABA) A receptor, epsilon	102			S -> A (in dbSNP:rs1139916). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9039914, ECO:0000269|PubMed:9084408}.		gamma-aminobutyric acid signaling pathway (GO:0007214)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|skin(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CTGTTGACGGAGATCTCAACA	0.517													a|||	2667	0.70649	0.3654	0.5591	3775	,	,		13577	0.6518		0.5318	False		,,,				2504	0.6176				p.S102A		Atlas-SNP	.											.	GABRE	141	.	0			c.T304G						PASS	.		ALA/SER	1933,1902		416,816,285,400,286	99.0	82.0	88.0		304	2.7	0.0	X	dbSNP_86	88	4511,2217		1089,1083,1250,256,622	yes	missense	GABRE	NM_004961.3	99	1505,1899,1535,656,908	CC,CA,C,AA,A		32.9518,49.5958,38.9946	possibly-damaging	102/507	151138179	6444,4119	2203	4300	6503	SO:0001583	missense	2564	exon3			TGACGGAGATCTC	Y09765	CCDS14703.1	Xq28	2012-06-22			ENSG00000102287	ENSG00000102287		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4085	protein-coding gene	gene with protein product	"""GABA(A) receptor, epsilon"""	300093				9039914, 9084408	Standard	NM_004961		Approved		uc004ffi.3	P78334	OTTHUMG00000024176	ENST00000370328.3:c.304T>G	X.37:g.151138179A>C	ENSP00000359353:p.Ser102Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_004961	E7ET93|O15345|O15346|Q6PCD2|Q99520	Missense_Mutation	SNP	ENST00000370328.3	37	CCDS14703.1	1143	0.6889692585895117	123	0.30295566502463056	139	0.5791666666666667	245	0.7291666666666666	293	0.5790513833992095	a	9.301	1.052992	0.19907	0.504042	0.670482	ENSG00000102287	ENST00000370328;ENST00000370325	T;T	0.77358	-1.09;-1.09	5.28	2.71	0.32032	Neurotransmitter-gated ion-channel ligand-binding (3);	0.340381	0.21783	N	0.069169	T	0.00012	0.0000	L	0.55990	1.75	0.46185	P	0.0010900000000000354	P	0.42456	0.78	B	0.43301	0.415	T	0.48468	-0.9033	9	0.17832	T	0.49	.	7.3801	0.26851	0.6457:0.0:0.0:0.3543	rs1139916;rs2071306;rs3203977;rs17846569;rs17859650;rs52790880;rs61218654;rs1139916	102	P78334	GBRE_HUMAN	A	102	ENSP00000359353:S102A;ENSP00000359350:S102A	ENSP00000359350:S102A	S	-	1	0	GABRE	150888835	0.998000	0.40836	0.001000	0.08648	0.024000	0.10985	3.505000	0.53356	0.204000	0.20548	0.483000	0.47432	TCC	A|0.369;C|0.631	0.631	strong		0.517	GABRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060903.1	NM_004961, NM_021990, NM_021984	
THBS1	7057	hgsc.bcm.edu	37	15	39880822	39880822	+	Missense_Mutation	SNP	A	A	G	rs2292305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:39880822A>G	ENST00000260356.5	+	10	1732	c.1567A>G	c.(1567-1569)Aca>Gca	p.T523A		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	523	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.		T -> A (in dbSNP:rs2292305). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2918029}.		activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.T523A(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CAACAACCCCACACCCCAGTT	0.542													A|||	1375	0.274561	0.4644	0.1412	5008	,	,		20016	0.3056		0.1312	False		,,,				2504	0.228				p.T523A		Atlas-SNP	.											THBS1,NS,carcinoma,0,1	THBS1	106	1	1	Substitution - Missense(1)	stomach(1)	c.A1567G						PASS	.	A	ALA/THR	1785,2615	527.1+/-372.1	368,1049,783	91.0	87.0	89.0		1567	-2.5	0.6	15	dbSNP_100	89	1134,7460	232.9+/-266.4	64,1006,3227	yes	missense	THBS1	NM_003246.2	58	432,2055,4010	GG,GA,AA		13.1953,40.5682,22.4642	benign	523/1171	39880822	2919,10075	2200	4297	6497	SO:0001583	missense	7057	exon10			AACCCCACACCCC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1567A>G	15.37:g.39880822A>G	ENSP00000260356:p.Thr523Ala	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	553	0.2532051282051282	216	0.43902439024390244	54	0.14917127071823205	190	0.3321678321678322	93	0.12269129287598944	A	8.764	0.924339	0.18056	0.405682	0.131953	ENSG00000137801	ENST00000260356	T	0.60040	0.22	5.87	-2.47	0.06442	.	0.716432	0.11505	N	0.557327	T	0.00012	0.0000	N	0.00436	-1.5	0.43953	P	0.0033800000000000496	B	0.02656	0.0	B	0.01281	0.0	T	0.32428	-0.9907	9	0.06365	T	0.9	4.0151	7.117	0.25423	0.3584:0.2348:0.4067:0.0	rs2292305;rs58566849;rs2292305	523	P07996	TSP1_HUMAN	A	523	ENSP00000260356:T523A	ENSP00000260356:T523A	T	+	1	0	THBS1	37668114	0.000000	0.05858	0.617000	0.29091	0.985000	0.73830	0.374000	0.20501	-0.734000	0.04843	-0.993000	0.02533	ACA	A|0.756;G|0.244	0.244	strong		0.542	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
SPRR1A	6698	hgsc.bcm.edu	37	1	152957832	152957832	+	Missense_Mutation	SNP	C	C	A	rs1611762|rs17882377|rs372951479	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152957832C>A	ENST00000368762.1	+	1	126	c.126C>A	c.(124-126)caC>caA	p.H42Q	SPRR1A_ENST00000307122.2_Missense_Mutation_p.H42Q			P35321	SPR1A_HUMAN	small proline-rich protein 1A	42	6 X 8 AA approximate tandem repeats.		H -> Q (in dbSNP:rs1611762). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8325635, ECO:0000269|Ref.3}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCCCTGCCACCCCAAGGTGC	0.647													C|||	2531	0.505391	0.4523	0.4395	5008	,	,		14293	0.5972		0.5348	False		,,,				2504	0.499				p.H42Q		Atlas-SNP	.											.	SPRR1A	17	.	0			c.C126A						PASS	.						122.0	126.0	125.0					1																	152957832		2203	4300	6503	SO:0001583	missense	6698	exon2			CTGCCACCCCAAG	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.126C>A	1.37:g.152957832C>A	ENSP00000357751:p.His42Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	37	CCDS1032.1	1174	0.5375457875457875	234	0.47560975609756095	180	0.4972375690607735	358	0.6258741258741258	402	0.5303430079155673	C	9.564	1.119172	0.20877	.	.	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.13657	2.57;2.57	4.77	1.54	0.23209	.	0.648090	0.12758	N	0.441596	T	0.03136	0.0092	.	.	.	0.52099	P	5.3999999999998494E-5	B	0.27013	0.166	B	0.24848	0.056	T	0.40850	-0.9541	8	0.36615	T	0.2	-2.9027	7.3544	0.26711	0.3386:0.4971:0.1643:0.0	rs1611762;rs17884470;rs58509799;rs1611762	42	P35321	SPR1A_HUMAN	Q	42	ENSP00000307340:H42Q;ENSP00000357751:H42Q	ENSP00000307340:H42Q	H	+	3	2	SPRR1A	151224456	0.620000	0.27068	0.970000	0.41538	0.731000	0.41821	0.156000	0.16382	0.397000	0.25310	0.549000	0.68633	CAC	C|0.457;A|0.543	0.543	strong		0.647	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987	
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 GAIIx	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_ENST00000449107.1_Silent_p.H418H|BTD_ENST00000437172.1_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		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	131	64	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 GAIIx	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_ENST00000344440.6_Missense_Mutation_p.L630R|SORCS1_ENST00000369698.1_Missense_Mutation_p.L165R	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	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	74	25	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	
USP42	84132	hgsc.bcm.edu	37	7	6194383	6194383	+	Silent	SNP	C	C	T	rs73058659	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6194383C>T	ENST00000306177.5	+	15	3356	c.3198C>T	c.(3196-3198)taC>taT	p.Y1066Y		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	1066	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)		ATGACAGGTACGCCCTGTACG	0.706													C|||	227	0.0453275	0.0068	0.0865	5008	,	,		7457	0.0		0.1392	False		,,,				2504	0.0184				p.Y1066Y		Atlas-SNP	.											USP42_ENST00000306177,NS,carcinoma,0,2	USP42	138	2	0			c.C3198T						PASS	.	C		96,3946		1,94,1926	8.0	10.0	10.0		3198	2.5	0.4	7	dbSNP_132	10	973,7321		38,897,3212	no	coding-synonymous	USP42	NM_032172.2		39,991,5138	TT,TC,CC		11.7314,2.3751,8.6657		1066/1317	6194383	1069,11267	2021	4147	6168	SO:0001819	synonymous_variant	84132	exon15			CAGGTACGCCCTG	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.3198C>T	7.37:g.6194383C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	27	7	0.259259	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	37	CCDS47535.1																																																																																			C|0.929;T|0.071	0.071	strong		0.706	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
AAMDC	28971	hgsc.bcm.edu	37	11	77553638	77553638	+	Silent	SNP	T	T	C	rs585721	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77553638T>C	ENST00000526415.1	+	3	269	c.96T>C	c.(94-96)ggT>ggC	p.G32G	AAMDC_ENST00000393427.2_Silent_p.G32G|AAMDC_ENST00000525409.1_Silent_p.G32G|AAMDC_ENST00000304716.8_Silent_p.G32G|AAMDC_ENST00000532481.1_Silent_p.G32G|AAMDC_ENST00000533193.1_Silent_p.G32G|RP11-91P24.7_ENST00000525594.1_RNA|AAMDC_ENST00000527134.1_Silent_p.G32G|AAMDC_ENST00000525034.1_Silent_p.G51G			Q9H7C9	AAMDC_HUMAN	adipogenesis associated, Mth938 domain containing	32	MTH138-like domain. {ECO:0000250}.				negative regulation of apoptotic process (GO:0043066)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)		p.G32G(1)									GGCCAGGGGGTAGTCGGACTT	0.433													C|||	1957	0.390775	0.5265	0.3948	5008	,	,		17605	0.2688		0.3688	False		,,,				2504	0.3528				p.G32G		Atlas-SNP	.											C11orf67,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.T96C						PASS	.	C		2296,2104	575.6+/-384.0	583,1130,487	69.0	67.0	68.0		96	-1.8	1.0	11	dbSNP_83	68	3162,5422	653.5+/-401.1	586,1990,1716	no	coding-synonymous	C11orf67	NM_024684.2		1169,3120,2203	CC,CT,TT		36.836,47.8182,42.0364		32/123	77553638	5458,7526	2200	4292	6492	SO:0001819	synonymous_variant	28971	exon2			AGGGGGTAGTCGG	BC016854	CCDS8254.1	11q14.1	2012-10-08	2012-10-08	2012-10-08	ENSG00000087884	ENSG00000087884			30205	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 67"""	C11orf67		12477932	Standard	NM_024684		Approved	PTD015, FLJ21035, CK067	uc001oyq.3	Q9H7C9	OTTHUMG00000166651	ENST00000526415.1:c.96T>C	11.37:g.77553638T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	73	0.901235	NM_024684	Q96AQ4|Q9Y6B1	Silent	SNP	ENST00000526415.1	37	CCDS8254.1																																																																																			T|0.588;C|0.412	0.412	strong		0.433	AAMDC-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390976.1	NM_024684	
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 GAIIx	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		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	130	30	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	
TMC1	117531	hgsc.bcm.edu	37	9	75315438	75315438	+	Missense_Mutation	SNP	G	G	A	rs1796993	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:75315438G>A	ENST00000297784.5	+	8	781	c.241G>A	c.(241-243)Gaa>Aaa	p.E81K	TMC1_ENST00000396237.3_Missense_Mutation_p.E81K|TMC1_ENST00000340019.3_Missense_Mutation_p.E81K	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	81	Arg/Asp/Glu/Lys-rich (highly charged).		E -> K (in dbSNP:rs1796993). {ECO:0000269|PubMed:11850618}.		auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						TTAAAGAGAAGAAGAAGAAAT	0.323													G|||	1384	0.276358	0.2708	0.2493	5008	,	,		12579	0.381		0.163	False		,,,				2504	0.3119				p.E81K	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.G241A						PASS	.	G	LYS/GLU	1157,3249	371.0+/-319.8	156,845,1202	71.0	82.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	241	5.5	1.0	9	dbSNP_89	78	1449,7143	256.2+/-280.8	116,1217,2963	yes	missense	TMC1	NM_138691.2	56	272,2062,4165	AA,AG,GG		16.8645,26.2596,20.0492	benign	81/761	75315438	2606,10392	2203	4296	6499	SO:0001583	missense	117531	exon8			AGAGAAGAAGAAG	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"""transmembrane, cochlear expressed, 1"""	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.241G>A	9.37:g.75315438G>A	ENSP00000297784:p.Glu81Lys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_138691	A8MVZ2|B1AM91	Missense_Mutation	SNP	ENST00000297784.5	37	CCDS6643.1	603	0.2760989010989011	142	0.2886178861788618	96	0.26519337016574585	234	0.4090909090909091	131	0.17282321899736147	G	16.23	3.064900	0.55432	0.262596	0.168645	ENSG00000165091	ENST00000297784;ENST00000340019;ENST00000542143;ENST00000396237	T;T;T	0.52295	0.67;0.67;0.67	5.48	5.48	0.80851	.	0.064987	0.64402	D	0.000014	T	0.00012	0.0000	L	0.41492	1.28	0.21445	P	0.99968547	B	0.26635	0.155	B	0.18871	0.023	T	0.36359	-0.9751	9	0.09084	T	0.74	-13.9321	18.494	0.90858	0.0:0.0:1.0:0.0	rs1796993;rs17058087;rs59785599;rs1796993	81	Q8TDI8	TMC1_HUMAN	K	81;81;75;81	ENSP00000297784:E81K;ENSP00000341433:E81K;ENSP00000379538:E81K	ENSP00000297784:E81K	E	+	1	0	TMC1	74505258	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.552000	0.67281	2.730000	0.93505	0.655000	0.94253	GAA	G|0.761;A|0.239	0.239	strong		0.323	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		
MS4A15	219995	hgsc.bcm.edu	37	11	60531264	60531264	+	Missense_Mutation	SNP	A	A	G	rs12363342	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:60531264A>G	ENST00000405633.3	+	2	137	c.58A>G	c.(58-60)Agt>Ggt	p.S20G	MS4A15_ENST00000528170.1_Missense_Mutation_p.S20G|MS4A15_ENST00000337911.4_Intron	NM_001098835.1	NP_001092305.1	Q8N5U1	M4A15_HUMAN	membrane-spanning 4-domains, subfamily A, member 15	20			S -> G (in dbSNP:rs12363342).			integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(3)	6						AAACAACGCCAGTGGCCTCTG	0.572													A|||	1321	0.263778	0.2398	0.2853	5008	,	,		20159	0.2123		0.3588	False		,,,				2504	0.2362				p.S20G		Atlas-SNP	.											.	MS4A15	37	.	0			c.A58G						PASS	.	A	GLY/SER,	1092,2998		168,756,1121	102.0	102.0	102.0		58,	4.1	1.0	11	dbSNP_120	102	3246,5118		639,1968,1575	yes	missense,intron	MS4A15	NM_001098835.1,NM_152717.2	56,	807,2724,2696	GG,GA,AA		38.8092,26.6993,34.8322	probably-damaging,	20/241,	60531264	4338,8116	2045	4182	6227	SO:0001583	missense	219995	exon2			AACGCCAGTGGCC	AY584608	CCDS7991.1, CCDS44617.1, CCDS60802.1	11q12.2	2008-03-25							28573	protein-coding gene	gene with protein product							Standard	NM_001098835		Approved		uc009ynf.1	Q8N5U1		ENST00000405633.3:c.58A>G	11.37:g.60531264A>G	ENSP00000386022:p.Ser20Gly	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	76	43	0.565789	NM_001098835	A9UJY6|A9UJY7|F2Z2J5	Missense_Mutation	SNP	ENST00000405633.3	37	CCDS44617.1	593	0.2715201465201465	108	0.21951219512195122	117	0.32320441988950277	99	0.17307692307692307	269	0.3548812664907652	A	13.46	2.242511	0.39598	0.266993	0.388092	ENSG00000166961	ENST00000528170;ENST00000405633	T;T	0.17213	2.29;2.87	5.21	4.07	0.47477	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.40139	P	0.02318600000000004	D;D	0.63880	0.993;0.982	P;D	0.67548	0.842;0.952	T	0.46062	-0.9218	8	0.51188	T	0.08	-21.4375	7.8754	0.29590	0.9042:0.0:0.0958:0.0	rs12363342	20;20	F2Z2J5;Q8N5U1	.;M4A15_HUMAN	G	20	ENSP00000434165:S20G;ENSP00000386022:S20G	ENSP00000386022:S20G	S	+	1	0	MS4A15	60287840	0.267000	0.24122	0.968000	0.41197	0.097000	0.18754	0.111000	0.15458	0.797000	0.33971	0.379000	0.24179	AGT	A|0.709;G|0.291	0.291	strong		0.572	MS4A15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395618.1		
JAG1	182	hgsc.bcm.edu	37	20	10625804	10625804	+	Silent	SNP	T	T	G	rs1801140	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:10625804T>G	ENST00000254958.5	-	17	2729	c.2214A>C	c.(2212-2214)acA>acC	p.T738T	JAG1_ENST00000423891.2_Silent_p.T579T|JAG1_ENST00000488480.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	738	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						TGTTACAGGTTGTTCCTTCCC	0.547									Alagille Syndrome				G|||	505	0.100839	0.0204	0.147	5008	,	,		19640	0.0476		0.1193	False		,,,				2504	0.2127				p.T738T		Atlas-SNP	.											.	JAG1	213	.	0			c.A2214C						PASS	.	G		151,4255	812.9+/-416.1	1,149,2053	106.0	88.0	94.0		2214	-11.7	0.0	20	dbSNP_89	94	831,7769	781.3+/-407.6	39,753,3508	no	coding-synonymous	JAG1	NM_000214.2		40,902,5561	GG,GT,TT		9.6628,3.4271,7.5504		738/1219	10625804	982,12024	2203	4300	6503	SO:0001819	synonymous_variant	182	exon17	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	ACAGGTTGTTCCT	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2214A>C	20.37:g.10625804T>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			T|0.921;G|0.079	0.079	strong		0.547	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
RTL1	388015	hgsc.bcm.edu	37	14	101348584	101348584	+	Missense_Mutation	SNP	C	C	G	rs11623267	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:101348584C>G	ENST00000534062.1	-	1	2600	c.2542G>C	c.(2542-2544)Gag>Cag	p.E848Q	MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA|MIR431_ENST00000385266.1_RNA|MIR432_ENST00000606207.1_RNA|MIR136_ENST00000385207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	848			E -> Q (in dbSNP:rs11623267).		multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TCTTGCTCCTCGACTCCCCAG	0.612													C|||	1006	0.200879	0.0915	0.1455	5008	,	,		17756	0.3482		0.2654	False		,,,				2504	0.1697				p.E848Q		Atlas-SNP	.											RTL1,NS,carcinoma,0,1	RTL1	120	1	0			c.G2542C						PASS	.						27.0	27.0	27.0					14																	101348584		692	1591	2283	SO:0001583	missense	388015	exon1			GCTCCTCGACTCC		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.2542G>C	14.37:g.101348584C>G	ENSP00000435342:p.Glu848Gln	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	37	CCDS53910.1	519	0.23763736263736263	42	0.08536585365853659	62	0.1712707182320442	205	0.3583916083916084	210	0.2770448548812665	C	11.41	1.629661	0.28978	.	.	ENSG00000254656	ENST00000534062	T	0.52526	0.66	3.33	3.33	0.38152	.	0.294433	0.19232	N	0.119389	T	0.00012	0.0000	L	0.56340	1.77	0.34432	P	0.30138699999999996	D	0.57571	0.98	P	0.53912	0.737	T	0.37888	-0.9686	9	0.34782	T	0.22	.	12.9629	0.58468	0.0:1.0:0.0:0.0	rs11623267;rs58725312;rs11623267	848	E9PKS8	.	Q	848	ENSP00000435342:E848Q	ENSP00000435342:E848Q	E	-	1	0	RTL1	100418337	0.992000	0.36948	0.816000	0.32577	0.297000	0.27493	3.624000	0.54231	2.180000	0.69256	0.561000	0.74099	GAG	C|0.751;G|0.249	0.249	strong		0.612	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
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 GAIIx	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*	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	40	8	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	
CCM2	83605	hgsc.bcm.edu	37	7	45113170	45113170	+	Splice_Site	SNP	G	G	A	rs2289367	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:45113170G>A	ENST00000258781.6	+	8	1064	c.915G>A	c.(913-915)acG>acA	p.T305T	CCM2_ENST00000474617.1_Splice_Site_p.T208T|CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000544363.1_Splice_Site_p.T214T|CCM2_ENST00000541586.1_Splice_Site_p.T247T|CCM2_ENST00000475551.1_Splice_Site_p.T299T|CCM2_ENST00000381112.3_Splice_Site_p.T326T	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	305	Harmonin homology domain.				blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						ACATGCTGACGGTAGGCCTCC	0.657													G|||	1101	0.219848	0.2277	0.2752	5008	,	,		17768	0.1895		0.2078	False		,,,				2504	0.2137				p.T326T		Atlas-SNP	.											CCM2,NS,carcinoma,0,1	CCM2	42	1	0			c.G978A						PASS	.	G	,,,	1127,3279	398.5+/-330.9	133,861,1209	52.0	43.0	46.0		978,741,642,915	-0.2	1.0	7	dbSNP_100	46	1830,6770	323.2+/-315.9	202,1426,2672	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CCM2	NM_001029835.2,NM_001167934.1,NM_001167935.1,NM_031443.3	,,,	335,2287,3881	AA,AG,GG		21.2791,25.5788,22.7357	,,,	326/466,247/387,214/354,305/445	45113170	2957,10049	2203	4300	6503	SO:0001630	splice_region_variant	83605	exon8			GCTGACGGTAGGC	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.915+1G>A	7.37:g.45113170G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	28	18	0.642857	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Silent	SNP	ENST00000258781.6	37	CCDS5500.1																																																																																			G|0.779;A|0.221	0.221	strong		0.657	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	Silent
DPY19L2	283417	hgsc.bcm.edu	37	12	63954300	63954300	+	Missense_Mutation	SNP	C	C	T	rs12314553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:63954300C>T	ENST00000324472.4	-	22	2452	c.2269G>A	c.(2269-2271)Gtt>Att	p.V757I	DPY19L2_ENST00000413230.2_Missense_Mutation_p.V204I	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	757			V -> I (in dbSNP:rs12314553).		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		TCTCAGTTAACCTTTAATACT	0.408													c|||	672	0.134185	0.2466	0.1239	5008	,	,		16421	0.0099		0.172	False		,,,				2504	0.0787				p.V757I		Atlas-SNP	.											.	DPY19L2	97	.	0			c.G2269A						PASS	.	C	ILE/VAL	1016,3390	374.6+/-321.3	105,806,1292	86.0	81.0	82.0		2269	2.1	0.4	12	dbSNP_120	82	1320,7280	259.7+/-282.8	101,1118,3081	yes	missense	DPY19L2	NM_173812.4	29	206,1924,4373	TT,TC,CC		15.3488,23.0595,17.9609	benign	757/759	63954300	2336,10670	2203	4300	6503	SO:0001583	missense	283417	exon22			AGTTAACCTTTAA		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.2269G>A	12.37:g.63954300C>T	ENSP00000315988:p.Val757Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	310	0.14194139194139194	129	0.2621951219512195	50	0.13812154696132597	6	0.01048951048951049	125	0.16490765171503957	C	12.42	1.934130	0.34096	0.230595	0.153488	ENSG00000177990	ENST00000324472;ENST00000413230	T;T	0.55588	0.51;0.51	3.0	2.07	0.26955	.	0.063133	0.64402	D	0.000007	T	0.00012	0.0000	L	0.35414	1.06	0.32875	P	0.490194	B	0.31581	0.329	B	0.40375	0.327	T	0.21621	-1.0240	8	.	.	.	.	5.5277	0.16967	0.0:0.8213:0.0:0.1787	rs12314553	757	Q6NUT2	D19L2_HUMAN	I	757;204	ENSP00000315988:V757I;ENSP00000439794:V204I	.	V	-	1	0	DPY19L2	62240567	1.000000	0.71417	0.389000	0.26208	0.194000	0.23727	2.462000	0.45049	0.345000	0.23873	0.162000	0.16502	GTT	C|0.836;T|0.164	0.164	strong		0.408	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
ARID5B	84159	hgsc.bcm.edu	37	10	63829539	63829539	+	Silent	SNP	C	C	T	rs76296217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:63829539C>T	ENST00000279873.7	+	8	1592	c.1182C>T	c.(1180-1182)acC>acT	p.T394T	ARID5B_ENST00000309334.5_Silent_p.T151T	NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	394	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				adipose tissue development (GO:0060612)|adrenal gland development (GO:0030325)|cell development (GO:0048468)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|fat pad development (GO:0060613)|female gonad development (GO:0008585)|fibroblast migration (GO:0010761)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|multicellular organism growth (GO:0035264)|muscle organ morphogenesis (GO:0048644)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(13)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	Prostate(12;0.016)|all_hematologic(501;0.215)					CCACTTGTACCCGCAGACATT	0.428													C|||	107	0.0213658	0.003	0.0389	5008	,	,		19689	0.0		0.0716	False		,,,				2504	0.0041				p.T394T		Atlas-SNP	.											.	ARID5B	125	.	0			c.C1182T						PASS	.	C		83,4323	70.9+/-108.8	1,81,2121	50.0	51.0	51.0		1182	-2.3	1.0	10	dbSNP_131	51	652,7948	166.7+/-218.6	28,596,3676	no	coding-synonymous	ARID5B	NM_032199.2		29,677,5797	TT,TC,CC		7.5814,1.8838,5.6512		394/1189	63829539	735,12271	2203	4300	6503	SO:0001819	synonymous_variant	84159	exon8			TTGTACCCGCAGA	M73837	CCDS31208.1, CCDS58082.1	10q11.22	2013-02-07			ENSG00000150347	ENSG00000150347		"""-"""	17362	protein-coding gene	gene with protein product		608538				11483573, 11478881	Standard	NM_032199		Approved	FLJ21150, MRF2	uc001jlt.2	Q14865	OTTHUMG00000018298	ENST00000279873.7:c.1182C>T	10.37:g.63829539C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Silent	SNP	ENST00000279873.7	37	CCDS31208.1																																																																																			C|0.954;T|0.046	0.046	strong		0.428	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482	
CSPG4	1464	hgsc.bcm.edu	37	15	75982085	75982085	+	Missense_Mutation	SNP	C	C	T	rs79463888	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:75982085C>T	ENST00000308508.5	-	3	1413	c.1321G>A	c.(1321-1323)Gag>Aag	p.E441K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	441	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						GTGCCCCCCTCGGCCACCACC	0.637																																					p.E441K		Atlas-SNP	.											CSPG4,NS,haematopoietic_neoplasm,0,1	CSPG4	175	1	0			c.G1321A						PASS	.						43.0	42.0	43.0					15																	75982085		2197	4292	6489	SO:0001583	missense	1464	exon3			CCCCCTCGGCCAC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1321G>A	15.37:g.75982085C>T	ENSP00000312506:p.Glu441Lys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	131	12	0.0916031	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	18.26	3.584924	0.65992	.	.	ENSG00000173546	ENST00000308508	T	0.31510	1.49	5.26	5.26	0.73747	.	0.170667	0.41001	D	0.000974	T	0.48642	0.1511	M	0.78049	2.395	0.80722	D	1	D	0.71674	0.998	P	0.56278	0.795	T	0.52041	-0.8628	10	0.59425	D	0.04	.	11.3564	0.49617	0.0:0.9168:0.0:0.0831	.	441	Q6UVK1	CSPG4_HUMAN	K	441	ENSP00000312506:E441K	ENSP00000312506:E441K	E	-	1	0	CSPG4	73769140	1.000000	0.71417	0.998000	0.56505	0.513000	0.34164	4.634000	0.61325	2.463000	0.83235	0.555000	0.69702	GAG	C|0.878;T|0.122	0.122	strong		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
OR5A2	219981	hgsc.bcm.edu	37	11	59190120	59190120	+	Missense_Mutation	SNP	A	A	G	rs17153691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:59190120A>G	ENST00000302040.4	-	1	329	c.307T>C	c.(307-309)Ttt>Ctt	p.F103L		NM_001001954.1	NP_001001954.1	Q8NGI9	OR5A2_HUMAN	olfactory receptor, family 5, subfamily A, member 2	103			F -> L (in dbSNP:rs17153691).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	21						CAGAAGACAAAGTACTGAGTG	0.512													A|||	225	0.0449281	0.0023	0.0951	5008	,	,		22914	0.0615		0.0258	False		,,,				2504	0.0695				p.F103L		Atlas-SNP	.											.	OR5A2	35	.	0			c.T307C						PASS	.	A	LEU/PHE	33,4369	38.4+/-70.7	0,33,2168	77.0	74.0	75.0		307	5.5	0.0	11	dbSNP_123	75	274,8316	102.9+/-164.1	6,262,4027	yes	missense	OR5A2	NM_001001954.1	22	6,295,6195	GG,GA,AA		3.1898,0.7497,2.363	probably-damaging	103/325	59190120	307,12685	2201	4295	6496	SO:0001583	missense	219981	exon1			AGACAAAGTACTG	AB065805	CCDS31560.1	11q12.1	2012-08-09			ENSG00000172324	ENSG00000172324		"""GPCR / Class A : Olfactory receptors"""	15249	protein-coding gene	gene with protein product							Standard	NM_001001954		Approved		uc010rkt.2	Q8NGI9	OTTHUMG00000167419	ENST00000302040.4:c.307T>C	11.37:g.59190120A>G	ENSP00000303834:p.Phe103Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001001954	B9EH21|Q6IFF4|Q96RB0	Missense_Mutation	SNP	ENST00000302040.4	37	CCDS31560.1	101	0.04624542124542125	2	0.0040650406504065045	34	0.09392265193370165	43	0.07517482517482517	22	0.029023746701846966	A	21.6	4.169148	0.78339	0.007497	0.031898	ENSG00000172324	ENST00000302040	T	0.00397	7.57	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36200	U	0.002735	T	0.00039	0.0001	M	0.75264	2.295	0.80722	P	0.0	D	0.76494	0.999	D	0.85130	0.997	T	0.74393	-0.3680	9	0.41790	T	0.15	.	13.7874	0.63119	1.0:0.0:0.0:0.0	rs17153691;rs17153691	103	Q8NGI9	OR5A2_HUMAN	L	103	ENSP00000303834:F103L	ENSP00000303834:F103L	F	-	1	0	OR5A2	58946696	0.203000	0.23435	0.040000	0.18447	0.930000	0.56654	4.339000	0.59322	2.212000	0.71576	0.477000	0.44152	TTT	A|0.965;G|0.035	0.035	strong		0.512	OR5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394552.1	NM_001001954	
EN2	2020	hgsc.bcm.edu	37	7	155255332	155255332	+	Silent	SNP	T	T	C	rs2361689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:155255332T>C	ENST00000297375.4	+	2	1201	c.952T>C	c.(952-954)Ttg>Ctg	p.L318L		NM_001427.3	NP_001418.2	P19622	HME2_HUMAN	engrailed homeobox 2	318					hindbrain development (GO:0030902)|midbrain development (GO:0030901)|multicellular organismal development (GO:0007275)|neuron development (GO:0048666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|large_intestine(1)|lung(2)	4	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.011)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GGCACAGGGCTTGTACAACCA	0.577													T|||	1855	0.370407	0.4334	0.438	5008	,	,		15241	0.2212		0.334	False		,,,				2504	0.4284				p.L318L		Atlas-SNP	.											.	EN2	14	.	0			c.T952C						PASS	.	T		1842,2562		379,1084,739	54.0	46.0	49.0		952	1.2	1.0	7	dbSNP_100	49	2877,5723		504,1869,1927	no	coding-synonymous	EN2	NM_001427.3		883,2953,2666	CC,CT,TT		33.4535,41.8256,36.2888		318/334	155255332	4719,8285	2202	4300	6502	SO:0001819	synonymous_variant	2020	exon2			CAGGGCTTGTACA		CCDS5940.1	7q36.2	2011-06-20	2007-02-15		ENSG00000164778	ENSG00000164778		"""Homeoboxes / ANTP class : NKL subclass"""	3343	protein-coding gene	gene with protein product		131310					Standard	NM_001427		Approved		uc003wmb.3	P19622	OTTHUMG00000151354	ENST00000297375.4:c.952T>C	7.37:g.155255332T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_001427	A4D252|Q549U3|Q9UD58	Silent	SNP	ENST00000297375.4	37	CCDS5940.1																																																																																			T|0.630;C|0.370	0.370	strong		0.577	EN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322337.1	NM_001427	
CCDC65	85478	hgsc.bcm.edu	37	12	49314994	49314994	+	Missense_Mutation	SNP	A	A	G	rs4760600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49314994A>G	ENST00000320516.4	+	8	1411	c.1223A>G	c.(1222-1224)tAc>tGc	p.Y408C	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Missense_Mutation_p.Y408C	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	408			Y -> C (in dbSNP:rs4760600).							breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						TGGAAAAGGTACAACAAAGTG	0.498													A|||	1543	0.308107	0.1014	0.4942	5008	,	,		18821	0.4444		0.4095	False		,,,				2504	0.2106				p.Y408C		Atlas-SNP	.											.	CCDC65	41	.	0			c.A1223G						PASS	.	A	CYS/TYR	695,3711	289.5+/-280.5	72,551,1580	56.0	52.0	54.0		1223	4.5	1.0	12	dbSNP_111	54	3287,5313	491.7+/-373.2	618,2051,1631	yes	missense	CCDC65	NM_033124.4	194	690,2602,3211	GG,GA,AA		38.2209,15.7739,30.6166	probably-damaging	408/485	49314994	3982,9024	2203	4300	6503	SO:0001583	missense	85478	exon8			AAAGGTACAACAA		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.1223A>G	12.37:g.49314994A>G	ENSP00000312706:p.Tyr408Cys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	776	0.3553113553113553	48	0.0975609756097561	160	0.4419889502762431	265	0.4632867132867133	303	0.3997361477572559	A	18.69	3.678629	0.68042	0.157739	0.382209	ENSG00000139537	ENST00000266984;ENST00000552942;ENST00000320516	T;T;T	0.02395	4.31;4.31;4.31	5.65	4.47	0.54385	.	0.194360	0.45361	D	0.000379	T	0.00012	0.0000	M	0.82323	2.585	0.21861	P	0.999501278	D	0.89917	1.0	D	0.83275	0.996	T	0.44544	-0.9321	9	0.54805	T	0.06	-9.0024	11.2624	0.49091	0.8628:0.0:0.0:0.1372	rs4760600;rs52816926;rs61316939;rs4760600	408	Q8IXS2	CCD65_HUMAN	C	408;305;408	ENSP00000266984:Y408C;ENSP00000446569:Y305C;ENSP00000312706:Y408C	ENSP00000266984:Y408C	Y	+	2	0	CCDC65	47601261	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.979000	0.56888	1.029000	0.39812	0.482000	0.46254	TAC	A|0.679;G|0.321	0.321	strong		0.498	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
ERCC6	2074	hgsc.bcm.edu	37	10	50678717	50678717	+	Missense_Mutation	SNP	T	T	C	rs2228526	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50678717T>C	ENST00000355832.5	-	18	3367	c.3289A>G	c.(3289-3291)Atg>Gtg	p.M1097V	ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000542458.1_Missense_Mutation_p.M467V	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1097			M -> V (in dbSNP:rs2228526). {ECO:0000269|PubMed:9443879, ECO:0000269|Ref.3}.		activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TTACTACTCATGTGAGGGTCA	0.403								Direct reversal of damage;Nucleotide excision repair (NER)					T|||	914	0.182508	0.1369	0.2104	5008	,	,		21456	0.0437		0.2078	False		,,,				2504	0.3415				p.M1097V		Atlas-SNP	.											.	ERCC6	162	.	0			c.A3289G	GRCh37	CM076169	ERCC6	M	rs2228526	PASS	.	T	VAL/MET	619,3787	265.9+/-266.9	60,499,1644	172.0	164.0	167.0		3289	-6.2	0.0	10	dbSNP_98	167	1864,6736	332.1+/-320.0	196,1472,2632	yes	missense	ERCC6	NM_000124.2	21	256,1971,4276	CC,CT,TT		21.6744,14.049,19.0912	benign	1097/1494	50678717	2483,10523	2203	4300	6503	SO:0001583	missense	2074	exon18			TACTCATGTGAGG	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.3289A>G	10.37:g.50678717T>C	ENSP00000348089:p.Met1097Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	342	0.1565934065934066	62	0.12601626016260162	83	0.2292817679558011	30	0.05244755244755245	167	0.22031662269129287	T	2.555	-0.303168	0.05495	0.14049	0.216744	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.81908	-1.55;-1.29	4.57	-6.21	0.02065	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.02437	-1.1159	8	0.23891	T	0.37	0.7226	3.2523	0.06819	0.1021:0.1951:0.4168:0.286	rs2228526;rs17702442;rs52816725;rs57248630;rs2228526	1097	Q03468	ERCC6_HUMAN	V	1097;474;467	ENSP00000348089:M1097V;ENSP00000445134:M467V	ENSP00000348089:M1097V	M	-	1	0	ERCC6	50348723	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.211000	0.09332	-1.189000	0.02702	-0.256000	0.11100	ATG	T|0.824;C|0.176	0.176	strong		0.403	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
ITGA9	3680	hgsc.bcm.edu	37	3	37536056	37536056	+	Silent	SNP	C	C	T	rs2507941	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:37536056C>T	ENST00000264741.5	+	5	865	c.609C>T	c.(607-609)acC>acT	p.T203T	ITGA9_ENST00000422441.1_Silent_p.T203T	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	203					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GCTTCTTCACCGAGGTGGGTG	0.517													C|||	235	0.0469249	0.0068	0.0749	5008	,	,		20842	0.0774		0.0537	False		,,,				2504	0.0429				p.T203T		Atlas-SNP	.											.	ITGA9	98	.	0			c.C609T						PASS	.	C		77,4329	66.4+/-103.9	0,77,2126	178.0	181.0	180.0		609	-6.6	0.9	3	dbSNP_100	180	488,8112	141.1+/-197.5	14,460,3826	yes	coding-synonymous	ITGA9	NM_002207.2		14,537,5952	TT,TC,CC		5.6744,1.7476,4.3441		203/1036	37536056	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon5			CTTCACCGAGGTG	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.609C>T	3.37:g.37536056C>T		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	288	126	0.4375	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			C|0.959;T|0.041	0.041	strong		0.517	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
MRPL17	63875	hgsc.bcm.edu	37	11	6703569	6703569	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6703569C>T	ENST00000288937.6	-	3	412	c.308G>A	c.(307-309)gGc>gAc	p.G103D	MRPL17_ENST00000532676.1_5'UTR	NM_022061.3	NP_071344.1	Q9NRX2	RM17_HUMAN	mitochondrial ribosomal protein L17	103					translation (GO:0006412)	mitochondrial inner membrane (GO:0005743)|ribosome (GO:0005840)	protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)			lung(4)	4		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TCTTGTGTAGCCCCCAGTTTG	0.507																																					p.G103D		Atlas-SNP	.											MRPL17,NS,carcinoma,-1,1	MRPL17	11	1	0			c.G308A						scavenged	.						125.0	119.0	121.0					11																	6703569		2201	4296	6497	SO:0001583	missense	63875	exon3			GTGTAGCCCCCAG	AB051620	CCDS31412.1	11p15.5-p15.4	2012-09-13				ENSG00000158042		"""Mitochondrial ribosomal proteins / large subunits"""	14053	protein-coding gene	gene with protein product		611830					Standard	NM_022061		Approved	RPML26, MRP-L26	uc001men.2	Q9NRX2		ENST00000288937.6:c.308G>A	11.37:g.6703569C>T	ENSP00000288937:p.Gly103Asp	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_022061	D3DQU3|Q6IAH8|Q96Q53|Q9C066	Missense_Mutation	SNP	ENST00000288937.6	37	CCDS31412.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223090	0.58668	.	.	ENSG00000158042	ENST00000288937;ENST00000532203	.	.	.	5.87	2.95	0.34219	.	0.323870	0.38058	N	0.001834	T	0.73892	0.3645	H	0.98089	4.145	0.28642	N	0.907107	B	0.22983	0.078	B	0.38194	0.267	T	0.72830	-0.4174	9	0.72032	D	0.01	-14.5211	6.8766	0.24151	0.0:0.669:0.0:0.331	.	103	Q9NRX2	RM17_HUMAN	D	103;80	.	ENSP00000288937:G103D	G	-	2	0	MRPL17	6660145	0.110000	0.22057	1.000000	0.80357	0.608000	0.37181	0.515000	0.22801	1.468000	0.48064	0.650000	0.86243	GGC	.	.	none		0.507	MRPL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384544.1	NM_022061	
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 GAIIx	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		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	54	23	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	
ALG6	29929	hgsc.bcm.edu	37	1	63872032	63872032	+	Missense_Mutation	SNP	T	T	C	rs35383149	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:63872032T>C	ENST00000371108.4	+	6	696	c.391T>C	c.(391-393)Tac>Cac	p.Y131H	ALG6_ENST00000263440.4_Missense_Mutation_p.Y131H	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	131			Y -> H (in CDG1C; dbSNP:rs35383149). {ECO:0000269|PubMed:11106564, ECO:0000269|PubMed:14517965}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						AGTGGTTTTGTACTGTTGTTG	0.343													T|||	67	0.0133786	0.0015	0.0245	5008	,	,		20154	0.0		0.0378	False		,,,				2504	0.0102				p.Y131H		Atlas-SNP	.											.	ALG6	33	.	0			c.T391C	GRCh37	CM033079	ALG6	M	rs35383149	PASS	.	T	HIS/TYR	26,4380	33.5+/-64.1	0,26,2177	174.0	158.0	163.0		391	4.8	1.0	1	dbSNP_126	163	354,8246	119.2+/-178.6	6,342,3952	yes	missense	ALG6	NM_013339.3	83	6,368,6129	CC,CT,TT		4.1163,0.5901,2.9217	benign	131/508	63872032	380,12626	2203	4300	6503	SO:0001583	missense	29929	exon6			GTTTTGTACTGTT	AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	2.4.1.267		23157	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	604566	"""asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""			10359825, 11875054	Standard	NM_013339		Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.391T>C	1.37:g.63872032T>C	ENSP00000360149:p.Tyr131His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	37	CCDS30735.1	39	0.017857142857142856	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	27	0.03562005277044855	T	15.07	2.725324	0.48833	0.005901	0.041163	ENSG00000088035	ENST00000371108;ENST00000263440	D;D	0.85484	-1.99;-1.99	5.87	4.75	0.60458	.	0.055745	0.85682	N	0.000000	T	0.76471	0.3992	M	0.70787	2.145	0.80722	D	1	B	0.15719	0.014	B	0.26693	0.072	T	0.73062	-0.4101	10	0.33940	T	0.23	-17.9966	11.8828	0.52586	0.0:0.0678:0.0:0.9321	rs35383149	131	A2A2G4	.	H	131	ENSP00000360149:Y131H;ENSP00000263440:Y131H	ENSP00000263440:Y131H	Y	+	1	0	ALG6	63644620	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	3.981000	0.56902	1.049000	0.40321	0.528000	0.53228	TAC	T|0.974;C|0.026	0.026	strong		0.343	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339	
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 GAIIx	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_ENST00000372308.3_Missense_Mutation_p.T147S|SFTPA1_ENST00000372313.5_Missense_Mutation_p.T88S|SFTPA1_ENST00000428376.2_Missense_Mutation_p.T147S|SFTPA1_ENST00000419470.2_Missense_Mutation_p.T162S	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	Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	299	115	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	
ADAM30	11085	hgsc.bcm.edu	37	1	120436751	120436751	+	Missense_Mutation	SNP	T	T	C	rs35273427	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:120436751T>C	ENST00000369400.1	-	1	2367	c.2209A>G	c.(2209-2211)Aca>Gca	p.T737A		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	737	5 X 9 AA approximate repeats.		T -> A (in dbSNP:rs35273427).		binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		ACAGTTTTTGTTTTAGATTCT	0.368													t|||	812	0.162141	0.3306	0.0865	5008	,	,		17633	0.0407		0.0606	False		,,,				2504	0.2178				p.T737A		Atlas-SNP	.											.	ADAM30	88	.	0			c.A2209G						PASS	.	T	ALA/THR	1222,3184	422.1+/-339.6	178,866,1159	196.0	205.0	202.0		2209	-1.9	0.0	1	dbSNP_126	202	495,8105	142.5+/-198.7	22,451,3827	yes	missense	ADAM30	NM_021794.3	58	200,1317,4986	CC,CT,TT		5.7558,27.7349,13.2016	benign	737/791	120436751	1717,11289	2203	4300	6503	SO:0001583	missense	11085	exon1			TTTTTGTTTTAGA	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"""ADAM metallopeptidase domain containing"""	208	protein-coding gene	gene with protein product		604779	"""a disintegrin and metalloproteinase domain 30"""				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.2209A>G	1.37:g.120436751T>C	ENSP00000358407:p.Thr737Ala	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	248	114	0.459677	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	260	0.11904761904761904	175	0.3556910569105691	30	0.08287292817679558	12	0.02097902097902098	43	0.05672823218997362	T	0.064	-1.217896	0.01542	0.277349	0.057558	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.01126	5.3	2.55	-1.93	0.07594	.	2.259650	0.03871	U	0.275554	T	0.00271	0.0008	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.45293	-0.9271	9	0.23891	T	0.37	.	7.691	0.28567	0.0:0.5507:0.0:0.4493	rs35273427;rs61752483	737	Q9UKF2	ADA30_HUMAN	A	737	ENSP00000358407:T737A	ENSP00000358407:T737A	T	-	1	0	ADAM30	120238274	0.330000	0.24705	0.000000	0.03702	0.009000	0.06853	-0.024000	0.12435	-0.586000	0.05898	0.482000	0.46254	ACA	T|0.878;C|0.122	0.122	strong		0.368	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794	
RNF145	153830	hgsc.bcm.edu	37	5	158603839	158603839	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:158603839A>G	ENST00000424310.2	-	5	781	c.422T>C	c.(421-423)aTg>aCg	p.M141T	RNF145_ENST00000521606.2_Missense_Mutation_p.M158T|RNF145_ENST00000518802.1_Missense_Mutation_p.M171T|RNF145_ENST00000520638.1_Missense_Mutation_p.M155T|RNF145_ENST00000519865.1_Missense_Mutation_p.M141T|RNF145_ENST00000274542.2_Missense_Mutation_p.M169T	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	141						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.M169T(4)		endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTTTGTTTTCATGACACAGGA	0.363																																					p.M171T		Atlas-SNP	.											RNF145,NS,carcinoma,0,4	RNF145	110	4	4	Substitution - Missense(4)	endometrium(3)|lung(1)	c.T512C						scavenged	.						35.0	33.0	34.0					5																	158603839		2201	4298	6499	SO:0001583	missense	153830	exon5			GTTTTCATGACAC	BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.422T>C	5.37:g.158603839A>G	ENSP00000409064:p.Met141Thr	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	172	8	0.0465116	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.282699	0.80692	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.77229	-1.08;-1.06;-1.06;-1.07;-1.07;-1.08;-1.07	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.81725	0.4883	L	0.44542	1.39	0.80722	D	1	D;D;D;D;D;D	0.57257	0.979;0.979;0.979;0.979;0.979;0.974	P;P;P;P;P;P	0.57846	0.828;0.828;0.828;0.828;0.76;0.736	D	0.83797	0.0234	10	0.72032	D	0.01	-20.3428	15.6548	0.77124	1.0:0.0:0.0:0.0	.	157;158;155;171;141;169	E7EW26;B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;.;RN145_HUMAN;.	T	169;141;141;157;158;171;141;155	ENSP00000274542:M169T;ENSP00000430397:M141T;ENSP00000409064:M141T;ENSP00000430753:M157T;ENSP00000445115:M158T;ENSP00000430955:M171T;ENSP00000429071:M155T	ENSP00000274542:M169T	M	-	2	0	RNF145	158536417	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.339000	0.96797	2.162000	0.67917	0.377000	0.23210	ATG	.	.	none		0.363	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
RILPL1	353116	hgsc.bcm.edu	37	12	124017850	124017850	+	Silent	SNP	G	G	C	rs28492040	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:124017850G>C	ENST00000376874.4	-	1	415	c.180C>G	c.(178-180)gtC>gtG	p.V60V		NM_178314.3	NP_847884.2	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	60					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)|regulation of neuron death (GO:1901214)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)		GGATCTCCAGGACGCGCACGA	0.687													G|||	590	0.117812	0.1225	0.121	5008	,	,		11260	0.0109		0.1909	False		,,,				2504	0.1442				p.V60V		Atlas-SNP	.											RILPL1,NS,carcinoma,0,1	RILPL1	23	1	0			c.C180G						PASS	.	G		592,3648		49,494,1577	10.0	15.0	13.0		180	0.9	1.0	12	dbSNP_125	13	1561,6859		151,1259,2800	no	coding-synonymous	RILPL1	NM_178314.3		200,1753,4377	CC,CG,GG		18.5392,13.9623,17.0063		60/404	124017850	2153,10507	2120	4210	6330	SO:0001819	synonymous_variant	353116	exon1			CTCCAGGACGCGC	AK097550	CCDS45006.1	12q24.31	2007-11-27			ENSG00000188026	ENSG00000188026			26814	protein-coding gene	gene with protein product		614092				14668488	Standard	NM_178314		Approved	FLJ39378	uc001ufe.2	Q5EBL4	OTTHUMG00000168686	ENST00000376874.4:c.180C>G	12.37:g.124017850G>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	27	17	0.62963	NM_178314	Q66K36|Q8N1M0	Silent	SNP	ENST00000376874.4	37	CCDS45006.1																																																																																			G|0.882;C|0.118	0.118	strong		0.687	RILPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400595.1	NM_178314	
CMYA5	202333	hgsc.bcm.edu	37	5	79029594	79029594	+	Missense_Mutation	SNP	T	T	C	rs1019762	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:79029594T>C	ENST00000446378.2	+	2	5037	c.5006T>C	c.(5005-5007)tTa>tCa	p.L1669S		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1669			L -> S (in dbSNP:rs1019762).		negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GATTCTGTTTTAGAAAAAGGC	0.403													T|||	555	0.110823	0.1172	0.1225	5008	,	,		19852	0.0188		0.164	False		,,,				2504	0.1339				p.L1669S		Atlas-SNP	.											.	CMYA5	643	.	0			c.T5006C						PASS	.	T	SER/LEU	469,3227		33,403,1412	59.0	60.0	60.0		5006	2.6	0.9	5	dbSNP_86	60	1272,6918		104,1064,2927	yes	missense	CMYA5	NM_153610.3	145	137,1467,4339	CC,CT,TT		15.5311,12.6894,14.6475	probably-damaging	1669/4070	79029594	1741,10145	1848	4095	5943	SO:0001583	missense	202333	exon2			CTGTTTTAGAAAA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.5006T>C	5.37:g.79029594T>C	ENSP00000394770:p.Leu1669Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	72	46	0.638889	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	242	0.1108058608058608	56	0.11382113821138211	48	0.13259668508287292	11	0.019230769230769232	127	0.16754617414248021	T	15.65	2.895293	0.52121	0.126894	0.155311	ENSG00000164309	ENST00000446378	T	0.61742	0.08	4.95	2.57	0.30868	.	0.488799	0.15222	N	0.273849	T	0.00300	0.0009	L	0.47190	1.495	0.80722	P	0.0	D	0.69078	0.997	P	0.59115	0.852	T	0.11991	-1.0565	9	0.87932	D	0	.	5.9191	0.19072	0.0:0.2058:0.0:0.7942	rs1019762;rs52808958;rs1019762	1669	Q8N3K9	CMYA5_HUMAN	S	1669	ENSP00000394770:L1669S	ENSP00000394770:L1669S	L	+	2	0	CMYA5	79065350	0.026000	0.19158	0.851000	0.33527	0.902000	0.53008	0.245000	0.18142	0.746000	0.32786	0.460000	0.39030	TTA	T|0.888;C|0.112	0.112	strong		0.403	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
OTC	5009	hgsc.bcm.edu	37	X	38226603	38226603	+	Missense_Mutation	SNP	A	A	G	rs1800321	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:38226603A>G	ENST00000039007.4	+	2	289	c.137A>G	c.(136-138)aAa>aGa	p.K46R	TM4SF2_ENST00000465127.1_Intron|OTC_ENST00000488812.1_3'UTR	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	46			K -> R (in dbSNP:rs1800321). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2474822}.		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)	CTCACTCTAAAAAACTTTACC	0.343													A|||	695	0.184106	0.2912	0.1167	3775	,	,		12634	0.002		0.2048	False		,,,				2504	0.0215				p.K46R		Atlas-SNP	.											.	OTC	60	.	0			c.A137G						PASS	.	A	ARG/LYS	1443,2390		252,726,213,653,358	46.0	46.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	137	4.2	0.9	X	dbSNP_89	46	1623,5104		155,862,451,1411,1420	yes	missense	OTC	NM_000531.5	26	407,1588,664,2064,1778	GG,GA,G,AA,A		24.1267,37.6468,29.0341	benign	46/355	38226603	3066,7494	2202	4299	6501	SO:0001583	missense	5009	exon2			CTCTAAAAAACTT	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.137A>G	X.37:g.38226603A>G	ENSP00000039007:p.Lys46Arg	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	162	116	0.716049	NM_000531	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	327	0.19710669077757687	82	0.20603015075376885	39	0.11337209302325581	1	0.0017482517482517483	101	0.15256797583081572	A	11.07	1.530492	0.27387	0.376468	0.241267	ENSG00000036473	ENST00000039007	D	0.98493	-4.96	5.39	4.23	0.50019	Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding (1);	0.207551	0.49305	N	0.000150	T	0.00012	0.0000	L	0.46614	1.455	0.27994	P	0.9355521	B	0.27679	0.185	B	0.29942	0.109	T	0.00361	-1.1789	9	0.21540	T	0.41	-29.6416	9.3789	0.38301	0.9133:0.0:0.0867:0.0	rs1800321;rs60302012;rs1800321	46	P00480	OTC_HUMAN	R	46	ENSP00000039007:K46R	ENSP00000039007:K46R	K	+	2	0	OTC	38111547	1.000000	0.71417	0.909000	0.35828	0.665000	0.39181	7.119000	0.77145	0.700000	0.31782	0.345000	0.21793	AAA	A|0.721;0|0.027	.	strong		0.343	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2		
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 GAIIx	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_ENST00000360416.3_Missense_Mutation_p.K1257T|MYH10_ENST00000396239.1_Missense_Mutation_p.K1247T|MYH10_ENST00000379980.4_Missense_Mutation_p.K1242T	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	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	154	50	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		
ZNF23	7571	hgsc.bcm.edu	37	16	71483497	71483497	+	Missense_Mutation	SNP	C	C	G	rs72795864	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:71483497C>G	ENST00000393539.2	-	6	1244	c.431G>C	c.(430-432)gGa>gCa	p.G144A	ZNF23_ENST00000539742.1_5'UTR|ZNF23_ENST00000358700.2_3'UTR|AC010547.9_ENST00000561908.1_3'UTR|ZNF23_ENST00000428724.2_Missense_Mutation_p.G86A|ZNF23_ENST00000497160.1_3'UTR|ZNF23_ENST00000357254.4_Missense_Mutation_p.G144A|ZNF23_ENST00000417828.1_Missense_Mutation_p.G144A|ZNF23_ENST00000564528.1_Missense_Mutation_p.G86A	NM_145911.1	NP_666016.1	P17027	ZNF23_HUMAN	zinc finger protein 23	144					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)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(14)|stomach(1)|urinary_tract(1)	29		Ovarian(137;0.00768)		BRCA - Breast invasive adenocarcinoma(221;0.0686)		TTTCCCCAATCCTGTACACCC	0.408													C|||	416	0.0830671	0.1407	0.0735	5008	,	,		19819	0.003		0.1441	False		,,,				2504	0.0317				p.G144A		Atlas-SNP	.											.	ZNF23	65	.	0			c.G431C						PASS	.	C	ALA/GLY	601,3795	262.5+/-264.9	32,537,1629	103.0	108.0	106.0		431	-0.9	0.0	16	dbSNP_130	106	1193,7407	242.9+/-272.7	84,1025,3191	yes	missense	ZNF23	NM_145911.1	60	116,1562,4820	GG,GC,CC		13.8721,13.6715,13.8042	benign	144/644	71483497	1794,11202	2198	4300	6498	SO:0001583	missense	7571	exon6			CCCAATCCTGTAC	X52347	CCDS10900.1	16q22.2	2013-03-28	2012-07-12		ENSG00000167377	ENSG00000167377		"""Zinc fingers, C2H2-type"""	13023	protein-coding gene	gene with protein product		194527	"""zinc finger protein 359"""	ZNF359			Standard	NM_145911		Approved	KOX16, Zfp612, ZNF612	uc002faf.3	P17027	OTTHUMG00000176797	ENST00000393539.2:c.431G>C	16.37:g.71483497C>G	ENSP00000377171:p.Gly144Ala	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	71	24	0.338028	NM_145911	Q8NDP5|Q96IT3|Q9UG42	Missense_Mutation	SNP	ENST00000393539.2	37	CCDS10900.1	208	0.09523809523809523	60	0.12195121951219512	25	0.06906077348066299	1	0.0017482517482517483	122	0.16094986807387862	C	14.13	2.442175	0.43326	0.136715	0.138721	ENSG00000167377	ENST00000393539;ENST00000357254;ENST00000417828;ENST00000428724;ENST00000539742	T;T;T;T	0.15139	2.45;2.45;2.45;2.45	3.63	-0.895	0.10560	.	0.693619	0.11908	N	0.517961	T	0.00039	0.0001	N	0.04260	-0.245	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37572	-0.9700	9	0.52906	T	0.07	-0.3386	4.1198	0.10099	0.0:0.3558:0.1805:0.4637	.	144;144	B3KR55;P17027	.;ZNF23_HUMAN	A	144;144;144;86;86	ENSP00000377171:G144A;ENSP00000349796:G144A;ENSP00000395712:G144A;ENSP00000387673:G86A	ENSP00000349796:G144A	G	-	2	0	ZNF23	70040998	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.196000	0.09532	-0.117000	0.11872	-0.367000	0.07326	GGA	A|0.000;C|0.878;G|0.122	0.122	strong		0.408	ZNF23-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268985.23	NM_145911	
MUC16	94025	hgsc.bcm.edu	37	19	9049396	9049396	+	Silent	SNP	C	C	G	rs10425044	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9049396C>G	ENST00000397910.4	-	5	32438	c.32235G>C	c.(32233-32235)ggG>ggC	p.G10745G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10747	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCTGTCTGTCCCAGAACTAG	0.478													C|||	939	0.1875	0.1566	0.2637	5008	,	,		22460	0.0258		0.2823	False		,,,				2504	0.2444				p.G10745G		Atlas-SNP	.											.	MUC16	4315	.	0			c.G32235C						PASS	.			624,3188		47,530,1329	173.0	156.0	161.0		32235	-1.9	0.0	19	dbSNP_119	161	2503,5737		402,1699,2019	no	coding-synonymous	MUC16	NM_024690.2		449,2229,3348	GG,GC,CC		30.3762,16.3694,25.9459		10745/14508	9049396	3127,8925	1906	4120	6026	SO:0001819	synonymous_variant	94025	exon5			GTCTGTCCCAGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32235G>C	19.37:g.9049396C>G		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	152	69	0.453947	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.781;G|0.219	0.219	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
APOA4	337	hgsc.bcm.edu	37	11	116691675	116691675	+	Missense_Mutation	SNP	T	T	A	rs675	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:116691675T>A	ENST00000357780.3	-	3	1213	c.1099A>T	c.(1099-1101)Act>Tct	p.T367S		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	367			T -> S (in allele APOA-IV*1A and allele Budapest-1; dbSNP:rs675). {ECO:0000269|PubMed:15108119, ECO:0000269|PubMed:1677358, ECO:0000269|PubMed:7728150}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		AGGGAGAGAGTCTTGTCCTGG	0.597													T|||	495	0.0988419	0.0923	0.1124	5008	,	,		19753	0.0		0.1789	False		,,,				2504	0.1176				p.T367S		Atlas-SNP	.											.	APOA4	51	.	0			c.A1099T	GRCh37	CM031126	APOA4	M	rs675	PASS	.	T	SER/THR	496,3906	229.4+/-244.0	24,448,1729	71.0	61.0	64.0		1099	0.0	0.0	11	dbSNP_36	64	1693,6893	310.8+/-310.0	145,1403,2745	yes	missense	APOA4	NM_000482.3	58	169,1851,4474	AA,AT,TT		19.7181,11.2676,16.854	benign	367/397	116691675	2189,10799	2201	4293	6494	SO:0001583	missense	337	exon3			AGAGAGTCTTGTC		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.1099A>T	11.37:g.116691675T>A	ENSP00000350425:p.Thr367Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	180	23	0.127778	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	37	CCDS31681.1	230	0.10531135531135531	44	0.08943089430894309	50	0.13812154696132597	0	0.0	136	0.17941952506596306	T	4.257	0.046734	0.08243	0.112676	0.197181	ENSG00000110244	ENST00000357780	T	0.73681	-0.77	4.7	0.0122	0.14090	.	0.640140	0.13188	N	0.407012	T	0.00073	0.0002	N	0.16478	0.41	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.02736	-1.1117	9	0.11182	T	0.66	-5.8048	2.0651	0.03601	0.0992:0.2603:0.282:0.3586	rs675;rs9282882;rs17250988;rs45474794;rs52810209;rs675	367	P06727	APOA4_HUMAN	S	367	ENSP00000350425:T367S	ENSP00000350425:T367S	T	-	1	0	APOA4	116196885	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	0.137000	0.15995	0.167000	0.19631	0.455000	0.32223	ACT	A|0.142;T|0.858	0.142	strong		0.597	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
CD69	969	hgsc.bcm.edu	37	12	9906146	9906146	+	Silent	SNP	T	T	C	rs117419783	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9906146T>C	ENST00000228434.3	-	5	611	c.531A>G	c.(529-531)aaA>aaG	p.K177K		NM_001781.2	NP_001772.1	Q07108	CD69_HUMAN	CD69 molecule	177	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular response to drug (GO:0035690)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(3)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)	10						CCTCTGTGTTTTTCAGAAAAA	0.318													T|||	18	0.00359425	0.0	0.0029	5008	,	,		-128	0.0		0.0109	False		,,,				2504	0.0051				p.K177K		Atlas-SNP	.											CD69,colon,carcinoma,0,1	CD69	23	1	0			c.A531G						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	58.0	57.0	57.0		531	-9.0	0.0	12	dbSNP_132	57	52,8548	34.3+/-88.2	0,52,4248	no	coding-synonymous	CD69	NM_001781.2		0,59,6444	CC,CT,TT		0.6047,0.1589,0.4536		177/200	9906146	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	969	exon5			TGTGTTTTTCAGA	Z22576	CCDS8604.1	12p13	2011-08-30	2006-03-28		ENSG00000110848	ENSG00000110848		"""C-type lectin domain containing"", ""CD molecules"""	1694	protein-coding gene	gene with protein product		107273	"""CD69 antigen (p60, early T-cell activation antigen)"""			1612643	Standard	NM_001781		Approved	CLEC2C	uc001qwk.3	Q07108	OTTHUMG00000168481	ENST00000228434.3:c.531A>G	12.37:g.9906146T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_001781		Silent	SNP	ENST00000228434.3	37	CCDS8604.1																																																																																			T|0.994;C|0.006	0.006	strong		0.318	CD69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399876.1		
MBD1	4152	hgsc.bcm.edu	37	18	47800179	47800179	+	Missense_Mutation	SNP	G	G	C	rs125555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:47800179G>C	ENST00000591416.1	-	12	1632	c.1201C>G	c.(1201-1203)Cca>Gca	p.P401A	MBD1_ENST00000588937.1_Missense_Mutation_p.P378A|MBD1_ENST00000587605.1_Missense_Mutation_p.P345A|MBD1_ENST00000382948.5_Missense_Mutation_p.P401A|MBD1_ENST00000353909.3_Missense_Mutation_p.P352A|MBD1_ENST00000591535.1_Missense_Mutation_p.P378A|MBD1_ENST00000269468.5_Missense_Mutation_p.P401A|MBD1_ENST00000590208.1_Missense_Mutation_p.P401A|MBD1_ENST00000436910.1_Missense_Mutation_p.P378A|MBD1_ENST00000349085.2_Missense_Mutation_p.P345A|MBD1_ENST00000398493.1_Missense_Mutation_p.P345A|MBD1_ENST00000398488.1_Missense_Mutation_p.P345A|MBD1_ENST00000585672.1_Missense_Mutation_p.P351A|MBD1_ENST00000398495.2_Missense_Mutation_p.P370A|MBD1_ENST00000457839.2_Missense_Mutation_p.P426A|MBD1_ENST00000424334.2_Missense_Mutation_p.P452A|MBD1_ENST00000585595.1_Missense_Mutation_p.P426A|MBD1_ENST00000339998.6_Missense_Mutation_p.P401A|MBD1_ENST00000347968.3_Missense_Mutation_p.P345A|MBD1_ENST00000269471.5_Missense_Mutation_p.P378A			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	401			P -> A (in dbSNP:rs125555). {ECO:0000269|PubMed:10441743}.		negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						CGGTAAGGTGGGGGCGATCCT	0.607													G|||	890	0.177716	0.1407	0.17	5008	,	,		16641	0.1806		0.1829	False		,,,				2504	0.2249				p.P426A		Atlas-SNP	.											.	MBD1	228	.	0			c.C1276G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	604,3802	261.3+/-264.2	49,506,1648	89.0	86.0	87.0		1201,1276,1273,1201,1108,1051,1201,1033,1132,1033,1033,1132,1201,1054	1.9	0.1	18	dbSNP_78	87	1692,6908	309.3+/-309.3	171,1350,2779	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	MBD1	NM_001204136.1,NM_001204137.1,NM_001204138.1,NM_001204139.1,NM_001204140.1,NM_001204141.1,NM_001204142.1,NM_001204143.1,NM_001204151.1,NM_002384.2,NM_015844.2,NM_015845.3,NM_015846.3,NM_015847.3	27,27,27,27,27,27,27,27,27,27,27,27,27,27	220,1856,4427	CC,CG,GG		19.6744,13.7086,17.6534	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	401/656,426/631,425/630,401/606,370/575,351/568,401/551,345/536,378/537,345/504,345/550,378/587,401/606,352/557	47800179	2296,10710	2203	4300	6503	SO:0001583	missense	4152	exon13			AAGGTGGGGGCGA	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.1201C>G	18.37:g.47800179G>C	ENSP00000467017:p.Pro401Ala	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Missense_Mutation	SNP	ENST00000591416.1	37	CCDS11943.1	385	0.1762820512820513	74	0.15040650406504066	66	0.18232044198895028	102	0.17832167832167833	143	0.18865435356200527	G	10.33	1.319949	0.23994	0.137086	0.196744	ENSG00000141644	ENST00000382948;ENST00000353909;ENST00000349085;ENST00000269468;ENST00000347968;ENST00000436910;ENST00000269471;ENST00000424334;ENST00000339998;ENST00000398495;ENST00000457839;ENST00000398493;ENST00000398488	D;D;D;D;D;D;D;D;D;D;D;D;D	0.98633	-3.89;-3.93;-4.78;-3.89;-5.04;-3.82;-3.82;-3.9;-3.84;-3.88;-3.88;-5.04;-4.78	4.98	1.89	0.25635	.	0.218980	0.32081	N	0.006607	T	0.02156	0.0067	L	0.32530	0.975	0.53688	P	2.599999999997049E-5	P;B;B;B;P;P;B;B;B;P;B;P	0.43314	0.803;0.409;0.081;0.245;0.51;0.644;0.359;0.433;0.154;0.681;0.245;0.681	B;B;B;B;B;B;B;B;B;B;B;B	0.44133	0.338;0.188;0.073;0.118;0.167;0.335;0.234;0.164;0.118;0.442;0.08;0.442	T	0.48514	-0.9029	9	0.44086	T	0.13	-0.1939	5.6276	0.17490	0.1987:0.1579:0.6434:0.0	rs125555;rs760283;rs52805720;rs60253010;rs125555	345;452;378;401;401;378;352;345;401;345;426;345	B4DUR3;B4DI41;Q9UIS9-8;A8K654;Q9UIS9-6;Q9UIS9-2;Q9UIS9-5;Q9UIS9-4;Q9UIS9;Q9UIS9-7;B4DXJ5;Q9UIS9-3	.;.;.;.;.;.;.;.;MBD1_HUMAN;.;.;.	A	401;352;345;401;345;378;378;452;401;401;426;345;345	ENSP00000372407:P401A;ENSP00000269469:P352A;ENSP00000342531:P345A;ENSP00000269468:P401A;ENSP00000285102:P345A;ENSP00000409561:P378A;ENSP00000269471:P378A;ENSP00000408846:P452A;ENSP00000339546:P401A;ENSP00000381508:P401A;ENSP00000405268:P426A;ENSP00000381506:P345A;ENSP00000381502:P345A	ENSP00000269468:P401A	P	-	1	0	MBD1	46054177	0.343000	0.24818	0.126000	0.21872	0.987000	0.75469	0.249000	0.18216	0.254000	0.21573	0.555000	0.69702	CCA	G|0.819;C|0.181	0.181	strong		0.607	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
CYP2C19	1557	hgsc.bcm.edu	37	10	96541616	96541616	+	Silent	SNP	G	G	A	rs4244285	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96541616G>A	ENST00000371321.3	+	5	763	c.681G>A	c.(679-681)ccG>ccA	p.P227P	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	227			P -> L (in allele CYP2C19*10; dbSNP:rs6413438). {ECO:0000269|PubMed:12464799}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|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)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	ATTATTTCCCGGGAACCCATA	0.294													G|||	1109	0.221446	0.1702	0.1052	5008	,	,		13926	0.3125		0.1451	False		,,,				2504	0.3579				p.P227P		Atlas-SNP	.											.	CYP2C19	88	.	0			c.G681A	GRCh37	CS941458	CYP2C19	S	rs4244285	PASS	.	G		728,3676	271.9+/-270.5	63,602,1537	50.0	55.0	53.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	681	-8.3	0.0	10	dbSNP_111	53	1276,7322	246.1+/-274.7	98,1080,3121	no	coding-synonymous	CYP2C19	NM_000769.1		161,1682,4658	AA,AG,GG		14.8407,16.5304,15.413		227/491	96541616	2004,10998	2202	4299	6501	SO:0001819	synonymous_variant	1557	exon5			TTTCCCGGGAACC	M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.681G>A	10.37:g.96541616G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_000769	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Silent	SNP	ENST00000371321.3	37	CCDS7436.1																																																																																			A|0.170;G|0.830	0.170	strong		0.294	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	
NCAPG	64151	hgsc.bcm.edu	37	4	17812796	17812796	+	Silent	SNP	C	C	T	rs16895792	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:17812796C>T	ENST00000251496.2	+	1	272	c.96C>T	c.(94-96)agC>agT	p.S32S	DCAF16_ENST00000536863.1_5'Flank|DCAF16_ENST00000507768.1_5'Flank|DCAF16_ENST00000382247.1_5'Flank	NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	32					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		TGGCGCTGAGCCGCACCTACC	0.736													C|||	274	0.0547125	0.0499	0.0101	5008	,	,		9862	0.0903		0.0249	False		,,,				2504	0.0869				p.S32S		Atlas-SNP	.											.	NCAPG	76	.	0			c.C96T						PASS	.	C		146,4160		2,142,2009	11.0	13.0	12.0		96	5.1	1.0	4	dbSNP_123	12	210,8202		1,208,3997	no	coding-synonymous	NCAPG	NM_022346.3		3,350,6006	TT,TC,CC		2.4964,3.3906,2.7992		32/1016	17812796	356,12362	2153	4206	6359	SO:0001819	synonymous_variant	64151	exon1			GCTGAGCCGCACC	AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"""chromosome condensation protein G"""	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.96C>T	4.37:g.17812796C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Silent	SNP	ENST00000251496.2	37	CCDS3424.1																																																																																			C|0.950;T|0.050	0.050	strong		0.736	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346	
HLA-C	3107	hgsc.bcm.edu	37	6	31239544	31239544	+	Silent	SNP	G	G	T	rs281860356		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31239544G>T	ENST00000376228.5	-	2	189	c.175C>A	c.(175-177)Cgg>Agg	p.R59R	HLA-C_ENST00000383329.3_Silent_p.R59R	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	59	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTGTCGAACCGCACGAACTGC	0.677																																					p.R59R		Atlas-SNP	.											HLA-C_ENST00000383329,colon,carcinoma,0,2	HLA-C	92	2	0			c.C175A						scavenged	.						40.0	39.0	39.0					6																	31239544		1511	2707	4218	SO:0001819	synonymous_variant	3107	exon2			CGAACCGCACGAA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.175C>A	6.37:g.31239544G>T		Somatic	105	2	0.0190476		WXS	Illumina HiSeq	Phase_I	109	19	0.174312	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	-	7.431	0.638746	0.14386	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	2.81	0.32909	.	.	.	.	.	T	0.46347	0.1388	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43065	-0.9414	4	.	.	.	.	9.2778	0.37709	0.0:0.0:1.0:0.0	.	.	.	.	E	58	.	.	A	-	2	0	HLA-C	31347523	0.000000	0.05858	1.000000	0.80357	0.308000	0.27856	0.040000	0.13905	1.886000	0.54624	0.305000	0.20034	GCG	.	.	weak		0.677	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
FBXL7	23194	hgsc.bcm.edu	37	5	15937010	15937010	+	Silent	SNP	C	C	T	rs61748187	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:15937010C>T	ENST00000504595.1	+	4	1672	c.1191C>T	c.(1189-1191)ctC>ctT	p.L397L	FBXL7_ENST00000510662.1_Silent_p.L350L|MIR887_ENST00000401258.1_RNA|FBXL7_ENST00000329673.7_Silent_p.L385L	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	397					cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(13)|lung(33)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	60						TGGAGTACCTCGCCAAGAACT	0.602													C|||	51	0.0101837	0.0015	0.013	5008	,	,		20130	0.0		0.0318	False		,,,				2504	0.0082				p.L397L		Atlas-SNP	.											FBXL7,NS,carcinoma,+2,1	FBXL7	138	1	0			c.C1191T						PASS	.	C		27,4305		0,27,2139	97.0	104.0	102.0		1191	-7.5	0.9	5	dbSNP_129	102	274,8230		6,262,3984	no	coding-synonymous	FBXL7	NM_012304.3		6,289,6123	TT,TC,CC		3.222,0.6233,2.345		397/492	15937010	301,12535	2166	4252	6418	SO:0001819	synonymous_variant	23194	exon4			GTACCTCGCCAAG	AB020647	CCDS54833.1, CCDS64129.1	5p15.1	2011-06-09				ENSG00000183580		"""F-boxes / Leucine-rich repeats"""	13604	protein-coding gene	gene with protein product		605656				10048485, 10531035	Standard	NM_012304		Approved	KIAA0840, FBL7, FBL6	uc003jfn.1	Q9UJT9		ENST00000504595.1:c.1191C>T	5.37:g.15937010C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_012304	B9EGF1|D6RDY7|O94926	Silent	SNP	ENST00000504595.1	37	CCDS54833.1																																																																																			C|0.982;T|0.018	0.018	strong		0.602	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304	
CCDC87	55231	hgsc.bcm.edu	37	11	66358126	66358126	+	Silent	SNP	C	C	T	rs486584	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:66358126C>T	ENST00000333861.3	-	1	2428	c.2361G>A	c.(2359-2361)ctG>ctA	p.L787L	CCS_ENST00000310190.4_5'Flank|CCS_ENST00000533244.1_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	787					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28						CTATCTCCTCCAGGAGGGAAA	0.507													C|||	2131	0.425519	0.1089	0.6268	5008	,	,		17655	0.4484		0.5129	False		,,,				2504	0.5971				p.L787L		Atlas-SNP	.											.	CCDC87	83	.	0			c.G2361A						PASS	.	C		843,3557	331.0+/-301.8	95,653,1452	134.0	141.0	139.0		2361	-1.6	0.5	11	dbSNP_83	139	4541,4049	596.0+/-393.5	1169,2203,923	no	coding-synonymous	CCDC87	NM_018219.2		1264,2856,2375	TT,TC,CC		47.1362,19.1591,41.4473		787/850	66358126	5384,7606	2200	4295	6495	SO:0001819	synonymous_variant	55231	exon1			CTCCTCCAGGAGG	BC034469	CCDS8145.1	11q13.2	2006-03-15			ENSG00000182791	ENSG00000182791			25579	protein-coding gene	gene with protein product						12477932	Standard	NM_018219		Approved	FLJ10786	uc001oiq.4	Q9NVE4	OTTHUMG00000167237	ENST00000333861.3:c.2361G>A	11.37:g.66358126C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_018219	Q8NE76	Silent	SNP	ENST00000333861.3	37	CCDS8145.1																																																																																			C|0.597;T|0.402	0.402	strong		0.507	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219	
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 GAIIx	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_ENST00000309065.3_Silent_p.T84T|SLC2A9_ENST00000506583.1_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		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	203	60	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		
EPHA7	2045	hgsc.bcm.edu	37	6	94067981	94067981	+	Silent	SNP	C	C	T	rs164544	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:94067981C>T	ENST00000369303.4	-	4	1165	c.981G>A	c.(979-981)gcG>gcA	p.A327A		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	327	Cys-rich.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CACTTGTGCACGCAACGTATG	0.403													T|||	3658	0.730431	0.8911	0.6455	5008	,	,		13541	0.8294		0.5527	False		,,,				2504	0.6544				p.A327A		Atlas-SNP	.											.	EPHA7	251	.	0			c.G981A						PASS	.	T		3659,747	306.3+/-289.4	1528,603,72	99.0	97.0	97.0		981	-11.8	0.1	6	dbSNP_79	97	4616,3984	552.9+/-386.2	1237,2142,921	no	coding-synonymous	EPHA7	NM_004440.3		2765,2745,993	TT,TC,CC		46.3256,16.9542,36.3755		327/999	94067981	8275,4731	2203	4300	6503	SO:0001819	synonymous_variant	2045	exon4			TGTGCACGCAACG	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.981G>A	6.37:g.94067981C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	37	CCDS5031.1																																																																																			C|0.322;T|0.678	0.678	strong		0.403	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
PHLDB2	90102	hgsc.bcm.edu	37	3	111688578	111688578	+	Silent	SNP	C	C	T	rs774854	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111688578C>T	ENST00000431670.2	+	16	3768	c.3357C>T	c.(3355-3357)gaC>gaT	p.D1119D	PHLDB2_ENST00000412622.1_Silent_p.D1076D|PHLDB2_ENST00000481953.1_Silent_p.D1076D|PHLDB2_ENST00000393925.3_Silent_p.D1119D|PHLDB2_ENST00000393923.3_Silent_p.D1103D|PHLDB2_ENST00000495180.1_Silent_p.D610D	NM_001134438.1	NP_001127910.1	Q86SQ0	PHLB2_HUMAN	pleckstrin homology-like domain, family B, member 2	1119						cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(8)|lung(23)|ovary(6)|skin(7)|stomach(1)	55						GGAAGGAAGACTTTGATTTGC	0.448													C|||	911	0.181909	0.289	0.1311	5008	,	,		16544	0.0655		0.1551	False		,,,				2504	0.2209				p.D1119D		Atlas-SNP	.											.	PHLDB2	449	.	0			c.C3357T						PASS	.	C	,,,	1210,3196	419.1+/-338.5	158,894,1151	81.0	84.0	83.0		3309,3357,3357,3228	3.8	1.0	3	dbSNP_86	83	1610,6990	297.1+/-303.3	155,1300,2845	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PHLDB2	NM_001134437.1,NM_001134438.1,NM_001134439.1,NM_145753.2	,,,	313,2194,3996	TT,TC,CC		18.7209,27.4626,21.6823	,,,	1103/1238,1119/1254,1119/1254,1076/1211	111688578	2820,10186	2203	4300	6503	SO:0001819	synonymous_variant	90102	exon16			GGAAGACTTTGAT		CCDS2962.1, CCDS46885.1, CCDS46886.1	3q13.13	2013-01-10			ENSG00000144824	ENSG00000144824		"""Pleckstrin homology (PH) domain containing"""	29573	protein-coding gene	gene with protein product		610298				12376540	Standard	NM_145753		Approved	LL5beta, FLJ21791, LL5b	uc003dyg.3	Q86SQ0	OTTHUMG00000159282	ENST00000431670.2:c.3357C>T	3.37:g.111688578C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001134439	A5PKZ3|Q59EA8|Q68CY3|Q6NT98|Q8N8U8|Q8NAB1|Q8NCU5	Silent	SNP	ENST00000431670.2	37	CCDS46886.1																																																																																			C|0.808;T|0.192	0.192	strong		0.448	PHLDB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354337.1	NM_145753	
KDELR3	11015	hgsc.bcm.edu	37	22	38877461	38877461	+	Missense_Mutation	SNP	T	T	G	rs12004	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:38877461T>G	ENST00000216014.4	+	4	768	c.596T>G	c.(595-597)gTg>gGg	p.V199G	KDELR3_ENST00000471268.1_3'UTR|KDELR3_ENST00000409006.3_Missense_Mutation_p.V199G	NM_006855.2	NP_006846.1	O43731	ERD23_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	199			V -> G (in dbSNP:rs12004). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein retention in ER lumen (GO:0006621)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ER retention sequence binding (GO:0046923)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)	13	Melanoma(58;0.0286)					TACTTGTATGTGACCAAAGGT	0.438													T|||	1278	0.255192	0.1657	0.1974	5008	,	,		20556	0.3542		0.3062	False		,,,				2504	0.2628				p.V199G	Ovarian(11;103 529 24120 28493 32980)	Atlas-SNP	.											.	KDELR3	39	.	0			c.T596G						PASS	.	T	GLY/VAL,GLY/VAL	824,3582	325.3+/-299.0	73,678,1452	138.0	125.0	129.0		596,596	4.7	1.0	22	dbSNP_52	129	2634,5966	426.6+/-355.3	402,1830,2068	yes	missense,missense	KDELR3	NM_006855.2,NM_016657.1	109,109	475,2508,3520	GG,GT,TT		30.6279,18.7018,26.5877	possibly-damaging,possibly-damaging	199/215,199/221	38877461	3458,9548	2203	4300	6503	SO:0001583	missense	11015	exon4			TGTATGTGACCAA	AL035081	CCDS13972.1, CCDS46705.1	22q13	2008-05-02			ENSG00000100196	ENSG00000100196			6306	protein-coding gene	gene with protein product							Standard	NM_006855		Approved		uc003avu.3	O43731	OTTHUMG00000153520	ENST00000216014.4:c.596T>G	22.37:g.38877461T>G	ENSP00000216014:p.Val199Gly	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_016657	A8K7T7|B8ZZ26|O95557|Q4V750|Q4V767|Q53FP4|Q53GK1	Missense_Mutation	SNP	ENST00000216014.4	37	CCDS13972.1	630	0.28846153846153844	89	0.18089430894308944	81	0.22375690607734808	219	0.38286713286713286	241	0.3179419525065963	T	16.69	3.193945	0.58017	0.187018	0.306279	ENSG00000100196	ENST00000216014;ENST00000409006	T;T	0.75704	-0.96;-0.96	4.65	4.65	0.58169	.	0.218747	0.39475	N	0.001353	T	0.00012	0.0000	M	0.81802	2.56	0.09310	P	0.999999999789922	B;P	0.43973	0.356;0.823	B;P	0.48141	0.197;0.568	T	0.01159	-1.1433	9	0.62326	D	0.03	-10.4461	14.226	0.65860	0.0:0.0:0.0:1.0	rs12004;rs3180098;rs17173760;rs17402570;rs52804343;rs57393871;rs12004	199;199	O43731;O43731-2	ERD23_HUMAN;.	G	199	ENSP00000216014:V199G;ENSP00000386918:V199G	ENSP00000216014:V199G	V	+	2	0	KDELR3	37207407	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.868000	0.87116	1.950000	0.56595	0.477000	0.44152	GTG	A|0.004;C|0.002	.	strong		0.438	KDELR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331474.1		
TPPP2	122664	hgsc.bcm.edu	37	14	21500121	21500121	+	Missense_Mutation	SNP	G	G	T	rs9624	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:21500121G>T	ENST00000321760.6	+	4	546	c.398G>T	c.(397-399)cGc>cTc	p.R133L	RP11-998D10.1_ENST00000531638.1_5'Flank|TPPP2_ENST00000530140.2_Missense_Mutation_p.R133L|AL161668.5_ENST00000533984.1_lincRNA|NDRG2_ENST00000403829.3_Intron	NM_173846.4	NP_776245.2	P59282	TPPP2_HUMAN	tubulin polymerization-promoting protein family member 2	133			R -> L (in dbSNP:rs9624). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		CACAAGGAGCGCTTTGATGAG	0.542													G|||	800	0.159744	0.0227	0.2651	5008	,	,		20356	0.2847		0.1322	False		,,,				2504	0.1697				p.R133L		Atlas-SNP	.											.	TPPP2	22	.	0			c.G398T						PASS	.	G	LEU/ARG	160,4246	108.6+/-147.0	3,154,2046	143.0	110.0	121.0		398	3.6	1.0	14	dbSNP_52	121	1088,7512	227.9+/-263.1	67,954,3279	yes	missense	TPPP2	NM_173846.4	102	70,1108,5325	TT,TG,GG		12.6512,3.6314,9.5956	probably-damaging	133/171	21500121	1248,11758	2203	4300	6503	SO:0001583	missense	122664	exon4			AGGAGCGCTTTGA	AY072034	CCDS9566.1	14q11.2	2014-01-21	2007-05-02	2007-05-02	ENSG00000179636	ENSG00000179636			19293	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 8"""	C14orf8		15590652, 17105200	Standard	NM_173846		Approved	p25beta, p18, CT152	uc001vzh.3	P59282	OTTHUMG00000029642	ENST00000321760.6:c.398G>T	14.37:g.21500121G>T	ENSP00000317595:p.Arg133Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	51	0.548387	NM_173846	Q2VYF3	Missense_Mutation	SNP	ENST00000321760.6	37	CCDS9566.1	356	0.163003663003663	15	0.03048780487804878	76	0.20994475138121546	171	0.29895104895104896	94	0.12401055408970976	G	22.1	4.239688	0.79800	0.036314	0.126512	ENSG00000179636	ENST00000321760;ENST00000530140	T;T	0.58797	0.31;0.31	4.49	3.59	0.41128	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.93763	3.455	0.09310	P	0.999999857937	D	0.71674	0.998	D	0.87578	0.998	T	0.02184	-1.1199	9	0.72032	D	0.01	1.1561	11.9813	0.53121	0.0:0.0:0.8258:0.1742	rs9624;rs1750658;rs3818610;rs17846241;rs17859260;rs52826016;rs61479083;rs9624	133	P59282	TPPP2_HUMAN	L	133	ENSP00000317595:R133L;ENSP00000435356:R133L	ENSP00000317595:R133L	R	+	2	0	TPPP2	20569961	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.796000	0.85898	1.227000	0.43598	0.650000	0.86243	CGC	G|0.882;T|0.118	0.118	strong		0.542	TPPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073914.3	NM_173846	
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 GAIIx	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_ENST00000555445.1_Missense_Mutation_p.G258V|PAPLN_ENST00000340738.5_Missense_Mutation_p.G231V|PAPLN_ENST00000381166.3_Missense_Mutation_p.G258V|PAPLN_ENST00000427855.1_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	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	146	76	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	
DENND5B	160518	hgsc.bcm.edu	37	12	31648826	31648826	+	Missense_Mutation	SNP	C	C	T	rs4930979	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:31648826C>T	ENST00000389082.5	-	2	419	c.155G>A	c.(154-156)aGa>aAa	p.R52K	DENND5B_ENST00000536562.1_Missense_Mutation_p.R87K|DENND5B_ENST00000354285.4_Missense_Mutation_p.R74K|DENND5B_ENST00000545147.1_5'UTR|DENND5B_ENST00000306833.6_Missense_Mutation_p.R87K	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	52	UDENN.		R -> K (in dbSNP:rs4930979). {ECO:0000269|PubMed:14702039}.		positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						GAATGTTCTTCTCAAAGGACT	0.333													C|||	1986	0.396565	0.084	0.6095	5008	,	,		16127	0.5734		0.4165	False		,,,				2504	0.4652				p.R52K		Atlas-SNP	.											.	DENND5B	114	.	0			c.G155A						PASS	.	C	LYS/ARG	458,3182		32,394,1394	113.0	101.0	105.0		155	3.7	1.0	12	dbSNP_111	105	3279,4887		678,1923,1482	yes	missense	DENND5B	NM_144973.3	26	710,2317,2876	TT,TC,CC		40.1543,12.5824,31.6534	benign	52/1275	31648826	3737,8069	1820	4083	5903	SO:0001583	missense	160518	exon2			GTTCTTCTCAAAG	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.155G>A	12.37:g.31648826C>T	ENSP00000373734:p.Arg52Lys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	908	0.4157509157509158	49	0.09959349593495935	206	0.569060773480663	334	0.583916083916084	319	0.420844327176781	C	13.73	2.323020	0.41096	0.125824	0.401543	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285;ENST00000546299	T;T;T;T;T	0.28895	3.82;1.59;1.59;3.35;3.34	4.6	3.71	0.42584	uDENN (3);	0.133121	0.49916	N	0.000128	T	0.00012	0.0000	N	0.25380	0.74	0.21697	P	0.999584744	B;B;B	0.11235	0.004;0.002;0.003	B;B;B	0.20577	0.03;0.008;0.017	T	0.41734	-0.9492	9	0.31617	T	0.26	-3.6645	11.8628	0.52476	0.0:0.9123:0.0:0.0877	rs4930979;rs4930979	74;52;87	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	K	52;87;87;74;4	ENSP00000373734:R52K;ENSP00000306482:R87K;ENSP00000444889:R87K;ENSP00000346238:R74K;ENSP00000442938:R4K	ENSP00000306482:R87K	R	-	2	0	DENND5B	31540093	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.535000	0.36061	1.277000	0.44412	0.650000	0.86243	AGA	C|0.605;T|0.395	0.395	strong		0.333	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
COQ5	84274	hgsc.bcm.edu	37	12	120966921	120966921	+	Silent	SNP	A	A	G	rs3742052	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:120966921A>G	ENST00000288532.6	-	1	64	c.24T>C	c.(22-24)gcT>gcC	p.A8A	COQ5_ENST00000445328.2_Silent_p.A8A	NM_032314.3	NP_115690.3	Q5HYK3	COQ5_HUMAN	coenzyme Q5 homolog, methyltransferase (S. cerevisiae)	8					small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(1)|prostate(1)|urinary_tract(3)	20	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGCTCCATAGAGCACAGCTCC	0.667													A|||	1325	0.264577	0.0809	0.2579	5008	,	,		14695	0.4921		0.2783	False		,,,				2504	0.2689				p.A8A		Atlas-SNP	.											.	COQ5	26	.	0			c.T24C						PASS	.	A		466,3938		24,418,1760	18.0	21.0	20.0		24	-1.4	0.0	12	dbSNP_107	20	2678,5920		424,1830,2045	no	coding-synonymous	COQ5	NM_032314.3		448,2248,3805	GG,GA,AA		31.1468,10.5813,24.1809		8/328	120966921	3144,9858	2202	4299	6501	SO:0001819	synonymous_variant	84274	exon1			CCATAGAGCACAG	AK057777	CCDS31912.1	12q24.31	2011-09-16	2006-04-04		ENSG00000110871	ENSG00000110871	2.1.1.201		28722	protein-coding gene	gene with protein product	"""2-methoxy-6-polyprenyl-1,4-benzoquinol methylase"""		"""coenzyme Q5 homolog, methyltransferase (yeast)"""				Standard	NM_032314		Approved	MGC4767	uc001tyn.3	Q5HYK3	OTTHUMG00000169375	ENST00000288532.6:c.24T>C	12.37:g.120966921A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_032314	B4DEJ4|Q32Q28|Q53HH0|Q96LV1|Q9BSP8	Silent	SNP	ENST00000288532.6	37	CCDS31912.1																																																																																			A|0.748;G|0.252	0.252	strong		0.667	COQ5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403767.2	NM_032314	
HLA-G	3135	hgsc.bcm.edu	37	6	29797639	29797639	+	Silent	SNP	C	C	T	rs1049033	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29797639C>T	ENST00000360323.6	+	5	966	c.942C>T	c.(940-942)ggC>ggT	p.G314G	HLA-G_ENST00000376815.3_Silent_p.G130G|HLA-G_ENST00000376818.3_Silent_p.G222G|HLA-G_ENST00000376828.2_Silent_p.G319G|HLA-G_ENST00000428701.1_Silent_p.G314G			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	314					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 peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TCGTTGCTGGCCTGGTTGTCC	0.597													N|||	1161	0.231829	0.2504	0.245	5008	,	,		20908	0.1091		0.2555	False		,,,				2504	0.2996				p.G314G		Atlas-SNP	.											.	HLA-G	90	.	0			c.C942T						PASS	.	C		1182,3224		158,866,1179	109.0	90.0	96.0		942	-0.2	0.0	6	dbSNP_86	96	2541,6059		367,1807,2126	no	coding-synonymous	HLA-G	NM_002127.5		525,2673,3305	TT,TC,CC		29.5465,26.8271,28.6252		314/339	29797639	3723,9283	2203	4300	6503	SO:0001819	synonymous_variant	3135	exon6			TGCTGGCCTGGTT		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.942C>T	6.37:g.29797639C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	140	105	0.75	NM_002127		Silent	SNP	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.738;T|0.262	0.262	strong		0.597	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
NLRC5	84166	hgsc.bcm.edu	37	16	57080528	57080528	+	Missense_Mutation	SNP	C	C	A	rs289723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57080528C>A	ENST00000262510.6	+	22	3538	c.3313C>A	c.(3313-3315)Cag>Aag	p.Q1105K	NLRC5_ENST00000539144.1_Missense_Mutation_p.Q1105K|NLRC5_ENST00000308149.7_Missense_Mutation_p.Q1105K|NLRC5_ENST00000436936.1_Missense_Mutation_p.Q1105K	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1105			Q -> K (in dbSNP:rs289723). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AGGGTTCCGTCAGCGCTGCAT	0.557													C|||	843	0.168331	0.034	0.2911	5008	,	,		15508	0.1081		0.2455	False		,,,				2504	0.2454				p.Q1105K		Atlas-SNP	.											.	NLRC5	186	.	0			c.C3313A						PASS	.	C	LYS/GLN	355,4041	182.2+/-210.1	8,339,1851	93.0	83.0	86.0		3313	1.5	0.0	16	dbSNP_79	86	2499,6101	411.7+/-350.6	368,1763,2169	yes	missense	NLRC5	NM_032206.3	53	376,2102,4020	AA,AC,CC		29.0581,8.0755,21.9606	benign	1105/1867	57080528	2854,10142	2198	4300	6498	SO:0001583	missense	84166	exon21			TTCCGTCAGCGCT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.3313C>A	16.37:g.57080528C>A	ENSP00000262510:p.Gln1105Lys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	389|389	0.17811355311355312|0.17811355311355312	20|20	0.04065040650406504|0.04065040650406504	104|104	0.287292817679558|0.287292817679558	74|74	0.12937062937062938|0.12937062937062938	191|191	0.2519788918205805|0.2519788918205805	C|C	5.154|5.154	0.213957|0.213957	0.09810|0.09810	0.080755|0.080755	0.290581|0.290581	ENSG00000140853|ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144|ENST00000538805	T;T;T;T|.	0.72942|.	-0.51;-0.53;-0.7;-0.53|.	3.55|3.55	1.52|1.52	0.23074|0.23074	.|.	1.238210|.	0.06245|.	N|.	0.691069|.	T|.	0.00012|.	0.0000|.	M|M	0.63428|0.63428	1.95|1.95	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.18013|.	0.017;0.017;0.025|.	B;B;B|.	0.15484|.	0.004;0.009;0.013|.	T|.	0.15607|.	-1.0431|.	9|.	0.02654|.	T|.	1|.	.|.	5.0579|5.0579	0.14542|0.14542	0.0:0.6681:0.2131:0.1188|0.0:0.6681:0.2131:0.1188	rs289723;rs59401549;rs289723|rs289723;rs59401549;rs289723	790;1105;1105|.	Q9H6Y0;Q86WI3-6;Q86WI3|.	.;.;NLRC5_HUMAN|.	K|X	1105|857	ENSP00000262510:Q1105K;ENSP00000308886:Q1105K;ENSP00000389739:Q1105K;ENSP00000441727:Q1105K|.	ENSP00000262510:Q1105K|.	Q|S	+|+	1|2	0|0	NLRC5|NLRC5	55638029|55638029	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	0.665000|0.665000	0.25083|0.25083	0.475000|0.475000	0.27415|0.27415	-0.254000|-0.254000	0.11334|0.11334	CAG|TCA	T|0.002;G|0.001	.	strong		0.557	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
IQUB	154865	hgsc.bcm.edu	37	7	123119990	123119990	+	Silent	SNP	T	T	C	rs10500091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:123119990T>C	ENST00000466202.1	-	8	1845	c.1269A>G	c.(1267-1269)caA>caG	p.Q423Q	IQUB_ENST00000324698.6_Silent_p.Q423Q|IQUB_ENST00000434450.1_Silent_p.Q423Q	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	423					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						CAGTAAAAGATTGGTTAATAC	0.378													T|||	1128	0.22524	0.0507	0.2478	5008	,	,		17942	0.3879		0.2853	False		,,,				2504	0.2157				p.Q423Q		Atlas-SNP	.											.	IQUB	117	.	0			c.A1269G						PASS	.	T		445,3961	212.5+/-232.4	22,401,1780	108.0	98.0	101.0		1269	-10.5	0.1	7	dbSNP_119	101	2325,6273	390.1+/-343.2	306,1713,2280	no	coding-synonymous	IQUB	NM_178827.4		328,2114,4060	CC,CT,TT		27.0412,10.0999,21.3011		423/792	123119990	2770,10234	2203	4299	6502	SO:0001819	synonymous_variant	154865	exon8			AAAAGATTGGTTA	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.1269A>G	7.37:g.123119990T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	121	68	0.561983	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Silent	SNP	ENST00000466202.1	37	CCDS5787.1																																																																																			T|0.782;C|0.218	0.218	strong		0.378	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
CAPN11	11131	hgsc.bcm.edu	37	6	44141088	44141088	+	Missense_Mutation	SNP	G	G	A	rs6938938	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:44141088G>A	ENST00000398776.1	+	7	834	c.796G>A	c.(796-798)Gtg>Atg	p.V266M	CAPN11_ENST00000542245.1_Missense_Mutation_p.V266M	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11	266	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		V -> M (in dbSNP:rs6938938).		proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TAGGAAGGCCGTGGAGCGATC	0.587													G|||	710	0.141773	0.239	0.072	5008	,	,		18803	0.1062		0.1083	False		,,,				2504	0.1309				p.V266M		Atlas-SNP	.											.	CAPN11	66	.	0			c.G796A						PASS	.	G	MET/VAL	731,3199		71,589,1305	26.0	29.0	28.0		796	-8.5	0.0	6	dbSNP_116	28	719,7565		30,659,3453	yes	missense	CAPN11	NM_007058.3	21	101,1248,4758	AA,AG,GG		8.6794,18.6005,11.8716	possibly-damaging	266/740	44141088	1450,10764	1965	4142	6107	SO:0001583	missense	11131	exon7			AAGGCCGTGGAGC	AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.796G>A	6.37:g.44141088G>A	ENSP00000381758:p.Val266Met	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_007058	B2RA64|Q5T3G1|Q8N4R5	Missense_Mutation	SNP	ENST00000398776.1	37	CCDS47436.1	278	0.12728937728937728	112	0.22764227642276422	19	0.052486187845303865	62	0.10839160839160839	85	0.11213720316622691	G	12.50	1.956180	0.34565	0.186005	0.086794	ENSG00000137225	ENST00000398776;ENST00000542245	D;D	0.89050	-2.46;-2.46	4.25	-8.51	0.00923	Peptidase C2, calpain, catalytic domain (3);	1.255730	0.05836	N	0.618473	T	0.60521	0.2275	L	0.48935	1.535	0.80722	P	0.0	P	0.34934	0.476	B	0.22386	0.039	T	0.53486	-0.8432	9	0.87932	D	0	.	4.2948	0.10895	0.1137:0.2636:0.4759:0.1468	rs6938938;rs57707167;rs6938938	266	Q9UMQ6	CAN11_HUMAN	M	266	ENSP00000381758:V266M;ENSP00000441078:V266M	ENSP00000381758:V266M	V	+	1	0	CAPN11	44249066	0.000000	0.05858	0.000000	0.03702	0.319000	0.28217	-1.323000	0.02692	-4.254000	0.00061	-0.355000	0.07637	GTG	G|0.864;A|0.136	0.136	strong		0.587	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3		
PRPS2	5634	hgsc.bcm.edu	37	X	12809661	12809661	+	Silent	SNP	G	G	A	rs1731469	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:12809661G>A	ENST00000380668.5	+	1	173	c.45G>A	c.(43-45)ctG>ctA	p.L15L	PRPS2_ENST00000398491.2_Silent_p.L15L|PRPS2_ENST00000489404.1_Silent_p.L15L	NM_001039091.2|NM_002765.4	NP_001034180.1|NP_002756.1	P11908	PRPS2_HUMAN	phosphoribosyl pyrophosphate synthetase 2	15					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|AMP biosynthetic process (GO:0006167)|nucleobase-containing compound metabolic process (GO:0006139)|organ regeneration (GO:0031100)	extracellular vesicular exosome (GO:0070062)|ribose phosphate diphosphokinase complex (GO:0002189)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|carbohydrate binding (GO:0030246)|GDP binding (GO:0019003)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	16						ATCAGGACCTGTCCCAGCGCG	0.721													g|||	2182	0.578013	0.3079	0.4769	3775	,	,		5715	0.6101		0.4662	False		,,,				2504	0.3681				p.L15L		Atlas-SNP	.											.	PRPS2	41	.	0			c.G45A						PASS	.		,	1726,2063		348,786,244,485,307	16.0	14.0	15.0		45,45	3.8	1.0	X	dbSNP_89	15	4189,2453		968,1104,1149,338,673	no	coding-synonymous,coding-synonymous	PRPS2	NM_001039091.2,NM_002765.4	,	1316,1890,1393,823,980	AA,AG,A,GG,G		36.9316,45.5529,43.294	,	15/322,15/319	12809661	5915,4516	2170	4232	6402	SO:0001819	synonymous_variant	5634	exon1			GGACCTGTCCCAG	Y00971	CCDS14150.1, CCDS43918.1	Xp22.2	2012-10-02			ENSG00000101911	ENSG00000101911	2.7.6.1		9465	protein-coding gene	gene with protein product	"""PRS II"", ""ribose-phosphate diphosphokinase 2"""	311860				1962753	Standard	NM_002765		Approved		uc004cva.3	P11908	OTTHUMG00000021139	ENST00000380668.5:c.45G>A	X.37:g.12809661G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	62	50	0.806452	NM_001039091	Q0VDH9|Q0VDI0|Q15245|Q2TAK7	Silent	SNP	ENST00000380668.5	37	CCDS14150.1																																																																																			G|0.430;A|0.570	0.570	strong		0.721	PRPS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055772.2	NM_002765	
HLA-C	3107	hgsc.bcm.edu	37	6	31239417	31239417	+	Missense_Mutation	SNP	C	C	T	rs2308557	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31239417C>T	ENST00000376228.5	-	2	316	c.302G>A	c.(301-303)aGc>aAc	p.S101N	HLA-C_ENST00000383329.3_Missense_Mutation_p.S101N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	101	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GTTCCGCAGGCTCACTCGGTC	0.706													c|||	1940	0.38738	0.5408	0.3862	5008	,	,		11155	0.1399		0.4125	False		,,,				2504	0.41				p.S101N		Atlas-SNP	.											.	HLA-C	92	.	0			c.G302A						PASS	.	C	ASN/SER	1619,1403		436,747,328	42.0	43.0	42.0		302	-4.1	0.0	6	dbSNP_126	42	2041,3377		375,1291,1043	yes	missense	HLA-C	NM_002117.5	46	811,2038,1371	TT,TC,CC		37.6707,46.4262,43.3649	benign	101/367	31239417	3660,4780	1511	2709	4220	SO:0001583	missense	3107	exon2			CGCAGGCTCACTC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.302G>A	6.37:g.31239417C>T	ENSP00000365402:p.Ser101Asn	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	180	23	0.127778	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	794	0.36355311355311354	264	0.5365853658536586	141	0.38950276243093923	80	0.13986013986013987	309	0.4076517150395778	N	6.683	0.494653	0.12702	0.535738	0.376707	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00686	5.85;5.85	2.81	-4.12	0.03916	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	2.590310	0.02414	U	0.082017	T	0.00109	0.0003	N	0.01535	-0.81	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.002;0.002;0.001	T	0.43507	-0.9387	9	0.08837	T	0.75	.	4.7356	0.12986	0.0:0.4159:0.166:0.4181	rs2308557;rs3177887;rs17416870	101;101;101;101	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	N	101;101;101;138	ENSP00000365402:S101N;ENSP00000372819:S101N	ENSP00000365402:S101N	S	-	2	0	HLA-C	31347396	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.592000	0.00421	-0.960000	0.03613	-0.727000	0.03589	AGC	T|0.404;G|0.000;C|0.595;A|0.000	0.404	strong		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
CCDC116	164592	hgsc.bcm.edu	37	22	21988599	21988599	+	Missense_Mutation	SNP	G	G	A	rs371513	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:21988599G>A	ENST00000292779.3	+	3	522	c.361G>A	c.(361-363)Gga>Aga	p.G121R	CCDC116_ENST00000607942.1_Missense_Mutation_p.G121R	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	121			G -> R (in dbSNP:rs371513).							endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					GCCAAGTGGTGGACGGCGGGC	0.662													G|||	649	0.129593	0.1135	0.1556	5008	,	,		15740	0.0417		0.2018	False		,,,				2504	0.1493				p.G121R		Atlas-SNP	.											.	CCDC116	56	.	0			c.G361A						PASS	.	G	ARG/GLY	478,3928	222.6+/-239.4	25,428,1750	92.0	86.0	88.0		361	-2.9	0.0	22	dbSNP_80	88	1636,6964	297.8+/-303.6	153,1330,2817	yes	missense	CCDC116	NM_152612.2	125	178,1758,4567	AA,AG,GG		19.0233,10.8488,16.254	benign	121/614	21988599	2114,10892	2203	4300	6503	SO:0001583	missense	164592	exon3			AGTGGTGGACGGC	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.361G>A	22.37:g.21988599G>A	ENSP00000292779:p.Gly121Arg	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	290	0.13278388278388278	57	0.11585365853658537	65	0.17955801104972377	24	0.04195804195804196	144	0.18997361477572558	G	0.011	-1.717935	0.00706	0.108488	0.190233	ENSG00000161180	ENST00000292779	T	0.21361	2.01	4.42	-2.88	0.05682	.	0.892392	0.09571	N	0.784163	T	0.00012	0.0000	N	0.04959	-0.14	0.80722	P	0.0	B;B	0.20887	0.012;0.049	B;B	0.17433	0.018;0.018	T	0.46062	-0.9218	8	.	.	.	-45.4808	8.7821	0.34798	0.5812:0.0:0.4188:0.0	rs371513;rs60165197;rs371513	121;121	B7Z7H5;Q8IYX3-2	.;.	R	121	ENSP00000292779:G121R	.	G	+	1	0	CCDC116	20318599	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.162000	0.03141	-0.552000	0.06167	-0.658000	0.03865	GGA	G|0.847;A|0.153	0.153	strong		0.662	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
FOXE1	2304	hgsc.bcm.edu	37	9	100616583	100616583	+	Silent	SNP	T	T	C	rs3021523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:100616583T>C	ENST00000375123.3	+	1	1048	c.387T>C	c.(385-387)ctT>ctC	p.L129L		NM_004473.3	NP_004464.2	O00358	FOXE1_HUMAN	forkhead box E1 (thyroid transcription factor 2)	129					anatomical structure morphogenesis (GO:0009653)|cell migration (GO:0016477)|embryonic organ morphogenesis (GO:0048562)|hair follicle morphogenesis (GO:0031069)|hard palate development (GO:0060022)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|pharynx development (GO:0060465)|positive regulation of transcription, DNA-templated (GO:0045893)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5		Acute lymphoblastic leukemia(62;0.158)				ACTGGGCGCTTGACCCCAACG	0.647													C|||	4421	0.882788	0.969	0.8271	5008	,	,		7122	0.9911		0.7604	False		,,,				2504	0.82				p.L129L		Atlas-SNP	.											.	FOXE1	19	.	0			c.T387C						PASS	.	C		4090,310	155.5+/-188.7	1900,290,10	31.0	35.0	34.0		387	0.3	1.0	9	dbSNP_101	34	6342,2254	355.3+/-329.8	2351,1640,307	no	coding-synonymous	FOXE1	NM_004473.3		4251,1930,317	CC,CT,TT		26.2215,7.0455,19.7291		129/374	100616583	10432,2564	2200	4298	6498	SO:0001819	synonymous_variant	2304	exon1			GGCGCTTGACCCC	U89995	CCDS35078.1	9q22	2008-09-05			ENSG00000178919	ENSG00000178919		"""Forkhead boxes"""	3806	protein-coding gene	gene with protein product		602617	"""forkhead box E2"""	FKHL15, TITF2, FOXE2		9169137, 9697705	Standard	NM_004473		Approved	TTF-2, HFKH4	uc004axu.3	O00358	OTTHUMG00000020333	ENST00000375123.3:c.387T>C	9.37:g.100616583T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_004473	O75765|Q5T109|Q99526	Silent	SNP	ENST00000375123.3	37	CCDS35078.1																																																																																			T|0.177;C|0.823	0.823	strong		0.647	FOXE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053341.1		
SLCO6A1	133482	hgsc.bcm.edu	37	5	101724472	101724472	+	Missense_Mutation	SNP	C	C	T	rs72779942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:101724472C>T	ENST00000506729.1	-	12	2108	c.1937G>A	c.(1936-1938)cGg>cAg	p.R646Q	SLCO6A1_ENST00000389019.3_Missense_Mutation_p.R584Q|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.R393Q|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.R393Q|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.R646Q			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	646						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.R646L(1)		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)		ATTAACATCCCGTAAAATACA	0.313													C|||	27	0.00539137	0.0	0.0101	5008	,	,		15044	0.0		0.0189	False		,,,				2504	0.001				p.R646Q		Atlas-SNP	.											SLCO6A1,caecum,carcinoma,-1,1	SLCO6A1	153	1	1	Substitution - Missense(1)	kidney(1)	c.G1937A						PASS	.	C	GLN/ARG	23,4381	29.0+/-57.7	1,21,2180	71.0	70.0	71.0		1937	2.3	0.0	5	dbSNP_130	71	156,8434	74.8+/-137.4	0,156,4139	yes	missense	SLCO6A1	NM_173488.3	43	1,177,6319	TT,TC,CC		1.8161,0.5223,1.3776	probably-damaging	646/720	101724472	179,12815	2202	4295	6497	SO:0001583	missense	133482	exon12			ACATCCCGTAAAA	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.1937G>A	5.37:g.101724472C>T	ENSP00000421339:p.Arg646Gln	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	198	94	0.474747	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	17	0.007783882783882784	0	0.0	4	0.011049723756906077	0	0.0	13	0.017150395778364115	C	12.49	1.952402	0.34471	0.005223	0.018161	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.38401	1.14;1.14;1.14;1.14;1.14	5.06	2.35	0.29111	Major facilitator superfamily domain, general substrate transporter (1);	0.984997	0.08296	N	0.967665	T	0.39358	0.1075	M	0.65975	2.015	0.09310	N	1	D;D;D	0.89917	1.0;0.997;1.0	D;D;D	0.72338	0.933;0.977;0.964	T	0.20338	-1.0278	10	0.54805	T	0.06	.	8.1625	0.31207	0.0:0.7531:0.0:0.2469	.	584;393;646	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	Q	646;646;584;393;393	ENSP00000421339:R646Q;ENSP00000369135:R646Q;ENSP00000373671:R584Q;ENSP00000421990:R393Q;ENSP00000369138:R393Q	ENSP00000369135:R646Q	R	-	2	0	SLCO6A1	101752371	0.081000	0.21417	0.000000	0.03702	0.000000	0.00434	1.806000	0.38892	0.320000	0.23234	-0.145000	0.13849	CGG	C|0.987;T|0.013	0.013	strong		0.313	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
ABCA13	154664	hgsc.bcm.edu	37	7	48313881	48313881	+	Missense_Mutation	SNP	T	T	C	rs17712299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48313881T>C	ENST00000435803.1	+	17	4642	c.4618T>C	c.(4618-4620)Ttt>Ctt	p.F1540L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1540			F -> L (in dbSNP:rs17712299).		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						TCCTAATCAGTTTCAAAATAT	0.303													T|||	483	0.0964457	0.143	0.0548	5008	,	,		17567	0.1498		0.0487	False		,,,				2504	0.0573				p.F1540L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T4618C						PASS	.	T	LEU/PHE	398,3212		23,352,1430	41.0	42.0	41.0		4618	5.3	0.8	7	dbSNP_123	41	468,7628		13,442,3593	yes	missense	ABCA13	NM_152701.3	22	36,794,5023	CC,CT,TT		5.7806,11.0249,7.3979	probably-damaging	1540/5059	48313881	866,10840	1805	4048	5853	SO:0001583	missense	154664	exon17			AATCAGTTTCAAA	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.4618T>C	7.37:g.48313881T>C	ENSP00000411096:p.Phe1540Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	39	31	0.794872	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	239	0.10943223443223443	80	0.16260162601626016	25	0.06906077348066299	96	0.16783216783216784	38	0.05013192612137203	T	17.56	3.420584	0.62622	0.110249	0.057806	ENSG00000179869	ENST00000435803	D	0.91631	-2.88	5.28	5.28	0.74379	.	0.000000	0.48286	D	0.000187	T	0.05456	0.0144	M	0.66939	2.045	0.09310	P	1.0	D	0.69078	0.997	D	0.75020	0.985	T	0.31971	-0.9924	8	.	.	.	.	13.2284	0.59927	0.0:0.0:0.0:1.0	rs17712299;rs17712299	1540	Q86UQ4	ABCAD_HUMAN	L	1540	ENSP00000411096:F1540L	.	F	+	1	0	ABCA13	48284427	0.614000	0.27017	0.788000	0.31933	0.576000	0.36127	2.325000	0.43840	2.125000	0.65367	0.460000	0.39030	TTT	T|0.884;C|0.116	0.116	strong		0.303	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
CUTC	51076	hgsc.bcm.edu	37	10	101502968	101502968	+	Silent	SNP	A	A	G	rs3740076	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101502968A>G	ENST00000370476.5	+	4	381	c.252A>G	c.(250-252)ccA>ccG	p.P84P	CUTC_ENST00000493385.1_3'UTR	NM_015960.2	NP_057044.2	Q9NTM9	CUTC_HUMAN	cutC copper transporter	84					copper ion homeostasis (GO:0055070)|copper ion transport (GO:0006825)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	copper ion binding (GO:0005507)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Colorectal(252;0.234)		Epithelial(162;3e-10)|all cancers(201;2.37e-08)		TGATTCGGCCACGGGGAGGTG	0.418													A|||	320	0.0638978	0.0053	0.1499	5008	,	,		19471	0.0228		0.1083	False		,,,				2504	0.0787				p.P84P		Atlas-SNP	.											.	CUTC	32	.	0			c.A252G						PASS	.	A		81,4325	69.2+/-107.0	1,79,2123	215.0	198.0	204.0		252	0.7	1.0	10	dbSNP_107	204	928,7672	204.0+/-246.8	49,830,3421	no	coding-synonymous	CUTC	NM_015960.2		50,909,5544	GG,GA,AA		10.7907,1.8384,7.758		84/274	101502968	1009,11997	2203	4300	6503	SO:0001819	synonymous_variant	51076	exon4			TCGGCCACGGGGA	AF132966	CCDS7483.1	10q24.31	2013-07-31	2013-07-31		ENSG00000119929	ENSG00000119929			24271	protein-coding gene	gene with protein product		610101	"""cutC copper transporter homolog (E. coli)"""			16182249	Standard	NM_015960		Approved	CGI-32	uc001kqd.4	Q9NTM9	OTTHUMG00000018889	ENST00000370476.5:c.252A>G	10.37:g.101502968A>G		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	212	103	0.485849	NM_015960	Q5TCZ8|Q9Y321	Silent	SNP	ENST00000370476.5	37	CCDS7483.1																																																																																			A|0.931;G|0.069	0.069	strong		0.418	CUTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049811.1	NM_015960	
MUC6	4588	hgsc.bcm.edu	37	11	1016825	1016825	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1016825G>A	ENST00000421673.2	-	31	6026	c.5976C>T	c.(5974-5976)acC>acT	p.T1992T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1992	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|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;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GATAGGTAGTGGTGGTCTGGA	0.552																																					p.T1992T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	0			c.C5976T						PASS	.						1487.0	1481.0	1483.0					11																	1016825		2203	4298	6501	SO:0001819	synonymous_variant	4588	exon31			GGTAGTGGTGGTC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5976C>T	11.37:g.1016825G>A		Somatic	607	0	0		WXS	Illumina HiSeq	Phase_I	825	38	0.0460606	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	none		0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
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 GAIIx	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_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Missense_Mutation_p.R109H	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	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	8	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		
SLC4A9	83697	hgsc.bcm.edu	37	5	139740454	139740454	+	Silent	SNP	C	C	T	rs34507975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139740454C>T	ENST00000230993.6	+	2	395	c.360C>T	c.(358-360)caC>caT	p.H120H	SLC4A9_ENST00000507527.1_Silent_p.H120H|SLC4A9_ENST00000506545.1_Silent_p.H96H|SLC4A9_ENST00000432095.2_Silent_p.H96H|SLC4A9_ENST00000506757.2_Silent_p.H96H	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	120					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGCCCCCCACGTGCCCACCC	0.627													C|||	1008	0.201278	0.0772	0.2104	5008	,	,		16034	0.2728		0.2326	False		,,,				2504	0.2566				p.H120H		Atlas-SNP	.											.	SLC4A9	125	.	0			c.C360T						PASS	.	C		354,3576		15,324,1626	18.0	21.0	20.0		288	-4.0	1.0	5	dbSNP_126	20	1941,6367		238,1465,2451	no	coding-synonymous	SLC4A9	NM_031467.2		253,1789,4077	TT,TC,CC		23.363,9.0076,18.7531		96/960	139740454	2295,9943	1965	4154	6119	SO:0001819	synonymous_variant	83697	exon2			CCCCCACGTGCCC	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"""Solute carriers"""	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.360C>T	5.37:g.139740454C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	133	56	0.421053	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Silent	SNP	ENST00000230993.6	37	CCDS58973.1																																																																																			C|0.790;T|0.210	0.210	strong		0.627	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467	
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 GAIIx	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_ENST00000326044.5_3'UTR|ZNF561_ENST00000495503.1_5'Flank|ZNF561_ENST00000354661.4_Silent_p.A237A|ZNF561_ENST00000424629.1_Silent_p.A304A	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		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	33	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	
TCEB3B	51224	hgsc.bcm.edu	37	18	44561619	44561619	+	Missense_Mutation	SNP	G	G	C	rs61738602	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44561619G>C	ENST00000332567.4	-	1	369	c.17C>G	c.(16-18)aCt>aGt	p.T6S	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	6	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GTGCAGCGTAGTGGACCCTGC	0.617													g|||	190	0.0379393	0.0499	0.0418	5008	,	,		16517	0.0069		0.0835	False		,,,				2504	0.0041				p.T6S		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C17G						PASS	.	C	SER/THR,	263,4141		9,245,1948	49.0	48.0	48.0		17,	-0.4	0.0	18	dbSNP_129	48	621,7977		28,565,3706	no	missense,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	58,	37,810,5654	CC,CG,GG		7.2226,5.9718,6.799	possibly-damaging,	6/754,	44561619	884,12118	2202	4299	6501	SO:0001583	missense	51224	exon1			AGCGTAGTGGACC	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.17C>G	18.37:g.44561619G>C	ENSP00000331302:p.Thr6Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_016427	Q9P2V9	Missense_Mutation	SNP	ENST00000332567.4	37	CCDS11932.1	121	0.0554029304029304	32	0.06504065040650407	17	0.04696132596685083	6	0.01048951048951049	66	0.0870712401055409	g	0.001	-3.777083	0.00004	0.059718	0.072226	ENSG00000206181	ENST00000332567	T	0.05025	3.51	0.195	-0.39	0.12450	Transcription factor IIS, N-terminal (2);	14.105800	0.01474	N	0.016384	T	0.00073	0.0002	N	0.00788	-1.185	0.80722	P	0.0	B	0.15141	0.012	B	0.08055	0.003	T	0.36601	-0.9741	8	0.02654	T	1	1.0064	.	.	.	rs61738602	6	Q8IYF1	ELOA2_HUMAN	S	6	ENSP00000331302:T6S	ENSP00000331302:T6S	T	-	2	0	TCEB3B	42815617	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.886000	0.01619	-2.617000	0.00442	-2.620000	0.00156	ACT	C|0.074;G|0.926;T|0.000	0.074	strong		0.617	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
ZNF845	91664	hgsc.bcm.edu	37	19	53856349	53856349	+	Missense_Mutation	SNP	A	A	T	rs55874600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:53856349A>T	ENST00000595091.1	+	5	2640	c.2421A>T	c.(2419-2421)gaA>gaT	p.E807D	ZNF845_ENST00000458035.1_Missense_Mutation_p.E807D			Q96IR2	ZN845_HUMAN	zinc finger protein 845	807				E -> D (in Ref. 3; AAH07307). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AGTGTAATGAATGTGGCAAGA	0.413													.|||	1021	0.203874	0.0431	0.2421	5008	,	,		22336	0.1052		0.3946	False		,,,				2504	0.2996				p.E807D		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2421T						PASS	.	A	ASP/GLU	121,1263		6,109,577	54.0	49.0	51.0		2421	-4.2	0.0	19	dbSNP_129	51	1299,1883		268,763,560	no	missense	ZNF845	NM_138374.1	45	274,872,1137	TT,TA,AA		40.8234,8.7428,31.0994	possibly-damaging	807/971	53856349	1420,3146	692	1591	2283	SO:0001583	missense	91664	exon4			TAATGAATGTGGC	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2421A>T	19.37:g.53856349A>T	ENSP00000470005:p.Glu807Asp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	473	0.21657509157509158	26	0.052845528455284556	91	0.2513812154696133	45	0.07867132867132867	311	0.4102902374670185	A	8.112	0.779021	0.16120	0.087428	0.408234	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.41758	0.99	2.1	-4.2	0.03823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.17631	0.505	0.80722	P	0.0	P	0.36647	0.563	B	0.43082	0.407	T	0.39583	-0.9607	8	0.38643	T	0.18	.	4.309	0.10962	0.4866:0.0:0.3554:0.1579	rs55874600;rs62115344	807	Q96IR2	ZN845_HUMAN	D	807;723	ENSP00000388311:E807D	ENSP00000412086:E723D	E	+	3	2	ZNF845	58548161	0.000000	0.05858	0.000000	0.03702	0.063000	0.16089	-6.159000	0.00078	-0.620000	0.05641	-0.650000	0.03912	GAA	A|0.782;T|0.218	0.218	strong		0.413	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
NR6A1	2649	hgsc.bcm.edu	37	9	127300464	127300464	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:127300464C>T	ENST00000487099.2	-	6	888	c.731G>A	c.(730-732)cGc>cAc	p.R244H	NR6A1_ENST00000416460.2_Missense_Mutation_p.R239H|NR6A1_ENST00000373584.3_Missense_Mutation_p.R240H|NR6A1_ENST00000344523.4_Missense_Mutation_p.R243H	NM_001278546.1	NP_001265475.1	Q15406	NR6A1_HUMAN	nuclear receptor subfamily 6, group A, member 1	244	Sufficient for interaction with UIMC1. {ECO:0000250}.				cell proliferation (GO:0008283)|gamete generation (GO:0007276)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(1)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	17						ATCCAGGCTGCGAGCTTGTTG	0.512																																					p.R244H	Esophageal Squamous(192;272 2884 6208 20560)	Atlas-SNP	.											NR6A1,NS,carcinoma,-1,1	NR6A1	38	1	0			c.G731A						scavenged	.						147.0	137.0	140.0					9																	127300464		2203	4300	6503	SO:0001583	missense	2649	exon6			AGGCTGCGAGCTT	U64876	CCDS35137.1, CCDS55340.1, CCDS65127.1	9q33.3	2014-01-21			ENSG00000148200	ENSG00000148200		"""Nuclear hormone receptors"""	7985	protein-coding gene	gene with protein product		602778		GCNF		9134503, 8982251	Standard	NM_001489		Approved	GCNF1, RTR, CT150	uc004bor.1	Q15406	OTTHUMG00000020661	ENST00000487099.2:c.731G>A	9.37:g.127300464C>T	ENSP00000420267:p.Arg244His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	108	2	0.0185185	NM_033334	O00551|O00603|Q5T6F4|Q8NHQ0|Q92898|Q99802	Missense_Mutation	SNP	ENST00000487099.2	37	CCDS35137.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.515050	0.64634	.	.	ENSG00000148200	ENST00000487099;ENST00000373584;ENST00000416460;ENST00000344523;ENST00000475178	D;D;D;D;D	0.94687	-3.1;-3.22;-3.22;-3.1;-3.49	5.39	5.39	0.77823	Nuclear hormone receptor, ligand-binding (1);	0.000000	0.85682	D	0.000000	D	0.94997	0.8381	L	0.44542	1.39	0.80722	D	1	D;D;P	0.71674	0.998;0.998;0.584	P;P;B	0.57101	0.813;0.771;0.059	D	0.94658	0.7845	10	0.45353	T	0.12	.	18.1297	0.89597	0.0:1.0:0.0:0.0	.	240;244;239	F1DAM1;Q15406;Q15406-5	.;NR6A1_HUMAN;.	H	244;240;239;243;202	ENSP00000420267:R244H;ENSP00000362686:R240H;ENSP00000413701:R239H;ENSP00000341135:R243H;ENSP00000420587:R202H	ENSP00000341135:R243H	R	-	2	0	NR6A1	126340285	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.434000	0.80377	2.529000	0.85273	0.561000	0.74099	CGC	.	.	none		0.512	NR6A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054043.4		
NSUN4	387338	hgsc.bcm.edu	37	1	46827456	46827456	+	Missense_Mutation	SNP	A	A	G	rs9865	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46827456A>G	ENST00000474844.1	+	6	1743	c.1093A>G	c.(1093-1095)Ata>Gta	p.I365V	NSUN4_ENST00000537428.1_Missense_Mutation_p.I316V|NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000536062.1_Missense_Mutation_p.I316V	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	365			I -> V (in dbSNP:rs9865). {ECO:0000269|PubMed:14702039}.		rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					GGAGCTGGTAATACCAAACCT	0.453													A|||	1020	0.203674	0.0552	0.1254	5008	,	,		24169	0.2798		0.1501	False		,,,				2504	0.4366				p.I365V		Atlas-SNP	.											.	NSUN4	26	.	0			c.A1093G						PASS	.	A	VAL/ILE	281,4125	157.4+/-190.3	8,265,1930	172.0	163.0	166.0		1093	3.0	1.0	1	dbSNP_52	166	1160,7440	237.5+/-269.3	76,1008,3216	yes	missense	NSUN4	NM_199044.2	29	84,1273,5146	GG,GA,AA		13.4884,6.3777,11.0795	benign	365/385	46827456	1441,11565	2203	4300	6503	SO:0001583	missense	387338	exon6			CTGGTAATACCAA	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"""NOP2/Sun domain containing"""	31802	protein-coding gene	gene with protein product	"""sperm head and tail associated protein"""	615394	"""NOL1/NOP2/Sun domain family 4"", ""NOL1/NOP2/Sun domain family, member 4"""				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.1093A>G	1.37:g.46827456A>G	ENSP00000419740:p.Ile365Val	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	290	154	0.531034	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Missense_Mutation	SNP	ENST00000474844.1	37	CCDS534.1	343	0.15705128205128205	21	0.042682926829268296	50	0.13812154696132597	173	0.30244755244755245	99	0.13060686015831136	A	10.53	1.375749	0.24857	0.063777	0.134884	ENSG00000117481	ENST00000474844;ENST00000536062;ENST00000537428	T;T;T	0.09073	3.02;3.02;3.02	5.43	3.01	0.34805	.	0.293446	0.35407	N	0.003224	T	0.00012	0.0000	L	0.31845	0.965	0.30466	P	0.773765	B;B	0.06786	0.001;0.001	B;B	0.09377	0.002;0.004	T	0.48175	-0.9058	9	0.27082	T	0.32	-9.8212	6.6119	0.22757	0.5345:0.3487:0.0:0.1167	rs9865;rs3170821;rs58670940;rs9865	232;365	B3KUM0;Q96CB9	.;NSUN4_HUMAN	V	365;316;316	ENSP00000419740:I365V;ENSP00000438912:I316V;ENSP00000437758:I316V	ENSP00000419740:I365V	I	+	1	0	NSUN4	46600043	0.991000	0.36638	1.000000	0.80357	0.993000	0.82548	1.173000	0.31920	1.038000	0.40049	0.533000	0.62120	ATA	A|0.862;G|0.138	0.138	strong		0.453	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
LENG1	79165	hgsc.bcm.edu	37	19	54662043	54662043	+	Missense_Mutation	SNP	C	C	T	rs35089861	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54662043C>T	ENST00000222224.3	-	2	475	c.289G>A	c.(289-291)Gag>Aag	p.E97K		NM_024316.1	NP_077292.1	Q96BZ8	LENG1_HUMAN	leukocyte receptor cluster (LRC) member 1	97			E -> K (in dbSNP:rs35089861).							breast(1)|endometrium(3)|large_intestine(2)|lung(1)|ovary(1)	8	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					TTTTCTTCCTCGTACTCTTTA	0.557													C|||	87	0.0173722	0.0023	0.0245	5008	,	,		17925	0.001		0.0616	False		,,,				2504	0.0041				p.E97K		Atlas-SNP	.											.	LENG1	19	.	0			c.G289A						PASS	.	C	LYS/GLU	30,4376	36.0+/-67.5	0,30,2173	188.0	160.0	169.0		289	5.1	1.0	19	dbSNP_126	169	465,8135	138.4+/-195.2	13,439,3848	yes	missense	LENG1	NM_024316.1	56	13,469,6021	TT,TC,CC		5.407,0.6809,3.8059	probably-damaging	97/265	54662043	495,12511	2203	4300	6503	SO:0001583	missense	79165	exon2			CTTCCTCGTACTC	AF211966	CCDS12881.1	19q13.4	2008-02-05			ENSG00000105617	ENSG00000105617			15502	protein-coding gene	gene with protein product						10941842	Standard	NM_024316		Approved		uc002qdm.3	Q96BZ8	OTTHUMG00000066486	ENST00000222224.3:c.289G>A	19.37:g.54662043C>T	ENSP00000222224:p.Glu97Lys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	139	56	0.402878	NM_024316	Q9HCU7	Missense_Mutation	SNP	ENST00000222224.3	37	CCDS12881.1	57	0.0260989010989011	0	0.0	8	0.022099447513812154	0	0.0	49	0.06464379947229551	C	31	5.072531	0.93950	0.006809	0.05407	ENSG00000105617	ENST00000222224	T	0.54479	0.57	5.14	5.14	0.70334	.	0.130543	0.51477	D	0.000081	T	0.26011	0.0634	M	0.93328	3.405	0.49299	D	0.999772	D	0.56287	0.975	P	0.50136	0.632	T	0.68161	-0.5482	10	0.59425	D	0.04	-31.1333	17.8251	0.88662	0.0:1.0:0.0:0.0	rs35089861;rs35089861	97	Q96BZ8	LENG1_HUMAN	K	97	ENSP00000222224:E97K	ENSP00000222224:E97K	E	-	1	0	LENG1	59353855	0.993000	0.37304	0.954000	0.39281	0.978000	0.69477	3.341000	0.52151	2.578000	0.87016	0.650000	0.86243	GAG	C|0.964;T|0.036	0.036	strong		0.557	LENG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142159.1	NM_024316	
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 GAIIx	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	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	63	10	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	
CERS2	29956	hgsc.bcm.edu	37	1	150940625	150940625	+	Missense_Mutation	SNP	T	T	G	rs267738	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:150940625T>G	ENST00000271688.6	-	4	730	c.344A>C	c.(343-345)gAg>gCg	p.E115A	CERS2_ENST00000345896.4_5'UTR|CERS2_ENST00000368954.5_Missense_Mutation_p.E115A|RP11-316M1.12_ENST00000561111.1_RNA|RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000561294.1_Missense_Mutation_p.E106A	NM_181746.3	NP_859530.1	Q96G23	CERS2_HUMAN	ceramide synthase 2	115			E -> A (in dbSNP:rs267738).		ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GAACCAACGCTCTACCTGGCG	0.607													T|||	341	0.0680911	0.0061	0.0951	5008	,	,		16202	0.0258		0.1909	False		,,,				2504	0.0501				p.E115A		Atlas-SNP	.											LASS2,colon,carcinoma,0,1	.	.	1	0			c.A344C						scavenged	.	T	ALA/GLU,ALA/GLU	176,4230	115.4+/-153.4	1,174,2028	67.0	73.0	71.0		344,344	4.9	1.0	1	dbSNP_79	71	1821,6779	325.8+/-317.1	200,1421,2679	yes	missense,missense	CERS2	NM_022075.4,NM_181746.3	107,107	201,1595,4707	GG,GT,TT		21.1744,3.9946,15.3545	probably-damaging,probably-damaging	115/381,115/381	150940625	1997,11009	2203	4300	6503	SO:0001583	missense	29956	exon4			CAACGCTCTACCT	AF189062	CCDS973.1	1q21.3	2012-09-20	2011-07-08	2011-07-08	ENSG00000143418	ENSG00000143418		"""Homeoboxes / CERS class"""	14076	protein-coding gene	gene with protein product		606920	"""longevity assurance (LAG1, S. cerevisiae) homolog 2"", ""LAG1 longevity assurance homolog 2 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 2"""	LASS2		11543633	Standard	NM_181746		Approved	SP260, FLJ10243	uc001evz.3	Q96G23	OTTHUMG00000035064	ENST00000271688.6:c.344A>C	1.37:g.150940625T>G	ENSP00000271688:p.Glu115Ala	Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	NM_022075	D3DV06|Q5SZE5|Q9HD96|Q9NW79	Missense_Mutation	SNP	ENST00000271688.6	37	CCDS973.1	217	0.09935897435897435	4	0.008130081300813009	40	0.11049723756906077	19	0.033216783216783216	154	0.20316622691292877	T	32	5.158232	0.94686	0.039946	0.211744	ENSG00000143418	ENST00000368954;ENST00000271688;ENST00000368949;ENST00000361419;ENST00000421609;ENST00000457392	D;D;D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89;-3.89;-3.89	4.9	4.9	0.64082	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.115318	0.64402	D	0.000015	D	0.95915	0.8670	M	0.81942	2.565	0.09310	P	0.999999635895	P	0.45634	0.863	P	0.54590	0.756	D	0.95090	0.8221	9	0.30078	T	0.28	-19.5384	14.3739	0.66860	0.0:0.0:0.0:1.0	rs267738;rs556626;rs56588434;rs60175401;rs267738	115	Q96G23	CERS2_HUMAN	A	115;115;135;115;115;115	ENSP00000357950:E115A;ENSP00000271688:E115A;ENSP00000357945:E135A;ENSP00000355020:E115A;ENSP00000393239:E115A;ENSP00000394012:E115A	ENSP00000271688:E115A	E	-	2	0	CERS2	149207249	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.460000	0.80816	2.058000	0.61347	0.533000	0.62120	GAG	T|0.878;G|0.122	0.122	strong		0.607	CERS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084897.2	NM_022075	
PROSER3	148137	hgsc.bcm.edu	37	19	36258842	36258842	+	Missense_Mutation	SNP	G	G	C	rs231217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36258842G>C	ENST00000544099.1	+	9	1158	c.1095G>C	c.(1093-1095)aaG>aaC	p.K365N	C19orf55_ENST00000396908.4_Missense_Mutation_p.K365N|AC002398.13_ENST00000589397.1_RNA			Q2NL68	PRSR3_HUMAN		365			K -> N (in dbSNP:rs231217).							cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCACAGTCAAGGCCTCGCCGC	0.716													G|||	510	0.101837	0.0915	0.1009	5008	,	,		12837	0.0744		0.1203	False		,,,				2504	0.1258				p.K365N		Atlas-SNP	.											.	C19orf55	39	.	0			c.G1095C						PASS	.	G	ASN/LYS	402,3532		21,360,1586	16.0	19.0	18.0		1095	0.6	0.0	19	dbSNP_79	18	865,7435		38,789,3323	yes	missense	C19orf55	NM_001039887.2	94	59,1149,4909	CC,CG,GG		10.4217,10.2186,10.3564	probably-damaging	365/481	36258842	1267,10967	1967	4150	6117	SO:0001583	missense	148137	exon9			AGTCAAGGCCTCG																												ENST00000544099.1:c.1095G>C	19.37:g.36258842G>C	ENSP00000467267:p.Lys365Asn	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000544099.1	37		216	0.0989010989010989	45	0.09146341463414634	37	0.10220994475138122	38	0.06643356643356643	96	0.1266490765171504	G	10.46	1.357114	0.24598	0.102186	0.104217	ENSG00000167595	ENST00000396908	T	0.33865	1.39	2.8	0.609	0.17575	.	.	.	.	.	T	0.00271	0.0008	L	0.50333	1.59	0.80722	P	0.0	B	0.32160	0.358	B	0.32864	0.154	T	0.10405	-1.0631	8	0.29301	T	0.29	0.5901	4.6861	0.12758	0.3155:0.0:0.6845:0.0	rs231217;rs59022087	365	E5RFB9	.	N	365	ENSP00000380116:K365N	ENSP00000380116:K365N	K	+	3	2	C19orf55	40950682	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.184000	0.16939	0.239000	0.21243	0.467000	0.42956	AAG	G|0.901;C|0.099	0.099	strong		0.716	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		
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 GAIIx	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	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	34	3	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	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011298	46011298	+	Silent	SNP	G	G	A	rs113437209	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46011298G>A	ENST00000400368.1	-	1	1088	c.1068C>T	c.(1066-1068)agC>agT	p.S356S	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	356						keratin filament (GO:0045095)		p.S356S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CAGAGCAGAGGCTGTAGCAGG	0.677																																					p.S356S		Atlas-SNP	.											KRTAP10-6,NS,carcinoma,0,1	KRTAP10-6	57	1	1	Substitution - coding silent(1)	stomach(1)	c.C1068T						scavenged	.						29.0	38.0	35.0					21																	46011298		2194	4298	6492	SO:0001819	synonymous_variant	386674	exon1			GCAGAGGCTGTAG	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.1068C>T	21.37:g.46011298G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	196	5	0.0255102	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			A|1.000;|0.000	1.000	weak		0.677	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
WDR81	124997	hgsc.bcm.edu	37	17	1637302	1637302	+	Silent	SNP	A	A	G	rs587780505|rs3809872	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1637302A>G	ENST00000409644.1	+	7	4971	c.4971A>G	c.(4969-4971)ctA>ctG	p.L1657L	WDR81_ENST00000419248.1_Silent_p.L430L|WDR81_ENST00000545662.1_Silent_p.L288L|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.L606L|WDR81_ENST00000446363.1_Silent_p.L296L|WDR81_ENST00000437219.2_Silent_p.L454L	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1657					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TGGCACCCCTAAGCAGCGAGG	0.662													G|||	3818	0.76238	0.7148	0.7089	5008	,	,		15982	0.9157		0.7137	False		,,,				2504	0.7566				p.L1657L		Atlas-SNP	.											.	WDR81	180	.	0			c.A4971G						PASS	.	G	,,,	3176,1230	417.0+/-337.8	1145,886,172	63.0	61.0	62.0		1362,4971,1290,1818	4.2	1.0	17	dbSNP_107	62	6224,2372	387.3+/-342.2	2239,1746,313	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	3384,2632,485	GG,GA,AA		27.5942,27.9165,27.7034	,,,	454/739,1657/1942,430/715,606/891	1637302	9400,3602	2203	4298	6501	SO:0001819	synonymous_variant	124997	exon7			ACCCCTAAGCAGC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.4971A>G	17.37:g.1637302A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	84	33	0.392857	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			A|0.257;G|0.743	0.743	strong		0.662	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
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 GAIIx	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		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	41	17	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	
PITRM1	10531	hgsc.bcm.edu	37	10	3207632	3207632	+	Missense_Mutation	SNP	A	A	G	rs3814596	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:3207632A>G	ENST00000224949.4	-	5	540	c.506T>C	c.(505-507)tTc>tCc	p.F169S	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.F169S|PITRM1_ENST00000451104.2_Missense_Mutation_p.F137S			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	169			F -> S (in dbSNP:rs3814596). {ECO:0000269|PubMed:10360838}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						TAAACATGGGAAAAAGGTGGC	0.383													A|||	667	0.133187	0.1407	0.1066	5008	,	,		18416	0.0526		0.1869	False		,,,				2504	0.1697				p.F169S		Atlas-SNP	.											PITRM1,colon,carcinoma,0,1	PITRM1	109	1	0			c.T506C						scavenged	.	A	SER/PHE,SER/PHE,SER/PHE	523,3215		49,425,1395	98.0	99.0	99.0		506,410,506	5.4	0.8	10	dbSNP_107	99	1599,6625		159,1281,2672	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	155,155,155	208,1706,4067	GG,GA,AA		19.4431,13.9914,17.7395	possibly-damaging,possibly-damaging,possibly-damaging	169/1039,137/940,169/1038	3207632	2122,9840	1869	4112	5981	SO:0001583	missense	10531	exon5			CATGGGAAAAAGG	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.506T>C	10.37:g.3207632A>G	ENSP00000224949:p.Phe169Ser	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	274	0.12545787545787546	60	0.12195121951219512	42	0.11602209944751381	29	0.050699300699300696	143	0.18865435356200527	a	17.90	3.501492	0.64298	0.139914	0.194431	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000451104	T;T;T	0.27104	1.69;1.69;1.69	5.37	5.37	0.77165	Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);Peptidase M16, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	M	0.79693	2.465	0.09310	P	0.99999623526	B;B;P;P;P	0.41498	0.377;0.11;0.708;0.752;0.752	B;B;P;P;P	0.53760	0.146;0.215;0.615;0.734;0.734	T	0.01105	-1.1450	9	0.33141	T	0.24	.	15.4166	0.74974	1.0:0.0:0.0:0.0	rs3814596;rs52789691;rs57308152;rs3814596	162;137;169;169;169	E9PDX6;E7ES23;Q5JRX3-2;C9JSL2;Q5JRX3	.;.;.;.;PREP_HUMAN	S	169;162;169;137	ENSP00000224949:F169S;ENSP00000370377:F169S;ENSP00000401201:F137S	ENSP00000224949:F169S	F	-	2	0	PITRM1	3197632	1.000000	0.71417	0.829000	0.32907	0.889000	0.51656	8.663000	0.91134	2.037000	0.60232	0.477000	0.44152	TTC	A|0.857;G|0.143	0.143	strong		0.383	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
OR5P2	120065	hgsc.bcm.edu	37	11	7817538	7817538	+	Missense_Mutation	SNP	T	T	C	rs7949771	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7817538T>C	ENST00000329434.2	-	1	982	c.952A>G	c.(952-954)Aat>Gat	p.N318D	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	318			N -> D (in dbSNP:rs7949771).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATATCATTATTTGAAGTTCTA	0.358													T|||	1185	0.236621	0.3472	0.2911	5008	,	,		18403	0.128		0.2763	False		,,,				2504	0.1196				p.N318D		Atlas-SNP	.											.	OR5P2	68	.	0			c.A952G						PASS	.	T	ASP/ASN	1362,2854		395,572,1141	89.0	125.0	113.0		952	-0.8	0.0	11	dbSNP_116	113	2420,6164		390,1640,2262	yes	missense	OR5P2	NM_153444.1	23	785,2212,3403	CC,CT,TT		28.192,32.3055,29.5469	possibly-damaging	318/323	7817538	3782,9018	2108	4292	6400	SO:0001583	missense	120065	exon1			CATTATTTGAAGT	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.952A>G	11.37:g.7817538T>C	ENSP00000331823:p.Asn318Asp	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	587	0.26877289377289376	180	0.36585365853658536	100	0.27624309392265195	85	0.1486013986013986	222	0.2928759894459103	T	1.029	-0.682344	0.03353	0.323055	0.28192	ENSG00000183303	ENST00000329434	T	0.00036	8.86	4.92	-0.787	0.10943	.	1.021990	0.07869	N	0.967611	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22604	0.072	B	0.14023	0.01	T	0.00068	-1.2139	9	0.30078	T	0.28	-0.4362	6.1083	0.20086	0.3063:0.137:0.0:0.5567	rs7949771;rs7949771	318	Q8WZ92	OR5P2_HUMAN	D	318	ENSP00000331823:N318D	ENSP00000331823:N318D	N	-	1	0	OR5P2	7774114	.	.	0.000000	0.03702	0.002000	0.02628	.	.	0.072000	0.16694	-0.425000	0.05940	AAT	T|0.748;C|0.252	0.252	strong		0.358	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
FMN2	56776	hgsc.bcm.edu	37	1	240371112	240371112	+	Silent	SNP	G	G	T	rs71646889	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:240371112G>T	ENST00000319653.9	+	5	3230	c.3000G>T	c.(2998-3000)ccG>ccT	p.P1000P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1000	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1143P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACCCCCTCCGCCCCCACTTC	0.716													G|||	1341	0.267772	0.357	0.1873	5008	,	,		4654	0.2927		0.2008	False		,,,				2504	0.2474				p.P1000P		Atlas-SNP	.											FMN2,NS,carcinoma,0,4	FMN2	451	4	1	Substitution - coding silent(1)	prostate(1)	c.G3000T						scavenged	.						4.0	6.0	6.0					1																	240371112		1774	3850	5624	SO:0001819	synonymous_variant	56776	exon5			CCCTCCGCCCCCA	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3000G>T	1.37:g.240371112G>T		Somatic	62	1	0.016129		WXS	Illumina HiSeq	Phase_I	51	13	0.254902	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			A|0.000;G|0.879;T|0.121	0.121	strong		0.716	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
AQP11	282679	hgsc.bcm.edu	37	11	77301341	77301341	+	Missense_Mutation	SNP	G	G	A	rs2276415	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77301341G>A	ENST00000313578.3	+	1	662	c.304G>A	c.(304-306)Ggc>Agc	p.G102S	AQP11_ENST00000528638.1_Intron	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	102			G -> S (in dbSNP:rs2276415).		endosomal lumen acidification (GO:0048388)|protein homooligomerization (GO:0051260)|proximal tubule development (GO:0072014)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			kidney(2)|large_intestine(1)|lung(5)	8	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			CAACCCGTGCGGCGTGATGAT	0.637													G|||	731	0.145966	0.1377	0.1902	5008	,	,		19940	0.1825		0.0964	False		,,,				2504	0.1391				p.G102S		Atlas-SNP	.											.	AQP11	14	.	0			c.G304A						PASS	.	G	SER/GLY	594,3806	258.0+/-262.2	40,514,1646	72.0	62.0	66.0		304	3.7	1.0	11	dbSNP_100	66	801,7783	187.3+/-234.6	34,733,3525	yes	missense	AQP11	NM_173039.2	56	74,1247,5171	AA,AG,GG		9.3313,13.5,10.744	probably-damaging	102/272	77301341	1395,11589	2200	4292	6492	SO:0001583	missense	282679	exon1			CCGTGCGGCGTGA	AB028147	CCDS8251.1	11q13.5	2008-02-05			ENSG00000178301	ENSG00000178301		"""Ion channels / Aquaporins"""	19940	protein-coding gene	gene with protein product		609914				16107722	Standard	NM_173039		Approved		uc001oyj.3	Q8NBQ7	OTTHUMG00000165194	ENST00000313578.3:c.304G>A	11.37:g.77301341G>A	ENSP00000318770:p.Gly102Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	88	0.897959	NM_173039		Missense_Mutation	SNP	ENST00000313578.3	37	CCDS8251.1	316	0.1446886446886447	74	0.15040650406504066	57	0.1574585635359116	113	0.19755244755244755	72	0.09498680738786279	G	17.49	3.402396	0.62288	0.135	0.093313	ENSG00000178301	ENST00000313578	D	0.84944	-1.92	5.54	3.68	0.42216	Aquaporin-like (2);	0.218216	0.47852	N	0.000215	T	0.00300	0.0009	M	0.63843	1.955	0.21762	P	0.99955712	P	0.52316	0.952	B	0.40602	0.334	T	0.07481	-1.0770	9	0.27082	T	0.32	-12.8909	9.8641	0.41131	0.2177:0.0:0.7823:0.0	rs2276415;rs52797374;rs59985599;rs2276415	102	Q8NBQ7	AQP11_HUMAN	S	102	ENSP00000318770:G102S	ENSP00000318770:G102S	G	+	1	0	AQP11	76978989	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.719000	0.47244	0.715000	0.32103	0.491000	0.48974	GGC	G|0.873;A|0.127	0.127	strong		0.637	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382582.1	NM_173039	
GPR144	347088	hgsc.bcm.edu	37	9	127217284	127217284	+	Missense_Mutation	SNP	G	G	A	rs77622235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:127217284G>A	ENST00000334810.1	+	7	1327	c.1327G>A	c.(1327-1329)Ggg>Agg	p.G443R				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	443					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)			central_nervous_system(1)|endometrium(3)	4						GGTGGCCCTCGGGGCTGGGGA	0.667													G|||	25	0.00499201	0.0	0.0058	5008	,	,		15897	0.0		0.0139	False		,,,				2504	0.0072				p.G443R		Atlas-SNP	.											.	GPR144	33	.	0			c.G1327A						PASS	.	G	ARG/GLY	6,1378		0,6,686	38.0	42.0	41.0		1327	3.0	0.0	9	dbSNP_132	41	67,3115		3,61,1527	yes	missense	GPR144	NM_001161808.1	125	3,67,2213	AA,AG,GG		2.1056,0.4335,1.5988	benign	443/964	127217284	73,4493	692	1591	2283	SO:0001583	missense	347088	exon7			GCCCTCGGGGCTG	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.1327G>A	9.37:g.127217284G>A	ENSP00000335156:p.Gly443Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	G	8.233	0.805098	0.16467	0.004335	0.021056	ENSG00000180264	ENST00000334810;ENST00000439837	T	0.47528	0.84	4.85	2.98	0.34508	.	.	.	.	.	T	0.15869	0.0382	L	0.43152	1.355	0.09310	N	1	P	0.40107	0.703	B	0.23716	0.048	T	0.04664	-1.0935	9	0.16896	T	0.51	.	8.1695	0.31247	0.1885:0.0:0.8115:0.0	.	443	Q7Z7M1	GP144_HUMAN	R	443;139	ENSP00000335156:G443R	ENSP00000335156:G443R	G	+	1	0	GPR144	126257105	0.145000	0.22656	0.003000	0.11579	0.080000	0.17528	1.557000	0.36299	0.547000	0.28938	0.561000	0.74099	GGG	G|0.990;A|0.010	0.010	strong		0.667	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
CENPJ	55835	hgsc.bcm.edu	37	13	25487103	25487103	+	Missense_Mutation	SNP	T	T	C	rs35498994	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25487103T>C	ENST00000381884.4	-	2	246	c.61A>G	c.(61-63)Atg>Gtg	p.M21V	CENPJ_ENST00000545981.1_Missense_Mutation_p.M21V	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	21			M -> V (in dbSNP:rs35498994).		cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		GGATTGGTCATCCACTGGGTT	0.433													T|||	777	0.155152	0.0794	0.1628	5008	,	,		18447	0.3462		0.1382	False		,,,				2504	0.0726				p.M21V		Atlas-SNP	.											.	CENPJ	116	.	0			c.A61G						PASS	.	T	VAL/MET	422,3984	207.8+/-229.1	25,372,1806	65.0	57.0	60.0		61	5.3	1.0	13	dbSNP_126	60	1162,7438	232.8+/-266.3	83,996,3221	yes	missense	CENPJ	NM_018451.3	21	108,1368,5027	CC,CT,TT		13.5116,9.5778,12.179	possibly-damaging	21/1339	25487103	1584,11422	2203	4300	6503	SO:0001583	missense	55835	exon2			TGGTCATCCACTG	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.61A>G	13.37:g.25487103T>C	ENSP00000371308:p.Met21Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	37	CCDS9310.1	390	0.17857142857142858	40	0.08130081300813008	50	0.13812154696132597	190	0.3321678321678322	110	0.14511873350923482	T	19.04	3.750856	0.69533	0.095778	0.135116	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	T;T	0.16743	2.32;2.32	5.28	5.28	0.74379	.	0.064543	0.64402	D	0.000004	T	0.00012	0.0000	M	0.78637	2.42	0.37049	P	0.10248000000000002	P	0.43431	0.807	B	0.35182	0.197	T	0.40850	-0.9541	9	0.87932	D	0	.	12.7331	0.57208	0.0:0.0:0.0:1.0	rs35498994;rs59706954	21	Q9HC77	CENPJ_HUMAN	V	21	ENSP00000371308:M21V;ENSP00000441090:M21V	ENSP00000371308:M21V	M	-	1	0	CENPJ	24385103	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.631000	0.46502	2.006000	0.58801	0.533000	0.62120	ATG	A|0.000;C|0.138;T|0.862	0.138	strong		0.433	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
GBP6	163351	hgsc.bcm.edu	37	1	89846152	89846152	+	Missense_Mutation	SNP	C	C	T	rs4582772	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:89846152C>T	ENST00000370456.4	+	6	926	c.833C>T	c.(832-834)aCc>aTc	p.T278I	GBP6_ENST00000535065.1_Missense_Mutation_p.T148I	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	278	GTPase domain (Globular). {ECO:0000250}.		T -> I (in dbSNP:rs4582772).		cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		CATGCAAGAACCAAGACCCTC	0.413													C|||	198	0.0395367	0.0045	0.0908	5008	,	,		18074	0.0		0.1203	False		,,,				2504	0.0082				p.T278I		Atlas-SNP	.											.	GBP6	87	.	0			c.C833T						PASS	.	C	ILE/THR	85,4321	70.9+/-108.8	2,81,2120	65.0	63.0	63.0		833	-0.3	0.1	1	dbSNP_111	63	938,7662	205.9+/-248.2	41,856,3403	yes	missense	GBP6	NM_198460.2	89	43,937,5523	TT,TC,CC		10.907,1.9292,7.8656	benign	278/634	89846152	1023,11983	2203	4300	6503	SO:0001583	missense	163351	exon6			CAAGAACCAAGAC	BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.833C>T	1.37:g.89846152C>T	ENSP00000359485:p.Thr278Ile	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	119	0.05448717948717949	1	0.0020325203252032522	40	0.11049723756906077	0	0.0	78	0.10290237467018469	C	7.099	0.573734	0.13623	0.019292	0.10907	ENSG00000183347	ENST00000544311;ENST00000370456;ENST00000535065	T;T	0.74002	-0.8;-0.8	4.8	-0.32	0.12721	Guanylate-binding protein, N-terminal (1);	1.288050	0.05235	N	0.511017	T	0.42314	0.1197	L	0.33792	1.035	0.58432	P	2.9999999999752447E-6	B	0.22909	0.077	B	0.21546	0.035	T	0.10177	-1.0641	9	0.28530	T	0.3	0.0055	8.6108	0.33801	0.0:0.5842:0.0:0.4157	rs4582772;rs17490113;rs4582772	278	Q6ZN66	GBP6_HUMAN	I	249;278;148	ENSP00000359485:T278I;ENSP00000442530:T148I	ENSP00000359485:T278I	T	+	2	0	GBP6	89618740	0.000000	0.05858	0.050000	0.19076	0.023000	0.10783	-0.671000	0.05250	-0.112000	0.11979	0.591000	0.81541	ACC	C|0.929;T|0.071	0.071	strong		0.413	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
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 GAIIx	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	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	88	6	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	
EPCAM	4072	hgsc.bcm.edu	37	2	47601106	47601106	+	Missense_Mutation	SNP	T	T	C	rs1126497|rs111849096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:47601106T>C	ENST00000263735.4	+	3	702	c.344T>C	c.(343-345)aTg>aCg	p.M115T	EPCAM_ENST00000405271.1_Missense_Mutation_p.M143T	NM_002354.2	NP_002345.2	P16422	EPCAM_HUMAN	epithelial cell adhesion molecule	115	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.		M -> T (in dbSNP:rs1126497). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2108441, ECO:0000269|PubMed:2463074, ECO:0000269|PubMed:2469722}.		negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|stem cell differentiation (GO:0048863)|ureteric bud development (GO:0001657)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	protein complex binding (GO:0032403)	p.0?(2)|p.?(1)		endometrium(3)|large_intestine(1)|liver(2)|lung(7)|skin(1)|stomach(1)	15						GGCACCTCCATGTGCTGGTGT	0.532													C|||	3336	0.666134	0.8888	0.5159	5008	,	,		17137	0.8323		0.4692	False		,,,				2504	0.5031				p.M115T		Atlas-SNP	.											.	EPCAM	27	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.T344C						PASS	.	C	THR/MET	3649,757	305.5+/-289.0	1530,589,84	74.0	69.0	70.0		344	1.7	0.4	2	dbSNP_86	70	3722,4878	618.5+/-396.8	801,2120,1379	yes	missense	EPCAM	NM_002354.2	81	2331,2709,1463	CC,CT,TT		43.2791,17.1811,43.3262	benign	115/315	47601106	7371,5635	2203	4300	6503	SO:0001583	missense	4072	exon3			CCTCCATGTGCTG	M33011	CCDS1833.1	2p21	2014-09-17	2008-12-16	2008-12-16	ENSG00000119888	ENSG00000119888		"""CD molecules"""	11529	protein-coding gene	gene with protein product		185535	"""antigen identified by monoclonal antibody AUA1"", ""tumor-associated calcium signal transducer 1"""	M4S1, MIC18, TACSTD1		8382772, 11306819	Standard	NM_002354		Approved	Ly74, TROP1, GA733-2, EGP34, EGP40, EGP-2, KSA, CD326, Ep-CAM, HEA125, KS1/4, MK-1, MH99, MOC31, 323/A3, 17-1A, TACST-1, CO-17A, ESA	uc002rvx.3	P16422	OTTHUMG00000128853	ENST00000263735.4:c.344T>C	2.37:g.47601106T>C	ENSP00000263735:p.Met115Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_002354	P18180|Q6FG26|Q6FG49|Q96C47|Q9UCD0	Missense_Mutation	SNP	ENST00000263735.4	37	CCDS1833.1	1440	0.6593406593406593	437	0.8882113821138211	182	0.5027624309392266	460	0.8041958041958042	361	0.4762532981530343	C	3.317	-0.139650	0.06669	0.828189	0.432791	ENSG00000119888	ENST00000405271;ENST00000263735;ENST00000419334	T;T;T	0.62105	0.05;0.05;0.05	5.93	1.71	0.24356	Thyroglobulin type-1 (6);	0.527053	0.22416	N	0.060350	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44251	-0.9340	9	0.02654	T	1	-4.742	11.8944	0.52648	0.0:0.6732:0.0:0.3268	rs1126497;rs3181550;rs17845436;rs17858308;rs52820371;rs57528354;rs1126497	115;143	P16422;B5MCA4	EPCAM_HUMAN;.	T	143;115;191	ENSP00000385476:M143T;ENSP00000263735:M115T;ENSP00000389028:M191T	ENSP00000263735:M115T	M	+	2	0	EPCAM	47454610	0.325000	0.24660	0.371000	0.25978	0.878000	0.50629	0.040000	0.13905	0.160000	0.19432	-0.119000	0.15052	ATG	T|0.385;C|0.615	0.615	strong		0.532	EPCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250792.2		
ABCA13	154664	hgsc.bcm.edu	37	7	48547511	48547511	+	Missense_Mutation	SNP	C	C	A	rs78634768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48547511C>A	ENST00000435803.1	+	50	13414	c.13390C>A	c.(13390-13392)Ctg>Atg	p.L4464M	ABCA13_ENST00000544596.1_Missense_Mutation_p.L194M	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4464					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						CTGCATCGTGCTGGGATTCTC	0.572													C|||	20	0.00399361	0.0008	0.0072	5008	,	,		20071	0.0		0.0139	False		,,,				2504	0.0				p.L4464M		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C13390A						PASS	.	C	MET/LEU	12,4246		0,12,2117	75.0	76.0	76.0		13390	3.6	1.0	7	dbSNP_131	76	91,8405		1,89,4158	yes	missense	ABCA13	NM_152701.3	15	1,101,6275	AA,AC,CC		1.0711,0.2818,0.8076	possibly-damaging	4464/5059	48547511	103,12651	2129	4248	6377	SO:0001583	missense	154664	exon50			ATCGTGCTGGGAT	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.13390C>A	7.37:g.48547511C>A	ENSP00000411096:p.Leu4464Met	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	95	59	0.621053	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	25|25	0.011446886446886446|0.011446886446886446	2|2	0.0040650406504065045|0.0040650406504065045	5|5	0.013812154696132596|0.013812154696132596	3|3	0.005244755244755245|0.005244755244755245	15|15	0.01978891820580475|0.01978891820580475	C|C	17.85|17.85	3.490833|3.490833	0.64074|0.64074	0.002818|0.002818	0.010711|0.010711	ENSG00000179869|ENSG00000179869	ENST00000435451|ENST00000435803;ENST00000411975;ENST00000544596	.|D;D;D	.|0.87809	.|-2.3;-2.3;-2.3	5.5|5.5	3.6|3.6	0.41247|0.41247	.|.	.|0.000000	.|0.40385	.|N	.|0.001110	D|D	0.82449|0.82449	0.5039|0.5039	L|L	0.50333|0.50333	1.59|1.59	0.35346|0.35346	D|D	0.786962|0.786962	.|P;D;D	.|0.89917	.|0.729;1.0;1.0	.|B;D;D	.|0.97110	.|0.343;0.995;1.0	D|D	0.85916|0.85916	0.1443|0.1443	5|10	.|0.30078	.|T	.|0.28	.|.	8.6054|8.6054	0.33769|0.33769	0.0:0.8104:0.0:0.1896|0.0:0.8104:0.0:0.1896	.|.	.|194;2166;4464	.|F5H7B7;Q86UQ4-3;Q86UQ4	.|.;.;ABCAD_HUMAN	D|M	15|4464;237;194	.|ENSP00000411096:L4464M;ENSP00000391042:L237M;ENSP00000442634:L194M	.|ENSP00000391042:L237M	A|L	+|+	2|1	0|2	ABCA13|ABCA13	48518057|48518057	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.998000|0.998000	0.95712|0.95712	0.886000|0.886000	0.28241|0.28241	1.209000|1.209000	0.43321|0.43321	0.650000|0.650000	0.86243|0.86243	GCT|CTG	C|0.989;A|0.011	0.011	strong		0.572	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
XIAP	331	hgsc.bcm.edu	37	X	123034511	123034511	+	Missense_Mutation	SNP	A	A	C	rs5956583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:123034511A>C	ENST00000371199.3	+	6	1567	c.1268A>C	c.(1267-1269)cAa>cCa	p.Q423P	XIAP_ENST00000468691.1_3'UTR|XIAP_ENST00000355640.3_Missense_Mutation_p.Q423P|XIAP_ENST00000434753.3_Missense_Mutation_p.Q423P	NM_001167.3	NP_001158.2	P98170	XIAP_HUMAN	X-linked inhibitor of apoptosis	423			Q -> P (in dbSNP:rs5956583). {ECO:0000269|PubMed:8654366, ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|copper ion homeostasis (GO:0055070)|inhibition of cysteine-type endopeptidase activity involved in apoptotic process (GO:1990001)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of protein ubiquitination (GO:0031398)|protein ubiquitination (GO:0016567)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell proliferation (GO:0042127)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)	25						GACAGTATGCAAGATGAGTCA	0.393									X-linked Lymphoproliferative syndrome				A|||	1146	0.303576	0.3722	0.2954	3775	,	,		14242	0.0655		0.2893	False		,,,				2504	0.0941				p.Q423P		Atlas-SNP	.											.	XIAP	56	.	0			c.A1268C						PASS	.	A	PRO/GLN,PRO/GLN	1810,2025		382,778,268,472,303	85.0	79.0	81.0		1268,1268	4.6	0.3	X	dbSNP_114	81	2379,4349		317,1104,641,1007,1231	yes	missense,missense	XIAP	NM_001167.3,NM_001204401.1	76,76	699,1882,909,1479,1534	CC,CA,C,AA,A		35.3597,47.1969,39.6573	benign,benign	423/498,423/498	123034511	4189,6374	2203	4300	6503	SO:0001583	missense	331	exon6	Familial Cancer Database	XLP, Duncan syndrome, Familial Fatal Epstein-Barr Infection, incl. XLP2	GTATGCAAGATGA	U45880	CCDS14606.1	Xq25	2014-09-17	2008-03-04	2008-03-04	ENSG00000101966	ENSG00000101966		"""Baculoviral IAP repeat containing"""	592	protein-coding gene	gene with protein product		300079	"""baculoviral IAP repeat-containing 4"""	API3, BIRC4		8552191, 8654366	Standard	NM_001167		Approved	hILP	uc010nqu.3	P98170	OTTHUMG00000022336	ENST00000371199.3:c.1268A>C	X.37:g.123034511A>C	ENSP00000360242:p.Gln423Pro	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	302	76	0.251656	NM_001204401	D3DTF2|Q9NQ14	Missense_Mutation	SNP	ENST00000371199.3	37	CCDS14606.1	540	0.325497287522604	125	0.32216494845360827	83	0.27483443708609273	24	0.043795620437956206	156	0.24299065420560748	a	6.132	0.392630	0.11638	0.471969	0.353597	ENSG00000101966	ENST00000434753;ENST00000371199;ENST00000355640	T;T;T	0.30448	1.53;1.53;1.53	4.61	4.61	0.57282	.	0.660669	0.14278	N	0.329725	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.42015	-0.9476	9	0.66056	D	0.02	-2.7599	7.8327	0.29353	0.8127:0.0:0.0:0.1873	rs5956583;rs17259511;rs52834392;rs5956583	423	P98170	XIAP_HUMAN	P	423	ENSP00000395230:Q423P;ENSP00000360242:Q423P;ENSP00000347858:Q423P	ENSP00000347858:Q423P	Q	+	2	0	XIAP	122862192	0.367000	0.25023	0.288000	0.24862	0.259000	0.26198	2.079000	0.41577	1.709000	0.51313	0.350000	0.21858	CAA	A|0.624;0|0.022	.	strong		0.393	XIAP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058165.5	NM_001167	
FAM35A	54537	hgsc.bcm.edu	37	10	88911841	88911841	+	Missense_Mutation	SNP	A	A	G	rs77879311	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:88911841A>G	ENST00000298784.1	+	3	844	c.730A>G	c.(730-732)Agt>Ggt	p.S244G	FAM35A_ENST00000298786.4_Missense_Mutation_p.S244G|RN7SL733P_ENST00000582253.1_RNA	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	244										endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						AGAATTTCTCAGTATAATTAC	0.383													A|||	747	0.149161	0.2466	0.1009	5008	,	,		19063	0.0218		0.169	False		,,,				2504	0.1626				p.S244G	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											.	FAM35A	48	.	0			c.A730G						PASS	.	A	GLY/SER	910,3496		95,720,1388	30.0	30.0	30.0		730	4.1	0.9	10	dbSNP_131	30	1339,7255		95,1149,3053	no	missense	FAM35A	NM_019054.2	56	190,1869,4441	GG,GA,AA		15.5806,20.6537,17.3	probably-damaging	244/836	88911841	2249,10751	2203	4297	6500	SO:0001583	missense	54537	exon3			TTTCTCAGTATAA	BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.730A>G	10.37:g.88911841A>G	ENSP00000298784:p.Ser244Gly	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	283	0.1295787545787546	99	0.20121951219512196	39	0.10773480662983426	10	0.017482517482517484	135	0.17810026385224276	a	16.76	3.211731	0.58452	0.206537	0.155806	ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313	T;T;T	0.30714	1.53;1.52;1.52	4.09	4.09	0.47781	.	0.268115	0.31963	N	0.006794	T	0.00039	0.0001	M	0.71581	2.175	0.29511	P	0.8541799999999999	D	0.60160	0.987	P	0.61533	0.89	T	0.06661	-1.0814	9	0.72032	D	0.01	-3.893	8.8322	0.35091	0.8326:0.0:0.0:0.1674	.	244	Q86V20	FA35A_HUMAN	G	244	ENSP00000298786:S244G;ENSP00000298784:S244G;ENSP00000351064:S244G	ENSP00000298784:S244G	S	+	1	0	FAM35A	88901821	1.000000	0.71417	0.854000	0.33618	0.963000	0.63663	4.382000	0.59594	1.733000	0.51620	0.438000	0.28831	AGT	A|0.850;G|0.150	0.150	strong		0.383	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054	
FBXO34	55030	hgsc.bcm.edu	37	14	55817708	55817708	+	Silent	SNP	T	T	C	rs10144418	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:55817708T>C	ENST00000313833.4	+	2	845	c.600T>C	c.(598-600)taT>taC	p.Y200Y	FBXO34_ENST00000440021.1_Silent_p.Y200Y	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	200								p.Y200Y(1)		breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						ATGGAGTCTATGCTGGGAGGC	0.502													T|||	1597	0.31889	0.2073	0.3012	5008	,	,		22020	0.3185		0.4155	False		,,,				2504	0.3834				p.Y200Y		Atlas-SNP	.											FBXO34,NS,carcinoma,0,1	FBXO34	61	1	1	Substitution - coding silent(1)	stomach(1)	c.T600C						PASS	.	T	,	1078,3328	392.1+/-328.4	130,818,1255	103.0	90.0	95.0		600,600	-3.2	0.0	14	dbSNP_119	95	3534,5066	514.5+/-378.4	751,2032,1517	no	coding-synonymous,coding-synonymous	FBXO34	NM_017943.3,NM_152231.1	,	881,2850,2772	CC,CT,TT		41.093,24.4666,35.4606	,	200/712,200/712	55817708	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	55030	exon2			AGTCTATGCTGGG	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.600T>C	14.37:g.55817708T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Silent	SNP	ENST00000313833.4	37	CCDS32086.1																																																																																			T|0.655;C|0.345	0.345	strong		0.502	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
SLC52A3	113278	hgsc.bcm.edu	37	20	744450	744450	+	Silent	SNP	G	G	A	rs3746805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:744450G>A	ENST00000217254.7	-	3	1006	c.765C>T	c.(763-765)ctC>ctT	p.L255L	SLC52A3_ENST00000381944.3_Silent_p.L255L|SLC52A3_ENST00000473664.1_Intron	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	255					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										GGTCATTGAGGAGGTCTTCCA	0.612													G|||	1546	0.308706	0.1278	0.4755	5008	,	,		18708	0.124		0.4881	False		,,,				2504	0.4407				p.L255L		Atlas-SNP	.											.	.	.	.	0			c.C765T						PASS	.	G		791,3615	317.7+/-295.3	78,635,1490	70.0	67.0	68.0		765	4.0	1.0	20	dbSNP_107	68	4089,4511	560.7+/-387.6	982,2125,1193	no	coding-synonymous	C20orf54	NM_033409.3		1060,2760,2683	AA,AG,GG		47.5465,17.9528,37.5211		255/470	744450	4880,8126	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon3			ATTGAGGAGGTCT	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.765C>T	20.37:g.744450G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	49	47	0.959184	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.667;A|0.333	0.333	strong		0.612	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
TGS1	96764	hgsc.bcm.edu	37	8	56711713	56711713	+	Missense_Mutation	SNP	A	A	G	rs10109493	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:56711713A>G	ENST00000260129.5	+	8	2260	c.1783A>G	c.(1783-1785)Act>Gct	p.T595A		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	595			T -> A (in dbSNP:rs10109493).		7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CTTGCTAGCAACTGTTCCAGA	0.433													A|||	575	0.114816	0.171	0.1167	5008	,	,		19247	0.0099		0.1103	False		,,,				2504	0.1503				p.T595A	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.A1783G						PASS	.	A	ALA/THR	730,3676	301.8+/-287.1	60,610,1533	79.0	77.0	78.0		1783	-7.3	0.0	8	dbSNP_119	78	925,7675	205.1+/-247.6	48,829,3423	yes	missense	TGS1	NM_024831.6	58	108,1439,4956	GG,GA,AA		10.7558,16.5683,12.7249	benign	595/854	56711713	1655,11351	2203	4300	6503	SO:0001583	missense	96764	exon8			CTAGCAACTGTTC	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.1783A>G	8.37:g.56711713A>G	ENSP00000260129:p.Thr595Ala	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	219	0.10027472527472528	92	0.18699186991869918	42	0.11602209944751381	0	0.0	85	0.11213720316622691	A	3.946	-0.013212	0.07727	0.165683	0.107558	ENSG00000137574	ENST00000260129	T	0.09073	3.02	5.94	-7.35	0.01422	.	1.979650	0.02270	N	0.068340	T	0.00012	0.0000	N	0.02830	-0.485	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38351	-0.9665	9	0.05959	T	0.93	0.0049	5.9341	0.19154	0.3639:0.0:0.3806:0.2556	rs10109493;rs57840550;rs10109493	595;595	B2RBJ7;Q96RS0	.;TGS1_HUMAN	A	595	ENSP00000260129:T595A	ENSP00000260129:T595A	T	+	1	0	TGS1	56874267	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.427000	0.06999	-1.389000	0.02090	-0.263000	0.10527	ACT	A|0.876;G|0.124	0.124	strong		0.433	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
THSD7A	221981	hgsc.bcm.edu	37	7	11581134	11581134	+	Silent	SNP	T	T	C	rs2074603	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:11581134T>C	ENST00000423059.4	-	6	1985	c.1734A>G	c.(1732-1734)gcA>gcG	p.A578A		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	578					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CCAGTCTCACTGCTTTCCAGT	0.527										HNSCC(18;0.044)			T|||	2362	0.471645	0.4902	0.3775	5008	,	,		17905	0.5387		0.4245	False		,,,				2504	0.4928				p.A578A		Atlas-SNP	.											.	THSD7A	219	.	0			c.A1734G						PASS	.	T		1846,2132		446,954,589	92.0	94.0	93.0		1734	-3.8	1.0	7	dbSNP_96	93	3470,4848		713,2044,1402	no	coding-synonymous	THSD7A	NM_015204.2		1159,2998,1991	CC,CT,TT		41.7168,46.4052,43.2336		578/1658	11581134	5316,6980	1989	4159	6148	SO:0001819	synonymous_variant	221981	exon6			TCTCACTGCTTTC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1734A>G	7.37:g.11581134T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	176	176	1	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			T|0.532;C|0.468	0.468	strong		0.527	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
BLVRA	644	hgsc.bcm.edu	37	7	43810764	43810764	+	Missense_Mutation	SNP	G	G	A	rs699512	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:43810764G>A	ENST00000402924.1	+	3	170	c.7G>A	c.(7-9)Gca>Aca	p.A3T	BLVRA_ENST00000265523.4_Missense_Mutation_p.A3T	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	3			A -> T (in dbSNP:rs699512). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8950184, ECO:0000269|Ref.4}.		heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						CAAGATGAATGCAGAGGTGAG	0.463													a|||	4112	0.821086	0.9576	0.8487	5008	,	,		22948	0.6825		0.7465	False		,,,				2504	0.8364				p.A3T		Atlas-SNP	.											.	BLVRA	26	.	0			c.G7A						PASS	.	A	THR/ALA	4086,320	171.2+/-201.5	1892,302,9	168.0	167.0	167.0		7	1.4	0.1	7	dbSNP_86	167	6579,2021	353.6+/-329.2	2545,1489,266	yes	missense	BLVRA	NM_000712.3	58	4437,1791,275	AA,AG,GG		23.5,7.2628,17.9994	benign	3/297	43810764	10665,2341	2203	4300	6503	SO:0001583	missense	644	exon3			ATGAATGCAGAGG	BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR			Standard	NM_001253823		Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.7G>A	7.37:g.43810764G>A	ENSP00000385757:p.Ala3Thr	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001253823	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	Missense_Mutation	SNP	ENST00000402924.1	37	CCDS5472.1	1728	0.7912087912087912	472	0.959349593495935	303	0.8370165745856354	388	0.6783216783216783	565	0.7453825857519789	A	0.006	-2.021544	0.00414	0.927372	0.765	ENSG00000106605	ENST00000265523;ENST00000402924;ENST00000424330	T;T;T	0.23147	1.92;1.92;1.92	3.24	1.38	0.22167	.	0.885863	0.09595	N	0.780983	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40478	-0.9561	9	0.02654	T	1	.	7.6037	0.28089	0.2506:0.0:0.7494:0.0	rs699512;rs1615795;rs10342114;rs17239474;rs52794979;rs58884429;rs699512	3	P53004	BIEA_HUMAN	T	3	ENSP00000265523:A3T;ENSP00000385757:A3T;ENSP00000412005:A3T	ENSP00000265523:A3T	A	+	1	0	BLVRA	43777289	0.038000	0.19896	0.078000	0.20375	0.441000	0.31987	-0.547000	0.06055	0.068000	0.16574	-1.390000	0.01156	GCA	G|0.184;A|0.816	0.816	strong		0.463	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	NM_000712	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133666209	133666209	+	Missense_Mutation	SNP	C	C	T	rs34550074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:133666209C>T	ENST00000310926.4	-	9	1459	c.1186G>A	c.(1186-1188)Gcc>Acc	p.A396T	SLCO2A1_ENST00000493729.1_Missense_Mutation_p.A320T	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	396			A -> T (in dbSNP:rs34550074). {ECO:0000269|PubMed:8787677, ECO:0000269|PubMed:9618293}.		lipid transport (GO:0006869)|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)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)	p.A396T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	CGGGGAATGGCTTGTAGAGAG	0.502													T|||	1421	0.283746	0.4297	0.2536	5008	,	,		19189	0.2817		0.1899	False		,,,				2504	0.2065				p.A396T		Atlas-SNP	.											SLCO2A1,NS,carcinoma,0,1	SLCO2A1	72	1	1	Substitution - Missense(1)	stomach(1)	c.G1186A						PASS	.	T	THR/ALA	1807,2599	640.3+/-397.3	388,1031,784	126.0	112.0	117.0		1186	4.6	1.0	3	dbSNP_126	117	1608,6992	743.2+/-407.2	152,1304,2844	yes	missense	SLCO2A1	NM_005630.2	58	540,2335,3628	TT,TC,CC		18.6977,41.0123,26.2571	benign	396/644	133666209	3415,9591	2203	4300	6503	SO:0001583	missense	6578	exon9			GAATGGCTTGTAG		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.1186G>A	3.37:g.133666209C>T	ENSP00000311291:p.Ala396Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_005630	Q86V98|Q8IUN2	Missense_Mutation	SNP	ENST00000310926.4	37	CCDS3084.1	605	0.27701465201465203	202	0.4105691056910569	95	0.26243093922651933	152	0.26573426573426573	156	0.20580474934036938	T	1.317	-0.600463	0.03744	0.410123	0.186977	ENSG00000174640	ENST00000310926;ENST00000493729	T;T	0.39229	1.09;1.09	5.72	4.55	0.56014	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.342974	0.34291	N	0.004099	T	0.00012	0.0000	N	0.03224	-0.385	0.47123	P	6.749999999999812E-4	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.47560	-0.9108	9	0.20519	T	0.43	.	8.1198	0.30965	0.0:0.2794:0.0:0.7206	rs34550074	320;396	E7EU40;Q92959	.;SO2A1_HUMAN	T	396;320	ENSP00000311291:A396T;ENSP00000418893:A320T	ENSP00000311291:A396T	A	-	1	0	SLCO2A1	135148899	0.959000	0.32827	1.000000	0.80357	0.096000	0.18686	0.518000	0.22847	0.437000	0.26423	-0.254000	0.11334	GCC	C|0.732;T|0.268	0.268	strong		0.502	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
CD68	968	hgsc.bcm.edu	37	17	7484101	7484101	+	Splice_Site	SNP	C	C	A	rs25679|rs9901673	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7484101C>A	ENST00000250092.6	+	4	971	c.760C>A	c.(760-762)Cag>Aag	p.Q254K	MPDU1_ENST00000250124.6_5'Flank|SNORA67_ENST00000384423.1_RNA|AC113189.5_ENST00000415124.1_RNA|AC113189.5_ENST00000417897.1_RNA|AC113189.5_ENST00000572046.1_RNA|MPDU1_ENST00000582151.1_5'Flank|AC113189.5_ENST00000573187.1_RNA|CD68_ENST00000380498.6_Splice_Site_p.Q227K|SENP3-EIF4A1_ENST00000579777.1_RNA	NM_001251.2	NP_001242.2	P34810	CD68_HUMAN	CD68 molecule	254			Q -> K (in dbSNP:rs25679). {ECO:0000269|PubMed:7680921}.		cellular response to organic substance (GO:0071310)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)				endometrium(1)|lung(1)|skin(1)	3						CCACGCAGCACGTAAGTAACC	0.572													C|||	789	0.157548	0.1657	0.121	5008	,	,		19669	0.1567		0.16	False		,,,				2504	0.1708				p.Q254K		Atlas-SNP	.											.	CD68	17	.	0			c.C760A						PASS	.	C	LYS/GLN,LYS/GLN	787,3619	318.8+/-295.8	68,651,1484	103.0	85.0	91.0		679,760	2.0	0.3	17	dbSNP_119	91	1443,7157	277.9+/-293.1	136,1171,2993	yes	missense-near-splice,missense-near-splice	CD68	NM_001040059.1,NM_001251.2	53,53	204,1822,4477	AA,AC,CC		16.7791,17.862,17.1459	possibly-damaging,possibly-damaging	227/328,254/355	7484101	2230,10776	2203	4300	6503	SO:0001630	splice_region_variant	968	exon4			GCAGCACGTAAGT	S57235	CCDS11114.1, CCDS58512.1	17p13	2011-11-24	2006-03-28		ENSG00000129226	ENSG00000129226		"""CD molecules"""	1693	protein-coding gene	gene with protein product	"""scavenger receptor class D, member 1"", ""CD68 antigen"", ""macrophage antigen CD68"""	153634	"""CD68 antigen"""			9790779	Standard	NM_001251		Approved	SCARD1, macrosialin, GP110, DKFZp686M18236, LAMP4	uc002ghv.3	P34810	OTTHUMG00000108146	ENST00000250092.6:c.760+1C>A	17.37:g.7484101C>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	162	83	0.512346	NM_001251	B4DVT4|Q53HR6|Q53XI3|Q96BI7	Missense_Mutation	SNP	ENST00000250092.6	37	CCDS11114.1	352	0.16117216117216118	83	0.16869918699186992	43	0.11878453038674033	104	0.18181818181818182	122	0.16094986807387862	C	10.69	1.422540	0.25639	0.17862	0.167791	ENSG00000129226	ENST00000250092;ENST00000380498	T	0.31769	1.48	5.16	1.97	0.26223	.	0.397176	0.21802	N	0.068903	T	0.00073	0.0002	M	0.72479	2.2	0.36687	P	0.12062600000000001	B;B	0.15141	0.012;0.012	B;B	0.18871	0.009;0.023	T	0.05305	-1.0893	9	0.42905	T	0.14	-1.8387	8.4898	0.33093	0.1656:0.5142:0.3201:0.0	rs9901673;rs60414741;rs9901673	254;227	P34810;B4DVT4	CD68_HUMAN;.	K	254;197	ENSP00000250092:Q254K	ENSP00000250092:Q254K	Q	+	1	0	CD68	7424825	0.565000	0.26610	0.295000	0.24960	0.028000	0.11728	0.685000	0.25378	0.294000	0.22547	-0.176000	0.13171	CAG	C|0.830;A|0.170	0.170	strong		0.572	CD68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226949.3	NM_001251	Missense_Mutation
APBA3	9546	hgsc.bcm.edu	37	19	3753769	3753769	+	Silent	SNP	C	C	T	rs3746120	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:3753769C>T	ENST00000316757.3	-	6	1205	c.1005G>A	c.(1003-1005)gcG>gcA	p.A335A	AC005954.4_ENST00000586503.1_RNA|AC005954.3_ENST00000591962.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	335	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		TCACGTCCTCCGCGTAGAATA	0.692													C|||	1703	0.340056	0.2405	0.4179	5008	,	,		13758	0.4474		0.3797	False		,,,				2504	0.2679				p.A335A		Atlas-SNP	.											APBA3,NS,carcinoma,0,1	APBA3	28	1	0			c.G1005A						PASS	.	C		1070,3286		139,792,1247	9.0	9.0	9.0		1005	-7.9	0.2	19	dbSNP_107	9	3082,5446		560,1962,1742	no	coding-synonymous	APBA3	NM_004886.3		699,2754,2989	TT,TC,CC		36.1398,24.5638,32.226		335/576	3753769	4152,8732	2178	4264	6442	SO:0001819	synonymous_variant	9546	exon6			GTCCTCCGCGTAG	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.1005G>A	19.37:g.3753769C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	31	9	0.290323	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			C|0.654;T|0.346	0.346	strong		0.692	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
C1orf94	84970	hgsc.bcm.edu	37	1	34663411	34663411	+	Missense_Mutation	SNP	C	C	G	rs1414474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:34663411C>G	ENST00000488417.1	+	2	1026	c.906C>G	c.(904-906)gaC>gaG	p.D302E	C1orf94_ENST00000373374.3_Missense_Mutation_p.D112E	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	302			D -> E (in dbSNP:rs1414474). {ECO:0000269|PubMed:15489334}.							central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CACGTCCTGACAAGCTCCCTG	0.607													C|||	836	0.166933	0.1369	0.2233	5008	,	,		19091	0.0863		0.2048	False		,,,				2504	0.2117				p.D302E		Atlas-SNP	.											.	C1orf94	156	.	0			c.C906G						PASS	.	C	GLU/ASP,GLU/ASP	742,3664	306.3+/-289.4	59,624,1520	56.0	51.0	53.0		906,336	1.3	0.7	1	dbSNP_88	53	2029,6571	352.5+/-328.7	240,1549,2511	yes	missense,missense	C1orf94	NM_001134734.1,NM_032884.3	45,45	299,2173,4031	GG,GC,CC		23.593,16.8407,21.3056	benign,benign	302/599,112/409	34663411	2771,10235	2203	4300	6503	SO:0001583	missense	84970	exon2			TCCTGACAAGCTC	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.906C>G	1.37:g.34663411C>G	ENSP00000435634:p.Asp302Glu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	37	CCDS44108.1	343	0.15705128205128205	75	0.1524390243902439	78	0.2154696132596685	43	0.07517482517482517	147	0.19393139841688653	C	8.449	0.852550	0.17106	0.168407	0.23593	ENSG00000142698	ENST00000373374;ENST00000488417	T;T	0.26223	1.75;1.75	4.46	1.31	0.21738	.	0.913614	0.09296	N	0.821662	T	0.00012	0.0000	L	0.40543	1.245	0.45777	P	0.0013370000000000326	B	0.13594	0.008	B	0.12156	0.007	T	0.31336	-0.9947	9	0.37606	T	0.19	-13.8187	6.5487	0.22420	0.0:0.5515:0.3483:0.1002	rs1414474;rs17484993;rs17845124;rs17857924;rs1414474	302	Q6P1W5	CA094_HUMAN	E	112;302	ENSP00000362472:D112E;ENSP00000435634:D302E	ENSP00000362472:D112E	D	+	3	2	C1orf94	34435998	0.958000	0.32768	0.721000	0.30653	0.408000	0.30992	-0.116000	0.10724	0.486000	0.27676	0.557000	0.71058	GAC	C|0.796;G|0.204	0.204	strong		0.607	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057958	46057958	+	Silent	SNP	C	C	T	rs4818951	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46057958C>T	ENST00000380095.1	+	1	686	c.624C>T	c.(622-624)tcC>tcT	p.S208S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	208	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCGTCCCCTCCTGCGGTGCCT	0.697													C|||	3206	0.640176	0.4092	0.6931	5008	,	,		18953	0.6687		0.7594	False		,,,				2504	0.7628				p.S208S		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C624T						PASS	.	C	,	1952,2454	547.0+/-377.2	407,1138,658	86.0	91.0	89.0		,624	2.3	0.5	21	dbSNP_111	89	6136,2464	691.7+/-404.5	2207,1722,371	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	2614,2860,1029	TT,TC,CC		28.6512,44.3032,37.8133	,	,208/252	46057958	8088,4918	2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CCCCTCCTGCGGT	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.624C>T	21.37:g.46057958C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	206	74	0.359223	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.368;T|0.632	0.632	strong		0.697	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
REG3A	5068	hgsc.bcm.edu	37	2	79385787	79385787	+	Missense_Mutation	SNP	G	G	A	rs77686105	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:79385787G>A	ENST00000409839.3	-	3	221	c.185C>T	c.(184-186)aCa>aTa	p.T62I	REG3A_ENST00000305165.2_Missense_Mutation_p.T62I|REG3A_ENST00000393878.1_Missense_Mutation_p.T62I|AC011754.1_ENST00000415201.1_RNA	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	62	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)			breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						ATCTGCATCTGTCCAGGATTT	0.552																																					p.T62I		Atlas-SNP	.											.	REG3A	76	.	0			c.C185T						PASS	.						130.0	118.0	122.0					2																	79385787		2203	4300	6503	SO:0001583	missense	5068	exon2			GCATCTGTCCAGG	S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"""pancreatitis-associated protein"""	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.185C>T	2.37:g.79385787G>A	ENSP00000386630:p.Thr62Ile	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	90	11	0.122222	NM_138938		Missense_Mutation	SNP	ENST00000409839.3	37	CCDS1965.1	.	.	.	.	.	.	.	.	.	.	G	3.884	-0.025360	0.07589	.	.	ENSG00000172016	ENST00000409839;ENST00000393878;ENST00000305165	T;T;T	0.19806	2.12;2.12;2.12	4.02	-4.6	0.03390	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.733660	0.02668	N	0.108266	T	0.11239	0.0274	N	0.17764	0.52	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.16778	-1.0391	10	0.22706	T	0.39	.	3.4681	0.07557	0.425:0.0:0.2967:0.2784	.	62	Q06141	REG3A_HUMAN	I	62	ENSP00000386630:T62I;ENSP00000377456:T62I;ENSP00000304311:T62I	ENSP00000304311:T62I	T	-	2	0	REG3A	79239295	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.065000	0.03458	-0.910000	0.03847	-1.155000	0.01812	ACA	G|0.894;A|0.106	0.106	strong		0.552	REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580	
TLR10	81793	hgsc.bcm.edu	37	4	38774785	38774785	+	Silent	SNP	A	A	G	rs10776482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38774785A>G	ENST00000308973.4	-	4	3032	c.2427T>C	c.(2425-2427)gaT>gaC	p.D809D	TLR10_ENST00000508334.1_Silent_p.D809D|TLR10_ENST00000506111.1_Silent_p.D809D|TLR10_ENST00000361424.2_Silent_p.D809D|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	809					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						TTTATAGACAATCTGTTCTCA	0.378													G|||	1496	0.298722	0.2126	0.3184	5008	,	,		18229	0.4325		0.2495	False		,,,				2504	0.3139				p.D809D		Atlas-SNP	.											TLR10,colon,carcinoma,0,1	TLR10	87	1	0			c.T2427C						PASS	.	G	,,,,	980,3426	732.4+/-410.4	100,780,1323	69.0	67.0	68.0		2427,2427,2427,2385,2427	0.1	0.1	4	dbSNP_120	68	1747,6853	734.7+/-406.9	188,1371,2741	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	,,,,	288,2151,4064	GG,GA,AA		20.314,22.2424,20.9672	,,,,	809/812,809/812,809/812,795/798,809/812	38774785	2727,10279	2203	4300	6503	SO:0001819	synonymous_variant	81793	exon2			TAGACAATCTGTT	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.2427T>C	4.37:g.38774785A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			A|0.739;G|0.261	0.261	strong		0.378	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
LRP1	4035	hgsc.bcm.edu	37	12	57593101	57593101	+	Silent	SNP	G	G	A	rs1140648	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:57593101G>A	ENST00000243077.3	+	61	10249	c.9783G>A	c.(9781-9783)acG>acA	p.T3261T		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3261					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)	ACAAGACCACGGGCACCAACA	0.592													g|||	2671	0.533347	0.2557	0.536	5008	,	,		20500	0.5		0.6839	False		,,,				2504	0.7863				p.T3261T		Atlas-SNP	.											.	LRP1	428	.	0			c.G9783A						PASS	.	A		1451,2955	468.5+/-355.1	257,937,1009	247.0	227.0	234.0		9783	-10.0	0.0	12	dbSNP_86	234	5862,2738	680.7+/-403.7	2007,1848,445	no	coding-synonymous	LRP1	NM_002332.2		2264,2785,1454	AA,AG,GG		31.8372,32.9324,43.7721		3261/4545	57593101	7313,5693	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon61			GACCACGGGCACC	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.9783G>A	12.37:g.57593101G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	57	55	0.964912	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			G|0.449;A|0.551	0.551	strong		0.592	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
STAM	8027	hgsc.bcm.edu	37	10	17756596	17756596	+	Silent	SNP	T	T	C	rs12221	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:17756596T>C	ENST00000377524.3	+	14	1655	c.1440T>C	c.(1438-1440)taT>taC	p.Y480Y	STAM_ENST00000540523.1_Silent_p.Y369Y	NM_003473.3	NP_003464.1	Q92783	STAM1_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 1	480					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	SH3/SH2 adaptor activity (GO:0005070)	p.Y480Y(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	26						CGCCAGTATATAGTCCTCCTC	0.463													T|||	763	0.152356	0.0787	0.1441	5008	,	,		14054	0.2262		0.2058	False		,,,				2504	0.1268				p.Y480Y		Atlas-SNP	.											STAM,NS,carcinoma,0,1	STAM	60	1	1	Substitution - coding silent(1)	stomach(1)	c.T1440C						PASS	.	T		483,3923	226.5+/-242.0	23,437,1743	71.0	69.0	70.0		1440	-4.4	0.4	10	dbSNP_52	70	1913,6687	341.0+/-323.9	223,1467,2610	no	coding-synonymous	STAM	NM_003473.3		246,1904,4353	CC,CT,TT		22.2442,10.9623,18.4223		480/541	17756596	2396,10610	2203	4300	6503	SO:0001819	synonymous_variant	8027	exon14			AGTATATAGTCCT	U43899	CCDS7122.1	10p14-p13	2009-04-29			ENSG00000136738	ENSG00000136738			11357	protein-coding gene	gene with protein product	"""HSE1 homolog (S. cerevisiae)"""	601899				8780729	Standard	NM_003473		Approved	STAM1	uc001ipj.2	Q92783	OTTHUMG00000017749	ENST00000377524.3:c.1440T>C	10.37:g.17756596T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	118	49	0.415254	NM_003473	B0YJ99|D3DRU5|Q8N6D9	Silent	SNP	ENST00000377524.3	37	CCDS7122.1																																																																																			T|0.815;C|0.185	0.185	strong		0.463	STAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047039.1	NM_003473	
BCO1	53630	hgsc.bcm.edu	37	16	81295780	81295780	+	Silent	SNP	C	C	A	rs35683292	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:81295780C>A	ENST00000258168.2	+	4	824	c.363C>A	c.(361-363)acC>acA	p.T121T	BCMO1_ENST00000425577.2_Silent_p.T52T|BCMO1_ENST00000564552.1_Silent_p.T121T	NM_017429.2	NP_059125.2														breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						CCGATTTCACCGACAACTGCC	0.488													C|||	85	0.0169728	0.0015	0.0202	5008	,	,		19127	0.002		0.0527	False		,,,				2504	0.0143				p.T121T		Atlas-SNP	.											.	BCMO1	53	.	0			c.C363A						PASS	.	C		42,4362	46.0+/-80.4	1,40,2161	188.0	179.0	182.0		363	-11.6	0.6	16	dbSNP_126	182	482,8118	141.1+/-197.5	14,454,3832	no	coding-synonymous	BCMO1	NM_017429.2		15,494,5993	AA,AC,CC		5.6047,0.9537,4.0295		121/548	81295780	524,12480	2202	4300	6502	SO:0001819	synonymous_variant	53630	exon4			TTTCACCGACAAC																												ENST00000258168.2:c.363C>A	16.37:g.81295780C>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_017429		Silent	SNP	ENST00000258168.2	37	CCDS10934.1																																																																																			C|0.965;A|0.035	0.035	strong		0.488	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269056.1		
LALBA	3906	hgsc.bcm.edu	37	12	48962869	48962869	+	Silent	SNP	A	A	G	rs2232566	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48962869A>G	ENST00000301046.2	-	2	313	c.288T>C	c.(286-288)tgT>tgC	p.C96C	LALBA_ENST00000549817.1_Silent_p.C96C	NM_002289.2	NP_002280.1	P00709	LALBA_HUMAN	lactalbumin, alpha-	96					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|lactose biosynthetic process (GO:0005989)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|lactose synthase activity (GO:0004461)			large_intestine(1)|stomach(2)	3						ACTCACTGTCACAGGAGATGT	0.478													A|||	482	0.096246	0.2269	0.0476	5008	,	,		20040	0.0278		0.0626	False		,,,				2504	0.0593				p.C96C		Atlas-SNP	.											.	LALBA	9	.	0			c.T288C						PASS	.	A		811,3595	323.7+/-298.2	70,671,1462	203.0	185.0	191.0		288	1.6	1.0	12	dbSNP_98	191	579,8021	154.8+/-208.9	16,547,3737	no	coding-synonymous	LALBA	NM_002289.2		86,1218,5199	GG,GA,AA		6.7326,18.4067,10.6874		96/143	48962869	1390,11616	2203	4300	6503	SO:0001819	synonymous_variant	3906	exon2			ACTGTCACAGGAG		CCDS8765.1	12q13	2012-10-02				ENSG00000167531			6480	protein-coding gene	gene with protein product		149750					Standard	XM_006719395		Approved	LYZL7	uc001rrt.3	P00709	OTTHUMG00000170391	ENST00000301046.2:c.288T>C	12.37:g.48962869A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_002289	Q6FGX0|Q9UDK4	Silent	SNP	ENST00000301046.2	37	CCDS8765.1																																																																																			A|0.903;G|0.097	0.097	strong		0.478	LALBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408836.1	NM_002289	
LRRC47	57470	hgsc.bcm.edu	37	1	3701663	3701663	+	Silent	SNP	T	T	C	rs2298227	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3701663T>C	ENST00000378251.1	-	3	1209	c.1182A>G	c.(1180-1182)ccA>ccG	p.P394P	RP1-286D6.5_ENST00000607459.1_RNA|RN7SL574P_ENST00000581512.1_RNA	NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	394							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		TGAGGTCCTGTGGGGGCCGGG	0.602													C|||	543	0.108427	0.1452	0.1023	5008	,	,		18489	0.1111		0.1213	False		,,,				2504	0.047				p.P394P		Atlas-SNP	.											.	LRRC47	42	.	0			c.A1182G						PASS	.	C		570,3836	768.5+/-413.6	29,512,1662	53.0	52.0	52.0		1182	-9.5	0.1	1	dbSNP_100	52	926,7674	774.1+/-407.7	48,830,3422	no	coding-synonymous	LRRC47	NM_020710.2		77,1342,5084	CC,CT,TT		10.7674,12.9369,11.5024		394/584	3701663	1496,11510	2203	4300	6503	SO:0001819	synonymous_variant	57470	exon3			GTCCTGTGGGGGC	AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.1182A>G	1.37:g.3701663T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_020710	Q9ULN5	Silent	SNP	ENST00000378251.1	37	CCDS51.1																																																																																			T|0.882;C|0.118	0.118	strong		0.602	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710	
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 GAIIx	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_ENST00000367421.3_Missense_Mutation_p.F66L|CFHR2_ENST00000476712.2_Missense_Mutation_p.F66L|CFHR2_ENST00000496448.1_Intron	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	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	219	14	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	
FCGBP	8857	hgsc.bcm.edu	37	19	40389741	40389741	+	Missense_Mutation	SNP	A	A	G	rs141158749		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40389741A>G	ENST00000221347.6	-	18	8448	c.8441T>C	c.(8440-8442)gTg>gCg	p.V2814A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2814	Cys-rich.		V -> A (in dbSNP:rs3746009). {ECO:0000269|PubMed:9182547}.			extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GACTTTACCCACATGGCACGT	0.637																																					p.V2814A		Atlas-SNP	.											FCGBP,NS,neuroblastoma,0,3	FCGBP	416	3	0			c.T8441C						scavenged	.						13.0	11.0	12.0					19																	40389741		2055	3702	5757	SO:0001583	missense	8857	exon18			TTACCCACATGGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8441T>C	19.37:g.40389741A>G	ENSP00000221347:p.Val2814Ala	Somatic	741	132	0.178138		WXS	Illumina HiSeq	Phase_I	593	212	0.357504	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	N	0.031	-1.331696	0.01298	.	.	ENSG00000090920	ENST00000221347	T	0.04603	3.59	2.94	-1.02	0.10135	von Willebrand factor, type C (1);	0.713318	0.11461	N	0.561738	T	0.01222	0.0040	N	0.00760	-1.21	0.80722	P	0.0	B	0.16603	0.018	B	0.18871	0.023	T	0.45760	-0.9239	9	0.07990	T	0.79	.	3.5552	0.07862	0.3816:0.1953:0.4231:0.0	.	2814	Q9Y6R7	FCGBP_HUMAN	A	2814	ENSP00000221347:V2814A	ENSP00000221347:V2814A	V	-	2	0	FCGBP	45081581	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.449000	0.21744	-0.587000	0.05890	-1.994000	0.00447	GTG	A|0.200;G|0.800	0.800	strong		0.637	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
SGK223	157285	hgsc.bcm.edu	37	8	8234219	8234219	+	Missense_Mutation	SNP	G	G	A	rs4840955|rs373458829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:8234219G>A	ENST00000520004.1	-	3	1964	c.1700C>T	c.(1699-1701)cCg>cTg	p.P567L	SGK223_ENST00000330777.4_Missense_Mutation_p.P567L			Q86YV5	SG223_HUMAN		569							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GTCAGCCAGCGGTGACACTGG	0.657													G|||	2270	0.453275	0.388	0.4323	5008	,	,		16798	0.6409		0.3002	False		,,,				2504	0.5204				p.P567L	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1700T						PASS	.	G	LEU/PRO	1293,2749		229,835,957	24.0	29.0	27.0		1700	4.9	0.0	8	dbSNP_111	27	2275,6025		338,1599,2213	yes	missense	SGK223	NM_001080826.1	98	567,2434,3170	AA,AG,GG		27.4096,31.9891,28.9094	probably-damaging	567/1403	8234219	3568,8774	2021	4150	6171	SO:0001583	missense	0	exon2			GCCAGCGGTGACA																												ENST00000520004.1:c.1700C>T	8.37:g.8234219G>A	ENSP00000428054:p.Pro567Leu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	906	0.41483516483516486	193	0.39227642276422764	131	0.36187845303867405	367	0.6416083916083916	215	0.2836411609498681	G	14.12	2.440334	0.43326	0.319891	0.274096	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59906	0.23;0.23	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	M	0.62723	1.935	0.32196	P	0.578445	B	0.25312	0.123	B	0.18871	0.023	T	0.48969	-0.8987	9	0.56958	D	0.05	.	7.8195	0.29280	0.0832:0.0:0.7549:0.1619	rs4840955;rs61637687	567	Q86YV5	SG223_HUMAN	L	567	ENSP00000330930:P567L;ENSP00000428054:P567L	ENSP00000330930:P567L	P	-	2	0	AC068353.1	8271629	1.000000	0.71417	0.040000	0.18447	0.002000	0.02628	4.250000	0.58772	2.446000	0.82766	0.563000	0.77884	CCG	G|0.631;A|0.369	0.369	strong		0.657	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
SVEP1	79987	hgsc.bcm.edu	37	9	113261483	113261483	+	Missense_Mutation	SNP	C	C	T	rs872665	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:113261483C>T	ENST00000401783.2	-	7	1855	c.1519G>A	c.(1519-1521)Gtc>Atc	p.V507I	SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374461.1_Missense_Mutation_p.V484I|SVEP1_ENST00000374469.1_Missense_Mutation_p.V484I|SVEP1_ENST00000302728.8_Missense_Mutation_p.V507I	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	507	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.		V -> I (in dbSNP:rs872665).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GATATGATGACATCTTTGGGC	0.463													C|||	1340	0.267572	0.3533	0.2622	5008	,	,		18368	0.1825		0.2535	False		,,,				2504	0.2577				p.V507I		Atlas-SNP	.											.	SVEP1	326	.	0			c.G1519A						PASS	.	C	ILE/VAL	1226,2836		190,846,995	54.0	53.0	54.0		1519	5.9	1.0	9	dbSNP_86	54	2174,6228		277,1620,2304	yes	missense	SVEP1	NM_153366.3	29	467,2466,3299	TT,TC,CC		25.8748,30.1822,27.2786	probably-damaging	507/3572	113261483	3400,9064	2031	4201	6232	SO:0001583	missense	79987	exon7			TGATGACATCTTT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.1519G>A	9.37:g.113261483C>T	ENSP00000384917:p.Val507Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	553	0.2532051282051282	170	0.34552845528455284	90	0.24861878453038674	102	0.17832167832167833	191	0.2519788918205805	C	6.191	0.403446	0.11754	0.301822	0.258748	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.91	5.91	0.95273	Complement control module (2);Sushi/SCR/CCP (2);	0.116309	0.64402	D	0.000020	T	0.00012	0.0000	L	0.36672	1.1	0.27382	P	0.9553831	D;B;D	0.67145	0.983;0.355;0.996	P;B;D	0.77557	0.753;0.1;0.99	T	0.03433	-1.1037	9	0.02654	T	1	.	19.0678	0.93119	0.0:1.0:0.0:0.0	rs872665;rs3818765;rs52802511;rs60471347;rs872665	507;507;507	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	I	507;484;507;484	ENSP00000384917:V507I;ENSP00000363593:V484I;ENSP00000304118:V507I;ENSP00000363585:V484I	ENSP00000304118:V507I	V	-	1	0	SVEP1	112301304	1.000000	0.71417	1.000000	0.80357	0.214000	0.24535	2.265000	0.43311	2.813000	0.96785	0.655000	0.94253	GTC	C|0.731;T|0.269	0.269	strong		0.463	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MAP2K3	5606	hgsc.bcm.edu	37	17	21203964	21203964	+	Silent	SNP	C	C	G	rs34458870	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:21203964C>G	ENST00000342679.4	+	4	522	c.273C>G	c.(271-273)gcC>gcG	p.A91A	MAP2K3_ENST00000361818.5_Silent_p.A62A|MAP2K3_ENST00000316920.6_Silent_p.A62A	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	91	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.A95A(1)							COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CCATCATGGCCGTGAAGGTGA	0.642																																					p.A91A		Atlas-SNP	.											MAP2K3_ENST00000316920,NS,lymphoid_neoplasm,0,1	MAP2K3	135	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C273G						PASS	.						38.0	36.0	36.0					17																	21203964		2202	4300	6502	SO:0001819	synonymous_variant	5606	exon4			CATGGCCGTGAAG	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.273C>G	17.37:g.21203964C>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	61	13	0.213115	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Silent	SNP	ENST00000342679.4	37	CCDS11217.1																																																																																			C|0.853;G|0.147	0.147	strong		0.642	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	
PIWIL4	143689	hgsc.bcm.edu	37	11	94320237	94320237	+	Silent	SNP	T	T	C	rs7110167	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:94320237T>C	ENST00000299001.6	+	7	949	c.738T>C	c.(736-738)ttT>ttC	p.F246F	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	246					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GGCCTGGGTTTGCCATTTCTG	0.358													T|||	2772	0.553514	0.8124	0.4524	5008	,	,		19065	0.5		0.4016	False		,,,				2504	0.4867				p.F246F		Atlas-SNP	.											PIWIL4,NS,carcinoma,+2,1	PIWIL4	70	1	0			c.T738C						scavenged	.	T		3284,1118	717.2+/-408.7	1239,806,156	144.0	153.0	150.0		738	-0.4	0.2	11	dbSNP_116	150	3427,5169	504.7+/-376.2	705,2017,1576	no	coding-synonymous	PIWIL4	NM_152431.2		1944,2823,1732	CC,CT,TT		39.8674,25.3975,48.369		246/853	94320237	6711,6287	2201	4298	6499	SO:0001819	synonymous_variant	143689	exon7			TGGGTTTGCCATT	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.738T>C	11.37:g.94320237T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	15	0.227273	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			T|0.476;C|0.524	0.524	strong		0.358	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
MTG1	92170	hgsc.bcm.edu	37	10	135205009	135205009	+	5'Flank	SNP	C	C	G	rs1046178	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135205009C>G	ENST00000317502.6	+	0	0				PAOX_ENST00000368535.2_3'UTR|MTG1_ENST00000477902.2_5'Flank|PAOX_ENST00000480071.2_3'UTR|PAOX_ENST00000357296.3_Silent_p.P476P|RP11-108K14.8_ENST00000468317.2_Intron|PAOX_ENST00000368539.4_3'UTR|PAOX_ENST00000278060.5_3'UTR	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1						GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		GGCTGGGACCCTCATTTCTTC	0.572													c|||	4236	0.845847	0.6785	0.8948	5008	,	,		18526	0.9812		0.8777	False		,,,				2504	0.865				p.P476P		Atlas-SNP	.											.	PAOX	82	.	0			c.C1428G						PASS	.	C	,,	3202,1120		1183,836,142	17.0	18.0	18.0		,,1428	-4.7	0.0	10	dbSNP_86	18	7454,1028		3285,884,72	no	utr-3,utr-3,coding-synonymous	PAOX	NM_152911.2,NM_207127.1,NM_207128.1	,,	4468,1720,214	GG,GC,CC		12.1198,25.9139,16.776	,,	,,476/487	135205009	10656,2148	2161	4241	6402	SO:0001631	upstream_gene_variant	196743	exon6			GGGACCCTCATTT		CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"""GTP-binding protein 7"", ""GTP-binding protein 7 (putative)"", ""mitochondrial GTPase 1 homolog (S. cerevisiae)"""	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564		10.37:g.135205009C>G	Exception_encountered	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_207128	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Silent	SNP	ENST00000317502.6	37	CCDS31320.1																																																																																			C|0.165;G|0.835	0.835	strong		0.572	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384	
AGGF1	55109	hgsc.bcm.edu	37	5	76359024	76359024	+	Missense_Mutation	SNP	C	C	A	rs34400049	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:76359024C>A	ENST00000312916.7	+	14	2474	c.2092C>A	c.(2092-2094)Cct>Act	p.P698T		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	698			P -> T (in dbSNP:rs34400049). {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)		AGAAACTAAGCCTCAAAAAGA	0.378													C|||	1027	0.205072	0.0802	0.3199	5008	,	,		16784	0.2728		0.2952	False		,,,				2504	0.1299				p.P698T		Atlas-SNP	.											.	AGGF1	71	.	0			c.C2092A						PASS	.	C	THR/PRO	440,3966	210.8+/-231.2	31,378,1794	83.0	88.0	86.0		2092	1.6	0.9	5	dbSNP_126	86	2499,6101	409.6+/-349.9	366,1767,2167	yes	missense	AGGF1	NM_018046.4	38	397,2145,3961	AA,AC,CC		29.0581,9.9864,22.5973	benign	698/715	76359024	2939,10067	2203	4300	6503	SO:0001583	missense	55109	exon14			ACTAAGCCTCAAA	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.2092C>A	5.37:g.76359024C>A	ENSP00000316109:p.Pro698Thr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	514	0.23534798534798534	47	0.09552845528455285	107	0.2955801104972376	143	0.25	217	0.2862796833773087	C	0.081	-1.184419	0.01620	0.099864	0.290581	ENSG00000164252	ENST00000312916	T	0.35421	1.31	5.47	1.61	0.23674	.	0.795454	0.12324	N	0.478965	T	0.00012	0.0000	L	0.29908	0.895	0.29291	P	0.869337	B	0.28713	0.22	B	0.19148	0.024	T	0.33497	-0.9866	9	0.02654	T	1	-18.1993	1.31	0.02096	0.1414:0.3459:0.1383:0.3744	rs34400049	698	Q8N302	AGGF1_HUMAN	T	698	ENSP00000316109:P698T	ENSP00000316109:P698T	P	+	1	0	AGGF1	76394780	0.008000	0.16893	0.924000	0.36721	0.903000	0.53119	-0.210000	0.09345	0.003000	0.14656	-0.145000	0.13849	CCT	A|0.225;C|0.775	0.225	strong		0.378	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552717	43552717	+	Silent	SNP	G	G	C	rs147243132	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43552717G>C	ENST00000430334.3	-	4	805	c.672C>G	c.(670-672)tcC>tcG	p.S224S	PLEKHM1_ENST00000421073.2_Silent_p.S135S	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	224					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CTGAAGAATGGGAAATGGAAT	0.562													G|||	412	0.0822684	0.0378	0.1556	5008	,	,		21763	0.001		0.1958	False		,,,				2504	0.0573				p.S224S		Atlas-SNP	.											PLEKHM1,caecum,carcinoma,-1,1	PLEKHM1	69	1	0			c.C672G						PASS	.						25.0	23.0	24.0					17																	43552717		2202	4294	6496	SO:0001819	synonymous_variant	9842	exon4			AGAATGGGAAATG	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.672C>G	17.37:g.43552717G>C		Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	171	161	0.94152	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			G|0.873;C|0.127	0.127	strong		0.562	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
XRCC3	7517	hgsc.bcm.edu	37	14	104165753	104165753	+	Missense_Mutation	SNP	G	G	A	rs861539	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:104165753G>A	ENST00000553264.1	-	6	1518	c.722C>T	c.(721-723)aCg>aTg	p.T241M	KLC1_ENST00000334553.6_Intron|XRCC3_ENST00000555832.1_5'Flank|RP11-73M18.8_ENST00000602422.1_RNA|XRCC3_ENST00000445556.1_Missense_Mutation_p.T241M|XRCC3_ENST00000555055.1_Missense_Mutation_p.T241M|KLC1_ENST00000554280.1_Intron|KLC1_ENST00000348520.6_Intron|XRCC3_ENST00000352127.7_Missense_Mutation_p.T241M|KLC1_ENST00000555836.1_Intron|KLC1_ENST00000557450.1_Intron|XRCC3_ENST00000554974.1_Missense_Mutation_p.T36M|KLC1_ENST00000452929.2_Intron|XRCC3_ENST00000554913.1_Missense_Mutation_p.T241M			O43542	XRCC3_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 3	241			T -> M (in CMM6 susceptibility; associated with cutaneous malignant melanoma; dbSNP:rs861539). {ECO:0000269|PubMed:11059748, ECO:0000269|PubMed:9660962, ECO:0000269|Ref.2}.		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|response to organic substance (GO:0010033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Rad51C-XRCC3 complex (GO:0033065)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)	p.T241M(1)		endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)	4		Melanoma(154;0.155)|all_epithelial(191;0.19)		Epithelial(152;0.239)		CTCACGCAGCGTGGCCCCCAG	0.637								Direct reversal of damage;Homologous recombination					G|||	1086	0.216853	0.1906	0.2291	5008	,	,		17489	0.0734		0.3936	False		,,,				2504	0.2096				p.T241M		Atlas-SNP	.											XRCC3,NS,carcinoma,0,1	XRCC3	16	1	1	Substitution - Missense(1)	prostate(1)	c.C722T	GRCh37	CM003625	XRCC3	M	rs861539	PASS	.	G	MET/THR,MET/THR,,MET/THR,	950,3452		98,754,1349	19.0	22.0	21.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	722,722,,722,	1.4	0.0	14	dbSNP_86	21	3252,5346		640,1972,1687	yes	missense,missense,intron,missense,intron	KLC1,XRCC3	NM_001100118.1,NM_001100119.1,NM_001130107.1,NM_005432.3,NM_182923.3	81,81,,81,	738,2726,3036	AA,AG,GG		37.8227,21.5811,32.3231	benign,benign,,benign,	241/347,241/347,,241/347,	104165753	4202,8798	2201	4299	6500	SO:0001583	missense	7517	exon8			CGCAGCGTGGCCC	AF035586	CCDS9984.1	14q32.3	2006-05-04				ENSG00000126215			12830	protein-coding gene	gene with protein product	"""RAD51-like"""	600675				7603995	Standard	NM_001100118		Approved		uc001ynz.4	O43542		ENST00000553264.1:c.722C>T	14.37:g.104165753G>A	ENSP00000451974:p.Thr241Met	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	NM_005432	O43568|Q9BU18	Missense_Mutation	SNP	ENST00000553264.1	37	CCDS9984.1	546	0.25	94	0.1910569105691057	96	0.26519337016574585	52	0.09090909090909091	304	0.40105540897097625	G	11.27	1.589788	0.28357	0.215811	0.378227	ENSG00000126215	ENST00000554913;ENST00000352127;ENST00000553264;ENST00000555055;ENST00000445556;ENST00000554974	T;T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05;1.05	4.78	1.35	0.21983	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.561051	0.19129	N	0.121979	T	0.00012	0.0000	L	0.38531	1.155	0.58432	P	5.000000000032756E-6	P	0.36171	0.541	B	0.34824	0.19	T	0.47355	-0.9124	9	0.26408	T	0.33	-18.8536	12.3156	0.54955	0.0:0.0:0.2693:0.7307	rs861539;rs1734804;rs3212111;rs17435402;rs17850783;rs56934996;rs861539	241	O43542	XRCC3_HUMAN	M	241;241;241;241;241;36	ENSP00000451362:T241M;ENSP00000343392:T241M;ENSP00000451974:T241M;ENSP00000452598:T241M;ENSP00000412990:T241M;ENSP00000451361:T36M	ENSP00000343392:T241M	T	-	2	0	XRCC3	103235506	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	0.642000	0.24735	0.376000	0.24707	0.462000	0.41574	ACG	G|0.729;A|0.271	0.271	strong		0.637	XRCC3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414631.1	NM_005432	
UCP3	7352	hgsc.bcm.edu	37	11	73717254	73717254	+	Silent	SNP	A	A	G	rs1800006	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:73717254A>G	ENST00000314032.4	-	3	849	c.297T>C	c.(295-297)taT>taC	p.Y99Y	UCP3_ENST00000426995.2_Silent_p.Y99Y|UCP3_ENST00000348534.4_Silent_p.Y99Y	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	99					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					TGACGGAGTCATAGAGGCCGA	0.622													G|||	1719	0.343251	0.6445	0.1556	5008	,	,		18847	0.2808		0.2416	False		,,,				2504	0.2382				p.Y99Y		Atlas-SNP	.											.	UCP3	31	.	0			c.T297C						PASS	.	G	,	2599,1801	528.9+/-372.5	772,1055,373	44.0	44.0	44.0		297,297	-7.6	0.3	11	dbSNP_89	44	2091,6495	715.0+/-406.0	256,1579,2458	no	coding-synonymous,coding-synonymous	UCP3	NM_003356.3,NM_022803.2	,	1028,2634,2831	GG,GA,AA		24.3536,40.9318,36.1158	,	99/313,99/276	73717254	4690,8296	2200	4293	6493	SO:0001819	synonymous_variant	7352	exon3			GGAGTCATAGAGG	AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"""Solute carriers"""	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.297T>C	11.37:g.73717254A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	53	5	0.0943396	NM_003356	O60475|Q96HL3	Silent	SNP	ENST00000314032.4	37	CCDS8229.1																																																																																			A|0.651;G|0.349	0.349	strong		0.622	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
KANSL1	284058	hgsc.bcm.edu	37	17	44117119	44117119	+	Missense_Mutation	SNP	A	A	G	rs34043286	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44117119A>G	ENST00000262419.6	-	8	2622	c.2152T>C	c.(2152-2154)Tca>Cca	p.S718P	KANSL1_ENST00000575318.1_Missense_Mutation_p.S718P|KANSL1_ENST00000432791.1_Missense_Mutation_p.S718P|KANSL1_ENST00000393476.3_Missense_Mutation_p.S75P|KANSL1_ENST00000574590.1_Missense_Mutation_p.S718P|KANSL1_ENST00000572904.1_Missense_Mutation_p.S718P	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	718			S -> P (in dbSNP:rs34043286).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TTACGAGCTGAATCTGGCAGA	0.498													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19661	0.001		0.2406	False		,,,				2504	0.0613				p.S718P		Atlas-SNP	.											.	.	.	.	0			c.T2152C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER	202,4204	807.9+/-415.9	5,192,2006	114.0	106.0	109.0		2152,2152,2152	6.1	1.0	17	dbSNP_126	109	1927,6673	726.3+/-406.6	220,1487,2593	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	74,74,74	225,1679,4599	GG,GA,AA		22.407,4.5847,16.3694	benign,benign,benign	718/1105,718/1106,718/1106	44117119	2129,10877	2203	4300	6503	SO:0001583	missense	284058	exon8			GAGCTGAATCTGG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2152T>C	17.37:g.44117119A>G	ENSP00000262419:p.Ser718Pro	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	8.847	0.943571	0.18281	0.045847	0.22407	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.22336	2.74;2.74;1.96	6.05	6.05	0.98169	.	0.072151	0.64402	N	0.000014	T	0.00012	0.0000	N	0.00308	-1.67	0.46678	P	8.470000000000422E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38045	-0.9679	9	0.17369	T	0.5	-5.2424	12.6915	0.56976	0.0762:0.0:0.9238:0.0	rs34043286	49;718	Q7Z3B3-2;Q7Z3B3	.;K1267_HUMAN	P	718;718;75	ENSP00000262419:S718P;ENSP00000387393:S718P;ENSP00000377117:S75P	ENSP00000262419:S718P	S	-	1	0	KIAA1267	41472966	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	4.936000	0.63506	1.587000	0.49959	-0.128000	0.14901	TCA	A|0.853;G|0.147	0.147	strong		0.498	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
SLC16A1	6566	hgsc.bcm.edu	37	1	113456546	113456546	+	Missense_Mutation	SNP	A	A	T	rs1049434	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:113456546A>T	ENST00000538576.1	-	5	2301	c.1470T>A	c.(1468-1470)gaT>gaA	p.D490E	SLC16A1_ENST00000369626.3_Missense_Mutation_p.D490E	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	490			D -> E (in dbSNP:rs1049434). {ECO:0000269|PubMed:10590411, ECO:0000269|PubMed:17081983, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:18691976, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:21406692, ECO:0000269|PubMed:7835905}.		behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	TGGGCCCTCCATCTGTGTCTT	0.463													T|||	3389	0.676717	0.9085	0.5519	5008	,	,		20043	0.6647		0.5626	False		,,,				2504	0.5818				p.D490E		Atlas-SNP	.											.	SLC16A1	61	.	0			c.T1470A						PASS	.	T	GLU/ASP,GLU/ASP	3721,685	288.9+/-280.1	1561,599,43	193.0	206.0	202.0		1470,1470	2.7	0.0	1	dbSNP_86	202	4944,3656	525.8+/-380.8	1422,2100,778	yes	missense,missense	SLC16A1	NM_001166496.1,NM_003051.3	45,45	2983,2699,821	TT,TA,AA		42.5116,15.547,33.3769	benign,benign	490/501,490/501	113456546	8665,4341	2203	4300	6503	SO:0001583	missense	6566	exon5			CCCTCCATCTGTG	BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"""Solute carriers"""	10922	protein-coding gene	gene with protein product		600682	"""solute carrier family 16 (monocarboxylic acid transporters), member 1"", ""solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"""			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.1470T>A	1.37:g.113456546A>T	ENSP00000441065:p.Asp490Glu	Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	273	129	0.472527	NM_001166496	Q49A45|Q5T8R6|Q9NSJ9	Missense_Mutation	SNP	ENST00000538576.1	37	CCDS858.1	1436	0.6575091575091575	443	0.9004065040650406	191	0.5276243093922652	373	0.6520979020979021	429	0.5659630606860159	T	0.009	-1.848859	0.00563	0.84453	0.574884	ENSG00000155380	ENST00000369626;ENST00000538576	T;T	0.20332	2.08;2.08	5.06	2.74	0.32292	.	1.028960	0.07686	N	0.937885	T	0.01592	0.0051	N	0.03608	-0.345	0.19775	P	0.999955287	B	0.02656	0.0	B	0.01281	0.0	T	0.43426	-0.9392	9	0.02654	T	1	.	2.5356	0.04713	0.1437:0.083:0.1728:0.6005	rs1049434;rs3189603;rs3789591;rs56625125;rs61493174;rs1049434	490	P53985	MOT1_HUMAN	E	490	ENSP00000358640:D490E;ENSP00000441065:D490E	ENSP00000358640:D490E	D	-	3	2	SLC16A1	113258069	0.089000	0.21612	0.013000	0.15412	0.018000	0.09664	-0.125000	0.10579	0.270000	0.21984	-0.265000	0.10407	GAT	A|0.340;T|0.660	0.660	strong		0.463	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051	
CBR3	874	hgsc.bcm.edu	37	21	37518582	37518582	+	Silent	SNP	G	G	A	rs17849671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:37518582G>A	ENST00000290354.5	+	3	887	c.606G>A	c.(604-606)acG>acA	p.T202T	CBR3-AS1_ENST00000427491.1_RNA|CBR3-AS1_ENST00000453159.1_RNA|CBR3-AS1_ENST00000608632.1_RNA|CBR3-AS1_ENST00000608641.1_RNA|CBR3-AS1_ENST00000608622.1_RNA|CBR3-AS1_ENST00000608690.1_RNA|CBR3-AS1_ENST00000413862.1_RNA	NM_001236.3	NP_001227.1	O75828	CBR3_HUMAN	carbonyl reductase 3	202					cognition (GO:0050890)|phylloquinone catabolic process (GO:0042376)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	3-keto sterol reductase activity (GO:0000253)|carbonyl reductase (NADPH) activity (GO:0004090)|NADPH binding (GO:0070402)			kidney(1)|large_intestine(1)|lung(1)	3					Doxorubicin(DB00997)	TGGGGGTCACGGTCTTATCGA	0.527													G|||	110	0.0219649	0.0	0.036	5008	,	,		18695	0.0		0.0606	False		,,,				2504	0.0245				p.T202T		Atlas-SNP	.											CBR3,NS,carcinoma,+1,1	CBR3	11	1	0			c.G606A						PASS	.	G		47,4359	48.9+/-83.8	0,47,2156	88.0	80.0	83.0		606	-9.6	0.4	21	dbSNP_123	83	478,8122	140.1+/-196.7	10,458,3832	no	coding-synonymous	CBR3	NM_001236.3		10,505,5988	AA,AG,GG		5.5581,1.0667,4.0366		202/278	37518582	525,12481	2203	4300	6503	SO:0001819	synonymous_variant	874	exon3			GGTCACGGTCTTA	AB004854	CCDS13642.1	21q22.2	2011-09-14			ENSG00000159231	ENSG00000159231	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	1549	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 21C, member 2"""	603608				9740676, 19027726	Standard	NM_001236		Approved	SDR21C2	uc002yve.3	O75828	OTTHUMG00000086617	ENST00000290354.5:c.606G>A	21.37:g.37518582G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_001236	Q6FHP2	Silent	SNP	ENST00000290354.5	37	CCDS13642.1																																																																																			G|0.964;A|0.036	0.036	strong		0.527	CBR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194632.1		
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 GAIIx	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_ENST00000378133.3_Silent_p.T386T|PCDHA1_ENST00000394633.3_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		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	100	18	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	
ST6GAL2	84620	hgsc.bcm.edu	37	2	107423188	107423188	+	Silent	SNP	G	G	A	rs1470591	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:107423188G>A	ENST00000409382.3	-	6	2146	c.1536C>T	c.(1534-1536)ccC>ccT	p.P512P	ST6GAL2_ENST00000361686.4_Silent_p.P512P	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	512					growth (GO:0040007)|multicellular organismal development (GO:0007275)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(30)|ovary(5)|pancreas(6)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	65						CCTGGAAGCCGGGAAGAACCA	0.542													G|||	1094	0.21845	0.1823	0.3285	5008	,	,		18730	0.0377		0.4533	False		,,,				2504	0.1339				p.P512P		Atlas-SNP	.											ST6GAL2,NS,carcinoma,-1,1	ST6GAL2	159	1	0			c.C1536T						scavenged	.	G	,	990,3416	370.8+/-319.7	101,788,1314	112.0	101.0	105.0		1536,1536	-11.6	0.0	2	dbSNP_88	105	3968,4632	551.5+/-385.9	900,2168,1232	no	coding-synonymous,coding-synonymous	ST6GAL2	NM_001142351.1,NM_032528.2	,	1001,2956,2546	AA,AG,GG		46.1395,22.4694,38.1209	,	512/530,512/530	107423188	4958,8048	2203	4300	6503	SO:0001819	synonymous_variant	84620	exon6			GAAGCCGGGAAGA	AB059555	CCDS2073.1, CCDS46380.1	2q11-q12	2008-02-05	2005-02-07	2005-02-07	ENSG00000144057	ENSG00000144057	2.4.99.2		10861	protein-coding gene	gene with protein product		608472	"""sialyltransferase 2 (monosialoganglioside sialyltransferase)"""	SIAT2			Standard	NM_032528		Approved	KIAA1877, St6gal2, St6GalII	uc002tdr.3	Q96JF0	OTTHUMG00000130923	ENST00000409382.3:c.1536C>T	2.37:g.107423188G>A		Somatic	89	2	0.0224719		WXS	Illumina HiSeq	Phase_I	68	66	0.970588	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	37	CCDS2073.1	568	0.2600732600732601	91	0.18495934959349594	119	0.3287292817679558	16	0.027972027972027972	342	0.45118733509234826	G	0.016	-1.537599	0.00942	0.224694	0.461395	ENSG00000144057	ENST00000361803	.	.	.	5.8	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999995177	.	.	.	.	.	.	T	0.08554	-1.0716	3	.	.	.	-32.3354	5.7615	0.18203	0.1271:0.0587:0.471:0.3432	rs1470591;rs3796113;rs17629922;rs1470591	.	.	.	W	78	.	.	R	-	1	2	ST6GAL2	106789620	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-5.699000	0.00104	-5.603000	0.00012	-5.073000	0.00001	CGG	G|0.679;A|0.321	0.321	strong		0.542	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528	
TAF4B	6875	hgsc.bcm.edu	37	18	23854692	23854692	+	Silent	SNP	C	C	T	rs17224558	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:23854692C>T	ENST00000269142.5	+	4	1661	c.663C>T	c.(661-663)acC>acT	p.T221T	TAF4B_ENST00000400466.2_Silent_p.T221T|TAF4B_ENST00000578121.1_Silent_p.T221T	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	221					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CTGTAACTACCCTGAAGCCTT	0.418													C|||	618	0.123403	0.1415	0.1182	5008	,	,		20318	0.1121		0.1074	False		,,,				2504	0.1309				p.T221T		Atlas-SNP	.											.	TAF4B	71	.	0			c.C663T						PASS	.	C		530,3254		32,466,1394	153.0	146.0	148.0		663	-0.2	0.4	18	dbSNP_123	148	890,7352		48,794,3279	no	coding-synonymous	TAF4B	NM_005640.1		80,1260,4673	TT,TC,CC		10.7983,14.0063,11.8077		221/863	23854692	1420,10606	1892	4121	6013	SO:0001819	synonymous_variant	6875	exon4			AACTACCCTGAAG	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.663C>T	18.37:g.23854692C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	37	CCDS42421.1																																																																																			C|0.875;T|0.125	0.125	strong		0.418	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
HEATR5B	54497	hgsc.bcm.edu	37	2	37227797	37227797	+	Missense_Mutation	SNP	C	C	G	rs62621396	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:37227797C>G	ENST00000233099.5	-	33	5572	c.5477G>C	c.(5476-5478)gGc>gCc	p.G1826A	HEATR5B_ENST00000354531.2_Missense_Mutation_p.G1737A	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1826						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TTTTTGAACGCCAGCCTCAGT	0.428													C|||	652	0.130192	0.2194	0.0548	5008	,	,		18957	0.1419		0.0507	False		,,,				2504	0.1329				p.G1826A		Atlas-SNP	.											.	HEATR5B	185	.	0			c.G5477C						PASS	.	C	ALA/GLY	903,3503	348.7+/-310.1	91,721,1391	144.0	143.0	143.0		5477	3.9	0.7	2	dbSNP_129	143	446,8154	134.7+/-192.1	11,424,3865	yes	missense	HEATR5B	NM_019024.1	60	102,1145,5256	GG,GC,CC		5.186,20.4948,10.3721	benign	1826/2072	37227797	1349,11657	2203	4300	6503	SO:0001583	missense	54497	exon33			TGAACGCCAGCCT	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.5477G>C	2.37:g.37227797C>G	ENSP00000233099:p.Gly1826Ala	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	129	59	0.457364	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	236	0.10805860805860806	115	0.23373983739837398	23	0.06353591160220995	64	0.11188811188811189	34	0.044854881266490766	C	10.85	1.465578	0.26335	0.204948	0.05186	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.40225	1.07;1.04	5.17	3.94	0.45596	Armadillo-like helical (1);Armadillo-type fold (1);	0.528090	0.22969	N	0.053446	T	0.00012	0.0000	N	0.08118	0	0.46260	P	0.001044000000000045	D;D	0.55605	0.972;0.972	P;P	0.62184	0.899;0.899	T	0.04128	-1.0975	9	0.11794	T	0.64	.	10.7169	0.46017	0.0:0.0762:0.0:0.9238	rs62621396	1826;1826	Q9P2D3;B9EK47	HTR5B_HUMAN;.	A	1826;1737	ENSP00000233099:G1826A;ENSP00000346531:G1737A	ENSP00000233099:G1826A	G	-	2	0	HEATR5B	37081301	0.996000	0.38824	0.687000	0.30102	0.708000	0.40852	3.276000	0.51646	0.803000	0.34113	-0.423000	0.05987	GGC	C|0.896;G|0.104	0.104	strong		0.428	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
PCDHGB4	8641	hgsc.bcm.edu	37	5	140769293	140769293	+	Silent	SNP	C	C	T	rs150721796	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140769293C>T	ENST00000519479.1	+	1	1842	c.1842C>T	c.(1840-1842)ctC>ctT	p.L614L	PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_003736.2|NM_018925.2|NM_032098.1	NP_003727.1|NP_061748.1|NP_115269.1	Q9UN71	PCDGG_HUMAN	protocadherin gamma subfamily B, 4	614	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(9)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(2)	37			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCCGGGCTCTTCAGCCTGG	0.682													.|||	101	0.0201677	0.003	0.0389	5008	,	,		16440	0.0		0.0666	False		,,,				2504	0.0031				p.L614L		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.C1842T						PASS	.	C	,,,,,,,,,,,	40,4216		0,40,2088	30.0	36.0	34.0		1842,,,,,,,,,,,1842	-3.0	1.0	5	dbSNP_134	34	477,8021		12,453,3784	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGB3,PCDHGB2,PCDHGB1,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_018922.2,NM_018923.2,NM_018924.2,NM_032098.1	,,,,,,,,,,,	12,493,5872	TT,TC,CC		5.6131,0.9398,4.0536	,,,,,,,,,,,	614/924,,,,,,,,,,,614/804	140769293	517,12237	2128	4249	6377	SO:0001819	synonymous_variant	8641	exon1			CGGGCTCTTCAGC	AF152520	CCDS54928.1, CCDS75337.1	5q31	2010-01-26				ENSG00000253953		"""Cadherins / Protocadherins : Clustered"""	8711	other	protocadherin	"""fibroblast cadherin FIB2"", ""cadherin 20"""	603058				10380929	Standard	NM_003736		Approved	FIB2, CDH20, PCDH-GAMMA-B4		Q9UN71		ENST00000519479.1:c.1842C>T	5.37:g.140769293C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_032098	O15099|Q2M267|Q9UN64	Silent	SNP	ENST00000519479.1	37	CCDS54928.1																																																																																			C|0.964;T|0.036	0.036	strong		0.682	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736	
MYH2	4620	hgsc.bcm.edu	37	17	10448769	10448769	+	Silent	SNP	A	A	T	rs11078850	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:10448769A>T	ENST00000245503.5	-	5	783	c.399T>A	c.(397-399)ccT>ccA	p.P133P	CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Silent_p.P133P|MYH2_ENST00000532183.2_Silent_p.P133P	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	133	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						GCTTATACACAGGCAGCCACT	0.502													T|||	2588	0.516773	0.3018	0.5144	5008	,	,		16718	0.8333		0.3847	False		,,,				2504	0.6186				p.P133P		Atlas-SNP	.											.	MYH2	390	.	0			c.T399A						PASS	.	T	,	1463,2943	680.4+/-403.8	244,975,984	90.0	94.0	92.0		399,399	-4.2	0.9	17	dbSNP_120	92	3511,5089	632.4+/-398.6	734,2043,1523	no	coding-synonymous,coding-synonymous	MYH2	NM_001100112.1,NM_017534.5	,	978,3018,2507	TT,TA,AA		40.8256,33.2047,38.2439	,	133/1942,133/1942	10448769	4974,8032	2203	4300	6503	SO:0001819	synonymous_variant	4620	exon5			ATACACAGGCAGC		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.399T>A	17.37:g.10448769A>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																			A|0.586;T|0.414	0.414	strong		0.502	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
KRT73	319101	hgsc.bcm.edu	37	12	53012128	53012128	+	Missense_Mutation	SNP	C	C	T	rs35417182	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53012128C>T	ENST00000305748.3	-	1	215	c.181G>A	c.(181-183)Gtg>Atg	p.V61M		NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	61	Gly-rich.|Head.		V -> M (in dbSNP:rs35417182).			extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		CCACTGGCCACATTGAAAGAG	0.637													C|||	406	0.0810703	0.1762	0.0519	5008	,	,		16167	0.0119		0.0318	False		,,,				2504	0.0951				p.V61M		Atlas-SNP	.											.	KRT73	101	.	0			c.G181A						PASS	.	C	MET/VAL	740,3666	285.7+/-278.4	62,616,1525	70.0	82.0	78.0		181	0.3	0.0	12	dbSNP_126	78	356,8244	114.4+/-174.4	6,344,3950	yes	missense	KRT73	NM_175068.2	21	68,960,5475	TT,TC,CC		4.1395,16.7953,8.4269	benign	61/541	53012128	1096,11910	2203	4300	6503	SO:0001583	missense	319101	exon1			TGGCCACATTGAA	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.181G>A	12.37:g.53012128C>T	ENSP00000307014:p.Val61Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	154	0.07051282051282051	99	0.20121951219512196	23	0.06353591160220995	7	0.012237762237762238	25	0.032981530343007916	C	2.818	-0.245510	0.05906	0.167953	0.041395	ENSG00000186049	ENST00000305748	T	0.75477	-0.94	4.64	0.269	0.15631	.	0.407546	0.20433	N	0.092431	T	0.00144	0.0004	L	0.52126	1.63	0.80722	P	0.0	B	0.12630	0.006	B	0.16289	0.015	T	0.08638	-1.0712	9	0.26408	T	0.33	.	10.3101	0.43704	0.0:0.5624:0.0:0.4376	rs35417182;rs61929572	61	Q86Y46	K2C73_HUMAN	M	61	ENSP00000307014:V61M	ENSP00000307014:V61M	V	-	1	0	KRT73	51298395	0.000000	0.05858	0.026000	0.17262	0.308000	0.27856	-0.053000	0.11846	-0.069000	0.12931	-0.136000	0.14681	GTG	C|0.927;T|0.073	0.073	strong		0.637	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
IPO4	79711	hgsc.bcm.edu	37	14	24647814	24647814	+	IGR	SNP	T	T	C	rs1885711	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24647814T>C	ENST00000354464.6	-	0	3646				REC8_ENST00000559919.1_Silent_p.P332P|REC8_ENST00000311457.3_Silent_p.P332P	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4						DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CTACACAGCCTATGGTGCAGC	0.567													C|||	3669	0.732628	0.9092	0.6614	5008	,	,		15515	0.87		0.507	False		,,,				2504	0.635				p.P332P		Atlas-SNP	.											.	REC8	47	.	0			c.T996C						PASS	.	C	,	3049,681		1247,555,63	53.0	60.0	58.0		996,996	-5.9	0.2	14	dbSNP_92	58	4041,4167		995,2051,1058	no	coding-synonymous,coding-synonymous	REC8	NM_001048205.1,NM_005132.2	,	2242,2606,1121	CC,CT,TT		49.2325,18.2574,40.6098	,	332/547,332/547	24647814	7090,4848	1865	4104	5969	SO:0001628	intergenic_variant	9985	exon13			ACAGCCTATGGTG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801		14.37:g.24647814T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_001048205	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																			T|0.305;C|0.695	0.695	strong		0.567	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
ABCA13	154664	hgsc.bcm.edu	37	7	48285485	48285485	+	Missense_Mutation	SNP	C	C	T	rs1880738	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48285485C>T	ENST00000435803.1	+	13	1541	c.1517C>T	c.(1516-1518)cCg>cTg	p.P506L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	506			P -> L (in dbSNP:rs1880738).		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						GCTGTCTGCCCGAATGGTCGT	0.468													C|||	2036	0.40655	0.1596	0.4366	5008	,	,		17442	0.6181		0.4115	False		,,,				2504	0.4959				p.P506L		Atlas-SNP	.											ABCA13_ENST00000435803,NS,carcinoma,0,2	ABCA13	1192	2	0			c.C1517T						scavenged	.	C	LEU/PRO	672,3066		67,538,1264	89.0	81.0	83.0		1517	-2.7	0.0	7	dbSNP_92	83	3535,4691		752,2031,1330	yes	missense	ABCA13	NM_152701.3	98	819,2569,2594	TT,TC,CC		42.9735,17.9775,35.1638	benign	506/5059	48285485	4207,7757	1869	4113	5982	SO:0001583	missense	154664	exon13			TCTGCCCGAATGG	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.1517C>T	7.37:g.48285485C>T	ENSP00000411096:p.Pro506Leu	Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	93	26	0.27957	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	866	0.3965201465201465	63	0.12804878048780488	156	0.430939226519337	340	0.5944055944055944	307	0.4050131926121372	C	10.17	1.276424	0.23307	0.179775	0.429735	ENSG00000179869	ENST00000435803	T	0.81330	-1.48	5.06	-2.68	0.06041	.	1.036610	0.07718	N	0.943236	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	0.41378	-0.9512	9	0.10377	T	0.69	.	0.6855	0.00882	0.1924:0.2748:0.1379:0.3948	rs1880738;rs17712198;rs52816810;rs59929558;rs1880738	506	Q86UQ4	ABCAD_HUMAN	L	506	ENSP00000411096:P506L	ENSP00000411096:P506L	P	+	2	0	ABCA13	48256031	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.065000	0.14466	-0.277000	0.09193	-0.136000	0.14681	CCG	C|0.624;T|0.376	0.376	strong		0.468	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
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 GAIIx	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_ENST00000392443.3_Silent_p.L11L|ATP13A4-AS1_ENST00000431512.1_RNA|ATP13A4_ENST00000295548.3_Silent_p.L11L|ATP13A4-AS1_ENST00000426459.1_RNA	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		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	118	12	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	
MORC4	79710	hgsc.bcm.edu	37	X	106221389	106221389	+	Missense_Mutation	SNP	T	T	C	rs41304048	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:106221389T>C	ENST00000355610.4	-	8	1251	c.977A>G	c.(976-978)aAt>aGt	p.N326S	MORC4_ENST00000535534.1_Missense_Mutation_p.N74S|MORC4_ENST00000255495.7_Missense_Mutation_p.N326S	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	326						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						CTGGTTACTATTCTTGCAAGA	0.383													t|||	25	0.00662252	0.0	0.0058	3775	,	,		12929	0.0		0.0199	False		,,,				2504	0.001				p.N326S		Atlas-SNP	.											.	MORC4	155	.	0			c.A977G						PASS	.	C	SER/ASN,SER/ASN	16,3819		0,11,5,1621,566	137.0	132.0	134.0		977,977	1.2	0.0	X	dbSNP_127	134	167,6561		5,100,57,2323,1815	yes	missense,missense	MORC4	NM_001085354.2,NM_024657.4	46,46	5,111,62,3944,2381	CC,CT,C,TT,T		2.4822,0.4172,1.7325	benign,benign	326/901,326/938	106221389	183,10380	2203	4300	6503	SO:0001583	missense	79710	exon8			TTACTATTCTTGC	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.977A>G	X.37:g.106221389T>C	ENSP00000347821:p.Asn326Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	79	19	0.240506	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	16	0.009644364074743821	0	0.0	1	0.0027624309392265192	0	0.0	13	0.017287234042553192	t	11.32	1.605313	0.28623	0.004172	0.024822	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.32988	2.65;1.43;2.64	4.99	1.23	0.21249	.	0.308537	0.32343	N	0.006223	T	0.10165	0.0249	L	0.35542	1.07	0.22142	N	0.999332	B;B;B	0.15473	0.013;0.003;0.01	B;B;B	0.11329	0.006;0.006;0.005	T	0.13045	-1.0524	10	0.42905	T	0.14	-1.1662	7.585	0.27987	0.0:0.2787:0.0:0.7213	rs41304048	74;326;326	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	S	326;74;326	ENSP00000347821:N326S;ENSP00000440359:N74S;ENSP00000255495:N326S	ENSP00000255495:N326S	N	-	2	0	MORC4	106108045	0.997000	0.39634	0.022000	0.16811	0.984000	0.73092	1.684000	0.37649	0.006000	0.14734	-0.408000	0.06270	AAT	T|0.984;C|0.016	0.016	strong		0.383	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
DKKL1	27120	hgsc.bcm.edu	37	19	49878115	49878115	+	Missense_Mutation	SNP	G	G	A	rs1054770	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49878115G>A	ENST00000221498.2	+	5	964	c.559G>A	c.(559-561)Ggc>Agc	p.G187S	DKKL1_ENST00000594268.1_Missense_Mutation_p.G45S|AC010524.2_ENST00000599433.1_RNA	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	187			G -> S (in dbSNP:rs1054770).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		CCTGGAGGGCGGCCACTGGCT	0.652													G|||	1583	0.316094	0.2844	0.2464	5008	,	,		15776	0.3373		0.2406	False		,,,				2504	0.4642				p.G187S		Atlas-SNP	.											.	DKKL1	23	.	0			c.G559A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	1216,3190		169,878,1156	26.0	28.0	28.0		466,334,559	-3.2	0.0	19	dbSNP_86	28	2242,6356		296,1650,2353	yes	missense,missense,missense	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	56,56,56	465,2528,3509	AA,AG,GG		26.0758,27.5987,26.5918	benign,benign,benign	156/212,112/168,187/243	49878115	3458,9546	2203	4299	6502	SO:0001583	missense	27120	exon5			GAGGGCGGCCACT	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.559G>A	19.37:g.49878115G>A	ENSP00000221498:p.Gly187Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	586	0.2683150183150183	130	0.26422764227642276	90	0.24861878453038674	186	0.32517482517482516	180	0.23746701846965698	G	9.816	1.184396	0.21870	0.275987	0.260758	ENSG00000104901	ENST00000221498	T	0.11385	2.78	4.15	-3.2	0.05156	.	0.951199	0.08710	N	0.905096	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B	0.27117	0.168	B	0.17979	0.02	T	0.43228	-0.9404	9	0.41790	T	0.15	-4.4785	8.8013	0.34909	0.5829:0.0:0.4171:0.0	rs1054770;rs3195287;rs1054770	187	Q9UK85	DKKL1_HUMAN	S	187	ENSP00000221498:G187S	ENSP00000221498:G187S	G	+	1	0	DKKL1	54569927	0.000000	0.05858	0.000000	0.03702	0.529000	0.34654	-1.471000	0.02344	-0.443000	0.07180	-0.302000	0.09304	GGC	G|0.733;A|0.267	0.267	strong		0.652	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	
CARD14	79092	hgsc.bcm.edu	37	17	78171944	78171944	+	Missense_Mutation	SNP	G	G	C	rs2066964	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78171944G>C	ENST00000573882.1	+	14	2177	c.1641G>C	c.(1639-1641)agG>agC	p.R547S	CARD14_ENST00000344227.2_Missense_Mutation_p.R547S|CARD14_ENST00000573754.1_3'UTR|CARD14_ENST00000392434.2_Missense_Mutation_p.R310S|CARD14_ENST00000570421.1_Missense_Mutation_p.R547S|RP11-334C17.5_ENST00000570309.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	547			R -> S (in dbSNP:rs2066964).		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)			CCCCTGGAAGGCTTGATGTCT	0.612													C|||	1854	0.370208	0.3079	0.2435	5008	,	,		19121	0.4554		0.4006	False		,,,				2504	0.4254				p.R547S		Atlas-SNP	.											CARD14_ENST00000309710,colon,carcinoma,0,2	CARD14	98	2	0			c.G1641C						PASS	.	C	SER/ARG,SER/ARG	1379,3027	687.2+/-404.8	220,939,1044	77.0	78.0	78.0		1641,930	0.7	0.0	17	dbSNP_96	78	3292,5308	643.5+/-399.9	634,2024,1642	yes	missense,missense	CARD14	NM_024110.3,NM_052819.2	110,110	854,2963,2686	CC,CG,GG		38.2791,31.2982,35.9142	benign,benign	547/1005,310/435	78171944	4671,8335	2203	4300	6503	SO:0001583	missense	79092	exon12			TGGAAGGCTTGAT	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.1641G>C	17.37:g.78171944G>C	ENSP00000458715:p.Arg547Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	847	0.38782051282051283	155	0.3150406504065041	97	0.26795580110497236	293	0.5122377622377622	302	0.39841688654353563	C	0.010	-1.787786	0.00628	0.312982	0.382791	ENSG00000141527	ENST00000344227;ENST00000392434;ENST00000309710	T;T	0.25912	1.77;2.46	2.81	0.71	0.18157	.	1.089900	0.07092	N	0.838903	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.46005	-0.9222	9	0.06365	T	0.9	-3.2662	6.6802	0.23115	0.0:0.3245:0.5565:0.119	rs2066964;rs56488425;rs2066964	310;547	E7ETJ2;Q9BXL6	.;CAR14_HUMAN	S	547;310;310	ENSP00000344549:R547S;ENSP00000376229:R310S	ENSP00000308507:R310S	R	+	3	2	CARD14	75786539	0.002000	0.14202	0.000000	0.03702	0.018000	0.09664	0.149000	0.16243	-0.043000	0.13513	-0.352000	0.07741	AGG	G|0.621;C|0.379	0.379	strong		0.612	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
DUSP12	11266	hgsc.bcm.edu	37	1	161721707	161721707	+	Silent	SNP	C	C	T	rs1063178	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161721707C>T	ENST00000367943.4	+	3	542	c.510C>T	c.(508-510)taC>taT	p.Y170Y		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	170					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CAATGGGATACGAAGTGGATA	0.333													C|||	1803	0.360024	0.407	0.2464	5008	,	,		18522	0.4831		0.2922	False		,,,				2504	0.32				p.Y170Y		Atlas-SNP	.											.	DUSP12	20	.	0			c.C510T						PASS	.	C		1715,2691	513.7+/-368.4	344,1027,832	95.0	103.0	100.0		510	0.1	0.7	1	dbSNP_86	100	2889,5711	452.1+/-362.9	453,1983,1864	no	coding-synonymous	DUSP12	NM_007240.1		797,3010,2696	TT,TC,CC		33.593,38.9242,35.399		170/341	161721707	4604,8402	2203	4300	6503	SO:0001819	synonymous_variant	11266	exon3			GGGATACGAAGTG	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3067	protein-coding gene	gene with protein product	"""serine/threonine specific protein phosphatase"", ""YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"""	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.510C>T	1.37:g.161721707C>T		Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	280	137	0.489286	NM_007240	Q5VXA8	Silent	SNP	ENST00000367943.4	37	CCDS1234.1																																																																																			C|0.639;N|0.000	.	strong		0.333	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240	
OR10Q1	219960	hgsc.bcm.edu	37	11	57995777	57995777	+	Missense_Mutation	SNP	G	G	A	rs11229301	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57995777G>A	ENST00000316770.2	-	1	613	c.571C>T	c.(571-573)Cgc>Tgc	p.R191C		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	191			R -> C (in dbSNP:rs11229301).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				CAGGCCAGGCGCAGGACGGGA	0.612													G|||	776	0.154952	0.1513	0.1873	5008	,	,		21565	0.123		0.163	False		,,,				2504	0.1616				p.R191C		Atlas-SNP	.											OR10Q1,NS,carcinoma,+1,2	OR10Q1	79	2	0			c.C571T						PASS	.	G	CYS/ARG	624,3778	271.9+/-270.5	53,518,1630	73.0	63.0	67.0		571	1.4	1.0	11	dbSNP_120	67	1199,7391	241.9+/-272.1	91,1017,3187	yes	missense	OR10Q1	NM_001004471.2	180	144,1535,4817	AA,AG,GG		13.9581,14.1754,14.0317	benign	191/320	57995777	1823,11169	2201	4295	6496	SO:0001583	missense	219960	exon1			CCAGGCGCAGGAC	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"""GPCR / Class A : Olfactory receptors"""	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.571C>T	11.37:g.57995777G>A	ENSP00000314324:p.Arg191Cys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	37	CCDS31547.1	325	0.1488095238095238	56	0.11382113821138211	71	0.19613259668508287	78	0.13636363636363635	120	0.158311345646438	G	5.949	0.359011	0.11239	0.141754	0.139581	ENSG00000180475	ENST00000316770	T	0.00158	8.65	4.47	1.43	0.22495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000943	T	0.00012	0.0000	M	0.80847	2.515	0.80722	P	0.0	B	0.29301	0.241	B	0.28784	0.094	T	0.36335	-0.9752	9	0.72032	D	0.01	.	6.7485	0.23474	0.0889:0.0:0.3361:0.575	rs11229301;rs56678494;rs11229301	191	Q8NGQ4	O10Q1_HUMAN	C	191	ENSP00000314324:R191C	ENSP00000314324:R191C	R	-	1	0	OR10Q1	57752353	0.000000	0.05858	0.986000	0.45419	0.101000	0.19017	-1.080000	0.03407	0.113000	0.18004	0.585000	0.79938	CGC	G|0.865;A|0.135	0.135	strong		0.612	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471	
PXK	54899	hgsc.bcm.edu	37	3	58382846	58382846	+	Silent	SNP	C	C	T	rs3191903	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:58382846C>T	ENST00000356151.2	+	10	1012	c.903C>T	c.(901-903)tgC>tgT	p.C301C	PXK_ENST00000479241.1_Silent_p.C284C|PXK_ENST00000484288.1_Silent_p.C301C|PXK_ENST00000536660.1_Silent_p.C164C|PXK_ENST00000383716.3_Silent_p.C268C|PXK_ENST00000463280.1_Silent_p.C268C|PXK_ENST00000302779.5_Silent_p.C284C|PXK_ENST00000383715.4_Silent_p.C284C	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		GGGACACTTGCCGGCTGCTGG	0.433													C|||	1005	0.200679	0.1959	0.2839	5008	,	,		18767	0.001		0.3777	False		,,,				2504	0.1718				p.C301C		Atlas-SNP	.											.	PXK	89	.	0			c.C903T						PASS	.	C		907,3499	350.8+/-311.0	89,729,1385	162.0	170.0	167.0		903	5.5	1.0	3	dbSNP_105	167	3210,5390	484.3+/-371.4	617,1976,1707	no	coding-synonymous	PXK	NM_017771.3		706,2705,3092	TT,TC,CC		37.3256,20.5856,31.6546		301/579	58382846	4117,8889	2203	4300	6503	SO:0001819	synonymous_variant	54899	exon10			CACTTGCCGGCTG	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.903C>T	3.37:g.58382846C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_017771		Silent	SNP	ENST00000356151.2	37	CCDS2889.1	493	0.22573260073260074	110	0.22357723577235772	110	0.30386740331491713	0	0.0	273	0.36015831134564646	C	10.37	1.332515	0.24167	0.205856	0.373256	ENSG00000168297	ENST00000479134	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.01452	-1.1351	3	.	.	.	-12.8138	19.5916	0.95514	0.0:1.0:0.0:0.0	rs3191903;rs17845192;rs17858004;rs17858288;rs3191903	.	.	.	V	56	.	.	A	+	2	0	PXK	58357886	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.606000	0.36826	2.861000	0.98227	0.655000	0.94253	GCC	C|0.701;T|0.299	0.299	strong		0.433	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771	
CD200R1	131450	hgsc.bcm.edu	37	3	112642572	112642572	+	Silent	SNP	T	T	C	rs79556290	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112642572T>C	ENST00000471858.1	-	7	1162	c.930A>G	c.(928-930)gcA>gcG	p.A310A	CD200R1_ENST00000295863.4_3'UTR|CD200R1_ENST00000308611.3_Silent_p.A333A	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	310					regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						ATGCCTCAGATGCCTTCACCT	0.373													C|||	375	0.0748802	0.0189	0.0159	5008	,	,		19261	0.2262		0.0328	False		,,,				2504	0.0798				p.A333A		Atlas-SNP	.											.	CD200R1	91	.	0			c.A999G						PASS	.	C	,	86,4320	817.5+/-416.3	0,86,2117	196.0	177.0	183.0		999,930	-10.5	0.0	3	dbSNP_131	183	325,8275	804.2+/-407.3	6,313,3981	no	coding-synonymous,coding-synonymous	CD200R1	NM_138806.3,NM_170780.2	,	6,399,6098	CC,CT,TT		3.7791,1.9519,3.1601	,	333/349,310/326	112642572	411,12595	2203	4300	6503	SO:0001819	synonymous_variant	131450	exon8			CTCAGATGCCTTC	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.930A>G	3.37:g.112642572T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	161	72	0.447205	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Silent	SNP	ENST00000471858.1	37	CCDS2970.1																																																																																			T|0.954;C|0.046	0.046	strong		0.373	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
RFPL4A	342931	hgsc.bcm.edu	37	19	56273285	56273285	+	Missense_Mutation	SNP	A	A	G	rs200422093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56273285A>G	ENST00000434937.2	+	2	290	c.119A>G	c.(118-120)aAg>aGg	p.K40R		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	40							zinc ion binding (GO:0008270)	p.K40R(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TCACTCCAGAAGGAGCCCGAT	0.502																																					p.K40R		Atlas-SNP	.											ENSG00000188683,NS,carcinoma,0,1	RFPL4A	8	1	1	Substitution - Missense(1)	stomach(1)	c.A119G						scavenged	.						3.0	2.0	2.0					19																	56273285		554	1274	1828	SO:0001583	missense	342931	exon2			TCCAGAAGGAGCC		CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.119A>G	19.37:g.56273285A>G	ENSP00000392936:p.Lys40Arg	Somatic	422	2	0.00473934		WXS	Illumina HiSeq	Phase_I	347	126	0.363112	NM_001145014		Missense_Mutation	SNP	ENST00000434937.2	37	CCDS46201.1	.	.	.	.	.	.	.	.	.	.	A	8.702	0.909908	0.17833	.	.	ENSG00000223638	ENST00000434937	T	0.10005	2.92	3.31	-0.759	0.11045	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);RDM domain, Ret finger protein-like (1);	.	.	.	.	T	0.12305	0.0299	M	0.72118	2.19	0.09310	N	1	B	0.32467	0.372	B	0.39531	0.302	T	0.35748	-0.9776	9	0.32370	T	0.25	-37.9873	0.4858	0.00555	0.4389:0.2097:0.1467:0.2047	.	40	A6NLU0	RFPLA_HUMAN	R	40	ENSP00000392936:K40R	ENSP00000392936:K40R	K	+	2	0	RFPL4A	60965097	0.000000	0.05858	0.000000	0.03702	0.144000	0.21451	-0.924000	0.03996	-0.357000	0.08175	0.383000	0.25322	AAG	.	.	weak		0.502	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1	XM_292796	
LTN1	26046	hgsc.bcm.edu	37	21	30339120	30339120	+	Missense_Mutation	SNP	C	C	A	rs34191159	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:30339120C>A	ENST00000361371.5	-	10	1772	c.1693G>T	c.(1693-1695)Ggc>Tgc	p.G565C	LTN1_ENST00000389194.2_Missense_Mutation_p.G611C|LTN1_ENST00000389195.2_Missense_Mutation_p.G611C			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	565			G -> C (in dbSNP:rs34191159).		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						AATTCCCAGCCTTCAATCTTC	0.353													C|||	970	0.19369	0.087	0.255	5008	,	,		20229	0.3849		0.1779	False		,,,				2504	0.1135				p.G611C		Atlas-SNP	.											.	LTN1	141	.	0			c.G1831T						PASS	.	C	CYS/GLY	422,3984	205.8+/-227.6	20,382,1801	60.0	55.0	57.0		1831	2.0	0.0	21	dbSNP_126	57	1351,7249	262.1+/-284.2	110,1131,3059	yes	missense	LTN1	NM_015565.2	159	130,1513,4860	AA,AC,CC		15.7093,9.5778,13.6322	probably-damaging	611/1813	30339120	1773,11233	2203	4300	6503	SO:0001583	missense	26046	exon10			CCCAGCCTTCAAT	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1693G>T	21.37:g.30339120C>A	ENSP00000354977:p.Gly565Cys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	42	0.591549	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		505	0.23122710622710624	49	0.09959349593495935	86	0.23756906077348067	233	0.40734265734265734	137	0.18073878627968337	C	9.941	1.217596	0.22373	0.095778	0.157093	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000389195	T;T;T	0.25414	2.15;2.16;1.8	4.75	1.97	0.26223	.	0.980624	0.08386	N	0.953805	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.69078	0.997	P	0.55667	0.781	T	0.47812	-0.9088	9	0.48119	T	0.1	.	6.5089	0.22210	0.0:0.7009:0.0:0.2991	rs34191159	565	O94822	LTN1_HUMAN	C	611;565;611	ENSP00000373846:G611C;ENSP00000354977:G565C;ENSP00000373847:G611C	ENSP00000354977:G565C	G	-	1	0	LTN1	29260991	0.010000	0.17322	0.002000	0.10522	0.002000	0.02628	0.745000	0.26259	0.318000	0.23185	-0.145000	0.13849	GGC	C|0.836;A|0.164	0.164	strong		0.353	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
NSRP1	84081	hgsc.bcm.edu	37	17	28511978	28511978	+	Silent	SNP	G	G	A	rs1979572	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:28511978G>A	ENST00000247026.5	+	7	1026	c.963G>A	c.(961-963)caG>caA	p.Q321Q	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	321	His-rich.				developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						ATCAGCACCAGCAGAAGCAAT	0.502													A|||	2911	0.58127	0.5333	0.5634	5008	,	,		21597	0.8224		0.4433	False		,,,				2504	0.5521				p.Q321Q		Atlas-SNP	.											.	NSRP1	49	.	0			c.G963A						PASS	.	A		2254,2152	580.6+/-385.2	562,1130,511	75.0	67.0	70.0		963	2.0	0.0	17	dbSNP_92	70	3963,4637	602.0+/-394.5	914,2135,1251	no	coding-synonymous	NSRP1	NM_032141.2		1476,3265,1762	AA,AG,GG		46.0814,48.8425,47.801		321/559	28511978	6217,6789	2203	4300	6503	SO:0001819	synonymous_variant	84081	exon7			GCACCAGCAGAAG	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"""coiled-coil domain containing 55"""	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.963G>A	17.37:g.28511978G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_032141	Q6FI71	Silent	SNP	ENST00000247026.5	37	CCDS11255.1																																																																																			G|0.483;A|0.517	0.517	strong		0.502	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141	
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 GAIIx	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_ENST00000405655.3_Missense_Mutation_p.L47M|PRAME_ENST00000406503.1_Missense_Mutation_p.L47M|PRAME_ENST00000485532.1_5'UTR|PRAME_ENST00000539862.1_Missense_Mutation_p.L31M|PRAME_ENST00000402697.1_Missense_Mutation_p.L47M|PRAME_ENST00000543184.1_Missense_Mutation_p.L47M|PRAME_ENST00000398743.2_Missense_Mutation_p.L47M|PRAME_ENST00000424204.2_Missense_Mutation_p.L31M	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	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	41	25	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	
PCSK5	5125	hgsc.bcm.edu	37	9	78937974	78937974	+	Missense_Mutation	SNP	C	C	T	rs3001772	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:78937974C>T	ENST00000545128.1	+	31	4566	c.4028C>T	c.(4027-4029)aCg>aTg	p.T1343M		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1343	CRM (Cys-rich motif).				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						CCAGAGTGCACGCCTGAGTTC	0.552													T|||	2451	0.489417	0.6846	0.4337	5008	,	,		18793	0.2093		0.5487	False		,,,				2504	0.4928				p.T1343M		Atlas-SNP	.											.	PCSK5	329	.	0			c.C4028T						PASS	.	T	MET/THR	1139,613		375,389,112	21.0	18.0	19.0		4028	5.7	1.0	9	dbSNP_101	19	2170,1812		603,964,424	yes	missense	PCSK5	NM_001190482.1	81	978,1353,536	TT,TC,CC		45.5048,34.9886,42.2916	benign	1343/1861	78937974	3309,2425	876	1991	2867	SO:0001583	missense	5125	exon31			AGTGCACGCCTGA		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.4028C>T	9.37:g.78937974C>T	ENSP00000446280:p.Thr1343Met	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	1020	0.46703296703296704	326	0.6626016260162602	164	0.4530386740331492	110	0.19230769230769232	420	0.554089709762533	T	10.28	1.305791	0.23736	0.650114	0.544952	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.30714	1.54;1.52	5.65	5.65	0.86999	.	0.444025	0.27340	N	0.019810	T	0.00012	0.0000	N	0.03071	-0.42	0.58432	P	6.999999999979245E-6	.	.	.	.	.	.	T	0.10019	-1.0648	7	0.40728	T	0.16	-8.0846	10.9166	0.47139	0.0:0.0746:0.0:0.9254	rs3001772;rs58696668	.	.	.	M	1343;1073;1043	ENSP00000446280:T1343M;ENSP00000411654:T1043M	ENSP00000365945:T1073M	T	+	2	0	PCSK5	78127794	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	1.767000	0.38501	0.976000	0.38417	-0.269000	0.10298	ACG	C|0.517;T|0.483	0.483	strong		0.552	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
RAB19	401409	hgsc.bcm.edu	37	7	140125750	140125750	+	Missense_Mutation	SNP	T	T	C	rs2948386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:140125750T>C	ENST00000356407.3	+	3	522	c.454T>C	c.(454-456)Tac>Cac	p.Y152H	RAB19_ENST00000537763.1_Missense_Mutation_p.Y152H|RAB19_ENST00000275874.5_Missense_Mutation_p.Y199H			A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family	152					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(3)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9	Melanoma(164;0.0142)					GGCTGAGAAGTACGGCCTCCT	0.517													T|||	733	0.146366	0.0356	0.1153	5008	,	,		18582	0.0704		0.2396	False		,,,				2504	0.3006				p.Y152H		Atlas-SNP	.											.	RAB19	21	.	0			c.T454C						PASS	.	T	HIS/TYR	269,4137	153.3+/-186.9	9,251,1943	108.0	111.0	110.0		454	-6.4	0.3	7	dbSNP_101	110	2302,6298	387.0+/-342.0	311,1680,2309	yes	missense	RAB19	NM_001008749.2	83	320,1931,4252	CC,CT,TT		26.7674,6.1053,19.7678	benign	152/218	140125750	2571,10435	2203	4300	6503	SO:0001583	missense	401409	exon4			GAGAAGTACGGCC		CCDS34762.1, CCDS34762.2	7q34	2014-05-09			ENSG00000146955	ENSG00000146955		"""RAB, member RAS oncogene"""	19982	protein-coding gene	gene with protein product							Standard	NM_001008749		Approved	RAB19B	uc010lni.2	A4D1S5	OTTHUMG00000157410	ENST00000356407.3:c.454T>C	7.37:g.140125750T>C	ENSP00000348778:p.Tyr152His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001008749	A4D1S6|B2RTS6|B5MDR2|Q9UL27	Missense_Mutation	SNP	ENST00000356407.3	37	CCDS34762.2	290	0.13278388278388278	21	0.042682926829268296	42	0.11602209944751381	36	0.06293706293706294	191	0.2519788918205805	T	10.72	1.430357	0.25726	0.061053	0.267674	ENSG00000146955	ENST00000275874;ENST00000537763;ENST00000356407	T;T;T	0.79454	-1.27;-1.27;-1.27	5.53	-6.44	0.01920	Small GTP-binding protein domain (1);	0.654754	0.17102	N	0.186978	T	0.00012	0.0000	N	0.00637	-1.305	0.54753	P	1.2000000000012001E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.13308	-1.0514	8	.	.	.	.	19.4309	0.94765	0.0:0.7041:0.0:0.2959	rs2948386;rs52792197;rs59698182;rs2948386	152	A4D1S5	RAB19_HUMAN	H	199;152;152	ENSP00000275874:Y199H;ENSP00000440167:Y152H;ENSP00000348778:Y152H	.	Y	+	1	0	RAB19	139772219	0.021000	0.18746	0.308000	0.25141	0.984000	0.73092	-0.209000	0.09358	-0.983000	0.03511	0.459000	0.35465	TAC	T|0.830;C|0.170	0.170	strong		0.517	RAB19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348740.1		
EXD1	161829	hgsc.bcm.edu	37	15	41483682	41483682	+	Silent	SNP	A	A	G	rs1971131	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:41483682A>G	ENST00000314992.5	-	8	838	c.648T>C	c.(646-648)ccT>ccC	p.P216P	EXD1_ENST00000458580.2_Silent_p.P274P|RN7SL497P_ENST00000476341.2_RNA	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	216							3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)	p.P216P(1)		large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						AGAGATATTTAGGGGCTACTT	0.383													A|||	1710	0.341454	0.5817	0.2161	5008	,	,		17705	0.2788		0.171	False		,,,				2504	0.3456				p.P216P		Atlas-SNP	.											EXD1,NS,carcinoma,0,2	EXD1	52	2	1	Substitution - coding silent(1)	prostate(1)	c.T648C						PASS	.	A		2261,2145	593.4+/-388.0	570,1121,512	87.0	92.0	90.0		648	-2.2	1.0	15	dbSNP_92	90	1382,7218	268.9+/-288.1	110,1162,3028	no	coding-synonymous	EXD1	NM_152596.2		680,2283,3540	GG,GA,AA		16.0698,48.6836,28.0101		216/515	41483682	3643,9363	2203	4300	6503	SO:0001819	synonymous_variant	161829	exon8			ATATTTAGGGGCT	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.648T>C	15.37:g.41483682A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	47	8	0.170213	NM_152596	A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	37	CCDS10072.1																																																																																			A|0.702;G|0.298	0.298	strong		0.383	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596	
NKX1-2	390010	hgsc.bcm.edu	37	10	126138345	126138345	+	Silent	SNP	C	C	T	rs112863004	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:126138345C>T	ENST00000451024.3	-	1	408	c.168G>A	c.(166-168)ggG>ggA	p.G56G	NKX1-2_ENST00000440536.2_Silent_p.G56G|RP13-238F13.3_ENST00000604581.1_RNA	NM_001146340.1	NP_001139812.1	Q9UD57	NKX12_HUMAN	NK1 homeobox 2	56					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)										TGGCATCTTTCCCCGCTTCGA	0.667													C|||	245	0.0489217	0.0106	0.0576	5008	,	,		12990	0.0079		0.1173	False		,,,				2504	0.0665				p.G56G		Atlas-SNP	.											.	NKX1-2	6	.	0			c.G168A						PASS	.						43.0	47.0	46.0					10																	126138345		692	1591	2283	SO:0001819	synonymous_variant	390010	exon1			ATCTTTCCCCGCT	CN285329	CCDS59221.1	10q26.13	2012-03-09	2007-07-09	2006-06-29		ENSG00000229544		"""Homeoboxes / ANTP class : NKL subclass"""	31652	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 121"", ""NK1 transcription factor related, locus 2 (Drosophila)"""	C10orf121		10681422	Standard	NM_001146340		Approved	bB238F13.2	uc010quf.2	Q9UD57		ENST00000451024.3:c.168G>A	10.37:g.126138345C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_001146340		Silent	SNP	ENST00000451024.3	37	CCDS59221.1																																																																																			C|0.946;T|0.054	0.054	strong		0.667	NKX1-2-001	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050861.3	XM_372331	
DOCK5	80005	hgsc.bcm.edu	37	8	25230168	25230168	+	Silent	SNP	C	C	T	rs2271108	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:25230168C>T	ENST00000276440.7	+	35	3662	c.3618C>T	c.(3616-3618)gaC>gaT	p.D1206D		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1206					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.D1206D(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		ACCTGCTGGACTATAGAACCA	0.537													C|||	2194	0.438099	0.382	0.464	5008	,	,		20146	0.3968		0.508	False		,,,				2504	0.4663				p.D1206D	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											DOCK5,NS,carcinoma,0,1	DOCK5	167	1	1	Substitution - coding silent(1)	stomach(1)	c.C3618T						PASS	.	C		1669,2737	507.8+/-366.8	322,1025,856	93.0	79.0	83.0		3618	3.5	1.0	8	dbSNP_100	83	4219,4381	570.7+/-389.4	1030,2159,1111	no	coding-synonymous	DOCK5	NM_024940.6		1352,3184,1967	TT,TC,CC		49.0581,37.8802,45.2714		1206/1871	25230168	5888,7118	2203	4300	6503	SO:0001819	synonymous_variant	80005	exon35			GCTGGACTATAGA		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3618C>T	8.37:g.25230168C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			C|0.562;T|0.438	0.438	strong		0.537	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
DSPP	1834	hgsc.bcm.edu	37	4	88536553	88536553	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88536553C>T	ENST00000282478.7	+	4	2772	c.2739C>T	c.(2737-2739)gaC>gaT	p.D913D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D913D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	913	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgacagcagtgata	0.478																																					p.D913D		Atlas-SNP	.											DSPP,NS,carcinoma,0,3	DSPP	174	3	0			c.C2739T						PASS	.						71.0	95.0	87.0					4																	88536553		1633	2974	4607	SO:0001819	synonymous_variant	1834	exon5			CAGTGACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2739C>T	4.37:g.88536553C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	83	7	0.0843373	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.478	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
OR10H2	26538	hgsc.bcm.edu	37	19	15839174	15839174	+	Silent	SNP	C	C	T	rs2285956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15839174C>T	ENST00000305899.3	+	1	341	c.321C>T	c.(319-321)ttC>ttT	p.F107F		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	107						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)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					CCTTCAGCTTCGGCTTCACCC	0.642																																					p.F107F		Atlas-SNP	.											.	OR10H2	59	.	0			c.C321T						PASS	.						60.0	56.0	58.0					19																	15839174		2202	4277	6479	SO:0001819	synonymous_variant	26538	exon1			CAGCTTCGGCTTC	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.321C>T	19.37:g.15839174C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	219	85	0.388128	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			T|1.000;|0.000	1.000	weak		0.642	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
LILRB4	11006	hgsc.bcm.edu	37	19	55178162	55178162	+	Missense_Mutation	SNP	A	A	G	rs11574576	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55178162A>G	ENST00000391736.1	+	12	1318	c.1003A>G	c.(1003-1005)Aac>Gac	p.N335D	LILRB4_ENST00000391733.3_Missense_Mutation_p.N336D|LILRB4_ENST00000270452.2_Missense_Mutation_p.N335D|LILRB4_ENST00000430952.2_Missense_Mutation_p.N335D|LILRB4_ENST00000391734.3_Missense_Mutation_p.N335D	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	335			N -> D (in dbSNP:rs11574576).		immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGCCGTGAAGAACACACAGCC	0.612													A|||	2247	0.448682	0.4395	0.3429	5008	,	,		17280	0.5615		0.2903	False		,,,				2504	0.5828				p.N335D		Atlas-SNP	.											.	LILRB4	86	.	0			c.A1003G						PASS	.	A	ASP/ASN,ASP/ASN	1749,2657	521.1+/-370.4	367,1015,821	125.0	113.0	117.0		1003,1003	-3.5	0.0	19	dbSNP_120	117	2451,6149	405.5+/-348.5	339,1773,2188	yes	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	23,23	706,2788,3009	GG,GA,AA		28.5,39.6959,32.2928	benign,benign	335/448,335/449	55178162	4200,8806	2203	4300	6503	SO:0001583	missense	11006	exon10			GTGAAGAACACAC	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1003A>G	19.37:g.55178162A>G	ENSP00000375616:p.Asn335Asp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	895	0.4097985347985348	215	0.4369918699186992	111	0.30662983425414364	337	0.5891608391608392	232	0.30606860158311344	A	0.007	-2.003554	0.00431	0.396959	0.285	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00454	7.33;7.33;7.34;7.32;7.35;7.36	1.9	-3.45	0.04781	.	.	.	.	.	T	0.00012	0.0000	N	0.00332	-1.63	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.0	T	0.24476	-1.0159	8	0.02654	T	1	.	6.5292	0.22318	0.6493:0.0:0.3507:0.0	rs11574576;rs13343440;rs52815740;rs59068627;rs11574576	335;334;336;335;335	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	D	335;335;335;335;336;334	ENSP00000375616:N335D;ENSP00000270452:N335D;ENSP00000408995:N335D;ENSP00000375614:N335D;ENSP00000375613:N336D;ENSP00000401962:N334D	ENSP00000270452:N335D	N	+	1	0	LILRB4	59869974	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.001000	0.13038	-0.842000	0.04195	-0.330000	0.08379	AAC	A|0.646;C|0.000;G|0.354	0.354	strong		0.612	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
ADH4	127	hgsc.bcm.edu	37	4	100048414	100048414	+	Missense_Mutation	SNP	T	T	C	rs1126671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100048414T>C	ENST00000265512.7	-	7	999	c.925A>G	c.(925-927)Att>Gtt	p.I309V	ADH4_ENST00000508393.1_Missense_Mutation_p.I328V|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000423445.1_Missense_Mutation_p.I328V|ADH4_ENST00000505590.1_Missense_Mutation_p.I328V	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	309			I -> V (in dbSNP:rs1126671). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		TCTGGAAAAATAGTCAATCCT	0.408													T|||	4242	0.847045	0.8608	0.7709	5008	,	,		13467	0.999		0.6968	False		,,,				2504	0.8804				p.I309V		Atlas-SNP	.											.	ADH4	35	.	0			c.A925G	GRCh37	CM025885	ADH4	M	rs1126671	PASS	.	T	VAL/ILE	3626,780	752.9+/-412.3	1487,652,64	89.0	89.0	89.0		925	-7.3	0.0	4	dbSNP_86	89	5880,2720	682.3+/-403.8	1991,1898,411	yes	missense	ADH4	NM_000670.3	29	3478,2550,475	CC,CT,TT		31.6279,17.7031,26.9107	benign	309/381	100048414	9506,3500	2203	4300	6503	SO:0001583	missense	127	exon7			GAAAAATAGTCAA	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"""Alcohol dehydrogenases"""	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.925A>G	4.37:g.100048414T>C	ENSP00000265512:p.Ile309Val	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	37	CCDS34032.1	1791	0.820054945054945	414	0.8414634146341463	274	0.7569060773480663	572	1.0	531	0.7005277044854882	T	0.061	-1.223333	0.01530	0.822969	0.683721	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590	T;T;T;T	0.06142	3.34;3.34;3.34;3.34	3.65	-7.29	0.01451	Alcohol dehydrogenase, C-terminal (1);	0.604873	0.15181	N	0.276103	T	0.00012	0.0000	N	0.21448	0.665	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27773	-1.0064	9	0.59425	D	0.04	-15.3141	3.7678	0.08629	0.0954:0.3913:0.2897:0.2237	rs1126671;rs3181816;rs17407311;rs17845683;rs17858623;rs52793462;rs57095404;rs1126671	328;309	P08319-2;P08319	.;ADH4_HUMAN	V	328;309;328;328	ENSP00000424630:I328V;ENSP00000265512:I309V;ENSP00000397939:I328V;ENSP00000425416:I328V	ENSP00000265512:I309V	I	-	1	0	ADH4	100267437	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.757000	0.04772	-2.687000	0.00405	-1.417000	0.01113	ATT	T|0.213;C|0.787	0.787	strong		0.408	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	
SUGP1	57794	hgsc.bcm.edu	37	19	19413092	19413092	+	Missense_Mutation	SNP	C	C	T	rs17751061	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:19413092C>T	ENST00000247001.5	-	7	1216	c.869G>A	c.(868-870)cGt>cAt	p.R290H	SUGP1_ENST00000585763.1_Intron	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	290			R -> H (in dbSNP:rs17751061).		gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						CTGGTTCTCACGGTTGTTCTG	0.612													C|||	345	0.0688898	0.0061	0.1037	5008	,	,		16253	0.0		0.164	False		,,,				2504	0.1022				p.R290H		Atlas-SNP	.											.	SUGP1	63	.	0			c.G869A						PASS	.	C	HIS/ARG	134,4272	96.7+/-135.4	0,134,2069	183.0	151.0	162.0		869	5.0	1.0	19	dbSNP_123	162	1359,7241	266.0+/-286.5	104,1151,3045	yes	missense	SUGP1	NM_172231.3	29	104,1285,5114	TT,TC,CC		15.8023,3.0413,11.4793	probably-damaging	290/646	19413092	1493,11513	2203	4300	6503	SO:0001583	missense	57794	exon7			TTCTCACGGTTGT	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.869G>A	19.37:g.19413092C>T	ENSP00000247001:p.Arg290His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	162	0.07417582417582418	7	0.014227642276422764	44	0.12154696132596685	0	0.0	111	0.14643799472295516	C	29.1	4.973750	0.92919	0.030413	0.158023	ENSG00000105705	ENST00000247001	T	0.44083	0.93	5.03	5.03	0.67393	SWAP/Surp (3);	0.000000	0.85682	D	0.000000	T	0.00468	0.0015	M	0.74881	2.28	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00857	-1.1538	9	0.54805	T	0.06	.	16.9243	0.86172	0.0:1.0:0.0:0.0	rs17751061;rs17751061	290	Q8IWZ8	SUGP1_HUMAN	H	290	ENSP00000247001:R290H	ENSP00000247001:R290H	R	-	2	0	SUGP1	19274092	1.000000	0.71417	0.964000	0.40570	0.985000	0.73830	5.788000	0.69020	2.350000	0.79820	0.563000	0.77884	CGT	C|0.891;T|0.109	0.109	strong		0.612	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	
OR2T29	343563	hgsc.bcm.edu	37	1	248722659	248722659	+	Missense_Mutation	SNP	C	C	T	rs201896684	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248722659C>T	ENST00000328570.3	-	1	138	c.134G>A	c.(133-135)gGa>gAa	p.G45E	RP11-438F14.3_ENST00000438623.1_RNA	NM_001004694.2	NP_001004694.2	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T, member 29	45						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|lung(4)	5	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)			GACAGCATTTCCAGACAACGC	0.468													.|||	1884	0.376198	0.5545	0.2795	5008	,	,		18263	0.3849		0.2535	False		,,,				2504	0.3211				p.G45E		Atlas-SNP	.											.	OR2T29	8	.	0			c.G134A						PASS	.						19.0	12.0	15.0					1																	248722659		2093	3766	5859	SO:0001583	missense	343563	exon1			GCATTTCCAGACA		CCDS55695.1	1q44	2012-08-09			ENSG00000182783	ENSG00000182783		"""GPCR / Class A : Olfactory receptors"""	31253	protein-coding gene	gene with protein product							Standard	NM_001004694		Approved		uc001ieo.2	Q8NH02	OTTHUMG00000040382	ENST00000328570.3:c.134G>A	1.37:g.248722659C>T	ENSP00000331774:p.Gly45Glu	Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	428	150	0.350467	NM_001004694		Missense_Mutation	SNP	ENST00000328570.3	37	CCDS55695.1	.	.	.	.	.	.	.	.	.	.	t	2.377	-0.343086	0.05243	.	.	ENSG00000182783	ENST00000328570	T	0.00538	6.71	2.73	1.8	0.24995	GPCR, rhodopsin-like superfamily (1);	0.315091	0.22855	N	0.054817	T	0.00754	0.0025	M	0.82823	2.61	0.54753	P	2.0000000000020002E-5	B	0.21606	0.058	B	0.25759	0.063	T	0.13764	-1.0497	9	0.56958	D	0.05	.	4.0976	0.09998	0.0:0.6121:0.2429:0.1449	.	45	Q8NH02	O2T29_HUMAN	E	45	ENSP00000331774:G45E	ENSP00000331774:G45E	G	-	2	0	OR2T29	246789282	0.000000	0.05858	0.968000	0.41197	0.022000	0.10575	0.495000	0.22483	0.370000	0.24538	-1.024000	0.02432	GGA	C|0.250;T|0.750	0.750	weak		0.468	OR2T29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097132.1	NM_001004694	
SECISBP2L	9728	hgsc.bcm.edu	37	15	49293194	49293194	+	Missense_Mutation	SNP	C	C	A	rs11854184	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:49293194C>A	ENST00000559471.1	-	15	2391	c.2128G>T	c.(2128-2130)Gta>Tta	p.V710L	SECISBP2L_ENST00000559122.1_5'UTR|SECISBP2L_ENST00000261847.3_Missense_Mutation_p.V665L	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	710							poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTTGCTCTTACAGGATCTTTT	0.378													C|||	385	0.076877	0.0408	0.1081	5008	,	,		17414	0.003		0.2018	False		,,,				2504	0.0511				p.V710L		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.G2128T						PASS	.	C	LEU/VAL,LEU/VAL	275,4119	154.8+/-188.1	10,255,1932	123.0	108.0	113.0		2128,1993	4.2	1.0	15	dbSNP_120	113	1897,6693	335.5+/-321.5	195,1507,2593	yes	missense,missense	SECISBP2L	NM_001193489.1,NM_014701.3	32,32	205,1762,4525	AA,AC,CC		22.0838,6.2585,16.7283	benign,benign	710/1102,665/1057	49293194	2172,10812	2197	4295	6492	SO:0001583	missense	9728	exon15			CTCTTACAGGATC	BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2128G>T	15.37:g.49293194C>A	ENSP00000453854:p.Val710Leu	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	208	204	0.980769	NM_001193489	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	219	0.10027472527472528	24	0.04878048780487805	42	0.11602209944751381	2	0.0034965034965034965	151	0.19920844327176782	C	14.83	2.651974	0.47362	0.062585	0.220838	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.56611	0.45	5.09	4.17	0.49024	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.361874	0.29046	N	0.013316	T	0.00039	0.0001	N	0.22421	0.69	0.29397	P	0.862182	B;B	0.18610	0.029;0.013	B;B	0.15870	0.014;0.008	T	0.06267	-1.0836	9	0.49607	T	0.09	.	8.8473	0.35179	0.0:0.7802:0.0:0.2198	rs11854184;rs52809376;rs59584512;rs11854184	710;665	Q93073;Q93073-2	SBP2L_HUMAN;.	L	665;710	ENSP00000261847:V665L	ENSP00000261847:V665L	V	-	1	0	SECISBP2L	47080486	1.000000	0.71417	0.956000	0.39512	0.900000	0.52787	3.043000	0.49823	1.282000	0.44496	-0.251000	0.11542	GTA	C|0.860;A|0.140	0.140	strong		0.378	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701	
CCDC91	55297	hgsc.bcm.edu	37	12	28412372	28412372	+	Missense_Mutation	SNP	G	G	A	rs11049488	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:28412372G>A	ENST00000545336.1	+	6	525	c.106G>A	c.(106-108)Gca>Aca	p.A36T	CCDC91_ENST00000381256.1_Missense_Mutation_p.A36T|CCDC91_ENST00000539107.1_Missense_Mutation_p.A36T|CCDC91_ENST00000381259.1_Missense_Mutation_p.A36T			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	36				A -> T (in Ref. 1; AAP42284). {ECO:0000305}.	protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					TGCCTTTCCTGCAGGTATTGG	0.388													A|||	624	0.124601	0.0182	0.1239	5008	,	,		14041	0.0427		0.2972	False		,,,				2504	0.1759				p.A36T		Atlas-SNP	.											.	CCDC91	63	.	0			c.G106A						PASS	.	A	THR/ALA	243,4163	803.2+/-415.7	8,227,1968	112.0	93.0	100.0		106	-0.5	1.0	12	dbSNP_120	100	2641,5957	685.6+/-404.1	403,1835,2061	yes	missense	CCDC91	NM_018318.3	58	411,2062,4029	AA,AG,GG		30.7164,5.5152,22.1778	benign	36/442	28412372	2884,10120	2203	4299	6502	SO:0001583	missense	55297	exon2			TTTCCTGCAGGTA	AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"""GGA binding partner"""					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.106G>A	12.37:g.28412372G>A	ENSP00000438040:p.Ala36Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_018318	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	37	CCDS8716.1	331	0.15155677655677655	16	0.032520325203252036	50	0.13812154696132597	31	0.05419580419580419	234	0.3087071240105541	A	5.392	0.257578	0.10239	0.055152	0.307164	ENSG00000123106	ENST00000538586;ENST00000539107;ENST00000536442;ENST00000545336;ENST00000543534;ENST00000545737;ENST00000381259;ENST00000381256	T;T;T;T;T;T	0.30448	1.56;1.53;1.54;1.53;1.54;1.56	5.57	-0.515	0.11954	.	0.204155	0.34268	N	0.004109	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999920092	B	0.02656	0.0	B	0.08055	0.003	T	0.38373	-0.9664	9	0.09843	T	0.71	-2.8834	1.3506	0.02172	0.4348:0.1422:0.2856:0.1374	rs11049488;rs52814885;rs58237387;rs11049488	36	Q7Z6B0	CCD91_HUMAN	T	36	ENSP00000440513:A36T;ENSP00000445660:A36T;ENSP00000438040:A36T;ENSP00000442544:A36T;ENSP00000370658:A36T;ENSP00000370655:A36T	ENSP00000370655:A36T	A	+	1	0	CCDC91	28303639	0.388000	0.25197	0.992000	0.48379	0.931000	0.56810	-0.115000	0.10741	-0.272000	0.09259	-0.254000	0.11334	GCA	G|0.816;A|0.184	0.184	strong		0.388	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1	NM_018318	
PDE6C	5146	hgsc.bcm.edu	37	10	95389041	95389041	+	Silent	SNP	G	G	A	rs714550	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:95389041G>A	ENST00000371447.3	+	8	1236	c.1098G>A	c.(1096-1098)gcG>gcA	p.A366A		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	366	GAF 2.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	ATGCCCCTGCGGATGAATACT	0.507													G|||	1982	0.395767	0.4493	0.389	5008	,	,		21297	0.4792		0.3459	False		,,,				2504	0.2935				p.A366A		Atlas-SNP	.											.	PDE6C	97	.	0			c.G1098A						PASS	.	G		1894,2512	544.9+/-376.7	426,1042,735	175.0	153.0	160.0		1098	-8.3	0.7	10	dbSNP_86	160	2870,5730	451.3+/-362.6	474,1922,1904	no	coding-synonymous	PDE6C	NM_006204.3		900,2964,2639	AA,AG,GG		33.3721,42.9868,36.6292		366/859	95389041	4764,8242	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon8			CCCTGCGGATGAA	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1098G>A	10.37:g.95389041G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			G|0.622;A|0.378	0.378	strong		0.507	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
ASGR2	433	hgsc.bcm.edu	37	17	7011225	7011225	+	Splice_Site	SNP	T	T	G	rs61731746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7011225T>G	ENST00000380952.2	-	5	618	c.354A>C	c.(352-354)ggA>ggC	p.G118G	ASGR2_ENST00000355035.5_Splice_Site_p.G118G|ASGR2_ENST00000446679.2_Splice_Site_p.G99G|ASGR2_ENST00000254850.7_Splice_Site_p.G94G	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	118					bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)	p.G118G(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	CCACGCTGCCTCCTGGAAGCG	0.652													T|||	584	0.116613	0.2738	0.0461	5008	,	,		18665	0.0952		0.0507	False		,,,				2504	0.044				p.G118G		Atlas-SNP	.											ASGR2,NS,carcinoma,0,1	ASGR2	38	1	1	Substitution - coding silent(1)	stomach(1)	c.A354C						PASS	.	T	,,,,	1075,3331	391.2+/-328.0	142,791,1270	193.0	132.0	152.0		354,339,354,282,297	-0.1	0.7	17	dbSNP_129	152	387,8213	125.1+/-183.8	15,357,3928	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	,,,,	157,1148,5198	GG,GT,TT		4.5,24.3985,11.241	,,,,	118/312,113/307,118/312,94/288,99/293	7011225	1462,11544	2203	4300	6503	SO:0001630	splice_region_variant	433	exon5			GCTGCCTCCTGGA	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.353-1A>C	17.37:g.7011225T>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	48	0.440367	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Silent	SNP	ENST00000380952.2	37	CCDS32544.1																																																																																			T|0.891;G|0.109	0.109	strong		0.652	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	Silent
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97922851	97922851	+	Silent	SNP	C	C	T	rs12728	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:97922851C>T	ENST00000005260.8	-	14	1733	c.1518G>A	c.(1516-1518)tcG>tcA	p.S506S		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	506	Binds F-actin.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			TGATGGGTGCCGAGCGATCAT	0.562													C|||	1333	0.266174	0.1392	0.3458	5008	,	,		16342	0.2688		0.4801	False		,,,				2504	0.1585				p.S506S		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.G1518A						PASS	.	C		881,3525	341.2+/-306.6	84,713,1406	128.0	125.0	126.0		1518	-9.9	0.2	7	dbSNP_52	126	4338,4262	580.7+/-391.1	1103,2132,1065	no	coding-synonymous	BAIAP2L1	NM_018842.4		1187,2845,2471	TT,TC,CC		49.5581,19.9955,40.1276		506/512	97922851	5219,7787	2203	4300	6503	SO:0001819	synonymous_variant	55971	exon14			GGGTGCCGAGCGA	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1518G>A	7.37:g.97922851C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																			C|0.634;T|0.366	0.366	strong		0.562	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
CASP7	840	hgsc.bcm.edu	37	10	115457264	115457264	+	Missense_Mutation	SNP	T	T	G	rs11555408	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:115457264T>G	ENST00000345633.4	+	3	396	c.12T>G	c.(10-12)gaT>gaG	p.D4E	CASP7_ENST00000369321.2_Missense_Mutation_p.D37E|CASP7_ENST00000369315.1_Missense_Mutation_p.D4E|CASP7_ENST00000369331.4_Missense_Mutation_p.D4E|CASP7_ENST00000369318.3_Missense_Mutation_p.D4E	NM_033339.4	NP_203125.1	P55210	CASP7_HUMAN	caspase 7, apoptosis-related cysteine peptidase	4			D -> E (in dbSNP:rs11593766). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway (GO:0097193)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)	8		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)		TGGCAGATGATCAGGGCTGTA	0.453													T|||	529	0.105631	0.146	0.0807	5008	,	,		21630	0.0883		0.1044	False		,,,				2504	0.0879				p.I79S		Atlas-SNP	.											.	CASP7	21	.	0			c.T236G						PASS	.	T	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	542,3864	246.2+/-254.9	35,472,1696	182.0	178.0	180.0		12,111,12,12	2.0	0.1	10	dbSNP_120	180	892,7708	201.3+/-244.8	59,774,3467	yes	missense,missense,missense,missense	CASP7	NM_001227.3,NM_033338.4,NM_033339.3,NM_033340.2	45,45,45,45	94,1246,5163	GG,GT,TT		10.3721,12.3014,11.0257	benign,benign,benign,benign	4/304,37/337,4/304,4/254	115457264	1434,11572	2203	4300	6503	SO:0001583	missense	840	exon2			AGATGATCAGGGC	U37448	CCDS7580.1, CCDS7581.1, CCDS7582.1, CCDS58096.1, CCDS73200.1	10q25	2006-02-17	2005-08-17		ENSG00000165806	ENSG00000165806		"""Caspases"""	1508	protein-coding gene	gene with protein product		601761	"""caspase 7, apoptosis-related cysteine protease"""			8521391, 8576161	Standard	NM_033338		Approved	MCH3, CMH-1, ICE-LAP3	uc010qsa.3	P55210	OTTHUMG00000019076	ENST00000345633.4:c.12T>G	10.37:g.115457264T>G	ENSP00000298701:p.Asp4Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	54	0.650602	NM_001267057	B4DQU7|B5BU45|D3DRB8|Q13364|Q53YD5|Q5SVL0|Q5SVL3|Q96BA0	Missense_Mutation	SNP	ENST00000345633.4	37	CCDS7581.1	231	0.10576923076923077	74	0.15040650406504066	32	0.08839779005524862	45	0.07867132867132867	80	0.10554089709762533	T	13.38	2.220932	0.39201	0.123014	0.103721	ENSG00000165806	ENST00000429617;ENST00000369331;ENST00000369321;ENST00000345633;ENST00000369318;ENST00000442393;ENST00000369319;ENST00000369316;ENST00000369315	T;T;T;T;T;T	0.11495	3.74;2.77;4.28;4.37;4.37;4.37	4.39	2.04	0.26737	.	0.454251	0.19939	N	0.102697	T	0.00073	0.0002	M	0.62723	1.935	0.36861	P	0.11158199999999996	B;B;P	0.45715	0.041;0.147;0.865	B;B;P	0.45310	0.026;0.042;0.476	T	0.20974	-1.0259	9	0.30078	T	0.28	.	5.7337	0.18055	0.0:0.2196:0.0:0.7804	rs11593766;rs17845478;rs17858357;rs11593766	37;4;4	P55210-3;P55210;P55210-2	.;CASP7_HUMAN;.	E	4;4;37;4;4;4;4;4;4	ENSP00000400094:D4E;ENSP00000358337:D4E;ENSP00000358327:D37E;ENSP00000298701:D4E;ENSP00000358324:D4E;ENSP00000358321:D4E	ENSP00000298701:D4E	D	+	3	2	CASP7	115447254	0.144000	0.22641	0.110000	0.21437	0.309000	0.27889	0.009000	0.13219	0.317000	0.23160	0.533000	0.62120	GAT	T|0.889;G|0.111	0.111	strong		0.453	CASP7-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050439.1	NM_033338	
CPXM2	119587	hgsc.bcm.edu	37	10	125528048	125528048	+	Silent	SNP	G	G	A	rs1219725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:125528048G>A	ENST00000241305.3	-	9	1447	c.1293C>T	c.(1291-1293)taC>taT	p.Y431Y	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	431					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		TTACCCCTTCGTAGGCCTTCT	0.612													G|||	1897	0.378794	0.1528	0.4784	5008	,	,		11886	0.5992		0.3738	False		,,,				2504	0.3916				p.Y431Y		Atlas-SNP	.											.	CPXM2	120	.	0			c.C1293T						PASS	.	G		844,3562	331.8+/-302.1	73,698,1432	68.0	56.0	60.0		1293	-4.3	0.4	10	dbSNP_87	60	3228,5372	485.9+/-371.8	614,2000,1686	no	coding-synonymous	CPXM2	NM_198148.2		687,2698,3118	AA,AG,GG		37.5349,19.1557,31.3086		431/757	125528048	4072,8934	2203	4300	6503	SO:0001819	synonymous_variant	119587	exon9			CCCTTCGTAGGCC	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase"""					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.1293C>T	10.37:g.125528048G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	24	23	0.958333	NM_198148	B4E3Q2	Silent	SNP	ENST00000241305.3	37	CCDS7637.1																																																																																			G|0.654;A|0.346	0.346	strong		0.612	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148	
SCLY	51540	hgsc.bcm.edu	37	2	238999883	238999883	+	Silent	SNP	T	T	C	rs1128552	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238999883T>C	ENST00000555827.1	+	8	973	c.909T>C	c.(907-909)gcT>gcC	p.A303A	SCLY_ENST00000373332.3_Silent_p.A221A|SCLY_ENST00000429612.2_Intron|SCLY_ENST00000254663.6_Silent_p.A311A|SCLY_ENST00000409736.2_Silent_p.A303A|SCLY_ENST00000422984.2_Silent_p.A209A			Q96I15	SCLY_HUMAN	selenocysteine lyase	303					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)	p.A303A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		CAATGATTGCTGGCCTTGGGA	0.478													C|||	1074	0.214457	0.1838	0.2349	5008	,	,		18815	0.0704		0.2177	False		,,,				2504	0.3865				p.A311A	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											SCLY,NS,carcinoma,0,1	SCLY	51	1	1	Substitution - coding silent(1)	stomach(1)	c.T933C						scavenged	.	C		866,3540	744.4+/-411.6	86,694,1423	252.0	236.0	242.0		933	-3.9	1.0	2	dbSNP_86	242	1927,6673	726.6+/-406.6	222,1483,2595	no	coding-synonymous	SCLY	NM_016510.5		308,2177,4018	CC,CT,TT		22.407,19.655,21.4747		311/454	238999883	2793,10213	2203	4300	6503	SO:0001819	synonymous_variant	51540	exon8			GATTGCTGGCCTT	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.909T>C	2.37:g.238999883T>C		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	226	113	0.5	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Silent	SNP	ENST00000555827.1	37		389|389	0.17811355311355312|0.17811355311355312	104|104	0.21138211382113822|0.21138211382113822	81|81	0.22375690607734808|0.22375690607734808	29|29	0.050699300699300696|0.050699300699300696	175|175	0.23087071240105542|0.23087071240105542	C|C	10.29|10.29	1.309196|1.309196	0.23821|0.23821	0.19655|0.19655	0.22407|0.22407	ENSG00000132330|ENSG00000132330	ENST00000440143;ENST00000433750|ENST00000437134	.|.	.|.	.|.	5.48|5.48	-3.93|-3.93	0.04143|0.04143	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24621|0.24621	-1.0155|-1.0155	3|3	.|.	.|.	.|.	-27.6118|-27.6118	10.8593|10.8593	0.46817|0.46817	0.0:0.1559:0.1139:0.7302|0.0:0.1559:0.1139:0.7302	rs1128552;rs3185626;rs1128552|rs1128552;rs3185626;rs1128552	.|.	.|.	.|.	P|R	45|147	.|.	.|.	L|W	+|+	2|1	0|0	SCLY|SCLY	238664622|238664622	0.000000|0.000000	0.05858|0.05858	0.959000|0.959000	0.39883|0.39883	0.838000|0.838000	0.47535|0.47535	-3.358000|-3.358000	0.00499|0.00499	-0.637000|-0.637000	0.05516|0.05516	-1.651000|-1.651000	0.00758|0.00758	CTG|TGG	T|0.801;C|0.199	0.199	strong		0.478	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
PODXL	5420	hgsc.bcm.edu	37	7	131196062	131196062	+	Silent	SNP	C	C	T	rs17744792	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:131196062C>T	ENST00000378555.3	-	2	478	c.231G>A	c.(229-231)tcG>tcA	p.S77S	PODXL_ENST00000537928.1_Silent_p.S77S|PODXL_ENST00000322985.9_Silent_p.S77S|PODXL_ENST00000465001.1_5'UTR|PODXL_ENST00000541194.1_Silent_p.S79S			O00592	PODXL_HUMAN	podocalyxin-like	77	Thr-rich.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					TCGCCTTGACCGAGGCCAAGA	0.572													C|||	502	0.10024	0.0567	0.1369	5008	,	,		18838	0.0099		0.1849	False		,,,				2504	0.1391				p.S77S		Atlas-SNP	.											.	PODXL	53	.	0			c.G231A						PASS	.	C	,	334,4072	175.5+/-204.9	14,306,1883	174.0	167.0	169.0		231,231	-5.2	0.0	7	dbSNP_123	169	1477,7123	280.6+/-294.6	129,1219,2952	no	coding-synonymous,coding-synonymous	PODXL	NM_001018111.2,NM_005397.3	,	143,1525,4835	TT,TC,CC		17.1744,7.5806,13.9243	,	77/559,77/527	131196062	1811,11195	2203	4300	6503	SO:0001819	synonymous_variant	5420	exon2			CTTGACCGAGGCC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.231G>A	7.37:g.131196062C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	37	CCDS34755.1																																																																																			C|0.871;T|0.129	0.129	strong		0.572	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
THRB	7068	hgsc.bcm.edu	37	3	24184995	24184995	+	Silent	SNP	G	G	A	rs3752874	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:24184995G>A	ENST00000356447.4	-	7	1019	c.735C>T	c.(733-735)ttC>ttT	p.F245F	THRB_ENST00000416420.1_Silent_p.F245F|THRB_ENST00000280696.5_Silent_p.F260F|THRB_ENST00000396671.2_Silent_p.F245F	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	245	Interaction with NR2F6.|Ligand-binding.				female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GCCTTACCAGGAATTTCCGTT	0.488													G|||	789	0.157548	0.1536	0.1873	5008	,	,		21207	0.0605		0.1531	False		,,,				2504	0.2464				p.F245F	Melanoma(21;896 1043 15021 37958)	Atlas-SNP	.											.	THRB	52	.	0			c.C735T						PASS	.	G	,,	660,3746	280.5+/-275.4	56,548,1599	128.0	133.0	131.0		735,735,735	-1.0	1.0	3	dbSNP_107	131	1338,7262	261.3+/-283.8	117,1104,3079	no	coding-synonymous,coding-synonymous,coding-synonymous	THRB	NM_000461.4,NM_001128176.1,NM_001128177.1	,,	173,1652,4678	AA,AG,GG		15.5581,14.9796,15.3621	,,	245/462,245/462,245/462	24184995	1998,11008	2203	4300	6503	SO:0001819	synonymous_variant	7068	exon7			TACCAGGAATTTC		CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090		"""Nuclear hormone receptors"""	11799	protein-coding gene	gene with protein product	"""avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2"", ""oncogene ERBA2"", ""generalized resistance to thyroid hormone"", ""thyroid hormone receptor beta 1"""	190160	"""thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2)"", ""pituitary resistance to thyroid hormone"", ""thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)"""	ERBA2, PRTH		1973914, 8040303	Standard	NM_000461		Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.735C>T	3.37:g.24184995G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	147	75	0.510204	NM_000461	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	Silent	SNP	ENST00000356447.4	37	CCDS2641.1																																																																																			G|0.858;A|0.142	0.142	strong		0.488	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252877.3	NM_000461	
MACROD1	28992	hgsc.bcm.edu	37	11	63884453	63884453	+	Intron	SNP	C	C	T	rs3751120	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:63884453C>T	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.R238R	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						CCAACCAGCGCATCGCCGACG	0.657													C|||	1768	0.353035	0.6014	0.1873	5008	,	,		19038	0.5377		0.0865	False		,,,				2504	0.2188				p.R238R		Atlas-SNP	.											.	FLRT1	46	.	0			c.C714T						PASS	.	C	,	2191,2211	546.4+/-377.0	556,1079,566	33.0	31.0	32.0		714,	2.5	1.0	11	dbSNP_107	32	616,7978	154.3+/-208.6	29,558,3710	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	585,1637,4276	TT,TC,CC		7.1678,49.7728,21.599	,	238/675,	63884453	2807,10189	2201	4297	6498	SO:0001627	intron_variant	23769	exon2			CCAGCGCATCGCC	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+34257G>A	11.37:g.63884453C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	59	18	0.305085	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			C|0.702;T|0.298	0.298	strong		0.657	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
PCNXL3	399909	hgsc.bcm.edu	37	11	65387012	65387012	+	Silent	SNP	C	C	T	rs57318451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:65387012C>T	ENST00000355703.3	+	7	2249	c.1710C>T	c.(1708-1710)gcC>gcT	p.A570A		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	570						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						GGGCAGCGGCCGAGGAGACTG	0.647													C|||	547	0.109225	0.1278	0.3055	5008	,	,		17444	0.1577		0.004	False		,,,				2504	0.0031				p.A570A		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C1710T						PASS	.	C		451,3695		26,399,1648	16.0	22.0	20.0		1710	-6.3	0.1	11	dbSNP_129	20	22,8334		0,22,4156	no	coding-synonymous	PCNXL3	NM_032223.2		26,421,5804	TT,TC,CC		0.2633,10.878,3.7834		570/2035	65387012	473,12029	2073	4178	6251	SO:0001819	synonymous_variant	399909	exon7			AGCGGCCGAGGAG	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.1710C>T	11.37:g.65387012C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			C|0.904;T|0.096	0.096	strong		0.647	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
OR8B4	283162	hgsc.bcm.edu	37	11	124294377	124294377	+	Missense_Mutation	SNP	A	A	G	rs4057750	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124294377A>G	ENST00000356130.3	-	1	412	c.391T>C	c.(391-393)Tac>Cac	p.Y131H		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	131			Y -> H (in dbSNP:rs4057750). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GTGACCATGTAGAGCAGGGGG	0.502													A|||	1302	0.259984	0.3843	0.1931	5008	,	,		22069	0.2163		0.1978	False		,,,				2504	0.2485				p.Y131H		Atlas-SNP	.											OR8B4,NS,carcinoma,+1,1	OR8B4	60	1	0			c.T391C						PASS	.	A	HIS/TYR	1502,2900	478.5+/-358.2	263,976,962	90.0	84.0	86.0		391	4.6	0.9	11	dbSNP_108	86	1963,6635	344.7+/-325.5	219,1525,2555	no	missense	OR8B4	NM_001005196.1	83	482,2501,3517	GG,GA,AA		22.8309,34.1209,26.6538	probably-damaging	131/310	124294377	3465,9535	2201	4299	6500	SO:0001583	missense	283162	exon1			CCATGTAGAGCAG	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.391T>C	11.37:g.124294377A>G	ENSP00000348449:p.Tyr131His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	85	73	0.858824	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	543	0.24862637362637363	214	0.4349593495934959	70	0.19337016574585636	107	0.18706293706293706	152	0.20052770448548812	a	18.02	3.530106	0.64860	0.341209	0.228309	ENSG00000198657	ENST00000356130	T	0.00392	7.58	4.62	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000198	T	0.00012	0.0000	M	0.93106	3.38	0.22156	P	0.999323742	D	0.89917	1.0	D	0.91635	0.999	T	0.44682	-0.9312	9	0.72032	D	0.01	.	14.1353	0.65284	1.0:0.0:0.0:0.0	rs4057750;rs52820788;rs4057750	131	Q96RC9	OR8B4_HUMAN	H	131	ENSP00000348449:Y131H	ENSP00000348449:Y131H	Y	-	1	0	OR8B4	123799587	1.000000	0.71417	0.928000	0.36995	0.531000	0.34715	8.756000	0.91651	2.073000	0.62155	0.533000	0.62120	TAC	A|0.742;G|0.258	0.258	strong		0.502	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
ANKS3	124401	hgsc.bcm.edu	37	16	4748825	4748825	+	Silent	SNP	C	C	T	rs841214	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4748825C>T	ENST00000304283.4	-	13	1821	c.1527G>A	c.(1525-1527)caG>caA	p.Q509Q	ANKS3_ENST00000585773.1_Silent_p.Q436Q|ANKS3_ENST00000446014.2_Silent_p.Q380Q	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	509										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						TGGCGAGCTCCTGCATCTCAG	0.667													C|||	2028	0.404952	0.146	0.4611	5008	,	,		13432	0.624		0.4602	False		,,,				2504	0.4325				p.Q509Q		Atlas-SNP	.											ANKS3,NS,carcinoma,0,1	ANKS3	44	1	0			c.G1527A						scavenged	.	C	,	955,3437		106,743,1347	49.0	61.0	57.0		1206,1527	2.2	1.0	16	dbSNP_86	57	4020,4576		994,2032,1272	no	coding-synonymous,coding-synonymous	ANKS3	NM_001242929.1,NM_133450.3	,	1100,2775,2619	TT,TC,CC		46.7659,21.7441,38.3046	,	402/550,509/657	4748825	4975,8013	2196	4298	6494	SO:0001819	synonymous_variant	124401	exon13			GAGCTCCTGCATC	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.1527G>A	16.37:g.4748825C>T		Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_133450	B4DWU4|D3DUE2|Q8TF25	Silent	SNP	ENST00000304283.4	37	CCDS10520.1																																																																																			C|0.602;T|0.398	0.398	strong		0.667	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450	
FMNL2	114793	hgsc.bcm.edu	37	2	153435434	153435434	+	Silent	SNP	C	C	T	rs16831399	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:153435434C>T	ENST00000288670.9	+	8	1105	c.738C>T	c.(736-738)caC>caT	p.H246H		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	246	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						CTCATCCACACGCTGTCAATG	0.388													C|||	715	0.142772	0.2897	0.1268	5008	,	,		19052	0.0367		0.1312	False		,,,				2504	0.0767				p.H246H		Atlas-SNP	.											.	FMNL2	75	.	0			c.C738T						PASS	.	C		971,2891		126,719,1086	78.0	75.0	76.0		738	-0.8	1.0	2	dbSNP_123	76	1127,7203		75,977,3113	no	coding-synonymous	FMNL2	NM_052905.3		201,1696,4199	TT,TC,CC		13.5294,25.1424,17.208		246/1093	153435434	2098,10094	1931	4165	6096	SO:0001819	synonymous_variant	114793	exon8			TCCACACGCTGTC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.738C>T	2.37:g.153435434C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	50	13	0.26	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																			C|0.842;N|0.000	.	strong		0.388	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
CARNS1	57571	hgsc.bcm.edu	37	11	67186271	67186271	+	Missense_Mutation	SNP	C	C	A	rs868167	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67186271C>A	ENST00000307823.3	+	4	492	c.40C>A	c.(40-42)Cca>Aca	p.P14T	CARNS1_ENST00000423745.2_Missense_Mutation_p.P14T|CARNS1_ENST00000531040.1_Missense_Mutation_p.P137T|CARNS1_ENST00000445895.2_Missense_Mutation_p.P137T	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	14			P -> T (in dbSNP:rs868167).		ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						GATGAAGGTGCCAGCACCCGG	0.637													C|||	887	0.177117	0.4887	0.2983	5008	,	,		16953	0.0288		0.005	False		,,,				2504	0.0				p.P137T		Atlas-SNP	.											.	CARNS1	60	.	0			c.C409A						PASS	.	C	THR/PRO,THR/PRO	1457,2409		268,921,744	28.0	30.0	29.0		409,40	3.0	1.0	11	dbSNP_86	29	54,8194		1,52,4071	yes	missense,missense	CARNS1	NM_001166222.1,NM_020811.1	38,38	269,973,4815	AA,AC,CC		0.6547,37.6875,12.4732	benign,benign	137/951,14/828	67186271	1511,10603	1933	4124	6057	SO:0001583	missense	57571	exon5			AAGGTGCCAGCAC		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.40C>A	11.37:g.67186271C>A	ENSP00000308268:p.Pro14Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	58	11	0.189655	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Missense_Mutation	SNP	ENST00000307823.3	37	CCDS44658.1	328	0.15018315018315018	228	0.4634146341463415	81	0.22375690607734808	15	0.026223776223776224	4	0.005277044854881266	C	14.00	2.404566	0.42613	0.376875	0.006547	ENSG00000172508	ENST00000531040;ENST00000307823;ENST00000542831;ENST00000539452;ENST00000423745;ENST00000445895	T;T;T;T	0.41065	1.01;1.24;1.24;1.07	3.98	3.03	0.35002	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.41198	P	0.013645000000000018	P;P;P	0.47762	0.835;0.745;0.9	P;B;P	0.44990	0.466;0.276;0.466	T	0.47195	-0.9136	8	0.62326	D	0.03	.	12.1121	0.53846	0.0:0.817:0.183:0.0	rs868167;rs1790732;rs868167	137;14;153	F5H427;A5YM72;A5YM72-3	.;CRNS1_HUMAN;.	T	137;14;137;153;14;137	ENSP00000431670:P137T;ENSP00000308268:P14T;ENSP00000401519:P14T;ENSP00000389009:P137T	ENSP00000308268:P14T	P	+	1	0	CARNS1	66942847	0.998000	0.40836	0.976000	0.42696	0.946000	0.59487	1.492000	0.35594	0.843000	0.35070	0.561000	0.74099	CCA	C|0.835;A|0.165	0.165	strong		0.637	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811	
GRIA2	2891	hgsc.bcm.edu	37	4	158238830	158238830	+	Silent	SNP	T	T	C	rs4302506	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:158238830T>C	ENST00000264426.9	+	5	966	c.687T>C	c.(685-687)caT>caC	p.H229H	GRIA2_ENST00000449365.1_Silent_p.H182H|GRIA2_ENST00000393815.2_Silent_p.H182H|GRIA2_ENST00000296526.7_Silent_p.H229H|GRIA2_ENST00000507898.1_Silent_p.H182H	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	229					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)	p.H229H(2)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TTGGAAAACATGTTAAAGGGT	0.234													T|||	3306	0.660144	0.4841	0.755	5008	,	,		13798	0.7897		0.6252	False		,,,				2504	0.7331				p.H229H		Atlas-SNP	.											GRIA2_ENST00000264426,NS,carcinoma,0,2	GRIA2	358	2	2	Substitution - coding silent(2)	prostate(2)	c.T687C						PASS	.	T	,,	2251,2137	563.4+/-381.2	600,1051,543	37.0	38.0	38.0		687,687,546	1.4	1.0	4	dbSNP_111	38	5547,3029	632.6+/-398.6	1812,1923,553	no	coding-synonymous,coding-synonymous,coding-synonymous	GRIA2	NM_000826.3,NM_001083619.1,NM_001083620.1	,,	2412,2974,1096	CC,CT,TT		35.3195,48.701,39.8488	,,	229/884,229/884,182/837	158238830	7798,5166	2194	4288	6482	SO:0001819	synonymous_variant	2891	exon5			AAAACATGTTAAA		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.687T>C	4.37:g.158238830T>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_000826	A8MT92|I6L997|Q96FP6	Silent	SNP	ENST00000264426.9	37	CCDS43274.1																																																																																			T|0.364;C|0.636	0.636	strong		0.234	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
PZP	5858	hgsc.bcm.edu	37	12	9321501	9321501	+	Missense_Mutation	SNP	C	C	T	rs3213832	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9321501C>T	ENST00000261336.2	-	17	2099	c.2071G>A	c.(2071-2073)Gtg>Atg	p.V691M	PZP_ENST00000381997.2_Missense_Mutation_p.V560M|PZP_ENST00000539983.1_5'Flank	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	691	Bait region.		V -> M (in dbSNP:rs3213832). {ECO:0000269|PubMed:1692292}.		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						CCTGCAGACACGGAAGGGATG	0.378													C|||	472	0.0942492	0.1785	0.036	5008	,	,		-128	0.0476		0.0636	False		,,,				2504	0.1012				p.V691M	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.G2071A						PASS	.	C	MET/VAL	663,3743	281.4+/-275.9	51,561,1591	126.0	126.0	126.0		2071	-2.9	0.0	12	dbSNP_106	126	525,8075	148.0+/-203.3	12,501,3787	yes	missense	PZP	NM_002864.2	21	63,1062,5378	TT,TC,CC		6.1047,15.0477,9.1342	benign	691/1483	9321501	1188,11818	2203	4300	6503	SO:0001583	missense	5858	exon17			CAGACACGGAAGG	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2071G>A	12.37:g.9321501C>T	ENSP00000261336:p.Val691Met	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	67	39	0.58209	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	175	0.08012820512820513	86	0.17479674796747968	15	0.04143646408839779	26	0.045454545454545456	48	0.0633245382585752	C	1.030	-0.682213	0.03353	0.150477	0.061047	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.35048	1.53;1.33	1.69	-2.88	0.05682	.	45.459000	0.00357	U	0.000025	T	0.00073	0.0002	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.16396	0.0;0.017;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.12760	-1.0535	9	0.33141	T	0.24	.	6.16	0.20358	0.0:0.5927:0.0:0.4073	rs3213832;rs52791055;rs3213832	691;560;691	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	M	691;560	ENSP00000261336:V691M;ENSP00000371427:V560M	ENSP00000261336:V691M	V	-	1	0	PZP	9212768	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.232000	0.02936	-0.588000	0.05882	-1.458000	0.01028	GTG	C|0.907;T|0.093	0.093	strong		0.378	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
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 GAIIx	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_ENST00000448525.1_Silent_p.A276A|CLCN7_ENST00000262318.8_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		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	24	14	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	
TCTN2	79867	hgsc.bcm.edu	37	12	124179417	124179417	+	Silent	SNP	T	T	C	rs7966867	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:124179417T>C	ENST00000303372.5	+	10	1256	c.1128T>C	c.(1126-1128)ccT>ccC	p.P376P	TCTN2_ENST00000426174.2_Silent_p.P375P	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	376					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000163)|Epithelial(86;0.000502)|all cancers(50;0.00451)		GATCAACCCCTAGAATTGTGA	0.338													C|||	2415	0.482228	0.8744	0.366	5008	,	,		19895	0.1508		0.4185	False		,,,				2504	0.4417				p.P376P		Atlas-SNP	.											.	TCTN2	50	.	0			c.T1128C						PASS	.	C	,	3602,804	304.4+/-288.4	1482,638,83	64.0	71.0	68.0		1125,1128	3.2	0.0	12	dbSNP_116	68	3841,4759	604.9+/-394.9	844,2153,1303	no	coding-synonymous,coding-synonymous	TCTN2	NM_001143850.1,NM_024809.3	,	2326,2791,1386	CC,CT,TT		44.6628,18.2478,42.7726	,	375/697,376/698	124179417	7443,5563	2203	4300	6503	SO:0001819	synonymous_variant	79867	exon10			AACCCCTAGAATT	AK056924	CCDS9253.1, CCDS45007.1	12q24.31	2011-04-12	2007-08-20	2007-08-20	ENSG00000168778	ENSG00000168778		"""Tectonic proteins"""	25774	protein-coding gene	gene with protein product	"""Meckel syndrome, type 8"""	613846	"""chromosome 12 open reading frame 38"""	C12orf38		21462283	Standard	NM_024809		Approved	FLJ12975, TECT2, MKS8	uc001ufp.3	Q96GX1	OTTHUMG00000168700	ENST00000303372.5:c.1128T>C	12.37:g.124179417T>C		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	194	82	0.42268	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	37	CCDS9253.1																																																																																			C|0.521;N|0.000	0.521	strong		0.338	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809	
NUP62CL	54830	hgsc.bcm.edu	37	X	106396455	106396455	+	Silent	SNP	A	A	G	rs1285590	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:106396455A>G	ENST00000372466.4	-	7	728	c.477T>C	c.(475-477)cgT>cgC	p.R159R	NUP62CL_ENST00000372461.3_3'UTR	NM_017681.2	NP_060151.2	Q9H1M0	N62CL_HUMAN	nucleoporin 62kDa C-terminal like	159					protein transport (GO:0015031)	nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			lung(4)	4						CACTCTGGTCACGCGTAGACT	0.388													G|||	1811	0.479735	0.6566	0.3199	3775	,	,		14359	0.3333		0.1521	False		,,,				2504	0.2372				p.R159R		Atlas-SNP	.											.	NUP62CL	10	.	0			c.T477C						PASS	.	G		2886,949		925,604,432,103,139	149.0	164.0	159.0		477	-1.8	0.0	X	dbSNP_87	159	1226,5502		66,739,355,1623,1517	no	coding-synonymous	NUP62CL	NM_017681.2		991,1343,787,1726,1656	GG,GA,G,AA,A		18.2224,24.7458,38.9283		159/185	106396455	4112,6451	2203	4300	6503	SO:0001819	synonymous_variant	54830	exon7			CTGGTCACGCGTA	AK000137	CCDS14527.1	Xq22.3	2008-02-05			ENSG00000198088	ENSG00000198088			25960	protein-coding gene	gene with protein product						12477932	Standard	NM_017681		Approved	FLJ20130	uc004ena.3	Q9H1M0	OTTHUMG00000022159	ENST00000372466.4:c.477T>C	X.37:g.106396455A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	220	59	0.268182	NM_017681	D3DUX4|Q8WVL6|Q9NXP2	Silent	SNP	ENST00000372466.4	37	CCDS14527.1	738	0.4448462929475588	217	0.7138157894736842	67	0.23591549295774647	137	0.315668202764977	77	0.11290322580645161	G	5.024	0.190194	0.09547	0.752542	0.182224	ENSG00000198088	ENST00000432145	.	.	.	5.44	-1.77	0.07982	.	.	.	.	.	.	.	.	.	.	.	0.32452	P	0.5452330000000001	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.6833	1.1076	0.01698	0.4443:0.1715:0.1106:0.2735	rs1285590;rs56440588;rs1285590	.	.	.	R	91	.	.	X	-	1	0	NUP62CL	106283111	0.824000	0.29247	0.000000	0.03702	0.000000	0.00434	-0.019000	0.12546	-1.064000	0.03172	-4.419000	0.00006	TGA	A|0.553;G|0.447	0.447	strong		0.388	NUP62CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057828.1	NM_017681	
SPACA7	122258	hgsc.bcm.edu	37	13	113053470	113053470	+	Missense_Mutation	SNP	T	T	A	rs10816	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:113053470T>A	ENST00000283550.3	+	4	399	c.332T>A	c.(331-333)gTc>gAc	p.V111D	SPACA7_ENST00000375699.3_Missense_Mutation_p.V80D	NM_145248.4	NP_660291.2	Q96KW9	SPAC7_HUMAN	sperm acrosome associated 7	111			V -> D (in dbSNP:rs10816). {ECO:0000269|PubMed:15489334}.			acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)				large_intestine(5)|lung(4)|skin(3)|urinary_tract(1)	13						GGCATTGAGGTCAAAATTTCC	0.423													A|||	3340	0.666933	0.7905	0.6081	5008	,	,		18900	0.624		0.5716	False		,,,				2504	0.684				p.V111D		Atlas-SNP	.											SPACA7,NS,adenoma,0,1	SPACA7	36	1	0			c.T332A						scavenged	.	A	ASP/VAL	3445,961	360.9+/-315.4	1357,731,115	70.0	71.0	71.0		332	0.4	0.0	13	dbSNP_52	71	5185,3415	503.2+/-375.9	1577,2031,692	yes	missense	SPACA7	NM_145248.4	152	2934,2762,807	AA,AT,TT		39.7093,21.8112,33.646	benign	111/196	113053470	8630,4376	2203	4300	6503	SO:0001583	missense	122258	exon4			TTGAGGTCAAAAT	BC016750	CCDS9524.1	13q34	2013-10-11	2011-03-15	2011-03-15	ENSG00000153498	ENSG00000153498			29575	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 28"""	C13orf28		22495889	Standard	NM_145248		Approved		uc001vsd.2	Q96KW9	OTTHUMG00000017365	ENST00000283550.3:c.332T>A	13.37:g.113053470T>A	ENSP00000283550:p.Val111Asp	Somatic	155	2	0.0129032		WXS	Illumina HiSeq	Phase_I	80	57	0.7125	NM_145248	Q5T8L1	Missense_Mutation	SNP	ENST00000283550.3	37	CCDS9524.1	1381	0.6323260073260073	382	0.7764227642276422	229	0.6325966850828729	344	0.6013986013986014	426	0.5620052770448549	A	0.743	-0.775762	0.02951	0.781888	0.602907	ENSG00000153498	ENST00000283550;ENST00000414180;ENST00000443541;ENST00000375699	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	3.03	0.446	0.16602	.	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36383	-0.9750	8	0.09843	T	0.71	-4.0574	0.5289	0.00625	0.4371:0.2203:0.129:0.2136	rs10816;rs1132162;rs3192694;rs11554437;rs17294556;rs17845503;rs17858390;rs60368660;rs10816	111	Q96KW9	SPAC7_HUMAN	D	111;99;97;80	ENSP00000283550:V111D;ENSP00000416096:V99D;ENSP00000406733:V97D;ENSP00000364851:V80D	ENSP00000283550:V111D	V	+	2	0	SPACA7	112101471	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.204000	0.09425	-0.169000	0.10834	-0.265000	0.10407	GTC	T|0.343;A|0.657	0.657	strong		0.423	SPACA7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045820.2	NM_145248	
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 GAIIx	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	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	55	4	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	
DNAH8	1769	hgsc.bcm.edu	37	6	38800164	38800164	+	Missense_Mutation	SNP	G	G	A	rs9357283	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:38800164G>A	ENST00000359357.3	+	29	3858	c.3604G>A	c.(3604-3606)Gaa>Aaa	p.E1202K	DNAH8_ENST00000441566.1_Missense_Mutation_p.E1202K|DNAH8_ENST00000449981.2_Missense_Mutation_p.E1419K			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1202			E -> K (in dbSNP:rs9357283). {ECO:0000269|PubMed:12297094}.		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)	p.E1202K(1)		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						TGAGTCTGTGGAAGTTTTTCG	0.343													G|||	913	0.182308	0.1415	0.1556	5008	,	,		20049	0.3423		0.1074	False		,,,				2504	0.1687				p.E1419K		Atlas-SNP	.											DNAH8_ENST00000359357,NS,carcinoma,0,1	DNAH8	1239	1	1	Substitution - Missense(1)	stomach(1)	c.G4255A						PASS	.	G	LYS/GLU	638,3768	272.5+/-270.8	45,548,1610	130.0	122.0	125.0		4255	4.5	1.0	6	dbSNP_119	125	1188,7412	240.8+/-271.4	71,1046,3183	yes	missense	DNAH8	NM_001206927.1	56	116,1594,4793	AA,AG,GG		13.814,14.4803,14.0397	benign	1419/4708	38800164	1826,11180	2203	4300	6503	SO:0001583	missense	1769	exon31			TCTGTGGAAGTTT	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.3604G>A	6.37:g.38800164G>A	ENSP00000352312:p.Glu1202Lys	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	115	24	0.208696	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		381	0.17445054945054944	63	0.12804878048780488	50	0.13812154696132597	195	0.3409090909090909	73	0.09630606860158311	G	8.047	0.765224	0.15914	0.144803	0.13814	ENSG00000124721	ENST00000449981;ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.25912	1.83;1.82;1.77	5.41	4.53	0.55603	.	0.264968	0.36066	N	0.002816	T	0.06096	0.0158	L	0.31157	0.91	0.30677	P	0.75271	B	0.02656	0.0	B	0.06405	0.002	T	0.23048	-1.0199	9	0.10377	T	0.69	.	10.1478	0.42774	0.073:0.1359:0.7911:0.0	rs9357283;rs59127177;rs9357283	1202	Q96JB1	DYH8_HUMAN	K	1407;1407;1202;1202	ENSP00000333363:E1407K;ENSP00000352312:E1202K;ENSP00000402294:E1202K	ENSP00000333363:E1407K	E	+	1	0	DNAH8	38908142	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	2.663000	0.46774	1.261000	0.44149	0.563000	0.77884	GAA	G|0.840;A|0.160	0.160	strong		0.343	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
PREX2	80243	hgsc.bcm.edu	37	8	69046409	69046409	+	Silent	SNP	G	G	A	rs3793379	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:69046409G>A	ENST00000288368.4	+	32	4159	c.3882G>A	c.(3880-3882)aaG>aaA	p.K1294K		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1294					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						ACAACAGCAAGGAAAATGAGA	0.498													G|||	606	0.121006	0.0212	0.2003	5008	,	,		17557	0.1865		0.1153	False		,,,				2504	0.138				p.K1294K		Atlas-SNP	.											PREX2,colon,carcinoma,+1,1	PREX2	614	1	0			c.G3882A						PASS	.	G		164,4242	110.4+/-148.6	2,160,2041	103.0	96.0	99.0		3882	2.0	1.0	8	dbSNP_107	99	1147,7453	235.0+/-267.7	74,999,3227	no	coding-synonymous	PREX2	NM_024870.2		76,1159,5268	AA,AG,GG		13.3372,3.7222,10.08		1294/1607	69046409	1311,11695	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon32			CAGCAAGGAAAAT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.3882G>A	8.37:g.69046409G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			G|0.894;A|0.106	0.106	strong		0.498	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
AP2M1	1173	hgsc.bcm.edu	37	3	183901281	183901281	+	Silent	SNP	G	G	A	rs2231224	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183901281G>A	ENST00000292807.5	+	12	1333	c.1185G>A	c.(1183-1185)gcG>gcA	p.A395A	ABCF3_ENST00000429586.2_5'Flank|AP2M1_ENST00000439647.1_Silent_p.A393A|AP2M1_ENST00000411763.2_Silent_p.A420A|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Silent_p.A393A|AP2M1_ENST00000461733.1_3'UTR|ABCF3_ENST00000292808.5_5'Flank	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	395	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGCCATTCGCGCCCTCTGGCC	0.562													G|||	368	0.0734824	0.0182	0.0749	5008	,	,		18192	0.004		0.1372	False		,,,				2504	0.1534				p.A393A		Atlas-SNP	.											.	AP2M1	35	.	0			c.G1179A						PASS	.	G	,	122,3952		1,120,1916	89.0	94.0	93.0		1179,1185	-5.8	0.1	3	dbSNP_98	93	1214,7118		85,1044,3037	yes	coding-synonymous,coding-synonymous	AP2M1	NM_001025205.1,NM_004068.3	,	86,1164,4953	AA,AG,GG		14.5703,2.9946,10.769	,	393/434,395/436	183901281	1336,11070	2037	4166	6203	SO:0001819	synonymous_variant	1173	exon11			ATTCGCGCCCTCT	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, medium 1"", ""plasma membrane adaptor AP-2 50kDA protein"", ""clathrin coat adaptor protein AP50"", ""clathrin adaptor complex AP2, mu subunit"", ""HA2 50 kDA subunit"", ""clathrin assembly protein complex 2 medium chain"", ""AP-2 mu 2 chain"""	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.1185G>A	3.37:g.183901281G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	147	57	0.387755	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Silent	SNP	ENST00000292807.5	37	CCDS43177.1																																																																																			G|0.921;A|0.079	0.079	strong		0.562	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068	
CTXN3	613212	hgsc.bcm.edu	37	5	126993249	126993249	+	Silent	SNP	G	G	C	rs45074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:126993249G>C	ENST00000379445.3	+	3	587	c.36G>C	c.(34-36)gtG>gtC	p.V12V	CTC-548H10.2_ENST00000512352.1_RNA|CTXN3_ENST00000395322.3_Silent_p.V12V	NM_001048252.2	NP_001041717.1	Q4LDR2	CTXN3_HUMAN	cortexin 3	12						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		CATCCCTAGTGCCCCTTGGGA	0.473													G|||	3260	0.650958	0.7602	0.6037	5008	,	,		20597	0.6141		0.6551	False		,,,				2504	0.5706				p.V12V		Atlas-SNP	.											.	CTXN3	19	.	0			c.G36C						PASS	.	G	,	3388,1018	728.1+/-409.9	1302,784,117	115.0	101.0	106.0		36,36	2.7	0.9	5	dbSNP_79	106	5785,2815	675.6+/-403.2	1929,1927,444	yes	coding-synonymous,coding-synonymous	CTXN3	NM_001048252.2,NM_001127385.1	,	3231,2711,561	CC,CG,GG		32.7326,23.1049,29.471	,	12/82,12/82	126993249	9173,3833	2203	4300	6503	SO:0001819	synonymous_variant	613212	exon3			CCTAGTGCCCCTT	AB219764	CCDS34221.1	5q23.2	2006-09-21				ENSG00000205279			31110	protein-coding gene	gene with protein product							Standard	NM_001048252		Approved		uc003kum.4	Q4LDR2		ENST00000379445.3:c.36G>C	5.37:g.126993249G>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_001048252	B2RV32|D3DQ82	Silent	SNP	ENST00000379445.3	37	CCDS34221.1																																																																																			G|0.308;C|0.692	0.692	strong		0.473	CTXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372467.1	XM_932841	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68705820	68705820	+	Missense_Mutation	SNP	G	G	A	rs2275996	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:68705820G>A	ENST00000255078.3	+	14	2893	c.2782G>A	c.(2782-2784)Gag>Aag	p.E928K		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	928			E -> K (in dbSNP:rs2275996).		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)			CCACCTGCCCGAGGTATGTCG	0.637													G|||	118	0.0235623	0.0008	0.0735	5008	,	,		16892	0.0655		0.0	False		,,,				2504	0.0				p.E928K		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.G2782A						PASS	.	G	LYS/GLU	14,4384		0,14,2185	19.0	17.0	17.0		2782	4.8	1.0	11	dbSNP_100	17	11,8567		0,11,4278	yes	missense	IGHMBP2	NM_002180.2	56	0,25,6463	AA,AG,GG		0.1282,0.3183,0.1927	probably-damaging	928/994	68705820	25,12951	2199	4289	6488	SO:0001583	missense	3508	exon14			CTGCCCGAGGTAT	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.2782G>A	11.37:g.68705820G>A	ENSP00000255078:p.Glu928Lys	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	27	7	0.259259	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	66	0.03021978021978022	0	0.0	23	0.06353591160220995	43	0.07517482517482517	0	0.0	G	35	5.458236	0.96240	0.003183	0.001282	ENSG00000132740	ENST00000255078	T	0.52526	0.66	4.82	4.82	0.62117	Zinc finger, AN1-type (4);	0.141344	0.47093	D	0.000259	T	0.15349	0.0370	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.63166	-0.6698	10	0.87932	D	0	-10.0293	16.6598	0.85238	0.0:0.0:1.0:0.0	rs2275996;rs2275996	928	P38935	SMBP2_HUMAN	K	928	ENSP00000255078:E928K	ENSP00000255078:E928K	E	+	1	0	IGHMBP2	68462396	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	9.118000	0.94355	2.221000	0.72209	0.462000	0.41574	GAG	G|0.983;A|0.017	0.017	strong		0.637	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
PRSS1	5644	hgsc.bcm.edu	37	7	142458437	142458437	+	Silent	SNP	C	C	T	rs372637371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:142458437C>T	ENST00000311737.7	+	2	78	c.72C>T	c.(70-72)atC>atT	p.I24I	PRSS1_ENST00000486171.1_Silent_p.I24I	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	24	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	ATGACAAGATCGTTGGGGGCT	0.542													C|||	2	0.000399361	0.0	0.0	5008	,	,		19985	0.002		0.0	False		,,,				2504	0.0				p.I24I		Atlas-SNP	.											PRSS1,NS,carcinoma,0,1	PRSS1	68	1	0			c.C72T						scavenged	.						158.0	156.0	157.0					7																	142458437		2203	4300	6503	SO:0001819	synonymous_variant	5644	exon2			CAAGATCGTTGGG	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.72C>T	7.37:g.142458437C>T		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	156	17	0.108974	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Silent	SNP	ENST00000311737.7	37	CCDS5872.1																																																																																			.	.	weak		0.542	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
C6orf15	29113	hgsc.bcm.edu	37	6	31079703	31079703	+	Missense_Mutation	SNP	C	C	G	rs2233978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31079703C>G	ENST00000259870.3	-	2	436	c.433G>C	c.(433-435)Gct>Cct	p.A145P	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	145			A -> P (in dbSNP:rs2233978).		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						CTGCCCGGAGCGAGGGCCGCA	0.642													C|||	926	0.184904	0.0492	0.1671	5008	,	,		16912	0.3899		0.0974	False		,,,				2504	0.2597				p.A145P		Atlas-SNP	.											.	C6orf15	29	.	0			c.G433C						PASS	.	C	PRO/ALA	169,3723		1,167,1778	31.0	33.0	32.0		433	-1.1	0.0	6	dbSNP_98	32	650,7084		32,586,3249	yes	missense	C6orf15	NM_014070.2	27	33,753,5027	GG,GC,CC		8.4044,4.3422,7.0446	benign	145/326	31079703	819,10807	1946	3867	5813	SO:0001583	missense	29113	exon2			CCGGAGCGAGGGC	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.433G>C	6.37:g.31079703C>G	ENSP00000259870:p.Ala145Pro	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	122	18	0.147541	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	366	0.16758241758241757	36	0.07317073170731707	40	0.11049723756906077	222	0.3881118881118881	68	0.08970976253298153	C	0.096	-1.158850	0.01686	0.043422	0.084044	ENSG00000204542	ENST00000259870	T	0.07567	3.18	4.57	-1.07	0.09968	.	0.957425	0.08616	N	0.919178	T	0.00356	0.0011	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46275	-0.9203	9	0.02654	T	1	.	0.5112	0.00596	0.2071:0.1654:0.3016:0.3259	rs2233978;rs3823390	145	Q6UXA7	CF015_HUMAN	P	145	ENSP00000259870:A145P	ENSP00000259870:A145P	A	-	1	0	C6orf15	31187682	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	-0.126000	0.10563	-0.096000	0.12329	-0.865000	0.03005	GCT	C|0.892;G|0.108	0.108	strong		0.642	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
PEX14	5195	hgsc.bcm.edu	37	1	10689942	10689942	+	Silent	SNP	G	G	T	rs11539794	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10689942G>T	ENST00000356607.4	+	9	1112	c.1032G>T	c.(1030-1032)ggG>ggT	p.G344G	PEX14_ENST00000538836.1_Silent_p.G280G	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	344					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		ACTGCCTGGGGGTGCAGAGGG	0.657													G|||	519	0.103634	0.0197	0.1326	5008	,	,		16747	0.0228		0.1948	False		,,,				2504	0.1861				p.G344G		Atlas-SNP	.											PEX14,NS,carcinoma,0,1	PEX14	40	1	0			c.G1032T						PASS	.	G		200,4202	123.7+/-161.0	3,194,2004	183.0	190.0	188.0		1032	0.2	1.0	1	dbSNP_120	188	1631,6969	298.5+/-303.9	148,1335,2817	no	coding-synonymous	PEX14	NM_004565.2		151,1529,4821	TT,TG,GG		18.9651,4.5434,14.0824		344/378	10689942	1831,11171	2201	4300	6501	SO:0001819	synonymous_variant	5195	exon9			CCTGGGGGTGCAG	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.1032G>T	1.37:g.10689942G>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			G|0.875;T|0.125	0.125	strong		0.657	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
MLPH	79083	hgsc.bcm.edu	37	2	238427194	238427194	+	Missense_Mutation	SNP	T	T	C	rs3751109	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238427194T>C	ENST00000264605.3	+	5	752	c.458T>C	c.(457-459)cTg>cCg	p.L153P	MLPH_ENST00000338530.4_Missense_Mutation_p.L153P|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Missense_Mutation_p.L153P|MLPH_ENST00000409373.1_Missense_Mutation_p.L153P|MLPH_ENST00000410032.1_Missense_Mutation_p.L153P	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	153			L -> P (in dbSNP:rs3751109).		melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		GGGCCTGAACTGATATCTGAA	0.542													N|||	895	0.178714	0.3714	0.0994	5008	,	,		18796	0.0843		0.1412	False		,,,				2504	0.1104				p.L153P		Atlas-SNP	.											.	MLPH	41	.	0			c.T458C						PASS	.		PRO/LEU,PRO/LEU	1523,2881		256,1011,935	66.0	65.0	65.0		458,458	-2.8	0.0	2	dbSNP_107	65	1456,7144		126,1204,2970	yes	missense,missense	MLPH	NM_001042467.1,NM_024101.5	98,98	382,2215,3905	CC,CT,TT		16.9302,34.5822,22.9083	benign,benign	153/573,153/601	238427194	2979,10025	2202	4300	6502	SO:0001583	missense	79083	exon5			CTGAACTGATATC	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.458T>C	2.37:g.238427194T>C	ENSP00000264605:p.Leu153Pro	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	134	72	0.537313	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	370	0.16941391941391942	174	0.35365853658536583	38	0.10497237569060773	47	0.08216783216783216	111	0.14643799472295516	N	2.707	-0.269709	0.05716	0.345822	0.169302	ENSG00000115648	ENST00000410032;ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T;T;T;T;T	0.27557	1.67;2.09;2.08;1.92;1.66	2.24	-2.76	0.05896	.	228.317000	0.01298	U	0.010207	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.001;0.001;0.0;0.0;0.0;0.0;0.0	T	0.36286	-0.9754	9	0.30078	T	0.28	0.0312	0.1965	0.00140	0.3586:0.227:0.1603:0.2541	rs3751109;rs52817184;rs58583705;rs3751109	153;37;153;153;153;153;153	B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36;G5E9G5	.;.;.;.;.;MELPH_HUMAN;.	P	153	ENSP00000386338:L153P;ENSP00000264605:L153P;ENSP00000414849:L153P;ENSP00000341845:L153P;ENSP00000386780:L153P	ENSP00000264605:L153P	L	+	2	0	MLPH	238091933	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.672000	0.05244	-1.189000	0.02702	-1.342000	0.01247	CTG	T|0.795;C|0.205	0.205	strong		0.542	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
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 GAIIx	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	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	77	40	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		
CAMLG	819	hgsc.bcm.edu	37	5	134076812	134076812	+	Missense_Mutation	SNP	G	G	A	rs12657663	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134076812G>A	ENST00000297156.2	+	2	352	c.232G>A	c.(232-234)Gtt>Att	p.V78I	CAMLG_ENST00000514518.1_Intron	NM_001745.3	NP_001736.1	P49069	CAMLG_HUMAN	calcium modulating ligand	78			V -> I (in dbSNP:rs12657663).		defense response (GO:0006952)|epidermal growth factor receptor signaling pathway (GO:0007173)|receptor recycling (GO:0001881)|signal transduction (GO:0007165)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|cervix(1)|kidney(3)|lung(3)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Cyclosporine(DB00091)	CTCCCTCAGCGTTCCTTCCGT	0.453													G|||	734	0.146565	0.0136	0.1787	5008	,	,		19311	0.2808		0.1332	False		,,,				2504	0.1789				p.V78I		Atlas-SNP	.											.	CAMLG	27	.	0			c.G232A						PASS	.	G	ILE/VAL	112,4294	86.3+/-125.0	2,108,2093	86.0	84.0	85.0		232	-11.7	0.0	5	dbSNP_120	85	885,7715	200.4+/-244.2	47,791,3462	yes	missense	CAMLG	NM_001745.3	29	49,899,5555	AA,AG,GG		10.2907,2.542,7.6657	benign	78/297	134076812	997,12009	2203	4300	6503	SO:0001583	missense	819	exon2			CTCAGCGTTCCTT	AF068179.1	CCDS4178.1	5q23	2008-07-18			ENSG00000164615	ENSG00000164615			1471	protein-coding gene	gene with protein product	"""calcium-modulating cyclophilin ligand"", ""calcium-signal modulating cyclophilin ligand"", ""cyclophilin B-binding protein"""	601118				8824814	Standard	NM_001745		Approved	CAML	uc003kzt.3	P49069	OTTHUMG00000129116	ENST00000297156.2:c.232G>A	5.37:g.134076812G>A	ENSP00000297156:p.Val78Ile	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_001745	A1L3Y3	Missense_Mutation	SNP	ENST00000297156.2	37	CCDS4178.1	330	0.1510989010989011	11	0.022357723577235773	50	0.13812154696132597	168	0.2937062937062937	101	0.13324538258575197	G	5.074	0.199353	0.09652	0.02542	0.102907	ENSG00000164615	ENST00000297156	T	0.30981	1.51	5.86	-11.7	0.00046	.	1.190980	0.05515	N	0.561025	T	0.00012	0.0000	N	0.12182	0.205	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.09662	-1.0664	9	0.05620	T	0.96	-1.7125	3.5917	0.07991	0.5114:0.2134:0.1321:0.1431	rs12657663;rs52822059;rs12657663	78	P49069	CAMLG_HUMAN	I	78	ENSP00000297156:V78I	ENSP00000297156:V78I	V	+	1	0	CAMLG	134104711	0.000000	0.05858	0.000000	0.03702	0.958000	0.62258	-1.489000	0.02306	-3.248000	0.00205	-0.812000	0.03155	GTT	G|0.890;A|0.110	0.110	strong		0.453	CAMLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251161.1	NM_001745	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227216662	227216662	+	Silent	SNP	T	T	C	rs1929861	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:227216662T>C	ENST00000366769.3	-	29	5314	c.4023A>G	c.(4021-4023)aaA>aaG	p.K1341K	CDC42BPA_ENST00000366765.3_Silent_p.K1354K|CDC42BPA_ENST00000366766.2_Silent_p.K1376K|CDC42BPA_ENST00000366767.3_Silent_p.K1260K|CDC42BPA_ENST00000535525.1_Silent_p.K1321K|CDC42BPA_ENST00000334218.5_Silent_p.K1341K|CDC42BPA_ENST00000366764.2_Silent_p.K1313K	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CTTGAATTTCTTTAAATTTTC	0.448													C|||	2025	0.404353	0.4796	0.4179	5008	,	,		19580	0.4038		0.4652	False		,,,				2504	0.2311				p.K1341K		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.A4023G						PASS	.	C	,	2058,2348	606.5+/-390.8	470,1118,615	77.0	73.0	74.0		4023,3780	1.4	1.0	1	dbSNP_92	74	3933,4667	603.0+/-394.6	883,2167,1250	no	coding-synonymous,coding-synonymous	CDC42BPA	NM_003607.3,NM_014826.4	,	1353,3285,1865	CC,CT,TT		45.7326,46.709,46.0634	,	1341/1720,1260/1639	227216662	5991,7015	2203	4300	6503	SO:0001819	synonymous_variant	8476	exon29			AATTTCTTTAAAT	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.4023A>G	1.37:g.227216662T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	34	11	0.323529	NM_003607		Silent	SNP	ENST00000366769.3	37	CCDS1558.1	999	0.4574175824175824	244	0.4959349593495935	150	0.4143646408839779	245	0.42832167832167833	360	0.47493403693931396	C	7.579	0.668292	0.14776	0.46709	0.457326	ENSG00000143776	ENST00000448940;ENST00000442054;ENST00000429440;ENST00000441725	.	.	.	5.32	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48198	-0.9056	3	.	.	.	.	11.2028	0.48751	0.0:0.5565:0.0:0.4435	rs1929861;rs3738730;rs58935232;rs1929861	.	.	.	G	544;670;239;566	.	.	R	-	1	2	CDC42BPA	225283285	0.998000	0.40836	0.996000	0.52242	0.969000	0.65631	0.685000	0.25378	-0.114000	0.11936	-0.962000	0.02626	AGA	T|0.544;C|0.456	0.456	strong		0.448	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
RNF5	6048	hgsc.bcm.edu	37	6	32147696	32147696	+	Silent	SNP	G	G	A	rs3130349	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32147696G>A	ENST00000375094.3	+	4	473	c.315G>A	c.(313-315)ccG>ccA	p.P105P	RNF5_ENST00000427134.2_Silent_p.P105P|AGPAT1_ENST00000336984.6_5'Flank|AGPAT1_ENST00000490711.1_5'Flank|AGPAT1_ENST00000395497.1_5'Flank|AGPAT1_ENST00000375104.2_5'Flank|AGPAT1_ENST00000395499.1_5'Flank	NM_006913.3	NP_008844.1	Q99942	RNF5_HUMAN	ring finger protein 5, E3 ubiquitin protein ligase	105					cellular protein catabolic process (GO:0044257)|ER-associated misfolded protein catabolic process (GO:0071712)|negative regulation of autophagy (GO:0010507)|protein destabilization (GO:0031648)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of autophagic vacuole assembly (GO:2000785)|response to bacterium (GO:0009617)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(7)|urinary_tract(2)	10						GACCAGCTCCGGAGAGCAGAG	0.542													A|||	667	0.133187	0.1241	0.0865	5008	,	,		18422	0.0933		0.159	False		,,,				2504	0.1933				p.P105P		Atlas-SNP	.											.	RNF5	16	.	0			c.G315A						PASS	.	A		500,3906	773.7+/-414.0	29,442,1732	92.0	107.0	102.0		315	-10.3	0.3	6	dbSNP_103	102	1568,7032	742.8+/-407.2	140,1288,2872	yes	coding-synonymous	RNF5	NM_006913.3		169,1730,4604	AA,AG,GG		18.2326,11.3482,15.9004		105/181	32147696	2068,10938	2203	4300	6503	SO:0001819	synonymous_variant	6048	exon4			AGCTCCGGAGAGC	U89336	CCDS4745.1	6p21.31	2013-01-09	2012-02-23			ENSG00000204308		"""RING-type (C3HC4) zinc fingers"""	10068	protein-coding gene	gene with protein product		602677	"""ring finger protein 5"""			9533025	Standard	NM_006913		Approved	NG2, G16, RING5, RMA1	uc031snv.1	Q99942	OTTHUMG00000031093	ENST00000375094.3:c.315G>A	6.37:g.32147696G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	191	139	0.727749	NM_006913	A2BFI6|B2R4K3|Q0VDB7|Q9UMQ2	Silent	SNP	ENST00000375094.3	37	CCDS4745.1																																																																																			G|0.863;A|0.137	0.137	strong		0.542	RNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076133.2	NM_006913	
NLRC5	84166	hgsc.bcm.edu	37	16	57091977	57091977	+	Splice_Site	SNP	T	T	C	rs7206703	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57091977T>C	ENST00000262510.6	+	28	3972	c.3747T>C	c.(3745-3747)gaT>gaC	p.D1249D	RP11-322D14.2_ENST00000562970.1_RNA|NLRC5_ENST00000539144.1_Splice_Site_p.G1220G|NLRC5_ENST00000308149.7_Splice_Site_p.G1220G|NLRC5_ENST00000436936.1_Splice_Site_p.D1249D	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1249					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				CCCCCTACAGTCTCTCAGCAA	0.587													c|||	549	0.109625	0.1755	0.1023	5008	,	,		20498	0.1319		0.0835	False		,,,				2504	0.0297				p.D1249D		Atlas-SNP	.											.	NLRC5	186	.	0			c.T3747C						PASS	.	C		728,3668	754.8+/-412.5	62,604,1532	53.0	44.0	47.0		3747	2.6	1.0	16	dbSNP_116	47	529,8071	791.2+/-407.6	20,489,3791	yes	coding-synonymous-near-splice	NLRC5	NM_032206.3		82,1093,5323	CC,CT,TT		6.1512,16.5605,9.6722		1249/1867	57091977	1257,11739	2198	4300	6498	SO:0001630	splice_region_variant	84166	exon27			CTACAGTCTCTCA	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.3747-1T>C	16.37:g.57091977T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	17	0.386364	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	252	0.11538461538461539	72	0.14634146341463414	35	0.09668508287292818	85	0.1486013986013986	60	0.079155672823219	C	5.031	0.191377	0.09547	0.165605	0.061512	ENSG00000140853	ENST00000538805;ENST00000399221	.	.	.	4.68	2.59	0.31030	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	P	0.9999999999998842	.	.	.	.	.	.	T	0.09207	-1.0685	3	.	.	.	.	5.625	0.17477	0.0:0.6489:0.0:0.3511	rs7206703;rs7206703	.	.	.	P	1001;1	.	.	S	+	1	0	NLRC5	55649478	1.000000	0.71417	0.993000	0.49108	0.032000	0.12392	0.367000	0.20382	0.609000	0.30018	-0.235000	0.12190	TCT	T|0.893;C|0.107	0.107	strong		0.587	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	Silent
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 GAIIx	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_ENST00000394184.3_Silent_p.G60G|PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000370197.1_Silent_p.G49G|PTBP2_ENST00000609116.1_Silent_p.G49G|PTBP2_ENST00000370198.1_Silent_p.G49G|PTBP2_ENST00000541987.1_Silent_p.G18G	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		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	33	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		
HHIPL2	79802	hgsc.bcm.edu	37	1	222713631	222713631	+	Missense_Mutation	SNP	G	G	C	rs3748666	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:222713631G>C	ENST00000343410.6	-	4	1229	c.1171C>G	c.(1171-1173)Cat>Gat	p.H391D		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	391			H -> D (in dbSNP:rs3748666).		carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		CGCTTGCCATGTGAGCCTGCC	0.527													C|||	1881	0.375599	0.3434	0.5058	5008	,	,		17707	0.5089		0.2604	False		,,,				2504	0.3078				p.H391D		Atlas-SNP	.											.	HHIPL2	122	.	0			c.C1171G						PASS	.	C	ASP/HIS	1448,2958	681.8+/-404.0	222,1004,977	70.0	66.0	68.0		1171	1.0	0.0	1	dbSNP_107	68	2505,6095	694.4+/-404.7	365,1775,2160	yes	missense	HHIPL2	NM_024746.3	81	587,2779,3137	CC,CG,GG		29.1279,32.8643,30.3937	benign	391/725	222713631	3953,9053	2203	4300	6503	SO:0001583	missense	79802	exon4			TGCCATGTGAGCC	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1171C>G	1.37:g.222713631G>C	ENSP00000342118:p.His391Asp	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	37	CCDS1530.2	822	0.37637362637362637	177	0.3597560975609756	151	0.4171270718232044	296	0.5174825174825175	198	0.2612137203166227	C	0	-2.657277	0.00108	0.328643	0.291279	ENSG00000143512	ENST00000343410	T	0.11169	2.8	4.43	1.02	0.19986	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	1.441690	0.04055	N	0.305409	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47471	-0.9115	9	0.05620	T	0.96	0.189	3.6679	0.08262	0.2757:0.379:0.2683:0.077	rs3748666	391	Q6UWX4	HIPL2_HUMAN	D	391	ENSP00000342118:H391D	ENSP00000342118:H391D	H	-	1	0	HHIPL2	220780254	0.000000	0.05858	0.000000	0.03702	0.194000	0.23727	0.545000	0.23268	0.046000	0.15833	-0.647000	0.03941	CAT	G|0.678;C|0.322	0.322	strong		0.527	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
TMEM120B	144404	hgsc.bcm.edu	37	12	122186317	122186317	+	Missense_Mutation	SNP	G	G	A	rs28655666	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:122186317G>A	ENST00000449592.2	+	3	375	c.274G>A	c.(274-276)Gac>Aac	p.D92N		NM_001080825.2	NP_001074294.2	A0PK00	T120B_HUMAN	transmembrane protein 120B	92				D -> N (in Ref. 2; AAI27770). {ECO:0000305}.		integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		CGTCTTCTTCGACATGGAGGC	0.612													G|||	2133	0.425919	0.2103	0.4481	5008	,	,		18243	0.5179		0.5467	False		,,,				2504	0.4826				p.D92N		Atlas-SNP	.											TMEM120B_ENST00000449592,brain,glioma,0,2	TMEM120B	43	2	0			c.G274A						PASS	.	G	ASN/ASP	1071,3125		161,749,1188	57.0	62.0	60.0		274	3.5	1.0	12	dbSNP_125	60	4584,3818		1263,2058,880	yes	missense	TMEM120B	NM_001080825.2	23	1424,2807,2068	AA,AG,GG		45.4416,25.5243,44.8881	benign	92/340	122186317	5655,6943	2098	4201	6299	SO:0001583	missense	144404	exon3			TTCTTCGACATGG	BC127768	CCDS41852.1	12q24.31	2007-08-01			ENSG00000188735	ENSG00000188735			32008	protein-coding gene	gene with protein product							Standard	NM_001080825		Approved		uc001ubc.4	A0PK00	OTTHUMG00000169076	ENST00000449592.2:c.274G>A	12.37:g.122186317G>A	ENSP00000404991:p.Asp92Asn	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	164	83	0.506098	NM_001080825	A0PK01|B3KX33	Missense_Mutation	SNP	ENST00000449592.2	37	CCDS41852.1	1017	0.46565934065934067	112	0.22764227642276422	172	0.47513812154696133	310	0.541958041958042	423	0.558047493403694	G	16.64	3.180210	0.57800	0.255243	0.545584	ENSG00000188735	ENST00000449592;ENST00000541467	T;T	0.36340	1.26;1.26	5.31	3.45	0.39498	.	0.145167	0.64402	D	0.000012	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	1.0	B	0.13145	0.007	B	0.18561	0.022	T	0.44283	-0.9338	9	0.54805	T	0.06	-29.1623	11.9916	0.53178	0.1553:0.0:0.8447:0.0	rs28655666	92	A0PK00	T120B_HUMAN	N	92;71	ENSP00000404991:D92N;ENSP00000442105:D71N	ENSP00000345152:D92N	D	+	1	0	TMEM120B	120670700	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	5.310000	0.65780	1.384000	0.46424	-0.250000	0.11733	GAC	G|0.502;A|0.498	0.498	strong		0.612	TMEM120B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402158.1	NM_001080825	
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 GAIIx	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_ENST00000578993.1_Missense_Mutation_p.Q3L|LIMD2_ENST00000582055.1_5'Flank|LIMD2_ENST00000583211.1_5'UTR|LIMD2_ENST00000578061.1_Missense_Mutation_p.Q3L|LIMD2_ENST00000578402.1_Missense_Mutation_p.Q3L	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	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	96	20	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	
RXFP2	122042	hgsc.bcm.edu	37	13	32371361	32371361	+	Missense_Mutation	SNP	A	A	G	rs17076657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:32371361A>G	ENST00000298386.2	+	17	1881	c.1810A>G	c.(1810-1812)Atc>Gtc	p.I604V	RXFP2_ENST00000380314.1_Missense_Mutation_p.I580V	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	604			I -> V (in dbSNP:rs17076657). {ECO:0000269|PubMed:12217959}.		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)		GGCTTTTCTCATCATTGTGTT	0.403													A|||	700	0.139776	0.1021	0.1657	5008	,	,		17890	0.1905		0.1551	False		,,,				2504	0.1043				p.I604V		Atlas-SNP	.											RXFP2,NS,carcinoma,-2,1	RXFP2	95	1	0			c.A1810G						PASS	.	A	VAL/ILE,VAL/ILE	660,3746	278.4+/-274.2	43,574,1586	146.0	145.0	146.0		1738,1810	1.8	1.0	13	dbSNP_123	146	1227,7373	247.1+/-275.3	89,1049,3162	yes	missense,missense	RXFP2	NM_001166058.1,NM_130806.3	29,29	132,1623,4748	GG,GA,AA		14.2674,14.9796,14.5087	benign,benign	580/731,604/755	32371361	1887,11119	2203	4300	6503	SO:0001583	missense	122042	exon17			TTTCTCATCATTG	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.1810A>G	13.37:g.32371361A>G	ENSP00000298386:p.Ile604Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	176	88	0.5	NM_130806	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	335	0.1533882783882784	55	0.11178861788617886	53	0.1464088397790055	110	0.19230769230769232	117	0.15435356200527706	A	10.64	1.408258	0.25378	0.149796	0.142674	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.37584	1.19;1.19	5.65	1.75	0.24633	GPCR, rhodopsin-like superfamily (1);	0.298620	0.37393	N	0.002114	T	0.00039	0.0001	N	0.25485	0.75	0.33242	P	0.442655	B;B	0.12013	0.005;0.005	B;B	0.17979	0.009;0.02	T	0.26608	-1.0098	9	0.08837	T	0.75	.	6.4112	0.21692	0.7249:0.1324:0.1427:0.0	rs17076657;rs52824466;rs17076657	580;604	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	V	580;604	ENSP00000369670:I580V;ENSP00000298386:I604V	ENSP00000298386:I604V	I	+	1	0	RXFP2	31269361	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.108000	0.31123	0.439000	0.26476	0.528000	0.53228	ATC	A|0.855;G|0.145	0.145	strong		0.403	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806	
PRR14L	253143	hgsc.bcm.edu	37	22	32113269	32113269	+	Missense_Mutation	SNP	C	C	A	rs112531886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:32113269C>A	ENST00000327423.6	-	4	745	c.556G>T	c.(556-558)Gta>Tta	p.V186L	PRR14L_ENST00000434485.1_Missense_Mutation_p.V186L|PRR14L_ENST00000461722.1_5'UTR|PRR14L_ENST00000397493.2_Missense_Mutation_p.V186L	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	186										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GTAATCTGTACATTTCCTTCT	0.353													C|||	166	0.033147	0.0015	0.0173	5008	,	,		20285	0.0268		0.0388	False		,,,				2504	0.0879				p.V186L		Atlas-SNP	.											PRR14L_ENST00000397493,NS,carcinoma,0,2	PRR14L	198	2	0			c.G556T						PASS	.						161.0	118.0	131.0					22																	32113269		692	1591	2283	SO:0001583	missense	253143	exon4			TCTGTACATTTCC	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.556G>T	22.37:g.32113269C>A	ENSP00000331845:p.Val186Leu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	65	0.02976190476190476	3	0.006097560975609756	10	0.027624309392265192	20	0.03496503496503497	32	0.04221635883905013	C	15.04	2.715474	0.48622	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.09630	2.96;2.98;2.96	5.21	4.19	0.49359	.	0.154521	0.29806	N	0.011152	T	0.04407	0.0121	M	0.62723	1.935	0.80722	D	1	D	0.57571	0.98	P	0.50934	0.654	T	0.00299	-1.1836	10	0.56958	D	0.05	-8.4182	11.3719	0.49704	0.0:0.9163:0.0:0.0837	.	186	Q5THK1	PR14L_HUMAN	L	186	ENSP00000380630:V186L;ENSP00000331845:V186L;ENSP00000388314:V186L	ENSP00000331845:V186L	V	-	1	0	PRR14L	30443269	1.000000	0.71417	0.956000	0.39512	0.199000	0.23934	1.154000	0.31688	1.195000	0.43115	0.650000	0.86243	GTA	C|0.969;A|0.031	0.031	strong		0.353	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
SWT1	54823	hgsc.bcm.edu	37	1	185171869	185171869	+	Missense_Mutation	SNP	A	A	G	rs6698109	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:185171869A>G	ENST00000367500.4	+	11	1772	c.1607A>G	c.(1606-1608)cAc>cGc	p.H536R	SWT1_ENST00000367501.3_Missense_Mutation_p.H536R	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	536			H -> R (in dbSNP:rs6698109). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						GAGTTATTACACTTATCTCTG	0.353													A|||	1380	0.275559	0.2179	0.2464	5008	,	,		12733	0.1964		0.341	False		,,,				2504	0.3885				p.H536R		Atlas-SNP	.											.	SWT1	88	.	0			c.A1607G						PASS	.	A	ARG/HIS,ARG/HIS	1090,3316	393.3+/-328.8	138,814,1251	88.0	89.0	89.0		1607,1607	-0.0	0.0	1	dbSNP_116	89	3038,5562	466.1+/-366.7	551,1936,1813	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	29,29	689,2750,3064	GG,GA,AA		35.3256,24.739,31.7392	benign,benign	536/901,536/901	185171869	4128,8878	2203	4300	6503	SO:0001583	missense	54823	exon11			TATTACACTTATC	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.1607A>G	1.37:g.185171869A>G	ENSP00000356470:p.His536Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	134	67	0.5	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	615	0.2815934065934066	130	0.26422764227642276	87	0.24033149171270718	140	0.24475524475524477	258	0.3403693931398417	A	7.659	0.684572	0.14973	0.24739	0.353256	ENSG00000116668	ENST00000367501;ENST00000367500	T;T	0.16457	2.34;2.34	5.49	-0.0357	0.13891	.	0.525254	0.22752	N	0.056064	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	0.49194	-0.8965	9	0.23302	T	0.38	.	4.8888	0.13717	0.5657:0.1491:0.2852:0.0	rs6698109;rs17856891;rs52826833;rs61051695;rs6698109	536	Q5T5J6	SWT1_HUMAN	R	536	ENSP00000356471:H536R;ENSP00000356470:H536R	ENSP00000356470:H536R	H	+	2	0	SWT1	183438492	0.844000	0.29557	0.003000	0.11579	0.720000	0.41350	0.715000	0.25822	-0.187000	0.10516	-0.274000	0.10170	CAC	A|0.699;G|0.301	0.301	strong		0.353	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
WASF3	10810	hgsc.bcm.edu	37	13	27257004	27257004	+	Missense_Mutation	SNP	C	C	T	rs17084492	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:27257004C>T	ENST00000335327.5	+	9	1422	c.1244C>T	c.(1243-1245)tCg>tTg	p.S415L	WASF3_ENST00000361042.4_Missense_Mutation_p.S412L	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	415			S -> L (in dbSNP:rs17084492).		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)		TCTTCTCTTTCGTCCTCCCCA	0.677													C|||	288	0.057508	0.0817	0.0562	5008	,	,		9678	0.0645		0.0209	False		,,,				2504	0.0562				p.S415L		Atlas-SNP	.											.	WASF3	68	.	0			c.C1244T						PASS	.	C	LEU/SER	311,4081		11,289,1896	51.0	62.0	58.0		1244	5.6	0.2	13	dbSNP_123	58	130,8448		1,128,4160	yes	missense	WASF3	NM_006646.5	145	12,417,6056	TT,TC,CC		1.5155,7.0811,3.4002	benign	415/503	27257004	441,12529	2196	4289	6485	SO:0001583	missense	10810	exon9			CTCTTTCGTCCTC	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.1244C>T	13.37:g.27257004C>T	ENSP00000335055:p.Ser415Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_006646	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	37	CCDS9318.1	110	0.05036630036630037	41	0.08333333333333333	19	0.052486187845303865	32	0.055944055944055944	18	0.023746701846965697	C	8.639	0.895539	0.17686	0.070811	0.015155	ENSG00000132970	ENST00000361042;ENST00000335327	T;T	0.55413	0.52;0.52	5.61	5.61	0.85477	.	0.352176	0.32273	N	0.006339	T	0.01489	0.0048	N	0.08118	0	0.48830	D	0.99971	D;B	0.54772	0.968;0.013	B;B	0.30716	0.119;0.003	T	0.04165	-1.0972	10	0.40728	T	0.16	-22.9197	17.1028	0.86654	0.0:1.0:0.0:0.0	rs17084492;rs17084492	412;415	Q86VQ2;Q9UPY6	.;WASF3_HUMAN	L	412;415	ENSP00000354325:S412L;ENSP00000335055:S415L	ENSP00000335055:S415L	S	+	2	0	WASF3	26155004	0.988000	0.35896	0.193000	0.23327	0.477000	0.33069	4.973000	0.63763	2.630000	0.89119	0.491000	0.48974	TCG	C|0.957;T|0.043	0.043	strong		0.677	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1		
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 GAIIx	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	OMA1_ENST00000467063.1_5'UTR|OMA1_ENST00000358603.2_Silent_p.G279G|DAB1_ENST00000485760.1_Intron	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		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	231	89	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	
BTNL8	79908	hgsc.bcm.edu	37	5	180374523	180374523	+	Missense_Mutation	SNP	G	G	A	rs7724813	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180374523G>A	ENST00000340184.4	+	4	891	c.685G>A	c.(685-687)Gag>Aag	p.E229K	BTNL8_ENST00000511704.1_Missense_Mutation_p.E113K|BTNL8_ENST00000508408.1_Missense_Mutation_p.E229K|BTNL8_ENST00000231229.4_Missense_Mutation_p.E229K|BTNL8_ENST00000505126.1_Missense_Mutation_p.E22K|BTNL8_ENST00000400707.3_Missense_Mutation_p.E104K|BTNL8_ENST00000533815.2_Missense_Mutation_p.E45K	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	229			E -> K (in dbSNP:rs7724813). {ECO:0000269|PubMed:15489334}.		immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.E229K(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TACCTTTTTCGAGCCTATATC	0.398													G|||	1197	0.239018	0.5605	0.1254	5008	,	,		18594	0.0962		0.1103	False		,,,				2504	0.1646				p.E229K		Atlas-SNP	.											BTNL8_ENST00000340184,NS,carcinoma,0,2	BTNL8	114	2	2	Substitution - Missense(2)	prostate(2)	c.G685A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	2246,2160	594.7+/-388.3	589,1068,546	198.0	214.0	209.0		685,337,685,310,133,685	-0.3	0.0	5	dbSNP_116	209	1033,7559	219.7+/-257.6	52,929,3315	yes	missense,missense,missense,missense,missense,missense	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	56,56,56,56,56,56	641,1997,3861	AA,AG,GG		12.0228,49.0241,25.227	benign,benign,benign,benign,benign,benign	229/501,113/385,229/341,104/376,45/317,229/348	180374523	3279,9719	2203	4296	6499	SO:0001583	missense	79908	exon4			TTTTTCGAGCCTA	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.685G>A	5.37:g.180374523G>A	ENSP00000342197:p.Glu229Lys	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	191	107	0.560209	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	487	0.222985347985348	306	0.6219512195121951	45	0.12430939226519337	49	0.08566433566433566	87	0.11477572559366754	G	0.005	-2.227809	0.00280	0.509759	0.120228	ENSG00000113303	ENST00000231229;ENST00000340184;ENST00000400707;ENST00000508408;ENST00000511704;ENST00000505126;ENST00000533815	T;T;T;T;T;T;T	0.59638	4.9;1.39;0.7;4.9;0.7;0.25;0.3	1.52	-0.353	0.12594	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B	0.10296	0.0;0.0;0.002;0.003;0.001	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.001;0.0	T	0.46005	-0.9222	8	0.22109	T	0.4	.	3.747	0.08552	0.2797:0.4417:0.2786:0.0	rs7724813;rs7724813	104;113;229;229;229	E9PG07;E9PEF6;F2Z2B2;A6NEX6;Q6UX41	.;.;.;.;BTNL8_HUMAN	K	229;229;104;229;113;22;45	ENSP00000231229:E229K;ENSP00000342197:E229K;ENSP00000383543:E104K;ENSP00000424585:E229K;ENSP00000425207:E113K;ENSP00000427441:E22K;ENSP00000435098:E45K	ENSP00000231229:E229K	E	+	1	0	BTNL8	180307129	0.850000	0.29656	0.040000	0.18447	0.004000	0.04260	0.037000	0.13840	-0.137000	0.11455	-1.953000	0.00484	GAG	G|0.732;A|0.268	0.268	strong		0.398	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
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 GAIIx	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		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	43	12	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	
UTP18	51096	hgsc.bcm.edu	37	17	49338275	49338275	+	Silent	SNP	G	G	A	rs8907	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:49338275G>A	ENST00000225298.7	+	1	387	c.330G>A	c.(328-330)ctG>ctA	p.L110L	MBTD1_ENST00000376381.2_5'Flank|MBTD1_ENST00000586178.1_5'Flank	NM_016001.2	NP_057085.2	Q9Y5J1	UTP18_HUMAN	UTP18 small subunit (SSU) processome component homolog (yeast)	110					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(3)|kidney(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16			BRCA - Breast invasive adenocarcinoma(22;2.09e-07)			TGCGGCGTCTGCGAGGCCCGA	0.756													G|||	480	0.0958466	0.2526	0.0562	5008	,	,		10725	0.0		0.0567	False		,,,				2504	0.0511				p.L110L		Atlas-SNP	.											.	UTP18	28	.	0			c.G330A						PASS	.	G		637,2915		53,531,1192	7.0	9.0	8.0		330	1.4	1.0	17	dbSNP_52	8	458,7282		12,434,3424	no	coding-synonymous	UTP18	NM_016001.2		65,965,4616	AA,AG,GG		5.9173,17.9336,9.6971		110/557	49338275	1095,10197	1776	3870	5646	SO:0001819	synonymous_variant	51096	exon1			GCGTCTGCGAGGC	AF151806	CCDS42362.1	17q21.33	2013-05-21	2011-12-09	2006-05-16	ENSG00000011260	ENSG00000011260		"""WD repeat domain containing"""	24274	protein-coding gene	gene with protein product		612816	"""WD repeat domain 50"""	WDR50		10810093, 8619474, 15590835	Standard	NM_016001		Approved	CGI-48	uc002its.3	Q9Y5J1	OTTHUMG00000162370	ENST00000225298.7:c.330G>A	17.37:g.49338275G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_016001	Q9H4N6	Silent	SNP	ENST00000225298.7	37	CCDS42362.1																																																																																			G|0.909;A|0.091	0.091	strong		0.756	UTP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368654.1	NM_016001	
HSPG2	3339	hgsc.bcm.edu	37	1	22160043	22160043	+	Missense_Mutation	SNP	C	C	T	rs2229493	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22160043C>T	ENST00000374695.3	-	79	10974	c.10895G>A	c.(10894-10896)cGa>cAa	p.R3632Q	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3632	Ig-like C2-type 22.		R -> Q (in dbSNP:rs2229493). {ECO:0000269|PubMed:1730768}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GTCCTGGGGTCGGACTGAGGG	0.622													c|||	430	0.0858626	0.1672	0.0504	5008	,	,		19458	0.0		0.0676	False		,,,				2504	0.1084				p.R3632Q		Atlas-SNP	.											.	HSPG2	311	.	0			c.G10895A						PASS	.	T	GLN/ARG	763,3643	310.8+/-291.8	66,631,1506	62.0	49.0	54.0		10895	-1.1	0.1	1	dbSNP_98	54	661,7939	166.7+/-218.6	26,609,3665	yes	missense	HSPG2	NM_005529.5	43	92,1240,5171	TT,TC,CC		7.686,17.3173,10.9488	benign	3632/4392	22160043	1424,11582	2203	4300	6503	SO:0001583	missense	3339	exon79			TGGGGTCGGACTG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.10895G>A	1.37:g.22160043C>T	ENSP00000363827:p.Arg3632Gln	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	165	0.07554945054945054	93	0.18902439024390244	23	0.06353591160220995	0	0.0	49	0.06464379947229551	c	3.442	-0.113760	0.06881	0.173173	0.07686	ENSG00000142798	ENST00000374695;ENST00000426143	T;T	0.65364	-0.15;2.78	4.19	-1.15	0.09709	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.976806	0.08314	N	0.964930	T	0.00073	0.0002	N	0.11673	0.155	0.80722	P	0.0	B;B	0.23806	0.003;0.091	B;B	0.19666	0.015;0.026	T	0.09640	-1.0665	9	0.14252	T	0.57	.	8.8503	0.35194	0.0:0.4632:0.0:0.5368	rs2229493;rs11552566;rs52806904;rs2229493	1572;3632	Q59EG0;P98160	.;PGBM_HUMAN	Q	3632;184	ENSP00000363827:R3632Q;ENSP00000392022:R184Q	ENSP00000363827:R3632Q	R	-	2	0	HSPG2	22032630	0.001000	0.12720	0.061000	0.19648	0.123000	0.20343	-0.065000	0.11617	-0.314000	0.08716	-1.984000	0.00453	CGA	T|0.098;G|0.000;C|0.902;A|0.000	0.098	strong		0.622	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
FAM71B	153745	hgsc.bcm.edu	37	5	156589660	156589660	+	Missense_Mutation	SNP	C	C	T	rs147753755	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:156589660C>T	ENST00000302938.4	-	2	1711	c.1616G>A	c.(1615-1617)aGg>aAg	p.R539K		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	539						nucleus (GO:0005634)				NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCTGAGGCTCCTTAAAAAAGA	0.458													C|||	3	0.000599042	0.0	0.0014	5008	,	,		19510	0.0		0.002	False		,,,				2504	0.0				p.R539K		Atlas-SNP	.											.	FAM71B	145	.	0			c.G1616A						PASS	.	C	LYS/ARG	1,4405	2.1+/-5.4	0,1,2202	135.0	138.0	137.0		1616	-0.2	0.0	5	dbSNP_134	137	31,8569	22.2+/-67.0	0,31,4269	yes	missense	FAM71B	NM_130899.2	26	0,32,6471	TT,TC,CC		0.3605,0.0227,0.246	probably-damaging	539/606	156589660	32,12974	2203	4300	6503	SO:0001583	missense	153745	exon2			AGGCTCCTTAAAA		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1616G>A	5.37:g.156589660C>T	ENSP00000305596:p.Arg539Lys	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	197	93	0.472081	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	10.61	1.398734	0.25205	2.27E-4	0.003605	ENSG00000170613	ENST00000302938	T	0.18960	2.18	3.87	-0.241	0.13043	.	0.524512	0.16000	N	0.234351	T	0.19765	0.0475	M	0.78637	2.42	0.09310	N	1	B	0.33857	0.429	B	0.23716	0.048	T	0.12477	-1.0546	10	0.87932	D	0	-16.7023	6.76	0.23536	0.0:0.5486:0.0:0.4514	.	539	Q8TC56	FA71B_HUMAN	K	539	ENSP00000305596:R539K	ENSP00000305596:R539K	R	-	2	0	FAM71B	156522238	0.254000	0.23992	0.000000	0.03702	0.007000	0.05969	-0.208000	0.09371	-0.074000	0.12820	0.655000	0.94253	AGG	C|0.997;T|0.003	0.003	strong		0.458	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
OAS2	4939	hgsc.bcm.edu	37	12	113448288	113448288	+	Nonstop_Mutation	SNP	A	A	G	rs15895	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:113448288A>G	ENST00000342315.4	+	11	2373	c.2159A>G	c.(2158-2160)tAg>tGg	p.*720W	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_3'UTR	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	0					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						AGAAACTTCTAGAGATCATCT	0.433													A|||	4329	0.864417	0.9879	0.7781	5008	,	,		17863	0.997		0.6441	False		,,,				2504	0.8487				p.X720W	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.A2159G	GRCh37	CM068051	OAS2	M	rs15895	PASS	.	A	,TRP/stop	4112,294		1920,272,11	114.0	123.0	120.0		,2159	0.9	0.1	12	dbSNP_52	120	5639,2961		1862,1915,523	yes	utr-3,stop-lost	OAS2	NM_002535.2,NM_016817.2	,	3782,2187,534	GG,GA,AA		34.4302,6.6727,25.0269	,	,720/720	113448288	9751,3255	2203	4300	6503	SO:0001578	stop_lost	4939	exon11			ACTTCTAGAGATC	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.2159A>G	12.37:g.113448288A>G	ENSP00000342278:p.*720Trpext*8	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_016817	A8K9T1|Q6PJ33|Q86XX8	Missense_Mutation	SNP	ENST00000342315.4	37	CCDS31906.1	1817	0.831959706959707	483	0.9817073170731707	272	0.7513812154696132	569	0.9947552447552448	493	0.6503957783641161	.	2.470	-0.322201	0.05350	0.933273	0.655698	ENSG00000111335	ENST00000342315	.	.	.	3.29	0.85	0.18980	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.3003	0.06980	0.6241:0.2435:0.1324:0.0	rs15895;rs3199142;rs17253693;rs52791245;rs60582125;rs15895	.	.	.	W	720	.	.	X	+	2	0	OAS2	111932671	0.010000	0.17322	0.097000	0.21041	0.068000	0.16541	0.040000	0.13905	0.163000	0.19507	0.459000	0.35465	TAG	T|0.004;G|0.782	0.782	strong		0.433	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
TTN	7273	hgsc.bcm.edu	37	2	179457147	179457147	+	Missense_Mutation	SNP	G	G	A	rs16866406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179457147G>A	ENST00000591111.1	-	251	54886	c.54662C>T	c.(54661-54663)cCa>cTa	p.P18221L	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P19862L|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P10989L|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P10922L|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P10797L|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P17294L|TTN-AS1_ENST00000589907.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18221	Ig-like 105.		P -> L. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGAACCAGCTGGATTCTCCAC	0.333													G|||	1067	0.213059	0.0666	0.1527	5008	,	,		19552	0.4573		0.1392	False		,,,				2504	0.2781				p.P19862L		Atlas-SNP	.											.	TTN	18412	.	0			c.C59585T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	283,3415		10,263,1576	153.0	147.0	149.0		32966,32765,51881,32390	5.2	1.0	2	dbSNP_123	149	1205,6973		91,1023,2975	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	98,98,98,98	101,1286,4551	AA,AG,GG		14.7347,7.6528,12.5295	benign,benign,benign,benign	10989/27119,10922/27052,17294/33424,10797/26927	179457147	1488,10388	1849	4089	5938	SO:0001583	missense	7273	exon301			CCAGCTGGATTCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.54662C>T	2.37:g.179457147G>A	ENSP00000465570:p.Pro18221Leu	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	110	40	0.363636	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		425	0.1945970695970696	30	0.06097560975609756	46	0.1270718232044199	244	0.42657342657342656	105	0.13852242744063326	G	11.43	1.636872	0.29157	0.076528	0.147347	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	6.03	5.16	0.70880	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.55213	1.73	0.21878	P	0.999490043	B;B;B;B	0.13594	0.008;0.008;0.008;0.008	B;B;B;B	0.20767	0.031;0.031;0.031;0.031	T	0.28839	-1.0031	8	0.87932	D	0	.	12.5317	0.56120	0.1336:0.0:0.8664:0.0	rs16866406;rs52804325;rs16866406	10797;10922;10989;18221	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	17294;10797;10989;10922;10795	ENSP00000343764:P17294L;ENSP00000434586:P10797L;ENSP00000340554:P10989L;ENSP00000352154:P10922L	ENSP00000340554:P10989L	P	-	2	0	TTN	179165393	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.667000	0.61561	1.568000	0.49683	0.557000	0.71058	CCA	G|0.808;A|0.191	0.191	strong		0.333	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ACPT	93650	hgsc.bcm.edu	37	19	51294098	51294098	+	Missense_Mutation	SNP	C	C	T	rs145475625	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51294098C>T	ENST00000270593.1	+	3	284	c.284C>T	c.(283-285)cCg>cTg	p.P95L	ACPT_ENST00000270594.3_Intron|CTD-2568A17.8_ENST00000594114.1_RNA	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	95						integral component of membrane (GO:0016021)	acid phosphatase activity (GO:0003993)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(3)	11		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		TTCCTGAGTCCGGAGTACCGG	0.667													C|||	167	0.0333466	0.0756	0.0331	5008	,	,		13358	0.001		0.0338	False		,,,				2504	0.0092				p.P95L		Atlas-SNP	.											ACPT,NS,carcinoma,0,1	ACPT	43	1	0			c.C284T						PASS	.	C	LEU/PRO	226,3510		8,210,1650	13.0	19.0	17.0		284	3.6	0.9	19	dbSNP_134	17	215,6889		1,213,3338	no	missense	ACPT	NM_033068.2	98	9,423,4988	TT,TC,CC		3.0265,6.0493,4.0683	probably-damaging	95/427	51294098	441,10399	1868	3552	5420	SO:0001583	missense	93650	exon3			TGAGTCCGGAGTA	AF321918	CCDS12802.1	19q13.33	2012-10-02			ENSG00000142513	ENSG00000142513			14376	protein-coding gene	gene with protein product		606362				11414767	Standard	NM_033068		Approved		uc002pta.1	Q9BZG2		ENST00000270593.1:c.284C>T	19.37:g.51294098C>T	ENSP00000270593:p.Pro95Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Missense_Mutation	SNP	ENST00000270593.1	37	CCDS12802.1	78	0.03571428571428571	39	0.07926829268292683	16	0.04419889502762431	1	0.0017482517482517483	22	0.029023746701846966	c	11.70	1.716556	0.30413	0.060493	0.030265	ENSG00000142513	ENST00000270593	T	0.18338	2.22	4.71	3.57	0.40892	.	0.255076	0.33346	N	0.005016	T	0.01976	0.0062	M	0.77486	2.375	0.58432	D	0.999998	D	0.67145	0.996	P	0.58391	0.838	T	0.00095	-1.2076	10	0.36615	T	0.2	-10.3187	11.3942	0.49832	0.2204:0.7796:0.0:0.0	.	95	Q9BZG2	PPAT_HUMAN	L	95	ENSP00000270593:P95L	ENSP00000270593:P95L	P	+	2	0	ACPT	55985910	0.460000	0.25776	0.927000	0.36925	0.158000	0.22134	1.614000	0.36911	2.336000	0.79503	0.561000	0.74099	CCG	C|0.964;T|0.036	0.036	strong		0.667	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	
HLA-A	3105	hgsc.bcm.edu	37	6	29910402	29910402	+	Splice_Site	SNP	G	G	A	rs1136656	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29910402G>A	ENST00000396634.1	+	3	413	c.72G>A	c.(70-72)gcG>gcA	p.A24A	HLA-A_ENST00000376806.5_Splice_Site_p.A24A|HLA-A_ENST00000376802.2_Splice_Site_p.A24A|HLA-A_ENST00000376809.5_Splice_Site_p.A24A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	24					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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGACCTGGGCGGGTGAGTGCG	0.736									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	782	0.15615	0.1362	0.1772	5008	,	,		13109	0.2034		0.1123	False		,,,				2504	0.1646				p.A24A		Atlas-SNP	.											.	HLA-A	89	.	0			c.G72A						PASS	.	G		591,3805		42,507,1649	20.0	22.0	21.0		72	0.2	1.0	6	dbSNP_86	21	907,7677		52,803,3437	no	coding-synonymous-near-splice	HLA-A	NM_002116.7		94,1310,5086	AA,AG,GG		10.5662,13.444,11.5408		24/366	29910402	1498,11482	2198	4292	6490	SO:0001630	splice_region_variant	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CTGGGCGGGTGAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.73+1G>A	6.37:g.29910402G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	63	12	0.190476	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.870;A|0.130	0.130	strong		0.736	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	Silent
FAM220A	84792	hgsc.bcm.edu	37	7	6370194	6370194	+	Missense_Mutation	SNP	C	C	T	rs6952125	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6370194C>T	ENST00000313324.4	-	2	1059	c.592G>A	c.(592-594)Gtg>Atg	p.V198M	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	198			V -> M (in dbSNP:rs6952125). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			nucleus (GO:0005634)											TCGGGATACACGTGCAGCGTT	0.488													C|||	3669	0.732628	0.8994	0.6614	5008	,	,		19902	0.8839		0.4553	False		,,,				2504	0.6871				p.V198M		Atlas-SNP	.											.	.	.	.	0			c.G592A						PASS	.	C	MET/VAL	3719,687	762.0+/-413.1	1588,543,72	103.0	111.0	109.0		592	-1.2	0.0	7	dbSNP_116	109	4108,4492	562.0+/-387.9	976,2156,1168	yes	missense	C7orf70	NM_001037163.1	21	2564,2699,1240	TT,TC,CC		47.7674,15.5924,39.8201	benign	198/260	6370194	7827,5179	2203	4300	6503	SO:0001583	missense	84792	exon2			GATACACGTGCAG	BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"""STAT3-interacting protein as a repressor"""		"""chromosome 7 open reading frame 70"""	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.592G>A	7.37:g.6370194C>T	ENSP00000317289:p.Val198Met	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	135	88	0.651852	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	Missense_Mutation	SNP	ENST00000313324.4	37	CCDS34599.1	1519	0.6955128205128205	440	0.8943089430894309	229	0.6325966850828729	505	0.8828671328671329	345	0.4551451187335092	C	11.43	1.635657	0.29068	0.844076	0.477674	ENSG00000178397	ENST00000313324	T	0.07908	3.15	5.2	-1.16	0.09678	.	1.225150	0.06349	N	0.709569	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.33637	0.42	B	0.31751	0.135	T	0.09079	-1.0691	9	0.48119	T	0.1	-1.1277	1.7656	0.03001	0.1303:0.4507:0.1266:0.2924	rs6952125;rs10304725;rs17775264;rs52819484;rs57403160;rs6952125	198	Q7Z4H9	SIPAR_HUMAN	M	198	ENSP00000317289:V198M	ENSP00000317289:V198M	V	-	1	0	C7orf70	6336719	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.236000	0.09003	-0.596000	0.05821	-0.140000	0.14226	GTG	C|0.342;N|0.000	.	strong		0.488	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163	
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 GAIIx	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_ENST00000454497.2_Missense_Mutation_p.V502M|OTUD4_ENST00000455611.2_5'UTR			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	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	35	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	
ANPEP	290	hgsc.bcm.edu	37	15	90334240	90334240	+	Silent	SNP	A	A	G	rs25654	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90334240A>G	ENST00000300060.6	-	19	2926	c.2613T>C	c.(2611-2613)atT>atC	p.I871I		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	871	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	GACCTTGCCCAATGACGTTGT	0.542													G|||	1570	0.313498	0.3812	0.2493	5008	,	,		20459	0.2341		0.2952	False		,,,				2504	0.3681				p.I871I	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.T2613C						PASS	.	G		1584,2816	665.6+/-401.6	290,1004,906	154.0	134.0	141.0		2613	-9.0	0.0	15	dbSNP_72	141	2734,5864	680.3+/-403.6	405,1924,1970	no	coding-synonymous	ANPEP	NM_001150.2		695,2928,2876	GG,GA,AA		31.7981,36.0,33.2205		871/968	90334240	4318,8680	2200	4299	6499	SO:0001819	synonymous_variant	290	exon19			TTGCCCAATGACG	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2613T>C	15.37:g.90334240A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	176	79	0.448864	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	37	CCDS10356.1																																																																																			A|0.675;G|0.325	0.325	strong		0.542	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
ACVR2A	92	hgsc.bcm.edu	37	2	148657117	148657117	+	Silent	SNP	G	G	A	rs1128919	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:148657117G>A	ENST00000241416.7	+	3	990	c.354G>A	c.(352-354)ccG>ccA	p.P118P	ACVR2A_ENST00000404590.1_Silent_p.P118P|AC009480.3_ENST00000402410.2_RNA|ACVR2A_ENST00000535787.1_Silent_p.P10P	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	118					activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		CTTATTTTCCGGAGATGGAAG	0.343													G|||	1766	0.352636	0.2852	0.4611	5008	,	,		15465	0.4673		0.327	False		,,,				2504	0.2751				p.P118P		Atlas-SNP	.											.	ACVR2A	125	.	0			c.G354A						PASS	.	G		1368,3036	424.0+/-340.3	223,922,1057	151.0	159.0	156.0		354	0.4	1.0	2	dbSNP_86	156	2710,5888	427.5+/-355.6	419,1872,2008	no	coding-synonymous	ACVR2A	NM_001616.3		642,2794,3065	AA,AG,GG		31.519,31.0627,31.3644		118/514	148657117	4078,8924	2202	4299	6501	SO:0001819	synonymous_variant	92	exon3			TTTTCCGGAGATG		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.354G>A	2.37:g.148657117G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Silent	SNP	ENST00000241416.7	37	CCDS33301.1																																																																																			G|0.657;A|0.343	0.343	strong		0.343	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	
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 GAIIx	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		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	93	32	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	
TMEM232	642987	hgsc.bcm.edu	37	5	109960989	109960989	+	Silent	SNP	A	A	G	rs61730920	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:109960989A>G	ENST00000455884.2	-	7	797	c.747T>C	c.(745-747)taT>taC	p.Y249Y	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Silent_p.Y249Y			C9JQI7	TM232_HUMAN	transmembrane protein 232	249						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						CTGTGTTCTCATATCTTTTCT	0.363													A|||	798	0.159345	0.3457	0.1354	5008	,	,		17424	0.0833		0.0905	False		,,,				2504	0.0736				p.Y249Y		Atlas-SNP	.											.	TMEM232	57	.	0			c.T747C						PASS	.	A		427,957		71,285,336	262.0	227.0	238.0		747	3.3	0.0	5	dbSNP_129	238	293,2889		14,265,1312	no	coding-synonymous	TMEM232	NM_001039763.3		85,550,1648	GG,GA,AA		9.208,30.8526,15.7687		249/658	109960989	720,3846	692	1591	2283	SO:0001819	synonymous_variant	642987	exon7			GTTCTCATATCTT	AK125070	CCDS47253.1, CCDS47253.2	5q22.1	2014-02-12	2009-10-02		ENSG00000186952	ENSG00000186952			37270	protein-coding gene	gene with protein product							Standard	NM_001039763		Approved	FLJ43080	uc011cvh.2	C9JQI7	OTTHUMG00000163297	ENST00000455884.2:c.747T>C	5.37:g.109960989A>G		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	210	93	0.442857	NM_001039763	B4DKF4	Silent	SNP	ENST00000455884.2	37	CCDS47253.2																																																																																			A|0.859;G|0.141	0.141	strong		0.363	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
PRRG4	79056	hgsc.bcm.edu	37	11	32852172	32852172	+	Missense_Mutation	SNP	G	G	A	rs33962176	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:32852172G>A	ENST00000257836.3	+	2	350	c.97G>A	c.(97-99)Gaa>Aaa	p.E33K		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	33			E -> K (in dbSNP:rs33962176).			extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.E33K(1)		large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					GCATGCGGGAGAAGAAGGTAA	0.488													G|||	364	0.0726837	0.0688	0.0504	5008	,	,		14880	0.0		0.1193	False		,,,				2504	0.1207				p.E33K		Atlas-SNP	.											PRRG4,NS,carcinoma,0,1	PRRG4	15	1	1	Substitution - Missense(1)	prostate(1)	c.G97A						PASS	.	G	LYS/GLU	329,4075	173.7+/-203.5	11,307,1884	90.0	80.0	84.0		97	2.8	0.6	11	dbSNP_126	84	1049,7549	220.9+/-258.5	48,953,3298	yes	missense	PRRG4	NM_024081.5	56	59,1260,5182	AA,AG,GG		12.2005,7.4705,10.5984	benign	33/227	32852172	1378,11624	2202	4299	6501	SO:0001583	missense	79056	exon2			GCGGGAGAAGAAG	AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.97G>A	11.37:g.32852172G>A	ENSP00000257836:p.Glu33Lys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_024081		Missense_Mutation	SNP	ENST00000257836.3	37	CCDS7881.1	154	0.07051282051282051	31	0.06300813008130081	18	0.049723756906077346	0	0.0	105	0.13852242744063326	G	6.368	0.436089	0.12104	0.074705	0.122005	ENSG00000135378	ENST00000257836	D	0.97731	-4.51	4.99	2.84	0.33178	Gamma-carboxyglutamic acid-rich (GLA) domain (1);	0.376451	0.29172	N	0.012929	T	0.07234	0.0183	N	0.12746	0.255	0.42859	P	0.005898999999999988	B	0.06786	0.001	B	0.08055	0.003	T	0.66388	-0.5936	9	0.07175	T	0.84	-10.946	4.509	0.11901	0.3813:0.0:0.6187:0.0	rs33962176	33	Q9BZD6	TMG4_HUMAN	K	33	ENSP00000257836:E33K	ENSP00000257836:E33K	E	+	1	0	PRRG4	32808748	0.617000	0.27043	0.589000	0.28718	0.051000	0.14879	0.807000	0.27140	1.086000	0.41228	-0.192000	0.12808	GAA	G|0.902;A|0.098	0.098	strong		0.488	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081	
DNAJC10	54431	hgsc.bcm.edu	37	2	183584755	183584755	+	Missense_Mutation	SNP	G	G	A	rs6729801	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:183584755G>A	ENST00000264065.7	+	4	641	c.226G>A	c.(226-228)Gat>Aat	p.D76N	DNAJC10_ENST00000537515.1_Missense_Mutation_p.D76N|DNAJC10_ENST00000469118.1_3'UTR	NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10	76	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.		D -> N (in dbSNP:rs6729801). {ECO:0000269|PubMed:14587667, ECO:0000269|PubMed:17974005}.		cell redox homeostasis (GO:0045454)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATPase activity (GO:0032781)|protein folding in endoplasmic reticulum (GO:0034975)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|disulfide oxidoreductase activity (GO:0015036)|Hsp70 protein binding (GO:0030544)|misfolded protein binding (GO:0051787)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide oxidoreductase activity (GO:0015035)			breast(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(15)|ovary(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			TGCACATGGCGATTTTTTAAA	0.284													G|||	1763	0.352037	0.093	0.3833	5008	,	,		15193	0.2996		0.5586	False		,,,				2504	0.5215				p.D76N	Pancreas(56;860 1183 25669 35822 48585)	Atlas-SNP	.											.	DNAJC10	76	.	0			c.G226A						PASS	.	G	ASN/ASP	771,3635	283.7+/-277.2	67,637,1499	49.0	51.0	50.0		226	5.1	1.0	2	dbSNP_116	50	4894,3706	605.8+/-395.0	1376,2142,782	yes	missense	DNAJC10	NM_018981.1	23	1443,2779,2281	AA,AG,GG		43.093,17.4989,43.5568	benign	76/794	183584755	5665,7341	2203	4300	6503	SO:0001583	missense	54431	exon4			CATGGCGATTTTT		CCDS33345.1, CCDS74613.1	2q32.1	2011-11-23			ENSG00000077232	ENSG00000077232		"""Heat shock proteins / DNAJ (HSP40)"", ""Protein disulfide isomerases"""	24637	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 19"""	607987				12411443, 12446677	Standard	NM_018981		Approved	ERdj5, PDIA19	uc002uow.2	Q8IXB1	OTTHUMG00000154209	ENST00000264065.7:c.226G>A	2.37:g.183584755G>A	ENSP00000264065:p.Asp76Asn	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_001271581	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Missense_Mutation	SNP	ENST00000264065.7	37	CCDS33345.1	781	0.3576007326007326	46	0.09349593495934959	157	0.43370165745856354	153	0.2674825174825175	425	0.5606860158311345	G	15.80	2.939858	0.52972	0.174989	0.56907	ENSG00000077232	ENST00000264065;ENST00000392392;ENST00000537410;ENST00000537515	T;T	0.29917	1.55;1.55	5.93	5.05	0.67936	Heat shock protein DnaJ, N-terminal (5);	0.417622	0.28760	N	0.014230	T	0.00012	0.0000	N	0.13098	0.295	0.27389	P	0.9551818	B;B	0.12630	0.002;0.006	B;B	0.04013	0.001;0.001	T	0.46470	-0.9189	9	0.17832	T	0.49	.	5.7114	0.17937	0.2546:0.0:0.7454:0.0	rs6729801;rs52808466;rs6729801	76;76	Q8IXB1-2;Q8IXB1	.;DJC10_HUMAN	N	76	ENSP00000264065:D76N;ENSP00000441560:D76N	ENSP00000264065:D76N	D	+	1	0	DNAJC10	183293000	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.065000	0.64344	2.802000	0.96397	0.563000	0.77884	GAT	G|0.597;A|0.403	0.403	strong		0.284	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981	
DOCK5	80005	hgsc.bcm.edu	37	8	25222165	25222165	+	Missense_Mutation	SNP	A	A	G	rs2271111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:25222165A>G	ENST00000276440.7	+	30	3112	c.3068A>G	c.(3067-3069)cAg>cGg	p.Q1023R		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1023			Q -> R (in dbSNP:rs2271111).		positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.Q1023R(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GCTATAAATCAGTTTGCTGAA	0.418													A|||	1230	0.245607	0.0711	0.304	5008	,	,		18344	0.3562		0.3698	False		,,,				2504	0.1984				p.Q1023R	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											DOCK5,NS,carcinoma,0,1	DOCK5	167	1	1	Substitution - Missense(1)	stomach(1)	c.A3068G						PASS	.	A	ARG/GLN	487,3919	213.8+/-233.3	26,435,1742	137.0	117.0	124.0		3068	4.3	1.0	8	dbSNP_100	124	2886,5714	414.1+/-351.3	498,1890,1912	yes	missense	DOCK5	NM_024940.6	43	524,2325,3654	GG,GA,AA		33.5581,11.0531,25.9342	benign	1023/1871	25222165	3373,9633	2203	4300	6503	SO:0001583	missense	80005	exon30			TAAATCAGTTTGC		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3068A>G	8.37:g.25222165A>G	ENSP00000276440:p.Gln1023Arg	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	146	57	0.390411	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	634	0.2902930402930403	37	0.07520325203252033	120	0.3314917127071823	189	0.3304195804195804	288	0.37994722955145116	A	10.21	1.287145	0.23478	0.110531	0.335581	ENSG00000147459	ENST00000276440	T	0.23950	1.88	5.62	4.34	0.51931	.	0.058883	0.64402	D	0.000001	T	0.00012	0.0000	L	0.41710	1.295	0.23920	P	0.99646016	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.41858	-0.9485	9	0.08837	T	0.75	.	7.572	0.27913	0.7907:0.0:0.073:0.1362	rs2271111;rs52835832;rs58353884;rs2271111	1013;1023	D3DSS6;Q9H7D0	.;DOCK5_HUMAN	R	1023	ENSP00000276440:Q1023R	ENSP00000276440:Q1023R	Q	+	2	0	DOCK5	25278082	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.300000	0.59079	2.142000	0.66516	0.528000	0.53228	CAG	A|0.749;G|0.251	0.251	strong		0.418	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
SEC23B	10483	hgsc.bcm.edu	37	20	18513372	18513372	+	Missense_Mutation	SNP	C	C	T	rs17807673	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:18513372C>T	ENST00000336714.3	+	11	1730	c.1298C>T	c.(1297-1299)cCg>cTg	p.P433L	SEC23B_ENST00000377465.1_Missense_Mutation_p.P433L|SEC23B_ENST00000262544.2_Missense_Mutation_p.P433L|SEC23B_ENST00000377475.3_Missense_Mutation_p.P433L	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	433			P -> L (in dbSNP:rs17807673). {ECO:0000269|PubMed:15489334}.		ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						GTGAAAGGACCGTGTGTGTCA	0.453													C|||	307	0.0613019	0.0061	0.1095	5008	,	,		22089	0.003		0.1302	False		,,,				2504	0.091				p.P433L		Atlas-SNP	.											SEC23B,NS,carcinoma,-1,1	SEC23B	70	1	0			c.C1298T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	133,4273	95.3+/-134.0	4,125,2074	135.0	128.0	130.0		1298,1244,1298,1298,1298	4.8	1.0	20	dbSNP_123	130	1235,7365	248.6+/-276.2	95,1045,3160	yes	missense,missense,missense,missense,missense	SEC23B	NM_001172745.1,NM_001172746.1,NM_006363.4,NM_032985.4,NM_032986.3	98,98,98,98,98	99,1170,5234	TT,TC,CC		14.3605,3.0186,10.5182	benign,benign,benign,benign,benign	433/768,415/750,433/768,433/768,433/768	18513372	1368,11638	2203	4300	6503	SO:0001583	missense	10483	exon11			AAGGACCGTGTGT	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"""Sec23 (S. cerevisiae) homolog B"", ""congenital dyserythropoietic anemia, type II"""	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.1298C>T	20.37:g.18513372C>T	ENSP00000338844:p.Pro433Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	37	CCDS13137.1	133	0.060897435897435896	6	0.012195121951219513	31	0.0856353591160221	1	0.0017482517482517483	95	0.12532981530343007	C	19.62	3.860872	0.71834	0.030186	0.143605	ENSG00000101310	ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	4.75	4.75	0.60458	Sec23/Sec24 beta-sandwich (1);	0.217145	0.48767	D	0.000178	T	0.02929	0.0087	M	0.90595	3.13	0.09310	P	0.9999999999602158	P	0.35411	0.5	B	0.42282	0.382	T	0.57837	-0.7742	9	0.72032	D	0.01	-11.4113	17.2702	0.87099	0.0:1.0:0.0:0.0	rs17807673;rs17849993;rs56617302;rs17807673	433	Q15437	SC23B_HUMAN	L	433	ENSP00000338844:P433L;ENSP00000262544:P433L;ENSP00000366695:P433L;ENSP00000366685:P433L	ENSP00000262544:P433L	P	+	2	0	SEC23B	18461372	0.998000	0.40836	0.977000	0.42913	0.989000	0.77384	7.109000	0.77062	2.631000	0.89168	0.655000	0.94253	CCG	C|0.909;T|0.091	0.091	strong		0.453	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5		
CEP290	80184	hgsc.bcm.edu	37	12	88505078	88505078	+	Silent	SNP	T	T	C	rs2468255	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:88505078T>C	ENST00000552810.1	-	22	2611	c.2268A>G	c.(2266-2268)tcA>tcG	p.S756S	CEP290_ENST00000309041.7_Silent_p.S758S|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	756					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						AAACAACATTTGATCCTTCTG	0.333													T|||	3829	0.764577	0.3245	0.8804	5008	,	,		14474	0.9673		0.9225	False		,,,				2504	0.9059				p.S756S		Atlas-SNP	.											.	CEP290	195	.	0			c.A2268G						PASS	.	T		1570,2064		350,870,597	60.0	52.0	54.0		2268	-1.3	1.0	12	dbSNP_100	54	7514,630		3473,568,31	no	coding-synonymous	CEP290	NM_025114.3		3823,1438,628	CC,CT,TT		7.7358,43.2031,22.8732		756/2480	88505078	9084,2694	1817	4072	5889	SO:0001819	synonymous_variant	80184	exon22			AACATTTGATCCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.2268A>G	12.37:g.88505078T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	196	87	0.443878	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	37	CCDS55858.1																																																																																			T|0.224;C|0.776	0.776	strong		0.333	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
SNRNP48	154007	hgsc.bcm.edu	37	6	7590624	7590624	+	Missense_Mutation	SNP	C	C	T	rs2757594	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:7590624C>T	ENST00000342415.5	+	1	193	c.134C>T	c.(133-135)cCc>cTc	p.P45L		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	45			P -> L (in dbSNP:rs2757594). {ECO:0000269|PubMed:15489334}.		mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						AGTCTGGATCCCGGGGAAGAG	0.687													C|||	1070	0.213658	0.1415	0.2435	5008	,	,		12876	0.0744		0.3817	False		,,,				2504	0.2607				p.P45L		Atlas-SNP	.											.	SNRNP48	32	.	0			c.C134T						PASS	.	C	LEU/PRO	702,3610		72,558,1526	11.0	13.0	13.0		134	2.3	0.7	6	dbSNP_100	13	3045,5415		579,1887,1764	yes	missense	SNRNP48	NM_152551.3	98	651,2445,3290	TT,TC,CC		35.9929,16.2801,29.3376	benign	45/340	7590624	3747,9025	2156	4230	6386	SO:0001583	missense	154007	exon1			TGGATCCCGGGGA	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"""U11/U12 snRNP 48K"""		"""chromosome 6 open reading frame 151"""	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.134C>T	6.37:g.7590624C>T	ENSP00000339834:p.Pro45Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	108	16	0.148148	NM_152551	A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Missense_Mutation	SNP	ENST00000342415.5	37	CCDS4502.1	507	0.23214285714285715	77	0.1565040650406504	103	0.2845303867403315	36	0.06293706293706294	291	0.3839050131926121	C	15.96	2.985607	0.53934	0.162801	0.359929	ENSG00000168566	ENST00000342415;ENST00000397475	T	0.30182	1.54	5.16	2.33	0.28932	.	0.471174	0.19972	N	0.101950	T	0.06325	0.0163	N	0.19112	0.55	0.28431	P	0.9172821	B	0.02656	0.0	B	0.06405	0.002	T	0.24584	-1.0156	9	0.33940	T	0.23	-0.0562	5.8231	0.18538	0.0:0.6621:0.1573:0.1807	rs2757594;rs17397753;rs52799491;rs59594751;rs2757594	45	Q6IEG0	SNR48_HUMAN	L	45	ENSP00000339834:P45L	ENSP00000339834:P45L	P	+	2	0	SNRNP48	7535623	0.012000	0.17670	0.748000	0.31131	0.993000	0.82548	0.390000	0.20768	0.545000	0.28902	0.563000	0.77884	CCC	C|0.778;T|0.222	0.222	strong		0.687	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551	
PLEC	5339	hgsc.bcm.edu	37	8	145004185	145004185	+	Silent	SNP	C	C	T	rs78012434	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145004185C>T	ENST00000322810.4	-	22	3238	c.3069G>A	c.(3067-3069)ttG>ttA	p.L1023L	PLEC_ENST00000354589.3_Silent_p.L886L|PLEC_ENST00000357649.2_Silent_p.L890L|PLEC_ENST00000436759.2_Silent_p.L913L|PLEC_ENST00000354958.2_Silent_p.L864L|PLEC_ENST00000527096.1_Silent_p.L909L|PLEC_ENST00000345136.3_Silent_p.L886L|PLEC_ENST00000356346.3_Silent_p.L872L|PLEC_ENST00000398774.2_Silent_p.L854L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1023	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TGTCCACGTGCAACTGGTGCC	0.697													C|||	326	0.0650958	0.2284	0.0317	5008	,	,		16413	0.0		0.002	False		,,,				2504	0.0				p.L1023L		Atlas-SNP	.											.	PLEC	1144	.	0			c.G3069A						PASS	.	C	,,,,,,,	823,3569		84,655,1457	26.0	34.0	31.0		2739,2616,2592,3069,2562,2658,2670,2658	-0.4	1.0	8	dbSNP_132	31	20,8550		0,20,4265	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	84,675,5722	TT,TC,CC		0.2334,18.7386,6.5036	,,,,,,,	913/4575,872/4534,864/4526,1023/4685,854/4516,886/4548,890/4552,886/4548	145004185	843,12119	2196	4285	6481	SO:0001819	synonymous_variant	5339	exon22			CACGTGCAACTGG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.3069G>A	8.37:g.145004185C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			C|0.963;T|0.037	0.037	strong		0.697	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
ANKRD6	22881	hgsc.bcm.edu	37	6	90340276	90340276	+	Silent	SNP	G	G	A	rs3210511	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90340276G>A	ENST00000522441.1	+	16	2378	c.1737G>A	c.(1735-1737)tcG>tcA	p.S579S	ANKRD6_ENST00000339746.4_Silent_p.S579S|ANKRD6_ENST00000520793.1_Silent_p.S515S|LYRM2_ENST00000520441.1_Intron|ANKRD6_ENST00000369408.5_Silent_p.S544S|ANKRD6_ENST00000447838.2_Silent_p.S574S	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	579					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		AGGAGCTGTCGTCTTCTGACT	0.587													G|||	3009	0.600839	0.5749	0.7003	5008	,	,		19233	0.9077		0.4662	False		,,,				2504	0.3875				p.S579S		Atlas-SNP	.											.	ANKRD6	51	.	0			c.G1737A						PASS	.	G	,,,,	2331,1589		714,903,343	31.0	33.0	32.0		1737,1737,1632,1545,1722	-3.7	1.0	6	dbSNP_105	32	3938,4334		969,2000,1167	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANKRD6	NM_001242809.1,NM_001242811.1,NM_001242813.1,NM_001242814.1,NM_014942.4	,,,,	1683,2903,1510	AA,AG,GG		47.6064,40.5357,48.581	,,,,	579/728,579/728,544/693,515/664,574/723	90340276	6269,5923	1960	4136	6096	SO:0001819	synonymous_variant	22881	exon16			GCTGTCGTCTTCT	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1737G>A	6.37:g.90340276G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Silent	SNP	ENST00000522441.1	37	CCDS56441.1																																																																																			G|0.381;A|0.619	0.619	strong		0.587	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
OR1S2	219958	hgsc.bcm.edu	37	11	57971171	57971171	+	Silent	SNP	C	C	T	rs200697120	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57971171C>T	ENST00000302592.6	-	1	482	c.483G>A	c.(481-483)tcG>tcA	p.S161S		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGAGGAACCACGAGATGACTG	0.498																																					p.S161S		Atlas-SNP	.											.	OR1S2	119	.	0			c.G483A						PASS	.						209.0	196.0	200.0					11																	57971171		2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			GAACCACGAGATG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.483G>A	11.37:g.57971171C>T		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	155	23	0.148387	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			C|0.928;T|0.072	0.072	strong		0.498	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
WDFY4	57705	hgsc.bcm.edu	37	10	50013402	50013402	+	Missense_Mutation	SNP	T	T	C	rs2170132	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50013402T>C	ENST00000325239.5	+	25	4609	c.4582T>C	c.(4582-4584)Tcc>Ccc	p.S1528P	WDFY4_ENST00000413659.2_Intron	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1528						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CTCCAAGATCTCCACCATCAT	0.587													C|||	2889	0.576877	0.7905	0.3977	5008	,	,		17153	0.8304		0.2962	False		,,,				2504	0.4427				p.S1528P		Atlas-SNP	.											.	WDFY4	205	.	0			c.T4582C						PASS	.	C	PRO/SER	1011,373		373,265,54	92.0	82.0	85.0		4582	1.5	1.0	10	dbSNP_96	85	996,2186		136,724,731	yes	missense	WDFY4	NM_020945.1	74	509,989,785	CC,CT,TT		31.3011,26.9509,43.9553	benign	1528/3185	50013402	2007,2559	692	1591	2283	SO:0001583	missense	57705	exon26			AAGATCTCCACCA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.4582T>C	10.37:g.50013402T>C	ENSP00000320563:p.Ser1528Pro	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	1202|1202	0.5503663003663004|0.5503663003663004	377|377	0.766260162601626|0.766260162601626	139|139	0.3839779005524862|0.3839779005524862	465|465	0.8129370629370629|0.8129370629370629	221|221	0.29155672823219|0.29155672823219	C|C	7.506|7.506	0.653714|0.653714	0.14580|0.14580	0.730491|0.730491	0.313011|0.313011	ENSG00000128815|ENSG00000128815	ENST00000312002;ENST00000374161|ENST00000426033;ENST00000325239	.|T	.|0.55234	.|0.53	5.01|5.01	1.47|1.47	0.22746|0.22746	.|.	.|0.231982	.|0.36101	.|N	.|0.002791	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04508|0.04508	-0.205|-0.205	0.09310|0.09310	P|P	0.99999999718745|0.99999999718745	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.28038|0.28038	-1.0056|-1.0056	4|8	.|.	.|.	.|.	.|.	4.1496|4.1496	0.10232|0.10232	0.4526:0.3487:0.0:0.1987|0.4526:0.3487:0.0:0.1987	rs2170132;rs17772022;rs52834656;rs2170132|rs2170132;rs17772022;rs52834656;rs2170132	.|56;1528	.|F2Z372;Q6ZS81	.|.;WDFY4_HUMAN	P|P	618;74|1528	.|ENSP00000320563:S1528P	.|.	L|S	+|+	2|1	0|0	WDFY4|WDFY4	49683408|49683408	0.490000|0.490000	0.26012|0.26012	0.989000|0.989000	0.46669|0.46669	0.577000|0.577000	0.36160|0.36160	-0.165000|-0.165000	0.09968|0.09968	0.219000|0.219000	0.20840|0.20840	-0.821000|-0.821000	0.03111|0.03111	CTC|TCC	T|0.443;C|0.557	0.557	strong		0.587	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
GCNT2	2651	hgsc.bcm.edu	37	6	10587056	10587056	+	Intron	SNP	A	A	G	rs71548508	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:10587056A>G	ENST00000379597.3	+	2	1481				GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000316170.3_Intron|GCNT2_ENST00000265012.4_Silent_p.L278L			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.L278L(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		ACTTTGTTCTACGTGACCAAA	0.418													A|||	256	0.0511182	0.0121	0.062	5008	,	,		19022	0.0079		0.1471	False		,,,				2504	0.0419				p.L278L		Atlas-SNP	.											GCNT2_ENST00000265012,NS,carcinoma,0,1	GCNT2	123	1	1	Substitution - coding silent(1)	stomach(1)	c.A834G						PASS	.	A	,,	152,4254	105.6+/-144.1	5,142,2056	90.0	84.0	86.0		,,834	-1.1	0.0	6	dbSNP_130	86	1270,7330	253.0+/-278.9	105,1060,3135	no	intron,intron,coding-synonymous	GCNT2	NM_001491.2,NM_145649.4,NM_145655.3	,,	110,1202,5191	GG,GA,AA		14.7674,3.4498,10.9334	,,	,,278/403	10587056	1422,11584	2203	4300	6503	SO:0001627	intron_variant	2651	exon1			TGTTCTACGTGAC	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-34528A>G	6.37:g.10587056A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	133	26	0.195489	NM_145655		Silent	SNP	ENST00000379597.3	37	CCDS34338.1																																																																																			A|0.899;G|0.101	0.101	strong		0.418	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
PDE5A	8654	hgsc.bcm.edu	37	4	120474859	120474859	+	Silent	SNP	A	A	G	rs11947234	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:120474859A>G	ENST00000354960.3	-	8	1561	c.1242T>C	c.(1240-1242)taT>taC	p.Y414Y	RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000394439.1_Silent_p.Y362Y|PDE5A_ENST00000264805.5_Silent_p.Y372Y	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	414	GAF 2.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	TATTTTTGACATACTGAGCAT	0.358													A|||	1331	0.265775	0.2118	0.2867	5008	,	,		18474	0.3929		0.2863	False		,,,				2504	0.1718				p.Y414Y		Atlas-SNP	.											.	PDE5A	83	.	0			c.T1242C						PASS	.	A	,,	917,3489	351.8+/-311.4	104,709,1390	233.0	226.0	228.0		1242,1116,1086	3.3	1.0	4	dbSNP_120	228	2462,6138	404.9+/-348.3	347,1768,2185	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE5A	NM_001083.3,NM_033430.2,NM_033437.3	,,	451,2477,3575	GG,GA,AA		28.6279,20.8125,25.9803	,,	414/876,372/834,362/824	120474859	3379,9627	2203	4300	6503	SO:0001819	synonymous_variant	8654	exon8			TTTGACATACTGA	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"""Phosphodiesterases"""	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1242T>C	4.37:g.120474859A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	160	68	0.425	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Silent	SNP	ENST00000354960.3	37	CCDS3713.1																																																																																			A|0.732;G|0.268	0.268	strong		0.358	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	
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 GAIIx	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_ENST00000354613.1_Missense_Mutation_p.E702K|MLXIPL_ENST00000429400.2_Missense_Mutation_p.E704K|MLXIPL_ENST00000414749.2_Missense_Mutation_p.E721K|MLXIPL_ENST00000395189.1_Missense_Mutation_p.E630K|MLXIPL_ENST00000434326.1_Missense_Mutation_p.E629K	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	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	35	16	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	
LAMA5	3911	hgsc.bcm.edu	37	20	60903419	60903419	+	Silent	SNP	C	C	T	rs7262393	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60903419C>T	ENST00000252999.3	-	35	4596	c.4530G>A	c.(4528-4530)ctG>ctA	p.L1510L		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1510	Laminin EGF-like 13. {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)			GCTGGCACAGCAGGCAGTCGG	0.682													C|||	924	0.184505	0.2458	0.1542	5008	,	,		15666	0.1062		0.2306	False		,,,				2504	0.1564				p.L1510L		Atlas-SNP	.											LAMA5,colon,carcinoma,0,1	LAMA5	268	1	0			c.G4530A						PASS	.	C		1187,3181		154,879,1151	20.0	21.0	21.0		4530	0.2	0.0	20	dbSNP_116	21	1850,6724		196,1458,2633	no	coding-synonymous	LAMA5	NM_005560.3		350,2337,3784	TT,TC,CC		21.5769,27.1749,23.4662		1510/3696	60903419	3037,9905	2184	4287	6471	SO:0001819	synonymous_variant	3911	exon35			GCACAGCAGGCAG	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.4530G>A	20.37:g.60903419C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			C|0.782;T|0.218	0.218	strong		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
FAM160A2	84067	hgsc.bcm.edu	37	11	6239139	6239139	+	Silent	SNP	A	A	G	rs11040809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6239139A>G	ENST00000449352.2	-	9	1940	c.1677T>C	c.(1675-1677)cgT>cgC	p.R559R	FAM160A2_ENST00000265978.4_Silent_p.R573R|FAM160A2_ENST00000529360.1_5'Flank|FAM160A2_ENST00000524416.1_Silent_p.R559R			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	559					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCACACCACGACGTGCCTCAC	0.642													A|||	547	0.109225	0.0106	0.1167	5008	,	,		11293	0.0456		0.2336	False		,,,				2504	0.1748				p.R573R		Atlas-SNP	.											.	FAM160A2	100	.	0			c.T1719C						PASS	.	A	,	207,4195	127.0+/-164.0	7,193,2001	65.0	61.0	62.0		1677,1719	1.6	1.0	11	dbSNP_120	62	2176,6416	366.5+/-334.3	280,1616,2400	no	coding-synonymous,coding-synonymous	FAM160A2	NM_001098794.1,NM_032127.3	,	287,1809,4401	GG,GA,AA		25.3259,4.7024,18.3392	,	559/973,573/987	6239139	2383,10611	2201	4296	6497	SO:0001819	synonymous_variant	84067	exon9			ACCACGACGTGCC		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 56"""	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.1677T>C	11.37:g.6239139A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Silent	SNP	ENST00000449352.2	37	CCDS44530.1																																																																																			A|0.841;G|0.159;N|0.000;T|0.000	0.159	strong		0.642	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
F13A1	2162	hgsc.bcm.edu	37	6	6152140	6152140	+	Missense_Mutation	SNP	C	C	T	rs5987	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:6152140C>T	ENST00000264870.3	-	14	2216	c.1951G>A	c.(1951-1953)Gtt>Att	p.V651I		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	651			V -> I (in allele F13A*2A and allele F13A*2B; dbSNP:rs5987). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:3026437, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	GTAAACTCAACTGTCACAGTC	0.448													C|||	362	0.0722843	0.034	0.0504	5008	,	,		20395	0.0903		0.0746	False		,,,				2504	0.1186				p.V651I		Atlas-SNP	.											.	F13A1	135	.	0			c.G1951A						PASS	.	C	ILE/VAL	134,4272	95.7+/-134.4	2,130,2071	87.0	78.0	81.0		1951	5.4	1.0	6	dbSNP_52	81	510,8090	145.0+/-200.8	15,480,3805	yes	missense	F13A1	NM_000129.3	29	17,610,5876	TT,TC,CC		5.9302,3.0413,4.9516	benign	651/733	6152140	644,12362	2203	4300	6503	SO:0001583	missense	2162	exon14			ACTCAACTGTCAC	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1951G>A	6.37:g.6152140C>T	ENSP00000264870:p.Val651Ile	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	43	11	0.255814	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	147|147	0.0673076923076923|0.0673076923076923	13|13	0.026422764227642278|0.026422764227642278	19|19	0.052486187845303865|0.052486187845303865	59|59	0.10314685314685315|0.10314685314685315	56|56	0.07387862796833773|0.07387862796833773	C|C	5.956|5.956	0.360336|0.360336	0.11296|0.11296	0.030413|0.030413	0.059302|0.059302	ENSG00000124491|ENSG00000124491	ENST00000441301|ENST00000264870	.|T	.|0.71103	.|-0.54	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	.|0.061993	.|0.64402	.|D	.|0.000004	T|T	0.41971|0.41971	0.1182|0.1182	L|L	0.31526|0.31526	0.94|0.94	0.21147|0.21147	P|P	0.999776622|0.999776622	.|B	.|0.30563	.|0.285	.|B	.|0.39119	.|0.291	T|T	0.23726|0.23726	-1.0180|-1.0180	5|9	0.52906|0.06891	T|T	0.07|0.86	.|.	9.9271|9.9271	0.41498|0.41498	0.0:0.9109:0.0:0.0891|0.0:0.9109:0.0:0.0891	rs5987;rs5987|rs5987;rs5987	.|651	.|P00488	.|F13A_HUMAN	K|I	588|651	.|ENSP00000264870:V651I	ENSP00000416127:E588K|ENSP00000264870:V651I	E|V	-|-	1|1	0|0	F13A1|F13A1	6097139|6097139	0.682000|0.682000	0.27624|0.27624	0.998000|0.998000	0.56505|0.56505	0.505000|0.505000	0.33919|0.33919	1.433000|1.433000	0.34947|0.34947	2.788000|2.788000	0.95919|0.95919	0.650000|0.650000	0.86243|0.86243	GAA|GTT	C|0.943;T|0.057	0.057	strong		0.448	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
NOP9	161424	hgsc.bcm.edu	37	14	24771285	24771285	+	Missense_Mutation	SNP	G	G	A	rs4280164	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24771285G>A	ENST00000267425.3	+	4	1016	c.923G>A	c.(922-924)aGt>aAt	p.S308N	NOP9_ENST00000396802.3_Missense_Mutation_p.S308N|DHRS1_ENST00000396813.1_5'Flank|DHRS1_ENST00000288111.7_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	308			S -> N (in dbSNP:rs4280164). {ECO:0000269|PubMed:15489334}.				poly(A) RNA binding (GO:0044822)										GGCTACCTGAGTACTCGCGGT	0.507													G|||	753	0.150359	0.1581	0.3473	5008	,	,		21235	0.004		0.1849	False		,,,				2504	0.1155				p.S308N		Atlas-SNP	.											.	.	.	.	0			c.G923A						PASS	.	G	ASN/SER	736,3670	303.2+/-287.8	63,610,1530	122.0	117.0	118.0		923	5.2	1.0	14	dbSNP_111	118	1783,6817	322.1+/-315.4	189,1405,2706	yes	missense	C14orf21	NM_174913.1	46	252,2015,4236	AA,AG,GG		20.7326,16.7045,19.368	possibly-damaging	308/637	24771285	2519,10487	2203	4300	6503	SO:0001583	missense	161424	exon4			ACCTGAGTACTCG		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.923G>A	14.37:g.24771285G>A	ENSP00000267425:p.Ser308Asn	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	336	0.15384615384615385	72	0.14634146341463414	108	0.2983425414364641	4	0.006993006993006993	152	0.20052770448548812	G	18.02	3.531149	0.64972	0.167045	0.207326	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.14022	2.54;2.54	5.21	5.21	0.72293	Armadillo-type fold (1);	0.219735	0.45606	D	0.000347	T	0.00012	0.0000	L	0.54323	1.7	0.29261	P	0.871328	P	0.50819	0.939	P	0.50378	0.639	T	0.51458	-0.8703	9	0.17369	T	0.5	-6.0418	13.4219	0.61003	0.0:0.1579:0.8421:0.0	rs4280164;rs17852257;rs52803285;rs56947421;rs4280164	308	Q86U38	CN021_HUMAN	N	308	ENSP00000267425:S308N;ENSP00000380020:S308N	ENSP00000267425:S308N	S	+	2	0	C14orf21	23841125	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	3.940000	0.56599	2.717000	0.92951	0.655000	0.94253	AGT	G|0.835;A|0.165	0.165	strong		0.507	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
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 GAIIx	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_ENST00000348007.3_Missense_Mutation_p.K243Q|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.K214Q|CTAGE5_ENST00000396158.2_Missense_Mutation_p.K248Q|CTAGE5_ENST00000556148.1_Missense_Mutation_p.K168Q|CTAGE5_ENST00000341502.5_Missense_Mutation_p.K243Q|CTAGE5_ENST00000341749.3_Missense_Mutation_p.K231Q|CTAGE5_ENST00000553352.1_Missense_Mutation_p.K214Q|CTAGE5_ENST00000557038.1_Missense_Mutation_p.K163Q|CTAGE5_ENST00000396165.4_Missense_Mutation_p.K214Q|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.K778Q			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	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	60	25	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	
SPERT	220082	hgsc.bcm.edu	37	13	46287373	46287373	+	Nonsense_Mutation	SNP	C	C	A	rs80072371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:46287373C>A	ENST00000310521.1	+	3	293	c.213C>A	c.(211-213)tgC>tgA	p.C71*	SPERT_ENST00000378966.3_Nonsense_Mutation_p.C35*	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	71						cytoplasmic membrane-bounded vesicle (GO:0016023)		p.C71C(1)		NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		CCCCTCGCTGCGCGCAGCAGG	0.647													C|||	341	0.0680911	0.1573	0.0461	5008	,	,		15204	0.001		0.0487	False		,,,				2504	0.0521				p.C71X		Atlas-SNP	.											SPERT,caecum,carcinoma,0,1	SPERT	54	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C213A						PASS	.	C	stop/CYS	560,3844		41,478,1683	29.0	30.0	30.0		213	-0.6	0.0	13	dbSNP_131	30	414,8184		10,394,3895	yes	stop-gained	SPERT	NM_152719.1		51,872,5578	AA,AC,CC		4.8151,12.7157,7.4912		71/449	46287373	974,12028	2202	4299	6501	SO:0001587	stop_gained	220082	exon3			TCGCTGCGCGCAG	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"""spermatid flower-like structure protein"", ""testis specific leucine zipper protein nurit"", ""chibby homolog 2 (Drosophila)"""					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.213C>A	13.37:g.46287373C>A	ENSP00000309189:p.Cys71*	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	78	28	0.358974	NM_152719	A8K8I5|Q8NHV2	Nonsense_Mutation	SNP	ENST00000310521.1	37	CCDS9399.1	122	0.055860805860805864	67	0.13617886178861788	18	0.049723756906077346	0	0.0	37	0.048812664907651716	C	17.83	3.484572	0.63962	0.127157	0.048151	ENSG00000174015	ENST00000310521;ENST00000533564;ENST00000378966	.	.	.	5.1	-0.559	0.11792	.	0.000000	0.52532	D	0.000074	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.9892	0.14205	0.0:0.4336:0.1462:0.4202	.	.	.	.	X	71;44;35	.	ENSP00000309189:C71X	C	+	3	2	SPERT	45185374	0.034000	0.19679	0.018000	0.16275	0.118000	0.20060	0.036000	0.13819	-0.368000	0.08040	-0.142000	0.14014	TGC	C|0.930;A|0.070	0.070	strong		0.647	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719	
HDGFRP2	84717	hgsc.bcm.edu	37	19	4493708	4493708	+	Silent	SNP	A	A	G	rs892161	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4493708A>G	ENST00000301284.4	+	7	751	c.687A>G	c.(685-687)ccA>ccG	p.P229P	HDGFRP2_ENST00000586684.1_Silent_p.P229P	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		229	Ser-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGAAGGCGCCATCAGCCTCCG	0.697													g|||	2915	0.582069	0.6702	0.6484	5008	,	,		12206	0.4236		0.6243	False		,,,				2504	0.5358				p.P229P		Atlas-SNP	.											HDGF2,NS,carcinoma,0,1	.	.	1	0			c.A687G						PASS	.		,	2808,1320		1014,780,270	12.0	15.0	14.0		687,687	-9.9	0.0	19	dbSNP_86	14	5167,3075		1714,1739,668	no	coding-synonymous,coding-synonymous	HDGFRP2	NM_001001520.1,NM_032631.2	,	2728,2519,938	GG,GA,AA		37.3089,31.9767,35.5295	,	229/677,229/676	4493708	7975,4395	2064	4121	6185	SO:0001819	synonymous_variant	0	exon7			GGCGCCATCAGCC																												ENST00000301284.4:c.687A>G	19.37:g.4493708A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	Silent	SNP	ENST00000301284.4	37	CCDS42472.1																																																																																			A|0.431;G|0.569	0.569	strong		0.697	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1		
PM20D1	148811	hgsc.bcm.edu	37	1	205812912	205812912	+	Missense_Mutation	SNP	A	A	G	rs7518979	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205812912A>G	ENST00000367136.4	-	6	754	c.710T>C	c.(709-711)aTt>aCt	p.I237T	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	237			I -> T (in dbSNP:rs7518979). {ECO:0000269|PubMed:15489334}.		negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			TGAGACTGCAATCCTGTAGAA	0.493													A|||	1275	0.254593	0.3691	0.1398	5008	,	,		18869	0.3829		0.169	False		,,,				2504	0.137				p.I237T		Atlas-SNP	.											.	PM20D1	56	.	0			c.T710C						PASS	.	A	THR/ILE	1466,2940	471.7+/-356.1	234,998,971	93.0	87.0	89.0		710	4.9	0.0	1	dbSNP_116	89	1248,7352	250.0+/-277.0	85,1078,3137	yes	missense	PM20D1	NM_152491.4	89	319,2076,4108	GG,GA,AA		14.5116,33.2728,20.8673	possibly-damaging	237/503	205812912	2714,10292	2203	4300	6503	SO:0001583	missense	148811	exon6			ACTGCAATCCTGT		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.710T>C	1.37:g.205812912A>G	ENSP00000356104:p.Ile237Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	581	0.266025641025641	193	0.39227642276422764	45	0.12430939226519337	218	0.3811188811188811	125	0.16490765171503957	A	12.48	1.950833	0.34471	0.332728	0.145116	ENSG00000162877	ENST00000367136	T	0.09911	2.93	6.06	4.92	0.64577	.	0.242071	0.49305	D	0.000152	T	0.00012	0.0000	M	0.89287	3.02	0.32399	P	0.5521769999999999	D	0.67145	0.996	D	0.70716	0.97	T	0.35798	-0.9774	9	0.52906	T	0.07	.	13.2167	0.59865	0.867:0.133:0.0:0.0	rs7518979;rs52830461;rs7518979	237	Q6GTS8	P20D1_HUMAN	T	237	ENSP00000356104:I237T	ENSP00000356104:I237T	I	-	2	0	PM20D1	204079535	0.999000	0.42202	0.009000	0.14445	0.017000	0.09413	6.988000	0.76212	1.085000	0.41206	0.533000	0.62120	ATT	A|0.764;G|0.236	0.236	strong		0.493	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
FUT6	2528	hgsc.bcm.edu	37	19	5831840	5831840	+	Missense_Mutation	SNP	C	C	T	rs17855739	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5831840C>T	ENST00000318336.4	-	3	1933	c.739G>A	c.(739-741)Gag>Aag	p.E247K	FUT6_ENST00000592563.1_Missense_Mutation_p.E247K|FUT6_ENST00000286955.5_Missense_Mutation_p.E247K|FUT6_ENST00000524754.1_Missense_Mutation_p.E247K|FUT6_ENST00000527106.1_Missense_Mutation_p.E247K	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	247			E -> K (found in alpha(1,3)- fucosyltransferase-deficient individuals; complete enzyme inactivation; dbSNP:rs17855739). {ECO:0000269|PubMed:11102976, ECO:0000269|PubMed:8175676}.		fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						AAGGAGTTCTCGAAGGCCAGA	0.627													C|||	805	0.160743	0.351	0.0461	5008	,	,		17359	0.1319		0.0417	False		,,,				2504	0.137				p.E247K		Atlas-SNP	.											FUT6,NS,carcinoma,+2,1	FUT6	30	1	0			c.G739A	GRCh37	CM940795	FUT6	M	rs17855739	PASS	.	C	LYS/GLU,LYS/GLU	1273,3133	433.5+/-343.6	156,961,1086	88.0	88.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	739,739	2.0	0.9	19	dbSNP_123	88	389,8207	124.1+/-182.9	12,365,3921	no	missense,missense	FUT6	NM_000150.2,NM_001040701.1	56,56	168,1326,5007	TT,TC,CC		4.5254,28.8924,12.7826	benign,benign	247/360,247/360	5831840	1662,11340	2203	4298	6501	SO:0001583	missense	2528	exon3			AGTTCTCGAAGGC		CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"""Fucosyltransferases"""	4017	protein-coding gene	gene with protein product	"""alpha-(1,3)-fucosyltransferase"", ""galactoside 3-L-fucosyltransferase"""	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.739G>A	19.37:g.5831840C>T	ENSP00000313398:p.Glu247Lys	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	234	101	0.431624	NM_000150	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	37	CCDS12152.1	278	0.12728937728937728	190	0.3861788617886179	18	0.049723756906077346	35	0.06118881118881119	35	0.04617414248021108	C	16.35	3.099891	0.56183	0.288924	0.045254	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530	T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39	3.07	1.97	0.26223	.	0.000000	0.64402	D	0.000016	T	0.00012	0.0000	H	0.99261	4.49	0.27631	P	0.9480265999999999	P;P	0.52170	0.951;0.917	P;P	0.58077	0.832;0.832	T	0.02352	-1.1172	9	0.72032	D	0.01	.	10.1858	0.42998	0.0:0.7931:0.2069:0.0	rs17855739	247;247	C9J8A2;P51993	.;FUT6_HUMAN	K	247	ENSP00000431708:E247K;ENSP00000432954:E247K;ENSP00000313398:E247K;ENSP00000286955:E247K	ENSP00000286955:E247K	E	-	1	0	FUT6	5782840	0.963000	0.33076	0.857000	0.33713	0.070000	0.16714	2.244000	0.43124	0.548000	0.28955	0.430000	0.28490	GAG	C|0.878;T|0.122	0.122	strong		0.627	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150	
SMC5	23137	hgsc.bcm.edu	37	9	72933774	72933774	+	Missense_Mutation	SNP	A	A	G	rs11142365	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:72933774A>G	ENST00000361138.5	+	15	2103	c.2045A>G	c.(2044-2046)cAt>cGt	p.H682R		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	682			H -> R (in dbSNP:rs11142365).		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|mitotic nuclear division (GO:0007067)|positive regulation of maintenance of mitotic sister chromatid cohesion (GO:0034184)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|telomere maintenance via recombination (GO:0000722)	cell junction (GO:0030054)|chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(4)	35						ACAAGCAAACATCTGGAGCAC	0.318													A|||	436	0.0870607	0.1664	0.0821	5008	,	,		16017	0.0139		0.1044	False		,,,				2504	0.0409				p.H682R		Atlas-SNP	.											.	SMC5	96	.	0			c.A2045G						PASS	.	A	ARG/HIS	670,3726		53,564,1581	48.0	50.0	49.0		2045	0.2	0.0	9	dbSNP_120	49	1012,7584		62,888,3348	no	missense	SMC5	NM_015110.3	29	115,1452,4929	GG,GA,AA		11.7729,15.2411,12.9464	benign	682/1102	72933774	1682,11310	2198	4298	6496	SO:0001583	missense	23137	exon15			GCAAACATCTGGA	AB011166	CCDS6632.1	9q21.11	2008-02-05	2006-07-06	2006-07-06	ENSG00000198887	ENSG00000198887		"""Structural maintenance of chromosomes proteins"""	20465	protein-coding gene	gene with protein product		609386	"""SMC5 structural maintenance of chromosomes 5-like 1 (yeast)"""	SMC5L1		9628581	Standard	NM_015110		Approved	KIAA0594	uc004ahr.2	Q8IY18	OTTHUMG00000019992	ENST00000361138.5:c.2045A>G	9.37:g.72933774A>G	ENSP00000354957:p.His682Arg	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	210	0.09615384615384616	93	0.18902439024390244	32	0.08839779005524862	5	0.008741258741258742	80	0.10554089709762533	A	3.138	-0.176891	0.06380	0.152411	0.117729	ENSG00000198887	ENST00000361138	T	0.16196	2.36	5.3	0.161	0.14977	RecF/RecN/SMC (1);	1.282520	0.04800	N	0.433287	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.39375	-0.9617	9	0.17832	T	0.49	-0.7879	4.1705	0.10327	0.4124:0.0:0.2134:0.3742	rs11142365	682	Q8IY18	SMC5_HUMAN	R	682	ENSP00000354957:H682R	ENSP00000354957:H682R	H	+	2	0	SMC5	72123594	0.000000	0.05858	0.005000	0.12908	0.889000	0.51656	0.330000	0.19715	0.008000	0.14787	0.472000	0.43445	CAT	A|0.888;G|0.112	0.112	strong		0.318	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110	
KRTAP12-1	353332	hgsc.bcm.edu	37	21	46101993	46101993	+	Missense_Mutation	SNP	C	C	T	rs55881656	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46101993C>T	ENST00000391617.1	-	1	85	c.46G>A	c.(46-48)Gcg>Acg	p.A16T	TSPEAR_ENST00000323084.4_Intron	NM_181686.1	NP_859014.1	P59990	KR121_HUMAN	keratin associated protein 12-1	16	14 X 5 AA approximate repeats.					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|skin(2)	5						GGGCTGGGCGCGCAGCAGGCT	0.672													C|||	214	0.0427316	0.0545	0.0504	5008	,	,		15533	0.001		0.0736	False		,,,				2504	0.0327				p.A16T		Atlas-SNP	.											.	KRTAP12-1	9	.	0			c.G46A						PASS	.	C	,THR/ALA	198,4122		5,188,1967	34.0	42.0	39.0		,46	-0.0	0.0	21	dbSNP_129	39	553,7967		19,515,3726	no	intron,missense	TSPEAR,KRTAP12-1	NM_144991.2,NM_181686.1	,58	24,703,5693	TT,TC,CC		6.4906,4.5833,5.8489	,benign	,16/97	46101993	751,12089	2160	4260	6420	SO:0001583	missense	353332	exon1			TGGGCGCGCAGCA	AJ566388	CCDS42966.1	21q22.3	2006-03-13			ENSG00000187175	ENSG00000187175		"""Keratin associated proteins"""	20529	protein-coding gene	gene with protein product							Standard	NM_181686		Approved	KRTAP12.1, KAP12.1	uc002zfv.3	P59990	OTTHUMG00000057639	ENST00000391617.1:c.46G>A	21.37:g.46101993C>T	ENSP00000375475:p.Ala16Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_181686	Q0VAS3	Missense_Mutation	SNP	ENST00000391617.1	37	CCDS42966.1	105	0.04807692307692308	28	0.056910569105691054	19	0.052486187845303865	3	0.005244755244755245	55	0.07255936675461741	c	0.007	-1.973663	0.00452	0.045833	0.064906	ENSG00000187175	ENST00000391617	T	0.01335	5.0	3.27	-0.0243	0.13939	.	5.317050	0.00921	N	0.002593	T	0.00109	0.0003	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45352	-0.9267	8	0.12103	T	0.63	.	4.4259	0.11503	0.0:0.5436:0.1877:0.2687	rs55881656	16	P59990	KR121_HUMAN	T	16	ENSP00000375475:A16T	ENSP00000375475:A16T	A	-	1	0	KRTAP12-1	44926421	0.000000	0.05858	0.016000	0.15963	0.010000	0.07245	-1.539000	0.02202	0.107000	0.17824	0.407000	0.27541	GCG	C|0.947;T|0.053	0.053	strong		0.672	KRTAP12-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128043.1	NM_181686	
FRMD1	79981	hgsc.bcm.edu	37	6	168462626	168462626	+	Silent	SNP	G	G	A	rs12197610	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:168462626G>A	ENST00000283309.6	-	8	970	c.906C>T	c.(904-906)ccC>ccT	p.P302P	FRMD1_ENST00000440994.2_Silent_p.P234P|FRMD1_ENST00000537786.1_Silent_p.P73P|FRMD1_ENST00000432403.1_5'UTR	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	302	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					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)		TCTGTGCTGCGGGCAGCCCAT	0.622													G|||	1070	0.213658	0.4463	0.183	5008	,	,		18029	0.0407		0.2018	False		,,,				2504	0.1115				p.P302P	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											FRMD1,NS,carcinoma,-1,1	FRMD1	52	1	0			c.C906T						PASS	.	G	,	1770,2636		363,1044,796	25.0	27.0	26.0		702,906	-4.8	0.0	6	dbSNP_120	26	1904,6696		209,1486,2605	no	coding-synonymous,coding-synonymous	FRMD1	NM_001122841.1,NM_024919.3	,	572,2530,3401	AA,AG,GG		22.1395,40.1725,28.2485	,	234/482,302/550	168462626	3674,9332	2203	4300	6503	SO:0001819	synonymous_variant	79981	exon8			TGCTGCGGGCAGC		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.906C>T	6.37:g.168462626G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Silent	SNP	ENST00000283309.6	37	CCDS5306.1																																																																																			G|0.739;A|0.261	0.261	strong		0.622	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
FCGBP	8857	hgsc.bcm.edu	37	19	40408128	40408128	+	Silent	SNP	C	C	T	rs4803310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40408128C>T	ENST00000221347.6	-	9	4600	c.4593G>A	c.(4591-4593)gaG>gaA	p.E1531E		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1531	Cys-rich.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TCGGAGGGCACTCCATGGCTG	0.657													c|||	953	0.190296	0.3555	0.1383	5008	,	,		17537	0.1319		0.1829	False		,,,				2504	0.0716				p.E1531E		Atlas-SNP	.											FCGBP,NS,malignant_melanoma,0,2	FCGBP	416	2	0			c.G4593A						PASS	.	C		1295,3111	410.0+/-335.2	208,879,1116	48.0	49.0	49.0		4593	0.1	0.3	19	dbSNP_111	49	1245,7355	234.3+/-267.3	96,1053,3151	no	coding-synonymous	FCGBP	NM_003890.2		304,1932,4267	TT,TC,CC		14.4767,29.3917,19.5294		1531/5406	40408128	2540,10466	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon9			AGGGCACTCCATG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4593G>A	19.37:g.40408128C>T		Somatic	292	1	0.00342466		WXS	Illumina HiSeq	Phase_I	283	155	0.547703	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			C|0.824;T|0.176	0.176	strong		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
HSPG2	3339	hgsc.bcm.edu	37	1	22168801	22168801	+	Missense_Mutation	SNP	T	T	C	rs2229491	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22168801T>C	ENST00000374695.3	-	68	9062	c.8983A>G	c.(8983-8985)Agc>Ggc	p.S2995G		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2995	Ig-like C2-type 15.		S -> G (in dbSNP:rs2229491). {ECO:0000269|PubMed:1730768}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCTGGGCCGCTGGCTGCACGA	0.642													C|||	444	0.0886581	0.1762	0.0533	5008	,	,		17453	0.0		0.0676	False		,,,				2504	0.1084				p.S2995G		Atlas-SNP	.											.	HSPG2	311	.	0			c.A8983G						PASS	.	C	GLY/SER	799,3607	748.2+/-411.9	73,653,1477	48.0	44.0	46.0		8983	1.0	0.0	1	dbSNP_98	46	660,7940	788.1+/-407.6	26,608,3666	yes	missense	HSPG2	NM_005529.5	56	99,1261,5143	CC,CT,TT		7.6744,18.1344,11.2179	benign	2995/4392	22168801	1459,11547	2203	4300	6503	SO:0001583	missense	3339	exon68			GGCCGCTGGCTGC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8983A>G	1.37:g.22168801T>C	ENSP00000363827:p.Ser2995Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	170	0.07783882783882784	98	0.1991869918699187	23	0.06353591160220995	0	0.0	49	0.06464379947229551	C	0.020	-1.435149	0.01108	0.181344	0.076744	ENSG00000142798	ENST00000374695	T	0.43688	0.94	4.95	1.0	0.19881	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.192817	0.25411	N	0.030867	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23013	-1.0200	9	0.22109	T	0.4	.	1.5458	0.02565	0.1402:0.3054:0.1367:0.4177	rs2229491;rs7528230;rs2229491	935;2995	Q59EG0;P98160	.;PGBM_HUMAN	G	2995	ENSP00000363827:S2995G	ENSP00000363827:S2995G	S	-	1	0	HSPG2	22041388	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.066000	0.11598	-0.063000	0.13065	-1.212000	0.01626	AGC	T|0.899;G|0.000;C|0.101;A|0.000	0.101	strong		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
MYH15	22989	hgsc.bcm.edu	37	3	108189627	108189627	+	Missense_Mutation	SNP	C	C	T	rs4299484	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:108189627C>T	ENST00000273353.3	-	14	1417	c.1361G>A	c.(1360-1362)cGg>cAg	p.R454Q		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	454	Myosin motor.		R -> Q (in dbSNP:rs4299484).			cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R454Q(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						CCTGTTGATCCGTGCCACTAG	0.458													C|||	505	0.100839	0.0098	0.1873	5008	,	,		14327	0.0		0.2932	False		,,,				2504	0.0685				p.R454Q		Atlas-SNP	.											MYH15,NS,carcinoma,0,1	MYH15	223	1	1	Substitution - Missense(1)	prostate(1)	c.G1361A						PASS	.	C	GLN/ARG	222,3770		8,206,1782	94.0	89.0	90.0		1361	2.6	0.0	3	dbSNP_111	90	2495,5801		374,1747,2027	yes	missense	MYH15	NM_014981.1	43	382,1953,3809	TT,TC,CC		30.0747,5.5611,22.111	probably-damaging	454/1947	108189627	2717,9571	1996	4148	6144	SO:0001583	missense	22989	exon14			TTGATCCGTGCCA	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1361G>A	3.37:g.108189627C>T	ENSP00000273353:p.Arg454Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	37	CCDS43127.1	318	0.14560439560439561	10	0.02032520325203252	79	0.21823204419889503	0	0.0	229	0.3021108179419525	C	23.4	4.411069	0.83340	0.055611	0.300747	ENSG00000144821	ENST00000273353	D	0.88431	-2.38	5.77	2.58	0.30949	Myosin head, motor domain (2);	.	.	.	.	T	0.00039	0.0001	M	0.88181	2.935	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00015	-1.2392	8	0.87932	D	0	.	7.0191	0.24904	0.1319:0.6992:0.0:0.1689	rs4299484;rs17538845;rs52826675;rs56656800;rs4299484	454	Q9Y2K3	MYH15_HUMAN	Q	454	ENSP00000273353:R454Q	ENSP00000273353:R454Q	R	-	2	0	MYH15	109672317	0.000000	0.05858	0.001000	0.08648	0.977000	0.68977	0.405000	0.21015	0.557000	0.29117	0.650000	0.86243	CGG	C|0.833;T|0.167	0.167	strong		0.458	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
LZTR1	8216	hgsc.bcm.edu	37	22	21348914	21348914	+	Silent	SNP	C	C	T	rs4822790	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:21348914C>T	ENST00000215739.8	+	15	2042	c.1683C>T	c.(1681-1683)cgC>cgT	p.R561R	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Silent_p.R542R	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	561					anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)	42	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			AGTTGTGCCGCCTGGAGCAGC	0.627													C|||	846	0.16893	0.1997	0.1124	5008	,	,		16176	0.2262		0.1352	False		,,,				2504	0.1431				p.R561R		Atlas-SNP	.											.	LZTR1	99	.	0			c.C1683T						PASS	.	C		791,3613	314.1+/-293.5	65,661,1476	63.0	49.0	54.0		1683	3.7	1.0	22	dbSNP_111	54	1023,7577	218.3+/-256.7	54,915,3331	no	coding-synonymous	LZTR1	NM_006767.3		119,1576,4807	TT,TC,CC		11.8953,17.9609,13.9496		561/841	21348914	1814,11190	2202	4300	6502	SO:0001819	synonymous_variant	8216	exon15			GTGCCGCCTGGAG	D38496	CCDS33606.1	22q11.21	2013-01-09	2004-12-10		ENSG00000099949	ENSG00000099949		"""BTB/POZ domain containing"""	6742	protein-coding gene	gene with protein product		600574	"""leucine-zipper-like transcriptional regulator 1"""			7633402, 16356934	Standard	NM_006767		Approved	LZTR-1, BTBD29	uc002zto.3	Q8N653	OTTHUMG00000150878	ENST00000215739.8:c.1683C>T	22.37:g.21348914C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	52	11	0.211538	NM_006767	Q14776|Q20WK0	Silent	SNP	ENST00000215739.8	37	CCDS33606.1																																																																																			C|0.855;T|0.145	0.145	strong		0.627	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	
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 GAIIx	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		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	107	52	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	
KLHL23	151230	hgsc.bcm.edu	37	2	170592709	170592709	+	Silent	SNP	A	A	G	rs2288331	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:170592709A>G	ENST00000392647.2	+	2	1429	c.1185A>G	c.(1183-1185)aaA>aaG	p.K395K	KLHL23_ENST00000272797.4_Silent_p.K395K|KLHL23_ENST00000602521.1_Intron	NM_144711.5	NP_653312.2	Q8NBE8	KLH23_HUMAN	kelch-like family member 23	395										breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(4)|skin(1)|urinary_tract(1)	16						TAAAAGAGAAATGGATTCCTA	0.413													A|||	783	0.15635	0.1831	0.1369	5008	,	,		20251	0.1766		0.1581	False		,,,				2504	0.1115				p.K395K		Atlas-SNP	.											.	KLHL23	52	.	0			c.A1185G						PASS	.	A	,	677,3729	284.3+/-277.5	58,561,1584	95.0	102.0	100.0		1185,1185	-2.5	1.0	2	dbSNP_100	100	1393,7207	267.5+/-287.3	126,1141,3033	no	coding-synonymous,coding-synonymous	KLHL23,PHOSPHO2-KLHL23	NM_001199290.1,NM_144711.5	,	184,1702,4617	GG,GA,AA		16.1977,15.3654,15.9157	,	395/559,395/559	170592709	2070,10936	2203	4300	6503	SO:0001819	synonymous_variant	151230	exon2			AGAGAAATGGATT	BC010437	CCDS2236.1	2q31.1	2013-01-30	2013-01-30		ENSG00000213160	ENSG00000213160		"""Kelch-like"", ""BTB/POZ domain containing"""	27506	protein-coding gene	gene with protein product			"""kelch-like 23 (Drosophila)"""				Standard	NM_144711		Approved	MGC2610, FLJ37812, MGC22679	uc002ufi.2	Q8NBE8	OTTHUMG00000132213	ENST00000392647.2:c.1185A>G	2.37:g.170592709A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_144711	Q8N9B9|Q96FT8	Silent	SNP	ENST00000392647.2	37	CCDS2236.1																																																																																			A|0.835;G|0.165	0.165	strong		0.413	KLHL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255271.2	NM_144711	
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 GAIIx	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	PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA1_ENST00000517417.1_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	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	139	71	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	
FGA	2243	hgsc.bcm.edu	37	4	155507590	155507590	+	Missense_Mutation	SNP	T	T	C	rs6050	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:155507590T>C	ENST00000302053.3	-	5	1069	c.991A>G	c.(991-993)Act>Gct	p.T331A	FGA_ENST00000403106.3_Missense_Mutation_p.T331A	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	331			T -> A (in dbSNP:rs6050). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)	p.T331A(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	CAGCTTCCAGTACTTCCAGGT	0.572													T|||	1638	0.327077	0.4334	0.2176	5008	,	,		16658	0.4315		0.2356	False		,,,				2504	0.2474				p.T331A	NSCLC(143;340 1922 20892 22370 48145)	Atlas-SNP	.											FGA,NS,carcinoma,0,1	FGA	179	1	1	Substitution - Missense(1)	prostate(1)	c.A991G	GRCh37	CM994632	FGA	M	rs6050	scavenged	.	T	ALA/THR,ALA/THR	1603,2803	496.9+/-363.7	292,1019,892	91.0	98.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	991,991	-6.7	0.0	4	dbSNP_52	96	2168,6432	371.1+/-336.1	293,1582,2425	yes	missense,missense	FGA	NM_000508.3,NM_021871.2	58,58	585,2601,3317	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	25.2093,36.3822,28.9943	benign,benign	331/867,331/645	155507590	3771,9235	2203	4300	6503	SO:0001583	missense	2243	exon5			TTCCAGTACTTCC		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.991A>G	4.37:g.155507590T>C	ENSP00000306361:p.Thr331Ala	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_000508	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	37	CCDS3787.1	720	0.32967032967032966	181	0.3678861788617886	80	0.22099447513812154	280	0.48951048951048953	179	0.23614775725593667	T	5.196	0.221707	0.09863	0.363822	0.252093	ENSG00000171560	ENST00000302053;ENST00000403106	T;T	0.70986	-0.53;-0.53	4.95	-6.65	0.01795	.	3.217810	0.01539	N	0.019120	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B	0.18013	0.001;0.025	B;B	0.12837	0.003;0.008	T	0.22800	-1.0206	9	0.07325	T	0.83	.	1.1703	0.01824	0.4201:0.2848:0.1048:0.1903	rs6050;rs2070019;rs2236789;rs56492214;rs6050	331;331	P02671-2;P02671	.;FIBA_HUMAN	A	331	ENSP00000306361:T331A;ENSP00000385981:T331A	ENSP00000306361:T331A	T	-	1	0	FGA	155727040	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-6.952000	0.00048	-0.905000	0.03871	0.528000	0.53228	ACT	T|0.700;C|0.300	0.300	strong		0.572	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
SSTR4	6754	hgsc.bcm.edu	37	20	23016970	23016970	+	Missense_Mutation	SNP	T	T	G	rs3746726	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:23016970T>G	ENST00000255008.3	+	1	914	c.850T>G	c.(850-852)Ttc>Gtc	p.F284V	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	284			F -> V (in dbSNP:rs3746726). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8483934, ECO:0000269|PubMed:8512564, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GCTGAACCTCTTCGTGACCAG	0.557													T|||	1530	0.305511	0.2179	0.281	5008	,	,		18337	0.2351		0.3698	False		,,,				2504	0.4479				p.F284V	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,colon,carcinoma,0,1	SSTR4	83	1	0			c.T850G						PASS	.	T	VAL/PHE	1031,3375	359.9+/-315.0	134,763,1306	197.0	205.0	202.0		850	3.4	0.5	20	dbSNP_107	202	3321,5279	483.4+/-371.1	672,1977,1651	yes	missense	SSTR4	NM_001052.2	50	806,2740,2957	GG,GT,TT		38.6163,23.3999,33.4615	benign	284/389	23016970	4352,8654	2203	4300	6503	SO:0001583	missense	6754	exon1			AACCTCTTCGTGA		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.850T>G	20.37:g.23016970T>G	ENSP00000255008:p.Phe284Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	648	0.2967032967032967	113	0.22967479674796748	112	0.30939226519337015	148	0.25874125874125875	275	0.3627968337730871	T	7.979	0.750733	0.15778	0.233999	0.386163	ENSG00000132671	ENST00000255008	T	0.39406	1.08	3.36	3.36	0.38483	GPCR, rhodopsin-like superfamily (1);	0.090253	0.44483	U	0.000451	T	0.00012	0.0000	L	0.47190	1.495	0.37728	P	0.07484000000000002	B	0.11235	0.004	B	0.17098	0.017	T	0.38373	-0.9664	9	0.02654	T	1	.	6.6396	0.22901	0.0:0.1196:0.0:0.8804	rs3746726;rs60613961;rs3746726	284	P31391	SSR4_HUMAN	V	284	ENSP00000255008:F284V	ENSP00000255008:F284V	F	+	1	0	SSTR4	22964970	0.846000	0.29590	0.479000	0.27329	0.626000	0.37791	1.296000	0.33389	1.384000	0.46424	0.533000	0.62120	TTC	T|0.674;G|0.326	0.326	strong		0.557	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
KLHL5	51088	hgsc.bcm.edu	37	4	39064162	39064162	+	Missense_Mutation	SNP	A	A	C	rs2711941	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:39064162A>C	ENST00000504108.1	+	1	311	c.28A>C	c.(28-30)Att>Ctt	p.I10L	KLHL5_ENST00000359687.2_Missense_Mutation_p.I10L|KLHL5_ENST00000508137.2_Intron|KLHL5_ENST00000261426.5_Missense_Mutation_p.I10L|KLHL5_ENST00000261425.3_Intron|KLHL5_ENST00000381930.3_Missense_Mutation_p.I10L	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	10			I -> L (in dbSNP:rs2711941). {ECO:0000269|PubMed:11590829, ECO:0000269|PubMed:14672410, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						TCCTTTACATATTTTTGTTGT	0.328													C|||	3688	0.736422	0.6104	0.7882	5008	,	,		21124	0.8274		0.7465	False		,,,				2504	0.7658				p.I10L		Atlas-SNP	.											.	KLHL5	75	.	0			c.A28C						PASS	.	C	,,LEU/ILE,LEU/ILE	2872,1534	476.8+/-357.7	926,1020,257	133.0	128.0	130.0		,,28,28	3.1	1.0	4	dbSNP_100	130	6424,2176	368.2+/-335.0	2391,1642,267	yes	intron,intron,missense,missense	KLHL5	NM_001007075.2,NM_001171654.1,NM_199039.3,NM_015990.4	,,5,5	3317,2662,524	CC,CA,AA		25.3023,34.8162,28.5253	,,benign,benign	,,10/695,10/756	39064162	9296,3710	2203	4300	6503	SO:0001583	missense	51088	exon1			TTACATATTTTTG	AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"""Kelch-like"", ""BTB/POZ domain containing"""	6356	protein-coding gene	gene with protein product		608064	"""kelch (Drosophila)-like 5"", ""kelch-like 5 (Drosophila)"""			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.28A>C	4.37:g.39064162A>C	ENSP00000423897:p.Ile10Leu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	149	147	0.986577	NM_015990	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Missense_Mutation	SNP	ENST00000504108.1	37	CCDS33974.1	1651	0.7559523809523809	309	0.6280487804878049	296	0.8176795580110497	480	0.8391608391608392	566	0.7467018469656992	C	1.835	-0.468826	0.04445	0.651838	0.746977	ENSG00000109790	ENST00000504108;ENST00000359687;ENST00000381930;ENST00000261426	T;T;T;T	0.70986	-0.41;-0.32;-0.35;-0.53	4.95	3.13	0.36017	.	0.421653	0.17293	N	0.179567	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43327	-0.9398	9	0.02654	T	1	.	4.5544	0.12130	0.1248:0.6049:0.1215:0.1488	rs2711941;rs52812365;rs2711941	10;10;10	F8WAE7;Q96PQ7;Q96PQ7-2	.;KLHL5_HUMAN;.	L	10	ENSP00000423897:I10L;ENSP00000352716:I10L;ENSP00000371355:I10L;ENSP00000261426:I10L	ENSP00000261426:I10L	I	+	1	0	KLHL5	38740557	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	0.818000	0.27295	0.581000	0.29539	-0.127000	0.14921	ATT	A|0.260;C|0.740	0.740	strong		0.328	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1		
INPP5E	56623	hgsc.bcm.edu	37	9	139324740	139324740	+	Silent	SNP	C	C	T	rs10870182	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139324740C>T	ENST00000371712.3	-	9	2193	c.1791G>A	c.(1789-1791)ccG>ccA	p.P597P		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		TGTCTCGCCCCGGCCTCACTT	0.622													C|||	643	0.128395	0.0371	0.245	5008	,	,		16229	0.1478		0.1213	False		,,,				2504	0.1564				p.P597P		Atlas-SNP	.											.	INPP5E	18	.	0			c.G1791A						PASS	.			204,3944		4,196,1874	57.0	48.0	51.0		1791	-10.2	0.2	9	dbSNP_120	51	1012,7156		57,898,3129	no	coding-synonymous	INPP5E	NM_019892.4		61,1094,5003	TT,TC,CC		12.3898,4.918,9.8733		597/645	139324740	1216,11100	2074	4084	6158	SO:0001819	synonymous_variant	56623	exon9			TCGCCCCGGCCTC	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1791G>A	9.37:g.139324740C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			C|0.894;T|0.106	0.106	strong		0.622	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
SFTA2	389376	hgsc.bcm.edu	37	6	30899524	30899524	+	Missense_Mutation	SNP	T	T	C	rs3131787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30899524T>C	ENST00000359086.3	-	2	188	c.110A>G	c.(109-111)aAt>aGt	p.N37S	Y_RNA_ENST00000516952.1_RNA	NM_205854.2	NP_995326.1	Q6UW10	SFTA2_HUMAN	surfactant associated 2	37			N -> S (in dbSNP:rs3131787).			extracellular region (GO:0005576)				lung(2)	2						ATAGGAGGAATTTGTCAGAAA	0.507													T|||	412	0.0822684	0.0968	0.0663	5008	,	,		19669	0.0218		0.1551	False		,,,				2504	0.0613				p.N37S		Atlas-SNP	.											.	SFTA2	6	.	0			c.A110G						PASS	.	T	SER/ASN	367,2655		15,337,1159	89.0	104.0	98.0		110	3.0	0.0	6	dbSNP_103	98	1047,4371		94,859,1756	yes	missense	SFTA2	NM_205854.2	46	109,1196,2915	CC,CT,TT		19.3245,12.1443,16.7536	possibly-damaging	37/79	30899524	1414,7026	1511	2709	4220	SO:0001583	missense	389376	exon2			GAGGAATTTGTCA	AY102070	CCDS4691.1	6p21.3	2008-08-26	2008-08-26	2008-08-26	ENSG00000196260	ENSG00000196260			18386	protein-coding gene	gene with protein product			"""surfactant associated protein G"""	SFTPG			Standard	NM_205854		Approved		uc003nsf.3	Q6UW10	OTTHUMG00000031183	ENST00000359086.3:c.110A>G	6.37:g.30899524T>C	ENSP00000351989:p.Asn37Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	87	74	0.850575	NM_205854	A2ABK7|A2ACH1|B7ZCJ7	Missense_Mutation	SNP	ENST00000359086.3	37	CCDS4691.1	246	0.11263736263736264	71	0.1443089430894309	27	0.07458563535911603	20	0.03496503496503497	128	0.16886543535620052	T	13.67	2.305613	0.40795	0.121443	0.193245	ENSG00000196260	ENST00000359086	T	0.47869	0.83	4.12	2.96	0.34315	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.80722	P	0.0	B	0.33318	0.408	B	0.25987	0.065	T	0.05115	-1.0905	7	0.40728	T	0.16	.	5.9551	0.19269	0.0:0.1188:0.0:0.8812	rs3131787;rs17196060;rs52836965;rs3131787	37	Q6UW10	SFTA2_HUMAN	S	37	ENSP00000351989:N37S	ENSP00000351989:N37S	N	-	2	0	SFTA2	31007503	0.012000	0.17670	0.002000	0.10522	0.310000	0.27922	1.306000	0.33505	0.649000	0.30751	0.383000	0.25322	AAT	T|0.854;C|0.146	0.146	strong		0.507	SFTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076360.2	NM_205854	
NOTCH4	4855	hgsc.bcm.edu	37	6	32168771	32168771	+	Silent	SNP	G	G	T	rs3134942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32168771G>T	ENST00000375023.3	-	23	4290	c.4152C>A	c.(4150-4152)gtC>gtA	p.V1384V		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1384					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						CCACACCCATGACCACCACAA	0.602													T|||	389	0.0776757	0.0991	0.0476	5008	,	,		17672	0.0278		0.1034	False		,,,				2504	0.0951				p.V1384V		Atlas-SNP	.											NOTCH4,colon,carcinoma,0,1	NOTCH4	201	1	0			c.C4152A						PASS	.	T		276,2746		11,254,1246	75.0	50.0	59.0		4152	0.8	1.0	6	dbSNP_103	59	699,4719		45,609,2055	no	coding-synonymous	NOTCH4	NM_004557.3		56,863,3301	TT,TG,GG		12.9014,9.133,11.5521		1384/2004	32168771	975,7465	1511	2709	4220	SO:0001819	synonymous_variant	4855	exon23			ACCCATGACCACC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4152C>A	6.37:g.32168771G>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	103	86	0.834951	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			G|0.909;T|0.091	0.091	strong		0.602	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
COL5A3	50509	hgsc.bcm.edu	37	19	10084460	10084460	+	Missense_Mutation	SNP	A	A	G	rs62638750	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10084460A>G	ENST00000264828.3	-	49	3669	c.3584T>C	c.(3583-3585)gTt>gCt	p.V1195A		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1195	Triple-helical region.				axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TGGCTGACCAACTCCTCCAGG	0.577													A|||	14	0.00279553	0.0015	0.0029	5008	,	,		18984	0.0		0.008	False		,,,				2504	0.002				p.V1195A		Atlas-SNP	.											.	COL5A3	243	.	0			c.T3584C						PASS	.	A	ALA/VAL	9,4397	15.5+/-35.6	0,9,2194	76.0	85.0	82.0		3584	3.5	0.5	19	dbSNP_129	82	95,8501	51.5+/-111.7	0,95,4203	yes	missense	COL5A3	NM_015719.3	64	0,104,6397	GG,GA,AA		1.1052,0.2043,0.7999	probably-damaging	1195/1746	10084460	104,12898	2203	4298	6501	SO:0001583	missense	50509	exon49			TGACCAACTCCTC	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.3584T>C	19.37:g.10084460A>G	ENSP00000264828:p.Val1195Ala	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	12	0.005494505494505495	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	7	0.009234828496042216	A	14.63	2.593279	0.46214	0.002043	0.011052	ENSG00000080573	ENST00000264828	D	0.96168	-3.93	4.48	3.47	0.39725	.	0.000000	0.64402	D	0.000006	T	0.80037	0.4550	N	0.04260	-0.245	0.09310	N	1	B	0.22800	0.075	B	0.18263	0.021	T	0.70281	-0.4915	10	0.09084	T	0.74	.	5.6932	0.17841	0.7885:0.0:0.2115:0.0	.	1195	P25940	CO5A3_HUMAN	A	1195	ENSP00000264828:V1195A	ENSP00000264828:V1195A	V	-	2	0	COL5A3	9945460	0.018000	0.18449	0.457000	0.27056	0.955000	0.61496	2.775000	0.47702	0.753000	0.32945	0.402000	0.26972	GTT	A|0.992;G|0.008	0.008	strong		0.577	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
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 GAIIx	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	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	81	40	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		
OR11H12	440153	hgsc.bcm.edu	37	14	19377881	19377881	+	Missense_Mutation	SNP	G	G	A	rs138502172	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:19377881G>A	ENST00000550708.1	+	1	360	c.288G>A	c.(286-288)atG>atA	p.M96I		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	96						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)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTCCCAAGATGTTGGTCAACT	0.403																																					p.M96I		Atlas-SNP	.											OR11H12,NS,carcinoma,0,1	OR11H12	58	1	0			c.G288A						scavenged	.						5.0	5.0	5.0					14																	19377881		1160	2711	3871	SO:0001583	missense	440153	exon1			CAAGATGTTGGTC		CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"""GPCR / Class A : Olfactory receptors"""	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.288G>A	14.37:g.19377881G>A	ENSP00000449002:p.Met96Ile	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	357	25	0.070028	NM_001013354		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	g	11.75	1.732631	0.30684	.	.	ENSG00000257115	ENST00000550708	T	0.05513	3.43	0.585	0.585	0.17428	GPCR, rhodopsin-like superfamily (1);	0.289165	0.23960	N	0.042866	T	0.11239	0.0274	M	0.78223	2.4	0.22675	N	0.998867	P	0.51537	0.946	P	0.47528	0.549	T	0.14282	-1.0478	9	0.59425	D	0.04	.	7.1009	0.25336	1.0E-4:0.0:0.9999:0.0	.	96	B2RN74	O11HC_HUMAN	I	96	ENSP00000449002:M96I	ENSP00000449002:M96I	M	+	3	0	CR383656.1	18447881	0.814000	0.29104	0.980000	0.43619	0.268000	0.26511	0.362000	0.20284	0.619000	0.30197	0.064000	0.15345	ATG	G|0.973;A|0.027	0.027	strong		0.403	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354	
RASA1	5921	hgsc.bcm.edu	37	5	86564564	86564564	+	Missense_Mutation	SNP	C	C	T	rs111840875	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:86564564C>T	ENST00000274376.6	+	1	860	c.296C>T	c.(295-297)gCt>gTt	p.A99V	RASA1_ENST00000512763.1_5'Flank|RASA1_ENST00000456692.2_5'Flank|RASA1_ENST00000506290.1_5'Flank	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	99					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.A99_A106delAAGVAGAA(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		gctggtgctgctgctggcgtg	0.647													C|||	63	0.0125799	0.003	0.0245	5008	,	,		14161	0.0		0.0368	False		,,,				2504	0.0051				p.A99V		Atlas-SNP	.											.	RASA1	213	.	1	Deletion - In frame(1)	large_intestine(1)	c.C296T						PASS	.	C	VAL/ALA	35,4371	40.0+/-72.8	0,35,2168	48.0	36.0	40.0		296	0.6	0.1	5	dbSNP_132	40	246,8354	96.1+/-157.9	0,246,4054	yes	missense	RASA1	NM_002890.2	64	0,281,6222	TT,TC,CC		2.8605,0.7944,2.1605	benign	99/1048	86564564	281,12725	2203	4300	6503	SO:0001583	missense	5921	exon1			GTGCTGCTGCTGG		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	9871	protein-coding gene	gene with protein product	"""capillary malformation-arteriovenous malformation"""	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.296C>T	5.37:g.86564564C>T	ENSP00000274376:p.Ala99Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_002890	B2R6W3|Q9UDI1	Missense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	36	0.016483516483516484	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	23	0.030343007915567283	C	3.718	-0.058129	0.07317	0.007944	0.028605	ENSG00000145715	ENST00000274376;ENST00000534133	T	0.74209	-0.82	1.6	0.623	0.17654	.	2.236220	0.02643	N	0.105591	T	0.25158	0.0611	N	0.08118	0	0.80722	D	1	P;B	0.51933	0.949;0.334	B;B	0.34346	0.18;0.014	T	0.40739	-0.9547	10	0.36615	T	0.2	.	4.8392	0.13481	0.3611:0.6389:0.0:0.0	.	132;99	Q59GK3;P20936	.;RASA1_HUMAN	V	99;132	ENSP00000274376:A99V	ENSP00000274376:A99V	A	+	2	0	RASA1	86600320	0.999000	0.42202	0.103000	0.21229	0.047000	0.14425	2.605000	0.46283	0.192000	0.20272	0.655000	0.94253	GCT	C|0.982;T|0.018	0.018	strong		0.647	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890	
OR2D3	120775	hgsc.bcm.edu	37	11	6942952	6942952	+	Silent	SNP	T	T	C	rs2035844	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6942952T>C	ENST00000317834.3	+	1	748	c.720T>C	c.(718-720)acT>acC	p.T240T		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	240						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)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTATCTCCACTGTTATCCAGA	0.463													T|||	2040	0.407348	0.6241	0.3329	5008	,	,		20687	0.4464		0.1948	False		,,,				2504	0.3456				p.T240T		Atlas-SNP	.											.	OR2D3	51	.	0			c.T720C						PASS	.	T		2479,1923	626.0+/-394.6	692,1095,414	110.0	98.0	102.0		720	-0.1	1.0	11	dbSNP_94	102	1701,6891	310.0+/-309.6	172,1357,2767	no	coding-synonymous	OR2D3	NM_001004684.1		864,2452,3181	CC,CT,TT		19.7975,43.6847,32.1687		240/331	6942952	4180,8814	2201	4296	6497	SO:0001819	synonymous_variant	120775	exon1			CTCCACTGTTATC	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.720T>C	11.37:g.6942952T>C		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	225	126	0.56	NM_001004684	B2RP06|Q6IFG8|Q96R51	Silent	SNP	ENST00000317834.3	37	CCDS31417.1																																																																																			T|0.667;C|0.333	0.333	strong		0.463	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
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 GAIIx	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		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	74	23	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	
ZNF154	7710	hgsc.bcm.edu	37	19	58213773	58213773	+	Missense_Mutation	SNP	G	G	C	rs2188736	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58213773G>C	ENST00000512439.2	-	3	740	c.544C>G	c.(544-546)Ctt>Gtt	p.L182V	AC003006.7_ENST00000594684.1_Intron|AC003006.7_ENST00000599221.1_Intron|ZNF154_ENST00000426889.1_Missense_Mutation_p.L182V|ZNF551_ENST00000596085.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	182			L -> V (in dbSNP:rs2188736).		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(1)|kidney(1)|large_intestine(7)|lung(3)	12		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;0.0257)		CCAGTGTGAAGTCTCCAATGG	0.453													C|||	622	0.124201	0.1589	0.111	5008	,	,		23592	0.0843		0.1948	False		,,,				2504	0.0552				p.L182V		Atlas-SNP	.											.	ZNF154	34	.	0			c.C544G						PASS	.	C	VAL/LEU	648,3704	694.5+/-405.8	61,526,1589	167.0	167.0	167.0		544	-3.6	0.0	19	dbSNP_96	167	1419,7161	734.1+/-406.9	115,1189,2986	yes	missense	ZNF154	NM_001085384.1	32	176,1715,4575	CC,CG,GG		16.5385,14.8897,15.9836	benign	182/438	58213773	2067,10865	2176	4290	6466	SO:0001583	missense	7710	exon3			TGTGAAGTCTCCA	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"""Zinc fingers, C2H2-type"", ""-"""	12939	protein-coding gene	gene with protein product		604085	"""zinc finger protein 154 (pHZ-92)"""			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.544C>G	19.37:g.58213773G>C	ENSP00000421258:p.Leu182Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Missense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	331	0.15155677655677655	79	0.16056910569105692	51	0.1408839779005525	54	0.0944055944055944	147	0.19393139841688653	C	13.24	2.178466	0.38511	0.148897	0.165385	ENSG00000179909	ENST00000512439;ENST00000426889	T;T	0.07216	3.21;3.21	2.6	-3.59	0.04583	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.10645	0.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47086	-0.9144	8	0.30078	T	0.28	.	6.6787	0.23108	0.0:0.2123:0.1497:0.638	rs2188736;rs2188736	182	Q13106	ZN154_HUMAN	V	182	ENSP00000421258:L182V;ENSP00000442370:L182V	ENSP00000442370:L182V	L	-	1	0	ZNF154	62905585	0.000000	0.05858	0.001000	0.08648	0.933000	0.57130	-1.922000	0.01568	-1.235000	0.02545	-0.216000	0.12614	CTT	G|0.847;C|0.153	0.153	strong		0.453	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2		
DOCK1	1793	hgsc.bcm.edu	37	10	129160458	129160458	+	Silent	SNP	G	G	A	rs2296635	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:129160458G>A	ENST00000280333.6	+	33	3460	c.3351G>A	c.(3349-3351)tcG>tcA	p.S1117S		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1117					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AATTCCATTCGACCCGAAGCT	0.493													G|||	1023	0.204273	0.1747	0.1628	5008	,	,		17732	0.1359		0.2684	False		,,,				2504	0.2781				p.S1117S		Atlas-SNP	.											.	DOCK1	188	.	0			c.G3351A						PASS	.	G		732,3446		67,598,1424	62.0	61.0	62.0		3306	-10.3	0.0	10	dbSNP_100	62	2277,6223		315,1647,2288	no	coding-synonymous	DOCK1	NM_001380.3		382,2245,3712	AA,AG,GG		26.7882,17.5203,23.734		1102/1851	129160458	3009,9669	2089	4250	6339	SO:0001819	synonymous_variant	1793	exon33			CCATTCGACCCGA	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.3351G>A	10.37:g.129160458G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				G|0.808;A|0.192	0.192	strong		0.493	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
PGD	5226	hgsc.bcm.edu	37	1	10473196	10473196	+	Silent	SNP	C	C	T	rs2229687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10473196C>T	ENST00000270776.8	+	8	770	c.732C>T	c.(730-732)gaC>gaT	p.D244D	PGD_ENST00000538557.1_Silent_p.D231D|PGD_ENST00000541529.1_Silent_p.D222D	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	244					carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)	p.D244D(1)		NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	AGTTCCAAGACACCGATGGCA	0.532													c|||	1678	0.335064	0.3457	0.3732	5008	,	,		21311	0.3403		0.338	False		,,,				2504	0.2853				p.D244D		Atlas-SNP	.											PGD,NS,carcinoma,0,1	PGD	39	1	1	Substitution - coding silent(1)	stomach(1)	c.C732T						PASS	.	T		1453,2953	682.7+/-404.2	254,945,1004	86.0	82.0	83.0		732	-10.1	0.0	1	dbSNP_98	83	2817,5783	676.6+/-403.3	487,1843,1970	no	coding-synonymous	PGD	NM_002631.2		741,2788,2974	TT,TC,CC		32.7558,32.9778,32.831		244/484	10473196	4270,8736	2203	4300	6503	SO:0001819	synonymous_variant	5226	exon8			CCAAGACACCGAT	BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	1.1.1.43		8891	protein-coding gene	gene with protein product		172200					Standard	NM_002631		Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.732C>T	1.37:g.10473196C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_002631	A8K2Y9|B4DQJ8|Q9BWD8	Silent	SNP	ENST00000270776.8	37	CCDS113.1																																																																																			C|0.656;T|0.344	0.344	strong		0.532	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005398.1	NM_002631	
CLEC4F	165530	hgsc.bcm.edu	37	2	71043461	71043461	+	Missense_Mutation	SNP	C	C	T	rs722896	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71043461C>T	ENST00000272367.2	-	4	1128	c.1052G>A	c.(1051-1053)cGt>cAt	p.R351H	CLEC4F_ENST00000426626.1_Missense_Mutation_p.R351H	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	351			R -> H (in dbSNP:rs722896).		endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						CTGGTCCAGACGGCCATTTGC	0.403													C|||	1693	0.338059	0.1195	0.4006	5008	,	,		21626	0.5248		0.3101	False		,,,				2504	0.4254				p.R351H	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.G1052A						PASS	.	C	HIS/ARG	739,3667	303.5+/-288.0	60,619,1524	86.0	83.0	84.0		1052	-5.1	0.0	2	dbSNP_86	84	2597,6003	421.6+/-353.8	431,1735,2134	yes	missense	CLEC4F	NM_173535.2	29	491,2354,3658	TT,TC,CC		30.1977,16.7726,25.6497	benign	351/590	71043461	3336,9670	2203	4300	6503	SO:0001583	missense	165530	exon4			TCCAGACGGCCAT	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.1052G>A	2.37:g.71043461C>T	ENSP00000272367:p.Arg351His	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	115	77	0.669565	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	753	0.3447802197802198	58	0.11788617886178862	124	0.3425414364640884	343	0.5996503496503497	228	0.3007915567282322	C	7.700	0.692882	0.15039	0.167726	0.301977	ENSG00000152672	ENST00000272367;ENST00000426626	D;D	0.82893	-1.66;-1.66	3.79	-5.05	0.02955	.	1.546170	0.04013	N	0.298500	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B;B	0.12630	0.002;0.006	B;B	0.04013	0.001;0.001	T	0.16600	-1.0397	9	0.13470	T	0.59	.	11.5395	0.50659	0.0:0.2236:0.0:0.7764	rs722896;rs59663124;rs722896	351;351	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	H	351	ENSP00000272367:R351H;ENSP00000390581:R351H	ENSP00000272367:R351H	R	-	2	0	CLEC4F	70896969	0.000000	0.05858	0.000000	0.03702	0.779000	0.44077	-1.034000	0.03567	-1.226000	0.02574	0.467000	0.42956	CGT	C|0.704;T|0.296	0.296	strong		0.403	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
FLNC	2318	hgsc.bcm.edu	37	7	128488734	128488734	+	Missense_Mutation	SNP	G	G	A	rs2291569	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128488734G>A	ENST00000325888.8	+	27	4961	c.4700G>A	c.(4699-4701)cGg>cAg	p.R1567Q	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.R1567Q	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1567			R -> Q (in dbSNP:rs2291569).		cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						ATCGACGCACGGGACGCGGGC	0.662													G|||	313	0.0625	0.0106	0.0447	5008	,	,		15225	0.1111		0.0765	False		,,,				2504	0.0808				p.R1567Q		Atlas-SNP	.											.	FLNC	339	.	0			c.G4700A						PASS	.	G	GLN/ARG,GLN/ARG	102,4070		1,100,1985	105.0	116.0	112.0		4700,4700	5.1	1.0	7	dbSNP_100	112	716,7706		28,660,3523	yes	missense,missense	FLNC	NM_001127487.1,NM_001458.4	43,43	29,760,5508	AA,AG,GG		8.5015,2.4449,6.4952	possibly-damaging,possibly-damaging	1567/2693,1567/2726	128488734	818,11776	2086	4211	6297	SO:0001583	missense	2318	exon27			ACGCACGGGACGC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.4700G>A	7.37:g.128488734G>A	ENSP00000327145:p.Arg1567Gln	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	154	0.07051282051282051	7	0.014227642276422764	19	0.052486187845303865	64	0.11188811188811189	64	0.08443271767810026	G	16.99	3.273010	0.59649	0.024449	0.085015	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.86164	-2.08;-2.08	5.09	5.09	0.68999	Immunoglobulin E-set (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.33904	0.0879	M	0.89968	3.075	0.22066	P	0.999382205	D;P	0.89917	1.0;0.907	D;P	0.85130	0.997;0.547	T	0.71185	-0.4667	9	0.51188	T	0.08	.	12.7242	0.57162	0.0868:0.0:0.9132:0.0	rs2291569;rs17477492	1567;1567	Q14315-2;Q14315	.;FLNC_HUMAN	Q	1567	ENSP00000327145:R1567Q;ENSP00000344002:R1567Q	ENSP00000327145:R1567Q	R	+	2	0	FLNC	128275970	0.436000	0.25586	0.995000	0.50966	0.033000	0.12548	3.398000	0.52579	2.513000	0.84729	0.655000	0.94253	CGG	G|0.921;A|0.079	0.079	strong		0.662	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
TMEM51	55092	hgsc.bcm.edu	37	1	15546077	15546077	+	Silent	SNP	G	G	A	rs3753313	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:15546077G>A	ENST00000428417.1	+	3	1046	c.600G>A	c.(598-600)ccG>ccA	p.P200P	TMEM51_ENST00000376008.2_Silent_p.P200P|TMEM51_ENST00000434578.2_3'UTR|TMEM51_ENST00000400796.3_Silent_p.P200P|TMEM51_ENST00000376014.3_Silent_p.P200P	NM_001136217.1	NP_001129689.1	Q9NW97	TMM51_HUMAN	transmembrane protein 51	200						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(3)|large_intestine(2)|lung(5)|prostate(2)	14		Renal(390;0.00145)|Breast(348;0.00186)|Colorectal(325;0.00215)|all_lung(284;0.00459)|Lung NSC(340;0.0104)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;2.07e-06)|COAD - Colon adenocarcinoma(227;7.14e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000175)|KIRC - Kidney renal clear cell carcinoma(229;0.00141)|STAD - Stomach adenocarcinoma(313;0.00644)|READ - Rectum adenocarcinoma(331;0.0751)		GACTGAAACCGCTGAAAGTTC	0.532													G|||	1023	0.204273	0.0741	0.2003	5008	,	,		17895	0.0754		0.3499	False		,,,				2504	0.3661				p.P200P		Atlas-SNP	.											TMEM51,NS,lymphoid_neoplasm,+1,1	TMEM51	28	1	0			c.G600A						scavenged	.	G	,,,	535,3871	242.1+/-252.3	29,477,1697	70.0	81.0	77.0		600,600,600,600	-8.2	0.6	1	dbSNP_107	77	3040,5560	468.0+/-367.2	566,1908,1826	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TMEM51	NM_001136216.1,NM_001136217.1,NM_001136218.1,NM_018022.2	,,,	595,2385,3523	AA,AG,GG		35.3488,12.1425,27.4873	,,,	200/254,200/254,200/254,200/254	15546077	3575,9431	2203	4300	6503	SO:0001819	synonymous_variant	55092	exon3			GAAACCGCTGAAA	AK098467	CCDS154.1	1p36.21	2008-02-05	2005-05-22	2005-05-22	ENSG00000171729	ENSG00000171729			25488	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 72"""	C1orf72		12477932	Standard	NM_018022		Approved	FLJ10199	uc001avx.3	Q9NW97	OTTHUMG00000002046	ENST00000428417.1:c.600G>A	1.37:g.15546077G>A		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_018022	A8K819	Silent	SNP	ENST00000428417.1	37	CCDS154.1																																																																																			G|0.767;A|0.233	0.233	strong		0.532	TMEM51-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005699.3	NM_018022	
ZNF211	10520	hgsc.bcm.edu	37	19	58153000	58153000	+	Silent	SNP	T	T	C	rs3746218	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58153000T>C	ENST00000347302.3	+	3	1325	c.1146T>C	c.(1144-1146)ttT>ttC	p.F382F	ZNF211_ENST00000299871.5_Silent_p.F447F|ZNF211_ENST00000254182.7_Silent_p.F373F|ZNF211_ENST00000420680.1_Silent_p.F386F|ZNF211_ENST00000240731.4_Silent_p.F395F|ZNF211_ENST00000544273.1_Silent_p.F394F|ZNF211_ENST00000541801.1_Silent_p.F373F|ZNF211_ENST00000391703.3_Silent_p.F321F	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	382					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(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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;0.026)		GCCAAAACTTTAGCCTGATCT	0.468													t|||	1072	0.214058	0.2352	0.1297	5008	,	,		22300	0.3214		0.159	False		,,,				2504	0.1912				p.F447F		Atlas-SNP	.											.	ZNF211	78	.	0			c.T1341C						PASS	.	C	,	979,3427	730.9+/-410.2	117,745,1341	70.0	76.0	74.0		1185,1146	-4.8	0.0	19	dbSNP_107	74	1346,7254	756.1+/-407.5	97,1152,3051	no	coding-synonymous,coding-synonymous	ZNF211	NM_006385.3,NM_198855.2	,	214,1897,4392	CC,CT,TT		15.6512,22.2197,17.8764	,	395/578,382/565	58153000	2325,10681	2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			AAACTTTAGCCTG	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1146T>C	19.37:g.58153000T>C		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	30	12	0.4	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	37	CCDS12957.1	485	0.22206959706959706	135	0.27439024390243905	52	0.143646408839779	180	0.3146853146853147	118	0.15567282321899736	c	7.735	0.700102	0.15106	0.222197	0.156512	ENSG00000121417	ENST00000407202	.	.	.	3.57	-4.82	0.03171	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.8423	0.05533	0.1604:0.184:0.1095:0.5462	rs3746218;rs3746218	.	.	.	Q	386	.	.	X	+	1	0	ZNF211	62844812	0.000000	0.05858	0.000000	0.03702	0.974000	0.67602	-2.277000	0.01160	-0.956000	0.03631	-0.197000	0.12766	TAG	T|0.792;C|0.208	0.208	strong		0.468	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
SYNE3	161176	hgsc.bcm.edu	37	14	95906321	95906321	+	Missense_Mutation	SNP	G	G	A	rs9671369	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:95906321G>A	ENST00000334258.5	-	11	2017	c.2003C>T	c.(2002-2004)aCg>aTg	p.T668M	SYNE3_ENST00000557275.1_Missense_Mutation_p.T668M|SYNE3_ENST00000554873.1_Missense_Mutation_p.T425M	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	668			T -> M (in dbSNP:rs9671369). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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						CAGCTTTTGCGTGGTCACAAC	0.647													G|||	2066	0.41254	0.1914	0.5562	5008	,	,		16914	0.6399		0.3807	False		,,,				2504	0.408				p.T668M		Atlas-SNP	.											SYNE3_ENST00000334258,NS,carcinoma,0,3	SYNE3	130	3	0			c.C2003T						PASS	.	G	MET/THR	973,3433	363.6+/-316.6	119,735,1349	81.0	84.0	83.0		2003	3.9	0.0	14	dbSNP_119	83	3220,5380	479.3+/-370.1	585,2050,1665	yes	missense	C14orf49	NM_152592.3	81	704,2785,3014	AA,AG,GG		37.4419,22.0835,32.239	probably-damaging	668/976	95906321	4193,8813	2203	4300	6503	SO:0001583	missense	161176	exon11			TTTTGCGTGGTCA	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.2003C>T	14.37:g.95906321G>A	ENSP00000334308:p.Thr668Met	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	944	0.43223443223443225	106	0.21544715447154472	184	0.5082872928176796	364	0.6363636363636364	290	0.38258575197889183	G	15.33	2.802166	0.50315	0.220835	0.374419	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.34072	1.38;1.38;1.38	4.93	3.9	0.45041	.	0.348520	0.20892	N	0.083808	T	0.00012	0.0000	M	0.70595	2.14	0.42751	P	0.006221000000000032	D;D	0.76494	0.999;0.999	P;D	0.65874	0.899;0.939	T	0.47459	-0.9116	9	0.45353	T	0.12	-9.251	10.0543	0.42235	0.0:0.0:0.6125:0.3874	rs9671369;rs56526633;rs59880763;rs9671369	668;668	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	M	668;425;668	ENSP00000334308:T668M;ENSP00000452154:T425M;ENSP00000450562:T668M	ENSP00000334308:T668M	T	-	2	0	C14orf49	94976074	0.040000	0.19996	0.025000	0.17156	0.005000	0.04900	0.891000	0.28309	2.435000	0.82474	0.561000	0.74099	ACG	G|0.638;A|0.362	0.362	strong		0.647	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
LAMA5	3911	hgsc.bcm.edu	37	20	60899182	60899182	+	Missense_Mutation	SNP	C	C	T	rs11698080	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60899182C>T	ENST00000252999.3	-	43	5788	c.5722G>A	c.(5722-5724)Gcc>Acc	p.A1908T		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1908	Laminin EGF-like 17. {ECO:0000255|PROSITE-ProRule:PRU00460}.		A -> T (in dbSNP:rs11698080).		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)			ACACAGGGGGCGCTGGGGTCG	0.672													.|||	1077	0.215056	0.2458	0.2363	5008	,	,		15727	0.1895		0.2406	False		,,,				2504	0.1585				p.A1908T		Atlas-SNP	.											LAMA5,caecum,carcinoma,0,1	LAMA5	268	1	0			c.G5722A						PASS	.	C	THR/ALA	1186,3188		159,868,1160	21.0	24.0	23.0		5722	0.0	0.2	20	dbSNP_120	23	1879,6663		206,1467,2598	yes	missense	LAMA5	NM_005560.3	58	365,2335,3758	TT,TC,CC		21.9972,27.1148,23.7303	benign	1908/3696	60899182	3065,9851	2187	4271	6458	SO:0001583	missense	3911	exon43			AGGGGGCGCTGGG	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.5722G>A	20.37:g.60899182C>T	ENSP00000252999:p.Ala1908Thr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	487	0.222985347985348	131	0.266260162601626	83	0.2292817679558011	104	0.18181818181818182	169	0.22295514511873352	C	9.488	1.099832	0.20552	0.271148	0.219972	ENSG00000130702	ENST00000252999	T	0.61392	0.11	4.05	0.0403	0.14208	EGF-like, laminin (4);	0.386612	0.25625	U	0.029398	T	0.00012	0.0000	L	0.33137	0.985	0.46874	P	7.700000000000484E-4	B	0.24576	0.106	B	0.13407	0.009	T	0.23619	-1.0183	9	0.19590	T	0.45	.	8.6324	0.33928	0.287:0.6297:0.0:0.0834	rs11698080;rs11698080	1908	O15230	LAMA5_HUMAN	T	1908	ENSP00000252999:A1908T	ENSP00000252999:A1908T	A	-	1	0	LAMA5	60332577	0.019000	0.18553	0.211000	0.23655	0.031000	0.12232	1.445000	0.35079	0.150000	0.19136	-0.350000	0.07774	GCC	C|0.759;T|0.241	0.241	strong		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
HSPG2	3339	hgsc.bcm.edu	37	1	22180723	22180723	+	Silent	SNP	C	C	T	rs12742444	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22180723C>T	ENST00000374695.3	-	50	6481	c.6402G>A	c.(6400-6402)gtG>gtA	p.V2134V	HSPG2_ENST00000430507.1_Intron	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2134	Ig-like C2-type 6.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGCCGTGGAGCACAGACACAG	0.627													G|||	173	0.0345447	0.0015	0.0245	5008	,	,		16741	0.0		0.0487	False		,,,				2504	0.1074				p.V2134V		Atlas-SNP	.											.	HSPG2	311	.	0			c.G6402A						PASS	.	G		41,4353		0,41,2156	21.0	22.0	22.0		6402	2.5	1.0	1	dbSNP_121	22	470,8122		13,444,3839	no	coding-synonymous	HSPG2	NM_005529.5		13,485,5995	TT,TC,CC		5.4702,0.9331,3.935		2134/4392	22180723	511,12475	2197	4296	6493	SO:0001819	synonymous_variant	3339	exon50			GTGGAGCACAGAC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6402G>A	1.37:g.22180723C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			C|0.971;G|0.000;T|0.029	0.029	strong		0.627	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
ACKR1	2532	hgsc.bcm.edu	37	1	159175527	159175527	+	Missense_Mutation	SNP	G	G	A	rs13962	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:159175527G>A	ENST00000368122.2	+	2	977	c.298G>A	c.(298-300)Gca>Aca	p.A100T	DARC_ENST00000368121.2_Missense_Mutation_p.A102T|DARC_ENST00000537147.1_Missense_Mutation_p.A100T|CTA-134P22.2_ENST00000609696.1_RNA	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		100			A -> T (in dbSNP:rs13962). {ECO:0000269|PubMed:9731074, ECO:0000269|PubMed:9886340}.		chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					GCCTGTCCTGGCACAGCTGGC	0.617													G|||	345	0.0688898	0.0045	0.0937	5008	,	,		21381	0.0		0.1839	False		,,,				2504	0.091				p.A102T		Atlas-SNP	.											.	DARC	76	.	0			c.G304A	GRCh37	CM983824	DARC	M	rs13962	PASS	.	G	THR/ALA,THR/ALA	140,4266	100.3+/-138.9	5,130,2068	105.0	100.0	102.0	http://www.ncbi.nlm.nih.gov/pubmed?term	304,298	3.1	0.2	1	dbSNP_52	102	1467,7133	279.1+/-293.8	127,1213,2960	yes	missense,missense	DARC	NM_001122951.2,NM_002036.3	58,58	132,1343,5028	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	17.0581,3.1775,12.3558	probably-damaging,probably-damaging	102/339,100/337	159175527	1607,11399	2203	4300	6503	SO:0001583	missense	2532	exon1			GTCCTGGCACAGC																												ENST00000368122.2:c.298G>A	1.37:g.159175527G>A	ENSP00000357104:p.Ala100Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_001122951	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	37	CCDS1183.1	178	0.0815018315018315	1	0.0020325203252032522	38	0.10497237569060773	0	0.0	139	0.18337730870712401	G	14.11	2.438188	0.43326	0.031775	0.170581	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000435307;ENST00000368121	T;T;T;T	0.37915	1.17;1.17;1.66;1.17	5.09	3.07	0.35406	.	0.300710	0.17478	U	0.172829	T	0.22513	0.0543	L	0.38175	1.15	0.58432	P	1.0000000000287557E-6	D;D	0.54772	0.968;0.968	P;P	0.54889	0.763;0.763	T	0.06552	-1.0820	9	0.45353	T	0.12	-3.8727	5.8028	0.18424	0.0989:0.0:0.7105:0.1906	rs13962;rs13962	102;100	Q5Y7A1;Q16570	.;DUFFY_HUMAN	T	100;100;100;102;102	ENSP00000357104:A100T;ENSP00000441985:A100T;ENSP00000398406:A102T;ENSP00000357103:A102T	ENSP00000352341:A100T	A	+	1	0	DARC	157442151	0.098000	0.21812	0.224000	0.23877	0.170000	0.22686	0.380000	0.20602	1.259000	0.44117	0.561000	0.74099	GCA	.	.	none		0.617	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2		
ZNF750	79755	hgsc.bcm.edu	37	17	80788465	80788465	+	Silent	SNP	T	T	C	rs12938126	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:80788465T>C	ENST00000269394.3	-	3	2558	c.1725A>G	c.(1723-1725)gcA>gcG	p.A575A	TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron|ZNF750_ENST00000572562.1_Silent_p.A176A|TBCD_ENST00000539345.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	575					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			CAGCAGGTTCTGCAGCTCGTG	0.627													T|||	1849	0.369209	0.4017	0.3343	5008	,	,		16310	0.3522		0.4195	False		,,,				2504	0.316				p.A575A		Atlas-SNP	.											.	ZNF750	60	.	0			c.A1725G						PASS	.	T	,	1764,2642	519.9+/-370.1	364,1036,803	56.0	60.0	59.0		,1725	-6.2	0.0	17	dbSNP_121	59	3532,5068	510.5+/-377.5	715,2102,1483	no	intron,coding-synonymous	TBCD,ZNF750	NM_005993.4,NM_024702.2	,	1079,3138,2286	CC,CT,TT		41.0698,40.0363,40.7197	,	,575/724	80788465	5296,7710	2203	4300	6503	SO:0001819	synonymous_variant	79755	exon3			AGGTTCTGCAGCT	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.1725A>G	17.37:g.80788465T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_024702	Q9H899	Silent	SNP	ENST00000269394.3	37	CCDS11819.1																																																																																			T|0.600;C|0.400	0.400	strong		0.627	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
OR6N1	128372	hgsc.bcm.edu	37	1	158736445	158736445	+	Missense_Mutation	SNP	C	C	T	rs1864346	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158736445C>T	ENST00000335094.2	-	1	47	c.28G>A	c.(28-30)Gca>Aca	p.A10T		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	10			A -> T (in dbSNP:rs1864346).			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(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					ATGAATTCTGCTACCTGGCTC	0.458													T|||	1233	0.246206	0.0182	0.3314	5008	,	,		20003	0.4246		0.334	False		,,,				2504	0.2198				p.A10T		Atlas-SNP	.											.	OR6N1	96	.	0			c.G28A						PASS	.	T	THR/ALA	280,4126	783.8+/-414.6	9,262,1932	47.0	43.0	44.0		28	2.5	0.8	1	dbSNP_92	44	2756,5844	662.9+/-402.0	455,1846,1999	yes	missense	OR6N1	NM_001005185.1	58	464,2108,3931	TT,TC,CC		32.0465,6.355,23.3431	benign	10/313	158736445	3036,9970	2203	4300	6503	SO:0001583	missense	128372	exon1			ATTCTGCTACCTG	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.28G>A	1.37:g.158736445C>T	ENSP00000335535:p.Ala10Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	40	13	0.325	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	620	0.2838827838827839	14	0.028455284552845527	115	0.31767955801104975	243	0.42482517482517484	248	0.32717678100263853	T	1.784	-0.481159	0.04383	0.06355	0.320465	ENSG00000197403	ENST00000335094	T	0.00606	6.26	4.83	2.52	0.30459	.	0.302038	0.23821	N	0.044234	T	0.00039	0.0001	N	0.00132	-2.035	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.04946	-1.0916	9	0.02654	T	1	0.1271	3.4356	0.07445	0.1622:0.2701:0.0:0.5677	rs1864346;rs56643362;rs59875632;rs1864346	10	Q8NGY5	OR6N1_HUMAN	T	10	ENSP00000335535:A10T	ENSP00000335535:A10T	A	-	1	0	OR6N1	157003069	0.000000	0.05858	0.816000	0.32577	0.965000	0.64279	-0.296000	0.08287	0.040000	0.15660	-0.254000	0.11334	GCA	C|0.753;N|0.000	.	strong		0.458	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
HLA-C	3107	hgsc.bcm.edu	37	6	31238931	31238931	+	Missense_Mutation	SNP	G	G	C	rs697743	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31238931G>C	ENST00000376228.5	-	3	552	c.538C>G	c.(538-540)Ctg>Gtg	p.L180V	HLA-C_ENST00000383329.3_Missense_Mutation_p.L180V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	180	Alpha-2.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)	p.L180L(2)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TAGGCTCTCAGCTGCTCCGCC	0.682																																					p.L180V		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,0,4	HLA-C	92	4	2	Substitution - coding silent(2)	prostate(2)	c.C538G						scavenged	.						43.0	30.0	34.0					6																	31238931		2197	4291	6488	SO:0001583	missense	3107	exon3			CTCTCAGCTGCTC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.538C>G	6.37:g.31238931G>C	ENSP00000365402:p.Leu180Val	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	154	13	0.0844156	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.115|0.115	-1.133170|-1.133170	0.01756|0.01756	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.00009	.|9.46;9.46	2.81|2.81	-5.62|-5.62	0.02481|0.02481	.|MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|115.764000	.|0.00166	.|U	.|0.000008	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.39514|0.39514	1.22|1.22	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.19331	.|0.035;0.01;0.005;0.01	.|B;B;B;B	.|0.31812	.|0.136;0.056;0.04;0.056	T|T	0.44065|0.44065	-0.9352|-0.9352	5|10	.|0.18710	.|T	.|0.47	.|.	2.8574|2.8574	0.05576|0.05576	0.25:0.4691:0.1066:0.1744|0.25:0.4691:0.1066:0.1744	rs697743;rs2308591;rs3176036;rs3179868;rs3200237;rs3204480;rs12721958;rs17839941;rs28732104|rs697743;rs2308591;rs3176036;rs3179868;rs3200237;rs3204480;rs12721958;rs17839941;rs28732104	.|180;180;180;180	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	G|V	179|180;180;180;217	.|ENSP00000365402:L180V;ENSP00000372819:L180V	.|ENSP00000365402:L180V	A|L	-|-	2|1	0|2	HLA-C|HLA-C	31346910|31346910	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-12.042000|-12.042000	0.00002|0.00002	-4.714000|-4.714000	0.00035|0.00035	-1.872000|-1.872000	0.00552|0.00552	GCT|CTG	G|0.777;C|0.108;A|0.115	0.108	strong		0.682	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
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 GAIIx	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*	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	129	31	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		
WDR81	124997	hgsc.bcm.edu	37	17	1639350	1639350	+	Silent	SNP	C	C	T	rs587780507|rs117522064	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1639350C>T	ENST00000409644.1	+	9	5343	c.5343C>T	c.(5341-5343)ggC>ggT	p.G1781G	WDR81_ENST00000419248.1_Silent_p.G554G|WDR81_ENST00000545662.1_Silent_p.G412G|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.G730G|WDR81_ENST00000446363.1_Silent_p.G420G|WDR81_ENST00000437219.2_Silent_p.G578G	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1781					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TCCGACTGGGCGGTGGGCTGA	0.667													C|||	71	0.0141773	0.0	0.0187	5008	,	,		14948	0.0		0.0268	False		,,,				2504	0.0317				p.G1781G		Atlas-SNP	.											.	WDR81	180	.	0			c.C5343T						PASS	.	C	,,,	47,4359	46.0+/-80.4	0,47,2156	53.0	49.0	50.0		1734,5343,1662,2190	-11.6	0.3	17	dbSNP_132	50	278,8318	103.3+/-164.5	6,266,4026	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	6,313,6182	TT,TC,CC		3.2341,1.0667,2.4996	,,,	578/739,1781/1942,554/715,730/891	1639350	325,12677	2203	4298	6501	SO:0001819	synonymous_variant	124997	exon9			ACTGGGCGGTGGG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5343C>T	17.37:g.1639350C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	33	0.6875	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.978;T|0.022	0.022	strong		0.667	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
TUBA3D	113457	hgsc.bcm.edu	37	2	132237927	132237927	+	Missense_Mutation	SNP	C	C	A	rs200147665	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:132237927C>A	ENST00000321253.6	+	4	768	c.661C>A	c.(661-663)Cgt>Agt	p.R221S		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	221					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R221S(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		GGACATTGAACGTCCCACGTA	0.542																																					p.R221S	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											TUBA3D,trunk,malignant_melanoma,0,1	TUBA3D	60	1	1	Substitution - Missense(1)	skin(1)	c.C661A						scavenged	.						62.0	76.0	71.0					2																	132237927		2203	4296	6499	SO:0001583	missense	113457	exon4			ATTGAACGTCCCA	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.661C>A	2.37:g.132237927C>A	ENSP00000326042:p.Arg221Ser	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	137	13	0.0948905	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000321253.6	37	CCDS33290.1	.	.	.	.	.	.	.	.	.	.	c	3.464	-0.109452	0.06924	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	T	0.68903	-0.36	2.24	1.33	0.21861	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.44483	U	0.000448	T	0.58666	0.2138	L	0.47190	1.495	0.44036	D	0.996764	B	0.17465	0.022	B	0.32805	0.153	T	0.55049	-0.8201	10	0.87932	D	0	.	6.8167	0.23835	0.0:0.8406:0.0:0.1594	.	221	Q13748	TBA3C_HUMAN	S	221	ENSP00000326042:R221S	ENSP00000326042:R221S	R	+	1	0	TUBA3D	131954397	1.000000	0.71417	0.987000	0.45799	0.044000	0.14063	2.392000	0.44433	0.267000	0.21916	0.194000	0.17425	CGT	C|0.500;A|0.500	0.500	weak		0.542	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
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 GAIIx	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_ENST00000302463.6_Nonsense_Mutation_p.Y224*|SETD5_ENST00000407969.1_Nonsense_Mutation_p.Y341*|SETD5_ENST00000402198.1_Nonsense_Mutation_p.Y322*|SETD5_ENST00000402466.1_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*	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	47	17	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 GAIIx	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		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	102	57	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	
Unknown	0	hgsc.bcm.edu	37	17	17326604	17326604	+	IGR	SNP	C	C	T	rs370938128|rs7225976	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:17326604C>T								NT5M (75629 upstream) : Y_RNA (37153 downstream)																							CATGATGGGGCAAATGCCAGA	0.473													T|||	2100	0.419329	0.7912	0.2651	5008	,	,		23244	0.1875		0.3201	False		,,,				2504	0.3671				p.A140V		Atlas-SNP	.											.	.	.	.	0			c.C419T						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			ATGGGGCAAATGC																													17.37:g.17326604C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_001243312		Missense_Mutation	SNP		37																																																																																				C|0.662;T|0.338	0.338	strong	0	0.473								
SLC39A6	25800	hgsc.bcm.edu	37	18	33702162	33702162	+	Silent	SNP	G	G	A	rs3737466	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:33702162G>A	ENST00000590986.1	-	5	1501	c.1212C>T	c.(1210-1212)ttC>ttT	p.F404F	SLC39A6_ENST00000440549.2_Silent_p.F129F|SLC39A6_ENST00000269187.5_Silent_p.F404F			Q13433	S39A6_HUMAN	solute carrier family 39 (zinc transporter), member 6	404					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|lamellipodium membrane (GO:0031258)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	41						ACAGATGACTGAAAAGTGGTC	0.388													G|||	464	0.0926518	0.1014	0.1052	5008	,	,		18537	0.1667		0.0527	False		,,,				2504	0.0368				p.F404F		Atlas-SNP	.											.	SLC39A6	81	.	0			c.C1212T						PASS	.	G	,	367,3429		19,329,1550	192.0	181.0	184.0		387,1212	3.4	1.0	18	dbSNP_107	184	507,7769		13,481,3644	no	coding-synonymous,coding-synonymous	SLC39A6	NM_001099406.1,NM_012319.3	,	32,810,5194	AA,AG,GG		6.1261,9.6681,7.2399	,	129/434,404/756	33702162	874,11198	1898	4138	6036	SO:0001819	synonymous_variant	25800	exon5			ATGACTGAAAAGT	U41060	CCDS42428.1, CCDS45854.1	18q12.2	2013-05-22				ENSG00000141424		"""Solute carriers"""	18607	protein-coding gene	gene with protein product		608731	"""solute carrier family 39 (metal ion transporter), member 6"""			12659941, 12839489	Standard	NM_012319		Approved	LIV-1	uc010dmy.3	Q13433		ENST00000590986.1:c.1212C>T	18.37:g.33702162G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	131	75	0.572519	NM_012319	B4DR49|B4E224|Q8IXR3|Q96HP5	Silent	SNP	ENST00000590986.1	37	CCDS42428.1																																																																																			G|0.903;A|0.097	0.097	strong		0.388	SLC39A6-004	NOVEL	alternative_5_UTR|not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000444136.1		
FREM1	158326	hgsc.bcm.edu	37	9	14819370	14819370	+	Missense_Mutation	SNP	G	G	T	rs7023244	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:14819370G>T	ENST00000380880.3	-	14	3191	c.2408C>A	c.(2407-2409)tCt>tAt	p.S803Y	FREM1_ENST00000422223.2_Missense_Mutation_p.S803Y|FREM1_ENST00000380881.4_Missense_Mutation_p.S804Y			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	803			S -> Y (in dbSNP:rs7023244).		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)		ATCTGCATCAGAAATTAGAAT	0.478													G|||	822	0.164137	0.0832	0.255	5008	,	,		18171	0.0794		0.2525	False		,,,				2504	0.2055				p.S803Y		Atlas-SNP	.											.	FREM1	261	.	0			c.C2408A						PASS	.	G	TYR/SER	455,3437		31,393,1522	114.0	109.0	111.0		2408	5.9	1.0	9	dbSNP_116	111	2046,6238		276,1494,2372	yes	missense	FREM1	NM_144966.5	144	307,1887,3894	TT,TG,GG		24.6982,11.6906,20.5404	possibly-damaging	803/2180	14819370	2501,9675	1946	4142	6088	SO:0001583	missense	158326	exon15			GCATCAGAAATTA	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.2408C>A	9.37:g.14819370G>T	ENSP00000370262:p.Ser803Tyr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	374	0.17124542124542125	37	0.07520325203252033	89	0.24585635359116023	55	0.09615384615384616	193	0.2546174142480211	G	20.5	4.005732	0.74932	0.116906	0.246982	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.27256	1.68;1.68;1.68	5.86	5.86	0.93980	.	0.225793	0.47852	D	0.000210	T	0.00012	0.0000	M	0.85041	2.73	0.09310	P	0.9999956479	D	0.65815	0.995	P	0.62649	0.905	T	0.00071	-1.2130	9	0.87932	D	0	-15.0418	20.1931	0.98233	0.0:0.0:1.0:0.0	rs7023244;rs56569639;rs7023244	803	Q5H8C1	FREM1_HUMAN	Y	804;803;803	ENSP00000370263:S804Y;ENSP00000412940:S803Y;ENSP00000370262:S803Y	ENSP00000370257:S806Y	S	-	2	0	FREM1	14809370	1.000000	0.71417	0.993000	0.49108	0.383000	0.30230	8.582000	0.90791	2.771000	0.95319	0.563000	0.77884	TCT	G|0.830;T|0.170	0.170	strong		0.478	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
DAPP1	27071	hgsc.bcm.edu	37	4	100784980	100784980	+	Silent	SNP	C	C	T	rs3737484	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100784980C>T	ENST00000512369.1	+	7	722	c.654C>T	c.(652-654)ttC>ttT	p.F218F	DAPP1_ENST00000296414.7_Silent_p.F218F	NM_014395.2	NP_055210.2	Q9UN19	DAPP1_HUMAN	dual adaptor of phosphotyrosine and 3-phosphoinositides	218	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.			VQFDYSQERVNCFC -> MICNILCSFFCPIS (in Ref. 6). {ECO:0000305}.	protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|lung(4)	6				OV - Ovarian serous cystadenocarcinoma(123;7.04e-09)		CTGTACAATTCGATTATTCAC	0.308													C|||	1337	0.266973	0.4713	0.2363	5008	,	,		20193	0.1528		0.2565	False		,,,				2504	0.1411				p.F218F		Atlas-SNP	.											.	DAPP1	47	.	0			c.C654T						PASS	.	C		1438,2188		295,848,670	82.0	83.0	83.0		654	-0.8	1.0	4	dbSNP_107	83	1955,6193		228,1499,2347	no	coding-synonymous	DAPP1	NM_014395.2		523,2347,3017	TT,TC,CC		23.9936,39.658,28.8177		218/281	100784980	3393,8381	1813	4074	5887	SO:0001819	synonymous_variant	27071	exon7			ACAATTCGATTAT	AF186022	CCDS47112.1	4q25-q27	2013-02-14			ENSG00000070190	ENSG00000070190		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	16500	protein-coding gene	gene with protein product		605768				10432293	Standard	NM_014395		Approved	BAM32	uc003hvf.4	Q9UN19	OTTHUMG00000160974	ENST00000512369.1:c.654C>T	4.37:g.100784980C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	17	0.333333	NM_014395	Q8TCK5|Q9UHF2	Silent	SNP	ENST00000512369.1	37	CCDS47112.1																																																																																			C|0.705;T|0.295	0.295	strong		0.308	DAPP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363215.1		
FHAD1	114827	hgsc.bcm.edu	37	1	15616139	15616139	+	Missense_Mutation	SNP	G	G	A	rs486557	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:15616139G>A	ENST00000375998.4	+	3	545	c.545G>A	c.(544-546)cGc>cAc	p.R182H	FHAD1_ENST00000417793.1_Missense_Mutation_p.R182H|FHAD1_ENST00000375999.3_Missense_Mutation_p.R182H|FHAD1_ENST00000358897.4_Missense_Mutation_p.R182H			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	182										skin(1)|stomach(1)	2						GACGACGCCCGCAAGCCACCC	0.612													G|||	1042	0.208067	0.2073	0.2089	5008	,	,		16676	0.0417		0.326	False		,,,				2504	0.2587				p.R182H		Atlas-SNP	.											.	FHAD1	78	.	0			c.G545A						PASS	.						28.0	36.0	34.0					1																	15616139		692	1591	2283	SO:0001583	missense	114827	exon4			ACGCCCGCAAGCC	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.545G>A	1.37:g.15616139G>A	ENSP00000365166:p.Arg182His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	52	19	0.365385	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		473	0.21657509157509158	110	0.22357723577235772	100	0.27624309392265195	22	0.038461538461538464	241	0.3179419525065963	G	5.490	0.275364	0.10403	.	.	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998	T;T;T;T	0.46819	0.88;0.87;0.86;0.88	3.77	-7.54	0.01332	.	1.620530	0.04279	N	0.343560	T	0.00012	0.0000	N	0.02539	-0.55	0.50313	P	1.36000000000025E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.17228	-1.0376	9	0.36615	T	0.2	-1.7323	12.0544	0.53527	0.1394:0.6827:0.178:0.0	rs486557;rs3765352;rs52797627;rs60426766;rs486557	182	B1AJZ9	FHAD1_HUMAN	H	182	ENSP00000351770:R182H;ENSP00000407615:R182H;ENSP00000365167:R182H;ENSP00000365166:R182H	ENSP00000351770:R182H	R	+	2	0	FHAD1	15488726	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.847000	0.04331	-1.849000	0.01171	-1.154000	0.01816	CGC	G|0.777;A|0.223	0.223	strong		0.612	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
CYP27A1	1593	hgsc.bcm.edu	37	2	219677690	219677690	+	Silent	SNP	A	A	G	rs61733619	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:219677690A>G	ENST00000258415.4	+	5	1315	c.888A>G	c.(886-888)caA>caG	p.Q296Q		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	296					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cholestanetriol 26-monooxygenase activity (GO:0047749)|cholesterol 26-hydroxylase activity (GO:0031073)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(3)|urinary_tract(1)	26		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Chenodeoxycholic acid(DB06777)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Pegvisomant(DB00082)	TGGAGGCCCAACTGCAGGCAG	0.547													A|||	46	0.0091853	0.0015	0.0202	5008	,	,		22147	0.0		0.0258	False		,,,				2504	0.0041				p.Q296Q		Atlas-SNP	.											.	CYP27A1	52	.	0			c.A888G						PASS	.	A		28,4378	34.3+/-65.2	0,28,2175	79.0	81.0	81.0		888	-1.5	0.2	2	dbSNP_129	81	200,8400	86.1+/-148.5	7,186,4107	no	coding-synonymous	CYP27A1	NM_000784.3		7,214,6282	GG,GA,AA		2.3256,0.6355,1.753		296/532	219677690	228,12778	2203	4300	6503	SO:0001819	synonymous_variant	1593	exon5			GGCCCAACTGCAG	BC017044	CCDS2423.1	2q35	2013-09-19	2003-01-14		ENSG00000135929	ENSG00000135929		"""Cytochrome P450s"""	2605	protein-coding gene	gene with protein product	"""cerebrotendinous xanthomatosis"""	606530	"""cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1"""	CYP27		2019602	Standard	NM_000784		Approved	CTX, CP27	uc002viz.4	Q02318	OTTHUMG00000048238	ENST00000258415.4:c.888A>G	2.37:g.219677690A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	137	53	0.386861	NM_000784	A8K303|Q6LDB4|Q86YQ6	Silent	SNP	ENST00000258415.4	37	CCDS2423.1																																																																																			A|0.983;G|0.017	0.017	strong		0.547	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4		
TAS2R42	353164	hgsc.bcm.edu	37	12	11338669	11338669	+	Missense_Mutation	SNP	C	C	T	rs1669412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11338669C>T	ENST00000334266.1	-	1	874	c.875G>A	c.(874-876)cGa>cAa	p.R292Q		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	292			R -> Q (in dbSNP:rs1669412).		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			AGCTGTCTGTCGCAGCTTGCT	0.408													C|||	1102	0.220048	0.2474	0.2305	5008	,	,		18104	0.1944		0.2167	False		,,,				2504	0.2055				p.R292Q	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.G875A						PASS	.	C	GLN/ARG	1067,3339	386.3+/-326.1	137,793,1273	76.0	71.0	73.0		875	2.2	0.0	12	dbSNP_89	73	2041,6559	356.6+/-330.4	248,1545,2507	yes	missense	TAS2R42	NM_181429.1	43	385,2338,3780	TT,TC,CC		23.7326,24.217,23.8967	probably-damaging	292/315	11338669	3108,9898	2203	4300	6503	SO:0001583	missense	353164	exon1			GTCTGTCGCAGCT	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.875G>A	12.37:g.11338669C>T	ENSP00000334050:p.Arg292Gln	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	37	CCDS31747.1	491	0.22481684981684982	114	0.23170731707317074	77	0.212707182320442	126	0.2202797202797203	174	0.22955145118733508	C	15.20	2.763624	0.49574	0.24217	0.237326	ENSG00000186136	ENST00000334266	T	0.01025	5.43	4.02	2.17	0.27698	.	0.165147	0.40064	N	0.001188	T	0.00012	0.0000	M	0.80028	2.48	0.80722	P	0.0	D	0.89917	1.0	D	0.80764	0.994	T	0.43814	-0.9368	9	0.72032	D	0.01	.	6.581	0.22594	0.0:0.7685:0.0:0.2315	rs1669412	292	Q7RTR8	T2R42_HUMAN	Q	292	ENSP00000334050:R292Q	ENSP00000334050:R292Q	R	-	2	0	TAS2R42	11229936	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.018000	0.13422	0.318000	0.23185	-0.145000	0.13849	CGA	C|0.762;T|0.238	0.238	strong		0.408	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429	
IL32	9235	hgsc.bcm.edu	37	16	3119167	3119167	+	Silent	SNP	T	T	C	rs34184287	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3119167T>C	ENST00000534507.1	+	6	727	c.516T>C	c.(514-516)gtT>gtC	p.V172V	IL32_ENST00000396887.3_Intron|IL32_ENST00000549213.1_Intron|RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000552356.1_Silent_p.V106V|IL32_ENST00000526464.2_Silent_p.V126V|IL32_ENST00000551513.1_Silent_p.V163V|IL32_ENST00000530538.2_Silent_p.V126V|IL32_ENST00000008180.9_Silent_p.V106V|IL32_ENST00000533097.2_Silent_p.V126V|IL32_ENST00000440815.3_Silent_p.V126V|IL32_ENST00000325568.5_Silent_p.V126V|IL32_ENST00000525643.2_Silent_p.V126V|IL32_ENST00000552664.1_Silent_p.V126V|IL32_ENST00000396890.2_Silent_p.V172V|IL32_ENST00000548652.1_Silent_p.V117V|IL32_ENST00000528163.2_Silent_p.V126V|IL32_ENST00000529550.1_Silent_p.V126V|IL32_ENST00000529699.1_Silent_p.V106V|IL32_ENST00000382213.3_Silent_p.V117V|IL32_ENST00000548246.1_Silent_p.V86V|IL32_ENST00000444393.3_Silent_p.V126V|IL32_ENST00000552936.1_Silent_p.V150V|IL32_ENST00000548476.1_Silent_p.V172V|IL32_ENST00000530890.1_Silent_p.V106V|IL32_ENST00000551122.1_Intron|IL32_ENST00000531965.1_Silent_p.V116V			P24001	IL32_HUMAN	interleukin 32	172					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						GGCACGGGGTTCTGGCCTGGG	0.597													T|||	1775	0.354433	0.2307	0.366	5008	,	,		18195	0.3839		0.4046	False		,,,				2504	0.4315				p.V126V		Atlas-SNP	.											.	IL32	32	.	0			c.T378C						PASS	.						21.0	25.0	24.0					16																	3119167		2192	4276	6468	SO:0001819	synonymous_variant	9235	exon7			CGGGGTTCTGGCC	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.516T>C	16.37:g.3119167T>C		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	257	122	0.474708	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Silent	SNP	ENST00000534507.1	37																																																																																				T|0.235;C|0.765	0.765	strong		0.597	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
CPSF3L	54973	hgsc.bcm.edu	37	1	1249187	1249187	+	Silent	SNP	G	G	A	rs12142199	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1249187G>A	ENST00000435064.1	-	9	964	c.882C>T	c.(880-882)ttC>ttT	p.F294F	CPSF3L_ENST00000545578.1_Silent_p.F265F|CPSF3L_ENST00000419704.1_Silent_p.F193F|CPSF3L_ENST00000540437.1_Silent_p.F300F|CPSF3L_ENST00000421495.2_Silent_p.F36F|CPSF3L_ENST00000450926.2_Silent_p.F272F|CPSF3L_ENST00000462432.1_5'UTR|CPSF3L_ENST00000411962.1_Silent_p.F196F	NM_001256460.1|NM_017871.5	NP_001243389.1|NP_060341.2	Q5TA45	INT11_HUMAN	cleavage and polyadenylation specific factor 3-like	294					snRNA processing (GO:0016180)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|integrator complex (GO:0032039)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(3)	13	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(86;4.35e-21)|Colorectal(212;0.000166)|COAD - Colon adenocarcinoma(227;0.000196)|Kidney(185;0.00235)|BRCA - Breast invasive adenocarcinoma(365;0.00255)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0349)|Lung(427;0.201)		TCCTCTGCACGAAAGTCTTGC	0.577													G|||	1553	0.310104	0.0651	0.4395	5008	,	,		21021	0.0188		0.8052	False		,,,				2504	0.3405				p.F300F		Atlas-SNP	.											.	CPSF3L	33	.	0			c.C900T						PASS	.	G		765,3639	308.6+/-290.6	65,635,1502	196.0	147.0	163.0		882	-3.6	0.8	1	dbSNP_120	163	6861,1739	734.5+/-406.9	2748,1365,187	no	coding-synonymous	CPSF3L	NM_017871.4		2813,2000,1689	AA,AG,GG		20.2209,17.3706,41.3565		294/601	1249187	7626,5378	2202	4300	6502	SO:0001819	synonymous_variant	54973	exon11			CTGCACGAAAGTC	AL136813	CCDS21.1, CCDS57959.1, CCDS57960.1, CCDS57961.1, CCDS72678.1	1p36.33	2008-02-05			ENSG00000127054	ENSG00000127054			26052	protein-coding gene	gene with protein product	"""integrator complex subunit 11"""	611354				15684398, 16239144	Standard	NM_001256456		Approved	FLJ20542, RC-68, CPSF73L, INT11, INTS11	uc001aee.2	Q5TA45	OTTHUMG00000003330	ENST00000435064.1:c.882C>T	1.37:g.1249187G>A		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	175	174	0.994286	NM_001256456	A8K5S2|B3KPR3|B4DM87|G3V1S5|Q5TA46|Q5TA48|Q5TA52|Q5TA53|Q5TA54|Q7L3D7|Q96HY1|Q9BW36|Q9H0F9|Q9H8R5|Q9HAA6|Q9NWX9	Silent	SNP	ENST00000435064.1	37	CCDS21.1																																																																																			G|0.517;A|0.483	0.483	strong		0.577	CPSF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009360.2	NM_017871	
ANKH	56172	hgsc.bcm.edu	37	5	14741984	14741984	+	Silent	SNP	T	T	C	rs2288474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:14741984T>C	ENST00000284268.6	-	8	1293	c.963A>G	c.(961-963)gcA>gcG	p.A321A	ANKH_ENST00000503939.1_5'UTR|ANKH_ENST00000535119.1_Silent_p.A123A	NM_054027.4	NP_473368.1	Q9HCJ1	ANKH_HUMAN	ANKH inorganic pyrophosphate transport regulator	321					locomotory behavior (GO:0007626)|regulation of bone mineralization (GO:0030500)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	inorganic diphosphate transmembrane transporter activity (GO:0030504)|inorganic phosphate transmembrane transporter activity (GO:0005315)|phosphate ion transmembrane transporter activity (GO:0015114)	p.A321A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	29						TGATGTGGGCTGCCGTGACTG	0.512													C|||	420	0.0838658	0.0794	0.1441	5008	,	,		17110	0.121		0.0427	False		,,,				2504	0.0511				p.A321A		Atlas-SNP	.											ANKH,NS,carcinoma,0,1	ANKH	64	1	1	Substitution - coding silent(1)	stomach(1)	c.A963G						PASS	.	C		373,4033	792.2+/-415.1	14,345,1844	169.0	128.0	142.0		963	-10.8	0.0	5	dbSNP_100	142	385,8215	802.2+/-407.3	9,367,3924	no	coding-synonymous	ANKH	NM_054027.4		23,712,5768	CC,CT,TT		4.4767,8.4657,5.8281		321/493	14741984	758,12248	2203	4300	6503	SO:0001819	synonymous_variant	56172	exon8			GTGGGCTGCCGTG	AF274753	CCDS3885.1	5p15.2	2013-06-19	2013-06-19		ENSG00000154122	ENSG00000154122			15492	protein-coding gene	gene with protein product		605145	"""ankylosis, progressive (mouse) homolog"", ""craniometaphyseal dysplasia, Jackson type (dominant)"", ""ankylosis, progressive homolog (mouse)"""	CCAL2, CMDJ		10894769, 12297989, 11326338	Standard	NM_054027		Approved	HANK, ANK, CPPDD	uc003jfm.4	Q9HCJ1	OTTHUMG00000090539	ENST00000284268.6:c.963A>G	5.37:g.14741984T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	148	67	0.452703	NM_054027	B2RCA7|B3KMG4|D3DTD4|Q9NQW2	Silent	SNP	ENST00000284268.6	37	CCDS3885.1																																																																																			T|0.932;C|0.068	0.068	strong		0.512	ANKH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207063.1	NM_054027	
LRIG1	26018	hgsc.bcm.edu	37	3	66434668	66434668	+	Silent	SNP	G	G	A	rs34993786	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:66434668G>A	ENST00000273261.3	-	14	2342	c.1818C>T	c.(1816-1818)caC>caT	p.H606H	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.H630H	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	606	Ig-like C2-type 2.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TGGTTATGTCGTGGGGCGTTT	0.547													G|||	68	0.0135783	0.003	0.0159	5008	,	,		17720	0.001		0.0437	False		,,,				2504	0.0082				p.H606H		Atlas-SNP	.											.	LRIG1	138	.	0			c.C1818T						PASS	.	G		34,4372	39.2+/-71.8	0,34,2169	230.0	222.0	225.0		1818	-12.3	0.0	3	dbSNP_126	225	389,8211	126.7+/-185.1	9,371,3920	no	coding-synonymous	LRIG1	NM_015541.2		9,405,6089	AA,AG,GG		4.5233,0.7717,3.2523		606/1094	66434668	423,12583	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon14			TATGTCGTGGGGC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1818C>T	3.37:g.66434668G>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	223	82	0.367713	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			A|0.031;C|0.000;G|0.969	0.031	strong		0.547	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
MIS18BP1	55320	hgsc.bcm.edu	37	14	45711340	45711340	+	Missense_Mutation	SNP	G	G	C	rs34168608	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:45711340G>C	ENST00000310806.4	-	4	1498	c.1040C>G	c.(1039-1041)cCa>cGa	p.P347R	MIS18BP1_ENST00000492652.1_5'UTR	NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	347			P -> R (in dbSNP:rs34168608).		CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						ATGAAGTCTTGGTGTTGCAAG	0.353													G|||	20	0.00399361	0.0	0.0086	5008	,	,		18273	0.0		0.0129	False		,,,				2504	0.001				p.P347R		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.C1040G						PASS	.	G	ARG/PRO	18,4388	25.3+/-52.1	0,18,2185	93.0	96.0	95.0		1040	4.8	0.7	14	dbSNP_126	95	118,8482	62.8+/-124.8	1,116,4183	yes	missense	MIS18BP1	NM_018353.4	103	1,134,6368	CC,CG,GG		1.3721,0.4085,1.0457	probably-damaging	347/1133	45711340	136,12870	2203	4300	6503	SO:0001583	missense	55320	exon4			AGTCTTGGTGTTG	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"""kinetochore null 2 homolog (C. elegans)"""		"""chromosome 14 open reading frame 106"""	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1040C>G	14.37:g.45711340G>C	ENSP00000309790:p.Pro347Arg	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	10	0.004578754578754579	0	0.0	4	0.011049723756906077	0	0.0	6	0.0079155672823219	G	18.52	3.640752	0.67244	0.004085	0.013721	ENSG00000129534	ENST00000310806	T	0.65732	-0.17	4.83	4.83	0.62350	.	0.067290	0.64402	D	0.000013	T	0.62417	0.2426	L	0.36672	1.1	0.43088	D	0.994755	D	0.76494	0.999	D	0.69142	0.962	T	0.70766	-0.4783	10	0.87932	D	0	-2.823	13.7618	0.62971	0.0:0.0:1.0:0.0	rs34168608	347	Q6P0N0	M18BP_HUMAN	R	347	ENSP00000309790:P347R	ENSP00000309790:P347R	P	-	2	0	MIS18BP1	44781090	1.000000	0.71417	0.681000	0.30009	0.945000	0.59286	4.904000	0.63279	2.383000	0.81215	0.591000	0.81541	CCA	G|0.991;C|0.009	0.009	strong		0.353	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
CEACAM4	1089	hgsc.bcm.edu	37	19	42132314	42132314	+	Missense_Mutation	SNP	G	G	C	rs1126454	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:42132314G>C	ENST00000221954.2	-	2	195	c.85C>G	c.(85-87)Cac>Gac	p.H29D	CEACAM4_ENST00000600925.1_Missense_Mutation_p.H29D	NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	29			H -> D (in dbSNP:rs1126454). {ECO:0000269|PubMed:2050678}.			integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						GTGGGCGGGTGCCAGAAGGTT	0.517													C|||	3053	0.609625	0.4599	0.4669	5008	,	,		15995	0.8919		0.5417	False		,,,				2504	0.6922				p.H29D		Atlas-SNP	.											.	CEACAM4	42	.	0			c.C85G						PASS	.	C	ASP/HIS	2085,2321	593.8+/-388.1	492,1101,610	58.0	61.0	60.0		85	0.7	0.0	19	dbSNP_86	60	4402,4198	565.8+/-388.6	1139,2124,1037	yes	missense	CEACAM4	NM_001817.2	81	1631,3225,1647	CC,CG,GG		48.814,47.3218,49.877	benign	29/245	42132314	6487,6519	2203	4300	6503	SO:0001583	missense	1089	exon2			GCGGGTGCCAGAA	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"""Immunoglobulin superfamily / V-set domain containing"""	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.85C>G	19.37:g.42132314G>C	ENSP00000221954:p.His29Asp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	37	CCDS33033.1	1311	0.6002747252747253	218	0.44308943089430897	169	0.46685082872928174	500	0.8741258741258742	424	0.5593667546174143	C	3.674	-0.066967	0.07273	0.473218	0.51186	ENSG00000105352	ENST00000221954	T	0.01139	5.28	1.76	0.701	0.18104	.	.	.	.	.	T	0.00012	0.0000	N	0.04355	-0.22	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04203	-1.0969	8	0.44086	T	0.13	.	2.3678	0.04323	0.0:0.2005:0.304:0.4955	rs1126454;rs3815381;rs17266713;rs1126454	29;29	E7EMX3;O75871	.;CEAM4_HUMAN	D	29	ENSP00000221954:H29D	ENSP00000221954:H29D	H	-	1	0	CEACAM4	46824154	0.010000	0.17322	0.023000	0.16930	0.075000	0.17131	-0.344000	0.07780	-0.213000	0.10094	-0.980000	0.02579	CAC	G|0.462;C|0.537	0.537	strong		0.517	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49379167	49379167	+	Silent	SNP	C	C	T	rs386810065|rs524	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49379167C>T	ENST00000200453.5	+	3	2231	c.1962C>T	c.(1960-1962)gcC>gcT	p.A654A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	654					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		AAGCTGTGGCCACACCTTCCC	0.587													C|||	1786	0.356629	0.5764	0.2896	5008	,	,		15979	0.1984		0.2803	False		,,,				2504	0.3487				p.A654A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.C1962T						PASS	.	C		2270,2136	590.6+/-387.4	567,1136,500	85.0	83.0	83.0		1962	2.1	0.0	19	dbSNP_36	83	2469,6131	402.4+/-347.5	352,1765,2183	no	coding-synonymous	PPP1R15A	NM_014330.3		919,2901,2683	TT,TC,CC		28.7093,48.4793,36.437		654/675	49379167	4739,8267	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon3			TGTGGCCACACCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1962C>T	19.37:g.49379167C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			C|0.647;T|0.353	0.353	strong		0.587	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
PRMT8	56341	hgsc.bcm.edu	37	12	3701464	3701464	+	Silent	SNP	G	G	A	rs34000611	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:3701464G>A	ENST00000382622.3	+	9	1437	c.1047G>A	c.(1045-1047)cgG>cgA	p.R349R	PRMT8_ENST00000452611.2_Silent_p.R340R|PRMT8_ENST00000261252.4_3'UTR	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	349	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(31;0.0109)|COAD - Colon adenocarcinoma(12;0.0264)			TCACTGTCCGGAGGGGGGAGG	0.547													G|||	516	0.103035	0.1218	0.0836	5008	,	,		19044	0.1052		0.1332	False		,,,				2504	0.0583				p.R349R		Atlas-SNP	.											PRMT8_ENST00000452611,NS,carcinoma,+1,2	PRMT8	97	2	0			c.G1047A						PASS	.	G		580,3826	258.9+/-262.7	37,506,1660	120.0	122.0	121.0		1047	1.1	1.0	12	dbSNP_126	121	1145,7455	236.2+/-268.5	81,983,3236	no	coding-synonymous	PRMT8	NM_019854.3		118,1489,4896	AA,AG,GG		13.314,13.1639,13.2631		349/395	3701464	1725,11281	2203	4300	6503	SO:0001819	synonymous_variant	56341	exon9			TGTCCGGAGGGGG	AF263539	CCDS8521.2, CCDS58200.1	12p13.3	2006-03-03	2006-02-16	2006-02-16	ENSG00000111218	ENSG00000111218		"""Protein arginine methyltransferases"""	5188	protein-coding gene	gene with protein product		610086	"""HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"", ""HMT1 hnRNP methyltransferase-like 4 (S. cerevisiae)"""	HRMT1L3, HRMT1L4		16051612	Standard	NM_019854		Approved		uc001qmf.4	Q9NR22	OTTHUMG00000128493	ENST00000382622.3:c.1047G>A	12.37:g.3701464G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	43	14	0.325581	NM_019854	B2RDP0|Q8TBJ8	Silent	SNP	ENST00000382622.3	37	CCDS8521.2																																																																																			G|0.881;A|0.119	0.119	strong		0.547	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026138	176026138	+	Missense_Mutation	SNP	T	T	A	rs142779818|rs550332435|rs201635586|rs371149640|rs386695335	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176026138T>A	ENST00000303991.4	-	2	875	c.698A>T	c.(697-699)gAg>gTg	p.E233V		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	233				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAGGATCCTCCTTCCTCGG	0.488																																					p.E233V		Atlas-SNP	.											.	GPRIN1	77	.	0			c.A698T						PASS	.						87.0	88.0	88.0					5																	176026138		2153	4218	6371	SO:0001583	missense	114787	exon2			GGATCCTCCTTCC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.698A>T	5.37:g.176026138T>A	ENSP00000305839:p.Glu233Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	85	22	0.258824	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	37	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	T	12.30	1.897302	0.33535	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.09163	3.01	4.92	2.48	0.30137	.	0.222228	0.23132	N	0.051562	T	0.12561	0.0305	M	0.77103	2.36	0.09310	N	1	B	0.30146	0.27	B	0.31337	0.128	T	0.18429	-1.0337	10	0.40728	T	0.16	-7.1862	3.6069	0.08046	0.1625:0.1858:0.0:0.6517	.	233	Q7Z2K8	GRIN1_HUMAN	V	233	ENSP00000305839:E233V	ENSP00000305839:E233V	E	-	2	0	GPRIN1	175958744	0.024000	0.19004	0.794000	0.32065	0.466000	0.32739	1.906000	0.39887	0.731000	0.32448	0.260000	0.18958	GAG	T|0.795;A|0.205	0.205	strong		0.488	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
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 GAIIx	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_ENST00000348911.6_Silent_p.L1488L|SBF1_ENST00000380817.3_Silent_p.L1513L|SBF1_ENST00000476293.1_5'Flank			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		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	56	35	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 GAIIx	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	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	46	25	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	
PPL	5493	hgsc.bcm.edu	37	16	4935636	4935636	+	Missense_Mutation	SNP	G	G	A	rs2075639	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4935636G>A	ENST00000345988.2	-	22	3109	c.3020C>T	c.(3019-3021)gCg>gTg	p.A1007V	PPL_ENST00000590782.2_Missense_Mutation_p.A1005V	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1007			A -> V (in dbSNP:rs2075639).		keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						GACCTCATCCGCCTGGGCCCT	0.697													G|||	598	0.119409	0.0061	0.1888	5008	,	,		17164	0.2242		0.0785	False		,,,				2504	0.1575				p.A1007V		Atlas-SNP	.											.	PPL	168	.	0			c.C3020T						PASS	.	G	VAL/ALA	108,4286	80.4+/-118.8	1,106,2090	76.0	79.0	78.0		3020	-2.7	0.0	16	dbSNP_96	78	701,7897	165.1+/-217.3	30,641,3628	yes	missense	PPL	NM_002705.4	64	31,747,5718	AA,AG,GG		8.1531,2.4579,6.2269	benign	1007/1757	4935636	809,12183	2197	4299	6496	SO:0001583	missense	5493	exon22			TCATCCGCCTGGG	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3020C>T	16.37:g.4935636G>A	ENSP00000340510:p.Ala1007Val	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	258	0.11813186813186813	7	0.014227642276422764	61	0.1685082872928177	132	0.23076923076923078	58	0.07651715039577836	G	10.45	1.354545	0.24512	0.024579	0.081531	ENSG00000118898	ENST00000345988	T	0.46063	0.88	4.89	-2.67	0.06059	.	0.297452	0.31531	N	0.007490	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	5.000000000032756E-6	B	0.29253	0.239	B	0.14023	0.01	T	0.09164	-1.0687	9	0.51188	T	0.08	.	3.0003	0.06011	0.1392:0.1079:0.2588:0.4941	rs2075639;rs52834399;rs57621226;rs2075639	1007	O60437	PEPL_HUMAN	V	1007	ENSP00000340510:A1007V	ENSP00000340510:A1007V	A	-	2	0	PPL	4875637	0.970000	0.33590	0.020000	0.16555	0.202000	0.24057	1.726000	0.38085	-0.515000	0.06479	0.484000	0.47621	GCG	G|0.915;A|0.085	0.085	strong		0.697	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
OR4L1	122742	hgsc.bcm.edu	37	14	20528207	20528207	+	Missense_Mutation	SNP	G	G	A	rs1958715	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20528207G>A	ENST00000315683.1	+	1	4	c.4G>A	c.(4-6)Gat>Aat	p.D2N		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	2			D -> N (in dbSNP:rs1958715).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		TGAGTAAATGGATCTTAAAAA	0.299													g|||	2688	0.536741	0.4902	0.5562	5008	,	,		17781	0.5734		0.3857	False		,,,				2504	0.7035				p.D2N		Atlas-SNP	.											.	OR4L1	98	.	0			c.G4A						PASS	.		ASN/ASP	2146,2260		521,1104,578	103.0	112.0	109.0		4	1.4	0.8	14	dbSNP_92	109	3457,5141		730,1997,1572	yes	missense	OR4L1	NM_001004717.1	23	1251,3101,2150	AA,AG,GG		40.207,48.7063,43.0867	possibly-damaging	2/313	20528207	5603,7401	2203	4299	6502	SO:0001583	missense	122742	exon1			TAAATGGATCTTA		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.4G>A	14.37:g.20528207G>A	ENSP00000319217:p.Asp2Asn	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_001004717	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	1083	0.4958791208791209	255	0.5182926829268293	192	0.5303867403314917	320	0.5594405594405595	316	0.41688654353562005	.	8.093	0.775042	0.16051	0.487063	0.40207	ENSG00000176246	ENST00000315683	T	0.03004	4.08	3.28	1.4	0.22301	.	0.569745	0.15717	N	0.248106	T	0.00012	0.0000	L	0.33245	0.995	0.39736	P	0.02832199999999996	B	0.09022	0.002	B	0.10450	0.005	T	0.20739	-1.0266	9	0.25751	T	0.34	.	6.4376	0.21831	0.1113:0.1873:0.7014:0.0	rs1958715;rs17126014;rs52801958;rs61492536;rs1958715	2	Q8NH43	OR4L1_HUMAN	N	2	ENSP00000319217:D2N	ENSP00000319217:D2N	D	+	1	0	OR4L1	19598047	0.000000	0.05858	0.786000	0.31890	0.504000	0.33889	-0.124000	0.10595	0.395000	0.25257	0.639000	0.83563	GAT	G|0.535;A|0.465	0.465	strong		0.299	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
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 GAIIx	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_ENST00000349097.3_Missense_Mutation_p.E940D|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.E940D|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395477.2_Missense_Mutation_p.E1328D	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	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	91	28	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	
ZFP2	80108	hgsc.bcm.edu	37	5	178358857	178358857	+	Silent	SNP	C	C	T	rs61744382	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178358857C>T	ENST00000361362.2	+	5	1073	c.543C>T	c.(541-543)acC>acT	p.T181T	ZFP2_ENST00000503510.2_Silent_p.T181T|ZFP2_ENST00000523286.1_Silent_p.T181T|ZFP2_ENST00000520301.1_Silent_p.T181T	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	181					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)		GAACTCACACCGGAGAGAAAC	0.398													C|||	212	0.0423323	0.0159	0.0648	5008	,	,		21720	0.0		0.1103	False		,,,				2504	0.0358				p.T181T		Atlas-SNP	.											.	ZFP2	70	.	0			c.C543T						PASS	.	C		131,4275	93.4+/-132.2	2,127,2074	50.0	49.0	50.0		543	3.5	1.0	5	dbSNP_129	50	905,7693	199.6+/-243.6	48,809,3442	no	coding-synonymous	ZFP2	NM_030613.2		50,936,5516	TT,TC,CC		10.5257,2.9732,7.9668		181/462	178358857	1036,11968	2203	4299	6502	SO:0001819	synonymous_variant	80108	exon5			TCACACCGGAGAG	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.543C>T	5.37:g.178358857C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Silent	SNP	ENST00000361362.2	37	CCDS4440.1																																																																																			C|0.925;T|0.075	0.075	strong		0.398	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613	
TNK1	8711	hgsc.bcm.edu	37	17	7286266	7286266	+	Silent	SNP	C	C	T	rs1554947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7286266C>T	ENST00000576812.1	+	2	390	c.21C>T	c.(19-21)tcC>tcT	p.S7S	TNK1_ENST00000311668.2_Silent_p.S7S|TNK1_ENST00000570896.1_Silent_p.S7S	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				AGGCTGGCTCCCTGTGGCTAC	0.557													.|||	1372	0.273962	0.0356	0.3934	5008	,	,		20569	0.4593		0.4056	False		,,,				2504	0.1851				p.S7S		Atlas-SNP	.											.	TNK1	31	.	0			c.C21T						PASS	.	C		409,3943		19,371,1786	53.0	57.0	56.0		21	2.6	0.9	17	dbSNP_88	56	3381,5181		662,2057,1562	no	coding-synonymous	TNK1	NM_003985.3		681,2428,3348	TT,TC,CC		39.4884,9.398,29.348		7/662	7286266	3790,9124	2176	4281	6457	SO:0001819	synonymous_variant	8711	exon2			TGGCTCCCTGTGG	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.21C>T	17.37:g.7286266C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_003985		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			C|0.631;T|0.369	0.369	strong		0.557	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	
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 GAIIx	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		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	108	28	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	
TMEM173	340061	hgsc.bcm.edu	37	5	138861078	138861078	+	Missense_Mutation	SNP	C	C	T	rs11554776	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:138861078C>T	ENST00000330794.4	-	3	545	c.212G>A	c.(211-213)cGc>cAc	p.R71H	TMEM173_ENST00000511850.1_5'UTR	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	71			R -> H (in dbSNP:rs11554776).		activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GTGGATGTGGCGCAGCTCCTC	0.617													C|||	1017	0.203075	0.0121	0.2781	5008	,	,		18966	0.4008		0.1471	False		,,,				2504	0.2618				p.R71H		Atlas-SNP	.											TMEM173,NS,carcinoma,0,1	TMEM173	19	1	0			c.G212A						scavenged	.	C	HIS/ARG	163,4243	103.8+/-142.4	5,153,2045	53.0	53.0	53.0		212	1.8	0.0	5	dbSNP_120	53	1200,7400	236.4+/-268.6	89,1022,3189	yes	missense	TMEM173	NM_198282.2	29	94,1175,5234	TT,TC,CC		13.9535,3.6995,10.4798	possibly-damaging	71/380	138861078	1363,11643	2203	4300	6503	SO:0001583	missense	340061	exon3			ATGTGGCGCAGCT		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.212G>A	5.37:g.138861078C>T	ENSP00000331288:p.Arg71His	Somatic	129	2	0.0155039		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	438	0.20054945054945056	11	0.022357723577235773	82	0.2265193370165746	232	0.40559440559440557	113	0.14907651715039577	C	4.677	0.125829	0.08931	0.036995	0.139535	ENSG00000184584	ENST00000330794;ENST00000510817	T;T	0.41758	0.99;0.99	5.58	1.84	0.25277	.	0.590726	0.19132	N	0.121905	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.13594	0.008	B	0.06405	0.002	T	0.43278	-0.9401	9	0.40728	T	0.16	-1.9834	3.65	0.08199	0.2713:0.4307:0.0:0.2979	rs11554776;rs11742049;rs52823365;rs57564432;rs11554776	71	Q86WV6	TM173_HUMAN	H	71	ENSP00000331288:R71H;ENSP00000427455:R71H	ENSP00000331288:R71H	R	-	2	0	TMEM173	138841262	0.000000	0.05858	0.028000	0.17463	0.331000	0.28603	-0.120000	0.10660	0.053000	0.16036	0.561000	0.74099	CGC	C|0.867;T|0.133	0.133	strong		0.617	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
TMCO3	55002	hgsc.bcm.edu	37	13	114175038	114175038	+	Missense_Mutation	SNP	G	G	A	rs7319493	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:114175038G>A	ENST00000434316.2	+	8	1692	c.1333G>A	c.(1333-1335)Gca>Aca	p.A445T	TMCO3_ENST00000474393.1_3'UTR|TMCO3_ENST00000375391.1_Intron	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	445			A -> T (in dbSNP:rs7319493). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)			NS(1)|endometrium(4)|large_intestine(9)|liver(1)|lung(8)|prostate(1)|stomach(1)	25	Lung NSC(43;0.0161)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0145)|all_epithelial(44;0.00286)|all_lung(25;0.0273)|Breast(118;0.0411)|Lung NSC(25;0.0983)	all cancers(43;0.0317)			GGGCGCCAGTGCATCTTCTAG	0.473													G|||	960	0.191693	0.205	0.3199	5008	,	,		16465	0.123		0.1302	False		,,,				2504	0.2168				p.A445T		Atlas-SNP	.											.	TMCO3	77	.	0			c.G1333A						PASS	.	G	THR/ALA	929,3477	354.9+/-312.8	100,729,1374	78.0	71.0	73.0		1333	-9.9	0.0	13	dbSNP_116	73	1256,7344	251.8+/-278.1	84,1088,3128	yes	missense	TMCO3	NM_017905.4	58	184,1817,4502	AA,AG,GG		14.6047,21.0849,16.7999	benign	445/678	114175038	2185,10821	2203	4300	6503	SO:0001583	missense	55002	exon8			GCCAGTGCATCTT	BC012564	CCDS9537.1	13q34	2008-02-05	2005-07-22	2005-07-22	ENSG00000150403	ENSG00000150403			20329	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 11"""	C13orf11			Standard	NM_017905		Approved	FLJ20623	uc001vtu.4	Q6UWJ1	OTTHUMG00000017389	ENST00000434316.2:c.1333G>A	13.37:g.114175038G>A	ENSP00000389399:p.Ala445Thr	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	69	16	0.231884	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	37	CCDS9537.1	349	0.15979853479853479	101	0.20528455284552846	95	0.26243093922651933	62	0.10839160839160839	91	0.12005277044854881	G	5.097	0.203455	0.09704	0.210849	0.146047	ENSG00000150403	ENST00000434316	T	0.15372	2.43	4.94	-9.87	0.00470	Cation/H+ exchanger (1);	0.637765	0.16438	N	0.214420	T	0.00012	0.0000	N	0.11818	0.18	0.46028	P	0.0011799999999999589	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.26430	-1.0103	9	0.13108	T	0.6	-11.3682	2.3263	0.04223	0.244:0.0853:0.3363:0.3343	rs7319493;rs60291985;rs7319493	445;445	Q6UWJ1;Q6UWJ1-2	TMCO3_HUMAN;.	T	445	ENSP00000389399:A445T	ENSP00000389399:A445T	A	+	1	0	TMCO3	113223039	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.505000	0.06367	-5.105000	0.00021	-2.375000	0.00234	GCA	G|0.835;A|0.165	0.165	strong		0.473	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
KRTAP12-4	386684	hgsc.bcm.edu	37	21	46074202	46074202	+	Silent	SNP	A	A	G	rs9984726	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46074202A>G	ENST00000391618.1	-	1	374	c.330T>C	c.(328-330)acT>acC	p.T110T	TSPEAR_ENST00000323084.4_Intron	NM_198698.1	NP_941971.1	P60329	KR124_HUMAN	keratin associated protein 12-4	110						keratin filament (GO:0045095)				lung(4)|ovary(1)|prostate(1)	6						CTCAGCAGCCAGTGGGGGTGC	0.617													G|||	3932	0.785144	0.9191	0.7493	5008	,	,		17808	0.6458		0.7624	False		,,,				2504	0.7965				p.T110T		Atlas-SNP	.											.	KRTAP12-4	10	.	0			c.T330C						PASS	.	G	,	3598,422		1616,366,28	27.0	33.0	31.0		,330	0.9	0.0	21	dbSNP_119	31	5942,2410		2151,1640,385	no	intron,coding-synonymous	TSPEAR,KRTAP12-4	NM_144991.2,NM_198698.1	,	3767,2006,413	GG,GA,AA		28.8554,10.4975,22.8904	,	,110/113	46074202	9540,2832	2010	4176	6186	SO:0001819	synonymous_variant	386684	exon1			GCAGCCAGTGGGG	AB076360	CCDS42963.1	21q22.3	2006-03-13			ENSG00000212933	ENSG00000212933		"""Keratin associated proteins"""	20532	protein-coding gene	gene with protein product							Standard	NM_198698		Approved	KRTAP12.4	uc002zfs.1	P60329	OTTHUMG00000057633	ENST00000391618.1:c.330T>C	21.37:g.46074202A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	144	60	0.416667	NM_198698	Q08AF5	Silent	SNP	ENST00000391618.1	37	CCDS42963.1																																																																																			A|0.264;G|0.736	0.736	strong		0.617	KRTAP12-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128036.1		
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 GAIIx	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	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	223	107	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	
MAPT	4137	hgsc.bcm.edu	37	17	44061036	44061036	+	Missense_Mutation	SNP	T	T	C	rs62063787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44061036T>C	ENST00000571987.1	+	5	866	c.866T>C	c.(865-867)gTa>gCa	p.V289A	MAPT_ENST00000334239.8_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.V289A|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.V289A|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.V289A|MAPT_ENST00000574436.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	289			V -> A (risk factor for PSNP1; dbSNP:rs62063787). {ECO:0000269|PubMed:10534245, ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GGGCCCAGTGTAGGGCGGGCC	0.617													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		16077	0.001		0.2406	False		,,,				2504	0.0613				p.V289A		Atlas-SNP	.											.	MAPT	135	.	0			c.T866C						PASS	.	C	ALA/VAL,,,,,,ALA/VAL,	227,4179	791.3+/-415.1	7,213,1983	41.0	46.0	44.0		866,,,,,,866,	-1.4	0.0	17	dbSNP_129	44	1928,6672	716.3+/-406.1	221,1486,2593	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	64,,,,,,64,	228,1699,4576	CC,CT,TT		22.4186,5.1521,16.5693	benign,,,,,,benign,	289/777,,,,,,289/759,	44061036	2155,10851	2203	4300	6503	SO:0001583	missense	4137	exon6			CCAGTGTAGGGCG	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.866T>C	17.37:g.44061036T>C	ENSP00000458742:p.Val289Ala	Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	0.533	-0.857132	0.02630	0.051521	0.224186	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.09723	2.95;2.95;2.95	4.68	-1.36	0.09085	.	1.284980	0.05582	N	0.573067	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43589	-0.9382	9	0.05620	T	0.96	1.7099	0.2163	0.00162	0.3062:0.2538:0.1395:0.3005	rs62063787	289;289	P10636-9;P10636	.;TAU_HUMAN	A	289	ENSP00000340820:V289A;ENSP00000262410:V289A;ENSP00000410838:V289A	ENSP00000262410:V289A	V	+	2	0	MAPT	41416873	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.211000	0.17474	-0.068000	0.12953	-1.163000	0.01768	GTA	T|0.849;C|0.151	0.151	strong		0.617	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
MYO3B	140469	hgsc.bcm.edu	37	2	171073887	171073887	+	Silent	SNP	G	G	A	rs2161916	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:171073887G>A	ENST00000408978.4	+	6	728	c.585G>A	c.(583-585)ccG>ccA	p.P195P	MYO3B_ENST00000409044.3_Silent_p.P195P|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Silent_p.P204P	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	195	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						TTGGCACCCCGTTCTGGATGG	0.433													A|||	2888	0.576677	0.6316	0.4179	5008	,	,		19832	0.5714		0.5636	False		,,,				2504	0.6339				p.P195P		Atlas-SNP	.											.	MYO3B	320	.	0			c.G585A						PASS	.	A	,,	2426,1418		753,920,249	226.0	221.0	222.0		585,585,585	-7.8	0.5	2	dbSNP_96	222	4542,3728		1261,2020,854	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	2014,2940,1103	AA,AG,GG		45.0786,36.8887,42.4798	,,	195/1315,195/1276,195/1342	171073887	6968,5146	1922	4135	6057	SO:0001819	synonymous_variant	140469	exon6			CACCCCGTTCTGG		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.585G>A	2.37:g.171073887G>A		Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	192	191	0.994792	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1	1227	0.5618131868131868	290	0.5894308943089431	170	0.4696132596685083	327	0.5716783216783217	440	0.5804749340369393	A	7.686	0.690037	0.15039	0.631113	0.549214	ENSG00000071909	ENST00000442690	.	.	.	6.06	-7.85	0.01192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999954	.	.	.	.	.	.	T	0.04178	-1.0971	3	.	.	.	.	12.0644	0.53580	0.1929:0.4715:0.3356:0.0	rs2161916;rs17496561;rs58706986;rs2161916	.	.	.	I	195	.	.	V	+	1	0	MYO3B	170782133	0.000000	0.05858	0.468000	0.27192	0.841000	0.47740	-1.854000	0.01664	-2.287000	0.00669	-0.254000	0.11334	GTT	G|0.433;A|0.567	0.567	strong		0.433	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
ZBTB3	79842	hgsc.bcm.edu	37	11	62521475	62521475	+	Silent	SNP	T	T	C	rs201229122|rs72929471	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:62521475T>C	ENST00000394807.3	-	1	185	c.60A>G	c.(58-60)cgA>cgG	p.R20R		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	20					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(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						GAGATCTTTTTCGCTCCCAGG	0.622													T|||	690	0.13778	0.0968	0.1556	5008	,	,		14457	0.0853		0.1938	False		,,,				2504	0.1769				p.R20R		Atlas-SNP	.											.	ZBTB3	47	.	0			c.A60G						PASS	.	T		534,3870	244.7+/-253.9	33,468,1701	99.0	88.0	92.0		60	1.4	0.1	11	dbSNP_130	92	1901,6697	336.2+/-321.7	221,1459,2619	no	coding-synonymous	ZBTB3	NM_024784.3		254,1927,4320	CC,CT,TT		22.1098,12.1253,18.7279		20/575	62521475	2435,10567	2202	4299	6501	SO:0001819	synonymous_variant	79842	exon1			TCTTTTTCGCTCC	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.60A>G	11.37:g.62521475T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_024784		Silent	SNP	ENST00000394807.3	37	CCDS8034.1																																																																																			T|0.821;C|0.179	0.179	strong		0.622	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
EIF2B5	8893	hgsc.bcm.edu	37	3	183860335	183860335	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183860335G>T	ENST00000273783.3	+	10	1612	c.1490G>T	c.(1489-1491)tGg>tTg	p.W497L	EIF2B5_ENST00000444495.1_Missense_Mutation_p.W497L	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	497					astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			GGCTACCTCTGGAAAGCTGCA	0.552																																					p.W497L		Atlas-SNP	.											EIF2B5,colon,carcinoma,-1,1	EIF2B5	62	1	0			c.G1490T						scavenged	.						48.0	49.0	49.0					3																	183860335		2203	4300	6503	SO:0001583	missense	8893	exon10			ACCTCTGGAAAGC	U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191			3261	protein-coding gene	gene with protein product		603945	"""eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)"""			8688466	Standard	NM_003907		Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000273783.3:c.1490G>T	3.37:g.183860335G>T	ENSP00000273783:p.Trp497Leu	Somatic	249	2	0.00803213		WXS	Illumina HiSeq	Phase_I	240	5	0.0208333	NM_003907	Q541Z1|Q96D04	Missense_Mutation	SNP	ENST00000273783.3	37	CCDS3252.1	.	.	.	.	.	.	.	.	.	.	g	25.4	4.635275	0.87760	.	.	ENSG00000145191	ENST00000273783;ENST00000444495;ENST00000544027	D;D	0.98937	-5.16;-5.25	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.99146	0.9705	M	0.81942	2.565	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.986;0.997	D	0.99525	1.0959	10	0.45353	T	0.12	.	19.8955	0.96956	0.0:0.0:1.0:0.0	.	497;497	E9PC74;Q13144	.;EI2BE_HUMAN	L	497;497;253	ENSP00000273783:W497L;ENSP00000409142:W497L	ENSP00000273783:W497L	W	+	2	0	EIF2B5	185343029	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	9.270000	0.95690	2.711000	0.92665	0.561000	0.74099	TGG	.	.	none		0.552	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1		
GIMAP7	168537	hgsc.bcm.edu	37	7	150217335	150217335	+	Silent	SNP	G	G	T	rs3735079	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150217335G>T	ENST00000313543.4	+	2	430	c.273G>T	c.(271-273)ggG>ggT	p.G91G		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	91	AIG1-type G.				GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCTGCCCAGGGCCCCATGCTA	0.547													G|||	549	0.109625	0.0416	0.1138	5008	,	,		19563	0.1855		0.1272	False		,,,				2504	0.1022				p.G91G		Atlas-SNP	.											.	GIMAP7	47	.	0			c.G273T						PASS	.	G		215,4191	130.6+/-167.2	2,211,1990	47.0	48.0	48.0		273	-6.0	0.8	7	dbSNP_107	48	1111,7489	231.2+/-265.3	78,955,3267	no	coding-synonymous	GIMAP7	NM_153236.3		80,1166,5257	TT,TG,GG		12.9186,4.8797,10.1953		91/301	150217335	1326,11680	2203	4300	6503	SO:0001819	synonymous_variant	168537	exon2			CCCAGGGCCCCAT	BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"""GTPases, IMAP"""	22404	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 7"""					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.273G>T	7.37:g.150217335G>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_153236		Silent	SNP	ENST00000313543.4	37	CCDS5903.1																																																																																			G|0.893;T|0.107	0.107	strong		0.547	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236	
MTMR11	10903	hgsc.bcm.edu	37	1	149906167	149906167	+	Missense_Mutation	SNP	T	T	G	rs41302101	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:149906167T>G	ENST00000439741.2	-	7	850	c.600A>C	c.(598-600)gaA>gaC	p.E200D	MTMR11_ENST00000361405.6_Missense_Mutation_p.E200D|MTMR11_ENST00000406732.3_Missense_Mutation_p.E172D|MTMR11_ENST00000492824.1_5'UTR|MTMR11_ENST00000369140.3_Missense_Mutation_p.E128D	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	200	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			TCTCCCAGTCTTCCGCTGTCT	0.567													T|||	122	0.024361	0.0008	0.0346	5008	,	,		19615	0.001		0.0875	False		,,,				2504	0.0082				p.E200D		Atlas-SNP	.											.	MTMR11	136	.	0			c.A600C						PASS	.	T	ASP/GLU,ASP/GLU	51,4355	52.9+/-88.7	0,51,2152	83.0	77.0	79.0		600,384	3.8	1.0	1	dbSNP_127	79	638,7962	164.3+/-216.7	33,572,3695	yes	missense,missense	MTMR11	NM_001145862.1,NM_181873.3	45,45	33,623,5847	GG,GT,TT		7.4186,1.1575,5.2976	benign,benign	200/710,128/641	149906167	689,12317	2203	4300	6503	SO:0001583	missense	10903	exon7			CCAGTCTTCCGCT	AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	24307	protein-coding gene	gene with protein product	"""cisplatin resistance associated"""					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.600A>C	1.37:g.149906167T>G	ENSP00000391668:p.Glu200Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Missense_Mutation	SNP	ENST00000439741.2	37	CCDS53360.1	91	0.041666666666666664	1	0.0020325203252032522	15	0.04143646408839779	1	0.0017482517482517483	74	0.09762532981530343	T	18.66	3.670978	0.67814	0.011575	0.074186	ENSG00000014914	ENST00000369140;ENST00000439741;ENST00000361405;ENST00000406732;ENST00000405710	D;D;T;D	0.90385	-2.66;-2.66;0.85;-2.66	6.07	3.81	0.43845	Myotubularin phosphatase domain (1);	0.354602	0.30890	N	0.008666	D	0.83538	0.5276	L	0.38838	1.175	0.34698	D	0.726433	P;P;D;D	0.62365	0.94;0.94;0.991;0.985	P;P;P;P	0.56563	0.546;0.546;0.801;0.637	T	0.81618	-0.0851	10	0.26408	T	0.33	.	4.2414	0.10650	0.1608:0.1327:0.0:0.7065	rs41302101	42;172;128;200	F8W8W0;A4FU01-6;A4FU01-4;A4FU01	.;.;.;MTMRB_HUMAN	D	128;200;200;172;42	ENSP00000358136:E128D;ENSP00000391668:E200D;ENSP00000354941:E200D;ENSP00000383948:E172D	ENSP00000354941:E200D	E	-	3	2	MTMR11	148172791	0.936000	0.31750	1.000000	0.80357	0.984000	0.73092	0.496000	0.22499	2.326000	0.78906	0.533000	0.62120	GAA	T|0.948;G|0.052	0.052	strong		0.567	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873	
USP45	85015	hgsc.bcm.edu	37	6	99894086	99894086	+	Missense_Mutation	SNP	C	C	G	rs41288947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:99894086C>G	ENST00000327681.6	-	14	2094	c.1562G>C	c.(1561-1563)aGa>aCa	p.R521T	USP45_ENST00000539675.1_Intron|USP45_ENST00000500704.2_Missense_Mutation_p.R521T|USP45_ENST00000369233.2_Missense_Mutation_p.R473T|USP45_ENST00000392738.2_Missense_Mutation_p.R201T	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	521	USP.		R -> T (in dbSNP:rs41288947). {ECO:0000269|PubMed:15489334}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		ACTACTGGATCTGAACAGCCC	0.488													C|||	1102	0.220048	0.1566	0.3386	5008	,	,		18812	0.0923		0.3171	False		,,,				2504	0.2536				p.R521T		Atlas-SNP	.											.	USP45	56	.	0			c.G1562C						PASS	.	C	THR/ARG	807,3599	323.7+/-298.2	81,645,1477	83.0	69.0	74.0		1562	4.2	0.0	6	dbSNP_127	74	2833,5767	446.1+/-361.2	481,1871,1948	yes	missense	USP45	NM_001080481.1	71	562,2516,3425	GG,GC,CC		32.9419,18.3159,27.9871	benign	521/815	99894086	3640,9366	2203	4300	6503	SO:0001583	missense	85015	exon14			CTGGATCTGAACA	AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"""Ubiquitin-specific peptidases"""	20080	protein-coding gene	gene with protein product			"""ubiquitin specific protease 45"""			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.1562G>C	6.37:g.99894086C>G	ENSP00000333376:p.Arg521Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Missense_Mutation	SNP	ENST00000327681.6	37	CCDS34501.1	492	0.22527472527472528	79	0.16056910569105692	121	0.3342541436464088	54	0.0944055944055944	238	0.31398416886543534	C	12.74	2.029739	0.35797	0.183159	0.329419	ENSG00000123552	ENST00000392738;ENST00000500704;ENST00000327681;ENST00000369233	T;T;T;T	0.17054	2.3;3.81;3.81;3.78	5.09	4.2	0.49525	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.629809	0.15993	N	0.234732	T	0.06735	0.0172	L	0.40543	1.245	0.38176	P	0.06051399999999996	P;P	0.39404	0.669;0.672	B;B	0.38225	0.265;0.268	T	0.20605	-1.0270	9	0.14656	T	0.56	.	15.0365	0.71751	0.0:0.7131:0.2869:0.0	rs41288947;rs62432293	521;201	Q70EL2;Q70EL2-3	UBP45_HUMAN;.	T	201;521;521;473	ENSP00000376495:R201T;ENSP00000424372:R521T;ENSP00000333376:R521T;ENSP00000358236:R473T	ENSP00000333376:R521T	R	-	2	0	USP45	100000807	0.004000	0.15560	0.002000	0.10522	0.079000	0.17450	1.774000	0.38573	1.320000	0.45209	0.655000	0.94253	AGA	C|0.737;G|0.263	0.263	strong		0.488	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
ZNF682	91120	hgsc.bcm.edu	37	19	20135066	20135066	+	Silent	SNP	G	G	T	rs61739376	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:20135066G>T	ENST00000397165.2	-	2	283	c.123C>A	c.(121-123)gtC>gtA	p.V41V	ZNF682_ENST00000596019.1_Silent_p.V41V|ZNF682_ENST00000397162.1_Silent_p.V9V|ZNF682_ENST00000358523.5_Silent_p.V9V|ZNF682_ENST00000595736.1_Intron|ZNF682_ENST00000597972.1_Silent_p.V47V|ZNF682_ENST00000593468.1_Silent_p.V41V|AC006539.1_ENST00000578235.1_RNA	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	41	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						CACCCAGAGAGACCAGGTTTC	0.393													g|||	460	0.091853	0.028	0.147	5008	,	,		15833	0.2093		0.0229	False		,,,				2504	0.089				p.V41V		Atlas-SNP	.											.	ZNF682	51	.	0			c.C123A						PASS	.	G	,	132,4258	89.2+/-127.9	2,128,2065	74.0	81.0	78.0		27,123	0.9	0.3	19	dbSNP_129	78	181,8415	80.4+/-143.0	1,179,4118	no	coding-synonymous,coding-synonymous	ZNF682	NM_001077349.1,NM_033196.2	,	3,307,6183	TT,TG,GG		2.1056,3.0068,2.4103	,	9/467,41/499	20135066	313,12673	2195	4298	6493	SO:0001819	synonymous_variant	91120	exon2			CAGAGAGACCAGG	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.123C>A	19.37:g.20135066G>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_033196	B3KU64|E9PFJ5|Q96JV9	Silent	SNP	ENST00000397165.2	37	CCDS42533.1																																																																																			G|0.937;T|0.063	0.063	strong		0.393	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
ACSM3	6296	hgsc.bcm.edu	37	16	20796387	20796387	+	Missense_Mutation	SNP	G	G	C	rs5716	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20796387G>C	ENST00000289416.5	+	8	1576	c.1101G>C	c.(1099-1101)aaG>aaC	p.K367N	ACSM3_ENST00000440284.2_Missense_Mutation_p.K367N|ACSM3_ENST00000450120.2_Missense_Mutation_p.K359N|RNU6-944P_ENST00000364023.1_RNA|ERI2_ENST00000300005.3_Intron|ACSM3_ENST00000567387.1_3'UTR	NM_005622.3	NP_005613.2	Q53FZ2	ACSM3_HUMAN	acyl-CoA synthetase medium-chain family member 3	367			K -> N (in dbSNP:rs5716). {ECO:0000269|PubMed:17278971, ECO:0000269|Ref.4}.		cholesterol homeostasis (GO:0042632)|fatty acid biosynthetic process (GO:0006633)|regulation of blood pressure (GO:0008217)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	21						GGAGAAACAAGACGGGCCTGG	0.418													G|||	465	0.0928514	0.0151	0.0519	5008	,	,		16439	0.2202		0.0706	False		,,,				2504	0.1186				p.K367N		Atlas-SNP	.											.	ACSM3	113	.	0			c.G1101C	GRCh37	CM070002	ACSM3	M	rs5716	PASS	.	G	ASN/LYS,,ASN/LYS	136,4266	97.6+/-136.3	4,128,2069	134.0	122.0	126.0		1101,,1101	2.1	0.1	16	dbSNP_52	126	772,7828	184.2+/-232.2	28,716,3556	yes	missense,intron,missense	ACSM3,ERI2	NM_005622.3,NM_080663.2,NM_202000.2	94,,94	32,844,5625	CC,CG,GG		8.9767,3.0895,6.9835	benign,,benign	367/587,,367/439	20796387	908,12094	2201	4300	6501	SO:0001583	missense	6296	exon8			AAACAAGACGGGC	D16350	CCDS10589.1, CCDS45435.1	16p13.11	2006-02-08	2005-09-08	2005-09-08	ENSG00000005187	ENSG00000005187		"""Acyl-CoA synthetase family"""	10522	protein-coding gene	gene with protein product		145505	"""SA (rat hypertension-associated) homolog"", ""SA hypertension-associated homolog (rat)"""	SAH		7843754, 7907320, 11470804	Standard	NM_005622		Approved	SA	uc002dhr.3	Q53FZ2	OTTHUMG00000131552	ENST00000289416.5:c.1101G>C	16.37:g.20796387G>C	ENSP00000289416:p.Lys367Asn	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_202000	O60363|Q13732|Q15425|Q7KYM6|Q9BUA2	Missense_Mutation	SNP	ENST00000289416.5	37	CCDS10589.1	182	0.08333333333333333	9	0.018292682926829267	12	0.03314917127071823	102	0.17832167832167833	59	0.07783641160949868	G	9.858	1.195592	0.22037	0.030895	0.089767	ENSG00000005187	ENST00000289416;ENST00000440284;ENST00000450120	T;T;T	0.42900	0.96;0.96;0.96	5.34	2.11	0.27256	AMP-dependent synthetase/ligase (1);	0.803410	0.11646	N	0.543268	T	0.00073	0.0002	L	0.31578	0.945	0.09310	P	0.9999999477389	B;B;B	0.33612	0.336;0.166;0.419	B;B;B	0.33121	0.158;0.102;0.133	T	0.15178	-1.0446	9	0.28530	T	0.3	-12.9705	6.8068	0.23782	0.2151:0.1283:0.6567:0.0	rs5716;rs52821460;rs56500245;rs5716	359;367;367	E7ETR5;Q53FZ2;Q53FZ2-2	.;ACSM3_HUMAN;.	N	367;367;359	ENSP00000289416:K367N;ENSP00000394565:K367N;ENSP00000395297:K359N	ENSP00000289416:K367N	K	+	3	2	ACSM3	20703888	0.006000	0.16342	0.127000	0.21898	0.854000	0.48673	0.010000	0.13242	0.747000	0.32809	0.655000	0.94253	AAG	G|0.919;C|0.081	0.081	strong		0.418	ACSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254414.2	NM_005622	
ZDHHC11	79844	hgsc.bcm.edu	37	5	843723	843723	+	Missense_Mutation	SNP	C	C	A	rs3863148		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:843723C>A	ENST00000283441.8	-	4	1003	c.620G>T	c.(619-621)aGg>aTg	p.R207M	ZDHHC11_ENST00000511539.1_5'UTR|ZDHHC11_ENST00000503758.2_5'Flank|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.R207M	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	207						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			ACCTTCATACCTGGGGTCCGT	0.657																																					p.R207M		Atlas-SNP	.											ZDHHC11_ENST00000424784,rectum,carcinoma,0,2	ZDHHC11	97	2	0			c.G620T						PASS	.						56.0	47.0	50.0					5																	843723		2201	4290	6491	SO:0001583	missense	79844	exon4			TCATACCTGGGGT	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.620G>T	5.37:g.843723C>A	ENSP00000283441:p.Arg207Met	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	379	93	0.245383	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	601	0.2751831501831502	211	0.42886178861788615	83	0.2292817679558011	121	0.21153846153846154	186	0.24538258575197888	t	11.12	1.543781	0.27563	.	.	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.25085	1.82;1.82	3.98	-2.98	0.05513	.	16.107500	0.01230	U	0.008323	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	B	0.06786	0.001	B	0.14023	0.01	T	0.44143	-0.9347	9	0.36615	T	0.2	0.0249	3.3426	0.07124	0.353:0.2826:0.0:0.3644	rs3863148;rs4993147	207	Q9H8X9	ZDH11_HUMAN	M	207	ENSP00000397719:R207M;ENSP00000283441:R207M	ENSP00000283441:R207M	R	-	2	0	ZDHHC11	896723	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.765000	0.04730	-1.644000	0.01517	-0.858000	0.03015	AGG	C|0.500;A|0.500	0.500	weak		0.657	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
OR51B6	390058	hgsc.bcm.edu	37	11	5373497	5373497	+	Missense_Mutation	SNP	G	G	C	rs7106330	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5373497G>C	ENST00000380219.1	+	1	760	c.760G>C	c.(760-762)Gtt>Ctt	p.V254L	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	254			V -> L (in dbSNP:rs7106330).		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)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCACTGTAGTTTGTCTGAC	0.453													G|||	528	0.105431	0.0303	0.1599	5008	,	,		23552	0.0754		0.1541	False		,,,				2504	0.1493				p.V254L		Atlas-SNP	.											.	OR51B6	53	.	0			c.G760C						PASS	.	G	LEU/VAL	241,4161	141.1+/-176.5	4,233,1964	239.0	212.0	221.0		760	4.0	0.8	11	dbSNP_116	221	1306,7288	258.6+/-282.2	117,1072,3108	yes	missense	OR51B6	NM_001004750.1	32	121,1305,5072	CC,CG,GG		15.1966,5.4748,11.9037	benign	254/313	5373497	1547,11449	2201	4297	6498	SO:0001583	missense	390058	exon1			ACTGTAGTTTGTC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.760G>C	11.37:g.5373497G>C	ENSP00000369568:p.Val254Leu	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	179	74	0.413408	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	261	0.11950549450549451	26	0.052845528455284556	57	0.1574585635359116	50	0.08741258741258741	128	0.16886543535620052	G	11.83	1.757108	0.31137	0.054748	0.151966	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.32023	1.47	4.89	3.98	0.46160	GPCR, rhodopsin-like superfamily (1);	0.278687	0.25453	N	0.030580	T	0.00039	0.0001	N	0.03000	-0.44	0.58432	P	1.999999999946489E-6	B	0.23249	0.082	B	0.29077	0.098	T	0.09885	-1.0654	9	0.59425	D	0.04	.	5.1329	0.14919	0.1815:0.1715:0.647:0.0	rs7106330;rs52837250;rs7106330	254	Q9H340	O51B6_HUMAN	L	253;254	ENSP00000369568:V254L	ENSP00000369568:V254L	V	+	1	0	OR51B6	5330073	0.000000	0.05858	0.793000	0.32043	0.887000	0.51463	-0.090000	0.11163	1.272000	0.44329	0.557000	0.71058	GTT	G|0.883;C|0.117	0.117	strong		0.453	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
DHDH	27294	hgsc.bcm.edu	37	19	49445817	49445817	+	Missense_Mutation	SNP	T	T	C	rs11666105	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49445817T>C	ENST00000221403.2	+	5	780	c.740T>C	c.(739-741)gTa>gCa	p.V247A	DHDH_ENST00000523250.1_Missense_Mutation_p.V108A|DHDH_ENST00000522614.1_Intron	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	247			V -> A (in dbSNP:rs11666105).		carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		AAGGGCATGGTACAGGTGAGG	0.612													C|||	2271	0.453474	0.6967	0.2954	5008	,	,		19234	0.5704		0.2058	False		,,,				2504	0.3712				p.V247A		Atlas-SNP	.											.	DHDH	35	.	0			c.T740C						PASS	.	C	ALA/VAL	2770,1636	497.6+/-363.9	892,986,325	53.0	48.0	50.0		740	2.5	0.7	19	dbSNP_120	50	1489,7111	745.4+/-407.3	130,1229,2941	yes	missense	DHDH	NM_014475.3	64	1022,2215,3266	CC,CT,TT		17.314,37.1312,32.7464	benign	247/335	49445817	4259,8747	2203	4300	6503	SO:0001583	missense	27294	exon5			GCATGGTACAGGT	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.740T>C	19.37:g.49445817T>C	ENSP00000221403:p.Val247Ala	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	903	0.41346153846153844	325	0.6605691056910569	94	0.2596685082872928	313	0.5472027972027972	171	0.22559366754617413	C	3.572	-0.087501	0.07097	0.628688	0.17314	ENSG00000104808	ENST00000221403;ENST00000523250	T;T	0.23552	1.9;1.9	4.67	2.52	0.30459	.	0.241349	0.41712	N	0.000836	T	0.00012	0.0000	N	0.03238	-0.38	0.22500	P	0.999045546	B	0.02656	0.0	B	0.06405	0.002	T	0.30060	-0.9991	9	0.49607	T	0.09	-9.8612	4.3945	0.11356	0.0:0.5637:0.1657:0.2706	rs11666105;rs52799598;rs61101818;rs11666105	247	Q9UQ10	DHDH_HUMAN	A	247;108	ENSP00000221403:V247A;ENSP00000428935:V108A	ENSP00000221403:V247A	V	+	2	0	DHDH	54137629	0.981000	0.34729	0.748000	0.31131	0.041000	0.13682	2.693000	0.47027	0.301000	0.22738	-0.684000	0.03749	GTA	T|0.634;C|0.366	0.366	strong		0.612	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
TAS2R20	259295	hgsc.bcm.edu	37	12	11149720	11149720	+	Missense_Mutation	SNP	A	A	G	rs10845280	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11149720A>G	ENST00000538986.1	-	1	754	c.755T>C	c.(754-756)tTt>tCt	p.F252S	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	252			F -> S (in dbSNP:rs10845280). {ECO:0000269|PubMed:15496549}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TCGCATCTTAAAATTCCAAAA	0.388													G|||	2118	0.422923	0.0651	0.3847	5008	,	,		19131	0.755		0.3817	False		,,,				2504	0.6339				p.F252S		Atlas-SNP	.											.	TAS2R20	17	.	0			c.T755C						PASS	.	G	SER/PHE	442,3964	211.5+/-231.7	19,404,1780	112.0	111.0	112.0		755	-2.3	0.0	12	dbSNP_120	112	3016,5584	464.9+/-366.4	544,1928,1828	yes	missense	TAS2R20	NM_176889.2	155	563,2332,3608	GG,GA,AA		35.0698,10.0318,26.5877	benign	252/310	11149720	3458,9548	2203	4300	6503	SO:0001583	missense	259295	exon1			ATCTTAAAATTCC	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.755T>C	12.37:g.11149720A>G	ENSP00000441624:p.Phe252Ser	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	121	46	0.380165	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	a	0.490	-0.875796	0.02550	0.100318	0.350698	ENSG00000255837	ENST00000538986	T	0.35421	1.31	2.49	-2.3	0.06785	.	1.140010	0.06894	N	0.804836	T	0.00012	0.0000	N	0.04203	-0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.36601	-0.9741	9	0.21540	T	0.41	.	5.6602	0.17664	0.4396:0.0:0.4277:0.1326	rs10845280;rs17743814;rs52818991;rs10845280	252	P59543	T2R20_HUMAN	S	252	ENSP00000441624:F252S	ENSP00000441624:F252S	F	-	2	0	TAS2R20	11040987	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.736000	0.01845	-1.545000	0.01719	-3.103000	0.00063	TTT	A|0.670;G|0.329	0.329	strong		0.388	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
FAM122B	159090	hgsc.bcm.edu	37	X	133923139	133923139	+	Silent	SNP	T	T	C	rs17317849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:133923139T>C	ENST00000370790.1	-	4	1180	c.252A>G	c.(250-252)caA>caG	p.Q84Q	FAM122B_ENST00000343004.5_Silent_p.Q103Q|FAM122B_ENST00000486347.1_Silent_p.Q84Q|FAM122B_ENST00000298090.6_Silent_p.Q103Q|FAM122B_ENST00000493333.1_5'UTR	NM_001166599.2|NM_145284.5	NP_001160071.1|NP_660327.2	Q7Z309	F122B_HUMAN	family with sequence similarity 122B	84										breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|skin(1)	6	Acute lymphoblastic leukemia(192;0.000127)					CATCCCATGATTGGCTTATCT	0.388													T|||	38	0.0100662	0.0008	0.0086	3775	,	,		14405	0.0		0.0298	False		,,,				2504	0.001				p.Q103Q		Atlas-SNP	.											.	FAM122B	20	.	0			c.A309G						PASS	.	T	,,,,	17,3818		0,16,1,1616,570	118.0	92.0	101.0		252,309,309,150,252	-11.6	0.1	X	dbSNP_123	101	185,6543		2,139,42,2287,1830	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FAM122B	NM_001166599.2,NM_001166600.2,NM_001170756.1,NM_001170757.1,NM_145284.5	,,,,	2,155,43,3903,2400	CC,CT,C,TT,T		2.7497,0.4433,1.9123	,,,,	84/248,103/242,103/267,50/190,84/249	133923139	202,10361	2203	4300	6503	SO:0001819	synonymous_variant	159090	exon5			CCATGATTGGCTT	BX538218	CCDS14643.1, CCDS55497.1, CCDS55498.1	Xq26.3	2008-02-05			ENSG00000156504	ENSG00000156504			30490	protein-coding gene	gene with protein product						12477932	Standard	NM_145284		Approved	DKFZp686L20116, RP11-308B5.5	uc004exq.3	Q7Z309	OTTHUMG00000022461	ENST00000370790.1:c.252A>G	X.37:g.133923139T>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	197	150	0.761421	NM_001170756	A8K902|Q6PIM2|Q6ZU47|Q6ZV64|Q6ZVE4|Q8TB75	Silent	SNP	ENST00000370790.1	37	CCDS55497.1																																																																																			0|0.003;C|0.018	0.018	strong		0.388	FAM122B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058382.1	NM_145284	
C1orf85	112770	hgsc.bcm.edu	37	1	156264000	156264000	+	Missense_Mutation	SNP	G	G	A	rs10908496	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156264000G>A	ENST00000362007.1	-	4	633	c.607C>T	c.(607-609)Cca>Tca	p.P203S	C1orf85_ENST00000482579.1_5'Flank	NM_001256604.1|NM_001256609.1|NM_144580.2	NP_001243533.1|NP_001243538.1|NP_653181.1	Q8WWB7	NCUG1_HUMAN	chromosome 1 open reading frame 85	203			P -> S (in dbSNP:rs10908496). {ECO:0000269|PubMed:15489334}.		intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(2)|skin(3)	14	Hepatocellular(266;0.158)					GGTTGGGCTGGTCGGCTGGAC	0.592													G|||	998	0.199281	0.0681	0.2738	5008	,	,		19636	0.2272		0.2694	False		,,,				2504	0.2229				p.P203S		Atlas-SNP	.											.	C1orf85	41	.	0			c.C607T						PASS	.	G	SER/PRO	423,3983	206.2+/-227.9	22,379,1802	42.0	43.0	43.0		607	4.6	0.8	1	dbSNP_120	43	2519,6081	408.6+/-349.5	381,1757,2162	yes	missense	C1orf85	NM_144580.1	74	403,2136,3964	AA,AG,GG		29.2907,9.6005,22.6203	probably-damaging	203/407	156264000	2942,10064	2203	4300	6503	SO:0001583	missense	112770	exon4			GGGCTGGTCGGCT	BC011575	CCDS1139.1, CCDS72947.1, CCDS72948.1, CCDS72949.1	1q22	2014-08-07			ENSG00000198715	ENSG00000198715			29436	protein-coding gene	gene with protein product	"""kidney lysosomal membrane protein"""					12975309, 18021396, 19489740	Standard	NM_144580		Approved	MGC31963, NCU-G1	uc001foh.4	Q8WWB7	OTTHUMG00000019789	ENST00000362007.1:c.607C>T	1.37:g.156264000G>A	ENSP00000354553:p.Pro203Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	57	22	0.385965	NM_001256608	A6NH16|B4DJN4|Q5SZX4|Q6UX96|Q8IV07|Q96F65	Missense_Mutation	SNP	ENST00000362007.1	37	CCDS1139.1	455	0.20833333333333334	33	0.06707317073170732	82	0.2265193370165746	135	0.23601398601398602	205	0.2704485488126649	G	11.35	1.612711	0.28712	0.096005	0.292907	ENSG00000198715	ENST00000362007;ENST00000368264	T;T	0.19806	2.12;2.12	5.53	4.59	0.56863	.	0.284991	0.32987	N	0.005403	T	0.16938	0.0407	M	0.67953	2.075	0.54753	P	1.799999999996249E-5	D;D	0.53312	0.959;0.959	P;P	0.51615	0.675;0.675	T	0.08764	-1.0706	9	0.12103	T	0.63	-0.8596	12.4594	0.55723	0.0:0.3244:0.6756:0.0	rs10908496;rs60798557;rs10908496	122;203	Q8WWB7-2;Q8WWB7	.;NCUG1_HUMAN	S	203;117	ENSP00000354553:P203S;ENSP00000357247:P117S	ENSP00000354553:P203S	P	-	1	0	C1orf85	154530624	0.890000	0.30428	0.777000	0.31699	0.989000	0.77384	1.928000	0.40104	1.277000	0.44412	0.462000	0.41574	CCA	G|0.796;A|0.204	0.204	strong		0.592	C1orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052108.1	NM_144580	
CCDC114	93233	hgsc.bcm.edu	37	19	48800338	48800338	+	Silent	SNP	A	A	G	rs7252988	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48800338A>G	ENST00000315396.7	-	14	2590	c.1908T>C	c.(1906-1908)tcT>tcC	p.S636S		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	636	Ser-rich.				outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		CGCTCGAATCAGACGCTGTGC	0.677													g|||	2327	0.464657	0.5068	0.4597	5008	,	,		15208	0.2619		0.66	False		,,,				2504	0.4192				p.S636S		Atlas-SNP	.											.	CCDC114	100	.	0			c.T1908C						PASS	.	C		2366,2040	564.1+/-381.3	627,1112,464	72.0	70.0	71.0		1908	-8.8	0.0	19	dbSNP_116	71	5731,2869	447.9+/-361.7	1919,1893,488	yes	coding-synonymous	CCDC114	NM_144577.3		2546,3005,952	GG,GA,AA		33.3605,46.3005,37.7441		636/671	48800338	8097,4909	2203	4300	6503	SO:0001819	synonymous_variant	93233	exon14			CGAATCAGACGCT	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.1908T>C	19.37:g.48800338A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	49	47	0.959184	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Silent	SNP	ENST00000315396.7	37	CCDS12714.2																																																																																			A|0.435;G|0.565	0.565	strong		0.677	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
BTNL8	79908	hgsc.bcm.edu	37	5	180338368	180338368	+	Missense_Mutation	SNP	A	A	G	rs386695827|rs2276995	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180338368A>G	ENST00000340184.4	+	3	633	c.427A>G	c.(427-429)Acg>Gcg	p.T143A	BTNL8_ENST00000511704.1_Missense_Mutation_p.T27A|BTNL8_ENST00000505126.1_5'UTR|Y_RNA_ENST00000410920.1_RNA|BTNL8_ENST00000533815.2_5'UTR|BTNL8_ENST00000231229.4_Missense_Mutation_p.T143A|BTNL8_ENST00000508408.1_Missense_Mutation_p.T143A|BTNL8_ENST00000400707.3_Missense_Mutation_p.T18A	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	143	Ig-like V-type 2.		T -> A (in dbSNP:rs2276995). {ECO:0000269|PubMed:15489334}.		immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATTTCCATCACGGGATATGT	0.527													G|||	2166	0.432508	0.6702	0.4236	5008	,	,		20380	0.3462		0.3757	False		,,,				2504	0.2648				p.T143A		Atlas-SNP	.											BTNL8,colon,carcinoma,-2,1	BTNL8	114	1	0			c.A427G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR,ALA/THR,,ALA/THR	2834,1572	658.7+/-400.4	925,984,294	248.0	272.0	264.0		427,79,427,52,,427	-5.4	0.0	5	dbSNP_100	264	3247,5345	485.0+/-371.5	625,1997,1674	yes	missense,missense,missense,missense,utr-5,missense	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	58,58,58,58,,58	1550,2981,1968	GG,GA,AA		37.791,35.6786,46.7841	benign,benign,benign,benign,,benign	143/501,27/385,143/341,18/376,,143/348	180338368	6081,6917	2203	4296	6499	SO:0001583	missense	79908	exon3			TCCATCACGGGAT	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.427A>G	5.37:g.180338368A>G	ENSP00000342197:p.Thr143Ala	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	176	174	0.988636	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	983	0.4500915750915751	338	0.6869918699186992	143	0.39502762430939226	204	0.35664335664335667	298	0.39313984168865435	a	7.914	0.737065	0.15574	0.643214	0.37791	ENSG00000113303	ENST00000231229;ENST00000340184;ENST00000400707;ENST00000508408;ENST00000511704	T;T;T;T;T	0.06371	3.31;3.31;3.31;3.31;3.31	3.86	-5.37	0.02681	.	.	.	.	.	T	0.00012	0.0000	N	0.25485	0.75	0.54753	P	1.4999999999987246E-5	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.26326	-1.0106	8	0.25751	T	0.34	.	6.8869	0.24208	0.5006:0.1261:0.3733:0.0	rs2276995;rs17704309;rs62406680;rs2276995	18;27;143;143;143	E9PG07;E9PEF6;F2Z2B2;A6NEX6;Q6UX41	.;.;.;.;BTNL8_HUMAN	A	143;143;18;143;27	ENSP00000231229:T143A;ENSP00000342197:T143A;ENSP00000383543:T18A;ENSP00000424585:T143A;ENSP00000425207:T27A	ENSP00000231229:T143A	T	+	1	0	BTNL8	180270974	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.743000	0.01834	-1.000000	0.03438	-2.568000	0.00172	ACG	A|0.529;G|0.471	0.471	strong		0.527	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
RNF20	56254	hgsc.bcm.edu	37	9	104309445	104309445	+	Silent	SNP	T	T	C	rs2273976	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:104309445T>C	ENST00000389120.3	+	8	1011	c.921T>C	c.(919-921)taT>taC	p.Y307Y	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	307					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		ATAAGGTGTATGGAGCGGGGA	0.413													T|||	551	0.110024	0.0847	0.1513	5008	,	,		20243	0.1111		0.1461	False		,,,				2504	0.0767				p.Y307Y		Atlas-SNP	.											.	RNF20	110	.	0			c.T921C						PASS	.	T		437,3969	209.8+/-230.5	17,403,1783	128.0	122.0	124.0		921	0.6	1.0	9	dbSNP_100	124	1389,7211	269.8+/-288.6	118,1153,3029	no	coding-synonymous	RNF20	NM_019592.5		135,1556,4812	CC,CT,TT		16.1512,9.9183,14.0397		307/976	104309445	1826,11180	2203	4300	6503	SO:0001819	synonymous_variant	56254	exon8			GGTGTATGGAGCG	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"""RING-type (C3HC4) zinc fingers"""	10062	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"""	607699	"""ring finger protein 20"""			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.921T>C	9.37:g.104309445T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	129	47	0.364341	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Silent	SNP	ENST00000389120.3	37	CCDS35084.1																																																																																			T|0.867;C|0.133	0.133	strong		0.413	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592	
RNF213	57674	hgsc.bcm.edu	37	17	78272294	78272294	+	Missense_Mutation	SNP	C	C	T	rs72849841	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78272294C>T	ENST00000582970.1	+	11	2329	c.2186C>T	c.(2185-2187)cCg>cTg	p.P729L	RNF213_ENST00000456466.1_Missense_Mutation_p.P729L|RNF213_ENST00000319921.4_Missense_Mutation_p.P729L|RNF213_ENST00000508628.2_Missense_Mutation_p.P778L	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	729					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			TCCTTCTCACCGTTCCGGGAA	0.572													c|||	570	0.113818	0.1997	0.0692	5008	,	,		17967	0.0149		0.1402	False		,,,				2504	0.1043				p.P729L		Atlas-SNP	.											RNF213_ENST00000456466,colon,carcinoma,-1,3	RNF213	766	3	0			c.C2186T						PASS	.	C	LEU/PRO,LEU/PRO	707,3699	295.6+/-283.7	56,595,1552	82.0	70.0	74.0		2333,2186	2.1	0.0	17	dbSNP_130	74	1182,7418	239.4+/-270.5	82,1018,3200	yes	missense,missense	RNF213	NM_020914.4,NM_020954.2	98,98	138,1613,4752	TT,TC,CC		13.7442,16.0463,14.5241	benign,benign	778/5257,729/1064	78272294	1889,11117	2203	4300	6503	SO:0001583	missense	57674	exon11			TCTCACCGTTCCG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.2186C>T	17.37:g.78272294C>T	ENSP00000464087:p.Pro729Leu	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	245	0.11217948717948718	112	0.22764227642276422	27	0.07458563535911603	9	0.015734265734265736	97	0.1279683377308707	c	1.845	-0.466542	0.04476	0.160463	0.137442	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T;T	0.14144	2.53;2.53	4.45	2.14	0.27477	.	0.990181	0.08196	N	0.982985	T	0.00012	0.0000	N	0.08118	0	0.51767	P	6.399999999995298E-5	B;B	0.23806	0.045;0.091	B;B	0.17098	0.017;0.017	T	0.42582	-0.9443	9	0.48119	T	0.1	-14.6717	10.3194	0.43756	0.4867:0.5133:0.0:0.0	.	729;729	Q9HCF4;Q9HCF4-2	ALO17_HUMAN;.	L	729;778;729;729	ENSP00000392123:P729L;ENSP00000324392:P729L	ENSP00000324392:P729L	P	+	2	0	RNF213	75886889	0.001000	0.12720	0.040000	0.18447	0.004000	0.04260	0.629000	0.24538	0.300000	0.22699	-0.280000	0.10049	CCG	C|0.869;T|0.131	0.131	strong		0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
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 GAIIx	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		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	35	13	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 GAIIx	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	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	103	51	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	
SMG6	23293	hgsc.bcm.edu	37	17	2186100	2186100	+	Silent	SNP	C	C	T	rs749240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2186100C>T	ENST00000263073.6	-	8	2552	c.2502G>A	c.(2500-2502)caG>caA	p.Q834Q	SMG6_ENST00000544865.1_Silent_p.Q803Q	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	834					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTTTCCGCCACTGGTCAGGGC	0.502													T|||	2135	0.426318	0.6914	0.3573	5008	,	,		22864	0.2371		0.3618	False		,,,				2504	0.3783				p.Q834Q	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.G2502A						PASS	.	T	,	2686,1720	517.8+/-369.5	821,1044,338	126.0	119.0	121.0		2409,2502	-10.5	0.2	17	dbSNP_86	121	3004,5596	664.9+/-402.2	542,1920,1838	no	coding-synonymous,coding-synonymous	SMG6	NM_001170957.1,NM_017575.4	,	1363,2964,2176	TT,TC,CC		34.9302,39.0377,43.749	,	803/1389,834/1420	2186100	5690,7316	2203	4300	6503	SO:0001819	synonymous_variant	23293	exon8			CCGCCACTGGTCA	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.2502G>A	17.37:g.2186100C>T		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	235	119	0.506383	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	37	CCDS11016.1																																																																																			C|0.573;N|0.001	.	strong		0.502	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
TADA2B	93624	hgsc.bcm.edu	37	4	7055796	7055796	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:7055796T>C	ENST00000310074.7	+	2	467	c.278T>C	c.(277-279)aTg>aCg	p.M93T	TADA2B_ENST00000512388.1_Missense_Mutation_p.M18T|TADA2B_ENST00000515646.1_Start_Codon_SNP_p.M1T	NM_152293.2	NP_689506.2	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2B	93	SANT. {ECO:0000255|PROSITE- ProRule:PRU00624}.				chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	SAGA-type complex (GO:0070461)|STAGA complex (GO:0030914)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	18						TAGGAAGATATGGCTGCCCAC	0.542																																					p.M93T		Atlas-SNP	.											TADA2B,colon,adenoma,0,1	TADA2B	29	1	0			c.T278C						scavenged	.						23.0	30.0	28.0					4																	7055796		2032	4163	6195	SO:0001583	missense	93624	exon2			AAGATATGGCTGC	AK026299	CCDS47007.1	4p16.1	2009-10-02			ENSG00000173011	ENSG00000173011			30781	protein-coding gene	gene with protein product		608790				12972612, 18936164	Standard	NM_152293		Approved	MGC21874	uc003gjw.4	Q86TJ2	OTTHUMG00000159983	ENST00000310074.7:c.278T>C	4.37:g.7055796T>C	ENSP00000308022:p.Met93Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	88	3	0.0340909	NM_152293	A0AUJ8|A4QMR7|B3KSN0|B3KU86|Q6MZG9	Missense_Mutation	SNP	ENST00000310074.7	37	CCDS47007.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.310990	0.40895	.	.	ENSG00000173011	ENST00000506692;ENST00000310074;ENST00000512388;ENST00000515646;ENST00000510704	T;T;T;T;T	0.45276	0.9;0.98;0.97;0.96;0.94	5.33	5.33	0.75918	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.000000	0.85682	D	0.000000	T	0.39226	0.1070	L	0.29908	0.895	0.58432	D	0.999998	P;P	0.41214	0.693;0.742	B;B	0.43728	0.219;0.429	T	0.38090	-0.9677	10	0.87932	D	0	-60.0988	15.2838	0.73810	0.0:0.0:0.0:1.0	.	18;93	Q86TJ2-2;Q86TJ2	.;TAD2B_HUMAN	T	1;93;18;1;1	ENSP00000422398:M1T;ENSP00000308022:M93T;ENSP00000423947:M18T;ENSP00000423181:M1T;ENSP00000425731:M1T	ENSP00000308022:M93T	M	+	2	0	TADA2B	7106697	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	7.262000	0.78410	2.024000	0.59613	0.459000	0.35465	ATG	.	.	none		0.542	TADA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358687.2	NM_152293	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274150	39274150	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39274150T>A	ENST00000391413.2	-	1	456	c.418A>T	c.(418-420)Agc>Tgc	p.S140C		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	140	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.S140C(2)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ctggagatgctgcagctgggg	0.672																																					p.S140C		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,5	KRTAP4-11	94	5	2	Substitution - Missense(2)	prostate(1)|kidney(1)	c.A418T						scavenged	.						8.0	13.0	12.0					17																	39274150		686	1587	2273	SO:0001583	missense	653240	exon1			AGATGCTGCAGCT	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.418A>T	17.37:g.39274150T>A	ENSP00000375232:p.Ser140Cys	Somatic	57	2	0.0350877		WXS	Illumina HiSeq	Phase_I	51	7	0.137255	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	6.114	0.389323	0.11581	.	.	ENSG00000212721	ENST00000391413	T	0.00832	5.64	3.95	-4.72	0.03269	.	.	.	.	.	T	0.00178	0.0005	N	0.00010	-3.035	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48139	-0.9061	9	0.02654	T	1	.	4.7994	0.13289	0.3484:0.2238:0.0:0.4278	.	140	Q9BYQ6	KR411_HUMAN	C	140	ENSP00000375232:S140C	ENSP00000375232:S140C	S	-	1	0	KRTAP4-11	36527676	0.000000	0.05858	0.000000	0.03702	0.829000	0.46940	0.038000	0.13862	-0.681000	0.05204	-0.924000	0.02725	AGC	.	.	none		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
LIMD1	8994	hgsc.bcm.edu	37	3	45637253	45637253	+	Silent	SNP	C	C	T	rs267237	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:45637253C>T	ENST00000273317.4	+	1	903	c.882C>T	c.(880-882)acC>acT	p.T294T	LIMD1_ENST00000465039.1_Intron|LIMD1_ENST00000440097.1_Silent_p.T294T	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	294					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		AGCCCAGGACCCCTTCTGTGT	0.632													C|||	3431	0.685104	0.5915	0.6542	5008	,	,		18786	0.9345		0.5497	False		,,,				2504	0.7157				p.T294T		Atlas-SNP	.											LIMD1,NS,carcinoma,0,1	LIMD1	34	1	0			c.C882T						PASS	.	C		2630,1776	636.1+/-396.5	788,1054,361	46.0	49.0	48.0		882	1.3	0.0	3	dbSNP_79	48	4934,3666	611.0+/-395.8	1430,2074,796	no	coding-synonymous	LIMD1	NM_014240.2		2218,3128,1157	TT,TC,CC		42.6279,40.3087,41.8422		294/677	45637253	7564,5442	2203	4300	6503	SO:0001819	synonymous_variant	8994	exon1			CAGGACCCCTTCT	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.882C>T	3.37:g.45637253C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Silent	SNP	ENST00000273317.4	37	CCDS2729.1																																																																																			C|0.394;T|0.606	0.606	strong		0.632	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240	
SHD	56961	hgsc.bcm.edu	37	19	4280186	4280186	+	Silent	SNP	C	C	T	rs10419363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4280186C>T	ENST00000543264.2	+	1	1589	c.126C>T	c.(124-126)ttC>ttT	p.F42F	SHD_ENST00000599689.1_Silent_p.F42F	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	42										breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCTGGACTTCGAGGACCCCT	0.677													C|||	1627	0.32488	0.2821	0.2565	5008	,	,		12837	0.4038		0.3549	False		,,,				2504	0.319				p.F42F		Atlas-SNP	.											.	SHD	33	.	0			c.C126T						PASS	.	C		1316,3088	397.4+/-330.4	194,928,1080	25.0	30.0	28.0		126	-3.0	1.0	19	dbSNP_119	28	2929,5669	429.2+/-356.1	500,1929,1870	no	coding-synonymous	SHD	NM_020209.3		694,2857,2950	TT,TC,CC		34.0661,29.8819,32.6488		42/341	4280186	4245,8757	2202	4299	6501	SO:0001819	synonymous_variant	56961	exon1			GGACTTCGAGGAC	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"""SH2 domain containing"""	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.126C>T	19.37:g.4280186C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_020209	Q96NC2	Silent	SNP	ENST00000543264.2	37	CCDS12125.1																																																																																			C|0.681;N|0.000	.	strong		0.677	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209	
ZNF587	84914	hgsc.bcm.edu	37	19	58371274	58371274	+	Silent	SNP	G	G	T	rs10405892	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58371274G>T	ENST00000339656.5	+	3	1676	c.1494G>T	c.(1492-1494)ggG>ggT	p.G498G	ZNF814_ENST00000597652.1_5'Flank|ZNF587_ENST00000419854.1_Silent_p.G455G|ZNF814_ENST00000595295.1_Intron|ZNF587_ENST00000423137.1_Silent_p.G497G|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	498					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(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		GTGAATGTGGGAAATCATTTC	0.408																																					p.G498G	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											ZNF587,NS,carcinoma,+2,1	ZNF587	53	1	0			c.G1494T						PASS	.						132.0	136.0	134.0					19																	58371274		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			ATGTGGGAAATCA	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1494G>T	19.37:g.58371274G>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	230	21	0.0913043	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			G|0.822;T|0.178	0.178	strong		0.408	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553784	140553784	+	Silent	SNP	C	C	T	rs7702701	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140553784C>T	ENST00000231137.3	+	1	1542	c.1368C>T	c.(1366-1368)taC>taT	p.Y456Y		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	456	Cadherin 5. {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(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AAACCTCCTACACCCTGTTTG	0.602													C|||	310	0.061901	0.202	0.0447	5008	,	,		17936	0.0		0.0119	False		,,,				2504	0.0				p.Y456Y		Atlas-SNP	.											.	PCDHB7	231	.	0			c.C1368T						PASS	.	C		780,3626	315.5+/-294.2	78,624,1501	143.0	136.0	138.0		1368	3.5	1.0	5	dbSNP_116	138	119,8481	62.4+/-124.4	0,119,4181	no	coding-synonymous	PCDHB7	NM_018940.2		78,743,5682	TT,TC,CC		1.3837,17.7031,6.9122		456/794	140553784	899,12107	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			CTCCTACACCCTG	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1368C>T	5.37:g.140553784C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			C|0.934;T|0.066	0.066	strong		0.602	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
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 GAIIx	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_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Silent_p.D26D	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		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	30	14	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 GAIIx	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		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	100	44	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 GAIIx	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	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	131	10	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 GAIIx	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	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	43	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	
SLC1A7	6512	hgsc.bcm.edu	37	1	53600078	53600078	+	Silent	SNP	A	A	G	rs3737989	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:53600078A>G	ENST00000371494.4	-	2	286	c.159T>C	c.(157-159)ccT>ccC	p.P53P	SLC1A7_ENST00000371491.4_Silent_p.P53P	NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	53					dicarboxylic acid transport (GO:0006835)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Colorectal(1306;0.234)		GGAGCTCTCCAGGGAACTGGA	0.507													A|||	942	0.188099	0.1293	0.3718	5008	,	,		20833	0.2907		0.159	False		,,,				2504	0.0613				p.P53P	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											.	SLC1A7	65	.	0			c.T159C						PASS	.	A		614,3792	266.5+/-267.3	40,534,1629	74.0	68.0	70.0		159	-3.0	1.0	1	dbSNP_107	70	1445,7155	274.2+/-291.1	103,1239,2958	no	coding-synonymous	SLC1A7	NM_006671.4		143,1773,4587	GG,GA,AA		16.8023,13.9355,15.8312		53/561	53600078	2059,10947	2203	4300	6503	SO:0001819	synonymous_variant	6512	exon2			CTCTCCAGGGAAC	U76362	CCDS574.1, CCDS72796.1, CCDS72797.1, CCDS72798.1	1p32.3	2013-05-22			ENSG00000162383	ENSG00000162383		"""Solute carriers"""	10945	protein-coding gene	gene with protein product		604471				9108121	Standard	NM_001287597		Approved	EAAT5	uc001cuy.3	O00341	OTTHUMG00000008937	ENST00000371494.4:c.159T>C	1.37:g.53600078A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Silent	SNP	ENST00000371494.4	37	CCDS574.1																																																																																			A|0.820;G|0.180	0.180	strong		0.507	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671	
KLK14	43847	hgsc.bcm.edu	37	19	51584951	51584951	+	Missense_Mutation	SNP	T	T	C	rs35287116	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51584951T>C	ENST00000156499.2	-	4	316	c.98A>G	c.(97-99)cAg>cGg	p.Q33R	KLK14_ENST00000391802.1_Missense_Mutation_p.Q33R			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	33			Q -> R (in dbSNP:rs35287116). {ECO:0000269|PubMed:15489334}.		epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		CTCTTGGCTCTGTGTCATGGC	0.567													N|||	2074	0.414137	0.6717	0.2781	5008	,	,		17406	0.0952		0.3966	False		,,,				2504	0.5092				p.Q33R	GBM(117;2161 2172 2448 22911)	Atlas-SNP	.											.	KLK14	49	.	0			c.A98G						PASS	.		ARG/GLN	2268,1724		697,874,425	32.0	33.0	33.0		98	3.5	0.8	19	dbSNP_126	33	3132,5144		653,1826,1659	yes	missense	KLK14	NM_022046.4	43	1350,2700,2084	CC,CT,TT		37.8444,43.1864,44.017	benign	33/268	51584951	5400,6868	1996	4138	6134	SO:0001583	missense	43847	exon4			TGGCTCTGTGTCA	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"""Kallikreins"""	6362	protein-coding gene	gene with protein product		606135	"""kallikrein 14"""			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.98A>G	19.37:g.51584951T>C	ENSP00000156499:p.Gln33Arg	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	84	31	0.369048	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Missense_Mutation	SNP	ENST00000156499.2	37	CCDS12823.2	747	0.34203296703296704	302	0.6138211382113821	111	0.30662983425414364	43	0.07517482517482517	291	0.3839050131926121	.	10.13	1.264708	0.23136	0.568136	0.378444	ENSG00000129437	ENST00000156499;ENST00000391802	D;D	0.92752	-3.1;-3.1	4.57	3.55	0.40652	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.48830	P	2.8600000000000847E-4	B	0.13145	0.007	B	0.09377	0.004	T	0.47923	-0.9079	8	0.23891	T	0.37	.	8.7263	0.34471	0.0:0.1015:0.0:0.8985	rs35287116;rs61747483	33	Q9P0G3	KLK14_HUMAN	R	33	ENSP00000156499:Q33R;ENSP00000375678:Q33R	ENSP00000156499:Q33R	Q	-	2	0	KLK14	56276763	0.590000	0.26815	0.771000	0.31576	0.682000	0.39822	0.745000	0.26259	0.373000	0.24621	-1.351000	0.01236	CAG	T|0.653;C|0.347	0.347	strong		0.567	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	
TMSB10	9168	hgsc.bcm.edu	37	2	85133216	85133216	+	Silent	SNP	G	G	A	rs7148	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85133216G>A	ENST00000233143.4	+	2	184	c.75G>A	c.(73-75)gaG>gaA	p.E25E		NM_021103.3	NP_066926.1	P63313	TYB10_HUMAN	thymosin beta 10	25					actin cytoskeleton organization (GO:0030036)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)	1						AGACGCAGGAGAAGAACACCC	0.562													G|||	222	0.0443291	0.0008	0.1196	5008	,	,		13919	0.0089		0.0577	False		,,,				2504	0.0726				p.E25E		Atlas-SNP	.											.	TMSB10	2	.	0			c.G75A						PASS	.	G		70,4336	61.7+/-98.7	1,68,2134	62.0	64.0	63.0		75	3.9	1.0	2	dbSNP_52	63	644,7956	164.2+/-216.6	20,604,3676	no	coding-synonymous	TMSB10	NM_021103.3		21,672,5810	AA,AG,GG		7.4884,1.5887,5.4898		25/45	85133216	714,12292	2203	4300	6503	SO:0001819	synonymous_variant	9168	exon2			GCAGGAGAAGAAC		CCDS1970.1	2p11.2	2008-02-25	2008-02-25		ENSG00000034510	ENSG00000034510			11879	protein-coding gene	gene with protein product		188399				3365256, 10487837	Standard	NM_021103		Approved	TB10	uc002sow.1	P63313	OTTHUMG00000130027	ENST00000233143.4:c.75G>A	2.37:g.85133216G>A		Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	111	83	0.747748	NM_021103	P13472|Q596K9	Silent	SNP	ENST00000233143.4	37	CCDS1970.1																																																																																			A|0.049;C|0.000;G|0.951	0.049	strong		0.562	TMSB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252302.2	NM_021103	
ALPK3	57538	hgsc.bcm.edu	37	15	85383640	85383640	+	Missense_Mutation	SNP	G	G	A	rs3803405	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:85383640G>A	ENST00000258888.5	+	5	1903	c.1736G>A	c.(1735-1737)gGg>gAg	p.G579E		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	579			G -> E (in dbSNP:rs3803405). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GCTGCACGGGGGCCTGGGTCC	0.672													G|||	691	0.137979	0.0159	0.1643	5008	,	,		14771	0.1329		0.2575	False		,,,				2504	0.1667				p.G579E		Atlas-SNP	.											.	ALPK3	289	.	0			c.G1736A						PASS	.	G	GLU/GLY	243,4159		11,221,1969	21.0	24.0	23.0		1736	2.7	0.1	15	dbSNP_107	23	2322,6274		315,1692,2291	yes	missense	ALPK3	NM_020778.4	98	326,1913,4260	AA,AG,GG		27.0126,5.5202,19.7338	probably-damaging	579/1908	85383640	2565,10433	2201	4298	6499	SO:0001583	missense	57538	exon5			CACGGGGGCCTGG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.1736G>A	15.37:g.85383640G>A	ENSP00000258888:p.Gly579Glu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	359	0.16437728937728938	7	0.014227642276422764	72	0.19889502762430938	81	0.14160839160839161	199	0.262532981530343	G	15.43	2.831448	0.50845	0.055202	0.270126	ENSG00000136383	ENST00000258888	T	0.58797	0.31	4.63	2.68	0.31781	.	0.701763	0.13520	N	0.381774	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.27997	0.197	B	0.28638	0.092	T	0.12915	-1.0529	9	0.42905	T	0.14	-25.0097	6.5307	0.22326	0.1001:0.1836:0.7163:0.0	rs3803405;rs60841515;rs3803405	579	Q96L96	ALPK3_HUMAN	E	579	ENSP00000258888:G579E	ENSP00000258888:G579E	G	+	2	0	ALPK3	83184644	0.004000	0.15560	0.136000	0.22124	0.102000	0.19082	0.123000	0.15708	1.163000	0.42636	-0.300000	0.09419	GGG	G|0.815;A|0.185	0.185	strong		0.672	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
KIF15	56992	hgsc.bcm.edu	37	3	44881909	44881909	+	Silent	SNP	A	A	G	rs76526953	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:44881909A>G	ENST00000326047.4	+	28	3530	c.3381A>G	c.(3379-3381)caA>caG	p.Q1127Q	KIF15_ENST00000425755.1_Silent_p.Q762Q	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1127					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		AAATGAGGCAACTAGAACATG	0.338													A|||	295	0.0589058	0.0696	0.098	5008	,	,		17908	0.0437		0.0567	False		,,,				2504	0.0348				p.Q1127Q		Atlas-SNP	.											.	KIF15	103	.	0			c.A3381G						PASS	.	A		300,4106	164.0+/-195.7	5,290,1908	118.0	113.0	115.0		3381	-11.5	0.2	3	dbSNP_132	115	429,8171	132.6+/-190.3	8,413,3879	no	coding-synonymous	KIF15	NM_020242.2		13,703,5787	GG,GA,AA		4.9884,6.8089,5.6051		1127/1389	44881909	729,12277	2203	4300	6503	SO:0001819	synonymous_variant	56992	exon28			GAGGCAACTAGAA	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3381A>G	3.37:g.44881909A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Silent	SNP	ENST00000326047.4	37	CCDS33744.1																																																																																			A|0.943;G|0.057	0.057	strong		0.338	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
PITRM1	10531	hgsc.bcm.edu	37	10	3206027	3206027	+	Silent	SNP	A	A	G	rs4609511	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:3206027A>G	ENST00000224949.4	-	7	715	c.681T>C	c.(679-681)ccT>ccC	p.P227P	PITRM1-AS1_ENST00000598280.1_RNA|PITRM1-AS1_ENST00000601046.1_RNA|PITRM1_ENST00000380989.2_Silent_p.P227P|PITRM1_ENST00000451104.2_Silent_p.P195P			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	227					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						ACGTGTGGTCAGGAAGAAGTC	0.443													G|||	3126	0.624201	0.5393	0.5793	5008	,	,		18869	0.6032		0.6988	False		,,,				2504	0.7157				p.P227P		Atlas-SNP	.											.	PITRM1	109	.	0			c.T681C						PASS	.	G	,,	2335,1529		721,893,318	122.0	119.0	120.0		681,585,681	-3.0	0.9	10	dbSNP_111	120	5958,2302		2124,1710,296	no	coding-synonymous,coding-synonymous,coding-synonymous	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	,,	2845,2603,614	GG,GA,AA		27.8692,39.5704,31.5985	,,	227/1039,195/940,227/1038	3206027	8293,3831	1932	4130	6062	SO:0001819	synonymous_variant	10531	exon7			GTGGTCAGGAAGA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.681T>C	10.37:g.3206027A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	37	CCDS59208.1																																																																																			A|0.358;G|0.642	0.642	strong		0.443	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
C1orf189	388701	hgsc.bcm.edu	37	1	154178079	154178079	+	Silent	SNP	G	G	A	rs74957241	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:154178079G>A	ENST00000368525.3	-	2	94	c.69C>T	c.(67-69)gtC>gtT	p.V23V	C1orf43_ENST00000483282.1_5'Flank	NM_001010979.1	NP_001010979.1	Q5VU69	CA189_HUMAN	chromosome 1 open reading frame 189	23										kidney(1)|large_intestine(3)|lung(1)|skin(2)	7	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					ATTACCTGTCGACCGTCTTCT	0.473													G|||	192	0.0383387	0.003	0.0677	5008	,	,		18138	0.001		0.1163	False		,,,				2504	0.0235				p.V23V		Atlas-SNP	.											C1orf189,NS,carcinoma,-2,1	C1orf189	17	1	0			c.C69T						PASS	.	G		82,4324	71.4+/-109.4	2,78,2123	166.0	148.0	154.0		69	-2.7	0.1	1	dbSNP_132	154	926,7674	205.1+/-247.6	55,816,3429	no	coding-synonymous	C1orf189	NM_001010979.1		57,894,5552	AA,AG,GG		10.7674,1.8611,7.7503		23/102	154178079	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	388701	exon2			CCTGTCGACCGTC		CCDS30876.1	1q21.3	2012-07-27			ENSG00000163263	ENSG00000163263			32305	protein-coding gene	gene with protein product							Standard	NM_001010979		Approved		uc001fee.2	Q5VU69	OTTHUMG00000035982	ENST00000368525.3:c.69C>T	1.37:g.154178079G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_001010979	A1L4E3	Silent	SNP	ENST00000368525.3	37	CCDS30876.1																																																																																			G|0.926;A|0.074	0.074	strong		0.473	C1orf189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087672.1	NM_001010979	
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 GAIIx	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|ZBTB16_ENST00000535379.1_3'UTR|RP11-64D24.2_ENST00000544925.1_RNA	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	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	131	25	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	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32551935	32551935	+	Silent	SNP	G	G	A	rs11554463	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32551935G>A	ENST00000360004.5	-	2	426	c.321C>T	c.(319-321)taC>taT	p.Y107Y		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	107	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TGTGTCTGCAGTAGGTGTCCA	0.672										Multiple Myeloma(14;0.17)																											p.Y107Y		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C321T						PASS	.						31.0	32.0	32.0					6																	32551935		2150	4260	6410	SO:0001819	synonymous_variant	3123	exon2			TCTGCAGTAGGTG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.321C>T	6.37:g.32551935G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	13	6	0.461538	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			T|0.033;G|0.900;A|0.067	0.067	strong		0.672	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
DENND6B	414918	hgsc.bcm.edu	37	22	50752150	50752150	+	Missense_Mutation	SNP	C	C	T	rs68178377	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50752150C>T	ENST00000413817.3	-	15	1278	c.1207G>A	c.(1207-1209)Gtg>Atg	p.V403M	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	403					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										TTCTTCTGCACGCCCTGCAGG	0.672													C|||	1407	0.28095	0.1982	0.3199	5008	,	,		9059	0.1994		0.2922	False		,,,				2504	0.4376				p.V403M		Atlas-SNP	.											.	.	.	.	0			c.G1207A						PASS	.	C	MET/VAL	834,3260		89,656,1302	19.0	22.0	21.0		1207	-2.6	0.0	22	dbSNP_130	21	2487,5839		382,1723,2058	yes	missense	FAM116B	NM_001001794.3	21	471,2379,3360	TT,TC,CC		29.8703,20.3713,26.7391	benign	403/586	50752150	3321,9099	2047	4163	6210	SO:0001583	missense	414918	exon15			TCTGCACGCCCTG	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.1207G>A	22.37:g.50752150C>T	ENSP00000391524:p.Val403Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_001001794	A6X8I5	Missense_Mutation	SNP	ENST00000413817.3	37	CCDS46732.1	548	0.2509157509157509	105	0.21341463414634146	101	0.27900552486187846	113	0.19755244755244755	229	0.3021108179419525	C	9.702	1.154751	0.21371	0.203713	0.298703	ENSG00000205593	ENST00000413817	.	.	.	4.82	-2.63	0.06133	.	0.554792	0.18959	N	0.126460	T	0.00012	0.0000	N	0.16266	0.395	0.54753	P	1.0999999999983245E-5	B;B	0.24317	0.101;0.101	B;B	0.11329	0.004;0.006	T	0.39292	-0.9621	8	0.27785	T	0.31	-3.5588	6.125	0.20174	0.0:0.2459:0.3228:0.4313	.	403;403	Q8NEG7;C9JIV6	F116B_HUMAN;.	M	403	.	ENSP00000391524:V403M	V	-	1	0	FAM116B	49094722	0.041000	0.20044	0.032000	0.17829	0.733000	0.41908	0.249000	0.18216	-0.577000	0.05967	0.462000	0.41574	GTG	C|0.747;T|0.253	0.253	strong		0.672	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
KRT72	140807	hgsc.bcm.edu	37	12	52985293	52985293	+	Silent	SNP	A	A	G	rs12824366	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52985293A>G	ENST00000537672.2	-	5	928	c.918T>C	c.(916-918)atT>atC	p.I306I	KRT72_ENST00000354310.4_Silent_p.I306I|KRT72_ENST00000293745.2_Silent_p.I306I|KRT72_ENST00000398066.3_Silent_p.I118I	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	306	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		TCTTTAGGGCAATCTCCTCGT	0.597													G|||	1865	0.372404	0.1914	0.2406	5008	,	,		21236	0.5655		0.3638	False		,,,				2504	0.5204				p.I306I		Atlas-SNP	.											.	KRT72	70	.	0			c.T918C						PASS	.	G	,,	1138,3268	716.0+/-408.5	156,826,1221	156.0	117.0	130.0		918,918,918	-3.6	0.0	12	dbSNP_121	130	3279,5321	647.6+/-400.4	598,2083,1619	no	coding-synonymous,coding-synonymous,coding-synonymous	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	,,	754,2909,2840	GG,GA,AA		38.1279,25.8284,33.9612	,,	306/512,306/470,306/512	52985293	4417,8589	2203	4300	6503	SO:0001819	synonymous_variant	140807	exon5			TAGGGCAATCTCC	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.918T>C	12.37:g.52985293A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	116	51	0.439655	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Silent	SNP	ENST00000537672.2	37	CCDS8833.1																																																																																			A|0.651;G|0.349	0.349	strong		0.597	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
OTUD6B	51633	hgsc.bcm.edu	37	8	92097062	92097062	+	Missense_Mutation	SNP	G	G	A	rs3210518	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:92097062G>A	ENST00000285420.4	+	7	1037	c.938G>A	c.(937-939)cGg>cAg	p.R313Q	OTUD6B_ENST00000404789.3_Missense_Mutation_p.R182Q	NM_016023.3	NP_057107.3	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B	283							cysteine-type peptidase activity (GO:0008234)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11			BRCA - Breast invasive adenocarcinoma(11;0.0187)			TCGGTTACACGGTTGGTAAAC	0.289													G|||	203	0.0405351	0.087	0.0288	5008	,	,		15666	0.0437		0.0189	False		,,,				2504	0.0051				p.R313Q		Atlas-SNP	.											.	OTUD6B	28	.	0			c.G938A						PASS	.	G	GLN/ARG	311,4095	159.2+/-191.8	10,291,1902	85.0	80.0	81.0		938	-7.1	0.6	8	dbSNP_105	81	280,8312	100.1+/-161.6	2,276,4018	yes	missense	OTUD6B	NM_016023.3	43	12,567,5920	AA,AG,GG		3.2588,7.0586,4.5469	benign	313/324	92097062	591,12407	2203	4296	6499	SO:0001583	missense	51633	exon7			TTACACGGTTGGT		CCDS6253.2, CCDS69513.1	8q21.3	2013-01-21			ENSG00000155100	ENSG00000155100		"""OTU domain containing"""	24281	protein-coding gene	gene with protein product		612021					Standard	NM_016023		Approved	CGI-77, DUBA5	uc003yeu.4	Q8N6M0	OTTHUMG00000150758	ENST00000285420.4:c.938G>A	8.37:g.92097062G>A	ENSP00000285420:p.Arg313Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_016023	A8K6I1|B4DEY0|Q9NTA4|Q9Y387	Missense_Mutation	SNP	ENST00000285420.4	37	CCDS6253.2	97	0.044413919413919416	47	0.09552845528455285	14	0.03867403314917127	24	0.04195804195804196	12	0.0158311345646438	G	8.675	0.903743	0.17760	0.070586	0.032588	ENSG00000155100	ENST00000285420;ENST00000404789	T;T	0.44881	0.91;0.91	5.98	-7.05	0.01573	Ovarian tumour, otubain (1);	1.463720	0.03677	N	0.244978	T	0.00524	0.0017	N	0.25245	0.725	0.09310	N	0.999993	B;B	0.10296	0.002;0.003	B;B	0.04013	0.0;0.001	T	0.08269	-1.0730	10	0.10902	T	0.67	3.7178	3.9119	0.09207	0.5123:0.2449:0.1098:0.133	rs3210518;rs17297951;rs52830475;rs3210518	182;283	B4DEY0;Q8N6M0	.;OTU6B_HUMAN	Q	313;182	ENSP00000285420:R313Q;ENSP00000384190:R182Q	ENSP00000285420:R313Q	R	+	2	0	OTUD6B	92166238	0.001000	0.12720	0.579000	0.28588	0.969000	0.65631	-1.801000	0.01743	-1.300000	0.02341	-0.218000	0.12543	CGG	G|0.954;A|0.046	0.046	strong		0.289	OTUD6B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319968.1	NM_016023	
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 GAIIx	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	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	209	94	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	
IL19	29949	hgsc.bcm.edu	37	1	207013248	207013248	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207013248G>A	ENST00000270218.6	+	5	1203	c.264G>A	c.(262-264)agG>agA	p.R88R	IL19_ENST00000340758.2_Silent_p.R126R	NM_013371.3	NP_037503.2	Q9UHD0	IL19_HUMAN	interleukin 19	88					apoptotic process (GO:0006915)|immune response (GO:0006955)|interleukin-6 biosynthetic process (GO:0042226)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|reactive oxygen species metabolic process (GO:0072593)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)			central_nervous_system(2)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7			BRCA - Breast invasive adenocarcinoma(75;0.211)			ACGTGGACAGGGTGTTCAAGG	0.468																																					p.R126R		Atlas-SNP	.											IL19_ENST00000340758,NS,carcinoma,+1,2	IL19	31	2	0			c.G378A						scavenged	.						269.0	252.0	258.0					1																	207013248		2203	4300	6503	SO:0001819	synonymous_variant	29949	exon4			GGACAGGGTGTTC	AF192498	CCDS1468.1, CCDS1469.1	1q32.2	2008-07-18			ENSG00000142224	ENSG00000142224		"""Interleukins and interleukin receptors"""	5990	protein-coding gene	gene with protein product	"""melanoma differentiation associated protein-like protein"""	605687				11196675	Standard	NM_153758		Approved	IL-19, MDA1, ZMDA1, IL-10C, NG.1	uc001heo.3	Q9UHD0	OTTHUMG00000036387	ENST00000270218.6:c.264G>A	1.37:g.207013248G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	183	2	0.010929	NM_153758	B6VEV9|Q5VUT3|Q96QR4|Q9NUA0	Silent	SNP	ENST00000270218.6	37	CCDS1469.1																																																																																			.	.	none		0.468	IL19-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088567.2	NM_153758	
DIMT1	27292	hgsc.bcm.edu	37	5	61694379	61694379	+	Silent	SNP	T	T	C	rs247264	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:61694379T>C	ENST00000199320.4	-	6	565	c.405A>G	c.(403-405)tcA>tcG	p.S135S	DIMT1_ENST00000506390.1_Silent_p.S135S|KIF2A_ENST00000509663.2_Intron	NM_014473.2	NP_055288.1	Q9UNQ2	DIM1_HUMAN	DIM1 dimethyladenosine transferase 1 homolog (S. cerevisiae)	135						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity (GO:0052909)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)										AGACAAAAGGTGAAGAGATCT	0.378													C|||	2924	0.583866	0.7179	0.5029	5008	,	,		19644	0.6806		0.4771	False		,,,				2504	0.4703				p.S135S		Atlas-SNP	.											.	.	.	.	0			c.A405G						PASS	.	C		3070,1336	443.7+/-347.1	1075,920,208	128.0	134.0	132.0		405	-0.3	1.0	5	dbSNP_79	132	4059,4541	594.3+/-393.3	960,2139,1201	no	coding-synonymous	DIMT1	NM_014473.2		2035,3059,1409	CC,CT,TT		47.1977,30.3223,45.1868		135/314	61694379	7129,5877	2203	4300	6503	SO:0001819	synonymous_variant	27292	exon6			AAAAGGTGAAGAG	AF102147	CCDS3981.1	5q12.1	2011-08-11	2011-08-11	2011-08-11	ENSG00000086189	ENSG00000086189			30217	protein-coding gene	gene with protein product		612499	"""DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)"""	DIMT1L		11124703	Standard	NM_014473		Approved	HSA9761	uc003jta.3	Q9UNQ2	OTTHUMG00000131223	ENST00000199320.4:c.405A>G	5.37:g.61694379T>C		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	208	205	0.985577	NM_014473	O76025|Q9BU77|Q9UES1	Silent	SNP	ENST00000199320.4	37	CCDS3981.1																																																																																			T|0.437;C|0.563	0.563	strong		0.378	DIMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253967.1	NM_014473	
PCDH1	5097	hgsc.bcm.edu	37	5	141248437	141248437	+	Silent	SNP	G	G	A	rs142655578	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:141248437G>A	ENST00000394536.3	-	2	739	c.600C>T	c.(598-600)aaC>aaT	p.N200N	PCDH1_ENST00000503492.1_Silent_p.N200N|PCDH1_ENST00000456271.1_Silent_p.N200N|PCDH1_ENST00000287008.3_Silent_p.N200N|PCDH1_ENST00000511044.1_5'Flank|PCDH1_ENST00000536585.1_Silent_p.N178N	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	200	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		ATGCCACACCGTTGGGACCAG	0.597													G|||	26	0.00519169	0.0008	0.0115	5008	,	,		18845	0.0		0.0169	False		,,,				2504	0.0				p.N200N	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.C600T						PASS	.	G	,	11,4395	19.1+/-41.9	0,11,2192	205.0	196.0	199.0		600,600	-6.2	0.8	5	dbSNP_134	199	113,8487	60.6+/-122.4	0,113,4187	no	coding-synonymous,coding-synonymous	PCDH1	NM_002587.3,NM_032420.2	,	0,124,6379	AA,AG,GG		1.314,0.2497,0.9534	,	200/1061,200/1238	141248437	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	5097	exon2			CACACCGTTGGGA	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"""Cadherins / Protocadherins : Non-clustered"""	8655	protein-coding gene	gene with protein product		603626	"""protocadherin 1 (cadherin-like 1)"""			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.600C>T	5.37:g.141248437G>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	225	100	0.444444	NM_032420	Q8IUP2	Silent	SNP	ENST00000394536.3	37	CCDS43375.1																																																																																			G|0.990;A|0.010	0.010	strong		0.597	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420	
WDR81	124997	hgsc.bcm.edu	37	17	1637458	1637458	+	Silent	SNP	G	G	A	rs587780506|rs398088774|rs8065251	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1637458G>A	ENST00000409644.1	+	7	5127	c.5127G>A	c.(5125-5127)ccG>ccA	p.P1709P	WDR81_ENST00000419248.1_Silent_p.P482P|WDR81_ENST00000545662.1_Silent_p.P340P|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.P658P|WDR81_ENST00000446363.1_Silent_p.P348P|WDR81_ENST00000437219.2_Silent_p.P506P	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1709					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TTGAGGCCCCGCAGCACGTGG	0.672													G|||	1236	0.246805	0.2519	0.2061	5008	,	,		15192	0.1855		0.1978	False		,,,				2504	0.3824				p.P1709P		Atlas-SNP	.											WDR81_ENST00000437219,NS,carcinoma,0,3	WDR81	180	3	0			c.G5127A						scavenged	.	G	,,,	1057,3347		118,821,1263	30.0	32.0	31.0		1518,5127,1446,1974	-8.9	0.1	17	dbSNP_116	31	1802,6794		188,1426,2684	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	306,2247,3947	AA,AG,GG		20.9632,24.0009,21.9923	,,,	506/739,1709/1942,482/715,658/891	1637458	2859,10141	2202	4298	6500	SO:0001819	synonymous_variant	124997	exon7			GGCCCCGCAGCAC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5127G>A	17.37:g.1637458G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			G|0.782;A|0.218	0.218	strong		0.672	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
SSH3	54961	hgsc.bcm.edu	37	11	67079177	67079177	+	Missense_Mutation	SNP	G	G	A	rs1573536	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67079177G>A	ENST00000308127.4	+	14	1977	c.1799G>A	c.(1798-1800)cGc>cAc	p.R600H	SSH3_ENST00000308298.7_Missense_Mutation_p.R335H|SSH3_ENST00000376757.5_3'UTR	NM_017857.3	NP_060327.3	Q8TE77	SSH3_HUMAN	slingshot protein phosphatase 3	600			R -> H (in dbSNP:rs1573536).		protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|DNA binding (GO:0003677)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CTGAAGTCCCGCCAGTCAGTG	0.672													G|||	350	0.0698882	0.0998	0.2651	5008	,	,		16248	0.0298		0.004	False		,,,				2504	0.0				p.R600H		Atlas-SNP	.											.	SSH3	54	.	0			c.G1799A						PASS	.	G	HIS/ARG	341,4059	175.9+/-205.1	9,323,1868	44.0	43.0	44.0		1799	2.5	1.0	11	dbSNP_88	44	37,8553	22.2+/-67.0	1,35,4259	yes	missense	SSH3	NM_017857.3	29	10,358,6127	AA,AG,GG		0.4307,7.75,2.9099	probably-damaging	600/660	67079177	378,12612	2200	4295	6495	SO:0001583	missense	54961	exon14			AGTCCCGCCAGTC	AF085851	CCDS8157.1	11q13	2013-03-05	2013-03-05		ENSG00000172830	ENSG00000172830		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30581	protein-coding gene	gene with protein product		606780	"""slingshot homolog 3 (Drosophila)"""			11832213	Standard	NM_017857		Approved	FLJ20515, FLJ10928	uc001okj.3	Q8TE77	OTTHUMG00000167105	ENST00000308127.4:c.1799G>A	11.37:g.67079177G>A	ENSP00000312081:p.Arg600His	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	77	16	0.207792	NM_017857	Q6PK42|Q76I75|Q8N9L8|Q8WYL0|Q9NV45|Q9NWZ7	Missense_Mutation	SNP	ENST00000308127.4	37	CCDS8157.1	136	0.06227106227106227	48	0.0975609756097561	71	0.19613259668508287	14	0.024475524475524476	3	0.00395778364116095	G	10.90	1.481567	0.26598	0.0775	0.004307	ENSG00000172830	ENST00000308127;ENST00000308298	T;T	0.54675	3.32;0.56	4.4	2.53	0.30540	.	2.303910	0.01656	N	0.024843	T	0.00039	0.0001	L	0.27053	0.805	0.09310	P	0.999999999815732	P;P	0.48640	0.834;0.913	B;B	0.40677	0.337;0.271	T	0.05920	-1.0856	9	0.59425	D	0.04	-6.9983	7.2681	0.26242	0.2038:0.0:0.7962:0.0	rs1573536;rs1573536	454;600	Q8TE77-3;Q8TE77	.;SSH3_HUMAN	H	600;335	ENSP00000312081:R600H;ENSP00000310055:R335H	ENSP00000312081:R600H	R	+	2	0	SSH3	66835753	0.998000	0.40836	0.993000	0.49108	0.026000	0.11368	0.450000	0.21762	0.619000	0.30197	-0.224000	0.12420	CGC	G|0.958;A|0.042	0.042	strong		0.672	SSH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393167.1	NM_018276	
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 GAIIx	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_ENST00000380800.3_Silent_p.T1311T|BRWD1_ENST00000342449.3_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		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	116	74	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	
P2RX6	9127	hgsc.bcm.edu	37	22	21377650	21377650	+	Missense_Mutation	SNP	G	G	A	rs2277838	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:21377650G>A	ENST00000413302.2	+	7	873	c.725G>A	c.(724-726)cGc>cAc	p.R242H	P2RX6_ENST00000402329.3_3'UTR|P2RX6_ENST00000336296.2_Missense_Mutation_p.R232H|P2RX6_ENST00000401443.1_Missense_Mutation_p.R216H|P2RX6_ENST00000443995.3_Missense_Mutation_p.R189H			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6	242			R -> H (in dbSNP:rs2277838). {ECO:0000269|PubMed:15489334}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										CCCGTGTTCCGCATTGGGGAC	0.612													G|||	390	0.0778754	0.0083	0.1254	5008	,	,		18765	0.0159		0.1948	False		,,,				2504	0.0818				p.R242H		Atlas-SNP	.											.	.	.	.	0			c.G725A						PASS	.	G	HIS/ARG,HIS/ARG	163,4243	110.4+/-148.6	7,149,2047	115.0	110.0	112.0		647,725	4.4	1.0	22	dbSNP_100	112	1571,7029	293.5+/-301.4	144,1283,2873	yes	missense,missense	P2RX6	NM_001159554.1,NM_005446.3	29,29	151,1432,4920	AA,AG,GG		18.2674,3.6995,13.3323	benign,benign	216/416,242/442	21377650	1734,11272	2203	4300	6503	SO:0001583	missense	9127	exon7			TGTTCCGCATTGG		CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8538	protein-coding gene	gene with protein product		608077	"""purinergic receptor P2X-like 1, orphan receptor"""	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689	ENST00000413302.2:c.725G>A	22.37:g.21377650G>A	ENSP00000416193:p.Arg242His	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_005446	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Missense_Mutation	SNP	ENST00000413302.2	37	CCDS13788.2	225	0.10302197802197802	7	0.014227642276422764	43	0.11878453038674033	12	0.02097902097902098	163	0.21503957783641162	G	15.41	2.824709	0.50739	0.036995	0.182674	ENSG00000099957	ENST00000413302;ENST00000336296;ENST00000401443;ENST00000443995	T;T;T;T	0.05199	3.48;3.48;3.48;3.48	5.44	4.4	0.53042	.	0.350072	0.24518	N	0.037824	T	0.00012	0.0000	M	0.76727	2.345	0.34749	P	0.26844199999999996	B;P	0.48350	0.019;0.909	B;B	0.37422	0.011;0.249	T	0.39035	-0.9633	9	0.66056	D	0.02	-12.0015	7.7709	0.29008	0.0863:0.1659:0.7478:0.0	rs2277838;rs17820577;rs57147063;rs2277838	242;216	O15547;F6V3D7	P2RX6_HUMAN;.	H	242;232;216;189	ENSP00000416193:R242H;ENSP00000338797:R232H;ENSP00000385309:R216H;ENSP00000408088:R189H	ENSP00000338797:R232H	R	+	2	0	P2RX6	19707650	1.000000	0.71417	0.983000	0.44433	0.509000	0.34042	2.810000	0.47979	1.379000	0.46325	0.655000	0.94253	CGC	G|0.895;A|0.105	0.105	strong		0.612	P2RX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319625.2	NM_005446	
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 GAIIx	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_ENST00000361052.3_Missense_Mutation_p.C109Y|CTSE_ENST00000360218.2_Missense_Mutation_p.C109Y|CTSE_ENST00000432969.2_Missense_Mutation_p.C34Y	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	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	88	13	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	
SLIT1	6585	hgsc.bcm.edu	37	10	98820528	98820528	+	Silent	SNP	C	C	G	rs33970910	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:98820528C>G	ENST00000266058.4	-	9	1055	c.810G>C	c.(808-810)ggG>ggC	p.G270G	SLIT1_ENST00000371041.3_Silent_p.G270G|SLIT1_ENST00000371070.4_Silent_p.G270G|ARHGAP19-SLIT1_ENST00000453547.2_3'UTR	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	270					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		TGGGCACGCGCCCCGCTTCTC	0.637													C|||	485	0.096845	0.1271	0.0994	5008	,	,		19661	0.002		0.175	False		,,,				2504	0.0716				p.G270G		Atlas-SNP	.											.	SLIT1	154	.	0			c.G810C						PASS	.	C		525,3881		39,447,1717	33.0	27.0	29.0		810	-0.3	0.0	10	dbSNP_126	29	1244,7356		81,1082,3137	no	coding-synonymous	SLIT1	NM_003061.2		120,1529,4854	GG,GC,CC		14.4651,11.9156,13.6014		270/1535	98820528	1769,11237	2203	4300	6503	SO:0001819	synonymous_variant	6585	exon9			CACGCGCCCCGCT	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.810G>C	10.37:g.98820528C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Silent	SNP	ENST00000266058.4	37	CCDS7453.1																																																																																			C|0.870;G|0.130	0.130	strong		0.637	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
CAGE1	285782	hgsc.bcm.edu	37	6	7374207	7374207	+	Missense_Mutation	SNP	T	T	G	rs2876098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:7374207T>G	ENST00000512086.1	-	5	1047	c.845A>C	c.(844-846)gAg>gCg	p.E282A	CAGE1_ENST00000338150.4_Missense_Mutation_p.E282A|CAGE1_ENST00000296742.7_Missense_Mutation_p.E146A|CAGE1_ENST00000509324.1_5'UTR|CAGE1_ENST00000379918.4_Missense_Mutation_p.E282A|CAGE1_ENST00000502583.1_Missense_Mutation_p.E282A			Q8TC20	CAGE1_HUMAN	cancer antigen 1	282			E -> A (in dbSNP:rs2876098).							breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					CTCACAGTTCTCCCGACATGC	0.458													T|||	513	0.102436	0.0703	0.1455	5008	,	,		19557	0.1062		0.1491	False		,,,				2504	0.0634				p.E282A		Atlas-SNP	.											.	CAGE1	165	.	0			c.A845C						PASS	.	T	ALA/GLU,ALA/GLU,ALA/GLU	360,3568		13,334,1617	99.0	96.0	97.0		845,845,437	3.2	0.0	6	dbSNP_101	97	1179,7115		106,967,3074	yes	missense,missense,missense	CAGE1	NM_001170692.1,NM_001170693.1,NM_205864.2	107,107,107	119,1301,4691	GG,GT,TT		14.2151,9.165,12.592	possibly-damaging,possibly-damaging,possibly-damaging	282/840,282/825,146/642	7374207	1539,10683	1964	4147	6111	SO:0001583	missense	285782	exon5			CAGTTCTCCCGAC	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"""cancer/testis antigen 95"""	608304	"""cancer/testis antigen 3"""	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.845A>C	6.37:g.7374207T>G	ENSP00000427583:p.Glu282Ala	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	114	69	0.605263	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	37		276	0.12637362637362637	42	0.08536585365853659	53	0.1464088397790055	63	0.11013986013986014	118	0.15567282321899736	T	16.25	3.071426	0.55646	0.09165	0.142151	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000296742;ENST00000512086;ENST00000338150;ENST00000542431;ENST00000512691	T;T;T;T;T;T	0.35048	1.33;1.33;1.33;1.33;1.33;1.33	5.66	3.23	0.37069	.	0.542419	0.18024	N	0.154151	T	0.19446	0.0467	L	0.55481	1.735	0.80722	P	0.0	P;P;P	0.48294	0.908;0.775;0.86	B;B;P	0.44561	0.436;0.356;0.453	T	0.04635	-1.0937	9	0.54805	T	0.06	-0.3094	7.542	0.27744	0.0:0.1713:0.0:0.8287	rs2876098;rs17673083;rs60779509;rs2876098	282;282;282	Q8TC20-3;D6RCT9;Q8TC20	.;.;CAGE1_HUMAN	A	282;282;282;146;282;282;282;294	ENSP00000369250:E282A;ENSP00000425493:E282A;ENSP00000296742:E146A;ENSP00000427583:E282A;ENSP00000338107:E282A;ENSP00000423789:E294A	ENSP00000296742:E146A	E	-	2	0	CAGE1	7319206	0.008000	0.16893	0.001000	0.08648	0.005000	0.04900	0.785000	0.26830	0.410000	0.25675	0.482000	0.46254	GAG	T|0.882;G|0.118	0.118	strong		0.458	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745	
ANKRD50	57182	hgsc.bcm.edu	37	4	125592869	125592869	+	Silent	SNP	G	G	A	rs114589928	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:125592869G>A	ENST00000504087.1	-	4	2600	c.1563C>T	c.(1561-1563)gcC>gcT	p.A521A	ANKRD50_ENST00000515641.1_Silent_p.A342A	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	521										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CTCTTTCTAAGGCTTGTCGAA	0.413													G|||	21	0.00419329	0.0008	0.0072	5008	,	,		22385	0.0		0.0139	False		,,,				2504	0.001				p.A521A		Atlas-SNP	.											.	ANKRD50	136	.	0			c.C1563T						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	117.0	114.0	115.0		1026,1563	3.9	1.0	4	dbSNP_132	115	72,8528	40.8+/-97.7	0,72,4228	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	0,76,6427	AA,AG,GG		0.8372,0.0908,0.5843	,	342/1251,521/1430	125592869	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			TTCTAAGGCTTGT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.1563C>T	4.37:g.125592869G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	33	0.383721	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			G|0.994;A|0.006	0.006	strong		0.413	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
MYO15A	51168	hgsc.bcm.edu	37	17	18058521	18058521	+	Silent	SNP	C	C	T	rs712272	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18058521C>T	ENST00000205890.5	+	46	8660	c.8322C>T	c.(8320-8322)tcC>tcT	p.S2774S	MYO15A_ENST00000418233.3_Silent_p.S38S|MYO15A_ENST00000585180.1_Silent_p.S38S	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2774	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TCTACTTCTCCCGCATCTTCC	0.602													C|||	1078	0.215256	0.1846	0.2983	5008	,	,		17398	0.0675		0.3907	False		,,,				2504	0.1697				p.S2774S		Atlas-SNP	.											.	MYO15A	268	.	0			c.C8322T						PASS	.	C		956,3260		106,744,1258	40.0	49.0	46.0		8322	-0.5	1.0	17	dbSNP_86	46	3446,4990		723,2000,1495	no	coding-synonymous	MYO15A	NM_016239.3		829,2744,2753	TT,TC,CC		40.8487,22.6755,34.7929		2774/3531	18058521	4402,8250	2108	4218	6326	SO:0001819	synonymous_variant	51168	exon45			CTTCTCCCGCATC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8322C>T	17.37:g.18058521C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																			C|0.696;T|0.304	0.304	strong		0.602	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
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 GAIIx	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	HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_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		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	81	8	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	
CPAMD8	27151	hgsc.bcm.edu	37	19	17104379	17104379	+	Silent	SNP	G	G	A	rs75991134	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17104379G>A	ENST00000443236.1	-	12	1285	c.1254C>T	c.(1252-1254)ccC>ccT	p.P418P	CPAMD8_ENST00000388925.4_Silent_p.P371P	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	371						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GGCTGCCATCGGGGTAGGATA	0.532													G|||	195	0.0389377	0.0862	0.0288	5008	,	,		18821	0.002		0.0358	False		,,,				2504	0.0235				p.P418P		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C1254T						PASS	.	G		234,3730		10,214,1758	61.0	59.0	60.0		1254	-6.1	0.1	19	dbSNP_131	60	247,8063		7,233,3915	no	coding-synonymous	CPAMD8	NM_015692.2		17,447,5673	AA,AG,GG		2.9723,5.9031,3.9189		418/1933	17104379	481,11793	1982	4155	6137	SO:0001819	synonymous_variant	27151	exon12			GCCATCGGGGTAG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1254C>T	19.37:g.17104379G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	82	0.037545787545787544	42	0.08536585365853659	15	0.04143646408839779	1	0.0017482517482517483	24	0.0316622691292876	G	0.055	-1.238061	0.01493	0.059031	0.029723	ENSG00000160111	ENST00000443236	.	.	.	3.04	-6.09	0.02145	.	0.000000	0.64402	D	0.000003	T	0.00967	0.0032	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39961	-0.9588	6	0.12103	T	0.63	.	2.2852	0.04124	0.2507:0.1564:0.3948:0.1981	.	.	.	.	L	429	.	ENSP00000402505:P429L	P	-	2	0	CPAMD8	16965379	0.000000	0.05858	0.134000	0.22075	0.180000	0.23129	-2.818000	0.00751	-2.672000	0.00413	-1.172000	0.01736	CCG	G|0.966;A|0.034	0.034	strong		0.532	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
KIAA1211	57482	hgsc.bcm.edu	37	4	57181629	57181629	+	Missense_Mutation	SNP	C	C	T	rs61750793	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57181629C>T	ENST00000504228.1	+	6	2066	c.1961C>T	c.(1960-1962)cCc>cTc	p.P654L	KIAA1211_ENST00000541073.1_Missense_Mutation_p.P647L|KIAA1211_ENST00000264229.6_Missense_Mutation_p.P654L			Q6ZU35	K1211_HUMAN	KIAA1211	654				P -> L (in Ref. 2; BAC86392). {ECO:0000305}.						endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AAGGCTAAGCCCCGCCAGGAG	0.682													C|||	1008	0.201278	0.1415	0.196	5008	,	,		13963	0.254		0.2823	False		,,,				2504	0.1483				p.P654L		Atlas-SNP	.											.	KIAA1211	178	.	0			c.C1961T						PASS	.	C	LEU/PRO	5,3863		0,5,1929	18.0	22.0	21.0		1961	-0.8	0.0	4	dbSNP_129	21	45,8165		5,35,4065	no	missense	KIAA1211	NM_020722.1	98	5,40,5994	TT,TC,CC		0.5481,0.1293,0.414	benign	654/1234	57181629	50,12028	1934	4105	6039	SO:0001583	missense	57482	exon8			CTAAGCCCCGCCA	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1961C>T	4.37:g.57181629C>T	ENSP00000423366:p.Pro654Leu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	496	0.2271062271062271	72	0.14634146341463414	76	0.20994475138121546	140	0.24475524475524477	208	0.27440633245382584	C	3.586	-0.084625	0.07097	0.001293	0.005481	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.01745	4.66;4.66;4.66	4.38	-0.764	0.11027	.	.	.	.	.	T	0.00012	0.0000	L	0.38531	1.155	0.50632	P	1.1600000000000499E-4	B;B	0.12013	0.005;0.005	B;B	0.08055	0.002;0.003	T	0.41070	-0.9529	8	0.11794	T	0.64	-4.4597	4.0737	0.09894	0.407:0.2333:0.0:0.3598	rs61750793	647;654	F5H1N7;Q6ZU35	.;K1211_HUMAN	L	654;654;647;564	ENSP00000264229:P654L;ENSP00000423366:P654L;ENSP00000444006:P647L	ENSP00000264229:P654L	P	+	2	0	KIAA1211	56876386	0.013000	0.17824	0.016000	0.15963	0.002000	0.02628	0.689000	0.25437	-0.084000	0.12595	-1.008000	0.02478	CCC	C|0.760;T|0.240	0.240	strong		0.682	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
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 GAIIx	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	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	73	23	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	
GMPPA	29926	hgsc.bcm.edu	37	2	220371035	220371035	+	Silent	SNP	C	C	G	rs1046474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:220371035C>G	ENST00000358215.3	+	12	1422	c.1053C>G	c.(1051-1053)gcC>gcG	p.A351A	AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373917.3_Silent_p.A404A|GMPPA_ENST00000341142.3_Silent_p.A351A|GMPPA_ENST00000313597.5_Silent_p.A351A|GMPPA_ENST00000373908.1_Silent_p.A351A	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	351					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		GACGCTGGGCCCGCGTGGAGG	0.622													C|||	263	0.052516	0.0129	0.0908	5008	,	,		18788	0.001		0.161	False		,,,				2504	0.0204				p.A351A		Atlas-SNP	.											.	GMPPA	50	.	0			c.C1053G						PASS	.	C	,	171,4235	115.4+/-153.4	7,157,2039	73.0	73.0	73.0		1053,1053	0.6	0.9	2	dbSNP_86	73	1430,7170	274.6+/-291.3	112,1206,2982	no	coding-synonymous,coding-synonymous	GMPPA	NM_013335.3,NM_205847.2	,	119,1363,5021	GG,GC,CC		16.6279,3.8811,12.3097	,	351/421,351/421	220371035	1601,11405	2203	4300	6503	SO:0001819	synonymous_variant	29926	exon12			CTGGGCCCGCGTG	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.1053C>G	2.37:g.220371035C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Silent	SNP	ENST00000358215.3	37	CCDS2441.1																																																																																			C|0.888;G|0.112	0.112	strong		0.622	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136308542	136308542	+	Silent	SNP	C	C	T	rs3124767	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136308542C>T	ENST00000371929.3	+	19	2724	c.2280C>T	c.(2278-2280)ggC>ggT	p.G760G	ADAMTS13_ENST00000355699.2_Silent_p.G760G|ADAMTS13_ENST00000485925.1_Intron|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000356589.2_Silent_p.G729G|ADAMTS13_ENST00000536611.1_Intron	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	760	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)		CCTGTGGGGGCGGCCTGCGGG	0.731													C|||	2488	0.496805	0.3298	0.4755	5008	,	,		16807	0.8026		0.4006	False		,,,				2504	0.5215				p.G760G		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.C2280T						PASS	.	C	,,	1414,2922		273,868,1027	10.0	10.0	10.0		2280,2187,2280	-9.3	0.0	9	dbSNP_103	10	3549,4931		809,1931,1500	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	1082,2799,2527	TT,TC,CC		41.8514,32.6107,38.725	,,	760/1428,729/1341,760/1372	136308542	4963,7853	2168	4240	6408	SO:0001819	synonymous_variant	11093	exon19			TGGGGGCGGCCTG	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.2280C>T	9.37:g.136308542C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	25	19	0.76	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			C|0.512;T|0.488	0.488	strong		0.731	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
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 GAIIx	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	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	63	35	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 GAIIx	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	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	37	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	
MYLK	4638	hgsc.bcm.edu	37	3	123411589	123411589	+	Silent	SNP	G	G	A	rs40305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:123411589G>A	ENST00000475616.1	-	16	3557	c.3558C>T	c.(3556-3558)acC>acT	p.T1186T	MYLK-AS2_ENST00000515464.1_RNA|MYLK_ENST00000360304.3_Silent_p.T1186T|MYLK_ENST00000346322.5_Silent_p.T1117T|MYLK_ENST00000359169.1_Silent_p.T1186T|MYLK_ENST00000354792.5_5'Flank|MYLK_ENST00000360772.3_Silent_p.T1186T|MYLK_ENST00000510775.1_5'UTR|MYLK-AS2_ENST00000510827.1_RNA			Q15746	MYLK_HUMAN	myosin light chain kinase	1186	Actin-binding (calcium/calmodulin- insensitive). {ECO:0000250}.|Ig-like C2-type 7.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TACCATCCACGGTGACTTGGC	0.587													G|||	1666	0.332668	0.0643	0.4856	5008	,	,		17004	0.0685		0.7594	False		,,,				2504	0.4202				p.T1186T		Atlas-SNP	.											.	MYLK	224	.	0			c.C3558T						PASS	.	G	,,,	769,3637	311.6+/-292.2	55,659,1489	97.0	73.0	81.0		3558,3351,3558,3351	-5.4	0.9	3	dbSNP_76	81	6558,2042	718.3+/-406.2	2522,1514,264	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	2577,2173,1753	AA,AG,GG		23.7442,17.4535,43.6645	,,,	1186/1915,1117/1846,1186/1864,1117/1795	123411589	7327,5679	2203	4300	6503	SO:0001819	synonymous_variant	4638	exon19			ATCCACGGTGACT	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.3558C>T	3.37:g.123411589G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	37	CCDS46896.1																																																																																			G|0.525;A|0.475	0.475	strong		0.587	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161017556	161017556	+	Silent	SNP	C	C	T	rs2774279	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161017556C>T	ENST00000368013.3	-	12	3575	c.3255G>A	c.(3253-3255)agG>agA	p.R1085R	USF1_ENST00000368020.1_5'Flank|USF1_ENST00000368021.3_5'Flank|USF1_ENST00000435396.1_5'Flank|ARHGAP30_ENST00000368015.1_Silent_p.R908R|ARHGAP30_ENST00000368016.3_Silent_p.R874R	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	1085					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			ATGCATATGACCTGCGCTGAG	0.552													C|||	1093	0.218251	0.1422	0.2003	5008	,	,		20077	0.1389		0.333	False		,,,				2504	0.2975				p.R1085R		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.G3255A						PASS	.	C	,	846,3560	333.3+/-302.9	80,686,1437	87.0	87.0	87.0		3255,2622	-1.2	0.0	1	dbSNP_100	87	2856,5744	448.2+/-361.8	460,1936,1904	no	coding-synonymous,coding-synonymous	ARHGAP30	NM_001025598.1,NM_181720.2	,	540,2622,3341	TT,TC,CC		33.2093,19.2011,28.4638	,	1085/1102,874/891	161017556	3702,9304	2203	4300	6503	SO:0001819	synonymous_variant	257106	exon12			ATATGACCTGCGC	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.3255G>A	1.37:g.161017556C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	37	CCDS30918.1																																																																																			C|0.752;T|0.248	0.248	strong		0.552	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
ALS2CR11	151254	hgsc.bcm.edu	37	2	202436684	202436684	+	Silent	SNP	T	T	A	rs55872838	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:202436684T>A	ENST00000286195.3	-	8	857	c.813A>T	c.(811-813)ccA>ccT	p.P271P	ALS2CR11_ENST00000439140.1_Silent_p.P271P|ALS2CR11_ENST00000439802.1_Silent_p.P271P|ALS2CR11_ENST00000450242.1_Silent_p.P271P	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	271										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						CTGTTCTTTCTGGAGGTGGTG	0.353													T|||	209	0.0417332	0.0915	0.0476	5008	,	,		19354	0.0		0.0477	False		,,,				2504	0.0072				p.P271P		Atlas-SNP	.											.	ALS2CR11	194	.	0			c.A813T						PASS	.	T	,,,	324,4082	172.3+/-202.3	14,296,1893	127.0	120.0	123.0		813,813,813,813	0.4	1.0	2	dbSNP_129	123	462,8138	137.1+/-194.1	14,434,3852	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ALS2CR11	NM_001168216.1,NM_001168217.1,NM_001168221.1,NM_152525.5	,,,	28,730,5745	AA,AT,TT		5.3721,7.3536,6.0434	,,,	271/396,271/551,271/1821,271/624	202436684	786,12220	2203	4300	6503	SO:0001819	synonymous_variant	151254	exon8			TCTTTCTGGAGGT	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.813A>T	2.37:g.202436684T>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	134	56	0.41791	NM_001168217	C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Silent	SNP	ENST00000286195.3	37	CCDS2349.1																																																																																			T|0.948;A|0.052	0.052	strong		0.353	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525	
ELF1	1997	hgsc.bcm.edu	37	13	41515286	41515286	+	Missense_Mutation	SNP	T	T	A	rs1056820	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:41515286T>A	ENST00000239882.3	-	8	1341	c.1027A>T	c.(1027-1029)Aca>Tca	p.T343S	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Missense_Mutation_p.T319S	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	343			T -> S (in dbSNP:rs1056820). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		TTTAGAACTGTAGTGGCTCCT	0.473													T|||	2071	0.413538	0.152	0.6657	5008	,	,		17563	0.1538		0.7097	False		,,,				2504	0.5511				p.T343S		Atlas-SNP	.											ELF1,colon,carcinoma,0,1	ELF1	65	1	0			c.A1027T						scavenged	.	T	SER/THR,SER/THR	972,3434	363.6+/-316.6	103,766,1334	167.0	155.0	159.0		955,1027	4.3	1.0	13	dbSNP_86	159	5834,2766	679.4+/-403.6	1961,1912,427	yes	missense,missense	ELF1	NM_001145353.1,NM_172373.3	58,58	2064,2678,1761	AA,AT,TT		32.1628,22.0608,47.6703	possibly-damaging,possibly-damaging	319/596,343/620	41515286	6806,6200	2203	4300	6503	SO:0001583	missense	1997	exon8			GAACTGTAGTGGC	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1027A>T	13.37:g.41515286T>A	ENSP00000239882:p.Thr343Ser	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	146	105	0.719178	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	955	0.43727106227106227	82	0.16666666666666666	229	0.6325966850828729	93	0.16258741258741258	551	0.7269129287598944	T	10.55	1.382206	0.24944	0.220608	0.678372	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.53640	0.61;0.61	5.47	4.3	0.51218	.	0.614496	0.17112	N	0.186597	T	0.00012	0.0000	L	0.36672	1.1	0.29711	P	0.839398	B;B	0.13594	0.004;0.008	B;B	0.16722	0.011;0.016	T	0.41378	-0.9512	9	0.07175	T	0.84	.	5.6684	0.17709	0.1273:0.1416:0.0:0.7311	rs1056820;rs3197446;rs17447529;rs1056820	319;343	E9PDQ9;P32519	.;ELF1_HUMAN	S	319;85;343	ENSP00000405580:T319S;ENSP00000239882:T343S	ENSP00000239882:T343S	T	-	1	0	ELF1	40413286	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.626000	0.24492	1.026000	0.39733	0.533000	0.62120	ACA	T|0.513;A|0.487	0.487	strong		0.473	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
TMEM120B	144404	hgsc.bcm.edu	37	12	122186268	122186268	+	Silent	SNP	C	C	T	rs28651018	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:122186268C>T	ENST00000449592.2	+	3	326	c.225C>T	c.(223-225)ctC>ctT	p.L75L		NM_001080825.2	NP_001074294.2	A0PK00	T120B_HUMAN	transmembrane protein 120B	75						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)	11	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;5.75e-05)|Epithelial(86;0.000128)|BRCA - Breast invasive adenocarcinoma(302;0.238)		AGGCGGAGCTCGTTCAGCAGA	0.622													C|||	2136	0.426518	0.2103	0.4496	5008	,	,		19037	0.5188		0.5487	False		,,,				2504	0.4816				p.L75L		Atlas-SNP	.											.	TMEM120B	43	.	0			c.C225T						PASS	.	C		1089,3123		168,753,1185	66.0	70.0	69.0		225	-10.6	0.0	12	dbSNP_125	69	4601,3823		1271,2059,882	no	coding-synonymous	TMEM120B	NM_001080825.2		1439,2812,2067	TT,TC,CC		45.3822,25.8547,45.0301		75/340	122186268	5690,6946	2106	4212	6318	SO:0001819	synonymous_variant	144404	exon3			GGAGCTCGTTCAG	BC127768	CCDS41852.1	12q24.31	2007-08-01			ENSG00000188735	ENSG00000188735			32008	protein-coding gene	gene with protein product							Standard	NM_001080825		Approved		uc001ubc.4	A0PK00	OTTHUMG00000169076	ENST00000449592.2:c.225C>T	12.37:g.122186268C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	180	89	0.494444	NM_001080825	A0PK01|B3KX33	Silent	SNP	ENST00000449592.2	37	CCDS41852.1																																																																																			C|0.500;G|0.000;T|0.499	0.499	strong		0.622	TMEM120B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402158.1	NM_001080825	
ARHGAP24	83478	hgsc.bcm.edu	37	4	86844835	86844835	+	Silent	SNP	A	A	G	rs6824722	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:86844835A>G	ENST00000395184.1	+	4	769	c.303A>G	c.(301-303)gaA>gaG	p.E101E	ARHGAP24_ENST00000503995.1_Silent_p.E101E|ARHGAP24_ENST00000395183.2_Silent_p.E6E	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	101	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CAAATCATGAAAGCTACCTCC	0.493													G|||	1985	0.396366	0.4304	0.3689	5008	,	,		17440	0.3601		0.2744	False		,,,				2504	0.5327				p.E101E		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.A303G						PASS	.	G	,	1765,2641	644.4+/-398.0	365,1035,803	101.0	92.0	95.0		303,18	3.4	1.0	4	dbSNP_116	95	2352,6248	703.2+/-405.3	329,1694,2277	no	coding-synonymous,coding-synonymous	ARHGAP24	NM_001025616.2,NM_001042669.1	,	694,2729,3080	GG,GA,AA		27.3488,40.059,31.6546	,	101/749,6/654	86844835	4117,8889	2203	4300	6503	SO:0001819	synonymous_variant	83478	exon4			TCATGAAAGCTAC	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.303A>G	4.37:g.86844835A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	37	CCDS34025.1																																																																																			A|0.669;G|0.331	0.331	strong		0.493	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
MXRA5	25878	hgsc.bcm.edu	37	X	3241050	3241050	+	Silent	SNP	G	G	A	rs1635247	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3241050G>A	ENST00000217939.6	-	5	2830	c.2676C>T	c.(2674-2676)tcC>tcT	p.S892S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	892						extracellular vesicular exosome (GO:0070062)		p.S892S(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CAGTCTTCTCGGAAAGGTCAT	0.483													G|||	1966	0.520795	0.4486	0.415	3775	,	,		16627	0.2728		0.4602	False		,,,				2504	0.3548				p.S892S		Atlas-SNP	.											.	MXRA5	815	.	1	Substitution - coding silent(1)	stomach(1)	c.C2676T						PASS	.	A		2244,1591		555,795,339,282,232	95.0	83.0	87.0		2676	-5.6	0.0	X	dbSNP_89	87	3846,2882		796,1187,1067,445,805	no	coding-synonymous	MXRA5	NM_015419.3		1351,1982,1406,727,1037	AA,AG,A,GG,G		42.8359,41.4863,42.3459		892/2829	3241050	6090,4473	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			CTTCTCGGAAAGG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2676C>T	X.37:g.3241050G>A		Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	120	118	0.983333	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			0|0.003;A|0.559	0.559	strong		0.483	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
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 GAIIx	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	MIR548AA1_ENST00000384971.2_RNA|ATAD2_ENST00000521903.1_5'UTR	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		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	73	26	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	
RPS6KA4	8986	hgsc.bcm.edu	37	11	64138805	64138805	+	Silent	SNP	T	T	C	rs11542299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64138805T>C	ENST00000334205.4	+	17	2237	c.2172T>C	c.(2170-2172)aaT>aaC	p.N724N	RPS6KA4_ENST00000528057.1_Silent_p.N717N|MIR1237_ENST00000408346.1_RNA|RPS6KA4_ENST00000294261.4_Silent_p.N476N	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	724					axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						GCGTGGAGAATGCACCCCTGG	0.706													C|||	1267	0.252995	0.0514	0.3833	5008	,	,		9149	0.2113		0.3708	False		,,,				2504	0.3548				p.N724N		Atlas-SNP	.											RPS6KA4_ENST00000334205,NS,carcinoma,+1,2	RPS6KA4	85	2	0			c.T2172C						PASS	.	C	,	433,3879		36,361,1759	38.0	43.0	42.0		2154,2172	1.6	1.0	11	dbSNP_120	42	2938,5552		502,1934,1809	no	coding-synonymous,coding-synonymous	RPS6KA4	NM_001006944.1,NM_003942.2	,	538,2295,3568	CC,CT,TT		34.6054,10.0417,26.3318	,	718/767,724/773	64138805	3371,9431	2156	4245	6401	SO:0001819	synonymous_variant	8986	exon17			GGAGAATGCACCC	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"""ribosomal protein S6 kinase, 90kD, polypeptide 4"""			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.2172T>C	11.37:g.64138805T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_003942	A8K7Z8|O75585|Q53ES8	Silent	SNP	ENST00000334205.4	37	CCDS8073.1																																																																																			T|0.729;C|0.271	0.271	strong		0.706	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942	
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 GAIIx	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	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	61	4	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	
ACP6	51205	hgsc.bcm.edu	37	1	147124310	147124310	+	Silent	SNP	T	T	G	rs386635276|rs2153463	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:147124310T>G	ENST00000369238.6	-	7	1270	c.823A>C	c.(823-825)Agg>Cgg	p.R275R	ACP6_ENST00000460583.1_5'Flank	NM_016361.3	NP_057445.4	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	275					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)					TCGATCATCCTTGCAAATCTC	0.498																																					p.R275R		Atlas-SNP	.											.	ACP6	36	.	0			c.A823C						PASS	.	G		3356,1050	385.4+/-325.7	1284,788,131	124.0	112.0	116.0		823	3.4	0.0	1	dbSNP_96	116	6082,2518	412.1+/-350.7	2169,1744,387	no	coding-synonymous	ACP6	NM_016361.3		3453,2532,518	GG,GT,TT		29.2791,23.8311,27.4335		275/429	147124310	9438,3568	2203	4300	6503	SO:0001819	synonymous_variant	51205	exon7			TCATCCTTGCAAA	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.823A>C	1.37:g.147124310T>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	91	51	0.56044	NM_016361	Q59G61|Q5T490|Q6IAQ3|Q7LG81|Q9UIG6	Silent	SNP	ENST00000369238.6	37	CCDS928.1																																																																																			G|0.729;N|0.000	0.729	strong		0.498	ACP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039420.2	NM_016361	
MDN1	23195	hgsc.bcm.edu	37	6	90482397	90482397	+	Missense_Mutation	SNP	T	T	C	rs12110451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90482397T>C	ENST00000369393.3	-	14	2093	c.1978A>G	c.(1978-1980)Atc>Gtc	p.I660V	MDN1_ENST00000428876.1_Missense_Mutation_p.I660V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	660			I -> V (in dbSNP:rs12110451).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AGCTGCTCGATGAGAACAGAG	0.512													T|||	822	0.164137	0.1793	0.1398	5008	,	,		16706	0.2163		0.1809	False		,,,				2504	0.09				p.I660V		Atlas-SNP	.											.	MDN1	478	.	0			c.A1978G						PASS	.	T	VAL/ILE	848,3558	333.3+/-302.9	87,674,1442	107.0	110.0	109.0		1978	4.5	1.0	6	dbSNP_120	109	1539,7061	290.5+/-299.9	142,1255,2903	yes	missense	MDN1	NM_014611.1	29	229,1929,4345	CC,CT,TT		17.8953,19.2465,18.3531	benign	660/5597	90482397	2387,10619	2203	4300	6503	SO:0001583	missense	23195	exon14			GCTCGATGAGAAC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.1978A>G	6.37:g.90482397T>C	ENSP00000358400:p.Ile660Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	19	0.327586	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	410	0.18772893772893773	93	0.18902439024390244	46	0.1270718232044199	127	0.22202797202797203	144	0.18997361477572558	T	11.71	1.718341	0.30503	0.192465	0.178953	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.40476	1.03;1.03;1.03	5.65	4.47	0.54385	.	0.212692	0.41605	D	0.000848	T	0.12135	0.0295	N	0.11201	0.11	0.35477	P	0.20219200000000004	B;B	0.18610	0.007;0.029	B;B	0.20384	0.011;0.029	T	0.04855	-1.0922	9	0.62326	D	0.03	.	11.8001	0.52122	0.0:0.0:0.2879:0.7121	rs12110451;rs52821586;rs60532094;rs12110451	587;660	Q5T795;Q9NU22	.;MDN1_HUMAN	V	660;660;587	ENSP00000358400:I660V;ENSP00000413970:I660V;ENSP00000409664:I587V	ENSP00000358400:I660V	I	-	1	0	MDN1	90539118	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.720000	0.47252	0.953000	0.37825	0.528000	0.53228	ATC	T|0.817;C|0.183	0.183	strong		0.512	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
DCHS2	54798	hgsc.bcm.edu	37	4	155411939	155411939	+	Missense_Mutation	SNP	A	A	C	rs17373874	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:155411939A>C	ENST00000339452.1	-	1	929	c.569T>G	c.(568-570)gTt>gGt	p.V190G	DCHS2_ENST00000456341.2_Missense_Mutation_p.V183G|DCHS2_ENST00000443500.1_Missense_Mutation_p.V190G	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1396	Cadherin 2. {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)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ATCGTGGGCAACTGGCAGGCG	0.662													C|||	2034	0.40615	0.466	0.4986	5008	,	,		15381	0.1667		0.4632	False		,,,				2504	0.4479				p.V190G		Atlas-SNP	.											.	DCHS2	594	.	0			c.T569G						PASS	.	C	GLY/VAL,GLY/VAL	695,689		176,343,173	25.0	33.0	31.0		569,569	3.8	0.4	4	dbSNP_123	31	1428,1754		333,762,496	yes	missense,missense	DCHS2	NM_001142552.1,NM_001142553.1	109,109	509,1105,669	CC,CA,AA		44.8774,49.7832,46.4958	,	190/1370,190/710	155411939	2123,2443	692	1591	2283	SO:0001583	missense	54798	exon1			TGGGCAACTGGCA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.569T>G	4.37:g.155411939A>C	ENSP00000345062:p.Val190Gly	Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	37	CCDS47150.1	829	0.37957875457875456	219	0.4451219512195122	175	0.48342541436464087	82	0.14335664335664336	353	0.4656992084432718	C	0.010	-1.759958	0.00657	0.502168	0.448774	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.59906	0.23;0.23;0.23	4.72	3.81	0.43845	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.27730	P	0.9448348	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41466	-0.9507	7	0.06757	T	0.87	.	8.3588	0.32346	0.1347:0.4827:0.3826:0.0	rs17373874;rs17373874	190;190	E9PG03;E9PC11	.;.	G	190;190;183;190	ENSP00000345062:V190G;ENSP00000408543:V183G;ENSP00000395539:V190G	ENSP00000345062:V190G	V	-	2	0	DCHS2	155631389	0.480000	0.25933	0.436000	0.26797	0.097000	0.18754	2.713000	0.47194	0.988000	0.38734	-0.358000	0.07595	GTT	A|0.634;C|0.366	0.366	strong		0.662	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
SHMT1	6470	hgsc.bcm.edu	37	17	18232096	18232096	+	Missense_Mutation	SNP	G	G	A	rs1979277	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18232096G>A	ENST00000316694.3	-	12	1554	c.1420C>T	c.(1420-1422)Ctc>Ttc	p.L474F	RP1-178F10.3_ENST00000577764.1_lincRNA|SHMT1_ENST00000354098.3_Missense_Mutation_p.L435F|SHMT1_ENST00000539052.1_Missense_Mutation_p.L336F|SHMT1_ENST00000352886.6_Missense_Mutation_p.L394F	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	474			L -> F (in dbSNP:rs1979277). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|folic acid metabolic process (GO:0046655)|glycine biosynthetic process from serine (GO:0019264)|L-serine catabolic process (GO:0006565)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase biosynthetic process (GO:0009113)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	amino acid binding (GO:0016597)|glycine hydroxymethyltransferase activity (GO:0004372)|L-allo-threonine aldolase activity (GO:0008732)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)	13					Glycine(DB00145)|Mimosine(DB01055)|Tetrahydrofolic acid(DB00116)	AGAGGGAAGAGAGAGGCGAAG	0.637													G|||	1141	0.227835	0.3313	0.2695	5008	,	,		15016	0.0605		0.3082	False		,,,				2504	0.1483				p.L474F		Atlas-SNP	.											SHMT1,colon,carcinoma,0,1	SHMT1	36	1	0			c.C1420T	GRCh37	CM014391	SHMT1	M	rs1979277	PASS	.	G	PHE/LEU,PHE/LEU	1485,2921		237,1011,955	24.0	24.0	24.0		1420,1303	-4.5	0.0	17	dbSNP_92	24	2608,5988		386,1836,2076	no	missense,missense	SHMT1	NM_004169.3,NM_148918.1	22,22	623,2847,3031	AA,AG,GG		30.3397,33.704,31.4798	benign,benign	474/484,435/445	18232096	4093,8909	2203	4298	6501	SO:0001583	missense	6470	exon12			GGAAGAGAGAGGC		CCDS11196.1, CCDS11197.1, CCDS62112.1	17p11.2	2010-04-23			ENSG00000176974	ENSG00000176974	2.1.2.1		10850	protein-coding gene	gene with protein product	"""cytoplasmic serine hydroxymethyltransferase"", ""14 kDa protein"""	182144				8505317	Standard	NM_004169		Approved	CSHMT, SHMT, MGC15229, MGC24556	uc002gta.3	P34896	OTTHUMG00000059094	ENST00000316694.3:c.1420C>T	17.37:g.18232096G>A	ENSP00000318868:p.Leu474Phe	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_004169	B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Missense_Mutation	SNP	ENST00000316694.3	37	CCDS11196.1	538	0.24633699633699635	165	0.3353658536585366	102	0.281767955801105	33	0.057692307692307696	238	0.31398416886543534	G	10.03	1.239397	0.22711	0.33704	0.303397	ENSG00000176974	ENST00000316694;ENST00000395684;ENST00000352886;ENST00000539052;ENST00000354098;ENST00000395685	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.37	-4.52	0.03472	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.898574	0.09830	N	0.750310	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B;B;B	0.27140	0.0;0.169;0.0	B;B;B	0.25140	0.001;0.058;0.0	T	0.45571	-0.9252	9	0.59425	D	0.04	-2.2252	5.6984	0.17869	0.0733:0.4502:0.1512:0.3252	rs1979277;rs2230025;rs3183766;rs17850285;rs57933897;rs1979277	437;435;474	A8MYA6;P34896-2;P34896	.;.;GLYC_HUMAN	F	474;249;394;336;435;437	ENSP00000318868:L474F;ENSP00000345881:L394F;ENSP00000440089:L336F;ENSP00000318805:L435F	ENSP00000318868:L474F	L	-	1	0	SHMT1	18172821	0.000000	0.05858	0.006000	0.13384	0.247000	0.25773	0.542000	0.23222	-0.245000	0.09625	-0.211000	0.12701	CTC	G|0.719;A|0.281	0.281	strong		0.637	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169	
MUC16	94025	hgsc.bcm.edu	37	19	9056513	9056513	+	Silent	SNP	G	G	A	rs553859469		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9056513G>A	ENST00000397910.4	-	3	31136	c.30933C>T	c.(30931-30933)ggC>ggT	p.G10311G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10313	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATCCCCAGGGCCTGACTCTG	0.517													G|||	1	0.000199681	0.0	0.0	5008	,	,		21056	0.0		0.001	False		,,,				2504	0.0				p.G10311G		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-2,2	MUC16	4315	2	0			c.C30933T						scavenged	.						100.0	102.0	102.0					19																	9056513		2069	4205	6274	SO:0001819	synonymous_variant	94025	exon3			CCCAGGGCCTGAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30933C>T	19.37:g.9056513G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	97	2	0.0206186	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			.	.	none		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CTLA4	1493	hgsc.bcm.edu	37	2	204732714	204732714	+	Missense_Mutation	SNP	A	A	G	rs231775	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:204732714A>G	ENST00000302823.3	+	1	206	c.49A>G	c.(49-51)Acc>Gcc	p.T17A	CTLA4_ENST00000487393.1_3'UTR|CTLA4_ENST00000295854.6_Missense_Mutation_p.T17A|CTLA4_ENST00000427473.2_5'Flank|CTLA4_ENST00000472206.1_Missense_Mutation_p.T17A	NM_005214.4	NP_005205.2	P16410	CTLA4_HUMAN	cytotoxic T-lymphocyte-associated protein 4	17			T -> A (increased risk for Graves disease, insulin-dependent diabetes mellitus, thyroid-associated orbitopathy, systemic lupus erythematosus and susceptibility to HBV infection; dbSNP:rs231775). {ECO:0000269|PubMed:10475192, ECO:0000269|PubMed:10903931, ECO:0000269|PubMed:10924276, ECO:0000269|PubMed:15452244, ECO:0000269|PubMed:1713603, ECO:0000269|PubMed:18595775, ECO:0000269|PubMed:9259273}.		B cell receptor signaling pathway (GO:0050853)|cellular response to DNA damage stimulus (GO:0006974)|immune response (GO:0006955)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of immune response (GO:0050777)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of apoptotic process (GO:0043065)|T cell costimulation (GO:0031295)	clathrin-coated endocytic vesicle (GO:0045334)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)				large_intestine(4)|lung(4)|skin(1)	9					Ipilimumab(DB06186)	GAACCTGGCTACCAGGACCTG	0.507													A|||	2140	0.427316	0.388	0.4625	5008	,	,		18012	0.6369		0.3588	False		,,,				2504	0.3098				p.T17A		Atlas-SNP	.											.	CTLA4	24	.	0			c.A49G	GRCh37	CM970403	CTLA4	M	rs231775	PASS	.	A	ALA/THR,ALA/THR	1629,2777	501.5+/-365.0	288,1053,862	154.0	133.0	140.0	http://omim.org/entry/123890#0001	49,49	-2.8	0.0	2	dbSNP_79	140	3176,5424	481.5+/-370.7	593,1990,1717	yes	missense,missense	CTLA4	NM_001037631.2,NM_005214.4	58,58	881,3043,2579	GG,GA,AA		36.9302,36.9723,36.9445	benign,benign	17/175,17/224	204732714	4805,8201	2203	4300	6503	SO:0001583	missense	1493	exon1			CTGGCTACCAGGA		CCDS2362.1, CCDS42803.1	2q33	2014-02-03			ENSG00000163599	ENSG00000163599		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	2505	protein-coding gene	gene with protein product		123890	"""celiac disease 3"", ""insulin-dependent diabetes mellitus 12"""	CELIAC3, IDDM12		3220103, 8817351	Standard	NM_005214		Approved	CD152, CD, GSE, CD28, ICOS	uc002vak.2	P16410	OTTHUMG00000132877	ENST00000302823.3:c.49A>G	2.37:g.204732714A>G	ENSP00000303939:p.Thr17Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	128	68	0.53125	NM_005214	A0N1S0|E9PDH0|O95653|Q0PP65|Q52MC1|Q53TD5|Q5S005|Q8WXJ1|Q96P43|Q9UKN9	Missense_Mutation	SNP	ENST00000302823.3	37	CCDS2362.1	987	0.4519230769230769	197	0.40040650406504064	147	0.40607734806629836	367	0.6416083916083916	276	0.3641160949868074	A	0.643	-0.812512	0.02798	0.369723	0.369302	ENSG00000163599	ENST00000302823;ENST00000541886;ENST00000295854;ENST00000472206	T;T;T	0.26518	1.73;1.73;1.73	3.94	-2.84	0.05751	.	1.862500	0.02307	N	0.071771	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B;B	0.15930	0.015;0.007;0.007	B;B;B	0.11329	0.006;0.003;0.002	T	0.47886	-0.9082	9	0.49607	T	0.09	-6.4144	4.3597	0.11196	0.2102:0.4297:0.0:0.3601	rs231775;rs57563726;rs231775	17;17;17	P16410-4;Q8TDA6;P16410	.;.;CTLA4_HUMAN	A	17	ENSP00000303939:T17A;ENSP00000295854:T17A;ENSP00000417779:T17A	ENSP00000295854:T17A	T	+	1	0	CTLA4	204440959	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.318000	0.08050	-0.514000	0.06488	-0.438000	0.05819	ACC	A|0.592;G|0.408	0.408	strong		0.507	CTLA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256365.1	NM_005214	
EPHX2	2053	hgsc.bcm.edu	37	8	27401964	27401964	+	Silent	SNP	A	A	C	rs1126452	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27401964A>C	ENST00000521400.1	+	19	2023	c.1593A>C	c.(1591-1593)ccA>ccC	p.P531P	EPHX2_ENST00000518379.1_Silent_p.P499P|EPHX2_ENST00000380476.3_Silent_p.P478P|EPHX2_ENST00000521780.1_Silent_p.P465P|EPHX2_ENST00000517536.1_Silent_p.P348P	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	531	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		CCCCCAGGCCAACCGAGGTGA	0.532													C|||	2158	0.430911	0.7655	0.255	5008	,	,		19379	0.4147		0.2366	False		,,,				2504	0.32				p.P531P		Atlas-SNP	.											EPHX2,NS,carcinoma,+2,1	EPHX2	57	1	0			c.A1593C						PASS	.	C		2862,1544	483.7+/-359.8	941,980,282	98.0	106.0	103.0		1593	-4.5	0.0	8	dbSNP_86	103	2310,6290	703.8+/-405.4	337,1636,2327	no	coding-synonymous	EPHX2	NM_001979.4		1278,2616,2609	CC,CA,AA		26.8605,35.0431,39.7663		531/556	27401964	5172,7834	2203	4300	6503	SO:0001819	synonymous_variant	2053	exon19			CAGGCCAACCGAG	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1593A>C	8.37:g.27401964A>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1																																																																																			A|0.594;C|0.406	0.406	strong		0.532	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
SAMD9	54809	hgsc.bcm.edu	37	7	92733975	92733975	+	Missense_Mutation	SNP	G	G	A	rs78564070	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92733975G>A	ENST00000379958.2	-	3	1705	c.1436C>T	c.(1435-1437)aCg>aTg	p.T479M		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	479						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AGTAGAAATCGTCTCATTTGG	0.393													G|||	417	0.0832668	0.0802	0.0389	5008	,	,		19308	0.0377		0.0507	False		,,,				2504	0.1994				p.T479M		Atlas-SNP	.											SAMD9,NS,carcinoma,+1,1	SAMD9	239	1	0			c.C1436T						PASS	.	G	MET/THR,MET/THR	316,4090	168.0+/-198.9	10,296,1897	81.0	80.0	81.0		1436,1436	-1.3	0.1	7	dbSNP_131	81	372,8226	122.9+/-181.8	8,356,3935	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	81,81	18,652,5832	AA,AG,GG		4.3266,7.172,5.2907	possibly-damaging,possibly-damaging	479/1590,479/1590	92733975	688,12316	2203	4299	6502	SO:0001583	missense	54809	exon2			GAAATCGTCTCAT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1436C>T	7.37:g.92733975G>A	ENSP00000369292:p.Thr479Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	113	0.051739926739926737	39	0.07926829268292683	19	0.052486187845303865	18	0.03146853146853147	37	0.048812664907651716	G	6.546	0.469062	0.12461	0.07172	0.043266	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.13778	2.56;2.56	4.38	-1.3	0.09259	.	0.537042	0.15112	N	0.279916	T	0.00356	0.0011	N	0.14661	0.345	0.09310	N	0.999996	B	0.12013	0.005	B	0.04013	0.001	T	0.32508	-0.9904	10	0.52906	T	0.07	-0.5196	6.2499	0.20839	0.3958:0.0:0.1379:0.4664	.	479	Q5K651	SAMD9_HUMAN	M	479	ENSP00000369292:T479M;ENSP00000414529:T479M	ENSP00000369292:T479M	T	-	2	0	SAMD9	92571911	0.000000	0.05858	0.057000	0.19452	0.833000	0.47200	-0.067000	0.11579	-0.279000	0.09167	-1.222000	0.01597	ACG	G|0.947;A|0.053	0.053	strong		0.393	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
SLC52A1	55065	hgsc.bcm.edu	37	17	4937351	4937351	+	Silent	SNP	G	G	T	rs56126318	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4937351G>T	ENST00000424747.1	-	3	1145	c.433C>A	c.(433-435)Cgg>Agg	p.R145R	SLC52A1_ENST00000254853.5_Silent_p.R145R|SLC52A1_ENST00000512825.2_Silent_p.R145R	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	145					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										AAGAAAGACCGTAAGAAAGGA	0.592													G|||	332	0.0662939	0.0204	0.1268	5008	,	,		21137	0.0744		0.0875	False		,,,				2504	0.0552				p.R145R		Atlas-SNP	.											GPR172B,NS,carcinoma,+1,1	.	.	1	0			c.C433A						PASS	.	G	,	112,4294	83.4+/-121.9	0,112,2091	137.0	135.0	136.0		433,433	0.2	1.0	17	dbSNP_129	136	709,7891	174.2+/-224.5	35,639,3626	no	coding-synonymous,coding-synonymous	GPR172B	NM_001104577.1,NM_017986.3	,	35,751,5717	TT,TG,GG		8.2442,2.542,6.3125	,	145/449,145/449	4937351	821,12185	2203	4300	6503	SO:0001819	synonymous_variant	55065	exon3			AAGACCGTAAGAA	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"""Solute carriers"""	30225	protein-coding gene	gene with protein product	"""riboflavin transporter 1"""	607883	"""G protein-coupled receptor 172B"""	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.433C>A	17.37:g.4937351G>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	91	51	0.56044	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Silent	SNP	ENST00000424747.1	37	CCDS11066.1																																																																																			G|0.931;T|0.069	0.069	strong		0.592	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
SLFN11	91607	hgsc.bcm.edu	37	17	33680811	33680811	+	Missense_Mutation	SNP	C	C	A	rs9898983	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33680811C>A	ENST00000394566.1	-	6	1738	c.1466G>T	c.(1465-1467)cGc>cTc	p.R489L	SLFN11_ENST00000308377.4_Missense_Mutation_p.R489L	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	489			R -> L (in dbSNP:rs9898983).		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)	p.R489L(2)		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)		AAAGGCGGTGCGAGTGCAGTA	0.562													C|||	1707	0.340855	0.4266	0.3415	5008	,	,		9159	0.4464		0.159	False		,,,				2504	0.3027				p.R489L		Atlas-SNP	.											SLFN11,NS,carcinoma,0,2	SLFN11	112	2	2	Substitution - Missense(2)	stomach(2)	c.G1466T						scavenged	.						16.0	14.0	15.0					17																	33680811		2181	4250	6431	SO:0001583	missense	91607	exon4			GCGGTGCGAGTGC	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.1466G>T	17.37:g.33680811C>A	ENSP00000378067:p.Arg489Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	72	0.626087	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	709	0.32463369963369965	229	0.4654471544715447	113	0.31215469613259667	239	0.4178321678321678	128	0.16886543535620052	c	1.872	-0.460031	0.04508	.	.	ENSG00000172716	ENST00000308377;ENST00000394566	T;T	0.02032	4.49;4.49	3.69	-7.38	0.01407	.	1.539480	0.03869	N	0.275369	T	0.00012	0.0000	L	0.48362	1.52	0.80722	P	0.0	B	0.17667	0.023	B	0.13407	0.009	T	0.47114	-0.9142	9	0.10636	T	0.68	.	4.2916	0.10881	0.1177:0.1683:0.1165:0.5975	rs9898983	489	Q7Z7L1	SLN11_HUMAN	L	489	ENSP00000312402:R489L;ENSP00000378067:R489L	ENSP00000312402:R489L	R	-	2	0	SLFN11	30704924	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-6.906000	0.00050	-1.990000	0.00978	-0.903000	0.02851	CGC	C|0.694;A|0.306	0.306	strong		0.562	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
FCGBP	8857	hgsc.bcm.edu	37	19	40368391	40368391	+	Silent	SNP	G	G	A	rs76288738	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40368391G>A	ENST00000221347.6	-	28	12964	c.12957C>T	c.(12955-12957)gaC>gaT	p.D4319D		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4319						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGCAAAGAATGTCACGGTCCC	0.622													G|||	594	0.11861	0.264	0.0447	5008	,	,		26515	0.0516		0.0557	False		,,,				2504	0.1084				p.D4319D		Atlas-SNP	.											.	FCGBP	416	.	0			c.C12957T						PASS	.						176.0	178.0	177.0					19																	40368391		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon28			AAGAATGTCACGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12957C>T	19.37:g.40368391G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	286	39	0.136364	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.967;A|0.033	0.033	strong		0.622	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF236	7776	hgsc.bcm.edu	37	18	74639433	74639433	+	Silent	SNP	G	G	A	rs117481741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:74639433G>A	ENST00000253159.8	+	24	4566	c.4368G>A	c.(4366-4368)ccG>ccA	p.P1456P	ZNF236_ENST00000320610.9_Silent_p.P1458P	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1456					cellular response to glucose stimulus (GO:0071333)|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(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		CCATAGGCCCGCTGTCTGAGC	0.527													G|||	36	0.0071885	0.0	0.0029	5008	,	,		18269	0.0		0.0149	False		,,,				2504	0.0194				p.P1456P		Atlas-SNP	.											.	ZNF236	325	.	0			c.G4368A						PASS	.	G		7,4079		0,7,2036	53.0	53.0	53.0		4368	-11.6	0.3	18	dbSNP_132	53	108,8298		1,106,4096	no	coding-synonymous	ZNF236	NM_007345.3		1,113,6132	AA,AG,GG		1.2848,0.1713,0.9206		1456/1846	74639433	115,12377	2043	4203	6246	SO:0001819	synonymous_variant	7776	exon24			AGGCCCGCTGTCT	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.4368G>A	18.37:g.74639433G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_007345	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	CCDS42447.1																																																																																			G|0.992;A|0.008	0.008	strong		0.527	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
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 GAIIx	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-TE_ENST00000387459.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-ND5_ENST00000361567.2_5'Flank|MT-TG_ENST00000387429.1_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		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	17	6	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	
MUC16	94025	hgsc.bcm.edu	37	19	9083143	9083143	+	Missense_Mutation	SNP	G	G	A	rs7245949	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9083143G>A	ENST00000397910.4	-	1	8875	c.8672C>T	c.(8671-8673)aCa>aTa	p.T2891I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2892	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AAACTCAAATGTCAAGGTAGA	0.517													G|||	1134	0.226438	0.27	0.2983	5008	,	,		21087	0.0228		0.3111	False		,,,				2504	0.2393				p.T2891I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C8672T						PASS	.	G	ILE/THR	1009,2791		143,723,1034	69.0	64.0	66.0		8672	0.8	0.0	19	dbSNP_116	66	2724,5530		461,1802,1864	yes	missense	MUC16	NM_024690.2	89	604,2525,2898	AA,AG,GG		33.0022,26.5526,30.969	probably-damaging	2891/14508	9083143	3733,8321	1900	4127	6027	SO:0001583	missense	94025	exon1			TCAAATGTCAAGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8672C>T	19.37:g.9083143G>A	ENSP00000381008:p.Thr2891Ile	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	175	81	0.462857	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	490	0.22435897435897437	127	0.258130081300813	111	0.30662983425414364	14	0.024475524475524476	238	0.31398416886543534	g	1.396	-0.579371	0.03854	0.265526	0.330022	ENSG00000181143	ENST00000397910	T	0.02472	4.28	0.773	0.773	0.18516	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.62365	0.991	D	0.65323	0.934	T	0.55049	-0.8201	8	0.87932	D	0	.	4.823	0.13400	0.0:0.0:1.0:0.0	rs7245949;rs56689992;rs7245949	2891	B5ME49	.	I	2891	ENSP00000381008:T2891I	ENSP00000381008:T2891I	T	-	2	0	MUC16	8944143	0.016000	0.18221	0.002000	0.10522	0.009000	0.06853	1.193000	0.32162	0.680000	0.31366	0.313000	0.20887	ACA	G|0.771;A|0.229	0.229	strong		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
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 GAIIx	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		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	38	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	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907843	12907843	+	Silent	SNP	T	T	G	rs2982093		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907843T>G	ENST00000317869.6	-	2	525	c.300A>C	c.(298-300)tcA>tcC	p.S100S		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	100						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						TCTCCGCTGCTGATCGTTTCA	0.488																																					p.S100S		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,-1,1	HNRNPCL1	68	1	0			c.A300C						PASS	.						133.0	126.0	129.0					1																	12907843		2203	4300	6503	SO:0001819	synonymous_variant	343069	exon2			CGCTGCTGATCGT	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.300A>C	1.37:g.12907843T>G		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	236	45	0.190678	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	37	CCDS30591.1																																																																																			T|1.000;|0.000	.	weak		0.488	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
C1QTNF9	338872	hgsc.bcm.edu	37	13	24895631	24895631	+	Missense_Mutation	SNP	T	T	A	rs78083136	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:24895631T>A	ENST00000382071.2	+	4	812	c.727T>A	c.(727-729)Tgc>Agc	p.C243S	C1QTNF9-AS1_ENST00000449656.1_RNA|C1QTNF9_ENST00000332018.4_Missense_Mutation_p.C243S|AL359736.1_ENST00000422229.2_5'Flank			P0C862	C1T9A_HUMAN	C1q and tumor necrosis factor related protein 9	243	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				endometrium(1)|kidney(2)|lung(6)	9		all_cancers(29;3.55e-20)|all_epithelial(30;4.25e-17)|all_lung(29;1.04e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.00565)|Epithelial(112;0.027)|OV - Ovarian serous cystadenocarcinoma(117;0.115)|Lung(94;0.159)		GAAATTCACGTGCCACATTGC	0.408																																					p.C243S		Atlas-SNP	.											.	C1QTNF9	22	.	0			c.T727A						PASS	.						193.0	170.0	178.0					13																	24895631		2203	4300	6503	SO:0001583	missense	338872	exon4			TTCACGTGCCACA	BC040438	CCDS9306.1	13q12.12	2010-08-18			ENSG00000240654	ENSG00000240654			28732	protein-coding gene	gene with protein product		614285				12975309, 18787108	Standard	NM_178540		Approved	MGC48915, CTRP9, C1QTNF9A, AQL1	uc001upj.3	P0C862	OTTHUMG00000016576	ENST00000382071.2:c.727T>A	13.37:g.24895631T>A	ENSP00000371503:p.Cys243Ser	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	228	42	0.184211	NM_178540	A2A3T6|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	Missense_Mutation	SNP	ENST00000382071.2	37	CCDS9306.1	148	0.06776556776556776	29	0.05894308943089431	19	0.052486187845303865	1	0.0017482517482517483	99	0.13060686015831136	N	14.79	2.640291	0.47153	.	.	ENSG00000240654	ENST00000382071;ENST00000332018	T;T	0.79454	-1.27;-1.27	3.96	3.96	0.45880	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.000000	0.85682	D	0.000000	T	0.06645	0.0170	M	0.84219	2.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.53085	-0.8488	10	0.62326	D	0.03	.	8.8982	0.35479	0.0:0.0:0.1885:0.8115	.	243	P0C862	C1T9A_HUMAN	S	243	ENSP00000371503:C243S;ENSP00000333737:C243S	ENSP00000333737:C243S	C	+	1	0	C1QTNF9	23793631	1.000000	0.71417	0.988000	0.46212	0.363000	0.29612	7.715000	0.84713	1.768000	0.52137	0.352000	0.21897	TGC	T|0.930;A|0.070	0.070	strong		0.408	C1QTNF9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044177.1	NM_178540	
PREX2	80243	hgsc.bcm.edu	37	8	69009268	69009268	+	Silent	SNP	C	C	T	rs3812458	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:69009268C>T	ENST00000288368.4	+	22	2662	c.2385C>T	c.(2383-2385)ttC>ttT	p.F795F	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	795					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TTGACAAATTCAACACTATGG	0.383													C|||	1333	0.266174	0.2731	0.2435	5008	,	,		17724	0.1885		0.2783	False		,,,				2504	0.3405				p.F795F		Atlas-SNP	.											.	PREX2	614	.	0			c.C2385T						PASS	.	C	,	1201,3205	419.3+/-338.6	169,863,1171	132.0	121.0	124.0		2385,2385	2.2	1.0	8	dbSNP_107	124	2270,6330	383.0+/-340.6	311,1648,2341	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	480,2511,3512	TT,TC,CC		26.3953,27.2583,26.6877	,	795/1607,795/980	69009268	3471,9535	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon22			CAAATTCAACACT	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2385C>T	8.37:g.69009268C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	88	31	0.352273	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			C|0.740;T|0.260	0.260	strong		0.383	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
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 GAIIx	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_ENST00000368956.2_Missense_Mutation_p.S52W|DMBT1_ENST00000368955.3_Missense_Mutation_p.S52W|DMBT1_ENST00000359586.6_Missense_Mutation_p.S52W|DMBT1_ENST00000344338.3_Missense_Mutation_p.S52W|DMBT1_ENST00000330163.4_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	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	192	94	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	
OAS3	4940	hgsc.bcm.edu	37	12	113398919	113398919	+	Silent	SNP	G	G	A	rs2072136	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:113398919G>A	ENST00000228928.7	+	8	1880	c.1701G>A	c.(1699-1701)tcG>tcA	p.S567S	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	567	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						AGGTCTACTCGAGGCTCCTCA	0.537													G|||	1580	0.315495	0.0862	0.2752	5008	,	,		18330	0.6577		0.2346	False		,,,				2504	0.3845				p.S567S		Atlas-SNP	.											.	OAS3	63	.	0			c.G1701A						PASS	.	G		430,3478		30,370,1554	45.0	46.0	46.0		1701	-8.9	0.0	12	dbSNP_96	46	1909,6421		221,1467,2477	no	coding-synonymous	OAS3	NM_006187.2		251,1837,4031	AA,AG,GG		22.9172,11.0031,19.1126		567/1088	113398919	2339,9899	1954	4165	6119	SO:0001819	synonymous_variant	4940	exon8			CTACTCGAGGCTC	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.1701G>A	12.37:g.113398919G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			G|0.696;N|0.000	.	strong		0.537	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
DNAJC11	55735	hgsc.bcm.edu	37	1	6705874	6705874	+	Missense_Mutation	SNP	G	G	C	rs200454	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:6705874G>C	ENST00000377577.5	-	8	992	c.869C>G	c.(868-870)aCc>aGc	p.T290S	DNAJC11_ENST00000377573.5_Missense_Mutation_p.T200S|DNAJC11_ENST00000349363.6_Intron|DNAJC11_ENST00000294401.7_Missense_Mutation_p.T290S|DNAJC11_ENST00000542246.1_Missense_Mutation_p.T252S|DNAJC11_ENST00000465508.1_5'Flank	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	290			T -> A (in dbSNP:rs200454).|T -> S (in dbSNP:rs200454). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(11)|lung(8)|ovary(2)|skin(1)|urinary_tract(1)	32	Ovarian(185;0.0265)|all_lung(157;0.154)	all_cancers(23;1.97e-27)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;2.34e-07)|COAD - Colon adenocarcinoma(227;2.05e-05)|Kidney(185;7.67e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000639)|KIRC - Kidney renal clear cell carcinoma(229;0.00128)|STAD - Stomach adenocarcinoma(132;0.00179)|READ - Rectum adenocarcinoma(331;0.0649)		GAAGTGGCTGGTTTTAGTGTC	0.592													G|||	807	0.161142	0.1982	0.3559	5008	,	,		17937	0.002		0.2266	False		,,,				2504	0.0695				p.T290S		Atlas-SNP	.											.	DNAJC11	93	.	0			c.C869G						PASS	.	G	SER/THR	986,3420	353.3+/-312.1	113,760,1330	138.0	131.0	133.0		869	4.3	1.0	1	dbSNP_79	133	1771,6829	306.6+/-308.0	170,1431,2699	yes	missense	DNAJC11	NM_018198.3	58	283,2191,4029	CC,CG,GG		20.593,22.3786,21.1979	benign	290/560	6705874	2757,10249	2203	4300	6503	SO:0001583	missense	55735	exon8			TGGCTGGTTTTAG	AF306695	CCDS87.1	1p36.23	2011-09-02			ENSG00000007923	ENSG00000007923		"""Heat shock proteins / DNAJ (HSP40)"""	25570	protein-coding gene	gene with protein product		614827				12964007	Standard	NM_018198		Approved	FLJ10737	uc001aof.2	Q9NVH1	OTTHUMG00000001443	ENST00000377577.5:c.869C>G	1.37:g.6705874G>C	ENSP00000366800:p.Thr290Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	111	63	0.567568	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Missense_Mutation	SNP	ENST00000377577.5	37	CCDS87.1	406	0.1858974358974359	113	0.22967479674796748	118	0.3259668508287293	2	0.0034965034965034965	173	0.22823218997361477	G	9.833	1.188875	0.21954	0.223786	0.20593	ENSG00000007923	ENST00000377577;ENST00000294401;ENST00000542246;ENST00000377573;ENST00000426784	T;T;T;T;T	0.22336	2.56;2.55;2.29;1.96;2.51	5.27	4.33	0.51752	.	0.136479	0.64402	D	0.000003	T	0.00012	0.0000	N	0.11427	0.14	0.24466	P	0.99441492	B;B;B	0.12013	0.0;0.003;0.005	B;B;B	0.10450	0.0;0.005;0.002	T	0.42582	-0.9443	9	0.09084	T	0.74	-16.7799	12.0357	0.53423	0.0:0.0:0.6861:0.3139	rs200454;rs201177;rs3949837;rs200454	200;290;290	B4DGD5;Q9NVH1-3;Q9NVH1	.;.;DJC11_HUMAN	S	290;290;252;200;320	ENSP00000366800:T290S;ENSP00000294401:T290S;ENSP00000444020:T252S;ENSP00000366796:T200S;ENSP00000410194:T320S	ENSP00000294401:T290S	T	-	2	0	DNAJC11	6628461	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.913000	0.39956	1.172000	0.42781	0.650000	0.86243	ACC	G|0.786;C|0.214	0.214	strong		0.592	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198	
HYAL4	23553	hgsc.bcm.edu	37	7	123517000	123517000	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:123517000G>A	ENST00000223026.4	+	5	1875	c.1237G>A	c.(1237-1239)Ggg>Agg	p.G413R	HYAL4_ENST00000476325.1_Missense_Mutation_p.G413R	NM_012269.2	NP_036401.2	Q2M3T9	HYAL4_HUMAN	hyaluronoglucosaminidase 4	413					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|glycosaminoglycan catabolic process (GO:0006027)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	hyalurononglucosaminidase activity (GO:0004415)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	23						CTCTGAGGACGGGGAGTTTAC	0.483																																					p.G413R		Atlas-SNP	.											.	HYAL4	65	.	0			c.G1237A						PASS	.						128.0	124.0	125.0					7																	123517000		2203	4300	6503	SO:0001583	missense	23553	exon5			GAGGACGGGGAGT	AF009010	CCDS5789.1	7q31.3	2010-01-14			ENSG00000106302	ENSG00000106302			5323	protein-coding gene	gene with protein product	"""hyaluronidase 4"""	604510				10493834	Standard	NM_012269		Approved		uc003vlc.3	Q2M3T9	OTTHUMG00000157349	ENST00000223026.4:c.1237G>A	7.37:g.123517000G>A	ENSP00000223026:p.Gly413Arg	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	171	89	0.520468	NM_012269	D0VXG1|Q9UL99|Q9Y6T9	Missense_Mutation	SNP	ENST00000223026.4	37	CCDS5789.1	.	.	.	.	.	.	.	.	.	.	G	4.708	0.131577	0.08981	.	.	ENSG00000106302	ENST00000223026;ENST00000476325	T;T	0.18810	2.19;2.19	5.86	4.05	0.47172	Epidermal growth factor-like (1);	0.190664	0.44483	N	0.000452	T	0.21921	0.0528	M	0.75615	2.305	0.09310	N	0.999994	B	0.23128	0.08	B	0.17722	0.019	T	0.22800	-1.0206	10	0.18276	T	0.48	-6.474	8.9867	0.35999	0.1403:0.1543:0.7054:0.0	.	413	Q2M3T9	HYAL4_HUMAN	R	413	ENSP00000223026:G413R;ENSP00000417186:G413R	ENSP00000223026:G413R	G	+	1	0	HYAL4	123304236	0.559000	0.26562	0.013000	0.15412	0.020000	0.10135	3.240000	0.51368	0.924000	0.37069	-0.142000	0.14014	GGG	.	.	none		0.483	HYAL4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348545.1	NM_012269	
AFAP1	60312	hgsc.bcm.edu	37	4	7857230	7857230	+	Silent	SNP	C	C	T	rs61742221	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:7857230C>T	ENST00000360265.4	-	3	531	c.297G>A	c.(295-297)ccG>ccA	p.P99P	AFAP1_ENST00000358461.2_Silent_p.P99P|AFAP1_ENST00000420658.1_Silent_p.P99P|AFAP1_ENST00000382543.3_Silent_p.P99P			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	99	Pro-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						CGGGGCTCAGCGGCACAGCTT	0.552													C|||	892	0.178115	0.0477	0.2464	5008	,	,		18081	0.0645		0.4443	False		,,,				2504	0.1493				p.P99P		Atlas-SNP	.											.	AFAP1	93	.	0			c.G297A						PASS	.	C	,	441,3965	213.8+/-233.3	20,401,1782	90.0	77.0	81.0		297,297	-9.3	0.6	4	dbSNP_129	81	3760,4840	535.6+/-382.8	836,2088,1376	no	coding-synonymous,coding-synonymous	AFAP1	NM_001134647.1,NM_198595.2	,	856,2489,3158	TT,TC,CC		43.7209,10.0091,32.3005	,	99/815,99/731	7857230	4201,8805	2203	4300	6503	SO:0001819	synonymous_variant	60312	exon4			GCTCAGCGGCACA	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.297G>A	4.37:g.7857230C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	69	67	0.971014	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			C|0.700;T|0.300	0.300	strong		0.552	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
DSCAML1	57453	hgsc.bcm.edu	37	11	117308795	117308795	+	Silent	SNP	G	G	A	rs2253440	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:117308795G>A	ENST00000321322.6	-	25	4429	c.4428C>T	c.(4426-4428)ttC>ttT	p.F1476F	DSCAML1_ENST00000527706.1_Silent_p.F1206F	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1416	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		ACTGTAGCACGAAGCCTGCGG	0.627													G|||	823	0.164337	0.1725	0.1254	5008	,	,		16762	0.0565		0.2187	False		,,,				2504	0.2362				p.F1476F		Atlas-SNP	.											DSCAML1,colon,carcinoma,0,1	DSCAML1	286	1	0			c.C4428T						PASS	.	G		882,3520	340.5+/-306.2	82,718,1401	61.0	48.0	52.0		4428	-3.0	1.0	11	dbSNP_100	52	2041,6551	351.5+/-328.3	242,1557,2497	no	coding-synonymous	DSCAML1	NM_020693.2		324,2275,3898	AA,AG,GG		23.7547,20.0363,22.495		1476/2114	117308795	2923,10071	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon25			TAGCACGAAGCCT		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.4428C>T	11.37:g.117308795G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	117	93	0.794872	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			G|0.808;A|0.192	0.192	strong		0.627	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
UNC13D	201294	hgsc.bcm.edu	37	17	73827205	73827205	+	Missense_Mutation	SNP	T	T	C	rs1135688	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73827205T>C	ENST00000207549.4	-	27	2978	c.2599A>G	c.(2599-2601)Aag>Gag	p.K867E	UNC13D_ENST00000412096.2_Missense_Mutation_p.K867E	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	867	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.		K -> E (in dbSNP:rs1135688).		defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGCAGGGCCTTGGGTGGCAGG	0.612									Familial Hemophagocytic Lymphohistiocytosis				C|||	2501	0.499401	0.9032	0.2968	5008	,	,		13362	0.4266		0.336	False		,,,				2504	0.3405				p.K867E		Atlas-SNP	.											.	UNC13D	68	.	0			c.A2599G						PASS	.	C	GLU/LYS	3612,794	315.2+/-294.0	1486,640,77	63.0	64.0	63.0		2599	3.7	0.3	17	dbSNP_86	63	2800,5798	676.1+/-403.3	458,1884,1957	yes	missense	UNC13D	NM_199242.2	56	1944,2524,2034	CC,CT,TT		32.5657,18.0209,49.3079	benign	867/1091	73827205	6412,6592	2203	4299	6502	SO:0001583	missense	201294	exon27	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GGGCCTTGGGTGG	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.2599A>G	17.37:g.73827205T>C	ENSP00000207549:p.Lys867Glu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	37	CCDS11730.1	1082	0.49542124542124544	441	0.8963414634146342	119	0.3287292817679558	280	0.48951048951048953	242	0.31926121372031663	C	0.028	-1.352212	0.01256	0.819791	0.325657	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.72282	-0.64;-0.64	4.67	3.7	0.42460	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.389639	0.26394	N	0.024634	T	0.00012	0.0000	N	0.00193	-1.875	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41875	-0.9484	9	0.02654	T	1	-0.9421	9.48	0.38895	0.0:0.835:0.0:0.165	rs1135688;rs3198548;rs28622144;rs61662805	867	Q70J99	UN13D_HUMAN	E	867	ENSP00000207549:K867E;ENSP00000388093:K867E	ENSP00000207549:K867E	K	-	1	0	UNC13D	71338800	0.073000	0.21202	0.342000	0.25602	0.004000	0.04260	1.088000	0.30877	0.583000	0.29574	-0.733000	0.03571	AAG	T|0.510;C|0.490	0.490	strong		0.612	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
MAP1B	4131	hgsc.bcm.edu	37	5	71494906	71494906	+	Silent	SNP	G	G	A	rs61734262	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:71494906G>A	ENST00000296755.7	+	5	6022	c.5724G>A	c.(5722-5724)aaG>aaA	p.K1908K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1908					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)		ACTATGAGAAGATAGAGAGAA	0.448													G|||	412	0.0822684	0.1021	0.0461	5008	,	,		19259	0.0317		0.1173	False		,,,				2504	0.0971				p.K1908K	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.G5724A						PASS	.	G		482,3924	203.5+/-225.9	20,442,1741	61.0	65.0	64.0		5724	3.5	0.7	5	dbSNP_129	64	1019,7581	206.8+/-248.7	62,895,3343	no	coding-synonymous	MAP1B	NM_005909.3		82,1337,5084	AA,AG,GG		11.8488,10.9396,11.5408		1908/2469	71494906	1501,11505	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			TGAGAAGATAGAG	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.5724G>A	5.37:g.71494906G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			G|0.900;A|0.100	0.100	strong		0.448	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
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 GAIIx	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_ENST00000576776.1_Silent_p.F37F|AIPL1_ENST00000576307.1_Intron|AIPL1_ENST00000575265.1_Silent_p.F37F|AIPL1_ENST00000250087.5_Silent_p.F37F|AIPL1_ENST00000571740.1_Silent_p.F37F|AIPL1_ENST00000574506.1_Intron	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		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	38	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 GAIIx	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	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	97	42	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 GAIIx	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		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	102	48	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	
BTBD6	90135	hgsc.bcm.edu	37	14	105716034	105716034	+	Silent	SNP	C	C	T	rs2816606	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105716034C>T	ENST00000392554.3	+	4	780	c.483C>T	c.(481-483)taC>taT	p.Y161Y	BRF1_ENST00000440513.3_Intron|BRF1_ENST00000379932.4_5'Flank|BRF1_ENST00000546474.1_Intron|BRF1_ENST00000327359.3_Intron|BTBD6_ENST00000536364.1_Silent_p.Y161Y|BTBD6_ENST00000327471.3_Silent_p.Y86Y|BRF1_ENST00000379937.2_Intron|BRF1_ENST00000392557.4_5'Flank|BRF1_ENST00000551787.1_5'Flank|BRF1_ENST00000446501.2_5'Flank|BTBD6_ENST00000463376.2_Silent_p.Y86Y			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	161						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		CCACTCTGTACGCTGCTAAGA	0.572													C|||	917	0.183107	0.1248	0.1801	5008	,	,		18024	0.1091		0.2833	False		,,,				2504	0.2372				p.Y161Y		Atlas-SNP	.											.	BTBD6	24	.	0			c.C483T						PASS	.	C	,,,,	644,3760	274.3+/-271.8	44,556,1602	55.0	56.0	56.0		,,,,483	-3.5	0.6	14	dbSNP_100	56	2328,6272	388.6+/-342.6	301,1726,2273	no	intron,intron,intron,intron,coding-synonymous	BRF1,BTBD6	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001519.3,NM_033271.2	,,,,	345,2282,3875	TT,TC,CC		27.0698,14.6231,22.8545	,,,,	,,,,161/486	105716034	2972,10032	2202	4300	6502	SO:0001819	synonymous_variant	90135	exon5			TCTGTACGCTGCT	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"""BTB/POZ domain containing"""	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.483C>T	14.37:g.105716034C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	43	0.597222	NM_033271	Q8IVQ7|Q9BR94	Silent	SNP	ENST00000392554.3	37	CCDS10002.2																																																																																			C|0.776;T|0.224	0.224	strong		0.572	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4		
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25255506	25255506	+	Silent	SNP	C	C	T	rs11642611	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:25255506C>T	ENST00000328086.7	-	6	2384	c.1581G>A	c.(1579-1581)aaG>aaA	p.K527K		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	527					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		ACAATTTGCTCTTCCGATGAC	0.498													C|||	1672	0.333866	0.4713	0.3026	5008	,	,		18387	0.3294		0.2107	False		,,,				2504	0.3016				p.K527K		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.G1581A						PASS	.	C		1983,2411	548.5+/-377.6	450,1083,664	68.0	68.0	68.0		1581	2.3	1.0	16	dbSNP_120	68	1784,6816	316.7+/-312.9	181,1422,2697	no	coding-synonymous	ZKSCAN2	NM_001012981.4		631,2505,3361	TT,TC,CC		20.7442,45.1297,28.9903		527/968	25255506	3767,9227	2197	4300	6497	SO:0001819	synonymous_variant	342357	exon6			TTTGCTCTTCCGA	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.1581G>A	16.37:g.25255506C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_001012981	A1L3B4|Q6ZN77	Silent	SNP	ENST00000328086.7	37	CCDS32410.1																																																																																			C|0.698;T|0.302	0.302	strong		0.498	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
SLC11A2	4891	hgsc.bcm.edu	37	12	51386066	51386066	+	Silent	SNP	A	A	G	rs1048230	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:51386066A>G	ENST00000262051.7	-	13	1341	c.1254T>C	c.(1252-1254)atT>atC	p.I418I	SLC11A2_ENST00000547198.1_Silent_p.I418I|SLC11A2_ENST00000394904.3_Silent_p.I447I|SLC11A2_ENST00000545993.2_Silent_p.I414I|SLC11A2_ENST00000547688.1_Silent_p.I447I|SLC11A2_ENST00000262052.5_Silent_p.I418I|SLC11A2_ENST00000541174.2_Silent_p.I418I|SLC11A2_ENST00000546743.1_Silent_p.I339I	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	418					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						GGATGATGGCAATAGAGCGAG	0.473													A|||	691	0.137979	0.0484	0.1037	5008	,	,		21367	0.1151		0.1809	False		,,,				2504	0.2628				p.I447I		Atlas-SNP	.											.	SLC11A2	51	.	0			c.T1341C						PASS	.	A	,,,,,,	304,4102	166.9+/-198.0	9,286,1908	148.0	117.0	128.0		1254,1341,1254,1254,1254,1254,1242	3.0	1.0	12	dbSNP_86	128	1675,6925	308.4+/-308.9	164,1347,2789	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC11A2	NM_000617.2,NM_001174125.1,NM_001174126.1,NM_001174127.1,NM_001174128.1,NM_001174129.1,NM_001174130.1	,,,,,,	173,1633,4697	GG,GA,AA		19.4767,6.8997,15.2161	,,,,,,	418/562,447/591,418/569,418/569,418/562,418/562,414/558	51386066	1979,11027	2203	4300	6503	SO:0001819	synonymous_variant	4891	exon13			GATGGCAATAGAG	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1254T>C	12.37:g.51386066A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Silent	SNP	ENST00000262051.7	37	CCDS53792.1																																																																																			A|0.856;G|0.144	0.144	strong		0.473	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
ACADSB	36	hgsc.bcm.edu	37	10	124768583	124768583	+	Missense_Mutation	SNP	G	G	A	rs12263012	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124768583G>A	ENST00000358776.4	+	1	52	c.38G>A	c.(37-39)aGg>aAg	p.R13K	IKZF5_ENST00000479103.1_5'Flank|IKZF5_ENST00000368886.5_5'Flank|ACADSB_ENST00000368869.4_5'UTR	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	13			R -> K (in dbSNP:rs12263012). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	CGCGGCAGCAGGCTGGTGAGT	0.716													G|||	1032	0.20607	0.0938	0.2839	5008	,	,		11892	0.1042		0.3946	False		,,,				2504	0.2137				p.R13K		Atlas-SNP	.											ACADSB,NS,carcinoma,0,1	ACADSB	45	1	0			c.G38A	GRCh37	CM070001	ACADSB	M	rs12263012	PASS	.	G	LYS/ARG	388,2908		30,328,1290	28.0	30.0	30.0		38	0.8	0.0	10	dbSNP_120	30	2125,3743		387,1351,1196	no	missense	ACADSB	NM_001609.3	26	417,1679,2486	AA,AG,GG		36.2134,11.7718,27.4225	benign	13/433	124768583	2513,6651	1648	2934	4582	SO:0001583	missense	36	exon1			GCAGCAGGCTGGT	U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"""acyl-Coenzyme A dehydrogenase, short/branched chain"""			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.38G>A	10.37:g.124768583G>A	ENSP00000357873:p.Arg13Lys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Missense_Mutation	SNP	ENST00000358776.4	37	CCDS7634.1	515	0.2358058608058608	47	0.09552845528455285	100	0.27624309392265195	64	0.11188811188811189	304	0.40105540897097625	G	5.395	0.258103	0.10239	0.117718	0.362134	ENSG00000196177	ENST00000358776	D	0.97016	-4.21	3.97	0.817	0.18773	.	2.154850	0.01961	N	0.043396	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15141	0.012	B	0.10450	0.005	T	0.43376	-0.9395	9	0.30078	T	0.28	.	5.8893	0.18899	0.1253:0.4602:0.4145:0.0	rs12263012;rs17553774;rs17851061;rs57929037;rs12263012	13	P45954	ACDSB_HUMAN	K	13	ENSP00000357873:R13K	ENSP00000357873:R13K	R	+	2	0	ACADSB	124758573	0.004000	0.15560	0.016000	0.15963	0.023000	0.10783	0.020000	0.13466	0.447000	0.26695	0.561000	0.74099	AGG	G|0.772;A|0.228	0.228	strong		0.716	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609	
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 GAIIx	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	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	98	50	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	
CFAP44	55779	hgsc.bcm.edu	37	3	113085143	113085143	+	Missense_Mutation	SNP	T	T	C	rs74521061	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:113085143T>C	ENST00000295868.2	-	19	2620	c.2458A>G	c.(2458-2460)Atg>Gtg	p.M820V	WDR52_ENST00000393845.2_Missense_Mutation_p.M820V	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						CAAAACATCATAACTTTGTTA	0.308													T|||	55	0.0109824	0.0023	0.0216	5008	,	,		18775	0.0		0.0278	False		,,,				2504	0.0092				p.M820V		Atlas-SNP	.											.	WDR52	151	.	0			c.A2458G						PASS	.	T	VAL/MET,VAL/MET	35,4371	40.8+/-73.8	0,35,2168	68.0	63.0	65.0		2458,2458	-0.0	0.3	3	dbSNP_131	65	308,8290	110.0+/-170.5	5,298,3996	yes	missense,missense	WDR52	NM_001164496.1,NM_018338.3	21,21	5,333,6164	CC,CT,TT		3.5822,0.7944,2.6376	benign,benign	820/1855,820/983	113085143	343,12661	2203	4299	6502	SO:0001583	missense	55779	exon19			ACATCATAACTTT																												ENST00000295868.2:c.2458A>G	3.37:g.113085143T>C	ENSP00000295868:p.Met820Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	185	95	0.513514	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	34	0.015567765567765568	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	20	0.026385224274406333	T	12.82	2.054011	0.36277	0.007944	0.035822	ENSG00000206530	ENST00000393845;ENST00000295868	T;T	0.16196	2.36;2.36	5.59	-0.00862	0.14004	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	.	.	.	.	T	0.02083	0.0065	L	0.40543	1.245	0.54753	D	0.999985	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.29427	-1.0012	8	.	.	.	.	2.2302	0.03994	0.2381:0.0746:0.3492:0.3381	.	820;820	Q96MT7;Q96MT7-2	WDR52_HUMAN;.	V	820	ENSP00000377428:M820V;ENSP00000295868:M820V	.	M	-	1	0	WDR52	114567833	0.005000	0.15991	0.252000	0.24328	0.817000	0.46193	-0.421000	0.07053	0.117000	0.18138	0.528000	0.53228	ATG	T|0.978;C|0.022	0.022	strong		0.308	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
NTRK1	4914	hgsc.bcm.edu	37	1	156848995	156848995	+	Silent	SNP	C	C	T	rs6337	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156848995C>T	ENST00000524377.1	+	15	1928	c.1887C>T	c.(1885-1887)gcC>gcT	p.A629A	NTRK1_ENST00000392302.2_Silent_p.A593A|NTRK1_ENST00000358660.3_Silent_p.A626A|NTRK1_ENST00000368196.3_Silent_p.A623A	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	629	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	AGCTGCTGGCCGTGGCTAGCC	0.642			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)			C|||	1673	0.334065	0.1384	0.5735	5008	,	,		16679	0.0437		0.7127	False		,,,				2504	0.3384				p.A629A		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	NTRK1	287	.	0			c.C1887T						PASS	.	C	,,	996,3408		118,760,1324	27.0	28.0	28.0		1779,1869,1887	-7.3	0.9	1	dbSNP_52	28	6245,2355		2273,1699,328	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	,,	2391,2459,1652	TT,TC,CC		27.3837,22.6158,44.3171	,,	593/761,623/791,629/797	156848995	7241,5763	2202	4300	6502	SO:0001819	synonymous_variant	4914	exon15			GCTGGCCGTGGCT	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.1887C>T	1.37:g.156848995C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_002529	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Silent	SNP	ENST00000524377.1	37	CCDS1161.1																																																																																			C|0.533;T|0.467	0.467	strong		0.642	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	
CIDEC	63924	hgsc.bcm.edu	37	3	9918861	9918861	+	Silent	SNP	C	C	A	rs456168	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9918861C>A	ENST00000336832.2	-	3	235	c.96G>T	c.(94-96)ctG>ctT	p.L32L	CIDEC_ENST00000430427.1_Silent_p.L32L|CIDEC_ENST00000383817.1_Silent_p.L32L|CIDEC_ENST00000423850.1_Intron|CIDEC_ENST00000455015.1_Intron|CIDEC_ENST00000443115.1_Silent_p.L32L	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	32					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					TGGGCTCCGACAGCAGCTGCT	0.647													C|||	1569	0.313299	0.4962	0.3458	5008	,	,		18973	0.248		0.1998	False		,,,				2504	0.227				p.L45L		Atlas-SNP	.											CIDEC,NS,carcinoma,0,1	CIDEC	22	1	0			c.G135T						PASS	.	C	,,,	1785,2463		385,1015,724	27.0	27.0	27.0		96,96,135,96	4.2	0.0	3	dbSNP_80	27	1568,6736		155,1258,2739	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIDEC	NM_001199551.1,NM_001199552.1,NM_001199623.1,NM_022094.3	,,,	540,2273,3463	AA,AC,CC		18.8825,42.0198,26.7129	,,,	32/249,32/239,45/252,32/239	9918861	3353,9199	2124	4152	6276	SO:0001819	synonymous_variant	63924	exon3			CTCCGACAGCAGC		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.96G>T	3.37:g.9918861C>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	68	41	0.602941	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Silent	SNP	ENST00000336832.2	37	CCDS2587.1																																																																																			C|0.678;A|0.322	0.322	strong		0.647	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094	
OR2B2	81697	hgsc.bcm.edu	37	6	27879982	27879982	+	Missense_Mutation	SNP	A	A	G	rs61742093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27879982A>G	ENST00000303324.2	-	1	192	c.116T>C	c.(115-117)aTc>aCc	p.I39T		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	39						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(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						ATTGCCAAAGATTGTCAAGAT	0.403													A|||	109	0.0217652	0.0106	0.0303	5008	,	,		18381	0.0		0.0736	False		,,,				2504	0.0				p.I39T		Atlas-SNP	.											.	OR2B2	54	.	0			c.T116C						PASS	.	A	THR/ILE	159,4247	106.0+/-144.5	4,151,2048	103.0	102.0	102.0		116	4.4	1.0	6	dbSNP_129	102	753,7847	180.3+/-229.3	35,683,3582	yes	missense	OR2B2	NM_033057.2	89	39,834,5630	GG,GA,AA		8.7558,3.6087,7.0121	possibly-damaging	39/358	27879982	912,12094	2203	4300	6503	SO:0001583	missense	81697	exon1			CCAAAGATTGTCA	Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"""GPCR / Class A : Olfactory receptors"""	13966	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 9"""	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.116T>C	6.37:g.27879982A>G	ENSP00000304419:p.Ile39Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	68	53	0.779412	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	74	0.03388278388278388	6	0.012195121951219513	10	0.027624309392265192	0	0.0	58	0.07651715039577836	A	10.95	1.496750	0.26861	0.036087	0.087558	ENSG00000168131	ENST00000303324	T	0.00635	6.06	4.37	4.37	0.52481	.	0.000000	0.39909	U	0.001233	T	0.01061	0.0035	M	0.84433	2.695	0.51012	P	9.599999999998499E-5	P	0.48911	0.917	P	0.49301	0.606	T	0.42531	-0.9446	9	0.87932	D	0	.	12.1623	0.54110	1.0:0.0:0.0:0.0	rs61742093	39	Q9GZK3	OR2B2_HUMAN	T	39	ENSP00000304419:I39T	ENSP00000304419:I39T	I	-	2	0	OR2B2	27987961	0.732000	0.28121	0.994000	0.49952	0.124000	0.20399	5.072000	0.64389	1.901000	0.55032	0.460000	0.39030	ATC	A|0.943;G|0.057	0.057	strong		0.403	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
CNRIP1	25927	hgsc.bcm.edu	37	2	68511584	68511584	+	Silent	SNP	A	A	G	rs735815	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:68511584A>G	ENST00000409559.3	-	3	362	c.363T>C	c.(361-363)tcT>tcC	p.S121S		NM_001111101.1	NP_001104571.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	0								p.S121S(1)		kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						CATATGTAAGAGAGATCTCTT	0.378													A|||	1974	0.394169	0.121	0.4481	5008	,	,		21161	0.5516		0.4404	False		,,,				2504	0.5153				p.S121S		Atlas-SNP	.											CNRIP1_ENST00000409559,NS,carcinoma,0,1	CNRIP1	45	1	1	Substitution - coding silent(1)	stomach(1)	c.T363C						PASS	.	A		267,1117		24,219,449	124.0	109.0	114.0		363	0.5	0.0	2	dbSNP_86	114	1368,1814		309,750,532	no	coding-synonymous	CNRIP1	NM_001111101.1		333,969,981	GG,GA,AA		42.9918,19.2919,35.8081		121/129	68511584	1635,2931	692	1591	2283	SO:0001819	synonymous_variant	25927	exon3			TGTAAGAGAGATC	AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 32"""	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000409559.3:c.363T>C	2.37:g.68511584A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_001111101	B2R4D0|Q49AN4|Q9UFZ0	Silent	SNP	ENST00000409559.3	37	CCDS46311.1																																																																																			A|0.599;G|0.401	0.401	strong		0.378	CNRIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326817.2	NM_015463	
GRM1	2911	hgsc.bcm.edu	37	6	146755515	146755515	+	Silent	SNP	T	T	G	rs6923864	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:146755515T>G	ENST00000282753.1	+	8	3403	c.3168T>G	c.(3166-3168)ggT>ggG	p.G1056G	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000361719.2_Silent_p.G1056G|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000492807.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1056					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CAGGCCCCGGTGGTCCCGGGA	0.672													G|||	3459	0.690695	0.947	0.5101	5008	,	,		13498	0.6131		0.5815	False		,,,				2504	0.6646				p.G1056G		Atlas-SNP	.											GRM1,NS,carcinoma,+2,1	GRM1	419	1	0			c.T3168G						scavenged	.	G	,	3890,496		1733,424,36	19.0	24.0	22.0		3168,	3.7	0.2	6	dbSNP_116	22	4840,3722		1420,2000,861	no	coding-synonymous,utr-3	GRM1	NM_000838.3,NM_001114329.1	,	3153,2424,897	GG,GT,TT		43.4712,11.3087,32.5765	,	1056/1195,	146755515	8730,4218	2193	4281	6474	SO:0001819	synonymous_variant	2911	exon9			CCCCGGTGGTCCC	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3168T>G	6.37:g.146755515T>G		Somatic	140	10	0.0714286		WXS	Illumina HiSeq	Phase_I	59	21	0.355932	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																			T|0.366;G|0.634	0.634	strong		0.672	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
ABCD4	5826	hgsc.bcm.edu	37	14	74766352	74766352	+	Silent	SNP	A	A	G	rs2301345	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74766352A>G	ENST00000356924.4	-	3	327	c.184T>C	c.(184-186)Ttg>Ctg	p.L62L	ABCD4_ENST00000557554.1_5'UTR|ABCD4_ENST00000557588.1_Silent_p.L62L|ABCD4_ENST00000298816.7_5'UTR	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	62	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		CTGGGGATCAAGCCAACCTGG	0.478													A|||	1315	0.26258	0.1195	0.2695	5008	,	,		20179	0.247		0.3857	False		,,,				2504	0.3405				p.L62L		Atlas-SNP	.											.	ABCD4	54	.	0			c.T184C						PASS	.	A		766,3640	309.1+/-290.9	64,638,1501	103.0	84.0	90.0		184	-2.6	1.0	14	dbSNP_100	90	3123,5477	472.3+/-368.3	551,2021,1728	no	coding-synonymous	ABCD4	NM_005050.3		615,2659,3229	GG,GA,AA		36.314,17.3854,29.9016		62/607	74766352	3889,9117	2203	4300	6503	SO:0001819	synonymous_variant	5826	exon3			GGATCAAGCCAAC	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"""ATP binding cassette transporters / subfamily D"""	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.184T>C	14.37:g.74766352A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Silent	SNP	ENST00000356924.4	37	CCDS9828.1																																																																																			A|0.717;G|0.283	0.283	strong		0.478	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
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 GAIIx	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		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	92	24	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 GAIIx	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_ENST00000427880.2_5'Flank|HIST2H2BF_ENST00000545683.1_5'Flank|RP11-196G18.21_ENST00000420462.1_RNA|HIST2H2BF_ENST00000469483.1_5'Flank|HIST2H2BF_ENST00000369167.1_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	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	238	15	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	
RBM11	54033	hgsc.bcm.edu	37	21	15599466	15599466	+	Missense_Mutation	SNP	A	A	G	rs7280643	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:15599466A>G	ENST00000400577.3	+	5	707	c.698A>G	c.(697-699)cAc>cGc	p.H233R	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	233					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)	p.H233R(1)		endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		AAATGGACTCACCAACAACCA	0.428													A|||	530	0.105831	0.1831	0.0807	5008	,	,		22211	0.0198		0.1103	False		,,,				2504	0.1033				p.H233R		Atlas-SNP	.											RBM11,NS,carcinoma,0,1	RBM11	41	1	1	Substitution - Missense(1)	stomach(1)	c.A698G						PASS	.	A	ARG/HIS	641,3235		58,525,1355	208.0	200.0	203.0		698	3.5	0.3	21	dbSNP_116	203	958,7314		37,884,3215	yes	missense	RBM11	NM_144770.3	29	95,1409,4570	GG,GA,AA		11.5812,16.5377,13.1627	benign	233/282	15599466	1599,10549	1938	4136	6074	SO:0001583	missense	54033	exon5			GGACTCACCAACA	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"""RNA binding motif (RRM) containing"""	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.698A>G	21.37:g.15599466A>G	ENSP00000383421:p.His233Arg	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	196	69	0.352041	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	202	0.0924908424908425	84	0.17073170731707318	25	0.06906077348066299	5	0.008741258741258742	88	0.11609498680738786	A	7.001	0.554944	0.13436	0.165377	0.115812	ENSG00000185272	ENST00000400577	T	0.08546	3.08	4.72	3.54	0.40534	.	.	.	.	.	T	0.00039	0.0001	L	0.47716	1.5	0.58432	P	9.000000000036756E-6	B	0.30763	0.294	B	0.24974	0.057	T	0.39251	-0.9623	8	0.23302	T	0.38	-2.9027	9.3897	0.38365	0.8398:0.0:0.0:0.1602	rs7280643	233	P57052	RBM11_HUMAN	R	233	ENSP00000383421:H233R	ENSP00000383421:H233R	H	+	2	0	RBM11	14521337	0.000000	0.05858	0.267000	0.24556	0.677000	0.39632	0.143000	0.16115	0.873000	0.35799	0.528000	0.53228	CAC	A|0.907;G|0.093	0.093	strong		0.428	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770	
OR52E4	390081	hgsc.bcm.edu	37	11	5906291	5906291	+	Missense_Mutation	SNP	T	T	C	rs11823842	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5906291T>C	ENST00000316987.2	+	1	791	c.769T>C	c.(769-771)Ttt>Ctt	p.F257L		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	257			F -> L (in dbSNP:rs11823842).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACACCAGCATTTTTTTCTTT	0.433													T|||	1790	0.357428	0.3207	0.402	5008	,	,		21006	0.3641		0.4085	False		,,,				2504	0.316				p.F257L		Atlas-SNP	.											.	OR52E4	65	.	0			c.T769C						PASS	.	T	LEU/PHE	1495,2907	473.5+/-356.7	259,977,965	217.0	197.0	204.0		769	3.9	1.0	11	dbSNP_120	204	3624,4968	522.1+/-380.0	780,2064,1452	yes	missense	OR52E4	NM_001005165.1	22	1039,3041,2417	CC,CT,TT		42.1788,33.9618,39.3951	benign	257/313	5906291	5119,7875	2201	4296	6497	SO:0001583	missense	390081	exon1			CCAGCATTTTTTT	AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"""GPCR / Class A : Olfactory receptors"""	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.769T>C	11.37:g.5906291T>C	ENSP00000321426:p.Phe257Leu	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	139	74	0.532374	NM_001005165	Q6IFG0	Missense_Mutation	SNP	ENST00000316987.2	37	CCDS31401.1	828	0.3791208791208791	154	0.3130081300813008	153	0.42265193370165743	204	0.35664335664335667	317	0.4182058047493404	T	6.783	0.513407	0.12944	0.339618	0.421788	ENSG00000180974	ENST00000316987	T	0.00025	8.95	5.1	3.94	0.45596	GPCR, rhodopsin-like superfamily (1);	0.128823	0.35466	N	0.003198	T	0.00012	0.0000	N	0.04275	-0.24	0.42048	P	0.008894999999999986	B	0.02656	0.0	B	0.12837	0.008	T	0.00024	-1.2322	9	0.15499	T	0.54	.	6.8055	0.23774	0.0:0.1821:0.0:0.8179	rs11823842;rs17807520;rs52828559;rs57975452;rs11823842	257	Q8NGH9	O52E4_HUMAN	L	257	ENSP00000321426:F257L	ENSP00000321426:F257L	F	+	1	0	OR52E4	5862867	0.000000	0.05858	0.980000	0.43619	0.990000	0.78478	-0.489000	0.06490	0.923000	0.37045	0.523000	0.50628	TTT	T|0.627;C|0.373	0.373	strong		0.433	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165	
PREX1	57580	hgsc.bcm.edu	37	20	47267940	47267940	+	Silent	SNP	G	G	A	rs61748372	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47267940G>A	ENST00000371941.3	-	22	2671	c.2649C>T	c.(2647-2649)acC>acT	p.T883T	PREX1_ENST00000396220.1_Silent_p.T883T	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	883					actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			AGACCTTGGCGGTGAGGCCGA	0.612													G|||	755	0.150759	0.0197	0.2118	5008	,	,		19711	0.1528		0.1849	False		,,,				2504	0.2474				p.T883T		Atlas-SNP	.											.	PREX1	441	.	0			c.C2649T						PASS	.	G		249,4157	138.4+/-174.2	10,229,1964	40.0	36.0	37.0		2649	-4.4	0.4	20	dbSNP_129	37	1621,6979	284.4+/-296.6	149,1323,2828	no	coding-synonymous	PREX1	NM_020820.3		159,1552,4792	AA,AG,GG		18.8488,5.6514,14.378		883/1660	47267940	1870,11136	2203	4300	6503	SO:0001819	synonymous_variant	57580	exon22			CTTGGCGGTGAGG	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.2649C>T	20.37:g.47267940G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			A|0.145;C|0.000;G|0.855	0.145	strong		0.612	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
KANSL1	284058	hgsc.bcm.edu	37	17	44110532	44110532	+	Silent	SNP	G	G	A	rs36076725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44110532G>A	ENST00000262419.6	-	13	3221	c.2751C>T	c.(2749-2751)ttC>ttT	p.F917F	KANSL1_ENST00000575318.1_Silent_p.F853F|KANSL1_ENST00000432791.1_Silent_p.F917F|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000393476.3_Silent_p.F211F|KANSL1_ENST00000574590.1_Silent_p.F917F|KANSL1_ENST00000572904.1_Silent_p.F917F	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	917	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GCAGGGCGGCGAAGGCTGCGT	0.602													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19745	0.001		0.2406	False		,,,				2504	0.0613				p.F917F		Atlas-SNP	.											.	.	.	.	0			c.C2751T						PASS	.	G	,,	201,4205	118.8+/-156.5	5,191,2007	59.0	59.0	59.0		2748,2751,2751	-5.2	0.9	17	dbSNP_126	59	1915,6685	305.0+/-307.2	214,1487,2599	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	219,1678,4606	AA,AG,GG		22.2674,4.562,16.2694	,,	916/1105,917/1106,917/1106	44110532	2116,10890	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon13			GGCGGCGAAGGCT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2751C>T	17.37:g.44110532G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.143;C|0.000;G|0.856;T|0.000	0.143	strong		0.602	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
C7	730	hgsc.bcm.edu	37	5	40964885	40964885	+	Missense_Mutation	SNP	A	A	T	rs60714178	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:40964885A>T	ENST00000313164.9	+	14	2151	c.1792A>T	c.(1792-1794)Act>Tct	p.T598S		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	598	CCP 1.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cellular sodium ion homeostasis (GO:0006883)|complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)							Ovarian(839;0.0112)				TGTAGTGTACACTTGCAATGA	0.403													A|||	331	0.0660942	0.0272	0.1081	5008	,	,		18463	0.001		0.1481	False		,,,				2504	0.0716				p.T598S		Atlas-SNP	.											.	C7	136	.	0			c.A1792T						PASS	.	A	SER/THR	180,3684		6,168,1758	163.0	161.0	162.0		1792	-0.2	0.6	5	dbSNP_129	162	1278,6984		83,1112,2936	yes	missense	C7	NM_000587.2	58	89,1280,4694	TT,TA,AA		15.4684,4.6584,12.0238	benign	598/844	40964885	1458,10668	1932	4131	6063	SO:0001583	missense	730	exon14			GTGTACACTTGCA	J03507	CCDS47201.1	5p13.1	2014-09-17			ENSG00000112936	ENSG00000112936		"""Complement system"""	1346	protein-coding gene	gene with protein product		217070					Standard	NM_000587		Approved		uc003jmh.3	P10643	OTTHUMG00000150340	ENST00000313164.9:c.1792A>T	5.37:g.40964885A>T	ENSP00000322061:p.Thr598Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	155	80	0.516129	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	177	0.08104395604395605	15	0.03048780487804878	37	0.10220994475138122	1	0.0017482517482517483	124	0.16358839050131926	A	11.28	1.591300	0.28357	0.046584	0.154684	ENSG00000112936	ENST00000313164;ENST00000440677	T	0.63744	-0.06	6.04	-0.173	0.13322	Complement control module (2);Sushi/SCR/CCP (3);	0.363303	0.29100	N	0.013144	T	0.00144	0.0004	N	0.20304	0.555	0.45118	P	0.0018700000000000383	B	0.20550	0.046	B	0.23574	0.047	T	0.04178	-1.0971	9	0.16420	T	0.52	-8.1559	4.3042	0.10938	0.3711:0.0:0.1734:0.4555	rs60714178;rs61741887	598	P10643	CO7_HUMAN	S	598;438	ENSP00000322061:T598S	ENSP00000322061:T598S	T	+	1	0	C7	41000642	0.340000	0.24792	0.595000	0.28798	0.893000	0.52053	0.756000	0.26419	0.035000	0.15519	0.460000	0.39030	ACT	A|0.902;T|0.098	0.098	strong		0.403	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
WDR11	55717	hgsc.bcm.edu	37	10	122645376	122645376	+	Silent	SNP	A	A	T	rs7899928	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:122645376A>T	ENST00000263461.6	+	15	2145	c.1899A>T	c.(1897-1899)gcA>gcT	p.A633A	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|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)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.A633A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AGCAACTTGCAACTCGAGAGG	0.473													T|||	1981	0.395567	0.4297	0.4366	5008	,	,		18356	0.4177		0.334	False		,,,				2504	0.3609				p.A633A		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.A1899T						PASS	.	T		1846,2560	635.2+/-396.3	392,1062,749	138.0	133.0	135.0		1899	-5.2	0.9	10	dbSNP_116	135	2894,5706	671.5+/-402.8	471,1952,1877	no	coding-synonymous	WDR11	NM_018117.11		863,3014,2626	TT,TA,AA		33.6512,41.8974,36.4447		633/1225	122645376	4740,8266	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon15			ACTTGCAACTCGA	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.1899A>T	10.37:g.122645376A>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	54	29	0.537037	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			A|0.640;T|0.360	0.360	strong		0.473	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
SERPINA9	327657	hgsc.bcm.edu	37	14	94933473	94933473	+	Missense_Mutation	SNP	C	C	A	rs28618118	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94933473C>A	ENST00000380365.3	-	3	953	c.875G>T	c.(874-876)aGa>aTa	p.R292I	SERPINA9_ENST00000448305.2_Missense_Mutation_p.R212I|SERPINA9_ENST00000337425.5_Missense_Mutation_p.R310I|SERPINA9_ENST00000424550.2_Missense_Mutation_p.R161I|SERPINA9_ENST00000539349.1_5'Flank|RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000546329.1_Missense_Mutation_p.R274I|SERPINA9_ENST00000298845.7_Missense_Mutation_p.R210I			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	292			R -> I (in dbSNP:rs28618118). {ECO:0000269|PubMed:12975309}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		GCTCCACTTTCTCAGTGTTCT	0.537													C|||	1614	0.322284	0.1452	0.3847	5008	,	,		21972	0.4643		0.3101	False		,,,				2504	0.3834				p.R310I		Atlas-SNP	.											.	SERPINA9	105	.	0			c.G929T						PASS	.	C	ILE/ARG,ILE/ARG	641,3347		54,533,1407	116.0	110.0	112.0		629,929	2.6	0.1	14	dbSNP_125	112	2518,5864		381,1756,2054	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	97,97	435,2289,3461	AA,AC,CC		30.0406,16.0732,25.5376	probably-damaging,probably-damaging	210/336,310/436	94933473	3159,9211	1994	4191	6185	SO:0001583	missense	327657	exon3			CACTTTCTCAGTG	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.875G>T	14.37:g.94933473C>A	ENSP00000369723:p.Arg292Ile	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	163	70	0.429448	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		721	0.3301282051282051	79	0.16056910569105692	127	0.35082872928176795	275	0.4807692307692308	240	0.316622691292876	C	11.91	1.778992	0.31502	0.160732	0.300406	ENSG00000170054	ENST00000448305;ENST00000298845;ENST00000424550;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87;-1.87	3.48	2.57	0.30868	Serpin domain (3);	0.260319	0.31976	N	0.006767	T	0.00012	0.0000	L	0.37697	1.125	0.51233	P	8.799999999997699E-5	B;B;B;B;B	0.18741	0.004;0.002;0.0;0.0;0.03	B;B;B;B;B	0.17979	0.008;0.018;0.004;0.003;0.02	T	0.36841	-0.9731	9	0.22109	T	0.4	.	9.3187	0.37950	0.0:0.8933:0.0:0.1067	rs28618118	274;292;212;310;210	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7;Q86WD7-2	.;SPA9_HUMAN;.;.;.	I	212;210;161;310;292;274	ENSP00000414092:R212I;ENSP00000298845:R210I;ENSP00000409012:R161I;ENSP00000337133:R310I;ENSP00000369723:R292I;ENSP00000445476:R274I	ENSP00000298845:R210I	R	-	2	0	SERPINA9	94003226	0.000000	0.05858	0.103000	0.21229	0.961000	0.63080	-0.880000	0.04183	0.790000	0.33803	0.462000	0.41574	AGA	C|0.677;A|0.323	0.323	strong		0.537	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
OR2T3	343173	hgsc.bcm.edu	37	1	248637381	248637381	+	Missense_Mutation	SNP	G	G	A	rs139789199	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248637381G>A	ENST00000359594.2	+	1	755	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	244						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(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	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)			GAAGGCCTTGGCCACCTGCTC	0.562																																					p.A244T		Atlas-SNP	.											OR2T3,NS,carcinoma,0,3	OR2T3	79	3	0			c.G730A						scavenged	.	G	THR/ALA	108,4298	63.5+/-100.7	4,100,2099	200.0	168.0	179.0		730	-4.7	0.0	1	dbSNP_134	179	4,8596	3.0+/-9.4	0,4,4296	no	missense	OR2T3	NM_001005495.1	58	4,104,6395	AA,AG,GG		0.0465,2.4512,0.8611	benign	244/319	248637381	112,12894	2203	4300	6503	SO:0001583	missense	343173	exon1			GCCTTGGCCACCT		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.730G>A	1.37:g.248637381G>A	ENSP00000352604:p.Ala244Thr	Somatic	419	0	0		WXS	Illumina HiSeq	Phase_I	344	54	0.156977	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	56	0.02564102564102564	16	0.032520325203252036	7	0.019337016574585635	21	0.03671328671328671	12	0.0158311345646438	g	8.134	0.783767	0.16189	0.024512	4.65E-4	ENSG00000196539	ENST00000359594	T	0.00063	8.78	2.37	-4.74	0.03249	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.32530	0.975	0.09310	N	1	B	0.29531	0.247	B	0.37888	0.26	T	0.02167	-1.1202	9	0.27082	T	0.32	.	3.8534	0.08965	0.2803:0.0:0.43:0.2897	.	244	Q8NH03	OR2T3_HUMAN	T	244	ENSP00000352604:A244T	ENSP00000352604:A244T	A	+	1	0	OR2T3	246704004	0.000000	0.05858	0.001000	0.08648	0.247000	0.25773	-1.692000	0.01918	-1.238000	0.02535	0.186000	0.17326	GCC	G|0.987;A|0.013	0.013	strong		0.562	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
GIMAP5	55340	hgsc.bcm.edu	37	7	150440043	150440043	+	Silent	SNP	C	C	T	rs1046355	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150440043C>T	ENST00000358647.3	+	3	1183	c.816C>T	c.(814-816)ctC>ctT	p.L272L	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	272					myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACAAGGCGCTCCTCAGAGTCA	0.418													C|||	1754	0.35024	0.5363	0.2565	5008	,	,		22097	0.3006		0.3082	False		,,,				2504	0.2597				p.L476L		Atlas-SNP	.											.	.	.	.	0			c.C1428T						PASS	.	C	,	2334,2072	605.8+/-390.6	633,1068,502	98.0	73.0	81.0		1428,816	-2.6	0.0	7	dbSNP_86	81	2638,5962	425.0+/-354.8	388,1862,2050	no	coding-synonymous,coding-synonymous	GIMAP5,GIMAP1-GIMAP5	NM_001199577.1,NM_018384.4	,	1021,2930,2552	TT,TC,CC		30.6744,47.0268,38.2285	,	476/512,272/308	150440043	4972,8034	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			GGCGCTCCTCAGA	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"""GTPases, IMAP"""	18005	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 5"""	608086	"""immune associated nucleotide 4 like 1 (mouse)"""	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.816C>T	7.37:g.150440043C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Silent	SNP	ENST00000358647.3	37	CCDS5907.1																																																																																			C|0.620;T|0.380	0.380	strong		0.418	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384	
TJP2	9414	hgsc.bcm.edu	37	9	71862987	71862987	+	Silent	SNP	G	G	A	rs2095876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:71862987G>A	ENST00000377245.4	+	19	2935	c.2727G>A	c.(2725-2727)gcG>gcA	p.A909A	TJP2_ENST00000498204.1_3'UTR|TJP2_ENST00000453658.2_Silent_p.A886A|TJP2_ENST00000348208.4_Silent_p.A909A|TJP2_ENST00000265384.7_Silent_p.A909A|TJP2_ENST00000539225.1_Silent_p.A940A|TJP2_ENST00000535702.1_Silent_p.A913A	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	909					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						CCATGGGCGCGGACTATCTGA	0.562													G|||	1423	0.284145	0.1664	0.4539	5008	,	,		18637	0.4504		0.2197	False		,,,				2504	0.2178				p.A940A		Atlas-SNP	.											TJP2,colon,carcinoma,+2,1	TJP2	120	1	0			c.G2820A						PASS	.	G	,,,,,	755,3651	306.9+/-289.7	78,599,1526	84.0	76.0	79.0		2658,2739,2820,2727,2727,2727	3.0	1.0	9	dbSNP_96	79	1812,6788	321.1+/-314.9	196,1420,2684	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,,,,	274,2019,4210	AA,AG,GG		21.0698,17.1357,19.737	,,,,,	886/1021,913/1158,940/1222,909/994,909/1191,909/1044	71862987	2567,10439	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon19			GGGCGCGGACTAT	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.2727G>A	9.37:g.71862987G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			G|0.763;A|0.237	0.237	strong		0.562	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
ZNF665	79788	hgsc.bcm.edu	37	19	53668549	53668549	+	Silent	SNP	T	T	G	rs10409924	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:53668549T>G	ENST00000600412.1	-	2	1114	c.999A>C	c.(997-999)ggA>ggC	p.G333G	CTD-2245F17.2_ENST00000600257.1_RNA|ZNF665_ENST00000396424.3_Silent_p.G398G			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	333					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)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		AAGGCTTTTCTCCGGTATGGA	0.393													T|||	1081	0.215855	0.4304	0.1484	5008	,	,		23571	0.0972		0.1342	False		,,,				2504	0.18				p.G398G		Atlas-SNP	.											.	ZNF665	136	.	0			c.A1194C						PASS	.	T		1573,2833	468.3+/-355.1	286,1001,916	96.0	101.0	99.0		1194	-2.4	0.0	19	dbSNP_119	99	1325,7269	255.4+/-280.3	99,1127,3071	no	coding-synonymous	ZNF665	NM_024733.3		385,2128,3987	GG,GT,TT		15.4177,35.7013,22.2923		398/679	53668549	2898,10102	2203	4297	6500	SO:0001819	synonymous_variant	79788	exon4			CTTTTCTCCGGTA		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.999A>C	19.37:g.53668549T>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_024733	A8K5T8	Silent	SNP	ENST00000600412.1	37																																																																																				T|0.774;G|0.226	0.226	strong		0.393	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
OR10W1	81341	hgsc.bcm.edu	37	11	58034543	58034543	+	Missense_Mutation	SNP	C	C	T	rs10792156	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:58034543C>T	ENST00000395079.2	-	1	1189	c.788G>A	c.(787-789)cGg>cAg	p.R263Q		NM_207374.3	NP_997257.2	Q8NGF6	O10W1_HUMAN	olfactory receptor, family 10, subfamily W, member 1	263			R -> Q (in dbSNP:rs10792156). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(2)|large_intestine(2)|lung(19)|ovary(2)|skin(1)	26		Breast(21;0.0589)				TGAGATGAACCGATCTTGCTT	0.547													t|||	2572	0.513578	0.4841	0.4942	5008	,	,		20037	0.6954		0.3787	False		,,,				2504	0.5184				p.R263Q		Atlas-SNP	.											OR10W1,NS,malignant_melanoma,-1,1	OR10W1	58	1	0			c.G788A						PASS	.	T	GLN/ARG	2180,2222	591.8+/-387.6	530,1120,551	97.0	89.0	92.0		788	-2.6	0.0	11	dbSNP_120	92	3483,5107	633.6+/-398.8	698,2087,1510	yes	missense	OR10W1	NM_207374.3	43	1228,3207,2061	TT,TC,CC		40.5471,49.5229,43.5884	benign	263/306	58034543	5663,7329	2201	4295	6496	SO:0001583	missense	81341	exon1			ATGAACCGATCTT	AB065850	CCDS7968.1	11q12.1	2012-08-09	2004-03-04	2004-03-05		ENSG00000172772		"""GPCR / Class A : Olfactory receptors"""	15139	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily W, member 1 pseudogene"""	OR10W1P			Standard	NM_207374		Approved		uc001nmq.1	Q8NGF6		ENST00000395079.2:c.788G>A	11.37:g.58034543C>T	ENSP00000378516:p.Arg263Gln	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	168	74	0.440476	NM_207374	A2RUD2|A8MTE1|Q6UXQ2	Missense_Mutation	SNP	ENST00000395079.2	37	CCDS7968.1	1099	0.5032051282051282	257	0.5223577235772358	181	0.5	373	0.6520979020979021	288	0.37994722955145116	T	5.977	0.364124	0.11296	0.495229	0.405471	ENSG00000172772	ENST00000395079	T	0.00084	8.75	5.7	-2.59	0.06209	GPCR, rhodopsin-like superfamily (1);	0.444434	0.19155	N	0.121349	T	0.00012	0.0000	L	0.28776	0.89	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48937	-0.8990	9	0.52906	T	0.07	.	4.216	0.10535	0.0956:0.3595:0.0984:0.4466	rs10792156;rs52791449;rs60718842;rs10792156	263	Q8NGF6	O10W1_HUMAN	Q	263	ENSP00000378516:R263Q	ENSP00000378516:R263Q	R	-	2	0	OR10W1	57791119	0.000000	0.05858	0.013000	0.15412	0.397000	0.30659	-0.521000	0.06245	-0.762000	0.04664	-1.062000	0.02293	CGG	C|0.523;T|0.477	0.477	strong		0.547	OR10W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394704.1	NM_207374	
PDILT	204474	hgsc.bcm.edu	37	16	20410488	20410488	+	Silent	SNP	G	G	A	rs7185940	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20410488G>A	ENST00000302451.4	-	2	383	c.135C>T	c.(133-135)ctC>ctT	p.L45L		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	45					cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						TTAGCACTAGGAGACTGCGTT	0.577													G|||	1735	0.346446	0.4644	0.3876	5008	,	,		18405	0.1528		0.3091	False		,,,				2504	0.3957				p.L45L		Atlas-SNP	.											.	PDILT	120	.	0			c.C135T						PASS	.	G		1872,2534	540.5+/-375.5	373,1126,704	149.0	136.0	140.0		135	1.0	0.2	16	dbSNP_116	140	2466,6134	405.8+/-348.6	326,1814,2160	no	coding-synonymous	PDILT	NM_174924.1		699,2940,2864	AA,AG,GG		28.6744,42.4875,33.3538		45/585	20410488	4338,8668	2203	4300	6503	SO:0001819	synonymous_variant	204474	exon2			CACTAGGAGACTG		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"""Protein disulfide isomerases"""	27338	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 7"", ""protein disulfide isomerase-like protein of the testis"""					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.135C>T	16.37:g.20410488G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_174924	Q8IVQ5	Silent	SNP	ENST00000302451.4	37	CCDS10584.1																																																																																			G|0.676;A|0.324	0.324	strong		0.577	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924	
C5orf52	100190949	hgsc.bcm.edu	37	5	157102159	157102159	+	Missense_Mutation	SNP	G	G	A	rs10051838	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:157102159G>A	ENST00000409999.3	+	2	334	c.272G>A	c.(271-273)cGg>cAg	p.R91Q		NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	91										endometrium(2)|lung(1)	3						CATTTATCTCGGGTGATTATT	0.448													.|||	913	0.182308	0.3071	0.111	5008	,	,		19662	0.119		0.1252	False		,,,				2504	0.1881				p.R91Q		Atlas-SNP	.											C5orf52,NS,carcinoma,+1,1	C5orf52	17	1	0			c.G272A						PASS	.	G	GLN/ARG	412,972		53,306,333	123.0	111.0	115.0		272	2.2	1.0	5	dbSNP_119	115	431,2751		32,367,1192	yes	missense	C5orf52	NM_001145132.1	43	85,673,1525	AA,AG,GG		13.5449,29.7688,18.4625	probably-damaging	91/160	157102159	843,3723	692	1591	2283	SO:0001583	missense	100190949	exon2			TATCTCGGGTGAT	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.272G>A	5.37:g.157102159G>A	ENSP00000387027:p.Arg91Gln	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_001145132		Missense_Mutation	SNP	ENST00000409999.3	37	CCDS47329.1	355	0.16254578754578755	148	0.3008130081300813	39	0.10773480662983426	74	0.12937062937062938	94	0.12401055408970976	G	11.63	1.697086	0.30142	0.297688	0.135449	ENSG00000187658	ENST00000409999	T	0.36878	1.23	2.22	2.22	0.28083	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	0.39575	P	0.030656000000000017	P	0.46952	0.887	B	0.32211	0.142	T	0.37753	-0.9692	8	0.66056	D	0.02	-17.8701	7.8836	0.29637	0.0:0.0:1.0:0.0	rs10051838;rs52825189;rs61469151;rs10051838	91	A6NGY3	CE052_HUMAN	Q	91	ENSP00000387027:R91Q	ENSP00000387027:R91Q	R	+	2	0	C5orf52	157034737	0.989000	0.36119	0.998000	0.56505	0.581000	0.36288	0.228000	0.17814	1.235000	0.43724	0.313000	0.20887	CGG	G|0.823;A|0.177	0.177	strong		0.448	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
OTOP3	347741	hgsc.bcm.edu	37	17	72943126	72943126	+	Silent	SNP	G	G	A	rs8066909	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72943126G>A	ENST00000328801.4	+	6	1176	c.1176G>A	c.(1174-1176)gcG>gcA	p.A392A		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	392						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					CGTGCCTGGCGGGCACAGCCA	0.607													G|||	1456	0.290735	0.1672	0.4885	5008	,	,		18262	0.0655		0.5109	False		,,,				2504	0.3231				p.A392A		Atlas-SNP	.											OTOP3,NS,carcinoma,0,1	OTOP3	64	1	0			c.G1176A						PASS	.						74.0	66.0	69.0					17																	72943126		2203	4300	6503	SO:0001819	synonymous_variant	347741	exon6			CCTGGCGGGCACA	BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.1176G>A	17.37:g.72943126G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_178233		Silent	SNP	ENST00000328801.4	37	CCDS11709.1																																																																																			G|0.683;A|0.317	0.317	strong		0.607	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
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 GAIIx	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		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	116	13	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 GAIIx	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_ENST00000413996.3_Splice_Site_p.H65H|SGK1_ENST00000367857.5_Splice_Site_p.H41H|SGK1_ENST00000475719.2_Splice_Site_p.H51H|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367858.5_Splice_Site_p.H146H|SGK1_ENST00000528577.1_Splice_Site_p.H79H	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		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	21	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
MYO5B	4645	hgsc.bcm.edu	37	18	47398549	47398549	+	Silent	SNP	G	G	A	rs3826579	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:47398549G>A	ENST00000285039.7	-	27	3890	c.3591C>T	c.(3589-3591)taC>taT	p.Y1197Y	Y_RNA_ENST00000364798.1_RNA|MYO5B_ENST00000324581.6_Silent_p.Y338Y|MYO5B_ENST00000587895.1_5'UTR	NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	1197					endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		TCAGACTATTGTAGGCCAGAT	0.512													G|||	1502	0.29992	0.2753	0.2291	5008	,	,		18058	0.4256		0.2177	False		,,,				2504	0.3384				p.Y1197Y		Atlas-SNP	.											.	MYO5B	178	.	0			c.C3591T						PASS	.	G		973,2901		123,727,1087	370.0	354.0	359.0		3591	2.5	1.0	18	dbSNP_107	359	1632,6638		163,1306,2666	no	coding-synonymous	MYO5B	NM_001080467.2		286,2033,3753	AA,AG,GG		19.734,25.1162,21.4509		1197/1849	47398549	2605,9539	1937	4135	6072	SO:0001819	synonymous_variant	4645	exon27			ACTATTGTAGGCC	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.3591C>T	18.37:g.47398549G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	122	61	0.5	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			G|0.718;A|0.282	0.282	strong		0.512	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
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 GAIIx	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_ENST00000483239.2_Silent_p.T596T|TTC12_ENST00000393020.1_Silent_p.T590T|TTC12_ENST00000314756.3_Silent_p.T590T	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		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	74	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	
HEPACAM	220296	hgsc.bcm.edu	37	11	124793716	124793716	+	Silent	SNP	G	G	A	rs10790716	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124793716G>A	ENST00000298251.4	-	3	1023	c.618C>T	c.(616-618)cgC>cgT	p.R206R		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	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;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		CCATGAGCACGCGGGTGATGG	0.587													G|||	681	0.135982	0.1074	0.1513	5008	,	,		20947	0.0714		0.2624	False		,,,				2504	0.1002				p.R206R		Atlas-SNP	.											.	HEPACAM	64	.	0			c.C618T						PASS	.	G		602,3800	264.4+/-266.0	42,518,1641	112.0	86.0	95.0		618	-11.3	0.1	11	dbSNP_120	95	2292,6306	385.3+/-341.4	319,1654,2326	no	coding-synonymous	HEPACAM	NM_152722.4		361,2172,3967	AA,AG,GG		26.6574,13.6756,22.2615		206/417	124793716	2894,10106	2201	4299	6500	SO:0001819	synonymous_variant	220296	exon3			GAGCACGCGGGTG	AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26361	protein-coding gene	gene with protein product	"""glial cell adhesion molecule"""	611642	"""hepatocyte cell adhesion molecule"""			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.618C>T	11.37:g.124793716G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	51	0.822581	NM_152722		Silent	SNP	ENST00000298251.4	37	CCDS8456.1																																																																																			G|0.814;A|0.186	0.186	strong		0.587	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722	
ZNF91	7644	hgsc.bcm.edu	37	19	23545250	23545250	+	Silent	SNP	A	A	G	rs1044095	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:23545250A>G	ENST00000300619.7	-	4	736	c.531T>C	c.(529-531)acT>acC	p.T177T	ZNF91_ENST00000397082.2_Silent_p.T145T|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	177					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				ATTTCTTTCCAGTATGTCTTA	0.323													A|||	1911	0.381589	0.2693	0.4841	5008	,	,		15093	0.1558		0.5964	False		,,,				2504	0.4724				p.T177T		Atlas-SNP	.											ZNF91_ENST00000300619,caecum,carcinoma,0,2	ZNF91	349	2	0			c.T531C						PASS	.	A		1201,2873		199,803,1035	69.0	68.0	68.0		531	0.8	0.0	19	dbSNP_86	68	4900,3546		1421,2058,744	no	coding-synonymous	ZNF91	NM_003430.2		1620,2861,1779	GG,GA,AA		41.9844,29.4796,48.73		177/1192	23545250	6101,6419	2037	4223	6260	SO:0001819	synonymous_variant	7644	exon4			CTTTCCAGTATGT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.531T>C	19.37:g.23545250A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			A|0.600;G|0.400	0.400	strong		0.323	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
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 GAIIx	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_ENST00000381869.3_Missense_Mutation_p.V908G|MTUS1_ENST00000544260.1_Missense_Mutation_p.V107G|MTUS1_ENST00000519263.1_Missense_Mutation_p.V908G|MTUS1_ENST00000297488.6_Missense_Mutation_p.V128G|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000400046.1_Missense_Mutation_p.V34G|MTUS1_ENST00000381861.3_Missense_Mutation_p.V209G	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	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	128	27	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	
ARHGAP15	55843	hgsc.bcm.edu	37	2	144194565	144194565	+	Silent	SNP	C	C	T	rs17230746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:144194565C>T	ENST00000295095.6	+	8	824	c.657C>T	c.(655-657)taC>taT	p.Y219Y	AC096558.1_ENST00000549032.1_RNA|RP11-570L15.2_ENST00000546678.1_RNA|AC096558.1_ENST00000442794.1_RNA|AC096558.1_ENST00000550516.1_RNA	NM_018460.3	NP_060930.3	Q53QZ3	RHG15_HUMAN	Rho GTPase activating protein 15	219					positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)			endometrium(1)|kidney(5)|large_intestine(8)|liver(2)|lung(15)|ovary(1)|skin(2)	34				BRCA - Breast invasive adenocarcinoma(221;0.151)		TAAGTCACTACGACAGTGATA	0.348													C|||	461	0.0920527	0.0325	0.0879	5008	,	,		18129	0.003		0.2058	False		,,,				2504	0.1503				p.Y219Y		Atlas-SNP	.											.	ARHGAP15	99	.	0			c.C657T						PASS	.	C		265,4141	147.6+/-182.1	9,247,1947	76.0	74.0	75.0		657	-3.3	0.4	2	dbSNP_123	75	1956,6644	343.2+/-324.8	242,1472,2586	no	coding-synonymous	ARHGAP15	NM_018460.3		251,1719,4533	TT,TC,CC		22.7442,6.0145,17.0767		219/476	144194565	2221,10785	2203	4300	6503	SO:0001819	synonymous_variant	55843	exon8			TCACTACGACAGT	AY219338	CCDS2184.1	2q22.2-q22.3	2013-01-10			ENSG00000075884	ENSG00000075884		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	21030	protein-coding gene	gene with protein product		610578				12650940, 11042152	Standard	NM_018460		Approved	BM046	uc002tvm.4	Q53QZ3	OTTHUMG00000131845	ENST00000295095.6:c.657C>T	2.37:g.144194565C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	119	86	0.722689	NM_018460	Q53R36|Q53RD7|Q53RT6|Q53SX9|Q584N9|Q6PJE6|Q86WP1|Q8IXX1|Q9NRL8|Q9NZ77|Q9NZ91	Silent	SNP	ENST00000295095.6	37	CCDS2184.1																																																																																			C|0.853;T|0.147	0.147	strong		0.348	ARHGAP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254793.2	NM_018460	
CCRL2	9034	hgsc.bcm.edu	37	3	46450297	46450297	+	Missense_Mutation	SNP	A	A	G	rs3204850	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46450297A>G	ENST00000399036.3	+	2	1079	c.727A>G	c.(727-729)Ata>Gta	p.I243V	CCRL2_ENST00000400882.2_Missense_Mutation_p.I243V|RP11-24F11.2_ENST00000451485.1_RNA|CCRL2_ENST00000400880.3_Missense_Mutation_p.I243V|CCRL2_ENST00000357392.4_Missense_Mutation_p.I255V	NM_003965.4	NP_003956.2	O00421	CCRL2_HUMAN	chemokine (C-C motif) receptor-like 2	243			I -> V (in dbSNP:rs3204850). {ECO:0000269|Ref.3}.		chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CCR chemokine receptor binding (GO:0048020)|chemokine receptor activity (GO:0004950)|chemokine receptor binding (GO:0042379)			lung(3)|ovary(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)		TGTTTTTGCCATAATGGTAGT	0.418													A|||	353	0.0704872	0.003	0.0403	5008	,	,		21215	0.0288		0.0934	False		,,,				2504	0.2025				p.I255V		Atlas-SNP	.											.	CCRL2	23	.	0			c.A763G						PASS	.	A	VAL/ILE,VAL/ILE	66,3808		2,62,1873	246.0	243.0	244.0		763,727	0.2	0.0	3	dbSNP_105	244	690,7562		27,636,3463	yes	missense,missense	CCRL2	NM_001130910.1,NM_003965.4	29,29	29,698,5336	GG,GA,AA		8.3616,1.7037,6.2345	benign,benign	255/357,243/345	46450297	756,11370	1937	4126	6063	SO:0001583	missense	9034	exon2			TTTGCCATAATGG	AF014958	CCDS43079.1, CCDS46814.1	3p21	2013-07-18	2013-07-18	2013-07-18	ENSG00000121797	ENSG00000121797		"""GPCR / Class A : Chemokine receptors : Atypical"""	1612	protein-coding gene	gene with protein product	"""atypical chemokine receptor 5"""	608379				9473515	Standard	NM_001130910		Approved	HCR, CRAM-B, CKRX, CRAM-A, ACKR5	uc003cpp.4	O00421	OTTHUMG00000156318	ENST00000399036.3:c.727A>G	3.37:g.46450297A>G	ENSP00000381994:p.Ile243Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	189	84	0.444444	NM_001130910	B4DKQ8|O75307|Q4VBB0|Q6IPX0|Q7KYQ9|Q96KP5|Q9UPG0	Missense_Mutation	SNP	ENST00000399036.3	37	CCDS43079.1	111	0.050824175824175824	4	0.008130081300813009	11	0.03038674033149171	21	0.03671328671328671	75	0.09894459102902374	A	14.23	2.473282	0.43942	0.017037	0.083616	ENSG00000121797	ENST00000399036;ENST00000357392;ENST00000400880;ENST00000400882	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.24	0.16	0.14972	GPCR, rhodopsin-like superfamily (1);	0.356870	0.25636	N	0.029306	T	0.00637	0.0021	L	0.37630	1.12	0.80722	P	0.0	B;B	0.24258	0.1;0.046	B;B	0.22152	0.022;0.038	T	0.06006	-1.0851	9	0.48119	T	0.1	.	8.7445	0.34578	0.5761:0.0:0.4239:0.0	rs3204850;rs17715546;rs35223756;rs61754204	255;243	O00421-2;O00421	.;CCRL2_HUMAN	V	243;255;243;243	ENSP00000381994:I243V;ENSP00000349967:I255V;ENSP00000383677:I243V;ENSP00000383678:I243V	ENSP00000349967:I255V	I	+	1	0	CCRL2	46425301	0.002000	0.14202	0.011000	0.14972	0.917000	0.54804	-0.076000	0.11412	-0.202000	0.10268	0.397000	0.26171	ATA	A|0.948;G|0.052	0.052	strong		0.418	CCRL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343909.2		
SP140L	93349	hgsc.bcm.edu	37	2	231258150	231258150	+	Missense_Mutation	SNP	C	C	T	rs7590429	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:231258150C>T	ENST00000415673.2	+	13	1215	c.1129C>T	c.(1129-1131)Cca>Tca	p.P377S	SP140L_ENST00000243810.6_Missense_Mutation_p.P377S|SP140L_ENST00000444636.1_Missense_Mutation_p.P377S|SP140L_ENST00000396563.4_Missense_Mutation_p.P342S	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	377			P -> S (in dbSNP:rs7590429).			nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						ACCTAATCCTCCAAGAATATA	0.353													C|||	2087	0.416733	0.4811	0.3919	5008	,	,		19709	0.2143		0.4404	False		,,,				2504	0.5317				p.P377S		Atlas-SNP	.											.	SP140L	68	.	0			c.C1129T						PASS	.	C	SER/PRO	1657,2025		374,909,558	64.0	63.0	63.0		1129	2.1	0.1	2	dbSNP_116	63	3556,4600		781,1994,1303	yes	missense	SP140L	NM_138402.4	74	1155,2903,1861	TT,TC,CC		43.5998,45.0027,44.0362	benign	377/581	231258150	5213,6625	1841	4078	5919	SO:0001583	missense	93349	exon13			AATCCTCCAAGAA	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.1129C>T	2.37:g.231258150C>T	ENSP00000397911:p.Pro377Ser	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	36	10	0.277778	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	812	0.3717948717948718	223	0.4532520325203252	131	0.36187845303867405	133	0.23251748251748253	325	0.4287598944591029	C	8.266	0.812214	0.16537	0.450027	0.435998	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	3.94	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;B	0.27625	0.183;0.089	B;B	0.32393	0.145;0.068	T	0.41645	-0.9497	8	0.38643	T	0.18	.	6.5031	0.22180	0.0:0.7764:0.0:0.2236	rs7590429;rs52792690;rs56807857;rs7590429	342;377	Q9H930-2;Q9H930-4	.;.	S	377;377;377;342	ENSP00000395195:P377S;ENSP00000397911:P377S;ENSP00000243810:P377S;ENSP00000379811:P342S	ENSP00000243810:P377S	P	+	1	0	SP140L	230966394	0.081000	0.21417	0.055000	0.19348	0.004000	0.04260	1.716000	0.37981	0.436000	0.26393	-0.966000	0.02617	CCA	C|0.605;T|0.395	0.395	strong		0.353	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
SCN10A	6336	hgsc.bcm.edu	37	3	38748833	38748833	+	Silent	SNP	T	T	C	rs6790627	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:38748833T>C	ENST00000449082.2	-	25	4322	c.4323A>G	c.(4321-4323)aaA>aaG	p.K1441K		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1441					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.K1441K(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CATTGTAGTATTTCTTCTGCT	0.542													C|||	1214	0.242412	0.3578	0.2104	5008	,	,		19164	0.3115		0.1571	False		,,,				2504	0.1258				p.K1441K		Atlas-SNP	.											SCN10A,NS,carcinoma,0,1	SCN10A	359	1	1	Substitution - coding silent(1)	stomach(1)	c.A4323G						PASS	.	C		1500,2906	676.4+/-403.2	263,974,966	131.0	139.0	136.0		4323	1.7	1.0	3	dbSNP_116	136	1230,7370	762.2+/-407.6	75,1080,3145	no	coding-synonymous	SCN10A	NM_006514.2		338,2054,4111	CC,CT,TT		14.3023,34.0445,20.9903		1441/1957	38748833	2730,10276	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon25			GTAGTATTTCTTC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.4323A>G	3.37:g.38748833T>C		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	227	103	0.453745	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			T|0.796;C|0.204	0.204	strong		0.542	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
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 GAIIx	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		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	113	70	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	
KCNMB2	10242	hgsc.bcm.edu	37	3	178546026	178546026	+	Silent	SNP	T	T	C	rs9831934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:178546026T>C	ENST00000432997.1	+	4	640	c.288T>C	c.(286-288)aaT>aaC	p.N96N	RP11-385J1.2_ENST00000432385.1_RNA|RP11-385J1.2_ENST00000425330.1_RNA|RP11-385J1.2_ENST00000451742.1_RNA|KCNMB2_ENST00000358316.3_Silent_p.N96N|KCNMB2_ENST00000420517.2_Silent_p.N96N|RP11-385J1.2_ENST00000437488.1_RNA|KCNMB2_ENST00000452583.1_Silent_p.N96N	NM_001278911.1	NP_001265840.1	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 2	108					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(2)|endometrium(4)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	12	all_cancers(143;5.38e-18)|Ovarian(172;0.00769)|Breast(254;0.125)		OV - Ovarian serous cystadenocarcinoma(80;1.32e-27)|GBM - Glioblastoma multiforme(14;0.0321)|BRCA - Breast invasive adenocarcinoma(182;0.0841)		Miconazole(DB01110)|Procaine(DB00721)	AAACATTTAATTGCTCCTTCA	0.522													T|||	2919	0.582867	0.9289	0.5245	5008	,	,		20296	0.2252		0.5825	False		,,,				2504	0.5256				p.N96N		Atlas-SNP	.											.	KCNMB2	35	.	0			c.T288C						PASS	.	T	,	3833,573	773.0+/-413.9	1669,495,39	140.0	117.0	125.0		288,288	-4.7	1.0	3	dbSNP_119	125	5039,3561	629.7+/-398.3	1511,2017,772	no	coding-synonymous,coding-synonymous	KCNMB2	NM_005832.3,NM_181361.1	,	3180,2512,811	CC,CT,TT		41.407,13.005,31.7853	,	96/236,96/236	178546026	8872,4134	2203	4300	6503	SO:0001819	synonymous_variant	10242	exon5			ATTTAATTGCTCC	AF099137	CCDS3223.1	3q26.32	2005-10-13			ENSG00000197584	ENSG00000197584		"""Potassium channels"""	6286	protein-coding gene	gene with protein product		605214				10097176	Standard	NM_181361		Approved		uc003fjd.3	Q9Y691	OTTHUMG00000157264	ENST00000432997.1:c.288T>C	3.37:g.178546026T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_005832	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Silent	SNP	ENST00000432997.1	37	CCDS3223.1																																																																																			T|0.360;C|0.640	0.640	strong		0.522	KCNMB2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348251.1	NM_181361	
ITPKB	3707	hgsc.bcm.edu	37	1	226923938	226923938	+	Missense_Mutation	SNP	A	A	C	rs6667260	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226923938A>C	ENST00000272117.3	-	1	1221	c.1222T>G	c.(1222-1224)Tcc>Gcc	p.S408A	ITPKB_ENST00000429204.1_Missense_Mutation_p.S408A|ITPKB_ENST00000366784.1_Missense_Mutation_p.S408A			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	408			S -> A (in dbSNP:rs6667260). {ECO:0000269|PubMed:11846419, ECO:0000269|PubMed:15489334}.		cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				CAGCTCAGGGAATCAGAGGAC	0.677													C|||	3057	0.610423	0.6067	0.6599	5008	,	,		16260	0.6786		0.5258	False		,,,				2504	0.5971				p.S408A	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	0			c.T1222G						PASS	.	C	ALA/SER	2536,1860		729,1078,391	33.0	40.0	38.0		1222	1.0	0.0	1	dbSNP_116	38	4146,4452		1040,2066,1193	yes	missense	ITPKB	NM_002221.3	99	1769,3144,1584	CC,CA,AA		48.2205,42.3112,48.5763	benign	408/947	226923938	6682,6312	2198	4299	6497	SO:0001583	missense	3707	exon2			TCAGGGAATCAGA	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1222T>G	1.37:g.226923938A>C	ENSP00000272117:p.Ser408Ala	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	59	0.967213	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	1305	0.5975274725274725	282	0.573170731707317	229	0.6325966850828729	387	0.6765734265734266	407	0.5369393139841688	C	0.132	-1.111789	0.01813	0.576888	0.482205	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.20598	2.07;2.07;2.06	4.1	1.01	0.19927	.	0.990786	0.08197	N	0.982952	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42649	-0.9439	9	0.02654	T	1	-1.6525	3.0407	0.06138	0.324:0.3961:0.0:0.28	rs6667260;rs17856474;rs58231934;rs6667260	408	P27987	IP3KB_HUMAN	A	408	ENSP00000272117:S408A;ENSP00000411152:S408A;ENSP00000355748:S408A	ENSP00000272117:S408A	S	-	1	0	ITPKB	224990561	0.000000	0.05858	0.001000	0.08648	0.072000	0.16883	0.079000	0.14782	-0.121000	0.11787	-0.323000	0.08544	TCC	A|0.444;C|0.556	0.556	strong		0.677	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
FHL2	2274	hgsc.bcm.edu	37	2	105977776	105977776	+	Silent	SNP	G	G	A	rs3087523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:105977776G>A	ENST00000409807.1	-	6	1138	c.804C>T	c.(802-804)gaC>gaT	p.D268D	FHL2_ENST00000393353.3_Silent_p.D268D|FHL2_ENST00000409177.1_Silent_p.D384D|FHL2_ENST00000393352.3_Silent_p.D268D|FHL2_ENST00000344213.4_Silent_p.D378D|FHL2_ENST00000336660.5_3'UTR|AC012360.6_ENST00000457290.2_RNA|FHL2_ENST00000358129.4_Silent_p.D268D|FHL2_ENST00000322142.8_Silent_p.D268D|FHL2_ENST00000408995.1_Silent_p.D268D			Q14192	FHL2_HUMAN	four and a half LIM domains 2	268	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|atrial cardiac muscle cell development (GO:0055014)|cellular lipid metabolic process (GO:0044255)|heart trabecula formation (GO:0060347)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|M band (GO:0031430)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Z disc (GO:0030018)	androgen receptor binding (GO:0050681)|identical protein binding (GO:0042802)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						ACAGGATGTCGTCCCTCTCTG	0.483													G|||	259	0.0517173	0.0068	0.1066	5008	,	,		20376	0.0238		0.1103	False		,,,				2504	0.0419				p.D268D		Atlas-SNP	.											FHL2,colon,carcinoma,0,1	FHL2	18	1	0			c.C804T						PASS	.	G	,,,	116,4290	88.2+/-126.9	1,114,2088	122.0	110.0	114.0		804,804,804,804	-11.0	0.0	2	dbSNP_102	114	1092,7508	227.9+/-263.1	63,966,3271	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FHL2	NM_001039492.2,NM_001450.3,NM_201555.1,NM_201557.3	,,,	64,1080,5359	AA,AG,GG		12.6977,2.6328,9.288	,,,	268/280,268/280,268/280,268/280	105977776	1208,11798	2203	4300	6503	SO:0001819	synonymous_variant	2274	exon7			GATGTCGTCCCTC		CCDS2070.1	2q12.2	2014-09-17			ENSG00000115641	ENSG00000115641			3703	protein-coding gene	gene with protein product		602633				8753811	Standard	NM_201557		Approved	SLIM3, DRAL	uc002tcy.3	Q14192	OTTHUMG00000153120	ENST00000409807.1:c.804C>T	2.37:g.105977776G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	32	0.410256	NM_001039492	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	Silent	SNP	ENST00000409807.1	37	CCDS2070.1																																																																																			G|0.921;A|0.079	0.079	strong		0.483	FHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329654.1		
NLRP6	171389	hgsc.bcm.edu	37	11	284341	284341	+	Silent	SNP	G	G	A	rs7108246	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:284341G>A	ENST00000312165.5	+	6	2313	c.2313G>A	c.(2311-2313)gcG>gcA	p.A771A	RP11-326C3.2_ENST00000533924.1_RNA|NLRP6_ENST00000534750.1_Silent_p.A770A	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	771					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCAGTGAGGCGGGACTGCGTA	0.687													g|||	96	0.0191693	0.0038	0.0216	5008	,	,		16726	0.0		0.0577	False		,,,				2504	0.0184				p.A771A		Atlas-SNP	.											NALP6,colon,carcinoma,+1,1	NLRP6	4	1	0			c.G2313A						PASS	.	A		55,4351	816.0+/-416.2	0,55,2148	41.0	42.0	42.0		2313	-6.1	0.0	11	dbSNP_116	42	587,8013	790.4+/-407.6	13,561,3726	no	coding-synonymous	NLRP6	NM_138329.1		13,616,5874	AA,AG,GG		6.8256,1.2483,4.9362		771/893	284341	642,12364	2203	4300	6503	SO:0001819	synonymous_variant	171389	exon6			TGAGGCGGGACTG	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2313G>A	11.37:g.284341G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			G|0.961;A|0.039	0.039	strong		0.687	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
C1orf127	148345	hgsc.bcm.edu	37	1	11024271	11024271	+	5'UTR	SNP	G	G	T	rs11121662	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11024271G>T	ENST00000377008.4	-	0	429				C1orf127_ENST00000377004.4_Silent_p.R144R			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)		CGATCACTCCGCTCCAACCCC	0.483													G|||	449	0.0896565	0.0469	0.0836	5008	,	,		21247	0.2302		0.0527	False		,,,				2504	0.045				p.R144R		Atlas-SNP	.											.	C1orf127	134	.	0			c.C430A						PASS	.	G		180,4226	117.1+/-155.0	8,164,2031	109.0	94.0	99.0		430	2.4	0.7	1	dbSNP_120	99	361,8239	120.8+/-180.0	10,341,3949	no	coding-synonymous	C1orf127	NM_001170754.1		18,505,5980	TT,TG,GG		4.1977,4.0853,4.1596		144/824	11024271	541,12465	2203	4300	6503	SO:0001623	5_prime_UTR_variant	148345	exon5			CACTCCGCTCCAA	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.-18C>A	1.37:g.11024271G>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	47	0.594937	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		229	0.10485347985347986	26	0.052845528455284556	23	0.06353591160220995	135	0.23601398601398602	45	0.059366754617414245	G	2.109	-0.404314	0.04832	0.040853	0.041977	ENSG00000175262	ENST00000520253	.	.	.	4.35	2.43	0.29744	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999678	.	.	.	.	.	.	T	0.14811	-1.0459	3	.	.	.	.	7.6668	0.28437	0.0955:0.1651:0.7394:0.0	rs11121662	.	.	.	R	121	.	.	S	-	3	2	C1orf127	10946858	1.000000	0.71417	0.731000	0.30826	0.210000	0.24377	1.485000	0.35519	0.286000	0.22352	0.561000	0.74099	AGC	G|0.919;T|0.081	0.081	strong		0.483	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
PPP1R26	9858	hgsc.bcm.edu	37	9	138376649	138376649	+	Missense_Mutation	SNP	T	T	C	rs3748192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138376649T>C	ENST00000356818.2	+	4	842	c.293T>C	c.(292-294)gTc>gCc	p.V98A	PPP1R26_ENST00000605286.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000605660.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Missense_Mutation_p.V98A|PPP1R26_ENST00000401470.3_Missense_Mutation_p.V98A	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	98			V -> A (in dbSNP:rs3748192). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GCGTTGGCTGTCTGTGGTCTC	0.627													C|||	2095	0.418331	0.2905	0.4899	5008	,	,		16315	0.6528		0.2117	False		,,,				2504	0.5112				p.V98A		Atlas-SNP	.											KIAA0649,NS,carcinoma,0,1	.	.	1	0			c.T293C						scavenged	.	C	ALA/VAL	1113,3291		132,849,1221	41.0	48.0	46.0		293	3.4	0.1	9	dbSNP_107	46	1777,6821		195,1387,2717	no	missense	KIAA0649	NM_014811.3	64	327,2236,3938	CC,CT,TT		20.6676,25.2725,22.2273	benign	98/1210	138376649	2890,10112	2202	4299	6501	SO:0001583	missense	9858	exon4			TGGCTGTCTGTGG	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.293T>C	9.37:g.138376649T>C	ENSP00000349274:p.Val98Ala	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	833	0.3814102564102564	122	0.24796747967479674	158	0.43646408839779005	394	0.6888111888111889	159	0.20976253298153033	C	0.007	-2.011636	0.00422	0.252725	0.206676	ENSG00000196422	ENST00000356818;ENST00000401470	T;T	0.46063	0.88;0.88	4.39	3.41	0.39046	.	0.854487	0.10136	N	0.711490	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	9	0.02654	T	1	-12.6961	7.3836	0.26870	0.2105:0.6922:0.0:0.0973	rs3748192;rs17846422;rs17859468;rs3748192	98	Q5T8A7	PPR26_HUMAN	A	98	ENSP00000349274:V98A;ENSP00000385826:V98A	ENSP00000349274:V98A	V	+	2	0	KIAA0649	137516470	0.006000	0.16342	0.106000	0.21319	0.067000	0.16453	1.185000	0.32065	1.085000	0.41206	-0.119000	0.15052	GTC	T|0.723;C|0.277	0.277	strong		0.627	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
DHRS3	9249	hgsc.bcm.edu	37	1	12640650	12640650	+	Silent	SNP	C	C	T	rs11540058	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12640650C>T	ENST00000376223.2	-	2	623	c.240G>A	c.(238-240)acG>acA	p.T80T	DHRS3_ENST00000482265.1_5'UTR	NM_004753.4	NP_004744.2	O75911	DHRS3_HUMAN	dehydrogenase/reductase (SDR family) member 3	80					bone morphogenesis (GO:0060349)|cardiac septum morphogenesis (GO:0060411)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|phototransduction, visible light (GO:0007603)|regulation of ossification (GO:0030278)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|photoreceptor outer segment membrane (GO:0042622)	electron carrier activity (GO:0009055)|NADP-retinol dehydrogenase activity (GO:0052650)|nucleotide binding (GO:0000166)|retinol dehydrogenase activity (GO:0004745)			cervix(1)|large_intestine(4)|lung(2)|prostate(1)|skin(1)	9	Ovarian(185;0.249)	Lung NSC(185;4.11e-05)|all_lung(284;4.58e-05)|Renal(390;0.000147)|Colorectal(325;0.000585)|Breast(348;0.000596)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|Colorectal(212;9.25e-07)|COAD - Colon adenocarcinoma(227;0.000326)|BRCA - Breast invasive adenocarcinoma(304;0.000344)|Kidney(185;0.00235)|KIRC - Kidney renal clear cell carcinoma(229;0.00656)|STAD - Stomach adenocarcinoma(313;0.00798)|READ - Rectum adenocarcinoma(331;0.0419)	Vitamin A(DB00162)	GGATCTCCTCCGTCGTCTCCT	0.537													C|||	399	0.0796725	0.0446	0.0764	5008	,	,		17584	0.002		0.1918	False		,,,				2504	0.0941				p.T80T		Atlas-SNP	.											.	DHRS3	18	.	0			c.G240A						PASS	.	C		294,4112	161.1+/-193.3	10,274,1919	74.0	71.0	72.0		240	-4.2	0.4	1	dbSNP_120	72	1781,6819	321.8+/-315.3	194,1393,2713	no	coding-synonymous	DHRS3	NM_004753.4		204,1667,4632	TT,TC,CC		20.7093,6.6727,15.9542		80/303	12640650	2075,10931	2203	4300	6503	SO:0001819	synonymous_variant	9249	exon2			CTCCTCCGTCGTC	AF061741	CCDS146.1	1p36.1	2011-09-20			ENSG00000162496	ENSG00000162496	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	17693	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 1"""	612830				9705317, 12226107, 19027726	Standard	XM_005263533		Approved	retSDR1, Rsdr1, SDR1, RDH17, SDR16C1	uc001auc.3	O75911	OTTHUMG00000001885	ENST00000376223.2:c.240G>A	1.37:g.12640650C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_004753	B2R7F3|Q5VUY3|Q6UY38|Q9BUC8	Silent	SNP	ENST00000376223.2	37	CCDS146.1																																																																																			C|0.868;T|0.132	0.132	strong		0.537	DHRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005318.1	NM_004753	
CFHR1	3078	hgsc.bcm.edu	37	1	196801042	196801042	+	Silent	SNP	G	G	T	rs4230	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196801042G>T	ENST00000320493.5	+	6	994	c.906G>T	c.(904-906)cgG>cgT	p.R302R	CFHR2_ENST00000367421.3_Intron|CFHR1_ENST00000367424.4_Silent_p.R243R	NM_002113.2	NP_002104.2	Q03591	FHR1_HUMAN	complement factor H-related 1	302	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|kidney(1)|large_intestine(2)|lung(7)	11						TGTGTAAACGGGGATATCGTC	0.383													-|||	2541	0.507388	0.6157	0.5187	5008	,	,		12798	0.5437		0.4463	False		,,,				2504	0.3783				p.R302R		Atlas-SNP	.											CFHR1,right_upper_lobe,carcinoma,+1,2	CFHR1	47	2	0			c.G906T						PASS	.	T		2442,1332		1044,354,489	117.0	131.0	127.0		906	0.1	0.0	1	dbSNP_36	127	3358,4906		1015,1328,1789	no	coding-synonymous	CFHR1	NM_002113.2		2059,1682,2278	TT,TG,GG		40.6341,35.2941,48.1808		302/331	196801042	5800,6238	1887	4132	6019	SO:0001819	synonymous_variant	3078	exon6			TAAACGGGGATAT	M65292	CCDS1386.1	1q32	2014-09-17	2004-08-09	2006-02-28	ENSG00000244414	ENSG00000244414		"""Complement system"""	4888	protein-coding gene	gene with protein product		134371	"""H factor (complement)-like 1"", ""complement factor H-related 1 pseudogene"", ""H factor (complement)-like 2"""	HFL1, CFHL1, CFHR1P, HFL2, CFHL1P		1711047, 1826708	Standard	NM_002113		Approved	H36-1, FHR1, CFHL, H36-2		Q03591	OTTHUMG00000036276	ENST00000320493.5:c.906G>T	1.37:g.196801042G>T		Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	537	237	0.441341	NM_002113	A8K465|Q3B774|Q9UJ17	Silent	SNP	ENST00000320493.5	37	CCDS1386.1																																																																																			G|0.519;T|0.481	0.481	strong		0.383	CFHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088251.2	NM_002113	
MORC1	27136	hgsc.bcm.edu	37	3	108719470	108719470	+	Silent	SNP	C	C	G	rs3762698	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:108719470C>G	ENST00000483760.1	-	20	2101	c.2058G>C	c.(2056-2058)ctG>ctC	p.L686L	MORC1_ENST00000232603.5_Silent_p.L707L					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						CTACAAAGTTCAGACTCTGCT	0.358													C|||	1038	0.207268	0.2693	0.2003	5008	,	,		18160	0.0278		0.2694	False		,,,				2504	0.2495				p.L707L		Atlas-SNP	.											.	MORC1	211	.	0			c.G2121C						PASS	.	C		1265,3141	432.0+/-343.1	188,889,1126	177.0	173.0	174.0		2121	-2.0	0.0	3	dbSNP_107	174	2422,6176	400.8+/-346.9	354,1714,2231	no	coding-synonymous	MORC1	NM_014429.3		542,2603,3357	GG,GC,CC		28.1693,28.7108,28.3528		707/985	108719470	3687,9317	2203	4299	6502	SO:0001819	synonymous_variant	27136	exon21			AAAGTTCAGACTC	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2058G>C	3.37:g.108719470C>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																				C|0.734;G|0.266	0.266	strong		0.358	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
CDHR1	92211	hgsc.bcm.edu	37	10	85960395	85960395	+	Silent	SNP	A	A	G	rs4933975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:85960395A>G	ENST00000372117.3	+	6	580	c.477A>G	c.(475-477)gcA>gcG	p.A159A	CDHR1_ENST00000332904.3_Silent_p.A159A|CDHR1_ENST00000440770.2_5'Flank	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	159	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						AGGTCCATGCAGTGGACAGGG	0.597													G|||	2584	0.515974	0.711	0.5202	5008	,	,		19219	0.3948		0.4612	False		,,,				2504	0.4305				p.A159A		Atlas-SNP	.											CDHR1,NS,carcinoma,+2,1	CDHR1	122	1	0			c.A477G						PASS	.	G	,	2949,1457	466.0+/-354.4	1006,937,260	112.0	79.0	90.0		477,477	-10.6	0.0	10	dbSNP_111	90	3878,4722	604.6+/-394.8	859,2160,1281	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	1865,3097,1541	GG,GA,AA		45.093,33.0685,47.5088	,	159/746,159/860	85960395	6827,6179	2203	4300	6503	SO:0001819	synonymous_variant	92211	exon6			CCATGCAGTGGAC	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.477A>G	10.37:g.85960395A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	165	80	0.484848	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			A|0.487;G|0.513	0.513	strong		0.597	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
CD276	80381	hgsc.bcm.edu	37	15	73994847	73994847	+	Missense_Mutation	SNP	C	C	A	rs7173476	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:73994847C>A	ENST00000318443.5	+	3	633	c.331C>A	c.(331-333)Cgc>Agc	p.R111S	CD276_ENST00000537340.2_5'UTR|CD276_ENST00000318424.5_Missense_Mutation_p.R111S|CD276_ENST00000561213.1_Missense_Mutation_p.R111S|CD276_ENST00000564751.1_Missense_Mutation_p.R111S	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	111	Ig-like V-type 1.		R -> S (in dbSNP:rs7173476).		cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GAGGCTGCAGCGCGTGCGTGT	0.682													C|||	1004	0.200479	0.4289	0.1023	5008	,	,		18424	0.1349		0.0964	False		,,,				2504	0.136				p.R111S		Atlas-SNP	.											.	CD276	29	.	0			c.C331A						PASS	.	C	SER/ARG,SER/ARG	1698,2698	497.7+/-363.9	352,994,852	44.0	39.0	41.0		331,331	2.0	1.0	15	dbSNP_116	41	840,7750	190.8+/-237.2	33,774,3488	no	missense,missense	CD276	NM_001024736.1,NM_025240.2	110,110	385,1768,4340	AA,AC,CC		9.7788,38.626,19.5441	benign,benign	111/535,111/317	73994847	2538,10448	2198	4295	6493	SO:0001583	missense	80381	exon3			CTGCAGCGCGTGC	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.331C>A	15.37:g.73994847C>A	ENSP00000320084:p.Arg111Ser	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_025240	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	394	0.1804029304029304	207	0.42073170731707316	41	0.1132596685082873	73	0.12762237762237763	73	0.09630606860158311	C	12.30	1.896302	0.33442	0.38626	0.097788	ENSG00000103855	ENST00000318424;ENST00000318443;ENST00000379823	T;T	0.02345	4.33;4.33	2.94	1.99	0.26369	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.20304	0.555	0.25280	P	0.9894434	P;B;P;P	0.49090	0.841;0.414;0.919;0.901	B;B;P;P	0.50162	0.283;0.067;0.633;0.499	T	0.52779	-0.8530	8	0.38643	T	0.18	-16.0534	12.1282	0.53928	0.0:0.824:0.176:0.0	rs7173476	57;111;111;111	B4DK26;Q5ZPR3-2;Q5ZPR3;Q5ZPR3-4	.;.;CD276_HUMAN;.	S	111	ENSP00000320058:R111S;ENSP00000320084:R111S	ENSP00000320058:R111S	R	+	1	0	CD276	71781900	0.632000	0.27172	0.997000	0.53966	0.617000	0.37484	0.357000	0.20199	0.774000	0.33427	0.313000	0.20887	CGC	C|0.813;A|0.187	0.187	strong		0.682	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
IFT140	9742	hgsc.bcm.edu	37	16	1608082	1608082	+	Silent	SNP	A	A	G	rs2076436	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1608082A>G	ENST00000426508.2	-	19	2616	c.2253T>C	c.(2251-2253)ccT>ccC	p.P751P	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	751					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.P751P(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				ACACCATCTGAGGGATGTGGT	0.547													A|||	1740	0.347444	0.5507	0.1844	5008	,	,		18218	0.3433		0.2087	False		,,,				2504	0.3354				p.P751P		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	1	1	Substitution - coding silent(1)	stomach(1)	c.T2253C						PASS	.	A		2135,2263	579.6+/-385.0	518,1099,582	146.0	144.0	145.0		2253	0.7	0.3	16	dbSNP_96	145	1861,6739	333.7+/-320.7	197,1467,2636	no	coding-synonymous	IFT140	NM_014714.3		715,2566,3218	GG,GA,AA		21.6395,48.5448,30.7432		751/1463	1608082	3996,9002	2199	4300	6499	SO:0001819	synonymous_variant	9742	exon19			CATCTGAGGGATG	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.2253T>C	16.37:g.1608082A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																			A|0.687;G|0.313	0.313	strong		0.547	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
SPATA17	128153	hgsc.bcm.edu	37	1	217856626	217856626	+	Silent	SNP	G	G	A	rs12068167	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:217856626G>A	ENST00000366933.4	+	5	373	c.318G>A	c.(316-318)agG>agA	p.R106R		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	106	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		GAGGCTATAGGGTTCGGAAGT	0.313													G|||	877	0.17512	0.3011	0.1268	5008	,	,		11797	0.0962		0.173	False		,,,				2504	0.1227				p.R106R		Atlas-SNP	.											.	SPATA17	59	.	0			c.G318A						PASS	.	G		1198,3200	373.4+/-320.8	166,866,1167	91.0	109.0	103.0		318	3.5	0.9	1	dbSNP_120	103	1365,7233	258.6+/-282.2	110,1145,3044	no	coding-synonymous	SPATA17	NM_138796.2		276,2011,4211	AA,AG,GG		15.8758,27.2397,19.7215		106/362	217856626	2563,10433	2199	4299	6498	SO:0001819	synonymous_variant	128153	exon5			CTATAGGGTTCGG	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"""IQ motif containing H"""	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.318G>A	1.37:g.217856626G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			G|0.826;A|0.174	0.174	strong		0.313	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
PZP	5858	hgsc.bcm.edu	37	12	9317784	9317784	+	Missense_Mutation	SNP	A	A	G	rs2277413	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9317784A>G	ENST00000261336.2	-	19	2466	c.2438T>C	c.(2437-2439)gTc>gCc	p.V813A	PZP_ENST00000381997.2_Missense_Mutation_p.V682A|PZP_ENST00000539983.1_5'UTR	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	813			V -> A (in dbSNP:rs2277413).		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						GAGTGTGAAGACCTCTCCACG	0.498													A|||	1934	0.386182	0.3411	0.2421	5008	,	,		-128	0.5357		0.3419	False		,,,				2504	0.4407				p.V813A	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											.	PZP	422	.	0			c.T2438C						PASS	.	A	ALA/VAL	1464,2942	463.4+/-353.5	261,942,1000	127.0	120.0	122.0		2438	-0.9	1.0	12	dbSNP_100	122	2537,6063	408.7+/-349.6	381,1775,2144	no	missense	PZP	NM_002864.2	64	642,2717,3144	GG,GA,AA		29.5,33.2274,30.7627	benign	813/1483	9317784	4001,9005	2203	4300	6503	SO:0001583	missense	5858	exon19			GTGAAGACCTCTC	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.2438T>C	12.37:g.9317784A>G	ENSP00000261336:p.Val813Ala	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	139	72	0.517986	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	732	0.33516483516483514	137	0.2784552845528455	97	0.26795580110497236	282	0.493006993006993	216	0.2849604221635884	A	0.003	-2.442208	0.00180	0.332274	0.295	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.24908	1.83;1.83	3.7	-0.929	0.10444	Alpha-2-macroglobulin (1);	0.671497	0.13428	N	0.388670	T	0.00012	0.0000	N	0.02420	-0.555	0.80722	P	0.0	B;B;B	0.16802	0.001;0.019;0.001	B;B;B	0.15484	0.002;0.013;0.002	T	0.43360	-0.9396	9	0.02654	T	1	.	3.0317	0.06109	0.268:0.1205:0.4895:0.122	rs2277413;rs59075755;rs2277413	813;682;813	B2R950;P20742-2;P20742	.;.;PZP_HUMAN	A	813;682	ENSP00000261336:V813A;ENSP00000371427:V682A	ENSP00000261336:V813A	V	-	2	0	PZP	9209051	0.000000	0.05858	0.990000	0.47175	0.212000	0.24457	-1.395000	0.02516	0.004000	0.14682	-1.483000	0.00984	GTC	A|0.677;G|0.323	0.323	strong		0.498	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
GPR123	84435	hgsc.bcm.edu	37	10	134942166	134942166	+	Silent	SNP	A	A	G	rs2806452	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:134942166A>G	ENST00000392607.3	+	7	1270	c.834A>G	c.(832-834)tcA>tcG	p.S278S	GPR123_ENST00000392606.2_Silent_p.S181S|GPR123_ENST00000607359.1_Silent_p.S997S	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	278					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		TGGCGGTGTCACAGGGCCACT	0.652													G|||	2450	0.489217	0.4826	0.621	5008	,	,		13237	0.5357		0.4145	False		,,,				2504	0.4335				p.S278S		Atlas-SNP	.											.	GPR123	118	.	0			c.A834G						PASS	.	G		2082,2306		513,1056,625	29.0	22.0	25.0		834	-9.5	0.1	10	dbSNP_100	25	3242,5342		623,1996,1673	no	coding-synonymous	GPR123	NM_001083909.1		1136,3052,2298	GG,GA,AA		37.7679,47.4476,41.0422		278/561	134942166	5324,7648	2194	4292	6486	SO:0001819	synonymous_variant	84435	exon7			GGTGTCACAGGGC	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.834A>G	10.37:g.134942166A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	37	CCDS41580.1																																																																																			A|0.559;G|0.441	0.441	strong		0.652	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2		
TRPV1	7442	hgsc.bcm.edu	37	17	3494361	3494361	+	Silent	SNP	G	G	A	rs222748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3494361G>A	ENST00000571088.1	-	4	714	c.501C>T	c.(499-501)caC>caT	p.H167H	TRPV1_ENST00000399756.4_Silent_p.H167H|TRPV1_ENST00000399759.3_Silent_p.H167H|TRPV1_ENST00000174621.6_Silent_p.H165H|TRPV1_ENST00000425167.2_Silent_p.H167H|SHPK_ENST00000572705.1_Silent_p.H167H|TRPV1_ENST00000310522.5_Silent_p.H167H|TRPV1_ENST00000576351.1_Silent_p.H167H	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	167					calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	TCTGTCCGTCGTGCAGGTTGA	0.612													G|||	813	0.16234	0.0242	0.1383	5008	,	,		20067	0.2659		0.1352	False		,,,				2504	0.2873				p.H167H	Melanoma(38;962 1762 15789)	Atlas-SNP	.											TRPV1_ENST00000399756,caecum,carcinoma,0,2	TRPV1	99	2	0			c.C501T						PASS	.	G	,,,	167,4093		2,163,1965	83.0	85.0	84.0		501,501,501,501	-9.0	0.0	17	dbSNP_79	84	916,7562		54,808,3377	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	,,,	56,971,5342	AA,AG,GG		10.8044,3.9202,8.5021	,,,	167/840,167/840,167/840,167/840	3494361	1083,11655	2130	4239	6369	SO:0001819	synonymous_variant	7442	exon4			TCCGTCGTGCAGG	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.501C>T	17.37:g.3494361G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	154	68	0.441558	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Silent	SNP	ENST00000571088.1	37	CCDS45576.1																																																																																			G|0.863;A|0.137	0.137	strong		0.612	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
OR5P2	120065	hgsc.bcm.edu	37	11	7818056	7818056	+	Missense_Mutation	SNP	T	T	C	rs73406604	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7818056T>C	ENST00000329434.2	-	1	464	c.434A>G	c.(433-435)tAc>tGc	p.Y145C	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ACCAGCTATGTAAACTACTAA	0.408													T|||	1184	0.236422	0.3472	0.2911	5008	,	,		19685	0.128		0.2763	False		,,,				2504	0.1186				p.Y145C		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	0			c.A434G						PASS	.	T	CYS/TYR	1369,2829		401,567,1131	63.0	75.0	71.0		434	3.2	0.2	11	dbSNP_130	71	2425,6159		393,1639,2260	yes	missense	OR5P2	NM_153444.1	194	794,2206,3391	CC,CT,TT		28.2502,32.6108,29.6824	benign	145/323	7818056	3794,8988	2099	4292	6391	SO:0001583	missense	120065	exon1			GCTATGTAAACTA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.434A>G	11.37:g.7818056T>C	ENSP00000331823:p.Tyr145Cys	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	586	0.2683150183150183	180	0.36585365853658536	100	0.27624309392265195	84	0.14685314685314685	222	0.2928759894459103	T	5.438	0.265978	0.10294	0.326108	0.282502	ENSG00000183303	ENST00000329434	T	0.38240	1.15	5.5	3.18	0.36537	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000015	T	0.00012	0.0000	M	0.68952	2.095	0.80722	P	0.0	B	0.17667	0.023	B	0.33750	0.169	T	0.32402	-0.9908	9	0.66056	D	0.02	-38.8562	4.4769	0.11748	0.3014:0.0807:0.0:0.6179	.	145	Q8WZ92	OR5P2_HUMAN	C	145	ENSP00000331823:Y145C	ENSP00000331823:Y145C	Y	-	2	0	OR5P2	7774632	0.000000	0.05858	0.166000	0.22797	0.001000	0.01503	0.078000	0.14761	0.511000	0.28236	-0.456000	0.05471	TAC	T|0.738;C|0.262	0.262	strong		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
USP42	84132	hgsc.bcm.edu	37	7	6193752	6193752	+	Missense_Mutation	SNP	G	G	A	rs61753119	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6193752G>A	ENST00000306177.5	+	15	2725	c.2567G>A	c.(2566-2568)aGt>aAt	p.S856N		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	856	Pro-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)		GAAGGGTTGAGTCCGGCTCCG	0.701													G|||	342	0.0682907	0.0484	0.1225	5008	,	,		11334	0.0089		0.1382	False		,,,				2504	0.046				p.S856N		Atlas-SNP	.											USP42_ENST00000306177,NS,carcinoma,0,2	USP42	138	2	0			c.G2567A						scavenged	.	G	ASN/SER	214,3498		2,210,1644	19.0	25.0	23.0		2567	3.4	0.1	7	dbSNP_129	23	941,7121		45,851,3135	no	missense	USP42	NM_032172.2	46	47,1061,4779	AA,AG,GG		11.672,5.7651,9.8098	probably-damaging	856/1317	6193752	1155,10619	1856	4031	5887	SO:0001583	missense	84132	exon15			GGTTGAGTCCGGC	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.2567G>A	7.37:g.6193752G>A	ENSP00000301962:p.Ser856Asn	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	9	4	0.444444	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	37	CCDS47535.1	165	0.07554945054945054	26	0.052845528455284556	42	0.11602209944751381	2	0.0034965034965034965	95	0.12532981530343007	G	18.30	3.593525	0.66219	0.057651	0.11672	ENSG00000106346	ENST00000306177;ENST00000426246	T;T	0.17854	2.25;2.67	5.2	3.37	0.38596	.	0.312951	0.33670	N	0.004665	T	0.00144	0.0004	L	0.29908	0.895	0.53688	P	2.199999999996649E-5	P;B	0.36909	0.573;0.437	B;B	0.39217	0.294;0.154	T	0.22906	-1.0203	9	0.39692	T	0.17	.	7.3813	0.26858	0.0973:0.2021:0.7005:0.0	rs61753119	856;856	Q9H9J4-2;Q9H9J4	.;UBP42_HUMAN	N	856;702	ENSP00000301962:S856N;ENSP00000408217:S702N	ENSP00000301962:S856N	S	+	2	0	USP42	6160277	0.129000	0.22400	0.053000	0.19242	0.001000	0.01503	3.032000	0.49736	0.786000	0.33708	-0.136000	0.14681	AGT	G|0.919;A|0.081	0.081	strong		0.701	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
PARP12	64761	hgsc.bcm.edu	37	7	139724555	139724555	+	Silent	SNP	C	C	T	rs3735352	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:139724555C>T	ENST00000263549.3	-	12	2784	c.1911G>A	c.(1909-1911)ccG>ccA	p.P637P		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	637	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					CCTTGGCCGGCGGACGGACAA	0.592													G|||	1881	0.375599	0.5522	0.3876	5008	,	,		19852	0.498		0.2117	False		,,,				2504	0.1708				p.P637P		Atlas-SNP	.											.	PARP12	59	.	0			c.G1911A						PASS	.	G		2796,1610		1038,720,445	111.0	93.0	99.0		1911	-2.0	0.9	7	dbSNP_107	99	1944,6656		262,1420,2618	no	coding-synonymous	PARP12	NM_022750.2		1300,2140,3063	TT,TC,CC		22.6047,36.5411,36.4447		637/702	139724555	4740,8266	2203	4300	6503	SO:0001819	synonymous_variant	64761	exon12			GGCCGGCGGACGG	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1911G>A	7.37:g.139724555C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_022750	Q9H610|Q9NP36|Q9NTI3	Silent	SNP	ENST00000263549.3	37	CCDS5857.1																																																																																			T|0.364;G|0.008;C|0.628	0.364	strong		0.592	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37421199	37421199	+	Missense_Mutation	SNP	C	C	T	rs34042320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:37421199C>T	ENST00000602533.1	+	4	473	c.374C>T	c.(373-375)aCg>aTg	p.T125M	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.T125M|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.T125M|RNU6-811P_ENST00000384069.1_RNA			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	181					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CTATCCATAACGAAAAGAAGT	0.284													C|||	164	0.0327476	0.0045	0.0288	5008	,	,		17241	0.0387		0.0517	False		,,,				2504	0.0481				p.T125M		Atlas-SNP	.											ANKRD30A_ENST00000602533,NS,carcinoma,-1,3	ANKRD30A	448	3	0			c.C374T						scavenged	.	C	MET/THR	55,3543		0,55,1744	63.0	61.0	61.0		374	-4.7	0.0	10	dbSNP_126	61	479,7661		18,443,3609	yes	missense	ANKRD30A	NM_052997.2	81	18,498,5353	TT,TC,CC		5.8845,1.5286,4.5493	benign	125/1342	37421199	534,11204	1799	4070	5869	SO:0001583	missense	91074	exon4			CCATAACGAAAAG	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.374C>T	10.37:g.37421199C>T	ENSP00000473551:p.Thr125Met	Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	214	99	0.462617	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		70	0.03205128205128205	3	0.006097560975609756	10	0.027624309392265192	19	0.033216783216783216	38	0.05013192612137203	.	6.950	0.545211	0.13312	0.015286	0.058845	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.64991	-0.1;-0.13	2.37	-4.74	0.03249	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.03871	0.0109	N	0.11789	0.175	0.09310	N	1	B	0.26547	0.152	B	0.14578	0.011	T	0.04255	-1.0965	9	0.36615	T	0.2	.	0.4082	0.00437	0.2455:0.3071:0.1679:0.2795	rs34042320;rs34042320	181	Q9BXX3	AN30A_HUMAN	M	125	ENSP00000354432:T125M;ENSP00000363792:T125M	ENSP00000354432:T125M	T	+	2	0	ANKRD30A	37461205	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.683000	0.01934	-1.230000	0.02561	-1.036000	0.02392	ACG	C|0.962;T|0.038	0.038	strong		0.284	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
PLEKHS1	79949	hgsc.bcm.edu	37	10	115529576	115529576	+	Missense_Mutation	SNP	T	T	A	rs41292632	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:115529576T>A	ENST00000369310.3	+	6	1013	c.451T>A	c.(451-453)Ttc>Atc	p.F151I	PLEKHS1_ENST00000361048.1_Missense_Mutation_p.F157I|PLEKHS1_ENST00000354462.3_5'Flank|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.F69I|PLEKHS1_ENST00000369309.1_5'Flank	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	151																	AAGAACCCTCTTCTACTCCAG	0.502													T|||	1003	0.20028	0.1195	0.1628	5008	,	,		18665	0.3175		0.162	False		,,,				2504	0.2546				p.F157I		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.T469A						PASS	.	T	ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE	532,3874	242.1+/-252.3	37,458,1708	125.0	119.0	121.0		205,205,469,451	4.8	0.0	10	dbSNP_127	121	1430,7170	275.6+/-291.8	138,1154,3008	yes	missense,missense,missense,missense	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4,NM_182601.1	21,21,21,21	175,1612,4716	AA,AT,TT		16.6279,12.0744,15.0853	benign,benign,benign,benign	69/367,69/367,157/364,151/466	115529576	1962,11044	2203	4300	6503	SO:0001583	missense	79949	exon7			ACCCTCTTCTACT	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.451T>A	10.37:g.115529576T>A	ENSP00000358316:p.Phe151Ile	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	46	29	0.630435	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	37	CCDS53580.1	410	0.18772893772893773	67	0.13617886178861788	55	0.15193370165745856	175	0.30594405594405594	113	0.14907651715039577	T	14.13	2.444684	0.43429	0.120744	0.166279	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310	T;T;T	0.28666	1.6;1.6;1.6	5.93	4.76	0.60689	.	0.459548	0.23019	N	0.052872	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;P;P	0.47302	0.893;0.63;0.744	B;B;B	0.42653	0.394;0.131;0.196	T	0.39702	-0.9601	9	0.52906	T	0.07	-34.7055	10.0062	0.41959	0.0:0.0:0.1698:0.8302	rs41292632;rs57607073	151;151;157	Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	.;.;.	I	157;69;151	ENSP00000354332:F157I;ENSP00000358318:F69I;ENSP00000358316:F151I	ENSP00000354332:F157I	F	+	1	0	C10orf81	115519566	0.359000	0.24955	0.009000	0.14445	0.001000	0.01503	2.190000	0.42630	1.015000	0.39444	0.533000	0.62120	TTC	T|0.838;A|0.162	0.162	strong		0.502	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889	
HIST1H3J	8356	hgsc.bcm.edu	37	6	27858421	27858421	+	Silent	SNP	A	A	G	rs200973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27858421A>G	ENST00000359303.2	-	1	149	c.150T>C	c.(148-150)cgT>cgC	p.R50R	HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	50					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						GGCGGATCTCACGCAAGGCCA	0.612													G|||	722	0.144169	0.2095	0.1542	5008	,	,		15341	0.0714		0.1461	False		,,,				2504	0.1217				p.R50R		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.T150C						PASS	.	G		883,3523	732.2+/-410.3	90,703,1410	47.0	49.0	48.0		150	3.1	1.0	6	dbSNP_79	48	1387,7213	744.2+/-407.2	114,1159,3027	no	coding-synonymous	HIST1H3J	NM_003535.2		204,1862,4437	GG,GA,AA		16.1279,20.0409,17.4535		50/137	27858421	2270,10736	2203	4300	6503	SO:0001819	synonymous_variant	8356	exon1			GATCTCACGCAAG	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.150T>C	6.37:g.27858421A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	55	0.820895	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000359303.2	37	CCDS4638.1																																																																																			A|0.839;G|0.161	0.161	strong		0.612	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535	
PYCRL	65263	hgsc.bcm.edu	37	8	144689289	144689289	+	Missense_Mutation	SNP	C	C	T	rs11549789	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144689289C>T	ENST00000220966.6	-	3	235	c.206G>A	c.(205-207)cGg>cAg	p.R69Q	PYCRL_ENST00000495276.1_5'UTR|PYCRL_ENST00000377579.3_5'UTR	NM_023078.3	NP_075566.2	Q53H96	P5CR3_HUMAN	pyrroline-5-carboxylate reductase-like	57					L-proline biosynthetic process (GO:0055129)		pyrroline-5-carboxylate reductase activity (GO:0004735)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	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;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		L-Proline(DB00172)	GTGCGTGGTCCGGCAACCCAG	0.642													C|||	211	0.0421326	0.0862	0.0346	5008	,	,		20629	0.0		0.0507	False		,,,				2504	0.0225				p.R69Q		Atlas-SNP	.											.	PYCRL	14	.	0			c.G206A						PASS	.	C	GLN/ARG	367,4023		18,331,1846	37.0	30.0	33.0		206	-1.1	1.0	8	dbSNP_120	33	491,8087		8,475,3806	yes	missense	PYCRL	NM_023078.3	43	26,806,5652	TT,TC,CC		5.7239,8.3599,6.6163	benign	69/287	144689289	858,12110	2195	4289	6484	SO:0001583	missense	65263	exon3			GTGGTCCGGCAAC	AF086378	CCDS6407.2	8q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000104524	ENSG00000104524			25846	protein-coding gene	gene with protein product							Standard	NM_023078		Approved	FLJ13852	uc003yyy.3	Q53H96	OTTHUMG00000157010	ENST00000220966.6:c.206G>A	8.37:g.144689289C>T	ENSP00000220966:p.Arg69Gln	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_023078	B3KMB5|B4DVT6|H0Y6C3|Q8N3N9|Q96HX4|Q9H896	Missense_Mutation	SNP	ENST00000220966.6	37	CCDS6407.2	96	0.04395604395604396	44	0.08943089430894309	14	0.03867403314917127	0	0.0	38	0.05013192612137203	C	1.565	-0.535559	0.04082	0.083599	0.057239	ENSG00000104524	ENST00000220966;ENST00000433751	T;T	0.41758	0.99;0.99	4.67	-1.09	0.09904	NAD(P)-binding domain (1);	0.692488	0.14411	N	0.321292	T	0.00666	0.0022	N	0.10874	0.06	0.80722	D	1	B;B	0.15719	0.01;0.014	B;B	0.12156	0.005;0.007	T	0.19063	-1.0317	10	0.14252	T	0.57	-11.155	9.7567	0.40508	0.0:0.5729:0.0:0.4271	rs11549789;rs57054652;rs11549789	69;57	D3DWK4;Q53H96	.;P5CR3_HUMAN	Q	69;64	ENSP00000220966:R69Q;ENSP00000404493:R64Q	ENSP00000220966:R69Q	R	-	2	0	PYCRL	144760432	0.707000	0.27866	0.998000	0.56505	0.226000	0.24999	0.198000	0.17217	-0.169000	0.10834	-1.587000	0.00848	CGG	C|0.935;T|0.065	0.065	strong		0.642	PYCRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347081.2	NM_023078	
CETN1	1068	hgsc.bcm.edu	37	18	580623	580623	+	Missense_Mutation	SNP	T	T	C	rs61734344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:580623T>C	ENST00000327228.3	+	1	257	c.215T>C	c.(214-216)aTg>aCg	p.M72T		NM_004066.1	NP_004057.1	Q12798	CETN1_HUMAN	centrin, EF-hand protein, 1	72	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to heat (GO:0034605)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|photoreceptor connecting cilium (GO:0032391)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|calcium ion binding (GO:0005509)|nucleic acid binding (GO:0003676)			breast(2)|cervix(1)|endometrium(3)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(2)	25						ATGAAGAAAATGATCTCCGAG	0.552													T|||	900	0.179712	0.2322	0.1239	5008	,	,		17797	0.244		0.1292	False		,,,				2504	0.1339				p.M72T		Atlas-SNP	.											.	CETN1	48	.	0			c.T215C						PASS	.	T	THR/MET	910,3496	350.8+/-311.0	116,678,1409	75.0	60.0	65.0		215	5.2	1.0	18	dbSNP_129	65	1254,7346	251.8+/-278.1	100,1054,3146	yes	missense	CETN1	NM_004066.1	81	216,1732,4555	CC,CT,TT		14.5814,20.6537,16.6385	probably-damaging	72/173	580623	2164,10842	2203	4300	6503	SO:0001583	missense	1068	exon1			AGAAAATGATCTC	U03270	CCDS11820.1	18p11.32	2013-01-10			ENSG00000177143	ENSG00000177143		"""EF-hand domain containing"""	1866	protein-coding gene	gene with protein product		603187		CETN		8175926	Standard	NM_004066		Approved	CEN1	uc002kko.1	Q12798	OTTHUMG00000131471	ENST00000327228.3:c.215T>C	18.37:g.580623T>C	ENSP00000319052:p.Met72Thr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_004066	B2R536	Missense_Mutation	SNP	ENST00000327228.3	37	CCDS11820.1	373	0.1707875457875458	129	0.2621951219512195	45	0.12430939226519337	101	0.17657342657342656	98	0.12928759894459102	T	15.06	2.720817	0.48728	0.206537	0.145814	ENSG00000177143	ENST00000327228	T	0.39056	1.1	5.2	5.2	0.72013	EF-hand-like domain (1);	0.045696	0.85682	D	0.000000	T	0.00039	0.0001	M	0.80982	2.52	0.09310	P	0.99999999872817	D	0.55172	0.97	D	0.85130	0.997	T	0.02431	-1.1160	9	0.87932	D	0	.	13.3624	0.60663	0.0:0.0:0.0:1.0	rs61734344	72	Q12798	CETN1_HUMAN	T	72	ENSP00000319052:M72T	ENSP00000319052:M72T	M	+	2	0	CETN1	570623	1.000000	0.71417	0.995000	0.50966	0.042000	0.13812	7.846000	0.86887	2.324000	0.78689	0.533000	0.62120	ATG	T|0.833;C|0.167	0.167	strong		0.552	CETN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254314.2	NM_004066	
AOAH	313	hgsc.bcm.edu	37	7	36656035	36656035	+	Missense_Mutation	SNP	G	G	C	rs3735386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:36656035G>C	ENST00000258749.5	-	11	1196	c.797C>G	c.(796-798)gCt>gGt	p.A266G	AOAH_ENST00000431169.1_Missense_Mutation_p.A266G|AOAH_ENST00000535891.1_Missense_Mutation_p.A234G	NM_001637.3	NP_001628.1	P28039	AOAH_HUMAN	acyloxyacyl hydrolase (neutrophil)	266			A -> G (in dbSNP:rs3735386).		inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|lipopolysaccharide metabolic process (GO:0008653)|negative regulation of inflammatory response (GO:0050728)	extracellular region (GO:0005576)	acyloxyacyl hydrolase activity (GO:0050528)|catalytic activity (GO:0003824)|lipoprotein lipase activity (GO:0004465)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(21)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	41						GTGAAAATGAGCCCCAGCTGA	0.443													G|||	344	0.0686901	0.0083	0.1297	5008	,	,		19766	0.0308		0.1272	False		,,,				2504	0.0859				p.A266G		Atlas-SNP	.											.	AOAH	79	.	0			c.C797G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	154,4252	105.6+/-144.1	1,152,2050	92.0	81.0	84.0		797,701,797	4.8	1.0	7	dbSNP_107	84	1188,7412	240.0+/-270.9	85,1018,3197	yes	missense,missense,missense	AOAH	NM_001177506.1,NM_001177507.1,NM_001637.3	60,60,60	86,1170,5247	CC,CG,GG		13.814,3.4952,10.3183	probably-damaging,probably-damaging,probably-damaging	266/689,234/544,266/576	36656035	1342,11664	2203	4300	6503	SO:0001583	missense	313	exon11			AAATGAGCCCCAG	BC025698	CCDS5448.1, CCDS55102.1, CCDS75584.1	7p14-p12	2014-03-14			ENSG00000136250	ENSG00000136250	3.1.1.77		548	protein-coding gene	gene with protein product		102593				1883828	Standard	NM_001637		Approved		uc022abu.1	P28039	OTTHUMG00000023566	ENST00000258749.5:c.797C>G	7.37:g.36656035G>C	ENSP00000258749:p.Ala266Gly	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	42	16	0.380952	NM_001637	A4D1Y5|B7Z490|Q53F13	Missense_Mutation	SNP	ENST00000258749.5	37	CCDS5448.1	168	0.07692307692307693	8	0.016260162601626018	38	0.10497237569060773	23	0.04020979020979021	99	0.13060686015831136	G	21.0	4.081487	0.76528	0.034952	0.13814	ENSG00000136250	ENST00000535891;ENST00000258749;ENST00000431169;ENST00000544647	T;T;T	0.16897	2.31;2.31;2.31	4.83	4.83	0.62350	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);	0.000000	0.64402	D	0.000003	T	0.00356	0.0011	.	.	.	0.09310	P	1.0	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.97110	0.994;1.0;1.0	T	0.00628	-1.1637	8	0.72032	D	0.01	.	14.9585	0.71138	0.0:0.0:1.0:0.0	rs3735386;rs52832007;rs56437548;rs3735386	234;266;266	B7Z490;C9J8T1;P28039	.;.;AOAH_HUMAN	G	234;266;266;266	ENSP00000441101:A234G;ENSP00000258749:A266G;ENSP00000405683:A266G	ENSP00000258749:A266G	A	-	2	0	AOAH	36622560	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.280000	0.65603	2.486000	0.83907	0.655000	0.94253	GCT	G|0.910;C|0.090	0.090	strong		0.443	AOAH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219829.2	NM_001637	
DNMBP	23268	hgsc.bcm.edu	37	10	101715899	101715899	+	Silent	SNP	G	G	A	rs2862923	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101715899G>A	ENST00000324109.4	-	4	1423	c.1332C>T	c.(1330-1332)ccC>ccT	p.P444P	DNMBP_ENST00000342239.3_Silent_p.P444P|DNMBP-AS1_ENST00000434409.1_RNA	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	444					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		GAAGAAGGTCGGGGTACTGTT	0.502													A|||	2211	0.441494	0.6558	0.4352	5008	,	,		19500	0.2579		0.4175	False		,,,				2504	0.3701				p.P444P		Atlas-SNP	.											.	DNMBP	173	.	0			c.C1332T						PASS	.			2746,1660	506.6+/-366.4	858,1030,315	86.0	92.0	90.0		1332	0.6	0.0	10	dbSNP_101	90	3661,4939	621.1+/-397.1	757,2147,1396	no	coding-synonymous	DNMBP	NM_015221.2		1615,3177,1711	AA,AG,GG		42.5698,37.6759,49.2619		444/1578	101715899	6407,6599	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon4			AAGGTCGGGGTAC	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.1332C>T	10.37:g.101715899G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	118	115	0.974576	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			G|0.534;A|0.466	0.466	strong		0.502	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
ZNF407	55628	hgsc.bcm.edu	37	18	72347482	72347482	+	Silent	SNP	T	T	C	rs12327359	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72347482T>C	ENST00000299687.5	+	1	4507	c.4507T>C	c.(4507-4509)Tta>Cta	p.L1503L	ZNF407_ENST00000577538.1_Silent_p.L1503L|ZNF407_ENST00000309902.6_Silent_p.L1503L|ZNF407_ENST00000582337.1_Silent_p.L1503L	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1503					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.L1503L(1)		central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAATTTATTTTTACATATTAA	0.473													C|||	2123	0.423922	0.7201	0.3271	5008	,	,		19354	0.1845		0.4175	False		,,,				2504	0.3456				p.L1503L		Atlas-SNP	.											ZNF407,NS,carcinoma,0,1	ZNF407	231	1	1	Substitution - coding silent(1)	prostate(1)	c.T4507C						PASS	.	C	,,	2571,1165		885,801,182	41.0	43.0	43.0		4507,4507,4507	4.8	0.9	18	dbSNP_120	43	3538,4686		754,2030,1328	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	1639,2831,1510	CC,CT,TT		43.0204,31.1831,48.9214	,,	1503/1816,1503/1661,1503/2249	72347482	6109,5851	1868	4112	5980	SO:0001819	synonymous_variant	55628	exon1			TTATTTTTACATA	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.4507T>C	18.37:g.72347482T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			T|0.567;C|0.433	0.433	strong		0.473	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
PIGB	9488	hgsc.bcm.edu	37	15	55632859	55632859	+	Missense_Mutation	SNP	G	G	T	rs678892	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:55632859G>T	ENST00000164305.5	+	8	1187	c.896G>T	c.(895-897)tGg>tTg	p.W299L	CCPG1_ENST00000563294.1_Intron|PIGB_ENST00000539642.1_Missense_Mutation_p.W104L	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	299			W -> L (in dbSNP:rs678892). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		CTGCAGAACTGGGGAACATTT	0.388													T|||	3011	0.601238	0.888	0.4063	5008	,	,		14382	0.7639		0.3479	False		,,,				2504	0.4448				p.W299L		Atlas-SNP	.											.	PIGB	36	.	0			c.G896T						PASS	.	T	LEU/TRP	2869,877		1102,665,106	96.0	96.0	96.0		896	4.8	0.3	15	dbSNP_83	96	2713,5491		457,1799,1846	yes	missense	PIGB	NM_004855.4	61	1559,2464,1952	TT,TG,GG		33.0692,23.4116,46.7113	benign	299/555	55632859	5582,6368	1873	4102	5975	SO:0001583	missense	9488	exon8			AGAACTGGGGAAC	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8959	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 3"", ""dol-P-Man dependent GPI mannosyltransferase"""	604122	"""phosphatidylinositol glycan, class B"""			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.896G>T	15.37:g.55632859G>T	ENSP00000164305:p.Trp299Leu	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_004855	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	37		1249	0.5718864468864469	426	0.8658536585365854	148	0.4088397790055249	426	0.7447552447552448	249	0.32849604221635886	T	10.68	1.417882	0.25552	0.765884	0.330692	ENSG00000069943	ENST00000164305;ENST00000539642	T;T	0.60672	0.17;0.17	5.94	4.82	0.62117	.	0.302551	0.32884	N	0.005524	T	0.00012	0.0000	N	0.00011	-2.99	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43829	-0.9367	9	0.16896	T	0.51	-0.3896	8.2258	0.31568	0.0:0.0687:0.135:0.7963	rs678892;rs17856548;rs52830794;rs58644582;rs678892	299	Q92521	PIGB_HUMAN	L	299;104	ENSP00000164305:W299L;ENSP00000438963:W104L	ENSP00000164305:W299L	W	+	2	0	PIGB	53420151	1.000000	0.71417	0.284000	0.24805	0.979000	0.70002	3.056000	0.49923	0.510000	0.28216	-0.363000	0.07495	TGG	G|0.418;T|0.582	0.582	strong		0.388	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855	
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 GAIIx	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	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	44	17	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	
TRIM3	10612	hgsc.bcm.edu	37	11	6477831	6477831	+	Silent	SNP	C	C	T	rs10606	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6477831C>T	ENST00000525074.1	-	6	1519	c.1125G>A	c.(1123-1125)ccG>ccA	p.P375P	TRIM3_ENST00000529058.1_5'UTR|TRIM3_ENST00000345851.3_Silent_p.P375P|TRIM3_ENST00000359518.3_Silent_p.P375P|TRIM3_ENST00000536344.1_Silent_p.P256P|TRIM3_ENST00000537602.1_Silent_p.P297P	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	375					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P375P(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCACTGGCACCGGAAGGCGCG	0.637													C|||	940	0.1877	0.2973	0.1772	5008	,	,		18660	0.0188		0.1849	False		,,,				2504	0.2239				p.P375P	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											TRIM3,NS,lymphoid_neoplasm,0,1	TRIM3	67	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1125A						PASS	.	C	,	1261,3125		180,901,1112	31.0	31.0	31.0		1125,1125	-10.3	0.0	11	dbSNP_52	31	1738,6816		198,1342,2737	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	378,2243,3849	TT,TC,CC		20.318,28.7506,23.1762	,	375/745,375/745	6477831	2999,9941	2193	4277	6470	SO:0001819	synonymous_variant	10612	exon6			TGGCACCGGAAGG	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1125G>A	11.37:g.6477831C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			C|0.791;T|0.209	0.209	strong		0.637	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
B4GALNT2	124872	hgsc.bcm.edu	37	17	47210469	47210469	+	Missense_Mutation	SNP	G	G	A	rs117575112	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:47210469G>A	ENST00000300404.2	+	1	141	c.82G>A	c.(82-84)Gag>Aag	p.E28K	B4GALNT2_ENST00000504681.1_Intron|B4GALNT2_ENST00000393354.2_Intron	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	28					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			GGGGACGCCCGAGTGTGGGAA	0.662													g|||	280	0.0559105	0.0166	0.0432	5008	,	,		13276	0.0724		0.0716	False		,,,				2504	0.0849				p.E28K	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.G82A						PASS	.		,,LYS/GLU	112,4294		2,108,2093	15.0	16.0	16.0		,,82	2.4	0.0	17	dbSNP_132	16	496,8102		18,460,3821	yes	intron,intron,missense	B4GALNT2	NM_001159387.1,NM_001159388.1,NM_153446.2	,,56	20,568,5914	AA,AG,GG		5.7688,2.542,4.6755	,,benign	,,28/567	47210469	608,12396	2203	4299	6502	SO:0001583	missense	124872	exon1			ACGCCCGAGTGTG	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.82G>A	17.37:g.47210469G>A	ENSP00000300404:p.Glu28Lys	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_153446	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	120	0.054945054945054944	5	0.01016260162601626	20	0.055248618784530384	38	0.06643356643356643	57	0.07519788918205805	-	13.96	2.392587	0.42410	0.02542	0.057688	ENSG00000167080	ENST00000300404	T	0.20069	2.1	2.36	2.36	0.29203	.	.	.	.	.	T	0.00440	0.0014	N	0.08118	0	0.09310	N	1	P	0.37083	0.581	B	0.28139	0.086	T	0.24764	-1.0151	9	0.25106	T	0.35	-0.2559	8.3567	0.32335	0.0:0.0:1.0:0.0	.	28	Q8NHY0	B4GN2_HUMAN	K	28	ENSP00000300404:E28K	ENSP00000300404:E28K	E	+	1	0	B4GALNT2	44565468	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-0.172000	0.09868	1.623000	0.50342	0.550000	0.68814	GAG	G|0.954;A|0.046	0.046	strong		0.662	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446	
TLR10	81793	hgsc.bcm.edu	37	4	38776180	38776180	+	Silent	SNP	C	C	A	rs11096956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38776180C>A	ENST00000308973.4	-	4	1637	c.1032G>T	c.(1030-1032)ccG>ccT	p.P344P	TLR10_ENST00000508334.1_Silent_p.P344P|TLR10_ENST00000506111.1_Silent_p.P344P|TLR10_ENST00000361424.2_Silent_p.P344P|TLR10_ENST00000507953.1_5'Flank	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	344					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						TAGGATAATTCGGGAAAAGCA	0.323													A|||	1495	0.298522	0.2118	0.3184	5008	,	,		21199	0.4325		0.2495	False		,,,				2504	0.3139				p.P344P		Atlas-SNP	.											TLR10,NS,malignant_melanoma,-2,2	TLR10	87	2	0			c.G1032T						PASS	.	A	,,,,	979,3425	724.9+/-409.6	100,779,1323	94.0	96.0	95.0		1032,1032,1032,990,1032	1.0	0.5	4	dbSNP_120	95	1748,6852	729.1+/-406.7	189,1370,2741	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	,,,,	289,2149,4064	AA,AC,CC		20.3256,22.2298,20.9705	,,,,	344/812,344/812,344/812,330/798,344/812	38776180	2727,10277	2202	4300	6502	SO:0001819	synonymous_variant	81793	exon2			ATAATTCGGGAAA	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.1032G>T	4.37:g.38776180C>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	56	0.528302	NM_001017388	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Silent	SNP	ENST00000308973.4	37	CCDS3445.1																																																																																			C|0.732;A|0.268	0.268	strong		0.323	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
LPA	4018	hgsc.bcm.edu	37	6	161007538	161007538	+	Missense_Mutation	SNP	G	G	C	rs7765803	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:161007538G>C	ENST00000316300.5	-	25	4116	c.4072C>G	c.(4072-4074)Ctc>Gtc	p.L1358V	LPA_ENST00000447678.1_Missense_Mutation_p.L1358V			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3866	Kringle 12. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GTTGTGAGGAGAGTTGATTCC	0.517													C|||	2049	0.409145	0.5772	0.268	5008	,	,		19647	0.4107		0.3648	False		,,,				2504	0.3262				p.L1358V		Atlas-SNP	.											.	LPA	237	.	0			c.C4072G						PASS	.	C	VAL/LEU	2242,1964		617,1008,478	137.0	137.0	137.0		4072	-2.6	0.0	6	dbSNP_116	137	2935,5587		530,1875,1856	yes	missense	LPA	NM_005577.2	32	1147,2883,2334	CC,CG,GG		34.4403,46.6952,40.6741	benign	1358/2041	161007538	5177,7551	2103	4261	6364	SO:0001583	missense	4018	exon26			TGAGGAGAGTTGA	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4072C>G	6.37:g.161007538G>C	ENSP00000321334:p.Leu1358Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	74	28	0.378378	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	931	0.42628205128205127	303	0.6158536585365854	99	0.27348066298342544	240	0.4195804195804196	289	0.3812664907651715	c	0.004	-2.377643	0.00207	0.533048	0.344403	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.61980	0.06;0.06	2.04	-2.6	0.06190	Kringle (1);Kringle-like fold (1);	.	.	.	.	T	0.04092	0.0114	N	0.00138	-2.015	0.80722	P	0.0	B	0.26483	0.15	B	0.17722	0.019	T	0.17684	-1.0361	8	0.02654	T	1	.	6.4809	0.22063	0.1895:0.2458:0.5647:0.0	rs7765803;rs7765803	3866	P08519	APOA_HUMAN	V	1358	ENSP00000321334:L1358V;ENSP00000395608:L1358V	ENSP00000321334:L1358V	L	-	1	0	LPA	160927528	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.546000	0.02188	-0.794000	0.04468	-0.980000	0.02579	CTC	G|0.569;C|0.431	0.431	strong		0.517	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
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 GAIIx	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		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	117	58	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	
GCNT4	51301	hgsc.bcm.edu	37	5	74324548	74324548	+	Missense_Mutation	SNP	G	G	A	rs3811987	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:74324548G>A	ENST00000322348.4	-	1	2176	c.1315C>T	c.(1315-1317)Ccc>Tcc	p.P439S		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	439			P -> S (in dbSNP:rs3811987).		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.P439S(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		TTTTCTGAGGGCAAAGTGATC	0.383													N|||	2187	0.436701	0.7504	0.3732	5008	,	,		19802	0.2897		0.3002	False		,,,				2504	0.3497				p.P439S		Atlas-SNP	.											GCNT4,NS,carcinoma,0,1	GCNT4	46	1	1	Substitution - Missense(1)	stomach(1)	c.C1315T						PASS	.	A	SER/PRO	2950,1456		999,952,252	101.0	105.0	103.0		1315	4.8	0.9	5	dbSNP_107	103	2336,6264		329,1678,2293	yes	missense	GCNT4	NM_016591.2	74	1328,2630,2545	AA,AG,GG		27.1628,33.0458,40.6428	benign	439/454	74324548	5286,7720	2203	4300	6503	SO:0001583	missense	51301	exon1			CTGAGGGCAAAGT	AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	17973	protein-coding gene	gene with protein product	"""core 2 beta-1,6-N-acetylglucosaminyltransferase 3"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"""		"""glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.1315C>T	5.37:g.74324548G>A	ENSP00000317027:p.Pro439Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	108	43	0.398148	NM_016591		Missense_Mutation	SNP	ENST00000322348.4	37	CCDS4026.1	884	0.40476190476190477	365	0.741869918699187	124	0.3425414364640884	163	0.28496503496503495	232	0.30606860158311344	.	1.278	-0.611098	0.03690	0.669542	0.271628	ENSG00000176928	ENST00000322348	T	0.06687	3.27	5.96	4.79	0.61399	.	0.159465	0.42420	N	0.000703	T	0.00012	0.0000	N	0.01576	-0.805	0.42947	P	0.005631000000000053	B	0.02656	0.0	B	0.01281	0.0	T	0.18398	-1.0338	9	0.07813	T	0.8	-6.8075	10.6701	0.45753	0.8705:0.0:0.1295:0.0	rs3811987;rs52807678;rs57800056;rs3811987	439	Q9P109	GCNT4_HUMAN	S	439	ENSP00000317027:P439S	ENSP00000317027:P439S	P	-	1	0	GCNT4	74360304	1.000000	0.71417	0.944000	0.38274	0.851000	0.48451	3.881000	0.56152	0.497000	0.27926	-0.269000	0.10298	CCC	G|0.584;A|0.416	0.416	strong		0.383	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591	
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 GAIIx	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	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	135	35	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	
NPW	283869	hgsc.bcm.edu	37	16	2070568	2070568	+	Missense_Mutation	SNP	A	A	C	rs2286472	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:2070568A>C	ENST00000566435.1	+	2	803	c.290A>C	c.(289-291)gAc>gCc	p.D97A	NPW_ENST00000329610.4_Missense_Mutation_p.D149A			Q8N729	NPW_HUMAN	neuropeptide W	149					feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				kidney(1)	1						CCAGCGGTGGACCCCGCAGCA	0.726													C|||	1810	0.361422	0.6218	0.2579	5008	,	,		11024	0.3313		0.329	False		,,,				2504	0.1472				p.D149A		Atlas-SNP	.											NPW,NS,carcinoma,0,2	NPW	4	2	0			c.A446C						scavenged	.	C	ALA/ASP	2209,1627		693,823,402	17.0	23.0	21.0		446	-0.2	0.0	16	dbSNP_100	21	2599,5625		402,1795,1915	yes	missense	NPW	NM_001099456.2	126	1095,2618,2317	CC,CA,AA		31.6026,42.414,39.8673	benign	149/166	2070568	4808,7252	1918	4112	6030	SO:0001583	missense	283869	exon2			CGGTGGACCCCGC	AB084276	CCDS42102.1	16p13.3	2013-02-26			ENSG00000183971	ENSG00000183971		"""Endogenous ligands"""	30509	protein-coding gene	gene with protein product	"""prepro-neuropeptide W"""	607997				12118011, 12401809	Standard	NM_001099456		Approved	PPL8	uc002coh.4	Q8N729	OTTHUMG00000176914	ENST00000566435.1:c.290A>C	16.37:g.2070568A>C	ENSP00000456974:p.Asp97Ala	Somatic	45	1	0.0222222		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_001099456		Missense_Mutation	SNP	ENST00000566435.1	37		820	0.37545787545787546	303	0.6158536585365854	105	0.2900552486187845	173	0.30244755244755245	239	0.3153034300791557	N	0.008	-1.886957	0.00527	0.57586	0.316026	ENSG00000183971	ENST00000329610	T	0.54071	0.59	2.21	-0.235	0.13071	.	0.833798	0.10009	N	0.727475	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	0.45338	-0.9268	9	0.09590	T	0.72	.	2.1559	0.03811	0.2384:0.3075:0.0:0.4541	rs2286472;rs56777272;rs2286472	149	Q8N729	NPW_HUMAN	A	149	ENSP00000330070:D149A	ENSP00000330070:D149A	D	+	2	0	NPW	2010569	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	-0.827000	0.04424	-0.424000	0.07382	-2.803000	0.00113	GAC	A|0.624;C|0.376	0.376	strong		0.726	NPW-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000434312.1	NM_001099456	
ZNF860	344787	hgsc.bcm.edu	37	3	32031135	32031135	+	Silent	SNP	A	A	G	rs6419811	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:32031135A>G	ENST00000360311.4	+	2	1113	c.564A>G	c.(562-564)tcA>tcG	p.S188S		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	188					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(3)|lung(4)|ovary(1)	8						ATGCTTCCTCAGTTCTAACGT	0.358													G|||	2356	0.470447	0.7988	0.3602	5008	,	,		20726	0.4524		0.1968	False		,,,				2504	0.4049				p.S188S		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	0			c.A564G						PASS	.	G		938,446		325,288,79	58.0	44.0	48.0		564	0.3	0.0	3	dbSNP_116	48	608,2574		58,492,1041	no	coding-synonymous	ZNF860	NM_001137674.2		383,780,1120	GG,GA,AA		19.1075,32.2254,33.859		188/633	32031135	1546,3020	692	1591	2283	SO:0001819	synonymous_variant	344787	exon2			TTCCTCAGTTCTA	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.564A>G	3.37:g.32031135A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	NM_001137674	B4DFA4	Silent	SNP	ENST00000360311.4	37	CCDS46784.1																																																																																			A|0.567;G|0.433	0.433	strong		0.358	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
MUC2	4583	hgsc.bcm.edu	37	11	1101078	1101078	+	Missense_Mutation	SNP	A	A	G	rs11245954	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1101078A>G	ENST00000441003.2	+	41	7504	c.7477A>G	c.(7477-7479)Agc>Ggc	p.S2493G		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4855					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)	CAAGAGGTGCAGCCAGAAGCC	0.587													A|||	426	0.0850639	0.1573	0.0403	5008	,	,		20234	0.0456		0.0775	False		,,,				2504	0.0675				p.S2489G		Atlas-SNP	.											.	MUC2	614	.	0			c.A7465G						PASS	.	A	GLY/SER	506,3726		27,452,1637	81.0	90.0	87.0		7462	-2.3	0.0	11	dbSNP_120	87	594,7860		18,558,3651	yes	missense	MUC2	NM_002457.2	56	45,1010,5288	GG,GA,AA		7.0263,11.9565,8.671	benign	2488/2813	1101078	1100,11586	2116	4227	6343	SO:0001583	missense	4583	exon42			AGGTGCAGCCAGA	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.7477A>G	11.37:g.1101078A>G	ENSP00000415183:p.Ser2493Gly	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	93	60	0.645161	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		164	0.07509157509157509	73	0.1483739837398374	15	0.04143646408839779	19	0.033216783216783216	57	0.07519788918205805	A	7.456	0.643762	0.14451	0.119565	0.070263	ENSG00000198788	ENST00000441003	T	0.42900	0.96	2.95	-2.26	0.06867	.	.	.	.	.	T	0.00144	0.0004	L	0.40543	1.245	0.80722	P	0.0	B	0.28470	0.213	B	0.21151	0.033	T	0.18840	-1.0324	8	0.20519	T	0.43	.	8.0542	0.30596	0.3112:0.5846:0.1042:0.0	rs11245954;rs11245954	2493	E7EUV1	.	G	2493	ENSP00000415183:S2493G	ENSP00000415183:S2493G	S	+	1	0	MUC2	1091078	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	-1.367000	0.02583	-0.205000	0.10219	0.392000	0.25879	AGC	A|0.924;G|0.076	0.076	strong		0.587	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ABCA13	154664	hgsc.bcm.edu	37	7	48315796	48315796	+	Missense_Mutation	SNP	C	C	A	rs1880736	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48315796C>A	ENST00000435803.1	+	17	6557	c.6533C>A	c.(6532-6534)gCa>gAa	p.A2178E		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2178			A -> E (in dbSNP:rs1880736).		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						ATATCTAGAGCAGGCAATTTT	0.348													A|||	4071	0.812899	0.8457	0.7954	5008	,	,		17238	0.9881		0.6083	False		,,,				2504	0.8108				p.A2178E		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C6533A						PASS	.	A	GLU/ALA	2936,668		1203,530,69	30.0	28.0	29.0		6533	5.0	0.0	7	dbSNP_92	29	5239,2885		1684,1871,507	yes	missense	ABCA13	NM_152701.3	107	2887,2401,576	AA,AC,CC		35.5121,18.535,30.295	benign	2178/5059	48315796	8175,3553	1802	4062	5864	SO:0001583	missense	154664	exon17			CTAGAGCAGGCAA	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.6533C>A	7.37:g.48315796C>A	ENSP00000411096:p.Ala2178Glu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	1709	0.7825091575091575	409	0.8313008130081301	282	0.7790055248618785	567	0.9912587412587412	451	0.5949868073878628	A	0.007	-1.936584	0.00484	0.81465	0.644879	ENSG00000179869	ENST00000435803	T	0.04454	3.62	4.99	4.99	0.66335	.	0.245798	0.28476	N	0.015208	T	0.00012	0.0000	N	0.00182	-1.905	0.50171	P	1.48000000000037E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.34725	-0.9817	8	.	.	.	.	10.3522	0.43943	0.8349:0.1651:0.0:0.0	rs1880736;rs17547907;rs61164907;rs1880736	2178	Q86UQ4	ABCAD_HUMAN	E	2178	ENSP00000411096:A2178E	.	A	+	2	0	ABCA13	48286342	0.918000	0.31147	0.002000	0.10522	0.083000	0.17756	1.125000	0.31332	0.852000	0.35287	-0.512000	0.04463	GCA	C|0.216;A|0.784	0.784	strong		0.348	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
FRAS1	80144	hgsc.bcm.edu	37	4	78987157	78987157	+	Missense_Mutation	SNP	A	A	G	rs4859905	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:78987157A>G	ENST00000325942.6	+	2	535	c.95A>G	c.(94-96)gAt>gGt	p.D32G	FRAS1_ENST00000264895.6_Missense_Mutation_p.D32G|FRAS1_ENST00000264899.6_Missense_Mutation_p.D32G	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	32	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.		D -> G (in dbSNP:rs4859905).		cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GTCTATCAGGATTCCTTGTTG	0.408													G|||	2762	0.551518	0.7519	0.4654	5008	,	,		18692	0.5407		0.4195	False		,,,				2504	0.4888				p.D32G		Atlas-SNP	.											.	FRAS1	779	.	0			c.A95G						PASS	.	G	GLY/ASP,GLY/ASP	2527,1199		884,759,220	232.0	215.0	220.0		95,95	5.9	1.0	4	dbSNP_111	220	3285,4913		664,1957,1478	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	94,94	1548,2716,1698	GG,GA,AA		40.0707,32.1793,48.742	benign,benign	32/1977,32/4013	78987157	5812,6112	1863	4099	5962	SO:0001583	missense	80144	exon2			ATCAGGATTCCTT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.95A>G	4.37:g.78987157A>G	ENSP00000326330:p.Asp32Gly	Somatic	326	1	0.00306748		WXS	Illumina HiSeq	Phase_I	307	148	0.482085	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	1127	0.5160256410256411	352	0.7154471544715447	173	0.47790055248618785	301	0.5262237762237763	301	0.3970976253298153	G	5.385	0.256325	0.10185	0.678207	0.400707	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000264899;ENST00000380674	T;T;T	0.56611	0.45;0.45;0.45	5.9	5.9	0.94986	.	0.162317	0.41194	N	0.000924	T	0.00012	0.0000	.	.	.	0.45261	P	0.0017329999999999846	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35201	-0.9798	8	0.02654	T	1	.	12.5489	0.56216	0.0777:0.0:0.9222:0.0	rs4859905;rs58160615;rs4859905	32;32	E9PHH6;A2RRR8	.;.	G	32	ENSP00000326330:D32G;ENSP00000264895:D32G;ENSP00000264899:D32G	ENSP00000264895:D32G	D	+	2	0	FRAS1	79206181	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	2.691000	0.47010	1.517000	0.48917	-0.213000	0.12676	GAT	A|0.473;G|0.527	0.527	strong		0.408	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
WDR93	56964	hgsc.bcm.edu	37	15	90260145	90260145	+	Missense_Mutation	SNP	T	T	A	rs7163367	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90260145T>A	ENST00000268130.7	+	7	861	c.760T>A	c.(760-762)Tcc>Acc	p.S254T	RNU6-132P_ENST00000383863.1_RNA|WDR93_ENST00000560294.1_Missense_Mutation_p.S254T	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	254			S -> T (in dbSNP:rs7163367).		electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TTCTCAGAACTCCCTTGGTCC	0.338													A|||	1879	0.3752	0.4766	0.3112	5008	,	,		15609	0.2044		0.3956	False		,,,				2504	0.4387				p.S254T		Atlas-SNP	.											WDR93,NS,carcinoma,-1,2	WDR93	63	2	0			c.T760A						PASS	.	A	THR/SER	2074,2326	603.5+/-390.1	483,1108,609	100.0	100.0	100.0		760	-2.3	0.0	15	dbSNP_116	100	3788,4810	613.1+/-396.1	816,2156,1327	yes	missense	WDR93	NM_020212.1	58	1299,3264,1936	AA,AT,TT		44.0568,47.1364,45.0992	benign	254/687	90260145	5862,7136	2200	4299	6499	SO:0001583	missense	56964	exon7			CAGAACTCCCTTG		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.760T>A	15.37:g.90260145T>A	ENSP00000268130:p.Ser254Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	757	0.3466117216117216	201	0.40853658536585363	125	0.3453038674033149	132	0.23076923076923078	299	0.3944591029023747	A	0.011	-1.739211	0.00681	0.471364	0.440568	ENSG00000140527	ENST00000268130	T	0.21361	2.01	3.21	-2.28	0.06826	WD40 repeat-like-containing domain (1);	0.687039	0.13286	N	0.399397	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32798	-0.9893	9	0.02654	T	1	-0.901	0.9508	0.01376	0.2657:0.319:0.1032:0.3121	rs7163367;rs52812393;rs7163367	254;254	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	T	254	ENSP00000268130:S254T	ENSP00000268130:S254T	S	+	1	0	WDR93	88061149	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.435000	0.06931	-0.913000	0.03832	-0.336000	0.08194	TCC	A|0.415;N|0.000	0.415	strong		0.338	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057393	46057393	+	Missense_Mutation	SNP	T	T	A	rs2838602	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46057393T>A	ENST00000380095.1	+	1	121	c.59T>A	c.(58-60)gTc>gAc	p.V20D	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	20			V -> D (in dbSNP:rs2838602).			keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						TGGCGGGTAGTCGACTGCCCA	0.672													A|||	3915	0.781749	0.9183	0.745	5008	,	,		16189	0.6468		0.7694	False		,,,				2504	0.7751				p.V20D		Atlas-SNP	.											KRTAP10-10,NS,carcinoma,-1,1	KRTAP10-10	37	1	0			c.T59A						PASS	.	A	,ASP/VAL	3896,510		1748,400,55	87.0	91.0	89.0		,59	3.5	1.0	21	dbSNP_100	89	6081,2519		2262,1557,481	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,152	4010,1957,536	AA,AT,TT		29.2907,11.5751,23.2893	,benign	,20/252	46057393	9977,3029	2203	4300	6503	SO:0001583	missense	353333	exon1			GGGTAGTCGACTG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.59T>A	21.37:g.46057393T>A	ENSP00000369438:p.Val20Asp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	1670	0.7646520146520146	454	0.9227642276422764	278	0.7679558011049724	354	0.6188811188811189	584	0.7704485488126649	a	0.006	-2.111369	0.00353	0.884249	0.707093	ENSG00000221859	ENST00000380095	T	0.02737	4.18	3.52	3.52	0.40303	.	.	.	.	.	T	0.00012	0.0000	N	0.00084	-2.21	0.34049	P	0.34411400000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.17048	-1.0382	8	0.02654	T	1	.	3.1103	0.06356	0.6704:0.0:0.1185:0.2111	rs2838602;rs58907408;rs2838602	20	P60014	KR10A_HUMAN	D	20	ENSP00000369438:V20D	ENSP00000369438:V20D	V	+	2	0	KRTAP10-10	44881821	0.166000	0.22962	0.998000	0.56505	0.104000	0.19210	0.966000	0.29331	0.357000	0.24183	-0.522000	0.04353	GTC	T|0.231;A|0.769	0.769	strong		0.672	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
CCDC22	28952	hgsc.bcm.edu	37	X	49103224	49103224	+	Silent	SNP	G	G	A	rs2294020	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49103224G>A	ENST00000376227.3	+	7	917	c.747G>A	c.(745-747)caG>caA	p.Q249Q		NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	249										NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						AGCGGCTGCAGAAGCAACTGA	0.672													G|||	1760	0.466225	0.4425	0.389	3775	,	,		11394	0.4851		0.2028	False		,,,				2504	0.2168				p.Q249Q		Atlas-SNP	.											.	CCDC22	69	.	0			c.G747A						PASS	.			2100,1688		528,744,300,351,242	9.0	9.0	9.0		747	0.8	0.7	X	dbSNP_100	9	1815,4840		200,917,498,1300,1323	no	coding-synonymous	CCDC22	NM_014008.3		728,1661,798,1651,1565	AA,AG,A,GG,G		27.2727,44.5618,37.4892		249/628	49103224	3915,6528	2165	4238	6403	SO:0001819	synonymous_variant	28952	exon7			GCTGCAGAAGCAA	BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"""chromosome X open reading frame 37"""	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.747G>A	X.37:g.49103224G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	35	8	0.228571	NM_014008	A8K7G1	Silent	SNP	ENST00000376227.3	37	CCDS14322.1																																																																																			0|0.005;A|0.488	0.488	strong		0.672	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008	
RNFT1	51136	hgsc.bcm.edu	37	17	58031412	58031412	+	Silent	SNP	A	A	G	rs11368	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:58031412A>G	ENST00000305783.8	-	8	1222	c.1167T>C	c.(1165-1167)atT>atC	p.I389I	RP11-178C3.1_ENST00000591035.1_Intron|RNFT1_ENST00000442346.2_3'UTR	NM_016125.3	NP_057209.3	Q5M7Z0	RNFT1_HUMAN	ring finger protein, transmembrane 1	389						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(5;1.58e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;7.95e-12)|all cancers(12;1.34e-10)			TTACCTGACAAATGAGAAGAA	0.328													G|||	2901	0.579273	0.8797	0.5	5008	,	,		19138	0.5764		0.4195	False		,,,				2504	0.3967				p.I389I		Atlas-SNP	.											.	RNFT1	30	.	0			c.T1167C						PASS	.	G		2953,719		1192,569,75	51.0	50.0	50.0		1167	0.9	1.0	17	dbSNP_52	50	3587,4589		816,1955,1317	no	coding-synonymous	RNFT1	NM_016125.3		2008,2524,1392	GG,GA,AA		43.8723,19.5806,44.8008		389/436	58031412	6540,5308	1836	4088	5924	SO:0001819	synonymous_variant	51136	exon8			CTGACAAATGAGA	BC006971	CCDS11622.2	17q23.2	2013-01-09			ENSG00000189050	ENSG00000189050		"""RING-type (C3HC4) zinc fingers"""	30206	protein-coding gene	gene with protein product		615172				12477932	Standard	NM_016125		Approved	PTD016	uc002iya.3	Q5M7Z0	OTTHUMG00000148658	ENST00000305783.8:c.1167T>C	17.37:g.58031412A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	NM_016125	Q8N7D0|Q96IZ9|Q9Y686	Silent	SNP	ENST00000305783.8	37	CCDS11622.2																																																																																			A|0.499;G|0.501	0.501	strong		0.328	RNFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308958.1	NM_016125	
KIF16B	55614	hgsc.bcm.edu	37	20	16410559	16410559	+	Silent	SNP	A	A	T	rs34550969	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:16410559A>T	ENST00000354981.2	-	13	1528	c.1371T>A	c.(1369-1371)atT>atA	p.I457I	KIF16B_ENST00000355755.3_Silent_p.I457I|KIF16B_ENST00000408042.1_Silent_p.I457I|KIF16B_ENST00000378003.2_5'UTR	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	457					ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CATCGATGCCAATCAAATGAG	0.358													A|||	391	0.0780751	0.0076	0.1196	5008	,	,		17147	0.0179		0.173	False		,,,				2504	0.1084				p.I457I		Atlas-SNP	.											.	KIF16B	305	.	0			c.T1371A						PASS	.	A	,,	138,4268	96.7+/-135.4	1,136,2066	94.0	86.0	89.0		1371,1371,1371	4.0	1.0	20	dbSNP_126	89	1400,7200	270.2+/-288.9	113,1174,3013	no	coding-synonymous,coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	,,	114,1310,5079	TT,TA,AA		16.2791,3.1321,11.8253	,,	457/1267,457/1393,457/1318	16410559	1538,11468	2203	4300	6503	SO:0001819	synonymous_variant	55614	exon13			GATGCCAATCAAA	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.1371T>A	20.37:g.16410559A>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	32	21	0.65625	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			A|0.898;T|0.102	0.102	strong		0.358	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
WDR81	124997	hgsc.bcm.edu	37	17	1630992	1630992	+	Silent	SNP	G	G	A	rs9912287|rs587780502	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1630992G>A	ENST00000409644.1	+	1	2739	c.2739G>A	c.(2737-2739)ctG>ctA	p.L913L	WDR81_ENST00000419248.1_Intron|WDR81_ENST00000545662.1_5'Flank|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000437219.2_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	913					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GCGCGGTGCTGAAGGACATCA	0.617													G|||	1232	0.246006	0.239	0.2061	5008	,	,		19324	0.1845		0.1948	False		,,,				2504	0.3998				p.L913L		Atlas-SNP	.											.	WDR81	180	.	0			c.G2739A						PASS	.	G	,,,	318,1066		38,242,412	56.0	54.0	54.0		,2739,,	2.7	0.8	17	dbSNP_119	54	689,2493		64,561,966	no	intron,coding-synonymous,intron,intron	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	102,803,1378	AA,AG,GG		21.653,22.9769,22.0543	,,,	,913/1942,,	1630992	1007,3559	692	1591	2283	SO:0001819	synonymous_variant	124997	exon1			GGTGCTGAAGGAC	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.2739G>A	17.37:g.1630992G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	48	0.533333	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			G|0.790;A|0.208	0.208	strong		0.617	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
SLC39A14	23516	hgsc.bcm.edu	37	8	22262418	22262418	+	Silent	SNP	A	A	G	rs2293144	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:22262418A>G	ENST00000381237.1	+	2	314	c.195A>G	c.(193-195)ctA>ctG	p.L65L	SLC39A14_ENST00000240095.6_Silent_p.L65L|SLC39A14_ENST00000289952.5_Silent_p.L65L|SLC39A14_ENST00000359741.5_Silent_p.L65L	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	65					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		TGAAGGCCCTACTCAACCACC	0.607													G|||	3379	0.67472	0.8298	0.5576	5008	,	,		19822	0.7798		0.505	False		,,,				2504	0.6145				p.L65L		Atlas-SNP	.											.	SLC39A14	59	.	0			c.A195G						PASS	.	G	,,,	3387,1019	377.3+/-322.4	1302,783,118	68.0	64.0	65.0		195,195,195,195	0.6	0.9	8	dbSNP_100	65	4079,4521	593.1+/-393.1	961,2157,1182	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A14	NM_001128431.2,NM_001135153.1,NM_001135154.1,NM_015359.4	,,,	2263,2940,1300	GG,GA,AA		47.4302,23.1276,42.5957	,,,	65/493,65/493,65/482,65/493	22262418	7466,5540	2203	4300	6503	SO:0001819	synonymous_variant	23516	exon2			GGCCCTACTCAAC	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.195A>G	8.37:g.22262418A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Silent	SNP	ENST00000381237.1	37	CCDS47823.1																																																																																			A|0.386;G|0.614	0.614	strong		0.607	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
DDR1	780	hgsc.bcm.edu	37	6	30862423	30862423	+	Silent	SNP	C	C	T	rs1264319	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30862423C>T	ENST00000324771.8	+	13	2036	c.1488C>T	c.(1486-1488)tcC>tcT	p.S496S	DDR1_ENST00000376570.4_Silent_p.S496S|DDR1_ENST00000508312.1_Silent_p.S514S|DDR1_ENST00000361741.4_Missense_Mutation_p.P200L|DDR1_ENST00000376569.3_Silent_p.S496S|DDR1_ENST00000454612.2_Silent_p.S496S|DDR1_ENST00000418800.2_Silent_p.S496S|DDR1_ENST00000376568.3_Silent_p.S496S|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000513240.1_Silent_p.S496S|DDR1_ENST00000376567.2_Silent_p.S496S|DDR1_ENST00000452441.1_Silent_p.S496S|DDR1_ENST00000376575.3_Silent_p.S496S			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	496	Gly/Pro-rich.		S -> A (in a lung squamous cell carcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	CGCCCCACTCCGCTCCCTGTG	0.582													C|||	642	0.128195	0.177	0.0951	5008	,	,		19738	0.0585		0.162	False		,,,				2504	0.1227				p.P469L		Atlas-SNP	.											.	DDR1	213	.	0			c.C1406T						PASS	.	C	,LEU/PRO,,,,	858,3548	335.7+/-304.0	90,678,1435	75.0	75.0	75.0		1488,1406,1542,1488,1488,1488	2.7	1.0	6	dbSNP_87	75	1699,6901	311.0+/-310.2	162,1375,2763	yes	coding-synonymous,missense,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,98,,,,	252,2053,4198	TT,TC,CC		19.7558,19.4734,19.6602	,,,,,	496/509,469/768,514/895,496/877,496/914,496/920	30862423	2557,10449	2203	4300	6503	SO:0001819	synonymous_variant	780	exon10			CCACTCCGCTCCC	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1488C>T	6.37:g.30862423C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	34	0.772727	NM_001202522	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	341|341	0.15613553113553114|0.15613553113553114	127|127	0.258130081300813|0.258130081300813	44|44	0.12154696132596685|0.12154696132596685	39|39	0.06818181818181818|0.06818181818181818	131|131	0.17282321899736147|0.17282321899736147	C|C	7.986|7.986	0.752226|0.752226	0.15778|0.15778	0.194734|0.194734	0.197558|0.197558	ENSG00000204580|ENSG00000204580	ENST00000417521;ENST00000361741;ENST00000451954|ENST00000514434	T;T|.	0.79454|.	-1.19;-1.27|.	5.24|5.24	2.73|2.73	0.32206|0.32206	.|.	.|.	.|.	.|.	.|.	T|T	0.26268|0.26268	0.0641|0.0641	.|.	.|.	.|.	0.26362|0.26362	P|P	0.9770315|0.9770315	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.08207|0.08207	-1.0733|-1.0733	7|3	0.20519|.	T|.	0.43|.	.|.	7.4808|7.4808	0.27404|0.27404	0.0:0.1817:0.0:0.8183|0.0:0.1817:0.0:0.8183	rs1264319;rs1264319|rs1264319;rs1264319	265|.	A2ABM8|.	.|.	L|C	265;200;152|25	ENSP00000398682:P265L;ENSP00000354844:P200L|.	ENSP00000354844:P200L|.	P|R	+|+	2|1	0|0	DDR1|DDR1	30970402|30970402	0.976000|0.976000	0.34144|0.34144	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	0.405000|0.405000	0.21015|0.21015	0.837000|0.837000	0.34925|0.34925	-0.455000|-0.455000	0.05494|0.05494	CCG|CGC	C|0.820;T|0.180	0.180	strong		0.582	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340841	55340841	+	Silent	SNP	G	G	C	rs150471749	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55340841G>C	ENST00000391728.4	+	7	1059	c.1026G>C	c.(1024-1026)ctG>ctC	p.L342L	KIR3DL1_ENST00000358178.4_Silent_p.L247L|KIR3DL1_ENST00000326542.7_Silent_p.L325L|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000538269.1_Silent_p.L342L|KIR3DL1_ENST00000541392.1_Silent_p.L325L	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	342					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TGCACATTCTGATTGGGACCT	0.453													g|||	526	0.105032	0.0938	0.1427	5008	,	,		16179	0.001		0.2475	False		,,,				2504	0.0542				p.L342L		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.G1026C						PASS	.	G		318,4030		79,160,1935	273.0	206.0	229.0		1026	0.7	0.1	19	dbSNP_134	229	1261,7047		387,487,3280	no	coding-synonymous	KIR3DL1	NM_013289.2		466,647,5215	CC,CG,GG		15.1781,7.3137,12.4763		342/445	55340841	1579,11077	2174	4154	6328	SO:0001819	synonymous_variant	3811	exon7			CATTCTGATTGGG	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1026G>C	19.37:g.55340841G>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_013289	O43473|Q14946|Q16541	Silent	SNP	ENST00000391728.4	37	CCDS42621.1																																																																																			G|0.905;C|0.096	0.096	strong		0.453	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
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 GAIIx	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		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	53	35	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		
TMC4	147798	hgsc.bcm.edu	37	19	54664209	54664209	+	Missense_Mutation	SNP	G	G	C	rs36657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54664209G>C	ENST00000376591.4	-	14	2196	c.2065C>G	c.(2065-2067)Cag>Gag	p.Q689E	TMC4_ENST00000416963.1_Missense_Mutation_p.Q271E|TMC4_ENST00000301187.4_Missense_Mutation_p.Q683E|LENG1_ENST00000222224.3_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	689			Q -> E (in dbSNP:rs36657).		ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CTCACCGTCTGTCTCtgacgt	0.592													C|||	2565	0.512181	0.6082	0.4597	5008	,	,		18746	0.255		0.5268	False		,,,				2504	0.6697				p.Q689E		Atlas-SNP	.											TMC4_ENST00000416963,NS,carcinoma,0,2	TMC4	89	2	0			c.C2065G						scavenged	.	C	GLU/GLN,GLU/GLN	2482,1924	547.6+/-377.3	657,1168,378	58.0	61.0	60.0		2065,2047	-1.9	0.4	19	dbSNP_76	60	4469,4131	562.7+/-388.0	1151,2167,982	yes	missense,missense	TMC4	NM_001145303.1,NM_144686.2	29,29	1808,3335,1360	CC,CG,GG		48.0349,43.6677,46.5554	benign,benign	689/713,683/707	54664209	6951,6055	2203	4300	6503	SO:0001583	missense	147798	exon14			CCGTCTGTCTCTG	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.2065C>G	19.37:g.54664209G>C	ENSP00000365776:p.Gln689Glu	Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	37	CCDS46174.1	1008	0.46153846153846156	296	0.6016260162601627	172	0.47513812154696133	140	0.24475524475524477	400	0.5277044854881267	C	1.992	-0.431517	0.04669	0.563323	0.519651	ENSG00000167608	ENST00000301187;ENST00000416963;ENST00000376591	T;T;T	0.71817	-0.6;-0.6;-0.6	4.52	-1.94	0.07571	.	0.460533	0.25264	N	0.031925	T	0.00012	0.0000	N	0.05259	-0.085	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.002;0.001	T	0.37267	-0.9713	9	0.02654	T	1	-10.0165	7.8637	0.29524	0.0:0.2708:0.5565:0.1727	rs36657;rs605399;rs1129911;rs3188228;rs11538073;rs16985414;rs61129573;rs36657	689;683;271	Q7Z404;Q7Z404-1;Q7Z404-3	TMC4_HUMAN;.;.	E	683;271;689	ENSP00000301187:Q683E;ENSP00000405023:Q271E;ENSP00000365776:Q689E	ENSP00000301187:Q683E	Q	-	1	0	TMC4	59356021	0.008000	0.16893	0.364000	0.25888	0.960000	0.62799	-0.626000	0.05527	-0.205000	0.10219	-0.125000	0.14975	CAG	G|0.492;C|0.508	0.508	strong		0.592	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
PNPLA3	80339	hgsc.bcm.edu	37	22	44342116	44342116	+	Missense_Mutation	SNP	A	A	G	rs2294918	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44342116A>G	ENST00000216180.3	+	9	1473	c.1300A>G	c.(1300-1302)Aag>Gag	p.K434E	PNPLA3_ENST00000423180.2_Missense_Mutation_p.K430E	NM_025225.2	NP_079501.2	Q9NST1	PLPL3_HUMAN	patatin-like phospholipase domain containing 3	434			K -> E (in dbSNP:rs2294918). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		acylglycerol acyl-chain remodeling (GO:0036155)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	diolein transacylation activity (GO:0051265)|mono-olein transacylation activity (GO:0051264)|phospholipase A2 activity (GO:0004623)|triglyceride lipase activity (GO:0004806)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|prostate(1)|skin(1)|stomach(2)	19		Ovarian(80;0.024)|all_neural(38;0.0416)				CTGCTCCCCCAAGGGCTGTCC	0.597											OREG0026623	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3945	0.78774	0.8964	0.7882	5008	,	,		19066	0.8185		0.6292	False		,,,				2504	0.772				p.K434E		Atlas-SNP	.											.	PNPLA3	53	.	0			c.A1300G						PASS	.	G	GLU/LYS	3766,640	276.3+/-273.0	1608,550,45	117.0	123.0	121.0		1300	-5.5	0.0	22	dbSNP_100	121	5083,3517	513.2+/-378.1	1496,2091,713	yes	missense	PNPLA3	NM_025225.2	56	3104,2641,758	GG,GA,AA		40.8953,14.5256,31.9622	benign	434/482	44342116	8849,4157	2203	4300	6503	SO:0001583	missense	80339	exon9			TCCCCCAAGGGCT		CCDS14054.1	22q13.31	2014-03-14	2006-05-26	2006-05-26	ENSG00000100344	ENSG00000100344	3.1.1.3	"""Patatin-like phospholipase domain containing"""	18590	protein-coding gene	gene with protein product		609567	"""chromosome 22 open reading frame 20"", ""adiponutrin"""	C22orf20, ADPN		16799181, 19029121	Standard	NM_025225		Approved	dJ796I17.1, FLJ22012, adiponutrin, iPLA2epsilon	uc003bei.1	Q9NST1	OTTHUMG00000150555	ENST00000216180.3:c.1300A>G	22.37:g.44342116A>G	ENSP00000216180:p.Lys434Glu	Somatic	87	0	0	923	WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_025225	B0QYI0|B2RCL3|B3KW00|Q6P1A1|Q96CB4	Missense_Mutation	SNP	ENST00000216180.3	37	CCDS14054.1	1683	0.7706043956043956	438	0.8902439024390244	275	0.7596685082872928	485	0.8479020979020979	485	0.6398416886543535	G	0.030	-1.343700	0.01277	0.854744	0.591047	ENSG00000100344	ENST00000216180;ENST00000423180	T;T	0.34472	1.36;1.36	2.74	-5.47	0.02600	.	19.533000	0.00166	N	0.000015	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	0.31779	-0.9931	9	0.27785	T	0.31	.	1.4741	0.02422	0.4592:0.1451:0.2489:0.1468	rs2294918;rs5764418;rs17494815;rs17845418;rs17855950;rs17858284;rs60922966;rs2294918	434	Q9NST1	PLPL3_HUMAN	E	434;430	ENSP00000216180:K434E;ENSP00000397987:K430E	ENSP00000216180:K434E	K	+	1	0	PNPLA3	42673449	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.202000	0.01235	-1.617000	0.01570	-1.163000	0.01768	AAG	A|0.280;G|0.720	0.720	strong		0.597	PNPLA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318891.1	NM_025225	
SYNJ2	8871	hgsc.bcm.edu	37	6	158507981	158507981	+	Silent	SNP	G	G	A	rs2296506	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:158507981G>A	ENST00000355585.4	+	23	3378	c.3303G>A	c.(3301-3303)cgG>cgA	p.R1101R	SYNJ2_ENST00000367112.1_Silent_p.R186R|SYNJ2_ENST00000367122.2_Intron|SYNJ2_ENST00000367121.3_Silent_p.R1101R	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1101	Pro-rich.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		TCCCCAACCGGCCTCGGCCAC	0.652													G|||	2644	0.527955	0.5719	0.3386	5008	,	,		14003	0.5913		0.5099	False		,,,				2504	0.5562				p.R1101R		Atlas-SNP	.											SYNJ2,NS,carcinoma,0,1	SYNJ2	111	1	0			c.G3303A						PASS	.	G	,	2440,1966	615.6+/-392.6	668,1104,431	40.0	43.0	42.0		2592,3303	4.8	1.0	6	dbSNP_100	42	4371,4229	576.2+/-390.3	1097,2177,1026	no	coding-synonymous,coding-synonymous	SYNJ2	NM_001178088.1,NM_003898.3	,	1765,3281,1457	AA,AG,GG		49.1744,44.621,47.6319	,	864/1260,1101/1497	158507981	6811,6195	2203	4300	6503	SO:0001819	synonymous_variant	8871	exon23			CAACCGGCCTCGG	AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.3303G>A	6.37:g.158507981G>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	18	15	0.833333	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Silent	SNP	ENST00000355585.4	37	CCDS5254.1																																																																																			G|0.477;A|0.523	0.523	strong		0.652	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2		
EIF2AK1	27102	hgsc.bcm.edu	37	7	6066461	6066461	+	Silent	SNP	T	T	C	rs2639	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6066461T>C	ENST00000199389.6	-	14	1808	c.1662A>G	c.(1660-1662)ccA>ccG	p.P554P	EIF2AK1_ENST00000536084.1_Silent_p.P430P	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	554	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of hemoglobin biosynthetic process (GO:0046986)|negative regulation of translational initiation by iron (GO:0045993)|protein autophosphorylation (GO:0046777)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|response to external stimulus (GO:0009605)|response to stress (GO:0006950)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|heme binding (GO:0020037)|protein homodimerization activity (GO:0042803)	p.P554P(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	27		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.106)|OV - Ovarian serous cystadenocarcinoma(56;5.22e-14)		TGGCTTGCACTGGACACCTTT	0.468													T|||	1690	0.33746	0.4448	0.219	5008	,	,		19204	0.4425		0.2048	False		,,,				2504	0.3047				p.P554P		Atlas-SNP	.											EIF2AK1,NS,carcinoma,0,1	EIF2AK1	76	1	1	Substitution - coding silent(1)	stomach(1)	c.A1662G						scavenged	.	T	,	1932,2474	551.2+/-378.2	416,1100,687	140.0	128.0	132.0		1659,1662	-5.5	0.0	7	dbSNP_36	132	1688,6912	310.0+/-309.6	176,1336,2788	no	coding-synonymous,coding-synonymous	EIF2AK1	NM_001134335.1,NM_014413.3	,	592,2436,3475	CC,CT,TT		19.6279,43.8493,27.8333	,	553/630,554/631	6066461	3620,9386	2203	4300	6503	SO:0001819	synonymous_variant	27102	exon14			TTGCACTGGACAC	BC006524	CCDS5345.1	7p22	2005-01-20			ENSG00000086232	ENSG00000086232			24921	protein-coding gene	gene with protein product	"""heme regulated initiation factor 2 alpha kinase"""	613635				7709427, 10718198	Standard	NM_014413		Approved	HRI, KIAA1369	uc003spp.3	Q9BQI3	OTTHUMG00000090689	ENST00000199389.6:c.1662A>G	7.37:g.6066461T>C		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	191	70	0.366492	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Silent	SNP	ENST00000199389.6	37	CCDS5345.1																																																																																			T|0.699;C|0.301	0.301	strong		0.468	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413	
LPO	4025	hgsc.bcm.edu	37	17	56344867	56344867	+	Silent	SNP	G	G	A	rs8178409	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:56344867G>A	ENST00000262290.4	+	12	2167	c.1851G>A	c.(1849-1851)ccG>ccA	p.P617P	LPO_ENST00000543544.1_Silent_p.P558P|LPO_ENST00000421678.2_Silent_p.P534P|LPO_ENST00000582328.1_Silent_p.P534P	NM_006151.2	NP_006142.1	P22079	PERL_HUMAN	lactoperoxidase	617					defense response to bacterium (GO:0042742)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|hydrogen peroxide catabolic process (GO:0042744)|response to oxidative stress (GO:0006979)|thiocyanate metabolic process (GO:0018969)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|thiocyanate peroxidase activity (GO:0036393)			breast(5)|cervix(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30						TTGCTGAGCCGCTGGTGGAAA	0.592													G|||	847	0.169129	0.18	0.1369	5008	,	,		18884	0.12		0.1938	False		,,,				2504	0.2025				p.P617P		Atlas-SNP	.											.	LPO	73	.	0			c.G1851A						PASS	.	G	,	810,3596	324.2+/-298.5	69,672,1462	57.0	59.0	58.0		1602,1851	0.2	1.0	17	dbSNP_117	58	1757,6843	317.8+/-313.4	173,1411,2716	no	coding-synonymous,coding-synonymous	LPO	NM_001160102.1,NM_006151.2	,	242,2083,4178	AA,AG,GG		20.4302,18.384,19.737	,	534/630,617/713	56344867	2567,10439	2203	4300	6503	SO:0001819	synonymous_variant	4025	exon12			TGAGCCGCTGGTG	M58151	CCDS32689.1, CCDS54149.1	17q23.1	2008-02-05				ENSG00000167419	1.11.1.7		6678	protein-coding gene	gene with protein product		150205				2222811, 8964511	Standard	NM_006151		Approved	SPO	uc002ivt.3	P22079		ENST00000262290.4:c.1851G>A	17.37:g.56344867G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_006151	A5JUY4|E7EMJ3|Q13408|Q3KNQ2	Silent	SNP	ENST00000262290.4	37	CCDS32689.1																																																																																			G|0.824;A|0.176	0.176	strong		0.592	LPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443961.1		
UCHL1	7345	hgsc.bcm.edu	37	4	41259633	41259633	+	Missense_Mutation	SNP	C	C	A	rs5030732	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:41259633C>A	ENST00000284440.4	+	3	197	c.53C>A	c.(52-54)tCc>tAc	p.S18Y	UCHL1_ENST00000504818.1_3'UTR|UCHL1_ENST00000503431.1_Missense_Mutation_p.S18Y|UCHL1_ENST00000512788.1_Missense_Mutation_p.S18Y|UCHL1_ENST00000508768.1_Missense_Mutation_p.S18Y|UCHL1-AS1_ENST00000510073.1_RNA|UCHL1-AS1_ENST00000507190.1_RNA	NM_004181.4	NP_004172.2	P09936	UCHL1_HUMAN	ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)	18			S -> Y (found in patients with cataract; unknown pathological significance; loss of dimerization ability; impaired ligase activity; confers an antioxidant protective function when expressed at physiological levels in neuroblastoma cells and primary cortical neurons; dbSNP:rs5030732). {ECO:0000269|PubMed:10203348, ECO:0000269|PubMed:11027850, ECO:0000269|PubMed:15048890, ECO:0000269|PubMed:16450370, ECO:0000269|PubMed:21268678}.		adult walking behavior (GO:0007628)|axon target recognition (GO:0007412)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|cell proliferation (GO:0008283)|eating behavior (GO:0042755)|muscle fiber development (GO:0048747)|negative regulation of MAP kinase activity (GO:0043407)|neuromuscular process (GO:0050905)|protein deubiquitination (GO:0016579)|response to ischemia (GO:0002931)|sensory perception of pain (GO:0019233)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	alpha-2A adrenergic receptor binding (GO:0031694)|cysteine-type endopeptidase activity (GO:0004197)|ligase activity (GO:0016874)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(2)	8						CAGGTGCTGTCCCGGCTGGGG	0.766													C|||	1272	0.253994	0.0121	0.2939	5008	,	,		10899	0.5437		0.1809	False		,,,				2504	0.3292				p.S18Y		Atlas-SNP	.											.	UCHL1	19	.	0			c.C53A	GRCh37	CM994452	UCHL1	M	rs5030732	PASS	.	C	TYR/SER	114,4064		2,110,1977	6.0	8.0	7.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	53	2.8	0.9	4	dbSNP_113	7	1114,7164		61,992,3086	no	missense	UCHL1	NM_004181.4	144	63,1102,5063	AA,AC,CC		13.4574,2.7286,9.8587	benign	18/224	41259633	1228,11228	2089	4139	6228	SO:0001583	missense	7345	exon3			TGCTGTCCCGGCT	BC000332	CCDS3462.1	4p13	2011-07-21			ENSG00000154277	ENSG00000154277	3.4.19.12	"""Parkinson disease"""	12513	protein-coding gene	gene with protein product		191342		PARK5		1840236	Standard	NM_004181		Approved	PGP9.5, Uch-L1	uc003gvo.3	P09936	OTTHUMG00000099377	ENST00000284440.4:c.53C>A	4.37:g.41259633C>A	ENSP00000284440:p.Ser18Tyr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	21	9	0.428571	NM_004181	Q4W5K6|Q71UM0	Missense_Mutation	SNP	ENST00000284440.4	37	CCDS3462.1	528	0.24175824175824176	16	0.032520325203252036	97	0.26795580110497236	282	0.493006993006993	133	0.17546174142480211	C	8.406	0.842968	0.16963	0.027286	0.134574	ENSG00000154277	ENST00000514924;ENST00000503431;ENST00000284440;ENST00000508768;ENST00000512788	T;T;T;T;T	0.56275	0.47;0.47;0.47;0.47;0.47	3.7	2.84	0.33178	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (4);	1.003210	0.08035	N	0.994193	T	0.00012	0.0000	L	0.37697	1.125	0.28202	P	0.9273172	P	0.38300	0.626	B	0.36567	0.228	T	0.44406	-0.9330	9	0.23891	T	0.37	-1.0546	13.1671	0.59577	0.0:0.8388:0.1611:0.0	rs5030732	18	P09936	UCHL1_HUMAN	Y	18	ENSP00000426634:S18Y;ENSP00000422542:S18Y;ENSP00000284440:S18Y;ENSP00000426895:S18Y;ENSP00000423623:S18Y	ENSP00000284440:S18Y	S	+	2	0	UCHL1	40954390	0.422000	0.25473	0.940000	0.37924	0.849000	0.48306	1.040000	0.30278	0.724000	0.32296	0.462000	0.41574	TCC	C|0.758;A|0.242	0.242	strong		0.766	UCHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216827.1	NM_004181	
OBSCN	84033	hgsc.bcm.edu	37	1	228496014	228496014	+	Silent	SNP	G	G	A	rs876180	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228496014G>A	ENST00000422127.1	+	47	12713	c.12669G>A	c.(12667-12669)acG>acA	p.T4223T	OBSCN_ENST00000284548.11_Silent_p.T4223T|OBSCN_ENST00000366709.4_Silent_p.T1342T|OBSCN_ENST00000366707.4_Silent_p.T1857T|OBSCN_ENST00000570156.2_Silent_p.T5180T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4223	Ig-like 43.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGGCGTGACGCCCGAGGACG	0.637													G|||	1067	0.213059	0.32	0.2781	5008	,	,		18436	0.1825		0.161	False		,,,				2504	0.1074				p.T5180T		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	0			c.G15540A						PASS	.	G	,	1355,2893		229,897,998	36.0	40.0	39.0		12669,12669	-12.1	0.0	1	dbSNP_86	39	1498,6956		141,1216,2870	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	370,2113,3868	AA,AG,GG		17.7194,31.8974,22.461	,	4223/7969,4223/6621	228496014	2853,9849	2124	4227	6351	SO:0001819	synonymous_variant	84033	exon58			CGTGACGCCCGAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12669G>A	1.37:g.228496014G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.776;A|0.224	0.224	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
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 GAIIx	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_ENST00000465202.1_Intron|CCR2_ENST00000292301.4_Missense_Mutation_p.Y188S|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	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	143	51	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 GAIIx	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_ENST00000309359.1_Missense_Mutation_p.N351K|SOX5_ENST00000537393.1_Missense_Mutation_p.N329K|SOX5_ENST00000546136.1_Missense_Mutation_p.N351K|SOX5_ENST00000541536.1_Missense_Mutation_p.N351K|SOX5_ENST00000545921.1_Missense_Mutation_p.N354K|SOX5_ENST00000381381.2_Missense_Mutation_p.N351K			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	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	124	9	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 GAIIx	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_ENST00000254299.4_5'UTR|GCH1_ENST00000395514.1_Missense_Mutation_p.Q110R|GCH1_ENST00000536224.2_Missense_Mutation_p.Q110R	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	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	41	15	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		
SAMD9	54809	hgsc.bcm.edu	37	7	92734983	92734983	+	Missense_Mutation	SNP	A	A	G	rs6969691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92734983A>G	ENST00000379958.2	-	3	697	c.428T>C	c.(427-429)aTa>aCa	p.I143T		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	143			I -> T (in dbSNP:rs6969691).			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TTTATCTTCTATGAGCTCAAC	0.358													A|||	764	0.152556	0.2905	0.1268	5008	,	,		20645	0.1359		0.1292	False		,,,				2504	0.0256				p.I143T		Atlas-SNP	.											.	SAMD9	239	.	0			c.T428C						PASS	.	A	THR/ILE,THR/ILE	1183,3223	414.6+/-336.9	164,855,1184	123.0	134.0	130.0		428,428	-4.0	0.0	7	dbSNP_116	130	1116,7484	230.1+/-264.6	84,948,3268	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	89,89	248,1803,4452	GG,GA,AA		12.9767,26.8498,17.6765	benign,benign	143/1590,143/1590	92734983	2299,10707	2203	4300	6503	SO:0001583	missense	54809	exon2			TCTTCTATGAGCT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.428T>C	7.37:g.92734983A>G	ENSP00000369292:p.Ile143Thr	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	151	78	0.516556	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	382	0.1749084249084249	146	0.2967479674796748	51	0.1408839779005525	94	0.16433566433566432	91	0.12005277044854881	A	4.275	0.050167	0.08243	0.268498	0.129767	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.13089	2.62;2.62	4.32	-4.02	0.04034	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47560	-0.9108	8	0.11182	T	0.66	.	5.2975	0.15760	0.367:0.0:0.397:0.2361	rs6969691;rs10363606;rs60909665;rs6969691	143	Q5K651	SAMD9_HUMAN	T	143	ENSP00000369292:I143T;ENSP00000414529:I143T	ENSP00000369292:I143T	I	-	2	0	SAMD9	92572919	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.406000	0.07187	-0.592000	0.05851	-0.322000	0.08575	ATA	A|0.818;G|0.182	0.182	strong		0.358	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
PLEKHA4	57664	hgsc.bcm.edu	37	19	49368843	49368843	+	Missense_Mutation	SNP	T	T	C	rs506425	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49368843T>C	ENST00000263265.6	-	3	664	c.109A>G	c.(109-111)Atc>Gtc	p.I37V	PLEKHA4_ENST00000355496.5_Missense_Mutation_p.I37V	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	37			I -> V (in dbSNP:rs506425). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		AAGGCGTGGATCTTGTTTACT	0.597													C|||	2192	0.4377	0.8661	0.3242	5008	,	,		16677	0.1111		0.3032	False		,,,				2504	0.4141				p.I37V		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.A109G						PASS	.	C	VAL/ILE,VAL/ILE	3475,931	357.6+/-314.0	1375,725,103	123.0	95.0	105.0		109,109	4.0	1.0	19	dbSNP_83	105	2607,5993	689.4+/-404.4	396,1815,2089	yes	missense,missense	PLEKHA4	NM_001161354.1,NM_020904.2	29,29	1771,2540,2192	CC,CT,TT		30.314,21.1303,46.763	benign,benign	37/584,37/780	49368843	6082,6924	2203	4300	6503	SO:0001583	missense	57664	exon3			CGTGGATCTTGTT	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.109A>G	19.37:g.49368843T>C	ENSP00000263265:p.Ile37Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_001161354	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	831	0.3804945054945055	407	0.8272357723577236	123	0.3397790055248619	67	0.11713286713286714	234	0.3087071240105541	C	4.078	0.012294	0.07912	0.788697	0.30314	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.11385	2.78;2.78	5.04	3.98	0.46160	.	0.000000	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00382	-1.575	0.45035	P	0.0019419999999999993	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31586	-0.9938	9	0.02654	T	1	.	10.4978	0.44788	0.0:0.8265:0.0:0.1735	rs506425;rs17855917;rs57752905;rs506425	37;37	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	V	37	ENSP00000263265:I37V;ENSP00000347683:I37V	ENSP00000263265:I37V	I	-	1	0	PLEKHA4	54060655	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.044000	0.49830	1.270000	0.44297	-0.213000	0.12676	ATC	T|0.549;G|0.003	.	strong		0.597	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		
TNRC18	84629	hgsc.bcm.edu	37	7	5352949	5352949	+	Missense_Mutation	SNP	G	G	C	rs76882791	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:5352949G>C	ENST00000430969.1	-	27	7921	c.7573C>G	c.(7573-7575)Ctc>Gtc	p.L2525V	TNRC18_ENST00000399537.4_Missense_Mutation_p.L2525V	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2525							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TCCTGGGCGAGGTCCCCGTCG	0.721													G|||	694	0.138578	0.0923	0.2752	5008	,	,		9519	0.1468		0.1133	False		,,,				2504	0.1217				p.L2525V		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7573G						PASS	.	G	VAL/LEU	182,2532		6,170,1181	3.0	3.0	3.0		7573	3.3	0.7	7	dbSNP_131	3	598,5770		19,560,2605	no	missense	TNRC18	NM_001080495.2	32	25,730,3786	CC,CG,GG		9.3907,6.706,8.5884	possibly-damaging	2525/2969	5352949	780,8302	1357	3184	4541	SO:0001583	missense	84629	exon27			GGGCGAGGTCCCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7573C>G	7.37:g.5352949G>C	ENSP00000395538:p.Leu2525Val	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	44	29	0.659091	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	285|285	0.1304945054945055|0.1304945054945055	55|55	0.11178861788617886|0.11178861788617886	83|83	0.2292817679558011|0.2292817679558011	57|57	0.09965034965034965|0.09965034965034965	90|90	0.11873350923482849|0.11873350923482849	g|g	8.857|8.857	0.946106|0.946106	0.18356|0.18356	0.06706|0.06706	0.093907|0.093907	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000328270	T;T|.	0.11712|.	2.75;2.75|.	4.24|4.24	3.34|3.34	0.38264|0.38264	.|.	0.552403|.	0.13692|.	N|.	0.369441|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	P|P	0.0|0.0	P|.	0.35328|.	0.495|.	B|.	0.31442|.	0.13|.	T|T	0.08932|0.08932	-1.0698|-1.0698	9|4	0.02654|.	T|.	1|.	.|.	8.8698|8.8698	0.35309|0.35309	0.087:0.1541:0.7588:0.0|0.087:0.1541:0.7588:0.0	.|.	2525|.	O15417|.	TNC18_HUMAN|.	V|R	2525|338	ENSP00000382452:L2525V;ENSP00000395538:L2525V|.	ENSP00000382452:L2525V|.	L|P	-|-	1|2	0|0	TNRC18|TNRC18	5319475|5319475	0.000000|0.000000	0.05858|0.05858	0.692000|0.692000	0.30179|0.30179	0.216000|0.216000	0.24613|0.24613	0.405000|0.405000	0.21015|0.21015	2.282000|2.282000	0.76494|0.76494	0.561000|0.561000	0.74099|0.74099	CTC|CCT	G|0.869;C|0.131	0.131	strong		0.721	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
FOXS1	2307	hgsc.bcm.edu	37	20	30433139	30433139	+	Silent	SNP	G	G	A	rs6089096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:30433139G>A	ENST00000375978.3	-	1	281	c.207C>T	c.(205-207)aaC>aaT	p.N69N		NM_004118.3	NP_004109.1	O43638	FOXS1_HUMAN	forkhead box S1	69					blood vessel development (GO:0001568)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|positive regulation of multicellular organism growth (GO:0040018)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	9						TGAGTGACAGGTTGTGGCGGA	0.627													G|||	254	0.0507188	0.0045	0.0663	5008	,	,		16028	0.001		0.1054	False		,,,				2504	0.0971				p.N69N		Atlas-SNP	.											.	FOXS1	29	.	0			c.C207T						PASS	.	G		98,4308	78.8+/-117.2	1,96,2106	89.0	72.0	78.0		207	3.8	1.0	20	dbSNP_114	78	976,7624	211.7+/-252.2	54,868,3378	no	coding-synonymous	FOXS1	NM_004118.3		55,964,5484	AA,AG,GG		11.3488,2.2242,8.2577		69/331	30433139	1074,11932	2203	4300	6503	SO:0001819	synonymous_variant	2307	exon1			TGACAGGTTGTGG	AF042831	CCDS13192.1	20q11.1-q11.2	2008-04-10	2008-04-10	2008-04-10	ENSG00000179772	ENSG00000179772		"""Forkhead boxes"""	3735	protein-coding gene	gene with protein product		602939	"""forkhead (Drosophila)-like 18"", ""forkhead-like 18 (Drosophila)"""	FKHL18		9325056, 17062144	Standard	NM_004118		Approved	FREAC10	uc002wwt.1	O43638	OTTHUMG00000032183	ENST00000375978.3:c.207C>T	20.37:g.30433139G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_004118	Q96D28	Silent	SNP	ENST00000375978.3	37	CCDS13192.1																																																																																			G|0.929;A|0.071	0.071	strong		0.627	FOXS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078560.2	NM_004118	
GNAQ	2776	hgsc.bcm.edu	37	9	80537112	80537112	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:80537112T>A	ENST00000286548.4	-	2	508	c.286A>T	c.(286-288)Aca>Tca	p.T96S		NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	96					action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.T96S(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						ATCTTGAGTGTGTCCATGGCT	0.473			Mis		uveal melanoma																																p.T96S		Atlas-SNP	.		Dom	yes		9	9q21	2776	"""guanine nucleotide binding protein (G protein), q polypeptide"""		E	GNAQ,NS,carcinoma,0,2	GNAQ	384	2	1	Substitution - Missense(1)	prostate(1)	c.A286T						scavenged	.																																			SO:0001583	missense	2776	exon2			TGAGTGTGTCCAT		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052			4390	protein-coding gene	gene with protein product		600998				8825633	Standard	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.286A>T	9.37:g.80537112T>A	ENSP00000286548:p.Thr96Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	135	3	0.0222222	NM_002072	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.141103	0.37825	.	.	ENSG00000156052	ENST00000286548;ENST00000411677	D;D	0.87809	-2.3;-2.3	5.86	5.86	0.93980	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.84170	0.5413	L	0.52126	1.63	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.79122	-0.1933	10	0.29301	T	0.29	.	16.2652	0.82574	0.0:0.0:0.0:1.0	.	96	P50148	GNAQ_HUMAN	S	96;67	ENSP00000286548:T96S;ENSP00000391501:T67S	ENSP00000286548:T96S	T	-	1	0	GNAQ	79726932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.145000	0.64839	2.241000	0.73720	0.528000	0.53228	ACA	.	.	none		0.473	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1	NM_002072	
SEC16A	9919	hgsc.bcm.edu	37	9	139371786	139371786	+	Silent	SNP	A	A	C	rs6560632	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139371786A>C	ENST00000313050.7	-	1	355	c.282T>G	c.(280-282)gtT>gtG	p.V94V	SEC16A_ENST00000431893.2_5'Flank|SEC16A_ENST00000290037.6_5'Flank|SEC16A_ENST00000371706.3_5'Flank	NM_014866.1	NP_055681.1	O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	0					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GTGTGTGAGGAACAAGCAAAC	0.587													C|||	1909	0.38119	0.4266	0.6124	5008	,	,		19570	0.2153		0.4105	False		,,,				2504	0.2965				p.V94V		Atlas-SNP	.											.	SEC16A	249	.	0			c.T282G						PASS	.	C		1609,2377		332,945,716	74.0	78.0	77.0		282	1.1	0.0	9	dbSNP_116	77	3719,4601		818,2083,1259	no	coding-synonymous	SEC16A	NM_014866.1		1150,3028,1975	CC,CA,AA		44.6995,40.3663,43.296		94/2358	139371786	5328,6978	1993	4160	6153	SO:0001819	synonymous_variant	9919	exon3			GTGAGGAACAAGC	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000313050.7:c.282T>G	9.37:g.139371786A>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	63	0.516393	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000313050.7	37	CCDS55351.1																																																																																			A|0.601;C|0.399	0.399	strong		0.587	SEC16A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088459	
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 GAIIx	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	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	40	11	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		
KLK3	354	hgsc.bcm.edu	37	19	51359497	51359497	+	Splice_Site	SNP	T	T	C	rs17849961|rs11573	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51359497T>C	ENST00000326003.2	+	2	89	c.48T>C	c.(46-48)ggT>ggC	p.G16G	KLK3_ENST00000595952.1_Splice_Site_p.G16G|KLK3_ENST00000593997.1_Splice_Site_p.G16G|KLK3_ENST00000360617.3_Splice_Site_p.G16G|KLK3_ENST00000597483.1_Splice_Site_p.G16G	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	16					cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		CCTCTGCAGGTGCTGCACCCC	0.582													C|||	1702	0.339856	0.1921	0.4914	5008	,	,		19205	0.4851		0.4195	False		,,,				2504	0.2004				p.G16G	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.T48C						PASS	.	C	,,,	1066,3340	722.5+/-409.3	139,788,1276	92.0	82.0	85.0		48,48,48,48	-1.4	0.0	19	dbSNP_52	85	3589,5011	627.5+/-398.0	767,2055,1478	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	KLK3	NM_001030047.1,NM_001030048.1,NM_001030050.1,NM_001648.2	,,,	906,2843,2754	CC,CT,TT		41.7326,24.1943,35.7912	,,,	16/239,16/219,16/70,16/262	51359497	4655,8351	2203	4300	6503	SO:0001630	splice_region_variant	354	exon2			TGCAGGTGCTGCA	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.47-1T>C	19.37:g.51359497T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001030050	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			T|0.629;C|0.371	0.371	strong		0.582	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	Silent
PABPC4	8761	hgsc.bcm.edu	37	1	40036944	40036944	+	Silent	SNP	G	G	A	rs61743745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:40036944G>A	ENST00000372857.3	-	3	1257	c.465C>T	c.(463-465)atC>atT	p.I155I	PABPC4_ENST00000529216.1_5'Flank|PABPC4_ENST00000372858.3_Silent_p.I155I|PABPC4_ENST00000372856.3_Silent_p.I155I|PABPC4_ENST00000372862.3_Silent_p.I155I|RP11-69E11.8_ENST00000415255.1_RNA	NM_003819.3	NP_003810.1	Q13310	PABP4_HUMAN	poly(A) binding protein, cytoplasmic 4 (inducible form)	155	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				blood coagulation (GO:0007596)|RNA catabolic process (GO:0006401)|RNA processing (GO:0006396)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(3)	21	Lung NSC(20;1.55e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;2.89e-18)|Epithelial(16;6.17e-17)|all cancers(16;1.18e-15)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			TCATCTTCTCGATGGCCTTGT	0.562													G|||	64	0.0127796	0.0008	0.0144	5008	,	,		21418	0.0		0.0249	False		,,,				2504	0.0286				p.I155I		Atlas-SNP	.											.	PABPC4	56	.	0			c.C465T						PASS	.	G	,,	27,4379	34.3+/-65.2	0,27,2176	248.0	209.0	223.0		465,465,465	1.6	1.0	1	dbSNP_129	223	219,8381	92.3+/-154.4	2,215,4083	no	coding-synonymous,coding-synonymous,coding-synonymous	PABPC4	NM_001135653.1,NM_001135654.1,NM_003819.3	,,	2,242,6259	AA,AG,GG		2.5465,0.6128,1.8914	,,	155/661,155/632,155/645	40036944	246,12760	2203	4300	6503	SO:0001819	synonymous_variant	8761	exon3			CTTCTCGATGGCC	U33818	CCDS438.1, CCDS44114.1, CCDS44115.1	1p34.2	2013-02-12	2001-11-28		ENSG00000090621	ENSG00000090621		"""RNA binding motif (RRM) containing"""	8557	protein-coding gene	gene with protein product		603407	"""poly(A)-binding protein, cytoplasmic 4 (inducible form)"""			10543404	Standard	NM_001135653		Approved	iPABP, APP-1	uc001cdl.2	Q13310	OTTHUMG00000009097	ENST00000372857.3:c.465C>T	1.37:g.40036944G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	154	80	0.519481	NM_001135653	B1ANQ8|Q4VC03|Q6P0N3	Silent	SNP	ENST00000372857.3	37	CCDS438.1	24	0.01098901098901099	0	0.0	6	0.016574585635359115	0	0.0	18	0.023746701846965697	G	9.946	1.218715	0.22373	0.006128	0.025465	ENSG00000090621	ENST00000421687;ENST00000474378	.	.	.	5.85	1.59	0.23543	.	.	.	.	.	T	0.20659	0.0497	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.09335	-1.0679	4	.	.	.	.	2.9296	0.05795	0.1291:0.1157:0.3979:0.3573	.	.	.	.	L	57;68	.	.	S	-	2	0	PABPC4	39809531	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.788000	0.26872	0.350000	0.24002	0.556000	0.70494	TCG	G|0.982;A|0.018	0.018	strong		0.562	PABPC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025220.1	NM_001135653	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244166	11244166	+	Silent	SNP	G	G	C	rs35720106	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11244166G>C	ENST00000531678.1	-	1	746	c.663C>G	c.(661-663)acC>acG	p.T221T	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	221					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)	p.T221T(1)		endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TGTGGACCTTGGTGCTGGGAT	0.398													.|||	3199	0.638778	0.1218	0.7205	5008	,	,		13366	0.9405		0.7793	False		,,,				2504	0.8241				p.T221T		Atlas-SNP	.											TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	1	Substitution - coding silent(1)	prostate(1)	c.C663G						PASS	.						130.0	112.0	118.0					12																	11244166		2176	4249	6425	SO:0001819	synonymous_variant	259289	exon1			GACCTTGGTGCTG	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.663C>G	12.37:g.11244166G>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	97	83	0.85567	NM_176884	P59546|Q645X4	Silent	SNP	ENST00000531678.1	37	CCDS53749.1																																																																																			G|0.614;C|0.386	0.386	strong		0.398	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
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 GAIIx	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	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	132	72	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		
ZFP90	146198	hgsc.bcm.edu	37	16	68598007	68598007	+	Silent	SNP	A	A	G	rs1177648	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:68598007A>G	ENST00000570495.1	+	5	1609	c.1317A>G	c.(1315-1317)caA>caG	p.Q439Q	ZFP90_ENST00000563169.2_Silent_p.Q439Q|ZFP90_ENST00000398253.2_Silent_p.Q439Q			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	439					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)		CTCTCACTCAAGATGAAAGCA	0.408													A|||	2648	0.528754	0.1884	0.6167	5008	,	,		23241	0.7659		0.5676	False		,,,				2504	0.6421				p.Q439Q		Atlas-SNP	.											ZFP90,NS,carcinoma,+1,1	ZFP90	67	1	0			c.A1317G						PASS	.	A		1043,2963		157,729,1117	93.0	90.0	91.0		1317	2.1	0.1	16	dbSNP_87	91	4990,3378		1470,2050,664	no	coding-synonymous	ZFP90	NM_133458.2		1627,2779,1781	GG,GA,AA		40.3681,26.0359,48.7555		439/637	68598007	6033,6341	2003	4184	6187	SO:0001819	synonymous_variant	146198	exon4			CACTCAAGATGAA	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.1317A>G	16.37:g.68598007A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_133458	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Silent	SNP	ENST00000570495.1	37	CCDS42183.1																																																																																			A|0.462;G|0.538	0.538	strong		0.408	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375	
FAM114A1	92689	hgsc.bcm.edu	37	4	38933859	38933859	+	Missense_Mutation	SNP	G	G	A	rs17429619	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38933859G>A	ENST00000358869.2	+	12	1503	c.1327G>A	c.(1327-1329)Gta>Ata	p.V443I	FAM114A1_ENST00000515037.1_Missense_Mutation_p.V236I	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	443			V -> I (in dbSNP:rs17429619).			cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						ATTTCAGGAAGTATACATGTC	0.353													G|||	545	0.108826	0.0507	0.2046	5008	,	,		17700	0.0764		0.1551	False		,,,				2504	0.1053				p.V443I		Atlas-SNP	.											.	FAM114A1	42	.	0			c.G1327A						PASS	.	G	ILE/VAL	344,4062	177.6+/-206.5	10,324,1869	58.0	57.0	57.0		1327	4.4	0.9	4	dbSNP_123	57	1540,7060	288.6+/-298.9	135,1270,2895	yes	missense	FAM114A1	NM_138389.2	29	145,1594,4764	AA,AG,GG		17.907,7.8075,14.4856	benign	443/564	38933859	1884,11122	2203	4300	6503	SO:0001583	missense	92689	exon12			CAGGAAGTATACA		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1327G>A	4.37:g.38933859G>A	ENSP00000351740:p.Val443Ile	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	244	86	0.352459	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	278	0.12728937728937728	33	0.06707317073170732	74	0.20441988950276244	45	0.07867132867132867	126	0.1662269129287599	G	0.718	-0.784474	0.02907	0.078075	0.17907	ENSG00000197712	ENST00000515037;ENST00000358869;ENST00000355404	T;T	0.19532	2.14;3.05	5.22	4.38	0.52667	.	0.292600	0.37136	N	0.002227	T	0.00012	0.0000	N	0.21097	0.63	0.24090	P	0.99591241	B;B	0.15141	0.012;0.005	B;B	0.12156	0.007;0.006	T	0.34775	-0.9815	9	0.02654	T	1	-12.6019	3.702	0.08386	0.2198:0.0:0.5886:0.1915	rs17429619;rs52811231;rs17429619	236;443	Q6MZV4;Q8IWE2	.;NXP20_HUMAN	I	236;443;236	ENSP00000424115:V236I;ENSP00000351740:V443I	ENSP00000347569:V236I	V	+	1	0	FAM114A1	38610254	0.994000	0.37717	0.940000	0.37924	0.397000	0.30659	1.397000	0.34543	1.435000	0.47434	0.563000	0.77884	GTA	G|0.869;A|0.131	0.131	strong		0.353	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
PRKACG	5568	hgsc.bcm.edu	37	9	71628207	71628207	+	Missense_Mutation	SNP	G	G	C	rs3730386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:71628207G>C	ENST00000377276.2	-	1	832	c.802C>G	c.(802-804)Cat>Gat	p.H268D		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		H -> D (in dbSNP:rs3730386). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2342480, ECO:0000269|Ref.3}.		activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CGCAGCAGATGCTTGAGGTCA	0.592													C|||	1609	0.321286	0.3752	0.1772	5008	,	,		17415	0.3145		0.2684	False		,,,				2504	0.4121				p.H268D	Esophageal Squamous(110;2236 2623 32146)	Atlas-SNP	.											.	PRKACG	65	.	0			c.C802G						PASS	.	C	ASP/HIS	1596,2810	665.1+/-401.5	295,1006,902	89.0	89.0	89.0		802	1.6	0.0	9	dbSNP_107	89	2203,6397	710.5+/-405.8	275,1653,2372	yes	missense	PRKACG	NM_002732.3	81	570,2659,3274	CC,CG,GG		25.6163,36.2233,29.2096	benign	268/352	71628207	3799,9207	2203	4300	6503	SO:0001583	missense	5568	exon1			GCAGATGCTTGAG	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.802C>G	9.37:g.71628207G>C	ENSP00000366488:p.His268Asp	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_002732	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	37	CCDS6625.1	599	0.2742673992673993	179	0.3638211382113821	68	0.1878453038674033	159	0.27797202797202797	193	0.2546174142480211	C	0.149	-1.093767	0.01858	0.362233	0.256163	ENSG00000165059	ENST00000377276	T	0.05139	3.49	1.62	1.62	0.23740	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.00049	-2.415	0.51482	P	7.299999999998974E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.44757	-0.9307	8	0.02654	T	1	.	7.527	0.27660	0.0:0.7289:0.2711:0.0	rs3730386;rs3730386	268	P22612	KAPCG_HUMAN	D	268	ENSP00000366488:H268D	ENSP00000366488:H268D	H	-	1	0	PRKACG	70818027	1.000000	0.71417	0.001000	0.08648	0.024000	0.10985	2.604000	0.46274	0.027000	0.15297	-0.224000	0.12420	CAT	G|0.707;C|0.293	0.293	strong		0.592	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1		
DEPTOR	64798	hgsc.bcm.edu	37	8	120940652	120940652	+	Silent	SNP	C	C	T	rs16893299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:120940652C>T	ENST00000286234.5	+	2	265	c.135C>T	c.(133-135)caC>caT	p.H45H	DEPTOR_ENST00000523492.1_Intron	NM_022783.2	NP_073620.2	Q8TB45	DPTOR_HUMAN	DEP domain containing MTOR-interacting protein	45	DEP 1. {ECO:0000255|PROSITE- ProRule:PRU00066}.				intracellular signal transduction (GO:0035556)|negative regulation of cell size (GO:0045792)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of TOR signaling (GO:0032007)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)	intracellular (GO:0005622)				endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	18						TCAGGCTGCACGAAGAAAAGG	0.373													T|||	1246	0.248802	0.379	0.1873	5008	,	,		19141	0.0367		0.2416	False		,,,				2504	0.3425				p.H45H		Atlas-SNP	.											.	DEPTOR	41	.	0			c.C135T						PASS	.	T		1585,2821	666.2+/-401.7	285,1015,903	91.0	93.0	92.0		135	2.3	1.0	8	dbSNP_123	92	2268,6332	708.0+/-405.6	292,1684,2324	no	coding-synonymous	DEPTOR	NM_022783.2		577,2699,3227	TT,TC,CC		26.3721,35.9737,29.6248		45/410	120940652	3853,9153	2203	4300	6503	SO:0001819	synonymous_variant	64798	exon2			GCTGCACGAAGAA		CCDS6331.1, CCDS64960.1	8q24.12	2011-12-13	2010-12-08	2010-12-08	ENSG00000155792	ENSG00000155792			22953	protein-coding gene	gene with protein product		612974	"""DEP domain containing 6"""	DEPDC6		19446321	Standard	NM_022783		Approved	DEP.6, FLJ12428	uc003yow.4	Q8TB45	OTTHUMG00000165052	ENST00000286234.5:c.135C>T	8.37:g.120940652C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_022783	B2RCL9|B4DN97|E7EV87|Q96EQ1|Q9H0R7|Q9H894|Q9HA07	Silent	SNP	ENST00000286234.5	37	CCDS6331.1																																																																																			C|0.743;T|0.257	0.257	strong		0.373	DEPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381601.1	NM_022783	
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 GAIIx	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_ENST00000252826.5_5'Flank|TRPM4_ENST00000427978.2_5'Flank|HRC_ENST00000595625.1_Silent_p.S50S|TRPM4_ENST00000355712.5_5'Flank	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		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	27	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	
TMEM61	199964	hgsc.bcm.edu	37	1	55457710	55457710	+	Silent	SNP	G	G	A	rs2500326	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:55457710G>A	ENST00000371268.3	+	3	841	c.567G>A	c.(565-567)gcG>gcA	p.A189A	RP11-12C17.2_ENST00000436960.1_RNA	NM_182532.1	NP_872338.1	Q8N0U2	TMM61_HUMAN	transmembrane protein 61	189						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	4						CCGTTTCTGCGGAGACGACAC	0.597													A|||	3944	0.78754	0.8162	0.8876	5008	,	,		16935	0.6379		0.8002	False		,,,				2504	0.819				p.A189A		Atlas-SNP	.											.	TMEM61	22	.	0			c.G567A						PASS	.	A		3628,778	316.1+/-294.4	1484,660,59	113.0	110.0	111.0		567	0.8	0.0	1	dbSNP_100	111	6953,1647	305.8+/-307.6	2813,1327,160	no	coding-synonymous	TMEM61	NM_182532.1		4297,1987,219	AA,AG,GG		19.1512,17.6577,18.6452		189/211	55457710	10581,2425	2203	4300	6503	SO:0001819	synonymous_variant	199964	exon3			TTCTGCGGAGACG	BC029775	CCDS601.1	1p32.3	2008-02-05			ENSG00000143001	ENSG00000143001			27296	protein-coding gene	gene with protein product						12477932	Standard	NM_182532		Approved		uc001cyd.3	Q8N0U2	OTTHUMG00000009991	ENST00000371268.3:c.567G>A	1.37:g.55457710G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_182532		Silent	SNP	ENST00000371268.3	37	CCDS601.1																																																																																			G|0.200;A|0.800	0.800	strong		0.597	TMEM61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027683.1	NM_182532	
NDRG4	65009	hgsc.bcm.edu	37	16	58545426	58545426	+	Silent	SNP	A	A	G	rs42945	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:58545426A>G	ENST00000570248.1	+	15	1111	c.1005A>G	c.(1003-1005)tcA>tcG	p.S335S	NDRG4_ENST00000569923.1_Silent_p.S267S|NDRG4_ENST00000258187.5_Silent_p.S354S|NDRG4_ENST00000566192.1_Silent_p.S322S|NDRG4_ENST00000394279.2_Silent_p.S354S|NDRG4_ENST00000356752.4_Silent_p.S352S|NDRG4_ENST00000568640.1_Silent_p.S340S|NDRG4_ENST00000394282.4_Silent_p.S374S|NDRG4_ENST00000562999.1_Silent_p.S310S|NDRG4_ENST00000563799.1_Silent_p.S340S	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	335					cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						GCACCCACTCAGAGAGCAGCG	0.682													G|||	4078	0.814297	0.9561	0.7392	5008	,	,		15744	0.9673		0.5577	False		,,,				2504	0.7822				p.S374S		Atlas-SNP	.											.	NDRG4	29	.	0			c.A1122G						PASS	.	G	,,,,,,	3883,513	222.3+/-239.2	1720,443,35	61.0	58.0	59.0		1122,1056,1020,1005,966,1062,1062	-8.2	0.1	16	dbSNP_76	59	4614,3980	526.3+/-380.9	1237,2140,920	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDRG4	NM_001130487.1,NM_001242833.1,NM_001242834.1,NM_001242835.1,NM_001242836.1,NM_020465.3,NM_022910.3	,,,,,,	2957,2583,955	GG,GA,AA		46.3114,11.6697,34.5881	,,,,,,	374/392,352/370,340/358,335/353,322/340,354/372,354/372	58545426	8497,4493	2198	4297	6495	SO:0001819	synonymous_variant	65009	exon16			CCACTCAGAGAGC	AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.1005A>G	16.37:g.58545426A>G		Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	121	120	0.991736	NM_001130487	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Silent	SNP	ENST00000570248.1	37	CCDS58466.1																																																																																			A|0.274;G|0.726	0.726	strong		0.682	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2		
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 GAIIx	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		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	79	44	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
C1orf94	84970	hgsc.bcm.edu	37	1	34663180	34663180	+	Silent	SNP	G	G	A	rs3795412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:34663180G>A	ENST00000488417.1	+	2	795	c.675G>A	c.(673-675)agG>agA	p.R225R	C1orf94_ENST00000373374.3_Silent_p.R35R	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	225										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				CAGAGGACAGGGGCCGCATCC	0.547													G|||	576	0.115016	0.1346	0.1124	5008	,	,		20597	0.0575		0.164	False		,,,				2504	0.0992				p.R225R		Atlas-SNP	.											.	C1orf94	156	.	0			c.G675A						PASS	.	G	,	694,3712	292.7+/-282.2	47,600,1556	87.0	76.0	80.0		675,105	0.7	0.0	1	dbSNP_107	80	1680,6920	307.8+/-308.6	170,1340,2790	yes	coding-synonymous,coding-synonymous	C1orf94	NM_001134734.1,NM_032884.3	,	217,1940,4346	AA,AG,GG		19.5349,15.7512,18.2531	,	225/599,35/409	34663180	2374,10632	2203	4300	6503	SO:0001819	synonymous_variant	84970	exon2			GGACAGGGGCCGC	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.675G>A	1.37:g.34663180G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_001134734	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	37	CCDS44108.1																																																																																			G|0.833;A|0.167	0.167	strong		0.547	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
LCE1E	353135	hgsc.bcm.edu	37	1	152760106	152760106	+	Missense_Mutation	SNP	G	G	A	rs56313719	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152760106G>A	ENST00000368770.3	+	2	384	c.331G>A	c.(331-333)Ggc>Agc	p.G111S	LCE1E_ENST00000368771.1_Missense_Mutation_p.G111S	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	111	Cys-rich.		G -> S (in dbSNP:rs56313719).		keratinization (GO:0031424)					lung(5)|stomach(1)	6	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;0.206)			AGGGGGCAGCGGCCAGCACTC	0.602													G|||	351	0.0700879	0.149	0.0418	5008	,	,		15029	0.0		0.1093	False		,,,				2504	0.0153				p.G111S		Atlas-SNP	.											LCE1E,neck,malignant_melanoma,-1,1	LCE1E	26	1	0			c.G331A						PASS	.	G	SER/GLY	484,3896		34,416,1740	41.0	59.0	53.0		331	-4.3	0.0	1	dbSNP_129	53	801,7775		44,713,3531	no	missense	LCE1E	NM_178353.1	56	78,1129,5271	AA,AG,GG		9.34,11.0502,9.9182	benign	111/119	152760106	1285,11671	2190	4288	6478	SO:0001583	missense	353135	exon2			GGCAGCGGCCAGC	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"""Late cornified envelopes"""	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.331G>A	1.37:g.152760106G>A	ENSP00000357759:p.Gly111Ser	Somatic	497	0	0		WXS	Illumina HiSeq	Phase_I	490	204	0.416327	NM_178353	D3DV30	Missense_Mutation	SNP	ENST00000368770.3	37	CCDS1024.1	169	0.07738095238095238	71	0.1443089430894309	14	0.03867403314917127	0	0.0	84	0.11081794195250659	G	2.174	-0.389269	0.04932	0.110502	0.0934	ENSG00000186226	ENST00000368771;ENST00000368770	T;T	0.05081	3.5;3.5	3.91	-4.31	0.03698	.	0.993514	0.08151	N	0.990096	T	0.01905	0.0060	L	0.51422	1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50048	-0.8873	9	0.87932	D	0	.	5.3981	0.16281	0.6845:0.0:0.1596:0.1559	rs56313719	111	Q5T753	LCE1E_HUMAN	S	111	ENSP00000357760:G111S;ENSP00000357759:G111S	ENSP00000357759:G111S	G	+	1	0	LCE1E	151026730	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.961000	0.03845	-0.449000	0.07117	-0.351000	0.07748	GGC	G|0.913;A|0.087	0.087	strong		0.602	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353	
TRIM16	10626	hgsc.bcm.edu	37	17	15531942	15531942	+	Missense_Mutation	SNP	C	C	A	rs1060903	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:15531942C>A	ENST00000578237.1	-	11	2537	c.1682G>T	c.(1681-1683)gGg>gTg	p.G561V	TRIM16_ENST00000577886.1_Missense_Mutation_p.G345V|RP11-385D13.1_ENST00000455584.2_Intron|TRIM16_ENST00000336708.7_Missense_Mutation_p.G561V|TRIM16_ENST00000416464.2_Missense_Mutation_p.G431V			O95361	TRI16_HUMAN	tripartite motif containing 16	561			G -> V (in dbSNP:rs1060903). {ECO:0000269|PubMed:11919186, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9817599, ECO:0000269|Ref.3}.		histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		GGGAGCAGTCCCCACCAAGGA	0.527													C|||	1202	0.240016	0.1399	0.2867	5008	,	,		16230	0.3135		0.2127	False		,,,				2504	0.2945				p.G561V		Atlas-SNP	.											.	TRIM16	45	.	0			c.G1682T						PASS	.						16.0	18.0	17.0					17																	15531942		2202	4280	6482	SO:0001583	missense	10626	exon9			GCAGTCCCCACCA	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.1682G>T	17.37:g.15531942C>A	ENSP00000463188:p.Gly561Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Missense_Mutation	SNP	ENST00000578237.1	37	CCDS11171.1	478	0.21886446886446886	69	0.1402439024390244	93	0.2569060773480663	158	0.2762237762237762	158	0.20844327176781002	.	8.259	0.810699	0.16537	.	.	ENSG00000221926	ENST00000336708;ENST00000416464	T;T	0.65916	0.07;-0.18	4.72	0.866	0.19079	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.19583	0.037;0.004	B;B	0.15484	0.013;0.008	T	0.15150	-1.0447	8	0.52906	T	0.07	.	3.8982	0.09149	0.0:0.2021:0.1836:0.6143	rs62070417	431;561	B3KP96;O95361	.;TRI16_HUMAN	V	561;431	ENSP00000338989:G561V;ENSP00000399918:G431V	ENSP00000338989:G561V	G	-	2	0	TRIM16	15472667	0.000000	0.05858	0.008000	0.14137	0.007000	0.05969	-0.150000	0.10189	0.251000	0.21505	-0.247000	0.11927	GGG	C|0.785;A|0.215	0.215	strong		0.527	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	
VPS35	55737	hgsc.bcm.edu	37	16	46705710	46705710	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:46705710T>C	ENST00000299138.7	-	12	1489	c.1431A>G	c.(1429-1431)gaA>gaG	p.E477E	VPS35_ENST00000568642.1_5'Flank	NM_018206.4	NP_060676.2	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35 homolog (S. cerevisiae)	477					cell death (GO:0008219)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|retromer complex (GO:0030904)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|pancreas(1)|prostate(1)|urinary_tract(1)	23		all_cancers(37;7.65e-05)|all_epithelial(9;0.000154)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				GATCAGGGTCTTCTACAGGTT	0.488																																					p.E477E		Atlas-SNP	.											VPS35,NS,carcinoma,0,1	VPS35	49	1	0			c.A1431G						scavenged	.						67.0	59.0	62.0					16																	46705710		2203	4300	6503	SO:0001819	synonymous_variant	55737	exon12			AGGGTCTTCTACA	AF175265	CCDS10721.1	16q12	2012-06-27	2006-12-19		ENSG00000069329	ENSG00000069329		"""Parkinson disease"""	13487	protein-coding gene	gene with protein product		601501	"""vacuolar protein sorting 35 (yeast homolog)"", ""vacuolar protein sorting 35 (yeast)"""			11112353, 21763482	Standard	NM_018206		Approved	FLJ10752, MEM3, PARK17	uc002eef.4	Q96QK1	OTTHUMG00000132542	ENST00000299138.7:c.1431A>G	16.37:g.46705710T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	202	4	0.019802	NM_018206	Q561W2|Q9H016|Q9H096|Q9H4P3|Q9H8J0|Q9NRS7|Q9NVG2|Q9NX80|Q9NZK2	Silent	SNP	ENST00000299138.7	37	CCDS10721.1																																																																																			.	.	none		0.488	VPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255742.3		
PRSS3	5646	hgsc.bcm.edu	37	9	33798052	33798052	+	Silent	SNP	C	C	T	rs377380263	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33798052C>T	ENST00000361005.5	+	3	597	c.597C>T	c.(595-597)tcC>tcT	p.S199S	PRSS3_ENST00000429677.3_Silent_p.S135S|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000342836.4_Silent_p.S156S|PRSS3_ENST00000379405.3_Silent_p.S142S	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	199	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)	p.S142S(2)|p.S199S(1)		large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			GCCTCATCTCCGGCTGGGGCA	0.567													c|||	2	0.000399361	0.0	0.0	5008	,	,		20608	0.0		0.002	False		,,,				2504	0.0				p.S199S		Atlas-SNP	.											PRSS3_ENST00000361005,NS,carcinoma,0,3	PRSS3	79	3	3	Substitution - coding silent(3)	pancreas(2)|upper_aerodigestive_tract(1)	c.C597T						scavenged	.						144.0	118.0	127.0					9																	33798052		2203	4300	6503	SO:0001819	synonymous_variant	5646	exon3			CATCTCCGGCTGG		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.597C>T	9.37:g.33798052C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	74	6	0.0810811	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Silent	SNP	ENST00000361005.5	37	CCDS47958.1																																																																																			.	.	weak		0.567	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
EPS8L2	64787	hgsc.bcm.edu	37	11	720197	720197	+	Silent	SNP	C	C	T	rs3087546	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:720197C>T	ENST00000533256.1	+	6	676	c.301C>T	c.(301-303)Ctg>Ttg	p.L101L	EPS8L2_ENST00000526198.1_Silent_p.L101L|EPS8L2_ENST00000318562.8_Silent_p.L101L|EPS8L2_ENST00000530636.1_Silent_p.L101L|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	101	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGACCAGTCGCTGCGGCTGCT	0.657													C|||	2463	0.491813	0.5651	0.647	5008	,	,		17050	0.2222		0.5457	False		,,,				2504	0.5051				p.L101L		Atlas-SNP	.											EPS8L2,rectum,carcinoma,0,1	EPS8L2	42	1	0			c.C301T						scavenged	.	C		2361,2045	601.6+/-389.7	622,1117,464	58.0	49.0	52.0		301	0.3	0.4	11	dbSNP_102	52	5037,3563	623.5+/-397.5	1480,2077,743	no	coding-synonymous	EPS8L2	NM_022772.3		2102,3194,1207	TT,TC,CC		41.4302,46.414,43.1186		101/716	720197	7398,5608	2203	4300	6503	SO:0001819	synonymous_variant	64787	exon5			CAGTCGCTGCGGC	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.301C>T	11.37:g.720197C>T		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	138	60	0.434783	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			C|0.473;T|0.527	0.527	strong		0.657	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
OR13C2	392376	hgsc.bcm.edu	37	9	107367008	107367008	+	Missense_Mutation	SNP	T	T	C	rs10156474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107367008T>C	ENST00000542196.1	-	1	943	c.901A>G	c.(901-903)Aag>Gag	p.K301E		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	301			K -> E (in dbSNP:rs10156474).			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(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						TTCACATCCTTGTTTCTAAGA	0.373													T|||	2155	0.430312	0.6256	0.2248	5008	,	,		20518	0.5774		0.1789	False		,,,				2504	0.4192				p.K301E		Atlas-SNP	.											.	OR13C2	46	.	0			c.A901G						PASS	.	T	GLU/LYS	2508,1894	629.6+/-395.3	759,990,452	163.0	161.0	162.0		901	3.5	1.0	9	dbSNP_119	162	1668,6932	307.4+/-308.4	183,1302,2815	no	missense	OR13C2	NM_001004481.1	56	942,2292,3267	CC,CT,TT		19.3953,43.0259,32.1181	probably-damaging	301/319	107367008	4176,8826	2201	4300	6501	SO:0001583	missense	392376	exon1			CATCCTTGTTTCT		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.901A>G	9.37:g.107367008T>C	ENSP00000438815:p.Lys301Glu	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	195	91	0.466667	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	826	0.3782051282051282	284	0.5772357723577236	79	0.21823204419889503	331	0.5786713286713286	132	0.1741424802110818	T	13.90	2.373626	0.42105	0.569741	0.193953	ENSG00000257019	ENST00000542196	T	0.44083	0.93	3.53	3.53	0.40419	.	0.000000	0.38436	U	0.001685	T	0.00012	0.0000	M	0.87038	2.855	0.39415	P	0.03319000000000005	P	0.39883	0.693	B	0.38500	0.275	T	0.48433	-0.9036	9	0.87932	D	0	.	6.7989	0.23740	0.0:0.0:0.2401:0.7599	rs10156474;rs59534843	301	Q8NGS9	O13C2_HUMAN	E	301	ENSP00000438815:K301E	ENSP00000438815:K301E	K	-	1	0	OR13C2	106406829	0.437000	0.25593	0.996000	0.52242	0.867000	0.49689	1.835000	0.39181	1.475000	0.48197	0.379000	0.24179	AAG	T|0.639;C|0.361	0.361	strong		0.373	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
KLHL4	56062	hgsc.bcm.edu	37	X	86887244	86887244	+	Silent	SNP	C	C	T	rs222084	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:86887244C>T	ENST00000373119.4	+	7	1504	c.1359C>T	c.(1357-1359)acC>acT	p.T453T	KLHL4_ENST00000373114.4_Silent_p.T453T	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	453						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						ACCTCAGGACCAACAGTTGGC	0.383													C|||	2112	0.55947	0.3238	0.3199	3775	,	,		13544	0.4335		0.5775	False		,,,				2504	0.454				p.T453T		Atlas-SNP	.											.	KLHL4	263	.	0			c.C1359T						PASS	.	C	,	1692,2143		310,817,255,505,316	88.0	74.0	79.0		1359,1359	1.2	0.0	X	dbSNP_79	79	5000,1728		1334,943,1389,151,483	no	coding-synonymous,coding-synonymous	KLHL4	NM_019117.4,NM_057162.2	,	1644,1760,1644,656,799	TT,TC,T,CC,C		25.6837,44.1199,36.6468	,	453/719,453/721	86887244	6692,3871	2203	4300	6503	SO:0001819	synonymous_variant	56062	exon7			CAGGACCAACAGT	AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.1359C>T	X.37:g.86887244C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	NM_019117	B2RTW2|Q9Y3J5	Silent	SNP	ENST00000373119.4	37	CCDS14457.1																																																																																			0|0.003;T|0.605	0.605	strong		0.383	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1		
FGFR4	2264	hgsc.bcm.edu	37	5	176516631	176516631	+	Missense_Mutation	SNP	G	G	A	rs1966265	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176516631G>A	ENST00000292408.4	+	2	273	c.28G>A	c.(28-30)Gtc>Atc	p.V10I	FGFR4_ENST00000507708.1_3'UTR|FGFR4_ENST00000502906.1_Missense_Mutation_p.V10I|FGFR4_ENST00000393637.1_Missense_Mutation_p.V10I|FGFR4_ENST00000393648.2_Missense_Mutation_p.V10I|FGFR4_ENST00000292410.3_Missense_Mutation_p.V10I	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	10			V -> I (in dbSNP:rs1966265). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:21882254, ECO:0000269|Ref.8}.		alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	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)		Palifermin(DB00039)|Ponatinib(DB08901)	CCTGTTGGGGGTCCTGCTGAG	0.607										TSP Lung(9;0.080)			g|||	1146	0.228834	0.0182	0.3184	5008	,	,		17888	0.5069		0.1799	False		,,,				2504	0.2137				p.V10I		Atlas-SNP	.											.	FGFR4	174	.	0			c.G28A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	269,4137	148.8+/-183.1	6,257,1940	59.0	54.0	55.0		28,28,28	-2.2	0.6	5	dbSNP_92	55	1952,6648	332.9+/-320.3	235,1482,2583	yes	missense,missense,missense	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	29,29,29	241,1739,4523	AA,AG,GG		22.6977,6.1053,17.0767	benign,benign,benign	10/803,10/763,10/803	176516631	2221,10785	2203	4300	6503	SO:0001583	missense	2264	exon1			TTGGGGGTCCTGC	AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.28G>A	5.37:g.176516631G>A	ENSP00000292408:p.Val10Ile	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	545	0.24954212454212454	13	0.026422764227642278	95	0.26243093922651933	304	0.5314685314685315	133	0.17546174142480211	g	0.003	-2.512008	0.00153	0.061053	0.226977	ENSG00000160867	ENST00000292408;ENST00000503708;ENST00000393648;ENST00000514472;ENST00000502906;ENST00000292410;ENST00000510911;ENST00000513166;ENST00000393637	T;T;T;D;T;T;T;D;T	0.88509	-1.17;-0.84;-1.13;-2.39;-1.17;-1.17;0.9;-2.32;-1.17	4.63	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	6.999999999979245E-6	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0	T	0.36648	-0.9739	8	0.31617	T	0.26	.	1.5311	0.02536	0.3612:0.135:0.3665:0.1373	rs1966265;rs2230268;rs17839798;rs59346453;rs1966265	10;10;10;10;10	B5A965;B4DVP5;P22455-2;E7EWF4;P22455	.;.;.;.;FGFR4_HUMAN	I	10	ENSP00000292408:V10I;ENSP00000424905:V10I;ENSP00000377259:V10I;ENSP00000426492:V10I;ENSP00000424960:V10I;ENSP00000292410:V10I;ENSP00000427222:V10I;ENSP00000422889:V10I;ENSP00000377254:V10I	ENSP00000292408:V10I	V	+	1	0	FGFR4	176449237	0.864000	0.29904	0.612000	0.29024	0.022000	0.10575	-0.136000	0.10405	-0.406000	0.07588	-1.652000	0.00757	GTC	G|0.804;A|0.196	0.196	strong		0.607	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
ZNF469	84627	hgsc.bcm.edu	37	16	88501034	88501034	+	Missense_Mutation	SNP	G	G	C	rs12598474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88501034G>C	ENST00000437464.1	+	2	7072	c.7072G>C	c.(7072-7074)Ggg>Cgg	p.G2358R	ZNF469_ENST00000565624.1_Missense_Mutation_p.G2386R	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2358			G -> R (in dbSNP:rs12598474). {ECO:0000269|PubMed:11347906}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G2358R(1)		breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CCCTGAGACCGGGCGCTCTGG	0.662													g|||	1478	0.295128	0.2231	0.2997	5008	,	,		15260	0.377		0.3807	False		,,,				2504	0.2168				p.G2358R		Atlas-SNP	.											ZNF469,NS,carcinoma,0,1	ZNF469	121	1	1	Substitution - Missense(1)	kidney(1)	c.G7072C						PASS	.						27.0	36.0	33.0					16																	88501034		692	1590	2282	SO:0001583	missense	84627	exon2			GAGACCGGGCGCT	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.7072G>C	16.37:g.88501034G>C	ENSP00000402343:p.Gly2358Arg	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	682	0.31227106227106227	104	0.21138211382113822	99	0.27348066298342544	195	0.3409090909090909	284	0.37467018469656993	g	7.137	0.581006	0.13686	.	.	ENSG00000225614	ENST00000437464	T	0.05513	3.43	3.66	-2.17	0.07059	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.32781	0.384	B	0.25884	0.064	T	0.47873	-0.9083	8	0.30078	T	0.28	.	4.2493	0.10686	0.4349:0.1731:0.392:0.0	rs12598474	2358	Q96JG9	ZN469_HUMAN	R	2358	ENSP00000402343:G2358R	ENSP00000402343:G2358R	G	+	1	0	ZNF469	87028535	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.132000	0.03235	-0.239000	0.09710	-0.320000	0.08662	GGG	G|0.685;C|0.315	0.315	strong		0.662	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
BBS12	166379	hgsc.bcm.edu	37	4	123664457	123664457	+	Silent	SNP	C	C	T	rs13135445	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:123664457C>T	ENST00000314218.3	+	2	1603	c.1410C>T	c.(1408-1410)tgC>tgT	p.C470C	BBS12_ENST00000542236.1_Silent_p.C470C	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	470					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						ACGGGGTCTGCGTGACCTTCT	0.478									Bardet-Biedl syndrome				T|||	606	0.121006	0.1293	0.1297	5008	,	,		19655	0.0		0.2346	False		,,,				2504	0.1115				p.C470C		Atlas-SNP	.											.	BBS12	63	.	0			c.C1410T						PASS	.	T	,	599,3807	770.2+/-413.7	38,523,1642	80.0	78.0	79.0		1410,1410	-0.7	0.0	4	dbSNP_121	79	2108,6492	716.6+/-406.1	255,1598,2447	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	293,2121,4089	TT,TC,CC		24.5116,13.5951,20.8135	,	470/711,470/711	123664457	2707,10299	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGTCTGCGTGACC	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1410C>T	4.37:g.123664457C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			C|0.818;T|0.182	0.182	strong		0.478	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
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 GAIIx	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_ENST00000416123.2_Silent_p.D2484D|COL12A1_ENST00000483888.2_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		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	67	22	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	
GRIK4	2900	hgsc.bcm.edu	37	11	120823608	120823608	+	Silent	SNP	G	G	A	rs2298725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:120823608G>A	ENST00000527524.2	+	15	1922	c.1635G>A	c.(1633-1635)ccG>ccA	p.P545P	GRIK4_ENST00000438375.2_Silent_p.P545P	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	545					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)			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)		CATTTTCTCCGGGCGTCTGGC	0.532											OREG0021429	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1291	0.257788	0.0772	0.3674	5008	,	,		15891	0.3264		0.334	False		,,,				2504	0.2751				p.P545P		Atlas-SNP	.											.	GRIK4	149	.	0			c.G1635A						PASS	.	G		511,3895	234.2+/-247.1	31,449,1723	144.0	133.0	136.0		1635	-11.2	0.1	11	dbSNP_100	136	2697,5901	432.8+/-357.2	427,1843,2029	no	coding-synonymous	GRIK4	NM_014619.2		458,2292,3752	AA,AG,GG		31.3678,11.5978,24.6693		545/957	120823608	3208,9796	2203	4299	6502	SO:0001819	synonymous_variant	2900	exon13			TTCTCCGGGCGTC	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.1635G>A	11.37:g.120823608G>A		Somatic	120	0	0	1506	WXS	Illumina HiSeq	Phase_I	115	19	0.165217	NM_014619	A8K9L1	Silent	SNP	ENST00000527524.2	37	CCDS8433.1																																																																																			G|0.752;A|0.248	0.248	strong		0.532	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
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 GAIIx	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	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	201	69	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 GAIIx	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_ENST00000369975.1_Missense_Mutation_p.L529W|MYO6_ENST00000369981.3_Missense_Mutation_p.L529W|RNA5SP209_ENST00000411237.1_RNA|MYO6_ENST00000369985.4_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	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	124	6	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	
SGK223	157285	hgsc.bcm.edu	37	8	8234218	8234218	+	Silent	SNP	C	C	T	rs4840954|rs373458829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:8234218C>T	ENST00000520004.1	-	3	1965	c.1701G>A	c.(1699-1701)ccG>ccA	p.P567P	SGK223_ENST00000330777.4_Silent_p.P567P			Q86YV5	SG223_HUMAN		569							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGTCAGCCAGCGGTGACACTG	0.662													C|||	2272	0.453674	0.3896	0.4323	5008	,	,		16883	0.6409		0.3002	False		,,,				2504	0.5204				p.P567P	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G1701A						PASS	.	C		1303,2737		237,829,954	24.0	29.0	27.0		1701	-9.8	0.0	8	dbSNP_127	27	2269,6033		341,1587,2223	no	coding-synonymous	SGK223	NM_001080826.1		578,2416,3177	TT,TC,CC		27.3308,32.2525,28.9418		567/1403	8234218	3572,8770	2020	4151	6171	SO:0001819	synonymous_variant	0	exon2			AGCCAGCGGTGAC																												ENST00000520004.1:c.1701G>A	8.37:g.8234218C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.631;T|0.369	0.369	strong		0.662	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
MAGEB18	286514	hgsc.bcm.edu	37	X	26157220	26157220	+	Missense_Mutation	SNP	C	C	T	rs5944317	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:26157220C>T	ENST00000325250.1	+	2	305	c.118C>T	c.(118-120)Cct>Tct	p.P40S		NM_173699.3	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	40			P -> S (in dbSNP:rs5944317). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(17)|skin(2)|stomach(1)|urinary_tract(2)	33						GTCACCCTCCCCTGCCTATCT	0.582													T|||	2793	0.739868	0.6339	0.5504	3775	,	,		13555	0.6935		0.3141	False		,,,				2504	0.5706				p.P40S		Atlas-SNP	.											.	MAGEB18	67	.	0			c.C118T						PASS	.	T	SER/PRO	3042,791		1013,547,469,71,102	50.0	44.0	46.0		118	-6.6	0.0	X	dbSNP_114	46	2836,3892		443,1164,786,821,1086	yes	missense	MAGEB18	NM_173699.3	74	1456,1711,1255,892,1188	TT,TC,T,CC,C		42.1522,20.6366,44.3424	benign	40/344	26157220	5878,4683	2202	4300	6502	SO:0001583	missense	286514	exon2			CCCTCCCCTGCCT	AK057361	CCDS14216.1	Xp21.3	2008-02-05			ENSG00000176774	ENSG00000176774			28515	protein-coding gene	gene with protein product							Standard	NM_173699		Approved	MGC33889	uc004dbq.2	Q96M61	OTTHUMG00000021282	ENST00000325250.1:c.118C>T	X.37:g.26157220C>T	ENSP00000314543:p.Pro40Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	131	32	0.244275	NM_173699		Missense_Mutation	SNP	ENST00000325250.1	37	CCDS14216.1	1129	0.6805304400241109	216	0.7105263157894737	117	0.5176991150442478	258	0.8376623376623377	161	0.27288135593220336	T	0.019	-1.457964	0.01071	0.793634	0.421522	ENSG00000176774	ENST00000325250	T	0.02280	4.36	4.17	-6.57	0.01842	Melanoma associated antigen, MAGE, N-terminal (1);	2.302700	0.02191	N	0.061355	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.46303	-0.9201	9	0.02654	T	1	.	12.8095	0.57631	0.1225:0.715:0.0:0.1625	rs5944317;rs6526550;rs17845895;rs17858870;rs58835272;rs5944317	40	Q96M61	MAGBI_HUMAN	S	40	ENSP00000314543:P40S	ENSP00000314543:P40S	P	+	1	0	MAGEB18	26067141	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.829000	0.00356	-2.305000	0.00654	-1.286000	0.01371	CCT	C|0.372;T|0.628	0.628	strong		0.582	MAGEB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056120.1	NM_173699	
CST2	1470	hgsc.bcm.edu	37	20	23805955	23805955	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:23805955C>A	ENST00000304725.2	-	2	304	c.234G>T	c.(232-234)gtG>gtT	p.V78V		NM_001322.2	NP_001313.1	P09228	CYTT_HUMAN	cystatin SA	78					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|cervix(1)|large_intestine(1)|liver(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	10						TCACCCCGCCCACGATCTACA	0.537																																					p.V78V	Pancreas(193;496 3017 22514 29918)	Atlas-SNP	.											CST2,colon,carcinoma,-2,1	CST2	39	1	0			c.G234T						scavenged	.						221.0	172.0	189.0					20																	23805955		2203	4300	6503	SO:0001819	synonymous_variant	1470	exon2			CCCGCCCACGATC	M19671	CCDS13161.1	20p11.2	2007-11-29			ENSG00000170369	ENSG00000170369			2474	protein-coding gene	gene with protein product	"""cystatin 2"""	123856					Standard	NM_001322		Approved		uc002wtq.1	P09228	OTTHUMG00000032086	ENST00000304725.2:c.234G>T	20.37:g.23805955C>A		Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	95	3	0.0315789	NM_001322	Q9UCQ7	Silent	SNP	ENST00000304725.2	37	CCDS13161.1																																																																																			.	.	none		0.537	CST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078352.2		
MATN3	4148	hgsc.bcm.edu	37	2	20202929	20202929	+	Silent	SNP	C	C	T	rs28452699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:20202929C>T	ENST00000407540.3	-	3	971	c.909G>A	c.(907-909)acG>acA	p.T303T	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Intron	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	303	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> M (in dbSNP:rs28939676). {ECO:0000269|PubMed:12736871, ECO:0000269|PubMed:14729835, ECO:0000269|PubMed:15459972}.		extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACCTGAACACGTTTTCTTGT	0.527													C|||	731	0.145966	0.1407	0.1974	5008	,	,		18880	0.0367		0.1978	False		,,,				2504	0.1759				p.T303T		Atlas-SNP	.											.	MATN3	28	.	0			c.G909A						PASS	.	C		574,3468		38,498,1485	125.0	117.0	120.0		909	-11.0	0.0	2	dbSNP_125	120	1796,6544		189,1418,2563	no	coding-synonymous	MATN3	NM_002381.4		227,1916,4048	TT,TC,CC		21.5348,14.2009,19.1407		303/487	20202929	2370,10012	2021	4170	6191	SO:0001819	synonymous_variant	4148	exon3			TGAACACGTTTTC	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.909G>A	2.37:g.20202929C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_002381	B2CPU0|Q4ZG02	Silent	SNP	ENST00000407540.3	37	CCDS46226.1																																																																																			C|0.827;T|0.173	0.173	strong		0.527	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573442	140573442	+	Silent	SNP	C	C	G	rs622424	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140573442C>G	ENST00000239446.4	+	1	1501	c.1317C>G	c.(1315-1317)gtC>gtG	p.V439V		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	439	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACATAACGGTCCTGGTCTCCG	0.592													G|||	2442	0.48762	0.5076	0.5461	5008	,	,		13937	0.5685		0.4076	False		,,,				2504	0.4182				p.V439V		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C1317G						PASS	.						80.0	77.0	78.0					5																	140573442		2203	4299	6502	SO:0001819	synonymous_variant	56126	exon1			AACGGTCCTGGTC	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1317C>G	5.37:g.140573442C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.549;G|0.451	0.451	strong		0.592	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
ACSL3	2181	hgsc.bcm.edu	37	2	223783841	223783841	+	Silent	SNP	G	G	A	rs13000358	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:223783841G>A	ENST00000357430.3	+	7	1257	c.726G>A	c.(724-726)ccG>ccA	p.P242P	AC097461.4_ENST00000446709.1_RNA|ACSL3_ENST00000392066.3_Silent_p.P242P	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	242					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	GAAAGCCACCGACCTGGTCCG	0.483			T	ETV1	prostate								g|||	113	0.0225639	0.0113	0.0346	5008	,	,		16458	0.0		0.0537	False		,,,				2504	0.0204				p.P242P		Atlas-SNP	.		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	.	ACSL3	107	.	0			c.G726A						PASS	.	G	,	85,4321	72.5+/-110.5	0,85,2118	120.0	102.0	108.0		726,726	-11.3	0.0	2	dbSNP_121	108	466,8134	138.1+/-194.9	14,438,3848	no	coding-synonymous,coding-synonymous	ACSL3	NM_004457.3,NM_203372.1	,	14,523,5966	AA,AG,GG		5.4186,1.9292,4.2365	,	242/721,242/721	223783841	551,12455	2203	4300	6503	SO:0001819	synonymous_variant	2181	exon6			GCCACCGACCTGG	D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"""Acyl-CoA synthetase family"""	3570	protein-coding gene	gene with protein product		602371	"""fatty-acid-Coenzyme A ligase, long-chain 3"""	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.726G>A	2.37:g.223783841G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	158	88	0.556962	NM_203372	Q60I92|Q8IUM9	Silent	SNP	ENST00000357430.3	37	CCDS2455.1																																																																																			G|0.963;A|0.037	0.037	strong		0.483	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457	
B4GALNT3	283358	hgsc.bcm.edu	37	12	661656	661656	+	Missense_Mutation	SNP	A	A	G	rs7298766	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:661656A>G	ENST00000266383.5	+	13	1245	c.1232A>G	c.(1231-1233)aAg>aGg	p.K411R		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	411			K -> R (in dbSNP:rs7298766). {ECO:0000269|PubMed:12966086}.		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)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GAGTACATCAAGATTGACCAG	0.597													A|||	1363	0.272165	0.3026	0.2349	5008	,	,		17742	0.1726		0.329	False		,,,				2504	0.3016				p.K411R		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A1232G						PASS	.	A	ARG/LYS	1459,2947	471.1+/-356.0	251,957,995	57.0	54.0	55.0		1232	4.3	1.0	12	dbSNP_116	55	2628,5972	422.4+/-354.0	392,1844,2064	yes	missense	B4GALNT3	NM_173593.3	26	643,2801,3059	GG,GA,AA		30.5581,33.1139,31.424	probably-damaging	411/999	661656	4087,8919	2203	4300	6503	SO:0001583	missense	283358	exon13			ACATCAAGATTGA	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1232A>G	12.37:g.661656A>G	ENSP00000266383:p.Lys411Arg	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	242	113	0.466942	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	575	0.2632783882783883	153	0.31097560975609756	103	0.2845303867403315	86	0.15034965034965034	233	0.3073878627968338	A	16.60	3.168671	0.57584	0.331139	0.305581	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.46063	2.95;0.88	5.47	4.3	0.51218	.	0.416227	0.28946	N	0.013626	T	0.00012	0.0000	M	0.64997	1.995	0.31212	P	0.698553	P;P	0.48503	0.911;0.779	B;B	0.42282	0.382;0.251	T	0.28933	-1.0028	9	0.66056	D	0.02	-31.4663	9.5586	0.39355	0.8431:0.0:0.0:0.1569	rs7298766;rs60883111;rs7298766	313;411	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	R	411;313	ENSP00000266383:K411R;ENSP00000322953:K313R	ENSP00000266383:K411R	K	+	2	0	B4GALNT3	531917	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.437000	0.59955	0.885000	0.36088	0.533000	0.62120	AAG	A|0.704;G|0.296	0.296	strong		0.597	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
SYNPO2	171024	hgsc.bcm.edu	37	4	119948046	119948046	+	Missense_Mutation	SNP	A	A	C	rs17263971	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:119948046A>C	ENST00000429713.2	+	3	704	c.522A>C	c.(520-522)caA>caC	p.Q174H	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.Q174H|SYNPO2_ENST00000434046.2_Missense_Mutation_p.Q174H	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	174			Q -> H (in dbSNP:rs17263971).			actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CTGACTCCCAAAGAGGACGCG	0.557													A|||	1110	0.221645	0.2133	0.219	5008	,	,		18571	0.1577		0.2644	False		,,,				2504	0.2566				p.Q174H		Atlas-SNP	.											.	SYNPO2	353	.	0			c.A522C						PASS	.	A	HIS/GLN,HIS/GLN,HIS/GLN	1006,3400	342.8+/-307.3	115,776,1312	36.0	41.0	40.0		522,522,522	-1.5	0.0	4	dbSNP_123	40	2140,6460	354.8+/-329.6	264,1612,2424	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	24,24,24	379,2388,3736	CC,CA,AA		24.8837,22.8325,24.1888	benign,benign,benign	174/1094,174/1110,174/1262	119948046	3146,9860	2203	4300	6503	SO:0001583	missense	171024	exon3			CTCCCAAAGAGGA	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.522A>C	4.37:g.119948046A>C	ENSP00000395143:p.Gln174His	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	463|463	0.211996336996337|0.211996336996337	87|87	0.17682926829268292|0.17682926829268292	88|88	0.2430939226519337|0.2430939226519337	90|90	0.15734265734265734|0.15734265734265734	198|198	0.2612137203166227|0.2612137203166227	A|A	6.546|6.546	0.469035|0.469035	0.12461|0.12461	0.228325|0.228325	0.248837|0.248837	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	.|T;T;T	.|0.09073	.|3.02;3.03;3.02	5.24|5.24	-1.52|-1.52	0.08637|0.08637	.|.	.|1.114660	.|0.06829	.|N	.|0.793679	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	P|P	0.0|0.0	.|P;B;B	.|0.41569	.|0.755;0.0;0.0	.|B;B;B	.|0.37346	.|0.247;0.001;0.001	T|T	0.44143|0.44143	-0.9347|-0.9347	4|9	.|0.30854	.|T	.|0.27	0.4447|0.4447	5.7472|5.7472	0.18126|0.18126	0.4363:0.2693:0.2945:0.0|0.4363:0.2693:0.2945:0.0	rs17263971;rs17263971|rs17263971;rs17263971	.|174;174;174	.|Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;SYNP2_HUMAN	Q|H	126|174	.|ENSP00000306015:Q174H;ENSP00000395143:Q174H;ENSP00000390965:Q174H	.|ENSP00000306015:Q174H	K|Q	+|+	1|3	0|2	SYNPO2|SYNPO2	120167494|120167494	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.201000|0.201000	0.24016|0.24016	-0.045000|-0.045000	0.12003|0.12003	-0.240000|-0.240000	0.09696|0.09696	0.455000|0.455000	0.32223|0.32223	AAG|CAA	A|0.774;C|0.226	0.226	strong		0.557	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
FBN3	84467	hgsc.bcm.edu	37	19	8176640	8176640	+	Missense_Mutation	SNP	C	C	T	rs12975322	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8176640C>T	ENST00000600128.1	-	32	4390	c.3976G>A	c.(3976-3978)Gtc>Atc	p.V1326I	FBN3_ENST00000601739.1_Missense_Mutation_p.V1326I|FBN3_ENST00000270509.2_Missense_Mutation_p.V1326I			Q75N90	FBN3_HUMAN	fibrillin 3	1326	EGF-like 20; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		V -> I (in dbSNP:rs12975322). {ECO:0000269|PubMed:11347906}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TCCTGGGAGACGCATTCATCC	0.622													C|||	1416	0.282748	0.2322	0.3905	5008	,	,		10528	0.4206		0.2326	False		,,,				2504	0.184				p.V1326I		Atlas-SNP	.											FBN3,colon,carcinoma,0,1	FBN3	300	1	0			c.G3976A						PASS	.	C	ILE/VAL	1126,3280	396.3+/-330.0	135,856,1212	50.0	49.0	49.0		3976	1.7	0.0	19	dbSNP_121	49	2080,6520	357.9+/-330.9	242,1596,2462	yes	missense	FBN3	NM_032447.3	29	377,2452,3674	TT,TC,CC		24.186,25.5561,24.6502	benign	1326/2810	8176640	3206,9800	2203	4300	6503	SO:0001583	missense	84467	exon31			GGGAGACGCATTC		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.3976G>A	19.37:g.8176640C>T	ENSP00000470498:p.Val1326Ile	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	683	0.31272893772893773	129	0.2621951219512195	126	0.34806629834254144	248	0.43356643356643354	180	0.23746701846965698	C	8.020	0.759456	0.15846	0.255561	0.24186	ENSG00000142449	ENST00000270509	D	0.87179	-2.22	3.95	1.72	0.24424	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.503112	0.19831	U	0.105085	T	0.00012	0.0000	N	0.03917	-0.325	0.80722	P	0.0	P	0.36535	0.557	B	0.29440	0.102	T	0.35847	-0.9772	9	0.37606	T	0.19	.	6.808	0.23788	0.0:0.6905:0.0:0.3095	rs12975322;rs56654013;rs12975322	1326	Q75N90	FBN3_HUMAN	I	1326	ENSP00000270509:V1326I	ENSP00000270509:V1326I	V	-	1	0	FBN3	8082640	0.000000	0.05858	0.000000	0.03702	0.324000	0.28378	-0.922000	0.04004	0.131000	0.18576	0.313000	0.20887	GTC	C|0.722;T|0.278	0.278	strong		0.622	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
GRID1	2894	hgsc.bcm.edu	37	10	87898729	87898729	+	Silent	SNP	G	G	A	rs17106320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:87898729G>A	ENST00000327946.7	-	4	658	c.573C>T	c.(571-573)gaC>gaT	p.D191D		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	191					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						GTAAAGAGACGTCAAGGCCCA	0.507										Multiple Myeloma(13;0.14)			g|||	906	0.180911	0.2579	0.1715	5008	,	,		21189	0.0893		0.1531	False		,,,				2504	0.2065				p.D191D		Atlas-SNP	.											.	GRID1	204	.	0			c.C573T						PASS	.			1100,3306	398.8+/-331.0	146,808,1249	189.0	169.0	176.0		573	-10.3	0.0	10	dbSNP_123	176	1248,7352	249.3+/-276.6	102,1044,3154	no	coding-synonymous	GRID1	NM_017551.2		248,1852,4403	AA,AG,GG		14.5116,24.966,18.0532		191/1010	87898729	2348,10658	2203	4300	6503	SO:0001819	synonymous_variant	2894	exon4			AGAGACGTCAAGG	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.573C>T	10.37:g.87898729G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																			G|0.823;A|0.177	0.177	strong		0.507	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18473928	18473928	+	Silent	SNP	T	T	C	rs12309666	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:18473928T>C	ENST00000266497.5	+	6	1208	c.1170T>C	c.(1168-1170)aaT>aaC	p.N390N	PIK3C2G_ENST00000538779.1_Silent_p.N390N|PIK3C2G_ENST00000535651.1_Silent_p.N390N|PIK3C2G_ENST00000433979.1_Silent_p.N390N|RERGL_ENST00000541632.1_5'Flank			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	390					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.N390N(1)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TTTATCTGAATCAACTTCTAG	0.318													C|||	1121	0.223842	0.4145	0.2233	5008	,	,		16827	0.2312		0.1083	False		,,,				2504	0.0777				p.N390N		Atlas-SNP	.											PIK3C2G,NS,carcinoma,0,1	PIK3C2G	315	1	1	Substitution - coding silent(1)	stomach(1)	c.T1170C						PASS	.	C		1472,2130		299,874,628	52.0	51.0	51.0		1170	1.7	1.0	12	dbSNP_120	51	688,7436		22,644,3396	no	coding-synonymous	PIK3C2G	NM_004570.4		321,1518,4024	CC,CT,TT		8.4687,40.8662,18.4206		390/1446	18473928	2160,9566	1801	4062	5863	SO:0001819	synonymous_variant	5288	exon7			TCTGAATCAACTT	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1170T>C	12.37:g.18473928T>C		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	197	102	0.517766	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			T|0.786;C|0.214	0.214	strong		0.318	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
KRT72	140807	hgsc.bcm.edu	37	12	52994955	52994955	+	Silent	SNP	G	G	A	rs61747192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52994955G>A	ENST00000537672.2	-	1	292	c.282C>T	c.(280-282)ccC>ccT	p.P94P	KRT72_ENST00000354310.4_Silent_p.P94P|RP11-641A6.2_ENST00000551089.1_RNA|KRT72_ENST00000293745.2_Silent_p.P94P|KRT72_ENST00000398066.3_5'UTR	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	94	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		GGATGCCCCCGGGTGGGCACA	0.746													G|||	876	0.17492	0.0862	0.0879	5008	,	,		14031	0.4444		0.1223	False		,,,				2504	0.1329				p.P94P		Atlas-SNP	.											.	KRT72	70	.	0			c.C282T						PASS	.	G	,,	506,3900	229.8+/-244.2	34,438,1731	35.0	36.0	36.0		282,282,282	-8.3	0.1	12	dbSNP_131	36	1080,7520	223.3+/-260.1	68,944,3288	no	coding-synonymous,coding-synonymous,coding-synonymous	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	,,	102,1382,5019	AA,AG,GG		12.5581,11.4843,12.1944	,,	94/512,94/470,94/512	52994955	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	140807	exon1			GCCCCCGGGTGGG	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.282C>T	12.37:g.52994955G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Silent	SNP	ENST00000537672.2	37	CCDS8833.1	424	0.19413919413919414	42	0.08536585365853659	33	0.09116022099447514	254	0.44405594405594406	95	0.12532981530343007	G	13.71	2.316979	0.40996	0.114843	0.125581	ENSG00000170486	ENST00000549979	.	.	.	4.49	-8.29	0.01009	.	0.000000	0.52532	D	0.000075	T	0.00012	0.0000	.	.	.	0.22446	P	0.999095179	.	.	.	.	.	.	T	0.28038	-1.0056	4	.	.	.	.	3.2959	0.06966	0.2814:0.4304:0.1238:0.1645	.	.	.	.	L	80	.	.	P	-	2	0	KRT72	51281222	0.000000	0.05858	0.051000	0.19133	0.895000	0.52256	-7.169000	0.00042	-1.814000	0.01224	-0.311000	0.09066	CCG	G|0.856;A|0.144	0.144	strong		0.746	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
MYBPC2	4606	hgsc.bcm.edu	37	19	50957397	50957397	+	Missense_Mutation	SNP	G	G	A	rs25665	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50957397G>A	ENST00000357701.5	+	17	1921	c.1870G>A	c.(1870-1872)Gtc>Atc	p.V624I		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	624	Ig-like C2-type 5.		V -> I (in dbSNP:rs25665).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CACCAACCCCGTCGGCGAGGA	0.632													g|||	1184	0.236422	0.034	0.2824	5008	,	,		18456	0.3829		0.2515	False		,,,				2504	0.3108				p.V624I		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G1870A						PASS	.	G	ILE/VAL	263,3941		7,249,1846	34.0	38.0	37.0		1870	-0.5	0.0	19	dbSNP_72	37	1778,6626		196,1386,2620	yes	missense	MYBPC2	NM_004533.3	29	203,1635,4466	AA,AG,GG		21.1566,6.2559,16.1881	benign	624/1142	50957397	2041,10567	2102	4202	6304	SO:0001583	missense	4606	exon17			AACCCCGTCGGCG		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.1870G>A	19.37:g.50957397G>A	ENSP00000350332:p.Val624Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	526	0.24084249084249085	19	0.03861788617886179	91	0.2513812154696133	228	0.3986013986013986	188	0.24802110817941952	g	9.583	1.124179	0.20959	0.062559	0.211566	ENSG00000086967	ENST00000357701	T	0.68181	-0.31	3.26	-0.485	0.12067	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	15.483300	0.02223	U	0.064183	T	0.00012	0.0000	L	0.58810	1.83	0.80722	P	0.0	B	0.20052	0.041	B	0.17098	0.017	T	0.15723	-1.0427	9	0.20519	T	0.43	.	3.9465	0.09350	0.0969:0.1597:0.579:0.1645	rs25665;rs2230838;rs2272322;rs12978290;rs17804237;rs52823468;rs25665	624	Q14324	MYPC2_HUMAN	I	624	ENSP00000350332:V624I	ENSP00000350332:V624I	V	+	1	0	MYBPC2	55649209	0.007000	0.16637	0.010000	0.14722	0.324000	0.28378	1.574000	0.36482	-0.057000	0.13199	-0.555000	0.04198	GTC	G|0.772;A|0.227	0.227	strong		0.632	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
NPHP4	261734	hgsc.bcm.edu	37	1	5937327	5937327	+	Silent	SNP	C	C	T	rs3747990	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:5937327C>T	ENST00000378156.4	-	20	2908	c.2643G>A	c.(2641-2643)gcG>gcA	p.A881A	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	881					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)		TGTCCACGTCCGCCAGCTTCT	0.647													C|||	448	0.0894569	0.0083	0.1153	5008	,	,		16487	0.0833		0.1571	False		,,,				2504	0.1176				p.A881A		Atlas-SNP	.											.	NPHP4	119	.	0			c.G2643A						PASS	.	C		124,4156		4,116,2020	27.0	27.0	27.0		2643	-10.2	0.0	1	dbSNP_107	27	1477,7005		141,1195,2905	no	coding-synonymous	NPHP4	NM_015102.3		145,1311,4925	TT,TC,CC		17.4133,2.8972,12.5451		881/1427	5937327	1601,11161	2140	4241	6381	SO:0001819	synonymous_variant	261734	exon20			CACGTCCGCCAGC	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.2643G>A	1.37:g.5937327C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	160	159	0.99375	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			C|0.906;T|0.094	0.094	strong		0.647	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
PPP1R17	10842	hgsc.bcm.edu	37	7	31732089	31732089	+	Missense_Mutation	SNP	C	C	G	rs3735422	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:31732089C>G	ENST00000342032.3	+	2	662	c.34C>G	c.(34-36)Ctc>Gtc	p.L12V	PPP1R17_ENST00000409146.3_Missense_Mutation_p.L12V	NM_006658.4	NP_006649.2	O96001	PPR17_HUMAN	protein phosphatase 1, regulatory subunit 17	12			L -> V (in dbSNP:rs3735422). {ECO:0000269|PubMed:10051666, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9920894}.		central nervous system development (GO:0007417)|intracellular signal transduction (GO:0035556)|regulation of phosphatase activity (GO:0010921)		protein serine/threonine phosphatase inhibitor activity (GO:0004865)	p.L12V(1)									GCCACTGGAACTCTCAGAAGA	0.448													C|||	797	0.159145	0.2057	0.1095	5008	,	,		19782	0.2341		0.1153	False		,,,				2504	0.0992				p.L12V		Atlas-SNP	.											C7orf16,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.C34G						PASS	.	C	VAL/LEU,VAL/LEU	757,3649	308.0+/-290.3	61,635,1507	117.0	102.0	107.0		34,34	4.3	1.0	7	dbSNP_107	107	962,7638	210.3+/-251.2	55,852,3393	yes	missense,missense	C7orf16	NM_001145123.2,NM_006658.4	32,32	116,1487,4900	GG,GC,CC		11.186,17.1811,13.217	benign,benign	12/105,12/156	31732089	1719,11287	2203	4300	6503	SO:0001583	missense	10842	exon2			CTGGAACTCTCAG	AF071789	CCDS5436.1, CCDS47570.1	7p15	2012-04-17	2011-10-11	2011-10-11	ENSG00000106341	ENSG00000106341		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16973	protein-coding gene	gene with protein product	"""G-substrate"""	604088	"""chromosome 7 open reading frame 16"""	C7orf16		10051666, 9920894	Standard	NM_006658		Approved	GSBS	uc003tcl.3	O96001	OTTHUMG00000128629	ENST00000342032.3:c.34C>G	7.37:g.31732089C>G	ENSP00000340125:p.Leu12Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	65	19	0.292308	NM_006658	B4DE58|Q9UDQ0	Missense_Mutation	SNP	ENST00000342032.3	37	CCDS5436.1	337	0.1543040293040293	88	0.17886178861788618	37	0.10220994475138122	131	0.229020979020979	81	0.10686015831134564	C	12.87	2.068223	0.36470	0.171811	0.11186	ENSG00000106341	ENST00000342032;ENST00000409146	T;T	0.36157	1.27;1.28	6.16	4.32	0.51571	.	0.255877	0.33235	N	0.005132	T	0.00012	0.0000	L	0.47716	1.5	0.35108	P	0.23413399999999995	P;B	0.37207	0.587;0.3	B;B	0.35182	0.197;0.164	T	0.23368	-1.0190	9	0.46703	T	0.11	-1.8379	5.263	0.15584	0.2395:0.5777:0.1105:0.0722	rs3735422;rs17852495;rs3735422	12;12	B4DE58;O96001	.;PPR17_HUMAN	V	12	ENSP00000340125:L12V;ENSP00000386459:L12V	ENSP00000340125:L12V	L	+	1	0	C7orf16	31698614	1.000000	0.71417	0.999000	0.59377	0.844000	0.47949	2.986000	0.49370	0.886000	0.36113	0.650000	0.86243	CTC	C|0.856;G|0.144	0.144	strong		0.448	PPP1R17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250498.1	NM_006658	
MUC16	94025	hgsc.bcm.edu	37	19	9072975	9072975	+	Missense_Mutation	SNP	G	G	A	rs17000816	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9072975G>A	ENST00000397910.4	-	3	14674	c.14471C>T	c.(14470-14472)aCg>aTg	p.T4824M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4826	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GGAAGGATGCGTTGTCTCTAT	0.448													G|||	936	0.186901	0.0923	0.2536	5008	,	,		23617	0.3254		0.1322	False		,,,				2504	0.181				p.T4824M		Atlas-SNP	.											MUC16_ENST00000397910,rectum,carcinoma,0,3	MUC16	4315	3	0			c.C14471T						PASS	.		MET/THR	399,3763		17,365,1699	165.0	153.0	157.0		14471	-1.5	0.0	19	dbSNP_123	157	1164,7258		73,1018,3120	yes	missense	MUC16	NM_024690.2	81	90,1383,4819	AA,AG,GG		13.8209,9.5867,12.4205	benign	4824/14508	9072975	1563,11021	2081	4211	6292	SO:0001583	missense	94025	exon3			GGATGCGTTGTCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14471C>T	19.37:g.9072975G>A	ENSP00000381008:p.Thr4824Met	Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	332	135	0.406626	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	439	0.20100732600732601	56	0.11382113821138211	80	0.22099447513812154	205	0.3583916083916084	98	0.12928759894459102	g	1.725	-0.495688	0.04291	0.095867	0.138209	ENSG00000181143	ENST00000397910	T	0.20332	2.08	2.02	-1.54	0.08584	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.46005	-0.9222	8	0.87932	D	0	.	5.65	0.17610	0.644:0.0:0.356:0.0	rs17000816;rs56515928;rs17000816	4824	B5ME49	.	M	4824	ENSP00000381008:T4824M	ENSP00000381008:T4824M	T	-	2	0	MUC16	8933975	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.495000	0.02294	-0.474000	0.06862	-0.692000	0.03713	ACG	G|0.810;A|0.190	0.190	strong		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
BTNL8	79908	hgsc.bcm.edu	37	5	180374534	180374534	+	Silent	SNP	G	G	A	rs3733756	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180374534G>A	ENST00000340184.4	+	4	902	c.696G>A	c.(694-696)tcG>tcA	p.S232S	BTNL8_ENST00000511704.1_Silent_p.S116S|BTNL8_ENST00000508408.1_Silent_p.S232S|BTNL8_ENST00000231229.4_Silent_p.S232S|BTNL8_ENST00000505126.1_Silent_p.S25S|BTNL8_ENST00000400707.3_Silent_p.S107S|BTNL8_ENST00000533815.2_Silent_p.S48S	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	232					immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.S232S(2)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCCTATATCGTGGCACCTGG	0.398													A|||	2208	0.440895	0.6641	0.4496	5008	,	,		19003	0.3462		0.4036	False		,,,				2504	0.2689				p.S232S		Atlas-SNP	.											BTNL8_ENST00000340184,NS,carcinoma,0,2	BTNL8	114	2	2	Substitution - coding silent(2)	prostate(2)	c.G696A						PASS	.	A	,,,,,	2840,1566	490.4+/-361.8	924,992,287	216.0	230.0	225.0		696,348,696,321,144,696	-1.3	0.0	5	dbSNP_107	225	3469,5123	636.0+/-399.0	705,2059,1532	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	,,,,,	1629,3051,1819	AA,AG,GG		40.3748,35.5424,48.5382	,,,,,	232/501,116/385,232/341,107/376,48/317,232/348	180374534	6309,6689	2203	4296	6499	SO:0001819	synonymous_variant	79908	exon4			TATATCGTGGCAC	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.696G>A	5.37:g.180374534G>A		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_001159708	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Silent	SNP	ENST00000340184.4	37	CCDS43413.1																																																																																			G|0.508;A|0.492	0.492	strong		0.398	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
RGPD4	285190	hgsc.bcm.edu	37	2	108475928	108475928	+	Missense_Mutation	SNP	C	C	T	rs143215949	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:108475928C>T	ENST00000408999.3	+	11	1629	c.1552C>T	c.(1552-1554)Ctt>Ttt	p.L518F	RGPD4_ENST00000354986.4_Missense_Mutation_p.L518F	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	518					protein targeting to Golgi (GO:0000042)			p.L518F(1)		breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						ATGCCTGCCCCTTCCTGTATG	0.393																																					p.L518F		Atlas-SNP	.											RGPD4,extremity,malignant_melanoma,0,1	RGPD4	112	1	1	Substitution - Missense(1)	skin(1)	c.C1552T						scavenged	.	C	PHE/LEU	20,1364		0,20,672	115.0	99.0	104.0		1552	1.7	1.0	2	dbSNP_134	104	15,3167		0,15,1576	no	missense	RGPD4	NM_182588.2	22	0,35,2248	TT,TC,CC		0.4714,1.4451,0.7665	probably-damaging	518/1759	108475928	35,4531	692	1591	2283	SO:0001583	missense	285190	exon11			CTGCCCCTTCCTG	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.1552C>T	2.37:g.108475928C>T	ENSP00000386810:p.Leu518Phe	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	211	15	0.0710901	NM_182588	B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	-	5.511	0.279200	0.10458	0.014451	0.004714	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000439322	T;T	0.50548	0.74;0.74	2.6	1.7	0.24286	.	.	.	.	.	T	0.34803	0.0910	M	0.69823	2.125	0.27171	N	0.960928	B	0.06786	0.001	B	0.06405	0.002	T	0.33317	-0.9873	9	0.38643	T	0.18	-11.7549	6.3947	0.21605	0.0:0.7319:0.0:0.2681	.	518	Q7Z3J3	RGPD4_HUMAN	F	518;518;276	ENSP00000347081:L518F;ENSP00000386810:L518F	ENSP00000347081:L518F	L	+	1	0	RGPD4	107842360	0.830000	0.29337	0.968000	0.41197	0.263000	0.26337	1.503000	0.35715	0.308000	0.22923	0.152000	0.16155	CTT	.	.	weak		0.393	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
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 GAIIx	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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	87	15	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	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33566234	33566234	+	Silent	SNP	C	C	T	rs62559879	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33566234C>T	ENST00000290943.6	+	13	2388	c.2292C>T	c.(2290-2292)gcC>gcT	p.A764A		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	764										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						ATCTTATGGCCGAGAAGGAAG	0.328													.|||	799	0.159545	0.0121	0.196	5008	,	,		17645	0.2083		0.2455	False		,,,				2504	0.1943				p.A763A		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.C2289T						PASS	.																																			SO:0001819	synonymous_variant	441459	exon13			TATGGCCGAGAAG			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2292C>T	9.37:g.33566234C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				T|1.000;|0.000	1.000	weak		0.328	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
PARP12	64761	hgsc.bcm.edu	37	7	139727135	139727135	+	Silent	SNP	G	G	A	rs2286196	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:139727135G>A	ENST00000263549.3	-	10	2442	c.1569C>T	c.(1567-1569)ttC>ttT	p.F523F		NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	523	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					GAACAAAGTAGAAAGGCAGCG	0.507													G|||	1513	0.302117	0.2799	0.3631	5008	,	,		21451	0.5258		0.1998	False		,,,				2504	0.1636				p.F523F		Atlas-SNP	.											.	PARP12	59	.	0			c.C1569T						PASS	.	G		1231,3175	425.7+/-340.9	196,839,1168	103.0	96.0	98.0		1569	3.7	0.3	7	dbSNP_100	98	1731,6869	314.6+/-311.9	165,1401,2734	no	coding-synonymous	PARP12	NM_022750.2		361,2240,3902	AA,AG,GG		20.1279,27.9392,22.7741		523/702	139727135	2962,10044	2203	4300	6503	SO:0001819	synonymous_variant	64761	exon10			AAAGTAGAAAGGC	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1569C>T	7.37:g.139727135G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	135	75	0.555556	NM_022750	Q9H610|Q9NP36|Q9NTI3	Silent	SNP	ENST00000263549.3	37	CCDS5857.1																																																																																			G|0.728;T|0.002	.	strong		0.507	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
EXPH5	23086	hgsc.bcm.edu	37	11	108409784	108409784	+	Missense_Mutation	SNP	T	T	A	rs2640785	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:108409784T>A	ENST00000265843.4	-	3	520	c.410A>T	c.(409-411)gAg>gTg	p.E137V	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000428840.1_Missense_Mutation_p.E61V|EXPH5_ENST00000525344.1_Missense_Mutation_p.E130V|EXPH5_ENST00000443411.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	137			E -> V (in dbSNP:rs2640785).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTTTGAAGTCTCCTTTCCAGA	0.433													T|||	1264	0.252396	0.0393	0.3501	5008	,	,		17701	0.5804		0.17	False		,,,				2504	0.2178				p.E137V		Atlas-SNP	.											.	EXPH5	193	.	0			c.A410T						PASS	.	T	VAL/GLU	281,4121	156.6+/-189.7	4,273,1924	144.0	141.0	142.0		410	5.0	0.8	11	dbSNP_100	142	1462,7134	279.8+/-294.2	141,1180,2977	yes	missense	EXPH5	NM_015065.2	121	145,1453,4901	AA,AT,TT		17.0079,6.3835,13.4098	probably-damaging	137/1990	108409784	1743,11255	2201	4298	6499	SO:0001583	missense	23086	exon3			GAAGTCTCCTTTC		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.410A>T	11.37:g.108409784T>A	ENSP00000265843:p.Glu137Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	117	19	0.162393	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	638	0.29212454212454214	31	0.06300813008130081	111	0.30662983425414364	356	0.6223776223776224	140	0.18469656992084432	T	22.7	4.322784	0.81580	0.063835	0.170079	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000525344;ENST00000526312;ENST00000531386	T;T;T;T;T	0.40756	3.92;3.84;3.92;3.74;1.02	4.99	4.99	0.66335	.	0.347910	0.24755	N	0.035872	T	0.00012	0.0000	M	0.69823	2.125	0.09310	P	1.0	D	0.61080	0.989	P	0.58266	0.836	T	0.50013	-0.8877	9	0.87932	D	0	-6.9937	11.3852	0.49780	0.0:0.0:0.0:1.0	rs2640785;rs3741047;rs52819845;rs2640785	137	Q8NEV8	EXPH5_HUMAN	V	137;61;130;61;61	ENSP00000265843:E137V;ENSP00000391966:E61V;ENSP00000432546:E130V;ENSP00000432683:E61V;ENSP00000433909:E61V	ENSP00000265843:E137V	E	-	2	0	EXPH5	107914994	0.997000	0.39634	0.799000	0.32177	0.948000	0.59901	4.094000	0.57721	2.012000	0.59069	0.528000	0.53228	GAG	T|0.797;A|0.203	0.203	strong		0.433	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
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 GAIIx	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		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	49	13	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	
HDC	3067	hgsc.bcm.edu	37	15	50534514	50534514	+	Missense_Mutation	SNP	T	T	G	rs2073440	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:50534514T>G	ENST00000267845.3	-	12	2334	c.1932A>C	c.(1930-1932)gaA>gaC	p.E644D	RN7SL494P_ENST00000461517.2_RNA|HDC_ENST00000543581.1_Missense_Mutation_p.E611D	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	175					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		GAGAGCTGCATTCAGGAAAGC	0.493													T|||	358	0.0714856	0.1581	0.0173	5008	,	,		19660	0.1081		0.0219	False		,,,				2504	0.0061				p.E644D	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.A1932C						PASS	.	T	ASP/GLU	558,3834	250.9+/-257.8	37,484,1675	79.0	81.0	80.0		1932	-1.0	1.0	15	dbSNP_96	80	240,8350	96.1+/-157.9	2,236,4057	yes	missense	HDC	NM_002112.3	45	39,720,5732	GG,GT,TT		2.7939,12.7049,6.147	probably-damaging	644/663	50534514	798,12184	2196	4295	6491	SO:0001583	missense	3067	exon12			GCTGCATTCAGGA		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1932A>C	15.37:g.50534514T>G	ENSP00000267845:p.Glu644Asp	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	146	0.06684981684981685	81	0.16463414634146342	7	0.019337016574585635	43	0.07517482517482517	15	0.01978891820580475	T	15.05	2.717664	0.48622	0.127049	0.027939	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.13196	2.91;2.61	5.61	-0.982	0.10266	.	0.101592	0.43260	D	0.000582	T	0.00039	0.0001	N	0.14661	0.345	0.32265	P	0.569707	B;P	0.49253	0.262;0.921	B;B	0.42882	0.053;0.401	T	0.40664	-0.9551	9	0.87932	D	0	-20.8974	6.6694	0.23060	0.0:0.3652:0.1288:0.5059	rs2073440;rs52811273;rs2073440	611;644	B7ZM01;P19113	.;DCHS_HUMAN	D	644;611	ENSP00000267845:E644D;ENSP00000440252:E611D	ENSP00000267845:E644D	E	-	3	2	HDC	48321806	1.000000	0.71417	0.996000	0.52242	0.703000	0.40648	0.846000	0.27682	0.106000	0.17784	-0.256000	0.11100	GAA	T|0.929;G|0.071	0.071	strong		0.493	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
ADH4	127	hgsc.bcm.edu	37	4	100045616	100045616	+	Splice_Site	SNP	C	C	T	rs1126673	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100045616C>T	ENST00000265512.7	-	9	1194	c.1120G>A	c.(1120-1122)Gtc>Atc	p.V374I	ADH4_ENST00000508393.1_Splice_Site_p.V393I|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000423445.1_Splice_Site_p.V393I|ADH4_ENST00000505590.1_Splice_Site_p.V393I	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	374			V -> I (in dbSNP:rs1126673). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		ATTGTTCGGACGCTGTTAATA	0.318													C|||	4243	0.847244	0.8608	0.7709	5008	,	,		16198	0.999		0.6978	False		,,,				2504	0.8804				p.V374I		Atlas-SNP	.											.	ADH4	35	.	0			c.G1120A						PASS	.	C	ILE/VAL	3623,781	729.6+/-410.1	1487,649,66	32.0	33.0	33.0		1120	0.6	1.0	4	dbSNP_86	33	5868,2728	666.1+/-402.3	1986,1896,416	yes	missense-near-splice	ADH4	NM_000670.3	29	3473,2545,482	TT,TC,CC		31.7357,17.7339,26.9923	benign	374/381	100045616	9491,3509	2202	4298	6500	SO:0001630	splice_region_variant	127	exon9			TTCGGACGCTGTT	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"""Alcohol dehydrogenases"""	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.1119-1G>A	4.37:g.100045616C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	145	142	0.97931	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Missense_Mutation	SNP	ENST00000265512.7	37	CCDS34032.1	1792	0.8205128205128205	414	0.8414634146341463	274	0.7569060773480663	572	1.0	532	0.7018469656992085	C	0.007	-1.995442	0.00435	0.822661	0.682643	ENSG00000198099	ENST00000508393;ENST00000265512;ENST00000423445;ENST00000505590	T;T;T;T	0.02916	4.11;4.11;4.11;4.11	3.16	0.629	0.17687	GroES-like (1);	0.170390	0.35525	N	0.003142	T	0.00012	0.0000	N	0.02751	-0.505	0.49213	P	2.3099999999998122E-4	B;B	0.11235	0.004;0.0	B;B	0.08055	0.003;0.001	T	0.30794	-0.9966	9	0.02654	T	1	-3.5331	3.5916	0.07990	0.0:0.1249:0.2267:0.6484	rs1126673;rs1540055;rs3181820;rs17410005;rs17856657;rs52807892;rs57345384;rs1126673	393;374	P08319-2;P08319	.;ADH4_HUMAN	I	393;374;393;393	ENSP00000424630:V393I;ENSP00000265512:V374I;ENSP00000397939:V393I;ENSP00000425416:V393I	ENSP00000265512:V374I	V	-	1	0	ADH4	100264639	0.998000	0.40836	0.985000	0.45067	0.282000	0.26991	0.511000	0.22739	0.133000	0.18654	-0.294000	0.09567	GTC	C|0.225;T|0.775	0.775	strong		0.318	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	Missense_Mutation
KIR3DL1	3811	hgsc.bcm.edu	37	19	55330019	55330019	+	Missense_Mutation	SNP	C	C	T	rs143159382|rs368503966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55330019C>T	ENST00000391728.4	+	3	353	c.320C>T	c.(319-321)tCg>tTg	p.S107L	KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.S107L|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.S107L|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.S107L|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.S107L	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	107					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ACTGGGTGGTCGGCACCCAGC	0.582													c|||	507	0.101238	0.087	0.1398	5008	,	,		12571	0.001		0.2416	False		,,,				2504	0.0521				p.S107L		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.C320T	GRCh37	CM035771	KIR3DL1	M	rs143159382	PASS	.	C	LEU/SER	471,3883		73,325,1779	69.0	67.0	67.0		320	0.1	0.0	19	dbSNP_134	67	1730,6508		431,868,2820	no	missense	KIR3DL1	NM_013289.2	145	504,1193,4599	TT,TC,CC		21.0002,10.8176,17.4794		107/445	55330019	2201,10391	2177	4119	6296	SO:0001583	missense	3811	exon3			GGTGGTCGGCACC	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.320C>T	19.37:g.55330019C>T	ENSP00000375608:p.Ser107Leu	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	246	0.11263736263736264	32	0.06504065040650407	43	0.11878453038674033	0	0.0	171	0.22559366754617413	-	12.28	1.891501	0.33442	0.108176	0.210002	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.01145	5.27;5.27;5.27;5.27;5.27	1.25	0.0636	0.14349	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	H	0.99011	4.4	0.80722	P	0.0	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.995	T	0.04840	-1.0923	8	0.66056	D	0.02	.	5.1966	0.15241	0.0:0.6264:0.3736:0.0	.	107;107;107	Q15702;F6QF33;P43629	.;.;KI3L1_HUMAN	L	107;107;107;85;107;107	ENSP00000384528:S107L;ENSP00000443350:S107L;ENSP00000442355:S107L;ENSP00000375608:S107L;ENSP00000326868:S107L	ENSP00000326868:S107L	S	+	2	0	KIR3DL1	60021831	0.004000	0.15560	0.001000	0.08648	0.056000	0.15407	0.687000	0.25407	0.096000	0.17463	0.184000	0.17185	TCG	C|0.884;T|0.116	0.116	strong		0.582	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
GALNT10	55568	hgsc.bcm.edu	37	5	153783753	153783753	+	Silent	SNP	C	C	T	rs6580076	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:153783753C>T	ENST00000297107.6	+	8	1283	c.1146C>T	c.(1144-1146)gcC>gcT	p.A382A	GALNT10_ENST00000377657.3_Silent_p.A53A|SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000519544.1_3'UTR|SAP30L-AS1_ENST00000524264.1_RNA|GALNT10_ENST00000377661.2_Silent_p.A320A	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	382	Flexible loop.				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)	p.A382A(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			AGGTCCCGGCCGGAGTCAGCC	0.632													C|||	1429	0.285343	0.5083	0.1585	5008	,	,		19763	0.1637		0.1571	False		,,,				2504	0.3313				p.A382A		Atlas-SNP	.											GALNT10,NS,carcinoma,0,1	GALNT10	70	1	1	Substitution - coding silent(1)	stomach(1)	c.C1146T						scavenged	.	C		1935,2471	545.4+/-376.8	432,1071,700	63.0	56.0	59.0		1146	-10.8	0.7	5	dbSNP_116	59	1471,7129	279.3+/-293.9	110,1251,2939	no	coding-synonymous	GALNT10	NM_198321.3		542,2322,3639	TT,TC,CC		17.1047,43.9174,26.1879		382/604	153783753	3406,9600	2203	4300	6503	SO:0001819	synonymous_variant	55568	exon8			CCCGGCCGGAGTC	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.1146C>T	5.37:g.153783753C>T		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Silent	SNP	ENST00000297107.6	37	CCDS4325.1																																																																																			C|0.733;T|0.267	0.267	strong		0.632	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321	
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 GAIIx	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		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	38	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	
SEC24D	9871	hgsc.bcm.edu	37	4	119736613	119736613	+	Silent	SNP	C	C	T	rs115118317	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:119736613C>T	ENST00000280551.6	-	5	904	c.666G>A	c.(664-666)ccG>ccA	p.P222P	SEC24D_ENST00000379735.5_Silent_p.P222P|SEC24D_ENST00000419654.2_5'UTR			O94855	SC24D_HUMAN	SEC24 family member D	222	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						TACCCTGCTGCGGAGGATATC	0.552													C|||	94	0.01877	0.0113	0.0231	5008	,	,		18988	0.001		0.0547	False		,,,				2504	0.0072				p.P222P		Atlas-SNP	.											SEC24D,NS,carcinoma,-1,1	SEC24D	96	1	0			c.G666A						PASS	.	C		104,4302	82.4+/-120.9	0,104,2099	69.0	67.0	68.0		666	-11.4	0.1	4	dbSNP_132	68	530,8070	148.5+/-203.7	12,506,3782	no	coding-synonymous	SEC24D	NM_014822.2		12,610,5881	TT,TC,CC		6.1628,2.3604,4.8747		222/1033	119736613	634,12372	2203	4300	6503	SO:0001819	synonymous_variant	9871	exon5			CTGCTGCGGAGGA	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.666G>A	4.37:g.119736613C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	75	29	0.386667	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			C|0.960;T|0.040	0.040	strong		0.552	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
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 GAIIx	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	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	49	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	
MXRA5	25878	hgsc.bcm.edu	37	X	3241284	3241284	+	Silent	SNP	A	A	G	rs34450504|rs1635248	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3241284A>G	ENST00000217939.6	-	5	2596	c.2442T>C	c.(2440-2442)agT>agC	p.S814S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	814						extracellular vesicular exosome (GO:0070062)		p.S814S(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TGACTTCTAGACTCAAGGATG	0.488													A|||	1752	0.464106	0.2988	0.3991	3775	,	,		13908	0.2728		0.4583	False		,,,				2504	0.3517				p.S814S		Atlas-SNP	.											.	MXRA5	815	.	1	Substitution - coding silent(1)	stomach(1)	c.T2442C						PASS	.	A		1534,2301		247,803,237,582,334	156.0	151.0	153.0		2442	-3.6	0.0	X	dbSNP_89	153	3841,2887		793,1189,1066,446,806	no	coding-synonymous	MXRA5	NM_015419.3		1040,1992,1303,1028,1140	GG,GA,G,AA,A		42.9102,40.0,49.1148		814/2829	3241284	5375,5188	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			TTCTAGACTCAAG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2442T>C	X.37:g.3241284A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			A|0.511;0|0.003	.	strong		0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
PIEZO1	9780	hgsc.bcm.edu	37	16	88780175	88780175	+	IGR	SNP	G	G	A	rs4782321	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88780175G>A	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Missense_Mutation_p.V332I|CTU2_ENST00000567949.1_Missense_Mutation_p.V403I|CTU2_ENST00000378384.3_Missense_Mutation_p.V245I|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.V332I	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						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						CACACCAGCCGTCGACACCAA	0.642													G|||	197	0.0393371	0.0234	0.0375	5008	,	,		20075	0.0		0.1282	False		,,,				2504	0.0112				p.V332I		Atlas-SNP	.											.	CTU2	66	.	0			c.G994A						PASS	.	G	ILE/VAL,ILE/VAL	155,4235	105.2+/-143.6	4,147,2044	117.0	113.0	114.0		994,994	-5.8	0.0	16	dbSNP_111	114	1171,7425	238.2+/-269.8	80,1011,3207	yes	missense,missense	CTU2	NM_001012759.1,NM_001012762.1	29,29	84,1158,5251	AA,AG,GG		13.6226,3.5308,10.211	benign,benign	332/516,332/486	88780175	1326,11660	2195	4298	6493	SO:0001628	intergenic_variant	348180	exon9			CCAGCCGTCGACA	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		16.37:g.88780175G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	40	0.421053	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	143	0.06547619047619048	16	0.032520325203252036	13	0.03591160220994475	0	0.0	114	0.1503957783641161	G	2.451	-0.326271	0.05350	0.035308	0.136226	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.43294	0.95;0.95;0.95	4.96	-5.78	0.02362	.	0.445492	0.21407	N	0.075058	T	0.00073	0.0002	N	0.02854	-0.475	0.80722	P	0.0	B;B;B	0.18610	0.01;0.029;0.006	B;B;B	0.11329	0.004;0.006;0.005	T	0.15954	-1.0419	9	0.12103	T	0.63	.	3.8935	0.09128	0.1945:0.419:0.2837:0.1028	rs4782321;rs60745289;rs4782321	245;332;332	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	I	245;332;332	ENSP00000367635:V245I;ENSP00000308617:V332I;ENSP00000388320:V332I	ENSP00000308617:V332I	V	+	1	0	CTU2	87307676	0.000000	0.05858	0.000000	0.03702	0.168000	0.22595	-0.746000	0.04829	-1.464000	0.01902	-0.302000	0.09304	GTC	G|0.912;A|0.088	0.088	strong		0.642	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
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 GAIIx	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	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	306	85	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	
MRPL28	10573	hgsc.bcm.edu	37	16	420140	420140	+	Missense_Mutation	SNP	G	G	A	rs3194151	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:420140G>A	ENST00000199706.8	-	2	114	c.79C>T	c.(79-81)Cac>Tac	p.H27Y	MRPL28_ENST00000389675.2_Missense_Mutation_p.H27Y|MRPL28_ENST00000429738.1_5'Flank	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	27			H -> Y (in dbSNP:rs3194151). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				CGCAGGTAGTGGCCGGGCAGG	0.662													G|||	565	0.112819	0.0151	0.085	5008	,	,		10068	0.1508		0.163	False		,,,				2504	0.1738				p.H27Y		Atlas-SNP	.											.	MRPL28	15	.	0			c.C79T						PASS	.	G	TYR/HIS	170,4194		7,156,2019	34.0	33.0	33.0		79	4.7	0.7	16	dbSNP_105	33	1457,7129		111,1235,2947	yes	missense	MRPL28	NM_006428.4	83	118,1391,4966	AA,AG,GG		16.9695,3.8955,12.5637	probably-damaging	27/257	420140	1627,11323	2182	4293	6475	SO:0001583	missense	10573	exon2			GGTAGTGGCCGGG	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.79C>T	16.37:g.420140G>A	ENSP00000199706:p.His27Tyr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Missense_Mutation	SNP	ENST00000199706.8	37	CCDS32349.1	225	0.10302197802197802	7	0.014227642276422764	33	0.09116022099447514	69	0.12062937062937062	116	0.15303430079155672	G	15.59	2.880014	0.51801	0.038955	0.169695	ENSG00000086504	ENST00000397735;ENST00000199706;ENST00000397734;ENST00000389675;ENST00000441883;ENST00000447696;ENST00000450882	T;T;T;T;T	0.33438	1.82;1.82;1.83;1.41;1.41	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.00300	0.0009	M	0.90595	3.13	0.22639	P	0.99890068	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.966;0.966;0.982	T	0.13710	-1.0499	9	0.52906	T	0.07	-49.4999	13.0978	0.59202	0.0805:0.0:0.9195:0.0	rs3194151;rs17849390;rs3194151	27;27;27	A2IDC6;Q13084;Q4TT38	.;RM28_HUMAN;.	Y	27	ENSP00000199706:H27Y;ENSP00000374326:H27Y;ENSP00000398684:H27Y;ENSP00000390399:H27Y;ENSP00000395305:H27Y	ENSP00000199706:H27Y	H	-	1	0	MRPL28	360141	1.000000	0.71417	0.733000	0.30861	0.077000	0.17291	5.096000	0.64535	2.175000	0.68902	0.561000	0.74099	CAC	G|0.896;A|0.104	0.104	strong		0.662	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
OR2W5	441932	hgsc.bcm.edu	37	1	247655275	247655275	+	RNA	SNP	T	T	C	rs12141850	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247655275T>C	ENST00000522351.1	+	0	906							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)			ACCATCGTCATTCCCAGCATC	0.522													C|||	1620	0.323482	0.4629	0.2406	5008	,	,		16411	0.2619		0.3241	False		,,,				2504	0.2566				p.H282H		Atlas-SNP	.											.	OR2W5	97	.	0			c.T846C						PASS	.	C		1982,2424	618.2+/-393.1	459,1064,680	114.0	104.0	107.0		846	3.1	0.4	1	dbSNP_120	107	2614,5986	688.3+/-404.3	397,1820,2083	no	coding-synonymous	OR2W5	NM_001004698.2		856,2884,2763	CC,CT,TT		30.3953,44.9841,35.3375		282/321	247655275	4596,8410	2203	4300	6503			441932	exon1			TCGTCATTCCCAG			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.247655275T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	139	65	0.467626	NM_001004698	B9EH85	Silent	SNP	ENST00000522351.1	37																																																																																				T|0.648;C|0.352	0.352	strong		0.522	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698	
PHF10	55274	hgsc.bcm.edu	37	6	170110404	170110404	+	Silent	SNP	T	T	C	rs17860601	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:170110404T>C	ENST00000339209.4	-	9	1164	c.1041A>G	c.(1039-1041)aaA>aaG	p.K347K	PHF10_ENST00000366780.4_Silent_p.K345K	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	347					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		CAGCTTTGTCTTTTGATTTCT	0.488													T|||	281	0.0561102	0.031	0.0403	5008	,	,		13886	0.0169		0.0189	False		,,,				2504	0.18				p.K347K		Atlas-SNP	.											.	PHF10	76	.	0			c.A1041G						PASS	.	T	,	136,4270	89.7+/-128.4	3,130,2070	105.0	108.0	107.0		1041,1035	3.7	1.0	6	dbSNP_123	107	228,8370	85.6+/-148.0	4,220,4075	no	coding-synonymous,coding-synonymous	PHF10	NM_018288.3,NM_133325.2	,	7,350,6145	CC,CT,TT		2.6518,3.0867,2.7991	,	347/499,345/497	170110404	364,12640	2203	4299	6502	SO:0001819	synonymous_variant	55274	exon9			TTTGTCTTTTGAT	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"""Zinc fingers, PHD-type"""	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.1041A>G	6.37:g.170110404T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	147	62	0.421769	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Silent	SNP	ENST00000339209.4	37	CCDS5308.2																																																																																			T|0.969;C|0.031	0.031	strong		0.488	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288	
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 GAIIx	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		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	33	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	
ALDH3B2	222	hgsc.bcm.edu	37	11	67431914	67431914	+	Missense_Mutation	SNP	G	G	A	rs17856219	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67431914G>A	ENST00000349015.3	-	8	1264	c.826C>T	c.(826-828)Cgg>Tgg	p.R276W	ALDH3B2_ENST00000531881.1_5'Flank|ALDH3B2_ENST00000530069.1_Missense_Mutation_p.R276W	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	276			R -> W (in dbSNP:rs17856219). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)	p.R276W(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						TTCTCCTGCCGGTTGATGAAC	0.642													G|||	355	0.0708866	0.0628	0.0591	5008	,	,		16318	0.0903		0.1123	False		,,,				2504	0.0276				p.R276W		Atlas-SNP	.											ALDH3B2,NS,carcinoma,0,1	ALDH3B2	46	1	1	Substitution - Missense(1)	stomach(1)	c.C826T						PASS	.	G	TRP/ARG,TRP/ARG	296,4104	162.9+/-194.8	15,266,1919	135.0	121.0	126.0		826,826	-2.0	0.0	11	dbSNP_123	126	855,7733	195.1+/-240.3	39,777,3478	no	missense,missense	ALDH3B2	NM_000695.3,NM_001031615.1	101,101	54,1043,5397	AA,AG,GG		9.9558,6.7273,8.862	probably-damaging,probably-damaging	276/386,276/386	67431914	1151,11837	2200	4294	6494	SO:0001583	missense	222	exon8			CCTGCCGGTTGAT	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"""Aldehyde dehydrogenases"""	411	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 8"", ""acetaldehyde dehydrogenase 8"""	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.826C>T	11.37:g.67431914G>A	ENSP00000255084:p.Arg276Trp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	55	0.696203	NM_001031615	Q53Y98|Q8NAL5|Q96IB2	Missense_Mutation	SNP	ENST00000349015.3	37	CCDS31622.1	172|172	0.07875457875457875|0.07875457875457875	30|30	0.06097560975609756|0.06097560975609756	27|27	0.07458563535911603|0.07458563535911603	35|35	0.06118881118881119|0.06118881118881119	80|80	0.10554089709762533|0.10554089709762533	G|G	10.23|10.23	1.294046|1.294046	0.23564|0.23564	0.067273|0.067273	0.099558|0.099558	ENSG00000132746|ENSG00000132746	ENST00000531248|ENST00000530069;ENST00000349015	.|D;D	.|0.85013	.|-1.93;-1.93	3.94|3.94	-1.95|-1.95	0.07548|0.07548	.|Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	.|1.051190	.|0.07515	.|U	.|0.909500	T|T	0.18341|0.18341	0.0440|0.0440	M|M	0.83483|0.83483	2.645|2.645	0.58432|0.58432	P|P	1.999999999946489E-6|1.999999999946489E-6	.|D;D	.|0.76494	.|0.999;0.997	.|P;D	.|0.65140	.|0.901;0.932	T|T	0.63695|0.63695	-0.6579|-0.6579	4|9	.|0.62326	.|D	.|0.03	.|.	1.5443|1.5443	0.02562|0.02562	0.1715:0.1439:0.3753:0.3094|0.1715:0.1439:0.3753:0.3094	rs17856219;rs58497255|rs17856219;rs58497255	.|161;276	.|B4DSX1;P48448	.|.;AL3B2_HUMAN	L|W	46|276	.|ENSP00000431595:R276W;ENSP00000255084:R276W	.|ENSP00000255084:R276W	P|R	-|-	2|1	0|2	ALDH3B2|ALDH3B2	67188490|67188490	0.000000|0.000000	0.05858|0.05858	0.004000|0.004000	0.12327|0.12327	0.080000|0.080000	0.17528|0.17528	-2.243000|-2.243000	0.01194|0.01194	-0.131000|-0.131000	0.11578|0.11578	-1.781000|-1.781000	0.00649|0.00649	CCG|CGG	G|0.913;A|0.087	0.087	strong		0.642	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695	
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 GAIIx	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_ENST00000389312.4_Silent_p.P269P|NBR1_ENST00000589872.1_Silent_p.P269P|NBR1_ENST00000542611.1_Silent_p.P248P	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		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	107	48	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	
CSMD1	64478	hgsc.bcm.edu	37	8	2820895	2820895	+	Silent	SNP	C	C	T	rs35515847	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:2820895C>T	ENST00000520002.1	-	61	9861	c.9306G>A	c.(9304-9306)ccG>ccA	p.P3102P	CSMD1_ENST00000400186.3_Silent_p.P2925P|CSMD1_ENST00000542608.1_Silent_p.P2924P|CSMD1_ENST00000602557.1_Silent_p.P3102P|CSMD1_ENST00000537824.1_Silent_p.P3101P|CSMD1_ENST00000602723.1_Silent_p.P2925P			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3102	Sushi 25. {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)		TCTGCACCGGCGGCGGCTGAG	0.537													C|||	28	0.00559105	0.0	0.0014	5008	,	,		14808	0.0099		0.008	False		,,,				2504	0.0092				p.P3101P		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G9303A						PASS	.	C		9,3829		0,9,1910	132.0	137.0	135.0		9303	-7.9	0.0	8	dbSNP_126	135	127,8175		0,127,4024	no	coding-synonymous	CSMD1	NM_033225.5		0,136,5934	TT,TC,CC		1.5298,0.2345,1.1203		3101/3565	2820895	136,12004	1919	4151	6070	SO:0001819	synonymous_variant	64478	exon60			CACCGGCGGCGGC			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.9306G>A	8.37:g.2820895C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		15	0.006868131868131868	0	0.0	0	0.0	9	0.015734265734265736	6	0.0079155672823219	C	4.194	0.034756	0.08101	0.002345	0.015298	ENSG00000183117	ENST00000335551	.	.	.	6.03	-7.88	0.01178	.	.	.	.	.	T	0.21468	0.0517	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36744	-0.9735	4	.	.	.	.	3.3513	0.07154	0.1885:0.3343:0.3241:0.1531	rs35515847	.	.	.	T	2519	.	.	A	-	1	0	CSMD1	2808302	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.703000	0.05063	-2.275000	0.00679	-3.395000	0.00039	GCC	C|0.991;T|0.009	0.009	strong		0.537	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
CDH23	64072	hgsc.bcm.edu	37	10	73558886	73558886	+	Missense_Mutation	SNP	G	G	A	rs4747194	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73558886G>A	ENST00000224721.6	+	50	7093	c.7088G>A	c.(7087-7089)cGg>cAg	p.R2363Q	CDH23_ENST00000398788.3_Missense_Mutation_p.R118Q|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2358	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.R2363Q(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ATTGCCAACCGGACAGTGGAC	0.572													G|||	1709	0.341254	0.267	0.3501	5008	,	,		19822	0.5298		0.2783	False		,,,				2504	0.3057				p.R2358Q		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - Missense(1)	stomach(1)	c.G7073A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	1060,2966		127,806,1080	85.0	95.0	92.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7073,353,353	2.7	1.0	10	dbSNP_111	92	2191,6191		309,1573,2309	yes	missense,missense,missense	CDH23	NM_022124.5,NM_001171934.1,NM_001171933.1	43,43,43	436,2379,3389	AA,AG,GG		26.1393,26.3289,26.2008	benign,benign,benign	2358/3355,118/1080,118/1115	73558886	3251,9157	2013	4191	6204	SO:0001583	missense	64072	exon49			CCAACCGGACAGT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7088G>A	10.37:g.73558886G>A	ENSP00000224721:p.Arg2363Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		765	0.35027472527472525	144	0.2926829268292683	109	0.3011049723756906	300	0.5244755244755245	212	0.2796833773087071	G	14.24	2.477311	0.44044	0.263289	0.261393	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.01725	4.67	5.55	2.71	0.32032	Cadherin (4);Cadherin-like (1);	0.138749	0.45867	N	0.000323	T	0.00012	0.0000	L	0.53617	1.68	0.20764	P	0.999855664	B;B	0.18310	0.004;0.027	B;B	0.16289	0.01;0.015	T	0.22941	-1.0202	9	0.08179	T	0.78	.	10.5972	0.45345	0.2081:0.0:0.7919:0.0	rs4747194;rs52818762;rs57656556;rs4747194	2358;2358	E9PEX1;Q9H251	.;CAD23_HUMAN	Q	2363;2358;2361;118	ENSP00000381768:R118Q	ENSP00000224721:R2363Q	R	+	2	0	CDH23	73228892	1.000000	0.71417	0.958000	0.39756	0.856000	0.48823	0.823000	0.27366	0.314000	0.23086	-0.137000	0.14449	CGG	G|0.658;A|0.342	0.342	strong		0.572	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
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 GAIIx	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	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	97	48	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	
CCDC153	283152	hgsc.bcm.edu	37	11	119064558	119064558	+	Silent	SNP	G	G	A	rs12417928	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119064558G>A	ENST00000503566.2	-	3	173	c.174C>T	c.(172-174)tcC>tcT	p.S58S	CCDC153_ENST00000415318.1_Silent_p.S58S			Q494R4	CC153_HUMAN	coiled-coil domain containing 153	58										lung(3)|stomach(1)	4						GCTGGTCTTCGGAAGCCTTGG	0.612													G|||	353	0.0704872	0.0053	0.304	5008	,	,		16839	0.0565		0.0467	False		,,,				2504	0.0317				p.S58S		Atlas-SNP	.											.	CCDC153	19	.	0			c.C174T						PASS	.	G		14,1370		0,14,678	96.0	89.0	91.0		174	-9.3	0.1	11	dbSNP_120	91	171,3011		5,161,1425	no	coding-synonymous	CCDC153	NM_001145018.1		5,175,2103	AA,AG,GG		5.374,1.0116,4.0517		58/211	119064558	185,4381	692	1591	2283	SO:0001819	synonymous_variant	283152	exon4			GTCTTCGGAAGCC		CCDS44753.1	11q23.3	2011-07-22			ENSG00000248712	ENSG00000248712			27446	protein-coding gene	gene with protein product						12477932	Standard	NM_001145018		Approved	LOC283152	uc010rze.2	Q494R4	OTTHUMG00000156903	ENST00000503566.2:c.174C>T	11.37:g.119064558G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	64	6	0.09375	NM_001145018		Silent	SNP	ENST00000503566.2	37	CCDS44753.1																																																																																			G|0.934;A|0.066	0.066	strong		0.612	CCDC153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388331.2	NM_001033658	
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 GAIIx	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	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	122	59	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 GAIIx	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_ENST00000532434.1_Missense_Mutation_p.T218S|NELL1_ENST00000298925.5_Missense_Mutation_p.T246S|NELL1_ENST00000325319.5_Missense_Mutation_p.T161S	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	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	20	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29911272	29911272	+	Missense_Mutation	SNP	T	T	G	rs76185201	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29911272T>G	ENST00000396634.1	+	5	912	c.571T>G	c.(571-573)Tgg>Ggg	p.W191G	HLA-A_ENST00000376806.5_Missense_Mutation_p.W191G|HLA-A_ENST00000376802.2_Missense_Mutation_p.W191G|HLA-A_ENST00000376809.5_Missense_Mutation_p.W191G			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	191	Alpha-2.		EW -> DG (in allele A*31:05).		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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GTGCGTGGAGTGGCTCCGCAG	0.677									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	1062	0.212061	0.1672	0.2075	5008	,	,		13907	0.2173		0.2058	False		,,,				2504	0.2771				p.W191G		Atlas-SNP	.											HLA-A,colon,carcinoma,0,1	HLA-A	89	1	0			c.T571G						PASS	.						49.0	39.0	43.0					6																	29911272		1510	2705	4215	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTGGAGTGGCTCC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.571T>G	6.37:g.29911272T>G	ENSP00000379873:p.Trp191Gly	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	418	0.19139194139194138	56	0.11382113821138211	77	0.212707182320442	139	0.243006993006993	146	0.19261213720316622	.	8.499	0.863893	0.17250	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00014	9.21;9.21;9.21;9.21	3.78	-2.67	0.06059	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	2.778300	0.01729	U	0.028724	T	0.00039	0.0001	M	0.83483	2.645	0.80722	P	0.0	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.001;0.0;0.001;0.001	T	0.37979	-0.9682	9	0.59425	D	0.04	.	4.7021	0.12832	0.0:0.188:0.3051:0.5069	rs3098019;rs9260161;rs41558617;rs52818888	70;191;191;191;191;191;191	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	G	191	ENSP00000379873:W191G;ENSP00000366002:W191G;ENSP00000366005:W191G;ENSP00000365998:W191G	ENSP00000365998:W191G	W	+	1	0	HLA-A	30019251	0.737000	0.28175	0.000000	0.03702	0.112000	0.19704	0.741000	0.26202	-0.555000	0.06142	0.397000	0.26171	TGG	A|0.001;G|0.178;T|0.821	0.178	strong		0.677	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SLC16A13	201232	hgsc.bcm.edu	37	17	6942111	6942111	+	Silent	SNP	G	G	T	rs33979567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6942111G>T	ENST00000308027.6	+	3	1292	c.984G>T	c.(982-984)gtG>gtT	p.V328V		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	328						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CCTTCTCCGTGCTGCCTGAAC	0.602													G|||	986	0.196885	0.3086	0.1643	5008	,	,		17805	0.0615		0.2068	False		,,,				2504	0.1984				p.V328V		Atlas-SNP	.											SLC16A13,colon,carcinoma,0,1	SLC16A13	28	1	0			c.G984T						PASS	.	G		1273,3133	421.3+/-339.3	177,919,1107	73.0	81.0	78.0		984	-2.0	0.9	17	dbSNP_126	78	1845,6755	320.3+/-314.5	206,1433,2661	no	coding-synonymous	SLC16A13	NM_201566.2		383,2352,3768	TT,TG,GG		21.4535,28.8924,23.9736		328/427	6942111	3118,9888	2203	4300	6503	SO:0001819	synonymous_variant	201232	exon3			CTCCGTGCTGCCT	BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"""Solute carriers"""	31037	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 13"""		"""solute carrier family 16 (monocarboxylic acid transporters), member 13"""				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.984G>T	17.37:g.6942111G>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_201566	A3KMG3|A5PKU5|Q2VP92	Silent	SNP	ENST00000308027.6	37	CCDS11085.1																																																																																			G|0.773;T|0.227	0.227	strong		0.602	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2		
SLC38A8	146167	hgsc.bcm.edu	37	16	84070500	84070500	+	Silent	SNP	C	C	G	rs1317524	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84070500C>G	ENST00000299709.3	-	2	194	c.195G>C	c.(193-195)tcG>tcC	p.S65S		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	65					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GGAAGACCAACGAGACCTGCG	0.657													G|||	2209	0.441094	0.5416	0.3646	5008	,	,		11922	0.5863		0.33	False		,,,				2504	0.3241				p.S65S		Atlas-SNP	.											.	SLC38A8	60	.	0			c.G195C						PASS	.	G		2096,2304	585.5+/-386.3	484,1128,588	47.0	40.0	42.0		195	2.0	1.0	16	dbSNP_88	42	2718,5882	667.3+/-402.5	448,1822,2030	no	coding-synonymous	SLC38A8	NM_001080442.1		932,2950,2618	GG,GC,CC		31.6047,47.6364,37.0308		65/436	84070500	4814,8186	2200	4300	6500	SO:0001819	synonymous_variant	146167	exon2			GACCAACGAGACC		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.195G>C	16.37:g.84070500C>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_001080442		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																			C|0.617;G|0.383	0.383	strong		0.657	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629936	32629936	+	Missense_Mutation	SNP	C	C	T	rs1049107	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32629936C>T	ENST00000399082.3	-	2	243	c.199G>A	c.(199-201)Ggc>Agc	p.G67S	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.G157S|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.G157S|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.G157S|HLA-DQB1-AS1_ENST00000419852.1_RNA|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.G157S			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	157	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TTGATCTGGCCTGGATAGAAA	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1048	0.209265	0.2216	0.1484	5008	,	,		12445	0.2431		0.1958	False		,,,				2504	0.2147				p.G157S	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G469A						PASS	.	C	SER/GLY	838,3180		119,600,1290	30.0	29.0	29.0		469	-1.2	0.1	6	dbSNP_86	29	1469,6921		227,1015,2953	no	missense	HLA-DQB1	NM_002123.4	56	346,1615,4243	TT,TC,CC		17.5089,20.8561,18.5928	benign	157/262	32629936	2307,10101	2009	4195	6204	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCTGGCCTGGATA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.199G>A	6.37:g.32629936C>T	ENSP00000382032:p.Gly67Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		450	0.20604395604395603	119	0.241869918699187	70	0.19337016574585636	90	0.15734265734265734	171	0.22559366754617413	.	5.815	0.334684	0.11013	0.208561	0.175089	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.02737	4.18;4.18;4.18;4.18;4.18	4.52	-1.24	0.09435	.	1.197420	0.06155	N	0.674887	T	0.00666	0.0022	N	0.10664	0.02	0.80722	P	0.0	B;B;B;B	0.13145	0.006;0.003;0.003;0.007	B;B;B;B	0.27887	0.05;0.05;0.05;0.084	T	0.49643	-0.8918	9	0.72032	D	0.01	.	6.026	0.19656	0.0:0.4008:0.1358:0.4634	rs1049107;rs16870483	157;122;157;157	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	S	67;157;157;157;157;93	ENSP00000382032:G67S;ENSP00000382029:G157S;ENSP00000364080:G157S;ENSP00000407332:G157S;ENSP00000382034:G157S	ENSP00000364080:G157S	G	-	1	0	HLA-DQB1	32737914	0.000000	0.05858	0.059000	0.19551	0.264000	0.26372	-0.490000	0.06482	-0.179000	0.10654	0.313000	0.20887	GGC	C|0.812;T|0.188	0.188	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
HLX	3142	hgsc.bcm.edu	37	1	221053545	221053545	+	Missense_Mutation	SNP	T	T	C	rs12141189	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:221053545T>C	ENST00000366903.6	+	1	1847	c.346T>C	c.(346-348)Tca>Cca	p.S116P	HLA-AS1_ENST00000552026.1_RNA|HLX_ENST00000549319.1_5'Flank	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	116	Pro-rich.		S -> P (in dbSNP:rs12141189). {ECO:0000269|PubMed:7806220}.		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)			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)		GTCTCCGCTCTCAGCCGCCTA	0.706													T|||	1056	0.210863	0.171	0.2767	5008	,	,		10735	0.2252		0.2505	False		,,,				2504	0.1626				p.S116P		Atlas-SNP	.											HLX,NS,carcinoma,0,1	HLX	67	1	0			c.T346C						scavenged	.	T	PRO/SER	846,3544		97,652,1446	13.0	18.0	16.0		346	3.4	1.0	1	dbSNP_120	16	1904,6676		215,1474,2601	no	missense	HLX	NM_021958.3	74	312,2126,4047	CC,CT,TT		22.1911,19.2711,21.2028	probably-damaging	116/489	221053545	2750,10220	2195	4290	6485	SO:0001583	missense	3142	exon1			CCGCTCTCAGCCG	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.346T>C	1.37:g.221053545T>C	ENSP00000355870:p.Ser116Pro	Somatic	67	5	0.0746269		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	511	0.23397435897435898	87	0.17682926829268292	104	0.287292817679558	124	0.21678321678321677	196	0.25857519788918204	T	20.7	4.040183	0.75732	0.192711	0.221911	ENSG00000136630	ENST00000366903	T	0.34472	1.36	4.57	3.44	0.39384	.	0.000000	0.39083	N	0.001465	T	0.00012	0.0000	N	0.11560	0.145	0.09310	P	1.0	B	0.20780	0.048	B	0.18871	0.023	T	0.40251	-0.9573	9	0.26408	T	0.33	-6.9827	7.6547	0.28369	0.0:0.1681:0.0:0.8319	rs12141189;rs12141189	116	Q14774	HLX_HUMAN	P	116	ENSP00000355870:S116P	ENSP00000355870:S116P	S	+	1	0	HLX	219120168	0.713000	0.27926	0.991000	0.47740	0.943000	0.58893	1.154000	0.31688	0.894000	0.36317	0.533000	0.62120	TCA	T|0.782;C|0.218	0.218	strong		0.706	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
MUC5B	727897	hgsc.bcm.edu	37	11	1272800	1272800	+	Missense_Mutation	SNP	C	C	T	rs55693520	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1272800C>T	ENST00000529681.1	+	31	14748	c.14690C>T	c.(14689-14691)tCg>tTg	p.S4897L	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S4900L	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4897	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)		GTTCCCAGCTCGTCCACCGTG	0.652													C|||	144	0.028754	0.0038	0.0346	5008	,	,		18033	0.002		0.0378	False		,,,				2504	0.0767				p.S4897L		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C14690T						PASS	.	C	LEU/SER	36,4284		0,36,2124	42.0	55.0	51.0		14690	0.6	0.0	11	dbSNP_129	51	288,8198		5,278,3960	yes	missense	MUC5B	NM_002458.2	145	5,314,6084	TT,TC,CC		3.3938,0.8333,2.5301	benign	4897/5763	1272800	324,12482	2160	4243	6403	SO:0001583	missense	727897	exon31			CCAGCTCGTCCAC	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.14690C>T	11.37:g.1272800C>T	ENSP00000436812:p.Ser4897Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	48	0.02197802197802198	1	0.0020325203252032522	16	0.04419889502762431	1	0.0017482517482517483	30	0.0395778364116095	C	5.836	0.338504	0.11069	0.008333	0.033938	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.19105	2.17;2.35	1.82	0.628	0.17681	.	.	.	.	.	T	0.03477	0.0100	L	0.39898	1.24	0.09310	N	1	B;B	0.21452	0.056;0.056	B;B	0.09377	0.002;0.004	T	0.19063	-1.0317	9	0.87932	D	0	.	6.9468	0.24522	0.0:0.7911:0.0:0.2089	rs55693520;rs61744629	5219;4900	A7Y9J9;E9PBJ0	.;.	L	4897;4900;4841;4596	ENSP00000436812:S4897L;ENSP00000415793:S4900L	ENSP00000343037:S4841L	S	+	2	0	MUC5B	1229376	0.010000	0.17322	0.000000	0.03702	0.002000	0.02628	0.004000	0.13106	0.198000	0.20407	0.485000	0.47835	TCG	C|0.974;T|0.026	0.026	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
DDR1	780	hgsc.bcm.edu	37	6	30864829	30864829	+	Silent	SNP	T	T	C	rs1049623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30864829T>C	ENST00000324771.8	+	16	2456	c.1908T>C	c.(1906-1908)gtT>gtC	p.V636V	DDR1_ENST00000376570.4_Silent_p.V599V|DDR1_ENST00000508312.1_Silent_p.V617V|DDR1_ENST00000361741.4_Silent_p.V303V|DDR1_ENST00000376569.3_Silent_p.V599V|DDR1_ENST00000454612.2_Silent_p.V599V|DDR1_ENST00000418800.2_Silent_p.V599V|DDR1_ENST00000376568.3_Silent_p.V636V|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000513240.1_Silent_p.V636V|DDR1_ENST00000376567.2_Silent_p.V599V|DDR1_ENST00000452441.1_Silent_p.V636V|DDR1_ENST00000376575.3_Silent_p.V636V			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	636	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	AAGATCTGGTTAGTCTTGATT	0.512													C|||	2683	0.535743	0.4531	0.5245	5008	,	,		14894	0.6667		0.3847	False		,,,				2504	0.6759				p.V636V		Atlas-SNP	.											DDR1_ENST00000376575,NS,adenoma,0,3	DDR1	213	3	0			c.T1908C	GRCh37	CM076148	DDR1	M	rs1049623	PASS	.	C	,,,,,	2008,2398	615.9+/-392.7	473,1062,668	203.0	181.0	189.0		,1470,1851,1797,1908,1908	5.3	1.0	6	dbSNP_86	189	3287,5313	648.3+/-400.5	620,2047,1633	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	,,,,,	1093,3109,2301	CC,CT,TT		38.2209,45.5742,40.712	,,,,,	,490/768,617/895,599/877,636/914,636/920	30864829	5295,7711	2203	4300	6503	SO:0001819	synonymous_variant	780	exon13			TCTGGTTAGTCTT	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1908T>C	6.37:g.30864829T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	166	129	0.777108	NM_013994	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Silent	SNP	ENST00000324771.8	37	CCDS34385.1	1109	0.5077838827838828	252	0.5121951219512195	189	0.5220994475138122	349	0.6101398601398601	319	0.420844327176781	C	10.41	1.343892	0.24339	0.455742	0.382209	ENSG00000204580	ENST00000514434	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999912	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.79	0.29114	0.0:0.7501:0.1626:0.0873	rs1049623;rs1264316;rs2228636;rs3173380;rs17413087;rs58133601;rs1049623	.	.	.	Q	128	.	.	X	+	1	0	DDR1	30972808	0.012000	0.17670	1.000000	0.80357	0.871000	0.50021	0.586000	0.23894	1.250000	0.43966	-0.215000	0.12644	TAG	T|0.539;C|0.461	0.461	strong		0.512	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
FBN3	84467	hgsc.bcm.edu	37	19	8176569	8176569	+	Silent	SNP	G	G	A	rs35306870	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8176569G>A	ENST00000600128.1	-	32	4461	c.4047C>T	c.(4045-4047)tgC>tgT	p.C1349C	FBN3_ENST00000601739.1_Silent_p.C1349C|FBN3_ENST00000270509.2_Silent_p.C1349C			Q75N90	FBN3_HUMAN	fibrillin 3	1349	EGF-like 20; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						AGCCCTGGCGGCAGGTGCAGC	0.632													G|||	1287	0.256989	0.1331	0.3876	5008	,	,		10551	0.4226		0.2346	False		,,,				2504	0.184				p.C1349C		Atlas-SNP	.											FBN3,colon,carcinoma,0,1	FBN3	300	1	0			c.C4047T						PASS	.	G		755,3651	297.6+/-284.8	59,637,1507	32.0	32.0	32.0		4047	1.6	0.3	19	dbSNP_126	32	2078,6522	351.7+/-328.4	242,1594,2464	no	coding-synonymous	FBN3	NM_032447.3		301,2231,3971	AA,AG,GG		24.1628,17.1357,21.7823		1349/2810	8176569	2833,10173	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon31			CTGGCGGCAGGTG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.4047C>T	19.37:g.8176569G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.761;A|0.239	0.239	strong		0.632	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
CHN2	1124	hgsc.bcm.edu	37	7	29440195	29440195	+	Silent	SNP	C	C	T	rs34045356	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:29440195C>T	ENST00000222792.6	+	6	857	c.327C>T	c.(325-327)caC>caT	p.H109H	CHN2_ENST00000435288.2_Intron|CHN2_ENST00000539389.1_Intron|CHN2_ENST00000495789.2_Silent_p.H122H|CHN2_ENST00000546235.1_Silent_p.H94H|CHN2_ENST00000539406.1_Silent_p.H184H	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	109	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						GGCTCTTCCACGACGGGAAAC	0.448													C|||	270	0.0539137	0.0938	0.0346	5008	,	,		20550	0.0099		0.0765	False		,,,				2504	0.0358				p.H109H	Ovarian(1;44 48 13232 18918 31480)	Atlas-SNP	.											.	CHN2	98	.	0			c.C327T						PASS	.	C		411,3995	201.1+/-224.2	10,391,1802	98.0	93.0	95.0		327	-12.1	0.1	7	dbSNP_126	95	518,8082	147.3+/-202.7	15,488,3797	no	coding-synonymous	CHN2	NM_004067.2		25,879,5599	TT,TC,CC		6.0233,9.3282,7.1429		109/469	29440195	929,12077	2203	4300	6503	SO:0001819	synonymous_variant	1124	exon6			CTTCCACGACGGG	L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"""Rho GTPase activating proteins"", ""SH2 domain containing"""	1944	protein-coding gene	gene with protein product	"""beta chimerin"", ""chimaerin 2"""	602857	"""chimerin (chimaerin) 2"""			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.327C>T	7.37:g.29440195C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	44	34	0.772727	NM_004067	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Silent	SNP	ENST00000222792.6	37	CCDS5420.1																																																																																			C|0.932;T|0.068	0.068	strong		0.448	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136333487G>A	ENST00000316948.4	+	5	508				CACFD1_ENST00000542192.1_Missense_Mutation_p.A110T|SLC2A6_ENST00000485978.1_5'Flank|CACFD1_ENST00000291722.7_Intron|CACFD1_ENST00000540581.1_Missense_Mutation_p.A152T	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		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	6	5	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	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100814570	100814570	+	Silent	SNP	A	A	G	rs543146	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:100814570A>G	ENST00000298815.8	+	10	1017	c.1014A>G	c.(1012-1014)cgA>cgG	p.R338R	ARHGAP42_ENST00000524892.2_Silent_p.R304R	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	338	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGACAAACGATTCTGCTTTG	0.328													A|||	2058	0.410942	0.1362	0.4308	5008	,	,		17776	0.7312		0.2565	False		,,,				2504	0.5971				p.R338R		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A1014G						PASS	.	A		276,1108		24,228,440	120.0	97.0	104.0		1014	-1.1	1.0	11	dbSNP_83	104	911,2271		127,657,807	no	coding-synonymous	ARHGAP42	NM_152432.2		151,885,1247	GG,GA,AA		28.6298,19.9422,25.9965		338/875	100814570	1187,3379	692	1591	2283	SO:0001819	synonymous_variant	143872	exon10			CAAACGATTCTGC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.1014A>G	11.37:g.100814570A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	65	0.970149	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.643;G|0.357	0.357	strong		0.328	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
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 GAIIx	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		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	56	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		
FRAS1	80144	hgsc.bcm.edu	37	4	79437155	79437155	+	Silent	SNP	C	C	T	rs3749487	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:79437155C>T	ENST00000264895.6	+	66	10817	c.10377C>T	c.(10375-10377)acC>acT	p.T3459T		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3455					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.T3459T(2)|p.T3460T(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GCTCTGTAACCGCTGACTTCC	0.507													C|||	884	0.176518	0.177	0.1398	5008	,	,		18849	0.2242		0.2058	False		,,,				2504	0.1227				p.T3459T		Atlas-SNP	.											FRAS1_ENST00000264895,NS,carcinoma,0,2	FRAS1	779	2	3	Substitution - coding silent(3)	prostate(3)	c.C10377T						PASS	.	C		762,3516		66,630,1443	69.0	74.0	72.0		10377	-4.6	0.7	4	dbSNP_107	72	1551,6979		140,1271,2854	no	coding-synonymous	FRAS1	NM_025074.6		206,1901,4297	TT,TC,CC		18.1829,17.8121,18.059		3459/4013	79437155	2313,10495	2139	4265	6404	SO:0001819	synonymous_variant	80144	exon66			TGTAACCGCTGAC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.10377C>T	4.37:g.79437155C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	432	0.1978021978021978	96	0.1951219512195122	58	0.16022099447513813	128	0.22377622377622378	150	0.19788918205804748	C	1.309	-0.602724	0.03744	0.178121	0.181829	ENSG00000138759	ENST00000512123	.	.	.	5.97	-4.61	0.03380	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33929	-0.9849	3	.	.	.	.	2.7957	0.05400	0.1827:0.3609:0.0961:0.3603	rs3749487;rs57228815	.	.	.	C	1688	.	.	R	+	1	0	FRAS1	79656179	0.002000	0.14202	0.743000	0.31040	0.168000	0.22595	-1.645000	0.02000	-0.358000	0.08162	-0.606000	0.04082	CGC	C|0.803;T|0.197	0.197	strong		0.507	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PSD4	23550	hgsc.bcm.edu	37	2	113940839	113940839	+	Missense_Mutation	SNP	G	G	C	rs4849167	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:113940839G>C	ENST00000245796.6	+	2	1001	c.806G>C	c.(805-807)gGg>gCg	p.G269A	PSD4_ENST00000441564.3_Missense_Mutation_p.G269A	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	269			G -> A (in dbSNP:rs4849167). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.		neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTTTCCTGGGGGGCTTCAGAC	0.592													G|||	2589	0.516973	0.5272	0.5	5008	,	,		18291	0.6012		0.4423	False		,,,				2504	0.5051				p.G269A		Atlas-SNP	.											.	PSD4	74	.	0			c.G806C						PASS	.	G	ALA/GLY	2223,2183	591.5+/-387.6	561,1101,541	71.0	73.0	73.0		806	0.9	0.1	2	dbSNP_111	73	3507,5093	512.2+/-377.9	730,2047,1523	yes	missense	PSD4	NM_012455.2	60	1291,3148,2064	CC,CG,GG		40.7791,49.5461,44.0566	possibly-damaging	269/1057	113940839	5730,7276	2203	4300	6503	SO:0001583	missense	23550	exon2			CCTGGGGGGCTTC	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.806G>C	2.37:g.113940839G>C	ENSP00000245796:p.Gly269Ala	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	37	CCDS33276.1	1171	0.5361721611721612	283	0.5752032520325203	185	0.511049723756906	353	0.6171328671328671	350	0.46174142480211083	G	15.48	2.844789	0.51164	0.504539	0.407791	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.12255	2.76;2.7	5.83	0.861	0.19048	.	0.493472	0.20113	N	0.098974	T	0.00012	0.0000	L	0.27053	0.805	0.36052	P	0.159169	P;P	0.41524	0.753;0.639	B;B	0.37091	0.241;0.122	T	0.25082	-1.0142	8	.	.	.	.	5.1622	0.15068	0.3159:0.1389:0.5452:0.0	rs4849167;rs17846131;rs17859138;rs4849167	269;269	Q8NDX1-2;Q8NDX1	.;PSD4_HUMAN	A	269	ENSP00000245796:G269A;ENSP00000413997:G269A	.	G	+	2	0	PSD4	113657310	0.007000	0.16637	0.054000	0.19295	0.733000	0.41908	-0.260000	0.08708	-0.120000	0.11809	0.655000	0.94253	GGG	G|0.507;C|0.493	0.493	strong		0.592	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
BSND	7809	hgsc.bcm.edu	37	1	55474262	55474262	+	Silent	SNP	G	G	A	rs33938617	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:55474262G>A	ENST00000371265.4	+	4	1178	c.924G>A	c.(922-924)ccG>ccA	p.P308P		NM_057176.2	NP_476517.1	Q8WZ55	BSND_HUMAN	barttin CLCNK-type chloride channel accessory beta subunit	308					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	chloride channel activity (GO:0005254)|chloride channel regulator activity (GO:0017081)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17						ACCTCCTCCCGGACAAGGAGC	0.577													g|||	581	0.116014	0.211	0.098	5008	,	,		18850	0.001		0.1859	False		,,,				2504	0.047				p.P308P	Ovarian(191;1657 2078 22894 42033 48899)	Atlas-SNP	.											.	BSND	36	.	0			c.G924A						PASS	.			829,3577	326.4+/-299.6	87,655,1461	86.0	84.0	85.0		924	-9.2	0.0	1	dbSNP_126	85	1768,6832	319.9+/-314.4	182,1404,2714	no	coding-synonymous	BSND	NM_057176.2		269,2059,4175	AA,AG,GG		20.5581,18.8153,19.9677		308/321	55474262	2597,10409	2203	4300	6503	SO:0001819	synonymous_variant	7809	exon4			CCTCCCGGACAAG	AY034632	CCDS602.1	1p32.3	2014-06-17	2014-06-17		ENSG00000162399	ENSG00000162399			16512	protein-coding gene	gene with protein product		606412	"""deafness, autosomal recessive 73"", ""Bartter syndrome, infantile, with sensorineural deafness (Barttin)"""	DFNB73		11687798, 11734858, 19646679	Standard	NM_057176		Approved	BART	uc001cye.3	Q8WZ55	OTTHUMG00000008112	ENST00000371265.4:c.924G>A	1.37:g.55474262G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_057176	Q6NT28	Silent	SNP	ENST00000371265.4	37	CCDS602.1																																																																																			G|0.824;A|0.176	0.176	strong		0.577	BSND-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022213.4	NM_057176	
MSH4	4438	hgsc.bcm.edu	37	1	76269460	76269460	+	Missense_Mutation	SNP	G	G	A	rs5745325	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:76269460G>A	ENST00000263187.3	+	2	393	c.289G>A	c.(289-291)Gca>Aca	p.A97T		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	97			A -> T (in dbSNP:rs5745325). {ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						AAACACAGTTGCATCAAATTT	0.323								Mismatch excision repair (MMR)					G|||	1066	0.212859	0.3026	0.2032	5008	,	,		14851	0.0228		0.3091	False		,,,				2504	0.1953				p.A97T		Atlas-SNP	.											.	MSH4	147	.	0			c.G289A						PASS	.	G	THR/ALA	1324,3082	433.7+/-343.7	176,972,1055	71.0	73.0	72.0		289	0.6	0.2	1	dbSNP_114	72	2572,6028	417.0+/-352.3	382,1808,2110	yes	missense	MSH4	NM_002440.3	58	558,2780,3165	AA,AG,GG		29.907,30.0499,29.9554	benign	97/937	76269460	3896,9110	2203	4300	6503	SO:0001583	missense	4438	exon2			ACAGTTGCATCAA	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"""mutS (E. coli) homolog 4"", ""mutS homolog 4 (E. coli)"""			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.289G>A	1.37:g.76269460G>A	ENSP00000263187:p.Ala97Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	106	38	0.358491	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	467	0.21382783882783882	136	0.2764227642276423	75	0.20718232044198895	17	0.02972027972027972	239	0.3153034300791557	G	6.675	0.493057	0.12702	0.300499	0.29907	ENSG00000057468	ENST00000263187	D	0.87256	-2.23	4.73	0.632	0.17705	.	0.895901	0.09711	N	0.765669	T	0.54398	0.1856	L	0.32530	0.975	0.58432	P	8.000000000008E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.14699	-1.0463	9	0.02654	T	1	0.7272	5.9083	0.19014	0.4471:0.132:0.4209:0.0	rs5745325;rs17594581;rs52829653;rs60345283;rs5745325	97	O15457	MSH4_HUMAN	T	97	ENSP00000263187:A97T	ENSP00000263187:A97T	A	+	1	0	MSH4	76042048	0.001000	0.12720	0.190000	0.23270	0.138000	0.21146	0.652000	0.24888	-0.148000	0.11234	-0.315000	0.08773	GCA	G|0.737;A|0.263	0.263	strong		0.323	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	
SDCCAG3	10807	hgsc.bcm.edu	37	9	139299637	139299637	+	Missense_Mutation	SNP	C	C	T	rs3812577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139299637C>T	ENST00000357365.3	-	7	1040	c.911G>A	c.(910-912)cGg>cAg	p.R304Q	SDCCAG3_ENST00000461693.1_5'UTR|SDCCAG3_ENST00000371725.3_Missense_Mutation_p.R231Q|SDCCAG3_ENST00000298537.7_Missense_Mutation_p.R281Q	NM_001039707.1	NP_001034796.1	Q96C92	SDCG3_HUMAN	serologically defined colon cancer antigen 3	304			R -> Q (in dbSNP:rs3812577). {ECO:0000269|Ref.1}.			cytoplasm (GO:0005737)				NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)	16		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.18e-06)|Epithelial(140;9.31e-06)		TTCTAACTTCCGCTCAAGCGT	0.463													C|||	548	0.109425	0.0098	0.2349	5008	,	,		19347	0.1359		0.1093	False		,,,				2504	0.1278				p.R304Q		Atlas-SNP	.											.	SDCCAG3	41	.	0			c.G911A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	95,3699		1,93,1803	116.0	110.0	112.0		911,692,842	4.5	1.0	9	dbSNP_107	112	1032,7206		68,896,3155	yes	missense,missense,missense	SDCCAG3	NM_001039707.1,NM_001039708.1,NM_006643.3	43,43,43	69,989,4958	TT,TC,CC		12.5273,2.504,9.3667	probably-damaging,probably-damaging,probably-damaging	304/436,231/363,281/413	139299637	1127,10905	1897	4119	6016	SO:0001583	missense	10807	exon7			AACTTCCGCTCAA	AF039688	CCDS6999.2, CCDS43903.1, CCDS43904.1	9q34.3	2010-10-27			ENSG00000165689	ENSG00000165689			10667	protein-coding gene	gene with protein product						9610721	Standard	XM_005266050		Approved	NY-CO-3	uc004chi.3	Q96C92	OTTHUMG00000020928	ENST00000357365.3:c.911G>A	9.37:g.139299637C>T	ENSP00000349929:p.Arg304Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	26	0.346667	NM_001039707	A6NCP1|O60525|Q5SXN1|Q5SXN2|Q5SXN3|Q5SXN4|Q5SXN8|Q6V704|Q9NVY5	Missense_Mutation	SNP	ENST00000357365.3	37	CCDS43904.1	241|241	0.11034798534798534|0.11034798534798534	6|6	0.012195121951219513|0.012195121951219513	68|68	0.1878453038674033|0.1878453038674033	73|73	0.12762237762237763|0.12762237762237763	94|94	0.12401055408970976|0.12401055408970976	C|C	11.89|11.89	1.772521|1.772521	0.31411|0.31411	0.02504|0.02504	0.125273|0.125273	ENSG00000165689|ENSG00000165689	ENST00000417512|ENST00000357365;ENST00000298537;ENST00000371725	.|T;T;T	.|0.78595	.|-1.19;-1.19;-1.19	4.53|4.53	4.53|4.53	0.55603|0.55603	.|.	.|0.192442	.|0.43919	.|D	.|0.000513	T|T	0.00328|0.00328	0.0010|0.0010	L|L	0.58810|0.58810	1.83|1.83	0.28814|0.28814	P|P	0.89807|0.89807	.|P;D;D	.|0.59767	.|0.956;0.986;0.986	.|B;P;P	.|0.47941	.|0.408;0.562;0.562	T|T	0.09684|0.09684	-1.0663|-1.0663	4|9	.|0.37606	.|T	.|0.19	-15.0759|-15.0759	12.2017|12.2017	0.54331|0.54331	0.0:0.9132:0.0:0.0868|0.0:0.9132:0.0:0.0868	rs3812577;rs52833688;rs57736081;rs3812577|rs3812577;rs52833688;rs57736081;rs3812577	.|231;281;304	.|Q96C92-4;Q96C92-2;Q96C92	.|.;.;SDCG3_HUMAN	R|Q	45|304;281;231	.|ENSP00000349929:R304Q;ENSP00000298537:R281Q;ENSP00000360790:R231Q	.|ENSP00000298537:R281Q	G|R	-|-	1|2	0|0	SDCCAG3|SDCCAG3	138419458|138419458	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.291000|0.291000	0.27294|0.27294	1.174000|1.174000	0.31932|0.31932	2.218000|2.218000	0.71995|0.71995	0.563000|0.563000	0.77884|0.77884	GGA|CGG	C|0.886;T|0.114	0.114	strong		0.463	SDCCAG3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055060.2	NM_006643	
RYR1	6261	hgsc.bcm.edu	37	19	38995510	38995510	+	Silent	SNP	T	T	C	rs2915951	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38995510T>C	ENST00000359596.3	+	51	8190	c.8190T>C	c.(8188-8190)gaT>gaC	p.D2730D	RYR1_ENST00000360985.3_Silent_p.D2730D|RYR1_ENST00000355481.4_Silent_p.D2730D			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2730	6 X approximate repeats.		D -> G (in MHS1). {ECO:0000269|PubMed:19191329}.		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.D2730D(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCACAGTGGATGCTGAAGGCA	0.597													C|||	2089	0.417133	0.5182	0.3703	5008	,	,		16497	0.3532		0.3072	False		,,,				2504	0.4928				p.D2730D		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	1	1	Substitution - coding silent(1)	stomach(1)	c.T8190C						PASS	.	C	,	2020,2386	612.1+/-391.9	460,1100,643	61.0	57.0	58.0		8190,8190	-8.4	0.1	19	dbSNP_101	58	2189,6411	712.0+/-405.9	298,1593,2409	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	758,2693,3052	CC,CT,TT		25.4535,45.8466,32.362	,	2730/5039,2730/5034	38995510	4209,8797	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon51			AGTGGATGCTGAA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.8190T>C	19.37:g.38995510T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			T|0.653;C|0.347	0.347	strong		0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
FCGR2B	2213	hgsc.bcm.edu	37	1	161642985	161642985	+	Silent	SNP	G	G	A	rs182968886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161642985G>A	ENST00000358671.5	+	4	693	c.612G>A	c.(610-612)ctG>ctA	p.L204L	FCGR2B_ENST00000403078.3_Silent_p.L204L|FCGR2B_ENST00000367961.4_Silent_p.L197L|FCGR2B_ENST00000236937.9_Silent_p.L204L|FCGR2B_ENST00000367962.4_Silent_p.L204L|FCGR2B_ENST00000428605.2_Silent_p.L204L|RP11-25K21.1_ENST00000453111.1_RNA|FCGR2B_ENST00000367960.5_Silent_p.L197L	NM_001002275.2|NM_004001.4	NP_001002275.1|NP_003992.3	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor (CD32)	204	Ig-like C2-type 2.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)						all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Antithymocyte globulin(DB00098)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GCTACACGCTGTACTCATCCA	0.517			T	?	ALL								G|||	552	0.110224	0.1694	0.0821	5008	,	,		21322	0.006		0.0944	False		,,,				2504	0.1738				p.L204L		Atlas-SNP	.		Dom	yes		1	1q23	2213	"""Fc fragment of IgG, low affinity IIb, receptor for (CD32)"""		L	.	FCGR2B	33	.	0			c.G612A						PASS	.	G	,,,,	717,3669		101,515,1577	42.0	43.0	43.0		609,612,609,591,612	-6.2	0.0	1		43	1003,7593		66,871,3361	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCGR2B	NM_001002273.2,NM_001002274.2,NM_001002275.2,NM_001190828.1,NM_004001.4	,,,,	167,1386,4938	AA,AG,GG		11.6682,16.3475,13.2491	,,,,	203/291,204/292,203/310,197/304,204/311	161642985	1720,11262	2193	4298	6491	SO:0001819	synonymous_variant	2213	exon4			CACGCTGTACTCA	BC031992	CCDS30924.1, CCDS30925.1, CCDS53414.1	1q23	2013-01-11	2005-02-02		ENSG00000072694	ENSG00000072694		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3618	protein-coding gene	gene with protein product		604590	"""Fc fragment of IgG, low affinity IIb, receptor for (CD32)"""	FCG2, FCGR2		2139735	Standard	NM_004001		Approved	CD32, CD32B	uc001gaz.2	P31994	OTTHUMG00000034470	ENST00000358671.5:c.612G>A	1.37:g.161642985G>A		Somatic	528	1	0.00189394		WXS	Illumina HiSeq	Phase_I	322	217	0.673913	NM_001002274	A6H8N3|O95649|Q53X85|Q5VXA9|Q8NIA1	Silent	SNP	ENST00000358671.5	37	CCDS30924.1																																																																																			G|0.895;A|0.105	0.105	strong		0.517	FCGR2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083337.4	NM_004001	
THAP10	56906	hgsc.bcm.edu	37	15	71184278	71184278	+	Silent	SNP	G	G	T	rs2959174	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:71184278G>T	ENST00000249861.4	-	1	846	c.334C>A	c.(334-336)Cga>Aga	p.R112R	LRRC49_ENST00000260382.5_5'Flank|LRRC49_ENST00000544974.2_Intron|LRRC49_ENST00000560369.1_5'Flank|LRRC49_ENST00000443425.2_5'Flank	NM_020147.3	NP_064532.1	Q9P2Z0	THA10_HUMAN	THAP domain containing 10	112							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|kidney(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						AGCTCTCCTCGCGTGTCCAGG	0.687													T|||	2750	0.549121	0.7731	0.2954	5008	,	,		14020	0.5823		0.4066	False		,,,				2504	0.5389				p.R112R		Atlas-SNP	.											.	THAP10	19	.	0			c.C334A						PASS	.	T		3117,1281	427.2+/-341.4	1113,891,195	33.0	34.0	34.0		334	-1.1	0.0	15	dbSNP_101	34	3501,5093	620.8+/-397.1	700,2101,1496	no	coding-synonymous	THAP10	NM_020147.3		1813,2992,1691	TT,TG,GG		40.7377,29.1269,49.061		112/258	71184278	6618,6374	2199	4297	6496	SO:0001819	synonymous_variant	56906	exon1			CTCCTCGCGTGTC	AL360202	CCDS10237.1	15q22.32	2013-01-25			ENSG00000129028	ENSG00000129028		"""THAP (C2CH-type zinc finger) domain containing"""	23193	protein-coding gene	gene with protein product		612538				12575992	Standard	NM_020147		Approved		uc002asv.3	Q9P2Z0	OTTHUMG00000133388	ENST00000249861.4:c.334C>A	15.37:g.71184278G>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_020147	B2R8R0	Silent	SNP	ENST00000249861.4	37	CCDS10237.1																																																																																			G|0.471;T|0.529	0.529	strong		0.687	THAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257242.2	NM_020147	
GPR37	2861	hgsc.bcm.edu	37	7	124404371	124404371	+	Silent	SNP	G	G	A	rs61744942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:124404371G>A	ENST00000303921.2	-	1	1310	c.660C>T	c.(658-660)gcC>gcT	p.A220A		NM_005302.3	NP_005293.1	O15354	GPR37_HUMAN	G protein-coupled receptor 37 (endothelin receptor type B-like)	220					dopamine biosynthetic process (GO:0042416)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotion involved in locomotory behavior (GO:0031987)|positive regulation of dopamine metabolic process (GO:0045964)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ubiquitin ligase complex (GO:0000151)	G-protein coupled receptor activity (GO:0004930)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|ubiquitin protein ligase binding (GO:0031625)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(11)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						ATCCATTCTGGGCCAGCGCCC	0.642													G|||	509	0.101637	0.2201	0.0591	5008	,	,		12246	0.0		0.0835	False		,,,				2504	0.0951				p.A220A		Atlas-SNP	.											GPR37,rectum,carcinoma,-1,1	GPR37	89	1	0			c.C660T						PASS	.	G		826,3580	320.7+/-296.8	67,692,1444	36.0	40.0	39.0		660	-3.0	1.0	7	dbSNP_129	39	711,7889	172.0+/-222.8	29,653,3618	no	coding-synonymous	GPR37	NM_005302.2		96,1345,5062	AA,AG,GG		8.2674,18.7472,11.8176		220/614	124404371	1537,11469	2203	4300	6503	SO:0001819	synonymous_variant	2861	exon1			ATTCTGGGCCAGC		CCDS5792.1	7q31	2012-08-21			ENSG00000170775	ENSG00000170775		"""GPCR / Class A : Orphans"""	4494	protein-coding gene	gene with protein product		602583				9339362	Standard	NM_005302		Approved	EDNRBL, hET(B)R-LP, PAELR	uc003vli.4	O15354	OTTHUMG00000157197	ENST00000303921.2:c.660C>T	7.37:g.124404371G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_005302	A4D0Y6|O00348|O14768|Q8TD39	Silent	SNP	ENST00000303921.2	37	CCDS5792.1																																																																																			G|0.889;A|0.111	0.111	strong		0.642	GPR37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347873.1	NM_005302	
QRICH2	84074	hgsc.bcm.edu	37	17	74289705	74289705	+	Missense_Mutation	SNP	A	A	G	rs6501880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74289705A>G	ENST00000262765.5	-	4	784	c.605T>C	c.(604-606)tTg>tCg	p.L202S		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	202			L -> S (in dbSNP:rs6501880).							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						GTCTCTGGCCAAGGGTAAGTC	0.522													G|||	2317	0.46266	0.6815	0.3084	5008	,	,		24481	0.5724		0.2753	False		,,,				2504	0.3558				p.L202S		Atlas-SNP	.											.	QRICH2	143	.	0			c.T605C						PASS	.	G	SER/LEU	2837,1569	489.0+/-361.4	920,997,286	132.0	101.0	111.0		605	-4.5	0.0	17	dbSNP_116	111	2486,6114	696.3+/-404.9	348,1790,2162	yes	missense	QRICH2	NM_032134.1	145	1268,2787,2448	GG,GA,AA		28.907,35.6105,40.9273	benign	202/1664	74289705	5323,7683	2203	4300	6503	SO:0001583	missense	84074	exon4			CTGGCCAAGGGTA	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.605T>C	17.37:g.74289705A>G	ENSP00000262765:p.Leu202Ser	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	383	179	0.467363	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	971	0.44459706959706957	337	0.6849593495934959	106	0.292817679558011	332	0.5804195804195804	196	0.25857519788918204	G	3.851	-0.031778	0.07543	0.643895	0.28907	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.17691	2.26	3.69	-4.53	0.03462	.	.	.	.	.	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.06405	0.001;0.002	T	0.35549	-0.9784	8	0.07813	T	0.8	.	7.1823	0.25780	0.6822:0.0:0.17:0.1478	rs6501880;rs60042941;rs6501880	202;202	B5MD94;Q9H0J4	.;QRIC2_HUMAN	S	202	ENSP00000262765:L202S	ENSP00000262765:L202S	L	-	2	0	QRICH2	71801300	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.980000	0.03770	-1.269000	0.02436	-1.945000	0.00491	TTG	A|0.564;G|0.436	0.436	strong		0.522	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
INPP5E	56623	hgsc.bcm.edu	37	9	139326304	139326304	+	Silent	SNP	G	G	A	rs10870188	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139326304G>A	ENST00000371712.3	-	7	1923	c.1521C>T	c.(1519-1521)caC>caT	p.H507H		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		TGAGCTGGTCGTGCTGCAGCA	0.701													g|||	608	0.121406	0.0151	0.2435	5008	,	,		8607	0.1429		0.1213	False		,,,				2504	0.1564				p.H507H		Atlas-SNP	.											INPP5E,NS,carcinoma,0,1	INPP5E	18	1	0			c.C1521T						PASS	.	G		168,4224		2,164,2030	24.0	24.0	24.0		1521	-10.2	0.0	9	dbSNP_120	24	1145,7439		72,1001,3219	no	coding-synonymous	INPP5E	NM_019892.4		74,1165,5249	AA,AG,GG		13.3388,3.8251,10.1187		507/645	139326304	1313,11663	2196	4292	6488	SO:0001819	synonymous_variant	56623	exon7			CTGGTCGTGCTGC	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1521C>T	9.37:g.139326304G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	104	61	0.586538	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			G|0.898;A|0.102	0.102	strong		0.701	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
HSD3B1	3283	hgsc.bcm.edu	37	1	120057158	120057158	+	Silent	SNP	C	C	T	rs6203	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:120057158C>T	ENST00000369413.3	+	4	1157	c.1012C>T	c.(1012-1014)Ctg>Ttg	p.L338L	HSD3B1_ENST00000235547.6_Silent_p.L340L|HSD3B1_ENST00000528909.1_Silent_p.L338L			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	338					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	TCAGCGAGATCTGGCGTATAA	0.512													C|||	1837	0.366813	0.0333	0.4813	5008	,	,		21293	0.6528		0.4254	False		,,,				2504	0.3814				p.L338L		Atlas-SNP	.											.	HSD3B1	53	.	0			c.C1012T	GRCh37	CM021275	HSD3B1	M	rs6203	PASS	.	C		457,3949	217.4+/-235.8	28,401,1774	88.0	77.0	81.0		1012	1.3	0.9	1	dbSNP_52	81	3730,4870	530.5+/-381.8	818,2094,1388	no	coding-synonymous	HSD3B1	NM_000862.2		846,2495,3162	TT,TC,CC		43.3721,10.3722,32.1928		338/374	120057158	4187,8819	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			CGAGATCTGGCGT	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.1012C>T	1.37:g.120057158C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			C|0.647;T|0.353	0.353	strong		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
APOB	338	hgsc.bcm.edu	37	2	21231524	21231524	+	Missense_Mutation	SNP	G	G	A	rs676210	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:21231524G>A	ENST00000233242.1	-	26	8343	c.8216C>T	c.(8215-8217)cCa>cTa	p.P2739L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2739			P -> L (in dbSNP:rs676210). {ECO:0000269|PubMed:22095935, ECO:0000269|PubMed:2216805, ECO:0000269|PubMed:9490296}.		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGGAATTCTGGTATGTGAAG	0.398													G|||	1834	0.366214	0.1241	0.2493	5008	,	,		21164	0.7192		0.2177	False		,,,				2504	0.5654				p.P2739L		Atlas-SNP	.											.	APOB	761	.	0			c.C8216T	GRCh37	CM980093	APOB	M	rs676210	PASS	.	G	LEU/PRO	694,3712	289.5+/-280.5	52,590,1561	185.0	186.0	186.0		8216	5.2	1.0	2	dbSNP_83	186	1862,6738	331.8+/-319.8	227,1408,2665	yes	missense	APOB	NM_000384.2	98	279,1998,4226	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	21.6512,15.7512,19.6525	probably-damaging	2739/4564	21231524	2556,10450	2203	4300	6503	SO:0001583	missense	338	exon26			AATTCTGGTATGT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8216C>T	2.37:g.21231524G>A	ENSP00000233242:p.Pro2739Leu	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	201	201	1	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	737	0.3374542124542125	77	0.1565040650406504	79	0.21823204419889503	406	0.7097902097902098	175	0.23087071240105542	G	24.9	4.580663	0.86748	0.157512	0.216512	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.01185	5.21	5.22	5.22	0.72569	.	0.000000	0.52532	D	0.000061	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.08597	-1.0714	9	0.87932	D	0	.	18.7715	0.91893	0.0:0.0:1.0:0.0	rs676210;rs17240903;rs52830519;rs60113879;rs676210	2739	P04114	APOB_HUMAN	L	2739	ENSP00000233242:P2739L	ENSP00000233242:P2739L	P	-	2	0	APOB	21085029	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	9.803000	0.99136	2.437000	0.82529	0.561000	0.74099	CCA	G|0.731;A|0.269	0.269	strong		0.398	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
CEP192	55125	hgsc.bcm.edu	37	18	13056333	13056333	+	Silent	SNP	C	C	T	rs2282541	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:13056333C>T	ENST00000325971.8	+	17	3549	c.1956C>T	c.(1954-1956)caC>caT	p.H652H	CEP192_ENST00000506447.1_Silent_p.H1248H|CEP192_ENST00000430049.2_Silent_p.H773H			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	652					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CTGCTGTGCACGCACTCTTGA	0.532													C|||	1233	0.246206	0.1974	0.3905	5008	,	,		23081	0.1835		0.34	False		,,,				2504	0.1779				p.H1248H		Atlas-SNP	.											.	CEP192	340	.	0			c.C3744T						PASS	.	C		970,3436	367.1+/-318.1	110,750,1343	86.0	68.0	74.0		3744	-3.9	0.0	18	dbSNP_100	74	2852,5748	448.4+/-361.8	462,1928,1910	no	coding-synonymous	CEP192	NM_032142.3		572,2678,3253	TT,TC,CC		33.1628,22.0154,29.3864		1248/2538	13056333	3822,9184	2203	4300	6503	SO:0001819	synonymous_variant	55125	exon19			TGTGCACGCACTC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.1956C>T	18.37:g.13056333C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																				C|0.713;T|0.287	0.287	strong		0.532	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
OR2T34	127068	hgsc.bcm.edu	37	1	248737230	248737230	+	Missense_Mutation	SNP	T	T	C	rs199863869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248737230T>C	ENST00000328782.2	-	1	850	c.829A>G	c.(829-831)Atg>Gtg	p.M277V		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M277V(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	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)			GACACCATCATGTCCTGCTCA	0.532													t|||	796	0.158946	0.3079	0.111	5008	,	,		8657	0.0942		0.1044	False		,,,				2504	0.1145				p.M277V		Atlas-SNP	.											OR2T34,NS,carcinoma,0,1	OR2T34	72	1	1	Substitution - Missense(1)	stomach(1)	c.A829G						scavenged	.						20.0	14.0	16.0					1																	248737230		2093	4220	6313	SO:0001583	missense	127068	exon1			CCATCATGTCCTG	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.829A>G	1.37:g.248737230T>C	ENSP00000330904:p.Met277Val	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	180	59	0.327778	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	292	0.1336996336996337	132	0.2682926829268293	37	0.10220994475138122	42	0.07342657342657342	81	0.10686015831134564	.	2.413	-0.334881	0.05278	.	.	ENSG00000183310	ENST00000328782	T	0.00054	8.8	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	L	0.39326	1.205	0.80722	P	0.0	B	0.19583	0.037	B	0.24006	0.05	T	0.11767	-1.0574	8	0.87932	D	0	.	6.6859	0.23144	0.0:0.0:0.2414:0.7586	.	277	Q8NGX1	O2T34_HUMAN	V	277	ENSP00000330904:M277V	ENSP00000330904:M277V	M	-	1	0	OR2T34	246803853	0.001000	0.12720	0.987000	0.45799	0.354000	0.29330	0.758000	0.26447	0.964000	0.38108	0.104000	0.15600	ATG	T|0.875;C|0.125	0.125	strong		0.532	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42434254	42434254	+	Silent	SNP	G	G	A	rs655427	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42434254G>A	ENST00000382396.4	-	20	2564	c.2478C>T	c.(2476-2478)aaC>aaT	p.N826N	PLA2G4F_ENST00000397272.3_Silent_p.N828N			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	826	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		AGGTCTCCACGTTGTTCAGGA	0.602													A|||	2000	0.399361	0.3964	0.415	5008	,	,		16500	0.3452		0.5487	False		,,,				2504	0.2945				p.N826N		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.C2478T						PASS	.	A		1819,2587	638.6+/-397.0	370,1079,754	81.0	76.0	77.0		2478	-10.4	0.0	15	dbSNP_83	77	4536,4062	560.1+/-387.5	1203,2130,966	no	coding-synonymous	PLA2G4F	NM_213600.3		1573,3209,1720	AA,AG,GG		47.2435,41.2846,48.8696		826/850	42434254	6355,6649	2203	4299	6502	SO:0001819	synonymous_variant	255189	exon20			CTCCACGTTGTTC		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.2478C>T	15.37:g.42434254G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																			G|0.540;N|0.000	.	strong		0.602	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
SRP68	6730	hgsc.bcm.edu	37	17	74056413	74056413	+	Silent	SNP	C	C	T	rs2665998	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74056413C>T	ENST00000307877.2	-	7	974	c.813G>A	c.(811-813)gaG>gaA	p.E271E	SRP68_ENST00000539137.1_Silent_p.E233E|SRP68_ENST00000355113.5_Silent_p.E170E	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	271					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						CCAAGAGACCCTCAGTGCCCC	0.438													C|||	2774	0.553914	0.9213	0.5764	5008	,	,		14229	0.4722		0.3926	False		,,,				2504	0.2914				p.E271E		Atlas-SNP	.											SRP68,NS,carcinoma,-2,1	SRP68	61	1	0			c.G813A						PASS	.	C		3634,772	753.4+/-412.4	1510,614,79	82.0	82.0	82.0		813	0.6	1.0	17	dbSNP_100	82	3481,5119	509.6+/-377.3	706,2069,1525	no	coding-synonymous	SRP68	NM_014230.2		2216,2683,1604	TT,TC,CC		40.4767,17.5216,45.2945		271/628	74056413	7115,5891	2203	4300	6503	SO:0001819	synonymous_variant	6730	exon7			GAGACCCTCAGTG	AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"""signal recognition particle 68kD"""			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.813G>A	17.37:g.74056413C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	25	0.337838	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Silent	SNP	ENST00000307877.2	37	CCDS11738.1																																																																																			C|0.433;T|0.567	0.567	strong		0.438	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230	
PSG1	5669	hgsc.bcm.edu	37	19	43382374	43382374	+	Missense_Mutation	SNP	C	C	G	rs707744	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43382374C>G	ENST00000436291.2	-	2	237	c.121G>C	c.(121-123)Gag>Cag	p.E41Q	PSG1_ENST00000312439.6_Missense_Mutation_p.E41Q|PSG1_ENST00000403380.3_Missense_Mutation_p.E41Q|PSG1_ENST00000595124.1_Missense_Mutation_p.E41Q|PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000244296.2_Missense_Mutation_p.E41Q|PSG1_ENST00000595356.1_Missense_Mutation_p.E41Q	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	41	Ig-like V-type.		E -> Q (in dbSNP:rs707744).	EPT -> QPP (in Ref. 4, 5 and 6). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TTGGTTGGCTCGGCTTCAATC	0.473													.|||	2124	0.424121	0.503	0.4207	5008	,	,		18131	0.4276		0.2505	False		,,,				2504	0.4949				p.E41Q		Atlas-SNP	.											.	PSG1	196	.	0			c.G121C						PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	2154,2252		582,990,631	147.0	166.0	160.0		121,121,121	-1.2	0.0	19	dbSNP_86	160	2121,6477		320,1481,2498	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	29,29,29	902,2471,3129	GG,GC,CC		24.6685,48.8879,32.8745	,,	41/420,41/418,41/427	43382374	4275,8729	2203	4299	6502	SO:0001583	missense	5669	exon2			TTGGCTCGGCTTC		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.121G>C	19.37:g.43382374C>G	ENSP00000413041:p.Glu41Gln	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	124	46	0.370968	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	0.484	-0.878652	0.02550	0.488879	0.246685	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	1.46	-1.17	0.09648	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00061	-2.33	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.11235	0.004;0.0;0.0;0.0;0.0;0.001;0.003;0.0	B;B;B;B;B;B;B;B	0.13407	0.008;0.003;0.001;0.004;0.003;0.007;0.009;0.004	T	0.43988	-0.9357	8	0.22706	T	0.39	.	4.7175	0.12903	0.0:0.5961:0.2282:0.1757	rs707744;rs3205494;rs16976238;rs61289360	41;41;41;41;41;41;41;41	O75238;P11464-4;G5E9F7;P11464;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.	Q	41	ENSP00000413041:E41Q;ENSP00000385386:E41Q;ENSP00000308970:E41Q;ENSP00000244296:E41Q	ENSP00000244296:E41Q	E	-	1	0	PSG1	48074214	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.330000	0.07925	-0.696000	0.05098	-1.122000	0.02009	GAG	C|0.695;G|0.305	0.305	strong		0.473	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
OR10K2	391107	hgsc.bcm.edu	37	1	158390252	158390252	+	Silent	SNP	T	T	G	rs12239443	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158390252T>G	ENST00000314902.2	-	1	404	c.405A>C	c.(403-405)ctA>ctC	p.L135L		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	135						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)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					CATGTCCCATTAGCACTGAGT	0.502													G|||	1453	0.290136	0.2526	0.2709	5008	,	,		21765	0.1687		0.4592	False		,,,				2504	0.3057				p.L135L		Atlas-SNP	.											.	OR10K2	69	.	0			c.A405C						PASS	.	G		1183,3223	710.9+/-407.9	164,855,1184	185.0	176.0	179.0		405	0.8	0.4	1	dbSNP_120	179	3770,4830	616.0+/-396.4	808,2154,1338	no	coding-synonymous	OR10K2	NM_001004476.1		972,3009,2522	GG,GT,TT		43.8372,26.8498,38.0824		135/313	158390252	4953,8053	2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			TCCCATTAGCACT	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"""GPCR / Class A : Olfactory receptors"""	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.405A>C	1.37:g.158390252T>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	189	105	0.555556	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			T|0.635;G|0.365	0.365	strong		0.502	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476	
STRN	6801	hgsc.bcm.edu	37	2	37111123	37111123	+	Missense_Mutation	SNP	G	G	A	rs80243841	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:37111123G>A	ENST00000263918.4	-	9	1146	c.1138C>T	c.(1138-1140)Ccc>Tcc	p.P380S	STRN_ENST00000379213.2_Missense_Mutation_p.P331S	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	380					dendrite development (GO:0016358)|locomotory behavior (GO:0007626)|negative regulation of cell proliferation (GO:0008285)|tight junction assembly (GO:0070830)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|estrogen receptor binding (GO:0030331)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33		Ovarian(717;0.0129)|all_hematologic(82;0.21)				GAGCTGCTGGGTCTGGAAGGT	0.423													G|||	56	0.0111821	0.0015	0.0058	5008	,	,		16376	0.002		0.0249	False		,,,				2504	0.0235				p.P380S		Atlas-SNP	.											.	STRN	71	.	0			c.C1138T						PASS	.	G	SER/PRO	20,4386	26.2+/-53.5	0,20,2183	88.0	80.0	83.0		1138	5.8	1.0	2	dbSNP_131	83	178,8422	81.5+/-144.1	1,176,4123	yes	missense	STRN	NM_003162.3	74	1,196,6306	AA,AG,GG		2.0698,0.4539,1.5224	benign	380/781	37111123	198,12808	2203	4300	6503	SO:0001583	missense	6801	exon9			TGCTGGGTCTGGA	AJ223814	CCDS1784.1	2p22.2	2013-01-10	2001-11-28		ENSG00000115808	ENSG00000115808		"""WD repeat domain containing"""	11424	protein-coding gene	gene with protein product		614765	"""striatin, calmodulin-binding protein"""			9693043, 8769426	Standard	NM_003162		Approved	SG2NA	uc002rpn.3	O43815	OTTHUMG00000100959	ENST00000263918.4:c.1138C>T	2.37:g.37111123G>A	ENSP00000263918:p.Pro380Ser	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	214	110	0.514019	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Missense_Mutation	SNP	ENST00000263918.4	37	CCDS1784.1	21	0.009615384615384616	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	18	0.023746701846965697	G	10.45	1.354709	0.24512	0.004539	0.020698	ENSG00000115808	ENST00000263918;ENST00000538092;ENST00000379213	T;T	0.62498	0.02;0.04	5.83	5.83	0.93111	.	0.049883	0.85682	D	0.000000	T	0.26195	0.0639	N	0.03608	-0.345	0.80722	D	1	B;B	0.15930	0.015;0.001	B;B	0.20577	0.03;0.006	T	0.27400	-1.0075	10	0.15066	T	0.55	-7.7469	20.111	0.97911	0.0:0.0:1.0:0.0	.	331;380	O43815-2;O43815	.;STRN_HUMAN	S	380;355;331	ENSP00000263918:P380S;ENSP00000368513:P331S	ENSP00000263918:P380S	P	-	1	0	STRN	36964627	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.102000	0.71486	2.747000	0.94245	0.650000	0.86243	CCC	G|0.984;A|0.016	0.016	strong		0.423	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1		
METTL11B	149281	hgsc.bcm.edu	37	1	170135760	170135760	+	Missense_Mutation	SNP	T	T	C	rs6427235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:170135760T>C	ENST00000439373.2	+	3	555	c.448T>C	c.(448-450)Tcc>Ccc	p.S150P	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	150			S -> P (in dbSNP:rs6427235).			nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						TATGATGGAATCCTTTCTCCT	0.517													T|||	1459	0.291334	0.5076	0.2435	5008	,	,		18050	0.1349		0.2724	False		,,,				2504	0.2137				p.S150P		Atlas-SNP	.											.	METTL11B	18	.	0			c.T448C						PASS	.	T	PRO/SER	657,727		159,339,194	116.0	107.0	110.0		448	-1.3	0.6	1	dbSNP_116	110	885,2297		133,619,839	yes	missense	METTL11B	NM_001136107.1	74	292,958,1033	CC,CT,TT		27.8127,47.4711,33.7714	benign	150/284	170135760	1542,3024	692	1591	2283	SO:0001583	missense	149281	exon3			ATGGAATCCTTTC	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.448T>C	1.37:g.170135760T>C	ENSP00000408058:p.Ser150Pro	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	107	63	0.588785	NM_001136107	B2RXI0	Missense_Mutation	SNP	ENST00000439373.2	37	CCDS44275.1	610	0.2793040293040293	227	0.4613821138211382	93	0.2569060773480663	70	0.12237762237762238	220	0.29023746701846964	T	10.56	1.383329	0.25031	0.474711	0.278127	ENSG00000203740	ENST00000439373	T	0.22539	1.95	5.25	-1.26	0.09376	.	0.478630	0.25096	N	0.033178	T	0.01940	0.0061	N	0.02697	-0.525	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.44421	-0.9329	9	0.28530	T	0.3	-0.9035	5.4805	0.16721	0.2123:0.435:0.0:0.3527	rs6427235	150	Q5VVY1	NTM1B_HUMAN	P	150	ENSP00000408058:S150P	ENSP00000408058:S150P	S	+	1	0	METTL11B	168402384	0.799000	0.28903	0.609000	0.28983	0.989000	0.77384	0.422000	0.21296	0.078000	0.16900	0.533000	0.62120	TCC	T|0.719;C|0.281	0.281	strong		0.517	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
PTPRS	5802	hgsc.bcm.edu	37	19	5273571	5273571	+	Silent	SNP	T	T	G	rs1141371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5273571T>G	ENST00000587303.1	-	3	360	c.261A>C	c.(259-261)gcA>gcC	p.A87A	PTPRS_ENST00000590509.1_Silent_p.A87A|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000262963.6_Silent_p.A87A|PTPRS_ENST00000348075.2_Silent_p.A87A|PTPRS_ENST00000588012.1_Silent_p.A87A|PTPRS_ENST00000372412.4_Silent_p.A87A|PTPRS_ENST00000357368.4_Silent_p.A87A|PTPRS_ENST00000592099.1_Silent_p.A87A|PTPRS_ENST00000353284.2_Silent_p.A87A			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	87	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	GCACTGCCCCTGCACTCTCAT	0.582													T|||	819	0.163538	0.2943	0.1527	5008	,	,		20134	0.002		0.2266	False		,,,				2504	0.0961				p.A87A		Atlas-SNP	.											.	PTPRS	169	.	0			c.A261C						PASS	.	T	,,,	1168,3238	412.4+/-336.1	151,866,1186	94.0	82.0	86.0		261,261,261,261	-8.0	0.6	19	dbSNP_86	86	1924,6676	339.9+/-323.4	208,1508,2584	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	359,2374,3770	GG,GT,TT		22.3721,26.5093,23.7736	,,,	87/1949,87/1502,87/1911,87/1506	5273571	3092,9914	2203	4300	6503	SO:0001819	synonymous_variant	5802	exon4			TGCCCCTGCACTC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.261A>C	19.37:g.5273571T>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_130854	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			T|0.785;G|0.215;A|0.000	0.215	strong		0.582	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
HERC2	8924	hgsc.bcm.edu	37	15	28517436	28517436	+	Silent	SNP	T	T	C	rs75181529		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:28517436T>C	ENST00000261609.7	-	9	1116	c.1008A>G	c.(1006-1008)ccA>ccG	p.P336P		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		AGGGCAAAAGTGGGGCGCTGG	0.562																																					p.P336P		Atlas-SNP	.											.	HERC2	501	.	0			c.A1008G						PASS	.																																			SO:0001819	synonymous_variant	8924	exon9			CAAAAGTGGGGCG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.1008A>G	15.37:g.28517436T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	155	64	0.412903	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			T|0.500;C|0.500	0.500	weak		0.562	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
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 GAIIx	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_ENST00000600188.1_Silent_p.A13A|RSPH6A_ENST00000597055.1_Silent_p.A277A	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		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	64	33	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 GAIIx	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	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	38	11	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	
KANK1	23189	hgsc.bcm.edu	37	9	712599	712599	+	Silent	SNP	C	C	T	rs11789987	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:712599C>T	ENST00000382303.1	+	7	2485	c.1833C>T	c.(1831-1833)aaC>aaT	p.N611N	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Silent_p.N611N|KANK1_ENST00000382293.3_Silent_p.N453N	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	611					negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		AGTCTGTGAACGACCTCACAC	0.502													C|||	1267	0.252995	0.0923	0.2262	5008	,	,		24150	0.126		0.4105	False		,,,				2504	0.4581				p.N611N		Atlas-SNP	.											KANK1_ENST00000382303,colon,carcinoma,0,2	KANK1	231	2	0			c.C1833T						PASS	.	C	,	606,3800	263.8+/-265.7	50,506,1647	173.0	148.0	157.0		1833,1359	-7.5	0.1	9	dbSNP_120	157	3458,5142	508.6+/-377.1	678,2102,1520	no	coding-synonymous,coding-synonymous	KANK1	NM_015158.2,NM_153186.3	,	728,2608,3167	TT,TC,CC		40.2093,13.754,31.2471	,	611/1353,453/1195	712599	4064,8942	2203	4300	6503	SO:0001819	synonymous_variant	23189	exon7			TGTGAACGACCTC	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1833C>T	9.37:g.712599C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			C|0.719;T|0.281	0.281	strong		0.502	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
UBQLNL	143630	hgsc.bcm.edu	37	11	5536415	5536415	+	Silent	SNP	C	C	T	rs10769023	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5536415C>T	ENST00000380184.1	-	1	1520	c.1257G>A	c.(1255-1257)gaG>gaA	p.E419E	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	419										endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		AGCTGCTCTGCTCATCTGACA	0.483													C|||	1445	0.288538	0.2458	0.3184	5008	,	,		22239	0.371		0.2614	False		,,,				2504	0.2679				p.E419E		Atlas-SNP	.											.	UBQLNL	74	.	0			c.G1257A						PASS	.	C		1114,3288	400.8+/-331.7	147,820,1234	129.0	116.0	121.0		1257	-5.5	0.0	11	dbSNP_120	121	2345,6249	392.8+/-344.1	331,1683,2283	no	coding-synonymous	UBQLNL	NM_145053.4		478,2503,3517	TT,TC,CC		27.2865,25.3067,26.6159		419/476	5536415	3459,9537	2201	4297	6498	SO:0001819	synonymous_variant	143630	exon1			GCTCTGCTCATCT	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.1257G>A	11.37:g.5536415C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	228	102	0.447368	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	37	CCDS31385.1																																																																																			C|0.719;T|0.281	0.281	strong		0.483	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
SLC4A2	6522	hgsc.bcm.edu	37	7	150763655	150763655	+	Silent	SNP	T	T	A	rs2229549	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150763655T>A	ENST00000485713.1	+	6	1670	c.630T>A	c.(628-630)acT>acA	p.T210T	SLC4A2_ENST00000461735.1_Silent_p.T196T|SLC4A2_ENST00000413384.2_Silent_p.T210T|SLC4A2_ENST00000310317.5_Silent_p.T128T|SLC4A2_ENST00000392826.2_Silent_p.T201T	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	210	Pro-rich.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCAGTGGCACTGCAGGGGGTG	0.706													T|||	2682	0.535543	0.2935	0.6945	5008	,	,		13256	0.7034		0.6163	False		,,,				2504	0.4939				p.T210T		Atlas-SNP	.											.	SLC4A2	98	.	0			c.T630A						PASS	.	T	,,,	1267,2645		259,749,948	7.0	8.0	7.0		630,603,588,630	-10.0	0.5	7	dbSNP_98	7	3900,3724		1106,1688,1018	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	,,,	1365,2437,1966	AA,AT,TT		48.8458,32.3875,44.7902	,,,	210/1242,201/1233,196/1228,210/1242	150763655	5167,6369	1956	3812	5768	SO:0001819	synonymous_variant	6522	exon6			TGGCACTGCAGGG		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.630T>A	7.37:g.150763655T>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	37	CCDS5917.1																																																																																			T|0.406;A|0.594	0.594	strong		0.706	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
SH3TC1	54436	hgsc.bcm.edu	37	4	8220029	8220029	+	Missense_Mutation	SNP	G	G	A	rs1281138	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:8220029G>A	ENST00000245105.3	+	8	938	c.871G>A	c.(871-873)Gac>Aac	p.D291N	SH3TC1_ENST00000539824.1_Missense_Mutation_p.D215N	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	291			D -> N (in dbSNP:rs1281138).							NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GGACCCCATCGACGATGCCAT	0.577													G|||	35	0.00698882	0.0	0.0159	5008	,	,		15965	0.001		0.0229	False		,,,				2504	0.0				p.D291N	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											SH3TC1,colon,carcinoma,-2,1	SH3TC1	105	1	0			c.G871A						PASS	.	G	ASN/ASP	34,4372	39.2+/-71.8	0,34,2169	62.0	61.0	62.0		871	2.7	0.0	4	dbSNP_87	62	254,8346	99.9+/-161.4	3,248,4049	yes	missense	SH3TC1	NM_018986.3	23	3,282,6218	AA,AG,GG		2.9535,0.7717,2.2144	benign	291/1337	8220029	288,12718	2203	4300	6503	SO:0001583	missense	54436	exon8			CCCATCGACGATG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.871G>A	4.37:g.8220029G>A	ENSP00000245105:p.Asp291Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	26	0.011904761904761904	0	0.0	5	0.013812154696132596	0	0.0	21	0.027704485488126648	G	10.71	1.425684	0.25639	0.007717	0.029535	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265;ENST00000508641	T;T;T	0.17213	2.29;2.29;2.29	3.53	2.68	0.31781	.	0.421507	0.22889	N	0.054416	T	0.04048	0.0113	L	0.43152	1.355	0.09310	N	1	B	0.19817	0.039	B	0.12837	0.008	T	0.23440	-1.0188	10	0.22109	T	0.4	-7.8139	8.1531	0.31152	0.1177:0.0:0.8823:0.0	rs1281138;rs1678293;rs1281138	291	Q8TE82	S3TC1_HUMAN	N	29;291;215;120;100	ENSP00000245105:D291N;ENSP00000441045:D215N;ENSP00000426035:D100N	ENSP00000245105:D291N	D	+	1	0	SH3TC1	8270929	0.005000	0.15991	0.002000	0.10522	0.156000	0.22039	1.468000	0.35332	0.833000	0.34828	0.561000	0.74099	GAC	G|0.980;A|0.020	0.020	strong		0.577	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
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 GAIIx	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_ENST00000457268.1_Silent_p.S185S|TFEC_ENST00000393485.1_3'UTR	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		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	147	70	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	
MLPH	79083	hgsc.bcm.edu	37	2	238449107	238449107	+	Silent	SNP	A	A	G	rs2271809|rs386656756	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238449107A>G	ENST00000264605.3	+	10	1515	c.1221A>G	c.(1219-1221)gaA>gaG	p.E407E	MLPH_ENST00000338530.4_Silent_p.E379E|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Silent_p.E407E|MLPH_ENST00000409373.1_Silent_p.E339E|MLPH_ENST00000410032.1_Silent_p.E264E	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	407					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)	p.E407E(1)		NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		AGGAGGAGGAAGCCAAGGACG	0.622													G|||	2532	0.505591	0.8873	0.3573	5008	,	,		20291	0.4226		0.2485	False		,,,				2504	0.4448				p.E407E		Atlas-SNP	.											MLPH,NS,carcinoma,0,2	MLPH	41	2	1	Substitution - coding silent(1)	stomach(1)	c.A1221G						PASS	.	G	,	3403,1003		1421,561,221	77.0	74.0	75.0		1137,1221	0.8	0.0	2	dbSNP_100	75	2263,6335		360,1543,2396	no	coding-synonymous,coding-synonymous	MLPH	NM_001042467.1,NM_024101.5	,	1781,2104,2617	GG,GA,AA		26.3201,22.7644,43.5712	,	379/573,407/601	238449107	5666,7338	2203	4299	6502	SO:0001819	synonymous_variant	79083	exon10			GGAGGAAGCCAAG	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1221A>G	2.37:g.238449107A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Silent	SNP	ENST00000264605.3	37	CCDS2518.1	952|952	0.4358974358974359|0.4358974358974359	427|427	0.8678861788617886|0.8678861788617886	117|117	0.32320441988950277|0.32320441988950277	225|225	0.39335664335664333|0.39335664335664333	183|183	0.24142480211081793|0.24142480211081793	G|G	0.093|0.093	-1.163772|-1.163772	0.01673|0.01673	0.772356|0.772356	0.263201|0.263201	ENSG00000115648|ENSG00000115648	ENST00000436965|ENST00000415753	.|.	.|.	.|.	2.76|2.76	0.838|0.838	0.18902|0.18902	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.48341|0.48341	P|P	3.630000000000022E-4|3.630000000000022E-4	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.15150|0.15150	-1.0447|-1.0447	3|3	.|.	.|.	.|.	-5.625|-5.625	4.1178|4.1178	0.10090|0.10090	0.2496:0.1953:0.5551:0.0|0.2496:0.1953:0.5551:0.0	rs2271809|rs2271809	.|.	.|.	.|.	R|G	128|95	.|.	.|.	K|S	+|+	2|1	0|0	MLPH|MLPH	238113846|238113846	0.209000|0.209000	0.23505|0.23505	0.015000|0.015000	0.15790|0.15790	0.028000|0.028000	0.11728|0.11728	0.760000|0.760000	0.26475|0.26475	-0.372000|-0.372000	0.07992|0.07992	-0.128000|-0.128000	0.14901|0.14901	AAG|AGC	A|0.549;C|0.000;G|0.450;T|0.000	0.450	strong		0.622	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
SLFN12	55106	hgsc.bcm.edu	37	17	33749546	33749546	+	Missense_Mutation	SNP	A	A	G	rs2586514	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33749546A>G	ENST00000394562.1	-	4	1025	c.502T>C	c.(502-504)Tgt>Cgt	p.C168R	SLFN12_ENST00000452764.3_Missense_Mutation_p.C168R|SLFN12_ENST00000304905.5_Missense_Mutation_p.C168R|SLFN12_ENST00000460530.1_5'Flank			Q8IYM2	SLN12_HUMAN	schlafen family member 12	168			C -> R (in dbSNP:rs2586514). {ECO:0000269|PubMed:15489334}.				ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATATCAACACAGGGCCTCTTT	0.398													G|||	2954	0.589856	0.6278	0.6354	5008	,	,		17852	0.4504		0.5905	False		,,,				2504	0.6493				p.C168R		Atlas-SNP	.											.	SLFN12	56	.	0			c.T502C						PASS	.	G	ARG/CYS	2769,1625		875,1019,303	75.0	78.0	77.0		502	-6.5	0.0	17	dbSNP_100	77	5123,3463		1532,2059,702	yes	missense	SLFN12	NM_018042.3	180	2407,3078,1005	GG,GA,AA		40.3331,36.9822,39.1988	possibly-damaging	168/579	33749546	7892,5088	2197	4293	6490	SO:0001583	missense	55106	exon2			CAACACAGGGCCT	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.502T>C	17.37:g.33749546A>G	ENSP00000378063:p.Cys168Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	1267	0.5801282051282052	327	0.6646341463414634	223	0.6160220994475138	249	0.4353146853146853	468	0.6174142480211082	g	3.337	-0.135420	0.06711	0.630178	0.596669	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.03468	3.92;3.92;3.92	3.23	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36114	-0.9761	8	0.23891	T	0.37	.	1.5985	0.02669	0.3055:0.3582:0.2094:0.1269	rs2586514;rs3744368;rs16970955;rs17846142;rs17859150;rs52828558;rs58226663;rs2586514	168	Q8IYM2	SLN12_HUMAN	R	168	ENSP00000378063:C168R;ENSP00000302077:C168R;ENSP00000394903:C168R	ENSP00000302077:C168R	C	-	1	0	SLFN12	30773659	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.790000	0.04604	-2.103000	0.00844	-1.786000	0.00637	TGT	A|0.416;G|0.584	0.584	strong		0.398	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
GNS	2799	hgsc.bcm.edu	37	12	65141588	65141588	+	Silent	SNP	C	C	T	rs2230291	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:65141588C>T	ENST00000258145.3	-	3	533	c.363G>A	c.(361-363)aaG>aaA	p.K121K	GNS_ENST00000543646.1_Silent_p.K153K|GNS_ENST00000542058.1_Silent_p.K101K|GNS_ENST00000418919.2_Silent_p.K65K	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase	121					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(4)	15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		TCTGCCAGGACTTACTACTGC	0.448													C|||	195	0.0389377	0.0091	0.0634	5008	,	,		17354	0.0		0.1223	False		,,,				2504	0.0164				p.K121K		Atlas-SNP	.											.	GNS	41	.	0			c.G363A						PASS	.	C		110,4296	85.3+/-124.0	1,108,2094	207.0	193.0	198.0		363	-6.1	0.0	12	dbSNP_132	198	1165,7435	239.3+/-270.5	88,989,3223	no	coding-synonymous	GNS	NM_002076.3		89,1097,5317	TT,TC,CC		13.5465,2.4966,9.8032		121/553	65141588	1275,11731	2203	4300	6503	SO:0001819	synonymous_variant	2799	exon3			CCAGGACTTACTA		CCDS8970.1	12q14	2010-05-04	2008-08-01		ENSG00000135677	ENSG00000135677	3.1.6.14		4422	protein-coding gene	gene with protein product	"""Sanfilippo disease IIID"", ""N-acetylglucosamine-6-sulfatase"""	607664					Standard	NM_002076		Approved		uc001ssg.4	P15586	OTTHUMG00000168819	ENST00000258145.3:c.363G>A	12.37:g.65141588C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	229	108	0.471616	NM_002076	B4DYH8|Q53F05	Silent	SNP	ENST00000258145.3	37	CCDS8970.1																																																																																			T|0.080;G|0.000;C|0.920	0.080	strong		0.448	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2		
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743086	22743086	+	Missense_Mutation	SNP	C	C	T	rs201721928		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:22743086C>T	ENST00000560659.2	+	8	1321	c.1321C>T	c.(1321-1323)Cgg>Tgg	p.R441W	GOLGA6L1_ENST00000316397.3_Missense_Mutation_p.R491W			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	485										NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						ggagaagatacggaagcagga	0.562																																					p.R491W		Atlas-SNP	.											.	GOLGA6L1	20	.	0			c.C1471T						PASS	.						4.0	3.0	4.0					15																	22743086		1053	1506	2559	SO:0001583	missense	283767	exon8			AAGATACGGAAGC	AK097517	CCDS73699.1	15q11.2	2012-10-05	2010-02-12		ENSG00000197414	ENSG00000277865			37444	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 1"""				Standard	NM_001001413		Approved		uc010tzx.1	Q8N7Z2	OTTHUMG00000171883	ENST00000560659.2:c.1321C>T	15.37:g.22743086C>T	ENSP00000452626:p.Arg441Trp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	74	13	0.175676	NM_001001413		Missense_Mutation	SNP	ENST00000560659.2	37		.	.	.	.	.	.	.	.	.	.	.	2.598	-0.293699	0.05568	.	.	ENSG00000197414	ENST00000316397;ENST00000355145	T	0.11385	2.78	.	.	.	.	.	.	.	.	T	0.13500	0.0327	L	0.52573	1.65	0.09310	N	1	.	.	.	.	.	.	T	0.25257	-1.0137	5	0.62326	D	0.03	.	.	.	.	.	.	.	.	W	491	ENSP00000320207:R491W	ENSP00000320207:R491W	R	+	1	2	GOLGA6L1	20294450	0.006000	0.16342	0.011000	0.14972	0.011000	0.07611	-0.992000	0.03724	0.149000	0.19098	0.152000	0.16155	CGG	.	.	weak		0.562	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
STK10	6793	hgsc.bcm.edu	37	5	171533656	171533656	+	Silent	SNP	C	C	T	rs2306962	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:171533656C>T	ENST00000176763.5	-	6	1099	c.756G>A	c.(754-756)tcG>tcA	p.S252S		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	252	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TGGGAGGGTCCGACTTGGCGA	0.647											OREG0017039	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3428	0.684505	0.4153	0.7507	5008	,	,		13548	0.8532		0.7356	False		,,,				2504	0.7751				p.S252S		Atlas-SNP	.											.	STK10	100	.	0			c.G756A						PASS	.	C		2065,2341	567.0+/-382.0	492,1081,630	103.0	94.0	97.0		756	-4.6	0.4	5	dbSNP_100	97	6053,2547	691.9+/-404.5	2129,1795,376	no	coding-synonymous	STK10	NM_005990.3		2621,2876,1006	TT,TC,CC		29.6163,46.8679,37.5827		252/969	171533656	8118,4888	2203	4300	6503	SO:0001819	synonymous_variant	6793	exon6			AGGGTCCGACTTG	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.756G>A	5.37:g.171533656C>T		Somatic	131	0	0	1893	WXS	Illumina HiSeq	Phase_I	108	48	0.444444	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Silent	SNP	ENST00000176763.5	37	CCDS34290.1																																																																																			C|0.351;T|0.649	0.649	strong		0.647	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
COMT	1312	hgsc.bcm.edu	37	22	19951207	19951207	+	Silent	SNP	C	C	G	rs4818	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:19951207C>G	ENST00000361682.6	+	4	790	c.408C>G	c.(406-408)ctC>ctG	p.L136L	MIR4761_ENST00000585066.1_RNA|COMT_ENST00000449653.1_Silent_p.L86L|COMT_ENST00000403184.1_Silent_p.L136L|COMT_ENST00000407537.1_Silent_p.L86L|COMT_ENST00000493893.1_3'UTR|COMT_ENST00000403710.1_Silent_p.L136L|COMT_ENST00000406520.3_Silent_p.L136L	NM_000754.3	NP_000745.1	P21964	COMT_HUMAN	catechol-O-methyltransferase	136					cellular response to phosphate starvation (GO:0016036)|dopamine catabolic process (GO:0042420)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|learning (GO:0007612)|methylation (GO:0032259)|multicellular organismal reproductive process (GO:0048609)|negative regulation of dopamine metabolic process (GO:0045963)|negative regulation of smooth muscle cell proliferation (GO:0048662)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|positive regulation of homocysteine metabolic process (GO:0050668)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	catechol O-methyltransferase activity (GO:0016206)|magnesium ion binding (GO:0000287)|O-methyltransferase activity (GO:0008171)			kidney(1)|lung(1)|ovary(1)|prostate(1)|stomach(1)	5	Colorectal(54;0.0993)				Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Methyldopa(DB00968)|Micafungin(DB01141)|S-Adenosylmethionine(DB00118)|Testosterone Propionate(DB01420)|Tolcapone(DB00323)	GGGCGAGGCTCATCACCATCG	0.632													G|||	1487	0.296925	0.1702	0.2954	5008	,	,		16301	0.3413		0.4026	False		,,,				2504	0.3149				p.L136L		Atlas-SNP	.											.	COMT	10	.	0			c.C408G	GRCh37	CM970391	COMT	M	rs4818	PASS	.	G	,,,	864,3542	740.3+/-411.2	87,690,1426	61.0	50.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	408,408,408,258	-0.3	0.2	22	dbSNP_52	54	3396,5204	637.1+/-399.2	656,2084,1560	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COMT	NM_000754.3,NM_001135161.1,NM_001135162.1,NM_007310.2	,,,	743,2774,2986	GG,GC,CC		39.4884,19.6096,32.7541	,,,	136/272,136/272,136/272,86/222	19951207	4260,8746	2203	4300	6503	SO:0001819	synonymous_variant	1312	exon4			GAGGCTCATCACC		CCDS13770.1, CCDS46663.1	22q11.21	2012-10-02			ENSG00000093010	ENSG00000093010	2.1.1.6		2228	protein-coding gene	gene with protein product		116790				1572656	Standard	NM_000754		Approved		uc002zqu.3	P21964	OTTHUMG00000150529	ENST00000361682.6:c.408C>G	22.37:g.19951207C>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_000754	A8MPV9|Q6IB07|Q6ICE6|Q9BWC7	Silent	SNP	ENST00000361682.6	37	CCDS13770.1																																																																																			C|0.677;G|0.323	0.323	strong		0.632	COMT-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318936.2	NM_000754	
BTNL3	10917	hgsc.bcm.edu	37	5	180432416	180432416	+	Silent	SNP	C	C	T	rs7726150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180432416C>T	ENST00000342868.6	+	8	1129	c.945C>T	c.(943-945)ccC>ccT	p.P315P	RNU6-1036P_ENST00000383959.1_RNA	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	315	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GAAAAGCTCCCCAGGAGGTGC	0.547													C|||	2313	0.461861	0.6135	0.4856	5008	,	,		19347	0.3621		0.4414	False		,,,				2504	0.364				p.P315P		Atlas-SNP	.											BTNL3,NS,carcinoma,+1,1	BTNL3	55	1	0			c.C945T						PASS	.						57.0	63.0	61.0					5																	180432416		2193	4295	6488	SO:0001819	synonymous_variant	10917	exon8			AGCTCCCCAGGAG	AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1143	protein-coding gene	gene with protein product	"""butyrophilin-like receptor"""	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.945C>T	5.37:g.180432416C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	151	145	0.960265	NM_197975	Q496L7|Q9Y2C7	Silent	SNP	ENST00000342868.6	37	CCDS47358.1																																																																																			T|1.000;|0.000	1.000	weak		0.547	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2	NM_197975	
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 GAIIx	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_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000594706.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593931.1_5'Flank|PEG3_ENST00000423103.2_Missense_Mutation_p.E22G|PEG3_ENST00000593695.1_Intron	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	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	35	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		
PLEKHS1	79949	hgsc.bcm.edu	37	10	115540411	115540411	+	Silent	SNP	T	T	C	rs11196483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:115540411T>C	ENST00000354462.3	+	6	626	c.468T>C	c.(466-468)gcT>gcC	p.A156A	PLEKHS1_ENST00000361048.1_3'UTR|PLEKHS1_ENST00000369312.4_Silent_p.A324A|PLEKHS1_ENST00000369309.1_Silent_p.A240A			Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	420																	CATTCCATGCTGCATCCTGTA	0.418													T|||	1782	0.355831	0.2625	0.2968	5008	,	,		21245	0.4187		0.3926	False		,,,				2504	0.4213				p.A324A		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.T972C						PASS	.	T	,,	1260,3146	432.4+/-343.3	194,872,1137	88.0	82.0	84.0		972,972,	-1.5	0.0	10	dbSNP_120	84	3395,5205	501.5+/-375.5	696,2003,1601	no	coding-synonymous,coding-synonymous,utr-3	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4	,,	890,2875,2738	CC,CT,TT		39.4767,28.5974,35.7912	,,	324/367,324/367,	115540411	4655,8351	2203	4300	6503	SO:0001819	synonymous_variant	79949	exon11			CCATGCTGCATCC	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000354462.3:c.468T>C	10.37:g.115540411T>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001193435	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Silent	SNP	ENST00000354462.3	37																																																																																				T|0.631;C|0.369	0.369	strong		0.418	PLEKHS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050431.2	NM_024889	
VWF	7450	hgsc.bcm.edu	37	12	6167196	6167196	+	Silent	SNP	A	A	G	rs1800379	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6167196A>G	ENST00000261405.5	-	14	1802	c.1548T>C	c.(1546-1548)taT>taC	p.Y516Y		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	516	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TCTTCCCGGCATAGACGGGGG	0.587													G|||	1888	0.376997	0.6422	0.2709	5008	,	,		13058	0.2103		0.3628	False		,,,				2504	0.2802				p.Y516Y		Atlas-SNP	.											VWF,colon,carcinoma,0,2	VWF	338	2	0			c.T1548C						PASS	.	G		2581,1813		777,1027,393	32.0	34.0	33.0		1548	-1.8	0.0	12	dbSNP_89	33	3011,5573		549,1913,1830	yes	coding-synonymous	VWF	NM_000552.3		1326,2940,2223	GG,GA,AA		35.0769,41.2608,43.0883		516/2814	6167196	5592,7386	2197	4292	6489	SO:0001819	synonymous_variant	7450	exon14			CCCGGCATAGACG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.1548T>C	12.37:g.6167196A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			T|0.125;G|0.330	0.330	strong		0.587	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150046	11150046	+	Missense_Mutation	SNP	G	G	T	rs12226920	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11150046G>T	ENST00000538986.1	-	1	428	c.429C>A	c.(427-429)caC>caA	p.H143Q	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	143			H -> Q (in dbSNP:rs12226920).	VCH -> ICQ (in Ref. 3; AAU21140). {ECO:0000305}.	sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TCATCACAAGGTGACAAACCA	0.383													G|||	2119	0.423123	0.0651	0.3847	5008	,	,		20817	0.755		0.3827	False		,,,				2504	0.6339				p.H143Q		Atlas-SNP	.											.	TAS2R20	17	.	0			c.C429A						PASS	.	G	GLN/HIS	441,3965	211.2+/-231.4	18,405,1780	134.0	119.0	124.0		429	-4.8	0.0	12	dbSNP_120	124	3013,5587	463.2+/-365.9	544,1925,1831	yes	missense	TAS2R20	NM_176889.2	24	562,2330,3611	TT,TG,GG		35.0349,10.0091,26.557	benign	143/310	11150046	3454,9552	2203	4300	6503	SO:0001583	missense	259295	exon1			CACAAGGTGACAA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.429C>A	12.37:g.11150046G>T	ENSP00000441624:p.His143Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	G	4.234	0.042417	0.08196	0.100091	0.350349	ENSG00000255837	ENST00000538986	T	0.36520	1.25	2.93	-4.77	0.03219	.	1.298410	0.05758	N	0.604393	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.14805	0.011	B	0.22880	0.042	T	0.38329	-0.9666	9	0.27082	T	0.32	.	0.8786	0.01230	0.2054:0.1545:0.3359:0.3042	rs12226920;rs60423827;rs12226920	143	P59543	T2R20_HUMAN	Q	143	ENSP00000441624:H143Q	ENSP00000441624:H143Q	H	-	3	2	TAS2R20	11041313	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.459000	0.02370	-0.884000	0.03976	-0.312000	0.09012	CAC	G|0.671;T|0.329	0.329	strong		0.383	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
TG	7038	hgsc.bcm.edu	37	8	133899051	133899051	+	Silent	SNP	G	G	A	rs116254142	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:133899051G>A	ENST00000220616.4	+	9	1474	c.1434G>A	c.(1432-1434)gtG>gtA	p.V478V	TG_ENST00000377869.1_Silent_p.V478V	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	478					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AATTTTTGGTGAATGTTGGCC	0.463													G|||	16	0.00319489	0.0023	0.0	5008	,	,		19121	0.0		0.0129	False		,,,				2504	0.0				p.V478V		Atlas-SNP	.											TG,NS,carcinoma,0,1	TG	416	1	0			c.G1434A						PASS	.	G		11,4395	16.8+/-37.8	0,11,2192	76.0	80.0	79.0		1434	3.8	0.7	8	dbSNP_132	79	81,8519	45.8+/-104.6	0,81,4219	no	coding-synonymous	TG	NM_003235.4		0,92,6411	AA,AG,GG		0.9419,0.2497,0.7074		478/2769	133899051	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon9			TTTGGTGAATGTT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1434G>A	8.37:g.133899051G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	95	39	0.410526	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																			G|0.994;A|0.006	0.006	strong		0.463	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
PLEC	5339	hgsc.bcm.edu	37	8	145024570	145024570	+	Missense_Mutation	SNP	C	C	A	rs200335928		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145024570C>A	ENST00000322810.4	-	1	474	c.305G>T	c.(304-306)cGc>cTc	p.R102L	PLEC_ENST00000436759.2_Intron|PLEC_ENST00000354958.2_Intron|PLEC_ENST00000527096.1_Intron|PLEC_ENST00000356346.3_Intron	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	102	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GGCGACGGGGCGGCGCACGCG	0.706																																					p.R102L		Atlas-SNP	.											.	PLEC	1144	.	0			c.G305T						PASS	.						22.0	32.0	29.0					8																	145024570		2058	4148	6206	SO:0001583	missense	5339	exon1			ACGGGGCGGCGCA	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.305G>T	8.37:g.145024570C>A	ENSP00000323856:p.Arg102Leu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	c	16.09	3.024318	0.54683	.	.	ENSG00000178209	ENST00000322810	T	0.80033	-1.33	4.9	4.9	0.64082	Plectin/S10, N-terminal (1);	0.232355	0.21165	U	0.079097	D	0.87188	0.6115	M	0.78456	2.415	0.80722	D	1	D	0.58620	0.983	P	0.55508	0.777	D	0.89133	0.3511	10	0.87932	D	0	.	15.5576	0.76208	0.0:1.0:0.0:0.0	.	102	Q15149	PLEC_HUMAN	L	102	ENSP00000323856:R102L	ENSP00000323856:R102L	R	-	2	0	PLEC	145096558	0.525000	0.26290	0.998000	0.56505	0.989000	0.77384	1.289000	0.33307	2.263000	0.75096	0.563000	0.77884	CGC	A|0.005;C|0.996	0.005	weak		0.706	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
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 GAIIx	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	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_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		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	209	11	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 GAIIx	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	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	102	17	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		
MUC16	94025	hgsc.bcm.edu	37	19	9087758	9087758	+	Missense_Mutation	SNP	G	G	A	rs12611293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9087758G>A	ENST00000397910.4	-	1	4260	c.4057C>T	c.(4057-4059)Cat>Tat	p.H1353Y		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1353	Thr-rich.		H -> Y (in dbSNP:rs12611293).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCTTTGGATGGTTTTCTGTG	0.517													G|||	951	0.189896	0.0711	0.2709	5008	,	,		21703	0.3036		0.172	False		,,,				2504	0.1943				p.H1353Y		Atlas-SNP	.											.	MUC16	4315	.	0			c.C4057T						PASS	.	G	TYR/HIS	330,4064	156.6+/-189.7	6,318,1873	184.0	184.0	184.0		4057	0.6	0.0	19	dbSNP_120	184	1533,7063	282.0+/-295.3	132,1269,2897	yes	missense	MUC16	NM_024690.2	83	138,1587,4770	AA,AG,GG		17.8339,7.5102,14.3418	benign	1353/14508	9087758	1863,11127	2197	4298	6495	SO:0001583	missense	94025	exon1			TTGGATGGTTTTC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.4057C>T	19.37:g.9087758G>A	ENSP00000381008:p.His1353Tyr	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	338	141	0.41716	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	g	2.142	-0.396620	0.04899	0.075102	0.178339	ENSG00000181143	ENST00000397910	T	0.02525	4.26	1.62	0.548	0.17208	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.12630	0.006	B	0.06405	0.002	T	0.48103	-0.9064	8	0.87932	D	0	.	3.1685	0.06544	0.7238:0.0:0.2762:0.0	rs12611293;rs52827539;rs61560919;rs12611293	1353	B5ME49	.	Y	1353	ENSP00000381008:H1353Y	ENSP00000381008:H1353Y	H	-	1	0	MUC16	8948758	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.884000	0.01622	0.107000	0.17824	0.305000	0.20034	CAT	G|0.812;A|0.188	0.188	strong		0.517	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CDH23	64072	hgsc.bcm.edu	37	10	73544086	73544086	+	Missense_Mutation	SNP	G	G	A	rs3802711	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73544086G>A	ENST00000224721.6	+	41	5431	c.5426G>A	c.(5425-5427)cGg>cAg	p.R1809Q		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1804	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CTAAGGGTCCGGAAGGACGTG	0.617													g|||	696	0.138978	0.0575	0.1282	5008	,	,		17957	0.2401		0.1839	False		,,,				2504	0.1063				p.R1804Q		Atlas-SNP	.											.	CDH23	365	.	0			c.G5411A						PASS	.	G	GLN/ARG	310,3672		11,288,1692	68.0	77.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5411	5.4	1.0	10	dbSNP_107	74	1367,6945		114,1139,2903	yes	missense	CDH23	NM_022124.5	43	125,1427,4595	AA,AG,GG		16.4461,7.785,13.6408	probably-damaging	1804/3355	73544086	1677,10617	1991	4156	6147	SO:0001583	missense	64072	exon40			GGGTCCGGAAGGA	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.5426G>A	10.37:g.73544086G>A	ENSP00000224721:p.Arg1809Gln	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		334	0.15293040293040294	34	0.06910569105691057	39	0.10773480662983426	120	0.2097902097902098	141	0.18601583113456466	g	35	5.596016	0.96602	0.07785	0.164461	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.44	5.44	0.79542	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.00144	0.0004	L	0.37897	1.145	0.09310	P	1.0	D	0.89917	1.0	D	0.79784	0.993	T	0.00761	-1.1577	8	0.23891	T	0.37	.	18.8954	0.92421	0.0:0.0:1.0:0.0	rs3802711;rs52792628;rs3802711	1804	Q9H251	CAD23_HUMAN	Q	1809;1804;1807	.	ENSP00000224721:R1809Q	R	+	2	0	CDH23	73214092	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.676000	0.74498	2.556000	0.86216	0.450000	0.29827	CGG	G|0.843;A|0.157	0.157	strong		0.617	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
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 GAIIx	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-RDH14_ENST00000532967.1_Missense_Mutation_p.L107P|NT5C1B_ENST00000304081.4_Missense_Mutation_p.L47P|NT5C1B_ENST00000600945.1_Missense_Mutation_p.L107P|NT5C1B_ENST00000460052.1_5'UTR|RNU6-1215P_ENST00000384441.1_RNA	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	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	130	59	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		
IL22RA1	58985	hgsc.bcm.edu	37	1	24448084	24448084	+	Silent	SNP	G	G	A	rs17852648	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:24448084G>A	ENST00000270800.1	-	7	974	c.936C>T	c.(934-936)ccC>ccT	p.P312P		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	312					cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)	integral component of membrane (GO:0016021)	interferon receptor activity (GO:0004904)	p.P312P(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000992)|all_lung(284;0.00138)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-24)|Colorectal(126;6.43e-08)|COAD - Colon adenocarcinoma(152;3.51e-06)|GBM - Glioblastoma multiforme(114;5.06e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00104)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00911)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.148)		GAGCTCCTGCGGGCTCCCTGG	0.632													G|||	1028	0.205272	0.0787	0.2219	5008	,	,		17539	0.2649		0.3141	False		,,,				2504	0.1912				p.P312P		Atlas-SNP	.											IL22RA1,NS,carcinoma,0,1	IL22RA1	62	1	1	Substitution - coding silent(1)	stomach(1)	c.C936T						PASS	.	G		488,3918	227.8+/-242.9	31,426,1746	60.0	61.0	61.0		936	-0.6	0.0	1	dbSNP_123	61	2592,6008	421.1+/-353.6	396,1800,2104	no	coding-synonymous	IL22RA1	NM_021258.3		427,2226,3850	AA,AG,GG		30.1395,11.0758,23.6814		312/575	24448084	3080,9926	2203	4300	6503	SO:0001819	synonymous_variant	58985	exon7			TCCTGCGGGCTCC	AF286095	CCDS247.1	1p36.11	2009-10-06	2002-12-02	2002-12-06	ENSG00000142677	ENSG00000142677		"""Interleukins and interleukin receptors"""	13700	protein-coding gene	gene with protein product		605457	"""interleukin 22 receptor"""	IL22R		10875937	Standard	NM_021258		Approved	CRF2-9	uc001biq.2	Q8N6P7	OTTHUMG00000003041	ENST00000270800.1:c.936C>T	1.37:g.24448084G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_021258	A8K839|B2R9Y9|Q9HB22	Silent	SNP	ENST00000270800.1	37	CCDS247.1																																																																																			G|0.765;A|0.235	0.235	strong		0.632	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
HTR3A	3359	hgsc.bcm.edu	37	11	113860425	113860425	+	Silent	SNP	A	A	G	rs1176713	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:113860425A>G	ENST00000504030.2	+	9	1822	c.1377A>G	c.(1375-1377)ctA>ctG	p.L459L	HTR3A_ENST00000506841.2_Silent_p.L491L|HTR3A_ENST00000355556.2_Silent_p.L497L|HTR3A_ENST00000375498.2_Silent_p.L465L|HTR3A_ENST00000299961.5_Silent_p.L444L|HTR3A_ENST00000535865.1_Silent_p.L203L			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	459					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	TTTACCTGCTAGCGGTGCTGG	0.592													G|||	1387	0.276957	0.32	0.2983	5008	,	,		18540	0.2907		0.2078	False		,,,				2504	0.2607				p.L497L		Atlas-SNP	.											.	HTR3A	93	.	0			c.A1491G						PASS	.	G	,,	1264,3138	696.9+/-406.1	205,854,1142	95.0	86.0	89.0		1395,1332,1491	2.7	1.0	11	dbSNP_87	89	1834,6758	728.4+/-406.7	201,1432,2663	no	coding-synonymous,coding-synonymous,coding-synonymous	HTR3A	NM_000869.5,NM_001161772.2,NM_213621.3	,,	406,2286,3805	GG,GA,AA		21.3454,28.7142,23.8418	,,	465/485,444/464,497/517	113860425	3098,9896	2201	4296	6497	SO:0001819	synonymous_variant	3359	exon8			CCTGCTAGCGGTG	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5297	protein-coding gene	gene with protein product		182139	"""5-hydroxytryptamine (serotonin) receptor 3A"""	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.1377A>G	11.37:g.113860425A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	44	11	0.25	NM_213621	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Silent	SNP	ENST00000504030.2	37																																																																																				G|0.258;N|0.000	0.258	strong		0.592	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	
SPESP1	246777	hgsc.bcm.edu	37	15	69238445	69238445	+	Missense_Mutation	SNP	G	G	A	rs3743093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:69238445G>A	ENST00000310673.3	+	2	726	c.572G>A	c.(571-573)gGg>gAg	p.G191E	NOX5_ENST00000448182.3_Intron|NOX5_ENST00000455873.3_Intron|NOX5_ENST00000260364.5_Intron|RP11-809H16.2_ENST00000557966.1_RNA|SPESP1_ENST00000560188.1_3'UTR	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	191			G -> E (in dbSNP:rs3743093). {ECO:0000269|PubMed:12773409, ECO:0000269|PubMed:12975309}.		acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						ACTGGCATTGGGATCTCTACA	0.428													A|||	2677	0.534545	0.6399	0.464	5008	,	,		17700	0.4623		0.5905	False		,,,				2504	0.4591				p.G191E		Atlas-SNP	.											.	SPESP1	39	.	0			c.G572A						PASS	.	A	,GLU/GLY	2602,1798	528.2+/-372.3	763,1076,361	114.0	113.0	113.0		,572	-0.3	0.0	15	dbSNP_107	113	5216,3380	499.0+/-374.9	1575,2066,657	yes	intron,missense	NOX5,SPESP1	NM_001184780.1,NM_145658.3	,98	2338,3142,1018	AA,AG,GG		39.3206,40.8636,39.843	,benign	,191/351	69238445	7818,5178	2200	4298	6498	SO:0001583	missense	246777	exon2			GCATTGGGATCTC	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.572G>A	15.37:g.69238445G>A	ENSP00000312284:p.Gly191Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_145658	Q8NG22|Q8WVH8	Missense_Mutation	SNP	ENST00000310673.3	37	CCDS10230.1	1220	0.5586080586080586	311	0.6321138211382114	174	0.48066298342541436	282	0.493006993006993	453	0.5976253298153035	A	0.101	-1.152006	0.01700	0.591364	0.606794	ENSG00000258484	ENST00000310673	T	0.20200	2.09	4.83	-0.354	0.12591	.	1.232680	0.05997	N	0.647055	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	0.45571	-0.9252	9	0.02654	T	1	1.1412	1.0664	0.01611	0.3818:0.1581:0.3066:0.1535	rs3743093;rs57417471;rs3743093	191	Q6UW49	SPESP_HUMAN	E	191	ENSP00000312284:G191E	ENSP00000312284:G191E	G	+	2	0	SPESP1	67025499	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.155000	0.16362	-0.586000	0.05898	-0.360000	0.07572	GGG	G|0.426;A|0.574	0.574	strong		0.428	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658	
IMPG1	3617	hgsc.bcm.edu	37	6	76633385	76633385	+	Missense_Mutation	SNP	C	C	T	rs3778005	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:76633385C>T	ENST00000369950.3	-	16	2471	c.2282G>A	c.(2281-2283)aGt>aAt	p.S761N	IMPG1_ENST00000369963.3_3'UTR	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				CTTTTTAACACTAGTTTTGTA	0.289													C|||	622	0.124201	0.0212	0.2262	5008	,	,		17448	0.0546		0.2634	False		,,,				2504	0.1196				p.S761N	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.G2282A						PASS	.	C	ASN/SER	267,4137	149.2+/-183.4	7,253,1942	133.0	120.0	125.0		2282	0.1	0.0	6	dbSNP_107	125	2239,6355	366.0+/-334.1	314,1611,2372	yes	missense	IMPG1	NM_001563.2	46	321,1864,4314	TT,TC,CC		26.0531,6.0627,19.2799	benign	761/798	76633385	2506,10492	2202	4297	6499	SO:0001583	missense	3617	exon16			TTAACACTAGTTT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.2282G>A	6.37:g.76633385C>T	ENSP00000358966:p.Ser761Asn	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	36	0.330275	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	343	0.15705128205128205	12	0.024390243902439025	92	0.2541436464088398	31	0.05419580419580419	208	0.27440633245382584	C	0.005	-2.192799	0.00302	0.060627	0.260531	ENSG00000112706	ENST00000369950;ENST00000369952	T;T	0.20598	2.06;2.12	4.02	0.0666	0.14362	.	1.486350	0.04588	N	0.396120	T	0.03390	0.0098	N	0.19112	0.55	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.37979	-0.9682	9	0.22109	T	0.4	.	3.3272	0.07071	0.1838:0.514:0.0:0.3022	rs3778005;rs52805553;rs59953815;rs3778005	761	Q17R60	IMPG1_HUMAN	N	761;122	ENSP00000358966:S761N;ENSP00000358968:S122N	ENSP00000358966:S761N	S	-	2	0	IMPG1	76690105	0.000000	0.05858	0.001000	0.08648	0.103000	0.19146	0.064000	0.14437	-0.129000	0.11620	-0.157000	0.13467	AGT	C|0.832;T|0.168	0.168	strong		0.289	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:145274844C>T	ENST00000558170.2	-	2	1258		c.e2+1		ZEB2-AS1_ENST00000427278.3_RNA|ZEB2-AS1_ENST00000610265.1_RNA|ZEB2-AS1_ENST00000609819.1_RNA|ZEB2_ENST00000465070.1_Splice_Site|ZEB2_ENST00000470879.1_Splice_Site|ZEB2-AS1_ENST00000428623.1_RNA|ZEB2_ENST00000539609.3_Splice_Site|ZEB2-AS1_ENST00000595109.1_RNA|ZEB2_ENST00000303660.4_Splice_Site|ZEB2_ENST00000493689.1_Splice_Site|ZEB2-AS1_ENST00000608361.1_RNA|ZEB2-AS1_ENST00000421083.1_RNA|ZEB2_ENST00000409487.3_Splice_Site|ZEB2-AS1_ENST00000609842.1_RNA|ZEB2-AS1_ENST00000609376.1_RNA|ZEB2-AS1_ENST00000602006.1_RNA|ZEB2_ENST00000462355.1_Splice_Site	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		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	50	27	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
ALPK3	57538	hgsc.bcm.edu	37	15	85405995	85405995	+	Missense_Mutation	SNP	T	T	C	rs187316	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:85405995T>C	ENST00000258888.5	+	10	5032	c.4865T>C	c.(4864-4866)cTt>cCt	p.L1622P		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1622	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.		L -> P (in dbSNP:rs187316). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GGGTGTGGCCTTCGGAAGGCC	0.612													T|||	753	0.150359	0.0129	0.2219	5008	,	,		18170	0.1438		0.2714	False		,,,				2504	0.1677				p.L1622P		Atlas-SNP	.											.	ALPK3	289	.	0			c.T4865C						PASS	.	T	PRO/LEU	242,4164	142.3+/-177.5	10,222,1971	79.0	76.0	77.0		4865	3.7	0.5	15	dbSNP_79	77	2353,6245	392.1+/-343.9	316,1721,2262	yes	missense	ALPK3	NM_020778.4	98	326,1943,4233	CC,CT,TT		27.3668,5.4925,19.9554	probably-damaging	1622/1908	85405995	2595,10409	2203	4299	6502	SO:0001583	missense	57538	exon10			GTGGCCTTCGGAA	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4865T>C	15.37:g.85405995T>C	ENSP00000258888:p.Leu1622Pro	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	400	0.18315018315018314	9	0.018292682926829267	88	0.2430939226519337	88	0.15384615384615385	215	0.2836411609498681	T	15.74	2.923941	0.52653	0.054925	0.273668	ENSG00000136383	ENST00000258888	T	0.08193	3.12	4.86	3.7	0.42460	MHCK/EF2 kinase (3);Protein kinase-like domain (1);	0.418235	0.25050	N	0.033523	T	0.00012	0.0000	L	0.47716	1.5	0.29830	P	0.830098	D	0.62365	0.991	P	0.58172	0.834	T	0.40831	-0.9542	9	0.72032	D	0.01	-4.3524	9.7636	0.40548	0.0:0.0:0.1741:0.8259	rs187316;rs52801929;rs187316	1622	Q96L96	ALPK3_HUMAN	P	1622	ENSP00000258888:L1622P	ENSP00000258888:L1622P	L	+	2	0	ALPK3	83206999	0.094000	0.21725	0.465000	0.27155	0.906000	0.53458	1.711000	0.37930	0.838000	0.34948	0.533000	0.62120	CTT	T|0.815;C|0.185	0.185	strong		0.612	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
PRPSAP1	5635	hgsc.bcm.edu	37	17	74307737	74307737	+	Silent	SNP	T	T	C	rs10459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74307737T>C	ENST00000446526.3	-	10	1489	c.1044A>G	c.(1042-1044)caA>caG	p.Q348Q	PRPSAP1_ENST00000588364.1_5'UTR|PRPSAP1_ENST00000324684.4_Silent_p.Q245Q	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	319					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						TCTTGGGACATTGCAGCTTCT	0.453													C|||	1284	0.25639	0.3154	0.17	5008	,	,		22164	0.4444		0.1471	False		,,,				2504	0.1564				p.Q348Q		Atlas-SNP	.											.	PRPSAP1	32	.	0			c.A1044G						PASS	.	C		1373,3033	689.2+/-405.1	200,973,1030	147.0	116.0	127.0		1044	4.9	1.0	17	dbSNP_52	127	1316,7284	758.1+/-407.5	115,1086,3099	no	coding-synonymous	PRPSAP1	NM_002766.2		315,2059,4129	CC,CT,TT		15.3023,31.1621,20.6751		348/386	74307737	2689,10317	2203	4300	6503	SO:0001819	synonymous_variant	5635	exon10			GGGACATTGCAGC	D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.1044A>G	17.37:g.74307737T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_002766	B2R6M4|Q96H06	Silent	SNP	ENST00000446526.3	37	CCDS11743.2																																																																																			T|0.766;C|0.234	0.234	strong		0.453	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766	
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 GAIIx	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_ENST00000377861.3_Missense_Mutation_p.I128K|PCDH9_ENST00000544246.1_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	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	154	54	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 GAIIx	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	IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597029.1_Silent_p.A223A|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000352066.3_Silent_p.A223A|NUP62_ENST00000422090.2_Silent_p.A223A|NUP62_ENST00000597723.1_Silent_p.A223A|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000413454.1_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		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	39	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	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21932625	21932625	+	Silent	SNP	G	G	A	rs2275365	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:21932625G>A	ENST00000374765.4	-	18	1562	c.1362C>T	c.(1360-1362)acC>acT	p.T454T	RAP1GAP_ENST00000542643.2_Silent_p.T454T|RAP1GAP_ENST00000374763.2_Silent_p.T454T|RAP1GAP_ENST00000374761.2_Silent_p.T485T|RAP1GAP_ENST00000290101.4_Silent_p.T518T	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	454					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		TGGTGGACACGGTGTTGGGCT	0.677													g|||	704	0.140575	0.0295	0.2867	5008	,	,		14581	0.2401		0.0765	False		,,,				2504	0.1503				p.T518T		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C1554T						PASS	.	A	,,	217,4183		3,211,1986	61.0	36.0	44.0		1362,1554,1362	-10.1	0.4	1	dbSNP_100	44	893,7685		43,807,3439	no	coding-synonymous,coding-synonymous,coding-synonymous	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	46,1018,5425	AA,AG,GG		10.4104,4.9318,8.5529	,,	454/682,518/728,454/664	21932625	1110,11868	2200	4289	6489	SO:0001819	synonymous_variant	5909	exon18			GGACACGGTGTTG	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1362C>T	1.37:g.21932625G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			G|0.893;A|0.107	0.107	strong		0.677	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
FAT4	79633	hgsc.bcm.edu	37	4	126402890	126402890	+	Silent	SNP	G	G	A	rs6824160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:126402890G>A	ENST00000394329.3	+	15	12826	c.12813G>A	c.(12811-12813)gtG>gtA	p.V4271V	FAT4_ENST00000335110.5_Silent_p.V2512V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4271	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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						ACACTACTGTGAAGGTGAGAT	0.403													G|||	673	0.134385	0.0068	0.1124	5008	,	,		18179	0.2579		0.1302	False		,,,				2504	0.1994				p.V4271V		Atlas-SNP	.											.	FAT4	1752	.	0			c.G12813A						PASS	.	G		124,4282	92.0+/-130.7	5,114,2084	70.0	65.0	67.0		12813	4.9	1.0	4	dbSNP_116	67	1039,7561	219.2+/-257.4	59,921,3320	no	coding-synonymous	FAT4	NM_024582.4		64,1035,5404	AA,AG,GG		12.0814,2.8143,8.942		4271/4982	126402890	1163,11843	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon15			TACTGTGAAGGTG	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.12813G>A	4.37:g.126402890G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			G|0.890;A|0.110	0.110	strong		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
RASL12	51285	hgsc.bcm.edu	37	15	65347405	65347405	+	Silent	SNP	G	G	A	rs2232762	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:65347405G>A	ENST00000220062.4	-	5	909	c.633C>T	c.(631-633)acC>acT	p.T211T	RASL12_ENST00000434605.2_Silent_p.T200T|RASL12_ENST00000421977.3_Silent_p.T192T	NM_016563.2	NP_057647.1	Q9NYN1	RASLC_HUMAN	RAS-like, family 12	211					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			lung(1)|ovary(1)|skin(1)|urinary_tract(1)	4						CATGCCGCGCGGTGAGCGGGG	0.677													G|||	2122	0.423722	0.1876	0.5202	5008	,	,		17548	0.7837		0.4095	False		,,,				2504	0.318				p.T211T		Atlas-SNP	.											.	RASL12	32	.	0			c.C633T						PASS	.	G		1076,3324	371.0+/-319.8	136,804,1260	26.0	24.0	25.0		633	-10.5	0.0	15	dbSNP_98	25	3422,5176	475.0+/-369.0	689,2044,1566	no	coding-synonymous	RASL12	NM_016563.2		825,2848,2826	AA,AG,GG		39.8,24.4545,34.6053		211/267	65347405	4498,8500	2200	4299	6499	SO:0001819	synonymous_variant	51285	exon5			CCGCGCGGTGAGC	AF233588	CCDS10200.1	15q11.2-q22.33	2014-05-09			ENSG00000103710	ENSG00000103710			30289	protein-coding gene	gene with protein product	"""Ras family member Ris"""					12107412	Standard	NM_016563		Approved	RIS	uc002aoi.1	Q9NYN1	OTTHUMG00000133115	ENST00000220062.4:c.633C>T	15.37:g.65347405G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_016563	B2RC29|B4DJW2|B4DU82	Silent	SNP	ENST00000220062.4	37	CCDS10200.1																																																																																			G|0.606;A|0.394	0.394	strong		0.677	RASL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256782.2	NM_016563	
ZCRB1	85437	hgsc.bcm.edu	37	12	42707711	42707711	+	Silent	SNP	C	C	T	rs141493486		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:42707711C>T	ENST00000266529.3	-	6	594	c.411G>A	c.(409-411)aaG>aaA	p.K137K	ZCRB1_ENST00000552673.1_Silent_p.K96K|PPHLN1_ENST00000549190.1_Intron	NM_033114.3	NP_149105.3	Q8TBF4	ZCRB1_HUMAN	zinc finger CCHC-type and RNA binding motif 1	137	Poly-Lys.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.K137K(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)	8	all_cancers(12;0.000348)|Breast(8;0.221)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0689)		TCTTTTTTTTCTTTTTTTCTT	0.343																																					p.K137K		Atlas-SNP	.											ZCRB1,upper_arm,malignant_melanoma,0,1	ZCRB1	20	1	1	Substitution - coding silent(1)	skin(1)	c.G411A						scavenged	.						62.0	62.0	62.0					12																	42707711		2203	4300	6503	SO:0001819	synonymous_variant	85437	exon6			TTTTTTCTTTTTT	BC022543	CCDS8740.1	12q12	2013-02-12				ENSG00000139168		"""Zinc fingers, CCHC domain containing"", ""RNA binding motif (RRM) containing"""	29620	protein-coding gene	gene with protein product	"""U11/U12 snRNP 31K"""	610750				15146077, 16959469	Standard	NM_033114		Approved	MADP-1, MADP1, RBM36, ZCCHC19, SNRNP31	uc001rmz.3	Q8TBF4	OTTHUMG00000169382	ENST00000266529.3:c.411G>A	12.37:g.42707711C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	132	2	0.0151515	NM_033114	Q6PJX0|Q96TA6	Silent	SNP	ENST00000266529.3	37	CCDS8740.1																																																																																			.	.	weak		0.343	ZCRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403813.1	NM_033114	
PCSK5	5125	hgsc.bcm.edu	37	9	78938043	78938043	+	Missense_Mutation	SNP	G	G	A	rs2495207	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:78938043G>A	ENST00000545128.1	+	31	4635	c.4097G>A	c.(4096-4098)cGc>cAc	p.R1366H		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1366	CRM (Cys-rich motif).				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						GCAGACTCGCGCCACTGTGTC	0.567													G|||	1605	0.320487	0.4667	0.2349	5008	,	,		14582	0.1369		0.3529	False		,,,				2504	0.3395				p.R1366H		Atlas-SNP	.											.	PCSK5	329	.	0			c.G4097A						PASS	.	G	HIS/ARG	793,959		189,415,272	30.0	28.0	28.0		4097	-1.5	0.0	9	dbSNP_100	28	1346,2636		236,874,881	yes	missense	PCSK5	NM_001190482.1	29	425,1289,1153	AA,AG,GG		33.8021,45.2626,37.3038	possibly-damaging	1366/1861	78938043	2139,3595	876	1991	2867	SO:0001583	missense	5125	exon31			ACTCGCGCCACTG		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.4097G>A	9.37:g.78938043G>A	ENSP00000446280:p.Arg1366His	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	685	0.31364468864468864	239	0.48577235772357724	98	0.27071823204419887	76	0.13286713286713286	272	0.35883905013192613	G	12.57	1.976900	0.34848	0.452626	0.338021	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.29397	1.57;1.6	5.65	-1.45	0.08828	.	0.871179	0.10360	N	0.684122	T	0.00012	0.0000	M	0.62016	1.91	0.80722	P	0.0	.	.	.	.	.	.	T	0.47923	-0.9079	7	0.42905	T	0.14	-12.1217	7.6077	0.28112	0.4202:0.1113:0.4685:0.0	rs2495207;rs17721339;rs56436828;rs61557544;rs2495207	.	.	.	H	1366;1096;1066	ENSP00000446280:R1366H;ENSP00000411654:R1066H	ENSP00000365945:R1096H	R	+	2	0	PCSK5	78127863	0.000000	0.05858	0.013000	0.15412	0.082000	0.17680	-0.184000	0.09698	0.077000	0.16863	0.650000	0.86243	CGC	G|0.668;A|0.332	0.332	strong		0.567	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
B3GALT5	10317	hgsc.bcm.edu	37	21	41033062	41033062	+	Silent	SNP	G	G	A	rs734412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:41033062G>A	ENST00000380620.4	+	5	1168	c.576G>A	c.(574-576)agG>agA	p.R192R	AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000398714.2_Silent_p.R192R|B3GALT5_ENST00000380618.1_Silent_p.R192R|B3GALT5_ENST00000343118.4_Silent_p.R192R			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	192					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				TTCCCATCAGGCAGCCATTCA	0.468													G|||	106	0.0211661	0.0038	0.036	5008	,	,		16476	0.0		0.0656	False		,,,				2504	0.0102				p.R192R		Atlas-SNP	.											.	B3GALT5	40	.	0			c.G576A						PASS	.	G	,,,,	79,4327	70.3+/-108.2	3,73,2127	67.0	67.0	67.0		576,576,576,576,576	2.7	0.1	21	dbSNP_86	67	723,7877	175.9+/-225.9	36,651,3613	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	B3GALT5	NM_006057.1,NM_033170.1,NM_033171.1,NM_033172.1,NM_033173.1	,,,,	39,724,5740	AA,AG,GG		8.407,1.793,6.1664	,,,,	192/311,192/311,192/311,192/311,192/311	41033062	802,12204	2203	4300	6503	SO:0001819	synonymous_variant	10317	exon3			CATCAGGCAGCCA	AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"""Beta 3-glycosyltransferases"""	920	protein-coding gene	gene with protein product	"""homolog of C. elegans Bt toxin resistance gene bre-5"", ""GlcNAc-beta-1,3-galactosyltransferase 5"""	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.576G>A	21.37:g.41033062G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	75	25	0.333333	NM_033170	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Silent	SNP	ENST00000380620.4	37	CCDS13667.1																																																																																			G|0.950;A|0.050	0.050	strong		0.468	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170	
DHODH	1723	hgsc.bcm.edu	37	16	72042682	72042682	+	Missense_Mutation	SNP	A	A	C	rs3213422	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:72042682A>C	ENST00000219240.4	+	1	40	c.19A>C	c.(19-21)Aaa>Caa	p.K7Q	DHODH_ENST00000572887.1_Missense_Mutation_p.K7Q	NM_001361.4	NP_001352.2	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase (quinone)	7			K -> Q (in dbSNP:rs3213422). {ECO:0000269|PubMed:1446837, ECO:0000269|PubMed:14702039}.		'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of apoptotic process (GO:0043065)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of mitochondrial fission (GO:0090140)|response to caffeine (GO:0031000)|response to drug (GO:0042493)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|neuronal cell body (GO:0043025)	dihydroorotate dehydrogenase activity (GO:0004152)|dihydroorotate oxidase activity (GO:0004158)|drug binding (GO:0008144)|FMN binding (GO:0010181)|ubiquinone binding (GO:0048039)			breast(1)|endometrium(2)|large_intestine(4)|ovary(1)|skin(1)|stomach(1)	10		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)|Teriflunomide(DB08880)	GAGACACCTGAAAGTGAGTCC	0.657													A|||	2825	0.564097	0.5204	0.6441	5008	,	,		16500	0.7381		0.4901	False		,,,				2504	0.4632				p.K7Q		Atlas-SNP	.											DHODH,colon,carcinoma,0,1	DHODH	33	1	0			c.A19C						PASS	.	A	GLN/LYS	2268,1612		715,838,387	31.0	37.0	35.0		19	2.9	1.0	16	dbSNP_106	35	4234,3824		1200,1834,995	yes	missense	DHODH	NM_001361.4	53	1915,2672,1382	CC,CA,AA		47.4559,41.5464,45.5353	benign	7/396	72042682	6502,5436	1940	4029	5969	SO:0001583	missense	1723	exon1			CACCTGAAAGTGA		CCDS42192.1	16q22.2	2012-10-02	2011-09-05		ENSG00000102967	ENSG00000102967	1.3.5.2		2867	protein-coding gene	gene with protein product		126064	"""dihydroorotate dehydrogenase"""			8211381	Standard	NM_001361		Approved		uc002fbp.3	Q02127	OTTHUMG00000178093	ENST00000219240.4:c.19A>C	16.37:g.72042682A>C	ENSP00000219240:p.Lys7Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_001361	A8K8C8|Q6P176	Missense_Mutation	SNP	ENST00000219240.4	37	CCDS42192.1	1246	0.5705128205128205	237	0.4817073170731707	219	0.6049723756906077	413	0.722027972027972	377	0.4973614775725594	A	11.65	1.702177	0.30232	0.584536	0.525441	ENSG00000102967	ENST00000219240	D	0.85013	-1.93	4.01	2.88	0.33553	.	0.499875	0.21331	N	0.076300	T	0.00012	0.0000	L	0.48642	1.525	0.39894	P	0.02618699999999996	B	0.09022	0.002	B	0.10450	0.005	T	0.46233	-0.9206	9	0.30078	T	0.28	-4.161	7.4494	0.27229	0.7786:0.2214:0.0:0.0	rs3213422;rs17665243;rs52805696;rs61491058;rs3213422	7	Q02127	PYRD_HUMAN	Q	7	ENSP00000219240:K7Q	ENSP00000219240:K7Q	K	+	1	0	DHODH	70600183	0.938000	0.31826	0.995000	0.50966	0.471000	0.32888	1.402000	0.34600	0.851000	0.35264	0.472000	0.43445	AAA	A|0.433;C|0.567	0.567	strong		0.657	DHODH-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001361	
CCDC50	152137	hgsc.bcm.edu	37	3	191097966	191097966	+	Missense_Mutation	SNP	T	T	C	rs293813	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:191097966T>C	ENST00000392455.3	+	6	1065	c.467T>C	c.(466-468)aTg>aCg	p.M156T	CCDC50_ENST00000392456.3_Missense_Mutation_p.M332T	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50	156			M -> T (in dbSNP:rs293813).			cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)	p.M332T(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		CCAAGAGTGATGAAAGAAGCT	0.353													C|||	3228	0.644569	0.854	0.5764	5008	,	,		14198	0.6865		0.495	False		,,,				2504	0.5204				p.M332T		Atlas-SNP	.											CCDC50,NS,carcinoma,0,1	CCDC50	39	1	1	Substitution - Missense(1)	stomach(1)	c.T995C						scavenged	.	C	THR/MET,THR/MET	3482,924	351.8+/-311.4	1370,742,91	52.0	52.0	52.0		467,995	0.6	0.0	3	dbSNP_79	52	3965,4635	599.3+/-394.1	923,2119,1258	yes	missense,missense	CCDC50	NM_174908.3,NM_178335.2	81,81	2293,2861,1349	CC,CT,TT		46.1047,20.9714,42.7418	benign,benign	156/307,332/483	191097966	7447,5559	2203	4300	6503	SO:0001583	missense	152137	exon7			GAGTGATGAAAGA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.467T>C	3.37:g.191097966T>C	ENSP00000376249:p.Met156Thr	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	37	CCDS33913.1	1367	0.6259157509157509	411	0.8353658536585366	209	0.5773480662983426	371	0.6486013986013986	376	0.49604221635883905	C	2.262	-0.368957	0.05069	0.790286	0.461047	ENSG00000152492	ENST00000392455;ENST00000392456	T;T	0.28895	1.6;1.59	5.57	0.585	0.17428	.	1.051930	0.07306	N	0.874929	T	0.00012	0.0000	N	0.04746	-0.17	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27502	-1.0072	9	0.17369	T	0.5	.	8.5288	0.33321	0.0:0.4501:0.0:0.5499	rs293813;rs697908;rs1196016;rs11542548;rs17811313;rs52827949;rs293813	156;332	Q8IVM0;Q8IVM0-2	CCD50_HUMAN;.	T	156;332	ENSP00000376249:M156T;ENSP00000376250:M332T	ENSP00000376249:M156T	M	+	2	0	CCDC50	192580660	0.018000	0.18449	0.002000	0.10522	0.001000	0.01503	0.488000	0.22371	-0.118000	0.11851	-1.163000	0.01768	ATG	T|0.396;C|0.603	0.603	strong		0.353	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
MFSD6L	162387	hgsc.bcm.edu	37	17	8700982	8700982	+	Missense_Mutation	SNP	C	C	T	rs2242373	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:8700982C>T	ENST00000329805.4	-	1	1685	c.1457G>A	c.(1456-1458)cGc>cAc	p.R486H		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	486			R -> H (in dbSNP:rs2242373).			integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						CCTCTCCATGCGGGGAGTGGC	0.607													C|||	1001	0.19988	0.2156	0.1182	5008	,	,		19658	0.1915		0.1759	False		,,,				2504	0.2699				p.R486H		Atlas-SNP	.											.	MFSD6L	46	.	0			c.G1457A						PASS	.	C	HIS/ARG	919,3487	346.9+/-309.2	90,739,1374	40.0	41.0	41.0		1457	4.9	0.0	17	dbSNP_98	41	1625,6975	296.3+/-302.9	129,1367,2804	yes	missense	MFSD6L	NM_152599.3	29	219,2106,4178	TT,TC,CC		18.8953,20.8579,19.5602	probably-damaging	486/587	8700982	2544,10462	2203	4300	6503	SO:0001583	missense	162387	exon1			TCCATGCGGGGAG	AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.1457G>A	17.37:g.8700982C>T	ENSP00000330051:p.Arg486His	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_152599	Q6YL34|Q8NA76	Missense_Mutation	SNP	ENST00000329805.4	37	CCDS11146.1	395	0.18086080586080586	109	0.22154471544715448	50	0.13812154696132597	105	0.18356643356643357	131	0.17282321899736147	C	16.73	3.204461	0.58234	0.208579	0.188953	ENSG00000185156	ENST00000329805	D	0.94650	-3.48	4.9	4.9	0.64082	Major facilitator superfamily domain, general substrate transporter (1);	0.381561	0.24534	N	0.037696	T	0.00695	0.0023	L	0.47716	1.5	0.35896	P	0.16996	D	0.65815	0.995	P	0.51918	0.684	T	0.00003	-1.2597	9	0.40728	T	0.16	-7.5296	17.0129	0.86411	0.0:1.0:0.0:0.0	rs2242373;rs58580851;rs2242373	486	Q8IWD5	MFS6L_HUMAN	H	486	ENSP00000330051:R486H	ENSP00000330051:R486H	R	-	2	0	MFSD6L	8641707	0.140000	0.22579	0.025000	0.17156	0.175000	0.22909	4.132000	0.57977	2.531000	0.85337	0.563000	0.77884	CGC	C|0.815;T|0.185	0.185	strong		0.607	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599	
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 GAIIx	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_ENST00000562109.1_Missense_Mutation_p.R1276H|GRIN2A_ENST00000330684.3_Silent_p.S1390S|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R1119H|GRIN2A_ENST00000396575.2_Silent_p.S1390S|GRIN2A_ENST00000404927.2_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		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	32	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		
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057806	46057806	+	Missense_Mutation	SNP	G	G	A	rs4818950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46057806G>A	ENST00000380095.1	+	1	534	c.472G>A	c.(472-474)Gtg>Atg	p.V158M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	158	15 X 5 AA repeats of C-C-X(3).		V -> M (in dbSNP:rs4818950).			keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CGTCTGCTATGTGCCTGTGTG	0.617													G|||	3022	0.603435	0.4342	0.6671	5008	,	,		21756	0.6667		0.6928	False		,,,				2504	0.6299				p.V158M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G472A						PASS	.	G	,MET/VAL	2058,2348	567.7+/-382.2	480,1098,625	281.0	254.0	263.0		,472	-0.3	0.0	21	dbSNP_111	263	5738,2862	672.4+/-402.9	1911,1916,473	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,21	2391,3014,1098	AA,AG,GG		33.2791,46.709,40.0584	,benign	,158/252	46057806	7796,5210	2203	4300	6503	SO:0001583	missense	353333	exon1			TGCTATGTGCCTG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.472G>A	21.37:g.46057806G>A	ENSP00000369438:p.Val158Met	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	1354	0.61996336996337	221	0.4491869918699187	241	0.6657458563535912	369	0.6451048951048951	523	0.6899736147757256	g	0.902	-0.721876	0.03182	0.46709	0.667209	ENSG00000221859	ENST00000380095	T	0.01414	4.92	3.13	-0.278	0.12894	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.38677	0.642	P	0.48334	0.574	T	0.05402	-1.0887	8	0.48119	T	0.1	.	3.0811	0.06262	0.5855:0.0:0.2299:0.1845	rs4818950;rs17004668;rs57325201;rs4818950	158	P60014	KR10A_HUMAN	M	158	ENSP00000369438:V158M	ENSP00000369438:V158M	V	+	1	0	KRTAP10-10	44882234	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.385000	0.02540	-0.309000	0.08779	0.306000	0.20318	GTG	G|0.392;A|0.608	0.608	strong		0.617	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
SLC15A1	6564	hgsc.bcm.edu	37	13	99340771	99340771	+	Silent	SNP	G	G	A	rs8187832	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:99340771G>A	ENST00000376503.5	-	19	1582	c.1527C>T	c.(1525-1527)aaC>aaT	p.N509N		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	509					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	AGCTGCTGATGTTTGCATAAA	0.373													A|||	386	0.0770767	0.2186	0.036	5008	,	,		19652	0.002		0.0199	False		,,,				2504	0.0511				p.N509N		Atlas-SNP	.											.	SLC15A1	92	.	0			c.C1527T						PASS	.	A		850,3556	745.3+/-411.6	105,640,1458	132.0	129.0	130.0		1527	-7.8	0.0	13	dbSNP_119	130	340,8260	804.0+/-407.3	5,330,3965	no	coding-synonymous	SLC15A1	NM_005073.3		110,970,5423	AA,AG,GG		3.9535,19.2919,9.1496		509/709	99340771	1190,11816	2203	4300	6503	SO:0001819	synonymous_variant	6564	exon19			GCTGATGTTTGCA	U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"""Solute carriers"""	10920	protein-coding gene	gene with protein product	"""peptide transporter HPEPT1"", ""bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)"", ""solute carrier family 15 oligopeptide transporter member 1"""	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.1527C>T	13.37:g.99340771G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	110	72	0.654545	NM_005073	Q5VW82	Silent	SNP	ENST00000376503.5	37	CCDS9489.1																																																																																			G|0.925;A|0.075	0.075	strong		0.373	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073	
NUP188	23511	hgsc.bcm.edu	37	9	131767668	131767668	+	Silent	SNP	A	A	C	rs2287363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131767668A>C	ENST00000372577.2	+	40	4617	c.4596A>C	c.(4594-4596)tcA>tcC	p.S1532S	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1532					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						CCTCCTCCTCAAAGCAGCCCG	0.597													C|||	2262	0.451677	0.4728	0.4957	5008	,	,		19526	0.4067		0.4672	False		,,,				2504	0.4223				p.S1532S		Atlas-SNP	.											.	NUP188	140	.	0			c.A4596C						PASS	.	C		2007,2399	582.1+/-385.5	439,1129,635	37.0	38.0	38.0		4596	2.0	1.0	9	dbSNP_100	38	3525,5075	607.7+/-395.3	739,2047,1514	no	coding-synonymous	NUP188	NM_015354.1		1178,3176,2149	CC,CA,AA		40.9884,45.5515,42.5342		1532/1750	131767668	5532,7474	2203	4300	6503	SO:0001819	synonymous_variant	23511	exon40			CTCCTCAAAGCAG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.4596A>C	9.37:g.131767668A>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			A|0.553;C|0.447	0.447	strong		0.597	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
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 GAIIx	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	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	201	11	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	
MST1L	11223	hgsc.bcm.edu	37	1	17084569	17084569	+	RNA	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17084569G>A	ENST00000455405.2	-	0	320							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CTCATAGCCCGTGAGAGGCAT	0.572																																					p.T510M		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,2	.	.	2	0			c.C1529T						scavenged	.																																					11223	exon12			TAGCCCGTGAGAG	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17084569G>A		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	214	13	0.0607477	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	5.254	0.232248	0.09969	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.607170	0.04519	N	0.384290	T	0.20373	0.0490	.	.	.	.	.	.	P;B	0.34743	0.466;0.079	B;B	0.20184	0.02;0.028	T	0.18053	-1.0349	6	0.41790	T	0.15	.	5.8178	0.18506	0.001:0.0:0.999:0.0	.	510;536	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	M	505;510;536	.	ENSP00000439273:T510M	T	-	2	0	MST1P9	16957156	0.919000	0.31177	0.000000	0.03702	0.000000	0.00434	2.306000	0.43673	-0.000000	0.14550	0.000000	0.15137	ACG	.	.	none		0.572	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
DPP10	57628	hgsc.bcm.edu	37	2	116447277	116447277	+	Silent	SNP	G	G	A	rs35766316	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:116447277G>A	ENST00000410059.1	+	6	936	c.456G>A	c.(454-456)tcG>tcA	p.S152S	DPP10_ENST00000409163.1_Silent_p.S102S|DPP10_ENST00000488208.1_3'UTR|DPP10_ENST00000393147.2_Silent_p.S156S|DPP10_ENST00000310323.8_Silent_p.S145S	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	152						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						TTCATTATTCGTATACTGCTT	0.259													A|||	193	0.0385383	0.0038	0.0461	5008	,	,		15983	0.001		0.0885	False		,,,				2504	0.0675				p.S156S		Atlas-SNP	.											DPP10_ENST00000410059,ear,carcinoma,+1,4	DPP10	415	4	0			c.G468A						PASS	.	A	,,,,	87,4317	782.2+/-414.5	2,83,2117	79.0	75.0	77.0		435,468,306,444,456	-8.6	0.6	2	dbSNP_126	77	972,7622	738.1+/-407.0	62,848,3387	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DPP10	NM_001004360.3,NM_001178034.1,NM_001178036.1,NM_001178037.1,NM_020868.3	,,,,	64,931,5504	AA,AG,GG		11.3102,1.9755,8.1474	,,,,	145/790,156/801,102/747,148/793,152/797	116447277	1059,11939	2202	4297	6499	SO:0001819	synonymous_variant	57628	exon6			TTATTCGTATACT	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.456G>A	2.37:g.116447277G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	78	58	0.74359	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Silent	SNP	ENST00000410059.1	37	CCDS46400.1																																																																																			G|0.928;A|0.072	0.072	strong		0.259	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
SUPT20H	55578	hgsc.bcm.edu	37	13	37583831	37583831	+	Missense_Mutation	SNP	G	G	A	rs9469	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:37583831G>A	ENST00000350612.6	-	26	2538	c.2318C>T	c.(2317-2319)aCg>aTg	p.T773M	SUPT20H_ENST00000360252.4_3'UTR|SUPT20H_ENST00000475892.1_3'UTR|SUPT20H_ENST00000356185.3_3'UTR|SUPT20H_ENST00000464744.1_3'UTR	NM_001014286.2	NP_001014308.2	Q8NEM7	SP20H_HUMAN	suppressor of Ty 20 homolog (S. cerevisiae)	773			T -> M (in dbSNP:rs9469). {ECO:0000269|PubMed:15498874}.		autophagy (GO:0006914)|chromatin organization (GO:0006325)|gastrulation (GO:0007369)	SAGA complex (GO:0000124)|SAGA-type complex (GO:0070461)	transcription cofactor activity (GO:0003712)										AGTGGTTGGCGTGCCTCTCTT	0.398													G|||	2069	0.413139	0.0809	0.4222	5008	,	,		16399	0.7232		0.3787	False		,,,				2504	0.5716				p.T773M		Atlas-SNP	.											.	.	.	.	0			c.C2318T						PASS	.	G	MET/THR,	618,3788	266.8+/-267.5	45,528,1630	174.0	167.0	169.0		2318,	4.2	0.9	13	dbSNP_52	169	3425,5175	505.1+/-376.3	692,2041,1567	yes	missense,utr-3	FAM48A	NM_001014286.2,NM_017569.3	81,	737,2569,3197	AA,AG,GG		39.8256,14.0263,31.0857	probably-damaging,	773/780,	37583831	4043,8963	2203	4300	6503	SO:0001583	missense	55578	exon26			GTTGGCGTGCCTC	AF093250	CCDS9362.1, CCDS31959.1, CCDS61311.1	13q13	2012-11-29	2012-11-29	2012-11-29	ENSG00000102710	ENSG00000102710			20596	protein-coding gene	gene with protein product	"""p38 interacting protein"", ""transcription factor (p38 interacting protein)"""	613417	"""chromosome 13 open reading frame 19"", ""family with sequence similarity 48, member A"""	C13orf19, FAM48A		12070015 , 16685401	Standard	NM_001278480		Approved	SPT20, bA421P11.4, P38IP	uc001uwg.3	Q8NEM7	OTTHUMG00000016747	ENST00000350612.6:c.2318C>T	13.37:g.37583831G>A	ENSP00000218894:p.Thr773Met	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	209	89	0.425837	NM_001014286	E7ER46|Q71RF3|Q9Y6A6	Missense_Mutation	SNP	ENST00000350612.6	37	CCDS31959.1	909|909	0.41620879120879123|0.41620879120879123	55|55	0.11178861788617886|0.11178861788617886	154|154	0.425414364640884|0.425414364640884	402|402	0.7027972027972028|0.7027972027972028	298|298	0.39313984168865435|0.39313984168865435	G|G	8.546|8.546	0.874397|0.874397	0.17395|0.17395	0.140263|0.140263	0.398256|0.398256	ENSG00000102710|ENSG00000102710	ENST00000469488|ENST00000350612	.|T	.|0.33654	.|1.4	5.92|5.92	4.18|4.18	0.49190|0.49190	.|.	.|0.112689	.|0.40064	.|N	.|0.001198	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.21448|0.21448	0.665|0.665	0.09310|0.09310	P|P	0.9999999999926429|0.9999999999926429	.|B	.|0.12630	.|0.006	.|B	.|0.09377	.|0.004	T|T	0.28776|0.28776	-1.0033|-1.0033	4|9	.|0.40728	.|T	.|0.16	.|.	10.3486|10.3486	0.43920|0.43920	0.1524:0.0:0.8476:0.0|0.1524:0.0:0.8476:0.0	rs9469;rs3168739;rs52812678;rs60675753;rs9469|rs9469;rs3168739;rs52812678;rs60675753;rs9469	.|773	.|Q8NEM7	.|FA48A_HUMAN	C|M	316|773	.|ENSP00000218894:T773M	.|ENSP00000218894:T773M	R|T	-|-	1|2	0|0	FAM48A|FAM48A	36481831|36481831	1.000000|1.000000	0.71417|0.71417	0.874000|0.874000	0.34290|0.34290	0.857000|0.857000	0.48899|0.48899	3.130000|3.130000	0.50508|0.50508	0.832000|0.832000	0.34804|0.34804	-0.373000|-0.373000	0.07131|0.07131	CGC|ACG	G|0.646;A|0.354	0.354	strong		0.398	SUPT20H-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354766.1	NM_017569	
OR5AU1	390445	hgsc.bcm.edu	37	14	21623489	21623489	+	Silent	SNP	C	C	T	rs45462402	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:21623489C>T	ENST00000304418.3	-	1	733	c.696G>A	c.(694-696)ggG>ggA	p.G232G		NM_001004731.1	NP_001004731.1	Q8NGC0	O5AU1_HUMAN	olfactory receptor, family 5, subfamily AU, member 1	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(12)|pancreas(1)	21	all_cancers(95;0.00238)		Epithelial(56;6.88e-07)|all cancers(55;6.02e-06)	GBM - Glioblastoma multiforme(265;0.0192)		GGATGGGTGGCCCATCACAGA	0.478													T|||	2547	0.508586	0.7262	0.389	5008	,	,		22675	0.6607		0.2087	False		,,,				2504	0.4509				p.G232G		Atlas-SNP	.											.	OR5AU1	46	.	0			c.G696A						PASS	.	T		2886,1520	479.2+/-358.4	951,984,268	83.0	73.0	77.0		696	1.7	1.0	14	dbSNP_127	77	1618,6982	742.1+/-407.2	145,1328,2827	no	coding-synonymous	OR5AU1	NM_001004731.1		1096,2312,3095	TT,TC,CC		18.814,34.4984,34.6302		232/363	21623489	4504,8502	2203	4300	6503	SO:0001819	synonymous_variant	390445	exon1			GGGTGGCCCATCA	AL157687	CCDS32042.1	14q11.2	2013-09-23			ENSG00000169327	ENSG00000169327		"""GPCR / Class A : Olfactory receptors"""	15362	protein-coding gene	gene with protein product							Standard	NM_001004731		Approved		uc010tlp.2	Q8NGC0	OTTHUMG00000170753	ENST00000304418.3:c.696G>A	14.37:g.21623489C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_001004731	B2RP78|Q6IEU2|Q96R10	Silent	SNP	ENST00000304418.3	37	CCDS32042.1																																																																																			C|0.637;T|0.363	0.363	strong		0.478	OR5AU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410213.1		
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 GAIIx	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		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	66	23	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		
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499228	59499228	+	Missense_Mutation	SNP	C	C	T	rs3809529	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:59499228C>T	ENST00000307144.4	+	1	187	c.89C>T	c.(88-90)cCg>cTg	p.P30L	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	30			P -> L (in dbSNP:rs3809529). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						GCCCTGTGTCCGCGTCAAGCA	0.597													C|||	2460	0.491214	0.4735	0.4409	5008	,	,		20601	0.6131		0.34	False		,,,				2504	0.5808				p.P30L		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.C89T						PASS	.	C	,LEU/PRO	1879,2503	542.2+/-376.0	414,1051,726	61.0	55.0	57.0		,89	1.5	0.0	15	dbSNP_107	57	2756,5824	439.8+/-359.3	438,1880,1972	yes	intron,missense	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,98	852,2931,2698	TT,TC,CC		32.1212,42.88,35.7584	,benign	,30/382	59499228	4635,8327	2191	4290	6481	SO:0001583	missense	92483	exon1			TGTGTCCGCGTCA	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.89C>T	15.37:g.59499228C>T	ENSP00000302393:p.Pro30Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	37	CCDS10171.1	984	0.45054945054945056	217	0.4410569105691057	146	0.40331491712707185	363	0.6346153846153846	258	0.3403693931398417	C	7.523	0.657174	0.14580	0.4288	0.321212	ENSG00000171989	ENST00000307144	T	0.68765	-0.35	1.49	1.49	0.22878	.	0.733878	0.10584	U	0.657625	T	0.00012	0.0000	L	0.29908	0.895	0.45946	P	0.0012299999999999534	B	0.15719	0.014	B	0.06405	0.002	T	0.47005	-0.9150	9	0.30854	T	0.27	.	6.8004	0.23748	0.0:1.0:0.0:0.0	rs3809529;rs17856654;rs52793037;rs57306412;rs3809529	30	Q9BYZ2	LDH6B_HUMAN	L	30	ENSP00000302393:P30L	ENSP00000302393:P30L	P	+	2	0	LDHAL6B	57286520	0.011000	0.17503	0.018000	0.16275	0.036000	0.12997	1.945000	0.40273	0.710000	0.31997	0.305000	0.20034	CCG	C|0.613;T|0.387	0.387	strong		0.597	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
PCDHB7	56129	hgsc.bcm.edu	37	5	140554484	140554484	+	Missense_Mutation	SNP	G	G	T	rs1811236	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140554484G>T	ENST00000231137.3	+	1	2242	c.2068G>T	c.(2068-2070)Gtg>Ttg	p.V690L	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	690					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTACCTGGTGGTGGCGTTGGC	0.706													G|||	275	0.0549121	0.1755	0.0447	5008	,	,		22049	0.0		0.0119	False		,,,				2504	0.0				p.V690L		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G2068T						PASS	.	G	LEU/VAL	578,3820		46,486,1667	64.0	100.0	88.0		2068	-3.7	0.0	5	dbSNP_92	88	87,8507		0,87,4210	no	missense	PCDHB7	NM_018940.2	32	46,573,5877	TT,TG,GG		1.0123,13.1423,5.1185	benign	690/794	140554484	665,12327	2199	4297	6496	SO:0001583	missense	56129	exon1			CTGGTGGTGGCGT	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2068G>T	5.37:g.140554484G>T	ENSP00000231137:p.Val690Leu	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	121	34	0.280992	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	113	0.051739926739926737	88	0.17886178861788618	17	0.04696132596685083	0	0.0	8	0.010554089709762533	G	17.07	3.295086	0.60086	0.131423	0.010123	ENSG00000113212	ENST00000231137	T	0.14516	2.5	3.77	-3.74	0.04385	.	.	.	.	.	T	0.00039	0.0001	M	0.79475	2.455	0.40338	P	0.02099799999999996	B	0.22346	0.068	B	0.32805	0.153	T	0.28839	-1.0031	8	0.72032	D	0.01	.	11.8314	0.52297	0.823:0.0:0.177:0.0	rs1811236	690	Q9Y5E2	PCDB7_HUMAN	L	690	ENSP00000231137:V690L	ENSP00000231137:V690L	V	+	1	0	PCDHB7	140534668	0.000000	0.05858	0.003000	0.11579	0.950000	0.60333	0.026000	0.13599	-0.785000	0.04522	0.449000	0.29647	GTG	G|0.943;T|0.057	0.057	strong		0.706	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
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 GAIIx	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	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	110	24	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	
DOCK10	55619	hgsc.bcm.edu	37	2	225727431	225727431	+	Silent	SNP	T	T	C	rs7589474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:225727431T>C	ENST00000258390.7	-	14	1702	c.1635A>G	c.(1633-1635)caA>caG	p.Q545Q	DOCK10_ENST00000409592.3_Silent_p.Q539Q	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	545					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TGCTGCAGAATTGTCTGTTGG	0.318													C|||	860	0.171725	0.4788	0.0548	5008	,	,		16832	0.0317		0.0865	False		,,,				2504	0.0716				p.Q545Q		Atlas-SNP	.											.	DOCK10	308	.	0			c.A1635G						PASS	.	C		1527,2145		317,893,626	93.0	92.0	92.0		1635	1.3	1.0	2	dbSNP_116	92	673,7483		25,623,3430	no	coding-synonymous	DOCK10	NM_014689.2		342,1516,4056	CC,CT,TT		8.2516,41.585,18.5999		545/2187	225727431	2200,9628	1836	4078	5914	SO:0001819	synonymous_variant	55619	exon14			GCAGAATTGTCTG	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.1635A>G	2.37:g.225727431T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	92	31	0.336957	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																			T|0.830;C|0.170	0.170	strong		0.318	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
ATP2C2	9914	hgsc.bcm.edu	37	16	84485677	84485677	+	Missense_Mutation	SNP	T	T	A	rs62640926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84485677T>A	ENST00000262429.4	+	18	1900	c.1811T>A	c.(1810-1812)cTg>cAg	p.L604Q	ATP2C2_ENST00000416219.2_Missense_Mutation_p.L604Q|ATP2C2_ENST00000420010.2_3'UTR	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	604			L -> Q (in dbSNP:rs62640926). {ECO:0000269|PubMed:17974005}.		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						GGGGATGCCCTGGAGACGGCC	0.587													T|||	146	0.0291534	0.0068	0.0447	5008	,	,		17439	0.0069		0.0765	False		,,,				2504	0.0225				p.L604Q		Atlas-SNP	.											.	ATP2C2	75	.	0			c.T1811A						PASS	.	T	GLN/LEU	81,3981		2,77,1952	61.0	67.0	65.0		1811	4.0	1.0	16	dbSNP_129	65	603,7725		31,541,3592	yes	missense	ATP2C2	NM_014861.2	113	33,618,5544	AA,AT,TT		7.2406,1.9941,5.5206	benign	604/947	84485677	684,11706	2031	4164	6195	SO:0001583	missense	9914	exon18			ATGCCCTGGAGAC	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1811T>A	16.37:g.84485677T>A	ENSP00000262429:p.Leu604Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	37	CCDS42207.1	80	0.03663003663003663	3	0.006097560975609756	24	0.06629834254143646	1	0.0017482517482517483	52	0.06860158311345646	T	4.768	0.142831	0.09083	0.019941	0.072406	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	D;D	0.95756	-3.8;-3.8	5.06	3.95	0.45737	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.000000	0.52532	D	0.000066	T	0.38639	0.1048	N	0.03238	-0.38	0.42692	D	0.993589	B;B;B;B	0.14438	0.007;0.002;0.01;0.002	B;B;B;B	0.22880	0.026;0.015;0.025;0.042	T	0.67589	-0.5632	10	0.05436	T	0.98	.	10.4525	0.44531	0.146:0.0:0.0:0.854	rs62640926	604;453;621;604	E7ES94;F8WAA5;O75185-2;O75185	.;.;.;AT2C2_HUMAN	Q	604;604;453	ENSP00000397925:L604Q;ENSP00000262429:L604Q	ENSP00000262429:L604Q	L	+	2	0	ATP2C2	83043178	1.000000	0.71417	0.976000	0.42696	0.217000	0.24651	6.105000	0.71505	0.753000	0.32945	0.459000	0.35465	CTG	T|0.946;A|0.054	0.054	strong		0.587	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248925	48248925	+	Silent	SNP	C	C	A	rs144346550	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48248925C>A	ENST00000246802.5	+	1	147	c.109C>A	c.(109-111)Cgg>Agg	p.R37R	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	37						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GCTGAGGCGGCGGCGGCGAGG	0.662													C|||	61	0.0121805	0.0008	0.0216	5008	,	,		9582	0.0		0.0338	False		,,,				2504	0.0112				p.R37R	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.C109A						PASS	.	C		13,4393		0,13,2190	34.0	43.0	40.0		109	2.2	1.0	19	dbSNP_134	40	179,8417		5,169,4124	no	coding-synonymous	GLTSCR2	NM_015710.4		5,182,6314	AA,AC,CC		2.0824,0.2951,1.4767		37/479	48248925	192,12810	2203	4298	6501	SO:0001819	synonymous_variant	29997	exon1			AGGCGGCGGCGGC	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.109C>A	19.37:g.48248925C>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	138	75	0.543478	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			C|0.981;A|0.019	0.019	strong		0.662	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
TRIM77	390231	hgsc.bcm.edu	37	11	89447375	89447375	+	Missense_Mutation	SNP	C	C	T	rs17221124	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:89447375C>T	ENST00000398290.3	+	3	523	c.523C>T	c.(523-525)Cgg>Tgg	p.R175W		NM_001146162.1	NP_001139634.1	I1YAP6	TRI77_HUMAN	tripartite motif containing 77	175						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										TATAAATTTGCGGAGCATGAT	0.373													C|||	140	0.0279553	0.003	0.0461	5008	,	,		17103	0.0		0.0915	False		,,,				2504	0.0123				p.R175W		Atlas-SNP	.											.	.	.	.	0			c.C523T						PASS	.	C	TRP/ARG	31,1353		1,29,662	69.0	58.0	61.0		523	0.9	0.0	11	dbSNP_123	61	315,2867		14,287,1290	yes	missense	TRIM77P	NM_001146162.1	101	15,316,1952	TT,TC,CC		9.8994,2.2399,7.5777		175/451	89447375	346,4220	692	1591	2283	SO:0001583	missense	390231	exon3			AATTTGCGGAGCA		CCDS60929.1	11q14.3	2014-02-17	2013-01-14	2013-01-14	ENSG00000214414	ENSG00000214414		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	34228	protein-coding gene	gene with protein product			"""tripartite motif-containing 77"", ""tripartite motif containing 77, pseudogene"""	TRIM77P			Standard	NM_001146162		Approved		uc010rtw.2	I1YAP6	OTTHUMG00000167624	ENST00000398290.3:c.523C>T	11.37:g.89447375C>T	ENSP00000474003:p.Arg175Trp	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	75	10	0.133333	NM_001146162		Missense_Mutation	SNP	ENST00000398290.3	37																																																																																				C|0.957;T|0.043	0.043	strong		0.373	TRIM77-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146162	
PCSK5	5125	hgsc.bcm.edu	37	9	78942956	78942956	+	Silent	SNP	A	A	G	rs2259969	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:78942956A>G	ENST00000545128.1	+	32	4828	c.4290A>G	c.(4288-4290)tcA>tcG	p.S1430S		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1430	CRM (Cys-rich motif).				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						CCTGCTCATCATCTGGGACCT	0.607													G|||	2566	0.51238	0.7156	0.451	5008	,	,		18048	0.2123		0.6024	False		,,,				2504	0.498				p.S1430S		Atlas-SNP	.											.	PCSK5	329	.	0			c.A4290G						PASS	.	G		1177,575		406,365,105	394.0	337.0	355.0		4290	-10.4	0.0	9	dbSNP_100	355	2349,1633		705,939,347	no	coding-synonymous	PCSK5	NM_001190482.1		1111,1304,452	GG,GA,AA		41.0095,32.8196,38.5072		1430/1861	78942956	3526,2208	876	1991	2867	SO:0001819	synonymous_variant	5125	exon32			CTCATCATCTGGG		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.4290A>G	9.37:g.78942956A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_001190482	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			A|0.492;G|0.508	0.508	strong		0.607	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CYP4A22	284541	hgsc.bcm.edu	37	1	47609489	47609489	+	Missense_Mutation	SNP	T	T	C	rs10789501	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47609489T>C	ENST00000371891.3	+	6	722	c.691T>C	c.(691-693)Tgt>Cgt	p.C231R	CYP4A22_ENST00000294337.3_Missense_Mutation_p.C231R|CYP4A22_ENST00000371890.3_Intron|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000485117.1_3'UTR	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	231			C -> R (allele CYP4A22*2, allele CYP4A22*3, allele CYP4A22*4, allele CYP4A22*5, allele CYP4A22*6, allele CYP4A22*7, allele CYP4A22*8, allele CYP4A22*9, allele CYP4A22*10, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs10789501). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGTTTTTTGCTGTATGAGGAA	0.552													C|||	2908	0.580671	0.5015	0.464	5008	,	,		20346	0.9335		0.3489	False		,,,				2504	0.6452				p.C231R	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.T691C						PASS	.	C	ARG/CYS	2187,2219		554,1079,570	137.0	125.0	129.0		691	1.9	0.0	1	dbSNP_120	129	2907,5693		483,1941,1876	yes	missense	CYP4A22	NM_001010969.2	180	1037,3020,2446	CC,CT,TT		33.8023,49.6369,39.1665	benign	231/520	47609489	5094,7912	2203	4300	6503	SO:0001583	missense	284541	exon6			TTTTGCTGTATGA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.691T>C	1.37:g.47609489T>C	ENSP00000360958:p.Cys231Arg	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	1188	0.5439560439560439	243	0.49390243902439024	151	0.4171270718232044	539	0.9423076923076923	255	0.33641160949868076	N	0.003	-2.442517	0.00180	0.496369	0.338023	ENSG00000162365	ENST00000371891;ENST00000294337	T;T	0.65732	-0.17;-0.17	1.94	1.94	0.25998	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00000	-3.89	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44922	-0.9296	9	0.02654	T	1	.	3.8065	0.08779	0.4389:0.412:0.0:0.1491	rs10789501;rs56846047;rs10789501	231	Q5TCH4	CP4AM_HUMAN	R	231	ENSP00000360958:C231R;ENSP00000294337:C231R	ENSP00000294337:C231R	C	+	1	0	CYP4A22	47382076	0.014000	0.17966	0.002000	0.10522	0.001000	0.01503	0.053000	0.14184	0.188000	0.20168	-1.033000	0.02402	TGT	T|0.527;C|0.473	0.473	strong		0.552	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
WNT9A	7483	hgsc.bcm.edu	37	1	228113046	228113046	+	Silent	SNP	C	C	T	rs8192629	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228113046C>T	ENST00000272164.5	-	2	280	c.270G>A	c.(268-270)gcG>gcA	p.A90A		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	90					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				GGCACTCGAGCGCACTCATGC	0.697													C|||	414	0.0826677	0.0613	0.0576	5008	,	,		15553	0.0992		0.0696	False		,,,				2504	0.1258				p.A90A		Atlas-SNP	.											.	WNT9A	39	.	0			c.G270A						PASS	.	C		281,4117		5,271,1923	18.0	18.0	18.0		270	-10.2	0.0	1	dbSNP_117	18	803,7789		36,731,3529	no	coding-synonymous	WNT9A	NM_003395.2		41,1002,5452	TT,TC,CC		9.3459,6.3893,8.3449		90/366	228113046	1084,11906	2199	4296	6495	SO:0001819	synonymous_variant	7483	exon2			CTCGAGCGCACTC	AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.270G>A	1.37:g.228113046C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			C|0.927;T|0.073	0.073	strong		0.697	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
KBTBD2	25948	hgsc.bcm.edu	37	7	32909182	32909182	+	Silent	SNP	G	G	A	rs752730	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:32909182G>A	ENST00000304056.4	-	4	2346	c.1647C>T	c.(1645-1647)taC>taT	p.Y549Y	AVL9_ENST00000404479.1_Intron|KBTBD2_ENST00000485611.1_5'Flank	NM_015483.2	NP_056298.2	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2	549										endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|urinary_tract(1)	17			GBM - Glioblastoma multiforme(11;0.0499)			GGTAGGTGACGTATTTAGCTC	0.468													G|||	965	0.192692	0.0756	0.4207	5008	,	,		20479	0.2242		0.2018	False		,,,				2504	0.1472				p.Y549Y		Atlas-SNP	.											.	KBTBD2	37	.	0			c.C1647T						PASS	.	G		400,4006	198.4+/-222.2	15,370,1818	165.0	150.0	155.0		1647	-3.8	0.9	7	dbSNP_86	155	1865,6735	332.8+/-320.3	204,1457,2639	no	coding-synonymous	KBTBD2	NM_015483.2		219,1827,4457	AA,AG,GG		21.686,9.0785,17.415		549/624	32909182	2265,10741	2203	4300	6503	SO:0001819	synonymous_variant	25948	exon4			GGTGACGTATTTA	AB040922	CCDS34614.1	7p14.3	2013-01-08	2003-12-12	2003-12-12	ENSG00000170852	ENSG00000170852		"""BTB/POZ domain containing"""	21751	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 1"""	BKLHD1		10819331	Standard	NM_015483		Approved	DKFZP566C134	uc003tdb.2	Q8IY47	OTTHUMG00000152984	ENST00000304056.4:c.1647C>T	7.37:g.32909182G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	77	19	0.246753	NM_015483	A8K9T7|Q86Y62|Q9P239|Q9UFM7|Q9Y382	Silent	SNP	ENST00000304056.4	37	CCDS34614.1																																																																																			G|0.819;A|0.181	0.181	strong		0.468	KBTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328890.1	XM_291224	
DZIP1L	199221	hgsc.bcm.edu	37	3	137787041	137787041	+	Missense_Mutation	SNP	C	C	T	rs115489792	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:137787041C>T	ENST00000327532.2	-	13	2146	c.1784G>A	c.(1783-1785)gGa>gAa	p.G595E	DZIP1L_ENST00000488595.1_5'Flank	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	595					cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						TCCATGCAGTCCGGGGCGTGG	0.687													C|||	50	0.00998403	0.0008	0.0202	5008	,	,		14611	0.0		0.0308	False		,,,				2504	0.0041				p.G595E		Atlas-SNP	.											.	DZIP1L	88	.	0			c.G1784A						PASS	.	C	GLU/GLY	33,4373	37.6+/-69.7	0,33,2170	40.0	44.0	43.0		1784	2.0	0.0	3	dbSNP_132	43	295,8305	106.8+/-167.6	2,291,4007	yes	missense	DZIP1L	NM_173543.2	98	2,324,6177	TT,TC,CC		3.4302,0.749,2.5219	benign	595/768	137787041	328,12678	2203	4300	6503	SO:0001583	missense	199221	exon13			TGCAGTCCGGGGC	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1784G>A	3.37:g.137787041C>T	ENSP00000332148:p.Gly595Glu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_173543	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	31	0.014194139194139194	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	22	0.029023746701846966	C	9.958	1.222121	0.22457	0.00749	0.034302	ENSG00000158163	ENST00000327532	T	0.37411	1.2	4.91	2.03	0.26663	.	0.490245	0.20959	N	0.082592	T	0.05318	0.0141	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.15723	-1.0427	10	0.25751	T	0.34	-0.0435	7.0789	0.25219	0.0:0.5746:0.3331:0.0923	.	595	Q8IYY4	DZI1L_HUMAN	E	595	ENSP00000332148:G595E	ENSP00000332148:G595E	G	-	2	0	DZIP1L	139269731	0.037000	0.19845	0.002000	0.10522	0.020000	0.10135	0.308000	0.19314	0.623000	0.30267	-0.181000	0.13052	GGA	C|0.980;T|0.020	0.020	strong		0.687	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
NMB	4828	hgsc.bcm.edu	37	15	85200520	85200520	+	Missense_Mutation	SNP	G	G	T	rs1051168	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:85200520G>T	ENST00000360476.3	-	2	612	c.217C>A	c.(217-219)Ccc>Acc	p.P73T	WDR73_ENST00000434634.2_5'Flank|NMB_ENST00000394588.3_Missense_Mutation_p.P73T|WDR73_ENST00000398528.3_5'Flank			P08949	NMB_HUMAN	neuromedin B	73			P -> T (in dbSNP:rs1051168). {ECO:0000269|PubMed:15489334}.	PLGTAPHTS -> HWGQLPTPP (in Ref. 1; AAA59934). {ECO:0000305}.	arachidonic acid secretion (GO:0050482)|cell-cell signaling (GO:0007267)|glucose homeostasis (GO:0042593)|negative regulation of hormone secretion (GO:0046888)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hormone secretion (GO:0046887)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|neuron projection (GO:0043005)	hormone activity (GO:0005179)			endometrium(1)	1				all cancers(203;3.5e-06)		GAGGTGTGGGGAGCTGTCCCC	0.607													G|||	693	0.138379	0.0136	0.1816	5008	,	,		18979	0.1359		0.2584	False		,,,				2504	0.1554				p.P73T		Atlas-SNP	.											.	NMB	14	.	0			c.C217A	GRCh37	CM045181	NMB	M	rs1051168	PASS	.	G	THR/PRO,THR/PRO	228,4176		8,212,1982	33.0	26.0	28.0		217,217	-1.4	0.0	15	dbSNP_86	28	2288,6310		281,1726,2292	yes	missense,missense	NMB	NM_021077.3,NM_205858.1	38,38	289,1938,4274	TT,TG,GG		26.6108,5.1771,19.3509	possibly-damaging,possibly-damaging	73/122,73/155	85200520	2516,10486	2202	4299	6501	SO:0001583	missense	4828	exon2			TGTGGGGAGCTGT		CCDS10332.1, CCDS42076.1	15q25.2-q25.3	2013-09-19			ENSG00000197696	ENSG00000197696			7842	protein-coding gene	gene with protein product		162340				2458345	Standard	NM_021077		Approved	MGC2277, MGC3936, MGC17211	uc002bla.3	P08949	OTTHUMG00000148666	ENST00000360476.3:c.217C>A	15.37:g.85200520G>T	ENSP00000353664:p.Pro73Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_205858	Q96A06|Q96HH5	Missense_Mutation	SNP	ENST00000360476.3	37	CCDS10332.1	358	0.16391941391941392	5	0.01016260162601626	73	0.20165745856353592	81	0.14160839160839161	199	0.262532981530343	G	10.58	1.388808	0.25118	0.051771	0.266108	ENSG00000197696	ENST00000360476;ENST00000394588	T;T	0.47528	0.93;0.84	5.11	-1.37	0.09056	.	0.759821	0.12773	N	0.440331	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	B;B	0.22346	0.068;0.041	B;B	0.23419	0.046;0.021	T	0.23511	-1.0186	9	0.02654	T	1	-8.7065	4.2642	0.10756	0.4384:0.0:0.4065:0.1551	rs1051168;rs3191563;rs17850187;rs17850193;rs17857977;rs1051168	73;73	P08949-2;P08949	.;NMB_HUMAN	T	73	ENSP00000353664:P73T;ENSP00000378089:P73T	ENSP00000353664:P73T	P	-	1	0	NMB	83001524	0.077000	0.21312	0.001000	0.08648	0.943000	0.58893	0.191000	0.17076	0.065000	0.16485	-0.137000	0.14449	CCC	G|0.833;T|0.167	0.167	strong		0.607	NMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308995.1	NM_021077	
CACNA1G	8913	hgsc.bcm.edu	37	17	48703752	48703752	+	Silent	SNP	T	T	C	rs739925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48703752T>C	ENST00000359106.5	+	38	6774	c.6774T>C	c.(6772-6774)ccT>ccC	p.P2258P	CACNA1G_ENST00000358244.5_Silent_p.P2052P|CACNA1G_ENST00000513964.1_Silent_p.P2120P|CACNA1G_ENST00000514717.1_Silent_p.P2108P|CACNA1G_ENST00000360761.4_Silent_p.P2142P|CACNA1G_ENST00000507896.1_Silent_p.P2075P|CACNA1G_ENST00000510366.1_Silent_p.P2113P|CACNA1G_ENST00000352832.5_Silent_p.P2131P|CACNA1G_ENST00000515411.1_Silent_p.P2195P|CACNA1G_ENST00000513689.2_Silent_p.P2168P|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000354983.4_Silent_p.P2224P|CACNA1G_ENST00000502264.1_Silent_p.P2187P|CACNA1G_ENST00000515765.1_Silent_p.P2202P|CACNA1G_ENST00000507336.1_Silent_p.P2247P|CACNA1G_ENST00000503485.1_Silent_p.P2131P|CACNA1G_ENST00000512389.1_Silent_p.P2154P|CACNA1G_ENST00000510115.1_Silent_p.P2179P|CACNA1G_ENST00000514181.1_Silent_p.P2140P|CACNA1G_ENST00000515165.1_Silent_p.P2165P|CACNA1G_ENST00000514079.1_Silent_p.P2172P|CACNA1G_ENST00000442258.2_Silent_p.P2124P|CACNA1G_ENST00000507609.1_Silent_p.P2158P|CACNA1G_ENST00000429973.2_Silent_p.P2147P|CACNA1G_ENST00000505165.1_Silent_p.P2086P|CACNA1G_ENST00000507510.2_Silent_p.P2213P	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2258					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGCGCCGGCCTACGTCCTGGC	0.677											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1839	0.367212	0.5393	0.2651	5008	,	,		14167	0.1786		0.4433	False		,,,				2504	0.3231				p.P2258P		Atlas-SNP	.											.	CACNA1G	659	.	0			c.T6774C						PASS	.	C	,,,,,,,,,,,,,	2057,2001		538,981,510	16.0	21.0	19.0		6774,6156,6705,6462,6537,6606,6426,6561,6495,6639,6441,6393,6372,6672	-10.9	0.0	17	dbSNP_86	19	3608,4724		780,2048,1338	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1	,,,,,,,,,,,,,	1318,3029,1848	CC,CT,TT		43.3029,49.31,45.7224	,,,,,,,,,,,,,	2258/2378,2052/2172,2235/2355,2154/2274,2179/2299,2202/2322,2142/2262,2187/2307,2165/2285,2213/2333,2147/2267,2131/2251,2124/2244,2224/2344	48703752	5665,6725	2029	4166	6195	SO:0001819	synonymous_variant	8913	exon38			CCGGCCTACGTCC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.6774T>C	17.37:g.48703752T>C		Somatic	132	0	0	956	WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																			T|0.603;G|0.006	.	strong		0.677	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
SDCCAG8	10806	hgsc.bcm.edu	37	1	243579112	243579112	+	Silent	SNP	G	G	A	rs10927011	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:243579112G>A	ENST00000366541.3	+	14	1843	c.1725G>A	c.(1723-1725)gaG>gaA	p.E575E	SDCCAG8_ENST00000355875.4_Silent_p.E532E|SDCCAG8_ENST00000343783.6_Silent_p.E430E	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	575	Gln-rich.|Mediates interaction with OFD1.|Sufficient for homodimerization. {ECO:0000250}.				establishment of cell polarity (GO:0030010)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|tube formation (GO:0035148)	cell-cell junction (GO:0005911)|centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(71;0.000545)|all_epithelial(71;0.000509)|all_lung(81;0.0821)|Ovarian(71;0.0919)|all_neural(11;0.101)|Breast(184;0.218)	all_cancers(173;0.00395)	all cancers(7;1.58e-07)|GBM - Glioblastoma multiforme(7;5.12e-06)|OV - Ovarian serous cystadenocarcinoma(106;0.00392)	COAD - Colon adenocarcinoma(196;0.145)		AGCAAATGGAGGCCCAGCATG	0.512													G|||	2201	0.439497	0.0938	0.5403	5008	,	,		19283	0.7847		0.498	False		,,,				2504	0.4192				p.E575E		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.G1725A						PASS	.	G		724,3682	297.3+/-284.7	64,596,1543	80.0	72.0	75.0		1725	1.5	1.0	1	dbSNP_120	75	4377,4223	582.0+/-391.3	1102,2173,1025	no	coding-synonymous	SDCCAG8	NM_006642.3		1166,2769,2568	AA,AG,GG		49.1047,16.4321,39.2204		575/714	243579112	5101,7905	2203	4300	6503	SO:0001819	synonymous_variant	10806	exon14			AATGGAGGCCCAG	AF039690	CCDS31075.1	1q43	2011-08-02			ENSG00000054282	ENSG00000054282			10671	protein-coding gene	gene with protein product		613524				9610721, 20835237	Standard	NM_006642		Approved	NY-CO-8, CCCAP, SLSN7, NPHP10, BBS16	uc001hzw.3	Q86SQ7	OTTHUMG00000039996	ENST00000366541.3:c.1725G>A	1.37:g.243579112G>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	262	134	0.51145	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Silent	SNP	ENST00000366541.3	37	CCDS31075.1																																																																																			G|0.576;A|0.424	0.424	strong		0.512	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642	
TSPAN18	90139	hgsc.bcm.edu	37	11	44940828	44940828	+	Missense_Mutation	SNP	G	G	A	rs2291334	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:44940828G>A	ENST00000520358.2	+	7	812	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	TSPAN18_ENST00000340160.3_Missense_Mutation_p.V133I			Q96SJ8	TSN18_HUMAN	tetraspanin 18	133			V -> I (in dbSNP:rs2291334). {ECO:0000269|PubMed:12975309}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						CGACACAGACGTCTTCTCTGC	0.557													G|||	1738	0.347045	0.034	0.415	5008	,	,		21259	0.5575		0.329	False		,,,				2504	0.5235				p.V133I		Atlas-SNP	.											TSPAN18,colon,carcinoma,-2,1	TSPAN18	38	1	0			c.G397A						PASS	.	G	ILE/VAL	440,3966	212.5+/-232.4	25,390,1788	199.0	154.0	170.0		397	2.4	0.5	11	dbSNP_100	170	2937,5661	458.0+/-364.5	502,1933,1864	yes	missense	TSPAN18	NM_130783.4	29	527,2323,3652	AA,AG,GG		34.1591,9.9864,25.9689	benign	133/249	44940828	3377,9627	2203	4299	6502	SO:0001583	missense	90139	exon6			ACAGACGTCTTCT	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"""Tetraspanins"""	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.397G>A	11.37:g.44940828G>A	ENSP00000429993:p.Val133Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_130783	Q6UY44|Q8NBI9	Missense_Mutation	SNP	ENST00000520358.2	37	CCDS7910.1	743|743	0.3402014652014652|0.3402014652014652	20|20	0.04065040650406504|0.04065040650406504	154|154	0.425414364640884|0.425414364640884	316|316	0.5524475524475524|0.5524475524475524	253|253	0.3337730870712401|0.3337730870712401	G|G	11.55|11.55	1.671289|1.671289	0.29693|0.29693	0.099864|0.099864	0.341591|0.341591	ENSG00000157570|ENSG00000157570	ENST00000518429|ENST00000533786;ENST00000533080;ENST00000520358;ENST00000520999;ENST00000340160	.|T;D;D;T;D	.|0.86956	.|-1.27;-2.19;-2.19;-1.27;-2.19	5.29|5.29	2.4|2.4	0.29515|0.29515	.|Tetraspanin, EC2 domain (1);	.|0.405863	.|0.28989	.|N	.|0.013489	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38838|0.38838	1.175|1.175	0.09310|0.09310	P|P	0.9999999999999999|0.9999999999999999	.|B;B	.|0.32302	.|0.205;0.363	.|B;B	.|0.34385	.|0.04;0.181	T|T	0.44651|0.44651	-0.9314|-0.9314	4|9	.|0.36615	.|T	.|0.2	.|.	9.2617|9.2617	0.37616|0.37616	0.2416:0.0:0.7584:0.0|0.2416:0.0:0.7584:0.0	rs2291334;rs17787220;rs58600094;rs2291334|rs2291334;rs17787220;rs58600094;rs2291334	.|133;133	.|Q8WUV1;Q96SJ8	.|.;TSN18_HUMAN	H|I	136|133;68;133;143;133	.|ENSP00000433592:V133I;ENSP00000433362:V68I;ENSP00000429993:V133I;ENSP00000427942:V143I;ENSP00000339820:V133I	.|ENSP00000339820:V133I	R|V	+|+	2|1	0|0	TSPAN18|TSPAN18	44897404|44897404	1.000000|1.000000	0.71417|0.71417	0.546000|0.546000	0.28166|0.28166	0.227000|0.227000	0.25037|0.25037	5.142000|5.142000	0.64820|0.64820	0.622000|0.622000	0.30249|0.30249	0.462000|0.462000	0.41574|0.41574	CGT|GTC	G|0.711;A|0.289	0.289	strong		0.557	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	
RHOD	29984	hgsc.bcm.edu	37	11	66834252	66834252	+	Silent	SNP	C	C	T	rs2282502	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:66834252C>T	ENST00000308831.2	+	3	349	c.264C>T	c.(262-264)gaC>gaT	p.D88D	RHOD_ENST00000533360.1_Silent_p.D88D|RHOD_ENST00000532559.1_Intron	NM_014578.3	NP_055393	O00212	RHOD_HUMAN	ras homolog family member D	88					actin filament bundle assembly (GO:0051017)|focal adhesion assembly (GO:0048041)|GTP catabolic process (GO:0006184)|lamellipodium assembly (GO:0030032)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			lung(3)	3						TCTACCCTGACGCCAGCGTCC	0.617													c|||	1912	0.381789	0.1566	0.5115	5008	,	,		19622	0.4524		0.3628	False		,,,				2504	0.5409				p.D88D		Atlas-SNP	.											.	RHOD	8	.	0			c.C264T						PASS	.	T		832,3568	327.7+/-300.2	82,668,1450	160.0	144.0	149.0		264	-9.8	0.1	11	dbSNP_100	149	3126,5464	476.4+/-369.4	574,1978,1743	no	coding-synonymous	RHOD	NM_014578.3		656,2646,3193	TT,TC,CC		36.3912,18.9091,30.4696		88/211	66834252	3958,9032	2200	4295	6495	SO:0001819	synonymous_variant	29984	exon3			CCCTGACGCCAGC	D85815	CCDS8155.1, CCDS73330.1	11q14.3	2012-02-27	2012-02-27	2004-03-24	ENSG00000173156	ENSG00000173156			670	protein-coding gene	gene with protein product	"""Rho-related protein HP1"", ""Rho-related GTP-binding protein RhoD"""	605781	"""ras homolog gene family, member D"""	ARHD		9116026	Standard	NM_014578		Approved	RhoHP1, RhoD, Rho	uc001ojv.3	O00212	OTTHUMG00000167102	ENST00000308831.2:c.264C>T	11.37:g.66834252C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_014578		Silent	SNP	ENST00000308831.2	37	CCDS8155.1																																																																																			C|0.683;G|0.000;T|0.317	0.317	strong		0.617	RHOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393136.1	NM_014578	
KCNE3	10008	hgsc.bcm.edu	37	11	74168411	74168411	+	Silent	SNP	A	A	G	rs2270676	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:74168411A>G	ENST00000310128.4	-	3	617	c.198T>C	c.(196-198)ttT>ttC	p.F66F	RP11-702H23.6_ENST00000530510.1_RNA|RP11-702H23.4_ENST00000533008.1_RNA|KCNE3_ENST00000525550.1_Silent_p.F66F	NM_005472.4	NP_005463.1	Q9Y6H6	KCNE3_HUMAN	potassium voltage-gated channel, Isk-related family, member 3	66					regulation of potassium ion transport (GO:0043266)	integral component of membrane (GO:0016021)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			cervix(1)|large_intestine(1)|lung(1)|ovary(1)	4	Breast(11;2.86e-06)					CAGCAAATAGAAACATGACAA	0.542													A|||	707	0.141174	0.1241	0.0879	5008	,	,		19189	0.1627		0.1103	False		,,,				2504	0.2117				p.F66F		Atlas-SNP	.											.	KCNE3	7	.	0			c.T198C	GRCh37	CM057459	KCNE3	M	rs2270676	PASS	.	A		551,3849	246.5+/-255.1	32,487,1681	78.0	68.0	72.0	http://www.ncbi.nlm.nih.gov/pubmed?term	198	1.2	1.0	11	dbSNP_100	72	931,7655	205.6+/-248.0	57,817,3419	no	coding-synonymous	KCNE3	NM_005472.4		89,1304,5100	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	10.8432,12.5227,11.4123		66/104	74168411	1482,11504	2200	4293	6493	SO:0001819	synonymous_variant	10008	exon3			AAATAGAAACATG	AF076531	CCDS8232.1	11q13.4	2014-09-17				ENSG00000175538		"""Potassium channels"""	6243	protein-coding gene	gene with protein product		604433				10219239	Standard	NM_005472		Approved	MiRP2, HOKPP	uc001ovc.3	Q9Y6H6		ENST00000310128.4:c.198T>C	11.37:g.74168411A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	119	28	0.235294	NM_005472		Silent	SNP	ENST00000310128.4	37	CCDS8232.1																																																																																			A|0.881;G|0.119	0.119	strong		0.542	KCNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385531.1	NM_005472	
EPB41L2	2037	hgsc.bcm.edu	37	6	131179302	131179302	+	Missense_Mutation	SNP	C	C	G	rs61731767	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:131179302C>G	ENST00000337057.3	-	19	3173	c.2992G>C	c.(2992-2994)Gag>Cag	p.E998Q	EPB41L2_ENST00000529208.1_Missense_Mutation_p.E928Q|EPB41L2_ENST00000530757.1_Missense_Mutation_p.E194Q|EPB41L2_ENST00000527659.1_Missense_Mutation_p.E804Q|EPB41L2_ENST00000530481.1_Missense_Mutation_p.E845Q|EPB41L2_ENST00000524581.1_Missense_Mutation_p.E376Q|EPB41L2_ENST00000525271.1_Missense_Mutation_p.E666Q|EPB41L2_ENST00000525193.1_Missense_Mutation_p.E699Q|EPB41L2_ENST00000368128.2_Missense_Mutation_p.E998Q|EPB41L2_ENST00000531410.1_Missense_Mutation_p.E119Q|EPB41L2_ENST00000528282.1_Missense_Mutation_p.E740Q|EPB41L2_ENST00000445890.2_Missense_Mutation_p.E740Q|EPB41L2_ENST00000392427.3_Missense_Mutation_p.E666Q|EPB41L2_ENST00000527411.1_Missense_Mutation_p.E928Q	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	998	C-terminal (CTD).				cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		TCAGCCAACTCTGTTTCTTTG	0.522													C|||	61	0.0121805	0.0008	0.0159	5008	,	,		20718	0.0		0.0427	False		,,,				2504	0.0061				p.E998Q		Atlas-SNP	.											.	EPB41L2	96	.	0			c.G2992C						PASS	.	C	GLN/GLU,GLN/GLU,GLN/GLU,GLN/GLU,GLN/GLU	34,4372	38.4+/-70.7	1,32,2170	361.0	257.0	292.0		1996,1996,2533,2533,2992	5.3	0.0	6	dbSNP_129	292	409,8191	128.5+/-186.7	13,383,3904	yes	missense,missense,missense,missense,missense	EPB41L2	NM_001135554.1,NM_001135555.2,NM_001199388.1,NM_001199389.1,NM_001431.3	29,29,29,29,29	14,415,6074	GG,GC,CC		4.7558,0.7717,3.4061	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	666/674,666/674,845/853,845/853,998/1006	131179302	443,12563	2203	4300	6503	SO:0001583	missense	2037	exon19			CCAACTCTGTTTC	AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.2992G>C	6.37:g.131179302C>G	ENSP00000338481:p.Glu998Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001431	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Missense_Mutation	SNP	ENST00000337057.3	37	CCDS5141.1	41	0.018772893772893772	0	0.0	8	0.022099447513812154	0	0.0	33	0.04353562005277045	C	29.6	5.016111	0.93404	0.007717	0.047558	ENSG00000079819	ENST00000531410;ENST00000528282;ENST00000530481;ENST00000445890;ENST00000337057;ENST00000530757;ENST00000392427;ENST00000368128;ENST00000527411;ENST00000524581;ENST00000525271;ENST00000525193;ENST00000527659;ENST00000529208	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55;-1.55	6.16	5.29	0.74685	Band 4.1, C-terminal (1);	0.188928	0.56097	D	0.000039	D	0.88614	0.6484	M	0.77616	2.38	0.42425	D	0.992656	D;D;P;P;D;D	0.89917	0.996;0.99;0.901;0.774;0.999;1.0	D;D;P;D;D;D	0.79784	0.989;0.93;0.475;0.914;0.993;0.992	D	0.89107	0.3493	10	0.45353	T	0.12	.	15.4433	0.75204	0.0:0.9339:0.0:0.0661	rs61731767	666;845;998;740;376;165	B4DHI8;E9PPD9;O43491;Q68DV2;Q6R5J7;Q9UG62	.;.;E41L2_HUMAN;.;.;.	Q	119;740;845;740;998;194;666;998;928;376;666;699;804;928	ENSP00000434596:E119Q;ENSP00000434308:E740Q;ENSP00000434576:E845Q;ENSP00000402041:E740Q;ENSP00000338481:E998Q;ENSP00000436349:E194Q;ENSP00000376222:E666Q;ENSP00000357110:E998Q;ENSP00000436348:E928Q;ENSP00000437207:E376Q;ENSP00000432803:E666Q;ENSP00000431988:E699Q;ENSP00000431647:E804Q;ENSP00000436641:E928Q	ENSP00000338481:E998Q	E	-	1	0	EPB41L2	131220995	1.000000	0.71417	0.032000	0.17829	0.687000	0.40016	5.757000	0.68766	1.612000	0.50221	0.650000	0.86243	GAG	C|0.961;G|0.039	0.039	strong		0.522	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3		
OR4C6	219432	hgsc.bcm.edu	37	11	55432843	55432843	+	Silent	SNP	G	G	A	rs191322588		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:55432843G>A	ENST00000314259.3	+	1	230	c.201G>A	c.(199-201)ttG>ttA	p.L67L		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	67						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L67L(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						TGTCCCTTTTGGATGTCATGT	0.448													g|||	1	0.000199681	0.0008	0.0	5008	,	,		19868	0.0		0.0	False		,,,				2504	0.0				p.L67L		Atlas-SNP	.											OR4C6,NS,carcinoma,0,1	OR4C6	114	1	1	Substitution - coding silent(1)	lung(1)	c.G201A						scavenged	.						283.0	245.0	258.0					11																	55432843		2200	4296	6496	SO:0001819	synonymous_variant	219432	exon1			CCTTTTGGATGTC	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"""GPCR / Class A : Olfactory receptors"""	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.201G>A	11.37:g.55432843G>A		Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	246	3	0.0121951	NM_001004704	B2RP11|Q6IFD2	Silent	SNP	ENST00000314259.3	37	CCDS31506.1																																																																																			G|1.000;A|0.000	0.000	strong		0.448	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704	
SMU1	55234	hgsc.bcm.edu	37	9	33062128	33062128	+	Silent	SNP	G	G	A	rs2274764	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33062128G>A	ENST00000397149.3	-	5	599	c.549C>T	c.(547-549)acC>acT	p.T183T	SMU1_ENST00000536631.1_Silent_p.T22T	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	183						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|lung(4)|ovary(2)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)		ACAAATCTATGGTCATACCAG	0.423													G|||	346	0.0690895	0.0091	0.0951	5008	,	,		20251	0.122		0.0358	False		,,,				2504	0.1115				p.T183T		Atlas-SNP	.											.	SMU1	29	.	0			c.C549T						PASS	.	G		71,4335	65.8+/-103.3	1,69,2133	124.0	113.0	117.0		549	-2.0	1.0	9	dbSNP_100	117	313,8287	112.5+/-172.7	5,303,3992	no	coding-synonymous	SMU1	NM_018225.2		6,372,6125	AA,AG,GG		3.6395,1.6114,2.9525		183/514	33062128	384,12622	2203	4300	6503	SO:0001819	synonymous_variant	55234	exon5			ATCTATGGTCATA	AK001667	CCDS6534.1	9p12	2013-01-10			ENSG00000122692	ENSG00000122692		"""WD repeat domain containing"""	18247	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 57"""					11438655, 11410362	Standard	NM_018225		Approved	SMU-1, FLJ10805, BWD, fSAP57	uc003zsf.1	Q2TAY7	OTTHUMG00000019757	ENST00000397149.3:c.549C>T	9.37:g.33062128G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_018225	B4E3L0|Q9BU59|Q9HA96|Q9NVD1	Silent	SNP	ENST00000397149.3	37	CCDS6534.1																																																																																			G|0.960;A|0.040	0.040	strong		0.423	SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052022.1	NM_018225	
ESPL1	9700	hgsc.bcm.edu	37	12	53682326	53682326	+	Silent	SNP	G	G	A	rs1110720	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53682326G>A	ENST00000257934.4	+	20	4642	c.4551G>A	c.(4549-4551)ggG>ggA	p.G1517G	ESPL1_ENST00000552462.1_Silent_p.G1517G	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1517					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						CCCCAGGTGGGAAGACTCCAG	0.567											OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3232	0.645367	0.4327	0.6326	5008	,	,		17084	0.8204		0.6382	False		,,,				2504	0.7689				p.G1517G	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.G4551A						PASS	.	G		1951,2455		420,1111,672	27.0	26.0	26.0		4551	3.0	0.8	12	dbSNP_86	26	5464,3134		1747,1970,582	no	coding-synonymous	ESPL1	NM_012291.4		2167,3081,1254	AA,AG,GG		36.4503,44.2805,42.9791		1517/2121	53682326	7415,5589	2203	4299	6502	SO:0001819	synonymous_variant	9700	exon20			AGGTGGGAAGACT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.4551G>A	12.37:g.53682326G>A		Somatic	53	0	0	994	WXS	Illumina HiSeq	Phase_I	62	60	0.967742	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																			G|0.402;A|0.598	0.598	strong		0.567	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
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 GAIIx	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	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	137	20	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	
OR12D3	81797	hgsc.bcm.edu	37	6	29342775	29342775	+	Missense_Mutation	SNP	G	G	A	rs3749971	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29342775G>A	ENST00000396806.3	-	1	293	c.290C>T	c.(289-291)aCc>aTc	p.T97I	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	97			T -> I (in dbSNP:rs3749971). {ECO:0000269|PubMed:14574404}.			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						GTGTAGCTGGGTGATACAGCC	0.468													G|||	155	0.0309505	0.0106	0.0288	5008	,	,		20049	0.0327		0.0746	False		,,,				2504	0.0133				p.T97I		Atlas-SNP	.											OR12D3,NS,carcinoma,0,3	OR12D3	55	3	0			c.C290T						scavenged	.	G	ILE/THR	71,2949		1,69,1440	57.0	60.0	59.0		290	2.3	0.8	6	dbSNP_107	59	515,4901		28,459,2221	yes	missense	OR12D3	NM_030959.2	89	29,528,3661	AA,AG,GG		9.5089,2.351,6.9464	benign	97/317	29342775	586,7850	1510	2708	4218	SO:0001583	missense	81797	exon1			AGCTGGGTGATAC		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.290C>T	6.37:g.29342775G>A	ENSP00000380023:p.Thr97Ile	Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	76	62	0.815789	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	96	0.04395604395604396	8	0.016260162601626018	9	0.024861878453038673	18	0.03146853146853147	61	0.08047493403693931	G	2.381	-0.342065	0.05243	0.02351	0.095089	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.01240	5.12	4.18	2.32	0.28847	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00608	0.0020	L	0.35723	1.085	0.80722	P	0.0	B	0.17465	0.022	B	0.18561	0.022	T	0.41752	-0.9491	8	0.38643	T	0.18	-4.3866	9.8495	0.41048	0.1766:0.0:0.8234:0.0	rs3749971;rs17346008;rs58992854;rs3749971	97	Q9UGF7	O12D3_HUMAN	I	97	ENSP00000380023:T97I	ENSP00000366348:T97I	T	-	2	0	OR12D3	29450754	0.000000	0.05858	0.829000	0.32907	0.092000	0.18411	0.870000	0.28010	0.946000	0.37632	0.195000	0.17529	ACC	G|0.942;A|0.058	0.058	strong		0.468	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
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 GAIIx	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	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	23	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	
PTBP1	5725	hgsc.bcm.edu	37	19	808586	808586	+	Silent	SNP	C	C	G	rs13169	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:808586C>G	ENST00000349038.4	+	12	1282	c.1209C>G	c.(1207-1209)ccC>ccG	p.P403P	PTBP1_ENST00000356948.6_Silent_p.P429P|PTBP1_ENST00000394601.4_Silent_p.P422P|PTBP1_ENST00000350092.4_Silent_p.P69P	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	403	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)	p.P429P(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		ACGGGAAGCCCATCCGCATCA	0.697													C|||	805	0.160743	0.1339	0.2666	5008	,	,		9699	0.0218		0.1451	False		,,,				2504	0.2812				p.P429P		Atlas-SNP	.											PTBP1,NS,lymphoid_neoplasm,0,1	PTBP1	43	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1287G						PASS	.	C	,,,	558,3840		44,470,1685	37.0	29.0	31.0		1287,1266,1209,207	-10.3	0.3	19	dbSNP_52	31	1250,7346		87,1076,3135	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	131,1546,4820	GG,GC,CC		14.5416,12.6876,13.9141	,,,	429/558,422/551,403/532,69/198	808586	1808,11186	2199	4298	6497	SO:0001819	synonymous_variant	5725	exon13			GAAGCCCATCCGC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.1209C>G	19.37:g.808586C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_002819	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.867;G|0.133	0.133	strong		0.697	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
TMPRSS6	164656	hgsc.bcm.edu	37	22	37499386	37499386	+	Silent	SNP	C	C	T	rs11704654	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:37499386C>T	ENST00000346753.3	-	2	215	c.99G>A	c.(97-99)ccG>ccA	p.P33P	TMPRSS6_ENST00000381792.2_Silent_p.P24P|TMPRSS6_ENST00000406725.1_Silent_p.P24P|TMPRSS6_ENST00000442782.2_Silent_p.P33P|TMPRSS6_ENST00000406856.1_Silent_p.P24P	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	33					angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						ACATCCCCTCCGGCTCCGCTT	0.662													C|||	759	0.151558	0.1528	0.1124	5008	,	,		17102	0.131		0.1879	False		,,,				2504	0.1616				p.P33P		Atlas-SNP	.											TMPRSS6,NS,carcinoma,-2,2	TMPRSS6	99	2	0			c.G99A						scavenged	.	C		653,3753	276.6+/-273.2	45,563,1595	87.0	94.0	91.0		99	-8.1	0.8	22	dbSNP_120	91	1671,6929	307.4+/-308.4	164,1343,2793	no	coding-synonymous	TMPRSS6	NM_153609.2		209,1906,4388	TT,TC,CC		19.4302,14.8207,17.8687		33/812	37499386	2324,10682	2203	4300	6503	SO:0001819	synonymous_variant	164656	exon2			CCCCTCCGGCTCC	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.99G>A	22.37:g.37499386C>T		Somatic	71	1	0.0140845		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			C|0.825;T|0.175	0.175	strong		0.662	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
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 GAIIx	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		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	44	20	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	
BRDT	676	hgsc.bcm.edu	37	1	92445257	92445257	+	Missense_Mutation	SNP	C	C	G	rs3088232	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:92445257C>G	ENST00000362005.3	+	9	1648	c.1230C>G	c.(1228-1230)aaC>aaG	p.N410K	BRDT_ENST00000399546.2_Missense_Mutation_p.N410K|BRDT_ENST00000402388.1_Missense_Mutation_p.N410K|BRDT_ENST00000370389.2_Missense_Mutation_p.N337K|BRDT_ENST00000394530.3_Missense_Mutation_p.N364K	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	410			N -> K (in dbSNP:rs3088232). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		CTGAAGGGAACTCTTCTGATG	0.398													C|||	653	0.130391	0.0242	0.2392	5008	,	,		15081	0.0278		0.2167	False		,,,				2504	0.2137				p.N414K		Atlas-SNP	.											.	BRDT	133	.	0			c.C1242G						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN	260,4146	149.9+/-184.0	7,246,1950	110.0	108.0	109.0		1230,1242,1092,1092,1011,1230,1230	3.8	0.9	1	dbSNP_102	109	2137,6463	368.2+/-335.0	259,1619,2422	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	94,94,94,94,94,94,94	266,1865,4372	GG,GC,CC		24.8488,5.901,18.43	benign,benign,benign,benign,benign,benign,benign	410/948,414/952,364/902,364/902,337/875,410/948,410/948	92445257	2397,10609	2203	4300	6503	SO:0001583	missense	676	exon8			AGGGAACTCTTCT	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.1230C>G	1.37:g.92445257C>G	ENSP00000354568:p.Asn410Lys	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	147	145	0.986395	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	293	0.13415750915750915	20	0.04065040650406504	78	0.2154696132596685	18	0.03146853146853147	177	0.23350923482849603	C	8.787	0.929564	0.18131	0.05901	0.248488	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.09255	3.31;3.31;3.31;3.36;3.0;3.31	5.65	3.76	0.43208	.	0.950790	0.08804	N	0.891225	T	0.02304	0.0071	L	0.27053	0.805	0.37695	P	0.07602399999999998	B;B;B;B	0.15473	0.003;0.003;0.013;0.003	B;B;B;B	0.12156	0.002;0.002;0.007;0.002	T	0.44065	-0.9352	9	0.51188	T	0.08	-0.8136	2.5253	0.04689	0.1655:0.5348:0.1407:0.159	rs3088232;rs52821661;rs3088232	364;364;414;410	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	K	410;337;410;410;364;410;410	ENSP00000354568:N410K;ENSP00000359416:N337K;ENSP00000387822:N410K;ENSP00000378038:N364K;ENSP00000404969:N410K;ENSP00000384051:N410K	ENSP00000354568:N410K	N	+	3	2	BRDT	92217845	0.022000	0.18835	0.889000	0.34880	0.201000	0.24016	0.236000	0.17967	0.728000	0.32382	0.655000	0.94253	AAC	C|0.838;G|0.162	0.162	strong		0.398	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
RIMBP2	23504	hgsc.bcm.edu	37	12	130912757	130912757	+	Silent	SNP	C	C	T	rs2277356	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:130912757C>T	ENST00000261655.4	-	12	2491	c.2328G>A	c.(2326-2328)agG>agA	p.R776R		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	776					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		CGCTGGGCCGCCTCCTTCCCC	0.617													C|||	1446	0.288738	0.2148	0.3429	5008	,	,		17168	0.4077		0.165	False		,,,				2504	0.3548				p.R776R		Atlas-SNP	.											RIMBP2,NS,carcinoma,0,2	RIMBP2	220	2	0			c.G2328A						scavenged	.	C		938,3468	356.1+/-313.4	92,754,1357	78.0	60.0	66.0		2328	4.1	1.0	12	dbSNP_100	66	1116,7484	231.9+/-265.7	73,970,3257	no	coding-synonymous	RIMBP2	NM_015347.4		165,1724,4614	TT,TC,CC		12.9767,21.2892,15.7927		776/1053	130912757	2054,10952	2203	4300	6503	SO:0001819	synonymous_variant	23504	exon12			GGGCCGCCTCCTT	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.2328G>A	12.37:g.130912757C>T		Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_015347	Q96ID2	Silent	SNP	ENST00000261655.4	37	CCDS31925.1																																																																																			C|0.786;T|0.214	0.214	strong		0.617	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
OR5P2	120065	hgsc.bcm.edu	37	11	7818313	7818313	+	Silent	SNP	C	C	T	rs73406609	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7818313C>T	ENST00000329434.2	-	1	207	c.177G>A	c.(175-177)ctG>ctA	p.L59L	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCAAGTGGCTCAGAAAGAAAT	0.408													C|||	1185	0.236621	0.348	0.2911	5008	,	,		18246	0.128		0.2763	False		,,,				2504	0.1186				p.L59L		Atlas-SNP	.											.	OR5P2	68	.	0			c.G177A						PASS	.	C		1363,2839		399,565,1137	67.0	84.0	79.0		177	1.4	1.0	11	dbSNP_130	79	2421,6163		389,1643,2260	no	coding-synonymous	OR5P2	NM_153444.1		788,2208,3397	TT,TC,CC		28.2036,32.4369,29.5949		59/323	7818313	3784,9002	2101	4292	6393	SO:0001819	synonymous_variant	120065	exon1			GTGGCTCAGAAAG	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.177G>A	11.37:g.7818313C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			C|0.741;T|0.259	0.259	strong		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
ANO7	50636	hgsc.bcm.edu	37	2	242149010	242149010	+	Missense_Mutation	SNP	C	C	T	rs57677160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242149010C>T	ENST00000274979.8	+	13	1584	c.1481C>T	c.(1480-1482)gCg>gTg	p.A494V	ANO7_ENST00000402430.3_Missense_Mutation_p.A493V	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	494					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						AGGAGCCGCGCGCGCCGCATG	0.682													C|||	616	0.123003	0.0998	0.1571	5008	,	,		15793	0.0159		0.2565	False		,,,				2504	0.1033				p.A494V		Atlas-SNP	.											ANO7,NS,carcinoma,+2,1	ANO7	136	1	0			c.C1481T						PASS	.	C	VAL/ALA	556,3850	245.9+/-254.7	34,488,1681	46.0	49.0	48.0		1481	-0.2	0.0	2	dbSNP_129	48	2203,6397	371.3+/-336.2	288,1627,2385	yes	missense	ANO7	NM_001001891.3	64	322,2115,4066	TT,TC,CC		25.6163,12.6192,21.2133	benign	494/934	242149010	2759,10247	2203	4300	6503	SO:0001583	missense	50636	exon13			GCCGCGCGCGCCG	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.1481C>T	2.37:g.242149010C>T	ENSP00000274979:p.Ala494Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	182	103	0.565934	NM_001001891	Q6IWH6	Missense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	308	0.14102564102564102	52	0.10569105691056911	58	0.16022099447513813	5	0.008741258741258742	193	0.2546174142480211	C	1.607	-0.525135	0.04141	0.126192	0.256163	ENSG00000146205	ENST00000274979;ENST00000402430	T;T	0.63096	-0.02;-0.02	3.09	-0.242	0.13039	.	5.980880	0.00465	N	0.000112	T	0.00012	0.0000	N	0.04297	-0.235	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.06734	-1.0810	9	0.09084	T	0.74	.	7.1853	0.25797	0.0:0.1983:0.0:0.8017	rs57677160	494	Q6IWH7	ANO7_HUMAN	V	494;493	ENSP00000274979:A494V;ENSP00000385418:A493V	ENSP00000274979:A494V	A	+	2	0	ANO7	241797683	0.072000	0.21174	0.005000	0.12908	0.282000	0.26991	2.903000	0.48711	-0.078000	0.12730	0.306000	0.20318	GCG	C|0.812;T|0.188	0.188	strong		0.682	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
PFKM	5213	hgsc.bcm.edu	37	12	48526712	48526712	+	Missense_Mutation	SNP	G	G	A	rs2228500	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48526712G>A	ENST00000312352.7	+	5	338	c.299G>A	c.(298-300)cGa>cAa	p.R100Q	PFKM_ENST00000551804.1_Missense_Mutation_p.R100Q|PFKM_ENST00000395233.2_Missense_Mutation_p.R100Q|PFKM_ENST00000359794.5_Missense_Mutation_p.R100Q|PFKM_ENST00000340802.6_Missense_Mutation_p.R171Q|PFKM_ENST00000547587.1_Missense_Mutation_p.R100Q	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	100	N-terminal catalytic PFK domain 1.		R -> Q (in GSD7; Swiss; dbSNP:rs2228500). {ECO:0000269|PubMed:7825568}.		carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						GGACGACTCCGAGCTGCCTAC	0.582													G|||	740	0.147764	0.0484	0.1628	5008	,	,		20660	0.1935		0.2137	False		,,,				2504	0.1564				p.R171Q		Atlas-SNP	.											.	PFKM	117	.	0			c.G512A	GRCh37	CM950928	PFKM	M	rs2228500	PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	313,4093	168.0+/-198.9	12,289,1902	103.0	87.0	93.0		299,512,299,299	1.7	1.0	12	dbSNP_98	93	1923,6677	340.7+/-323.7	209,1505,2586	yes	missense,missense,missense,missense	PFKM	NM_000289.5,NM_001166686.1,NM_001166687.1,NM_001166688.1	43,43,43,43	221,1794,4488	AA,AG,GG		22.3605,7.1039,17.1921	benign,benign,benign,benign	100/781,171/852,100/781,100/781	48526712	2236,10770	2203	4300	6503	SO:0001583	missense	5213	exon7			GACTCCGAGCTGC	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 122"""	610681	"""phosphofructokinase, polypeptide X"""	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.299G>A	12.37:g.48526712G>A	ENSP00000309438:p.Arg100Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_001166686	J3KNX3|Q16814|Q16815|Q6ZTT1	Missense_Mutation	SNP	ENST00000312352.7	37	CCDS8760.1	369	0.16895604395604397	30	0.06097560975609756	63	0.17403314917127072	118	0.2062937062937063	158	0.20844327176781002	G	12.95	2.090597	0.36855	0.071039	0.223605	ENSG00000152556	ENST00000550345;ENST00000549003;ENST00000549941;ENST00000340802;ENST00000359794;ENST00000551339;ENST00000395233;ENST00000548345;ENST00000551804;ENST00000549022;ENST00000547587;ENST00000312352	T;T;T;T;T;T;T;T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38	4.54	1.73	0.24493	Phosphofructokinase domain (2);	0.279409	0.32901	N	0.005511	T	0.00039	0.0001	N	0.11818	0.18	0.28824	P	0.897532	B;B;B	0.21147	0.002;0.003;0.052	B;B;B	0.09377	0.004;0.001;0.003	T	0.02654	-1.1128	9	0.25751	T	0.34	-0.4464	6.7518	0.23491	0.4553:0.0:0.5447:0.0	rs2228500;rs2269934;rs10783229;rs57807152;rs2228500	100;100;171	P08237-2;P08237;Q6ZTT1	.;K6PF_HUMAN;.	Q	100;100;133;171;100;100;100;100;100;100;100;100	ENSP00000450369:R100Q;ENSP00000449835:R100Q;ENSP00000446829:R133Q;ENSP00000345771:R171Q;ENSP00000352842:R100Q;ENSP00000448253:R100Q;ENSP00000378656:R100Q;ENSP00000449269:R100Q;ENSP00000448177:R100Q;ENSP00000446805:R100Q;ENSP00000449426:R100Q;ENSP00000309438:R100Q	ENSP00000309438:R100Q	R	+	2	0	PFKM	46812979	0.020000	0.18652	0.999000	0.59377	0.998000	0.95712	1.053000	0.30442	0.413000	0.25759	0.555000	0.69702	CGA	G|0.825;A|0.175	0.175	strong		0.582	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289	
TBC1D9	23158	hgsc.bcm.edu	37	4	141598126	141598126	+	Silent	SNP	C	C	T	rs2303911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:141598126C>T	ENST00000442267.2	-	6	1055	c.981G>A	c.(979-981)caG>caA	p.Q327Q		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	327	GRAM 2.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				ACACAAACATCTGCCCCAAAA	0.428													C|||	503	0.100439	0.0991	0.072	5008	,	,		17329	0.0853		0.1581	False		,,,				2504	0.0787				p.Q327Q		Atlas-SNP	.											.	TBC1D9	198	.	0			c.G981A						PASS	.	C		443,3385		28,387,1499	120.0	117.0	118.0		981	2.7	1.0	4	dbSNP_100	118	1247,7015		83,1081,2967	no	coding-synonymous	TBC1D9	NM_015130.2		111,1468,4466	TT,TC,CC		15.0932,11.5726,13.9785		327/1267	141598126	1690,10400	1914	4131	6045	SO:0001819	synonymous_variant	23158	exon6			AAACATCTGCCCC	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"""EF-hand domain containing"""	21710	protein-coding gene	gene with protein product			"""TBC1 domain family, member 9"""			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.981G>A	4.37:g.141598126C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_015130	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	37	CCDS47136.1																																																																																			C|0.866;G|0.000;T|0.133	0.133	strong		0.428	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130	
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 GAIIx	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		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	18	8	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	
QRSL1	55278	hgsc.bcm.edu	37	6	107100396	107100396	+	Missense_Mutation	SNP	A	A	G	rs34221917	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:107100396A>G	ENST00000369046.4	+	7	892	c.788A>G	c.(787-789)aAt>aGt	p.N263S	QRSL1_ENST00000369044.1_Missense_Mutation_p.N263S	NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1											endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		GAACCTATTAATAAACCATTC	0.388													A|||	274	0.0547125	0.0053	0.0202	5008	,	,		19855	0.0913		0.0567	False		,,,				2504	0.1063				p.N263S	NSCLC(192;2127 2142 11668 26277 49545)	Atlas-SNP	.											.	QRSL1	30	.	0			c.A788G						PASS	.	A	SER/ASN	55,4351	54.2+/-90.2	0,55,2148	85.0	89.0	87.0		788	-0.8	0.2	6	dbSNP_126	87	401,8199	128.0+/-186.3	16,369,3915	yes	missense	QRSL1	NM_018292.4	46	16,424,6063	GG,GA,AA		4.6628,1.2483,3.5061	benign	263/529	107100396	456,12550	2203	4300	6503	SO:0001583	missense	55278	exon7			CTATTAATAAACC	AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348			21020	protein-coding gene	gene with protein product	"""glutamyl-tRNA(Gln) amidotransferase, subunit A"""					11230166, 19805282	Standard	NM_018292		Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.788A>G	6.37:g.107100396A>G	ENSP00000358042:p.Asn263Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	NM_018292		Missense_Mutation	SNP	ENST00000369046.4	37	CCDS5057.1	86	0.039377289377289376	1	0.0020325203252032522	7	0.019337016574585635	41	0.07167832167832168	37	0.048812664907651716	A	0.008	-1.875551	0.00537	0.012483	0.046628	ENSG00000130348	ENST00000369046;ENST00000369044	T;T	0.50813	0.73;0.73	0.427	-0.763	0.11030	.	2.470390	0.04136	U	0.318822	T	0.13200	0.0320	N	0.03983	-0.305	0.09310	N	1	B;P	0.37398	0.013;0.593	B;P	0.45577	0.009;0.486	T	0.17745	-1.0359	9	0.48119	T	0.1	.	.	.	.	rs34221917	263;263	Q9H0R6;Q9H0R6-2	GATA_HUMAN;.	S	263	ENSP00000358042:N263S;ENSP00000358040:N263S	ENSP00000358040:N263S	N	+	2	0	QRSL1	107207089	0.306000	0.24490	0.202000	0.23494	0.006000	0.05464	0.321000	0.19558	-0.455000	0.07054	-0.456000	0.05471	AAT	A|0.962;G|0.038	0.038	strong		0.388	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041667.1	NM_018292	
BAZ1A	11177	hgsc.bcm.edu	37	14	35263983	35263983	+	Silent	SNP	T	T	C	rs17102745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:35263983T>C	ENST00000382422.2	-	10	1662	c.1335A>G	c.(1333-1335)caA>caG	p.Q445Q	BAZ1A_ENST00000360310.1_Silent_p.Q445Q|BAZ1A_ENST00000358716.4_Silent_p.Q445Q			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	445	DDT. {ECO:0000255|PROSITE- ProRule:PRU00063}.				chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		GAAACTCATCTTGAAGATCAA	0.378													T|||	580	0.115815	0.118	0.0749	5008	,	,		18705	0.0377		0.1044	False		,,,				2504	0.2342				p.Q445Q		Atlas-SNP	.											.	BAZ1A	128	.	0			c.A1335G						PASS	.	T	,	471,3935	223.6+/-240.1	22,427,1754	92.0	89.0	90.0		1335,1335	2.3	1.0	14	dbSNP_123	90	840,7760	193.2+/-239.0	36,768,3496	no	coding-synonymous,coding-synonymous	BAZ1A	NM_013448.2,NM_182648.1	,	58,1195,5250	CC,CT,TT		9.7674,10.69,10.08	,	445/1557,445/1525	35263983	1311,11695	2203	4300	6503	SO:0001819	synonymous_variant	11177	exon11			CTCATCTTGAAGA	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.1335A>G	14.37:g.35263983T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_182648	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			T|0.899;C|0.101	0.101	strong		0.378	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
C6orf141	135398	hgsc.bcm.edu	37	6	49519048	49519048	+	Missense_Mutation	SNP	G	G	T	rs199917136		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:49519048G>T	ENST00000529246.2	+	1	936	c.543G>T	c.(541-543)atG>atT	p.M181I	C6orf141_ENST00000424426.1_Intron	NM_001145652.1	NP_001139124	Q5SZD1	CF141_HUMAN	chromosome 6 open reading frame 141	181										breast(1)|prostate(1)	2						AGGGTCGCATGACCACGAGGA	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		17341	0.0		0.001	False		,,,				2504	0.0				p.M181I		Atlas-SNP	.											.	C6orf141	7	.	0			c.G543T						PASS	.	G	ILE/MET	0,1384		0,0,692	69.0	64.0	66.0		543	5.5	1.0	6		66	3,3179		0,3,1588	yes	missense	C6orf141	NM_001145652.1	10	0,3,2280	TT,TG,GG		0.0943,0.0,0.0657	benign	181/245	49519048	3,4563	692	1591	2283	SO:0001583	missense	135398	exon1			TCGCATGACCACG	AK054918	CCDS55018.1	6p12.3	2012-02-06			ENSG00000197261	ENSG00000197261			21351	protein-coding gene	gene with protein product							Standard	NM_001145652		Approved	MGC46457	uc011dwo.2	Q5SZD1	OTTHUMG00000014820	ENST00000529246.2:c.543G>T	6.37:g.49519048G>T	ENSP00000434602:p.Met181Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_001145652	A8K1H4|Q8N400|Q96NQ1	Missense_Mutation	SNP	ENST00000529246.2	37	CCDS55018.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.089032	0.36855	0.0	9.43E-4	ENSG00000197261	ENST00000529246	T	0.33865	1.39	5.52	5.52	0.82312	.	0.154521	0.28624	U	0.014684	T	0.26448	0.0646	L	0.27053	0.805	0.33306	D	0.56545	P	0.52316	0.952	P	0.51385	0.668	T	0.05550	-1.0878	10	0.52906	T	0.07	.	15.3029	0.73969	0.0:0.0:1.0:0.0	.	181	Q5SZD1	CF141_HUMAN	I	181	ENSP00000434602:M181I	ENSP00000431184:M181I	M	+	3	0	C6orf141	49627007	0.997000	0.39634	0.956000	0.39512	0.585000	0.36419	2.896000	0.48656	2.745000	0.94114	0.655000	0.94253	ATG	.	.	weak		0.612	C6orf141-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390228.1	NM_153344	
BLMH	642	hgsc.bcm.edu	37	17	28576076	28576076	+	Missense_Mutation	SNP	T	T	C	rs1050565	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:28576076T>C	ENST00000261714.6	-	12	1501	c.1327A>G	c.(1327-1329)Atc>Gtc	p.I443V	RP11-354P11.2_ENST00000577420.1_RNA|SNORD63_ENST00000516303.1_RNA|BLMH_ENST00000394819.3_Missense_Mutation_p.I356V	NM_000386.3	NP_000377.1	Q13867	BLMH_HUMAN	bleomycin hydrolase	443			I -> V (common polymorphism; dbSNP:rs1050565). {ECO:0000269|PubMed:8639621, ECO:0000269|Ref.8}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|carboxypeptidase activity (GO:0004180)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|stomach(1)	13					Bleomycin(DB00290)	GCTGGCAGGATAATGGGTTCC	0.527													T|||	1271	0.253794	0.1989	0.3746	5008	,	,		18137	0.1736		0.329	False		,,,				2504	0.2474				p.I443V	Pancreas(127;628 1772 12912 33293 36203)	Atlas-SNP	.											.	BLMH	42	.	0			c.A1327G	GRCh37	CM980214	BLMH	M	rs1050565	PASS	.	T	VAL/ILE	941,3465	357.6+/-314.0	91,759,1353	161.0	129.0	140.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1327	1.5	0.6	17	dbSNP_86	140	2771,5829	439.7+/-359.3	460,1851,1989	yes	missense	BLMH	NM_000386.3	29	551,2610,3342	CC,CT,TT		32.2209,21.3572,28.5407	benign	443/456	28576076	3712,9294	2203	4300	6503	SO:0001583	missense	642	exon12			GCAGGATAATGGG	X92106	CCDS32604.1	17q11.2	2004-02-16				ENSG00000108578			1059	protein-coding gene	gene with protein product		602403				9407121, 9331073	Standard	NM_000386		Approved	BH	uc002hez.2	Q13867		ENST00000261714.6:c.1327A>G	17.37:g.28576076T>C	ENSP00000261714:p.Ile443Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	122	46	0.377049	NM_000386	B2R796|Q53F86|Q9UER9	Missense_Mutation	SNP	ENST00000261714.6	37	CCDS32604.1	598	0.27380952380952384	111	0.22560975609756098	128	0.35359116022099446	102	0.17832167832167833	257	0.3390501319261214	T	0.549	-0.850369	0.02651	0.213572	0.322209	ENSG00000108578	ENST00000261714;ENST00000394819	T;T	0.39787	1.06;1.06	5.83	1.54	0.23209	.	0.449653	0.24960	N	0.034224	T	0.00012	0.0000	N	0.00109	-2.105	0.54753	P	1.2000000000012001E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45056	-0.9287	9	0.02654	T	1	-4.5757	9.4628	0.38796	0.0:0.7023:0.0:0.2977	rs1050565;rs3190883;rs17767244;rs52825124;rs59661471;rs1050565	356;443	E7EMN3;Q13867	.;BLMH_HUMAN	V	443;356	ENSP00000261714:I443V;ENSP00000378296:I356V	ENSP00000261714:I443V	I	-	1	0	BLMH	25600202	0.494000	0.26043	0.649000	0.29536	0.957000	0.61999	1.148000	0.31614	0.080000	0.16959	-1.125000	0.01998	ATC	T|0.728;C|0.272	0.272	strong		0.527	BLMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447940.1	NM_000386	
FPGT	8790	hgsc.bcm.edu	37	1	74670172	74670172	+	Silent	SNP	A	A	G	rs12046751	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:74670172A>G	ENST00000609362.1	+	4	478	c.441A>G	c.(439-441)aaA>aaG	p.K147K	TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT_ENST00000534056.1_Intron|FPGT_ENST00000524915.1_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT_ENST00000467578.2_3'UTR|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370898.3_Silent_p.K160K|FPGT_ENST00000482102.2_3'UTR|FPGT_ENST00000370894.5_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	147					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TAGAATTAAAACTAGCCATGT	0.368													A|||	1186	0.236821	0.1362	0.428	5008	,	,		15853	0.1171		0.4085	False		,,,				2504	0.184				p.K147K		Atlas-SNP	.											.	FPGT	77	.	0			c.A441G						PASS	.	A	,,,,	854,3552	333.9+/-303.2	80,694,1429	106.0	113.0	111.0		,,,,441	3.3	1.0	1	dbSNP_120	111	3451,5149	505.6+/-376.4	704,2043,1553	no	intron,intron,intron,intron,coding-synonymous	FPGT,FPGT-TNNI3K	NM_001112808.2,NM_001199327.1,NM_001199328.1,NM_001199329.1,NM_003838.3	,,,,	784,2737,2982	GG,GA,AA		40.1279,19.3827,33.1001	,,,,	,,,,147/595	74670172	4305,8701	2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			ATTAAAACTAGCC	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.441A>G	1.37:g.74670172A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	37	CCDS663.1																																																																																			A|0.697;G|0.303	0.303	strong		0.368	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SERPINB10	5273	hgsc.bcm.edu	37	18	61582867	61582867	+	Missense_Mutation	SNP	A	A	G	rs8097425	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61582867A>G	ENST00000238508.3	+	2	182	c.123A>G	c.(121-123)atA>atG	p.I41M		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	41			I -> M (in dbSNP:rs8097425).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				CCTTGACCATAGTGTATTTGG	0.448													G|||	2366	0.472444	0.8464	0.3991	5008	,	,		17129	0.4623		0.2247	False		,,,				2504	0.2843				p.I41M		Atlas-SNP	.											.	SERPINB10	53	.	0			c.A123G						PASS	.	G	MET/ILE	3266,1140	406.9+/-334.0	1211,844,148	84.0	84.0	84.0		123	5.8	1.0	18	dbSNP_116	84	1752,6848	734.8+/-406.9	186,1380,2734	yes	missense	SERPINB10	NM_005024.1	10	1397,2224,2882	GG,GA,AA		20.3721,25.8738,38.5822		41/398	61582867	5018,7988	2203	4300	6503	SO:0001583	missense	5273	exon1			GACCATAGTGTAT	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.123A>G	18.37:g.61582867A>G	ENSP00000238508:p.Ile41Met	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	147	81	0.55102	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	933|933	0.4271978021978022|0.4271978021978022	392|392	0.7967479674796748|0.7967479674796748	136|136	0.3756906077348066|0.3756906077348066	243|243	0.42482517482517484|0.42482517482517484	162|162	0.21372031662269128|0.21372031662269128	G|G	0.542|0.542	-0.853253|-0.853253	0.02630|0.02630	0.741262|0.741262	0.203721|0.203721	ENSG00000242550|ENSG00000242550	ENST00000238508|ENST00000397996;ENST00000418725	D|.	0.82344|.	-1.6|.	5.85|5.85	5.85|5.85	0.93711|0.93711	Serpin domain (3);|.	0.000000|.	0.85682|.	N|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00022|0.00022	-2.735|-2.735	0.49915|0.49915	P|P	1.6199999999999548E-4|1.6199999999999548E-4	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.35895|0.35895	-0.9770|-0.9770	9|4	0.02654|.	T|.	1|.	.|.	13.9957|13.9957	0.64397|0.64397	0.0731:0.0:0.9269:0.0|0.0731:0.0:0.9269:0.0	rs8097425;rs52793663;rs60772677;rs8097425|rs8097425;rs52793663;rs60772677;rs8097425	41|.	P48595|.	SPB10_HUMAN|.	M|G	41|254;227	ENSP00000238508:I41M|.	ENSP00000238508:I41M|.	I|S	+|+	3|1	3|0	SERPINB10|SERPINB10	59733847|59733847	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.170000|0.170000	0.22686|0.22686	4.155000|4.155000	0.58131|0.58131	1.498000|1.498000	0.48600|0.48600	-0.128000|-0.128000	0.14901|0.14901	ATA|AGT	A|0.582;G|0.418	0.418	strong		0.448	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
RPS6KA3	6197	hgsc.bcm.edu	37	X	20204461	20204461	+	Silent	SNP	G	G	T	rs2230488	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:20204461G>T	ENST00000379565.3	-	10	1005	c.798C>A	c.(796-798)ctC>ctA	p.L266L	RPS6KA3_ENST00000540702.1_Silent_p.L238L|RPS6KA3_ENST00000544447.1_Silent_p.L238L|RPS6KA3_ENST00000379548.4_Silent_p.L237L	NM_004586.2	NP_004577.1	P51812	KS6A3_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 3	266	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|central nervous system development (GO:0007417)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(4)|central_nervous_system(4)|endometrium(3)|kidney(2)|large_intestine(5)|liver(14)|lung(7)|ovary(1)|stomach(1)	41					Acetylsalicylic acid(DB00945)	CTTGGAAAGGGAGTGTACCAG	0.294													T|||	868	0.229934	0.4123	0.1455	3775	,	,		13450	0.0208		0.1352	False		,,,				2504	0.0665				p.L266L		Atlas-SNP	.											.	RPS6KA3	110	.	0			c.C798A						PASS	.	T		1836,1999		380,828,248,424,323	107.0	106.0	107.0		798	2.7	1.0	X	dbSNP_120	107	1140,5587		66,672,336,1690,1535	no	coding-synonymous	RPS6KA3	NM_004586.2		446,1500,584,2114,1858	TT,TG,T,GG,G		16.9466,47.8748,28.1765		266/741	20204461	2976,7586	2203	4299	6502	SO:0001819	synonymous_variant	6197	exon10			GAAAGGGAGTGTA	U08316	CCDS14197.1	Xp22.2-p22.1	2013-06-03	2002-08-29		ENSG00000177189	ENSG00000177189			10432	protein-coding gene	gene with protein product		300075	"""ribosomal protein S6 kinase, 90kD, polypeptide 3"", ""mental retardation, X-linked 19"", ""Coffin-Lowry syndrome"""	MRX19, CLS		8141249, 11896450, 16879200	Standard	XM_005274573		Approved	RSK, RSK2, HU-3	uc004czu.3	P51812	OTTHUMG00000021231	ENST00000379565.3:c.798C>A	X.37:g.20204461G>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	135	88	0.651852	NM_004586	B2R9V4|Q4VAP3|Q59H26|Q5JPK8|Q7Z3Z7	Silent	SNP	ENST00000379565.3	37	CCDS14197.1																																																																																			0|0.003;T|0.273	0.273	strong		0.294	RPS6KA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056011.3	NM_004586	
KIAA0753	9851	hgsc.bcm.edu	37	17	6511781	6511781	+	Silent	SNP	A	A	G	rs4796519	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6511781A>G	ENST00000361413.3	-	10	2074	c.1716T>C	c.(1714-1716)gcT>gcC	p.A572A	KIAA0753_ENST00000572370.1_Silent_p.A273A|KIAA0753_ENST00000575027.1_5'Flank|KIAA0753_ENST00000589033.1_Silent_p.A28A|KIAA0753_ENST00000542606.1_Silent_p.A273A	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	572						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TTAGCCATGCAGCACTGAAAT	0.458													G|||	3322	0.663339	0.7307	0.6729	5008	,	,		16648	0.7103		0.5467	False		,,,				2504	0.637				p.A572A		Atlas-SNP	.											KIAA0753,colon,carcinoma,-1,1	KIAA0753	63	1	0			c.T1716C						scavenged	.	G		2749,1123		976,797,163	205.0	198.0	200.0		1716	0.2	0.5	17	dbSNP_111	200	4751,3521		1370,2011,755	yes	coding-synonymous	KIAA0753	NM_014804.2		2346,2808,918	GG,GA,AA		42.5653,29.0031,38.2411		572/968	6511781	7500,4644	1936	4136	6072	SO:0001819	synonymous_variant	9851	exon10			CCATGCAGCACTG		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1716T>C	17.37:g.6511781A>G		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Silent	SNP	ENST00000361413.3	37	CCDS42247.1																																																																																			A|0.360;G|0.640	0.640	strong		0.458	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
CYP2F1	1572	hgsc.bcm.edu	37	19	41622189	41622189	+	Silent	SNP	G	G	A	rs305968	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41622189G>A	ENST00000331105.2	+	2	168	c.96G>A	c.(94-96)ccG>ccA	p.P32P		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	32					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|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)|oxygen binding (GO:0019825)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						AGCTGCCTCCGGGACCCAGAC	0.547													A|||	2074	0.414137	0.5787	0.4957	5008	,	,		20578	0.2798		0.3131	False		,,,				2504	0.3763				p.P32P		Atlas-SNP	.											.	CYP2F1	60	.	0			c.G96A						PASS	.	A		2395,2011	561.6+/-380.8	657,1081,465	184.0	179.0	181.0		96	0.3	0.8	19	dbSNP_79	181	2632,5968	687.3+/-404.2	410,1812,2078	no	coding-synonymous	CYP2F1	NM_000774.3		1067,2893,2543	AA,AG,GG		30.6047,45.6423,38.6514		32/492	41622189	5027,7979	2203	4300	6503	SO:0001819	synonymous_variant	1572	exon2			GCCTCCGGGACCC	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.96G>A	19.37:g.41622189G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Silent	SNP	ENST00000331105.2	37	CCDS12572.1																																																																																			G|0.601;A|0.399	0.399	strong		0.547	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
CISD1	55847	hgsc.bcm.edu	37	10	60036963	60036963	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:60036963C>T	ENST00000333926.5	+	2	334	c.118C>T	c.(118-120)Cga>Tga	p.R40*	CISD1_ENST00000488388.2_3'UTR	NM_018464.4	NP_060934.1	Q9NZ45	CISD1_HUMAN	CDGSH iron sulfur domain 1	40					regulation of cellular respiration (GO:0043457)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)			breast(1)	1						TAAAGATCATCGAAATAAAGC	0.413																																					p.R40X		Atlas-SNP	.											CISD1,NS,carcinoma,-1,2	CISD1	7	2	0			c.C118T						scavenged	.						72.0	71.0	71.0					10																	60036963		2203	4300	6503	SO:0001587	stop_gained	55847	exon2			GATCATCGAAATA	AY960578	CCDS7251.1	10q21.3	2011-01-05	2007-08-10	2007-08-10	ENSG00000122873	ENSG00000122873		"""CDGSH iron sulfur domain containing"""	30880	protein-coding gene	gene with protein product		611932	"""chromosome 10 open reading frame 70"", ""zinc finger, CDGSH-type domain 1"""	C10orf70, ZCD1		17376863, 17584744	Standard	NM_018464		Approved	MDS029, mitoNEET	uc001jkc.5	Q9NZ45	OTTHUMG00000018266	ENST00000333926.5:c.118C>T	10.37:g.60036963C>T	ENSP00000363041:p.Arg40*	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	213	4	0.0187793	NM_018464	Q1X902	Nonsense_Mutation	SNP	ENST00000333926.5	37	CCDS7251.1	.	.	.	.	.	.	.	.	.	.	C	37	6.624407	0.97714	.	.	ENSG00000122873	ENST00000333926	.	.	.	5.99	5.08	0.68730	.	0.145675	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	-17.0192	7.8497	0.29446	0.1626:0.7578:0.0:0.0796	.	.	.	.	X	40	.	ENSP00000363041:R40X	R	+	1	2	CISD1	59706969	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	2.091000	0.41691	1.514000	0.48869	0.655000	0.94253	CGA	.	.	none		0.413	CISD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048137.1	NM_018464	
NSD1	64324	hgsc.bcm.edu	37	5	176721272	176721272	+	Silent	SNP	G	G	C	rs11740250	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176721272G>C	ENST00000439151.2	+	23	6948	c.6903G>C	c.(6901-6903)ggG>ggC	p.G2301G	NSD1_ENST00000354179.4_Silent_p.G2032G|NSD1_ENST00000347982.4_Silent_p.G2032G|NSD1_ENST00000361032.4_Silent_p.G2198G	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2301	Pro-rich.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)|Epithelial(233;0.198)	Kidney(146;0.235)		ACCTCGCTGGGTCAGGGACCA	0.572			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			G|||	541	0.108027	0.0106	0.1455	5008	,	,		18881	0.0		0.2475	False		,,,				2504	0.181				p.G2301G		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G6903C						PASS	.	G	,	184,4222	115.4+/-153.4	7,170,2026	55.0	57.0	57.0		6903,6096	-1.2	1.0	5	dbSNP_120	57	2158,6442	349.2+/-327.3	281,1596,2423	no	coding-synonymous,coding-synonymous	NSD1	NM_022455.4,NM_172349.2	,	288,1766,4449	CC,CG,GG		25.093,4.1761,18.0071	,	2301/2697,2032/2428	176721272	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CGCTGGGTCAGGG	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6903G>C	5.37:g.176721272G>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																			G|0.836;C|0.164	0.164	strong		0.572	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25263278	25263278	+	Missense_Mutation	SNP	G	G	A	rs2112811	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:25263278G>A	ENST00000328086.7	-	4	1560	c.757C>T	c.(757-759)Ctc>Ttc	p.L253F		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	253	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		L -> F (in dbSNP:rs2112811).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.L253F(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		TCCCGGTAGAGGTCCCTTTGG	0.463													G|||	1676	0.334665	0.475	0.3026	5008	,	,		18379	0.3284		0.2107	False		,,,				2504	0.3016				p.L253F		Atlas-SNP	.											ZKSCAN2,NS,adenoma,0,2	ZKSCAN2	90	2	1	Substitution - Missense(1)	stomach(1)	c.C757T						PASS	.	G	PHE/LEU	1987,2407	558.4+/-380.0	453,1081,663	112.0	107.0	109.0		757	2.5	0.4	16	dbSNP_96	109	1785,6815	321.8+/-315.3	181,1423,2696	yes	missense	ZKSCAN2	NM_001012981.4	22	634,2504,3359	AA,AG,GG		20.7558,45.2208,29.0288	probably-damaging	253/968	25263278	3772,9222	2197	4300	6497	SO:0001583	missense	342357	exon4			GGTAGAGGTCCCT	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.757C>T	16.37:g.25263278G>A	ENSP00000331626:p.Leu253Phe	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	664	0.304029304029304	234	0.47560975609756095	91	0.2513812154696133	178	0.3111888111888112	161	0.21240105540897097	G	6.020	0.372047	0.11409	0.452208	0.207558	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.01252	5.1	5.94	2.52	0.30459	Krueppel-associated box (3);	0.333284	0.26460	N	0.024258	T	0.00012	0.0000	M	0.83118	2.625	0.80722	P	0.0	B;B;B	0.24651	0.01;0.108;0.014	B;B;B	0.33799	0.019;0.17;0.008	T	0.24012	-1.0172	9	0.25106	T	0.35	-8.6474	8.299	0.32004	0.2803:0.0:0.7197:0.0	rs2112811;rs17717427;rs58715832;rs2112811	49;253;253	B4DYF0;Q63HK3-2;Q63HK3	.;.;ZKSC2_HUMAN	F	253	ENSP00000331626:L253F	ENSP00000331626:L253F	L	-	1	0	ZKSCAN2	25170779	0.020000	0.18652	0.390000	0.26220	0.512000	0.34134	0.592000	0.23984	0.866000	0.35629	0.561000	0.74099	CTC	G|0.696;N|0.000	.	strong		0.463	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
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 GAIIx	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	SARS2_ENST00000448145.2_Intron|MRPS12_ENST00000308018.4_Silent_p.T15T|SARS2_ENST00000594171.1_5'Flank|SARS2_ENST00000600042.1_5'Flank|SARS2_ENST00000430193.3_5'Flank|MRPS12_ENST00000402029.3_Silent_p.T15T|SARS2_ENST00000221431.6_5'Flank|CTC-360G5.8_ENST00000599996.1_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		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	94	27	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		
MUC4	4585	hgsc.bcm.edu	37	3	195512103	195512103	+	Silent	SNP	G	G	A	rs437805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195512103G>A	ENST00000463781.3	-	2	6807	c.6348C>T	c.(6346-6348)acC>acT	p.T2116T	MUC4_ENST00000475231.1_Silent_p.T2116T|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		AGGAAGCATCGGTGTCATGAA	0.562																																					p.T2116T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C6348T						PASS	.						81.0	69.0	72.0					3																	195512103		691	1590	2281	SO:0001819	synonymous_variant	4585	exon2			AGCATCGGTGTCA	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.6348C>T	3.37:g.195512103G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	232	28	0.12069	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|0.898;A|0.102	0.102	strong		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TAS2R31	259290	hgsc.bcm.edu	37	12	11183512	11183512	+	Silent	SNP	A	A	G	rs12370363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11183512A>G	ENST00000390675.2	-	1	494	c.423T>C	c.(421-423)gcT>gcC	p.A141A	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	141					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						AAAGTTGACAAGCCAAAAATA	0.368													.|||	1065	0.21266	0.2375	0.2406	5008	,	,		20162	0.1944		0.2068	False		,,,				2504	0.184				p.A141A		Atlas-SNP	.											.	TAS2R31	24	.	0			c.T423C						PASS	.	A		865,3205		79,707,1249	80.0	83.0	82.0		423	1.1	0.0	12	dbSNP_120	82	1835,6611		159,1517,2547	no	coding-synonymous	TAS2R31	NM_176885.2		238,2224,3796	GG,GA,AA		21.7263,21.2531,21.5724		141/310	11183512	2700,9816	2035	4223	6258	SO:0001819	synonymous_variant	259290	exon1			TTGACAAGCCAAA	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.423T>C	12.37:g.11183512A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	116	39	0.336207	NM_176885	P59547|Q17R84|Q645X5	Silent	SNP	ENST00000390675.2	37	CCDS53747.1																																																																																			A|0.785;G|0.215	0.215	strong		0.368	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
HLA-A	3105	hgsc.bcm.edu	37	6	29912086	29912086	+	Silent	SNP	G	G	A	rs199474634	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29912086G>A	ENST00000396634.1	+	6	1148	c.807G>A	c.(805-807)gcG>gcA	p.A269A	HLA-A_ENST00000376806.5_Silent_p.A269A|HLA-A_ENST00000376802.2_Silent_p.A269A|HLA-A_ENST00000376809.5_Silent_p.A269A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	269	Alpha-3.|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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGAAGTGGGCGGCTGTGGTGG	0.627									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	759	0.151558	0.1241	0.1744	5008	,	,		17320	0.2034		0.1113	False		,,,				2504	0.1605				p.A269A		Atlas-SNP	.											.	HLA-A	89	.	0			c.G807A						PASS	.						31.0	30.0	31.0					6																	29912086		1510	2704	4214	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTGGGCGGCTGTG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.807G>A	6.37:g.29912086G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	132	26	0.19697	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.580;A|0.420	0.420	strong		0.627	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
C6orf226	441150	hgsc.bcm.edu	37	6	42858524	42858524	+	Start_Codon_SNP	SNP	C	C	T	rs61732354	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42858524C>T	ENST00000408925.2	-	1	30	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_001008739.1	NP_001008739.1	Q5I0X4	CF226_HUMAN	chromosome 6 open reading frame 226	1										lung(2)	2						GGGGACGCTCCATGTCGGGTC	0.657													C|||	65	0.0129792	0.0151	0.0231	5008	,	,		16133	0.001		0.0149	False		,,,				2504	0.0133				p.M1I		Atlas-SNP	.											.	C6orf226	8	.	0			c.G3A						PASS	.	C	ILE/MET	57,3945		1,55,1945	24.0	31.0	29.0		3	4.1	0.9	6	dbSNP_129	29	235,8083		4,227,3928	yes	missense	C6orf226	NM_001008739.1	10	5,282,5873	TT,TC,CC		2.8252,1.4243,2.3701	possibly-damaging	1/102	42858524	292,12028	2001	4159	6160	SO:0001582	initiator_codon_variant	441150	exon1			ACGCTCCATGTCG	BC051007, BC060325	CCDS43463.1	6p21.1	2009-02-11			ENSG00000221821	ENSG00000221821			34431	protein-coding gene	gene with protein product							Standard	NM_001008739		Approved	LOC441150	uc003osw.3	Q5I0X4	OTTHUMG00000156926	ENST00000408925.2:c.3G>A	6.37:g.42858524C>T	ENSP00000386146:p.Met1Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	151	82	0.543046	NM_001008739		Missense_Mutation	SNP	ENST00000408925.2	37	CCDS43463.1	30	0.013736263736263736	8	0.016260162601626018	11	0.03038674033149171	0	0.0	11	0.014511873350923483	C	12.87	2.067055	0.36470	0.014243	0.028252	ENSG00000221821	ENST00000408925	.	.	.	4.14	4.14	0.48551	.	1.997660	0.03386	U	0.201174	T	0.58552	0.2130	.	.	.	0.80722	D	1	P	0.50156	0.932	P	0.51135	0.66	T	0.57300	-0.7835	8	0.87932	D	0	-7.5501	12.204	0.54342	0.0:1.0:0.0:0.0	rs61732354	1	Q5I0X4	CF226_HUMAN	I	1	.	ENSP00000386146:M1I	M	-	3	0	C6orf226	42966502	0.996000	0.38824	0.925000	0.36789	0.067000	0.16453	1.608000	0.36847	2.600000	0.87896	0.561000	0.74099	ATG	C|0.982;T|0.018	0.018	strong		0.657	C6orf226-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346635.1	NM_001008739	Missense_Mutation
TCP10L	140290	hgsc.bcm.edu	37	21	33956579	33956579	+	Silent	SNP	T	T	C	rs2017816	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:33956579T>C	ENST00000300258.3	-	2	149	c.36A>G	c.(34-36)aaA>aaG	p.K12K	AP000275.65_ENST00000553001.1_Intron|TCP10L_ENST00000472557.1_Intron	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	12					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						GGGTGCCCTCTTTGGGGTCCC	0.637													C|||	2175	0.434305	0.553	0.3703	5008	,	,		17914	0.3492		0.3767	False		,,,				2504	0.4663				p.K12K		Atlas-SNP	.											TCP10L,rectum,carcinoma,0,1	TCP10L	24	1	0			c.A36G						PASS	.	C		2319,2087		596,1127,480	48.0	44.0	46.0		36	-0.9	0.0	21	dbSNP_92	46	3178,5422		607,1964,1729	no	coding-synonymous	TCP10L	NM_144659.5		1203,3091,2209	CC,CT,TT		36.9535,47.3672,42.2651		12/216	33956579	5497,7509	2203	4300	6503	SO:0001819	synonymous_variant	140290	exon2			GCCCTCTTTGGGG	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"""t-complex 10 (a murine tcp homolog)-like"", ""t-complex 10 (mouse)-like"""			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.36A>G	21.37:g.33956579T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	189	189	1	NM_144659	Q53EW0|Q96LN5	Silent	SNP	ENST00000300258.3	37	CCDS13616.1																																																																																			T|0.582;C|0.418	0.418	strong		0.637	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659	
HLA-C	3107	hgsc.bcm.edu	37	6	31239449	31239449	+	Missense_Mutation	SNP	C	C	G	rs28626310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31239449C>G	ENST00000376228.5	-	2	284	c.270G>C	c.(268-270)aaG>aaC	p.K90N	HLA-C_ENST00000383329.3_Missense_Mutation_p.K90N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	90	Alpha-1.		K -> N (in dbSNP:rs28626310).		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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGCGCTTGTACTTCTGTGTCT	0.701													c|||	710	0.141773	0.1452	0.1282	5008	,	,		12148	0.0516		0.168	False		,,,				2504	0.2127				p.K90N		Atlas-SNP	.											.	HLA-C	92	.	0			c.G270C						PASS	.	C	ASN/LYS	438,2584		26,386,1099	48.0	49.0	48.0		270	-5.5	0.0	6	dbSNP_125	48	999,4419		91,817,1801	no	missense	HLA-C	NM_002117.5	94	117,1203,2900	GG,GC,CC		18.4385,14.4937,17.0261	benign	90/367	31239449	1437,7003	1511	2709	4220	SO:0001583	missense	3107	exon2			CTTGTACTTCTGT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.270G>C	6.37:g.31239449C>G	ENSP00000365402:p.Lys90Asn	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	190	186	0.978947	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	260|260	0.11904761904761904|0.11904761904761904	60|60	0.12195121951219512|0.12195121951219512	47|47	0.1298342541436464|0.1298342541436464	26|26	0.045454545454545456|0.045454545454545456	127|127	0.16754617414248021|0.16754617414248021	-|-	0.008|0.008	-1.894729|-1.894729	0.00522|0.00522	0.144937|0.144937	0.184385|0.184385	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.48;9.48|.	2.75|2.75	-5.49|-5.49	0.02584|0.02584	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	2211.810000|.	0.00541|.	N|.	0.000226|.	T|T	0.01489|0.01489	0.0048|0.0048	N|N	0.01751|0.01751	-0.74|-0.74	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.10296|.	0.003;0.003;0.001;0.003|.	B;B;B;B|.	0.21151|.	0.033;0.033;0.033;0.022|.	T|T	0.22941|0.22941	-1.0202|-1.0202	9|4	0.36615|.	T|.	0.2|.	.|.	3.7958|3.7958	0.08738|0.08738	0.0845:0.197:0.1701:0.5485|0.0845:0.197:0.1701:0.5485	rs28626310;rs41555912|rs28626310;rs41555912	90;90;90;90|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	N|L	90;90;90;127|90	ENSP00000365402:K90N;ENSP00000372819:K90N|.	ENSP00000365402:K90N|.	K|V	-|-	3|1	2|0	HLA-C|HLA-C	31347428|31347428	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-9.984000|-9.984000	0.00008|0.00008	-6.044000|-6.044000	0.00007|0.00007	-3.594000|-3.594000	0.00028|0.00028	AAG|GTA	C|0.840;G|0.160	0.160	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
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 GAIIx	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		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	28	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	
GPR112	139378	hgsc.bcm.edu	37	X	135426693	135426693	+	Missense_Mutation	SNP	A	A	G	rs4829829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135426693A>G	ENST00000394143.1	+	6	1119	c.828A>G	c.(826-828)atA>atG	p.I276M	GPR112_ENST00000394141.1_Missense_Mutation_p.I71M|GPR112_ENST00000370652.1_Missense_Mutation_p.I276M|GPR112_ENST00000287534.4_Missense_Mutation_p.I213M|GPR112_ENST00000412101.1_Missense_Mutation_p.I71M	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	276			I -> M (in dbSNP:rs4829829). {ECO:0000269|Ref.2}.		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(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GCATACCTATATTTGCAACTG	0.363													a|||	1702	0.450861	0.4228	0.3545	3775	,	,		15401	0.2024		0.3738	False		,,,				2504	0.3241				p.I276M		Atlas-SNP	.											.	GPR112	459	.	0			c.A828G						PASS	.		MET/ILE	2087,1748		484,812,307,336,264	199.0	154.0	169.0		828	-8.6	0.0	X	dbSNP_111	169	3203,3525		555,1185,908,688,964	yes	missense	GPR112	NM_153834.3	10	1039,1997,1215,1024,1228	GG,GA,G,AA,A		47.607,45.5802,49.9195	benign	276/3081	135426693	5290,5273	2203	4300	6503	SO:0001583	missense	139378	exon6			ACCTATATTTGCA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.828A>G	X.37:g.135426693A>G	ENSP00000377699:p.Ile276Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	140	102	0.728571	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	710	0.4279686558167571	138	0.372972972972973	80	0.27972027972027974	76	0.15702479338842976	187	0.3191126279863481	a	2.435	-0.329891	0.05314	0.544198	0.47607	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.30448	1.55;1.55;1.53;1.66;1.53	4.27	-8.55	0.00908	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.43228	-0.9404	8	0.37606	T	0.19	.	0.3544	0.00354	0.2435:0.2422:0.2647:0.2496	rs4829829;rs59872615;rs4829829	213;71;276	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	M	276;276;71;213;71	ENSP00000377699:I276M;ENSP00000359686:I276M;ENSP00000416526:I71M;ENSP00000287534:I213M;ENSP00000377697:I71M	ENSP00000287534:I213M	I	+	3	3	GPR112	135254359	0.001000	0.12720	0.000000	0.03702	0.050000	0.14768	-0.872000	0.04219	-2.190000	0.00757	-0.485000	0.04761	ATA	A|0.517;0|0.025	.	strong		0.363	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
S100A7A	338324	hgsc.bcm.edu	37	1	153391729	153391729	+	Missense_Mutation	SNP	G	G	A	rs3006414	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153391729G>A	ENST00000368729.4	+	3	307	c.250G>A	c.(250-252)Gca>Aca	p.A84T	S100A7A_ENST00000329256.2_Missense_Mutation_p.A84T|S100A7A_ENST00000368728.2_Missense_Mutation_p.A84T	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	84	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		A -> T (in dbSNP:rs3006414).			cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)	p.A84T(1)		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)			AGACATAGCCGCAGACTACCA	0.527													a|||	1047	0.209065	0.4766	0.1686	5008	,	,		16030	0.1379		0.0835	False		,,,				2504	0.0787				p.A84T		Atlas-SNP	.											S100A7A,rectum,carcinoma,0,2	S100A7A	24	2	1	Substitution - Missense(1)	stomach(1)	c.G250A						PASS	.	A	THR/ALA	1893,2513		408,1077,718	81.0	76.0	78.0		250	-2.9	0.0	1	dbSNP_101	78	765,7835		32,701,3567	no	missense	S100A7A	NM_176823.3	58	440,1778,4285	AA,AG,GG		8.8953,42.9641,20.4367	benign	84/102	153391729	2658,10348	2203	4300	6503	SO:0001583	missense	338324	exon3			ATAGCCGCAGACT	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.250G>A	1.37:g.153391729G>A	ENSP00000357718:p.Ala84Thr	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	258	117	0.453488	NM_176823	D3DV38|Q5SY69	Missense_Mutation	SNP	ENST00000368729.4	37	CCDS30872.1	436	0.19963369963369965	229	0.4654471544715447	55	0.15193370165745856	85	0.1486013986013986	67	0.08839050131926121	.	0.009	-1.820264	0.00595	0.429641	0.088953	ENSG00000184330	ENST00000368729;ENST00000368728;ENST00000329256	T;T;T	0.06142	3.34;3.34;3.34	1.7	-2.9	0.05648	EF-hand-like domain (1);	.	.	.	.	T	0.00328	0.0010	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37798	-0.9690	8	0.09843	T	0.71	.	3.6925	0.08351	0.2976:0.0:0.4869:0.2155	rs3006414;rs57686181;rs3006414	84	Q86SG5	S1A7A_HUMAN	T	84	ENSP00000357718:A84T;ENSP00000357717:A84T;ENSP00000329008:A84T	ENSP00000329008:A84T	A	+	1	0	S100A7A	151658353	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.964000	0.01512	-1.503000	0.01812	-2.435000	0.00213	GCA	.	.	weak		0.527	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823	
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 GAIIx	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_ENST00000418068.2_Missense_Mutation_p.V625I|PRSS36_ENST00000569305.1_Missense_Mutation_p.V620I	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	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	12	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	
PIFO	128344	hgsc.bcm.edu	37	1	111891170	111891170	+	Missense_Mutation	SNP	A	A	C	rs15396	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:111891170A>C	ENST00000369738.4	+	4	656	c.291A>C	c.(289-291)aaA>aaC	p.K97N	PIFO_ENST00000369737.4_Missense_Mutation_p.K64N|PIFO_ENST00000484512.1_3'UTR	NM_181643.4	NP_857594.2	Q8TCI5	PIFO_HUMAN	primary cilia formation	97			K -> N (in dbSNP:rs15396).		cell projection organization (GO:0030030)|positive regulation of kinase activity (GO:0033674)|regulation of cell projection organization (GO:0031344)	ciliary basal body (GO:0036064)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	beta-tubulin binding (GO:0048487)|gamma-tubulin binding (GO:0043015)|kinesin binding (GO:0019894)|protein kinase binding (GO:0019901)|Rab GTPase binding (GO:0017137)										GGTACCAGAAAGTAAGTCCTC	0.383													a|||	104	0.0207668	0.0068	0.0317	5008	,	,		19920	0.0		0.0636	False		,,,				2504	0.0092				p.K97N		Atlas-SNP	.											.	.	.	.	0			c.A291C						PASS	.	C	ASN/LYS	61,4345	57.4+/-93.9	1,59,2143	231.0	251.0	244.0		291	-0.6	0.0	1	dbSNP_52	244	578,8022	155.4+/-209.4	16,546,3738	yes	missense	C1orf88	NM_181643.4	94	17,605,5881	CC,CA,AA		6.7209,1.3845,4.9131	benign	97/192	111891170	639,12367	2203	4300	6503	SO:0001583	missense	128344	exon4			CCAGAAAGTAAGT	BC050319	CCDS833.1, CCDS72836.1	1p13.2	2012-10-10	2012-10-10	2012-10-10	ENSG00000173947	ENSG00000173947			27009	protein-coding gene	gene with protein product		614234	"""chromosome 1 open reading frame 88"""	C1orf88		20643351	Standard	XM_005270472		Approved	FLJ23853, pitchfork	uc001eaw.2	Q8TCI5	OTTHUMG00000011168	ENST00000369738.4:c.291A>C	1.37:g.111891170A>C	ENSP00000358753:p.Lys97Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_181643	D9J0A2|D9J0A3|Q4G0K4|Q52LJ6|Q5T5D5|Q5T5D6|Q8N310	Missense_Mutation	SNP	ENST00000369738.4	37	CCDS833.1	68	0.031135531135531136	4	0.008130081300813009	11	0.03038674033149171	0	0.0	53	0.06992084432717678	a	5.218	0.225661	0.09916	0.013845	0.067209	ENSG00000173947	ENST00000369738;ENST00000369737	T;T	0.33865	1.92;1.39	4.36	-0.598	0.11649	.	1.479250	0.03973	N	0.291991	T	0.07234	0.0183	L	0.29908	0.895	0.09310	N	1	B;B	0.26258	0.145;0.001	B;B	0.24541	0.054;0.002	T	0.18178	-1.0345	10	0.20519	T	0.43	0.1602	0.3038	0.00277	0.4124:0.182:0.2079:0.1977	rs15396;rs1058516;rs3199154;rs60989587;rs15396	64;97	Q8TCI5-3;Q8TCI5	.;PIFO_HUMAN	N	97;64	ENSP00000358753:K97N;ENSP00000358752:K64N	ENSP00000358752:K64N	K	+	3	2	C1orf88	111692693	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.030000	0.12308	-0.003000	0.14444	-0.559000	0.04183	AAA	A|0.957;C|0.043	0.043	strong		0.383	PIFO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030718.1	NM_181643	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035262	110035262	+	Silent	SNP	A	A	G	rs1026608	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:110035262A>G	ENST00000278590.3	+	6	1503	c.1452A>G	c.(1450-1452)cgA>cgG	p.R484R	ZC3H12C_ENST00000453089.2_Silent_p.R453R|ZC3H12C_ENST00000528673.1_Silent_p.R485R	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	484							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		ATGTCAAACGAGGTGCTCCAA	0.458													A|||	1103	0.220248	0.2186	0.2161	5008	,	,		23480	0.2004		0.2724	False		,,,				2504	0.1922				p.R484R		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A1452G						PASS	.	A		807,3057		89,629,1214	106.0	104.0	105.0		1452	-2.8	1.0	11	dbSNP_86	105	2087,6189		246,1595,2297	no	coding-synonymous	ZC3H12C	NM_033390.1		335,2224,3511	GG,GA,AA		25.2175,20.8851,23.8386		484/884	110035262	2894,9246	1932	4138	6070	SO:0001819	synonymous_variant	85463	exon6			CAAACGAGGTGCT		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1452A>G	11.37:g.110035262A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	85	16	0.188235	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			A|0.746;G|0.254	0.254	strong		0.458	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
SPANXD	64648	hgsc.bcm.edu	37	X	140785741	140785741	+	Missense_Mutation	SNP	A	A	C	rs144554749		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:140785741A>C	ENST00000370515.3	-	2	508	c.175T>G	c.(175-177)Ttt>Gtt	p.F59V		NM_032417.2|NM_145665.1	NP_115793.1|NP_663698.1	Q9BXN6	SPNXD_HUMAN	SPANX family, member D	59						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	Acute lymphoblastic leukemia(192;7.65e-05)					GTTCTTTTAAAGTTCCTCCTG	0.488																																					p.F59V		Atlas-SNP	.											.	.	.	.	0			c.T175G						PASS	.						233.0	182.0	199.0					X																	140785741		2202	4287	6489	SO:0001583	missense	171489	exon2			TTTTAAAGTTCCT	AJ457791	CCDS14675.1	Xq27.2	2014-06-19			ENSG00000196406	ENSG00000196406			14332	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 4"""	300670, 300671	"""SPANX family, member E"""	SPANXE			Standard	NM_032417		Approved	CT11.4		Q9BXN6	OTTHUMG00000022563	ENST00000370515.3:c.175T>G	X.37:g.140785741A>C	ENSP00000359546:p.Phe59Val	Somatic	372	0	0		WXS	Illumina HiSeq	Phase_I	587	81	0.13799	NM_145665	Q5JWI1	Missense_Mutation	SNP	ENST00000370515.3	37	CCDS14675.1	.	.	.	.	.	.	.	.	.	.	N	0	-2.675089	0.00104	.	.	ENSG00000196406	ENST00000370515	T	0.05319	3.46	.	.	.	.	.	.	.	.	T	0.02380	0.0073	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45011	-0.9290	6	0.15952	T	0.53	.	.	.	.	rs1059178;rs2933670;rs3176111;rs17845057;rs17857836;rs17859693	59	Q9BXN6	SPNXD_HUMAN	V	59	ENSP00000359546:F59V	ENSP00000359546:F59V	F	-	1	0	SPANXD	140613407	0.004000	0.15560	0.004000	0.12327	0.004000	0.04260	-2.376000	0.01070	-2.341000	0.00625	-2.441000	0.00211	TTT	.	.	weak		0.488	SPANXD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058598.1		
EP400	57634	hgsc.bcm.edu	37	12	132508389	132508389	+	Silent	SNP	A	A	G	rs7133119	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132508389A>G	ENST00000333577.4	+	25	4975	c.4866A>G	c.(4864-4866)ccA>ccG	p.P1622P	EP400_ENST00000389561.2_Silent_p.P1586P|EP400_ENST00000330386.6_Silent_p.P1505P|EP400_ENST00000389562.2_Silent_p.P1585P|EP400_ENST00000332482.4_Silent_p.P1549P			Q96L91	EP400_HUMAN	E1A binding protein p400	1622					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)	p.P1585P(1)		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)		TGGCTCAGCCAGAGACGCCGG	0.582													G|||	1646	0.328674	0.7973	0.1729	5008	,	,		15201	0.1458		0.1282	False		,,,				2504	0.2004				p.P1586P		Atlas-SNP	.											EP400,NS,carcinoma,0,1	EP400	370	1	1	Substitution - coding silent(1)	stomach(1)	c.A4758G						PASS	.	G		3023,1383	454.4+/-350.6	1055,913,235	48.0	49.0	49.0		4758	-10.4	0.6	12	dbSNP_116	49	982,7618	773.8+/-407.7	59,864,3377	no	coding-synonymous	EP400	NM_015409.4		1114,1777,3612	GG,GA,AA		11.4186,31.389,30.7935		1586/3124	132508389	4005,9001	2203	4300	6503	SO:0001819	synonymous_variant	57634	exon24			TCAGCCAGAGACG	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.4866A>G	12.37:g.132508389A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	179	92	0.513967	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				A|0.700;G|0.300	0.300	strong		0.582	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
PPT2	9374	hgsc.bcm.edu	37	6	32122472	32122472	+	Missense_Mutation	SNP	C	C	A	rs3096696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32122472C>A	ENST00000324816.6	+	2	669	c.101C>A	c.(100-102)gCg>gAg	p.A34E	PPT2-EGFL8_ENST00000453656.2_3'UTR|PPT2_ENST00000493548.1_3'UTR|PPT2_ENST00000445576.2_Missense_Mutation_p.A34E|PPT2_ENST00000395523.1_Missense_Mutation_p.A34E|PRRT1_ENST00000211413.5_5'Flank|PPT2-EGFL8_ENST00000422437.1_Missense_Mutation_p.A34E|PPT2_ENST00000361568.2_Missense_Mutation_p.A40E|PPT2_ENST00000375143.2_Missense_Mutation_p.A34E|PRRT1_ENST00000375150.2_5'Flank|PRRT1_ENST00000375152.2_5'Flank|PPT2_ENST00000437001.2_5'UTR|PPT2_ENST00000375137.2_Missense_Mutation_p.A34E			Q9UMR5	PPT2_HUMAN	palmitoyl-protein thioesterase 2	34			A -> E (in dbSNP:rs3096696). {ECO:0000269|PubMed:10051407, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14656967}.		cellular protein modification process (GO:0006464)|macromolecule depalmitoylation (GO:0098734)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	palmitoyl hydrolase activity (GO:0098599)|palmitoyl-(protein) hydrolase activity (GO:0008474)|thiolester hydrolase activity (GO:0016790)			NS(1)|endometrium(2)|large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	17						CCCCACCGCGCGTCCTACAAG	0.662													C|||	781	0.15595	0.2103	0.1023	5008	,	,		14262	0.0377		0.2018	False		,,,				2504	0.1953				p.A40E		Atlas-SNP	.											.	PPT2	19	.	0			c.C119A						PASS	.	C	GLU/ALA,GLU/ALA,GLU/ALA	574,2442		54,466,988	50.0	56.0	54.0		101,101,119	2.6	0.1	6	dbSNP_103	54	1143,4271		112,919,1676	yes	missense,missense,missense	PPT2	NM_001204103.1,NM_005155.6,NM_138717.2	107,107,107	166,1385,2664	AA,AC,CC		21.1119,19.0318,20.3677	benign,benign,benign	34/303,34/303,40/309	32122472	1717,6713	1508	2707	4215	SO:0001583	missense	9374	exon2			ACCGCGCGTCCTA	AF020543	CCDS4740.1, CCDS4742.1	6p21.3	2012-07-02			ENSG00000221988	ENSG00000221988	3.1.2.22		9326	protein-coding gene	gene with protein product		603298				9341199, 10051407	Standard	NM_138717		Approved		uc003nzw.3	Q9UMR5	OTTHUMG00000031257	ENST00000324816.6:c.101C>A	6.37:g.32122472C>A	ENSP00000320528:p.Ala34Glu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	83	0.838384	NM_138717	A2ABC9|A2ABD1|A2ARM7|A2BFH7|A2BFH9|A2BFI2|A8K9L4|B0S868|G8JLE1|O14799|Q0P6K0|Q5JP13|Q5JP14|Q5JQF0|Q5SSX4|Q5SSX5|Q5SSX6|Q5STJ4|Q5STJ5|Q5STJ6|Q6FI80|Q99945	Missense_Mutation	SNP	ENST00000324816.6	37	CCDS4742.1	312	0.14285714285714285	105	0.21341463414634146	33	0.09116022099447514	23	0.04020979020979021	151	0.19920844327176782	C	10.98	1.504887	0.26949	0.190318	0.211119	ENSG00000221988	ENST00000414204;ENST00000361568;ENST00000395523;ENST00000445576;ENST00000324816;ENST00000375137;ENST00000375143;ENST00000424499;ENST00000436118;ENST00000453656	D;D;D;D;D;D;D;D;T	0.94092	-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;-3.35;1.42	4.63	2.61	0.31194	.	1.033790	0.07631	N	0.928533	T	0.68732	0.3033	N	0.14661	0.345	0.46458	P	9.460000000000024E-4	P;B;B	0.35226	0.491;0.209;0.116	B;B;B	0.31614	0.133;0.125;0.095	T	0.60367	-0.7277	9	0.02654	T	1	-2.8103	6.931	0.24442	0.0:0.6957:0.1926:0.1117	rs3096696;rs17208035;rs61155654	34;34;40	Q9UMR5-2;Q9UMR5;B0S872	.;PPT2_HUMAN;.	E	34;40;34;34;34;34;34;34;34;34	ENSP00000398847:A34E;ENSP00000354608:A40E;ENSP00000378894:A34E;ENSP00000412381:A34E;ENSP00000320528:A34E;ENSP00000364279:A34E;ENSP00000364285:A34E;ENSP00000409877:A34E;ENSP00000395456:A34E	ENSP00000320528:A34E	A	+	2	0	PPT2	32230450	0.006000	0.16342	0.052000	0.19188	0.733000	0.41908	0.937000	0.28951	1.107000	0.41642	0.484000	0.47621	GCG	C|0.825;A|0.175	0.175	strong		0.662	PPT2-207	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076552.4	NM_138717	
CEP57	9702	hgsc.bcm.edu	37	11	95564259	95564259	+	Missense_Mutation	SNP	A	A	G	rs644799	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:95564259A>G	ENST00000325542.5	+	11	1580	c.1342A>G	c.(1342-1344)Aga>Gga	p.R448G	CEP57_ENST00000325486.5_Missense_Mutation_p.R422G|CEP57_ENST00000541150.1_Missense_Mutation_p.R439G|CEP57_ENST00000537677.1_Missense_Mutation_p.R421G	NM_001243776.1|NM_014679.4	NP_001230705.1|NP_055494.2	Q86XR8	CEP57_HUMAN	centrosomal protein 57kDa	448	Mediates interaction with microtubules. {ECO:0000250}.		R -> G (in dbSNP:rs644799). {ECO:0000269|PubMed:12717444, ECO:0000269|PubMed:14702039}.		fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|mitotic cell cycle (GO:0000278)|protein homooligomerization (GO:0051260)|protein import into nucleus, translocation (GO:0000060)|spermatid development (GO:0007286)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	fibroblast growth factor binding (GO:0017134)|protein homodimerization activity (GO:0042803)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				TGATGAAGAAAGAAACAGCAG	0.373									Mosaic Variegated Aneuploidy Syndrome				G|||	1031	0.205871	0.0772	0.2363	5008	,	,		13719	0.253		0.3738	False		,,,				2504	0.137				p.R448G		Atlas-SNP	.											CEP57,colon,carcinoma,0,1	CEP57	40	1	0			c.A1342G						PASS	.	G	GLY/ARG	546,3856	765.6+/-413.4	34,478,1689	56.0	58.0	58.0		1342	4.9	1.0	11	dbSNP_83	58	3286,5310	636.7+/-399.1	602,2082,1614	yes	missense	CEP57	NM_014679.4	125	636,2560,3303	GG,GA,AA		38.2271,12.4035,29.4815	benign	448/501	95564259	3832,9166	2201	4298	6499	SO:0001583	missense	9702	exon11	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GAAGAAAGAAACA	D42054	CCDS8304.1, CCDS58166.1, CCDS58167.1	11q21	2014-09-17			ENSG00000166037	ENSG00000166037			30794	protein-coding gene	gene with protein product		607951				7788527	Standard	NM_014679		Approved	Translokin, TSP57, KIAA0092	uc001pfp.2	Q86XR8	OTTHUMG00000167740	ENST00000325542.5:c.1342A>G	11.37:g.95564259A>G	ENSP00000317902:p.Arg448Gly	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	135	17	0.125926	NM_014679	A0PJH1|A8K5D0|B4DDP5|F5H5F7|Q14704|Q5JB46|Q8IXP0|Q9BVF9	Missense_Mutation	SNP	ENST00000325542.5	37	CCDS8304.1	590|590	0.27014652014652013|0.27014652014652013	44|44	0.08943089430894309|0.08943089430894309	102|102	0.281767955801105|0.281767955801105	163|163	0.28496503496503495|0.28496503496503495	281|281	0.370712401055409|0.370712401055409	G|G	4.527|4.527	0.097865|0.097865	0.08681|0.08681	0.124035|0.124035	0.382271|0.382271	ENSG00000166037|ENSG00000166037	ENST00000535224|ENST00000537677;ENST00000325542;ENST00000325486;ENST00000541150	.|T;T;T;T	.|0.30182	.|1.55;1.55;1.54;1.54	5.89|5.89	4.92|4.92	0.64577|0.64577	.|.	.|0.499946	.|0.20276	.|N	.|0.095553	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01219|0.01219	-0.95|-0.95	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.35251|0.35251	-0.9796|-0.9796	4|9	.|0.87932	.|D	.|0	-4.9723|-4.9723	6.4242|6.4242	0.21760|0.21760	0.1897:0.1507:0.6596:0.0|0.1897:0.1507:0.6596:0.0	rs644799;rs1150354;rs16922608;rs17228646;rs52796376;rs644799|rs644799;rs1150354;rs16922608;rs17228646;rs52796376;rs644799	.|439;422;448	.|F5H5F7;Q86XR8-2;Q86XR8	.|.;.;CEP57_HUMAN	R|G	237|421;448;422;439	.|ENSP00000441392:R421G;ENSP00000317902:R448G;ENSP00000317487:R422G;ENSP00000443436:R439G	.|ENSP00000317487:R422G	K|R	+|+	2|1	0|2	CEP57|CEP57	95203907|95203907	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.664000|0.664000	0.39144|0.39144	1.006000|1.006000	0.29847|0.29847	1.511000|1.511000	0.48818|0.48818	-0.226000|-0.226000	0.12346|0.12346	AAG|AGA	T|0.005;G|0.275;C|0.007;N|0.000;A|0.713	0.275	strong		0.373	CEP57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395983.1	NM_014679	
TSNARE1	203062	hgsc.bcm.edu	37	8	143425406	143425406	+	Silent	SNP	C	C	T	rs80309837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143425406C>T	ENST00000307180.3	-	4	783	c.666G>A	c.(664-666)acG>acA	p.T222T	TSNARE1_ENST00000524325.1_Silent_p.T222T|TSNARE1_ENST00000520166.1_Silent_p.T222T|TSNARE1_ENST00000519651.1_Intron	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	222					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GCTCCACGGGCGTGAGAGCCA	0.697													C|||	218	0.0435304	0.0477	0.0216	5008	,	,		10225	0.0833		0.0189	False		,,,				2504	0.0378				p.T222T		Atlas-SNP	.											.	TSNARE1	59	.	0			c.G666A						PASS	.	C		168,4178		3,162,2008	18.0	21.0	20.0		666	-7.8	0.0	8	dbSNP_131	20	177,8349		2,173,4088	no	coding-synonymous	TSNARE1	NM_145003.3		5,335,6096	TT,TC,CC		2.076,3.8656,2.6802		222/514	143425406	345,12527	2173	4263	6436	SO:0001819	synonymous_variant	203062	exon4			CACGGGCGTGAGA			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.666G>A	8.37:g.143425406C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_145003	B7ZLB0|Q14D03	Silent	SNP	ENST00000307180.3	37	CCDS6384.1																																																																																			C|0.971;T|0.029	0.029	strong		0.697	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
MAP2K2	5605	hgsc.bcm.edu	37	19	4102449	4102449	+	Silent	SNP	G	G	A	rs17851657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4102449G>A	ENST00000262948.5	-	4	706	c.453C>T	c.(451-453)gaC>gaT	p.D151D	MAP2K2_ENST00000394867.4_Silent_p.D54D|MAP2K2_ENST00000599345.1_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	151	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|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)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)	p.D151D(2)					Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	GGGAGCCGCCGTCCTAGAGGG	0.662													.|||	557	0.111222	0.0197	0.0994	5008	,	,		17424	0.0526		0.2038	False		,,,				2504	0.2086				p.D151D		Atlas-SNP	.											MAP2K2_ENST00000262948,NS,carcinoma,0,1	MAP2K2	72	1	2	Substitution - coding silent(2)	prostate(2)	c.C453T						PASS	.	A		193,4207		7,179,2014	44.0	36.0	39.0		453	-8.4	0.1	19	dbSNP_123	39	1662,6932		143,1376,2778	no	coding-synonymous	MAP2K2	NM_030662.3		150,1555,4792	AA,AG,GG		19.3391,4.3864,14.2758		151/401	4102449	1855,11139	2200	4297	6497	SO:0001819	synonymous_variant	5605	exon4			GCCGCCGTCCTAG	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.453C>T	19.37:g.4102449G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			G|0.865;A|0.135	0.135	strong		0.662	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
PLXNB3	5365	hgsc.bcm.edu	37	X	153035798	153035798	+	Missense_Mutation	SNP	G	G	A	rs2266879	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153035798G>A	ENST00000361971.5	+	9	1906	c.1792G>A	c.(1792-1794)Gtc>Atc	p.V598I	PLXNB3_ENST00000538543.1_Missense_Mutation_p.V148I|PLXNB3_ENST00000538776.1_Missense_Mutation_p.V251I|PLXNB3_ENST00000538282.1_Missense_Mutation_p.V208I|PLXNB3_ENST00000538966.1_Missense_Mutation_p.V621I	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	598			V -> I (in dbSNP:rs2266879). {ECO:0000269|PubMed:14702039}.		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)					CCCAGACCACGTCACTGTGCC	0.642													G|||	1137	0.301192	0.177	0.2378	3775	,	,		13509	0.0804		0.4791	False		,,,				2504	0.1789				p.V621I		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G1861A						PASS	.		ILE/VAL,ILE/VAL	1017,2810		131,607,148,892,419	76.0	50.0	59.0		1861,1792	-2.9	0.0	X	dbSNP_100	59	4336,2389		1034,1079,1189,315,680	yes	missense,missense	PLXNB3	NM_001163257.1,NM_005393.2	29,29	1165,1686,1337,1207,1099	AA,AG,A,GG,G		35.5242,26.5743,49.2703	benign,benign	621/1933,598/1910	153035798	5353,5199	2197	4297	6494	SO:0001583	missense	5365	exon10			GACCACGTCACTG	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.1792G>A	X.37:g.153035798G>A	ENSP00000355378:p.Val598Ile	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	145	141	0.972414	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	610	0.3676913803496082	78	0.18055555555555555	66	0.2185430463576159	31	0.05719557195571956	253	0.4755639097744361	g	5.719	0.317087	0.10845	0.265743	0.644758	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538543;ENST00000538282	T;T;T;T;T	0.70164	5.1;5.06;4.51;1.75;-0.46	4.78	-2.94	0.05581	.	1.088280	0.07055	N	0.832721	T	0.00012	0.0000	N	0.25245	0.725	0.52501	P	4.999999999999449E-5	B;P;B;B	0.44776	0.018;0.843;0.055;0.018	B;B;B;B	0.33295	0.007;0.161;0.026;0.012	T	0.36480	-0.9746	9	0.30078	T	0.28	.	11.2095	0.48790	0.5531:0.0:0.4469:0.0	rs2266879	251;148;621;598	B7Z3H9;F5GZZ4;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	I	621;598;251;148;208	ENSP00000442736:V621I;ENSP00000355378:V598I;ENSP00000445569:V251I;ENSP00000444086:V148I;ENSP00000441919:V208I	ENSP00000355378:V598I	V	+	1	0	PLXNB3	152688992	0.000000	0.05858	0.037000	0.18230	0.021000	0.10359	-0.430000	0.06973	-1.033000	0.03299	-0.303000	0.09236	GTC	G|0.542;A|0.458	0.458	strong		0.642	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
AFAP1	60312	hgsc.bcm.edu	37	4	7780582	7780582	+	Missense_Mutation	SNP	C	C	T	rs41264705	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:7780582C>T	ENST00000360265.4	-	12	1786	c.1552G>A	c.(1552-1554)Gtg>Atg	p.V518M	AFAP1_ENST00000358461.2_Missense_Mutation_p.V518M|AFAP1-AS1_ENST00000608442.1_RNA|AFAP1_ENST00000420658.1_Missense_Mutation_p.V602M|AFAP1_ENST00000513842.1_5'UTR|AFAP1_ENST00000382543.3_Missense_Mutation_p.V602M			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	518			V -> M (in dbSNP:rs41264705). {ECO:0000269|Ref.5}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TTAGACGCCACGGGGGGCTTT	0.428													C|||	554	0.110623	0.0106	0.1455	5008	,	,		17983	0.0615		0.2992	False		,,,				2504	0.0777				p.V602M		Atlas-SNP	.											.	AFAP1	93	.	0			c.G1804A						PASS	.	C	MET/VAL,MET/VAL	240,4166	141.9+/-177.2	7,226,1970	85.0	93.0	90.0		1804,1552	-0.2	0.0	4	dbSNP_127	90	2578,6022	418.9+/-352.9	409,1760,2131	yes	missense,missense	AFAP1	NM_001134647.1,NM_198595.2	21,21	416,1986,4101	TT,TC,CC		29.9767,5.4471,21.6669	possibly-damaging,possibly-damaging	602/815,518/731	7780582	2818,10188	2203	4300	6503	SO:0001583	missense	60312	exon14			ACGCCACGGGGGG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1552G>A	4.37:g.7780582C>T	ENSP00000353402:p.Val518Met	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Missense_Mutation	SNP	ENST00000360265.4	37	CCDS3397.1	335	0.1533882783882784	12	0.024390243902439025	68	0.1878453038674033	39	0.06818181818181818	216	0.2849604221635884	C	8.194	0.796722	0.16327	0.054471	0.299767	ENSG00000196526	ENST00000360265;ENST00000420658;ENST00000358461;ENST00000382543	T;T;T;T	0.15017	2.48;2.46;2.48;2.46	4.66	-0.23	0.13090	.	1.759780	0.02821	N	0.125536	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;P	0.44816	0.832;0.844	B;B	0.26969	0.036;0.075	T	0.42327	-0.9458	9	0.48119	T	0.1	-2.3154	5.8903	0.18909	0.0:0.4928:0.2336:0.2736	rs41264705;rs62289269	602;518	E9PDT7;Q8N556	.;AFAP1_HUMAN	M	518;602;518;602	ENSP00000353402:V518M;ENSP00000410689:V602M;ENSP00000351245:V518M;ENSP00000371983:V602M	ENSP00000351245:V518M	V	-	1	0	AFAP1	7831482	0.000000	0.05858	0.001000	0.08648	0.647000	0.38526	-0.488000	0.06497	-0.038000	0.13624	-0.742000	0.03525	GTG	C|0.800;T|0.200	0.200	strong		0.428	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
ZNF302	55900	hgsc.bcm.edu	37	19	35175592	35175592	+	Missense_Mutation	SNP	G	G	A	rs10425561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35175592G>A	ENST00000446502.2	+	6	990	c.782G>A	c.(781-783)aGt>aAt	p.S261N	ZNF302_ENST00000423823.2_Missense_Mutation_p.S217N|ZNF302_ENST00000457781.2_Missense_Mutation_p.S217N|ZNF302_ENST00000505242.1_Missense_Mutation_p.S217N|ZNF302_ENST00000505365.2_3'UTR			Q9NR11	ZN302_HUMAN	zinc finger protein 302	296					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)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TCAATCCTCAGTCGCCACTGG	0.443													A|||	595	0.11881	0.0666	0.0951	5008	,	,		18354	0.0694		0.1233	False		,,,				2504	0.2526				p.S217N		Atlas-SNP	.											ZNF302,right_upper_lobe,carcinoma,+1,1	ZNF302	27	1	0			c.G650A						scavenged	.	A	ASN/SER,ASN/SER	312,4080	726.3+/-409.7	8,296,1892	93.0	100.0	98.0		650,650	-0.1	0.8	19	dbSNP_119	98	1116,7476	746.8+/-407.3	72,972,3252	no	missense,missense	ZNF302	NM_001012320.1,NM_018443.2	46,46	80,1268,5144	AA,AG,GG		12.9888,7.1038,10.9982	benign,benign	217/400,217/400	35175592	1428,11556	2196	4296	6492	SO:0001583	missense	55900	exon5			TCCTCAGTCGCCA	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.782G>A	19.37:g.35175592G>A	ENSP00000396379:p.Ser261Asn	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	37		168	0.07692307692307693	31	0.06300813008130081	37	0.10220994475138122	19	0.033216783216783216	81	0.10686015831134564	A	0.014	-1.600804	0.00849	0.071038	0.129888	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000423823;ENST00000446502	T;T;T;T	0.18338	3.18;3.18;3.18;2.22	0.967	-0.1	0.13621	.	.	.	.	.	T	0.00073	0.0002	N	0.04880	-0.145	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41052	-0.9530	8	0.29301	T	0.29	.	6.1893	0.20516	0.3779:0.0:0.6221:0.0	rs10425561	261;217	E7EVR1;Q9NR11-2	.;.	N	217;217;217;261	ENSP00000391067:S217N;ENSP00000421028:S217N;ENSP00000405219:S217N;ENSP00000396379:S261N	ENSP00000405219:S217N	S	+	2	0	ZNF302	39867432	0.000000	0.05858	0.751000	0.31187	0.272000	0.26649	-0.848000	0.04326	-0.698000	0.05085	-1.673000	0.00743	AGT	G|0.500;A|0.500	0.500	weak		0.443	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
DOCK11	139818	hgsc.bcm.edu	37	X	117700141	117700141	+	Silent	SNP	A	A	G	rs2286977	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:117700141A>G	ENST00000276202.7	+	8	930	c.867A>G	c.(865-867)gcA>gcG	p.A289A	DOCK11_ENST00000276204.6_Silent_p.A289A	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	289					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TAGAAACAGCACAAGGTCAGA	0.373													A|||	1459	0.38649	0.1225	0.2911	3775	,	,		12894	0.4177		0.2753	False		,,,				2504	0.4059				p.A289A		Atlas-SNP	.											.	DOCK11	185	.	0			c.A867G						PASS	.	A		707,3128		51,503,102,1078,469	70.0	70.0	70.0		867	1.6	0.6	X	dbSNP_100	70	2489,4239		317,1174,681,937,1191	no	coding-synonymous	DOCK11	NM_144658.3		368,1677,783,2015,1660	GG,GA,G,AA,A		36.9946,18.4355,30.2566		289/2074	117700141	3196,7367	2203	4300	6503	SO:0001819	synonymous_variant	139818	exon8			AACAGCACAAGGT	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.867A>G	X.37:g.117700141A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	121	45	0.371901	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			0|0.012;G|0.317	0.317	strong		0.373	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
PARP1	142	hgsc.bcm.edu	37	1	226573364	226573364	+	Silent	SNP	A	A	G	rs1805414	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226573364A>G	ENST00000366794.5	-	7	995	c.852T>C	c.(850-852)gcT>gcC	p.A284A		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	284					base-excision repair (GO:0006284)|cellular response to insulin stimulus (GO:0032869)|DNA damage response, detection of DNA damage (GO:0042769)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|gene expression (GO:0010467)|macrophage differentiation (GO:0030225)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein ADP-ribosylation (GO:0006471)|protein autoprocessing (GO:0016540)|protein poly-ADP-ribosylation (GO:0070212)|regulation of growth rate (GO:0040009)|signal transduction involved in regulation of gene expression (GO:0023019)|telomere maintenance (GO:0000723)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NAD binding (GO:0051287)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(4)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	44	Breast(184;0.133)			GBM - Glioblastoma multiforme(131;0.0531)		CCATGCCATCAGCTACTCGGT	0.537								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA					G|||	2587	0.516573	0.5582	0.5029	5008	,	,		19644	0.7946		0.329	False		,,,				2504	0.3763				p.A284A		Atlas-SNP	.											.	PARP1	100	.	0			c.T852C	GRCh37	CM071915	PARP1	M	rs1805414	PASS	.	G		2366,2040	564.7+/-381.5	626,1114,463	80.0	73.0	75.0		852	-4.1	1.0	1	dbSNP_92	75	2937,5663	668.7+/-402.6	501,1935,1864	no	coding-synonymous	PARP1	NM_001618.3		1127,3049,2327	GG,GA,AA		34.1512,46.3005,40.7735		284/1015	226573364	5303,7703	2203	4300	6503	SO:0001819	synonymous_variant	142	exon7			GCCATCAGCTACT	BC037545	CCDS1554.1	1q41-q42	2010-02-16	2008-07-28	2004-08-26	ENSG00000143799	ENSG00000143799	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	270	protein-coding gene	gene with protein product		173870	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)"", ""poly (ADP-ribose) polymerase family, member 1"""	PPOL, ADPRT		10964595	Standard	NM_001618		Approved	PARP	uc001hqd.4	P09874	OTTHUMG00000037556	ENST00000366794.5:c.852T>C	1.37:g.226573364A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_001618	B1ANJ4|Q8IUZ9	Silent	SNP	ENST00000366794.5	37	CCDS1554.1																																																																																			A|0.543;G|0.457	0.457	strong		0.537	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618	
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 GAIIx	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	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	3	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 GAIIx	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	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	11	9	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		
NEU4	129807	hgsc.bcm.edu	37	2	242758203	242758203	+	Silent	SNP	T	T	C	rs2293763	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242758203T>C	ENST00000391969.2	+	5	1995	c.1284T>C	c.(1282-1284)gcT>gcC	p.A428A	NEU4_ENST00000405370.1_Silent_p.A428A|NEU4_ENST00000404257.1_Silent_p.A440A|NEU4_ENST00000325935.6_Silent_p.A441A|NEU4_ENST00000407683.1_Silent_p.A428A	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	428					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		TCGGGCCGGCTCCTGAGGGGG	0.652													C|||	2229	0.445088	0.4887	0.3458	5008	,	,		12581	0.4187		0.3847	False		,,,				2504	0.546				p.A441A		Atlas-SNP	.											NEU4,NS,carcinoma,0,1	NEU4	39	1	0			c.T1323C						scavenged	.		,,,,	1780,2412		436,908,752	11.0	15.0	14.0		1323,1284,1284,1284,1320	-6.6	0.0	2	dbSNP_100	14	2654,5640		489,1676,1982	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	925,2584,2734	CC,CT,TT		31.999,42.4618,35.5118	,,,,	441/498,428/485,428/485,428/485,440/497	242758203	4434,8052	2096	4147	6243	SO:0001819	synonymous_variant	129807	exon4			GCCGGCTCCTGAG	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.1284T>C	2.37:g.242758203T>C		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	90	32	0.355556	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1																																																																																			T|0.640;C|0.360	0.360	strong		0.652	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
PCDHB10	56126	hgsc.bcm.edu	37	5	140572729	140572729	+	Missense_Mutation	SNP	C	C	T	rs189437073	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140572729C>T	ENST00000239446.4	+	1	788	c.604C>T	c.(604-606)Cgg>Tgg	p.R202W		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	202	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGCACTGGATCGGGAGGAGCA	0.507																																					p.R202W		Atlas-SNP	.											PCDHB10,NS,lymphoid_neoplasm,0,1	PCDHB10	177	1	0			c.C604T						scavenged	.						115.0	128.0	124.0					5																	140572729		2203	4300	6503	SO:0001583	missense	56126	exon1			CTGGATCGGGAGG	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.604C>T	5.37:g.140572729C>T	ENSP00000239446:p.Arg202Trp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	86	2	0.0232558	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.672038	0.29693	.	.	ENSG00000120324	ENST00000239446	T	0.01725	4.67	3.41	-6.82	0.01698	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.05914	0.0154	H	0.98936	4.375	0.29699	N	0.840282	B	0.21606	0.058	B	0.21708	0.036	T	0.18178	-1.0345	9	0.72032	D	0.01	.	4.177	0.10356	0.3535:0.3064:0.0:0.34	.	202	Q9UN67	PCDBA_HUMAN	W	202	ENSP00000239446:R202W	ENSP00000239446:R202W	R	+	1	2	PCDHB10	140552913	0.000000	0.05858	0.418000	0.26571	0.610000	0.37248	-0.855000	0.04295	-1.907000	0.01087	-0.265000	0.10407	CGG	C|0.997;A|0.003	.	alt		0.507	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
TTN	7273	hgsc.bcm.edu	37	2	179582327	179582327	+	Missense_Mutation	SNP	C	C	T	rs13390491	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179582327C>T	ENST00000591111.1	-	85	24547	c.24323G>A	c.(24322-24324)aGc>aAc	p.S8108N	TTN_ENST00000589042.1_Missense_Mutation_p.S8425N|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S7181N			Q8WZ42	TITIN_HUMAN	titin	12299	Ig-like 63.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCCTATGTGGCTCTGGTCAGT	0.423													C|||	1221	0.24381	0.1936	0.183	5008	,	,		21045	0.4355		0.1571	False		,,,				2504	0.2464				p.S8425N		Atlas-SNP	.											.	TTN	18412	.	0			c.G25274A						PASS	.	C	,,,ASN/SER	613,3149		46,521,1314	76.0	78.0	77.0		,,,21542	5.5	1.0	2	dbSNP_121	77	1242,6996		96,1050,2973	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,46	142,1571,4287	TT,TC,CC		15.0765,16.2945,15.4583	,,,benign	,,,7181/33424	179582327	1855,10145	1881	4119	6000	SO:0001583	missense	7273	exon87			ATGTGGCTCTGGT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24323G>A	2.37:g.179582327C>T	ENSP00000465570:p.Ser8108Asn	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	227	108	0.475771	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		512	0.23443223443223443	98	0.1991869918699187	55	0.15193370165745856	243	0.42482517482517484	116	0.15303430079155672	C	8.404	0.842666	0.16963	0.162945	0.150765	ENSG00000155657	ENST00000342992	T	0.68903	-0.36	5.51	5.51	0.81932	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.61036	1.89	0.19945	P	0.999942837	B	0.26602	0.154	B	0.22753	0.041	T	0.31613	-0.9937	8	0.87932	D	0	.	10.3596	0.43984	0.0:0.7257:0.2009:0.0734	rs13390491;rs52812757;rs58114390;rs13390491	8108	Q8WZ42	TITIN_HUMAN	N	7181	ENSP00000343764:S7181N	ENSP00000343764:S7181N	S	-	2	0	TTN	179290572	0.357000	0.24938	1.000000	0.80357	0.939000	0.58152	0.935000	0.28924	2.738000	0.93877	0.655000	0.94253	AGC	C|0.774;T|0.226	0.226	strong		0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MED24	9862	hgsc.bcm.edu	37	17	38186106	38186106	+	Silent	SNP	C	C	T	rs11555255	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38186106C>T	ENST00000394128.2	-	13	1242	c.1161G>A	c.(1159-1161)gcG>gcA	p.A387A	MED24_ENST00000394126.1_Silent_p.A412A|MED24_ENST00000394127.2_Silent_p.A374A|MED24_ENST00000356271.3_Silent_p.A374A|MED24_ENST00000501516.3_Silent_p.A406A|SNORD124_ENST00000459577.1_RNA	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	387					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					GCTCTCGGTCCGCTTTGCTGT	0.557													C|||	528	0.105431	0.1551	0.1182	5008	,	,		20173	0.006		0.164	False		,,,				2504	0.0716				p.A387A		Atlas-SNP	.											.	MED24	89	.	0			c.G1161A						PASS	.	C	,	737,3669	304.1+/-288.3	63,611,1529	221.0	165.0	184.0		1122,1161	-4.2	0.2	17	dbSNP_120	184	1401,7199	270.7+/-289.1	115,1171,3014	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	178,1782,4543	TT,TC,CC		16.2907,16.7272,16.4386	,	374/977,387/990	38186106	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon13			TCGGTCCGCTTTG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1161G>A	17.37:g.38186106C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1																																																																																			T|0.119;G|0.156;C|0.699;A|0.025	0.119	strong		0.557	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
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 GAIIx	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_ENST00000410077.2_Silent_p.E380E|JAKMIP1_ENST00000409831.1_Silent_p.E545E|JAKMIP1_ENST00000409021.3_Silent_p.E545E|JAKMIP1_ENST00000409371.3_Silent_p.E360E	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		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	83	29	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	
HSD17B7	51478	hgsc.bcm.edu	37	1	162760622	162760622	+	Missense_Mutation	SNP	G	G	C	rs116929795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:162760622G>C	ENST00000254521.3	+	1	87	c.32G>C	c.(31-33)aGc>aCc	p.S11T	HSD17B7_ENST00000367917.3_Missense_Mutation_p.S11T|HSD17B7_ENST00000485405.1_3'UTR|HSD17B7_ENST00000367915.1_Missense_Mutation_p.S11T|HSD17B7_ENST00000367913.1_Missense_Mutation_p.S11T	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	11					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					ACCGGGGCTAGCAGGTGAGGC	0.622													G|||	55	0.0109824	0.0	0.0014	5008	,	,		17303	0.0387		0.002	False		,,,				2504	0.0133				p.S11T		Atlas-SNP	.											.	HSD17B7	25	.	0			c.G32C						PASS	.	G	THR/SER	5,4401	9.9+/-24.2	0,5,2198	56.0	49.0	52.0		32	4.8	1.0	1	dbSNP_132	52	17,8583	13.3+/-46.6	0,17,4283	yes	missense	HSD17B7	NM_016371.2	58	0,22,6481	CC,CG,GG		0.1977,0.1135,0.1692	benign	11/342	162760622	22,12984	2203	4300	6503	SO:0001583	missense	51478	exon1			GGGCTAGCAGGTG	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5215	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 37C, member 1"""	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.32G>C	1.37:g.162760622G>C	ENSP00000254521:p.Ser11Thr	Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	273	135	0.494505	NM_016371	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Missense_Mutation	SNP	ENST00000254521.3	37	CCDS1242.1	21	0.009615384615384616	0	0.0	0	0.0	20	0.03496503496503497	1	0.0013192612137203166	G	12.32	1.902208	0.33628	0.001135	0.001977	ENSG00000132196	ENST00000367915;ENST00000367917;ENST00000254521;ENST00000367913	D;T;D;D	0.86769	-2.17;2.81;-2.17;-2.17	4.83	4.83	0.62350	NAD(P)-binding domain (1);	0.147023	0.64402	D	0.000006	T	0.65626	0.2709	N	0.12887	0.27	0.35499	D	0.799637	B	0.19200	0.034	B	0.19666	0.026	T	0.61744	-0.7000	9	0.31617	T	0.26	-19.5809	13.611	0.62078	0.0:0.0:1.0:0.0	.	11	P56937	DHB7_HUMAN	T	11	ENSP00000356892:S11T;ENSP00000356894:S11T;ENSP00000254521:S11T;ENSP00000356889:S11T	ENSP00000254521:S11T	S	+	2	0	HSD17B7	161027246	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.456000	0.44997	2.660000	0.90430	0.655000	0.94253	AGC	G|0.996;C|0.004	0.004	strong		0.622	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371	
STX1A	6804	hgsc.bcm.edu	37	7	73122923	73122923	+	Silent	SNP	A	A	G	rs2228607	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:73122923A>G	ENST00000222812.3	-	3	230	c.204T>C	c.(202-204)gaT>gaC	p.D68D	STX1A_ENST00000395155.3_Silent_p.D68D|MIR4284_ENST00000578924.1_RNA|STX1A_ENST00000395156.3_Silent_p.D68D|STX1A_ENST00000395154.3_Silent_p.D68D	NM_004603.3	NP_004594.1	Q16623	STX1A_HUMAN	syntaxin 1A (brain)	68					calcium ion-dependent exocytosis (GO:0017156)|cellular protein metabolic process (GO:0044267)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|neurotransmitter secretion (GO:0007269)|positive regulation of exocytosis (GO:0045921)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of insulin secretion (GO:0050796)|response to gravity (GO:0009629)|secretion by cell (GO:0032940)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)	actomyosin (GO:0042641)|cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|SNARE complex (GO:0031201)|synaptic vesicle membrane (GO:0030672)|synaptobrevin 2-SNAP-25-syntaxin-1a complex (GO:0070044)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)	calcium channel inhibitor activity (GO:0019855)			large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5		Lung NSC(55;0.0908)|all_lung(88;0.198)				ACTCACTCTCATCGGGGTTGG	0.632													A|||	2289	0.457069	0.5008	0.3948	5008	,	,		15594	0.4067		0.5596	False		,,,				2504	0.3885				p.D68D		Atlas-SNP	.											.	STX1A	16	.	0			c.T204C	GRCh37	CM014827	STX1A	M	rs2228607	PASS	.	A	,	2228,2178	586.6+/-386.5	564,1100,539	85.0	62.0	70.0		204,204	-6.4	0.9	7	dbSNP_98	70	4870,3730	610.7+/-395.7	1398,2074,828	no	coding-synonymous,coding-synonymous	STX1A	NM_001165903.1,NM_004603.3	,	1962,3174,1367	GG,GA,AA		43.3721,49.4326,45.4252	,	68/252,68/289	73122923	7098,5908	2203	4300	6503	SO:0001819	synonymous_variant	6804	exon3			ACTCTCATCGGGG		CCDS34655.1, CCDS55120.1	7q11.2	2008-07-18			ENSG00000106089	ENSG00000106089			11433	protein-coding gene	gene with protein product		186590		STX1		1321498	Standard	NM_001165903		Approved	HPC-1, p35-1	uc003tyx.3	Q16623	OTTHUMG00000137422	ENST00000222812.3:c.204T>C	7.37:g.73122923A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_004603	O15447|O15448|Q12936|Q75MD9|Q7Z5K3|Q9BPZ6	Silent	SNP	ENST00000222812.3	37	CCDS34655.1																																																																																			A|0.473;G|0.527	0.527	strong		0.632	STX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268422.1	NM_004603	
TIMP1	7076	hgsc.bcm.edu	37	X	47444985	47444985	+	Silent	SNP	T	T	C	rs4898	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:47444985T>C	ENST00000218388.4	+	5	542	c.372T>C	c.(370-372)ttT>ttC	p.F124F	SYN1_ENST00000295987.7_Intron|TIMP1_ENST00000456754.2_3'UTR|MIR4769_ENST00000584126.1_RNA|TIMP1_ENST00000377018.2_Silent_p.F118F|TIMP1_ENST00000377017.1_Silent_p.F60F|SYN1_ENST00000340666.4_Intron	NM_003254.2	NP_003245.1	P01033	TIMP1_HUMAN	TIMP metallopeptidase inhibitor 1	124	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				aging (GO:0007568)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of trophoblast cell migration (GO:1901164)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell proliferation (GO:0008284)|regulation of integrin-mediated signaling pathway (GO:2001044)|response to cytokine (GO:0034097)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	cytokine activity (GO:0005125)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|large_intestine(2)	3						CCTGCAGTTTTGTGGCTCCCT	0.572													c|||	1772	0.469404	0.3676	0.3184	3775	,	,		10671	0.3472		0.3539	False		,,,				2504	0.3671				p.F124F		Atlas-SNP	.											.	TIMP1	12	.	0			c.T372C	GRCh37	CM991177	TIMP1	M	rs4898	PASS	.		,,	1814,2021		368,820,258,444,313	44.0	36.0	39.0		372,,	0.4	0.3	X	dbSNP_52	39	3078,3650		522,1211,823,695,1049	no	coding-synonymous,intron,intron	SYN1,TIMP1	NM_003254.2,NM_006950.3,NM_133499.2	,,	890,2031,1081,1139,1362	CC,CT,C,TT,T		45.7491,47.3012,46.3126	,,	124/208,,	47444985	4892,5671	2203	4300	6503	SO:0001819	synonymous_variant	7076	exon5			CAGTTTTGTGGCT		CCDS14281.1	Xp11.3-p11.23	2008-07-29	2005-08-08		ENSG00000102265	ENSG00000102265			11820	protein-coding gene	gene with protein product		305370	"""tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor)"""	TIMP, CLGI			Standard	XM_005272645		Approved	EPO	uc004dif.3	P01033	OTTHUMG00000021447	ENST00000218388.4:c.372T>C	X.37:g.47444985T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_003254	Q14252|Q9UCU1	Silent	SNP	ENST00000218388.4	37	CCDS14281.1	748	0.45087402049427366	101	0.27595628415300544	79	0.2762237762237762	124	0.2818181818181818	199	0.33166666666666667	c	3.324	-0.138159	0.06669	0.473012	0.457491	ENSG00000102265	ENST00000445623	.	.	.	5.29	0.454	0.16644	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.39430	P	0.03293199999999996	.	.	.	.	.	.	T	0.47381	-0.9122	3	.	.	.	.	9.163	0.37035	0.0:0.4676:0.0:0.5324	rs4898;rs1043945;rs6520277;rs17849372;rs57987733;rs4898	.	.	.	S	82	.	.	L	+	2	0	TIMP1	47329929	0.052000	0.20516	0.290000	0.24890	0.402000	0.30811	-1.200000	0.03029	-0.352000	0.08237	-1.181000	0.01715	TTG	T|0.536;C|0.464	0.464	strong		0.572	TIMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056423.1	NM_003254	
DTHD1	401124	hgsc.bcm.edu	37	4	36317970	36317970	+	Silent	SNP	T	T	C	rs9995922	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:36317970T>C	ENST00000456874.2	+	7	1885	c.1827T>C	c.(1825-1827)agT>agC	p.S609S	RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000507598.1_Silent_p.S649S|DTHD1_ENST00000357504.3_Silent_p.S444S	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	609					signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						GAAACTATAGTTGCCCTCATT	0.368													C|||	1794	0.358227	0.5287	0.3804	5008	,	,		17459	0.2153		0.3648	False		,,,				2504	0.2526				p.S609S		Atlas-SNP	.											.	DTHD1	63	.	0			c.T1827C						PASS	.	C	,	691,693		174,343,175	110.0	103.0	105.0		1332,1827	2.9	1.0	4	dbSNP_119	105	1155,2027		209,737,645	no	coding-synonymous,coding-synonymous	DTHD1	NM_001136536.3,NM_001170700.1	,	383,1080,820	CC,CT,TT		36.2979,49.9277,40.4293	,	444/617,609/782	36317970	1846,2720	692	1591	2283	SO:0001819	synonymous_variant	401124	exon7			CTATAGTTGCCCT	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1827T>C	4.37:g.36317970T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	72	42	0.583333	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			T|0.642;C|0.358	0.358	strong		0.368	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
C16orf71	146562	hgsc.bcm.edu	37	16	4790273	4790273	+	Silent	SNP	G	G	A	rs859305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4790273G>A	ENST00000299320.5	+	4	874	c.396G>A	c.(394-396)gaG>gaA	p.E132E	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Silent_p.E146E	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	132										breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GCTCTGGTGAGGTCAGCGCTC	0.572													G|||	2768	0.552716	0.4644	0.5548	5008	,	,		15556	0.6806		0.6044	False		,,,				2504	0.4857				p.E132E		Atlas-SNP	.											.	C16orf71	46	.	0			c.G396A						PASS	.	G		2273,2121	598.2+/-389.0	584,1105,508	88.0	93.0	91.0		396	-0.4	0.0	16	dbSNP_86	91	5285,3315	645.3+/-400.1	1620,2045,635	no	coding-synonymous	C16orf71	NM_139170.2		2204,3150,1143	AA,AG,GG		38.5465,48.2704,41.8347		132/521	4790273	7558,5436	2197	4300	6497	SO:0001819	synonymous_variant	146562	exon4			TGGTGAGGTCAGC	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.396G>A	16.37:g.4790273G>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	103	101	0.980583	NM_139170	Q8NCV0	Silent	SNP	ENST00000299320.5	37	CCDS10521.1																																																																																			G|0.414;A|0.586	0.586	strong		0.572	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
DHX37	57647	hgsc.bcm.edu	37	12	125461976	125461976	+	Missense_Mutation	SNP	C	C	T	rs33931896	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:125461976C>T	ENST00000308736.2	-	5	897	c.799G>A	c.(799-801)Gag>Aag	p.E267K	DHX37_ENST00000544745.1_Missense_Mutation_p.E54K	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	267	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		ATGGGGTGCTCGGCCACAGCC	0.567													C|||	75	0.014976	0.0	0.0245	5008	,	,		20975	0.001		0.0298	False		,,,				2504	0.0276				p.E267K		Atlas-SNP	.											.	DHX37	114	.	0			c.G799A						PASS	.	C	LYS/GLU	21,4385	27.2+/-55.0	1,19,2183	93.0	81.0	85.0		799	5.2	1.0	12	dbSNP_126	85	295,8305	108.2+/-168.9	9,277,4014	yes	missense	DHX37	NM_032656.3	56	10,296,6197	TT,TC,CC		3.4302,0.4766,2.4296	benign	267/1158	125461976	316,12690	2203	4300	6503	SO:0001583	missense	57647	exon5			GGTGCTCGGCCAC	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.799G>A	12.37:g.125461976C>T	ENSP00000311135:p.Glu267Lys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	155	66	0.425806	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	31	0.014194139194139194	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	22	0.029023746701846966	C	21.0	4.084767	0.76642	0.004766	0.034302	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.07114	3.22;3.22	5.23	5.23	0.72850	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.099871	0.64402	D	0.000002	T	0.07458	0.0188	L	0.53671	1.685	0.80722	D	1	D	0.65815	0.995	P	0.55965	0.788	T	0.00051	-1.2195	10	0.66056	D	0.02	-34.4922	18.3868	0.90469	0.0:1.0:0.0:0.0	rs33931896	267	Q8IY37	DHX37_HUMAN	K	267;54	ENSP00000311135:E267K;ENSP00000439009:E54K	ENSP00000311135:E267K	E	-	1	0	DHX37	124027929	1.000000	0.71417	0.994000	0.49952	0.002000	0.02628	7.023000	0.76437	2.444000	0.82710	0.591000	0.81541	GAG	C|0.980;T|0.020	0.020	strong		0.567	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
HLA-A	3105	hgsc.bcm.edu	37	6	29911957	29911957	+	Silent	SNP	G	G	A	rs12721755	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29911957G>A	ENST00000396634.1	+	6	1019	c.678G>A	c.(676-678)agG>agA	p.R226R	HLA-A_ENST00000376806.5_Silent_p.R226R|HLA-A_ENST00000376802.2_Silent_p.R226R|HLA-A_ENST00000376809.5_Silent_p.R226R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	226	Alpha-3.|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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CCACCCTGAGGTGCTGGGCCC	0.607									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	779	0.155551	0.1286	0.1787	5008	,	,		19595	0.2093		0.1113	False		,,,				2504	0.1656				p.R226R		Atlas-SNP	.											.	HLA-A	89	.	0			c.G678A						PASS	.	G		433,2583		61,311,1136	73.0	95.0	87.0		678	1.8	1.0	6	dbSNP_126	87	602,4810		55,492,2159	no	coding-synonymous	HLA-A	NM_002116.7		116,803,3295	AA,AG,GG		11.1234,14.3568,12.2805		226/366	29911957	1035,7393	1508	2706	4214	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCTGAGGTGCTGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.678G>A	6.37:g.29911957G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	280	26	0.0928571	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	weak		0.607	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
TRO	7216	hgsc.bcm.edu	37	X	54951464	54951464	+	Missense_Mutation	SNP	C	C	T	rs45448595		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:54951464C>T	ENST00000173898.7	+	6	1560	c.1448C>T	c.(1447-1449)cCa>cTa	p.P483L	TRO_ENST00000484031.1_3'UTR|TRO_ENST00000375022.4_Missense_Mutation_p.P483L|TRO_ENST00000399736.1_Missense_Mutation_p.P86L|TRO_ENST00000420798.2_Missense_Mutation_p.P14L|TRO_ENST00000375041.2_Missense_Mutation_p.P86L|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000319167.8_Missense_Mutation_p.P483L	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	483	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						GAATATTTCCCAGAAATCATT	0.502													C|||	88	0.0233113	0.0038	0.0216	3775	,	,		17063	0.001		0.0626	False		,,,				2504	0.0041				p.P483L		Atlas-SNP	.											.	TRO	246	.	0			c.C1448T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	59,3662		1,42,15,1532,556	62.0	56.0	58.0		1448,1448,1448	2.7	1.0	X	dbSNP_127	58	647,6006		20,441,166,1946,1673	yes	missense,missense,missense	TRO	NM_001039705.1,NM_016157.2,NM_177556.1	98,98,98	21,483,181,3478,2229	TT,TC,T,CC,C		9.7249,1.5856,6.8055	probably-damaging,probably-damaging,probably-damaging	483/1432,483/707,483/707	54951464	706,9668	2146	4246	6392	SO:0001583	missense	7216	exon6			ATTTCCCAGAAAT	U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.1448C>T	X.37:g.54951464C>T	ENSP00000173898:p.Pro483Leu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	213	150	0.704225	NM_016157	B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	37	CCDS43959.1	50	0.030138637733574444	4	0.008130081300813009	7	0.019337016574585635	1	0.0017482517482517483	23	0.03159340659340659	C	16.93	3.257175	0.59321	0.015856	0.097249	ENSG00000067445	ENST00000173898;ENST00000319167;ENST00000375022;ENST00000399736;ENST00000319179;ENST00000420798;ENST00000431115;ENST00000375041	T;T;T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4;3.4;3.4	2.66	2.66	0.31614	.	.	.	.	.	T	0.00552	0.0018	M	0.74467	2.265	0.22479	P	0.999063102	D;P;D;D	0.89917	0.996;0.875;1.0;0.991	D;P;D;P	0.97110	0.938;0.678;1.0;0.89	T	0.03433	-1.1037	8	0.72032	D	0.01	.	10.1955	0.43051	0.0:1.0:0.0:0.0	rs45448595	86;86;483;483	B1AKE9;B1AKF1;Q96SX2;Q12816	.;.;.;TROP_HUMAN	L	483;483;483;86;86;14;86;86	ENSP00000173898:P483L;ENSP00000318278:P483L;ENSP00000364162:P483L;ENSP00000382641:P86L;ENSP00000405126:P14L;ENSP00000407996:P86L;ENSP00000364181:P86L	ENSP00000173898:P483L	P	+	2	0	TRO	54968189	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	3.421000	0.52742	1.580000	0.49851	0.422000	0.28245	CCA	C|0.970;T|0.030	0.030	strong		0.502	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157	
TNFRSF8	943	hgsc.bcm.edu	37	1	12164437	12164437	+	Splice_Site	SNP	C	C	T	rs2230622	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12164437C>T	ENST00000263932.2	+	4	492	c.270C>T	c.(268-270)gaC>gaT	p.D90D	TNFRSF8_ENST00000417814.2_5'UTR	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	90					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	GTCCCTTAGACGACCTCGTGG	0.597													C|||	1466	0.292732	0.2118	0.379	5008	,	,		16676	0.3264		0.2296	False		,,,				2504	0.3712				p.D90D		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.C270T						PASS	.	C		956,3450		101,754,1348	109.0	89.0	96.0		270	-8.1	0.0	1	dbSNP_98	96	2082,6518		247,1588,2465	yes	coding-synonymous-near-splice	TNFRSF8	NM_001243.3		348,2342,3813	TT,TC,CC		24.2093,21.6977,23.3584		90/596	12164437	3038,9968	2203	4300	6503	SO:0001630	splice_region_variant	943	exon4			CTTAGACGACCTC	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.269-1C>T	1.37:g.12164437C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Silent	SNP	ENST00000263932.2	37	CCDS144.1																																																																																			C|0.611;A|0.050	.	strong		0.597	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1		Silent
IGSF8	93185	hgsc.bcm.edu	37	1	160062340	160062340	+	Silent	SNP	G	G	A	rs41265757	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:160062340G>A	ENST00000368086.1	-	5	1674	c.1458C>T	c.(1456-1458)gaC>gaT	p.D486D	IGSF8_ENST00000460351.1_5'Flank|IGSF8_ENST00000314485.7_Silent_p.D486D			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	486	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			TGAGCTCTCCGTCCTCTGGTC	0.697													G|||	474	0.0946486	0.0091	0.1643	5008	,	,		16969	0.1786		0.1004	False		,,,				2504	0.0685				p.D486D		Atlas-SNP	.											.	IGSF8	59	.	0			c.C1458T						PASS	.	G	,	101,4301		3,95,2103	19.0	21.0	20.0		1458,1458	-6.0	0.0	1	dbSNP_127	20	1055,7541		67,921,3310	no	coding-synonymous,coding-synonymous	IGSF8	NM_001206665.2,NM_052868.4	,	70,1016,5413	AA,AG,GG		12.2732,2.2944,8.8937	,	486/614,486/614	160062340	1156,11842	2201	4298	6499	SO:0001819	synonymous_variant	93185	exon5			CTCTCCGTCCTCT	AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.1458C>T	1.37:g.160062340G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Silent	SNP	ENST00000368086.1	37	CCDS1195.1																																																																																			G|0.910;A|0.090	0.090	strong		0.697	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868	
ZNF423	23090	hgsc.bcm.edu	37	16	49671218	49671218	+	Silent	SNP	C	C	T	rs16947741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:49671218C>T	ENST00000561648.1	-	4	1898	c.1845G>A	c.(1843-1845)ccG>ccA	p.P615P	ZNF423_ENST00000562871.1_Silent_p.P555P|ZNF423_ENST00000562520.1_Silent_p.P555P|ZNF423_ENST00000535559.1_Silent_p.P498P|ZNF423_ENST00000567169.1_Silent_p.P498P|ZNF423_ENST00000262383.2_Silent_p.P615P|ZNF423_ENST00000563137.2_Silent_p.P555P	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	615					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				GCTGCCGCTTCGGGGAAGACA	0.552													C|||	113	0.0225639	0.0144	0.0144	5008	,	,		22588	0.0149		0.0398	False		,,,				2504	0.0297				p.P615P		Atlas-SNP	.											ZNF423_ENST00000262383,NS,carcinoma,0,2	ZNF423	463	2	0			c.G1845A						PASS	.	C		91,4305	75.7+/-113.9	0,91,2107	88.0	74.0	79.0		1845	-9.6	0.8	16	dbSNP_123	79	274,8326	104.6+/-165.6	4,266,4030	no	coding-synonymous	ZNF423	NM_015069.2		4,357,6137	TT,TC,CC		3.186,2.0701,2.8086		615/1285	49671218	365,12631	2198	4300	6498	SO:0001819	synonymous_variant	23090	exon4			CCGCTTCGGGGAA	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1845G>A	16.37:g.49671218C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_015069	O94860|Q76N04|Q9NZ13	Silent	SNP	ENST00000561648.1	37	CCDS32445.1																																																																																			C|0.973;T|0.027	0.027	strong		0.552	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
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 GAIIx	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		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	77	33	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 GAIIx	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		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	33	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	
CCDC64B	146439	hgsc.bcm.edu	37	16	3085335	3085335	+	Missense_Mutation	SNP	G	G	C	rs7204908	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3085335G>C	ENST00000572449.1	-	2	225	c.163C>G	c.(163-165)Cag>Gag	p.Q55E	CCDC64B_ENST00000573514.1_5'Flank|RP11-473M20.5_ENST00000382225.3_RNA|CCDC64B_ENST00000389347.4_Missense_Mutation_p.Q55E			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	55			Q -> E (in dbSNP:rs7204908). {ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(2)|large_intestine(1)	4						TCCTTCTGCTGCAGCTGCAAG	0.657													G|||	1370	0.273562	0.2829	0.3573	5008	,	,		11851	0.1905		0.333	False		,,,				2504	0.226				p.Q55E		Atlas-SNP	.											CCDC64B,NS,carcinoma,0,1	CCDC64B	19	1	0			c.C163G						scavenged	.	G	GLU/GLN	1154,2692		209,736,978	11.0	12.0	12.0		163	5.1	1.0	16	dbSNP_116	12	2915,5327		562,1791,1768	yes	missense	CCDC64B	NM_001103175.1	29	771,2527,2746	CC,CG,GG		35.3676,30.0052,33.6615	benign	55/509	3085335	4069,8019	1923	4121	6044	SO:0001583	missense	146439	exon1			TCTGCTGCAGCTG	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.163C>G	16.37:g.3085335G>C	ENSP00000459043:p.Gln55Glu	Somatic	109	3	0.0275229		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	643	0.2944139194139194	146	0.2967479674796748	129	0.356353591160221	120	0.2097902097902098	248	0.32717678100263853	g	13.32	2.200816	0.38905	0.300052	0.353676	ENSG00000162069	ENST00000389347	T	0.04551	3.6	5.08	5.08	0.68730	.	0.297596	0.31010	N	0.008422	T	0.00012	0.0000	N	0.16478	0.41	0.31471	P	0.6683859999999999	B	0.28713	0.22	B	0.32289	0.143	T	0.39333	-0.9619	9	0.06099	T	0.92	-35.5726	11.814	0.52199	0.0:0.1772:0.8227:0.0	rs7204908;rs7204908	55	A1A5D9	BICR2_HUMAN	E	55	ENSP00000373998:Q55E	ENSP00000373998:Q55E	Q	-	1	0	CCDC64B	3025336	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.490000	0.53245	2.361000	0.80049	0.457000	0.33378	CAG	G|0.592;C|0.408	0.408	strong		0.657	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		
ALDH1A1	216	hgsc.bcm.edu	37	9	75545882	75545882	+	Silent	SNP	G	G	A	rs13959	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:75545882G>A	ENST00000297785.3	-	3	279	c.225C>T	c.(223-225)tcC>tcT	p.S75S	ALDH1A1_ENST00000376939.1_Silent_p.S75S|ALDH1A1_ENST00000482210.1_5'UTR	NM_000689.4	NP_000680.2	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1 family, member A1	75					cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|positive regulation of Ras GTPase activity (GO:0032320)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|androgen binding (GO:0005497)|Ras GTPase activator activity (GO:0005099)|retinal dehydrogenase activity (GO:0001758)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)	17					Tretinoin(DB00755)|Vitamin A(DB00162)	TACGCCACGGGGATCCAATCT	0.468													A|||	2050	0.409345	0.1664	0.4885	5008	,	,		18441	0.4554		0.503	False		,,,				2504	0.5378				p.S75S		Atlas-SNP	.											.	ALDH1A1	98	.	0			c.C225T						PASS	.	A		1101,3305	720.0+/-409.0	128,845,1230	84.0	87.0	86.0		225	-1.8	1.0	9	dbSNP_52	86	4295,4305	578.0+/-390.7	1051,2193,1056	no	coding-synonymous	ALDH1A1	NM_000689.4		1179,3038,2286	AA,AG,GG		49.9419,24.9887,41.4885		75/502	75545882	5396,7610	2203	4300	6503	SO:0001819	synonymous_variant	216	exon3			CCACGGGGATCCA	K03000	CCDS6644.1	9q21.13	2010-08-05			ENSG00000165092	ENSG00000165092	1.2.1.36, 1.2.1.3	"""Aldehyde dehydrogenases"""	402	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 1"""	100640		PUMB1, ALDH1		1709013	Standard	NM_000689		Approved	RALDH1	uc004ajd.3	P00352	OTTHUMG00000020019	ENST00000297785.3:c.225C>T	9.37:g.75545882G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_000689	O00768|Q5SYR1	Silent	SNP	ENST00000297785.3	37	CCDS6644.1																																																																																			G|0.598;A|0.402	0.402	strong		0.468	ALDH1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052679.1		
OR10H2	26538	hgsc.bcm.edu	37	19	15839459	15839459	+	Silent	SNP	G	G	A	rs11669315	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15839459G>A	ENST00000305899.3	+	1	626	c.606G>A	c.(604-606)ttG>ttA	p.L202L		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	202						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)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					GCGTGGGCTTGGTATGTATCA	0.517													G|||	764	0.152556	0.1278	0.121	5008	,	,		23239	0.123		0.17	False		,,,				2504	0.2209				p.L202L		Atlas-SNP	.											.	OR10H2	59	.	0			c.G606A						PASS	.	G		612,3794		46,520,1637	223.0	182.0	196.0		606	2.3	0.0	19	dbSNP_120	196	1652,6948		179,1294,2827	no	coding-synonymous	OR10H2	NM_013939.2		225,1814,4464	AA,AG,GG		19.2093,13.8901,17.4074		202/316	15839459	2264,10742	2203	4300	6503	SO:0001819	synonymous_variant	26538	exon1			GGGCTTGGTATGT	AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.606G>A	19.37:g.15839459G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	136	67	0.492647	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			G|0.839;A|0.161	0.161	strong		0.517	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
HRNR	388697	hgsc.bcm.edu	37	1	152186614	152186614	+	Silent	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152186614C>G	ENST00000368801.2	-	3	7566	c.7491G>C	c.(7489-7491)tcG>tcC	p.S2497S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2497					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGCCACAGCTCGATGACTGTC	0.557																																					p.S2497S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.G7491C						scavenged	.						1.0	1.0	1.0					1																	152186614		84	271	355	SO:0001819	synonymous_variant	388697	exon3			ACAGCTCGATGAC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.7491G>C	1.37:g.152186614C>G		Somatic	507	1	0.00197239		WXS	Illumina HiSeq	Phase_I	1337	55	0.0411369	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			.	.	none		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
PKHD1	5314	hgsc.bcm.edu	37	6	51720838	51720838	+	Silent	SNP	T	T	C	rs9349603	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:51720838T>C	ENST00000371117.3	-	49	8039	c.7764A>G	c.(7762-7764)ttA>ttG	p.L2588L	PKHD1_ENST00000340994.4_Silent_p.L2588L	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2588					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CAGTCATGGTTAAATCATAAG	0.383													T|||	2699	0.538938	0.4523	0.5634	5008	,	,		20327	0.8383		0.3191	False		,,,				2504	0.5562				p.L2588L		Atlas-SNP	.											.	PKHD1	927	.	0			c.A7764G						PASS	.	T	,	1903,2503	545.2+/-376.7	428,1047,728	142.0	147.0	146.0		7764,7764	3.8	1.0	6	dbSNP_119	146	2709,5891	433.8+/-357.5	466,1777,2057	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	894,2824,2785	CC,CT,TT		31.5,43.1911,35.4606	,	2588/4075,2588/3397	51720838	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon49			CATGGTTAAATCA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.7764A>G	6.37:g.51720838T>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	146	67	0.458904	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			T|0.577;C|0.423	0.423	strong		0.383	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
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 GAIIx	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_ENST00000444564.2_Silent_p.R148R|SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000468008.1_3'UTR	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		Somatic	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	191	132	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	
AK7	122481	hgsc.bcm.edu	37	14	96944878	96944878	+	Silent	SNP	G	G	A	rs76293597	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:96944878G>A	ENST00000267584.4	+	15	1676	c.1632G>A	c.(1630-1632)gcG>gcA	p.A544A		NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	544	Adenylate kinase.|LID. {ECO:0000250}.				axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GCATCGTGGCGGGGACCCACT	0.507													G|||	231	0.0461262	0.0045	0.0735	5008	,	,		14917	0.0556		0.0577	False		,,,				2504	0.0613				p.A544A		Atlas-SNP	.											.	AK7	69	.	0			c.G1632A						PASS	.	G		62,4344	58.7+/-95.3	1,60,2142	113.0	103.0	106.0		1632	-10.1	0.0	14	dbSNP_131	106	442,8158	134.3+/-191.7	13,416,3871	no	coding-synonymous	AK7	NM_152327.2		14,476,6013	AA,AG,GG		5.1395,1.4072,3.8751		544/724	96944878	504,12502	2203	4300	6503	SO:0001819	synonymous_variant	122481	exon15			CGTGGCGGGGACC	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.1632G>A	14.37:g.96944878G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_152327	Q8IYP6	Silent	SNP	ENST00000267584.4	37	CCDS9945.1																																																																																			G|0.957;A|0.043	0.043	strong		0.507	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1		
BLVRA	644	hgsc.bcm.edu	37	7	43846603	43846603	+	Silent	SNP	A	A	G	rs7738	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:43846603A>G	ENST00000402924.1	+	9	823	c.660A>G	c.(658-660)ggA>ggG	p.G220G	BLVRA_ENST00000265523.4_Silent_p.G220G	NM_001253823.1	NP_001240752.1	P53004	BIEA_HUMAN	biliverdin reductase A	220					heme catabolic process (GO:0042167)|oxidation-reduction process (GO:0055114)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	biliverdin reductase activity (GO:0004074)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(2)	12						AAGAAAAAGGACCTGGTCTAA	0.403													a|||	2379	0.47504	0.6059	0.3718	5008	,	,		21120	0.4048		0.3529	False		,,,				2504	0.5695				p.G220G		Atlas-SNP	.											.	BLVRA	26	.	0			c.A660G						PASS	.	A		2330,2076	599.9+/-389.4	606,1118,479	65.0	65.0	65.0		660	-4.6	0.0	7	dbSNP_52	65	3253,5347	484.2+/-371.3	621,2011,1668	no	coding-synonymous	BLVRA	NM_000712.3		1227,3129,2147	GG,GA,AA		37.8256,47.1176,42.9263		220/297	43846603	5583,7423	2203	4300	6503	SO:0001819	synonymous_variant	644	exon9			AAAAGGACCTGGT	BC008456	CCDS5472.1	7p13	2012-10-02			ENSG00000106605	ENSG00000106605	1.3.1.24		1062	protein-coding gene	gene with protein product		109750		BLVR			Standard	NM_001253823		Approved		uc003tir.3	P53004	OTTHUMG00000128953	ENST00000402924.1:c.660A>G	7.37:g.43846603A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	55	18	0.327273	NM_001253823	A8K747|O95019|Q86UX0|Q96QL4|Q9BRW8	Silent	SNP	ENST00000402924.1	37	CCDS5472.1																																																																																			A|0.555;G|0.445	0.445	strong		0.403	BLVRA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339006.1	NM_000712	
CDC20B	166979	hgsc.bcm.edu	37	5	54410099	54410099	+	Missense_Mutation	SNP	G	G	A	rs444527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:54410099G>A	ENST00000381375.2	-	12	1652	c.1507C>T	c.(1507-1509)Cgg>Tgg	p.R503W	CDC20B_ENST00000322374.6_Missense_Mutation_p.R461W|CDC20B_ENST00000334206.5_3'UTR|CDC20B_ENST00000296733.1_Missense_Mutation_p.R499W			Q86Y33	CD20B_HUMAN	cell division cycle 20B	503			R -> W (in dbSNP:rs444527). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.					p.R499W(1)		kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			gaaaacacccgggtctggtct	0.537													G|||	849	0.169529	0.0401	0.147	5008	,	,		17932	0.1865		0.2127	False		,,,				2504	0.2986				p.R503W		Atlas-SNP	.											CDC20B,bladder,carcinoma,+2,2	CDC20B	61	2	1	Substitution - Missense(1)	stomach(1)	c.C1507T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	270,4136	154.4+/-187.8	13,244,1946	96.0	90.0	92.0		1381,1507,1495	1.7	0.3	5	dbSNP_80	92	1642,6958	303.4+/-306.4	161,1320,2819	yes	missense,missense,missense	CDC20B	NM_001145734.2,NM_001170402.1,NM_152623.2	101,101,101	174,1564,4765	AA,AG,GG		19.093,6.128,14.7009	probably-damaging,probably-damaging,probably-damaging	461/478,503/520,499/516	54410099	1912,11094	2203	4300	6503	SO:0001583	missense	166979	exon12			ACACCCGGGTCTG	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.1507C>T	5.37:g.54410099G>A	ENSP00000370781:p.Arg503Trp	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	37	CCDS54852.1	339	0.15521978021978022	23	0.046747967479674794	59	0.16298342541436464	91	0.1590909090909091	166	0.21899736147757257	G	15.65	2.897041	0.52121	0.06128	0.19093	ENSG00000164287	ENST00000296733;ENST00000381375;ENST00000322374	T;T;T	0.60548	0.18;0.18;0.18	3.73	1.7	0.24286	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.521154	0.14995	N	0.286491	T	0.00039	0.0001	L	0.27975	0.815	0.58432	P	4.000000000004E-6	D;D;D	0.65815	0.993;0.995;0.986	P;P;P	0.58520	0.752;0.84;0.636	T	0.04961	-1.0915	9	0.72032	D	0.01	-18.0434	4.2399	0.10643	0.123:0.0:0.6533:0.2237	rs444527;rs17839390;rs59073991;rs444527	461;503;499	Q86Y33-3;Q86Y33;Q86Y33-2	.;CD20B_HUMAN;.	W	499;503;461	ENSP00000296733:R499W;ENSP00000370781:R503W;ENSP00000315720:R461W	ENSP00000296733:R499W	R	-	1	2	CDC20B	54445856	0.057000	0.20700	0.334000	0.25495	0.958000	0.62258	0.257000	0.18369	0.876000	0.35872	0.563000	0.77884	CGG	G|0.861;A|0.139	0.139	strong		0.537	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
ONECUT2	9480	hgsc.bcm.edu	37	18	55143766	55143766	+	Silent	SNP	C	C	T	rs3745074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:55143766C>T	ENST00000491143.2	+	2	1358	c.1326C>T	c.(1324-1326)ttC>ttT	p.F442F		NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	442					cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	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)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		GAACACTCTTCGCCATCTTCA	0.517													C|||	1965	0.392372	0.5136	0.4236	5008	,	,		18551	0.4673		0.2356	False		,,,				2504	0.2904				p.F442F		Atlas-SNP	.											ONECUT2,NS,carcinoma,+1,1	ONECUT2	42	1	0			c.C1326T						PASS	.	C		1811,2319		385,1041,639	62.0	69.0	66.0		1326	-10.2	0.4	18	dbSNP_107	66	1778,6648		177,1424,2612	no	coding-synonymous	ONECUT2	NM_004852.2		562,2465,3251	TT,TC,CC		21.1014,43.8499,28.5839		442/505	55143766	3589,8967	2065	4213	6278	SO:0001819	synonymous_variant	9480	exon2			ACTCTTCGCCATC	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"""Homeoboxes / CUT class"""	8139	protein-coding gene	gene with protein product		604894	"""one cut domain, family member 2"""			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.1326C>T	18.37:g.55143766C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_004852		Silent	SNP	ENST00000491143.2	37	CCDS42440.1	852	0.3901098901098901	240	0.4878048780487805	154	0.425414364640884	276	0.4825174825174825	182	0.24010554089709762	C	7.087	0.571487	0.13623	0.438499	0.211014	ENSG00000119547	ENST00000481727	.	.	.	6.02	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999699	.	.	.	.	.	.	T	0.11012	-1.0605	3	.	.	.	-10.8386	21.9508	0.99964	0.0:0.1873:0.0:0.8127	rs3745074;rs17831449;rs3745074	.	.	.	C	71	.	.	R	+	1	0	ONECUT2	53294764	0.000000	0.05858	0.399000	0.26333	0.993000	0.82548	-2.690000	0.00831	-2.195000	0.00752	-0.145000	0.13849	CGC	C|0.638;T|0.362	0.362	strong		0.517	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3		
CLDN16	10686	hgsc.bcm.edu	37	3	190106074	190106074	+	Missense_Mutation	SNP	G	G	C	rs386669518|rs3214506	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:190106074G>C	ENST00000264734.2	+	1	414	c.166G>C	c.(166-168)Gct>Cct	p.A56P	CLDN16_ENST00000456423.1_Missense_Mutation_p.A56P|CLDN16_ENST00000468220.1_Intron	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	56					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		TGGGGCCAGGGCTGGTGTCTG	0.507													G|||	586	0.117013	0.0681	0.1455	5008	,	,		20600	0.0208		0.2336	False		,,,				2504	0.1421				p.A56P		Atlas-SNP	.											.	CLDN16	59	.	0			c.G166C						PASS	.						161.0	140.0	147.0					3																	190106074		2203	4300	6503	SO:0001583	missense	10686	exon1			GCCAGGGCTGGTG	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"""Claudins"""	2037	protein-coding gene	gene with protein product	"""paracellin-1"", ""hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"""	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.166G>C	3.37:g.190106074G>C	ENSP00000264734:p.Ala56Pro	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	155	86	0.554839	NM_006580		Missense_Mutation	SNP	ENST00000264734.2	37	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	G	6.438	0.448874	0.12223	.	.	ENSG00000113946	ENST00000264734;ENST00000456423	D;D	0.93659	-2.9;-3.26	5.39	-3.93	0.04143	.	1.665760	0.03286	N	0.186971	D	0.84234	0.5427	N	0.19112	0.55	0.09310	N	1	B;B	0.12630	0.006;0.0	B;B	0.16289	0.015;0.002	T	0.70167	-0.4946	10	0.36615	T	0.2	-13.3321	0.4429	0.00489	0.347:0.1211:0.2211:0.3108	.	56;56	A0SDD8;Q9Y5I7	.;CLD16_HUMAN	P	56	ENSP00000264734:A56P;ENSP00000414136:A56P	ENSP00000264734:A56P	A	+	1	0	CLDN16	191588768	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	-0.121000	0.10643	-0.435000	0.07264	-0.535000	0.04281	GCT	G|0.753;C|0.247	0.247	strong		0.507	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580	
CDH17	1015	hgsc.bcm.edu	37	8	95158259	95158259	+	Silent	SNP	G	G	A	rs2251734	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:95158259G>A	ENST00000027335.3	-	15	2188	c.2064C>T	c.(2062-2064)ttC>ttT	p.F688F	CDH17_ENST00000450165.2_Silent_p.F688F|CDH17_ENST00000441892.2_Silent_p.F474F	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	688	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			CAGTAGCCTCGAAAATGAGAC	0.483													G|||	1563	0.312101	0.4523	0.3804	5008	,	,		18213	0.1597		0.2604	False		,,,				2504	0.2843				p.F688F		Atlas-SNP	.											.	CDH17	119	.	0			c.C2064T						PASS	.	G	,	1847,2559	537.1+/-374.7	390,1067,746	102.0	90.0	94.0		2064,2064	-11.7	0.0	8	dbSNP_100	94	2410,6190	398.7+/-346.2	358,1694,2248	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	748,2761,2994	AA,AG,GG		28.0233,41.9201,32.731	,	688/833,688/833	95158259	4257,8749	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon15			AGCCTCGAAAATG	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.2064C>T	8.37:g.95158259G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	147	68	0.462585	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			G|0.692;A|0.308	0.308	strong		0.483	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
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 GAIIx	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_ENST00000316997.4_Missense_Mutation_p.D135N|RBM44_ENST00000444524.2_Intron			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	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	44	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	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144863438	144863438	+	Missense_Mutation	SNP	G	G	T	rs140993521		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:144863438G>T	ENST00000369354.3	-	37	6154	c.5965C>A	c.(5965-5967)Cag>Aag	p.Q1989K	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.Q2125K|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.Q1883K|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.Q1989K|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.Q2074K|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1989					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGCTTGTGCTGCAGTCTGACC	0.527			T	PDGFRB	MPD																																p.Q1989K		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,NS,carcinoma,0,2	PDE4DIP	817	2	0			c.C5965A						scavenged	.						180.0	167.0	171.0					1																	144863438		2203	4300	6503	SO:0001583	missense	9659	exon37			TGTGCTGCAGTCT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.5965C>A	1.37:g.144863438G>T	ENSP00000358360:p.Gln1989Lys	Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	182	17	0.0934066	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.4|22.4	4.291537|4.291537	0.80914|0.80914	.|.	.|.	ENSG00000178104|ENSG00000178104	ENST00000530130|ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	.|T;T;T;T;T	.|0.03124	.|4.04;4.09;4.08;4.17;4.14	4.83|4.83	4.83|4.83	0.62350|0.62350	.|.	.|.	.|.	.|.	.|.	.|T	.|0.05777	.|0.0151	M|M	0.77313|0.77313	2.365|2.365	0.36029|0.36029	D|D	0.839278|0.839278	.|P;B	.|0.46784	.|0.884;0.261	.|P;B	.|0.46076	.|0.503;0.297	.|T	.|0.06250	.|-1.0837	.|9	.|0.66056	.|D	.|0.02	.|.	15.7693|15.7693	0.78152|0.78152	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1883;1989	.|Q5VU43-3;Q5VU43	.|.;MYOME_HUMAN	X|K	145|1883;1989;1989;2074;2125	.|ENSP00000327209:Q1883K;ENSP00000358360:Q1989K;ENSP00000358363:Q1989K;ENSP00000435654:Q2074K;ENSP00000358366:Q2125K	.|ENSP00000327209:Q1883K	C|Q	-|-	3|1	2|0	PDE4DIP|PDE4DIP	143574795|143574795	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.800000|0.800000	0.45204|0.45204	4.045000|4.045000	0.57368|0.57368	2.407000|2.407000	0.81776|0.81776	0.484000|0.484000	0.47621|0.47621	TGC|CAG	.	.	weak		0.527	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
GPRC6A	222545	hgsc.bcm.edu	37	6	117114290	117114290	+	Missense_Mutation	SNP	A	A	G	rs35937022	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:117114290A>G	ENST00000310357.3	-	6	1817	c.1796T>C	c.(1795-1797)aTt>aCt	p.I599T	GPRC6A_ENST00000368549.3_Missense_Mutation_p.I528T|GPRC6A_ENST00000530250.1_Missense_Mutation_p.I424T	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	599			I -> T (in dbSNP:rs35937022).		calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		TAGGGAGAGAATCAGGAGTAG	0.433													A|||	661	0.131989	0.0136	0.1556	5008	,	,		19254	0.0218		0.3042	False		,,,				2504	0.2117				p.I599T		Atlas-SNP	.											.	GPRC6A	152	.	0			c.T1796C						PASS	.	A	THR/ILE	270,4136	151.4+/-185.3	22,226,1955	107.0	103.0	104.0		1796	2.4	1.0	6	dbSNP_126	104	2652,5948	427.6+/-355.6	408,1836,2056	yes	missense	GPRC6A	NM_148963.2	89	430,2062,4011	GG,GA,AA		30.8372,6.128,22.4666	benign	599/927	117114290	2922,10084	2203	4300	6503	SO:0001583	missense	222545	exon6			GAGAGAATCAGGA	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.1796T>C	6.37:g.117114290A>G	ENSP00000309493:p.Ile599Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	304	0.1391941391941392	7	0.014227642276422764	59	0.16298342541436464	13	0.022727272727272728	225	0.29683377308707126	A	0.267	-0.995430	0.02145	0.06128	0.308372	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.90844	-2.51;-2.74;-2.73	5.17	2.37	0.29283	GPCR, family 3, C-terminal (1);	1.162580	0.06303	N	0.701252	T	0.59609	0.2206	N	0.08118	0	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.002	B;B;B	0.10450	0.002;0.005;0.001	T	0.44034	-0.9354	9	0.12430	T	0.62	.	4.4929	0.11822	0.2894:0.4026:0.308:0.0	rs35937022	528;424;599	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	T	599;528;424	ENSP00000309493:I599T;ENSP00000357537:I528T;ENSP00000433465:I424T	ENSP00000309493:I599T	I	-	2	0	GPRC6A	117220983	0.005000	0.15991	0.955000	0.39395	0.008000	0.06430	1.768000	0.38511	0.315000	0.23110	-1.182000	0.01712	ATT	A|0.803;G|0.197	0.197	strong		0.433	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
MAPT	4137	hgsc.bcm.edu	37	17	44071294	44071294	+	Intron	SNP	T	T	C	rs62063845	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44071294T>C	ENST00000571987.1	+	8	1507				MAPT_ENST00000334239.8_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000344290.5_Silent_p.T504T|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000415613.2_Silent_p.T504T|MAPT_ENST00000574436.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau						adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TTTAAGCGACTAAGCAAGTCC	0.557													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		18596	0.001		0.2406	False		,,,				2504	0.0613				p.T504T		Atlas-SNP	.											.	MAPT	135	.	0			c.T1512C						PASS	.	C	,,,,,,,	154,2966		6,142,1412	50.0	46.0	47.0		1512,,,,,,,	0.6	1.0	17	dbSNP_129	47	1577,5579		183,1211,2184	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,	189,1353,3596	CC,CT,TT		22.0375,4.9359,16.8451	,,,,,,,	504/777,,,,,,,	44071294	1731,8545	1560	3578	5138	SO:0001627	intron_variant	4137	exon10			AGCGACTAAGCAA	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1507+2342T>C	17.37:g.44071294T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			T|0.860;C|0.140	0.140	strong		0.557	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
ZNF37A	7587	hgsc.bcm.edu	37	10	38407519	38407519	+	Silent	SNP	A	A	G	rs176889	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:38407519A>G	ENST00000361085.5	+	7	1785	c.1440A>G	c.(1438-1440)tcA>tcG	p.S480S	ZNF37A_ENST00000351773.3_Silent_p.S480S	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	480					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(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|prostate(1)	28						GTCAGAAGTCAGCCCTAATTG	0.408													G|||	2349	0.46905	0.4947	0.513	5008	,	,		19435	0.5595		0.4901	False		,,,				2504	0.2883				p.S480S		Atlas-SNP	.											.	ZNF37A	118	.	0			c.A1440G						PASS	.	G	,,	2236,2170	579.2+/-384.9	560,1116,527	59.0	59.0	59.0		1440,1440,1440	1.1	0.8	10	dbSNP_79	59	4204,4396	583.6+/-391.6	998,2208,1094	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF37A	NM_001007094.2,NM_001178101.1,NM_003421.2	,,	1558,3324,1621	GG,GA,AA		48.8837,49.251,49.5156	,,	480/562,480/562,480/562	38407519	6440,6566	2203	4300	6503	SO:0001819	synonymous_variant	7587	exon7			GAAGTCAGCCCTA	X69115	CCDS31183.1	10p11.2	2013-01-08	2006-05-11		ENSG00000075407	ENSG00000075407		"""Zinc fingers, C2H2-type"", ""-"""	13102	protein-coding gene	gene with protein product			"""zinc finger protein 37a (KOX 21)"""			2014798, 8464732	Standard	NM_001178101		Approved	KOX21, ZNF37	uc001izl.3	P17032	OTTHUMG00000017990	ENST00000361085.5:c.1440A>G	10.37:g.38407519A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_003421	B3KRQ3|D3DRZ3|Q96B88	Silent	SNP	ENST00000361085.5	37	CCDS31183.1																																																																																			A|0.502;G|0.498	0.498	strong		0.408	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421	
CRISP1	167	hgsc.bcm.edu	37	6	49814379	49814379	+	Missense_Mutation	SNP	T	T	C	rs3209304	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:49814379T>C	ENST00000335847.4	-	5	390	c.289A>G	c.(289-291)Acc>Gcc	p.T97A	CRISP1_ENST00000536021.1_Missense_Mutation_p.T97A|CRISP1_ENST00000329411.5_Missense_Mutation_p.T97A|CRISP1_ENST00000355791.2_Missense_Mutation_p.T97A|CRISP1_ENST00000507853.1_Missense_Mutation_p.T97A|CRISP1_ENST00000505118.1_Missense_Mutation_p.T97A	NM_001131.2	NP_001122.2	P54107	CRIS1_HUMAN	cysteine-rich secretory protein 1	97	SCP.			T -> A (in Ref. 2; AAB35899 and 3; BAA07483). {ECO:0000305}.	binding of sperm to zona pellucida (GO:0007339)|fusion of sperm to egg plasma membrane (GO:0007342)|regulation of acrosome reaction (GO:0060046)	extracellular space (GO:0005615)|nucleus (GO:0005634)	calcium channel regulator activity (GO:0005246)			endometrium(1)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|upper_aerodigestive_tract(1)	27	Lung NSC(77;0.0358)					CCACAAAAGGTATCTGAAATG	0.368													T|||	220	0.0439297	0.0091	0.0504	5008	,	,		21396	0.0		0.1272	False		,,,				2504	0.046				p.T97A		Atlas-SNP	.											.	CRISP1	45	.	0			c.A289G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	144,4262	100.7+/-139.4	2,140,2061	134.0	119.0	124.0		289,289,289	2.8	0.2	6	dbSNP_105	124	1278,7322	255.0+/-280.0	106,1066,3128	yes	missense,missense,missense	CRISP1	NM_001131.2,NM_001205220.1,NM_170609.1	58,58,58	108,1206,5189	CC,CT,TT		14.8605,3.2683,10.9334	possibly-damaging,possibly-damaging,possibly-damaging	97/250,97/250,97/179	49814379	1422,11584	2203	4300	6503	SO:0001583	missense	167	exon5			AAAAGGTATCTGA	D38451	CCDS4931.1, CCDS4932.1	6p21.2-p21.1	2008-02-05	2003-09-03	2003-09-05	ENSG00000124812	ENSG00000124812			304	protein-coding gene	gene with protein product		601193	"""acidic epididymal glycoprotein-like 1"""	AEGL1		8838800	Standard	NM_001131		Approved	CRISP-1, ARP, HUMARP, HSCRISP1D, HSCRISP1G	uc003ozw.2	P54107	OTTHUMG00000014827	ENST00000335847.4:c.289A>G	6.37:g.49814379T>C	ENSP00000338276:p.Thr97Ala	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_001205220	B5BU98|O00698|Q13248|Q14082|Q96SF6	Missense_Mutation	SNP	ENST00000335847.4	37	CCDS4931.1	124	0.056776556776556776	7	0.014227642276422764	22	0.06077348066298342	0	0.0	95	0.12532981530343007	T	10.34	1.323035	0.24080	0.032683	0.148605	ENSG00000124812	ENST00000507853;ENST00000335847;ENST00000355791;ENST00000329411;ENST00000505118;ENST00000536021	T;T;T;T;T;T	0.07216	3.21;3.21;3.21;3.21;3.21;3.21	5.34	2.77	0.32553	CAP domain (3);	0.790058	0.11938	N	0.514962	T	0.06280	0.0162	L	0.58669	1.825	0.80722	P	0.0	P;D	0.57571	0.793;0.98	B;P	0.52454	0.256;0.699	T	0.28902	-1.0029	8	.	.	.	.	4.5062	0.11889	0.0:0.1067:0.1945:0.6988	rs3209304;rs12205497;rs17410390;rs17663949;rs52831968;rs12205497	97;97	P54107-2;P54107	.;CRIS1_HUMAN	A	97	ENSP00000425020:T97A;ENSP00000338276:T97A;ENSP00000348044:T97A;ENSP00000331317:T97A;ENSP00000427589:T97A;ENSP00000441798:T97A	.	T	-	1	0	CRISP1	49922338	0.001000	0.12720	0.220000	0.23810	0.052000	0.14988	0.287000	0.18920	0.842000	0.35045	0.528000	0.53228	ACC	T|0.762;G|0.006;C|0.078;A|0.154	0.078	strong		0.368	CRISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040875.2	NM_001131	
PPAP2C	8612	hgsc.bcm.edu	37	19	288062	288062	+	Silent	SNP	G	G	A	rs11542542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:288062G>A	ENST00000269812.3	-	2	211	c.162C>T	c.(160-162)caC>caT	p.H54H	PPAP2C_ENST00000327790.3_Silent_p.H75H|PPAP2C_ENST00000434325.2_De_novo_Start_OutOfFrame	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	54					dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-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)		CCATGAGCCCGTGGGTGATGG	0.617													G|||	195	0.0389377	0.0121	0.049	5008	,	,		14045	0.001		0.0954	False		,,,				2504	0.0491				p.H75H		Atlas-SNP	.											PPAP2C_ENST00000269812,NS,carcinoma,0,2	PPAP2C	38	2	0			c.C225T						PASS	.	G	,,	114,4292	86.3+/-125.0	2,110,2091	148.0	123.0	132.0		162,,225	-9.4	0.0	19	dbSNP_120	132	794,7806	186.0+/-233.6	37,720,3543	yes	coding-synonymous,utr-5,coding-synonymous	PPAP2C	NM_003712.2,NM_177526.1,NM_177543.1	,,	39,830,5634	AA,AG,GG		9.2326,2.5874,6.9814	,,	54/289,,75/310	288062	908,12098	2203	4300	6503	SO:0001819	synonymous_variant	8612	exon2			GAGCCCGTGGGTG	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.162C>T	19.37:g.288062G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	171	61	0.356725	NM_177543	A6NLV0|E9PAY8	Silent	SNP	ENST00000269812.3	37	CCDS12023.1																																																																																			G|0.935;A|0.065	0.065	strong		0.617	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2		
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 GAIIx	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		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	32	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 GAIIx	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_ENST00000509931.1_Intron|ZNF131_ENST00000306938.4_Silent_p.Y358Y|ZNF131_ENST00000509634.1_Silent_p.Y358Y|ZNF131_ENST00000509156.1_Silent_p.Y392Y|ZNF131_ENST00000505606.2_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		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	38	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	
NCK1	4690	hgsc.bcm.edu	37	3	136664737	136664737	+	Missense_Mutation	SNP	C	C	T	rs13320485	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:136664737C>T	ENST00000481752.1	+	3	703	c.539C>T	c.(538-540)gCa>gTa	p.A180V	NCK1_ENST00000469404.1_Missense_Mutation_p.A116V|NCK1_ENST00000288986.2_Missense_Mutation_p.A180V			P16333	NCK1_HUMAN	NCK adaptor protein 1	180			A -> V (in dbSNP:rs13320485).		actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)			cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						GAGAAATTAGCAGCAGTCGTC	0.423													C|||	43	0.00858626	0.0023	0.0274	5008	,	,		20979	0.0		0.0179	False		,,,				2504	0.0031				p.A180V		Atlas-SNP	.											.	NCK1	26	.	0			c.C539T						PASS	.	C	VAL/ALA,VAL/ALA	12,4394	19.1+/-41.9	0,12,2191	203.0	199.0	200.0		347,539	6.2	1.0	3	dbSNP_121	200	143,8457	70.3+/-132.9	1,141,4158	yes	missense,missense	NCK1	NM_001190796.1,NM_006153.4	64,64	1,153,6349	TT,TC,CC		1.6628,0.2724,1.1918	benign,benign	116/314,180/378	136664737	155,12851	2203	4300	6503	SO:0001583	missense	4690	exon3			AATTAGCAGCAGT	X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092		"""SH2 domain containing"""	7664	protein-coding gene	gene with protein product		600508		NCK		7806213, 9737977	Standard	XM_005247498		Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.539C>T	3.37:g.136664737C>T	ENSP00000417273:p.Ala180Val	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	142	79	0.556338	NM_006153	B7Z751|D3DNE3	Missense_Mutation	SNP	ENST00000481752.1	37	CCDS3092.1	24	0.01098901098901099	3	0.006097560975609756	10	0.027624309392265192	0	0.0	11	0.014511873350923483	C	27.5	4.836165	0.91117	0.002724	0.016628	ENSG00000158092	ENST00000288986;ENST00000481752;ENST00000469404	T;T;T	0.69175	-0.32;-0.32;-0.38	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.42449	0.1203	M	0.64997	1.995	0.80722	D	1	B;B	0.33512	0.415;0.243	B;B	0.30716	0.119;0.09	T	0.59112	-0.7515	10	0.54805	T	0.06	-5.3209	18.3537	0.90348	0.0:1.0:0.0:0.0	rs13320485;rs13320485	116;180	B7Z751;P16333	.;NCK1_HUMAN	V	180;180;116	ENSP00000288986:A180V;ENSP00000417273:A180V;ENSP00000419631:A116V	ENSP00000288986:A180V	A	+	2	0	NCK1	138147427	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.451000	0.60047	2.937000	0.99478	0.650000	0.86243	GCA	C|0.989;T|0.011	0.011	strong		0.423	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357307.1	NM_006153	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161017761	161017761	+	Missense_Mutation	SNP	C	C	T	rs112388093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161017761C>T	ENST00000368013.3	-	12	3370	c.3050G>A	c.(3049-3051)cGa>cAa	p.R1017Q	USF1_ENST00000368021.3_5'Flank|USF1_ENST00000435396.1_5'Flank|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.R840Q|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.R806Q	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	1017					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GGTCTGGGTTCGCCGAACTCC	0.587													C|||	43	0.00858626	0.0038	0.0086	5008	,	,		18547	0.001		0.0219	False		,,,				2504	0.0092				p.R1017Q		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.G3050A						PASS	.	C	GLN/ARG,GLN/ARG	42,4364	45.3+/-79.5	1,40,2162	71.0	71.0	71.0		3050,2417	4.2	1.0	1	dbSNP_132	71	234,8366	96.3+/-158.1	3,228,4069	yes	missense,missense	ARHGAP30	NM_001025598.1,NM_181720.2	43,43	4,268,6231	TT,TC,CC		2.7209,0.9532,2.1221	probably-damaging,probably-damaging	1017/1102,806/891	161017761	276,12730	2203	4300	6503	SO:0001583	missense	257106	exon12			TGGGTTCGCCGAA	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.3050G>A	1.37:g.161017761C>T	ENSP00000356992:p.Arg1017Gln	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	52	0.597701	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	CCDS30918.1	27	0.012362637362637362	3	0.006097560975609756	6	0.016574585635359115	1	0.0017482517482517483	17	0.022427440633245383	C	19.85	3.904021	0.72754	0.009532	0.027209	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368015	T;T;T	0.53640	1.93;2.08;0.61	4.21	4.21	0.49690	.	0.000000	0.37483	N	0.002074	T	0.55417	0.1919	M	0.69823	2.125	0.28290	N	0.923571	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.979	T	0.51148	-0.8742	10	0.87932	D	0	.	11.9335	0.52860	0.0:1.0:0.0:0.0	.	1017;806	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	Q	806;1017;840	ENSP00000356995:R806Q;ENSP00000356992:R1017Q;ENSP00000356994:R840Q	ENSP00000356992:R1017Q	R	-	2	0	ARHGAP30	159284385	0.996000	0.38824	1.000000	0.80357	0.967000	0.64934	1.946000	0.40283	2.164000	0.68074	0.455000	0.32223	CGA	C|0.980;T|0.020	0.020	strong		0.587	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
TTC7A	57217	hgsc.bcm.edu	37	2	47177617	47177617	+	Silent	SNP	C	C	T	rs61738825	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:47177617C>T	ENST00000319190.5	+	2	668	c.300C>T	c.(298-300)agC>agT	p.S100S	TTC7A_ENST00000461601.1_3'UTR|TTC7A_ENST00000536057.1_Silent_p.S100S|TTC7A_ENST00000394850.2_Silent_p.S100S|TTC7A_ENST00000409245.1_Silent_p.S66S|TTC7A_ENST00000263737.6_5'UTR	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	100					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			CGAAGATGAGCGAAGCCAAAA	0.507													C|||	254	0.0507188	0.0242	0.0576	5008	,	,		21040	0.0		0.1153	False		,,,				2504	0.0675				p.S100S		Atlas-SNP	.											.	TTC7A	80	.	0			c.C300T						PASS	.	C		157,4249	105.2+/-143.6	5,147,2051	110.0	99.0	103.0		300	-0.4	0.4	2	dbSNP_129	103	846,7754	194.9+/-240.2	42,762,3496	no	coding-synonymous	TTC7A	NM_020458.2		47,909,5547	TT,TC,CC		9.8372,3.5633,7.7118		100/859	47177617	1003,12003	2203	4300	6503	SO:0001819	synonymous_variant	57217	exon2			GATGAGCGAAGCC	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"""Tetratricopeptide (TTC) repeat domain containing"""	19750	protein-coding gene	gene with protein product		609332	"""tetratricopeptide repeat domain 7"""	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.300C>T	2.37:g.47177617C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	75	28	0.373333	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			C|0.928;T|0.072	0.072	strong		0.507	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927	
RBMXL3	139804	hgsc.bcm.edu	37	X	114425238	114425238	+	Missense_Mutation	SNP	G	G	A	rs55718100		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:114425238G>A	ENST00000424776.3	+	1	1276	c.1234G>A	c.(1234-1236)Ggc>Agc	p.G412S	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	412	Gly-rich.			G -> S (in Ref. 1; AK097568). {ECO:0000305}.			nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						CAACAGTTACGGCCAGAGCCA	0.667													G|||	340	0.0900662	0.0197	0.0778	3775	,	,		10374	0.0427		0.1481	False		,,,				2504	0.0695				p.G412S		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G1234A						PASS	.	G	SER/GLY,	33,1174		1,24,7,492,166	12.0	15.0	14.0		1234,	-0.7	0.0	X	dbSNP_129	14	383,1994		18,209,138,571,643	yes	missense,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	56,	19,233,145,1063,809	AA,AG,A,GG,G		16.1127,2.7341,11.6071	probably-damaging,	412/1068,	114425238	416,3168	690	1579	2269	SO:0001583	missense	139804	exon1			AGTTACGGCCAGA	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.1234G>A	X.37:g.114425238G>A	ENSP00000417451:p.Gly412Ser	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	35	12	0.342857	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	37	CCDS55478.1	117	0.0705244122965642	3	0.006122448979591836	20	0.056179775280898875	2	0.0034965034965034965	53	0.07703488372093023	G	4.885	0.164466	0.09287	0.027341	0.161127	ENSG00000175718	ENST00000424776	T	0.07216	3.21	0.341	-0.683	0.11335	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.25007	0.116	B	0.14023	0.01	T	0.44832	-0.9302	7	0.87932	D	0	.	.	.	.	rs55718100	412	Q8N7X1	RMXL3_HUMAN	S	412	ENSP00000417451:G412S	ENSP00000417451:G412S	G	+	1	0	RBMXL3	114331494	0.876000	0.30132	0.001000	0.08648	0.002000	0.02628	-0.224000	0.09164	-1.340000	0.02227	-1.442000	0.01069	GGC	G|0.930;A|0.070	0.070	strong		0.667	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
HHLA2	11148	hgsc.bcm.edu	37	3	108081277	108081277	+	Missense_Mutation	SNP	C	C	A	rs6779094	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:108081277C>A	ENST00000357759.5	+	7	1506	c.1092C>A	c.(1090-1092)agC>agA	p.S364R	HHLA2_ENST00000467761.1_Missense_Mutation_p.S364R|HHLA2_ENST00000467562.1_Missense_Mutation_p.S300R|HHLA2_ENST00000491820.1_Missense_Mutation_p.S364R|HHLA2_ENST00000489514.2_Missense_Mutation_p.S364R	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	364			S -> R (in dbSNP:rs6779094).		positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						TGATTTGGAGCGTAAAATGTT	0.413													A|||	546	0.109026	0.0809	0.1571	5008	,	,		17658	0.001		0.2336	False		,,,				2504	0.0961				p.S364R		Atlas-SNP	.											.	HHLA2	95	.	0			c.C1092A						PASS	.	A	ARG/SER	456,3216		30,396,1410	111.0	99.0	103.0		1092	-8.0	0.0	3	dbSNP_116	103	1906,6284		237,1432,2426	yes	missense	HHLA2	NM_007072.2	110	267,1828,3836	AA,AC,CC		23.2723,12.4183,19.9123	possibly-damaging	364/415	108081277	2362,9500	1836	4095	5931	SO:0001583	missense	11148	exon7			TTGGAGCGTAAAA	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1092C>A	3.37:g.108081277C>A	ENSP00000350402:p.Ser364Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	37	CCDS46883.1	299|299	0.13690476190476192|0.13690476190476192	44|44	0.08943089430894309|0.08943089430894309	66|66	0.18232044198895028|0.18232044198895028	0|0	0.0|0.0	189|189	0.24934036939313983|0.24934036939313983	A|A	0.596|0.596	-0.830853|-0.830853	0.02713|0.02713	0.124183|0.124183	0.232723|0.232723	ENSG00000114455|ENSG00000114455	ENST00000482099|ENST00000491820;ENST00000467562;ENST00000357759;ENST00000467761;ENST00000489514	.|T;T;T;T;T	.|0.10382	.|5.08;2.88;5.05;5.05;5.05	3.98|3.98	-7.96|-7.96	0.01144|0.01144	.|.	.|8.316520	.|0.00166	.|N	.|0.000010	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.01281	.|0.0;0.0;0.0	T|T	0.30851|0.30851	-0.9964|-0.9964	4|9	.|0.72032	.|D	.|0.01	-18.4602|-18.4602	5.9093|5.9093	0.19018|0.19018	0.1377:0.0963:0.5385:0.2274|0.1377:0.0963:0.5385:0.2274	rs6779094;rs17242385;rs52829163;rs59044069;rs6779094|rs6779094;rs17242385;rs52829163;rs59044069;rs6779094	.|300;364;364	.|B4DKN2;C9J7D0;Q9UM44	.|.;.;HHLA2_HUMAN	S|R	267|364;300;364;364;364	.|ENSP00000418284:S364R;ENSP00000418345:S300R;ENSP00000350402:S364R;ENSP00000419207:S364R;ENSP00000417856:S364R	.|ENSP00000350402:S364R	R|S	+|+	1|3	0|2	HHLA2|HHLA2	109563967|109563967	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.012000|0.012000	0.07955|0.07955	-2.044000|-2.044000	0.01411|0.01411	-3.721000|-3.721000	0.00115|0.00115	-1.066000|-1.066000	0.02275|0.02275	CGT|AGC	C|0.868;A|0.132	0.132	strong		0.413	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
BTBD2	55643	hgsc.bcm.edu	37	19	1986520	1986520	+	Silent	SNP	G	G	A	rs7253519	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1986520G>A	ENST00000255608.4	-	9	1561	c.1545C>T	c.(1543-1545)gaC>gaT	p.D515D	AC005306.3_ENST00000587498.1_RNA	NM_017797.3	NP_060267.2	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	515						cytoplasmic mRNA processing body (GO:0000932)				endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	12		Ovarian(11;2.11e-07)|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)		GGATCTGGCCGTCCTCCACGG	0.652													G|||	580	0.115815	0.0832	0.1398	5008	,	,		18950	0.1736		0.1312	False		,,,				2504	0.0675				p.D515D		Atlas-SNP	.											BTBD2,NS,carcinoma,0,1	BTBD2	31	1	0			c.C1545T						PASS	.	G		375,4031	189.2+/-215.4	15,345,1843	155.0	108.0	124.0		1545	1.1	0.9	19	dbSNP_116	124	1043,7557	221.9+/-259.1	61,921,3318	no	coding-synonymous	BTBD2	NM_017797.3		76,1266,5161	AA,AG,GG		12.1279,8.5111,10.9027		515/526	1986520	1418,11588	2203	4300	6503	SO:0001819	synonymous_variant	55643	exon9			CTGGCCGTCCTCC	AF355797	CCDS12078.1	19p13.3	2013-10-02			ENSG00000133243	ENSG00000133243		"""BTB/POZ domain containing"""	15504	protein-coding gene	gene with protein product		608531				11179693	Standard	XM_005259593		Approved		uc002lup.1	Q9BX70	OTTHUMG00000180017	ENST00000255608.4:c.1545C>T	19.37:g.1986520G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	135	66	0.488889	NM_017797	O60418|O75248|Q4VBZ1|Q6IAC5|Q7Z5W0|Q96SX8|Q9NPS1|Q9NX81	Silent	SNP	ENST00000255608.4	37	CCDS12078.1																																																																																			A|0.103;C|0.000;G|0.897	0.103	strong		0.652	BTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449300.2		
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 GAIIx	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	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	67	37	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	
DRC7	84229	hgsc.bcm.edu	37	16	57762401	57762401	+	Missense_Mutation	SNP	T	T	C	rs2923147	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57762401T>C	ENST00000360716.3	+	17	2517	c.2296T>C	c.(2296-2298)Tgc>Cgc	p.C766R	CCDC135_ENST00000394337.4_Missense_Mutation_p.C766R|CCDC135_ENST00000336825.8_Missense_Mutation_p.C701R			Q8IY82	CC135_HUMAN		766			C -> R (in dbSNP:rs2923147). {ECO:0000269|PubMed:11230166}.		cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				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						GAAACTAACATGCTGGCAGGC	0.622													c|||	1976	0.394569	0.7133	0.2954	5008	,	,		16930	0.3839		0.2256	False		,,,				2504	0.2188				p.C766R		Atlas-SNP	.											CCDC135,NS,carcinoma,0,1	CCDC135	97	1	0			c.T2296C						PASS	.	C	ARG/CYS	2798,1594	487.6+/-361.0	900,998,298	46.0	51.0	49.0		2296	4.2	0.8	16	dbSNP_101	49	1710,6882	732.0+/-406.8	169,1372,2755	yes	missense	CCDC135	NM_032269.5	180	1069,2370,3053	CC,CT,TT		19.9022,36.2933,34.7197	benign	766/875	57762401	4508,8476	2196	4296	6492	SO:0001583	missense	84229	exon16			CTAACATGCTGGC																												ENST00000360716.3:c.2296T>C	16.37:g.57762401T>C	ENSP00000353942:p.Cys766Arg	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	160	90	0.5625	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	843	0.385989010989011	344	0.6991869918699187	109	0.3011049723756906	218	0.3811188811188811	172	0.22691292875989447	c	0.059	-1.228281	0.01518	0.637067	0.199022	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.35973	1.28;1.28;1.28	5.15	4.16	0.48862	.	0.215200	0.37304	N	0.002154	T	0.00012	0.0000	N	0.00067	-2.295	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43180	-0.9407	9	0.02654	T	1	-14.2278	8.0328	0.30476	0.2595:0.6617:0.0:0.0788	rs2923147;rs3803595;rs57995451;rs2923147	701;766	Q8IY82-2;Q8IY82	.;CC135_HUMAN	R	766;701;766	ENSP00000377869:C766R;ENSP00000338938:C701R;ENSP00000353942:C766R	ENSP00000338938:C701R	C	+	1	0	CCDC135	56319902	0.054000	0.20591	0.822000	0.32727	0.661000	0.39034	1.019000	0.30014	1.184000	0.42957	-0.320000	0.08662	TGC	T|0.627;C|0.373	0.373	strong		0.622	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
TRIAP1	51499	hgsc.bcm.edu	37	12	120884328	120884328	+	5'Flank	SNP	C	C	T	rs2235217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:120884328C>T	ENST00000546954.1	-	0	0				TRIAP1_ENST00000302432.3_5'Flank|AL021546.6_ENST00000551806.1_Intron|GATC_ENST00000551765.1_Silent_p.G15G	NM_016399.2	NP_057483.1	O43715	TRIA1_HUMAN	TP53 regulated inhibitor of apoptosis 1						cellular response to UV (GO:0034644)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of membrane lipid distribution (GO:0097035)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	p53 binding (GO:0002039)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCCTCTGGGCGGGCGCCAGG	0.706													C|||	1299	0.259385	0.0794	0.2579	5008	,	,		14028	0.4901		0.2783	False		,,,				2504	0.2464				p.G15G		Atlas-SNP	.											.	GATC	12	.	0			c.C45T						PASS	.	C		466,3940	217.8+/-236.0	23,420,1760	46.0	52.0	50.0		45	-0.2	0.0	12	dbSNP_98	50	2719,5877	419.6+/-353.1	426,1867,2005	no	coding-synonymous	GATC	NM_176818.2		449,2287,3765	TT,TC,CC		31.631,10.5765,24.4962		15/137	120884328	3185,9817	2203	4298	6501	SO:0001631	upstream_gene_variant	283459	exon1			TCTGGGCGGGCGC		CCDS9198.1	12q24.31	2012-10-15			ENSG00000170855	ENSG00000170855			26937	protein-coding gene	gene with protein product	"""p53-inducible cell-survival factor"", ""mitochondrial distribution and morphology 35 homolog (S. cerevisiae)"""	614943				11042152, 15735003	Standard	NM_016399		Approved	P53CSV, WF-1, HSPC132, p53CSV, MDM35	uc001tyg.3	O43715	OTTHUMG00000047787		12.37:g.120884328C>T	Exception_encountered	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_176818	B2R4Z7|Q5RKS5|Q6LCA7	Silent	SNP	ENST00000546954.1	37	CCDS9198.1																																																																																			C|0.744;T|0.256	0.256	strong		0.706	TRIAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108980.3	NM_016399	
EPPK1	83481	hgsc.bcm.edu	37	8	144940331	144940331	+	Missense_Mutation	SNP	C	C	T	rs200585601		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144940331C>T	ENST00000525985.1	-	2	7162	c.7091G>A	c.(7090-7092)cGg>cAg	p.R2364Q				P58107	EPIPL_HUMAN	epiplakin 1	2364						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)	p.R2364Q(1)		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)			GTAGCCGCGCCGGTAGGCCAC	0.692																																					p.R2364Q		Atlas-SNP	.											EPPK1,NS,carcinoma,0,6	EPPK1	199	6	1	Substitution - Missense(1)	large_intestine(1)	c.G7091A						scavenged	.	C	GLN/ARG	194,4166		0,194,1986	217.0	211.0	213.0		7091	0.7	1.0	8	dbSNP_134	213	66,8462		0,66,4198	no	missense	EPPK1	NM_031308.1	43	0,260,6184	TT,TC,CC		0.7739,4.4495,2.0174	benign	2364/2420	144940331	260,12628	2180	4264	6444	SO:0001583	missense	83481	exon1			CCGCGCCGGTAGG	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.7091G>A	8.37:g.144940331C>T	ENSP00000436337:p.Arg2364Gln	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	176	45	0.255682	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	7.296	0.612142	0.14066	0.044495	0.007739	ENSG00000227184	ENST00000525985	T	0.74526	-0.85	4.42	0.661	0.17874	.	.	.	.	.	T	0.14184	0.0343	N	0.03903	-0.33	0.21579	N	0.999636	B	0.20550	0.046	B	0.12837	0.008	T	0.14254	-1.0479	9	0.02654	T	1	.	7.4216	0.27075	0.0:0.2871:0.0:0.7129	.	2364	E9PPU0	.	Q	2364	ENSP00000436337:R2364Q	ENSP00000436337:R2364Q	R	-	2	0	EPPK1	145012319	0.742000	0.28228	0.982000	0.44146	0.955000	0.61496	1.358000	0.34102	0.024000	0.15214	-0.482000	0.04802	CGG	C|0.997;T|0.003	0.003	weak		0.692	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
MAP10	54627	hgsc.bcm.edu	37	1	232941354	232941354	+	Silent	SNP	G	G	T	rs12567597	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:232941354G>T	ENST00000418460.1	+	1	712	c.585G>T	c.(583-585)ctG>ctT	p.L195L		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	53					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										CGCGCGGTCTGTGCCCCGCCG	0.716													G|||	613	0.122404	0.1263	0.1412	5008	,	,		13004	0.1726		0.0964	False		,,,				2504	0.0787				p.L195L		Atlas-SNP	.											.	.	.	.	0			c.G585T						PASS	.	G		372,3506		17,338,1584	4.0	6.0	6.0		585	2.2	0.1	1	dbSNP_120	6	833,7271		45,743,3264	no	coding-synonymous	KIAA1383	NM_019090.2		62,1081,4848	TT,TG,GG		10.2789,9.5926,10.0568		195/1048	232941354	1205,10777	1939	4052	5991	SO:0001819	synonymous_variant	54627	exon1			CGGTCTGTGCCCC	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.585G>T	1.37:g.232941354G>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	37	CCDS44334.1																																																																																			G|0.858;T|0.142	0.142	strong		0.716	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
FREM1	158326	hgsc.bcm.edu	37	9	14801738	14801738	+	Missense_Mutation	SNP	G	G	C	rs16932300	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:14801738G>C	ENST00000380880.3	-	20	4389	c.3606C>G	c.(3604-3606)agC>agG	p.S1202R	FREM1_ENST00000422223.2_Missense_Mutation_p.S1202R|FREM1_ENST00000380881.4_Missense_Mutation_p.S1203R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1202			S -> R (in dbSNP:rs16932300).		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)		AGAAGTCTTTGCTAAACCCCC	0.517													G|||	820	0.163738	0.3578	0.098	5008	,	,		18063	0.1002		0.0795	False		,,,				2504	0.1002				p.S1202R		Atlas-SNP	.											.	FREM1	261	.	0			c.C3606G						PASS	.	G	ARG/SER	1213,2779		181,851,964	147.0	145.0	145.0		3606	-2.4	0.0	9	dbSNP_123	145	542,7814		13,516,3649	yes	missense	FREM1	NM_144966.5	110	194,1367,4613	CC,CG,GG		6.4864,30.3858,14.2128	benign	1202/2180	14801738	1755,10593	1996	4178	6174	SO:0001583	missense	158326	exon21			GTCTTTGCTAAAC	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.3606C>G	9.37:g.14801738G>C	ENSP00000370262:p.Ser1202Arg	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	206	101	0.490291	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	341	0.15613553113553114	176	0.35772357723577236	38	0.10497237569060773	65	0.11363636363636363	62	0.08179419525065963	G	1.832	-0.469514	0.04445	0.303858	0.064864	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.54279	0.58;0.58;0.58	5.51	-2.39	0.06602	.	0.432154	0.30068	N	0.010492	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.38542	-0.9656	9	0.22706	T	0.39	-4.1075	4.321	0.11016	0.1358:0.304:0.4434:0.1168	rs16932300;rs58105230;rs16932300	1202	Q5H8C1	FREM1_HUMAN	R	1203;1202;1202	ENSP00000370263:S1203R;ENSP00000412940:S1202R;ENSP00000370262:S1202R	ENSP00000370257:S1205R	S	-	3	2	FREM1	14791738	0.104000	0.21937	0.001000	0.08648	0.023000	0.10783	0.018000	0.13422	-0.241000	0.09681	-0.282000	0.10007	AGC	G|0.839;C|0.161	0.161	strong		0.517	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
DPP4	1803	hgsc.bcm.edu	37	2	162929979	162929979	+	Silent	SNP	A	A	G	rs17574	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:162929979A>G	ENST00000360534.3	-	2	584	c.24T>C	c.(22-24)ctT>ctC	p.L8L	AC008063.2_ENST00000418335.1_RNA	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	8					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	GCAGTCCCAGAAGAACCTTCC	0.547													G|||	1065	0.21266	0.211	0.1744	5008	,	,		16929	0.0466		0.3459	False		,,,				2504	0.2761				p.L8L		Atlas-SNP	.											.	DPP4	90	.	0			c.T24C						PASS	.	G		1037,3369	726.6+/-409.7	121,795,1287	73.0	71.0	71.0		24	2.9	1.0	2	dbSNP_63	71	2979,5621	666.2+/-402.3	527,1925,1848	no	coding-synonymous	DPP4	NM_001935.3		648,2720,3135	GG,GA,AA		34.6395,23.5361,30.8781		8/767	162929979	4016,8990	2203	4300	6503	SO:0001819	synonymous_variant	1803	exon2			TCCCAGAAGAACC	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"""CD molecules"""	3009	protein-coding gene	gene with protein product		102720	"""dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)"", ""adenosine deaminase complexing protein 2"""	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.24T>C	2.37:g.162929979A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_001935	Q53TN1	Silent	SNP	ENST00000360534.3	37	CCDS2216.1																																																																																			A|0.720;G|0.280	0.280	strong		0.547	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2		
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 GAIIx	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	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	199	88	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	
ZBBX	79740	hgsc.bcm.edu	37	3	167000256	167000256	+	Missense_Mutation	SNP	G	G	C	rs12638625	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:167000256G>C	ENST00000392766.2	-	19	2247	c.1907C>G	c.(1906-1908)gCa>gGa	p.A636G	ZBBX_ENST00000455345.2_Missense_Mutation_p.A675G|ZBBX_ENST00000392767.2_Missense_Mutation_p.A636G|ZBBX_ENST00000307529.5_Missense_Mutation_p.A675G|ZBBX_ENST00000392764.1_Missense_Mutation_p.A607G	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	636			A -> G (in dbSNP:rs12638625). {ECO:0000269|PubMed:14702039}.			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						TGGAAAATTTGCTGTTGAAGG	0.338																																					p.A675G		Atlas-SNP	.											.	ZBBX	299	.	0			c.C2024G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	982,2656		134,714,971	124.0	120.0	121.0		2024,1820,1907	1.5	0.8	3	dbSNP_120	121	2451,5685		353,1745,1970	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	60,60,60	487,2459,2941	CC,CG,GG		30.1254,26.9929,29.1575	benign,benign,benign	675/840,607/772,636/801	167000256	3433,8341	1819	4068	5887	SO:0001583	missense	79740	exon20			AAATTTGCTGTTG	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.1907C>G	3.37:g.167000256G>C	ENSP00000376519:p.Ala636Gly	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	129	54	0.418605	NM_001199201	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	861	0.3942307692307692	135	0.27439024390243905	136	0.3756906077348066	370	0.6468531468531469	220	0.29023746701846964	G	6.009	0.370125	0.11352	0.269929	0.301254	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.14391	2.68;2.68;2.53;2.53;2.51	5.28	1.47	0.22746	.	0.759635	0.12007	N	0.508267	T	0.00012	0.0000	L	0.53249	1.67	0.49130	P	2.4400000000002198E-4	B;B	0.28760	0.221;0.141	B;B	0.33295	0.161;0.077	T	0.21724	-1.0237	9	0.40728	T	0.16	-1.7821	4.4295	0.11520	0.2482:0.0:0.5988:0.153	rs12638625;rs52789532;rs12638625	675;636	A8MT70-2;A8MT70	.;ZBBX_HUMAN	G	636;636;675;675;607	ENSP00000376519:A636G;ENSP00000376520:A636G;ENSP00000390232:A675G;ENSP00000305065:A675G;ENSP00000376517:A607G	ENSP00000305065:A675G	A	-	2	0	ZBBX	168482950	0.997000	0.39634	0.831000	0.32960	0.003000	0.03518	0.491000	0.22419	-0.014000	0.14175	-0.911000	0.02809	GCA	G|0.622;C|0.378	0.378	strong		0.338	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
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 GAIIx	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	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	150	89	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		
NEBL	10529	hgsc.bcm.edu	37	10	21134282	21134282	+	Missense_Mutation	SNP	C	C	G	rs41277370	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:21134282C>G	ENST00000377122.4	-	12	1528	c.1132G>C	c.(1132-1134)Gat>Cat	p.D378H	NEBL_ENST00000377159.4_Intron|NEBL_ENST00000417816.2_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	378			D -> H (in dbSNP:rs41277370).		cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.D378H(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TTCTCAAAATCCTCTTTGTAA	0.348													C|||	193	0.0385383	0.0053	0.0461	5008	,	,		16267	0.0268		0.0835	False		,,,				2504	0.044				p.D378H		Atlas-SNP	.											NEBL,NS,carcinoma,0,1	NEBL	199	1	1	Substitution - Missense(1)	stomach(1)	c.G1132C						PASS	.	C	,HIS/ASP,	81,4325	69.8+/-107.6	1,79,2123	113.0	110.0	111.0		,1132,	4.2	1.0	10	dbSNP_127	111	712,7886	174.2+/-224.5	27,658,3614	yes	intron,missense,intron	NEBL	NM_001173484.1,NM_006393.2,NM_213569.2	,81,	28,737,5737	GG,GC,CC		8.281,1.8384,6.0981	,probably-damaging,	,378/1015,	21134282	793,12211	2203	4299	6502	SO:0001583	missense	10529	exon12			CAAAATCCTCTTT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1132G>C	10.37:g.21134282C>G	ENSP00000366326:p.Asp378His	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	102	0.046703296703296704	8	0.016260162601626018	20	0.055248618784530384	15	0.026223776223776224	59	0.07783641160949868	C	16.21	3.059222	0.55325	0.018384	0.08281	ENSG00000078114	ENST00000377122	T	0.54071	0.59	6.14	4.24	0.50183	.	0.284706	0.36409	N	0.002617	T	0.12263	0.0298	M	0.86097	2.795	0.80722	D	1	P	0.48589	0.912	P	0.62298	0.9	T	0.47959	-0.9076	10	0.72032	D	0.01	.	9.0226	0.36209	0.0:0.8194:0.0:0.1806	rs41277370	378	O76041	NEBL_HUMAN	H	378	ENSP00000366326:D378H	ENSP00000366326:D378H	D	-	1	0	NEBL	21174288	0.999000	0.42202	0.978000	0.43139	0.719000	0.41307	3.614000	0.54160	0.869000	0.35703	-0.145000	0.13849	GAT	C|0.937;G|0.063	0.063	strong		0.348	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
CARNS1	57571	hgsc.bcm.edu	37	11	67191449	67191449	+	Silent	SNP	T	T	C	rs1790747	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67191449T>C	ENST00000307823.3	+	9	2313	c.1861T>C	c.(1861-1863)Ttg>Ctg	p.L621L	CARNS1_ENST00000423745.2_Silent_p.L621L|CARNS1_ENST00000531040.1_Silent_p.L718L|CARNS1_ENST00000445895.2_Silent_p.L744L	NM_020811.1	NP_065862.1	A5YM72	CRNS1_HUMAN	carnosine synthase 1	621	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				ATP catabolic process (GO:0006200)|carnosine biosynthetic process (GO:0035499)		ATP binding (GO:0005524)|ATPase activity (GO:0016887)|carnosine synthase activity (GO:0047730)|metal ion binding (GO:0046872)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)	11						TGGTGGGCGGTTGCTGGCTGC	0.652													C|||	1802	0.359824	0.8298	0.4063	5008	,	,		17757	0.2897		0.0835	False		,,,				2504	0.0481				p.L744L		Atlas-SNP	.											.	CARNS1	60	.	0			c.T2230C						PASS	.	C	,	2879,1419		993,893,263	119.0	143.0	135.0		2230,1861	3.9	0.8	11	dbSNP_89	135	653,7809		21,611,3599	no	coding-synonymous,coding-synonymous	CARNS1	NM_001166222.1,NM_020811.1	,	1014,1504,3862	CC,CT,TT		7.7169,33.0154,27.6803	,	744/951,621/828	67191449	3532,9228	2149	4231	6380	SO:0001819	synonymous_variant	57571	exon10			GGGCGGTTGCTGG		CCDS44658.1, CCDS53667.1	11q13.1	2010-03-25	2010-03-25	2010-03-25	ENSG00000172508	ENSG00000172508			29268	protein-coding gene	gene with protein product		613368	"""ATP-grasp domain containing 1"""	ATPGD1		20097752	Standard	NM_020811		Approved	KIAA1394	uc010rpr.2	A5YM72		ENST00000307823.3:c.1861T>C	11.37:g.67191449T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	70	13	0.185714	NM_001166222	A8K1M3|B4DFC6|E9PK38|F5H427|Q8N467|Q9P2F3	Silent	SNP	ENST00000307823.3	37	CCDS44658.1																																																																																			T|0.648;C|0.352	0.352	strong		0.652	CARNS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395501.1	NM_020811	
OBSCN	84033	hgsc.bcm.edu	37	1	228412228	228412228	+	Missense_Mutation	SNP	G	G	A	rs386640006|rs1757153	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228412228G>A	ENST00000422127.1	+	9	2766	c.2722G>A	c.(2722-2724)Gcc>Acc	p.A908T	OBSCN_ENST00000570156.2_Missense_Mutation_p.A1000T|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A908T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	908	Ig-like 9.		A -> T (in dbSNP:rs1757153).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGAGCCAGTGCCACACTGAG	0.617													G|||	1423	0.284145	0.3351	0.3559	5008	,	,		17550	0.1756		0.3618	False		,,,				2504	0.1963				p.A1000T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2998A						PASS	.						42.0	44.0	43.0					1																	228412228		2108	4221	6329	SO:0001583	missense	84033	exon10			GCCAGTGCCACAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2722G>A	1.37:g.228412228G>A	ENSP00000409493:p.Ala908Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	562	0.2573260073260073	124	0.25203252032520324	120	0.3314917127071823	90	0.15734265734265734	228	0.3007915567282322	.	12.46	1.944173	0.34283	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.05996	3.36;3.36	4.42	3.5	0.40072	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.187584	0.32753	N	0.005681	T	0.00012	0.0000	M	0.83384	2.64	0.09310	P	1.0	B;D	0.56968	0.437;0.978	B;P	0.52309	0.326;0.695	T	0.50775	-0.8788	9	0.30078	T	0.28	.	12.898	0.58109	0.0795:0.0:0.9205:0.0	rs1757153;rs1757153	908;908	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	T	908	ENSP00000284548:A908T;ENSP00000409493:A908T	ENSP00000284548:A908T	A	+	1	0	OBSCN	226478851	0.998000	0.40836	0.906000	0.35671	0.036000	0.12997	2.707000	0.47143	1.211000	0.43351	0.655000	0.94253	GCC	G|0.756;A|0.244	0.244	strong		0.617	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
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 GAIIx	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	Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	108	40	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	
ESRP1	54845	hgsc.bcm.edu	37	8	95690579	95690579	+	Silent	SNP	T	T	C	rs12677519	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:95690579T>C	ENST00000433389.2	+	13	1990	c.1800T>C	c.(1798-1800)aaT>aaC	p.N600N	ESRP1_ENST00000358397.5_Silent_p.N596N|ESRP1_ENST00000454170.2_Silent_p.N600N|ESRP1_ENST00000423620.2_Silent_p.N596N	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	600					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						TCTTCATGAATTACACAGCGT	0.502													C|||	2466	0.492412	0.1914	0.5346	5008	,	,		20607	0.5407		0.6223	False		,,,				2504	0.6861				p.N600N		Atlas-SNP	.											.	ESRP1	148	.	0			c.T1800C						PASS	.	C	,,,,	1101,3003		169,763,1120	83.0	79.0	80.0		1788,1800,1788,1788,1800	3.6	1.0	8	dbSNP_120	80	5055,3371		1542,1971,700	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	1711,2734,1820	CC,CT,TT		40.0071,26.8275,49.1301	,,,,	596/678,600/609,596/660,596/605,600/682	95690579	6156,6374	2052	4213	6265	SO:0001819	synonymous_variant	54845	exon13			CATGAATTACACA	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.1800T>C	8.37:g.95690579T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_001122825	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1																																																																																			T|0.494;C|0.506	0.506	strong		0.502	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
JAG1	182	hgsc.bcm.edu	37	20	10653469	10653469	+	Silent	SNP	C	C	T	rs1051415	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:10653469C>T	ENST00000254958.5	-	2	782	c.267G>A	c.(265-267)ggG>ggA	p.G89G	RP11-103J8.1_ENST00000605292.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	89					angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						TGCAGGGCCCCCCGGCCGTGA	0.667									Alagille Syndrome				C|||	327	0.0652955	0.003	0.1196	5008	,	,		13341	0.1091		0.1034	False		,,,				2504	0.0266				p.G89G		Atlas-SNP	.											.	JAG1	213	.	0			c.G267A						PASS	.	C		110,4296	81.4+/-119.9	4,102,2097	46.0	47.0	46.0		267	5.3	1.0	20	dbSNP_86	46	918,7682	195.1+/-240.3	53,812,3435	no	coding-synonymous	JAG1	NM_000214.2		57,914,5532	TT,TC,CC		10.6744,2.4966,7.904		89/1219	10653469	1028,11978	2203	4300	6503	SO:0001819	synonymous_variant	182	exon2	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGGCCCCCCGGCC	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.267G>A	20.37:g.10653469C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			C|0.922;T|0.078	0.078	strong		0.667	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
CHPT1	56994	hgsc.bcm.edu	37	12	102108301	102108301	+	Silent	SNP	T	T	C	rs2066920	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:102108301T>C	ENST00000229266.3	+	3	676	c.441T>C	c.(439-441)gcT>gcC	p.A147A	CHPT1_ENST00000550385.1_3'UTR|CHPT1_ENST00000549872.1_Silent_p.A147A	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	147					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CAGTGGGAGCTTCAATTGCCG	0.333													T|||	516	0.103035	0.0325	0.1614	5008	,	,		15157	0.1687		0.1143	False		,,,				2504	0.0777				p.A147A		Atlas-SNP	.											.	CHPT1	27	.	0			c.T441C						PASS	.	T		228,4178	135.3+/-171.4	8,212,1983	106.0	96.0	100.0		441	-3.0	0.8	12	dbSNP_94	100	1062,7538	223.4+/-260.2	67,928,3305	no	coding-synonymous	CHPT1	NM_020244.2		75,1140,5288	CC,CT,TT		12.3488,5.1748,9.9185		147/407	102108301	1290,11716	2203	4300	6503	SO:0001819	synonymous_variant	56994	exon3			GGGAGCTTCAATT		CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"""phosphatidylcholine synthesizing enzyme"""					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.441T>C	12.37:g.102108301T>C		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	165	85	0.515152	NM_020244	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Silent	SNP	ENST00000229266.3	37	CCDS9086.1																																																																																			C|0.107;T|0.893	0.107	strong		0.333	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1	NM_020244	
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 GAIIx	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	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	38	9	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	
SETX	23064	hgsc.bcm.edu	37	9	135172412	135172412	+	Silent	SNP	A	A	G	rs2296869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135172412A>G	ENST00000224140.5	-	14	5993	c.5811T>C	c.(5809-5811)gaT>gaC	p.D1937D	SETX_ENST00000372169.2_Silent_p.D1937D|SETX_ENST00000393220.1_Silent_p.D1937D	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1937					cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		CTTTCTTTTGATCTTCATTGA	0.348													G|||	2212	0.441693	0.6921	0.2262	5008	,	,		21263	0.6329		0.1382	False		,,,				2504	0.3712				p.D1937D		Atlas-SNP	.											.	SETX	234	.	0			c.T5811C						PASS	.	G		2658,1748	518.6+/-369.8	823,1012,368	134.0	110.0	118.0		5811	-0.0	1.0	9	dbSNP_100	118	1337,7263	755.9+/-407.5	97,1143,3060	no	coding-synonymous	SETX	NM_015046.5		920,2155,3428	GG,GA,AA		15.5465,39.6732,30.7166		1937/2678	135172412	3995,9011	2203	4300	6503	SO:0001819	synonymous_variant	23064	exon14			CTTTTGATCTTCA	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.5811T>C	9.37:g.135172412A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Silent	SNP	ENST00000224140.5	37	CCDS6947.1																																																																																			A|0.628;G|0.372	0.372	strong		0.348	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
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 GAIIx	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	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	115	74	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	
C9orf50	375759	hgsc.bcm.edu	37	9	132375432	132375432	+	Missense_Mutation	SNP	C	C	T	rs2302779	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:132375432C>T	ENST00000372478.4	-	6	1343	c.1142G>A	c.(1141-1143)cGa>cAa	p.R381Q	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	381			R -> Q (in dbSNP:rs2302779).							central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				GAGGCTGCTTCGCGGCCTCTG	0.602													C|||	1064	0.21246	0.1483	0.2637	5008	,	,		18459	0.2937		0.1869	False		,,,				2504	0.2055				p.R381Q		Atlas-SNP	.											.	C9orf50	25	.	0			c.G1142A						PASS	.	C	GLN/ARG	669,3737	274.9+/-272.2	54,561,1588	36.0	37.0	36.0		1142	0.0	0.0	9	dbSNP_100	36	1212,7388	237.2+/-269.1	80,1052,3168	yes	missense	C9orf50	NM_199350.3	43	134,1613,4756	TT,TC,CC		14.093,15.1838,14.4626	probably-damaging	381/432	132375432	1881,11125	2203	4300	6503	SO:0001583	missense	375759	exon6			CTGCTTCGCGGCC	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.1142G>A	9.37:g.132375432C>T	ENSP00000361556:p.Arg381Gln	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	454	0.2078754578754579	71	0.1443089430894309	77	0.212707182320442	160	0.27972027972027974	146	0.19261213720316622	C	15.01	2.706789	0.48412	0.151838	0.14093	ENSG00000179058	ENST00000372478	T	0.23147	1.92	3.59	0.0128	0.14093	.	0.237083	0.21078	N	0.080535	T	0.00012	0.0000	N	0.17082	0.46	0.80722	P	0.0	P	0.42161	0.772	B	0.25506	0.061	T	0.47328	-0.9126	9	0.87932	D	0	-7.4103	6.003	0.19531	0.0:0.5648:0.0:0.4352	rs2302779	381	Q5SZB4	CI050_HUMAN	Q	381	ENSP00000361556:R381Q	ENSP00000361556:R381Q	R	-	2	0	C9orf50	131415253	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.278000	0.02809	-0.001000	0.14495	0.435000	0.28638	CGA	C|0.835;T|0.165	0.165	strong		0.602	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350	
GPBP1L1	60313	hgsc.bcm.edu	37	1	46095272	46095272	+	Silent	SNP	T	T	C	rs1135812	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46095272T>C	ENST00000290795.3	-	11	2469	c.1248A>G	c.(1246-1248)aaA>aaG	p.K416K	GPBP1L1_ENST00000355105.3_Silent_p.K416K|GPBP1L1_ENST00000479235.1_5'UTR			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	416					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					TGTGGAACTCTTTGAGCTCAT	0.463													T|||	1598	0.319089	0.267	0.3473	5008	,	,		17762	0.3165		0.2833	False		,,,				2504	0.409				p.K416K		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.A1248G						PASS	.	T		1115,3291	400.8+/-331.7	145,825,1233	165.0	153.0	157.0		1248	3.9	1.0	1	dbSNP_86	157	2548,6052	414.0+/-351.3	386,1776,2138	no	coding-synonymous	GPBP1L1	NM_021639.4		531,2601,3371	CC,CT,TT		29.6279,25.3064,28.1639		416/475	46095272	3663,9343	2203	4300	6503	SO:0001819	synonymous_variant	60313	exon12			GAACTCTTTGAGC		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.1248A>G	1.37:g.46095272T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	86	34	0.395349	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	37	CCDS528.1																																																																																			T|0.709;C|0.291;A|0.000	0.291	strong		0.463	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
ATXN7	6314	hgsc.bcm.edu	37	3	63967900	63967900	+	Missense_Mutation	SNP	A	A	G	rs1053338	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:63967900A>G	ENST00000295900.6	+	7	1341	c.791A>G	c.(790-792)aAa>aGa	p.K264R	ATXN7_ENST00000488239.1_3'UTR|ATXN7_ENST00000484332.1_Missense_Mutation_p.K119R|ATXN7_ENST00000538065.1_Missense_Mutation_p.K264R|ATXN7_ENST00000487717.1_Missense_Mutation_p.K264R|ATXN7_ENST00000398590.3_Missense_Mutation_p.K264R	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	264			K -> R (in dbSNP:rs1053338). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9425224}.		cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		ATTCATCCGAAAATGGATGGC	0.522													A|||	574	0.114617	0.0121	0.1916	5008	,	,		16999	0.1478		0.1471	False		,,,				2504	0.1309				p.K264R		Atlas-SNP	.											.	ATXN7	126	.	0			c.A791G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	140,3846		3,134,1856	105.0	102.0	103.0		791,356,791	4.6	1.0	3	dbSNP_86	103	1091,7241		67,957,3142	yes	missense,missense,missense	ATXN7	NM_000333.3,NM_001128149.2,NM_001177387.1	26,26,26	70,1091,4998	GG,GA,AA		13.0941,3.5123,9.9935	probably-damaging,probably-damaging,probably-damaging	264/893,119/748,264/946	63967900	1231,11087	1993	4166	6159	SO:0001583	missense	6314	exon7			ATCCGAAAATGGA	AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.791A>G	3.37:g.63967900A>G	ENSP00000295900:p.Lys264Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_000333	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	37	CCDS43102.1	279	0.12774725274725274	5	0.01016260162601626	63	0.17403314917127072	101	0.17657342657342656	110	0.14511873350923482	A	16.90	3.251328	0.59212	0.035123	0.130941	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332	T;T;T;T;T	0.34667	1.35;1.35;1.35;1.35;1.35	5.72	4.57	0.56435	.	0.230389	0.44902	D	0.000408	T	0.00109	0.0003	L	0.39020	1.185	0.21416	P	0.999694523	D;P;P	0.69078	0.997;0.724;0.603	D;B;B	0.75020	0.985;0.183;0.089	T	0.03773	-1.1005	9	0.46703	T	0.11	-8.7245	11.6024	0.51010	0.9304:0.0:0.0696:0.0	rs1053338;rs3193849;rs3765033;rs17421116;rs52791474;rs61726608;rs1053338	119;264;264	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	R	264;264;264;264;119	ENSP00000381590:K264R;ENSP00000295900:K264R;ENSP00000420234:K264R;ENSP00000439585:K264R;ENSP00000428277:K119R	ENSP00000295900:K264R	K	+	2	0	ATXN7	63942940	1.000000	0.71417	1.000000	0.80357	0.764000	0.43329	4.062000	0.57492	1.005000	0.39183	0.459000	0.35465	AAA	A|0.876;G|0.124	0.124	strong		0.522	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333	
DPYSL4	10570	hgsc.bcm.edu	37	10	134013906	134013906	+	Silent	SNP	C	C	T	rs56326856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:134013906C>T	ENST00000338492.4	+	9	1022	c.858C>T	c.(856-858)gaC>gaT	p.D286D	DPYSL4_ENST00000368627.1_Silent_p.D186D|DPYSL4_ENST00000368629.1_Silent_p.D186D	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	286					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.D286D(3)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		TGGGCACCGACGGTTCACACT	0.672													T|||	751	0.14996	0.2708	0.098	5008	,	,		15549	0.001		0.159	False		,,,				2504	0.1677				p.D286D		Atlas-SNP	.											DPYSL4,caecum,carcinoma,+1,8	DPYSL4	91	8	3	Substitution - Missense(3)	central_nervous_system(2)|endometrium(1)	c.C858T						PASS	.	T		1004,3402	727.6+/-409.9	119,766,1318	119.0	107.0	112.0		858	-3.2	0.1	10	dbSNP_129	112	1324,7276	756.8+/-407.5	92,1140,3068	no	coding-synonymous	DPYSL4	NM_006426.2		211,1906,4386	TT,TC,CC		15.3953,22.7871,17.8994		286/573	134013906	2328,10678	2203	4300	6503	SO:0001819	synonymous_variant	10570	exon9			CACCGACGGTTCA	AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.858C>T	10.37:g.134013906C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	ENST00000338492.4	37	CCDS7665.1																																																																																			C|0.833;T|0.167	0.167	strong		0.672	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2		
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 GAIIx	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_ENST00000447133.3_Silent_p.N39N|PARP11_ENST00000427057.2_Silent_p.N39N|PARP11_ENST00000476985.1_5'Flank|PARP11_ENST00000397096.2_Silent_p.N113N	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		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	12	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		
PCSK1N	27344	hgsc.bcm.edu	37	X	48690749	48690749	+	Silent	SNP	C	C	T	rs11538178		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:48690749C>T	ENST00000218230.5	-	2	217	c.117G>A	c.(115-117)gaG>gaA	p.E39E	PCSK1N_ENST00000478242.1_5'UTR	NM_013271.2	NP_037403.1	Q9UHG2	PCSK1_HUMAN	proprotein convertase subtilisin/kexin type 1 inhibitor	39	ProSAAS(1-180). {ECO:0000250}.				neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|response to cold (GO:0009409)|response to dietary excess (GO:0002021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)	endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)										GGCCGCGGGGCTCCTGCGGGA	0.682													c|||	1198	0.317351	0.5234	0.0807	3775	,	,		6872	0.1151		0.0666	False		,,,				2504	0.273				p.E39E		Atlas-SNP	.											.	PCSK1N	6	.	0			c.G117A						PASS	.			1039,1413		118,601,202,343,126	2.0	2.0	2.0		117	0.3	0.9	X	dbSNP_120	2	346,4094		11,224,100,1486,898	yes	coding-synonymous	PCSK1N	NM_013271.2		129,825,302,1829,1024	TT,TC,T,CC,C		7.7928,42.3736,20.0958		39/261	48690749	1385,5507	1390	2719	4109	SO:0001819	synonymous_variant	27344	exon2			GCGGGGCTCCTGC	AF181562	CCDS14307.1	Xp11.23	2008-07-28			ENSG00000102109	ENSG00000102109			17301	protein-coding gene	gene with protein product		300399				10632593	Standard	NM_013271		Approved	SAAS	uc004dkz.4	Q9UHG2	OTTHUMG00000034502	ENST00000218230.5:c.117G>A	X.37:g.48690749C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	13	10	0.769231	NM_013271	Q4VC04	Silent	SNP	ENST00000218230.5	37	CCDS14307.1																																																																																			C|0.763;T|0.237	0.237	strong		0.682	PCSK1N-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083444.1	NM_013271	
KRT32	3882	hgsc.bcm.edu	37	17	39620399	39620399	+	Silent	SNP	C	C	T	rs12948056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39620399C>T	ENST00000225899.3	-	5	1030	c.927G>A	c.(925-927)caG>caA	p.Q309Q		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	309	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				TGATGTCTGACTGGTAGTTCT	0.582													C|||	1523	0.304113	0.2095	0.3818	5008	,	,		21394	0.3145		0.4215	False		,,,				2504	0.2454				p.Q309Q		Atlas-SNP	.											KRT32,rectum,carcinoma,0,1	KRT32	57	1	0			c.G927A						PASS	.	C		935,3471	357.1+/-313.8	98,739,1366	175.0	132.0	147.0		927	4.1	1.0	17	dbSNP_121	147	3179,5421	481.6+/-370.7	611,1957,1732	no	coding-synonymous	KRT32	NM_002278.3		709,2696,3098	TT,TC,CC		36.9651,21.2211,31.6316		309/449	39620399	4114,8892	2203	4300	6503	SO:0001819	synonymous_variant	3882	exon5			GTCTGACTGGTAG	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.927G>A	17.37:g.39620399C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_002278		Silent	SNP	ENST00000225899.3	37	CCDS11393.1																																																																																			C|0.683;N|0.000	.	strong		0.582	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
MAPT	4137	hgsc.bcm.edu	37	17	44061278	44061278	+	Missense_Mutation	SNP	C	C	T	rs17651549	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44061278C>T	ENST00000571987.1	+	5	1108	c.1108C>T	c.(1108-1110)Cgg>Tgg	p.R370W	MAPT_ENST00000334239.8_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.R370W|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.R370W|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.R370W|MAPT_ENST00000574436.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	370			R -> W (in dbSNP:rs17651549).		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GCCCGTCAGCCGGGTCCCTCA	0.647													C|||	429	0.0856629	0.0129	0.1571	5008	,	,		15403	0.001		0.2406	False		,,,				2504	0.0613				p.R370W		Atlas-SNP	.											.	MAPT	135	.	0			c.C1108T						PASS	.	C	TRP/ARG,,,,,,TRP/ARG,	171,3947		5,161,1893	65.0	79.0	75.0		1108,,,,,,1108,	4.5	1.0	17	dbSNP_123	75	1750,6338		186,1378,2480	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	101,,,,,,101,	191,1539,4373	TT,TC,CC		21.637,4.1525,15.7382	probably-damaging,,,,,,probably-damaging,	370/777,,,,,,370/759,	44061278	1921,10285	2059	4044	6103	SO:0001583	missense	4137	exon6			GTCAGCCGGGTCC	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1108C>T	17.37:g.44061278C>T	ENSP00000458742:p.Arg370Trp	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	253	0.11584249084249085	9	0.018292682926829267	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	18.18	3.567727	0.65651	0.041525	0.21637	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.15139	2.54;2.45;2.54	5.51	4.51	0.55191	.	0.000000	0.37857	N	0.001904	T	0.00012	0.0000	L	0.58101	1.795	0.09310	P	0.9999999999999999	D;D	0.71674	0.998;0.998	P;P	0.62491	0.903;0.774	T	0.07616	-1.0763	9	0.66056	D	0.02	-12.7384	12.1085	0.53825	0.0:0.827:0.173:0.0	rs17651549;rs52812169;rs17651549	370;370	P10636-9;P10636	.;TAU_HUMAN	W	370	ENSP00000340820:R370W;ENSP00000262410:R370W;ENSP00000410838:R370W	ENSP00000262410:R370W	R	+	1	2	MAPT	41417115	1.000000	0.71417	1.000000	0.80357	0.552000	0.35366	2.545000	0.45769	1.277000	0.44412	0.511000	0.50034	CGG	C|0.867;T|0.133	0.133	strong		0.647	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
ZC3H3	23144	hgsc.bcm.edu	37	8	144522387	144522387	+	Nonsense_Mutation	SNP	G	G	T	rs2272754	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144522387G>T	ENST00000262577.5	-	11	2670	c.2639C>A	c.(2638-2640)tCa>tAa	p.S880*		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	880	Poly-Ser.				mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			Gggaggggatgaggaggagga	0.652													G|||	560	0.111821	0.0363	0.1167	5008	,	,		17078	0.2431		0.1461	False		,,,				2504	0.0399				p.S880X		Atlas-SNP	.											.	ZC3H3	75	.	0			c.C2639A						PASS	.	G	stop/SER	220,4186		8,204,1991	29.0	28.0	29.0		2639	1.1	0.0	8	dbSNP_100	29	943,7655		116,711,3472	yes	stop-gained	ZC3H3	NM_015117.2		124,915,5463	TT,TG,GG		10.9677,4.9932,8.9434		880/949	144522387	1163,11841	2203	4299	6502	SO:0001587	stop_gained	23144	exon11			GGGGATGAGGAGG	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.2639C>A	8.37:g.144522387G>T	ENSP00000262577:p.Ser880*	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_015117	Q14163|Q8N4E2|Q9BUS4	Nonsense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	273	0.125	25	0.0508130081300813	42	0.11602209944751381	122	0.21328671328671328	84	0.11081794195250659	G	27.7	4.854259	0.91355	0.049932	0.109677	ENSG00000014164	ENST00000262577	.	.	.	4.25	1.07	0.20283	.	2.759650	0.01499	N	0.017425	.	.	.	.	.	.	0.09310	P	0.9999999999699166	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	2.0487	8.7374	0.34537	0.0967:0.5505:0.3527:0.0	rs2272754	.	.	.	X	880	.	ENSP00000262577:S880X	S	-	2	0	ZC3H3	144593530	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.528000	0.06193	-0.133000	0.11537	-0.444000	0.05651	TCA	G|0.879;T|0.121	0.121	strong		0.652	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
FLNC	2318	hgsc.bcm.edu	37	7	128470838	128470838	+	Silent	SNP	C	C	T	rs3734972	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128470838C>T	ENST00000325888.8	+	1	408	c.147C>T	c.(145-147)caC>caT	p.H49H	FLNC_ENST00000346177.6_Silent_p.H49H	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	49	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GCAATGAGCACCTCAAGTGCG	0.637													C|||	551	0.110024	0.0938	0.0908	5008	,	,		13918	0.1964		0.0825	False		,,,				2504	0.0849				p.H49H		Atlas-SNP	.											.	FLNC	339	.	0			c.C147T						PASS	.	C	,	487,3917	223.6+/-240.1	32,423,1747	47.0	47.0	47.0		147,147	1.6	1.0	7	dbSNP_107	47	732,7868	174.3+/-224.6	29,674,3597	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	61,1097,5344	TT,TC,CC		8.5116,11.0581,9.374	,	49/2693,49/2726	128470838	1219,11785	2202	4300	6502	SO:0001819	synonymous_variant	2318	exon1			TGAGCACCTCAAG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.147C>T	7.37:g.128470838C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	253	144	0.56917	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			C|0.885;T|0.115	0.115	strong		0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
OR2L8	391190	hgsc.bcm.edu	37	1	248112554	248112554	+	Missense_Mutation	SNP	T	T	C	rs202165563		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248112554T>C	ENST00000357191.3	+	1	395	c.395T>C	c.(394-396)cTc>cCc	p.L132P	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L132P(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			CTCCACTATCTCATCCGCATG	0.433																																					p.L132P		Atlas-SNP	.											OR2L8,trunk,malignant_melanoma,0,1	OR2L8	92	1	1	Substitution - Missense(1)	skin(1)	c.T395C						scavenged	.						294.0	255.0	269.0					1																	248112554		2203	4300	6503	SO:0001583	missense	391190	exon1			ACTATCTCATCCG	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.395T>C	1.37:g.248112554T>C	ENSP00000349719:p.Leu132Pro	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	178	22	0.123596	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.779851	0.00079	.	.	ENSG00000196936	ENST00000357191	T	0.00648	5.99	1.64	-3.28	0.05033	GPCR, rhodopsin-like superfamily (1);	0.569254	0.13211	N	0.405136	T	0.00210	0.0006	N	0.00554	-1.385	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32402	-0.9908	10	0.02654	T	1	.	2.9738	0.05930	0.1117:0.4051:0.1115:0.3717	.	132	Q8NGY9	OR2L8_HUMAN	P	132	ENSP00000349719:L132P	ENSP00000349719:L132P	L	+	2	0	OR2L8	246179177	0.000000	0.05858	0.002000	0.10522	0.242000	0.25591	-4.646000	0.00204	-2.286000	0.00670	-2.951000	0.00084	CTC	.	.	weak		0.433	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
SACS	26278	hgsc.bcm.edu	37	13	23911820	23911820	+	Silent	SNP	A	A	G	rs4143768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:23911820A>G	ENST00000382292.3	-	9	6468	c.6195T>C	c.(6193-6195)atT>atC	p.I2065I	SACS_ENST00000382298.3_Silent_p.I2065I|SACS_ENST00000402364.1_Silent_p.I1315I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2065					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CAATTTCTTGAATATTTGGAA	0.333													A|||	1302	0.259984	0.056	0.3617	5008	,	,		19205	0.3155		0.2783	False		,,,				2504	0.3875				p.I2065I		Atlas-SNP	.											.	SACS	871	.	0			c.T6195C						PASS	.	A		421,3981		22,377,1802	30.0	32.0	31.0		6195	-2.4	1.0	13	dbSNP_110	31	2223,6367		295,1633,2367	yes	coding-synonymous	SACS	NM_014363.4		317,2010,4169	GG,GA,AA		25.8789,9.5638,20.351		2065/4580	23911820	2644,10348	2201	4295	6496	SO:0001819	synonymous_variant	26278	exon10			TTCTTGAATATTT	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.6195T>C	13.37:g.23911820A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			A|0.760;G|0.240	0.240	strong		0.333	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
CCDC15	80071	hgsc.bcm.edu	37	11	124862514	124862514	+	Silent	SNP	A	A	G	rs6590113	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124862514A>G	ENST00000344762.5	+	10	2329	c.2070A>G	c.(2068-2070)gaA>gaG	p.E690E	CCDC15_ENST00000529051.1_Silent_p.E690E	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	690						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)		GAGTGAGAGAAGAATTGCCTC	0.363													G|||	1437	0.286941	0.4705	0.1801	5008	,	,		9619	0.1935		0.1958	False		,,,				2504	0.3047				p.E690E		Atlas-SNP	.											.	CCDC15	134	.	0			c.A2070G						PASS	.	G		1575,2085		356,863,611	66.0	60.0	62.0		2070	-2.2	0.0	11	dbSNP_116	62	1630,6548		170,1290,2629	no	coding-synonymous	CCDC15	NM_025004.2		526,2153,3240	GG,GA,AA		19.9315,43.0328,27.0738		690/952	124862514	3205,8633	1830	4089	5919	SO:0001819	synonymous_variant	80071	exon10			GAGAGAAGAATTG	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.2070A>G	11.37:g.124862514A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	43	0.826923	NM_025004	Q9H8U7	Silent	SNP	ENST00000344762.5	37	CCDS44756.1																																																																																			A|0.728;G|0.272	0.272	strong		0.363	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
SLC28A3	64078	hgsc.bcm.edu	37	9	86920236	86920236	+	Silent	SNP	T	T	C	rs7867504	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:86920236T>C	ENST00000376238.4	-	4	316	c.267A>G	c.(265-267)acA>acG	p.T89T	SLC28A3_ENST00000495823.1_5'UTR|SLC28A3_ENST00000537648.1_Silent_p.T20T	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	89					pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)			endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	AACCACATACTGTGTCATACC	0.398													C|||	2823	0.563698	0.8427	0.5764	5008	,	,		19630	0.6002		0.3211	False		,,,				2504	0.3896				p.T89T	Ovarian(106;425 1539 34835 42413 43572)	Atlas-SNP	.											SLC28A3,NS,carcinoma,-1,1	SLC28A3	72	1	0			c.A267G						PASS	.	C	,	3186,1220	422.1+/-339.6	1167,852,184	140.0	127.0	131.0		267,267	-7.4	0.0	9	dbSNP_116	131	2619,5981	688.4+/-404.3	391,1837,2072	no	coding-synonymous,coding-synonymous	SLC28A3	NM_001199633.1,NM_022127.2	,	1558,2689,2256	CC,CT,TT		30.4535,27.6895,44.6332	,	89/692,89/692	86920236	5805,7201	2203	4300	6503	SO:0001819	synonymous_variant	64078	exon4			ACATACTGTGTCA	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"""Solute carriers"""	16484	protein-coding gene	gene with protein product		608269	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"""			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.267A>G	9.37:g.86920236T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_001199633	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Silent	SNP	ENST00000376238.4	37	CCDS6670.1																																																																																			C|0.517;N|0.000	0.517	strong		0.398	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127	
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 GAIIx	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_ENST00000522826.1_Missense_Mutation_p.R869C|ENPP2_ENST00000427067.2_Missense_Mutation_p.R865C|ENPP2_ENST00000522167.1_Missense_Mutation_p.R479C|ENPP2_ENST00000259486.6_Missense_Mutation_p.R896C	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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	106	51	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		
ARFGAP3	26286	hgsc.bcm.edu	37	22	43195147	43195147	+	Silent	SNP	A	A	G	rs1128013	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:43195147A>G	ENST00000263245.5	-	15	1650	c.1431T>C	c.(1429-1431)agT>agC	p.S477S	ARFGAP3_ENST00000429508.2_Silent_p.S405S|ARFGAP3_ENST00000437119.2_Silent_p.S433S	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	477					intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						TGGGCAGCACACTGGACAGGC	0.572													G|||	1890	0.377396	0.5053	0.3847	5008	,	,		17264	0.0813		0.4642	False		,,,				2504	0.4151				p.S477S	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.T1431C						PASS	.	G	,	2270,2136	578.4+/-384.7	588,1094,521	130.0	114.0	120.0		1299,1431	0.5	0.3	22	dbSNP_86	120	4152,4448	588.6+/-392.4	1038,2076,1186	no	coding-synonymous,coding-synonymous	ARFGAP3	NM_001142293.1,NM_014570.4	,	1626,3170,1707	GG,GA,AA		48.2791,48.4793,49.3772	,	433/473,477/517	43195147	6422,6584	2203	4300	6503	SO:0001819	synonymous_variant	26286	exon15			CAGCACACTGGAC	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.1431T>C	22.37:g.43195147A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Silent	SNP	ENST00000263245.5	37	CCDS14042.1																																																																																			A|0.557;G|0.443	0.443	strong		0.572	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570	
DNHD1	144132	hgsc.bcm.edu	37	11	6569896	6569896	+	Missense_Mutation	SNP	G	G	A	rs11606889	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6569896G>A	ENST00000527990.2	+	22	7120	c.7120G>A	c.(7120-7122)Gtg>Atg	p.V2374M	DNHD1_ENST00000254579.6_Missense_Mutation_p.V2374M			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2374					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)		CTTGTATGTGGTGGACCTGCT	0.522													G|||	636	0.126997	0.0832	0.1729	5008	,	,		19672	0.0228		0.1829	False		,,,				2504	0.2035				p.V2374M		Atlas-SNP	.											.	DNHD1	198	.	0			c.G7120A						PASS	.	G	MET/VAL	136,1248		8,120,564	59.0	52.0	54.0		7120	4.9	1.0	11	dbSNP_120	54	619,2563		51,517,1023	yes	missense	DNHD1	NM_144666.2	21	59,637,1587	AA,AG,GG		19.4532,9.8266,16.5353	probably-damaging	2374/4754	6569896	755,3811	692	1591	2283	SO:0001583	missense	144132	exon24			TATGTGGTGGACC	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.7120G>A	11.37:g.6569896G>A	ENSP00000436180:p.Val2374Met	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	253	0.11584249084249085	47	0.09552845528455285	50	0.13812154696132597	18	0.03146853146853147	138	0.1820580474934037	G	15.97	2.988476	0.53934	0.098266	0.194532	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.29397	1.57;1.57	5.96	4.95	0.65309	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.39708	P	0.028714000000000017	D	0.63046	0.992	P	0.58077	0.832	T	0.06006	-1.0851	8	0.22706	T	0.39	.	9.6269	0.39757	0.1245:0.0:0.8755:0.0	rs11606889;rs58131910;rs11606889	2374	Q96M86	DNHD1_HUMAN	M	2374	ENSP00000254579:V2374M;ENSP00000436180:V2374M	ENSP00000254579:V2374M	V	+	1	0	DNHD1	6526472	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.820000	0.39032	2.813000	0.96785	0.655000	0.94253	GTG	G|0.887;A|0.113	0.113	strong		0.522	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51857774T>G	ENST00000309244.4	-	2	149				ETFB_ENST00000354232.4_Missense_Mutation_p.E40A|CTD-2616J11.11_ENST00000600067.1_Intron|CTD-2616J11.9_ENST00000600974.1_RNA	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		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	71	42	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		
REST	5978	hgsc.bcm.edu	37	4	57797414	57797414	+	Missense_Mutation	SNP	C	C	T	rs3796529	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57797414C>T	ENST00000309042.7	+	4	2704	c.2390C>T	c.(2389-2391)cCa>cTa	p.P797L		NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	797	Pro-rich.		P -> L (in dbSNP:rs3796529). {ECO:0000269|PubMed:8568247}.		cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|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 transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.P797L(2)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					CAGAGGGAGCCACCTCCTCCC	0.532													C|||	1306	0.260783	0.2738	0.2248	5008	,	,		18741	0.377		0.1849	False		,,,				2504	0.227				p.P797L		Atlas-SNP	.											REST,NS,carcinoma,0,1	REST	104	1	2	Substitution - Missense(2)	prostate(2)	c.C2390T						PASS	.	C	LEU/PRO,LEU/PRO	1121,3285	398.3+/-330.8	125,871,1207	108.0	120.0	116.0		2390,2390	0.4	0.0	4	dbSNP_107	116	1636,6964	302.2+/-305.8	141,1354,2805	yes	missense,missense	REST	NM_001193508.1,NM_005612.4	98,98	266,2225,4012	TT,TC,CC		19.0233,25.4426,21.1979	probably-damaging,probably-damaging	797/1098,797/1098	57797414	2757,10249	2203	4300	6503	SO:0001583	missense	5978	exon4			GGGAGCCACCTCC	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.2390C>T	4.37:g.57797414C>T	ENSP00000311816:p.Pro797Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Missense_Mutation	SNP	ENST00000309042.7	37	CCDS3509.1	544	0.2490842490842491	123	0.25	71	0.19613259668508287	208	0.36363636363636365	142	0.18733509234828497	C	12.13	1.845760	0.32606	0.254426	0.190233	ENSG00000084093	ENST00000309042;ENST00000358605	T	0.06218	3.33	3.08	0.384	0.16244	.	1.097820	0.07026	N	0.827581	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.001	B;B	0.09377	0.004;0.001	T	0.48007	-0.9072	9	0.42905	T	0.14	-0.8172	5.4341	0.16472	0.0:0.6053:0.0:0.3947	rs3796529;rs57306785;rs3796529	774;797	F8WAN5;Q13127	.;REST_HUMAN	L	797;774	ENSP00000311816:P797L	ENSP00000311816:P797L	P	+	2	0	REST	57492171	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.057000	0.03486	0.027000	0.15297	-0.192000	0.12808	CCA	C|0.784;T|0.216	0.216	strong		0.532	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
PEG3	5178	hgsc.bcm.edu	37	19	57327503	57327503	+	Silent	SNP	A	A	G	rs33931963	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57327503A>G	ENST00000326441.9	-	10	2670	c.2307T>C	c.(2305-2307)taT>taC	p.Y769Y	ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Silent_p.Y645Y|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000423103.2_Silent_p.Y769Y|PEG3_ENST00000593695.1_Silent_p.Y643Y	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	769					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)		ATTTTGCCTCATAGACATTTT	0.423													A|||	1006	0.200879	0.1876	0.2075	5008	,	,		20993	0.1062		0.2565	False		,,,				2504	0.2546				p.Y769Y		Atlas-SNP	.											ZIM2_ENST00000326441,NS,carcinoma,-1,2	PEG3	414	2	0			c.T2307C						PASS	.	A	,,,,,,,	985,3421	363.9+/-316.7	103,779,1321	166.0	165.0	165.0		2307,1929,2307,1935,,,2307,	-1.3	0.0	19	dbSNP_126	165	2248,6352	378.4+/-338.9	279,1690,2331	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	PEG3,ZIM2	NM_001146184.1,NM_001146185.1,NM_001146186.1,NM_001146187.1,NM_001146326.1,NM_001146327.1,NM_006210.2,NM_015363.4	,,,,,,,	382,2469,3652	GG,GA,AA		26.1395,22.3559,24.8578	,,,,,,,	769/1589,643/1463,769/1589,645/1465,,,769/1589,	57327503	3233,9773	2203	4300	6503	SO:0001819	synonymous_variant	5178	exon9			TGCCTCATAGACA	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.2307T>C	19.37:g.57327503A>G		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	220	119	0.540909	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	37	CCDS12948.1																																																																																			A|0.767;G|0.233	0.233	strong		0.423	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
NUMA1	4926	hgsc.bcm.edu	37	11	71726785	71726785	+	Silent	SNP	A	A	G	rs17161802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:71726785A>G	ENST00000393695.3	-	15	2095	c.1764T>C	c.(1762-1764)gcT>gcC	p.A588A	NUMA1_ENST00000351960.6_Intron|NUMA1_ENST00000358965.6_Silent_p.A588A|RP11-849H4.4_ENST00000502284.1_RNA	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						GCTCCTCTGCAGCAGTGGCCA	0.597			T	RARA	APL						OREG0021187	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	135	0.0269569	0.0008	0.1556	5008	,	,		21015	0.0248		0.001	False		,,,				2504	0.0				p.A588A		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.T1764C						PASS	.	A		10,4390	16.8+/-37.8	0,10,2190	73.0	73.0	73.0		1764	-1.8	0.0	11	dbSNP_123	73	5,8581	2.2+/-6.3	0,5,4288	no	coding-synonymous	NUMA1	NM_006185.2		0,15,6478	GG,GA,AA		0.0582,0.2273,0.1155		588/2116	71726785	15,12971	2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			CTCTGCAGCAGTG	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.1764T>C	11.37:g.71726785A>G		Somatic	89	0	0	1132	WXS	Illumina HiSeq	Phase_I	86	16	0.186047	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			A|0.992;G|0.008	0.008	strong		0.597	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
ABCG2	9429	hgsc.bcm.edu	37	4	89061114	89061114	+	Missense_Mutation	SNP	C	C	T	rs2231137	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:89061114C>T	ENST00000237612.3	-	2	579	c.34G>A	c.(34-36)Gtg>Atg	p.V12M	ABCG2_ENST00000515655.1_Missense_Mutation_p.V12M	NM_004827.2	NP_004818.2	Q9UNQ0	ABCG2_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 2 (Junior blood group)	12			V -> M (found in Jr(a-) blood group phenotype; dbSNP:rs2231137). {ECO:0000269|PubMed:12111378, ECO:0000269|PubMed:12544509, ECO:0000269|PubMed:16702730, ECO:0000269|PubMed:22246507, ECO:0000269|Ref.11}.		cellular iron ion homeostasis (GO:0006879)|drug export (GO:0046618)|drug transmembrane transport (GO:0006855)|embryonic process involved in female pregnancy (GO:0060136)|heme transport (GO:0015886)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|heme transporter activity (GO:0015232)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(13)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;7.02e-05)	Afatinib(DB08916)|Apixaban(DB06605)|Buprenorphine(DB00921)|Cabazitaxel(DB06772)|Carboplatin(DB00958)|Cisplatin(DB00515)|Cladribine(DB00242)|Clofarabine(DB00631)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Diethylstilbestrol(DB00255)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gefitinib(DB00317)|Glyburide(DB01016)|Hesperetin(DB01094)|Hydrocortisone(DB00741)|Imatinib(DB00619)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Methotrexate(DB00563)|Mitoxantrone(DB01204)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Nilotinib(DB04868)|Nitrofurantoin(DB00698)|Novobiocin(DB01051)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Prazosin(DB00457)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Teniposide(DB00444)|Teriflunomide(DB08880)|Testosterone(DB00624)|Topotecan(DB01030)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vincristine(DB00541)|Vismodegib(DB08828)|Zafirlukast(DB00549)|Zidovudine(DB00495)	CCTTGTGACACTGGGATAAAA	0.408													T|||	789	0.157548	0.0628	0.2378	5008	,	,		19663	0.3264		0.0606	False		,,,				2504	0.1544				p.V12M		Atlas-SNP	.											.	ABCG2	151	.	0			c.G34A	GRCh37	CM045703	ABCG2	M	rs2231137	PASS	.	T	MET/VAL	267,4139	801.2+/-415.6	6,255,1942	62.0	60.0	60.0		34	1.5	0.2	4	dbSNP_98	60	325,8275	804.5+/-407.3	6,313,3981	yes	missense	ABCG2	NM_004827.2	21	12,568,5923	TT,TC,CC		3.7791,6.0599,4.5517	benign	12/656	89061114	592,12414	2203	4300	6503	SO:0001583	missense	9429	exon2			GTGACACTGGGAT	AF103796	CCDS3628.1, CCDS58910.1	4q22.1	2014-08-27	2014-08-27		ENSG00000118777	ENSG00000118777		"""CD molecules"", ""ATP binding cassette transporters / subfamily G"""	74	protein-coding gene	gene with protein product		603756	"""ATP-binding cassette, sub-family G (WHITE), member 2"""			8894702, 9861027	Standard	NM_001257386		Approved	EST157481, MXR, BCRP, ABCP, CD338	uc003hrg.3	Q9UNQ0	OTTHUMG00000130601	ENST00000237612.3:c.34G>A	4.37:g.89061114C>T	ENSP00000237612:p.Val12Met	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	138	57	0.413043	NM_004827	A0A1W3|A8K1T5|O95374|Q4W5I3|Q53ZQ1|Q569L4|Q5YLG4|Q86V64|Q8IX16|Q96LD6|Q96TA8|Q9BY73|Q9NUS0	Missense_Mutation	SNP	ENST00000237612.3	37	CCDS3628.1	306	0.1401098901098901	39	0.07926829268292683	68	0.1878453038674033	152	0.26573426573426573	47	0.06200527704485488	T	0.006	-2.093527	0.00364	0.060599	0.037791	ENSG00000118777	ENST00000515655;ENST00000237612;ENST00000505480;ENST00000503830	D;D;T;T	0.86497	-2.13;-2.02;-0.24;-0.24	5.41	1.54	0.23209	.	0.312505	0.41938	N	0.000797	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.13145	0.007;0.0	B;B	0.12837	0.008;0.001	T	0.04165	-1.0972	9	0.02654	T	1	-0.874	9.7436	0.40433	0.0:0.2315:0.0:0.7685	rs2231137;rs2231137	12;12	Q9UNQ0-2;Q9UNQ0	.;ABCG2_HUMAN	M	12;12;50;30	ENSP00000426917:V12M;ENSP00000237612:V12M;ENSP00000426916:V50M;ENSP00000426934:V30M	ENSP00000237612:V12M	V	-	1	0	ABCG2	89280138	0.218000	0.23608	0.197000	0.23402	0.050000	0.14768	0.230000	0.17852	0.051000	0.15978	-0.988000	0.02552	GTG	C|0.925;T|0.075	0.075	strong		0.408	ABCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253051.1	NM_004827	
FAM24B	196792	hgsc.bcm.edu	37	10	124610027	124610027	+	Missense_Mutation	SNP	G	G	A	rs1891110	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124610027G>A	ENST00000368898.3	-	3	295	c.5C>T	c.(4-6)cCt>cTt	p.P2L	FAM24B_ENST00000462859.1_Intron|CUZD1_ENST00000545804.1_Intron|CUZD1_ENST00000368904.1_5'UTR|FAM24B_ENST00000368896.1_Missense_Mutation_p.P2L	NM_152644.2	NP_689857.2	Q8N5W8	FA24B_HUMAN	family with sequence similarity 24, member B	2			P -> L (in dbSNP:rs1891110). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_neural(114;0.0765)|Lung NSC(174;0.163)|all_lung(145;0.205)		Colorectal(40;0.136)|COAD - Colon adenocarcinoma(40;0.141)		AGCGATGACAGGCATAATCAC	0.502													A|||	2516	0.502396	0.4834	0.4597	5008	,	,		20107	0.4931		0.5785	False		,,,				2504	0.4898				p.P2L		Atlas-SNP	.											.	FAM24B	9	.	0			c.C5T						PASS	.	A	LEU/PRO,LEU/PRO	2292,2114	576.7+/-384.3	610,1072,521	185.0	154.0	164.0		5,5	3.0	0.0	10	dbSNP_92	164	4772,3828	541.1+/-383.9	1323,2126,851	yes	missense,missense	FAM24B	NM_152644.2,NM_001204364.1	98,98	1933,3198,1372	AA,AG,GG		44.5116,47.98,45.6866	benign,benign	2/95,2/95	124610027	7064,5942	2203	4300	6503	SO:0001583	missense	196792	exon3			ATGACAGGCATAA	BC031343	CCDS31303.1	10q26.13	2004-05-27			ENSG00000213185	ENSG00000213185			23475	protein-coding gene	gene with protein product						12477932	Standard	NM_152644		Approved	MGC45962, AC073585.2	uc021qai.1	Q8N5W8	OTTHUMG00000019194	ENST00000368898.3:c.5C>T	10.37:g.124610027G>A	ENSP00000357894:p.Pro2Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001204364	Q5JPG1	Missense_Mutation	SNP	ENST00000368898.3	37	CCDS31303.1	1150	0.5265567765567766	252	0.5121951219512195	162	0.44751381215469616	298	0.5209790209790209	438	0.5778364116094987	A	0.055	-1.238180	0.01493	0.5202	0.554884	ENSG00000213185	ENST00000368898;ENST00000368896	T;T	0.39056	1.1;1.1	3.0	3.0	0.34707	.	0.970919	0.08370	U	0.956308	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	8	0.33940	T	0.23	.	5.0762	0.14632	0.8615:0.0:0.1385:0.0	rs1891110;rs17653026;rs17845954;rs17858936;rs57906451;rs1891110	2	Q8N5W8	FA24B_HUMAN	L	2	ENSP00000357894:P2L;ENSP00000357892:P2L	ENSP00000357892:P2L	P	-	2	0	FAM24B	124600017	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	1.235000	0.32671	0.555000	0.29079	-0.516000	0.04426	CCT	G|0.475;A|0.525	0.525	strong		0.502	FAM24B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050825.1	NM_152644	
ATP10D	57205	hgsc.bcm.edu	37	4	47560002	47560002	+	Missense_Mutation	SNP	C	C	A	rs34208443	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:47560002C>A	ENST00000273859.3	+	12	2415	c.2146C>A	c.(2146-2148)Cca>Aca	p.P716T	AC092597.3_ENST00000508081.1_RNA	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	716			P -> T (in dbSNP:rs34208443).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						CCCTGGACAGCCATTGGCCTG	0.582													C|||	387	0.0772764	0.0272	0.0879	5008	,	,		19067	0.0079		0.1909	False		,,,				2504	0.092				p.P716T		Atlas-SNP	.											ATP10D,NS,carcinoma,-1,1	ATP10D	168	1	0			c.C2146A						PASS	.	C	THR/PRO	225,4181	134.5+/-170.7	4,217,1982	62.0	57.0	59.0		2146	0.4	0.0	4	dbSNP_126	59	1626,6974	301.2+/-305.3	163,1300,2837	yes	missense	ATP10D	NM_020453.3	38	167,1517,4819	AA,AC,CC		18.907,5.1067,14.2319	benign	716/1427	47560002	1851,11155	2203	4300	6503	SO:0001583	missense	57205	exon12			GGACAGCCATTGG	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.2146C>A	4.37:g.47560002C>A	ENSP00000273859:p.Pro716Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	211	0.09661172161172162	14	0.028455284552845527	42	0.11602209944751381	5	0.008741258741258742	150	0.19788918205804748	C	7.444	0.641307	0.14451	0.051067	0.18907	ENSG00000145246	ENST00000273859	T	0.38077	1.16	5.24	0.389	0.16269	HAD-like domain (1);	0.647822	0.16543	N	0.209830	T	0.00012	0.0000	N	0.25647	0.755	0.54753	P	1.6000000000016E-5	B	0.16802	0.019	B	0.16722	0.016	T	0.23583	-1.0184	9	0.10636	T	0.68	-8.4018	0.865	0.01202	0.1493:0.2624:0.2909:0.2974	rs34208443	716	Q9P241	AT10D_HUMAN	T	716	ENSP00000273859:P716T	ENSP00000273859:P716T	P	+	1	0	ATP10D	47254759	0.000000	0.05858	0.020000	0.16555	0.001000	0.01503	-0.414000	0.07114	0.374000	0.24650	-0.305000	0.09177	CCA	C|0.865;A|0.135	0.135	strong		0.582	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
RYR1	6261	hgsc.bcm.edu	37	19	39002725	39002725	+	Silent	SNP	A	A	G	rs2071089	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39002725A>G	ENST00000359596.3	+	62	9186	c.9186A>G	c.(9184-9186)ccA>ccG	p.P3062P	RYR1_ENST00000360985.3_Silent_p.P3062P|RYR1_ENST00000355481.4_Silent_p.P3062P			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3062					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CAGACGCCCCAGCTGTGGTCA	0.647													G|||	2038	0.406949	0.4856	0.366	5008	,	,		15860	0.3532		0.3022	False		,,,				2504	0.4928				p.P3062P		Atlas-SNP	.											.	RYR1	708	.	0			c.A9186G						PASS	.	G	,	1882,2524	629.2+/-395.2	397,1088,718	47.0	48.0	47.0		9186,9186	-8.1	0.1	19	dbSNP_96	47	2161,6439	712.2+/-405.9	294,1573,2433	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	691,2661,3151	GG,GA,AA		25.1279,42.7145,31.0857	,	3062/5039,3062/5034	39002725	4043,8963	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon62			CGCCCCAGCTGTG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.9186A>G	19.37:g.39002725A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	164	65	0.396341	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			A|0.669;G|0.331	0.331	strong		0.647	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
IL11	3589	hgsc.bcm.edu	37	19	55879872	55879872	+	Silent	SNP	C	C	T	rs1126757	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55879872C>T	ENST00000264563.2	-	3	308	c.246G>A	c.(244-246)gcG>gcA	p.A82A	IL11_ENST00000590625.1_Silent_p.A3A|IL11_ENST00000585513.1_Silent_p.A82A	NM_000641.3	NP_000632.1	P20809	IL11_HUMAN	interleukin 11	82					B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|fat cell differentiation (GO:0045444)|megakaryocyte differentiation (GO:0030219)|negative regulation of hormone secretion (GO:0046888)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|interleukin-11 receptor binding (GO:0005142)			large_intestine(1)|skin(1)	2	Breast(117;0.191)	Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		CCAGTGCCCCCGCACTCATGG	0.652													C|||	1975	0.394369	0.0234	0.4452	5008	,	,		12524	0.7093		0.4722	False		,,,				2504	0.455				p.A82A		Atlas-SNP	.											.	IL11	16	.	0			c.G246A						PASS	.	C		420,3986	198.7+/-222.5	21,378,1804	49.0	50.0	49.0	http://www.ncbi.nlm.nih.gov/pubmed?term	246	-7.7	0.0	19	dbSNP_86	49	4037,4563	538.2+/-383.4	954,2129,1217	yes	coding-synonymous	IL11	NM_000641.2		975,2507,3021	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	46.9419,9.5325,34.2688		82/200	55879872	4457,8549	2203	4300	6503	SO:0001819	synonymous_variant	3589	exon3			TGCCCCCGCACTC	X58377	CCDS12923.1, CCDS59423.1	19q13.3-q13.4	2014-01-30			ENSG00000095752	ENSG00000095752		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5966	protein-coding gene	gene with protein product	"""adipogenesis inhibitory factor"", ""oprelvekin"""	147681				1386338	Standard	NM_001267718		Approved	IL-11, AGIF	uc002qks.2	P20809		ENST00000264563.2:c.246G>A	19.37:g.55879872C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_000641	B4DQV5|Q96EB4	Silent	SNP	ENST00000264563.2	37	CCDS12923.1																																																																																			C|0.636;T|0.364	0.364	strong		0.652	IL11-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453027.1	NM_000641	
PON2	5445	hgsc.bcm.edu	37	7	95041016	95041016	+	Missense_Mutation	SNP	G	G	C	rs12026	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:95041016G>C	ENST00000222572.3	-	5	689	c.443C>G	c.(442-444)gCa>gGa	p.A148G	PON2_ENST00000483292.1_5'Flank|PON2_ENST00000433091.2_Missense_Mutation_p.A136G|PON2_ENST00000536183.1_Missense_Mutation_p.A169G			Q15165	PON2_HUMAN	paraoxonase 2	148			A -> G (associated with elevated mean fasting plasma glucose level; dbSNP:rs12026). {ECO:0000269|PubMed:9329371, ECO:0000269|PubMed:9714608, ECO:0000269|Ref.5}.		aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			AGAATTTTCTGCTTCTTCAAA	0.338													G|||	1413	0.282149	0.3283	0.232	5008	,	,		18002	0.1885		0.2485	False		,,,				2504	0.3865				p.A148G	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											PON2,rectum,carcinoma,-1,1	PON2	32	1	0			c.C443G	GRCh37	CM971237	PON2	M	rs12026	PASS	.	G	GLY/ALA,GLY/ALA	1243,3163	424.0+/-340.3	159,925,1119	70.0	72.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	443,407	2.5	1.0	7	dbSNP_52	71	1960,6640	343.5+/-324.9	224,1512,2564	yes	missense,missense	PON2	NM_000305.2,NM_001018161.1	60,60	383,2437,3683	CC,CG,GG		22.7907,28.2115,24.6271	benign,benign	148/355,136/343	95041016	3203,9803	2203	4300	6503	SO:0001583	missense	5445	exon5			TTTTCTGCTTCTT	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"""Paraoxonases"""	9205	protein-coding gene	gene with protein product	"""paraoxonase nirs"", ""arylesterase 2"""	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.443C>G	7.37:g.95041016G>C	ENSP00000222572:p.Ala148Gly	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	135	59	0.437037	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	37	CCDS5640.1	557	0.25503663003663	174	0.35365853658536583	86	0.23756906077348067	104	0.18181818181818182	193	0.2546174142480211	G	7.402	0.633000	0.14322	0.282115	0.227907	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.39229	2.27;1.09;2.27	4.94	2.55	0.30701	Six-bladed beta-propeller, TolB-like (1);	0.296339	0.41500	D	0.000871	T	0.00012	0.0000	N	0.19112	0.55	0.40899	P	0.01587000000000005	B;B	0.14012	0.002;0.009	B;B	0.12156	0.007;0.007	T	0.38394	-0.9663	9	0.02654	T	1	-16.649	8.3986	0.32572	0.1265:0.0:0.1426:0.7308	rs12026;rs1058082;rs3173814;rs11545941;rs17354640;rs17846386;rs17859428;rs17876142;rs61490355;rs12026	148;148	A4D1H7;Q15165	.;PON2_HUMAN	G	169;146;136;148	ENSP00000440282:A169G;ENSP00000404622:A136G;ENSP00000222572:A148G	ENSP00000222572:A148G	A	-	2	0	PON2	94878952	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	5.652000	0.67959	0.452000	0.26830	-1.640000	0.00773	GCA	G|0.746;C|0.253	0.253	strong		0.338	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305	
PRR22	163154	hgsc.bcm.edu	37	19	5783905	5783905	+	Missense_Mutation	SNP	G	G	A	rs3745640	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5783905G>A	ENST00000419421.2	-	3	457	c.353C>T	c.(352-354)cCt>cTt	p.P118L		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	118	Pro-rich.		P -> L (in dbSNP:rs3745640).							endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GTAGGGCTGAGGCTCCAGGAG	0.706													G|||	1540	0.307508	0.3147	0.1859	5008	,	,		10380	0.5437		0.165	False		,,,				2504	0.2873				p.P118L		Atlas-SNP	.											.	PRR22	25	.	0			c.C353T						PASS	.	G	LEU/PRO	990,3048		90,810,1119	4.0	6.0	5.0		353	4.5	0.4	19	dbSNP_107	5	1119,7019		66,987,3016	yes	missense	PRR22	NM_001134316.1	98	156,1797,4135	AA,AG,GG		13.7503,24.5171,17.321	possibly-damaging	118/423	5783905	2109,10067	2019	4069	6088	SO:0001583	missense	163154	exon3			GGCTGAGGCTCCA	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.353C>T	19.37:g.5783905G>A	ENSP00000407653:p.Pro118Leu	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	638	0.29212454212454214	154	0.3130081300813008	75	0.20718232044198895	282	0.493006993006993	127	0.16754617414248021	G	19.20	3.782414	0.70222	0.245171	0.137503	ENSG00000212123	ENST00000419421	T	0.45668	0.89	4.51	4.51	0.55191	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.28455	P	0.9161476	P;D	0.57571	0.944;0.98	P;P	0.51806	0.548;0.68	T	0.48790	-0.9004	8	0.72032	D	0.01	-9.3203	14.7247	0.69336	0.0:0.0:1.0:0.0	rs3745640;rs3745640	118;116	E9PB31;Q8IZ63	.;PRR22_HUMAN	L	118	ENSP00000407653:P118L	ENSP00000407653:P118L	P	-	2	0	PRR22	5734905	0.736000	0.28164	0.388000	0.26195	0.756000	0.42949	5.938000	0.70170	2.338000	0.79540	0.436000	0.28706	CCT	G|0.702;A|0.298	0.298	strong		0.706	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
LONRF3	79836	hgsc.bcm.edu	37	X	118108785	118108785	+	Silent	SNP	T	T	C	rs3813933	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:118108785T>C	ENST00000371628.3	+	1	73	c.42T>C	c.(40-42)gcT>gcC	p.A14A	LONRF3_ENST00000422289.2_5'Flank|LONRF3_ENST00000304778.7_Silent_p.A14A	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	14							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						GCTTGCCCGCTGAGGTCAGCA	0.647													C|||	1898	0.502781	0.2247	0.464	3775	,	,		12076	0.5923		0.327	False		,,,				2504	0.3609				p.A14A		Atlas-SNP	.											.	LONRF3	138	.	0			c.T42C						PASS	.	C	,	1211,2620		174,681,182,777,385	24.0	19.0	20.0		42,42	-1.1	0.5	X	dbSNP_107	20	2862,3854		444,1178,796,804,1068	no	coding-synonymous,coding-synonymous	LONRF3	NM_001031855.1,NM_024778.4	,	618,1859,978,1581,1453	CC,CT,C,TT,T		42.6147,31.6105,38.6176	,	14/760,14/719	118108785	4073,6474	2199	4290	6489	SO:0001819	synonymous_variant	79836	exon1			GCCCGCTGAGGTC	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.42T>C	X.37:g.118108785T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Silent	SNP	ENST00000371628.3	37	CCDS35374.1																																																																																			T|0.560;C|0.440	0.440	strong		0.647	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
CSPG4	1464	hgsc.bcm.edu	37	15	75981976	75981976	+	Missense_Mutation	SNP	C	C	T	rs200493777		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:75981976C>T	ENST00000308508.5	-	3	1522	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	477	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.			RH -> HY (in Ref. 1; CAA65529). {ECO:0000305}.	activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.R477H(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTCGCCATGGCGTGCCCCTCG	0.637																																					p.R477H		Atlas-SNP	.											CSPG4,NS,carcinoma,0,2	CSPG4	175	2	1	Substitution - Missense(1)	kidney(1)	c.G1430A						scavenged	.						67.0	61.0	63.0					15																	75981976		2197	4291	6488	SO:0001583	missense	1464	exon3			CCATGGCGTGCCC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1430G>A	15.37:g.75981976C>T	ENSP00000312506:p.Arg477His	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	156	7	0.0448718	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	9.517	1.107225	0.20714	.	.	ENSG00000173546	ENST00000308508	T	0.19532	2.14	5.12	4.19	0.49359	.	0.096704	0.44483	D	0.000447	T	0.17746	0.0426	L	0.57536	1.79	0.27465	N	0.953023	P	0.35628	0.513	B	0.27380	0.079	T	0.14783	-1.0460	10	0.41790	T	0.15	.	9.3594	0.38186	0.0:0.8315:0.0:0.1685	.	477	Q6UVK1	CSPG4_HUMAN	H	477	ENSP00000312506:R477H	ENSP00000312506:R477H	R	-	2	0	CSPG4	73769031	0.038000	0.19896	0.145000	0.22337	0.035000	0.12851	1.407000	0.34657	2.375000	0.81037	0.555000	0.69702	CGC	C|0.999;T|0.001	0.001	weak		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
CFAP46	54777	hgsc.bcm.edu	37	10	134648279	134648279	+	Splice_Site	SNP	C	C	T	rs12356978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:134648279C>T	ENST00000368586.5	-	48	6845	c.6745G>A	c.(6745-6747)Gaa>Aaa	p.E2249K	TTC40_ENST00000263170.5_Splice_Site_p.E410K	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CCTTCTGGTTCCTACCGCAAT	0.652													C|||	185	0.0369409	0.0015	0.0288	5008	,	,		15303	0.0605		0.0646	False		,,,				2504	0.0378				p.E2249K		Atlas-SNP	.											.	TTC40	100	.	0			c.G6745A						PASS	.	C	LYS/GLU	46,4358	49.6+/-84.7	1,44,2157	28.0	30.0	29.0		1681	-1.6	0.0	10	dbSNP_120	29	592,8008	150.3+/-205.2	17,558,3725	yes	missense-near-splice	C10orf92	NM_001200049.1	56	18,602,5882	TT,TC,CC		6.8837,1.0445,4.9062	benign	561/1028	134648279	638,12366	2202	4300	6502	SO:0001630	splice_region_variant	54777	exon48			CTGGTTCCTACCG																												ENST00000368586.5:c.6745-1G>A	10.37:g.134648279C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	104	0.047619047619047616	2	0.0040650406504065045	8	0.022099447513812154	43	0.07517482517482517	51	0.06728232189973615	C	9.265	1.044267	0.19748	0.010445	0.068837	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.11277	3.02;2.79	3.19	-1.56	0.08532	.	3.081050	0.01876	N	0.037588	T	0.00608	0.0020	L	0.56769	1.78	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.35574	-0.9783	10	0.52906	T	0.07	.	3.4896	0.07633	0.0:0.413:0.2001:0.3869	rs12356978;rs61009165;rs12356978	410	Q8IYW2	CJ092_HUMAN	K	2249;410	ENSP00000357575:E2249K;ENSP00000263170:E410K	ENSP00000263170:E410K	E	-	1	0	C10orf93	134498269	0.005000	0.15991	0.004000	0.12327	0.006000	0.05464	-0.321000	0.08018	-0.091000	0.12440	0.462000	0.41574	GAA	C|0.955;T|0.045	0.045	strong		0.652	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		Missense_Mutation
SGK3	23678	hgsc.bcm.edu	37	8	67748231	67748231	+	Silent	SNP	G	G	A	rs35809374	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:67748231G>A	ENST00000396596.1	+	10	877	c.663G>A	c.(661-663)ccG>ccA	p.P221P	SGK3_ENST00000521198.2_Silent_p.P221P|SGK3_ENST00000522398.1_Silent_p.P221P|C8orf44-SGK3_ENST00000519289.1_Silent_p.P221P|SGK3_ENST00000345714.4_Silent_p.P221P|SGK3_ENST00000520976.1_Silent_p.P221P	NM_013257.4	NP_037389.4	Q96BR1	SGK3_HUMAN	serum/glucocorticoid regulated kinase family, member 3	221	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ion transmembrane transport (GO:0034220)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|phosphatidylinositol binding (GO:0035091)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	18	Breast(64;0.186)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0046)|OV - Ovarian serous cystadenocarcinoma(28;0.0112)|all cancers(69;0.0141)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TGAAACATCCGTTTTTGGTTG	0.333													A|||	771	0.153954	0.3911	0.111	5008	,	,		18341	0.0258		0.0467	False		,,,				2504	0.1063				p.P221P		Atlas-SNP	.											.	SGK3	92	.	0			c.G663A						PASS	.	A	,,,	1417,2987	684.3+/-404.4	233,951,1018	148.0	151.0	150.0		663,663,663,663	-1.0	1.0	8	dbSNP_126	150	326,8274	804.1+/-407.3	6,314,3980	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGK3,C8orf44-SGK3	NM_001033578.2,NM_001204173.1,NM_013257.4,NM_170709.2	,,,	239,1265,4998	AA,AG,GG		3.7907,32.1753,13.4036	,,,	221/497,221/497,221/497,221/465	67748231	1743,11261	2202	4300	6502	SO:0001819	synonymous_variant	23678	exon10			ACATCCGTTTTTG		CCDS6195.1, CCDS6196.1	8q12	2008-07-28	2005-09-13	2005-09-13		ENSG00000104205			10812	protein-coding gene	gene with protein product		607591	"""serum/glucocorticoid regulated kinase-like"""	SGK2, SGKL		10585774, 10548550	Standard	NM_013257		Approved		uc003xwr.3	Q96BR1		ENST00000396596.1:c.663G>A	8.37:g.67748231G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	131	59	0.450382	NM_001033578	A8K5W3|B3KQC2|Q9P1Q7|Q9UKG5	Silent	SNP	ENST00000396596.1	37	CCDS6195.1																																																																																			G|0.875;A|0.125	0.125	strong		0.333	SGK3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379232.3		
RAI1	10743	hgsc.bcm.edu	37	17	17698254	17698254	+	Silent	SNP	G	G	A	rs8067439	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:17698254G>A	ENST00000353383.1	+	3	2461	c.1992G>A	c.(1990-1992)ccG>ccA	p.P664P	RAI1_ENST00000261641.6_Silent_p.P664P	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	664					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CTGGGGAGCCGGAGGCCCTGC	0.662													A|||	2002	0.39976	0.5522	0.4395	5008	,	,		18631	0.1617		0.5875	False		,,,				2504	0.2178				p.P664P		Atlas-SNP	.											.	RAI1	121	.	0			c.G1992A						PASS	.	A		2472,1934	541.7+/-375.8	694,1084,425	43.0	42.0	42.0		1992	-8.3	0.6	17	dbSNP_116	42	5346,3254	484.0+/-371.3	1682,1982,636	no	coding-synonymous	RAI1	NM_030665.3		2376,3066,1061	AA,AG,GG		37.8372,43.8947,39.8893		664/1907	17698254	7818,5188	2203	4300	6503	SO:0001819	synonymous_variant	10743	exon3			GGAGCCGGAGGCC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.1992G>A	17.37:g.17698254G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			G|0.457;A|0.543	0.543	strong		0.662	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
ZFAND6	54469	hgsc.bcm.edu	37	15	80414094	80414094	+	Silent	SNP	A	A	G	rs56296028	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:80414094A>G	ENST00000261749.6	+	4	617	c.195A>G	c.(193-195)caA>caG	p.Q65Q	ZFAND6_ENST00000559835.1_Silent_p.Q65Q|ZFAND6_ENST00000558087.1_Silent_p.Q65Q|ZFAND6_ENST00000559157.1_Silent_p.Q53Q|ZFAND6_ENST00000558494.1_Silent_p.Q65Q|ZFAND6_ENST00000558688.1_Silent_p.Q65Q|ZFAND6_ENST00000561060.1_Silent_p.Q65Q|ZFAND6_ENST00000559775.1_Silent_p.Q65Q	NM_001242913.1|NM_001242914.1|NM_019006.3	NP_001229842.1|NP_001229843.1|NP_061879.2	Q6FIF0	ZFAN6_HUMAN	zinc finger, AN1-type domain 6	65	Ser-rich.				apoptotic process (GO:0006915)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|protein targeting to peroxisome (GO:0006625)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|polyubiquitin binding (GO:0031593)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	11						TACCAGTTCAATGCACAGATG	0.423													a|||	7	0.00139776	0.0008	0.0	5008	,	,		17531	0.0		0.006	False		,,,				2504	0.0				p.Q65Q		Atlas-SNP	.											.	ZFAND6	18	.	0			c.A195G						PASS	.	G	,,,,,,,,,	6,4400	11.4+/-27.6	0,6,2197	126.0	106.0	113.0		195,195,195,195,195,195,159,195,195,195	3.4	1.0	15	dbSNP_129	113	70,8530	42.6+/-100.3	0,70,4230	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFAND6	NM_001242911.1,NM_001242912.1,NM_001242913.1,NM_001242914.1,NM_001242915.1,NM_001242916.1,NM_001242917.1,NM_001242918.1,NM_001242919.1,NM_019006.3	,,,,,,,,,	0,76,6427	GG,GA,AA		0.814,0.1362,0.5843	,,,,,,,,,	65/209,65/209,65/209,65/209,65/209,65/209,53/197,65/171,65/182,65/209	80414094	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	54469	exon5			AGTTCAATGCACA	BC005283	CCDS10313.1, CCDS58395.1	15q24.3	2013-01-09	2006-07-07	2006-07-07	ENSG00000086666	ENSG00000086666		"""Zinc fingers, AN1-type domain containing"""	30164	protein-coding gene	gene with protein product	"""protein associated with PRK1"""	610183	"""zinc finger, A20 domain containing 3"""	ZA20D3		11054541	Standard	NM_019006		Approved	ZFAND5B, AWP1	uc002bff.2	Q6FIF0	OTTHUMG00000144169	ENST00000261749.6:c.195A>G	15.37:g.80414094A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	141	71	0.503546	NM_001242913	D3DW92|D3DW94|O95792|Q9BQF7|Q9GZY3	Silent	SNP	ENST00000261749.6	37	CCDS10313.1																																																																																			A|0.996;G|0.004	0.004	strong		0.423	ZFAND6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291368.1	NM_019006	
SEC24C	9632	hgsc.bcm.edu	37	10	75527708	75527708	+	Silent	SNP	A	A	G	rs4746147	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:75527708A>G	ENST00000339365.2	+	16	2286	c.2124A>G	c.(2122-2124)acA>acG	p.T708T	SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000411652.2_Silent_p.T589T|SEC24C_ENST00000496827.1_Intron|SEC24C_ENST00000345254.4_Silent_p.T708T	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	708					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					ATGTGGCCACACTCTCTGTTG	0.552													G|||	723	0.144369	0.1528	0.1167	5008	,	,		12439	0.1171		0.1332	False		,,,				2504	0.1922				p.T708T		Atlas-SNP	.											SEC24C,NS,carcinoma,0,1	SEC24C	86	1	0			c.A2124G						PASS	.	G	,	653,3753	765.4+/-413.4	55,543,1605	160.0	142.0	148.0		2124,2124	-11.8	0.2	10	dbSNP_111	148	1232,7368	762.1+/-407.6	85,1062,3153	no	coding-synonymous,coding-synonymous	SEC24C	NM_004922.3,NM_198597.2	,	140,1605,4758	GG,GA,AA		14.3256,14.8207,14.4933	,	708/1095,708/1095	75527708	1885,11121	2203	4300	6503	SO:0001819	synonymous_variant	9632	exon15			GGCCACACTCTCT	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.2124A>G	10.37:g.75527708A>G		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	233	124	0.532189	NM_198597	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	37	CCDS7332.1																																																																																			A|0.856;G|0.144	0.144	strong		0.552	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
RHCE	6006	hgsc.bcm.edu	37	1	25717365	25717365	+	Missense_Mutation	SNP	C	C	G	rs609320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:25717365C>G	ENST00000294413.7	-	5	734	c.676G>C	c.(676-678)Gct>Cct	p.A226P	RHCE_ENST00000374352.2_Missense_Mutation_p.A210P|RHCE_ENST00000455194.1_Intron|RHCE_ENST00000349320.3_Missense_Mutation_p.A210P|RHCE_ENST00000425135.1_Missense_Mutation_p.A226P|RHCE_ENST00000243186.6_Missense_Mutation_p.A226P|RHCE_ENST00000346452.4_Intron|RHCE_ENST00000413854.1_Missense_Mutation_p.A226P|RHCE_ENST00000340849.4_Intron|RHCE_ENST00000349438.4_Missense_Mutation_p.A226P	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens	226			P -> A (in E/Rh5 antigen; dbSNP:rs609320). {ECO:0000269|PubMed:11380456, ECO:0000269|PubMed:11902138, ECO:0000269|PubMed:12393640, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16710414, ECO:0000269|Ref.11, ECO:0000269|Ref.12, ECO:0000269|Ref.13, ECO:0000269|Ref.8, ECO:0000269|Ref.9}.			integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			endometrium(8)|large_intestine(6)|lung(3)	17		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		CTCAGCAGAGCAGAGTTGACA	0.542													C|||	720	0.14377	0.0802	0.232	5008	,	,		19967	0.2024		0.16	False		,,,				2504	0.09				p.A226P		Atlas-SNP	.											.	RHCE	36	.	0			c.G676C	GRCh37	CM930646	RHCE	M	rs609320	PASS	.	C	PRO/ALA,,,PRO/ALA	508,3898	233.3+/-246.5	30,448,1725	176.0	157.0	163.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	676,,,676	3.2	0.9	1	dbSNP_83	163	1324,7276	259.4+/-282.6	99,1126,3075	yes	missense,intron,intron,missense	RHCE	NM_020485.4,NM_138616.3,NM_138617.3,NM_138618.3	27,,,27	129,1574,4800	GG,GC,CC		15.3953,11.5297,14.0858	benign,,,benign	226/418,,,226/355	25717365	1832,11174	2203	4300	6503	SO:0001583	missense	6006	exon5			GCAGAGCAGAGTT	BC075081	CCDS30634.1, CCDS30635.1, CCDS30636.1, CCDS30637.1	1p36.11	2014-09-17	2006-02-23		ENSG00000188672	ENSG00000188672		"""CD molecules"", ""Blood group antigens"""	10008	protein-coding gene	gene with protein product		111700	"""Rhesus blood group, CcEe antigens"""	RH		8220426	Standard	NM_138618		Approved	CD240CE	uc001bkf.3	P18577	OTTHUMG00000007650	ENST00000294413.7:c.676G>C	1.37:g.25717365C>G	ENSP00000294413:p.Ala226Pro	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	146	61	0.417808	NM_138618	A7DW68|B7UDF3|B7UDF4|B7UDF5|B7UDF6|B7UDF7|B7UDF8|B7UDF9|B7UDG0|B7UDG1|B7UDG2|B7UDG3|Q02163|Q02164|Q02165|Q16160|Q2MJW0|Q2VC86|Q3LTM6|Q6AZX5|Q6J2U3|Q7RU06|Q8IZT2|Q8IZT3|Q8IZT4|Q8IZT5|Q9UD13|Q9UD14|Q9UD15|Q9UD16|Q9UD73|Q9UD74|Q9UEC2|Q9UEC3|Q9UPN0	Missense_Mutation	SNP	ENST00000294413.7	37	CCDS30635.1	354	0.1620879120879121	38	0.07723577235772358	65	0.17955801104972377	126	0.2202797202797203	125	0.16490765171503957	c	12.85	2.061295	0.36373	0.115297	0.153953	ENSG00000188672	ENST00000413854;ENST00000539650;ENST00000374352;ENST00000243186;ENST00000425135;ENST00000349320;ENST00000294413;ENST00000447203;ENST00000349438	T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62	4.08	3.15	0.36227	.	0.434706	0.24222	N	0.040430	T	0.00012	0.0000	.	.	.	0.30859	P	0.733735	B;B	0.18968	0.032;0.026	B;B	0.32724	0.151;0.01	T	0.14868	-1.0457	8	0.59425	D	0.04	-2.9938	8.181	0.31311	0.0:0.887:0.0:0.113	rs609320;rs1053357;rs3765375;rs7543659;rs9660380;rs52813416;rs609320	210;226	Q5VSJ9;Q5VSJ8	.;.	P	226;168;210;226;226;210;226;226;226	ENSP00000415417:A226P;ENSP00000363472:A210P;ENSP00000243186:A226P;ENSP00000392809:A226P;ENSP00000311185:A210P;ENSP00000294413:A226P;ENSP00000334570:A226P	ENSP00000243186:A226P	A	-	1	0	RHCE	25589952	0.070000	0.21116	0.948000	0.38648	0.569000	0.35902	1.282000	0.33226	1.027000	0.39758	0.591000	0.81541	GCT	C|0.855;G|0.145	0.145	strong		0.542	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	NM_020485	
MED12L	116931	hgsc.bcm.edu	37	3	151090424	151090424	+	Missense_Mutation	SNP	G	G	A	rs3732765	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:151090424G>A	ENST00000474524.1	+	25	3667	c.3629G>A	c.(3628-3630)cGa>cAa	p.R1210Q	P2RY12_ENST00000302632.3_Intron|MED12L_ENST00000273432.4_Missense_Mutation_p.R1070Q	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1210			R -> Q (in dbSNP:rs3732765).			mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.R1210Q(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			AGAGGTTTGCGATGTGATGGG	0.388													G|||	1018	0.203275	0.0287	0.3055	5008	,	,		18878	0.1389		0.3807	False		,,,				2504	0.2505				p.R1210Q		Atlas-SNP	.											MED12L,NS,carcinoma,0,1	MED12L	271	1	1	Substitution - Missense(1)	stomach(1)	c.G3629A						PASS	.	G	,GLN/ARG	361,4045	185.0+/-212.2	15,331,1857	126.0	117.0	120.0		,3629	4.9	0.5	3	dbSNP_107	120	3235,5365	487.5+/-372.1	582,2071,1647	yes	intron,missense	P2RY12,MED12L	NM_022788.3,NM_053002.4	,43	597,2402,3504	AA,AG,GG		37.6163,8.1934,27.6488	,benign	,1210/2146	151090424	3596,9410	2203	4300	6503	SO:0001583	missense	116931	exon25			GTTTGCGATGTGA	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.3629G>A	3.37:g.151090424G>A	ENSP00000417235:p.Arg1210Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	494	0.2261904761904762	16	0.032520325203252036	120	0.3314917127071823	73	0.12762237762237763	285	0.3759894459102902	G	10.71	1.425534	0.25639	0.081934	0.376163	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.60040	0.44;0.22	5.9	4.95	0.65309	.	0.073163	0.56097	D	0.000028	T	0.00012	0.0000	N	0.19112	0.55	0.21762	P	0.999551663	P;B;B	0.44195	0.828;0.431;0.305	B;B;B	0.42959	0.403;0.028;0.068	T	0.36792	-0.9733	9	0.36615	T	0.2	-22.3073	11.0701	0.47997	0.0:0.0:0.7064:0.2936	rs3732765;rs17282989;rs52828592;rs61340099;rs3732765	1070;1209;1210	F8WAE6;Q86YW9-4;Q86YW9	.;.;MD12L_HUMAN	Q	1210;1070	ENSP00000417235:R1210Q;ENSP00000273432:R1070Q	ENSP00000273432:R1070Q	R	+	2	0	MED12L	152573114	0.956000	0.32656	0.518000	0.27811	0.971000	0.66376	3.813000	0.55636	2.788000	0.95919	0.650000	0.86243	CGA	G|0.766;A|0.234	0.234	strong		0.388	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
MUC16	94025	hgsc.bcm.edu	37	19	9060572	9060572	+	Silent	SNP	G	G	A	rs56405542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9060572G>A	ENST00000397910.4	-	3	27077	c.26874C>T	c.(26872-26874)ggC>ggT	p.G8958G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8960	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCTCTGGGAGGCCTGGATAAG	0.468													g|||	1012	0.202077	0.0968	0.2824	5008	,	,		22043	0.3254		0.167	False		,,,				2504	0.1963				p.G8958G		Atlas-SNP	.											.	MUC16	4315	.	0			c.C26874T						PASS	.	G		413,3555		18,377,1589	200.0	186.0	191.0		26874	-3.2	0.0	19	dbSNP_129	191	1521,6807		137,1247,2780	yes	coding-synonymous	MUC16	NM_024690.2		155,1624,4369	AA,AG,GG		18.2637,10.4083,15.7287		8958/14508	9060572	1934,10362	1984	4164	6148	SO:0001819	synonymous_variant	94025	exon3			TGGGAGGCCTGGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.26874C>T	19.37:g.9060572G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	216	97	0.449074	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.788;A|0.212	0.212	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NUP107	57122	hgsc.bcm.edu	37	12	69082805	69082805	+	Silent	SNP	G	G	A	rs2259588	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:69082805G>A	ENST00000229179.4	+	2	404	c.72G>A	c.(70-72)cgG>cgA	p.R24R	NUP107_ENST00000378905.2_5'UTR|NUP107_ENST00000539906.1_5'UTR|RP11-637A17.2_ENST00000500695.2_lincRNA	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	24					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			GGACTGCACGGAAACAGAGTG	0.383													G|||	1105	0.220647	0.0582	0.2983	5008	,	,		18358	0.3065		0.2903	False		,,,				2504	0.2249				p.R24R		Atlas-SNP	.											NUP107,NS,carcinoma,+2,1	NUP107	88	1	0			c.G72A						PASS	.	G		404,4002	200.4+/-223.7	20,364,1819	140.0	132.0	135.0		72	-1.5	0.9	12	dbSNP_100	135	2322,6278	390.4+/-343.3	314,1694,2292	no	coding-synonymous	NUP107	NM_020401.2		334,2058,4111	AA,AG,GG		27.0,9.1693,20.9596		24/926	69082805	2726,10280	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon2			TGCACGGAAACAG	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.72G>A	12.37:g.69082805G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			G|0.777;A|0.223	0.223	strong		0.383	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
PPL	5493	hgsc.bcm.edu	37	16	4934564	4934564	+	Silent	SNP	C	C	G	rs1049207	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4934564C>G	ENST00000345988.2	-	22	4181	c.4092G>C	c.(4090-4092)ctG>ctC	p.L1364L	PPL_ENST00000590782.2_Silent_p.L1362L	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1364					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CCTCGGCCCGCAGGCCTGGCT	0.677													C|||	2107	0.420727	0.1014	0.4697	5008	,	,		15767	0.6478		0.5308	False		,,,				2504	0.4703				p.L1364L		Atlas-SNP	.											.	PPL	168	.	0			c.G4092C						PASS	.	C		688,3706	285.5+/-278.2	56,576,1565	114.0	125.0	121.0		4092	2.4	0.4	16	dbSNP_86	121	4759,3841	607.2+/-395.2	1317,2125,858	no	coding-synonymous	PPL	NM_002705.4		1373,2701,2423	GG,GC,CC		44.6628,15.6577,41.9193		1364/1757	4934564	5447,7547	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			GGCCCGCAGGCCT	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.4092G>C	16.37:g.4934564C>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			C|0.573;G|0.427	0.427	strong		0.677	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
YY1AP1	55249	hgsc.bcm.edu	37	1	155658085	155658085	+	Intron	SNP	T	T	C	rs2666826	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:155658085T>C	ENST00000295566.4	-	2	71				DAP3_ENST00000535183.1_5'Flank|YY1AP1_ENST00000405763.3_Silent_p.E57E|DAP3_ENST00000368336.5_5'Flank|YY1AP1_ENST00000361831.5_Intron|DAP3_ENST00000343043.3_5'Flank|DAP3_ENST00000465375.1_5'Flank|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000476093.1_Intron|YY1AP1_ENST00000404643.1_Intron|YY1AP1_ENST00000347088.5_Intron|YY1AP1_ENST00000311573.5_5'UTR|DAP3_ENST00000471642.2_Intron|YY1AP1_ENST00000355499.4_Intron|YY1AP1_ENST00000368340.5_Silent_p.E57E|YY1AP1_ENST00000407221.1_Intron|YY1AP1_ENST00000359205.5_Intron|YY1AP1_ENST00000438245.2_5'UTR|DAP3_ENST00000421487.2_5'Flank|YY1AP1_ENST00000368339.5_Silent_p.E57E|YY1AP1_ENST00000368330.2_Intron|MSTO1_ENST00000538143.1_Intron	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1						regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					CTGGGATCGTTTCCCCTCGCA	0.637													.|||	2662	0.53155	0.8041	0.3631	5008	,	,		15905	0.6855		0.2972	False		,,,				2504	0.365				p.E57E		Atlas-SNP	.											YY1AP1_ENST00000368339,NS,carcinoma,0,1	YY1AP1	104	1	0			c.A171G						PASS	.																																			SO:0001627	intron_variant	55249	exon1			GATCGTTTCCCCT	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.48-93A>G	1.37:g.155658085T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_001198904	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Silent	SNP	ENST00000295566.4	37	CCDS1115.1																																																																																			T|0.472;C|0.528	0.528	strong		0.637	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118	
RBL2	5934	hgsc.bcm.edu	37	16	53503943	53503943	+	Silent	SNP	C	C	G	rs11540358	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:53503943C>G	ENST00000262133.6	+	15	2228	c.2091C>G	c.(2089-2091)cgC>cgG	p.R697R	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Intron	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	697	Pocket; binds E1A.|Spacer.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CGCCTGGGCGCATGCCCCCAC	0.552													C|||	1274	0.254393	0.3835	0.2406	5008	,	,		17307	0.0496		0.2992	False		,,,				2504	0.2546				p.R697R		Atlas-SNP	.											.	RBL2	115	.	0			c.C2091G						PASS	.	C		1532,2864	483.2+/-359.6	260,1012,926	73.0	70.0	71.0		2091	2.9	1.0	16	dbSNP_120	71	2726,5874	433.9+/-357.6	437,1852,2011	no	coding-synonymous	RBL2	NM_005611.3		697,2864,2937	GG,GC,CC		31.6977,34.8499,32.7639		697/1140	53503943	4258,8738	2198	4300	6498	SO:0001819	synonymous_variant	5934	exon15			TGGGCGCATGCCC	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2091C>G	16.37:g.53503943C>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	37	CCDS10748.1																																																																																			C|0.706;G|0.294	0.294	strong		0.552	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
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 GAIIx	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_ENST00000349097.3_Missense_Mutation_p.H933R|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.H933R|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395477.2_Missense_Mutation_p.H1321R	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	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	95	27	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	
MOV10	4343	hgsc.bcm.edu	37	1	113239382	113239382	+	Silent	SNP	G	G	A	rs17030651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:113239382G>A	ENST00000413052.2	+	14	2502	c.2112G>A	c.(2110-2112)gaG>gaA	p.E704E	MOV10_ENST00000369645.1_Silent_p.E704E|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000357443.2_Silent_p.E704E|MOV10_ENST00000369644.1_Silent_p.E648E|MOV10_ENST00000468624.1_3'UTR	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	704					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		CACTGCTGGAGCGGCTGCTCA	0.607													G|||	1175	0.234625	0.0787	0.281	5008	,	,		18993	0.4425		0.2346	False		,,,				2504	0.1984				p.E704E		Atlas-SNP	.											MOV10,NS,carcinoma,+2,1	MOV10	74	1	0			c.G2112A						PASS	.	G	,	425,3981	193.0+/-218.2	26,373,1804	63.0	49.0	53.0		2112,2112	1.2	1.0	1	dbSNP_123	53	1748,6852	294.4+/-301.9	179,1390,2731	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	205,1763,4535	AA,AG,GG		20.3256,9.6459,16.7077	,	704/1004,704/1004	113239382	2173,10833	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon14			GCTGGAGCGGCTG	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2112G>A	1.37:g.113239382G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			G|0.803;A|0.197	0.197	strong		0.607	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
DDR2	4921	hgsc.bcm.edu	37	1	162737116	162737116	+	Silent	SNP	C	C	G	rs2298258	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:162737116C>G	ENST00000367922.3	+	12	1698	c.1260C>G	c.(1258-1260)ctC>ctG	p.L420L	DDR2_ENST00000367921.3_Silent_p.L420L	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	420					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)	TCATCATCCTCTGGAGGCAGT	0.473													C|||	1745	0.348442	0.5023	0.353	5008	,	,		20143	0.4077		0.1461	False		,,,				2504	0.2843				p.L420L	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											DDR2_ENST00000367922,NS,carcinoma,+2,1	DDR2	228	1	0			c.C1260G						scavenged	.	C	,	2082,2324	572.6+/-383.4	502,1078,623	117.0	107.0	110.0		1260,1260	1.6	1.0	1	dbSNP_100	110	1264,7336	252.6+/-278.6	103,1058,3139	no	coding-synonymous,coding-synonymous	DDR2	NM_001014796.1,NM_006182.2	,	605,2136,3762	GG,GC,CC		14.6977,47.2537,25.7266	,	420/856,420/856	162737116	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	4921	exon12			CATCCTCTGGAGG	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.1260C>G	1.37:g.162737116C>G		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	141	68	0.482269	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1	705	0.3228021978021978	253	0.5142276422764228	113	0.31215469613259667	237	0.4143356643356643	102	0.1345646437994723	C	9.562	1.118647	0.20877	0.472537	0.146977	ENSG00000162733	ENST00000433757	T	0.74315	-0.83	5.79	1.65	0.23941	.	0.000000	0.85682	D	0.000000	T	0.67420	0.2891	.	.	.	0.31024	P	0.717955	.	.	.	.	.	.	T	0.68010	-0.5522	6	0.87932	D	0	.	9.3142	0.37924	0.0:0.5761:0.2821:0.1418	rs2298258;rs2298258	.	.	.	V	13	ENSP00000396864:L13V	ENSP00000396864:L13V	L	+	1	2	DDR2	161003740	0.991000	0.36638	0.998000	0.56505	0.995000	0.86356	0.218000	0.17622	0.034000	0.15491	0.655000	0.94253	CTG	C|0.718;G|0.282	0.282	strong		0.473	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182	
GPR133	283383	hgsc.bcm.edu	37	12	131622735	131622735	+	Silent	SNP	T	T	C	rs7302341	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:131622735T>C	ENST00000261654.5	+	24	3049	c.2490T>C	c.(2488-2490)tcT>tcC	p.S830S	GPR133_ENST00000543617.1_Silent_p.S349S|GPR133_ENST00000376682.4_Silent_p.S516S|GPR133_ENST00000535015.1_Silent_p.S862S|GPR133_ENST00000540207.1_3'UTR	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	830					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(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		CGAGCAGCTCTGCCCGCACCT	0.602													C|||	3325	0.663938	0.3495	0.7378	5008	,	,		16161	0.9306		0.6471	False		,,,				2504	0.7791				p.S830S		Atlas-SNP	.											.	GPR133	136	.	0			c.T2490C						PASS	.	C		1845,2561	634.3+/-396.2	381,1083,739	95.0	75.0	81.0		2490	-1.8	0.0	12	dbSNP_116	81	5396,3204	483.9+/-371.3	1691,2014,595	no	coding-synonymous	GPR133	NM_198827.3		2072,3097,1334	CC,CT,TT		37.2558,41.8747,44.3257		830/875	131622735	7241,5765	2203	4300	6503	SO:0001819	synonymous_variant	283383	exon24			CAGCTCTGCCCGC	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.2490T>C	12.37:g.131622735T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	33	21	0.636364	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Silent	SNP	ENST00000261654.5	37	CCDS9272.1	1458	0.6675824175824175	174	0.35365853658536583	258	0.712707182320442	531	0.9283216783216783	495	0.6530343007915568	C	5.077	0.199830	0.09652	0.418747	0.627442	ENSG00000111452	ENST00000335486	.	.	.	4.46	-1.77	0.07982	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.23232	P	0.9980725	.	.	.	.	.	.	T	0.23119	-1.0197	3	.	.	.	.	10.5216	0.44922	0.0:0.4617:0.0:0.5383	rs7302341;rs7302341	.	.	.	P	184	.	.	L	+	2	0	GPR133	130188688	0.000000	0.05858	0.008000	0.14137	0.015000	0.08874	-3.362000	0.00497	-0.786000	0.04516	-1.050000	0.02344	CTG	T|0.416;C|0.584	0.584	strong		0.602	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
DLGAP2	9228	hgsc.bcm.edu	37	8	1514009	1514009	+	Missense_Mutation	SNP	C	C	A	rs2301963	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:1514009C>A	ENST00000421627.2	+	3	1285	c.1151C>A	c.(1150-1152)cCa>cAa	p.P384Q	RP11-666I19.2_ENST00000518063.1_RNA	NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	463					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)				breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GCAATCCTACCAGAGCCGCTG	0.562													C|||	2307	0.460663	0.3434	0.5749	5008	,	,		16949	0.4484		0.4503	False		,,,				2504	0.5613				p.P384Q		Atlas-SNP	.											.	DLGAP2	292	.	0			c.C1151A						PASS	.	C	GLN/PRO	1604,2696		288,1028,834	35.0	40.0	39.0		1151	4.6	0.0	8	dbSNP_100	39	3828,4728		872,2084,1322	yes	missense	DLGAP2	NM_004745.3	76	1160,3112,2156	AA,AC,CC		44.7405,37.3023,42.2526	possibly-damaging	384/976	1514009	5432,7424	2150	4278	6428	SO:0001583	missense	9228	exon3			TCCTACCAGAGCC	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1151C>A	8.37:g.1514009C>A	ENSP00000400258:p.Pro384Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	66	22	0.333333	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	959|959	0.4391025641025641|0.4391025641025641	172|172	0.34959349593495936|0.34959349593495936	200|200	0.5524861878453039|0.5524861878453039	260|260	0.45454545454545453|0.45454545454545453	327|327	0.4313984168865435|0.4313984168865435	C|C	14.97|14.97	2.695380|2.695380	0.48202|0.48202	0.373023|0.373023	0.447405|0.447405	ENSG00000198010|ENSG00000198010	ENST00000356067;ENST00000421627|ENST00000520901	T|.	0.21932|.	1.98|.	4.55|4.55	4.55|4.55	0.56014|0.56014	.|.	0.333684|.	0.36409|.	N|.	0.002603|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.72479|0.72479	2.2|2.2	0.33270|0.33270	P|P	0.43908899999999995|0.43908899999999995	D;P|.	0.56521|.	0.976;0.918|.	P;B|.	0.50270|.	0.636;0.372|.	T|T	0.49707|0.49707	-0.8911|-0.8911	9|4	0.62326|.	D|.	0.03|.	-2.2526|-2.2526	17.7159|17.7159	0.88336|0.88336	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2301963;rs17748827;rs58660533;rs2301963|rs2301963;rs17748827;rs58660533;rs2301963	463;463|.	Q9P1A6-2;Q9P1A6|.	.;DLGP2_HUMAN|.	Q|K	429;384|401	ENSP00000400258:P384Q|.	ENSP00000348366:P429Q|.	P|Q	+|+	2|1	0|0	DLGAP2|DLGAP2	1501416|1501416	0.559000|0.559000	0.26562|0.26562	0.049000|0.049000	0.19019|0.19019	0.107000|0.107000	0.19398|0.19398	3.412000|3.412000	0.52679|0.52679	2.238000|2.238000	0.73509|0.73509	0.585000|0.585000	0.79938|0.79938	CCA|CAG	C|0.556;A|0.444	0.444	strong		0.562	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
CDH17	1015	hgsc.bcm.edu	37	8	95188850	95188850	+	Missense_Mutation	SNP	T	T	C	rs2243518	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:95188850T>C	ENST00000027335.3	-	5	467	c.343A>G	c.(343-345)Aaa>Gaa	p.K115E	CDH17_ENST00000450165.2_Missense_Mutation_p.K115E|CDH17_ENST00000441892.2_Missense_Mutation_p.K115E	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	115	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		K -> E (in dbSNP:rs2243518). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8153632}.		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TCCTTCACTTTTATGGTGATA	0.498													C|||	4018	0.802316	0.9531	0.7752	5008	,	,		20599	0.6359		0.7753	False		,,,				2504	0.817				p.K115E		Atlas-SNP	.											.	CDH17	119	.	0			c.A343G						PASS	.	C	GLU/LYS,GLU/LYS	4054,352	183.6+/-211.2	1865,324,14	198.0	166.0	177.0		343,343	4.1	1.0	8	dbSNP_100	177	6759,1841	331.1+/-319.5	2661,1437,202	yes	missense,missense	CDH17	NM_001144663.1,NM_004063.3	56,56	4526,1761,216	CC,CT,TT		21.407,7.9891,16.8614	benign,benign	115/833,115/833	95188850	10813,2193	2203	4300	6503	SO:0001583	missense	1015	exon5			TCACTTTTATGGT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.343A>G	8.37:g.95188850T>C	ENSP00000027335:p.Lys115Glu	Somatic	325	1	0.00307692		WXS	Illumina HiSeq	Phase_I	267	259	0.970037	NM_004063	Q15336|Q2M2E0	Missense_Mutation	SNP	ENST00000027335.3	37	CCDS6260.1	1679	0.7687728937728938	466	0.9471544715447154	279	0.7707182320441989	351	0.6136363636363636	583	0.7691292875989446	C	6.612	0.481388	0.12581	0.920109	0.78593	ENSG00000079112	ENST00000027335;ENST00000441892;ENST00000450165;ENST00000521491	T;T;T;T	0.60920	0.15;4.67;0.15;0.7	5.93	4.12	0.48240	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.56097	N	0.000038	T	0.00012	0.0000	N	0.04063	-0.285	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39683	-0.9602	9	0.10636	T	0.68	-21.0879	4.3334	0.11075	0.158:0.5651:0.0:0.277	rs2243518;rs56623970;rs2243518	115;115	E7EN24;Q12864	.;CAD17_HUMAN	E	115	ENSP00000027335:K115E;ENSP00000392811:K115E;ENSP00000401468:K115E;ENSP00000428189:K115E	ENSP00000027335:K115E	K	-	1	0	CDH17	95258026	0.954000	0.32549	1.000000	0.80357	0.952000	0.60782	0.537000	0.23144	1.546000	0.49388	-0.119000	0.15052	AAA	T|0.193;C|0.807	0.807	strong		0.498	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
PEG3	5178	hgsc.bcm.edu	37	19	57328920	57328920	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57328920T>A	ENST00000326441.9	-	10	1253	c.890A>T	c.(889-891)aAa>aTa	p.K297I	ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000598410.1_Missense_Mutation_p.K173I|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.K297I|PEG3_ENST00000593695.1_Missense_Mutation_p.K171I	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	297					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)		GTGGGTTGATTTTTTGGCTTC	0.468																																					p.K297I		Atlas-SNP	.											ZIM2_ENST00000326441,NS,carcinoma,-1,2	PEG3	414	2	0			c.A890T						scavenged	.						46.0	54.0	51.0					19																	57328920		2202	4292	6494	SO:0001583	missense	5178	exon9			GTTGATTTTTTGG	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.890A>T	19.37:g.57328920T>A	ENSP00000326581:p.Lys297Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	127	3	0.023622	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	T	18.78	3.697043	0.68386	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.02944	4.1;4.1	4.27	3.25	0.37280	.	0.131956	0.35124	N	0.003427	T	0.05318	0.0141	L	0.27053	0.805	.	.	.	D;D;D	0.65815	0.995;0.995;0.993	P;P;P	0.59221	0.854;0.854;0.694	T	0.24657	-1.0154	9	0.87932	D	0	-35.4037	8.1788	0.31298	0.0:0.0974:0.0:0.9026	.	173;297;232	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	I	297;297;267	ENSP00000326581:K297I;ENSP00000403051:K297I	ENSP00000292074:K267I	K	-	2	0	ZIM2	62020732	0.019000	0.18553	0.840000	0.33206	0.971000	0.66376	0.219000	0.17641	0.970000	0.38263	0.459000	0.35465	AAA	.	.	none		0.468	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
GPR123	84435	hgsc.bcm.edu	37	10	134942319	134942319	+	Silent	SNP	C	C	T	rs2806453	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:134942319C>T	ENST00000392607.3	+	7	1423	c.987C>T	c.(985-987)ccC>ccT	p.P329P	GPR123_ENST00000392606.2_Silent_p.P232P|GPR123_ENST00000607359.1_Silent_p.P1048P	NM_001083909.1	NP_001077378.1	Q86SQ6	GP123_HUMAN	G protein-coupled receptor 123	329					G-protein coupled receptor signaling pathway (GO:0007186)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(3)	14		all_cancers(35;1.8e-10)|all_epithelial(44;8.95e-09)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Colorectal(31;0.0585)|Melanoma(40;0.123)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;9.16e-06)|Epithelial(32;1.21e-05)|all cancers(32;1.63e-05)		ACGCCCACCCCGCACTTGACG	0.736													C|||	224	0.0447284	0.0015	0.1758	5008	,	,		11377	0.001		0.0706	False		,,,				2504	0.0286				p.P329P		Atlas-SNP	.											.	GPR123	118	.	0			c.C987T						PASS	.	C		42,4234		0,42,2096	16.0	16.0	16.0		987	-1.1	0.0	10	dbSNP_100	16	385,8017		9,367,3825	no	coding-synonymous	GPR123	NM_001083909.1		9,409,5921	TT,TC,CC		4.5822,0.9822,3.368		329/561	134942319	427,12251	2138	4201	6339	SO:0001819	synonymous_variant	84435	exon7			CCACCCCGCACTT	AB058731	CCDS41580.1	10q26	2014-08-08			ENSG00000197177	ENSG00000197177		"""-"", ""GPCR / Class B : Orphans"""	13838	protein-coding gene	gene with protein product		612302				12565841	Standard	XM_005252695		Approved	KIAA1828	uc001llw.3	Q86SQ6	OTTHUMG00000019304	ENST00000392607.3:c.987C>T	10.37:g.134942319C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_001083909	A5HL16|A6NG50|Q5T234|Q86SN7|Q96JJ9	Silent	SNP	ENST00000392607.3	37	CCDS41580.1																																																																																			C|0.959;T|0.041	0.041	strong		0.736	GPR123-003	NOVEL	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051113.2		
LTBP1	4052	hgsc.bcm.edu	37	2	33335818	33335818	+	Splice_Site	SNP	C	C	T	rs17012574	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:33335818C>T	ENST00000404816.2	+	4	1386	c.1033C>T	c.(1033-1035)Ctg>Ttg	p.L345L	LTBP1_ENST00000354476.3_Splice_Site_p.L345L			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	345					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)				ACCTTTTCAGCGTGAGTATAG	0.418													C|||	283	0.0565096	0.084	0.0274	5008	,	,		20669	0.0357		0.0318	False		,,,				2504	0.0869				p.L345L		Atlas-SNP	.											.	LTBP1	317	.	0			c.C1033T						PASS	.	C		317,4089	169.1+/-199.8	14,289,1900	111.0	106.0	108.0		1033	-2.2	1.0	2	dbSNP_123	108	292,8308	108.4+/-169.1	6,280,4014	yes	coding-synonymous-near-splice	LTBP1	NM_206943.2		20,569,5914	TT,TC,CC		3.3953,7.1947,4.6825		345/1722	33335818	609,12397	2203	4300	6503	SO:0001630	splice_region_variant	4052	exon4			TTTCAGCGTGAGT		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.1033+1C>T	2.37:g.33335818C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	181	91	0.502762	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			C|0.952;T|0.048	0.048	strong		0.418	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	Silent
ANKRD26	22852	hgsc.bcm.edu	37	10	27353007	27353007	+	Missense_Mutation	SNP	T	T	C	rs12359281	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27353007T>C	ENST00000376087.4	-	12	1438	c.1273A>G	c.(1273-1275)Atc>Gtc	p.I425V	ANKRD26_ENST00000436985.2_Missense_Mutation_p.I474V	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	425			I -> V (in dbSNP:rs12359281).		glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TTCTCAGAGATACTCTGTTAA	0.299													t|||	336	0.0670927	0.1021	0.0086	5008	,	,		16231	0.122		0.0239	False		,,,				2504	0.0491				p.I425V		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A1273G						PASS	.	T	VAL/ILE	318,3252		15,288,1482	68.0	62.0	64.0		1273	-2.8	0.1	10	dbSNP_120	64	164,7952		1,162,3895	yes	missense	ANKRD26	NM_014915.2	29	16,450,5377	CC,CT,TT		2.0207,8.9076,4.1246	possibly-damaging	425/1711	27353007	482,11204	1785	4058	5843	SO:0001583	missense	22852	exon12			CAGAGATACTCTG	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.1273A>G	10.37:g.27353007T>C	ENSP00000365255:p.Ile425Val	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	32	21	0.65625	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	133	0.060897435897435896	42	0.08536585365853659	5	0.013812154696132596	68	0.11888111888111888	18	0.023746701846965697	T	4.665	0.123575	0.08931	0.089076	0.020207	ENSG00000107890	ENST00000376087;ENST00000436985	T;T	0.31247	1.65;1.5	4.16	-2.81	0.05805	.	.	.	.	.	T	0.00241	0.0007	L	0.59436	1.845	0.52099	P	5.2000000000052005E-5	B;B;B	0.12013	0.002;0.001;0.005	B;B;B	0.09377	0.004;0.002;0.004	T	0.34976	-0.9807	8	0.02654	T	1	.	0.8735	0.01219	0.1656:0.3034:0.1705:0.3605	rs12359281;rs52819728;rs12359281	425;425;474	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	V	425;474	ENSP00000365255:I425V;ENSP00000405112:I474V	ENSP00000365255:I425V	I	-	1	0	ANKRD26	27393013	0.004000	0.15560	0.053000	0.19242	0.252000	0.25951	-0.541000	0.06099	-0.407000	0.07576	0.459000	0.35465	ATC	T|0.945;C|0.055	0.055	strong		0.299	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
GPR87	53836	hgsc.bcm.edu	37	3	151011969	151011969	+	Silent	SNP	G	G	A	rs1048408	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:151011969G>A	ENST00000260843.4	-	3	1529	c.1065C>T	c.(1063-1065)taC>taT	p.Y355Y	MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	355					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACACATCAGTGTAATCATAAT	0.348													A|||	2482	0.495607	0.4561	0.5692	5008	,	,		19851	0.5139		0.4642	False		,,,				2504	0.5102				p.Y355Y		Atlas-SNP	.											.	GPR87	52	.	0			c.C1065T						PASS	.	A	,	1921,2485	625.9+/-394.6	393,1135,675	136.0	137.0	137.0		1065,	-5.0	0.1	3	dbSNP_86	137	4040,4560	595.3+/-393.4	941,2158,1201	no	coding-synonymous,intron	GPR87,MED12L	NM_023915.3,NM_053002.4	,	1334,3293,1876	AA,AG,GG		46.9767,43.5996,45.8327	,	355/359,	151011969	5961,7045	2203	4300	6503	SO:0001819	synonymous_variant	53836	exon3			ATCAGTGTAATCA	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"""GPCR / Class A : Orphans"""	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.1065C>T	3.37:g.151011969G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Silent	SNP	ENST00000260843.4	37	CCDS3157.1																																																																																			G|0.533;A|0.467	0.467	strong		0.348	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		
SNAPC4	6621	hgsc.bcm.edu	37	9	139275204	139275204	+	Silent	SNP	A	A	C	rs3812570	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139275204A>C	ENST00000298532.2	-	19	2855	c.2487T>G	c.(2485-2487)gtT>gtG	p.V829V		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GCAGAAGATGAACTGGTGGGT	0.662													C|||	2064	0.412141	0.3858	0.6066	5008	,	,		17164	0.3214		0.4165	False		,,,				2504	0.3988				p.V829V		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T2487G						PASS	.			1679,2719	634.7+/-396.3	323,1033,843	53.0	46.0	48.0		2487	-4.0	0.0	9	dbSNP_107	48	3805,4789	598.1+/-393.9	845,2115,1337	no	coding-synonymous	SNAPC4	NM_003086.2		1168,3148,2180	CC,CA,AA		44.2751,38.1764,42.2106		829/1470	139275204	5484,7508	2199	4297	6496	SO:0001819	synonymous_variant	6621	exon19			AAGATGAACTGGT	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2487T>G	9.37:g.139275204A>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.591;C|0.409	0.409	strong		0.662	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
DEK	7913	hgsc.bcm.edu	37	6	18264210	18264210	+	Silent	SNP	G	G	A	rs11544757	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:18264210G>A	ENST00000397239.3	-	2	456	c.9C>T	c.(7-9)gcC>gcT	p.A3A	DEK_ENST00000244776.7_Silent_p.A3A	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	3					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			CAGGGGCCGAGGCGGACATGC	0.672			T	NUP214	AML								G|||	824	0.164537	0.031	0.1124	5008	,	,		12151	0.246		0.2087	False		,,,				2504	0.2526				p.A3A		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.C9T						PASS	.	G	,	297,4109	154.0+/-187.5	10,277,1916	25.0	27.0	26.0		9,9	-1.1	0.0	6	dbSNP_120	26	1789,6811	306.2+/-307.8	198,1393,2709	no	coding-synonymous,coding-synonymous	DEK	NM_001134709.1,NM_003472.3	,	208,1670,4625	AA,AG,GG		20.8023,6.7408,16.0388	,	3/342,3/376	18264210	2086,10920	2203	4300	6503	SO:0001819	synonymous_variant	7913	exon2			GGCCGAGGCGGAC	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.9C>T	6.37:g.18264210G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	27	6	0.222222	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																			G|0.838;C|0.000;A|0.162	0.162	strong		0.672	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
TBCK	93627	hgsc.bcm.edu	37	4	107133919	107133919	+	Silent	SNP	A	A	G	rs17036613	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:107133919A>G	ENST00000273980.5	-	21	2295	c.1848T>C	c.(1846-1848)ggT>ggC	p.G616G	TBCK_ENST00000394708.2_Silent_p.G616G|TBCK_ENST00000361687.4_Silent_p.G553G|TBCK_ENST00000432496.2_Silent_p.G616G|TBCK_ENST00000514689.1_5'UTR|TBCK_ENST00000394706.3_Silent_p.G577G					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						CTGGAATGAAACCAATCTCAT	0.323													G|||	1067	0.213059	0.2829	0.134	5008	,	,		17461	0.1468		0.1799	False		,,,				2504	0.2771				p.G616G		Atlas-SNP	.											TBCK,NS,carcinoma,0,2	TBCK	89	2	0			c.T1848C						scavenged	.	G	,,,	1198,3208	708.8+/-407.7	164,870,1169	147.0	151.0	150.0		1848,1848,1731,1659	2.2	1.0	4	dbSNP_123	150	1492,7104	747.9+/-407.3	141,1210,2947	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TBCK	NM_001163435.1,NM_001163436.1,NM_001163437.1,NM_033115.3	,,,	305,2080,4116	GG,GA,AA		17.3569,27.1902,20.6891	,,,	616/894,616/894,577/855,553/831	107133919	2690,10312	2203	4298	6501	SO:0001819	synonymous_variant	93627	exon20			AATGAAACCAATC		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1848T>C	4.37:g.107133919A>G		Somatic	302	2	0.00662252		WXS	Illumina HiSeq	Phase_I	255	130	0.509804	NM_001163436		Silent	SNP	ENST00000273980.5	37	CCDS54788.1																																																																																			A|0.802;G|0.198	0.198	strong		0.323	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
GPER1	2852	hgsc.bcm.edu	37	7	1132153	1132153	+	Silent	SNP	G	G	A	rs3808352	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:1132153G>A	ENST00000297469.3	+	2	1480	c.789G>A	c.(787-789)gcG>gcA	p.A263A	GPER1_ENST00000397088.3_Silent_p.A263A|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|GPER1_ENST00000397092.1_Silent_p.A263A|C7orf50_ENST00000357429.6_Intron|GPER1_ENST00000401670.1_Silent_p.A263A	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	263					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										TGATCCTCGCGGTGGTGCTGG	0.687													G|||	572	0.114217	0.0287	0.1427	5008	,	,		17727	0.1121		0.1759	False		,,,				2504	0.1483				p.A263A		Atlas-SNP	.											.	GPER	25	.	0			c.G789A						PASS	.		,,,,,	211,4195	126.6+/-163.6	10,191,2002	50.0	53.0	52.0		789,789,,,789,	-10.9	0.0	7	dbSNP_107	52	1599,7001	295.8+/-302.6	155,1289,2856	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	,,,,,	165,1480,4858	AA,AG,GG		18.593,4.7889,13.9167	,,,,,	263/376,263/376,,,263/376,	1132153	1810,11196	2203	4300	6503	SO:0001819	synonymous_variant	2852	exon2			CCTCGCGGTGGTG	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"""G protein-coupled receptor 30"""	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.789G>A	7.37:g.1132153G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	27	7	0.259259	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Silent	SNP	ENST00000297469.3	37	CCDS5322.1																																																																																			G|0.875;A|0.125	0.125	strong		0.687	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
ARMC5	79798	hgsc.bcm.edu	37	16	31473275	31473275	+	Missense_Mutation	SNP	A	A	G	rs35923277	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31473275A>G	ENST00000563544.1	+	3	1054	c.508A>G	c.(508-510)Atc>Gtc	p.I170V	ARMC5_ENST00000538189.1_Missense_Mutation_p.I202V|RP11-452L6.5_ENST00000564629.1_RNA|ARMC5_ENST00000268314.4_Missense_Mutation_p.I170V|ARMC5_ENST00000457010.2_Missense_Mutation_p.I170V|ARMC5_ENST00000408912.3_Missense_Mutation_p.I265V|ARMC5_ENST00000412665.2_Missense_Mutation_p.I6V			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	170			I -> V (in dbSNP:rs35923277). {ECO:0000269|PubMed:14702039}.							central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GACAGACAGCATCCAGAACCG	0.537													a|||	117	0.0233626	0.0023	0.0202	5008	,	,		21200	0.0		0.0567	False		,,,				2504	0.044				p.I170V		Atlas-SNP	.											.	ARMC5	94	.	0			c.A508G						PASS	.		VAL/ILE,VAL/ILE	36,4114		0,36,2039	136.0	143.0	141.0		508,508	4.2	1.0	16	dbSNP_126	141	387,8017		12,363,3827	yes	missense,missense	ARMC5	NM_001105247.1,NM_024742.2	29,29	12,399,5866	GG,GA,AA		4.605,0.8675,3.3694	benign,benign	170/936,170/726	31473275	423,12131	2075	4202	6277	SO:0001583	missense	79798	exon2			GACAGCATCCAGA	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.508A>G	16.37:g.31473275A>G	ENSP00000456877:p.Ile170Val	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_024742	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	54	0.024725274725274724	4	0.008130081300813009	5	0.013812154696132596	0	0.0	45	0.059366754617414245	a	15.46	2.838937	0.51057	0.008675	0.04605	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010;ENST00000412665	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.14	4.15	4.15	0.48705	Armadillo-like helical (1);Armadillo-type fold (1);	0.122188	0.53938	D	0.000057	T	0.08044	0.0201	L	0.49455	1.56	0.22292	N	0.999221	B;B;B;B;P	0.40638	0.311;0.311;0.311;0.311;0.725	B;B;B;B;P	0.52343	0.303;0.303;0.303;0.303;0.696	T	0.05131	-1.0904	10	0.11182	T	0.66	-9.2216	11.2092	0.48788	1.0:0.0:0.0:0.0	rs35923277	202;202;265;170;170	B4DH27;F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;.;ARMC5_HUMAN;.	V	265;202;170;170;6	ENSP00000386125:I265V;ENSP00000443995:I202V;ENSP00000268314:I170V;ENSP00000399561:I170V;ENSP00000400183:I6V	ENSP00000268314:I170V	I	+	1	0	ARMC5	31380776	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.176000	0.58269	1.762000	0.52044	0.454000	0.30748	ATC	A|0.964;G|0.036	0.036	strong		0.537	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919891	12919891	+	Nonsense_Mutation	SNP	G	G	T	rs75411676	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12919891G>T	ENST00000240189.2	+	3	718	c.631G>T	c.(631-633)Gaa>Taa	p.E211*		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	211					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)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGGGGAGCTGGAAATTCACAA	0.383																																					p.E211X		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G631T						PASS	.	G	stop/GLU	107,4295	81.9+/-120.4	1,105,2095	96.0	106.0	103.0		631	-0.5	0.0	1	dbSNP_131	103	385,8199	123.4+/-182.3	6,373,3913	yes	stop-gained	PRAMEF2	NM_023014.1		7,478,6008	TT,TG,GG		4.4851,2.4307,3.7887		211/475	12919891	492,12494	2201	4292	6493	SO:0001587	stop_gained	65122	exon3			GAGCTGGAAATTC		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.631G>T	1.37:g.12919891G>T	ENSP00000240189:p.Glu211*	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	131	46	0.351145	NM_023014		Nonsense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	171	0.0782967032967033	4	0.008130081300813009	10	0.027624309392265192	124	0.21678321678321677	33	0.04353562005277045	G	12.65	2.001461	0.35320	0.024307	0.044851	ENSG00000120952	ENST00000240189	.	.	.	0.842	-0.497	0.12023	.	1.227560	0.05797	N	0.611416	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	4.5732	0.12219	0.0:0.4102:0.5898:0.0	.	.	.	.	X	211	.	ENSP00000240189:E211X	E	+	1	0	PRAMEF2	12842478	0.002000	0.14202	0.006000	0.13384	0.017000	0.09413	-0.236000	0.09003	-0.146000	0.11274	0.194000	0.17425	GAA	G|0.952;T|0.048	0.048	strong		0.383	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
LAMA1	284217	hgsc.bcm.edu	37	18	7008591	7008591	+	Missense_Mutation	SNP	T	T	C	rs662471	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:7008591T>C	ENST00000389658.3	-	28	4111	c.4018A>G	c.(4018-4020)Atg>Gtg	p.M1340V		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1340	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.		M -> V (in dbSNP:rs662471). {ECO:0000269|PubMed:1714537}.		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)				CCAACCTCCATTGAAATGTCT	0.428													T|||	937	0.187101	0.2292	0.1945	5008	,	,		18687	0.0099		0.3012	False		,,,				2504	0.1902				p.M1340V		Atlas-SNP	.											.	LAMA1	458	.	0			c.A4018G						PASS	.	T	VAL/MET	1072,3334	387.9+/-326.7	136,800,1267	119.0	111.0	113.0		4018	-7.8	0.0	18	dbSNP_83	113	2578,6022	419.2+/-353.0	368,1842,2090	yes	missense	LAMA1	NM_005559.3	21	504,2642,3357	CC,CT,TT		29.9767,24.3305,28.064	possibly-damaging	1340/3076	7008591	3650,9356	2203	4300	6503	SO:0001583	missense	284217	exon28			CCTCCATTGAAAT	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.4018A>G	18.37:g.7008591T>C	ENSP00000374309:p.Met1340Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	426	0.19505494505494506	109	0.22154471544715448	84	0.23204419889502761	3	0.005244755244755245	230	0.3034300791556728	T	16.41	3.115673	0.56505	0.243305	0.299767	ENSG00000101680	ENST00000389658	T	0.36520	1.25	5.47	-7.83	0.01201	Laminin B type IV (2);Laminin B, subgroup (1);	0.264036	0.40908	N	0.000983	T	0.00012	0.0000	M	0.88450	2.955	0.43160	P	0.005055999999999949	P	0.36354	0.549	B	0.42625	0.393	T	0.04153	-1.0973	9	0.62326	D	0.03	.	5.1126	0.14817	0.094:0.122:0.4681:0.3159	rs662471;rs59106429;rs662471	1340	P25391	LAMA1_HUMAN	V	1340	ENSP00000374309:M1340V	ENSP00000374309:M1340V	M	-	1	0	LAMA1	6998591	0.009000	0.17119	0.006000	0.13384	0.427000	0.31564	-0.035000	0.12205	-0.925000	0.03775	-0.304000	0.09214	ATG	T|0.753;C|0.247	0.247	strong		0.428	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
EBI3	10148	hgsc.bcm.edu	37	19	4236996	4236996	+	Missense_Mutation	SNP	G	G	A	rs4740	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4236996G>A	ENST00000221847.5	+	5	654	c.601G>A	c.(601-603)Gtc>Atc	p.V201I		NM_005755.2	NP_005746.2	Q14213	IL27B_HUMAN	Epstein-Barr virus induced 3	201	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs4740). {ECO:0000269|Ref.2, ECO:0000269|Ref.4}.		cytokine-mediated signaling pathway (GO:0019221)|humoral immune response (GO:0006959)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|T-helper 1 type immune response (GO:0042088)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0336)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGTACTACGTCCAAGTGGC	0.607													g|||	2246	0.448482	0.6233	0.2738	5008	,	,		15690	0.4415		0.3052	False		,,,				2504	0.4908				p.V201I		Atlas-SNP	.											.	EBI3	15	.	0			c.G601A						PASS	.	G	ILE/VAL	2572,1834	633.1+/-396.0	752,1068,383	54.0	54.0	54.0		601	-8.9	0.0	19	dbSNP_52	54	2456,6144	401.9+/-347.3	368,1720,2212	yes	missense	EBI3	NM_005755.2	29	1120,2788,2595	AA,AG,GG		28.5581,41.6251,38.6591	benign	201/230	4236996	5028,7978	2203	4300	6503	SO:0001583	missense	10148	exon5			TACTACGTCCAAG	L08187	CCDS12123.1	19p13	2013-02-11	2008-09-12		ENSG00000105246	ENSG00000105246		"""Fibronectin type III domain containing"""	3129	protein-coding gene	gene with protein product	"""IL27 subunit"", ""IL35 subunit"""	605816				8551575	Standard	NM_005755		Approved		uc002lzu.3	Q14213		ENST00000221847.5:c.601G>A	19.37:g.4236996G>A	ENSP00000221847:p.Val201Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_005755	A0N0N2|O75269	Missense_Mutation	SNP	ENST00000221847.5	37	CCDS12123.1	889	0.40705128205128205	297	0.6036585365853658	100	0.27624309392265195	254	0.44405594405594406	238	0.31398416886543534	G	2.664	-0.279141	0.05642	0.583749	0.285581	ENSG00000105246	ENST00000221847	T	0.59083	0.29	5.41	-8.95	0.00765	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.720518	0.13155	N	0.409544	T	0.00012	0.0000	N	0.10664	0.02	0.80722	P	0.0	B	0.21753	0.06	B	0.18871	0.023	T	0.29822	-0.9999	9	0.20046	T	0.44	-22.3909	20.4741	0.99163	0.1443:0.0:0.8557:0.0	rs4740;rs82395;rs710083;rs3170371;rs3888633;rs17764870;rs57865374;rs4740	201	Q14213	IL27B_HUMAN	I	201	ENSP00000221847:V201I	ENSP00000221847:V201I	V	+	1	0	EBI3	4187996	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.447000	0.02396	-2.080000	0.00870	-1.223000	0.01593	GTC	A|0.399;C|0.003	0.399	strong		0.607	EBI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458005.1		
ASXL3	80816	hgsc.bcm.edu	37	18	31324934	31324934	+	Missense_Mutation	SNP	A	A	G	rs7232237	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:31324934A>G	ENST00000269197.5	+	12	5122	c.5122A>G	c.(5122-5124)Atg>Gtg	p.M1708V		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1708			M -> V (in dbSNP:rs7232237). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:14702039}.		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						AACACAGAACATGAAAGCTTC	0.552													G|||	3401	0.679113	0.7352	0.6816	5008	,	,		18940	0.8988		0.5189	False		,,,				2504	0.5399				p.M1708V		Atlas-SNP	.											.	ASXL3	405	.	0			c.A5122G						PASS	.	G	VAL/MET	3003,1067		1109,785,141	86.0	88.0	87.0		5122	-7.4	0.0	18	dbSNP_116	87	4324,4098		1104,2116,991	yes	missense	ASXL3	NM_030632.1	21	2213,2901,1132	GG,GA,AA		48.6583,26.2162,41.3465	benign	1708/2249	31324934	7327,5165	2035	4211	6246	SO:0001583	missense	80816	exon12			CAGAACATGAAAG	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.5122A>G	18.37:g.31324934A>G	ENSP00000269197:p.Met1708Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	1486	0.6804029304029304	353	0.717479674796748	233	0.643646408839779	517	0.9038461538461539	383	0.5052770448548812	G	0.001	-2.950943	0.00051	0.737838	0.513417	ENSG00000141431	ENST00000269197	T	0.12465	2.68	5.86	-7.36	0.01417	.	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.17319	-1.0373	8	0.12430	T	0.62	.	3.2945	0.06961	0.4653:0.0659:0.231:0.2378	rs7232237;rs17668829;rs57813627;rs7232237	1708	Q9C0F0	ASXL3_HUMAN	V	1708	ENSP00000269197:M1708V	ENSP00000269197:M1708V	M	+	1	0	ASXL3	29578932	0.000000	0.05858	0.000000	0.03702	0.136000	0.21042	-1.434000	0.02425	-1.640000	0.01525	-0.733000	0.03571	ATG	A|0.319;G|0.681	0.681	strong		0.552	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
GCSAML	148823	hgsc.bcm.edu	37	1	247719769	247719769	+	Splice_Site	SNP	G	G	A	rs56043070	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247719769G>A	ENST00000366488.4	+	2	193		c.e2+1		GCSAML_ENST00000536561.1_Intron|GCSAML_ENST00000366489.1_Intron|GCSAML_ENST00000366491.2_Intron|GCSAML_ENST00000527541.1_Intron|GCSAML_ENST00000463359.1_Splice_Site|GCSAML_ENST00000527084.1_Splice_Site	NM_001281836.1|NM_001281837.1|NM_001281853.1|NM_145278.3	NP_001268765.1|NP_001268766.1|NP_001268782.1|NP_660321.1	Q5JQS6	GSAML_HUMAN	germinal center-associated, signaling and motility-like																		AAAGAAAACGGTAAGAACAGA	0.378													G|||	195	0.0389377	0.0318	0.0447	5008	,	,		17829	0.0327		0.0596	False		,,,				2504	0.0297				.		Atlas-SNP	.											.	.	.	.	0			c.89+1G>A						PASS	.	G		160,4246	107.3+/-145.7	3,154,2046	85.0	99.0	94.0			3.0	0.3	1	dbSNP_129	94	603,7997	157.6+/-211.2	18,567,3715	yes	splice-5	C1orf150	NM_145278.3		21,721,5761	AA,AG,GG		7.0116,3.6314,5.8665			247719769	763,12243	2203	4300	6503	SO:0001630	splice_region_variant	148823	exon2			AAAACGGTAAGAA	AK126682	CCDS1635.1, CCDS60470.1, CCDS73058.1	1q44	2012-08-23	2012-08-23	2012-08-23	ENSG00000169224	ENSG00000169224			29583	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 150"""	C1orf150			Standard	NM_001281834		Approved	FLJ44728	uc001idf.3	Q5JQS6	OTTHUMG00000040648	ENST00000366488.4:c.89+1G>A	1.37:g.247719769G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_145278	B2R4Y5|B3KX46|Q5JQT3	Splice_Site	SNP	ENST00000366488.4	37	CCDS1635.1	102	0.046703296703296704	20	0.04065040650406504	16	0.04419889502762431	20	0.03496503496503497	46	0.06068601583113457	G	10.66	1.413798	0.25465	0.036314	0.070116	ENSG00000169224	ENST00000526896;ENST00000366488	.	.	.	3.0	3.0	0.34707	.	.	.	.	.	.	.	.	.	.	.	0.46749	D	0.999181	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.7317	0.40366	0.0:0.0:1.0:0.0	rs56043070	.	.	.	.	-1	.	.	.	+	.	.	C1orf150	245786392	0.961000	0.32948	0.331000	0.25455	0.175000	0.22909	2.220000	0.42908	1.987000	0.57996	0.491000	0.48974	.	G|0.941;A|0.059	0.059	strong		0.378	GCSAML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097745.4	NM_145278	Intron
MUC2	4583	hgsc.bcm.edu	37	11	1080954	1080954	+	Silent	SNP	G	G	A	rs11245929	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1080954G>A	ENST00000441003.2	+	10	1365	c.1338G>A	c.(1336-1338)acG>acA	p.T446T	MUC2_ENST00000359061.5_Silent_p.T446T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	446	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	GCCTGAAGACGGTGGTGCTGC	0.632													G|||	396	0.0790735	0.1233	0.0519	5008	,	,		15776	0.0506		0.0934	False		,,,				2504	0.0532				p.T446T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G1338A						scavenged	.	G		495,3653		33,429,1612	69.0	80.0	76.0		1338	-7.2	0.7	11	dbSNP_120	76	764,7612		35,694,3459	no	coding-synonymous	MUC2	NM_002457.2		68,1123,5071	AA,AG,GG		9.1213,11.9335,10.0527		446/2813	1080954	1259,11265	2074	4188	6262	SO:0001819	synonymous_variant	4583	exon10			GAAGACGGTGGTG	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.1338G>A	11.37:g.1080954G>A		Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	117	56	0.478632	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				G|0.919;A|0.081	0.081	strong		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
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 GAIIx	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	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	59	18	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		
CDCP1	64866	hgsc.bcm.edu	37	3	45153708	45153708	+	Silent	SNP	G	G	A	rs35501071	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:45153708G>A	ENST00000296129.1	-	3	656	c.522C>T	c.(520-522)atC>atT	p.I174I	CDCP1_ENST00000425231.2_Silent_p.I174I|CDCP1_ENST00000490471.1_5'Flank	NM_022842.3	NP_073753.3	Q9H5V8	CDCP1_HUMAN	CUB domain containing protein 1	174						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|skin(4)|urinary_tract(1)	29				BRCA - Breast invasive adenocarcinoma(193;0.00928)|KIRC - Kidney renal clear cell carcinoma(197;0.0519)|Kidney(197;0.0651)		AGAAGGTTCCGATCCTGACCA	0.577													G|||	689	0.13758	0.1301	0.1614	5008	,	,		18945	0.0456		0.1928	False		,,,				2504	0.1687				p.I174I		Atlas-SNP	.											CDCP1,colon,carcinoma,0,1	CDCP1	61	1	0			c.C522T						PASS	.	G	,	475,3931	223.0+/-239.6	30,415,1758	161.0	149.0	153.0		522,522	-2.3	0.6	3	dbSNP_126	153	1520,7080	288.0+/-298.5	112,1296,2892	no	coding-synonymous,coding-synonymous	CDCP1	NM_022842.3,NM_178181.1	,	142,1711,4650	AA,AG,GG		17.6744,10.7808,15.3391	,	174/837,174/344	45153708	1995,11011	2203	4300	6503	SO:0001819	synonymous_variant	64866	exon3			GGTTCCGATCCTG	AF468010	CCDS2727.1, CCDS46812.1	3p21.3	2006-03-28			ENSG00000163814	ENSG00000163814		"""CD molecules"""	24357	protein-coding gene	gene with protein product		611735				11466621	Standard	NM_022842		Approved	CD318, SIMA135	uc003com.3	Q9H5V8	OTTHUMG00000133090	ENST00000296129.1:c.522C>T	3.37:g.45153708G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_178181	Q49UB4|Q6NT71|Q6U9Y2|Q8WU91|Q96QU7|Q9H676|Q9H8C2	Silent	SNP	ENST00000296129.1	37	CCDS2727.1																																																																																			G|0.844;A|0.156	0.156	strong		0.577	CDCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256748.3	NM_022842	
SPAG17	200162	hgsc.bcm.edu	37	1	118583408	118583408	+	Silent	SNP	G	G	A	rs10923477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:118583408G>A	ENST00000336338.5	-	22	3176	c.3111C>T	c.(3109-3111)taC>taT	p.Y1037Y		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1037						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		AAGGATACAGGTAGTAATTTG	0.358													G|||	1445	0.288538	0.1573	0.4135	5008	,	,		19632	0.1567		0.4324	False		,,,				2504	0.365				p.Y1037Y		Atlas-SNP	.											.	SPAG17	263	.	0			c.C3111T						PASS	.	G		894,3512	347.7+/-309.6	87,720,1396	137.0	118.0	125.0		3111	-2.6	0.9	1	dbSNP_120	125	3923,4677	546.5+/-385.0	910,2103,1287	no	coding-synonymous	SPAG17	NM_206996.2		997,2823,2683	AA,AG,GG		45.6163,20.2905,37.0368		1037/2224	118583408	4817,8189	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon22			ATACAGGTAGTAA		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.3111C>T	1.37:g.118583408G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			G|0.677;A|0.323	0.323	strong		0.358	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
RBM19	9904	hgsc.bcm.edu	37	12	114261053	114261053	+	Silent	SNP	G	G	A	rs11066773	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:114261053G>A	ENST00000545145.2	-	24	2937	c.2859C>T	c.(2857-2859)agC>agT	p.S953S	RBM19_ENST00000261741.5_Silent_p.S953S|RBM19_ENST00000392561.3_Silent_p.S953S	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	953					multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					TCTGCTCCTCGCTGTCGCTGT	0.642													G|||	656	0.13099	0.0484	0.1182	5008	,	,		15453	0.1528		0.1024	False		,,,				2504	0.2587				p.S953S		Atlas-SNP	.											.	RBM19	117	.	0			c.C2859T						PASS	.	G	,,	286,4120	157.4+/-190.3	11,264,1928	49.0	43.0	45.0		2859,2859,2859	-4.5	0.0	12	dbSNP_120	45	1129,7471	230.5+/-264.8	90,949,3261	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	101,1213,5189	AA,AG,GG		13.1279,6.4911,10.8796	,,	953/961,953/961,953/961	114261053	1415,11591	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon24			CTCCTCGCTGTCG	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.2859C>T	12.37:g.114261053G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.894;A|0.106	0.106	strong		0.642	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73148481	73148481	+	Missense_Mutation	SNP	G	G	A	rs2973566	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:73148481G>A	ENST00000426542.2	+	13	1774	c.1754G>A	c.(1753-1755)aGa>aAa	p.R585K	ARHGEF28_ENST00000296799.4_Missense_Mutation_p.R272K|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.R585K|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.R585K|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.R585K|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.R585K|ARHGEF28_ENST00000513042.2_Missense_Mutation_p.R585K			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	585			R -> K (in dbSNP:rs2973566).		central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GTAGAGCAAAGAGCTTACAGC	0.378													G|||	821	0.163938	0.0877	0.2464	5008	,	,		21296	0.0754		0.2654	False		,,,				2504	0.1953				p.R585K		Atlas-SNP	.											.	.	.	.	0			c.G1754A						PASS	.	G	LYS/ARG,LYS/ARG	477,3293		35,407,1443	165.0	156.0	159.0		1754,1754	6.2	1.0	5	dbSNP_101	159	2289,5937		330,1629,2154	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	26,26	365,2036,3597	AA,AG,GG		27.8264,12.6525,23.0577	probably-damaging,probably-damaging	585/1732,585/1706	73148481	2766,9230	1885	4113	5998	SO:0001583	missense	64283	exon14			AGCAAAGAGCTTA		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1754G>A	5.37:g.73148481G>A	ENSP00000412175:p.Arg585Lys	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	374	0.17124542124542125	43	0.08739837398373984	88	0.2430939226519337	39	0.06818181818181818	204	0.2691292875989446	G	32	5.116278	0.94339	0.126525	0.278264	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799	T;T;T;T;T;T;T	0.13778	2.77;2.74;2.75;2.56;2.74;2.75;2.57	6.17	6.17	0.99709	.	.	.	.	.	T	0.00012	0.0000	M	0.66939	2.045	0.31753	P	0.634368	D;D;D;D	0.63046	0.986;0.986;0.986;0.992	P;P;P;P	0.60117	0.744;0.744;0.744;0.869	T	0.22277	-1.0221	8	0.41790	T	0.15	.	14.6223	0.68594	0.0696:0.0:0.9304:0.0	rs2973566;rs52806455;rs57829934;rs2973566	272;585;585;585	B5MDA3;Q8N1W1;E9PC75;Q8N1W1-4	.;RGNEF_HUMAN;.;.	K	585;585;585;585;585;585;272	ENSP00000296794:R585K;ENSP00000441913:R585K;ENSP00000441436:R585K;ENSP00000287898:R585K;ENSP00000411459:R585K;ENSP00000412175:R585K;ENSP00000296799:R272K	ENSP00000287898:R585K	R	+	2	0	RP11-428C6.1	73184237	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.093000	0.71422	2.941000	0.99782	0.655000	0.94253	AGA	G|0.830;A|0.170	0.170	strong		0.378	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
SMOX	54498	hgsc.bcm.edu	37	20	4158164	4158164	+	Silent	SNP	C	C	A	rs11552911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:4158164C>A	ENST00000305958.4	+	3	600	c.375C>A	c.(373-375)acC>acA	p.T125T	SMOX_ENST00000484515.1_3'UTR|SMOX_ENST00000379460.2_Silent_p.T125T|SMOX_ENST00000339123.6_Silent_p.T125T|SMOX_ENST00000278795.3_Silent_p.T125T|SMOX_ENST00000346595.2_Silent_p.T125T	NM_175839.2	NP_787033.1	Q9NWM0	SMOX_HUMAN	spermine oxidase	125					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|small molecule metabolic process (GO:0044281)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	N1-acetylspermine:oxygen oxidoreductase (N1-acetylspermidine-forming) activity (GO:0052895)|norspermine:oxygen oxidoreductase activity (GO:0052894)|polyamine oxidase activity (GO:0046592)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			breast(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(7)|lung(5)|skin(2)|urinary_tract(1)	26					Spermine(DB00127)	GCTACCTTACCAACCACGGCC	0.577													C|||	240	0.0479233	0.0045	0.0288	5008	,	,		17218	0.0268		0.0775	False		,,,				2504	0.1115				p.T125T		Atlas-SNP	.											.	SMOX	119	.	0			c.C375A						PASS	.	C	,,,	57,4349		0,57,2146	57.0	48.0	51.0		375,375,375,375	5.3	1.0	20	dbSNP_120	51	642,7956		17,608,3674	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SMOX	NM_175839.1,NM_175840.1,NM_175841.1,NM_175842.1	,,,	17,665,5820	AA,AC,CC		7.4669,1.2937,5.3753	,,,	125/556,125/503,125/191,125/533	4158164	699,12305	2203	4299	6502	SO:0001819	synonymous_variant	54498	exon3			CCTTACCAACCAC	AK000753	CCDS13075.1, CCDS13076.1, CCDS13077.1, CCDS13078.1, CCDS74702.1	20p13	2003-10-15	2003-10-15	2003-10-15	ENSG00000088826	ENSG00000088826			15862	protein-coding gene	gene with protein product		615854	"""chromosome 20 open reading frame 16"""	C20orf16		11454677, 12398765	Standard	NM_175839		Approved	FLJ20746, dJ779E11.1, PAO, PAOh1, MGC1010, SMO	uc002wkp.3	Q9NWM0	OTTHUMG00000031777	ENST00000305958.4:c.375C>A	20.37:g.4158164C>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_175839	A2A2P5|A2A2P6|A8BE87|D3DVZ4|Q5TE26|Q5TE27|Q6UY28|Q8IX00|Q96LC3|Q96LC4|Q96QT3|Q9BW38|Q9H6H1|Q9NP51|Q9NPY1|Q9NPY2	Silent	SNP	ENST00000305958.4	37	CCDS13075.1																																																																																			C|0.950;A|0.050	0.050	strong		0.577	SMOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077806.1	NM_175842	
CHRNE	1145	hgsc.bcm.edu	37	17	4802329	4802329	+	Silent	SNP	G	G	A	rs33978919	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4802329G>A	ENST00000293780.4	-	11	1303	c.1293C>T	c.(1291-1293)gcC>gcT	p.A431A	CHRNE_ENST00000575637.1_5'Flank|C17orf107_ENST00000521575.1_5'Flank|C17orf107_ENST00000381365.3_5'Flank	NM_000080.3	NP_000071.1	Q04844	ACHE_HUMAN	cholinergic receptor, nicotinic, epsilon (muscle)	431			A -> P (in FCCMS; causes an increase in distributions of rates for channel opening and closing increasing the range of activation kinetics). {ECO:0000269|PubMed:10962020}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12					Galantamine(DB00674)	TCGTGCTCTCGGCCACGAAGT	0.706													g|||	958	0.191294	0.3298	0.2176	5008	,	,		14907	0.0655		0.1461	False		,,,				2504	0.1616				p.A431A		Atlas-SNP	.											.	CHRNE	25	.	0			c.C1293T						PASS	.	G		1231,3173		154,923,1125	14.0	15.0	15.0		1293	-10.9	0.2	17	dbSNP_126	15	1203,7387		98,1007,3190	no	coding-synonymous	CHRNE	NM_000080.3		252,1930,4315	AA,AG,GG		14.0047,27.9519,18.7317		431/494	4802329	2434,10560	2202	4295	6497	SO:0001819	synonymous_variant	1145	exon11			GCTCTCGGCCACG	X66403	CCDS11058.1	17p13.2	2012-02-11	2012-02-07		ENSG00000108556	ENSG00000108556		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1966	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, epsilon (muscle)"""	100725	"""cholinergic receptor, nicotinic, epsilon"""			7688301	Standard	NM_000080		Approved	ACHRE	uc002fzk.1	Q04844	OTTHUMG00000090778	ENST00000293780.4:c.1293C>T	17.37:g.4802329G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	41	0.672131	NM_000080	D3DTK6	Silent	SNP	ENST00000293780.4	37	CCDS11058.1																																																																																			G|0.820;A|0.180	0.180	strong		0.706	CHRNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207560.3		
SFI1	9814	hgsc.bcm.edu	37	22	32014161	32014161	+	Silent	SNP	G	G	A	rs55735011	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:32014161G>A	ENST00000400288.2	+	32	3678	c.3573G>A	c.(3571-3573)ccG>ccA	p.P1191P	SFI1_ENST00000474741.1_Intron|PISD_ENST00000478893.1_5'Flank|SFI1_ENST00000443326.1_Silent_p.P1109P|SFI1_ENST00000540643.1_Silent_p.P1136P|SFI1_ENST00000414585.1_3'UTR|SFI1_ENST00000432498.1_Silent_p.P1160P|SFI1_ENST00000400289.1_Silent_p.P1109P|SFI1_ENST00000443011.1_Silent_p.P1038P	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	1191					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GAGAGGAGCCGGGGCCTGAGG	0.677													G|||	273	0.0545128	0.0915	0.0216	5008	,	,		17595	0.0069		0.0368	False		,,,				2504	0.0951				p.P1191P		Atlas-SNP	.											SFI1,NS,carcinoma,0,1	SFI1	78	1	0			c.G3573A						scavenged	.	G	,	231,3733		7,217,1758	23.0	29.0	27.0		3573,3480	-4.4	0.0	22	dbSNP_129	27	232,8116		3,226,3945	no	coding-synonymous,coding-synonymous	SFI1	NM_001007467.1,NM_014775.2	,	10,443,5703	AA,AG,GG		2.7791,5.8274,3.7606	,	1191/1243,1160/1212	32014161	463,11849	1982	4174	6156	SO:0001819	synonymous_variant	9814	exon32			GGAGCCGGGGCCT	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.3573G>A	22.37:g.32014161G>A		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	147	86	0.585034	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Silent	SNP	ENST00000400288.2	37	CCDS43004.1																																																																																			G|0.959;A|0.041	0.041	strong		0.677	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161019040	161019040	+	Missense_Mutation	SNP	G	G	C	rs3813609	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161019040G>C	ENST00000368013.3	-	12	2091	c.1771C>G	c.(1771-1773)Ctg>Gtg	p.L591V	ARHGAP30_ENST00000368015.1_Missense_Mutation_p.L414V|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.L591V	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	591			L -> V (in dbSNP:rs3813609). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GCGGAGTCCAGGGAACAGCAG	0.567													G|||	1983	0.395966	0.1815	0.4654	5008	,	,		21362	0.3333		0.6292	False		,,,				2504	0.4611				p.L591V		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.C1771G						PASS	.	G	VAL/LEU,VAL/LEU	1158,3248	410.6+/-335.4	145,868,1190	94.0	101.0	99.0		1771,1771	1.1	0.5	1	dbSNP_107	99	5222,3378	640.6+/-399.6	1560,2102,638	yes	missense,missense	ARHGAP30	NM_001025598.1,NM_181720.2	32,32	1705,2970,1828	CC,CG,GG		39.2791,26.2823,49.0543	benign,benign	591/1102,591/891	161019040	6380,6626	2203	4300	6503	SO:0001583	missense	257106	exon12			AGTCCAGGGAACA	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1771C>G	1.37:g.161019040G>C	ENSP00000356992:p.Leu591Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	81	32	0.395062	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	CCDS30918.1	939	0.42994505494505497	101	0.20528455284552846	173	0.47790055248618785	191	0.3339160839160839	474	0.6253298153034301	G	9.123	1.009373	0.19277	0.262823	0.607209	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.35421	2.92;2.84;1.31	5.18	1.1	0.20463	.	1.038190	0.07683	N	0.937368	T	0.10594	0.0259	L	0.59436	1.845	0.58432	P	1.999999999946489E-6	B;P	0.41848	0.361;0.763	B;B	0.39027	0.081;0.288	T	0.18935	-1.0321	9	0.10902	T	0.67	.	1.7083	0.02887	0.2435:0.1391:0.4746:0.1429	rs3813609;rs52800561;rs3813609	591;591	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	V	591;591;443;414	ENSP00000356995:L591V;ENSP00000356992:L591V;ENSP00000356994:L414V	ENSP00000356992:L591V	L	-	1	2	ARHGAP30	159285664	0.983000	0.35010	0.518000	0.27811	0.941000	0.58515	2.269000	0.43346	-0.047000	0.13423	-0.266000	0.10368	CTG	G|0.539;C|0.461	0.461	strong		0.567	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
RASSF1	11186	hgsc.bcm.edu	37	3	50369546	50369546	+	Missense_Mutation	SNP	C	C	A	rs2073498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:50369546C>A	ENST00000357043.2	-	3	444	c.409G>T	c.(409-411)Gct>Tct	p.A137S	RASSF1_ENST00000359365.4_Missense_Mutation_p.A133S|RASSF1_ENST00000327761.3_Missense_Mutation_p.A63S|RASSF1_ENST00000395126.3_5'UTR					Ras association (RalGDS/AF-6) domain family member 1											lung(2)|ovary(1)|skin(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		TCAATCTCAGCTTGAGAAAGG	0.547													C|||	356	0.0710863	0.0076	0.0807	5008	,	,		20741	0.0556		0.1183	False		,,,				2504	0.1176				p.A137S		Atlas-SNP	.											.	RASSF1	46	.	0			c.G409T	GRCh37	CM063088	RASSF1	M	rs2073498	PASS	.	C	,SER/ALA,,SER/ALA,SER/ALA	98,4308	79.3+/-117.8	0,98,2105	133.0	108.0	116.0		,397,,187,409	4.5	1.0	3	dbSNP_96	116	864,7736	196.3+/-241.3	38,788,3474	yes	utr-5,missense,utr-5,missense,missense	RASSF1	NM_001206957.1,NM_007182.4,NM_170712.2,NM_170713.2,NM_170714.1	,99,,99,99	38,886,5579	AA,AC,CC		10.0465,2.2242,7.3966	,benign,,benign,benign	,133/341,,63/271,137/345	50369546	962,12044	2203	4300	6503	SO:0001583	missense	11186	exon3			TCTCAGCTTGAGA	AF132675	CCDS2820.1, CCDS2821.1, CCDS2822.1, CCDS43096.1	3p21.3	2008-02-22	2008-02-22		ENSG00000068028	ENSG00000068028			9882	protein-coding gene	gene with protein product		605082					Standard	NM_170713		Approved	NORE2A, REH3P21, RDA32, 123F2	uc003dad.1	Q9NS23	OTTHUMG00000149958	ENST00000357043.2:c.409G>T	3.37:g.50369546C>A	ENSP00000349547:p.Ala137Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_170714		Missense_Mutation	SNP	ENST00000357043.2	37	CCDS2820.1	166	0.076007326007326	6	0.012195121951219513	28	0.07734806629834254	38	0.06643356643356643	94	0.12401055408970976	C	11.17	1.560853	0.27827	0.022242	0.100465	ENSG00000068028	ENST00000327761;ENST00000357043;ENST00000359365	T;T;T	0.75938	2.77;-0.98;-0.98	5.5	4.52	0.55395	.	0.278640	0.39834	N	0.001252	T	0.01189	0.0039	N	0.15975	0.35	0.25265	P	0.9895621	B;B;B	0.14012	0.004;0.009;0.003	B;B;B	0.15484	0.013;0.007;0.004	T	0.14924	-1.0455	9	0.23891	T	0.37	-11.3149	11.1963	0.48715	0.0:0.8767:0.0:0.1233	rs2073498;rs52807901;rs2073498	133;137;63	Q9NS23-2;Q9NS23;Q5TZT2	.;RASF1_HUMAN;.	S	63;137;133	ENSP00000333327:A63S;ENSP00000349547:A137S;ENSP00000352323:A133S	ENSP00000333327:A63S	A	-	1	0	RASSF1	50344550	0.917000	0.31117	1.000000	0.80357	0.978000	0.69477	2.556000	0.45862	2.590000	0.87494	0.462000	0.41574	GCT	C|0.925;A|0.075	0.075	strong		0.547	RASSF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314304.1		
PINX1	54984	hgsc.bcm.edu	37	8	10692242	10692242	+	Silent	SNP	G	G	A	rs1052523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:10692242G>A	ENST00000314787.3	-	2	182	c.63C>T	c.(61-63)gcC>gcT	p.A21A	PINX1_ENST00000426190.2_Silent_p.A19A|SOX7_ENST00000553390.1_Silent_p.A21A|PINX1_ENST00000519088.1_Silent_p.A21A|PINX1_ENST00000520018.2_5'UTR|SOX7_ENST00000554914.1_Silent_p.A21A	NM_017884.4	NP_060354.4	Q96BK5	PINX1_HUMAN	PIN2/TERF1 interacting, telomerase inhibitor 1	21					mitotic metaphase plate congression (GO:0007080)|negative regulation of cell proliferation (GO:0008285)|negative regulation of telomerase activity (GO:0051974)|regulation of telomerase activity (GO:0051972)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|spindle (GO:0005819)	telomerase inhibitor activity (GO:0010521)|telomeric RNA binding (GO:0070034)			kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)		CATTACTCCAGGCAGTGTTCT	0.458													G|||	259	0.0517173	0.0582	0.0692	5008	,	,		20469	0.001		0.0577	False		,,,				2504	0.0767				p.A21A		Atlas-SNP	.											.	PINX1	38	.	0			c.C63T						PASS	.	G		133,3733		3,127,1803	86.0	79.0	81.0		63	-11.6	0.0	8	dbSNP_86	81	455,7847		11,433,3707	no	coding-synonymous	PINX1	NM_017884.4		14,560,5510	AA,AG,GG		5.4806,3.4402,4.8323		21/329	10692242	588,11580	1933	4151	6084	SO:0001819	synonymous_variant	54984	exon2			ACTCCAGGCAGTG	AF418553	CCDS47801.1, CCDS64825.1	8p23	2013-01-28				ENSG00000254093		"""G patch domain containing"""	30046	protein-coding gene	gene with protein product	"""PIN2 interacting protein 1"", ""liver-related putative tumor suppressor"""	606505				11003615, 11701125	Standard	NM_001284356		Approved	PinX1, LPTL, LPTS, FLJ20565, MGC8850		Q96BK5		ENST00000314787.3:c.63C>T	8.37:g.10692242G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_017884	B2R9B1|Q548A5|Q6QWG9|Q7Z7J8|Q96QD7|Q9HBU7|Q9NWW2	Silent	SNP	ENST00000314787.3	37	CCDS47801.1																																																																																			G|0.958;A|0.042	0.042	strong		0.458	PINX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375683.1	NM_017884	
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 GAIIx	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_ENST00000483972.1_Intron|LTB_ENST00000446745.2_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		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	80	27	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		
ANKRD18B	441459	hgsc.bcm.edu	37	9	33568789	33568789	+	Silent	SNP	T	T	G	rs10971566	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33568789T>G	ENST00000290943.6	+	15	2985	c.2889T>G	c.(2887-2889)ctT>ctG	p.L963L	ANKRD18B_ENST00000426460.2_3'UTR	NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	963										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						TTGAAAATCTTAATAGTATAG	0.393													.|||	1000	0.199681	0.0454	0.2695	5008	,	,		16912	0.2143		0.3161	False		,,,				2504	0.2239				p.L962L		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.T2886G						PASS	.																																			SO:0001819	synonymous_variant	441459	exon15			AAATCTTAATAGT			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2889T>G	9.37:g.33568789T>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				T|0.756;G|0.244	0.244	strong		0.393	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
ZFHX3	463	hgsc.bcm.edu	37	16	72992221	72992221	+	Silent	SNP	G	G	A	rs61735550	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:72992221G>A	ENST00000268489.5	-	2	2496	c.1824C>T	c.(1822-1824)agC>agT	p.S608S	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	608					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CACCCTCTGTGCTTTCATTTG	0.617													G|||	416	0.0830671	0.0174	0.098	5008	,	,		18070	0.0		0.2306	False		,,,				2504	0.0951				p.S608S		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C1824T						PASS	.	G	,	239,4157	140.4+/-175.9	9,221,1968	102.0	95.0	97.0		,1824	4.3	1.0	16	dbSNP_129	97	2109,6491	364.6+/-333.6	259,1591,2450	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	268,1812,4418	AA,AG,GG		24.5233,5.4368,18.0671	,	,608/3704	72992221	2348,10648	2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCTGTGCTTTCA	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1824C>T	16.37:g.72992221G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	161	70	0.434783	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			G|0.830;A|0.170	0.170	strong		0.617	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
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 GAIIx	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		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	25	11	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	
INPP4B	8821	hgsc.bcm.edu	37	4	143033778	143033778	+	Silent	SNP	T	T	C	rs3822141	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:143033778T>C	ENST00000513000.1	-	23	2626	c.2193A>G	c.(2191-2193)ctA>ctG	p.L731L	INPP4B_ENST00000308502.4_Silent_p.L731L|INPP4B_ENST00000509777.1_Silent_p.L731L|INPP4B_ENST00000508116.1_Silent_p.L731L|INPP4B_ENST00000262992.4_Silent_p.L731L	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	731					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CTTTAATCTGTAGAGGTAGTG	0.398													T|||	375	0.0748802	0.003	0.0865	5008	,	,		17717	0.0764		0.0636	False		,,,				2504	0.1738				p.L731L		Atlas-SNP	.											.	INPP4B	132	.	0			c.A2193G						PASS	.	T	,	64,4342	60.5+/-97.4	0,64,2139	171.0	166.0	167.0		2193,2193	-11.4	0.0	4	dbSNP_107	167	643,7957	164.8+/-217.1	20,603,3677	no	coding-synonymous,coding-synonymous	INPP4B	NM_001101669.1,NM_003866.2	,	20,667,5816	CC,CT,TT		7.4767,1.4526,5.436	,	731/925,731/925	143033778	707,12299	2203	4300	6503	SO:0001819	synonymous_variant	8821	exon23			AATCTGTAGAGGT	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.2193A>G	4.37:g.143033778T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			C|0.057;T|0.943	0.057	strong		0.398	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377918	49377918	+	Missense_Mutation	SNP	G	G	T	rs35087747	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49377918G>T	ENST00000200453.5	+	2	1697	c.1428G>T	c.(1426-1428)agG>agT	p.R476S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	476	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.		R -> S (in dbSNP:rs35087747). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CGGACCAGAGGGCCCACTTCA	0.572													T|||	421	0.0840655	0.087	0.0793	5008	,	,		17447	0.003		0.164	False		,,,				2504	0.0849				p.R476S		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1428T						PASS	.	T	SER/ARG	578,3828	771.4+/-413.8	35,508,1660	71.0	70.0	70.0		1428	-5.6	0.0	19	dbSNP_126	70	1549,7051	745.0+/-407.3	129,1291,2880	yes	missense	PPP1R15A	NM_014330.3	110	164,1799,4540	TT,TG,GG		18.0116,13.1185,16.354	benign	476/675	49377918	2127,10879	2203	4300	6503	SO:0001583	missense	23645	exon2			CCAGAGGGCCCAC	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1428G>T	19.37:g.49377918G>T	ENSP00000200453:p.Arg476Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	198	0.09065934065934066	45	0.09146341463414634	30	0.08287292817679558	1	0.0017482517482517483	122	0.16094986807387862	T	0.463	-0.888184	0.02511	0.131185	0.180116	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05139	3.49	4.19	-5.56	0.02529	.	0.890365	0.09631	N	0.776241	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34925	-0.9809	9	0.02654	T	1	2.4026	3.0039	0.06023	0.2444:0.4426:0.1244:0.1886	rs35087747	476	O75807	PR15A_HUMAN	S	476;316;434	ENSP00000200453:R476S	ENSP00000200453:R476S	R	+	3	2	PPP1R15A	54069730	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.597000	0.00894	-1.820000	0.01215	-1.089000	0.02181	AGG	A|0.000;C|0.000;G|0.864;T|0.136	0.136	strong		0.572	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
RASGRF1	5923	hgsc.bcm.edu	37	15	79284127	79284127	+	Missense_Mutation	SNP	C	C	A	rs28603308	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:79284127C>A	ENST00000419573.3	-	22	3359	c.3085G>T	c.(3085-3087)Gtg>Ttg	p.V1029L	RASGRF1_ENST00000394745.3_Missense_Mutation_p.V245L|RASGRF1_ENST00000558480.2_Missense_Mutation_p.V1013L|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	1029					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TCAGCCTTCACGCCTTCAGCC	0.547													C|||	28	0.00559105	0.0076	0.0029	5008	,	,		18479	0.0		0.0129	False		,,,				2504	0.0031				p.V1029L		Atlas-SNP	.											.	RASGRF1	168	.	0			c.G3085T						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	54,4338	54.2+/-90.2	0,54,2142	94.0	83.0	87.0		3037,3085,733	3.2	1.0	15	dbSNP_125	87	182,8404	82.9+/-145.4	5,172,4116	yes	missense,missense,missense	RASGRF1	NM_001145648.1,NM_002891.4,NM_153815.2	32,32,32	5,226,6258	AA,AC,CC		2.1197,1.2295,1.8185	benign,benign,benign	1013/1258,1029/1274,245/490	79284127	236,12742	2196	4293	6489	SO:0001583	missense	5923	exon22			CCTTCACGCCTTC	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.3085G>T	15.37:g.79284127C>A	ENSP00000405963:p.Val1029Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	37	CCDS10309.1	20	0.009157509157509158	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	C	2.381	-0.342087	0.05243	0.012295	0.021197	ENSG00000058335	ENST00000419573;ENST00000394741;ENST00000394745	T;T	0.30182	1.54;1.54	4.13	3.21	0.36854	Ras guanine nucleotide exchange factor, domain (1);	0.353120	0.25971	N	0.027135	T	0.07773	0.0195	N	0.19112	0.55	0.33171	D	0.548287	B;B;B;B	0.16396	0.017;0.003;0.01;0.001	B;B;B;B	0.18263	0.021;0.006;0.008;0.008	T	0.19192	-1.0313	10	0.10636	T	0.68	.	7.2876	0.26348	0.0:0.8797:0.0:0.1203	rs28603308;rs28603308	425;1013;1031;1013	B7Z6Z6;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	L	1029;1013;245	ENSP00000405963:V1029L;ENSP00000378228:V245L	ENSP00000378224:V1013L	V	-	1	0	RASGRF1	77071182	0.076000	0.21285	0.996000	0.52242	0.222000	0.24845	0.673000	0.25203	0.943000	0.37553	0.650000	0.86243	GTG	C|0.986;A|0.014	0.014	strong		0.547	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
SNRNP200	23020	hgsc.bcm.edu	37	2	96963419	96963419	+	Missense_Mutation	SNP	T	T	C	rs142729495	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:96963419T>C	ENST00000323853.5	-	10	1236	c.1159A>G	c.(1159-1161)Atg>Gtg	p.M387V	SNRNP200_ENST00000349783.5_Missense_Mutation_p.M387V	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	387					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.M387V(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TCTGTGTCCATTCGAGACTGA	0.473													T|||	8	0.00159744	0.0	0.0014	5008	,	,		21476	0.0		0.005	False		,,,				2504	0.002				p.M387V		Atlas-SNP	.											SNRNP200,NS,lymphoid_neoplasm,0,1	SNRNP200	195	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1159G						scavenged	.	T	VAL/MET	9,4397	14.3+/-33.2	0,9,2194	111.0	100.0	104.0		1159	4.5	1.0	2	dbSNP_134	104	62,8538	38.8+/-94.9	1,60,4239	yes	missense	SNRNP200	NM_014014.4	21	1,69,6433	CC,CT,TT		0.7209,0.2043,0.5459	benign	387/2137	96963419	71,12935	2203	4300	6503	SO:0001583	missense	23020	exon10			TGTCCATTCGAGA	AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.1159A>G	2.37:g.96963419T>C	ENSP00000317123:p.Met387Val	Somatic	133	2	0.0150376		WXS	Illumina HiSeq	Phase_I	115	63	0.547826	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Missense_Mutation	SNP	ENST00000323853.5	37	CCDS2020.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	11.40	1.628939	0.28978	0.002043	0.007209	ENSG00000144028	ENST00000323853;ENST00000349783;ENST00000540328	T;T	0.66460	-0.21;1.58	5.69	4.54	0.55810	.	0.047537	0.85682	D	0.000000	T	0.32346	0.0826	N	0.04508	-0.205	0.35825	D	0.824846	B	0.02656	0.0	B	0.01281	0.0	T	0.32929	-0.9888	10	0.29301	T	0.29	-29.9429	8.0906	0.30799	0.0:0.1578:0.0:0.8422	.	387	O75643	U520_HUMAN	V	387;387;62	ENSP00000317123:M387V;ENSP00000326937:M387V	ENSP00000317123:M387V	M	-	1	0	SNRNP200	96327146	1.000000	0.71417	0.973000	0.42090	0.995000	0.86356	5.389000	0.66255	0.988000	0.38734	0.533000	0.62120	ATG	T|0.996;C|0.004	0.004	strong		0.473	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014	
TM6SF1	53346	hgsc.bcm.edu	37	15	83781631	83781631	+	Missense_Mutation	SNP	C	C	T	rs1989	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:83781631C>T	ENST00000322019.9	+	2	449	c.175C>T	c.(175-177)Ccc>Tcc	p.P59S	TM6SF1_ENST00000379390.6_Missense_Mutation_p.P59S|RP11-382A20.2_ENST00000565513.1_RNA|TM6SF1_ENST00000564988.1_3'UTR|TM6SF1_ENST00000379386.4_Missense_Mutation_p.P59S|TM6SF1_ENST00000565774.1_Missense_Mutation_p.P59S			Q9BZW5	TM6S1_HUMAN	transmembrane 6 superfamily member 1	59			P -> S (in dbSNP:rs1989).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						AAGAAAACCACCCCGGGACCC	0.483													C|||	229	0.0457268	0.0038	0.0562	5008	,	,		19407	0.001		0.1203	False		,,,				2504	0.0644				p.P59S		Atlas-SNP	.											.	TM6SF1	38	.	0			c.C175T						PASS	.	C	SER/PRO,SER/PRO	77,4329	68.1+/-105.8	1,75,2127	144.0	127.0	132.0		175,175	5.6	0.9	15	dbSNP_36	132	867,7733	196.6+/-241.5	51,765,3484	yes	missense,missense	TM6SF1	NM_001144903.1,NM_023003.3	74,74	52,840,5611	TT,TC,CC		10.0814,1.7476,7.2582	probably-damaging,probably-damaging	59/340,59/371	83781631	944,12062	2203	4300	6503	SO:0001583	missense	53346	exon2			AAACCACCCCGGG	AF255922	CCDS10323.1, CCDS45338.1	15q24-q26	2003-04-04			ENSG00000136404	ENSG00000136404			11860	protein-coding gene	gene with protein product		606562				11124529	Standard	NM_001144903		Approved		uc002bjp.3	Q9BZW5	OTTHUMG00000147365	ENST00000322019.9:c.175C>T	15.37:g.83781631C>T	ENSP00000317000:p.Pro59Ser	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	135	75	0.555556	NM_001144903	A8K7T5|H3BU56|Q4U0U5	Missense_Mutation	SNP	ENST00000322019.9	37	CCDS10323.1	120	0.054945054945054944	2	0.0040650406504065045	28	0.07734806629834254	1	0.0017482517482517483	89	0.11741424802110818	C	19.47	3.833608	0.71258	0.017476	0.100814	ENSG00000136404	ENST00000322019;ENST00000379386;ENST00000379384;ENST00000379390;ENST00000258909	T;T;T;T;T	0.60797	0.16;0.16;0.16;0.16;0.16	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.02193	0.0068	L	0.41632	1.29	0.58432	D	0.999997	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.996;0.961;0.996	T	0.04650	-1.0936	10	0.19590	T	0.45	-13.4727	18.3813	0.90452	0.0:1.0:0.0:0.0	rs1989;rs52798020;rs60024683;rs1989	59;59;59	E9PD04;Q6P4D7;Q9BZW5	.;.;TM6S1_HUMAN	S	59	ENSP00000317000:P59S;ENSP00000368696:P59S;ENSP00000368693:P59S;ENSP00000368700:P59S;ENSP00000258909:P59S	ENSP00000258909:P59S	P	+	1	0	TM6SF1	81572635	0.999000	0.42202	0.934000	0.37439	0.997000	0.91878	5.964000	0.70379	2.633000	0.89246	0.561000	0.74099	CCC	C|0.934;T|0.066	0.066	strong		0.483	TM6SF1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000304009.1	NM_023003	
PDIA2	64714	hgsc.bcm.edu	37	16	334732	334732	+	Silent	SNP	C	C	T	rs45593734	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:334732C>T	ENST00000219406.6	+	3	498	c.480C>T	c.(478-480)gaC>gaT	p.D160D	PDIA2_ENST00000404312.1_Silent_p.D160D	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	160					cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GGCTGGAGGACGAGGCGGCCG	0.716													c|||	640	0.127796	0.0862	0.0994	5008	,	,		12306	0.0962		0.16	False		,,,				2504	0.2035				p.D160D		Atlas-SNP	.											.	PDIA2	51	.	0			c.C480T						PASS	.	C		328,3770		14,300,1735	8.0	14.0	12.0		480	-3.5	0.3	16	dbSNP_127	12	1280,6964		99,1082,2941	no	coding-synonymous	PDIA2	NM_006849.2		113,1382,4676	TT,TC,CC		15.5264,8.0039,13.0287		160/526	334732	1608,10734	2049	4122	6171	SO:0001819	synonymous_variant	64714	exon3			GGAGGACGAGGCG	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"""Protein disulfide isomerases"""	14180	protein-coding gene	gene with protein product		608012	"""protein disulfide isomerase, pancreatic"", ""protein disulfide isomerase-associated 2"""	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.480C>T	16.37:g.334732C>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	6	4	0.666667	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Silent	SNP	ENST00000219406.6	37	CCDS42089.1	245	0.11217948717948718	33	0.06707317073170732	40	0.11049723756906077	54	0.0944055944055944	118	0.15567282321899736	c	0.097	-1.157292	0.01686	0.080039	0.155264	ENSG00000185615	ENST00000456379	.	.	.	3.75	-3.55	0.04639	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.44485	P	0.00257099999999999	.	.	.	.	.	.	T	0.21008	-1.0258	3	.	.	.	.	3.4234	0.07401	0.1195:0.1343:0.119:0.6272	rs45593734;rs62032217	.	.	.	M	157	.	.	T	+	2	0	PDIA2	274733	0.000000	0.05858	0.349000	0.25694	0.141000	0.21300	-2.516000	0.00954	-0.782000	0.04541	0.457000	0.33378	ACG	C|0.886;T|0.114	0.114	strong		0.716	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
SMURF1	57154	hgsc.bcm.edu	37	7	98650051	98650051	+	Silent	SNP	G	G	C	rs219797	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:98650051G>C	ENST00000361125.1	-	7	817	c.498C>G	c.(496-498)tcC>tcG	p.S166S	SMURF1_ENST00000480055.1_5'UTR|SMURF1_ENST00000361368.2_Silent_p.S166S	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	166					BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of ossification (GO:0030279)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein export from nucleus (GO:0006611)|protein localization to cell surface (GO:0034394)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activin binding (GO:0048185)|I-SMAD binding (GO:0070411)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|urinary_tract(1)	25	all_cancers(62;1.05e-08)|all_epithelial(64;4.34e-09)|Lung NSC(181;0.00902)|all_lung(186;0.0145)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)|Lung(104;0.224)			TCCCAGGCCCGGAGTCTTCAT	0.597													C|||	3413	0.68151	0.9561	0.5375	5008	,	,		18187	0.6498		0.504	False		,,,				2504	0.6278				p.S166S		Atlas-SNP	.											.	SMURF1	58	.	0			c.C498G						PASS	.	C	,,	3959,447	213.5+/-233.1	1782,395,26	35.0	35.0	35.0		498,498,498	-10.5	0.0	7	dbSNP_79	35	4367,4233	567.1+/-388.8	1133,2101,1066	no	coding-synonymous,coding-synonymous,coding-synonymous	SMURF1	NM_001199847.1,NM_020429.2,NM_181349.2	,,	2915,2496,1092	CC,CG,GG		49.2209,10.1453,35.9834	,,	166/729,166/758,166/732	98650051	8326,4680	2203	4300	6503	SO:0001819	synonymous_variant	57154	exon7			AGGCCCGGAGTCT	AB046845	CCDS34689.1, CCDS34690.1	7q21.1-q31.1	2004-07-29			ENSG00000198742	ENSG00000198742			16807	protein-coding gene	gene with protein product		605568				10458166	Standard	NM_020429		Approved	KIAA1625	uc003upu.2	Q9HCE7	OTTHUMG00000150272	ENST00000361125.1:c.498C>G	7.37:g.98650051G>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Silent	SNP	ENST00000361125.1	37	CCDS34690.1																																																																																			G|0.362;C|0.638	0.638	strong		0.597	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362209	105362209	+	Silent	SNP	T	T	C	rs4917396	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:105362209T>C	ENST00000369774.4	-	15	3042	c.2766A>G	c.(2764-2766)aaA>aaG	p.K922K	SH3PXD2A_ENST00000355946.2_Silent_p.K894K|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000538130.1_Silent_p.K757K|SH3PXD2A_ENST00000540321.1_Silent_p.K789K			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	922					superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|podosome (GO:0002102)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(18)|ovary(1)|skin(1)|urinary_tract(1)	38		Colorectal(252;0.0815)|Breast(234;0.131)		Epithelial(162;4.09e-10)|all cancers(201;2.73e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0119)		GGCTGTCTGATTTGCCTTCGT	0.607													C|||	4570	0.91254	0.9743	0.8876	5008	,	,		20101	0.999		0.7624	False		,,,				2504	0.9121				p.K894K		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.A2682G						PASS	.	C		4125,281	156.6+/-189.7	1936,253,14	128.0	120.0	123.0		2682	2.6	1.0	10	dbSNP_111	123	6723,1877	336.3+/-321.8	2622,1479,199	no	coding-synonymous	SH3PXD2A	NM_014631.2		4558,1732,213	CC,CT,TT		21.8256,6.3777,16.5923		894/1106	105362209	10848,2158	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			GTCTGATTTGCCT	AB007878	CCDS31278.1	10q25.1	2006-02-13	2006-02-13	2006-02-13	ENSG00000107957	ENSG00000107957			23664	protein-coding gene	gene with protein product	"""five SH3 domains"""		"""SH3 multiple domains 1"""	SH3MD1		9687503	Standard	XM_005270297		Approved	FISH, KIAA0418	uc001kxj.1	Q5TCZ1	OTTHUMG00000018997	ENST00000369774.4:c.2766A>G	10.37:g.105362209T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		1942	0.8891941391941391	479	0.9735772357723578	310	0.856353591160221	571	0.9982517482517482	582	0.7678100263852242	C	0.035	-1.311184	0.01342	0.936223	0.781744	ENSG00000107957	ENST00000420222	.	.	.	4.77	2.62	0.31277	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.27365	-1.0076	3	.	.	.	-31.869	7.2011	0.25881	0.0:0.4692:0.0:0.5308	rs4917396;rs4917396	.	.	.	V	849	.	.	I	-	1	0	SH3PXD2A	105352199	1.000000	0.71417	0.987000	0.45799	0.191000	0.23601	1.153000	0.31676	0.471000	0.27319	-0.227000	0.12334	ATC	T|0.147;C|0.853	0.853	strong		0.607	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
ZNF860	344787	hgsc.bcm.edu	37	3	32031643	32031643	+	Missense_Mutation	SNP	A	A	G	rs386659897|rs13065048	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:32031643A>G	ENST00000360311.4	+	2	1621	c.1072A>G	c.(1072-1074)Aca>Gca	p.T358A		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	358					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(3)|lung(4)|ovary(1)	8						TTCACACCTCACACAACACAC	0.403													a|||	2357	0.470647	0.7988	0.3602	5008	,	,		21395	0.4534		0.1968	False		,,,				2504	0.4049				p.T358A		Atlas-SNP	.											.	ZNF860	96	.	0			c.A1072G						PASS	.	G	ALA/THR	933,451		325,283,84	48.0	50.0	49.0		1072	-0.7	0.0	3	dbSNP_121	49	608,2574		57,494,1040	no	missense	ZNF860	NM_001137674.2	58	382,777,1124	GG,GA,AA		19.1075,32.5867,33.7495	benign	358/633	32031643	1541,3025	692	1591	2283	SO:0001583	missense	344787	exon2			CACCTCACACAAC	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1072A>G	3.37:g.32031643A>G	ENSP00000373274:p.Thr358Ala	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	913	0.41804029304029305	385	0.782520325203252	126	0.34806629834254144	249	0.4353146853146853	153	0.20184696569920843	a	0.001	-2.874949	0.00062	0.674133	0.191075	ENSG00000197385	ENST00000360311	T	0.06849	3.25	0.345	-0.691	0.11305	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.22034	-1.0228	7	.	.	.	.	2.7881	0.05379	0.2503:0.0:0.5021:0.2476	rs13065048;rs52806446;rs60333482;rs13065048	358	A6NHJ4	ZN860_HUMAN	A	358	ENSP00000373274:T358A	.	T	+	1	0	ZNF860	32006647	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.246000	0.18160	-2.012000	0.00950	-2.005000	0.00442	ACA	A|0.615;G|0.385	0.385	strong		0.403	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
EMR3	84658	hgsc.bcm.edu	37	19	14758168	14758168	+	Missense_Mutation	SNP	G	G	A	rs34226397	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:14758168G>A	ENST00000253673.5	-	8	807	c.707C>T	c.(706-708)gCc>gTc	p.A236V	EMR3_ENST00000344373.4_Missense_Mutation_p.A184V|EMR3_ENST00000599900.1_Missense_Mutation_p.A21V|EMR3_ENST00000443157.2_Missense_Mutation_p.A110V	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	236			A -> V (in dbSNP:rs34226397).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						AAAGGCAATGGCACTGGGACC	0.353													G|||	1493	0.298123	0.3691	0.2104	5008	,	,		21054	0.2738		0.3091	False		,,,				2504	0.2781				p.A236V		Atlas-SNP	.											.	EMR3	99	.	0			c.C707T						PASS	.	G	VAL/ALA	1628,2778	501.8+/-365.1	298,1032,873	70.0	68.0	69.0		707	3.9	0.1	19	dbSNP_126	69	2623,5977	423.5+/-354.4	410,1803,2087	yes	missense	EMR3	NM_032571.3	64	708,2835,2960	AA,AG,GG		30.5,36.9496,32.6849	benign	236/653	14758168	4251,8755	2203	4300	6503	SO:0001583	missense	84658	exon8			GCAATGGCACTGG	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"""-"", ""GPCR / Class B : Orphans"""	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.707C>T	19.37:g.14758168G>A	ENSP00000253673:p.Ala236Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	647	0.29624542124542125	196	0.3983739837398374	88	0.2430939226519337	141	0.2465034965034965	222	0.2928759894459103	G	0.010	-1.771288	0.00645	0.369496	0.305	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	T;T;T	0.42900	0.96;3.23;3.23	3.94	3.94	0.45596	.	.	.	.	.	T	0.00012	0.0000	L	0.48986	1.54	0.80722	P	0.0	B;B;B	0.23854	0.092;0.028;0.023	B;B;B	0.22753	0.017;0.015;0.041	T	0.40739	-0.9547	8	0.27082	T	0.32	.	11.5753	0.50858	0.0:0.0:1.0:0.0	rs34226397	110;184;236	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	V	110;236;184	ENSP00000396208:A110V;ENSP00000253673:A236V;ENSP00000340758:A184V	ENSP00000253673:A236V	A	-	2	0	EMR3	14619168	0.148000	0.22702	0.108000	0.21378	0.026000	0.11368	2.331000	0.43894	1.753000	0.51906	0.644000	0.83932	GCC	G|0.679;A|0.321	0.321	strong		0.353	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571	
MST1R	4486	hgsc.bcm.edu	37	3	49936102	49936102	+	Missense_Mutation	SNP	T	T	C	rs2230590	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49936102T>C	ENST00000296474.3	-	4	1595	c.1568A>G	c.(1567-1569)cAa>cGa	p.Q523R	MST1R_ENST00000344206.4_Missense_Mutation_p.Q523R|CTD-2330K9.2_ENST00000435478.1_RNA	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	523			Q -> R (in dbSNP:rs2230590). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8386824}.		cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)			cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		GCCAGGGCCTTGGATAGGTAC	0.597													C|||	2086	0.416534	0.7368	0.3761	5008	,	,		19719	0.1429		0.497	False		,,,				2504	0.2117				p.Q523R		Atlas-SNP	.											.	MST1R	205	.	0			c.A1568G						PASS	.	C	ARG/GLN	2941,1465	467.9+/-355.0	1002,937,264	49.0	58.0	55.0		1568	-6.8	0.1	3	dbSNP_98	55	4350,4250	570.7+/-389.4	1100,2150,1050	yes	missense	MST1R	NM_002447.2	43	2102,3087,1314	CC,CT,TT		49.4186,33.2501,43.9413	benign	523/1401	49936102	7291,5715	2203	4300	6503	SO:0001583	missense	4486	exon4			GGGCCTTGGATAG	X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"""CD molecules"""	7381	protein-coding gene	gene with protein product		600168	"""PTK8 protein tyrosine kinase 8"""	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.1568A>G	3.37:g.49936102T>C	ENSP00000296474:p.Gln523Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001244937	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	37	CCDS2807.1	916	0.4194139194139194	340	0.6910569105691057	132	0.36464088397790057	82	0.14335664335664336	362	0.47757255936675463	C	0.005	-2.227231	0.00280	0.667499	0.505814	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.39997	1.05;3.01	5.84	-6.78	0.01721	WD40/YVTN repeat-like-containing domain (1);	0.557246	0.19719	N	0.107633	T	0.00012	0.0000	L	0.35487	1.065	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.002;0.0	T	0.36311	-0.9753	9	0.05959	T	0.93	-0.871	7.5474	0.27775	0.0646:0.3007:0.0998:0.5348	rs2230590;rs2293019;rs57396014;rs2230590	417;523;523;523	Q04912-4;Q04912-6;Q04912-5;Q04912	.;.;.;RON_HUMAN	R	523	ENSP00000296474:Q523R;ENSP00000341325:Q523R	ENSP00000296474:Q523R	Q	-	2	0	MST1R	49911106	0.000000	0.05858	0.139000	0.22197	0.049000	0.14656	-1.163000	0.03138	-1.703000	0.01409	-2.395000	0.00226	CAA	T|0.495;C|0.505	0.505	strong		0.597	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
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 GAIIx	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	RP11-552F3.10_ENST00000587267.1_RNA|TRIM65_ENST00000269383.3_5'Flank|MRPL38_ENST00000409963.3_Missense_Mutation_p.P57L|MRPL38_ENST00000585475.1_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	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	57	21	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	
ANXA9	8416	hgsc.bcm.edu	37	1	150958836	150958836	+	Missense_Mutation	SNP	A	A	G	rs267733	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:150958836A>G	ENST00000368947.4	+	8	973	c.497A>G	c.(496-498)gAc>gGc	p.D166G		NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	166			D -> G (in dbSNP:rs267733). {ECO:0000269|PubMed:10899159, ECO:0000269|PubMed:9742942, ECO:0000269|Ref.5}.		single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCTGTGGATGACATCACATCT	0.567													A|||	318	0.0634984	0.0424	0.0735	5008	,	,		19507	0.0258		0.1382	False		,,,				2504	0.047				p.D166G		Atlas-SNP	.											.	ANXA9	28	.	0			c.A497G						PASS	.	A	GLY/ASP	271,4135	152.9+/-186.6	5,261,1937	81.0	69.0	73.0		497	5.1	1.0	1	dbSNP_79	73	1332,7268	261.3+/-283.8	112,1108,3080	yes	missense	ANXA9	NM_003568.2	94	117,1369,5017	GG,GA,AA		15.4884,6.1507,12.3251	probably-damaging	166/346	150958836	1603,11403	2203	4300	6503	SO:0001583	missense	8416	exon8			TGGATGACATCAC	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"""Annexins"""	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.497A>G	1.37:g.150958836A>G	ENSP00000357943:p.Asp166Gly	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	37	CCDS975.2	173	0.07921245421245421	21	0.042682926829268296	29	0.08011049723756906	19	0.033216783216783216	104	0.13720316622691292	A	14.34	2.507144	0.44558	0.061507	0.154884	ENSG00000143412	ENST00000368947	T	0.08634	3.07	5.1	5.1	0.69264	.	0.061224	0.64402	D	0.000005	T	0.24160	0.0585	M	0.91300	3.195	0.23589	P	0.99734447	D	0.61697	0.99	D	0.67231	0.95	T	0.27262	-1.0079	9	0.72032	D	0.01	.	11.5488	0.50708	1.0:0.0:0.0:0.0	rs267733;rs579783;rs17356291;rs17610363;rs61138212;rs267733	166	O76027	ANXA9_HUMAN	G	166	ENSP00000357943:D166G	ENSP00000357943:D166G	D	+	2	0	ANXA9	149225460	1.000000	0.71417	1.000000	0.80357	0.134000	0.20937	5.151000	0.64875	2.049000	0.60858	0.379000	0.24179	GAC	A|0.906;G|0.094	0.094	strong		0.567	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377319	49377319	+	Missense_Mutation	SNP	A	A	G	rs610308	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49377319A>G	ENST00000200453.5	+	2	1098	c.829A>G	c.(829-831)Aaa>Gaa	p.K277E		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	277	Glu-rich.		K -> E (in dbSNP:rs610308). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		AAAGGCACACAAAGAAACTGG	0.612													G|||	2228	0.444888	0.8033	0.3444	5008	,	,		17948	0.1141		0.3539	False		,,,				2504	0.4663				p.K277E		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.A829G						PASS	.	G	GLU/LYS	3295,1111	388.4+/-326.9	1232,831,140	63.0	78.0	73.0		829	-3.1	0.0	19	dbSNP_83	73	3002,5598	652.0+/-400.9	527,1948,1825	yes	missense	PPP1R15A	NM_014330.3	56	1759,2779,1965	GG,GA,AA		34.907,25.2156,48.4161	benign	277/675	49377319	6297,6709	2203	4300	6503	SO:0001583	missense	23645	exon2			GCACACAAAGAAA	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.829A>G	19.37:g.49377319A>G	ENSP00000200453:p.Lys277Glu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	81	31	0.382716	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	844	0.38644688644688646	383	0.7784552845528455	127	0.35082872928176795	68	0.11888111888111888	266	0.35092348284960423	G	0.655	-0.808008	0.02819	0.747844	0.34907	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05382	3.45	3.8	-3.11	0.05299	.	2.747870	0.01207	N	0.007758	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33675	-0.9859	9	0.02654	T	1	2.7997	5.5496	0.17083	0.5438:0.1519:0.3044:0.0	rs610308;rs3745701;rs52824100;rs58566411;rs610308	277	O75807	PR15A_HUMAN	E	277;117;235	ENSP00000200453:K277E	ENSP00000200453:K277E	K	+	1	0	PPP1R15A	54069131	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.530000	0.06179	-0.994000	0.03463	-1.110000	0.02074	AAA	A|0.546;G|0.454	0.454	strong		0.612	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
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 GAIIx	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		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	44	17	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	
MECOM	2122	hgsc.bcm.edu	37	3	169098992	169098992	+	Missense_Mutation	SNP	G	G	A	rs7622799	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:169098992G>A	ENST00000494292.1	-	2	455	c.358C>T	c.(358-360)Ccc>Tcc	p.P120S	MECOM_ENST00000485957.1_5'UTR	NM_004991.3	NP_004982.2	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	120			P -> S (in dbSNP:rs7622799).		regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P114S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CCATAACTGGGGTCTTTCAGG	0.408													G|||	766	0.152955	0.1362	0.3329	5008	,	,		20490	0.1558		0.1233	False		,,,				2504	0.0757				p.P120S		Atlas-SNP	.											MDS1,NS,carcinoma,0,1	MECOM	216	1	1	Substitution - Missense(1)	stomach(1)	c.C358T						PASS	.	G	,SER/PRO	483,3245		32,419,1413	90.0	87.0	88.0		,358	4.5	1.0	3	dbSNP_116	88	932,7278		53,826,3226	yes	intron,missense	MECOM	NM_001205194.1,NM_004991.3	,74	85,1245,4639	AA,AG,GG		11.352,12.956,11.8529	,possibly-damaging	,120/1240	169098992	1415,10523	1864	4105	5969	SO:0001583	missense	2122	exon2			AACTGGGGTCTTT	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000494292.1:c.358C>T	3.37:g.169098992G>A	ENSP00000417899:p.Pro120Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000494292.1	37		344	0.1575091575091575	59	0.11991869918699187	89	0.24585635359116023	94	0.16433566433566432	102	0.1345646437994723	G	1.493	-0.554124	0.03996	0.12956	0.11352	ENSG00000085276	ENST00000494292	T	0.71698	-0.59	5.4	4.52	0.55395	.	0.105398	0.42964	N	0.000640	T	0.00012	0.0000	N	0.12746	0.255	0.09310	P	1.0	B;B	0.30281	0.275;0.0	B;B	0.28916	0.096;0.002	T	0.06734	-1.0810	9	0.46703	T	0.11	.	13.2366	0.59972	0.0775:0.0:0.9225:0.0	rs7622799;rs52817261;rs59561788;rs7622799	120;120	Q13465;Q03112-3	MDS1_HUMAN;.	S	120	ENSP00000417899:P120S	ENSP00000417899:P120S	P	-	1	0	MECOM	170581686	1.000000	0.71417	0.974000	0.42286	0.381000	0.30169	2.496000	0.45346	1.252000	0.44001	0.650000	0.86243	CCC	G|0.861;A|0.139	0.139	strong		0.408	MECOM-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000351517.3	NM_005241, NM_004991	
FHAD1	114827	hgsc.bcm.edu	37	1	15702130	15702130	+	Silent	SNP	A	A	G	rs17368978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:15702130A>G	ENST00000375998.4	+	26	3543	c.3543A>G	c.(3541-3543)ctA>ctG	p.L1181L	FHAD1_ENST00000314740.8_Silent_p.L434L|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000417793.1_Silent_p.L1145L|FHAD1_ENST00000375999.3_Silent_p.L1181L|FHAD1_ENST00000358897.4_Silent_p.L1181L			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1181										skin(1)|stomach(1)	2						AATCATTTCTAGATTTAAAGA	0.358													A|||	252	0.0503195	0.0847	0.036	5008	,	,		18986	0.001		0.0467	False		,,,				2504	0.0685				p.L1181L		Atlas-SNP	.											.	FHAD1	78	.	0			c.A3543G						PASS	.	A		94,1290		3,88,601	115.0	94.0	100.0		3543	1.4	0.8	1	dbSNP_123	100	187,2995		6,175,1410	no	coding-synonymous	FHAD1	NM_052929.1		9,263,2011	GG,GA,AA		5.8768,6.7919,6.1542		1181/1413	15702130	281,4285	692	1591	2283	SO:0001819	synonymous_variant	114827	exon27			ATTTCTAGATTTA	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.3543A>G	1.37:g.15702130A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37		96	0.04395604395604396	41	0.08333333333333333	19	0.052486187845303865	0	0.0	36	0.047493403693931395	A	0.392	-0.923114	0.02377	0.067919	0.058768	ENSG00000142621	ENST00000444385	.	.	.	5.08	1.38	0.22167	.	.	.	.	.	.	.	.	.	.	.	0.47441	D	0.999425	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.4267	0.11507	0.6482:0.1692:0.1825:0.0	rs17368978;rs56584101;rs17368978	.	.	.	W	500	.	.	X	+	2	0	FHAD1	15574717	0.627000	0.27129	0.828000	0.32881	0.056000	0.15407	0.299000	0.19138	0.114000	0.18032	-0.250000	0.11733	TAG	A|0.944;G|0.056	0.056	strong		0.358	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
CENPQ	55166	hgsc.bcm.edu	37	6	49439805	49439805	+	Missense_Mutation	SNP	G	G	A	rs4267943	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:49439805G>A	ENST00000335783.3	+	4	281	c.187G>A	c.(187-189)Gga>Aga	p.G63R		NM_018132.3	NP_060602.2	Q7L2Z9	CENPQ_HUMAN	centromere protein Q	63			G -> R (in dbSNP:rs4267943).		CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(4)|ovary(2)|prostate(1)	11	Lung NSC(77;0.0128)					CCTAAAACACGGAAAGACAGC	0.378													G|||	1674	0.334265	0.4191	0.2305	5008	,	,		14881	0.2103		0.332	False		,,,				2504	0.4233				p.G63R		Atlas-SNP	.											.	CENPQ	23	.	0			c.G187A						PASS	.	G	ARG/GLY	1724,2682	516.8+/-369.3	331,1062,810	121.0	124.0	123.0		187	-6.5	0.0	6	dbSNP_111	123	3158,5442	479.9+/-370.2	584,1990,1726	yes	missense	CENPQ	NM_018132.3	125	915,3052,2536	AA,AG,GG		36.7209,39.1285,37.5365	benign	63/269	49439805	4882,8124	2203	4300	6503	SO:0001583	missense	55166	exon4			AAACACGGAAAGA	AK001407	CCDS4925.1	6p12.3	2013-11-05	2006-06-15	2006-06-15	ENSG00000031691	ENSG00000031691			21347	protein-coding gene	gene with protein product		611506	"""chromosome 6 open reading frame 139"""	C6orf139		16622420, 16622419	Standard	NM_018132		Approved	FLJ10545, CENP-Q	uc003ozh.1	Q7L2Z9	OTTHUMG00000014815	ENST00000335783.3:c.187G>A	6.37:g.49439805G>A	ENSP00000337289:p.Gly63Arg	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_018132	A8KAF1|Q6IN61|Q9NVS5	Missense_Mutation	SNP	ENST00000335783.3	37	CCDS4925.1	690	0.3159340659340659	205	0.4166666666666667	89	0.24585635359116023	112	0.1958041958041958	284	0.37467018469656993	G	4.427	0.079036	0.08533	0.391285	0.367209	ENSG00000031691	ENST00000335783;ENST00000371200	T	0.29142	1.58	4.44	-6.48	0.01896	.	0.695143	0.13866	N	0.357330	T	0.04363	0.0120	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.01281	0.0	T	0.33954	-0.9848	9	0.87932	D	0	-0.2957	9.5128	0.39087	0.5713:0.0989:0.3297:0.0	rs4267943;rs17186767;rs56644708;rs58394552;rs4267943	63	Q7L2Z9	CENPQ_HUMAN	R	63	ENSP00000337289:G63R	ENSP00000337289:G63R	G	+	1	0	CENPQ	49547764	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.832000	0.04400	-1.779000	0.01280	-1.345000	0.01243	GGA	G|0.653;A|0.347	0.347	strong		0.378	CENPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040855.2	NM_018132	
ITGBL1	9358	hgsc.bcm.edu	37	13	102220193	102220193	+	Missense_Mutation	SNP	G	G	T	rs1140605	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:102220193G>T	ENST00000376180.3	+	3	679	c.460G>T	c.(460-462)Gca>Tca	p.A154S	ITGBL1_ENST00000545560.2_Missense_Mutation_p.A13S|ITGBL1_ENST00000376162.3_Missense_Mutation_p.A61S	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	154	Cysteine-rich tandem repeats.		A -> S (in dbSNP:rs1140605).		cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CTGCTCTAATGCAGGTAAGAA	0.373													G|||	581	0.116014	0.2148	0.0692	5008	,	,		19898	0.125		0.0338	False		,,,				2504	0.091				p.A154S		Atlas-SNP	.											.	ITGBL1	83	.	0			c.G460T						PASS	.	G	SER/ALA	777,3629	313.3+/-293.0	77,623,1503	93.0	88.0	90.0		460	4.6	1.0	13	dbSNP_86	90	374,8226	122.2+/-181.2	11,352,3937	yes	missense	ITGBL1	NM_004791.1	99	88,975,5440	TT,TG,GG		4.3488,17.635,8.8498	benign	154/495	102220193	1151,11855	2203	4300	6503	SO:0001583	missense	9358	exon3			TCTAATGCAGGTA	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"""ten integrin EGF-like repeat domains protein"", ""ITGBL1, integrin beta-like 1"""	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.460G>T	13.37:g.102220193G>T	ENSP00000365351:p.Ala154Ser	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	28	20	0.714286	NM_004791	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Missense_Mutation	SNP	ENST00000376180.3	37	CCDS9499.1	237	0.10851648351648352	106	0.21544715447154472	27	0.07458563535911603	83	0.1451048951048951	21	0.027704485488126648	G	15.05	2.718934	0.48622	0.17635	0.043488	ENSG00000198542	ENST00000376180;ENST00000537118;ENST00000539955;ENST00000545560;ENST00000376162	D;D;D	0.92545	-3.06;-2.58;-3.06	5.44	4.58	0.56647	.	0.156948	0.56097	N	0.000025	T	0.00271	0.0008	L	0.31207	0.915	0.22226	P	0.999270791	B	0.26975	0.165	B	0.24848	0.056	T	0.30504	-0.9976	9	0.62326	D	0.03	.	14.1328	0.65266	0.0:0.0:0.8496:0.1504	rs1140605;rs2277441;rs3204596;rs17685895;rs52802409;rs1140605	154	O95965	ITGBL_HUMAN	S	154;62;13;13;61	ENSP00000365351:A154S;ENSP00000439903:A13S;ENSP00000365332:A61S	ENSP00000365332:A61S	A	+	1	0	ITGBL1	101018194	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	3.744000	0.55112	1.417000	0.47077	0.585000	0.79938	GCA	G|0.897;T|0.103	0.103	strong		0.373	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791	
KLK14	43847	hgsc.bcm.edu	37	19	51584916	51584916	+	Missense_Mutation	SNP	G	G	A	rs2569491	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51584916G>A	ENST00000156499.2	-	4	351	c.133C>T	c.(133-135)Cat>Tat	p.H45Y	KLK14_ENST00000391802.1_Missense_Mutation_p.H45Y			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	45	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		H -> Y (in dbSNP:rs2569491). {ECO:0000269|PubMed:15489334}.		epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		GTGCACGTATGGCCACCAATT	0.617													N|||	2032	0.405751	0.7436	0.2637	5008	,	,		16271	0.0952		0.3201	False		,,,				2504	0.4581				p.H45Y	GBM(117;2161 2172 2448 22911)	Atlas-SNP	.											.	KLK14	49	.	0			c.C133T						PASS	.		TYR/HIS	2483,1457		821,841,308	36.0	36.0	36.0		133	2.9	0.2	19	dbSNP_100	36	2584,5656		468,1648,2004	yes	missense	KLK14	NM_022046.4	83	1289,2489,2312	AA,AG,GG		31.3592,36.9797,41.601	benign	45/268	51584916	5067,7113	1970	4120	6090	SO:0001583	missense	43847	exon4			ACGTATGGCCACC	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"""Kallikreins"""	6362	protein-coding gene	gene with protein product		606135	"""kallikrein 14"""			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.133C>T	19.37:g.51584916G>A	ENSP00000156499:p.His45Tyr	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	78	31	0.397436	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Missense_Mutation	SNP	ENST00000156499.2	37	CCDS12823.2	714	0.3269230769230769	341	0.693089430894309	102	0.281767955801105	43	0.07517482517482517	228	0.3007915567282322	.	0.011	-1.694889	0.00731	0.630203	0.313592	ENSG00000129437	ENST00000156499;ENST00000391802	D;D	0.88818	-2.43;-2.43	5.04	2.91	0.33838	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.11698	0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	8	0.02654	T	1	.	4.6001	0.12348	0.5856:0.1572:0.2572:0.0	rs2569491;rs56473998;rs59256883;rs2569491	45	Q9P0G3	KLK14_HUMAN	Y	45	ENSP00000156499:H45Y;ENSP00000375678:H45Y	ENSP00000156499:H45Y	H	-	1	0	KLK14	56276728	0.992000	0.36948	0.154000	0.22540	0.287000	0.27160	2.724000	0.47285	0.411000	0.25702	-0.355000	0.07637	CAT	G|0.632;A|0.368	0.368	strong		0.617	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	
BAZ1A	11177	hgsc.bcm.edu	37	14	35242828	35242828	+	Silent	SNP	G	G	A	rs2275145	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:35242828G>A	ENST00000382422.2	-	19	3429	c.3102C>T	c.(3100-3102)gaC>gaT	p.D1034D	BAZ1A_ENST00000360310.1_Silent_p.D1034D|BAZ1A_ENST00000358716.4_Silent_p.D1002D			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1034					chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TCTCTTCTACGTCTTCATTCA	0.343													G|||	2581	0.515375	0.4387	0.5461	5008	,	,		16749	0.4911		0.5318	False		,,,				2504	0.6053				p.D1034D		Atlas-SNP	.											.	BAZ1A	128	.	0			c.C3102T						PASS	.	G	,	2076,2330	571.5+/-383.1	501,1074,628	175.0	160.0	165.0		3102,3006	3.2	0.6	14	dbSNP_100	165	4352,4246	579.9+/-391.0	1080,2192,1027	yes	coding-synonymous,coding-synonymous	BAZ1A	NM_013448.2,NM_182648.1	,	1581,3266,1655	AA,AG,GG		49.3836,47.1176,49.4309	,	1034/1557,1002/1525	35242828	6428,6576	2203	4299	6502	SO:0001819	synonymous_variant	11177	exon20			TTCTACGTCTTCA	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.3102C>T	14.37:g.35242828G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	214	211	0.985981	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			G|0.500;A|0.500	0.500	strong		0.343	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
C17orf112	100506650	hgsc.bcm.edu	37	17	51063068	51063068	+	Silent	SNP	A	A	G	rs12450084	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:51063068A>G	ENST00000441889.1	+	1	189	c.30A>G	c.(28-30)gtA>gtG	p.V10V		NM_001243552.1	NP_001230481.1	F2Z3M2	CQ112_HUMAN	chromosome 17 open reading frame 112	10																	CCACCTTCGTAGCATTTGCTG	0.398													A|||	488	0.0974441	0.0908	0.1801	5008	,	,		20248	0.1359		0.0099	False		,,,				2504	0.0982				p.V10V		Atlas-SNP	.											.	.	.	.	0			c.A30G						PASS	.																																			SO:0001819	synonymous_variant	100506650	exon1			CTTCGTAGCATTT		CCDS56040.1	17q22	2012-10-23			ENSG00000227011	ENSG00000227011			42963	protein-coding gene	gene with protein product							Standard	NM_001243552		Approved		uc021uaf.1	F2Z3M2	OTTHUMG00000132355	ENST00000441889.1:c.30A>G	17.37:g.51063068A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001243552		Silent	SNP	ENST00000441889.1	37	CCDS56040.1																																																																																			A|0.933;G|0.067	0.067	strong		0.398	C17orf112-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000255477.1	NM_001243552	
C3orf30	152405	hgsc.bcm.edu	37	3	118867047	118867047	+	Missense_Mutation	SNP	C	C	G	rs9289122	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:118867047C>G	ENST00000295622.1	+	2	1459	c.1419C>G	c.(1417-1419)gaC>gaG	p.D473E	IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_Intron|IGSF11_ENST00000425327.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	473			D -> E (in dbSNP:rs9289122).							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)		CAGAAATTGACCAAGGAAAGG	0.363													G|||	2352	0.469649	0.4818	0.4856	5008	,	,		18727	0.5119		0.4404	False		,,,				2504	0.4284				p.D473E		Atlas-SNP	.											.	C3orf30	64	.	0			c.C1419G						PASS	.	G	GLU/ASP	2098,2308	595.5+/-388.5	494,1110,599	81.0	88.0	86.0		1419	-2.6	0.0	3	dbSNP_119	86	4077,4523	590.5+/-392.7	984,2109,1207	yes	missense	C3orf30	NM_152539.2	45	1478,3219,1806	GG,GC,CC		47.407,47.6169,47.4781	benign	473/537	118867047	6175,6831	2203	4300	6503	SO:0001583	missense	152405	exon2			AATTGACCAAGGA	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.1419C>G	3.37:g.118867047C>G	ENSP00000295622:p.Asp473Glu	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	213	101	0.474178	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	1084	0.49633699633699635	256	0.5203252032520326	176	0.4861878453038674	303	0.5297202797202797	349	0.4604221635883905	G	0.041	-1.283573	0.01398	0.476169	0.47407	ENSG00000163424	ENST00000295622;ENST00000470341	T	0.11495	2.77	4.74	-2.61	0.06171	.	1.523470	0.04778	N	0.429264	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45629	-0.9248	9	0.02654	T	1	3.0155	0.727	0.00950	0.41:0.1284:0.2103:0.2513	rs9289122;rs52829346;rs9289122	473;473	E9PFE5;Q96M34	.;CC030_HUMAN	E	473	ENSP00000295622:D473E	ENSP00000295622:D473E	D	+	3	2	C3orf30	120349737	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.870000	0.01641	-0.718000	0.04949	-0.120000	0.15030	GAC	C|0.521;G|0.479	0.479	strong		0.363	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
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 GAIIx	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		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	201	16	0.079602	NM_001007249		Missense_Mutation	SNP		37																																																																																				A|0.996;G|0.005	0.005	strong	0	0.448								
GAL3ST1	9514	hgsc.bcm.edu	37	22	30953295	30953295	+	Missense_Mutation	SNP	C	C	T	rs2267161	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30953295C>T	ENST00000402321.1	-	2	402	c.85G>A	c.(85-87)Gtg>Atg	p.V29M	GAL3ST1_ENST00000406361.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000406955.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000443111.2_Missense_Mutation_p.V29M|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.V29M|GAL3ST1_ENST00000338911.5_Missense_Mutation_p.V29M			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	29			V -> M (in dbSNP:rs2267161). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.		galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						TAGGAGTACACCAGCAGCAGG	0.652													C|||	1552	0.309904	0.3646	0.2536	5008	,	,		17788	0.3502		0.326	False		,,,				2504	0.2178				p.V29M		Atlas-SNP	.											.	GAL3ST1	44	.	0			c.G85A						PASS	.	C	MET/VAL	1647,2759	502.0+/-365.1	326,995,882	89.0	91.0	91.0		85	1.1	0.9	22	dbSNP_100	91	2732,5868	436.8+/-358.4	420,1892,1988	yes	missense	GAL3ST1	NM_004861.1	21	746,2887,2870	TT,TC,CC		31.7674,37.3808,33.6691	benign	29/424	30953295	4379,8627	2203	4300	6503	SO:0001583	missense	9514	exon3			AGTACACCAGCAG	D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"""Sulfotransferases, membrane-bound"""	24240	protein-coding gene	gene with protein product	"""cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"""	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.85G>A	22.37:g.30953295C>T	ENSP00000385735:p.Val29Met	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	258	125	0.484496	NM_004861	Q96C63	Missense_Mutation	SNP	ENST00000402321.1	37	CCDS13879.1	691	0.3163919413919414	167	0.3394308943089431	90	0.24861878453038674	197	0.34440559440559443	237	0.31266490765171506	C	13.74	2.327313	0.41197	0.373808	0.317674	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111;ENST00000441967;ENST00000431313;ENST00000452827;ENST00000437282;ENST00000416358;ENST00000427899;ENST00000423299;ENST00000443136;ENST00000423371;ENST00000428682;ENST00000453479;ENST00000426220;ENST00000447224;ENST00000411821;ENST00000445645;ENST00000448604	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.18960	2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18;2.18	5.58	1.09	0.20402	.	0.269973	0.36268	N	0.002686	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.9999999999999958	B	0.25904	0.137	B	0.29716	0.106	T	0.49495	-0.8934	9	0.33141	T	0.24	-10.4855	7.6791	0.28502	0.2039:0.1191:0.677:0.0	rs2267161;rs17845430;rs17856591;rs17858302;rs61593263;rs2267161	29	Q99999	G3ST1_HUMAN	M	29	ENSP00000385825:V29M;ENSP00000385735:V29M;ENSP00000384122:V29M;ENSP00000384388:V29M;ENSP00000343234:V29M;ENSP00000385207:V29M;ENSP00000402587:V29M;ENSP00000390545:V29M;ENSP00000395080:V29M;ENSP00000405017:V29M;ENSP00000401426:V29M;ENSP00000391485:V29M;ENSP00000397092:V29M;ENSP00000391996:V29M;ENSP00000405381:V29M;ENSP00000401074:V29M;ENSP00000389876:V29M;ENSP00000398380:V29M;ENSP00000414542:V29M;ENSP00000412995:V29M;ENSP00000394912:V29M;ENSP00000399649:V29M;ENSP00000390068:V29M	ENSP00000343234:V29M	V	-	1	0	GAL3ST1	29283295	1.000000	0.71417	0.931000	0.37212	0.726000	0.41606	1.007000	0.29860	0.316000	0.23135	-0.147000	0.13772	GTG	C|0.671;T|0.329	0.329	strong		0.652	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861	
FXYD5	53827	hgsc.bcm.edu	37	19	35649281	35649281	+	Silent	SNP	A	A	G	rs1128882	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35649281A>G	ENST00000342879.3	+	3	955	c.177A>G	c.(175-177)ccA>ccG	p.P59P	FXYD5_ENST00000392218.2_Silent_p.P59P|FXYD5_ENST00000541435.2_Silent_p.P59P|FXYD5_ENST00000392219.2_Silent_p.P59P|FXYD5_ENST00000588699.1_Silent_p.P59P|FXYD5_ENST00000423817.3_Silent_p.P59P|FXYD5_ENST00000590686.1_Silent_p.P59P|FXYD5_ENST00000543307.1_Silent_p.P59P			Q96DB9	FXYD5_HUMAN	FXYD domain containing ion transport regulator 5	59					microvillus assembly (GO:0030033)|negative regulation of calcium-dependent cell-cell adhesion (GO:0046588)	integral component of membrane (GO:0016021)	actin binding (GO:0003779)|cadherin binding (GO:0045296)|ion channel activity (GO:0005216)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	all_lung(56;9.4e-09)|Lung NSC(56;1.4e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.75e-22)|OV - Ovarian serous cystadenocarcinoma(14;3.17e-20)|all cancers(14;7.07e-19)|LUSC - Lung squamous cell carcinoma(66;0.0221)			CCACCTCTCCAACCCCAACCT	0.537													a|||	1018	0.203275	0.1914	0.245	5008	,	,		16035	0.1171		0.1779	False		,,,				2504	0.3047				p.P59P		Atlas-SNP	.											.	FXYD5	41	.	0			c.A177G						PASS	.	G	,,	964,3442	364.1+/-316.8	100,764,1339	78.0	72.0	74.0		177,177,177	1.8	0.0	19	dbSNP_86	74	1469,7131	278.6+/-293.5	134,1201,2965	no	coding-synonymous,coding-synonymous,coding-synonymous	FXYD5	NM_001164605.1,NM_014164.5,NM_144779.2	,,	234,1965,4304	GG,GA,AA		17.0814,21.8793,18.7068	,,	59/179,59/179,59/179	35649281	2433,10573	2203	4300	6503	SO:0001819	synonymous_variant	53827	exon4			CTCTCCAACCCCA	AF161462	CCDS12447.1	19q13.12	2008-02-05	2002-01-14		ENSG00000089327	ENSG00000089327			4029	protein-coding gene	gene with protein product	"""dysadherin"""	606669	"""FXYD domain-containing ion transport regulator 5"""				Standard	NM_144779		Approved	OIT2	uc002nyg.2	Q96DB9	OTTHUMG00000048092	ENST00000342879.3:c.177A>G	19.37:g.35649281A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	35	0.388889	NM_014164	B7WNZ8|Q6UW44|Q9HC34|Q9P039	Silent	SNP	ENST00000342879.3	37	CCDS12447.1																																																																																			A|0.828;G|0.172	0.172	strong		0.537	FXYD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109443.1	NM_014164	
CCNT1	904	hgsc.bcm.edu	37	12	49087899	49087899	+	Silent	SNP	C	C	T	rs35678179	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49087899C>T	ENST00000261900.3	-	9	1320	c.1098G>A	c.(1096-1098)caG>caA	p.Q366Q		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	366					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						TTGAACCATCCTGTGGTAAGG	0.438													C|||	50	0.00998403	0.0008	0.013	5008	,	,		21831	0.0		0.0348	False		,,,				2504	0.0051				p.Q366Q		Atlas-SNP	.											.	CCNT1	55	.	0			c.G1098A						PASS	.	C		21,4385	28.1+/-56.4	0,21,2182	179.0	174.0	176.0		1098	-0.2	1.0	12	dbSNP_126	176	204,8396	88.1+/-150.5	1,202,4097	no	coding-synonymous	CCNT1	NM_001240.2		1,223,6279	TT,TC,CC		2.3721,0.4766,1.73		366/727	49087899	225,12781	2203	4300	6503	SO:0001819	synonymous_variant	904	exon9			ACCATCCTGTGGT	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1098G>A	12.37:g.49087899C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_001240	A9XU13|E7EX76|O60581	Silent	SNP	ENST00000261900.3	37	CCDS8766.1																																																																																			C|0.984;T|0.016	0.016	strong		0.438	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240	
MINK1	50488	hgsc.bcm.edu	37	17	4796286	4796286	+	Missense_Mutation	SNP	C	C	T	rs11556635	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4796286C>T	ENST00000355280.6	+	20	2520	c.2324C>T	c.(2323-2325)cCg>cTg	p.P775L	MINK1_ENST00000453408.3_Missense_Mutation_p.P755L|MINK1_ENST00000347992.7_Missense_Mutation_p.P738L	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						TCCTCCAAACCGGACAGCTCC	0.642													T|||	3507	0.70028	0.851	0.5461	5008	,	,		17870	0.9246		0.4066	False		,,,				2504	0.6769				p.P775L		Atlas-SNP	.											.	MINK1	110	.	0			c.C2324T						PASS	.	T	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	3005,1071		1139,727,172	23.0	29.0	27.0		2264,2213,2324,2213	5.0	1.0	17	dbSNP_120	27	3063,5283		587,1889,1697	yes	missense,missense,missense,missense	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	98,98,98,98	1726,2616,1869	TT,TC,CC		36.7002,26.2758,48.8488	benign,benign,benign,benign	755/1313,738/1296,775/1333,738/1304	4796286	6068,6354	2038	4173	6211	SO:0001583	missense	50488	exon20			CCAAACCGGACAG	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.2324C>T	17.37:g.4796286C>T	ENSP00000347427:p.Pro775Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_153827		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	1440	0.6593406593406593	435	0.8841463414634146	184	0.5082872928176796	527	0.9213286713286714	294	0.38786279683377306	T	11.58	1.681467	0.29872	0.737242	0.367002	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.72725	-0.66;-0.65;-0.68	4.98	4.98	0.66077	.	0.161017	0.41294	N	0.000918	T	0.00012	0.0000	N	0.00742	-1.23	0.42354	P	0.00761400000000001	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.37407	-0.9707	9	0.30854	T	0.27	.	8.9983	0.36066	0.0:0.0878:0.0:0.9122	rs11556635;rs12936135;rs58119627;rs11556635	738;755;775;738	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	L	775;755;738	ENSP00000347427:P775L;ENSP00000406487:P755L;ENSP00000269296:P738L	ENSP00000269296:P738L	P	+	2	0	MINK1	4737062	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.561000	0.36342	0.934000	0.37316	-0.254000	0.11334	CCG	C|0.313;T|0.687	0.687	strong		0.642	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
KLHL10	317719	hgsc.bcm.edu	37	17	40001659	40001659	+	Silent	SNP	T	T	C	rs34933374	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40001659T>C	ENST00000293303.4	+	3	1119	c.966T>C	c.(964-966)acT>acC	p.T322T		NM_152467.3	NP_689680.2	Q6JEL2	KLH10_HUMAN	kelch-like family member 10	322					cell morphogenesis (GO:0000902)|fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia morphogenesis (GO:0048808)|male gonad development (GO:0008584)|protein ubiquitination (GO:0016567)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26		Breast(137;0.000162)				TGAATGTTACTTGTGAGGAAG	0.502													T|||	103	0.0205671	0.0015	0.0504	5008	,	,		21132	0.0		0.0557	False		,,,				2504	0.0102				p.T322T		Atlas-SNP	.											.	KLHL10	67	.	0			c.T966C						PASS	.	T		36,3868		0,36,1916	80.0	78.0	79.0		966	1.2	1.0	17	dbSNP_126	79	519,7749		9,501,3624	no	coding-synonymous	KLHL10	NM_152467.3		9,537,5540	CC,CT,TT		6.2772,0.9221,4.5596		322/609	40001659	555,11617	1952	4134	6086	SO:0001819	synonymous_variant	317719	exon3			TGTTACTTGTGAG	AK057224	CCDS42340.1	17q21.2	2013-01-30	2013-01-30		ENSG00000161594	ENSG00000161594		"""Kelch-like"", ""BTB/POZ domain containing"""	18829	protein-coding gene	gene with protein product		608778	"""kelch-like 10 (Drosophila)"""				Standard	NM_152467		Approved	FLJ32662	uc010cxr.3	Q6JEL2	OTTHUMG00000152510	ENST00000293303.4:c.966T>C	17.37:g.40001659T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	91	50	0.549451	NM_152467	Q6NW28|Q96MC0	Silent	SNP	ENST00000293303.4	37	CCDS42340.1																																																																																			T|0.959;C|0.041	0.041	strong		0.502	KLHL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326535.1	NM_152467	
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 GAIIx	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_ENST00000394419.4_Missense_Mutation_p.T890S|ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S|ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S	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	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	46	25	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	
CLCA1	1179	hgsc.bcm.edu	37	1	86947975	86947975	+	Silent	SNP	A	A	T	rs1321694	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:86947975A>T	ENST00000234701.3	+	6	996	c.645A>T	c.(643-645)gtA>gtT	p.V215V	CLCA1_ENST00000394711.1_Silent_p.V215V			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	215					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)			NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		TCAATAAAGTAACAGGACTCT	0.398													A|||	1841	0.367612	0.2443	0.2939	5008	,	,		20995	0.505		0.3728	False		,,,				2504	0.4397				p.V215V		Atlas-SNP	.											.	CLCA1	109	.	0			c.A645T						PASS	.	A		1116,3290	398.8+/-331.0	140,836,1227	136.0	123.0	128.0		645	-2.2	0.1	1	dbSNP_88	128	3044,5556	467.7+/-367.1	534,1976,1790	no	coding-synonymous	CLCA1	NM_001285.3		674,2812,3017	TT,TA,AA		35.3953,25.3291,31.9852		215/915	86947975	4160,8846	2203	4300	6503	SO:0001819	synonymous_variant	1179	exon5			TAAAGTAACAGGA		CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"""chloride channel, calcium activated, family member 1"", ""chloride channel regulator 1"""			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.645A>T	1.37:g.86947975A>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Silent	SNP	ENST00000234701.3	37	CCDS709.1																																																																																			T|0.353;N|0.000	0.353	strong		0.398	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	
SLC52A1	55065	hgsc.bcm.edu	37	17	4936336	4936336	+	Silent	SNP	A	A	T	rs72822610	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4936336A>T	ENST00000424747.1	-	5	1975	c.1263T>A	c.(1261-1263)ctT>ctA	p.L421L	SLC52A1_ENST00000254853.5_Silent_p.L421L|SLC52A1_ENST00000512825.2_3'UTR	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	421					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										CACCGGCACCAAGCAGGGAGC	0.617													A|||	501	0.10004	0.1445	0.1066	5008	,	,		19163	0.0605		0.1441	False		,,,				2504	0.0307				p.L421L		Atlas-SNP	.											.	.	.	.	0			c.T1263A						PASS	.	A	,	598,3808	263.1+/-265.3	43,512,1648	83.0	79.0	81.0		1263,1263	-1.7	0.1	17	dbSNP_130	81	1231,7369	246.8+/-275.1	83,1065,3152	no	coding-synonymous,coding-synonymous	GPR172B	NM_001104577.1,NM_017986.3	,	126,1577,4800	TT,TA,AA		14.314,13.5724,14.0627	,	421/449,421/449	4936336	1829,11177	2203	4300	6503	SO:0001819	synonymous_variant	55065	exon5			GGCACCAAGCAGG	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"""Solute carriers"""	30225	protein-coding gene	gene with protein product	"""riboflavin transporter 1"""	607883	"""G protein-coupled receptor 172B"""	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.1263T>A	17.37:g.4936336A>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Silent	SNP	ENST00000424747.1	37	CCDS11066.1																																																																																			A|0.868;T|0.132	0.132	strong		0.617	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
MUC2	4583	hgsc.bcm.edu	37	11	1084362	1084362	+	Missense_Mutation	SNP	G	G	A	rs11245936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1084362G>A	ENST00000441003.2	+	19	2521	c.2494G>A	c.(2494-2496)Ggc>Agc	p.G832S	MUC2_ENST00000359061.5_Missense_Mutation_p.G832S	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	832			G -> S (in dbSNP:rs11245936).		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)		p.G832R(2)		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)	GTATTCTTCCGGCGCCAAGAT	0.642													G|||	273	0.0545128	0.0363	0.0461	5008	,	,		19772	0.0496		0.0905	False		,,,				2504	0.0532				p.G832S		Atlas-SNP	.											MUC2_ENST00000441003,mouth,carcinoma,0,2	MUC2	614	2	2	Substitution - Missense(2)	upper_aerodigestive_tract(2)	c.G2494A						scavenged	.	G	SER/GLY	168,4110		4,160,1975	82.0	92.0	89.0		2494	4.2	0.0	11	dbSNP_120	89	758,7724		34,690,3517	yes	missense	MUC2	NM_002457.2	56	38,850,5492	AA,AG,GG		8.9366,3.9271,7.2571	probably-damaging	832/2813	1084362	926,11834	2139	4241	6380	SO:0001583	missense	4583	exon19			TCTTCCGGCGCCA	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.2494G>A	11.37:g.1084362G>A	ENSP00000415183:p.Gly832Ser	Somatic	133	2	0.0150376		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		118	0.05402930402930403	15	0.03048780487804878	10	0.027624309392265192	26	0.045454545454545456	67	0.08839050131926121	G	12.65	2.003040	0.35320	0.039271	0.089366	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.28895	1.59;1.59	4.22	4.22	0.49857	.	0.000000	0.64402	D	0.000006	T	0.06962	0.0177	H	0.95004	3.61	0.22842	P	0.99866543	D	0.89917	1.0	D	0.87578	0.998	T	0.61686	-0.7012	9	0.87932	D	0	.	16.7715	0.85538	0.0:0.0:1.0:0.0	rs11245936;rs57489587;rs11245936	832	E7EUV1	.	S	832	ENSP00000415183:G832S;ENSP00000351956:G832S	ENSP00000351956:G832S	G	+	1	0	MUC2	1074362	1.000000	0.71417	0.038000	0.18304	0.006000	0.05464	6.454000	0.73493	2.175000	0.68902	0.555000	0.69702	GGC	G|0.945;A|0.055	0.055	strong		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
HELB	92797	hgsc.bcm.edu	37	12	66696410	66696410	+	Silent	SNP	C	C	T	rs3741604	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:66696410C>T	ENST00000247815.4	+	1	86	c.27C>T	c.(25-27)cgC>cgT	p.R9R		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	9					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		CGTACCTGCGCCAACTTCAGG	0.557													C|||	1519	0.303315	0.143	0.3256	5008	,	,		16059	0.1825		0.5308	False		,,,				2504	0.3947				p.R9R		Atlas-SNP	.											.	HELB	90	.	0			c.C27T						PASS	.	C		948,3458	360.9+/-315.4	100,748,1355	79.0	74.0	76.0		27	-5.0	0.0	12	dbSNP_107	76	4659,3941	604.2+/-394.8	1279,2101,920	no	coding-synonymous	HELB	NM_033647.2		1379,2849,2275	TT,TC,CC		45.8256,21.5161,43.1109		9/1088	66696410	5607,7399	2203	4300	6503	SO:0001819	synonymous_variant	92797	exon1			CCTGCGCCAACTT	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.27C>T	12.37:g.66696410C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	104	100	0.961538	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	37	CCDS8976.1																																																																																			C|0.620;T|0.380	0.380	strong		0.557	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
CALB2	794	hgsc.bcm.edu	37	16	71411636	71411636	+	Missense_Mutation	SNP	G	G	A	rs11545954	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:71411636G>A	ENST00000302628.4	+	4	405	c.328G>A	c.(328-330)Gcc>Acc	p.A110T	CALB2_ENST00000349553.5_Missense_Mutation_p.A110T	NM_001740.4	NP_001731.2	P22676	CALB2_HUMAN	calbindin 2	110	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.			A -> T (in Ref. 5; AAH15484). {ECO:0000305}.	cytosolic calcium ion homeostasis (GO:0051480)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18		Ovarian(137;0.125)				GGGCTCCAGCGCCGAGTTTAT	0.572													G|||	690	0.13778	0.1861	0.1052	5008	,	,		19624	0.0298		0.1292	False		,,,				2504	0.2157				p.A110T		Atlas-SNP	.											.	CALB2	46	.	0			c.G328A						PASS	.	G	THR/ALA,THR/ALA	751,3645	306.9+/-289.7	63,625,1510	94.0	84.0	88.0		328,328	1.2	0.9	16	dbSNP_120	88	1117,7483	232.6+/-266.2	72,973,3255	yes	missense,missense	CALB2	NM_001740.4,NM_007088.3	58,58	135,1598,4765	AA,AG,GG		12.9884,17.0837,14.3737	benign,benign	110/272,110/193	71411636	1868,11128	2198	4300	6498	SO:0001583	missense	794	exon4			TCCAGCGCCGAGT	X56667	CCDS10899.1	16q22.2	2013-01-10	2008-05-19		ENSG00000172137	ENSG00000172137		"""EF-hand domain containing"""	1435	protein-coding gene	gene with protein product	"""calretinin"""	114051	"""calbindin 2, 29kDa (calretinin)"""			1906795	Standard	NM_001740		Approved	CAL2	uc002faa.4	P22676	OTTHUMG00000137589	ENST00000302628.4:c.328G>A	16.37:g.71411636G>A	ENSP00000307508:p.Ala110Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_007088	A8K4Y1|Q53HD2|Q96BK4	Missense_Mutation	SNP	ENST00000302628.4	37	CCDS10899.1	264	0.12087912087912088	103	0.20934959349593496	51	0.1408839779005525	21	0.03671328671328671	89	0.11741424802110818	G	10.06	1.246691	0.22796	0.170837	0.129884	ENSG00000172137	ENST00000349553;ENST00000302628	T;T	0.68479	-0.33;-0.33	5.48	1.17	0.20885	EF-hand-like domain (1);	0.565985	0.20929	N	0.083122	T	0.00039	0.0001	L	0.41573	1.285	0.38374	P	0.05504600000000004	B;B	0.12013	0.005;0.003	B;B	0.11329	0.006;0.002	T	0.05517	-1.0880	9	0.27785	T	0.31	-1.4052	7.9909	0.30239	0.4237:0.0:0.5763:0.0	rs11545954;rs17851296;rs58508901	110;110	A6NER6;P22676	.;CALB2_HUMAN	T	110	ENSP00000340294:A110T;ENSP00000307508:A110T	ENSP00000307508:A110T	A	+	1	0	CALB2	69969137	0.811000	0.29063	0.926000	0.36857	0.935000	0.57460	0.203000	0.17315	0.057000	0.16193	0.603000	0.83216	GCC	G|0.867;A|0.133	0.133	strong		0.572	CALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268988.1	NM_001740	
ZC3H6	376940	hgsc.bcm.edu	37	2	113089267	113089267	+	Silent	SNP	T	T	C	rs7601200	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:113089267T>C	ENST00000409871.1	+	12	3173	c.2772T>C	c.(2770-2772)aaT>aaC	p.N924N	AC115115.2_ENST00000607612.1_RNA|ZC3H6_ENST00000343936.4_Silent_p.N924N	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	924							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						TTCATCAAAATACAGTGTCCA	0.398													C|||	3634	0.725639	0.9728	0.6455	5008	,	,		20981	0.7421		0.5477	False		,,,				2504	0.6145				p.N924N		Atlas-SNP	.											.	ZC3H6	93	.	0			c.T2772C						PASS	.	C		3350,364		1515,320,22	72.0	66.0	67.0		2772	0.1	0.0	2	dbSNP_116	67	4229,3971		1073,2083,944	no	coding-synonymous	ZC3H6	NM_198581.2		2588,2403,966	CC,CT,TT		48.4268,9.8008,36.3858		924/1190	113089267	7579,4335	1857	4100	5957	SO:0001819	synonymous_variant	376940	exon12			TCAAAATACAGTG	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.2772T>C	2.37:g.113089267T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_198581	A9JR71|Q6ZW96	Silent	SNP	ENST00000409871.1	37	CCDS46393.1																																																																																			T|0.273;C|0.727	0.727	strong		0.398	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
TAF1C	9013	hgsc.bcm.edu	37	16	84212928	84212928	+	Silent	SNP	G	G	A	rs3743642	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84212928G>A	ENST00000567759.1	-	14	2411	c.2229C>T	c.(2227-2229)ccC>ccT	p.P743P	TAF1C_ENST00000378541.4_Silent_p.P743P|TAF1C_ENST00000341690.6_Silent_p.P649P|TAF1C_ENST00000541676.1_Silent_p.P650P|TAF1C_ENST00000570117.1_Silent_p.P411P|TAF1C_ENST00000566732.1_Silent_p.P717P	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	743					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						TCTGTCTCCCGGGCTCCGAGG	0.672													G|||	771	0.153954	0.1914	0.0634	5008	,	,		13013	0.1498		0.1064	False		,,,				2504	0.2209				p.P743P		Atlas-SNP	.											.	TAF1C	60	.	0			c.C2229T						PASS	.	G	,	774,3600		65,644,1478	13.0	17.0	16.0		2229,1947	-3.5	0.0	16	dbSNP_107	16	772,7788		40,692,3548	no	coding-synonymous,coding-synonymous	TAF1C	NM_005679.3,NM_139353.2	,	105,1336,5026	AA,AG,GG		9.0187,17.6955,11.953	,	743/870,649/776	84212928	1546,11388	2187	4280	6467	SO:0001819	synonymous_variant	9013	exon14			TCTCCCGGGCTCC	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.2229C>T	16.37:g.84212928G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			G|0.867;A|0.133	0.133	strong		0.672	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
RARRES1	5918	hgsc.bcm.edu	37	3	158428642	158428642	+	Silent	SNP	G	G	A	rs2307064	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:158428642G>A	ENST00000237696.5	-	3	700	c.420C>T	c.(418-420)acC>acT	p.T140T	RARRES1_ENST00000498640.1_Intron|RARRES1_ENST00000479756.1_Silent_p.T140T	NM_206963.1	NP_996846.1	P49788	TIG1_HUMAN	retinoic acid receptor responder (tazarotene induced) 1	140					negative regulation of cell proliferation (GO:0008285)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)		Tretinoin(DB00755)	TTACATTGATGGTTGGTCTGG	0.413													G|||	806	0.160942	0.1225	0.1412	5008	,	,		20560	0.1498		0.2356	False		,,,				2504	0.1616				p.T140T		Atlas-SNP	.											.	RARRES1	22	.	0			c.C420T						PASS	.	G	,	604,3802	265.0+/-266.4	48,508,1647	201.0	184.0	190.0		420,420	1.8	0.0	3	dbSNP_100	190	2047,6553	356.6+/-330.4	253,1541,2506	no	coding-synonymous,coding-synonymous	RARRES1	NM_002888.2,NM_206963.1	,	301,2049,4153	AA,AG,GG		23.8023,13.7086,20.3829	,	140/229,140/295	158428642	2651,10355	2203	4300	6503	SO:0001819	synonymous_variant	5918	exon3			ATTGATGGTTGGT	U27185	CCDS3184.1, CCDS54665.1	3q25.32	2013-07-29			ENSG00000118849	ENSG00000118849			9867	protein-coding gene	gene with protein product	"""latexin-like"""	605090				8601727, 9270552	Standard	NM_002888		Approved	TIG1, LXNL	uc003fci.3	P49788	OTTHUMG00000158834	ENST00000237696.5:c.420C>T	3.37:g.158428642G>A		Somatic	368	0	0		WXS	Illumina HiSeq	Phase_I	318	146	0.459119	NM_206963	Q8N1D7	Silent	SNP	ENST00000237696.5	37	CCDS3184.1																																																																																			G|0.814;A|0.186	0.186	strong		0.413	RARRES1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352358.1		
GINS2	51659	hgsc.bcm.edu	37	16	85711860	85711860	+	Silent	SNP	C	C	T	rs1053328	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:85711860C>T	ENST00000253462.3	-	5	616	c.516G>A	c.(514-516)acG>acA	p.T172T		NM_016095.2	NP_057179.1	Q9Y248	PSF2_HUMAN	GINS complex subunit 2 (Psf2 homolog)	172					DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)	nucleoplasm (GO:0005654)				endometrium(2)|large_intestine(2)|lung(2)	6						GCTGGAGGTTCGTGCGGAGTT	0.537													C|||	1877	0.3748	0.2859	0.3156	5008	,	,		16030	0.494		0.3429	False		,,,				2504	0.4468				p.T172T		Atlas-SNP	.											GINS2,colon,carcinoma,-1,1	GINS2	15	1	0			c.G516A						PASS	.	C		1339,3057	447.5+/-348.4	199,941,1058	98.0	94.0	95.0		516	-6.7	0.9	16	dbSNP_86	95	3099,5501	474.0+/-368.7	563,1973,1764	no	coding-synonymous	GINS2	NM_016095.2		762,2914,2822	TT,TC,CC		36.0349,30.4595,34.149		172/186	85711860	4438,8558	2198	4300	6498	SO:0001819	synonymous_variant	51659	exon5			GAGGTTCGTGCGG	BC003186	CCDS10953.1	16q24.1	2008-02-05			ENSG00000131153	ENSG00000131153			24575	protein-coding gene	gene with protein product		610609				11042152, 10810093	Standard	NM_016095		Approved	PSF2, Pfs2	uc002fja.3	Q9Y248	OTTHUMG00000137646	ENST00000253462.3:c.516G>A	16.37:g.85711860C>T		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	NM_016095	D3DUM5|Q6IAG9	Silent	SNP	ENST00000253462.3	37	CCDS10953.1																																																																																			C|0.657;T|0.343	0.343	strong		0.537	GINS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269098.1	NM_016095	
RNF213	57674	hgsc.bcm.edu	37	17	78337584	78337584	+	Missense_Mutation	SNP	A	A	G	rs61740658	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78337584A>G	ENST00000582970.1	+	41	11887	c.11744A>G	c.(11743-11745)gAa>gGa	p.E3915G	CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.E1988G|RNF213_ENST00000508628.2_Missense_Mutation_p.E3964G|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3915			E -> G (in dbSNP:rs61740658). {ECO:0000269|PubMed:21048783}.		ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GTCATCAGGGAAGTCAGGTGA	0.612													A|||	406	0.0810703	0.1006	0.0576	5008	,	,		18004	0.0367		0.0885	False		,,,				2504	0.1094				p.E3915G		Atlas-SNP	.											.	RNF213	766	.	0			c.A11744G						PASS	.	A	GLY/GLU	357,4049	157.8+/-190.6	14,329,1860	35.0	29.0	31.0		11891	2.8	0.1	17	dbSNP_129	31	759,7841	158.5+/-212.0	44,671,3585	yes	missense	RNF213	NM_020914.4	98	58,1000,5445	GG,GA,AA		8.8256,8.1026,8.5807	benign	3964/5257	78337584	1116,11890	2203	4300	6503	SO:0001583	missense	57674	exon41			TCAGGGAAGTCAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11744A>G	17.37:g.78337584A>G	ENSP00000464087:p.Glu3915Gly	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	44	0.571429	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	156	0.07142857142857142	57	0.11585365853658537	24	0.06629834254143646	20	0.03496503496503497	55	0.07255936675461741	A	12.55	1.970631	0.34754	0.081026	0.088256	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.25579	1.79	5.03	2.81	0.32909	.	0.676131	0.15941	N	0.237167	T	0.00300	0.0009	L	0.55481	1.735	0.80722	P	0.0	B;P	0.40144	0.023;0.704	B;B	0.32762	0.023;0.152	T	0.07028	-1.0794	9	0.56958	D	0.05	.	8.7793	0.34781	0.845:0.0:0.155:0.0	rs61740658	3964;1988	C9JCP4;Q63HN8	.;RN213_HUMAN	G	3915;3964;1988	ENSP00000338218:E1988G	ENSP00000338218:E1988G	E	+	2	0	RNF213	75952179	0.026000	0.19158	0.079000	0.20413	0.024000	0.10985	1.513000	0.35823	0.761000	0.33130	-0.256000	0.11100	GAA	A|0.918;G|0.082	0.082	strong		0.612	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
TMIGD2	126259	hgsc.bcm.edu	37	19	4294623	4294623	+	Missense_Mutation	SNP	C	C	A	rs58237134	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4294623C>A	ENST00000301272.2	-	4	548	c.503G>T	c.(502-504)tGg>tTg	p.W168L	TMIGD2_ENST00000600114.1_Missense_Mutation_p.W48L|TMIGD2_ENST00000595645.1_Missense_Mutation_p.W168L|TMIGD2_ENST00000600349.1_Intron	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	168			W -> L (in dbSNP:rs58237134).		positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGGCACCCCACACGATCGC	0.637													A|||	894	0.178514	0.1543	0.1931	5008	,	,		13901	0.0873		0.2068	False		,,,				2504	0.2658				p.W168L		Atlas-SNP	.											.	TMIGD2	38	.	0			c.G503T						PASS	.	A	LEU/TRP,LEU/TRP	776,3630	751.6+/-412.2	69,638,1496	119.0	142.0	134.0		503,503	1.9	0.0	19	dbSNP_129	134	1785,6815	732.2+/-406.8	192,1401,2707	yes	missense,missense	TMIGD2	NM_001169126.1,NM_144615.2	61,61	261,2039,4203	AA,AC,CC		20.7558,17.6123,19.6909	benign,benign	168/279,168/283	4294623	2561,10445	2203	4300	6503	SO:0001583	missense	126259	exon4			GCACCCCACACGA	BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.503G>T	19.37:g.4294623C>A	ENSP00000301272:p.Trp168Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_144615	Q6UW59	Missense_Mutation	SNP	ENST00000301272.2	37	CCDS12126.1	374	0.17124542124542125	92	0.18699186991869918	71	0.19613259668508287	68	0.11888111888111888	143	0.18865435356200527	A	0.011	-1.720885	0.00700	0.176123	0.207558	ENSG00000167664	ENST00000301272	T	0.28454	1.61	2.94	1.86	0.25419	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39057	-0.9632	8	0.02654	T	1	.	7.1594	0.25654	0.536:0.464:0.0:0.0	rs58237134;rs61753894	168;168	Q96BF3-2;Q96BF3	.;TMIG2_HUMAN	L	168	ENSP00000301272:W168L	ENSP00000301272:W168L	W	-	2	0	TMIGD2	4245623	0.024000	0.19004	0.032000	0.17829	0.002000	0.02628	0.579000	0.23788	-0.036000	0.13669	-0.384000	0.06662	TGG	C|0.806;A|0.194	0.194	strong		0.637	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615	
STK31	56164	hgsc.bcm.edu	37	7	23757162	23757162	+	Missense_Mutation	SNP	G	G	C	rs6945306	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:23757162G>C	ENST00000355870.3	+	4	332	c.213G>C	c.(211-213)caG>caC	p.Q71H	STK31_ENST00000428484.1_Missense_Mutation_p.Q48H|STK31_ENST00000433467.2_Missense_Mutation_p.Q71H|STK31_ENST00000354639.3_Missense_Mutation_p.Q48H	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	71			Q -> H (in dbSNP:rs6945306). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.			acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTTGCCCCCAGGCCAGTTCAG	0.358																																					p.Q71H		Atlas-SNP	.											.	STK31	175	.	0			c.G213C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN	731,3675	299.8+/-286.0	72,587,1544	65.0	66.0	66.0		144,213,144	3.0	0.9	7	dbSNP_116	66	2492,6108	404.5+/-348.2	368,1756,2176	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	24,24,24	440,2343,3720	CC,CG,GG		28.9767,16.591,24.7809	benign,benign,benign	48/997,71/1020,48/997	23757162	3223,9783	2203	4300	6503	SO:0001583	missense	56164	exon4			CCCCCAGGCCAGT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.213G>C	7.37:g.23757162G>C	ENSP00000348132:p.Gln71His	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	162	40	0.246914	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	552|552	0.25274725274725274|0.25274725274725274	66|66	0.13414634146341464|0.13414634146341464	66|66	0.18232044198895028|0.18232044198895028	203|203	0.3548951048951049|0.3548951048951049	217|217	0.2862796833773087|0.2862796833773087	G|G	5.213|5.213	0.224817|0.224817	0.09916|0.09916	0.16591|0.16591	0.289767|0.289767	ENSG00000196335|ENSG00000196335	ENST00000422637|ENST00000355870;ENST00000456014;ENST00000433467;ENST00000354639;ENST00000444333;ENST00000428484	.|T;T;T;T;T;T	.|0.09817	.|2.94;2.94;2.94;2.94;2.94;2.94	5.23|5.23	2.95|2.95	0.34219|0.34219	.|Maternal tudor protein (1);	.|0.983616	.|0.08296	.|N	.|0.967629	.|T	.|0.00012	.|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.48087|0.48087	P|P	4.1400000000002546E-4|4.1400000000002546E-4	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.10450	.|0.001;0.005	.|T	.|0.48514	.|-0.9029	.|9	.|0.27785	.|T	.|0.31	.|-0.6565	6.0676|6.0676	0.19871|0.19871	0.1394:0.0:0.4391:0.4215|0.1394:0.0:0.4391:0.4215	rs6945306;rs11558824;rs17854998;rs52815535;rs6945306|rs6945306;rs11558824;rs17854998;rs52815535;rs6945306	.|71;71	.|B4DZ06;Q9BXU1	.|.;STK31_HUMAN	.|H	-1|71;48;71;48;48;48	.|ENSP00000348132:Q71H;ENSP00000389340:Q48H;ENSP00000411852:Q71H;ENSP00000346660:Q48H;ENSP00000398413:Q48H;ENSP00000406146:Q48H	.|ENSP00000346660:Q48H	.|Q	+|+	.|3	.|2	STK31|STK31	23723687|23723687	0.998000|0.998000	0.40836|0.40836	0.888000|0.888000	0.34837|0.34837	0.163000|0.163000	0.22366|0.22366	1.356000|1.356000	0.34079|0.34079	0.838000|0.838000	0.34948|0.34948	-0.518000|-0.518000	0.04402|0.04402	.|CAG	G|0.742;C|0.258	0.258	strong		0.358	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
ALMS1	7840	hgsc.bcm.edu	37	2	73717656	73717656	+	Missense_Mutation	SNP	A	A	G	rs10193972	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73717656A>G	ENST00000264448.6	+	10	8678	c.8567A>G	c.(8566-8568)aAc>aGc	p.N2856S	ALMS1_ENST00000409009.1_Missense_Mutation_p.N2814S|AC096546.1_ENST00000408160.1_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2856			N -> S (in dbSNP:rs10193972).		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						CTAGGAGTAAACAGATCGAGT	0.403													G|||	1794	0.358227	0.8578	0.3905	5008	,	,		20831	0.0089		0.2266	False		,,,				2504	0.1554				p.N2856S		Atlas-SNP	.											.	ALMS1	384	.	0			c.A8567G						PASS	.	G	SER/ASN	2743,1043		1007,729,157	78.0	74.0	75.0		8567	0.2	0.2	2	dbSNP_119	75	1947,6251		221,1505,2373	yes	missense	ALMS1	NM_015120.4	46	1228,2234,2530	GG,GA,AA		23.7497,27.5489,39.1355	benign	2856/4168	73717656	4690,7294	1893	4099	5992	SO:0001583	missense	7840	exon10			GAGTAAACAGATC	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.8567A>G	2.37:g.73717656A>G	ENSP00000264448:p.Asn2856Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	108	81	0.75	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	730	0.3342490842490842	418	0.8495934959349594	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	G	1.761	-0.486860	0.04352	0.724511	0.237497	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.06528	3.29;3.29	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	4.000000000004E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04900	-1.0919	7	0.16896	T	0.51	.	.	.	.	rs10193972;rs17434201;rs17848864;rs52794198;rs60480147;rs10193972	2856;2814;2856	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	S	2814;2856	ENSP00000386627:N2814S;ENSP00000264448:N2856S	ENSP00000264448:N2856S	N	+	2	0	ALMS1	73571164	0.532000	0.26346	0.192000	0.23308	0.725000	0.41563	-0.691000	0.05133	-0.690000	0.05142	-0.684000	0.03749	AAC	A|0.675;G|0.325	0.325	strong		0.403	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
TGFBI	7045	hgsc.bcm.edu	37	5	135392426	135392426	+	Silent	SNP	T	T	C	rs4669	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:135392426T>C	ENST00000442011.2	+	12	1781	c.1620T>C	c.(1618-1620)ttT>ttC	p.F540F	TGFBI_ENST00000305126.8_Silent_p.F540F|TGFBI_ENST00000508076.1_5'Flank	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	540	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082}.		F -> S (in CDL3A). {ECO:0000269|PubMed:15790870}.|Missing (in CDRB). {ECO:0000269|PubMed:10660331, ECO:0000269|PubMed:11923233}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACACAGTCTTTGCTCCCACAA	0.498													C|||	2106	0.420527	0.6687	0.3703	5008	,	,		17729	0.3433		0.2584	False		,,,				2504	0.3671				p.F540F		Atlas-SNP	.											.	TGFBI	76	.	0			c.T1620C						PASS	.	C		2356,1582		707,942,320	78.0	82.0	81.0		1620	-2.7	0.9	5	dbSNP_52	81	2249,6075		315,1619,2228	no	coding-synonymous	TGFBI	NM_000358.2		1022,2561,2548	CC,CT,TT		27.0183,40.1727,37.555		540/684	135392426	4605,7657	1969	4162	6131	SO:0001819	synonymous_variant	7045	exon12			AGTCTTTGCTCCC	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.1620T>C	5.37:g.135392426T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	205	100	0.487805	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1	852	0.3901098901098901	328	0.6666666666666666	128	0.35359116022099446	195	0.3409090909090909	201	0.26517150395778366	C	9.636	1.137809	0.21123	0.598273	0.270183	ENSG00000120708	ENST00000514554	.	.	.	5.82	-2.69	0.06022	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.28522	-1.0041	3	.	.	.	-1.5181	14.5145	0.67809	0.0:0.3811:0.0:0.6189	rs4669;rs1054164;rs2228406;rs3173019;rs7727187;rs17403539;rs17849263;rs17849891;rs56414978;rs59886758;rs4669	.	.	.	R	258	.	.	C	+	1	0	TGFBI	135420325	0.441000	0.25626	0.868000	0.34077	0.823000	0.46562	-0.359000	0.07632	-1.131000	0.02910	-1.551000	0.00897	TGC	T|0.599;C|0.401	0.401	strong		0.498	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
MYH13	8735	hgsc.bcm.edu	37	17	10231417	10231417	+	Silent	SNP	C	C	T	rs2277644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:10231417C>T	ENST00000418404.3	-	21	2620	c.2457G>A	c.(2455-2457)caG>caA	p.Q819Q	MYH13_ENST00000252172.4_Silent_p.Q819Q|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	819					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						GGATGTTGTACTGGATGCAGA	0.517											OREG0024177	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1379	0.275359	0.1974	0.2291	5008	,	,		20047	0.5159		0.167	False		,,,				2504	0.2771				p.Q819Q		Atlas-SNP	.											.	MYH13	533	.	0			c.G2457A						PASS	.	C		852,3536	312.5+/-292.6	85,682,1427	75.0	76.0	75.0		2457	4.0	1.0	17	dbSNP_100	75	1511,7085	278.0+/-293.2	141,1229,2928	no	coding-synonymous	MYH13	NM_003802.2		226,1911,4355	TT,TC,CC		17.5779,19.4166,18.1993		819/1939	10231417	2363,10621	2194	4298	6492	SO:0001819	synonymous_variant	8735	exon22			GTTGTACTGGATG	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.2457G>A	17.37:g.10231417C>T		Somatic	90	0	0	663	WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			C|0.729;T|0.271	0.271	strong		0.517	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	
SEMA4D	10507	hgsc.bcm.edu	37	9	91978783	91978783	+	Silent	SNP	G	G	A	rs45515192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:91978783G>A	ENST00000420987.1	-	18	2411	c.1965C>T	c.(1963-1965)ccC>ccT	p.P655P	SEMA4D_ENST00000339861.4_Silent_p.P655P|SEMA4D_ENST00000343780.4_Silent_p.P655P|SEMA4D_ENST00000455551.2_Silent_p.P655P|SEMA4D_ENST00000469653.1_5'UTR|SEMA4D_ENST00000420101.2_Silent_p.P40P	NM_001142287.1	NP_001135759.1	Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	0					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						CCCTGCCATCGGGCAGTGCAT	0.597													G|||	765	0.152756	0.0091	0.3646	5008	,	,		21139	0.2331		0.1203	False		,,,				2504	0.1472				p.P655P		Atlas-SNP	.											.	SEMA4D	81	.	0			c.C1965T						PASS	.	G		133,4273	95.3+/-134.0	3,127,2073	88.0	77.0	81.0		1965	-6.7	0.0	9	dbSNP_127	81	1143,7457	235.7+/-268.2	83,977,3240	no	coding-synonymous	SEMA4D	NM_001142287.1		86,1104,5313	AA,AG,GG		13.2907,3.0186,9.8109		655/739	91978783	1276,11730	2203	4300	6503	SO:0001819	synonymous_variant	10507	exon19			GCCATCGGGCAGT	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000420987.1:c.1965C>T	9.37:g.91978783G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_001142287	B2RPM6|Q7Z5S4|Q8N8B0	Silent	SNP	ENST00000420987.1	37	CCDS47991.1																																																																																			G|0.883;A|0.117	0.117	strong		0.597	SEMA4D-203	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402418.2	NM_006378	
NGFR	4804	hgsc.bcm.edu	37	17	47588000	47588000	+	Silent	SNP	C	C	T	rs11466155	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:47588000C>T	ENST00000172229.3	+	4	920	c.795C>T	c.(793-795)ggC>ggT	p.G265G	RP5-1029K10.2_ENST00000514506.1_RNA|NGFR_ENST00000504201.1_Silent_p.G171G	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	265					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					TGGTTGTGGGCCTTGTGGCCT	0.582													C|||	1151	0.229832	0.0477	0.3141	5008	,	,		20799	0.0823		0.3231	False		,,,				2504	0.4724				p.G265G		Atlas-SNP	.											NGFR,colon,carcinoma,0,2	NGFR	46	2	0			c.C795T						PASS	.	C		398,4008	197.7+/-221.8	15,368,1820	117.0	104.0	108.0		795	-0.8	1.0	17	dbSNP_120	108	2848,5752	448.3+/-361.8	484,1880,1936	no	coding-synonymous	NGFR	NM_002507.3		499,2248,3756	TT,TC,CC		33.1163,9.0331,24.9577		265/428	47588000	3246,9760	2203	4300	6503	SO:0001819	synonymous_variant	4804	exon4			TGTGGGCCTTGTG	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	7809	protein-coding gene	gene with protein product	"""low affinity nerve growth factor receptor"", ""TNFR superfamily, member 16"""	162010	"""nerve growth factor receptor (TNFR superfamily, member 16)"""			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.795C>T	17.37:g.47588000C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_002507	B2R961|B4E096	Silent	SNP	ENST00000172229.3	37	CCDS11549.1																																																																																			C|0.763;T|0.237	0.237	strong		0.582	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		
AP3B1	8546	hgsc.bcm.edu	37	5	77473165	77473165	+	Silent	SNP	A	A	G	rs4532349	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:77473165A>G	ENST00000255194.6	-	9	1213	c.1038T>C	c.(1036-1038)aaT>aaC	p.N346N	AP3B1_ENST00000519295.1_Silent_p.N297N	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	346					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		TGACCTACCTATTGCTACGAA	0.328									Hermansky-Pudlak syndrome				A|||	715	0.142772	0.0968	0.3026	5008	,	,		17278	0.0724		0.1968	False		,,,				2504	0.1084				p.N346N		Atlas-SNP	.											AP3B1,colon,carcinoma,0,1	AP3B1	94	1	0			c.T1038C						PASS	.	A		529,3877	240.9+/-251.5	39,451,1713	96.0	92.0	94.0		1038	3.0	1.0	5	dbSNP_111	94	1905,6695	338.0+/-322.5	232,1441,2627	no	coding-synonymous	AP3B1	NM_003664.3		271,1892,4340	GG,GA,AA		22.1512,12.0064,18.7144		346/1095	77473165	2434,10572	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon9	Familial Cancer Database	HPS, HPS1-8	CTACCTATTGCTA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1038T>C	5.37:g.77473165A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.832;G|0.168	0.168	strong		0.328	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
PPL	5493	hgsc.bcm.edu	37	16	4934549	4934549	+	Silent	SNP	G	G	A	rs1049208	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4934549G>A	ENST00000345988.2	-	22	4196	c.4107C>T	c.(4105-4107)agC>agT	p.S1369S	PPL_ENST00000590782.2_Silent_p.S1367S	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1369					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CGGCAAAGGCGCTCGCCTCGG	0.682													G|||	2035	0.40635	0.0598	0.4726	5008	,	,		15868	0.6339		0.5298	False		,,,				2504	0.4663				p.S1369S		Atlas-SNP	.											.	PPL	168	.	0			c.C4107T						PASS	.	G		574,3820	251.2+/-258.0	41,492,1664	100.0	109.0	106.0		4107	-0.4	0.3	16	dbSNP_86	106	4754,3846	604.9+/-394.9	1316,2122,862	no	coding-synonymous	PPL	NM_002705.4		1357,2614,2526	AA,AG,GG		44.7209,13.0633,41.0035		1369/1757	4934549	5328,7666	2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			AAAGGCGCTCGCC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.4107C>T	16.37:g.4934549G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			G|0.589;A|0.411	0.411	strong		0.682	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
C16orf46	123775	hgsc.bcm.edu	37	16	81095091	81095091	+	Missense_Mutation	SNP	A	A	G	rs7198494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:81095091A>G	ENST00000299578.5	-	4	1098	c.863T>C	c.(862-864)aTa>aCa	p.I288T	C16orf46_ENST00000378611.4_Missense_Mutation_p.I288T|C16orf46_ENST00000444657.3_5'Flank|RP11-303E16.8_ENST00000564536.1_RNA	NM_152337.2	NP_689550.2	Q6P387	CP046_HUMAN	chromosome 16 open reading frame 46	288			I -> T (in dbSNP:rs7198494).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|large_intestine(3)|lung(9)|prostate(1)|stomach(1)|urinary_tract(1)	18						CAGCAGGGATATCTGGGCCGC	0.577													G|||	790	0.157748	0.2791	0.1643	5008	,	,		17378	0.0198		0.2048	False		,,,				2504	0.0828				p.I288T		Atlas-SNP	.											.	C16orf46	57	.	0			c.T863C						PASS	.	G	THR/ILE,THR/ILE	1168,3236	707.8+/-407.5	143,882,1177	112.0	107.0	108.0		863,863	2.4	0.0	16	dbSNP_116	108	1943,6657	716.5+/-406.1	224,1495,2581	yes	missense,missense	C16orf46	NM_001100873.1,NM_152337.2	89,89	367,2377,3758	GG,GA,AA		22.593,26.5213,23.9234	benign,benign	288/389,288/396	81095091	3111,9893	2202	4300	6502	SO:0001583	missense	123775	exon3			AGGGATATCTGGG	BC064143	CCDS10932.1, CCDS42201.1	16q23.2	2012-10-09			ENSG00000166455	ENSG00000166455			26525	protein-coding gene	gene with protein product							Standard	NM_152337		Approved	FLJ32702	uc002fgc.4	Q6P387	OTTHUMG00000137629	ENST00000299578.5:c.863T>C	16.37:g.81095091A>G	ENSP00000299578:p.Ile288Thr	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	199	95	0.477387	NM_001100873	Q96MA7	Missense_Mutation	SNP	ENST00000299578.5	37	CCDS10932.1	372	0.17032967032967034	140	0.2845528455284553	69	0.19060773480662985	13	0.022727272727272728	150	0.19788918205804748	G	0.004	-2.315748	0.00235	0.265213	0.22593	ENSG00000166455	ENST00000378611;ENST00000444657;ENST00000299578	T;T	0.12774	2.65;2.65	5.53	2.4	0.29515	.	0.813420	0.11056	N	0.604525	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46624	-0.9178	9	0.02654	T	1	.	3.4169	0.07378	0.1687:0.1419:0.5584:0.131	rs7198494;rs61064956;rs7198494	288;288	Q6P387-2;Q6P387	.;CP046_HUMAN	T	288;15;288	ENSP00000367874:I288T;ENSP00000299578:I288T	ENSP00000299578:I288T	I	-	2	0	C16orf46	79652592	0.008000	0.16893	0.003000	0.11579	0.036000	0.12997	1.169000	0.31871	0.717000	0.32145	-0.213000	0.12676	ATA	A|0.792;G|0.208	0.208	strong		0.577	C16orf46-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269054.2	NM_152337	
AEN	64782	hgsc.bcm.edu	37	15	89169614	89169614	+	Silent	SNP	A	A	G	rs3743476	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89169614A>G	ENST00000332810.3	+	2	325	c.174A>G	c.(172-174)gaA>gaG	p.E58E	AEN_ENST00000379231.3_Silent_p.E58E	NM_022767.3	NP_073604.3	Q8WTP8	AEN_HUMAN	apoptosis enhancing nuclease	58					intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			NS(1)|kidney(1)|large_intestine(1)|lung(4)	7						TGCCTCCAGAACCAGGGTCCT	0.642													A|||	991	0.197883	0.0825	0.2061	5008	,	,		15751	0.1538		0.3618	False		,,,				2504	0.2249				p.E58E		Atlas-SNP	.											.	AEN	29	.	0			c.A174G						PASS	.	A		473,3925	207.8+/-229.1	25,423,1751	30.0	26.0	27.0		174	0.8	0.0	15	dbSNP_107	27	3014,5582	419.5+/-353.1	543,1928,1827	no	coding-synonymous	AEN	NM_022767.3		568,2351,3578	GG,GA,AA		35.0628,10.7549,26.8355		58/326	89169614	3487,9507	2199	4298	6497	SO:0001819	synonymous_variant	64782	exon2			TCCAGAACCAGGG	BC020988	CCDS10344.1	15q26.1	2008-07-15	2008-07-15	2008-07-15	ENSG00000181026	ENSG00000181026			25722	protein-coding gene	gene with protein product		610177	"""interferon stimulated exonuclease gene 20kDa-like 1"""	ISG20L1		18264133, 16171785	Standard	NM_022767		Approved	FLJ12484, FLJ12562	uc002bmt.2	Q8WTP8	OTTHUMG00000148681	ENST00000332810.3:c.174A>G	15.37:g.89169614A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_022767	C9J571|Q9BSA5|Q9H9X7	Silent	SNP	ENST00000332810.3	37	CCDS10344.1																																																																																			A|0.763;G|0.237	0.237	strong		0.642	AEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309071.1	NM_022767	
PNPLA5	150379	hgsc.bcm.edu	37	22	44287629	44287629	+	Silent	SNP	G	G	A	rs74445350	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44287629G>A	ENST00000597664.1	-	1	261	c.132C>T	c.(130-132)cgC>cgT	p.R44R	PNPLA5_ENST00000381198.2_Silent_p.R44R|PNPLA5_ENST00000593866.1_Silent_p.R44R|PNPLA5_ENST00000216177.4_Silent_p.R44R			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	44	Patatin.				lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)	16		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				AACCGTAGATGCGGCGGGCGC	0.726													G|||	667	0.133187	0.0053	0.1297	5008	,	,		12691	0.248		0.1034	False		,,,				2504	0.2209				p.R44R		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C132T						PASS	.	G	,	70,3548		0,70,1739	5.0	5.0	5.0		132,132	-3.6	0.1	22	dbSNP_131	5	524,6092		14,496,2798	no	coding-synonymous,coding-synonymous	PNPLA5	NM_001177675.1,NM_138814.3	,	14,566,4537	AA,AG,GG		7.9202,1.9348,5.8042	,	44/316,44/430	44287629	594,9640	1809	3308	5117	SO:0001819	synonymous_variant	150379	exon1			GTAGATGCGGCGG	Z97055	CCDS14053.1, CCDS54537.1	22q13.31	2009-01-12			ENSG00000100341	ENSG00000100341		"""Patatin-like phospholipase domain containing"""	24888	protein-coding gene	gene with protein product		611589				16799181, 19029121	Standard	NM_138814		Approved	dJ388M5.4, GS2L	uc003beg.3	Q7Z6Z6	OTTHUMG00000030779	ENST00000597664.1:c.132C>T	22.37:g.44287629G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Silent	SNP	ENST00000597664.1	37																																																																																				G|0.878;A|0.122	0.122	strong		0.726	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814	
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 GAIIx	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		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	32	10	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
LRPPRC	10128	hgsc.bcm.edu	37	2	44161960	44161960	+	Silent	SNP	T	T	C	rs4494798	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44161960T>C	ENST00000260665.7	-	24	2619	c.2562A>G	c.(2560-2562)gtA>gtG	p.V854V		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	854					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TCCTTGGTAATACTTTATACT	0.348													T|||	70	0.0139776	0.0008	0.0086	5008	,	,		18209	0.0		0.0119	False		,,,				2504	0.0521				p.V854V		Atlas-SNP	.											.	LRPPRC	105	.	0			c.A2562G						PASS	.	T		7,4399	11.4+/-27.6	0,7,2196	102.0	100.0	101.0		2562	-1.0	0.0	2	dbSNP_111	101	136,8464	68.0+/-130.5	1,134,4165	no	coding-synonymous	LRPPRC	NM_133259.3		1,141,6361	CC,CT,TT		1.5814,0.1589,1.0995		854/1395	44161960	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	10128	exon24			TGGTAATACTTTA	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.2562A>G	2.37:g.44161960T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			T|0.988;C|0.012	0.012	strong		0.348	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
BAD	572	hgsc.bcm.edu	37	11	64039175	64039175	+	Silent	SNP	G	G	A	rs2286615	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64039175G>A	ENST00000394532.3	-	2	558	c.288C>T	c.(286-288)cgC>cgT	p.R96R	BAD_ENST00000309032.3_Silent_p.R96R|BAD_ENST00000394531.3_Missense_Mutation_p.A143V|BAD_ENST00000544785.1_Intron	NM_004322.3	NP_004313.1	Q92934	BAD_HUMAN	BCL2-associated agonist of cell death	96					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ADP metabolic process (GO:0046031)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|ATP metabolic process (GO:0046034)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to chromate (GO:0071247)|cellular response to hypoxia (GO:0071456)|cellular response to lipid (GO:0071396)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose catabolic process (GO:0006007)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|pore complex assembly (GO:0046931)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of autophagy (GO:0010508)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane potential (GO:0010918)|positive regulation of neuron death (GO:1901216)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to amino acid (GO:0043200)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to oleic acid (GO:0034201)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|suppression by virus of host apoptotic process (GO:0019050)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|lipid binding (GO:0008289)|phospholipid binding (GO:0005543)|protein kinase binding (GO:0019901)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4						CCGAGCGCGAGCGGCCCCGAA	0.692													G|||	359	0.0716853	0.0159	0.0807	5008	,	,		11474	0.0565		0.1581	False		,,,				2504	0.0675				p.R96R		Atlas-SNP	.											BAD,NS,carcinoma,0,1	BAD	8	1	0			c.C288T						PASS	.	G	,	181,4173		6,169,2002	20.0	18.0	19.0		288,288	3.9	1.0	11	dbSNP_100	19	1290,7234		101,1088,3073	no	coding-synonymous,coding-synonymous	BAD	NM_004322.3,NM_032989.2	,	107,1257,5075	AA,AG,GG		15.1337,4.1571,11.4226	,	96/169,96/169	64039175	1471,11407	2177	4262	6439	SO:0001819	synonymous_variant	572	exon3			GCGCGAGCGGCCC	AF021792	CCDS8065.1	11q13.1	2014-03-07	2008-08-19		ENSG00000002330	ENSG00000002330			936	protein-coding gene	gene with protein product		603167				8929532	Standard	NM_004322		Approved	BCL2L8, BBC2	uc001nzd.3	Q92934	OTTHUMG00000134302	ENST00000394532.3:c.288C>T	11.37:g.64039175G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_032989	O14803|Q6FH21	Silent	SNP	ENST00000394532.3	37	CCDS8065.1	204	0.09340659340659341	11	0.022357723577235773	32	0.08839779005524862	40	0.06993006993006994	121	0.15963060686015831	G	14.80	2.644886	0.47258	0.041571	0.151337	ENSG00000002330	ENST00000394531	.	.	.	5.72	3.87	0.44632	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.17806	-1.0357	4	0.87932	D	0	-26.3086	9.227	0.37414	0.1676:0.0:0.8324:0.0	rs2286615;rs3209943;rs3729932	.	.	.	V	143	.	ENSP00000378039:A143V	A	-	2	0	BAD	63795751	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	0.795000	0.26972	0.788000	0.33755	-1.020000	0.02445	GCT	G|0.905;A|0.095	0.095	strong		0.692	BAD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259180.2	NM_032989	
Unknown	0	hgsc.bcm.edu	37	13	103410914	103410914	+	IGR	SNP	A	A	T	rs12855785	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103410914A>T								LINC00283 (13340 upstream) : TEX30 (7425 downstream)																							CTTTTGGGGCAACTGTCTTCC	0.284													A|||	1910	0.38139	0.1044	0.5029	5008	,	,		16341	0.4097		0.5089	False		,,,				2504	0.5092				p.C82S		Atlas-SNP	.											.	.	.	.	0			c.T244A						PASS	.	A	SER/CYS	262,1122		28,206,458	49.0	42.0	44.0		244	0.8	0.0	13	dbSNP_121	44	1592,1586		410,772,407	yes	missense	CCDC168	NM_001146197.1	112	438,978,865	TT,TA,AA		49.9056,18.9306,40.6401		82/7082	103410914	1854,2708	692	1589	2281	SO:0001628	intergenic_variant	643677	exon2			TGGGGCAACTGTC																													13.37:g.103410914A>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	41	27	0.658537	NM_001146197		Missense_Mutation	SNP		37																																																																																				A|0.627;T|0.373	0.373	strong	0	0.284								
SPRY3	10251	hgsc.bcm.edu	37	X	155004280	155004280	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:155004280A>G	ENST00000302805.2	+	2	1178	c.747A>G	c.(745-747)caA>caG	p.Q249Q		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	249	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATCTGTGCCAACAGGGCTATG	0.592													A|||	970	0.19369	0.2489	0.1744	5008	,	,		20237	0.0179		0.2992	False		,,,				2504	0.2055				p.Q249Q		Atlas-SNP	.											.	SPRY3	52	.	0			c.A747G						PASS	.	A		1040,3366		132,776,1295	207.0	192.0	197.0		747	2.0	1.0	X	dbSNP_134	197	2390,6202		328,1734,2234	no	coding-synonymous	SPRY3	NM_005840.1		460,2510,3529	GG,GA,AA		27.8166,23.6042,26.3887		249/289	155004280	3430,9568	2203	4296	6499	SO:0001819	synonymous_variant	10251	exon2			GTGCCAACAGGGC	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"""Pseudoautosomal regions / PAR2"""	11271	protein-coding gene	gene with protein product	"""antagonist of FGF signaling"""	300531	"""sprouty (Drosophila) homolog 2"""			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.747A>G	X.37:g.155004280A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	94	66	0.702128	NM_005840	A8K0H8	Silent	SNP	ENST00000302805.2	37	CCDS14769.4																																																																																			A|0.771;G|0.229	0.229	strong		0.592	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840	
INPP5A	3632	hgsc.bcm.edu	37	10	134459388	134459388	+	Missense_Mutation	SNP	A	A	G	rs1133400	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:134459388A>G	ENST00000368594.3	+	3	411	c.134A>G	c.(133-135)aAg>aGg	p.K45R	INPP5A_ENST00000368593.3_Missense_Mutation_p.K45R	NM_005539.3	NP_005530.3	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase, 40kDa	45			K -> R (in dbSNP:rs1133400).		inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|PH domain binding (GO:0042731)			cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		CACACACACAAGCCGCACTTC	0.607													A|||	1063	0.21226	0.1014	0.2565	5008	,	,		17008	0.3016		0.2137	False		,,,				2504	0.2372				p.K45R	Pancreas(63;823 1267 11107 20380 51626)	Atlas-SNP	.											.	INPP5A	77	.	0			c.A134G						PASS	.	A	ARG/LYS	475,3931	221.0+/-238.3	27,421,1755	139.0	84.0	103.0		134	-0.9	1.0	10	dbSNP_86	103	1745,6855	311.6+/-310.4	176,1393,2731	yes	missense	INPP5A	NM_005539.3	26	203,1814,4486	GG,GA,AA		20.2907,10.7808,17.069	benign	45/413	134459388	2220,10786	2203	4300	6503	SO:0001583	missense	3632	exon3			CACACAAGCCGCA	X77567	CCDS7669.2	10q26.3	2008-08-07	2002-08-29		ENSG00000068383	ENSG00000068383	3.1.3.56		6076	protein-coding gene	gene with protein product	"""CTCL tumor antigen HD-CL-02"", ""43 kDa inositol polyphosphate 5-phophatase"", ""inositol polyphosphate 5-phophatase, 40kDa"", ""InsP3 5-phosphatase"", ""type I inositol-1,4,5-trisphosphate 5-phosphatase"""	600106	"""inositol polyphosphate-5-phosphatase, 40kD"""			8013665	Standard	NM_005539		Approved	5PTASE	uc001llp.3	Q14642	OTTHUMG00000019293	ENST00000368594.3:c.134A>G	10.37:g.134459388A>G	ENSP00000357583:p.Lys45Arg	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_005539	D3DXI3|Q14640|Q5JSF1	Missense_Mutation	SNP	ENST00000368594.3	37	CCDS7669.2	505	0.23122710622710624	58	0.11788617886178862	98	0.27071823204419887	180	0.3146853146853147	169	0.22295514511873352	A	10.69	1.422128	0.25639	0.107808	0.202907	ENSG00000068383	ENST00000368594;ENST00000368593;ENST00000416326;ENST00000368595;ENST00000451873	T;T	0.42900	0.96;0.96	4.31	-0.882	0.10604	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.284900	0.37053	N	0.002266	T	0.00012	0.0000	N	0.25201	0.72	0.25964	P	0.9825875	B;B	0.09022	0.0;0.002	B;B	0.06405	0.001;0.002	T	0.43393	-0.9394	9	0.17832	T	0.49	-17.8059	8.6704	0.34147	0.6762:0.0:0.3238:0.0	rs1133400;rs3195167;rs3818511;rs11545720;rs59704452;rs1133400	45;45	Q14642;Q5T1B5	I5P1_HUMAN;.	R	45;45;45;45;41	ENSP00000357583:K45R;ENSP00000357582:K45R	ENSP00000357582:K45R	K	+	2	0	INPP5A	134309378	1.000000	0.71417	0.988000	0.46212	0.976000	0.68499	1.210000	0.32370	-0.258000	0.09446	0.533000	0.62120	AAG	A|0.804;G|0.196	0.196	strong		0.607	INPP5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051085.1	NM_005539	
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 GAIIx	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		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	58	11	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
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919302	51919302	+	Missense_Mutation	SNP	T	T	C	rs201376644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51919302T>C	ENST00000339313.5	-	5	990	c.874A>G	c.(874-876)Aac>Gac	p.N292D	SIGLEC10_ENST00000439889.2_Missense_Mutation_p.N234D|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.N244D|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.N292D|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.N209D|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.N292D|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.N234D|CTD-2616J11.2_ENST00000532688.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	292	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		AGGACTCTGTTCTGCAGGACC	0.652																																					p.N292D		Atlas-SNP	.											SIGLEC12_ENST00000439889,rectum,carcinoma,0,2	SIGLEC10	112	2	0			c.A874G						PASS	.						19.0	24.0	22.0					19																	51919302		2201	4299	6500	SO:0001583	missense	89790	exon5			CTCTGTTCTGCAG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.874A>G	19.37:g.51919302T>C	ENSP00000345243:p.Asn292Asp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	13	0.171053	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	7.755	0.704152	0.15172	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.40476	1.61;1.61;1.61;1.61;1.61;1.61;1.61;1.03	4.37	1.07	0.20283	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.427133	0.19965	N	0.102128	T	0.13841	0.0335	N	0.02854	-0.475	0.09310	N	1	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001	T	0.33701	-0.9858	10	0.02654	T	1	.	7.7519	0.28903	0.0:0.684:0.0:0.316	.	244;292;292;234;234;292	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	D	292;209;292;234;234;244;292;106	ENSP00000342389:N292D;ENSP00000396742:N209D;ENSP00000348646:N292D;ENSP00000408387:N234D;ENSP00000389132:N234D;ENSP00000414324:N244D;ENSP00000345243:N292D;ENSP00000435281:N106D	ENSP00000345243:N292D	N	-	1	0	SIGLEC10	56611114	0.000000	0.05858	0.002000	0.10522	0.047000	0.14425	0.182000	0.16900	-0.072000	0.12864	-1.945000	0.00491	AAC	T|0.998;C|0.002	0.002	strong		0.652	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
NRD1	4898	hgsc.bcm.edu	37	1	52266350	52266350	+	Silent	SNP	C	C	T	rs2273198	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:52266350C>T	ENST00000354831.7	-	23	2712	c.2523G>A	c.(2521-2523)ctG>ctA	p.L841L	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_Silent_p.L641L|RP4-657D16.3_ENST00000588291.1_RNA|RP4-657D16.3_ENST00000591675.1_RNA|RP4-657D16.3_ENST00000586761.1_RNA|RP4-657D16.6_ENST00000607338.1_RNA|NRD1_ENST00000539524.1_Silent_p.L709L|NRD1_ENST00000352171.7_Silent_p.L773L	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	772					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						TGAGCTGAAACAGTAGCTAAA	0.383													C|||	309	0.0617013	0.062	0.0793	5008	,	,		21108	0.0942		0.0219	False		,,,				2504	0.0562				p.L841L		Atlas-SNP	.											.	NRD1	89	.	0			c.G2523A						PASS	.	C	,,	229,4177	137.3+/-173.1	7,215,1981	92.0	87.0	89.0		2319,2127,2523	-3.7	0.9	1	dbSNP_100	89	258,8342	99.3+/-160.8	7,244,4049	no	coding-synonymous,coding-synonymous,coding-synonymous	NRD1	NM_001101662.1,NM_001242361.1,NM_002525.2	,,	14,459,6030	TT,TC,CC		3.0,5.1975,3.7444	,,	773/1152,709/1088,841/1220	52266350	487,12519	2203	4300	6503	SO:0001819	synonymous_variant	4898	exon23			CTGAAACAGTAGC	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.2523G>A	1.37:g.52266350C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	65	0.528455	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	37	CCDS559.1	139	0.06364468864468864	37	0.07520325203252033	27	0.07458563535911603	62	0.10839160839160839	13	0.017150395778364115	C	8.743	0.919346	0.17982	0.051975	0.03	ENSG00000078618	ENST00000440943	.	.	.	4.85	-3.72	0.04411	.	.	.	.	.	T	0.00784	0.0026	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19647	-1.0299	4	.	.	.	-5.5643	1.5623	0.02597	0.2009:0.295:0.3076:0.1965	rs2273198;rs52824051;rs56571057;rs2273198	.	.	.	I	188	.	.	V	-	1	0	NRD1	52038938	0.007000	0.16637	0.905000	0.35620	0.964000	0.63967	-1.003000	0.03682	-1.034000	0.03295	-0.305000	0.09177	GTT	C|0.946;T|0.054	0.054	strong		0.383	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
HCN2	610	hgsc.bcm.edu	37	19	605171	605171	+	Silent	SNP	T	T	C	rs12981860	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:605171T>C	ENST00000251287.2	+	3	1220	c.1167T>C	c.(1165-1167)ccT>ccC	p.P389P		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	389					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)		TCCTGGTGCCTATGCTGCAGG	0.627													c|||	3031	0.605232	0.5915	0.5418	5008	,	,		10661	0.7669		0.5994	False		,,,				2504	0.5082				p.P389P	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.T1167C						PASS	.	C		2474,1932		693,1088,422	98.0	77.0	84.0		1167	3.7	1.0	19	dbSNP_121	84	5505,3093		1750,2005,544	no	coding-synonymous	HCN2	NM_001194.3		2443,3093,966	CC,CT,TT		35.9735,43.8493,38.642		389/890	605171	7979,5025	2203	4299	6502	SO:0001819	synonymous_variant	610	exon3			GGTGCCTATGCTG	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.1167T>C	19.37:g.605171T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			T|0.381;C|0.619	0.619	strong		0.627	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194	
IFT88	8100	hgsc.bcm.edu	37	13	21189941	21189941	+	Missense_Mutation	SNP	G	G	A	rs2442455	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:21189941G>A	ENST00000319980.6	+	16	1476	c.1149G>A	c.(1147-1149)atG>atA	p.M383I	IFT88_ENST00000461115.1_3'UTR|IFT88_ENST00000382778.4_Missense_Mutation_p.M383I|IFT88_ENST00000537103.1_Missense_Mutation_p.M355I|IFT88_ENST00000351808.5_Missense_Mutation_p.M374I	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	383			M -> I (in dbSNP:rs2442455). {ECO:0000269|PubMed:15489334}.		anterior/posterior pattern specification (GO:0009952)|cardiac muscle cell differentiation (GO:0055007)|cardiac septum morphogenesis (GO:0060411)|cilium morphogenesis (GO:0060271)|cochlea development (GO:0090102)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|embryonic digit morphogenesis (GO:0042733)|epidermal stem cell homeostasis (GO:0036334)|epidermis development (GO:0008544)|epithelial cell morphogenesis (GO:0003382)|eye development (GO:0001654)|forebrain morphogenesis (GO:0048853)|heart formation (GO:0060914)|inner ear receptor stereocilium organization (GO:0060122)|kidney development (GO:0001822)|liver development (GO:0001889)|lung vasculature development (GO:0060426)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|protein localization (GO:0008104)|regulation of autophagic vacuole assembly (GO:2000785)|regulation of cilium assembly (GO:1902017)|regulation of fat cell differentiation (GO:0045598)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of protein processing (GO:0070613)|regulation of smoothened signaling pathway (GO:0008589)|response to fluid shear stress (GO:0034405)|smoothened signaling pathway (GO:0007224)|sperm axoneme assembly (GO:0007288)|spermatid nucleus elongation (GO:0007290)|spinal cord dorsal/ventral patterning (GO:0021513)|telencephalon development (GO:0021537)	acrosomal membrane (GO:0002080)|apical part of cell (GO:0045177)|axonemal basal plate (GO:0097541)|centriole (GO:0005814)|ciliary basal body (GO:0036064)|ciliary base (GO:0097546)|ciliary tip (GO:0097542)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|kinocilium (GO:0060091)|motile cilium (GO:0031514)|motile primary cilium (GO:0031512)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	27		all_cancers(29;5.79e-25)|all_epithelial(30;2.57e-20)|all_lung(29;3.13e-16)|Lung SC(185;0.0262)|Ovarian(182;0.0825)|Hepatocellular(188;0.244)		all cancers(112;0.000667)|Epithelial(112;0.00119)|OV - Ovarian serous cystadenocarcinoma(117;0.0141)|Lung(94;0.0183)|LUSC - Lung squamous cell carcinoma(192;0.0528)		GGAAAGCCATGGCAGAAAAAT	0.289													G|||	651	0.129992	0.2776	0.134	5008	,	,		15594	0.0		0.1382	False		,,,				2504	0.0532				p.M383I		Atlas-SNP	.											.	IFT88	83	.	0			c.G1149A						PASS	.	G	ILE/MET,ILE/MET	1094,3312	386.3+/-326.1	130,834,1239	79.0	89.0	85.0		1122,1149	4.7	1.0	13	dbSNP_100	85	1264,7328	250.1+/-277.1	95,1074,3127	yes	missense,missense	IFT88	NM_006531.3,NM_175605.3	10,10	225,1908,4366	AA,AG,GG		14.7114,24.8298,18.1413	benign,benign	374/825,383/834	21189941	2358,10640	2203	4296	6499	SO:0001583	missense	8100	exon16			AGCCATGGCAGAA	AK058172	CCDS31944.1, CCDS31945.1	13q12.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000032742	ENSG00000032742		"""Intraflagellar transport homologs"", ""Tetratricopeptide (TTC) repeat domain containing"""	20606	protein-coding gene	gene with protein product	"""polaris homolog"""	600595	"""tetratricopeptide repeat domain 10"", ""intraflagellar transport 88 homolog (Chlamydomonas)"""	TTC10		7633404	Standard	XM_005266546		Approved	hTg737, Tg737, D13S1056E, MGC26259	uc001uni.3	Q13099	OTTHUMG00000016517	ENST00000319980.6:c.1149G>A	13.37:g.21189941G>A	ENSP00000323580:p.Met383Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Missense_Mutation	SNP	ENST00000319980.6	37	CCDS31944.1	289	0.13232600732600733	136	0.2764227642276423	54	0.14917127071823205	0	0.0	99	0.13060686015831136	G	14.05	2.419414	0.42918	0.248298	0.147114	ENSG00000032742	ENST00000382778;ENST00000389374;ENST00000351808;ENST00000319980;ENST00000537103	T;T;T;T	0.28895	1.59;1.59;1.59;1.6	5.59	4.74	0.60224	.	0.243577	0.43110	D	0.000611	T	0.00012	0.0000	N	0.19112	0.55	0.28726	P	0.9027585	B;B;B;B	0.17667	0.001;0.002;0.0;0.023	B;B;B;B	0.11329	0.001;0.003;0.0;0.006	T	0.24728	-1.0152	9	0.35671	T	0.21	-20.9649	9.7533	0.40490	0.1501:0.0:0.8499:0.0	rs2442455;rs17852821;rs52832974;rs58218357;rs2442455	355;383;181;383	F5H6C2;E7EW86;Q6MZX0;Q13099	.;.;.;IFT88_HUMAN	I	383;246;374;383;355	ENSP00000372228:M383I;ENSP00000261632:M374I;ENSP00000323580:M383I;ENSP00000437719:M355I	ENSP00000323580:M383I	M	+	3	0	IFT88	20087941	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.179000	0.50887	2.625000	0.88918	0.650000	0.86243	ATG	G|0.837;A|0.163	0.163	strong		0.289	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531	
TRIM5	85363	hgsc.bcm.edu	37	11	5701001	5701001	+	Missense_Mutation	SNP	C	C	T	rs10838525	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5701001C>T	ENST00000380034.3	-	2	663	c.407G>A	c.(406-408)cGg>cAg	p.R136Q	TRIM5_ENST00000305836.5_Missense_Mutation_p.R136Q|TRIM5_ENST00000396853.4_Missense_Mutation_p.R136Q|TRIM5_ENST00000380027.1_Missense_Mutation_p.R136Q|TRIM5_ENST00000483835.1_5'UTR|TRIM5_ENST00000396847.3_Missense_Mutation_p.R136Q|TRIM5_ENST00000396855.3_Missense_Mutation_p.R136Q	NM_033034.2|NM_033092.2	NP_149023.2|NP_149083.2	Q9C035	TRIM5_HUMAN	tripartite motif containing 5	136			R -> Q (in dbSNP:rs10838525). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18312418, ECO:0000269|Ref.9}.		activation of innate immune response (GO:0002218)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|signaling pattern recognition receptor activity (GO:0008329)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R136Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		TTGGTACTCCCGGGCAACCTC	0.512													T|||	926	0.184904	0.1029	0.2349	5008	,	,		18833	0.0784		0.3847	False		,,,				2504	0.1646				p.R136Q		Atlas-SNP	.											TRIM5_ENST00000380034,NS,carcinoma,0,1	TRIM5	111	1	1	Substitution - Missense(1)	stomach(1)	c.G407A	GRCh37	CM068300	TRIM5	M	rs10838525	PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	633,3769	271.0+/-269.9	49,535,1617	105.0	92.0	97.0		407,407,407	0.2	0.0	11	dbSNP_120	97	3012,5582	465.6+/-366.6	554,1904,1839	yes	missense,missense,missense	TRIM5	NM_033034.2,NM_033092.2,NM_033093.2	43,43,43	603,2439,3456	TT,TC,CC		35.0477,14.3798,28.0471	benign,benign,benign	136/494,136/348,136/327	5701001	3645,9351	2201	4297	6498	SO:0001583	missense	85363	exon2			TACTCCCGGGCAA	AF220025	CCDS31392.1, CCDS31393.1, CCDS31394.1	11p15	2014-06-03	2011-01-25		ENSG00000132256	ENSG00000132256		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16276	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM5"", ""tripartite motif protein TRIM"""	608487	"""tripartite motif-containing 5"""			11331580	Standard	NM_033034		Approved	RNF88, TRIM5alpha	uc001mbm.2	Q9C035	OTTHUMG00000066893	ENST00000380034.3:c.407G>A	11.37:g.5701001C>T	ENSP00000369373:p.Arg136Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_033093	A6NGQ1|A8WFA8|D3DQS8|D3DQS9|G3GJY1|Q2MLV4|Q2MLV8|Q2MLV9|Q2MLW1|Q2MLW3|Q2MLW4|Q2MLW6|Q2MLW7|Q2MLX1|Q2MLX2|Q2MLX3|Q2MLX5|Q2MLY3|Q2MLY4|Q2V6Q6|Q6GX26|Q8WU46|Q96SR5|Q9C031|Q9C032|Q9C033|Q9C034	Missense_Mutation	SNP	ENST00000380034.3	37	CCDS31393.1	462|462	0.21153846153846154|0.21153846153846154	49|49	0.09959349593495935|0.09959349593495935	91|91	0.2513812154696133|0.2513812154696133	30|30	0.05244755244755245|0.05244755244755245	292|292	0.38522427440633245|0.38522427440633245	c|c	0.006|0.006	-2.061954|-2.061954	0.00386|0.00386	0.143798|0.143798	0.350477|0.350477	ENSG00000132256|ENSG00000132256	ENST00000438025|ENST00000396855;ENST00000305836;ENST00000380034;ENST00000380027;ENST00000396847;ENST00000396853;ENST00000412903	.|T;T;T;T;T;T;T	.|0.55413	.|0.52;0.52;0.52;0.52;0.52;0.52;0.52	4.07|4.07	0.203|0.203	0.15195|0.15195	.|.	.|0.418264	.|0.20632	.|N	.|0.088573	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00252|0.00252	-1.77|-1.77	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.13145	.|0.007;0.0;0.0	.|B;B;B	.|0.06405	.|0.002;0.002;0.0	T|T	0.36841|0.36841	-0.9731|-0.9731	4|9	.|0.02654	.|T	.|1	.|.	4.1195|4.1195	0.10099|0.10099	0.0:0.2902:0.1754:0.5344|0.0:0.2902:0.1754:0.5344	rs10838525;rs52810416;rs57044514;rs10838525|rs10838525;rs52810416;rs57044514;rs10838525	.|136;136;136	.|Q9C035-3;Q9C035-4;Q9C035	.|.;.;TRIM5_HUMAN	R|Q	13|136	.|ENSP00000380064:R136Q;ENSP00000307031:R136Q;ENSP00000369373:R136Q;ENSP00000369366:R136Q;ENSP00000380058:R136Q;ENSP00000380062:R136Q;ENSP00000388031:R136Q	.|ENSP00000307031:R136Q	G|R	-|-	1|2	0|0	TRIM5|TRIM5	5657577|5657577	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.761000|0.761000	0.26489|0.26489	0.015000|0.015000	0.14971|0.14971	-0.295000|-0.295000	0.09555|0.09555	GGG|CGG	C|0.763;T|0.237	0.237	strong		0.512	TRIM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143360.3	NM_033034	
TMEM175	84286	hgsc.bcm.edu	37	4	944210	944210	+	Splice_Site	SNP	A	A	C	rs34884217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:944210A>C	ENST00000264771.4	+	4	379	c.194A>C	c.(193-195)cAg>cCg	p.Q65P	TMEM175_ENST00000515740.1_5'UTR|TMEM175_ENST00000508204.1_5'UTR|TMEM175_ENST00000504180.1_Splice_Site	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	65			Q -> P (in dbSNP:rs34884217).			integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GTATTCCAGCAGTTCGACAGA	0.587													A|||	161	0.0321486	0.0023	0.049	5008	,	,		15929	0.001		0.0964	False		,,,				2504	0.0266				p.Q65P		Atlas-SNP	.											.	TMEM175	44	.	0			c.A194C						PASS	.	A	PRO/GLN	101,4305	79.9+/-118.3	4,93,2106	119.0	102.0	107.0		194	0.6	0.1	4	dbSNP_126	107	921,7679	203.5+/-246.5	63,795,3442	yes	missense-near-splice	TMEM175	NM_032326.2	76	67,888,5548	CC,CA,AA		10.7093,2.2923,7.8579	benign	65/505	944210	1022,11984	2203	4300	6503	SO:0001630	splice_region_variant	84286	exon4			TCCAGCAGTTCGA	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.193-1A>C	4.37:g.944210A>C		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	179	176	0.98324	NM_032326	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	37	CCDS3341.1	87|87	0.03983516483516483|0.03983516483516483	4|4	0.008130081300813009|0.008130081300813009	20|20	0.055248618784530384|0.055248618784530384	0|0	0.0|0.0	63|63	0.08311345646437995|0.08311345646437995	A|A	1.373|1.373	-0.585596|-0.585596	0.03827|0.03827	0.022923|0.022923	0.107093|0.107093	ENSG00000127419|ENSG00000127419	ENST00000507319|ENST00000264771;ENST00000514453;ENST00000514546	.|T;T;T	.|0.46451	.|0.87;1.0;0.87	4.9|4.9	0.563|0.563	0.17296|0.17296	.|.	.|0.685752	.|0.13840	.|N	.|0.359112	.|T	.|0.00300	.|0.0009	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	D|D	1|1	.|B	.|0.10296	.|0.003	.|B	.|0.10450	.|0.005	.|T	.|0.22277	.|-1.0221	.|10	.|0.30854	.|T	.|0.27	.|-4.2182	4.3737|4.3737	0.11260|0.11260	0.6118:0.1753:0.2129:0.0|0.6118:0.1753:0.2129:0.0	rs34884217|rs34884217	.|65	.|Q9BSA9	.|TM175_HUMAN	.|P	-1|65;52;65	.|ENSP00000264771:Q65P;ENSP00000425181:Q52P;ENSP00000425763:Q65P	.|ENSP00000264771:Q65P	.|Q	+|+	.|2	.|0	TMEM175|TMEM175	934210|934210	1.000000|1.000000	0.71417|0.71417	0.101000|0.101000	0.21167|0.21167	0.007000|0.007000	0.05969|0.05969	4.186000|4.186000	0.58337|0.58337	0.233000|0.233000	0.21120|0.21120	-0.396000|-0.396000	0.06452|0.06452	.|CAG	A|0.930;C|0.070	0.070	strong		0.587	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326	Missense_Mutation
AVL9	23080	hgsc.bcm.edu	37	7	32613020	32613020	+	Silent	SNP	A	A	G	rs1993050	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:32613020A>G	ENST00000318709.4	+	12	1781	c.1560A>G	c.(1558-1560)acA>acG	p.T520T	AVL9_ENST00000409301.1_Silent_p.T520T|AVL9_ENST00000404479.1_Intron	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	520					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)		p.T520T(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TGGCTGCCACACTGCAATTAG	0.458													A|||	2848	0.56869	0.3933	0.7147	5008	,	,		17731	0.6677		0.6551	False		,,,				2504	0.5112				p.T520T		Atlas-SNP	.											AVL9,NS,carcinoma,0,1	AVL9	66	1	1	Substitution - coding silent(1)	stomach(1)	c.A1560G						PASS	.	A		1900,2506	546.3+/-377.0	416,1068,719	89.0	77.0	81.0		1560	-11.0	0.2	7	dbSNP_92	81	5691,2909	671.1+/-402.8	1902,1887,511	no	coding-synonymous	AVL9	NM_015060.1		2318,2955,1230	GG,GA,AA		33.8256,43.123,41.6346		520/649	32613020	7591,5415	2203	4300	6503	SO:0001819	synonymous_variant	23080	exon12			TGCCACACTGCAA	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1560A>G	7.37:g.32613020A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	37	CCDS34613.1																																																																																			A|0.420;G|0.580	0.580	strong		0.458	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
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 GAIIx	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	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	76	9	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29910759	29910759	+	Missense_Mutation	SNP	T	T	C	rs1071742	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29910759T>C	ENST00000396634.1	+	4	640	c.299T>C	c.(298-300)gTg>gCg	p.V100A	HLA-A_ENST00000376806.5_Missense_Mutation_p.V100A|HLA-A_ENST00000376802.2_Missense_Mutation_p.V100A|HLA-A_ENST00000376809.5_Missense_Mutation_p.V100A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	100	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ACTGACCGAGTGGACCTGGGG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	774	0.154553	0.1445	0.1225	5008	,	,		10249	0.0704		0.1928	False		,,,				2504	0.2382				p.V100A		Atlas-SNP	.											HLA-A,rectum,carcinoma,0,1	HLA-A	89	1	0			c.T299C						scavenged	.	C	ALA/VAL	656,3732		158,340,1696	60.0	64.0	63.0		299	-6.7	0.0	6	dbSNP_86	63	2286,6282		597,1092,2595	yes	missense	HLA-A	NM_002116.7	64	755,1432,4291	CC,CT,TT		26.6807,14.9499,22.7076	benign	100/366	29910759	2942,10014	2194	4284	6478	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ACCGAGTGGACCT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.299T>C	6.37:g.29910759T>C	ENSP00000379873:p.Val100Ala	Somatic	189	2	0.010582		WXS	Illumina HiSeq	Phase_I	120	108	0.9	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	5.521	0.280982	0.10458	0.149499	0.266807	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00792	5.69;5.69;5.69;5.69	3.33	-6.67	0.01783	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	15.776400	0.01836	N	0.034989	T	0.00300	0.0009	M	0.67625	2.065	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.09377	0.004;0.003;0.002;0.001;0.004	T	0.46289	-0.9202	9	0.38643	T	0.18	.	0.4643	0.00521	0.2856:0.2905:0.146:0.2778	rs1071742;rs2231002;rs3129019;rs3173422;rs3200152;rs3200155;rs9256981;rs17423971;rs41551313	100;100;100;100;100	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	A	100	ENSP00000379873:V100A;ENSP00000366002:V100A;ENSP00000366005:V100A;ENSP00000365998:V100A	ENSP00000348012:V100A	V	+	2	0	HLA-A	30018738	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.538000	0.00938	-1.834000	0.01193	-3.111000	0.00062	GTG	A|0.129;C|0.082;T|0.790	0.082	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
JADE2	23338	hgsc.bcm.edu	37	5	133887780	133887780	+	Silent	SNP	G	G	A	rs12163993	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:133887780G>A	ENST00000402835.1	+	4	447	c.192G>A	c.(190-192)ccG>ccA	p.P64P	PHF15_ENST00000395003.1_Silent_p.P64P|PHF15_ENST00000282605.4_Silent_p.P64P|PHF15_ENST00000361895.2_Silent_p.P64P																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)			TGAAGATCCCGGACTCATACC	0.592													G|||	791	0.157947	0.0454	0.2147	5008	,	,		19516	0.2113		0.1571	False		,,,				2504	0.2157				p.P64P		Atlas-SNP	.											.	PHF15	60	.	0			c.G192A						PASS	.	G		231,4175	139.2+/-174.8	8,215,1980	96.0	92.0	93.0		192	-3.9	1.0	5	dbSNP_120	93	1226,7374	248.2+/-276.0	95,1036,3169	no	coding-synonymous	PHF15	NM_015288.4		103,1251,5149	AA,AG,GG		14.2558,5.2429,11.2025		64/791	133887780	1457,11549	2203	4300	6503	SO:0001819	synonymous_variant	23338	exon4			GATCCCGGACTCA																												ENST00000402835.1:c.192G>A	5.37:g.133887780G>A		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	279	125	0.448029	NM_015288		Silent	SNP	ENST00000402835.1	37																																																																																				G|0.879;A|0.121	0.121	strong		0.592	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1		
GAPVD1	26130	hgsc.bcm.edu	37	9	128069703	128069703	+	Silent	SNP	C	C	A	rs13299973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:128069703C>A	ENST00000495955.1	+	7	1418	c.1128C>A	c.(1126-1128)gcC>gcA	p.A376A	GAPVD1_ENST00000394084.1_Silent_p.A376A|GAPVD1_ENST00000265956.4_Silent_p.A376A|GAPVD1_ENST00000394105.2_Silent_p.A376A|GAPVD1_ENST00000297933.6_Silent_p.A376A|GAPVD1_ENST00000394104.2_Silent_p.A376A|GAPVD1_ENST00000394083.2_Silent_p.A376A|GAPVD1_ENST00000312123.9_Silent_p.A376A|GAPVD1_ENST00000470056.1_Silent_p.A376A			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	376					endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						GCTGTGTTGCCGCTTTCCTTG	0.408													C|||	189	0.0377396	0.0023	0.036	5008	,	,		15965	0.002		0.0765	False		,,,				2504	0.0838				p.A376A		Atlas-SNP	.											.	GAPVD1	124	.	0			c.C1128A						PASS	.	C		62,4344	58.7+/-95.3	0,62,2141	49.0	49.0	49.0		1128	2.8	1.0	9	dbSNP_121	49	630,7970	161.3+/-214.2	27,576,3697	no	coding-synonymous	GAPVD1	NM_015635.2		27,638,5838	AA,AC,CC		7.3256,1.4072,5.3206		376/1488	128069703	692,12314	2203	4300	6503	SO:0001819	synonymous_variant	26130	exon5			TGTTGCCGCTTTC		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.1128C>A	9.37:g.128069703C>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Silent	SNP	ENST00000495955.1	37		77|77	0.035256410256410256|0.035256410256410256	1|1	0.0020325203252032522|0.0020325203252032522	6|6	0.016574585635359115|0.016574585635359115	2|2	0.0034965034965034965|0.0034965034965034965	68|68	0.08970976253298153|0.08970976253298153	C|C	8.598|8.598	0.886212|0.886212	0.17540|0.17540	0.014072|0.014072	0.073256|0.073256	ENSG00000165219|ENSG00000165219	ENST00000431329|ENST00000436712	.|.	.|.	.|.	5.17|5.17	2.84|2.84	0.33178|0.33178	.|.	.|.	.|.	.|.	.|.	T|T	0.01695|0.01695	0.0054|0.0054	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.14117|0.14117	-1.0484|-1.0484	3|3	.|.	.|.	.|.	.|.	5.0939|5.0939	0.14723|0.14723	0.1336:0.1577:0.0:0.7087|0.1336:0.1577:0.0:0.7087	rs13299973;rs13299973|rs13299973;rs13299973	.|.	.|.	.|.	Q|S	239|207	.|.	.|.	P|R	+|+	2|1	0|0	GAPVD1|GAPVD1	127109524|127109524	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	1.279000|1.279000	0.33191|0.33191	0.389000|0.389000	0.25086|0.25086	-0.471000|-0.471000	0.05019|0.05019	CCG|CGC	A|0.046;C|0.954;G|0.000	0.046	strong		0.408	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1		
PLEKHA7	144100	hgsc.bcm.edu	37	11	16812397	16812397	+	Silent	SNP	G	G	A	rs35142528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:16812397G>A	ENST00000355661.3	-	21	3010	c.3000C>T	c.(2998-3000)ccC>ccT	p.P1000P	PLEKHA7_ENST00000332954.4_5'UTR|PLEKHA7_ENST00000531066.1_Silent_p.P1000P|PLEKHA7_ENST00000448080.2_Silent_p.P1001P|PLEKHA7_ENST00000532079.1_Intron			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	1000					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						GTCCTAGGGAGGGCTGGGCCA	0.642													G|||	322	0.0642971	0.025	0.0821	5008	,	,		18434	0.0714		0.1074	False		,,,				2504	0.0532				p.P1000P		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.C3000T						PASS	.	G		119,4281	79.9+/-118.3	1,117,2082	33.0	28.0	29.0		3000	4.7	1.0	11	dbSNP_126	29	825,7763	176.2+/-226.1	37,751,3506	yes	coding-synonymous	PLEKHA7	NM_175058.4		38,868,5588	AA,AG,GG		9.6064,2.7045,7.2682		1000/1122	16812397	944,12044	2200	4294	6494	SO:0001819	synonymous_variant	144100	exon21			TAGGGAGGGCTGG	BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"""Pleckstrin homology (PH) domain containing"""	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.3000C>T	11.37:g.16812397G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_175058	B4DK33|B4DWC3|Q86VZ7	Silent	SNP	ENST00000355661.3	37	CCDS31434.1	172	0.07875457875457875	11	0.022357723577235773	32	0.08839779005524862	49	0.08566433566433566	80	0.10554089709762533	G	10.05	1.243791	0.22796	0.027045	0.096064	ENSG00000166689	ENST00000530489	T	0.23950	1.88	5.63	4.66	0.58398	.	0.359291	0.33253	N	0.005108	T	0.00695	0.0023	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.12344	-1.0551	6	0.59425	D	0.04	-4.3793	8.9423	0.35738	0.2318:0.0:0.7682:0.0	rs35142528;rs61751348	.	.	.	L	632	ENSP00000433467:P632L	ENSP00000433467:P632L	P	-	2	0	PLEKHA7	16768973	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	1.569000	0.36428	1.384000	0.46424	0.561000	0.74099	CCT	G|0.926;A|0.074	0.074	strong		0.642	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058	
HFM1	164045	hgsc.bcm.edu	37	1	91784887	91784887	+	Silent	SNP	G	G	A	rs10493845	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:91784887G>A	ENST00000370425.3	-	24	2741	c.2643C>T	c.(2641-2643)acC>acT	p.T881T	HFM1_ENST00000370424.3_Silent_p.T560T|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_Silent_p.T113T	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	881	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.T881T(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AAATCTTTGCGGTATCTTGTG	0.338													G|||	1184	0.236422	0.2481	0.2781	5008	,	,		16268	0.1756		0.3072	False		,,,				2504	0.181				p.T881T		Atlas-SNP	.											HFM1,NS,carcinoma,0,1	HFM1	188	1	1	Substitution - coding silent(1)	stomach(1)	c.C2643T						PASS	.	G		1179,3227	413.0+/-336.3	153,873,1177	113.0	108.0	110.0		2643	-10.0	0.0	1	dbSNP_119	110	2875,5725	451.0+/-362.6	479,1917,1904	no	coding-synonymous	HFM1	NM_001017975.3		632,2790,3081	AA,AG,GG		33.4302,26.759,31.1702		881/1436	91784887	4054,8952	2203	4300	6503	SO:0001819	synonymous_variant	164045	exon24			CTTTGCGGTATCT	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2643C>T	1.37:g.91784887G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	173	78	0.450867	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2	548	0.2509157509157509	110	0.22357723577235772	118	0.3259668508287293	80	0.13986013986013987	240	0.316622691292876	G	0.178	-1.065163	0.01934	0.26759	0.334302	ENSG00000162669	ENST00000430465	.	.	.	5.0	-10.0	0.00425	.	.	.	.	.	T	0.04998	0.0134	.	.	.	0.40115	P	0.023468999999999962	.	.	.	.	.	.	T	0.08027	-1.0742	3	.	.	.	.	4.3723	0.11253	0.5367:0.0827:0.0881:0.2926	rs10493845;rs10493845	.	.	.	L	137	.	.	P	-	2	0	HFM1	91557475	0.000000	0.05858	0.000000	0.03702	0.240000	0.25518	-1.031000	0.03578	-3.005000	0.00274	-1.223000	0.01593	CCG	G|0.749;A|0.251	0.251	strong		0.338	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
TWF2	11344	hgsc.bcm.edu	37	3	52263967	52263967	+	Silent	SNP	G	G	A	rs34038856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:52263967G>A	ENST00000305533.5	-	7	972	c.729C>T	c.(727-729)caC>caT	p.H243H	TLR9_ENST00000597542.1_5'UTR|TWF2_ENST00000499914.2_Silent_p.H243H|TLR9_ENST00000494383.1_Missense_Mutation_p.H104Y	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	243	ADF-H 2. {ECO:0000255|PROSITE- ProRule:PRU00599}.				barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CCTCATGGGTGTGCTTGTAGA	0.647													G|||	94	0.01877	0.003	0.036	5008	,	,		17997	0.0		0.0596	False		,,,				2504	0.0051				p.H243H		Atlas-SNP	.											.	TWF2	33	.	0			c.C729T						PASS	.	G		49,4357	50.2+/-85.5	0,49,2154	48.0	53.0	51.0		729	1.4	1.0	3	dbSNP_126	51	434,8166	132.6+/-190.3	7,420,3873	no	coding-synonymous	TWF2	NM_007284.3		7,469,6027	AA,AG,GG		5.0465,1.1121,3.7137		243/350	52263967	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	11344	exon7			ATGGGTGTGCTTG	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"""protein tyrosine kinase 9-like (A6-related protein)"", ""PTK9L protein tyrosine kinase 9-like (A6-related protein)"", ""twinfilin, actin-binding protein, homolog 2 (Drosophila)"""	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.729C>T	3.37:g.52263967G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_007284	Q9Y3F5	Silent	SNP	ENST00000305533.5	37	CCDS2849.1	60	0.027472527472527472	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	43	0.05672823218997362	G	6.366	0.435655	0.12104	0.011121	0.050465	ENSG00000173366	ENST00000494383	T	0.29917	1.55	4.91	1.42	0.22433	.	.	.	.	.	T	0.06462	0.0166	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01557	-1.1325	6	0.87932	D	0	.	9.1548	0.36985	0.3544:0.0:0.6456:0.0	rs34038856	.	.	.	Y	104	ENSP00000417517:H104Y	ENSP00000417517:H104Y	H	-	1	0	RP11-330H6.5	52239007	1.000000	0.71417	0.997000	0.53966	0.614000	0.37383	1.501000	0.35693	0.240000	0.21263	0.561000	0.74099	CAC	G|0.968;A|0.032	0.032	strong		0.647	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2		
JAG1	182	hgsc.bcm.edu	37	20	10622501	10622501	+	Missense_Mutation	SNP	G	G	C	rs35761929	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:10622501G>C	ENST00000254958.5	-	22	3127	c.2612C>G	c.(2611-2613)cCa>cGa	p.P871R	JAG1_ENST00000423891.2_Missense_Mutation_p.P712R	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	871			P -> R (in biliary atresia; extrahepatic; dbSNP:rs35761929). {ECO:0000269|PubMed:12297837}.		angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GGCCCCATCTGGTATCACACT	0.522									Alagille Syndrome				G|||	265	0.0529153	0.003	0.0288	5008	,	,		22044	0.0258		0.0726	False		,,,				2504	0.1452				p.P871R		Atlas-SNP	.											.	JAG1	213	.	0			c.C2612G	GRCh37	CM023740|CP984551	JAG1	M|X	rs35761929	PASS	.	G	ARG/PRO	64,4342	60.5+/-97.4	1,62,2140	201.0	176.0	184.0		2612	3.9	0.8	20	dbSNP_126	184	562,8038	153.0+/-207.5	17,528,3755	yes	missense	JAG1	NM_000214.2	103	18,590,5895	CC,CG,GG		6.5349,1.4526,4.8132	possibly-damaging	871/1219	10622501	626,12380	2203	4300	6503	SO:0001583	missense	182	exon22	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CCATCTGGTATCA	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2612C>G	20.37:g.10622501G>C	ENSP00000254958:p.Pro871Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	93	0.042582417582417584	4	0.008130081300813009	13	0.03591160220994475	15	0.026223776223776224	61	0.08047493403693931	G	20.9	4.070375	0.76301	0.014526	0.065349	ENSG00000101384	ENST00000254958;ENST00000423891	T;D	0.85861	-0.11;-2.04	5.84	3.89	0.44902	von Willebrand factor, type C (1);	0.206142	0.51477	D	0.000084	T	0.36026	0.0952	L	0.52206	1.635	0.46954	D	0.999268	D	0.60575	0.988	P	0.60345	0.873	T	0.67154	-0.5742	10	0.52906	T	0.07	.	11.3551	0.49611	0.1463:0.0:0.8537:0.0	rs35761929;rs61729454	871	P78504	JAG1_HUMAN	R	871;712	ENSP00000254958:P871R;ENSP00000389519:P712R	ENSP00000254958:P871R	P	-	2	0	JAG1	10570501	1.000000	0.71417	0.815000	0.32552	0.991000	0.79684	3.993000	0.56987	0.794000	0.33899	0.650000	0.86243	CCA	G|0.949;C|0.051	0.051	strong		0.522	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
ACACB	32	hgsc.bcm.edu	37	12	109605730	109605730	+	Silent	SNP	C	C	T	rs4766516	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:109605730C>T	ENST00000338432.7	+	4	935	c.816C>T	c.(814-816)gcC>gcT	p.A272A	ACACB_ENST00000377848.3_Silent_p.A272A|ACACB_ENST00000377854.5_Silent_p.A272A			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	272	Biotin carboxylation.				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)	GGATTGCCGCCGTGAAGTGCA	0.597													C|||	1160	0.231629	0.0424	0.2089	5008	,	,		14485	0.5099		0.1769	False		,,,				2504	0.273				p.A272A		Atlas-SNP	.											.	ACACB	330	.	0			c.C816T						PASS	.	C		332,4074	172.7+/-202.6	13,306,1884	138.0	96.0	110.0		816	-8.6	0.3	12	dbSNP_111	110	1711,6889	312.7+/-311.0	179,1353,2768	no	coding-synonymous	ACACB	NM_001093.3		192,1659,4652	TT,TC,CC		19.8953,7.5352,15.7081		272/2459	109605730	2043,10963	2203	4300	6503	SO:0001819	synonymous_variant	32	exon3			TGCCGCCGTGAAG	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.816C>T	12.37:g.109605730C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	74	43	0.581081	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.805;T|0.195	0.195	strong		0.597	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
PDE6C	5146	hgsc.bcm.edu	37	10	95372764	95372764	+	Silent	SNP	C	C	T	rs12781149	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:95372764C>T	ENST00000371447.3	+	1	420	c.282C>T	c.(280-282)gaC>gaT	p.D94D		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	94	GAF 1.				phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	TCCAGGCTGACCGCTGCAGCA	0.652													C|||	215	0.0429313	0.0053	0.0793	5008	,	,		17246	0.001		0.0885	False		,,,				2504	0.0644				p.D94D		Atlas-SNP	.											.	PDE6C	97	.	0			c.C282T						PASS	.	C		106,4300	83.4+/-121.9	0,106,2097	34.0	35.0	35.0		282	1.4	1.0	10	dbSNP_121	35	832,7768	192.8+/-238.7	38,756,3506	no	coding-synonymous	PDE6C	NM_006204.3		38,862,5603	TT,TC,CC		9.6744,2.4058,7.2121		94/859	95372764	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon1			GGCTGACCGCTGC	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.282C>T	10.37:g.95372764C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			C|0.939;T|0.061	0.061	strong		0.652	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
APCS	325	hgsc.bcm.edu	37	1	159558150	159558150	+	Silent	SNP	G	G	A	rs28383572	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:159558150G>A	ENST00000255040.2	+	2	421	c.324G>A	c.(322-324)ccG>ccA	p.P108P		NM_001639.3	NP_001630.1	P02743	SAMP_HUMAN	amyloid P component, serum	108	Pentaxin.				acute-phase response (GO:0006953)|chaperone-mediated protein complex assembly (GO:0051131)|innate immune response (GO:0045087)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral process (GO:0048525)|negative regulation of wound healing (GO:0061045)|protein folding (GO:0006457)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|unfolded protein binding (GO:0051082)|virion binding (GO:0046790)			breast(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_hematologic(112;0.0429)					AAAAGTTCCCGGCTCCAGTGC	0.433													G|||	125	0.0249601	0.0008	0.0144	5008	,	,		20758	0.0317		0.0209	False		,,,				2504	0.0624				p.P108P		Atlas-SNP	.											.	APCS	48	.	0			c.G324A						PASS	.	G		20,4386	27.2+/-55.0	0,20,2183	81.0	82.0	82.0		324	-7.3	0.0	1	dbSNP_125	82	193,8407	84.8+/-147.2	4,185,4111	no	coding-synonymous	APCS	NM_001639.3		4,205,6294	AA,AG,GG		2.2442,0.4539,1.6377		108/224	159558150	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	325	exon2			GTTCCCGGCTCCA		CCDS1186.1	1q21-q23	2012-10-02			ENSG00000132703	ENSG00000132703			584	protein-coding gene	gene with protein product	"""pentaxin-related"", ""9.5S alpha-1-glycoprotein"""	104770				2987268	Standard	NM_001639		Approved	SAP, PTX2, MGC88159	uc001ftv.3	P02743	OTTHUMG00000022741	ENST00000255040.2:c.324G>A	1.37:g.159558150G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_001639		Silent	SNP	ENST00000255040.2	37	CCDS1186.1																																																																																			G|0.984;A|0.016	0.016	strong		0.433	APCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059024.2	NM_001639	
HDAC10	83933	hgsc.bcm.edu	37	22	50684415	50684415	+	Missense_Mutation	SNP	T	T	C	rs11553697	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50684415T>C	ENST00000216271.5	-	18	2109	c.1757A>G	c.(1756-1758)cAg>cGg	p.Q586R	TUBGCP6_ENST00000248846.5_5'Flank|MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000448072.1_Missense_Mutation_p.Q536R|TUBGCP6_ENST00000439308.2_5'Flank|HDAC10_ENST00000349505.4_Missense_Mutation_p.Q566R|HDAC10_ENST00000498366.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	586					chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GTGGGGGCCCTGCAGGCCATG	0.692													T|||	223	0.0445288	0.0008	0.0245	5008	,	,		17546	0.1379		0.0129	False		,,,				2504	0.0542				p.Q586R		Atlas-SNP	.											.	HDAC10	29	.	0			c.A1757G						PASS	.	T	ARG/GLN,ARG/GLN	8,4378		0,8,2185	21.0	24.0	22.0		1697,1757	1.8	0.3	22	dbSNP_120	22	95,8491		0,95,4198	no	missense,missense	HDAC10	NM_001159286.1,NM_032019.5	43,43	0,103,6383	CC,CT,TT		1.1065,0.1824,0.794	benign,benign	566/650,586/670	50684415	103,12869	2193	4293	6486	SO:0001583	missense	83933	exon18			GGGCCCTGCAGGC	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.1757A>G	22.37:g.50684415T>C	ENSP00000216271:p.Gln586Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Missense_Mutation	SNP	ENST00000216271.5	37	CCDS14088.1	101	0.04624542124542125	0	0.0	8	0.022099447513812154	81	0.14160839160839161	12	0.0158311345646438	T	12.67	2.007161	0.35415	0.001824	0.011065	ENSG00000100429	ENST00000216271;ENST00000448072;ENST00000349505	T;T;T	0.29142	1.58;1.58;1.58	5.31	1.79	0.24919	Histone deacetylase domain (1);	1.553380	0.03822	N	0.267611	T	0.00178	0.0005	L	0.39020	1.185	0.09310	N	0.999998	B;B;B;B	0.10296	0.003;0.002;0.002;0.002	B;B;B;B	0.09377	0.004;0.002;0.004;0.002	T	0.16070	-1.0415	10	0.54805	T	0.06	-4.4891	3.1256	0.06406	0.0:0.2746:0.221:0.5044	rs11553697	566;536;586;586	Q969S8-2;C9J8B8;Q969S8-4;Q969S8	.;.;.;HDA10_HUMAN	R	586;536;566	ENSP00000216271:Q586R;ENSP00000397542:Q536R;ENSP00000343540:Q566R	ENSP00000216271:Q586R	Q	-	2	0	HDAC10	49026542	0.000000	0.05858	0.277000	0.24703	0.850000	0.48378	0.138000	0.16016	0.448000	0.26722	0.459000	0.35465	CAG	T|0.978;C|0.022	0.022	strong		0.692	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	
COL4A2	1284	hgsc.bcm.edu	37	13	111155779	111155779	+	Silent	SNP	G	G	A	rs4773199	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:111155779G>A	ENST00000360467.5	+	43	4395	c.4089G>A	c.(4087-4089)gcG>gcA	p.A1363A	COL4A2-AS1_ENST00000417970.2_RNA	NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	1363	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)			CCACTGGGGCGGTGGGCGACA	0.612													G|||	933	0.186302	0.2617	0.1772	5008	,	,		18204	0.0496		0.2008	False		,,,				2504	0.2168				p.A1363A		Atlas-SNP	.											COL4A2,NS,carcinoma,0,1	COL4A2	178	1	0			c.G4089A						PASS	.	G		1100,2660		158,784,938	27.0	32.0	31.0		4089	-7.4	0.0	13	dbSNP_111	31	1798,6418		218,1362,2528	no	coding-synonymous	COL4A2	NM_001846.2		376,2146,3466	AA,AG,GG		21.8841,29.2553,24.1984		1363/1713	111155779	2898,9078	1880	4108	5988	SO:0001819	synonymous_variant	1284	exon43			TGGGGCGGTGGGC	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.4089G>A	13.37:g.111155779G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	56	19	0.339286	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			G|0.834;A|0.166	0.166	strong		0.612	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
DGKE	8526	hgsc.bcm.edu	37	17	54912339	54912339	+	Silent	SNP	G	G	A	rs1048159	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:54912339G>A	ENST00000284061.3	+	2	363	c.183G>A	c.(181-183)ggG>ggA	p.G61G	C17orf67_ENST00000397861.2_5'Flank|DGKE_ENST00000572810.1_Silent_p.G61G|C17orf67_ENST00000575658.1_5'Flank|C17orf67_ENST00000487705.1_Intron|DGKE_ENST00000576869.1_3'UTR	NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	61					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					GCAAGCACGGGTGGCGCGACA	0.677													G|||	511	0.102037	0.0666	0.1066	5008	,	,		16751	0.0179		0.1799	False		,,,				2504	0.1534				p.G61G		Atlas-SNP	.											DGKE,NS,carcinoma,+2,1	DGKE	47	1	0			c.G183A						PASS	.	G		395,4011	192.3+/-217.7	18,359,1826	52.0	60.0	57.0		183	-4.0	1.0	17	dbSNP_86	57	1264,7334	249.4+/-276.7	92,1080,3127	no	coding-synonymous	DGKE	NM_003647.2		110,1439,4953	AA,AG,GG		14.7011,8.965,12.7576		61/568	54912339	1659,11345	2203	4299	6502	SO:0001819	synonymous_variant	8526	exon2			GCACGGGTGGCGC	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"""diacylglycerol kinase, epsilon (64kD)"""			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.183G>A	17.37:g.54912339G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_003647	Q8TBM4|Q9UKQ3	Silent	SNP	ENST00000284061.3	37	CCDS11590.1																																																																																			G|0.882;A|0.118	0.118	strong		0.677	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647	
MANSC4	100287284	hgsc.bcm.edu	37	12	27916206	27916206	+	Missense_Mutation	SNP	G	G	A	rs11049125	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27916206G>A	ENST00000381273.3	-	3	487	c.488C>T	c.(487-489)aCg>aTg	p.T163M		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	163						integral component of membrane (GO:0016021)				kidney(1)	1						ACCATTTATCGTGGTGGTTTG	0.383													A|||	625	0.1248	0.0234	0.1023	5008	,	,		19906	0.2044		0.173	False		,,,				2504	0.1462				p.T163M		Atlas-SNP	.											.	MANSC4	9	.	0			c.C488T						PASS	.	A	MET/THR	63,1321		1,61,630	292.0	244.0	259.0		488	-9.5	0.0	12	dbSNP_120	259	485,2697		36,413,1142	yes	missense	MANSC4	NM_001146221.1	81	37,474,1772	AA,AG,GG		15.242,4.552,12.0018	benign	163/341	27916206	548,4018	692	1591	2283	SO:0001583	missense	100287284	exon3			TTTATCGTGGTGG		CCDS53770.1	12p11.22	2011-05-05			ENSG00000205693	ENSG00000205693			40023	protein-coding gene	gene with protein product							Standard	NM_001146221		Approved		uc010sjs.1	A6NHS7	OTTHUMG00000169216	ENST00000381273.3:c.488C>T	12.37:g.27916206G>A	ENSP00000370673:p.Thr163Met	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	241	98	0.406639	NM_001146221		Missense_Mutation	SNP	ENST00000381273.3	37	CCDS53770.1	295	0.13507326007326007	17	0.034552845528455285	34	0.09392265193370165	112	0.1958041958041958	132	0.1741424802110818	A	4.507	0.094008	0.08632	0.04552	0.15242	ENSG00000205693	ENST00000381273	T	0.44881	0.91	5.58	-9.5	0.00584	.	1.354920	0.04623	N	0.402308	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.15809	-1.0424	9	0.36615	T	0.2	2.5148	4.6531	0.12605	0.2368:0.0978:0.4738:0.1916	rs11049125;rs61212329;rs11049125	163	A6NHS7	MANS4_HUMAN	M	163	ENSP00000370673:T163M	ENSP00000370673:T163M	T	-	2	0	MANSC4	27807473	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-0.138000	0.10374	-2.593000	0.00455	-0.360000	0.07572	ACG	G|0.869;A|0.131	0.131	strong		0.383	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
NUP54	53371	hgsc.bcm.edu	37	4	77053834	77053834	+	Missense_Mutation	SNP	T	T	C	rs61750814	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:77053834T>C	ENST00000264883.3	-	6	889	c.749A>G	c.(748-750)aAt>aGt	p.N250S	NUP54_ENST00000515460.1_5'Flank|NUP54_ENST00000458189.2_Missense_Mutation_p.N70S|NUP54_ENST00000514987.1_Missense_Mutation_p.N202S|NUP54_ENST00000342467.6_Missense_Mutation_p.N70S	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	250	9 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						TGAAGTACCATTTGGCGAACG	0.378													T|||	708	0.141374	0.2156	0.2248	5008	,	,		14987	0.0278		0.172	False		,,,				2504	0.0675				p.N250S		Atlas-SNP	.											.	NUP54	48	.	0			c.A749G						PASS	.	T	SER/ASN	900,3506	346.2+/-308.9	92,716,1395	137.0	126.0	130.0		749	5.5	1.0	4	dbSNP_129	130	1343,7257	262.8+/-284.6	114,1115,3071	yes	missense	NUP54	NM_017426.2	46	206,1831,4466	CC,CT,TT		15.6163,20.4267,17.2459	benign	250/508	77053834	2243,10763	2203	4300	6503	SO:0001583	missense	53371	exon6			GTACCATTTGGCG	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.749A>G	4.37:g.77053834T>C	ENSP00000264883:p.Asn250Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	CCDS3576.1	318	0.14560439560439561	94	0.1910569105691057	86	0.23756906077348067	15	0.026223776223776224	123	0.16226912928759896	T	12.31	1.900725	0.33535	0.204267	0.156163	ENSG00000138750	ENST00000264883;ENST00000342467;ENST00000514987;ENST00000458189	.	.	.	5.46	5.46	0.80206	.	0.041245	0.85682	D	0.000000	T	0.00012	0.0000	L	0.41710	1.295	0.09310	P	0.999999830858	B;B;B	0.25955	0.085;0.138;0.085	B;B;B	0.21151	0.02;0.03;0.033	T	0.06716	-1.0811	8	0.22706	T	0.39	-13.6304	15.5414	0.76052	0.0:0.0:0.0:1.0	rs61750814	202;70;250	B4DT35;Q7Z3B4-2;Q7Z3B4	.;.;NUP54_HUMAN	S	250;70;202;70	.	ENSP00000264883:N250S	N	-	2	0	NUP54	77272858	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.857000	0.69525	2.087000	0.62958	0.528000	0.53228	AAT	T|0.836;C|0.164	0.164	strong		0.378	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
WDR43	23160	hgsc.bcm.edu	37	2	29169612	29169612	+	Silent	SNP	T	T	C	rs3087649	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:29169612T>C	ENST00000407426.3	+	18	2057	c.2001T>C	c.(1999-2001)gaT>gaC	p.D667D		NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	667						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					GAGATTCTGATTTAGATCCTG	0.433													C|||	3782	0.755192	0.7065	0.7911	5008	,	,		18943	0.8601		0.7068	False		,,,				2504	0.7372				p.D667D		Atlas-SNP	.											.	WDR43	38	.	0			c.T2001C						PASS	.	C		2805,1055		1020,765,145	48.0	53.0	51.0		2001	-3.0	0.9	2	dbSNP_102	51	5973,2287		2174,1625,331	no	coding-synonymous	WDR43	NM_015131.1		3194,2390,476	CC,CT,TT		27.6877,27.3316,27.5743		667/678	29169612	8778,3342	1930	4130	6060	SO:0001819	synonymous_variant	23160	exon18			TTCTGATTTAGAT	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"""WD repeat domain containing"""	28945	protein-coding gene	gene with protein product	"""UTP5, small subunit (SSU) processome component, homolog (yeast)"""					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.2001T>C	2.37:g.29169612T>C		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	24	13	0.541667	NM_015131	Q15395|Q92577	Silent	SNP	ENST00000407426.3	37	CCDS46251.1																																																																																			T|0.251;C|0.749	0.749	strong		0.433	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089	
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 GAIIx	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		Somatic	287	1	0.00348432		WXS	Illumina HiSeq	Phase_I	261	110	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		
PRRC2B	84726	hgsc.bcm.edu	37	9	134350458	134350458	+	Missense_Mutation	SNP	C	C	T	rs10751478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:134350458C>T	ENST00000357304.4	+	15	2997	c.2942C>T	c.(2941-2943)cCc>cTc	p.P981L	PRRC2B_ENST00000405995.1_Intron|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Intron	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	981				P -> L (in Ref. 5; CAH18678). {ECO:0000305}.			poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						GAGCAGAGCCCCACGGCAGAA	0.567													C|||	3850	0.76877	0.5227	0.7478	5008	,	,		15760	0.9395		0.7654	False		,,,				2504	0.9438				p.P981L		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C2942T						PASS	.	C	LEU/PRO	2496,1652		736,1024,314	39.0	45.0	43.0		2942	-10.7	0.0	9	dbSNP_120	43	6789,1611		2739,1311,150	yes	missense	PRRC2B	NM_013318.3	98	3475,2335,464	TT,TC,CC		19.1786,39.8264,26.0041	benign	981/2230	134350458	9285,3263	2074	4200	6274	SO:0001583	missense	84726	exon15			AGAGCCCCACGGC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.2942C>T	9.37:g.134350458C>T	ENSP00000349856:p.Pro981Leu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	19	19	1	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	1658	0.7591575091575091	261	0.5304878048780488	280	0.7734806629834254	535	0.9353146853146853	582	0.7678100263852242	C	0.050	-1.254689	0.01457	0.601736	0.808214	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.01705	4.68	5.87	-10.7	0.00240	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.23547	-1.0185	7	.	.	.	.	3.4277	0.07417	0.4155:0.3378:0.0936:0.1531	rs10751478;rs52834787;rs10751478	981	Q5JSZ5	PRC2B_HUMAN	L	981;277	ENSP00000349856:P981L	.	P	+	2	0	PRRC2B	133340279	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.817000	0.04472	-2.096000	0.00852	-0.165000	0.13383	CCC	C|0.231;G|0.000;T|0.769	0.769	strong		0.567	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OR1S1	219959	hgsc.bcm.edu	37	11	57982832	57982832	+	Missense_Mutation	SNP	T	T	A	rs2867400	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57982832T>A	ENST00000309433.6	+	1	616	c.616T>A	c.(616-618)Ttg>Atg	p.L206M		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	206			L -> M (in dbSNP:rs2867400).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L206M(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTCAGATACATTGATCAATGA	0.438													t|||	2629	0.52496	0.2829	0.5403	5008	,	,		19594	0.8046		0.4225	False		,,,				2504	0.6585				p.L206M		Atlas-SNP	.											OR1S1,NS,carcinoma,0,1	OR1S1	139	1	1	Substitution - Missense(1)	stomach(1)	c.T616A						PASS	.						179.0	140.0	153.0					11																	57982832		2201	4294	6495	SO:0001583	missense	219959	exon1			GATACATTGATCA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.616T>A	11.37:g.57982832T>A	ENSP00000311688:p.Leu206Met	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	980	0.44871794871794873	120	0.24390243902439024	175	0.48342541436464087	413	0.722027972027972	272	0.35883905013192613	T	0.120	-1.126825	0.01770	.	.	ENSG00000172774	ENST00000309433	T	0.00115	8.71	3.23	0.689	0.18033	GPCR, rhodopsin-like superfamily (1);	1.756970	0.02885	N	0.133431	T	0.00012	0.0000	L	0.56280	1.765	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.23583	-1.0184	9	0.49607	T	0.09	.	1.1022	0.01686	0.3279:0.1471:0.1014:0.4237	rs2867400;rs2867400	206	Q8NH92	OR1S1_HUMAN	M	206	ENSP00000311688:L206M	ENSP00000311688:L206M	L	+	1	2	OR1S1	57739408	0.000000	0.05858	0.005000	0.12908	0.171000	0.22731	-1.315000	0.02713	0.339000	0.23719	-0.562000	0.04174	TTG	T|0.703;A|0.297	0.297	strong		0.438	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
PKD1L2	114780	hgsc.bcm.edu	37	16	81253917	81253917	+	RNA	SNP	A	A	G	rs533693628|rs9924530	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:81253917A>G	ENST00000525539.1	-	0	58				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTCTGGCTTAACAGTGGTGGC	0.567													G|||	2680	0.535144	0.6014	0.562	5008	,	,		20950	0.4405		0.6501	False		,,,				2504	0.4059				p.V20A		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T59C						PASS	.	G	ALA/VAL,ALA/VAL	2630,1446		865,900,273	69.0	69.0	69.0		59,59	3.2	0.0	16	dbSNP_119	69	5299,3093		1657,1985,554	yes	missense,missense	PKD1L2	NM_052892.3,NM_001076780.1	64,64	2522,2885,827	GG,GA,AA		36.8565,35.476,36.4052	benign,benign	20/2460,20/992	81253917	7929,4539	2038	4196	6234			114780	exon1			GGCTTAACAGTGG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81253917A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		1251	0.5728021978021978	301	0.6117886178861789	226	0.6243093922651933	233	0.40734265734265734	491	0.6477572559366754	G	0.019	-1.453081	0.01071	0.64524	0.631435	ENSG00000166473	ENST00000337114	T	0.16196	2.36	4.17	3.22	0.36961	.	0.335569	0.23343	N	0.049204	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43861	-0.9365	8	0.02654	T	1	-0.5748	3.3619	0.07189	0.2937:0.0:0.5103:0.196	rs9924530;rs52790816;rs61536671;rs9924530	20;20	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	A	20	ENSP00000337397:V20A	ENSP00000337397:V20A	V	-	2	0	PKD1L2	79811418	0.009000	0.17119	0.001000	0.08648	0.013000	0.08279	1.062000	0.30555	0.426000	0.26116	-0.213000	0.12676	GTT	A|0.429;G|0.571	0.571	strong		0.567	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
BDNF	627	hgsc.bcm.edu	37	11	27679916	27679916	+	Missense_Mutation	SNP	C	C	T	rs6265	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:27679916C>T	ENST00000525528.1	-	1	1289	c.196G>A	c.(196-198)Gtg>Atg	p.V66M	BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000584049.1_5'UTR|BDNF_ENST00000420794.1_Missense_Mutation_p.V66M|BDNF-AS_ENST00000532965.1_RNA|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000530861.1_Missense_Mutation_p.V66M|BDNF_ENST00000532997.1_Missense_Mutation_p.V66M|BDNF-AS_ENST00000499568.2_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000395983.3_Missense_Mutation_p.V66M|BDNF_ENST00000533246.1_Missense_Mutation_p.V66M|BDNF_ENST00000439476.2_Missense_Mutation_p.V66M|BDNF_ENST00000395980.2_Missense_Mutation_p.V66M|BDNF_ENST00000314915.6_Missense_Mutation_p.V74M|BDNF_ENST00000438929.1_Missense_Mutation_p.V148M|BDNF_ENST00000525950.1_Missense_Mutation_p.V66M|BDNF-AS_ENST00000499008.3_RNA|BDNF_ENST00000356660.4_Missense_Mutation_p.V66M|BDNF_ENST00000533131.1_Missense_Mutation_p.V66M|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000395986.2_Missense_Mutation_p.V81M|BDNF_ENST00000418212.1_Missense_Mutation_p.V66M|BDNF_ENST00000395981.3_Missense_Mutation_p.V66M|BDNF_ENST00000395978.3_Missense_Mutation_p.V66M	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	66			V -> M (polymorphism that impairs localization to secretory granules or synapses; associated with poorer episodic memory; may have a protective effect in obsessive-compulsive disorder; dbSNP:rs6265). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12553913, ECO:0000269|PubMed:12836135, ECO:0000269|PubMed:12888803, ECO:0000269|PubMed:14566559, ECO:0000269|Ref.8}.		axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						TCTTCTATCACGTGTTCGAAA	0.527													C|||	1008	0.201278	0.0106	0.1527	5008	,	,		18573	0.4881		0.1968	False		,,,				2504	0.2025				p.V148M		Atlas-SNP	.											.	BDNF	63	.	0			c.G442A	GRCh37	CM020369	BDNF	M	rs6265	PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	184,4220	118.0+/-155.7	3,178,2021	207.0	197.0	200.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	196,196,196,196,283,442,196,196,196,196,196,196,220,196,196,241,196	5.2	1.0	11	dbSNP_52	200	1640,6958	303.3+/-306.4	166,1308,2825	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	BDNF	NM_001143805.1,NM_001143806.1,NM_001143807.1,NM_001143808.1,NM_001143809.1,NM_001143810.1,NM_001143811.1,NM_001143812.1,NM_001143813.1,NM_001143814.1,NM_001143816.1,NM_001709.4,NM_170731.4,NM_170732.4,NM_170733.3,NM_170734.3,NM_170735.5	21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21	169,1486,4846	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	19.0742,4.178,14.0286	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	66/248,66/248,66/248,66/248,95/277,148/330,66/248,66/248,66/248,66/248,66/248,66/248,74/256,66/248,66/248,81/263,66/248	27679916	1824,11178	2202	4299	6501	SO:0001583	missense	627	exon3			CTATCACGTGTTC	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"""Endogenous ligands"""	1033	protein-coding gene	gene with protein product	"""neurotrophin"""	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.196G>A	11.37:g.27679916C>T	ENSP00000437138:p.Val66Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_001143810	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000525528.1	37	CCDS7866.1	499	0.22847985347985347	7	0.014227642276422764	64	0.17679558011049723	274	0.479020979020979	154	0.20316622691292877	C	13.00	2.107047	0.37145	0.04178	0.190742	ENSG00000176697	ENST00000439476;ENST00000525528;ENST00000395986;ENST00000533131;ENST00000356660;ENST00000418212;ENST00000533246;ENST00000530861;ENST00000395983;ENST00000438929;ENST00000395980;ENST00000532997;ENST00000395981;ENST00000395978;ENST00000525950;ENST00000314915;ENST00000420794;ENST00000528035	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.55234	0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53;0.53	6.16	5.25	0.73442	.	0.063003	0.64402	N	0.000006	T	0.00012	0.0000	M	0.64997	1.995	0.09310	P	0.999999020481	D;P;D;D;D	0.76494	0.999;0.889;0.999;0.998;0.999	D;B;D;D;D	0.91635	0.999;0.134;0.991;0.981;0.991	T	0.42982	-0.9419	9	0.87932	D	0	-10.0315	15.4433	0.75204	0.0:0.9339:0.0:0.0661	rs6265;rs3829232;rs16917222;rs17855547;rs60760775;rs6265	95;148;74;66;81	P23560-5;P23560-4;P23560-2;P23560;P23560-3	.;.;.;BDNF_HUMAN;.	M	66;66;81;66;66;66;66;66;66;148;66;66;66;66;66;74;66;66	ENSP00000389345:V66M;ENSP00000437138:V66M;ENSP00000379309:V81M;ENSP00000432727:V66M;ENSP00000349084:V66M;ENSP00000400502:V66M;ENSP00000432376:V66M;ENSP00000435564:V66M;ENSP00000379307:V66M;ENSP00000414303:V148M;ENSP00000379304:V66M;ENSP00000435805:V66M;ENSP00000379305:V66M;ENSP00000379302:V66M;ENSP00000432035:V66M;ENSP00000320002:V74M;ENSP00000389564:V66M	ENSP00000320002:V74M	V	-	1	0	BDNF	27636492	0.999000	0.42202	0.996000	0.52242	0.911000	0.54048	3.967000	0.56802	1.612000	0.50221	0.650000	0.86243	GTG	C|0.815;T|0.185	0.185	strong		0.527	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
QSOX1	5768	hgsc.bcm.edu	37	1	180159657	180159657	+	Silent	SNP	C	C	T	rs1050154	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:180159657C>T	ENST00000367602.3	+	10	1304	c.1230C>T	c.(1228-1230)ctC>ctT	p.L410L	QSOX1_ENST00000367600.5_Silent_p.L410L			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	410	ERV/ALR sulfhydryl oxidase. {ECO:0000255|PROSITE-ProRule:PRU00654}.				cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						TGTGGGTCCTCTTCCACTTCT	0.597													C|||	629	0.125599	0.0832	0.1556	5008	,	,		18905	0.0734		0.1581	False		,,,				2504	0.182				p.L410L		Atlas-SNP	.											.	QSOX1	79	.	0			c.C1230T						PASS	.	C	,	390,4016		27,336,1840	134.0	120.0	125.0		1230,1230	-1.8	1.0	1	dbSNP_86	125	1353,7247		121,1111,3068	no	coding-synonymous,coding-synonymous	QSOX1	NM_001004128.2,NM_002826.4	,	148,1447,4908	TT,TC,CC		15.7326,8.8516,13.4015	,	410/605,410/748	180159657	1743,11263	2203	4300	6503	SO:0001819	synonymous_variant	5768	exon10			GGTCCTCTTCCAC	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1230C>T	1.37:g.180159657C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Silent	SNP	ENST00000367602.3	37	CCDS1337.1																																																																																			C|0.864;T|0.136	0.136	strong		0.597	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
FAM71F2	346653	hgsc.bcm.edu	37	7	128315882	128315882	+	Missense_Mutation	SNP	C	C	A	rs17169357	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128315882C>A	ENST00000480462.1	+	2	440	c.334C>A	c.(334-336)Cct>Act	p.P112T	FAM71F2_ENST00000460349.1_3'UTR|FAM71F2_ENST00000378704.3_Missense_Mutation_p.P103T|FAM71F2_ENST00000477515.1_Missense_Mutation_p.P112T			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	112			P -> T (in dbSNP:rs17169357). {ECO:0000269|PubMed:15489334}.							NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						CTGGAGCACACCTGGTGACGC	0.587													.|||	1655	0.330471	0.177	0.3098	5008	,	,		15407	0.5615		0.2903	False		,,,				2504	0.3558				p.P112T		Atlas-SNP	.											.	FAM71F2	19	.	0			c.C334A						PASS	.	C	THR/PRO,THR/PRO	735,3091		76,583,1254	46.0	43.0	44.0		334,307	1.8	0.0	7	dbSNP_123	44	2459,5803		379,1701,2051	yes	missense,missense	FAM71F2	NM_001012454.3,NM_001128926.1	38,38	455,2284,3305	AA,AC,CC		29.7628,19.2107,26.4229	benign,benign	112/310,103/301	128315882	3194,8894	1913	4131	6044	SO:0001583	missense	346653	exon2			AGCACACCTGGTG	BC047310	CCDS47701.1, CCDS47702.1	7q32.1	2009-04-17	2007-11-20	2007-11-20	ENSG00000205085	ENSG00000205085			27998	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member B"""	FAM137B		12477932	Standard	XM_006715964		Approved		uc003vnk.4	Q6NXP2	OTTHUMG00000158275	ENST00000480462.1:c.334C>A	7.37:g.128315882C>A	ENSP00000420140:p.Pro112Thr	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	708	0.3241758241758242	98	0.1991869918699187	101	0.27900552486187846	296	0.5174825174825175	213	0.28100263852242746	C	7.819	0.717347	0.15372	0.192107	0.297628	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001;ENST00000477515	T;T;T;T;T	0.35236	3.18;3.17;3.18;3.18;1.32	4.67	1.77	0.24775	.	0.291939	0.24851	N	0.035089	T	0.00012	0.0000	M	0.68593	2.085	0.80722	P	0.0	B;B	0.20671	0.047;0.028	B;B	0.21151	0.033;0.015	T	0.45891	-0.9230	9	0.20046	T	0.44	-12.2044	2.8366	0.05516	0.1903:0.5257:0.1841:0.0999	rs17169357;rs52807763;rs17169357	103;112	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	T	103;112;103;103;112	ENSP00000418907:P103T;ENSP00000420140:P112T;ENSP00000367976:P103T;ENSP00000401654:P103T;ENSP00000419649:P112T	ENSP00000367976:P103T	P	+	1	0	FAM71F2	128103118	0.014000	0.17966	0.005000	0.12908	0.419000	0.31324	1.082000	0.30803	0.653000	0.30826	0.557000	0.71058	CCT	C|0.664;A|0.335	0.335	strong		0.587	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
LAMA1	284217	hgsc.bcm.edu	37	18	6997818	6997818	+	Missense_Mutation	SNP	A	A	C	rs12961939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:6997818A>C	ENST00000389658.3	-	33	4822	c.4729T>G	c.(4729-4731)Tct>Gct	p.S1577A		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1577	Domain II and I.		S -> A (in dbSNP:rs12961939).		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)				AGGTTCAGAGAAAGAACGGCA	0.398													A|||	749	0.149561	0.1513	0.1758	5008	,	,		23170	0.0575		0.2684	False		,,,				2504	0.1012				p.S1577A		Atlas-SNP	.											.	LAMA1	458	.	0			c.T4729G						PASS	.	A	ALA/SER	658,3748	279.9+/-275.1	52,554,1597	205.0	187.0	193.0		4729	4.2	0.5	18	dbSNP_121	193	2311,6289	388.3+/-342.5	307,1697,2296	yes	missense	LAMA1	NM_005559.3	99	359,2251,3893	CC,CA,AA		26.8721,14.9342,22.8279	possibly-damaging	1577/3076	6997818	2969,10037	2203	4300	6503	SO:0001583	missense	284217	exon33			TCAGAGAAAGAAC	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.4729T>G	18.37:g.6997818A>C	ENSP00000374309:p.Ser1577Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	399	0.18269230769230768	76	0.15447154471544716	74	0.20441988950276244	40	0.06993006993006994	209	0.2757255936675462	A	10.49	1.363916	0.24684	0.149342	0.268721	ENSG00000101680	ENST00000389658	T	0.12039	2.72	5.36	4.18	0.49190	Laminin I (1);	0.281539	0.35615	N	0.003085	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	B	0.32324	0.364	B	0.33295	0.161	T	0.42816	-0.9429	9	0.14656	T	0.56	.	11.7865	0.52045	0.9275:0.0:0.0725:0.0	rs12961939;rs52825785;rs58740747;rs12961939	1577	P25391	LAMA1_HUMAN	A	1577	ENSP00000374309:S1577A	ENSP00000374309:S1577A	S	-	1	0	LAMA1	6987818	0.997000	0.39634	0.506000	0.27664	0.067000	0.16453	4.299000	0.59073	2.160000	0.67779	0.533000	0.62120	TCT	A|0.790;C|0.210	0.210	strong		0.398	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
OR13C9	286362	hgsc.bcm.edu	37	9	107380177	107380177	+	Silent	SNP	A	A	G	rs1813819	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107380177A>G	ENST00000259362.1	-	1	308	c.309T>C	c.(307-309)ctT>ctC	p.L103L		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	103						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)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						TGGCCAAGCCAAGGAACATCT	0.498													a|||	2155	0.430312	0.6271	0.2262	5008	,	,		20857	0.5754		0.1779	False		,,,				2504	0.4192				p.L103L		Atlas-SNP	.											.	OR13C9	42	.	0			c.T309C						PASS	.	G		2358,2048	598.6+/-389.1	674,1010,519	116.0	135.0	129.0		309	-3.7	0.9	9	dbSNP_92	129	1591,7009	286.3+/-297.7	184,1223,2893	no	coding-synonymous	OR13C9	NM_001001956.1		858,2233,3412	GG,GA,AA		18.5,46.4821,30.3629		103/319	107380177	3949,9057	2203	4300	6503	SO:0001819	synonymous_variant	286362	exon1			CAAGCCAAGGAAC		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.309T>C	9.37:g.107380177A>G		Somatic	294	0	0		WXS	Illumina HiSeq	Phase_I	223	83	0.372197	NM_001001956	Q6IFL2	Silent	SNP	ENST00000259362.1	37	CCDS35093.1																																																																																			A|0.694;G|0.306	0.306	strong		0.498	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
FGD2	221472	hgsc.bcm.edu	37	6	36995222	36995222	+	Silent	SNP	G	G	A	rs2274587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:36995222G>A	ENST00000274963.8	+	15	1794	c.1623G>A	c.(1621-1623)acG>acA	p.T541T		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	541					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|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)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						CCTCAGCCACGCCTGACCAGA	0.612													G|||	1139	0.227436	0.2035	0.2248	5008	,	,		19191	0.501		0.1054	False		,,,				2504	0.1053				p.T541T		Atlas-SNP	.											.	FGD2	65	.	0			c.G1623A						PASS	.	G		782,3624	315.8+/-294.3	78,626,1499	108.0	109.0	109.0		1623	-1.0	0.0	6	dbSNP_100	109	778,7822	185.0+/-232.9	36,706,3558	no	coding-synonymous	FGD2	NM_173558.3		114,1332,5057	AA,AG,GG		9.0465,17.7485,11.9945		541/656	36995222	1560,11446	2203	4300	6503	SO:0001819	synonymous_variant	221472	exon15			AGCCACGCCTGAC	AK097230	CCDS4829.1	6p21.2	2013-01-10	2004-08-24		ENSG00000146192	ENSG00000146192		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	3664	protein-coding gene	gene with protein product		605091	"""FGD1 family, member 2"""			10458911	Standard	NM_173558		Approved	ZFYVE4	uc010jwp.1	Q7Z6J4	OTTHUMG00000014616	ENST00000274963.8:c.1623G>A	6.37:g.36995222G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	128	94	0.734375	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Silent	SNP	ENST00000274963.8	37	CCDS4829.1																																																																																			G|0.824;A|0.175	0.175	strong		0.612	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558	
FUT3	2525	hgsc.bcm.edu	37	19	5844343	5844343	+	Missense_Mutation	SNP	C	C	T	rs3745635	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5844343C>T	ENST00000303225.6	-	3	1142	c.508G>A	c.(508-510)Ggc>Agc	p.G170S	FUT3_ENST00000589918.1_Missense_Mutation_p.G170S|FUT3_ENST00000593144.1_5'Flank|FUT3_ENST00000458379.2_Missense_Mutation_p.G170S|FUT3_ENST00000589620.1_Missense_Mutation_p.G170S	NM_000149.3	NP_000140	P21217	FUT3_HUMAN	fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group)	170			G -> S (in Le(-); completely inactive; dbSNP:rs28362464). {ECO:0000269|PubMed:8219240, ECO:0000269|PubMed:8240337, ECO:0000269|Ref.5}.		cell-cell recognition (GO:0009988)|fucosylation (GO:0036065)|macromolecule glycosylation (GO:0043413)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						TCCAGCCAGCCGTAGGGCGTG	0.647													C|||	769	0.153554	0.2988	0.219	5008	,	,		15232	0.1448		0.0159	False		,,,				2504	0.0613				p.G170S	Esophageal Squamous(82;745 1728 24593 44831)	Atlas-SNP	.											.	FUT3	30	.	0			c.G508A	GRCh37	CM930260	FUT3	M	rs3745635	PASS	.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY	1082,3304		129,824,1240	28.0	28.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	508,508,508,508	2.2	1.0	19	dbSNP_107	28	147,8393		0,147,4123	no	missense,missense,missense,missense	FUT3	NM_000149.3,NM_001097639.1,NM_001097640.1,NM_001097641.1	56,56,56,56	129,971,5363	TT,TC,CC		1.7213,24.6694,9.508	probably-damaging,probably-damaging,probably-damaging,probably-damaging	170/362,170/362,170/362,170/362	5844343	1229,11697	2193	4270	6463	SO:0001583	missense	2525	exon3			GCCAGCCGTAGGG		CCDS12153.1	19p13.3	2014-07-19	2006-01-12		ENSG00000171124	ENSG00000171124	2.4.1.65	"""CD molecules"", ""Blood group antigens"", ""Fucosyltransferases"""	4014	protein-coding gene	gene with protein product		111100	"""fucosyltransferase 3 (galactoside 3(4)-L-fucosyltransferase, Lewis blood group included)"""	LE		1977660, 1740457	Standard	NM_000149		Approved	CD174	uc002mdk.2	P21217	OTTHUMG00000180614	ENST00000303225.6:c.508G>A	19.37:g.5844343C>T	ENSP00000305603:p.Gly170Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	113	41	0.362832	NM_001097640	B5U7U9|B5U7V0|Q32NE7|Q99448|Q99449	Missense_Mutation	SNP	ENST00000303225.6	37	CCDS12153.1	303	0.13873626373626374	135	0.27439024390243905	65	0.17955801104972377	92	0.16083916083916083	11	0.014511873350923483	C	15.54	2.864545	0.51482	0.246694	0.017213	ENSG00000171124	ENST00000303225;ENST00000458379	T;T	0.32988	1.43;1.43	2.24	2.24	0.28232	.	0.000000	0.64402	D	0.000015	T	0.00012	0.0000	M	0.88775	2.98	0.27837	P	0.9412428	D;D;D;D	0.89917	1.0;0.999;0.999;0.999	D;D;D;D	0.83275	0.996;0.986;0.986;0.986	T	0.07673	-1.0760	9	0.62326	D	0.03	.	10.5177	0.44900	0.0:1.0:0.0:0.0	rs28362464	170;170;170;170	B3W6H0;A8K737;B3GVC1;P21217	.;.;.;FUT3_HUMAN	S	170	ENSP00000305603:G170S;ENSP00000416443:G170S	ENSP00000305603:G170S	G	-	1	0	FUT3	5795343	0.857000	0.29778	0.998000	0.56505	0.274000	0.26718	3.283000	0.51701	1.168000	0.42723	0.205000	0.17691	GGC	C|0.902;T|0.098	0.098	strong		0.647	FUT3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452204.1	NM_000149	
RECQL5	9400	hgsc.bcm.edu	37	17	73625286	73625286	+	Silent	SNP	G	G	A	rs820190	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73625286G>A	ENST00000317905.5	-	16	2376	c.2217C>T	c.(2215-2217)agC>agT	p.S739S	RECQL5_ENST00000423245.2_Silent_p.S712S|RECQL5_ENST00000443199.2_5'UTR	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	739					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)			TGGCAAGGGAGCTGCCCCCAG	0.647								Other identified genes with known or suspected DNA repair function					G|||	1144	0.228435	0.2247	0.2118	5008	,	,		16511	0.1577		0.3439	False		,,,				2504	0.1994				p.S739S		Atlas-SNP	.											.	RECQL5	77	.	0			c.C2217T						PASS	.	G		843,3013		99,645,1184	31.0	34.0	33.0		2217	-7.5	0.0	17	dbSNP_86	33	2670,5558		429,1812,1873	no	coding-synonymous	RECQL5	NM_004259.6		528,2457,3057	AA,AG,GG		32.4502,21.862,29.0715		739/992	73625286	3513,8571	1928	4114	6042	SO:0001819	synonymous_variant	9400	exon16			AAGGGAGCTGCCC	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.2217C>T	17.37:g.73625286G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			G|0.746;A|0.254	0.254	strong		0.647	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
NELL1	4745	hgsc.bcm.edu	37	11	21392487	21392487	+	Silent	SNP	C	C	T	rs4151056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:21392487C>T	ENST00000357134.5	+	15	1790	c.1638C>T	c.(1636-1638)tgC>tgT	p.C546C	NELL1_ENST00000532434.1_Silent_p.C546C|NELL1_ENST00000298925.5_Silent_p.C574C|NELL1_ENST00000529218.1_3'UTR|NELL1_ENST00000325319.5_Silent_p.C489C	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	546	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						GAAGCCACTGCGAGAAAGGTA	0.433													C|||	801	0.159944	0.2216	0.0735	5008	,	,		18435	0.2698		0.0726	False		,,,				2504	0.1145				p.C546C		Atlas-SNP	.											.	NELL1	179	.	0			c.C1638T						PASS	.	C	,	831,3575	325.3+/-299.0	81,669,1453	93.0	88.0	90.0		1638,1638	-7.8	0.6	11	dbSNP_110	90	469,8131	137.6+/-194.5	12,445,3843	no	coding-synonymous,coding-synonymous	NELL1	NM_006157.3,NM_201551.1	,	93,1114,5296	TT,TC,CC		5.4535,18.8606,9.9954	,	546/811,546/764	21392487	1300,11706	2203	4300	6503	SO:0001819	synonymous_variant	4745	exon15			CCACTGCGAGAAA	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.1638C>T	11.37:g.21392487C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	47	10	0.212766	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	37	CCDS7855.1																																																																																			C|0.868;T|0.132	0.132	strong		0.433	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
PRRG4	79056	hgsc.bcm.edu	37	11	32874919	32874919	+	Missense_Mutation	SNP	C	C	A	rs34139105	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:32874919C>A	ENST00000257836.3	+	6	780	c.527C>A	c.(526-528)cCa>cAa	p.P176Q		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	176			P -> Q (in dbSNP:rs34139105).			extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	7	Breast(20;0.206)					GCCTTGTCTCCATTGCCGCCT	0.517													C|||	271	0.0541134	0.0635	0.0346	5008	,	,		16129	0.0		0.0825	False		,,,				2504	0.0818				p.P176Q		Atlas-SNP	.											PRRG4,NS,carcinoma,+1,1	PRRG4	15	1	0			c.C527A						PASS	.	C	GLN/PRO	288,4116	159.2+/-191.8	8,272,1922	106.0	100.0	102.0		527	2.6	0.0	11	dbSNP_126	102	733,7865	176.6+/-226.4	26,681,3592	yes	missense	PRRG4	NM_024081.5	76	34,953,5514	AA,AC,CC		8.5252,6.5395,7.8526	possibly-damaging	176/227	32874919	1021,11981	2202	4299	6501	SO:0001583	missense	79056	exon6			TGTCTCCATTGCC	AF326351	CCDS7881.1	11p13	2008-02-05			ENSG00000135378	ENSG00000135378			30799	protein-coding gene	gene with protein product		611690				11171957	Standard	NM_024081		Approved	TMG4	uc001mtx.3	Q9BZD6	OTTHUMG00000166219	ENST00000257836.3:c.527C>A	11.37:g.32874919C>A	ENSP00000257836:p.Pro176Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_024081		Missense_Mutation	SNP	ENST00000257836.3	37	CCDS7881.1	115	0.052655677655677656	28	0.056910569105691054	14	0.03867403314917127	0	0.0	73	0.09630606860158311	C	6.598	0.478792	0.12521	0.065395	0.085252	ENSG00000135378	ENST00000257836	D	0.98012	-4.66	5.56	2.57	0.30868	.	0.152215	0.64402	D	0.000011	T	0.51568	0.1682	M	0.62723	1.935	0.09310	N	0.999997	P	0.50272	0.933	P	0.45577	0.486	T	0.71510	-0.4571	10	0.29301	T	0.29	-0.7029	6.8589	0.24056	0.0:0.6953:0.1443:0.1605	rs34139105	176	Q9BZD6	TMG4_HUMAN	Q	176	ENSP00000257836:P176Q	ENSP00000257836:P176Q	P	+	2	0	PRRG4	32831495	0.005000	0.15991	0.001000	0.08648	0.018000	0.09664	1.561000	0.36342	0.265000	0.21872	0.551000	0.68910	CCA	C|0.927;A|0.073	0.073	strong		0.517	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081	
RTP4	64108	hgsc.bcm.edu	37	3	187088656	187088656	+	Missense_Mutation	SNP	C	C	T	rs1047584	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:187088656C>T	ENST00000259030.2	+	2	346	c.236C>T	c.(235-237)aCa>aTa	p.T79I		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	79			T -> I (in dbSNP:rs1047584).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		GAGCACTGGACATCCCAGGGT	0.567													C|||	900	0.179712	0.1831	0.2363	5008	,	,		19987	0.0536		0.2376	False		,,,				2504	0.2055				p.T79I		Atlas-SNP	.											.	RTP4	20	.	0			c.C236T						PASS	.	C	ILE/THR	855,3551	336.5+/-304.4	92,671,1440	67.0	57.0	61.0		236	-7.8	0.0	3	dbSNP_86	61	2027,6573	353.4+/-329.1	231,1565,2504	yes	missense	RTP4	NM_022147.2	89	323,2236,3944	TT,TC,CC		23.5698,19.4054,22.159	possibly-damaging	79/247	187088656	2882,10124	2203	4300	6503	SO:0001583	missense	64108	exon2			ACTGGACATCCCA	BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"""Receptor transporter proteins"""	23992	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 4"""	609350	"""receptor transporter protein 4"""			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.236C>T	3.37:g.187088656C>T	ENSP00000259030:p.Thr79Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	190	91	0.478947	NM_022147	Q9H4F3	Missense_Mutation	SNP	ENST00000259030.2	37	CCDS33910.1	396	0.1813186813186813	92	0.18699186991869918	98	0.27071823204419887	36	0.06293706293706294	170	0.22427440633245382	C	6.698	0.497523	0.12762	0.194054	0.235698	ENSG00000136514	ENST00000259030	T	0.18810	2.19	3.89	-7.78	0.01223	.	1.733720	0.02687	N	0.110196	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.48089	0.905	P	0.49047	0.599	T	0.24548	-1.0157	9	0.44086	T	0.13	-0.034	0.4251	0.00462	0.1837:0.237:0.238:0.3414	rs1047584;rs3187602;rs1047584	79	Q96DX8	RTP4_HUMAN	I	79	ENSP00000259030:T79I	ENSP00000259030:T79I	T	+	2	0	RTP4	188571350	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.121000	0.03270	-3.035000	0.00265	-0.793000	0.03317	ACA	C|0.802;T|0.198	0.198	strong		0.567	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
COL22A1	169044	hgsc.bcm.edu	37	8	139642974	139642974	+	Silent	SNP	T	T	C	rs4131277	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:139642974T>C	ENST00000303045.6	-	50	4073	c.3627A>G	c.(3625-3627)gcA>gcG	p.A1209A	COL22A1_ENST00000435777.1_Silent_p.A1189A|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1209	Collagen-like 11.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CAGCAGCTCCTGCAATTCCAT	0.463										HNSCC(7;0.00092)			C|||	1312	0.261981	0.5439	0.2522	5008	,	,		20306	0.1974		0.0795	False		,,,				2504	0.1421				p.A1209A		Atlas-SNP	.											.	COL22A1	390	.	0			c.A3627G						PASS	.	C		2074,2332	603.9+/-390.2	484,1106,613	131.0	130.0	130.0		3627	-11.3	0.0	8	dbSNP_108	130	834,7766	781.4+/-407.6	50,734,3516	no	coding-synonymous	COL22A1	NM_152888.1		534,1840,4129	CC,CT,TT		9.6977,47.0722,22.3589		1209/1627	139642974	2908,10098	2203	4300	6503	SO:0001819	synonymous_variant	169044	exon50			AGCTCCTGCAATT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3627A>G	8.37:g.139642974T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			T|0.780;C|0.220	0.220	strong		0.463	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
OR5P2	120065	hgsc.bcm.edu	37	11	7817856	7817856	+	Missense_Mutation	SNP	C	C	T	rs78460198	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7817856C>T	ENST00000329434.2	-	1	664	c.634G>A	c.(634-636)Gtc>Atc	p.V212I	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V212I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		ATGTAGCAGACGGCTATGACA	0.493													C|||	1185	0.236621	0.3472	0.2911	5008	,	,		18815	0.128		0.2763	False		,,,				2504	0.1196				p.V212I		Atlas-SNP	.											OR5P2,colon,carcinoma,0,2	OR5P2	68	2	1	Substitution - Missense(1)	large_intestine(1)	c.G634A						PASS	.	C	ILE/VAL	1371,2839		401,569,1135	99.0	104.0	102.0		634	-11.0	0.0	11	dbSNP_131	102	2425,6159		393,1639,2260	no	missense	OR5P2	NM_153444.1	29	794,2208,3395	TT,TC,CC		28.2502,32.5653,29.6702	benign	212/323	7817856	3796,8998	2105	4292	6397	SO:0001583	missense	120065	exon1			AGCAGACGGCTAT	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.634G>A	11.37:g.7817856C>T	ENSP00000331823:p.Val212Ile	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	586	0.2683150183150183	180	0.36585365853658536	100	0.27624309392265195	84	0.14685314685314685	222	0.2928759894459103	C	0.005	-2.119520	0.00346	0.325653	0.282502	ENSG00000183303	ENST00000329434	T	0.37235	1.21	5.5	-11.0	0.00169	GPCR, rhodopsin-like superfamily (1);	0.814212	0.11083	N	0.601638	T	0.00012	0.0000	N	0.11000	0.08	0.80722	P	0.0	B	0.13594	0.008	B	0.18263	0.021	T	0.36578	-0.9742	9	0.02654	T	1	-5.754	20.7759	0.99721	0.0:0.328:0.0:0.672	.	212	Q8WZ92	OR5P2_HUMAN	I	212	ENSP00000331823:V212I	ENSP00000331823:V212I	V	-	1	0	OR5P2	7774432	0.000000	0.05858	0.000000	0.03702	0.379000	0.30106	-6.285000	0.00072	-3.387000	0.00174	-1.300000	0.01332	GTC	C|0.739;T|0.261	0.261	strong		0.493	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
AMPD3	272	hgsc.bcm.edu	37	11	10521764	10521764	+	Silent	SNP	T	T	C	rs3741041	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:10521764T>C	ENST00000396554.3	+	11	2057	c.1716T>C	c.(1714-1716)taT>taC	p.Y572Y	AMPD3_ENST00000444303.2_Silent_p.Y404Y|AMPD3_ENST00000530864.1_3'UTR	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	563					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		ACTACATGTATGCCAACATCA	0.547													T|||	1840	0.367412	0.0545	0.3991	5008	,	,		27067	0.6944		0.4145	False		,,,				2504	0.3824				p.Y572Y		Atlas-SNP	.											.	AMPD3	68	.	0			c.T1716C						PASS	.	T	,,,,	540,3862	244.0+/-253.5	31,478,1692	324.0	208.0	247.0		1716,1689,1710,1689,1212	-2.7	1.0	11	dbSNP_107	247	3545,5043	516.6+/-378.9	727,2091,1476	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	,,,,	758,2569,3168	CC,CT,TT		41.2785,12.2672,31.4473	,,,,	572/777,563/768,570/775,563/768,404/609	10521764	4085,8905	2201	4294	6495	SO:0001819	synonymous_variant	272	exon11			CATGTATGCCAAC	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.1716T>C	11.37:g.10521764T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	121	53	0.438017	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																			T|0.653;C|0.347	0.347	strong		0.547	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
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 GAIIx	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	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	58	33	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	
RNASE11	122651	hgsc.bcm.edu	37	14	21052259	21052259	+	Silent	SNP	T	T	C	rs1429539	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:21052259T>C	ENST00000610205.1	-	3	558	c.375A>G	c.(373-375)acA>acG	p.T125T	RNASE11_ENST00000432835.2_Silent_p.T125T|RNASE11_ENST00000398009.2_Silent_p.T125T|RNASE11_ENST00000555841.1_Silent_p.T125T|RNASE11_ENST00000553849.1_Silent_p.T125T|RNASE11_ENST00000398008.2_Silent_p.T125T	NM_145250.3	NP_660293.1	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)	125						extracellular region (GO:0005576)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(6)|lung(7)|ovary(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	21	all_cancers(95;0.00238)	all_lung(585;0.235)	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)		GCATCACTTCTGTGGAGCTGC	0.493													C|||	1842	0.367812	0.5484	0.2723	5008	,	,		21015	0.1905		0.3539	False		,,,				2504	0.3885				p.T125T		Atlas-SNP	.											.	RNASE11	44	.	0			c.A375G						PASS	.	C		2223,2183	585.8+/-386.3	575,1073,555	86.0	74.0	78.0		375	-1.9	0.0	14	dbSNP_88	78	3189,5411	653.4+/-401.0	604,1981,1715	no	coding-synonymous	RNASE11	NM_145250.3		1179,3054,2270	CC,CT,TT		37.0814,49.5461,41.6116		125/200	21052259	5412,7594	2203	4300	6503	SO:0001819	synonymous_variant	122651	exon3			CACTTCTGTGGAG	BC025410	CCDS9553.1	14q11.1	2013-08-05	2004-11-18	2004-11-18	ENSG00000173464	ENSG00000173464		"""Ribonucleases, RNase A"""	19269	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 6"""	C14orf6			Standard	NM_145250		Approved		uc001vxs.3	Q8TAA1	OTTHUMG00000170990	ENST00000610205.1:c.375A>G	14.37:g.21052259T>C		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	194	92	0.474227	NM_145250		Silent	SNP	ENST00000610205.1	37	CCDS9553.1																																																																																			T|0.613;C|0.387	0.387	strong		0.493	RNASE11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073662.3	NM_145250	
ZCCHC14	23174	hgsc.bcm.edu	37	16	87451273	87451273	+	Silent	SNP	G	G	T	rs56283442	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:87451273G>T	ENST00000268616.4	-	8	982	c.765C>A	c.(763-765)tcC>tcA	p.S255S		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	255							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		AGGGGGCGGCGGAGCCGGCCG	0.697													T|||	746	0.148962	0.5053	0.0533	5008	,	,		15812	0.0		0.0358	False		,,,				2504	0.0051				p.S255S		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.C765A						PASS	.	T		1774,2622	627.4+/-394.9	360,1054,784	43.0	51.0	49.0		765	-11.1	0.0	16	dbSNP_129	49	220,8378	798.3+/-407.4	1,218,4080	no	coding-synonymous	ZCCHC14	NM_015144.2		361,1272,4864	TT,TG,GG		2.5587,40.3549,15.3455		255/950	87451273	1994,11000	2198	4299	6497	SO:0001819	synonymous_variant	23174	exon8			GGCGGCGGAGCCG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.765C>A	16.37:g.87451273G>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																			G|0.859;T|0.141	0.141	strong		0.697	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
EHMT1	79813	hgsc.bcm.edu	37	9	140638416	140638416	+	Silent	SNP	G	G	A	rs1129767	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:140638416G>A	ENST00000460843.1	+	6	1071	c.1044G>A	c.(1042-1044)tcG>tcA	p.S348S	EHMT1_ENST00000334856.6_Silent_p.S317S|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Silent_p.S348S	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	348					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		AGATGGACTCGGATGAGGACG	0.632													G|||	763	0.152356	0.0068	0.3862	5008	,	,		18222	0.1012		0.167	False		,,,				2504	0.2209				p.S348S		Atlas-SNP	.											EHMT1_ENST00000460843,colon,carcinoma,+1,2	EHMT1	196	2	0			c.G1044A						PASS	.	G	,	169,4237	109.9+/-148.2	2,165,2036	56.0	50.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1044,1044	-10.8	0.0	9	dbSNP_86	52	1537,7063	288.9+/-299.0	144,1249,2907	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	146,1414,4943	AA,AG,GG		17.8721,3.8357,13.117	,	348/809,348/1299	140638416	1706,11300	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon6			GGACTCGGATGAG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1044G>A	9.37:g.140638416G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			G|0.862;A|0.138	0.138	strong		0.632	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
BRCA2	675	hgsc.bcm.edu	37	13	32929232	32929232	+	Silent	SNP	A	A	G	rs1799955	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:32929232A>G	ENST00000380152.3	+	14	7475	c.7242A>G	c.(7240-7242)tcA>tcG	p.S2414S	BRCA2_ENST00000544455.1_Silent_p.S2414S			P51587	BRCA2_HUMAN	breast cancer 2, early onset	2414	Interaction with FANCD2.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AAACTAAATCACATTTTCACA	0.333			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			A|||	1165	0.232628	0.2073	0.1988	5008	,	,		20134	0.369		0.2087	False		,,,				2504	0.1748				p.S2414S	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.A7242G						PASS	.	A		915,3491	350.3+/-310.7	85,745,1373	74.0	73.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7242	-2.2	0.5	13	dbSNP_89	74	1834,6766	328.4+/-318.3	188,1458,2654	no	coding-synonymous	BRCA2	NM_000059.3		273,2203,4027	GG,GA,AA		21.3256,20.7671,21.1364		2414/3419	32929232	2749,10257	2203	4300	6503	SO:0001819	synonymous_variant	675	exon14	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TAAATCACATTTT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.7242A>G	13.37:g.32929232A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			A|0.772;G|0.228	0.228	strong		0.333	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
FMO2	2327	hgsc.bcm.edu	37	1	171174531	171174531	+	Missense_Mutation	SNP	A	A	G	rs2020863	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171174531A>G	ENST00000209929.7	+	7	1099	c.941A>G	c.(940-942)gAg>gGg	p.E314G	FMO2_ENST00000529935.1_3'UTR|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.E314G|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	313					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.E314G(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GCCATCTTTGAGGATGGAACA	0.408													A|||	800	0.159744	0.0424	0.2277	5008	,	,		20245	0.2371		0.0905	False		,,,				2504	0.2618				p.E314G		Atlas-SNP	.											FMO2,NS,carcinoma,0,1	FMO2	66	1	1	Substitution - Missense(1)	stomach(1)	c.A941G						PASS	.	A	GLY/GLU	275,4131	153.3+/-186.9	9,257,1937	95.0	92.0	93.0		941	5.7	1.0	1	dbSNP_98	93	790,7810	186.3+/-233.8	35,720,3545	yes	missense	FMO2	NM_001460.2	98	44,977,5482	GG,GA,AA		9.186,6.2415,8.1885	possibly-damaging	314/472	171174531	1065,11941	2203	4300	6503	SO:0001583	missense	2327	exon7			TCTTTGAGGATGG	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.941A>G	1.37:g.171174531A>G	ENSP00000209929:p.Glu314Gly	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	296	0.13553113553113552	18	0.036585365853658534	61	0.1685082872928177	152	0.26573426573426573	65	0.08575197889182058	A	16.76	3.211991	0.58452	0.062415	0.09186	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.58940	0.3;0.3	5.67	5.67	0.87782	.	0.097167	0.64402	D	0.000002	T	0.67748	0.2926	M	0.88241	2.94	0.22591	P	0.99895097	P	0.35050	0.482	P	0.47705	0.555	T	0.75283	-0.3372	9	0.87932	D	0	-25.4404	14.8967	0.70649	1.0:0.0:0.0:0.0	rs2020863;rs2266707;rs61588049;rs2020863	314	Q99518	FMO2_HUMAN	G	314	ENSP00000209929:E314G;ENSP00000405905:E314G	ENSP00000209929:E314G	E	+	2	0	FMO2	169441155	1.000000	0.71417	0.969000	0.41365	0.738000	0.42128	4.940000	0.63533	2.154000	0.67381	0.533000	0.62120	GAG	A|0.884;G|0.116	0.116	strong		0.408	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
NDRG4	65009	hgsc.bcm.edu	37	16	58542901	58542901	+	Silent	SNP	G	G	A	rs867583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:58542901G>A	ENST00000570248.1	+	11	871	c.765G>A	c.(763-765)acG>acA	p.T255T	NDRG4_ENST00000569923.1_Silent_p.T200T|NDRG4_ENST00000258187.5_Silent_p.T287T|NDRG4_ENST00000566192.1_Silent_p.T255T|NDRG4_ENST00000394279.2_Silent_p.T287T|NDRG4_ENST00000356752.4_Silent_p.T285T|NDRG4_ENST00000568640.1_Silent_p.T273T|NDRG4_ENST00000394282.4_Silent_p.T307T|NDRG4_ENST00000562999.1_Silent_p.T255T|NDRG4_ENST00000563799.1_Silent_p.T273T	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	255	Poly-Thr.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						CGACCACTACGACCTTCCTGA	0.632													G|||	1797	0.358826	0.379	0.2392	5008	,	,		18235	0.5694		0.2127	False		,,,				2504	0.3497				p.T307T		Atlas-SNP	.											.	NDRG4	29	.	0			c.G921A						PASS	.	G	,,,,,,	1646,2750	501.2+/-364.9	320,1006,872	68.0	70.0	69.0		921,855,819,765,765,861,861	-7.5	0.8	16	dbSNP_86	69	1716,6884	313.1+/-311.2	163,1390,2747	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDRG4	NM_001130487.1,NM_001242833.1,NM_001242834.1,NM_001242835.1,NM_001242836.1,NM_020465.3,NM_022910.3	,,,,,,	483,2396,3619	AA,AG,GG		19.9535,37.4431,25.8695	,,,,,,	307/392,285/370,273/358,255/353,255/340,287/372,287/372	58542901	3362,9634	2198	4300	6498	SO:0001819	synonymous_variant	65009	exon13			CACTACGACCTTC	AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.765G>A	16.37:g.58542901G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_001130487	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Silent	SNP	ENST00000570248.1	37	CCDS58466.1																																																																																			G|0.696;A|0.304	0.304	strong		0.632	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2		
WFDC1	58189	hgsc.bcm.edu	37	16	84360533	84360533	+	Missense_Mutation	SNP	A	A	G	rs12933084	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84360533A>G	ENST00000219454.5	+	6	976	c.650A>G	c.(649-651)aAg>aGg	p.K217R	WFDC1_ENST00000568638.1_Missense_Mutation_p.K217R	NM_001282466.1|NM_001282467.1	NP_001269395.1|NP_001269396.1	Q9HC57	WFDC1_HUMAN	WAP four-disulfide core domain 1	217			K -> R (in dbSNP:rs12933084). {ECO:0000269|PubMed:10967136, ECO:0000269|Ref.4}.		negative regulation of cell growth (GO:0030308)|negative regulation of epithelial cell proliferation (GO:0050680)|response to drug (GO:0042493)|response to estradiol (GO:0032355)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)	9						GGACAACAGAAGCACTTTCAG	0.507													G|||	1494	0.298323	0.3275	0.2709	5008	,	,		21130	0.2788		0.3012	False		,,,				2504	0.2955				p.K217R		Atlas-SNP	.											.	WFDC1	17	.	0			c.A650G						PASS	.	G	ARG/LYS	1442,2958	682.0+/-404.1	240,962,998	133.0	122.0	125.0		650	1.4	0.0	16	dbSNP_121	125	2654,5946	685.3+/-404.0	444,1766,2090	yes	missense	WFDC1	NM_021197.2	26	684,2728,3088	GG,GA,AA		30.8605,32.7727,31.5077	benign	217/221	84360533	4096,8904	2200	4300	6500	SO:0001583	missense	58189	exon6			AACAGAAGCACTT	AF302109	CCDS10946.1	16q24.1	2013-01-21			ENSG00000103175	ENSG00000103175		"""WAP four-disulfide core domain containing"""	15466	protein-coding gene	gene with protein product		605322				10967136	Standard	NM_021197		Approved	PS20	uc002fhw.3	Q9HC57	OTTHUMG00000137641	ENST00000219454.5:c.650A>G	16.37:g.84360533A>G	ENSP00000219454:p.Lys217Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_021197	D3DUL7|Q8NC27|Q9HAU1	Missense_Mutation	SNP	ENST00000219454.5	37	CCDS10946.1	594	0.27197802197802196	128	0.2601626016260163	113	0.31215469613259667	145	0.2534965034965035	208	0.27440633245382584	G	0.095	-1.161164	0.01673	0.327727	0.308605	ENSG00000103175	ENST00000219454	T	0.33438	1.41	3.48	1.41	0.22369	.	0.129258	0.50627	N	0.000119	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	0.42189	-0.9466	9	0.02654	T	1	-8.1222	3.5776	0.07941	0.3283:0.192:0.4797:0.0	rs12933084;rs52824232;rs56778113;rs12933084	217	Q9HC57	WFDC1_HUMAN	R	217	ENSP00000219454:K217R	ENSP00000219454:K217R	K	+	2	0	WFDC1	82918034	0.993000	0.37304	0.001000	0.08648	0.159000	0.22180	0.806000	0.27126	0.111000	0.17947	-0.349000	0.07799	AAG	A|0.701;G|0.299	0.299	strong		0.507	WFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269083.2		
DDX5	1655	hgsc.bcm.edu	37	17	62496670	62496670	+	Missense_Mutation	SNP	A	A	C	rs1140409	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:62496670A>C	ENST00000225792.5	-	12	1839	c.1438T>G	c.(1438-1440)Tca>Gca	p.S480A	DDX5_ENST00000578804.1_Missense_Mutation_p.S480A|DDX5_ENST00000450599.2_Missense_Mutation_p.S401A|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000580026.1_5'UTR|MIR3064_ENST00000581130.1_RNA	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	480	Transactivation domain.		S -> A (in dbSNP:rs1140409).		cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			TCCTTACCTGAACCTCTGTCT	0.403			T	ETV4	prostate								A|||	146	0.0291534	0.003	0.0461	5008	,	,		21998	0.0		0.0835	False		,,,				2504	0.0266				p.S480A	NSCLC(22;406 813 4871 19580 40307)	Atlas-SNP	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	.	DDX5	101	.	0			c.T1438G	GRCh37	CM066777	DDX5	M	rs1140409	PASS	.	A	ALA/SER	51,4355	50.9+/-86.3	1,49,2153	88.0	78.0	81.0		1438	4.6	1.0	17	dbSNP_86	81	615,7985	158.6+/-212.1	27,561,3712	yes	missense	DDX5	NM_004396.3	99	28,610,5865	CC,CA,AA		7.1512,1.1575,5.1207	benign	480/615	62496670	666,12340	2203	4300	6503	SO:0001583	missense	1655	exon12			TACCTGAACCTCT	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"""DEAD-boxes"""	2746	protein-coding gene	gene with protein product		180630	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"""	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.1438T>G	17.37:g.62496670A>C	ENSP00000225792:p.Ser480Ala	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	135	54	0.4	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	37	CCDS11659.1	88	0.040293040293040296	3	0.006097560975609756	19	0.052486187845303865	0	0.0	66	0.0870712401055409	A	4.506	0.093795	0.08632	0.011575	0.071512	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	5.73	4.64	0.57946	.	0.338429	0.30311	N	0.009909	T	0.01800	0.0057	L	0.29908	0.895	0.38284	D	0.942529	B;B;B	0.17852	0.013;0.024;0.024	B;B;B	0.14023	0.004;0.01;0.01	T	0.04229	-1.0967	9	0.18710	T	0.47	.	7.5474	0.27775	0.7721:0.1564:0.0715:0.0	rs1140409;rs2229795;rs3179861;rs3204465;rs52828247;rs57832194;rs1140409	401;480;480	B4DLW8;B5BUE6;P17844	.;.;DDX5_HUMAN	A	480;410;469	.	ENSP00000225792:S469A	S	-	1	0	DDX5	59927132	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	4.358000	0.59442	1.096000	0.41439	0.533000	0.62120	TCA	A|0.953;C|0.047	0.047	strong		0.403	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396	
EVA1C	59271	hgsc.bcm.edu	37	21	33887131	33887131	+	Silent	SNP	G	G	A	rs1129157	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:33887131G>A	ENST00000300255.2	+	8	1430	c.957G>A	c.(955-957)ccG>ccA	p.P319P	EVA1C_ENST00000485488.1_3'UTR|EVA1C_ENST00000382699.3_Silent_p.P316P|EVA1C_ENST00000401402.3_Silent_p.P271P	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	319						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										CAGCCCACCCGGAGAGAGCTG	0.617													G|||	2458	0.490815	0.5976	0.5072	5008	,	,		17369	0.631		0.2922	False		,,,				2504	0.3947				p.P319P		Atlas-SNP	.											.	.	.	.	0			c.G957A						PASS	.	G		2457,1949	584.9+/-386.1	698,1061,444	38.0	39.0	39.0		957	-11.2	0.2	21	dbSNP_105	39	2363,6237	365.7+/-334.0	328,1707,2265	no	coding-synonymous	C21orf63	NM_058187.3		1026,2768,2709	AA,AG,GG		27.4767,44.2351,37.0598		319/442	33887131	4820,8186	2203	4300	6503	SO:0001819	synonymous_variant	59271	exon8			CCACCCGGAGAGA	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 64"", ""chromosome 21 open reading frame 63"", ""family with sequence similarity 176, member C"""	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.957G>A	21.37:g.33887131G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_058187	A6ND58|Q8IXZ0	Silent	SNP	ENST00000300255.2	37	CCDS13614.1																																																																																			G|0.575;A|0.425	0.425	strong		0.617	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187	
CCT2	10576	hgsc.bcm.edu	37	12	69986788	69986788	+	Silent	SNP	A	A	G	rs1043434	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:69986788A>G	ENST00000299300.6	+	9	971	c.783A>G	c.(781-783)acA>acG	p.T261T	CCT2_ENST00000543146.2_Silent_p.T214T|CCT2_ENST00000544368.2_Silent_p.T261T	NM_006431.2	NP_006422.1	P78371	TCPB_HUMAN	chaperonin containing TCP1, subunit 2 (beta)	261					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(1)	24	all_cancers(2;7.7e-106)|Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.72e-18)|GBM - Glioblastoma multiforme(2;2.58e-10)|Lung(24;0.000185)|OV - Ovarian serous cystadenocarcinoma(12;0.00126)|STAD - Stomach adenocarcinoma(21;0.00501)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			TTGACTCTACAGCAAAGGTTG	0.363													A|||	1086	0.216853	0.084	0.1888	5008	,	,		19934	0.3026		0.2565	False		,,,				2504	0.2873				p.T261T		Atlas-SNP	.											.	CCT2	49	.	0			c.A783G						PASS	.	A	,	459,3947	218.1+/-236.3	20,419,1764	81.0	82.0	82.0		642,783	4.6	1.0	12	dbSNP_86	82	1954,6646	345.9+/-325.9	204,1546,2550	no	coding-synonymous,coding-synonymous	CCT2	NM_001198842.1,NM_006431.2	,	224,1965,4314	GG,GA,AA		22.7209,10.4176,18.553	,	214/489,261/536	69986788	2413,10593	2203	4300	6503	SO:0001819	synonymous_variant	10576	exon9			CTCTACAGCAAAG	AF026293	CCDS8991.1, CCDS55843.1	12q14	2011-09-02						"""Heat Shock Proteins / Chaperonins"""	1615	protein-coding gene	gene with protein product		605139				9819444	Standard	NM_001198842		Approved	Cctb	uc001svb.1	P78371	OTTHUMG00000169383	ENST00000299300.6:c.783A>G	12.37:g.69986788A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_006431	A8K402|B5BTY7|B7Z243|B7Z7K4|B7ZAT2|Q14D36|Q6IAT3	Silent	SNP	ENST00000299300.6	37	CCDS8991.1																																																																																			A|0.800;G|0.200	0.200	strong		0.363	CCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403818.1	NM_006431	
KLHL38	340359	hgsc.bcm.edu	37	8	124664113	124664113	+	Missense_Mutation	SNP	T	T	A	rs11784175	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124664113T>A	ENST00000325995.7	-	1	1077	c.1054A>T	c.(1054-1056)Aat>Tat	p.N352Y	CTD-2552K11.2_ENST00000524355.1_RNA	NM_001081675.2	NP_001075144.2	Q2WGJ6	KLH38_HUMAN	kelch-like family member 38	352			N -> Y (in dbSNP:rs11784175).					p.N352Y(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(16)|pancreas(1)|prostate(3)|stomach(1)	38						ATGTAGACATTGTGACTGACC	0.577													T|||	401	0.0800719	0.0083	0.0735	5008	,	,		20926	0.0923		0.1541	False		,,,				2504	0.093				p.N352Y		Atlas-SNP	.											KLHL38,NS,carcinoma,0,1	KLHL38	81	1	1	Substitution - Missense(1)	stomach(1)	c.A1054T						PASS	.	T	TYR/ASN	100,3982		0,100,1941	65.0	67.0	66.0		1054	-4.1	0.0	8	dbSNP_120	66	1139,7235		86,967,3134	yes	missense	KLHL38	NM_001081675.2	143	86,1067,5075	AA,AT,TT		13.6016,2.4498,9.947	possibly-damaging	352/582	124664113	1239,11217	2041	4187	6228	SO:0001583	missense	340359	exon1			AGACATTGTGACT		CCDS43766.1	8q24.13	2013-02-22	2013-02-22		ENSG00000175946	ENSG00000175946		"""Kelch-like"", ""BTB/POZ domain containing"""	34435	protein-coding gene	gene with protein product			"""kelch-like 38 (Drosophila)"""				Standard	NM_001081675		Approved	C8ORFK36	uc003yqs.1	Q2WGJ6	OTTHUMG00000164983	ENST00000325995.7:c.1054A>T	8.37:g.124664113T>A	ENSP00000321475:p.Asn352Tyr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_001081675	A0PK12	Missense_Mutation	SNP	ENST00000325995.7	37	CCDS43766.1	197	0.0902014652014652	6	0.012195121951219513	38	0.10497237569060773	43	0.07517482517482517	110	0.14511873350923482	T	6.482	0.457164	0.12283	0.024498	0.136016	ENSG00000175946	ENST00000325995	T	0.66995	-0.24	5.18	-4.09	0.03951	Kelch-type beta propeller (1);	0.762878	0.12967	N	0.424462	T	0.00356	0.0011	L	0.43152	1.355	0.80722	P	0.0	B	0.20550	0.046	B	0.20184	0.028	T	0.09357	-1.0678	9	0.59425	D	0.04	.	6.3935	0.21599	0.0:0.2677:0.3269:0.4053	rs11784175;rs17341070;rs52808446;rs11784175	352	Q2WGJ6	KLH38_HUMAN	Y	352	ENSP00000321475:N352Y	ENSP00000321475:N352Y	N	-	1	0	KLHL38	124733294	0.001000	0.12720	0.000000	0.03702	0.263000	0.26337	0.548000	0.23314	-0.490000	0.06707	0.459000	0.35465	AAT	T|0.899;A|0.101	0.101	strong		0.577	KLHL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381288.1		
EMILIN3	90187	hgsc.bcm.edu	37	20	39991144	39991144	+	Silent	SNP	A	A	G	rs41307177	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:39991144A>G	ENST00000332312.3	-	4	1257	c.1065T>C	c.(1063-1065)ctT>ctC	p.L355L		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	355						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				CCCGGCCATCAAGGCTCTGGT	0.682													A|||	406	0.0810703	0.0598	0.1225	5008	,	,		15115	0.003		0.1799	False		,,,				2504	0.0593				p.L355L		Atlas-SNP	.											EMILIN3,rectum,carcinoma,0,1	EMILIN3	63	1	0			c.T1065C						PASS	.	A		377,4021		11,355,1833	13.0	16.0	15.0		1065	-1.5	1.0	20	dbSNP_127	15	1411,7175		132,1147,3014	no	coding-synonymous	EMILIN3	NM_052846.1		143,1502,4847	GG,GA,AA		16.4337,8.5721,13.7708		355/767	39991144	1788,11196	2199	4293	6492	SO:0001819	synonymous_variant	90187	exon4			GCCATCAAGGCTC	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1065T>C	20.37:g.39991144A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			A|0.888;G|0.112	0.112	strong		0.682	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
ZBTB46	140685	hgsc.bcm.edu	37	20	62378364	62378364	+	Silent	SNP	C	C	T	rs12625387	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62378364C>T	ENST00000245663.4	-	5	1839	c.1689G>A	c.(1687-1689)gcG>gcA	p.A563A	RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA|ZBTB46_ENST00000395104.1_Silent_p.A563A|ZBTB46_ENST00000302995.2_Silent_p.A563A	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	563					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CCTTGTCGTCCGCCAACAGCG	0.721													C|||	1350	0.269569	0.1392	0.3804	5008	,	,		10252	0.3452		0.3499	False		,,,				2504	0.2065				p.A563A		Atlas-SNP	.											ZBTB46,rectum,carcinoma,0,1	ZBTB46	72	1	0			c.G1689A						PASS	.	C		746,3652		73,600,1526	30.0	29.0	29.0		1689	-0.2	0.3	20	dbSNP_120	29	2911,5675		480,1951,1862	no	coding-synonymous	ZBTB46	NM_025224.3		553,2551,3388	TT,TC,CC		33.904,16.9623,28.1654		563/590	62378364	3657,9327	2199	4293	6492	SO:0001819	synonymous_variant	140685	exon5			GTCGTCCGCCAAC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1689G>A	20.37:g.62378364C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.724;T|0.276	0.276	strong		0.721	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
SPTBN5	51332	hgsc.bcm.edu	37	15	42159290	42159290	+	Missense_Mutation	SNP	C	C	T	rs2290553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42159290C>T	ENST00000320955.6	-	36	6574	c.6347G>A	c.(6346-6348)cGg>cAg	p.R2116Q	MIR4310_ENST00000582950.1_RNA	NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2116					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCGGGGGCGCCGGAGCGTCTT	0.736													c|||	711	0.141973	0.034	0.1671	5008	,	,		14161	0.0446		0.2833	False		,,,				2504	0.2249				p.R2081Q		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G6242A						PASS	.	C	GLN/ARG	191,3125		13,165,1480	3.0	4.0	4.0		6242	-4.3	0.0	15	dbSNP_100	4	1708,5692		230,1248,2222	no	missense	SPTBN5	NM_016642.2	43	243,1413,3702	TT,TC,CC		23.0811,5.76,17.7212	possibly-damaging	2081/3640	42159290	1899,8817	1658	3700	5358	SO:0001583	missense	51332	exon36			GGGCGCCGGAGCG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.6347G>A	15.37:g.42159290C>T	ENSP00000317790:p.Arg2116Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		308	0.14102564102564102	20	0.04065040650406504	61	0.1685082872928177	19	0.033216783216783216	208	0.27440633245382584	.	9.097	1.003238	0.19121	0.0576	0.230811	ENSG00000137877	ENST00000320955	T	0.47177	0.85	4.61	-4.26	0.03755	.	1.848070	0.02996	N	0.147432	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B	0.25743	0.133	B	0.17098	0.017	T	0.09292	-1.0681	9	0.14252	T	0.57	.	6.4787	0.22051	0.0:0.4092:0.1605:0.4303	rs2290553;rs17736981	2116	Q9NRC6	SPTN5_HUMAN	Q	2116	ENSP00000317790:R2116Q	ENSP00000317790:R2116Q	R	-	2	0	SPTBN5	39946582	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.487000	0.06505	-0.666000	0.05310	-0.389000	0.06534	CGG	C|0.858;T|0.142	0.142	strong		0.736	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
QRICH2	84074	hgsc.bcm.edu	37	17	74287389	74287389	+	Missense_Mutation	SNP	T	T	C	rs2279053	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74287389T>C	ENST00000262765.5	-	4	3100	c.2921A>G	c.(2920-2922)cAt>cGt	p.H974R		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	974			H -> R (in dbSNP:rs2279053).							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						AGGAATTCCATGTCGGTCCGA	0.527													C|||	2350	0.469249	0.7065	0.3098	5008	,	,		19962	0.5734		0.2744	False		,,,				2504	0.3548				p.H974R		Atlas-SNP	.											.	QRICH2	143	.	0			c.A2921G						PASS	.	C	ARG/HIS	2927,1479	472.8+/-356.5	979,969,255	68.0	68.0	68.0		2921	-9.4	0.0	17	dbSNP_100	68	2483,6117	696.2+/-404.9	348,1787,2165	yes	missense	QRICH2	NM_032134.1	29	1327,2756,2420	CC,CT,TT		28.8721,33.5679,41.5962	benign	974/1664	74287389	5410,7596	2203	4300	6503	SO:0001583	missense	84074	exon4			ATTCCATGTCGGT	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.2921A>G	17.37:g.74287389T>C	ENSP00000262765:p.His974Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	984	0.45054945054945056	350	0.7113821138211383	106	0.292817679558011	333	0.5821678321678322	195	0.25725593667546176	C	2.659	-0.280104	0.05642	0.664321	0.288721	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08102	3.13	4.68	-9.36	0.00629	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31696	-0.9934	8	0.19147	T	0.46	9.8215	1.7269	0.02924	0.4102:0.2666:0.0962:0.2269	rs2279053;rs56708258;rs2279053	974;974	B5MD94;Q9H0J4	.;QRIC2_HUMAN	R	974	ENSP00000262765:H974R	ENSP00000262765:H974R	H	-	2	0	QRICH2	71798984	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.988000	0.03739	-2.936000	0.00299	-3.824000	0.00019	CAT	T|0.545;C|0.455	0.455	strong		0.527	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
LPA	4018	hgsc.bcm.edu	37	6	161007496	161007496	+	Missense_Mutation	SNP	G	G	C	rs7765781	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:161007496G>C	ENST00000316300.5	-	25	4158	c.4114C>G	c.(4114-4116)Ctt>Gtt	p.L1372V	LPA_ENST00000447678.1_Missense_Mutation_p.L1372V			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3880	Kringle 12. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	TCAGAAGGAAGCTCTGTGCTT	0.478													C|||	2078	0.414936	0.6006	0.268	5008	,	,		20695	0.4107		0.3648	False		,,,				2504	0.3241				p.L1372V		Atlas-SNP	.											.	LPA	237	.	0			c.C4114G						PASS	.	C	VAL/LEU	2188,1720		625,938,391	116.0	112.0	114.0		4114	-2.2	0.0	6	dbSNP_116	114	2865,5499		510,1845,1827	yes	missense	LPA	NM_005577.2	32	1135,2783,2218	CC,CG,GG		34.2539,44.0123,41.175	benign	1372/2041	161007496	5053,7219	1954	4182	6136	SO:0001583	missense	4018	exon26			AAGGAAGCTCTGT	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4114C>G	6.37:g.161007496G>C	ENSP00000321334:p.Leu1372Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	940	0.43040293040293043	312	0.6341463414634146	99	0.27348066298342544	240	0.4195804195804196	289	0.3812664907651715	c	0.003	-2.485890	0.00163	0.559877	0.342539	ENSG00000198670	ENST00000316300;ENST00000447678	D;D	0.86956	-2.19;-2.19	2.39	-2.21	0.06973	Kringle (1);	.	.	.	.	T	0.34861	0.0912	N	0.01352	-0.895	0.80722	P	0.0	B	0.22683	0.073	B	0.12837	0.008	T	0.07083	-1.0791	8	0.13470	T	0.59	.	4.4369	0.11555	0.0:0.2799:0.1829:0.5372	rs7765781;rs52813570;rs7765781	3880	P08519	APOA_HUMAN	V	1372	ENSP00000321334:L1372V;ENSP00000395608:L1372V	ENSP00000321334:L1372V	L	-	1	0	LPA	160927486	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.349000	0.02627	-0.967000	0.03582	-0.444000	0.05651	CTT	G|0.582;C|0.418	0.418	strong		0.478	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
GPR148	344561	hgsc.bcm.edu	37	2	131486765	131486765	+	Missense_Mutation	SNP	C	C	G	rs80008074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:131486765C>G	ENST00000309926.4	+	1	123	c.41C>G	c.(40-42)gCt>gGt	p.A14G		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	14						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					GGCACTACAGCTTGGCCGGCC	0.617													.|||	344	0.0686901	0.202	0.0375	5008	,	,		19856	0.0		0.0308	False		,,,				2504	0.0204				p.A14G		Atlas-SNP	.											.	GPR148	54	.	0			c.C41G						PASS	.	C	GLY/ALA	756,3650		81,594,1528	99.0	100.0	100.0		41	0.6	0.0	2	dbSNP_131	100	234,8366		3,228,4069	yes	missense	GPR148	NM_207364.2	60	84,822,5597	GG,GC,CC		2.7209,17.1584,7.6119	benign	14/348	131486765	990,12016	2203	4300	6503	SO:0001583	missense	344561	exon1			CTACAGCTTGGCC	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"""GPCR / Class A : Orphans"""	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.41C>G	2.37:g.131486765C>G	ENSP00000308908:p.Ala14Gly	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	122	38	0.311475	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	37	CCDS2163.1	144	0.06593406593406594	108	0.21951219512195122	15	0.04143646408839779	0	0.0	21	0.027704485488126648	.	7.664	0.685580	0.14973	0.171584	0.027209	ENSG00000173302	ENST00000309926	T	0.09163	3.01	2.41	0.555	0.17247	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.26635	0.155	B	0.28305	0.088	T	0.46345	-0.9198	8	0.51188	T	0.08	-0.8278	4.6863	0.12758	0.0:0.6753:0.0:0.3247	.	14	Q8TDV2	GP148_HUMAN	G	14	ENSP00000308908:A14G	ENSP00000308908:A14G	A	+	2	0	GPR148	131203235	0.003000	0.15002	0.003000	0.11579	0.025000	0.11179	0.139000	0.16036	0.127000	0.18452	-0.448000	0.05591	GCT	C|0.932;G|0.068	0.068	strong		0.617	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092	
OBSL1	23363	hgsc.bcm.edu	37	2	220431631	220431631	+	Silent	SNP	G	G	T	rs1043537	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:220431631G>T	ENST00000404537.1	-	5	2111	c.2055C>A	c.(2053-2055)gcC>gcA	p.A685A	OBSL1_ENST00000265318.4_Silent_p.A685A|OBSL1_ENST00000289656.3_Silent_p.A272A|OBSL1_ENST00000373873.4_Silent_p.A685A|OBSL1_ENST00000373876.1_Silent_p.A685A|OBSL1_ENST00000603926.1_Silent_p.A685A	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	685					cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GGTGCTTGACGGCATGCAGGA	0.632													G|||	856	0.170927	0.0439	0.2003	5008	,	,		19484	0.1151		0.2425	False		,,,				2504	0.3057				p.A685A		Atlas-SNP	.											.	OBSL1	120	.	0			c.C2055A						PASS	.	G	,,	336,3798		8,320,1739	51.0	56.0	55.0		2055,2055,2055	-9.8	0.0	2	dbSNP_86	55	2110,6292		272,1566,2363	no	coding-synonymous,coding-synonymous,coding-synonymous	OBSL1	NM_001173408.1,NM_001173431.1,NM_015311.2	,,	280,1886,4102	TT,TG,GG		25.1131,8.1277,19.5118	,,	685/1026,685/1544,685/1897	220431631	2446,10090	2067	4201	6268	SO:0001819	synonymous_variant	23363	exon5			CTTGACGGCATGC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2055C>A	2.37:g.220431631G>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1																																																																																			T|0.187;G|0.813;C|0.000	0.187	strong		0.632	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
CCHCR1	54535	hgsc.bcm.edu	37	6	31122500	31122500	+	Missense_Mutation	SNP	G	G	A	rs130065	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31122500G>A	ENST00000376266.5	-	4	429	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W	CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396263.2_Missense_Mutation_p.R103W|CCHCR1_ENST00000396268.3_Missense_Mutation_p.R192W|CCHCR1_ENST00000451521.2_Missense_Mutation_p.R156W	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	103			R -> W (in allele HCR*WWCC; associated with psoriasis; dbSNP:rs130065). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						TCCTCCAGCCGCCGCAGCTCT	0.657													G|||	598	0.119409	0.1241	0.0793	5008	,	,		18354	0.0387		0.1918	False		,,,				2504	0.1503				p.R192W		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C574T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	410,2604		29,352,1126	31.0	36.0	34.0		466,574,307	4.4	1.0	6	dbSNP_78	34	1110,4304		120,870,1717	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	101,101,101	149,1222,2843	AA,AG,GG		20.5024,13.6032,18.0351	benign,benign,benign	156/836,192/872,103/783	31122500	1520,6908	1507	2707	4214	SO:0001583	missense	54535	exon4			CCAGCCGCCGCAG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.307C>T	6.37:g.31122500G>A	ENSP00000365442:p.Arg103Trp	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	50	0.833333	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	265	0.12133699633699634	62	0.12601626016260162	27	0.07458563535911603	26	0.045454545454545456	150	0.19788918205804748	G	18.11	3.550954	0.65311	0.136032	0.205024	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521;ENST00000448141;ENST00000508683;ENST00000448162;ENST00000513222;ENST00000503420;ENST00000515274;ENST00000507751;ENST00000455279;ENST00000412245;ENST00000503934;ENST00000426967;ENST00000502557;ENST00000507829	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.07327	3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2;3.2	5.33	4.37	0.52481	.	0.450693	0.21536	N	0.072963	T	0.05227	0.0139	M	0.69823	2.125	0.31057	P	0.7145239999999999	B;B;B;B;B	0.27997	0.019;0.019;0.019;0.197;0.066	B;B;B;B;B	0.25405	0.002;0.002;0.002;0.06;0.017	T	0.05178	-1.0901	9	0.59425	D	0.04	-22.3718	9.5976	0.39584	0.0:0.0:0.7385:0.2615	rs130065;rs3173361;rs17840019;rs58977051	103;103;103;156;192	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	W	192;103;103;103;156;67;67;103;77;67;103;103;103;129;103;201;103;103	ENSP00000379566:R192W;ENSP00000365442:R103W;ENSP00000379561:R103W;ENSP00000401039:R156W;ENSP00000414323:R67W;ENSP00000421393:R67W;ENSP00000390027:R103W;ENSP00000425682:R77W;ENSP00000421992:R67W;ENSP00000420941:R103W;ENSP00000398715:R103W;ENSP00000425595:R103W;ENSP00000402432:R201W;ENSP00000425377:R103W;ENSP00000420911:R103W	ENSP00000365442:R103W	R	-	1	2	CCHCR1	31230479	0.987000	0.35691	1.000000	0.80357	0.768000	0.43524	1.439000	0.35013	2.510000	0.84645	0.638000	0.83543	CGG	G|0.836;A|0.164	0.164	strong		0.657	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
TRERF1	55809	hgsc.bcm.edu	37	6	42232475	42232475	+	Silent	SNP	G	G	A	rs2295274	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42232475G>A	ENST00000372922.4	-	7	2164	c.1602C>T	c.(1600-1602)caC>caT	p.H534H	TRERF1_ENST00000372917.4_Silent_p.H534H|TRERF1_ENST00000340840.2_Silent_p.H534H|TRERF1_ENST00000354325.2_Silent_p.H534H|TRERF1_ENST00000541110.1_Silent_p.H534H	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	534	Interacts with CREBBP.				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)			TCATTCCCCCGTGGGACCGCA	0.572													G|||	754	0.150559	0.1362	0.1066	5008	,	,		19343	0.122		0.169	False		,,,				2504	0.2117				p.H534H		Atlas-SNP	.											.	TRERF1	124	.	0			c.C1602T						PASS	.	G		677,3729	286.9+/-279.0	49,579,1575	99.0	87.0	91.0		1602	-3.5	0.9	6	dbSNP_100	91	1413,7187	272.3+/-290.0	117,1179,3004	no	coding-synonymous	TRERF1	NM_033502.2		166,1758,4579	AA,AG,GG		16.4302,15.3654,16.0695		534/1201	42232475	2090,10916	2203	4300	6503	SO:0001819	synonymous_variant	55809	exon7			TCCCCCGTGGGAC	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.1602C>T	6.37:g.42232475G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	87	16	0.183908	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																			G|0.848;A|0.152	0.152	strong		0.572	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
CEP192	55125	hgsc.bcm.edu	37	18	13001512	13001512	+	5'UTR	SNP	G	G	C	rs4499304	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:13001512G>C	ENST00000325971.8	+	0	301				CEP192_ENST00000506447.1_Missense_Mutation_p.G74A			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.G74A(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GTTCCATCCGGGTCATCTCCC	0.383													G|||	2157	0.430711	0.528	0.4798	5008	,	,		17422	0.3552		0.4493	False		,,,				2504	0.3231				p.G74A		Atlas-SNP	.											CEP192_ENST00000506447,NS,carcinoma,0,1	CEP192	340	1	1	Substitution - Missense(1)	stomach(1)	c.G221C						PASS	.						150.0	130.0	136.0					18																	13001512		692	1591	2283	SO:0001623	5_prime_UTR_variant	55125	exon3			CATCCGGGTCATC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.-1293G>C	18.37:g.13001512G>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1013	0.46382783882783885	264	0.5365853658536586	174	0.48066298342541436	237	0.4143356643356643	338	0.44591029023746703	G	0.005	-2.151523	0.00325	.	.	ENSG00000101639	ENST00000506447	T	0.05025	3.51	4.76	-0.604	0.11626	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.53688	P	2.6999999999999247E-5	B	0.06786	0.001	B	0.04013	0.001	T	0.40421	-0.9564	8	0.02654	T	1	.	5.6865	0.17805	0.2963:0.5058:0.1979:0.0	rs4499304;rs17659973;rs4499304	74	E9PF99	.	A	74	ENSP00000427550:G74A	ENSP00000427550:G74A	G	+	2	0	CEP192	12991512	0.005000	0.15991	0.005000	0.12908	0.258000	0.26162	0.032000	0.13732	-0.105000	0.12132	0.205000	0.17691	GGG	G|0.535;C|0.465	0.465	strong		0.383	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
ANO7	50636	hgsc.bcm.edu	37	2	242129487	242129487	+	Silent	SNP	G	G	T	rs11695874	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242129487G>T	ENST00000274979.8	+	2	274	c.171G>T	c.(169-171)cgG>cgT	p.R57R	ANO7_ENST00000402430.3_Silent_p.R57R|ANO7_ENST00000402530.3_Silent_p.R57R	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	57					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						GGATGCTGCGGCGACGGGCCC	0.677													G|||	745	0.148762	0.0968	0.1888	5008	,	,		15980	0.0208		0.3052	False		,,,				2504	0.1616				p.R57R		Atlas-SNP	.											.	ANO7	136	.	0			c.G171T						PASS	.	G	,	571,3819		41,489,1665	29.0	28.0	28.0		171,171	0.4	0.0	2	dbSNP_120	28	2342,6220		335,1672,2274	no	coding-synonymous,coding-synonymous	ANO7	NM_001001666.3,NM_001001891.3	,	376,2161,3939	TT,TG,GG		27.3534,13.0068,22.4907	,	57/180,57/934	242129487	2913,10039	2195	4281	6476	SO:0001819	synonymous_variant	50636	exon2			GCTGCGGCGACGG	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.171G>T	2.37:g.242129487G>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	124	41	0.330645	NM_001001666	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			G|0.805;T|0.195	0.195	strong		0.677	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
GDF3	9573	hgsc.bcm.edu	37	12	7848202	7848202	+	Silent	SNP	G	G	C	rs17727707	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:7848202G>C	ENST00000329913.3	-	1	170	c.123C>G	c.(121-123)ccC>ccG	p.P41P		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	41					endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						GGAACTTCTGGGGTGAAGGCG	0.483													G|||	134	0.0267572	0.0023	0.0389	5008	,	,		-128	0.0		0.0686	False		,,,				2504	0.0358				p.P41P		Atlas-SNP	.											.	GDF3	68	.	0			c.C123G						PASS	.	G		68,4338	62.9+/-100.1	0,68,2135	48.0	49.0	48.0		123	-0.3	0.0	12	dbSNP_123	48	677,7923	169.1+/-220.5	39,599,3662	no	coding-synonymous	GDF3	NM_020634.1		39,667,5797	CC,CG,GG		7.8721,1.5433,5.7281		41/365	7848202	745,12261	2203	4300	6503	SO:0001819	synonymous_variant	9573	exon1			CTTCTGGGGTGAA	AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"""Endogenous ligands"""	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.123C>G	12.37:g.7848202G>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_020634	Q8NEJ4	Silent	SNP	ENST00000329913.3	37	CCDS8581.1																																																																																			G|0.951;C|0.049	0.049	strong		0.483	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1		
MUC2	4583	hgsc.bcm.edu	37	11	1093066	1093066	+	Missense_Mutation	SNP	C	C	A	rs56365200	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1093066C>A	ENST00000441003.2	+	30	4912	c.4885C>A	c.(4885-4887)Cca>Aca	p.P1629T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.P1596T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				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)	gaccccaaccccaacagccat	0.632																																					p.P1629T		Atlas-SNP	.											MUC2_ENST00000441003,caecum,carcinoma,0,4	MUC2	614	4	0			c.C4885A						scavenged	.						123.0	163.0	149.0					11																	1093066		1876	3602	5478	SO:0001583	missense	4583	exon30			CCAACCCCAACAG	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.4885C>A	11.37:g.1093066C>A	ENSP00000415183:p.Pro1629Thr	Somatic	23	1	0.0434783		WXS	Illumina HiSeq	Phase_I	32	4	0.125	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	T	0.903	-0.721580	0.03182	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12879	2.64;3.49	1.75	-3.49	0.04724	.	16.324000	0.00424	N	0.000074	T	0.04407	0.0121	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25502	-1.0130	9	0.05620	T	0.96	.	2.5689	0.04790	0.221:0.4621:0.0:0.317	rs56365200	1629	E7EUV1	.	T	1629;1596	ENSP00000415183:P1629T;ENSP00000351956:P1596T	ENSP00000351956:P1596T	P	+	1	0	MUC2	1083066	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.774000	0.00187	-0.960000	0.03613	-3.899000	0.00016	CCA	.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FCAR	2204	hgsc.bcm.edu	37	19	55396913	55396913	+	Missense_Mutation	SNP	G	G	A	rs11666735	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55396913G>A	ENST00000355524.3	+	3	347	c.337G>A	c.(337-339)Gac>Aac	p.D113N	FCAR_ENST00000391725.3_Missense_Mutation_p.D113N|FCAR_ENST00000391724.3_Missense_Mutation_p.D101N|FCAR_ENST00000359272.4_Missense_Mutation_p.D101N|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000353758.4_Intron|FCAR_ENST00000345937.4_Missense_Mutation_p.D113N|FCAR_ENST00000391723.3_Missense_Mutation_p.D101N|FCAR_ENST00000469767.1_Missense_Mutation_p.D113N|FCAR_ENST00000391726.3_Missense_Mutation_p.D101N	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	113			D -> N (in dbSNP:rs11666735). {ECO:0000269|PubMed:17548632}.		immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		CCGGTACAGTGACACCCTGGA	0.453													.|||	276	0.0551118	0.0469	0.049	5008	,	,		17334	0.0387		0.0755	False		,,,				2504	0.0665				p.D113N		Atlas-SNP	.											.	FCAR	110	.	0			c.G337A	GRCh37	CM066073	FCAR	M	rs11666735	PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,,ASN/ASP,ASN/ASP	193,4213	122.1+/-159.5	4,185,2014	62.0	57.0	58.0		337,337,337,301,301,301,,301,337	-0.1	0.0	19	dbSNP_120	58	709,7891	174.8+/-225.0	21,667,3612	yes	missense,missense,missense,missense,missense,missense,intron,missense,missense	FCAR	NM_002000.2,NM_133269.2,NM_133271.2,NM_133272.2,NM_133273.2,NM_133274.2,NM_133277.2,NM_133278.2,NM_133279.2	23,23,23,23,23,23,,23,23	25,852,5626	AA,AG,GG		8.2442,4.3804,6.9353	benign,benign,benign,benign,benign,benign,,benign,benign	113/288,113/266,113/192,101/276,101/180,101/210,,101/254,113/240	55396913	902,12104	2203	4300	6503	SO:0001583	missense	2204	exon3			TACAGTGACACCC	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.337G>A	19.37:g.55396913G>A	ENSP00000347714:p.Asp113Asn	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_133279	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	37	CCDS12907.1	137	0.06272893772893773	26	0.052845528455284556	24	0.06629834254143646	29	0.050699300699300696	58	0.07651715039577836	G	7.024	0.559366	0.13436	0.043804	0.082442	ENSG00000186431	ENST00000433231;ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000359272;ENST00000391723;ENST00000391724	T;T;T;T;T;T;T	0.12774	2.65;2.84;2.84;2.65;2.84;2.84;2.84	3.19	-0.126	0.13515	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.141140	0.06882	N	0.802795	T	0.00608	0.0020	L	0.41710	1.295	0.09310	N	1	B;B;B;P;B;B;B;B	0.34587	0.033;0.004;0.037;0.458;0.027;0.03;0.118;0.008	B;B;B;B;B;B;B;B	0.39027	0.078;0.009;0.024;0.288;0.033;0.016;0.133;0.011	T	0.39099	-0.9630	10	0.27082	T	0.32	.	5.3781	0.16176	0.3944:0.0:0.6056:0.0	rs11666735;rs52806707;rs11666735	101;101;101;101;113;113;113;113	Q92588;Q92593;Q92587;Q9UEK0;Q53X39;P24071-3;P24071;P24071-4	.;.;.;.;.;.;FCAR_HUMAN;.	N	113;101;113;113;113;101;101;101	ENSP00000375606:D101N;ENSP00000347714:D113N;ENSP00000375605:D113N;ENSP00000338257:D113N;ENSP00000352218:D101N;ENSP00000375603:D101N;ENSP00000375604:D101N	ENSP00000338257:D113N	D	+	1	0	FCAR	60088725	0.028000	0.19301	0.003000	0.11579	0.003000	0.03518	0.141000	0.16076	0.056000	0.16144	-0.244000	0.11960	GAC	G|0.933;A|0.067	0.067	strong		0.453	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000	
GABRR2	2570	hgsc.bcm.edu	37	6	89981413	89981413	+	Silent	SNP	T	T	C	rs282117	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:89981413T>C	ENST00000402938.3	-	3	382	c.249A>G	c.(247-249)gtA>gtG	p.V83V	GABRR2_ENST00000602808.1_5'UTR|GABRR2_ENST00000602399.1_Silent_p.V108V	NM_002043.3	NP_002034.3	P28476	GBRR2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, rho 2	83					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(10)|prostate(2)|urinary_tract(1)	21		all_cancers(76;1.67e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.77e-07)|all_epithelial(107;2.51e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0158)	Adinazolam(DB00546)|Bromazepam(DB01558)|Cinolazepam(DB01594)|Clotiazepam(DB01559)|Diazepam(DB00829)|Estazolam(DB01215)|Fludiazepam(DB01567)|Flurazepam(DB00690)|Halazepam(DB00801)|Midazolam(DB00683)|Nitrazepam(DB01595)|Oxazepam(DB00842)|Prazepam(DB01588)|Quazepam(DB01589)|Temazepam(DB00231)|Triazolam(DB00897)	TCTCCACCTGTACGTCCACGC	0.617													C|||	3467	0.692292	0.8207	0.5533	5008	,	,		18518	0.7292		0.5815	False		,,,				2504	0.6933				p.V83V		Atlas-SNP	.											GABRR2,NS,carcinoma,0,1	GABRR2	41	1	0			c.A249G						PASS	.	C		3447,959	355.6+/-313.1	1353,741,109	66.0	51.0	56.0		324	4.9	1.0	6	dbSNP_79	56	5161,3439	496.1+/-374.2	1540,2081,679	no	coding-synonymous	GABRR2	NM_002043.2		2893,2822,788	CC,CT,TT		39.9884,21.7658,33.8152		108/491	89981413	8608,4398	2203	4300	6503	SO:0001819	synonymous_variant	2570	exon3			CACCTGTACGTCC		CCDS5020.2, CCDS5020.3	6q15	2012-06-22	2012-02-03		ENSG00000111886	ENSG00000111886		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4091	protein-coding gene	gene with protein product	"""GABA(A) receptor, rho 2"""	137162	"""gamma-aminobutyric acid (GABA) receptor, rho 2"""			1315307	Standard	NM_002043		Approved		uc003pnb.3	P28476	OTTHUMG00000015198	ENST00000402938.3:c.249A>G	6.37:g.89981413T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_002043	A2BDE4|Q9H153	Silent	SNP	ENST00000402938.3	37	CCDS5020.3																																																																																			T|0.334;C|0.666	0.666	strong		0.617	GABRR2-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041482.3		
ZNF682	91120	hgsc.bcm.edu	37	19	20117685	20117685	+	Missense_Mutation	SNP	G	G	A	rs2075090	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:20117685G>A	ENST00000397165.2	-	4	786	c.626C>T	c.(625-627)aCc>aTc	p.T209I	ZNF682_ENST00000596019.1_Intron|ZNF682_ENST00000397162.1_Missense_Mutation_p.T177I|ZNF682_ENST00000358523.5_Missense_Mutation_p.T177I|ZNF682_ENST00000595736.1_Missense_Mutation_p.T133I|ZNF682_ENST00000597972.1_Missense_Mutation_p.T215I	NM_033196.2	NP_149973.1	O95780	ZN682_HUMAN	zinc finger protein 682	209			T -> I (in dbSNP:rs2075090). {ECO:0000269|PubMed:14702039}.		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)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	14						CCACTTAAAGGTTTTGCCACA	0.378													g|||	621	0.124002	0.1316	0.17	5008	,	,		19963	0.1954		0.0378	False		,,,				2504	0.0961				p.T209I		Atlas-SNP	.											.	ZNF682	51	.	0			c.C626T						PASS	.	G	ILE/THR,ILE/THR	456,3668		29,398,1635	50.0	52.0	52.0		530,626	-0.6	0.0	19	dbSNP_96	52	283,8185		5,273,3956	yes	missense,missense	ZNF682	NM_001077349.1,NM_033196.2	89,89	34,671,5591	AA,AG,GG		3.342,11.0572,5.8688	possibly-damaging,possibly-damaging	177/467,209/499	20117685	739,11853	2062	4234	6296	SO:0001583	missense	91120	exon4			TTAAAGGTTTTGC	AC006539	CCDS42533.1, CCDS42534.1	19p12	2014-02-13			ENSG00000197124	ENSG00000197124		"""Zinc fingers, C2H2-type"", ""-"""	28857	protein-coding gene	gene with protein product							Standard	NM_033196		Approved	BC39498_3	uc002noq.3	O95780	OTTHUMG00000182650	ENST00000397165.2:c.626C>T	19.37:g.20117685G>A	ENSP00000380351:p.Thr209Ile	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_033196	B3KU64|E9PFJ5|Q96JV9	Missense_Mutation	SNP	ENST00000397165.2	37	CCDS42533.1	252	0.11538461538461539	72	0.14634146341463414	50	0.13812154696132597	105	0.18356643356643357	25	0.032981530343007916	G	6.697	0.497203	0.12762	0.110572	0.03342	ENSG00000197124	ENST00000397165;ENST00000397162;ENST00000358523	T;T;T	0.36157	1.27;1.27;1.27	1.08	-0.578	0.11724	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	M	0.64080	1.96	0.58432	P	5.999999999950489E-6	B	0.23249	0.082	B	0.25987	0.065	T	0.12785	-1.0534	8	0.72032	D	0.01	.	5.2114	0.15318	0.244:0.0:0.756:0.0	rs2075090;rs60679185;rs2075090	209	O95780	ZN682_HUMAN	I	209;177;177	ENSP00000380351:T209I;ENSP00000380348:T177I;ENSP00000351324:T177I	ENSP00000351324:T177I	T	-	2	0	ZNF682	19978685	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.410000	0.07151	-0.354000	0.08212	-0.350000	0.07774	ACC	G|0.895;A|0.105	0.105	strong		0.378	ZNF682-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462888.1	NM_033196	
OR2L3	391192	hgsc.bcm.edu	37	1	248224587	248224587	+	Missense_Mutation	SNP	A	A	G	rs61525219	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248224587A>G	ENST00000359959.3	+	1	604	c.604A>G	c.(604-606)Acc>Gcc	p.T202A	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	202						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)			GTTTTTGAGCACCACCATCTT	0.493													a|||	288	0.057508	0.1218	0.0216	5008	,	,		24287	0.0704		0.0298	False		,,,				2504	0.0112				p.T202A		Atlas-SNP	.											OR2L3,NS,carcinoma,-1,1	OR2L3	97	1	0			c.A604G						scavenged	.						194.0	212.0	206.0					1																	248224587		2187	4300	6487	SO:0001583	missense	391192	exon1			TTGAGCACCACCA	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.604A>G	1.37:g.248224587A>G	ENSP00000353044:p.Thr202Ala	Somatic	347	2	0.00576369		WXS	Illumina HiSeq	Phase_I	228	12	0.0526316	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	.	.	.	.	.	.	.	.	.	.	A	0.713	-0.786430	0.02907	.	.	ENSG00000198128	ENST00000359959	T	0.36157	1.27	2.05	-0.724	0.11177	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34002	U	0.004342	T	0.19967	0.0480	N	0.11756	0.17	0.09310	N	1	B	0.18013	0.025	B	0.30646	0.118	T	0.21109	-1.0255	10	0.56958	D	0.05	.	7.7621	0.28959	0.3671:0.0:0.6329:0.0	rs61525219	202	Q8NG85	OR2L3_HUMAN	A	202	ENSP00000353044:T202A	ENSP00000353044:T202A	T	+	1	0	OR2L3	246291210	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.037000	0.01420	-0.358000	0.08162	-1.678000	0.00738	ACC	.	.	weak		0.493	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
RNF17	56163	hgsc.bcm.edu	37	13	25428002	25428002	+	Missense_Mutation	SNP	C	C	A	rs3783082	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25428002C>A	ENST00000255324.5	+	25	3382	c.3330C>A	c.(3328-3330)aaC>aaA	p.N1110K	RNF17_ENST00000381921.1_Missense_Mutation_p.N1110K|RNF17_ENST00000339524.3_Missense_Mutation_p.N162K	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1110			N -> K (in dbSNP:rs3783082).		multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		GAATTAATAACTTAGATAACA	0.318													A|||	605	0.120807	0.0802	0.1744	5008	,	,		6377	0.1835		0.1342	False		,,,				2504	0.0593				p.N1110K		Atlas-SNP	.											.	RNF17	259	.	0			c.C3330A						PASS	.	A	LYS/ASN,LYS/ASN	405,3995	767.3+/-413.5	23,359,1818	42.0	44.0	43.0		3318,3330	3.8	0.8	13	dbSNP_107	43	1153,7445	755.7+/-407.5	83,987,3229	yes	missense,missense	RNF17	NM_001184993.1,NM_031277.2	94,94	106,1346,5047	AA,AC,CC		13.4101,9.2045,11.9865	benign,benign	1106/1620,1110/1624	25428002	1558,11440	2200	4299	6499	SO:0001583	missense	56163	exon25			TAATAACTTAGAT	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"""RING-type (C3HC4) zinc fingers"", ""Tudor domain containing"""	10060	protein-coding gene	gene with protein product	"""spermatogenesis associated 23"""	605793	"""tudor domain containing 4"""	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.3330C>A	13.37:g.25428002C>A	ENSP00000255324:p.Asn1110Lys	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_031277	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	321	0.14697802197802198	42	0.08536585365853659	52	0.143646408839779	121	0.21153846153846154	106	0.13984168865435356	A	0.011	-1.714727	0.00706	0.092045	0.134101	ENSG00000132972	ENST00000255324;ENST00000381921;ENST00000429047;ENST00000418120;ENST00000339524	T;T;T;T	0.20598	3.63;3.63;2.87;2.06	4.96	3.78	0.43462	.	0.229124	0.39274	N	0.001413	T	0.00012	0.0000	N	0.00170	-1.935	0.18873	P	0.9999861813	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.36601	-0.9741	9	0.02654	T	1	-13.1537	5.1228	0.14869	0.7231:0.1838:0.0931:0.0	rs3783082;rs52827814;rs60804193;rs3783082	1106;162;1110;1110	B7Z7S1;Q5T6R1;Q9BXT8-5;Q9BXT8	.;.;.;RNF17_HUMAN	K	1110;1110;969;434;162	ENSP00000255324:N1110K;ENSP00000371346:N1110K;ENSP00000388892:N434K;ENSP00000344776:N162K	ENSP00000255324:N1110K	N	+	3	2	RNF17	24326002	0.996000	0.38824	0.787000	0.31911	0.385000	0.30292	2.231000	0.43009	0.466000	0.27193	-0.335000	0.08231	AAC	C|0.876;A|0.124	0.124	strong		0.318	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
MMP14	4323	hgsc.bcm.edu	37	14	23312554	23312554	+	Silent	SNP	C	C	G	rs2236302	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:23312554C>G	ENST00000311852.6	+	5	1038	c.777C>G	c.(775-777)ccC>ccG	p.P259P	MMP14_ENST00000548162.1_3'UTR	NM_004995.2	NP_004986.1	P50281	MMP14_HUMAN	matrix metallopeptidase 14 (membrane-inserted)	259					angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|branching morphogenesis of an epithelial tube (GO:0048754)|chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|endodermal cell differentiation (GO:0035987)|endothelial cell proliferation (GO:0001935)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|male gonad development (GO:0008584)|negative regulation of focal adhesion assembly (GO:0051895)|ovarian follicle development (GO:0001541)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to oxidative stress (GO:0006979)|tissue remodeling (GO:0048771)|zymogen activation (GO:0031638)	extracellular matrix (GO:0031012)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|peptidase activator activity (GO:0016504)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(95;9.47e-05)			GBM - Glioblastoma multiforme(265;0.00551)	Marimastat(DB00786)	TCATGGCACCCTTTTACCAGT	0.587													C|||	815	0.16274	0.3048	0.1383	5008	,	,		18326	0.13		0.1163	False		,,,				2504	0.0695				p.P259P		Atlas-SNP	.											.	MMP14	40	.	0			c.C777G						PASS	.	C		1263,3143	432.8+/-343.4	196,871,1136	107.0	104.0	105.0		777	-0.9	0.6	14	dbSNP_98	105	947,7653	208.7+/-250.1	50,847,3403	no	coding-synonymous	MMP14	NM_004995.2		246,1718,4539	GG,GC,CC		11.0116,28.6655,16.9922		259/583	23312554	2210,10796	2203	4300	6503	SO:0001819	synonymous_variant	4323	exon5			GGCACCCTTTTAC		CCDS9577.1	14q11-q12	2011-06-29	2005-08-08		ENSG00000157227	ENSG00000157227			7160	protein-coding gene	gene with protein product	"""membrane type 1 metalloprotease"""	600754	"""matrix metalloproteinase 14 (membrane-inserted)"""			8015608	Standard	NM_004995		Approved	MT1-MMP	uc001whc.3	P50281	OTTHUMG00000028704	ENST00000311852.6:c.777C>G	14.37:g.23312554C>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_004995	A8K5L0|Q6GSF3|Q92678	Silent	SNP	ENST00000311852.6	37	CCDS9577.1																																																																																			C|0.833;G|0.167	0.167	strong		0.587	MMP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071660.3	NM_004995	
DTD2	112487	hgsc.bcm.edu	37	14	31926584	31926584	+	Missense_Mutation	SNP	G	G	A	rs17097904	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:31926584G>A	ENST00000310850.4	-	1	132	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	DTD2_ENST00000356180.4_Missense_Mutation_p.R6W|RP11-176H8.1_ENST00000547378.1_Missense_Mutation_p.R6W	NM_080664.2	NP_542395.1	Q96FN9	DTD2_HUMAN	D-tyrosyl-tRNA deacylase 2 (putative)	6			R -> W (in dbSNP:rs17097904).		D-amino acid catabolic process (GO:0019478)	cytoplasm (GO:0005737)	hydrolase activity, acting on ester bonds (GO:0016788)	p.R6W(1)									TGAGGAATCCGGCTACCCTCA	0.697																																					p.R6W		Atlas-SNP	.											C14orf126,third_ventricle,glioma,0,2	.	.	2	1	Substitution - Missense(1)	skin(1)	c.C16T						scavenged	.						12.0	12.0	12.0					14																	31926584		2183	4278	6461	SO:0001583	missense	112487	exon1			GAATCCGGCTACC	BC010618	CCDS9643.1	14q12	2012-09-25	2012-09-25	2012-09-25	ENSG00000129480	ENSG00000129480			20277	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 126"""	C14orf126			Standard	NM_080664		Approved	MGC9912	uc001wrj.3	Q96FN9	OTTHUMG00000140205	ENST00000310850.4:c.16C>T	14.37:g.31926584G>A	ENSP00000312224:p.Arg6Trp	Somatic	90	5	0.0555556		WXS	Illumina HiSeq	Phase_I	85	8	0.0941176	NM_080664	D3DS87	Missense_Mutation	SNP	ENST00000310850.4	37	CCDS9643.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758136	0.69763	.	.	ENSG00000203546;ENSG00000129480;ENSG00000129480	ENST00000547378;ENST00000310850;ENST00000356180	T;T;T	0.55052	0.54;0.71;0.71	4.84	2.97	0.34412	D-Tyr tRNAtyr deacylase-like domain (1);	0.302778	0.30901	N	0.008651	T	0.52419	0.1733	M	0.69823	2.125	0.36855	D	0.888115	D	0.67145	0.996	B	0.43623	0.425	T	0.65220	-0.6221	10	0.87932	D	0	.	11.9711	0.53063	0.0:0.0:0.5428:0.4572	rs17097904	6	Q96FN9	DTD2_HUMAN	W	6	ENSP00000447056:R6W;ENSP00000312224:R6W;ENSP00000348503:R6W	ENSP00000312224:R6W	R	-	1	2	C14orf126;RP11-176H8.1	30996335	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	0.080000	0.14802	0.618000	0.30179	0.561000	0.74099	CGG	.	.	weak		0.697	DTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276614.2	NM_080664	
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 GAIIx	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	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	47	26	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 GAIIx	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	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	55	22	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	
C17orf107	100130311	hgsc.bcm.edu	37	17	4803711	4803711	+	Nonsense_Mutation	SNP	G	G	A	rs35400274	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4803711G>A	ENST00000381365.3	+	3	683	c.456G>A	c.(454-456)tgG>tgA	p.W152*	CHRNE_ENST00000575637.1_5'Flank|C17orf107_ENST00000521575.1_3'UTR|CHRNE_ENST00000293780.4_Intron	NM_001145536.1	NP_001139008.1	Q6ZR85	CQ107_HUMAN	chromosome 17 open reading frame 107	152										endometrium(2)	2						AGGGAGCATGGCTATGCCTGT	0.687													G|||	1110	0.221645	0.4145	0.2378	5008	,	,		15004	0.0863		0.1511	False		,,,				2504	0.1616				p.W152X		Atlas-SNP	.											.	C17orf107	8	.	0			c.G456A						PASS	.	G	,stop/TRP	494,890		84,326,282	22.0	30.0	28.0		,456	4.6	1.0	17	dbSNP_126	28	444,2738		34,376,1181	yes	intron,stop-gained	CHRNE,C17orf107	NM_000080.3,NM_001145536.1	,	118,702,1463	AA,AG,GG		13.9535,35.6936,20.5431	,	,152/191	4803711	938,3628	692	1591	2283	SO:0001587	stop_gained	100130311	exon3			AGCATGGCTATGC	AK128415	CCDS45591.1	17p13.2	2009-09-30			ENSG00000205710	ENSG00000205710			37238	protein-coding gene	gene with protein product							Standard	NM_001145536		Approved		uc002fzl.3	Q6ZR85	OTTHUMG00000164838	ENST00000381365.3:c.456G>A	17.37:g.4803711G>A	ENSP00000370770:p.Trp152*	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_001145536		Nonsense_Mutation	SNP	ENST00000381365.3	37	CCDS45591.1	452	0.20695970695970695	219	0.4451219512195122	84	0.23204419889502761	49	0.08566433566433566	100	0.13192612137203166	G	19.87	3.907762	0.72868	0.356936	0.139535	ENSG00000205710	ENST00000381365	.	.	.	4.62	4.62	0.57501	.	0.786555	0.10471	N	0.670805	.	.	.	.	.	.	0.09310	P	0.99999863135	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.5576	12.8268	0.57725	0.0:0.0:1.0:0.0	rs35400274;rs56837916	.	.	.	X	152	.	ENSP00000370770:W152X	W	+	3	0	C17orf107	4744490	0.793000	0.28825	0.994000	0.49952	0.119000	0.20118	1.993000	0.40747	2.411000	0.81874	0.561000	0.74099	TGG	G|0.791;A|0.209	0.209	strong		0.687	C17orf107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380556.1	NM_001145536	
CRB2	286204	hgsc.bcm.edu	37	9	126132919	126132919	+	Silent	SNP	G	G	A	rs33984675	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:126132919G>A	ENST00000373631.3	+	7	1588	c.1587G>A	c.(1585-1587)gcG>gcA	p.A529A	CRB2_ENST00000373629.2_Silent_p.A197A|CRB2_ENST00000359999.3_Silent_p.A529A	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	529	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						TCCATCTAGCGACCCTGGAGC	0.642													G|||	990	0.197684	0.059	0.1758	5008	,	,		19807	0.252		0.2753	False		,,,				2504	0.2648				p.A529A		Atlas-SNP	.											.	CRB2	86	.	0			c.G1587A						PASS	.	G		383,4023	192.3+/-217.7	17,349,1837	72.0	66.0	68.0		1587	3.0	0.5	9	dbSNP_126	68	2696,5904	430.3+/-356.5	430,1836,2034	no	coding-synonymous	CRB2	NM_173689.5		447,2185,3871	AA,AG,GG		31.3488,8.6927,23.6737		529/1286	126132919	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon7			TCTAGCGACCCTG	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.1587G>A	9.37:g.126132919G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			G|0.766;A|0.234	0.234	strong		0.642	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
LIG4	3981	hgsc.bcm.edu	37	13	108861913	108861913	+	Silent	SNP	A	A	G	rs1805386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:108861913A>G	ENST00000356922.4	-	2	1976	c.1704T>C	c.(1702-1704)gaT>gaC	p.D568D	LIG4_ENST00000442234.1_Silent_p.D568D|LIG4_ENST00000405925.1_Silent_p.D568D	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	568					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)					TTTTATACATATCACTGGGTA	0.423								Non-homologous end-joining					A|||	344	0.0686901	0.0507	0.1326	5008	,	,		19957	0.001		0.1481	False		,,,				2504	0.0358				p.D568D		Atlas-SNP	.											.	LIG4	91	.	0			c.T1704C						PASS	.	A	,,	352,4054	182.6+/-210.3	12,328,1863	98.0	91.0	93.0		1704,1704,1704	-11.5	0.1	13	dbSNP_92	93	1581,7019	295.9+/-302.6	145,1291,2864	no	coding-synonymous,coding-synonymous,coding-synonymous	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	,,	157,1619,4727	GG,GA,AA		18.3837,7.9891,14.8624	,,	568/912,568/912,568/912	108861913	1933,11073	2203	4300	6503	SO:0001819	synonymous_variant	3981	exon3			ATACATATCACTG	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.1704T>C	13.37:g.108861913A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	89	67	0.752809	NM_206937	Q8IY66|Q8TEU5	Silent	SNP	ENST00000356922.4	37	CCDS9508.1																																																																																			A|0.870;G|0.130	0.130	strong		0.423	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312	
GEMIN5	25929	hgsc.bcm.edu	37	5	154307070	154307070	+	Missense_Mutation	SNP	G	G	C	rs35522740	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:154307070G>C	ENST00000285873.7	-	7	1030	c.955C>G	c.(955-957)Cgg>Ggg	p.R319G		NM_001252156.1|NM_015465.4	NP_001239085.1|NP_056280.2	Q8TEQ6	GEMI5_HUMAN	gem (nuclear organelle) associated protein 5	319					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|protein complex assembly (GO:0006461)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)|snRNA binding (GO:0017069)			breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			GTGTATTTCCGTCTCCAAGAT	0.378													G|||	55	0.0109824	0.003	0.0115	5008	,	,		21838	0.0		0.0328	False		,,,				2504	0.0102				p.R319G		Atlas-SNP	.											.	GEMIN5	120	.	0			c.C955G						PASS	.	G	GLY/ARG	16,4390	22.3+/-47.3	0,16,2187	134.0	124.0	127.0		955	5.6	1.0	5	dbSNP_126	127	228,8372	94.0+/-155.9	6,216,4078	yes	missense	GEMIN5	NM_015465.3	125	6,232,6265	CC,CG,GG		2.6512,0.3631,1.8761	probably-damaging	319/1509	154307070	244,12762	2203	4300	6503	SO:0001583	missense	25929	exon7			ATTTCCGTCTCCA	AK022748	CCDS4330.1	5q34	2013-01-10			ENSG00000082516	ENSG00000082516		"""WD repeat domain containing"""	20043	protein-coding gene	gene with protein product		607005				11714716	Standard	NM_015465		Approved		uc003lvx.3	Q8TEQ6	OTTHUMG00000130189	ENST00000285873.7:c.955C>G	5.37:g.154307070G>C	ENSP00000285873:p.Arg319Gly	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	NM_015465	Q14CV0|Q8WWV4|Q969W4|Q9H9K3|Q9UFI5	Missense_Mutation	SNP	ENST00000285873.7	37	CCDS4330.1	32	0.014652014652014652	3	0.006097560975609756	5	0.013812154696132596	0	0.0	24	0.0316622691292876	G	28.4	4.916127	0.92178	0.003631	0.026512	ENSG00000082516	ENST00000285873	T	0.04758	3.56	5.64	5.64	0.86602	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.070336	0.64402	D	0.000010	T	0.04543	0.0124	L	0.41824	1.3	0.54753	D	0.999987	D;D	0.67145	0.996;0.996	D;D	0.63877	0.919;0.919	T	0.11665	-1.0578	10	0.26408	T	0.33	-20.5766	19.7174	0.96129	0.0:0.0:1.0:0.0	rs35522740	318;319	B7ZLC9;Q8TEQ6	.;GEMI5_HUMAN	G	319	ENSP00000285873:R319G	ENSP00000285873:R319G	R	-	1	2	GEMIN5	154287263	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.678000	0.61641	2.653000	0.90120	0.655000	0.94253	CGG	G|0.979;C|0.021	0.021	strong		0.378	GEMIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252507.1		
CCDC15	80071	hgsc.bcm.edu	37	11	124908352	124908352	+	Missense_Mutation	SNP	T	T	C	rs7107487	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124908352T>C	ENST00000344762.5	+	14	2696	c.2437T>C	c.(2437-2439)Tgt>Cgt	p.C813R	CCDC15_ENST00000529051.1_Missense_Mutation_p.C813R|CCDC15_ENST00000530061.1_3'UTR	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	813			C -> R (in dbSNP:rs7107487).			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)		AGAGCAAGAATGTTATGCTGC	0.308													C|||	1149	0.229433	0.3616	0.1398	5008	,	,		16654	0.1825		0.1481	False		,,,				2504	0.2464				p.C813R		Atlas-SNP	.											.	CCDC15	134	.	0			c.T2437C						PASS	.	C	ARG/CYS	1185,2417		202,781,818	34.0	30.0	32.0		2437	3.1	1.0	11	dbSNP_116	32	1268,6866		97,1074,2896	yes	missense	CCDC15	NM_025004.2	180	299,1855,3714	CC,CT,TT		15.5889,32.8984,20.9015	benign	813/952	124908352	2453,9283	1801	4067	5868	SO:0001583	missense	80071	exon14			CAAGAATGTTATG	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.2437T>C	11.37:g.124908352T>C	ENSP00000341684:p.Cys813Arg	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	129	110	0.852713	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	461	0.21108058608058608	181	0.3678861788617886	59	0.16298342541436464	106	0.1853146853146853	115	0.1517150395778364	C	0.627	-0.818673	0.02776	0.328984	0.155889	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.20332	2.16;2.08	5.0	3.11	0.35812	.	.	.	.	.	T	0.00012	0.0000	N	0.00152	-1.975	0.29734	P	0.8376250000000001	B	0.02656	0.0	B	0.01281	0.0	T	0.46162	-0.9211	8	0.02654	T	1	-0.3039	5.8186	0.18514	0.1537:0.6807:0.0:0.1656	rs7107487;rs52832936;rs60393511;rs7107487	813	Q0P6D6	CCD15_HUMAN	R	813	ENSP00000435403:C813R;ENSP00000341684:C813R	ENSP00000341684:C813R	C	+	1	0	CCDC15	124413562	0.991000	0.36638	0.973000	0.42090	0.926000	0.56050	1.147000	0.31602	0.244000	0.21351	-0.349000	0.07799	TGT	T|0.779;C|0.221	0.221	strong		0.308	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
TTN	7273	hgsc.bcm.edu	37	2	179598228	179598228	+	Silent	SNP	A	A	G	rs12993099	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179598228A>G	ENST00000591111.1	-	52	15065	c.14841T>C	c.(14839-14841)atT>atC	p.I4947I	TTN_ENST00000589042.1_Silent_p.I5264I|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.I4020I			Q8WZ42	TITIN_HUMAN	titin	12327	Ig-like 30.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCTCGCTCAATGATTTTGG	0.438													A|||	148	0.0295527	0.0023	0.062	5008	,	,		17704	0.0		0.0895	False		,,,				2504	0.0123				p.I5264I		Atlas-SNP	.											.	TTN	18412	.	0			c.T15792C						PASS	.	A	,,,	59,3795		1,57,1869	215.0	217.0	216.0		,12060,,	3.5	1.0	2	dbSNP_121	216	656,7622		18,620,3501	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	19,677,5370	GG,GA,AA		7.9246,1.5309,5.8935	,,,	,4020/33424,,	179598228	715,11417	1927	4139	6066	SO:0001819	synonymous_variant	7273	exon54			TCGCTCAATGATT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.14841T>C	2.37:g.179598228A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	30	18	0.6	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.957;G|0.043	0.043	strong		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KRT6A	3853	hgsc.bcm.edu	37	12	52886478	52886478	+	Silent	SNP	T	T	C	rs376545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52886478T>C	ENST00000330722.6	-	1	563	c.495A>G	c.(493-495)gaA>gaG	p.E165E		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	165	Coil 1A.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTTGATCTGTTCACGCTCCT	0.587													T|||	1808	0.361022	0.3238	0.3458	5008	,	,		19063	0.5397		0.3748	False		,,,				2504	0.2239				p.E165E		Atlas-SNP	.											.	KRT6A	89	.	0			c.A495G						PASS	.	T		1353,3053	449.6+/-349.1	213,927,1063	178.0	164.0	169.0		495	2.4	1.0	12	dbSNP_80	169	3145,5453	473.5+/-368.6	610,1925,1764	no	coding-synonymous	KRT6A	NM_005554.3		823,2852,2827	CC,CT,TT		36.5783,30.7081,34.5894		165/565	52886478	4498,8506	2203	4299	6502	SO:0001819	synonymous_variant	3853	exon1			GATCTGTTCACGC	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.495A>G	12.37:g.52886478T>C		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	223	77	0.345291	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																			T|0.615;C|0.385	0.385	strong		0.587	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
CARD8	22900	hgsc.bcm.edu	37	19	48715196	48715196	+	Missense_Mutation	SNP	T	T	C	rs34632751	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48715196T>C	ENST00000359009.4	-	10	1379	c.1067A>G	c.(1066-1068)cAa>cGa	p.Q356R	CARD8_ENST00000391898.3_Missense_Mutation_p.Q462R|CARD8_ENST00000520753.1_3'UTR|CARD8_ENST00000447740.2_Missense_Mutation_p.Q412R|CARD8_ENST00000520153.1_Missense_Mutation_p.Q412R|CARD8_ENST00000520015.1_3'UTR|CARD8_ENST00000357778.5_Intron|CARD8_ENST00000521613.1_Missense_Mutation_p.Q412R|CTC-453G23.8_ENST00000595201.1_RNA|CARD8_ENST00000519940.1_Missense_Mutation_p.Q462R|ZNF114_ENST00000597695.1_Intron			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	356	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		CATCCTGGCTTGGAGTTGCCG	0.507													T|||	44	0.00878594	0.0008	0.013	5008	,	,		20120	0.0		0.0328	False		,,,				2504	0.001				p.Q462R		Atlas-SNP	.											.	CARD8	53	.	0			c.A1385G						PASS	.	T	ARG/GLN,ARG/GLN,,,ARG/GLN	15,4391	22.3+/-47.3	0,15,2188	93.0	90.0	91.0		1385,1235,,,1235	-0.3	0.0	19	dbSNP_126	91	217,8383	90.6+/-152.8	2,213,4085	yes	missense,missense,utr-3,utr-3,missense	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	43,43,,,43	2,228,6273	CC,CT,TT		2.5233,0.3404,1.7838	possibly-damaging,possibly-damaging,,,possibly-damaging	462/538,412/488,,,412/488	48715196	232,12774	2203	4300	6503	SO:0001583	missense	22900	exon11			CTGGCTTGGAGTT	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.1067A>G	19.37:g.48715196T>C	ENSP00000351901:p.Gln356Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	139	57	0.410072	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Missense_Mutation	SNP	ENST00000359009.4	37		32	0.014652014652014652	0	0.0	8	0.022099447513812154	0	0.0	24	0.0316622691292876	T	12.17	1.856317	0.32791	0.003404	0.025233	ENSG00000105483	ENST00000447740;ENST00000391898;ENST00000359009;ENST00000520153;ENST00000521613;ENST00000519940	T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06	2.01	-0.336	0.12658	DEATH-like (2);Caspase Recruitment (3);	.	.	.	.	T	0.11281	0.0275	L	0.44542	1.39	0.09310	N	1	D;D;D;D	0.59357	0.985;0.985;0.981;0.985	D;D;D;D	0.71414	0.973;0.973;0.954;0.973	T	0.08932	-1.0698	9	0.66056	D	0.02	.	2.6107	0.04890	0.0:0.175:0.28:0.5451	rs34632751	381;462;412;356	B5KVR7;E9PEM7;G3XAM9;Q9Y2G2	.;.;.;CARD8_HUMAN	R	412;462;356;412;412;462	ENSP00000391248:Q412R;ENSP00000375767:Q462R;ENSP00000351901:Q356R;ENSP00000428736:Q412R;ENSP00000427858:Q412R;ENSP00000428883:Q462R	ENSP00000351901:Q356R	Q	-	2	0	CARD8	53407008	0.004000	0.15560	0.003000	0.11579	0.015000	0.08874	0.140000	0.16056	-0.166000	0.10890	0.482000	0.46254	CAA	T|0.983;C|0.017	0.017	strong		0.507	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
SSRP1	6749	hgsc.bcm.edu	37	11	57102096	57102096	+	Silent	SNP	A	A	G	rs2230649	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57102096A>G	ENST00000278412.2	-	3	347	c.81T>C	c.(79-81)cgT>cgC	p.R27R		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	27					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						TGATGCCCTGACGGCTCAACC	0.517													G|||	846	0.16893	0.3941	0.1326	5008	,	,		23311	0.0218		0.1451	False		,,,				2504	0.0665				p.R27R	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.T81C						PASS	.	G		1539,2863	670.1+/-402.3	248,1043,910	185.0	171.0	176.0		81	3.5	1.0	11	dbSNP_98	176	1434,7158	751.5+/-407.4	100,1234,2962	no	coding-synonymous	SSRP1	NM_003146.2		348,2277,3872	GG,GA,AA		16.6899,34.9614,22.8798		27/710	57102096	2973,10021	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon3			GCCCTGACGGCTC	M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 80 kDa subunit"""	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.81T>C	11.37:g.57102096A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	16	0.372093	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			A|0.799;G|0.201	0.201	strong		0.517	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146	
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 GAIIx	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_ENST00000400186.3_Missense_Mutation_p.V815D|CSMD1_ENST00000542608.1_Missense_Mutation_p.V814D|CSMD1_ENST00000602557.1_Missense_Mutation_p.V815D|CSMD1_ENST00000539096.1_Missense_Mutation_p.V814D|CSMD1_ENST00000537824.1_Missense_Mutation_p.V814D|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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	97	28	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	
SYCE1	93426	hgsc.bcm.edu	37	10	135370633	135370633	+	Silent	SNP	C	C	T	rs8181356	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135370633C>T	ENST00000343131.5	-	7	506	c.402G>A	c.(400-402)aaG>aaA	p.K134K	SYCE1_ENST00000432597.2_Silent_p.K98K|SYCE1_ENST00000368517.3_Silent_p.K98K|SPRN_ENST00000541506.1_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	134					synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)		p.K134K(1)|p.K98K(1)		breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		AAATTCTCTCCTTGCACTCCT	0.552													C|||	775	0.154752	0.0454	0.1715	5008	,	,		21865	0.2698		0.1093	False		,,,				2504	0.2188				p.K134K		Atlas-SNP	.											SYCE1_ENST00000343131,NS,carcinoma,0,2	SYCE1	81	2	2	Substitution - coding silent(2)	stomach(2)	c.G402A						PASS	.	C	,,	260,4146	142.7+/-177.9	6,248,1949	274.0	260.0	264.0		402,402,294	0.3	1.0	10	dbSNP_117	264	815,7785	186.2+/-233.7	45,725,3530	no	coding-synonymous,coding-synonymous,coding-synonymous	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	,,	51,973,5479	TT,TC,CC		9.4767,5.901,8.2654	,,	134/319,134/352,98/283	135370633	1075,11931	2203	4300	6503	SO:0001819	synonymous_variant	93426	exon7			TCTCTCCTTGCAC	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.402G>A	10.37:g.135370633C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Silent	SNP	ENST00000343131.5	37	CCDS44501.1																																																																																			C|0.889;T|0.111	0.111	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
KLHL5	51088	hgsc.bcm.edu	37	4	39116911	39116911	+	Silent	SNP	T	T	C	rs3733276	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:39116911T>C	ENST00000504108.1	+	10	2455	c.2172T>C	c.(2170-2172)acT>acC	p.T724T	KLHL5_ENST00000359687.2_Silent_p.T724T|KLHL5_ENST00000508137.2_Silent_p.T537T|RP11-360F5.1_ENST00000509449.1_RNA|KLHL5_ENST00000261426.5_Silent_p.T663T|KLHL5_ENST00000261425.3_Silent_p.T678T|KLHL5_ENST00000381930.3_Silent_p.T724T	NM_015990.4	NP_057074.3	Q96PQ7	KLHL5_HUMAN	kelch-like family member 5	724						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(1)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29						ACCTTAATACTGTGGAGGCTT	0.418													C|||	2467	0.492612	0.3411	0.5965	5008	,	,		15980	0.495		0.5765	False		,,,				2504	0.5348				p.T724T		Atlas-SNP	.											.	KLHL5	75	.	0			c.T2172C						PASS	.	C	,,,	1725,2681	651.6+/-399.3	332,1061,810	104.0	94.0	97.0		2034,1611,2172,1989	-3.4	0.9	4	dbSNP_107	97	5039,3561	517.0+/-379.0	1490,2059,751	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLHL5	NM_001007075.2,NM_001171654.1,NM_015990.4,NM_199039.3	,,,	1822,3120,1561	CC,CT,TT		41.407,39.1512,47.9932	,,,	678/710,537/569,724/756,663/695	39116911	6764,6242	2203	4300	6503	SO:0001819	synonymous_variant	51088	exon10			TAATACTGTGGAG	AF272976	CCDS3449.1, CCDS33974.1, CCDS33975.1, CCDS54756.1	4p15.1	2013-01-30	2013-01-30		ENSG00000109790	ENSG00000109790		"""Kelch-like"", ""BTB/POZ domain containing"""	6356	protein-coding gene	gene with protein product		608064	"""kelch (Drosophila)-like 5"", ""kelch-like 5 (Drosophila)"""			11590829, 14672410	Standard	NM_001007075		Approved		uc003gtp.3	Q96PQ7	OTTHUMG00000097819	ENST00000504108.1:c.2172T>C	4.37:g.39116911T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_015990	A8K170|B7WP68|E9PCF4|F8WAE7|G3XA92|Q6Y881|Q86XW0|Q9NUK3|Q9NV27|Q9NVA9|Q9Y2X2	Silent	SNP	ENST00000504108.1	37	CCDS33974.1	1173	0.5370879120879121	203	0.41260162601626016	227	0.6270718232044199	295	0.5157342657342657	448	0.5910290237467019	C	7.776	0.708499	0.15239	0.391512	0.58593	ENSG00000109790	ENST00000515612	.	.	.	6.06	-3.44	0.04796	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44967	-0.9293	3	.	.	.	.	0.6333	0.00798	0.2383:0.1979:0.2894:0.2744	rs3733276;rs17430718;rs3733276	.	.	.	R	236	.	.	C	+	1	0	KLHL5	38793306	0.012000	0.17670	0.901000	0.35422	0.859000	0.49053	-0.788000	0.04614	-0.927000	0.03766	-1.068000	0.02270	TGT	T|0.472;C|0.528	0.528	strong		0.418	KLHL5-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360604.1		
MAP3K1	4214	hgsc.bcm.edu	37	5	56178111	56178111	+	Silent	SNP	A	A	G	rs3822625	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:56178111A>G	ENST00000399503.3	+	14	3084	c.3084A>G	c.(3082-3084)caA>caG	p.Q1028Q		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1028					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)		TTTCTCTACAATTCCACAGAA	0.453													A|||	451	0.0900559	0.1195	0.0778	5008	,	,		22274	0.1081		0.0755	False		,,,				2504	0.0552				p.Q1028Q		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A3084G						PASS	.	A		357,3377		18,321,1528	65.0	64.0	65.0		3084	3.7	1.0	5	dbSNP_107	65	581,7625		23,535,3545	no	coding-synonymous	MAP3K1	NM_005921.1		41,856,5073	GG,GA,AA		7.0802,9.5608,7.8559		1028/1513	56178111	938,11002	1867	4103	5970	SO:0001819	synonymous_variant	4214	exon14			TCTACAATTCCAC	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.3084A>G	5.37:g.56178111A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_005921		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			A|0.910;G|0.090	0.090	strong		0.453	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
SERPINH1	871	hgsc.bcm.edu	37	11	75282882	75282882	+	Silent	SNP	G	G	A	rs585821	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:75282882G>A	ENST00000524558.1	+	5	2446	c.1011G>A	c.(1009-1011)ttG>ttA	p.L337L	SERPINH1_ENST00000525876.1_Silent_p.L120L|SERPINH1_ENST00000533603.1_Silent_p.L337L|SERPINH1_ENST00000358171.3_Silent_p.L337L			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	337					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					AGGCCGACTTGTCACGCATGT	0.587													G|||	1887	0.376797	0.4758	0.3775	5008	,	,		18407	0.2073		0.2972	False		,,,				2504	0.499				p.L337L		Atlas-SNP	.											.	SERPINH1	33	.	0			c.G1011A						PASS	.	G	,	1940,2460	550.6+/-378.1	437,1066,697	66.0	51.0	56.0		1011,1011	2.3	1.0	11	dbSNP_83	56	2609,5977	420.8+/-353.5	377,1855,2061	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	814,2921,2758	AA,AG,GG		30.3867,44.0909,35.03	,	337/419,337/419	75282882	4549,8437	2200	4293	6493	SO:0001819	synonymous_variant	871	exon5			CGACTTGTCACGC	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.1011G>A	11.37:g.75282882G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	36	6	0.166667	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			G|0.662;A|0.338	0.338	strong		0.587	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
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 GAIIx	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		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	47	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	
CTNND1	1500	hgsc.bcm.edu	37	11	57563991	57563991	+	Silent	SNP	C	C	T	rs10896644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57563991C>T	ENST00000399050.4	+	6	1019	c.483C>T	c.(481-483)gaC>gaT	p.D161D	CTNND1_ENST00000528621.1_Silent_p.D107D|CTNND1_ENST00000529919.1_Silent_p.D161D|CTNND1_ENST00000532649.1_Silent_p.D107D|CTNND1_ENST00000532463.1_Silent_p.D60D|CTNND1_ENST00000399039.4_Silent_p.D161D|CTNND1_ENST00000532787.1_Silent_p.D60D|CTNND1_ENST00000532844.1_Silent_p.D107D|CTNND1_ENST00000358694.6_Silent_p.D161D|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000532245.1_Silent_p.D60D|CTNND1_ENST00000534579.1_Silent_p.D107D|CTNND1_ENST00000426142.2_Silent_p.D60D|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000526938.1_Silent_p.D161D|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000526357.1_Silent_p.D107D|CTNND1_ENST00000529873.1_Silent_p.D107D|CTNND1_ENST00000528232.1_Silent_p.D60D|CTNND1_ENST00000361391.6_Silent_p.D161D|CTNND1_ENST00000529526.1_Silent_p.D107D|CTNND1_ENST00000361796.4_Silent_p.D161D|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000428599.2_Silent_p.D161D|CTNND1_ENST00000529986.1_Silent_p.D60D|CTNND1_ENST00000530094.1_Silent_p.D60D|CTNND1_ENST00000360682.6_Silent_p.D161D|CTNND1_ENST00000415361.2_Silent_p.D60D|CTNND1_ENST00000530748.1_Silent_p.D107D|CTNND1_ENST00000361332.4_Silent_p.D161D|CTNND1_ENST00000524630.1_Silent_p.D161D	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	161					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				TGGGACCAGACGGGTTGCCTG	0.463													C|||	1359	0.271366	0.1762	0.3314	5008	,	,		20175	0.1012		0.4284	False		,,,				2504	0.3712				p.D161D		Atlas-SNP	.											.	CTNND1	203	.	0			c.C483T						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,	893,3063		116,661,1201	82.0	86.0	85.0		483,483,483,483,483,180,180,180,180,180,180,180,321,321,483,321,321,321,321,180,321,483	-5.8	0.8	11	dbSNP_120	85	3413,4933		696,2021,1456	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CTNND1	NM_001085458.1,NM_001085459.1,NM_001085460.1,NM_001085461.1,NM_001085462.1,NM_001085463.1,NM_001085464.1,NM_001085465.1,NM_001085466.1,NM_001085467.1,NM_001085468.1,NM_001085469.1,NM_001206883.1,NM_001206884.1,NM_001206885.1,NM_001206886.1,NM_001206887.1,NM_001206888.1,NM_001206889.1,NM_001206890.1,NM_001206891.1,NM_001331.2	,,,,,,,,,,,,,,,,,,,,,	812,2682,2657	TT,TC,CC		40.8938,22.5733,35.0024	,,,,,,,,,,,,,,,,,,,,,	161/969,161/963,161/934,161/934,161/934,60/868,60/862,60/841,60/839,60/833,60/833,60/833,107/915,107/886,161/940,107/909,107/888,107/880,107/880,60/833,107/880,161/942	57563991	4306,7996	1978	4173	6151	SO:0001819	synonymous_variant	1500	exon6			ACCAGACGGGTTG	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"""Armadillo repeat containing"""	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.483C>T	11.37:g.57563991C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	114	62	0.54386	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Silent	SNP	ENST00000399050.4	37	CCDS44604.1																																																																																			C|0.728;T|0.272	0.272	strong		0.463	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331	
PRDM6	93166	hgsc.bcm.edu	37	5	122435627	122435627	+	Missense_Mutation	SNP	G	G	A	rs1008058	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:122435627G>A	ENST00000407847.4	+	3	1285	c.871G>A	c.(871-873)Gcc>Acc	p.A291T	PRDM6_ENST00000464424.1_3'UTR	NM_001136239.1	NP_001129711.1	Q9NQX0	PRDM6_HUMAN	PR domain containing 6	291	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of smooth muscle cell differentiation (GO:0051151)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	7						GCAGGCAGGCGCCGTGAGGAA	0.672													G|||	927	0.185104	0.0643	0.2334	5008	,	,		16270	0.3859		0.1054	False		,,,				2504	0.1892				p.A291T		Atlas-SNP	.											.	PRDM6	26	.	0			c.G871A						PASS	.	G	THR/ALA	84,1298		0,84,607	17.0	19.0	18.0		871	5.1	1.0	5	dbSNP_86	18	356,2826		17,322,1252	yes	missense	PRDM6	NM_001136239.1	58	17,406,1859	AA,AG,GG		11.1879,6.0781,9.6407	possibly-damaging	291/596	122435627	440,4124	691	1591	2282	SO:0001583	missense	93166	exon3			GCAGGCGCCGTGA	AF272898	CCDS47259.1	5q21-q23	2013-01-08			ENSG00000061455	ENSG00000061455		"""Zinc fingers, C2H2-type"""	9350	protein-coding gene	gene with protein product							Standard	NM_001136239		Approved		uc003kti.3	Q9NQX0	OTTHUMG00000150469	ENST00000407847.4:c.871G>A	5.37:g.122435627G>A	ENSP00000384725:p.Ala291Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	171	86	0.502924	NM_001136239	B5MCJ4|Q9NQW9	Missense_Mutation	SNP	ENST00000407847.4	37	CCDS47259.1	435	0.19917582417582416	42	0.08536585365853659	64	0.17679558011049723	254	0.44405594405594406	75	0.09894459102902374	G	20.4	3.989064	0.74589	0.060781	0.111879	ENSG00000061455	ENST00000407847	T	0.72615	-0.67	5.91	5.05	0.67936	SET domain (3);	0.188519	0.44483	N	0.000459	T	0.00012	0.0000	L	0.39514	1.22	0.24453	P	0.99447099	B	0.29862	0.259	B	0.19946	0.027	T	0.33497	-0.9866	9	0.31617	T	0.26	-5.1987	14.9405	0.70989	0.0682:0.0:0.9318:0.0	rs1008058;rs1008058	291	Q9NQX0	PRDM6_HUMAN	T	291	ENSP00000384725:A291T	ENSP00000384725:A291T	A	+	1	0	PRDM6	122463526	0.906000	0.30813	1.000000	0.80357	0.997000	0.91878	2.842000	0.48230	1.518000	0.48934	0.655000	0.94253	GCC	G|0.784;A|0.216	0.216	strong		0.672	PRDM6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318226.2	XM_049619	
MTHFD1	4522	hgsc.bcm.edu	37	14	64908845	64908845	+	Missense_Mutation	SNP	G	G	A	rs2236225	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:64908845G>A	ENST00000545908.1	+	20	2355	c.2126G>A	c.(2125-2127)cGg>cAg	p.R709Q	CTD-2555O16.2_ENST00000556640.1_RNA|MTHFD1_ENST00000216605.8_Missense_Mutation_p.R653Q|CTD-2555O16.4_ENST00000609125.1_RNA			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	653	Formyltetrahydrofolate synthetase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	ATTGCAGACCGGATCGCACTC	0.488													G|||	1712	0.341853	0.1581	0.5447	5008	,	,		20044	0.1984		0.4294	False		,,,				2504	0.5041				p.R653Q	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.G1958A	GRCh37	CM022820	MTHFD1	M	rs2236225	PASS	.	G	GLN/ARG	943,3463	358.4+/-314.3	103,737,1363	124.0	109.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1958	5.0	1.0	14	dbSNP_98	114	3934,4666	546.9+/-385.1	892,2150,1258	yes	missense	MTHFD1	NM_005956.3	43	995,2887,2621	AA,AG,GG		45.7442,21.4026,37.4981	benign	653/936	64908845	4877,8129	2203	4300	6503	SO:0001583	missense	4522	exon20			CAGACCGGATCGC	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.2126G>A	14.37:g.64908845G>A	ENSP00000438588:p.Arg709Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	37		757	0.3466117216117216	105	0.21341463414634146	193	0.5331491712707183	134	0.23426573426573427	325	0.4287598944591029	G	14.88	2.667518	0.47677	0.214026	0.457442	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605	T;T;T	0.21932	1.98;1.98;1.98	5.87	4.97	0.65823	.	0.052299	0.85682	D	0.000000	T	0.00012	0.0000	L	0.33668	1.02	0.26730	P	0.970606	B;B	0.31599	0.33;0.009	B;B	0.19666	0.026;0.016	T	0.47736	-0.9094	9	0.41790	T	0.15	-5.0748	5.9329	0.19148	0.2468:0.0:0.7532:0.0	rs2236225;rs17751608;rs17850560;rs52810262;rs56503831;rs58065500;rs2236225	709;653	F5H2F4;G3V2B8	.;.	Q	709;653;709	ENSP00000438588:R709Q;ENSP00000450560:R653Q;ENSP00000216605:R709Q	ENSP00000216605:R653Q	R	+	2	0	MTHFD1	63978598	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	5.247000	0.65416	2.941000	0.99782	0.655000	0.94253	CGG	G|0.641;N|0.000	.	strong		0.488	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1		
ITGAM	3684	hgsc.bcm.edu	37	16	31336719	31336719	+	Silent	SNP	G	G	A	rs1143682	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31336719G>A	ENST00000287497.8	+	20	2574	c.2499G>A	c.(2497-2499)acG>acA	p.T833T	ITGAM_ENST00000544665.3_Silent_p.T834T			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	833					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)	p.T833T(1)		endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						AGGTGTCCACGCTCCAGGTAG	0.562													G|||	1475	0.294529	0.0832	0.3329	5008	,	,		18561	0.6558		0.3519	False		,,,				2504	0.1217				p.T834T		Atlas-SNP	.											ITGAM,NS,carcinoma,0,3	ITGAM	137	3	1	Substitution - coding silent(1)	prostate(1)	c.G2502A						scavenged	.	G	,	576,3644		46,484,1580	68.0	72.0	71.0		2499,2502	-8.9	0.0	16	dbSNP_86	71	3164,5294		609,1946,1674	no	coding-synonymous,coding-synonymous	ITGAM	NM_000632.3,NM_001145808.1	,	655,2430,3254	AA,AG,GG		37.4084,13.6493,29.4999	,	833/1153,834/1154	31336719	3740,8938	2110	4229	6339	SO:0001819	synonymous_variant	3684	exon20			GTCCACGCTCCAG	J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.2499G>A	16.37:g.31336719G>A		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	67	62	0.925373	NM_001145808	Q4VAK0|Q4VAK1|Q4VAK2	Silent	SNP	ENST00000287497.8	37	CCDS45470.1																																																																																			G|0.631;A|0.369	0.369	strong		0.562	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1	NM_000632	
TRPA1	8989	hgsc.bcm.edu	37	8	72987638	72987638	+	Missense_Mutation	SNP	G	G	A	rs13268757	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:72987638G>A	ENST00000262209.4	-	1	214	c.7C>T	c.(7-9)Cgc>Tgc	p.R3C		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	3			R -> C (in dbSNP:rs13268757). {ECO:0000269|PubMed:10066796}.		calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CTCAGGCTGCGCTTCATTGAC	0.652													g|||	503	0.100439	0.0825	0.0735	5008	,	,		13603	0.0565		0.173	False		,,,				2504	0.1145				p.R3C		Atlas-SNP	.											.	TRPA1	256	.	0			c.C7T						PASS	.	A	CYS/ARG	365,4041	186.7+/-213.5	14,337,1852	66.0	69.0	68.0		7	2.7	1.0	8	dbSNP_121	68	1437,7163	276.4+/-292.3	117,1203,2980	yes	missense	TRPA1	NM_007332.2	180	131,1540,4832	AA,AG,GG		16.7093,8.2842,13.8551	probably-damaging	3/1120	72987638	1802,11204	2203	4300	6503	SO:0001583	missense	8989	exon1			GGCTGCGCTTCAT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.7C>T	8.37:g.72987638G>A	ENSP00000262209:p.Arg3Cys	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	223	0.1021062271062271	26	0.052845528455284556	28	0.07734806629834254	40	0.06993006993006994	129	0.17018469656992086	g	10.45	1.352754	0.24512	0.082842	0.167093	ENSG00000104321	ENST00000262209	T	0.42513	0.97	4.58	2.73	0.32206	.	0.173631	0.36134	N	0.002767	T	0.00109	0.0003	L	0.39147	1.195	0.25823	P	0.9842676	B	0.15141	0.012	B	0.04013	0.001	T	0.04723	-1.0931	9	0.87932	D	0	-1.0158	8.9297	0.35663	0.0844:0.0:0.7798:0.1358	rs13268757;rs58641623;rs13268757	3	O75762	TRPA1_HUMAN	C	3	ENSP00000262209:R3C	ENSP00000262209:R3C	R	-	1	0	TRPA1	73150192	0.997000	0.39634	0.999000	0.59377	0.224000	0.24922	0.071000	0.14594	0.256000	0.21614	-0.875000	0.02981	CGC	G|0.872;A|0.128	0.128	strong		0.652	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
ZNF253	56242	hgsc.bcm.edu	37	19	20002439	20002439	+	Missense_Mutation	SNP	G	G	T	rs75543118	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:20002439G>T	ENST00000589717.1	+	4	475	c.383G>T	c.(382-384)gGt>gTt	p.G128V	ZNF253_ENST00000355650.4_Missense_Mutation_p.G52V|AC011477.1_ENST00000578823.1_RNA|CTC-559E9.8_ENST00000585571.1_RNA	NM_021047.2	NP_066385.2	O75346	ZN253_HUMAN	zinc finger protein 253	128					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CACAAAGGAGGTTATAATGGA	0.338													g|||	420	0.0838658	0.0454	0.1326	5008	,	,		18915	0.1766		0.0189	False		,,,				2504	0.0726				p.G128V		Atlas-SNP	.											.	ZNF253	99	.	0			c.G383T						PASS	.	G	VAL/GLY	174,4122		5,164,1979	62.0	64.0	63.0		383	0.0	0.0	19	dbSNP_131	63	154,8408		1,152,4128	yes	missense	ZNF253	NM_021047.2	109	6,316,6107	TT,TG,GG		1.7986,4.0503,2.5509	benign	128/500	20002439	328,12530	2148	4281	6429	SO:0001583	missense	56242	exon4			AAGGAGGTTATAA	AF038951	CCDS42532.1	19p12	2014-02-12	2003-12-17		ENSG00000256771	ENSG00000256771		"""Zinc fingers, C2H2-type"", ""-"""	13497	protein-coding gene	gene with protein product		606954	"""zinc finger protein 411"""	ZNF411		10585455	Standard	NM_021047		Approved	BMZF-1, FLJ90391	uc002noj.3	O75346	OTTHUMG00000182369	ENST00000589717.1:c.383G>T	19.37:g.20002439G>T	ENSP00000468720:p.Gly128Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_021047	A4FVA7|Q0P6G3|Q6P0L2|Q8NCA3|Q8NCF9	Missense_Mutation	SNP	ENST00000589717.1	37	CCDS42532.1	156	0.07142857142857142	17	0.034552845528455285	39	0.10773480662983426	89	0.1555944055944056	11	0.014511873350923483	g	6.678	0.493674	0.12702	0.040503	0.017986	ENSG00000256771	ENST00000355650	.	.	.	1.4	0.0162	0.14107	.	.	.	.	.	T	0.00109	0.0003	L	0.27053	0.805	0.49483	P	2.0600000000003948E-4	B	0.28667	0.219	B	0.29716	0.106	T	0.22556	-1.0213	6	.	.	.	.	4.7194	0.12912	0.43:0.0:0.57:0.0	.	128	O75346	ZN253_HUMAN	V	128	.	.	G	+	2	0	ZNF253	19863439	0.266000	0.24112	0.018000	0.16275	0.017000	0.09413	0.226000	0.17776	-0.722000	0.04922	-0.708000	0.03648	GGT	G|0.945;T|0.055	0.055	strong		0.338	ZNF253-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460802.1	NM_021047	
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 GAIIx	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_ENST00000510516.1_Silent_p.L14L|LYRM7_ENST00000507584.1_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		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	48	23	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	
TBP	6908	hgsc.bcm.edu	37	6	170871052	170871052	+	Silent	SNP	G	G	A	rs112083427|rs369312237	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:170871052G>A	ENST00000392092.2	+	3	507	c.228G>A	c.(226-228)caG>caA	p.Q76Q	TBP_ENST00000540980.1_Silent_p.Q56Q|TBP_ENST00000230354.6_Silent_p.Q76Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	76	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q76Q(4)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcaacagcagcagcagcagc	0.572																																					p.Q76Q		Atlas-SNP	.											TBP,NS,carcinoma,0,5	TBP	58	5	4	Substitution - coding silent(4)	lung(3)|prostate(1)	c.G228A						scavenged	.						14.0	19.0	17.0					6																	170871052		1952	3842	5794	SO:0001819	synonymous_variant	6908	exon3			ACAGCAGCAGCAG	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.228G>A	6.37:g.170871052G>A		Somatic	44	1	0.0227273		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			G|0.500;A|0.500	0.500	strong		0.572	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
DENND3	22898	hgsc.bcm.edu	37	8	142200467	142200467	+	Silent	SNP	G	G	A	rs1045303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:142200467G>A	ENST00000262585.2	+	20	3368	c.3090G>A	c.(3088-3090)ccG>ccA	p.P1030P	DENND3_ENST00000519811.1_Silent_p.P1110P|DENND3_ENST00000523308.1_Silent_p.P80P|DENND3_ENST00000424248.1_Silent_p.P978P	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	1030					cellular protein catabolic process (GO:0044257)|endosome to lysosome transport (GO:0008333)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(4)|stomach(2)|urinary_tract(1)	55	all_cancers(97;7.36e-15)|all_epithelial(106;2.33e-13)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.105)			TCCAGCTGCCGCGAGGTGGCC	0.647													G|||	1882	0.375799	0.2035	0.3256	5008	,	,		16360	0.6171		0.2644	False		,,,				2504	0.5102				p.P1030P		Atlas-SNP	.											.	DENND3	127	.	0			c.G3090A						PASS	.	G		1034,3372	357.4+/-313.9	127,780,1296	51.0	48.0	49.0		3090	-10.6	0.0	8	dbSNP_86	49	2217,6383	357.4+/-330.7	286,1645,2369	no	coding-synonymous	DENND3	NM_014957.2		413,2425,3665	AA,AG,GG		25.7791,23.468,24.9962		1030/1199	142200467	3251,9755	2203	4300	6503	SO:0001819	synonymous_variant	22898	exon20			GCTGCCGCGAGGT	AB020677	CCDS34947.1	8q24.3	2013-01-10				ENSG00000105339		"""DENN/MADD domain containing"", ""WD repeat domain containing"""	29134	protein-coding gene	gene with protein product						10048485	Standard	NM_014957		Approved	KIAA0870	uc003yvy.3	A2RUS2		ENST00000262585.2:c.3090G>A	8.37:g.142200467G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	37	CCDS34947.1	779	0.3566849816849817	100	0.2032520325203252	126	0.34806629834254144	353	0.6171328671328671	200	0.2638522427440633	G	0.218	-1.031100	0.02029	0.23468	0.257791	ENSG00000105339	ENST00000518668	.	.	.	5.31	-10.6	0.00265	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.34903	P	0.25326899999999997	.	.	.	.	.	.	T	0.16808	-1.0390	3	.	.	.	-30.1385	15.5131	0.75798	0.175:0.6549:0.1108:0.0593	rs1045303;rs3185194;rs17407339;rs56738741;rs1045303	.	.	.	T	1035	.	.	A	+	1	0	DENND3	142269649	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.815000	0.01722	-4.470000	0.00047	-0.657000	0.03884	GCG	A|0.299;C|0.000;G|0.700	0.299	strong		0.647	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
APOBR	55911	hgsc.bcm.edu	37	16	28506428	28506428	+	Silent	SNP	C	C	T	rs151233	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28506428C>T	ENST00000431282.1	+	2	76	c.66C>T	c.(64-66)ctC>ctT	p.L22L	APOBR_ENST00000564831.1_Silent_p.L22L|CLN3_ENST00000569430.1_Intron|CLN3_ENST00000567160.1_Intron|CLN3_ENST00000360019.2_5'Flank|APOBR_ENST00000328423.5_Silent_p.L22L			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	22					cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						AGGATTCCCTCGGCACCTTTG	0.612													C|||	780	0.155751	0.112	0.1095	5008	,	,		16661	0.0079		0.1342	False		,,,				2504	0.4223				p.L22L		Atlas-SNP	.											.	APOBR	89	.	0			c.C66T						PASS	.	C		411,3383		24,363,1510	11.0	12.0	12.0		66	-0.5	0.6	16	dbSNP_79	12	1122,7086		75,972,3057	no	coding-synonymous	APOBR	NM_018690.3		99,1335,4567	TT,TC,CC		13.6696,10.8329,12.7729		22/1089	28506428	1533,10469	1897	4104	6001	SO:0001819	synonymous_variant	55911	exon2			TTCCCTCGGCACC	AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.66C>T	16.37:g.28506428C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Silent	SNP	ENST00000431282.1	37																																																																																				C|0.894;T|0.106	0.106	strong		0.612	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
ADAMTS13	11093	hgsc.bcm.edu	37	9	136304497	136304497	+	Silent	SNP	A	A	G	rs3124768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136304497A>G	ENST00000371929.3	+	15	2160	c.1716A>G	c.(1714-1716)acA>acG	p.T572T	ADAMTS13_ENST00000355699.2_Silent_p.T572T|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000356589.2_Silent_p.T541T|ADAMTS13_ENST00000536611.1_Silent_p.T244T	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	572	Spacer.				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)		AATATGTCACATTTCTGACAG	0.498													A|||	2584	0.515974	0.3699	0.4769	5008	,	,		20869	0.8115		0.4215	False		,,,				2504	0.5337				p.T572T		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.A1716G						PASS	.	A	,,	1577,2829	492.4+/-362.4	285,1007,911	158.0	133.0	142.0		1716,1623,1716	-10.3	0.2	9	dbSNP_103	142	3826,4774	539.8+/-383.7	854,2118,1328	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMTS13	NM_139025.3,NM_139026.3,NM_139027.3	,,	1139,3125,2239	GG,GA,AA		44.4884,35.7921,41.5424	,,	572/1428,541/1341,572/1372	136304497	5403,7603	2203	4300	6503	SO:0001819	synonymous_variant	11093	exon15			TGTCACATTTCTG	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.1716A>G	9.37:g.136304497A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			A|0.531;G|0.469	0.469	strong		0.498	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
CH25H	9023	hgsc.bcm.edu	37	10	90966393	90966393	+	Silent	SNP	G	G	A	rs17382301	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:90966393G>A	ENST00000371852.2	-	1	678	c.657C>T	c.(655-657)aaC>aaT	p.N219N		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	219					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)	p.N219N(1)		kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		ACCAAGGGAAGTTGTAGCCGG	0.587													G|||	415	0.0828674	0.0053	0.0706	5008	,	,		19855	0.0337		0.1233	False		,,,				2504	0.2055				p.N219N		Atlas-SNP	.											CH25H,NS,carcinoma,0,1	CH25H	19	1	1	Substitution - coding silent(1)	stomach(1)	c.C657T						PASS	.	G		134,4272	98.5+/-137.1	3,128,2072	119.0	100.0	106.0		657	3.1	1.0	10	dbSNP_123	106	1227,7373	247.2+/-275.4	92,1043,3165	no	coding-synonymous	CH25H	NM_003956.3		95,1171,5237	AA,AG,GG		14.2674,3.0413,10.4644		219/273	90966393	1361,11645	2203	4300	6503	SO:0001819	synonymous_variant	9023	exon1			AGGGAAGTTGTAG	AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"""Fatty acid hydroxylase domain containing"""	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.657C>T	10.37:g.90966393G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	NM_003956	B2RBY3	Silent	SNP	ENST00000371852.2	37	CCDS7400.1																																																																																			G|0.910;A|0.090	0.090	strong		0.587	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956	
LRRK1	79705	hgsc.bcm.edu	37	15	101606889	101606889	+	Missense_Mutation	SNP	G	G	A	rs375358524|rs386787404|rs2924835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:101606889G>A	ENST00000388948.3	+	33	6172	c.5813G>A	c.(5812-5814)gGc>gAc	p.G1938D	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.G1935D|LRRK1_ENST00000532145.1_3'UTR	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			AAGGATTCTGGCGCCCAGCGG	0.587													G|||	1363	0.272165	0.0794	0.3559	5008	,	,		18822	0.3403		0.3201	False		,,,				2504	0.3538				p.G1938D		Atlas-SNP	.											.	LRRK1	310	.	0			c.G5813A						PASS	.	G	ASP/GLY	418,3730		14,390,1670	160.0	175.0	170.0		5813	5.5	0.0	15	dbSNP_101	170	2545,5895		368,1809,2043	yes	missense	LRRK1	NM_024652.3	94	382,2199,3713	AA,AG,GG		30.154,10.0771,23.5383	benign	1938/2016	101606889	2963,9625	2074	4220	6294	SO:0001583	missense	79705	exon33			ATTCTGGCGCCCA	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.5813G>A	15.37:g.101606889G>A	ENSP00000373600:p.Gly1938Asp	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	37	CCDS42086.1	495|495	0.22664835164835165|0.22664835164835165	38|38	0.07723577235772358|0.07723577235772358	94|94	0.2596685082872928|0.2596685082872928	177|177	0.3094405594405594|0.3094405594405594	186|186	0.24538258575197888|0.24538258575197888	G|G	8.438|8.438	0.850072|0.850072	0.17034|0.17034	0.100771|0.100771	0.30154|0.30154	ENSG00000154237|ENSG00000154237	ENST00000542170|ENST00000388948;ENST00000284395;ENST00000529762	.|T;T	.|0.72725	.|-0.65;-0.68	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	.|0.111323	.|0.64402	.|D	.|0.000007	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.64997|0.64997	1.995|1.995	0.58432|0.58432	P|P	6.999999999979245E-6|6.999999999979245E-6	.|B	.|0.16166	.|0.016	.|B	.|0.12156	.|0.007	T|T	0.03840|0.03840	-1.0999|-1.0999	4|9	.|0.59425	.|D	.|0.04	.|.	15.7379|15.7379	0.77859|0.77859	0.0:0.1366:0.8634:0.0|0.0:0.1366:0.8634:0.0	rs2959197;rs33925554;rs2959197|rs2959197;rs33925554;rs2959197	.|1938	.|Q38SD2	.|LRRK1_HUMAN	T|D	492|1938;1935;629	.|ENSP00000373600:G1938D;ENSP00000284395:G1935D	.|ENSP00000284395:G1935D	A|G	+|+	1|2	0|0	LRRK1|LRRK1	99424412|99424412	0.994000|0.994000	0.37717|0.37717	0.014000|0.014000	0.15608|0.15608	0.043000|0.043000	0.13939|0.13939	3.321000|3.321000	0.51999|0.51999	2.582000|2.582000	0.87167|0.87167	0.655000|0.655000	0.94253|0.94253	GCG|GGC	.	.	alt		0.587	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
Unknown	0	hgsc.bcm.edu	37	13	103402522	103402522	+	IGR	SNP	C	C	T	rs9300760	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103402522C>T								LINC00283 (4948 upstream) : TEX30 (15817 downstream)																							GGCTTAGACACGTTTCCTCTA	0.343													C|||	3473	0.69349	0.5416	0.7493	5008	,	,		19401	0.5873		0.826	False		,,,				2504	0.8323				p.T175T		Atlas-SNP	.											.	.	.	.	0			c.G525A						PASS	.	C		773,611		217,339,136	244.0	179.0	199.0		525	0.1	0.0	13	dbSNP_119	199	2544,638		1024,496,71	no	coding-synonymous	CCDC168	NM_001146197.1		1241,835,207	TT,TC,CC		20.0503,44.1474,27.3544		175/7082	103402522	3317,1249	692	1591	2283	SO:0001628	intergenic_variant	643677	exon4			TAGACACGTTTCC																													13.37:g.103402522C>T		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001146197		Silent	SNP		37																																																																																				C|0.316;N|0.001	.	strong	0	0.343								
LGI2	55203	hgsc.bcm.edu	37	4	25005193	25005193	+	Silent	SNP	G	G	A	rs2232028	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:25005193G>A	ENST00000382114.4	-	8	1703	c.1518C>T	c.(1516-1518)taC>taT	p.Y506Y		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	506						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				GCGCCTGCACGTAAATCTCCT	0.408													A|||	3835	0.765775	0.9115	0.6455	5008	,	,		17150	0.9742		0.4632	False		,,,				2504	0.7505				p.Y506Y		Atlas-SNP	.											.	LGI2	62	.	0			c.C1518T						PASS	.	A		3719,687	287.8+/-279.5	1570,579,54	92.0	102.0	98.0		1518	-3.8	0.7	4	dbSNP_98	98	3924,4676	605.9+/-395.0	933,2058,1309	no	coding-synonymous	LGI2	NM_018176.3		2503,2637,1363	AA,AG,GG		45.6279,15.5924,41.2348		506/546	25005193	7643,5363	2203	4300	6503	SO:0001819	synonymous_variant	55203	exon8			CTGCACGTAAATC	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.1518C>T	4.37:g.25005193G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Silent	SNP	ENST00000382114.4	37	CCDS3431.1																																																																																			G|0.332;A|0.668	0.668	strong		0.408	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1		
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 GAIIx	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	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	100	49	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	
CAND2	23066	hgsc.bcm.edu	37	3	12857493	12857493	+	Missense_Mutation	SNP	C	C	T	rs2305397	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:12857493C>T	ENST00000456430.2	+	9	1468	c.1427C>T	c.(1426-1428)cCt>cTt	p.P476L	CAND2_ENST00000295989.5_Missense_Mutation_p.P383L	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	476			P -> L (in dbSNP:rs2305397).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GAGCATATGCCTGTGCTGGTA	0.627													C|||	1617	0.322883	0.3154	0.366	5008	,	,		19330	0.1766		0.5775	False		,,,				2504	0.1912				p.P476L	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											CAND2_ENST00000456430,caecum,carcinoma,0,2	CAND2	138	2	0			c.C1427T						PASS	.	C	LEU/PRO,LEU/PRO	1410,2662		251,908,877	57.0	63.0	61.0		1427,1148	5.1	0.8	3	dbSNP_100	61	4400,3966		1144,2112,927	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	98,98	1395,3020,1804	TT,TC,CC		47.4062,34.6267,46.7117	benign,benign	476/1237,383/1120	12857493	5810,6628	2036	4183	6219	SO:0001583	missense	23066	exon9			ATATGCCTGTGCT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1427C>T	3.37:g.12857493C>T	ENSP00000387641:p.Pro476Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	803	0.3676739926739927	162	0.32926829268292684	122	0.3370165745856354	88	0.15384615384615385	431	0.5686015831134564	C	12.11	1.841013	0.32513	0.346267	0.525938	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.11277	2.79;2.79	5.12	5.12	0.69794	Armadillo-like helical (1);Armadillo-type fold (1);	0.126888	0.53938	D	0.000055	T	0.00012	0.0000	M	0.69248	2.105	0.09310	P	1.0	B;B	0.25904	0.005;0.137	B;B	0.32533	0.009;0.147	T	0.45175	-0.9279	9	0.46703	T	0.11	-10.0664	16.0847	0.81038	0.0:1.0:0.0:0.0	rs2305397;rs17825005;rs52819689;rs59943117;rs2305397	476;383	O75155;O75155-2	CAND2_HUMAN;.	L	383;476	ENSP00000295989:P383L;ENSP00000387641:P476L	ENSP00000295989:P383L	P	+	2	0	CAND2	12832493	1.000000	0.71417	0.846000	0.33378	0.346000	0.29079	5.984000	0.70548	2.395000	0.81488	0.561000	0.74099	CCT	C|0.612;T|0.386	0.386	strong		0.627	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
KANK1	23189	hgsc.bcm.edu	37	9	712060	712060	+	Missense_Mutation	SNP	G	G	C	rs4465020	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:712060G>C	ENST00000382303.1	+	7	1946	c.1294G>C	c.(1294-1296)Gag>Cag	p.E432Q	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.E432Q|KANK1_ENST00000382293.3_Missense_Mutation_p.E274Q	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	432	Interaction with KIF21A.		E -> Q (in dbSNP:rs4465020). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)	p.E274Q(2)|p.E432Q(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GACACTTGTTGAGATGAGAAA	0.522													G|||	1178	0.235224	0.0303	0.2176	5008	,	,		21322	0.123		0.4066	False		,,,				2504	0.4642				p.E432Q		Atlas-SNP	.											KANK1_ENST00000382303,NS,carcinoma,0,2	KANK1	231	2	3	Substitution - Missense(3)	prostate(3)	c.G1294C						PASS	.	G	GLN/GLU,GLN/GLU	353,4053	182.2+/-210.1	15,323,1865	113.0	98.0	103.0		1294,820	4.8	0.1	9	dbSNP_111	103	3393,5207	502.5+/-375.7	648,2097,1555	yes	missense,missense	KANK1	NM_015158.2,NM_153186.3	29,29	663,2420,3420	CC,CG,GG		39.4535,8.0118,28.8021	benign,benign	432/1353,274/1195	712060	3746,9260	2203	4300	6503	SO:0001583	missense	23189	exon7			CTTGTTGAGATGA	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1294G>C	9.37:g.712060G>C	ENSP00000371740:p.Glu432Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	481	0.22023809523809523	25	0.0508130081300813	84	0.23204419889502761	60	0.1048951048951049	312	0.41160949868073876	G	2.483	-0.319282	0.05386	0.080118	0.394535	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.47177	0.85;0.85;0.92	5.73	4.81	0.61882	.	0.418748	0.20444	N	0.092235	T	0.00012	0.0000	L	0.49126	1.545	0.52501	P	4.700000000001925E-5	B;B	0.32203	0.36;0.36	B;B	0.28465	0.09;0.09	T	0.42949	-0.9421	9	0.22706	T	0.39	-3.643	9.3954	0.38399	0.0731:0.2712:0.6557:0.0	rs4465020;rs17853758;rs17853807;rs52805693	432;432	Q5W0W1;Q14678	.;KANK1_HUMAN	Q	432;432;432;274	ENSP00000371740:E432Q;ENSP00000371734:E432Q;ENSP00000371730:E274Q	ENSP00000346479:E432Q	E	+	1	0	KANK1	702060	0.546000	0.26457	0.120000	0.21714	0.005000	0.04900	2.053000	0.41326	2.721000	0.93114	0.655000	0.94253	GAG	G|0.734;C|0.266	0.266	strong		0.522	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
NRD1	4898	hgsc.bcm.edu	37	1	52290984	52290984	+	Silent	SNP	T	T	G	rs11205896	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:52290984T>G	ENST00000354831.7	-	8	1404	c.1215A>C	c.(1213-1215)ggA>ggC	p.G405G	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_Silent_p.G205G|NRD1_ENST00000539524.1_Silent_p.G273G|NRD1_ENST00000352171.7_Silent_p.G337G	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	336					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						CCATAGGATGTCCAGGTCTAG	0.294													T|||	2496	0.498403	0.2496	0.6009	5008	,	,		18122	0.8313		0.5239	False		,,,				2504	0.3926				p.G405G		Atlas-SNP	.											.	NRD1	89	.	0			c.A1215C						PASS	.	T	,,	1286,3120	435.5+/-344.3	172,942,1089	62.0	62.0	62.0		1011,819,1215	4.3	1.0	1	dbSNP_120	62	4311,4289	576.1+/-390.3	1077,2157,1066	no	coding-synonymous,coding-synonymous,coding-synonymous	NRD1	NM_001101662.1,NM_001242361.1,NM_002525.2	,,	1249,3099,2155	GG,GT,TT		49.8721,29.1875,43.034	,,	337/1152,273/1088,405/1220	52290984	5597,7409	2203	4300	6503	SO:0001819	synonymous_variant	4898	exon8			AGGATGTCCAGGT	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.1215A>C	1.37:g.52290984T>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	191	75	0.39267	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	37	CCDS559.1																																																																																			T|0.532;G|0.468	0.468	strong		0.294	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
WDPCP	51057	hgsc.bcm.edu	37	2	63401820	63401820	+	Missense_Mutation	SNP	T	T	C	rs61734468	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:63401820T>C	ENST00000272321.7	-	15	2590	c.2063A>G	c.(2062-2064)aAt>aGt	p.N688S	WDPCP_ENST00000398544.3_Missense_Mutation_p.N529S|WDPCP_ENST00000409120.1_Missense_Mutation_p.N496S|WDPCP_ENST00000409199.1_Missense_Mutation_p.N496S	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	688					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						AGAAGAGCCATTCAGTATTCT	0.388													T|||	15	0.00299521	0.0	0.0043	5008	,	,		16954	0.0		0.007	False		,,,				2504	0.0051				p.N688S		Atlas-SNP	.											.	WDPCP	79	.	0			c.A2063G						PASS	.	T	SER/ASN	12,3676		0,12,1832	124.0	114.0	117.0		2063	2.8	0.3	2	dbSNP_129	117	138,8036		2,134,3951	yes	missense	WDPCP	NM_015910.5	46	2,146,5783	CC,CT,TT		1.6883,0.3254,1.2645	benign	688/747	63401820	150,11712	1844	4087	5931	SO:0001583	missense	51057	exon15			GAGCCATTCAGTA		CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"""chromosome 2 open reading frame 86"""	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.2063A>G	2.37:g.63401820T>C	ENSP00000272321:p.Asn688Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	125	50	0.4	NM_015910	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	T	2.949	-0.217137	0.06101	0.003254	0.016883	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544	T;T;T;T	0.72394	-0.65;-0.06;-0.06;-0.06	5.29	2.75	0.32379	.	0.643092	0.13025	N	0.419775	T	0.35770	0.0943	L	0.29908	0.895	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.002;0.003	T	0.19418	-1.0306	10	0.13470	T	0.59	-5.1826	6.0461	0.19760	0.0:0.0959:0.1776:0.7265	.	688;529	O95876;O95876-3	FRITZ_HUMAN;.	S	688;496;496;529	ENSP00000272321:N688S;ENSP00000386592:N496S;ENSP00000386769:N496S;ENSP00000381552:N529S	ENSP00000272321:N688S	N	-	2	0	WDPCP	63255324	0.002000	0.14202	0.290000	0.24890	0.845000	0.48019	0.137000	0.15995	0.871000	0.35750	0.416000	0.27883	AAT	T|0.993;C|0.007	0.007	strong		0.388	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910	
DDX11	1663	hgsc.bcm.edu	37	12	31256517	31256517	+	Silent	SNP	C	C	T	rs140335402	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:31256517C>T	ENST00000407793.2	+	26	2789	c.2538C>T	c.(2536-2538)ggC>ggT	p.G846G	DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000545668.1_Silent_p.G846G|DDX11_ENST00000350437.4_Missense_Mutation_p.A798V|DDX11_ENST00000542838.1_Missense_Mutation_p.A848V|DDX11_ENST00000228264.6_Missense_Mutation_p.A822V	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	846					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GCAGGCAGGGCCATCAGGCAC	0.642										Multiple Myeloma(12;0.14)			C|||	212	0.0423323	0.0098	0.0778	5008	,	,		15220	0.002		0.1113	False		,,,				2504	0.0317				p.A848V		Atlas-SNP	.											DDX11_ENST00000407793,NS,haematopoietic_neoplasm,0,2	DDX11	188	2	0			c.C2543T						PASS	.	C	VAL/ALA,VAL/ALA,	70,4300		2,66,2117	17.0	25.0	22.0		2393,2543,2538	3.1	1.0	12	dbSNP_134	22	852,7726		41,770,3478	no	missense,missense,coding-synonymous	DDX11	NM_004399.2,NM_030653.3,NM_152438.1	64,64,	43,836,5595	TT,TC,CC		9.9324,1.6018,7.1208	,,	798/857,848/907,846/971	31256517	922,12026	2185	4289	6474	SO:0001819	synonymous_variant	1663	exon26			GCAGGGCCATCAG	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2538C>T	12.37:g.31256517C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	114|114	0.0521978021978022|0.0521978021978022	8|8	0.016260162601626018|0.016260162601626018	29|29	0.08011049723756906|0.08011049723756906	1|1	0.0017482517482517483|0.0017482517482517483	76|76	0.10026385224274406|0.10026385224274406	C|C	4.403|4.403	0.074498|0.074498	0.08485|0.08485	0.016018|0.016018	0.099324|0.099324	ENSG00000013573|ENSG00000013573	ENST00000542838;ENST00000228264;ENST00000350437|ENST00000404673;ENST00000539702	T;T;D|.	0.91011|.	-0.8;-0.8;-2.77|.	3.14|3.14	3.14|3.14	0.36123|0.36123	.|.	0.768466|.	0.12220|.	N|.	0.488518|.	T|T	0.01627|0.01627	0.0052|0.0052	L|L	0.43923|0.43923	1.385|1.385	0.09310|0.09310	P|P	1.0|1.0	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.999;0.999|.	T|T	0.12915|0.12915	-1.0529|-1.0529	9|5	0.72032|0.08837	D|T	0.01|0.75	.|.	11.816|11.816	0.52211|0.52211	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	822;798;848|.	Q96FC9-3;Q96FC9-4;Q96FC9-2|.	.;.;.|.	V|S	848;822;798|547;114	ENSP00000443426:A848V;ENSP00000228264:A822V;ENSP00000309965:A798V|.	ENSP00000228264:A822V|ENSP00000385471:P547S	A|P	+|+	2|1	0|0	DDX11|DDX11	31147784|31147784	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.804000|0.804000	0.45430|0.45430	6.568000|6.568000	0.73987|0.73987	1.582000|1.582000	0.49881|0.49881	0.430000|0.430000	0.28490|0.28490	GCC|CCA	C|0.931;T|0.069	0.069	strong		0.642	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
EDA2R	60401	hgsc.bcm.edu	37	X	65824986	65824986	+	Missense_Mutation	SNP	C	C	T	rs1385699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:65824986C>T	ENST00000374719.3	-	3	226	c.170G>A	c.(169-171)aGa>aAa	p.R57K	EDA2R_ENST00000456230.2_Missense_Mutation_p.R57K|EDA2R_ENST00000253392.5_Missense_Mutation_p.R57K|EDA2R_ENST00000451436.2_Intron|EDA2R_ENST00000450752.1_Missense_Mutation_p.R57K|EDA2R_ENST00000396050.1_Missense_Mutation_p.R57K	NM_021783.3	NP_068555	Q9HAV5	TNR27_HUMAN	ectodysplasin A2 receptor	57			R -> K (in dbSNP:rs1385699).		cell differentiation (GO:0030154)|embryo development (GO:0009790)|epidermis development (GO:0008544)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						ACTCTGACATCTGTGGTGGCC	0.542													C|||	2512	0.66543	0.0333	0.6326	3775	,	,		13681	0.7569		0.6123	False		,,,				2504	0.6646				p.R57K		Atlas-SNP	.											.	EDA2R	30	.	0			c.G170A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	547,3288		36,393,82,1203,489	131.0	76.0	95.0		170,170,170	4.0	1.0	X	dbSNP_88	95	5367,1361		1599,731,1438,98,434	yes	missense,missense,missense	EDA2R	NM_001199687.2,NM_001242310.1,NM_021783.3	26,26,26	1635,1124,1520,1301,923	TT,TC,T,CC,C		20.2289,14.2634,44.0121	benign,benign,benign	57/298,57/319,57/298	65824986	5914,4649	2203	4300	6503	SO:0001583	missense	60401	exon2			TGACATCTGTGGT	AF298812	CCDS14386.1, CCDS56603.1	Xq11.1	2013-05-22			ENSG00000131080	ENSG00000131080		"""Tumor necrosis factor receptor superfamily"""	17756	protein-coding gene	gene with protein product		300276				11039935	Standard	NM_021783		Approved	XEDAR, EDA-A2R, EDAA2R, TNFRSF27	uc004dwt.2	Q9HAV5	OTTHUMG00000021736	ENST00000374719.3:c.170G>A	X.37:g.65824986C>T	ENSP00000363851:p.Arg57Lys	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_001242310	Q5VYX9|Q5VYY0|Q6UWM2|Q8IZA6	Missense_Mutation	SNP	ENST00000374719.3	37	CCDS14386.1	1144	0.6895720313441832	26	0.05416666666666667	146	0.6636363636363637	284	1.0	326	0.6877637130801688	C	7.543	0.661064	0.14645	0.142634	0.797711	ENSG00000131080	ENST00000374719;ENST00000396050;ENST00000253392;ENST00000456230;ENST00000450752	T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13	4.04	4.04	0.47022	TNFR/CD27/30/40/95 cysteine-rich region (4);	0.314080	0.26542	N	0.023785	T	0.00012	0.0000	N	0.15975	0.35	0.09310	P	0.9999999999996072	B;B	0.33826	0.001;0.427	B;B	0.31245	0.002;0.126	T	0.51647	-0.8679	9	0.02654	T	1	-10.3612	12.6999	0.57026	0.0:1.0:0.0:0.0	rs1385699;rs52832922;rs61534432;rs1385699	57;57	Q9HAV5-2;Q9HAV5	.;TNR27_HUMAN	K	57	ENSP00000363851:R57K;ENSP00000379365:R57K;ENSP00000253392:R57K;ENSP00000393935:R57K;ENSP00000402929:R57K	ENSP00000253392:R57K	R	-	2	0	EDA2R	65741711	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.661000	0.54503	1.841000	0.53522	0.600000	0.82982	AGA	C|0.436;0|0.005	.	strong		0.542	EDA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057002.1	NM_021783	
MTMR2	8898	hgsc.bcm.edu	37	11	95657111	95657111	+	Missense_Mutation	SNP	T	T	G	rs3824874	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:95657111T>G	ENST00000346299.5	-	1	348	c.8A>C	c.(7-9)aAg>aCg	p.K3T	MTMR2_ENST00000393223.3_5'UTR|MTMR2_ENST00000484818.1_5'Flank|MTMR2_ENST00000409459.1_5'UTR|MTMR2_ENST00000352297.7_5'UTR	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	3			K -> T (in dbSNP:rs3824874). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCTCGAGCTCTTCTCCATCGC	0.711													T|||	1066	0.212859	0.0681	0.2406	5008	,	,		14532	0.2688		0.3857	False		,,,				2504	0.1534				p.K3T		Atlas-SNP	.											.	MTMR2	79	.	0			c.A8C						PASS	.	T	THR/LYS,,	384,3908		20,344,1782	6.0	6.0	6.0		8,,	0.8	1.0	11	dbSNP_107	6	2643,5687		423,1797,1945	yes	missense,utr-5,utr-5	MTMR2	NM_016156.5,NM_201278.2,NM_201281.2	78,,	443,2141,3727	GG,GT,TT		31.7287,8.9469,23.9819	benign,,	3/644,,	95657111	3027,9595	2146	4165	6311	SO:0001583	missense	8898	exon1			GAGCTCTTCTCCA	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.8A>C	11.37:g.95657111T>G	ENSP00000345752:p.Lys3Thr	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	224	26	0.116071	NM_016156	A6NN98|Q9UPS9	Missense_Mutation	SNP	ENST00000346299.5	37	CCDS8305.1	601	0.2751831501831502	37	0.07520325203252033	102	0.281767955801105	171	0.29895104895104896	291	0.3839050131926121	T	10.82	1.456942	0.26161	0.089469	0.317287	ENSG00000087053	ENST00000346299	D	0.95342	-3.68	4.49	0.819	0.18785	.	0.802256	0.11114	N	0.598149	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	0.999999999999761	B	0.19817	0.039	B	0.15870	0.014	T	0.05386	-1.0888	9	0.72032	D	0.01	.	7.154	0.25626	0.0:0.2881:0.0:0.7119	rs3824874;rs17230839;rs17854793;rs3824874	3	Q13614	MTMR2_HUMAN	T	3	ENSP00000345752:K3T	ENSP00000345752:K3T	K	-	2	0	MTMR2	95296759	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	1.345000	0.33953	0.264000	0.21851	0.459000	0.35465	AAG	G|0.251;N|0.000	0.251	strong		0.711	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156	
GABRQ	55879	hgsc.bcm.edu	37	X	151821277	151821277	+	Missense_Mutation	SNP	T	T	A	rs3810651|rs57198283|rs368602583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:151821277T>A	ENST00000370306.2	+	9	1452	c.1432T>A	c.(1432-1434)Ttt>Att	p.F478I		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	478			F -> I (in dbSNP:rs3810651). {ECO:0000269|PubMed:10804200, ECO:0000269|PubMed:15489334}.		neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGACAGTATTTTTCCTACCGA	0.547													A|||	1644	0.435497	0.2065	0.536	3775	,	,		16054	0.2688		0.4235	False		,,,				2504	0.3088				p.F478I		Atlas-SNP	.											.	GABRQ	131	.	0			c.T1432A						PASS	.						119.0	111.0	114.0					X																	151821277		2150	4298	6448	SO:0001583	missense	55879	exon9			AGTATTTTTCCTA	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1432T>A	X.37:g.151821277T>A	ENSP00000359329:p.Phe478Ile	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	118	79	0.669492	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	765	0.46112115732368897	78	0.18309859154929578	136	0.5619834710743802	89	0.1869747899159664	223	0.3982142857142857	A	0.120	-1.126593	0.01770	.	.	ENSG00000147402	ENST00000370306	T	0.76060	-0.99	4.59	-9.19	0.00685	Neurotransmitter-gated ion-channel transmembrane domain (2);	4.285530	0.00357	N	0.000025	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03287	-1.1052	9	0.02654	T	1	.	6.847	0.23994	0.1293:0.3351:0.4511:0.0844	rs3810651;rs52810409;rs3810651	478	Q9UN88	GBRT_HUMAN	I	478	ENSP00000359329:F478I	ENSP00000359329:F478I	F	+	1	0	GABRQ	151571933	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.939000	0.03933	-4.339000	0.00055	-1.197000	0.01672	TTT	0|0.046;A|0.417	0.417	strong		0.547	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
CCDC38	120935	hgsc.bcm.edu	37	12	96312686	96312686	+	Missense_Mutation	SNP	C	C	A	rs12368787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:96312686C>A	ENST00000344280.3	-	3	663	c.106G>T	c.(106-108)Gtc>Ttc	p.V36F	CCDC38_ENST00000549752.1_5'Flank	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	36			V -> F (in dbSNP:rs12368787).							breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TTTTCTTTGACAAGAAAGAGA	0.318													A|||	335	0.066893	0.0401	0.0749	5008	,	,		21521	0.0278		0.1372	False		,,,				2504	0.0654				p.V36F		Atlas-SNP	.											.	CCDC38	45	.	0			c.G106T						PASS	.	A	PHE/VAL	213,4191	806.9+/-415.9	4,205,1993	156.0	148.0	150.0		106	4.8	1.0	12	dbSNP_120	150	1070,7530	769.8+/-407.6	67,936,3297	yes	missense	CCDC38	NM_182496.2	50	71,1141,5290	AA,AC,CC		12.4419,4.8365,9.8662	benign	36/564	96312686	1283,11721	2202	4300	6502	SO:0001583	missense	120935	exon3			CTTTGACAAGAAA	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.106G>T	12.37:g.96312686C>A	ENSP00000345470:p.Val36Phe	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_182496	Q8N835	Missense_Mutation	SNP	ENST00000344280.3	37	CCDS9056.1	159	0.07280219780219781	24	0.04878048780487805	25	0.06906077348066299	10	0.017482517482517484	100	0.13192612137203166	A	3.234	-0.156872	0.06544	0.048365	0.124419	ENSG00000165972	ENST00000344280	T	0.26957	1.7	4.85	4.85	0.62838	.	0.267312	0.34777	N	0.003681	T	0.00073	0.0002	N	0.01168	-0.975	0.09310	P	0.9999999999622513	B	0.02656	0.0	B	0.01281	0.0	T	0.24476	-1.0159	9	0.12430	T	0.62	-4.2424	8.8974	0.35472	0.811:0.189:0.0:0.0	rs12368787;rs52827128;rs61694415;rs12368787	36	Q502W7	CCD38_HUMAN	F	36	ENSP00000345470:V36F	ENSP00000345470:V36F	V	-	1	0	CCDC38	94836817	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	2.491000	0.45303	0.983000	0.38602	-0.363000	0.07495	GTC	C|0.915;A|0.085	0.085	strong		0.318	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
AMER3	205147	hgsc.bcm.edu	37	2	131520945	131520945	+	Missense_Mutation	SNP	C	C	G	rs72854996	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:131520945C>G	ENST00000423981.1	+	2	1410	c.1300C>G	c.(1300-1302)Ctt>Gtt	p.L434V	AMER3_ENST00000321420.4_Missense_Mutation_p.L434V	NM_001105193.1|NM_001105194.1|NM_001105195.1|NM_152698.2	NP_001098663.1|NP_001098664.1|NP_001098665.1|NP_689911.2	Q8N944	AMER3_HUMAN	APC membrane recruitment protein 3	434					Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	lipid binding (GO:0008289)										CGAGGGTCCTCTTGGCCCCAG	0.662													G|||	291	0.058107	0.1808	0.0317	5008	,	,		15160	0.0		0.0219	False		,,,				2504	0.0082				p.L434V		Atlas-SNP	.											.	.	.	.	0			c.C1300G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	595,3811	754.3+/-412.4	49,497,1657	38.0	39.0	39.0		1300,1300,1300,1300	1.9	0.0	2	dbSNP_130	39	212,8388	797.5+/-407.4	2,208,4090	yes	missense,missense,missense,missense	FAM123C	NM_001105193.1,NM_001105194.1,NM_001105195.1,NM_152698.2	32,32,32,32	51,705,5747	GG,GC,CC		2.4651,13.5043,6.2048	benign,benign,benign,benign	434/862,434/862,434/862,434/862	131520945	807,12199	2203	4300	6503	SO:0001583	missense	205147	exon2			GGTCCTCTTGGCC	AK095696	CCDS2164.1	2q21.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000178171	ENSG00000178171		"""-"""	26771	protein-coding gene	gene with protein product			"""family with sequence similarity 123C"""	FAM123C		20843316	Standard	NM_001105195		Approved	FLJ38377	uc002trw.2	Q8N944	OTTHUMG00000131637	ENST00000423981.1:c.1300C>G	2.37:g.131520945C>G	ENSP00000392700:p.Leu434Val	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	30	9	0.3	NM_152698	B7ZLH6	Missense_Mutation	SNP	ENST00000423981.1	37	CCDS2164.1	115	0.052655677655677656	89	0.18089430894308944	12	0.03314917127071823	0	0.0	14	0.018469656992084433	G	0	-2.676327	0.00102	0.135043	0.024651	ENSG00000178171	ENST00000321420;ENST00000423981	T;T	0.18016	2.24;2.24	5.2	1.93	0.25924	.	1.263360	0.05731	N	0.599540	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35919	-0.9769	9	0.02654	T	1	.	4.1881	0.10407	0.3064:0.3238:0.3698:0.0	.	434	Q8N944	F123C_HUMAN	V	434	ENSP00000314914:L434V;ENSP00000392700:L434V	ENSP00000314914:L434V	L	+	1	0	FAM123C	131237415	0.631000	0.27164	0.017000	0.16124	0.004000	0.04260	1.635000	0.37134	0.317000	0.23160	-0.216000	0.12614	CTT	C|0.945;G|0.055	0.055	strong		0.662	AMER3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254531.3	NM_152698	
ELOVL2	54898	hgsc.bcm.edu	37	6	10989942	10989942	+	Silent	SNP	G	G	A	rs12195587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:10989942G>A	ENST00000354666.3	-	7	842	c.759C>T	c.(757-759)taC>taT	p.Y253Y		NM_017770.3	NP_060240.3	Q9NXB9	ELOV2_HUMAN	ELOVL fatty acid elongase 2	253					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	fatty acid elongase activity (GO:0009922)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(2)	14	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)			GTACCTGAACGTAAAAATTTA	0.413													G|||	272	0.0543131	0.0068	0.0778	5008	,	,		21775	0.002		0.1372	False		,,,				2504	0.0706				p.Y253Y		Atlas-SNP	.											.	ELOVL2	40	.	0			c.C759T						PASS	.	G		142,4264	101.2+/-139.8	6,130,2067	83.0	76.0	78.0		759	-8.7	0.0	6	dbSNP_120	78	1502,7098	285.5+/-297.2	132,1238,2930	no	coding-synonymous	ELOVL2	NM_017770.3		138,1368,4997	AA,AG,GG		17.4651,3.2229,12.6403		253/297	10989942	1644,11362	2203	4300	6503	SO:0001819	synonymous_variant	54898	exon7			CTGAACGTAAAAA	AK000341	CCDS4518.1	6p24.1	2011-05-25	2011-05-25		ENSG00000197977	ENSG00000197977			14416	protein-coding gene	gene with protein product		611814	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2"""			12371743, 16564093	Standard	NM_017770		Approved	Ssc2	uc003mzp.4	Q9NXB9	OTTHUMG00000014252	ENST00000354666.3:c.759C>T	6.37:g.10989942G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	80	0.851064	NM_017770	Q6P9E1|Q86W94	Silent	SNP	ENST00000354666.3	37	CCDS4518.1																																																																																			G|0.898;A|0.102	0.102	strong		0.413	ELOVL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039849.1		
FAT2	2196	hgsc.bcm.edu	37	5	150908813	150908813	+	Missense_Mutation	SNP	G	G	A	rs2304024	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150908813G>A	ENST00000261800.5	-	14	9964	c.9952C>T	c.(9952-9954)Cgg>Tgg	p.R3318W		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3318	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> Q (in dbSNP:rs7718054).|R -> W (in dbSNP:rs2304024).		epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AATTGGGGCCGGTGTTCATTG	0.527													G|||	484	0.0966454	0.0083	0.1571	5008	,	,		21748	0.125		0.1938	False		,,,				2504	0.044				p.R3318W		Atlas-SNP	.											.	FAT2	465	.	0			c.C9952T						PASS	.	G	TRP/ARG	161,4245	107.3+/-145.7	6,149,2048	144.0	137.0	139.0		9952	3.9	1.0	5	dbSNP_100	139	1815,6785	328.0+/-318.1	201,1413,2686	yes	missense	FAT2	NM_001447.2	101	207,1562,4734	AA,AG,GG		21.1047,3.6541,15.193	probably-damaging	3318/4350	150908813	1976,11030	2203	4300	6503	SO:0001583	missense	2196	exon14			GGGGCCGGTGTTC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.9952C>T	5.37:g.150908813G>A	ENSP00000261800:p.Arg3318Trp	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	288|288	0.13186813186813187|0.13186813186813187	6|6	0.012195121951219513|0.012195121951219513	65|65	0.17955801104972377|0.17955801104972377	81|81	0.14160839160839161|0.14160839160839161	136|136	0.17941952506596306|0.17941952506596306	G|G	17.07|17.07	3.295417|3.295417	0.60086|0.60086	0.036541|0.036541	0.211047|0.211047	ENSG00000086570|ENSG00000086570	ENST00000520200|ENST00000261800	.|T	.|0.61392	.|0.11	5.78|5.78	3.9|3.9	0.45041|0.45041	.|Cadherin (3);Cadherin-like (1);	.|1.332910	.|0.04805	.|N	.|0.434197	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.61036|0.61036	1.89|1.89	0.39169|0.39169	P|P	0.03744499999999995|0.03744499999999995	.|D;D	.|0.62365	.|0.991;0.989	.|P;B	.|0.46452	.|0.517;0.409	T|T	0.04153|0.04153	-1.0973|-1.0973	4|9	.|0.87932	.|D	.|0	.|.	6.7277|6.7277	0.23365|0.23365	0.1644:0.2384:0.5973:0.0|0.1644:0.2384:0.5973:0.0	rs2304024;rs17404244;rs52798374;rs2304024|rs2304024;rs17404244;rs52798374;rs2304024	.|3318;509	.|Q9NYQ8;E9PDJ8	.|FAT2_HUMAN;.	L|W	176|3318	.|ENSP00000261800:R3318W	.|ENSP00000261800:R3318W	P|R	-|-	2|1	0|2	FAT2|FAT2	150889006|150889006	0.204000|0.204000	0.23447|0.23447	0.977000|0.977000	0.42913|0.42913	0.589000|0.589000	0.36550|0.36550	0.780000|0.780000	0.26760|0.26760	1.450000|1.450000	0.47717|0.47717	-0.170000|-0.170000	0.13304|0.13304	CCG|CGG	G|0.858;N|0.001	.	strong		0.527	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
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 GAIIx	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_ENST00000441551.2_Missense_Mutation_p.E1813K|LOXHD1_ENST00000582408.1_Missense_Mutation_p.E846K|LOXHD1_ENST00000398686.4_Missense_Mutation_p.E258K|LOXHD1_ENST00000398705.2_Missense_Mutation_p.E258K|LOXHD1_ENST00000300591.6_Missense_Mutation_p.E908K|LOXHD1_ENST00000579038.1_Missense_Mutation_p.E812K|LOXHD1_ENST00000536736.1_Missense_Mutation_p.E1957K|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	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	60	30	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	
TMEM143	55260	hgsc.bcm.edu	37	19	48836673	48836673	+	Silent	SNP	G	G	T	rs3826828	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48836673G>T	ENST00000293261.3	-	8	1499	c.1183C>A	c.(1183-1185)Cgg>Agg	p.R395R	TMEM143_ENST00000435956.3_Silent_p.R360R|TMEM143_ENST00000377431.2_Silent_p.R295R|TMEM143_ENST00000436660.2_Silent_p.R330R|TMEM143_ENST00000541566.1_Silent_p.R285R	NM_018273.2	NP_060743.2	Q96AN5	TM143_HUMAN	transmembrane protein 143	395					hematopoietic progenitor cell differentiation (GO:0002244)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				endometrium(2)|kidney(1)|large_intestine(2)|lung(9)	14		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000149)|all cancers(93;0.000198)|Epithelial(262;0.0151)|GBM - Glioblastoma multiforme(486;0.0157)		ACCTCCGACCGGAGCCACCTG	0.627													G|||	1680	0.335463	0.2595	0.3847	5008	,	,		17868	0.3482		0.4175	False		,,,				2504	0.3057				p.R395R		Atlas-SNP	.											.	TMEM143	29	.	0			c.C1183A						PASS	.	G		1279,3127	423.6+/-340.2	197,885,1121	46.0	44.0	45.0		1183	4.5	1.0	19	dbSNP_107	45	3792,4808	520.4+/-379.7	839,2114,1347	no	coding-synonymous	TMEM143	NM_018273.2		1036,2999,2468	TT,TG,GG		44.093,29.0286,38.9897		395/460	48836673	5071,7935	2203	4300	6503	SO:0001819	synonymous_variant	55260	exon8			CCGACCGGAGCCA	AK129801	CCDS12716.1	19q13.32	2008-02-05				ENSG00000161558			25603	protein-coding gene	gene with protein product						12975309	Standard	NM_018273		Approved	FLJ10922	uc002pix.1	Q96AN5		ENST00000293261.3:c.1183C>A	19.37:g.48836673G>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_018273	A8K656|Q6UXY4|Q9NV49	Silent	SNP	ENST00000293261.3	37	CCDS12716.1																																																																																			G|0.645;T|0.355	0.355	strong		0.627	TMEM143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465622.1	NM_018273	
CALCR	799	hgsc.bcm.edu	37	7	93055753	93055753	+	Missense_Mutation	SNP	A	A	G	rs1801197	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:93055753A>G	ENST00000394441.1	-	13	1655	c.1340T>C	c.(1339-1341)cTg>cCg	p.L447P	CALCR_ENST00000421592.1_Missense_Mutation_p.L463P|CALCR_ENST00000359558.2_Missense_Mutation_p.L481P|CALCR_ENST00000426151.1_Missense_Mutation_p.L447P|CALCR_ENST00000360249.4_Missense_Mutation_p.L463P	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	481					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	TTCATTCCTCAGCTCCTGATG	0.557													G|||	2722	0.54353	0.5408	0.4308	5008	,	,		18060	0.8611		0.3052	False		,,,				2504	0.545				p.L481P		Atlas-SNP	.											CALCR_ENST00000359558,NS,adenoma,0,2	CALCR	200	2	0			c.T1442C	GRCh37	CM980299	CALCR	M	rs1801197	scavenged	.	G	PRO/LEU,PRO/LEU,PRO/LEU	2073,2333	606.2+/-390.7	470,1133,600	170.0	158.0	162.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1442,1340,1340	1.3	0.0	7	dbSNP_89	162	2187,6413	712.5+/-405.9	296,1595,2409	yes	missense,missense,missense	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	98,98,98	766,2728,3009	GG,GA,AA		25.4302,47.0495,32.7541	benign,benign,benign	481/509,447/475,447/475	93055753	4260,8746	2203	4300	6503	SO:0001583	missense	799	exon16			TTCCTCAGCTCCT	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.1340T>C	7.37:g.93055753A>G	ENSP00000377959:p.Leu447Pro	Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	124	57	0.459677	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Missense_Mutation	SNP	ENST00000394441.1	37	CCDS5631.1	1154	0.5283882783882784	274	0.556910569105691	157	0.43370165745856354	497	0.8688811188811189	226	0.29815303430079154	G	0.389	-0.924704	0.02377	0.470495	0.254302	ENSG00000004948	ENST00000359558;ENST00000360249;ENST00000421592;ENST00000394441;ENST00000426151	T;T;T;T;T	0.50001	0.76;0.78;0.78;0.91;0.91	5.11	1.3	0.21679	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53005	P	3.2000000000032E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15521	-1.0434	7	0.28530	T	0.3	.	4.6969	0.12808	0.3355:0.1492:0.5153:0.0	rs1801197;rs3181601;rs10368963;rs11769260;rs17165394;rs58887934;rs1801197	481;447	F5H605;A4D1G6	.;.	P	481;463;463;447;447	ENSP00000352561:L481P;ENSP00000353385:L463P;ENSP00000399552:L463P;ENSP00000377959:L447P;ENSP00000389295:L447P	ENSP00000352561:L481P	L	-	2	0	CALCR	92893689	0.940000	0.31905	0.014000	0.15608	0.178000	0.23041	1.787000	0.38704	-0.050000	0.13356	-0.790000	0.03334	CTG	A|0.561;G|0.439	0.439	strong		0.557	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150240	11150240	+	Missense_Mutation	SNP	T	T	C	rs7135018	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11150240T>C	ENST00000538986.1	-	1	234	c.235A>G	c.(235-237)Aaa>Gaa	p.K79E	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	79			K -> E (in dbSNP:rs7135018). {ECO:0000269|PubMed:15489334}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						ATTATTACTTTTAAATTAGAT	0.358													T|||	1039	0.207468	0.2171	0.2392	5008	,	,		17782	0.1964		0.2068	False		,,,				2504	0.184				p.K79E		Atlas-SNP	.											.	TAS2R20	17	.	0			c.A235G						PASS	.	T	GLU/LYS	889,3419		102,685,1367	36.0	40.0	39.0		235	-4.2	0.0	12	dbSNP_116	39	1950,6604		238,1474,2565	yes	missense	TAS2R20	NM_176889.2	56	340,2159,3932	CC,CT,TT		22.7964,20.636,22.0728	benign	79/310	11150240	2839,10023	2154	4277	6431	SO:0001583	missense	259295	exon1			TTACTTTTAAATT	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.235A>G	12.37:g.11150240T>C	ENSP00000441624:p.Lys79Glu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	465	0.2129120879120879	94	0.1910569105691057	76	0.20994475138121546	126	0.2202797202797203	169	0.22295514511873352	T	0.007	-2.002581	0.00431	0.20636	0.227964	ENSG00000255837	ENST00000538986	T	0.00737	5.76	2.65	-4.21	0.03812	.	2.421730	0.02456	N	0.086115	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.41805	-0.9488	9	0.02654	T	1	.	1.285	0.02049	0.1643:0.1796:0.1642:0.4919	rs7135018;rs60271229;rs7135018	79	P59543	T2R20_HUMAN	E	79	ENSP00000441624:K79E	ENSP00000441624:K79E	K	-	1	0	TAS2R20	11041507	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.986000	0.00660	-0.881000	0.03992	-1.251000	0.01509	AAA	T|0.779;C|0.221	0.221	strong		0.358	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
PITPNM3	83394	hgsc.bcm.edu	37	17	6441376	6441376	+	Missense_Mutation	SNP	G	G	A	rs28493751	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6441376G>A	ENST00000262483.8	-	2	136	c.49C>T	c.(49-51)Ccc>Tcc	p.P17S	PITPNM3_ENST00000421306.3_Missense_Mutation_p.P17S	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	17			P -> S (in dbSNP:rs28493751).		phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)	p.P17S(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		AGGTGCCAGGGGGCACCGCCG	0.552													G|||	267	0.0533147	0.0265	0.0648	5008	,	,		18689	0.002		0.1103	False		,,,				2504	0.0757				p.P17S		Atlas-SNP	.											PITPNM3,brain,glioma,0,1	PITPNM3	91	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.C49T						PASS	.	G	SER/PRO,SER/PRO	196,4210	119.6+/-157.3	4,188,2011	39.0	37.0	38.0		49,49	4.9	1.0	17	dbSNP_125	38	939,7661	200.3+/-244.1	62,815,3423	yes	missense,missense	PITPNM3	NM_001165966.1,NM_031220.3	74,74	66,1003,5434	AA,AG,GG		10.9186,4.4485,8.7267	possibly-damaging,possibly-damaging	17/939,17/975	6441376	1135,11871	2203	4300	6503	SO:0001583	missense	83394	exon2			GCCAGGGGGCACC	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.49C>T	17.37:g.6441376G>A	ENSP00000262483:p.Pro17Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	200	110	0.55	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	37	CCDS11076.1	127	0.05815018315018315	15	0.03048780487804878	28	0.07734806629834254	1	0.0017482517482517483	83	0.10949868073878628	G	18.04	3.534439	0.64972	0.044485	0.109186	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.41065	1.03;1.01	4.89	4.89	0.63831	.	0.182670	0.37219	N	0.002190	T	0.00496	0.0016	N	0.08118	0	0.36580	P	0.12648700000000002	P;P	0.42518	0.782;0.675	B;B	0.41174	0.349;0.19	T	0.08659	-1.0711	9	0.48119	T	0.1	0.2887	13.9315	0.63998	0.0:0.0:1.0:0.0	rs28493751	17;17	F8WEW5;Q9BZ71	.;PITM3_HUMAN	S	17	ENSP00000262483:P17S;ENSP00000407882:P17S	ENSP00000262483:P17S	P	-	1	0	PITPNM3	6382100	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.677000	0.54619	2.439000	0.82584	0.655000	0.94253	CCC	G|0.926;A|0.074	0.074	strong		0.552	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
PARP4	143	hgsc.bcm.edu	37	13	25052261	25052261	+	Silent	SNP	C	C	T	rs4770696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25052261C>T	ENST00000381989.3	-	13	1707	c.1602G>A	c.(1600-1602)tcG>tcA	p.S534S		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	534	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		AGGCTGTTTGCGAAACTCCAT	0.443													.|||	2727	0.544529	0.4289	0.5677	5008	,	,		16176	0.5992		0.5	False		,,,				2504	0.6738				p.S534S		Atlas-SNP	.											PARP4,mouth,carcinoma,-1,1	PARP4	142	1	0			c.G1602A						PASS	.	T		1900,2506	626.8+/-394.8	410,1080,713	74.0	65.0	68.0		1602	-0.2	0.0	13	dbSNP_111	68	4549,4051	557.5+/-387.1	1197,2155,948	no	coding-synonymous	PARP4	NM_006437.3		1607,3235,1661	TT,TC,CC		47.1047,43.123,49.5848		534/1725	25052261	6449,6557	2203	4300	6503	SO:0001819	synonymous_variant	143	exon13			TGTTTGCGAAACT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1602G>A	13.37:g.25052261C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.494;T|0.506	0.506	strong		0.443	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
PHLDB1	23187	hgsc.bcm.edu	37	11	118502121	118502121	+	Silent	SNP	A	A	G	rs17614795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:118502121A>G	ENST00000361417.2	+	8	2436	c.2025A>G	c.(2023-2025)ctA>ctG	p.L675L	PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000356063.5_Silent_p.L675L	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	675										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CCCAACGCCTATGGGAGAGTA	0.637													A|||	76	0.0151757	0.0015	0.0159	5008	,	,		18023	0.0		0.0417	False		,,,				2504	0.0215				p.L675L		Atlas-SNP	.											.	PHLDB1	103	.	0			c.A2025G						PASS	.	A	,,	31,4369	36.0+/-67.5	0,31,2169	28.0	30.0	29.0		2025,2025,2025	1.7	1.0	11	dbSNP_123	29	318,8272	111.8+/-172.0	7,304,3984	no	coding-synonymous,coding-synonymous,coding-synonymous	PHLDB1	NM_001144758.1,NM_001144759.1,NM_015157.2	,,	7,335,6153	GG,GA,AA		3.702,0.7045,2.6867	,,	675/1378,675/1320,675/1378	118502121	349,12641	2200	4295	6495	SO:0001819	synonymous_variant	23187	exon7			ACGCCTATGGGAG		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.2025A>G	11.37:g.118502121A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	29	6	0.206897	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	37	CCDS8401.1																																																																																			A|0.975;G|0.025	0.025	strong		0.637	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157	
NT5C2	22978	hgsc.bcm.edu	37	10	104849468	104849468	+	Silent	SNP	G	G	A	rs3740387	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:104849468G>A	ENST00000404739.3	-	17	1670	c.1647C>T	c.(1645-1647)gaC>gaT	p.D549D	NT5C2_ENST00000369857.4_5'UTR|CNNM2_ENST00000369878.4_3'UTR|NT5C2_ENST00000423468.2_Silent_p.D520D|NT5C2_ENST00000343289.5_Silent_p.D549D			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	549	Asp/Glu-rich (acidic).				cell death (GO:0008219)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|nucleobase-containing small molecule metabolic process (GO:0055086)|phosphorylation (GO:0016310)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleoside phosphotransferase activity (GO:0050146)|nucleotide binding (GO:0000166)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|urinary_tract(1)	16		all_hematologic(284;0.176)|Colorectal(252;0.178)		Epithelial(162;1.33e-08)|all cancers(201;1.04e-07)|BRCA - Breast invasive adenocarcinoma(275;0.159)	Adenosine triphosphate(DB00171)|Ribavirin(DB00811)	catcatcttcgtcATGGCAGT	0.498													A|||	2114	0.422125	0.3442	0.4135	5008	,	,		18060	0.499		0.4135	False		,,,				2504	0.4632				p.D549D		Atlas-SNP	.											.	NT5C2	41	.	0			c.C1647T						PASS	.	A	,	1652,2754	659.5+/-400.6	318,1016,869	97.0	87.0	90.0		1647,1647	2.3	1.0	10	dbSNP_107	90	3509,5091	633.3+/-398.7	701,2107,1492	no	coding-synonymous,coding-synonymous	NT5C2	NM_001134373.1,NM_012229.3	,	1019,3123,2361	AA,AG,GG		40.8023,37.4943,39.6817	,	549/562,549/562	104849468	5161,7845	2203	4300	6503	SO:0001819	synonymous_variant	22978	exon19			ATCTTCGTCATGG	D38524	CCDS7544.1	10q24.32	2014-03-03	2002-04-18	2002-04-19	ENSG00000076685	ENSG00000076685			8022	protein-coding gene	gene with protein product	"""purine 5' nucleotidase"""	600417	"""5'-nucleotidase (purine), cytosolic type B"""	NT5B		7999131, 24482476	Standard	NM_012229		Approved	PNT5, GMP, cN-II, SPG65	uc001kwq.3	P49902	OTTHUMG00000018981	ENST00000404739.3:c.1647C>T	10.37:g.104849468G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	254	129	0.507874	NM_012229	B7Z382|D3DR91|Q5JUV5	Silent	SNP	ENST00000404739.3	37	CCDS7544.1																																																																																			G|0.600;A|0.400	0.400	strong		0.498	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229	
DNAI1	27019	hgsc.bcm.edu	37	9	34500821	34500821	+	Missense_Mutation	SNP	G	G	A	rs11793196	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:34500821G>A	ENST00000242317.4	+	11	1174	c.1003G>A	c.(1003-1005)Gtc>Atc	p.V335I		NM_001281428.1|NM_012144.2	NP_001268357.1|NP_036276.1	Q9UI46	DNAI1_HUMAN	dynein, axonemal, intermediate chain 1	335			V -> I (in dbSNP:rs11793196).		cell projection organization (GO:0030030)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	motor activity (GO:0003774)			autonomic_ganglia(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|prostate(1)|skin(2)|urinary_tract(1)	34	all_epithelial(49;0.244)		LUSC - Lung squamous cell carcinoma(29;0.0107)|STAD - Stomach adenocarcinoma(86;0.212)	GBM - Glioblastoma multiforme(74;0.0222)		GCGCCTGTCCGTCACTGCCCT	0.537									Kartagener syndrome		OREG0019152	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	884	0.176518	0.3601	0.1455	5008	,	,		18776	0.0119		0.1561	False		,,,				2504	0.1411				p.V335I		Atlas-SNP	.											.	DNAI1	72	.	0			c.G1003A						PASS	.	G	ILE/VAL	1420,2986	463.2+/-353.5	229,962,1012	61.0	61.0	61.0		1003	5.0	1.0	9	dbSNP_120	61	1308,7292	258.4+/-282.1	114,1080,3106	yes	missense	DNAI1	NM_012144.2	29	343,2042,4118	AA,AG,GG		15.2093,32.2288,20.9749	probably-damaging	335/700	34500821	2728,10278	2203	4300	6503	SO:0001583	missense	27019	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CTGTCCGTCACTG	AF091619	CCDS6557.1, CCDS75829.1	9p13.3	2013-02-19	2006-09-04		ENSG00000122735	ENSG00000122735		"""Axonemal dyneins"", ""WD repeat domain containing"""	2954	protein-coding gene	gene with protein product		604366	"""dynein, axonemal, intermediate polypeptide 1"""			10577904, 21953912	Standard	NM_012144		Approved	DIC1, PCD, CILD1	uc003zum.3	Q9UI46	OTTHUMG00000019825	ENST00000242317.4:c.1003G>A	9.37:g.34500821G>A	ENSP00000242317:p.Val335Ile	Somatic	60	0	0	848	WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_012144	B7Z7U1|Q5T8G7|Q8NHQ7|Q9UEZ8	Missense_Mutation	SNP	ENST00000242317.4	37	CCDS6557.1	350	0.16025641025641027	168	0.34146341463414637	53	0.1464088397790055	8	0.013986013986013986	121	0.15963060686015831	G	17.37	3.372643	0.61624	0.322288	0.152093	ENSG00000122735	ENST00000242317	T	0.71579	-0.58	4.99	4.99	0.66335	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.065937	0.64402	D	0.000011	T	0.00012	0.0000	M	0.85710	2.77	0.09310	P	1.0	B	0.27700	0.186	B	0.25405	0.06	T	0.07635	-1.0762	9	0.54805	T	0.06	.	16.1322	0.81449	0.0:0.0:1.0:0.0	rs11793196;rs59607272;rs11793196	335	Q9UI46	DNAI1_HUMAN	I	335	ENSP00000242317:V335I	ENSP00000242317:V335I	V	+	1	0	DNAI1	34490821	1.000000	0.71417	0.979000	0.43373	0.880000	0.50808	7.069000	0.76755	2.470000	0.83445	0.462000	0.41574	GTC	G|0.812;A|0.188	0.188	strong		0.537	DNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052192.1		
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 GAIIx	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_ENST00000370994.4_Nonsense_Mutation_p.Q69*|SERBP1_ENST00000370990.5_Nonsense_Mutation_p.Q69*|SERBP1_ENST00000361219.6_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*	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	110	39	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228434395	228434395	+	Silent	SNP	T	T	C	rs7517088	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228434395T>C	ENST00000422127.1	+	13	3968	c.3924T>C	c.(3922-3924)gcT>gcC	p.A1308A	OBSCN_ENST00000570156.2_Silent_p.A1400A|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.A1308A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1308	Ig-like 13.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.A1308A(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCATAGAGGCTGCGGGCTGCA	0.642													C|||	3093	0.617612	0.7133	0.6542	5008	,	,		20385	0.5992		0.6412	False		,,,				2504	0.4571				p.A1400A		Atlas-SNP	.											OBSCN_ENST00000359599,NS,carcinoma,0,1	OBSCN	2142	1	1	Substitution - coding silent(1)	stomach(1)	c.T4200C						scavenged	.	C	,	3010,1108		1089,832,138	79.0	85.0	83.0		3924,3924	3.1	0.2	1	dbSNP_116	83	5752,2666		1994,1764,451	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	3083,2596,589	CC,CT,TT		31.6702,26.9063,30.1053	,	1308/7969,1308/6621	228434395	8762,3774	2059	4209	6268	SO:0001819	synonymous_variant	84033	exon14			AGAGGCTGCGGGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3924T>C	1.37:g.228434395T>C		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			T|0.373;C|0.627	0.627	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
FSTL5	56884	hgsc.bcm.edu	37	4	162307060	162307060	+	Silent	SNP	G	G	T	rs17040984	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:162307060G>T	ENST00000306100.5	-	16	2819	c.2383C>A	c.(2383-2385)Cgg>Agg	p.R795R	FSTL5_ENST00000379164.4_Silent_p.R794R|FSTL5_ENST00000427802.2_Silent_p.R785R|RP11-234O6.2_ENST00000508189.1_RNA|FSTL5_ENST00000536695.1_Silent_p.R794R	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	795						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CTGTTTTTCCGGTTCCAAGGC	0.458													G|||	912	0.182109	0.0416	0.1657	5008	,	,		18093	0.3175		0.2256	False		,,,				2504	0.1994				p.R795R		Atlas-SNP	.											FSTL5,NS,carcinoma,+2,1	FSTL5	207	1	0			c.C2383A						PASS	.	G	,,	323,4083	171.6+/-201.8	12,299,1892	225.0	201.0	209.0		2380,2353,2383	1.6	0.0	4	dbSNP_123	209	2173,6427	372.0+/-336.5	273,1627,2400	no	coding-synonymous,coding-synonymous,coding-synonymous	FSTL5	NM_001128427.1,NM_001128428.1,NM_020116.3	,,	285,1926,4292	TT,TG,GG		25.2674,7.3309,19.1911	,,	794/847,785/838,795/848	162307060	2496,10510	2203	4300	6503	SO:0001819	synonymous_variant	56884	exon16			TTTTCCGGTTCCA	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.2383C>A	4.37:g.162307060G>T		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	180	80	0.444444	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																			G|0.805;T|0.195	0.195	strong		0.458	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318912	21318912	+	Silent	SNP	C	C	A	rs35011501	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:21318912C>A	ENST00000583088.1	+	3	1153	c.258C>A	c.(256-258)atC>atA	p.I86I	KCNJ12_ENST00000331718.5_Silent_p.I86I	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	86					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	TGCTGCTCATCTTCTCGCTGG	0.612										Prostate(3;0.18)																											p.I86I		Atlas-SNP	.											.	.	.	.	0			c.C258A						PASS	.						190.0	116.0	141.0					17																	21318912		2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			GCTCATCTTCTCG	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.258C>A	17.37:g.21318912C>A		Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	180	19	0.105556	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			C|0.733;A|0.267	0.267	strong		0.612	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
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 GAIIx	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		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	51	27	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 GAIIx	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_ENST00000352040.3_Missense_Mutation_p.F742I|ADAMTS12_ENST00000504582.1_5'UTR	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	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	104	10	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	
KIAA1328	57536	hgsc.bcm.edu	37	18	34647176	34647176	+	Silent	SNP	T	T	C	rs3747895	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:34647176T>C	ENST00000280020.5	+	7	922	c.900T>C	c.(898-900)ccT>ccC	p.P300P	KIAA1328_ENST00000591619.1_Silent_p.P296P|KIAA1328_ENST00000435985.2_Silent_p.P16P|KIAA1328_ENST00000543923.1_Silent_p.P192P|KIAA1328_ENST00000586135.1_Silent_p.P16P|KIAA1328_ENST00000586501.1_Silent_p.P16P	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	300										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		ATCTTAAGCCTACTCCTAGTC	0.443													T|||	1297	0.258986	0.643	0.1311	5008	,	,		21398	0.1101		0.1292	False		,,,				2504	0.1176				p.P300P		Atlas-SNP	.											.	KIAA1328	39	.	0			c.T900C						PASS	.	T		2272,1844		625,1022,411	104.0	98.0	100.0		900	0.1	0.0	18	dbSNP_107	100	1148,7264		78,992,3136	no	coding-synonymous	KIAA1328	NM_020776.1		703,2014,3547	CC,CT,TT		13.6472,44.8008,27.2989		300/578	34647176	3420,9108	2058	4206	6264	SO:0001819	synonymous_variant	57536	exon7			TAAGCCTACTCCT	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.900T>C	18.37:g.34647176T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Silent	SNP	ENST00000280020.5	37	CCDS45855.1																																																																																			T|0.749;C|0.251	0.251	strong		0.443	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
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 GAIIx	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_ENST00000402845.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399591.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399621.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399637.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399595.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000480911.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399629.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000335762.5_Missense_Mutation_p.G37R|CACNA1C_ENST00000399649.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399655.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399617.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000344100.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399638.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399606.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399641.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399597.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399603.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399601.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000327702.7_Missense_Mutation_p.G37R|CACNA1C_ENST00000399634.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000406454.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399644.1_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	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	34	17	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	
GSDMA	284110	hgsc.bcm.edu	37	17	38121993	38121993	+	Missense_Mutation	SNP	G	G	A	rs3894194	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38121993G>A	ENST00000301659.4	+	2	171	c.53G>A	c.(52-54)cGa>cAa	p.R18Q		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	18			R -> Q (in dbSNP:rs3894194).		apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CTAAACCCTCGAGGGGACCTG	0.582													G|||	2158	0.430911	0.2587	0.5043	5008	,	,		18378	0.5397		0.4463	False		,,,				2504	0.4836				p.R18Q		Atlas-SNP	.											.	GSDMA	26	.	0			c.G53A	GRCh37	CM073116	GSDMA	M	rs3894194	PASS	.	G	GLN/ARG	1170,2796		170,830,983	54.0	59.0	58.0	http://www.ncbi.nlm.nih.gov/pubmed?term	53	3.3	1.0	17	dbSNP_108	58	3796,4528		879,2038,1245	yes	missense	GSDMA	NM_178171.4	43	1049,2868,2228	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	45.6031,29.5008,40.4068	benign	18/446	38121993	4966,7324	1983	4162	6145	SO:0001583	missense	284110	exon2			ACCCTCGAGGGGA	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.53G>A	17.37:g.38121993G>A	ENSP00000301659:p.Arg18Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	44	42	0.954545	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	930	0.4258241758241758	130	0.26422764227642276	181	0.5	284	0.4965034965034965	335	0.4419525065963061	G	13.55	2.270656	0.40194	0.295008	0.456031	ENSG00000167914	ENST00000301659	T	0.22743	1.94	5.36	3.34	0.38264	.	0.710982	0.12216	N	0.488832	T	0.00012	0.0000	L	0.49455	1.56	0.38224	P	0.05916500000000002	B	0.16166	0.016	B	0.14023	0.01	T	0.43393	-0.9394	9	0.20046	T	0.44	-4.2602	7.6027	0.28085	0.1926:0.0:0.8074:0.0	rs3894194;rs12948522;rs52814263;rs61411446;rs3894194	18	Q96QA5	GSDMA_HUMAN	Q	18	ENSP00000301659:R18Q	ENSP00000301659:R18Q	R	+	2	0	GSDMA	35375519	0.267000	0.24122	1.000000	0.80357	0.934000	0.57294	0.886000	0.28241	1.245000	0.43885	0.462000	0.41574	CGA	G|0.576;T|0.004	.	strong		0.582	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
CCDC18	343099	hgsc.bcm.edu	37	1	93676478	93676478	+	Missense_Mutation	SNP	A	A	C	rs76148185	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:93676478A>C	ENST00000343253.7	+	10	1831	c.1329A>C	c.(1327-1329)gaA>gaC	p.E443D	CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000557479.1_Missense_Mutation_p.E561D|CCDC18_ENST00000338949.4_Missense_Mutation_p.E242D|CCDC18_ENST00000401026.3_Missense_Mutation_p.E443D			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	443										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TGATTTCGGAATTGAGGTACA	0.383													A|||	47	0.00938498	0.0008	0.013	5008	,	,		17506	0.0		0.0278	False		,,,				2504	0.0092				p.E443D		Atlas-SNP	.											.	CCDC18	93	.	0			c.A1329C						PASS	.	A	ASP/GLU	17,3673		0,17,1828	82.0	78.0	79.0		1329	1.2	1.0	1	dbSNP_131	79	225,7975		2,221,3877	yes	missense	CCDC18	NM_206886.3	45	2,238,5705	CC,CA,AA		2.7439,0.4607,2.0353	benign	443/1300	93676478	242,11648	1845	4100	5945	SO:0001583	missense	343099	exon10			TTCGGAATTGAGG			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.1329A>C	1.37:g.93676478A>C	ENSP00000343377:p.Glu443Asp	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		24|24	0.01098901098901099|0.01098901098901099	1|1	0.0020325203252032522|0.0020325203252032522	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	18|18	0.023746701846965697|0.023746701846965697	A|A	10.40|10.40	1.339270|1.339270	0.24339|0.24339	0.004607|0.004607	0.027439|0.027439	ENSG00000122483|ENSG00000122483	ENST00000343253;ENST00000401026;ENST00000557479;ENST00000338949;ENST00000455267|ENST00000370276	T;T;T;T;T|.	0.19394|.	2.15;2.15;2.15;2.15;2.15|.	6.04|6.04	1.23|1.23	0.21249|0.21249	.|.	0.416730|.	0.25296|.	N|.	0.031686|.	T|T	0.21186|0.21186	0.0510|0.0510	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	B;B|.	0.18013|.	0.009;0.025|.	B;B|.	0.14023|.	0.006;0.01|.	T|T	0.05517|0.05517	-1.0880|-1.0880	10|5	0.16896|.	T|.	0.51|.	.|.	5.0648|5.0648	0.14576|0.14576	0.498:0.2315:0.2705:0.0|0.498:0.2315:0.2705:0.0	.|.	443;561|.	Q5T9S5;G3V388|.	CCD18_HUMAN;.|.	D|T	443;443;561;242;163|497	ENSP00000343377:E443D;ENSP00000383808:E443D;ENSP00000451099:E561D;ENSP00000344380:E242D;ENSP00000391151:E163D|.	ENSP00000344380:E242D|.	E|N	+|+	3|2	2|0	CCDC18|CCDC18	93449066|93449066	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.936000|0.936000	0.57629|0.57629	1.123000|1.123000	0.31308|0.31308	0.190000|0.190000	0.20209|0.20209	0.459000|0.459000	0.35465|0.35465	GAA|AAT	A|0.982;C|0.018	0.018	strong		0.383	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
SLCO4C1	353189	hgsc.bcm.edu	37	5	101631790	101631790	+	Silent	SNP	T	T	G	rs10479190	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:101631790T>G	ENST00000310954.6	-	1	463	c.177A>C	c.(175-177)ccA>ccC	p.P59P		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		GAGATGGCTCTGGTGACTTCT	0.582													T|||	711	0.141973	0.0121	0.1398	5008	,	,		15190	0.1558		0.2833	False		,,,				2504	0.1595				p.P59P		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.A177C						PASS	.	T		209,4197	126.1+/-163.2	7,195,2001	76.0	80.0	79.0		177	-2.2	0.0	5	dbSNP_119	79	2096,6504	361.0+/-332.2	262,1572,2466	no	coding-synonymous	SLCO4C1	NM_180991.4		269,1767,4467	GG,GT,TT		24.3721,4.7435,17.7226		59/725	101631790	2305,10701	2203	4300	6503	SO:0001819	synonymous_variant	353189	exon1			TGGCTCTGGTGAC	AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.177A>C	5.37:g.101631790T>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_180991		Silent	SNP	ENST00000310954.6	37	CCDS34205.1																																																																																			T|0.830;G|0.170	0.170	strong		0.582	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
C4orf17	84103	hgsc.bcm.edu	37	4	100443800	100443800	+	Missense_Mutation	SNP	G	G	A	rs17029087	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100443800G>A	ENST00000326581.4	+	3	633	c.271G>A	c.(271-273)Gag>Aag	p.E91K	C4orf17_ENST00000514652.1_Missense_Mutation_p.E91K|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	91			E -> K (in dbSNP:rs17029087). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		TGCAGTCCAGGAGAGCCCTGT	0.498													G|||	1032	0.20607	0.1838	0.1873	5008	,	,		16608	0.1161		0.2744	False		,,,				2504	0.272				p.E91K		Atlas-SNP	.											.	C4orf17	42	.	0			c.G271A						PASS	.	G	LYS/GLU	885,3521	342.0+/-307.0	101,683,1419	92.0	88.0	89.0		271	0.5	0.0	4	dbSNP_123	89	2356,6244	392.0+/-343.8	328,1700,2272	yes	missense	C4orf17	NM_032149.2	56	429,2383,3691	AA,AG,GG		27.3953,20.0862,24.9193	benign	91/360	100443800	3241,9765	2203	4300	6503	SO:0001583	missense	84103	exon3			GTCCAGGAGAGCC	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.271G>A	4.37:g.100443800G>A	ENSP00000322582:p.Glu91Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Missense_Mutation	SNP	ENST00000326581.4	37	CCDS3649.1	399	0.18269230769230768	64	0.13008130081300814	70	0.19337016574585636	66	0.11538461538461539	199	0.262532981530343	G	11.57	1.677464	0.29783	0.200862	0.273953	ENSG00000138813	ENST00000326581;ENST00000514652	T;T	0.17854	2.25;2.25	4.41	0.478	0.16789	.	2.099710	0.01389	N	0.013186	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B	0.20164	0.042	B	0.26310	0.068	T	0.37888	-0.9686	9	0.27785	T	0.31	0.2327	7.6519	0.28352	0.0955:0.4981:0.4064:0.0	rs17029087;rs52812387;rs17029087	91	Q53FE4	CD017_HUMAN	K	91	ENSP00000322582:E91K;ENSP00000427663:E91K	ENSP00000322582:E91K	E	+	1	0	C4orf17	100662823	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.370000	0.20433	0.048000	0.15891	-0.894000	0.02916	GAG	G|0.780;A|0.220	0.220	strong		0.498	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
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 GAIIx	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	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	247	64	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 GAIIx	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_ENST00000427143.2_Missense_Mutation_p.A896S|DIP2A_ENST00000318711.7_Missense_Mutation_p.A961S|DIP2A_ENST00000400274.1_Missense_Mutation_p.A956S			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	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	95	32	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	
PXMP4	11264	hgsc.bcm.edu	37	20	32295541	32295541	+	Missense_Mutation	SNP	C	C	T	rs910397	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:32295541C>T	ENST00000409299.3	-	4	702	c.610G>A	c.(610-612)Gtc>Atc	p.V204I	PXMP4_ENST00000217398.3_3'UTR|PXMP4_ENST00000344022.3_3'UTR	NM_007238.4	NP_009169.3	Q9Y6I8	PXMP4_HUMAN	peroxisomal membrane protein 4, 24kDa	204			V -> I (in dbSNP:rs910397). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				NS(1)|endometrium(2)|large_intestine(2)|lung(8)	13						TTGTTATAGACGAGGAAGTCT	0.537													c|||	3133	0.625599	0.6838	0.5447	5008	,	,		19954	0.7837		0.4811	False		,,,				2504	0.59				p.V204I		Atlas-SNP	.											.	PXMP4	20	.	0			c.G610A						PASS	.	C	ILE/VAL,	2790,1616	663.3+/-401.2	886,1018,299	139.0	124.0	129.0		610,	-2.5	1.0	20	dbSNP_86	129	4125,4475	563.8+/-388.2	997,2131,1172	yes	missense,utr-3	PXMP4	NM_007238.4,NM_183397.2	29,	1883,3149,1471	TT,TC,CC		47.9651,36.6773,46.8322	benign,	204/213,	32295541	6915,6091	2203	4300	6503	SO:0001583	missense	11264	exon4			TATAGACGAGGAA	AF072864	CCDS13225.1, CCDS13226.1	20q11.22	2008-07-02	2002-08-29		ENSG00000101417	ENSG00000101417			15920	protein-coding gene	gene with protein product	"""24 kDa peroxisomal intrinsic membrane protein"""		"""peroxisomal membrane protein 4 (24kD)"""			10366717	Standard	NM_183397		Approved	PMP24	uc002wzv.3	Q9Y6I8	OTTHUMG00000032273	ENST00000409299.3:c.610G>A	20.37:g.32295541C>T	ENSP00000386385:p.Val204Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	129	68	0.527132	NM_007238	A2A2I7|Q9H0T4	Missense_Mutation	SNP	ENST00000409299.3	37	CCDS13225.1	1371	0.6277472527472527	351	0.7134146341463414	193	0.5331491712707183	450	0.7867132867132867	377	0.4973614775725594	c	0.308	-0.969442	0.02232	0.633227	0.479651	ENSG00000101417	ENST00000409299	T	0.41065	1.01	5.83	-2.5	0.06384	.	0.333388	0.35677	N	0.003059	T	0.00012	0.0000	N	0.01705	-0.755	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32481	-0.9905	9	0.02654	T	1	-17.1965	6.6941	0.23189	0.0:0.2455:0.3347:0.4198	rs910397;rs17403865;rs17849429;rs58681389;rs910397	204	Q9Y6I8	PXMP4_HUMAN	I	204	ENSP00000386385:V204I	ENSP00000386385:V204I	V	-	1	0	PXMP4	31759202	0.981000	0.34729	0.990000	0.47175	0.170000	0.22686	0.196000	0.17176	-0.405000	0.07599	-1.272000	0.01410	GTC	C|0.421;N|0.000	.	strong		0.537	PXMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078739.2	NM_007238	
OBSL1	23363	hgsc.bcm.edu	37	2	220432014	220432014	+	Silent	SNP	G	G	A	rs61732787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:220432014G>A	ENST00000404537.1	-	4	1874	c.1818C>T	c.(1816-1818)ttC>ttT	p.F606F	OBSL1_ENST00000265318.4_Silent_p.F606F|OBSL1_ENST00000289656.3_Silent_p.F193F|OBSL1_ENST00000373873.4_Silent_p.F606F|OBSL1_ENST00000373876.1_Silent_p.F606F|OBSL1_ENST00000603926.1_Silent_p.F606F	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	606	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		CAGAACCGTGGAACACCACGT	0.637													G|||	860	0.171725	0.0454	0.2017	5008	,	,		19285	0.1151		0.2425	False		,,,				2504	0.3067				p.F606F		Atlas-SNP	.											.	OBSL1	120	.	0			c.C1818T						PASS	.	G	,,	378,3996		10,358,1819	39.0	50.0	46.0		1818,1818,1818	2.9	1.0	2	dbSNP_129	46	2155,6401		281,1593,2404	no	coding-synonymous,coding-synonymous,coding-synonymous	OBSL1	NM_001173408.1,NM_001173431.1,NM_015311.2	,,	291,1951,4223	AA,AG,GG		25.187,8.642,19.5901	,,	606/1026,606/1544,606/1897	220432014	2533,10397	2187	4278	6465	SO:0001819	synonymous_variant	23363	exon4			ACCGTGGAACACC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.1818C>T	2.37:g.220432014G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1																																																																																			G|0.816;A|0.184	0.184	strong		0.637	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
CCDC136	64753	hgsc.bcm.edu	37	7	128455916	128455916	+	Silent	SNP	G	G	A	rs2270590	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128455916G>A	ENST00000297788.4	+	16	3661	c.3294G>A	c.(3292-3294)gaG>gaA	p.E1098E	CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000471729.1_3'UTR|CCDC136_ENST00000378685.4_Intron	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	1098	Glu-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						aagaggaggaggaTGACGCCG	0.488													A|||	2110	0.421326	0.6793	0.2824	5008	,	,		21280	0.5833		0.1471	False		,,,				2504	0.2863				p.E1098E		Atlas-SNP	.											.	CCDC136	170	.	0			c.G3294A						PASS	.	A	,	2382,1680		694,994,343	108.0	124.0	119.0		,3294	-2.2	0.0	7	dbSNP_100	119	1309,7045		93,1123,2961	no	intron,coding-synonymous	CCDC136	NM_001201372.1,NM_022742.4	,	787,2117,3304	AA,AG,GG		15.6691,41.3589,29.7278	,	,1098/1155	128455916	3691,8725	2031	4177	6208	SO:0001819	synonymous_variant	64753	exon16			GGAGGAGGATGAC		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.3294G>A	7.37:g.128455916G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Silent	SNP	ENST00000297788.4	37	CCDS47704.1	853	0.39056776556776557	309	0.6280487804878049	93	0.2569060773480663	339	0.5926573426573427	112	0.14775725593667546	A	1.198	-0.633386	0.03584	0.586411	0.156691	ENSG00000128596	ENST00000494552	.	.	.	1.08	-2.17	0.07059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	T	0.42599	-0.9442	3	.	.	.	4.4954	3.2714	0.06883	0.2236:0.0:0.5398:0.2366	rs2270590;rs60406895;rs2270590	.	.	.	K	975	.	.	R	+	2	0	CCDC136	128243152	0.000000	0.05858	0.002000	0.10522	0.080000	0.17528	-2.626000	0.00874	-1.561000	0.01684	-1.361000	0.01213	AGG	G|0.609;A|0.391	0.391	strong		0.488	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742	
RAG2	5897	hgsc.bcm.edu	37	11	36615697	36615697	+	Missense_Mutation	SNP	C	C	T	rs150762709	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:36615697C>T	ENST00000311485.3	-	2	183	c.22G>A	c.(22-24)Gtc>Atc	p.V8I	C11orf74_ENST00000347206.4_5'Flank|C11orf74_ENST00000534635.1_5'Flank|C11orf74_ENST00000446510.2_5'Flank|C11orf74_ENST00000334307.5_5'Flank|RAG2_ENST00000528428.1_5'Flank	NM_000536.3|NM_001243785.1|NM_001243786.1	NP_000527.2|NP_001230714.1|NP_001230715.1	P55895	RAG2_HUMAN	recombination activating gene 2	8					B cell differentiation (GO:0030183)|chromatin modification (GO:0016568)|pre-B cell allelic exclusion (GO:0002331)|T cell differentiation in thymus (GO:0033077)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|zinc ion binding (GO:0008270)	p.V8I(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|pancreas(2)|prostate(1)|skin(4)	32	all_lung(20;0.226)	all_hematologic(20;0.00756)				TTATTACTGACTGTTACCATC	0.363									Familial Hemophagocytic Lymphohistiocytosis				C|||	4	0.000798722	0.0	0.0014	5008	,	,		20630	0.0		0.003	False		,,,				2504	0.0				p.V8I		Atlas-SNP	.											RAG2,NS,carcinoma,+2,2	RAG2	92	2	1	Substitution - Missense(1)	pancreas(1)	c.G22A						PASS	.	C	ILE/VAL	1,4403		0,1,2201	50.0	56.0	54.0		22	4.8	1.0	11	dbSNP_134	54	36,8558		0,36,4261	yes	missense	RAG2	NM_000536.3	29	0,37,6462	TT,TC,CC		0.4189,0.0227,0.2847	possibly-damaging	8/528	36615697	37,12961	2202	4297	6499	SO:0001583	missense	5897	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	TACTGACTGTTAC	AF080577	CCDS7903.1	11p13	2014-09-17				ENSG00000175097			9832	protein-coding gene	gene with protein product		179616				1283330	Standard	NM_000536		Approved		uc001mwv.4	P55895		ENST00000311485.3:c.22G>A	11.37:g.36615697C>T	ENSP00000308620:p.Val8Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_001243785	A8K9E9|Q8TBL4	Missense_Mutation	SNP	ENST00000311485.3	37	CCDS7903.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.86	3.238221	0.58886	2.27E-4	0.004189	ENSG00000175097	ENST00000311485;ENST00000529083;ENST00000527033	D;D;D	0.96232	-3.95;-3.14;-2.5	5.7	4.79	0.61399	.	0.206979	0.39475	N	0.001350	D	0.90789	0.7108	N	0.19112	0.55	0.26905	N	0.967021	B	0.06786	0.001	B	0.04013	0.001	T	0.82661	-0.0347	10	0.40728	T	0.16	-5.0002	8.1934	0.31381	0.0:0.7304:0.1294:0.1402	.	8	P55895	RAG2_HUMAN	I	8	ENSP00000308620:V8I;ENSP00000436327:V8I;ENSP00000436895:V8I	ENSP00000308620:V8I	V	-	1	0	RAG2	36572273	0.975000	0.34042	0.990000	0.47175	0.981000	0.71138	1.072000	0.30678	1.420000	0.47138	0.557000	0.71058	GTC	C|0.997;T|0.003	0.003	strong		0.363	RAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389536.1	NM_000536	
PPP1R26	9858	hgsc.bcm.edu	37	9	138376972	138376972	+	Missense_Mutation	SNP	A	A	G	rs3928777	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138376972A>G	ENST00000356818.2	+	4	1165	c.616A>G	c.(616-618)Aag>Gag	p.K206E	PPP1R26_ENST00000605286.1_Missense_Mutation_p.K206E|PPP1R26_ENST00000605660.1_Missense_Mutation_p.K206E|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Missense_Mutation_p.K206E|PPP1R26_ENST00000401470.3_Missense_Mutation_p.K206E	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	206			K -> E (in dbSNP:rs3928777). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGGATCCAGCAAGGACCAGGG	0.607													G|||	2059	0.411142	0.2927	0.4899	5008	,	,		17027	0.6319		0.2107	False		,,,				2504	0.4939				p.K206E		Atlas-SNP	.											.	.	.	.	0			c.A616G						PASS	.	G	GLU/LYS	1123,3281		138,847,1217	48.0	57.0	54.0		616	-5.0	0.0	9	dbSNP_108	54	1779,6809		195,1389,2710	yes	missense	KIAA0649	NM_014811.3	56	333,2236,3927	GG,GA,AA		20.715,25.4995,22.3368	benign	206/1210	138376972	2902,10090	2202	4294	6496	SO:0001583	missense	9858	exon4			TCCAGCAAGGACC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.616A>G	9.37:g.138376972A>G	ENSP00000349274:p.Lys206Glu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	34	23	0.676471	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	825	0.37774725274725274	124	0.25203252032520324	158	0.43646408839779005	385	0.6730769230769231	158	0.20844327176781002	G	1.359	-0.589194	0.03799	0.254995	0.20715	ENSG00000196422	ENST00000356818	T	0.08370	3.1	5.4	-4.97	0.03029	.	1.900700	0.02781	N	0.120907	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38134	-0.9675	9	0.02654	T	1	0.0044	4.3603	0.11199	0.2545:0.4099:0.2528:0.0828	rs3928777;rs17846423;rs17859469;rs56846731	206	Q5T8A7	PPR26_HUMAN	E	206	ENSP00000349274:K206E	ENSP00000349274:K206E	K	+	1	0	KIAA0649	137516793	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.040000	0.12104	-2.103000	0.00844	-2.245000	0.00285	AAG	A|0.724;G|0.276	0.276	strong		0.607	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
TENM1	10178	hgsc.bcm.edu	37	X	123526031	123526031	+	Silent	SNP	T	T	C	rs2076165	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:123526031T>C	ENST00000371130.3	-	27	5601	c.5538A>G	c.(5536-5538)tcA>tcG	p.S1846S	TENM1_ENST00000422452.2_Silent_p.S1853S|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1846					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)										ATCCCGAAGGTGAATATGTGA	0.413													T|||	659	0.17457	0.1021	0.1571	3775	,	,		14695	0.2569		0.0895	False		,,,				2504	0.0675				p.S1853S		Atlas-SNP	.											.	.	.	.	0			c.A5559G						PASS	.	T	,,	538,3297		30,395,83,1207,488	98.0	82.0	88.0		5559,5556,5538	1.4	1.0	X	dbSNP_96	88	759,5967		23,494,219,1910,1653	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	53,889,302,3117,2141	CC,CT,C,TT,T		11.2846,14.0287,12.281	,,	1853/2733,1852/2732,1846/2726	123526031	1297,9264	2203	4299	6502	SO:0001819	synonymous_variant	10178	exon28			CGAAGGTGAATAT	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.5538A>G	X.37:g.123526031T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	122	35	0.286885	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			0|0.003;C|0.153	0.153	strong		0.413	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
TACC2	10579	hgsc.bcm.edu	37	10	123846288	123846288	+	Missense_Mutation	SNP	G	G	A	rs4752642	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123846288G>A	ENST00000369005.1	+	4	4613	c.4273G>A	c.(4273-4275)Gcc>Acc	p.A1425T	TACC2_ENST00000334433.3_Missense_Mutation_p.A1425T|TACC2_ENST00000515603.1_Missense_Mutation_p.A1425T|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Missense_Mutation_p.A1425T|TACC2_ENST00000515273.1_Missense_Mutation_p.A1425T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1425			A -> T (in dbSNP:rs4752642).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				CGGAGCCCTGGCCACACCTGG	0.587													A|||	1025	0.204673	0.3071	0.1844	5008	,	,		19126	0.1002		0.2117	False		,,,				2504	0.181				p.A1425T		Atlas-SNP	.											.	TACC2	271	.	0			c.G4273A						PASS	.	A	,THR/ALA	1515,2891	673.4+/-402.8	257,1001,945	45.0	46.0	45.0		,4273	-1.9	0.0	10	dbSNP_111	45	1931,6669	725.9+/-406.6	215,1501,2584	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	472,2502,3529	AA,AG,GG		22.4535,34.3849,26.4955	,benign	,1425/2949	123846288	3446,9560	2203	4300	6503	SO:0001583	missense	10579	exon4			GCCCTGGCCACAC	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.4273G>A	10.37:g.123846288G>A	ENSP00000358001:p.Ala1425Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	462	0.21153846153846154	157	0.31910569105691056	79	0.21823204419889503	70	0.12237762237762238	156	0.20580474934036938	A	2.047	-0.418747	0.04766	0.343849	0.224535	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.02606	4.23;4.25;4.24;4.23;4.25	4.42	-1.87	0.07737	.	0.725799	0.11366	N	0.571365	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41662	-0.9496	9	0.07644	T	0.81	-0.7154	11.5586	0.50764	0.3549:0.0:0.6451:0.0	rs4752642;rs52796433;rs57437888;rs4752642	1425;1425;1425	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1425;1425;1425;1425;1425;1415	ENSP00000358001:A1425T;ENSP00000424467:A1425T;ENSP00000427618:A1425T;ENSP00000334280:A1425T;ENSP00000395048:A1425T	ENSP00000334280:A1425T	A	+	1	0	TACC2	123836278	0.009000	0.17119	0.000000	0.03702	0.001000	0.01503	0.072000	0.14617	-0.939000	0.03709	-0.380000	0.06706	GCC	G|0.754;A|0.246	0.246	strong		0.587	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
KIAA0753	9851	hgsc.bcm.edu	37	17	6515387	6515387	+	Missense_Mutation	SNP	A	A	G	rs2289642	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6515387A>G	ENST00000361413.3	-	8	1755	c.1397T>C	c.(1396-1398)cTg>cCg	p.L466P	KIAA0753_ENST00000572370.1_Missense_Mutation_p.L167P|KIAA0753_ENST00000589033.1_Intron|KIAA0753_ENST00000542606.1_Missense_Mutation_p.L167P	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	466			L -> P (in dbSNP:rs2289642). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		TCCTTCTTCCAGAACTATATC	0.443													G|||	3451	0.689097	0.8253	0.6801	5008	,	,		18156	0.7103		0.5467	False		,,,				2504	0.636				p.L466P		Atlas-SNP	.											.	KIAA0753	63	.	0			c.T1397C						PASS	.	G	PRO/LEU	2969,819		1169,631,94	154.0	155.0	155.0		1397	-3.8	0.0	17	dbSNP_100	155	4726,3512		1359,2008,752	yes	missense	KIAA0753	NM_014804.2	98	2528,2639,846	GG,GA,AA		42.6317,21.6209,36.0136	benign	466/968	6515387	7695,4331	1894	4119	6013	SO:0001583	missense	9851	exon8			TCTTCCAGAACTA		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1397T>C	17.37:g.6515387A>G	ENSP00000355250:p.Leu466Pro	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	175	87	0.497143	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	1439	0.6588827838827839	404	0.8211382113821138	243	0.6712707182320442	391	0.6835664335664335	401	0.5290237467018469	G	0.702	-0.790487	0.02884	0.783791	0.573683	ENSG00000198920	ENST00000361413;ENST00000542606	T;T	0.10477	2.87;2.87	4.43	-3.82	0.04281	.	1.416230	0.03928	N	0.284834	T	0.00012	0.0000	N	0.00483	-1.445	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.23940	-1.0174	9	0.20519	T	0.43	2.309	5.0425	0.14465	0.5171:0.0:0.2025:0.2804	rs2289642;rs17804248;rs52813277;rs59469410;rs2289642	466	Q2KHM9	K0753_HUMAN	P	466;167	ENSP00000355250:L466P;ENSP00000444634:L167P	ENSP00000355250:L466P	L	-	2	0	KIAA0753	6456111	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.776000	0.04674	-1.047000	0.03242	-0.119000	0.15052	CTG	A|0.342;G|0.658	0.658	strong		0.443	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
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 GAIIx	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	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	63	15	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	
KIAA1324	57535	hgsc.bcm.edu	37	1	109704525	109704525	+	Missense_Mutation	SNP	C	C	T	rs74920406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109704525C>T	ENST00000369939.3	+	2	346	c.163C>T	c.(163-165)Cac>Tac	p.H55Y	KIAA1324_ENST00000529753.1_Missense_Mutation_p.H55Y	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	55					cellular response to starvation (GO:0009267)|macroautophagy (GO:0016236)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of autophagic vacuole assembly (GO:2000786)|positive regulation of vacuole organization (GO:0044090)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34		all_epithelial(167;0.000102)|all_lung(203;0.000323)|Lung NSC(277;0.00063)		Colorectal(144;0.0188)|Lung(183;0.0527)|COAD - Colon adenocarcinoma(174;0.14)|Epithelial(280;0.21)|all cancers(265;0.249)		GTCTGAGTACCACTATGAGTA	0.587													C|||	56	0.0111821	0.0008	0.0173	5008	,	,		20125	0.0		0.0398	False		,,,				2504	0.0031				p.H55Y		Atlas-SNP	.											.	KIAA1324	77	.	0			c.C163T						PASS	.	C	TYR/HIS	44,4362	46.7+/-81.2	0,44,2159	93.0	71.0	78.0		163	5.6	1.0	1	dbSNP_131	78	387,8213	124.1+/-182.9	6,375,3919	yes	missense	KIAA1324	NM_020775.3	83	6,419,6078	TT,TC,CC		4.5,0.9986,3.3139	probably-damaging	55/1014	109704525	431,12575	2203	4300	6503	SO:0001583	missense	57535	exon2			GAGTACCACTATG	AK057647	CCDS794.1, CCDS58015.1	1p13.3	2008-09-18			ENSG00000116299	ENSG00000116299			29618	protein-coding gene	gene with protein product	"""estrogen induced gene 121"""	611298				10718198, 16322283	Standard	NM_020775		Approved	maba1, EIG121	uc021orb.1	Q6UXG2	OTTHUMG00000011725	ENST00000369939.3:c.163C>T	1.37:g.109704525C>T	ENSP00000358955:p.His55Tyr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	122	55	0.45082	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Missense_Mutation	SNP	ENST00000369939.3	37	CCDS794.1	30	0.013736263736263736	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	23	0.030343007915567283	C	21.8	4.197056	0.79015	0.009986	0.045	ENSG00000116299	ENST00000533147;ENST00000531664;ENST00000534476;ENST00000526264;ENST00000369939;ENST00000457623;ENST00000529753	T;T;T;T;T;T;T	0.47177	0.85;1.6;1.6;1.6;1.6;1.6;1.6	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.44008	0.1273	L	0.39397	1.21	0.32959	D	0.520846	P;D;D	0.89917	0.687;1.0;1.0	B;D;D	0.87578	0.301;0.998;0.998	T	0.31475	-0.9942	10	0.02654	T	1	-14.7801	19.1286	0.93396	0.0:1.0:0.0:0.0	.	55;55;55	Q6UXG2-3;C9J810;Q6UXG2	.;.;K1324_HUMAN	Y	55	ENSP00000431134:H55Y;ENSP00000431349:H55Y;ENSP00000432164:H55Y;ENSP00000435066:H55Y;ENSP00000358955:H55Y;ENSP00000393964:H55Y;ENSP00000434595:H55Y	ENSP00000358955:H55Y	H	+	1	0	KIAA1324	109506048	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.992000	0.70609	2.603000	0.88011	0.655000	0.94253	CAC	C|0.977;T|0.023	0.023	strong		0.587	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775	
OR5P2	120065	hgsc.bcm.edu	37	11	7818151	7818151	+	Silent	SNP	G	G	A	rs73406606	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7818151G>A	ENST00000329434.2	-	1	369	c.339C>T	c.(337-339)gcC>gcT	p.A113A	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	113						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CATAGGCCATGGCAGCCAGAA	0.478													G|||	1185	0.236621	0.348	0.2911	5008	,	,		18204	0.128		0.2763	False		,,,				2504	0.1186				p.A113A		Atlas-SNP	.											OR5P2,brain,glioma,0,1	OR5P2	68	1	0			c.C339T						PASS	.	G		1371,2837		401,569,1134	89.0	103.0	99.0		339	2.4	1.0	11	dbSNP_130	99	2425,6159		393,1639,2260	no	coding-synonymous	OR5P2	NM_153444.1		794,2208,3394	AA,AG,GG		28.2502,32.5808,29.6748		113/323	7818151	3796,8996	2104	4292	6396	SO:0001819	synonymous_variant	120065	exon1			GGCCATGGCAGCC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.339C>T	11.37:g.7818151G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			G|0.739;A|0.261	0.261	strong		0.478	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
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 GAIIx	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	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	30	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	
SNAPC4	6621	hgsc.bcm.edu	37	9	139273288	139273288	+	Silent	SNP	C	C	T	rs3829112	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139273288C>T	ENST00000298532.2	-	21	3359	c.2991G>A	c.(2989-2991)gaG>gaA	p.E997E		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		GGGCTGTGCCCTCGGCCTCTG	0.667													C|||	945	0.188698	0.0893	0.2594	5008	,	,		10947	0.2738		0.161	False		,,,				2504	0.2137				p.E997E		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G2991A						PASS	.	C		382,4000		17,348,1826	15.0	18.0	17.0		2991	1.9	0.0	9	dbSNP_107	17	1323,7263		102,1119,3072	no	coding-synonymous	SNAPC4	NM_003086.2		119,1467,4898	TT,TC,CC		15.4088,8.7175,13.1477		997/1470	139273288	1705,11263	2191	4293	6484	SO:0001819	synonymous_variant	6621	exon21			TGTGCCCTCGGCC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2991G>A	9.37:g.139273288C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	158	156	0.987342	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			C|0.845;T|0.155	0.155	strong		0.667	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
GABRA2	2555	hgsc.bcm.edu	37	4	46252540	46252540	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:46252540C>T	ENST00000510861.1	-	10	1314	c.1141G>A	c.(1141-1143)Gat>Aat	p.D381N	GABRA2_ENST00000514090.1_Missense_Mutation_p.D381N|GABRA2_ENST00000356504.1_Missense_Mutation_p.D381N|GABRA2_ENST00000381620.4_Missense_Mutation_p.D381N|GABRA2_ENST00000507069.1_Missense_Mutation_p.D441N|GABRA2_ENST00000540012.1_Missense_Mutation_p.D386N			P47869	GBRA2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 2	381					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|neurotransmitter transport (GO:0006836)|regulation of neurotransmitter levels (GO:0001505)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of synaptic vesicle membrane (GO:0030285)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	56					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	AGAACTGGATCTTTTGAAAGA	0.413																																					p.D381N		Atlas-SNP	.											GABRA2,caecum,carcinoma,+1,2	GABRA2	134	2	0			c.G1141A						scavenged	.						147.0	147.0	147.0					4																	46252540		2203	4299	6502	SO:0001583	missense	2555	exon10			CTGGATCTTTTGA		CCDS3471.1	4p12	2012-06-22			ENSG00000151834	ENSG00000151834		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4076	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 2"""	137140					Standard	NM_000807		Approved		uc010igc.2	P47869	OTTHUMG00000044266	ENST00000510861.1:c.1141G>A	4.37:g.46252540C>T	ENSP00000421828:p.Asp381Asn	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	212	7	0.0330189	NM_000807	A8K0U7|B7Z1H8|Q59G14	Missense_Mutation	SNP	ENST00000510861.1	37	CCDS3471.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141165	0.56936	.	.	ENSG00000151834	ENST00000510861;ENST00000514090;ENST00000381620;ENST00000356504;ENST00000540012;ENST00000507069	D;D;D;D;D;D	0.85258	-1.81;-1.81;-1.81;-1.81;-1.96;-1.96	5.96	5.96	0.96718	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.87454	0.6181	L	0.43923	1.385	0.30606	N	0.760055	D;B	0.55172	0.97;0.019	P;B	0.53450	0.726;0.034	D	0.85504	0.1193	10	0.51188	T	0.08	.	19.3998	0.94623	0.0:1.0:0.0:0.0	.	386;381	B7Z1H8;P47869	.;GBRA2_HUMAN	N	381;381;381;381;386;441	ENSP00000421828:D381N;ENSP00000421300:D381N;ENSP00000371033:D381N;ENSP00000348897:D381N;ENSP00000444409:D386N;ENSP00000427603:D441N	ENSP00000348897:D381N	D	-	1	0	GABRA2	45947297	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.818000	0.86416	2.827000	0.97445	0.655000	0.94253	GAT	.	.	none		0.413	GABRA2-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360848.2		
TXNDC2	84203	hgsc.bcm.edu	37	18	9887877	9887877	+	Silent	SNP	G	G	A	rs34362649	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:9887877G>A	ENST00000306084.6	+	2	1600	c.1401G>A	c.(1399-1401)ggG>ggA	p.G467G	TXNDC2_ENST00000357775.5_Silent_p.G400G|TXNDC2_ENST00000536353.2_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	467	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						AGGAGGCCGGGGAGAGGCTGG	0.567													G|||	78	0.0155751	0.0015	0.0173	5008	,	,		20053	0.0		0.0596	False		,,,				2504	0.0041				p.G467G		Atlas-SNP	.											.	TXNDC2	168	.	0			c.G1401A						PASS	.	G	,	31,4375	38.4+/-70.7	0,31,2172	61.0	50.0	54.0		1401,1200	-1.4	0.5	18	dbSNP_126	54	431,8169	130.7+/-188.6	12,407,3881	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	12,438,6053	AA,AG,GG		5.0116,0.7036,3.5522	,	467/554,400/487	9887877	462,12544	2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			GGCCGGGGAGAGG	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.1401G>A	18.37:g.9887877G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			G|0.960;A|0.040	0.040	strong		0.567	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
SPPL2C	162540	hgsc.bcm.edu	37	17	43924231	43924231	+	Silent	SNP	G	G	A	rs12373140	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43924231G>A	ENST00000329196.5	+	1	1976	c.1959G>A	c.(1957-1959)caG>caA	p.Q653Q	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	653						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										TCCATGCCCAGGCCCAGGCCC	0.627													G|||	431	0.0860623	0.0151	0.1571	5008	,	,		18478	0.001		0.2396	False		,,,				2504	0.0613				p.Q653Q		Atlas-SNP	.											.	.	.	.	0			c.G1959A						PASS	.	G		202,4204	120.0+/-157.7	5,192,2006	35.0	37.0	37.0		1959	3.0	0.9	17	dbSNP_120	37	1921,6679	320.1+/-314.5	221,1479,2600	no	coding-synonymous	IMP5	NM_175882.2		226,1671,4606	AA,AG,GG		22.3372,4.5847,16.3232		653/685	43924231	2123,10883	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			TGCCCAGGCCCAG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1959G>A	17.37:g.43924231G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			C|0.852;T|0.148	.	strong		0.627	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
USP8	9101	hgsc.bcm.edu	37	15	50782703	50782703	+	Missense_Mutation	SNP	A	A	G	rs11638390	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:50782703A>G	ENST00000396444.3	+	14	2553	c.2215A>G	c.(2215-2217)Aca>Gca	p.T739A	USP8_ENST00000425032.3_Missense_Mutation_p.T633A|USP8_ENST00000433963.1_Missense_Mutation_p.T739A|USP8_ENST00000307179.4_Missense_Mutation_p.T739A	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	739			T -> A (in dbSNP:rs11638390).		cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		AGTAACTCCAACAGTTAATCG	0.413													a|||	578	0.115415	0.0265	0.2406	5008	,	,		19297	0.002		0.1789	False		,,,				2504	0.1984				p.T739A		Atlas-SNP	.											.	USP8	90	.	0			c.A2215G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR	221,4171	129.8+/-166.5	6,209,1981	107.0	108.0	107.0		2215,2215,2215	-6.6	0.0	15	dbSNP_120	107	1571,7017	292.4+/-300.8	157,1257,2880	yes	missense,missense,missense	USP8	NM_001128610.1,NM_001128611.1,NM_005154.3	58,58,58	163,1466,4861	GG,GA,AA		18.293,5.0319,13.8059	benign,benign,benign	739/1119,739/1119,739/1119	50782703	1792,11188	2196	4294	6490	SO:0001583	missense	9101	exon14			ACTCCAACAGTTA	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2215A>G	15.37:g.50782703A>G	ENSP00000379721:p.Thr739Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	30	18	0.6	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	37	CCDS10137.1	236	0.10805860805860806	18	0.036585365853658534	88	0.2430939226519337	0	0.0	130	0.17150395778364116	a	0.126	-1.118975	0.01785	0.050319	0.18293	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.17213	2.29;2.29;2.29;4.38	5.6	-6.61	0.01818	.	0.928719	0.09316	N	0.818875	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47471	-0.9115	9	0.16896	T	0.51	-0.0226	8.1026	0.30865	0.2895:0.0902:0.5314:0.0889	rs11638390;rs17519682;rs52795257;rs11638390	633;739	B4DKA8;P40818	.;UBP8_HUMAN	A	739;739;739;633	ENSP00000379721:T739A;ENSP00000405537:T739A;ENSP00000302239:T739A;ENSP00000412682:T633A	ENSP00000302239:T739A	T	+	1	0	USP8	48569995	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-1.084000	0.03393	-1.515000	0.01784	-1.926000	0.00513	ACA	A|0.874;G|0.126	0.126	strong		0.413	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154	
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 GAIIx	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		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	110	40	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
ERN2	10595	hgsc.bcm.edu	37	16	23711925	23711925	+	Missense_Mutation	SNP	C	C	G	rs26764	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:23711925C>G	ENST00000457008.2	-	12	1342	c.1304G>C	c.(1303-1305)aGc>aCc	p.S435T	ERN2_ENST00000256797.4_Missense_Mutation_p.S535T					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		GCTCCTCCGGCTGGCCCCCGA	0.622													G|||	2177	0.434704	0.674	0.3228	5008	,	,		15017	0.4792		0.2734	False		,,,				2504	0.3108				p.S535T		Atlas-SNP	.											.	ERN2	131	.	0			c.G1604C						PASS	.	G	THR/SER	2612,1782	524.6+/-371.4	797,1018,382	74.0	74.0	74.0		1604	2.0	0.0	16	dbSNP_76	74	2197,6403	709.7+/-405.7	263,1671,2366	yes	missense	ERN2	NM_033266.3	58	1060,2689,2748	GG,GC,CC		25.5465,40.5553,37.0094	benign	535/975	23711925	4809,8185	2197	4300	6497	SO:0001583	missense	10595	exon13			CTCCGGCTGGCCC	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"""ER to nucleus signalling 2"""			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.1304G>C	16.37:g.23711925C>G	ENSP00000413812:p.Ser435Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_033266		Missense_Mutation	SNP	ENST00000457008.2	37		892	0.4084249084249084	314	0.6382113821138211	108	0.2983425414364641	261	0.4562937062937063	209	0.2757255936675462	G	0.763	-0.768622	0.02974	0.594447	0.255465	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.60299	0.2;0.26	4.1	2.02	0.26589	.	0.946701	0.08902	N	0.877043	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46005	-0.9222	9	0.10636	T	0.68	.	6.4926	0.22123	0.0993:0.3506:0.5501:0.0	rs26764;rs52832029;rs58295665;rs26764	435;487	E7ETG2;A5YM65	.;.	T	535;435	ENSP00000256797:S535T;ENSP00000413812:S435T	ENSP00000256797:S535T	S	-	2	0	ERN2	23619426	0.025000	0.19082	0.005000	0.12908	0.001000	0.01503	0.105000	0.15333	0.255000	0.21593	-0.216000	0.12614	AGC	C|0.619;G|0.381	0.381	strong		0.622	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1		
ATP2C2	9914	hgsc.bcm.edu	37	16	84474484	84474484	+	Missense_Mutation	SNP	G	G	A	rs2303853	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84474484G>A	ENST00000262429.4	+	14	1320	c.1231G>A	c.(1231-1233)Ggt>Agt	p.G411S	ATP2C2_ENST00000416219.2_Missense_Mutation_p.G411S|ATP2C2_ENST00000420010.2_3'UTR	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	411			G -> S (in dbSNP:rs2303853).		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TGGGTATGACGGTCAAGGGAC	0.507													G|||	204	0.0407348	0.0061	0.0764	5008	,	,		21580	0.0258		0.0736	False		,,,				2504	0.044				p.G411S		Atlas-SNP	.											.	ATP2C2	75	.	0			c.G1231A						PASS	.	G	SER/GLY	75,3957		0,75,1941	104.0	109.0	107.0		1231	4.8	0.0	16	dbSNP_100	107	586,7766		23,540,3613	yes	missense	ATP2C2	NM_014861.2	56	23,615,5554	AA,AG,GG		7.0163,1.8601,5.3375	benign	411/947	84474484	661,11723	2016	4176	6192	SO:0001583	missense	9914	exon14			TATGACGGTCAAG	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1231G>A	16.37:g.84474484G>A	ENSP00000262429:p.Gly411Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	37	CCDS42207.1	101	0.04624542124542125	3	0.006097560975609756	33	0.09116022099447514	14	0.024475524475524476	51	0.06728232189973615	G	9.107	1.005591	0.19199	0.018601	0.070163	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	T;T	0.69561	-0.41;-0.41	5.7	4.75	0.60458	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.850743	0.10388	N	0.680687	T	0.03564	0.0102	N	0.17872	0.535	0.30302	P	0.78938	B;B;B;B	0.23937	0.094;0.018;0.076;0.053	B;B;B;B	0.21917	0.036;0.014;0.031;0.037	T	0.29761	-1.0001	9	0.37606	T	0.19	.	13.5545	0.61751	0.0746:0.0:0.9254:0.0	rs2303853;rs52818805;rs58870704;rs2303853	411;260;428;411	E7ES94;F8WAA5;O75185-2;O75185	.;.;.;AT2C2_HUMAN	S	411;411;260	ENSP00000397925:G411S;ENSP00000262429:G411S	ENSP00000262429:G411S	G	+	1	0	ATP2C2	83031985	1.000000	0.71417	0.014000	0.15608	0.043000	0.13939	4.470000	0.60175	1.403000	0.46800	0.655000	0.94253	GGT	G|0.951;A|0.049	0.049	strong		0.507	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
TRMT10C	54931	hgsc.bcm.edu	37	3	101283792	101283792	+	Missense_Mutation	SNP	C	C	G	rs3762735	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:101283792C>G	ENST00000309922.6	+	2	321	c.167C>G	c.(166-168)cCc>cGc	p.P56R		NM_017819.2	NP_060289.2	Q7L0Y3	MRRP1_HUMAN	tRNA methyltransferase 10 homolog C (S. cerevisiae)	56			P -> R (in dbSNP:rs3762735). {ECO:0000269|PubMed:10508479}.		mitochondrial RNA 5'-end processing (GO:0000964)|tRNA processing (GO:0008033)	mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)										GAGAGTACACCCCCTTCTGAA	0.368													C|||	685	0.136781	0.1044	0.1066	5008	,	,		16403	0.1171		0.1461	False		,,,				2504	0.2127				p.P56R		Atlas-SNP	.											.	.	.	.	0			c.C167G						PASS	.	C	ARG/PRO	381,3359		17,347,1506	142.0	132.0	135.0		167	5.2	0.1	3	dbSNP_107	135	1330,6866		123,1084,2891	yes	missense	RG9MTD1	NM_017819.2	103	140,1431,4397	GG,GC,CC		16.2274,10.1872,14.3348	benign	56/404	101283792	1711,10225	1870	4098	5968	SO:0001583	missense	54931	exon2			GTACACCCCCTTC	AK000439	CCDS43122.1	3q12.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000174173	ENSG00000174173			26022	protein-coding gene	gene with protein product	"""mitochondrial RNase P subunit 1"""	615423	"""RNA (guanine-9-) methyltransferase domain containing 1"""	RG9MTD1		18984158	Standard	NM_017819		Approved	FLJ20432, MRPP1	uc003duz.4	Q7L0Y3	OTTHUMG00000159114	ENST00000309922.6:c.167C>G	3.37:g.101283792C>G	ENSP00000312356:p.Pro56Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_017819	Q9NRG5|Q9NX54|Q9Y596	Missense_Mutation	SNP	ENST00000309922.6	37	CCDS43122.1	281	0.12866300366300365	62	0.12601626016260162	47	0.1298342541436464	65	0.11363636363636363	107	0.14116094986807387	C	7.448	0.642048	0.14451	0.101872	0.162274	ENSG00000174173	ENST00000309922;ENST00000495642	T;T	0.22336	2.56;1.96	6.03	5.16	0.70880	.	0.953354	0.08828	N	0.887801	T	0.00073	0.0002	L	0.29908	0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.09707	-1.0662	9	0.48119	T	0.1	-12.4857	9.8176	0.40862	0.0:0.7852:0.1401:0.0747	rs3762735;rs52819925	56	Q7L0Y3	MRRP1_HUMAN	R	56	ENSP00000312356:P56R;ENSP00000419389:P56R	ENSP00000312356:P56R	P	+	2	0	RG9MTD1	102766482	0.001000	0.12720	0.084000	0.20598	0.440000	0.31957	1.431000	0.34925	1.545000	0.49373	0.655000	0.94253	CCC	C|0.864;G|0.136	0.136	strong		0.368	TRMT10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353400.2	NM_017819	
VWA7	80737	hgsc.bcm.edu	37	6	31733466	31733466	+	Missense_Mutation	SNP	T	T	C	rs3101017	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31733466T>C	ENST00000375688.4	-	17	2781	c.2581A>G	c.(2581-2583)Act>Gct	p.T861A	VWA7_ENST00000375686.3_3'UTR|VWA7_ENST00000467576.1_5'Flank|SAPCD1-AS1_ENST00000419679.1_RNA			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	861			T -> A (in dbSNP:rs3101017). {ECO:0000269|PubMed:14656967}.			extracellular region (GO:0005576)											CTGCCTTGAGTCACCAATGTG	0.652													T|||	169	0.033746	0.0567	0.0274	5008	,	,		14680	0.0		0.0746	False		,,,				2504	0.0				p.T861A		Atlas-SNP	.											.	.	.	.	0			c.A2581G						PASS	.	T	ALA/THR	194,2808		6,182,1313	26.0	18.0	21.0		2581	-0.7	0.5	6	dbSNP_103	21	536,4868		31,474,2197	yes	missense	C6orf27	NM_025258.2	58	37,656,3510	CC,CT,TT		9.9186,6.4624,8.6843	benign	861/892	31733466	730,7676	1501	2702	4203	SO:0001583	missense	80737	exon17			CTTGAGTCACCAA		CCDS4721.2	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000204396	ENSG00000204396			13939	protein-coding gene	gene with protein product		609693	"""chromosome 6 open reading frame 27"""	C6orf27			Standard	NM_025258		Approved	G7c, NG37	uc011dog.2	Q9Y334	OTTHUMG00000031132	ENST00000375688.4:c.2581A>G	6.37:g.31733466T>C	ENSP00000364840:p.Thr861Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	91	80	0.879121	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	37	CCDS4721.2	96	0.04395604395604396	28	0.056910569105691054	11	0.03038674033149171	0	0.0	57	0.07519788918205805	T	9.614	1.131932	0.21041	0.064624	0.099186	ENSG00000204396	ENST00000375688	T	0.12361	2.69	5.02	-0.686	0.11324	.	0.908575	0.09039	U	0.857619	T	0.01940	0.0061	L	0.32530	0.975	0.21445	N	0.999689	B	0.11235	0.004	B	0.11329	0.006	T	0.46359	-0.9197	10	0.06365	T	0.9	-3.144	4.3182	0.11003	0.0:0.1855:0.3361:0.4784	rs3101017	861	Q9Y334	G7C_HUMAN	A	861	ENSP00000364840:T861A	ENSP00000364840:T861A	T	-	1	0	C6orf27	31841445	0.760000	0.28428	0.467000	0.27180	0.163000	0.22366	0.058000	0.14301	0.096000	0.17463	0.528000	0.53228	ACT	T|0.956;C|0.044	0.044	strong		0.652	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258	
FAN1	22909	hgsc.bcm.edu	37	15	31197564	31197564	+	Missense_Mutation	SNP	G	G	A	rs4779794	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:31197564G>A	ENST00000362065.4	+	2	989	c.698G>A	c.(697-699)gGa>gAa	p.G233E	FAN1_ENST00000565466.1_Missense_Mutation_p.G233E|FAN1_ENST00000561594.1_Missense_Mutation_p.G233E|FAN1_ENST00000561607.1_Missense_Mutation_p.G233E	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	233			G -> E (in dbSNP:rs4779794). {ECO:0000269|PubMed:15489334}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						ATGGTAAGAGGAAGTAAAATA	0.408								Direct reversal of damage					G|||	2116	0.422524	0.0401	0.4539	5008	,	,		21085	0.7679		0.4374	False		,,,				2504	0.546				p.G233E		Atlas-SNP	.											FAN1,NS,carcinoma,+1,1	FAN1	77	1	0			c.G698A						scavenged	.	G	GLU/GLY,GLU/GLY,GLU/GLY,GLU/GLY	494,3910	225.6+/-241.4	34,426,1742	53.0	52.0	52.0		698,698,698,698	-2.2	0.0	15	dbSNP_111	52	3661,4939	522.8+/-380.2	760,2141,1399	yes	missense,missense,missense,missense	FAN1	NM_001146094.1,NM_001146095.1,NM_001146096.1,NM_014967.4	98,98,98,98	794,2567,3141	AA,AG,GG		42.5698,11.2171,31.9517	benign,benign,benign,benign	233/534,233/534,233/534,233/1018	31197564	4155,8849	2202	4300	6502	SO:0001583	missense	22909	exon2			TAAGAGGAAGTAA		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.698G>A	15.37:g.31197564G>A	ENSP00000354497:p.Gly233Glu	Somatic	43	2	0.0465116		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	37	CCDS32186.1	985	0.451007326007326	28	0.056910569105691054	157	0.43370165745856354	456	0.7972027972027972	344	0.45382585751978893	G	1.907	-0.451723	0.04572	0.112171	0.425698	ENSG00000198690	ENST00000362065	T	0.41065	1.01	5.18	-2.16	0.07080	.	1.092420	0.06802	N	0.788905	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.33583	0.146;0.418	B;B	0.30855	0.026;0.121	T	0.48547	-0.9026	9	0.02654	T	1	-2.2897	6.1061	0.20073	0.5001:0.0:0.3751:0.1248	rs4779794;rs17227870;rs57472252;rs4779794	233;233	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	E	233	ENSP00000354497:G233E	ENSP00000354497:G233E	G	+	2	0	FAN1	28984856	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.063000	0.11655	-0.319000	0.08652	-0.126000	0.14955	GGA	G|0.626;A|0.374	0.374	strong		0.408	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967	
TTC23	64927	hgsc.bcm.edu	37	15	99762052	99762052	+	Silent	SNP	A	A	G	rs76007555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:99762052A>G	ENST00000394132.2	-	6	1015	c.198T>C	c.(196-198)caT>caC	p.H66H	TTC23_ENST00000558613.1_Silent_p.H66H|TTC23_ENST00000262074.4_Silent_p.H66H|TTC23_ENST00000394135.3_Silent_p.H66H|TTC23_ENST00000394129.2_Silent_p.H66H|TTC23_ENST00000394130.1_Silent_p.H66H|TTC23_ENST00000394136.1_Silent_p.H66H|TTC23_ENST00000558663.1_Silent_p.H66H			Q5W5X9	TTC23_HUMAN	tetratricopeptide repeat domain 23	66										endometrium(2)|large_intestine(3)|lung(9)|urinary_tract(2)	16	all_cancers(4;1.49e-13)|Lung NSC(78;0.000545)|all_lung(78;0.00121)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		all cancers(5;8.11e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00215)			GCACAAGCTCATGGACGGCCT	0.433													G|||	230	0.0459265	0.0703	0.0418	5008	,	,		19732	0.0089		0.0596	False		,,,				2504	0.0399				p.H66H		Atlas-SNP	.											.	TTC23	33	.	0			c.T198C						PASS	.	G	,,,,,,	384,4010	790.3+/-415.0	23,338,1836	107.0	89.0	95.0		198,198,198,198,198,198,198	-10.8	0.0	15	dbSNP_132	95	640,7954	790.5+/-407.6	21,598,3678	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTC23	NM_001040655.1,NM_001040656.1,NM_001040657.1,NM_001040658.1,NM_001040659.1,NM_001040660.1,NM_022905.4	,,,,,,	44,936,5514	GG,GA,AA		7.4471,8.7392,7.8842	,,,,,,	66/448,66/448,66/448,66/448,66/448,66/448,66/448	99762052	1024,11964	2197	4297	6494	SO:0001819	synonymous_variant	64927	exon4			AAGCTCATGGACG		CCDS10379.2	15q26.3	2013-01-11			ENSG00000103852	ENSG00000103852		"""Tetratricopeptide (TTC) repeat domain containing"""	25730	protein-coding gene	gene with protein product						12477932	Standard	NM_001288615		Approved	FLJ12572, HCC-8	uc002bux.3	Q5W5X9	OTTHUMG00000147344	ENST00000394132.2:c.198T>C	15.37:g.99762052A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_001040657	A8K6M5|Q53HK0|Q96BC9|Q9H8W9|Q9H9S7	Silent	SNP	ENST00000394132.2	37	CCDS10379.2																																																																																			A|0.932;G|0.068	0.068	strong		0.433	TTC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303953.2	NM_022905	
OR2T29	343563	hgsc.bcm.edu	37	1	248722777	248722777	+	Missense_Mutation	SNP	T	T	A	rs77589892	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248722777T>A	ENST00000328570.3	-	1	20	c.16A>T	c.(16-18)Agg>Tgg	p.R6W	RP11-438F14.3_ENST00000438623.1_RNA	NM_001004694.2	NP_001004694.2	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T, member 29	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|lung(4)	5	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)			TTGGCCATCCTGGTGATGTTG	0.463																																					p.R6W		Atlas-SNP	.											.	OR2T29	8	.	0			c.A16T						PASS	.	A	TRP/ARG	2570,1836		591,1388,224	78.0	65.0	69.0		16	-0.6	0.0	1	dbSNP_131	69	2027,6569		69,1889,2340	no	missense	OR2T29	NM_001004694.2	101	660,3277,2564	AA,AT,TT		23.5807,41.6704,35.3561		6/316	248722777	4597,8405	2203	4298	6501	SO:0001583	missense	343563	exon1			CCATCCTGGTGAT		CCDS55695.1	1q44	2012-08-09			ENSG00000182783	ENSG00000182783		"""GPCR / Class A : Olfactory receptors"""	31253	protein-coding gene	gene with protein product							Standard	NM_001004694		Approved		uc001ieo.2	Q8NH02	OTTHUMG00000040382	ENST00000328570.3:c.16A>T	1.37:g.248722777T>A	ENSP00000331774:p.Arg6Trp	Somatic	599	0	0		WXS	Illumina HiSeq	Phase_I	908	253	0.278634	NM_001004694		Missense_Mutation	SNP	ENST00000328570.3	37	CCDS55695.1	.	.	.	.	.	.	.	.	.	.	N	7.770	0.707330	0.15239	0.583296	0.235807	ENSG00000182783	ENST00000328570	T	0.00466	7.23	2.34	-0.604	0.11626	.	0.645074	0.13113	N	0.412838	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	.	.	.	.	.	.	T	0.00006	-1.2513	7	0.20519	T	0.43	.	7.9651	0.30094	0.4093:0.0:0.0:0.5907	.	.	.	.	W	6	ENSP00000331774:R6W	ENSP00000331774:R6W	R	-	1	2	OR2T29	246789400	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.533000	0.06157	-0.193000	0.10415	-4.084000	0.00011	AGG	T|0.770;A|0.230	0.230	strong		0.463	OR2T29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097132.1	NM_001004694	
SAGE1	55511	hgsc.bcm.edu	37	X	134991078	134991078	+	Silent	SNP	A	A	G	rs5974570	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:134991078A>G	ENST00000370709.3	+	12	1497	c.1497A>G	c.(1495-1497)caA>caG	p.Q499Q	SAGE1_ENST00000535938.1_Silent_p.Q499Q|SAGE1_ENST00000537770.1_Intron|SAGE1_ENST00000324447.3_Silent_p.Q499Q			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	499						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					GCAAACCCCAAACTGATAAGG	0.443													a|||	611	0.161854	0.0673	0.1614	3775	,	,		15680	0.1012		0.2058	False		,,,				2504	0.1033				p.Q499Q		Atlas-SNP	.											.	SAGE1	160	.	0			c.A1497G						PASS	.	A		560,3275		31,427,71,1174,500	217.0	154.0	175.0		1497	-2.8	0.0	X	dbSNP_114	175	1754,4974		188,923,455,1317,1417	no	coding-synonymous	SAGE1	NM_018666.2		219,1350,526,2491,1917	GG,GA,G,AA,A		26.0702,14.6023,21.9067		499/905	134991078	2314,8249	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon13			ACCCCAAACTGAT	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.1497A>G	X.37:g.134991078A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	123	36	0.292683	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			A|0.806;G|0.194	0.194	strong		0.443	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
TBC1D31	93594	hgsc.bcm.edu	37	8	124121798	124121798	+	Silent	SNP	A	A	G	rs16897969	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124121798A>G	ENST00000287380.1	+	10	1464	c.1374A>G	c.(1372-1374)gcA>gcG	p.A458A	TBC1D31_ENST00000378080.2_Silent_p.A353A|TBC1D31_ENST00000521676.1_Silent_p.A335A|TBC1D31_ENST00000327098.5_Silent_p.A458A|TBC1D31_ENST00000309336.3_Silent_p.A458A|TBC1D31_ENST00000522420.1_Silent_p.A353A|TBC1D31_ENST00000518805.1_Silent_p.A91A	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	458	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										CTCATGTGGCATTTCTCAACC	0.388													a|||	1459	0.291334	0.3865	0.3588	5008	,	,		15919	0.1538		0.2903	False		,,,				2504	0.2577				p.A458A		Atlas-SNP	.											.	WDR67	97	.	0			c.A1374G						PASS	.	G	,	1633,2773	500.7+/-364.8	324,985,894	130.0	134.0	132.0		1374,1374	-10.0	0.6	8	dbSNP_123	132	2570,6030	417.1+/-352.3	363,1844,2093	no	coding-synonymous,coding-synonymous	WDR67	NM_001145088.1,NM_145647.3	,	687,2829,2987	GG,GA,AA		29.8837,37.0631,32.3159	,	458/971,458/1067	124121798	4203,8803	2203	4300	6503	SO:0001819	synonymous_variant	93594	exon10			TGTGGCATTTCTC	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.1374A>G	8.37:g.124121798A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	ENST00000287380.1	37	CCDS6338.1																																																																																			A|0.694;G|0.306	0.306	strong		0.388	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	
ELF1	1997	hgsc.bcm.edu	37	13	41517985	41517985	+	Silent	SNP	A	A	G	rs3764056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:41517985A>G	ENST00000239882.3	-	6	920	c.606T>C	c.(604-606)gaT>gaC	p.D202D	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Silent_p.D178D	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	202					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		TACCCTTTCCATCTTTGTTTT	0.368													A|||	2071	0.413538	0.152	0.6657	5008	,	,		17100	0.1538		0.7097	False		,,,				2504	0.5511				p.D202D		Atlas-SNP	.											.	ELF1	65	.	0			c.T606C						PASS	.	A	,	976,3430	362.4+/-316.1	103,770,1330	222.0	184.0	197.0		534,606	3.6	1.0	13	dbSNP_107	197	5838,2762	678.9+/-403.5	1962,1914,424	yes	coding-synonymous,coding-synonymous	ELF1	NM_001145353.1,NM_172373.3	,	2065,2684,1754	GG,GA,AA		32.1163,22.1516,47.6088	,	178/596,202/620	41517985	6814,6192	2203	4300	6503	SO:0001819	synonymous_variant	1997	exon6			CTTTCCATCTTTG	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.606T>C	13.37:g.41517985A>G		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	288	179	0.621528	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Silent	SNP	ENST00000239882.3	37	CCDS9374.1																																																																																			A|0.521;G|0.479	0.479	strong		0.368	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
SPARCL1	8404	hgsc.bcm.edu	37	4	88401616	88401616	+	Silent	SNP	A	A	G	rs9933	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88401616A>G	ENST00000282470.6	-	9	2195	c.1725T>C	c.(1723-1725)gaT>gaC	p.D575D	SPARCL1_ENST00000418378.1_Silent_p.D575D|SPARCL1_ENST00000503414.1_Silent_p.D450D	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	575					signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		TTAAGAGAAGATCAATGGGAT	0.428													G|||	3745	0.747804	0.9017	0.7939	5008	,	,		16227	0.631		0.5964	False		,,,				2504	0.7832				p.D575D		Atlas-SNP	.											.	SPARCL1	59	.	0			c.T1725C						PASS	.	G	,	3754,652	279.0+/-274.6	1597,560,46	127.0	128.0	128.0		1725,1725	2.3	1.0	4	dbSNP_52	128	5234,3366	500.1+/-375.1	1583,2068,649	no	coding-synonymous,coding-synonymous	SPARCL1	NM_001128310.1,NM_004684.4	,	3180,2628,695	GG,GA,AA		39.1395,14.798,30.8934	,	575/665,575/665	88401616	8988,4018	2203	4300	6503	SO:0001819	synonymous_variant	8404	exon9			GAGAAGATCAATG	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1725T>C	4.37:g.88401616A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_004684	B4E2Z0|E7ESU2|Q14800	Silent	SNP	ENST00000282470.6	37	CCDS3622.1																																																																																			G|0.689;C|0.000;A|0.310	0.689	strong		0.428	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
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 GAIIx	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	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	171	41	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	
HLA-C	3107	hgsc.bcm.edu	37	6	31239407	31239407	+	Missense_Mutation	SNP	G	G	T	rs17408553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31239407G>T	ENST00000376228.5	-	2	326	c.312C>A	c.(310-312)aaC>aaA	p.N104K	HLA-C_ENST00000383329.3_Missense_Mutation_p.N104K	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	104	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						AGCCGCGCAGGTTCCGCAGGC	0.716													g|||	1938	0.386981	0.5408	0.3862	5008	,	,		10850	0.1399		0.4115	False		,,,				2504	0.409				p.N104K		Atlas-SNP	.											.	HLA-C	92	.	0			c.C312A						PASS	.	G	LYS/ASN	1618,1404		435,748,328	40.0	41.0	41.0		312	-0.2	0.0	6	dbSNP_123	41	2036,3382		372,1292,1045	no	missense	HLA-C	NM_002117.5	94	807,2040,1373	TT,TG,GG		37.5784,46.4593,43.2938	benign	104/367	31239407	3654,4786	1511	2709	4220	SO:0001583	missense	3107	exon2			GCGCAGGTTCCGC	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.312C>A	6.37:g.31239407G>T	ENSP00000365402:p.Asn104Lys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	175	21	0.12	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	792|792	0.3626373626373626|0.3626373626373626	263|263	0.5345528455284553|0.5345528455284553	141|141	0.38950276243093923|0.38950276243093923	80|80	0.13986013986013987|0.13986013986013987	308|308	0.40633245382585753|0.40633245382585753	N|N	7.072|7.072	0.568503|0.568503	0.13560|0.13560	0.535407|0.535407	0.375784|0.375784	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00686|.	5.85;5.85|.	2.81|2.81	-0.203|-0.203	0.13204|0.13204	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	1.795410|.	0.05622|.	U|.	0.580150|.	T|T	0.33381|0.33381	0.0861|0.0861	M|M	0.76838|0.76838	2.35|2.35	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.21688|.	0.059;0.017;0.017;0.008|.	B;B;B;B|.	0.33890|.	0.172;0.066;0.097;0.045|.	T|T	0.23833|0.23833	-1.0177|-1.0177	9|4	0.37606|.	T|.	0.19|.	.|.	3.4973|3.4973	0.07659|0.07659	0.2649:0.2124:0.5227:0.0|0.2649:0.2124:0.5227:0.0	rs17408553;rs28393247;rs52821555|rs17408553;rs28393247;rs52821555	104;104;104;104|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	K|T	104;104;104;141|104	ENSP00000365402:N104K;ENSP00000372819:N104K|.	ENSP00000365402:N104K|.	N|P	-|-	3|1	2|0	HLA-C|HLA-C	31347386|31347386	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.046000|-0.046000	0.11983|0.11983	-0.060000|-0.060000	0.13132|0.13132	0.305000|0.305000	0.20034|0.20034	AAC|CCT	T|0.398;G|0.602	0.398	strong		0.716	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
RCOR3	55758	hgsc.bcm.edu	37	1	211451467	211451467	+	Silent	SNP	T	T	C	rs11577985	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:211451467T>C	ENST00000367005.4	+	5	492	c.351T>C	c.(349-351)gaT>gaC	p.D117D	RCOR3_ENST00000452621.2_Silent_p.D175D|RCOR3_ENST00000419091.2_Silent_p.D175D|RCOR3_ENST00000367006.4_Silent_p.D175D	NM_018254.3	NP_060724.1	Q9P2K3	RCOR3_HUMAN	REST corepressor 3	117	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D117D(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.00961)|all cancers(67;0.0999)|Epithelial(68;0.171)		AGCTTCCAGATAAGACAATTG	0.299													T|||	870	0.173722	0.3003	0.1643	5008	,	,		17065	0.0655		0.1421	False		,,,				2504	0.1534				p.D175D		Atlas-SNP	.											RCOR3,NS,carcinoma,0,1	RCOR3	51	1	1	Substitution - coding silent(1)	stomach(1)	c.T525C						PASS	.	T	,,,	1198,3208	394.0+/-329.1	179,840,1184	48.0	49.0	49.0		525,525,525,351	4.5	1.0	1	dbSNP_120	49	1268,7332	249.7+/-276.9	98,1072,3130	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RCOR3	NM_001136223.1,NM_001136224.2,NM_001136225.1,NM_018254.3	,,,	277,1912,4314	CC,CT,TT		14.7442,27.1902,18.9605	,,,	175/554,175/437,175/450,117/496	211451467	2466,10540	2203	4300	6503	SO:0001819	synonymous_variant	55758	exon6			TCCAGATAAGACA	AK001738	CCDS31016.1, CCDS44312.1, CCDS44313.1, CCDS44314.1	1q32.3	2008-02-05			ENSG00000117625	ENSG00000117625			25594	protein-coding gene	gene with protein product						10718198	Standard	NM_018254		Approved	FLJ10876	uc010psw.2	Q9P2K3	OTTHUMG00000036996	ENST00000367005.4:c.351T>C	1.37:g.211451467T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_001136223	B3KYA2|B4DYY7|Q5VT47|Q7L9I5|Q8N5U3|Q9NV83	Silent	SNP	ENST00000367005.4	37	CCDS31016.1																																																																																			T|0.830;C|0.170	0.170	strong		0.299	RCOR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089821.1	NM_018254	
SYNGR4	23546	hgsc.bcm.edu	37	19	48869178	48869178	+	Missense_Mutation	SNP	C	C	T	rs919804	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48869178C>T	ENST00000344846.2	+	2	329	c.79C>T	c.(79-81)Cgg>Tgg	p.R27W	TMEM143_ENST00000435956.3_5'Flank|TMEM143_ENST00000377431.2_5'Flank|TMEM143_ENST00000436660.2_5'Flank|TMEM143_ENST00000541566.1_5'Flank|TMEM143_ENST00000293261.3_5'Flank|TMEM143_ENST00000598012.1_5'Flank	NM_012451.3	NP_036583.2	O95473	SNG4_HUMAN	synaptogyrin 4	27	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.		R -> W (in dbSNP:rs919804).			integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(4)|lung(2)|skin(1)	10		all_epithelial(76;5.08e-07)|all_lung(116;5.76e-06)|Lung NSC(112;1.18e-05)|Prostate(7;0.0143)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000138)|all cancers(93;0.00017)|Epithelial(262;0.0138)|GBM - Glioblastoma multiforme(486;0.0146)		GACCATCACGCGGGTCTTCGA	0.622													C|||	260	0.0519169	0.0129	0.0346	5008	,	,		14921	0.1032		0.0527	False		,,,				2504	0.0634				p.R27W		Atlas-SNP	.											.	SYNGR4	31	.	0			c.C79T						PASS	.	C	TRP/ARG	117,4289	87.8+/-126.4	3,111,2089	87.0	86.0	87.0		79	2.5	0.4	19	dbSNP_86	87	383,8217	124.3+/-183.0	14,355,3931	yes	missense	SYNGR4	NM_012451.3	101	17,466,6020	TT,TC,CC		4.4535,2.6555,3.8444	probably-damaging	27/235	48869178	500,12506	2203	4300	6503	SO:0001583	missense	23546	exon2			ATCACGCGGGTCT	AJ011733	CCDS12717.1	19q13.3	2008-07-04				ENSG00000105467			11502	protein-coding gene	gene with protein product		608373					Standard	NM_012451		Approved		uc002piz.3	O95473		ENST00000344846.2:c.79C>T	19.37:g.48869178C>T	ENSP00000344041:p.Arg27Trp	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	34	11	0.323529	NM_012451	Q3KP58	Missense_Mutation	SNP	ENST00000344846.2	37	CCDS12717.1	126	0.057692307692307696	6	0.012195121951219513	19	0.052486187845303865	63	0.11013986013986014	38	0.05013192612137203	C	12.40	1.927319	0.34002	0.026555	0.044535	ENSG00000105467	ENST00000344846	T	0.41758	0.99	4.92	2.52	0.30459	Marvel (1);MARVEL-like domain (1);	0.133905	0.47852	D	0.000209	T	0.03136	0.0092	M	0.88105	2.93	0.24671	P	0.9934132	D	0.89917	1.0	D	0.91635	0.999	T	0.55373	-0.8151	9	0.87932	D	0	-17.8736	12.4776	0.55823	0.5228:0.4771:0.0:0.0	rs919804;rs919804	27	O95473	SNG4_HUMAN	W	27	ENSP00000344041:R27W	ENSP00000344041:R27W	R	+	1	2	SYNGR4	53560990	0.304000	0.24472	0.365000	0.25901	0.006000	0.05464	0.535000	0.23114	0.383000	0.24910	0.505000	0.49811	CGG	C|0.953;T|0.047	0.047	strong		0.622	SYNGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465704.1		
MXRA5	25878	hgsc.bcm.edu	37	X	3240343	3240343	+	Missense_Mutation	SNP	G	G	A	rs1635246	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3240343G>A	ENST00000217939.6	-	5	3537	c.3383C>T	c.(3382-3384)gCa>gTa	p.A1128V		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1128			A -> V (in dbSNP:rs1635246). {ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TGTTGTTGTTGCTGTTGTGGT	0.502													G|||	1964	0.520265	0.447	0.415	3775	,	,		15049	0.2728		0.4602	False		,,,				2504	0.3548				p.A1128V		Atlas-SNP	.											.	MXRA5	815	.	0			c.C3383T						PASS	.	-	VAL/ALA	2239,1596		552,796,339,284,232	107.0	88.0	94.0		3383	-6.3	0.0	X	dbSNP_89	94	3847,2881		796,1188,1067,444,805	yes	missense	MXRA5	NM_015419.3	64	1348,1984,1406,728,1037	AA,AG,A,GG,G		42.821,41.6167,42.3838	benign	1128/2829	3240343	6086,4477	2203	4300	6503	SO:0001583	missense	25878	exon5			GTTGTTGCTGTTG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.3383C>T	X.37:g.3240343G>A	ENSP00000217939:p.Ala1128Val	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	192	190	0.989583	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	878	0.5292344786015672	159	0.4441340782122905	93	0.33214285714285713	105	0.23863636363636365	242	0.4416058394160584	g	9.113	1.007028	0.19199	0.583833	0.57179	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.70399	-0.48	3.61	-6.31	0.02001	.	0.667190	0.12097	N	0.499817	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.39187	-0.9626	9	0.23302	T	0.38	.	3.9428	0.09334	0.1509:0.1155:0.6164:0.1172	rs1635246;rs3764755;rs56693232;rs1635246	1128	Q9NR99	MXRA5_HUMAN	V	1128	ENSP00000217939:A1128V	ENSP00000217939:A1128V	A	-	2	0	MXRA5	3250343	0.005000	0.15991	0.000000	0.03702	0.017000	0.09413	1.488000	0.35551	-1.519000	0.01775	0.519000	0.50382	GCA	G|0.441;A|0.559	0.559	strong		0.502	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
ZNF417	147687	hgsc.bcm.edu	37	19	58420152	58420152	+	Silent	SNP	C	C	A	rs17845779	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58420152C>A	ENST00000312026.5	-	3	1658	c.1494G>T	c.(1492-1494)ggG>ggT	p.G498G	ZNF417_ENST00000595559.1_Silent_p.G497G|CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000536263.1_Silent_p.G299G	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G498G(1)		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)		GAAATGATTTCCCACATTCAT	0.398													A|||	1399	0.279353	0.2761	0.2248	5008	,	,		21369	0.2847		0.2992	False		,,,				2504	0.2965				p.G498G		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - coding silent(1)	stomach(1)	c.G1494T						PASS	.						104.0	85.0	91.0					19																	58420152		2203	4296	6499	SO:0001819	synonymous_variant	147687	exon3			TGATTTCCCACAT	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.1494G>T	19.37:g.58420152C>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	142	48	0.338028	NM_152475	B4DEU1	Silent	SNP	ENST00000312026.5	37	CCDS12965.1																																																																																			C|0.765;A|0.235	0.235	strong		0.398	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
THRAP3	9967	hgsc.bcm.edu	37	1	36752433	36752433	+	Missense_Mutation	SNP	C	C	T	rs6425977	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:36752433C>T	ENST00000354618.5	+	4	826	c.602C>T	c.(601-603)gCc>gTc	p.A201V	THRAP3_ENST00000469141.2_Missense_Mutation_p.A201V	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	201	Ser-rich.		A -> V (in dbSNP:rs6425977). {ECO:0000269|PubMed:10198638, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GGAGATGAGGCCAAGGAGCAG	0.527			T	USP6	aneurysmal bone cysts								C|||	3984	0.795527	0.5197	0.8602	5008	,	,		18229	0.9484		0.8837	False		,,,				2504	0.8742				p.A201V	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3	93	.	0			c.C602T						PASS	.	C	VAL/ALA	2612,1794	633.7+/-396.1	790,1032,381	73.0	78.0	76.0		602	4.8	1.0	1	dbSNP_116	76	7549,1051	765.9+/-407.6	3312,925,63	no	missense	THRAP3	NM_005119.3	64	4102,1957,444	TT,TC,CC		12.2209,40.7172,21.8745	benign	201/956	36752433	10161,2845	2203	4300	6503	SO:0001583	missense	9967	exon4			ATGAGGCCAAGGA	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.602C>T	1.37:g.36752433C>T	ENSP00000346634:p.Ala201Val	Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	115	110	0.956522	NM_005119	D3DPS5|Q5VTK6	Missense_Mutation	SNP	ENST00000354618.5	37	CCDS405.1	1787	0.8182234432234432	261	0.5304878048780488	299	0.8259668508287292	551	0.9632867132867133	676	0.8918205804749341	C	12.40	1.925773	0.34002	0.592828	0.877791	ENSG00000054118	ENST00000354618;ENST00000469141	T;T	0.14022	2.54;2.54	5.72	4.79	0.61399	.	0.545093	0.18767	N	0.131733	T	0.00012	0.0000	N	0.14661	0.345	0.30829	P	0.736969	B	0.24426	0.103	B	0.25140	0.058	T	0.23119	-1.0197	9	0.41790	T	0.15	-0.4152	13.9728	0.64252	0.0:0.8486:0.1514:0.0	rs6425977;rs11545219;rs16837438;rs17844947;rs17857687;rs17858111;rs17859228;rs17859603;rs17859799;rs52829948;rs58522784;rs6425977	201	Q9Y2W1	TR150_HUMAN	V	201	ENSP00000346634:A201V;ENSP00000433825:A201V	ENSP00000346634:A201V	A	+	2	0	THRAP3	36525020	0.024000	0.19004	1.000000	0.80357	0.969000	0.65631	0.946000	0.29069	1.368000	0.46115	0.655000	0.94253	GCC	C|0.211;T|0.789	0.789	strong		0.527	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119	
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 GAIIx	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		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	19	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 GAIIx	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	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	39	20	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	
NLRP13	126204	hgsc.bcm.edu	37	19	56443519	56443519	+	Silent	SNP	C	C	T	rs12610617	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56443519C>T	ENST00000342929.3	-	1	158	c.159G>A	c.(157-159)ccG>ccA	p.P53P	NLRP13_ENST00000588751.1_Silent_p.P53P	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	53	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(58)|ovary(4)|pancreas(2)|prostate(2)|skin(13)|stomach(2)|urinary_tract(1)	109		Colorectal(82;3.48e-05)|Ovarian(87;0.0481)|Renal(1328;0.218)		GBM - Glioblastoma multiforme(193;0.0642)		AGGGGATACGCGGGAAGTGCC	0.552													C|||	497	0.0992412	0.1157	0.0447	5008	,	,		18654	0.2609		0.0109	False		,,,				2504	0.0399				p.P53P		Atlas-SNP	.											NLRP13,colon,carcinoma,-1,1	NLRP13	220	1	0			c.G159A						PASS	.	C		391,4015	193.0+/-218.2	16,359,1828	57.0	60.0	59.0		159	-1.8	0.0	19	dbSNP_120	59	78,8522	43.6+/-101.6	0,78,4222	no	coding-synonymous	NLRP13	NM_176810.2		16,437,6050	TT,TC,CC		0.907,8.8743,3.606		53/1044	56443519	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon1			GATACGCGGGAAG	AY154468	CCDS33119.1	19q13.43	2008-02-05	2006-12-08	2006-12-08	ENSG00000173572	ENSG00000173572		"""Nucleotide-binding domain and leucine rich repeat containing"""	22937	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 13"""	609660	"""NACHT, leucine rich repeat and PYD containing 13"""	NALP13		12563287	Standard	NM_176810		Approved	NOD14, PAN13, CLR19.7	uc010ygg.2	Q86W25	OTTHUMG00000167839	ENST00000342929.3:c.159G>A	19.37:g.56443519C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			C|0.928;T|0.072	0.072	strong		0.552	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
TM4SF20	79853	hgsc.bcm.edu	37	2	228230945	228230945	+	Missense_Mutation	SNP	G	G	A	rs76547437	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:228230945G>A	ENST00000304568.3	-	3	302	c.265C>T	c.(265-267)Ctt>Ttt	p.L89F		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	89				L -> F (in Ref. 1; AAQ89034 and 4; AAH35754). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.L89F(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		ACACTGAAAAGTGATGAAAGA	0.383													G|||	369	0.0736821	0.0076	0.0836	5008	,	,		20917	0.0873		0.1481	False		,,,				2504	0.0654				p.L89F		Atlas-SNP	.											TM4SF20,NS,carcinoma,0,1	TM4SF20	24	1	1	Substitution - Missense(1)	stomach(1)	c.C265T						scavenged	.	G	PHE/LEU	126,4280	93.0+/-131.7	4,118,2081	106.0	103.0	104.0		265	-2.0	0.0	2	dbSNP_131	104	1337,7263	261.3+/-283.8	108,1121,3071	yes	missense	TM4SF20	NM_024795.3	22	112,1239,5152	AA,AG,GG		15.5465,2.8597,11.2487	benign	89/230	228230945	1463,11543	2203	4300	6503	SO:0001583	missense	79853	exon3			TGAAAAGTGATGA	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.265C>T	2.37:g.228230945G>A	ENSP00000303028:p.Leu89Phe	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	CCDS2466.1	219	0.10027472527472528	10	0.02032520325203252	32	0.08839779005524862	71	0.12412587412587413	106	0.13984168865435356	G	5.841	0.339381	0.11069	0.028597	0.155465	ENSG00000168955	ENST00000304568	T	0.41758	0.99	6.03	-1.95	0.07548	.	0.387117	0.24485	N	0.038110	T	0.00109	0.0003	L	0.50333	1.59	0.80722	P	0.0	B	0.18166	0.026	B	0.19946	0.027	T	0.05733	-1.0867	9	0.32370	T	0.25	-7.9097	0.947	0.01368	0.4163:0.1354:0.2617:0.1865	.	89	Q53R12	T4S20_HUMAN	F	89	ENSP00000303028:L89F	ENSP00000303028:L89F	L	-	1	0	TM4SF20	227939189	0.031000	0.19500	0.007000	0.13788	0.135000	0.20990	0.320000	0.19540	0.010000	0.14839	-0.136000	0.14681	CTT	G|0.895;A|0.105	0.105	strong		0.383	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795	
RCN3	57333	hgsc.bcm.edu	37	19	50045916	50045916	+	Silent	SNP	T	T	C	rs34459162	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50045916T>C	ENST00000270645.3	+	6	1233	c.786T>C	c.(784-786)gaT>gaC	p.D262D		NM_020650.2	NP_065701.2	Q96D15	RCN3_HUMAN	reticulocalbin 3, EF-hand calcium binding domain	262	EF-hand 5. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0159)		GGCACCTGGATGGGAGTGAGG	0.662													C|||	535	0.106829	0.2209	0.0749	5008	,	,		14979	0.0258		0.0835	False		,,,				2504	0.0828				p.D262D		Atlas-SNP	.											.	RCN3	28	.	0			c.T786C						PASS	.	C		904,3498		102,700,1399	36.0	35.0	35.0		786	-4.9	0.1	19	dbSNP_126	35	658,7940		23,612,3664	no	coding-synonymous	RCN3	NM_020650.2		125,1312,5063	CC,CT,TT		7.6529,20.5361,12.0154		262/329	50045916	1562,11438	2201	4299	6500	SO:0001819	synonymous_variant	57333	exon6			CCTGGATGGGAGT	AY195859	CCDS12771.1	19q13.33	2013-01-10				ENSG00000142552		"""EF-hand domain containing"""	21145	protein-coding gene	gene with protein product							Standard	NM_020650		Approved	RLP49	uc002poj.3	Q96D15		ENST00000270645.3:c.786T>C	19.37:g.50045916T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_020650	Q9HBZ8	Silent	SNP	ENST00000270645.3	37	CCDS12771.1																																																																																			T|0.891;C|0.109	0.109	strong		0.662	RCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465261.1	NM_020650	
TARM1	441864	hgsc.bcm.edu	37	19	54578105	54578105	+	Missense_Mutation	SNP	C	C	T	rs80087697	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54578105C>T	ENST00000432826.1	-	3	356	c.332G>A	c.(331-333)cGc>cAc	p.R111H	TARM1_ENST00000446034.2_Missense_Mutation_p.R119H	NM_001135686.1	NP_001129158.2	B6A8C7	TARM1_HUMAN	T cell-interacting, activating receptor on myeloid cells 1	111	Ig-like C2-type 1.		R -> H (in dbSNP:rs80087697).			integral component of membrane (GO:0016021)		p.R111H(1)		endometrium(1)|stomach(2)	3						GACGTCACTGCGCTGTGAAAG	0.522													C|||	176	0.0351438	0.0015	0.111	5008	,	,		17416	0.0268		0.0636	False		,,,				2504	0.0061				p.R111H		Atlas-SNP	.											TARM1,NS,carcinoma,0,1	TARM1	10	1	1	Substitution - Missense(1)	stomach(1)	c.G332A						PASS	.						118.0	107.0	111.0					19																	54578105		692	1591	2283	SO:0001583	missense	441864	exon3			TCACTGCGCTGTG		CCDS46173.1	19q13.42	2013-01-29			ENSG00000248385	ENSG00000248385		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	37250	protein-coding gene	gene with protein product							Standard	XM_005258952		Approved		uc010yei.1	B6A8C7		ENST00000432826.1:c.332G>A	19.37:g.54578105C>T	ENSP00000439454:p.Arg111His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_001135686	B4DWY4	Missense_Mutation	SNP	ENST00000432826.1	37	CCDS46173.1	109	0.04990842490842491	2	0.0040650406504065045	37	0.10220994475138122	16	0.027972027972027972	54	0.0712401055408971	C	10.40	1.338388	0.24253	.	.	ENSG00000248385	ENST00000432826;ENST00000446034	T;T	0.00760	5.73;5.73	3.6	-7.2	0.01495	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.17278	0.47	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44667	-0.9313	8	0.33141	T	0.24	.	1.5596	0.02592	0.1733:0.3006:0.3151:0.2109	.	111	B6A8C7	TARM1_HUMAN	H	111;119	ENSP00000439454:R111H;ENSP00000441055:R119H	ENSP00000439454:R111H	R	-	2	0	TARM1	59269917	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.655000	0.01982	-1.385000	0.02101	-1.061000	0.02294	CGC	C|0.950;T|0.050	0.050	strong		0.522	TARM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465679.1	NM_001135686	
BTBD10	84280	hgsc.bcm.edu	37	11	13443250	13443250	+	Silent	SNP	C	C	T	rs3789325	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:13443250C>T	ENST00000278174.5	-	3	482	c.237G>A	c.(235-237)acG>acA	p.T79T	BTBD10_ENST00000530907.1_Silent_p.T87T|BTBD10_ENST00000532261.1_5'UTR|BTBD10_ENST00000528120.1_Silent_p.T31T	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	79						nucleus (GO:0005634)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		GCTGAGACTCCGTTCTTTCAT	0.418													T|||	702	0.140176	0.0545	0.2997	5008	,	,		18962	0.1687		0.1481	False		,,,				2504	0.1053				p.T79T		Atlas-SNP	.											.	BTBD10	43	.	0			c.G237A						PASS	.	T		292,4108	799.4+/-415.5	16,260,1924	152.0	125.0	134.0		237	3.8	1.0	11	dbSNP_107	134	1492,7096	747.9+/-407.3	117,1258,2919	no	coding-synonymous	BTBD10	NM_032320.5		133,1518,4843	TT,TC,CC		17.3731,6.6364,13.7358		79/476	13443250	1784,11204	2200	4294	6494	SO:0001819	synonymous_variant	84280	exon3			AGACTCCGTTCTT	AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"""BTB/POZ domain containing"""	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.237G>A	11.37:g.13443250C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	NM_032320	B7Z228|Q86WG1	Silent	SNP	ENST00000278174.5	37	CCDS7811.1																																																																																			C|0.866;T|0.134	0.134	strong		0.418	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
ANKRD17	26057	hgsc.bcm.edu	37	4	73956736	73956736	+	Silent	SNP	G	G	A	rs6855349	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:73956736G>A	ENST00000358602.4	-	29	6725	c.6609C>T	c.(6607-6609)ctC>ctT	p.L2203L	ANKRD17_ENST00000330838.6_Silent_p.L1952L|ANKRD17_ENST00000509867.2_Silent_p.L2090L	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2203					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GATTGACACTGAGGACTGCAA	0.458													G|||	1762	0.351837	0.2375	0.2968	5008	,	,		20331	0.3849		0.4483	False		,,,				2504	0.4121				p.L2203L		Atlas-SNP	.											.	ANKRD17	214	.	0			c.C6609T						PASS	.	G	,	1217,3189	422.5+/-339.8	185,847,1171	134.0	141.0	139.0		6609,5856	3.7	1.0	4	dbSNP_116	139	3585,5015	519.3+/-379.4	736,2113,1451	no	coding-synonymous,coding-synonymous	ANKRD17	NM_032217.3,NM_198889.1	,	921,2960,2622	AA,AG,GG		41.686,27.6214,36.9214	,	2203/2604,1952/2353	73956736	4802,8204	2203	4300	6503	SO:0001819	synonymous_variant	26057	exon29			GACACTGAGGACT	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.6609C>T	4.37:g.73956736G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	130	64	0.492308	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																			G|0.639;A|0.361	0.361	strong		0.458	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
ZRANB2	9406	hgsc.bcm.edu	37	1	71536574	71536574	+	Missense_Mutation	SNP	G	G	C	rs11583800	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:71536574G>C	ENST00000370920.3	-	7	920	c.619C>G	c.(619-621)Cga>Gga	p.R207G	ZRANB2_ENST00000254821.6_Missense_Mutation_p.R207G	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	207	Arg/Ser-rich.|Required for nuclear targeting.		R -> G (in dbSNP:rs11583800). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6}.		mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						TGTGAAGATCGAGACTTTGAG	0.423													G|||	231	0.0461262	0.0098	0.0663	5008	,	,		13730	0.003		0.1203	False		,,,				2504	0.0491				p.R207G		Atlas-SNP	.											.	ZRANB2	75	.	0			c.C619G						PASS	.	G	GLY/ARG,GLY/ARG	74,4332	65.3+/-102.7	0,74,2129	279.0	258.0	265.0		619,619	6.1	1.0	1	dbSNP_120	265	886,7714	198.7+/-243.0	41,804,3455	yes	missense,missense	ZRANB2	NM_005455.4,NM_203350.2	125,125	41,878,5584	CC,CG,GG		10.3023,1.6795,7.3812	probably-damaging,probably-damaging	207/321,207/331	71536574	960,12046	2203	4300	6503	SO:0001583	missense	9406	exon7			AAGATCGAGACTT	AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"""Zinc fingers, RAN-binding domain containing"""	13058	protein-coding gene	gene with protein product		604347	"""zinc finger protein 265"""	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.619C>G	1.37:g.71536574G>C	ENSP00000359958:p.Arg207Gly	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	55	16	0.290909	NM_203350	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Missense_Mutation	SNP	ENST00000370920.3	37	CCDS659.1	126	0.057692307692307696	6	0.012195121951219513	28	0.07734806629834254	2	0.0034965034965034965	90	0.11873350923482849	G	14.27	2.484245	0.44147	0.016795	0.103023	ENSG00000132485	ENST00000370920;ENST00000254821	T;T	0.65549	-0.16;-0.14	6.06	6.06	0.98353	.	0.179999	0.50627	D	0.000109	T	0.63283	0.2498	L	0.27053	0.805	0.09310	P	0.99999692137	D;D	0.63046	0.962;0.992	D;D	0.70487	0.931;0.969	T	0.57452	-0.7809	9	0.29301	T	0.29	.	20.6397	0.99537	0.0:0.0:1.0:0.0	rs11583800;rs17846263;rs17859285;rs52834710;rs11583800	207;207	O95218;O95218-2	ZRAB2_HUMAN;.	G	207	ENSP00000359958:R207G;ENSP00000254821:R207G	ENSP00000254821:R207G	R	-	1	2	ZRANB2	71309162	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.778000	0.75043	2.880000	0.98712	0.650000	0.86243	CGA	G|0.937;C|0.063	0.063	strong		0.423	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350	
SMOC1	64093	hgsc.bcm.edu	37	14	70477508	70477508	+	Silent	SNP	C	C	T	rs3825739	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:70477508C>T	ENST00000381280.4	+	8	955	c.702C>T	c.(700-702)gcC>gcT	p.A234A	SMOC1_ENST00000361956.3_Silent_p.A234A	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	234	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GGCAGAGTGCCCTGGAAGAGG	0.537													C|||	1030	0.205671	0.0061	0.3213	5008	,	,		19744	0.4196		0.173	False		,,,				2504	0.2065				p.A234A		Atlas-SNP	.											SMOC1,colon,carcinoma,+1,1	SMOC1	61	1	0			c.C702T						PASS	.	C	,	212,4194	131.0+/-167.6	10,192,2001	111.0	118.0	116.0		702,702	4.6	1.0	14	dbSNP_107	116	1567,7033	295.1+/-302.2	143,1281,2876	no	coding-synonymous,coding-synonymous	SMOC1	NM_001034852.2,NM_022137.5	,	153,1473,4877	TT,TC,CC		18.2209,4.8116,13.6783	,	234/436,234/435	70477508	1779,11227	2203	4300	6503	SO:0001819	synonymous_variant	64093	exon8			GAGTGCCCTGGAA	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.702C>T	14.37:g.70477508C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001034852	A8K1S3|B2R7P5|Q96F78	Silent	SNP	ENST00000381280.4	37	CCDS9798.1																																																																																			C|0.825;T|0.175	0.175	strong		0.537	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1		
MAPT	4137	hgsc.bcm.edu	37	17	44060775	44060775	+	Missense_Mutation	SNP	C	C	T	rs63750417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44060775C>T	ENST00000571987.1	+	5	605	c.605C>T	c.(604-606)cCg>cTg	p.P202L	MAPT_ENST00000334239.8_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.P202L|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.P202L|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.P202L|MAPT_ENST00000574436.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	202					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	GAGGGGCCGCCGCTGAAGGGG	0.677													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		15400	0.001		0.2406	False		,,,				2504	0.0613				p.P202L		Atlas-SNP	.											.	MAPT	135	.	0			c.C605T						PASS	.	C	LEU/PRO,,,,,,LEU/PRO,	220,4094		7,206,1944	19.0	16.0	17.0		605,,,,,,605,	-0.9	0.0	17	dbSNP_130	17	1886,6602		231,1424,2589	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	98,,,,,,98,	238,1630,4533	TT,TC,CC		22.2196,5.0997,16.4506	probably-damaging,,,,,,probably-damaging,	202/777,,,,,,202/759,	44060775	2106,10696	2157	4244	6401	SO:0001583	missense	4137	exon6			GGCCGCCGCTGAA	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.605C>T	17.37:g.44060775C>T	ENSP00000458742:p.Pro202Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	15.24	2.774625	0.49786	0.050997	0.222196	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.12255	2.71;2.7;2.71	5.05	-0.928	0.10448	.	0.827349	0.10194	N	0.704208	T	0.00012	0.0000	L	0.59436	1.845	0.58432	P	1.0000000000287557E-6	D;D	0.71674	0.996;0.998	P;P	0.55871	0.786;0.688	T	0.24048	-1.0171	9	0.87932	D	0	0.2179	3.6703	0.08272	0.1676:0.4266:0.0:0.4058	rs63750417	202;202	P10636-9;P10636	.;TAU_HUMAN	L	202	ENSP00000340820:P202L;ENSP00000262410:P202L;ENSP00000410838:P202L	ENSP00000262410:P202L	P	+	2	0	MAPT	41416612	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.208000	0.17415	-0.048000	0.13401	-0.367000	0.07326	CCG	C|0.552;A|0.040	.	strong		0.677	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
NBPF3	84224	hgsc.bcm.edu	37	1	21795388	21795388	+	Missense_Mutation	SNP	A	A	G	rs1827293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:21795388A>G	ENST00000318249.5	+	3	691	c.341A>G	c.(340-342)tAc>tGc	p.Y114C	NBPF3_ENST00000342104.5_Missense_Mutation_p.Y114C|NBPF3_ENST00000318220.6_Missense_Mutation_p.Y58C|NBPF3_ENST00000454000.2_Intron	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	114			Y -> C (in dbSNP:rs1827293). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CAAAATAATTACGGTAAGTTC	0.448											OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	2123	0.423922	0.1445	0.4755	5008	,	,		19838	0.5804		0.5417	False		,,,				2504	0.4826				p.A114G		Atlas-SNP	.											NBPF3,NS,carcinoma,0,1	NBPF3	55	1	0			c.C341G						scavenged	.	A	CYS/TYR	970,3436		104,762,1337	48.0	53.0	51.0		341	-2.2	0.0	1	dbSNP_92	51	4756,3844		1332,2092,876	yes	missense	NBPF3	NM_032264.2	194	1436,2854,2213	GG,GA,AA		44.6977,22.0154,44.0258	probably-damaging	114/634	21795388	5726,7280	2203	4300	6503	SO:0001583	missense	84224	exon3			ATAATTACGGTAA	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.341A>G	1.37:g.21795388A>G	ENSP00000316782:p.Tyr114Cys	Somatic	105	1	0.00952381	751	WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Missense_Mutation	SNP	ENST00000318249.5	37	CCDS216.1	999	0.4574175824175824	88	0.17886178861788618	187	0.5165745856353591	318	0.5559440559440559	406	0.5356200527704486	.	10.34	1.323132	0.24080	0.220154	0.553023	ENSG00000142794	ENST00000318220;ENST00000318249;ENST00000417552;ENST00000342104;ENST00000434838	T;T;T;T	0.04970	3.69;3.52;3.55;3.69	1.08	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	M	0.72353	2.195	0.80722	P	0.0	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.979	T	0.48547	-0.9026	8	0.87932	D	0	.	1.9892	0.03442	0.3991:0.302:0.0:0.2989	rs1827293;rs3738102;rs17420230;rs17856707;rs52824093;rs58179675;rs1827293	114;114	Q9H094-3;Q9H094	.;NBPF3_HUMAN	C	58;114;58;114;58	ENSP00000316739:Y58C;ENSP00000316782:Y114C;ENSP00000340336:Y114C;ENSP00000391865:Y58C	ENSP00000316739:Y58C	Y	+	2	0	NBPF3	21667975	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	-0.056000	0.11787	-0.776000	0.04578	0.327000	0.21459	TAC	A|0.554;G|0.446	0.446	strong		0.448	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
C3orf18	51161	hgsc.bcm.edu	37	3	50598396	50598396	+	Silent	SNP	G	G	A	rs41291736	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:50598396G>A	ENST00000357203.3	-	5	899	c.360C>T	c.(358-360)gaC>gaT	p.D120D	C3orf18_ENST00000426034.1_Silent_p.D120D|C3orf18_ENST00000486175.1_5'UTR|C3orf18_ENST00000441239.1_Silent_p.D100D|C3orf18_ENST00000449241.1_Silent_p.D120D|C3orf18_ENST00000422619.1_Silent_p.D68D	NM_016210.4	NP_057294.2	Q9UK00	CC018_HUMAN	chromosome 3 open reading frame 18	120						integral component of membrane (GO:0016021)				lung(1)|pancreas(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)		CAGAGGCGGCGTCCCGCCCAT	0.632													G|||	280	0.0559105	0.0242	0.0937	5008	,	,		18530	0.0		0.1243	False		,,,				2504	0.0593				p.D120D		Atlas-SNP	.											.	C3orf18	12	.	0			c.C360T						PASS	.	G	,,,	179,4227	115.9+/-153.8	2,175,2026	95.0	83.0	87.0		360,360,300,360	-4.8	0.1	3	dbSNP_127	87	1140,7460	234.9+/-267.6	68,1004,3228	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C3orf18	NM_001171740.2,NM_001171741.2,NM_001171743.2,NM_016210.4	,,,	70,1179,5254	AA,AG,GG		13.2558,4.0626,10.1415	,,,	120/163,120/163,100/143,120/163	50598396	1319,11687	2203	4300	6503	SO:0001819	synonymous_variant	51161	exon5			GGCGGCGTCCCGC	AF188706	CCDS2829.1, CCDS54589.1	3p21.3	2006-01-11			ENSG00000088543	ENSG00000088543			24837	protein-coding gene	gene with protein product						12477932	Standard	NM_016210		Approved	G20	uc010hlp.3	Q9UK00	OTTHUMG00000156854	ENST00000357203.3:c.360C>T	3.37:g.50598396G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_016210	C9JNP0	Silent	SNP	ENST00000357203.3	37	CCDS2829.1																																																																																			G|0.908;A|0.092	0.092	strong		0.632	C3orf18-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346260.2	NM_016210	
ZFAND4	93550	hgsc.bcm.edu	37	10	46143958	46143958	+	Missense_Mutation	SNP	T	T	G	rs17854567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:46143958T>G	ENST00000344646.5	-	5	568	c.353A>C	c.(352-354)aAg>aCg	p.K118T	ZFAND4_ENST00000374366.3_Missense_Mutation_p.K44T|ZFAND4_ENST00000374370.1_5'UTR|ZFAND4_ENST00000374371.2_Missense_Mutation_p.K118T	NM_001128324.2|NM_174890.2	NP_001121796.1|NP_777550.2	Q86XD8	ZFAN4_HUMAN	zinc finger, AN1-type domain 4	118			K -> T (in dbSNP:rs17854567). {ECO:0000269|PubMed:14702039}.				zinc ion binding (GO:0008270)										CTCTGCCATCTTCCTAAGTGG	0.393													T|||	495	0.0988419	0.0068	0.2205	5008	,	,		18196	0.0317		0.1521	False		,,,				2504	0.1513				p.K118T		Atlas-SNP	.											.	.	.	.	0			c.A353C						PASS	.	T	THR/LYS,THR/LYS	133,4273	95.3+/-134.0	4,125,2074	101.0	97.0	98.0		353,353	5.8	1.0	10	dbSNP_123	98	1094,7506	228.0+/-263.2	69,956,3275	yes	missense,missense	ANUBL1	NM_001128324.1,NM_174890.2	78,78	73,1081,5349	GG,GT,TT		12.7209,3.0186,9.4341	benign,benign	118/728,118/728	46143958	1227,11779	2203	4300	6503	SO:0001583	missense	93550	exon5			GCCATCTTCCTAA	AF311324	CCDS7214.1, CCDS60520.1	10q11.22	2013-01-09	2011-11-10	2011-11-10	ENSG00000172671	ENSG00000172671		"""Zinc fingers, AN1-type domain containing"""	23504	protein-coding gene	gene with protein product			"""AN1, ubiquitin-like, homolog (Xenopus laevis)"""	ANUBL1			Standard	XM_005271837		Approved	FLJ40185	uc001jcp.4	Q86XD8	OTTHUMG00000018085	ENST00000344646.5:c.353A>C	10.37:g.46143958T>G	ENSP00000339484:p.Lys118Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_001128324	A8K8V4|B2RAX2|Q5VVY5	Missense_Mutation	SNP	ENST00000344646.5	37	CCDS7214.1	201	0.09203296703296704	6	0.012195121951219513	67	0.1850828729281768	14	0.024475524475524476	114	0.1503957783641161	T	16.40	3.113419	0.56398	0.030186	0.127209	ENSG00000172671	ENST00000344646;ENST00000374371;ENST00000374366;ENST00000374376	T;T;T	0.46819	1.91;0.86;1.96	5.78	5.78	0.91487	.	2.856830	0.01859	N	0.036460	T	0.00073	0.0002	N	0.14661	0.345	0.29438	P	0.859326	B;B	0.23937	0.002;0.094	B;B	0.15870	0.001;0.014	T	0.04065	-1.0980	9	0.87932	D	0	-18.3348	14.0663	0.64831	0.0:0.0:0.0:1.0	rs17854567;rs17854567	118;118	Q5VVY4;Q86XD8	.;ANUB1_HUMAN	T	118;118;44;118	ENSP00000339484:K118T;ENSP00000363491:K118T;ENSP00000363486:K44T	ENSP00000339484:K118T	K	-	2	0	ANUBL1	45463964	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	4.665000	0.61547	2.198000	0.70561	0.477000	0.44152	AAG	T|0.909;G|0.091	0.091	strong		0.393	ZFAND4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047790.1	NM_174890	
PEAR1	375033	hgsc.bcm.edu	37	1	156883493	156883493	+	Missense_Mutation	SNP	G	G	A	rs11264581	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156883493G>A	ENST00000338302.3	+	22	2879	c.2654G>A	c.(2653-2655)cGc>cAc	p.R885H	PEAR1_ENST00000292357.7_Missense_Mutation_p.R885H			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	885	Pro-rich.		R -> H (in dbSNP:rs11264581).		recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GGGAGCAGCCGCCTGGACCGA	0.612													G|||	1161	0.231829	0.0469	0.2954	5008	,	,		16121	0.4732		0.1759	False		,,,				2504	0.2454				p.R885H		Atlas-SNP	.											.	PEAR1	118	.	0			c.G2654A						PASS	.	G	HIS/ARG	293,4113	159.6+/-192.1	7,279,1917	37.0	38.0	38.0		2654	-3.7	0.7	1	dbSNP_120	38	1577,7023	291.1+/-300.1	149,1279,2872	yes	missense	PEAR1	NM_001080471.1	29	156,1558,4789	AA,AG,GG		18.3372,6.65,14.378	benign	885/1038	156883493	1870,11136	2203	4300	6503	SO:0001583	missense	375033	exon21			GCAGCCGCCTGGA	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.2654G>A	1.37:g.156883493G>A	ENSP00000344465:p.Arg885His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	488	0.22344322344322345	26	0.052845528455284556	79	0.21823204419889503	251	0.4388111888111888	132	0.1741424802110818	G	13.25	2.182510	0.38511	0.0665	0.183372	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.88975	-2.45;-2.45	5.78	-3.72	0.04411	.	0.543959	0.15501	N	0.259052	T	0.45975	0.1369	N	0.03608	-0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.28396	-1.0045	9	0.15066	T	0.55	.	5.0929	0.14718	0.2315:0.0:0.3078:0.4608	rs11264581;rs59112747;rs11264581	885	Q5VY43	PEAR1_HUMAN	H	885	ENSP00000344465:R885H;ENSP00000292357:R885H	ENSP00000292357:R885H	R	+	2	0	PEAR1	155150117	0.000000	0.05858	0.737000	0.30932	0.740000	0.42216	-0.451000	0.06795	-0.439000	0.07222	0.563000	0.77884	CGC	G|0.832;A|0.168	0.168	strong		0.612	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
NOC3L	64318	hgsc.bcm.edu	37	10	96114835	96114835	+	Missense_Mutation	SNP	G	G	A	rs12572897	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96114835G>A	ENST00000371361.3	-	6	681	c.581C>T	c.(580-582)cCt>cTt	p.P194L	NOC3L_ENST00000543788.1_5'Flank|NOC3L_ENST00000371350.1_Missense_Mutation_p.P194L|NOC3L_ENST00000463649.1_5'UTR	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	194			P -> L (in dbSNP:rs12572897).		fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				CTCTTGAATAGGATCTTCAAT	0.323													G|||	1032	0.20607	0.1649	0.0908	5008	,	,		17156	0.2917		0.1213	False		,,,				2504	0.3425				p.P194L		Atlas-SNP	.											.	NOC3L	67	.	0			c.C581T						PASS	.	G	LEU/PRO	718,3686	293.6+/-282.7	63,592,1547	154.0	158.0	157.0		581	4.0	0.1	10	dbSNP_120	157	1041,7557	218.7+/-257.0	65,911,3323	yes	missense	NOC3L	NM_022451.9	98	128,1503,4870	AA,AG,GG		12.1075,16.3034,13.5287	benign	194/801	96114835	1759,11243	2202	4299	6501	SO:0001583	missense	64318	exon6			TGAATAGGATCTT	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"""chromosome 10 open reading frame 117"""	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.581C>T	10.37:g.96114835G>A	ENSP00000360412:p.Pro194Leu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	106	53	0.5	NM_022451	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	399	0.18269230769230768	89	0.18089430894308944	38	0.10497237569060773	181	0.31643356643356646	91	0.12005277044854881	G	11.91	1.779336	0.31502	0.163034	0.121075	ENSG00000173145	ENST00000371361;ENST00000371350	T;T	0.13307	2.6;2.6	5.86	4.02	0.46733	.	0.233884	0.43260	D	0.000584	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.99999465797	B	0.06786	0.001	B	0.06405	0.002	T	0.48547	-0.9026	9	0.30078	T	0.28	-0.03	12.0319	0.53401	0.1383:0.0:0.8617:0.0	rs12572897;rs52833406;rs60029470;rs12572897	194	Q8WTT2	NOC3L_HUMAN	L	194	ENSP00000360412:P194L;ENSP00000360401:P194L	ENSP00000360401:P194L	P	-	2	0	NOC3L	96104825	1.000000	0.71417	0.142000	0.22268	0.601000	0.36947	4.602000	0.61098	1.490000	0.48466	0.655000	0.94253	CCT	G|0.847;A|0.153	0.153	strong		0.323	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	
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 GAIIx	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	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	61	32	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		
GAS2	2620	hgsc.bcm.edu	37	11	22696451	22696451	+	Silent	SNP	A	A	G	rs922571	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:22696451A>G	ENST00000454584.2	+	2	341	c.36A>G	c.(34-36)ggA>ggG	p.G12G	GAS2_ENST00000278187.3_Silent_p.G12G|GAS2_ENST00000433790.1_Silent_p.G12G|GAS2_ENST00000533092.1_3'UTR	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	12					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|regulation of cell shape (GO:0008360)	actin filament (GO:0005884)|cytosol (GO:0005829)|membrane (GO:0016020)		p.G12G(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(4)|stomach(1)	24						TACGCAGTGGACCTGGCCTCT	0.428													A|||	2625	0.524161	0.1747	0.6095	5008	,	,		18535	0.749		0.67	False		,,,				2504	0.5542				p.G12G		Atlas-SNP	.											GAS2,NS,carcinoma,0,1	GAS2	46	1	1	Substitution - coding silent(1)	stomach(1)	c.A36G						scavenged	.	A	,,	1132,3274	401.0+/-331.8	144,844,1215	98.0	93.0	95.0		36,36,36	0.2	1.0	11	dbSNP_86	95	5943,2657	685.3+/-404.0	2048,1847,405	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS2	NM_001143830.1,NM_005256.3,NM_177553.2	,,	2192,2691,1620	GG,GA,AA		30.8953,25.6922,45.602	,,	12/314,12/314,12/314	22696451	7075,5931	2203	4300	6503	SO:0001819	synonymous_variant	2620	exon2			CAGTGGACCTGGC	BC040470	CCDS7858.1	11p14.3	2005-10-11			ENSG00000148935	ENSG00000148935			4167	protein-coding gene	gene with protein product		602835				9521882	Standard	NM_005256		Approved		uc001mqo.3	O43903	OTTHUMG00000166071	ENST00000454584.2:c.36A>G	11.37:g.22696451A>G		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_177553	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Silent	SNP	ENST00000454584.2	37	CCDS7858.1																																																																																			A|0.457;G|0.543	0.543	strong		0.428	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553	
BOD1	91272	hgsc.bcm.edu	37	5	173036394	173036394	+	Missense_Mutation	SNP	C	C	T	rs72822197	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:173036394C>T	ENST00000311086.4	-	3	629	c.406G>A	c.(406-408)Gtg>Atg	p.V136M	BOD1_ENST00000480951.1_Intron|BOD1_ENST00000471339.1_5'Flank|BOD1_ENST00000285908.5_Intron	NM_138369.2	NP_612378.1	Q96IK1	BOD1_HUMAN	biorientation of chromosomes in cell division 1	136					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|kinetochore (GO:0000776)				endometrium(1)|large_intestine(2)|lung(2)|ovary(2)	7						GGATCCACCACCTGAGAAATA	0.468																																					p.V136M		Atlas-SNP	.											.	BOD1	15	.	0			c.G406A						PASS	.						150.0	136.0	141.0					5																	173036394		2203	4300	6503	SO:0001583	missense	91272	exon3			CCACCACCTGAGA	AY303777	CCDS4389.1, CCDS54951.1	5q35.2	2013-10-11	2009-03-04	2009-03-04	ENSG00000145919	ENSG00000145919			25114	protein-coding gene	gene with protein product	"""biorientation defective 1"""		"""family with sequence similarity 44, member B"""	FAM44B		17938248	Standard	NM_138369		Approved		uc003mcq.2	Q96IK1	OTTHUMG00000130540	ENST00000311086.4:c.406G>A	5.37:g.173036394C>T	ENSP00000309644:p.Val136Met	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	216	33	0.152778	NM_138369	B4DXH8|Q9BTW1	Missense_Mutation	SNP	ENST00000311086.4	37	CCDS4389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.1|27.1	4.803392|4.803392	0.90623|0.90623	.|.	.|.	ENSG00000145919|ENSG00000145919	ENST00000477985|ENST00000311086;ENST00000462674	.|.	.|.	.|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71367|0.71367	0.3331|0.3331	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	.|P	.|0.46987	.|0.888	.|P	.|0.46825	.|0.528	T|T	0.75470|0.75470	-0.3306|-0.3306	5|9	.|0.72032	.|D	.|0.01	-25.5605|-25.5605	19.7198|19.7198	0.96137|0.96137	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|136	.|Q96IK1	.|BOD1_HUMAN	D|M	68|136;31	.|.	.|ENSP00000309644:V136M	G|V	-|-	2|1	0|0	BOD1|BOD1	172969000|172969000	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.474000|7.474000	0.81024|0.81024	2.668000|2.668000	0.90789|0.90789	0.655000|0.655000	0.94253|0.94253	GGT|GTG	C|0.946;T|0.054	0.054	strong		0.468	BOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252963.1	NM_138369	
MACF1	23499	hgsc.bcm.edu	37	1	39838174	39838174	+	Silent	SNP	T	T	C	rs80197726	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:39838174T>C	ENST00000372915.3	+	51	13221	c.13134T>C	c.(13132-13134)agT>agC	p.S4378S	MACF1_ENST00000539005.1_Silent_p.S2311S|MACF1_ENST00000567887.1_Silent_p.S4410S|MACF1_ENST00000361689.2_Silent_p.S2311S|MACF1_ENST00000317713.7_Silent_p.S2311S|MACF1_ENST00000289893.4_Silent_p.S2813S|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000564288.1_Silent_p.S4373S|MACF1_ENST00000545844.1_Silent_p.S2311S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4378					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACTGGGCAAGTAAGGGAACTC	0.403													T|||	288	0.057508	0.1127	0.0375	5008	,	,		17162	0.0		0.0378	False		,,,				2504	0.0767				p.S2311S		Atlas-SNP	.											.	MACF1	909	.	0			c.T6933C						PASS	.	T	,	452,3954	214.8+/-234.0	16,420,1767	76.0	76.0	76.0		6933,8439	3.4	1.0	1	dbSNP_132	76	321,8279	114.4+/-174.4	7,307,3986	no	coding-synonymous,coding-synonymous	MACF1	NM_012090.4,NM_033044.3	,	23,727,5753	CC,CT,TT		3.7326,10.2587,5.9434	,	2311/5431,2813/5939	39838174	773,12233	2203	4300	6503	SO:0001819	synonymous_variant	23499	exon48			GGCAAGTAAGGGA	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.13134T>C	1.37:g.39838174T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	159	98	0.616352	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37		98	0.04487179487179487	57	0.11585365853658537	15	0.04143646408839779	0	0.0	26	0.03430079155672823	T	10.19	1.282607	0.23392	0.102587	0.037326	ENSG00000127603	ENST00000372925	.	.	.	5.87	3.38	0.38709	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999999320644	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2318	0.31603	0.1158:0.0:0.4627:0.4215	.	.	.	.	Q	1445	.	.	X	+	1	0	MACF1	39610761	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	0.558000	0.23469	1.025000	0.39708	0.529000	0.55759	TAA	T|0.945;C|0.055	0.055	strong		0.403	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
CHD1L	9557	hgsc.bcm.edu	37	1	146766122	146766122	+	Silent	SNP	C	C	G	rs45563244	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:146766122C>G	ENST00000369258.4	+	22	2558	c.2538C>G	c.(2536-2538)gcC>gcG	p.A846A	CHD1L_ENST00000369259.3_Silent_p.A642A|CHD1L_ENST00000361293.5_Silent_p.A565A|CHD1L_ENST00000431239.1_Silent_p.A752A|CHD1L_ENST00000467213.1_3'UTR	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	846	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					TTGGACATGCCACGAAAGGTT	0.398													C|||	44	0.00878594	0.0015	0.0115	5008	,	,		19433	0.0		0.0288	False		,,,				2504	0.0051				p.A846A		Atlas-SNP	.											.	CHD1L	72	.	0			c.C2538G						PASS	.	C		28,4378	34.3+/-65.2	0,28,2175	252.0	223.0	233.0		2538	-0.1	1.0	1	dbSNP_127	233	250,8350	99.3+/-160.8	5,240,4055	no	coding-synonymous	CHD1L	NM_004284.3		5,268,6230	GG,GC,CC		2.907,0.6355,2.1375		846/898	146766122	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	9557	exon22			ACATGCCACGAAA	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.2538C>G	1.37:g.146766122C>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Silent	SNP	ENST00000369258.4	37	CCDS927.1																																																																																			C|0.980;G|0.020	0.020	strong		0.398	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	
CDH3	1001	hgsc.bcm.edu	37	16	68719113	68719113	+	Missense_Mutation	SNP	G	G	A	rs34494880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:68719113G>A	ENST00000264012.4	+	11	1974	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H	CDH3_ENST00000581171.1_Missense_Mutation_p.R422H|CDH3_ENST00000429102.2_Missense_Mutation_p.R477H	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	477	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> H (in dbSNP:rs34494880).		adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TCCAGCTACCGCATCCTGAGA	0.542													G|||	130	0.0259585	0.0023	0.0173	5008	,	,		20212	0.0		0.0596	False		,,,				2504	0.0562				p.R477H		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G1430A						PASS	.	G	HIS/ARG	65,4331	61.1+/-98.1	0,65,2133	80.0	70.0	73.0		1430	0.6	1.0	16	dbSNP_126	73	645,7955	166.1+/-218.1	26,593,3681	yes	missense	CDH3	NM_001793.4	29	26,658,5814	AA,AG,GG		7.5,1.4786,5.4632	benign	477/830	68719113	710,12286	2198	4300	6498	SO:0001583	missense	1001	exon11			GCTACCGCATCCT	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1430G>A	16.37:g.68719113G>A	ENSP00000264012:p.Arg477His	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	40	38	0.95	NM_001793	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	37	CCDS10868.1	63	0.028846153846153848	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	55	0.07255936675461741	G	11.26	1.584836	0.28268	0.014786	0.075	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.53640	0.61;0.61	5.58	0.567	0.17325	Cadherin (4);Cadherin-like (1);	0.911629	0.09141	N	0.842988	T	0.02193	0.0068	L	0.28014	0.82	0.24544	N	0.994051	B	0.13145	0.007	B	0.12837	0.008	T	0.13548	-1.0505	10	0.35671	T	0.21	.	0.9118	0.01296	0.4382:0.1566:0.2544:0.1508	rs34494880	477	P22223	CADH3_HUMAN	H	477;477;422	ENSP00000398485:R477H;ENSP00000264012:R477H	ENSP00000264012:R477H	R	+	2	0	CDH3	67276614	0.000000	0.05858	0.999000	0.59377	0.725000	0.41563	-0.843000	0.04350	0.072000	0.16694	-0.672000	0.03802	CGC	G|0.953;A|0.047	0.047	strong		0.542	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
IGSF9B	22997	hgsc.bcm.edu	37	11	133815981	133815981	+	Silent	SNP	C	C	G	rs10894768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:133815981C>G	ENST00000321016.8	-	2	467	c.237G>C	c.(235-237)ccG>ccC	p.P79P	IGSF9B_ENST00000533871.2_Silent_p.P79P			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	79	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCACGTGCGGCGGGTAGTAGC	0.617													G|||	1776	0.354633	0.3011	0.438	5008	,	,		16482	0.5208		0.2992	False		,,,				2504	0.2536				p.P79P		Atlas-SNP	.											.	IGSF9B	290	.	0			c.G237C						PASS	.	G		1154,3082		154,846,1118	48.0	59.0	55.0		237	-11.4	0.0	11	dbSNP_120	55	2510,5934		370,1770,2082	no	coding-synonymous	IGSF9B	NM_014987.1		524,2616,3200	GG,GC,CC		29.7252,27.2427,28.8959		79/1350	133815981	3664,9016	2118	4222	6340	SO:0001819	synonymous_variant	22997	exon2			GTGCGGCGGGTAG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.237G>C	11.37:g.133815981C>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	156	25	0.160256	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				C|0.633;G|0.367	0.367	strong		0.617	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
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 GAIIx	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_ENST00000374500.5_Missense_Mutation_p.R184H|CUTA_ENST00000607266.1_Missense_Mutation_p.R142H|CUTA_ENST00000492510.1_5'Flank|CUTA_ENST00000374496.3_Missense_Mutation_p.R142H|CUTA_ENST00000440279.3_Missense_Mutation_p.R142H|CUTA_ENST00000494751.1_Intron|CUTA_ENST00000488478.1_Silent_p.A148A	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	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	173	142	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 GAIIx	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		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	66	33	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		
GSAP	54103	hgsc.bcm.edu	37	7	76984572	76984572	+	Silent	SNP	G	G	A	rs2037753	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:76984572G>A	ENST00000257626.7	-	16	1374	c.1296C>T	c.(1294-1296)tgC>tgT	p.C432C		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	432					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										AGTAGAGCGCGCAGTGCAACG	0.478													A|||	2664	0.531949	0.8253	0.4798	5008	,	,		19035	0.504		0.2962	False		,,,				2504	0.4438				p.C432C		Atlas-SNP	.											.	PION	74	.	0			c.C1296T						PASS	.	A		3255,1151	408.2+/-334.5	1219,817,167	75.0	74.0	74.0		1296	-2.2	0.0	7	dbSNP_94	74	2729,5871	681.2+/-403.7	418,1893,1989	no	coding-synonymous	PION	NM_017439.3		1637,2710,2156	AA,AG,GG		31.7326,26.1235,46.0095		432/855	76984572	5984,7022	2203	4300	6503	SO:0001819	synonymous_variant	54103	exon16			GAGCGCGCAGTGC		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.1296C>T	7.37:g.76984572G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Silent	SNP	ENST00000257626.7	37	CCDS34672.2																																																																																			G|0.528;A|0.472	0.472	strong		0.478	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
GNB4	59345	hgsc.bcm.edu	37	3	179137273	179137273	+	Silent	SNP	A	A	G	rs1362650	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:179137273A>G	ENST00000232564.3	-	4	403	c.117T>C	c.(115-117)tcT>tcC	p.S39S	GNB4_ENST00000468623.1_Silent_p.S39S	NM_021629.3	NP_067642.1	Q9HAV0	GBB4_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 4	39					cell death (GO:0008219)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	16	all_cancers(143;2.01e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.237)			TTCGACCCACAGAGTCCATAT	0.383													G|||	2369	0.473043	0.4455	0.5058	5008	,	,		17180	0.4365		0.5	False		,,,				2504	0.4969				p.S39S	Melanoma(105;1405 1491 7265 20440 33721)	Atlas-SNP	.											.	GNB4	37	.	0			c.T117C						PASS	.	G		2021,2385	614.5+/-392.4	461,1099,643	180.0	171.0	174.0		117	-2.8	0.9	3	dbSNP_88	174	4036,4564	597.2+/-393.7	948,2140,1212	no	coding-synonymous	GNB4	NM_021629.3		1409,3239,1855	GG,GA,AA		46.9302,45.8693,46.5708		39/341	179137273	6057,6949	2203	4300	6503	SO:0001819	synonymous_variant	59345	exon4			ACCCACAGAGTCC	AF300648	CCDS3230.1	3q27.1	2013-01-10			ENSG00000114450	ENSG00000114450		"""WD repeat domain containing"""	20731	protein-coding gene	gene with protein product		610863				10644457, 11842130	Standard	NM_021629		Approved		uc003fjv.4	Q9HAV0	OTTHUMG00000157440	ENST00000232564.3:c.117T>C	3.37:g.179137273A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_021629	B3KMH5|D3DNR8	Silent	SNP	ENST00000232564.3	37	CCDS3230.1																																																																																			A|0.538;G|0.462	0.462	strong		0.383	GNB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258218.1	NM_021629	
CCDC183	84960	hgsc.bcm.edu	37	9	139694521	139694521	+	Missense_Mutation	SNP	T	T	G	rs4546744	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139694521T>G	ENST00000338005.6	+	4	373	c.338T>G	c.(337-339)cTg>cGg	p.L113R	RP11-216L13.18_ENST00000471502.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.L143R|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		113			L -> R (in dbSNP:rs4546744).							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CTGATCCACCTGGTGCGGCGG	0.667													T|||	1327	0.264976	0.3003	0.2954	5008	,	,		10067	0.2421		0.2177	False		,,,				2504	0.2679				p.L113R		Atlas-SNP	.											KIAA1984,NS,carcinoma,0,1	KIAA1984	39	1	0			c.T338G						PASS	.	T	ARG/LEU	1040,3066		153,734,1166	14.0	17.0	16.0		338	4.8	1.0	9	dbSNP_111	16	1716,6654		209,1298,2678	yes	missense	KIAA1984	NM_001039374.4	102	362,2032,3844	GG,GT,TT		20.5018,25.3288,22.0904	probably-damaging	113/535	139694521	2756,9720	2053	4185	6238	SO:0001583	missense	84960	exon4			TCCACCTGGTGCG																												ENST00000338005.6:c.338T>G	9.37:g.139694521T>G	ENSP00000338013:p.Leu113Arg	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	513	0.2348901098901099	132	0.2682926829268293	98	0.27071823204419887	124	0.21678321678321677	159	0.20976253298153033	T	20.4	3.987669	0.74589	0.253288	0.205018	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.11495	2.77	4.85	4.85	0.62838	.	0.569511	0.13099	U	0.413906	T	0.00012	0.0000	M	0.61703	1.905	0.24583	P	0.99386576	D	0.57257	0.979	P	0.59487	0.858	T	0.37549	-0.9701	9	0.15952	T	0.53	-15.2278	10.827	0.46638	0.0:0.0:0.0:1.0	rs4546744;rs60974315;rs4546744	113	Q5T5S1	K1984_HUMAN	R	113	ENSP00000338013:L113R	ENSP00000338013:L113R	L	+	2	0	KIAA1984	138814342	0.931000	0.31567	1.000000	0.80357	0.960000	0.62799	0.669000	0.25142	1.808000	0.52836	0.379000	0.24179	CTG	T|0.772;G|0.228	0.228	strong		0.667	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
PLCG2	5336	hgsc.bcm.edu	37	16	81971403	81971403	+	Silent	SNP	T	T	C	rs1071644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:81971403T>C	ENST00000359376.3	+	28	3307	c.3093T>C	c.(3091-3093)aaT>aaC	p.N1031N		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1031	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						TTTCTCTCAATGGGCGCACGG	0.547													T|||	1572	0.313898	0.0764	0.3199	5008	,	,		20866	0.3442		0.504	False		,,,				2504	0.4039				p.N1031N		Atlas-SNP	.											.	PLCG2	276	.	0			c.T3093C						PASS	.	T		636,3558		55,526,1516	102.0	99.0	100.0		3093	-5.8	0.9	16	dbSNP_86	100	4490,3954		1225,2040,957	no	coding-synonymous	PLCG2	NM_002661.3		1280,2566,2473	CC,CT,TT		46.8261,15.1645,40.5602		1031/1266	81971403	5126,7512	2097	4222	6319	SO:0001819	synonymous_variant	5336	exon28			TCTCAATGGGCGC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3093T>C	16.37:g.81971403T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			C|0.387;N|0.000	0.387	strong		0.547	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
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 GAIIx	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	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	73	18	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 GAIIx	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		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	20	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	
CMYA5	202333	hgsc.bcm.edu	37	5	79028726	79028726	+	Missense_Mutation	SNP	A	A	G	rs13158477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:79028726A>G	ENST00000446378.2	+	2	4169	c.4138A>G	c.(4138-4140)Atc>Gtc	p.I1380V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1380			I -> V (in dbSNP:rs13158477).		negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TTCATCTCTTATCACTCCTGT	0.398													G|||	557	0.111222	0.1172	0.1254	5008	,	,		21072	0.0188		0.164	False		,,,				2504	0.1339				p.I1380V		Atlas-SNP	.											.	CMYA5	643	.	0			c.A4138G						PASS	.	G	VAL/ILE	469,3255		33,403,1426	37.0	36.0	36.0		4138	-0.9	0.0	5	dbSNP_121	36	1285,6907		105,1075,2916	yes	missense	CMYA5	NM_153610.3	29	138,1478,4342	GG,GA,AA		15.686,12.594,14.7197	benign	1380/4070	79028726	1754,10162	1862	4096	5958	SO:0001583	missense	202333	exon2			TCTCTTATCACTC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.4138A>G	5.37:g.79028726A>G	ENSP00000394770:p.Ile1380Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	244	0.11172161172161173	56	0.11382113821138211	50	0.13812154696132597	11	0.019230769230769232	127	0.16754617414248021	G	0.003	-2.531967	0.00145	0.12594	0.15686	ENSG00000164309	ENST00000446378	T	0.03413	3.94	6.17	-0.879	0.10613	.	0.706453	0.12896	N	0.430196	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.42832	-0.9428	9	0.02654	T	1	.	0.3063	0.00280	0.2386:0.2567:0.2478:0.2568	rs13158477;rs17254056;rs60369806;rs13158477	1380	Q8N3K9	CMYA5_HUMAN	V	1380	ENSP00000394770:I1380V	ENSP00000394770:I1380V	I	+	1	0	CMYA5	79064482	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.304000	0.02741	0.054000	0.16065	-0.119000	0.15052	ATC	A|0.895;G|0.105	0.105	strong		0.398	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
KLF11	8462	hgsc.bcm.edu	37	2	10186419	10186419	+	Missense_Mutation	SNP	A	A	G	rs35927125	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:10186419A>G	ENST00000305883.1	+	2	347	c.185A>G	c.(184-186)cAg>cGg	p.Q62R	KLF11_ENST00000535335.1_Missense_Mutation_p.Q45R|KLF11_ENST00000540845.1_Missense_Mutation_p.Q45R	NM_003597.4	NP_003588.1	O14901	KLF11_HUMAN	Kruppel-like factor 11	62			Q -> R (high frequency in individuals with diabetes mellitus type 2; increased repression activity; increased binding to SIN3A; impairs activation of insulin promoter; dbSNP:rs35927125). {ECO:0000269|PubMed:15774581}.		apoptotic process (GO:0006915)|cellular response to peptide (GO:1901653)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	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)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.133)|OV - Ovarian serous cystadenocarcinoma(76;0.228)		CAAAGATCCCAGAAAGGTGAC	0.537													A|||	290	0.0579073	0.034	0.072	5008	,	,		19962	0.003		0.1233	False		,,,				2504	0.0695				p.Q62R	Melanoma(56;431 1507 23687 50789)	Atlas-SNP	.											.	KLF11	45	.	0			c.A185G	GRCh37	CM057336	KLF11	M	rs35927125	PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN	189,4217	120.8+/-158.4	1,187,2015	102.0	97.0	99.0		134,134,185	-0.5	0.2	2	dbSNP_126	99	1044,7556	221.5+/-258.9	63,918,3319	yes	missense,missense,missense	KLF11	NM_001177716.1,NM_001177718.1,NM_003597.4	43,43,43	64,1105,5334	GG,GA,AA		12.1395,4.2896,9.4802	probably-damaging,probably-damaging,probably-damaging	45/496,45/496,62/513	10186419	1233,11773	2203	4300	6503	SO:0001583	missense	8462	exon2			GATCCCAGAAAGG	AF028008	CCDS1668.1, CCDS54333.1	2p25	2013-01-08	2004-11-29	2004-12-01	ENSG00000172059	ENSG00000172059		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	11811	protein-coding gene	gene with protein product		603301	"""TGFB inducible early growth response 2"""	TIEG2		9748269, 11087666	Standard	NM_001177716		Approved	Tieg3, MODY7	uc002raf.1	O14901	OTTHUMG00000119004	ENST00000305883.1:c.185A>G	2.37:g.10186419A>G	ENSP00000307023:p.Gln62Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_003597	B4DZE7|Q9EPF4	Missense_Mutation	SNP	ENST00000305883.1	37	CCDS1668.1	138	0.06318681318681318	17	0.034552845528455285	36	0.09944751381215469	1	0.0017482517482517483	84	0.11081794195250659	A	11.43	1.636632	0.29068	0.042896	0.121395	ENSG00000172059	ENST00000401510;ENST00000305883;ENST00000448523;ENST00000540845;ENST00000440320;ENST00000535335	T;T;T;T;T;T	0.64438	-0.08;2.54;-0.1;2.53;-0.07;2.53	5.03	-0.464	0.12160	.	0.531770	0.21425	N	0.074747	T	0.01092	0.0036	M	0.72894	2.215	0.35218	P	0.224271	B	0.10296	0.003	B	0.08055	0.003	T	0.15065	-1.0450	9	0.59425	D	0.04	.	5.9364	0.19169	0.6594:0.1265:0.214:0.0	rs35927125;rs61754179	62	O14901	KLF11_HUMAN	R	45;62;45;45;45;45	ENSP00000386058:Q45R;ENSP00000307023:Q62R;ENSP00000387866:Q45R;ENSP00000444690:Q45R;ENSP00000388263:Q45R;ENSP00000442722:Q45R	ENSP00000307023:Q62R	Q	+	2	0	KLF11	10103870	1.000000	0.71417	0.190000	0.23270	0.671000	0.39405	2.349000	0.44054	-0.043000	0.13513	0.379000	0.24179	CAG	T|0.000;G|0.084;A|0.916	0.084	strong		0.537	KLF11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000239202.3	NM_003597	
BTNL9	153579	hgsc.bcm.edu	37	5	180472513	180472513	+	Silent	SNP	A	A	G	rs6894087	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180472513A>G	ENST00000327705.9	+	2	255	c.24A>G	c.(22-24)ccA>ccG	p.P8P	BTNL9_ENST00000376842.3_Silent_p.P8P|BTNL9_ENST00000515271.1_Intron|BTNL9_ENST00000376841.2_Silent_p.P8P	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	8						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGTCTCCCCAGACTCCTTGA	0.602													G|||	2530	0.505192	0.6596	0.5245	5008	,	,		17341	0.3919		0.5189	False		,,,				2504	0.3855				p.P8P		Atlas-SNP	.											.	BTNL9	58	.	0			c.A24G						PASS	.	G		2806,1598	496.2+/-363.5	899,1008,295	108.0	93.0	98.0		24	1.9	0.0	5	dbSNP_116	98	4501,4097	561.7+/-387.8	1170,2161,968	no	coding-synonymous	BTNL9	NM_152547.4		2069,3169,1263	GG,GA,AA		47.6506,36.2852,43.801		8/536	180472513	7307,5695	2202	4299	6501	SO:0001819	synonymous_variant	153579	exon2			CTCCCCAGACTCC	AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.24A>G	5.37:g.180472513A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_152547	A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	37	CCDS4460.2																																																																																			A|0.458;G|0.542	0.542	strong		0.602	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3	NM_152547	
MUC2	4583	hgsc.bcm.edu	37	11	1092692	1092692	+	Missense_Mutation	SNP	C	C	T	rs199884046		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1092692C>T	ENST00000441003.2	+	30	4538	c.4511C>T	c.(4510-4512)aCg>aTg	p.T1504M	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1505M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4239	Approximate repeats.			M -> T (in Ref. 3; AAA59875). {ECO:0000305}.	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)	agccctccaacgactacgccc	0.632																																					p.T1504M		Atlas-SNP	.											.	MUC2	614	.	0			c.C4511T						PASS	.						420.0	612.0	545.0					11																	1092692		1787	3356	5143	SO:0001583	missense	4583	exon30			CTCCAACGACTAC	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.4511C>T	11.37:g.1092692C>T	ENSP00000415183:p.Thr1504Met	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	301	23	0.076412	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	-	3.987	-0.005205	0.07773	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15487	2.48;2.42	1.51	0.444	0.16592	.	0.577884	0.11519	U	0.555967	T	0.15262	0.0368	.	.	.	0.09310	N	1	D	0.71674	0.998	B	0.44085	0.44	T	0.17471	-1.0368	9	0.46703	T	0.11	.	8.0965	0.30831	0.2426:0.7574:0.0:0.0	.	1504	E7EUV1	.	M	1504;1505	ENSP00000415183:T1504M;ENSP00000351956:T1505M	ENSP00000351956:T1505M	T	+	2	0	MUC2	1082692	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.088000	0.14979	0.040000	0.15660	0.000000	0.15137	ACG	.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
BTC	685	hgsc.bcm.edu	37	4	75675841	75675841	+	Missense_Mutation	SNP	A	A	T	rs11938093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:75675841A>T	ENST00000395743.3	-	4	730	c.370T>A	c.(370-372)Ttg>Atg	p.L124M		NM_001729.2	NP_001720.1	P35070	BTC_HUMAN	betacellulin	124			L -> M (in dbSNP:rs11938093). {ECO:0000269|PubMed:15489334}.		epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitosis (GO:0045840)|positive regulation of urine volume (GO:0035810)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	10			Lung(101;0.219)			ACTGCTATCAAACAAATCACC	0.358													A|||	1001	0.19988	0.2428	0.2003	5008	,	,		16216	0.0407		0.2555	False		,,,				2504	0.2485				p.L124M		Atlas-SNP	.											.	BTC	23	.	0			c.T370A						PASS	.	A	MET/LEU	1191,3215	415.4+/-337.2	152,887,1164	188.0	198.0	195.0		370	2.9	1.0	4	dbSNP_120	195	2282,6318	383.8+/-340.9	296,1690,2314	yes	missense	BTC	NM_001729.2	15	448,2577,3478	TT,TA,AA		26.5349,27.0313,26.7031	probably-damaging	124/179	75675841	3473,9533	2203	4300	6503	SO:0001583	missense	685	exon4			CTATCAAACAAAT	S55606	CCDS3566.1	4q13.3	2012-09-20			ENSG00000174808	ENSG00000174808			1121	protein-coding gene	gene with protein product		600345				8439318, 11522793	Standard	NM_001729		Approved		uc003hig.2	P35070	OTTHUMG00000130107	ENST00000395743.3:c.370T>A	4.37:g.75675841A>T	ENSP00000379092:p.Leu124Met	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	204	100	0.490196	NM_001729	Q96F48	Missense_Mutation	SNP	ENST00000395743.3	37	CCDS3566.1	392	0.1794871794871795	115	0.23373983739837398	81	0.22375690607734808	13	0.022727272727272728	183	0.24142480211081793	A	16.81	3.224906	0.58668	0.270313	0.265349	ENSG00000174808	ENST00000395743	T	0.15139	2.45	5.32	2.94	0.34122	.	0.163209	0.44285	D	0.000462	T	0.00012	0.0000	L	0.27053	0.805	0.35815	P	0.17586800000000002	D	0.76494	0.999	D	0.74023	0.982	T	0.26950	-1.0088	9	0.54805	T	0.06	-3.2024	5.9362	0.19167	0.7332:0.0:0.2668:0.0	rs11938093;rs17845298;rs17858133;rs52824759;rs11938093	124	P35070	BTC_HUMAN	M	124	ENSP00000379092:L124M	ENSP00000379092:L124M	L	-	1	2	BTC	75894865	0.974000	0.33945	1.000000	0.80357	0.723000	0.41478	0.064000	0.14437	1.101000	0.41535	0.460000	0.39030	TTG	A|0.755;T|0.245	0.245	strong		0.358	BTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252413.1		
AOC1	26	hgsc.bcm.edu	37	7	150554887	150554887	+	Silent	SNP	G	G	A	rs2071514	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150554887G>A	ENST00000493429.1	+	4	1913	c.1329G>A	c.(1327-1329)gcG>gcA	p.A443A	AOC1_ENST00000467291.1_Silent_p.A443A|AOC1_ENST00000360937.4_Silent_p.A443A|AOC1_ENST00000416793.2_Silent_p.A443A			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	443					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)	p.A443A(1)								Amiloride(DB00594)	ACTTCTATGCGGGGCTGAAGG	0.517													A|||	1504	0.300319	0.2564	0.2939	5008	,	,		17333	0.4444		0.1511	False		,,,				2504	0.3691				p.A443A		Atlas-SNP	.											ABP1,NS,carcinoma,+1,2	ABP1	92	2	1	Substitution - coding silent(1)	stomach(1)	c.G1329A						PASS	.	A		773,3145		73,627,1259	58.0	63.0	61.0		1329	-9.9	0.0	7	dbSNP_96	61	1502,6776		138,1226,2775	no	coding-synonymous	ABP1	NM_001091.2		211,1853,4034	AA,AG,GG		18.1445,19.7295,18.6537		443/752	150554887	2275,9921	1959	4139	6098	SO:0001819	synonymous_variant	26	exon2			CTATGCGGGGCTG	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1329G>A	7.37:g.150554887G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																			G|0.717;A|0.283	0.283	strong		0.517	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
HNMT	3176	hgsc.bcm.edu	37	2	138759649	138759649	+	Missense_Mutation	SNP	C	C	T	rs11558538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:138759649C>T	ENST00000280097.3	+	4	496	c.314C>T	c.(313-315)aCa>aTa	p.T105I	HNMT_ENST00000410115.1_Missense_Mutation_p.T105I|HNMT_ENST00000485653.1_3'UTR	NM_006895.2	NP_008826.1	P50135	HNMT_HUMAN	histamine N-methyltransferase	105			T -> I (in dbSNP:rs1801105). {ECO:0000269|PubMed:10803682, ECO:0000269|PubMed:9547362}.		brain development (GO:0007420)|hyperosmotic response (GO:0006972)|respiratory gaseous exchange (GO:0007585)|response to amine (GO:0014075)|response to cocaine (GO:0042220)|response to glucocorticoid (GO:0051384)|response to interleukin-1 (GO:0070555)|response to tumor cell (GO:0002347)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	histamine N-methyltransferase activity (GO:0046539)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.125)	Amodiaquine(DB00613)|Chlorhexidine(DB00878)|Histamine Phosphate(DB00667)|Quinacrine(DB01103)	GTAGCCAAGACATCGAACCTC	0.368													C|||	298	0.0595048	0.003	0.0778	5008	,	,		14767	0.0317		0.1044	False		,,,				2504	0.1053				p.T105I		Atlas-SNP	.											.	HNMT	42	.	0			c.C314T	GRCh37	CM983499	HNMT	M	rs11558538	PASS	.	C	ILE/THR	105,4301	81.9+/-120.4	0,105,2098	65.0	61.0	62.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	314	5.3	1.0	2	dbSNP_120	62	901,7699	201.6+/-245.0	36,829,3435	yes	missense	HNMT	NM_006895.2	89	36,934,5533	TT,TC,CC		10.4767,2.3831,7.7349	probably-damaging	105/293	138759649	1006,12000	2203	4300	6503	SO:0001583	missense	3176	exon4			CCAAGACATCGAA		CCDS2181.1, CCDS33296.1, CCDS33297.1	2q22.1	2008-02-05			ENSG00000150540	ENSG00000150540	2.1.1.8		5028	protein-coding gene	gene with protein product		605238					Standard	NM_001024074		Approved		uc002tvf.3	P50135	OTTHUMG00000131751	ENST00000280097.3:c.314C>T	2.37:g.138759649C>T	ENSP00000280097:p.Thr105Ile	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	134	41	0.30597	NM_006895	B2R9J3|Q546Z6|Q7Z7I2|Q8IU56|Q8WW98|Q9BRW6	Missense_Mutation	SNP	ENST00000280097.3	37	CCDS2181.1	122	0.055860805860805864	2	0.0040650406504065045	26	0.0718232044198895	18	0.03146853146853147	76	0.10026385224274406	C	21.1	4.101588	0.76983	0.023831	0.104767	ENSG00000150540	ENST00000410115;ENST00000280097	T;T	0.41758	0.99;0.99	6.16	5.27	0.74061	Methyltransferase type 12 (1);	0.306570	0.39341	N	0.001399	T	0.02230	0.0069	M	0.69823	2.125	0.80722	D	1	P	0.40794	0.729	P	0.49192	0.602	T	0.01074	-1.1460	10	0.22109	T	0.4	-4.2676	15.1706	0.72869	0.1411:0.8589:0.0:0.0	rs61727980	105	P50135	HNMT_HUMAN	I	105	ENSP00000386940:T105I;ENSP00000280097:T105I	ENSP00000280097:T105I	T	+	2	0	HNMT	138476119	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.284000	0.65627	1.580000	0.49851	0.650000	0.86243	ACA	C|0.931;T|0.069	0.069	strong		0.368	HNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254673.1		
ESRP1	54845	hgsc.bcm.edu	37	8	95680229	95680229	+	Silent	SNP	C	C	T	rs1549466	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:95680229C>T	ENST00000433389.2	+	10	1174	c.984C>T	c.(982-984)gtC>gtT	p.V328V	ESRP1_ENST00000358397.5_Silent_p.V328V|ESRP1_ENST00000454170.2_Silent_p.V328V|ESRP1_ENST00000423620.2_Silent_p.V328V	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	328	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						AAGTCATTGTCCGCATGCGGG	0.483													C|||	1765	0.352436	0.0514	0.3804	5008	,	,		19140	0.5387		0.3897	False		,,,				2504	0.5092				p.V328V		Atlas-SNP	.											ESRP1_ENST00000433389,NS,carcinoma,+2,2	ESRP1	148	2	0			c.C984T						PASS	.	C	,,,,	393,3341		21,351,1495	61.0	60.0	60.0		984,984,984,984,984	-0.6	1.0	8	dbSNP_88	60	3101,5085		579,1943,1571	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	600,2294,3066	TT,TC,CC		37.8817,10.5249,29.3121	,,,,	328/678,328/609,328/660,328/605,328/682	95680229	3494,8426	1867	4093	5960	SO:0001819	synonymous_variant	54845	exon10			CATTGTCCGCATG	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.984C>T	8.37:g.95680229C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1	780	0.35714285714285715	28	0.056910569105691054	135	0.3729281767955801	307	0.5367132867132867	310	0.40897097625329815	C	9.611	1.131193	0.21041	0.105249	0.378817	ENSG00000104413	ENST00000519505	.	.	.	5.78	-0.637	0.11504	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47761	-0.9092	3	.	.	.	-9.6706	9.8714	0.41177	0.0:0.28:0.5332:0.1868	rs1549466;rs17717111;rs1549466	.	.	.	S	194	.	.	P	+	1	0	ESRP1	95749405	0.112000	0.22096	0.981000	0.43875	0.994000	0.84299	-0.523000	0.06230	-0.440000	0.07211	-0.302000	0.09304	CCG	C|0.648;T|0.352	0.352	strong		0.483	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
SRRM5	100170229	hgsc.bcm.edu	37	19	44117052	44117052	+	Missense_Mutation	SNP	C	C	T	rs77545563	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:44117052C>T	ENST00000607544.1	+	3	1101	c.779C>T	c.(778-780)aCt>aTt	p.T260I	SRRM5_ENST00000526798.1_Missense_Mutation_p.T275I|ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000417606.1_Missense_Mutation_p.T260I			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	260	Ser-rich.									endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						TACAGCCCCACTGAAATGTCC	0.527													C|||	79	0.0157748	0.0	0.0288	5008	,	,		17478	0.0		0.0527	False		,,,				2504	0.0061				p.T260I		Atlas-SNP	.											.	SRRM5	38	.	0			c.C779T						PASS	.	C	ILE/THR,	15,1369		0,15,677	102.0	97.0	99.0		779,	-3.0	0.0	19	dbSNP_132	99	169,3013		6,157,1428	yes	missense,intron	ZNF428,SRRM5	NM_001145641.1,NM_182498.3	89,	6,172,2105	TT,TC,CC		5.3111,1.0838,4.0298	possibly-damaging,	260/716,	44117052	184,4382	692	1591	2283	SO:0001583	missense	100170229	exon1			GCCCCACTGAAAT	AK297891	CCDS46095.1	19q13.31	2013-09-20			ENSG00000226763	ENSG00000226763			37248	protein-coding gene	gene with protein product							Standard	NM_001145641		Approved		uc010xwr.2	B3KS81	OTTHUMG00000165480	ENST00000607544.1:c.779C>T	19.37:g.44117052C>T	ENSP00000476253:p.Thr260Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	89	51	0.573034	NM_001145641	B4DNF0	Missense_Mutation	SNP	ENST00000607544.1	37	CCDS46095.1	46	0.021062271062271064	0	0.0	8	0.022099447513812154	0	0.0	38	0.05013192612137203	C	11.65	1.702164	0.30232	0.010838	0.053111	ENSG00000226763	ENST00000526798;ENST00000417606	.	.	.	4.89	-2.98	0.05513	.	.	.	.	.	T	0.02688	0.0081	N	0.24115	0.695	0.09310	N	1	B	0.21606	0.058	B	0.16289	0.015	T	0.20273	-1.0280	8	0.62326	D	0.03	.	0.8784	0.01229	0.3666:0.289:0.1196:0.2248	.	260	B3KS81	SRRM5_HUMAN	I	275;260	.	ENSP00000414512:T260I	T	+	2	0	SRRM5	48808892	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	-1.586000	0.02110	-0.449000	0.07117	0.563000	0.77884	ACT	C|0.977;T|0.023	0.023	strong		0.527	SRRM5-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000384398.2	NM_001145641	
MUC2	4583	hgsc.bcm.edu	37	11	1090343	1090343	+	Silent	SNP	T	T	C	rs12221966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1090343T>C	ENST00000441003.2	+	27	3666	c.3639T>C	c.(3637-3639)tgT>tgC	p.C1213C	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_5'Flank|MUC2_ENST00000359061.5_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1213					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)	GCAGCGTGTGTACCAACTCCT	0.647													C|||	422	0.0842652	0.0537	0.0893	5008	,	,		17608	0.0685		0.1163	False		,,,				2504	0.1053				p.C1213C		Atlas-SNP	.											.	MUC2	614	.	0			c.T3639C						PASS	.			298,4082		12,274,1904	64.0	73.0	70.0		3639	0.3	0.0	11	dbSNP_120	70	945,7609		47,851,3379	no	coding-synonymous	MUC2	NM_002457.2		59,1125,5283	CC,CT,TT		11.0475,6.8037,9.6103		1213/2813	1090343	1243,11691	2190	4277	6467	SO:0001819	synonymous_variant	4583	exon27			CGTGTGTACCAAC	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.3639T>C	11.37:g.1090343T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.916;C|0.084	0.084	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
TMPRSS3	64699	hgsc.bcm.edu	37	21	43805637	43805637	+	Silent	SNP	C	C	T	rs2839501	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43805637C>T	ENST00000291532.3	-	6	1408	c.453G>A	c.(451-453)gtG>gtA	p.V151V	TMPRSS3_ENST00000398405.1_Silent_p.V149V|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000380399.1_Silent_p.V235V|TMPRSS3_ENST00000433957.2_Silent_p.V151V|TMPRSS3_ENST00000398397.3_Silent_p.V151V	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	151	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TATCTGAACTCACATAGCTGC	0.488													T|||	2319	0.463059	0.8896	0.3646	5008	,	,		21554	0.2758		0.3429	False		,,,				2504	0.273				p.V151V		Atlas-SNP	.											TMPRSS3,colon,carcinoma,0,1	TMPRSS3	40	1	0			c.G453A						PASS	.	T	,	3541,865	338.6+/-305.4	1420,701,82	127.0	131.0	130.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	453,453	-4.8	0.0	21	dbSNP_100	130	3127,5473	658.4+/-401.6	579,1969,1752	no	coding-synonymous,coding-synonymous	TMPRSS3	NM_024022.2,NM_032405.1	,	1999,2670,1834	TT,TC,CC		36.3605,19.6323,48.7314	,	151/455,151/345	43805637	6668,6338	2203	4300	6503	SO:0001819	synonymous_variant	64699	exon6			TGAACTCACATAG	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.453G>A	21.37:g.43805637C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Silent	SNP	ENST00000291532.3	37	CCDS13686.1																																																																																			C|0.505;A|0.004	.	strong		0.488	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		
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 GAIIx	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	ATAD2_ENST00000521903.1_Silent_p.H181H|RNU6-875P_ENST00000516488.1_RNA	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		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	91	40	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	
ADCY10	55811	hgsc.bcm.edu	37	1	167849414	167849414	+	Silent	SNP	A	A	G	rs203849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:167849414A>G	ENST00000367851.4	-	11	1339	c.1155T>C	c.(1153-1155)ggT>ggC	p.G385G	ADCY10_ENST00000545172.1_Silent_p.G232G|ADCY10_ENST00000367848.1_Silent_p.G293G	NM_018417.4	NP_060887.2	Q96PN6	ADCYA_HUMAN	adenylate cyclase 10 (soluble)	385	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				cAMP biosynthetic process (GO:0006171)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	apical part of cell (GO:0045177)|axon (GO:0030424)|basal part of cell (GO:0045178)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)	p.G385G(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(26)|ovary(2)|prostate(4)|skin(6)|stomach(1)|urinary_tract(1)	63						CACTGGCAACACCGATGGATA	0.483													G|||	2470	0.493211	0.6687	0.4597	5008	,	,		19729	0.3224		0.504	False		,,,				2504	0.4448				p.G385G		Atlas-SNP	.											ADCY10,NS,carcinoma,0,1	ADCY10	175	1	1	Substitution - coding silent(1)	stomach(1)	c.T1155C						PASS	.	G	,	2826,1580	492.2+/-362.3	903,1020,280	66.0	59.0	61.0		696,1155	-1.5	0.1	1	dbSNP_79	61	4122,4476	585.4+/-391.9	1002,2118,1179	yes	coding-synonymous,coding-synonymous	ADCY10	NM_001167749.1,NM_018417.4	,	1905,3138,1459	GG,GA,AA		47.9414,35.8602,46.5703	,	232/1458,385/1611	167849414	6948,6056	2203	4299	6502	SO:0001819	synonymous_variant	55811	exon11			GGCAACACCGATG	AF271058	CCDS1265.1, CCDS53426.1, CCDS72977.1	1q24	2013-02-04			ENSG00000143199	ENSG00000143199	4.6.1.1	"""Adenylate cyclases"""	21285	protein-coding gene	gene with protein product	"""soluble adenylyl cyclase"", ""Hypercalciuria, absorptive, 2"""	605205					Standard	XM_006711449		Approved	SAC, Sacy, SACI, HCA2, RP1-313L4.2	uc001ger.3	Q96PN6	OTTHUMG00000034573	ENST00000367851.4:c.1155T>C	1.37:g.167849414A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	51	0.41129	NM_018417	B4DZF0|F5GWS5|O95558|Q5R329|Q5R330|Q8WXV4|Q9NNX0	Silent	SNP	ENST00000367851.4	37	CCDS1265.1																																																																																			G|0.516;N|0.000	0.516	strong		0.483	ADCY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083663.1	NM_018417	
HOXA9	3205	hgsc.bcm.edu	37	7	27204732	27204732	+	Silent	SNP	C	C	A	rs35355140	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:27204732C>A	ENST00000343483.6	-	1	417	c.345G>T	c.(343-345)acG>acT	p.T115T	RP1-170O19.20_ENST00000465941.1_Intron|RP1-170O19.20_ENST00000470747.4_Intron|HOXA9_ENST00000497089.1_Intron|HOXA9_ENST00000396345.1_Intron	NM_152739.3	NP_689952.1	P31269	HXA9_HUMAN	homeobox A9	115					endothelial cell activation (GO:0042118)|multicellular organismal development (GO:0007275)|negative regulation of myeloid cell differentiation (GO:0045638)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|endometrium(1)|lung(5)|prostate(1)	8						GCGCACCGGGCGTGGGCTCCA	0.687			T	"""NUP98, MSI2"""	AML*								C|||	333	0.0664936	0.0015	0.0533	5008	,	,		12010	0.1984		0.0646	False		,,,				2504	0.0297				p.T115T		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3205	homeo box A9		L	HOXA9,right_upper_lobe,carcinoma,-1,3	HOXA9	20	3	0			c.G345T						PASS	.	C		73,4327		1,71,2128	14.0	17.0	16.0		345	5.6	1.0	7	dbSNP_126	16	590,8004		16,558,3723	no	coding-synonymous	HOXA9	NM_152739.3		17,629,5851	AA,AC,CC		6.8653,1.6591,5.1024		115/273	27204732	663,12331	2200	4297	6497	SO:0001819	synonymous_variant	3205	exon1			ACCGGGCGTGGGC		CCDS5409.1	7p15.2	2011-06-20	2005-12-22		ENSG00000078399	ENSG00000078399		"""Homeoboxes / ANTP class : HOXL subclass"""	5109	protein-coding gene	gene with protein product		142956	"""homeo box A9"""	HOX1G, HOX1		1973146, 1358459	Standard	NM_152739		Approved		uc003syt.3	P31269	OTTHUMG00000023220	ENST00000343483.6:c.345G>T	7.37:g.27204732C>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	18	15	0.833333	NM_152739	O43369|O43429|Q99820	Silent	SNP	ENST00000343483.6	37	CCDS5409.1																																																																																			C|0.937;A|0.063	0.063	strong		0.687	HOXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358706.2		
DND1	373863	hgsc.bcm.edu	37	5	140050926	140050926	+	Silent	SNP	G	G	A	rs62384220	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140050926G>A	ENST00000542735.1	-	4	1057	c.1014C>T	c.(1012-1014)aaC>aaT	p.N338N	WDR55_ENST00000358337.5_3'UTR|WDR55_ENST00000520764.1_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	338					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)	p.N338N(1)		central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCACAGGAGGTTGGCCCCAG	0.587													G|||	20	0.00399361	0.0008	0.0072	5008	,	,		20122	0.0		0.0109	False		,,,				2504	0.0031				p.N338N		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	1	Substitution - coding silent(1)	prostate(1)	c.C1014T						PASS	.						73.0	65.0	67.0					5																	140050926		1984	4006	5990	SO:0001819	synonymous_variant	373863	exon4			CAGGAGGTTGGCC	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1014C>T	5.37:g.140050926G>A		Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	683	158	0.231332	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			G|0.970;A|0.030	0.030	strong		0.587	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189601	11189601	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11189601G>T	ENST00000382435.4	+	1	1205	c.986G>T	c.(985-987)aGc>aTc	p.S329I		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	329						integral component of membrane (GO:0016021)											CGGAACCTCAGCTGTGAGAGG	0.517																																					p.S329I		Atlas-SNP	.											AMAC1L2,NS,carcinoma,-1,1	.	.	1	0			c.G986T						scavenged	.						67.0	68.0	68.0					8																	11189601		2203	4300	6503	SO:0001583	missense	83650	exon1			ACCTCAGCTGTGA	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.986G>T	8.37:g.11189601G>T	ENSP00000371872:p.Ser329Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	69	6	0.0869565	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	g	0.299	-0.974907	0.02215	.	.	ENSG00000177710	ENST00000382435	T	0.28666	1.6	.	.	.	.	0.000000	0.52532	D	0.000061	T	0.22244	0.0536	L	0.54323	1.7	0.26188	N	0.979621	B	0.02656	0.0	B	0.06405	0.002	T	0.18241	-1.0343	8	0.22706	T	0.39	-1.3917	.	.	.	.	329	Q96KT7	S35G5_HUMAN	I	329	ENSP00000371872:S329I	ENSP00000371872:S329I	S	+	2	0	SLC35G5	11227011	0.173000	0.23056	0.298000	0.25002	0.299000	0.27559	0.335000	0.19806	0.064000	0.16427	0.064000	0.15345	AGC	.	.	none		0.517	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
NUP205	23165	hgsc.bcm.edu	37	7	135279315	135279315	+	Silent	SNP	A	A	C	rs7800214	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:135279315A>C	ENST00000285968.6	+	13	1877	c.1851A>C	c.(1849-1851)gcA>gcC	p.A617A	NUP205_ENST00000440390.2_Intron	NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	617					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						CTCGCTTGGCACTCTGTGAAC	0.423													A|||	1721	0.34365	0.2421	0.3213	5008	,	,		18147	0.2579		0.4841	False		,,,				2504	0.4407				p.A617A		Atlas-SNP	.											NUP205,colon,carcinoma,0,1	NUP205	198	1	0			c.A1851C						PASS	.	A		1165,3241	410.0+/-335.2	156,853,1194	99.0	100.0	100.0		1851	-10.7	0.3	7	dbSNP_116	100	4276,4324	575.1+/-390.2	1081,2114,1105	no	coding-synonymous	NUP205	NM_015135.2		1237,2967,2299	CC,CA,AA		49.7209,26.4412,41.8345		617/2013	135279315	5441,7565	2203	4300	6503	SO:0001819	synonymous_variant	23165	exon13			CTTGGCACTCTGT	D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.1851A>C	7.37:g.135279315A>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	37	0.377551	NM_015135	A6H8X3|Q86YC1	Silent	SNP	ENST00000285968.6	37	CCDS34759.1																																																																																			A|0.596;C|0.404	0.404	strong		0.423	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
EFHD1	80303	hgsc.bcm.edu	37	2	233537125	233537125	+	Missense_Mutation	SNP	A	A	G	rs11550699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233537125A>G	ENST00000264059.3	+	3	1034	c.557A>G	c.(556-558)aAa>aGa	p.K186R	EFHD1_ENST00000409613.1_Missense_Mutation_p.K90R|EFHD1_ENST00000410095.1_Missense_Mutation_p.K74R|EFHD1_ENST00000409708.1_Missense_Mutation_p.K74R	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	186			K -> R (in dbSNP:rs11550699). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		GAGGGTGTCAAAGGTGCCAAG	0.577													A|||	1735	0.346446	0.1483	0.464	5008	,	,		18935	0.4891		0.3469	False		,,,				2504	0.3834				p.K186R		Atlas-SNP	.											.	EFHD1	28	.	0			c.A557G						PASS	.	A	ARG/LYS	810,3596	324.8+/-298.8	83,644,1476	132.0	129.0	130.0		557	-0.4	0.9	2	dbSNP_120	130	3173,5427	482.0+/-370.8	597,1979,1724	yes	missense	EFHD1	NM_025202.3	26	680,2623,3200	GG,GA,AA		36.8953,18.384,30.6243	benign	186/240	233537125	3983,9023	2203	4300	6503	SO:0001583	missense	80303	exon3			GTGTCAAAGGTGC		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"""EF-hand domain containing"""	29556	protein-coding gene	gene with protein product	"""swiprosin-2"""	611617	"""EF hand domain containing 1"""			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.557A>G	2.37:g.233537125A>G	ENSP00000264059:p.Lys186Arg	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_025202	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Missense_Mutation	SNP	ENST00000264059.3	37	CCDS2497.1	754	0.34523809523809523	73	0.1483739837398374	152	0.4198895027624309	272	0.4755244755244755	257	0.3390501319261214	A	9.677	1.148271	0.21288	0.18384	0.368953	ENSG00000115468	ENST00000409613;ENST00000264059;ENST00000540187;ENST00000409708;ENST00000427698;ENST00000410095	T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74	4.96	-0.41	0.12374	.	0.207888	0.48767	N	0.000164	T	0.00012	0.0000	L	0.53780	1.695	0.32928	P	0.48319999999999996	B;B	0.17268	0.002;0.021	B;B	0.15484	0.001;0.013	T	0.44513	-0.9323	9	0.30854	T	0.27	-1.3083	4.7049	0.12844	0.5494:0.1545:0.2961:0.0	rs11550699;rs17844998;rs17857759;rs52815265;rs59739742;rs11550699	90;186	E9PFH3;Q9BUP0	.;EFHD1_HUMAN	R	90;186;89;74;74;74	ENSP00000386556:K90R;ENSP00000264059:K186R;ENSP00000386243:K74R;ENSP00000401073:K74R;ENSP00000386685:K74R	ENSP00000264059:K186R	K	+	2	0	EFHD1	233245369	0.388000	0.25197	0.930000	0.37139	0.370000	0.29829	0.160000	0.16462	-0.331000	0.08501	-0.379000	0.06801	AAA	A|0.685;G|0.315	0.315	strong		0.577	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202	
COL2A1	1280	hgsc.bcm.edu	37	12	48375568	48375568	+	Silent	SNP	A	A	G	rs1635553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48375568A>G	ENST00000380518.3	-	36	2564	c.2400T>C	c.(2398-2400)aaT>aaC	p.N800N	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Silent_p.N731N	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	800	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)	CCTTCTCGCCATTAGCACCAG	0.637													G|||	2418	0.482827	0.4879	0.3703	5008	,	,		17163	0.5476		0.4632	False		,,,				2504	0.5092				p.N800N		Atlas-SNP	.											COL2A1_ENST00000380518,NS,carcinoma,0,2	COL2A1	368	2	0			c.T2400C						PASS	.	G	,	1927,2385		453,1021,682	51.0	38.0	43.0		2400,2193	-8.6	0.4	12	dbSNP_89	43	3856,4604		908,2040,1282	yes	coding-synonymous,coding-synonymous	COL2A1	NM_001844.4,NM_033150.2	,	1361,3061,1964	GG,GA,AA		45.5792,44.6892,45.2787	,	800/1488,731/1419	48375568	5783,6989	2156	4230	6386	SO:0001819	synonymous_variant	1280	exon36			CTCGCCATTAGCA	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.2400T>C	12.37:g.48375568A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	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																																																																																			A|0.519;G|0.481	0.481	strong		0.637	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
PTCHD1	139411	hgsc.bcm.edu	37	X	23398214	23398214	+	Silent	SNP	T	T	C	rs5926304	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:23398214T>C	ENST00000379361.4	+	2	1718	c.858T>C	c.(856-858)tgT>tgC	p.C286C		NM_173495.2	NP_775766.2	Q96NR3	PTHD1_HUMAN	patched domain containing 1	286	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				cognition (GO:0050890)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(4)|endometrium(3)|kidney(3)|large_intestine(9)|lung(14)|ovary(4)|skin(2)|urinary_tract(2)	42						CCATCCTGTGTTGCTCTATGC	0.567													C|||	2399	0.635497	0.7118	0.4308	3775	,	,		15053	0.4216		0.4543	False		,,,				2504	0.2832				p.C286C		Atlas-SNP	.											.	PTCHD1	213	.	0			c.T858C						PASS	.	C		3351,484		1244,364,499,24,72	140.0	118.0	126.0		858	3.1	1.0	X	dbSNP_114	126	4118,2610		901,1165,1151,362,721	no	coding-synonymous	PTCHD1	NM_173495.2		2145,1529,1650,386,793	CC,CT,C,TT,T		38.7931,12.6206,29.2909		286/889	23398214	7469,3094	2203	4300	6503	SO:0001819	synonymous_variant	139411	exon2			CCTGTGTTGCTCT	AK054858	CCDS35215.2	Xp22.13	2008-02-05			ENSG00000165186	ENSG00000165186			26392	protein-coding gene	gene with protein product		300828					Standard	NM_173495		Approved	FLJ30296	uc004dal.4	Q96NR3	OTTHUMG00000021251	ENST00000379361.4:c.858T>C	X.37:g.23398214T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_173495	B4DQH0|Q0IJ60|Q6P6B8	Silent	SNP	ENST00000379361.4	37	CCDS35215.2																																																																																			T|0.313;C|0.687	0.687	strong		0.567	PTCHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056047.2	NM_173495	
CHPF2	54480	hgsc.bcm.edu	37	7	150931268	150931268	+	Silent	SNP	C	C	G	rs2608293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150931268C>G	ENST00000035307.2	+	1	1684	c.171C>G	c.(169-171)tcC>tcG	p.S57S	CHPF2_ENST00000495645.1_Silent_p.S49S	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	57					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						ATCCAGATTCCAGAGCTCGGC	0.587													G|||	2245	0.448283	0.3207	0.4207	5008	,	,		18057	0.7183		0.4493	False		,,,				2504	0.3609				p.S57S		Atlas-SNP	.											.	CHPF2	52	.	0			c.C171G						PASS	.	G		1500,2906	676.7+/-403.3	259,982,962	71.0	75.0	74.0		171	-3.7	0.0	7	dbSNP_100	74	3525,5075	632.4+/-398.6	709,2107,1484	no	coding-synonymous	CHPF2	NM_019015.1		968,3089,2446	GG,GC,CC		40.9884,34.0445,38.636		57/773	150931268	5025,7981	2203	4300	6503	SO:0001819	synonymous_variant	54480	exon1			AGATTCCAGAGCT	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.171C>G	7.37:g.150931268C>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Silent	SNP	ENST00000035307.2	37	CCDS34779.1																																																																																			C|0.584;G|0.416	0.416	strong		0.587	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
METTL21A	151194	hgsc.bcm.edu	37	2	208477956	208477956	+	Silent	SNP	C	C	T	rs2709416	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:208477956C>T	ENST00000411432.1	-	4	687	c.471G>A	c.(469-471)caG>caA	p.Q157Q	METTL21A_ENST00000448007.2_Silent_p.Q157Q|METTL21A_ENST00000458426.1_Intron|METTL21A_ENST00000272839.3_Silent_p.Q175Q|METTL21A_ENST00000477919.1_5'Flank|METTL21A_ENST00000406927.2_Silent_p.Q157Q|METTL21A_ENST00000425132.1_Intron|METTL21A_ENST00000426075.1_Silent_p.Q157Q|METTL21A_ENST00000448823.2_3'UTR|METTL21A_ENST00000442521.1_Silent_p.Q157Q|METTL21A_ENST00000432416.1_Intron	NM_001127395.1	NP_001120867.1	Q8WXB1	MT21A_HUMAN	methyltransferase like 21A	157					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	cytoplasm (GO:0005737)	ATPase binding (GO:0051117)|Hsp70 protein binding (GO:0030544)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|stomach(1)	10						GTTCCAGTGTCTGAAGAAGAT	0.403													T|||	4528	0.904153	0.8646	0.879	5008	,	,		21003	0.998		0.831	False		,,,				2504	0.954				p.Q157Q		Atlas-SNP	.											.	METTL21A	24	.	0			c.G471A						PASS	.	T	,	3826,580	258.0+/-262.2	1661,504,38	127.0	129.0	128.0		471,471	-9.3	0.3	2	dbSNP_100	128	7027,1573	295.4+/-302.4	2857,1313,130	no	coding-synonymous,coding-synonymous	METTL21A	NM_001127395.1,NM_145280.4	,	4518,1817,168	TT,TC,CC		18.2907,13.1639,16.5539	,	157/219,157/219	208477956	10853,2153	2203	4300	6503	SO:0001819	synonymous_variant	151194	exon4			CAGTGTCTGAAGA	AK093812, AF455817	CCDS2376.1	2q33.3	2013-09-30	2011-03-03	2011-03-03	ENSG00000144401	ENSG00000144401			30476	protein-coding gene	gene with protein product	"""Hepatocellular carcinoma-associated antigen 557b"", ""heat shock protein 70kDa lysine (K) methyltransferase"""	615257	"""family with sequence similarity 119, member A"""	FAM119A		23921388	Standard	NM_145280		Approved	LOC151194, HCA557b, HSPA-KMT	uc010fuk.1	Q8WXB1	OTTHUMG00000132934	ENST00000411432.1:c.471G>A	2.37:g.208477956C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	83	27	0.325301	NM_145280	Q53RV0|Q8N1Z9|Q96GH6	Silent	SNP	ENST00000411432.1	37	CCDS2376.1																																																																																			C|0.146;T|0.854	0.854	strong		0.403	METTL21A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337044.1	NM_145280	
BRINP1	1620	hgsc.bcm.edu	37	9	121929575	121929575	+	Silent	SNP	T	T	C	rs28453	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:121929575T>C	ENST00000265922.3	-	8	2534	c.2073A>G	c.(2071-2073)tcA>tcG	p.S691S	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	691					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											GGAGCATCACTGACGAAGAGG	0.572													C|||	933	0.186302	0.5136	0.1124	5008	,	,		18193	0.004		0.0915	False		,,,				2504	0.0818				p.S691S		Atlas-SNP	.											.	DBC1	194	.	0			c.A2073G						PASS	.	C		1908,2498	626.9+/-394.8	431,1046,726	130.0	127.0	128.0		2073	-11.0	0.0	9	dbSNP_79	128	717,7883	786.8+/-407.6	35,647,3618	no	coding-synonymous	DBC1	NM_014618.2		466,1693,4344	CC,CT,TT		8.3372,43.3046,20.183		691/762	121929575	2625,10381	2203	4300	6503	SO:0001819	synonymous_variant	1620	exon8			CATCACTGACGAA	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.2073A>G	9.37:g.121929575T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	125	53	0.424	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																			T|0.797;C|0.203	0.203	strong		0.572	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
TRAK2	66008	hgsc.bcm.edu	37	2	202245423	202245423	+	Missense_Mutation	SNP	A	A	T	rs34594680	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:202245423A>T	ENST00000332624.3	-	16	3016	c.2588T>A	c.(2587-2589)aTt>aAt	p.I863N		NM_015049.2	NP_055864.2	O60296	TRAK2_HUMAN	trafficking protein, kinesin binding 2	863			I -> N (in dbSNP:rs34594680). {ECO:0000269|PubMed:15489334}.		protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|endosome (GO:0005768)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GABA receptor binding (GO:0050811)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	23						TTGAGGACCAATTTCTGCCTC	0.453													A|||	263	0.052516	0.1233	0.0562	5008	,	,		20783	0.001		0.0527	False		,,,				2504	0.0072				p.I863N		Atlas-SNP	.											.	TRAK2	62	.	0			c.T2588A						PASS	.	A	ASN/ILE	450,3956	214.5+/-233.7	19,412,1772	81.0	86.0	84.0		2588	-2.3	0.0	2	dbSNP_126	84	494,8106	141.7+/-198.0	16,462,3822	yes	missense	TRAK2	NM_015049.2	149	35,874,5594	TT,TA,AA		5.7442,10.2133,7.2582	benign	863/915	202245423	944,12062	2203	4300	6503	SO:0001583	missense	66008	exon16			GGACCAATTTCTG	AB038951	CCDS2347.1	2q33.1	2012-03-05	2005-12-13	2005-12-13	ENSG00000115993	ENSG00000115993			13206	protein-coding gene	gene with protein product	"""gamma-aminobutyric acid(A) receptor-interacting factor"", ""milton homolog 2 (Drosophila)"", ""O-linked N-acetylglucosamine transferase interacting protein 98"""	607334	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 3"""	ALS2CR3		11161814, 16380713, 20230862	Standard	NM_015049		Approved	CALS-C, KIAA0549, GRIF-1, OIP98, MILT2	uc002uyb.4	O60296	OTTHUMG00000132822	ENST00000332624.3:c.2588T>A	2.37:g.202245423A>T	ENSP00000328875:p.Ile863Asn	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_015049	E7EV21|Q8WVH7|Q96NS2|Q9C0K5|Q9C0K6	Missense_Mutation	SNP	ENST00000332624.3	37	CCDS2347.1	115|115	0.052655677655677656|0.052655677655677656	52|52	0.10569105691056911|0.10569105691056911	18|18	0.049723756906077346|0.049723756906077346	1|1	0.0017482517482517483|0.0017482517482517483	44|44	0.05804749340369393|0.05804749340369393	A|A	1.705|1.705	-0.500469|-0.500469	0.04291|0.04291	0.102133|0.102133	0.057442|0.057442	ENSG00000115993|ENSG00000115993	ENST00000332624|ENST00000542292	T|.	0.06933|.	3.24|.	6.17|6.17	-2.31|-2.31	0.06765|0.06765	.|.	1.354340|.	0.04289|.	N|.	0.345106|.	T|T	0.00300|0.00300	0.0009|0.0009	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.17501|0.17501	-1.0367|-1.0367	10|6	0.15499|0.36615	T|T	0.54|0.2	.|.	4.7814|4.7814	0.13204|0.13204	0.4558:0.0:0.3155:0.2286|0.4558:0.0:0.3155:0.2286	rs34594680;rs59285166|rs34594680;rs59285166	863|.	O60296|.	TRAK2_HUMAN|.	N|M	863|769	ENSP00000328875:I863N|.	ENSP00000328875:I863N|ENSP00000445053:L769M	I|L	-|-	2|1	0|2	TRAK2|TRAK2	201953668|201953668	0.001000|0.001000	0.12720|0.12720	0.014000|0.014000	0.15608|0.15608	0.249000|0.249000	0.25844|0.25844	0.062000|0.062000	0.14389|0.14389	-0.627000|-0.627000	0.05589|0.05589	-0.290000|-0.290000	0.09829|0.09829	ATT|TTG	A|0.935;T|0.065	0.065	strong		0.453	TRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256284.3	NM_015049	
CDHR2	54825	hgsc.bcm.edu	37	5	176017455	176017455	+	Missense_Mutation	SNP	C	C	T	rs2291442	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176017455C>T	ENST00000510636.1	+	27	3657	c.3383C>T	c.(3382-3384)aCg>aTg	p.T1128M	CDHR2_ENST00000506348.1_Missense_Mutation_p.T1128M|CDHR2_ENST00000261944.5_Missense_Mutation_p.T1128M	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1128			T -> M (in dbSNP:rs2291442). {ECO:0000269|PubMed:12117771, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						GACTCGCTGACGCAGCTGCTG	0.637													c|||	1413	0.282149	0.3033	0.2334	5008	,	,		16317	0.3194		0.2445	False		,,,				2504	0.2883				p.T1128M		Atlas-SNP	.											CDHR2,colon,carcinoma,0,1	CDHR2	152	1	0			c.C3383T						scavenged	.		MET/THR,MET/THR	1332,3074	446.3+/-348.0	180,972,1051	65.0	67.0	66.0		3383,3383	0.3	0.0	5	dbSNP_100	66	2337,6263	389.7+/-343.0	298,1741,2261	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	81,81	478,2713,3312	TT,TC,CC		27.1744,30.2315,28.2101	benign,benign	1128/1311,1128/1311	176017455	3669,9337	2203	4300	6503	SO:0001583	missense	54825	exon27			CGCTGACGCAGCT	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.3383C>T	5.37:g.176017455C>T	ENSP00000424565:p.Thr1128Met	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	616	0.28205128205128205	138	0.2804878048780488	104	0.287292817679558	181	0.31643356643356646	193	0.2546174142480211	c	3.170	-0.170179	0.06461	0.302315	0.271744	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.55760	0.5;0.5;0.5	4.61	0.292	0.15737	.	.	.	.	.	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.30149	-0.9988	8	0.45353	T	0.12	-2.7345	3.7294	0.08487	0.1833:0.5449:0.112:0.1598	rs2291442;rs59204096;rs2291442	1128	Q9BYE9	CDHR2_HUMAN	M	1128	ENSP00000424565:T1128M;ENSP00000261944:T1128M;ENSP00000421078:T1128M	ENSP00000261944:T1128M	T	+	2	0	CDHR2	175950061	0.000000	0.05858	0.030000	0.17652	0.184000	0.23303	-1.990000	0.01479	-0.169000	0.10834	-1.263000	0.01449	ACG	C|0.719;T|0.281	0.281	strong		0.637	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
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 GAIIx	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	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	4	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	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318773	21318773	+	Missense_Mutation	SNP	G	G	A	rs3752034	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:21318773G>A	ENST00000583088.1	+	3	1014	c.119G>A	c.(118-120)cGc>cAc	p.R40H	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R40H	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	40					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CACACGCGGCGCAGGTGCCGC	0.612										Prostate(3;0.18)			.|||	1734	0.346246	0.1505	0.366	5008	,	,		36495	0.4812		0.3559	False		,,,				2504	0.4479				p.R40H		Atlas-SNP	.											KCNJ12,NS,carcinoma,+1,1	.	.	1	0			c.G119A						PASS	.	G	HIS/ARG	626,3780		0,626,1577	122.0	91.0	101.0		119	5.3	1.0	17	dbSNP_107	101	2643,5957		0,2643,1657	yes	missense	KCNJ12	NM_021012.4	29	0,3269,3234	AA,AG,GG		30.7326,14.2079,25.1346	benign	40/434	21318773	3269,9737	2203	4300	6503	SO:0001583	missense	100134444	exon3			CGCGGCGCAGGTG	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.119G>A	17.37:g.21318773G>A	ENSP00000463778:p.Arg40His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	116	41	0.353448	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	717	0.3282967032967033	78	0.15853658536585366	120	0.3314917127071823	270	0.47202797202797203	249	0.32849604221635886	G	17.23	3.337271	0.60963	0.142079	0.307326	ENSG00000184185	ENST00000331718	T	0.36699	1.24	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.175986	0.42964	N	0.000638	T	0.00012	0.0000	L	0.47716	1.5	0.53005	D	0.999968	B	0.20780	0.048	B	0.21546	0.035	T	0.50056	-0.8872	10	0.62326	D	0.03	.	19.026	0.92932	0.0:0.0:1.0:0.0	rs3752034;rs3752034	40	Q14500	IRK12_HUMAN	H	40	ENSP00000328150:R40H	ENSP00000328150:R40H	R	+	2	0	KCNJ12	21259366	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.619000	0.74219	2.506000	0.84524	0.591000	0.81541	CGC	G|0.744;A|0.256	0.256	strong		0.612	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
TAS2R20	259295	hgsc.bcm.edu	37	12	11149711	11149711	+	Missense_Mutation	SNP	C	C	A	rs10845279	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11149711C>A	ENST00000538986.1	-	1	763	c.764G>T	c.(763-765)cGa>cTa	p.R255L	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	255			R -> L (in dbSNP:rs10845279). {ECO:0000269|PubMed:15496549}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.R255Q(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						TTCTTTTGGTCGCATCTTAAA	0.373													C|||	2119	0.423123	0.0651	0.3847	5008	,	,		18928	0.755		0.3827	False		,,,				2504	0.6339				p.R255L		Atlas-SNP	.											TAS2R20,colon,carcinoma,0,1	TAS2R20	17	1	1	Substitution - Missense(1)	large_intestine(1)	c.G764T						PASS	.	C	LEU/ARG	442,3964	212.8+/-232.6	18,406,1779	110.0	109.0	109.0		764	-5.3	0.0	12	dbSNP_120	109	3016,5584	465.2+/-366.4	544,1928,1828	yes	missense	TAS2R20	NM_176889.2	102	562,2334,3607	AA,AC,CC		35.0698,10.0318,26.5877	benign	255/310	11149711	3458,9548	2203	4300	6503	SO:0001583	missense	259295	exon1			TTTGGTCGCATCT	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.764G>T	12.37:g.11149711C>A	ENSP00000441624:p.Arg255Leu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	122	47	0.385246	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	C	0.008	-1.921931	0.00498	0.100318	0.350698	ENSG00000255837	ENST00000538986	T	0.00753	5.74	2.66	-5.32	0.02722	.	2.067560	0.05057	N	0.479233	T	0.00012	0.0000	N	0.00017	-2.83	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46638	-0.9177	9	0.02654	T	1	.	4.8332	0.13451	0.2999:0.1236:0.0:0.5765	rs10845279;rs60755728;rs10845279	255	P59543	T2R20_HUMAN	L	255	ENSP00000441624:R255L	ENSP00000441624:R255L	R	-	2	0	TAS2R20	11040978	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.312000	0.02720	-1.408000	0.02040	-0.383000	0.06682	CGA	C|0.671;A|0.329	0.329	strong		0.373	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
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 GAIIx	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		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	128	80	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	
PLEC	5339	hgsc.bcm.edu	37	8	144996029	144996029	+	Missense_Mutation	SNP	A	A	G	rs7833924	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144996029A>G	ENST00000322810.4	-	32	8540	c.8371T>C	c.(8371-8373)Tca>Cca	p.S2791P	PLEC_ENST00000354589.3_Missense_Mutation_p.S2654P|PLEC_ENST00000357649.2_Missense_Mutation_p.S2658P|PLEC_ENST00000436759.2_Missense_Mutation_p.S2681P|PLEC_ENST00000354958.2_Missense_Mutation_p.S2632P|PLEC_ENST00000527096.1_Missense_Mutation_p.S2677P|PLEC_ENST00000345136.3_Missense_Mutation_p.S2654P|PLEC_ENST00000356346.3_Missense_Mutation_p.S2640P|PLEC_ENST00000398774.2_Missense_Mutation_p.S2622P	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2791	Globular 2.		S -> P (in dbSNP:rs7833924).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTCTGAGCTGACACCTTCCGC	0.687													G|||	2337	0.466653	0.8775	0.3674	5008	,	,		16760	0.1429		0.4354	False		,,,				2504	0.3476				p.S2791P		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,9	PLEC	1144	9	0			c.T8371C						scavenged	.	G	PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER	3507,739		1479,549,95	13.0	16.0	15.0		8041,7918,7894,8371,7864,7960,7972,7960	1.3	0.6	8	dbSNP_116	15	3635,4801		854,1927,1437	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	74,74,74,74,74,74,74,74	2333,2476,1532	GG,GA,AA		43.0891,17.4046,43.684	benign,benign,benign,benign,benign,benign,benign,benign	2681/4575,2640/4534,2632/4526,2791/4685,2622/4516,2654/4548,2658/4552,2654/4548	144996029	7142,5540	2123	4218	6341	SO:0001583	missense	5339	exon32			GAGCTGACACCTT	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.8371T>C	8.37:g.144996029A>G	ENSP00000323856:p.Ser2791Pro	Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	978	0.4478021978021978	423	0.8597560975609756	137	0.3784530386740331	94	0.16433566433566432	324	0.42744063324538256	G	9.708	1.156295	0.21454	0.825954	0.430891	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43	4.16	1.26	0.21427	.	0.000000	0.64402	N	0.000006	T	0.00012	0.0000	N	0.05441	-0.05	0.46678	P	8.430000000000382E-4	B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.42766	-0.9432	9	0.02654	T	1	.	3.6953	0.08361	0.4852:0.1979:0.317:0.0	rs7833924	2681;2640;2632;2791;2622;2654;2658;2654	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	P	2654;2658;2654;2622;2791;2632;2640;2681;2677	ENSP00000344848:S2654P;ENSP00000350277:S2658P;ENSP00000346602:S2654P;ENSP00000381756:S2622P;ENSP00000323856:S2791P;ENSP00000347044:S2632P;ENSP00000348702:S2640P;ENSP00000388180:S2681P;ENSP00000434583:S2677P	ENSP00000323856:S2791P	S	-	1	0	PLEC	145068017	0.803000	0.28956	0.551000	0.28230	0.791000	0.44710	0.441000	0.21611	0.147000	0.19030	-0.380000	0.06706	TCA	A|0.560;G|0.440	0.440	strong		0.687	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
BAI2	576	hgsc.bcm.edu	37	1	32196647	32196647	+	Silent	SNP	C	C	G	rs909001|rs35020949	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:32196647C>G	ENST00000373658.3	-	29	4475	c.4134G>C	c.(4132-4134)ccG>ccC	p.P1378P	BAI2_ENST00000257070.4_Silent_p.P1345P|BAI2_ENST00000398547.1_Silent_p.P1311P|BAI2_ENST00000398556.3_Silent_p.P1293P|BAI2_ENST00000398538.1_Silent_p.P1366P|BAI2_ENST00000440175.2_Silent_p.P987P|BAI2_ENST00000373655.2_Silent_p.P1378P|BAI2_ENST00000527361.1_Silent_p.P1345P|BAI2_ENST00000398542.1_Silent_p.P1278P|BAI2_ENST00000465256.1_5'UTR	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1378					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		GGGTCCCCTCCGGCCGGGCCC	0.711													G|||	1930	0.385383	0.7579	0.2594	5008	,	,		12912	0.2331		0.159	False		,,,				2504	0.3609				p.P1378P		Atlas-SNP	.											.	BAI2	128	.	0			c.G4134C						PASS	.	G		2507,1833		741,1025,404	8.0	11.0	10.0		4134	-10.9	0.0	1	dbSNP_86	10	1364,7136		119,1126,3005	no	coding-synonymous	BAI2	NM_001703.2		860,2151,3409	GG,GC,CC		16.0471,42.235,30.148		1378/1586	32196647	3871,8969	2170	4250	6420	SO:0001819	synonymous_variant	576	exon29			CCCCTCCGGCCGG	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.4134G>C	1.37:g.32196647C>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	37	CCDS346.2																																																																																			C|0.675;G|0.325	0.325	strong		0.711	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
DHX58	79132	hgsc.bcm.edu	37	17	40257055	40257055	+	Missense_Mutation	SNP	T	T	C	rs34016093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40257055T>C	ENST00000251642.3	-	10	1604	c.1382A>G	c.(1381-1383)aAt>aGt	p.N461S		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	461	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GGAGATTTCATTGGTCAAGAG	0.577													T|||	204	0.0407348	0.0144	0.049	5008	,	,		18811	0.0109		0.0487	False		,,,				2504	0.093				p.N461S		Atlas-SNP	.											.	DHX58	39	.	0			c.A1382G						PASS	.	T	SER/ASN	73,4333	65.3+/-102.7	0,73,2130	96.0	96.0	96.0		1382	4.8	1.0	17	dbSNP_126	96	416,8184	129.8+/-187.9	14,388,3898	yes	missense	DHX58	NM_024119.2	46	14,461,6028	CC,CT,TT		4.8372,1.6568,3.7598	probably-damaging	461/679	40257055	489,12517	2203	4300	6503	SO:0001583	missense	79132	exon10			ATTTCATTGGTCA	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"""RNA helicase LGP2"""	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.1382A>G	17.37:g.40257055T>C	ENSP00000251642:p.Asn461Ser	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	34	23	0.676471	NM_024119	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	37	CCDS11416.1	67	0.030677655677655676	4	0.008130081300813009	16	0.04419889502762431	7	0.012237762237762238	40	0.052770448548812667	T	21.4	4.147356	0.77888	0.016568	0.048372	ENSG00000108771	ENST00000251642;ENST00000423748	T	0.73047	-0.71	4.77	4.77	0.60923	Helicase, C-terminal (3);	0.099220	0.64402	D	0.000003	T	0.32941	0.0846	L	0.31804	0.96	0.52501	D	0.999957	D;P	0.71674	0.998;0.914	D;P	0.67231	0.95;0.666	T	0.55127	-0.8189	10	0.15066	T	0.55	-15.8552	13.263	0.60117	0.0:0.0:0.0:1.0	rs34016093	454;461	B7Z455;Q96C10	.;DHX58_HUMAN	S	461;424	ENSP00000251642:N461S	ENSP00000251642:N461S	N	-	2	0	DHX58	37510581	1.000000	0.71417	0.999000	0.59377	0.964000	0.63967	7.836000	0.86788	2.015000	0.59207	0.379000	0.24179	AAT	T|0.965;C|0.035	0.035	strong		0.577	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119	
WDR73	84942	hgsc.bcm.edu	37	15	85189464	85189464	+	Silent	SNP	T	T	G	rs2271431	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:85189464T>G	ENST00000434634.2	-	6	528	c.468A>C	c.(466-468)cgA>cgC	p.R156R	WDR73_ENST00000398528.3_5'UTR	NM_032856.2	NP_116245.2	Q6P4I2	WDR73_HUMAN	WD repeat domain 73	156										cervix(1)|large_intestine(1)|lung(1)	3						CCTGCAGACTTCGGAGCCTCG	0.602													G|||	737	0.147165	0.0287	0.1902	5008	,	,		17725	0.1379		0.2734	False		,,,				2504	0.1564				p.R156R		Atlas-SNP	.											.	WDR73	15	.	0			c.A468C						PASS	.	G		247,3761		7,233,1764	47.0	51.0	50.0		468	-2.1	0.0	15	dbSNP_100	50	2280,6066		290,1700,2183	no	coding-synonymous	WDR73	NM_032856.2		297,1933,3947	GG,GT,TT		27.3185,6.1627,20.4549		156/379	85189464	2527,9827	2004	4173	6177	SO:0001819	synonymous_variant	84942	exon6			CAGACTTCGGAGC	AK027200	CCDS45339.1	15q25.2	2013-01-09				ENSG00000177082		"""WD repeat domain containing"""	25928	protein-coding gene	gene with protein product						12477932	Standard	NM_032856		Approved	FLJ14888, HSPC264	uc002bkw.2	Q6P4I2		ENST00000434634.2:c.468A>C	15.37:g.85189464T>G		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_032856	Q96JZ1|Q9P0B7	Silent	SNP	ENST00000434634.2	37	CCDS45339.1																																																																																			T|0.830;G|0.170	0.170	strong		0.602	WDR73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418195.1	NM_032856	
MANSC4	100287284	hgsc.bcm.edu	37	12	27916224	27916224	+	Missense_Mutation	SNP	A	A	G	rs11049126	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27916224A>G	ENST00000381273.3	-	3	469	c.470T>C	c.(469-471)tTa>tCa	p.L157S		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	157						integral component of membrane (GO:0016021)				kidney(1)	1						TTGTTTATCTAAATTCATAGC	0.403													A|||	625	0.1248	0.0234	0.1023	5008	,	,		19740	0.2044		0.173	False		,,,				2504	0.1462				p.L157S		Atlas-SNP	.											.	MANSC4	9	.	0			c.T470C						PASS	.						249.0	211.0	222.0					12																	27916224		692	1591	2283	SO:0001583	missense	100287284	exon3			TTATCTAAATTCA		CCDS53770.1	12p11.22	2011-05-05			ENSG00000205693	ENSG00000205693			40023	protein-coding gene	gene with protein product							Standard	NM_001146221		Approved		uc010sjs.1	A6NHS7	OTTHUMG00000169216	ENST00000381273.3:c.470T>C	12.37:g.27916224A>G	ENSP00000370673:p.Leu157Ser	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	238	99	0.415966	NM_001146221		Missense_Mutation	SNP	ENST00000381273.3	37	CCDS53770.1	295	0.13507326007326007	17	0.034552845528455285	34	0.09392265193370165	112	0.1958041958041958	132	0.1741424802110818	A	16.47	3.131562	0.56828	.	.	ENSG00000205693	ENST00000381273	T	0.49139	0.79	5.41	-2.67	0.06059	.	1.334070	0.05107	N	0.488297	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.28760	0.221	B	0.22386	0.039	T	0.05869	-1.0859	9	0.17832	T	0.49	0.1944	5.4929	0.16787	0.4742:0.0:0.3901:0.1357	rs11049126;rs11049126	157	A6NHS7	MANS4_HUMAN	S	157	ENSP00000370673:L157S	ENSP00000370673:L157S	L	-	2	0	MANSC4	27807491	0.018000	0.18449	0.000000	0.03702	0.794000	0.44872	0.074000	0.14662	-0.497000	0.06641	0.460000	0.39030	TTA	A|0.859;G|0.141	0.141	strong		0.403	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
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 GAIIx	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		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	101	48	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	
NOTCH4	4855	hgsc.bcm.edu	37	6	32190406	32190406	+	Silent	SNP	A	A	G	rs443198	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32190406A>G	ENST00000375023.3	-	3	471	c.333T>C	c.(331-333)ggT>ggC	p.G111G		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	111	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						GGCATCTCTCACCAGTGAAGC	0.632													a|||	2307	0.460663	0.4705	0.3775	5008	,	,		19302	0.5615		0.3638	False		,,,				2504	0.502				p.G111G		Atlas-SNP	.											.	NOTCH4	201	.	0			c.T333C	GRCh37	CM030916	NOTCH4	M	rs443198	PASS	.	A		2013,2393	560.0+/-380.4	466,1081,656	72.0	75.0	74.0	http://www.ncbi.nlm.nih.gov/pubmed?term	333	-8.3	0.1	6	dbSNP_80	74	3241,5359	486.8+/-372.0	614,2013,1673	no	coding-synonymous	NOTCH4	NM_004557.3		1080,3094,2329	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	37.686,45.6877,40.3967		111/2004	32190406	5254,7752	2203	4300	6503	SO:0001819	synonymous_variant	4855	exon3			TCTCTCACCAGTG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.333T>C	6.37:g.32190406A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	149	148	0.993289	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			A|0.576;G|0.424	0.424	strong		0.632	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
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 GAIIx	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	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	50	20	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	
POM121L12	285877	hgsc.bcm.edu	37	7	53103554	53103554	+	Missense_Mutation	SNP	C	C	G	rs11238247	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:53103554C>G	ENST00000408890.4	+	1	206	c.190C>G	c.(190-192)Cag>Gag	p.Q64E		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	64			Q -> E (in dbSNP:rs11238247). {ECO:0000269|PubMed:14702039}.							endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						GAGCCATATTCAGTACTTCCA	0.697													C|||	1680	0.335463	0.1921	0.4323	5008	,	,		12258	0.3095		0.4861	False		,,,				2504	0.3323				p.Q64E		Atlas-SNP	.											.	POM121L12	146	.	0			c.C190G						PASS	.	C	GLU/GLN	852,3038		105,642,1198	29.0	33.0	32.0		190	1.1	0.0	7	dbSNP_120	32	4217,4067		1064,2089,989	yes	missense	POM121L12	NM_182595.3	29	1169,2731,2187	GG,GC,CC		49.0946,21.9023,41.6379	possibly-damaging	64/297	53103554	5069,7105	1945	4142	6087	SO:0001583	missense	285877	exon1			CATATTCAGTACT		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.190C>G	7.37:g.53103554C>G	ENSP00000386133:p.Gln64Glu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	29	28	0.965517	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	806	0.36904761904761907	102	0.2073170731707317	154	0.425414364640884	175	0.30594405594405594	375	0.4947229551451187	C	6.806	0.517760	0.13005	0.219023	0.509054	ENSG00000221900	ENST00000408890	T	0.23348	1.91	1.11	1.11	0.20524	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.43701	0.815	B	0.33690	0.168	T	0.43065	-0.9414	8	0.66056	D	0.02	.	5.5761	0.17225	0.0:1.0:0.0:0.0	rs11238247;rs52794294;rs11238247	64	Q8N7R1	P1L12_HUMAN	E	64	ENSP00000386133:Q64E	ENSP00000386133:Q64E	Q	+	1	0	POM121L12	53071048	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.130000	0.15850	0.903000	0.36546	0.313000	0.20887	CAG	C|0.588;G|0.412	0.412	strong		0.697	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
DLGAP2	9228	hgsc.bcm.edu	37	8	1616640	1616640	+	Silent	SNP	G	G	A	rs4565482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:1616640G>A	ENST00000421627.2	+	6	1850	c.1716G>A	c.(1714-1716)ccG>ccA	p.P572P		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	651					neuron-neuron synaptic transmission (GO:0007270)	cell junction (GO:0030054)|neurofilament (GO:0005883)|postsynaptic membrane (GO:0045211)		p.P616P(1)|p.P594P(1)		breast(1)|endometrium(6)|lung(31)|prostate(3)	41		Ovarian(12;0.0271)|Hepatocellular(245;0.0838)|Colorectal(14;0.0846)		BRCA - Breast invasive adenocarcinoma(11;0.000169)|READ - Rectum adenocarcinoma(644;0.171)		GGATGTCCCCGTGGCCCCAGG	0.672													G|||	367	0.0732827	0.0106	0.0951	5008	,	,		13887	0.003		0.1958	False		,,,				2504	0.089				p.P572P		Atlas-SNP	.											DLGAP2_ENST00000356067,NS,carcinoma,0,5	DLGAP2	292	5	2	Substitution - coding silent(2)	prostate(2)	c.G1716A						PASS	.	G		159,3979		1,157,1911	12.0	18.0	16.0		1716	-11.1	0.0	8	dbSNP_111	16	1716,6654		188,1340,2657	no	coding-synonymous	DLGAP2	NM_004745.3		189,1497,4568	AA,AG,GG		20.5018,3.8424,14.9904		572/976	1616640	1875,10633	2069	4185	6254	SO:0001819	synonymous_variant	9228	exon6			GTCCCCGTGGCCC	AB000275	CCDS47760.1, CCDS75689.1	8p23	2007-12-06	2001-11-28		ENSG00000198010	ENSG00000198010			2906	protein-coding gene	gene with protein product		605438	"""discs, large (Drosophila) homolog-associated protein 2"""			9286858, 10854099	Standard	NM_004745		Approved	DAP-2	uc003wpl.4	Q9P1A6	OTTHUMG00000163599	ENST00000421627.2:c.1716G>A	8.37:g.1616640G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Silent	SNP	ENST00000421627.2	37	CCDS47760.1	193	0.08836996336996338	4	0.008130081300813009	46	0.1270718232044199	1	0.0017482517482517483	142	0.18733509234828497	G	3.107	-0.183454	0.06340	0.038424	0.205018	ENSG00000198010	ENST00000520901	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.99999280338	.	.	.	.	.	.	T	0.05937	-1.0855	3	.	.	.	-10.5133	11.1444	0.48422	0.4809:0.3504:0.1687:0.0	rs4565482	.	.	.	H	589	.	.	R	+	2	0	DLGAP2	1604047	0.000000	0.05858	0.010000	0.14722	0.388000	0.30384	-3.479000	0.00457	-2.726000	0.00386	-1.619000	0.00793	CGT	G|0.894;A|0.106	0.106	strong		0.672	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745	
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 GAIIx	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_ENST00000348328.5_Intron|ACVR1C_ENST00000409680.3_Missense_Mutation_p.N100H	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	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	134	33	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	
FSIP1	161835	hgsc.bcm.edu	37	15	39910431	39910431	+	Missense_Mutation	SNP	A	A	G	rs10152640	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:39910431A>G	ENST00000350221.3	-	11	1413	c.1204T>C	c.(1204-1206)Tgt>Cgt	p.C402R		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	402			C -> R (in dbSNP:rs10152640). {ECO:0000269|Ref.3}.					p.C402R(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCAGAGAGACATGATGTGGAC	0.318													G|||	2063	0.411941	0.7458	0.2594	5008	,	,		20215	0.3095		0.3072	False		,,,				2504	0.2822				p.C402R		Atlas-SNP	.											FSIP1,NS,carcinoma,0,2	FSIP1	53	2	1	Substitution - Missense(1)	stomach(1)	c.T1204C						scavenged	.	G	ARG/CYS	2789,1577		917,955,311	44.0	48.0	47.0		1204	-0.4	0.1	15	dbSNP_119	47	2544,5964		382,1780,2092	yes	missense	FSIP1	NM_152597.4	180	1299,2735,2403	GG,GA,AA		29.9013,36.12,41.4246	benign	402/582	39910431	5333,7541	2183	4254	6437	SO:0001583	missense	161835	exon11			AGAGACATGATGT	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1204T>C	15.37:g.39910431A>G	ENSP00000280236:p.Cys402Arg	Somatic	77	2	0.025974		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	872	0.3992673992673993	346	0.7032520325203252	106	0.292817679558011	188	0.32867132867132864	232	0.30606860158311344	G	0.009	-1.857666	0.00558	0.6388	0.299013	ENSG00000150667	ENST00000350221	T	0.10668	2.85	5.06	-0.452	0.12205	.	0.738656	0.11694	N	0.538597	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15723	-1.0427	8	.	.	.	8.7668	2.7672	0.05323	0.2845:0.4014:0.2062:0.1079	rs10152640;rs52803468;rs57454183;rs10152640	402	Q8NA03	FSIP1_HUMAN	R	402	ENSP00000280236:C402R	.	C	-	1	0	FSIP1	37697723	0.001000	0.12720	0.088000	0.20740	0.012000	0.07955	-0.124000	0.10595	-0.082000	0.12640	-0.726000	0.03593	TGT	A|0.599;G|0.401	0.401	strong		0.318	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
KCNK5	8645	hgsc.bcm.edu	37	6	39159379	39159379	+	Missense_Mutation	SNP	G	G	A	rs150380866	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:39159379G>A	ENST00000359534.3	-	5	1125	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W		NM_003740.3	NP_003731.1	O95279	KCNK5_HUMAN	potassium channel, subfamily K, member 5	263					excretion (GO:0007588)|potassium ion transport (GO:0006813)	integral component of plasma membrane (GO:0005887)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(4)|skin(3)	19						GACTCCTTCCGTCGCCGCCGC	0.562													G|||	12	0.00239617	0.0015	0.0014	5008	,	,		16035	0.0		0.005	False		,,,				2504	0.0041				p.R263W		Atlas-SNP	.											.	KCNK5	57	.	0			c.C787T						PASS	.	G	TRP/ARG	4,4402	8.1+/-20.4	0,4,2199	78.0	85.0	83.0		787	2.9	1.0	6	dbSNP_134	83	44,8556	29.0+/-79.6	0,44,4256	yes	missense	KCNK5	NM_003740.3	101	0,48,6455	AA,AG,GG		0.5116,0.0908,0.3691	probably-damaging	263/500	39159379	48,12958	2203	4300	6503	SO:0001583	missense	8645	exon5			CCTTCCGTCGCCG	AF084830	CCDS4841.1	6p21	2012-03-07			ENSG00000164626	ENSG00000164626		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6280	protein-coding gene	gene with protein product		603493				9812978, 16382106	Standard	XM_005249456		Approved	K2p5.1, TASK-2	uc003oon.3	O95279	OTTHUMG00000014642	ENST00000359534.3:c.787C>T	6.37:g.39159379G>A	ENSP00000352527:p.Arg263Trp	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	52	0.83871	NM_003740	B2RAQ6|B5TJL2|Q5VV76	Missense_Mutation	SNP	ENST00000359534.3	37	CCDS4841.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	0	0.0	3	0.00395778364116095	G	18.69	3.677471	0.68042	9.08E-4	0.005116	ENSG00000164626	ENST00000359534	T	0.26067	1.76	5.05	2.92	0.33932	.	1.216240	0.05744	N	0.601915	T	0.30479	0.0766	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.13602	-1.0503	10	0.87932	D	0	.	12.738	0.57236	0.0:0.0:0.5882:0.4117	.	263	O95279	KCNK5_HUMAN	W	263	ENSP00000352527:R263W	ENSP00000352527:R263W	R	-	1	2	KCNK5	39267357	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.852000	0.48310	1.240000	0.43803	0.561000	0.74099	CGG	G|0.997;A|0.003	0.003	strong		0.562	KCNK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040449.1	NM_003740	
DSPP	1834	hgsc.bcm.edu	37	4	88537444	88537444	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88537444C>T	ENST00000282478.7	+	4	3663	c.3630C>T	c.(3628-3630)agC>agT	p.S1210S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1210S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1210	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcagtgacagcagtgacagca	0.557																																					p.S1210S		Atlas-SNP	.											DSPP,NS,carcinoma,0,1	DSPP	174	1	0			c.C3630T						scavenged	.						44.0	65.0	57.0					4																	88537444		1604	2918	4522	SO:0001819	synonymous_variant	1834	exon5			TGACAGCAGTGAC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3630C>T	4.37:g.88537444C>T		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	112	13	0.116071	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497917	32497917	+	Missense_Mutation	SNP	C	C	A	rs71549220	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32497917C>A	ENST00000374975.3	-	1	147	c.85G>T	c.(85-87)Gct>Tct	p.A29S		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5									p.A29S(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						GTGTCCCCAGCCAAAGCCAGT	0.547													C|||	443	0.0884585	0.0847	0.111	5008	,	,		20515	0.0417		0.1372	False		,,,				2504	0.0757				p.A29S		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	1	Substitution - Missense(1)	stomach(1)	c.G85T						scavenged	.	C	SER/ALA	315,4091		5,305,1893	102.0	105.0	104.0		85	3.6	0.0	6	dbSNP_130	104	739,7861		26,687,3587	no	missense	HLA-DRB5	NM_002125.3	99	31,992,5480	AA,AC,CC		8.593,7.1493,8.104	benign	29/267	32497917	1054,11952	2203	4300	6503	SO:0001583	missense	3127	exon1			CCCCAGCCAAAGC		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.85G>T	6.37:g.32497917C>A	ENSP00000364114:p.Ala29Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	109	19	0.174312	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	12.42	1.933464	0.34096	0.071493	0.08593	ENSG00000198502	ENST00000374975	T	0.00256	8.42	4.54	3.61	0.41365	MHC classes I/II-like antigen recognition protein (1);	0.581841	0.16240	N	0.223213	T	0.00073	0.0002	L	0.54965	1.715	0.09310	N	1	B	0.12630	0.006	B	0.19666	0.026	T	0.40850	-0.9541	10	0.62326	D	0.03	.	9.2292	0.37425	0.2691:0.7309:0.0:0.0	.	29	Q30154	DRB5_HUMAN	S	29	ENSP00000364114:A29S	ENSP00000364114:A29S	A	-	1	0	HLA-DRB5	32605895	0.017000	0.18338	0.005000	0.12908	0.148000	0.21650	0.184000	0.16939	1.002000	0.39104	0.485000	0.47835	GCT	C|0.956;A|0.044	0.044	strong		0.547	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
SLC38A6	145389	hgsc.bcm.edu	37	14	61448049	61448049	+	Silent	SNP	C	C	G	rs17097938	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:61448049C>G	ENST00000267488.4	+	1	170	c.54C>G	c.(52-54)gtC>gtG	p.V18V	SLC38A6_ENST00000354886.2_Silent_p.V18V|SLC38A6_ENST00000456840.2_5'Flank|RP11-193F5.1_ENST00000553946.1_RNA|SLC38A6_ENST00000554304.1_3'UTR|TRMT5_ENST00000261249.6_5'UTR	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	18					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		ATGTCTCTGTCCAGCAGCCTG	0.612											OREG0007220	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=TRMT5|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	C|||	176	0.0351438	0.0023	0.0231	5008	,	,		18153	0.0813		0.0517	False		,,,				2504	0.0235				p.V18V		Atlas-SNP	.											.	SLC38A6	87	.	0			c.C54G						PASS	.	C	,	43,4363	45.3+/-79.5	0,43,2160	70.0	67.0	68.0		54,54	0.9	0.0	14	dbSNP_123	68	279,8319	101.0+/-162.3	3,273,4023	no	coding-synonymous,coding-synonymous	SLC38A6	NM_001172702.1,NM_153811.2	,	3,316,6183	GG,GC,CC		3.2449,0.9759,2.4762	,	18/522,18/457	61448049	322,12682	2203	4299	6502	SO:0001819	synonymous_variant	145389	exon1			CTCTGTCCAGCAG	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.54C>G	14.37:g.61448049C>G		Somatic	52	0	0	1053	WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_153811	C9JWA6|Q86SY5	Silent	SNP	ENST00000267488.4	37	CCDS9751.1																																																																																			C|0.968;G|0.032	0.032	strong		0.612	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1		
LANCL3	347404	hgsc.bcm.edu	37	X	37527659	37527659	+	Intron	SNP	T	T	C	rs28503960	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:37527659T>C	ENST00000378619.3	+	4	1322				TM4SF2_ENST00000465127.1_Intron|LANCL3_ENST00000378621.3_Missense_Mutation_p.L381P	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)								catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						gaacatctgctgtataccaga	0.294													T|||	568	0.150464	0.1256	0.0994	3775	,	,		9346	0.0496		0.1123	False		,,,				2504	0.1738				p.L381P		Atlas-SNP	.											.	LANCL3	42	.	0			c.T1142C						PASS	.	T	,PRO/LEU	697,3136		55,490,97,1086,474	54.0	49.0	51.0		,1142	2.2	0.0	X	dbSNP_125	51	1168,5558		84,695,305,1648,1567	yes	intron,missense	LANCL3	NM_001170331.1,NM_198511.2	,98	139,1185,402,2734,2041	CC,CT,C,TT,T		17.3654,18.1842,17.6627	,benign	,381/389	37527659	1865,8694	2202	4299	6501	SO:0001627	intron_variant	347404	exon5			ATCTGCTGTATAC	AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.1103+917T>C	X.37:g.37527659T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	163	36	0.220859	NM_198511	A6NHE3	Missense_Mutation	SNP	ENST00000378619.3	37	CCDS55398.1	214	0.1289933694996986	46	0.10222222222222223	20	0.060240963855421686	16	0.02877697841726619	63	0.08898305084745763	T	4.137	0.023659	0.08006	0.181842	0.173654	ENSG00000147036	ENST00000378621	.	.	.	2.17	2.17	0.27698	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.32968	0.392	B	0.27500	0.08	T	0.13872	-1.0493	6	0.30078	T	0.28	.	5.629	0.17499	0.0:0.0:0.0:1.0	rs28503960	381	Q6ZV70-2	.	P	381	.	ENSP00000367885:L381P	L	+	2	0	LANCL3	37412578	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.193000	0.17116	1.111000	0.41721	0.430000	0.28490	CTG	T|0.847;C|0.153	0.153	strong		0.294	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511	
BFAR	51283	hgsc.bcm.edu	37	16	14742400	14742400	+	Missense_Mutation	SNP	T	T	G	rs11546303	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:14742400T>G	ENST00000261658.2	+	3	696	c.419T>G	c.(418-420)aTg>aGg	p.M140R	BFAR_ENST00000563971.1_Intron|BFAR_ENST00000426842.2_Intron	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	140			M -> R (in dbSNP:rs11546303).		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						AATCAGCAGATGGGAGGGGGA	0.507													G|||	1262	0.251997	0.1172	0.4049	5008	,	,		17221	0.1558		0.3917	False		,,,				2504	0.2812				p.M140R		Atlas-SNP	.											BFAR,colon,carcinoma,0,1	BFAR	38	1	0			c.T419G						scavenged	.	G	ARG/MET	775,3619	752.4+/-412.3	65,645,1487	207.0	204.0	205.0		419	6.1	1.0	16	dbSNP_120	205	3346,5254	643.3+/-399.9	658,2030,1612	yes	missense	BFAR	NM_016561.2	91	723,2675,3099	GG,GT,TT		38.907,17.6377,31.7146	benign	140/451	14742400	4121,8873	2197	4300	6497	SO:0001583	missense	51283	exon3			AGCAGATGGGAGG	AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"""RING-type (C3HC4) zinc fingers"", ""Sterile alpha motif (SAM) domain containing"""	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.419T>G	16.37:g.14742400T>G	ENSP00000261658:p.Met140Arg	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	127	64	0.503937	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	37	CCDS10554.1	592	0.27106227106227104	64	0.13008130081300814	136	0.3756906077348066	90	0.15734265734265734	302	0.39841688654353563	G	2.593	-0.294767	0.05568	0.176377	0.38907	ENSG00000103429	ENST00000261658	T	0.05855	3.38	6.08	6.08	0.98989	.	0.094567	0.64402	N	0.000001	T	0.00012	0.0000	N	0.01048	-1.04	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45877	-0.9231	9	0.02654	T	1	.	16.121	0.81357	0.0:0.0:0.8652:0.1348	rs11546303;rs52806449;rs11546303	140	Q9NZS9	BFAR_HUMAN	R	140	ENSP00000261658:M140R	ENSP00000261658:M140R	M	+	2	0	BFAR	14649901	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	3.507000	0.53371	1.599000	0.50093	-0.121000	0.15023	ATG	T|0.708;G|0.292	0.292	strong		0.507	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561	
UNC79	57578	hgsc.bcm.edu	37	14	94088369	94088369	+	Missense_Mutation	SNP	T	T	C	rs28670114	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94088369T>C	ENST00000393151.2	+	30	4790	c.4790T>C	c.(4789-4791)gTa>gCa	p.V1597A	UNC79_ENST00000555664.1_Missense_Mutation_p.V1597A|UNC79_ENST00000256339.4_Missense_Mutation_p.V1420A|UNC79_ENST00000553484.1_Missense_Mutation_p.V1619A			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1597			V -> A (in dbSNP:rs28670114).		behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						GACTCGCCGGTAAAGCCTGCT	0.478													T|||	594	0.11861	0.1634	0.134	5008	,	,		19307	0.004		0.2038	False		,,,				2504	0.0777				p.V1420A		Atlas-SNP	.											.	UNC79	366	.	0			c.T4259C						PASS	.	T	ALA/VAL	675,3731	284.6+/-277.7	54,567,1582	69.0	73.0	72.0		4259	-10.5	0.0	14	dbSNP_125	72	1535,7065	288.0+/-298.5	140,1255,2905	yes	missense	UNC79	NM_020818.3	64	194,1822,4487	CC,CT,TT		17.8488,15.32,16.9922	benign	1420/2459	94088369	2210,10796	2203	4300	6503	SO:0001583	missense	57578	exon30			CGCCGGTAAAGCC	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.4790T>C	14.37:g.94088369T>C	ENSP00000376858:p.Val1597Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		296	0.13553113553113552	77	0.1565040650406504	55	0.15193370165745856	1	0.0017482517482517483	163	0.21503957783641162	T	1.765	-0.485748	0.04352	0.1532	0.178488	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.17054	2.3;2.31;2.3;2.3	5.85	-10.5	0.00291	.	1.244990	0.05238	N	0.511633	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36311	-0.9753	9	0.07990	T	0.79	1.8056	7.1867	0.25803	0.0888:0.115:0.523:0.2731	rs28670114	1619	C9JQL1	.	A	1420;1597;1619;1597;1619	ENSP00000256339:V1420A;ENSP00000450868:V1597A;ENSP00000451360:V1619A;ENSP00000376858:V1597A	ENSP00000256339:V1420A	V	+	2	0	KIAA1409	93158122	0.000000	0.05858	0.000000	0.03702	0.230000	0.25150	-0.415000	0.07106	-1.287000	0.02381	-0.680000	0.03767	GTA	T|0.833;C|0.167	0.167	strong		0.478	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
STAG3	10734	hgsc.bcm.edu	37	7	99799845	99799845	+	Silent	SNP	T	T	A	rs1043915	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99799845T>A	ENST00000426455.1	+	24	2852	c.2445T>A	c.(2443-2445)atT>atA	p.I815I	STAG3_ENST00000440830.1_3'UTR|STAG3_ENST00000317296.5_Silent_p.I815I|STAG3_ENST00000394018.2_Silent_p.I757I|GATS_ENST00000543273.1_RNA|GATS_ENST00000436886.2_3'UTR	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	815					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CTCAGATGATTGTTGGGGGCC	0.458													T|||	1969	0.393171	0.3343	0.5173	5008	,	,		19641	0.621		0.2664	False		,,,				2504	0.2802				p.I815I		Atlas-SNP	.											.	STAG3	121	.	0			c.T2445A						PASS	.	T	,	1502,2904		245,1012,946	144.0	153.0	150.0		2445,	-0.2	0.1	7	dbSNP_86	150	2263,6337		305,1653,2342	no	coding-synonymous,utr-3	STAG3,GATS	NM_012447.2,NM_178831.6	,	550,2665,3288	AA,AT,TT		26.314,34.0899,28.9482	,	815/1226,	99799845	3765,9241	2203	4300	6503	SO:0001819	synonymous_variant	10734	exon24			GATGATTGTTGGG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.2445T>A	7.37:g.99799845T>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	37	CCDS34703.1																																																																																			T|0.679;A|0.321	0.321	strong		0.458	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
MTFR1	9650	hgsc.bcm.edu	37	8	66620359	66620359	+	Intron	SNP	G	G	A	rs13274205	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:66620359G>A	ENST00000262146.4	+	7	1059				MTFR1_ENST00000458689.2_Intron	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1						aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			AAAGGGAGGTGATACAGGATT	0.413													G|||	1389	0.277356	0.3215	0.3156	5008	,	,		19512	0.0		0.5348	False		,,,				2504	0.2117				p.X349X		Atlas-SNP	.											.	MTFR1	26	.	0			c.G1046A						PASS	.	G	,,	472,912		83,306,303	46.0	38.0	41.0		,1046,	-0.1	0.0	8	dbSNP_121	41	1761,1421		480,801,310	no	intron,coding-synonymous,intron	MTFR1	NM_001145838.1,NM_001145839.1,NM_014637.3	,,	563,1107,613	AA,AG,GG		44.6574,34.104,48.9049	,,	,349/349,	66620359	2233,2333	692	1591	2283	SO:0001627	intron_variant	9650	exon7			GGAGGTGATACAG		CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"""likely ortholog of chicken chondrocyte protein with a poly proline region"""					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.933+113G>A	8.37:g.66620359G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	15	8	0.533333	NM_001145839	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Silent	SNP	ENST00000262146.4	37	CCDS6182.1																																																																																			G|0.693;A|0.307	0.307	strong		0.413	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637	
KIF1B	23095	hgsc.bcm.edu	37	1	10342522	10342522	+	Silent	SNP	G	G	A	rs17034660	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10342522G>A	ENST00000377086.1	+	15	1567	c.1365G>A	c.(1363-1365)acG>acA	p.T455T	KIF1B_ENST00000377081.1_Silent_p.T455T|KIF1B_ENST00000377083.1_Silent_p.T409T|KIF1B_ENST00000263934.6_Silent_p.T409T|KIF1B_ENST00000377093.4_Silent_p.T409T			O60333	KIF1B_HUMAN	kinesin family member 1B	455					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TGGGCTTGACGTCTGTGACCA	0.478													G|||	206	0.0411342	0.0575	0.0403	5008	,	,		20144	0.0585		0.0288	False		,,,				2504	0.0143				p.T409T		Atlas-SNP	.											.	KIF1B	242	.	0			c.G1227A						PASS	.	G	,	211,4195	129.0+/-165.8	5,201,1997	165.0	151.0	155.0		1227,1227	-6.1	0.6	1	dbSNP_123	155	222,8378	92.8+/-154.8	2,218,4080	no	coding-synonymous,coding-synonymous	KIF1B	NM_015074.3,NM_183416.3	,	7,419,6077	AA,AG,GG		2.5814,4.7889,3.3292	,	409/1771,409/1154	10342522	433,12573	2203	4300	6503	SO:0001819	synonymous_variant	23095	exon13			CTTGACGTCTGTG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.1365G>A	1.37:g.10342522G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	100	56	0.56	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																				G|0.962;A|0.038	0.038	strong		0.478	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
SLCO2A1	6578	hgsc.bcm.edu	37	3	133670073	133670073	+	Silent	SNP	T	T	C	rs6767412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:133670073T>C	ENST00000310926.4	-	6	1113	c.840A>G	c.(838-840)cgA>cgG	p.R280R	SLCO2A1_ENST00000493729.1_Silent_p.R204R	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	280					lipid transport (GO:0006869)|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)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)	p.R280R(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	TGGGCATTGCTCGAGGGAAGA	0.488													T|||	1274	0.254393	0.3215	0.2421	5008	,	,		19409	0.2827		0.1909	False		,,,				2504	0.2086				p.R280R		Atlas-SNP	.											SLCO2A1,NS,carcinoma,0,1	SLCO2A1	72	1	1	Substitution - coding silent(1)	stomach(1)	c.A840G						PASS	.	T		1395,3011	456.5+/-351.3	220,955,1028	87.0	96.0	93.0		840	1.0	0.0	3	dbSNP_116	93	1627,6973	300.6+/-305.0	154,1319,2827	no	coding-synonymous	SLCO2A1	NM_005630.2		374,2274,3855	CC,CT,TT		18.9186,31.6614,23.2354		280/644	133670073	3022,9984	2203	4300	6503	SO:0001819	synonymous_variant	6578	exon6			CATTGCTCGAGGG		CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.840A>G	3.37:g.133670073T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	37	CCDS3084.1																																																																																			T|0.773;C|0.227	0.227	strong		0.488	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
ARHGAP4	393	hgsc.bcm.edu	37	X	153176254	153176254	+	Silent	SNP	A	A	G	rs2070097	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153176254A>G	ENST00000350060.5	-	15	1757	c.1716T>C	c.(1714-1716)caT>caC	p.H572H	ARHGAP4_ENST00000370016.1_Silent_p.H551H|ARHGAP4_ENST00000393721.1_Silent_p.H394H|ARHGAP4_ENST00000537206.1_Silent_p.H549H|ARHGAP4_ENST00000370028.3_Silent_p.H612H|ARHGAP4_ENST00000467421.1_5'UTR	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	572	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|negative regulation of axon extension (GO:0030517)|negative regulation of fibroblast migration (GO:0010764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)	Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGTCCAGGTCATGGGCAGTGC	0.682											OREG0003617	type=REGULATORY REGION|Gene=ARHGAP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	2661	0.704901	0.6914	0.4928	3775	,	,		6158	0.5437		0.3062	False		,,,				2504	0.5613				p.H612H		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.T1836C						PASS	.	G	,	3240,563		1191,370,488,60,73	13.0	15.0	15.0		1836,1716	-6.9	0.0	X	dbSNP_96	15	2616,4076		384,1102,746,931,1112	no	coding-synonymous,coding-synonymous	ARHGAP4	NM_001164741.1,NM_001666.4	,	1575,1472,1234,991,1185	GG,GA,G,AA,A		39.0915,14.8041,44.202	,	612/987,572/947	153176254	5856,4639	2182	4275	6457	SO:0001819	synonymous_variant	393	exon16			CAGGTCATGGGCA	X78817	CCDS14736.1, CCDS55540.1	Xq28	2010-02-09			ENSG00000089820	ENSG00000089820		"""Rho GTPase activating proteins"""	674	protein-coding gene	gene with protein product	"""Rho-GAP hematopoietic protein C1"""	300023				8570618	Standard	NM_001666		Approved	KIAA0131, C1, p115, RhoGAP4, SrGAP4	uc004fjk.2	P98171	OTTHUMG00000024226	ENST00000350060.5:c.1716T>C	X.37:g.153176254A>G		Somatic	31	0	0	1753	WXS	Illumina HiSeq	Phase_I	53	15	0.283019	NM_001164741	Q14144|Q86UY3	Silent	SNP	ENST00000350060.5	37	CCDS14736.1	1043	0.6286919831223629	234	0.7959183673469388	118	0.44696969696969696	218	0.5828877005347594	163	0.26547231270358307	a	0.105	-1.146679	0.01714	0.851959	0.390915	ENSG00000089820	ENST00000454164;ENST00000442172	.	.	.	4.61	-6.94	0.01633	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.24137	P	0.99574145	.	.	.	.	.	.	T	0.07009	-1.0795	3	.	.	.	.	7.0917	0.25287	0.6809:0.0919:0.1343:0.0929	rs2070097;rs17846493;rs17859557;rs61248836;rs2070097	.	.	.	T	72;61	.	.	M	-	2	0	ARHGAP4	152829448	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.160000	0.03147	-2.323000	0.00639	-2.187000	0.00313	ATG	A|0.354;G|0.646	0.646	strong		0.682	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666	
ULK4	54986	hgsc.bcm.edu	37	3	41877414	41877414	+	Missense_Mutation	SNP	T	T	C	rs3774372	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:41877414T>C	ENST00000301831.4	-	18	2168	c.1706A>G	c.(1705-1707)aAa>aGa	p.K569R		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	569			K -> R (in dbSNP:rs3774372).	AIVLLTELIRENFRNSKLKQCLLPTLGE -> TTSSIGIGI LNCLVQHSTPVPRQCLVYV (in Ref. 3; AAH14794). {ECO:0000305}.	cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		CTGTTTTAATTTGCTGTTCCT	0.363													T|||	865	0.172724	0.1974	0.1369	5008	,	,		14471	0.1458		0.1849	False		,,,				2504	0.18				p.K569R		Atlas-SNP	.											.	ULK4	150	.	0			c.A1706G						PASS	.	T	ARG/LYS	766,2902		74,618,1142	135.0	134.0	135.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1706	5.5	1.0	3	dbSNP_107	135	1373,6785		118,1137,2824	yes	missense	ULK4	NM_017886.2	26	192,1755,3966	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	16.8301,20.8833,18.0873	possibly-damaging	569/1276	41877414	2139,9687	1834	4079	5913	SO:0001583	missense	54986	exon18			TTTAATTTGCTGT	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1706A>G	3.37:g.41877414T>C	ENSP00000301831:p.Lys569Arg	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	188	87	0.462766	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	392	0.1794871794871795	105	0.21341463414634146	51	0.1408839779005525	88	0.15384615384615385	148	0.19525065963060687	T	13.98	2.400184	0.42613	0.208833	0.168301	ENSG00000168038	ENST00000301831	T	0.64438	-0.1	5.48	5.48	0.80851	Armadillo-like helical (1);Armadillo-type fold (2);	0.057123	0.64402	U	0.000002	T	0.00039	0.0001	L	0.33485	1.01	0.09310	P	1.0	P	0.42456	0.78	B	0.39027	0.288	T	0.09100	-1.0690	9	0.14252	T	0.57	.	14.0999	0.65049	0.0:0.0:0.0:1.0	rs3774372;rs17216668;rs56443480;rs3774372	569	Q96C45	ULK4_HUMAN	R	569	ENSP00000301831:K569R	ENSP00000301831:K569R	K	-	2	0	ULK4	41852418	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.095000	0.57728	2.204000	0.70986	0.528000	0.53228	AAA	T|0.818;C|0.182	0.182	strong		0.363	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
PDDC1	347862	hgsc.bcm.edu	37	11	772490	772490	+	Silent	SNP	G	G	A	rs12224894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:772490G>A	ENST00000319863.8	-	5	408	c.387C>T	c.(385-387)gcC>gcT	p.A129A	PDDC1_ENST00000397472.2_Silent_p.A129A|PDDC1_ENST00000526325.1_Silent_p.A129A|PDDC1_ENST00000529966.1_5'UTR|PDDC1_ENST00000442059.2_Silent_p.A79A|PDDC1_ENST00000524550.1_Silent_p.A93A	NM_182612.2	NP_872418.1	Q8NB37	PDDC1_HUMAN	Parkinson disease 7 domain containing 1	129						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(3)|urinary_tract(1)	5		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;3.66e-26)|Epithelial(43;2.43e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-19)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCACAGGGCGGCGACACCGT	0.667													g|||	1539	0.307308	0.1687	0.5893	5008	,	,		17437	0.2827		0.4354	False		,,,				2504	0.1881				p.A129A		Atlas-SNP	.											.	PDDC1	16	.	0			c.C387T						PASS	.			957,3449		101,755,1347	145.0	130.0	135.0		387	-8.5	0.1	11	dbSNP_120	135	4144,4456		1005,2134,1161	no	coding-synonymous	PDDC1	NM_182612.2		1106,2889,2508	AA,AG,GG		48.186,21.7204,39.2204		129/221	772490	5101,7905	2203	4300	6503	SO:0001819	synonymous_variant	347862	exon5			CAGGGCGGCGACA	AK128653	CCDS7713.1	11p15.5	2005-10-26			ENSG00000177225	ENSG00000177225			26616	protein-coding gene	gene with protein product							Standard	XM_005252898		Approved	FLJ34283	uc001lrc.3	Q8NB37	OTTHUMG00000133315	ENST00000319863.8:c.387C>T	11.37:g.772490G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_182612	B7ZKW5|Q2NL76|Q6ZQY0|Q8NAE0	Silent	SNP	ENST00000319863.8	37	CCDS7713.1																																																																																			G|0.633;A|0.367	0.367	strong		0.667	PDDC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258051.2	NM_182612	
TSKU	25987	hgsc.bcm.edu	37	11	76506888	76506888	+	Silent	SNP	G	G	A	rs11546727	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:76506888G>A	ENST00000527881.1	+	2	1254	c.228G>A	c.(226-228)tcG>tcA	p.S76S	TSKU_ENST00000333090.4_Silent_p.S76S			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	76					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					TGAATGAGTCGGTGTTGGCGG	0.637													G|||	221	0.0441294	0.1044	0.0317	5008	,	,		17779	0.0		0.0497	False		,,,				2504	0.0112				p.S76S		Atlas-SNP	.											TSKU,right_lower_lobe,carcinoma,+1,1	TSKU	26	1	0			c.G228A						PASS	.	G		381,4019	190.2+/-216.2	21,339,1840	70.0	56.0	61.0		228	-10.8	0.0	11	dbSNP_120	61	455,8129	134.4+/-191.8	13,429,3850	no	coding-synonymous	TSKU	NM_015516.3		34,768,5690	AA,AG,GG		5.3006,8.6591,6.4387		76/354	76506888	836,12148	2200	4292	6492	SO:0001819	synonymous_variant	25987	exon2			TGAGTCGGTGTTG	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"""leucine rich repeat containing 54"", ""tsukushin"", ""tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"""	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.228G>A	11.37:g.76506888G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	15	0.157895	NM_015516	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	Silent	SNP	ENST00000527881.1	37	CCDS8246.1																																																																																			G|0.939;A|0.061	0.061	strong		0.637	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516	
GPR112	139378	hgsc.bcm.edu	37	X	135429503	135429503	+	Missense_Mutation	SNP	C	C	A	rs4829830	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135429503C>A	ENST00000394143.1	+	6	3929	c.3638C>A	c.(3637-3639)aCc>aAc	p.T1213N	GPR112_ENST00000394141.1_Missense_Mutation_p.T1008N|GPR112_ENST00000370652.1_Missense_Mutation_p.T1213N|GPR112_ENST00000287534.4_Missense_Mutation_p.T1150N|GPR112_ENST00000412101.1_Missense_Mutation_p.T1008N	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1213			T -> N (in dbSNP:rs4829830).		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(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GTTGATGAGACCACACCCTCA	0.473													c|||	1760	0.466225	0.4289	0.3573	3775	,	,		15390	0.246		0.3797	False		,,,				2504	0.3221				p.T1213N		Atlas-SNP	.											.	GPR112	459	.	0			c.C3638A						PASS	.		ASN/THR	2122,1713		502,805,313,325,258	214.0	183.0	193.0		3638	-1.5	0.0	X	dbSNP_111	193	3220,3508		566,1176,912,686,960	yes	missense	GPR112	NM_153834.3	65	1068,1981,1225,1011,1218	AA,AC,A,CC,C		47.8597,44.6675,49.4272	benign	1213/3081	135429503	5342,5221	2203	4300	6503	SO:0001583	missense	139378	exon6			ATGAGACCACACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.3638C>A	X.37:g.135429503C>A	ENSP00000377699:p.Thr1213Asn	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	136	91	0.669118	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	746	0.4496684749849307	138	0.372972972972973	83	0.2902097902097902	99	0.21063829787234042	190	0.3242320819112628	c	6.546	0.469051	0.12461	0.553325	0.478597	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.33865	1.43;1.43;1.39;1.52;1.39	2.98	-1.46	0.08800	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.15930	0.015;0.001;0.001	B;B;B	0.14578	0.011;0.003;0.001	T	0.46190	-0.9209	8	0.37606	T	0.19	.	0.3457	0.00341	0.2044:0.3206:0.1987:0.2763	rs4829830;rs58174019;rs4829830	1150;1008;1213	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	N	1213;1213;1008;1150;1008	ENSP00000377699:T1213N;ENSP00000359686:T1213N;ENSP00000416526:T1008N;ENSP00000287534:T1150N;ENSP00000377697:T1008N	ENSP00000287534:T1150N	T	+	2	0	GPR112	135257169	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.312000	0.08113	-0.347000	0.08299	-0.313000	0.08912	ACC	0|0.015;A|0.479	0.479	strong		0.473	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
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 GAIIx	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_ENST00000483485.1_5'UTR|SNX5_ENST00000377759.4_Missense_Mutation_p.R160H	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	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	30	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		
WDR81	124997	hgsc.bcm.edu	37	17	1639458	1639458	+	Silent	SNP	A	A	G	rs11549259|rs587780508	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1639458A>G	ENST00000409644.1	+	9	5451	c.5451A>G	c.(5449-5451)acA>acG	p.T1817T	WDR81_ENST00000419248.1_Silent_p.T590T|WDR81_ENST00000545662.1_Silent_p.T448T|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000309182.5_Silent_p.T766T|WDR81_ENST00000446363.1_Silent_p.T456T|WDR81_ENST00000437219.2_Silent_p.T614T	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1817					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		ACACCCGCACAGGCCTGGTTC	0.677													G|||	3594	0.717652	0.6225	0.6772	5008	,	,		14523	0.8383		0.7177	False		,,,				2504	0.7505				p.T1817T		Atlas-SNP	.											WDR81_ENST00000437219,NS,carcinoma,0,3	WDR81	180	3	0			c.A5451G						PASS	.	G	,,,	2793,1613	493.4+/-362.7	889,1015,299	58.0	59.0	58.0		1842,5451,1770,2298	-11.3	0.2	17	dbSNP_120	58	6229,2369	391.1+/-343.5	2243,1743,313	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	3132,2758,612	GG,GA,AA		27.5529,36.6092,30.6213	,,,	614/739,1817/1942,590/715,766/891	1639458	9022,3982	2203	4299	6502	SO:0001819	synonymous_variant	124997	exon9			CCGCACAGGCCTG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.5451A>G	17.37:g.1639458A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			A|0.293;G|0.707	0.707	strong		0.677	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
RYR2	6262	hgsc.bcm.edu	37	1	237814783	237814783	+	Silent	SNP	C	C	T	rs684923	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:237814783C>T	ENST00000366574.2	+	51	8123	c.7806C>T	c.(7804-7806)caC>caT	p.H2602H	RYR2_ENST00000542537.1_Silent_p.H2586H|RYR2_ENST00000360064.6_Silent_p.H2600H	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2602	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TAAATGAACACGCAAAGATGC	0.318													C|||	2779	0.554912	0.4864	0.5029	5008	,	,		17313	0.7956		0.4324	False		,,,				2504	0.5624				p.H2602H		Atlas-SNP	.											.	RYR2	1273	.	0			c.C7806T						PASS	.	C		1777,1899		437,903,498	78.0	70.0	72.0		7806	-1.3	1.0	1	dbSNP_83	72	3575,4623		779,2017,1303	no	coding-synonymous	RYR2	NM_001035.2		1216,2920,1801	TT,TC,CC		43.6082,48.3406,45.0733		2602/4968	237814783	5352,6522	1838	4099	5937	SO:0001819	synonymous_variant	6262	exon51			TGAACACGCAAAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7806C>T	1.37:g.237814783C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	165	68	0.412121	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			C|0.455;T|0.545	0.545	strong		0.318	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
POLE	5426	hgsc.bcm.edu	37	12	133236000	133236000	+	Silent	SNP	C	C	T	rs5744857	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:133236000C>T	ENST00000320574.5	-	26	3199	c.3156G>A	c.(3154-3156)acG>acA	p.T1052T	POLE_ENST00000535270.1_Silent_p.T1025T	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1052					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|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)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	TGCTGATGGACGTAGACTTCT	0.567								DNA polymerases (catalytic subunits)					T|||	3032	0.605431	0.7602	0.5317	5008	,	,		19097	0.6736		0.4314	False		,,,				2504	0.5573				p.T1052T		Atlas-SNP	.											POLE_ENST00000320574,caecum,carcinoma,-1,2	POLE	416	2	0			c.G3156A						PASS	.	T		3091,1315	441.8+/-346.5	1076,939,188	90.0	81.0	84.0		3156	-11.7	0.0	12	dbSNP_114	84	3704,4896	619.9+/-397.0	798,2108,1394	no	coding-synonymous	POLE	NM_006231.2		1874,3047,1582	TT,TC,CC		43.0698,29.8457,47.7549		1052/2287	133236000	6795,6211	2203	4300	6503	SO:0001819	synonymous_variant	5426	exon26			GATGGACGTAGAC		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.3156G>A	12.37:g.133236000C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			C|0.443;T|0.557	0.557	strong		0.567	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
ACAP3	116983	hgsc.bcm.edu	37	1	1229538	1229538	+	Silent	SNP	C	C	T	rs148138514	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1229538C>T	ENST00000354700.5	-	22	2383	c.2181G>A	c.(2179-2181)gcG>gcA	p.A727A	ACAP3_ENST00000379037.2_5'Flank|ACAP3_ENST00000353662.3_Silent_p.A652A	NM_030649.2	NP_085152.2	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	727					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			endometrium(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	14						GGTTCACGTCCGCTCCGTTTT	0.716													C|||	24	0.00479233	0.0023	0.0058	5008	,	,		7408	0.002		0.0139	False		,,,				2504	0.001				p.A727A		Atlas-SNP	.											.	ACAP3	87	.	0			c.G2181A						PASS	.	C		15,4333		0,15,2159	19.0	23.0	22.0		2181	-8.4	0.5	1	dbSNP_134	22	111,8431		1,109,4161	no	coding-synonymous	ACAP3	NM_030649.2		1,124,6320	TT,TC,CC		1.2995,0.345,0.9775		727/835	1229538	126,12764	2174	4271	6445	SO:0001819	synonymous_variant	116983	exon22			CACGTCCGCTCCG	AF411981	CCDS19.2	1p36	2013-01-10	2008-09-22	2008-09-22	ENSG00000131584	ENSG00000131584		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16754	protein-coding gene	gene with protein product			"""centaurin, beta 5"""	CENTB5			Standard	NM_030649		Approved	KIAA1716	uc001aeb.2	Q96P50	OTTHUMG00000002235	ENST00000354700.5:c.2181G>A	1.37:g.1229538C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	43	13	0.302326	NM_030649	B1AMF5|Q5TA42|Q5TA43|Q86UT3|Q9BSR9|Q9C0E7	Silent	SNP	ENST00000354700.5	37	CCDS19.2																																																																																			C|0.993;T|0.007	0.007	strong		0.716	ACAP3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006366.2	NM_030649	
INPP4B	8821	hgsc.bcm.edu	37	4	143067054	143067054	+	Silent	SNP	G	G	A	rs35390852	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:143067054G>A	ENST00000513000.1	-	19	2092	c.1659C>T	c.(1657-1659)ggC>ggT	p.G553G	INPP4B_ENST00000308502.4_Silent_p.G553G|INPP4B_ENST00000509777.1_Silent_p.G553G|INPP4B_ENST00000508116.1_Silent_p.G553G|INPP4B_ENST00000262992.4_Silent_p.G553G	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	553					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CATTGTTGCCGCCACTGCCTT	0.443													G|||	480	0.0958466	0.0083	0.1052	5008	,	,		17327	0.0615		0.1163	False		,,,				2504	0.2219				p.G553G		Atlas-SNP	.											.	INPP4B	132	.	0			c.C1659T						PASS	.	G	,	149,4257	102.1+/-140.7	2,145,2056	194.0	162.0	173.0		1659,1659	-1.8	0.0	4	dbSNP_126	173	1038,7562	221.0+/-258.6	58,922,3320	yes	coding-synonymous,coding-synonymous	INPP4B	NM_001101669.1,NM_003866.2	,	60,1067,5376	AA,AG,GG		12.0698,3.3818,9.1266	,	553/925,553/925	143067054	1187,11819	2203	4300	6503	SO:0001819	synonymous_variant	8821	exon19			GTTGCCGCCACTG	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.1659C>T	4.37:g.143067054G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	168	88	0.52381	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			G|0.911;A|0.089	0.089	strong		0.443	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	
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 GAIIx	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_ENST00000359484.4_Missense_Mutation_p.V988I|SLC4A5_ENST00000358683.4_Missense_Mutation_p.V988I|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Missense_Mutation_p.V1009I|SLC4A5_ENST00000357822.5_Missense_Mutation_p.V1106I|SLC4A5_ENST00000423644.1_3'UTR|SLC4A5_ENST00000346834.4_Missense_Mutation_p.V1009I|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000394019.2_Missense_Mutation_p.V1090I					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	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	82	47	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		
MAT2A	4144	hgsc.bcm.edu	37	2	85769711	85769711	+	Silent	SNP	C	C	G	rs1078004	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85769711C>G	ENST00000306434.3	+	7	915	c.792C>G	c.(790-792)cgC>cgG	p.R264R	MAT2A_ENST00000409017.1_Silent_p.R201R	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	264					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)	p.R264R(1)		breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TGACTGGACGCAAAATCATTG	0.453													G|||	2468	0.492812	0.7194	0.3934	5008	,	,		20209	0.3859		0.494	False		,,,				2504	0.3661				p.R264R		Atlas-SNP	.											MAT2A,NS,carcinoma,0,1	MAT2A	23	1	1	Substitution - coding silent(1)	stomach(1)	c.C792G						PASS	.	G		2978,1428	464.2+/-353.8	1016,946,241	132.0	141.0	138.0		792	2.8	1.0	2	dbSNP_86	138	3955,4645	602.6+/-394.5	911,2133,1256	yes	coding-synonymous	MAT2A	NM_005911.5		1927,3079,1497	GG,GC,CC		45.9884,32.4103,46.6938		264/396	85769711	6933,6073	2203	4300	6503	SO:0001819	synonymous_variant	4144	exon7			TGGACGCAAAATC		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.792C>G	2.37:g.85769711C>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	119	93	0.781513	NM_005911	A8K511|B4DN45|D6W5L1|Q53SP5	Silent	SNP	ENST00000306434.3	37	CCDS1977.1																																																																																			C|0.483;G|0.517	0.517	strong		0.453	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911	
NUP210	23225	hgsc.bcm.edu	37	3	13421150	13421150	+	Missense_Mutation	SNP	C	C	T	rs7628051	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:13421150C>T	ENST00000254508.5	-	7	971	c.889G>A	c.(889-891)Gcc>Acc	p.A297T		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	297			A -> T (in dbSNP:rs7628051).		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					ACCGGCCGGGCTGGGTCTCCT	0.572													C|||	2589	0.516973	0.8215	0.4236	5008	,	,		15632	0.3323		0.5239	False		,,,				2504	0.3548				p.A297T		Atlas-SNP	.											.	NUP210	182	.	0			c.G889A						PASS	.	C	THR/ALA	3338,1068	721.2+/-409.1	1265,808,130	44.0	45.0	45.0		889	3.0	0.1	3	dbSNP_116	45	4672,3928	601.7+/-394.4	1281,2110,909	yes	missense	NUP210	NM_024923.2	58	2546,2918,1039	TT,TC,CC		45.6744,24.2397,38.413	benign	297/1888	13421150	8010,4996	2203	4300	6503	SO:0001583	missense	23225	exon7			GCCGGGCTGGGTC	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.889G>A	3.37:g.13421150C>T	ENSP00000254508:p.Ala297Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	1153	0.5279304029304029	396	0.8048780487804879	161	0.4447513812154696	208	0.36363636363636365	388	0.5118733509234829	C	5.556	0.287518	0.10513	0.757603	0.543256	ENSG00000132182	ENST00000254508	T	0.05382	3.45	5.15	2.96	0.34315	.	0.781060	0.12576	N	0.456838	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08186	-1.0734	9	0.18276	T	0.48	-21.9636	8.5655	0.33536	0.1293:0.7062:0.0:0.1645	rs7628051;rs17780361;rs56732558;rs7628051	297	Q8TEM1	PO210_HUMAN	T	297	ENSP00000254508:A297T	ENSP00000254508:A297T	A	-	1	0	NUP210	13396150	0.000000	0.05858	0.090000	0.20809	0.099000	0.18886	0.152000	0.16302	1.129000	0.42072	0.655000	0.94253	GCC	C|0.416;T|0.584	0.584	strong		0.572	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
NIPAL2	79815	hgsc.bcm.edu	37	8	99208190	99208190	+	Silent	SNP	A	A	C	rs3779721	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:99208190A>C	ENST00000341166.3	-	9	1179	c.924T>G	c.(922-924)acT>acG	p.T308T	NIPAL2_ENST00000430223.2_Silent_p.T308T|NIPAL2_ENST00000520545.1_5'UTR	NM_024759.1	NP_079035.1	Q9H841	NPAL2_HUMAN	NIPA-like domain containing 2	308						integral component of membrane (GO:0016021)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(3)|kidney(1)|large_intestine(2)|lung(5)|stomach(1)	12						ATATAAATACAGTGAGAAAAG	0.328													A|||	2040	0.407348	0.3026	0.4841	5008	,	,		15920	0.4325		0.3479	False		,,,				2504	0.5297				p.T308T		Atlas-SNP	.											.	NIPAL2	23	.	0			c.T924G						PASS	.	A		1347,3059	436.8+/-344.8	198,951,1054	51.0	52.0	51.0		924	0.5	0.4	8	dbSNP_107	51	3080,5518	464.2+/-366.2	564,1952,1783	yes	coding-synonymous	NIPAL2	NM_024759.1		762,2903,2837	CC,CA,AA		35.8223,30.5719,34.0434		308/369	99208190	4427,8577	2203	4299	6502	SO:0001819	synonymous_variant	79815	exon9			AAATACAGTGAGA	AK024017	CCDS6278.1	8q22.2	2009-03-24		2009-03-24	ENSG00000104361	ENSG00000104361			25854	protein-coding gene	gene with protein product				NPAL2		14702039	Standard	NM_024759		Approved	FLJ13955	uc003yil.1	Q9H841	OTTHUMG00000164668	ENST00000341166.3:c.924T>G	8.37:g.99208190A>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_024759	A2RTY8	Silent	SNP	ENST00000341166.3	37	CCDS6278.1																																																																																			A|0.642;C|0.358	0.358	strong		0.328	NIPAL2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379677.1	NM_024759	
MRPL37	51253	hgsc.bcm.edu	37	1	54683856	54683856	+	Silent	SNP	C	C	G	rs15921	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:54683856C>G	ENST00000360840.5	+	7	1283	c.1206C>G	c.(1204-1206)ggC>ggG	p.G402G	MRPL37_ENST00000336230.6_Silent_p.G271G|MRPL37_ENST00000605337.1_Intron	NM_016491.3	NP_057575.2	Q9BZE1	RM37_HUMAN	mitochondrial ribosomal protein L37	402					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(4)|skin(2)	19						AACCTGTTGGCCCAGTTGGTT	0.448													G|||	2031	0.405551	0.3502	0.3545	5008	,	,		20898	0.5942		0.2078	False		,,,				2504	0.5256				p.G402G		Atlas-SNP	.											MRPL37,NS,carcinoma,0,2	MRPL37	36	2	0			c.C1206G						scavenged	.	G		1355,3051	691.3+/-405.4	217,921,1065	199.0	208.0	205.0		1206	0.8	1.0	1	dbSNP_52	205	1862,6738	729.9+/-406.7	190,1482,2628	no	coding-synonymous	MRPL37	NM_016491.3		407,2403,3693	GG,GC,CC		21.6512,30.7535,24.7347		402/424	54683856	3217,9789	2203	4300	6503	SO:0001819	synonymous_variant	51253	exon7			TGTTGGCCCAGTT	AB051344	CCDS589.1	1p32.1	2012-09-13			ENSG00000116221	ENSG00000116221		"""Mitochondrial ribosomal proteins / large subunits"""	14034	protein-coding gene	gene with protein product		611843				10600119	Standard	NM_016491		Approved	RPML2, MRP-L2	uc001cxa.4	Q9BZE1	OTTHUMG00000008118	ENST00000360840.5:c.1206C>G	1.37:g.54683856C>G		Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	141	57	0.404255	NM_016491	Q96Q67|Q9BWR1|Q9P0P3	Silent	SNP	ENST00000360840.5	37	CCDS589.1																																																																																			C|0.704;G|0.296	0.296	strong		0.448	MRPL37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022224.1	NM_016491	
RAB34	83871	hgsc.bcm.edu	37	17	27044004	27044004	+	Silent	SNP	C	C	T	rs11545699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27044004C>T	ENST00000395245.3	-	2	689	c.63G>A	c.(61-63)agG>agA	p.R21R	RAB34_ENST00000395242.2_Silent_p.R21R|RAB34_ENST00000447716.1_Silent_p.R78R|RAB34_ENST00000395243.3_Silent_p.R21R|RAB34_ENST00000415040.2_Silent_p.R21R|RAB34_ENST00000301043.6_Silent_p.R21R|RAB34_ENST00000436730.3_Silent_p.R21R|RPL23A_ENST00000422514.2_5'Flank|RAB34_ENST00000450529.1_Silent_p.R21R|RAB34_ENST00000453384.3_Silent_p.R78R	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family	21					antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					CGGCCTCCTTCCTCAGGCACT	0.652													C|||	36	0.0071885	0.0008	0.0086	5008	,	,		17009	0.0		0.0239	False		,,,				2504	0.0051				p.E169K	Pancreas(175;216 2049 29940 32498 41589)	Atlas-SNP	.											.	.	.	.	0			c.G505A						PASS	.	C	,,,,	27,4379	32.6+/-62.9	0,27,2176	64.0	64.0	64.0		234,234,63,234,63	4.4	1.0	17	dbSNP_120	64	230,8370	93.1+/-155.1	5,220,4075	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAB34	NM_001142624.2,NM_001142625.2,NM_001144942.1,NM_001144943.1,NM_031934.5	,,,,	5,247,6251	TT,TC,CC		2.6744,0.6128,1.976	,,,,	78/309,78/269,21/252,78/317,21/260	27044004	257,12749	2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			CTCCTTCCTCAGG	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"""RAB, member RAS oncogene"""	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680	ENST00000395245.3:c.63G>A	17.37:g.27044004C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_001256281	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	37	CCDS11240.1	26	0.011904761904761904	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	11.42	1.634497	0.29068	0.006128	0.026744	ENSG00000109113	ENST00000419712	.	.	.	5.39	4.42	0.53409	.	.	.	.	.	T	0.27489	0.0675	.	.	.	.	.	.	.	.	.	.	.	.	T	0.55835	-0.8078	3	.	.	.	-13.2002	9.2331	0.37450	0.0:0.8359:0.0:0.1641	rs11545699;rs16964527;rs11545699	.	.	.	E	41	.	.	G	-	2	0	RAB34	24068131	0.980000	0.34600	1.000000	0.80357	0.994000	0.84299	0.275000	0.18698	1.509000	0.48786	0.561000	0.74099	GGA	C|0.983;T|0.017	0.017	strong		0.652	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345906.1	NM_031934	
SPACA7	122258	hgsc.bcm.edu	37	13	113052388	113052388	+	Silent	SNP	A	A	G	rs2296895	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:113052388A>G	ENST00000283550.3	+	3	244	c.177A>G	c.(175-177)ttA>ttG	p.L59L	SPACA7_ENST00000375699.3_Silent_p.L28L	NM_145248.4	NP_660291.2	Q96KW9	SPAC7_HUMAN	sperm acrosome associated 7	59						acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)				large_intestine(5)|lung(4)|skin(3)|urinary_tract(1)	13						AGGAGATTTTAGATCTGAATA	0.488													G|||	3379	0.67472	0.8154	0.6196	5008	,	,		20762	0.624		0.5696	False		,,,				2504	0.684				p.L59L		Atlas-SNP	.											SPACA7,NS,adenoma,0,1	SPACA7	36	1	0			c.A177G						PASS	.	G		3464,942	356.9+/-313.7	1368,728,107	142.0	137.0	138.0		177	2.8	0.0	13	dbSNP_100	138	5061,3535	514.4+/-378.4	1515,2031,752	no	coding-synonymous	SPACA7	NM_145248.4		2883,2759,859	GG,GA,AA		41.1238,21.3799,34.4332		59/196	113052388	8525,4477	2203	4298	6501	SO:0001819	synonymous_variant	122258	exon3			GATTTTAGATCTG	BC016750	CCDS9524.1	13q34	2013-10-11	2011-03-15	2011-03-15	ENSG00000153498	ENSG00000153498			29575	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 28"""	C13orf28		22495889	Standard	NM_145248		Approved		uc001vsd.2	Q96KW9	OTTHUMG00000017365	ENST00000283550.3:c.177A>G	13.37:g.113052388A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	67	53	0.791045	NM_145248	Q5T8L1	Silent	SNP	ENST00000283550.3	37	CCDS9524.1																																																																																			A|0.363;G|0.637	0.637	strong		0.488	SPACA7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045820.2	NM_145248	
DISP1	84976	hgsc.bcm.edu	37	1	223176275	223176275	+	Silent	SNP	G	G	A	rs61738819	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:223176275G>A	ENST00000284476.6	+	8	1700	c.1536G>A	c.(1534-1536)gtG>gtA	p.V512V		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	512	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		TAGCCATTGTGATTGTCCTTT	0.383													G|||	287	0.0573083	0.0121	0.0692	5008	,	,		23825	0.0		0.1392	False		,,,				2504	0.0849				p.V512V		Atlas-SNP	.											.	DISP1	145	.	0			c.G1536A						PASS	.	G		177,4229	114.6+/-152.6	6,165,2032	129.0	121.0	124.0		1536	1.5	0.0	1	dbSNP_129	124	1299,7301	256.6+/-281.0	97,1105,3098	no	coding-synonymous	DISP1	NM_032890.3		103,1270,5130	AA,AG,GG		15.1047,4.0172,11.3486		512/1525	223176275	1476,11530	2203	4300	6503	SO:0001819	synonymous_variant	84976	exon10			CATTGTGATTGTC	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.1536G>A	1.37:g.223176275G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Silent	SNP	ENST00000284476.6	37	CCDS1536.1																																																																																			G|0.899;A|0.101	0.101	strong		0.383	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
BTN3A2	11118	hgsc.bcm.edu	37	6	26370707	26370707	+	Silent	SNP	T	T	C	rs9379862	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26370707T>C	ENST00000356386.2	+	5	779	c.591T>C	c.(589-591)gaT>gaC	p.D197D	BTN3A2_ENST00000527422.1_Silent_p.D197D|BTN3A2_ENST00000377708.2_Silent_p.D197D|BTN3A2_ENST00000396934.3_Silent_p.D174D|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000396948.1_Silent_p.D197D|BTN3A2_ENST00000508906.2_Silent_p.D155D	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	197					interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						TGGTTGCAGATGGAGTGGGCC	0.567													t|||	1182	0.236022	0.3109	0.1931	5008	,	,		18947	0.124		0.2396	False		,,,				2504	0.2771				p.D197D		Atlas-SNP	.											.	BTN3A2	44	.	0			c.T591C						PASS	.	C	,,,,	1355,3051		203,949,1051	153.0	143.0	146.0		591,591,522,465,591	-4.6	0.0	6	dbSNP_119	146	2112,6488		249,1614,2437	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	452,2563,3488	CC,CT,TT		24.5581,30.7535,26.6569	,,,,	197/335,197/335,174/312,155/293,197/335	26370707	3467,9539	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon3			TGCAGATGGAGTG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.591T>C	6.37:g.26370707T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	156	23	0.147436	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			T|0.752;C|0.248	0.248	strong		0.567	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
TRIOBP	11078	hgsc.bcm.edu	37	22	38120429	38120429	+	Silent	SNP	T	T	C	rs6000868	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:38120429T>C	ENST00000406386.3	+	7	2121	c.1866T>C	c.(1864-1866)gaT>gaC	p.D622D		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	622					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CCACACGAGATAACCCCAGAA	0.587																																					p.D622D		Atlas-SNP	.											TRIOBP_ENST00000344404,colon,carcinoma,0,1	TRIOBP	262	1	0			c.T1866C						scavenged	.						124.0	138.0	134.0					22																	38120429		1941	4148	6089	SO:0001819	synonymous_variant	11078	exon7			ACGAGATAACCCC	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1866T>C	22.37:g.38120429T>C		Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	171	13	0.0760234	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			T|0.625;C|0.375	0.375	strong		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
PCSK5	5125	hgsc.bcm.edu	37	9	78936492	78936492	+	Missense_Mutation	SNP	A	A	G	rs1110223	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:78936492A>G	ENST00000545128.1	+	30	4496	c.3958A>G	c.(3958-3960)Aag>Gag	p.K1320E		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1320	CRM (Cys-rich motif).				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						CGTGGCTGTGAAGGGGGTATG	0.557													G|||	1597	0.31889	0.4592	0.2378	5008	,	,		19341	0.1369		0.341	False		,,,				2504	0.3517				p.K1320E		Atlas-SNP	.											.	PCSK5	329	.	0			c.A3958G						PASS	.	G	GLU/LYS	773,979		180,413,283	107.0	87.0	93.0		3958	4.8	0.9	9	dbSNP_86	93	1314,2668		221,872,898	yes	missense	PCSK5	NM_001190482.1	56	401,1285,1181	GG,GA,AA		32.9985,44.121,36.3969	benign	1320/1861	78936492	2087,3647	876	1991	2867	SO:0001583	missense	5125	exon30			GCTGTGAAGGGGG		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.3958A>G	9.37:g.78936492A>G	ENSP00000446280:p.Lys1320Glu	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	670	0.3067765567765568	234	0.47560975609756095	99	0.27348066298342544	76	0.13286713286713286	261	0.34432717678100266	G	1.456	-0.563675	0.03939	0.44121	0.329985	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.49432	0.78;1.64	5.68	4.78	0.61160	.	0.398150	0.27397	N	0.019557	T	0.00012	0.0000	N	0.02736	-0.51	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.42949	-0.9421	7	0.02654	T	1	-9.562	9.362	0.38201	0.0773:0.1438:0.7788:0.0	rs1110223;rs2803426;rs60945756	.	.	.	E	1320;1050;1020	ENSP00000446280:K1320E;ENSP00000411654:K1020E	ENSP00000365945:K1050E	K	+	1	0	PCSK5	78126312	1.000000	0.71417	0.887000	0.34795	0.398000	0.30690	2.286000	0.43496	0.753000	0.32945	-0.802000	0.03209	AAG	A|0.687;G|0.313	0.313	strong		0.557	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PYGB	5834	hgsc.bcm.edu	37	20	25264814	25264814	+	Silent	SNP	T	T	C	rs2227892	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:25264814T>C	ENST00000216962.4	+	14	1805	c.1695T>C	c.(1693-1695)gaT>gaC	p.D565D		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	565					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						CCATGTTCGATGTGCATGTGA	0.552													C|||	2689	0.536941	0.4516	0.3473	5008	,	,		20398	0.9107		0.4334	False		,,,				2504	0.5082				p.D565D		Atlas-SNP	.											.	PYGB	84	.	0			c.T1695C						PASS	.	C		1903,2503	629.0+/-395.2	401,1101,701	228.0	159.0	183.0		1695	-4.5	0.9	20	dbSNP_98	183	3754,4846	616.5+/-396.5	813,2128,1359	no	coding-synonymous	PYGB	NM_002862.3		1214,3229,2060	CC,CT,TT		43.6512,43.1911,43.4953		565/844	25264814	5657,7349	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon14			GTTCGATGTGCAT		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.1695T>C	20.37:g.25264814T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			T|0.523;C|0.477	0.477	strong		0.552	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
KANSL1	284058	hgsc.bcm.edu	37	17	44249096	44249096	+	Silent	SNP	A	A	C	rs571568457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44249096A>C	ENST00000262419.6	-	2	884	c.414T>G	c.(412-414)ctT>ctG	p.L138L	KANSL1_ENST00000575318.1_Silent_p.L138L|KANSL1_ENST00000432791.1_Silent_p.L138L|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.L138L|KANSL1_ENST00000572904.1_Silent_p.L138L|KANSL1_ENST00000576248.1_5'Flank	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	138					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											TCATGGTTCTAAGATTTTCTA	0.428													A|||	364	0.0726837	0.0113	0.1398	5008	,	,		24050	0.001		0.1998	False		,,,				2504	0.0511				p.L138L		Atlas-SNP	.											.	.	.	.	0			c.T414G						PASS	.	A	,,	169,4237		0,169,2034	140.0	201.0	180.0		414,414,414	0.8	1.0	17	dbSNP_123	180	1588,7012		0,1588,2712	yes	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	0,1757,4746	CC,CA,AA		18.4651,3.8357,13.5091	,,	138/1105,138/1106,138/1106	44249096	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			GGTTCTAAGATTT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.414T>G	17.37:g.44249096A>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.888;C|0.112	0.112	strong		0.428	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
HRNR	388697	hgsc.bcm.edu	37	1	152191051	152191051	+	Silent	SNP	G	G	A	rs74868796	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152191051G>A	ENST00000368801.2	-	3	3129	c.3054C>T	c.(3052-3054)tcC>tcT	p.S1018S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1018					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AAGACTGCCCGGAACCAGACC	0.607													A|||	147	0.029353	0.0023	0.0461	5008	,	,		21218	0.0		0.0994	False		,,,				2504	0.0123				p.S1018S		Atlas-SNP	.											.	HRNR	403	.	0			c.C3054T						PASS	.	A		71,4335	63.5+/-100.7	1,69,2133	136.0	151.0	146.0		3054	-6.0	0.0	1	dbSNP_131	146	764,7836	181.0+/-229.8	33,698,3569	no	coding-synonymous	HRNR	NM_001009931.1		34,767,5702	AA,AG,GG		8.8837,1.6114,6.4201		1018/2851	152191051	835,12171	2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			CTGCCCGGAACCA	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.3054C>T	1.37:g.152191051G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			G|0.942;A|0.058	0.058	strong		0.607	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
NFATC1	4772	hgsc.bcm.edu	37	18	77170477	77170477	+	Missense_Mutation	SNP	C	C	A	rs1051978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:77170477C>A	ENST00000427363.2	+	2	202	c.202C>A	c.(202-204)Ccg>Acg	p.P68T	NFATC1_ENST00000591814.1_Missense_Mutation_p.P68T|NFATC1_ENST00000329101.4_Missense_Mutation_p.P55T|NFATC1_ENST00000253506.5_Missense_Mutation_p.P68T|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000318065.5_Missense_Mutation_p.P55T|NFATC1_ENST00000586434.1_Missense_Mutation_p.P55T|NFATC1_ENST00000592223.1_Missense_Mutation_p.P55T|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000587635.1_Missense_Mutation_p.P68T|NFATC1_ENST00000542384.1_Missense_Mutation_p.P68T			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	68			P -> T (in dbSNP:rs1051978).		calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	CCTGCCGGCCCCGTGCCACAA	0.652													C|||	234	0.0467252	0.0068	0.1527	5008	,	,		14100	0.0		0.0934	False		,,,				2504	0.0256				p.P68T	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C202A						PASS	.	C	THR/PRO,THR/PRO,,THR/PRO,THR/PRO	100,4306	77.8+/-116.1	1,98,2104	59.0	68.0	65.0		202,163,,163,202	3.5	0.0	18	dbSNP_86	65	935,7663	205.9+/-248.2	54,827,3418	yes	missense,missense,intron,missense,missense	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	38,38,,38,38	55,925,5522	AA,AC,CC		10.8746,2.2696,7.9591	possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	68/826,55/931,,55/813,68/717	77170477	1035,11969	2203	4299	6502	SO:0001583	missense	4772	exon2			CCGGCCCCGTGCC	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.202C>A	18.37:g.77170477C>A	ENSP00000389377:p.Pro68Thr	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		128	0.05860805860805861	4	0.008130081300813009	50	0.13812154696132597	0	0.0	74	0.09762532981530343	C	10.32	1.318656	0.23994	0.022696	0.108746	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384;ENST00000329101;ENST00000427363;ENST00000397794	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	4.39	3.49	0.39957	.	0.118056	0.64402	D	0.000016	T	0.00328	0.0010	M	0.70275	2.135	0.09310	P	1.0	B;B;B;B;B;B;B	0.34181	0.306;0.306;0.306;0.306;0.306;0.44;0.306	B;B;B;B;B;B;B	0.30646	0.08;0.118;0.05;0.08;0.08;0.08;0.05	T	0.10543	-1.0625	9	0.66056	D	0.02	-10.9661	8.6371	0.33955	0.0:0.7533:0.1611:0.0856	rs1051978;rs2230114;rs16958940;rs1051978	55;55;68;68;68;55;68	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	T	68;68;68;55;55;32	ENSP00000316553:P68T;ENSP00000253506:P68T;ENSP00000442435:P68T;ENSP00000327850:P55T	ENSP00000253506:P68T	P	+	1	0	NFATC1	75271465	0.236000	0.23804	0.006000	0.13384	0.137000	0.21094	2.714000	0.47202	1.013000	0.39391	0.561000	0.74099	CCG	C|0.931;A|0.069	0.069	strong		0.652	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
ZNF331	55422	hgsc.bcm.edu	37	19	54080144	54080144	+	Silent	SNP	A	A	G	rs8109631	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54080144A>G	ENST00000253144.9	+	7	1663	c.330A>G	c.(328-330)agA>agG	p.R110R	ZNF331_ENST00000449416.1_Silent_p.R110R|ZNF331_ENST00000513999.1_Silent_p.R110R|ZNF331_ENST00000411977.2_Silent_p.R110R|ZNF331_ENST00000511593.2_Silent_p.R110R|ZNF331_ENST00000512387.1_Silent_p.R110R|ZNF331_ENST00000511154.1_Silent_p.R110R|ZNF331_ENST00000513265.1_Intron	NM_001253801.1|NM_018555.5	NP_001240730.1|NP_061025.5	Q9NQX6	ZN331_HUMAN	zinc finger protein 331	110					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R110R(1)		NS(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	10				GBM - Glioblastoma multiforme(134;0.00555)		ATGTCAAAAGACCTGCTACTA	0.463			T	?	follicular thyroid adenoma								G|||	3725	0.74381	0.9266	0.5965	5008	,	,		18003	0.6954		0.6958	False		,,,				2504	0.7004				p.R110R		Atlas-SNP	.		Dom	yes		19	19q13.3-q13.4	55422	zinc finger protein 331		E	ZNF331,NS,carcinoma,0,1	ZNF331	66	1	1	Substitution - coding silent(1)	stomach(1)	c.A330G						scavenged	.	G	,,	3906,500	231.0+/-245.0	1735,436,32	92.0	95.0	94.0		330,330,330	-5.3	0.0	19	dbSNP_116	94	6136,2464	407.5+/-349.2	2204,1728,368	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF331	NM_001079906.1,NM_001079907.1,NM_018555.5	,,	3939,2164,400	GG,GA,AA		28.6512,11.3482,22.7895	,,	110/464,110/464,110/464	54080144	10042,2964	2203	4300	6503	SO:0001819	synonymous_variant	55422	exon5			CAAAAGACCTGCT	AF251515	CCDS33102.1	19q13	2013-12-10				ENSG00000130844		"""Zinc fingers, C2H2-type"", ""-"""	15489	protein-coding gene	gene with protein product	"""rearranged in thyroid adenomas"""	606043					Standard	NM_001079906		Approved	RITA, ZNF463, ZNF361	uc021uzh.1	Q9NQX6		ENST00000253144.9:c.330A>G	19.37:g.54080144A>G		Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	82	52	0.634146	NM_001253801	Q96GJ4	Silent	SNP	ENST00000253144.9	37	CCDS33102.1																																																																																			A|0.243;G|0.757	0.757	strong		0.463	ZNF331-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371366.1	NM_018555	
ZNF211	10520	hgsc.bcm.edu	37	19	58152361	58152361	+	Silent	SNP	T	T	A	rs3746219	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58152361T>A	ENST00000347302.3	+	3	686	c.507T>A	c.(505-507)acT>acA	p.T169T	ZNF211_ENST00000299871.5_Silent_p.T234T|ZNF211_ENST00000254182.7_Silent_p.T160T|ZNF211_ENST00000420680.1_Silent_p.T173T|ZNF211_ENST00000240731.4_Silent_p.T182T|ZNF211_ENST00000544273.1_Silent_p.T181T|ZNF211_ENST00000541801.1_Silent_p.T160T|ZNF211_ENST00000391703.3_Silent_p.T108T	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	169					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(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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;0.026)		ATGTGGACACTGCCTCGTTTA	0.463													A|||	1072	0.214058	0.2352	0.1297	5008	,	,		22324	0.3214		0.159	False		,,,				2504	0.1912				p.T234T		Atlas-SNP	.											.	ZNF211	78	.	0			c.T702A						PASS	.	A	,	980,3426	732.6+/-410.4	117,746,1340	94.0	84.0	88.0		546,507	-3.0	0.0	19	dbSNP_107	88	1346,7254	756.5+/-407.5	97,1152,3051	no	coding-synonymous,coding-synonymous	ZNF211	NM_006385.3,NM_198855.2	,	214,1898,4391	AA,AT,TT		15.6512,22.2424,17.8841	,	182/578,169/565	58152361	2326,10680	2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			GGACACTGCCTCG	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.507T>A	19.37:g.58152361T>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	37	CCDS12957.1	485	0.22206959706959706	135	0.27439024390243905	52	0.143646408839779	180	0.3146853146853147	118	0.15567282321899736	a	3.445	-0.113268	0.06881	0.222424	0.156512	ENSG00000121417	ENST00000407202	.	.	.	3.01	-3.05	0.05396	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.39333	-0.9619	3	.	.	.	.	1.5958	0.02663	0.21:0.1384:0.3799:0.2718	rs3746219;rs58797181;rs3746219	.	.	.	S	173	.	.	C	+	1	0	ZNF211	62844173	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.114000	0.01329	-1.426000	0.01994	-3.087000	0.00065	TGC	T|0.805;A|0.195	0.195	strong		0.463	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
GLT6D1	360203	hgsc.bcm.edu	37	9	138516128	138516128	+	Missense_Mutation	SNP	C	C	T	rs61739510	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138516128C>T	ENST00000371763.1	-	5	899	c.646G>A	c.(646-648)Gct>Act	p.A216T		NM_182974.2	NP_892019.2	Q7Z4J2	GL6D1_HUMAN	glycosyltransferase 6 domain containing 1	216					carbohydrate metabolic process (GO:0005975)	integral component of membrane (GO:0016021)	transferase activity, transferring hexosyl groups (GO:0016758)			endometrium(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	15		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;4.3e-07)|Epithelial(140;1.58e-06)|all cancers(34;5.36e-05)		GGGATGCAAGCTGCTGAGGTC	0.517													C|||	221	0.0441294	0.0038	0.0706	5008	,	,		19738	0.0675		0.0477	False		,,,				2504	0.0521				p.A216T		Atlas-SNP	.											.	GLT6D1	56	.	0			c.G646A						PASS	.	C	THR/ALA	44,3796		0,44,1876	98.0	98.0	98.0		646	3.5	0.0	9	dbSNP_129	98	558,7702		22,514,3594	yes	missense	GLT6D1	NM_182974.2	58	22,558,5470	TT,TC,CC		6.7554,1.1458,4.9752	probably-damaging	216/277	138516128	602,11498	1920	4130	6050	SO:0001583	missense	360203	exon5			TGCAAGCTGCTGA	AY336054	CCDS43900.1	9q34.3	2013-02-22	2004-09-16	2004-09-17	ENSG00000204007	ENSG00000204007		"""Glycosyltransferase family 6 domain containing"""	23671	protein-coding gene	gene with protein product		613699	"""galactosyltransferase family 6 domain containing 1"""	GLTDC1			Standard	NM_182974		Approved		uc010nbd.1	Q7Z4J2	OTTHUMG00000020911	ENST00000371763.1:c.646G>A	9.37:g.138516128C>T	ENSP00000360829:p.Ala216Thr	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_182974		Missense_Mutation	SNP	ENST00000371763.1	37	CCDS43900.1	112	0.05128205128205128	4	0.008130081300813009	25	0.06906077348066299	39	0.06818181818181818	44	0.05804749340369393	C	21.7	4.192627	0.78902	0.011458	0.067554	ENSG00000204007	ENST00000371763	T	0.02140	4.43	3.49	3.49	0.39957	.	0.000000	0.53938	D	0.000045	T	0.01061	0.0035	M	0.90922	3.16	0.43874	D	0.996482	D	0.89917	1.0	D	0.97110	1.0	T	0.00202	-1.1925	10	0.87932	D	0	-40.4359	13.325	0.60454	0.0:1.0:0.0:0.0	rs61739510	216	Q7Z4J2	GL6D1_HUMAN	T	216	ENSP00000360829:A216T	ENSP00000360829:A216T	A	-	1	0	GLT6D1	137655949	0.995000	0.38212	0.048000	0.18961	0.008000	0.06430	4.249000	0.58766	2.268000	0.75426	0.655000	0.94253	GCT	C|0.947;T|0.053	0.053	strong		0.517	GLT6D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055005.2	NM_182974	
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 GAIIx	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	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	38	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		
NPAP1	23742	hgsc.bcm.edu	37	15	24922208	24922208	+	Silent	SNP	C	C	G	rs12905237	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:24922208C>G	ENST00000329468.2	+	1	1668	c.1194C>G	c.(1192-1194)gcC>gcG	p.A398A		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	398	Pro-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCCAGCCTGCCCCTTCTTTCT	0.527													C|||	615	0.122804	0.0787	0.0821	5008	,	,		17130	0.1528		0.17	False		,,,				2504	0.1319				p.A398A		Atlas-SNP	.											.	.	.	.	0			c.C1194G						PASS	.	C		401,4005		16,369,1818	69.0	70.0	70.0		1194	-0.1	0.0	15	dbSNP_121	70	1404,7196		115,1174,3011	no	coding-synonymous	C15orf2	NM_018958.2		131,1543,4829	GG,GC,CC		16.3256,9.1012,13.8782		398/1157	24922208	1805,11201	2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			GCCTGCCCCTTCT	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.1194C>G	15.37:g.24922208C>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_018958		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			C|0.867;G|0.133	0.133	strong		0.527	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
SORL1	6653	hgsc.bcm.edu	37	11	121460846	121460846	+	Silent	SNP	C	C	T	rs2276412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:121460846C>T	ENST00000260197.7	+	30	4305	c.4176C>T	c.(4174-4176)aaC>aaT	p.N1392N	SORL1_ENST00000525532.1_Silent_p.N336N|SORL1_ENST00000532694.1_Silent_p.N238N|SORL1_ENST00000527934.1_5'Flank|SORL1_ENST00000534286.1_Silent_p.N302N	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1392	LDL-receptor class A 8. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		ACAGGGAGAACGACTGTGGGG	0.547													C|||	421	0.0840655	0.2262	0.0375	5008	,	,		18894	0.0645		0.0149	False		,,,				2504	0.0164				p.N1392N		Atlas-SNP	.											.	SORL1	218	.	0			c.C4176T						PASS	.	C		801,3605	322.9+/-297.8	80,641,1482	174.0	180.0	178.0		4176	-4.7	0.9	11	dbSNP_100	178	158,8440	75.1+/-137.7	0,158,4141	no	coding-synonymous	SORL1	NM_003105.5		80,799,5623	TT,TC,CC		1.8376,18.1798,7.3747		1392/2215	121460846	959,12045	2203	4299	6502	SO:0001819	synonymous_variant	6653	exon30			GGAGAACGACTGT	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.4176C>T	11.37:g.121460846C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	129	21	0.162791	NM_003105	B2RNX7|Q92856	Silent	SNP	ENST00000260197.7	37	CCDS8436.1																																																																																			C|0.924;T|0.076	0.076	strong		0.547	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
CHAF1A	10036	hgsc.bcm.edu	37	19	4409756	4409756	+	Splice_Site	SNP	A	A	G	rs2230636	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4409756A>G	ENST00000301280.5	+	3	1061	c.960A>G	c.(958-960)agA>agG	p.R320R		NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	320					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCTCCGCAGAGTGAGTATCT	0.627								Chromatin Structure					A|||	692	0.138179	0.0492	0.3055	5008	,	,		18632	0.0198		0.2406	False		,,,				2504	0.1564				p.R320R		Atlas-SNP	.											.	CHAF1A	69	.	0			c.A960G						PASS	.	A		393,4013	194.3+/-219.2	17,359,1827	50.0	48.0	49.0		960	-2.2	0.8	19	dbSNP_126	49	2129,6471	350.0+/-327.7	262,1605,2433	yes	coding-synonymous-near-splice	CHAF1A	NM_005483.2		279,1964,4260	GG,GA,AA		24.7558,8.9197,19.3911		320/957	4409756	2522,10484	2203	4300	6503	SO:0001630	splice_region_variant	10036	exon3			CCGCAGAGTGAGT	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.960+1A>G	19.37:g.4409756A>G		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	27	9	0.333333	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Silent	SNP	ENST00000301280.5	37	CCDS32875.1																																																																																			A|0.809;G|0.191	0.191	strong		0.627	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483	Silent
CPN2	1370	hgsc.bcm.edu	37	3	194062519	194062519	+	Missense_Mutation	SNP	C	C	T	rs3732477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:194062519C>T	ENST00000323830.3	-	2	1002	c.913G>A	c.(913-915)Gct>Act	p.A305T	CPN2_ENST00000429275.1_Missense_Mutation_p.A305T	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	305			A -> T (in dbSNP:rs3732477).		protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		GTGCCCTCAGCGACAGTCTCC	0.597													C|||	1835	0.366414	0.4561	0.2752	5008	,	,		19539	0.3185		0.3131	False		,,,				2504	0.4141				p.A305T		Atlas-SNP	.											.	CPN2	56	.	0			c.G913A						PASS	.	C	THR/ALA	1807,2599	527.8+/-372.2	364,1079,760	51.0	47.0	48.0		913	-10.6	0.0	3	dbSNP_107	48	2431,6169	402.3+/-347.4	348,1735,2217	yes	missense	CPN2	NM_001080513.2	58	712,2814,2977	TT,TC,CC		28.2674,41.0123,32.585	benign	305/546	194062519	4238,8768	2203	4300	6503	SO:0001583	missense	1370	exon2			CCTCAGCGACAGT	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"""carboxypeptidase N, polypeptide 2, 83kD"""	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.913G>A	3.37:g.194062519C>T	ENSP00000319464:p.Ala305Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	42	0.43299	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	799	0.3658424908424908	213	0.4329268292682927	122	0.3370165745856354	208	0.36363636363636365	256	0.33773087071240104	C	5.221	0.226234	0.09916	0.410123	0.282674	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.58358	0.34;0.34	5.29	-10.6	0.00265	.	1.554000	0.04255	N	0.339262	T	0.00012	0.0000	N	0.17312	0.475	0.80722	P	0.0	B	0.16396	0.017	B	0.13407	0.009	T	0.30357	-0.9981	9	0.05436	T	0.98	.	13.9695	0.64230	0.0607:0.1435:0.6345:0.1614	rs3732477;rs56776099;rs3732477	305	P22792	CPN2_HUMAN	T	305	ENSP00000319464:A305T;ENSP00000402232:A305T	ENSP00000319464:A305T	A	-	1	0	CPN2	195544214	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.271000	0.08572	-2.493000	0.00515	-0.165000	0.13383	GCT	C|0.653;T|0.347	0.347	strong		0.597	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513	
APOL5	80831	hgsc.bcm.edu	37	22	36123083	36123083	+	Missense_Mutation	SNP	C	C	T	rs2076672	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36123083C>T	ENST00000249044.2	+	3	968	c.968C>T	c.(967-969)aCg>aTg	p.T323M		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	323			T -> M (in dbSNP:rs2076672).		lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						GGGGCAAGGACGGAGACAGCA	0.612													C|||	744	0.148562	0.0923	0.2032	5008	,	,		18198	0.0804		0.2545	False		,,,				2504	0.1472				p.T323M		Atlas-SNP	.											.	APOL5	45	.	0			c.C968T						PASS	.	C	MET/THR	523,3883	234.2+/-247.1	28,467,1708	43.0	43.0	43.0		968	1.8	0.0	22	dbSNP_96	43	2264,6336	376.9+/-338.3	292,1680,2328	yes	missense	APOL5	NM_030642.1	81	320,2147,4036	TT,TC,CC		26.3256,11.8702,21.4286	probably-damaging	323/434	36123083	2787,10219	2203	4300	6503	SO:0001583	missense	80831	exon3			CAAGGACGGAGAC	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"""Apolipoproteins"""	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.968C>T	22.37:g.36123083C>T	ENSP00000249044:p.Thr323Met	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	18	0.5625	NM_030642	Q5TFL9|Q9UGW5	Missense_Mutation	SNP	ENST00000249044.2	37	CCDS13920.1	386	0.17673992673992675	55	0.11178861788617886	88	0.2430939226519337	38	0.06643356643356643	205	0.2704485488126649	C	13.49	2.253235	0.39797	0.118702	0.263256	ENSG00000128313	ENST00000249044	T	0.04119	3.7	3.9	1.78	0.24846	.	0.611094	0.13858	U	0.357864	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	D	0.71674	0.998	P	0.58331	0.837	T	0.47142	-0.9140	9	0.87932	D	0	.	7.0387	0.25008	0.0:0.7788:0.0:0.2212	rs2076672;rs52809043;rs60873045;rs2076672	323	Q9BWW9	APOL5_HUMAN	M	323	ENSP00000249044:T323M	ENSP00000249044:T323M	T	+	2	0	APOL5	34453029	0.001000	0.12720	0.000000	0.03702	0.065000	0.16274	0.985000	0.29578	0.174000	0.19809	0.655000	0.94253	ACG	C|0.812;T|0.188	0.188	strong		0.612	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
MCF2	4168	hgsc.bcm.edu	37	X	138679712	138679712	+	Silent	SNP	T	T	A	rs1051619	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:138679712T>A	ENST00000370576.4	-	18	2171	c.1962A>T	c.(1960-1962)ggA>ggT	p.G654G	MCF2_ENST00000520602.1_Silent_p.G714G|MCF2_ENST00000370573.4_Silent_p.G654G|MCF2_ENST00000414978.1_Silent_p.G714G|MCF2_ENST00000519895.1_Silent_p.G730G|MCF2_ENST00000338585.6_Silent_p.G670G|AL033403.1_ENST00000401295.2_RNA|MCF2_ENST00000370578.4_Silent_p.G799G|MCF2_ENST00000536274.1_Silent_p.G615G	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence	654	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|dendrite development (GO:0016358)|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)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(15)|lung(34)|pancreas(1)|pleura(1)|prostate(1)	62	Acute lymphoblastic leukemia(192;0.000127)					ACAGAGCAGATCCTTCACAGT	0.328													T|||	726	0.192318	0.0204	0.2075	3775	,	,		14365	0.0466		0.3728	False		,,,				2504	0.136				p.G730G		Atlas-SNP	.											.	MCF2	432	.	0			c.A2190T						PASS	.	T	,,,,,	362,3473		17,274,54,1341,517	103.0	87.0	93.0		2142,2190,1845,1962,2010,1962	1.5	0.0	X	dbSNP_86	93	3458,3266		620,1261,957,546,913	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MCF2	NM_001099855.1,NM_001171876.1,NM_001171877.1,NM_001171878.1,NM_001171879.1,NM_005369.4	,,,,,	637,1535,1011,1887,1430	AA,AT,A,TT,T		48.5723,9.4394,36.1777	,,,,,	714/986,730/1002,615/822,654/861,670/942,654/926	138679712	3820,6739	2203	4297	6500	SO:0001819	synonymous_variant	4168	exon22			AGCAGATCCTTCA		CCDS14667.1, CCDS48175.1, CCDS55514.1, CCDS55515.1, CCDS55516.1, CCDS55517.1	Xq26.3-q27.1	2012-07-24			ENSG00000101977	ENSG00000101977		"""Rho guanine nucleotide exchange factors"""	6940	protein-coding gene	gene with protein product	"""Oncogene MCF2 (oncogene DBL)"""	311030				2577874, 1611909	Standard	NM_001099855		Approved	DBL, ARHGEF21	uc011mwo.1	P10911	OTTHUMG00000022537	ENST00000370576.4:c.1962A>T	X.37:g.138679712T>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	199	48	0.241206	NM_001171876	B7Z3Y5|B7Z869|B7ZAV1|E9PH77|F5H091|P14919|Q5JYJ2|Q5JYJ3|Q5JYJ4|Q8IUF3|Q8IUF4|Q9UJB3	Silent	SNP	ENST00000370576.4	37	CCDS14667.1	405	0.244122965641953	12	0.02459016393442623	60	0.19480519480519481	22	0.039711191335740074	191	0.32154882154882153	T	1.295	-0.606460	0.03717	0.094394	0.514277	ENSG00000101977	ENST00000437564	.	.	.	5.69	1.45	0.22620	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19300	P	0.999970659	.	.	.	.	.	.	T	0.48375	-0.9041	3	.	.	.	.	5.805	0.18434	0.1285:0.2461:0.0:0.6255	rs1051619;rs3192018;rs17284775;rs17879934;rs1051619	.	.	.	F	158	.	.	I	-	1	0	MCF2	138507378	0.002000	0.14202	0.021000	0.16686	0.333000	0.28666	-0.162000	0.10012	0.279000	0.22186	0.486000	0.48141	ATC	T|0.720;0|0.003	.	strong		0.328	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	NM_005369	
DOCK7	85440	hgsc.bcm.edu	37	1	62960101	62960101	+	Silent	SNP	A	A	G	rs10889335	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:62960101A>G	ENST00000340370.5	-	39	4986	c.4969T>C	c.(4969-4971)Ttg>Ctg	p.L1657L	DOCK7_ENST00000251157.5_Silent_p.L1679L	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1688					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						AACCAGGTCAATCGCAGATCT	0.468													A|||	1751	0.349641	0.4228	0.3573	5008	,	,		18621	0.1815		0.3171	False		,,,				2504	0.4519				p.L1679L		Atlas-SNP	.											.	DOCK7	184	.	0			c.T5035C						PASS	.	A		1726,2680	518.5+/-369.7	350,1026,827	102.0	79.0	87.0		4969	-8.7	0.0	1	dbSNP_120	87	2870,5730	451.3+/-362.6	508,1854,1938	no	coding-synonymous	DOCK7	NM_033407.2		858,2880,2765	GG,GA,AA		33.3721,39.1739,35.3375		1657/2110	62960101	4596,8410	2203	4300	6503	SO:0001819	synonymous_variant	85440	exon40			AGGTCAATCGCAG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.4969T>C	1.37:g.62960101A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	105	61	0.580952	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	37	CCDS30734.1	667	0.30540293040293043	204	0.4146341463414634	116	0.32044198895027626	100	0.17482517482517482	247	0.3258575197889182	A	8.164	0.790280	0.16258	0.391739	0.333721	ENSG00000116641	ENST00000454575	.	.	.	5.9	-8.68	0.00859	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999740427	.	.	.	.	.	.	T	0.27365	-1.0076	3	.	.	.	.	22.854	0.99977	0.2653:0.0:0.7347:0.0	rs10889335;rs59629051;rs10889335	.	.	.	T	850	.	.	I	-	2	0	DOCK7	62732689	0.003000	0.15002	0.003000	0.11579	0.990000	0.78478	-0.049000	0.11924	-1.661000	0.01484	-0.353000	0.07706	ATT	A|0.670;G|0.330	0.330	strong		0.468	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
ARMCX1	51309	hgsc.bcm.edu	37	X	100808222	100808222	+	Silent	SNP	C	C	T	rs1044275	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:100808222C>T	ENST00000372829.3	+	4	680	c.309C>T	c.(307-309)ggC>ggT	p.G103G		NM_016608.1	NP_057692.1	Q9P291	ARMX1_HUMAN	armadillo repeat containing, X-linked 1	103						integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(2)|ovary(3)|pancreas(1)|urinary_tract(1)	19						GCGGAGGTGGCCTAGAGGCCA	0.562													C|||	100	0.0264901	0.0053	0.036	3775	,	,		14022	0.0		0.0616	False		,,,				2504	0.0061				p.G103G		Atlas-SNP	.											.	ARMCX1	67	.	0			c.C309T						PASS	.	C		63,3772		0,52,11,1580,560	68.0	62.0	64.0		309	0.2	1.0	X	dbSNP_86	64	675,6053		39,418,179,1971,1693	no	coding-synonymous	ARMCX1	NM_016608.1		39,470,190,3551,2253	TT,TC,T,CC,C		10.0327,1.6428,6.9867		103/454	100808222	738,9825	2203	4300	6503	SO:0001819	synonymous_variant	51309	exon4			AGGTGGCCTAGAG	AB039670	CCDS14487.1	Xq21.33-q22.2	2014-03-21			ENSG00000126947	ENSG00000126947		"""Armadillo repeat containing"""	18073	protein-coding gene	gene with protein product		300362				11162520, 16221301, 22569362	Standard	NM_016608		Approved	ALEX1, GASP7	uc004ehv.3	Q9P291	OTTHUMG00000022033	ENST00000372829.3:c.309C>T	X.37:g.100808222C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	59	13	0.220339	NM_016608	Q53HK2|Q9H2Q0	Silent	SNP	ENST00000372829.3	37	CCDS14487.1																																																																																			C|0.948;T|0.052	0.052	strong		0.562	ARMCX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057561.1	NM_016608	
TNFRSF4	7293	hgsc.bcm.edu	37	1	1148445	1148445	+	Silent	SNP	G	G	A	rs34160451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1148445G>A	ENST00000379236.3	-	3	301	c.297C>T	c.(295-297)tgC>tgT	p.C99C	TNFRSF4_ENST00000453580.1_5'UTR	NM_003327.3	NP_003318.1	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily, member 4	99					cellular defense response (GO:0006968)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin secretion (GO:0051024)|regulation of apoptotic process (GO:0042981)|regulation of protein kinase activity (GO:0045859)|T cell proliferation (GO:0042098)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			large_intestine(1)|lung(2)|urinary_tract(1)	4	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GTGTGGCCGTGCACAGCTGCT	0.697													g|||	38	0.00758786	0.0	0.0058	5008	,	,		12685	0.001		0.0249	False		,,,				2504	0.0082				p.C99C		Atlas-SNP	.											.	TNFRSF4	12	.	0			c.C297T						PASS	.			13,4377		0,13,2182	16.0	18.0	17.0		297	2.8	0.8	1	dbSNP_126	17	202,8378		1,200,4089	no	coding-synonymous	TNFRSF4	NM_003327.3		1,213,6271	AA,AG,GG		2.3543,0.2961,1.6577		99/278	1148445	215,12755	2195	4290	6485	SO:0001819	synonymous_variant	7293	exon3			GGCCGTGCACAGC	X75962	CCDS11.1	1p36	2008-02-05			ENSG00000186827	ENSG00000186827		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11918	protein-coding gene	gene with protein product		600315		TXGP1L		7510240, 2828930	Standard	NM_003327		Approved	ACT35, OX40, CD134	uc001ade.3	P43489	OTTHUMG00000001415	ENST00000379236.3:c.297C>T	1.37:g.1148445G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	134	62	0.462687	NM_003327	Q13663|Q2M312|Q5T7M0	Silent	SNP	ENST00000379236.3	37	CCDS11.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	17	0.022427440633245383	g	1.251	-0.618691	0.03663	0.002961	0.023543	ENSG00000186827	ENST00000453580	.	.	.	3.69	2.77	0.32553	.	.	.	.	.	T	0.38188	0.1031	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	T	0.37244	-0.9714	4	.	.	.	-16.94	6.0225	0.19636	0.2369:0.0:0.7631:0.0	rs34160451	.	.	.	Y	45	.	.	H	-	1	0	TNFRSF4	1138308	0.990000	0.36364	0.821000	0.32701	0.081000	0.17604	0.269000	0.18589	0.908000	0.36671	0.472000	0.43445	CAC	G|0.988;A|0.012	0.012	strong		0.697	TNFRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004086.1		
RC3H2	54542	hgsc.bcm.edu	37	9	125618080	125618080	+	Silent	SNP	T	T	G	rs7033878	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:125618080T>G	ENST00000373670.1	-	13	3132	c.2532A>C	c.(2530-2532)atA>atC	p.I844I	RC3H2_ENST00000423239.2_Silent_p.I844I|RC3H2_ENST00000357244.2_Silent_p.I844I			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	844					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						TACAGGAGCCTATGGTGCCAC	0.388													T|||	233	0.0465256	0.1006	0.049	5008	,	,		15984	0.0		0.0596	False		,,,				2504	0.0061				p.I844I		Atlas-SNP	.											.	RC3H2	150	.	0			c.A2532C						PASS	.	T	,	328,3430		8,312,1559	106.0	102.0	103.0		2532,2532	3.0	1.0	9	dbSNP_116	103	539,7669		14,511,3579	no	coding-synonymous,coding-synonymous	RC3H2	NM_001100588.1,NM_018835.2	,	22,823,5138	GG,GT,TT		6.5668,8.728,7.2455	,	844/1192,844/1065	125618080	867,11099	1879	4104	5983	SO:0001819	synonymous_variant	54542	exon14			GGAGCCTATGGTG	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	21461	protein-coding gene	gene with protein product		615231	"""membrane associated DNA binding protein"", ""ring finger and CCCH-type zinc finger domains 2"""	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.2532A>C	9.37:g.125618080T>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	26	0.382353	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Silent	SNP	ENST00000373670.1	37	CCDS43874.1																																																																																			T|0.932;G|0.068	0.068	strong		0.388	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835	
KIAA1143	57456	hgsc.bcm.edu	37	3	44794881	44794881	+	Missense_Mutation	SNP	A	A	C	rs112645395	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:44794881A>C	ENST00000296121.4	-	3	476	c.417T>G	c.(415-417)atT>atG	p.I139M	KIAA1143_ENST00000484437.1_5'UTR	NM_020696.3	NP_065747.1	Q96AT1	K1143_HUMAN	KIAA1143	139			I -> M (in dbSNP:rs3853404). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							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)		TACTATTTTTAATTTGTTTTT	0.299													A|||	190	0.0379393	0.0083	0.0764	5008	,	,		15712	0.0446		0.0467	False		,,,				2504	0.0348				p.I139M		Atlas-SNP	.											.	KIAA1143	10	.	0			c.T417G						PASS	.	A	MET/ILE	68,4336		0,68,2134	69.0	77.0	74.0		417	-10.3	0.4	3	dbSNP_132	74	335,8259		5,325,3967	no	missense	KIAA1143	NM_020696.3	10	5,393,6101	CC,CA,AA		3.8981,1.5441,3.1005	benign	139/155	44794881	403,12595	2202	4297	6499	SO:0001583	missense	57456	exon3			ATTTTTAATTTGT	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.417T>G	3.37:g.44794881A>C	ENSP00000296121:p.Ile139Met	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_020696	A8K0I4|Q96HJ8|Q9ULS7	Missense_Mutation	SNP	ENST00000296121.4	37	CCDS2721.1	87	0.03983516483516483	4	0.008130081300813009	23	0.06353591160220995	22	0.038461538461538464	38	0.05013192612137203	A	14.05	2.420633	0.42918	0.015441	0.038981	ENSG00000163807	ENST00000296121	T	0.42900	0.96	5.17	-10.3	0.00346	.	0.373750	0.30483	N	0.009523	T	0.05318	0.0141	L	0.53249	1.67	0.24096	N	0.995892	P	0.35908	0.527	P	0.44518	0.452	T	0.44143	-0.9347	10	0.56958	D	0.05	-2.9024	14.2241	0.65848	0.1135:0.0:0.1644:0.7221	.	139	Q96AT1	K1143_HUMAN	M	139	ENSP00000296121:I139M	ENSP00000296121:I139M	I	-	3	3	KIAA1143	44769885	0.000000	0.05858	0.395000	0.26283	0.780000	0.44128	-3.926000	0.00333	-2.050000	0.00905	-0.917000	0.02746	ATT	A|1.000;|0.000	.	weak		0.299	KIAA1143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256746.1	NM_020696	
PYDC2	152138	hgsc.bcm.edu	37	3	191179193	191179193	+	Missense_Mutation	SNP	A	A	G	rs293833	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:191179193A>G	ENST00000518817.1	+	1	242	c.242A>G	c.(241-243)cAa>cGa	p.Q81R		NM_001083308.1	NP_001076777.1	Q56P42	PYDC2_HUMAN	pyrin domain containing 2	81	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		Q -> R (in dbSNP:rs293833).			cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10						AAGATGAATCAAACGCATCTG	0.512													A|||	3155	0.629992	0.7534	0.6268	5008	,	,		17407	0.4196		0.7256	False		,,,				2504	0.5838				p.Q81R		Atlas-SNP	.											.	PYDC2	24	.	0			c.A242G						PASS	.	A	ARG/GLN	3332,966		1297,738,114	94.0	99.0	97.0		242	-0.6	0.0	3	dbSNP_79	97	6367,2191		2383,1601,295	yes	missense	PYDC2	NM_001083308.1	43	3680,2339,409	GG,GA,AA		25.6018,22.4756,24.5566	benign	81/98	191179193	9699,3157	2149	4279	6428	SO:0001583	missense	152138	exon1			TGAATCAAACGCA			3q28	2008-07-29				ENSG00000253548			33512	protein-coding gene	gene with protein product		615701				17178784	Standard	NM_001083308		Approved	POP2	uc011bso.2	Q56P42		ENST00000518817.1:c.242A>G	3.37:g.191179193A>G	ENSP00000428325:p.Gln81Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	42	0.4	NM_001083308		Missense_Mutation	SNP	ENST00000518817.1	37		1406	0.6437728937728938	371	0.7540650406504065	239	0.6602209944751382	233	0.40734265734265734	563	0.7427440633245382	A	0	-2.667632	0.00105	0.775244	0.743982	ENSG00000253548	ENST00000518817	T	0.47869	0.83	0.621	-0.631	0.11526	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40194	-0.9576	6	0.02654	T	1	.	.	.	.	rs293833;rs479670;rs56471858;rs58411821;rs293833	81	Q56P42	PYDC2_HUMAN	R	81	ENSP00000428325:Q81R	ENSP00000428325:Q81R	Q	+	2	0	PYDC2	192661887	0.149000	0.22717	0.000000	0.03702	0.007000	0.05969	0.934000	0.28910	-0.282000	0.09128	0.172000	0.16884	CAA	A|0.344;G|0.656	0.656	strong		0.512	PYDC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000343231.2	NM_001083308	
IL23R	149233	hgsc.bcm.edu	37	1	67633812	67633812	+	Missense_Mutation	SNP	G	G	T	rs1884444	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:67633812G>T	ENST00000347310.5	+	2	180	c.9G>T	c.(7-9)caG>caT	p.Q3H	IL23R_ENST00000371002.1_Missense_Mutation_p.Q3H|C1orf141_ENST00000371007.2_Intron	NM_144701.2	NP_653302.2	Q5VWK5	IL23R_HUMAN	interleukin 23 receptor	3			Q -> H (in dbSNP:rs1884444). {ECO:0000269|PubMed:17068223}.		defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|interleukin-23-mediated signaling pathway (GO:0038155)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of granulocyte macrophage colony-stimulating factor production (GO:0032725)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)	interleukin-23 receptor complex (GO:0072536)|receptor complex (GO:0043235)				breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	21						ACATGAATCAGGTCACTATTC	0.323													G|||	2655	0.530152	0.4713	0.3689	5008	,	,		17689	0.6369		0.5239	False		,,,				2504	0.6207				p.Q3H		Atlas-SNP	.											.	IL23R	52	.	0			c.G9T						PASS	.	G	HIS/GLN	2203,2203	589.1+/-387.1	549,1105,549	216.0	182.0	193.0		9	2.0	0.9	1	dbSNP_92	193	4540,4060	595.0+/-393.4	1203,2134,963	yes	missense	IL23R	NM_144701.2	24	1752,3239,1512	TT,TG,GG		47.2093,50.0,48.1547	benign	3/630	67633812	6743,6263	2203	4300	6503	SO:0001583	missense	149233	exon2			GAATCAGGTCACT	AF461422	CCDS637.1	1p31.2	2008-02-05			ENSG00000162594	ENSG00000162594			19100	protein-coding gene	gene with protein product		607562				12023369	Standard	NM_144701		Approved	IL-23R	uc001ddo.3	Q5VWK5	OTTHUMG00000009092	ENST00000347310.5:c.9G>T	1.37:g.67633812G>T	ENSP00000321345:p.Gln3His	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_144701	C9JGX4|Q4VGP1|Q4VGP2|Q4VGP3|Q4VGP4|Q4VGP5|Q4VGP6|Q5VWK7|Q8IW84|Q8NFQ9|Q96AS1	Missense_Mutation	SNP	ENST00000347310.5	37	CCDS637.1	1129	0.516941391941392	226	0.45934959349593496	142	0.39226519337016574	360	0.6293706293706294	401	0.5290237467018469	G	4.001	-0.002532	0.07819	0.5	0.527907	ENSG00000162594	ENST00000347310;ENST00000371002	D;D	0.85339	-1.97;-1.97	5.41	2.03	0.26663	.	0.684055	0.14296	N	0.328617	T	0.53738	0.1815	N	0.22421	0.69	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.19844	-1.0293	9	0.18276	T	0.48	-8.8637	5.912	0.19033	0.1103:0.4066:0.4832:0.0	rs1884444;rs41538148;rs52798390;rs57078543;rs1884444	3	Q5VWK5	IL23R_HUMAN	H	3	ENSP00000321345:Q3H;ENSP00000360041:Q3H	ENSP00000321345:Q3H	Q	+	3	2	IL23R	67406400	0.352000	0.24895	0.917000	0.36280	0.002000	0.02628	0.723000	0.25939	1.232000	0.43678	0.591000	0.81541	CAG	G|0.477;T|0.523	0.523	strong		0.323	IL23R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025199.2	NM_144701	
DYNLRB2	83657	hgsc.bcm.edu	37	16	80583497	80583497	+	Silent	SNP	C	C	T	rs11866734	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:80583497C>T	ENST00000305904.6	+	3	316	c.196C>T	c.(196-198)Ctg>Ttg	p.L66L	DYNLRB2_ENST00000562982.1_Silent_p.L95L|DYNLRB2_ENST00000568035.1_Intron|RP11-525K10.3_ENST00000568776.1_RNA|DYNLRB2_ENST00000570222.1_3'UTR|RP11-109P11.1_ENST00000568275.1_RNA	NM_130897.1	NP_570967.1	Q8TF09	DLRB2_HUMAN	dynein, light chain, roadblock-type 2	66					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|transport (GO:0006810)	cytoplasmic dynein complex (GO:0005868)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			large_intestine(1)|lung(4)|prostate(1)	6						TCAGAACGACCTGACTTTTCT	0.383													C|||	750	0.14976	0.2443	0.1585	5008	,	,		16697	0.0129		0.2515	False		,,,				2504	0.0521				p.L66L		Atlas-SNP	.											DYNLRB2,NS,carcinoma,0,3	DYNLRB2	17	3	0			c.C196T						PASS	.	C		1124,3282	400.1+/-331.5	145,834,1224	115.0	107.0	110.0		196	4.1	1.0	16	dbSNP_120	110	2070,6530	359.0+/-331.4	246,1578,2476	no	coding-synonymous	DYNLRB2	NM_130897.1		391,2412,3700	TT,TC,CC		24.0698,25.5107,24.5579		66/97	80583497	3194,9812	2203	4300	6503	SO:0001819	synonymous_variant	83657	exon3			AACGACCTGACTT	AF125108	CCDS10929.1	16q23.3	2008-02-05	2005-11-25	2005-11-25	ENSG00000168589	ENSG00000168589		"""Cytoplasmic dyneins"""	15467	protein-coding gene	gene with protein product	"""roadblock domain containing 2"""	607168	"""dynein, cytoplasmic, light polypeptide 2B"""	DNCL2B		11750132, 16260502	Standard	NM_130897		Approved	DNLC2B, ROBLD2	uc002ffo.3	Q8TF09	OTTHUMG00000137622	ENST00000305904.6:c.196C>T	16.37:g.80583497C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_130897		Silent	SNP	ENST00000305904.6	37	CCDS10929.1																																																																																			C|0.779;T|0.221	0.221	strong		0.383	DYNLRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269043.1	NM_130897	
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 GAIIx	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		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	87	29	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	
NEB	4703	hgsc.bcm.edu	37	2	152427080	152427080	+	Silent	SNP	C	C	A	rs140688592	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:152427080C>A	ENST00000172853.10	-	80	12093	c.11946G>T	c.(11944-11946)gcG>gcT	p.A3982A	NEB_ENST00000397345.3_Silent_p.A5683A|NEB_ENST00000603639.1_Silent_p.A5683A|NEB_ENST00000409198.1_Silent_p.A3982A|NEB_ENST00000604864.1_Silent_p.A5683A|NEB_ENST00000427231.2_Silent_p.A5683A			P20929	NEBU_HUMAN	nebulin	3982					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)			NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		CATCACAGCCCGCCTTCATTT	0.483													C|||	11	0.00219649	0.0	0.0058	5008	,	,		17858	0.0		0.006	False		,,,				2504	0.001				p.A5683A		Atlas-SNP	.											.	NEB	1697	.	0			c.G17049T						PASS	.	C	,,	5,3847		0,5,1921	25.0	27.0	26.0		17049,17049,11946	2.6	1.0	2	dbSNP_134	26	110,8216		1,108,4054	yes	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	1,113,5975	AA,AC,CC		1.3212,0.1298,0.9443	,,	5683/8526,5683/8526,3982/6670	152427080	115,12063	1926	4163	6089	SO:0001819	synonymous_variant	4703	exon108			ACAGCCCGCCTTC	X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.11946G>T	2.37:g.152427080C>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	107	15	0.140187	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				C|0.995;A|0.005	0.005	strong		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
KAL1	3730	hgsc.bcm.edu	37	X	8503641	8503641	+	Silent	SNP	G	G	A	rs809446	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:8503641G>A	ENST00000262648.3	-	12	1982	c.1833C>T	c.(1831-1833)atC>atT	p.I611I	KAL1_ENST00000481896.1_5'UTR	NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	611	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						CGGAAGGCAGGATCTGGGACT	0.488													G|||	1819	0.481854	0.2307	0.3458	3775	,	,		14845	0.506		0.505	False		,,,				2504	0.2618				p.I611I		Atlas-SNP	.											.	KAL1	78	.	0			c.C1833T						PASS	.	G		1347,2488		196,756,199,680,372	158.0	116.0	130.0		1833	-0.4	1.0	X	dbSNP_86	130	4483,2245		1086,1063,1248,279,624	no	coding-synonymous	KAL1	NM_000216.2		1282,1819,1447,959,996	AA,AG,A,GG,G		33.368,35.1239,44.8073		611/681	8503641	5830,4733	2203	4300	6503	SO:0001819	synonymous_variant	3730	exon12			AGGCAGGATCTGG		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1833C>T	X.37:g.8503641G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	237	236	0.995781	NM_000216	B2RPF8	Silent	SNP	ENST00000262648.3	37	CCDS14130.1																																																																																			G|0.471;0|0.003	.	strong		0.488	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
C1orf86	199990	hgsc.bcm.edu	37	1	2125172	2125172	+	Missense_Mutation	SNP	G	G	A	rs1058411	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:2125172G>A	ENST00000378546.4	-	3	400	c.376C>T	c.(376-378)Ccc>Tcc	p.P126S	C1orf86_ENST00000400919.3_5'UTR|C1orf86_ENST00000378545.3_Missense_Mutation_p.P229S|C1orf86_ENST00000487186.1_5'UTR	NM_182533.2	NP_872339	Q6NZ36	FAP20_HUMAN	chromosome 1 open reading frame 86	126			P -> S (in dbSNP:rs1058411).		cellular response to DNA damage stimulus (GO:0006974)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	cell junction (GO:0030054)|chromosome (GO:0005694)|Fanconi anaemia nuclear complex (GO:0043240)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)			central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		GCCCTGCAGGGATCAGGTGCC	0.731													G|||	1041	0.207867	0.528	0.0836	5008	,	,		12708	0.0615		0.1004	False		,,,				2504	0.1247				p.P126S		Atlas-SNP	.											.	C1orf86	20	.	0			c.C376T						PASS	.	G	,SER/PRO	1734,2482		363,1008,737	13.0	18.0	16.0		363,376	1.1	0.0	1	dbSNP_86	16	803,7637		52,699,3469	no	coding-synonymous,missense	C1orf86	NM_001146310.1,NM_182533.2	,74	415,1707,4206	AA,AG,GG		9.5142,41.129,20.0458	,possibly-damaging	121/231,126/181	2125172	2537,10119	2108	4220	6328	SO:0001583	missense	199990	exon3			TGCAGGGATCAGG	AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585			26428	protein-coding gene	gene with protein product		615183				14702039	Standard	NM_182533		Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000378546.4:c.376C>T	1.37:g.2125172G>A	ENSP00000367808:p.Pro126Ser	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	NM_001256946	A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	Missense_Mutation	SNP	ENST00000378546.4	37	CCDS38.2	400	0.18315018315018314	253	0.5142276422764228	37	0.10220994475138122	36	0.06293706293706294	74	0.09762532981530343	G	10.64	1.407716	0.25378	0.41129	0.095142	ENSG00000162585	ENST00000400918;ENST00000378546;ENST00000378545	T;T;T	0.39592	1.19;1.2;1.07	3.09	1.1	0.20463	.	0.922212	0.09100	N	0.848630	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.28971	0.229	B	0.28385	0.089	T	0.47235	-0.9133	8	0.30078	T	0.28	-4.6427	3.1153	0.06372	0.1507:0.0:0.585:0.2643	rs1058411;rs3205435	126	Q6NZ36	CA086_HUMAN	S	126;126;229	ENSP00000383709:P126S;ENSP00000367808:P126S;ENSP00000367807:P229S	ENSP00000367807:P229S	P	-	1	0	C1orf86	2115032	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.374000	0.20501	0.284000	0.22305	0.561000	0.74099	CCC	G|0.825;A|0.175	0.175	strong		0.731	C1orf86-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316541.1	NM_182533	
POLRMT	5442	hgsc.bcm.edu	37	19	617614	617614	+	Silent	SNP	G	G	A	rs41551212	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:617614G>A	ENST00000588649.2	-	19	3621	c.3537C>T	c.(3535-3537)atC>atT	p.I1179I	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1179	Mediates interaction with TEFM.				gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		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)		GGTCCTGCAGGATGGGCTCGC	0.632													g|||	455	0.0908546	0.028	0.1052	5008	,	,		12482	0.005		0.1541	False		,,,				2504	0.1892				p.I1179I		Atlas-SNP	.											.	POLRMT	91	.	0			c.C3537T						PASS	.	G		245,4161		6,233,1964	42.0	40.0	41.0		3537	1.2	1.0	19	dbSNP_127	41	1459,7141		112,1235,2953	no	coding-synonymous	POLRMT	NM_005035.3		118,1468,4917	AA,AG,GG		16.9651,5.5606,13.1016		1179/1231	617614	1704,11302	2203	4300	6503	SO:0001819	synonymous_variant	5442	exon19			CTGCAGGATGGGC		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.3537C>T	19.37:g.617614G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.881;A|0.119	0.119	strong		0.632	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
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 GAIIx	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		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	143	73	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		
DUS1L	64118	hgsc.bcm.edu	37	17	80020812	80020812	+	Silent	SNP	C	C	T	rs11542332	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:80020812C>T	ENST00000354321.7	-	4	920	c.435G>A	c.(433-435)acG>acA	p.T145T	DUS1L_ENST00000306796.5_Silent_p.T145T			Q6P1R4	DUS1L_HUMAN	dihydrouridine synthase 1-like (S. cerevisiae)	145							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	6	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			GGATTTTGCACGTGACAGGAA	0.612													c|||	638	0.127396	0.2617	0.1225	5008	,	,		18591	0.0377		0.0537	False		,,,				2504	0.1176				p.T145T		Atlas-SNP	.											DUS1L,colon,carcinoma,-1,1	DUS1L	25	1	0			c.G435A						PASS	.	C		959,3445	360.1+/-315.1	102,755,1345	63.0	61.0	62.0		435	-7.2	0.7	17	dbSNP_120	62	409,8191	128.0+/-186.3	9,391,3900	no	coding-synonymous	DUS1L	NM_022156.3		111,1146,5245	TT,TC,CC		4.7558,21.7757,10.5198		145/474	80020812	1368,11636	2202	4300	6502	SO:0001819	synonymous_variant	64118	exon5			TTTGCACGTGACA		CCDS32775.1	17q25.3	2005-08-09				ENSG00000169718			30086	protein-coding gene	gene with protein product						12477932	Standard	NM_022156		Approved	PP3111, DUS1	uc002kdr.4	Q6P1R4		ENST00000354321.7:c.435G>A	17.37:g.80020812C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_022156	A6NHV4|Q96AI3	Silent	SNP	ENST00000354321.7	37	CCDS32775.1																																																																																			C|0.901;T|0.099	0.099	strong		0.612	DUS1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442347.1	NM_022156	
PYGL	5836	hgsc.bcm.edu	37	14	51387782	51387782	+	Missense_Mutation	SNP	C	C	T	rs946616	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:51387782C>T	ENST00000216392.7	-	6	996	c.664G>A	c.(664-666)Gtc>Atc	p.V222I	PYGL_ENST00000532462.1_Missense_Mutation_p.V222I|PYGL_ENST00000544180.2_Missense_Mutation_p.V188I	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	222			V -> I (in dbSNP:rs946616). {ECO:0000269|PubMed:9529348}.		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)	AGAGCCAGGACCACCTGTGGG	0.512													C|||	468	0.0934505	0.2027	0.0533	5008	,	,		18099	0.0169		0.0736	False		,,,				2504	0.0736				p.V222I		Atlas-SNP	.											.	PYGL	77	.	0			c.G664A						PASS	.	C	ILE/VAL,ILE/VAL	807,3599	324.0+/-298.4	66,675,1462	66.0	71.0	69.0		562,664	5.8	1.0	14	dbSNP_86	69	558,8042	152.5+/-207.1	17,524,3759	yes	missense,missense	PYGL	NM_001163940.1,NM_002863.4	29,29	83,1199,5221	TT,TC,CC		6.4884,18.3159,10.4952	possibly-damaging,possibly-damaging	188/814,222/848	51387782	1365,11641	2203	4300	6503	SO:0001583	missense	5836	exon6			CCAGGACCACCTG		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.664G>A	14.37:g.51387782C>T	ENSP00000216392:p.Val222Ile	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	101	42	0.415842	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	37	CCDS32080.1	190	0.08699633699633699	98	0.1991869918699187	20	0.055248618784530384	15	0.026223776223776224	57	0.07519788918205805	C	20.6	4.021222	0.75275	0.183159	0.064884	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.95690	-3.21;-3.21;-3.78	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.01489	0.0048	L	0.52206	1.635	0.09310	P	0.999999999655194	B;B;B	0.26845	0.064;0.016;0.161	B;B;B	0.34536	0.073;0.185;0.132	T	0.44483	-0.9325	9	0.34782	T	0.22	-13.3483	19.3504	0.94381	0.0:1.0:0.0:0.0	rs946616;rs1126548;rs3181652;rs17425135;rs52832805;rs946616	188;222;222	F5H816;E9PK47;P06737	.;.;PYGL_HUMAN	I	222;188;222	ENSP00000431657:V222I;ENSP00000443787:V188I;ENSP00000216392:V222I	ENSP00000216392:V222I	V	-	1	0	PYGL	50457532	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	3.269000	0.51592	2.885000	0.99019	0.655000	0.94253	GTC	C|0.897;T|0.103	0.103	strong		0.512	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	
LYST	1130	hgsc.bcm.edu	37	1	235971763	235971763	+	Silent	SNP	A	A	G	rs3768066	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:235971763A>G	ENST00000389794.3	-	5	2529	c.2355T>C	c.(2353-2355)ctT>ctC	p.L785L	LYST_ENST00000389793.2_Silent_p.L785L|LYST_ENST00000536965.1_Silent_p.L785L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	785					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)			ACCTGGATTTAAGCAGGATAG	0.448													A|||	354	0.0706869	0.056	0.0965	5008	,	,		16372	0.0407		0.1481	False		,,,				2504	0.0235				p.L785L		Atlas-SNP	.											.	LYST	370	.	0			c.T2355C						PASS	.	A		340,4066	175.9+/-205.1	6,328,1869	66.0	63.0	64.0		2355	-5.7	1.0	1	dbSNP_107	64	1175,7425	241.0+/-271.5	74,1027,3199	no	coding-synonymous	LYST	NM_000081.2		80,1355,5068	GG,GA,AA		13.6628,7.7167,11.6485		785/3802	235971763	1515,11491	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon5			GGATTTAAGCAGG	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.2355T>C	1.37:g.235971763A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	108	66	0.611111	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			A|0.898;G|0.102	0.102	strong		0.448	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
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 GAIIx	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_ENST00000441566.1_Silent_p.S3076S|DNAH8_ENST00000449981.2_Silent_p.S3329S			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		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	103	79	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	
PDE6C	5146	hgsc.bcm.edu	37	10	95395364	95395364	+	Silent	SNP	C	C	G	rs3737228	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:95395364C>G	ENST00000371447.3	+	10	1518	c.1380C>G	c.(1378-1380)acC>acG	p.T460T		NM_006204.3	NP_006195.3	P51160	PDE6C_HUMAN	phosphodiesterase 6C, cGMP-specific, cone, alpha prime	460					phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|visual perception (GO:0007601)	plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.123)			Caffeine(DB00201)	TGAACCAAACCAAAGCCACTC	0.368													C|||	1178	0.235224	0.1112	0.3199	5008	,	,		19136	0.3661		0.2922	False		,,,				2504	0.1493				p.T460T		Atlas-SNP	.											.	PDE6C	97	.	0			c.C1380G						PASS	.	C		582,3824	258.9+/-262.7	36,510,1657	129.0	115.0	120.0		1380	2.4	1.0	10	dbSNP_107	120	2398,6202	397.8+/-345.9	310,1778,2212	no	coding-synonymous	PDE6C	NM_006204.3		346,2288,3869	GG,GC,CC		27.8837,13.2093,22.9125		460/859	95395364	2980,10026	2203	4300	6503	SO:0001819	synonymous_variant	5146	exon10			CCAAACCAAAGCC	U31973	CCDS7429.1	10q24	2013-01-23			ENSG00000095464	ENSG00000095464	3.1.4.17	"""Phosphodiesterases"""	8787	protein-coding gene	gene with protein product		600827					Standard	NM_006204		Approved	PDEA2, ACHM5, COD4	uc001kiu.4	P51160	OTTHUMG00000018775	ENST00000371447.3:c.1380C>G	10.37:g.95395364C>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_006204	A6NCR6|Q5VY29	Silent	SNP	ENST00000371447.3	37	CCDS7429.1																																																																																			C|0.752;G|0.248	0.248	strong		0.368	PDE6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049437.1	NM_006204	
AGL	178	hgsc.bcm.edu	37	1	100358103	100358103	+	Missense_Mutation	SNP	C	C	T	rs3753494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:100358103C>T	ENST00000294724.4	+	24	3677	c.3199C>T	c.(3199-3201)Cct>Tct	p.P1067S	AGL_ENST00000370161.2_Missense_Mutation_p.P1051S|AGL_ENST00000361915.3_Missense_Mutation_p.P1067S|AGL_ENST00000361522.4_Missense_Mutation_p.P1050S|AGL_ENST00000361302.3_Missense_Mutation_p.P1051S|AGL_ENST00000370163.3_Missense_Mutation_p.P1067S|AGL_ENST00000370165.3_Missense_Mutation_p.P1067S	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	1067			P -> S (in dbSNP:rs3753494).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		AATGGATGTACCTTATAGGTT	0.378													C|||	554	0.110623	0.1203	0.0951	5008	,	,		15854	0.0278		0.1551	False		,,,				2504	0.1483				p.P1067S		Atlas-SNP	.											.	AGL	137	.	0			c.C3199T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	557,3849	249.0+/-256.6	36,485,1682	99.0	94.0	96.0		3199,3199,3199,3199,3148,3151	5.2	0.4	1	dbSNP_107	96	1257,7343	251.5+/-278.0	96,1065,3139	yes	missense,missense,missense,missense,missense,missense	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	74,74,74,74,74,74	132,1550,4821	TT,TC,CC		14.6163,12.6419,13.9474	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1067/1533,1067/1533,1067/1533,1067/1533,1050/1516,1051/1517	100358103	1814,11192	2203	4300	6503	SO:0001583	missense	178	exon24			GATGTACCTTATA	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.3199C>T	1.37:g.100358103C>T	ENSP00000294724:p.Pro1067Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	237	0.10851648351648352	69	0.1402439024390244	43	0.11878453038674033	13	0.022727272727272728	112	0.14775725593667546	C	13.10	2.137783	0.37728	0.126419	0.146163	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	T;T;T;T;T;T;T	0.74947	-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-0.89	5.2	5.2	0.72013	.	0.111526	0.64402	D	0.000006	T	0.66703	0.2816	M	0.67953	2.075	0.09310	P	0.999999999670201	B;B;B	0.26318	0.12;0.12;0.146	B;B;B	0.29353	0.047;0.047;0.101	T	0.66460	-0.5918	9	0.37606	T	0.19	.	19.1022	0.93277	0.0:1.0:0.0:0.0	rs3753494;rs17449932;rs52793848;rs56862711;rs3753494	1050;1051;1067	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	S	1067;1067;1067;1067;1051;1051;1050	ENSP00000355106:P1067S;ENSP00000359184:P1067S;ENSP00000359182:P1067S;ENSP00000294724:P1067S;ENSP00000354971:P1051S;ENSP00000359180:P1051S;ENSP00000354635:P1050S	ENSP00000294724:P1067S	P	+	1	0	AGL	100130691	1.000000	0.71417	0.412000	0.26496	0.008000	0.06430	7.230000	0.78097	2.553000	0.86117	0.573000	0.79308	CCT	C|0.869;T|0.131	0.131	strong		0.378	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
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 GAIIx	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_ENST00000448849.2_Intron|BIVM_ENST00000419638.1_Silent_p.L134L	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		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	66	21	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		
UPF2	26019	hgsc.bcm.edu	37	10	12043790	12043790	+	Silent	SNP	T	T	G	rs11595168	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:12043790T>G	ENST00000356352.2	-	5	2012	c.1539A>C	c.(1537-1539)tcA>tcC	p.S513S	UPF2_ENST00000357604.5_Silent_p.S513S|UPF2_ENST00000397053.2_Silent_p.S513S			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	513					gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				CATCGGGACTTGATACCTCCT	0.358													T|||	158	0.0315495	0.003	0.0274	5008	,	,		16786	0.001		0.0855	False		,,,				2504	0.0491				p.S513S		Atlas-SNP	.											.	UPF2	111	.	0			c.A1539C						PASS	.	T	,	79,4325	66.4+/-103.9	0,79,2123	99.0	93.0	95.0		1539,1539	3.1	1.0	10	dbSNP_120	95	688,7912	168.3+/-219.8	27,634,3639	no	coding-synonymous,coding-synonymous	UPF2	NM_015542.2,NM_080599.1	,	27,713,5762	GG,GT,TT		8.0,1.7938,5.8982	,	513/1273,513/1273	12043790	767,12237	2202	4300	6502	SO:0001819	synonymous_variant	26019	exon6			GGGACTTGATACC	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"""smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.1539A>C	10.37:g.12043790T>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Silent	SNP	ENST00000356352.2	37	CCDS7086.1																																																																																			T|0.947;G|0.053	0.053	strong		0.358	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1		
SEMA5B	54437	hgsc.bcm.edu	37	3	122645277	122645277	+	Silent	SNP	C	C	T	rs2276777	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:122645277C>T	ENST00000357599.3	-	9	1484	c.1098G>A	c.(1096-1098)ccG>ccA	p.P366P	SEMA5B_ENST00000451055.2_Silent_p.P420P|AC078794.1_ENST00000408284.1_RNA|SEMA5B_ENST00000195173.4_Silent_p.P366P	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	366	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GGTCCTGCTCCGGCAAGTGGA	0.597													C|||	400	0.0798722	0.0666	0.1037	5008	,	,		18764	0.0605		0.0736	False		,,,				2504	0.1074				p.P420P		Atlas-SNP	.											SEMA5B_ENST00000451055,NS,carcinoma,0,2	SEMA5B	303	2	0			c.G1260A						PASS	.	C		279,4127	157.4+/-190.3	10,259,1934	35.0	33.0	34.0		1098	-9.0	0.0	3	dbSNP_100	34	634,7966	162.5+/-215.2	16,602,3682	no	coding-synonymous	SEMA5B	NM_001031702.2		26,861,5616	TT,TC,CC		7.3721,6.3323,7.0198		366/1152	122645277	913,12093	2203	4300	6503	SO:0001819	synonymous_variant	54437	exon9			CTGCTCCGGCAAG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1098G>A	3.37:g.122645277C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1																																																																																			C|0.925;T|0.075	0.075	strong		0.597	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
PGD	5226	hgsc.bcm.edu	37	1	10479791	10479791	+	Silent	SNP	G	G	A	rs41274480	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10479791G>A	ENST00000270776.8	+	13	1475	c.1437G>A	c.(1435-1437)tcG>tcA	p.S479S	PGD_ENST00000538557.1_Silent_p.S466S|PGD_ENST00000541529.1_Silent_p.S457S|PGD_ENST00000498356.1_3'UTR	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	479					carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.14e-07)|COAD - Colon adenocarcinoma(227;7.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000294)|Kidney(185;0.000728)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	TGTCATCCTCGTCATACAATG	0.562													G|||	191	0.038139	0.0582	0.0403	5008	,	,		21663	0.0446		0.0288	False		,,,				2504	0.0123				p.S479S		Atlas-SNP	.											.	PGD	39	.	0			c.G1437A						PASS	.	G		209,4197	128.2+/-165.1	4,201,1998	208.0	174.0	186.0		1437	-1.4	0.1	1	dbSNP_127	186	218,8382	91.9+/-153.9	2,214,4084	no	coding-synonymous	PGD	NM_002631.2		6,415,6082	AA,AG,GG		2.5349,4.7435,3.2831		479/484	10479791	427,12579	2203	4300	6503	SO:0001819	synonymous_variant	5226	exon13			ATCCTCGTCATAC	BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	1.1.1.43		8891	protein-coding gene	gene with protein product		172200					Standard	NM_002631		Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.1437G>A	1.37:g.10479791G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_002631	A8K2Y9|B4DQJ8|Q9BWD8	Silent	SNP	ENST00000270776.8	37	CCDS113.1																																																																																			A|0.035;C|0.000;G|0.965	0.035	strong		0.562	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005398.1	NM_002631	
MUC1	4582	hgsc.bcm.edu	37	1	155162067	155162067	+	Silent	SNP	C	C	T	rs4072037	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:155162067C>T	ENST00000368395.1	-	2	137	c.66G>A	c.(64-66)acG>acA	p.T22T	MUC1_ENST00000337604.5_Silent_p.T22T|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000368392.3_Silent_p.T31T|MUC1_ENST00000368389.2_Silent_p.T22T|MUC1_ENST00000338684.5_Silent_p.T31T|MIR92B_ENST00000607575.1_RNA|MUC1_ENST00000368390.3_Silent_p.T22T|MUC1_ENST00000438413.1_Silent_p.T22T|MUC1_ENST00000368393.3_Silent_p.T22T|MUC1_ENST00000368398.3_Silent_p.T22T|MUC1_ENST00000342482.4_Silent_p.T31T|MUC1_ENST00000343256.5_Silent_p.T22T|MUC1_ENST00000462215.1_5'UTR|MUC1_ENST00000368396.4_Silent_p.T31T|MUC1_ENST00000457295.2_Silent_p.T31T	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	22					cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GACCAGAACCCGTAACAACTG	0.458			T	IGH@	B-NHL								T|||	3149	0.628794	0.6044	0.7133	5008	,	,		16591	0.7619		0.5477	False		,,,				2504	0.5481				p.T31T		Atlas-SNP	.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	MUC1_ENST00000368395,caecum,carcinoma,-1,3	MUC1	94	3	0			c.G93A						PASS	.	T	,,,,,,,,,,,,,,,,,,,	2839,1567	489.7+/-361.6	910,1019,274	118.0	127.0	124.0	http://www.ncbi.nlm.nih.gov/pubmed?term	93,66,66,66,93,66,66,93,93,93,93,,93,93,66,66,93,93,93,66	0.3	0.0	1	dbSNP_108	124	4605,3995	552.3+/-386.1	1231,2143,926	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MUC1	NM_001018016.2,NM_001018017.2,NM_001044390.2,NM_001044391.2,NM_001044392.2,NM_001044393.2,NM_001204285.1,NM_001204286.1,NM_001204287.1,NM_001204288.1,NM_001204289.1,NM_001204290.1,NM_001204291.1,NM_001204292.1,NM_001204293.1,NM_001204294.1,NM_001204295.1,NM_001204296.1,NM_001204297.1,NM_002456.5	,,,,,,,,,,,,,,,,,,,	2141,3162,1200	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	46.4535,35.5651,42.7649	,,,,,,,,,,,,,,,,,,,	31/265,22/256,22/204,22/151,31/160,22/159,22/476,31/485,31/283,31/220,31/239,,31/242,31/240,22/199,22/231,31/190,31/213,31/178,22/274	155162067	7444,5562	2203	4300	6503	SO:0001819	synonymous_variant	4582	exon2			AGAACCCGTAACA	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.66G>A	1.37:g.155162067C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Silent	SNP	ENST00000368395.1	37	CCDS55640.1																																																																																			C|0.385;T|0.615	0.615	strong		0.458	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
SLFN12	55106	hgsc.bcm.edu	37	17	33749919	33749919	+	Missense_Mutation	SNP	A	A	C	rs1849733	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33749919A>C	ENST00000394562.1	-	4	652	c.129T>G	c.(127-129)agT>agG	p.S43R	SLFN12_ENST00000452764.3_Missense_Mutation_p.S43R|SLFN12_ENST00000304905.5_Missense_Mutation_p.S43R|SLFN12_ENST00000460530.1_5'Flank			Q8IYM2	SLN12_HUMAN	schlafen family member 12	43			S -> R (in dbSNP:rs1849733). {ECO:0000269|PubMed:15489334}.				ATP binding (GO:0005524)			breast(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTCGTGAGACACTTTCATTCT	0.403													A|||	1884	0.376198	0.2685	0.5375	5008	,	,		18787	0.3462		0.4881	False		,,,				2504	0.3231				p.S43R		Atlas-SNP	.											SLFN12,NS,adenoma,0,1	SLFN12	56	1	0			c.T129G						PASS	.	A	ARG/SER	1433,2973	466.2+/-354.4	241,951,1011	142.0	121.0	128.0		129	-6.4	0.0	17	dbSNP_92	128	4207,4393	569.1+/-389.1	1014,2179,1107	yes	missense	SLFN12	NM_018042.3	110	1255,3130,2118	CC,CA,AA		48.9186,32.5238,43.3646	benign	43/579	33749919	5640,7366	2203	4300	6503	SO:0001583	missense	55106	exon2			TGAGACACTTTCA	AK001122	CCDS11295.1	17q12	2006-04-05			ENSG00000172123	ENSG00000172123			25500	protein-coding gene	gene with protein product		614955				12477932	Standard	NM_018042		Approved	FLJ10260	uc002hji.4	Q8IYM2	OTTHUMG00000132952	ENST00000394562.1:c.129T>G	17.37:g.33749919A>C	ENSP00000378063:p.Ser43Arg	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	177	177	1	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	910	0.4166666666666667	134	0.27235772357723576	182	0.5027624309392266	201	0.3513986013986014	393	0.5184696569920845	a	2.100	-0.406307	0.04832	0.325238	0.489186	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764;ENST00000447040;ENST00000445092	T;T;T;T;T	0.28666	3.93;3.93;3.93;2.02;1.6	3.2	-6.41	0.01938	.	.	.	.	.	T	0.00012	0.0000	N	0.11313	0.125	0.80722	P	0.0	B	0.19331	0.035	B	0.08055	0.003	T	0.47341	-0.9125	8	0.09338	T	0.73	.	3.679	0.08304	0.1948:0.0:0.3113:0.4939	rs1849733;rs17548986;rs17846141;rs17859149;rs52813912;rs56957697;rs1849733	43	Q8IYM2	SLN12_HUMAN	R	43	ENSP00000378063:S43R;ENSP00000302077:S43R;ENSP00000394903:S43R;ENSP00000398315:S43R;ENSP00000404175:S43R	ENSP00000302077:S43R	S	-	3	2	SLFN12	30774032	0.000000	0.05858	0.000000	0.03702	0.155000	0.21991	-2.082000	0.01365	-0.829000	0.04268	0.358000	0.22013	AGT	A|0.586;C|0.414	0.414	strong		0.403	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042	
PON2	5445	hgsc.bcm.edu	37	7	95034775	95034775	+	Missense_Mutation	SNP	G	G	C	rs7493	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:95034775G>C	ENST00000222572.3	-	9	1178	c.932C>G	c.(931-933)tCt>tGt	p.S311C	PON2_ENST00000483292.1_5'UTR|PON2_ENST00000433091.2_Missense_Mutation_p.S299C|PON2_ENST00000536183.1_Missense_Mutation_p.S332C			Q15165	PON2_HUMAN	paraoxonase 2	311			C -> S (associated with increased risk of coronary heart disease; CHD; dbSNP:rs7493). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8661009, ECO:0000269|PubMed:9443862, ECO:0000269|PubMed:9714608, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			AGGCTTCTCAGATAGAATGTT	0.438													G|||	1419	0.283347	0.3321	0.2334	5008	,	,		18192	0.1885		0.2485	False		,,,				2504	0.3865				p.S311C	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.C932G	GRCh37	CM981611	PON2	M	rs7493	PASS	.	G	CYS/SER,CYS/SER	1250,3156	429.9+/-342.4	159,932,1112	169.0	147.0	154.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	932,896	3.7	1.0	7	dbSNP_52	154	1961,6639	344.9+/-325.5	224,1513,2563	yes	missense,missense	PON2	NM_000305.2,NM_001018161.1	112,112	383,2445,3675	CC,CG,GG		22.8023,28.3704,24.6886	benign,benign	311/355,299/343	95034775	3211,9795	2203	4300	6503	SO:0001583	missense	5445	exon9			TTCTCAGATAGAA	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"""Paraoxonases"""	9205	protein-coding gene	gene with protein product	"""paraoxonase nirs"", ""arylesterase 2"""	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.932C>G	7.37:g.95034775G>C	ENSP00000222572:p.Ser311Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	37	CCDS5640.1	561	0.25686813186813184	177	0.3597560975609756	87	0.24033149171270718	104	0.18181818181818182	193	0.2546174142480211	G	12.38	1.920948	0.33908	0.283704	0.228023	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.51817	0.69;0.69;0.69	4.58	3.7	0.42460	.	0.108239	0.64402	D	0.000004	T	0.00012	0.0000	.	.	.	0.21897	P	0.999480547	B	0.15473	0.013	B	0.12837	0.008	T	0.31392	-0.9945	8	0.59425	D	0.04	-23.1358	12.9946	0.58640	0.0782:0.0:0.9218:0.0	rs7493;rs1058131;rs3173813;rs6954345;rs17876171;rs56451431;rs60345618;rs7493	311	A4D1H7	.	C	332;309;299;311	ENSP00000440282:S332C;ENSP00000404622:S299C;ENSP00000222572:S311C	ENSP00000222572:S311C	S	-	2	0	PON2	94872711	1.000000	0.71417	0.994000	0.49952	0.773000	0.43773	9.118000	0.94355	1.303000	0.44873	-0.136000	0.14681	TCT	G|0.747;C|0.253	0.253	strong		0.438	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305	
METTL21B	25895	hgsc.bcm.edu	37	12	58174306	58174306	+	Silent	SNP	T	T	C	rs923829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:58174306T>C	ENST00000300209.8	+	3	683	c.558T>C	c.(556-558)caT>caC	p.H186H	TSFM_ENST00000454289.3_5'Flank|TSFM_ENST00000540550.1_5'Flank|RP11-571M6.15_ENST00000553083.1_Intron|METTL21B_ENST00000551420.1_Silent_p.H5H|RP11-571M6.15_ENST00000471530.1_Intron|TSFM_ENST00000543727.1_5'Flank|TSFM_ENST00000550559.1_5'Flank|METTL21B_ENST00000333012.5_3'UTR|TSFM_ENST00000350762.5_5'Flank|TSFM_ENST00000323833.8_5'Flank|TSFM_ENST00000548851.1_5'Flank	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B	186						cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						GAAAGGAGCATGGGACAGAGA	0.567													t|||	2024	0.404153	0.2141	0.2767	5008	,	,		21672	0.6468		0.3191	False		,,,				2504	0.589				p.H186H		Atlas-SNP	.											.	METTL21B	16	.	0			c.T558C						PASS	.	T	,	1018,3388	377.5+/-322.5	116,786,1301	69.0	60.0	63.0		558,	-2.5	1.0	12	dbSNP_86	63	2755,5845	438.5+/-358.9	456,1843,2001	no	coding-synonymous,utr-3	METTL21B	NM_015433.2,NM_206914.1	,	572,2629,3302	CC,CT,TT		32.0349,23.1049,29.0097	,	186/227,	58174306	3773,9233	2203	4300	6503	SO:0001819	synonymous_variant	25895	exon3			GGAGCATGGGACA	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"""family with sequence similarity 119, member B"""	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459	ENST00000300209.8:c.558T>C	12.37:g.58174306T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_015433	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	37	CCDS8957.1																																																																																			T|0.672;C|0.328	0.328	strong		0.567	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433	
DAP3	7818	hgsc.bcm.edu	37	1	155699118	155699118	+	Silent	SNP	T	T	C	rs4933	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:155699118T>C	ENST00000368336.5	+	9	928	c.804T>C	c.(802-804)ctT>ctC	p.L268L	DAP3_ENST00000535183.1_Silent_p.L227L|DAP3_ENST00000343043.3_Silent_p.L268L|MSTO1_ENST00000452804.2_Intron|DAP3_ENST00000471642.2_Silent_p.L227L|DAP3_ENST00000421487.2_Silent_p.L234L|MSTO1_ENST00000538143.1_Intron	NM_001199849.1|NM_004632.3	NP_001186778.1|NP_004623.1	P51398	RT29_HUMAN	death associated protein 3	268					apoptotic mitochondrial changes (GO:0008637)|apoptotic signaling pathway (GO:0097190)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	24	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					TCAATGCTCTTTGGGGAAGAA	0.453													T|||	292	0.0583067	0.1316	0.0418	5008	,	,		18175	0.0		0.0557	False		,,,				2504	0.0337				p.L268L		Atlas-SNP	.											.	DAP3	46	.	0			c.T804C						PASS	.	T	,,,,	454,3952	211.8+/-231.9	22,410,1771	103.0	101.0	101.0		804,702,681,804,804	1.3	1.0	1	dbSNP_52	101	429,8171	130.5+/-188.4	9,411,3880	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DAP3	NM_001199849.1,NM_001199850.1,NM_001199851.1,NM_004632.3,NM_033657.2	,,,,	31,821,5651	CC,CT,TT		4.9884,10.3041,6.7892	,,,,	268/399,234/365,227/358,268/399,268/399	155699118	883,12123	2203	4300	6503	SO:0001819	synonymous_variant	7818	exon9			TGCTCTTTGGGGA	X83544	CCDS1120.1, CCDS55646.1, CCDS55647.1	1q22	2012-11-14			ENSG00000132676	ENSG00000132676		"""Mitochondrial ribosomal proteins / small subunits"""	2673	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S29"""	602074				7499268, 9284927	Standard	NM_004632		Approved	MRPS29, DAP-3, MRP-S29, bMRP-10, MGC126058, MGC126059, DKFZp686G12159	uc001flr.3	P51398	OTTHUMG00000035439	ENST00000368336.5:c.804T>C	1.37:g.155699118T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_033657	B4DP59|B4DY62|E7EM60|Q13044|Q68CT7|Q96Q20	Silent	SNP	ENST00000368336.5	37	CCDS1120.1																																																																																			A|0.000;C|0.066;G|0.000;T|0.934	0.066	strong		0.453	DAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086042.1	NM_004632	
POTEC	388468	hgsc.bcm.edu	37	18	14543098	14543098	+	Silent	SNP	C	C	T	rs11873462	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:14543098C>T	ENST00000358970.5	-	1	47	c.48G>A	c.(46-48)aaG>aaA	p.K16K	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	16										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GATCGAATGGCTTCTTCACAG	0.572													.|||	1371	0.273762	0.2655	0.2507	5008	,	,		19912	0.4216		0.1511	False		,,,				2504	0.2751				p.K16K		Atlas-SNP	.											.	POTEC	129	.	0			c.G48A						PASS	.						122.0	101.0	107.0					18																	14543098		692	1591	2283	SO:0001819	synonymous_variant	388468	exon1			GAATGGCTTCTTC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.48G>A	18.37:g.14543098C>T		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	278	119	0.428058	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			C|0.744;T|0.256	0.256	strong		0.572	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
PLEC	5339	hgsc.bcm.edu	37	8	144992862	144992862	+	Silent	SNP	A	A	G	rs7819099	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144992862A>G	ENST00000322810.4	-	32	11707	c.11538T>C	c.(11536-11538)gcT>gcC	p.A3846A	PLEC_ENST00000354589.3_Silent_p.A3709A|PLEC_ENST00000357649.2_Silent_p.A3713A|PLEC_ENST00000436759.2_Silent_p.A3736A|PLEC_ENST00000354958.2_Silent_p.A3687A|PLEC_ENST00000527096.1_Silent_p.A3732A|PLEC_ENST00000345136.3_Silent_p.A3709A|PLEC_ENST00000356346.3_Silent_p.A3695A|PLEC_ENST00000398774.2_Silent_p.A3677A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3846	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTTTCTTGAGAGCCTGGTAGA	0.662													G|||	2234	0.446086	0.7844	0.3703	5008	,	,		16512	0.1448		0.4364	False		,,,				2504	0.363				p.A3846A		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	0			c.T11538C						scavenged	.	G	,,,,,,,	2861,1041		1085,691,175	25.0	31.0	29.0		11208,11085,11061,11538,11031,11127,11139,11127	-0.3	1.0	8	dbSNP_116	29	3625,4607		868,1889,1359	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	1953,2580,1534	GG,GA,AA		44.0355,26.6786,46.5469	,,,,,,,	3736/4575,3695/4534,3687/4526,3846/4685,3677/4516,3709/4548,3713/4552,3709/4548	144992862	6486,5648	1951	4116	6067	SO:0001819	synonymous_variant	5339	exon32			CTTGAGAGCCTGG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11538T>C	8.37:g.144992862A>G		Somatic	76	2	0.0263158		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.555;G|0.445	0.445	strong		0.662	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
CCDC88B	283234	hgsc.bcm.edu	37	11	64109208	64109208	+	Silent	SNP	G	G	C	rs61735121	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64109208G>C	ENST00000356786.5	+	7	713	c.669G>C	c.(667-669)ggG>ggC	p.G223G	CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	223						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GTGACCTGGGGGCCCAGGTAG	0.662													G|||	185	0.0369409	0.0	0.1037	5008	,	,		13404	0.1081		0.003	False		,,,				2504	0.001				p.G223G		Atlas-SNP	.											.	CCDC88B	89	.	0			c.G669C						PASS	.	G		28,4362		0,28,2167	16.0	20.0	19.0		669	-1.4	1.0	11	dbSNP_129	19	24,8562		0,24,4269	no	coding-synonymous	CCDC88B	NM_032251.5		0,52,6436	CC,CG,GG		0.2795,0.6378,0.4007		223/1477	64109208	52,12924	2195	4293	6488	SO:0001819	synonymous_variant	283234	exon7			CCTGGGGGCCCAG	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.669G>C	11.37:g.64109208G>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.980;C|0.020	0.020	strong		0.662	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
OTOGL	283310	hgsc.bcm.edu	37	12	80747209	80747209	+	Missense_Mutation	SNP	C	C	G	rs7312569	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:80747209C>G	ENST00000547103.1	+	45	5455	c.5449C>G	c.(5449-5451)Cta>Gta	p.L1817V	OTOGL_ENST00000546620.1_5'Flank|OTOGL_ENST00000458043.2_Missense_Mutation_p.L1829V			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1817					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						CTGTTTGAATCTAAGAGAAGA	0.458													C|||	868	0.173323	0.1846	0.2075	5008	,	,		16401	0.0575		0.1819	False		,,,				2504	0.2444				p.L1829V		Atlas-SNP	.											.	OTOGL	235	.	0			c.C5485G						PASS	.	C	VAL/LEU	688,3198		61,566,1316	72.0	69.0	70.0		5485	0.4	0.1	12	dbSNP_116	70	1621,6675		159,1303,2686	yes	missense	OTOGL	NM_173591.3	32	220,1869,4002	GG,GC,CC		19.5395,17.7046,18.9542		1829/2345	80747209	2309,9873	1943	4148	6091	SO:0001583	missense	283310	exon45			TTGAATCTAAGAG	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5449C>G	12.37:g.80747209C>G	ENSP00000447211:p.Leu1817Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	58	0.591837	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		327|327	0.14972527472527472|0.14972527472527472	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	30|30	0.05244755244755245|0.05244755244755245	136|136	0.17941952506596306|0.17941952506596306	C|C	5.903|5.903	0.350723|0.350723	0.11182|0.11182	0.177046|0.177046	0.195395|0.195395	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043	.|T;T	.|0.55052	.|0.54;0.54	5.74|5.74	0.452|0.452	0.16634|0.16634	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.45285|0.45285	1.41|1.41	0.54753|0.54753	P|P	1.799999999996249E-5|1.799999999996249E-5	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.10847|0.10847	-1.0612|-1.0612	4|6	.|0.31617	.|T	.|0.26	.|.	3.0832|3.0832	0.06269|0.06269	0.1146:0.1279:0.1196:0.6379|0.1146:0.1279:0.1196:0.6379	rs7312569;rs17249560;rs7312569|rs7312569;rs17249560;rs7312569	.|.	.|.	.|.	M|V	271|1817;1829	.|ENSP00000447211:L1817V;ENSP00000400895:L1829V	.|ENSP00000400895:L1829V	I|L	+|+	3|1	3|2	OTOGL|OTOGL	79271340|79271340	0.049000|0.049000	0.20398|0.20398	0.071000|0.071000	0.20095|0.20095	0.298000|0.298000	0.27526|0.27526	0.246000|0.246000	0.18160|0.18160	-0.156000|-0.156000	0.11079|0.11079	-0.294000|-0.294000	0.09567|0.09567	ATC|CTA	C|0.844;G|0.156	0.156	strong		0.458	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39496336	39496336	+	Missense_Mutation	SNP	G	G	T	rs139293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39496336G>T	ENST00000401756.1	+	2	129	c.53G>T	c.(52-54)cGc>cTc	p.R18L	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.R18L|APOBEC3H_ENST00000421988.2_Missense_Mutation_p.R18L|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.R18L	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	18			R -> L (in dbSNP:rs139293). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					AACAAGCGCCGCCTCAGAAGG	0.522													G|||	1010	0.201677	0.0666	0.2421	5008	,	,		17467	0.1587		0.2932	False		,,,				2504	0.3057				p.R18L		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G53T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG	365,4041		14,337,1852	82.0	73.0	76.0		53,53,53,53	-0.2	0.0	22	dbSNP_78	76	2353,6247		307,1739,2254	yes	missense,missense,missense,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	102,102,102,102	321,2076,4106	TT,TG,GG		27.3605,8.2842,20.898	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	18/183,18/201,18/155,18/184	39496336	2718,10288	2203	4300	6503	SO:0001583	missense	164668	exon2			AGCGCCGCCTCAG	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.53G>T	22.37:g.39496336G>T	ENSP00000385741:p.Arg18Leu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	439	0.20100732600732601	30	0.06097560975609756	83	0.2292817679558011	89	0.1555944055944056	237	0.31266490765171506	.	12.72	2.022317	0.35701	0.082842	0.273605	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000421988;ENST00000401756	T;T;T;T	0.63580	0.04;0.04;-0.05;0.01	3.01	-0.212	0.13169	.	.	.	.	.	T	0.00012	0.0000	M	0.64404	1.975	0.80722	P	0.0	D	0.61080	0.989	D	0.64410	0.925	T	0.24154	-1.0168	8	0.13470	T	0.59	2.1365	5.1589	0.15050	0.4171:0.0:0.5829:0.0	rs139293;rs52833502;rs139293	18	B7TQM3	.	L	18	ENSP00000216123:R18L;ENSP00000411754:R18L;ENSP00000393520:R18L;ENSP00000385741:R18L	ENSP00000216123:R18L	R	+	2	0	APOBEC3H	37826282	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.120000	0.10660	0.030000	0.15379	-0.481000	0.04817	CGC	A|0.000;G|0.804;T|0.196	0.196	strong		0.522	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
PRDM9	56979	hgsc.bcm.edu	37	5	23527469	23527469	+	Missense_Mutation	SNP	C	C	A	rs112501567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:23527469C>A	ENST00000296682.3	+	11	2454	c.2272C>A	c.(2272-2274)Cgc>Agc	p.R758S		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	758					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						GCGGGGCTTTCGCGATAAGTC	0.572										HNSCC(3;0.000094)			A|||	79	0.0157748	0.0514	0.0014	5008	,	,		9432	0.002		0.002	False		,,,				2504	0.0061				p.R758S		Atlas-SNP	.											PRDM9,NS,carcinoma,-1,2	PRDM9	344	2	0			c.C2272A						scavenged	.						61.0	85.0	77.0					5																	23527469		2096	4292	6388	SO:0001583	missense	56979	exon11			GGCTTTCGCGATA	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.2272C>A	5.37:g.23527469C>A	ENSP00000296682:p.Arg758Ser	Somatic	76	2	0.0263158		WXS	Illumina HiSeq	Phase_I	41	13	0.317073	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	70	0.03205128205128205	47	0.09552845528455285	10	0.027624309392265192	7	0.012237762237762238	6	0.0079155672823219	A	0.001	-3.244943	0.00022	.	.	ENSG00000164256	ENST00000296682	T	0.35605	1.3	2.65	2.65	0.31530	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00412	0.0013	N	0.20574	0.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24048	-1.0171	8	0.05620	T	0.96	.	3.4855	0.07618	0.534:0.2366:0.0:0.2294	.	758	Q9NQV7	PRDM9_HUMAN	S	758	ENSP00000296682:R758S	ENSP00000296682:R758S	R	+	1	0	PRDM9	23563226	0.000000	0.05858	0.052000	0.19188	0.010000	0.07245	-0.386000	0.07370	0.423000	0.26033	-0.512000	0.04463	CGC	C|0.978;A|0.022	0.022	strong		0.572	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
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 GAIIx	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_ENST00000370994.4_Missense_Mutation_p.K76Q|SERBP1_ENST00000370990.5_Missense_Mutation_p.K76Q|SERBP1_ENST00000361219.6_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	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	149	50	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	
SLC36A3	285641	hgsc.bcm.edu	37	5	150666962	150666962	+	Missense_Mutation	SNP	G	G	A	rs12520516	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150666962G>A	ENST00000335230.3	-	6	964	c.553C>T	c.(553-555)Ccc>Tcc	p.P185S	SLC36A3_ENST00000377713.3_Missense_Mutation_p.P226S	NM_181774.3	NP_861439.3	Q495N2	S36A3_HUMAN	solute carrier family 36, member 3	185			P -> S (in dbSNP:rs12520516).			integral component of membrane (GO:0016021)		p.P185S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	21		Medulloblastoma(196;0.109)|all_hematologic(541;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCCAGGATGGGGGTCAGCGTC	0.507													G|||	495	0.0988419	0.0204	0.0605	5008	,	,		20215	0.2192		0.0845	False		,,,				2504	0.1227				p.P226S		Atlas-SNP	.											SLC36A3,NS,carcinoma,0,1	SLC36A3	54	1	1	Substitution - Missense(1)	stomach(1)	c.C676T						PASS	.	G	SER/PRO,SER/PRO	148,4258	103.8+/-142.4	5,138,2060	153.0	143.0	146.0		676,553	2.1	0.5	5	dbSNP_120	146	869,7731	196.8+/-241.6	52,765,3483	yes	missense,missense	SLC36A3	NM_001145017.1,NM_181774.3	74,74	57,903,5543	AA,AG,GG		10.1047,3.3591,7.8195	benign,benign	226/512,185/471	150666962	1017,11989	2203	4300	6503	SO:0001583	missense	285641	exon7			GGATGGGGGTCAG	AY162215	CCDS4314.1, CCDS47316.1	5q33.1	2013-07-17	2013-07-17		ENSG00000186334	ENSG00000186334		"""Solute carriers"""	19659	protein-coding gene	gene with protein product		608332				12809675	Standard	NM_181774		Approved	PAT3, TRAMD2, tramdorin2	uc003ltw.2	Q495N2	OTTHUMG00000130128	ENST00000335230.3:c.553C>T	5.37:g.150666962G>A	ENSP00000334750:p.Pro185Ser	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_001145017	Q495N3|Q6ZMU7|Q6ZRU4|Q7Z6B4	Missense_Mutation	SNP	ENST00000335230.3	37	CCDS4314.1	214	0.09798534798534798	14	0.028455284552845527	22	0.06077348066298342	109	0.19055944055944055	69	0.09102902374670185	G	11.88	1.769949	0.31320	0.033591	0.101047	ENSG00000186334	ENST00000335230;ENST00000377713	T;T	0.02177	4.41;4.41	4.86	2.1	0.27182	.	0.305040	0.36854	N	0.002372	T	0.00012	0.0000	L	0.54965	1.715	0.29987	P	0.817211	B;B;B	0.19073	0.004;0.018;0.033	B;B;B	0.21360	0.022;0.034;0.033	T	0.45056	-0.9287	9	0.06236	T	0.91	.	5.1441	0.14975	0.2509:0.15:0.5991:0.0	rs12520516;rs52834166;rs60939954;rs12520516	226;185;170	Q495N2-3;Q495N2;Q495N2-2	.;S36A3_HUMAN;.	S	185;226	ENSP00000334750:P185S;ENSP00000366942:P226S	ENSP00000334750:P185S	P	-	1	0	SLC36A3	150647155	0.993000	0.37304	0.532000	0.27989	0.574000	0.36063	2.181000	0.42547	0.257000	0.21650	0.655000	0.94253	CCC	G|0.909;A|0.091	0.091	strong		0.507	SLC36A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252436.1	NM_181774	
SLC1A1	6505	hgsc.bcm.edu	37	9	4564432	4564432	+	Silent	SNP	G	G	A	rs2228622	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:4564432G>A	ENST00000262352.3	+	4	650	c.414G>A	c.(412-414)acG>acA	p.T138T	SLC1A1_ENST00000490167.1_3'UTR	NM_004170.5	NP_004161.4	P43005	EAA3_HUMAN	solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1	138					D-aspartate import (GO:0070779)|ion transport (GO:0006811)|L-glutamate import (GO:0051938)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glutamate binding (GO:0016595)|glutamate:sodium symporter activity (GO:0015501)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			endometrium(1)|kidney(1)|large_intestine(7)|lung(4)|pancreas(1)|skin(1)	15		Acute lymphoblastic leukemia(2;0.0359)|Breast(48;0.0457)		GBM - Glioblastoma multiforme(50;0.0124)|Lung(218;0.183)	L-Aspartic Acid(DB00128)|Pregabalin(DB00230)	AAGTCAGTACGGTGGATGCCA	0.512													G|||	1644	0.328275	0.1921	0.4582	5008	,	,		21504	0.2361		0.4095	False		,,,				2504	0.4315				p.T138T		Atlas-SNP	.											.	SLC1A1	43	.	0			c.G414A						PASS	.	G		970,3436	364.6+/-317.1	87,796,1320	160.0	116.0	131.0		414	-9.0	0.1	9	dbSNP_98	131	3665,4935	522.1+/-380.0	772,2121,1407	no	coding-synonymous	SLC1A1	NM_004170.5		859,2917,2727	AA,AG,GG		42.6163,22.0154,35.6374		138/525	4564432	4635,8371	2203	4300	6503	SO:0001819	synonymous_variant	6505	exon4			CAGTACGGTGGAT		CCDS6452.1	9p24	2013-05-22			ENSG00000106688	ENSG00000106688		"""Solute carriers"""	10939	protein-coding gene	gene with protein product		133550				8020993	Standard	NM_004170		Approved	EAAC1, EAAT3	uc003zij.2	P43005	OTTHUMG00000019468	ENST00000262352.3:c.414G>A	9.37:g.4564432G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_004170	O75587|Q5VZ24|Q8N199|Q9UEW2	Silent	SNP	ENST00000262352.3	37	CCDS6452.1																																																																																			G|0.657;A|0.343	0.343	strong		0.512	SLC1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051571.1		
SLC6A5	9152	hgsc.bcm.edu	37	11	20648364	20648364	+	Missense_Mutation	SNP	G	G	C	rs3740870	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:20648364G>C	ENST00000525748.1	+	8	1644	c.1371G>C	c.(1369-1371)aaG>aaC	p.K457N		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	457			K -> N (in dbSNP:rs3740870).		glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	TCACACCCAAGTGGGAGAAAC	0.562													G|||	453	0.0904553	0.0091	0.0922	5008	,	,		17456	0.0744		0.1392	False		,,,				2504	0.1656				p.K457N		Atlas-SNP	.											SLC6A5,caecum,carcinoma,0,1	SLC6A5	151	1	0			c.G1371C						PASS	.	G	ASN/LYS	134,4272	93.9+/-132.6	3,128,2072	123.0	114.0	117.0		1371	5.1	1.0	11	dbSNP_107	117	1384,7216	269.3+/-288.3	109,1166,3025	yes	missense	SLC6A5	NM_004211.3	94	112,1294,5097	CC,CG,GG		16.093,3.0413,11.6715	benign	457/798	20648364	1518,11488	2203	4300	6503	SO:0001583	missense	9152	exon8			ACCCAAGTGGGAG	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1371G>C	11.37:g.20648364G>C	ENSP00000434364:p.Lys457Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	193	0.08836996336996338	8	0.016260162601626018	35	0.09668508287292818	45	0.07867132867132867	105	0.13852242744063326	G	11.51	1.659351	0.29515	0.030413	0.16093	ENSG00000165970	ENST00000525748	T	0.73363	-0.74	6.04	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.00300	0.0009	N	0.17474	0.49	0.09310	P	0.999999255195	B	0.20261	0.043	B	0.20577	0.03	T	0.05305	-1.0893	9	0.09843	T	0.71	.	10.6233	0.45493	0.1431:0.0:0.8569:0.0	rs3740870;rs52812307;rs3740870	457	Q9Y345	SC6A5_HUMAN	N	457	ENSP00000434364:K457N	ENSP00000434364:K457N	K	+	3	2	SLC6A5	20604940	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.250000	0.32850	2.873000	0.98535	0.561000	0.74099	AAG	G|0.895;C|0.105	0.105	strong		0.562	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
PNLDC1	154197	hgsc.bcm.edu	37	6	160225012	160225012	+	Silent	SNP	T	T	G	rs35435543	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:160225012T>G	ENST00000610273.1	+	5	402	c.231T>G	c.(229-231)tcT>tcG	p.S77S	PNLDC1_ENST00000609334.1_3'UTR|PNLDC1_ENST00000392167.3_Silent_p.S88S	NM_001271862.1|NM_173516.1	NP_001258791.1|NP_775787.1	Q8NA58	PNDC1_HUMAN	poly(A)-specific ribonuclease (PARN)-like domain containing 1	77						integral component of membrane (GO:0016021)|nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	31		Breast(66;0.00519)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;1.55e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TAGCCCATTCTTGTAACTTCT	0.413													G|||	1879	0.3752	0.236	0.5865	5008	,	,		18181	0.1627		0.5109	False		,,,				2504	0.4928				p.S77S		Atlas-SNP	.											.	PNLDC1	66	.	0			c.T231G						PASS	.	G		1196,3210	707.9+/-407.6	163,870,1170	123.0	127.0	126.0		231	-10.4	0.8	6	dbSNP_126	126	4692,3908	545.9+/-384.9	1312,2068,920	no	coding-synonymous	PNLDC1	NM_173516.1		1475,2938,2090	GG,GT,TT		45.4419,27.1448,45.2714		77/521	160225012	5888,7118	2203	4300	6503	SO:0001819	synonymous_variant	154197	exon5			CCATTCTTGTAAC	AK097559	CCDS5271.1, CCDS5271.2, CCDS64561.1	6q25.3	2008-02-05			ENSG00000146453	ENSG00000146453			21185	protein-coding gene	gene with protein product							Standard	NM_001271862		Approved	FLJ40240, dJ195P10.2	uc003qsy.2	Q8NA58	OTTHUMG00000015941	ENST00000610273.1:c.231T>G	6.37:g.160225012T>G		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	203	202	0.995074	NM_173516	Q5TAP7|Q8N7X5	Silent	SNP	ENST00000610273.1	37	CCDS5271.1																																																																																			T|0.564;G|0.436	0.436	strong		0.413	PNLDC1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_173516	
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 GAIIx	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	RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000561530.1_Silent_p.S52S|CARHSP1_ENST00000311052.5_Silent_p.S52S|CARHSP1_ENST00000567554.1_Silent_p.S52S|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		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	141	63	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	
CR1	1378	hgsc.bcm.edu	37	1	207782931	207782931	+	Missense_Mutation	SNP	A	A	G	rs6691117	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207782931A>G	ENST00000367049.4	+	37	6193	c.6193A>G	c.(6193-6195)Atc>Gtc	p.I2065V	CR1_ENST00000367052.1_Missense_Mutation_p.I1615V|CR1_ENST00000367051.1_Missense_Mutation_p.I1615V|CR1_ENST00000367053.1_Missense_Mutation_p.I1615V|CR1_ENST00000400960.2_Missense_Mutation_p.I1615V	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1615					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CACTGAGATCATCAGATTTAG	0.498													G|||	2471	0.493411	0.8722	0.3761	5008	,	,		19776	0.3433		0.2256	False		,,,				2504	0.4949				p.I2065V		Atlas-SNP	.											.	CR1	354	.	0			c.A6193G						PASS	.	G	VAL/ILE,VAL/ILE	2892,958		1089,714,122	36.0	37.0	37.0		4843,6193	2.5	0.0	1	dbSNP_116	37	1761,6497		162,1437,2530	yes	missense,missense	CR1	NM_000573.3,NM_000651.4	29,29	1251,2151,2652	GG,GA,AA		21.3248,24.8831,38.4291	benign,benign	1615/2040,2065/2490	207782931	4653,7455	1925	4129	6054	SO:0001583	missense	1378	exon37			GAGATCATCAGAT	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6193A>G	1.37:g.207782931A>G	ENSP00000356016:p.Ile2065Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	850	0.3891941391941392	408	0.8292682926829268	135	0.3729281767955801	143	0.25	164	0.21635883905013192	G	0.017	-1.509804	0.00984	0.751169	0.213248	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17	2.54	2.54	0.30619	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.10450	0.0;0.0;0.005	T	0.38866	-0.9641	8	0.02654	T	1	.	5.5311	0.16985	0.1589:0.0:0.8411:0.0	rs6691117;rs59510794;rs6691117	1615;1615;2065	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	V	1615;1615;1615;1615;2065	ENSP00000356019:I1615V;ENSP00000356018:I1615V;ENSP00000356020:I1615V;ENSP00000383744:I1615V;ENSP00000356016:I2065V	ENSP00000356016:I2065V	I	+	1	0	CR1	205849554	0.801000	0.28930	0.004000	0.12327	0.078000	0.17371	2.671000	0.46842	0.637000	0.30526	-0.355000	0.07637	ATC	A|0.601;G|0.399	0.399	strong		0.498	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
MLPH	79083	hgsc.bcm.edu	37	2	238443226	238443226	+	Missense_Mutation	SNP	A	A	G	rs2292884	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238443226A>G	ENST00000264605.3	+	9	1334	c.1040A>G	c.(1039-1041)cAt>cGt	p.H347R	MLPH_ENST00000338530.4_Intron|MLPH_ENST00000468178.1_Intron|MLPH_ENST00000445024.2_Missense_Mutation_p.H347R|MLPH_ENST00000409373.1_Intron|MLPH_ENST00000410032.1_Intron	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	347			H -> R (in dbSNP:rs2292884).		melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		CTGAATAAGCATATTTCAGCT	0.552													G|||	1860	0.371406	0.621	0.3098	5008	,	,		20283	0.2748		0.2097	False		,,,				2504	0.3436				p.H347R		Atlas-SNP	.											.	MLPH	41	.	0			c.A1040G						PASS	.	G	,ARG/HIS	2503,1903	545.1+/-376.7	712,1079,412	132.0	126.0	128.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,1040	0.0	0.0	2	dbSNP_100	128	2189,6411	711.9+/-405.9	269,1651,2380	yes	intron,missense	MLPH	NM_001042467.1,NM_024101.5	,29	981,2730,2792	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	25.4535,43.1911,36.0757	,benign	,347/601	238443226	4692,8314	2203	4300	6503	SO:0001583	missense	79083	exon9			ATAAGCATATTTC	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1040A>G	2.37:g.238443226A>G	ENSP00000264605:p.His347Arg	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	131	57	0.435115	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	723	0.33104395604395603	305	0.6199186991869918	98	0.27071823204419887	159	0.27797202797202797	161	0.21240105540897097	G	0.005	-2.149150	0.00328	0.568089	0.254535	ENSG00000115648	ENST00000264605;ENST00000445024;ENST00000437893	T;T;T	0.14144	3.1;3.01;2.53	3.99	0.0132	0.14094	.	0.873451	0.09484	N	0.795883	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43015	-0.9417	9	0.02654	T	1	-1.4822	8.7039	0.34343	0.4573:0.0:0.5427:0.0	rs2292884;rs11539362;rs60898014;rs2292884	8;347	Q53QV8;Q9BV36	.;MELPH_HUMAN	R	347;347;107	ENSP00000264605:H347R;ENSP00000414849:H347R;ENSP00000412438:H107R	ENSP00000264605:H347R	H	+	2	0	MLPH	238107965	0.000000	0.05858	0.000000	0.03702	0.557000	0.35523	0.241000	0.18065	-0.177000	0.10690	-0.119000	0.15052	CAT	A|0.644;G|0.356	0.356	strong		0.552	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
INTS1	26173	hgsc.bcm.edu	37	7	1542814	1542814	+	Silent	SNP	T	T	C	rs3752715	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:1542814T>C	ENST00000404767.3	-	3	157	c.72A>G	c.(70-72)ccA>ccG	p.P24P	INTS1_ENST00000493531.1_5'Flank|INTS1_ENST00000389470.4_Silent_p.P152P	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	24					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TGAAGTCTCCTGGGGGAGGGT	0.557													C|||	2928	0.584665	0.7746	0.4179	5008	,	,		18049	0.7063		0.4642	False		,,,				2504	0.4448				p.P24P		Atlas-SNP	.											INTS1,colon,carcinoma,-1,1	INTS1	145	1	0			c.A72G						PASS	.			2592,1218		883,826,196	44.0	49.0	48.0		72	-9.5	0.0	7	dbSNP_107	48	3412,4838		681,2050,1394	no	coding-synonymous	INTS1	NM_001080453.2		1564,2876,1590	CC,CT,TT		41.3576,31.9685,49.7844		24/2191	1542814	6004,6056	1905	4125	6030	SO:0001819	synonymous_variant	26173	exon3			GTCTCCTGGGGGA	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.72A>G	7.37:g.1542814T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	163	99	0.607362	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			T|0.412;C|0.588	0.588	strong		0.557	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
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 GAIIx	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_ENST00000487848.1_Missense_Mutation_p.P267H|GATA2_ENST00000430265.2_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	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	31	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	
C11orf1	64776	hgsc.bcm.edu	37	11	111754574	111754574	+	Silent	SNP	A	A	C	rs1045282	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:111754574A>C	ENST00000260276.3	+	4	760	c.423A>C	c.(421-423)tcA>tcC	p.S141S	C11orf1_ENST00000530214.1_Missense_Mutation_p.Q119P|C11orf1_ENST00000529270.1_Silent_p.S181S|C11orf1_ENST00000528125.1_Silent_p.S95S	NM_022761.2	NP_073598.1	Q9H5F2	CK001_HUMAN	chromosome 11 open reading frame 1	141						nucleus (GO:0005634)				kidney(2)|lung(3)	5		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)		CAGAAAAGTCAACTTACATGA	0.398													A|||	1200	0.239617	0.1952	0.3069	5008	,	,		18184	0.1905		0.3231	False		,,,				2504	0.2168				p.S141S		Atlas-SNP	.											.	C11orf1	15	.	0			c.A423C						PASS	.	A		963,3439	363.1+/-316.4	106,751,1344	114.0	108.0	110.0		423	4.2	1.0	11	dbSNP_86	110	2579,6015	419.8+/-353.2	394,1791,2112	no	coding-synonymous	C11orf1	NM_022761.2		500,2542,3456	CC,CA,AA		30.0093,21.8764,27.2545		141/151	111754574	3542,9454	2201	4297	6498	SO:0001819	synonymous_variant	64776	exon4			AAAGTCAACTTAC	AJ250229	CCDS8350.1	11q23.1	2012-05-30			ENSG00000137720	ENSG00000137720			1163	protein-coding gene	gene with protein product						10873569	Standard	NM_022761		Approved	FLJ23499	uc001pmd.3	Q9H5F2	OTTHUMG00000166884	ENST00000260276.3:c.423A>C	11.37:g.111754574A>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	56	45	0.803571	NM_022761	Q6I9X7|Q9NQC6	Silent	SNP	ENST00000260276.3	37	CCDS8350.1	583	0.26694139194139194	114	0.23170731707317074	126	0.34806629834254144	101	0.17657342657342656	242	0.31926121372031663	A	10.58	1.389114	0.25118	0.218764	0.300093	ENSG00000137720	ENST00000530214	T	0.25085	1.82	5.37	4.22	0.49857	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999994803	.	.	.	.	.	.	T	0.43196	-0.9406	5	0.62326	D	0.03	-22.8715	5.7886	0.18347	0.5843:0.3324:0.0833:0.0	rs1045282;rs3168261;rs17489575;rs59543330;rs1045282	.	.	.	P	119	ENSP00000435864:Q119P	ENSP00000435864:Q119P	Q	+	2	0	C11orf1	111259784	0.960000	0.32886	0.982000	0.44146	0.994000	0.84299	1.708000	0.37899	1.017000	0.39495	0.528000	0.53228	CAA	A|0.734;C|0.266	0.266	strong		0.398	C11orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391650.1	NM_022761	
TRIM9	114088	hgsc.bcm.edu	37	14	51446216	51446216	+	Missense_Mutation	SNP	T	T	G	rs2275462	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:51446216T>G	ENST00000298355.3	-	9	3080	c.1959A>C	c.(1957-1959)ttA>ttC	p.L653F	TRIM9_ENST00000338969.5_Missense_Mutation_p.L734F	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	653	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		L -> F (in dbSNP:rs2275462). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9179496}.		negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TTTTTCTATTTAAGTCGAGGA	0.448													T|||	2954	0.589856	0.4372	0.7262	5008	,	,		19323	0.6925		0.5537	False		,,,				2504	0.6309				p.L653F		Atlas-SNP	.											TRIM9_ENST00000338969,NS,carcinoma,-2,2	TRIM9	188	2	0			c.A1959C						PASS	.	T	PHE/LEU	1944,2462	551.4+/-378.3	432,1080,691	198.0	218.0	211.0		1959	3.5	1.0	14	dbSNP_100	211	4883,3717	618.6+/-396.8	1386,2111,803	yes	missense	TRIM9	NM_015163.5	22	1818,3191,1494	GG,GT,TT		43.2209,44.1217,47.5088	benign	653/711	51446216	6827,6179	2203	4300	6503	SO:0001583	missense	114088	exon9			TCTATTTAAGTCG	AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1959A>C	14.37:g.51446216T>G	ENSP00000298355:p.Leu653Phe	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_015163	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	37	CCDS9703.1	1278	0.5851648351648352	207	0.42073170731707316	241	0.6657458563535912	408	0.7132867132867133	422	0.5567282321899736	T	15.58	2.876985	0.51801	0.441217	0.567791	ENSG00000100505	ENST00000298355;ENST00000338969	T;T	0.73363	-0.44;-0.74	5.89	3.54	0.40534	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.122414	0.56097	N	0.000032	T	0.00012	0.0000	L	0.41236	1.265	0.09310	P	1.0	B;B	0.21606	0.058;0.012	B;B	0.29663	0.105;0.077	T	0.48387	-0.9040	9	0.11182	T	0.66	.	1.0846	0.01650	0.1734:0.1282:0.1816:0.5167	rs2275462;rs17795996;rs17855888;rs60258718;rs2275462	734;653	Q9C026-4;Q9C026	.;TRIM9_HUMAN	F	653;734	ENSP00000298355:L653F;ENSP00000342970:L734F	ENSP00000298355:L653F	L	-	3	2	TRIM9	50515966	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	0.502000	0.22594	1.035000	0.39972	0.455000	0.32223	TTA	T|0.451;G|0.549	0.549	strong		0.448	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163	
MAT2B	27430	hgsc.bcm.edu	37	5	162940999	162940999	+	Splice_Site	SNP	A	A	G	rs11546512	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:162940999A>G	ENST00000321757.6	+	4	664	c.525A>G	c.(523-525)ctA>ctG	p.L175L	MAT2B_ENST00000280969.5_Splice_Site_p.L164L|MAT2B_ENST00000518095.1_Splice_Site_p.L175L	NM_013283.3	NP_037415.1	Q9NZL9	MAT2B_HUMAN	methionine adenosyltransferase II, beta	175					cellular nitrogen compound metabolic process (GO:0034641)|extracellular polysaccharide biosynthetic process (GO:0045226)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|regulation of catalytic activity (GO:0050790)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|methionine adenosyltransferase complex (GO:0048269)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dTDP-4-dehydrorhamnose reductase activity (GO:0008831)|enzyme binding (GO:0019899)|methionine adenosyltransferase regulator activity (GO:0048270)			endometrium(3)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)	14	Renal(175;0.000281)	Medulloblastoma(196;0.0208)|all_neural(177;0.0765)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.027)|OV - Ovarian serous cystadenocarcinoma(192;0.0406)|Epithelial(171;0.0797)	L-Methionine(DB00134)	AGAACAATCTAGGTAAGACCT	0.323													A|||	410	0.081869	0.0371	0.0836	5008	,	,		13745	0.0129		0.17	False		,,,				2504	0.1217				p.L175L		Atlas-SNP	.											.	MAT2B	42	.	0			c.A525G						PASS	.	A	,	239,4167	137.3+/-173.1	7,225,1971	58.0	58.0	58.0		525,492	1.9	1.0	5	dbSNP_123	58	1303,7297	253.3+/-279.0	107,1089,3104	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	MAT2B	NM_013283.3,NM_182796.1	,	114,1314,5075	GG,GA,AA		15.1512,5.4244,11.8561	,	175/335,164/324	162940999	1542,11464	2203	4300	6503	SO:0001630	splice_region_variant	27430	exon4			CAATCTAGGTAAG	AF182814	CCDS4364.1, CCDS4365.1	5q34-q35	2011-09-14			ENSG00000038274	ENSG00000038274		"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	6905	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 23E, member 1"""	605527				9055605, 10644686, 19027726	Standard	NM_182796		Approved	MATIIbeta, SDR23E1	uc003lzk.4	Q9NZL9	OTTHUMG00000130379	ENST00000321757.6:c.526+1A>G	5.37:g.162940999A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_013283	B2R5Y6|Q1WAI7|Q27J92|Q3LIE8|Q567T7|Q6NYC7|Q9BS89|Q9H3E1|Q9UJ54	Silent	SNP	ENST00000321757.6	37	CCDS4365.1																																																																																			A|0.889;G|0.111	0.111	strong		0.323	MAT2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252749.2	NM_013283	Silent
B3GNTL1	146712	hgsc.bcm.edu	37	17	80904844	80904844	+	Missense_Mutation	SNP	C	C	T	rs7225887	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:80904844C>T	ENST00000320865.3	-	12	1034	c.1021G>A	c.(1021-1023)Gcc>Acc	p.A341T	B3GNTL1_ENST00000576599.1_Missense_Mutation_p.A230T	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	341			A -> T (in dbSNP:rs7225887).				transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)	all_cancers(8;0.0396)|all_epithelial(8;0.0556)	BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			TCCTCAAAGGCGCCCCCTGTG	0.622													C|||	781	0.15595	0.0582	0.2046	5008	,	,		14879	0.1577		0.2535	False		,,,				2504	0.1513				p.A341T		Atlas-SNP	.											B3GNTL1,NS,carcinoma,+2,1	B3GNTL1	40	1	0			c.G1021A						PASS	.	C	THR/ALA	319,4081		5,309,1886	56.0	47.0	50.0		1021	4.0	1.0	17	dbSNP_116	50	1806,6778		189,1428,2675	yes	missense	B3GNTL1	NM_001009905.1	58	194,1737,4561	TT,TC,CC		21.0391,7.25,16.3663	benign	341/362	80904844	2125,10859	2200	4292	6492	SO:0001583	missense	146712	exon12			CAAAGGCGCCCCC	AY634364	CCDS32778.1	17q25.3	2013-02-22	2004-01-13	2004-01-14	ENSG00000175711	ENSG00000175711		"""Glycosyltransferase family 2 domain containing"""	21727	protein-coding gene	gene with protein product		615337					Standard	NM_001009905		Approved	B3GNT8	uc002kgg.1	Q67FW5	OTTHUMG00000177788	ENST00000320865.3:c.1021G>A	17.37:g.80904844C>T	ENSP00000319979:p.Ala341Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_001009905	Q6GV30|Q8WUT3	Missense_Mutation	SNP	ENST00000320865.3	37	CCDS32778.1	380	0.17399267399267399	30	0.06097560975609756	76	0.20994475138121546	90	0.15734265734265734	184	0.24274406332453827	C	12.22	1.871294	0.33069	0.0725	0.210391	ENSG00000175711	ENST00000320865	T	0.41400	1.0	4.0	4.0	0.46444	.	0.419285	0.23201	N	0.050795	T	0.00012	0.0000	N	0.19112	0.55	0.36786	P	0.115429	B	0.15473	0.013	B	0.08055	0.003	T	0.17289	-1.0374	8	.	.	.	-14.9116	14.4067	0.67088	0.0:1.0:0.0:0.0	rs7225887;rs17344847;rs52802513;rs57810247;rs7225887	341	Q67FW5	B3GNL_HUMAN	T	341	ENSP00000319979:A341T	.	A	-	1	0	B3GNTL1	78498133	0.136000	0.22515	0.965000	0.40720	0.950000	0.60333	3.322000	0.52007	2.171000	0.68590	0.563000	0.77884	GCC	C|0.840;T|0.160	0.160	strong		0.622	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
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 GAIIx	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_ENST00000529450.1_Silent_p.N428N|SLC44A3_ENST00000446120.2_Silent_p.N424N|SLC44A3_ENST00000527077.1_Silent_p.N392N|SLC44A3_ENST00000532427.1_Silent_p.N380N|SLC44A3_ENST00000467909.1_Silent_p.N412N|SLC44A3_ENST00000530397.1_3'UTR	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		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	51	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	
ANKRD26	22852	hgsc.bcm.edu	37	10	27381349	27381349	+	Silent	SNP	T	T	C	rs2297145	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27381349T>C	ENST00000376087.4	-	4	789	c.624A>G	c.(622-624)gtA>gtG	p.V208V	ANKRD26_ENST00000436985.2_Silent_p.V208V	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	208					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						CCAACTTATCTACTGCATTTA	0.313													C|||	1736	0.346645	0.3207	0.1873	5008	,	,		17605	0.5427		0.2137	False		,,,				2504	0.4294				p.V208V		Atlas-SNP	.											.	ANKRD26	179	.	0			c.A624G						PASS	.	C		1119,2493		165,789,852	97.0	95.0	96.0		624	-8.6	0.0	10	dbSNP_100	96	1351,6793		102,1147,2823	no	coding-synonymous	ANKRD26	NM_014915.2		267,1936,3675	CC,CT,TT		16.5889,30.9801,21.0105		208/1711	27381349	2470,9286	1806	4072	5878	SO:0001819	synonymous_variant	22852	exon4			CTTATCTACTGCA	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.624A>G	10.37:g.27381349T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Silent	SNP	ENST00000376087.4	37	CCDS41499.1																																																																																			T|0.691;C|0.309	0.309	strong		0.313	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
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 GAIIx	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	MIR4783_ENST00000580343.1_RNA|PROC_ENST00000409048.1_Missense_Mutation_p.R38W|PROC_ENST00000453608.2_Missense_Mutation_p.R59W|PROC_ENST00000422777.3_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	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	127	47	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	
BCDIN3D	144233	hgsc.bcm.edu	37	12	50232496	50232496	+	Silent	SNP	T	T	C	rs17260403	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:50232496T>C	ENST00000333924.4	-	2	578	c.537A>G	c.(535-537)ctA>ctG	p.L179L	BCDIN3D-AS1_ENST00000549124.1_RNA|BCDIN3D-AS1_ENST00000548872.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	179	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						GGAACTCCCATAGGCCATGGT	0.512											OREG0021805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	179	0.0357428	0.0045	0.0461	5008	,	,		20862	0.001		0.1302	False		,,,				2504	0.0092				p.L179L		Atlas-SNP	.											.	BCDIN3D	20	.	0			c.A537G						PASS	.	T		92,4314	77.8+/-116.1	1,90,2112	97.0	82.0	87.0		537	-1.2	0.4	12	dbSNP_123	87	898,7702	201.8+/-245.2	44,810,3446	no	coding-synonymous	BCDIN3D	NM_181708.2		45,900,5558	CC,CT,TT		10.4419,2.0881,7.6119		179/293	50232496	990,12016	2203	4300	6503	SO:0001819	synonymous_variant	144233	exon2			CTCCCATAGGCCA		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.537A>G	12.37:g.50232496T>C		Somatic	61	0	0	968	WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_181708	A8K829	Silent	SNP	ENST00000333924.4	37	CCDS8790.1																																																																																			T|0.938;C|0.062	0.062	strong		0.512	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708	
HHLA2	11148	hgsc.bcm.edu	37	3	108095365	108095365	+	Silent	SNP	G	G	A	rs2124736	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:108095365G>A	ENST00000357759.5	+	9	1599	c.1185G>A	c.(1183-1185)gaG>gaA	p.E395E	HHLA2_ENST00000467761.1_Silent_p.E395E|HHLA2_ENST00000467562.1_Silent_p.E331E|HHLA2_ENST00000491820.1_Silent_p.E378E|HHLA2_ENST00000489514.2_Silent_p.E395E	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	395					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						CTCCTGGTGAGCGCTGTCCCA	0.363													G|||	449	0.0896565	0.0136	0.1527	5008	,	,		19715	0.001		0.2326	False		,,,				2504	0.092				p.E395E		Atlas-SNP	.											.	HHLA2	95	.	0			c.G1185A						PASS	.	G		212,3540		5,202,1669	82.0	84.0	83.0		1185	-2.5	0.0	3	dbSNP_96	83	1901,6307		236,1429,2439	no	coding-synonymous	HHLA2	NM_007072.2		241,1631,4108	AA,AG,GG		23.1603,5.6503,17.6672		395/415	108095365	2113,9847	1876	4104	5980	SO:0001819	synonymous_variant	11148	exon9			TGGTGAGCGCTGT	AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.1185G>A	3.37:g.108095365G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Silent	SNP	ENST00000357759.5	37	CCDS46883.1	256	0.11721611721611722	7	0.014227642276422764	64	0.17679558011049723	0	0.0	185	0.24406332453825857	G	1.601	-0.526518	0.04141	0.056503	0.231603	ENSG00000114455	ENST00000482099	.	.	.	3.44	-2.48	0.06423	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.34601	-0.9822	3	.	.	.	-15.1402	1.081	0.01643	0.2254:0.3121:0.3019:0.1606	rs2124736;rs17373363;rs2124736	.	.	.	T	298	.	.	A	+	1	0	HHLA2	109578055	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.141000	0.10327	-0.545000	0.06224	0.561000	0.74099	GCG	G|0.881;A|0.119	0.119	strong		0.363	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
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 GAIIx	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_ENST00000542181.1_Intron|ELP3_ENST00000523760.1_3'UTR|ELP3_ENST00000524103.1_5'UTR|ELP3_ENST00000537665.1_5'UTR|ELP3_ENST00000521015.1_Silent_p.V57V	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		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	27	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	
DFNA5	1687	hgsc.bcm.edu	37	7	24758795	24758795	+	Silent	SNP	T	T	C	rs78941420|rs876305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:24758795T>C	ENST00000342947.3	-	4	872	c.447A>G	c.(445-447)gaA>gaG	p.E149E	DFNA5_ENST00000409970.1_5'UTR|DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000419307.1_5'UTR|DFNA5_ENST00000559637.1_5'UTR|DFNA5_ENST00000409775.3_Silent_p.E149E	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	149					apoptotic process (GO:0006915)|inner ear receptor cell differentiation (GO:0060113)|negative regulation of cell proliferation (GO:0008285)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)|stomach(1)	19						CATTCCTTCCTTCCAGCACCT	0.493													C|||	3694	0.73762	0.8275	0.6643	5008	,	,		23268	0.9841		0.4135	False		,,,				2504	0.7474				p.E149E	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.A447G						PASS	.	C	,,	3370,1036	379.0+/-323.1	1295,780,128	161.0	143.0	149.0		447,,447	3.3	0.9	7	dbSNP_86	149	3619,4981	624.4+/-397.6	755,2109,1436	no	coding-synonymous,utr-5,coding-synonymous	DFNA5	NM_001127453.1,NM_001127454.1,NM_004403.2	,,	2050,2889,1564	CC,CT,TT		42.0814,23.5134,46.2633	,,	149/497,,149/497	24758795	6989,6017	2203	4300	6503	SO:0001819	synonymous_variant	1687	exon4			CCTTCCTTCCAGC	AF007790	CCDS5389.1, CCDS47563.1	7p15	2011-07-01			ENSG00000105928	ENSG00000105928			2810	protein-coding gene	gene with protein product		608798				8589696, 9450185	Standard	NM_004403		Approved	ICERE-1	uc010kus.1	O60443	OTTHUMG00000023237	ENST00000342947.3:c.447A>G	7.37:g.24758795T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	13	0.288889	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Silent	SNP	ENST00000342947.3	37	CCDS5389.1																																																																																			T|0.394;C|0.606	0.606	strong		0.493	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403	
CENPU	79682	hgsc.bcm.edu	37	4	185655171	185655171	+	Splice_Site	SNP	C	C	T	rs902174	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:185655171C>T	ENST00000281453.5	-	1	116	c.46G>A	c.(46-48)Ggc>Agc	p.G16S	MLF1IP_ENST00000541971.1_Splice_Site_p.G16S	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		AGTACTTACCCCTCAGACCTG	0.726													C|||	1689	0.33726	0.1044	0.389	5008	,	,		12283	0.7321		0.2306	False		,,,				2504	0.318				p.G16S		Atlas-SNP	.											.	MLF1IP	33	.	0			c.G46A						PASS	.	C	SER/GLY	509,3827		38,433,1697	10.0	11.0	11.0		46	-0.2	0.1	4	dbSNP_86	11	1949,6555		232,1485,2535	yes	missense-near-splice	MLF1IP	NM_024629.3	56	270,1918,4232	TT,TC,CC		22.9186,11.7389,19.1433	possibly-damaging	16/419	185655171	2458,10382	2168	4252	6420	SO:0001630	splice_region_variant	79682	exon1			CTTACCCCTCAGA																												ENST00000281453.5:c.47+1G>A	4.37:g.185655171C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_024629		Missense_Mutation	SNP	ENST00000281453.5	37	CCDS3838.1	746|746	0.3415750915750916|0.3415750915750916	53|53	0.10772357723577236|0.10772357723577236	128|128	0.35359116022099446|0.35359116022099446	387|387	0.6765734265734266|0.6765734265734266	178|178	0.23482849604221637|0.23482849604221637	C|C	9.719|9.719	1.159177|1.159177	0.21454|0.21454	0.117389|0.117389	0.229186|0.229186	ENSG00000151725|ENSG00000151725	ENST00000541665|ENST00000281453;ENST00000541971	.|T;T	.|0.19669	.|2.19;2.13	3.66|3.66	-0.251|-0.251	0.13003|0.13003	.|.	.|0.854162	.|0.10010	.|N	.|0.727321	.|T	.|0.00012	.|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.51233|0.51233	P|P	8.20000000000265E-5|8.20000000000265E-5	.|P;P	.|0.43857	.|0.819;0.608	.|B;B	.|0.35114	.|0.196;0.151	.|T	.|0.30765	.|-0.9967	.|9	.|0.48119	.|T	.|0.1	.|-7.3742	7.1902|7.1902	0.25821|0.25821	0.0:0.3724:0.5225:0.1051|0.0:0.3724:0.5225:0.1051	rs902174;rs1137716;rs3201524;rs11542157;rs17625279;rs60983112;rs902174|rs902174;rs1137716;rs3201524;rs11542157;rs17625279;rs60983112;rs902174	.|16;16	.|Q09GN1;Q71F23	.|.;CENPU_HUMAN	.|S	-1|16	.|ENSP00000281453:G16S;ENSP00000445862:G16S	.|ENSP00000281453:G16S	.|G	-|-	.|1	.|0	MLF1IP|MLF1IP	185892165|185892165	0.024000|0.024000	0.19004|0.19004	0.062000|0.062000	0.19696|0.19696	0.005000|0.005000	0.04900|0.04900	-0.164000|-0.164000	0.09983|0.09983	-0.082000|-0.082000	0.12640|0.12640	0.655000|0.655000	0.94253|0.94253	.|GGC	C|0.641;T|0.359	0.359	strong		0.726	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		Missense_Mutation
BTN3A2	11118	hgsc.bcm.edu	37	6	26370748	26370748	+	Missense_Mutation	SNP	G	G	A	rs35183513	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26370748G>A	ENST00000356386.2	+	5	820	c.632G>A	c.(631-633)aGa>aAa	p.R211K	BTN3A2_ENST00000527422.1_Missense_Mutation_p.R211K|BTN3A2_ENST00000377708.2_Missense_Mutation_p.R211K|BTN3A2_ENST00000396934.3_Missense_Mutation_p.R188K|BTN3A2_ENST00000532994.1_3'UTR|BTN3A2_ENST00000396948.1_Missense_Mutation_p.R211K|BTN3A2_ENST00000508906.2_Missense_Mutation_p.R169K	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	211			R -> K (in dbSNP:rs35183513).	RG -> KS (in Ref. 3; AAF76140). {ECO:0000305}.	interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						GTGATCATGAGAGGCGGCTCC	0.557													G|||	524	0.104633	0.1233	0.1095	5008	,	,		18498	0.0248		0.1173	False		,,,				2504	0.1452				p.R211K		Atlas-SNP	.											.	BTN3A2	44	.	0			c.G632A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	646,3760	279.0+/-274.6	43,560,1600	145.0	141.0	142.0		632,632,563,506,632	1.2	0.0	6	dbSNP_126	142	1062,7538	224.5+/-260.9	66,930,3304	yes	missense,missense,missense,missense,missense	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	26,26,26,26,26	109,1490,4904	AA,AG,GG		12.3488,14.6618,13.1324	benign,benign,benign,benign,benign	211/335,211/335,188/312,169/293,211/335	26370748	1708,11298	2203	4300	6503	SO:0001583	missense	11118	exon3			TCATGAGAGGCGG	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.632G>A	6.37:g.26370748G>A	ENSP00000348751:p.Arg211Lys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	163	26	0.159509	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Missense_Mutation	SNP	ENST00000356386.2	37	CCDS4605.1	207	0.09478021978021978	67	0.13617886178861788	45	0.12430939226519337	10	0.017482517482517484	85	0.11213720316622691	g	10.17	1.277326	0.23307	0.146618	0.123488	ENSG00000186470	ENST00000532865;ENST00000535620;ENST00000527422;ENST00000356386;ENST00000396934;ENST00000377708;ENST00000396948;ENST00000508906	T;T;T;T;T;T;T	0.75938	-0.98;3.34;3.34;3.34;3.34;3.34;3.34	2.31	1.22	0.21188	Immunoglobulin-like fold (1);	.	.	.	.	T	0.41604	0.1166	L	0.38649	1.16	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.002	T	0.15492	-1.0435	8	0.66056	D	0.02	.	4.3959	0.11363	0.2525:0.0:0.7475:0.0	rs35183513	188;211	F8W6E0;P78410	.;BT3A2_HUMAN	K	169;211;211;211;188;211;211;169	ENSP00000435952:R169K;ENSP00000432138:R211K;ENSP00000348751:R211K;ENSP00000380140:R188K;ENSP00000366937:R211K;ENSP00000380152:R211K;ENSP00000442687:R169K	ENSP00000348751:R211K	R	+	2	0	BTN3A2	26478727	0.000000	0.05858	0.006000	0.13384	0.282000	0.26991	-0.711000	0.05019	0.351000	0.24027	0.405000	0.27470	AGA	G|0.877;A|0.123	0.123	strong		0.557	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
OR10A5	144124	hgsc.bcm.edu	37	11	6867462	6867462	+	Silent	SNP	G	G	A	rs543931840		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6867462G>A	ENST00000299454.4	+	1	580	c.549G>A	c.(547-549)ccG>ccA	p.P183P	OR10A5_ENST00000379831.2_Silent_p.P187P			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	183					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)	p.P183P(2)		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)		GTGACAGCCCGCCTGTGCTGA	0.527													A|||	1	0.000199681	0.0	0.0	5008	,	,		23000	0.001		0.0	False		,,,				2504	0.0				p.P183P	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											OR10A5,NS,carcinoma,0,3	OR10A5	48	3	2	Substitution - coding silent(2)	kidney(2)	c.G549A						scavenged	.						180.0	152.0	161.0					11																	6867462		2201	4296	6497	SO:0001819	synonymous_variant	144124	exon1			CAGCCCGCCTGTG	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.549G>A	11.37:g.6867462G>A		Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	186	5	0.0268817	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	37	CCDS7773.1																																																																																			.	.	none		0.527	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168	
GIMAP2	26157	hgsc.bcm.edu	37	7	150389856	150389856	+	Missense_Mutation	SNP	A	A	G	rs2075078	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150389856A>G	ENST00000223293.5	+	3	576	c.482A>G	c.(481-483)cAc>cGc	p.H161R		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	161	AIG1-type G.		H -> R (in dbSNP:rs2075078).			cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GATTACATGCACGACTCAGAT	0.502													G|||	1383	0.276158	0.441	0.1888	5008	,	,		21862	0.2431		0.1968	False		,,,				2504	0.2311				p.H161R		Atlas-SNP	.											.	GIMAP2	39	.	0			c.A482G						PASS	.	G	ARG/HIS	1675,2731	655.2+/-399.9	329,1017,857	89.0	66.0	74.0		482	-5.8	0.0	7	dbSNP_96	74	1707,6893	738.2+/-407.0	179,1349,2772	yes	missense	GIMAP2	NM_015660.2	29	508,2366,3629	GG,GA,AA		19.8488,38.0163,26.0034	benign	161/338	150389856	3382,9624	2203	4300	6503	SO:0001583	missense	26157	exon3			ACATGCACGACTC	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"""GTPases, IMAP"""	21789	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 12"""	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.482A>G	7.37:g.150389856A>G	ENSP00000223293:p.His161Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	139	79	0.568345	NM_015660	Q96L25	Missense_Mutation	SNP	ENST00000223293.5	37	CCDS5905.1	548	0.2509157509157509	187	0.3800813008130081	67	0.1850828729281768	133	0.23251748251748253	161	0.21240105540897097	G	3.917	-0.018824	0.07681	0.380163	0.198488	ENSG00000106560	ENST00000223293	T	0.04917	3.53	3.68	-5.76	0.02376	AIG1 (1);	2.358640	0.01635	N	0.023758	T	0.00012	0.0000	N	0.01631	-0.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42666	-0.9438	9	0.02654	T	1	.	5.9694	0.19342	0.5414:0.0:0.3374:0.1212	rs2075078;rs61565028;rs2075078	161	Q9UG22	GIMA2_HUMAN	R	161	ENSP00000223293:H161R	ENSP00000223293:H161R	H	+	2	0	GIMAP2	150020789	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.344000	0.00130	-1.789000	0.01264	-0.855000	0.03028	CAC	A|0.741;G|0.259	0.259	strong		0.502	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660	
MAEL	84944	hgsc.bcm.edu	37	1	166958601	166958601	+	Silent	SNP	T	T	C	rs2296837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:166958601T>C	ENST00000367872.4	+	1	256	c.12T>C	c.(10-12)cgT>cgC	p.R4R	MAEL_ENST00000367870.2_Silent_p.R4R	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	4					cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						TGCCGAACCGTAAGGCCAGCC	0.617													C|||	1512	0.301917	0.559	0.1715	5008	,	,		16556	0.247		0.2247	False		,,,				2504	0.183				p.R4R		Atlas-SNP	.											.	MAEL	95	.	0			c.T12C						PASS	.	C		2297,2109	557.3+/-379.7	590,1117,496	51.0	45.0	47.0		12	4.3	1.0	1	dbSNP_100	47	2135,6465	696.9+/-404.9	255,1625,2420	no	coding-synonymous	MAEL	NM_032858.1		845,2742,2916	CC,CT,TT		24.8256,47.8665,34.0766		4/435	166958601	4432,8574	2203	4300	6503	SO:0001819	synonymous_variant	84944	exon1			GAACCGTAAGGCC	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"""cancer/testis antigen 128"", ""spermatogenesis associated 35"""	611368	"""maelstrom homolog (Drosophila)"""			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.12T>C	1.37:g.166958601T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Silent	SNP	ENST00000367872.4	37	CCDS1257.1																																																																																			T|0.682;G|0.000;C|0.317;A|0.000	0.317	strong		0.617	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858	
DNMBP	23268	hgsc.bcm.edu	37	10	101639877	101639877	+	Missense_Mutation	SNP	A	A	C	rs11190305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101639877A>C	ENST00000324109.4	-	16	4330	c.4239T>G	c.(4237-4239)tgT>tgG	p.C1413W	DNMBP_ENST00000540316.1_Missense_Mutation_p.C349W|DNMBP_ENST00000342239.3_Missense_Mutation_p.C1437W|DNMBP_ENST00000543621.1_Missense_Mutation_p.C659W	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1413	Ser-rich.		C -> W (in dbSNP:rs11190305). {ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TTCCTTGGTCACATTCTTTTG	0.542													A|||	1388	0.277157	0.1437	0.3329	5008	,	,		19778	0.244		0.3917	False		,,,				2504	0.3344				p.C1413W		Atlas-SNP	.											.	DNMBP	173	.	0			c.T4239G						PASS	.		TRP/CYS	827,3579	328.5+/-300.6	82,663,1458	194.0	191.0	192.0		4239	0.6	0.0	10	dbSNP_120	192	3271,5329	490.7+/-372.9	638,1995,1667	yes	missense	DNMBP	NM_015221.2	215	720,2658,3125	CC,CA,AA		38.0349,18.7699,31.5085	benign	1413/1578	101639877	4098,8908	2203	4300	6503	SO:0001583	missense	23268	exon16			TTGGTCACATTCT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.4239T>G	10.37:g.101639877A>C	ENSP00000315659:p.Cys1413Trp	Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	252	103	0.40873	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	630	0.28846153846153844	55	0.11178861788617886	133	0.3674033149171271	150	0.26223776223776224	292	0.38522427440633245	A	9.817	1.184720	0.21870	0.187699	0.380349	ENSG00000107554	ENST00000342239;ENST00000324109;ENST00000393570;ENST00000543621;ENST00000540316	T;T;T;T	0.34275	2.81;2.76;2.42;1.37	5.77	0.604	0.17547	.	2.318410	0.01492	N	0.017126	T	0.00012	0.0000	N	0.14661	0.345	0.44104	P	0.003125999999999962	B;P;B	0.37573	0.328;0.6;0.102	B;B;B	0.41202	0.094;0.35;0.078	T	0.28618	-1.0038	9	0.37606	T	0.19	11.0357	1.0338	0.01543	0.3826:0.2917:0.1845:0.1411	rs11190305;rs17495998;rs17846312;rs17859342;rs52793133;rs56919867;rs11190305	1413;659;1437	Q6XZF7;Q6XZF7-2;Q5SVK8	DNMBP_HUMAN;.;.	W	1437;1413;659;659;349	ENSP00000344914:C1437W;ENSP00000315659:C1413W;ENSP00000443657:C659W;ENSP00000443573:C349W	ENSP00000315659:C1413W	C	-	3	2	DNMBP	101629867	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	-0.874000	0.04210	-0.132000	0.11557	-0.366000	0.07423	TGT	A|0.708;C|0.292	0.292	strong		0.542	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
OR5A1	219982	hgsc.bcm.edu	37	11	59211421	59211421	+	Silent	SNP	C	C	T	rs17591107	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:59211421C>T	ENST00000302030.2	+	1	805	c.780C>T	c.(778-780)ttC>ttT	p.F260F		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						CAGCCCTTTTCGTGTACTTGC	0.537													C|||	630	0.125799	0.0242	0.1326	5008	,	,		21088	0.1111		0.2525	False		,,,				2504	0.1431				p.F260F		Atlas-SNP	.											OR5A1,NS,adenoma,0,1	OR5A1	72	1	0			c.C780T						PASS	.	C		251,4151	146.9+/-181.5	10,231,1960	265.0	215.0	232.0		780	6.0	1.0	11	dbSNP_123	232	2264,6326	383.3+/-340.7	283,1698,2314	no	coding-synonymous	OR5A1	NM_001004728.1		293,1929,4274	TT,TC,CC		26.3562,5.702,19.3581		260/316	59211421	2515,10477	2201	4295	6496	SO:0001819	synonymous_variant	219982	exon1			CCTTTTCGTGTAC	AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"""GPCR / Class A : Olfactory receptors"""	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.780C>T	11.37:g.59211421C>T		Somatic	258	1	0.00387597		WXS	Illumina HiSeq	Phase_I	248	127	0.512097	NM_001004728	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																			C|0.815;T|0.185	0.185	strong		0.537	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728	
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 GAIIx	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_ENST00000477795.1_3'UTR|PARVB_ENST00000404989.1_Missense_Mutation_p.M38V|PARVB_ENST00000406477.3_Missense_Mutation_p.M108V	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	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	35	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	
CRHR1	1394	hgsc.bcm.edu	37	17	43910507	43910507	+	Silent	SNP	C	C	T	rs16940674	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43910507C>T	ENST00000398285.3	+	10	861	c.861C>T	c.(859-861)tgC>tgT	p.C287C	CRHR1_ENST00000293493.7_Silent_p.C83C|CRHR1_ENST00000314537.5_Silent_p.C258C|CRHR1_ENST00000339069.5_Silent_p.C157C|CRHR1_ENST00000352855.5_Silent_p.C218C|CRHR1_ENST00000577353.1_Silent_p.C258C	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	287					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CTTCTAGGTGCTGGTTTGGCA	0.612													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		20400	0.001		0.2396	False		,,,				2504	0.0613				p.C287C	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.C861T	GRCh37	CM044865	CRHR1	M	rs16940674	PASS	.	C	,,,	173,3815		5,163,1826	123.0	128.0	127.0		861,654,774,774	4.2	1.0	17	dbSNP_123	127	1831,6495		203,1425,2535	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRHR1	NM_001145146.1,NM_001145147.1,NM_001145148.1,NM_004382.4	,,,	208,1588,4361	TT,TC,CC		21.9914,4.338,16.2742	,,,	287/445,218/376,258/402,258/416	43910507	2004,10310	1994	4163	6157	SO:0001819	synonymous_variant	1394	exon10			TAGGTGCTGGTTT	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2357	protein-coding gene	gene with protein product	"""corticotropin-releasing factor receptor"""	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.861C>T	17.37:g.43910507C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001145146	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Silent	SNP	ENST00000398285.3	37	CCDS45712.1																																																																																			C|0.860;T|0.140	0.140	strong		0.612	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		
MUC2	4583	hgsc.bcm.edu	37	11	1081074	1081074	+	Splice_Site	SNP	T	T	C	rs41411848	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1081074T>C	ENST00000441003.2	+	11	1397	c.1370T>C	c.(1369-1371)gTg>gCg	p.V457A	MUC2_ENST00000359061.5_Splice_Site_p.V457A	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	457	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	TCCCTGCAGGTGGTGGTCTTC	0.657													T|||	1816	0.36262	0.4206	0.366	5008	,	,		16156	0.372		0.2207	False		,,,				2504	0.4182				p.V457A		Atlas-SNP	.											.	MUC2	614	.	0			c.T1370C						PASS	.	T	ALA/VAL	1534,2400		311,912,744	39.0	45.0	43.0		1370	2.2	1.0	11	dbSNP_127	43	1706,6598		183,1340,2629	no	missense-near-splice	MUC2	NM_002457.2	64	494,2252,3373	CC,CT,TT		20.5443,38.9934,26.4749	benign	457/2813	1081074	3240,8998	1967	4152	6119	SO:0001630	splice_region_variant	4583	exon11			TGCAGGTGGTGGT	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.1369-1T>C	11.37:g.1081074T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		678	0.31043956043956045	185	0.37601626016260165	108	0.2983425414364641	222	0.3881118881118881	163	0.21503957783641162	T	8.556	0.876751	0.17395	0.389934	0.205443	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.65549	-0.16;-0.16	3.43	2.25	0.28309	.	0.231656	0.26470	U	0.024184	T	0.00012	0.0000	.	.	.	0.34554	P	0.28835500000000003	B	0.33379	0.41	B	0.41174	0.349	T	0.40156	-0.9578	8	0.39692	T	0.17	.	7.978	0.30166	0.0:0.1046:0.0:0.8954	rs41411848;rs61738283	457	E7EUV1	.	A	457	ENSP00000415183:V457A;ENSP00000351956:V457A	ENSP00000351956:V457A	V	+	2	0	MUC2	1071074	1.000000	0.71417	1.000000	0.80357	0.029000	0.11900	2.109000	0.41863	1.441000	0.47550	0.358000	0.22013	GTG	T|0.714;C|0.286	0.286	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	Missense_Mutation
SLC22A25	387601	hgsc.bcm.edu	37	11	62951221	62951221	+	Missense_Mutation	SNP	C	C	G	rs11231397	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:62951221C>G	ENST00000306494.6	-	5	898	c.899G>C	c.(898-900)aGa>aCa	p.R300T	SLC22A10_ENST00000525620.1_Intron|SLC22A25_ENST00000403374.2_Missense_Mutation_p.R134T|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						TGCAGCTTTTCTAAGTTCCTT	0.483													C|||	2105	0.420327	0.2617	0.4438	5008	,	,		21198	0.5317		0.3946	False		,,,				2504	0.5297				p.R300T		Atlas-SNP	.											.	SLC22A25	87	.	0			c.G899C						PASS	.	C	THR/ARG	1306,3096	439.8+/-345.8	175,956,1070	290.0	263.0	272.0		899	-3.9	0.4	11	dbSNP_120	272	3239,5355	487.8+/-372.2	637,1965,1695	yes	missense	SLC22A25	NM_199352.3	71	812,2921,2765	GG,GC,CC		37.6891,29.6683,34.9723	probably-damaging	300/548	62951221	4545,8451	2201	4297	6498	SO:0001583	missense	387601	exon5			GCTTTTCTAAGTT	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.899G>C	11.37:g.62951221C>G	ENSP00000307443:p.Arg300Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	126	46	0.365079	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	875	0.40064102564102566	120	0.24390243902439024	135	0.3729281767955801	333	0.5821678321678322	287	0.3786279683377309	C	1.583	-0.531111	0.04112	0.296683	0.376891	ENSG00000196600	ENST00000306494;ENST00000403374	T;T	0.74526	0.27;-0.85	2.56	-3.87	0.04218	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.468291	0.22454	N	0.059854	T	0.00012	0.0000	M	0.88450	2.955	0.24720	P	0.99315045	D;D	0.67145	0.984;0.996	D;D	0.66497	0.925;0.944	T	0.44726	-0.9309	9	0.62326	D	0.03	.	3.2969	0.06969	0.1915:0.3105:0.0:0.498	rs11231397;rs52813421;rs11231397	298;300	A4IF29;Q6T423	.;S22AP_HUMAN	T	300;134	ENSP00000307443:R300T;ENSP00000384208:R134T	ENSP00000307443:R300T	R	-	2	0	SLC22A25	62707797	0.000000	0.05858	0.366000	0.25914	0.539000	0.34962	-0.657000	0.05335	-1.156000	0.02818	0.121000	0.15741	AGA	C|0.621;G|0.379	0.379	strong		0.483	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
RGS11	8786	hgsc.bcm.edu	37	16	320992	320992	+	Nonsense_Mutation	SNP	C	C	A	rs61759901	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:320992C>A	ENST00000397770.3	-	13	987	c.970G>T	c.(970-972)Gag>Tag	p.E324*	RGS11_ENST00000316163.5_Nonsense_Mutation_p.E303*|RGS11_ENST00000359740.5_Nonsense_Mutation_p.E313*|ARHGDIG_ENST00000464609.1_Intron			O94810	RGS11_HUMAN	regulator of G-protein signaling 11	324	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)	8		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				CCACTGAACTCCTTTCCCAGA	0.672													C|||	9	0.00179712	0.0	0.0043	5008	,	,		13030	0.0		0.006	False		,,,				2504	0.0				p.E324X		Atlas-SNP	.											.	RGS11	29	.	0			c.G970T						PASS	.	C	stop/GLU,stop/GLU	6,4284		0,6,2139	13.0	18.0	16.0		907,970	4.8	0.9	16	dbSNP_129	16	79,8361		0,79,4141	yes	stop-gained,stop-gained	RGS11	NM_003834.1,NM_183337.1	,	0,85,6280	AA,AC,CC		0.936,0.1399,0.6677	,	303/447,324/468	320992	85,12645	2145	4220	6365	SO:0001587	stop_gained	8786	exon13			TGAACTCCTTTCC	AF035153	CCDS10403.1, CCDS42088.1, CCDS66884.1	16p13.3	2008-07-28	2007-08-14		ENSG00000076344	ENSG00000076344		"""Regulators of G-protein signaling"""	9993	protein-coding gene	gene with protein product		603895	"""regulator of G-protein signalling 11"""			9789084	Standard	NM_001286486		Approved		uc002cgj.1	O94810	OTTHUMG00000064893	ENST00000397770.3:c.970G>T	16.37:g.320992C>A	ENSP00000380876:p.Glu324*	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	24	0.342857	NM_183337	O75883|Q4TT71|Q4TT72	Nonsense_Mutation	SNP	ENST00000397770.3	37	CCDS42088.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	25.0	4.592050	0.86953	0.001399	0.00936	ENSG00000076344	ENST00000397770;ENST00000316163;ENST00000359740	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-18.0187	15.0006	0.71469	0.0:1.0:0.0:0.0	rs61759901	.	.	.	X	324;303;313	.	ENSP00000319069:E303X	E	-	1	0	RGS11	260993	1.000000	0.71417	0.942000	0.38095	0.913000	0.54294	7.206000	0.77891	2.201000	0.70794	0.448000	0.29417	GAG	C|0.996;A|0.004	0.004	strong		0.672	RGS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139325.2		
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2929674	2929674	+	Silent	SNP	T	T	C	rs12941934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2929674T>C	ENST00000254695.8	+	21	1986	c.1896T>C	c.(1894-1896)cgT>cgC	p.R632R	RAP1GAP2_ENST00000542807.1_Silent_p.R632R|RAP1GAP2_ENST00000366401.4_Silent_p.R617R|RAP1GAP2_ENST00000540393.2_Silent_p.R613R	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	632	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.R632R(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						AAAACGGCCGTGCCATCTCCC	0.672													C|||	2914	0.581869	0.4312	0.6744	5008	,	,		16616	0.6429		0.5606	False		,,,				2504	0.6789				p.R632R		Atlas-SNP	.											RAP1GAP2_ENST00000254695,NS,lymphoid_neoplasm,0,2	RAP1GAP2	90	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1896C						scavenged	.	C	,	1939,2059		530,879,590	15.0	18.0	17.0		1851,1896	-9.8	0.3	17	dbSNP_121	17	4907,3181		1615,1677,752	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	2145,2556,1342	CC,CT,TT		39.3299,48.4992,43.3559	,	617/716,632/731	2929674	6846,5240	1999	4044	6043	SO:0001819	synonymous_variant	23108	exon21			CGGCCGTGCCATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1896T>C	17.37:g.2929674T>C		Somatic	150	2	0.0133333		WXS	Illumina HiSeq	Phase_I	168	80	0.47619	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			T|0.421;C|0.579	0.579	strong		0.672	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
RNF152	220441	hgsc.bcm.edu	37	18	59483202	59483202	+	Silent	SNP	G	G	C	rs4538107	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:59483202G>C	ENST00000312828.3	-	2	1594	c.495C>G	c.(493-495)acC>acG	p.T165T		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	165					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				CCCCCGACCAGGTGGAGCTTT	0.602													G|||	112	0.0223642	0.0106	0.0187	5008	,	,		18489	0.0		0.0746	False		,,,				2504	0.0102				p.T165T		Atlas-SNP	.											.	RNF152	37	.	0			c.C495G						PASS	.	G		113,4293	85.8+/-124.5	0,113,2090	119.0	108.0	111.0		495	-2.5	1.0	18	dbSNP_111	111	539,8061	148.6+/-203.8	19,501,3780	no	coding-synonymous	RNF152	NM_173557.2		19,614,5870	CC,CG,GG		6.2674,2.5647,5.0131		165/204	59483202	652,12354	2203	4300	6503	SO:0001819	synonymous_variant	220441	exon2			CGACCAGGTGGAG	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"""RING-type (C3HC4) zinc fingers"""	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.495C>G	18.37:g.59483202G>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	140	64	0.457143	NM_173557	B3KV99|Q52LA4	Silent	SNP	ENST00000312828.3	37	CCDS11978.1																																																																																			G|0.959;C|0.041	0.041	strong		0.602	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557	
XCR1	2829	hgsc.bcm.edu	37	3	46063329	46063329	+	Silent	SNP	T	T	C	rs2230322	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46063329T>C	ENST00000309285.3	-	2	467	c.111A>G	c.(109-111)ctA>ctG	p.L37L	XCR1_ENST00000542109.1_Silent_p.L37L	NM_001024644.1	NP_001019815.1	P46094	XCR1_HUMAN	chemokine (C motif) receptor 1	37					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol (GO:0051209)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			NS(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(2)	14				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CCAGGCAGTATAGGACAGTGG	0.557													C|||	1166	0.232827	0.4425	0.0908	5008	,	,		17479	0.0466		0.1243	False		,,,				2504	0.3538				p.L37L		Atlas-SNP	.											.	XCR1	51	.	0			c.A111G						PASS	.	C	,	1744,2662	648.0+/-398.6	342,1060,801	113.0	107.0	109.0		111,111	-2.5	0.8	3	dbSNP_98	109	971,7629	774.7+/-407.7	46,879,3375	no	coding-synonymous,coding-synonymous	XCR1	NM_001024644.1,NM_005283.2	,	388,1939,4176	CC,CT,TT		11.2907,39.5824,20.875	,	37/334,37/334	46063329	2715,10291	2203	4300	6503	SO:0001819	synonymous_variant	2829	exon2			GCAGTATAGGACA		CCDS2736.1	3p21.3-p21.1	2012-11-19	2006-01-13	2002-08-23	ENSG00000173578	ENSG00000173578		"""GPCR / Class A : Chemokine receptors : X-C motif"""	1625	protein-coding gene	gene with protein product		600552	"""chemokine (C motif) XC receptor 1"""	GPR5, CCXCR1		7832990, 10400311	Standard	NM_005283		Approved		uc003cpf.3	P46094	OTTHUMG00000133449	ENST00000309285.3:c.111A>G	3.37:g.46063329T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_001024644		Silent	SNP	ENST00000309285.3	37	CCDS2736.1																																																																																			T|0.794;C|0.206	0.206	strong		0.557	XCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257322.2		
ZBTB21	49854	hgsc.bcm.edu	37	21	43413651	43413651	+	Missense_Mutation	SNP	T	T	C	rs871545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43413651T>C	ENST00000310826.5	-	3	737	c.554A>G	c.(553-555)aAt>aGt	p.N185S	ZBTB21_ENST00000398505.3_Missense_Mutation_p.N185S|ZBTB21_ENST00000398511.3_Missense_Mutation_p.N185S|ZBTB21_ENST00000465968.1_Intron|ZBTB21_ENST00000398499.1_Missense_Mutation_p.N185S	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	185			N -> S (in dbSNP:rs871545).		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										CTTATTGGTATTGGCCTTGAC	0.418													T|||	498	0.0994409	0.0378	0.0764	5008	,	,		20866	0.0655		0.1938	False		,,,				2504	0.137				p.N185S		Atlas-SNP	.											ZNF295,NS,carcinoma,+1,1	.	.	1	0			c.A554G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	271,4135	154.0+/-187.5	7,257,1939	187.0	174.0	179.0		554,554,554	-3.0	0.0	21	dbSNP_86	179	1625,6975	301.0+/-305.2	152,1321,2827	yes	missense,missense,missense	ZNF295	NM_001098402.1,NM_001098403.1,NM_020727.4	46,46,46	159,1578,4766	CC,CT,TT		18.8953,6.1507,14.5779	benign,benign,benign	185/1067,185/866,185/1067	43413651	1896,11110	2203	4300	6503	SO:0001583	missense	49854	exon3			TTGGTATTGGCCT	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.554A>G	21.37:g.43413651T>C	ENSP00000308759:p.Asn185Ser	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	347	118	0.340058	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Missense_Mutation	SNP	ENST00000310826.5	37	CCDS13678.1	237	0.10851648351648352	15	0.03048780487804878	27	0.07458563535911603	35	0.06118881118881119	160	0.21108179419525067	T	3.401	-0.122323	0.06795	0.061507	0.188953	ENSG00000173276	ENST00000398505;ENST00000310826;ENST00000398499;ENST00000398511	T;T;T;T	0.06768	3.52;3.26;3.26;3.26	5.81	-2.96	0.05547	.	0.698049	0.13293	N	0.398833	T	0.00012	0.0000	N	0.01800	-0.715	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.43196	-0.9406	9	0.02654	T	1	-3.3374	8.3118	0.32075	0.0:0.4223:0.1033:0.4744	rs871545;rs52802180;rs871545	185;185	Q9ULJ3-2;Q9ULJ3	.;ZN295_HUMAN	S	185	ENSP00000381517:N185S;ENSP00000308759:N185S;ENSP00000381512:N185S;ENSP00000381523:N185S	ENSP00000308759:N185S	N	-	2	0	ZNF295	42286720	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.417000	0.07088	-0.353000	0.08224	-0.256000	0.11100	AAT	T|0.878;C|0.122	0.122	strong		0.418	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
PAG1	55824	hgsc.bcm.edu	37	8	81905397	81905397	+	Silent	SNP	A	A	G	rs2016465	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:81905397A>G	ENST00000220597.4	-	4	776	c.66T>C	c.(64-66)gcT>gcC	p.A22A		NM_018440.3	NP_060910.3	Q9NWQ8	PHAG1_HUMAN	phosphoprotein membrane anchor with glycosphingolipid microdomains 1	22					epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)|positive regulation of signal transduction (GO:0009967)|regulation of T cell activation (GO:0050863)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	SH2 domain binding (GO:0042169)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(2)	11	Lung NSC(7;5.76e-06)|all_lung(9;2e-05)		BRCA - Breast invasive adenocarcinoma(6;0.0567)|Epithelial(68;0.0634)|all cancers(69;0.197)			TGGCGACAGCAGCCAGACTTC	0.567													G|||	2624	0.523962	0.8487	0.3156	5008	,	,		18022	0.5268		0.326	False		,,,				2504	0.4335				p.A22A		Atlas-SNP	.											.	PAG1	39	.	0			c.T66C						PASS	.	G		3250,1156	410.4+/-335.4	1214,822,167	81.0	75.0	77.0		66	-10.7	0.0	8	dbSNP_92	77	2778,5822	678.6+/-403.5	439,1900,1961	no	coding-synonymous	PAG1	NM_018440.3		1653,2722,2128	GG,GA,AA		32.3023,26.2369,46.3478		22/433	81905397	6028,6978	2203	4300	6503	SO:0001819	synonymous_variant	55824	exon4			GACAGCAGCCAGA	AF240634	CCDS6227.1	8q21.13	2014-04-30	2014-04-30						30043	protein-coding gene	gene with protein product	"""Csk-binding protein"", ""transmembrane adaptor protein PAG"""	605767	"""phosphoprotein associated with glycosphingolipid microdomains 1"""			10790433	Standard	XM_006716461		Approved	PAG, CBP	uc003ybz.3	Q9NWQ8		ENST00000220597.4:c.66T>C	8.37:g.81905397A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_018440	A8K1A3|Q2M1Z9|Q5BKU4|Q9NYK0	Silent	SNP	ENST00000220597.4	37	CCDS6227.1																																																																																			A|0.513;G|0.487	0.487	strong		0.567	PAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379352.3	NM_018440	
KCNA1	3736	hgsc.bcm.edu	37	12	5021228	5021228	+	Silent	SNP	T	T	C	rs1048500	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:5021228T>C	ENST00000382545.3	+	2	1791	c.684T>C	c.(682-684)tgT>tgC	p.C228C	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	228					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	AAACGCTGTGTATCATCTGGT	0.512													T|||	2449	0.489018	0.4183	0.5072	5008	,	,		20287	0.631		0.498	False		,,,				2504	0.4162				p.C228C		Atlas-SNP	.											KCNA1,colon,carcinoma,0,1	KCNA1	112	1	0			c.T684C						PASS	.	T		1794,2612	528.7+/-372.5	342,1110,751	114.0	87.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	684	-0.1	1.0	12	dbSNP_86	96	4306,4294	577.7+/-390.6	1078,2150,1072	no	coding-synonymous	KCNA1	NM_000217.2		1420,3260,1823	CC,CT,TT		49.9302,40.7172,46.9014		228/496	5021228	6100,6906	2203	4300	6503	SO:0001819	synonymous_variant	3736	exon2			GCTGTGTATCATC	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.684T>C	12.37:g.5021228T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_000217	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	37	CCDS8535.1																																																																																			T|0.498;C|0.502	0.502	strong		0.512	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
RLF	6018	hgsc.bcm.edu	37	1	40705726	40705726	+	Missense_Mutation	SNP	A	A	T	rs10889205	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:40705726A>T	ENST00000372771.4	+	8	5379	c.5352A>T	c.(5350-5352)gaA>gaT	p.E1784D		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1784			E -> D (in dbSNP:rs10889205).		chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|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(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			AAGAGAAAGAAGATGATTTTG	0.358													A|||	743	0.148363	0.2542	0.1671	5008	,	,		20224	0.0625		0.1819	False		,,,				2504	0.046				p.E1784D		Atlas-SNP	.											RLF,NS,carcinoma,0,1	RLF	152	1	0			c.A5352T						PASS	.	A	ASP/GLU	1001,3405	364.6+/-317.1	110,781,1312	57.0	59.0	59.0		5352	-11.7	0.1	1	dbSNP_120	59	1718,6882	307.4+/-308.4	150,1418,2732	yes	missense	RLF	NM_012421.3	45	260,2199,4044	TT,TA,AA		19.9767,22.719,20.9057	benign	1784/1915	40705726	2719,10287	2203	4300	6503	SO:0001583	missense	6018	exon8			GAAAGAAGATGAT		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.5352A>T	1.37:g.40705726A>T	ENSP00000361857:p.Glu1784Asp	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	337	0.1543040293040293	106	0.21544715447154472	47	0.1298342541436464	40	0.06993006993006994	144	0.18997361477572558	A	0.133	-1.111075	0.01813	0.22719	0.199767	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.13420	2.59	5.87	-11.7	0.00046	.	0.534594	0.21335	N	0.076226	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.799999999996249E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.25779	-1.0122	9	0.12103	T	0.63	-0.2135	9.5397	0.39244	0.0786:0.1215:0.1152:0.6846	rs10889205;rs52823391;rs10889205	1477;1784	F5H2M5;Q13129	.;RLF_HUMAN	D	1784;1477	ENSP00000361857:E1784D	ENSP00000361857:E1784D	E	+	3	2	RLF	40478313	0.000000	0.05858	0.059000	0.19551	0.979000	0.70002	-3.576000	0.00425	-3.937000	0.00089	-0.301000	0.09380	GAA	A|0.804;T|0.196	0.196	strong		0.358	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421	
AACS	65985	hgsc.bcm.edu	37	12	125561151	125561151	+	Missense_Mutation	SNP	A	A	G	rs11549081	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:125561151A>G	ENST00000316519.6	+	3	558	c.352A>G	c.(352-354)Att>Gtt	p.I118V	AACS_ENST00000261686.6_Missense_Mutation_p.I118V	NM_023928.3	NP_076417.2	Q86V21	AACS_HUMAN	acetoacetyl-CoA synthetase	118			I -> V (in dbSNP:rs12831803). {ECO:0000269|PubMed:15489334}.		adipose tissue development (GO:0060612)|cellular response to cholesterol (GO:0071397)|cellular response to glucose stimulus (GO:0071333)|cellular response to testosterone stimulus (GO:0071394)|fatty acid metabolic process (GO:0006631)|liver development (GO:0001889)|positive regulation of insulin secretion (GO:0032024)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to oleic acid (GO:0034201)|response to purine-containing compound (GO:0014074)|response to starvation (GO:0042594)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)	acetoacetate-CoA ligase activity (GO:0030729)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(4)|liver(1)|lung(16)|ovary(1)|stomach(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;9.82e-05)|Epithelial(86;0.000642)|all cancers(50;0.00843)		TGCCCTTTACATTGCAAGTAA	0.493													G|||	1105	0.220647	0.3548	0.1888	5008	,	,		20430	0.1171		0.1441	False		,,,				2504	0.2474				p.I118V		Atlas-SNP	.											.	AACS	59	.	0			c.A352G						PASS	.	A	VAL/ILE	1292,3114	439.6+/-345.7	198,896,1109	111.0	107.0	109.0		352	3.4	0.0	12	dbSNP_121	109	1229,7371	245.7+/-274.4	102,1025,3173	yes	missense	AACS	NM_023928.3	29	300,1921,4282	GG,GA,AA		14.2907,29.3236,19.3834	benign	118/673	125561151	2521,10485	2203	4300	6503	SO:0001583	missense	65985	exon3			CTTTACATTGCAA	AK022451	CCDS9263.1	12q24.31	2010-09-29			ENSG00000081760	ENSG00000081760	6.2.1.16	"""Acyl-CoA synthetase family"""	21298	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 1"""	614364				12623130, 17762044	Standard	NM_023928		Approved	FLJ12389, SUR-5, ACSF1	uc001uhc.3	Q86V21	OTTHUMG00000168550	ENST00000316519.6:c.352A>G	12.37:g.125561151A>G	ENSP00000324842:p.Ile118Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_023928	Q49AB9|Q49AC3|Q658Q8|Q8IWD2|Q8NEW5|Q9BSJ9|Q9H829|Q9HA19	Missense_Mutation	SNP	ENST00000316519.6	37	CCDS9263.1	406	0.1858974358974359	167	0.3394308943089431	65	0.17955801104972377	78	0.13636363636363635	96	0.1266490765171504	a	0.149	-1.093357	0.01858	0.293236	0.142907	ENSG00000081760	ENST00000316519;ENST00000536752;ENST00000261686	T;T;T	0.10192	2.9;2.91;2.9	5.27	3.44	0.39384	.	0.251297	0.38548	N	0.001649	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47328	-0.9126	9	0.10636	T	0.68	.	6.2699	0.20949	0.1585:0.0:0.6938:0.1477	rs12831803;rs17854015;rs61595606;rs12831803	118;118	Q86V21-2;Q86V21	.;AACS_HUMAN	V	118	ENSP00000324842:I118V;ENSP00000442691:I118V;ENSP00000261686:I118V	ENSP00000261686:I118V	I	+	1	0	AACS	124127104	1.000000	0.71417	0.003000	0.11579	0.009000	0.06853	5.025000	0.64097	0.720000	0.32209	-0.221000	0.12465	ATT	A|0.803;G|0.197	0.197	strong		0.493	AACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400202.1	NM_023928	
CCL3	6348	hgsc.bcm.edu	37	17	34416537	34416537	+	Silent	SNP	G	G	A	rs1130371	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:34416537G>A	ENST00000225245.5	-	2	262	c.180C>T	c.(178-180)ccC>ccT	p.P60P	AC069363.1_ENST00000441575.1_RNA|AC069363.1_ENST00000590992.1_RNA|AC069363.1_ENST00000592728.1_RNA	NM_002983.2	NP_002974.1	P10147	CCL3_HUMAN	chemokine (C-C motif) ligand 3	60					astrocyte cell migration (GO:0043615)|behavior (GO:0007610)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|cellular response to interferon-gamma (GO:0071346)|cellular response to interleukin-1 (GO:0071347)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|eosinophil degranulation (GO:0043308)|exocytosis (GO:0006887)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|monocyte chemotaxis (GO:0002548)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of bone mineralization (GO:0030502)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoclast differentiation (GO:0045671)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive chemotaxis (GO:0050918)|positive regulation of calcium ion import (GO:0090280)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell migration (GO:0030335)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of tumor necrosis factor production (GO:0032760)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|response to toxic substance (GO:0009636)|signaling (GO:0023052)|T cell chemotaxis (GO:0010818)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular (GO:0005622)	calcium-dependent protein kinase C activity (GO:0004698)|CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemoattractant activity (GO:0042056)|chemokine activity (GO:0008009)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|protein kinase activity (GO:0004672)			breast(2)|lung(3)|urinary_tract(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ACATGACACCGGGCTTGGAGC	0.582													G|||	1107	0.221046	0.1331	0.1182	5008	,	,		18931	0.3532		0.2505	False		,,,				2504	0.2464				p.P60P		Atlas-SNP	.											.	CCL3	8	.	0			c.C180T						PASS	.	G		611,3795		40,531,1632	155.0	150.0	152.0		180	-10.8	1.0	17	dbSNP_86	152	2001,6599		243,1515,2542	no	coding-synonymous	CCL3	NM_002983.2		283,2046,4174	AA,AG,GG		23.2674,13.8675,20.083		60/93	34416537	2612,10394	2203	4300	6503	SO:0001819	synonymous_variant	6348	exon2			GACACCGGGCTTG	M23178	CCDS11307.1	17q12	2014-05-06	2002-08-22	2002-08-23	ENSG00000006075	ENSG00000277632		"""Chemokine ligands"", ""Endogenous ligands"""	10627	protein-coding gene	gene with protein product		182283	"""small inducible cytokine A3 (homologous to mouse Mip-1a)"""	SCYA3			Standard	NM_002983		Approved	G0S19-1, LD78ALPHA, MIP-1-alpha	uc002hkv.3	P10147	OTTHUMG00000188413	ENST00000225245.5:c.180C>T	17.37:g.34416537G>A		Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	266	262	0.984962	NM_002983		Silent	SNP	ENST00000225245.5	37	CCDS11307.1																																																																																			G|0.795;A|0.205	0.205	strong		0.582	CCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256581.1	NM_002983	
KRT14	3861	hgsc.bcm.edu	37	17	39743081	39743081	+	Silent	SNP	G	G	A	rs11551759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39743081G>A	ENST00000167586.6	-	1	92	c.6C>T	c.(4-6)acC>acT	p.T2T		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	2	Head.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				GGCTGCAGGTGGTCATGGTGC	0.627													G|||	3408	0.680511	0.4788	0.7248	5008	,	,		14228	0.9425		0.5845	False		,,,				2504	0.7505				p.T2T		Atlas-SNP	.											.	KRT14	65	.	0			c.C6T						PASS	.	G		1977,1915		557,863,526	6.0	6.0	6.0		6	4.8	1.0	17	dbSNP_120	6	4461,3347		1355,1751,798	no	coding-synonymous	KRT14	NM_000526.4		1912,2614,1324	AA,AG,GG		42.8663,49.2035,44.9744		2/473	39743081	6438,5262	1946	3904	5850	SO:0001819	synonymous_variant	3861	exon1			GCAGGTGGTCATG	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.6C>T	17.37:g.39743081G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Silent	SNP	ENST00000167586.6	37	CCDS11400.1																																																																																			G|0.355;A|0.645	0.645	strong		0.627	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
PCDHB16	57717	hgsc.bcm.edu	37	5	140563586	140563586	+	Silent	SNP	C	C	T	rs61745655	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140563586C>T	ENST00000361016.2	+	1	2607	c.1452C>T	c.(1450-1452)gcC>gcT	p.A484A		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	484	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			GCACCAACGCCCAGGTCACCT	0.657													C|||	304	0.0607029	0.1974	0.0447	5008	,	,		11640	0.0		0.0119	False		,,,				2504	0.0				p.A484A		Atlas-SNP	.											PCDHB16,NS,carcinoma,+2,1	PCDHB16	159	1	0			c.C1452T						scavenged	.	C		779,3627		78,623,1502	51.0	48.0	49.0		1452	1.4	1.0	5	dbSNP_129	49	122,8432		3,116,4158	no	coding-synonymous	PCDHB16	NM_020957.1		81,739,5660	TT,TC,CC		1.4262,17.6804,6.9522		484/777	140563586	901,12059	2203	4277	6480	SO:0001819	synonymous_variant	57717	exon1			CAACGCCCAGGTC	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.1452C>T	5.37:g.140563586C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	56	43	0.767857	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																			C|0.937;T|0.063	0.063	strong		0.657	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
SULF2	55959	hgsc.bcm.edu	37	20	46365636	46365636	+	Missense_Mutation	SNP	C	C	T	rs56218501	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:46365636C>T	ENST00000359930.4	-	3	1077	c.226G>A	c.(226-228)Gcg>Acg	p.A76T	SULF2_ENST00000361612.4_Missense_Mutation_p.A76T|SULF2_ENST00000484875.1_Missense_Mutation_p.A76T|SULF2_ENST00000478766.1_5'UTR|SULF2_ENST00000467815.1_Missense_Mutation_p.A76T	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	76			A -> T (in dbSNP:rs56218501). {ECO:0000269|PubMed:10574462}.		bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						ATGAAGTGCGCCCCGCCCTGC	0.607													C|||	389	0.0776757	0.0061	0.1354	5008	,	,		18064	0.001		0.2167	False		,,,				2504	0.0695				p.A76T		Atlas-SNP	.											SULF2,colon,carcinoma,+2,3	SULF2	131	3	0			c.G226A						scavenged	.	C	THR/ALA,THR/ALA,THR/ALA	168,4238	110.8+/-149.0	8,152,2043	206.0	164.0	178.0		226,226,226	5.4	1.0	20	dbSNP_129	178	1848,6752	331.5+/-319.7	219,1410,2671	yes	missense,missense,missense	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	58,58,58	227,1562,4714	TT,TC,CC		21.4884,3.813,15.5005	benign,benign,benign	76/871,76/871,76/868	46365636	2016,10990	2203	4300	6503	SO:0001583	missense	55959	exon3			AGTGCGCCCCGCC	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.226G>A	20.37:g.46365636C>T	ENSP00000353007:p.Ala76Thr	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	218	0.09981684981684982	2	0.0040650406504065045	60	0.16574585635359115	0	0.0	156	0.20580474934036938	C	13.86	2.362478	0.41902	0.03813	0.214884	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815;ENST00000437955	D;D;D;D;D	0.98455	-4.94;-4.94;-4.94;-4.94;-4.94	5.44	5.44	0.79542	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.103148	0.64402	D	0.000002	T	0.00754	0.0025	N	0.05534	-0.03	0.23809	P	0.99678531	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.09377	0.002;0.002;0.004	T	0.55405	-0.8146	9	0.27785	T	0.31	-14.4645	8.5077	0.33197	0.1539:0.7697:0.0:0.0764	rs56218501;rs61741658	76;76;76	G3XAE6;Q8IWU5-2;Q8IWU5	.;.;SULF2_HUMAN	T	76	ENSP00000353007:A76T;ENSP00000418290:A76T;ENSP00000354662:A76T;ENSP00000418442:A76T;ENSP00000410026:A76T	ENSP00000353007:A76T	A	-	1	0	SULF2	45799043	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	2.973000	0.49264	2.559000	0.86315	0.561000	0.74099	GCG	C|0.856;G|0.000;T|0.144	0.144	strong		0.607	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
MATN3	4148	hgsc.bcm.edu	37	2	20205680	20205680	+	Silent	SNP	C	C	T	rs28401180	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:20205680C>T	ENST00000407540.3	-	2	677	c.615G>A	c.(613-615)gaG>gaA	p.E205E	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Silent_p.E205E	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	205	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAGCCGCCACCTCATTCACCT	0.597													C|||	2626	0.524361	0.528	0.4625	5008	,	,		17859	0.619		0.4026	False		,,,				2504	0.591				p.E205E		Atlas-SNP	.											.	MATN3	28	.	0			c.G615A						PASS	.	C		1964,2134		494,976,579	21.0	25.0	23.0		615	3.5	1.0	2	dbSNP_125	23	3408,4988		716,1976,1506	no	coding-synonymous	MATN3	NM_002381.4		1210,2952,2085	TT,TC,CC		40.5908,47.9258,42.9966		205/487	20205680	5372,7122	2049	4198	6247	SO:0001819	synonymous_variant	4148	exon2			CGCCACCTCATTC	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.615G>A	2.37:g.20205680C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	101	40	0.39604	NM_002381	B2CPU0|Q4ZG02	Silent	SNP	ENST00000407540.3	37	CCDS46226.1																																																																																			C|0.513;T|0.487	0.487	strong		0.597	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
CLEC10A	10462	hgsc.bcm.edu	37	17	6981397	6981397	+	Missense_Mutation	SNP	A	A	G	rs90951	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6981397A>G	ENST00000254868.4	-	3	431	c.103T>C	c.(103-105)Tgc>Cgc	p.C35R	CLEC10A_ENST00000576617.1_Missense_Mutation_p.C35R|CLEC10A_ENST00000571664.1_Missense_Mutation_p.C35R|CLEC10A_ENST00000416562.2_Missense_Mutation_p.C35R	NM_182906.2	NP_878910.1	Q8IUN9	CLC10_HUMAN	C-type lectin domain family 10, member A	35			C -> R (in dbSNP:rs90951). {ECO:0000269|PubMed:8598452}.		endocytosis (GO:0006897)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	10						GGCCCAGAGCAGAGACGCTGC	0.627													G|||	2604	0.519968	0.9266	0.3473	5008	,	,		16452	0.4702		0.3608	False		,,,				2504	0.3078				p.C35R		Atlas-SNP	.											.	CLEC10A	40	.	0			c.T103C						PASS	.	G	ARG/CYS,ARG/CYS	3608,798	320.4+/-296.6	1492,624,87	102.0	106.0	104.0		103,103	-0.4	0.0	17	dbSNP_80	104	3053,5547	661.7+/-401.9	556,1941,1803	yes	missense,missense	CLEC10A	NM_006344.2,NM_182906.2	180,180	2048,2565,1890	GG,GA,AA		35.5,18.1117,48.7852	benign,benign	35/293,35/317	6981397	6661,6345	2203	4300	6503	SO:0001583	missense	10462	exon3			CAGAGCAGAGACG	D50532	CCDS11087.1, CCDS45597.1	17p13.2	2014-05-20	2005-02-09	2005-02-11		ENSG00000132514		"""C-type lectin domain containing"", ""CD molecules"""	16916	protein-coding gene	gene with protein product	"""macrophage lectin 2 (calcium dependent)"""	605999	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 14 (macrophage-derived)"""	CLECSF13, CLECSF14		8598452	Standard	XM_005256411		Approved	HML2, HML, CD301	uc002gej.3	Q8IUN9		ENST00000254868.4:c.103T>C	17.37:g.6981397A>G	ENSP00000254868:p.Cys35Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_182906	A8K8J8|Q14538|Q6PIW3	Missense_Mutation	SNP	ENST00000254868.4	37	CCDS11087.1	1115	0.5105311355311355	443	0.9004065040650406	119	0.3287292817679558	283	0.49475524475524474	270	0.3562005277044855	G	7.930	0.740365	0.15642	0.818883	0.355	ENSG00000132514	ENST00000254868;ENST00000416562	T;T	0.20738	2.05;2.05	4.43	-0.382	0.12481	Hepatic lectin, N-terminal (1);	0.629715	0.15066	N	0.282488	T	0.00012	0.0000	L	0.31371	0.925	0.80722	P	0.0	B;B;B	0.10296	0.003;0.0;0.003	B;B;B	0.21708	0.002;0.001;0.036	T	0.08432	-1.0722	9	0.37606	T	0.19	.	8.7412	0.34558	0.547:0.0:0.453:0.0	rs90951;rs747025;rs1048153;rs3765149;rs17806200;rs52801524;rs61010712;rs90951	35;35;35	Q8IUN9-3;Q8IUN9;Q8IUN9-2	.;CLC10_HUMAN;.	R	35	ENSP00000254868:C35R;ENSP00000414938:C35R	ENSP00000254868:C35R	C	-	1	0	CLEC10A	6922121	0.081000	0.21417	0.000000	0.03702	0.013000	0.08279	0.674000	0.25218	-0.472000	0.06881	-1.140000	0.01884	TGC	A|0.467;G|0.532	0.532	strong		0.627	CLEC10A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439837.2	NM_006344	
AKAP11	11215	hgsc.bcm.edu	37	13	42872866	42872866	+	Missense_Mutation	SNP	A	A	G	rs75739749	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:42872866A>G	ENST00000025301.2	+	7	724	c.549A>G	c.(547-549)atA>atG	p.I183M		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	183					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		TGTCATCCATAGAGGATGACT	0.393																																					p.I183M		Atlas-SNP	.											.	AKAP11	146	.	0			c.A549G						PASS	.	A	MET/ILE	3,4403	6.2+/-15.9	0,3,2200	150.0	126.0	134.0		549	-6.2	1.0	13	dbSNP_131	134	8,8590	6.4+/-24.3	0,8,4291	yes	missense	AKAP11	NM_016248.3	10	0,11,6491	GG,GA,AA		0.093,0.0681,0.0846	probably-damaging	183/1902	42872866	11,12993	2203	4299	6502	SO:0001583	missense	11215	exon7			ATCCATAGAGGAT	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.549A>G	13.37:g.42872866A>G	ENSP00000025301:p.Ile183Met	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	201	134	0.666667	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	22.4	4.285277	0.80803	6.81E-4	9.3E-4	ENSG00000023516	ENST00000025301	T	0.31510	1.49	6.07	-6.17	0.02091	.	0.000000	0.85682	D	0.000000	T	0.44244	0.1284	M	0.72118	2.19	0.44908	D	0.997923	D	0.89917	1.0	D	0.91635	0.999	T	0.55289	-0.8164	10	0.87932	D	0	.	9.6397	0.39831	0.1485:0.1745:0.0:0.677	.	183	Q9UKA4	AKA11_HUMAN	M	183	ENSP00000025301:I183M	ENSP00000025301:I183M	I	+	3	3	AKAP11	41770866	0.987000	0.35691	0.991000	0.47740	0.984000	0.73092	0.261000	0.18442	-0.474000	0.06862	0.533000	0.62120	ATA	A|1.000;G|0.000	0.000	strong		0.393	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
FSCB	84075	hgsc.bcm.edu	37	14	44975511	44975511	+	Missense_Mutation	SNP	G	G	A	rs372153461|rs45478391	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:44975511G>A	ENST00000340446.4	-	1	971	c.680C>T	c.(679-681)cCg>cTg	p.P227L	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	227						sperm fibrous sheath (GO:0035686)|sperm principal piece (GO:0097228)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(47)|ovary(2)|pancreas(1)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	89				GBM - Glioblastoma multiforme(112;0.128)		TAAAAGTACCGGGGGACCTTT	0.408													G|||	541	0.108027	0.0053	0.1009	5008	,	,		18318	0.0833		0.2296	False		,,,				2504	0.1524				p.P227L		Atlas-SNP	.											.	FSCB	173	.	0			c.C680T						PASS	.	G	LEU/PRO	169,4237	111.2+/-149.4	2,165,2036	97.0	99.0	98.0		680	-6.0	0.0	14	dbSNP_127	98	1818,6782	326.4+/-317.4	186,1446,2668	yes	missense	FSCB	NM_032135.3	98	188,1611,4704	AA,AG,GG		21.1395,3.8357,15.2776	benign	227/826	44975511	1987,11019	2203	4300	6503	SO:0001583	missense	84075	exon1			AGTACCGGGGGAC	AK124110	CCDS9679.1	14q21.3	2007-11-22	2007-11-22	2007-11-22	ENSG00000189139	ENSG00000189139			20494	protein-coding gene	gene with protein product		611779	"""chromosome 14 open reading frame 155"""	C14orf155		17855365	Standard	NM_032135		Approved	DKFZP434F1017	uc001wvn.3	Q5H9T9	OTTHUMG00000140262	ENST00000340446.4:c.680C>T	14.37:g.44975511G>A	ENSP00000344579:p.Pro227Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	287	0.13141025641025642	4	0.008130081300813009	49	0.13535911602209943	49	0.08566433566433566	185	0.24406332453825857	G	5.123	0.208391	0.09757	0.038357	0.211395	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.23754	1.89	4.24	-5.98	0.02220	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.23891	0.093	B	0.16722	0.016	T	0.39121	-0.9629	8	0.30078	T	0.28	7.679	2.1036	0.03686	0.4745:0.1129:0.2656:0.147	rs45478391;rs61739486	227	Q5H9T9	FSCB_HUMAN	L	227	ENSP00000344579:P227L	ENSP00000344579:P227L	P	-	2	0	FSCB	44045261	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.326000	0.07965	-1.143000	0.02866	-0.140000	0.14226	CCG	G|0.852;A|0.148	0.148	strong		0.408	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
SPTBN5	51332	hgsc.bcm.edu	37	15	42168400	42168400	+	Missense_Mutation	SNP	C	C	T	rs2290559	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42168400C>T	ENST00000320955.6	-	21	4261	c.4034G>A	c.(4033-4035)cGc>cAc	p.R1345H		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1345			R -> H (in dbSNP:rs2290559).		actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		GATGTTTCTGCGCGCTCCGGA	0.632													C|||	786	0.156949	0.0461	0.1888	5008	,	,		18058	0.0476		0.3121	False		,,,				2504	0.2372				p.R1310H		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G3929A						PASS	.	C	HIS/ARG	379,3911		21,337,1787	46.0	51.0	50.0		3929	3.0	0.0	15	dbSNP_100	50	2645,5891		408,1829,2031	yes	missense	SPTBN5	NM_016642.2	29	429,2166,3818	TT,TC,CC		30.9864,8.8345,23.5771	benign	1310/3640	42168400	3024,9802	2145	4268	6413	SO:0001583	missense	51332	exon21			TTTCTGCGCGCTC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.4034G>A	15.37:g.42168400C>T	ENSP00000317790:p.Arg1345His	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		340	0.15567765567765568	27	0.054878048780487805	69	0.19060773480662985	20	0.03496503496503497	224	0.2955145118733509	.	17.09	3.300924	0.60195	0.088345	0.309864	ENSG00000137877	ENST00000320955	T	0.49720	0.77	4.94	3.0	0.34707	.	0.710907	0.12920	N	0.428223	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.51791	0.948	P	0.45794	0.493	T	0.33599	-0.9862	9	0.72032	D	0.01	.	14.2271	0.65868	0.0:0.3011:0.6989:0.0	rs2290559;rs17686159;rs60823875;rs2290559	1345	Q9NRC6	SPTN5_HUMAN	H	1345	ENSP00000317790:R1345H	ENSP00000317790:R1345H	R	-	2	0	SPTBN5	39955692	0.979000	0.34478	0.000000	0.03702	0.000000	0.00434	4.573000	0.60893	0.562000	0.29204	-0.147000	0.13772	CGC	C|0.835;T|0.165	0.165	strong		0.632	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
ANPEP	290	hgsc.bcm.edu	37	15	90335788	90335788	+	Missense_Mutation	SNP	C	C	T	rs25651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90335788C>T	ENST00000300060.6	-	17	2568	c.2255G>A	c.(2254-2256)aGc>aAc	p.S752N		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	752	Metalloprotease.		S -> N (in dbSNP:rs25651).		angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	ATTAACCTCGCTGTACCTGCC	0.577													T|||	1756	0.350639	0.5144	0.2622	5008	,	,		17122	0.2331		0.2962	False		,,,				2504	0.3691				p.S752N	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.G2255A						PASS	.	T	ASN/SER	2142,2258	595.9+/-388.5	542,1058,600	104.0	85.0	91.0		2255	-4.4	0.0	15	dbSNP_72	91	2737,5861	679.9+/-403.6	405,1927,1967	yes	missense	ANPEP	NM_001150.2	46	947,2985,2567	TT,TC,CC		31.833,48.6818,37.5365	benign	752/968	90335788	4879,8119	2200	4299	6499	SO:0001583	missense	290	exon17			ACCTCGCTGTACC	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2255G>A	15.37:g.90335788C>T	ENSP00000300060:p.Ser752Asn	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Missense_Mutation	SNP	ENST00000300060.6	37	CCDS10356.1	689	0.31547619047619047	231	0.4695121951219512	94	0.2596685082872928	144	0.2517482517482518	220	0.29023746701846964	T	0.008	-1.901246	0.00517	0.486818	0.31833	ENSG00000166825	ENST00000300060	T	0.05513	3.43	4.58	-4.38	0.03622	.	0.497865	0.21743	N	0.069790	T	0.00012	0.0000	N	0.01405	-0.89	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45411	-0.9263	9	0.22706	T	0.39	.	14.2567	0.66058	0.0:0.6451:0.0:0.3549	rs25651;rs1126609;rs3181738;rs8179194;rs16943596;rs17402988;rs52810845;rs25651	752	P15144	AMPN_HUMAN	N	752	ENSP00000300060:S752N	ENSP00000300060:S752N	S	-	2	0	ANPEP	88136792	0.002000	0.14202	0.006000	0.13384	0.005000	0.04900	-0.012000	0.12699	-1.792000	0.01259	-1.271000	0.01417	AGC	C|0.642;T|0.358	0.358	strong		0.577	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
TRIOBP	11078	hgsc.bcm.edu	37	22	38164106	38164106	+	Silent	SNP	C	C	T	rs4821708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:38164106C>T	ENST00000406386.3	+	19	6753	c.6498C>T	c.(6496-6498)taC>taT	p.Y2166Y	TRIOBP_ENST00000403663.2_Silent_p.Y453Y	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	2166					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					AGAAGGCCTACCAGGAAGAGC	0.612													C|||	1326	0.264776	0.0408	0.2997	5008	,	,		18755	0.2927		0.336	False		,,,				2504	0.4407				p.Y2166Y		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,1	TRIOBP	262	1	0			c.C6498T						PASS	.	C	,	303,3729		11,281,1724	33.0	37.0	35.0		6498,1359	1.0	1.0	22	dbSNP_111	35	2561,5783		367,1827,1978	no	coding-synonymous,coding-synonymous	TRIOBP	NM_001039141.2,NM_007032.5	,	378,2108,3702	TT,TC,CC		30.6927,7.5149,23.1416	,	2166/2366,453/653	38164106	2864,9512	2016	4172	6188	SO:0001819	synonymous_variant	11078	exon19			GGCCTACCAGGAA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.6498C>T	22.37:g.38164106C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.739;T|0.261	0.261	strong		0.612	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
TIAM1	7074	hgsc.bcm.edu	37	21	32493031	32493031	+	Silent	SNP	A	A	G	rs762194	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:32493031A>G	ENST00000286827.3	-	29	4902	c.4431T>C	c.(4429-4431)ggT>ggC	p.G1477G	TIAM1_ENST00000541036.1_Silent_p.G1417G	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1477					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CAGTGTCCCCACCACCGGGGG	0.567													A|||	2681	0.535343	0.531	0.598	5008	,	,		16126	0.7639		0.4712	False		,,,				2504	0.3272				p.G1477G		Atlas-SNP	.											.	TIAM1	522	.	0			c.T4431C						PASS	.	A		2288,2118	599.7+/-389.3	593,1102,508	64.0	63.0	64.0		4431	2.1	1.0	21	dbSNP_86	64	3950,4650	549.3+/-385.5	877,2196,1227	no	coding-synonymous	TIAM1	NM_003253.2		1470,3298,1735	GG,GA,AA		45.9302,48.0708,47.9625		1477/1592	32493031	6238,6768	2203	4300	6503	SO:0001819	synonymous_variant	7074	exon29			GTCCCCACCACCG		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.4431T>C	21.37:g.32493031A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	56	32	0.571429	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																			A|0.482;G|0.518	0.518	strong		0.567	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
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 GAIIx	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		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	78	29	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	
TGFBI	7045	hgsc.bcm.edu	37	5	135391374	135391374	+	Silent	SNP	C	C	T	rs1133170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:135391374C>T	ENST00000442011.2	+	11	1577	c.1416C>T	c.(1414-1416)ctC>ctT	p.L472L	TGFBI_ENST00000305126.8_Silent_p.L472L	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	472	FAS1 3. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TGCAGAGCCTCTGCATTGAGA	0.562													G|||	1403	0.280152	0.3011	0.2133	5008	,	,		17398	0.247		0.2565	False		,,,				2504	0.3579				p.L472L		Atlas-SNP	.											TGFBI,NS,carcinoma,+2,1	TGFBI	76	1	0			c.C1416T						PASS	.	G		1182,2662		173,836,913	40.0	40.0	40.0		1416	3.4	1.0	5	dbSNP_86	40	2201,6035		306,1589,2223	no	coding-synonymous	TGFBI	NM_000358.2		479,2425,3136	TT,TC,CC		26.7241,30.7492,28.005		472/684	135391374	3383,8697	1922	4118	6040	SO:0001819	synonymous_variant	7045	exon11			GAGCCTCTGCATT	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.1416C>T	5.37:g.135391374C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1																																																																																			C|0.738;T|0.262	0.262	strong		0.562	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
EIF4A3	9775	hgsc.bcm.edu	37	17	78113832	78113832	+	Silent	SNP	G	G	A	rs2241886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78113832G>A	ENST00000269349.3	-	5	701	c.480C>T	c.(478-480)gtC>gtT	p.V160V		NM_014740.3	NP_055555.1	P38919	IF4A3_HUMAN	eukaryotic translation initiation factor 4A3	160	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|cytokine-mediated signaling pathway (GO:0019221)|embryonic cranial skeleton morphogenesis (GO:0048701)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|mRNA binding (GO:0003729)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	10	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)			GAGTGCCCGCGACAACATGCT	0.498													g|||	650	0.129792	0.0272	0.2262	5008	,	,		17672	0.1022		0.174	False		,,,				2504	0.183				p.V160V		Atlas-SNP	.											EIF4A3,NS,adenoma,0,1	EIF4A3	35	1	0			c.C480T						PASS	.	G		219,4187	133.7+/-170.0	6,207,1990	86.0	72.0	76.0		480	-11.3	0.0	17	dbSNP_98	76	1727,6873	315.7+/-312.4	159,1409,2732	no	coding-synonymous	EIF4A3	NM_014740.3		165,1616,4722	AA,AG,GG		20.0814,4.9705,14.9623		160/412	78113832	1946,11060	2203	4300	6503	SO:0001819	synonymous_variant	9775	exon5			GCCCGCGACAACA	BC004386	CCDS11767.1	17q25.3	2010-02-10	2010-02-10	2006-11-27		ENSG00000141543		"""DEAD-boxes"""	18683	protein-coding gene	gene with protein product		608546	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 48"", ""eukaryotic translation initiation factor 4A, isoform 3"""	DDX48		10623621, 14730019	Standard	NM_014740		Approved	KIAA0111, EIF4AIII	uc002jxs.3	P38919		ENST00000269349.3:c.480C>T	17.37:g.78113832G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_014740	Q15033|Q6IBQ2|Q96A18	Silent	SNP	ENST00000269349.3	37	CCDS11767.1																																																																																			G|0.864;A|0.136	0.136	strong		0.498	EIF4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437446.1	NM_014740	
MISP	126353	hgsc.bcm.edu	37	19	757241	757241	+	Missense_Mutation	SNP	G	G	A	rs45477999	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:757241G>A	ENST00000215582.6	+	2	398	c.295G>A	c.(295-297)Gcc>Acc	p.A99T		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	99			A -> T (in dbSNP:rs45477999).		mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCGCCTGGGCGCCAGGGATGC	0.657													G|||	30	0.00599042	0.0008	0.013	5008	,	,		17905	0.0		0.0129	False		,,,				2504	0.0072				p.A99T		Atlas-SNP	.											C19orf21,caecum,carcinoma,0,1	C19orf21	56	1	0			c.G295A						PASS	.	G	THR/ALA	12,4394	20.2+/-43.8	0,12,2191	57.0	51.0	53.0		295	-2.3	0.0	19	dbSNP_127	53	140,8458	69.0+/-131.5	0,140,4159	yes	missense	C19orf21	NM_173481.2	58	0,152,6350	AA,AG,GG		1.6283,0.2724,1.1689	benign	99/680	757241	152,12852	2203	4299	6502	SO:0001583	missense	126353	exon2			CTGGGCGCCAGGG	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"""mitotic interactor and substrate of Plk1"""	615289	"""chromosome 19 open reading frame 21"""	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.295G>A	19.37:g.757241G>A	ENSP00000215582:p.Ala99Thr	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	32	0.363636	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	37	CCDS12042.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	0.519	-0.863201	0.02610	0.002724	0.016283	ENSG00000099812	ENST00000215582	T	0.14391	2.51	1.18	-2.35	0.06684	.	7.882870	0.00397	N	0.000047	T	0.02193	0.0068	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.22906	-1.0203	10	0.07482	T	0.82	.	2.4213	0.04448	0.2755:0.3183:0.4063:0.0	rs45477999	99	Q8IVT2	CS021_HUMAN	T	99	ENSP00000215582:A99T	ENSP00000215582:A99T	A	+	1	0	C19orf21	708241	0.008000	0.16893	0.003000	0.11579	0.048000	0.14542	0.889000	0.28282	-0.412000	0.07519	-0.657000	0.03884	GCC	G|0.989;A|0.011	0.011	strong		0.657	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
SLC44A3	126969	hgsc.bcm.edu	37	1	95294089	95294089	+	Silent	SNP	T	T	C	rs2640065	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:95294089T>C	ENST00000271227.6	+	5	558	c.456T>C	c.(454-456)taT>taC	p.Y152Y	SLC44A3_ENST00000529450.1_Silent_p.Y120Y|SLC44A3_ENST00000446120.2_Silent_p.Y116Y|SLC44A3_ENST00000527077.1_Silent_p.Y84Y|SLC44A3_ENST00000532427.1_Silent_p.Y72Y|SLC44A3_ENST00000467909.1_Silent_p.Y104Y|SLC44A3_ENST00000530397.1_3'UTR	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	152					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)		p.Y104Y(1)		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)	CCTTCAACTATACCCACAGTC	0.428													C|||	1012	0.202077	0.2466	0.1398	5008	,	,		18783	0.1012		0.2117	False		,,,				2504	0.2802				p.Y152Y		Atlas-SNP	.											SLC44A3,NS,carcinoma,0,1	SLC44A3	109	1	1	Substitution - coding silent(1)	stomach(1)	c.T456C						PASS	.	C	,	1101,3305	720.1+/-409.0	151,799,1253	162.0	151.0	155.0		456,312	-1.5	0.3	1	dbSNP_100	155	1758,6842	734.9+/-406.9	179,1400,2721	no	coding-synonymous,coding-synonymous	SLC44A3	NM_001114106.1,NM_152369.3	,	330,2199,3974	CC,CT,TT		20.4419,24.9887,21.9822	,	152/654,104/606	95294089	2859,10147	2203	4300	6503	SO:0001819	synonymous_variant	126969	exon5			CAACTATACCCAC	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.456T>C	1.37:g.95294089T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	37	CCDS44176.1																																																																																			T|0.790;C|0.210	0.210	strong		0.428	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369	
C12orf4	57102	hgsc.bcm.edu	37	12	4627414	4627414	+	Silent	SNP	C	C	T	rs35924298	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4627414C>T	ENST00000261250.3	-	8	930	c.843G>A	c.(841-843)caG>caA	p.Q281Q	C12orf4_ENST00000545746.1_Silent_p.Q281Q	NM_020374.2	NP_065107.1	Q9NQ89	CL004_HUMAN	chromosome 12 open reading frame 4	281										NS(1)|endometrium(1)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)	BRCA - Breast invasive adenocarcinoma(232;0.0281)		TGGTCTTCAACTGGGCTCCTG	0.428													C|||	238	0.047524	0.0023	0.0735	5008	,	,		16358	0.003		0.1282	False		,,,				2504	0.0532				p.Q281Q		Atlas-SNP	.											.	C12orf4	58	.	0			c.G843A						PASS	.	C		87,4319	73.6+/-111.7	0,87,2116	105.0	108.0	107.0		843	4.3	1.0	12	dbSNP_126	107	1016,7584	217.4+/-256.1	63,890,3347	no	coding-synonymous	C12orf4	NM_020374.2		63,977,5463	TT,TC,CC		11.814,1.9746,8.4807		281/553	4627414	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	57102	exon8			CTTCAACTGGGCT	AJ272205	CCDS8528.1	12p13.3	2012-08-10			ENSG00000047621	ENSG00000047621			1184	protein-coding gene	gene with protein product							Standard	NM_020374		Approved		uc001qms.3	Q9NQ89	OTTHUMG00000168258	ENST00000261250.3:c.843G>A	12.37:g.4627414C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_020374	D3DUQ8|Q6MZH5	Silent	SNP	ENST00000261250.3	37	CCDS8528.1																																																																																			C|0.922;T|0.078	0.078	strong		0.428	C12orf4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398992.1	NM_020374	
KRT6B	3854	hgsc.bcm.edu	37	12	52844243	52844243	+	Silent	SNP	A	A	G	rs28414881	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52844243A>G	ENST00000252252.3	-	2	749	c.702T>C	c.(700-702)cgT>cgC	p.R234R		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	234	Coil 1B.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		CCGAGTCCAGACGACCCCGTT	0.552													A|||	394	0.0786741	0.0061	0.0821	5008	,	,		24489	0.1875		0.0875	False		,,,				2504	0.0532				p.R234R		Atlas-SNP	.											KRT6B,NS,carcinoma,-1,1	KRT6B	90	1	0			c.T702C						scavenged	.						211.0	184.0	193.0					12																	52844243		2203	4300	6503	SO:0001819	synonymous_variant	3854	exon2			GTCCAGACGACCC	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.702T>C	12.37:g.52844243A>G		Somatic	208	7	0.0336538		WXS	Illumina HiSeq	Phase_I	226	44	0.19469	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			A|0.959;G|0.041	0.041	strong		0.552	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
FAM83F	113828	hgsc.bcm.edu	37	22	40417820	40417820	+	Missense_Mutation	SNP	A	A	G	rs5995794	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:40417820A>G	ENST00000333407.6	+	4	1400	c.1306A>G	c.(1306-1308)Agg>Ggg	p.R436G	FAM83F_ENST00000473717.1_Missense_Mutation_p.R268G	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	436			R -> G (in dbSNP:rs5995794).							breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						CGCCCCCGCCAGGCGCTTCAG	0.657													A|||	1358	0.271166	0.3359	0.1585	5008	,	,		14624	0.0863		0.2863	False		,,,				2504	0.4387				p.R436G		Atlas-SNP	.											FAM83F,NS,carcinoma,0,1	FAM83F	29	1	0			c.A1306G						PASS	.	A	GLY/ARG	1193,3207		184,825,1191	18.0	22.0	21.0		1306	2.7	0.9	22	dbSNP_114	21	2403,6191		332,1739,2226	yes	missense	FAM83F	NM_138435.2	125	516,2564,3417	GG,GA,AA		27.9614,27.1136,27.6743	possibly-damaging	436/501	40417820	3596,9398	2200	4297	6497	SO:0001583	missense	113828	exon4			CCCGCCAGGCGCT		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1306A>G	22.37:g.40417820A>G	ENSP00000330432:p.Arg436Gly	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_138435	Q96FD6	Missense_Mutation	SNP	ENST00000333407.6	37	CCDS14000.2	500	0.22893772893772893	165	0.3353658536585366	62	0.1712707182320442	43	0.07517482517482517	230	0.3034300791556728	A	7.297	0.612217	0.14066	0.271136	0.279614	ENSG00000133477	ENST00000333407	T	0.10099	2.91	3.79	2.72	0.32119	.	0.560877	0.14341	N	0.325730	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.22276	0.067	B	0.19391	0.025	T	0.46091	-0.9216	9	0.42905	T	0.14	-11.3454	8.8472	0.35177	0.8099:0.1901:0.0:0.0	rs5995794;rs5995794	436	Q8NEG4	FA83F_HUMAN	G	436	ENSP00000330432:R436G	ENSP00000330432:R436G	R	+	1	2	FAM83F	38747766	0.996000	0.38824	0.875000	0.34327	0.027000	0.11550	3.639000	0.54339	0.478000	0.27488	0.374000	0.22700	AGG	A|0.766;G|0.234	0.234	strong		0.657	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
LRIG1	26018	hgsc.bcm.edu	37	3	66433676	66433676	+	Silent	SNP	A	A	G	rs900171	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:66433676A>G	ENST00000273261.3	-	15	2745	c.2221T>C	c.(2221-2223)Ttg>Ctg	p.L741L	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.L718L	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	741	Ig-like C2-type 3.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TCAGGGGTCAAGTGGTGCCGC	0.632													A|||	3478	0.694489	0.7247	0.6441	5008	,	,		19173	0.8036		0.5974	False		,,,				2504	0.6769				p.L741L		Atlas-SNP	.											.	LRIG1	138	.	0			c.T2221C						PASS	.	A		3087,1319	696.1+/-406.0	1077,933,193	69.0	66.0	67.0		2221	5.7	1.0	3	dbSNP_86	67	4828,3772	614.9+/-396.3	1375,2078,847	no	coding-synonymous	LRIG1	NM_015541.2		2452,3011,1040	GG,GA,AA		43.8605,29.9365,39.1435		741/1094	66433676	7915,5091	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon15			GGGTCAAGTGGTG	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2221T>C	3.37:g.66433676A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	97	58	0.597938	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			A|0.361;G|0.639	0.639	strong		0.632	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
GCAT	23464	hgsc.bcm.edu	37	22	38205989	38205989	+	Intron	SNP	T	T	C	rs2285178	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:38205989T>C	ENST00000248924.6	+	2	252				GCAT_ENST00000415371.1_Intron|GCAT_ENST00000323205.6_Missense_Mutation_p.L77S	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase						biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	GGCCTGCCCTTGCCCCACCTG	0.557													.|||	1380	0.275559	0.1014	0.3098	5008	,	,		18233	0.3135		0.332	False		,,,				2504	0.3896				p.L77S		Atlas-SNP	.											.	GCAT	27	.	0			c.T230C						PASS	.	T	SER/LEU,	618,3788	253.4+/-259.3	47,524,1632	66.0	43.0	51.0		230,	0.0	0.0	22	dbSNP_100	51	2672,5926	399.5+/-346.5	383,1906,2010	yes	missense,intron	GCAT	NM_001171690.1,NM_014291.3	145,	430,2430,3642	CC,CT,TT		31.077,14.0263,25.2999	,	77/446,	38205989	3290,9714	2203	4299	6502	SO:0001627	intron_variant	23464	exon2			TGCCCTTGCCCCA	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"""2-amino-3-ketobutyrate coenzyme A ligase"""	607422	"""glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"""				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.197-45T>C	22.37:g.38205989T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	121	58	0.479339	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	37	CCDS13957.1	614	0.28113553113553114	54	0.10975609756097561	114	0.3149171270718232	195	0.3409090909090909	251	0.3311345646437995	t	5.786	0.329321	0.10956	0.140263	0.31077	ENSG00000100116	ENST00000323205;ENST00000445195;ENST00000394944	D;D	0.94793	-3.52;-1.86	3.68	0.00572	0.14064	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	B	0.19583	0.037	B	0.13407	0.009	T	0.09378	-1.0677	7	0.87932	D	0	.	4.1025	0.10020	0.3637:0.0:0.1877:0.4486	rs2285178;rs59294489;rs2285178	77	E2QC23	.	S	77	ENSP00000371110:L77S;ENSP00000406719:L77S	ENSP00000371110:L77S	L	+	2	0	GCAT	36535935	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	0.213000	0.17521	-0.072000	0.12864	0.402000	0.26972	TTG	T|0.723;C|0.277	0.277	strong		0.557	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	
KIAA0754	643314	hgsc.bcm.edu	37	1	39878815	39878815	+	Missense_Mutation	SNP	A	A	G	rs1746842	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:39878815A>G	ENST00000530275.1	+	1	2665	c.2470A>G	c.(2470-2472)Att>Gtt	p.I824V	MACF1_ENST00000539005.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	824	Ala-rich.		I -> V (in dbSNP:rs1746842).							central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TGCTTTAGCTATTACAGTACC	0.577													A|||	288	0.057508	0.1127	0.0375	5008	,	,		17391	0.0		0.0378	False		,,,				2504	0.0767				p.I960V		Atlas-SNP	.											.	KIAA0754	93	.	0			c.A2878G						PASS	.	A	,,VAL/ILE	403,3687		13,377,1655	27.0	30.0	29.0		,,2878	-0.6	0.0	1	dbSNP_89	29	310,8076		5,300,3888	yes	intron,intron,missense	MACF1,KIAA0754	NM_012090.4,NM_033044.3,NM_015038.1	,,29	18,677,5543	GG,GA,AA		3.6966,9.8533,5.715	,,benign	,,960/1428	39878815	713,11763	2045	4193	6238	SO:0001583	missense	643314	exon1			TTAGCTATTACAG			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.2470A>G	1.37:g.39878815A>G	ENSP00000431179:p.Ile824Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		98	0.04487179487179487	57	0.11585365853658537	15	0.04143646408839779	0	0.0	26	0.03430079155672823	A	0.825	-0.747244	0.03065	0.098533	0.036966	ENSG00000255103	ENST00000530275	T	0.23754	1.89	2.85	-0.579	0.11720	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35871	-0.9771	8	0.02654	T	1	.	4.6926	0.12788	0.1162:0.0:0.5113:0.3726	rs1746842;rs1746842	824	O94854	K0754_HUMAN	V	824	ENSP00000431179:I824V	ENSP00000431179:I824V	I	+	1	0	RP4-562N20.1	39651402	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.595000	0.05727	-0.238000	0.09724	-1.778000	0.00651	ATT	A|0.949;G|0.051	0.051	strong		0.577	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
TACR2	6865	hgsc.bcm.edu	37	10	71164655	71164655	+	Missense_Mutation	SNP	C	C	T	rs2229170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:71164655C>T	ENST00000373306.4	-	5	1667	c.1124G>A	c.(1123-1125)cGt>cAt	p.R375H	TACR2_ENST00000373307.1_Missense_Mutation_p.R163H	NM_001057.2	NP_001048.2	P21452	NK2R_HUMAN	tachykinin receptor 2	375			R -> H (in dbSNP:rs2229170). {ECO:0000269|PubMed:1848773}.		excretion (GO:0007588)|intestine smooth muscle contraction (GO:0014827)|muscle contraction (GO:0006936)|negative regulation of luteinizing hormone secretion (GO:0033685)|operant conditioning (GO:0035106)|positive regulation of acetylcholine secretion, neurotransmission (GO:0014057)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vascular permeability (GO:0043117)|prolactin secretion (GO:0070459)|tachykinin receptor signaling pathway (GO:0007217)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	substance K receptor activity (GO:0016497)|tachykinin receptor activity (GO:0004995)			endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	11						ATCCTGGGGACGCCCCGCCTC	0.562													C|||	630	0.125799	0.0166	0.17	5008	,	,		18632	0.1161		0.1889	False		,,,				2504	0.1871				p.R375H		Atlas-SNP	.											.	TACR2	37	.	0			c.G1124A						PASS	.	C	HIS/ARG	175,4231	113.8+/-151.8	5,165,2033	60.0	60.0	60.0		1124	2.2	0.0	10	dbSNP_98	60	1648,6952	304.8+/-307.1	159,1330,2811	yes	missense	TACR2	NM_001057.2	29	164,1495,4844	TT,TC,CC		19.1628,3.9719,14.0166	benign	375/399	71164655	1823,11183	2203	4300	6503	SO:0001583	missense	6865	exon5			TGGGGACGCCCCG		CCDS7293.1	10q22.1	2012-09-20			ENSG00000075073	ENSG00000075073		"""GPCR / Class A : Tachykinin receptors"""	11527	protein-coding gene	gene with protein product		162321		TAC2R, NKNAR			Standard	NM_001057		Approved	SKR, NK2R	uc001jpn.2	P21452	OTTHUMG00000018377	ENST00000373306.4:c.1124G>A	10.37:g.71164655C>T	ENSP00000362403:p.Arg375His	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_001057	A8K7I1|Q4QRI5|Q8NGQ8|Q9UDE6|Q9UDE7	Missense_Mutation	SNP	ENST00000373306.4	37	CCDS7293.1	266	0.12179487179487179	10	0.02032520325203252	61	0.1685082872928177	64	0.11188811188811189	131	0.17282321899736147	C	11.04	1.522797	0.27211	0.039719	0.191628	ENSG00000075073	ENST00000373307;ENST00000373306	T;T	0.72282	0.12;-0.64	4.99	2.15	0.27550	.	1.929900	0.02113	N	0.055001	T	0.00109	0.0003	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.03315	-1.1049	9	0.22706	T	0.39	.	6.3885	0.21574	0.0:0.7037:0.0:0.2963	rs2229170	375	P21452	NK2R_HUMAN	H	163;375	ENSP00000362404:R163H;ENSP00000362403:R375H	ENSP00000362403:R375H	R	-	2	0	TACR2	70834661	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.612000	0.24283	0.779000	0.33543	-0.137000	0.14449	CGT	C|0.868;T|0.132	0.132	strong		0.562	TACR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048411.1		
RNF5	6048	hgsc.bcm.edu	37	6	32148031	32148031	+	Silent	SNP	A	A	G	rs1062070	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32148031A>G	ENST00000375094.3	+	6	629	c.471A>G	c.(469-471)ccA>ccG	p.P157P	RNF5_ENST00000427134.2_Intron|AGPAT1_ENST00000336984.6_5'Flank|AGPAT1_ENST00000490711.1_5'Flank|AGPAT1_ENST00000395497.1_5'Flank|AGPAT1_ENST00000375104.2_5'Flank	NM_006913.3	NP_008844.1	Q99942	RNF5_HUMAN	ring finger protein 5, E3 ubiquitin protein ligase	157					cellular protein catabolic process (GO:0044257)|ER-associated misfolded protein catabolic process (GO:0071712)|negative regulation of autophagy (GO:0010507)|protein destabilization (GO:0031648)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of autophagic vacuole assembly (GO:2000785)|response to bacterium (GO:0009617)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|lung(7)|urinary_tract(2)	10						AGGGTCACCCAGCCTCCAGCT	0.567													G|||	668	0.133387	0.1241	0.0865	5008	,	,		18465	0.0942		0.159	False		,,,				2504	0.1933				p.P157P		Atlas-SNP	.											.	RNF5	16	.	0			c.A471G						PASS	.	G		362,2660		23,316,1172	240.0	257.0	251.0		471	0.5	1.0	6	dbSNP_86	251	974,4444		83,808,1818	no	coding-synonymous	RNF5	NM_006913.3		106,1124,2990	GG,GA,AA		17.9771,11.9788,15.8294		157/181	32148031	1336,7104	1511	2709	4220	SO:0001819	synonymous_variant	6048	exon6			TCACCCAGCCTCC	U89336	CCDS4745.1	6p21.31	2013-01-09	2012-02-23			ENSG00000204308		"""RING-type (C3HC4) zinc fingers"""	10068	protein-coding gene	gene with protein product		602677	"""ring finger protein 5"""			9533025	Standard	NM_006913		Approved	NG2, G16, RING5, RMA1	uc031snv.1	Q99942	OTTHUMG00000031093	ENST00000375094.3:c.471A>G	6.37:g.32148031A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	44	40	0.909091	NM_006913	A2BFI6|B2R4K3|Q0VDB7|Q9UMQ2	Silent	SNP	ENST00000375094.3	37	CCDS4745.1																																																																																			A|0.860;G|0.140	0.140	strong		0.567	RNF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076133.2	NM_006913	
BTNL8	79908	hgsc.bcm.edu	37	5	180376974	180376974	+	Missense_Mutation	SNP	T	T	G	rs386695831|rs146303629	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180376974T>G	ENST00000340184.4	+	8	1139	c.933T>G	c.(931-933)caT>caG	p.H311Q	BTNL8_ENST00000511704.1_Missense_Mutation_p.H195Q|BTNL8_ENST00000508408.1_3'UTR|BTNL8_ENST00000231229.4_3'UTR|BTNL8_ENST00000505126.1_Missense_Mutation_p.H104Q|BTNL8_ENST00000400707.3_Missense_Mutation_p.H186Q|BTNL8_ENST00000533815.2_Missense_Mutation_p.H127Q	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	311	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		H -> Q (in dbSNP:rs146303629). {ECO:0000269|PubMed:15489334}.	H -> E (in Ref. 2; BAH12847). {ECO:0000305}.	immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTGTAACCCATAGAAAAGCTC	0.532													t|||	1447	0.288938	0.4796	0.1527	5008	,	,		14284	0.1825		0.2266	False		,,,				2504	0.3016				p.H311Q		Atlas-SNP	.											.	BTNL8	114	.	0			c.T933G						PASS	.	G	GLN/HIS,GLN/HIS,,GLN/HIS,GLN/HIS,	1823,2407		505,813,797	37.0	37.0	37.0		933,585,,558,381,	-1.0	0.0	5	dbSNP_134	37	1992,5814		598,796,2509	no	missense,missense,utr-3,missense,missense,utr-3	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	24,24,,24,24,	1103,1609,3306	GG,GT,TT		25.5188,43.0969,31.6966	probably-damaging,probably-damaging,,probably-damaging,probably-damaging,	311/501,195/385,,186/376,127/317,	180376974	3815,8221	2115	3903	6018	SO:0001583	missense	79908	exon8			AACCCATAGAAAA	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.933T>G	5.37:g.180376974T>G	ENSP00000342197:p.His311Gln	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	51	41	0.803922	NM_001040462	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Missense_Mutation	SNP	ENST00000340184.4	37	CCDS43413.1	621	0.28434065934065933	259	0.5264227642276422	67	0.1850828729281768	108	0.1888111888111888	187	0.24670184696569922	t	7.936	0.741652	0.15642	0.430969	0.255188	ENSG00000113303	ENST00000340184;ENST00000400707;ENST00000511704;ENST00000505126;ENST00000533815	T;T;T;T;T	0.10382	2.88;2.88;2.88;2.88;2.88	1.89	-1.04	0.10068	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.00012	0.0000	M	0.66378	2.025	0.80722	P	0.0	D;P;D	0.65815	0.961;0.802;0.995	P;B;P	0.60789	0.462;0.303;0.879	T	0.44406	-0.9330	8	0.29301	T	0.29	.	2.8916	0.05678	0.0:0.3265:0.2529:0.4206	.	186;195;311	E9PG07;E9PEF6;Q6UX41	.;.;BTNL8_HUMAN	Q	311;186;195;104;127	ENSP00000342197:H311Q;ENSP00000383543:H186Q;ENSP00000425207:H195Q;ENSP00000427441:H104Q;ENSP00000435098:H127Q	ENSP00000342197:H311Q	H	+	3	2	BTNL8	180309580	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.302000	0.02746	-0.398000	0.07679	-0.720000	0.03607	CAT	T|1.000;|0.000	.	weak		0.532	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
H1FNT	341567	hgsc.bcm.edu	37	12	48723784	48723784	+	Missense_Mutation	SNP	C	C	T	rs2291483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48723784C>T	ENST00000335017.1	+	1	1022	c.710C>T	c.(709-711)tCc>tTc	p.S237F		NM_181788.1	NP_861453.1	Q75WM6	H1FNT_HUMAN	H1 histone family, member N, testis-specific	237			S -> F (in a Japanese man; dbSNP:rs2291483). {ECO:0000269|PubMed:16533358}.		chromosome condensation (GO:0030261)|multicellular organismal development (GO:0007275)|sperm chromatin condensation (GO:0035092)|spermatid nucleus elongation (GO:0007290)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.S237F(1)		endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	13						AGGCGAAGCTCCAAGCCCAGG	0.652													C|||	1032	0.20607	0.2829	0.1311	5008	,	,		14762	0.121		0.2435	False		,,,				2504	0.2045				p.S237F		Atlas-SNP	.											H1FNT,NS,carcinoma,0,1	H1FNT	30	1	1	Substitution - Missense(1)	stomach(1)	c.C710T						PASS	.	C	PHE/SER	1270,3098	419.1+/-338.5	180,910,1094	48.0	59.0	55.0		710	1.8	0.0	12	dbSNP_100	55	1788,6800	305.0+/-307.2	177,1434,2683	yes	missense	H1FNT	NM_181788.1	155	357,2344,3777	TT,TC,CC		20.8197,29.0751,23.603	possibly-damaging	237/256	48723784	3058,9898	2184	4294	6478	SO:0001583	missense	341567	exon1			GAAGCTCCAAGCC	AY302593	CCDS8762.1	12q13.11	2011-01-27				ENSG00000187166		"""Histones / Replication-independent"""	24893	protein-coding gene	gene with protein product						15710904	Standard	NM_181788		Approved	HANP1, H1T2	uc001rrm.3	Q75WM6		ENST00000335017.1:c.710C>T	12.37:g.48723784C>T	ENSP00000334805:p.Ser237Phe	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_181788	Q147U8|Q5GKZ5|Q7Z694	Missense_Mutation	SNP	ENST00000335017.1	37	CCDS8762.1	470	0.21520146520146521	140	0.2845528455284553	46	0.1270718232044199	82	0.14335664335664336	202	0.26649076517150394	C	16.43	3.121223	0.56613	0.290751	0.208197	ENSG00000187166	ENST00000335017	T	0.22539	1.95	4.66	1.78	0.24846	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	D	0.61697	0.99	D	0.64410	0.925	T	0.31364	-0.9946	8	0.59425	D	0.04	-3.2202	6.29	0.21054	0.0:0.6714:0.1526:0.176	rs2291483;rs60062142;rs2291483	237	Q75WM6	H1FNT_HUMAN	F	237	ENSP00000334805:S237F	ENSP00000334805:S237F	S	+	2	0	H1FNT	47010051	0.003000	0.15002	0.003000	0.11579	0.138000	0.21146	0.403000	0.20982	0.135000	0.18707	0.655000	0.94253	TCC	C|0.772;T|0.228	0.228	strong		0.652	H1FNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406516.1	NM_181788	
NOSTRIN	115677	hgsc.bcm.edu	37	2	169721381	169721381	+	Silent	SNP	A	A	G	rs3931	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:169721381A>G	ENST00000317647.7	+	16	1651	c.1422A>G	c.(1420-1422)ggA>ggG	p.G474G	NOSTRIN_ENST00000421711.2_Silent_p.G446G|NOSTRIN_ENST00000458381.2_Silent_p.G531G|NOSTRIN_ENST00000397206.2_Silent_p.G396G|NOSTRIN_ENST00000397209.2_Silent_p.G446G|NOSTRIN_ENST00000445023.2_Silent_p.G396G|NOSTRIN_ENST00000444448.2_Silent_p.G531G	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	474	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						AAGAAGGAGGATGGTGGTTTG	0.428													A|||	1038	0.207268	0.087	0.1974	5008	,	,		20541	0.2688		0.2903	False		,,,				2504	0.228				p.G531G		Atlas-SNP	.											.	NOSTRIN	68	.	0			c.A1593G						PASS	.	A	,,,	376,3372		16,344,1514	156.0	142.0	146.0		1422,1593,1338,1188	2.3	1.0	2	dbSNP_36	146	2608,5608		418,1772,1918	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOSTRIN	NM_001039724.3,NM_001171631.1,NM_001171632.1,NM_052946.3	,,,	434,2116,3432	GG,GA,AA		31.7429,10.032,24.9415	,,,	474/507,531/564,446/479,396/429	169721381	2984,8980	1874	4108	5982	SO:0001819	synonymous_variant	115677	exon21			AGGAGGATGGTGG	AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"""nitric oxide synthase trafficker"""			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.1422A>G	2.37:g.169721381A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_001171631	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Silent	SNP	ENST00000317647.7	37	CCDS42771.1																																																																																			A|0.757;G|0.243	0.243	strong		0.428	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333356.4	NM_052946	
GOLGB1	2804	hgsc.bcm.edu	37	3	121415610	121415610	+	Missense_Mutation	SNP	G	G	A	rs33988592	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:121415610G>A	ENST00000340645.5	-	13	3870	c.3745C>T	c.(3745-3747)Cca>Tca	p.P1249S	GOLGB1_ENST00000393667.3_Missense_Mutation_p.P1254S	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1249			P -> S (in dbSNP:rs33988592).		Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		TCTGTGCTTGGGAGTTTTCCG	0.438													G|||	736	0.146965	0.1286	0.1383	5008	,	,		21254	0.0923		0.2833	False		,,,				2504	0.0941				p.P1254S		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C3760T						PASS	.	G	SER/PRO	667,3739	282.8+/-276.7	50,567,1586	203.0	182.0	189.0		3745	1.9	0.0	3	dbSNP_126	189	2468,6132	405.4+/-348.5	368,1732,2200	yes	missense	GOLGB1	NM_004487.3	74	418,2299,3786	AA,AG,GG		28.6977,15.1384,24.1043	benign	1249/3260	121415610	3135,9871	2203	4300	6503	SO:0001583	missense	2804	exon13			TGCTTGGGAGTTT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.3745C>T	3.37:g.121415610G>A	ENSP00000341848:p.Pro1249Ser	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	279	129	0.462366	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	377	0.17261904761904762	65	0.13211382113821138	48	0.13259668508287292	55	0.09615384615384616	209	0.2757255936675462	G	0.041	-1.284513	0.01398	0.151384	0.286977	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	T;T;T	0.22539	2.56;2.54;1.95	6.07	1.91	0.25777	.	0.655467	0.14262	N	0.330719	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B;B;B;B;B	0.12630	0.006;0.006;0.006;0.006;0.006	B;B;B;B;B	0.10450	0.005;0.005;0.003;0.003;0.003	T	0.41395	-0.9511	9	0.09843	T	0.71	.	2.4289	0.04466	0.1581:0.1242:0.4626:0.2551	rs33988592	1174;1213;1254;1254;1249	F1T0J2;E7EU81;E7EP74;B2ZZ91;Q14789	.;.;.;.;GOGB1_HUMAN	S	1249;1254;1213	ENSP00000341848:P1249S;ENSP00000377275:P1254S;ENSP00000418231:P1213S	ENSP00000341848:P1249S	P	-	1	0	GOLGB1	122898300	0.000000	0.05858	0.004000	0.12327	0.083000	0.17756	-0.819000	0.04462	0.410000	0.25675	0.655000	0.94253	CCA	G|0.780;A|0.220	0.220	strong		0.438	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
CYP4Z1	199974	hgsc.bcm.edu	37	1	47571905	47571905	+	Silent	SNP	C	C	T	rs28463559	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47571905C>T	ENST00000334194.3	+	9	1176	c.1173C>T	c.(1171-1173)acC>acT	p.T391T	CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_178134.2	NP_835235.1	Q86W10	CP4Z1_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 1	391						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			cervix(1)|large_intestine(4)|lung(4)|skin(1)|stomach(1)	11						AACCCATCACCTTTCCAGATG	0.448													C|||	2902	0.579473	0.4766	0.4654	5008	,	,		17755	0.9563		0.339	False		,,,				2504	0.6585				p.T391T		Atlas-SNP	.											.	CYP4Z1	43	.	0			c.C1173T						PASS	.						93.0	86.0	89.0					1																	47571905		2203	4300	6503	SO:0001819	synonymous_variant	199974	exon9			CATCACCTTTCCA	AY262056	CCDS545.1	1p33	2008-02-05			ENSG00000186160	ENSG00000186160		"""Cytochrome P450s"""	20583	protein-coding gene	gene with protein product						15059886	Standard	NM_178134		Approved	CYP4A20	uc001cqu.1	Q86W10	OTTHUMG00000008019	ENST00000334194.3:c.1173C>T	1.37:g.47571905C>T		Somatic	315	1	0.0031746		WXS	Illumina HiSeq	Phase_I	275	105	0.381818	NM_178134	Q5VVE4	Silent	SNP	ENST00000334194.3	37	CCDS545.1																																																																																			C|0.568;T|0.432	0.432	strong		0.448	CYP4Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022020.1	NM_178134	
OBSCN	84033	hgsc.bcm.edu	37	1	228433217	228433217	+	Silent	SNP	A	A	G	rs2487384	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228433217A>G	ENST00000422127.1	+	12	3629	c.3585A>G	c.(3583-3585)acA>acG	p.T1195T	OBSCN_ENST00000570156.2_Silent_p.T1287T|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.T1195T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1195	Ig-like 12.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGCCCCAGACAGAGGTGACGT	0.602													G|||	3088	0.616613	0.7095	0.6542	5008	,	,		17687	0.5992		0.6412	False		,,,				2504	0.4571				p.T1287T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A3861G						PASS	.	G	,	3040,1116		1101,838,139	87.0	85.0	86.0		3585,3585	-9.0	0.0	1	dbSNP_100	86	5725,2663		1984,1757,453	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	3085,2595,592	GG,GA,AA		31.7477,26.8527,30.126	,	1195/7969,1195/6621	228433217	8765,3779	2078	4194	6272	SO:0001819	synonymous_variant	84033	exon13			CCAGACAGAGGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3585A>G	1.37:g.228433217A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	191	105	0.549738	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			A|0.366;G|0.634	0.634	strong		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
GNB1L	54584	hgsc.bcm.edu	37	22	19789541	19789541	+	Missense_Mutation	SNP	A	A	C	rs2073770	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:19789541A>C	ENST00000329517.6	-	7	951	c.715T>G	c.(715-717)Tgg>Ggg	p.W239G	GNB1L_ENST00000403325.1_Missense_Mutation_p.W239G|GNB1L_ENST00000460402.1_5'UTR|GNB1L_ENST00000405009.1_Intron	NM_053004.2	NP_443730.1	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	239			W -> G (in dbSNP:rs2073770).		G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|social behavior (GO:0035176)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)				breast(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	12	Colorectal(54;0.0993)					GCCTGCTGCCAGTCCAGGCTC	0.592													C|||	1032	0.20607	0.0348	0.2392	5008	,	,		15897	0.4792		0.1183	False		,,,				2504	0.2229				p.W239G		Atlas-SNP	.											.	GNB1L	34	.	0			c.T715G						PASS	.	C	GLY/TRP	172,4226		8,156,2035	19.0	18.0	18.0		715	4.8	1.0	22	dbSNP_96	18	968,7626		71,826,3400	yes	missense	GNB1L	NM_053004.2	184	79,982,5435	CC,CA,AA		11.2637,3.9109,8.7746	benign	239/328	19789541	1140,11852	2199	4297	6496	SO:0001583	missense	54584	exon7			GCTGCCAGTCCAG	AF238328	CCDS13768.1	22q11.2	2013-05-21			ENSG00000185838	ENSG00000185838		"""WD repeat domain containing"""	4397	protein-coding gene	gene with protein product		610778				11072084	Standard	NM_053004		Approved	GY2, WDR14	uc002zqf.1	Q9BYB4	OTTHUMG00000150279	ENST00000329517.6:c.715T>G	22.37:g.19789541A>C	ENSP00000331313:p.Trp239Gly	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_053004	Q9H2S2|Q9H4M4	Missense_Mutation	SNP	ENST00000329517.6	37	CCDS13768.1	488	0.22344322344322345	18	0.036585365853658534	89	0.24585635359116023	296	0.5174825174825175	85	0.11213720316622691	C	4.473	0.087593	0.08583	0.039109	0.112637	ENSG00000185838	ENST00000329517;ENST00000403325	T;T	0.16597	2.33;2.33	5.79	4.78	0.61160	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.762820	0.12420	N	0.470532	T	0.00012	0.0000	N	0.01705	-0.755	0.09310	P	0.99999999842471	B	0.02656	0.0	B	0.01281	0.0	T	0.42599	-0.9442	9	0.31617	T	0.26	-7.8749	7.5444	0.27757	0.1265:0.6861:0.1218:0.0656	rs2073770;rs17817304;rs2073770	239	Q9BYB4	GNB1L_HUMAN	G	239	ENSP00000331313:W239G;ENSP00000385154:W239G	ENSP00000331313:W239G	W	-	1	0	GNB1L	18169541	0.997000	0.39634	0.991000	0.47740	0.578000	0.36192	1.876000	0.39588	0.822000	0.34565	-0.979000	0.02580	TGG	A|0.844;C|0.156	0.156	strong		0.592	GNB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075202.1		
DTNB	1838	hgsc.bcm.edu	37	2	25655772	25655772	+	Silent	SNP	T	T	C	rs7583475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:25655772T>C	ENST00000406818.3	-	14	1689	c.1440A>G	c.(1438-1440)gcA>gcG	p.A480A	DTNB_ENST00000405222.1_Silent_p.A450A|DTNB_ENST00000404103.3_Silent_p.A480A|DTNB_ENST00000288642.8_Silent_p.A480A|DTNB_ENST00000407661.3_Silent_p.A480A|DTNB_ENST00000545439.1_Silent_p.A276A|DTNB_ENST00000496972.2_Silent_p.A423A|DTNB_ENST00000407038.3_Silent_p.A450A|DTNB_ENST00000407186.1_Silent_p.A450A	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	480						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)					GCCGCAGCTCTGCCAGCAGCG	0.567													T|||	1199	0.239417	0.3298	0.2104	5008	,	,		19600	0.005		0.3489	False		,,,				2504	0.2669				p.A480A		Atlas-SNP	.											.	DTNB	43	.	0			c.A1440G						PASS	.	T	,,,,	1405,2935		240,925,1005	23.0	28.0	27.0		1440,1440,1350,1440,1350	-9.0	0.9	2	dbSNP_116	27	2850,5716		493,1864,1926	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	,,,,	733,2789,2931	CC,CT,TT		33.2711,32.3733,32.9692	,,,,	480/628,480/598,450/568,480/610,450/561	25655772	4255,8651	2170	4283	6453	SO:0001819	synonymous_variant	1838	exon14			CAGCTCTGCCAGC	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.1440A>G	2.37:g.25655772T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Silent	SNP	ENST00000406818.3	37	CCDS46237.1																																																																																			T|0.743;C|0.257	0.257	strong		0.567	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147	
CDH23	64072	hgsc.bcm.edu	37	10	73558952	73558952	+	Missense_Mutation	SNP	C	C	T	rs4747195	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73558952C>T	ENST00000224721.6	+	50	7159	c.7154C>T	c.(7153-7155)cCg>cTg	p.P2385L	CDH23_ENST00000398788.3_Missense_Mutation_p.P140L|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2380	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.P2385L(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						AACGGGTCCCCGCCCCGGGCA	0.592													C|||	1644	0.328275	0.2443	0.3473	5008	,	,		19778	0.5298		0.2744	False		,,,				2504	0.2761				p.P2380L		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - Missense(1)	stomach(1)	c.C7139T						scavenged	.	C	LEU/PRO,LEU/PRO,LEU/PRO	966,3058		114,738,1160	70.0	80.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	419,419,7139	5.6	1.0	10	dbSNP_111	77	2173,6145		304,1565,2290	yes	missense,missense,missense	CDH23	NM_001171933.1,NM_001171934.1,NM_022124.5	98,98,98	418,2303,3450	TT,TC,CC		26.1241,24.006,25.4335	probably-damaging,probably-damaging,probably-damaging	140/1115,140/1080,2380/3355	73558952	3139,9203	2012	4159	6171	SO:0001583	missense	64072	exon49			GGTCCCCGCCCCG	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7154C>T	10.37:g.73558952C>T	ENSP00000224721:p.Pro2385Leu	Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		749	0.34294871794871795	133	0.2703252032520325	108	0.2983425414364641	300	0.5244755244755245	208	0.27440633245382584	C	22.5	4.304758	0.81247	0.24006	0.261241	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398788	T	0.00792	5.69	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.82716	2.605	0.09310	P	0.99999999999995	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.981	T	0.53373	-0.8448	9	0.62326	D	0.03	.	19.516	0.95165	0.0:1.0:0.0:0.0	rs4747195;rs60719007;rs4747195	2380;2380	E9PEX1;Q9H251	.;CAD23_HUMAN	L	2385;2380;2383;140	ENSP00000381768:P140L	ENSP00000224721:P2385L	P	+	2	0	CDH23	73228958	1.000000	0.71417	0.994000	0.49952	0.319000	0.28217	7.786000	0.85741	2.623000	0.88846	0.655000	0.94253	CCG	C|0.668;T|0.332	0.332	strong		0.592	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
PRR18	285800	hgsc.bcm.edu	37	6	166721211	166721211	+	Silent	SNP	G	G	T	rs13204594	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:166721211G>T	ENST00000322583.3	-	1	660	c.420C>A	c.(418-420)acC>acA	p.T140T		NM_175922.3	NP_787118.2	Q8N4B5	PRR18_HUMAN	proline rich 18	140								p.T140T(1)		haematopoietic_and_lymphoid_tissue(2)|lung(1)	3		Breast(66;2.35e-05)|Ovarian(120;0.0606)|Prostate(117;0.0959)		OV - Ovarian serous cystadenocarcinoma(33;1.5e-19)|BRCA - Breast invasive adenocarcinoma(81;4.45e-06)|GBM - Glioblastoma multiforme(31;7.96e-05)		CGGCCTCGGGGGTGAGATTCA	0.731													G|||	3827	0.764177	0.7322	0.6124	5008	,	,		6273	0.9206		0.7455	False		,,,				2504	0.773				p.T140T		Atlas-SNP	.											PRR18,NS,lymphoid_neoplasm,0,1	PRR18	4	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C420A						PASS	.	G		3047,1071		1145,757,157	7.0	9.0	9.0		420	0.3	1.0	6	dbSNP_121	9	6150,2074		2328,1494,290	no	coding-synonymous	PRR18	NM_175922.3		3473,2251,447	TT,TG,GG		25.2189,26.0078,25.4821		140/296	166721211	9197,3145	2059	4112	6171	SO:0001819	synonymous_variant	285800	exon1			CTCGGGGGTGAGA	BC034775	CCDS5291.1	6q27	2009-01-27	2009-01-27						28574	protein-coding gene	gene with protein product			"""proline rich region 18"""			12477932	Standard	NM_175922		Approved	MGC35308	uc003quw.1	Q8N4B5		ENST00000322583.3:c.420C>A	6.37:g.166721211G>T		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_175922		Silent	SNP	ENST00000322583.3	37	CCDS5291.1																																																																																			G|0.224;T|0.776	0.776	strong		0.731	PRR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392563.3	NM_175922	
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 GAIIx	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	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	166	16	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 GAIIx	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|MCF2L2_ENST00000473233.1_Intron|B3GNT5_ENST00000465010.1_Missense_Mutation_p.R2K|B3GNT5_ENST00000460419.1_Missense_Mutation_p.R2K	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	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	26	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	
GALR1	2587	hgsc.bcm.edu	37	18	74980601	74980601	+	Missense_Mutation	SNP	A	A	T	rs77169818	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:74980601A>T	ENST00000299727.3	+	3	793	c.793A>T	c.(793-795)Atc>Ttc	p.I265F		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	265					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		GCCGCACCACATCATCCATCT	0.557													A|||	207	0.0413339	0.0015	0.0908	5008	,	,		14586	0.0565		0.0507	False		,,,				2504	0.0348				p.I265F		Atlas-SNP	.											.	GALR1	53	.	0			c.A793T						PASS	.	A	PHE/ILE	57,4349	55.5+/-91.7	2,53,2148	135.0	134.0	134.0		793	0.5	0.7	18	dbSNP_131	134	345,8255	118.8+/-178.2	5,335,3960	yes	missense	GALR1	NM_001480.3	21	7,388,6108	TT,TA,AA		4.0116,1.2937,3.0909	benign	265/350	74980601	402,12604	2203	4300	6503	SO:0001583	missense	2587	exon3			CACCACATCATCC	U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"""GPCR / Class A : Galanin receptors"""	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.793A>T	18.37:g.74980601A>T	ENSP00000299727:p.Ile265Phe	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_001480	Q4VBL7	Missense_Mutation	SNP	ENST00000299727.3	37	CCDS12012.1	117	0.05357142857142857	0	0.0	39	0.10773480662983426	35	0.06118881118881119	43	0.05672823218997362	A	13.23	2.174445	0.38413	0.012937	0.040116	ENSG00000166573	ENST00000299727	T	0.59638	0.25	4.74	0.465	0.16711	GPCR, rhodopsin-like superfamily (1);	0.195753	0.43260	D	0.000600	T	0.02649	0.0080	M	0.76574	2.34	0.37387	D	0.912277	B	0.30542	0.284	P	0.45610	0.487	T	0.42481	-0.9449	10	0.72032	D	0.01	.	9.0874	0.36590	0.4241:0.0:0.5759:0.0	.	265	P47211	GALR1_HUMAN	F	265	ENSP00000299727:I265F	ENSP00000299727:I265F	I	+	1	0	GALR1	73109589	0.940000	0.31905	0.727000	0.30756	0.147000	0.21601	1.474000	0.35398	-0.244000	0.09639	-0.376000	0.06991	ATC	A|0.965;T|0.035	0.035	strong		0.557	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1		
SPATA13	221178	hgsc.bcm.edu	37	13	24797913	24797913	+	Intron	SNP	C	C	T	rs1220546	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:24797913C>T	ENST00000382095.4	+	2	185				RP11-307N16.6_ENST00000382141.4_Silent_p.D282D|SPATA13_ENST00000382108.3_Silent_p.D282D|SPATA13_ENST00000424834.2_Silent_p.D282D	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.D282D(2)		breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		CGGCCCATGACGCACGGGTAC	0.567													C|||	1315	0.26258	0.1097	0.196	5008	,	,		19459	0.4405		0.2942	False		,,,				2504	0.3006				p.D282D		Atlas-SNP	.											.	SPATA13	92	.	2	Substitution - coding silent(2)	endometrium(2)	c.C846T						PASS	.	C	,	205,1179		17,171,504	72.0	65.0	67.0		846,	-9.2	0.0	13	dbSNP_87	67	988,2194		154,680,757	no	coding-synonymous,intron	SPATA13	NM_001166271.1,NM_153023.2	,	171,851,1261	TT,TC,CC		31.0497,14.8121,26.1279	,	282/1278,	24797913	1193,3373	692	1591	2283	SO:0001627	intron_variant	221178	exon2			CCATGACGCACGG	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-222-25702C>T	13.37:g.24797913C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	37	CCDS9305.1	610	0.2793040293040293	64	0.13008130081300814	76	0.20994475138121546	240	0.4195804195804196	230	0.3034300791556728	C	3.895	-0.023136	0.07634	0.148121	0.310497	ENSG00000182957	ENST00000424834	.	.	.	4.62	-9.24	0.00669	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.21484	-1.0244	3	.	.	.	.	2.1055	0.03690	0.4112:0.2767:0.1656:0.1465	rs1220546;rs17365668;rs56504932;rs60383945;rs1220546	.	.	.	C	320	.	.	R	+	1	0	SPATA13	23695913	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.827000	0.00746	-3.430000	0.00165	-1.555000	0.00892	CGC	C|0.720;T|0.280	0.280	strong		0.567	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
C5orf42	65250	hgsc.bcm.edu	37	5	37196028	37196028	+	Missense_Mutation	SNP	C	C	T	rs72736758	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:37196028C>T	ENST00000508244.1	-	20	3836	c.3743G>A	c.(3742-3744)gGt>gAt	p.G1248D	C5orf42_ENST00000274258.7_Missense_Mutation_p.G129D|C5orf42_ENST00000425232.2_Missense_Mutation_p.G1248D			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1248						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AAATGCGATACCTCCTTTACA	0.383													C|||	97	0.019369	0.0045	0.0303	5008	,	,		16480	0.0		0.0398	False		,,,				2504	0.0307				p.G1248D		Atlas-SNP	.											.	C5orf42	422	.	0			c.G3743A						PASS	.	C	ASP/GLY	39,4367	43.1+/-76.7	1,37,2165	105.0	102.0	103.0		3743	5.2	0.9	5	dbSNP_130	103	369,8231	122.7+/-181.7	10,349,3941	yes	missense	C5orf42	NM_023073.3	94	11,386,6106	TT,TC,CC		4.2907,0.8852,3.137	benign	1248/3198	37196028	408,12598	2203	4300	6503	SO:0001583	missense	65250	exon21			GCGATACCTCCTT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.3743G>A	5.37:g.37196028C>T	ENSP00000421690:p.Gly1248Asp	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	216	93	0.430556	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	45	0.020604395604395604	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	30	0.0395778364116095	C	18.05	3.537916	0.65085	0.008852	0.042907	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.27557	1.8;1.8;1.66;1.68	5.21	5.21	0.72293	.	0.153741	0.30791	N	0.008879	T	0.10766	0.0263	N	0.14661	0.345	0.32954	D	0.520092	D;D	0.76494	0.999;0.999	D;D	0.72075	0.976;0.967	T	0.24905	-1.0147	10	0.46703	T	0.11	.	12.947	0.58376	0.0:0.915:0.0:0.085	.	1248;129	E9PH94;Q9H799	.;CE042_HUMAN	D	1248;1248;129;296;129	ENSP00000421690:G1248D;ENSP00000389014:G1248D;ENSP00000274258:G129D;ENSP00000424223:G296D	ENSP00000274258:G129D	G	-	2	0	C5orf42	37231785	0.005000	0.15991	0.924000	0.36721	0.532000	0.34746	1.971000	0.40530	2.601000	0.87937	0.655000	0.94253	GGT	C|0.972;T|0.028	0.028	strong		0.383	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
IFITM2	10581	hgsc.bcm.edu	37	11	309127	309127	+	Missense_Mutation	SNP	A	A	G	rs1059091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:309127A>G	ENST00000399817.4	+	2	391	c.361A>G	c.(361-363)Atc>Gtc	p.I121V	RP11-326C3.7_ENST00000526612.1_RNA|IFITM2_ENST00000533141.1_Missense_Mutation_p.I101V|IFITM2_ENST00000602569.1_Missense_Mutation_p.I101V	NM_006435.2	NP_006426.2	Q01629	IFM2_HUMAN	interferon induced transmembrane protein 2	121			I -> V (in dbSNP:rs1059091). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1906403}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4		all_cancers(49;2e-09)|all_epithelial(84;3.36e-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;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		CATTCTGCTCATCATCATCCC	0.577													N|||	2707	0.540535	0.5976	0.4553	5008	,	,		21628	0.6944		0.332	False		,,,				2504	0.5798				p.I121V		Atlas-SNP	.											.	IFITM2	21	.	0			c.A361G						PASS	.	G	VAL/ILE	2248,1872		615,1018,427	83.0	84.0	84.0		361	-3.8	0.0	11	dbSNP_86	84	2757,5609		453,1851,1879	yes	missense	IFITM2	NM_006435.2	29	1068,2869,2306	GG,GA,AA		32.9548,45.4369,40.0849	benign	121/133	309127	5005,7481	2060	4183	6243	SO:0001583	missense	10581	exon2			CTGCTCATCATCA	X57351	CCDS41583.1	11p15.5	2012-03-13	2012-03-13		ENSG00000185201	ENSG00000185201			5413	protein-coding gene	gene with protein product		605578	"""interferon induced transmembrane protein 2 (1-8D)"""			1906403	Standard	NM_006435		Approved	1-8D	uc001lox.4	Q01629		ENST00000399817.4:c.361A>G	11.37:g.309127A>G	ENSP00000382714:p.Ile121Val	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	267	132	0.494382	NM_006435	Q6FH82|Q96DA8	Missense_Mutation	SNP	ENST00000399817.4	37	CCDS41583.1	1097|1097	0.5022893772893773|0.5022893772893773	287|287	0.5833333333333334|0.5833333333333334	160|160	0.4419889502762431|0.4419889502762431	396|396	0.6923076923076923|0.6923076923076923	254|254	0.33509234828496043|0.33509234828496043	G|G	8.381|8.381	0.837569|0.837569	0.16891|0.16891	0.545631|0.545631	0.329548|0.329548	ENSG00000185201|ENSG00000185201	ENST00000327366|ENST00000533141;ENST00000399817	.|D;D	.|0.86627	.|-2.15;-2.15	2.35|2.35	-3.77|-3.77	0.04346|0.04346	.|.	1.013090|.	0.07963|.	N|.	0.982712|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.69463|0.69463	2.115|2.115	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	6|8	0.87932|0.35671	D|T	0|0.21	-6.1667|-6.1667	4.3203|4.3203	0.11013|0.11013	0.3671:0.0:0.4565:0.1764|0.3671:0.0:0.4565:0.1764	rs1059091;rs3168356;rs3765194;rs17845234;rs17858050;rs1059091|rs1059091;rs3168356;rs3765194;rs17845234;rs17858050;rs1059091	.|121	.|Q01629	.|IFM2_HUMAN	R|V	117|101;121	.|ENSP00000434443:I101V;ENSP00000382714:I121V	ENSP00000327996:H117R|ENSP00000382714:I121V	H|I	+|+	2|1	0|0	IFITM2|IFITM2	299127|299127	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-0.264000|-0.264000	0.08658|0.08658	-1.307000|-1.307000	0.02321|0.02321	-2.523000|-2.523000	0.00184|0.00184	CAT|ATC	A|0.607;C|0.000;G|0.393	0.393	strong		0.577	IFITM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383591.1	NM_006435	
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194944	18194944	+	Silent	SNP	T	T	A	rs11024531	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18194944T>A	ENST00000314254.3	+	1	561	c.141T>A	c.(139-141)gtT>gtA	p.V47V	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						GAAACGCGGTTGTGCTCTGGC	0.557													T|||	1374	0.274361	0.0862	0.3617	5008	,	,		21062	0.504		0.2734	False		,,,				2504	0.2311				p.V47V		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.T141A						PASS	.	T		534,3864	243.4+/-253.1	29,476,1694	145.0	129.0	134.0		141	-1.1	0.0	11	dbSNP_120	134	2251,6335	380.7+/-339.8	310,1631,2352	no	coding-synonymous	MRGPRX4	NM_054032.3		339,2107,4046	AA,AT,TT		26.2171,12.1419,21.4495		47/323	18194944	2785,10199	2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			CGCGGTTGTGCTC	AY042216	CCDS7831.1	11p15.1	2013-10-10			ENSG00000179817	ENSG00000179817		"""GPCR / Class A : Orphans"""	17617	protein-coding gene	gene with protein product		607230				11551509	Standard	NM_054032		Approved	MRGX4	uc001mnv.1	Q96LA9	OTTHUMG00000166442	ENST00000314254.3:c.141T>A	11.37:g.18194944T>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	37	CCDS7831.1																																																																																			T|0.760;A|0.240	0.240	strong		0.557	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
CCDC181	57821	hgsc.bcm.edu	37	1	169390957	169390957	+	Missense_Mutation	SNP	A	A	T	rs35107735	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:169390957A>T	ENST00000367806.3	-	3	864	c.712T>A	c.(712-714)Ttt>Att	p.F238I	CCDC181_ENST00000367805.3_Missense_Mutation_p.F238I|CCDC181_ENST00000491570.1_5'UTR|CCDC181_ENST00000545005.1_Missense_Mutation_p.F238I	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	238			F -> I (in dbSNP:rs35107735). {ECO:0000269|Ref.2}.			nucleus (GO:0005634)											GGAGGCAAAAACCCCTGACTG	0.403													A|||	720	0.14377	0.0696	0.1873	5008	,	,		19575	0.001		0.3678	False		,,,				2504	0.1299				p.F238I		Atlas-SNP	.											.	C1orf114	67	.	0			c.T712A						PASS	.	A	ILE/PHE	516,3890	237.7+/-249.4	30,456,1717	114.0	115.0	115.0		712	1.5	0.2	1	dbSNP_126	115	3158,5442	479.7+/-370.2	580,1998,1722	no	missense	C1orf114	NM_021179.1	21	610,2454,3439	TT,TA,AA		36.7209,11.7113,28.2485	benign	238/509	169390957	3674,9332	2203	4300	6503	SO:0001583	missense	57821	exon3			GCAAAAACCCCTG	AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 114"""	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.712T>A	1.37:g.169390957A>T	ENSP00000356780:p.Phe238Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	162	161	0.993827	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Missense_Mutation	SNP	ENST00000367806.3	37		404	0.184981684981685	41	0.08333333333333333	80	0.22099447513812154	0	0.0	283	0.3733509234828496	A	13.39	2.224273	0.39300	0.117113	0.367209	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005;ENST00000456107	T;T;T;T	0.22539	1.96;1.96;1.96;1.95	5.31	1.53	0.23141	.	0.170180	0.53938	D	0.000060	T	0.10423	0.0255	M	0.67953	2.075	0.37524	D	0.917639	B;P;P	0.47841	0.103;0.901;0.901	B;B;B	0.41135	0.082;0.348;0.348	T	0.06552	-1.0820	9	0.52906	T	0.07	-0.8188	9.1053	0.36694	0.5219:0.3623:0.0:0.1158	rs35107735;rs61808029	238;238;238	Q5TID7-2;Q5TID7;Q5TID7-3	.;CA114_HUMAN;.	I	238	ENSP00000356779:F238I;ENSP00000356780:F238I;ENSP00000442297:F238I;ENSP00000411000:F238I	ENSP00000356779:F238I	F	-	1	0	C1orf114	167657581	0.981000	0.34729	0.172000	0.22920	0.884000	0.51177	2.390000	0.44416	-0.002000	0.14469	0.455000	0.32223	TTT	A|0.752;T|0.248	0.248	strong		0.403	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179	
SGPL1	8879	hgsc.bcm.edu	37	10	72629567	72629567	+	Silent	SNP	C	C	T	rs827249	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72629567C>T	ENST00000373202.3	+	9	923	c.723C>T	c.(721-723)gcC>gcT	p.A241A		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	241					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117)			large_intestine(4)	4						CCCAAAGTGCCCATGCTGCAT	0.463													C|||	344	0.0686901	0.0492	0.0807	5008	,	,		18915	0.1369		0.0517	False		,,,				2504	0.0337				p.A241A	Colon(151;1054 2458 6676 40971)	Atlas-SNP	.											.	SGPL1	37	.	0			c.C723T						PASS	.	C		188,4218	120.4+/-158.0	1,186,2016	101.0	97.0	98.0		723	3.7	1.0	10	dbSNP_86	98	330,8270	115.2+/-175.0	5,320,3975	no	coding-synonymous	SGPL1	NM_003901.3		6,506,5991	TT,TC,CC		3.8372,4.2669,3.9828		241/569	72629567	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	8879	exon9			AAGTGCCCATGCT	AI128825	CCDS31216.1	10q21	2008-08-01			ENSG00000166224	ENSG00000166224			10817	protein-coding gene	gene with protein product		603729				9464245, 17090686	Standard	NM_003901		Approved	SPL	uc001jrm.3	O95470	OTTHUMG00000018421	ENST00000373202.3:c.723C>T	10.37:g.72629567C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	163	77	0.472393	NM_003901	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	Silent	SNP	ENST00000373202.3	37	CCDS31216.1																																																																																			C|0.943;T|0.057	0.057	strong		0.463	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048533.1	NM_003901	
LYRM2	57226	hgsc.bcm.edu	37	6	90347511	90347511	+	Missense_Mutation	SNP	T	T	C	rs34012596	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90347511T>C	ENST00000523377.1	-	2	172	c.136A>G	c.(136-138)Aaa>Gaa	p.K46E	LYRM2_ENST00000517396.1_5'UTR|LYRM2_ENST00000520318.1_Missense_Mutation_p.K46E|LYRM2_ENST00000520441.1_Missense_Mutation_p.K46E	NM_020466.4	NP_065199.1	Q9NU23	LYRM2_HUMAN	LYR motif containing 2	46			K -> E (in dbSNP:rs34012596). {ECO:0000269|PubMed:14702039}.			mitochondrion (GO:0005739)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(76;2.76e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;3.72e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0131)		GCCCAATCTTTCAGGTATTTG	0.398													T|||	810	0.161741	0.118	0.1124	5008	,	,		16926	0.0407		0.2078	False		,,,				2504	0.3333				p.K46E		Atlas-SNP	.											.	LYRM2	6	.	0			c.A136G						PASS	.	T	GLU/LYS	523,3883	238.7+/-250.0	34,455,1714	173.0	169.0	170.0		136	2.4	1.0	6	dbSNP_126	170	1770,6830	319.9+/-314.4	166,1438,2696	yes	missense	LYRM2	NM_020466.4	56	200,1893,4410	CC,CT,TT		20.5814,11.8702,17.6303	benign	46/89	90347511	2293,10713	2203	4300	6503	SO:0001583	missense	57226	exon2			AATCTTTCAGGTA	BC009782	CCDS5023.1	6q15	2006-09-19			ENSG00000083099	ENSG00000083099		"""LYR motif containing"""	25229	protein-coding gene	gene with protein product						12477932	Standard	NM_020466		Approved	DJ122O8.2	uc003pnm.3	Q9NU23	OTTHUMG00000015203	ENST00000523377.1:c.136A>G	6.37:g.90347511T>C	ENSP00000430025:p.Lys46Glu	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	182	98	0.538462	NM_020466	B2R4U2|E1P517	Missense_Mutation	SNP	ENST00000523377.1	37	CCDS5023.1	269	0.12316849816849818	43	0.08739837398373984	48	0.13259668508287292	23	0.04020979020979021	155	0.20448548812664907	T	16.48	3.135484	0.56828	0.118702	0.205814	ENSG00000083099	ENST00000520441;ENST00000523377;ENST00000520318	T;T;T	0.70164	-0.46;-0.46;-0.46	6.03	2.37	0.29283	.	0.307844	0.34853	N	0.003635	T	0.45836	0.1362	.	.	.	0.40731	P	0.017251000000000016	B	0.19583	0.037	B	0.25614	0.062	T	0.46748	-0.9169	8	0.59425	D	0.04	.	14.7249	0.69339	0.0:0.0:0.4496:0.5504	rs34012596;rs56863728;rs34012596	46	Q9NU23	LYRM2_HUMAN	E	46	ENSP00000427859:K46E;ENSP00000430025:K46E;ENSP00000428207:K46E	ENSP00000430316:K46E	K	-	1	0	LYRM2	90404232	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	0.931000	0.28871	0.488000	0.27723	0.455000	0.32223	AAA	T|0.844;C|0.156	0.156	strong		0.398	LYRM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041498.2	NM_020466	
GGT1	2678	hgsc.bcm.edu	37	22	24982254	24982254	+	Intron	SNP	G	G	A	rs41277319	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:24982254G>A	ENST00000248923.4	+	1	59				FAM211B_ENST00000495297.1_5'Flank|FAM211B_ENST00000318753.8_Missense_Mutation_p.A183V	NM_013430.2	NP_038347.2	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1						arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	GTCCAGCACCGCCAGCACAGC	0.652													G|||	45	0.00898562	0.0008	0.0086	5008	,	,		18690	0.0		0.0318	False		,,,				2504	0.0061				p.A183V		Atlas-SNP	.											.	.	.	.	0			c.C548T						PASS	.	G	,VAL/ALA	27,4339	27.2+/-55.0	0,27,2156	100.0	112.0	108.0		,548	1.9	0.0	22	dbSNP_127	108	250,8330	95.9+/-157.7	1,248,4041	yes	intron,missense	GGT1,C22orf36	NM_013430.2,NM_207644.2	,64	1,275,6197	AA,AG,GG		2.9138,0.6184,2.1397	,benign	,183/316	24982254	277,12669	2183	4290	6473	SO:0001627	intron_variant	388886	exon4			AGCACCGCCAGCA	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000248923.4:c.-429+2478G>A	22.37:g.24982254G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	133	68	0.511278	NM_207644	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000248923.4	37	CCDS42992.1	31	0.014194139194139194	0	0.0	5	0.013812154696132596	0	0.0	26	0.03430079155672823	G	7.999	0.754982	0.15846	0.006184	0.029138	ENSG00000178026	ENST00000318753	T	0.28069	1.63	3.4	1.87	0.25490	.	0.354983	0.25532	N	0.030023	T	0.05868	0.0153	N	0.22421	0.69	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.17745	-1.0359	10	0.22706	T	0.39	-1.208	8.4432	0.32826	0.1701:0.0:0.8299:0.0	rs41277319	183	Q2VPJ9	LRC6X_HUMAN	V	183	ENSP00000320520:A183V	ENSP00000320520:A183V	A	-	2	0	C22orf36	23312254	0.005000	0.15991	0.005000	0.12908	0.026000	0.11368	0.802000	0.27069	0.390000	0.25115	0.561000	0.74099	GCG	G|0.983;A|0.017	0.017	strong		0.652	GGT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319110.1	NM_013430	
LILRB4	11006	hgsc.bcm.edu	37	19	55179342	55179342	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55179342C>T	ENST00000391736.1	+	14	1534	c.1219C>T	c.(1219-1221)Ccc>Tcc	p.P407S	LILRB4_ENST00000391733.3_Missense_Mutation_p.P408S|LILRB4_ENST00000270452.2_Missense_Mutation_p.P407S|LILRB4_ENST00000430952.2_Missense_Mutation_p.P406S|LILRB4_ENST00000391734.3_Missense_Mutation_p.P354S	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	407					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)	p.P407S(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		ATCTGAAGCCCCCCAGGATGT	0.647																																					p.P407S		Atlas-SNP	.											LILRB4,NS,carcinoma,0,1	LILRB4	86	1	1	Substitution - Missense(1)	lung(1)	c.C1219T						scavenged	.						62.0	67.0	66.0					19																	55179342		2203	4300	6503	SO:0001583	missense	11006	exon12			GAAGCCCCCCAGG	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1219C>T	19.37:g.55179342C>T	ENSP00000375616:p.Pro407Ser	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	184	6	0.0326087	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	C	11.16	1.556618	0.27827	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733	T;T;T;T;T	0.00505	7.11;7.11;7.11;6.93;7.12	2.07	2.07	0.26955	.	.	.	.	.	T	0.00906	0.0030	L	0.48935	1.535	0.20764	N	0.999854	D;D;B;B	0.76494	0.999;0.999;0.007;0.001	D;D;B;B	0.76575	0.972;0.988;0.01;0.001	T	0.57946	-0.7723	9	0.22706	T	0.39	.	7.5752	0.27931	0.0:1.0:0.0:0.0	.	354;408;406;407	A8MUE1;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	S	407;407;406;354;408	ENSP00000375616:P407S;ENSP00000270452:P407S;ENSP00000408995:P406S;ENSP00000375614:P354S;ENSP00000375613:P408S	ENSP00000270452:P407S	P	+	1	0	LILRB4	59871154	0.007000	0.16637	0.721000	0.30653	0.421000	0.31385	0.250000	0.18235	1.166000	0.42689	0.407000	0.27541	CCC	.	.	none		0.647	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
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 GAIIx	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_ENST00000409125.4_Intron|GPD2_ENST00000409674.1_Silent_p.L122L|GPD2_ENST00000438166.2_Silent_p.L122L|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		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	144	107	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 GAIIx	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	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	81	40	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 GAIIx	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_ENST00000444481.1_Silent_p.E191E|VCX3B_ENST00000453306.1_Intron|VCX3B_ENST00000440654.2_Silent_p.E171E|VCX3B_ENST00000381029.4_Silent_p.E189E	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		Somatic	326	0	0		WXS	Illumina HiSeq	Phase_I	450	135	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		
ARL13A	392509	hgsc.bcm.edu	37	X	100242536	100242536	+	Missense_Mutation	SNP	C	C	T	rs41307262	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:100242536C>T	ENST00000450049.2	+	6	757	c.644C>T	c.(643-645)tCa>tTa	p.S215L		NM_001162491.1	NP_001155963.1	Q5H913	AR13A_HUMAN	ADP-ribosylation factor-like 13A	215					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			endometrium(1)|ovary(1)	2						GAAAGATGCTCATCACACAGG	0.483													C|||	477	0.126358	0.1596	0.1254	3775	,	,		14995	0.0069		0.1093	False		,,,				2504	0.0634				p.S215L		Atlas-SNP	.											.	ARL13A	7	.	0			c.C644T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	637,2639		40,434,123,879,447	92.0	80.0	84.0		644,644,644	1.6	0.0	X	dbSNP_127	84	797,5656		24,525,224,1784,1563	yes	missense,missense,missense	ARL13A	NM_001012990.3,NM_001162490.1,NM_001162491.1	145,145,145	64,959,347,2663,2010	TT,TC,T,CC,C		12.3508,19.4444,14.7394	benign,benign,benign	215/291,215/291,215/257	100242536	1434,8295	1923	4120	6043	SO:0001583	missense	392509	exon6			GATGCTCATCACA		CCDS55463.1	Xq22.1	2014-05-09	2005-11-18	2005-11-18	ENSG00000174225	ENSG00000174225		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31709	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 13"""	ARL13			Standard	NM_001162491		Approved		uc011mrf.2	Q5H913	OTTHUMG00000022013	ENST00000450049.2:c.644C>T	X.37:g.100242536C>T	ENSP00000398637:p.Ser215Leu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	39	28	0.717949	NM_001162490	B2RTT6|B4DX50	Missense_Mutation	SNP	ENST00000450049.2	37	CCDS55463.1	222	0.13381555153707053	58	0.13679245283018868	25	0.07668711656441718	2	0.0035087719298245615	63	0.08798882681564246	C	1.182	-0.637841	0.03557	0.194444	0.123508	ENSG00000174225	ENST00000450049;ENST00000372953	T	0.59638	0.25	4.43	1.61	0.23674	.	1.389140	0.04468	N	0.375547	T	0.00073	0.0002	N	0.11560	0.145	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.04976	-1.0914	9	0.37606	T	0.19	.	3.5007	0.07672	0.1977:0.5836:0.0:0.2187	rs41307262;rs61747478	215;215	B2RTT6;Q5H913	.;AR13A_HUMAN	L	215;89	ENSP00000398637:S215L	ENSP00000362044:S89L	S	+	2	0	ARL13A	100129192	0.059000	0.20769	0.001000	0.08648	0.040000	0.13550	0.159000	0.16442	0.202000	0.20498	-0.322000	0.08575	TCA	C|0.866;T|0.134	0.134	strong		0.483	ARL13A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000057504.2	XM_373358	
RAG1	5896	hgsc.bcm.edu	37	11	36595600	36595600	+	Missense_Mutation	SNP	A	A	G	rs3740955	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:36595600A>G	ENST00000299440.5	+	2	858	c.746A>G	c.(745-747)cAc>cGc	p.H249R		NM_000448.2	NP_000439	P15918	RAG1_HUMAN	recombination activating gene 1	249	Interaction with importin alpha-1.		H -> R (in dbSNP:rs3740955). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2598259, ECO:0000269|PubMed:8844221}.		adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|DNA recombination (GO:0006310)|histone monoubiquitination (GO:0010390)|immune response (GO:0006955)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|pre-B cell allelic exclusion (GO:0002331)|protein autoubiquitination (GO:0051865)|regulation of T cell differentiation (GO:0045580)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|V(D)J recombination (GO:0033151)	nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	65	all_lung(20;0.226)	all_hematologic(20;0.107)				GCCCGTCAGCACAAGAGAAGA	0.498									Familial Hemophagocytic Lymphohistiocytosis				G|||	3072	0.613419	0.7708	0.6052	5008	,	,		24019	0.756		0.3648	False		,,,				2504	0.5153				p.H249R	Pancreas(43;321 1249 3212 48200)|Esophageal Squamous(38;49 1003 17530 24363)	Atlas-SNP	.											.	RAG1	151	.	0			c.A746G						PASS	.	G	ARG/HIS	3200,1204	420.4+/-339.0	1162,876,164	79.0	71.0	74.0		746	-2.0	0.0	11	dbSNP_107	74	2888,5708	672.0+/-402.9	470,1948,1880	yes	missense	RAG1	NM_000448.2	29	1632,2824,2044	GG,GA,AA		33.597,27.3388,46.8308	benign	249/1044	36595600	6088,6912	2202	4298	6500	SO:0001583	missense	5896	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GTCAGCACAAGAG	M29474	CCDS7902.1	11p13	2014-09-17				ENSG00000166349		"""RING-type (C3HC4) zinc fingers"""	9831	protein-coding gene	gene with protein product	"""recombination activating protein 1"", ""RING finger protein 74"", ""V(D)J recombination-activating protein 1"""	179615				1612612, 1283330	Standard	NM_000448		Approved	RNF74, MGC43321	uc001mwu.4	P15918		ENST00000299440.5:c.746A>G	11.37:g.36595600A>G	ENSP00000299440:p.His249Arg	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	35	0.59322	NM_000448	E9PPC4|Q8IY72|Q8NER2	Missense_Mutation	SNP	ENST00000299440.5	37	CCDS7902.1	1291	0.5911172161172161	364	0.7398373983739838	200	0.5524861878453039	448	0.7832167832167832	279	0.36807387862796836	G	0.188	-1.055818	0.01965	0.726612	0.33597	ENSG00000166349	ENST00000534663;ENST00000299440	T;T	0.36878	1.23;1.23	5.6	-1.98	0.07480	.	1.564430	0.03609	N	0.234553	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45920	-0.9228	9	0.51188	T	0.08	.	10.2304	0.43252	0.5804:0.1383:0.2812:0.0	rs3740955;rs12797306;rs17629075;rs17857143;rs56430511;rs58718336;rs3740955	249	P15918	RAG1_HUMAN	R	249	ENSP00000434610:H249R;ENSP00000299440:H249R	ENSP00000299440:H249R	H	+	2	0	RAG1	36552176	0.004000	0.15560	0.000000	0.03702	0.057000	0.15508	0.169000	0.16641	-0.541000	0.06257	-0.738000	0.03535	CAC	A|0.471;G|0.529	0.529	strong		0.498	RAG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389535.1	NM_000448	
CD1D	912	hgsc.bcm.edu	37	1	158151974	158151974	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158151974T>G	ENST00000368171.3	+	4	980	c.481T>G	c.(481-483)Ttg>Gtg	p.L161V		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	161					antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					TTGGGTAAACTTGGCCATTCA	0.493																																					p.L161V		Atlas-SNP	.											CD1D,NS,carcinoma,0,2	CD1D	60	2	0			c.T481G						scavenged	.						156.0	165.0	162.0					1																	158151974		2203	4300	6503	SO:0001583	missense	912	exon4			GTAAACTTGGCCA	BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1637	protein-coding gene	gene with protein product		188410	"""CD1D antigen, d polypeptide"", ""CD1d antigen"""			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.481T>G	1.37:g.158151974T>G	ENSP00000357153:p.Leu161Val	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	198	7	0.0353535	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Missense_Mutation	SNP	ENST00000368171.3	37	CCDS1173.1	.	.	.	.	.	.	.	.	.	.	T	3.001	-0.206066	0.06180	.	.	ENSG00000158473	ENST00000368171	T	0.17528	2.27	4.44	-8.88	0.00789	MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	3.577100	0.00616	N	0.000421	T	0.01940	0.0061	N	0.20986	0.625	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15407	-1.0438	10	0.31617	T	0.26	1.4747	1.1115	0.01705	0.248:0.3259:0.1226:0.3035	.	161	P15813	CD1D_HUMAN	V	161	ENSP00000357153:L161V	ENSP00000357153:L161V	L	+	1	2	CD1D	156418598	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.831000	0.00743	-3.564000	0.00140	-1.262000	0.01453	TTG	.	.	none		0.493	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766	
MT1A	4489	hgsc.bcm.edu	37	16	56673828	56673828	+	Missense_Mutation	SNP	A	A	G	rs8052394	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:56673828A>G	ENST00000290705.8	+	3	225	c.152A>G	c.(151-153)aAa>aGa	p.K51R	MT1JP_ENST00000564564.1_RNA	NM_005946.2	NP_005937.2	P04731	MT1A_HUMAN	metallothionein 1A	51	Alpha.		K -> R (in dbSNP:rs8052394).		cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(1)	3					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCATCTGCAAAGGGGCATCA	0.552													.|||	884	0.176518	0.1604	0.1671	5008	,	,		18390	0.2292		0.1441	False		,,,				2504	0.184				p.K51R		Atlas-SNP	.											.	MT1A	4	.	0			c.A152G						PASS	.	A	ARG/LYS	764,3632	311.4+/-292.0	70,624,1504	111.0	107.0	108.0		152	2.0	1.0	16	dbSNP_116	108	1108,7492	229.1+/-263.9	72,964,3264	no	missense	MT1A	NM_005946.2	26	142,1588,4768	GG,GA,AA		12.8837,17.3794,14.4044	benign	51/62	56673828	1872,11124	2198	4300	6498	SO:0001583	missense	4489	exon3			TCTGCAAAGGGGC	BC029475	CCDS32454.1	16q13	2012-10-02	2007-03-02			ENSG00000205362		"""Metallothioneins"""	7393	protein-coding gene	gene with protein product		156350	"""metallothionein 1S"""	MT1, MT1S		6089206, 6327055	Standard	NM_005946		Approved		uc002ejq.3	P04731		ENST00000290705.8:c.152A>G	16.37:g.56673828A>G	ENSP00000290705:p.Lys51Arg	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_005946	Q86YX5	Missense_Mutation	SNP	ENST00000290705.8	37	CCDS32454.1	349	0.15979853479853479	72	0.14634146341463414	55	0.15193370165745856	118	0.2062937062937063	104	0.13720316622691292	A	7.939	0.742314	0.15642	0.173794	0.128837	ENSG00000205362	ENST00000290705	T	0.12879	2.64	3.07	1.95	0.26073	Metallothionein domain, vertebrate (1);Metallothionein domain (1);	0.000000	0.64402	U	0.000010	T	0.00012	0.0000	.	.	.	0.33189	P	0.44935499999999995	B	0.24618	0.107	B	0.23852	0.049	T	0.32745	-0.9895	8	0.66056	D	0.02	.	6.2045	0.20595	0.8704:0.0:0.1296:0.0	rs8052394	51	P04731	MT1A_HUMAN	R	51	ENSP00000290705:K51R	ENSP00000290705:K51R	K	+	2	0	MT1A	55231329	1.000000	0.71417	0.976000	0.42696	0.004000	0.04260	4.890000	0.63178	0.358000	0.24211	-0.624000	0.04008	AAA	A|0.853;G|0.147	0.147	strong		0.552	MT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434324.1	NM_005946	
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 GAIIx	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	RP5-994D16.3_ENST00000414339.1_lincRNA|YBX1_ENST00000467957.1_3'UTR	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		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	104	28	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	
NUP210	23225	hgsc.bcm.edu	37	3	13395579	13395579	+	Missense_Mutation	SNP	C	C	A	rs2280084	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:13395579C>A	ENST00000254508.5	-	17	2439	c.2357G>T	c.(2356-2358)cGg>cTg	p.R786L		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	786			R -> L (polymorphism confirmed at protein level; dbSNP:rs2280084). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17488105}.		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					CAGGTCCAGCCGGGGGTTGCG	0.632													A|||	2880	0.57508	0.8971	0.4452	5008	,	,		18550	0.3998		0.5467	False		,,,				2504	0.4417				p.R786L		Atlas-SNP	.											NUP210,NS,carcinoma,0,1	NUP210	182	1	0			c.G2357T						PASS	.	A	LEU/ARG	3663,741		1528,607,67	18.0	15.0	16.0		2357	4.2	1.0	3	dbSNP_100	16	4875,3717		1397,2081,818	yes	missense	NUP210	NM_024923.2	102	2925,2688,885	AA,AC,CC		43.2612,16.8256,34.3029	benign	786/1888	13395579	8538,4458	2202	4296	6498	SO:0001583	missense	23225	exon17			TCCAGCCGGGGGT	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.2357G>T	3.37:g.13395579C>A	ENSP00000254508:p.Arg786Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	139	75	0.539568	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	1244	0.5695970695970696	429	0.8719512195121951	173	0.47790055248618785	242	0.4230769230769231	400	0.5277044854881267	A	1.769	-0.484919	0.04352	0.831744	0.567388	ENSG00000132182	ENST00000254508	T	0.19394	2.15	5.53	4.25	0.50352	.	0.365106	0.24698	N	0.036332	T	0.00012	0.0000	N	0.00677	-1.265	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18524	-1.0334	9	0.22109	T	0.4	-5.3448	9.7463	0.40448	0.7628:0.114:0.0:0.1233	rs2280084;rs17175429;rs52795349;rs59726611;rs2280084	786;786	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	L	786	ENSP00000254508:R786L	ENSP00000254508:R786L	R	-	2	0	NUP210	13370579	0.380000	0.25131	0.993000	0.49108	0.162000	0.22319	3.340000	0.52143	0.938000	0.37419	-0.362000	0.07510	CGG	C|0.358;A|0.642	0.642	strong		0.632	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
EXPH5	23086	hgsc.bcm.edu	37	11	108384661	108384661	+	Missense_Mutation	SNP	C	C	A	rs12146448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:108384661C>A	ENST00000265843.4	-	6	1683	c.1573G>T	c.(1573-1575)Gtt>Ttt	p.V525F	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Missense_Mutation_p.V449F|EXPH5_ENST00000525344.1_Missense_Mutation_p.V518F|EXPH5_ENST00000443411.1_Missense_Mutation_p.V337F	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	525			V -> F (in dbSNP:rs12146448).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TCAGAAGAAACATTATGGCCA	0.403													C|||	92	0.0183706	0.0023	0.0231	5008	,	,		21017	0.0149		0.0378	False		,,,				2504	0.0204				p.V525F		Atlas-SNP	.											.	EXPH5	193	.	0			c.G1573T						PASS	.	C	PHE/VAL	33,4369	37.6+/-69.7	0,33,2168	69.0	69.0	69.0		1573	2.5	0.9	11	dbSNP_120	69	341,8255	117.0+/-176.6	9,323,3966	yes	missense	EXPH5	NM_015065.2	50	9,356,6134	AA,AC,CC		3.967,0.7497,2.8774	possibly-damaging	525/1990	108384661	374,12624	2201	4298	6499	SO:0001583	missense	23086	exon6			AAGAAACATTATG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.1573G>T	11.37:g.108384661C>A	ENSP00000265843:p.Val525Phe	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	77	59	0.766234	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	45	0.020604395604395604	3	0.006097560975609756	10	0.027624309392265192	5	0.008741258741258742	27	0.03562005277044855	C	8.345	0.829492	0.16749	0.007497	0.03967	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.05025	4.12;4.04;3.9;4.12;3.96;3.51	5.82	2.53	0.30540	.	0.538297	0.16886	N	0.195489	T	0.01835	0.0058	M	0.64997	1.995	0.09310	N	1	P	0.36837	0.571	B	0.39027	0.288	T	0.15896	-1.0421	10	0.87932	D	0	-1.0716	7.873	0.29578	0.0:0.6684:0.0:0.3316	rs12146448;rs52826351;rs12146448	525	Q8NEV8	EXPH5_HUMAN	F	525;449;337;518;369;449;337	ENSP00000265843:V525F;ENSP00000391966:V449F;ENSP00000411390:V337F;ENSP00000432546:V518F;ENSP00000432683:V449F;ENSP00000446434:V337F	ENSP00000265843:V525F	V	-	1	0	EXPH5	107889871	0.000000	0.05858	0.891000	0.34965	0.181000	0.23173	-0.136000	0.10405	0.820000	0.34516	0.467000	0.42956	GTT	C|0.975;A|0.025	0.025	strong		0.403	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
PRDM5	11107	hgsc.bcm.edu	37	4	121706201	121706201	+	Silent	SNP	A	A	G	rs12499000	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:121706201A>G	ENST00000264808.3	-	11	1474	c.1234T>C	c.(1234-1236)Ttg>Ctg	p.L412L	PRDM5_ENST00000515109.1_Silent_p.L381L|PRDM5_ENST00000428209.2_Silent_p.L381L	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	412					histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|mitotic cell cycle (GO:0000278)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.L412L(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(17)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GTCCGGAACAAAGCTTTACAT	0.408													A|||	688	0.13738	0.0113	0.1931	5008	,	,		15439	0.1895		0.2674	False		,,,				2504	0.0808				p.L412L		Atlas-SNP	.											PRDM5,NS,carcinoma,0,1	PRDM5	76	1	1	Substitution - coding silent(1)	stomach(1)	c.T1234C						PASS	.	A		255,4151	146.9+/-181.5	11,233,1959	108.0	97.0	101.0		1234	-1.3	0.8	4	dbSNP_120	101	2344,6256	392.4+/-344.0	329,1686,2285	no	coding-synonymous	PRDM5	NM_018699.2		340,1919,4244	GG,GA,AA		27.2558,5.7876,19.9831		412/631	121706201	2599,10407	2203	4300	6503	SO:0001819	synonymous_variant	11107	exon11			GGAACAAAGCTTT	AF272897	CCDS3716.1, CCDS75187.1, CCDS75188.1	4q25-q26	2013-01-08			ENSG00000138738	ENSG00000138738		"""Zinc fingers, C2H2-type"""	9349	protein-coding gene	gene with protein product		614161					Standard	XM_005262706		Approved	PFM2	uc003idn.3	Q9NQX1	OTTHUMG00000132970	ENST00000264808.3:c.1234T>C	4.37:g.121706201A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Silent	SNP	ENST00000264808.3	37	CCDS3716.1																																																																																			A|0.807;G|0.193	0.193	strong		0.408	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2		
TMC4	147798	hgsc.bcm.edu	37	19	54664752	54664752	+	Silent	SNP	A	A	C	rs36656	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54664752A>C	ENST00000376591.4	-	13	1985	c.1854T>G	c.(1852-1854)ctT>ctG	p.L618L	TMC4_ENST00000416963.1_Silent_p.L200L|TMC4_ENST00000301187.4_Silent_p.L612L|LENG1_ENST00000222224.3_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	618					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					ATGGACCACAAAGCTTAGAAG	0.577													C|||	2173	0.433906	0.441	0.4222	5008	,	,		16302	0.2073		0.5149	False		,,,				2504	0.5828				p.L618L		Atlas-SNP	.											.	TMC4	89	.	0			c.T1854G						PASS	.	C	,	1865,2541	627.0+/-394.8	374,1117,712	45.0	52.0	50.0		1854,1836	3.7	0.7	19	dbSNP_76	50	4262,4338	575.8+/-390.3	1027,2208,1065	no	coding-synonymous,coding-synonymous	TMC4	NM_001145303.1,NM_144686.2	,	1401,3325,1777	CC,CA,AA		49.5581,42.3286,47.109	,	618/713,612/707	54664752	6127,6879	2203	4300	6503	SO:0001819	synonymous_variant	147798	exon13			ACCACAAAGCTTA	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.1854T>G	19.37:g.54664752A>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	37	CCDS46174.1																																																																																			A|0.558;C|0.442	0.442	strong		0.577	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
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 GAIIx	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	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	112	30	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	
TOPORS	10210	hgsc.bcm.edu	37	9	32542204	32542204	+	Silent	SNP	A	A	G	rs10971019	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:32542204A>G	ENST00000360538.2	-	3	2435	c.2319T>C	c.(2317-2319)tcT>tcC	p.S773S	TOPORS_ENST00000379858.1_Silent_p.S708S	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	773	Arg-rich.|Interaction with TOP1.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		ATCTGTTACTAGACAGGCTCC	0.423													A|||	897	0.179113	0.0681	0.2003	5008	,	,		20185	0.1071		0.2078	False		,,,				2504	0.3589				p.S773S		Atlas-SNP	.											.	TOPORS	127	.	0			c.T2319C						PASS	.	A	,	425,3981	205.8+/-227.6	25,375,1803	109.0	109.0	109.0		2124,2319	-2.4	1.0	9	dbSNP_120	109	1908,6692	338.9+/-322.9	222,1464,2614	no	coding-synonymous,coding-synonymous	TOPORS	NM_001195622.1,NM_005802.4	,	247,1839,4417	GG,GA,AA		22.186,9.6459,17.9379	,	708/981,773/1046	32542204	2333,10673	2203	4300	6503	SO:0001819	synonymous_variant	10210	exon3			GTTACTAGACAGG	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2319T>C	9.37:g.32542204A>G		Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	333	166	0.498498	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Silent	SNP	ENST00000360538.2	37	CCDS6527.1																																																																																			A|0.836;G|0.164	0.164	strong		0.423	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
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 GAIIx	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		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	132	65	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	
USP6NL	9712	hgsc.bcm.edu	37	10	11505743	11505743	+	Missense_Mutation	SNP	G	G	A	rs113611342	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:11505743G>A	ENST00000609104.1	-	15	1578	c.1184C>T	c.(1183-1185)cCg>cTg	p.P395L	USP6NL_ENST00000277575.5_Missense_Mutation_p.P412L|USP6NL_ENST00000379237.2_Missense_Mutation_p.P418L	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	395					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						CAGCGGGCTCGGCCGGCCCAC	0.672													g|||	47	0.00938498	0.0008	0.0115	5008	,	,		13488	0.0		0.0268	False		,,,				2504	0.0112				p.P412L		Atlas-SNP	.											.	USP6NL	57	.	0			c.C1235T						PASS	.	A	LEU/PRO,LEU/PRO	15,3779		0,15,1882	17.0	21.0	19.0		1235,1184	3.5	0.1	10	dbSNP_132	19	215,7965		2,211,3877	yes	missense,missense	USP6NL	NM_001080491.2,NM_014688.2	98,98	2,226,5759	AA,AG,GG		2.6284,0.3954,1.9208	benign,benign	412/846,395/829	11505743	230,11744	1897	4090	5987	SO:0001583	missense	9712	exon14			GGGCTCGGCCGGC	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1184C>T	10.37:g.11505743G>A	ENSP00000476462:p.Pro395Leu	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	23	16	0.695652	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	37	CCDS53492.1	28	0.01282051282051282	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	20	0.026385224274406333	g	14.16	2.453347	0.43531	0.003954	0.026284	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.03831	3.79;3.79	5.42	3.52	0.40303	.	0.822752	0.11219	N	0.586941	T	0.00998	0.0033	N	0.11427	0.14	0.09310	N	1	B;B	0.16396	0.003;0.017	B;B	0.09377	0.0;0.004	T	0.44907	-0.9297	10	0.46703	T	0.11	.	7.1336	0.25515	0.0872:0.0:0.7439:0.1689	.	395;412	Q92738;Q92738-2	US6NL_HUMAN;.	L	395;412;395	ENSP00000277575:P412L;ENSP00000368539:P395L	ENSP00000277575:P412L	P	-	2	0	USP6NL	11545749	0.377000	0.25106	0.095000	0.20976	0.104000	0.19210	1.504000	0.35726	0.741000	0.32674	-0.185000	0.12909	CCG	G|0.986;A|0.014	0.014	strong		0.672	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
CCDC13	152206	hgsc.bcm.edu	37	3	42772038	42772038	+	Missense_Mutation	SNP	A	A	T	rs12495805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42772038A>T	ENST00000310232.6	-	13	1722	c.1639T>A	c.(1639-1641)Tca>Aca	p.S547T	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	547			S -> T (in dbSNP:rs12495805).							endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						TTGATCTCTGACACTTGTGCC	0.592													T|||	1022	0.204073	0.2451	0.1844	5008	,	,		18415	0.1081		0.1849	False		,,,				2504	0.2812				p.S547T		Atlas-SNP	.											.	CCDC13	71	.	0			c.T1639A						PASS	.	T	THR/SER	1077,3329	722.4+/-409.3	108,861,1234	87.0	85.0	85.0		1639	-3.3	0.0	3	dbSNP_120	85	1567,7033	744.7+/-407.2	123,1321,2856	yes	missense	CCDC13	NM_144719.3	58	231,2182,4090	TT,TA,AA		18.2209,24.4439,20.3291	benign	547/716	42772038	2644,10362	2203	4300	6503	SO:0001583	missense	152206	exon13			TCTCTGACACTTG	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.1639T>A	3.37:g.42772038A>T	ENSP00000309836:p.Ser547Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	107	61	0.570093	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	427	0.1955128205128205	139	0.28252032520325204	75	0.20718232044198895	71	0.12412587412587413	142	0.18733509234828497	T	0.599	-0.829686	0.02734	0.244439	0.182209	ENSG00000244607	ENST00000310232	T	0.10573	2.86	5.76	-3.26	0.05064	.	0.453819	0.24400	N	0.038850	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	9	0.12766	T	0.61	.	10.1473	0.42771	0.1103:0.5632:0.0:0.3265	rs12495805;rs52834773;rs12495805	547	Q8IYE1	CCD13_HUMAN	T	547	ENSP00000309836:S547T	ENSP00000309836:S547T	S	-	1	0	CCDC13	42747042	0.002000	0.14202	0.006000	0.13384	0.575000	0.36095	-0.454000	0.06770	-0.933000	0.03737	-1.051000	0.02340	TCA	A|0.792;T|0.208	0.208	strong		0.592	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
THBS1	7057	hgsc.bcm.edu	37	15	39885301	39885301	+	Silent	SNP	T	T	C	rs2228263	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:39885301T>C	ENST00000260356.5	+	18	3033	c.2868T>C	c.(2866-2868)gaT>gaC	p.D956D	CTD-2033D15.1_ENST00000560769.1_RNA	NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	956					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		GTGAGACCGATTTCCGCCGAT	0.502													T|||	574	0.114617	0.2224	0.1037	5008	,	,		20624	0.002		0.159	False		,,,				2504	0.047				p.D956D		Atlas-SNP	.											.	THBS1	106	.	0			c.T2868C						PASS	.	T		920,3480	351.3+/-311.2	108,704,1388	81.0	69.0	73.0		2868	2.2	1.0	15	dbSNP_98	73	1461,7133	277.5+/-292.9	110,1241,2946	no	coding-synonymous	THBS1	NM_003246.2		218,1945,4334	CC,CT,TT		17.0002,20.9091,18.3238		956/1171	39885301	2381,10613	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon18			GACCGATTTCCGC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.2868T>C	15.37:g.39885301T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			T|0.841;C|0.159	0.159	strong		0.502	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
MMP20	9313	hgsc.bcm.edu	37	11	102495998	102495998	+	Missense_Mutation	SNP	T	T	G	rs2245803	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102495998T>G	ENST00000260228.2	-	1	65	c.53A>C	c.(52-54)aAg>aCg	p.K18T	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	0					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	AGTGGAAAACTTCAAAGCCAT	0.537													T|||	3388	0.676518	0.6036	0.6816	5008	,	,		16935	0.8016		0.6262	False		,,,				2504	0.6943				p.K18T		Atlas-SNP	.											.	MMP20	52	.	0			c.A53C						PASS	.	T	THR/LYS	2751,1655	657.1+/-400.2	857,1037,309	129.0	103.0	112.0		53	4.1	0.7	11	dbSNP_100	112	5538,3060	660.5+/-401.8	1773,1992,534	yes	missense	MMP20	NM_004771.3	78	2630,3029,843	GG,GT,TT		35.5897,37.5624,36.2581	benign	18/484	102495998	8289,4715	2203	4299	6502	SO:0001583	missense	9313	exon1			GAAAACTTCAAAG	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.53A>C	11.37:g.102495998T>G	ENSP00000260228:p.Lys18Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	82	15	0.182927	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	1483	0.6790293040293041	301	0.6117886178861789	247	0.6823204419889503	462	0.8076923076923077	473	0.6240105540897097	T	5.964	0.361845	0.11296	0.624376	0.644103	ENSG00000137674	ENST00000260228	T	0.12774	2.65	5.26	4.12	0.48240	.	1.072100	0.07112	N	0.842373	T	0.00012	0.0000	N	0.08118	0	0.36335	P	0.14090899999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.25984	-1.0116	9	0.12766	T	0.61	.	11.56	0.50772	0.0:0.0:0.1499:0.8501	rs2245803;rs11565201;rs17099166;rs58085681;rs2245803	18	O60882	MMP20_HUMAN	T	18	ENSP00000260228:K18T	ENSP00000260228:K18T	K	-	2	0	MMP20	102001208	0.997000	0.39634	0.727000	0.30756	0.562000	0.35680	2.004000	0.40854	0.999000	0.39023	0.460000	0.39030	AAG	T|0.342;G|0.658	0.658	strong		0.537	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
FAM178B	51252	hgsc.bcm.edu	37	2	97559759	97559759	+	Silent	SNP	G	G	A	rs11677797	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:97559759G>A	ENST00000417561.3	-	18	2123	c.2124C>T	c.(2122-2124)ctC>ctT	p.L708L	FAM178B_ENST00000393526.2_5'UTR|FAM178B_ENST00000470789.1_5'UTR|FAM178B_ENST00000490605.2_Silent_p.L560L|FAM178B_ENST00000327896.3_Silent_p.L528L			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	708										large_intestine(1)|ovary(1)	2						ATGGCCTCATGAGGCCCAGGA	0.622													.|||	2146	0.428514	0.236	0.4424	5008	,	,		17897	0.6766		0.1491	False		,,,				2504	0.7106				p.L560L		Atlas-SNP	.											.	FAM178B	35	.	0			c.C1680T						PASS	.	G	,,	1122,3282	394.7+/-329.4	151,820,1231	65.0	59.0	61.0		1680,57,	2.6	1.0	2	dbSNP_120	61	1572,7024	290.9+/-300.1	138,1296,2864	no	coding-synonymous,coding-synonymous,utr-5	FAM178B	NM_001122646.2,NM_001172667.1,NM_016490.4	,,	289,2116,4095	AA,AG,GG		18.2876,25.4768,20.7231	,,	560/680,19/139,	97559759	2694,10306	2202	4298	6500	SO:0001819	synonymous_variant	51252	exon14			CCTCATGAGGCCC	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.2124C>T	2.37:g.97559759G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Silent	SNP	ENST00000417561.3	37																																																																																				G|0.745;A|0.255	0.255	strong		0.622	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
FANK1	92565	hgsc.bcm.edu	37	10	127585221	127585221	+	Nonsense_Mutation	SNP	C	C	T	rs202109621		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127585221C>T	ENST00000368693.1	+	1	114	c.10C>T	c.(10-12)Cag>Tag	p.Q4*	FANK1_ENST00000368695.1_5'UTR|FANK1_ENST00000449042.2_5'UTR			Q8TC84	FANK1_HUMAN	fibronectin type III and ankyrin repeat domains 1	4						cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(10)|ovary(1)|urinary_tract(1)	21		all_lung(145;0.00752)|Lung NSC(174;0.0115)|Colorectal(57;0.0847)|all_neural(114;0.0936)				CATGGAGCCCCAGAGTAAGGg	0.756																																					p.Q4X		Atlas-SNP	.											.	FANK1	46	.	0			c.C10T						PASS	.						8.0	12.0	11.0					10																	127585221		2169	4258	6427	SO:0001587	stop_gained	92565	exon1			GAGCCCCAGAGTA	BC024189	CCDS31309.1	10q26.2	2013-02-11	2005-03-01		ENSG00000203780	ENSG00000203780		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	23527	protein-coding gene	gene with protein product		611640	"""fibronectin type 3 and ankyrin repeat domains 1"""			12477932	Standard	NM_145235		Approved		uc001ljh.4	Q8TC84	OTTHUMG00000019241	ENST00000368693.1:c.10C>T	10.37:g.127585221C>T	ENSP00000357682:p.Gln4*	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	31	4	0.129032	NM_145235	Q6UXY9|Q6X7T6	Nonsense_Mutation	SNP	ENST00000368693.1	37	CCDS31309.1	.	.	.	.	.	.	.	.	.	.	C	32	5.122908	0.94429	.	.	ENSG00000203780	ENST00000368693	.	.	.	2.62	1.68	0.24146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	6.8436	0.23977	0.274:0.726:0.0:0.0	.	.	.	.	X	4	.	ENSP00000357682:Q4X	Q	+	1	0	FANK1	127575211	1.000000	0.71417	0.999000	0.59377	0.552000	0.35366	1.578000	0.36525	0.621000	0.30232	0.462000	0.41574	CAG	.	.	weak		0.756	FANK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145235	
PWP1	11137	hgsc.bcm.edu	37	12	108096769	108096769	+	Missense_Mutation	SNP	G	G	C	rs11547907	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:108096769G>C	ENST00000412830.3	+	9	1032	c.864G>C	c.(862-864)ttG>ttC	p.L288F	PWP1_ENST00000541166.1_Missense_Mutation_p.L226F	NM_007062.1	NP_008993.1	Q13610	PWP1_HUMAN	PWP1 homolog (S. cerevisiae)	288			L -> F (in dbSNP:rs11547907).		transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(3)|endometrium(4)|kidney(1)|large_intestine(8)|lung(6)|urinary_tract(1)	23						ATATGTCCTTGGGGAAACCAG	0.403													G|||	226	0.0451278	0.0098	0.0245	5008	,	,		17751	0.0774		0.0348	False		,,,				2504	0.0849				p.L288F		Atlas-SNP	.											.	PWP1	43	.	0			c.G864C						PASS	.	G	PHE/LEU	84,4322	72.0+/-110.0	2,80,2121	121.0	111.0	114.0		864	4.8	1.0	12	dbSNP_120	114	340,8260	117.6+/-177.1	5,330,3965	yes	missense	PWP1	NM_007062.1	22	7,410,6086	CC,CG,GG		3.9535,1.9065,3.26	benign	288/502	108096769	424,12582	2203	4300	6503	SO:0001583	missense	11137	exon9			GTCCTTGGGGAAA	BC000067	CCDS9114.1	12q23.3	2013-06-10				ENSG00000136045		"""WD repeat domain containing"""	17015	protein-coding gene	gene with protein product	"""endonuclein"""					7828893, 11850830	Standard	NM_007062		Approved	IEF-SSP-9502	uc001tmo.1	Q13610	OTTHUMG00000169913	ENST00000412830.3:c.864G>C	12.37:g.108096769G>C	ENSP00000387365:p.Leu288Phe	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_007062	A8K3R6|Q7Z3X9	Missense_Mutation	SNP	ENST00000412830.3	37	CCDS9114.1	87	0.03983516483516483	11	0.022357723577235773	11	0.03038674033149171	37	0.06468531468531469	28	0.036939313984168866	G	14.02	2.410319	0.42715	0.019065	0.039535	ENSG00000136045	ENST00000412830;ENST00000258531;ENST00000541166	T;T	0.29142	1.58;2.23	5.71	4.82	0.62117	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.543212	0.20171	N	0.097733	T	0.02418	0.0074	L	0.27053	0.805	0.29613	N	0.846797	B	0.17667	0.023	B	0.25140	0.058	T	0.04767	-1.0928	10	0.56958	D	0.05	.	8.9358	0.35700	0.2248:0.0:0.7752:0.0	rs11547907;rs52791867;rs11547907	288	Q13610	PWP1_HUMAN	F	288;288;226	ENSP00000387365:L288F;ENSP00000445249:L226F	ENSP00000258531:L288F	L	+	3	2	PWP1	106620899	1.000000	0.71417	0.991000	0.47740	0.961000	0.63080	2.422000	0.44696	1.422000	0.47177	-0.140000	0.14226	TTG	G|0.964;C|0.036	0.036	strong		0.403	PWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406539.1	NM_007062	
ARNT	405	hgsc.bcm.edu	37	1	150789884	150789884	+	Missense_Mutation	SNP	C	C	T	rs1805133	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:150789884C>T	ENST00000358595.5	-	16	1731	c.1531G>A	c.(1531-1533)Gac>Aac	p.D511N	ARNT_ENST00000354396.2_Missense_Mutation_p.D511N|ARNT_ENST00000505755.1_Missense_Mutation_p.D496N|ARNT_ENST00000515192.1_Missense_Mutation_p.D497N	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	511			D -> N (in dbSNP:rs1805133).		cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGTACCATGTCCAATTCTGTT	0.408			T	ETV6	AML								C|||	8	0.00159744	0.0	0.0043	5008	,	,		17959	0.0		0.005	False		,,,				2504	0.0				p.D511N		Atlas-SNP	.		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	.	ARNT	68	.	0			c.G1531A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	10,4396	16.8+/-37.8	0,10,2193	155.0	133.0	140.0		1486,1531,1486	5.6	1.0	1	dbSNP_89	140	81,8519	47.6+/-106.9	1,79,4220	yes	missense,missense,missense	ARNT	NM_001197325.1,NM_001668.3,NM_178427.2	23,23,23	1,89,6413	TT,TC,CC		0.9419,0.227,0.6997	benign,benign,benign	496/774,511/790,496/775	150789884	91,12915	2203	4300	6503	SO:0001583	missense	405	exon16			CCATGTCCAATTC	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"""Basic helix-loop-helix proteins"""	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.1531G>A	1.37:g.150789884C>T	ENSP00000351407:p.Asp511Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_001668	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Missense_Mutation	SNP	ENST00000358595.5	37	CCDS970.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	18.40	3.614958	0.66672	0.00227	0.009419	ENSG00000143437	ENST00000358595;ENST00000354396;ENST00000515192;ENST00000394700;ENST00000505755	T;T;T;T	0.05382	3.56;3.53;3.56;3.45	5.6	5.6	0.85130	.	0.979822	0.08335	N	0.961696	T	0.05456	0.0144	L	0.54323	1.7	0.58432	D	0.999997	P;B;B;B;B	0.36753	0.568;0.38;0.38;0.38;0.258	B;B;B;B;B	0.33846	0.168;0.171;0.171;0.171;0.064	T	0.48536	-0.9027	10	0.36615	T	0.2	.	19.6047	0.95576	0.0:1.0:0.0:0.0	rs1805133	496;511;497;496;511	A8K6P0;F8WAP6;P27540-3;P27540-2;P27540	.;.;.;.;ARNT_HUMAN	N	511;511;497;463;496	ENSP00000351407:D511N;ENSP00000346372:D511N;ENSP00000423851:D497N;ENSP00000427571:D496N	ENSP00000346372:D511N	D	-	1	0	ARNT	149056508	0.999000	0.42202	0.957000	0.39632	0.990000	0.78478	4.476000	0.60216	2.638000	0.89438	0.591000	0.81541	GAC	C|0.994;T|0.006	0.006	strong		0.408	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2		
MYOM2	9172	hgsc.bcm.edu	37	8	2005883	2005883	+	Missense_Mutation	SNP	C	C	T	rs17064618	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:2005883C>T	ENST00000262113.4	+	5	686	c.545C>T	c.(544-546)aCg>aTg	p.T182M	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	182	Ig-like C2-type 1.		T -> M (in dbSNP:rs17064618).		muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GGATTTCCCACGCCCGTGGTG	0.562													C|||	313	0.0625	0.1445	0.049	5008	,	,		15859	0.0367		0.0348	False		,,,				2504	0.0164				p.T182M		Atlas-SNP	.											.	MYOM2	251	.	0			c.C545T						PASS	.	C	MET/THR	587,3819	259.8+/-263.3	37,513,1653	70.0	67.0	68.0		545	3.7	0.5	8	dbSNP_123	68	419,8181	131.2+/-189.0	8,403,3889	yes	missense	MYOM2	NM_003970.2	81	45,916,5542	TT,TC,CC		4.8721,13.3227,7.7349	probably-damaging	182/1466	2005883	1006,12000	2203	4300	6503	SO:0001583	missense	9172	exon5			TTCCCACGCCCGT		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.545C>T	8.37:g.2005883C>T	ENSP00000262113:p.Thr182Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	110	0.05036630036630037	61	0.12398373983739837	17	0.04696132596685083	9	0.015734265734265736	23	0.030343007915567283	C	11.19	1.566768	0.28003	0.133227	0.048721	ENSG00000036448	ENST00000262113	T	0.68624	-0.34	4.62	3.74	0.42951	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.339710	0.28062	N	0.016760	T	0.01730	0.0055	L	0.58302	1.8	0.09310	P	1.0	D	0.57571	0.98	P	0.51895	0.683	T	0.45175	-0.9279	9	0.54805	T	0.06	.	13.7064	0.62641	0.1556:0.8444:0.0:0.0	rs17064618;rs52804853;rs17064618	182	P54296	MYOM2_HUMAN	M	182	ENSP00000262113:T182M	ENSP00000262113:T182M	T	+	2	0	MYOM2	1993290	0.826000	0.29277	0.532000	0.27989	0.194000	0.23727	2.735000	0.47377	0.918000	0.36919	-0.310000	0.09108	ACG	C|0.929;T|0.071	0.071	strong		0.562	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
SETMAR	6419	hgsc.bcm.edu	37	3	4354697	4354697	+	Missense_Mutation	SNP	G	G	A	rs6801634	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:4354697G>A	ENST00000358065.4	+	2	339	c.272G>A	c.(271-273)cGc>cAc	p.R91H	SETMAR_ENST00000430981.1_Missense_Mutation_p.R91H|SETMAR_ENST00000425863.1_Missense_Mutation_p.R91H|SETMAR_ENST00000462115.1_3'UTR|SUMF1_ENST00000534863.1_Intron	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	91	Histone-lysine N-methyltransferase.|Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.			R -> H (in Ref. 1; BAG63636). {ECO:0000305}.	DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		TCCTGTCTCCGCCATGGAGAG	0.483								Chromatin Structure					G|||	609	0.121605	0.1014	0.1167	5008	,	,		18899	0.0982		0.16	False		,,,				2504	0.137				p.R91H		Atlas-SNP	.											.	SETMAR	30	.	0			c.G272A						PASS	.	G	HIS/ARG	458,3948	220.4+/-237.8	24,410,1769	84.0	76.0	79.0		272	1.0	0.8	3	dbSNP_116	79	1215,7385	245.6+/-274.3	70,1075,3155	yes	missense	SETMAR	NM_006515.3	29	94,1485,4924	AA,AG,GG		14.1279,10.3949,12.8633	possibly-damaging	91/685	4354697	1673,11333	2203	4300	6503	SO:0001583	missense	6419	exon2			GTCTCCGCCATGG	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.272G>A	3.37:g.4354697G>A	ENSP00000373354:p.Arg91His	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	126	51	0.404762	NM_001243723	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	37	CCDS2563.2	273	0.125	54	0.10975609756097561	43	0.11878453038674033	54	0.0944055944055944	122	0.16094986807387862	G	9.041	0.989745	0.18966	0.103949	0.141279	ENSG00000170364	ENST00000358065;ENST00000430981;ENST00000425863	D;D;T	0.89552	-2.53;-2.53;-1.09	5.13	1.01	0.19927	Pre-SET zinc-binding sub-group (1);Pre-SET domain (2);	.	.	.	.	T	0.01124	0.0037	M	0.64567	1.98	0.58432	P	1.0000000000287557E-6	P;P;B	0.43750	0.816;0.699;0.031	B;B;B	0.29716	0.106;0.058;0.006	T	0.41680	-0.9495	8	0.56958	D	0.05	.	3.9103	0.09201	0.1543:0.1976:0.5295:0.1185	rs6801634;rs52791578;rs58831512;rs6801634	91;78;91	E7EN68;Q53H47;C9JHK2	.;SETMR_HUMAN;.	H	91	ENSP00000373354:R91H;ENSP00000403000:R91H;ENSP00000403145:R91H	ENSP00000373354:R91H	R	+	2	0	SETMAR	4329697	0.003000	0.15002	0.809000	0.32408	0.376000	0.30014	0.089000	0.15002	0.571000	0.29365	-0.262000	0.10625	CGC	G|0.871;A|0.129	0.129	strong		0.483	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515	
REM1	28954	hgsc.bcm.edu	37	20	30070239	30070239	+	Silent	SNP	C	C	A	rs2233832	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:30070239C>A	ENST00000201979.2	+	4	866	c.573C>A	c.(571-573)atC>atA	p.I191I		NM_014012.4	NP_054731.2	O75628	REM1_HUMAN	RAS (RAD and GEM)-like GTP-binding 1	191					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			kidney(3)|large_intestine(3)|lung(14)|pancreas(2)|upper_aerodigestive_tract(1)	23	all_cancers(5;0.000119)|Lung NSC(7;1.32e-05)|all_lung(7;2.14e-05)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TGCCCATCATCCTCGTGGGCA	0.607													C|||	711	0.141973	0.0764	0.1383	5008	,	,		20109	0.246		0.0905	False		,,,				2504	0.1789				p.I191I		Atlas-SNP	.											.	REM1	54	.	0			c.C573A						PASS	.	C		422,3984	206.5+/-228.1	21,380,1802	89.0	78.0	82.0		573	5.0	1.0	20	dbSNP_98	82	718,7882	175.6+/-225.6	27,664,3609	no	coding-synonymous	REM1	NM_014012.4		48,1044,5411	AA,AC,CC		8.3488,9.5778,8.7652		191/299	30070239	1140,11866	2203	4300	6503	SO:0001819	synonymous_variant	28954	exon4			CATCATCCTCGTG	AF152863	CCDS13181.1	20q11.21	2014-05-09	2004-04-14	2004-04-16	ENSG00000088320	ENSG00000088320			15922	protein-coding gene	gene with protein product	"""GTPase GES"""	610388	"""RAS (RAD and GEM)-like GTP-binding"""	REM		10831614, 14623965	Standard	NM_014012		Approved	GES	uc002wwa.3	O75628	OTTHUMG00000032168	ENST00000201979.2:c.573C>A	20.37:g.30070239C>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_014012	E1P5L1|Q5TZR7|Q5TZR8|Q9NP57	Silent	SNP	ENST00000201979.2	37	CCDS13181.1																																																																																			C|0.886;A|0.114	0.114	strong		0.607	REM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078508.2	NM_014012	
POTEB2	100287399	hgsc.bcm.edu	37	15	21071492	21071492	+	Missense_Mutation	SNP	G	G	T	rs536533463	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:21071492G>T	ENST00000454856.4	-	1	151	c.119C>A	c.(118-120)aCg>aAg	p.T40K		NM_001277303.1	NP_001264232.1	H3BUK9	POTB2_HUMAN	POTE ankyrin domain family, member B2	40																	CACATTGCTCGTGCCGCTCCC	0.582													G|||	2239	0.447085	0.4206	0.513	5008	,	,		15782	0.4742		0.4274	False		,,,				2504	0.4284				p.T40K		Atlas-SNP	.											ENSG00000230031,NS,carcinoid-endocrine_tumour,0,1	POTEB	22	1	0			c.C119A						scavenged	.																																			SO:0001583	missense	339010	exon1			TTGCTCGTGCCGC		CCDS59248.1	15q11.2	2014-01-29			ENSG00000230031	ENSG00000230031		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	48327	protein-coding gene	gene with protein product							Standard	NM_001277303		Approved			H3BUK9	OTTHUMG00000185829	ENST00000454856.4:c.119C>A	15.37:g.21071492G>T	ENSP00000456953:p.Thr40Lys	Somatic	154	42	0.272727		WXS	Illumina HiSeq	Phase_I	156	104	0.666667	NM_207355		Missense_Mutation	SNP	ENST00000454856.4	37	CCDS59248.1																																																																																			.	.	weak		0.582	POTEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471435.1		
AIM1	202	hgsc.bcm.edu	37	6	106967778	106967778	+	Missense_Mutation	SNP	T	T	C	rs3747787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:106967778T>C	ENST00000369066.3	+	2	1958	c.1471T>C	c.(1471-1473)Tgc>Cgc	p.C491R		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CAGTTTCCCATGCACTGATCT	0.458													T|||	872	0.174121	0.1808	0.1354	5008	,	,		22330	0.1161		0.2515	False		,,,				2504	0.1728				p.C491R		Atlas-SNP	.											.	AIM1	161	.	0			c.T1471C						PASS	.	T	ARG/CYS	733,3673	297.8+/-285.0	58,617,1528	83.0	89.0	87.0		1471	-5.8	0.0	6	dbSNP_107	87	2104,6496	356.3+/-330.2	259,1586,2455	yes	missense	AIM1	NM_001624.2	180	317,2203,3983	CC,CT,TT		24.4651,16.6364,21.813	benign	491/1724	106967778	2837,10169	2203	4300	6503	SO:0001583	missense	202	exon2			TTCCCATGCACTG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.1471T>C	6.37:g.106967778T>C	ENSP00000358062:p.Cys491Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	390	0.17857142857142858	92	0.18699186991869918	57	0.1574585635359116	56	0.0979020979020979	185	0.24406332453825857	T	10.37	1.330824	0.24167	0.166364	0.244651	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.71341	-0.56	6.17	-5.75	0.02384	.	1.231230	0.05863	N	0.623317	T	0.23210	0.0561	N	0.20685	0.6	0.53005	P	3.500000000000725E-5	B	0.06786	0.001	B	0.06405	0.002	T	0.05131	-1.0904	9	0.23891	T	0.37	.	2.4107	0.04423	0.2004:0.1489:0.4535:0.1972	rs3747787;rs17495394;rs52819883;rs58298313;rs3747787	491	Q9Y4K1	AIM1_HUMAN	R	899;491	ENSP00000358062:C491R	ENSP00000285105:C899R	C	+	1	0	AIM1	107074471	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.826000	0.04429	-0.749000	0.04747	0.533000	0.62120	TGC	T|0.805;C|0.195	0.195	strong		0.458	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
MUC2	4583	hgsc.bcm.edu	37	11	1092891	1092891	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1092891C>A	ENST00000441003.2	+	30	4737	c.4710C>A	c.(4708-4710)acC>acA	p.T1570T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1571T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				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)		p.T1571T(1)|p.T1570T(1)		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)	CCACGGTGaccccaaccccaa	0.642																																					p.T1570T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - coding silent(2)	ovary(2)	c.C4710A						PASS	.						116.0	157.0	142.0					11																	1092891		1961	3652	5613	SO:0001819	synonymous_variant	4583	exon30			GGTGACCCCAACC	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.4710C>A	11.37:g.1092891C>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	4	0.097561	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ATP8B3	148229	hgsc.bcm.edu	37	19	1806667	1806667	+	Missense_Mutation	SNP	C	C	T	rs45574836	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1806667C>T	ENST00000310127.6	-	7	875	c.637G>A	c.(637-639)Gcc>Acc	p.A213T	ATP8B3_ENST00000526092.2_Missense_Mutation_p.A160T|ATP8B3_ENST00000525591.1_Missense_Mutation_p.A160T|ATP8B3_ENST00000539485.1_Missense_Mutation_p.A213T	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	213					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		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)		TTGTTGATGGCTCTGTCACTC	0.667													c|||	310	0.061901	0.0136	0.0504	5008	,	,		13981	0.0942		0.0606	False		,,,				2504	0.1033				p.A213T		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G637A						PASS	.	C	THR/ALA,THR/ALA	49,4023		0,49,1987	42.0	49.0	47.0		478,637	-8.1	0.0	19	dbSNP_127	47	373,7911		8,357,3777	yes	missense,missense	ATP8B3	NM_001178002.1,NM_138813.2	58,58	8,406,5764	TT,TC,CC		4.5027,1.2033,3.4153	benign,benign	160/1264,213/1301	1806667	422,11934	2036	4142	6178	SO:0001583	missense	148229	exon7			TGATGGCTCTGTC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.637G>A	19.37:g.1806667C>T	ENSP00000311336:p.Ala213Thr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	129	0.059065934065934064	7	0.014227642276422764	14	0.03867403314917127	61	0.10664335664335664	47	0.06200527704485488	c	9.701	1.154504	0.21371	0.012033	0.045027	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591;ENST00000526092;ENST00000382339	D;D;D;D	0.90197	-2.63;-2.63;-2.63;-2.63	4.08	-8.15	0.01065	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	2.158490	0.02032	N	0.048604	T	0.09598	0.0236	L	0.31752	0.955	0.09310	N	1	B;B;B	0.25719	0.132;0.01;0.03	B;B;B	0.23574	0.047;0.018;0.018	T	0.61686	-0.7012	10	0.33940	T	0.23	.	9.4352	0.38635	0.0939:0.3028:0.0:0.6033	rs45574836	160;213;160	F5H3R9;O60423;Q7Z485	.;AT8B3_HUMAN;.	T	213;213;160;160;160	ENSP00000311336:A213T;ENSP00000443574:A213T;ENSP00000437115:A160T;ENSP00000445204:A160T	ENSP00000311336:A213T	A	-	1	0	ATP8B3	1757667	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	-1.593000	0.02096	-1.983000	0.00987	-2.069000	0.00389	GCC	C|0.941;T|0.059	0.059	strong		0.667	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
ERCC5	2073	hgsc.bcm.edu	37	13	103504517	103504517	+	Silent	SNP	T	T	C	rs1047768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103504517T>C	ENST00000355739.4	+	2	1561	c.138T>C	c.(136-138)caT>caC	p.H46H	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.W472R|ERCC5_ENST00000535557.1_Silent_p.H46H	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	46	N-domain.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GGGATCGCCATGGGAACTCAA	0.393			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	2469	0.493011	0.6778	0.3991	5008	,	,		14964	0.25		0.5845	False		,,,				2504	0.4663				p.H500H		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	.	.	.	.	0			c.T1500C						PASS	.	C	,	2912,1494	478.3+/-358.2	970,972,261	148.0	149.0	149.0		138,1500	-0.4	0.9	13	dbSNP_86	149	5045,3555	516.8+/-378.9	1464,2117,719	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	2434,3089,980	CC,CT,TT		41.3372,33.9083,38.8205	,	46/1187,500/1641	103504517	7957,5049	2203	4300	6503	SO:0001819	synonymous_variant	0	exon10	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TCGCCATGGGAAC	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.138T>C	13.37:g.103504517T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			T|0.449;C|0.551	0.551	strong		0.393	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
IBSP	3381	hgsc.bcm.edu	37	4	88732763	88732763	+	Missense_Mutation	SNP	A	A	G	rs17013181	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88732763A>G	ENST00000226284.5	+	7	722	c.655A>G	c.(655-657)Agg>Ggg	p.R219G		NM_004967.3	NP_004958.2	P21815	SIAL_HUMAN	integrin-binding sialoprotein	219			R -> G (in dbSNP:rs17013181). {ECO:0000269|PubMed:2404984, ECO:0000269|PubMed:8406493}.		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cellular response to growth factor stimulus (GO:0071363)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)	21		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000333)|COAD - Colon adenocarcinoma(81;0.154)		AGAGACCGGAAGGCAGGGCAA	0.537													G|||	1302	0.259984	0.3979	0.2651	5008	,	,		18038	0.2302		0.1928	False		,,,				2504	0.1697				p.R219G		Atlas-SNP	.											.	IBSP	53	.	0			c.A655G						PASS	.	G	GLY/ARG	1590,2816	662.4+/-401.0	293,1004,906	135.0	134.0	134.0		655	3.3	0.0	4	dbSNP_123	134	1890,6710	726.8+/-406.6	208,1474,2618	yes	missense	IBSP	NM_004967.3	125	501,2478,3524	GG,GA,AA		21.9767,36.0872,26.7569	benign	219/318	88732763	3480,9526	2203	4300	6503	SO:0001583	missense	3381	exon7			ACCGGAAGGCAGG		CCDS3624.1	4q21.1	2008-07-28	2008-07-28		ENSG00000029559	ENSG00000029559			5341	protein-coding gene	gene with protein product	"""bone sialoprotein"", ""bone sialoprotein II"""	147563				8406493	Standard	NM_004967		Approved	BSP, SP-II, BSP-II	uc003hqx.4	P21815	OTTHUMG00000130600	ENST00000226284.5:c.655A>G	4.37:g.88732763A>G	ENSP00000226284:p.Arg219Gly	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_004967		Missense_Mutation	SNP	ENST00000226284.5	37	CCDS3624.1	579	0.2651098901098901	210	0.4268292682926829	97	0.26795580110497236	127	0.22202797202797203	145	0.19129287598944592	G	7.604	0.673451	0.14776	0.360872	0.219767	ENSG00000029559	ENST00000226284	T	0.11930	2.73	4.15	3.27	0.37495	.	1.270430	0.05318	N	0.526129	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48490	-0.9031	9	0.24483	T	0.36	.	7.4088	0.27006	0.2177:0.0:0.7823:0.0	rs17013181;rs52811255;rs57322105;rs17013181	219	P21815	SIAL_HUMAN	G	219	ENSP00000226284:R219G	ENSP00000226284:R219G	R	+	1	2	IBSP	88951787	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	0.404000	0.20999	0.478000	0.27488	-0.186000	0.12905	AGG	A|0.733;G|0.267	0.267	strong		0.537	IBSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253050.2		
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 GAIIx	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		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	51	29	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
DMBT1	1755	hgsc.bcm.edu	37	10	124339378	124339378	+	Missense_Mutation	SNP	A	A	G	rs1969620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124339378A>G	ENST00000338354.3	+	10	1070	c.964A>G	c.(964-966)Aac>Gac	p.N322D	DMBT1_ENST00000368909.3_Missense_Mutation_p.N322D|DMBT1_ENST00000368956.2_Missense_Mutation_p.N322D|DMBT1_ENST00000368955.3_Missense_Mutation_p.N322D|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.N322D|DMBT1_ENST00000330163.4_Missense_Mutation_p.N322D			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	322	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		N -> D (in dbSNP:rs1969620). {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)				GCTCACCCACAACTGTGGCCA	0.567													A|||	507	0.101238	0.1339	0.0951	5008	,	,		19316	0.1994		0.006	False		,,,				2504	0.0583				p.N322D	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.A964G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN	385,3441		18,349,1546	84.0	83.0	84.0		964,964,964	3.9	0.7	10	dbSNP_92	84	71,8213		0,71,4071	no	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	23,23,23	18,420,5617	GG,GA,AA		0.8571,10.0627,3.7655	benign,benign,benign	322/1786,322/2414,322/2404	124339378	456,11654	1913	4142	6055	SO:0001583	missense	1755	exon10			ACCCACAACTGTG		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.964A>G	10.37:g.124339378A>G	ENSP00000342210:p.Asn322Asp	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	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		222	0.10164835164835165	62	0.12601626016260162	30	0.08287292817679558	128	0.22377622377622378	2	0.002638522427440633	A	17.31	3.357713	0.61403	0.100627	0.008571	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9	3.94	3.94	0.45596	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.00039	0.0001	L	0.52011	1.625	0.09310	P	1.0	B;D;B;D;B	0.62365	0.31;0.989;0.211;0.991;0.231	P;D;B;D;P	0.80764	0.617;0.987;0.165;0.994;0.65	T	0.02646	-1.1129	8	0.38643	T	0.18	.	13.1512	0.59490	1.0:0.0:0.0:0.0	rs1969620;rs3980989;rs52823791;rs1969620	322;322;322;322;322	Q9UGM3-4;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	D	322	ENSP00000342210:N322D;ENSP00000343175:N322D;ENSP00000327747:N322D;ENSP00000357905:N322D;ENSP00000357951:N322D;ENSP00000357952:N322D	ENSP00000331522:N322D	N	+	1	0	DMBT1	124329368	0.999000	0.42202	0.730000	0.30809	0.034000	0.12701	4.137000	0.58010	1.580000	0.49851	0.414000	0.27820	AAC	A|0.909;G|0.091	0.091	strong		0.567	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907633	12907633	+	Silent	SNP	G	G	A	rs75660350	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907633G>A	ENST00000317869.6	-	2	735	c.510C>T	c.(508-510)tcC>tcT	p.S170S		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	170						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						TTCCAGACTTGGAAGATCCCC	0.468																																					p.S170S		Atlas-SNP	.											.	HNRNPCL1	68	.	0			c.C510T						PASS	.	G		93,4305		1,91,2107	149.0	161.0	157.0		510	1.1	0.8	1	dbSNP_131	157	374,8208		4,366,3921	no	coding-synonymous	HNRNPCL1	NM_001013631.1		5,457,6028	AA,AG,GG		4.358,2.1146,3.5978		170/294	12907633	467,12513	2199	4291	6490	SO:0001819	synonymous_variant	343069	exon2			AGACTTGGAAGAT	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.510C>T	1.37:g.12907633G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	156	45	0.288462	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	37	CCDS30591.1																																																																																			G|0.950;A|0.050	0.050	strong		0.468	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
WDR93	56964	hgsc.bcm.edu	37	15	90245174	90245174	+	Missense_Mutation	SNP	T	T	A	rs4287542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90245174T>A	ENST00000268130.7	+	2	298	c.197T>A	c.(196-198)cTt>cAt	p.L66H	WDR93_ENST00000558000.1_Missense_Mutation_p.L66H|RP11-300G22.2_ENST00000557964.1_RNA|WDR93_ENST00000560294.1_Missense_Mutation_p.L66H	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	66			L -> H (in dbSNP:rs4287542).		electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CTGGTGAACCTTCTGTTTGAC	0.502													T|||	1963	0.391973	0.5061	0.3617	5008	,	,		20048	0.2063		0.4026	False		,,,				2504	0.4397				p.L66H		Atlas-SNP	.											.	WDR93	63	.	0			c.T197A						PASS	.	T	HIS/LEU	2141,2259	581.7+/-385.4	529,1083,588	88.0	78.0	82.0		197	0.1	0.0	15	dbSNP_111	82	3848,4750	541.6+/-384.0	846,2156,1297	yes	missense	WDR93	NM_020212.1	99	1375,3239,1885	AA,AT,TT		44.7546,48.6591,46.0763	benign	66/687	90245174	5989,7009	2200	4299	6499	SO:0001583	missense	56964	exon2			TGAACCTTCTGTT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.197T>A	15.37:g.90245174T>A	ENSP00000268130:p.Leu66His	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	115	113	0.982609	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	787	0.36034798534798534	218	0.44308943089430897	141	0.38950276243093923	124	0.21678321678321677	304	0.40105540897097625	T	1.654	-0.513158	0.04200	0.486591	0.447546	ENSG00000140527	ENST00000268130	T	0.22134	1.97	5.59	0.0743	0.14394	.	0.586451	0.15989	N	0.234922	T	0.00012	0.0000	N	0.12746	0.255	0.58432	P	4.000000000004E-6	B;B;B	0.20261	0.01;0.043;0.01	B;B;B	0.18561	0.01;0.022;0.01	T	0.45352	-0.9267	9	0.13470	T	0.59	-1.9233	1.6993	0.02869	0.4348:0.0838:0.1407:0.3407	rs4287542;rs57513749;rs4287542	66;66;66	Q6P2C0-2;B4E3E2;Q6P2C0	.;.;WDR93_HUMAN	H	66	ENSP00000268130:L66H	ENSP00000268130:L66H	L	+	2	0	WDR93	88046178	0.011000	0.17503	0.008000	0.14137	0.289000	0.27227	-0.054000	0.11826	0.039000	0.15632	0.528000	0.53228	CTT	T|0.574;A|0.426	0.426	strong		0.502	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520254	72520254	+	Missense_Mutation	SNP	C	C	T	rs61736607	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72520254C>T	ENST00000373207.1	+	22	3317	c.3317C>T	c.(3316-3318)cCt>cTt	p.P1106L	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.P1109L	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1106	Pro-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						ggcccagaccctggcccaacc	0.637													C|||	140	0.0279553	0.0038	0.0461	5008	,	,		15277	0.001		0.0805	False		,,,				2504	0.0215				p.P1109L		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.C3326T						PASS	.	C	LEU/PRO,LEU/PRO	62,4344	57.4+/-93.9	1,60,2142	54.0	52.0	53.0		3317,3326	3.5	0.0	10	dbSNP_129	53	733,7867	177.2+/-226.9	35,663,3602	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	98,98	36,723,5744	TT,TC,CC		8.5233,1.4072,6.1126	benign,benign	1106/1224,1109/1227	72520254	795,12211	2203	4300	6503	SO:0001583	missense	140766	exon22			CAGACCCTGGCCC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3317C>T	10.37:g.72520254C>T	ENSP00000362303:p.Pro1106Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	78	0.03571428571428571	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	55	0.07255936675461741	C	9.658	1.143274	0.21205	0.014072	0.085233	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.61859	0.07;0.1	4.44	3.53	0.40419	.	0.685543	0.12145	N	0.495514	T	0.01189	0.0039	N	0.02916	-0.46	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.08055	0.003;0.003	T	0.01591	-1.1317	10	0.15066	T	0.55	.	12.2683	0.54691	0.0:0.9166:0.0:0.0834	rs61736607	1106;1109	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	L	1109;1106	ENSP00000362304:P1109L;ENSP00000362303:P1106L	ENSP00000362303:P1106L	P	+	2	0	ADAMTS14	72190260	0.002000	0.14202	0.017000	0.16124	0.263000	0.26337	1.076000	0.30729	1.220000	0.43490	0.655000	0.94253	CCT	C|0.944;T|0.056	0.056	strong		0.637	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
TBATA	219793	hgsc.bcm.edu	37	10	72537086	72537086	+	Silent	SNP	C	C	T	rs4747099	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72537086C>T	ENST00000299290.1	-	7	902	c.513G>A	c.(511-513)gaG>gaA	p.E171E	TBATA_ENST00000456372.2_Silent_p.E171E	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	171					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											CCTCCTTCTGCTCCTTCTGCT	0.642													C|||	465	0.0928514	0.0492	0.2104	5008	,	,		16641	0.1825		0.0368	False		,,,				2504	0.0337				p.E171E		Atlas-SNP	.											.	.	.	.	0			c.G513A						PASS	.	C		198,4208	123.7+/-161.0	6,186,2011	34.0	38.0	37.0		513	-2.3	0.2	10	dbSNP_111	37	248,8352	97.7+/-159.3	3,242,4055	no	coding-synonymous	C10orf27	NM_152710.2		9,428,6066	TT,TC,CC		2.8837,4.4939,3.4292		171/352	72537086	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	219793	exon7			CTTCTGCTCCTTC	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"""chromosome 10 open reading frame 27"""	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.513G>A	10.37:g.72537086C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_152710	A4QPA8|B2RPQ2|Q5T4G2	Silent	SNP	ENST00000299290.1	37	CCDS7308.1																																																																																			C|0.940;T|0.060	0.060	strong		0.642	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710	
EP400	57634	hgsc.bcm.edu	37	12	132547093	132547093	+	Silent	SNP	A	A	G	rs10902490|rs528214697	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132547093A>G	ENST00000333577.4	+	48	8398	c.8289A>G	c.(8287-8289)caA>caG	p.Q2763Q	EP400_ENST00000389561.2_Silent_p.Q2727Q|EP400_ENST00000330386.6_Silent_p.Q2646Q|EP400_ENST00000389562.2_Silent_p.Q2726Q|EP400_ENST00000332482.4_Silent_p.Q2690Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2763	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				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)	p.Q2726Q(9)		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)		agcagcaacaacagcagcagc	0.567																																					p.Q2727Q		Atlas-SNP	.											EP400,NS,carcinoma,0,15	EP400	370	15	9	Substitution - coding silent(9)	lung(3)|kidney(2)|endometrium(2)|central_nervous_system(2)	c.A8181G						scavenged	.						25.0	29.0	28.0					12																	132547093		2173	4217	6390	SO:0001819	synonymous_variant	57634	exon47			GCAACAACAGCAG	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.8289A>G	12.37:g.132547093A>G		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	83	24	0.289157	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				A|0.500;G|0.500	0.500	weak		0.567	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
LCT	3938	hgsc.bcm.edu	37	2	136574968	136574968	+	Silent	SNP	G	G	C	rs35093754	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:136574968G>C	ENST00000264162.2	-	6	1660	c.1650C>G	c.(1648-1650)ggC>ggG	p.G550G	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	550	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CGGTGCCATAGCCTGCGTAGC	0.577													G|||	251	0.0501198	0.1059	0.0202	5008	,	,		16966	0.0516		0.0288	False		,,,				2504	0.0164				p.G550G		Atlas-SNP	.											.	LCT	309	.	0			c.C1650G						PASS	.	G		483,3923	226.2+/-241.8	31,421,1751	85.0	80.0	82.0		1650	0.9	1.0	2	dbSNP_126	82	186,8414	82.3+/-144.9	3,180,4117	no	coding-synonymous	LCT	NM_002299.2		34,601,5868	CC,CG,GG		2.1628,10.9623,5.1438		550/1928	136574968	669,12337	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon6			GCCATAGCCTGCG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1650C>G	2.37:g.136574968G>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.950;C|0.050	0.050	strong		0.577	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
TGM5	9333	hgsc.bcm.edu	37	15	43545728	43545728	+	Silent	SNP	G	G	A	rs555001	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:43545728G>A	ENST00000220420.5	-	5	667	c.660C>T	c.(658-660)taC>taT	p.Y220Y	TGM5_ENST00000349114.4_Silent_p.Y138Y	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	220					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CTCTGCTGACGTAGACGGGGC	0.612													G|||	2388	0.476837	0.7579	0.3228	5008	,	,		18010	0.4127		0.336	False		,,,				2504	0.4172				p.Y220Y		Atlas-SNP	.											.	TGM5	88	.	0			c.C660T						PASS	.	G	,	2884,1520	673.0+/-402.7	961,962,279	70.0	63.0	65.0		414,660	-2.3	0.8	15	dbSNP_83	65	2798,5800	443.5+/-360.4	466,1866,1967	no	coding-synonymous,coding-synonymous	TGM5	NM_004245.3,NM_201631.3	,	1427,2828,2246	AA,AG,GG		32.5425,34.5141,43.701	,	138/639,220/721	43545728	5682,7320	2202	4299	6501	SO:0001819	synonymous_variant	9333	exon5			GCTGACGTAGACG	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.660C>T	15.37:g.43545728G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	18	14	0.777778	NM_201631	O43549|Q0VF40|Q9UEZ4	Silent	SNP	ENST00000220420.5	37	CCDS32212.1																																																																																			G|0.539;A|0.461	0.461	strong		0.612	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
APOL6	80830	hgsc.bcm.edu	37	22	36055406	36055406	+	Silent	SNP	A	A	C	rs34014315	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36055406A>C	ENST00000409652.4	+	3	1071	c.795A>C	c.(793-795)acA>acC	p.T265T		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	265					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						GAGCAAGGACAAAGTTTGCGG	0.532													A|||	110	0.0219649	0.0038	0.0375	5008	,	,		21399	0.0		0.0398	False		,,,				2504	0.0399				p.T265T		Atlas-SNP	.											.	APOL6	26	.	0			c.A795C						PASS	.	A		36,4370	41.6+/-74.8	0,36,2167	79.0	77.0	77.0		795	-8.8	0.0	22	dbSNP_126	77	404,8196	127.0+/-185.4	14,376,3910	no	coding-synonymous	APOL6	NM_030641.3		14,412,6077	CC,CA,AA		4.6977,0.8171,3.3831		265/344	36055406	440,12566	2203	4300	6503	SO:0001819	synonymous_variant	80830	exon3			AAGGACAAAGTTT	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"""Apolipoproteins"""	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.795A>C	22.37:g.36055406A>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	80	55	0.6875	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Silent	SNP	ENST00000409652.4	37	CCDS13919.1																																																																																			A|0.965;C|0.035	0.035	strong		0.532	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641	
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 GAIIx	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	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	79	21	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	
PIWIL4	143689	hgsc.bcm.edu	37	11	94322352	94322352	+	Missense_Mutation	SNP	A	A	T	rs11020845|rs386756343	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:94322352A>T	ENST00000299001.6	+	8	1191	c.980A>T	c.(979-981)cAg>cTg	p.Q327L	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	327	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.		Q -> L (in dbSNP:rs11020845). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CACACCTTTCAGAAGCGGGAT	0.398													A|||	942	0.188099	0.0598	0.1873	5008	,	,		18440	0.2817		0.2813	False		,,,				2504	0.1697				p.Q327L		Atlas-SNP	.											.	PIWIL4	70	.	0			c.A980T						PASS	.	A	LEU/GLN	24,4378		9,6,2186	177.0	161.0	166.0		980	-3.5	0.7	11	dbSNP_120	166	314,8282		126,62,4110	yes	missense	PIWIL4	NM_152431.2	113	135,68,6296	TT,TA,AA		3.6529,0.5452,2.6004	benign	327/853	94322352	338,12660	2201	4298	6499	SO:0001583	missense	143689	exon8			CCTTTCAGAAGCG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.980A>T	11.37:g.94322352A>T	ENSP00000299001:p.Gln327Leu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	175	29	0.165714	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Missense_Mutation	SNP	ENST00000299001.6	37	CCDS31656.1	370	0.16941391941391942	21	0.042682926829268296	69	0.19060773480662985	116	0.20279720279720279	164	0.21635883905013192	A	14.47	2.546340	0.45383	0.005452	0.036529	ENSG00000134627	ENST00000299001	T	0.14144	2.53	4.96	-3.53	0.04667	Argonaute/Dicer protein, PAZ (4);	0.810725	0.11154	N	0.593796	T	0.00012	0.0000	L	0.58969	1.84	0.09310	P	0.999999830308	B	0.26708	0.157	B	0.33121	0.158	T	0.41448	-0.9508	9	0.44086	T	0.13	-1.6396	2.9704	0.05920	0.3688:0.1246:0.3849:0.1216	rs11020845;rs11020845	327	Q7Z3Z4	PIWL4_HUMAN	L	327	ENSP00000299001:Q327L	ENSP00000299001:Q327L	Q	+	2	0	PIWIL4	93962000	0.291000	0.24352	0.714000	0.30535	0.988000	0.76386	-0.490000	0.06482	-0.492000	0.06687	-0.388000	0.06559	CAG	A|0.793;T|0.207	0.207	strong		0.398	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
IKBKE	9641	hgsc.bcm.edu	37	1	206669465	206669465	+	Missense_Mutation	SNP	C	C	T	rs3748022	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:206669465C>T	ENST00000367120.3	+	22	2511	c.2138C>T	c.(2137-2139)cCt>cTt	p.P713L	C1orf147_ENST00000367119.1_Intron|IKBKE_ENST00000537984.1_Missense_Mutation_p.P628L	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	713			P -> L (in dbSNP:rs3748022). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GTCCCAGCACCTCCTGATGTC	0.532													C|||	742	0.148163	0.0182	0.3256	5008	,	,		22926	0.1935		0.2326	False		,,,				2504	0.0644				p.P713L		Atlas-SNP	.											IKBKE,NS,adenoma,0,1	IKBKE	77	1	0			c.C2138T						PASS	.	C	LEU/PRO,,LEU/PRO	195,4211	122.9+/-160.3	7,181,2015	132.0	107.0	116.0		1883,,2138	3.5	0.1	1	dbSNP_107	116	1876,6724	335.6+/-321.5	182,1512,2606	yes	missense,utr-3,missense	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	98,,98	189,1693,4621	TT,TC,CC		21.814,4.4258,15.9234	benign,,benign	628/632,,713/717	206669465	2071,10935	2203	4300	6503	SO:0001583	missense	9641	exon22			CAGCACCTCCTGA	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.2138C>T	1.37:g.206669465C>T	ENSP00000356087:p.Pro713Leu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	135	57	0.422222	NM_014002	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	407	0.18635531135531136	15	0.03048780487804878	105	0.2900552486187845	107	0.18706293706293706	180	0.23746701846965698	C	13.59	2.281232	0.40394	0.044258	0.21814	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.62639	0.01;0.16	4.38	3.45	0.39498	.	0.940554	0.08970	N	0.867304	T	0.00012	0.0000	N	0.14661	0.345	0.50632	P	1.1700000000003374E-4	B	0.18741	0.03	B	0.18561	0.022	T	0.11299	-1.0593	9	0.36615	T	0.2	1.8782	8.6908	0.34264	0.0:0.8967:0.0:0.1033	rs3748022;rs17434096;rs61028264;rs3748022	713	Q14164	IKKE_HUMAN	L	713;628	ENSP00000356087:P713L;ENSP00000444529:P628L	ENSP00000356087:P713L	P	+	2	0	IKBKE	204736088	0.003000	0.15002	0.057000	0.19452	0.813000	0.45954	1.861000	0.39438	1.401000	0.46761	0.655000	0.94253	CCT	C|0.844;T|0.156	0.156	strong		0.532	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
ITGAE	3682	hgsc.bcm.edu	37	17	3661052	3661052	+	Missense_Mutation	SNP	G	G	A	rs71366574	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3661052G>A	ENST00000263087.4	-	9	1066	c.968C>T	c.(967-969)aCg>aTg	p.T323M		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	323	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GATGACTGTCGTAAGGTTGAG	0.577													G|||	82	0.0163738	0.0023	0.0115	5008	,	,		19476	0.0308		0.0229	False		,,,				2504	0.0174				p.T323M	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.C968T						PASS	.	G	MET/THR	36,4370	40.8+/-73.8	0,36,2167	229.0	216.0	220.0		968	0.8	0.3	17	dbSNP_130	220	210,8390	89.9+/-152.1	4,202,4094	yes	missense	ITGAE	NM_002208.4	81	4,238,6261	AA,AG,GG		2.4419,0.8171,1.8914	probably-damaging	323/1180	3661052	246,12760	2203	4300	6503	SO:0001583	missense	3682	exon9			ACTGTCGTAAGGT	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.968C>T	17.37:g.3661052G>A	ENSP00000263087:p.Thr323Met	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	39	0.017857142857142856	0	0.0	5	0.013812154696132596	16	0.027972027972027972	18	0.023746701846965697	G	9.981	1.228175	0.22542	0.008171	0.024419	ENSG00000083457	ENST00000263087	D	0.83506	-1.73	5.56	0.793	0.18632	von Willebrand factor, type A (3);	.	.	.	.	T	0.72614	0.3482	L	0.54323	1.7	0.09310	N	1	D	0.89917	1.0	D	0.71414	0.973	T	0.69331	-0.5173	9	0.56958	D	0.05	.	9.4127	0.38503	0.0:0.3634:0.3893:0.2472	.	323	P38570	ITAE_HUMAN	M	323	ENSP00000263087:T323M	ENSP00000263087:T323M	T	-	2	0	ITGAE	3607801	0.011000	0.17503	0.287000	0.24848	0.010000	0.07245	0.349000	0.20055	0.339000	0.23719	-0.414000	0.06135	ACG	G|0.979;A|0.021	0.021	strong		0.577	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
TTLL2	83887	hgsc.bcm.edu	37	6	167753691	167753691	+	Silent	SNP	C	C	T	rs877653	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:167753691C>T	ENST00000239587.5	+	3	391	c.303C>T	c.(301-303)agC>agT	p.S101S		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	101	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		TGGTGCAAAGCGTCCTCCTGG	0.542													C|||	1552	0.309904	0.1679	0.2824	5008	,	,		20342	0.5079		0.2664	False		,,,				2504	0.362				p.S101S		Atlas-SNP	.											.	TTLL2	82	.	0			c.C303T						PASS	.	C		840,3566	329.6+/-301.1	80,680,1443	62.0	57.0	59.0		303	-6.0	0.2	6	dbSNP_86	59	2537,6063	415.1+/-351.7	364,1809,2127	no	coding-synonymous	TTLL2	NM_031949.4		444,2489,3570	TT,TC,CC		29.5,19.0649,25.9649		101/593	167753691	3377,9629	2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			GCAAAGCGTCCTC	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.303C>T	6.37:g.167753691C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	37	CCDS5301.1																																																																																			C|0.724;T|0.276	0.276	strong		0.542	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
AGBL3	340351	hgsc.bcm.edu	37	7	134678253	134678253	+	Missense_Mutation	SNP	T	T	A	rs2348049	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:134678253T>A	ENST00000436302.2	+	4	387	c.134T>A	c.(133-135)tTt>tAt	p.F45Y	AGBL3_ENST00000458078.1_Missense_Mutation_p.F19Y|AGBL3_ENST00000494702.2_3'UTR|AGBL3_ENST00000435976.2_Missense_Mutation_p.F45Y|AGBL3_ENST00000359383.3_Missense_Mutation_p.F45Y	NM_178563.3	NP_848658.3	Q8NEM8	CBPC3_HUMAN	ATP/GTP binding protein-like 3	45			F -> Y (in dbSNP:rs2348049).			cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|lung(2)|skin(3)	10						GCTGACTCTTTTGGTGATCCC	0.398													T|||	1148	0.229233	0.2844	0.1801	5008	,	,		18336	0.1845		0.2714	False		,,,				2504	0.1922				p.F45Y		Atlas-SNP	.											.	AGBL3	45	.	0			c.T134A						PASS	.						189.0	145.0	158.0					7																	134678253		692	1591	2283	SO:0001583	missense	340351	exon4			ACTCTTTTGGTGA	BC030651	CCDS47718.1	7q33	2014-06-23			ENSG00000146856	ENSG00000146856			27981	protein-coding gene	gene with protein product							Standard	NM_178563		Approved	MGC32955, CCP3	uc011kpw.2	Q8NEM8	OTTHUMG00000155406	ENST00000436302.2:c.134T>A	7.37:g.134678253T>A	ENSP00000388275:p.Phe45Tyr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	140	53	0.378571	NM_178563	B7Z827|Q9H965	Missense_Mutation	SNP	ENST00000436302.2	37	CCDS47718.1	503	0.2303113553113553	139	0.28252032520325204	70	0.19337016574585636	96	0.16783216783216784	198	0.2612137203166227	T	9.842	1.191184	0.21954	.	.	ENSG00000146856	ENST00000436302;ENST00000359383;ENST00000458078;ENST00000435976	T;T;T;T	0.33865	2.89;1.39;2.87;2.9	5.66	1.36	0.22044	.	0.822350	0.10654	N	0.649568	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.31790	0.34	B	0.28709	0.093	T	0.33497	-0.9866	9	0.54805	T	0.06	-2.0438	3.9919	0.09541	0.136:0.0812:0.1241:0.6587	rs2348049;rs52793726;rs2348049	45	Q8NEM8-4	.	Y	45;45;19;45	ENSP00000388275:F45Y;ENSP00000352343:F45Y;ENSP00000395969:F19Y;ENSP00000401220:F45Y	ENSP00000275763:F45Y	F	+	2	0	AGBL3	134328793	0.004000	0.15560	0.001000	0.08648	0.041000	0.13682	1.544000	0.36158	0.358000	0.24211	0.528000	0.53228	TTT	T|0.760;A|0.240	0.240	strong		0.398	AGBL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376655.1	NM_178563	
SVIL	6840	hgsc.bcm.edu	37	10	29783908	29783908	+	Missense_Mutation	SNP	A	A	G	rs78773460		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:29783908A>G	ENST00000355867.4	-	20	4528	c.3776T>C	c.(3775-3777)aTg>aCg	p.M1259T	SVIL_ENST00000535393.1_Missense_Mutation_p.M173T|SVIL_ENST00000538146.1_Missense_Mutation_p.M51T|SVIL_ENST00000375398.2_Missense_Mutation_p.M1259T|SVIL_ENST00000375400.3_Missense_Mutation_p.M833T	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	1259					cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)	p.M1259T(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TTCTAACTGCATATCTGGTCT	0.502																																					p.M1259T		Atlas-SNP	.											SVIL,NS,carcinoma,0,2	SVIL	226	2	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.T3776C						PASS	.						180.0	172.0	175.0					10																	29783908		2203	4300	6503	SO:0001583	missense	6840	exon20			AACTGCATATCTG	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.3776T>C	10.37:g.29783908A>G	ENSP00000348128:p.Met1259Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	29	0.226562	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	A	17.38	3.374630	0.61735	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393;ENST00000535994;ENST00000538146	T;T;T;T;T	0.27557	2.68;2.67;2.67;2.59;1.66	4.41	4.41	0.53225	.	0.084190	0.85682	D	0.000000	T	0.39937	0.1097	M	0.71581	2.175	0.47476	D	0.999433	B;P;B;P	0.44429	0.336;0.835;0.104;0.774	B;B;B;P	0.45913	0.268;0.295;0.054;0.497	T	0.33497	-0.9866	10	0.40728	T	0.16	-28.221	13.8415	0.63441	1.0:0.0:0.0:0.0	.	173;51;833;1259	F5H2Q5;F5GXV0;O95425-2;O95425	.;.;.;SVIL_HUMAN	T	833;1259;1259;173;213;51	ENSP00000364549:M833T;ENSP00000364547:M1259T;ENSP00000348128:M1259T;ENSP00000445472:M173T;ENSP00000440343:M51T	ENSP00000348128:M1259T	M	-	2	0	SVIL	29823914	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	8.642000	0.91036	1.854000	0.53819	0.254000	0.18369	ATG	A|0.500;G|0.500	0.500	strong		0.502	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
TTN	7273	hgsc.bcm.edu	37	2	179436020	179436020	+	Missense_Mutation	SNP	G	G	A	rs744426	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179436020G>A	ENST00000591111.1	-	276	70140	c.69916C>T	c.(69916-69918)Cgc>Tgc	p.R23306C	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R24947C|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R16074C|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R16007C|TTN_ENST00000460472.2_Missense_Mutation_p.R15882C|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R22379C			Q8WZ42	TITIN_HUMAN	titin	23306	Fibronectin type-III 69. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> C. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTTCCTTGCGTTCTAGATGA	0.428													G|||	1042	0.208067	0.0666	0.1455	5008	,	,		23224	0.4504		0.1372	False		,,,				2504	0.2669				p.R24947C		Atlas-SNP	.											TTN_ENST00000359218,brain,glioma,+1,10	TTN	18412	10	0			c.C74839T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	288,3574		10,268,1653	124.0	117.0	120.0		47644,67135,48019,48220	4.5	1.0	2	dbSNP_86	120	1195,7091		90,1015,3038	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	180,180,180,180	100,1283,4691	AA,AG,GG		14.4219,7.4573,12.2078	probably-damaging,probably-damaging,probably-damaging,probably-damaging	15882/26927,22379/33424,16007/27052,16074/27119	179436020	1483,10665	1931	4143	6074	SO:0001583	missense	7273	exon326			CCTTGCGTTCTAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.69916C>T	2.37:g.179436020G>A	ENSP00000465570:p.Arg23306Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		415	0.190018315018315	30	0.06097560975609756	42	0.11602209944751381	239	0.4178321678321678	104	0.13720316622691292	G	10.62	1.402466	0.25291	0.074573	0.144219	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	5.39	4.5	0.54988	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.63428	1.95	0.09310	P	0.99999816646	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	P;P;P;P	0.60609	0.877;0.877;0.877;0.877	T	0.34576	-0.9823	8	0.87932	D	0	.	13.6593	0.62357	0.0:0.0:0.7197:0.2803	rs744426;rs3731742;rs52810886;rs61022663;rs744426	15882;16007;16074;23306	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	C	22379;15882;16074;16007;15880	ENSP00000343764:R22379C;ENSP00000434586:R15882C;ENSP00000340554:R16074C;ENSP00000352154:R16007C	ENSP00000340554:R16074C	R	-	1	0	TTN	179144266	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.109000	0.50345	1.394000	0.46624	0.650000	0.86243	CGC	G|0.817;N|0.001	.	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TFG	10342	hgsc.bcm.edu	37	3	100467018	100467018	+	Silent	SNP	T	T	C	rs11353	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:100467018T>C	ENST00000240851.4	+	8	1186	c.846T>C	c.(844-846)ccT>ccC	p.P282P	TFG_ENST00000418917.2_Silent_p.P278P|TFG_ENST00000476228.1_Silent_p.P278P|TFG_ENST00000481203.1_3'UTR|TFG_ENST00000490574.1_Silent_p.P282P	NM_001195478.1|NM_001195479.1|NM_006070.5	NP_001182407.1|NP_001182408.1|NP_006061.2	Q92734	TFG_HUMAN	TRK-fused gene	282					cell death (GO:0008219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	signal transducer activity (GO:0004871)		TFG/NR4A3(2)|TFG/NTRK1_ENST00000392302(5)|TFG/ALK(9)	large_intestine(4)|lung(2)|prostate(1)|stomach(1)	8						AGACTGGACCTCAACAACCTC	0.448			T	"""NTRK1, ALK"""	"""papillary thyroid, ALCL, NSCLC"""								C|||	3571	0.713059	0.646	0.8055	5008	,	,		19679	0.6518		0.6412	False		,,,				2504	0.8753				p.P282P		Atlas-SNP	.		Dom	yes		3	3q11-q12	10342	TRK-fused gene		"""E, L"""	.	TFG	42	.	0			c.T846C						PASS	.	C	,,,	2872,1534		946,980,277	82.0	83.0	82.0		846,846,834,846	4.8	1.0	3	dbSNP_52	82	5648,2952		1851,1946,503	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TFG	NM_001007565.2,NM_001195478.1,NM_001195479.1,NM_006070.5	,,,	2797,2926,780	CC,CT,TT		34.3256,34.8162,34.4918	,,,	282/401,282/401,278/397,282/401	100467018	8520,4486	2203	4300	6503	SO:0001819	synonymous_variant	10342	exon8			TGGACCTCAACAA	BC009241	CCDS2939.1, CCDS56266.1	3q12.2	2013-03-13	2001-12-04		ENSG00000114354	ENSG00000114354			11758	protein-coding gene	gene with protein product		602498				9169129, 23479643	Standard	NM_001007565		Approved	TF6, FLJ36137, SPG57	uc003dui.3	Q92734	OTTHUMG00000159085	ENST00000240851.4:c.846T>C	3.37:g.100467018T>C		Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	180	180	1	NM_006070	D3DN49|G5E9V1|Q15656|Q969I2	Silent	SNP	ENST00000240851.4	37	CCDS2939.1	1442	0.6602564102564102	309	0.6280487804878049	292	0.8066298342541437	355	0.6206293706293706	486	0.6411609498680739	C	4.324	0.059524	0.08339	0.651838	0.656744	ENSG00000114354	ENST00000443578	.	.	.	5.64	4.77	0.60923	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999999	.	.	.	.	.	.	T	0.20806	-1.0264	3	.	.	.	-1.4612	5.7931	0.18371	0.0:0.592:0.132:0.276	rs11353;rs1059445;rs3200128;rs6441516;rs57273775;rs6441516	.	.	.	P	278	.	.	L	+	2	0	TFG	101949708	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	1.055000	0.30467	0.953000	0.37825	-0.128000	0.14901	CTC	T|0.339;C|0.661	0.661	strong		0.448	TFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353242.1	NM_006070	
LINC00283	100874057	hgsc.bcm.edu	37	13	103394716	103394716	+	RNA	SNP	T	T	C	rs9585987	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103394716T>C	ENST00000430111.1	+	0	0									long intergenic non-protein coding RNA 283																		GAGAAATAGATGTGTAGGGAT	0.393													T|||	3479	0.694688	0.5431	0.7493	5008	,	,		20859	0.5913		0.826	False		,,,				2504	0.8323				p.T2777T		Atlas-SNP	.											.	.	.	.	0			c.A8331G						PASS	.	T		775,609		217,341,134	51.0	37.0	41.0		8331	-1.7	0.0	13	dbSNP_119	41	2541,639		1022,497,71	no	coding-synonymous	CCDC168	NM_001146197.1		1239,838,205	CC,CT,TT		20.0943,44.0029,27.3444		2777/7082	103394716	3316,1248	692	1590	2282			643677	exon4			AATAGATGTGTAG			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103394716T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_001146197		Silent	SNP	ENST00000430111.1	37																																																																																				T|0.305;C|0.695	0.695	strong		0.393	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
PAK7	57144	hgsc.bcm.edu	37	20	9520133	9520133	+	Silent	SNP	G	G	A	rs6039495	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:9520133G>A	ENST00000378429.3	-	11	2682	c.2136C>T	c.(2134-2136)ctC>ctT	p.L712L	PAK7_ENST00000353224.5_Silent_p.L712L|PAK7_ENST00000378423.1_Silent_p.L712L	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	712					apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			ATTGTCTCATGAGGGGGACGA	0.493													G|||	153	0.0305511	0.0673	0.0202	5008	,	,		20117	0.0		0.0318	False		,,,				2504	0.0184				p.L712L		Atlas-SNP	.											.	PAK7	194	.	0			c.C2136T						PASS	.	G	,	257,4149	149.2+/-183.4	9,239,1955	230.0	214.0	220.0		2136,2136	4.5	1.0	20	dbSNP_114	220	290,8310	106.6+/-167.4	6,278,4016	no	coding-synonymous,coding-synonymous	PAK7	NM_020341.3,NM_177990.2	,	15,517,5971	AA,AG,GG		3.3721,5.833,4.2058	,	712/720,712/720	9520133	547,12459	2203	4300	6503	SO:0001819	synonymous_variant	57144	exon10			TCTCATGAGGGGG	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"""p21(CDKN1A)-activated kinase 7"""			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.2136C>T	20.37:g.9520133G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	98	61	0.622449	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Silent	SNP	ENST00000378429.3	37	CCDS13107.1																																																																																			G|0.962;A|0.038	0.038	strong		0.493	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
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 GAIIx	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		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	100	45	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 GAIIx	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	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	37	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	
MMP3	4314	hgsc.bcm.edu	37	11	102709425	102709425	+	Silent	SNP	A	A	G	rs520540	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102709425A>G	ENST00000299855.5	-	8	1342	c.1086T>C	c.(1084-1086)gcT>gcC	p.A362A	WTAPP1_ENST00000525739.2_RNA	NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	362					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	TTCCTCTGATAGCCCAGAATT	0.398													G|||	3117	0.622404	0.5598	0.6643	5008	,	,		17460	0.6706		0.5298	False		,,,				2504	0.7229				p.A362A		Atlas-SNP	.											.	MMP3	60	.	0			c.T1086C						PASS	.	G		2389,2017	561.6+/-380.8	643,1103,457	69.0	64.0	66.0		1086	2.2	1.0	11	dbSNP_83	66	4298,4300	577.8+/-390.6	1064,2170,1065	no	coding-synonymous	MMP3	NM_002422.3		1707,3273,1522	GG,GA,AA		49.9884,45.7785,48.5774		362/478	102709425	6687,6317	2203	4299	6502	SO:0001819	synonymous_variant	4314	exon8			TCTGATAGCCCAG	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.1086T>C	11.37:g.102709425A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Silent	SNP	ENST00000299855.5	37	CCDS8323.1	1308	0.5989010989010989	285	0.5792682926829268	226	0.6243093922651933	387	0.6765734265734266	410	0.5408970976253298	G	8.240	0.806639	0.16467	0.542215	0.499884	ENSG00000149968	ENST00000434103	.	.	.	5.07	2.15	0.27550	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999977	.	.	.	.	.	.	T	0.38436	-0.9661	3	.	.	.	.	6.7088	0.23266	0.5951:0.0:0.4049:0.0	rs520540;rs3740933;rs60233336;rs520540	.	.	.	P	6	.	.	L	-	2	0	MMP3	102214635	0.374000	0.25081	1.000000	0.80357	0.655000	0.38815	1.162000	0.31786	0.394000	0.25230	-0.186000	0.12905	CTA	A|0.461;G|0.539	0.539	strong		0.398	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
MB	4151	hgsc.bcm.edu	37	22	36007045	36007045	+	Silent	SNP	G	G	A	rs7292	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36007045G>A	ENST00000397326.2	-	2	402	c.204C>T	c.(202-204)acC>acT	p.T68T	MB_ENST00000406324.1_Silent_p.T68T|MB_ENST00000359787.1_Silent_p.T68T|MB_ENST00000397328.1_Silent_p.T68T|MB_ENST00000401702.1_Silent_p.T13T	NM_005368.2	NP_005359.1	P02144	MYG_HUMAN	myoglobin	68					brown fat cell differentiation (GO:0050873)|enucleate erythrocyte differentiation (GO:0043353)|heart development (GO:0007507)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)			lung(1)	1						CGGTGAGCACGGTGGCACCAT	0.552													G|||	2826	0.564297	0.5703	0.4798	5008	,	,		21661	0.747		0.4493	False		,,,				2504	0.546				p.T68T	GBM(49;694 1113 16998 18419)|Esophageal Squamous(101;120 1973 10459 37086)	Atlas-SNP	.											.	MB	7	.	0			c.C204T						PASS	.	G	,,	2425,1981	618.2+/-393.1	678,1069,456	130.0	100.0	110.0		204,204,204	-10.6	0.0	22	dbSNP_52	110	4022,4578	556.1+/-386.8	958,2106,1236	no	coding-synonymous,coding-synonymous,coding-synonymous	MB	NM_005368.2,NM_203377.1,NM_203378.1	,,	1636,3175,1692	AA,AG,GG		46.7674,44.9614,49.5694	,,	68/155,68/155,68/155	36007045	6447,6559	2203	4300	6503	SO:0001819	synonymous_variant	4151	exon3			GAGCACGGTGGCA		CCDS13917.1	22q13.1	2012-10-02			ENSG00000198125	ENSG00000198125			6915	protein-coding gene	gene with protein product		160000				10591208, 2989088	Standard	NM_005368		Approved	PVALB	uc003anz.3	P02144	OTTHUMG00000150606	ENST00000397326.2:c.204C>T	22.37:g.36007045G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_203377	Q52H51|Q5THY7	Silent	SNP	ENST00000397326.2	37	CCDS13917.1																																																																																			G|0.474;A|0.526	0.526	strong		0.552	MB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319057.2	NM_203377	
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 GAIIx	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		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	118	35	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	
TNRC18	84629	hgsc.bcm.edu	37	7	5391702	5391702	+	Missense_Mutation	SNP	C	C	G	rs3801048	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:5391702C>G	ENST00000430969.1	-	17	5566	c.5218G>C	c.(5218-5220)Gaa>Caa	p.E1740Q	TNRC18_ENST00000399537.4_Missense_Mutation_p.E1740Q	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1740							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TTCAGGAATTCTTCGTCTTCC	0.507													C|||	950	0.189696	0.2526	0.1844	5008	,	,		19265	0.0625		0.2147	False		,,,				2504	0.2137				p.E1740Q		Atlas-SNP	.											.	TNRC18	311	.	0			c.G5218C						PASS	.	C	GLN/GLU	779,2357		85,609,874	39.0	36.0	37.0		5218	4.0	0.0	7	dbSNP_107	37	1211,5953		101,1009,2472	yes	missense	TNRC18	NM_001080495.2	29	186,1618,3346	GG,GC,CC		16.904,24.8406,19.3204	benign	1740/2969	5391702	1990,8310	1568	3582	5150	SO:0001583	missense	84629	exon17			GGAATTCTTCGTC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.5218G>C	7.37:g.5391702C>G	ENSP00000395538:p.Glu1740Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	121	40	0.330579	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	389	0.17811355311355312	130	0.26422764227642276	63	0.17403314917127072	30	0.05244755244755245	166	0.21899736147757257	c	14.58	2.578239	0.45902	0.248406	0.16904	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.48201	2.64;2.64;0.82	4.92	4.0	0.46444	.	0.946100	0.08634	N	0.916650	T	0.00012	0.0000	L	0.50333	1.59	0.48975	P	2.609999999999557E-4	B;B	0.20164	0.001;0.042	B;B	0.16722	0.005;0.016	T	0.14282	-1.0478	9	0.24483	T	0.36	.	14.7976	0.69889	0.0:0.8547:0.1453:0.0	rs3801048;rs10384278;rs60343046;rs3801048	795;1740	A8MSW5;O15417	.;TNC18_HUMAN	Q	1740;1740;795;230	ENSP00000382452:E1740Q;ENSP00000395538:E1740Q;ENSP00000395990:E230Q	ENSP00000382452:E1740Q	E	-	1	0	TNRC18	5358228	0.733000	0.28132	0.005000	0.12908	0.952000	0.60782	2.845000	0.48254	0.997000	0.38969	0.561000	0.74099	GAA	C|0.797;G|0.203	0.203	strong		0.507	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
SIX4	51804	hgsc.bcm.edu	37	14	61180336	61180336	+	Missense_Mutation	SNP	C	C	T	rs112624131	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:61180336C>T	ENST00000216513.4	-	3	2194	c.2135G>A	c.(2134-2136)cGt>cAt	p.R712H		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	712					anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R712L(1)		breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		CAGAACCAAACGATGTTCTTG	0.443													C|||	27	0.00539137	0.0068	0.0058	5008	,	,		22171	0.0		0.0119	False		,,,				2504	0.002				p.R712H		Atlas-SNP	.											SIX4,NS,carcinoma,0,1	SIX4	69	1	1	Substitution - Missense(1)	lung(1)	c.G2135A						PASS	.	C	HIS/ARG	31,4375	36.8+/-68.6	0,31,2172	99.0	96.0	97.0		2135	3.7	1.0	14	dbSNP_132	97	91,8509	51.5+/-111.7	0,91,4209	yes	missense	SIX4	NM_017420.4	29	0,122,6381	TT,TC,CC		1.0581,0.7036,0.938	benign	712/782	61180336	122,12884	2203	4300	6503	SO:0001583	missense	51804	exon3			ACCAAACGATGTT	AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"""Homeoboxes / SINE class"""	10890	protein-coding gene	gene with protein product		606342	"""sine oculis homeobox (Drosophila) homolog 4"", ""sine oculis homeobox homolog 4 (Drosophila)"""			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.2135G>A	14.37:g.61180336C>T	ENSP00000216513:p.Arg712His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	141	61	0.432624	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	15	0.006868131868131868	3	0.006097560975609756	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	11.76	1.734903	0.30774	0.007036	0.010581	ENSG00000100625	ENST00000216513;ENST00000554079	D;T	0.91407	-2.84;0.78	5.63	3.73	0.42828	.	0.409847	0.21022	N	0.081482	T	0.74981	0.3788	N	0.14661	0.345	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.70375	-0.4889	10	0.46703	T	0.11	.	7.0186	0.24902	0.0:0.7034:0.1429:0.1537	.	712	Q9UIU6	SIX4_HUMAN	H	712;385	ENSP00000216513:R712H;ENSP00000451537:R385H	ENSP00000216513:R712H	R	-	2	0	SIX4	60250089	0.811000	0.29063	0.967000	0.41034	0.940000	0.58332	0.542000	0.23222	0.777000	0.33496	0.563000	0.77884	CGT	C|0.991;T|0.009	0.009	strong		0.443	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2		
MFF	56947	hgsc.bcm.edu	37	2	228221725	228221725	+	Silent	SNP	A	A	G	rs4844	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:228221725A>G	ENST00000353339.3	+	11	1362	c.921A>G	c.(919-921)ctA>ctG	p.L307L	MFF_ENST00000476924.1_3'UTR|MFF_ENST00000409565.1_Silent_p.L183L|MFF_ENST00000409616.1_Silent_p.L203L|MFF_ENST00000349901.7_Silent_p.L203L|MFF_ENST00000337110.7_Silent_p.L208L|MFF_ENST00000524634.1_Silent_p.L54L|MFF_ENST00000354503.6_Silent_p.L183L|MFF_ENST00000304593.9_Silent_p.L256L|MFF_ENST00000392059.1_Silent_p.L307L	NM_001277061.1	NP_001263990.1	Q9GZY8	MFF_HUMAN	mitochondrial fission factor	307					mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion morphogenesis (GO:0070584)|peroxisome fission (GO:0016559)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|regulation of peroxisome organization (GO:1900063)|release of cytochrome c from mitochondria (GO:0001836)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of mitochondrial membrane (GO:0032592)|mitochondrial outer membrane (GO:0005741)|peroxisome (GO:0005777)|synapse (GO:0045202)	protein homodimerization activity (GO:0042803)	p.L307L(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(7)|lung(4)|stomach(2)	21						ATAGACGTCTACAACTTCTGG	0.333													A|||	654	0.130591	0.1997	0.1138	5008	,	,		18914	0.0933		0.1461	False		,,,				2504	0.0716				p.L307L		Atlas-SNP	.											MFF,NS,carcinoma,0,1	MFF	48	1	1	Substitution - coding silent(1)	stomach(1)	c.A921G						PASS	.	A		917,3489	349.0+/-310.2	66,785,1352	105.0	102.0	103.0		921	-5.4	1.0	2	dbSNP_131	103	1318,7282	258.7+/-282.2	97,1124,3079	no	coding-synonymous	MFF	NM_020194.4		163,1909,4431	GG,GA,AA		15.3256,20.8125,17.1844		307/343	228221725	2235,10771	2203	4300	6503	SO:0001819	synonymous_variant	56947	exon11			ACGTCTACAACTT	AF258660	CCDS2465.1, CCDS63139.1, CCDS63140.1, CCDS63141.1, CCDS63142.1, CCDS74662.1	2q36	2008-05-29	2008-05-29	2008-05-29	ENSG00000168958	ENSG00000168958			24858	protein-coding gene	gene with protein product		614785	"""chromosome 2 open reading frame 33"""	C2orf33		18353969	Standard	NM_001277061		Approved	GL004	uc002voy.4	Q9GZY8	OTTHUMG00000133180	ENST00000353339.3:c.921A>G	2.37:g.228221725A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_020194	Q567U1|Q658R6|Q9BVZ1|Q9H690|Q9NRG8	Silent	SNP	ENST00000353339.3	37	CCDS2465.1																																																																																			A|0.847;G|0.153	0.153	strong		0.333	MFF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256887.2	NM_020194	
DEPDC5	9681	hgsc.bcm.edu	37	22	32194581	32194581	+	Silent	SNP	A	A	G	rs16989495	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:32194581A>G	ENST00000382112.3	+	13	955	c.885A>G	c.(883-885)caA>caG	p.Q295Q	DEPDC5_ENST00000536766.1_Silent_p.Q267Q|DEPDC5_ENST00000382105.2_Silent_p.Q295Q|DEPDC5_ENST00000400249.2_Silent_p.Q295Q|DEPDC5_ENST00000382111.2_Silent_p.Q295Q|DEPDC5_ENST00000400246.1_Silent_p.Q295Q|DEPDC5_ENST00000400248.2_Silent_p.Q295Q|DEPDC5_ENST00000400242.3_Silent_p.Q295Q|DEPDC5_ENST00000266091.3_Silent_p.Q295Q|DEPDC5_ENST00000535622.1_Silent_p.Q295Q	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	295					intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GCTTTCCTCAAGGAGATAATT	0.413													a|||	192	0.0383387	0.0242	0.0187	5008	,	,		4706	0.0218		0.0408	False		,,,				2504	0.0859				p.Q295Q		Atlas-SNP	.											.	DEPDC5	266	.	0			c.A885G						PASS	.	A	,,,,	74,3622		0,74,1774	88.0	76.0	79.0		885,885,885,885,885	0.1	1.0	22	dbSNP_123	79	239,7987		3,233,3877	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DEPDC5	NM_001007188.2,NM_001136029.2,NM_001242896.1,NM_001242897.1,NM_014662.3	,,,,	3,307,5651	GG,GA,AA		2.9054,2.0022,2.6254	,,,,	295/560,295/1595,295/1604,295/1504,295/1573	32194581	313,11609	1848	4113	5961	SO:0001819	synonymous_variant	9681	exon14			TCCTCAAGGAGAT	AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.885A>G	22.37:g.32194581A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_001242897	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382112.3	37	CCDS46692.1																																																																																			A|0.965;G|0.035	0.035	strong		0.413	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
MTOR	2475	hgsc.bcm.edu	37	1	11190646	11190646	+	Silent	SNP	G	G	A	rs2275527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11190646G>A	ENST00000361445.4	-	39	5629	c.5553C>T	c.(5551-5553)agC>agT	p.S1851S	MTOR_ENST00000495435.1_5'Flank|MTOR_ENST00000376838.1_Silent_p.S56S	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1851	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TCTCGGCCTCGCTCTCACTGT	0.627													G|||	1145	0.228634	0.4486	0.1542	5008	,	,		17004	0.0794		0.2356	False		,,,				2504	0.1309				p.S1851S		Atlas-SNP	.											.	MTOR	327	.	0			c.C5553T						PASS	.	G		1927,2479	549.0+/-377.7	407,1113,683	107.0	88.0	95.0		5553	-5.7	0.9	1	dbSNP_100	95	2052,6548	356.5+/-330.3	249,1554,2497	no	coding-synonymous	MTOR	NM_004958.3		656,2667,3180	AA,AG,GG		23.8605,43.7358,30.5936		1851/2550	11190646	3979,9027	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon39			GGCCTCGCTCTCA	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.5553C>T	1.37:g.11190646G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			G|0.716;A|0.284	0.284	strong		0.627	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
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 GAIIx	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	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	42	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	
OSBPL9	114883	hgsc.bcm.edu	37	1	52231560	52231560	+	Missense_Mutation	SNP	C	C	T	rs61739207	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:52231560C>T	ENST00000428468.1	+	12	847	c.845C>T	c.(844-846)aCa>aTa	p.T282I	OSBPL9_ENST00000361556.5_Missense_Mutation_p.T172I|OSBPL9_ENST00000453295.1_Missense_Mutation_p.T265I|OSBPL9_ENST00000530544.1_Missense_Mutation_p.T201I|OSBPL9_ENST00000337809.4_Missense_Mutation_p.T287I|OSBPL9_ENST00000447887.1_Missense_Mutation_p.T292I|OSBPL9_ENST00000462759.1_Missense_Mutation_p.T104I|OSBPL9_ENST00000531828.1_Missense_Mutation_p.T117I|OSBPL9_ENST00000371710.3_Missense_Mutation_p.T300I|OSBPL9_ENST00000435686.2_Missense_Mutation_p.T117I|OSBPL9_ENST00000371714.1_Missense_Mutation_p.T269I|OSBPL9_ENST00000486942.1_Missense_Mutation_p.T104I			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	282					lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						TCTCCAAATACAGTCCCAGAG	0.428													C|||	8	0.00159744	0.0008	0.0029	5008	,	,		16897	0.0		0.005	False		,,,				2504	0.0				p.T292I		Atlas-SNP	.											.	OSBPL9	192	.	0			c.C875T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR,ILE/THR,ILE/THR,ILE/THR,ILE/THR	5,4401	9.9+/-24.2	0,5,2198	107.0	96.0	100.0		845,311,311,794,515,806,875	5.0	1.0	1	dbSNP_129	100	81,8519	46.3+/-105.2	2,77,4221	yes	missense,missense,missense,missense,missense,missense,missense	OSBPL9	NM_024586.5,NM_148904.3,NM_148905.3,NM_148906.2,NM_148907.2,NM_148908.3,NM_148909.3	89,89,89,89,89,89,89	2,82,6419	TT,TC,CC		0.9419,0.1135,0.6612	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	282/737,104/559,104/559,265/720,172/627,269/724,292/747	52231560	86,12920	2203	4300	6503	SO:0001583	missense	114883	exon12			CAAATACAGTCCC	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.845C>T	1.37:g.52231560C>T	ENSP00000407168:p.Thr282Ile	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	274	127	0.463504	NM_148909	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Missense_Mutation	SNP	ENST00000428468.1	37	CCDS41332.3	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	21.3	4.125491	0.77436	0.001135	0.009419	ENSG00000117859	ENST00000371714;ENST00000371710;ENST00000337809;ENST00000447887;ENST00000435686;ENST00000428468;ENST00000453295;ENST00000530544;ENST00000532975;ENST00000531828;ENST00000361556;ENST00000462759;ENST00000486942	T;T;T;T;T;T;T;T;T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54;2.54	5.01	5.01	0.66863	.	0.049550	0.85682	D	0.000000	T	0.22589	0.0545	L	0.44542	1.39	0.58432	D	0.999992	D;D;D;P;P	0.71674	0.998;0.971;0.96;0.951;0.951	D;P;P;P;P	0.75484	0.986;0.65;0.556;0.447;0.447	T	0.00496	-1.1705	10	0.25106	T	0.35	-24.3341	18.8802	0.92353	0.0:1.0:0.0:0.0	rs61739207	265;172;298;282;287	Q86YQ3;Q96SU4-3;B1AKJ7;Q96SU4;B1AKJ6	.;.;.;OSBL9_HUMAN;.	I	269;300;287;292;117;282;265;201;104;117;172;104;104	ENSP00000360779:T269I;ENSP00000360775:T300I;ENSP00000337265:T287I;ENSP00000412733:T292I;ENSP00000402646:T117I;ENSP00000407168:T282I;ENSP00000413263:T265I;ENSP00000433675:T201I;ENSP00000432801:T104I;ENSP00000433083:T117I;ENSP00000354970:T172I;ENSP00000433279:T104I;ENSP00000431980:T104I	ENSP00000337265:T287I	T	+	2	0	OSBPL9	52004148	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.127000	0.77210	2.748000	0.94277	0.650000	0.86243	ACA	C|0.994;T|0.006	0.006	strong		0.428	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4		
MAN2B2	23324	hgsc.bcm.edu	37	4	6596360	6596360	+	Missense_Mutation	SNP	G	G	A	rs2301795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:6596360G>A	ENST00000285599.3	+	7	994	c.958G>A	c.(958-960)Gtg>Atg	p.V320M	MAN2B2_ENST00000504248.1_Missense_Mutation_p.V269M	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	320			V -> M (in dbSNP:rs2301795). {ECO:0000269|PubMed:17974005}.		mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CGGTGTCTCGGTGCAGTATGC	0.602													G|||	2281	0.455471	0.4387	0.4755	5008	,	,		20498	0.3879		0.5388	False		,,,				2504	0.4479				p.V320M		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G958A						PASS	.	G	MET/VAL	1930,2476	549.9+/-377.9	431,1068,704	127.0	95.0	106.0		958	2.8	0.0	4	dbSNP_100	106	4455,4145	588.1+/-392.3	1138,2179,983	yes	missense	MAN2B2	NM_015274.1	21	1569,3247,1687	AA,AG,GG		48.1977,43.8039,49.0927	benign	320/1010	6596360	6385,6621	2203	4300	6503	SO:0001583	missense	23324	exon7			GTCTCGGTGCAGT	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.958G>A	4.37:g.6596360G>A	ENSP00000285599:p.Val320Met	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	1021	0.4674908424908425	233	0.4735772357723577	169	0.46685082872928174	216	0.3776223776223776	403	0.5316622691292876	G	6.829	0.522162	0.13066	0.438039	0.518023	ENSG00000013288	ENST00000285599;ENST00000504248	T;T	0.76709	-1.04;-1.04	4.52	2.76	0.32466	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	0.350241	0.28927	N	0.013700	T	0.00012	0.0000	L	0.53671	1.685	0.39621	P	0.029962000000000044	B;B;B	0.33299	0.37;0.126;0.407	B;B;B	0.40477	0.33;0.138;0.167	T	0.45833	-0.9234	9	0.40728	T	0.16	-6.2654	8.0974	0.30837	0.0849:0.0:0.7574:0.1577	rs2301795;rs17724940;rs60981402;rs2301795	269;320;320	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	M	320;269	ENSP00000285599:V320M;ENSP00000423129:V269M	ENSP00000285599:V320M	V	+	1	0	MAN2B2	6647261	0.998000	0.40836	0.001000	0.08648	0.090000	0.18270	3.562000	0.53777	0.341000	0.23771	0.543000	0.68304	GTG	G|0.522;A|0.478	0.478	strong		0.602	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
SEH1L	81929	hgsc.bcm.edu	37	18	12951878	12951878	+	Missense_Mutation	SNP	G	G	A	rs117978838	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:12951878G>A	ENST00000262124.11	+	2	263	c.136G>A	c.(136-138)Gat>Aat	p.D46N	SEH1L_ENST00000399892.2_Missense_Mutation_p.D46N	NM_031216.3	NP_112493.2	Q96EE3	SEH1_HUMAN	SEH1-like (S. cerevisiae)	46					attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|carbohydrate metabolic process (GO:0005975)|cytokine production involved in inflammatory response (GO:0002534)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore organization (GO:0006999)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.D46N(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	11						TGAAAGTGGTGATTGGCATTG	0.259													G|||	38	0.00758786	0.0	0.0202	5008	,	,		15251	0.0		0.0209	False		,,,				2504	0.0031				p.D46N		Atlas-SNP	.											SEH1L,NS,carcinoma,0,1	SEH1L	33	1	1	Substitution - Missense(1)	pancreas(1)	c.G136A						PASS	.	G	ASN/ASP,ASN/ASP	11,4393	17.9+/-39.9	0,11,2191	104.0	112.0	110.0		136,136	5.5	0.9	18	dbSNP_132	110	173,8427	78.4+/-141.0	2,169,4129	yes	missense,missense	SEH1L	NM_001013437.1,NM_031216.3	23,23	2,180,6320	AA,AG,GG		2.0116,0.2498,1.4149	benign,benign	46/422,46/361	12951878	184,12820	2202	4300	6502	SO:0001583	missense	81929	exon2			AGTGGTGATTGGC	BC012430	CCDS32791.1, CCDS45832.1	18p11.21	2013-01-10				ENSG00000085415		"""WD repeat domain containing"""	30379	protein-coding gene	gene with protein product	"""sec13 like protein"", ""nucleoporin Seh1"""	609263				12196509, 14517296	Standard	XM_005258152		Approved	SEH1A, SEH1B, Seh1, SEC13L	uc002krq.3	Q96EE3		ENST00000262124.11:c.136G>A	18.37:g.12951878G>A	ENSP00000262124:p.Asp46Asn	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	53	20	0.377358	NM_001013437	A8K5B1|Q8NFU6|Q96MH3|Q9C069	Missense_Mutation	SNP	ENST00000262124.11	37	CCDS45832.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	15.33	2.800785	0.50315	0.002498	0.020116	ENSG00000085415	ENST00000399892;ENST00000262124	T;T	0.65549	-0.16;-0.16	5.48	5.48	0.80851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.235730	0.49916	D	0.000133	T	0.29158	0.0725	N	0.11818	0.18	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.29397	-1.0013	10	0.13108	T	0.6	-5.0864	19.3601	0.94434	0.0:0.0:1.0:0.0	.	46;46	Q96EE3;Q96EE3-1	SEH1_HUMAN;.	N	46	ENSP00000382779:D46N;ENSP00000262124:D46N	ENSP00000262124:D46N	D	+	1	0	SEH1L	12941878	1.000000	0.71417	0.917000	0.36280	0.972000	0.66771	9.413000	0.97351	2.593000	0.87608	0.491000	0.48974	GAT	G|0.988;A|0.012	0.012	strong		0.259	SEH1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458254.1	NM_031216	
HMCN1	83872	hgsc.bcm.edu	37	1	186050417	186050417	+	Missense_Mutation	SNP	A	A	G	rs10798035	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186050417A>G	ENST00000271588.4	+	56	8907	c.8678A>G	c.(8677-8679)gAg>gGg	p.E2893G	HMCN1_ENST00000367492.2_Missense_Mutation_p.E2893G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2893	Ig-like C2-type 27.		E -> G (in dbSNP:rs10798035). {ECO:0000269|PubMed:14570714}.		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						GCACTGATAGAGTGTTTATCC	0.463													A|||	2918	0.582668	0.6952	0.6311	5008	,	,		14601	0.5694		0.499	False		,,,				2504	0.4959				p.E2893G		Atlas-SNP	.											HMCN1,NS,carcinoma,0,2	HMCN1	797	2	0			c.A8678G						PASS	.	A	GLY/GLU	2939,1467	678.7+/-403.6	1003,933,267	159.0	152.0	155.0		8678	5.9	1.0	1	dbSNP_120	155	4279,4321	576.2+/-390.4	1079,2121,1100	yes	missense	HMCN1	NM_031935.2	98	2082,3054,1367	GG,GA,AA		49.7558,33.2955,44.5025	possibly-damaging	2893/5636	186050417	7218,5788	2203	4300	6503	SO:0001583	missense	83872	exon56			TGATAGAGTGTTT	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.8678A>G	1.37:g.186050417A>G	ENSP00000271588:p.Glu2893Gly	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	87	29	0.333333	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1286	0.5888278388278388	327	0.6646341463414634	228	0.6298342541436464	344	0.6013986013986014	387	0.5105540897097626	A	27.2	4.808057	0.90707	0.667045	0.497558	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.30182	1.54;1.54	5.86	5.86	0.93980	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.188863	0.56097	D	0.000030	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	0.99999577304	D	0.76494	0.999	D	0.83275	0.996	T	0.46638	-0.9177	9	0.48119	T	0.1	.	14.8163	0.70036	1.0:0.0:0.0:0.0	rs10798035;rs52812505;rs56779083;rs10798035	2893	Q96RW7	HMCN1_HUMAN	G	2893	ENSP00000271588:E2893G;ENSP00000356462:E2893G	ENSP00000271588:E2893G	E	+	2	0	HMCN1	184317040	1.000000	0.71417	0.995000	0.50966	0.856000	0.48823	8.904000	0.92590	2.241000	0.73720	0.533000	0.62120	GAG	A|0.425;G|0.575	0.575	strong		0.463	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
THUMPD3	25917	hgsc.bcm.edu	37	3	9422210	9422210	+	Silent	SNP	T	T	C	rs2596916	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9422210T>C	ENST00000345094.3	+	7	1366	c.1032T>C	c.(1030-1032)tgT>tgC	p.C344C	THUMPD3_ENST00000515662.2_Silent_p.C344C|SETD5-AS1_ENST00000468186.1_RNA|THUMPD3_ENST00000452837.2_Silent_p.C344C	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	344						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		GGTCTGACTGTTTCCATATTG	0.333													T|||	3091	0.617212	0.5446	0.5908	5008	,	,		17264	0.5665		0.6093	False		,,,				2504	0.7945				p.C344C		Atlas-SNP	.											.	THUMPD3	46	.	0			c.T1032C						PASS	.	T	,	2446,1960	620.6+/-393.6	685,1076,442	103.0	101.0	102.0		1032,1032	3.2	1.0	3	dbSNP_100	102	5219,3381	639.7+/-399.5	1589,2041,670	no	coding-synonymous,coding-synonymous	THUMPD3	NM_001114092.1,NM_015453.2	,	2274,3117,1112	CC,CT,TT		39.314,44.4848,41.0657	,	344/508,344/508	9422210	7665,5341	2203	4300	6503	SO:0001819	synonymous_variant	25917	exon7			TGACTGTTTCCAT	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.1032T>C	3.37:g.9422210T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Silent	SNP	ENST00000345094.3	37	CCDS2573.1	1254	0.5741758241758241	265	0.5386178861788617	210	0.580110497237569	327	0.5716783216783217	452	0.5963060686015831	T	8.071	0.770195	0.15983	0.555152	0.60686	ENSG00000134077	ENST00000441127	.	.	.	5.55	3.2	0.36748	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.46162	-0.9211	3	.	.	.	-15.3779	7.1043	0.25354	0.0:0.2685:0.0:0.7315	rs2596916;rs17849507;rs56489598;rs60900250;rs2596916	.	.	.	A	201	.	.	V	+	2	0	THUMPD3	9397210	1.000000	0.71417	0.993000	0.49108	0.708000	0.40852	1.117000	0.31234	0.943000	0.37553	0.454000	0.30748	GTT	T|0.410;C|0.590	0.590	strong		0.333	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453	
FAM111A	63901	hgsc.bcm.edu	37	11	58920492	58920492	+	Missense_Mutation	SNP	C	C	G	rs116918730	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:58920492C>G	ENST00000528737.1	+	5	4169	c.1351C>G	c.(1351-1353)Caa>Gaa	p.Q451E	FAM111A_ENST00000420244.1_Missense_Mutation_p.Q451E|FAM111A_ENST00000531147.1_Missense_Mutation_p.Q451E|FAM111A_ENST00000533703.1_Missense_Mutation_p.Q451E|FAM111A_ENST00000361723.3_Missense_Mutation_p.Q451E			Q96PZ2	F111A_HUMAN	family with sequence similarity 111, member A	451	Interaction with SV40 large T antigen.				defense response to virus (GO:0051607)|DNA replication (GO:0006260)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_epithelial(135;0.139)				AAATGGACAACAAGTACCTAT	0.363													C|||	77	0.0153754	0.0023	0.0288	5008	,	,		22708	0.001		0.0437	False		,,,				2504	0.0092				p.Q451E		Atlas-SNP	.											.	FAM111A	57	.	0			c.C1351G						PASS	.	C	GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN	38,4364	43.1+/-76.7	0,38,2163	90.0	93.0	92.0		1351,1351,1351,1351,1351	-1.8	0.0	11	dbSNP_132	92	413,8177	129.8+/-187.9	15,383,3897	yes	missense,missense,missense,missense,missense	FAM111A	NM_001142519.1,NM_001142520.1,NM_001142521.1,NM_022074.3,NM_198847.2	29,29,29,29,29	15,421,6060	GG,GC,CC		4.8079,0.8632,3.4714	benign,benign,benign,benign,benign	451/612,451/612,451/612,451/612,451/612	58920492	451,12541	2201	4295	6496	SO:0001583	missense	63901	exon5			GGACAACAAGTAC	AK092953	CCDS7973.1	11q12.1	2014-03-13				ENSG00000166801			24725	protein-coding gene	gene with protein product		615292				11572484, 23996431, 23684011	Standard	NM_022074		Approved	FLJ22794, KIAA1895	uc001nnq.3	Q96PZ2		ENST00000528737.1:c.1351C>G	11.37:g.58920492C>G	ENSP00000434435:p.Gln451Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_001142520	A8K5Y8|Q5RKS9|Q5XKM2|Q68DK9|Q6IPR7|Q9H5Y1	Missense_Mutation	SNP	ENST00000528737.1	37	CCDS7973.1	52	0.023809523809523808	3	0.006097560975609756	15	0.04143646408839779	1	0.0017482517482517483	33	0.04353562005277045	C	0.427	-0.905422	0.02453	0.008632	0.048079	ENSG00000166801	ENST00000528737;ENST00000420244;ENST00000361723;ENST00000533703;ENST00000531147	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	5.04	-1.75	0.08031	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	1.264940	0.05268	N	0.516963	T	0.04092	0.0114	N	0.17474	0.49	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.15206	-1.0445	10	0.09843	T	0.71	-16.2634	9.6028	0.39615	0.4381:0.2104:0.3516:0.0	.	451	Q96PZ2	F111A_HUMAN	E	451	ENSP00000434435:Q451E;ENSP00000406683:Q451E;ENSP00000355264:Q451E;ENSP00000433154:Q451E;ENSP00000431631:Q451E	ENSP00000355264:Q451E	Q	+	1	0	FAM111A	58677068	0.000000	0.05858	0.000000	0.03702	0.180000	0.23129	-2.314000	0.01125	-0.376000	0.07943	-0.211000	0.12701	CAA	C|0.966;G|0.034	0.034	strong		0.363	FAM111A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393975.1	NM_022074	
LOXHD1	125336	hgsc.bcm.edu	37	18	44057673	44057673	+	Missense_Mutation	SNP	C	C	T	rs74316327	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44057673C>T	ENST00000398722.4	-	34	5749	c.5750G>A	c.(5749-5751)cGc>cAc	p.R1917H	LOXHD1_ENST00000441551.2_Missense_Mutation_p.R1989H|LOXHD1_ENST00000582408.1_Missense_Mutation_p.R1022H|LOXHD1_ENST00000398686.4_Missense_Mutation_p.R434H|LOXHD1_ENST00000398705.2_Missense_Mutation_p.R434H|LOXHD1_ENST00000300591.6_Missense_Mutation_p.R1084H|LOXHD1_ENST00000579038.1_Missense_Mutation_p.R988H|LOXHD1_ENST00000536736.1_Missense_Mutation_p.R2133H|LOXHD1_ENST00000441893.2_Missense_Mutation_p.R1066H			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1917	PLAT 14. {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						GAAGAGGTTGCGCATTTTCTG	0.617													C|||	136	0.0271565	0.0008	0.0605	5008	,	,		21838	0.001		0.0765	False		,,,				2504	0.0153				p.R2133H		Atlas-SNP	.											LOXHD1_ENST00000398722,NS,carcinoma,-1,4	LOXHD1	367	4	0			c.G6398A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	20,1364		0,20,672	96.0	92.0	93.0		6398,1301,1301,3251	4.3	1.0	18	dbSNP_131	93	254,2928		13,228,1350	yes	missense,missense,missense,missense	LOXHD1	NM_144612.6,NM_001173129.1,NM_001145473.2,NM_001145472.2	29,29,29,29	13,248,2022	TT,TC,CC		7.9824,1.4451,6.0009	benign,benign,benign,benign	2133/2212,434/458,434/513,1084/1115	44057673	274,4292	692	1591	2283	SO:0001583	missense	125336	exon40			AGGTTGCGCATTT	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.5750G>A	18.37:g.44057673C>T	ENSP00000381707:p.Arg1917His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		79	0.036172161172161175	0	0.0	29	0.08011049723756906	1	0.0017482517482517483	49	0.06464379947229551	C	15.74	2.922300	0.52653	0.014451	0.079824	ENSG00000167210	ENST00000300591;ENST00000398722;ENST00000398705;ENST00000536736;ENST00000441893;ENST00000398686	T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52	5.14	4.26	0.50523	Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1);	.	.	.	.	T	0.01489	0.0048	L	0.48218	1.51	0.47009	D	0.999281	B;B;B	0.27971	0.004;0.004;0.196	B;B;B	0.23852	0.006;0.006;0.049	T	0.01795	-1.1272	9	0.49607	T	0.09	.	13.8868	0.63712	0.0:0.9248:0.0:0.0752	.	2133;1066;1917	F5GZB4;F8WA52;Q8IVV2	.;.;LOXH1_HUMAN	H	1084;1917;434;2133;1066;434	ENSP00000300591:R1084H;ENSP00000381707:R1917H;ENSP00000381692:R434H;ENSP00000444586:R2133H;ENSP00000409062:R1066H;ENSP00000381676:R434H	ENSP00000300591:R1084H	R	-	2	0	LOXHD1	42311671	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.944000	0.63561	2.401000	0.81631	0.561000	0.74099	CGC	C|0.959;T|0.041	0.041	strong		0.617	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
TAS2R14	50840	hgsc.bcm.edu	37	12	11091693	11091693	+	Silent	SNP	T	T	A	rs7138535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11091693T>A	ENST00000537503.1	-	1	169	c.114A>T	c.(112-114)ggA>ggT	p.G38G	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_023922.1	NP_076411.1	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	38					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						AGATCTTTCTTCCCTTGACCC	0.378													T|||	1117	0.223043	0.2337	0.2911	5008	,	,		20154	0.2073		0.2147	False		,,,				2504	0.1851				p.G38G		Atlas-SNP	.											.	TAS2R14	26	.	0			c.A114T						PASS	.	T		984,3422	364.6+/-317.1	116,752,1335	68.0	67.0	67.0		114	-1.9	0.0	12	dbSNP_116	67	2072,6528	352.1+/-328.5	259,1554,2487	no	coding-synonymous	TAS2R14	NM_023922.1		375,2306,3822	AA,AT,TT		24.093,22.3332,23.4968		38/318	11091693	3056,9950	2203	4300	6503	SO:0001819	synonymous_variant	50840	exon1			CTTTCTTCCCTTG	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.114A>T	12.37:g.11091693T>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_023922	Q645X3	Silent	SNP	ENST00000537503.1	37	CCDS8637.1																																																																																			T|0.766;A|0.234	0.234	strong		0.378	TAS2R14-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370194.4	NM_023922	
RNF213	57674	hgsc.bcm.edu	37	17	78346870	78346870	+	Missense_Mutation	SNP	C	C	A	rs62077764	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78346870C>A	ENST00000582970.1	+	49	12990	c.12847C>A	c.(12847-12849)Ctc>Atc	p.L4283I	CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.L2356I|RNF213_ENST00000508628.2_Missense_Mutation_p.L4332I|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	4283					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GGTGCGGAAGCTCAGCAGCCA	0.622													C|||	120	0.0239617	0.003	0.0432	5008	,	,		10496	0.0		0.0716	False		,,,				2504	0.0143				p.L4283I		Atlas-SNP	.											.	RNF213	766	.	0			c.C12847A						PASS	.	C	ILE/LEU	72,4334	65.3+/-102.7	1,70,2132	66.0	66.0	66.0		12994	4.5	0.3	17	dbSNP_129	66	635,7965	164.2+/-216.6	30,575,3695	yes	missense	RNF213	NM_020914.4	5	31,645,5827	AA,AC,CC		7.3837,1.6341,5.436	benign	4332/5257	78346870	707,12299	2203	4300	6503	SO:0001583	missense	57674	exon49			CGGAAGCTCAGCA	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.12847C>A	17.37:g.78346870C>A	ENSP00000464087:p.Leu4283Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	41	0.602941	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	82	0.037545787545787544	3	0.006097560975609756	23	0.06353591160220995	0	0.0	56	0.07387862796833773	C	8.154	0.788020	0.16258	0.016341	0.073837	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T;T	0.34275	1.77;1.37	5.5	4.53	0.55603	.	0.331493	0.28135	N	0.016478	T	0.03305	0.0096	L	0.55990	1.75	0.25926	N	0.983053	P;B	0.46784	0.884;0.219	P;B	0.45610	0.487;0.042	T	0.01909	-1.1249	10	0.39692	T	0.17	.	8.6985	0.34312	0.1588:0.7623:0.0:0.0789	rs62077764	4332;2356	C9JCP4;Q63HN8	.;RN213_HUMAN	I	4283;4332;2356	ENSP00000425956:L4283I;ENSP00000338218:L2356I	ENSP00000338218:L2356I	L	+	1	0	RNF213	75961465	0.964000	0.33143	0.303000	0.25071	0.155000	0.21991	1.367000	0.34204	1.313000	0.45069	-0.140000	0.14226	CTC	C|0.953;A|0.047	0.047	strong		0.622	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
PLEC	5339	hgsc.bcm.edu	37	8	144991176	144991176	+	Silent	SNP	T	T	C	rs6558405	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144991176T>C	ENST00000322810.4	-	32	13393	c.13224A>G	c.(13222-13224)tcA>tcG	p.S4408S	PLEC_ENST00000354589.3_Silent_p.S4271S|PLEC_ENST00000357649.2_Silent_p.S4275S|PLEC_ENST00000436759.2_Silent_p.S4298S|PLEC_ENST00000354958.2_Silent_p.S4249S|PLEC_ENST00000527096.1_Silent_p.S4294S|PLEC_ENST00000345136.3_Silent_p.S4271S|PLEC_ENST00000356346.3_Silent_p.S4257S|PLEC_ENST00000398774.2_Silent_p.S4239S	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4408	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CAGTGGGGTCTGACCAGGAGG	0.667													t|||	2396	0.478435	0.9002	0.3746	5008	,	,		16195	0.1528		0.4423	False		,,,				2504	0.3548				p.S4408S		Atlas-SNP	.											.	PLEC	1144	.	0			c.A13224G						PASS	.	C	,,,,,,,	3321,637		1397,527,55	30.0	38.0	36.0		12894,12771,12747,13224,12717,12813,12825,12813	-10.5	0.1	8	dbSNP_116	36	3608,4686		825,1958,1364	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	2222,2485,1419	CC,CT,TT		43.5013,16.094,43.446	,,,,,,,	4298/4575,4257/4534,4249/4526,4408/4685,4239/4516,4271/4548,4275/4552,4271/4548	144991176	6929,5323	1979	4147	6126	SO:0001819	synonymous_variant	5339	exon32			GGGGTCTGACCAG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.13224A>G	8.37:g.144991176T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			T|0.548;C|0.452	0.452	strong		0.667	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
CNTN2	6900	hgsc.bcm.edu	37	1	205031116	205031116	+	Missense_Mutation	SNP	C	C	T	rs2229866	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205031116C>T	ENST00000331830.4	+	9	1381	c.1097C>T	c.(1096-1098)cCt>cTt	p.P366L	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	366	Ig-like C2-type 4.		P -> L (in dbSNP:rs2229866).		adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AACGGGGAGCCTCTGGCCTCC	0.652											OREG0014144	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2760	0.551118	0.323	0.5591	5008	,	,		15503	0.876		0.339	False		,,,				2504	0.7372				p.P366L	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C1097T						PASS	.	C	LEU/PRO	1480,2924		251,978,973	16.0	18.0	17.0		1097	4.9	1.0	1	dbSNP_98	17	2953,5641		552,1849,1896	yes	missense	CNTN2	NM_005076.3	98	803,2827,2869	TT,TC,CC		34.3612,33.6058,34.1052	benign	366/1041	205031116	4433,8565	2202	4297	6499	SO:0001583	missense	6900	exon9			GGGAGCCTCTGGC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.1097C>T	1.37:g.205031116C>T	ENSP00000330633:p.Pro366Leu	Somatic	69	0	0	2149	WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	1085	0.4967948717948718	153	0.31097560975609756	182	0.5027624309392266	498	0.8706293706293706	252	0.3324538258575198	C	20.8	4.055142	0.75960	0.336058	0.343612	ENSG00000184144	ENST00000331830	T	0.68025	-0.3	4.94	4.94	0.65067	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000078	T	0.00012	0.0000	M	0.66560	2.04	0.09310	P	0.999999999241044	B;B	0.18610	0.029;0.013	B;B	0.18871	0.023;0.014	T	0.40289	-0.9571	9	0.62326	D	0.03	.	17.7437	0.88414	0.0:1.0:0.0:0.0	rs2229866;rs4951164	366;366	A1L3A3;Q02246	.;CNTN2_HUMAN	L	366	ENSP00000330633:P366L	ENSP00000330633:P366L	P	+	2	0	CNTN2	203297739	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	4.643000	0.61390	2.284000	0.76573	0.557000	0.71058	CCT	C|0.586;T|0.414	0.414	strong		0.652	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
C4orf26	152816	hgsc.bcm.edu	37	4	76489345	76489345	+	Missense_Mutation	SNP	C	C	T	rs2306175	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:76489345C>T	ENST00000311623.4	+	2	124	c.89C>T	c.(88-90)cCt>cTt	p.P30L	C4orf26_ENST00000435974.2_Missense_Mutation_p.L45F	NM_001257072.1|NM_178497.3	NP_001244001.1|NP_848592.2	Q17RF5	CD026_HUMAN	chromosome 4 open reading frame 26	30			P -> L (in dbSNP:rs2306175). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)		p.P30L(1)		kidney(1)|large_intestine(4)|stomach(1)	6			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			GTATTTACGCCTCCTGGAGAT	0.542													C|||	1220	0.24361	0.3238	0.1715	5008	,	,		18003	0.244		0.2276	False		,,,				2504	0.2025				p.L45F		Atlas-SNP	.											C4orf26,NS,carcinoma,0,1	C4orf26	24	1	1	Substitution - Missense(1)	stomach(1)	c.C133T						PASS	.	C	PHE/LEU,LEU/PRO	1354,3052	450.0+/-349.2	201,952,1050	69.0	73.0	72.0		133,89	2.8	0.3	4	dbSNP_100	72	2014,6586	351.0+/-328.1	261,1492,2547	yes	missense,missense	C4orf26	NM_001206981.1,NM_178497.3	22,98	462,2444,3597	TT,TC,CC		23.4186,30.7308,25.8957	possibly-damaging,possibly-damaging	45/177,30/131	76489345	3368,9638	2203	4300	6503	SO:0001583	missense	152816	exon3			TTACGCCTCCTGG	AK074237	CCDS3569.1, CCDS56334.1, CCDS75142.1	4q21.1	2012-10-31			ENSG00000174792	ENSG00000174792			26300	protein-coding gene	gene with protein product		614829				22901946	Standard	NM_001206981		Approved	FLJ23657	uc011cbo.2	Q17RF5	OTTHUMG00000130104	ENST00000311623.4:c.89C>T	4.37:g.76489345C>T	ENSP00000311307:p.Pro30Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_001206981	B4DTI3|E7ETQ0|Q8TEC3	Missense_Mutation	SNP	ENST00000311623.4	37	CCDS3569.1	567|567	0.25961538461538464|0.25961538461538464	184|184	0.37398373983739835|0.37398373983739835	65|65	0.17955801104972377|0.17955801104972377	145|145	0.2534965034965035|0.2534965034965035	173|173	0.22823218997361477|0.22823218997361477	C|C	14.06|14.06	2.423024|2.423024	0.43020|0.43020	0.307308|0.307308	0.234186|0.234186	ENSG00000174792|ENSG00000174792	ENST00000435974|ENST00000311623	T|T	0.60424|0.64618	0.19|-0.11	4.6|4.6	2.84|2.84	0.33178|0.33178	.|.	.|0.145749	.|0.32120	.|N	.|0.006545	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.29908|0.29908	0.895|0.895	0.48185|0.48185	P|P	3.950000000000342E-4|3.950000000000342E-4	P|P	0.50943|0.35107	0.94|0.484	P|B	0.47015|0.35655	0.534|0.207	T|T	0.37103|0.37103	-0.9720|-0.9720	8|9	0.87932|0.33940	D|T	0|0.23	.|.	6.3991|6.3991	0.21628|0.21628	0.0:0.7141:0.1857:0.1002|0.0:0.7141:0.1857:0.1002	rs2306175;rs52816760;rs61113264;rs2306175|rs2306175;rs52816760;rs61113264;rs2306175	45|30	E7ETQ0|Q17RF5	.|CD026_HUMAN	F|L	45|30	ENSP00000406925:L45F|ENSP00000311307:P30L	ENSP00000406925:L45F|ENSP00000311307:P30L	L|P	+|+	1|2	0|0	C4orf26|C4orf26	76708369|76708369	0.182000|0.182000	0.23173|0.23173	0.304000|0.304000	0.25085|0.25085	0.213000|0.213000	0.24496|0.24496	1.953000|1.953000	0.40352|0.40352	0.663000|0.663000	0.31027|0.31027	0.551000|0.551000	0.68910|0.68910	CTC|CCT	C|0.741;T|0.259	0.259	strong		0.542	C4orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252410.1	NM_178497	
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 GAIIx	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|CDKN1C_ENST00000414822.3_5'Flank|SLC22A18AS_ENST00000526203.1_Missense_Mutation_p.P119L|CDKN1C_ENST00000430149.2_5'Flank|CDKN1C_ENST00000313407.6_5'Flank|CDKN1C_ENST00000380725.1_5'Flank|SLC22A18AS_ENST00000455942.2_Missense_Mutation_p.P119L	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	Somatic	49	0	0	607	WXS	Illumina HiSeq	Phase_I	60	33	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	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919111	12919111	+	Missense_Mutation	SNP	G	G	A	rs9728577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12919111G>A	ENST00000240189.2	+	2	334	c.247G>A	c.(247-249)Gaa>Aaa	p.E83K		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	83			E -> K (in dbSNP:rs9728577).		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)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGCATTGCTGGAAGGGCTTCA	0.562																																					p.E83K		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G247A						PASS	.	G	LYS/GLU	88,4314	64.1+/-101.4	1,86,2114	170.0	182.0	178.0		247	0.8	0.1	1	dbSNP_119	178	334,8258	102.9+/-164.1	0,334,3962	yes	missense	PRAMEF2	NM_023014.1	56	1,420,6076	AA,AG,GG		3.8873,1.9991,3.2477	benign	83/475	12919111	422,12572	2201	4296	6497	SO:0001583	missense	65122	exon2			TTGCTGGAAGGGC		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.247G>A	1.37:g.12919111G>A	ENSP00000240189:p.Glu83Lys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	160	48	0.3	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	166	0.076007326007326	3	0.006097560975609756	9	0.024861878453038673	123	0.21503496503496503	31	0.040897097625329816	G	8.310	0.821883	0.16678	0.019991	0.038873	ENSG00000120952	ENST00000240189	T	0.04502	3.61	0.842	0.842	0.18927	.	0.749866	0.12459	N	0.467115	T	0.00012	0.0000	M	0.72894	2.215	0.09310	N	1	B	0.15141	0.012	B	0.16289	0.015	T	0.45116	-0.9283	10	0.56958	D	0.05	.	5.0452	0.14480	0.0:0.0:1.0:0.0	rs9728577;rs52822181;rs9728577	83	O60811	PRAM2_HUMAN	K	83	ENSP00000240189:E83K	ENSP00000240189:E83K	E	+	1	0	PRAMEF2	12841698	0.042000	0.20092	0.117000	0.21633	0.093000	0.18481	0.689000	0.25437	0.759000	0.33084	0.194000	0.17425	GAA	G|0.953;A|0.047	0.047	strong		0.562	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
EPHX1	2052	hgsc.bcm.edu	37	1	226033030	226033030	+	Silent	SNP	G	G	C	rs4149230	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226033030G>C	ENST00000366837.4	+	9	1546	c.1350G>C	c.(1348-1350)tcG>tcC	p.S450S	EPHX1_ENST00000272167.5_Silent_p.S450S|RP11-285F7.2_ENST00000424332.1_RNA	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	450					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					AGTTCCTGTCGGTGCTGGAGC	0.617													G|||	353	0.0704872	0.0008	0.072	5008	,	,		8496	0.1587		0.0487	False		,,,				2504	0.0951				p.S450S		Atlas-SNP	.											.	EPHX1	57	.	0			c.G1350C						PASS	.	G	,	31,4375	36.8+/-68.6	0,31,2172	32.0	33.0	32.0		1350,1350	-4.5	0.0	1	dbSNP_110	32	349,8251	115.3+/-175.2	3,343,3954	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	3,374,6126	CC,CG,GG		4.0581,0.7036,2.9217	,	450/456,450/456	226033030	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon9			CCTGTCGGTGCTG	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.1350G>C	1.37:g.226033030G>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			G|0.955;C|0.045	0.045	strong		0.617	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
MYZAP	100820829	hgsc.bcm.edu	37	15	57918069	57918069	+	Silent	SNP	A	A	G	rs2069133	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:57918069A>G	ENST00000267853.5	+	5	598	c.504A>G	c.(502-504)gcA>gcG	p.A168A	GCOM1_ENST00000572390.1_Silent_p.A168A|GCOM1_ENST00000380568.3_Silent_p.A168A|MYZAP_ENST00000380565.4_Silent_p.A168A|GCOM1_ENST00000396180.1_Silent_p.A137A|GCOM1_ENST00000574161.1_Silent_p.A168A|GCOM1_ENST00000380560.2_Intron|GCOM1_ENST00000380569.2_Silent_p.A168A|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000380561.2_Silent_p.A137A|GCOM1_ENST00000587652.1_Silent_p.A168A			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	168					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											CAGCCTTGGCATCAGATTCCA	0.488													G|||	2677	0.534545	0.5825	0.5821	5008	,	,		20643	0.5536		0.4026	False		,,,				2504	0.5521				p.A168A		Atlas-SNP	.											.	GCOM1	66	.	0			c.A504G						PASS	.	G	,,,	2428,1956	554.0+/-378.9	679,1070,443	132.0	112.0	119.0		504,504,504,504	-8.3	0.0	15	dbSNP_96	119	3477,5107	634.0+/-398.8	686,2105,1501	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GCOM1	NM_001018090.3,NM_001018091.3,NM_001018100.3,NM_152451.6	,,,	1365,3175,1944	GG,GA,AA		40.5056,44.6168,45.5352	,,,	168/551,168/446,168/467,168/439	57918069	5905,7063	2192	4292	6484	SO:0001819	synonymous_variant	145781	exon5			CTTGGCATCAGAT	FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"""myocardium-enriched zonula adherens protein"""	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.504A>G	15.37:g.57918069A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Silent	SNP	ENST00000267853.5	37	CCDS10162.1																																																																																			A|0.516;G|0.484	0.484	strong		0.488	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100	
ITIH1	3697	hgsc.bcm.edu	37	3	52820403	52820403	+	Silent	SNP	C	C	T	rs142797927		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:52820403C>T	ENST00000273283.2	+	13	1710	c.1686C>T	c.(1684-1686)gtC>gtT	p.V562V	ITIH1_ENST00000540715.1_Silent_p.V420V|ITIH1_ENST00000405128.3_5'Flank|ITIH1_ENST00000537050.1_Silent_p.V274V|ITIH1_ENST00000542827.1_Silent_p.V562V	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	562	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.V562V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		AGAACCACGTCGAGCGCCTCT	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		17597	0.0		0.001	False		,,,				2504	0.0				p.V562V		Atlas-SNP	.											ITIH1,caecum,carcinoma,0,1	ITIH1	108	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1686T						PASS	.	C	,,,	1,4405		0,1,2202	42.0	34.0	37.0		1260,822,822,1686	-9.6	0.0	3	dbSNP_134	37	7,8583		0,7,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	,,,	0,8,6490	TT,TC,CC		0.0815,0.0227,0.0616	,,,	420/770,274/624,274/624,562/912	52820403	8,12988	2203	4295	6498	SO:0001819	synonymous_variant	3697	exon13			CCACGTCGAGCGC		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.1686C>T	3.37:g.52820403C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	170	87	0.511765	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Silent	SNP	ENST00000273283.2	37	CCDS2864.1																																																																																			C|1.000;T|0.000	0.000	strong		0.617	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
UBC	7316	hgsc.bcm.edu	37	12	125397061	125397061	+	Silent	SNP	G	G	A	rs17840844	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:125397061G>A	ENST00000536769.1	-	1	2833	c.1257C>T	c.(1255-1257)gaC>gaT	p.D419D	UBC_ENST00000546120.1_Silent_p.D343D|UBC_ENST00000538617.1_Intron|UBC_ENST00000536661.1_5'Flank|UBC_ENST00000339647.5_Silent_p.D419D			P0CG48	UBC_HUMAN	ubiquitin C	419	Ubiquitin-like 6. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|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)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			breast(3)|endometrium(4)|kidney(4)|large_intestine(2)|lung(13)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.17e-05)|Epithelial(86;0.000207)|all cancers(50;0.00308)		ACCTCTGCTGGTCAGGAGGGA	0.537													G|||	1838	0.367013	0.1657	0.4308	5008	,	,		31861	0.2103		0.5686	False		,,,				2504	0.5481				p.D419D		Atlas-SNP	.											UBC,NS,carcinoma,-2,1	UBC	79	1	0			c.C1257T						scavenged	.						54.0	52.0	53.0					12																	125397061		2150	4211	6361	SO:0001819	synonymous_variant	7316	exon2			CTGCTGGTCAGGA		CCDS9260.1	12q24.3	2008-09-08			ENSG00000150991	ENSG00000150991			12468	protein-coding gene	gene with protein product	"""polyubiquitin-C"""	191340				1315303, 11872750	Standard	NM_021009		Approved		uc001ugs.4	P0CG48		ENST00000536769.1:c.1257C>T	12.37:g.125397061G>A		Somatic	278	1	0.00359712		WXS	Illumina HiSeq	Phase_I	262	206	0.78626	NM_021009	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000536769.1	37	CCDS9260.1																																																																																			G|0.625;A|0.375	0.375	strong		0.537	UBC-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400177.1	NM_021009	
ZNF180	7733	hgsc.bcm.edu	37	19	44981883	44981883	+	Missense_Mutation	SNP	C	C	G	rs1897820	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:44981883C>G	ENST00000221327.4	-	5	1096	c.815G>C	c.(814-816)tGc>tCc	p.C272S	ZNF180_ENST00000391956.4_Missense_Mutation_p.C247S|ZNF180_ENST00000592529.1_Missense_Mutation_p.C245S|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	272			C -> S (in dbSNP:rs1897820). {ECO:0000269|PubMed:12743021}.		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)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				AAATCCATAGCATTTATCTTT	0.328													G|||	2176	0.434505	0.6218	0.2939	5008	,	,		18677	0.4177		0.4583	False		,,,				2504	0.274				p.C272S	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.G815C						PASS	.	G	SER/CYS	2621,1785	516.3+/-369.1	784,1053,366	76.0	83.0	81.0		815	4.2	0.0	19	dbSNP_92	81	3685,4911	615.7+/-396.4	800,2085,1413	yes	missense	ZNF180	NM_013256.3	112	1584,3138,1779	GG,GC,CC		42.8688,40.5129,48.5002	benign	272/693	44981883	6306,6696	2203	4298	6501	SO:0001583	missense	7733	exon5			CCATAGCATTTAT	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.815G>C	19.37:g.44981883C>G	ENSP00000221327:p.Cys272Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	993	0.45467032967032966	277	0.5630081300813008	118	0.3259668508287293	258	0.45104895104895104	340	0.44854881266490765	G	2.681	-0.275458	0.05679	0.594871	0.428688	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.05649	3.41;3.43	5.3	4.2	0.49525	.	0.366777	0.20138	N	0.098426	T	0.00012	0.0000	N	0.03608	-0.345	0.49915	P	1.64000000000053E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.17319	-1.0373	9	0.36615	T	0.2	-0.6346	9.886	0.41262	0.0:0.1515:0.6916:0.1568	rs1897820;rs52836449;rs1897820	247;271;272	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	S	272;247	ENSP00000221327:C272S;ENSP00000375818:C247S	ENSP00000221327:C272S	C	-	2	0	ZNF180	49673723	0.000000	0.05858	0.019000	0.16419	0.310000	0.27922	0.026000	0.13599	1.237000	0.43756	-0.120000	0.15030	TGC	C|0.530;G|0.470	0.470	strong		0.328	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
CDH17	1015	hgsc.bcm.edu	37	8	95161102	95161102	+	Splice_Site	SNP	G	G	A	rs35792427	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:95161102G>A	ENST00000027335.3	-	14	1921	c.1797C>T	c.(1795-1797)agC>agT	p.S599S	CDH17_ENST00000450165.2_Splice_Site_p.S599S|CDH17_ENST00000441892.2_Splice_Site_p.S385S	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	599	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)			NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			TCAGTGAATAGCTTCATCAAA	0.418													G|||	635	0.126797	0.0106	0.2305	5008	,	,		15416	0.1587		0.1143	False		,,,				2504	0.1902				p.S599S		Atlas-SNP	.											.	CDH17	119	.	0			c.C1797T						PASS	.	G	,	134,4272	95.3+/-134.0	3,128,2072	99.0	84.0	89.0		1797,1797	-6.6	0.9	8	dbSNP_126	89	1166,7434	237.8+/-269.5	82,1002,3216	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CDH17	NM_001144663.1,NM_004063.3	,	85,1130,5288	AA,AG,GG		13.5581,3.0413,9.9954	,	599/833,599/833	95161102	1300,11706	2203	4300	6503	SO:0001630	splice_region_variant	1015	exon14			TGAATAGCTTCAT	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.1797-1C>T	8.37:g.95161102G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	92	34	0.369565	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			G|0.892;A|0.108	0.108	strong		0.418	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	Silent
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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.L82F|SGK1_ENST00000367857.5_Missense_Mutation_p.L58F|SGK1_ENST00000475719.2_Missense_Mutation_p.L68F|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367858.5_Missense_Mutation_p.L163F|SGK1_ENST00000528577.1_Missense_Mutation_p.L96F	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	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	72	21	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		
NUP88	4927	hgsc.bcm.edu	37	17	5294976	5294976	+	Silent	SNP	T	T	A	rs14231	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5294976T>A	ENST00000573584.1	-	10	1898	c.1389A>T	c.(1387-1389)ccA>ccT	p.P463P		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	463					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						GAATTGGAGCTGGCTGCCTGG	0.478													T|||	2766	0.552316	0.3971	0.4236	5008	,	,		23299	0.8254		0.4404	False		,,,				2504	0.6871				p.P463P		Atlas-SNP	.											.	NUP88	47	.	0			c.A1389T						PASS	.	T		1846,2560	537.0+/-374.6	407,1032,764	106.0	93.0	97.0		1389	-3.3	0.9	17	dbSNP_52	97	3390,5210	501.8+/-375.5	665,2060,1575	no	coding-synonymous	NUP88	NM_002532.4		1072,3092,2339	AA,AT,TT		39.4186,41.8974,40.2583		463/742	5294976	5236,7770	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon10			TGGAGCTGGCTGC	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1389A>T	17.37:g.5294976T>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			T|0.571;A|0.429	0.429	strong		0.478	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
KIF16B	55614	hgsc.bcm.edu	37	20	16493533	16493533	+	Silent	SNP	T	T	C	rs6135775	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:16493533T>C	ENST00000354981.2	-	5	541	c.384A>G	c.(382-384)ggA>ggG	p.G128G	KIF16B_ENST00000355755.3_Silent_p.G128G|KIF16B_ENST00000408042.1_Silent_p.G128G|KIF16B_ENST00000378003.2_5'UTR	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	128	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GACTGAAGAGTCCTTCACAGA	0.463													C|||	1208	0.241214	0.0582	0.2839	5008	,	,		19635	0.38		0.2843	False		,,,				2504	0.271				p.G128G		Atlas-SNP	.											.	KIF16B	305	.	0			c.A384G						PASS	.	C	,,	459,3947	784.2+/-414.7	28,403,1772	108.0	96.0	100.0		384,384,384	-3.9	0.9	20	dbSNP_114	100	2642,5958	686.7+/-404.1	386,1870,2044	no	coding-synonymous,coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	,,	414,2273,3816	CC,CT,TT		30.7209,10.4176,23.8428	,,	128/1267,128/1393,128/1318	16493533	3101,9905	2203	4300	6503	SO:0001819	synonymous_variant	55614	exon5			GAAGAGTCCTTCA	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.384A>G	20.37:g.16493533T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	45	31	0.688889	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			T|0.759;C|0.241	0.241	strong		0.463	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
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 GAIIx	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	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	66	21	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	
ADH4	127	hgsc.bcm.edu	37	4	100052733	100052733	+	Silent	SNP	C	C	A	rs1126670	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100052733C>A	ENST00000265512.7	-	6	839	c.765G>T	c.(763-765)ccG>ccT	p.P255P	ADH4_ENST00000508393.1_Silent_p.P274P|RP11-696N14.1_ENST00000500358.2_RNA|ADH4_ENST00000423445.1_Silent_p.P274P|ADH4_ENST00000505590.1_Silent_p.P274P	NM_000670.3	NP_000661.2	P08319	ADH4_HUMAN	alcohol dehydrogenase 4 (class II), pi polypeptide	255					alcohol catabolic process (GO:0046164)|alcohol metabolic process (GO:0006066)|cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|quinone metabolic process (GO:1901661)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase (NAD) activity (GO:0004022)|alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|all-trans retinal binding (GO:0005503)|benzaldehyde dehydrogenase activity (GO:0019115)|ethanol binding (GO:0035276)|NAD binding (GO:0051287)|NADPH:quinone reductase activity (GO:0003960)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)|retinol binding (GO:0019841)|retinol dehydrogenase activity (GO:0004745)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(123;4.48e-08)		CTTCCTGGATCGGTTTATGTA	0.438													C|||	4243	0.847244	0.8608	0.7709	5008	,	,		19123	0.999		0.6978	False		,,,				2504	0.8804				p.P255P		Atlas-SNP	.											ADH4,NS,carcinoma,-1,1	ADH4	35	1	0			c.G765T						PASS	.	C		3626,780	752.9+/-412.3	1487,652,64	121.0	122.0	122.0		765	-0.6	0.2	4	dbSNP_86	122	5885,2715	682.6+/-403.8	1994,1897,409	no	coding-synonymous	ADH4	NM_000670.3		3481,2549,473	AA,AC,CC		31.5698,17.7031,26.8722		255/381	100052733	9511,3495	2203	4300	6503	SO:0001819	synonymous_variant	127	exon6			CTGGATCGGTTTA	M15943	CCDS34032.1	4q22	2008-02-05				ENSG00000198099	1.1.1.1	"""Alcohol dehydrogenases"""	252	protein-coding gene	gene with protein product		103740					Standard	NM_000670		Approved	ADH-2	uc003hun.3	P08319		ENST00000265512.7:c.765G>T	4.37:g.100052733C>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_000670	A8K470|B4DIE7|C9J4A9|Q8TCD7	Silent	SNP	ENST00000265512.7	37	CCDS34032.1																																																																																			C|0.217;A|0.783	0.783	strong		0.438	ADH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364220.2	NM_000670	
OR2T29	343563	hgsc.bcm.edu	37	1	248722671	248722671	+	Missense_Mutation	SNP	T	T	A	rs140437806	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248722671T>A	ENST00000328570.3	-	1	126	c.122A>T	c.(121-123)aAg>aTg	p.K41M	RP11-438F14.3_ENST00000438623.1_RNA	NM_001004694.2	NP_001004694.2	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T, member 29	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|lung(4)	5	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)			AGACAACGCCTTCAGGAAAAC	0.478													.|||	2494	0.498003	0.6399	0.4222	5008	,	,		17465	0.5427		0.338	False		,,,				2504	0.4785				p.K41M		Atlas-SNP	.											.	OR2T29	8	.	0			c.A122T						PASS	.						25.0	15.0	19.0					1																	248722671		2117	3771	5888	SO:0001583	missense	343563	exon1			AACGCCTTCAGGA		CCDS55695.1	1q44	2012-08-09			ENSG00000182783	ENSG00000182783		"""GPCR / Class A : Olfactory receptors"""	31253	protein-coding gene	gene with protein product							Standard	NM_001004694		Approved		uc001ieo.2	Q8NH02	OTTHUMG00000040382	ENST00000328570.3:c.122A>T	1.37:g.248722671T>A	ENSP00000331774:p.Lys41Met	Somatic	372	0	0		WXS	Illumina HiSeq	Phase_I	467	175	0.374732	NM_001004694		Missense_Mutation	SNP	ENST00000328570.3	37	CCDS55695.1	.	.	.	.	.	.	.	.	.	.	N	0	-2.755629	0.00085	.	.	ENSG00000182783	ENST00000328570	T	0.00424	7.45	2.73	2.73	0.32206	.	0.130450	0.36409	N	0.002609	T	0.00073	0.0002	N	0.00022	-2.74	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20706	-1.0267	9	0.02654	T	1	.	6.2239	0.20698	0.7754:0.0:0.0:0.2246	.	41	Q8NH02	O2T29_HUMAN	M	41	ENSP00000331774:K41M	ENSP00000331774:K41M	K	-	2	0	OR2T29	246789294	0.001000	0.12720	0.995000	0.50966	0.024000	0.10985	1.554000	0.36266	0.191000	0.20236	-1.231000	0.01572	AAG	T|0.250;A|0.750	0.750	weak		0.478	OR2T29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097132.1	NM_001004694	
C15orf52	388115	hgsc.bcm.edu	37	15	40633138	40633138	+	Silent	SNP	A	A	T	rs4924455	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:40633138A>T	ENST00000559313.1	-	1	30	c.15T>A	c.(13-15)gcT>gcA	p.A5A	C15orf52_ENST00000557973.1_5'Flank|C15orf52_ENST00000397536.2_5'Flank	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	5							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		TTCGCTGCTCAGCACACGAGA	0.647													A|||	1053	0.210264	0.0045	0.3098	5008	,	,		15062	0.5833		0.0915	False		,,,				2504	0.1554				p.A5A		Atlas-SNP	.											.	C15orf52	47	.	0			c.T15A						PASS	.	A		68,3672		0,68,1802	10.0	13.0	12.0		15	3.4	1.0	15	dbSNP_111	12	618,7568		18,582,3493	no	coding-synonymous	C15orf52	NM_207380.2		18,650,5295	TT,TA,AA		7.5495,1.8182,5.7521		5/535	40633138	686,11240	1870	4093	5963	SO:0001819	synonymous_variant	388115	exon1			CTGCTCAGCACAC	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.15T>A	15.37:g.40633138A>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	78	61	0.782051	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Silent	SNP	ENST00000559313.1	37	CCDS10055.2																																																																																			A|0.762;T|0.238	0.238	strong		0.647	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
SKA3	221150	hgsc.bcm.edu	37	13	21746637	21746637	+	Missense_Mutation	SNP	C	C	T	rs11546983	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:21746637C>T	ENST00000314759.5	-	3	296	c.172G>A	c.(172-174)Gtt>Att	p.V58I	SKA3_ENST00000400018.3_Missense_Mutation_p.V58I	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3	58			V -> I (in dbSNP:rs11546983). {ECO:0000269|PubMed:15489334}.		chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|regulation of microtubule polymerization or depolymerization (GO:0031110)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|spindle microtubule (GO:0005876)				breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGAATATTAACATCATCCTTT	0.249													C|||	45	0.00898562	0.0023	0.0115	5008	,	,		17666	0.0		0.0288	False		,,,				2504	0.0051				p.V58I		Atlas-SNP	.											.	SKA3	76	.	0			c.G172A						PASS	.	C	ILE/VAL,ILE/VAL	32,4330		0,32,2149	33.0	34.0	34.0		172,172	4.1	0.9	13	dbSNP_120	34	322,8228		5,312,3958	yes	missense,missense	SKA3	NM_001166017.1,NM_145061.5	29,29	5,344,6107	TT,TC,CC		3.7661,0.7336,2.7416	probably-damaging,probably-damaging	58/389,58/413	21746637	354,12558	2181	4275	6456	SO:0001583	missense	221150	exon3			TATTAACATCATC	AF361358	CCDS31946.1, CCDS53856.1	13q11	2013-01-17	2009-08-19	2009-08-19	ENSG00000165480	ENSG00000165480			20262	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 3"""	C13orf3		19387489, 19289083, 19646878, 19360002	Standard	NM_145061		Approved	MGC4832, RAMA1	uc001unt.3	Q8IX90	OTTHUMG00000016539	ENST00000314759.5:c.172G>A	13.37:g.21746637C>T	ENSP00000319417:p.Val58Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Missense_Mutation	SNP	ENST00000314759.5	37	CCDS31946.1	34	0.015567765567765568	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	24	0.0316622691292876	C	15.74	2.922622	0.52653	0.007336	0.037661	ENSG00000165480	ENST00000314759;ENST00000400018	T;T	0.24151	1.87;1.87	5.81	4.06	0.47325	.	0.252908	0.40554	N	0.001076	T	0.04137	0.0115	L	0.50333	1.59	0.33351	D	0.571094	P;B	0.41450	0.75;0.141	B;B	0.29524	0.103;0.067	T	0.21381	-1.0247	10	0.38643	T	0.18	-7.2162	10.0581	0.42257	0.0:0.8397:0.0:0.1603	rs11546983;rs17855680;rs11546983	58;58	Q8IX90-3;Q8IX90	.;SKA3_HUMAN	I	58	ENSP00000319417:V58I;ENSP00000382896:V58I	ENSP00000319417:V58I	V	-	1	0	SKA3	20644637	0.997000	0.39634	0.941000	0.38009	0.867000	0.49689	0.532000	0.23067	1.456000	0.47831	0.591000	0.81541	GTT	C|0.980;T|0.020	0.020	strong		0.249	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	
CCDC137	339230	hgsc.bcm.edu	37	17	79637367	79637367	+	Missense_Mutation	SNP	C	C	G	rs7226091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79637367C>G	ENST00000329214.8	+	3	784	c.381C>G	c.(379-381)caC>caG	p.H127Q		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	127			H -> Q (in dbSNP:rs7226091).				poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CCTATATCCACCGCATGCAGC	0.577													G|||	1198	0.239217	0.3472	0.1484	5008	,	,		17806	0.2252		0.2515	False		,,,				2504	0.1595				p.H127Q		Atlas-SNP	.											CCDC137,NS,carcinoma,0,2	CCDC137	27	2	0			c.C381G						PASS	.	G	GLN/HIS	1319,2607		239,841,883	31.0	37.0	35.0		381	0.3	0.5	17	dbSNP_116	35	1782,6530		200,1382,2574	yes	missense	CCDC137	NM_199287.2	24	439,2223,3457	GG,GC,CC		21.4389,33.5965,25.3391	benign	127/290	79637367	3101,9137	1963	4156	6119	SO:0001583	missense	339230	exon3			TATCCACCGCATG	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.381C>G	17.37:g.79637367C>G	ENSP00000329360:p.His127Gln	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_199287		Missense_Mutation	SNP	ENST00000329214.8	37	CCDS42400.1	546	0.25	187	0.3800813008130081	59	0.16298342541436464	124	0.21678321678321677	176	0.23218997361477572	G	0.012	-1.648770	0.00785	0.335965	0.214389	ENSG00000185298	ENST00000329214	T	0.15952	2.38	4.88	0.343	0.16001	.	0.377525	0.26539	N	0.023820	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45629	-0.9248	9	0.14656	T	0.56	-12.8019	2.9796	0.05949	0.2238:0.2606:0.4154:0.1002	rs7226091;rs60336178;rs7226091	127	Q6PK04	CC137_HUMAN	Q	127	ENSP00000329360:H127Q	ENSP00000329360:H127Q	H	+	3	2	CCDC137	77247772	0.017000	0.18338	0.502000	0.27614	0.234000	0.25298	-0.066000	0.11598	0.022000	0.15160	-0.709000	0.03644	CAC	C|0.754;G|0.245	0.245	strong		0.577	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
APOBEC3H	164668	hgsc.bcm.edu	37	22	39497404	39497404	+	Missense_Mutation	SNP	G	G	C	rs139297	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39497404G>C	ENST00000401756.1	+	3	389	c.313G>C	c.(313-315)Ggc>Cgc	p.G105R	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.G105R|APOBEC3H_ENST00000421988.2_Missense_Mutation_p.G105R|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.G105R	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	105			G -> R (in allele A3H-Var; haplotype 2; allele presenting a higher expression and which is more effective in retrotransposons and HIV-1 restriction; increases protein stability and exhibits a cytoplasmic localization; dbSNP:rs139297). {ECO:0000269|PubMed:15461802}.		cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					TCTGAACCTGGGCATCTTCGC	0.612													C|||	2628	0.52476	0.8752	0.3833	5008	,	,		4666	0.3155		0.4642	False		,,,				2504	0.4294				p.G105R		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G313C						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3573,833		1455,663,85	91.0	67.0	75.0		313,313,313,313	-4.6	0.0	22	dbSNP_78	75	3964,4636		887,2190,1223	yes	missense,missense,missense,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	125,125,125,125	2342,2853,1308	CC,CG,GG		46.093,18.906,42.0498	benign,benign,benign,benign	105/183,105/201,105/155,105/184	39497404	7537,5469	2203	4300	6503	SO:0001583	missense	164668	exon3			AACCTGGGCATCT	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.313G>C	22.37:g.39497404G>C	ENSP00000385741:p.Gly105Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	1088	0.4981684981684982	427	0.8678861788617886	127	0.35082872928176795	172	0.3006993006993007	362	0.47757255936675463	.	0.023	-1.398362	0.01175	0.81094	0.46093	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000421988;ENST00000401756	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	3.33	-4.63	0.03359	.	.	.	.	.	T	0.00012	0.0000	N	0.00030	-2.605	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38112	-0.9676	8	0.02654	T	1	-0.0266	7.6083	0.28115	0.5538:0.2197:0.2266:0.0	rs139297;rs52798787;rs61578228;rs139297	105	B7TQM3	.	R	105	ENSP00000216123:G105R;ENSP00000411754:G105R;ENSP00000393520:G105R;ENSP00000385741:G105R	ENSP00000216123:G105R	G	+	1	0	APOBEC3H	37827350	0.000000	0.05858	0.001000	0.08648	0.040000	0.13550	-1.028000	0.03589	-1.275000	0.02417	-0.365000	0.07479	GGC	G|0.456;C|0.544	0.544	strong		0.612	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
ASGR2	433	hgsc.bcm.edu	37	17	7012077	7012077	+	Splice_Site	SNP	C	C	T	rs2304979	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7012077C>T	ENST00000380952.2	-	3	519	c.255G>A	c.(253-255)ggG>ggA	p.G85G	ASGR2_ENST00000355035.5_Splice_Site_p.G85G|ASGR2_ENST00000446679.2_Splice_Site_p.G66G|ASGR2_ENST00000254850.7_Intron	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	85			G -> R (in dbSNP:rs2304978). {ECO:0000269|PubMed:1371982, ECO:0000269|PubMed:3863106, ECO:0000269|Ref.4}.		bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)	p.G85G(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	CCTGCTGGCCCCCGTGACCCT	0.632													C|||	1277	0.254992	0.0703	0.3689	5008	,	,		14724	0.2887		0.2724	False		,,,				2504	0.3712				p.G85G		Atlas-SNP	.											ASGR2,NS,carcinoma,-2,2	ASGR2	38	2	1	Substitution - coding silent(1)	stomach(1)	c.G255A						PASS	.	C	,,,,	474,3932	216.1+/-234.9	30,414,1759	68.0	60.0	63.0		255,,255,,198	-0.3	0.0	17	dbSNP_100	63	2427,6173	390.0+/-343.1	362,1703,2235	no	coding-synonymous-near-splice,intron,coding-synonymous-near-splice,intron,coding-synonymous-near-splice	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	,,,,	392,2117,3994	TT,TC,CC		28.2209,10.7581,22.3051	,,,,	85/312,,85/312,,66/293	7012077	2901,10105	2203	4300	6503	SO:0001630	splice_region_variant	433	exon3			CTGGCCCCCGTGA	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.256+1G>A	17.37:g.7012077C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Silent	SNP	ENST00000380952.2	37	CCDS32544.1																																																																																			C|0.777;T|0.223	0.223	strong		0.632	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	Silent
NCR1	9437	hgsc.bcm.edu	37	19	55420801	55420801	+	Silent	SNP	C	C	A	rs3765013	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55420801C>A	ENST00000291890.4	+	4	591	c.553C>A	c.(553-555)Cga>Aga	p.R185R	NCR1_ENST00000594765.1_Silent_p.R185R|NCR1_ENST00000598576.1_Silent_p.R173R|NCR1_ENST00000447255.1_Silent_p.R185R|NCR1_ENST00000357397.5_Silent_p.R78R|NCR1_ENST00000350790.5_Silent_p.R90R|NCR1_ENST00000338835.5_Silent_p.R185R	NM_004829.5	NP_004820.2	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	185	Ig-like 2.				cellular defense response (GO:0006968)|intracellular signal transduction (GO:0035556)|natural killer cell activation (GO:0030101)|regulation of natural killer cell mediated cytotoxicity (GO:0042269)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|SWI/SNF complex (GO:0016514)	receptor signaling protein activity (GO:0005057)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		CACAGCCCACCGAGGGACATA	0.567													.|||	2420	0.483227	0.7148	0.4236	5008	,	,		17754	0.5268		0.2286	False		,,,				2504	0.4294				p.R185R		Atlas-SNP	.											.	NCR1	60	.	0			c.C553A						PASS	.	A	,,,,	2787,1619	498.4+/-364.1	868,1051,284	84.0	82.0	82.0		553,553,268,268,553	-1.5	0.0	19	dbSNP_107	82	1935,6665	726.6+/-406.6	226,1483,2591	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCR1	NM_001145457.1,NM_001145458.1,NM_001242356.1,NM_001242357.1,NM_004829.5	,,,,	1094,2534,2875	AA,AC,CC		22.5,36.7453,36.3063	,,,,	185/304,185/288,90/210,90/193,185/305	55420801	4722,8284	2203	4300	6503	SO:0001819	synonymous_variant	9437	exon4			GCCCACCGAGGGA	AJ001383	CCDS12911.1, CCDS46181.1, CCDS46182.1, CCDS56103.1	19q13.42	2013-09-20	2002-11-13	2002-11-15	ENSG00000189430	ENSG00000189430		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6731	protein-coding gene	gene with protein product		604530	"""lymphocyte antigen 94 (mouse) homolog (activating NK-receptor; NK-p46)"""	LY94		9730896	Standard	NM_001145457		Approved	NK-p46, NKP46, CD335	uc002qib.2	O76036	OTTHUMG00000183212	ENST00000291890.4:c.553C>A	19.37:g.55420801C>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_001145458	B0V3L2|B0V3L3|B0V3L4|B0V3L5|B8JL03|O76016|O76017|O76018	Silent	SNP	ENST00000291890.4	37	CCDS12911.1																																																																																			C|0.604;A|0.396	0.396	strong		0.567	NCR1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465680.1		
TMX4	56255	hgsc.bcm.edu	37	20	7963041	7963041	+	Missense_Mutation	SNP	C	C	T	rs2076015	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:7963041C>T	ENST00000246024.2	-	8	1122	c.907G>A	c.(907-909)Gga>Aga	p.G303R		NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	303	Glu-rich.		G -> R (in dbSNP:rs2076015). {ECO:0000269|PubMed:15489334}.		cell redox homeostasis (GO:0045454)|oxidation-reduction process (GO:0055114)|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(2)|lung(11)|skin(1)	17						CCGTCCTCTCCTGGGGGCCCC	0.582													C|||	1773	0.354034	0.6483	0.2334	5008	,	,		16298	0.5883		0.0726	False		,,,				2504	0.09				p.G303R		Atlas-SNP	.											.	TMX4	39	.	0			c.G907A						PASS	.	C	ARG/GLY	2456,1950	623.1+/-394.1	683,1090,430	140.0	123.0	129.0		907	-0.6	0.0	20	dbSNP_96	129	581,8019	156.0+/-209.9	22,537,3741	yes	missense	TMX4	NM_021156.2	125	705,1627,4171	TT,TC,CC		6.7558,44.2578,23.3508	benign	303/350	7963041	3037,9969	2203	4300	6503	SO:0001583	missense	56255	exon8			CCTCTCCTGGGGG		CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827		"""Protein disulfide isomerases"""	25237	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 14"""		"""thioredoxin domain containing 13"""	TXNDC13			Standard	NM_021156		Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.907G>A	20.37:g.7963041C>T	ENSP00000246024:p.Gly303Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Missense_Mutation	SNP	ENST00000246024.2	37	CCDS13101.1	764	0.3498168498168498	308	0.6260162601626016	73	0.20165745856353592	325	0.5681818181818182	58	0.07651715039577836	C	2.423	-0.332568	0.05314	0.557422	0.067558	ENSG00000125827	ENST00000246024	T	0.09255	3.0	5.72	-0.564	0.11774	.	0.974158	0.08471	N	0.940949	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33033	-0.9884	9	0.10111	T	0.7	0.0112	5.9282	0.19124	0.0:0.2476:0.1306:0.6218	rs2076015;rs17846062;rs17859056;rs52797785;rs60332072;rs2076015	303	Q9H1E5	TMX4_HUMAN	R	303	ENSP00000246024:G303R	ENSP00000246024:G303R	G	-	1	0	TMX4	7911041	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.068000	0.03447	-0.104000	0.12154	-1.353000	0.01230	GGA	C|0.693;T|0.307	0.307	strong		0.582	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156	
SBF1	6305	hgsc.bcm.edu	37	22	50894987	50894987	+	Silent	SNP	G	G	A	rs79468232	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50894987G>A	ENST00000390679.3	-	29	4126	c.3942C>T	c.(3940-3942)ccC>ccT	p.P1314P	SBF1_ENST00000348911.6_Silent_p.P1315P|SBF1_ENST00000380817.3_Silent_p.P1340P|SBF1_ENST00000476293.1_5'Flank			O95248	MTMR5_HUMAN	SET binding factor 1	1314	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)		AGCCCGGGTCGGGAGGGCCCC	0.706													G|||	214	0.0427316	0.0598	0.0245	5008	,	,		9310	0.0		0.0517	False		,,,				2504	0.0675				p.P1340P		Atlas-SNP	.											.	SBF1	211	.	0			c.C4020T						PASS	.	G		195,3583		1,193,1695	7.0	8.0	8.0		4020	-9.3	0.0	22	dbSNP_131	8	397,7793		7,383,3705	no	coding-synonymous	SBF1	NM_002972.2		8,576,5400	AA,AG,GG		4.8474,5.1615,4.9465		1340/1894	50894987	592,11376	1889	4095	5984	SO:0001819	synonymous_variant	6305	exon30			CGGGTCGGGAGGG	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.3942C>T	22.37:g.50894987G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				G|0.963;A|0.037	0.037	strong		0.706	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
POLD1	5424	hgsc.bcm.edu	37	19	50909765	50909765	+	Silent	SNP	C	C	T	rs2230245	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50909765C>T	ENST00000440232.2	+	12	1538	c.1485C>T	c.(1483-1485)acC>acT	p.T495T	POLD1_ENST00000595904.1_Silent_p.T495T|POLD1_ENST00000599857.1_Silent_p.T495T	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	495					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|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)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GCATCATCACCGACCTGCAGG	0.632								DNA polymerases (catalytic subunits)					C|||	388	0.077476	0.0318	0.0749	5008	,	,		17886	0.0099		0.1252	False		,,,				2504	0.1616				p.T495T		Atlas-SNP	.											POLD1_ENST00000440232,colon,carcinoma,0,2	POLD1	174	2	0			c.C1485T						PASS	.	C		172,4226		7,158,2034	79.0	47.0	58.0		1485	-8.9	0.9	19	dbSNP_98	58	986,7608		52,882,3363	no	coding-synonymous	POLD1	NM_002691.2		59,1040,5397	TT,TC,CC		11.4731,3.9109,8.9132		495/1108	50909765	1158,11834	2199	4297	6496	SO:0001819	synonymous_variant	5424	exon12			CATCACCGACCTG		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.1485C>T	19.37:g.50909765C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_002691	Q8NER3|Q96H98	Silent	SNP	ENST00000440232.2	37	CCDS12795.1																																																																																			C|0.925;T|0.075	0.075	strong		0.632	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
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 GAIIx	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	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	120	26	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	
ITPKB	3707	hgsc.bcm.edu	37	1	226924642	226924642	+	Missense_Mutation	SNP	C	C	T	rs3754415	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:226924642C>T	ENST00000272117.3	-	1	517	c.518G>A	c.(517-519)cGc>cAc	p.R173H	ITPKB_ENST00000429204.1_Missense_Mutation_p.R173H|ITPKB_ENST00000366784.1_Missense_Mutation_p.R173H			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	173				R -> H (in Ref. 2; CAC40650 and 4; AAH15009). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				GGAGGGCGAGCGAGCCCTGCC	0.672													C|||	1137	0.227037	0.1694	0.2032	5008	,	,		15203	0.3393		0.2127	False		,,,				2504	0.2209				p.R173H	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,NS,carcinoma,0,1	ITPKB	158	1	0			c.G518A						PASS	.	C	HIS/ARG	773,3615		65,643,1486	48.0	54.0	52.0		518	4.6	1.0	1	dbSNP_107	52	1557,7003		156,1245,2879	yes	missense	ITPKB	NM_002221.3	29	221,1888,4365	TT,TC,CC		18.1893,17.6162,17.9951	probably-damaging	173/947	226924642	2330,10618	2194	4280	6474	SO:0001583	missense	3707	exon2			GGCGAGCGAGCCC	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.518G>A	1.37:g.226924642C>T	ENSP00000272117:p.Arg173His	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	521	0.23855311355311357	88	0.17886178861788618	80	0.22099447513812154	186	0.32517482517482516	167	0.22031662269129287	C	20.6	4.025053	0.75390	0.176162	0.181893	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.37752	1.24;1.24;1.18	4.6	4.6	0.57074	.	0.000000	0.53938	D	0.000055	T	0.00012	0.0000	L	0.27053	0.805	0.32169	P	0.581978	P	0.51537	0.946	B	0.36418	0.224	T	0.40040	-0.9584	9	0.54805	T	0.06	.	9.1902	0.37195	0.0:0.8609:0.0:0.1391	rs3754415;rs17851263	173	P27987	IP3KB_HUMAN	H	173	ENSP00000272117:R173H;ENSP00000411152:R173H;ENSP00000355748:R173H	ENSP00000272117:R173H	R	-	2	0	ITPKB	224991265	0.985000	0.35326	0.998000	0.56505	0.888000	0.51559	2.942000	0.49018	2.374000	0.81015	0.561000	0.74099	CGC	C|0.795;T|0.205	0.205	strong		0.672	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
PTPRS	5802	hgsc.bcm.edu	37	19	5210762	5210762	+	Silent	SNP	G	G	A	rs1143699	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5210762G>A	ENST00000587303.1	-	33	5388	c.5289C>T	c.(5287-5289)gaC>gaT	p.D1763D	PTPRS_ENST00000588012.1_Silent_p.D1725D|PTPRS_ENST00000588552.1_5'UTR|PTPRS_ENST00000372412.4_Silent_p.D1764D|PTPRS_ENST00000262963.6_Silent_p.D1743D|PTPRS_ENST00000348075.2_Silent_p.D1725D|PTPRS_ENST00000357368.4_Silent_p.D1763D|PTPRS_ENST00000592099.1_Silent_p.D1316D|PTPRS_ENST00000353284.2_Silent_p.D1316D			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	1763	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|corpus callosum development (GO:0022038)|extracellular matrix organization (GO:0030198)|hippocampus development (GO:0021766)|peptidyl-tyrosine dephosphorylation (GO:0035335)|spinal cord development (GO:0021510)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(9)|ovary(4)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)	61				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0321)|Lung(535;0.182)	Alendronate(DB00630)|Etidronic acid(DB01077)	TGCGCCAGAAGTCTTCCGTGG	0.662													G|||	504	0.100639	0.2216	0.0807	5008	,	,		18976	0.0		0.0994	False		,,,				2504	0.0562				p.D1763D		Atlas-SNP	.											.	PTPRS	169	.	0			c.C5289T						PASS	.	G	,,,	819,3587	325.0+/-298.9	87,645,1471	98.0	77.0	84.0		5289,3948,5175,3960	-2.7	1.0	19	dbSNP_86	84	875,7725	197.5+/-242.1	46,783,3471	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRS	NM_002850.3,NM_130853.2,NM_130854.2,NM_130855.2	,,,	133,1428,4942	AA,AG,GG		10.1744,18.5883,13.0248	,,,	1763/1949,1316/1502,1725/1911,1320/1506	5210762	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	5802	exon34			CCAGAAGTCTTCC	U35234	CCDS12139.1, CCDS12140.1, CCDS45930.1, CCDS74265.1	19p13.3	2013-02-11				ENSG00000105426		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9681	protein-coding gene	gene with protein product		601576				8954782, 8524829	Standard	NM_002850		Approved		uc002mbv.3	Q13332		ENST00000587303.1:c.5289C>T	19.37:g.5210762G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	35	0.380435	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Silent	SNP	ENST00000587303.1	37	CCDS45930.1																																																																																			G|0.874;A|0.126	0.126	strong		0.662	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2		
ACSM5	54988	hgsc.bcm.edu	37	16	20442613	20442613	+	Silent	SNP	T	T	C	rs77351186	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20442613T>C	ENST00000331849.4	+	10	1425	c.1278T>C	c.(1276-1278)acT>acC	p.T426T		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	426					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						TCAGACCCACTCGGCCCTTCT	0.498																																					p.T426T		Atlas-SNP	.											ACSM5,NS,carcinoma,0,1	ACSM5	101	1	0			c.T1278C						PASS	.						171.0	145.0	154.0					16																	20442613		2203	4300	6503	SO:0001819	synonymous_variant	54988	exon10			ACCCACTCGGCCC		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1278T>C	16.37:g.20442613T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	125	15	0.12	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Silent	SNP	ENST00000331849.4	37	CCDS10585.1																																																																																			T|0.997;C|0.003	0.003	strong		0.498	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
PLEC	5339	hgsc.bcm.edu	37	8	144994916	144994916	+	Missense_Mutation	SNP	C	C	T	rs35027700	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144994916C>T	ENST00000322810.4	-	32	9653	c.9484G>A	c.(9484-9486)Gtc>Atc	p.V3162I	PLEC_ENST00000354589.3_Missense_Mutation_p.V3025I|PLEC_ENST00000357649.2_Missense_Mutation_p.V3029I|PLEC_ENST00000436759.2_Missense_Mutation_p.V3052I|PLEC_ENST00000354958.2_Missense_Mutation_p.V3003I|PLEC_ENST00000527096.1_Missense_Mutation_p.V3048I|PLEC_ENST00000345136.3_Missense_Mutation_p.V3025I|PLEC_ENST00000356346.3_Missense_Mutation_p.V3011I|PLEC_ENST00000398774.2_Missense_Mutation_p.V2993I	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3162	Globular 2.		V -> I (in dbSNP:rs35027700).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCCGCGATGACGTTGGCACCC	0.637													C|||	419	0.0836661	0.2965	0.036	5008	,	,		16170	0.0		0.002	False		,,,				2504	0.0				p.V3162I		Atlas-SNP	.											.	PLEC	1144	.	0			c.G9484A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	851,3279		83,685,1297	28.0	33.0	32.0		9154,9031,9007,9484,8977,9073,9085,9073	2.2	0.0	8	dbSNP_126	32	21,8257		0,21,4118	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	29,29,29,29,29,29,29,29	83,706,5415	TT,TC,CC		0.2537,20.6053,7.0277	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	3052/4575,3011/4534,3003/4526,3162/4685,2993/4516,3025/4548,3029/4552,3025/4548	144994916	872,11536	2065	4139	6204	SO:0001583	missense	5339	exon32			CGATGACGTTGGC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.9484G>A	8.37:g.144994916C>T	ENSP00000323856:p.Val3162Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	61	38	0.622951	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	149	0.06822344322344322	134	0.27235772357723576	14	0.03867403314917127	0	0.0	1	0.0013192612137203166	C	1.718	-0.497466	0.04291	0.206053	0.002537	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72;-0.72;-0.72;-0.72;-0.72;-0.72	4.1	2.25	0.28309	.	0.269957	0.28859	U	0.013903	T	0.00012	0.0000	N	0.22421	0.69	0.49687	P	1.8499999999999073E-4	B;B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001;0.001;0.001;0.001	T	0.08166	-1.0735	9	0.31617	T	0.26	.	7.8073	0.29211	0.1602:0.7502:0.0:0.0896	rs35027700	3052;3011;3003;3162;2993;3025;3029;3025	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	I	3025;3029;3025;2993;3162;3003;3011;3052;3048	ENSP00000344848:V3025I;ENSP00000350277:V3029I;ENSP00000346602:V3025I;ENSP00000381756:V2993I;ENSP00000323856:V3162I;ENSP00000347044:V3003I;ENSP00000348702:V3011I;ENSP00000388180:V3052I;ENSP00000434583:V3048I	ENSP00000323856:V3162I	V	-	1	0	PLEC	145066904	0.069000	0.21087	0.012000	0.15200	0.011000	0.07611	0.487000	0.22356	0.300000	0.22699	-0.480000	0.04831	GTC	C|0.953;T|0.047	0.047	strong		0.637	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
TGFA	7039	hgsc.bcm.edu	37	2	70677994	70677994	+	Silent	SNP	G	G	A	rs2166975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:70677994G>A	ENST00000295400.6	-	6	727	c.480C>T	c.(478-480)gtC>gtT	p.V160V	TGFA_ENST00000418333.2_Silent_p.V159V|TGFA_ENST00000445399.1_Intron|TGFA_ENST00000444975.1_Silent_p.V166V|TGFA_ENST00000450929.1_Silent_p.V165V	NM_001099691.2|NM_003236.3	NP_001093161.1|NP_003227.1	P01135	TGFA_HUMAN	transforming growth factor, alpha	160					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|mammary gland alveolus development (GO:0060749)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell division (GO:0051781)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mitosis (GO:0045840)|response to drug (GO:0042493)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)	p.V160V(1)		haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	4						GGGCTCTTCAGACCACTGGCA	0.537													G|||	1039	0.207468	0.1309	0.1326	5008	,	,		19477	0.2877		0.2565	False		,,,				2504	0.2311				p.V160V		Atlas-SNP	.											TGFA,NS,lymphoid_neoplasm,0,1	TGFA	14	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C480T						PASS	.	G	,	729,3677	292.7+/-282.2	51,627,1525	62.0	50.0	54.0		477,480	2.1	1.0	2	dbSNP_96	54	2330,6270	374.2+/-337.3	324,1682,2294	no	coding-synonymous,coding-synonymous	TGFA	NM_001099691.2,NM_003236.3	,	375,2309,3819	AA,AG,GG		27.093,16.5456,23.5199	,	159/160,160/161	70677994	3059,9947	2203	4300	6503	SO:0001819	synonymous_variant	7039	exon6			TCTTCAGACCACT		CCDS1905.1, CCDS46316.1	2p13	2012-10-02			ENSG00000163235	ENSG00000163235			11765	protein-coding gene	gene with protein product		190170				3459638, 10552925	Standard	NM_003236		Approved		uc002sgs.4	P01135	OTTHUMG00000129669	ENST00000295400.6:c.480C>T	2.37:g.70677994G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_003236	A8K286|Q15577|Q53SK7|Q9BS56|Q9UEI3|Q9UKM1|Q9UKM2|Q9UKM3	Silent	SNP	ENST00000295400.6	37	CCDS1905.1																																																																																			G|0.782;A|0.218	0.218	strong		0.537	TGFA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251870.2		
MYPOP	339344	hgsc.bcm.edu	37	19	46394268	46394268	+	Silent	SNP	G	G	A	rs150220406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46394268G>A	ENST00000322217.5	-	3	899	c.813C>T	c.(811-813)aaC>aaT	p.N271N		NM_001012643.2	NP_001012661.1	Q86VE0	MYPOP_HUMAN	Myb-related transcription factor, partner of profilin	271	Pro-rich.					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 negative regulation of transcription (GO:0001078)			large_intestine(2)|lung(1)|skin(1)	4						CCCGGATGGCGTTGGCAGTCT	0.697													G|||	46	0.0091853	0.0008	0.0216	5008	,	,		4924	0.0		0.0268	False		,,,				2504	0.0031				p.N271N		Atlas-SNP	.											.	MYPOP	23	.	0			c.C813T						PASS	.	G		27,4251		0,27,2112	7.0	6.0	6.0		813	-2.8	1.0	19	dbSNP_134	6	254,8110		0,254,3928	no	coding-synonymous	MYPOP	NM_001012643.2		0,281,6040	AA,AG,GG		3.0368,0.6311,2.2227		271/400	46394268	281,12361	2139	4182	6321	SO:0001819	synonymous_variant	339344	exon3			GATGGCGTTGGCA	BC044311	CCDS33055.1	19q13.32	2014-06-13			ENSG00000176182	ENSG00000176182			20178	protein-coding gene	gene with protein product	"""p42 Myb-related transcription factor, partner of profilin"""					15615774	Standard	NM_001012643		Approved	P42pop	uc002pdt.3	Q86VE0	OTTHUMG00000182486	ENST00000322217.5:c.813C>T	19.37:g.46394268G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_001012643		Silent	SNP	ENST00000322217.5	37	CCDS33055.1																																																																																			G|0.988;A|0.012	0.012	strong		0.697	MYPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461684.1	NM_001012643	
RXFP2	122042	hgsc.bcm.edu	37	13	32360547	32360547	+	Silent	SNP	A	A	G	rs7325513	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:32360547A>G	ENST00000298386.2	+	12	1028	c.957A>G	c.(955-957)gaA>gaG	p.E319E	RXFP2_ENST00000380314.1_Silent_p.E295E	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	319					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)		CGATAACGGAACTATCACCTC	0.353													G|||	3174	0.633786	0.6044	0.5072	5008	,	,		18811	0.7758		0.5676	False		,,,				2504	0.6851				p.E319E		Atlas-SNP	.											.	RXFP2	95	.	0			c.A957G						PASS	.	G	,	2721,1685	510.9+/-367.7	843,1035,325	115.0	105.0	109.0		885,957	2.9	1.0	13	dbSNP_116	109	5153,3447	505.3+/-376.3	1548,2057,695	no	coding-synonymous,coding-synonymous	RXFP2	NM_001166058.1,NM_130806.3	,	2391,3092,1020	GG,GA,AA		40.0814,38.2433,39.4587	,	295/731,319/755	32360547	7874,5132	2203	4300	6503	SO:0001819	synonymous_variant	122042	exon12			AACGGAACTATCA	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.957A>G	13.37:g.32360547A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_130806	B1ALE9|Q3KU23	Silent	SNP	ENST00000298386.2	37	CCDS9342.1																																																																																			A|0.387;G|0.613	0.613	strong		0.353	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806	
CEACAM5	1048	hgsc.bcm.edu	37	19	42213744	42213744	+	Silent	SNP	T	T	C	rs10402825	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:42213744T>C	ENST00000221992.6	+	2	324	c.210T>C	c.(208-210)ggT>ggC	p.G70G	CEA_ENST00000598976.1_Silent_p.G70G|CEACAM5_ENST00000405816.1_Silent_p.G70G|CEACAM7_ENST00000599715.1_5'Flank|CEACAM5_ENST00000398599.4_Silent_p.G70G	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	70	Ig-like 1.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		GGTACAAAGGTGAAAGAGTGG	0.483													N|||	687	0.137181	0.3056	0.0922	5008	,	,		19385	0.0		0.1958	False		,,,				2504	0.0225				p.G70G		Atlas-SNP	.											CEACAM5,NS,carcinoma,+1,1	CEACAM5	84	1	0			c.T210C						scavenged	.	G		1322,3084		205,912,1086	153.0	148.0	150.0		210	-6.2	0.0	19	dbSNP_119	150	1389,7211		116,1157,3027	no	coding-synonymous	CEACAM5	NM_004363.2		321,2069,4113	CC,CT,TT		16.1512,30.0045,20.8442		70/703	42213744	2711,10295	2203	4300	6503	SO:0001819	synonymous_variant	1048	exon2			CAAAGGTGAAAGA	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.210T>C	19.37:g.42213744T>C		Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	165	100	0.606061	NM_004363	H9KVA7	Silent	SNP	ENST00000221992.6	37	CCDS12584.1	285	0.1304945054945055	112	0.22764227642276422	38	0.10497237569060773	0	0.0	135	0.17810026385224276	-	11.13	1.548573	0.27652	0.300045	0.161512	ENSG00000105388	ENST00000398599	.	.	.	3.09	-6.19	0.02078	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8066	0.13323	0.4678:0.0:0.2992:0.233	rs10402825;rs12973300	.	.	.	R	67	.	.	X	+	1	0	CEACAM5	46905584	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.408000	0.01042	-2.845000	0.00333	-3.352000	0.00042	TGA	C|0.181;G|0.000;T|0.819	0.181	strong		0.483	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951584	130951584	+	Silent	SNP	T	T	C	rs7340507	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:130951584T>C	ENST00000312988.7	-	4	931	c.831A>G	c.(829-831)tcA>tcG	p.S277S		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	277					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					CCTTCTCAGCTGAGATGACTG	0.597													.|||	2348	0.46885	0.587	0.5014	5008	,	,		20424	0.4365		0.3628	False		,,,				2504	0.4284				p.S277S		Atlas-SNP	.											.	TUBA3E	73	.	0			c.A831G						PASS	.	T		2294,2112		349,1596,258	116.0	102.0	107.0		831	-5.8	0.6	2	dbSNP_116	107	3043,5557		544,1955,1801	no	coding-synonymous	TUBA3E	NM_207312.2		893,3551,2059	CC,CT,TT		35.3837,47.9346,41.0349		277/451	130951584	5337,7669	2203	4300	6503	SO:0001819	synonymous_variant	112714	exon4			CTCAGCTGAGATG	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.831A>G	2.37:g.130951584T>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	110	22	0.2	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			T|0.595;C|0.405	0.405	strong		0.597	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
OR10G7	390265	hgsc.bcm.edu	37	11	123909671	123909671	+	Missense_Mutation	SNP	G	G	A	rs11827843	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:123909671G>A	ENST00000330487.5	-	1	46	c.38C>T	c.(37-39)aCg>aTg	p.T13M		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	13			T -> M (in dbSNP:rs11827843).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		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;0.0521)		GGGAAGGCCCGTGAGGATGAA	0.547													A|||	393	0.0784744	0.1558	0.0288	5008	,	,		17247	0.0744		0.0139	False		,,,				2504	0.0798				p.T13M		Atlas-SNP	.											.	OR10G7	103	.	0			c.C38T						PASS	.	A	MET/THR	632,3768	268.6+/-268.5	46,540,1614	99.0	90.0	93.0		38	-2.3	0.2	11	dbSNP_120	93	156,8442	73.5+/-136.2	2,152,4145	yes	missense	OR10G7	NM_001004463.1	81	48,692,5759	AA,AG,GG		1.8144,14.3636,6.0625	benign	13/312	123909671	788,12210	2200	4299	6499	SO:0001583	missense	390265	exon1			AGGCCCGTGAGGA	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.38C>T	11.37:g.123909671G>A	ENSP00000329689:p.Thr13Met	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	171	143	0.836257	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	141	0.06456043956043957	66	0.13414634146341464	10	0.027624309392265192	52	0.09090909090909091	13	0.017150395778364115	g	5.259	0.233252	0.09969	0.143636	0.018144	ENSG00000182634	ENST00000330487	T	0.00421	7.46	3.27	-2.34	0.06704	.	1.119520	0.06816	N	0.791289	T	0.00012	0.0000	N	0.12887	0.27	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.09684	-1.0663	9	0.36615	T	0.2	.	3.5223	0.07747	0.5545:0.0:0.2732:0.1724	rs11827843	13	Q8NGN6	O10G7_HUMAN	M	13	ENSP00000329689:T13M	ENSP00000329689:T13M	T	-	2	0	OR10G7	123414881	0.000000	0.05858	0.247000	0.24249	0.028000	0.11728	-1.233000	0.02934	-0.569000	0.06030	-1.158000	0.01797	ACG	G|0.939;A|0.061	0.061	strong		0.547	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
HR	55806	hgsc.bcm.edu	37	8	21984650	21984650	+	Silent	SNP	A	A	G	rs12675745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:21984650A>G	ENST00000381418.4	-	3	2785	c.1305T>C	c.(1303-1305)ttT>ttC	p.F435F	HR_ENST00000312841.8_Silent_p.F435F	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	435					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CAGTGCCTGGAAAAGGGTCCG	0.647													G|||	2901	0.579273	0.6906	0.4914	5008	,	,		13552	0.3948		0.5984	False		,,,				2504	0.6616				p.F435F		Atlas-SNP	.											HR,NS,carcinoma,0,1	HR	71	1	0			c.T1305C						PASS	.	G	,	3080,1284		1107,866,209	53.0	60.0	57.0		1305,1305	5.0	0.9	8	dbSNP_120	57	5323,3205		1717,1889,658	no	coding-synonymous,coding-synonymous	HR	NM_005144.4,NM_018411.4	,	2824,2755,867	GG,GA,AA		37.5821,29.4225,34.82	,	435/1190,435/1135	21984650	8403,4489	2182	4264	6446	SO:0001819	synonymous_variant	55806	exon3			GCCTGGAAAAGGG	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1305T>C	8.37:g.21984650A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_018411	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			A|0.372;G|0.628	0.628	strong		0.647	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
DAAM1	23002	hgsc.bcm.edu	37	14	59797373	59797373	+	Silent	SNP	G	G	A	rs28927674	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:59797373G>A	ENST00000395125.1	+	12	1550	c.1527G>A	c.(1525-1527)gcG>gcA	p.A509A	DAAM1_ENST00000351081.1_Silent_p.A509A|DAAM1_ENST00000360909.3_Silent_p.A509A	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	509					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AGCAGGTGGCGGACCTCACAG	0.522													G|||	153	0.0305511	0.0053	0.0375	5008	,	,		19108	0.0109		0.0924	False		,,,				2504	0.0164				p.A509A		Atlas-SNP	.											DAAM1,colon,carcinoma,+1,1	DAAM1	95	1	0			c.G1527A						PASS	.	G		70,4336	66.4+/-103.9	0,70,2133	71.0	71.0	71.0		1527	-12.0	0.4	14	dbSNP_125	71	814,7786	188.9+/-235.7	33,748,3519	no	coding-synonymous	DAAM1	NM_014992.1		33,818,5652	AA,AG,GG		9.4651,1.5887,6.7969		509/1079	59797373	884,12122	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon13			GGTGGCGGACCTC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.1527G>A	14.37:g.59797373G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	143	64	0.447552	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.939;A|0.061	0.061	strong		0.522	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
DOCK5	80005	hgsc.bcm.edu	37	8	25159885	25159885	+	Silent	SNP	G	G	A	rs907157	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:25159885G>A	ENST00000276440.7	+	10	935	c.891G>A	c.(889-891)gtG>gtA	p.V297V	DOCK5_ENST00000481100.1_Silent_p.V297V	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	297					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		TCAGCCTTGTGTGCCAGATTG	0.582													G|||	1392	0.277955	0.0514	0.3646	5008	,	,		18282	0.244		0.498	False		,,,				2504	0.3313				p.V297V	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.G891A						PASS	.	G		485,3921	227.5+/-242.7	24,437,1742	93.0	71.0	79.0		891	4.7	1.0	8	dbSNP_86	79	4017,4583	547.9+/-385.3	924,2169,1207	no	coding-synonymous	DOCK5	NM_024940.6		948,2606,2949	AA,AG,GG		46.7093,11.0077,34.6148		297/1871	25159885	4502,8504	2203	4300	6503	SO:0001819	synonymous_variant	80005	exon10			CCTTGTGTGCCAG		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.891G>A	8.37:g.25159885G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1	681	0.3118131868131868	28	0.056910569105691054	145	0.4005524861878453	138	0.24125874125874125	370	0.48812664907651715	G	10.41	1.341314	0.24339	0.110077	0.467093	ENSG00000147459	ENST00000444569	T	0.18502	2.21	5.55	4.67	0.58626	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48681	-0.9014	6	0.87932	D	0	.	10.5137	0.44876	0.1514:0.0:0.8486:0.0	rs907157;rs17775605;rs17845314;rs17858153;rs61496588;rs907157	.	.	.	M	69	ENSP00000414125:V69M	ENSP00000414125:V69M	V	+	1	0	DOCK5	25215802	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	1.503000	0.35715	1.332000	0.45431	0.650000	0.86243	GTG	G|0.698;N|0.000	.	strong		0.582	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
MTG1	92170	hgsc.bcm.edu	37	10	135204950	135204950	+	5'Flank	SNP	C	C	G	rs1046175	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135204950C>G	ENST00000317502.6	+	0	0				PAOX_ENST00000368535.2_3'UTR|MTG1_ENST00000477902.2_5'Flank|PAOX_ENST00000480071.2_3'UTR|PAOX_ENST00000357296.3_Missense_Mutation_p.Q457E|RP11-108K14.8_ENST00000468317.2_Intron|PAOX_ENST00000368539.4_3'UTR|PAOX_ENST00000278060.5_Silent_p.P509P	NM_138384.2	NP_612393.2	Q9BT17	MTG1_HUMAN	mitochondrial ribosome-associated GTPase 1						GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|all cancers(32;1.69e-06)|Epithelial(32;1.94e-06)		AGCCCAGGCCCAGGCTCTAGC	0.632													N|||	4232	0.845048	0.68	0.8948	5008	,	,		17472	0.9792		0.8738	False		,,,				2504	0.865				p.Q457E		Atlas-SNP	.											PAOX_ENST00000357296,NS,carcinoma,0,2	PAOX	82	2	0			c.C1369G						PASS	.	G	,,GLU/GLN	3246,1160		1188,870,145	28.0	31.0	30.0		1527,,1369	2.3	0.0	10	dbSNP_86	30	7529,1069		3303,923,73	yes	coding-synonymous,utr-3,missense	PAOX	NM_152911.2,NM_207127.1,NM_207128.1	,,29	4491,1793,218	GG,GC,CC		12.4331,26.3277,17.1409	,,	509/512,,457/487	135204950	10775,2229	2203	4299	6502	SO:0001631	upstream_gene_variant	196743	exon6			CAGGCCCAGGCTC		CCDS31320.1	10q26.3	2013-05-24	2013-05-24	2006-01-09	ENSG00000148824	ENSG00000148824			32159	protein-coding gene	gene with protein product			"""GTP-binding protein 7"", ""GTP-binding protein 7 (putative)"", ""mitochondrial GTPase 1 homolog (S. cerevisiae)"""	GTPBP7		12808030, 23396448	Standard	NM_138384		Approved		uc001lnd.3	Q9BT17	OTTHUMG00000166564		10.37:g.135204950C>G	Exception_encountered	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_207128	Q5VWX8|Q6PIY9|Q8IYJ4|Q8NC48|Q9BVU8	Missense_Mutation	SNP	ENST00000317502.6	37	CCDS31320.1	1869|1869	0.8557692307692307|0.8557692307692307	330|330	0.6707317073170732|0.6707317073170732	313|313	0.8646408839779005|0.8646408839779005	553|553	0.9667832167832168|0.9667832167832168	673|673	0.8878627968337731|0.8878627968337731	N|N	0.017|0.017	-1.496625|-1.496625	0.01001|0.01001	0.736723|0.736723	0.875669|0.875669	ENSG00000148832|ENSG00000148832	ENST00000368544;ENST00000368534|ENST00000357296	.|T	.|0.44482	.|0.92	4.26|4.26	2.32|2.32	0.28847|0.28847	.|.	1.187630|.	0.05854|.	N|.	0.621810|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.41556|0.41556	-0.9502|-0.9502	5|7	0.38643|0.02654	T|T	0.18|1	-23.986|-23.986	7.5043|7.5043	0.27536|0.27536	0.0:0.7112:0.1777:0.1111|0.0:0.7112:0.1777:0.1111	rs1046175;rs3827685;rs17846017;rs17859001;rs59057363|rs1046175;rs3827685;rs17846017;rs17859001;rs59057363	.|457	.|Q6QHF9-4	.|.	R|E	68;98|457	.|ENSP00000349847:Q457E	ENSP00000357522:P98R|ENSP00000349847:Q457E	P|Q	+|+	2|1	0|0	PAOX|PAOX	135054940|135054940	0.000000|0.000000	0.05858|0.05858	0.007000|0.007000	0.13788|0.13788	0.011000|0.011000	0.07611|0.07611	-1.219000|-1.219000	0.02973|0.02973	0.097000|0.097000	0.17492|0.17492	-1.313000|-1.313000	0.01306|0.01306	CCA|CAG	C|0.163;G|0.837	0.837	strong		0.632	MTG1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051166.1	NM_138384	
PAH	5053	hgsc.bcm.edu	37	12	103246700	103246700	+	Silent	SNP	C	C	T	rs1042503	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:103246700C>T	ENST00000553106.1	-	7	1207	c.735G>A	c.(733-735)gtG>gtA	p.V245V	PAH_ENST00000551988.1_5'Flank|PAH_ENST00000307000.2_Silent_p.V240V	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	245			V -> A (in PKU, HPA and non-PKU HPA; haplotypes 3,7). {ECO:0000269|PubMed:12501224, ECO:0000269|PubMed:22513348, ECO:0000269|PubMed:8088845, ECO:0000269|PubMed:8889590}.|V -> E (in PKU; haplotype 11).|V -> L (in PKU).		catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	GCAGGCCAGCCACAGGTCGGA	0.527													C|||	1577	0.314896	0.0129	0.196	5008	,	,		21210	0.7629		0.2594	False		,,,				2504	0.4029				p.V245V		Atlas-SNP	.											.	PAH	77	.	0			c.G735A	GRCh37	CX056901	PAH	X	rs1042503	PASS	.	C		245,4161	142.7+/-177.9	2,241,1960	69.0	76.0	73.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	735	3.0	1.0	12	dbSNP_86	73	2116,6484	364.1+/-333.4	253,1610,2437	no	coding-synonymous	PAH	NM_000277.1		255,1851,4397	TT,TC,CC		24.6047,5.5606,18.1532		245/453	103246700	2361,10645	2203	4300	6503	SO:0001819	synonymous_variant	5053	exon7			GCCAGCCACAGGT	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.735G>A	12.37:g.103246700C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_000277	Q16717|Q8TC14	Silent	SNP	ENST00000553106.1	37	CCDS9092.1																																																																																			C|0.723;T|0.276	0.276	strong		0.527	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.P87S|SGK1_ENST00000367857.5_Missense_Mutation_p.P63S|SGK1_ENST00000475719.2_Missense_Mutation_p.P73S|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367858.5_Missense_Mutation_p.P168S|SGK1_ENST00000528577.1_Missense_Mutation_p.P101S	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	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	60	12	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		
CDH23	64072	hgsc.bcm.edu	37	10	73377054	73377054	+	Silent	SNP	G	G	A	rs74608315	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73377054G>A	ENST00000224721.6	+	10	1058	c.1053G>A	c.(1051-1053)ccG>ccA	p.P351P	CDH23_ENST00000461841.3_Silent_p.P391P|CDH23_ENST00000299366.7_Silent_p.P391P|CDH23_ENST00000398842.3_Silent_p.P346P|CDH23_ENST00000398809.4_Silent_p.P346P	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	346	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ACAATGCCCCGGAGTTCAACA	0.552													g|||	110	0.0219649	0.0	0.0086	5008	,	,		21728	0.0625		0.0159	False		,,,				2504	0.0256				p.P346P		Atlas-SNP	.											.	CDH23	365	.	0			c.G1038A						PASS	.	A	,,,,	4,4356	6.2+/-15.9	0,4,2176	81.0	84.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1038,1038,1038,1038,1038	-10.9	0.1	10	dbSNP_132	83	81,8487	45.8+/-104.6	0,81,4203	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_001171932.1,NM_022124.5,NM_052836.3	,,,,	0,85,6379	AA,AG,GG		0.9454,0.0917,0.6575	,,,,	346/1382,346/1062,346/407,346/3355,346/531	73377054	85,12843	2180	4284	6464	SO:0001819	synonymous_variant	64072	exon11			TGCCCCGGAGTTC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.1053G>A	10.37:g.73377054G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				G|0.972;A|0.028	0.028	strong		0.552	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
NCAPD2	9918	hgsc.bcm.edu	37	12	6639981	6639981	+	Missense_Mutation	SNP	C	C	G	rs2240871	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6639981C>G	ENST00000315579.5	+	30	4761	c.3962C>G	c.(3961-3963)aCt>aGt	p.T1321S	NCAPD2_ENST00000545962.1_Missense_Mutation_p.T1276S|RP5-940J5.3_ENST00000537921.1_RNA	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1321			T -> S (in dbSNP:rs2240871). {ECO:0000269|PubMed:15489334}.		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						AAACCATCCACTGGTACGTAA	0.522													C|||	920	0.183706	0.0658	0.1988	5008	,	,		18395	0.3671		0.1829	False		,,,				2504	0.1442				p.T1321S		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3962G						PASS	.	C	SER/THR	330,4076	173.4+/-203.2	13,304,1886	62.0	64.0	63.0		3962	2.4	0.0	12	dbSNP_98	63	1523,7077	283.6+/-296.2	135,1253,2912	yes	missense	NCAPD2	NM_014865.3	58	148,1557,4798	GG,GC,CC		17.7093,7.4898,14.2473	benign	1321/1402	6639981	1853,11153	2203	4300	6503	SO:0001583	missense	9918	exon30			CATCCACTGGTAC	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.3962C>G	12.37:g.6639981C>G	ENSP00000325017:p.Thr1321Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	37	CCDS8548.1	459	0.21016483516483517	33	0.06707317073170732	73	0.20165745856353592	214	0.3741258741258741	139	0.18337730870712401	C	1.095	-0.662912	0.03454	0.074898	0.177093	ENSG00000010292	ENST00000315579;ENST00000545962	T;T	0.16897	2.58;2.31	5.42	2.4	0.29515	.	1.768640	0.02053	N	0.050195	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.43212	-0.9405	9	0.15066	T	0.55	1.0634	8.1283	0.31012	0.0:0.6505:0.1269:0.2226	rs2240871;rs11545059;rs17852509;rs2240871	1276;1321	F5GZJ1;Q15021	.;CND1_HUMAN	S	1321;1276	ENSP00000325017:T1321S;ENSP00000444417:T1276S	ENSP00000325017:T1321S	T	+	2	0	NCAPD2	6510242	0.000000	0.05858	0.001000	0.08648	0.066000	0.16364	0.129000	0.15830	0.664000	0.31047	0.561000	0.74099	ACT	C|0.834;G|0.166	0.166	strong		0.522	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
OR2F1	26211	hgsc.bcm.edu	37	7	143657473	143657473	+	Missense_Mutation	SNP	A	A	G	rs2072165	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143657473A>G	ENST00000392899.1	+	1	447	c.410A>G	c.(409-411)cAt>cGt	p.H137R	RP4-669B10.3_ENST00000466281.1_lincRNA	NM_012369.2	NP_036501.2	Q13607	OR2F1_HUMAN	olfactory receptor, family 2, subfamily F, member 1 (gene/pseudogene)	137			H -> R (in dbSNP:rs2072165).		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(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|skin(4)	34	Melanoma(164;0.0903)					GCCATCATGCATGGAGGGCTG	0.567													A|||	1132	0.226038	0.4463	0.2378	5008	,	,		21578	0.1627		0.1093	False		,,,				2504	0.1053				p.H137R		Atlas-SNP	.											.	OR2F1	71	.	0			c.A410G						PASS	.	A	ARG/HIS	1711,2695	515.5+/-368.9	335,1041,827	154.0	132.0	140.0		410	3.2	0.6	7	dbSNP_96	140	776,7824	183.3+/-231.6	34,708,3558	yes	missense	OR2F1	NM_012369.2	29	369,1749,4385	GG,GA,AA		9.0233,38.8334,19.1219	benign	137/318	143657473	2487,10519	2203	4300	6503	SO:0001583	missense	26211	exon1			TCATGCATGGAGG	U56421	CCDS5887.1	7q35	2013-06-03	2013-06-03		ENSG00000213215	ENSG00000213215		"""GPCR / Class A : Olfactory receptors"""	8246	protein-coding gene	gene with protein product		608497	"""olfactory receptor, family 2, subfamily F, member 1"""	OR2F4, OR2F5, OR2F3, OR2F3P		9500546	Standard	NM_012369		Approved	OLF3, OR7-140, OR7-139, OR14-60	uc003wds.1	Q13607	OTTHUMG00000157771	ENST00000392899.1:c.410A>G	7.37:g.143657473A>G	ENSP00000376633:p.His137Arg	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_012369	A4D2G1|Q6IFP7|Q96R49|Q9UDX1	Missense_Mutation	SNP	ENST00000392899.1	37	CCDS5887.1	476	0.21794871794871795	202	0.4105691056910569	88	0.2430939226519337	102	0.17832167832167833	84	0.11081794195250659	A	2.960	-0.214763	0.06101	0.388334	0.090233	ENSG00000213215	ENST00000392899	T	0.35421	1.31	5.53	3.17	0.36434	GPCR, rhodopsin-like superfamily (1);	0.229512	0.30911	N	0.008621	T	0.00012	0.0000	N	0.20483	0.58	0.46499	P	9.299999999999864E-4	B	0.06786	0.001	B	0.06405	0.002	T	0.43294	-0.9400	9	0.56958	D	0.05	-7.694	7.008	0.24848	0.7489:0.0:0.2511:0.0	rs2072165;rs60798611	137	Q13607	OR2F1_HUMAN	R	137	ENSP00000376633:H137R	ENSP00000376633:H137R	H	+	2	0	OR2F1	143288406	0.000000	0.05858	0.568000	0.28447	0.033000	0.12548	0.163000	0.16520	0.524000	0.28502	-0.256000	0.11100	CAT	A|0.807;G|0.193	0.193	strong		0.567	OR2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349581.1		
GPR113	165082	hgsc.bcm.edu	37	2	26534112	26534112	+	Silent	SNP	G	G	A	rs77088392	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:26534112G>A	ENST00000311519.1	-	11	2483	c.2484C>T	c.(2482-2484)ggC>ggT	p.G828G	GPR113_ENST00000421160.2_Silent_p.G759G|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000333478.6_Silent_p.G629G|GPR113_ENST00000541401.1_Silent_p.G431G	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	828					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)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAATGGGGCGCCCAGGAAGC	0.612													G|||	47	0.00938498	0.0015	0.0259	5008	,	,		18199	0.0		0.0209	False		,,,				2504	0.0061				p.G828G		Atlas-SNP	.											.	GPR113	134	.	0			c.C2484T						PASS	.	G	,,	23,4383	26.2+/-53.5	0,23,2180	33.0	25.0	28.0		2484,2277,1887	-11.6	0.0	2	dbSNP_132	28	201,8399	83.7+/-146.2	2,197,4101	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	,,	2,220,6281	AA,AG,GG		2.3372,0.522,1.7223	,,	828/1080,759/998,629/874	26534112	224,12782	2203	4300	6503	SO:0001819	synonymous_variant	165082	exon11			TGGGGCGCCCAGG	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.2484C>T	2.37:g.26534112G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Silent	SNP	ENST00000311519.1	37	CCDS46239.1																																																																																			G|0.985;A|0.015	0.015	strong		0.612	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
ZNF584	201514	hgsc.bcm.edu	37	19	58928786	58928786	+	Missense_Mutation	SNP	A	A	G	rs7257872	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58928786A>G	ENST00000306910.4	+	4	1424	c.901A>G	c.(901-903)Aca>Gca	p.T301A	CTD-2619J13.16_ENST00000596296.1_lincRNA|ZNF584_ENST00000599238.1_3'UTR|ZNF584_ENST00000593920.1_Missense_Mutation_p.T256A	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	301			T -> A (in dbSNP:rs7257872). {ECO:0000269|PubMed:14702039}.		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(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		CTATGAGTGTACAGAATGTGG	0.443													A|||	1457	0.290935	0.4592	0.1787	5008	,	,		22805	0.2708		0.2465	False		,,,				2504	0.2096				p.T301A		Atlas-SNP	.											.	ZNF584	31	.	0			c.A901G						PASS	.	A	ALA/THR	1985,2421	559.0+/-380.1	450,1085,668	76.0	78.0	77.0		901	0.2	0.8	19	dbSNP_116	77	2339,6261	391.7+/-343.7	309,1721,2270	yes	missense	ZNF584	NM_173548.1	58	759,2806,2938	GG,GA,AA		27.1977,45.0522,33.2462	benign	301/422	58928786	4324,8682	2203	4300	6503	SO:0001583	missense	201514	exon4			GAGTGTACAGAAT	AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"""Zinc fingers, C2H2-type"", ""-"""	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.901A>G	19.37:g.58928786A>G	ENSP00000306756:p.Thr301Ala	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	92	54	0.586957	NM_173548	A8K203	Missense_Mutation	SNP	ENST00000306910.4	37	CCDS12979.1	644	0.2948717948717949	220	0.44715447154471544	77	0.212707182320442	151	0.263986013986014	196	0.25857519788918204	A	9.916	1.210741	0.22289	0.450522	0.271977	ENSG00000171574	ENST00000306910;ENST00000354635	T	0.07216	3.21	3.78	0.242	0.15498	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	2.9999999999752447E-6	B	0.06786	0.001	B	0.10450	0.005	T	0.44452	-0.9327	8	0.40728	T	0.16	.	1.8084	0.03085	0.3614:0.3782:0.1017:0.1587	rs7257872;rs52798108;rs59404846;rs7257872	301	Q8IVC4	ZN584_HUMAN	A	301;160	ENSP00000306756:T301A	ENSP00000306756:T301A	T	+	1	0	ZNF584	63620598	0.000000	0.05858	0.822000	0.32727	0.947000	0.59692	-4.685000	0.00198	-0.127000	0.11661	0.454000	0.30748	ACA	A|0.686;G|0.314	0.314	strong		0.443	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548	
DIS3	22894	hgsc.bcm.edu	37	13	73350079	73350079	+	Missense_Mutation	SNP	T	T	C	rs4883918	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:73350079T>C	ENST00000377767.4	-	5	906	c.806A>G	c.(805-807)aAt>aGt	p.N269S	DIS3_ENST00000545453.1_Missense_Mutation_p.N107S|DIS3_ENST00000377780.4_Missense_Mutation_p.N239S	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	269			N -> S (in dbSNP:rs4883918). {ECO:0000269|PubMed:11935316, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		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)		ATTTTCTTCATTGTCGCCATG	0.303										Multiple Myeloma(4;0.011)			T|||	1638	0.327077	0.0825	0.4741	5008	,	,		15022	0.4534		0.2634	False		,,,				2504	0.4888				p.N269S		Atlas-SNP	.											.	DIS3	103	.	0			c.A806G						PASS	.	T	SER/ASN,SER/ASN	502,3902	230.7+/-244.8	40,422,1740	74.0	69.0	70.0		716,806	-8.1	0.0	13	dbSNP_111	70	2548,6048	413.0+/-351.0	386,1776,2136	yes	missense,missense	DIS3	NM_001128226.1,NM_014953.3	46,46	426,2198,3876	CC,CT,TT		29.6417,11.3987,23.4615	benign,benign	239/929,269/959	73350079	3050,9950	2202	4298	6500	SO:0001583	missense	22894	exon5			TCTTCATTGTCGC	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.806A>G	13.37:g.73350079T>C	ENSP00000366997:p.Asn269Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	88	28	0.318182	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	697	0.3191391941391941	54	0.10975609756097561	158	0.43646408839779005	278	0.486013986013986	207	0.27308707124010556	T	1.751	-0.489183	0.04352	0.113987	0.296417	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.20200	2.09;2.09;2.09	5.66	-8.07	0.01098	.	1.579370	0.03238	N	0.179867	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43572	-0.9383	9	0.08837	T	0.75	.	14.0915	0.64993	0.0:0.1368:0.2749:0.5883	rs4883918;rs52826006;rs4883918	239;269	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	S	269;239;107	ENSP00000366997:N269S;ENSP00000367011:N239S;ENSP00000440058:N107S	ENSP00000366997:N269S	N	-	2	0	DIS3	72248080	0.000000	0.05858	0.000000	0.03702	0.631000	0.37964	0.585000	0.23879	-1.333000	0.02247	-2.015000	0.00435	AAT	T|0.726;C|0.274	0.274	strong		0.303	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953	
IL6R	3570	hgsc.bcm.edu	37	1	154426970	154426970	+	Missense_Mutation	SNP	A	A	C	rs2228145	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:154426970A>C	ENST00000368485.3	+	9	1510	c.1073A>C	c.(1072-1074)gAt>gCt	p.D358A	IL6R_ENST00000344086.4_Intron|IL6R_ENST00000507256.1_3'UTR	NM_000565.3	NP_000556.1	P08887	IL6RA_HUMAN	interleukin 6 receptor	358			D -> A (significantly associated with circulating levels of IL6 and soluble IL6R; dbSNP:rs2228145). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17357077}.		acute-phase response (GO:0006953)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|endocrine pancreas development (GO:0031018)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatic immune response (GO:0002384)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of interleukin-8 production (GO:0032717)|neutrophil mediated immunity (GO:0002446)|positive regulation of activation of Janus kinase activity (GO:0010536)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|response to cytokine (GO:0034097)	apical plasma membrane (GO:0016324)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)|plasma membrane (GO:0005886)	ciliary neurotrophic factor binding (GO:0070119)|cytokine receptor activity (GO:0004896)|enzyme binding (GO:0019899)|interleukin-6 binding (GO:0019981)|protein homodimerization activity (GO:0042803)		IL6R/ATP8B2(2)	breast(2)|large_intestine(1)|ovary(3)	6	all_lung(78;1.72e-29)|Lung NSC(65;2.96e-27)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)		Tocilizumab(DB06273)	CTAGTGCAAGATTCTTCTTCA	0.473													A|||	1468	0.293131	0.087	0.536	5008	,	,		19463	0.3234		0.3598	False		,,,				2504	0.2996				p.D358A		Atlas-SNP	.											.	IL6R	47	.	0			c.A1073C	GRCh37	CM034737	IL6R	M	rs2228145	PASS	.	A	ALA/ASP,	641,3765	274.0+/-271.7	46,549,1608	74.0	65.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1073,	2.8	0.7	1	dbSNP_98	68	3480,5120	508.5+/-377.1	706,2068,1526	yes	missense,intron	IL6R	NM_000565.3,NM_181359.2	126,	752,2617,3134	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	40.4651,14.5483,31.6854	benign,	358/469,	154426970	4121,8885	2203	4300	6503	SO:0001583	missense	3570	exon9			TGCAAGATTCTTC	X12830	CCDS1067.1, CCDS1068.1, CCDS72927.1	1q21	2013-01-11			ENSG00000160712	ENSG00000160712		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6019	protein-coding gene	gene with protein product		147880					Standard	NM_000565		Approved	CD126	uc001fez.2	P08887	OTTHUMG00000036073	ENST00000368485.3:c.1073A>C	1.37:g.154426970A>C	ENSP00000357470:p.Asp358Ala	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	35	21	0.6	NM_000565	A8KAE8|B2R6V4|Q16202|Q53EQ7|Q5FWG2|Q5VZ23	Missense_Mutation	SNP	ENST00000368485.3	37	CCDS1067.1	698|698	0.31959706959706957|0.31959706959706957	43|43	0.08739837398373984|0.08739837398373984	175|175	0.48342541436464087|0.48342541436464087	207|207	0.3618881118881119|0.3618881118881119	273|273	0.36015831134564646|0.36015831134564646	A|A	10.96|10.96	1.499781|1.499781	0.26861|0.26861	0.145483|0.145483	0.404651|0.404651	ENSG00000160712|ENSG00000160712	ENST00000368485|ENST00000515190	T|.	0.16457|.	2.34|.	4.03|4.03	2.85|2.85	0.33270|0.33270	.|.	7.394690|.	0.00166|.	N|.	0.000000|.	T|T	0.41743|0.41743	0.1172|0.1172	M|M	0.70595|0.70595	2.14|2.14	0.21822|0.21822	P|P	0.999521233|0.999521233	B|.	0.25312|.	0.123|.	B|.	0.17979|.	0.02|.	T|T	0.35992|0.35992	-0.9766|-0.9766	9|4	0.25106|.	T|.	0.35|.	-2.254|-2.254	6.5|6.5	0.22164|0.22164	0.8858:0.0:0.1142:0.0|0.8858:0.0:0.1142:0.0	rs2228145;rs8192284;rs52837205;rs58037860;rs8192284|rs2228145;rs8192284;rs52837205;rs58037860;rs8192284	358|.	P08887|.	IL6RA_HUMAN|.	A|L	358|161	ENSP00000357470:D358A|.	ENSP00000357470:D358A|.	D|I	+|+	2|1	0|0	IL6R|IL6R	152693594|152693594	0.167000|0.167000	0.22975|0.22975	0.672000|0.672000	0.29872|0.29872	0.291000|0.291000	0.27294|0.27294	0.915000|0.915000	0.28638|0.28638	0.662000|0.662000	0.31006|0.31006	0.454000|0.454000	0.30748|0.30748	GAT|ATT	A|0.687;C|0.313;T|0.000	0.313	strong		0.473	IL6R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087911.1	NM_000565	
KRTAP10-5	386680	hgsc.bcm.edu	37	21	45999908	45999908	+	Missense_Mutation	SNP	A	A	C	rs380585	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45999908A>C	ENST00000400372.1	-	1	573	c.548T>G	c.(547-549)tTc>tGc	p.F183C	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	183	22 X 5 AA repeats of C-C-X(3).		F -> C (in dbSNP:rs380585).			keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GATGGGTTTGAAGCAGACAGG	0.602													.|||	730	0.145767	0.2489	0.0692	5008	,	,		22219	0.1964		0.0378	False		,,,				2504	0.1196				p.F183C		Atlas-SNP	.											.	KRTAP10-5	43	.	0			c.T548G						PASS	.	C	,CYS/PHE	944,3462	734.8+/-410.6	116,712,1375	190.0	196.0	194.0		,548	0.9	0.1	21	dbSNP_80	194	264,8336	806.2+/-407.2	4,256,4040	no	intron,missense	TSPEAR,KRTAP10-5	NM_144991.2,NM_198694.2	,205	120,968,5415	CC,CA,AA		3.0698,21.4253,9.288	,benign	,183/272	45999908	1208,11798	2203	4300	6503	SO:0001583	missense	386680	exon1			GGTTTGAAGCAGA	AJ566384	CCDS42958.1	21q22.3	2007-10-05			ENSG00000241123	ENSG00000241123		"""Keratin associated proteins"""	22969	protein-coding gene	gene with protein product				KRTAP18-5			Standard	NM_198694		Approved	KAP10.5, KAP18.5	uc002zfl.1	P60370	OTTHUMG00000057638	ENST00000400372.1:c.548T>G	21.37:g.45999908A>C	ENSP00000383223:p.Phe183Cys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	124	73	0.58871	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	286	0.13095238095238096	119	0.241869918699187	27	0.07458563535911603	119	0.20804195804195805	21	0.027704485488126648	c	0.001	-3.150025	0.00029	0.214253	0.030698	ENSG00000241123	ENST00000400372	T	0.00768	5.72	2.89	0.948	0.19561	.	.	.	.	.	T	0.00012	0.0000	N	0.00016	-2.86	0.53005	P	3.100000000000325E-5	B	0.12013	0.005	B	0.01281	0.0	T	0.39961	-0.9588	8	0.02654	T	1	.	2.2902	0.04136	0.1834:0.3404:0.3598:0.1164	rs380585	183	P60370	KR105_HUMAN	C	183	ENSP00000383223:F183C	ENSP00000383223:F183C	F	-	2	0	KRTAP10-5	44824336	0.053000	0.20554	0.129000	0.21949	0.017000	0.09413	-0.206000	0.09398	-0.183000	0.10585	-0.677000	0.03784	TTC	A|0.902;C|0.098	0.098	strong		0.602	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
MTMR10	54893	hgsc.bcm.edu	37	15	31267147	31267147	+	Silent	SNP	C	C	T	rs1133642	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:31267147C>T	ENST00000435680.1	-	4	415	c.318G>A	c.(316-318)gaG>gaA	p.E106E	MTMR10_ENST00000314404.8_5'Flank|MTMR10_ENST00000425768.1_Silent_p.E106E|MTMR10_ENST00000563714.1_Silent_p.E24E	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	106							phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TGACAATTTGCTCAATACATG	0.323													C|||	2404	0.480032	0.1884	0.4741	5008	,	,		17120	0.8313		0.4453	False		,,,				2504	0.5521				p.E106E		Atlas-SNP	.											.	MTMR10	74	.	0			c.G318A						PASS	.	C		834,2826		112,610,1108	61.0	56.0	58.0		318	0.8	1.0	15	dbSNP_86	58	3577,4575		780,2017,1279	no	coding-synonymous	MTMR10	NM_017762.2		892,2627,2387	TT,TC,CC		43.8788,22.7869,37.3434		106/778	31267147	4411,7401	1830	4076	5906	SO:0001819	synonymous_variant	54893	exon4			AATTTGCTCAATA	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.318G>A	15.37:g.31267147C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_017762	Q6P4Q6	Silent	SNP	ENST00000435680.1	37	CCDS45204.1																																																																																			A|0.000;C|0.421;T|0.579	0.579	strong		0.323	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762	
WDR72	256764	hgsc.bcm.edu	37	15	54003091	54003091	+	Missense_Mutation	SNP	G	G	A	rs551225	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:54003091G>A	ENST00000396328.1	-	9	1156	c.917C>T	c.(916-918)cCt>cTt	p.P306L	WDR72_ENST00000360509.5_Missense_Mutation_p.P306L|WDR72_ENST00000557913.1_Missense_Mutation_p.P305L|WDR72_ENST00000559418.1_Missense_Mutation_p.P318L	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	306				P -> L (in Ref. 1; CAD97880 and 3; AAI01617/AAI01615). {ECO:0000305}.						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)		CAGTAAATGAGGATAAATGGT	0.398													G|||	1607	0.320887	0.1626	0.3156	5008	,	,		16888	0.2014		0.494	False		,,,				2504	0.4836				p.P306L		Atlas-SNP	.											.	WDR72	177	.	0			c.C917T						PASS	.	G	LEU/PRO	949,3439	359.6+/-314.9	114,721,1359	142.0	127.0	132.0		917	5.6	1.0	15	dbSNP_83	132	4304,4282	576.9+/-390.5	1067,2170,1056	yes	missense	WDR72	NM_182758.2	98	1181,2891,2415	AA,AG,GG		49.8719,21.6272,40.4887	probably-damaging	306/1103	54003091	5253,7721	2194	4293	6487	SO:0001583	missense	256764	exon9			AAATGAGGATAAA	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.917C>T	15.37:g.54003091G>A	ENSP00000379619:p.Pro306Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	690	0.3159340659340659	67	0.13617886178861788	132	0.36464088397790057	119	0.20804195804195805	372	0.49076517150395776	G	20.7	4.027819	0.75390	0.216272	0.501281	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.18016	2.24;2.24	5.58	5.58	0.84498	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.45137	1.4	0.09310	P	0.999999221283	D	0.89917	1.0	D	0.74674	0.984	T	0.51647	-0.8679	9	0.59425	D	0.04	.	18.919	0.92518	0.0:0.0:1.0:0.0	rs551225;rs52834404;rs59983782;rs551225	306	Q3MJ13	WDR72_HUMAN	L	306	ENSP00000379619:P306L;ENSP00000353699:P306L	ENSP00000353699:P306L	P	-	2	0	WDR72	51790383	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.344000	0.72991	2.778000	0.95560	0.655000	0.94253	CCT	G|0.619;A|0.381	0.381	strong		0.398	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
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 GAIIx	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*	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	183	40	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	
POU5F1	5460	hgsc.bcm.edu	37	6	31138107	31138107	+	Silent	SNP	G	G	A	rs1062630	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31138107G>A	ENST00000259915.8	-	1	363	c.291C>T	c.(289-291)ggC>ggT	p.G97G	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	97					anatomical structure morphogenesis (GO:0009653)|blastocyst development (GO:0001824)|BMP signaling pathway involved in heart induction (GO:0003130)|cardiac cell fate determination (GO:0060913)|cell fate commitment involved in formation of primary germ layer (GO:0060795)|endodermal cell fate specification (GO:0001714)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of gene silencing by miRNA (GO:0060965)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of asymmetric cell division (GO:0009786)|regulation of gene expression (GO:0010468)|regulation of heart induction by regulation of canonical Wnt signaling pathway (GO:0090081)|regulation of methylation-dependent chromatin silencing (GO:0090308)|regulation of transcription, DNA-templated (GO:0006355)|response to wounding (GO:0009611)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)		EWSR1/POU5F1(10)	breast(1)|large_intestine(2)|lung(3)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	13					Dopamine(DB00988)|Norepinephrine(DB00368)	CTCCTGCTTCGCCCTCAGGCT	0.672			T	EWSR1	sarcoma								G|||	847	0.169129	0.2678	0.1412	5008	,	,		15076	0.0377		0.2008	False		,,,				2504	0.1585				p.G97G		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"""POU domain, class 5, transcription factor 1"""		M	POU5F1,colon,carcinoma,0,2	POU5F1	25	2	0			c.C291T						PASS	.	G		809,2213		106,597,808	33.0	34.0	33.0		291	0.1	0.4	6	dbSNP_86	33	1252,4160		159,934,1613	no	coding-synonymous	POU5F1	NM_002701.4		265,1531,2421	AA,AG,GG		23.1338,26.7704,24.4368		97/361	31138107	2061,6373	1511	2706	4217	SO:0001819	synonymous_variant	5460	exon1			TGCTTCGCCCTCA	Z11898	CCDS34391.1, CCDS47398.1, CCDS47398.2, CCDS75420.1	6p21.33	2011-06-20	2007-07-13		ENSG00000204531	ENSG00000204531		"""Homeoboxes / POU class"""	9221	protein-coding gene	gene with protein product		164177	"""POU domain class 5, transcription factor 1"""	OTF3		1408763	Standard	NM_002701		Approved	OCT3, Oct4, MGC22487	uc003nsv.3	Q01860	OTTHUMG00000031206	ENST00000259915.8:c.291C>T	6.37:g.31138107G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	44	0.721311	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Silent	SNP	ENST00000259915.8	37	CCDS34391.1																																																																																			G|0.784;A|0.216	0.216	strong		0.672	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701	
SLC15A1	6564	hgsc.bcm.edu	37	13	99376181	99376181	+	Missense_Mutation	SNP	C	C	T	rs2297322	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:99376181C>T	ENST00000376503.5	-	5	405	c.350G>A	c.(349-351)aGc>aAc	p.S117N		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	117			S -> N (in dbSNP:rs2297322). {ECO:0000269|PubMed:12436193, ECO:0000269|PubMed:16258023}.|S -> R (in dbSNP:rs8187821). {ECO:0000269|PubMed:16258023}.		digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CACAGGAAGGCTGTCGGGGGT	0.512													C|||	1545	0.308506	0.3548	0.2363	5008	,	,		21342	0.4385		0.1292	False		,,,				2504	0.3476				p.S117N		Atlas-SNP	.											.	SLC15A1	92	.	0			c.G350A						PASS	.	C	ASN/SER	1315,3091	443.1+/-346.9	190,935,1078	250.0	184.0	206.0		350	-11.3	0.0	13	dbSNP_100	206	947,7653	206.9+/-248.8	53,841,3406	yes	missense	SLC15A1	NM_005073.3	46	243,1776,4484	TT,TC,CC		11.0116,29.8457,17.392	benign	117/709	99376181	2262,10744	2203	4300	6503	SO:0001583	missense	6564	exon5			GGAAGGCTGTCGG	U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"""Solute carriers"""	10920	protein-coding gene	gene with protein product	"""peptide transporter HPEPT1"", ""bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)"", ""solute carrier family 15 oligopeptide transporter member 1"""	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.350G>A	13.37:g.99376181C>T	ENSP00000365686:p.Ser117Asn	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	132	78	0.590909	NM_005073	Q5VW82	Missense_Mutation	SNP	ENST00000376503.5	37	CCDS9489.1	602	0.27564102564102566	161	0.32723577235772355	95	0.26243093922651933	241	0.42132867132867136	105	0.13852242744063326	C	11.28	1.591231	0.28357	0.298457	0.110116	ENSG00000088386	ENST00000376503;ENST00000376494;ENST00000313260	T	0.04603	3.59	5.65	-11.3	0.00108	Major facilitator superfamily domain, general substrate transporter (1);	0.486708	0.24735	N	0.036040	T	0.00012	0.0000	N	0.04880	-0.145	0.58432	P	8.000000000008E-6	B;B	0.16603	0.018;0.0	B;B	0.20577	0.03;0.006	T	0.41556	-0.9502	9	0.10377	T	0.69	-18.7336	13.485	0.61359	0.0618:0.084:0.1096:0.7445	rs2297322;rs10285589;rs2297322	85;117	Q9BZ22;P46059	.;S15A1_HUMAN	N	117;85;127	ENSP00000365686:S117N	ENSP00000318937:S127N	S	-	2	0	SLC15A1	98174182	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.084000	0.03393	-2.807000	0.00349	-0.136000	0.14681	AGC	C|0.768;T|0.232	0.232	strong		0.512	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073	
UBE4B	10277	hgsc.bcm.edu	37	1	10218439	10218439	+	Silent	SNP	T	T	C	rs2273299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10218439T>C	ENST00000253251.8	+	21	3404	c.2565T>C	c.(2563-2565)agT>agC	p.S855S	UBE4B_ENST00000343090.6_Silent_p.S984S|UBE4B_ENST00000377157.3_Silent_p.S739S					ubiquitination factor E4B									p.S855S(1)		NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		GAGCCACCAGTGAGTTTTATG	0.398													C|||	1832	0.365815	0.8033	0.1873	5008	,	,		19632	0.2956		0.1392	False		,,,				2504	0.2065				p.S984S		Atlas-SNP	.											UBE4B,NS,carcinoma,0,1	UBE4B	233	1	1	Substitution - coding silent(1)	stomach(1)	c.T2952C						PASS	.	C	,	2942,1464	472.0+/-356.2	996,950,257	137.0	140.0	139.0		2952,2565	-0.9	1.0	1	dbSNP_100	139	1135,7465	767.0+/-407.6	81,973,3246	no	coding-synonymous,coding-synonymous	UBE4B	NM_001105562.2,NM_006048.4	,	1077,1923,3503	CC,CT,TT		13.1977,33.2274,31.3471	,	984/1303,855/1174	10218439	4077,8929	2203	4300	6503	SO:0001819	synonymous_variant	10277	exon22			CACCAGTGAGTTT	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2565T>C	1.37:g.10218439T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	43	0.40566	NM_001105562		Silent	SNP	ENST00000253251.8	37	CCDS110.1																																																																																			T|0.658;C|0.342	0.342	strong		0.398	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
LAMA5	3911	hgsc.bcm.edu	37	20	60897488	60897488	+	Silent	SNP	G	G	A	rs2274933	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60897488G>A	ENST00000252999.3	-	47	6249	c.6183C>T	c.(6181-6183)ttC>ttT	p.F2061F		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2061	Laminin EGF-like 20. {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)			CGCAGCCATCGAAACCAAAAT	0.677													.|||	848	0.169329	0.1059	0.2061	5008	,	,		11140	0.1885		0.2187	False		,,,				2504	0.1585				p.F2061F		Atlas-SNP	.											.	LAMA5	268	.	0			c.C6183T						PASS	.	A		539,3757		30,479,1639	9.0	11.0	11.0		6183	-4.8	0.1	20	dbSNP_100	11	1731,6767		193,1345,2711	no	coding-synonymous	LAMA5	NM_005560.3		223,1824,4350	AA,AG,GG		20.3695,12.5466,17.7427		2061/3696	60897488	2270,10524	2148	4249	6397	SO:0001819	synonymous_variant	3911	exon47			GCCATCGAAACCA	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.6183C>T	20.37:g.60897488G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.817;C|0.000;A|0.183	0.183	strong		0.677	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
CABLES2	81928	hgsc.bcm.edu	37	20	60968596	60968596	+	Silent	SNP	A	A	G	rs1570027	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60968596A>G	ENST00000279101.5	-	6	788	c.780T>C	c.(778-780)caT>caC	p.H260H		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	260					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCAGCAGGCCATGGCTGTCAC	0.592													A|||	1014	0.202476	0.2035	0.2666	5008	,	,		19142	0.1498		0.2336	False		,,,				2504	0.1779				p.H260H		Atlas-SNP	.											.	CABLES2	30	.	0			c.T780C						PASS	.	A		1036,3370	381.6+/-324.1	114,808,1281	119.0	117.0	117.0		780	-6.5	0.1	20	dbSNP_88	117	1917,6683	338.5+/-322.8	228,1461,2611	no	coding-synonymous	CABLES2	NM_031215.2		342,2269,3892	GG,GA,AA		22.2907,23.5134,22.7049		260/479	60968596	2953,10053	2203	4300	6503	SO:0001819	synonymous_variant	81928	exon6			CAGGCCATGGCTG	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 150"""	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.780T>C	20.37:g.60968596A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_031215	Q5JWL0|Q9BYK0	Silent	SNP	ENST00000279101.5	37	CCDS33503.1	436	0.19963369963369965	104	0.21138211382113822	102	0.281767955801105	64	0.11188811188811189	166	0.21899736147757257	A	0.144	-1.099321	0.01843	0.235134	0.222907	ENSG00000149679	ENST00000453274	.	.	.	5.15	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.12192	-1.0557	3	.	.	.	-24.4711	14.808	0.69971	0.4038:0.0:0.5962:0.0	rs1570027;rs1570027	.	.	.	T	54	.	.	M	-	2	0	CABLES2	60401991	0.000000	0.05858	0.058000	0.19502	0.035000	0.12851	-1.013000	0.03645	-1.179000	0.02737	-0.468000	0.05107	ATG	A|0.785;G|0.215	0.215	strong		0.592	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265	
S100A7L2	645922	hgsc.bcm.edu	37	1	153410822	153410822	+	Splice_Site	SNP	C	C	A	rs10888561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153410822C>A	ENST00000368725.2	-	2	16	c.17G>T	c.(16-18)gGc>gTc	p.G6V		NM_001045479.1	NP_001038944.2	Q5SY68	S1A7B_HUMAN	S100 calcium binding protein A7-like 2	0							calcium ion binding (GO:0005509)			NS(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)	8	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)			TTTCAAAAAGCCTTCAGGAAA	0.408													C|||	3076	0.614217	0.5	0.7061	5008	,	,		22923	0.6042		0.7376	False		,,,				2504	0.5869				p.G6V		Atlas-SNP	.											.	S100A7L2	36	.	0			c.G17T						PASS	.	C	VAL/GLY	2349,2057		632,1085,486	109.0	96.0	100.0		17	-1.5	0.0	1	dbSNP_120	100	6331,2269		2331,1669,300	yes	missense-near-splice	S100A7L2	NM_001045479.1	109	2963,2754,786	AA,AC,CC		26.3837,46.6863,33.2616	benign	6/113	153410822	8680,4326	2203	4300	6503	SO:0001630	splice_region_variant	645922	exon2			AAAAAGCCTTCAG			1q21.3	2013-01-10			ENSG00000197364	ENSG00000197364		"""EF-hand domain containing"""	21655	protein-coding gene	gene with protein product							Standard	NM_001045479		Approved	s100a7b	uc010pdx.2	Q5SY68	OTTHUMG00000013129	ENST00000368725.2:c.17-1G>T	1.37:g.153410822C>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_001045479		Missense_Mutation	SNP	ENST00000368725.2	37		1382	0.6327838827838828	242	0.491869918699187	264	0.7292817679558011	311	0.5437062937062938	565	0.7453825857519789	.	9.346	1.064220	0.20067	0.533137	0.736163	ENSG00000197364	ENST00000453814	T	0.12361	2.69	1.36	-1.48	0.08745	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.38001	-0.9681	5	0.66056	D	0.02	.	2.9716	0.05925	0.0:0.2884:0.405:0.3066	rs10888561	.	.	.	V	6	ENSP00000405610:G6V	ENSP00000405610:G6V	G	-	2	0	S100A7L2	151677446	0.005000	0.15991	0.001000	0.08648	0.001000	0.01503	-0.069000	0.11542	-0.390000	0.07774	-0.714000	0.03626	GGC	C|0.875;G|0.125	.	alt		0.408	S100A7L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000036797.2	NM_001045479	Missense_Mutation
RNF213	57674	hgsc.bcm.edu	37	17	78335610	78335610	+	Silent	SNP	G	G	A	rs61741791	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78335610G>A	ENST00000582970.1	+	39	11420	c.11277G>A	c.(11275-11277)ccG>ccA	p.P3759P	CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Silent_p.P1832P|RNF213_ENST00000508628.2_Silent_p.P3808P|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3759					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			ATGGAGAGCCGCAGCAGGAAC	0.498													G|||	203	0.0405351	0.0325	0.0303	5008	,	,		19738	0.0278		0.0636	False		,,,				2504	0.0481				p.P3759P		Atlas-SNP	.											.	RNF213	766	.	0			c.G11277A						PASS	.	G		123,4283	92.0+/-130.7	1,121,2081	68.0	66.0	66.0		11424	3.5	0.5	17	dbSNP_129	66	484,8116	140.3+/-196.8	17,450,3833	no	coding-synonymous	RNF213	NM_020914.4		18,571,5914	AA,AG,GG		5.6279,2.7916,4.6671		3808/5257	78335610	607,12399	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon39			AGAGCCGCAGCAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11277G>A	17.37:g.78335610G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	83	27	0.325301	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			G|0.955;A|0.045	0.045	strong		0.498	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
MGLL	11343	hgsc.bcm.edu	37	3	127413881	127413881	+	Silent	SNP	T	T	C	rs4881	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:127413881T>C	ENST00000434178.2	-	7	1619	c.723A>G	c.(721-723)ctA>ctG	p.L241L	MGLL_ENST00000398104.1_Silent_p.L241L|MGLL_ENST00000453507.2_Silent_p.L221L|MGLL_ENST00000265052.5_Silent_p.L251L|MGLL_ENST00000476682.1_5'UTR|MGLL_ENST00000398101.3_Silent_p.L215L			Q99685	MGLL_HUMAN	monoglyceride lipase	241					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						TGCTGTCACATAGGCGATCGG	0.622													C|||	503	0.100439	0.1974	0.0778	5008	,	,		17787	0.0129		0.0944	False		,,,				2504	0.0818				p.L251L		Atlas-SNP	.											.	MGLL	19	.	0			c.A753G						PASS	.	C	,	652,3480		50,552,1464	50.0	57.0	55.0		723,753	-0.9	1.0	3	dbSNP_52	55	783,7603		42,699,3452	no	coding-synonymous,coding-synonymous	MGLL	NM_001003794.1,NM_007283.5	,	92,1251,4916	CC,CT,TT		9.337,15.7793,11.4635	,	241/304,251/314	127413881	1435,11083	2066	4193	6259	SO:0001819	synonymous_variant	11343	exon7			GTCACATAGGCGA	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.723A>G	3.37:g.127413881T>C		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	205	92	0.44878	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Silent	SNP	ENST00000434178.2	37	CCDS43148.1	199	0.09111721611721611	87	0.17682926829268292	35	0.09668508287292818	7	0.012237762237762238	70	0.09234828496042216	C	11.08	1.534009	0.27387	0.157793	0.09337	ENSG00000074416	ENST00000496306	.	.	.	5.02	-0.899	0.10547	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999997122	.	.	.	.	.	.	T	0.21759	-1.0236	3	.	.	.	-7.5383	5.3013	0.15780	0.2029:0.3099:0.4138:0.0734	rs4881;rs2070258;rs3183250;rs4881	.	.	.	C	147	.	.	Y	-	2	0	MGLL	128896571	0.944000	0.32072	0.975000	0.42487	0.991000	0.79684	-0.074000	0.11450	-0.464000	0.06963	-0.186000	0.12905	TAT	T|0.903;C|0.097	0.097	strong		0.622	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283	
ACOT2	10965	hgsc.bcm.edu	37	14	74036500	74036500	+	Missense_Mutation	SNP	C	C	T	rs146968042	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74036500C>T	ENST00000238651.5	+	1	738	c.556C>T	c.(556-558)Cgg>Tgg	p.R186W	ACOT2_ENST00000538782.1_Intron	NM_006821.5	NP_006812.3	P49753	ACOT2_HUMAN	acyl-CoA thioesterase 2	186					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.0639)		GTGCCAGACGCGGCACGAGCG	0.746													C|||	40	0.00798722	0.0	0.0159	5008	,	,		10149	0.0		0.0278	False		,,,				2504	0.001				p.R186W		Atlas-SNP	.											.	ACOT2	24	.	0			c.C556T						PASS	.	C	TRP/ARG	12,3898		0,12,1943	8.0	8.0	8.0		556	0.1	0.0	14	dbSNP_134	8	151,7611		1,149,3731	no	missense	ACOT2	NM_006821.4	101	1,161,5674	TT,TC,CC		1.9454,0.3069,1.3965	probably-damaging	186/484	74036500	163,11509	1955	3881	5836	SO:0001583	missense	10965	exon1			CAGACGCGGCACG	AY005822, AK001939	CCDS9816.1	14q24.3	2013-09-20			ENSG00000119673	ENSG00000119673		"""Acyl CoA thioesterases"""	18431	protein-coding gene	gene with protein product	"""mitochondrial acyl-CoA thioesterase 1"""	609972				16103133, 16940157	Standard	NM_006821		Approved	Mte1, ZAP128	uc001xon.5	P49753	OTTHUMG00000171608	ENST00000238651.5:c.556C>T	14.37:g.74036500C>T	ENSP00000238651:p.Arg186Trp	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	18	14	0.777778	NM_006821	Q3I5F8|Q53EK4|Q9NUX4	Missense_Mutation	SNP	ENST00000238651.5	37	CCDS9816.1	31	0.014194139194139194	3	0.006097560975609756	7	0.019337016574585635	0	0.0	21	0.027704485488126648	C	7.032	0.560848	0.13498	0.003069	0.019454	ENSG00000119673	ENST00000238651	T	0.71222	-0.55	3.38	0.0757	0.14400	Acyl-CoA thioester hydrolase/bile acid-CoA amino acid N-acetyltransferase (1);	0.993165	0.08180	N	0.985593	T	0.47967	0.1474	M	0.68593	2.085	0.09310	N	1	B	0.18166	0.026	B	0.17433	0.018	T	0.58200	-0.7678	10	0.72032	D	0.01	-2.9385	15.4993	0.75684	0.0:0.5948:0.4052:0.0	.	186	P49753	ACOT2_HUMAN	W	186	ENSP00000238651:R186W	ENSP00000238651:R186W	R	+	1	2	ACOT2	73106253	0.000000	0.05858	0.022000	0.16811	0.009000	0.06853	-0.346000	0.07760	-0.275000	0.09219	0.313000	0.20887	CGG	C|0.986;T|0.014	0.014	strong		0.746	ACOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414435.1	NM_006821	
CHRD	8646	hgsc.bcm.edu	37	3	184102396	184102396	+	Silent	SNP	C	C	T	rs16858778	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:184102396C>T	ENST00000204604.1	+	13	1758	c.1512C>T	c.(1510-1512)aaC>aaT	p.N504N	CHRD_ENST00000450923.1_Silent_p.N504N|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000545352.1_Silent_p.N134N|CHRD_ENST00000348986.3_Silent_p.N464N	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	504	CHRD 3. {ECO:0000255|PROSITE- ProRule:PRU00230}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCTTCCTGAACGTGGGCACCA	0.642													C|||	602	0.120208	0.0227	0.2522	5008	,	,		18257	0.2024		0.0507	False		,,,				2504	0.1452				p.N504N		Atlas-SNP	.											.	CHRD	149	.	0			c.C1512T						PASS	.	C		182,4224	115.9+/-153.8	3,176,2024	79.0	78.0	78.0		1512	-3.9	1.0	3	dbSNP_123	78	707,7893	173.3+/-223.8	35,637,3628	no	coding-synonymous	CHRD	NM_003741.2		38,813,5652	TT,TC,CC		8.2209,4.1307,6.8353		504/956	184102396	889,12117	2203	4300	6503	SO:0001819	synonymous_variant	8646	exon13			CCTGAACGTGGGC	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.1512C>T	3.37:g.184102396C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Silent	SNP	ENST00000204604.1	37	CCDS3266.1																																																																																			C|0.909;T|0.091	0.091	strong		0.642	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
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 GAIIx	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_ENST00000414689.2_Missense_Mutation_p.T129I|TMEM219_ENST00000561899.2_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	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	95	7	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	
PLA2G6	8398	hgsc.bcm.edu	37	22	38525510	38525510	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:38525510C>T	ENST00000332509.3	-	8	1320	c.1137G>A	c.(1135-1137)ccG>ccA	p.P379P	PLA2G6_ENST00000490473.1_5'Flank|PLA2G6_ENST00000402064.1_Silent_p.P379P|PLA2G6_ENST00000335539.3_Silent_p.P379P	NM_003560.2	NP_003551.2	O60733	PLPL9_HUMAN	phospholipase A2, group VI (cytosolic, calcium-independent)	379					cardiolipin acyl-chain remodeling (GO:0035965)|cardiolipin biosynthetic process (GO:0032049)|cell death (GO:0008219)|chemotaxis (GO:0006935)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of exocytosis (GO:0045921)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of vasodilation (GO:0045909)|regulation of store-operated calcium channel activity (GO:1901339)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|urinary bladder smooth muscle contraction (GO:0014832)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipase A2 activity (GO:0004623)			breast(2)|endometrium(6)|kidney(1)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	24	Melanoma(58;0.045)				Quinacrine(DB01103)	CAAAGTCATTCGGGGTGTCCA	0.552																																					p.P379P		Atlas-SNP	.											PLA2G6,NS,malignant_melanoma,-1,1	PLA2G6	54	1	0			c.G1137A						scavenged	.						189.0	160.0	170.0					22																	38525510		2203	4300	6503	SO:0001819	synonymous_variant	8398	exon8			GTCATTCGGGGTG	AF064594	CCDS13967.1, CCDS33645.1	22q13.1	2013-01-10			ENSG00000184381	ENSG00000184381	3.1.1.4	"""Patatin-like phospholipase domain containing"", ""Parkinson disease"", ""Ankyrin repeat domain containing"""	9039	protein-coding gene	gene with protein product	"""neurodegeneration with brain iron accumulation 2"""	603604				9417066, 16799181, 19029121	Standard	NM_001199562		Approved	iPLA2, PNPLA9, PARK14, iPLA2beta, NBIA2	uc003aux.1	O60733	OTTHUMG00000151246	ENST00000332509.3:c.1137G>A	22.37:g.38525510C>T		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	181	2	0.0110497	NM_003560	A8K597|B0QYE8|O75645|Q8N452|Q9UG29|Q9UIT0|Q9Y671	Silent	SNP	ENST00000332509.3	37	CCDS13967.1	.	.	.	.	.	.	.	.	.	.	C	10.69	1.421551	0.25639	.	.	ENSG00000184381	ENST00000452794;ENST00000427114	.	.	.	5.34	-10.7	0.00240	.	.	.	.	.	T	0.42359	0.1199	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50197	-0.8856	4	.	.	.	-31.8142	5.7505	0.18144	0.065:0.126:0.3295:0.4795	.	.	.	.	Q	36;184	.	.	R	-	2	0	PLA2G6	36855456	0.000000	0.05858	0.554000	0.28268	0.968000	0.65278	-2.771000	0.00779	-2.024000	0.00936	-0.140000	0.14226	CGA	.	.	none		0.552	PLA2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321860.1	NM_001004426	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923654	43923654	+	Missense_Mutation	SNP	G	G	C	rs12185233	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43923654G>C	ENST00000329196.5	+	1	1399	c.1382G>C	c.(1381-1383)cGc>cCc	p.R461P	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	461			R -> P (in dbSNP:rs12185233).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										TACTGTTGCCGCTTTGATGTG	0.587													G|||	431	0.0860623	0.0151	0.1571	5008	,	,		22035	0.001		0.2396	False		,,,				2504	0.0613				p.R461P		Atlas-SNP	.											IMP5,NS,carcinoma,0,1	.	.	1	0			c.G1382C						PASS	.	G	PRO/ARG	203,4203	127.0+/-164.0	5,193,2005	153.0	117.0	129.0		1382	5.2	1.0	17	dbSNP_120	129	1928,6672	340.3+/-323.5	221,1486,2593	yes	missense	IMP5	NM_175882.2	103	226,1679,4598	CC,CG,GG		22.4186,4.6074,16.3847	possibly-damaging	461/685	43923654	2131,10875	2203	4300	6503	SO:0001583	missense	162540	exon1			GTTGCCGCTTTGA		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1382G>C	17.37:g.43923654G>C	ENSP00000332488:p.Arg461Pro	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	G	15.02	2.709293	0.48517	0.046074	0.224186	ENSG00000185294	ENST00000329196	T	0.27104	1.69	5.2	5.2	0.72013	.	0.000000	0.41823	D	0.000810	T	0.00039	0.0001	M	0.91768	3.24	0.09310	P	0.9999999837478	P	0.36712	0.566	B	0.44133	0.442	T	0.02781	-1.1111	9	0.87932	D	0	-2.5538	16.2754	0.82642	0.0:0.0:1.0:0.0	rs12185233;rs17763711;rs12185233	461	Q8IUH8	IMP5_HUMAN	P	461	ENSP00000332488:R461P	ENSP00000332488:R461P	R	+	2	0	AC217771.1	41279434	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	6.410000	0.73294	2.698000	0.92095	0.563000	0.77884	CGC	G|0.509;C|0.491	0.491	strong		0.587	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
FMO2	2327	hgsc.bcm.edu	37	1	171168584	171168584	+	Missense_Mutation	SNP	C	C	T	rs386636736|rs2020862	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171168584C>T	ENST00000209929.7	+	5	742	c.584C>T	c.(583-585)tCa>tTa	p.S195L	FMO2_ENST00000529935.1_Intron|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.S195L|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	195					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.S195L(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ATGGGAAACTCAGGCTCAGAT	0.488													C|||	2368	0.472843	0.5265	0.4827	5008	,	,		19421	0.5456		0.2962	False		,,,				2504	0.5				p.S195L		Atlas-SNP	.											FMO2,NS,carcinoma,-1,2	FMO2	66	2	1	Substitution - Missense(1)	stomach(1)	c.C584T	GRCh37	CM033900	FMO2	M	rs2020862	PASS	.	C	LEU/SER	2174,2232	585.1+/-386.2	561,1052,590	134.0	140.0	138.0		584	6.2	1.0	1	dbSNP_98	138	2753,5847	439.1+/-359.1	448,1857,1995	yes	missense	FMO2	NM_001460.2	145	1009,2909,2585	TT,TC,CC		32.0116,49.3418,37.8825	probably-damaging	195/472	171168584	4927,8079	2203	4300	6503	SO:0001583	missense	2327	exon5			GAAACTCAGGCTC	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.584C>T	1.37:g.171168584C>T	ENSP00000209929:p.Ser195Leu	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	153	152	0.993464	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	788	0.3608058608058608	190	0.3861788617886179	136	0.3756906077348066	272	0.4755244755244755	190	0.25065963060686014	C	22.4	4.283324	0.80803	0.493418	0.320116	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.60548	0.18;0.18	6.17	6.17	0.99709	.	0.056199	0.85682	D	0.000000	T	0.80824	0.4697	H	0.99689	4.705	0.09310	P	0.9999999445746	B	0.29232	0.238	B	0.41764	0.366	T	0.82810	-0.0273	9	0.87932	D	0	-3.8921	19.6509	0.95805	0.0:1.0:0.0:0.0	rs2020862;rs2266706;rs58871762;rs2020862	195	Q99518	FMO2_HUMAN	L	195	ENSP00000209929:S195L;ENSP00000405905:S195L	ENSP00000209929:S195L	S	+	2	0	FMO2	169435208	1.000000	0.71417	0.969000	0.41365	0.124000	0.20399	5.980000	0.70516	2.941000	0.99782	0.655000	0.94253	TCA	C|0.606;T|0.394	0.394	strong		0.488	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
WNT10B	7480	hgsc.bcm.edu	37	12	49359989	49359989	+	Silent	SNP	G	G	A	rs1051886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49359989G>A	ENST00000301061.4	-	5	1407	c.1059C>T	c.(1057-1059)caC>caT	p.H353H	WNT10B_ENST00000407467.1_3'UTR|WNT10B_ENST00000403957.1_3'UTR	NM_003394.3	NP_003385.2	O00744	WN10B_HUMAN	wingless-type MMTV integration site family, member 10B	353					bone trabecula formation (GO:0060346)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to cAMP (GO:0071320)|cellular response to hydrostatic pressure (GO:0071464)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fungiform papilla development (GO:0061196)|G2/M transition of mitotic cell cycle (GO:0000086)|hematopoietic stem cell proliferation (GO:0071425)|lipid metabolic process (GO:0006629)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of anagen (GO:0051885)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of skeletal muscle tissue development (GO:0048641)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			central_nervous_system(1)|large_intestine(5)|lung(12)|prostate(1)|skin(4)	23						GGAGCACGTTGTGCCCACGGC	0.622													G|||	1558	0.311102	0.1021	0.4957	5008	,	,		16965	0.4494		0.4155	False		,,,				2504	0.2127				p.H353H		Atlas-SNP	.											.	WNT10B	41	.	0			c.C1059T						PASS	.	G		692,3714	284.9+/-277.9	68,556,1579	60.0	48.0	52.0		1059	2.8	1.0	12	dbSNP_86	52	3289,5311	489.3+/-372.6	620,2049,1631	no	coding-synonymous	WNT10B	NM_003394.3		688,2605,3210	AA,AG,GG		38.2442,15.7059,30.6089		353/390	49359989	3981,9025	2203	4300	6503	SO:0001819	synonymous_variant	7480	exon5			CACGTTGTGCCCA	X97057	CCDS8775.1	12q13	2009-01-02			ENSG00000169884	ENSG00000169884		"""Wingless-type MMTV integration sites"""	12775	protein-coding gene	gene with protein product		601906				9121776, 9284937, 18515319	Standard	NM_003394		Approved	WNT-12, SHFM6	uc001rss.3	O00744	OTTHUMG00000150734	ENST00000301061.4:c.1059C>T	12.37:g.49359989G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_003394	B2R7A5|O00747|Q4VAJ4|Q4VAJ5|Q8WZ97	Silent	SNP	ENST00000301061.4	37	CCDS8775.1																																																																																			G|0.679;A|0.321	0.321	strong		0.622	WNT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319864.1	NM_003394	
CR1L	1379	hgsc.bcm.edu	37	1	207851611	207851611	+	Missense_Mutation	SNP	A	A	G	rs2296158	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207851611A>G	ENST00000508064.2	+	3	406	c.346A>G	c.(346-348)Aga>Gga	p.R116G	CR1L_ENST00000530905.1_3'UTR	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	116	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.		R -> G (in dbSNP:rs2296158).			cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CATCCAGTTCAGATCCCAAAT	0.413													N|||	2637	0.526558	0.4493	0.379	5008	,	,		21965	0.6984		0.492	False		,,,				2504	0.5941				p.R116G		Atlas-SNP	.											.	CR1L	97	.	0			c.A346G						PASS	.	G	GLY/ARG	1799,1957		420,959,499	155.0	146.0	149.0		346	2.7	0.2	1	dbSNP_100	149	4309,3941		1127,2055,943	yes	missense	CR1L	NM_175710.1	125	1547,3014,1442	GG,GA,AA		47.7697,47.8967,49.1254	benign	116/570	207851611	6108,5898	1878	4125	6003	SO:0001583	missense	1379	exon3			CAGTTCAGATCCC	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.346A>G	1.37:g.207851611A>G	ENSP00000421736:p.Arg116Gly	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	1129	0.516941391941392	229	0.4654471544715447	147	0.40607734806629836	374	0.6538461538461539	379	0.5	G	0.455	-0.892119	0.02491	0.478967	0.522303	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.56941	0.43	2.73	2.73	0.32206	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.00018	-2.82	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46148	-0.9212	8	0.02654	T	1	.	5.8622	0.18754	0.1578:0.0:0.8422:0.0	rs2296158;rs17259122;rs2296158	116	Q2VPA4	CR1L_HUMAN	G	116	ENSP00000421736:R116G	ENSP00000434864:R60G	R	+	1	2	CR1L	205918234	1.000000	0.71417	0.219000	0.23793	0.114000	0.19823	2.122000	0.41987	0.466000	0.27193	-1.063000	0.02288	AGA	A|0.473;G|0.527	0.527	strong		0.413	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
DNAH7	56171	hgsc.bcm.edu	37	2	196851911	196851911	+	Missense_Mutation	SNP	G	G	A	rs10931715	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:196851911G>A	ENST00000312428.6	-	14	1733	c.1633C>T	c.(1633-1635)Cgt>Tgt	p.R545C		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	545	Stem. {ECO:0000250}.		R -> C (in dbSNP:rs10931715). {ECO:0000269|PubMed:10231032}.		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						ATTCCTAAACGAATAGTCTGC	0.294													G|||	2708	0.540735	0.1664	0.6326	5008	,	,		16139	0.6359		0.664	False		,,,				2504	0.7566				p.R545C		Atlas-SNP	.											.	DNAH7	512	.	0			c.C1633T						PASS	.	G	CYS/ARG	934,2678		131,672,1003	72.0	61.0	64.0		1633	4.9	0.8	2	dbSNP_120	64	5239,2893		1663,1913,490	yes	missense	DNAH7	NM_018897.2	180	1794,2585,1493	AA,AG,GG		35.5755,25.8583,47.437	benign	545/4025	196851911	6173,5571	1806	4066	5872	SO:0001583	missense	56171	exon14			CTAAACGAATAGT	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.1633C>T	2.37:g.196851911G>A	ENSP00000311273:p.Arg545Cys	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	146	66	0.452055	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	1204	0.5512820512820513	86	0.17479674796747968	219	0.6049723756906077	385	0.6730769230769231	514	0.6781002638522428	G	13.06	2.125790	0.37533	0.258583	0.644245	ENSG00000118997	ENST00000312428	T	0.23147	1.92	5.75	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.76002	2.32	0.09310	P	1.0	B	0.15719	0.014	B	0.12156	0.007	T	0.32214	-0.9915	9	0.38643	T	0.18	.	9.7376	0.40397	0.072:0.0:0.789:0.139	rs10931715;rs52824549;rs59453802;rs10931715	545	Q8WXX0	DYH7_HUMAN	C	545	ENSP00000311273:R545C	ENSP00000311273:R545C	R	-	1	0	DNAH7	196560156	1.000000	0.71417	0.809000	0.32408	0.949000	0.60115	3.997000	0.57016	1.398000	0.46701	0.563000	0.77884	CGT	G|0.453;A|0.547	0.547	strong		0.294	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
COL11A2	1302	hgsc.bcm.edu	37	6	33136310	33136310	+	Missense_Mutation	SNP	G	G	T	rs2229784	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33136310G>T	ENST00000374708.4	-	52	3946	c.3688C>A	c.(3688-3690)Cca>Aca	p.P1230T	COL11A2_ENST00000341947.2_Missense_Mutation_p.P1316T|COL11A2_ENST00000374714.1_Missense_Mutation_p.P1290T|COL11A2_ENST00000374712.1_Missense_Mutation_p.P1235T|COL11A2_ENST00000374713.1_Missense_Mutation_p.P1269T|COL11A2_ENST00000357486.1_Missense_Mutation_p.P1295T|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000361917.1_Missense_Mutation_p.P1209T|COL11A2_ENST00000395197.1_Missense_Mutation_p.P1256T	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1316	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TTTCCAAGTGGCCCTGGGGGT	0.632													G|||	288	0.057508	0.0908	0.0403	5008	,	,		15707	0.0883		0.0308	False		,,,				2504	0.0204				p.P1316T	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.C3946A						PASS	.	G	THR/PRO,THR/PRO,THR/PRO	194,2828		6,182,1323	55.0	50.0	52.0		3625,3946,3688	3.4	1.0	6	dbSNP_98	52	168,5250		2,164,2543	yes	missense,missense,missense	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	38,38,38	8,346,3866	TT,TG,GG		3.1008,6.4196,4.2891	probably-damaging,probably-damaging,probably-damaging	1209/1630,1316/1737,1230/1651	33136310	362,8078	1511	2709	4220	SO:0001583	missense	1302	exon54			CAAGTGGCCCTGG	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.3688C>A	6.37:g.33136310G>T	ENSP00000363840:p.Pro1230Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	70	8	0.114286	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Missense_Mutation	SNP	ENST00000374708.4	37	CCDS43452.1	117	0.05357142857142857	35	0.07113821138211382	13	0.03591160220994475	52	0.09090909090909091	17	0.022427440633245383	G	15.27	2.785207	0.49997	0.064196	0.031008	ENSG00000204248	ENST00000374708;ENST00000341947;ENST00000357486;ENST00000374714;ENST00000374713;ENST00000395197;ENST00000374712;ENST00000361917	D;D;D;D;D;D;D;D	0.96856	-3.2;-4.15;-4.15;-4.15;-4.15;-3.2;-4.15;-4.15	4.25	3.38	0.38709	.	0.066730	0.64402	N	0.000010	D	0.95781	0.8627	M	0.64404	1.975	0.58432	D	0.999998	D;D;D	0.58268	0.982;0.982;0.97	P;P;P	0.60236	0.871;0.871;0.746	D	0.95434	0.8519	10	0.72032	D	0.01	.	9.8222	0.40889	0.1015:0.0:0.8985:0.0	rs2229784;rs2272904;rs45631887;rs59414740;rs2229784	1209;1230;1316	P13942-8;P13942-6;P13942	.;.;COBA2_HUMAN	T	1230;1316;1295;1290;1269;1256;1235;1209	ENSP00000363840:P1230T;ENSP00000339915:P1316T;ENSP00000350079:P1295T;ENSP00000363846:P1290T;ENSP00000363845:P1269T;ENSP00000378623:P1256T;ENSP00000363844:P1235T;ENSP00000355123:P1209T	ENSP00000339915:P1316T	P	-	1	0	COL11A2	33244288	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.325000	0.79124	1.008000	0.39264	0.551000	0.68910	CCA	G|0.947;T|0.053	0.053	strong		0.632	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
CACNA1F	778	hgsc.bcm.edu	37	X	49061742	49061742	+	Missense_Mutation	SNP	C	C	T	rs33910054	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49061742C>T	ENST00000376265.2	-	48	5850	c.5789G>A	c.(5788-5790)cGc>cAc	p.R1930H	CACNA1F_ENST00000323022.5_Missense_Mutation_p.R1919H|SYP-AS1_ENST00000433499.1_RNA|CACNA1F_ENST00000376251.1_Missense_Mutation_p.R1865H|AF196779.1_ENST00000583131.1_RNA	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1930			R -> H (in dbSNP:rs33910054).		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)	CAGCGTCAGGCGACACGCATC	0.597													C|||	457	0.12106	0.0113	0.0317	3775	,	,		14844	0.1468		0.0676	False		,,,				2504	0.2086				p.R1930H		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G5789A						PASS	.	C	HIS/ARG	82,3753		0,66,16,1566,555	92.0	53.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5789	1.1	1.0	X	dbSNP_126	67	569,6159		18,376,157,2034,1715	yes	missense	CACNA1F	NM_005183.2	29	18,442,173,3600,2270	TT,TC,T,CC,C		8.4572,2.1382,6.163	benign	1930/1978	49061742	651,9912	2203	4300	6503	SO:0001583	missense	778	exon48			GTCAGGCGACACG	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.5789G>A	X.37:g.49061742C>T	ENSP00000365441:p.Arg1930His	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	110	68	0.618182	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	151	0.09101868595539482	6	0.012244897959183673	5	0.014044943820224719	61	0.11685823754789272	32	0.044444444444444446	C	13.46	2.244305	0.39697	0.021382	0.084572	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	T;T;T	0.54866	0.55;0.55;0.55	4.95	1.07	0.20283	.	0.332987	0.31760	N	0.007102	T	0.00300	0.0009	N	0.02142	-0.665	0.40294	P	0.021468000000000043	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.06625	-1.0816	9	0.35671	T	0.21	.	7.565	0.27874	0.0:0.406:0.0:0.594	rs33910054;rs33910054	1919;1930	F5CIQ9;O60840	.;CAC1F_HUMAN	H	1865;1919;1930	ENSP00000365427:R1865H;ENSP00000321618:R1919H;ENSP00000365441:R1930H	ENSP00000321618:R1919H	R	-	2	0	CACNA1F	48948686	1.000000	0.71417	0.985000	0.45067	0.979000	0.70002	1.872000	0.39549	0.091000	0.17302	0.529000	0.55759	CGC	C|0.926;T|0.074	0.074	strong		0.597	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
AGXT2	64902	hgsc.bcm.edu	37	5	34998877	34998877	+	Missense_Mutation	SNP	C	C	A	rs16899974	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:34998877C>A	ENST00000231420.6	-	14	1692	c.1492G>T	c.(1492-1494)Gta>Tta	p.V498L		NM_031900.3	NP_114106.1	Q9BYV1	AGT2_HUMAN	alanine--glyoxylate aminotransferase 2	498			V -> L (in dbSNP:rs16899974). {ECO:0000269|Ref.3}.		cellular nitrogen compound metabolic process (GO:0034641)|glycine biosynthetic process, by transamination of glyoxylate (GO:0019265)|glyoxylate catabolic process (GO:0009436)|glyoxylate metabolic process (GO:0046487)|L-alanine catabolic process, by transamination (GO:0019481)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|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)	(R)-3-amino-2-methylpropionate-pyruvate transaminase activity (GO:0047305)|alanine-glyoxylate transaminase activity (GO:0008453)|beta-alanine-pyruvate transaminase activity (GO:0016223)|pyridoxal phosphate binding (GO:0030170)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(18)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	41	all_lung(31;4.52e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)	GBM - Glioblastoma multiforme(108;0.181)	Glycine(DB00145)|L-Alanine(DB00160)|Pyruvic acid(DB00119)	AATACTTCTACTGCAAAATCA	0.373													C|||	1180	0.235623	0.0461	0.2608	5008	,	,		21622	0.4216		0.2266	False		,,,				2504	0.2914				p.V498L		Atlas-SNP	.											.	AGXT2	89	.	0			c.G1492T						PASS	.	C	LEU/VAL	333,4073	175.1+/-204.6	9,315,1879	203.0	182.0	189.0		1492	3.8	1.0	5	dbSNP_123	189	1972,6628	346.5+/-326.2	219,1534,2547	yes	missense	AGXT2	NM_031900.3	32	228,1849,4426	AA,AC,CC		22.9302,7.5579,17.7226	benign	498/515	34998877	2305,10701	2203	4300	6503	SO:0001583	missense	64902	exon14			CTTCTACTGCAAA	AJ292204	CCDS3908.1	5p13	2010-05-07	2010-05-07		ENSG00000113492	ENSG00000113492	2.6.1.44		14412	protein-coding gene	gene with protein product	"""beta-alanine-pyruvate aminotransferase"", ""beta-ALAAT II"""	612471	"""alanine-glyoxylate aminotransferase 2"""			15240345	Standard	NM_031900		Approved	AGT2	uc003jjf.3	Q9BYV1	OTTHUMG00000090788	ENST00000231420.6:c.1492G>T	5.37:g.34998877C>A	ENSP00000231420:p.Val498Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_031900	B7ZM47|E9PDL7|Q53FB4|Q53FY7|Q53G03|Q5W7Q1	Missense_Mutation	SNP	ENST00000231420.6	37	CCDS3908.1	519	0.23763736263736263	20	0.04065040650406504	93	0.2569060773480663	240	0.4195804195804196	166	0.21899736147757257	C	9.105	1.005038	0.19199	0.075579	0.229302	ENSG00000113492	ENST00000231420	T	0.17691	2.26	5.69	3.85	0.44370	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.481828	0.23060	N	0.052393	T	0.00012	0.0000	L	0.43152	1.355	0.42398	P	0.007441000000000031	B;B	0.23591	0.088;0.002	B;B	0.22753	0.041;0.006	T	0.46816	-0.9164	9	0.16420	T	0.52	-17.7656	10.6159	0.45449	0.1359:0.7889:0.0:0.0753	rs16899974;rs52832203;rs60642487;rs16899974	423;498	E9PDL7;Q9BYV1	.;AGT2_HUMAN	L	498	ENSP00000231420:V498L	ENSP00000231420:V498L	V	-	1	0	AGXT2	35034634	0.992000	0.36948	0.981000	0.43875	0.050000	0.14768	1.044000	0.30329	0.313000	0.23062	-0.813000	0.03139	GTA	C|0.795;A|0.205	0.205	strong		0.373	AGXT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207574.2	NM_031900	
CCDC85C	317762	hgsc.bcm.edu	37	14	100070030	100070030	+	Silent	SNP	G	G	A	rs78667152	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:100070030G>A	ENST00000380243.4	-	1	333	c.267C>T	c.(265-267)tgC>tgT	p.C89C	RP11-543C4.1_ENST00000502101.2_lincRNA	NM_001144995.1	NP_001138467.1	A6NKD9	CC85C_HUMAN	coiled-coil domain containing 85C	89					cerebral cortex development (GO:0021987)	apical junction complex (GO:0043296)|tight junction (GO:0005923)				endometrium(1)|skin(1)	2						CGTCGAGGAAGCAGCAGAGCT	0.716													g|||	954	0.190495	0.264	0.3069	5008	,	,		6915	0.3433		0.0199	False		,,,				2504	0.0266				p.C89C		Atlas-SNP	.											.	CCDC85C	3	.	0			c.C267T						PASS	.						2.0	5.0	4.0					14																	100070030		575	1385	1960	SO:0001819	synonymous_variant	317762	exon1			GAGGAAGCAGCAG		CCDS45161.1	14q32.31	2009-02-18				ENSG00000205476			35459	protein-coding gene	gene with protein product							Standard	NM_001144995		Approved		uc010avr.3	A6NKD9		ENST00000380243.4:c.267C>T	14.37:g.100070030G>A		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	13	4	0.307692	NM_001144995		Silent	SNP	ENST00000380243.4	37	CCDS45161.1																																																																																			G|0.808;A|0.192	0.192	strong		0.716	CCDC85C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413802.1	NM_001144995	
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 GAIIx	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_ENST00000435176.1_Missense_Mutation_p.I121V|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000539477.1_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	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	73	38	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	
ARFGEF2	10564	hgsc.bcm.edu	37	20	47626847	47626847	+	Silent	SNP	T	T	C	rs2295580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47626847T>C	ENST00000371917.4	+	27	3663	c.3663T>C	c.(3661-3663)ggT>ggC	p.G1221G		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	1221					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			TCCGCTCAGGTTGGAAGAACA	0.567													C|||	1774	0.354233	0.5976	0.2752	5008	,	,		21249	0.1905		0.3171	False		,,,				2504	0.2883				p.G1221G	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											ARFGEF2,colon,carcinoma,0,1	ARFGEF2	160	1	0			c.T3663C						PASS	.	C		2283,2123	577.7+/-384.5	594,1095,514	139.0	109.0	119.0		3663	0.6	1.0	20	dbSNP_100	119	2970,5630	666.7+/-402.4	496,1978,1826	no	coding-synonymous	ARFGEF2	NM_006420.2		1090,3073,2340	CC,CT,TT		34.5349,48.1843,40.3891		1221/1786	47626847	5253,7753	2203	4300	6503	SO:0001819	synonymous_variant	10564	exon27			CTCAGGTTGGAAG	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.3663T>C	20.37:g.47626847T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	93	43	0.462366	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			A|0.003;C|0.372;G|0.003;T|0.622	0.372	strong		0.567	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
GRIN2B	2904	hgsc.bcm.edu	37	12	13720043	13720043	+	Silent	SNP	G	G	A	rs3026160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:13720043G>A	ENST00000609686.1	-	12	2723	c.2514C>T	c.(2512-2514)tgC>tgT	p.C838C		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	838					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	AAAGGTGTTCGCAGATGAAGG	0.502													G|||	208	0.0415335	0.0045	0.0403	5008	,	,		20273	0.001		0.1074	False		,,,				2504	0.0665				p.C838C		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C2514T						PASS	.	G		107,4299	82.4+/-120.9	2,103,2098	133.0	112.0	119.0		2514	-7.1	0.7	12	dbSNP_102	119	1117,7483	231.7+/-265.6	71,975,3254	no	coding-synonymous	GRIN2B	NM_000834.3		73,1078,5352	AA,AG,GG		12.9884,2.4285,9.411		838/1485	13720043	1224,11782	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon12			GTGTTCGCAGATG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.2514C>T	12.37:g.13720043G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.922;A|0.078	0.078	strong		0.502	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
KY	339855	hgsc.bcm.edu	37	3	134369716	134369716	+	Silent	SNP	C	C	A	rs13060869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:134369716C>A	ENST00000423778.2	-	1	148	c.87G>T	c.(85-87)acG>acT	p.T29T	KY_ENST00000503669.1_Silent_p.T29T|KY_ENST00000508956.1_Silent_p.T29T	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	29					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGTCTGAGAGCGTACCCTGTG	0.662													C|||	711	0.141973	0.1097	0.1758	5008	,	,		13584	0.0208		0.2863	False		,,,				2504	0.138				p.T29T		Atlas-SNP	.											.	KY	92	.	0			c.G87T						PASS	.	C		507,3631		29,449,1591	39.0	44.0	43.0		87	2.8	0.6	3	dbSNP_121	43	2394,6006		339,1716,2145	no	coding-synonymous	KY	NM_178554.4		368,2165,3736	AA,AC,CC		28.5,12.2523,23.1377		29/662	134369716	2901,9637	2069	4200	6269	SO:0001819	synonymous_variant	339855	exon1			TGAGAGCGTACCC	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.87G>T	3.37:g.134369716C>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			C|0.832;A|0.168	0.168	strong		0.662	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
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 GAIIx	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_ENST00000472232.3_5'Flank|CHMP5_ENST00000419016.2_Missense_Mutation_p.K46T|BAG1_ENST00000379704.2_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	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	29	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 GAIIx	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_ENST00000566203.2_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000453892.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000433764.1_RNA|MMP24-AS1_ENST00000438751.1_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	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	57	15	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	
SVEP1	79987	hgsc.bcm.edu	37	9	113169631	113169631	+	Missense_Mutation	SNP	G	G	A	rs71492888|rs7030192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:113169631G>A	ENST00000401783.2	-	38	8585	c.8249C>T	c.(8248-8250)gCa>gTa	p.A2750V	SVEP1_ENST00000297826.5_Missense_Mutation_p.A676V|SVEP1_ENST00000374469.1_Missense_Mutation_p.A2727V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2750	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.		A -> V (in dbSNP:rs7030192). {ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GTCAGAGCCTGCTAGAATGTG	0.458													A|||	2138	0.426917	0.5726	0.3256	5008	,	,		22620	0.4365		0.328	False		,,,				2504	0.3937				p.A2750V		Atlas-SNP	.											.	SVEP1	326	.	0			c.C8249T						PASS	.	A	VAL/ALA	1929,2047		465,999,524	75.0	79.0	78.0		8249	4.7	0.1	9	dbSNP_116	78	2601,5709		391,1819,1945	yes	missense	SVEP1	NM_153366.3	64	856,2818,2469	AA,AG,GG		31.2996,48.5161,36.8712	benign	2750/3572	113169631	4530,7756	1988	4155	6143	SO:0001583	missense	79987	exon38			GAGCCTGCTAGAA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8249C>T	9.37:g.113169631G>A	ENSP00000384917:p.Ala2750Val	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	214	106	0.495327	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	742	0.33974358974358976	212	0.43089430894308944	108	0.2983425414364641	213	0.3723776223776224	209	0.2757255936675462	A	0	-2.739132	0.00088	0.485161	0.312996	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.62364	0.03;0.03;0.03	5.87	4.71	0.59529	Complement control module (2);Sushi/SCR/CCP (3);	0.717443	0.14280	N	0.329611	T	0.00012	0.0000	N	0.00205	-1.85	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.45934	-0.9227	9	0.25106	T	0.35	.	6.1143	0.20117	0.568:0.0:0.0664:0.3656	rs7030192;rs60576083;rs7030192	2750	Q4LDE5	SVEP1_HUMAN	V	2750;2727;676;422	ENSP00000384917:A2750V;ENSP00000363593:A2727V;ENSP00000297826:A676V	ENSP00000297826:A676V	A	-	2	0	SVEP1	112209452	0.005000	0.15991	0.139000	0.22197	0.028000	0.11728	1.821000	0.39041	0.451000	0.26802	-0.352000	0.07741	GCA	A|0.380;G|0.620	0.380	strong		0.458	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TRIM45	80263	hgsc.bcm.edu	37	1	117660754	117660754	+	Missense_Mutation	SNP	C	C	T	rs749902	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117660754C>T	ENST00000256649.4	-	2	1650	c.1124G>A	c.(1123-1125)tGt>tAt	p.C375Y	TRIM45_ENST00000369461.3_Missense_Mutation_p.C318Y|TRIM45_ENST00000369464.3_Missense_Mutation_p.C375Y	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	375			C -> Y (in dbSNP:rs749902). {ECO:0000269|Ref.3}.		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)		CTCCTGAGGACAGAAGCGTAT	0.468													C|||	1125	0.224641	0.2103	0.3674	5008	,	,		21820	0.0327		0.3529	False		,,,				2504	0.2086				p.C375Y		Atlas-SNP	.											.	TRIM45	55	.	0			c.G1124A						PASS	.	C	TYR/CYS,TYR/CYS	1014,3392	379.7+/-323.4	123,768,1312	127.0	127.0	127.0		1124,1124	0.7	0.9	1	dbSNP_86	127	2832,5768	447.2+/-361.5	470,1892,1938	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	194,194	593,2660,3250	TT,TC,CC		32.9302,23.0141,29.571	benign,benign	375/563,375/581	117660754	3846,9160	2203	4300	6503	SO:0001583	missense	80263	exon2			TGAGGACAGAAGC		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.1124G>A	1.37:g.117660754C>T	ENSP00000256649:p.Cys375Tyr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_001145635	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	509	0.23305860805860806	103	0.20934959349593496	125	0.3453038674033149	17	0.02972027972027972	264	0.3482849604221636	C	0.003	-2.538963	0.00143	0.230141	0.329302	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	T;D;T	0.81996	-1.38;-1.56;-1.09	4.75	0.722	0.18225	.	0.676676	0.15867	N	0.240719	T	0.31918	0.0812	N	0.03608	-0.345	0.47698	P	5.020000000000024E-4	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.03945	-1.0990	9	0.07482	T	0.82	-0.4557	5.3998	0.16288	0.2396:0.2863:0.4741:0.0	rs749902;rs52795064;rs58937492;rs749902	375;375	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	Y	375;375;318	ENSP00000256649:C375Y;ENSP00000358476:C375Y;ENSP00000358473:C318Y	ENSP00000256649:C375Y	C	-	2	0	TRIM45	117462277	0.990000	0.36364	0.888000	0.34837	0.040000	0.13550	1.358000	0.34102	-0.013000	0.14199	-0.165000	0.13383	TGT	C|0.742;T|0.258	0.258	strong		0.468	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
PPL	5493	hgsc.bcm.edu	37	16	4942099	4942099	+	Missense_Mutation	SNP	C	C	T	rs1049205	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4942099C>T	ENST00000345988.2	-	15	1855	c.1766G>A	c.(1765-1767)cGg>cAg	p.R589Q	PPL_ENST00000590782.2_Missense_Mutation_p.R587Q	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	589			R -> Q (in dbSNP:rs1049205). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9412476, ECO:0000269|PubMed:9628581, ECO:0000269|Ref.5}.		keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						GTCCTCCACCCGGGTCCTCAG	0.642													C|||	2002	0.39976	0.034	0.4654	5008	,	,		17542	0.6399		0.5388	False		,,,				2504	0.4571				p.R589Q		Atlas-SNP	.											PPL,NS,carcinoma,0,1	PPL	168	1	0			c.G1766A						PASS	.	C	GLN/ARG	513,3881	233.3+/-246.5	36,441,1720	59.0	58.0	59.0		1766	5.3	1.0	16	dbSNP_86	59	4754,3846	609.6+/-395.6	1318,2118,864	yes	missense	PPL	NM_002705.4	43	1354,2559,2584	TT,TC,CC		44.7209,11.675,40.5341	possibly-damaging	589/1757	4942099	5267,7727	2197	4300	6497	SO:0001583	missense	5493	exon15			TCCACCCGGGTCC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.1766G>A	16.37:g.4942099C>T	ENSP00000340510:p.Arg589Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	970	0.4441391941391941	24	0.04878048780487805	164	0.4530386740331492	370	0.6468531468531469	412	0.5435356200527705	C	14.43	2.534249	0.45073	0.11675	0.552791	ENSG00000118898	ENST00000345988	T	0.36520	1.25	5.35	5.35	0.76521	.	0.079955	0.51477	D	0.000092	T	0.00012	0.0000	L	0.44542	1.39	0.27437	P	0.9538222	P	0.41710	0.76	B	0.30401	0.115	T	0.40869	-0.9540	9	0.14656	T	0.56	.	6.9724	0.24656	0.0:0.7881:0.0:0.2119	rs1049205;rs3189307;rs56845948;rs1049205	589	O60437	PEPL_HUMAN	Q	589	ENSP00000340510:R589Q	ENSP00000340510:R589Q	R	-	2	0	PPL	4882100	1.000000	0.71417	1.000000	0.80357	0.352000	0.29268	5.278000	0.65592	2.519000	0.84933	0.549000	0.68633	CGG	C|0.588;T|0.412	0.412	strong		0.642	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
NES	10763	hgsc.bcm.edu	37	1	156640678	156640678	+	Missense_Mutation	SNP	G	G	A	rs2886443	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156640678G>A	ENST00000368223.3	-	4	3434	c.3302C>T	c.(3301-3303)cCg>cTg	p.P1101L		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1101	Tail.		P -> L (in dbSNP:rs2886443). {ECO:0000269|PubMed:1478958}.		brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCCCTGCCCCGGGCCTGGCTC	0.647													G|||	3116	0.622204	0.3858	0.67	5008	,	,		11968	0.8621		0.6481	False		,,,				2504	0.6339				p.P1101L		Atlas-SNP	.											NES,NS,carcinoma,0,1	NES	196	1	0			c.C3302T						PASS	.	G	LEU/PRO	1788,2592		377,1034,779	18.0	22.0	21.0		3302	-4.2	0.0	1	dbSNP_101	21	5445,3117		1815,1815,651	yes	missense	NES	NM_006617.1	98	2192,2849,1430	AA,AG,GG		36.405,40.8219,44.1122	probably-damaging	1101/1622	156640678	7233,5709	2190	4281	6471	SO:0001583	missense	10763	exon4			TGCCCCGGGCCTG	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3302C>T	1.37:g.156640678G>A	ENSP00000357206:p.Pro1101Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	125	60	0.48	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	1421	0.6506410256410257	199	0.40447154471544716	242	0.6685082872928176	489	0.8548951048951049	491	0.6477572559366754	G	6.686	0.495244	0.12762	0.408219	0.63595	ENSG00000132688	ENST00000368223	D	0.84873	-1.91	4.16	-4.17	0.03857	.	1.304050	0.05885	N	0.627213	T	0.55305	0.1912	L	0.56769	1.78	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.32903	-0.9889	9	0.07030	T	0.85	.	4.0525	0.09801	0.2772:0.0:0.3442:0.3786	rs2886443;rs3748572;rs57956552;rs2886443	1101	P48681	NEST_HUMAN	L	1101	ENSP00000357206:P1101L	ENSP00000357206:P1101L	P	-	2	0	NES	154907302	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.984000	0.00320	-0.966000	0.03587	-1.141000	0.01876	CCG	G|0.356;A|0.644	0.644	strong		0.647	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
MUC4	4585	hgsc.bcm.edu	37	3	195505822	195505822	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195505822G>T	ENST00000463781.3	-	2	13088	c.12629C>A	c.(12628-12630)cCt>cAt	p.P4210H	MUC4_ENST00000475231.1_Missense_Mutation_p.P4210H|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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)		GTCGGTGACAGGAAGAGGGGT	0.592																																					p.P4210H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C12629A						scavenged	.						18.0	16.0	17.0					3																	195505822		688	1572	2260	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	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.12629C>A	3.37:g.195505822G>T	ENSP00000417498:p.Pro4210His	Somatic	81	2	0.0246914		WXS	Illumina HiSeq	Phase_I	74	7	0.0945946	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	2.410	-0.335654	0.05278	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37058	1.22;1.26	.	.	.	.	.	.	.	.	T	0.32912	0.0845	N	0.14661	0.345	0.09310	N	0.999993	D	0.76494	0.999	D	0.72338	0.977	T	0.14117	-1.0484	7	.	.	.	.	2.6645	0.05037	0.4931:0.0:0.5069:0.0	.	4082	E7ESK3	.	H	4210	ENSP00000417498:P4210H;ENSP00000420243:P4210H	.	P	-	2	0	MUC4	196990601	.	.	0.023000	0.16930	0.027000	0.11550	.	.	0.088000	0.17205	0.089000	0.15464	CCT	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
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 GAIIx	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		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	148	78	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 GAIIx	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	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	159	83	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	
SVIL	6840	hgsc.bcm.edu	37	10	29754535	29754535	+	Missense_Mutation	SNP	G	G	A	rs17694739	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:29754535G>A	ENST00000355867.4	-	34	6874	c.6122C>T	c.(6121-6123)gCg>gTg	p.A2041V	PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.A955V|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000375398.2_Missense_Mutation_p.A2041V|SVIL_ENST00000375400.3_Missense_Mutation_p.A1615V|PTCHD3P1_ENST00000413405.1_RNA|PTCHD3P1_ENST00000414457.1_RNA	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2041			A -> V (in dbSNP:rs17694739).		cytoskeleton organization (GO:0007010)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|costamere (GO:0043034)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(24)|lung(35)|ovary(8)|prostate(2)|skin(4)|stomach(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	112		Breast(68;0.103)				TGGCTGGGGCGCGCTGTACAG	0.542													G|||	246	0.0491214	0.0189	0.0504	5008	,	,		17538	0.0198		0.1352	False		,,,				2504	0.0307				p.A2041V		Atlas-SNP	.											SVIL,colon,carcinoma,+1,1	SVIL	226	1	0			c.C6122T						PASS	.	G	VAL/ALA,VAL/ALA	151,4255	99.4+/-138.0	0,151,2052	38.0	41.0	40.0		4844,6122	4.7	0.2	10	dbSNP_123	40	1126,7472	211.1+/-251.8	82,962,3255	no	missense,missense	SVIL	NM_003174.3,NM_021738.2	64,64	82,1113,5307	AA,AG,GG		13.0961,3.4271,9.8201	benign,benign	1615/1789,2041/2215	29754535	1277,11727	2203	4299	6502	SO:0001583	missense	6840	exon34			TGGGGCGCGCTGT	AF051851	CCDS7163.1, CCDS7164.1	10p11.2	2008-07-29			ENSG00000197321	ENSG00000197321			11480	protein-coding gene	gene with protein product	"""archvillin"""	604126				9382871	Standard	NM_003174		Approved		uc001iut.1	O95425	OTTHUMG00000017882	ENST00000355867.4:c.6122C>T	10.37:g.29754535G>A	ENSP00000348128:p.Ala2041Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	139	0.06364468864468864	8	0.016260162601626018	23	0.06353591160220995	7	0.012237762237762238	101	0.13324538258575197	G	16.70	3.195070	0.58017	0.034271	0.130961	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393	T;T;T;T	0.14640	2.49;2.49;2.49;2.49	4.72	4.72	0.59763	.	0.046563	0.85682	D	0.000000	T	0.00210	0.0006	M	0.74258	2.255	0.09310	P	1.0	P;P;P	0.46656	0.882;0.582;0.791	B;B;B	0.39152	0.292;0.245;0.177	T	0.14671	-1.0464	9	0.42905	T	0.14	-23.0313	17.8597	0.88777	0.0:0.0:1.0:0.0	rs17694739	955;1615;2041	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	V	1615;2041;2041;955	ENSP00000364549:A1615V;ENSP00000364547:A2041V;ENSP00000348128:A2041V;ENSP00000445472:A955V	ENSP00000348128:A2041V	A	-	2	0	SVIL	29794541	1.000000	0.71417	0.245000	0.24217	0.158000	0.22134	7.706000	0.84615	2.428000	0.82296	0.650000	0.86243	GCG	G|0.917;A|0.083	0.083	strong		0.542	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1		
LY6K	54742	hgsc.bcm.edu	37	8	143782044	143782044	+	Silent	SNP	A	A	G	rs2585174	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143782044A>G	ENST00000292430.6	+	1	516	c.99A>G	c.(97-99)cgA>cgG	p.R33R	LY6K_ENST00000561179.1_Silent_p.R91R|LY6K_ENST00000518841.1_Silent_p.R33R|CTD-2292P10.4_ENST00000520572.1_RNA|LY6K_ENST00000522591.1_Silent_p.R33R|LY6K_ENST00000519387.1_Silent_p.R33R			Q17RY6	LY6K_HUMAN	lymphocyte antigen 6 complex, locus K	33						anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)	10	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					ACTCCCAGCGAACGGGTGAGC	0.716													G|||	2576	0.514377	0.7065	0.4611	5008	,	,		9524	0.4524		0.4722	False		,,,				2504	0.3998				p.R33R		Atlas-SNP	.											.	LY6K	23	.	0			c.A99G						PASS	.	G	,,	2883,1457		1011,861,298	13.0	15.0	14.0		99,99,99	0.2	0.0	8	dbSNP_100	14	4048,4492		1004,2040,1226	no	coding-synonymous,coding-synonymous,coding-synonymous	LY6K	NM_001160354.1,NM_001160355.1,NM_017527.3	,,	2015,2901,1524	GG,GA,AA		47.4005,33.5714,46.1879	,,	33/121,33/106,33/166	143782044	6931,5949	2170	4270	6440	SO:0001819	synonymous_variant	54742	exon1			CCAGCGAACGGGT	AK092545	CCDS6385.1, CCDS6385.2, CCDS59114.1	8q24.3	2009-08-06				ENSG00000160886			24225	protein-coding gene	gene with protein product	"""cancer/testis antigen 97"""	615093				12516096	Standard	NM_017527		Approved	HSJ001348, FLJ35226, CT97	uc011ljv.2	Q17RY6		ENST00000292430.6:c.99A>G	8.37:g.143782044A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_001160354	G3V116|O15227|Q9BVD7	Silent	SNP	ENST00000292430.6	37	CCDS6385.2	1070	0.4899267399267399	329	0.6686991869918699	146	0.40331491712707185	239	0.4178321678321678	356	0.46965699208443273	G	5.291	0.239083	0.10023	0.664286	0.474005	ENSG00000160886	ENST00000522591	.	.	.	0.149	0.149	0.14863	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.40021	-0.9585	2	.	.	.	.	.	.	.	rs2585174;rs3188888;rs3736007;rs17412659;rs2585174	.	.	.	G	52	.	.	E	+	2	0	LY6K	143779046	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.521000	0.02239	-1.066000	0.03164	-1.063000	0.02288	GAA	A|0.482;G|0.518	0.518	strong		0.716	LY6K-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379893.2	NM_017527	
PARP12	64761	hgsc.bcm.edu	37	7	139734069	139734069	+	Missense_Mutation	SNP	C	C	T	rs35456446	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:139734069C>T	ENST00000263549.3	-	8	2260	c.1387G>A	c.(1387-1389)Gtg>Atg	p.V463M	PARP12_ENST00000470515.1_5'UTR	NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	463			V -> M (in dbSNP:rs35456446).			nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					TGGGGAGACACGTATTTGGGT	0.463													C|||	302	0.0603035	0.0855	0.0346	5008	,	,		18790	0.001		0.0437	False		,,,				2504	0.1227				p.V463M		Atlas-SNP	.											.	PARP12	59	.	0			c.G1387A						PASS	.	C	MET/VAL	290,4116	158.9+/-191.5	10,270,1923	87.0	79.0	82.0		1387	4.1	0.9	7	dbSNP_126	82	376,8224	123.2+/-182.1	12,352,3936	yes	missense	PARP12	NM_022750.2	21	22,622,5859	TT,TC,CC		4.3721,6.5819,5.1207	possibly-damaging	463/702	139734069	666,12340	2203	4300	6503	SO:0001583	missense	64761	exon8			GAGACACGTATTT	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	21919	protein-coding gene	gene with protein product		612481	"""zinc finger CCCH-type domain containing 1"""	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1387G>A	7.37:g.139734069C>T	ENSP00000263549:p.Val463Met	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_022750	Q9H610|Q9NP36|Q9NTI3	Missense_Mutation	SNP	ENST00000263549.3	37	CCDS5857.1	101	0.04624542124542125	42	0.08536585365853659	19	0.052486187845303865	0	0.0	40	0.052770448548812667	C	18.59	3.656556	0.67586	0.065819	0.043721	ENSG00000059378	ENST00000263549;ENST00000489809	T;T	0.60548	1.52;0.18	5.84	4.05	0.47172	.	0.062472	0.64402	N	0.000005	T	0.08626	0.0214	M	0.69358	2.11	0.43637	D	0.996032	D	0.89917	1.0	D	0.70935	0.971	T	0.42155	-0.9468	10	0.62326	D	0.03	.	10.7226	0.46048	0.0:0.8542:0.0:0.1458	rs35456446	463	Q9H0J9	PAR12_HUMAN	M	463;101	ENSP00000263549:V463M;ENSP00000417606:V101M	ENSP00000263549:V463M	V	-	1	0	PARP12	139380538	0.276000	0.24211	0.895000	0.35142	0.825000	0.46686	0.726000	0.25984	1.489000	0.48450	-0.234000	0.12200	GTG	C|0.953;T|0.047	0.047	strong		0.463	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750	
KMT2B	9757	hgsc.bcm.edu	37	19	36222857	36222857	+	Missense_Mutation	SNP	C	C	T	rs16970649	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36222857C>T	ENST00000222270.7	+	27	5486	c.5486C>T	c.(5485-5487)cCt>cTt	p.P1829L	KMT2B_ENST00000420124.1_Missense_Mutation_p.P1829L|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1829			P -> L (in dbSNP:rs16970649).		chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GTTCTTGTCCCTGGAGCTCCT	0.627													C|||	502	0.10024	0.0794	0.0994	5008	,	,		15311	0.0883		0.1203	False		,,,				2504	0.1207				p.P1829L		Atlas-SNP	.											.	MLL4	229	.	0			c.C5486T						PASS	.	C	LEU/PRO	307,3673		10,287,1693	38.0	44.0	42.0		5486	4.3	0.9	19	dbSNP_123	42	797,7501		33,731,3385	yes	missense	MLL4	NM_014727.1	98	43,1018,5078	TT,TC,CC		9.6047,7.7136,8.9917	benign	1829/2716	36222857	1104,11174	1990	4149	6139	SO:0001583	missense	8085	exon27			TTGTCCCTGGAGC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.5486C>T	19.37:g.36222857C>T	ENSP00000222270:p.Pro1829Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	37	CCDS46055.1	223	0.1021062271062271	45	0.09146341463414634	36	0.09944751381215469	48	0.08391608391608392	94	0.12401055408970976	C	8.457	0.854334	0.17106	0.077136	0.096047	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.84146	-1.81;-1.81	5.33	4.3	0.51218	.	0.338090	0.21603	N	0.071911	T	0.05777	0.0151	L	0.49126	1.545	0.09310	P	1.0	B	0.12630	0.006	B	0.12156	0.007	T	0.61724	-0.7004	9	0.66056	D	0.02	.	13.0361	0.58873	0.0:0.9206:0.0:0.0794	rs16970649;rs56612720;rs60126381;rs16970649	1829	Q9UMN6	MLL4_HUMAN	L	1829	ENSP00000222270:P1829L;ENSP00000398837:P1829L	ENSP00000222270:P1829L	P	+	2	0	AD000671.1	40914697	0.132000	0.22450	0.860000	0.33809	0.622000	0.37654	1.659000	0.37387	1.390000	0.46547	0.655000	0.94253	CCT	C|0.902;T|0.098	0.098	strong		0.627	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499179	59499179	+	Missense_Mutation	SNP	G	G	A	rs3809530	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:59499179G>A	ENST00000307144.4	+	1	138	c.40G>A	c.(40-42)Gtg>Atg	p.V14M	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	14			V -> M (in dbSNP:rs3809530). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						CAGCCAGAGAGTGAGCTCGGT	0.587													G|||	2017	0.402756	0.2814	0.3905	5008	,	,		20610	0.5496		0.2714	False		,,,				2504	0.5593				p.V14M		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.G40A						PASS	.	G	,MET/VAL	1272,3110	430.6+/-342.6	197,878,1116	41.0	39.0	39.0		,40	1.5	0.0	15	dbSNP_107	39	2368,6212	392.2+/-343.9	323,1722,2245	yes	intron,missense	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,21	520,2600,3361	AA,AG,GG		27.5991,29.0278,28.0821	,benign	,14/382	59499179	3640,9322	2191	4290	6481	SO:0001583	missense	92483	exon1			CAGAGAGTGAGCT	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.40G>A	15.37:g.59499179G>A	ENSP00000302393:p.Val14Met	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	92	31	0.336957	NM_033195	Q6DUY4|Q96LI2	Missense_Mutation	SNP	ENST00000307144.4	37	CCDS10171.1	793	0.3630952380952381	137	0.2784552845528455	122	0.3370165745856354	330	0.5769230769230769	204	0.2691292875989446	G	7.458	0.644080	0.14451	0.290278	0.275991	ENSG00000171989	ENST00000307144	T	0.72051	-0.62	1.49	1.49	0.22878	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.19200	0.034	B	0.14023	0.01	T	0.46721	-0.9171	8	0.37606	T	0.19	.	6.8004	0.23748	0.0:0.0:1.0:0.0	rs3809530;rs17856653;rs52798006;rs3809530	14	Q9BYZ2	LDH6B_HUMAN	M	14	ENSP00000302393:V14M	ENSP00000302393:V14M	V	+	1	0	LDHAL6B	57286471	0.088000	0.21588	0.003000	0.11579	0.113000	0.19764	0.474000	0.22148	0.710000	0.31997	0.305000	0.20034	GTG	G|0.690;A|0.310	0.310	strong		0.587	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
IL3RA	3563	hgsc.bcm.edu	37	X	1497644	1497644	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:1497644G>C	ENST00000331035.4	+	10	1316	c.967G>C	c.(967-969)Gtg>Ctg	p.V323L	IL3RA_ENST00000381469.2_Missense_Mutation_p.V245L	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	323			V -> L (in dbSNP:rs17883366). {ECO:0000269|Ref.5}.		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)			lung(1)|skin(2)	3		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)			Sargramostim(DB00020)	CTGTGTCTTCGTGATCTGCAG	0.592													g|||	525	0.104832	0.0378	0.1297	5008	,	,		16681	0.0694		0.2058	False		,,,				2504	0.1104				p.V323L		Atlas-SNP	.											.	IL3RA	49	.	0			c.G967C						PASS	.		LEU/VAL	293,4109		12,269,1920	130.0	106.0	114.0		967	-1.6	0.0	X	dbSNP_134	114	1580,7012		144,1292,2860	no	missense	IL3RA	NM_002183.2	32	156,1561,4780	CC,CG,GG		18.3892,6.6561,14.4143	benign	323/379	1497644	1873,11121	2201	4296	6497	SO:0001583	missense	3563	exon10			GTCTTCGTGATCT	M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"""Pseudoautosomal regions / PAR1"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.967G>C	X.37:g.1497644G>C	ENSP00000327890:p.Val323Leu	Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	142	92	0.647887	NM_002183	A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Missense_Mutation	SNP	ENST00000331035.4	37	CCDS14113.1	283	0.1295787545787546	21	0.042682926829268296	54	0.14917127071823205	53	0.09265734265734266	155	0.20448548812664907	.	0	-2.808565	0.00074	0.066561	0.183892	ENSG00000185291	ENST00000331035;ENST00000381469	T;D	0.96522	1.74;-4.04	0.798	-1.6	0.08426	.	0.471891	0.15240	N	0.272951	T	0.00271	0.0008	N	0.00841	-1.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.51957	-0.8639	9	0.06757	T	0.87	.	.	.	.	.	244;323	P26951-2;P26951	.;IL3RA_HUMAN	L	323;245	ENSP00000327890:V323L;ENSP00000370878:V245L	ENSP00000327890:V323L	V	+	1	0	IL3RA	1457644	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.991000	0.03728	-2.554000	0.00477	-2.540000	0.00180	GTG	G|0.868;C|0.132	0.132	strong		0.592	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3		
PDE4DIP	9659	hgsc.bcm.edu	37	1	144906508	144906508	+	Missense_Mutation	SNP	C	C	T	rs34169189	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:144906508C>T	ENST00000369354.3	-	18	2538	c.2349G>A	c.(2347-2349)atG>atA	p.M783I	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.M920I|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.M570I|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.M783I|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.M946I|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.M783I|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.M849I|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.M783I|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.M920I|PDE4DIP_ENST00000524974.1_Intron|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.M946I			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	783				M -> I (in Ref. 4; CAD38529 and 6; AAI32718). {ECO:0000305}.	cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CCTGCACAGCCATCATGGACT	0.418			T	PDGFRB	MPD								C|||	467	0.0932508	0.0227	0.1974	5008	,	,		20695	0.0268		0.1342	False		,,,				2504	0.1411				p.M946I		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G2838A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	179,4227	111.2+/-149.4	6,167,2030	92.0	92.0	92.0		2349,2349,2547,2349,2838	2.0	1.0	1	dbSNP_126	92	1266,7320	243.8+/-273.2	80,1106,3107	yes	missense,missense,missense,missense,missense	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1,NM_001002812.1,NM_001002811.1	10,10,10,10,10	86,1273,5137	TT,TC,CC		14.7449,4.0626,11.1222	benign,benign,benign,benign,benign	783/2347,783/2363,849/2241,783/970,946/1133	144906508	1445,11547	2203	4293	6496	SO:0001583	missense	9659	exon14			CACAGCCATCATG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.2349G>A	1.37:g.144906508C>T	ENSP00000358360:p.Met783Ile	Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	259	126	0.486486	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	187	0.08562271062271062	10	0.02032520325203252	67	0.1850828729281768	13	0.022727272727272728	97	0.1279683377308707	C	10.64	1.407063	0.25378	0.040626	0.147449	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.10860	4.85;4.94;4.94;4.94;4.94;3.93;3.94;2.86;2.85;2.83	6.07	1.96	0.26148	.	.	.	.	.	T	0.01124	0.0037	N	0.12182	0.205	0.09310	P	0.9999999999993228	B;B;B;B;B	0.18461	0.0;0.0;0.0;0.028;0.0	B;B;B;B;B	0.13407	0.001;0.0;0.001;0.009;0.0	T	0.47018	-0.9149	8	0.06099	T	0.92	.	3.6148	0.08073	0.1196:0.5183:0.2102:0.1519	rs34169189	946;783;946;849;783	E9PL24;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;MYOME_HUMAN	I	849;783;783;946;920;920;783;783;946;946;570	ENSP00000327209:M849I;ENSP00000358360:M783I;ENSP00000358363:M783I;ENSP00000435654:M920I;ENSP00000358366:M920I;ENSP00000358357:M783I;ENSP00000358355:M783I;ENSP00000316434:M946I;ENSP00000433392:M946I;ENSP00000436791:M570I	ENSP00000327209:M849I	M	-	3	0	PDE4DIP	143617865	0.689000	0.27690	1.000000	0.80357	0.965000	0.64279	-0.084000	0.11268	0.929000	0.37192	0.638000	0.83543	ATG	C|0.898;T|0.102	0.102	strong		0.418	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
CSPP1	79848	hgsc.bcm.edu	37	8	68074137	68074137	+	Missense_Mutation	SNP	G	G	A	rs16933182	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:68074137G>A	ENST00000262210.5	+	20	2646	c.2615G>A	c.(2614-2616)cGt>cAt	p.R872H	CSPP1_ENST00000412460.1_Missense_Mutation_p.R527H|CSPP1_ENST00000521168.1_3'UTR	NM_024790.6	NP_079066.5	Q1MSJ5	CSPP1_HUMAN	centrosome and spindle pole associated protein 1	907					positive regulation of cell division (GO:0051781)|positive regulation of cytokinesis (GO:0032467)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|spindle (GO:0005819)|spindle pole (GO:0000922)				NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(17)|ovary(5)|prostate(3)|skin(1)|urinary_tract(1)	49	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00145)|OV - Ovarian serous cystadenocarcinoma(28;0.00589)|all cancers(69;0.0069)|BRCA - Breast invasive adenocarcinoma(89;0.153)			AGCATCATACGTTCCTTTATT	0.353													G|||	727	0.145168	0.3638	0.1052	5008	,	,		18340	0.0248		0.0437	False		,,,				2504	0.1063				p.R872H		Atlas-SNP	.											.	CSPP1	129	.	0			c.G2615A						PASS	.	G	HIS/ARG	1081,2631		156,769,931	183.0	177.0	179.0		2615	0.8	1.0	8	dbSNP_123	179	266,7920		3,260,3830	yes	missense	CSPP1	NM_024790.6	29	159,1029,4761	AA,AG,GG		3.2495,29.1218,11.3212	benign	872/1222	68074137	1347,10551	1856	4093	5949	SO:0001583	missense	79848	exon20			TCATACGTTCCTT	AJ583433	CCDS43744.1	8q13.2	2014-02-24			ENSG00000104218	ENSG00000104218			26193	protein-coding gene	gene with protein product		611654				15580290, 24360807	Standard	NM_024790		Approved	FLJ22490, CSPP, JBTS21	uc003xxj.3	Q1MSJ5	OTTHUMG00000164564	ENST00000262210.5:c.2615G>A	8.37:g.68074137G>A	ENSP00000262210:p.Arg872His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	123	47	0.382114	NM_024790	A6ND63|Q70F00|Q8TBC1	Missense_Mutation	SNP	ENST00000262210.5	37	CCDS43744.1	264	0.12087912087912088	173	0.3516260162601626	35	0.09668508287292818	18	0.03146853146853147	38	0.05013192612137203	G	14.92	2.678370	0.47886	0.291218	0.032495	ENSG00000104218	ENST00000262210;ENST00000389042;ENST00000412460;ENST00000519668	T;T;T	0.30448	1.53;1.54;1.54	4.56	0.842	0.18927	.	0.673644	0.15627	N	0.252588	T	0.00012	0.0000	N	0.08118	0	0.44469	P	0.0026000000000000467	P;P;P	0.35844	0.524;0.524;0.524	B;B;B	0.30855	0.121;0.091;0.091	T	0.47420	-0.9119	9	0.41790	T	0.15	-6.6099	6.4721	0.22013	0.2507:0.429:0.3202:0.0	rs16933182;rs17852119;rs52829429;rs16933182	527;872;907	Q1MSJ5-2;Q1MSJ5-1;Q1MSJ5	.;.;CSPP1_HUMAN	H	872;907;527;527	ENSP00000262210:R872H;ENSP00000415782:R527H;ENSP00000430092:R527H	ENSP00000262210:R872H	R	+	2	0	CSPP1	68236691	0.993000	0.37304	0.999000	0.59377	0.967000	0.64934	0.216000	0.17585	0.143000	0.18926	0.650000	0.86243	CGT	G|0.883;A|0.117	0.117	strong		0.353	CSPP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379254.1	NM_024790	
CST1	1469	hgsc.bcm.edu	37	20	23731494	23731494	+	Missense_Mutation	SNP	A	A	G	rs6076122	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:23731494A>G	ENST00000304749.2	-	1	80	c.10T>C	c.(10-12)Tat>Cat	p.Y4H	CST1_ENST00000398402.1_Missense_Mutation_p.Y4H	NM_001898.2	NP_001889.2	P01037	CYTN_HUMAN	cystatin SN	4			Y -> H (in dbSNP:rs6076122). {ECO:0000269|PubMed:2837486, ECO:0000269|PubMed:3446578}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			kidney(1)|large_intestine(1)|lung(8)|ovary(1)|stomach(1)|urinary_tract(1)	13	Lung NSC(19;0.0676)|all_lung(19;0.148)					GTACTCAGATACTGGGCCATG	0.632													.|||	4155	0.829673	0.9607	0.7133	5008	,	,		13985	0.9048		0.7068	False		,,,				2504	0.7843				p.Y4H		Atlas-SNP	.											.	CST1	37	.	0			c.T10C						PASS	.	G	HIS/TYR	4056,350	171.6+/-201.8	1868,320,15	37.0	34.0	35.0		10	0.3	0.0	20	dbSNP_114	35	6004,2594	403.1+/-347.7	2093,1818,388	yes	missense	CST1	NM_001898.2	83	3961,2138,403	GG,GA,AA		30.1698,7.9437,22.6392	benign	4/142	23731494	10060,2944	2203	4299	6502	SO:0001583	missense	1469	exon1			TCAGATACTGGGC	M19169	CCDS13160.1	20p11.2	2008-04-15			ENSG00000170373	ENSG00000170373			2473	protein-coding gene	gene with protein product		123855					Standard	NM_001898		Approved		uc002wtp.3	P01037	OTTHUMG00000032085	ENST00000304749.2:c.10T>C	20.37:g.23731494A>G	ENSP00000305731:p.Tyr4His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001898	Q96LE6|Q9UCQ6	Missense_Mutation	SNP	ENST00000304749.2	37	CCDS13160.1	1773	0.8118131868131868	475	0.9654471544715447	258	0.712707182320442	516	0.9020979020979021	524	0.6912928759894459	G	4.328	0.060322	0.08339	0.920563	0.698302	ENSG00000170373	ENST00000304749;ENST00000398402	T;T	0.07216	3.21;3.21	1.38	0.348	0.16026	.	0.950640	0.08797	N	0.892372	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.01281	0.0	T	0.13045	-1.0524	9	0.15066	T	0.55	.	4.1273	0.10133	0.4469:0.0:0.5531:0.0	rs6076122;rs7274985;rs17233610;rs60834128;rs6076122	4	P01037	CYTN_HUMAN	H	4	ENSP00000305731:Y4H;ENSP00000381439:Y4H	ENSP00000305731:Y4H	Y	-	1	0	CST1	23679494	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.844000	0.04345	-0.243000	0.09653	-1.160000	0.01791	TAT	A|0.194;G|0.806	0.806	strong		0.632	CST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078351.2	NM_001898	
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 GAIIx	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	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	26	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 GAIIx	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	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	93	48	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	
DCHS2	54798	hgsc.bcm.edu	37	4	155410667	155410667	+	Missense_Mutation	SNP	G	G	A	rs55810732	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:155410667G>A	ENST00000339452.1	-	1	2201	c.1841C>T	c.(1840-1842)gCg>gTg	p.A614V	DCHS2_ENST00000456341.2_Missense_Mutation_p.A607V|DCHS2_ENST00000443500.1_Missense_Mutation_p.A614V	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1739	Cadherin 5. {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)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AGTGCTGATCGCACCGCTTTC	0.597													G|||	860	0.171725	0.0356	0.3084	5008	,	,		18458	0.1558		0.2117	False		,,,				2504	0.2342				p.A614V		Atlas-SNP	.											DCHS2_ENST00000443500,NS,carcinoma,+1,2	DCHS2	594	2	0			c.C1841T						PASS	.	G	VAL/ALA,VAL/ALA	78,1306		6,66,620	48.0	48.0	48.0		1841,1841	0.1	0.0	4	dbSNP_129	48	554,2628		56,442,1093	yes	missense,missense	DCHS2	NM_001142552.1,NM_001142553.1	64,64	62,508,1713	AA,AG,GG		17.4104,5.6358,13.8414	,	614/1370,614/710	155410667	632,3934	692	1591	2283	SO:0001583	missense	54798	exon1			CTGATCGCACCGC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000339452.1:c.1841C>T	4.37:g.155410667G>A	ENSP00000345062:p.Ala614Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	37	CCDS47150.1	359	0.16437728937728938	17	0.034552845528455285	96	0.26519337016574585	81	0.14160839160839161	165	0.21767810026385223	G	0	-2.743134	0.00087	0.056358	0.174104	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.49720	0.77;0.77;0.77	5.17	0.0543	0.14310	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.30765	-0.9967	7	0.02654	T	1	.	9.3402	0.38076	0.6058:0.0:0.3942:0.0	rs55810732	614;614	E9PG03;E9PC11	.;.	V	614;614;607;614	ENSP00000345062:A614V;ENSP00000408543:A607V;ENSP00000395539:A614V	ENSP00000345062:A614V	A	-	2	0	DCHS2	155630117	0.000000	0.05858	0.002000	0.10522	0.037000	0.13140	0.599000	0.24089	-0.096000	0.12329	-1.298000	0.01336	GCG	G|0.837;A|0.163	0.163	strong		0.597	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
STAT1	6772	hgsc.bcm.edu	37	2	191874667	191874667	+	Silent	SNP	A	A	G	rs2066802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:191874667A>G	ENST00000361099.3	-	3	450	c.63T>C	c.(61-63)ctT>ctC	p.L21L	STAT1_ENST00000540176.1_Silent_p.L21L|STAT1_ENST00000409465.1_Silent_p.L21L|STAT1_ENST00000392323.2_Silent_p.L23L|STAT1_ENST00000392322.3_Silent_p.L21L	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	21					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			TGTCATCATAAAGCTGGTGAA	0.393													A|||	574	0.114617	0.0734	0.0504	5008	,	,		19108	0.2272		0.0696	False		,,,				2504	0.1462				p.L21L		Atlas-SNP	.											.	STAT1	93	.	0			c.T63C						PASS	.	A	,	320,4086	171.6+/-201.8	10,300,1893	157.0	149.0	152.0		63,63	-2.9	1.0	2	dbSNP_94	152	532,8068	147.7+/-203.1	17,498,3785	no	coding-synonymous,coding-synonymous	STAT1	NM_007315.3,NM_139266.2	,	27,798,5678	GG,GA,AA		6.186,7.2628,6.5508	,	21/751,21/713	191874667	852,12154	2203	4300	6503	SO:0001819	synonymous_variant	6772	exon3			ATCATAAAGCTGG		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.63T>C	2.37:g.191874667A>G		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Silent	SNP	ENST00000361099.3	37	CCDS2309.1																																																																																			A|0.909;G|0.091	0.091	strong		0.393	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766776	27766776	+	Silent	SNP	G	G	A	rs45553337	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:27766776G>A	ENST00000451261.2	+	5	2163	c.1764G>A	c.(1762-1764)acG>acA	p.T588T		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	588								p.T555T(1)		central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						GTCACGTGACGCAGAGAGGTC	0.507													A|||	620	0.164238	0.1324	0.1167	3775	,	,		15143	0.0546		0.2078	False		,,,				2504	0.1022				p.T588T		Atlas-SNP	.											.	DCAF8L2	79	.	1	Substitution - coding silent(1)	kidney(1)	c.G1764A						PASS	.	A		250,959		19,183,29,315,146	83.0	59.0	67.0		1764	2.5	0.0	X	dbSNP_127	67	671,1720		61,306,243,433,548	no	coding-synonymous	DCAF8L2	NM_001136533.1		80,489,272,748,694	AA,AG,A,GG,G		28.0636,20.6782,25.5833		588/632	27766776	921,2679	692	1591	2283	SO:0001819	synonymous_variant	347442	exon1			CGTGACGCAGAGA		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1764G>A	X.37:g.27766776G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	184	141	0.766304	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			G|0.816;A|0.184	0.184	strong		0.507	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
CGB2	114336	hgsc.bcm.edu	37	19	49536390	49536390	+	Missense_Mutation	SNP	C	C	A	rs62126039	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49536390C>A	ENST00000359342.6	+	3	522	c.404C>A	c.(403-405)gCc>gAc	p.A135D	CTB-60B18.6_ENST00000591656.1_Intron	NM_033378.1	NP_203696.2	Q6NT52	CGB2_HUMAN	chorionic gonadotropin, beta polypeptide 2	167						extracellular region (GO:0005576)		p.A135D(1)		large_intestine(1)|lung(1)|stomach(1)	3		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		CGCTTCCAGGCCTCCTCTTCC	0.637													c|||	1481	0.295727	0.3381	0.3718	5008	,	,		12440	0.1567		0.336	False		,,,				2504	0.2863				p.A135D		Atlas-SNP	.											CGB2,NS,carcinoma,0,1	CGB2	6	1	1	Substitution - Missense(1)	stomach(1)	c.C404A						scavenged	.						19.0	27.0	24.0					19																	49536390		2161	4265	6426	SO:0001583	missense	114336	exon3			TCCAGGCCTCCTC	K03184	CCDS12750.2	19q13.32	2008-02-05			ENSG00000104818	ENSG00000104818			16722	protein-coding gene	gene with protein product		608824				6194155	Standard	NM_033378		Approved		uc002plw.3	Q6NT52	OTTHUMG00000150185	ENST00000359342.6:c.404C>A	19.37:g.49536390C>A	ENSP00000352295:p.Ala135Asp	Somatic	161	10	0.0621118		WXS	Illumina HiSeq	Phase_I	107	30	0.280374	NM_033378	B9ZVM5	Missense_Mutation	SNP	ENST00000359342.6	37	CCDS12750.2	.	.	.	.	.	.	.	.	.	.	c	0.395	-0.921146	0.02396	.	.	ENSG00000104818	ENST00000359342	T	0.36520	1.25	1.79	0.719	0.18208	.	.	.	.	.	T	0.11707	0.0285	N	0.02916	-0.46	0.47905	P	4.6000000000001595E-4	.	.	.	.	.	.	T	0.34254	-0.9836	6	0.11182	T	0.66	.	5.5188	0.16921	0.3275:0.6725:0.0:0.0	.	.	.	.	D	135	ENSP00000352295:A135D	ENSP00000352295:A135D	A	+	2	0	CGB2	54228202	0.010000	0.17322	0.167000	0.22817	0.014000	0.08584	0.011000	0.13264	0.323000	0.23307	-1.276000	0.01395	GCC	A|1.000;|0.000	1.000	weak		0.637	CGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316745.1	NM_033378	
TNNC2	7125	hgsc.bcm.edu	37	20	44452697	44452697	+	Silent	SNP	C	C	A	rs4629	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44452697C>A	ENST00000372555.3	-	5	476	c.384G>T	c.(382-384)acG>acT	p.T128T	TNNC2_ENST00000372557.1_Silent_p.T113T	NM_003279.2	NP_003270.1	P02585	TNNC2_HUMAN	troponin C type 2 (fast)	128	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				muscle filament sliding (GO:0030049)|regulation of muscle contraction (GO:0006937)|skeletal muscle contraction (GO:0003009)	cytosol (GO:0005829)|troponin complex (GO:0005861)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5		Myeloproliferative disorder(115;0.0122)			Felodipine(DB01023)	TCTCCTCGTCCGTCACGTGCT	0.612													C|||	2027	0.404752	0.1815	0.5476	5008	,	,		17060	0.5308		0.5378	False		,,,				2504	0.3384				p.T128T		Atlas-SNP	.											.	TNNC2	12	.	0			c.G384T						PASS	.	C		1148,3258	406.4+/-333.9	155,838,1210	162.0	141.0	148.0		384	-5.9	0.9	20	dbSNP_52	148	4562,4038	596.6+/-393.6	1206,2150,944	no	coding-synonymous	TNNC2	NM_003279.2		1361,2988,2154	AA,AC,CC		46.9535,26.0554,43.9028		128/161	44452697	5710,7296	2203	4300	6503	SO:0001819	synonymous_variant	7125	exon5			CTCGTCCGTCACG		CCDS13375.1	20q12-q13.11	2013-01-10	2005-09-12		ENSG00000101470	ENSG00000101470		"""EF-hand domain containing"""	11944	protein-coding gene	gene with protein product		191039	"""troponin C2, fast"""			2373703	Standard	NM_003279		Approved		uc002xpr.3	P02585	OTTHUMG00000032623	ENST00000372555.3:c.384G>T	20.37:g.44452697C>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_003279	Q6FH92	Silent	SNP	ENST00000372555.3	37	CCDS13375.1																																																																																			C|0.569;A|0.431	0.431	strong		0.612	TNNC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079524.3	NM_003279	
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 GAIIx	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	C17orf74_ENST00000574034.1_3'UTR|RP11-104H15.7_ENST00000575310.1_RNA	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	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	61	41	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	
BANK1	55024	hgsc.bcm.edu	37	4	102751076	102751076	+	Missense_Mutation	SNP	G	G	A	rs10516487	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:102751076G>A	ENST00000322953.4	+	2	456	c.182G>A	c.(181-183)cGc>cAc	p.R61H	BANK1_ENST00000428908.1_Intron|BANK1_ENST00000504592.1_Missense_Mutation_p.R46H|BANK1_ENST00000444316.2_Missense_Mutation_p.R31H|BANK1_ENST00000508653.1_Intron	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	61	Interaction with ITPR2.		R -> H (influences susceptibility to SLE; dbSNP:rs10516487). {ECO:0000269|PubMed:18204447}.		B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		CTGTTATATCGCTTGGAGAAT	0.353													G|||	1094	0.21845	0.2239	0.1859	5008	,	,		16221	0.1875		0.2972	False		,,,				2504	0.1851				p.R61H		Atlas-SNP	.											.	BANK1	95	.	0			c.G182A	GRCh37	CM080095	BANK1	M	rs10516487	PASS	.	G	HIS/ARG,,HIS/ARG	1075,3331	385.8+/-325.9	139,797,1267	77.0	78.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	92,,182	-1.2	0.0	4	dbSNP_119	78	2610,5990	420.8+/-353.5	395,1820,2085	yes	missense,intron,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	29,,29	534,2617,3352	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	30.3488,24.3985,28.3331	benign,,benign	31/756,,61/786	102751076	3685,9321	2203	4300	6503	SO:0001583	missense	55024	exon2			TATATCGCTTGGA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.182G>A	4.37:g.102751076G>A	ENSP00000320509:p.Arg61His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	81	32	0.395062	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	490	0.22435897435897437	115	0.23373983739837398	74	0.20441988950276244	84	0.14685314685314685	217	0.2862796833773087	G	11.15	1.553737	0.27739	0.243985	0.303488	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000444316	T;T;T	0.09445	2.98;2.98;2.98	5.18	-1.16	0.09678	.	0.869969	0.09740	N	0.762056	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.21753	0.06;0.06	B;B	0.15870	0.014;0.014	T	0.47799	-0.9089	9	0.42905	T	0.14	.	2.2057	0.03935	0.4512:0.1608:0.2727:0.1153	rs10516487;rs17200720;rs56600798;rs56700821;rs10516487	61;46	Q8NDB2;Q8NDB2-2	BANK1_HUMAN;.	H	46;61;31	ENSP00000421443:R46H;ENSP00000320509:R61H;ENSP00000388817:R31H	ENSP00000320509:R61H	R	+	2	0	BANK1	102970099	0.002000	0.14202	0.001000	0.08648	0.909000	0.53808	0.550000	0.23345	-0.749000	0.04747	0.650000	0.86243	CGC	G|0.748;A|0.252	0.252	strong		0.353	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
SPTB	6710	hgsc.bcm.edu	37	14	65216120	65216120	+	Silent	SNP	C	C	T	rs57421986	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:65216120C>T	ENST00000556626.1	-	36	7033	c.6891G>A	c.(6889-6891)gcG>gcA	p.A2297A	SPTB_ENST00000389722.3_Silent_p.A2297A|SPTB_ENST00000342835.4_5'UTR			P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	0					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GCAGGCTCTGCGCCTTGACGC	0.632													C|||	523	0.104433	0.2421	0.0346	5008	,	,		13049	0.0317		0.0775	False		,,,				2504	0.0706				p.A2297A		Atlas-SNP	.											.	SPTB	378	.	0			c.G6891A						PASS	.	C		979,3427	354.6+/-312.7	114,751,1338	56.0	50.0	52.0		6891	-9.5	0.4	14	dbSNP_129	52	509,8091	139.8+/-196.4	16,477,3807	no	coding-synonymous	SPTB	NM_001024858.2		130,1228,5145	TT,TC,CC		5.9186,22.2197,11.4409		2297/2329	65216120	1488,11518	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon35			GCTCTGCGCCTTG		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000556626.1:c.6891G>A	14.37:g.65216120C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000556626.1	37	CCDS32099.1																																																																																			A|0.000;C|0.891;T|0.108	0.108	strong		0.632	SPTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414076.1		
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 GAIIx	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_ENST00000394827.3_Silent_p.Q224Q|PTPN3_ENST00000446349.1_Silent_p.Q580Q|PTPN3_ENST00000412145.1_Silent_p.Q625Q|PTPN3_ENST00000262539.3_Silent_p.Q602Q	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		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	41	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		
BTNL8	79908	hgsc.bcm.edu	37	5	180377331	180377331	+	Silent	SNP	T	T	C	rs2278689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180377331T>C	ENST00000340184.4	+	8	1496	c.1290T>C	c.(1288-1290)taT>taC	p.Y430Y	BTNL8_ENST00000511704.1_Silent_p.Y314Y|BTNL8_ENST00000508408.1_3'UTR|BTNL8_ENST00000231229.4_3'UTR|BTNL8_ENST00000505126.1_Silent_p.Y223Y|BTNL8_ENST00000400707.3_Silent_p.Y305Y|BTNL8_ENST00000533815.2_Silent_p.Y246Y	NM_001040462.2	NP_001035552.1	Q6UX41	BTNL8_HUMAN	butyrophilin-like 8	430	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	28	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCTTATTTATACCCTGACAT	0.478													t|||	1246	0.248802	0.5787	0.1182	5008	,	,		16037	0.1171		0.1163	False		,,,				2504	0.1677				p.Y430Y		Atlas-SNP	.											.	BTNL8	114	.	0			c.T1290C						PASS	.	T	,,,,,	2010,1748		638,734,507	177.0	142.0	153.0		1290,942,,915,738,	1.9	0.6	5	dbSNP_100	153	1078,6516		293,492,3012	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous,coding-synonymous,utr-3	BTNL8	NM_001040462.2,NM_001159707.1,NM_001159708.1,NM_001159709.1,NM_001159710.1,NM_024850.2	,,,,,	931,1226,3519	CC,CT,TT		14.1954,46.5141,27.2023	,,,,,	430/501,314/385,,305/376,246/317,	180377331	3088,8264	1879	3797	5676	SO:0001819	synonymous_variant	79908	exon8			TATTTATACCCTG	AK025111	CCDS4459.1, CCDS43413.1, CCDS54956.1, CCDS54957.1, CCDS54958.1, CCDS54959.1	5q35.3	2014-01-14			ENSG00000113303	ENSG00000113303		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	26131	protein-coding gene	gene with protein product		615606				12975309	Standard	NM_024850		Approved	FLJ21458, BTN9.2	uc003mmp.3	Q6UX41	OTTHUMG00000130932	ENST00000340184.4:c.1290T>C	5.37:g.180377331T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001040462	A4QMZ8|A6NEX6|B7Z409|B7Z5B1|E9PEF6|E9PG07|F2Z2B2|F8W712|Q9H730	Silent	SNP	ENST00000340184.4	37	CCDS43413.1																																																																																			T|0.757;C|0.243	0.243	strong		0.478	BTNL8-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368440.1	NM_024850	
FANCA	2175	hgsc.bcm.edu	37	16	89836323	89836323	+	Missense_Mutation	SNP	C	C	T	rs7195066	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89836323C>T	ENST00000389301.3	-	26	2456	c.2426G>A	c.(2425-2427)gGt>gAt	p.G809D	FANCA_ENST00000567284.2_5'Flank|FANCA_ENST00000568369.1_Missense_Mutation_p.G809D	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	809			G -> D (common polymorphism; dbSNP:rs7195066). {ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:9371798, ECO:0000269|PubMed:9399890, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		AAGGCCAGCACCAGGTGCAGG	0.617			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	3339	0.666733	0.7398	0.5821	5008	,	,		17886	0.9881		0.3221	False		,,,				2504	0.6513				p.G809D		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,NS,carcinoma,0,1	FANCA	99	1	0			c.G2426A						PASS	.	T	ASP/GLY	2895,1501	476.3+/-357.6	953,989,256	92.0	68.0	76.0		2426	-0.2	0.0	16	dbSNP_116	76	2702,5898	682.3+/-403.8	438,1826,2036	yes	missense	FANCA	NM_000135.2	94	1391,2815,2292	TT,TC,CC		31.4186,34.1447,43.0671	benign	809/1456	89836323	5597,7399	2198	4300	6498	SO:0001583	missense	2175	exon26	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CCAGCACCAGGTG	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.2426G>A	16.37:g.89836323C>T	ENSP00000373952:p.Gly809Asp	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	1344	0.6153846153846154	348	0.7073170731707317	190	0.5248618784530387	565	0.9877622377622378	241	0.3179419525065963	T	3.507	-0.100499	0.06967	0.658553	0.314186	ENSG00000187741	ENST00000389301	D	0.84442	-1.85	3.13	-0.167	0.13347	.	0.597657	0.15671	N	0.250384	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27054	-1.0085	9	0.18710	T	0.47	-0.0117	2.3692	0.04326	0.1117:0.3478:0.3548:0.1856	rs7195066;rs17233043;rs60022722;rs7195066	809;809	B4DRI7;O15360	.;FANCA_HUMAN	D	809	ENSP00000373952:G809D	ENSP00000373952:G809D	G	-	2	0	FANCA	88363824	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.305000	0.19254	-0.200000	0.10300	-1.562000	0.00884	GGT	C|0.485;T|0.515	0.515	strong		0.617	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
DOCK2	1794	hgsc.bcm.edu	37	5	169483706	169483706	+	Silent	SNP	C	C	T	rs17647491	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:169483706C>T	ENST00000256935.8	+	43	4394	c.4314C>T	c.(4312-4314)taC>taT	p.Y1438Y	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Silent_p.Y930Y|DOCK2_ENST00000540750.1_Silent_p.Y499Y	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1438	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AATCCAACTACGTGCAAAGGT	0.572													C|||	28	0.00559105	0.0	0.0173	5008	,	,		19455	0.0		0.0149	False		,,,				2504	0.001				p.Y1438Y		Atlas-SNP	.											.	DOCK2	389	.	0			c.C4314T						PASS	.	C		10,4396	17.9+/-39.9	0,10,2193	106.0	95.0	99.0		4314	-3.8	1.0	5	dbSNP_123	99	157,8443	75.1+/-137.7	1,155,4144	no	coding-synonymous	DOCK2	NM_004946.2		1,165,6337	TT,TC,CC		1.8256,0.227,1.284		1438/1831	169483706	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon43			CAACTACGTGCAA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4314C>T	5.37:g.169483706C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			C|0.989;T|0.011	0.011	strong		0.572	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
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 GAIIx	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_ENST00000416245.1_Missense_Mutation_p.A7T|ZP3_ENST00000336517.4_Missense_Mutation_p.A132T	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	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	21	13	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		
CHMP4C	92421	hgsc.bcm.edu	37	8	82670747	82670747	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:82670747G>T	ENST00000297265.4	+	5	863	c.670G>T	c.(670-672)Gat>Tat	p.D224Y		NM_152284.3	NP_689497.1	Q96CF2	CHM4C_HUMAN	charged multivesicular body protein 4C	224	Intramolecular interaction with N- terminus. {ECO:0000250}.				abscission (GO:0009838)|cytokinesis checkpoint (GO:0031565)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of cytokinesis (GO:0032466)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|membrane (GO:0016020)|midbody (GO:0030496)	protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	10						AGAGGATGATGATATCAAACA	0.318																																					p.D224Y		Atlas-SNP	.											CHMP4C,bladder,carcinoma,0,1	CHMP4C	28	1	0			c.G670T						scavenged	.						99.0	100.0	100.0					8																	82670747		2203	4299	6502	SO:0001583	missense	92421	exon5			GATGATGATATCA	AK000049	CCDS6233.1	8q21.13	2011-09-21	2011-09-21		ENSG00000164695	ENSG00000164695		"""Charged multivesicular body proteins"""	30599	protein-coding gene	gene with protein product	"""Snf7 homologue associated with Alix 3"""	610899	"""chromatin modifying protein 4C"""			12860994 , 14678797	Standard	NM_152284		Approved	MGC22825, Shax3, VPS32C	uc003ycl.3	Q96CF2	OTTHUMG00000164726	ENST00000297265.4:c.670G>T	8.37:g.82670747G>T	ENSP00000297265:p.Asp224Tyr	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	143	5	0.034965	NM_152284	B2RBZ1	Missense_Mutation	SNP	ENST00000297265.4	37	CCDS6233.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.586062	0.86748	.	.	ENSG00000164695	ENST00000297265	T	0.56776	0.44	6.11	6.11	0.99139	.	0.041199	0.85682	D	0.000000	T	0.55800	0.1943	N	0.08118	0	0.80722	D	1	D	0.76494	0.999	D	0.67231	0.95	T	0.64668	-0.6353	10	0.87932	D	0	-11.5446	19.5057	0.95114	0.0:0.0:1.0:0.0	.	224	Q96CF2	CHM4C_HUMAN	Y	224	ENSP00000297265:D224Y	ENSP00000297265:D224Y	D	+	1	0	CHMP4C	82833302	1.000000	0.71417	0.977000	0.42913	0.986000	0.74619	7.784000	0.85713	2.906000	0.99361	0.655000	0.94253	GAT	.	.	none		0.318	CHMP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379927.1	NM_152284	
MUC16	94025	hgsc.bcm.edu	37	19	9057896	9057896	+	Missense_Mutation	SNP	G	G	C	rs12984471	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9057896G>C	ENST00000397910.4	-	3	29753	c.29550C>G	c.(29548-29550)gaC>gaG	p.D9850E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9852	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGTGGTATCGTCCACAGCGG	0.473													C|||	1046	0.208866	0.2352	0.219	5008	,	,		21466	0.0258		0.3121	False		,,,				2504	0.2485				p.D9850E		Atlas-SNP	.											.	MUC16	4315	.	0			c.C29550G						PASS	.	C	GLU/ASP	931,3103		102,727,1188	156.0	149.0	151.0		29550	-1.6	0.0	19	dbSNP_121	151	2825,5553		499,1827,1863	yes	missense	MUC16	NM_024690.2	45	601,2554,3051	CC,CG,GG		33.7193,23.0788,30.261	benign	9850/14508	9057896	3756,8656	2017	4189	6206	SO:0001583	missense	94025	exon3			GGTATCGTCCACA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.29550C>G	19.37:g.9057896G>C	ENSP00000381008:p.Asp9850Glu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	455	0.20833333333333334	123	0.25	82	0.2265193370165746	11	0.019230769230769232	239	0.3153034300791557	c	5.757	0.324052	0.10900	0.230788	0.337193	ENSG00000181143	ENST00000397910	T	0.19806	2.12	2.43	-1.59	0.08453	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.45687	-0.9244	8	0.87932	D	0	.	4.2005	0.10464	0.0:0.4824:0.185:0.3325	rs12984471;rs52797430;rs57305113;rs12984471	9850	B5ME49	.	E	9850	ENSP00000381008:D9850E	ENSP00000381008:D9850E	D	-	3	2	MUC16	8918896	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.110000	0.00293	-0.660000	0.05352	-0.224000	0.12420	GAC	G|0.760;C|0.240	0.240	strong		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
C2CD2	25966	hgsc.bcm.edu	37	21	43327856	43327856	+	Silent	SNP	A	A	G	rs3746906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43327856A>G	ENST00000380486.3	-	9	1297	c.1056T>C	c.(1054-1056)ttT>ttC	p.F352F	C2CD2_ENST00000329623.7_Silent_p.F197F	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	352						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						GCTGCTTCTTAAATAAGTCCA	0.622													A|||	3042	0.607428	0.6248	0.5159	5008	,	,		17172	0.5923		0.6491	False		,,,				2504	0.6217				p.F352F		Atlas-SNP	.											.	C2CD2	47	.	0			c.T1056C						PASS	.	A	,	2707,1699	639.3+/-397.1	838,1031,334	34.0	38.0	37.0		1056,591	-0.9	0.9	21	dbSNP_107	37	5543,3057	645.7+/-400.2	1784,1975,541	no	coding-synonymous,coding-synonymous	C2CD2	NM_015500.1,NM_199050.2	,	2622,3006,875	GG,GA,AA		35.5465,38.5611,36.5677	,	352/697,197/542	43327856	8250,4756	2203	4300	6503	SO:0001819	synonymous_variant	25966	exon9			CTTCTTAAATAAG	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1056T>C	21.37:g.43327856A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Silent	SNP	ENST00000380486.3	37	CCDS42933.1																																																																																			A|0.367;G|0.633	0.633	strong		0.622	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
SHROOM2	357	hgsc.bcm.edu	37	X	9914947	9914947	+	Missense_Mutation	SNP	G	G	C	rs2073942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:9914947G>C	ENST00000380913.3	+	10	4911	c.4821G>C	c.(4819-4821)ttG>ttC	p.L1607F	SHROOM2_ENST00000418909.2_Missense_Mutation_p.L442F	NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	1607	ASD2. {ECO:0000255|PROSITE- ProRule:PRU00638}.		L -> F (in dbSNP:rs2073942).		apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				AGTGCTTATTGGACAGCCTTC	0.567													C|||	1751	0.463841	0.5787	0.3429	3775	,	,		12496	0.4276		0.1819	False		,,,				2504	0.137				p.L1607F		Atlas-SNP	.											.	SHROOM2	139	.	0			c.G4821C						PASS	.	C	PHE/LEU	2631,1199		774,690,393,168,173	27.0	22.0	24.0		4821	-9.4	0.0	X	dbSNP_96	24	1645,5081		165,878,437,1385,1433	yes	missense	SHROOM2	NM_001649.2	22	939,1568,830,1553,1606	CC,CG,C,GG,G		24.4573,31.3055,40.5078	benign	1607/1617	9914947	4276,6280	2198	4298	6496	SO:0001583	missense	357	exon10			CTTATTGGACAGC	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.4821G>C	X.37:g.9914947G>C	ENSP00000370299:p.Leu1607Phe	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	73	15	0.205479	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	37	CCDS14135.1	831	0.5009041591320073	219	0.6801242236024845	84	0.28378378378378377	180	0.47368421052631576	83	0.12691131498470948	C	8.484	0.860544	0.17178	0.686945	0.244573	ENSG00000146950	ENST00000380913;ENST00000418909	T;T	0.30714	1.52;1.52	4.69	-9.37	0.00626	Apx/shroom, ASD2 (2);	1.014080	0.07897	N	0.972089	T	0.00012	0.0000	L	0.28115	0.83	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.23655	-1.0182	9	0.31617	T	0.26	-3.6589	11.2952	0.49274	0.0:0.4623:0.2526:0.2851	rs2073942;rs17255327;rs2073942	1607	Q13796	SHRM2_HUMAN	F	1607;442	ENSP00000370299:L1607F;ENSP00000415229:L442F	ENSP00000370299:L1607F	L	+	3	2	SHROOM2	9874947	0.000000	0.05858	0.003000	0.11579	0.729000	0.41735	-3.530000	0.00440	-2.894000	0.00314	-2.367000	0.00236	TTG	0|0.003;C|0.476	0.476	strong		0.567	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
LIPC	3990	hgsc.bcm.edu	37	15	58838010	58838010	+	Missense_Mutation	SNP	A	A	G	rs6083	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:58838010A>G	ENST00000356113.6	+	7	1259	c.644A>G	c.(643-645)aAt>aGt	p.N215S	LIPC_ENST00000299022.5_Missense_Mutation_p.N215S|LIPC_ENST00000414170.3_Missense_Mutation_p.N215S|LIPC_ENST00000433326.2_Missense_Mutation_p.N154S			P11150	LIPC_HUMAN	lipase, hepatic	215			N -> S (in dbSNP:rs6083). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2324091, ECO:0000269|PubMed:2447084, ECO:0000269|PubMed:2828141}.		cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron remnant clearance (GO:0034382)|fatty acid biosynthetic process (GO:0006633)|high-density lipoprotein particle remodeling (GO:0034375)|intermediate-density lipoprotein particle remodeling (GO:0034373)|low-density lipoprotein particle remodeling (GO:0034374)|phosphatidylcholine catabolic process (GO:0034638)|reverse cholesterol transport (GO:0043691)|triglyceride catabolic process (GO:0019433)|triglyceride homeostasis (GO:0070328)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular space (GO:0005615)|high-density lipoprotein particle (GO:0034364)	apolipoprotein binding (GO:0034185)|heparin binding (GO:0008201)|low-density lipoprotein particle binding (GO:0030169)|phospholipase activity (GO:0004620)|triglyceride lipase activity (GO:0004806)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Colorectal(260;0.215)		GBM - Glioblastoma multiforme(80;0.00213)|all cancers(107;0.00548)		GATGATGCCAATTTTGTGGAT	0.547													A|||	3048	0.608626	0.7141	0.4928	5008	,	,		17425	0.7917		0.3847	False		,,,				2504	0.59				p.N215S		Atlas-SNP	.											.	LIPC	56	.	0			c.A644G	GRCh37	CM910256	LIPC	M	rs6083	PASS	.	A	SER/ASN	2974,1410	683.7+/-404.3	1008,958,226	102.0	97.0	99.0		644	-0.1	0.2	15	dbSNP_52	99	3117,5467	477.4+/-369.6	585,1947,1760	yes	missense	LIPC	NM_000236.2	46	1593,2905,1986	GG,GA,AA		36.3117,32.1624,46.9695	benign	215/500	58838010	6091,6877	2192	4292	6484	SO:0001583	missense	3990	exon5			ATGCCAATTTTGT		CCDS10166.1	15q21-q23	2012-10-02			ENSG00000166035	ENSG00000166035	3.1.1.3		6619	protein-coding gene	gene with protein product		151670					Standard	NM_000236		Approved	HL, HTGL	uc002afa.2	P11150	OTTHUMG00000132632	ENST00000356113.6:c.644A>G	15.37:g.58838010A>G	ENSP00000348425:p.Asn215Ser	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	53	32	0.603774	NM_000236	A2RUB4|A8K9B6|O43571|P78529|Q99465	Missense_Mutation	SNP	ENST00000356113.6	37	CCDS10166.1	1284	0.5879120879120879	340	0.6910569105691057	173	0.47790055248618785	484	0.8461538461538461	287	0.3786279683377309	A	10.60	1.396310	0.25205	0.678376	0.363117	ENSG00000166035	ENST00000356113;ENST00000414170;ENST00000299022;ENST00000433326	D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61	5.44	-0.0709	0.13745	Lipase, N-terminal (1);	0.579236	0.19650	N	0.109222	T	0.00012	0.0000	L	0.47190	1.495	0.80722	P	0.0	B;B	0.18461	0.028;0.003	B;B	0.15870	0.014;0.011	T	0.31420	-0.9944	9	0.59425	D	0.04	.	2.8406	0.05528	0.5107:0.2771:0.0788:0.1334	rs6083;rs3184021;rs17269369;rs58086367;rs6083	154;215	E7EUK6;P11150	.;LIPC_HUMAN	S	215;215;215;154	ENSP00000348425:N215S;ENSP00000395569:N215S;ENSP00000299022:N215S;ENSP00000395002:N154S	ENSP00000299022:N215S	N	+	2	0	LIPC	56625302	0.005000	0.15991	0.226000	0.23910	0.397000	0.30659	2.059000	0.41384	0.025000	0.15241	-0.490000	0.04691	AAT	A|0.457;G|0.543	0.543	strong		0.547	LIPC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416209.1		
NKTR	4820	hgsc.bcm.edu	37	3	42679486	42679486	+	Missense_Mutation	SNP	A	A	G	rs150528581	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42679486A>G	ENST00000232978.8	+	13	2478	c.2290A>G	c.(2290-2292)Aaa>Gaa	p.K764E	RP4-613B23.1_ENST00000434363.1_RNA|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	764	Arg/Ser-rich.				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)		ATCCAGTGGGAAAAAAAATAG	0.378													A|||	14	0.00279553	0.0	0.0101	5008	,	,		20549	0.0		0.007	False		,,,				2504	0.0				p.K764E		Atlas-SNP	.											NKTR,NS,carcinoma,-1,1	NKTR	116	1	0			c.A2290G						PASS	.	A	GLU/LYS	13,4393	6.2+/-15.9	0,13,2190	86.0	86.0	86.0		2290	0.2	0.0	3	dbSNP_134	86	108,8492	34.8+/-89.0	1,106,4193	yes	missense	NKTR	NM_005385.3	56	1,119,6383	GG,GA,AA		1.2558,0.2951,0.9303	benign	764/1463	42679486	121,12885	2203	4300	6503	SO:0001583	missense	4820	exon13			AGTGGGAAAAAAA		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.2290A>G	3.37:g.42679486A>G	ENSP00000232978:p.Lys764Glu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	37	CCDS2702.1	10	0.004578754578754579	0	0.0	5	0.013812154696132596	0	0.0	5	0.006596306068601583	A	5.258	0.233021	0.09969	0.002951	0.012558	ENSG00000114857	ENST00000232978	T	0.11930	2.73	5.64	0.224	0.15297	.	0.627824	0.17249	N	0.181233	T	0.09423	0.0232	M	0.61703	1.905	0.09310	N	1	B;B	0.16802	0.019;0.003	B;B	0.14578	0.011;0.002	T	0.19582	-1.0301	10	0.72032	D	0.01	-4.6749	6.7187	0.23318	0.524:0.3408:0.1351:0.0	.	464;764	Q6M1B8;P30414	.;NKTR_HUMAN	E	764	ENSP00000232978:K764E	ENSP00000232978:K764E	K	+	1	0	NKTR	42654490	0.624000	0.27102	0.001000	0.08648	0.156000	0.22039	1.871000	0.39539	0.083000	0.17047	0.482000	0.46254	AAA	A|0.992;G|0.008	0.008	strong		0.378	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
NALCN	259232	hgsc.bcm.edu	37	13	101881777	101881777	+	Silent	SNP	G	G	A	rs3916906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:101881777G>A	ENST00000251127.6	-	13	1674	c.1593C>T	c.(1591-1593)gtC>gtT	p.V531V	NALCN_ENST00000470333.1_5'UTR|NALCN_ENST00000376196.3_Silent_p.V531V	NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	531					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.V531V(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					CCAGTTCTTCGACAAAGCAGA	0.343													G|||	963	0.192292	0.1029	0.1888	5008	,	,		15730	0.0417		0.3519	False		,,,				2504	0.3067				p.V531V		Atlas-SNP	.											NALCN,NS,carcinoma,0,1	NALCN	431	1	1	Substitution - coding silent(1)	stomach(1)	c.C1593T						scavenged	.	G		589,3817	260.4+/-263.7	35,519,1649	100.0	104.0	103.0		1593	-10.4	0.5	13	dbSNP_108	103	3091,5509	471.9+/-368.2	534,2023,1743	no	coding-synonymous	NALCN	NM_052867.2		569,2542,3392	AA,AG,GG		35.9419,13.3681,28.2946		531/1739	101881777	3680,9326	2203	4300	6503	SO:0001819	synonymous_variant	259232	exon13			TTCTTCGACAAAG	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.1593C>T	13.37:g.101881777G>A		Somatic	47	1	0.0212766		WXS	Illumina HiSeq	Phase_I	32	19	0.59375	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			G|0.766;N|0.000	.	strong		0.343	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
FCGBP	8857	hgsc.bcm.edu	37	19	40399383	40399383	+	Silent	SNP	T	T	C	rs138090709		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40399383T>C	ENST00000221347.6	-	13	6319	c.6312A>G	c.(6310-6312)ggA>ggG	p.G2104G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2104	VWFD 5. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCAAGGGTGGTCCGTGGCAGG	0.597																																					p.G2104G		Atlas-SNP	.											FCGBP,NS,carcinoma,-2,2	FCGBP	416	2	0			c.A6312G						scavenged	.	T		120,2044		0,120,962	8.0	11.0	10.0		6312	-6.0	0.0	19	dbSNP_134	10	158,4042		0,158,1942	no	coding-synonymous	FCGBP	NM_003890.2		0,278,2904	CC,CT,TT		3.7619,5.5453,4.3683		2104/5406	40399383	278,6086	1082	2100	3182	SO:0001819	synonymous_variant	8857	exon13			GGGTGGTCCGTGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6312A>G	19.37:g.40399383T>C		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	187	37	0.197861	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			T|1.000;C|0.000	0.000	weak		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CFH	3075	hgsc.bcm.edu	37	1	196709774	196709774	+	Missense_Mutation	SNP	G	G	T	rs1065489	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196709774G>T	ENST00000367429.4	+	18	3048	c.2808G>T	c.(2806-2808)gaG>gaT	p.E936D		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	936	Sushi 16. {ECO:0000255|PROSITE- ProRule:PRU00302}.		E -> D (polymorphism associated with hemolytic uremic syndrome and basal laminar drusen; dbSNP:rs1065489). {ECO:0000269|PubMed:14583443, ECO:0000269|PubMed:18252232, ECO:0000269|PubMed:20513133, ECO:0000269|Ref.2}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						CTCCACCTGAGATTTCTCATG	0.333													G|||	1018	0.203275	0.0378	0.196	5008	,	,		16282	0.5079		0.1769	False		,,,				2504	0.1452				p.E936D		Atlas-SNP	.											.	CFH	251	.	0			c.G2808T	GRCh37	CM033784	CFH	M	rs1065489	PASS	.	G	ASP/GLU	292,4114		10,272,1921	117.0	114.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2808	-2.4	0.0	1	dbSNP_86	115	1503,7097		142,1219,2939	yes	missense	CFH	NM_000186.3	45	152,1491,4860	TT,TG,GG		17.4767,6.6273,13.8013	possibly-damaging	936/1232	196709774	1795,11211	2203	4300	6503	SO:0001583	missense	3075	exon18			ACCTGAGATTTCT	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2808G>T	1.37:g.196709774G>T	ENSP00000356399:p.Glu936Asp	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	508	0.2326007326007326	18	0.036585365853658534	69	0.19060773480662985	283	0.49475524475524474	138	0.1820580474934037	.	13.70	2.316299	0.40996	0.066273	0.174767	ENSG00000000971	ENST00000367429	T	0.63096	-0.02	6.16	-2.39	0.06602	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.20881	0.62	0.58432	P	2.9999999999752447E-6	P	0.41450	0.75	B	0.35114	0.196	T	0.40905	-0.9538	8	0.12430	T	0.62	.	7.0098	0.24855	0.5627:0.1248:0.3124:0.0	rs1065489;rs2297092;rs52801055;rs57838443;rs1065489	936	P08603	CFAH_HUMAN	D	936	ENSP00000356399:E936D	ENSP00000356399:E936D	E	+	3	2	CFH	194976397	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.208000	0.03005	-0.248000	0.09583	-0.355000	0.07637	GAG	G|0.828;T|0.172	0.172	strong		0.333	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
KRT9	3857	hgsc.bcm.edu	37	17	39728050	39728050	+	Silent	SNP	G	G	A	rs8070680	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39728050G>A	ENST00000246662.4	-	1	260	c.195C>T	c.(193-195)ggC>ggT	p.G65G	KRT9_ENST00000588431.1_Intron	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	65	Head.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				AACTGCCACCGCCTCCCCTCC	0.612													A|||	3911	0.78095	0.6377	0.7709	5008	,	,		10331	1.0		0.667	False		,,,				2504	0.8732				p.G65G		Atlas-SNP	.											.	KRT9	78	.	0			c.C195T						PASS	.	A		2781,1625	494.6+/-363.0	887,1007,309	86.0	65.0	72.0		195	-9.3	0.0	17	dbSNP_116	72	5545,3055	464.1+/-366.1	1766,2013,521	no	coding-synonymous	KRT9	NM_000226.3		2653,3020,830	AA,AG,GG		35.5233,36.8815,35.9834		65/624	39728050	8326,4680	2203	4300	6503	SO:0001819	synonymous_variant	3857	exon1			GCCACCGCCTCCC		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.195C>T	17.37:g.39728050G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	155	70	0.451613	NM_000226	O00109|Q0IJ47|Q14665	Silent	SNP	ENST00000246662.4	37	CCDS32654.1																																																																																			A|0.670;G|0.330	0.670	strong		0.612	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226	
C20orf194	25943	hgsc.bcm.edu	37	20	3362033	3362033	+	Silent	SNP	T	T	C	rs6051818	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3362033T>C	ENST00000252032.9	-	3	343	c.276A>G	c.(274-276)gtA>gtG	p.V92V	U3_ENST00000364476.1_RNA	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	92										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						TACCATCTAGTACTTCTTCAG	0.328													C|||	1190	0.23762	0.3759	0.1873	5008	,	,		18843	0.1657		0.2197	False		,,,				2504	0.1789				p.V92V		Atlas-SNP	.											.	C20orf194	83	.	0			c.A276G						PASS	.	C		1332,2322		243,846,738	81.0	79.0	79.0		276	2.5	1.0	20	dbSNP_114	79	1730,6448		184,1362,2543	no	coding-synonymous	C20orf194	NM_001009984.1		427,2208,3281	CC,CT,TT		21.1543,36.4532,25.879		92/1178	3362033	3062,8770	1827	4089	5916	SO:0001819	synonymous_variant	25943	exon3			ATCTAGTACTTCT	AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.276A>G	20.37:g.3362033T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Silent	SNP	ENST00000252032.9	37	CCDS42851.1																																																																																			T|0.757;C|0.243	0.243	strong		0.328	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	
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 GAIIx	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|HYLS1_ENST00000356438.3_Intron|HYLS1_ENST00000526028.1_Intron|PUS3_ENST00000227474.3_Missense_Mutation_p.L324V			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	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	62	8	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	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596241	48596241	+	Missense_Mutation	SNP	A	A	G	rs11168459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48596241A>G	ENST00000310248.2	-	1	929	c.835T>C	c.(835-837)Tac>Cac	p.Y279H		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	279			Y -> H (in dbSNP:rs11168459).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y279H(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						ATGATGGTGTACAGGAGGGAG	0.493													A|||	983	0.196286	0.2579	0.1916	5008	,	,		22103	0.1935		0.2117	False		,,,				2504	0.1033				p.Y279H		Atlas-SNP	.											OR10AD1,NS,carcinoma,0,1	OR10AD1	24	1	1	Substitution - Missense(1)	stomach(1)	c.T835C						PASS	.	A	HIS/TYR	1143,3263	405.8+/-333.6	133,877,1193	123.0	122.0	122.0		835	3.8	1.0	12	dbSNP_120	122	1857,6743	331.6+/-319.7	197,1463,2640	yes	missense	OR10AD1	NM_001004134.1	83	330,2340,3833	GG,GA,AA		21.593,25.9419,23.0663	probably-damaging	279/318	48596241	3000,10006	2203	4300	6503	SO:0001583	missense	121275	exon1			TGGTGTACAGGAG		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.835T>C	12.37:g.48596241A>G	ENSP00000308689:p.Tyr279His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	79	50	0.632911	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	473	0.21657509157509158	125	0.2540650406504065	76	0.20994475138121546	121	0.21153846153846154	151	0.19920844327176782	A	17.45	3.393798	0.62066	0.259419	0.21593	ENSG00000172640	ENST00000310248	T	0.00321	8.11	4.96	3.81	0.43845	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35466	N	0.003189	T	0.00012	0.0000	M	0.90198	3.095	0.31492	P	0.665852	D	0.61697	0.99	P	0.62184	0.899	T	0.43686	-0.9376	9	0.87932	D	0	-26.9109	9.0035	0.36097	0.9115:0.0:0.0885:0.0	rs11168459;rs52836532;rs58095204;rs11168459	279	Q8NGE0	O10AD_HUMAN	H	279	ENSP00000308689:Y279H	ENSP00000308689:Y279H	Y	-	1	0	OR10AD1	46882508	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	8.441000	0.90313	1.030000	0.39839	0.533000	0.62120	TAC	A|0.772;G|0.228	0.228	strong		0.493	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
ZNF675	171392	hgsc.bcm.edu	37	19	23837145	23837145	+	Missense_Mutation	SNP	A	A	G	rs11671053	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:23837145A>G	ENST00000359788.4	-	4	758	c.590T>C	c.(589-591)gTg>gCg	p.V197A	ZNF675_ENST00000601935.1_Intron|ZNF675_ENST00000600313.1_Intron|ZNF675_ENST00000596211.1_Intron	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675	197			V -> A (in dbSNP:rs11671053).	Missing (in Ref. 2; BAC04216). {ECO:0000305}.	bone resorption (GO:0045453)|cytokine-mediated signaling pathway (GO:0019221)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA binding (GO:0003677)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				GCAGAAATTCACCTTGGTATA	0.303													A|||	1864	0.372204	0.3593	0.4424	5008	,	,		18306	0.125		0.6173	False		,,,				2504	0.3425				p.V197A		Atlas-SNP	.											.	ZNF675	88	.	0			c.T590C						PASS	.	A	ALA/VAL	1689,2713		329,1031,841	42.0	41.0	42.0		590	-2.2	0.0	19	dbSNP_120	42	5328,3268		1655,2018,625	yes	missense	ZNF675	NM_138330.2	64	1984,3049,1466	GG,GA,AA		38.0177,38.3689,46.0148	benign	197/569	23837145	7017,5981	2201	4298	6499	SO:0001583	missense	171392	exon4			AAATTCACCTTGG		CCDS32981.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	30768	protein-coding gene	gene with protein product	"""TRAF6 inhibitory zinc finger"""					11751921	Standard	NM_138330		Approved	TIZ, TBZF	uc002nri.3	Q8TD23		ENST00000359788.4:c.590T>C	19.37:g.23837145A>G	ENSP00000352836:p.Val197Ala	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	59	57	0.966102	NM_138330	Q8N211	Missense_Mutation	SNP	ENST00000359788.4	37	CCDS32981.1	881	0.4033882783882784	160	0.3252032520325203	167	0.4613259668508287	85	0.1486013986013986	469	0.6187335092348285	.	9.716	1.158276	0.21454	0.383689	0.619823	ENSG00000197372	ENST00000359788	T	0.15139	2.45	1.08	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	L	0.31371	0.925	0.43399	P	0.004471000000000003	B	0.28439	0.212	B	0.29353	0.101	T	0.37244	-0.9714	8	0.66056	D	0.02	.	5.106	0.14785	0.2747:0.0:0.0:0.7252	rs11671053;rs52791469;rs11671053	197	Q8TD23	ZN675_HUMAN	A	197	ENSP00000352836:V197A	ENSP00000352836:V197A	V	-	2	0	ZNF675	23628985	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	-0.105000	0.10907	-0.617000	0.05664	-0.686000	0.03744	GTG	A|0.544;G|0.456	0.456	strong		0.303	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330	
SOAT1	6646	hgsc.bcm.edu	37	1	179310262	179310262	+	Silent	SNP	C	C	T	rs11576517	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:179310262C>T	ENST00000367619.3	+	7	740	c.597C>T	c.(595-597)ccC>ccT	p.P199P	SOAT1_ENST00000535686.1_5'UTR|SOAT1_ENST00000540564.1_Silent_p.P141P|SOAT1_ENST00000539888.1_Silent_p.P134P	NM_003101.5	NP_003092.4	P35610	SOAT1_HUMAN	sterol O-acyltransferase 1	199					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol storage (GO:0010878)|macrophage derived foam cell differentiation (GO:0010742)|positive regulation of amyloid precursor protein biosynthetic process (GO:0042986)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|sterol O-acyltransferase activity (GO:0004772)	p.P199P(1)		central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|stomach(1)	20					Ezetimibe(DB00973)|Hesperetin(DB01094)	TTTCAGTTCCCTATTTTCTGT	0.453													C|||	1414	0.282348	0.1354	0.2406	5008	,	,		16077	0.4782		0.2406	False		,,,				2504	0.3517				p.P199P		Atlas-SNP	.											SOAT1,NS,carcinoma,0,1	SOAT1	53	1	1	Substitution - coding silent(1)	stomach(1)	c.C597T						PASS	.	C		596,3810	259.5+/-263.1	39,518,1646	204.0	187.0	193.0		597	-1.8	1.0	1	dbSNP_120	193	1822,6778	325.9+/-317.1	177,1468,2655	no	coding-synonymous	SOAT1	NM_003101.4		216,1986,4301	TT,TC,CC		21.186,13.527,18.5914		199/551	179310262	2418,10588	2203	4300	6503	SO:0001819	synonymous_variant	6646	exon7			AGTTCCCTATTTT	L21934	CCDS1330.1, CCDS58047.1, CCDS58048.1	1q25	2008-08-26	2008-08-26		ENSG00000057252	ENSG00000057252	2.3.1.26		11177	protein-coding gene	gene with protein product	"""acyl-Coenzyme A: cholesterol acyltransferase"""	102642	"""sterol O-acyltransferase (acyl-Coenzyme A: cholesterol acyltransferase) 1"""	SOAT, STAT		8407899	Standard	NM_003101		Approved	ACAT	uc001gml.3	P35610	OTTHUMG00000035253	ENST00000367619.3:c.597C>T	1.37:g.179310262C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	157	91	0.579618	NM_003101	A6NC40|A8K3P4|A9Z1V7|B4DU95|Q5T0X4|Q8N1E4	Silent	SNP	ENST00000367619.3	37	CCDS1330.1																																																																																			C|0.773;T|0.227	0.227	strong		0.453	SOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085286.2	NM_003101	
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 GAIIx	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	TENM1_ENST00000422452.2_Missense_Mutation_p.F1737V|STAG2_ENST00000469481.1_Intron	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	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	60	25	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	
BABAM1	29086	hgsc.bcm.edu	37	19	17389704	17389704	+	Silent	SNP	G	G	A	rs8170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17389704G>A	ENST00000359435.4	+	9	1030	c.837G>A	c.(835-837)aaG>aaA	p.K279K	CTD-2278I10.6_ENST00000596542.1_Intron|ANKLE1_ENST00000394458.3_5'Flank|ANKLE1_ENST00000594072.1_5'Flank|BABAM1_ENST00000598188.1_Silent_p.K279K|ANKLE1_ENST00000404085.1_5'Flank|BABAM1_ENST00000595632.1_Silent_p.K204K|BABAM1_ENST00000447614.2_Silent_p.K279K|ANKLE1_ENST00000433424.2_5'Flank|BABAM1_ENST00000601043.1_Silent_p.K279K	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	279	VWFA-like.				chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						CCAGCTACAAGTATGAGGTGG	0.612													G|||	563	0.11242	0.1861	0.0951	5008	,	,		17800	0.001		0.163	False		,,,				2504	0.0879				p.K279K		Atlas-SNP	.											C19orf62,NS,carcinoma,0,2	BABAM1	14	2	0			c.G837A						PASS	.	G	,	723,3299		60,603,1348	35.0	40.0	38.0	http://www.ncbi.nlm.nih.gov/pubmed?term	837,837	2.8	1.0	19	dbSNP_52	38	1503,6797		145,1213,2792	yes	coding-synonymous,coding-synonymous	BABAM1	NM_001033549.1,NM_014173.2	,	205,1816,4140	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	18.1084,17.9761,18.0652	,	279/330,279/330	17389704	2226,10096	2011	4150	6161	SO:0001819	synonymous_variant	29086	exon9			CTACAAGTATGAG	AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"""Mediator of Rap80 Interactions and Targeting 40 kD"", ""new component of the BRCA1 A complex"""	612766	"""chromosome 19 open reading frame 62"""	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.837G>A	19.37:g.17389704G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_014173	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Silent	SNP	ENST00000359435.4	37	CCDS46012.1																																																																																			G|0.869;A|0.131	0.131	strong		0.612	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173	
TMED6	146456	hgsc.bcm.edu	37	16	69385641	69385641	+	Missense_Mutation	SNP	A	A	G	rs76116020	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:69385641A>G	ENST00000288025.3	-	1	71	c.16T>C	c.(16-18)Ttt>Ctt	p.F6L	RP11-343C2.9_ENST00000563634.1_Intron|RP11-343C2.7_ENST00000564737.1_5'Flank	NM_144676.3	NP_653277.2	Q8WW62	TMED6_HUMAN	transmembrane emp24 protein transport domain containing 6	6					transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)	9						CCAGCCCCAAAGAGCAAAGGG	0.572													A|||	52	0.0103834	0.0015	0.0101	5008	,	,		16560	0.0		0.0308	False		,,,				2504	0.0123				p.F6L		Atlas-SNP	.											.	TMED6	19	.	0			c.T16C						PASS	.	A	LEU/PHE	35,4361	39.2+/-71.8	0,35,2163	55.0	55.0	55.0		16	-0.4	0.0	16	dbSNP_131	55	328,8272	111.6+/-171.8	9,310,3981	yes	missense	TMED6	NM_144676.3	22	9,345,6144	GG,GA,AA		3.814,0.7962,2.7932	benign	6/241	69385641	363,12633	2198	4300	6498	SO:0001583	missense	146456	exon1			CCCCAAAGAGCAA	BC020827	CCDS10878.1	16q22.1	2008-02-05			ENSG00000157315	ENSG00000157315			28331	protein-coding gene	gene with protein product						12477932	Standard	NM_144676		Approved	MGC23911	uc002exc.2	Q8WW62	OTTHUMG00000137571	ENST00000288025.3:c.16T>C	16.37:g.69385641A>G	ENSP00000288025:p.Phe6Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_144676	Q6UXN5	Missense_Mutation	SNP	ENST00000288025.3	37	CCDS10878.1	33	0.01510989010989011	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	29	0.03825857519788918	A	1.177	-0.639365	0.03557	0.007962	0.03814	ENSG00000157315	ENST00000288025	T	0.24723	1.84	5.91	-0.443	0.12249	.	0.610400	0.16351	N	0.218219	T	0.01765	0.0056	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25398	-1.0133	10	0.23302	T	0.38	-0.5314	2.7235	0.05207	0.2866:0.143:0.4309:0.1395	.	6	Q8WW62	TMED6_HUMAN	L	6	ENSP00000288025:F6L	ENSP00000288025:F6L	F	-	1	0	TMED6	67943142	0.000000	0.05858	0.014000	0.15608	0.395000	0.30598	0.092000	0.15066	-0.328000	0.08539	-0.256000	0.11100	TTT	A|0.979;G|0.021	0.021	strong		0.572	TMED6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268951.1	NM_144676	
NT5C1B	93034	hgsc.bcm.edu	37	2	18757501	18757501	+	Silent	SNP	G	G	C	rs3902946	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:18757501G>C	ENST00000359846.2	-	9	1535	c.1458C>G	c.(1456-1458)ctC>ctG	p.L486L	NT5C1B-RDH14_ENST00000532967.1_Silent_p.L486L|NT5C1B_ENST00000304081.4_Silent_p.L426L|NT5C1B_ENST00000600945.1_Silent_p.L486L	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	486					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)				AGAATTTGTCGAGCCCATGCT	0.398													C|||	1574	0.314297	0.6649	0.3127	5008	,	,		17787	0.1081		0.1948	False		,,,				2504	0.1769				p.L503L		Atlas-SNP	.											.	NT5C1B	72	.	0			c.C1509G						PASS	.	C	,,,,,,	2591,1815	530.8+/-373.0	754,1083,366	81.0	76.0	78.0		1458,1407,1509,1464,1284,1458,1278	2.0	1.0	2	dbSNP_108	78	1796,6804	732.6+/-406.8	195,1406,2699	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NT5C1B,NT5C1B-RDH14	NM_001002006.2,NM_001199086.1,NM_001199087.1,NM_001199088.1,NM_001199103.1,NM_001199104.1,NM_033253.3	,,,,,,	949,2489,3065	CC,CG,GG		20.8837,41.1938,33.7306	,,,,,,	486/611,469/594,503/628,488/613,428/651,486/603,426/551	18757501	4387,8619	2203	4300	6503	SO:0001819	synonymous_variant	93034	exon9			TTTGTCGAGCCCA	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.1458C>G	2.37:g.18757501G>C		Somatic	313	1	0.00319489		WXS	Illumina HiSeq	Phase_I	296	156	0.527027	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Silent	SNP	ENST00000359846.2	37	CCDS33150.1	648	0.2967032967032967	323	0.6565040650406504	104	0.287292817679558	64	0.11188811188811189	157	0.20712401055408972	C	0.259	-1.000911	0.02128	0.588062	0.208837	ENSG00000185013	ENST00000418427	.	.	.	5.33	1.98	0.26296	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41034	-0.9531	3	.	.	.	-1.9764	6.9441	0.24508	0.0:0.5707:0.1303:0.299	rs3902946;rs58362593;rs3902946	.	.	.	G	141	.	.	R	-	1	2	NT5C1B	18620982	0.389000	0.25205	1.000000	0.80357	0.042000	0.13812	-0.321000	0.08018	0.324000	0.23333	-0.120000	0.15030	CGA	G|0.689;C|0.311	0.311	strong		0.398	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1		
BMP10	27302	hgsc.bcm.edu	37	2	69093312	69093312	+	Silent	SNP	A	A	G	rs2231344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:69093312A>G	ENST00000295379.1	-	2	884	c.726T>C	c.(724-726)gaT>gaC	p.D242D		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	242					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						GGGCACTGGTATCTATTTCTA	0.488													G|||	710	0.141773	0.3048	0.0908	5008	,	,		21484	0.1151		0.0606	False		,,,				2504	0.0685				p.D242D		Atlas-SNP	.											.	BMP10	70	.	0			c.T726C						PASS	.	G		1168,3238	713.3+/-408.2	158,852,1193	106.0	95.0	98.0		726	3.2	1.0	2	dbSNP_98	98	570,8030	793.8+/-407.5	17,536,3747	no	coding-synonymous	BMP10	NM_014482.1		175,1388,4940	GG,GA,AA		6.6279,26.5093,13.3631		242/425	69093312	1738,11268	2203	4300	6503	SO:0001819	synonymous_variant	27302	exon2			ACTGGTATCTATT	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.726T>C	2.37:g.69093312A>G		Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	208	60	0.288462	NM_014482	Q53R17|Q6NTE0	Silent	SNP	ENST00000295379.1	37	CCDS1890.1																																																																																			A|0.870;G|0.130	0.130	strong		0.488	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482	
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 GAIIx	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	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	156	57	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	
METTL13	51603	hgsc.bcm.edu	37	1	171751236	171751236	+	Silent	SNP	T	T	C	rs2294720	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171751236T>C	ENST00000361735.3	+	1	395	c.129T>C	c.(127-129)caT>caC	p.H43H	METTL13_ENST00000458517.1_Silent_p.H42H|METTL13_ENST00000362019.3_Intron|METTL13_ENST00000367737.5_Silent_p.H43H	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	43							methyltransferase activity (GO:0008168)	p.H43H(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GGGTGCTACATAAATATATCA	0.517													C|||	2673	0.533746	0.73	0.4395	5008	,	,		17775	0.6577		0.4443	False		,,,				2504	0.2996				p.H43H		Atlas-SNP	.											METTL13,NS,carcinoma,0,1	METTL13	67	1	1	Substitution - coding silent(1)	stomach(1)	c.T129C						PASS	.	C	,,	3080,1326	445.1+/-347.6	1091,898,214	74.0	79.0	77.0		129,,129	5.5	1.0	1	dbSNP_100	77	4046,4554	595.7+/-393.5	940,2166,1194	no	coding-synonymous,intron,coding-synonymous	METTL13	NM_001007239.1,NM_014955.2,NM_015935.4	,,	2031,3064,1408	CC,CT,TT		47.0465,30.0953,45.2099	,,	43/544,,43/700	171751236	7126,5880	2203	4300	6503	SO:0001819	synonymous_variant	51603	exon1			GCTACATAAATAT	AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.129T>C	1.37:g.171751236T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_015935	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Silent	SNP	ENST00000361735.3	37	CCDS1299.1																																																																																			T|0.439;C|0.561	0.561	strong		0.517	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
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 GAIIx	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-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TG_ENST00000387429.1_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		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	6	6	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	
SP140	11262	hgsc.bcm.edu	37	2	231118041	231118041	+	Missense_Mutation	SNP	A	A	C	rs3820975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:231118041A>C	ENST00000392045.3	+	11	1182	c.1068A>C	c.(1066-1068)ttA>ttC	p.L356F	SP140_ENST00000420434.3_Missense_Mutation_p.L356F|SP140_ENST00000350136.5_Intron|SP140_ENST00000417495.3_Intron|SP140_ENST00000343805.6_Intron|SP140_ENST00000486687.2_Missense_Mutation_p.L280F	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	356			L -> F (in dbSNP:rs3820975).	LSA -> FST (in Ref. 1; AAB18617). {ECO:0000305}.	defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		TTTCTTGTTTATCTGCAGAGA	0.473													a|||	617	0.123203	0.1815	0.1081	5008	,	,		19243	0.0952		0.1332	False		,,,				2504	0.0736				p.L356F		Atlas-SNP	.											.	SP140	121	.	0			c.A1068C						PASS	.	C	PHE/LEU	635,3141		55,525,1308	150.0	135.0	140.0		1068	1.7	0.0	2	dbSNP_107	140	1092,7140		84,924,3108	yes	missense	SP140	NM_007237.4	22	139,1449,4416	CC,CA,AA		13.2653,16.8167,14.3821	benign	356/868	231118041	1727,10281	1888	4116	6004	SO:0001583	missense	11262	exon11			TTGTTTATCTGCA	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"""Zinc fingers, PHD-type"""	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.1068A>C	2.37:g.231118041A>C	ENSP00000375899:p.Leu356Phe	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	280	0.1282051282051282	96	0.1951219512195122	40	0.11049723756906077	50	0.08741258741258741	94	0.12401055408970976	a	0.090	-1.168032	0.01660	0.168167	0.132653	ENSG00000079263	ENST00000486687;ENST00000392045;ENST00000420434	T;T;T	0.59772	0.24;0.52;0.56	2.55	1.67	0.24075	.	.	.	.	.	T	0.00039	0.0001	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16394	-1.0404	8	0.09338	T	0.73	.	3.289	0.06942	0.2553:0.6001:0.0:0.1446	rs3820975;rs52809113;rs3820975	356;356	E7EUR5;Q13342	.;LY10_HUMAN	F	280;356;356	ENSP00000440107:L280F;ENSP00000375899:L356F;ENSP00000398210:L356F	ENSP00000375899:L356F	L	+	3	2	SP140	230826285	0.001000	0.12720	0.008000	0.14137	0.003000	0.03518	0.332000	0.19751	0.189000	0.20188	-0.290000	0.09829	TTA	A|0.867;C|0.133	0.133	strong		0.473	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237	
A4GALT	53947	hgsc.bcm.edu	37	22	43089055	43089055	+	Silent	SNP	G	G	C	rs6002904	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:43089055G>C	ENST00000401850.1	-	2	1392	c.903C>G	c.(901-903)ccC>ccG	p.P301P	A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000249005.2_Silent_p.P301P|A4GALT_ENST00000381278.3_Silent_p.P301P			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	301					globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						GCAGCTCCTCGGGGTTGATGT	0.662													G|||	3482	0.695288	0.8608	0.6052	5008	,	,		16794	0.7063		0.5915	False		,,,				2504	0.6309				p.P301P		Atlas-SNP	.											.	A4GALT	35	.	0			c.C903G	GRCh37	CD045904	A4GALT	D	rs6002904	PASS	.	G		3610,794	747.2+/-411.8	1487,636,79	65.0	53.0	57.0		903	0.5	0.9	22	dbSNP_114	57	4885,3715	616.0+/-396.4	1371,2143,786	no	coding-synonymous	A4GALT	NM_017436.4		2858,2779,865	CC,CG,GG		43.1977,18.0291,34.6739		301/354	43089055	8495,4509	2202	4300	6502	SO:0001819	synonymous_variant	53947	exon3			CTCCTCGGGGTTG		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"""Gb3 synthase"", ""CD77 synthase"", ""globotriaosylceramide synthase"", ""lactosylceramide 4-alpha-galactosyltransferase"""	607922	"""alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"""			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.903C>G	22.37:g.43089055G>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_017436	B2R7C4|Q9P1X5	Silent	SNP	ENST00000401850.1	37	CCDS14041.1																																																																																			G|0.332;C|0.668	0.668	strong		0.662	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
TAS2R42	353164	hgsc.bcm.edu	37	12	11338750	11338750	+	Missense_Mutation	SNP	T	T	C	rs1451772	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11338750T>C	ENST00000334266.1	-	1	793	c.794A>G	c.(793-795)tAc>tGc	p.Y265C		NM_181429.1	NP_852094.1	Q7RTR8	T2R42_HUMAN	taste receptor, type 2, member 42	265			Y -> C (in dbSNP:rs1451772).		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(2)|lung(4)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(49;0.0455)			AAACTTTATGTACTTGTTGTT	0.398													T|||	1102	0.220048	0.2474	0.2305	5008	,	,		19207	0.1944		0.2167	False		,,,				2504	0.2055				p.Y265C	Melanoma(15;352 722 10077 19546 48810)	Atlas-SNP	.											.	TAS2R42	30	.	0			c.A794G						PASS	.	T	CYS/TYR	1067,3339	387.5+/-326.5	137,793,1273	90.0	82.0	84.0		794	-0.4	0.0	12	dbSNP_92	84	2040,6560	356.5+/-330.3	248,1544,2508	yes	missense	TAS2R42	NM_181429.1	194	385,2337,3781	CC,CT,TT		23.7209,24.217,23.889	possibly-damaging	265/315	11338750	3107,9899	2203	4300	6503	SO:0001583	missense	353164	exon1			TTTATGTACTTGT	AX097739, AB199241	CCDS31747.1	12p13	2012-08-22			ENSG00000186136	ENSG00000186136		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18888	protein-coding gene	gene with protein product		613966				12679530	Standard	NM_181429		Approved	T2R24, T2R55, hT2R55, TAS2R55	uc001qzr.1	Q7RTR8	OTTHUMG00000168567	ENST00000334266.1:c.794A>G	12.37:g.11338750T>C	ENSP00000334050:p.Tyr265Cys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_181429	A2RRP4|Q645X0	Missense_Mutation	SNP	ENST00000334266.1	37	CCDS31747.1	491	0.22481684981684982	114	0.23170731707317074	77	0.212707182320442	126	0.2202797202797203	174	0.22955145118733508	T	7.012	0.557044	0.13436	0.24217	0.237209	ENSG00000186136	ENST00000334266	T	0.00737	5.76	3.59	-0.391	0.12446	GPCR, rhodopsin-like superfamily (1);	4.835580	0.00857	N	0.001895	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	P	0.47841	0.901	B	0.40066	0.318	T	0.43278	-0.9401	9	0.45353	T	0.12	.	2.6081	0.04883	0.4343:0.0:0.2782:0.2874	rs1451772;rs1650018;rs17817145	265	Q7RTR8	T2R42_HUMAN	C	265	ENSP00000334050:Y265C	ENSP00000334050:Y265C	Y	-	2	0	TAS2R42	11230017	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.540000	0.06106	0.078000	0.16900	0.528000	0.53228	TAC	C|0.238;N|0.001	0.238	strong		0.398	TAS2R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400243.1	NM_181429	
GPR141	353345	hgsc.bcm.edu	37	7	37780799	37780799	+	Silent	SNP	C	C	A	rs61729279	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:37780799C>A	ENST00000447769.1	+	4	1093	c.804C>A	c.(802-804)atC>atA	p.I268I	EPDR1_ENST00000476620.1_Intron|GPR141_ENST00000334425.1_Silent_p.I268I|GPR141_ENST00000461610.1_Intron			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	268						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						ATAACGAAATCTTCTTGAGTG	0.378													C|||	690	0.13778	0.0129	0.1124	5008	,	,		20949	0.253		0.0895	False		,,,				2504	0.2556				p.I268I		Atlas-SNP	.											.	GPR141	79	.	0			c.C804A						PASS	.	C		91,4315	73.6+/-111.7	2,87,2114	156.0	150.0	152.0		804	4.3	1.0	7	dbSNP_129	152	761,7839	181.6+/-230.3	32,697,3571	no	coding-synonymous	GPR141	NM_181791.1		34,784,5685	AA,AC,CC		8.8488,2.0654,6.5508		268/306	37780799	852,12154	2203	4300	6503	SO:0001819	synonymous_variant	353345	exon1			CGAAATCTTCTTG	AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"""GPCR / Class A : Orphans"""	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.804C>A	7.37:g.37780799C>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	100	69	0.69	NM_181791	A4D1X7|Q0VAR5|Q86SP3	Silent	SNP	ENST00000447769.1	37	CCDS5451.1																																																																																			C|0.923;A|0.077	0.077	strong		0.378	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791	
PRR3	80742	hgsc.bcm.edu	37	6	30530245	30530245	+	Silent	SNP	T	T	C	rs2074504	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30530245T>C	ENST00000376560.3	+	4	999	c.540T>C	c.(538-540)caT>caC	p.H180H	PRR3_ENST00000376557.3_Silent_p.H159H|PRR3_ENST00000498336.1_3'UTR	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	180							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						CCTTCTACCATCCAGGCGTCA	0.522													.|||	3769	0.752596	0.8419	0.6153	5008	,	,		20539	0.6994		0.6988	False		,,,				2504	0.8395				p.H180H		Atlas-SNP	.											PRR3,NS,carcinoma,+2,1	PRR3	5	1	0			c.T540C						PASS	.	C	,	3413,657		1434,545,56	167.0	167.0	167.0		477,540	0.9	1.0	6	dbSNP_96	167	5915,2519		2099,1717,401	yes	coding-synonymous,coding-synonymous	PRR3	NM_001077497.2,NM_025263.3	,	3533,2262,457	CC,CT,TT		29.8672,16.1425,25.3999	,	159/168,180/189	30530245	9328,3176	2035	4217	6252	SO:0001819	synonymous_variant	80742	exon4			CTACCATCCAGGC	AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576		"""Zinc fingers, CCCH-type domain containing"""	21149	protein-coding gene	gene with protein product			"""proline-rich polpeptide 3"""				Standard	NM_025263		Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.540T>C	6.37:g.30530245T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Silent	SNP	ENST00000376560.3	37	CCDS43440.1																																																																																			T|0.274;C|0.726	0.726	strong		0.522	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263	
TAF1L	138474	hgsc.bcm.edu	37	9	32632860	32632860	+	Silent	SNP	A	A	G	rs142256340		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:32632860A>G	ENST00000242310.4	-	1	2807	c.2718T>C	c.(2716-2718)gcT>gcC	p.A906A	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	906					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGCTATAATAAGCACAGCACT	0.448													A|||	1	0.000199681	0.0008	0.0	5008	,	,		21255	0.0		0.0	False		,,,				2504	0.0				p.A906A		Atlas-SNP	.											.	TAF1L	382	.	0			c.T2718C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	201.0	181.0	187.0		2718	1.0	1.0	9	dbSNP_134	187	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	TAF1L	NM_153809.2		0,12,6491	GG,GA,AA		0.1047,0.0681,0.0923		906/1827	32632860	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			ATAATAAGCACAG	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.2718T>C	9.37:g.32632860A>G		Somatic	380	1	0.00263158		WXS	Illumina HiSeq	Phase_I	344	181	0.526163	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			A|1.000;G|0.000	0.000	strong		0.448	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
OR2B2	81697	hgsc.bcm.edu	37	6	27879200	27879200	+	Missense_Mutation	SNP	C	C	A	rs34788973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27879200C>A	ENST00000303324.2	-	1	974	c.898G>T	c.(898-900)Gcc>Tcc	p.A300S		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	300			A -> S (in dbSNP:rs34788973).			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(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						CTTTTAAAGGCTTCCTTTACC	0.378													C|||	109	0.0217652	0.0106	0.0303	5008	,	,		16685	0.0		0.0736	False		,,,				2504	0.0				p.A300S		Atlas-SNP	.											.	OR2B2	54	.	0			c.G898T						PASS	.	C	SER/ALA	159,4247	106.0+/-144.5	4,151,2048	79.0	80.0	79.0		898	3.6	1.0	6	dbSNP_126	79	753,7847	179.9+/-228.9	35,683,3582	yes	missense	OR2B2	NM_033057.2	99	39,834,5630	AA,AC,CC		8.7558,3.6087,7.0121	possibly-damaging	300/358	27879200	912,12094	2203	4300	6503	SO:0001583	missense	81697	exon1			TAAAGGCTTCCTT	Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"""GPCR / Class A : Olfactory receptors"""	13966	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 9"""	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.898G>T	6.37:g.27879200C>A	ENSP00000304419:p.Ala300Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	82	69	0.841463	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Missense_Mutation	SNP	ENST00000303324.2	37	CCDS4641.1	74	0.03388278388278388	6	0.012195121951219513	10	0.027624309392265192	0	0.0	58	0.07651715039577836	C	11.14	1.551573	0.27739	0.036087	0.087558	ENSG00000168131	ENST00000303324	T	0.44482	0.92	3.6	3.6	0.41247	.	0.000000	0.38959	U	0.001518	T	0.24967	0.0606	N	0.25060	0.705	0.52099	P	5.900000000003125E-5	D	0.54772	0.968	P	0.50405	0.64	T	0.13202	-1.0518	9	0.87932	D	0	.	11.0202	0.47713	0.0:1.0:0.0:0.0	rs34788973;rs61758134	300	Q9GZK3	OR2B2_HUMAN	S	300	ENSP00000304419:A300S	ENSP00000304419:A300S	A	-	1	0	OR2B2	27987179	0.165000	0.22948	0.998000	0.56505	0.577000	0.36160	0.875000	0.28079	2.293000	0.77203	0.313000	0.20887	GCC	C|0.943;A|0.057	0.057	strong		0.378	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
STRN4	29888	hgsc.bcm.edu	37	19	47223949	47223949	+	Silent	SNP	G	G	A	rs313841	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47223949G>A	ENST00000263280.6	-	17	2221	c.2172C>T	c.(2170-2172)caC>caT	p.H724H	STRN4_ENST00000539396.1_Silent_p.H605H|STRN4_ENST00000594357.2_5'Flank|STRN4_ENST00000391910.3_Silent_p.H731H	NM_001039877.1|NM_013403.2	NP_001034966.1|NP_037535.2	Q9NRL3	STRN4_HUMAN	striatin, calmodulin binding protein 4	724						cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000563)|all cancers(93;0.00138)|Epithelial(262;0.0217)|GBM - Glioblastoma multiforme(486;0.035)		TGGCCTCCTCGTGCTTCTTGC	0.627													G|||	389	0.0776757	0.0454	0.0663	5008	,	,		19982	0.0427		0.1421	False		,,,				2504	0.0992				p.H731H		Atlas-SNP	.											.	STRN4	33	.	0			c.C2193T						PASS	.	G	,	243,4163	140.8+/-176.2	5,233,1965	159.0	110.0	127.0		2193,2172	-6.1	0.9	19	dbSNP_79	127	1124,7476	232.1+/-265.8	76,972,3252	no	coding-synonymous,coding-synonymous	STRN4	NM_001039877.1,NM_013403.2	,	81,1205,5217	AA,AG,GG		13.0698,5.5152,10.5105	,	731/761,724/754	47223949	1367,11639	2203	4300	6503	SO:0001819	synonymous_variant	29888	exon17			CTCCTCGTGCTTC	AF212940	CCDS12690.1, CCDS42581.1	19q13.32	2013-01-10			ENSG00000090372	ENSG00000090372		"""WD repeat domain containing"""	15721	protein-coding gene	gene with protein product		614767				10748158	Standard	XM_006723171		Approved	zinedin, ZIN	uc002pfm.3	Q9NRL3		ENST00000263280.6:c.2172C>T	19.37:g.47223949G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	211	100	0.473934	NM_001039877	A0A024R0V2|B4DQH7|F8VYA6|Q8NE53	Silent	SNP	ENST00000263280.6	37	CCDS12690.1																																																																																			G|0.913;N|0.000	.	strong		0.627	STRN4-001	KNOWN	NMD_exception|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466607.2		
DNAH7	56171	hgsc.bcm.edu	37	2	196892695	196892695	+	Missense_Mutation	SNP	T	T	C	rs62203391	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:196892695T>C	ENST00000312428.6	-	6	575	c.475A>G	c.(475-477)Aaa>Gaa	p.K159E	DNAH7_ENST00000410072.1_Missense_Mutation_p.K159E	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	159	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						AAGATGTCTTTCTCTATAGCA	0.378													T|||	122	0.024361	0.0015	0.0173	5008	,	,		17050	0.0		0.0895	False		,,,				2504	0.0184				p.K159E		Atlas-SNP	.											.	DNAH7	512	.	0			c.A475G						PASS	.	T	GLU/LYS	46,3610		0,46,1782	185.0	178.0	180.0		475	5.3	1.0	2	dbSNP_129	180	584,7592		23,538,3527	yes	missense	DNAH7	NM_018897.2	56	23,584,5309	CC,CT,TT		7.1429,1.2582,5.3245	possibly-damaging	159/4025	196892695	630,11202	1828	4088	5916	SO:0001583	missense	56171	exon6			TGTCTTTCTCTAT	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.475A>G	2.37:g.196892695T>C	ENSP00000311273:p.Lys159Glu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	80	0.03663003663003663	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	73	0.09630606860158311	T	18.85	3.712231	0.68730	0.012582	0.071429	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23552	1.9;2.68	5.29	5.29	0.74685	.	0.939336	0.08938	N	0.871994	T	0.00608	0.0020	L	0.52573	1.65	0.43913	D	0.996555	P	0.40578	0.722	B	0.36719	0.231	T	0.12041	-1.0563	10	0.08837	T	0.75	.	12.7614	0.57367	0.0:0.0:0.0:1.0	rs62203391	159	Q8WXX0	DYH7_HUMAN	E	159	ENSP00000311273:K159E;ENSP00000386260:K159E	ENSP00000311273:K159E	K	-	1	0	DNAH7	196600940	1.000000	0.71417	1.000000	0.80357	0.498000	0.33706	4.735000	0.62051	1.993000	0.58246	0.533000	0.62120	AAA	T|0.949;C|0.051	0.051	strong		0.378	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
SUN1	23353	hgsc.bcm.edu	37	7	897496	897496	+	Missense_Mutation	SNP	G	G	A	rs59910530	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:897496G>A	ENST00000405266.1	+	14	1561	c.1537G>A	c.(1537-1539)Gag>Aag	p.E513K	SUN1_ENST00000413514.2_Missense_Mutation_p.E274K|SUN1_ENST00000389574.3_Missense_Mutation_p.E393K|SUN1_ENST00000425407.2_Missense_Mutation_p.E393K|SUN1_ENST00000401592.1_Missense_Mutation_p.E476K|SUN1_ENST00000456758.2_Missense_Mutation_p.E665K|SUN1_ENST00000452783.2_Missense_Mutation_p.E373K			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	503					cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCCACAGTCGAGCACCTCCA	0.562													G|||	843	0.168331	0.0772	0.2406	5008	,	,		15787	0.1359		0.1849	False		,,,				2504	0.2566				p.E476K		Atlas-SNP	.											.	SUN1	157	.	0			c.G1426A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	354,3828		19,316,1756	162.0	176.0	171.0		1426,1117,1177	-10.3	0.0	7	dbSNP_129	171	1365,7061		105,1155,2953	yes	missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_025154.5	56,56,56	124,1471,4709	AA,AG,GG		16.1999,8.4648,13.6342	benign,benign,benign	476/786,373/683,393/703	897496	1719,10889	2091	4213	6304	SO:0001583	missense	23353	exon13			ACAGTCGAGCACC	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.1537G>A	7.37:g.897496G>A	ENSP00000384116:p.Glu513Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_001130965	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		359|359	0.16437728937728938|0.16437728937728938	49|49	0.09959349593495935|0.09959349593495935	86|86	0.23756906077348067|0.23756906077348067	89|89	0.1555944055944056|0.1555944055944056	135|135	0.17810026385224276|0.17810026385224276	G|G	8.800|8.800	0.932697|0.932697	0.18131|0.18131	0.084648|0.084648	0.161999|0.161999	ENSG00000164828|ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000452783;ENST00000405266;ENST00000401592;ENST00000297445;ENST00000425407;ENST00000429178;ENST00000413514|ENST00000433212	T;T;T;T;T;T;T;T|.	0.22336|.	2.31;2.31;2.32;2.31;2.31;2.31;1.99;1.96|.	5.15|5.15	-10.3|-10.3	0.00346|0.00346	.|.	1.071220|.	0.06979|.	N|.	0.819504|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.17268|.	0.002;0.002;0.003;0.021;0.003;0.005|.	B;B;B;B;B;B|.	0.09377|.	0.002;0.002;0.003;0.004;0.002;0.004|.	T|T	0.22243|0.22243	-1.0222|-1.0222	9|4	0.06236|.	T|.	0.91|.	-4.5311|-4.5311	9.0345|9.0345	0.36280|0.36280	0.2149:0.5051:0.28:0.0|0.2149:0.5051:0.28:0.0	rs59910530;rs61743533|rs59910530;rs61743533	274;373;476;665;503;393|.	E7EP45;E9PDU4;E9PF23;A4D2Q0;O94901;O94901-5|.	.;.;.;.;SUN1_HUMAN;.|.	K|Q	665;393;373;513;476;503;393;401;274|324	ENSP00000388743:E665K;ENSP00000374225:E393K;ENSP00000413439:E373K;ENSP00000384116:E513K;ENSP00000384015:E476K;ENSP00000392309:E393K;ENSP00000409909:E401K;ENSP00000389313:E274K|.	ENSP00000297445:E503K|.	E|R	+|+	1|2	0|0	SUN1|SUN1	864022|864022	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.212000|-0.212000	0.09319|0.09319	-2.067000|-2.067000	0.00885|0.00885	-0.302000|-0.302000	0.09304|0.09304	GAG|CGA	G|0.839;A|0.161	0.161	strong		0.562	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
SUSD5	26032	hgsc.bcm.edu	37	3	33194990	33194990	+	Missense_Mutation	SNP	C	C	A	rs6810039	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:33194990C>A	ENST00000309558.3	-	5	1551	c.1134G>T	c.(1132-1134)gaG>gaT	p.E378D		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	378			E -> D (in dbSNP:rs6810039). {ECO:0000269|PubMed:9628581}.		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						TCCAAGCCCCCTCTGTCACAG	0.557													A|||	3305	0.659944	0.7307	0.6441	5008	,	,		21284	0.8542		0.3936	False		,,,				2504	0.6493				p.E378D		Atlas-SNP	.											.	SUSD5	53	.	0			c.G1134T						PASS	.	A	ASP/GLU	2899,1285		1014,871,207	99.0	107.0	105.0		1134	-9.8	0.0	3	dbSNP_116	105	3273,5189		644,1985,1602	yes	missense	SUSD5	NM_015551.1	45	1658,2856,1809	AA,AC,CC		38.6788,30.7122,48.8059	benign	378/630	33194990	6172,6474	2092	4231	6323	SO:0001583	missense	26032	exon5			AGCCCCCTCTGTC	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.1134G>T	3.37:g.33194990C>A	ENSP00000308727:p.Glu378Asp	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_015551		Missense_Mutation	SNP	ENST00000309558.3	37	CCDS46787.1	1384	0.6336996336996337	362	0.7357723577235772	205	0.5662983425414365	510	0.8916083916083916	307	0.4050131926121372	A	2.099	-0.406519	0.04832	0.692878	0.386788	ENSG00000173705	ENST00000309558	T	0.05996	3.36	5.84	-9.81	0.00487	.	0.218834	0.37955	N	0.001879	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41270	-0.9518	9	0.08381	T	0.77	-19.8019	8.3556	0.32329	0.1666:0.1655:0.5626:0.1052	rs6810039;rs52836781;rs56655667;rs6810039	378	O60279	SUSD5_HUMAN	D	378	ENSP00000308727:E378D	ENSP00000308727:E378D	E	-	3	2	SUSD5	33169994	0.057000	0.20700	0.005000	0.12908	0.820000	0.46376	-0.950000	0.03889	-2.418000	0.00566	-0.996000	0.02517	GAG	C|0.374;A|0.626	0.626	strong		0.557	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054	
DNAH2	146754	hgsc.bcm.edu	37	17	7630505	7630505	+	Silent	SNP	T	T	C	rs11867551	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7630505T>C	ENST00000572933.1	+	4	1754	c.294T>C	c.(292-294)caT>caC	p.H98H	DNAH2_ENST00000570791.1_Silent_p.H98H|DNAH2_ENST00000082259.3_Silent_p.H98H|DNAH2_ENST00000389173.2_Silent_p.H98H			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	98	Stem. {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(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CACAGGAGCATGATGCCATTC	0.542													C|||	432	0.086262	0.112	0.072	5008	,	,		19153	0.0		0.167	False		,,,				2504	0.0675				p.H98H		Atlas-SNP	.											.	DNAH2	498	.	0			c.T294C						PASS	.	C		517,3889	778.0+/-414.3	30,457,1716	265.0	182.0	210.0		294	-8.8	0.0	17	dbSNP_120	210	1433,7167	751.6+/-407.4	128,1177,2995	no	coding-synonymous	DNAH2	NM_020877.2		158,1634,4711	CC,CT,TT		16.6628,11.734,14.9931		98/4428	7630505	1950,11056	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon3			GGAGCATGATGCC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.294T>C	17.37:g.7630505T>C		Somatic	221	1	0.00452489		WXS	Illumina HiSeq	Phase_I	220	106	0.481818	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			T|0.866;C|0.134	0.134	strong		0.542	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
ZNF501	115560	hgsc.bcm.edu	37	3	44775962	44775962	+	Missense_Mutation	SNP	A	A	G	rs4682752	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:44775962A>G	ENST00000396048.2	+	3	486	c.49A>G	c.(49-51)Atg>Gtg	p.M17V		NM_001258280.1|NM_145044.3	NP_001245209.1|NP_659481.2	Q96CX3	ZN501_HUMAN	zinc finger protein 501	17			M -> V (in dbSNP:rs4682752). {ECO:0000269|PubMed:14702039}.		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)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00843)|KIRC - Kidney renal clear cell carcinoma(197;0.0463)|Kidney(197;0.0579)		GAGAGTTAACATGCAGAAGAA	0.403													A|||	3482	0.695288	0.6112	0.6643	5008	,	,		21877	0.881		0.5954	False		,,,				2504	0.7423				p.M17V		Atlas-SNP	.											.	ZNF501	27	.	0			c.A49G						PASS	.	A	VAL/MET	2638,1528		844,950,289	97.0	97.0	97.0		49	2.4	0.0	3	dbSNP_111	97	4720,3776		1303,2114,831	yes	missense	ZNF501	NM_145044.2	21	2147,3064,1120	GG,GA,AA		44.4444,36.6779,41.8891	benign	17/272	44775962	7358,5304	2083	4248	6331	SO:0001583	missense	115560	exon3			GTTAACATGCAGA	BC013762	CCDS2720.2	3p21.32	2013-01-08			ENSG00000186446	ENSG00000186446		"""Zinc fingers, C2H2-type"""	23717	protein-coding gene	gene with protein product			"""zinc finger protein 52"""	ZNF52		1505991	Standard	NM_145044		Approved	MGC21738	uc003cnu.2	Q96CX3	OTTHUMG00000133048	ENST00000396048.2:c.49A>G	3.37:g.44775962A>G	ENSP00000379363:p.Met17Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_001258280	B4DLY7|Q96NU9	Missense_Mutation	SNP	ENST00000396048.2	37	CCDS2720.2	1501	0.6872710622710623	288	0.5853658536585366	247	0.6823204419889503	514	0.8986013986013986	452	0.5963060686015831	A	12.92	2.082127	0.36758	0.633221	0.555556	ENSG00000186446	ENST00000396048;ENST00000332489	T	0.38401	1.14	2.39	2.39	0.29439	.	.	.	.	.	T	0.00012	0.0000	L	0.35854	1.095	0.37504	P	0.08313000000000004	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28933	-1.0028	8	0.72032	D	0.01	.	9.9914	0.41874	1.0:0.0:0.0:0.0	rs4682752;rs17624679;rs61047958;rs4682752	17;17	Q96CX3-2;Q96CX3	.;ZN501_HUMAN	V	17	ENSP00000379363:M17V	ENSP00000330388:M17V	M	+	1	0	ZNF501	44750966	0.001000	0.12720	0.009000	0.14445	0.251000	0.25915	1.006000	0.29847	1.351000	0.45789	0.455000	0.32223	ATG	A|0.329;G|0.671	0.671	strong		0.403	ZNF501-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256654.4	NM_145044	
IMMT	10989	hgsc.bcm.edu	37	2	86371883	86371883	+	Silent	SNP	T	T	C	rs8244	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:86371883T>C	ENST00000410111.3	-	15	2172	c.1785A>G	c.(1783-1785)gcA>gcG	p.A595A	IMMT_ENST00000449247.2_Silent_p.A584A|IMMT_ENST00000254636.5_Silent_p.A496A|IMMT_ENST00000442664.2_Silent_p.A594A|IMMT_ENST00000409051.2_Silent_p.A548A	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	595					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TGGCCTCAACTGCACTACCCA	0.502													T|||	1306	0.260783	0.0582	0.3703	5008	,	,		18972	0.1488		0.4761	False		,,,				2504	0.3507				p.A595A		Atlas-SNP	.											IMMT,colon,carcinoma,-1,1	IMMT	65	1	0			c.A1785G						PASS	.	T	,,	434,3420		27,380,1520	90.0	87.0	88.0		1782,1752,1785	-10.5	0.0	2	dbSNP_52	88	4158,4106		1034,2090,1008	no	coding-synonymous,coding-synonymous,coding-synonymous	IMMT	NM_001100169.1,NM_001100170.1,NM_006839.2	,,	1061,2470,2528	CC,CT,TT		49.6854,11.261,37.894	,,	594/758,584/748,595/759	86371883	4592,7526	1927	4132	6059	SO:0001819	synonymous_variant	10989	exon15			CTCAACTGCACTA	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"""mitofilin"", ""mitochondrial inner membrane organizing system 2"""	600378	"""inner membrane protein, mitochondrial (mitofilin)"""			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1785A>G	2.37:g.86371883T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	620	0.2838827838827839	32	0.06504065040650407	143	0.39502762430939226	94	0.16433566433566432	351	0.4630606860158311	T	0.334	-0.954617	0.02285	0.11261	0.503146	ENSG00000132305	ENST00000419070	.	.	.	5.27	-10.5	0.00291	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999958	.	.	.	.	.	.	T	0.18085	-1.0348	3	.	.	.	-13.0405	5.2624	0.15582	0.1877:0.432:0.2424:0.1379	rs8244;rs17431880;rs17849575;rs8244	.	.	.	G	450	.	.	S	-	1	0	IMMT	86225394	0.000000	0.05858	0.002000	0.10522	0.292000	0.27327	-5.190000	0.00143	-3.336000	0.00184	-0.320000	0.08662	AGT	T|0.689;G|0.000;C|0.310;A|0.000	0.310	strong		0.502	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
HERC2	8924	hgsc.bcm.edu	37	15	28483809	28483809	+	Silent	SNP	G	G	A	rs149204675	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:28483809G>A	ENST00000261609.7	-	24	3795	c.3687C>T	c.(3685-3687)gaC>gaT	p.D1229D		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		ACACCTTCCCGTCAATCACAG	0.373													G|||	26	0.00519169	0.0129	0.0	5008	,	,		17942	0.0		0.004	False		,,,				2504	0.0051				p.D1229D		Atlas-SNP	.											HERC2,NS,carcinoma,0,1	HERC2	501	1	0			c.C3687T						scavenged	.						73.0	68.0	70.0					15																	28483809		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon24			CTTCCCGTCAATC	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.3687C>T	15.37:g.28483809G>A		Somatic	328	3	0.00914634		WXS	Illumina HiSeq	Phase_I	275	5	0.0181818	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.998;A|0.002	0.002	strong		0.373	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
DKKL1	27120	hgsc.bcm.edu	37	19	49869051	49869051	+	Splice_Site	SNP	T	T	G	rs2303759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49869051T>G	ENST00000221498.2	+	4	731	c.326T>G	c.(325-327)aTg>aGg	p.M109R	DKKL1_ENST00000594268.1_Intron|AC010524.2_ENST00000599433.1_RNA	NM_014419.3	NP_055234.1	Q9UK85	DKKL1_HUMAN	dickkopf-like 1	109			M -> R (in dbSNP:rs2303759).		anatomical structure morphogenesis (GO:0009653)|positive regulation of fat cell differentiation (GO:0045600)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	signal transducer activity (GO:0004871)			large_intestine(2)|upper_aerodigestive_tract(1)	3		all_lung(116;1.66e-06)|Lung NSC(112;5.89e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0456)		TCCTCACAGATGACCGACAAC	0.562													T|||	1594	0.318291	0.292	0.2464	5008	,	,		17401	0.3373		0.2396	False		,,,				2504	0.4663				p.M109R		Atlas-SNP	.											.	DKKL1	23	.	0			c.T326G						PASS	.	T	,ARG/MET,ARG/MET	1266,3140	430.6+/-342.6	182,902,1119	102.0	89.0	93.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,101,326	4.3	1.0	19	dbSNP_100	93	2278,6322	384.0+/-341.0	302,1674,2324	no	intron,missense-near-splice,missense-near-splice	DKKL1	NM_001197301.1,NM_001197302.1,NM_014419.3	,91,91	484,2576,3443	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	26.4884,28.7335,27.249	,benign,benign	,34/168,109/243	49869051	3544,9462	2203	4300	6503	SO:0001630	splice_region_variant	27120	exon4			CACAGATGACCGA	AB047816	CCDS12762.1	19q13.3	2010-10-12	2010-10-12		ENSG00000104901	ENSG00000104901			16528	protein-coding gene	gene with protein product	"""cancer/testis antigen 34"", ""soggy"""	605418	"""dickkopf-like 1 (soggy)"""			10570958	Standard	NM_001197301		Approved	SGY-1, CT34	uc002pnk.3	Q9UK85		ENST00000221498.2:c.325-1T>G	19.37:g.49869051T>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_014419		Missense_Mutation	SNP	ENST00000221498.2	37	CCDS12762.1	590	0.27014652014652013	134	0.27235772357723576	90	0.24861878453038674	186	0.32517482517482516	180	0.23746701846965698	T	10.98	1.504113	0.26949	0.287335	0.264884	ENSG00000104901	ENST00000221498	T	0.11930	2.73	4.35	4.35	0.52113	.	0.503678	0.16898	N	0.195029	T	0.00012	0.0000	N	0.08118	0	0.20764	P	0.99985795	B	0.32620	0.378	B	0.29353	0.101	T	0.43245	-0.9403	9	0.72032	D	0.01	-11.7793	10.1284	0.42663	0.0:0.0:0.0:1.0	rs2303759;rs52827084;rs59086630;rs2303759	109	Q9UK85	DKKL1_HUMAN	R	109	ENSP00000221498:M109R	ENSP00000221498:M109R	M	+	2	0	DKKL1	54560863	1.000000	0.71417	1.000000	0.80357	0.376000	0.30014	3.671000	0.54576	1.980000	0.57719	0.459000	0.35465	ATG	T|0.710;G|0.290	0.290	strong		0.562	DKKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465454.2	NM_014419	Missense_Mutation
FDXACB1	91893	hgsc.bcm.edu	37	11	111747297	111747297	+	Silent	SNP	A	A	G	rs7124696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:111747297A>G	ENST00000260257.4	-	4	647	c.600T>C	c.(598-600)ttT>ttC	p.F200F	C11orf1_ENST00000530214.1_5'Flank|ALG9_ENST00000527377.1_5'UTR|FDXACB1_ENST00000542429.1_Silent_p.F51F|C11orf1_ENST00000528125.1_5'Flank|ALG9_ENST00000524880.1_Silent_p.F200F|C11orf1_ENST00000260276.3_5'Flank	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	200					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						GAGAACCTTCAAAAGGTAAGC	0.423													G|||	1228	0.245208	0.1982	0.3228	5008	,	,		20985	0.1944		0.33	False		,,,				2504	0.2188				p.F200F		Atlas-SNP	.											.	FDXACB1	74	.	0			c.T600C						PASS	.	G		805,2911		85,635,1138	127.0	123.0	124.0		600	0.9	0.0	11	dbSNP_116	124	2534,5660		397,1740,1960	no	coding-synonymous	FDXACB1	NM_138378.2		482,2375,3098	GG,GA,AA		30.9251,21.6631,28.0353		200/625	111747297	3339,8571	1858	4097	5955	SO:0001819	synonymous_variant	91893	exon4			ACCTTCAAAAGGT		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"""hypothetical protein BC006136"""						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.600T>C	11.37:g.111747297A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	121	105	0.867769	NM_138378	A0PJW7|B4DUU2	Silent	SNP	ENST00000260257.4	37	CCDS44729.1																																																																																			A|0.738;G|0.262	0.262	strong		0.423	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378	
ZNF600	162966	hgsc.bcm.edu	37	19	53269614	53269614	+	Silent	SNP	G	G	A	rs58262989	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:53269614G>A	ENST00000338230.3	-	3	1662	c.1395C>T	c.(1393-1395)acC>acT	p.T465T		NM_198457.2	NP_940859	Q6ZNG1	ZN600_HUMAN	zinc finger protein 600	465					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(2)|endometrium(2)|kidney(4)|large_intestine(9)|liver(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(262;0.0241)|GBM - Glioblastoma multiforme(134;0.0404)		GTTTCTCTCCGGTGTGAATTA	0.373													-|||	316	0.063099	0.003	0.0432	5008	,	,		23044	0.1925		0.0278	False		,,,				2504	0.0613				p.T465T	Esophageal Squamous(196;1235 2112 2375 33339 34207)	Atlas-SNP	.											ZNF600,caecum,carcinoma,0,1	ZNF600	75	1	0			c.C1395T						PASS	.	G		46,4360		0,46,2157	122.0	124.0	123.0		1395	0.4	0.3	19	dbSNP_129	123	253,8347		7,239,4054	no	coding-synonymous	ZNF600	NM_198457.2		7,285,6211	AA,AG,GG		2.9419,1.044,2.2989		465/723	53269614	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	162966	exon3			CTCTCCGGTGTGA	U52096	CCDS12856.1	19q13.42	2013-01-08				ENSG00000189190		"""Zinc fingers, C2H2-type"""	30951	protein-coding gene	gene with protein product						12576331	Standard	NM_198457		Approved	KR-ZNF1, DKFZp686F06123	uc002qab.4	Q6ZNG1		ENST00000338230.3:c.1395C>T	19.37:g.53269614G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_198457	Q6MZR0	Silent	SNP	ENST00000338230.3	37	CCDS12856.1																																																																																			G|0.962;A|0.038	0.038	strong		0.373	ZNF600-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463093.1	NM_198457	
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 GAIIx	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	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	48	26	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 GAIIx	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_ENST00000405222.1_Silent_p.V531V|DTNB_ENST00000404103.3_Silent_p.V568V|DTNB_ENST00000288642.8_Silent_p.V568V|DTNB_ENST00000407661.3_Silent_p.V568V|DTNB_ENST00000545439.1_Silent_p.V357V|DTNB_ENST00000496972.2_Silent_p.V504V|DTNB_ENST00000407038.3_Silent_p.V538V|DTNB_ENST00000407186.1_Silent_p.V531V	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		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	36	22	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	
TMEM200A	114801	hgsc.bcm.edu	37	6	130761804	130761804	+	Silent	SNP	C	C	T	rs12200105	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:130761804C>T	ENST00000296978.3	+	3	1108	c.237C>T	c.(235-237)gcC>gcT	p.A79A	TMEM200A_ENST00000392429.1_Silent_p.A79A|TMEM200A_ENST00000545622.1_Silent_p.A79A	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	79						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TTGCTATGGCCGTTCTTGGAT	0.418													C|||	1312	0.261981	0.5408	0.2248	5008	,	,		19198	0.1339		0.172	False		,,,				2504	0.136				p.A79A		Atlas-SNP	.											.	TMEM200A	108	.	0			c.C237T						PASS	.	C		2008,2398	562.1+/-380.9	465,1078,660	99.0	100.0	100.0		237	-9.9	0.9	6	dbSNP_120	100	1382,7218	268.3+/-287.8	119,1144,3037	no	coding-synonymous	TMEM200A	NM_052913.2		584,2222,3697	TT,TC,CC		16.0698,45.5742,26.0649		79/492	130761804	3390,9616	2203	4300	6503	SO:0001819	synonymous_variant	114801	exon3			TATGGCCGTTCTT	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.237C>T	6.37:g.130761804C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_001258277	Q96PX5	Silent	SNP	ENST00000296978.3	37	CCDS5140.1																																																																																			C|0.743;T|0.257	0.257	strong		0.418	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
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 GAIIx	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		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	72	14	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 GAIIx	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_ENST00000416245.1_Missense_Mutation_p.P45R|ZP3_ENST00000336517.4_Missense_Mutation_p.P170R	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	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	59	26	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		
ZNF578	147660	hgsc.bcm.edu	37	19	53014851	53014851	+	Missense_Mutation	SNP	A	A	T	rs35720624	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:53014851A>T	ENST00000421239.2	+	6	1461	c.1217A>T	c.(1216-1218)aAg>aTg	p.K406M	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	406					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GAATGTGGCAAGGCTTTTAAT	0.373													A|||	35	0.00698882	0.0	0.0086	5008	,	,		25239	0.0		0.0239	False		,,,				2504	0.0051				p.K406M		Atlas-SNP	.											.	.	.	.	0			c.A1217T						PASS	.	A	MET/LYS	16,4390		0,16,2187	91.0	94.0	93.0		1217	0.2	0.1	19	dbSNP_126	93	165,8435		0,165,4135	no	missense	ZNF578	NM_001099694.1	95	0,181,6322	TT,TA,AA		1.9186,0.3631,1.3917	probably-damaging	406/591	53014851	181,12825	2203	4300	6503	SO:0001583	missense	147660	exon6			GTGGCAAGGCTTT	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1217A>T	19.37:g.53014851A>T	ENSP00000459216:p.Lys406Met	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	-	14.01	2.407495	0.42715	0.003631	0.019186	ENSG00000258405	ENST00000553364	.	.	.	1.48	0.247	0.15521	.	.	.	.	.	T	0.26810	0.0656	M	0.81497	2.545	0.23632	N	0.997249	P	0.41366	0.747	B	0.41174	0.349	T	0.20472	-1.0274	7	.	.	.	.	5.4535	0.16578	0.7501:0.0:0.0:0.2498	rs35720624	406	G3V4F6	.	M	406	.	.	K	+	2	0	ZNF578	57706663	0.803000	0.28956	0.060000	0.19600	0.137000	0.21094	4.419000	0.59835	-0.138000	0.11434	0.246000	0.17985	AAG	A|0.992;T|0.008	0.008	strong		0.373	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
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 GAIIx	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	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	73	20	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	
CYP2A13	1553	hgsc.bcm.edu	37	19	41594389	41594389	+	Missense_Mutation	SNP	G	G	T	rs71579358		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41594389G>T	ENST00000330436.3	+	1	13	c.13G>T	c.(13-15)Ggg>Tgg	p.G5W		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	5					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(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	GCTGGCCTCAGGGCTGCTTCT	0.557																																					p.G5W		Atlas-SNP	.											CYP2A13,colon,carcinoma,-1,2	CYP2A13	90	2	0			c.G13T						scavenged	.						63.0	52.0	56.0					19																	41594389		2203	4300	6503	SO:0001583	missense	1553	exon1			GCCTCAGGGCTGC	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"""Cytochrome P450s"""	2608	protein-coding gene	gene with protein product		608055	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"""			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.13G>T	19.37:g.41594389G>T	ENSP00000332679:p.Gly5Trp	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	120	2	0.0166667	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	.	.	.	.	.	.	.	.	.	.	.	12.37	1.917225	0.33815	.	.	ENSG00000197838	ENST00000330436	T	0.69926	-0.44	3.3	3.3	0.37823	.	0.285165	0.29438	U	0.012142	T	0.77157	0.4089	M	0.68952	2.095	0.29522	N	0.853405	D	0.89917	1.0	D	0.71184	0.972	T	0.72194	-0.4364	10	0.41790	T	0.15	.	12.5425	0.56179	0.0:0.0:1.0:0.0	.	5	Q16696	CP2AD_HUMAN	W	5	ENSP00000332679:G5W	ENSP00000332679:G5W	G	+	1	0	CYP2A13	46286229	0.998000	0.40836	0.989000	0.46669	0.961000	0.63080	5.281000	0.65609	1.860000	0.53959	0.430000	0.28490	GGG	.	.	alt		0.557	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766	
ZNF354B	117608	hgsc.bcm.edu	37	5	178294060	178294060	+	Missense_Mutation	SNP	G	G	A	rs11955074|rs386695542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178294060G>A	ENST00000322434.3	+	4	470	c.244G>A	c.(244-246)Gtc>Atc	p.V82I		NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	82	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	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)			CAGTTCTGGTGTCTCCTCTCT	0.507													G|||	592	0.118211	0.2655	0.1066	5008	,	,		17688	0.0		0.1213	False		,,,				2504	0.046				p.V82I		Atlas-SNP	.											.	ZNF354B	67	.	0			c.G244A						PASS	.	G	ILE/VAL	925,3481		122,681,1400	147.0	138.0	141.0		244	0.8	0.0	5	dbSNP_120	141	911,7689		64,783,3453	yes	missense	ZNF354B	NM_058230.2	29	186,1464,4853	AA,AG,GG		10.593,20.9941,14.1166	benign	82/613	178294060	1836,11170	2203	4300	6503	SO:0001583	missense	117608	exon4			TCTGGTGTCTCCT	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.244G>A	5.37:g.178294060G>A	ENSP00000327143:p.Val82Ile	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	NM_058230	A8K0V2|Q5U5Z4	Missense_Mutation	SNP	ENST00000322434.3	37	CCDS4439.1	218	0.09981684981684982	113	0.22967479674796748	35	0.09668508287292818	0	0.0	70	0.09234828496042216	G	3.804	-0.041079	0.07452	0.209941	0.10593	ENSG00000178338	ENST00000322434;ENST00000520377	T;T	0.05580	3.42;6.24	3.74	0.785	0.18584	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.14012	0.009	B	0.11329	0.006	T	0.46091	-0.9216	8	0.48119	T	0.1	.	4.3661	0.11225	0.211:0.0:0.6034:0.1855	rs11955074;rs57002972	82	Q96LW1	Z354B_HUMAN	I	82	ENSP00000327143:V82I;ENSP00000429827:V82I	ENSP00000327143:V82I	V	+	1	0	ZNF354B	178226666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.168000	0.16622	0.027000	0.15297	-0.671000	0.03813	GTC	G|0.854;A|0.146	0.146	strong		0.507	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
DNAH8	1769	hgsc.bcm.edu	37	6	38951998	38951998	+	Missense_Mutation	SNP	C	C	T	rs1537232	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:38951998C>T	ENST00000359357.3	+	85	12571	c.12317C>T	c.(12316-12318)aCg>aTg	p.T4106M	DNAH8_ENST00000441566.1_Missense_Mutation_p.T4070M			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	4106			T -> M (in dbSNP:rs1537232).		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						TCATGGAATACGGTTCGGTAC	0.368													C|||	859	0.171526	0.0477	0.1182	5008	,	,		19108	0.3462		0.167	False		,,,				2504	0.2014				p.T4323M		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C12968T						PASS	.	C	MET/THR	295,4111	160.3+/-192.7	7,281,1915	122.0	118.0	119.0		12968	6.0	1.0	6	dbSNP_88	119	1265,7335	251.9+/-278.2	85,1095,3120	yes	missense	DNAH8	NM_001206927.1	81	92,1376,5035	TT,TC,CC		14.7093,6.6954,11.9945	probably-damaging	4323/4708	38951998	1560,11446	2203	4300	6503	SO:0001583	missense	1769	exon87			GGAATACGGTTCG	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.12317C>T	6.37:g.38951998C>T	ENSP00000352312:p.Thr4106Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	112	84	0.75	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	37		400	0.18315018315018314	27	0.054878048780487805	40	0.11049723756906077	196	0.34265734265734266	137	0.18073878627968337	C	20.3	3.959637	0.74016	0.066954	0.147093	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.09630	2.96;2.96;2.96	6.02	6.02	0.97574	Dynein heavy chain (1);	0.125135	0.51477	D	0.000083	T	0.41465	0.1160	M	0.93328	3.405	0.20563	P	0.999882234	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.52983	-0.8502	9	0.72032	D	0.01	.	20.5407	0.99260	0.0:1.0:0.0:0.0	rs1537232;rs52791759;rs57517872;rs1537232	4070;4106	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	M	4311;4106;4070	ENSP00000333363:T4311M;ENSP00000352312:T4106M;ENSP00000402294:T4070M	ENSP00000333363:T4311M	T	+	2	0	DNAH8	39059976	1.000000	0.71417	0.966000	0.40874	0.755000	0.42902	5.884000	0.69729	2.865000	0.98341	0.655000	0.94253	ACG	C|0.843;T|0.157	0.157	strong		0.368	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
FSD1	79187	hgsc.bcm.edu	37	19	4306311	4306311	+	Silent	SNP	T	T	C	rs4807578	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4306311T>C	ENST00000221856.6	+	3	375	c.228T>C	c.(226-228)cgT>cgC	p.R76R	FSD1_ENST00000597590.1_Silent_p.R76R	NM_024333.2	NP_077309.1	Q9BTV5	FSD1_HUMAN	fibronectin type III and SPRY domain containing 1	76					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.034)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGCCAGCCGTACCTACGAGC	0.572													c|||	2921	0.583267	0.553	0.6412	5008	,	,		16805	0.4107		0.663	False		,,,				2504	0.6789				p.R76R		Atlas-SNP	.											.	FSD1	51	.	0			c.T228C						PASS	.			2595,1811	528.1+/-372.3	763,1069,371	58.0	57.0	58.0		228	-4.5	1.0	19	dbSNP_111	58	5479,3121	472.5+/-368.4	1718,2043,539	no	coding-synonymous	FSD1	NM_024333.2		2481,3112,910	CC,CT,TT		36.2907,41.103,37.921		76/497	4306311	8074,4932	2203	4300	6503	SO:0001819	synonymous_variant	79187	exon3			CAGCCGTACCTAC	AF316829	CCDS12127.1	19p13.3	2013-02-11	2005-03-01			ENSG00000105255		"""Fibronectin type III domain containing"""	13745	protein-coding gene	gene with protein product		609828	"""fibronectin type 3 and SPRY domain containing 1"""			11267680	Standard	NM_024333		Approved	MGC3213, MIR1	uc002lzy.2	Q9BTV5		ENST00000221856.6:c.228T>C	19.37:g.4306311T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_024333	B2RDT0|Q9BXN0|Q9HAG4	Silent	SNP	ENST00000221856.6	37	CCDS12127.1																																																																																			T|0.402;C|0.598	0.598	strong		0.572	FSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458091.1	NM_024333	
OR5A1	219982	hgsc.bcm.edu	37	11	59210761	59210761	+	Silent	SNP	C	C	G	rs11605572	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:59210761C>G	ENST00000302030.2	+	1	145	c.120C>G	c.(118-120)acC>acG	p.T40T		NM_001004728.1	NP_001004728.1	Q8NGJ0	OR5A1_HUMAN	olfactory receptor, family 5, subfamily A, member 1	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	28						TCTATCTTACCACCCTGGCCT	0.502													.|||	642	0.128195	0.0333	0.1326	5008	,	,		19888	0.1111		0.2525	False		,,,				2504	0.1431				p.T40T		Atlas-SNP	.											OR5A1,right_upper_lobe,carcinoma,+1,1	OR5A1	72	1	0			c.C120G						PASS	.	G		287,4115	799.4+/-415.5	12,263,1926	135.0	129.0	131.0		120	-2.2	0.0	11	dbSNP_120	131	2264,6326	707.1+/-405.6	283,1698,2314	no	coding-synonymous	OR5A1	NM_001004728.1		295,1961,4240	GG,GC,CC		26.3562,6.5198,19.6352		40/316	59210761	2551,10441	2201	4295	6496	SO:0001819	synonymous_variant	219982	exon1			TCTTACCACCCTG	AB065804	CCDS31561.1	11q12.1	2012-08-09			ENSG00000172320	ENSG00000172320		"""GPCR / Class A : Olfactory receptors"""	8319	protein-coding gene	gene with protein product				OR5A1P			Standard	NM_001004728		Approved	OST181	uc001nnx.1	Q8NGJ0	OTTHUMG00000167339	ENST00000302030.2:c.120C>G	11.37:g.59210761C>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001004728	B9EH58|Q6IFF2|Q96RB1	Silent	SNP	ENST00000302030.2	37	CCDS31561.1																																																																																			C|0.809;G|0.191	0.191	strong		0.502	OR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394233.1	NM_001004728	
NCOA3	8202	hgsc.bcm.edu	37	20	46279866	46279866	+	Silent	SNP	A	A	G	rs578139784|rs112826888|rs1132443	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:46279866A>G	ENST00000371998.3	+	20	3983	c.3792A>G	c.(3790-3792)caA>caG	p.Q1264Q	NCOA3_ENST00000341724.6_Silent_p.Q1190Q|NCOA3_ENST00000372004.3_Silent_p.Q1260Q|NCOA3_ENST00000371997.3_Silent_p.Q1255Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1264	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcagcaacagcaacagc	0.567													G|||	599	0.119609	0.2186	0.0663	5008	,	,		14499	0.0873		0.0726	False		,,,				2504	0.1053				p.Q1264Q		Atlas-SNP	.											NCOA3,colon,carcinoma,0,1	NCOA3	156	1	0			c.A3792G						PASS	.	G	,,,	561,3841		126,309,1766	56.0	66.0	62.0		3789,3765,3780,3792	0.0	0.2	20	dbSNP_86	62	436,8164		30,376,3894	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	156,685,5660	GG,GA,AA		5.0698,12.7442,7.6681	,,,	1263/1424,1255/1416,1260/1421,1264/1425	46279866	997,12005	2201	4300	6501	SO:0001819	synonymous_variant	8202	exon20			GCAGCAACAGCAA	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3792A>G	20.37:g.46279866A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			A|0.870;G|0.130	0.130	strong		0.567	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
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 GAIIx	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_ENST00000415482.2_Missense_Mutation_p.G611D|PTPN12_ENST00000435495.2_Missense_Mutation_p.G600D	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	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	101	47	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		
RPAP1	26015	hgsc.bcm.edu	37	15	41813279	41813279	+	Silent	SNP	C	C	T	rs3743031	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:41813279C>T	ENST00000304330.4	-	22	3221	c.3105G>A	c.(3103-3105)agG>agA	p.R1035R	RPAP1_ENST00000561603.1_Intron	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	1035	Leu-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		ACCGAGGGACCCTGCTGCTTC	0.602													C|||	1495	0.298522	0.1256	0.3285	5008	,	,		17963	0.2758		0.4324	False		,,,				2504	0.3967				p.R1035R		Atlas-SNP	.											RPAP1,NS,carcinoma,0,1	RPAP1	111	1	0			c.G3105A						PASS	.	C		794,3612		79,636,1488	45.0	49.0	47.0		3105	3.9	0.0	15	dbSNP_107	47	3684,4914		816,2052,1431	no	coding-synonymous	RPAP1	NM_015540.2		895,2688,2919	TT,TC,CC		42.8472,18.0209,34.4356		1035/1394	41813279	4478,8526	2203	4299	6502	SO:0001819	synonymous_variant	26015	exon22			AGGGACCCTGCTG	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.3105G>A	15.37:g.41813279C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	116	25	0.215517	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Silent	SNP	ENST00000304330.4	37	CCDS10079.1																																																																																			C|0.680;T|0.320	0.320	strong		0.602	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
PRDM8	56978	hgsc.bcm.edu	37	4	81124596	81124596	+	Silent	SNP	G	G	C	rs12780	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:81124596G>C	ENST00000504452.1	+	8	2819	c.1980G>C	c.(1978-1980)cgG>cgC	p.R660R	PRDM8_ENST00000415738.2_Silent_p.R660R|PRDM8_ENST00000339711.4_Silent_p.R660R			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	660					corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						TGGTGAAGCGGCGGCGAGAGG	0.572													G|||	1745	0.348442	0.1672	0.3372	5008	,	,		12837	0.626		0.2724	False		,,,				2504	0.3937				p.R660R		Atlas-SNP	.											PRDM8,colon,carcinoma,0,1	PRDM8	44	1	0			c.G1980C						PASS	.	G	,	746,3544		70,606,1469	32.0	38.0	36.0		1980,1980	1.1	1.0	4	dbSNP_52	36	2160,6384		289,1582,2401	no	coding-synonymous,coding-synonymous	PRDM8	NM_001099403.1,NM_020226.3	,	359,2188,3870	CC,CG,GG		25.2809,17.3893,22.643	,	660/690,660/690	81124596	2906,9928	2145	4272	6417	SO:0001819	synonymous_variant	56978	exon4			GAAGCGGCGGCGA	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.1980G>C	4.37:g.81124596G>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	105	56	0.533333	NM_001099403	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	CCDS43243.1																																																																																			G|0.671;C|0.329	0.329	strong		0.572	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1		
WDFY4	57705	hgsc.bcm.edu	37	10	50025446	50025446	+	Missense_Mutation	SNP	G	G	T	rs12268007	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50025446G>T	ENST00000325239.5	+	31	5524	c.5497G>T	c.(5497-5499)Gcc>Tcc	p.A1833S	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1833						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CCCCCTGGGAGCCCAAAAGGT	0.622													G|||	833	0.166334	0.2905	0.1542	5008	,	,		18222	0.1071		0.1223	False		,,,				2504	0.1135				p.A1833S		Atlas-SNP	.											.	WDFY4	205	.	0			c.G5497T						PASS	.	G	SER/ALA	397,987		60,277,355	24.0	31.0	29.0		5497	-1.6	0.0	10	dbSNP_120	29	338,2844		18,302,1271	yes	missense	WDFY4	NM_020945.1	99	78,579,1626	TT,TG,GG		10.6223,28.685,16.0972	benign	1833/3185	50025446	735,3831	692	1591	2283	SO:0001583	missense	57705	exon32			CTGGGAGCCCAAA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5497G>T	10.37:g.50025446G>T	ENSP00000320563:p.Ala1833Ser	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	339|339	0.15521978021978022|0.15521978021978022	124|124	0.25203252032520324|0.25203252032520324	52|52	0.143646408839779|0.143646408839779	71|71	0.12412587412587413|0.12412587412587413	92|92	0.12137203166226913|0.12137203166226913	G|G	1.092|1.092	-0.663764|-0.663764	0.03428|0.03428	0.28685|0.28685	0.106223|0.106223	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000312002;ENST00000374161	T|.	0.55760|.	0.5|.	5.24|5.24	-1.59|-1.59	0.08453|0.08453	.|.	0.981883|.	0.08311|.	N|.	0.965312|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02011|0.02011	-0.69|-0.69	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.12630|.	0.006;0.0|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.42548|0.42548	-0.9445|-0.9445	8|4	.|.	.|.	.|.	.|.	5.3947|5.3947	0.16263|0.16263	0.3875:0.2776:0.335:0.0|0.3875:0.2776:0.335:0.0	rs12268007;rs12268007|rs12268007;rs12268007	361;1833|.	F2Z372;Q6ZS81|.	.;WDFY4_HUMAN|.	S|I	1833|923;379	ENSP00000320563:A1833S|.	.|.	A|S	+|+	1|2	0|0	WDFY4|WDFY4	49695452|49695452	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.080000|0.080000	0.17528|0.17528	-1.238000|-1.238000	0.02919|0.02919	-0.578000|-0.578000	0.05959|0.05959	-0.302000|-0.302000	0.09304|0.09304	GCC|AGC	G|0.836;T|0.164	0.164	strong		0.622	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
NLRC5	84166	hgsc.bcm.edu	37	16	57060213	57060213	+	Missense_Mutation	SNP	C	C	T	rs9938543	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57060213C>T	ENST00000262510.6	+	6	1583	c.1358C>T	c.(1357-1359)cCc>cTc	p.P453L	NLRC5_ENST00000539144.1_Missense_Mutation_p.P453L|NLRC5_ENST00000308149.7_Missense_Mutation_p.P453L|NLRC5_ENST00000436936.1_Missense_Mutation_p.P453L	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	453	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		P -> L (in dbSNP:rs9938543). {ECO:0000269|PubMed:12693554}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GGGCACTTGCCCACCTCGTCC	0.602													C|||	435	0.086861	0.1566	0.0519	5008	,	,		20395	0.0179		0.1173	False		,,,				2504	0.0573				p.P453L		Atlas-SNP	.											.	NLRC5	186	.	0			c.C1358T						PASS	.	C	LEU/PRO	753,3643	297.0+/-284.5	74,605,1519	41.0	39.0	40.0		1358	-2.9	0.0	16	dbSNP_119	40	817,7783	182.6+/-231.0	45,727,3528	yes	missense	NLRC5	NM_032206.3	98	119,1332,5047	TT,TC,CC		9.5,17.1292,12.0806	benign	453/1867	57060213	1570,11426	2198	4300	6498	SO:0001583	missense	84166	exon5			ACTTGCCCACCTC	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1358C>T	16.37:g.57060213C>T	ENSP00000262510:p.Pro453Leu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	194	0.08882783882783883	72	0.14634146341463414	18	0.049723756906077346	16	0.027972027972027972	88	0.11609498680738786	C	1.239	-0.621900	0.03636	0.171292	0.095	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	T;T;T;T	0.76060	-0.8;-0.82;-0.99;-0.82	5.21	-2.88	0.05682	.	0.811645	0.10069	N	0.719919	T	0.00210	0.0006	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B	0.15141	0.012;0.007;0.001;0.0	B;B;B;B	0.12156	0.005;0.005;0.007;0.001	T	0.05257	-1.0896	9	0.19590	T	0.45	.	0.1538	0.00096	0.2642:0.2625:0.2094:0.2638	rs9938543;rs58059842;rs9938543	453;453;453;453	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.;.;.;NLRC5_HUMAN	L	453	ENSP00000262510:P453L;ENSP00000308886:P453L;ENSP00000389739:P453L;ENSP00000441727:P453L	ENSP00000262510:P453L	P	+	2	0	NLRC5	55617714	0.000000	0.05858	0.000000	0.03702	0.181000	0.23173	-0.231000	0.09069	-0.738000	0.04817	0.561000	0.74099	CCC	C|0.891;T|0.109	0.109	strong		0.602	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
MUC16	94025	hgsc.bcm.edu	37	19	9047267	9047267	+	Missense_Mutation	SNP	C	C	T	rs10410169	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9047267C>T	ENST00000397910.4	-	5	34567	c.34364G>A	c.(34363-34365)gGt>gAt	p.G11455D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11457	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTTTGATGCACCAGGGGAGAC	0.493													C|||	949	0.189497	0.1982	0.1988	5008	,	,		24195	0.0258		0.2823	False		,,,				2504	0.2444				p.G11455D		Atlas-SNP	.											.	MUC16	4315	.	0			c.G34364A						PASS	.		ASP/GLY	754,3276		70,614,1331	173.0	169.0	170.0		34364	0.9	0.0	19	dbSNP_119	170	2524,5826		402,1720,2053	yes	missense	MUC16	NM_024690.2	94	472,2334,3384	TT,TC,CC		30.2275,18.7097,26.4782	possibly-damaging	11455/14508	9047267	3278,9102	2015	4175	6190	SO:0001583	missense	94025	exon5			GATGCACCAGGGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.34364G>A	19.37:g.9047267C>T	ENSP00000381008:p.Gly11455Asp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	408	0.18681318681318682	103	0.20934959349593496	76	0.20994475138121546	11	0.019230769230769232	218	0.287598944591029	c	7.617	0.676019	0.14841	0.187097	0.302275	ENSG00000181143	ENST00000397910	T	0.04862	3.54	3.05	0.877	0.19145	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	.	.	.	P	0.36086	0.536	B	0.39339	0.297	T	0.49234	-0.8961	8	0.87932	D	0	.	5.0244	0.14378	0.0:0.7109:0.0:0.2891	rs10410169;rs52822154;rs58775557;rs10410169	11455	B5ME49	.	D	11455	ENSP00000381008:G11455D	ENSP00000381008:G11455D	G	-	2	0	MUC16	8908267	0.000000	0.05858	0.001000	0.08648	0.182000	0.23217	-1.197000	0.03038	0.307000	0.22880	0.306000	0.20318	GGT	C|0.788;T|0.212	0.212	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MATN2	4147	hgsc.bcm.edu	37	8	99045866	99045866	+	Missense_Mutation	SNP	G	G	A	rs17831160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:99045866G>A	ENST00000520016.1	+	17	2918	c.2794G>A	c.(2794-2796)Gta>Ata	p.V932I	MATN2_ENST00000522025.2_Missense_Mutation_p.V648I|MATN2_ENST00000521689.1_Missense_Mutation_p.V913I|MATN2_ENST00000524308.1_Missense_Mutation_p.V891I|MATN2_ENST00000254898.5_Missense_Mutation_p.V932I|RPL30_ENST00000518164.1_Intron			O00339	MATN2_HUMAN	matrilin 2	932			V -> I (in dbSNP:rs17831160).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			AAACGAAGAAGTAAGAAAATT	0.353													G|||	55	0.0109824	0.0008	0.0144	5008	,	,		22730	0.0		0.0378	False		,,,				2504	0.0061				p.V932I		Atlas-SNP	.											.	MATN2	165	.	0			c.G2794A						PASS	.	G	ILE/VAL,ILE/VAL	16,3644		0,16,1814	87.0	79.0	81.0		2794,2737	4.8	1.0	8	dbSNP_123	81	257,7927		3,251,3838	yes	missense,missense	MATN2	NM_002380.3,NM_030583.2	29,29	3,267,5652	AA,AG,GG		3.1403,0.4372,2.305	probably-damaging,probably-damaging	932/957,913/938	99045866	273,11571	1830	4092	5922	SO:0001583	missense	4147	exon18			GAAGAAGTAAGAA	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.2794G>A	8.37:g.99045866G>A	ENSP00000430487:p.Val932Ile	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	34|34|34	0.015567765567765568|0.015567765567765568|0.015567765567765568	0|0|0	0.0|0.0|0.0	7|7|7	0.019337016574585635|0.019337016574585635|0.019337016574585635	0|0|0	0.0|0.0|0.0	27|27|27	0.03562005277044855|0.03562005277044855|0.03562005277044855	G|G|G	18.50|18.50|18.50	3.636558|3.636558|3.636558	0.67130|0.67130|0.67130	0.004372|0.004372|0.004372	0.031403|0.031403|0.031403	ENSG00000132561|ENSG00000132561|ENSG00000132561	ENST00000519582|ENST00000518154|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|.|T;T;T;T;T	.|.|0.37752	.|.|1.18;1.18;1.18;1.18;1.18	5.73|5.73|5.73	4.84|4.84|4.84	0.62591|0.62591|0.62591	.|.|Matrilin, coiled-coil trimerisation domain (2);	.|.|6.163480	.|.|0.00447	.|.|N	.|.|0.000093	.|T|T	.|0.20414|0.20414	.|0.0491|0.0491	L|L|L	0.28274|0.28274|0.28274	0.84|0.84|0.84	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|D;D;P;D	.|.|0.69078	.|.|0.963;0.963;0.954;0.997	.|.|P;P;P;D	.|.|0.80764	.|.|0.891;0.84;0.752;0.994	.|T|T	.|0.25606|0.25606	.|-1.0127|-1.0127	.|5|10	.|.|0.33940	.|.|T	.|.|0.23	.|0.016|0.016	12.8072|12.8072|12.8072	0.57619|0.57619|0.57619	0.0753:0.0:0.9247:0.0|0.0753:0.0:0.9247:0.0|0.0753:0.0:0.9247:0.0	rs17831160;rs52795510;rs17831160|rs17831160;rs52795510;rs17831160|rs17831160;rs52795510;rs17831160	.|.|891;913;913;932	.|.|C9JH87;E9PF03;O00339-2;O00339	.|.|.;.;.;MATN2_HUMAN	.|N|I	-1|695|913;932;891;891;648;932	.|.|ENSP00000429977:V913I;ENSP00000254898:V932I;ENSP00000430221:V891I;ENSP00000429010:V648I;ENSP00000430487:V932I	.|.|ENSP00000254898:V932I	.|S|V	+|+|+	.|2|1	.|0|0	MATN2|MATN2|MATN2	99115042|99115042|99115042	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.997000|0.997000|0.997000	0.91878|0.91878|0.91878	3.851000|3.851000|3.851000	0.55926|0.55926|0.55926	2.861000|2.861000|2.861000	0.98227|0.98227|0.98227	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	.|AGT|GTA	G|0.979;A|0.021	0.021	strong		0.353	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
CBLB	868	hgsc.bcm.edu	37	3	105438957	105438957	+	Silent	SNP	T	T	G	rs2305036	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:105438957T>G	ENST00000264122.4	-	10	1662	c.1341A>C	c.(1339-1341)ctA>ctC	p.L447L	CBLB_ENST00000403724.1_Silent_p.L447L|CBLB_ENST00000405772.1_Silent_p.L447L|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000394027.3_Silent_p.L469L	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	447					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						CGTCCAAGTCTAGCATCGGCA	0.463			Mis S		AML								G|||	1053	0.210264	0.1936	0.2968	5008	,	,		20280	0.2192		0.2376	False		,,,				2504	0.1339				p.L447L	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.A1341C						PASS	.	G		815,3591	749.3+/-412.0	76,663,1464	118.0	100.0	106.0		1341	0.9	1.0	3	dbSNP_100	106	1843,6757	730.6+/-406.8	207,1429,2664	no	coding-synonymous	CBLB	NM_170662.3		283,2092,4128	GG,GT,TT		21.4302,18.4975,20.4367		447/983	105438957	2658,10348	2203	4300	6503	SO:0001819	synonymous_variant	868	exon10			CAAGTCTAGCATC	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.1341A>C	3.37:g.105438957T>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	147	72	0.489796	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	37	CCDS2948.1																																																																																			T|0.786;G|0.214	0.214	strong		0.463	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
PSG4	5672	hgsc.bcm.edu	37	19	43708245	43708245	+	Missense_Mutation	SNP	G	G	C	rs3170216	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43708245G>C	ENST00000405312.3	-	2	460	c.223C>G	c.(223-225)Ctc>Gtc	p.L75V	PSG4_ENST00000244295.9_Missense_Mutation_p.L75V|PSG4_ENST00000433626.2_Missense_Mutation_p.L75V	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	75	Ig-like V-type.		L -> V (in dbSNP:rs3170216). {ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2271648, ECO:0000269|PubMed:7794280}.		female pregnancy (GO:0007565)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	24		Prostate(69;0.00682)				TAATGGTAGAGGTATGTCATT	0.423													G|||	864	0.172524	0.2791	0.1643	5008	,	,		18097	0.005		0.2893	False		,,,				2504	0.0869				p.T75A		Atlas-SNP	.											.	PSG4	129	.	0			c.A223G						PASS	.	G	VAL/LEU,VAL/LEU	1246,3024		350,546,1239	196.0	207.0	203.0		223,223	-3.3	0.0	19	dbSNP_105	203	2389,6153		487,1415,2369	yes	missense,missense	PSG4	NM_002780.3,NM_213633.1	32,32	837,1961,3608	CC,CG,GG		27.9677,29.1803,28.3718	,	75/420,75/327	43708245	3635,9177	2135	4271	6406	SO:0001583	missense	5672	exon2			GGTAGAGGTATGT		CCDS33039.1, CCDS46093.1, CCDS62695.1	19q13.2	2013-01-29			ENSG00000243137	ENSG00000243137		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9521	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1-glycoprotein 4"""	176393				2783133	Standard	NM_002780		Approved		uc002ovy.4	Q00888	OTTHUMG00000151544	ENST00000405312.3:c.223C>G	19.37:g.43708245G>C	ENSP00000384770:p.Leu75Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Missense_Mutation	SNP	ENST00000405312.3	37	CCDS46093.1	402	0.18406593406593408	114	0.23170731707317074	61	0.1685082872928177	5	0.008741258741258742	222	0.2928759894459103	N	0.023	-1.397258	0.01175	0.291803	0.279677	ENSG00000243137	ENST00000244295;ENST00000405312;ENST00000433626;ENST00000451895	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	1.65	-3.31	0.04988	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	0.80722	P	0.0	P;P;B	0.46706	0.883;0.694;0.058	P;B;B	0.49140	0.601;0.379;0.056	T	0.08472	-1.0720	8	0.12766	T	0.61	.	2.9373	0.05818	0.2951:0.0:0.3242:0.3807	rs3170216;rs17680844	75;75;75	E7EX79;Q00888-2;Q00888	.;.;PSG4_HUMAN	V	75;75;75;91	ENSP00000244295:L75V;ENSP00000384770:L75V;ENSP00000387864:L75V;ENSP00000388134:L91V	ENSP00000244295:L75V	L	-	1	0	PSG4	48400085	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-3.219000	0.00553	-2.341000	0.00625	0.173000	0.16961	CTC	G|0.800;C|0.200	0.200	strong		0.423	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918135	51918135	+	Missense_Mutation	SNP	G	G	T	rs1833785	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51918135G>T	ENST00000339313.5	-	8	1674	c.1558C>A	c.(1558-1560)Cgc>Agc	p.R520S	SIGLEC10_ENST00000439889.2_Missense_Mutation_p.R462S|SIGLEC10_ENST00000436984.2_Intron|SIGLEC10_ENST00000353836.5_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000432469.2_Intron|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.R520S|SIGLEC10_ENST00000441969.3_Intron|CTD-2616J11.2_ENST00000532688.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	520			R -> S (in dbSNP:rs1833785).		cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		GCCTCACAGCGGAGCCTGAGG	0.667													t|||	1217	0.243011	0.3828	0.1974	5008	,	,		15822	0.2113		0.1501	False		,,,				2504	0.2147				p.R520S		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C1558A						PASS	.	T	SER/ARG,,,,,,SER/ARG	1520,2884		258,1004,940	44.0	52.0	49.0		1384,,,,,,1558	-2.3	0.8	19	dbSNP_92	49	1283,7315		99,1085,3115	yes	missense,intron,intron,intron,intron,intron,missense	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	110,,,,,,110	357,2089,4055	TT,TG,GG		14.9221,34.5141,21.5582	benign,,,,,,benign	462/640,,,,,,520/698	51918135	2803,10199	2202	4299	6501	SO:0001583	missense	89790	exon8			CACAGCGGAGCCT	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.1558C>A	19.37:g.51918135G>T	ENSP00000345243:p.Arg520Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	461	0.21108058608058608	178	0.3617886178861789	65	0.17955801104972377	108	0.1888111888111888	110	0.14511873350923482	.	2.864	-0.235411	0.05983	0.345141	0.149221	ENSG00000142512	ENST00000356298;ENST00000439889;ENST00000339313	D;D;D	0.85484	-1.99;-1.99;-1.99	4.83	-2.29	0.06805	.	0.523323	0.19200	N	0.120203	T	0.00012	0.0000	N	0.00385	-1.57	0.58432	P	9.000000000036756E-6	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.12243	-1.0555	9	0.02654	T	1	.	11.8093	0.52173	0.0:0.086:0.7091:0.2048	rs1833785;rs3810100;rs16982678	462;520	Q96LC7-3;Q96LC7	.;SIG10_HUMAN	S	520;462;520	ENSP00000348646:R520S;ENSP00000389132:R462S;ENSP00000345243:R520S	ENSP00000345243:R520S	R	-	1	0	SIGLEC10	56609947	0.006000	0.16342	0.838000	0.33150	0.003000	0.03518	-0.988000	0.03739	-0.803000	0.04415	-1.915000	0.00519	CGC	G|0.776;T|0.224	0.224	strong		0.667	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
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 GAIIx	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		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	240	102	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
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919872	12919872	+	Missense_Mutation	SNP	T	T	G	rs3204798	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12919872T>G	ENST00000240189.2	+	3	699	c.612T>G	c.(610-612)atT>atG	p.I204M		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	204					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)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TAATATACATTAATAGTATTG	0.373													.|||	389	0.0776757	0.0189	0.0231	5008	,	,		22686	0.2292		0.0388	False		,,,				2504	0.0798				p.I204M		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.T612G						PASS	.	G	MET/ILE	106,4296	794.0+/-415.2	1,104,2096	98.0	113.0	108.0		612	-0.3	0.0	1	dbSNP_105	108	386,8198	793.2+/-407.5	7,372,3913	yes	missense	PRAMEF2	NM_023014.1	10	8,476,6009	GG,GT,TT		4.4967,2.408,3.7887	benign	204/475	12919872	492,12494	2201	4292	6493	SO:0001583	missense	65122	exon3			ATACATTAATAGT		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.612T>G	1.37:g.12919872T>G	ENSP00000240189:p.Ile204Met	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	139	48	0.345324	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	194	0.08882783882783883	4	0.008130081300813009	14	0.03867403314917127	134	0.23426573426573427	42	0.055408970976253295	G	3.131	-0.178427	0.06380	0.02408	0.044967	ENSG00000120952	ENST00000240189	T	0.01119	5.31	0.842	-0.295	0.12828	.	0.519605	0.18636	N	0.135435	T	0.00012	0.0000	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.17433	0.018	T	0.49312	-0.8953	10	0.46703	T	0.11	.	1.5253	0.02524	0.3007:0.0:0.3642:0.3351	rs3204798	204	O60811	PRAM2_HUMAN	M	204	ENSP00000240189:I204M	ENSP00000240189:I204M	I	+	3	3	PRAMEF2	12842459	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.627000	0.05521	-0.696000	0.05098	-1.044000	0.02363	ATT	T|0.947;G|0.053	0.053	strong		0.373	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
KBTBD12	166348	hgsc.bcm.edu	37	3	127703085	127703085	+	Silent	SNP	G	G	A	rs13100951	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:127703085G>A	ENST00000405109.1	+	6	2303	c.1836G>A	c.(1834-1836)ccG>ccA	p.P612P	KBTBD12_ENST00000492025.1_3'UTR|KBTBD12_ENST00000405256.1_Silent_p.P612P|KBTBD12_ENST00000407609.3_Silent_p.P219P|KBTBD12_ENST00000343941.4_Silent_p.P187P			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12	612										endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						TCATCCCCCCGCCTTCAGATT	0.537													G|||	1097	0.21905	0.1241	0.2983	5008	,	,		20696	0.2887		0.2614	False		,,,				2504	0.1759				p.P612P		Atlas-SNP	.											.	KBTBD12	41	.	0			c.G1836A						PASS	.	G		655,3751	278.1+/-274.1	54,547,1602	97.0	90.0	93.0		1836	-9.4	0.3	3	dbSNP_121	93	2157,6443	369.1+/-335.3	290,1577,2433	no	coding-synonymous	KBTBD12	NM_207335.2		344,2124,4035	AA,AG,GG		25.0814,14.8661,21.6208		612/624	127703085	2812,10194	2203	4300	6503	SO:0001819	synonymous_variant	166348	exon5			CCCCCCGCCTTCA		CCDS33848.2	3q21.3	2013-01-08	2009-10-01	2009-10-01	ENSG00000187715	ENSG00000187715		"""BTB/POZ domain containing"""	25731	protein-coding gene	gene with protein product			"""kelch domain containing 6"""	KLHDC6			Standard	NM_207335		Approved	FLJ46299	uc010hsr.3	Q3ZCT8	OTTHUMG00000150508	ENST00000405109.1:c.1836G>A	3.37:g.127703085G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_207335	B5MCC6|Q6ZRK1	Silent	SNP	ENST00000405109.1	37	CCDS33848.2																																																																																			G|0.771;A|0.229	0.229	strong		0.537	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335	
ALMS1	7840	hgsc.bcm.edu	37	2	73677833	73677833	+	Silent	SNP	A	A	G	rs6546836	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73677833A>G	ENST00000264448.6	+	8	4287	c.4176A>G	c.(4174-4176)caA>caG	p.Q1392Q	ALMS1_ENST00000409009.1_Silent_p.Q1350Q|ALMS1_ENST00000377715.1_Silent_p.Q1392Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1392	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						TTTTCTACCAACAGTCGTTGC	0.473													A|||	1694	0.338259	0.7859	0.3847	5008	,	,		21223	0.0089		0.2256	False		,,,				2504	0.1554				p.Q1392Q		Atlas-SNP	.											ALMS1,colon,carcinoma,0,1	ALMS1	384	1	0			c.A4176G						PASS	.	A		2499,1227		847,805,211	91.0	93.0	92.0		4176	-6.8	0.0	2	dbSNP_116	92	1942,6272		217,1508,2382	no	coding-synonymous	ALMS1	NM_015120.4		1064,2313,2593	GG,GA,AA		23.6426,32.9308,37.1943		1392/4168	73677833	4441,7499	1863	4107	5970	SO:0001819	synonymous_variant	7840	exon8			CTACCAACAGTCG	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.4176A>G	2.37:g.73677833A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			A|0.737;G|0.263	0.263	strong		0.473	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
LILRB3	11025	hgsc.bcm.edu	37	19	54724443	54724443	+	Missense_Mutation	SNP	G	G	A	rs201735825	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54724443G>A	ENST00000391750.1	-	7	1349	c.1213C>T	c.(1213-1215)Cac>Tac	p.H405Y	LILRB3_ENST00000407860.2_Missense_Mutation_p.H405Y|LILRA6_ENST00000440558.2_Missense_Mutation_p.H405Y|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.H405Y|LILRA6_ENST00000270464.5_Missense_Mutation_p.H405Y|LILRB3_ENST00000346401.6_Missense_Mutation_p.H405Y|LILRB3_ENST00000424807.1_Missense_Mutation_p.H405Y|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	405	Ig-like C2-type 4.		H -> Y (in dbSNP:rs1132604). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GACAGCAGGTGGGGGTTGGAG	0.627													.|||	941	0.187899	0.4085	0.1772	5008	,	,		7731	0.005		0.1481	False		,,,				2504	0.1268				p.H405Y		Atlas-SNP	.											.	LILRB3	67	.	0			c.C1213T						PASS	.						16.0	9.0	11.0					19																	54724443		2160	3980	6140	SO:0001583	missense	11025	exon6			GCAGGTGGGGGTT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1213C>T	19.37:g.54724443G>A	ENSP00000375630:p.His405Tyr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	39	30	0.769231	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	g	0.003	-2.389985	0.00200	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464	T;T;T;T;T;T;T	0.00669	5.9;5.9;5.9;5.9;5.9;5.9;5.9	2.87	-5.11	0.02901	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.167250	0.06702	N	0.771663	T	0.00271	0.0008	N	0.00329	-1.635	0.58432	P	1.0000000000287557E-6	B;B;B;B;B;B	0.09022	0.0;0.0;0.0;0.002;0.0;0.0	B;B;B;B;B;B	0.08055	0.001;0.001;0.001;0.003;0.0;0.0	T	0.45977	-0.9224	9	0.02654	T	1	.	10.4418	0.44471	0.4586:0.0:0.5414:0.0	.	405;405;405;405;405;405	B5MCX0;F8WCY4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;LIRB3_HUMAN;.	Y	405	ENSP00000375630:H405Y;ENSP00000412771:H405Y;ENSP00000345184:H405Y;ENSP00000245620:H405Y;ENSP00000384274:H405Y;ENSP00000390120:H405Y;ENSP00000270464:H405Y	ENSP00000270464:H405Y	H	-	1	0	LILRB3;LILRA6	59416255	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.211000	0.02997	-1.561000	0.01684	-1.799000	0.00621	CAC	G|0.860;A|0.140	0.140	strong		0.627	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
CHEK2	11200	hgsc.bcm.edu	37	22	29091840	29091840	+	Missense_Mutation	SNP	T	T	C	rs142470496	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:29091840T>C	ENST00000405598.1	-	12	1308	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	CHEK2_ENST00000403642.1_Missense_Mutation_p.K282E|CHEK2_ENST00000402731.1_Missense_Mutation_p.K344E|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382580.2_Missense_Mutation_p.K416E|CHEK2_ENST00000382578.1_Missense_Mutation_p.K282E|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Missense_Mutation_p.K373E|CHEK2_ENST00000404276.1_Missense_Mutation_p.K373E|CHEK2_ENST00000348295.3_Missense_Mutation_p.K344E|CHEK2_ENST00000544772.1_Missense_Mutation_p.K152E			O96017	CHK2_HUMAN	checkpoint kinase 2	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.K373E(9)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCCAAAATCTTGGAGTGCCCA	0.418			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.K416E		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	CHEK2,NS,carcinoma,0,36	CHEK2	438	36	9	Substitution - Missense(9)	kidney(4)|prostate(2)|endometrium(1)|stomach(1)|central_nervous_system(1)	c.A1246G						scavenged	.																																			SO:0001583	missense	11200	exon12			AAATCTTGGAGTG	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1117A>G	22.37:g.29091840T>C	ENSP00000386087:p.Lys373Glu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	7	0.0693069	NM_001005735	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	T	19.06	3.754336	0.69648	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731	T;T;T;T;T;T;T;T;T	0.54071	0.9;0.59;0.59;0.59;0.59;0.59;0.59;0.59;0.9	5.89	5.89	0.94794	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043710	0.85682	D	0.000000	T	0.56292	0.1975	N	0.11756	0.17	0.80722	D	1	D;D;D;D;D;D	0.76494	0.996;0.999;0.998;0.998;0.993;0.991	P;D;D;D;D;P	0.74674	0.905;0.984;0.943;0.969;0.923;0.896	T	0.64769	-0.6329	10	0.87932	D	0	-1.7726	15.4726	0.75453	0.0:0.0:0.0:1.0	.	282;152;373;344;373;416	O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;CHK2_HUMAN;.	E	344;282;152;373;373;373;416;282;344	ENSP00000329012:K344E;ENSP00000372021:K282E;ENSP00000442458:K152E;ENSP00000329178:K373E;ENSP00000385747:K373E;ENSP00000386087:K373E;ENSP00000372023:K416E;ENSP00000384919:K282E;ENSP00000384835:K344E	ENSP00000329178:K373E	K	-	1	0	CHEK2	27421840	1.000000	0.71417	1.000000	0.80357	0.479000	0.33129	4.270000	0.58896	2.248000	0.74166	0.528000	0.53228	AAG	.	.	weak		0.418	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735	
SMARCA2	6595	hgsc.bcm.edu	37	9	2191309	2191309	+	Missense_Mutation	SNP	C	C	G	rs2296212	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:2191309C>G	ENST00000382203.1	+	33	4847	c.4638C>G	c.(4636-4638)gaC>gaG	p.D1546E	SMARCA2_ENST00000382185.1_Missense_Mutation_p.D192E|SMARCA2_ENST00000382194.1_Missense_Mutation_p.D1528E|SMARCA2_ENST00000349721.2_Missense_Mutation_p.D1546E|SMARCA2_ENST00000357248.2_Missense_Mutation_p.D1528E|SMARCA2_ENST00000302401.3_Missense_Mutation_p.D234E|SMARCA2_ENST00000382186.1_Missense_Mutation_p.D210E|SMARCA2_ENST00000324954.5_Missense_Mutation_p.D192E			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1546			D -> E (in dbSNP:rs2296212).		aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		AAAAAGATGACAAAGGCCGGG	0.413													G|||	1120	0.223642	0.3071	0.2061	5008	,	,		20895	0.2163		0.0984	False		,,,				2504	0.2597				p.D1546E		Atlas-SNP	.											.	SMARCA2	313	.	0			c.C4638G						PASS	.	G	GLU/ASP,GLU/ASP	1187,3219	710.9+/-407.9	149,889,1165	111.0	95.0	100.0	http://omim.org/entry/600014	4584,4638	3.8	1.0	9	dbSNP_100	100	962,7638	775.6+/-407.7	53,856,3391	yes	missense,missense	SMARCA2	NM_139045.2,NM_003070.3	45,45	202,1745,4556	GG,GC,CC		11.186,26.9405,16.5231	benign,benign	1528/1573,1546/1591	2191309	2149,10857	2203	4300	6503	SO:0001583	missense	6595	exon33			AGATGACAAAGGC	D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.4638C>G	9.37:g.2191309C>G	ENSP00000371638:p.Asp1546Glu	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	103	61	0.592233	NM_003070	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	397	0.18177655677655677	143	0.29065040650406504	70	0.19337016574585636	115	0.20104895104895104	69	0.09102902374670185	G	5.237	0.229183	0.09916	0.269405	0.11186	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194;ENST00000302401;ENST00000324954;ENST00000382186;ENST00000417599;ENST00000382185;ENST00000382183;ENST00000382182	D;D;D;D;T;T;T;T;T;T	0.86956	-2.19;-2.13;-2.19;-2.13;3.19;3.34;3.12;3.35;3.34;3.34	5.71	3.76	0.43208	.	0.232312	0.35466	N	0.003181	T	0.00012	0.0000	N	0.03115	-0.41	0.49798	P	1.7100000000003224E-4	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.04090	-1.0978	9	0.02654	T	1	-24.9	12.6243	0.56620	0.0717:0.5959:0.3323:0.0	rs2296212;rs2296212	232;234;1528;1546	B4DNT1;B1ALF6;P51531-2;P51531	.;.;.;SMCA2_HUMAN	E	1546;1528;1546;1528;234;192;210;232;192;192;75	ENSP00000265773:D1546E;ENSP00000349788:D1528E;ENSP00000371638:D1546E;ENSP00000371629:D1528E;ENSP00000305411:D234E;ENSP00000324770:D192E;ENSP00000371621:D210E;ENSP00000387486:D232E;ENSP00000371620:D192E;ENSP00000371618:D192E	ENSP00000305411:D234E	D	+	3	2	SMARCA2	2181309	0.982000	0.34865	1.000000	0.80357	0.994000	0.84299	0.094000	0.15107	0.742000	0.32697	-0.127000	0.14921	GAC	C|0.831;G|0.169	0.169	strong		0.413	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
BEND7	222389	hgsc.bcm.edu	37	10	13481427	13481427	+	Silent	SNP	T	T	A	rs12415754	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:13481427T>A	ENST00000396900.2	-	9	1304	c.1305A>T	c.(1303-1305)tcA>tcT	p.S435S	BEND7_ENST00000486542.1_5'UTR|BEND7_ENST00000341083.3_Silent_p.S384S			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	435						extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						TTGTCTGAGGTGAGCTCTGCA	0.537													T|||	1668	0.333067	0.0257	0.3401	5008	,	,		20712	0.6667		0.3559	False		,,,				2504	0.3763				p.S384S		Atlas-SNP	.											.	BEND7	85	.	0			c.A1152T						PASS	.	T		354,4052	182.6+/-210.3	12,330,1861	105.0	92.0	97.0		1152	-0.7	0.0	10	dbSNP_120	97	2890,5710	452.6+/-363.0	484,1922,1894	no	coding-synonymous	BEND7	NM_152751.2		496,2252,3755	AA,AT,TT		33.6047,8.0345,24.9423		384/469	13481427	3244,9762	2203	4300	6503	SO:0001819	synonymous_variant	222389	exon9			CTGAGGTGAGCTC	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.1305A>T	10.37:g.13481427T>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_152751	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				T|0.703;A|0.297	0.297	strong		0.537	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
COL4A4	1286	hgsc.bcm.edu	37	2	227892619	227892619	+	Splice_Site	SNP	C	C	T	rs2228556	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:227892619C>T	ENST00000396625.3	-	42	4287	c.4080G>A	c.(4078-4080)ccG>ccA	p.P1360P	COL4A4_ENST00000329662.7_Splice_Site_p.P1360P	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1360	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GAAGCTCACCCGGAAGACCAG	0.463													T|||	2463	0.491813	0.5651	0.4769	5008	,	,		14265	0.4028		0.4384	False		,,,				2504	0.5501				p.P1360P		Atlas-SNP	.											.	COL4A4	215	.	0			c.G4080A						PASS	.	T		1957,1765		499,959,403	52.0	59.0	56.0		4080	3.4	1.0	2	dbSNP_107	56	3455,4727		729,1997,1365	no	coding-synonymous-near-splice	COL4A4	NM_000092.4		1228,2956,1768	TT,TC,CC		42.2268,47.4207,45.4637		1360/1691	227892619	5412,6492	1861	4091	5952	SO:0001630	splice_region_variant	1286	exon42			CTCACCCGGAAGA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4081+1G>A	2.37:g.227892619C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			C|0.556;T|0.444	0.444	strong		0.463	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	Silent
DCBLD2	131566	hgsc.bcm.edu	37	3	98541116	98541116	+	Silent	SNP	G	G	A	rs828616	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:98541116G>A	ENST00000326840.6	-	6	1148	c.786C>T	c.(784-786)atC>atT	p.I262I	DCBLD2_ENST00000326857.9_Silent_p.I262I|DCBLD2_ENST00000469648.1_5'Flank	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	262	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						CATAATAGGGGATACCTTTAC	0.393													G|||	1933	0.385982	0.0772	0.5115	5008	,	,		18220	0.6806		0.3757	False		,,,				2504	0.4213				p.I262I		Atlas-SNP	.											.	DCBLD2	62	.	0			c.C786T						PASS	.	G		439,3373		30,379,1497	63.0	58.0	59.0		786	2.8	1.0	3	dbSNP_86	59	2903,5363		495,1913,1725	no	coding-synonymous	DCBLD2	NM_080927.3		525,2292,3222	AA,AG,GG		35.1198,11.5163,27.6701		262/776	98541116	3342,8736	1906	4133	6039	SO:0001819	synonymous_variant	131566	exon6			ATAGGGGATACCT		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.786C>T	3.37:g.98541116G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	120	52	0.433333	NM_080927	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Silent	SNP	ENST00000326840.6	37	CCDS46878.1																																																																																			G|0.593;A|0.407	0.407	strong		0.393	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927	
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 GAIIx	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_ENST00000265662.5_Silent_p.A2092A|ABCA2_ENST00000341511.6_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		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	63	30	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	
TTYH2	94015	hgsc.bcm.edu	37	17	72248512	72248512	+	Missense_Mutation	SNP	C	C	T	rs12600564	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72248512C>T	ENST00000269346.4	+	11	1330	c.1256C>T	c.(1255-1257)aCc>aTc	p.T419I	TTYH2_ENST00000441391.2_Missense_Mutation_p.T98I|TTYH2_ENST00000529107.1_Missense_Mutation_p.T398I	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	419			T -> I (in dbSNP:rs12600564).			chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						CACTTCACCACCAGGTGGGCT	0.612													C|||	428	0.0854633	0.0197	0.134	5008	,	,		18189	0.0456		0.1412	False		,,,				2504	0.1237				p.T419I		Atlas-SNP	.											.	TTYH2	63	.	0			c.C1256T						PASS	.	C	ILE/THR,ILE/THR	191,4215	118.8+/-156.5	5,181,2017	47.0	40.0	42.0		1256,293	0.6	0.7	17	dbSNP_120	42	1279,7321	251.9+/-278.2	100,1079,3121	yes	missense,missense	TTYH2	NM_032646.5,NM_052869.1	89,89	105,1260,5138	TT,TC,CC		14.8721,4.335,11.3025	benign,benign	419/535,98/214	72248512	1470,11536	2203	4300	6503	SO:0001583	missense	94015	exon11			TCACCACCAGGTG		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.1256C>T	17.37:g.72248512C>T	ENSP00000269346:p.Thr419Ile	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	31	18	0.580645	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	180	0.08241758241758242	5	0.01016260162601626	38	0.10497237569060773	25	0.043706293706293704	112	0.14775725593667546	C	12.31	1.898732	0.33535	0.04335	0.148721	ENSG00000141540	ENST00000269346;ENST00000529107;ENST00000441391	T;T;T	0.11604	2.76;2.76;2.76	5.79	0.617	0.17619	.	0.817264	0.11849	N	0.523478	T	0.00039	0.0001	L	0.33485	1.01	0.54753	P	2.0000000000020002E-5	B;B	0.19706	0.038;0.012	B;B	0.16722	0.016;0.011	T	0.35724	-0.9777	9	0.38643	T	0.18	-19.0966	4.4593	0.11659	0.1353:0.3925:0.3718:0.1004	rs12600564;rs58697289;rs12600564	398;419	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	I	419;398;98	ENSP00000269346:T419I;ENSP00000433089:T398I;ENSP00000394576:T98I	ENSP00000269346:T419I	T	+	2	0	TTYH2	69760107	0.004000	0.15560	0.711000	0.30485	0.998000	0.95712	-0.018000	0.12568	0.710000	0.31997	0.655000	0.94253	ACC	C|0.907;T|0.093	0.093	strong		0.612	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
EPHA5	2044	hgsc.bcm.edu	37	4	66535284	66535284	+	Silent	SNP	G	G	A	rs55860557	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:66535284G>A	ENST00000273854.3	-	1	777	c.177C>T	c.(175-177)aaC>aaT	p.N59N	RP11-807H7.1_ENST00000509473.1_lincRNA|EPHA5_ENST00000511294.1_Silent_p.N59N|EPHA5_ENST00000354839.4_Silent_p.N59N|EPHA5_ENST00000432638.2_Silent_p.N59N	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	59					axon guidance (GO:0007411)|cAMP-mediated signaling (GO:0019933)|ephrin receptor signaling pathway (GO:0048013)|hippocampus development (GO:0021766)|negative regulation of synapse assembly (GO:0051964)|neuron development (GO:0048666)|positive regulation of CREB transcription factor activity (GO:0032793)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of Rac GTPase activity (GO:0032314)	dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|GPI-linked ephrin receptor activity (GO:0005004)|transmembrane-ephrin receptor activity (GO:0005005)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(25)|liver(1)|lung(76)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	142						CCCTACCTTCGTTGCTGGGGC	0.716										TSP Lung(17;0.13)			G|||	576	0.115016	0.1157	0.0965	5008	,	,		10587	0.0159		0.2117	False		,,,				2504	0.1299				p.N59N		Atlas-SNP	.											EPHA5,brain,glioma,0,1	EPHA5	315	1	0			c.C177T						PASS	.	G	,	465,3869		30,405,1732	12.0	14.0	13.0		177,177	1.8	1.0	4	dbSNP_129	13	1687,6839		180,1327,2756	no	coding-synonymous,coding-synonymous	EPHA5	NM_004439.5,NM_182472.2	,	210,1732,4488	AA,AG,GG		19.7865,10.7291,16.7341	,	59/1038,59/1016	66535284	2152,10708	2167	4263	6430	SO:0001819	synonymous_variant	2044	exon1			ACCTTCGTTGCTG	L36644	CCDS3513.1, CCDS3514.1, CCDS75131.1, CCDS75132.1, CCDS75133.1	4q13.1	2013-02-11	2004-10-28		ENSG00000145242	ENSG00000145242		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3389	protein-coding gene	gene with protein product		600004	"""EphA5"""			9267020, 7528718	Standard	NM_004439		Approved	Hek7, TYRO4, CEK7, EHK1	uc003hcy.3	P54756	OTTHUMG00000129273	ENST00000273854.3:c.177C>T	4.37:g.66535284G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	131	75	0.572519	NM_004439	Q7Z3F2	Silent	SNP	ENST00000273854.3	37	CCDS3513.1																																																																																			G|0.861;A|0.139	0.139	strong		0.716	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634369	32634369	+	Missense_Mutation	SNP	C	C	A	rs1049056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32634369C>A	ENST00000399082.3	-	1	60	c.16G>T	c.(16-18)Gct>Tct	p.A6S	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.A6S|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.A6S|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.A6S|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.A6S			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	6			A -> S (in allele DQB1*05:01 and allele DQB1*05:02; dbSNP:rs1049056).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	ATCCGCAAAGCCTTCTTCCAA	0.527									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1072	0.214058	0.2322	0.1527	5008	,	,		13934	0.2411		0.2008	False		,,,				2504	0.2188				p.A6S	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G16T						PASS	.	C	SER/ALA	803,3049		125,553,1248	41.0	40.0	41.0		16	-0.0	0.0	6	dbSNP_86	41	1475,6725		255,965,2880	yes	missense	HLA-DQB1	NM_002123.4	99	380,1518,4128	AA,AC,CC		17.9878,20.8463,18.9014	benign	6/262	32634369	2278,9774	1926	4100	6026	SO:0001583	missense	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GCAAAGCCTTCTT		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.16G>T	6.37:g.32634369C>A	ENSP00000382032:p.Ala6Ser	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		456	0.2087912087912088	125	0.2540650406504065	70	0.19337016574585636	90	0.15734265734265734	171	0.22559366754617413	.	11.39	1.624062	0.28889	0.208463	0.179878	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.05786	3.39;6.02;6.02;5.99;5.99	4.09	-0.0275	0.13926	.	2.706550	0.03300	U	0.188815	T	0.01835	0.0058	L	0.41415	1.275	0.80722	P	0.0	B;B;B;B	0.28512	0.214;0.004;0.002;0.002	B;B;B;B	0.24848	0.056;0.012;0.01;0.008	T	0.44314	-0.9336	9	0.56958	D	0.05	.	3.2401	0.06778	0.3581:0.4329:0.0:0.209	rs1049056;rs3189132	16;6;6;6	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	S	6	ENSP00000382032:A6S;ENSP00000382029:A6S;ENSP00000364080:A6S;ENSP00000407332:A6S;ENSP00000382034:A6S	ENSP00000364080:A6S	A	-	1	0	HLA-DQB1	32742347	0.001000	0.12720	0.024000	0.17045	0.005000	0.04900	0.222000	0.17699	0.070000	0.16634	0.460000	0.39030	GCT	C|0.811;A|0.189	0.189	strong		0.527	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
VWA8	23078	hgsc.bcm.edu	37	13	42442546	42442546	+	Missense_Mutation	SNP	A	A	G	rs3742262	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:42442546A>G	ENST00000379310.3	-	10	1216	c.1148T>C	c.(1147-1149)aTg>aCg	p.M383T	VWA8_ENST00000281496.6_Missense_Mutation_p.M383T	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	383			M -> T (in dbSNP:rs3742262). {ECO:0000269|PubMed:17974005}.			extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										ATGGTTTTCCATCATCTTCTC	0.358													A|||	1113	0.222244	0.056	0.3026	5008	,	,		17551	0.1895		0.3231	False		,,,				2504	0.32				p.M383T		Atlas-SNP	.											.	.	.	.	0			c.T1148C						PASS	.	A	THR/MET,THR/MET	381,4025	191.2+/-216.9	10,361,1832	145.0	130.0	135.0		1148,1148	0.9	0.0	13	dbSNP_107	135	2773,5827	440.8+/-359.6	453,1867,1980	yes	missense,missense	KIAA0564	NM_001009814.1,NM_015058.1	81,81	463,2228,3812	GG,GA,AA		32.2442,8.6473,24.2503	benign,benign	383/1040,383/1906	42442546	3154,9852	2203	4300	6503	SO:0001583	missense	23078	exon10			TTTTCCATCATCT	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1148T>C	13.37:g.42442546A>G	ENSP00000368612:p.Met383Thr	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	263	186	0.707224	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	523	0.23946886446886448	32	0.06504065040650407	116	0.32044198895027626	121	0.21153846153846154	254	0.33509234828496043	A	0.004	-2.267391	0.00259	0.086473	0.322442	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496;ENST00000398857	T;T	0.10192	3.09;2.9	4.63	0.953	0.19590	.	0.927533	0.09044	N	0.856935	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47611	-0.9104	9	0.13853	T	0.58	.	5.1762	0.15137	0.2184:0.0:0.4149:0.3667	rs3742262;rs17534800;rs60079135;rs3742262	383	A3KMH1	K0564_HUMAN	T	287;383;383;383	ENSP00000368612:M383T;ENSP00000281496:M383T	ENSP00000251030:M287T	M	-	2	0	KIAA0564	41340546	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.140000	0.16056	0.025000	0.15241	-0.147000	0.13772	ATG	A|0.760;G|0.240	0.240	strong		0.358	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
ZNF717	100131827	hgsc.bcm.edu	37	3	75790797	75790797	+	De_novo_Start_InFrame	SNP	C	C	T	rs147946451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:75790797C>T	ENST00000478296.1	-	0	274				ZNF717_ENST00000400845.3_Missense_Mutation_p.V43M|ZNF717_ENST00000477374.1_Missense_Mutation_p.V50M|ZNF717_ENST00000491507.1_5'UTR|ZNF717_ENST00000422325.1_Missense_Mutation_p.V50M			Q9BY31	ZN717_HUMAN	zinc finger protein 717						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)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TCCAGCATCACGTCCCTGTAC	0.502																																					p.V50M		Atlas-SNP	.											ZNF717,NS,malignant_melanoma,0,1	ZNF717	160	1	0			c.G148A						scavenged	.						16.0	13.0	14.0					3																	75790797		444	1237	1681			100131827	exon3			GCATCACGTCCCT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965		3.37:g.75790797C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	27	4	0.148148	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		562	0.2573260073260073	83	0.16869918699186992	111	0.30662983425414364	134	0.23426573426573427	234	0.3087071240105541	.	14.80	2.645039	0.47258	.	.	ENSG00000227124	ENST00000477374;ENST00000422325;ENST00000400845;ENST00000468296	T;T;T;T	0.04015	3.73;3.73;3.73;3.73	1.97	1.97	0.26223	.	.	.	.	.	T	0.00012	0.0000	M	0.92833	3.35	0.36926	P	0.10836100000000004	D	0.89917	1.0	D	0.64776	0.929	T	0.22417	-1.0217	8	0.72032	D	0.01	.	9.6897	0.40120	0.0:1.0:0.0:0.0	.	50	C9JSV9	.	M	50;50;43;50	ENSP00000417902:V50M;ENSP00000409514:V50M;ENSP00000383643:V43M;ENSP00000418187:V50M	ENSP00000383643:V43M	V	-	1	0	ZNF717	75873487	0.243000	0.23878	0.981000	0.43875	0.552000	0.35366	1.184000	0.32053	1.127000	0.42034	0.545000	0.68477	GTG	C|0.753;T|0.247	0.247	strong		0.502	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
MUC16	94025	hgsc.bcm.edu	37	19	9083174	9083174	+	Missense_Mutation	SNP	G	G	A	rs7245960	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9083174G>A	ENST00000397910.4	-	1	8844	c.8641C>T	c.(8641-8643)Cca>Tca	p.P2881S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2881	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCCCAAGTTGGGGGAGCTGTA	0.527													G|||	1135	0.226637	0.2708	0.2983	5008	,	,		21319	0.0228		0.3111	False		,,,				2504	0.2393				p.P2881S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C8641T						PASS	.	G	SER/PRO	1025,2837		145,735,1051	65.0	61.0	62.0		8641	-1.5	0.0	19	dbSNP_116	62	2725,5561		461,1803,1879	yes	missense	MUC16	NM_024690.2	74	606,2538,2930	AA,AG,GG		32.8868,26.5407,30.8693	benign	2881/14508	9083174	3750,8398	1931	4143	6074	SO:0001583	missense	94025	exon1			AAGTTGGGGGAGC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8641C>T	19.37:g.9083174G>A	ENSP00000381008:p.Pro2881Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	181	87	0.480663	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	490	0.22435897435897437	127	0.258130081300813	111	0.30662983425414364	14	0.024475524475524476	238	0.31398416886543534	g	0.010	-1.770807	0.00645	0.265407	0.328868	ENSG00000181143	ENST00000397910	T	0.03124	4.04	0.773	-1.55	0.08558	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.48281	-0.9049	8	0.87932	D	0	.	3.4546	0.07511	0.2113:0.0:0.551:0.2378	rs7245960;rs7245960	2881	B5ME49	.	S	2881	ENSP00000381008:P2881S	ENSP00000381008:P2881S	P	-	1	0	MUC16	8944174	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.153000	0.03169	-2.439000	0.00551	-2.281000	0.00270	CCA	G|0.757;A|0.243	0.243	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
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 GAIIx	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_ENST00000166534.4_Silent_p.V410V|P4HA2_ENST00000379100.2_Silent_p.V410V|P4HA2_ENST00000360568.3_Silent_p.V410V|P4HA2_ENST00000379086.1_Silent_p.V410V|P4HA2_ENST00000379104.2_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		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	136	64	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	
PRR32	100130613	hgsc.bcm.edu	37	X	125954964	125954964	+	Missense_Mutation	SNP	C	C	G	rs12835991		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:125954964C>G	ENST00000371125.3	+	2	423	c.343C>G	c.(343-345)Ctg>Gtg	p.L115V		NM_001122716.1	NP_001116188.1	B1ATL7	PRR32_HUMAN		115			L -> V (in dbSNP:rs12835991).														CTCTGATGCACTGGCAGGCTG	0.547													C|||	189	0.0500662	0.0227	0.0303	3775	,	,		13540	0.001		0.0706	False		,,,				2504	0.0675				p.L115V		Atlas-SNP	.											.	.	.	.	0			c.C343G						PASS	.	C	VAL/LEU	51,1158		1,42,7,474,168	31.0	27.0	28.0		343	-0.8	0.0	X	dbSNP_121	28	212,2179		5,135,67,660,724	yes	missense	CXorf64	NM_001122716.1	32	6,177,74,1134,892	GG,GC,G,CC,C		8.8666,4.2184,7.3056	possibly-damaging	115/299	125954964	263,3337	692	1591	2283	SO:0001583	missense	100130613	exon2			GATGCACTGGCAG																												ENST00000371125.3:c.343C>G	X.37:g.125954964C>G	ENSP00000360166:p.Leu115Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	89	61	0.685393	NM_001122716		Missense_Mutation	SNP	ENST00000371125.3	37	CCDS48163.1	90	0.054249547920433995	11	0.02301255230125523	12	0.03389830508474576	0	0.0	36	0.05013927576601671	C	6.120	0.390313	0.11581	0.042184	0.088666	ENSG00000183631	ENST00000371125	T	0.39229	1.09	4.01	-0.763	0.11030	.	0.355410	0.16216	N	0.224251	T	0.01695	0.0054	L	0.32530	0.975	0.80722	P	0.0	D	0.54047	0.964	P	0.55260	0.772	T	0.16247	-1.0409	9	0.40728	T	0.16	-0.2952	7.3865	0.26884	0.0:0.4272:0.0:0.5728	rs12835991	115	B1ATL7	CX064_HUMAN	V	115	ENSP00000360166:L115V	ENSP00000360166:L115V	L	+	1	2	CXorf64	125782645	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-1.032000	0.03574	-0.335000	0.08451	-0.928000	0.02712	CTG	C|0.945;G|0.055	0.055	strong		0.547	CXorf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058188.1		
LRP6	4040	hgsc.bcm.edu	37	12	12334006	12334006	+	Silent	SNP	G	G	C	rs10082834	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:12334006G>C	ENST00000261349.4	-	6	1420	c.1344C>G	c.(1342-1344)ccC>ccG	p.P448P	LRP6_ENST00000543091.1_Silent_p.P448P	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	448	Beta-propeller 2.				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)				CAATAGCCCGGGGTTCCTCTA	0.428													.|||	244	0.048722	0.0212	0.147	5008	,	,		20171	0.002		0.0815	False		,,,				2504	0.0307				p.P448P		Atlas-SNP	.											.	LRP6	170	.	0			c.C1344G						PASS	.	G		168,4238	109.1+/-147.4	4,160,2039	68.0	66.0	66.0		1344	2.8	1.0	12	dbSNP_119	66	777,7821	180.3+/-229.3	40,697,3562	no	coding-synonymous	LRP6	NM_002336.2		44,857,5601	CC,CG,GG		9.037,3.813,7.267		448/1614	12334006	945,12059	2203	4299	6502	SO:0001819	synonymous_variant	4040	exon6			AGCCCGGGGTTCC	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.1344C>G	12.37:g.12334006G>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_002336	Q17RZ2	Silent	SNP	ENST00000261349.4	37	CCDS8647.1																																																																																			G|0.935;C|0.065	0.065	strong		0.428	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
FRMD3	257019	hgsc.bcm.edu	37	9	85863091	85863091	+	Silent	SNP	A	A	G	rs10114696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:85863091A>G	ENST00000304195.3	-	14	1742	c.1536T>C	c.(1534-1536)taT>taC	p.Y512Y	FRMD3_ENST00000465485.1_5'UTR|FRMD3_ENST00000376434.1_Silent_p.Y318Y|FRMD3_ENST00000328788.1_Silent_p.Y169Y|FRMD3_ENST00000376438.1_Silent_p.Y512Y	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	512						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						TCAGAATGTCATAGCTCCACG	0.507													.|||	1404	0.280351	0.1415	0.2767	5008	,	,		19160	0.2014		0.3936	False		,,,				2504	0.4356				p.Y512Y		Atlas-SNP	.											.	FRMD3	96	.	0			c.T1536C						PASS	.	A		696,3268		61,574,1347	80.0	83.0	82.0		1536	4.6	1.0	9	dbSNP_119	82	3451,4897		728,1995,1451	no	coding-synonymous	FRMD3	NM_174938.4		789,2569,2798	GG,GA,AA		41.3392,17.558,33.6826		512/598	85863091	4147,8165	1982	4174	6156	SO:0001819	synonymous_variant	257019	exon14			AATGTCATAGCTC	AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159			24125	protein-coding gene	gene with protein product		607619				12601556	Standard	NM_174938		Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.1536T>C	9.37:g.85863091A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_174938	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	Silent	SNP	ENST00000304195.3	37	CCDS43840.1																																																																																			A|0.685;G|0.315	0.315	strong		0.507	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157355.1	NM_174938	
ROS1	6098	hgsc.bcm.edu	37	6	117683821	117683821	+	Missense_Mutation	SNP	G	G	A	rs2229079	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:117683821G>A	ENST00000368508.3	-	21	3524	c.3326C>T	c.(3325-3327)tCa>tTa	p.S1109L	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Missense_Mutation_p.S1104L	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1109	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> L (in dbSNP:rs2229079). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		AGACATCACTGAGGGAGTGAC	0.368			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								G|||	249	0.0497204	0.025	0.0403	5008	,	,		17334	0.003		0.0924	False		,,,				2504	0.0941				p.S1109L		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.C3326T						PASS	.	G	LEU/SER	229,4177	135.7+/-171.8	6,217,1980	129.0	121.0	124.0		3326	4.1	0.6	6	dbSNP_98	124	764,7836	181.9+/-230.5	44,676,3580	yes	missense	ROS1	NM_002944.2	145	50,893,5560	AA,AG,GG		8.8837,5.1975,7.6349	possibly-damaging	1109/2348	117683821	993,12013	2203	4300	6503	SO:0001583	missense	6098	exon21			ATCACTGAGGGAG	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.3326C>T	6.37:g.117683821G>A	ENSP00000357494:p.Ser1109Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	114	0.0521978021978022	15	0.03048780487804878	18	0.049723756906077346	2	0.0034965034965034965	79	0.10422163588390501	G	12.28	1.889490	0.33348	0.051975	0.088837	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.59224	0.28;0.28	5.03	4.14	0.48551	.	0.350015	0.24803	N	0.035467	T	0.35008	0.0917	M	0.62723	1.935	0.22940	N	0.998533	B	0.15719	0.014	B	0.19666	0.026	T	0.35549	-0.9784	10	0.52906	T	0.07	.	8.8243	0.35045	0.0804:0.1527:0.7669:0.0	rs2229079;rs59204588;rs2229079	1109	P08922	ROS1_HUMAN	L	1109;1104	ENSP00000357494:S1109L;ENSP00000357493:S1104L	ENSP00000357493:S1104L	S	-	2	0	ROS1	117790514	0.227000	0.23707	0.636000	0.29352	0.741000	0.42261	2.689000	0.46993	1.404000	0.46819	0.655000	0.94253	TCA	G|0.939;A|0.061	0.061	strong		0.368	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
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 GAIIx	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	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	67	39	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	
TOPORS	10210	hgsc.bcm.edu	37	9	32541532	32541532	+	Silent	SNP	A	A	G	rs12348918	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:32541532A>G	ENST00000360538.2	-	3	3107	c.2991T>C	c.(2989-2991)gaT>gaC	p.D997D	TOPORS_ENST00000379858.1_Silent_p.D932D	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	997					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D997D(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		CTTCTCTTACATCGAGAGTTT	0.423													A|||	572	0.114217	0.093	0.1412	5008	,	,		20493	0.0079		0.2545	False		,,,				2504	0.089				p.D997D		Atlas-SNP	.											TOPORS_ENST00000360538,NS,carcinoma,0,2	TOPORS	127	2	1	Substitution - coding silent(1)	prostate(1)	c.T2991C						PASS	.	A	,	551,3855	248.4+/-256.2	34,483,1686	164.0	158.0	160.0		2796,2991	3.1	1.0	9	dbSNP_120	160	2111,6489	363.7+/-333.3	260,1591,2449	no	coding-synonymous,coding-synonymous	TOPORS	NM_001195622.1,NM_005802.4	,	294,2074,4135	GG,GA,AA		24.5465,12.5057,20.4675	,	932/981,997/1046	32541532	2662,10344	2203	4300	6503	SO:0001819	synonymous_variant	10210	exon3			TCTTACATCGAGA	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2991T>C	9.37:g.32541532A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	113	44	0.389381	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Silent	SNP	ENST00000360538.2	37	CCDS6527.1																																																																																			A|0.832;G|0.168	0.168	strong		0.423	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
C6orf15	29113	hgsc.bcm.edu	37	6	31079371	31079371	+	Silent	SNP	C	C	G	rs2233983	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31079371C>G	ENST00000259870.3	-	2	768	c.765G>C	c.(763-765)cgG>cgC	p.R255R		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	255	Gly-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						CTCCTGGATACCGATTAATAT	0.527													C|||	521	0.104034	0.0068	0.0994	5008	,	,		16226	0.2361		0.0785	False		,,,				2504	0.1288				p.R255R		Atlas-SNP	.											.	C6orf15	29	.	0			c.G765C						PASS	.	C		52,3420		0,52,1684	56.0	66.0	62.0		765	-4.2	0.0	6	dbSNP_98	62	449,6123		19,411,2856	no	coding-synonymous	C6orf15	NM_014070.2		19,463,4540	GG,GC,CC		6.832,1.4977,4.9881		255/326	31079371	501,9543	1736	3286	5022	SO:0001819	synonymous_variant	29113	exon2			TGGATACCGATTA	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.765G>C	6.37:g.31079371C>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	128	18	0.140625	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			C|0.932;G|0.068	0.068	strong		0.527	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
ICAM5	7087	hgsc.bcm.edu	37	19	10403368	10403368	+	Missense_Mutation	SNP	G	G	A	rs2228615	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10403368G>A	ENST00000221980.4	+	5	1105	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	348	Ig-like C2-type 4.		A -> T (in dbSNP:rs2228615). {ECO:0000269|PubMed:8995416}.		phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CGCAGCTGGGGCCCAAGCTCT	0.657													G|||	1449	0.289337	0.0439	0.5202	5008	,	,		15041	0.2371		0.4066	False		,,,				2504	0.3906				p.A348T		Atlas-SNP	.											.	ICAM5	53	.	0			c.G1042A	GRCh37	CM065278	ICAM5	M	rs2228615	PASS	.	G	THR/ALA	437,3969	208.2+/-229.3	19,399,1785	40.0	39.0	39.0		1042	-0.8	0.0	19	dbSNP_98	39	3346,5254	493.3+/-373.5	664,2018,1618	yes	missense	ICAM5	NM_003259.3	58	683,2417,3403	AA,AG,GG		38.907,9.9183,29.0866	benign	348/925	10403368	3783,9223	2203	4300	6503	SO:0001583	missense	7087	exon5			GCTGGGGCCCAAG	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1042G>A	19.37:g.10403368G>A	ENSP00000221980:p.Ala348Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_003259	Q9Y6F3	Missense_Mutation	SNP	ENST00000221980.4	37	CCDS12233.1	643	0.2944139194139194	11	0.022357723577235773	175	0.48342541436464087	145	0.2534965034965035	312	0.41160949868073876	G	12.92	2.082357	0.36758	0.099183	0.38907	ENSG00000105376	ENST00000221980	T	0.12672	2.66	5.61	-0.808	0.10868	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.562319	0.17184	N	0.183799	T	0.00012	0.0000	L	0.55743	1.74	0.80722	P	0.0	B	0.09022	0.002	B	0.09377	0.004	T	0.43410	-0.9393	9	0.49607	T	0.09	-7.5346	5.0792	0.14647	0.2826:0.3719:0.3454:0.0	rs2228615;rs17856760;rs56676893;rs2228615	348	Q9UMF0	ICAM5_HUMAN	T	348	ENSP00000221980:A348T	ENSP00000221980:A348T	A	+	1	0	ICAM5	10264368	0.000000	0.05858	0.001000	0.08648	0.579000	0.36224	-1.124000	0.03260	0.041000	0.15688	0.561000	0.74099	GCC	G|0.713;A|0.287	0.287	strong		0.657	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
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 GAIIx	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		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	196	141	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	
EVPLL	645027	hgsc.bcm.edu	37	17	18291559	18291559	+	Silent	SNP	T	T	C	rs9890369	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18291559T>C	ENST00000399134.4	+	10	1261	c.903T>C	c.(901-903)caT>caC	p.H301H	EVPLL_ENST00000583003.1_3'UTR|RP1-37N7.1_ENST00000579352.1_RNA	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	301										NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						CCTCTCCTCATTGACTCTGCA	0.463													.|||	1328	0.265176	0.4342	0.2032	5008	,	,		12834	0.1637		0.1849	False		,,,				2504	0.2679				p.H301H		Atlas-SNP	.											EVPLL,NS,NS,+2,1	EVPLL	10	1	0			c.T903C						PASS	.	T		503,881		91,321,280	73.0	63.0	66.0		903	0.1	0.0	17	dbSNP_119	66	659,2523		64,531,996	no	coding-synonymous	EVPLL	NM_001145127.1		155,852,1276	CC,CT,TT		20.7102,36.3439,25.449		301/302	18291559	1162,3404	692	1591	2283	SO:0001819	synonymous_variant	645027	exon10			TCCTCATTGACTC		CCDS45626.1	17p11.2	2009-08-25			ENSG00000214860	ENSG00000214860			35236	protein-coding gene	gene with protein product							Standard	NM_001145127		Approved		uc002gte.3	A8MZ36	OTTHUMG00000059095	ENST00000399134.4:c.903T>C	17.37:g.18291559T>C		Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	256	138	0.539062	NM_001145127	B4DPD4	Silent	SNP	ENST00000399134.4	37	CCDS45626.1																																																																																			T|0.770;C|0.230	0.230	strong		0.463	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127	
PER2	8864	hgsc.bcm.edu	37	2	239165636	239165636	+	Silent	SNP	C	C	T	rs2304670	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:239165636C>T	ENST00000254657.3	-	17	2271	c.1992G>A	c.(1990-1992)gcG>gcA	p.A664A	AC096574.4_ENST00000456601.1_RNA|PER2_ENST00000254658.3_3'UTR	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	664	CSNK1E binding domain. {ECO:0000250}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|fatty acid metabolic process (GO:0006631)|gluconeogenesis (GO:0006094)|glycogen biosynthetic process (GO:0005978)|histone H3 deacetylation (GO:0070932)|lactate biosynthetic process (GO:0019249)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of DNA-templated transcription, termination (GO:0060567)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of glutamate uptake involved in transmission of nerve impulse (GO:0051946)|regulation of insulin secretion (GO:0050796)|regulation of neurogenesis (GO:0050767)|regulation of vasoconstriction (GO:0019229)|response to ischemia (GO:0002931)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	pre-mRNA binding (GO:0036002)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding transcription factor activity (GO:0000989)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|ubiquitin binding (GO:0043130)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0423)|all_lung(227;0.114)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Lung NSC(271;0.223)|Hepatocellular(293;0.244)		Epithelial(121;6.84e-24)|OV - Ovarian serous cystadenocarcinoma(60;9.73e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;6.77e-05)|Lung(119;0.00941)|LUSC - Lung squamous cell carcinoma(224;0.0161)		TGGTGAGCGACGCCACACTCT	0.617											OREG0015336	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	468	0.0934505	0.1089	0.0605	5008	,	,		14426	0.0585		0.1024	False		,,,				2504	0.1227				p.A664A		Atlas-SNP	.											.	PER2	85	.	0			c.G1992A						PASS	.	C		455,3951	221.3+/-238.5	21,413,1769	84.0	82.0	83.0		1992	0.5	1.0	2	dbSNP_100	83	774,7826	183.5+/-231.7	29,716,3555	no	coding-synonymous	PER2	NM_022817.2		50,1129,5324	TT,TC,CC		9.0,10.3268,9.4495		664/1256	239165636	1229,11777	2203	4300	6503	SO:0001819	synonymous_variant	8864	exon17			GAGCGACGCCACA	AB002345	CCDS2528.1	2q37.3	2012-12-13	2012-12-13		ENSG00000132326	ENSG00000132326			8846	protein-coding gene	gene with protein product		603426	"""period (Drosophila) homolog 2"", ""period homolog 2 (Drosophila)"""			9427249, 17218255	Standard	NM_022817		Approved	KIAA0347	uc002vyc.3	O15055	OTTHUMG00000152884	ENST00000254657.3:c.1992G>A	2.37:g.239165636C>T		Somatic	73	0	0	2409	WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Silent	SNP	ENST00000254657.3	37	CCDS2528.1																																																																																			C|0.913;T|0.087	0.087	strong		0.617	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817	
SERPINA6	866	hgsc.bcm.edu	37	14	94772429	94772429	+	Silent	SNP	G	G	A	rs2228543	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94772429G>A	ENST00000341584.3	-	4	1157	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	337					glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	TCAGCTGGGCGTCCTGGGTGA	0.468													G|||	770	0.153754	0.3343	0.0965	5008	,	,		22300	0.0069		0.1531	False		,,,				2504	0.1022				p.D337D		Atlas-SNP	.											SERPINA6_ENST00000341584,NS,carcinoma,-2,2	SERPINA6	102	2	0			c.C1011T						PASS	.	G		1457,2949	470.7+/-355.8	247,963,993	136.0	122.0	127.0		1011	-4.2	0.0	14	dbSNP_98	127	1226,7374	246.9+/-275.2	86,1054,3160	no	coding-synonymous	SERPINA6	NM_001756.3		333,2017,4153	AA,AG,GG		14.2558,33.0685,20.6289		337/406	94772429	2683,10323	2203	4300	6503	SO:0001819	synonymous_variant	866	exon4			CTGGGCGTCCTGG	J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"""Serine (or cysteine) peptidase inhibitors"""	1540	protein-coding gene	gene with protein product	"""corticosteroid binding globulin"", ""transcortin"""	122500	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"""	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.1011C>T	14.37:g.94772429G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_001756	A8K456|Q7Z2Q9	Silent	SNP	ENST00000341584.3	37	CCDS9924.1																																																																																			G|0.677;T|0.043	.	strong		0.468	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756	
CDH23	64072	hgsc.bcm.edu	37	10	73562744	73562744	+	Silent	SNP	G	G	A	rs10823849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73562744G>A	ENST00000224721.6	+	53	7592	c.7587G>A	c.(7585-7587)gcG>gcA	p.A2529A	CDH23_ENST00000398788.3_Silent_p.A284A|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2524	Cadherin 24. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.A2529A(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ATGAGCCGGCGGGCACCTCGG	0.577													G|||	1645	0.328474	0.2307	0.3444	5008	,	,		20495	0.5298		0.2783	False		,,,				2504	0.2935				p.A2524A		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - coding silent(1)	stomach(1)	c.G7572A						scavenged	.	G	,,	904,3136		96,712,1212	69.0	73.0	72.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	852,852,7572	-10.0	0.4	10	dbSNP_120	72	2180,6174		306,1568,2303	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171933.1,NM_001171934.1,NM_022124.5	,,	402,2280,3515	AA,AG,GG		26.0953,22.3762,24.883	,,	284/1115,284/1080,2524/3355	73562744	3084,9310	2020	4177	6197	SO:0001819	synonymous_variant	64072	exon52			GCCGGCGGGCACC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.7587G>A	10.37:g.73562744G>A		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				G|0.681;A|0.319	0.319	strong		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
CFH	3075	hgsc.bcm.edu	37	1	196695742	196695742	+	Silent	SNP	A	A	G	rs3753396	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196695742A>G	ENST00000367429.4	+	13	2256	c.2016A>G	c.(2014-2016)caA>caG	p.Q672Q		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	672	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)			NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ATAAAATTCAATGTGTTGATG	0.299													A|||	1016	0.202875	0.0378	0.1916	5008	,	,		15851	0.5099		0.1759	False		,,,				2504	0.1452				p.Q672Q		Atlas-SNP	.											CFH,NS,carcinoma,+2,3	CFH	251	3	0			c.A2016G	GRCh37	CM033783	CFH	M	rs3753396	PASS	.	A		293,4113	159.2+/-191.8	10,273,1920	95.0	98.0	97.0		2016	-2.2	0.9	1	dbSNP_107	97	1488,7112	281.7+/-295.2	140,1208,2952	no	coding-synonymous	CFH	NM_000186.3		150,1481,4872	GG,GA,AA		17.3023,6.65,13.6937		672/1232	196695742	1781,11225	2203	4300	6503	SO:0001819	synonymous_variant	3075	exon13			AATTCAATGTGTT	Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2016A>G	1.37:g.196695742A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000367429.4	37	CCDS1385.1																																																																																			A|0.777;G|0.223	0.223	strong		0.299	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
CFAP61	26074	hgsc.bcm.edu	37	20	20257958	20257958	+	Silent	SNP	C	C	T	rs2424317	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:20257958C>T	ENST00000245957.5	+	22	2728	c.2652C>T	c.(2650-2652)agC>agT	p.S884S	C20orf26_ENST00000377309.2_Silent_p.S240S	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		884										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		CGGTGGAGAGCGCCGTGGCGG	0.652													C|||	671	0.133986	0.0976	0.2089	5008	,	,		15156	0.004		0.2296	False		,,,				2504	0.1656				p.S884S		Atlas-SNP	.											.	C20orf26	188	.	0			c.C2652T						PASS	.	C		562,3844	251.2+/-258.0	39,484,1680	57.0	57.0	57.0		2652	-8.6	0.0	20	dbSNP_100	57	2112,6488	363.5+/-333.2	258,1596,2446	no	coding-synonymous	C20orf26	NM_015585.3		297,2080,4126	TT,TC,CC		24.5581,12.7553,20.5597		884/1238	20257958	2674,10332	2203	4300	6503	SO:0001819	synonymous_variant	26074	exon22			GGAGAGCGCCGTG																												ENST00000245957.5:c.2652C>T	20.37:g.20257958C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Silent	SNP	ENST00000245957.5	37	CCDS33447.1																																																																																			C|0.824;T|0.176	0.176	strong		0.652	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
BTBD10	84280	hgsc.bcm.edu	37	11	13441126	13441126	+	Silent	SNP	A	A	G	rs7114113	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:13441126A>G	ENST00000278174.5	-	4	710	c.465T>C	c.(463-465)aaT>aaC	p.N155N	BTBD10_ENST00000530907.1_Silent_p.N163N|BTBD10_ENST00000532261.1_5'UTR|BTBD10_ENST00000528120.1_Silent_p.N107N	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	155	Interaction with AKT family members. {ECO:0000250|UniProtKB:Q80X66}.					nucleus (GO:0005634)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		CTTCTTTTGCATTTTCATATA	0.428													A|||	742	0.148163	0.084	0.3012	5008	,	,		16577	0.1687		0.1481	False		,,,				2504	0.1053				p.N155N		Atlas-SNP	.											.	BTBD10	43	.	0			c.T465C						PASS	.	A		379,4021	191.6+/-217.2	19,341,1840	238.0	229.0	232.0		465	4.2	1.0	11	dbSNP_116	232	1493,7095	284.4+/-296.6	117,1259,2918	no	coding-synonymous	BTBD10	NM_032320.5		136,1600,4758	GG,GA,AA		17.3847,8.6136,14.4133		155/476	13441126	1872,11116	2200	4294	6494	SO:0001819	synonymous_variant	84280	exon4			TTTTGCATTTTCA	AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"""BTB/POZ domain containing"""	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.465T>C	11.37:g.13441126A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	171	85	0.497076	NM_032320	B7Z228|Q86WG1	Silent	SNP	ENST00000278174.5	37	CCDS7811.1																																																																																			A|0.855;G|0.145	0.145	strong		0.428	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
NDUFS2	4720	hgsc.bcm.edu	37	1	161182208	161182208	+	Missense_Mutation	SNP	C	C	G	rs11576415	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161182208C>G	ENST00000367993.3	+	11	1502	c.1054C>G	c.(1054-1056)Cct>Gct	p.P352A	NDUFS2_ENST00000465923.1_3'UTR|FCER1G_ENST00000367992.3_5'Flank|NDUFS2_ENST00000392179.4_Missense_Mutation_p.P352A|FCER1G_ENST00000289902.1_5'Flank	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	352			P -> A (in dbSNP:rs11576415).		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NAD binding (GO:0051287)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|quinone binding (GO:0048038)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|prostate(1)|skin(1)	18	all_cancers(52;1.16e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Doxorubicin(DB00997)	AAACAAGATGCCTCCTGGGGA	0.527													C|||	247	0.0493211	0.0068	0.0317	5008	,	,		17350	0.0099		0.1083	False		,,,				2504	0.0992				p.P352A		Atlas-SNP	.											NDUFS2,lymph_node,lymphoid_neoplasm,0,1	NDUFS2	33	1	0			c.C1054G						PASS	.	C	ALA/PRO,ALA/PRO	80,4326	70.9+/-108.8	2,76,2125	106.0	87.0	93.0		1054,1054	4.9	1.0	1	dbSNP_120	93	813,7787	190.0+/-236.6	40,733,3527	yes	missense,missense	NDUFS2	NM_001166159.1,NM_004550.4	27,27	42,809,5652	GG,GC,CC		9.4535,1.8157,6.8661	probably-damaging,probably-damaging	352/458,352/464	161182208	893,12113	2203	4300	6503	SO:0001583	missense	4720	exon10			AAGATGCCTCCTG	BC008868	CCDS1224.1, CCDS53404.1	1q23.3	2011-07-04	2002-08-29		ENSG00000158864	ENSG00000158864	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7708	protein-coding gene	gene with protein product	"""complex I 49kDa subunit"", ""NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial"""	602985	"""NADH dehydrogenase (ubiquinone) Fe-S protein 2 (49kD) (NADH-coenzyme Q reductase)"""			1832859, 9585441	Standard	NM_004550		Approved	CI-49	uc001fyw.3	O75306	OTTHUMG00000034344	ENST00000367993.3:c.1054C>G	1.37:g.161182208C>G	ENSP00000356972:p.Pro352Ala	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_001166159	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Missense_Mutation	SNP	ENST00000367993.3	37	CCDS1224.1	112	0.05128205128205128	6	0.012195121951219513	14	0.03867403314917127	6	0.01048951048951049	86	0.11345646437994723	C	25.4	4.634647	0.87660	0.018157	0.094535	ENSG00000158864	ENST00000367993;ENST00000392179	D;D	0.90261	-2.64;-2.64	4.86	4.86	0.63082	NADH-quinone oxidoreductase, subunit D (1);	0.000000	0.85682	D	0.000000	D	0.95843	0.8647	M	0.89785	3.06	0.54753	P	1.7000000000044757E-5	D;P;P	0.89917	1.0;0.83;0.83	D;P;P	0.97110	1.0;0.734;0.734	D	0.96599	0.9443	9	0.87932	D	0	.	17.14	0.86750	0.0:1.0:0.0:0.0	rs11576415;rs52789797;rs11576415	301;352;352	B7Z792;Q53HG2;O75306	.;.;NDUS2_HUMAN	A	352	ENSP00000356972:P352A;ENSP00000376018:P352A	ENSP00000356972:P352A	P	+	1	0	NDUFS2	159448832	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.129000	0.77225	2.412000	0.81896	0.650000	0.86243	CCT	C|0.937;G|0.063	0.063	strong		0.527	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550	
TEX15	56154	hgsc.bcm.edu	37	8	30702525	30702525	+	Missense_Mutation	SNP	A	A	C	rs323344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:30702525A>C	ENST00000256246.2	-	1	4083	c.4009T>G	c.(4009-4011)Tta>Gta	p.L1337V		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1337			L -> V (in dbSNP:rs323344). {ECO:0000269|PubMed:11279525}.		fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		GCGGCTGATAACTGAGGAATA	0.383													A|||	1635	0.326478	0.8449	0.1571	5008	,	,		20923	0.0704		0.1272	False		,,,				2504	0.2147				p.L1337V		Atlas-SNP	.											.	TEX15	350	.	0			c.T4009G						PASS	.	A	VAL/LEU	3181,1225	696.4+/-406.1	1153,875,175	115.0	130.0	125.0		4009	3.6	0.0	8	dbSNP_79	125	1010,7588	214.8+/-254.3	66,878,3355	yes	missense	TEX15	NM_031271.3	32	1219,1753,3530	CC,CA,AA		11.7469,27.803,32.2285	possibly-damaging	1337/2790	30702525	4191,8813	2203	4299	6502	SO:0001583	missense	56154	exon1			CTGATAACTGAGG	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.4009T>G	8.37:g.30702525A>C	ENSP00000256246:p.Leu1337Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	604	0.2765567765567766	411	0.8353658536585366	61	0.1685082872928177	39	0.06818181818181818	93	0.12269129287598944	A	9.942	1.217641	0.22373	0.72197	0.117469	ENSG00000133863	ENST00000256246	T	0.23552	1.9	6.07	3.57	0.40892	.	0.794140	0.11065	N	0.603508	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.37122	0.583	B	0.34652	0.187	T	0.12863	-1.0531	9	0.87932	D	0	.	6.4494	0.21896	0.7626:0.1567:0.0807:0.0	rs323344;rs52799274;rs59808187;rs323344	1337	Q9BXT5	TEX15_HUMAN	V	1337	ENSP00000256246:L1337V	ENSP00000256246:L1337V	L	-	1	2	TEX15	30822067	0.008000	0.16893	0.000000	0.03702	0.019000	0.09904	0.681000	0.25320	0.465000	0.27167	0.533000	0.62120	TTA	A|0.701;C|0.299	0.299	strong		0.383	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
CEP192	55125	hgsc.bcm.edu	37	18	13069782	13069782	+	Missense_Mutation	SNP	C	C	T	rs6505780	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:13069782C>T	ENST00000325971.8	+	25	4906	c.3313C>T	c.(3313-3315)Ctc>Ttc	p.L1105F	CEP192_ENST00000506447.1_Missense_Mutation_p.L1701F|CEP192_ENST00000430049.2_Missense_Mutation_p.L1226F			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1105			L -> F (in dbSNP:rs6505780). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12693554, ECO:0000269|PubMed:15498874}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						AAAGAATCTACTCCTTAAACC	0.368													T|||	3857	0.770168	0.9486	0.6455	5008	,	,		22039	0.8105		0.6193	False		,,,				2504	0.7311				p.L1701F		Atlas-SNP	.											.	CEP192	340	.	0			c.C5101T						PASS	.	T	PHE/LEU	3886,520	236.8+/-248.8	1713,460,30	102.0	105.0	104.0		5101	5.5	0.6	18	dbSNP_116	104	5329,3271	490.5+/-372.9	1664,2001,635	yes	missense	CEP192	NM_032142.3	22	3377,2461,665	TT,TC,CC		38.0349,11.8021,29.1481	benign	1701/2538	13069782	9215,3791	2203	4300	6503	SO:0001583	missense	55125	exon27			AATCTACTCCTTA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.3313C>T	18.37:g.13069782C>T	ENSP00000317156:p.Leu1105Phe	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	52	22	0.423077	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1635	0.7486263736263736	461	0.9369918699186992	238	0.6574585635359116	464	0.8111888111888111	472	0.6226912928759895	T	2.206	-0.381800	0.04966	0.881979	0.619651	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.42900	0.96;0.96;0.96	5.47	5.47	0.80525	.	0.062950	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00263	-1.745	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40646	-0.9552	9	0.02654	T	1	-10.6382	10.4557	0.44548	0.0:0.0773:0.0:0.9227	rs6505780;rs17660946;rs59425635;rs6505780	1226;1701;303	C9JT09;E9PF99;Q9HCK3	.;.;.	F	1701;1105;1105;1226	ENSP00000427550:L1701F;ENSP00000317156:L1105F;ENSP00000389190:L1226F	ENSP00000317156:L1105F	L	+	1	0	CEP192	13059782	0.968000	0.33430	0.621000	0.29145	0.743000	0.42351	2.323000	0.43823	0.927000	0.37143	-0.361000	0.07541	CTC	C|0.258;T|0.742	0.742	strong		0.368	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
SERPINB10	5273	hgsc.bcm.edu	37	18	61587067	61587067	+	Missense_Mutation	SNP	C	C	T	rs9967382	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61587067C>T	ENST00000238508.3	+	5	477	c.418C>T	c.(418-420)Cct>Tct	p.P140S		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	140			P -> S (in dbSNP:rs9967382).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				AGAACCTCAGCCTGTTAACTT	0.383													T|||	2258	0.450879	0.767	0.3963	5008	,	,		18282	0.4623		0.2247	False		,,,				2504	0.2832				p.P140S		Atlas-SNP	.											.	SERPINB10	53	.	0			c.C418T						PASS	.	T	SER/PRO	3002,1404	459.8+/-352.4	1012,978,213	72.0	85.0	81.0		418	2.9	0.9	18	dbSNP_119	81	1751,6847	734.6+/-406.9	186,1379,2734	yes	missense	SERPINB10	NM_005024.1	74	1198,2357,2947	TT,TC,CC		20.3652,31.8656,36.5503		140/398	61587067	4753,8251	2203	4299	6502	SO:0001583	missense	5273	exon4			CCTCAGCCTGTTA	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.418C>T	18.37:g.61587067C>T	ENSP00000238508:p.Pro140Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	69	38	0.550725	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	894	0.40934065934065933	354	0.7195121951219512	135	0.3729281767955801	243	0.42482517482517484	162	0.21372031662269128	T	7.093	0.572494	0.13623	0.681344	0.203652	ENSG00000242550	ENST00000238508	D	0.83837	-1.77	5.33	2.88	0.33553	Serpin domain (3);	0.381500	0.27640	N	0.018475	T	0.00012	0.0000	N	0.00339	-1.615	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44697	-0.9311	9	0.10377	T	0.69	.	4.5016	0.11867	0.0:0.1756:0.1663:0.6581	rs9967382;rs52818279;rs60017388;rs9967382	140	P48595	SPB10_HUMAN	S	140	ENSP00000238508:P140S	ENSP00000238508:P140S	P	+	1	0	SERPINB10	59738047	1.000000	0.71417	0.948000	0.38648	0.982000	0.71751	0.684000	0.25364	0.029000	0.15352	-0.254000	0.11334	CCT	C|0.604;N|0.000	.	strong		0.383	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
RCN3	57333	hgsc.bcm.edu	37	19	50046365	50046365	+	Silent	SNP	T	T	C	rs3187346	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50046365T>C	ENST00000270645.3	+	7	1329	c.882T>C	c.(880-882)gaT>gaC	p.D294D		NM_020650.2	NP_065701.2	Q96D15	RCN3_HUMAN	reticulocalbin 3, EF-hand calcium binding domain	294	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.					endoplasmic reticulum (GO:0005783)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0159)		CCCTCCAGGATGGGCGGCTGA	0.592													C|||	493	0.0984425	0.1906	0.072	5008	,	,		17537	0.0258		0.0835	False		,,,				2504	0.0828				p.D294D		Atlas-SNP	.											.	RCN3	28	.	0			c.T882C						PASS	.	C		780,3626	752.4+/-412.3	61,658,1484	63.0	52.0	56.0		882	-7.5	0.3	19	dbSNP_105	56	655,7945	789.4+/-407.6	22,611,3667	no	coding-synonymous	RCN3	NM_020650.2		83,1269,5151	CC,CT,TT		7.6163,17.7031,11.0334		294/329	50046365	1435,11571	2203	4300	6503	SO:0001819	synonymous_variant	57333	exon7			CCAGGATGGGCGG	AY195859	CCDS12771.1	19q13.33	2013-01-10				ENSG00000142552		"""EF-hand domain containing"""	21145	protein-coding gene	gene with protein product							Standard	NM_020650		Approved	RLP49	uc002poj.3	Q96D15		ENST00000270645.3:c.882T>C	19.37:g.50046365T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_020650	Q9HBZ8	Silent	SNP	ENST00000270645.3	37	CCDS12771.1																																																																																			T|0.895;C|0.105	0.105	strong		0.592	RCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465261.1	NM_020650	
WARS2	10352	hgsc.bcm.edu	37	1	119584949	119584949	+	Silent	SNP	G	G	A	rs33960696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:119584949G>A	ENST00000235521.4	-	4	479	c.453C>T	c.(451-453)caC>caT	p.H151H	WARS2_ENST00000369426.5_Silent_p.H151H|WARS2_ENST00000537870.1_Silent_p.H57H	NM_015836.3|NM_201263.2	NP_056651.1|NP_957715.1	Q9UGM6	SYWM_HUMAN	tryptophanyl tRNA synthetase 2, mitochondrial	151				H -> R (in Ref. 3; BAD96917). {ECO:0000305}.	gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|tryptophanyl-tRNA aminoacylation (GO:0006436)|vasculogenesis (GO:0001570)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|tryptophan-tRNA ligase activity (GO:0004830)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(2)	15	all_neural(166;0.187)	all_lung(203;2.48e-06)|Lung NSC(69;1.74e-05)|all_epithelial(167;0.000564)		Lung(183;0.0629)	L-Tryptophan(DB00150)	CCGTGCCATCGTGCTTCTGCT	0.453													G|||	290	0.0579073	0.0522	0.0403	5008	,	,		16602	0.004		0.0706	False		,,,				2504	0.1207				p.H151H		Atlas-SNP	.											.	WARS2	69	.	0			c.C453T						PASS	.	G	,	215,4191	129.4+/-166.1	4,207,1992	148.0	134.0	139.0		453,453	-11.3	0.0	1	dbSNP_126	139	647,7953	164.8+/-217.1	27,593,3680	no	coding-synonymous,coding-synonymous	WARS2	NM_015836.3,NM_201263.2	,	31,800,5672	AA,AG,GG		7.5233,4.8797,6.6277	,	151/361,151/221	119584949	862,12144	2203	4300	6503	SO:0001819	synonymous_variant	10352	exon4			GCCATCGTGCTTC	BC021722	CCDS900.1, CCDS30817.1	1p12	2011-07-01	2007-02-23		ENSG00000116874	ENSG00000116874	6.1.1.2	"""Aminoacyl tRNA synthetases / Class I"""	12730	protein-coding gene	gene with protein product	"""tryptophan tRNA ligase 2, mitochondrial"""	604733				10072595, 10828066	Standard	NM_201263		Approved	TrpRS	uc001ehn.3	Q9UGM6	OTTHUMG00000012335	ENST00000235521.4:c.453C>T	1.37:g.119584949G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	121	56	0.46281	NM_015836	B1ALR1|B2R9D4|Q53FT4|Q5VUD2|Q86TQ0	Silent	SNP	ENST00000235521.4	37	CCDS900.1																																																																																			G|0.937;A|0.063	0.063	strong		0.453	WARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034362.1	NM_015836	
ZFP64	55734	hgsc.bcm.edu	37	20	50803573	50803573	+	Silent	SNP	G	G	A	rs34351592	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:50803573G>A	ENST00000216923.4	-	2	433	c.84C>T	c.(82-84)ccC>ccT	p.P28P	ZFP64_ENST00000346617.4_Silent_p.P28P|ZFP64_ENST00000371515.4_Silent_p.P26P|ZFP64_ENST00000361387.2_Silent_p.P28P|ZFP64_ENST00000371518.2_Silent_p.P28P	NM_018197.2|NM_199426.1	NP_060667.2|NP_955458.1	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	28					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(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						TATGGATGTCGGGAGTCAGCT	0.512													G|||	846	0.16893	0.3185	0.1643	5008	,	,		19634	0.1736		0.0706	False		,,,				2504	0.0665				p.P28P		Atlas-SNP	.											.	ZFP64	240	.	0			c.C84T						PASS	.	G	,,,	1206,3200	418.5+/-338.3	170,866,1167	66.0	59.0	62.0		84,84,78,84	-10.6	0.1	20	dbSNP_126	62	493,8107	142.0+/-198.3	9,475,3816	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZFP64	NM_018197.2,NM_022088.4,NM_199426.1,NM_199427.2	,,,	179,1341,4983	AA,AG,GG		5.7326,27.3718,13.0632	,,,	28/682,28/628,26/680,28/646	50803573	1699,11307	2203	4300	6503	SO:0001819	synonymous_variant	55734	exon2			GATGTCGGGAGTC	AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000216923.4:c.84C>T	20.37:g.50803573G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_018197	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000216923.4	37	CCDS13440.1																																																																																			G|0.864;A|0.136	0.136	strong		0.512	ZFP64-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079744.1	NM_018197	
RANBP2	5903	hgsc.bcm.edu	37	2	109371498	109371498	+	Silent	SNP	G	G	A	rs373469365	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:109371498G>A	ENST00000283195.6	+	16	2466	c.2340G>A	c.(2338-2340)ccG>ccA	p.P780P		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	780					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						ATTCTACACCGTCTCCTACCA	0.353													G|||	3	0.000599042	0.0008	0.0	5008	,	,		15081	0.001		0.0	False		,,,				2504	0.001				p.P780P		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	0			c.G2340A						scavenged	.						98.0	103.0	101.0					2																	109371498		2198	4282	6480	SO:0001819	synonymous_variant	5903	exon16			TACACCGTCTCCT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2340G>A	2.37:g.109371498G>A		Somatic	241	2	0.00829876		WXS	Illumina HiSeq	Phase_I	276	5	0.0181159	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																			.	.	alt		0.353	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
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 GAIIx	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	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	106	59	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 GAIIx	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	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	186	8	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	
OR13C5	138799	hgsc.bcm.edu	37	9	107361129	107361129	+	Missense_Mutation	SNP	C	C	T	rs4117966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107361129C>T	ENST00000374779.2	-	1	659	c.566G>A	c.(565-567)tGt>tAt	p.C189Y		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	189			C -> Y (in dbSNP:rs4117966).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						GATGTCAGCACAGGCCAGTTT	0.388													C|||	1820	0.363419	0.3994	0.2133	5008	,	,		24769	0.5645		0.1789	False		,,,				2504	0.4039				p.C189Y		Atlas-SNP	.											.	OR13C5	60	.	0			c.G566A						PASS	.	C	TYR/CYS	1567,2839	492.0+/-362.3	283,1001,919	183.0	169.0	173.0		566	4.2	0.3	9	dbSNP_108	173	1660,6940	306.8+/-308.1	182,1296,2822	no	missense	OR13C5	NM_001004482.1	194	465,2297,3741	TT,TC,CC		19.3023,35.5651,24.8116	probably-damaging	189/319	107361129	3227,9779	2203	4300	6503	SO:0001583	missense	138799	exon1			TCAGCACAGGCCA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.566G>A	9.37:g.107361129C>T	ENSP00000363911:p.Cys189Tyr	Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	270	122	0.451852	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	700	0.32051282051282054	174	0.35365853658536583	72	0.19889502762430938	322	0.5629370629370629	132	0.1741424802110818	C	19.12	3.766581	0.69878	0.355651	0.193023	ENSG00000255800	ENST00000374779	T	0.00462	7.26	4.17	4.17	0.49024	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40469	U	0.001090	T	0.00012	0.0000	H	0.97077	3.935	0.28200	P	0.9273963000000001	D	0.89917	1.0	D	0.97110	1.0	T	0.13124	-1.0521	9	0.87932	D	0	.	14.0519	0.64742	0.0:1.0:0.0:0.0	rs4117966;rs52805780;rs57944987;rs4117966	189	Q8NGS8	O13C5_HUMAN	Y	189	ENSP00000363911:C189Y	ENSP00000363911:C189Y	C	-	2	0	OR13C5	106400950	0.971000	0.33674	0.337000	0.25536	0.483000	0.33249	2.706000	0.47135	2.169000	0.68431	0.531000	0.56144	TGT	C|0.726;T|0.274	0.274	strong		0.388	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
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 GAIIx	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		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	138	67	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	
KIAA1614	57710	hgsc.bcm.edu	37	1	180905448	180905448	+	Missense_Mutation	SNP	G	G	T	rs3795504	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:180905448G>T	ENST00000367588.4	+	5	2458	c.2403G>T	c.(2401-2403)ttG>ttT	p.L801F	KIAA1614_ENST00000367587.1_Missense_Mutation_p.L422F	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	801			L -> F (in dbSNP:rs3795504). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039}.							NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CAGCTTCCTTGTGTCCTGAAG	0.612													T|||	2021	0.403554	0.3548	0.428	5008	,	,		19313	0.2748		0.4533	False		,,,				2504	0.5337				p.L801F		Atlas-SNP	.											.	KIAA1614	75	.	0			c.G2403T						PASS	.	T	PHE/LEU	1469,2525		285,899,813	67.0	71.0	69.0		2403	2.4	0.0	1	dbSNP_107	69	3670,4648		807,2056,1296	yes	missense	KIAA1614	NM_020950.1	22	1092,2955,2109	TT,TG,GG		44.1212,36.7802,41.7398	benign	801/1191	180905448	5139,7173	1997	4159	6156	SO:0001583	missense	57710	exon5			TTCCTTGTGTCCT	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2403G>T	1.37:g.180905448G>T	ENSP00000356560:p.Leu801Phe	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	842	0.38553113553113555	181	0.3678861788617886	175	0.48342541436464087	146	0.25524475524475526	340	0.44854881266490765	T	2.589	-0.295649	0.05532	0.367802	0.441212	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.42513	0.97;0.97	4.3	2.38	0.29361	.	0.948451	0.08769	N	0.896507	T	0.00012	0.0000	N	0.11560	0.145	0.20821	P	0.999844	B	0.02656	0.0	B	0.04013	0.001	T	0.48468	-0.9033	9	0.14252	T	0.57	-0.1445	4.419	0.11470	0.0:0.5393:0.1748:0.2859	rs3795504;rs17302221;rs59561360;rs3795504	801	Q5VZ46	K1614_HUMAN	F	801;422	ENSP00000356560:L801F;ENSP00000356559:L422F	ENSP00000356559:L422F	L	+	3	2	KIAA1614	179172071	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.066000	0.14489	0.277000	0.22141	-1.202000	0.01658	TTG	G|0.614;T|0.386	0.386	strong		0.612	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
C19orf10	56005	hgsc.bcm.edu	37	19	4670236	4670236	+	Silent	SNP	C	C	G	rs10401515	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4670236C>G	ENST00000262947.3	-	1	146	c.111G>C	c.(109-111)acG>acC	p.T37T	C19orf10_ENST00000599630.1_Silent_p.T37T	NM_019107.3	NP_061980.1	Q969H8	CS010_HUMAN	chromosome 19 open reading frame 10	37					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.015)		CAAACGCCACCGTCGTGGGCT	0.721													c|||	620	0.123802	0.23	0.062	5008	,	,		7770	0.1022		0.0785	False		,,,				2504	0.093				p.T37T		Atlas-SNP	.											.	C19orf10	9	.	0			c.G111C						PASS	.	C		741,3555		57,627,1464	13.0	11.0	12.0		111	-4.1	1.0	19	dbSNP_119	12	547,7865		26,495,3685	no	coding-synonymous	C19orf10	NM_019107.3		83,1122,5149	GG,GC,CC		6.5026,17.2486,10.1353		37/174	4670236	1288,11420	2148	4206	6354	SO:0001819	synonymous_variant	56005	exon1			CGCCACCGTCGTG	AF282264	CCDS12133.1	19p13.3	2013-11-27	2003-06-25	2003-06-27	ENSG00000074842	ENSG00000074842			16948	protein-coding gene	gene with protein product		606746	"""interleukin 27 working designation"""	IL27, IL27w		17362502, 21128247	Standard	NM_019107		Approved	R33729_1, IL25, SF20, IL-25, IL-27	uc002may.3	Q969H8		ENST00000262947.3:c.111G>C	19.37:g.4670236C>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	15	10	0.666667	NM_019107	D6W628|O75256|O75272|Q9BTK7|Q9NP69	Silent	SNP	ENST00000262947.3	37	CCDS12133.1																																																																																			C|0.891;G|0.109	0.109	strong		0.721	C19orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458937.1	NM_019107	
CHDH	55349	hgsc.bcm.edu	37	3	53856653	53856653	+	Silent	SNP	C	C	T	rs2241808	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:53856653C>T	ENST00000315251.6	-	4	1157	c.720G>A	c.(718-720)gcG>gcA	p.A240A		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	240					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	AGGCACAGGCCGCGCTCCACC	0.647													C|||	2217	0.442692	0.1581	0.4438	5008	,	,		19438	0.5655		0.5268	False		,,,				2504	0.6135				p.A240A		Atlas-SNP	.											CHDH,colon,carcinoma,-2,1	CHDH	34	1	0			c.G720A						PASS	.	C		986,3420	368.8+/-318.8	111,764,1328	74.0	62.0	66.0		720	-11.3	0.0	3	dbSNP_98	66	4716,3884	606.1+/-395.1	1280,2156,864	no	coding-synonymous	CHDH	NM_018397.4		1391,2920,2192	TT,TC,CC		45.1628,22.3786,43.8413		240/595	53856653	5702,7304	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon4			ACAGGCCGCGCTC	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.720G>A	3.37:g.53856653C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			C|0.555;T|0.444	0.444	strong		0.647	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
KDM6A	7403	hgsc.bcm.edu	37	X	44938563	44938563	+	Silent	SNP	G	G	A	rs20539	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:44938563G>A	ENST00000377967.4	+	20	3152	c.3111G>A	c.(3109-3111)caG>caA	p.Q1037Q	KDM6A_ENST00000382899.4_Silent_p.Q1044Q|KDM6A_ENST00000543216.1_Silent_p.Q958Q|KDM6A_ENST00000536777.1_Silent_p.Q992Q	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1037	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						AATATGCACAGTACCAGGCCT	0.358			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""								G|||	837	0.221722	0.0091	0.3386	3775	,	,		12635	0.2381		0.16	False		,,,				2504	0.1933				p.Q1037Q	Colon(129;1273 1667 15230 27352 52914)	Atlas-SNP	.		Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	.	KDM6A	274	.	6	Whole gene deletion(6)	oesophagus(2)|breast(2)|pancreas(2)	c.G3111A						PASS	.	G		126,3709		5,103,13,1524,558	136.0	109.0	118.0		3111	0.2	1.0	X	dbSNP_67	118	1268,5460		79,761,349,1588,1523	no	coding-synonymous	KDM6A	NM_021140.2		84,864,362,3112,2081	AA,AG,A,GG,G		18.8466,3.2855,13.197		1037/1402	44938563	1394,9169	2203	4300	6503	SO:0001819	synonymous_variant	7403	exon20			TGCACAGTACCAG	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.3111G>A	X.37:g.44938563G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	279	85	0.304659	NM_021140	Q52LL9|Q5JVQ7	Silent	SNP	ENST00000377967.4	37	CCDS14265.1	374	0.22543701024713683	7	0.014285714285714285	69	0.24820143884892087	90	0.18518518518518517	86	0.12536443148688048	G	7.673	0.687468	0.14973	0.032855	0.188466	ENSG00000147050	ENST00000414389;ENST00000433797	.	.	.	5.6	0.226	0.15353	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16660	-1.0395	3	.	.	.	-8.1414	11.1997	0.48734	0.3721:0.0:0.6279:0.0	rs20539;rs4824526;rs17245004;rs52822280;rs4824526	.	.	.	I	635;680	.	.	V	+	1	0	KDM6A	44823507	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.819000	0.39022	-0.032000	0.13758	-0.198000	0.12761	GTA	0|0.018;A|0.156	0.156	strong		0.358	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	
EXOG	9941	hgsc.bcm.edu	37	3	38565576	38565576	+	Missense_Mutation	SNP	G	G	T	rs1141223	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:38565576G>T	ENST00000287675.5	+	6	926	c.830G>T	c.(829-831)gGa>gTa	p.G277V	EXOG_ENST00000358249.2_Intron|EXOG_ENST00000422077.2_Missense_Mutation_p.G227V	NM_005107.3	NP_005098.2	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	277			G -> V (abolishes catalytic activity; dbSNP:rs1141223). {ECO:0000269|PubMed:10231028}.		DNA catabolic process, endonucleolytic (GO:0000737)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			central_nervous_system(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	17						AAGTTGTCAGGACTGGTGTTT	0.498													G|||	23	0.00459265	0.0	0.0101	5008	,	,		18037	0.0		0.0139	False		,,,				2504	0.002				p.G277V		Atlas-SNP	.											.	EXOG	29	.	0			c.G830T						PASS	.	G	VAL/GLY,VAL/GLY	12,4394	19.1+/-41.9	0,12,2191	121.0	131.0	128.0		680,830	5.5	1.0	3	dbSNP_86	128	103,8497	56.8+/-118.0	1,101,4198	yes	missense,missense	EXOG	NM_001145464.1,NM_005107.3	109,109	1,113,6389	TT,TG,GG		1.1977,0.2724,0.8842	probably-damaging,probably-damaging	227/319,277/369	38565576	115,12891	2203	4300	6503	SO:0001583	missense	9941	exon6			TGTCAGGACTGGT	AB020523	CCDS2680.1, CCDS46795.1	3p21.3	2010-05-07	2009-01-08	2009-01-08	ENSG00000157036	ENSG00000157036	3.1.30.-		3347	protein-coding gene	gene with protein product		604051	"""endonuclease G-like 1"", ""endonuclease G-like 2"""	ENDOGL1, ENDOGL2		10231028, 18187503	Standard	NM_005107		Approved	ENGL-a, ENGL, ENGL-b	uc003cih.2	Q9Y2C4	OTTHUMG00000131295	ENST00000287675.5:c.830G>T	3.37:g.38565576G>T	ENSP00000287675:p.Gly277Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	108	39	0.361111	NM_005107	A8K242|B4DVG2|Q3SXM9|Q9Y2C8	Missense_Mutation	SNP	ENST00000287675.5	37	CCDS2680.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	G	24.3	4.511010	0.85389	0.002724	0.011977	ENSG00000157036	ENST00000287675;ENST00000422077	T;T	0.77098	-1.07;-1.07	5.54	5.54	0.83059	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.000000	0.85682	D	0.000000	D	0.91016	0.7174	H	0.97896	4.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93584	0.6915	10	0.87932	D	0	-23.5108	19.6787	0.95950	0.0:0.0:1.0:0.0	rs1141223;rs1141223	227;277	Q9Y2C4-4;Q9Y2C4	.;EXOG_HUMAN	V	277;227	ENSP00000287675:G277V;ENSP00000404305:G227V	ENSP00000287675:G277V	G	+	2	0	EXOG	38540580	1.000000	0.71417	0.957000	0.39632	0.999000	0.98932	7.311000	0.78958	2.884000	0.98904	0.655000	0.94253	GGA	G|0.993;T|0.007	0.007	strong		0.498	EXOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254063.2	NM_005107	
NBEAL2	23218	hgsc.bcm.edu	37	3	47045846	47045846	+	Missense_Mutation	SNP	C	C	T	rs2305637	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:47045846C>T	ENST00000450053.3	+	37	6340	c.6161C>T	c.(6160-6162)tCc>tTc	p.S2054F	NBEAL2_ENST00000292309.5_Missense_Mutation_p.S1870F|NBEAL2_ENST00000383740.2_Missense_Mutation_p.S333F	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2054	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.		S -> F (in dbSNP:rs2305637).		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)		AGCAGCCGCTCCCCCCAGGAG	0.652													C|||	634	0.126597	0.0197	0.1571	5008	,	,		15380	0.2073		0.2038	False		,,,				2504	0.0869				p.S2054F		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C6161T						PASS	.	C	PHE/SER	185,3781		9,167,1807	29.0	34.0	33.0		6161	5.0	1.0	3	dbSNP_100	33	1392,6916		125,1142,2887	yes	missense	NBEAL2	NM_015175.1	155	134,1309,4694	TT,TC,CC		16.7549,4.6646,12.8483	probably-damaging	2054/2755	47045846	1577,10697	1983	4154	6137	SO:0001583	missense	23218	exon37			GCCGCTCCCCCCA	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.6161C>T	3.37:g.47045846C>T	ENSP00000415034:p.Ser2054Phe	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	359|359	0.16437728937728938|0.16437728937728938	17|17	0.034552845528455285|0.034552845528455285	62|62	0.1712707182320442|0.1712707182320442	120|120	0.2097902097902098|0.2097902097902098	160|160	0.21108179419525067|0.21108179419525067	C|C	25.6|25.6	4.650975|4.650975	0.87958|0.87958	0.046646|0.046646	0.167549|0.167549	ENSG00000160796|ENSG00000160796	ENST00000416683|ENST00000292309;ENST00000383740;ENST00000450053	.|T;T;T	.|0.77358	.|-1.09;-1.09;-1.09	4.98|4.98	4.98|4.98	0.66077|0.66077	.|BEACH domain (2);	.|0.111193	.|0.64402	.|D	.|0.000006	T|T	0.00524|0.00524	0.0017|0.0017	M|M	0.91406|0.91406	3.205|3.205	0.09310|0.09310	P|P	0.99999999621455|0.99999999621455	.|D;D	.|0.89917	.|1.0;0.988	.|D;D	.|0.87578	.|0.998;0.958	T|T	0.02676|0.02676	-1.1125|-1.1125	4|9	.|0.87932	.|D	.|0	.|.	16.985|16.985	0.86338|0.86338	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2305637;rs2305637|rs2305637;rs2305637	.|1870;2054	.|Q6ZNJ1-2;Q6ZNJ1	.|.;NBEL2_HUMAN	S|F	1342|1870;333;2054	.|ENSP00000292309:S1870F;ENSP00000373246:S333F;ENSP00000415034:S2054F	.|ENSP00000292309:S1870F	P|S	+|+	1|2	0|0	NBEAL2|NBEAL2	47020850|47020850	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	5.794000|5.794000	0.69067|0.69067	2.606000|2.606000	0.88127|0.88127	0.491000|0.491000	0.48974|0.48974	CCC|TCC	C|0.844;T|0.156	0.156	strong		0.652	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
HOMER3	9454	hgsc.bcm.edu	37	19	19049194	19049194	+	Silent	SNP	G	G	A	rs11540741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:19049194G>A	ENST00000539827.1	-	3	923	c.271C>T	c.(271-273)Ctg>Ttg	p.L91L	HOMER3_ENST00000392351.3_Silent_p.L91L|AC005932.1_ENST00000601106.1_RNA|HOMER3_ENST00000221222.11_Silent_p.L91L|HOMER3_ENST00000433218.2_Silent_p.L91L|HOMER3_ENST00000542541.2_Silent_p.L91L|HOMER3_ENST00000355887.6_Silent_p.L91L|HOMER3_ENST00000594439.1_Silent_p.L91L|HOMER3_ENST00000594794.1_Intron			Q9NSC5	HOME3_HUMAN	homer homolog 3 (Drosophila)	91	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				G-protein coupled glutamate receptor signaling pathway (GO:0007216)|protein targeting (GO:0006605)	basal part of cell (GO:0045178)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				endometrium(3)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10			Epithelial(12;0.0107)			GCAAAGCCCAGGCCGTAGACT	0.597													G|||	331	0.0660942	0.0091	0.0951	5008	,	,		15228	0.0565		0.1451	False		,,,				2504	0.0511				p.L91L		Atlas-SNP	.											.	HOMER3	19	.	0			c.C271T						PASS	.	G	,,,	132,4274	96.7+/-135.4	3,126,2074	106.0	100.0	102.0		271,271,271,271	3.2	0.8	19	dbSNP_120	102	1325,7275	254.6+/-279.8	108,1109,3083	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HOMER3	NM_001145721.1,NM_001145722.1,NM_001145724.1,NM_004838.3	,,,	111,1235,5157	AA,AG,GG		15.407,2.9959,11.2025	,,,	91/359,91/362,91/326,91/362	19049194	1457,11549	2203	4300	6503	SO:0001819	synonymous_variant	9454	exon4			AGCCCAGGCCGTA	Y18894	CCDS12391.1, CCDS46022.1, CCDS46023.1	19p13.1	2008-02-05				ENSG00000051128			17514	protein-coding gene	gene with protein product		604800				10653696, 9808459	Standard	NM_004838		Approved	HOMER-3	uc002nkv.2	Q9NSC5		ENST00000539827.1:c.271C>T	19.37:g.19049194G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_001145722	E9PCW9|O14580|O95350|Q9NSB9|Q9NSC0|Q9NSC1	Silent	SNP	ENST00000539827.1	37	CCDS12391.1																																																																																			G|0.895;A|0.105	0.105	strong		0.597	HOMER3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464607.1		
SLC28A1	9154	hgsc.bcm.edu	37	15	85447431	85447431	+	Missense_Mutation	SNP	G	G	A	rs2290272	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:85447431G>A	ENST00000286749.3	+	6	655	c.565G>A	c.(565-567)Gtc>Atc	p.V189I	SLC28A1_ENST00000538177.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000394573.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000537703.1_Missense_Mutation_p.V111I|SLC28A1_ENST00000537624.1_Missense_Mutation_p.V189I|SLC28A1_ENST00000537216.1_Missense_Mutation_p.V189I			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	189			V -> I (in A; dbSNP:rs2290272). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9124315}.		nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)	p.V189I(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	CTGCGTGTTCGTCGCTCTCCT	0.587													A|||	1919	0.383187	0.1914	0.5058	5008	,	,		20264	0.375		0.3638	False		,,,				2504	0.5838				p.V189I		Atlas-SNP	.											SLC28A1,NS,carcinoma,0,1	SLC28A1	118	1	1	Substitution - Missense(1)	stomach(1)	c.G565A	GRCh37	CM045806	SLC28A1	M	rs2290272	PASS	.	A	ILE/VAL	962,3444	734.2+/-410.6	104,754,1345	171.0	146.0	155.0		565	-5.9	0.0	15	dbSNP_100	155	3013,5585	663.4+/-402.1	524,1965,1810	yes	missense	SLC28A1	NM_004213.3	29	628,2719,3155	AA,AG,GG		35.043,21.8339,30.5675	benign	189/650	85447431	3975,9029	2203	4299	6502	SO:0001583	missense	9154	exon7			GTGTTCGTCGCTC	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.565G>A	15.37:g.85447431G>A	ENSP00000286749:p.Val189Ile	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Missense_Mutation	SNP	ENST00000286749.3	37	CCDS10334.1	762	0.3489010989010989	93	0.18902439024390244	175	0.48342541436464087	208	0.36363636363636365	286	0.37730870712401055	A	0.006	-2.043950	0.00398	0.218339	0.35043	ENSG00000156222	ENST00000537216;ENST00000538177;ENST00000537624;ENST00000286749;ENST00000394573;ENST00000537703	T;T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7;2.7	4.38	-5.87	0.02297	Na dependent nucleoside transporter (1);	0.579854	0.17850	N	0.159890	T	0.00012	0.0000	N	0.02357	-0.585	0.80722	P	0.0	B;B;B;B;B	0.19331	0.005;0.001;0.035;0.001;0.002	B;B;B;B;B	0.19148	0.006;0.003;0.024;0.004;0.006	T	0.16808	-1.0390	9	0.02654	T	1	3.2539	9.4688	0.38829	0.2123:0.2511:0.5366:0.0	rs2290272;rs17222253;rs17536477;rs52799974;rs58773874;rs2290272	189;189;189;111;189	B7Z533;F5H560;B7Z3L6;B7Z3M4;O00337	.;.;.;.;S28A1_HUMAN	I	189;189;189;189;189;111	ENSP00000440546:V189I;ENSP00000443752:V189I;ENSP00000444700:V189I;ENSP00000286749:V189I;ENSP00000378074:V189I;ENSP00000443764:V111I	ENSP00000286749:V189I	V	+	1	0	SLC28A1	83248435	0.142000	0.22610	0.003000	0.11579	0.001000	0.01503	-0.604000	0.05667	-1.600000	0.01603	-1.157000	0.01802	GTC	G|0.674;A|0.326	0.326	strong		0.587	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
RIF1	55183	hgsc.bcm.edu	37	2	152314385	152314385	+	Silent	SNP	G	G	A	rs16830047	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:152314385G>A	ENST00000243326.5	+	23	3246	c.2763G>A	c.(2761-2763)ctG>ctA	p.L921L	RIF1_ENST00000430328.2_Silent_p.L921L|RIF1_ENST00000428287.2_Silent_p.L921L|RIF1_ENST00000444746.2_Silent_p.L921L|RIF1_ENST00000453091.2_Silent_p.L921L			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TAATATTTCTGCACAAGAATA	0.378													G|||	1244	0.248403	0.093	0.3631	5008	,	,		15359	0.3224		0.3211	False		,,,				2504	0.226				p.L921L		Atlas-SNP	.											.	RIF1	244	.	0			c.G2763A						PASS	.	G	,,,	557,3849	250.9+/-257.8	38,481,1684	91.0	90.0	90.0		2763,2763,2763,2763	0.4	1.0	2	dbSNP_123	90	2428,6172	400.3+/-346.7	337,1754,2209	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	,,,	375,2235,3893	AA,AG,GG		28.2326,12.6419,22.9509	,,,	921/2447,921/2447,921/2447,921/2473	152314385	2985,10021	2203	4300	6503	SO:0001819	synonymous_variant	55183	exon24			ATTTCTGCACAAG	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.2763G>A	2.37:g.152314385G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	67	18	0.268657	NM_018151	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																			G|0.749;A|0.251	0.251	strong		0.378	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
YBX1	4904	hgsc.bcm.edu	37	1	43166630	43166630	+	Missense_Mutation	SNP	G	G	A	rs200741644		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:43166630G>A	ENST00000321358.7	+	7	1058	c.919G>A	c.(919-921)Gat>Aat	p.D307N		NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	307					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)	p.D307N(1)		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)				AAAAGCAGCCGATCCACCAGC	0.562																																					p.D307N		Atlas-SNP	.											YBX1,mouth,carcinoma,0,1	YBX1	49	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G919A						scavenged	.						56.0	58.0	57.0					1																	43166630		2203	4299	6502	SO:0001583	missense	4904	exon7			GCAGCCGATCCAC	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.919G>A	1.37:g.43166630G>A	ENSP00000361626:p.Asp307Asn	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	122	17	0.139344	NM_004559	P16990|P16991|Q14972|Q15325|Q5FVF0	Missense_Mutation	SNP	ENST00000321358.7	37	CCDS470.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735579	0.69189	.	.	ENSG00000065978	ENST00000321358;ENST00000318612	T	0.31510	1.49	5.39	5.39	0.77823	.	0.236880	0.49916	N	0.000136	T	0.22044	0.0531	N	0.17379	0.485	0.54753	D	0.999989	B	0.25312	0.123	B	0.15052	0.012	T	0.04078	-1.0979	10	0.62326	D	0.03	-3.4519	16.6483	0.85182	0.0:0.0:1.0:0.0	.	307	P67809	YBOX1_HUMAN	N	307;297	ENSP00000361626:D307N	ENSP00000361621:D297N	D	+	1	0	YBX1	42939217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.018000	0.93657	2.505000	0.84491	0.557000	0.71058	GAT	G|0.998;A|0.002	0.002	weak		0.562	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559	
KIAA0753	9851	hgsc.bcm.edu	37	17	6513329	6513329	+	Missense_Mutation	SNP	G	G	A	rs2304977	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6513329G>A	ENST00000361413.3	-	9	2055	c.1697C>T	c.(1696-1698)cCa>cTa	p.P566L	KIAA0753_ENST00000572370.1_Missense_Mutation_p.P267L|KIAA0753_ENST00000589033.1_Missense_Mutation_p.P22L|KIAA0753_ENST00000542606.1_Missense_Mutation_p.P267L	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	566			P -> L (in dbSNP:rs2304977).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		AGGAGACGCTGGTGGGGATGT	0.473													G|||	1361	0.271765	0.0303	0.3876	5008	,	,		16778	0.3562		0.3459	False		,,,				2504	0.3528				p.P566L		Atlas-SNP	.											.	KIAA0753	63	.	0			c.C1697T						PASS	.	G	LEU/PRO	325,3485		15,295,1595	155.0	154.0	154.0		1697	4.2	1.0	17	dbSNP_100	154	3087,5129		548,1991,1569	yes	missense	KIAA0753	NM_014804.2	98	563,2286,3164	AA,AG,GG		37.573,8.5302,28.3719	probably-damaging	566/968	6513329	3412,8614	1905	4108	6013	SO:0001583	missense	9851	exon9			GACGCTGGTGGGG		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1697C>T	17.37:g.6513329G>A	ENSP00000355250:p.Pro566Leu	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	203	92	0.453202	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	601	0.2751831501831502	20	0.04065040650406504	148	0.4088397790055249	178	0.3111888111888112	255	0.33641160949868076	G	18.74	3.688818	0.68271	0.085302	0.37573	ENSG00000198920	ENST00000361413;ENST00000542606;ENST00000542826	D;D	0.85702	-2.02;-2.02	5.14	4.15	0.48705	.	0.112488	0.64402	D	0.000007	T	0.00012	0.0000	M	0.78916	2.43	0.20563	P	0.99988895	D	0.57257	0.979	P	0.54270	0.747	T	0.01409	-1.1362	9	0.27785	T	0.31	-9.5145	11.2919	0.49256	0.0:0.0:0.8174:0.1826	rs2304977;rs17731495;rs52796942;rs60289833;rs2304977	566	Q2KHM9	K0753_HUMAN	L	566;267;22	ENSP00000355250:P566L;ENSP00000444634:P267L	ENSP00000355250:P566L	P	-	2	0	KIAA0753	6454053	0.999000	0.42202	0.998000	0.56505	0.886000	0.51366	2.037000	0.41174	1.275000	0.44379	0.650000	0.86243	CCA	G|0.714;A|0.286	0.286	strong		0.473	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
PRKCQ	5588	hgsc.bcm.edu	37	10	6527143	6527143	+	Missense_Mutation	SNP	G	G	A	rs2236379	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:6527143G>A	ENST00000263125.5	-	10	1088	c.989C>T	c.(988-990)cCg>cTg	p.P330L	PRKCQ_ENST00000539722.1_Missense_Mutation_p.P205L|PRKCQ_ENST00000397176.2_Missense_Mutation_p.P330L	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	330			P -> L (in dbSNP:rs2236379). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7686153, ECO:0000269|Ref.4}.		apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of T cell apoptotic process (GO:0070233)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T-helper 17 type immune response (GO:2000318)|positive regulation of T-helper 2 cell activation (GO:2000570)|protein ubiquitination (GO:0016567)|regulation of cell growth (GO:0001558)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of transcription, DNA-templated (GO:0006355)|rhodopsin mediated signaling pathway (GO:0016056)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|immunological synapse (GO:0001772)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin-protein transferase activity (GO:0004842)	p.P330L(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(2)	45					Tamoxifen(DB00675)	TAAACATGGCGGCCTTGCTTC	0.458													.|||	1830	0.365415	0.3744	0.3674	5008	,	,		19593	0.38		0.2316	False		,,,				2504	0.4744				p.P330L	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											PRKCQ,NS,carcinoma,0,1	PRKCQ	113	1	1	Substitution - Missense(1)	stomach(1)	c.C989T						PASS	.	G	LEU/PRO,LEU/PRO	1535,2871		277,981,945	180.0	173.0	175.0		989,989	-2.7	0.0	10	dbSNP_98	175	2147,6453		281,1585,2434	yes	missense,missense	PRKCQ	NM_001242413.1,NM_006257.3	98,98	558,2566,3379	AA,AG,GG		24.9651,34.8389,28.31	benign,benign	330/644,330/707	6527143	3682,9324	2203	4300	6503	SO:0001583	missense	5588	exon10			CATGGCGGCCTTG	L07032	CCDS7079.1, CCDS55701.1, CCDS60482.1	10p15	2009-07-10			ENSG00000065675	ENSG00000065675	2.7.11.1		9410	protein-coding gene	gene with protein product		600448				8444877	Standard	NM_001282645		Approved		uc001ijj.2	Q04759	OTTHUMG00000017623	ENST00000263125.5:c.989C>T	10.37:g.6527143G>A	ENSP00000263125:p.Pro330Leu	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Missense_Mutation	SNP	ENST00000263125.5	37	CCDS7079.1	704|704	0.32234432234432236|0.32234432234432236	175|175	0.3556910569105691|0.3556910569105691	141|141	0.38950276243093923|0.38950276243093923	220|220	0.38461538461538464|0.38461538461538464	168|168	0.22163588390501318|0.22163588390501318	.|.	8.301|8.301	0.819958|0.819958	0.16678|0.16678	0.348389|0.348389	0.249651|0.249651	ENSG00000065675|ENSG00000065675	ENST00000263125;ENST00000397176;ENST00000539722|ENST00000397178	T;T;T|.	0.68025|.	-0.3;-0.25;-0.28|.	5.22|5.22	-2.67|-2.67	0.06059|0.06059	.|.	0.528439|.	0.20037|.	N|.	0.100581|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02916|0.02916	-0.46|-0.46	0.51767|0.51767	P|P	6.700000000003925E-5|6.700000000003925E-5	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.0;0.0;0.0|.	T|T	0.46582|0.46582	-0.9181|-0.9181	9|4	0.23302|.	T|.	0.38|.	.|.	5.4646|5.4646	0.16635|0.16635	0.4512:0.0:0.4134:0.1355|0.4512:0.0:0.4134:0.1355	rs2236379;rs61306241;rs2236379|rs2236379;rs61306241;rs2236379	205;102;330;330|.	B4DF52;Q5JUN8;Q04759-2;Q04759|.	.;.;.;KPCT_HUMAN|.	L|C	330;330;205|103	ENSP00000263125:P330L;ENSP00000380361:P330L;ENSP00000441752:P205L|.	ENSP00000263125:P330L|.	P|R	-|-	2|1	0|0	PRKCQ|PRKCQ	6567149|6567149	0.011000|0.011000	0.17503|0.17503	0.003000|0.003000	0.11579|0.11579	0.004000|0.004000	0.04260|0.04260	0.733000|0.733000	0.26087|0.26087	-0.676000|-0.676000	0.05238|0.05238	0.655000|0.655000	0.94253|0.94253	CCG|CGC	G|0.675;T|0.002	.	strong		0.458	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
KRTAP12-3	386683	hgsc.bcm.edu	37	21	46077946	46077946	+	Missense_Mutation	SNP	A	A	G	rs9306111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46077946A>G	ENST00000397907.1	+	1	98	c.50A>G	c.(49-51)cAc>cGc	p.H17R	TSPEAR_ENST00000323084.4_Intron	NM_198697.2	NP_941970.2	P60328	KR123_HUMAN	keratin associated protein 12-3	17	14 X 5 AA approximate repeats.		H -> R (in dbSNP:rs9306111). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				central_nervous_system(1)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						TGCTGCATACACAGCCCCTGC	0.647													a|||	3954	0.789537	0.9198	0.7507	5008	,	,		18260	0.6637		0.7624	False		,,,				2504	0.7986				p.H17R		Atlas-SNP	.											.	KRTAP12-3	18	.	0			c.A50G						PASS	.	G	,ARG/HIS	3882,478		1732,418,30	73.0	88.0	83.0		,50	3.0	0.0	21	dbSNP_119	83	6083,2455		2194,1695,380	yes	intron,missense	TSPEAR,KRTAP12-3	NM_144991.2,NM_198697.2	,29	3926,2113,410	GG,GA,AA		28.7538,10.9633,22.74	,benign	,17/97	46077946	9965,2933	2180	4269	6449	SO:0001583	missense	386683	exon1			GCATACACAGCCC	AB076361	CCDS42964.1	21q22.3	2006-03-13			ENSG00000205439	ENSG00000205439		"""Keratin associated proteins"""	20531	protein-coding gene	gene with protein product							Standard	NM_198697		Approved	KRTAP12.3	uc002zft.3	P60328	OTTHUMG00000057630	ENST00000397907.1:c.50A>G	21.37:g.46077946A>G	ENSP00000381005:p.His17Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	197	75	0.380711	NM_198697		Missense_Mutation	SNP	ENST00000397907.1	37	CCDS42964.1	1680	0.7692307692307693	455	0.9247967479674797	279	0.7707182320441989	366	0.6398601398601399	580	0.7651715039577837	N	4.837	0.155633	0.09236	0.890367	0.712462	ENSG00000205439	ENST00000546091;ENST00000397907	T	0.01304	5.03	4.9	3.03	0.35002	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08764	-1.0706	7	0.54805	T	0.06	.	3.3378	0.07107	0.1737:0.56:0.1678:0.0985	rs9306111;rs57807884	17	P60328	KR123_HUMAN	R	31;17	ENSP00000381005:H17R	ENSP00000381005:H17R	H	+	2	0	KRTAP12-3	44902374	0.000000	0.05858	0.022000	0.16811	0.028000	0.11728	-0.359000	0.07632	0.116000	0.18110	-2.261000	0.00279	CAC	A|0.246;G|0.754	0.754	strong		0.647	KRTAP12-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128033.1		
C1orf101	257044	hgsc.bcm.edu	37	1	244715966	244715966	+	Silent	SNP	G	G	A	rs35587664	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:244715966G>A	ENST00000366534.4	+	9	933	c.879G>A	c.(877-879)tcG>tcA	p.S293S	C1orf101_ENST00000473875.1_Intron|C1orf101_ENST00000366533.4_Silent_p.S293S|C1orf101_ENST00000366531.3_Silent_p.S142S	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	293						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)			TGATCTTATCGCGGGATGGAA	0.398													G|||	589	0.117612	0.3116	0.0562	5008	,	,		15582	0.0		0.0696	False		,,,				2504	0.0695				p.S293S		Atlas-SNP	.											.	C1orf101	158	.	0			c.G879A						PASS	.	G	,,	1212,3194	422.3+/-339.7	168,876,1159	171.0	161.0	164.0		879,426,879	-11.2	0.0	1	dbSNP_126	164	523,8077	146.6+/-202.2	14,495,3791	no	coding-synonymous,coding-synonymous,coding-synonymous	C1orf101	NM_001130957.1,NM_001242340.1,NM_173807.4	,,	182,1371,4950	AA,AG,GG		6.0814,27.5079,13.34	,,	293/952,142/801,293/833	244715966	1735,11271	2203	4300	6503	SO:0001819	synonymous_variant	257044	exon9			CTTATCGCGGGAT	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.879G>A	1.37:g.244715966G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	144	59	0.409722	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																			G|0.880;A|0.120	0.120	strong		0.398	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807	
EPHA1	2041	hgsc.bcm.edu	37	7	143097100	143097100	+	Missense_Mutation	SNP	A	A	G	rs4725617	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143097100A>G	ENST00000275815.3	-	4	565	c.479T>C	c.(478-480)gTg>gCg	p.V160A		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	160	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.		V -> A (in dbSNP:rs4725617). {ECO:0000269|PubMed:10369740, ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:2825356, ECO:0000269|Ref.6}.		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)				GGAGCCAGACACAAGGTCTCG	0.607													G|||	4725	0.94349	0.8722	0.9726	5008	,	,		16915	0.9921		0.9195	False		,,,				2504	0.9939				p.V160A		Atlas-SNP	.											.	EPHA1	193	.	0			c.T479C						PASS	.	G	ALA/VAL	3813,593	245.0+/-254.1	1649,515,39	30.0	32.0	32.0		479	3.9	0.0	7	dbSNP_111	32	7935,665	161.0+/-214.0	3668,599,33	yes	missense	EPHA1	NM_005232.4	64	5317,1114,72	GG,GA,AA		7.7326,13.4589,9.6725	benign	160/977	143097100	11748,1258	2203	4300	6503	SO:0001583	missense	2041	exon4			CCAGACACAAGGT	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.479T>C	7.37:g.143097100A>G	ENSP00000275815:p.Val160Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	2029	0.9290293040293041	423	0.8597560975609756	352	0.9723756906077348	565	0.9877622377622378	689	0.9089709762532981	G	5.079	0.200225	0.09652	0.865411	0.922674	ENSG00000146904	ENST00000275815	T	0.03358	3.96	4.79	3.88	0.44766	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.110618	0.40302	N	0.001125	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34675	-0.9819	9	0.33940	T	0.23	.	7.0943	0.25301	0.0831:0.0:0.5974:0.3195	rs4725617;rs57667339;rs4725617	160	P21709	EPHA1_HUMAN	A	160	ENSP00000275815:V160A	ENSP00000275815:V160A	V	-	2	0	EPHA1	142807222	0.103000	0.21917	0.003000	0.11579	0.179000	0.23085	0.994000	0.29693	0.577000	0.29470	-0.119000	0.15052	GTG	A|0.081;G|0.919	0.919	strong		0.607	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
UBXN6	80700	hgsc.bcm.edu	37	19	4454083	4454083	+	Missense_Mutation	SNP	C	C	T	rs1127888	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4454083C>T	ENST00000301281.6	-	2	215	c.91G>A	c.(91-93)Gcc>Acc	p.A31T	UBXN6_ENST00000394765.3_5'UTR|CTB-50L17.9_ENST00000592034.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	31			A -> T (in dbSNP:rs1127888).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						TCTTTGTGGGCCTTTTCCCTG	0.662													C|||	836	0.166933	0.09	0.3213	5008	,	,		14937	0.0645		0.2624	False		,,,				2504	0.1687				p.A31T		Atlas-SNP	.											.	UBXN6	27	.	0			c.G91A						PASS	.	C	,THR/ALA	527,3879	242.1+/-252.3	30,467,1706	103.0	117.0	112.0		,91	2.0	1.0	19	dbSNP_86	112	2330,6270	388.9+/-342.7	319,1692,2289	yes	utr-5,missense	UBXN6	NM_001171091.1,NM_025241.2	,58	349,2159,3995	TT,TC,CC		27.093,11.961,21.9668	,benign	,31/442	4454083	2857,10149	2203	4300	6503	SO:0001583	missense	80700	exon2			TGTGGGCCTTTTC	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.91G>A	19.37:g.4454083C>T	ENSP00000301281:p.Ala31Thr	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	381	0.17445054945054944	48	0.0975609756097561	104	0.287292817679558	37	0.06468531468531469	192	0.2532981530343008	C	8.633	0.894076	0.17613	0.11961	0.27093	ENSG00000167671	ENST00000301281	T	0.43294	0.95	4.13	1.96	0.26148	.	1.015050	0.07885	N	0.970198	T	0.00012	0.0000	L	0.50333	1.59	0.09310	P	1.0	B	0.06786	0.001	B	0.08055	0.003	T	0.33929	-0.9849	9	0.10902	T	0.67	-9.49	6.9264	0.24418	0.0:0.7783:0.0:0.2217	rs1127888;rs11558243	31	Q9BZV1	UBXN6_HUMAN	T	31	ENSP00000301281:A31T	ENSP00000301281:A31T	A	-	1	0	UBXN6	4405083	0.996000	0.38824	0.990000	0.47175	0.138000	0.21146	0.552000	0.23376	0.211000	0.20683	0.484000	0.47621	GCC	T|0.211;G|0.000;C|0.788	0.211	strong		0.662	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
MOV10L1	54456	hgsc.bcm.edu	37	22	50538028	50538028	+	Missense_Mutation	SNP	G	G	A	rs146380250		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50538028G>A	ENST00000262794.5	+	3	522	c.439G>A	c.(439-441)Gaa>Aaa	p.E147K	MOV10L1_ENST00000475190.1_3'UTR|MOV10L1_ENST00000540615.1_Missense_Mutation_p.E127K|MOV10L1_ENST00000545383.1_Missense_Mutation_p.E147K|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.E147K	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	147					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		GAGTGTGTGCGAAGGTATGCT	0.512													G|||	1	0.000199681	0.0	0.0	5008	,	,		21026	0.0		0.001	False		,,,				2504	0.0				p.E147K		Atlas-SNP	.											MOV10L1_ENST00000540615,NS,malignant_melanoma,0,2	MOV10L1	238	2	0			c.G439A						scavenged	.	G	LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	110.0	93.0	99.0		439,379,439	2.6	1.0	22	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	147/1166,127/1166,147/1212	50538028	1,13005	2203	4300	6503	SO:0001583	missense	54456	exon3			GTGTGCGAAGGTA	AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.439G>A	22.37:g.50538028G>A	ENSP00000262794:p.Glu147Lys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	9.418	1.082369	0.20309	0.0	1.16E-4	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615;ENST00000428564	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.76	2.56	0.30785	.	0.293590	0.37261	N	0.002178	T	0.39733	0.1089	L	0.43923	1.385	0.80722	D	1	B;B;B;B	0.29627	0.252;0.236;0.095;0.095	B;B;B;B	0.17979	0.02;0.02;0.009;0.009	T	0.21861	-1.0233	10	0.52906	T	0.07	-17.5766	9.2821	0.37735	0.2268:0.0:0.7732:0.0	.	127;127;147;147	F5H403;E7EPK8;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	K	147;147;147;127;127	ENSP00000438978:E147K;ENSP00000262794:E147K;ENSP00000379199:E147K;ENSP00000438542:E127K	ENSP00000262794:E147K	E	+	1	0	MOV10L1	48880155	1.000000	0.71417	0.964000	0.40570	0.003000	0.03518	4.036000	0.57304	0.375000	0.24679	-0.793000	0.03317	GAA	G|1.000;A|0.000	0.000	strong		0.512	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
LRRC4C	57689	hgsc.bcm.edu	37	11	40137543	40137543	+	Silent	SNP	T	T	C	rs2953310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:40137543T>C	ENST00000278198.2	-	2	2263	c.300A>G	c.(298-300)agA>agG	p.R100R	LRRC4C_ENST00000528697.1_Silent_p.R100R|LRRC4C_ENST00000530763.1_Silent_p.R100R|LRRC4C_ENST00000527150.1_Silent_p.R100R			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	100					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)		p.R100R(1)		NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TTTCCAAGTGTCTCAAGTGCT	0.473													C|||	2501	0.499401	0.7027	0.5058	5008	,	,		19910	0.6052		0.3728	False		,,,				2504	0.2413				p.R100R		Atlas-SNP	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	1	Substitution - coding silent(1)	stomach(1)	c.A300G						scavenged	.	C		2917,1489	477.0+/-357.8	981,955,267	96.0	90.0	92.0		300	3.9	1.0	11	dbSNP_101	92	3562,5038	629.9+/-398.3	730,2102,1468	no	coding-synonymous	LRRC4C	NM_020929.1		1711,3057,1735	CC,CT,TT		41.4186,33.7948,49.8155		100/641	40137543	6479,6527	2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			CAAGTGTCTCAAG	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.300A>G	11.37:g.40137543T>C		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	149	64	0.42953	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																			T|0.478;C|0.522	0.522	strong		0.473	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
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 GAIIx	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	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	239	25	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 GAIIx	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	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_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	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	103	12	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	
MCTP1	79772	hgsc.bcm.edu	37	5	94050487	94050487	+	Silent	SNP	T	T	A	rs2636	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:94050487T>A	ENST00000515393.1	-	20	2714	c.2715A>T	c.(2713-2715)atA>atT	p.I905I	MCTP1_ENST00000514040.1_5'UTR|MCTP1_ENST00000505078.1_Silent_p.I421I|MCTP1_ENST00000429576.2_Silent_p.I598I|ANKRD32_ENST00000493934.1_Intron|MCTP1_ENST00000312216.8_Silent_p.I684I	NM_024717.4	NP_078993.4	Q6DN14	MCTP1_HUMAN	multiple C2 domains, transmembrane 1	905					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(13)|liver(2)|lung(13)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	41		all_cancers(142;1.68e-05)|all_epithelial(76;1.51e-07)|all_lung(232;0.0167)|Lung NSC(167;0.0207)|Ovarian(225;0.0218)|Colorectal(57;0.207)		all cancers(79;9.1e-17)		CTCACTTCTTTATCCTTTCGC	0.443													T|||	1988	0.396965	0.1853	0.4827	5008	,	,		17048	0.4345		0.4662	False		,,,				2504	0.5123				p.I905I		Atlas-SNP	.											.	MCTP1	110	.	0			c.A2715T						PASS	.	T	,	1030,3376	381.1+/-324.0	107,816,1280	207.0	199.0	201.0		2052,2715	0.1	1.0	5	dbSNP_36	201	3919,4681	547.9+/-385.3	881,2157,1262	no	coding-synonymous,coding-synonymous	MCTP1	NM_001002796.2,NM_024717.4	,	988,2973,2542	AA,AT,TT		45.5698,23.3772,38.0517	,	684/779,905/1000	94050487	4949,8057	2203	4300	6503	SO:0001819	synonymous_variant	79772	exon20			CTTCTTTATCCTT		CCDS34203.1, CCDS47247.1, CCDS75275.1	5q15	2008-02-05			ENSG00000175471	ENSG00000175471			26183	protein-coding gene	gene with protein product						15528213	Standard	XM_005272082		Approved	FLJ22344	uc003kkx.2	Q6DN14	OTTHUMG00000162742	ENST00000515393.1:c.2715A>T	5.37:g.94050487T>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_024717	Q6DN13|Q8N2W1|Q8NBA2|Q96LX0|Q9H6E8	Silent	SNP	ENST00000515393.1	37	CCDS34203.1																																																																																			T|0.597;N|0.000	.	strong		0.443	MCTP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370280.3	NM_024717	
CYP4F2	8529	hgsc.bcm.edu	37	19	15996820	15996820	+	Missense_Mutation	SNP	G	G	A	rs2074900	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15996820G>A	ENST00000011989.7	-	7	863	c.515C>T	c.(514-516)aCc>aTc	p.T172I	CYP4F2_ENST00000221700.6_Silent_p.H343H					cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						GCTTTGCAAGGTGGTACAGGA	0.597													.|||	1167	0.233027	0.1725	0.2421	5008	,	,		17400	0.2222		0.2972	False		,,,				2504	0.2536				p.H343H		Atlas-SNP	.											.	CYP4F2	97	.	0			c.C1029T						PASS	.	G		836,3570	331.2+/-301.9	75,686,1442	89.0	79.0	82.0		1029	1.5	1.0	19	dbSNP_96	82	2708,5892	433.6+/-357.5	435,1838,2027	no	coding-synonymous	CYP4F2	NM_001082.3		510,2524,3469	AA,AG,GG		31.4884,18.9741,27.249		343/521	15996820	3544,9462	2203	4300	6503	SO:0001583	missense	8529	exon9			TGCAAGGTGGTAC	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000011989.7:c.515C>T	19.37:g.15996820G>A	ENSP00000011989:p.Thr172Ile	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_001082		Silent	SNP	ENST00000011989.7	37		556	0.25457875457875456	107	0.21747967479674796	79	0.21823204419889503	135	0.23601398601398602	235	0.3100263852242744	g	9.429	1.085048	0.20390	0.189741	0.314884	ENSG00000186115	ENST00000011989	T	0.25414	1.8	2.63	1.49	0.22878	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46678	P	8.430000000000382E-4	B	0.11235	0.004	B	0.13407	0.009	T	0.35748	-0.9776	7	0.87932	D	0	.	5.1868	0.15187	0.3008:0.0:0.6992:0.0	rs2074900;rs2230747;rs61124408	172	B4DV75	.	I	172	ENSP00000011989:T172I	ENSP00000011989:T172I	T	-	2	0	CYP4F2	15857820	1.000000	0.71417	0.969000	0.41365	0.423000	0.31445	2.531000	0.45650	0.379000	0.24794	0.313000	0.20887	ACC	G|0.734;A|0.266	0.266	strong		0.597	CYP4F2-201	KNOWN	basic	protein_coding	protein_coding		NM_001082	
KRT76	51350	hgsc.bcm.edu	37	12	53165949	53165949	+	Missense_Mutation	SNP	C	C	T	rs12296548	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53165949C>T	ENST00000332411.2	-	5	1119	c.1066G>A	c.(1066-1068)Gag>Aag	p.E356K		NM_015848.4	NP_056932.2	Q01546	K22O_HUMAN	keratin 76	356	Coil 2.|Rod.			E -> K (in Ref. 3; BAG61375). {ECO:0000305}.	cytoskeleton organization (GO:0007010)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GCGCGGACCTCGGCAATGATG	0.597													C|||	690	0.13778	0.0817	0.0965	5008	,	,		20630	0.0972		0.1014	False		,,,				2504	0.3221				p.E356K		Atlas-SNP	.											.	KRT76	72	.	0			c.G1066A						PASS	.	C	LYS/GLU	476,3930	223.3+/-239.8	33,410,1760	88.0	75.0	79.0		1066	4.4	0.9	12	dbSNP_120	79	1043,7557	221.2+/-258.7	71,901,3328	yes	missense	KRT76	NM_015848.4	56	104,1311,5088	TT,TC,CC		12.1279,10.8034,11.6792	probably-damaging	356/639	53165949	1519,11487	2203	4300	6503	SO:0001583	missense	51350	exon5			GGACCTCGGCAAT	M99063	CCDS8838.1	12q13.13	2013-06-25			ENSG00000185069	ENSG00000185069		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24430	protein-coding gene	gene with protein product						1282112, 16831889	Standard	NM_015848		Approved	HUMCYT2A, KRT2B, KRT2P	uc001sax.3	Q01546	OTTHUMG00000169797	ENST00000332411.2:c.1066G>A	12.37:g.53165949C>T	ENSP00000330101:p.Glu356Lys	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	136	67	0.492647	NM_015848	B4DRR3|Q7Z795	Missense_Mutation	SNP	ENST00000332411.2	37	CCDS8838.1	218	0.09981684981684982	45	0.09146341463414634	42	0.11602209944751381	62	0.10839160839160839	69	0.09102902374670185	C	21.6	4.179986	0.78564	0.108034	0.121279	ENSG00000185069	ENST00000332411	D	0.92199	-2.99	4.42	4.42	0.53409	Filament (1);	0.000000	0.44902	D	0.000406	T	0.42245	0.1194	M	0.89904	3.07	0.09310	P	0.99999385671	D	0.89917	1.0	D	0.81914	0.995	T	0.66555	-0.5894	9	0.72032	D	0.01	.	17.8977	0.88893	0.0:1.0:0.0:0.0	rs12296548	356	Q01546	K22O_HUMAN	K	356	ENSP00000330101:E356K	ENSP00000330101:E356K	E	-	1	0	KRT76	51452216	1.000000	0.71417	0.920000	0.36463	0.272000	0.26649	6.020000	0.70826	2.398000	0.81561	0.462000	0.41574	GAG	C|0.889;T|0.111	0.111	strong		0.597	KRT76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405928.1	NM_015848	
SLC13A3	64849	hgsc.bcm.edu	37	20	45242269	45242269	+	Silent	SNP	G	G	C	rs2273024	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:45242269G>C	ENST00000279027.4	-	2	225	c.207C>G	c.(205-207)ctC>ctG	p.L69L	SLC13A3_ENST00000413164.2_Silent_p.L69L|SLC13A3_ENST00000339636.3_Silent_p.L69L|SLC13A3_ENST00000472148.1_Silent_p.L22L|SLC13A3_ENST00000372121.1_Silent_p.L69L|SLC13A3_ENST00000290317.5_Silent_p.L22L|SLC13A3_ENST00000435032.1_5'UTR|SLC13A3_ENST00000417157.2_Silent_p.L22L|SLC13A3_ENST00000396360.1_Silent_p.L22L|SLC13A3_ENST00000495082.1_Silent_p.L22L	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	69					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	TGAAGGGGAAGAGGACGATGG	0.612													G|||	1548	0.309105	0.2088	0.3617	5008	,	,		14974	0.2798		0.3539	False		,,,				2504	0.3916				p.L69L		Atlas-SNP	.											.	SLC13A3	88	.	0			c.C207G						PASS	.	G	,,,,	1028,3378	373.4+/-320.8	116,796,1291	74.0	55.0	61.0		66,207,66,,207	-0.3	1.0	20	dbSNP_100	61	2852,5748	440.6+/-359.6	451,1950,1899	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	SLC13A3	NM_001011554.2,NM_001193339.1,NM_001193340.1,NM_001193342.1,NM_022829.5	,,,,	567,2746,3190	CC,CG,GG		33.1628,23.3318,29.8324	,,,,	22/556,69/553,22/521,,69/603	45242269	3880,9126	2203	4300	6503	SO:0001819	synonymous_variant	64849	exon2			GGGGAAGAGGACG	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"""Solute carriers"""	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.207C>G	20.37:g.45242269G>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Silent	SNP	ENST00000279027.4	37	CCDS13400.1																																																																																			G|0.680;C|0.320	0.320	strong		0.612	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2		
IVL	3713	hgsc.bcm.edu	37	1	152882979	152882979	+	Missense_Mutation	SNP	C	C	T	rs17855670		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152882979C>T	ENST00000368764.3	+	2	770	c.706C>T	c.(706-708)Cca>Tca	p.P236S	IVL_ENST00000392667.2_Missense_Mutation_p.P90S			P07476	INVO_HUMAN	involucrin	236	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		P -> S (in dbSNP:rs17855670). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2873896}.		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)			gctggagctcccacagcagca	0.677																																					p.P236S		Atlas-SNP	.											IVL,colon,carcinoma,0,2	IVL	100	2	0			c.C706T						PASS	.																																			SO:0001583	missense	3713	exon2			GAGCTCCCACAGC	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.706C>T	1.37:g.152882979C>T	ENSP00000357753:p.Pro236Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	51	8	0.156863	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	126	0.057692307692307696	14	0.028455284552845527	19	0.052486187845303865	65	0.11363636363636363	28	0.036939313984168866	C	0.481	-0.879883	0.02530	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10960	3.06;2.82	3.86	-2.86	0.05717	.	.	.	.	.	T	0.01387	0.0045	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.48198	-0.9056	9	0.09590	T	0.72	.	4.7558	0.13082	0.3537:0.2977:0.3486:0.0	rs17855670	236	P07476	INVO_HUMAN	S	236;90	ENSP00000357753:P236S;ENSP00000376435:P90S	ENSP00000357753:P236S	P	+	1	0	IVL	151149603	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.107000	0.15375	-0.341000	0.08376	-0.883000	0.02948	CCA	C|0.943;T|0.057	0.057	strong		0.677	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
SPRR3	6707	hgsc.bcm.edu	37	1	152975763	152975763	+	Silent	SNP	C	C	A	rs1977734	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152975763C>A	ENST00000295367.4	+	2	309	c.267C>A	c.(265-267)ggC>ggA	p.G89G	SPRR3_ENST00000542696.1_Silent_p.G89G|SPRR3_ENST00000331860.3_Silent_p.G89G	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	89	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGAGCCAGGCTGTACCAAGG	0.602													T|||	2627	0.524561	0.5	0.4323	5008	,	,		17476	0.6319		0.5318	False		,,,				2504	0.5051				p.G89G		Atlas-SNP	.											.	SPRR3	45	.	0			c.C267A						PASS	.	C	,	2311,2095		594,1123,486	72.0	60.0	64.0		267,267	1.5	0.0	1	dbSNP_92	64	4670,3928		1279,2112,908	no	coding-synonymous,coding-synonymous	SPRR3	NM_001097589.1,NM_005416.2	,	1873,3235,1394	AA,AC,CC		45.685,47.5488,46.3165	,	89/170,89/170	152975763	6981,6023	2203	4299	6502	SO:0001819	synonymous_variant	6707	exon2			GCCAGGCTGTACC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.267C>A	1.37:g.152975763C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	69	24	0.347826	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			T|0.000;C|0.476;A|0.524	0.524	strong		0.602	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
MYCBP2	23077	hgsc.bcm.edu	37	13	77738664	77738664	+	Silent	SNP	A	A	G	rs2274547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:77738664A>G	ENST00000544440.2	-	43	6375	c.6358T>C	c.(6358-6360)Ttg>Ctg	p.L2120L	MYCBP2_ENST00000407578.2_Silent_p.L2158L|MYCBP2_ENST00000357337.6_Silent_p.L2120L|MYCBP2_ENST00000360084.5_5'UTR					MYC binding protein 2, E3 ubiquitin protein ligase											NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		TCTTTTTCCAATTGGATGACT	0.368													A|||	1153	0.230232	0.093	0.0965	5008	,	,		19334	0.3661		0.169	False		,,,				2504	0.4335				p.L2158L		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.T6472C						PASS	.	A		520,3886	235.5+/-248.0	28,464,1711	90.0	84.0	86.0		6472	0.5	1.0	13	dbSNP_100	86	1459,7141	277.8+/-293.0	105,1249,2946	no	coding-synonymous	MYCBP2	NM_015057.4		133,1713,4657	GG,GA,AA		16.9651,11.8021,15.2161		2158/4679	77738664	1979,11027	2203	4300	6503	SO:0001819	synonymous_variant	23077	exon43			TTTCCAATTGGAT	AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.6358T>C	13.37:g.77738664A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	134	50	0.373134	NM_015057		Silent	SNP	ENST00000544440.2	37																																																																																				A|0.832;G|0.168	0.168	strong		0.368	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766045	27766045	+	Missense_Mutation	SNP	A	A	G	rs5926895	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:27766045A>G	ENST00000451261.2	+	5	1432	c.1033A>G	c.(1033-1035)Acc>Gcc	p.T345A		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	345			T -> A (in dbSNP:rs5926895).							central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TGTTGTCTTCACCATTGACCT	0.478													A|||	627	0.166093	0.0613	0.1427	3775	,	,		14904	0.0575		0.2714	False		,,,				2504	0.1186				p.T345A		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A1033G						PASS	.	A	ALA/THR	164,1045		7,129,21,381,154	89.0	62.0	70.0		1033	0.1	0.0	X	dbSNP_114	70	886,1505		111,355,309,334,482	yes	missense	DCAF8L2	NM_001136533.1	58	118,484,330,715,636	GG,GA,G,AA,A		37.0556,13.5649,29.1667	benign	345/632	27766045	1050,2550	692	1591	2283	SO:0001583	missense	347442	exon1			GTCTTCACCATTG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1033A>G	X.37:g.27766045A>G	ENSP00000462745:p.Thr345Ala	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	130	93	0.715385	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			A|0.784;0|0.046	.	strong		0.478	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
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 GAIIx	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	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	61	3	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 GAIIx	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	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	25	15	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	
TRIM31	11074	hgsc.bcm.edu	37	6	30078275	30078275	+	Missense_Mutation	SNP	C	C	T	rs2523989	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30078275C>T	ENST00000376734.3	-	4	819	c.694G>A	c.(694-696)Gtt>Att	p.V232I	TRIM31_ENST00000485864.1_5'UTR|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Missense_Mutation_p.V232I	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	232			V -> I (in dbSNP:rs2523989). {ECO:0000269|PubMed:14574404}.	ASTEPQLNDLKKLVDSLK -> EIPLMPTVERSQEARCYP (in Ref. 6; CAA69165). {ECO:0000305}.	innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						AGGGAATCAACGAGCTTCTTG	0.552													T|||	374	0.0746805	0.0492	0.1239	5008	,	,		18612	0.0486		0.1203	False		,,,				2504	0.0542				p.V232I		Atlas-SNP	.											.	TRIM31	40	.	0			c.G694A						PASS	.	T	ILE/VAL	296,4110	799.7+/-415.5	11,274,1918	199.0	180.0	186.0		694	0.4	0.0	6	dbSNP_100	186	1207,7393	763.5+/-407.6	76,1055,3169	yes	missense	TRIM31	NM_007028.3	29	87,1329,5087	TT,TC,CC		14.0349,6.7181,11.5562	benign	232/426	30078275	1503,11503	2203	4300	6503	SO:0001583	missense	11074	exon4			AATCAACGAGCTT	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.694G>A	6.37:g.30078275C>T	ENSP00000365924:p.Val232Ile	Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	130	103	0.792308	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Missense_Mutation	SNP	ENST00000376734.3	37	CCDS34374.1	199	0.09111721611721611	14	0.028455284552845527	53	0.1464088397790055	38	0.06643356643356643	94	0.12401055408970976	T	0.019	-1.464264	0.01053	0.067181	0.140349	ENSG00000204616	ENST00000376734;ENST00000376728;ENST00000540829	T;T	0.61980	0.06;0.06	3.26	0.419	0.16438	.	.	.	.	.	T	0.07728	0.0194	N	0.01874	-0.695	0.80722	P	0.0	B	0.19583	0.037	B	0.11329	0.006	T	0.22173	-1.0224	8	0.02654	T	1	.	3.1145	0.06370	0.0:0.3495:0.2401:0.4104	rs2523989;rs6457153;rs17389049;rs17851467;rs52820560;rs56648206;rs58929461;rs2523989	232	Q9BZY9	TRI31_HUMAN	I	232	ENSP00000365924:V232I;ENSP00000444311:V232I	ENSP00000365918:V232I	V	-	1	0	TRIM31	30186254	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	0.141000	0.16076	0.013000	0.14918	-0.891000	0.02926	GTT	C|0.898;T|0.102	0.102	strong		0.552	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
CDH5	1003	hgsc.bcm.edu	37	16	66432423	66432423	+	Missense_Mutation	SNP	T	T	C	rs1049970|rs386791725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:66432423T>C	ENST00000341529.3	+	10	1698	c.1550T>C	c.(1549-1551)aTc>aCc	p.I517T	CDH5_ENST00000539168.1_5'UTR	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	517	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> T (in dbSNP:rs1049970). {ECO:0000269|PubMed:10861224, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7627717}.		adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)	p.I517T(1)		central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	TTCAAATTCATCTTGAATACT	0.473													C|||	3728	0.744409	0.7474	0.83	5008	,	,		21203	0.8224		0.6869	False		,,,				2504	0.6585				p.I517T		Atlas-SNP	.											CDH5,NS,carcinoma,0,2	CDH5	111	2	1	Substitution - Missense(1)	prostate(1)	c.T1550C						PASS	.	C	THR/ILE	2722,1680		1096,530,575	150.0	127.0	135.0		1550	4.0	0.9	16	dbSNP_86	135	4823,3777		1885,1053,1362	yes	missense	CDH5	NM_001795.3	89	2981,1583,1937	CC,CT,TT		43.9186,38.1645,41.9705	benign	517/785	66432423	7545,5457	2201	4300	6501	SO:0001583	missense	1003	exon10			AATTCATCTTGAA	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"""CD molecules"", ""Cadherins / Major cadherins"""	1764	protein-coding gene	gene with protein product	"""VE-cadherin"""	601120	"""cadherin 5, type 2, VE-cadherin (vascular epithelium)"""			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.1550T>C	16.37:g.66432423T>C	ENSP00000344115:p.Ile517Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001795	Q4VAI5|Q4VAI6	Missense_Mutation	SNP	ENST00000341529.3	37	CCDS10804.1	1542	0.7060439560439561	328	0.6666666666666666	269	0.7430939226519337	453	0.791958041958042	492	0.6490765171503958	C	8.228	0.803910	0.16467	0.618355	0.560814	ENSG00000179776	ENST00000341529;ENST00000379531;ENST00000539262	T	0.59502	0.26	4.95	3.99	0.46301	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.01188	-0.97	0.09310	P	0.9999999999986131	B	0.02656	0.0	B	0.04013	0.001	T	0.31364	-0.9946	8	0.48119	T	0.1	.	7.3952	0.26931	0.1654:0.7492:0.0:0.0854	rs1049970;rs3190184;rs52795742;rs61244397;rs1049970	517	P33151	CADH5_HUMAN	T	517;402;258	ENSP00000344115:I517T	ENSP00000344115:I517T	I	+	2	0	CDH5	64989924	0.998000	0.40836	0.911000	0.35937	0.055000	0.15305	1.933000	0.40153	0.699000	0.31761	-0.215000	0.12644	ATC	T|0.282;C|0.718	0.718	strong		0.473	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795	
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 GAIIx	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		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	126	72	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	
MYH2	4620	hgsc.bcm.edu	37	17	10450816	10450816	+	Silent	SNP	T	T	C	rs12600539	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:10450816T>C	ENST00000245503.5	-	4	708	c.324A>G	c.(322-324)gaA>gaG	p.E108E	CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000397183.2_Silent_p.E108E|MYH2_ENST00000532183.2_Silent_p.E108E	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	108	Myosin motor.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CTGCATAACGTTCTTTGAGGT	0.483													C|||	2722	0.54353	0.3797	0.5216	5008	,	,		20805	0.8492		0.3917	False		,,,				2504	0.6217				p.E108E		Atlas-SNP	.											MYH2,NS,carcinoma,-2,1	MYH2	390	1	0			c.A324G						PASS	.	C	,	1764,2642	645.7+/-398.2	344,1076,783	330.0	280.0	297.0		324,324	5.9	1.0	17	dbSNP_120	297	3548,5052	630.3+/-398.3	747,2054,1499	no	coding-synonymous,coding-synonymous	MYH2	NM_001100112.1,NM_017534.5	,	1091,3130,2282	CC,CT,TT		41.2558,40.0363,40.8427	,	108/1942,108/1942	10450816	5312,7694	2203	4300	6503	SO:0001819	synonymous_variant	4620	exon4			ATAACGTTCTTTG		CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.324A>G	17.37:g.10450816T>C		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	242	119	0.491736	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																			T|0.540;C|0.460	0.460	strong		0.483	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534	
MUC4	4585	hgsc.bcm.edu	37	3	195505742	195505742	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195505742G>C	ENST00000463781.3	-	2	13168	c.12709C>G	c.(12709-12711)Cac>Gac	p.H4237D	MUC4_ENST00000475231.1_Missense_Mutation_p.H4237D|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	994					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.H4237D(1)		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)		GGGGTGGCGTGACCTGTGGAT	0.587																																					p.H4237D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	lung(1)	c.C12709G						scavenged	.						49.0	50.0	49.0					3																	195505742		2110	4203	6313	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.12709C>G	3.37:g.195505742G>C	ENSP00000417498:p.His4237Asp	Somatic	89	5	0.0561798		WXS	Illumina HiSeq	Phase_I	74	5	0.0675676	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	2.170	-0.390211	0.04932	.	.	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.30448	1.55;1.53	2.31	-0.661	0.11417	.	.	.	.	.	T	0.21841	0.0526	L	0.38175	1.15	0.09310	N	1	P;P	0.47604	0.797;0.898	B;B	0.43623	0.343;0.425	T	0.13019	-1.0525	8	.	.	.	.	4.9563	0.14041	0.5176:0.0:0.4824:0.0	.	4109;994	E7ESK3;Q99102	.;MUC4_HUMAN	D	4237;4237;963	ENSP00000417498:H4237D;ENSP00000420243:H4237D	.	H	-	1	0	MUC4	196990521	0.025000	0.19082	0.033000	0.17914	0.009000	0.06853	1.101000	0.31037	-0.196000	0.10366	-0.213000	0.12676	CAC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR1S1	219959	hgsc.bcm.edu	37	11	57982620	57982620	+	Missense_Mutation	SNP	A	A	G	rs1966834	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57982620A>G	ENST00000309433.6	+	1	404	c.404A>G	c.(403-405)cAc>cGc	p.H135R		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	135			H -> R (in dbSNP:rs1966834).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GCCTATGACCACTTTGTGGCG	0.438													G|||	2598	0.51877	0.2844	0.5418	5008	,	,		22010	0.8036		0.4205	False		,,,				2504	0.6268				p.H135R		Atlas-SNP	.											.	OR1S1	139	.	0			c.A404G	GRCh37	CM035848	OR1S1	M	rs1966834	PASS	.	G	ARG/HIS	1324,3078	695.1+/-405.9	197,930,1074	182.0	173.0	176.0		404	3.5	1.0	11	dbSNP_92	176	3621,4971	625.0+/-397.7	779,2063,1454	yes	missense	OR1S1	NM_001004458.1	29	976,2993,2528	GG,GA,AA		42.1439,30.0772,38.056	benign	135/326	57982620	4945,8049	2201	4296	6497	SO:0001583	missense	219959	exon1			ATGACCACTTTGT	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.404A>G	11.37:g.57982620A>G	ENSP00000311688:p.His135Arg	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	189	188	0.994709	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1083	0.4958791208791209	148	0.3008130081300813	187	0.5165745856353591	433	0.756993006993007	315	0.4155672823218997	G	0.809	-0.752849	0.03041	0.300772	0.421439	ENSG00000172774	ENST00000309433	T	0.04809	3.55	3.45	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	N	0.000173	T	0.00012	0.0000	N	0.00006	-3.19	0.46458	P	9.470000000000312E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.32107	-0.9919	9	0.02654	T	1	.	10.0632	0.42288	0.102:0.0:0.898:0.0	rs1966834;rs52803988;rs1966834	135	Q8NH92	OR1S1_HUMAN	R	135	ENSP00000311688:H135R	ENSP00000311688:H135R	H	+	2	0	OR1S1	57739196	1.000000	0.71417	1.000000	0.80357	0.381000	0.30169	6.004000	0.70709	0.671000	0.31185	-0.348000	0.07805	CAC	A|0.569;G|0.431	0.431	strong		0.438	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14752601	14752601	+	Silent	SNP	A	A	G	rs200428778	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:14752601A>G	ENST00000358984.4	+	2	438	c.258A>G	c.(256-258)gcA>gcG	p.A86A	ANKRD30B_ENST00000447268.2_Silent_p.A86A|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	86										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						ATGGCCATGCAGAAGTAGTAA	0.448													a|||	12	0.00239617	0.0008	0.0	5008	,	,		17952	0.0		0.0099	False		,,,				2504	0.001				p.A86A		Atlas-SNP	.											ANKRD30B_ENST00000358984,NS,carcinoma,+2,2	ANKRD30B	237	2	0			c.A258G						PASS	.	A		1,1383		0,1,691	69.0	61.0	64.0		258	-3.2	0.0	18		64	16,3166		0,16,1575	no	coding-synonymous	ANKRD30B	NM_001145029.1		0,17,2266	GG,GA,AA		0.5028,0.0723,0.3723		86/1393	14752601	17,4549	692	1591	2283	SO:0001819	synonymous_variant	374860	exon2			CCATGCAGAAGTA	BC028407	CCDS54182.1	18p11.21	2013-01-10			ENSG00000180777	ENSG00000180777		"""Ankyrin repeat domain containing"""	24165	protein-coding gene	gene with protein product						11280766	Standard	NM_001145029		Approved	NY-BR-1.1	uc010dlo.2	Q9BXX2		ENST00000358984.4:c.258A>G	18.37:g.14752601A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	CCDS54182.1																																																																																			A|0.992;G|0.008	0.008	strong		0.448	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
MAPT	4137	hgsc.bcm.edu	37	17	44067400	44067400	+	Missense_Mutation	SNP	T	T	C	rs10445337	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44067400T>C	ENST00000571987.1	+	7	1339	c.1339T>C	c.(1339-1341)Tcc>Ccc	p.S447P	MAPT_ENST00000334239.8_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000344290.5_Missense_Mutation_p.S447P|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Missense_Mutation_p.S447P|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000431008.3_Intron|MAPT_ENST00000415613.2_Missense_Mutation_p.S447P|MAPT_ENST00000574436.1_Intron			P10636	TAU_HUMAN	microtubule-associated protein tau	447			S -> P (in dbSNP:rs10445337). {ECO:0000269|PubMed:9629852}.		adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	TTCTGTCACTTCCCGAACTGG	0.532													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		17709	0.001		0.2406	False		,,,				2504	0.0613				p.S447P		Atlas-SNP	.											.	MAPT	135	.	0			c.T1339C						PASS	.	C	PRO/SER,,,,,,PRO/SER,	225,4181	804.2+/-415.7	6,213,1984	125.0	126.0	125.0		1339,,,,,,1339,	4.1	1.0	17	dbSNP_119	125	1917,6683	721.4+/-406.4	220,1477,2603	yes	missense,intron,intron,intron,intron,intron,missense,intron	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	74,,,,,,74,	226,1690,4587	CC,CT,TT		22.2907,5.1067,16.4693	benign,,,,,,benign,	447/777,,,,,,447/759,	44067400	2142,10864	2203	4300	6503	SO:0001583	missense	4137	exon8			GTCACTTCCCGAA	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1339T>C	17.37:g.44067400T>C	ENSP00000458742:p.Ser447Pro	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Missense_Mutation	SNP	ENST00000571987.1	37	CCDS11501.1	256	0.11721611721611722	12	0.024390243902439025	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	C	4.363	0.066874	0.08388	0.051067	0.222907	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000415613	T;T;T	0.22539	1.95;1.95;1.95	5.17	4.14	0.48551	.	0.000000	0.41396	N	0.000891	T	0.00012	0.0000	N	0.00436	-1.5	0.09310	P	0.9999999999986787	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37842	-0.9688	9	0.02654	T	1	-9.971	6.5764	0.22569	0.0:0.7842:0.0:0.2158	rs10445337;rs52822487;rs10445337	447;447	P10636-9;P10636	.;TAU_HUMAN	P	447	ENSP00000340820:S447P;ENSP00000262410:S447P;ENSP00000410838:S447P	ENSP00000262410:S447P	S	+	1	0	MAPT	41423237	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.033000	0.30191	1.427000	0.47276	-0.320000	0.08662	TCC	T|0.856;C|0.144	0.144	strong		0.532	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
BCAS1	8537	hgsc.bcm.edu	37	20	52573971	52573971	+	Splice_Site	SNP	T	T	G	rs35575210	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:52573971T>G	ENST00000395961.3	-	10	1582	c.1416A>C	c.(1414-1416)caA>caC	p.Q472H	BCAS1_ENST00000371435.2_Intron|BCAS1_ENST00000434986.2_Intron|BCAS1_ENST00000371440.3_Intron	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	472			Q -> H (in dbSNP:rs35575210).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			GGTCACTTACTTGGCAGCTGG	0.433													T|||	662	0.132188	0.0265	0.1354	5008	,	,		20559	0.1429		0.1899	False		,,,				2504	0.2025				p.Q472H		Atlas-SNP	.											.	BCAS1	77	.	0			c.A1416C						PASS	.	T	HIS/GLN	205,4201	125.7+/-162.9	3,199,2001	225.0	181.0	196.0		1416	4.4	1.0	20	dbSNP_126	196	1645,6955	302.6+/-306.0	151,1343,2806	yes	missense-near-splice	BCAS1	NM_003657.2	24	154,1542,4807	GG,GT,TT		19.1279,4.6527,14.2242	probably-damaging	472/585	52573971	1850,11156	2203	4300	6503	SO:0001630	splice_region_variant	8537	exon10			ACTTACTTGGCAG	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.1416+1A>C	20.37:g.52573971T>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	181	84	0.464088	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	278|278	0.12728937728937728|0.12728937728937728	10|10	0.02032520325203252|0.02032520325203252	58|58	0.16022099447513813|0.16022099447513813	68|68	0.11888111888111888|0.11888111888111888	142|142	0.18733509234828497|0.18733509234828497	T|T	18.88|18.88	3.717957|3.717957	0.68844|0.68844	0.046527|0.046527	0.191279|0.191279	ENSG00000064787|ENSG00000064787	ENST00000422805|ENST00000395961	.|T	.|0.21361	.|2.01	5.55|5.55	4.43|4.43	0.53597|0.53597	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.58101|0.58101	1.795|1.795	0.09310|0.09310	P|P	0.9999999999999795|0.9999999999999795	.|P;P	.|0.35348	.|0.496;0.496	.|B;B	.|0.34242	.|0.178;0.178	T|T	0.21177|0.21177	-1.0253|-1.0253	4|7	.|.	.|.	.|.	.|.	6.56|6.56	0.22481|0.22481	0.1465:0.0:0.1745:0.679|0.1465:0.0:0.1745:0.679	rs35575210;rs61749686|rs35575210;rs61749686	.|472;472	.|A0AVG7;O75363	.|.;BCAS1_HUMAN	T|H	135|472	.|ENSP00000379290:Q472H	.|.	K|Q	-|-	2|3	0|2	BCAS1|BCAS1	52007378|52007378	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.912000|0.912000	0.54170|0.54170	1.178000|1.178000	0.31981|0.31981	0.908000|0.908000	0.36671|0.36671	0.459000|0.459000	0.35465|0.35465	AAA|CAA	T|0.857;G|0.143	0.143	strong		0.433	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	Missense_Mutation
IL3	3562	hgsc.bcm.edu	37	5	131396478	131396478	+	Missense_Mutation	SNP	C	C	T	rs40401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131396478C>T	ENST00000296870.2	+	1	257	c.79C>T	c.(79-81)Ccc>Tcc	p.P27S		NM_000588.3	NP_000579.2	P08700	IL3_HUMAN	interleukin 3	27			P -> S (in dbSNP:rs40401). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2544122, ECO:0000269|Ref.4}.		cell-cell signaling (GO:0007267)|embryonic hemopoiesis (GO:0035162)|immune response (GO:0006955)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-3 receptor binding (GO:0005135)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)	10		all_cancers(142;7.42e-12)|Lung NSC(810;4.25e-07)|all_lung(232;1.93e-06)|Prostate(281;0.00741)|Breast(839;0.0544)|Lung SC(612;0.122)|Ovarian(839;0.223)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	GBM - Glioblastoma multiforme(465;0.0161)|Lung(113;0.105)	Amlexanox(DB01025)	CCAGACAACGCCCTTGAAGAC	0.537													T|||	2101	0.419529	0.5703	0.3156	5008	,	,		21475	0.5714		0.2515	False		,,,				2504	0.3057				p.P27S		Atlas-SNP	.											IL3,NS,carcinoma,0,1	IL3	28	1	0			c.C79T						PASS	.	T	SER/PRO	2268,2138	578.4+/-384.7	588,1092,523	100.0	97.0	98.0		79	1.2	0.0	5	dbSNP_76	98	1951,6649	725.2+/-406.5	226,1499,2575	yes	missense	IL3	NM_000588.3	74	814,2591,3098	TT,TC,CC		22.686,48.5247,32.4389	benign	27/153	131396478	4219,8787	2203	4300	6503	SO:0001583	missense	3562	exon1			ACAACGCCCTTGA	M14743	CCDS4149.1	5q23-q31	2014-04-04	2014-04-04		ENSG00000164399	ENSG00000164399		"""Interleukins and interleukin receptors"""	6011	protein-coding gene	gene with protein product	"""multilineage-colony-stimulating factor"", ""hematopoietic growth factor"", ""P-cell stimulating factor"", ""mast-cell growth factor"", ""colony-stimulating factor, multiple"""	147740	"""interleukin 3 (colony-stimulating factor, multiple)"""			3489530	Standard	NM_000588		Approved	IL-3, MULTI-CSF, MCGF, MGC79398, MGC79399	uc003kwe.1	P08700	OTTHUMG00000059640	ENST00000296870.2:c.79C>T	5.37:g.131396478C>T	ENSP00000296870:p.Pro27Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_000588	Q6GS87	Missense_Mutation	SNP	ENST00000296870.2	37	CCDS4149.1	911	0.41712454212454214	291	0.5914634146341463	100	0.27624309392265195	319	0.5576923076923077	201	0.26517150395778366	T	0.343	-0.949559	0.02304	0.514753	0.22686	ENSG00000164399	ENST00000296870	T	0.26373	1.74	3.24	1.18	0.20946	.	1.255760	0.05782	N	0.608778	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.18968	0.032	B	0.20577	0.03	T	0.43766	-0.9371	9	0.07644	T	0.81	-2.5392	6.6006	0.22699	0.0:0.6449:0.2355:0.1196	rs40401;rs657709;rs3181636;rs52803049;rs59548569;rs40401	27	P08700	IL3_HUMAN	S	27	ENSP00000296870:P27S	ENSP00000296870:P27S	P	+	1	0	IL3	131424377	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.640000	0.00108	0.009000	0.14813	-0.834000	0.03071	CCC	C|0.616;N|0.000	.	strong		0.537	IL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132639.1	NM_000588	
ZNF83	55769	hgsc.bcm.edu	37	19	53117017	53117017	+	Silent	SNP	T	T	G	rs7248435	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:53117017T>G	ENST00000597597.1	-	2	3054	c.801A>C	c.(799-801)ggA>ggC	p.G267G	ZNF83_ENST00000544146.1_Silent_p.G267G|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000536937.1_Silent_p.G267G|ZNF83_ENST00000545872.1_Silent_p.G267G|ZNF83_ENST00000391789.4_Silent_p.G267G|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Silent_p.G267G|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000301096.3_Silent_p.G267G			P51522	ZNF83_HUMAN	zinc finger protein 83	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		GGAAGACCTTTCCACATACAT	0.403													T|||	1368	0.273163	0.1649	0.4323	5008	,	,		17989	0.497		0.2137	False		,,,				2504	0.137				p.G267G		Atlas-SNP	.											.	ZNF83	73	.	0			c.A801C						PASS	.	T	,,,,,,,,	384,4022		38,308,1857	84.0	78.0	80.0		801,801,801,801,801,801,801,801,801	0.5	0.1	19	dbSNP_116	80	907,7693		116,675,3509	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF83	NM_001105549.1,NM_001105550.1,NM_001105551.1,NM_001105552.1,NM_001105553.1,NM_001105554.1,NM_001242531.1,NM_001242538.1,NM_018300.3	,,,,,,,,	154,983,5366	GG,GT,TT		10.5465,8.7154,9.9262	,,,,,,,,	267/517,267/517,267/517,267/517,267/489,267/489,267/489,267/489,267/517	53117017	1291,11715	2203	4300	6503	SO:0001819	synonymous_variant	55769	exon3			GACCTTTCCACAT	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.801A>C	19.37:g.53117017T>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Silent	SNP	ENST00000597597.1	37	CCDS12854.1	.	.	.	.	.	.	.	.	.	.	-	0.039	-1.293052	0.01375	0.087154	0.105465	ENSG00000167766	ENST00000434535	.	.	.	1.64	0.536	0.17138	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999998759	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.1646	0.10300	0.0:0.2128:0.3331:0.4541	rs7248435;rs7248435	.	.	.	.	-1	.	.	.	-	.	.	ZNF83	57808829	0.000000	0.05858	0.070000	0.20053	0.008000	0.06430	-3.515000	0.00445	0.214000	0.20742	-0.811000	0.03165	.	T|0.881;G|0.119	0.119	strong		0.403	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
TBCK	93627	hgsc.bcm.edu	37	4	107156462	107156462	+	Missense_Mutation	SNP	C	C	T	rs34961213	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:107156462C>T	ENST00000273980.5	-	16	1860	c.1413G>A	c.(1411-1413)atG>atA	p.M471I	TBCK_ENST00000394708.2_Missense_Mutation_p.M471I|TBCK_ENST00000361687.4_Missense_Mutation_p.M408I|TBCK_ENST00000432496.2_Missense_Mutation_p.M471I|TBCK_ENST00000394706.3_Missense_Mutation_p.M432I					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TTAAACCTCTCATAAGAGGAG	0.358													C|||	684	0.136581	0.0076	0.1167	5008	,	,		14619	0.1468		0.1789	False		,,,				2504	0.271				p.M471I		Atlas-SNP	.											.	TBCK	89	.	0			c.G1413A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET,ILE/MET	144,4262	99.8+/-138.5	2,140,2061	82.0	73.0	76.0		1413,1413,1296,1224	5.9	1.0	4	dbSNP_126	76	1484,7116	279.9+/-294.2	139,1206,2955	yes	missense,missense,missense,missense	TBCK	NM_001163435.1,NM_001163436.1,NM_001163437.1,NM_033115.3	10,10,10,10	141,1346,5016	TT,TC,CC		17.2558,3.2683,12.5173	benign,benign,benign,benign	471/894,471/894,432/855,408/831	107156462	1628,11378	2203	4300	6503	SO:0001583	missense	93627	exon15			ACCTCTCATAAGA		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1413G>A	4.37:g.107156462C>T	ENSP00000273980:p.Met471Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	37	CCDS54788.1	284	0.13003663003663005	7	0.014227642276422764	51	0.1408839779005525	95	0.1660839160839161	131	0.17282321899736147	C	16.03	3.007829	0.54361	0.032683	0.172558	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708;ENST00000503516	T;T;T;T;T;T	0.09538	2.97;2.97;2.97;2.97;2.97;2.97	5.9	5.9	0.94986	Rab-GAP/TBC domain (4);	0.193345	0.56097	D	0.000023	T	0.00039	0.0001	N	0.20685	0.6	0.25671	P	0.9858951	B;B;B	0.18310	0.001;0.027;0.004	B;B;B	0.13407	0.001;0.007;0.009	T	0.44772	-0.9306	9	0.59425	D	0.04	.	20.2789	0.98501	0.0:1.0:0.0:0.0	rs34961213;rs61733979	471;432;408	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	I	471;471;408;432;471;1	ENSP00000273980:M471I;ENSP00000405847:M471I;ENSP00000355338:M408I;ENSP00000378196:M432I;ENSP00000378198:M471I;ENSP00000423834:M1I	ENSP00000273980:M471I	M	-	3	0	TBCK	107375911	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	1.989000	0.40707	2.788000	0.95919	0.650000	0.86243	ATG	C|0.876;T|0.124	0.124	strong		0.358	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743249	22743249	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:22743249T>A	ENST00000560659.2	+	8	1484	c.1484T>A	c.(1483-1485)aTg>aAg	p.M495K	GOLGA6L1_ENST00000316397.3_Missense_Mutation_p.M545K			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	538										NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						caggaggagatgatgcaggaa	0.552																																					p.M545K		Atlas-SNP	.											GOLGA6L1,caecum,carcinoma,0,1	GOLGA6L1	20	1	0			c.T1634A						scavenged	.																																			SO:0001583	missense	283767	exon8			AGGAGATGATGCA	AK097517	CCDS73699.1	15q11.2	2012-10-05	2010-02-12		ENSG00000197414	ENSG00000277865			37444	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 1"""				Standard	NM_001001413		Approved		uc010tzx.1	Q8N7Z2	OTTHUMG00000171883	ENST00000560659.2:c.1484T>A	15.37:g.22743249T>A	ENSP00000452626:p.Met495Lys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	26	2	0.0769231	NM_001001413		Missense_Mutation	SNP	ENST00000560659.2	37		.	.	.	.	.	.	.	.	.	.	.	0.004	-2.347201	0.00219	.	.	ENSG00000197414	ENST00000316397	T	0.07688	3.17	.	.	.	.	.	.	.	.	T	0.01976	0.0062	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.37197	-0.9716	5	0.02654	T	1	.	1.3913	0.02251	0.3258:0.0:0.3254:0.3488	.	.	.	.	K	545	ENSP00000320207:M545K	ENSP00000320207:M545K	M	+	2	0	GOLGA6L1	20294613	0.232000	0.23762	0.009000	0.14445	0.009000	0.06853	-1.148000	0.03185	-1.878000	0.01128	-2.010000	0.00438	ATG	.	.	none		0.552	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
OR8B4	283162	hgsc.bcm.edu	37	11	124294236	124294236	+	Missense_Mutation	SNP	A	A	G	rs4057749	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124294236A>G	ENST00000356130.3	-	1	553	c.532T>C	c.(532-534)Tgt>Cgt	p.C178R		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	178			C -> R (in dbSNP:rs4057749). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AGAACGTCACACAGATAATGG	0.507													A|||	1410	0.28155	0.4637	0.196	5008	,	,		21494	0.2163		0.1988	False		,,,				2504	0.2485				p.C178R		Atlas-SNP	.											.	OR8B4	60	.	0			c.T532C						PASS	.	A	ARG/CYS	1714,2688	514.1+/-368.5	337,1040,824	92.0	63.0	73.0		532	4.0	1.0	11	dbSNP_108	73	1966,6632	344.6+/-325.4	219,1528,2552	yes	missense	OR8B4	NM_001005196.1	180	556,2568,3376	GG,GA,AA		22.8658,38.9368,28.3077	probably-damaging	178/310	124294236	3680,9320	2201	4299	6500	SO:0001583	missense	283162	exon1			CGTCACACAGATA	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.532T>C	11.37:g.124294236A>G	ENSP00000348449:p.Cys178Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	96	85	0.885417	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	580	0.26556776556776557	249	0.5060975609756098	71	0.19613259668508287	107	0.18706293706293706	153	0.20184696569920843	a	16.05	3.011484	0.54468	0.389368	0.228658	ENSG00000198657	ENST00000356130	T	0.62498	0.02	4.02	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000019	T	0.00012	0.0000	H	0.96048	3.76	0.09310	P	0.9999999884866	D	0.89917	1.0	D	0.81914	0.995	T	0.38499	-0.9658	9	0.72032	D	0.01	.	13.7135	0.62682	1.0:0.0:0.0:0.0	rs4057749;rs4057749	178	Q96RC9	OR8B4_HUMAN	R	178	ENSP00000348449:C178R	ENSP00000348449:C178R	C	-	1	0	OR8B4	123799446	1.000000	0.71417	1.000000	0.80357	0.486000	0.33341	7.016000	0.76393	2.070000	0.61991	0.529000	0.55759	TGT	A|0.720;G|0.280	0.280	strong		0.507	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
NID2	22795	hgsc.bcm.edu	37	14	52520746	52520746	+	Missense_Mutation	SNP	G	G	T	rs35657569	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:52520746G>T	ENST00000216286.5	-	4	1060	c.1061C>A	c.(1060-1062)cCt>cAt	p.P354H	NID2_ENST00000541773.1_Missense_Mutation_p.P301H	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	354			P -> H (in dbSNP:rs35657569).		basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					ACCCTCTAAAGGCTTTGTATC	0.483													G|||	139	0.0277556	0.0038	0.0519	5008	,	,		20528	0.0		0.0895	False		,,,				2504	0.0082				p.P354H		Atlas-SNP	.											.	NID2	201	.	0			c.C1061A						PASS	.	G	HIS/PRO	71,4335	63.5+/-100.7	0,71,2132	92.0	91.0	92.0		1061	1.3	0.0	14	dbSNP_126	92	787,7813	185.3+/-233.1	34,719,3547	yes	missense	NID2	NM_007361.3	77	34,790,5679	TT,TG,GG		9.1512,1.6114,6.597	possibly-damaging	354/1376	52520746	858,12148	2203	4300	6503	SO:0001583	missense	22795	exon4			TCTAAAGGCTTTG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1061C>A	14.37:g.52520746G>T	ENSP00000216286:p.Pro354His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	99	56	0.565657	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	91	0.041666666666666664	5	0.01016260162601626	26	0.0718232044198895	0	0.0	60	0.079155672823219	G	14.90	2.674903	0.47781	0.016114	0.091512	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	D;D	0.83992	-1.79;-1.69	5.48	1.27	0.21489	.	0.804485	0.10712	N	0.642768	T	0.15825	0.0381	L	0.29908	0.895	0.09310	N	1	D;P	0.65815	0.995;0.761	P;B	0.60473	0.875;0.338	T	0.46679	-0.9174	10	0.59425	D	0.04	.	2.5868	0.04832	0.0946:0.153:0.4015:0.3509	rs35657569	301;354	Q14112-2;Q14112	.;NID2_HUMAN	H	354;301;356	ENSP00000216286:P354H;ENSP00000443730:P301H	ENSP00000216286:P354H	P	-	2	0	NID2	51590496	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	0.286000	0.18902	0.664000	0.31047	0.563000	0.77884	CCT	G|0.939;T|0.061	0.061	strong		0.483	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29911271	29911271	+	Missense_Mutation	SNP	G	G	C	rs3098019	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29911271G>C	ENST00000396634.1	+	5	911	c.570G>C	c.(568-570)gaG>gaC	p.E190D	HLA-A_ENST00000376806.5_Missense_Mutation_p.E190D|HLA-A_ENST00000376802.2_Missense_Mutation_p.E190D|HLA-A_ENST00000376809.5_Missense_Mutation_p.E190D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	190	Alpha-2.		EW -> DG (in allele A*31:05).		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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CGTGCGTGGAGTGGCTCCGCA	0.677									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	1082	0.216054	0.1679	0.2089	5008	,	,		13958	0.2183		0.2167	False		,,,				2504	0.2832				p.E190D		Atlas-SNP	.											HLA-A,colon,carcinoma,0,1	HLA-A	89	1	0			c.G570C						PASS	.	G	ASP/GLU	8,3012		1,6,1503	48.0	39.0	42.0		570	0.6	0.0	6	dbSNP_131	42	10,5400		1,8,2696	no	missense	HLA-A	NM_002116.7	45	2,14,4199	CC,CG,GG		0.1848,0.2649,0.2135	benign	190/366	29911271	18,8412	1510	2705	4215	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGTGGAGTGGCTC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.570G>C	6.37:g.29911271G>C	ENSP00000379873:p.Glu190Asp	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	419	0.19184981684981686	56	0.11382113821138211	78	0.2154696132596685	139	0.243006993006993	146	0.19261213720316622	.	9.897	1.205898	0.22205	0.002649	0.001848	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00995	5.46;5.46;5.46;5.46	3.78	0.557	0.17260	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	1.991270	0.03551	U	0.225458	T	0.00637	0.0021	M	0.78916	2.43	0.80722	P	0.0	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.001;0.0;0.001;0.0;0.001;0.001	T	0.46582	-0.9181	9	0.62326	D	0.03	.	4.9635	0.14078	0.111:0.0:0.5236:0.3654	rs3129016;rs9260160;rs41553132	69;190;190;190;190;190;190	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	D	190	ENSP00000379873:E190D;ENSP00000366002:E190D;ENSP00000366005:E190D;ENSP00000365998:E190D	ENSP00000365998:E190D	E	+	3	2	HLA-A	30019250	0.578000	0.26717	0.003000	0.11579	0.119000	0.20118	1.433000	0.34947	-0.016000	0.14127	0.485000	0.47835	GAG	C|0.644;G|0.356	0.644	strong		0.677	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
AQP8	343	hgsc.bcm.edu	37	16	25239805	25239805	+	Missense_Mutation	SNP	G	G	C	rs2287798	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:25239805G>C	ENST00000219660.5	+	6	903	c.778G>C	c.(778-780)Gct>Cct	p.A260P	AQP8_ENST00000566125.1_Missense_Mutation_p.A254P	NM_001169.2	NP_001160.2	O94778	AQP8_HUMAN	aquaporin 8	260			A -> P (in dbSNP:rs2287798).		canalicular bile acid transport (GO:0015722)|cellular response to cAMP (GO:0071320)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)	p.A260P(2)		NS(1)|breast(1)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	16				GBM - Glioblastoma multiforme(48;0.044)		CATCCTGAAGGCTCGGTGAAG	0.592													G|||	2074	0.414137	0.4077	0.4308	5008	,	,		19369	0.5298		0.3459	False		,,,				2504	0.362				p.A260P		Atlas-SNP	.											AQP8_ENST00000219660,NS,carcinoma,0,2	AQP8	75	2	2	Substitution - Missense(2)	stomach(2)	c.G778C						PASS	.	G	PRO/ALA	1822,2572	533.3+/-373.7	378,1066,753	97.0	84.0	88.0		778	-1.5	0.0	16	dbSNP_100	88	3191,5409	482.4+/-370.9	578,2035,1687	yes	missense	AQP8	NM_001169.2	27	956,3101,2440	CC,CG,GG		37.1047,41.4656,38.5793	benign	260/262	25239805	5013,7981	2197	4300	6497	SO:0001583	missense	343	exon6			CTGAAGGCTCGGT	BC040630	CCDS10626.1	16p12	2008-02-05			ENSG00000103375	ENSG00000103375		"""Ion channels / Aquaporins"""	642	protein-coding gene	gene with protein product		603750				9806845, 10393433	Standard	NM_001169		Approved		uc002doc.3	O94778	OTTHUMG00000097013	ENST00000219660.5:c.778G>C	16.37:g.25239805G>C	ENSP00000219660:p.Ala260Pro	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_001169	Q8IUU3|Q9UIA4	Missense_Mutation	SNP	ENST00000219660.5	37	CCDS10626.1	903	0.41346153846153844	203	0.41260162601626016	146	0.40331491712707185	291	0.5087412587412588	263	0.3469656992084433	G	9.751	1.167366	0.21621	0.414656	0.371047	ENSG00000103375	ENST00000219660	D	0.90844	-2.74	4.71	-1.46	0.08800	Aquaporin-like (1);	2.407790	0.01641	N	0.024060	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.26975	0.165	B	0.23018	0.043	T	0.21449	-1.0245	9	0.40728	T	0.16	1.6603	8.6705	0.34147	0.0:0.1258:0.4556:0.4186	rs2287798;rs56573772;rs2287798	260	O94778	AQP8_HUMAN	P	260	ENSP00000219660:A260P	ENSP00000219660:A260P	A	+	1	0	AQP8	25147306	0.174000	0.23070	0.003000	0.11579	0.003000	0.03518	0.297000	0.19101	-0.007000	0.14345	-0.831000	0.03077	GCT	G|0.599;C|0.401	0.401	strong		0.592	AQP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214102.2	NM_001169	
OR52E4	390081	hgsc.bcm.edu	37	11	5906143	5906143	+	Silent	SNP	T	T	C	rs11823809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5906143T>C	ENST00000316987.2	+	1	643	c.621T>C	c.(619-621)taT>taC	p.Y207Y		NM_001005165.1	NP_001005165.1	Q8NGH9	O52E4_HUMAN	olfactory receptor, family 52, subfamily E, member 4	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(2)|prostate(1)|skin(2)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.24e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGATTTCTTATATTATTGTGG	0.448													T|||	1792	0.357827	0.3222	0.402	5008	,	,		21992	0.3641		0.4085	False		,,,				2504	0.316				p.Y207Y		Atlas-SNP	.											.	OR52E4	65	.	0			c.T621C						PASS	.	T		1502,2900	477.5+/-357.9	262,978,961	298.0	257.0	271.0		621	-0.4	0.9	11	dbSNP_120	271	3625,4967	522.8+/-380.2	780,2065,1451	no	coding-synonymous	OR52E4	NM_001005165.1		1042,3043,2412	CC,CT,TT		42.1904,34.1209,39.4567		207/313	5906143	5127,7867	2201	4296	6497	SO:0001819	synonymous_variant	390081	exon1			TTCTTATATTATT	AB065817	CCDS31401.1	11p15.4	2012-08-09			ENSG00000180974	ENSG00000180974		"""GPCR / Class A : Olfactory receptors"""	15213	protein-coding gene	gene with protein product							Standard	NM_001005165		Approved		uc010qzs.2	Q8NGH9	OTTHUMG00000168804	ENST00000316987.2:c.621T>C	11.37:g.5906143T>C		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	288	140	0.486111	NM_001005165	Q6IFG0	Silent	SNP	ENST00000316987.2	37	CCDS31401.1																																																																																			T|0.611;C|0.389	0.389	strong		0.448	OR52E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401146.1	NM_001005165	
KLHL40	131377	hgsc.bcm.edu	37	3	42728144	42728144	+	Missense_Mutation	SNP	A	A	G	rs6805421	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42728144A>G	ENST00000287777.4	+	1	1134	c.1034A>G	c.(1033-1035)aAc>aGc	p.N345S		NM_152393.2	NP_689606.2	Q2TBA0	KLH40_HUMAN	kelch-like family member 40	345			N -> S (in dbSNP:rs6805421). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)		p.N345S(1)									TCCCTCTCCAACCAGGTCCCC	0.557													A|||	3118	0.622604	0.3638	0.5922	5008	,	,		20403	0.8343		0.672	False		,,,				2504	0.7249				p.N345S		Atlas-SNP	.											KBTBD5,colon,carcinoma,0,2	.	.	2	1	Substitution - Missense(1)	stomach(1)	c.A1034G						PASS	.	A	SER/ASN	1828,2578	535.8+/-374.3	385,1058,760	86.0	76.0	79.0		1034	3.2	1.0	3	dbSNP_116	79	5454,3146	656.0+/-401.3	1730,1994,576	yes	missense	KBTBD5	NM_152393.2	46	2115,3052,1336	GG,GA,AA		36.5814,41.4889,44.0105	benign	345/622	42728144	7282,5724	2203	4300	6503	SO:0001583	missense	131377	exon1			TCTCCAACCAGGT	AK056577	CCDS2703.1	3p21.33	2013-07-30	2013-02-22	2013-01-08	ENSG00000157119	ENSG00000157119		"""Kelch-like"", ""BTB/POZ domain containing"""	30372	protein-coding gene	gene with protein product	"""sarcosynapsin"", ""nemaline myopathy type 8"""	615340	"""kelch repeat and BTB (POZ) domain containing 5"", ""kelch-like 40 (Drosophila)"""	KBTBD5		23746549	Standard	NM_152393		Approved	SRYP, NEM8	uc003clv.1	Q2TBA0	OTTHUMG00000133045	ENST00000287777.4:c.1034A>G	3.37:g.42728144A>G	ENSP00000287777:p.Asn345Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_152393	Q86SI1|Q96MR2	Missense_Mutation	SNP	ENST00000287777.4	37	CCDS2703.1	1409	0.6451465201465202	211	0.42886178861788615	229	0.6325966850828729	460	0.8041958041958042	509	0.6715039577836411	A	6.854	0.526858	0.13066	0.414889	0.634186	ENSG00000157119	ENST00000287777;ENST00000452129	T	0.66099	-0.19	5.08	3.24	0.37175	Kelch-type beta propeller (1);	0.201582	0.52532	D	0.000072	T	0.00012	0.0000	N	0.02539	-0.55	0.46631	P	8.700000000000374E-4	B	0.09022	0.002	B	0.04013	0.001	T	0.40059	-0.9583	9	0.07325	T	0.83	.	11.0302	0.47767	0.1611:0.7139:0.125:0.0	rs6805421;rs6805421	345	Q2TBA0	KBTB5_HUMAN	S	345;90	ENSP00000287777:N345S	ENSP00000287777:N345S	N	+	2	0	KBTBD5	42703148	0.915000	0.31059	0.993000	0.49108	0.996000	0.88848	1.917000	0.39996	0.518000	0.28383	-0.280000	0.10049	AAC	A|0.408;G|0.592	0.592	strong		0.557	KLHL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256651.1	NM_152393	
LCTL	197021	hgsc.bcm.edu	37	15	66850362	66850362	+	Missense_Mutation	SNP	C	C	T	rs1030986	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:66850362C>T	ENST00000341509.5	-	7	849	c.718G>A	c.(718-720)Gcc>Acc	p.A240T	LCTL_ENST00000537670.1_Missense_Mutation_p.A67T	NM_207338.2	NP_997221.2	Q6UWM7	LCTL_HUMAN	lactase-like	240			A -> T (in dbSNP:rs1030986).		carbohydrate metabolic process (GO:0005975)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GAATGCCAGGCTTTGGCGTGG	0.552													C|||	291	0.058107	0.034	0.1167	5008	,	,		17544	0.0893		0.0229	False		,,,				2504	0.0532				p.A240T		Atlas-SNP	.											.	LCTL	73	.	0			c.G718A						PASS	.	C	THR/ALA	122,4280	90.6+/-129.3	3,116,2082	127.0	113.0	118.0		718	5.0	1.0	15	dbSNP_86	118	116,8482	59.8+/-121.6	0,116,4183	yes	missense	LCTL	NM_207338.2	58	3,232,6265	TT,TC,CC		1.3492,2.7715,1.8308	possibly-damaging	240/568	66850362	238,12762	2201	4299	6500	SO:0001583	missense	197021	exon7			GCCAGGCTTTGGC	AY358729	CCDS10220.1, CCDS61678.1	15q21.3	2008-02-05			ENSG00000188501	ENSG00000188501			15583	protein-coding gene	gene with protein product	"""klotho gamma"", ""KL lactase phlorizin hydrolase"""					12084582	Standard	NM_207338		Approved	KLPH, FLJ33279, KLG	uc002aqc.3	Q6UWM7	OTTHUMG00000133207	ENST00000341509.5:c.718G>A	15.37:g.66850362C>T	ENSP00000343490:p.Ala240Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_207338	B3KQY0	Missense_Mutation	SNP	ENST00000341509.5	37	CCDS10220.1	116	0.05311355311355311	17	0.034552845528455285	31	0.0856353591160221	50	0.08741258741258741	18	0.023746701846965697	C	17.54	3.415609	0.62511	0.027715	0.013492	ENSG00000188501	ENST00000537670;ENST00000341509	T;T	0.59224	0.28;1.14	4.99	4.99	0.66335	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.150400	0.64402	D	0.000014	T	0.04634	0.0126	M	0.68952	2.095	0.45194	D	0.998209	B	0.22080	0.064	B	0.22753	0.041	T	0.27157	-1.0082	10	0.59425	D	0.04	-15.3831	17.8088	0.88609	0.0:1.0:0.0:0.0	rs1030986;rs56618400;rs1030986	240	Q6UWM7	LCTL_HUMAN	T	67;240	ENSP00000445419:A67T;ENSP00000343490:A240T	ENSP00000343490:A240T	A	-	1	0	LCTL	64637416	0.999000	0.42202	0.963000	0.40424	0.542000	0.35054	4.072000	0.57563	2.752000	0.94435	0.655000	0.94253	GCC	C|0.963;T|0.037	0.037	strong		0.552	LCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256921.2	NM_207338	
CBFA2T2	9139	hgsc.bcm.edu	37	20	32212690	32212690	+	Silent	SNP	C	C	T	rs3803939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:32212690C>T	ENST00000346541.3	+	7	1377	c.840C>T	c.(838-840)ccC>ccT	p.P280P	CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000492345.1_Silent_p.P251P|CBFA2T2_ENST00000375279.2_Silent_p.P280P|CBFA2T2_ENST00000397800.1_Silent_p.P251P|CBFA2T2_ENST00000342704.6_Silent_p.P271P|CBFA2T2_ENST00000359606.3_Silent_p.P290P	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	280					epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.P280P(1)		breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						TCATGAATCCCGGGGGCCAAT	0.532													T|||	3351	0.669129	0.8638	0.5692	5008	,	,		20127	0.754		0.4871	False		,,,				2504	0.5767				p.P280P	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											CBFA2T2,NS,carcinoma,0,1	CBFA2T2	93	1	1	Substitution - coding silent(1)	prostate(1)	c.C840T						PASS	.	T	,,	3418,988	368.3+/-318.6	1327,764,112	121.0	100.0	107.0		813,753,840	-8.9	0.0	20	dbSNP_107	107	4152,4448	588.8+/-392.4	1013,2126,1161	no	coding-synonymous,coding-synonymous,coding-synonymous	CBFA2T2	NM_001032999.2,NM_001039709.1,NM_005093.3	,,	2340,2890,1273	TT,TC,CC		48.2791,22.424,41.7961	,,	271/596,251/576,280/605	32212690	7570,5436	2203	4300	6503	SO:0001819	synonymous_variant	9139	exon7			GAATCCCGGGGGC	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"""Zinc fingers, MYND-type"""	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.840C>T	20.37:g.32212690C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Silent	SNP	ENST00000346541.3	37	CCDS13221.1																																																																																			T|0.624;G|0.002;C|0.371;N|0.000;A|0.003	0.624	strong		0.532	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999	
GOLGA7	51125	hgsc.bcm.edu	37	8	41355096	41355096	+	Silent	SNP	C	C	T	rs17656952	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:41355096C>T	ENST00000357743.4	+	2	381	c.180C>T	c.(178-180)ctC>ctT	p.L60L	GOLGA7_ENST00000518270.1_Silent_p.L60L|GOLGA7_ENST00000405786.2_Silent_p.L60L|GOLGA7_ENST00000520817.1_Silent_p.L60L	NM_001002296.1	NP_001002296.1	Q7Z5G4	GOGA7_HUMAN	golgin A7	60					Golgi to plasma membrane protein transport (GO:0043001)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|Golgi stack (GO:0005795)|intrinsic component of Golgi membrane (GO:0031228)|palmitoyltransferase complex (GO:0002178)				breast(1)|large_intestine(1)	2	Ovarian(28;0.014)|Colorectal(14;0.0234)|Lung SC(25;0.211)	all_lung(54;0.000771)|Lung NSC(58;0.0031)|Hepatocellular(245;0.014)|Esophageal squamous(32;0.0559)	Colorectal(10;0.0014)|OV - Ovarian serous cystadenocarcinoma(14;0.00596)|LUSC - Lung squamous cell carcinoma(45;0.0137)|COAD - Colon adenocarcinoma(11;0.0147)			CAGAGAAGCTCGGCGGCCAGT	0.368													C|||	465	0.0928514	0.1165	0.1297	5008	,	,		19845	0.0		0.1471	False		,,,				2504	0.0746				p.L60L		Atlas-SNP	.											.	GOLGA7	10	.	0			c.C180T						PASS	.	C	,,	628,3778	272.5+/-270.8	46,536,1621	152.0	160.0	157.0		180,180,180	-2.6	1.0	8	dbSNP_123	157	1260,7340	253.0+/-278.9	81,1098,3121	no	coding-synonymous,coding-synonymous,coding-synonymous	GOLGA7	NM_001002296.1,NM_001174124.1,NM_016099.2	,,	127,1634,4742	TT,TC,CC		14.6512,14.2533,14.5164	,,	60/138,60/135,60/138	41355096	1888,11118	2203	4300	6503	SO:0001819	synonymous_variant	51125	exon2			GAAGCTCGGCGGC	AF125102	CCDS34887.1, CCDS55226.1	8p11.21	2011-10-25	2010-02-12		ENSG00000147533	ENSG00000147533			24876	protein-coding gene	gene with protein product		609453	"""golgi autoantigen, golgin subfamily a, 7"""			11042152	Standard	NM_001174124		Approved	GCP16, HSPC041, GOLGA3AP1, GOLGA7A	uc003xnu.3	Q7Z5G4	OTTHUMG00000164077	ENST00000357743.4:c.180C>T	8.37:g.41355096C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_001002296	D3DSX9|J3KQ24|Q96EQ4|Q9P1S0|Q9Y5U7	Silent	SNP	ENST00000357743.4	37	CCDS34887.1																																																																																			C|0.876;T|0.124	0.124	strong		0.368	GOLGA7-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377142.1	NM_016099	
CYP1B1	1545	hgsc.bcm.edu	37	2	38298203	38298203	+	Missense_Mutation	SNP	C	C	G	rs1056836	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:38298203C>G	ENST00000260630.3	-	3	1695	c.1294G>C	c.(1294-1296)Gtg>Ctg	p.V432L	CYP1B1_ENST00000494864.1_5'UTR|CYP1B1_ENST00000407341.1_Missense_Mutation_p.V432L	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	432			L -> V (in allele CYP1B1*3, allele CYP1B1*5, allele CYP1B1*6 and allele CYP1B1*7; 1.6-fold increase in 17beta- estradiol 4-hydroxylation activity but no change in 17beta-estradiol 2- hydroxylation activity; 2-fold reduction in testosterone 6beta-hydroxylation activity and 3-fold reduction in testosterone affinity; 6-fold and 4-fold increase in progesterone 6beta- and 16alpha-hydroxylation activity, respectively and 7-fold reduction in progesterone affinity; dbSNP:rs1056836). {ECO:0000269|PubMed:10655546, ECO:0000269|PubMed:10739169, ECO:0000269|PubMed:11527932, ECO:0000269|PubMed:11774072, ECO:0000269|PubMed:11854439, ECO:0000269|PubMed:11980847, ECO:0000269|PubMed:12036985, ECO:0000269|PubMed:12525557, ECO:0000269|PubMed:14635112, ECO:0000269|PubMed:15342693, ECO:0000269|PubMed:15475877, ECO:0000269|PubMed:16688110, ECO:0000269|PubMed:9497261, ECO:0000269|PubMed:9823305, ECO:0000269|Ref.5}.		angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|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)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	GGCCACTTCACTGGGTCATGA	0.493													C|||	3079	0.614816	0.1831	0.7233	5008	,	,		19209	0.9087		0.6024	False		,,,				2504	0.8313				p.V432L		Atlas-SNP	.											CYP1B1,caecum,carcinoma,0,1	CYP1B1	39	1	0			c.G1294C	GRCh37	CM004465	CYP1B1	M	rs1056836	PASS	.	C	LEU/VAL	1014,3392	374.9+/-321.4	137,740,1326	73.0	64.0	67.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1294	5.9	0.0	2	dbSNP_86	67	4781,3819	612.4+/-396.0	1344,2093,863	yes	missense	CYP1B1	NM_000104.3	32	1481,2833,2189	GG,GC,CC		44.407,23.0141,44.5564	benign	432/544	38298203	5795,7211	2203	4300	6503	SO:0001583	missense	1545	exon3			ACTTCACTGGGTC	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.1294G>C	2.37:g.38298203C>G	ENSP00000260630:p.Val432Leu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_000104	Q5TZW8|Q93089|Q9H316	Missense_Mutation	SNP	ENST00000260630.3	37	CCDS1793.1	1340	0.6135531135531136	95	0.19308943089430894	249	0.6878453038674033	517	0.9038461538461539	479	0.6319261213720316	C	9.985	1.229235	0.22542	0.230141	0.55593	ENSG00000138061	ENST00000260630;ENST00000407341	T;T	0.68025	-0.3;-0.3	5.95	5.95	0.96441	.	1.219440	0.05416	N	0.543299	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.53041	-0.8494	8	0.27785	T	0.31	.	13.4692	0.61273	0.0:0.8433:0.1567:0.0	rs1056836;rs3731848;rs17405323;rs52802961;rs59494749;rs1056836	432	Q53TK1	.	L	432	ENSP00000260630:V432L;ENSP00000384972:V432L	ENSP00000260630:V432L	V	-	1	0	CYP1B1	38151707	0.000000	0.05858	0.033000	0.17914	0.966000	0.64601	0.163000	0.16520	2.824000	0.97209	0.655000	0.94253	GTG	C|0.487;G|0.513	0.513	strong		0.493	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
COL4A4	1286	hgsc.bcm.edu	37	2	227896976	227896976	+	Silent	SNP	C	C	T	rs10203363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:227896976C>T	ENST00000396625.3	-	39	3801	c.3594G>A	c.(3592-3594)ggG>ggA	p.G1198G	COL4A4_ENST00000329662.7_Silent_p.G1198G	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1198	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GACCAGGTGGCCCCACATCAT	0.493													C|||	2479	0.495008	0.5613	0.4769	5008	,	,		18481	0.4028		0.4364	False		,,,				2504	0.5736				p.G1198G		Atlas-SNP	.											.	COL4A4	215	.	0			c.G3594A						PASS	.	C		1929,1773		493,943,415	35.0	36.0	36.0		3594	-3.7	1.0	2	dbSNP_119	36	3443,4761		726,1991,1385	no	coding-synonymous	COL4A4	NM_000092.4		1219,2934,1800	TT,TC,CC		41.9673,47.893,45.1201		1198/1691	227896976	5372,6534	1851	4102	5953	SO:0001819	synonymous_variant	1286	exon39			AGGTGGCCCCACA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3594G>A	2.37:g.227896976C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			C|0.544;T|0.456	0.456	strong		0.493	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
ARSG	22901	hgsc.bcm.edu	37	17	66364691	66364691	+	Missense_Mutation	SNP	C	C	G	rs1558876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:66364691C>G	ENST00000448504.2	+	7	1503	c.707C>G	c.(706-708)aCc>aGc	p.T236S	ARSG_ENST00000582154.1_3'UTR|ARSG_ENST00000452479.2_Missense_Mutation_p.T72S	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	236			T -> S (in dbSNP:rs1558876).		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)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGTTTCAGCACCAGCGGGAGG	0.597													C|||	1382	0.275958	0.1914	0.3934	5008	,	,		18964	0.126		0.4076	False		,,,				2504	0.3262				p.T236S		Atlas-SNP	.											.	ARSG	55	.	0			c.C707G						PASS	.	C	SER/THR	984,3422	363.6+/-316.6	121,742,1340	62.0	62.0	62.0		707	4.2	1.0	17	dbSNP_88	62	3769,4831	530.3+/-381.8	834,2101,1365	yes	missense	ARSG	NM_014960.3	58	955,2843,2705	GG,GC,CC		43.8256,22.3332,36.5447	benign	236/526	66364691	4753,8253	2203	4300	6503	SO:0001583	missense	22901	exon7			TCAGCACCAGCGG	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.707C>G	17.37:g.66364691C>G	ENSP00000407193:p.Thr236Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	36	0.654545	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	37	CCDS11676.1	624	0.2857142857142857	92	0.18699186991869918	137	0.3784530386740331	80	0.13986013986013987	315	0.4155672823218997	C	3.051	-0.195352	0.06259	0.223332	0.438256	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.26	4.24	0.50183	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.713760	0.13649	N	0.372438	T	0.00012	0.0000	N	0.16478	0.41	0.44492	P	0.002569999999999961	B	0.18166	0.026	B	0.18871	0.023	T	0.37126	-0.9719	8	0.38643	T	0.18	.	12.9999	0.58670	0.2038:0.7962:0.0:0.0	rs1558876;rs3826352;rs17739339;rs52794112;rs58616018;rs1558876	236	Q96EG1	ARSG_HUMAN	S	236;135	.	ENSP00000407193:T135S	T	+	2	0	ARSG	63876286	0.184000	0.23200	0.962000	0.40283	0.373000	0.29922	2.123000	0.41996	2.733000	0.93635	0.655000	0.94253	ACC	C|0.673;G|0.327	0.327	strong		0.597	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
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 GAIIx	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_ENST00000337852.6_Missense_Mutation_p.T202I|AF196970.3_ENST00000416061.1_RNA|SUV39H1_ENST00000453214.2_Intron	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	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	94	52	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	
CEP112	201134	hgsc.bcm.edu	37	17	64023642	64023642	+	Silent	SNP	A	A	G	rs11079628	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:64023642A>G	ENST00000392769.2	-	16	1851	c.1633T>C	c.(1633-1635)Tta>Cta	p.L545L	CEP112_ENST00000535342.2_Silent_p.L545L|CEP112_ENST00000537949.1_Silent_p.L503L|CEP112_ENST00000541355.1_Silent_p.L180L	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa	545					receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						ATGTGTTTTAAATGACTTTTC	0.239													A|||	2686	0.536342	0.233	0.6585	5008	,	,		16280	0.873		0.4384	False		,,,				2504	0.6135				p.L545L		Atlas-SNP	.											.	CEP112	192	.	0			c.T1633C						PASS	.	A	,	1082,3192		161,760,1216	40.0	37.0	38.0		1633,1633	5.4	1.0	17	dbSNP_120	38	3290,5132		711,1868,1632	no	coding-synonymous,coding-synonymous	CEP112	NM_001199165.1,NM_145036.3	,	872,2628,2848	GG,GA,AA		39.0644,25.3159,34.436	,	545/956,545/956	64023642	4372,8324	2137	4211	6348	SO:0001819	synonymous_variant	201134	exon16			GTTTTAAATGACT	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.1633T>C	17.37:g.64023642A>G		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	143	143	1	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Silent	SNP	ENST00000392769.2	37	CCDS32710.1																																																																																			A|0.561;G|0.439	0.439	strong		0.239	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
PCNXL4	64430	hgsc.bcm.edu	37	14	60585131	60585131	+	Missense_Mutation	SNP	A	A	G	rs308998	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:60585131A>G	ENST00000406854.1	+	7	2217	c.1663A>G	c.(1663-1665)Aaa>Gaa	p.K555E	PCNXL4_ENST00000535349.1_5'Flank|PCNXL4_ENST00000406949.1_Missense_Mutation_p.K321E|PCNXL4_ENST00000404681.2_Missense_Mutation_p.K555E|PCNXL4_ENST00000317623.4_Missense_Mutation_p.K321E			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	555				EK -> QE (in Ref. 2; CAH56141). {ECO:0000305}.		integral component of membrane (GO:0016021)											ATGGACAGAGAAAAAACAACG	0.368													A|||	1708	0.341054	0.5794	0.1398	5008	,	,		18327	0.3462		0.1183	False		,,,				2504	0.3855				p.K321E		Atlas-SNP	.											.	.	.	.	0			c.A961G						PASS	.	A	GLU/LYS	2099,2213		511,1077,568	97.0	96.0	96.0		961	4.9	1.0	14	dbSNP_79	96	1072,7478		73,926,3276	yes	missense	C14orf135	NM_022495.5	56	584,2003,3844	GG,GA,AA		12.538,48.6781,24.654	benign	321/939	60585131	3171,9691	2156	4275	6431	SO:0001583	missense	64430	exon6			ACAGAGAAAAAAC	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1663A>G	14.37:g.60585131A>G	ENSP00000384801:p.Lys555Glu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	222	220	0.990991	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		602	0.27564102564102566	269	0.5467479674796748	56	0.15469613259668508	197	0.34440559440559443	80	0.10554089709762533	A	17.38	3.374655	0.61735	0.486781	0.12538	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681	T;T;T;T	0.27890	1.74;1.74;1.64;1.74	6.07	4.93	0.64822	.	.	.	.	.	T	0.00012	0.0000	M	0.78637	2.42	0.09310	P	1.0	B;B	0.15930	0.015;0.005	B;B	0.14578	0.011;0.01	T	0.40590	-0.9555	8	0.21540	T	0.41	.	12.334	0.55056	0.9343:0.0:0.0657:0.0	rs308998;rs308998	555;321	Q63HM2;B5MC47	CN135_HUMAN;.	E	321;555;321;555	ENSP00000317396:K321E;ENSP00000384801:K555E;ENSP00000385201:K321E;ENSP00000385713:K555E	ENSP00000317396:K321E	K	+	1	0	C14orf135	59654884	1.000000	0.71417	0.996000	0.52242	0.989000	0.77384	5.726000	0.68515	1.116000	0.41820	-0.280000	0.10049	AAA	A|0.702;G|0.298	0.298	strong		0.368	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
PLCB2	5330	hgsc.bcm.edu	37	15	40589002	40589002	+	Silent	SNP	A	A	G	rs2229691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:40589002A>G	ENST00000260402.3	-	14	1680	c.1431T>C	c.(1429-1431)acT>acC	p.T477T	PLCB2_ENST00000456256.2_Silent_p.T477T|PLCB2_ENST00000557821.1_Silent_p.T477T	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	477					activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		CCTCCCCACCAGTATCCTTAC	0.607													A|||	1779	0.355232	0.1293	0.4755	5008	,	,		19466	0.6736		0.2167	False		,,,				2504	0.3896				p.T477T		Atlas-SNP	.											.	PLCB2	177	.	0			c.T1431C						PASS	.	A		635,3191		58,519,1336	54.0	54.0	54.0		1431	-0.3	0.0	15	dbSNP_98	54	1913,6327		223,1467,2430	no	coding-synonymous	PLCB2	NM_004573.2		281,1986,3766	GG,GA,AA		23.216,16.597,21.1172		477/1186	40589002	2548,9518	1913	4120	6033	SO:0001819	synonymous_variant	5330	exon14			CCCACCAGTATCC		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1431T>C	15.37:g.40589002A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	37	CCDS42020.1																																																																																			A|0.697;G|0.303	0.303	strong		0.607	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
SEC22C	9117	hgsc.bcm.edu	37	3	42610374	42610374	+	Silent	SNP	A	A	G	rs2271186	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42610374A>G	ENST00000264454.3	-	2	308	c.165T>C	c.(163-165)ggT>ggC	p.G55G	SEC22C_ENST00000423701.2_Silent_p.G55G|SEC22C_ENST00000273156.7_Silent_p.G55G|SEC22C_ENST00000493107.1_5'UTR|SEC22C_ENST00000536332.1_5'UTR|SEC22C_ENST00000417572.1_Silent_p.G55G			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	55	Longin. {ECO:0000255|PROSITE- ProRule:PRU00231}.				ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)	3				KIRC - Kidney renal clear cell carcinoma(284;0.222)		TAAAGTCACAACCTTCTGCAG	0.383													G|||	2684	0.535942	0.7958	0.2968	5008	,	,		18703	0.5843		0.337	False		,,,				2504	0.5092				p.G55G		Atlas-SNP	.											.	SEC22C	27	.	0			c.T165C						PASS	.	G	,,,	3067,1339	447.5+/-348.4	1075,917,211	57.0	63.0	61.0		165,165,165,165	3.3	0.1	3	dbSNP_100	61	2798,5802	676.4+/-403.3	470,1858,1972	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEC22C	NM_001201572.1,NM_001201584.1,NM_004206.3,NM_032970.3	,,,	1545,2775,2183	GG,GA,AA		32.5349,30.3904,45.0946	,,,	55/251,55/229,55/251,55/304	42610374	5865,7141	2203	4300	6503	SO:0001819	synonymous_variant	9117	exon2			GTCACAACCTTCT	AF039568	CCDS2699.1, CCDS2700.1, CCDS56246.1	3p24.3-p22.1	2006-04-25	2006-04-25	2006-04-25	ENSG00000093183	ENSG00000093183			16828	protein-coding gene	gene with protein product		604028	"""SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)"""	SEC22L3		9501016, 11001058	Standard	NM_004206		Approved	MGC13261, MGC5373	uc003clj.3	Q9BRL7	OTTHUMG00000131797	ENST00000264454.3:c.165T>C	3.37:g.42610374A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	116	50	0.431034	NM_001201584	O95152|Q68CX3|Q6UW18	Silent	SNP	ENST00000264454.3	37	CCDS2700.1																																																																																			A|0.520;G|0.480	0.480	strong		0.383	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206	
ADAM23	8745	hgsc.bcm.edu	37	2	207459467	207459467	+	Silent	SNP	C	C	T	rs3732079	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:207459467C>T	ENST00000264377.3	+	23	2413	c.2085C>T	c.(2083-2085)gcC>gcT	p.A695A	ADAM23_ENST00000374415.3_Silent_p.A695A|ADAM23_ENST00000374416.1_Silent_p.A695A	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	695					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.A695A(1)		NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		TTAGTGGTGCCCATGTAGTTT	0.428													T|||	896	0.178914	0.2595	0.2205	5008	,	,		21136	0.1736		0.1193	False		,,,				2504	0.1074				p.A695A	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											ADAM23,NS,carcinoma,0,1	ADAM23	239	1	1	Substitution - coding silent(1)	stomach(1)	c.C2085T						PASS	.	T		980,3426	732.4+/-410.4	108,764,1331	171.0	174.0	173.0		2085	0.8	1.0	2	dbSNP_107	173	855,7745	780.2+/-407.7	52,751,3497	no	coding-synonymous	ADAM23	NM_003812.2		160,1515,4828	TT,TC,CC		9.9419,22.2424,14.1089		695/833	207459467	1835,11171	2203	4300	6503	SO:0001819	synonymous_variant	8745	exon23			TGGTGCCCATGTA	AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"""ADAM metallopeptidase domain containing"""	202	protein-coding gene	gene with protein product		603710	"""a disintegrin and metalloproteinase domain 23"""			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.2085C>T	2.37:g.207459467C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	195	99	0.507692	NM_003812	A2RU59	Silent	SNP	ENST00000264377.3	37	CCDS2369.1																																																																																			C|0.856;G|0.000;T|0.144	0.144	strong		0.428	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	
FDFT1	2222	hgsc.bcm.edu	37	8	11667179	11667179	+	Silent	SNP	C	C	T	rs8417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11667179C>T	ENST00000220584.4	+	3	423	c.201C>T	c.(199-201)aaC>aaT	p.N67N	FDFT1_ENST00000530664.1_Silent_p.N3N|FDFT1_ENST00000525900.1_Silent_p.N60N|FDFT1_ENST00000446331.2_Intron|FDFT1_ENST00000443614.2_Silent_p.N67N|FDFT1_ENST00000538689.1_5'UTR|FDFT1_ENST00000528812.1_Silent_p.N3N|FDFT1_ENST00000528643.1_5'UTR|FDFT1_ENST00000525777.1_5'UTR	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	67					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		TTTACAGCAACGCAGTGTGCA	0.393													C|||	1191	0.237819	0.0923	0.2406	5008	,	,		20475	0.4474		0.1918	False		,,,				2504	0.2638				p.N67N		Atlas-SNP	.											.	FDFT1	25	.	0			c.C201T						PASS	.	C		514,3892	235.8+/-248.2	25,464,1714	74.0	70.0	72.0		201	-2.9	0.5	8	dbSNP_52	72	1652,6948	305.2+/-307.3	168,1316,2816	no	coding-synonymous	FDFT1	NM_004462.3		193,1780,4530	TT,TC,CC		19.2093,11.6659,16.6539		67/418	11667179	2166,10840	2203	4300	6503	SO:0001819	synonymous_variant	2222	exon3			CAGCAACGCAGTG	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.201C>T	8.37:g.11667179C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Silent	SNP	ENST00000220584.4	37	CCDS5985.1																																																																																			C|0.809;T|0.191	0.191	strong		0.393	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
SYNE3	161176	hgsc.bcm.edu	37	14	95918625	95918625	+	Silent	SNP	T	T	C	rs4905318	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:95918625T>C	ENST00000334258.5	-	6	1247	c.1233A>G	c.(1231-1233)ccA>ccG	p.P411P	SYNE3_ENST00000557275.1_Silent_p.P411P|SYNE3_ENST00000554873.1_Silent_p.P168P|SYNE3_ENST00000553340.1_Silent_p.P411P	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	411					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						TATCAGAGAGTGGCTTCAGGT	0.612											OREG0022900	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2308	0.460863	0.382	0.6023	5008	,	,		17704	0.5655		0.4105	False		,,,				2504	0.411				p.P411P		Atlas-SNP	.											.	SYNE3	130	.	0			c.A1233G						PASS	.	T		1715,2691	515.5+/-368.9	338,1039,826	116.0	97.0	104.0		1233	-9.4	0.1	14	dbSNP_111	104	3637,4963	522.0+/-380.0	752,2133,1415	no	coding-synonymous	C14orf49	NM_152592.3		1090,3172,2241	CC,CT,TT		42.2907,38.9242,41.1502		411/976	95918625	5352,7654	2203	4300	6503	SO:0001819	synonymous_variant	161176	exon6			AGAGAGTGGCTTC	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.1233A>G	14.37:g.95918625T>C		Somatic	79	0	0	1316	WXS	Illumina HiSeq	Phase_I	97	97	1	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	CCDS9935.1																																																																																			T|0.562;C|0.438	0.438	strong		0.612	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
RBM15B	29890	hgsc.bcm.edu	37	3	51430657	51430657	+	Silent	SNP	A	A	C	rs3804766	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:51430657A>C	ENST00000323686.4	+	1	1927	c.1827A>C	c.(1825-1827)tcA>tcC	p.S609S		NM_013286.4	NP_037418.3	Q8NDT2	RB15B_HUMAN	RNA binding motif protein 15B	609					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|large_intestine(5)|lung(3)	12				BRCA - Breast invasive adenocarcinoma(193;0.000224)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		CAACCCATTCACCATATGAGG	0.627													C|||	743	0.148363	0.1172	0.245	5008	,	,		18301	0.3532		0.0199	False		,,,				2504	0.0429				p.S609S		Atlas-SNP	.											.	RBM15B	47	.	0			c.A1827C						PASS	.	C		400,4004	781.6+/-414.5	20,360,1822	61.0	57.0	58.0		1827	-1.0	1.0	3	dbSNP_107	58	179,8421	810.0+/-407.1	3,173,4124	no	coding-synonymous	RBM15B	NM_013286.4		23,533,5946	CC,CA,AA		2.0814,9.0827,4.4525		609/891	51430657	579,12425	2202	4300	6502	SO:0001819	synonymous_variant	29890	exon1			CCATTCACCATAT	AL831838	CCDS33764.1	3p21.1	2013-02-12			ENSG00000179837	ENSG00000259956		"""RNA binding motif (RRM) containing"""	24303	protein-coding gene	gene with protein product		612602				16129689	Standard	NM_013286		Approved	HUMAGCGB, OTT3	uc003dbd.3	Q8NDT2	OTTHUMG00000156896	ENST00000323686.4:c.1827A>C	3.37:g.51430657A>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_013286	A4QPG7|Q6QE19|Q9BV96	Silent	SNP	ENST00000323686.4	37	CCDS33764.1																																																																																			A|0.905;C|0.095	0.095	strong		0.627	RBM15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346489.1	NM_013286	
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 GAIIx	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	Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000534699.1_Missense_Mutation_p.N440S|CSDE1_ENST00000339438.6_Missense_Mutation_p.N409S|CSDE1_ENST00000530886.1_Missense_Mutation_p.N310S|CSDE1_ENST00000369530.1_Missense_Mutation_p.N455S|CSDE1_ENST00000438362.2_Missense_Mutation_p.N486S|CSDE1_ENST00000261443.5_Missense_Mutation_p.N409S	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	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	108	39	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	
TIMM17B	10245	hgsc.bcm.edu	37	X	48751471	48751471	+	Silent	SNP	A	A	G	rs1128363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:48751471A>G	ENST00000376582.3	-	5	376	c.228T>C	c.(226-228)atT>atC	p.I76I	TIMM17B_ENST00000495490.2_Silent_p.I96I|TIMM17B_ENST00000396779.3_Silent_p.I126I|TIMM17B_ENST00000472645.1_5'UTR|TIMM17B_ENST00000465150.2_Silent_p.I126I	NM_005834.3	NP_005825.1	O60830	TI17B_HUMAN	translocase of inner mitochondrial membrane 17 homolog B (yeast)	76					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane presequence translocase complex (GO:0005744)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)	6						GGCCACAGTCAATGGTGGAGA	0.587													a|||	2762	0.731656	0.7368	0.4063	3775	,	,		12441	0.5714		0.3757	False		,,,				2504	0.5644				p.I126I		Atlas-SNP	.											.	TIMM17B	15	.	0			c.T378C						PASS	.	A	,	3514,320		1376,242,520,14,50	47.0	43.0	45.0		378,228	-4.1	0.9	X	dbSNP_86	45	3604,3124		722,1169,991,537,881	no	coding-synonymous,coding-synonymous	TIMM17B	NM_001167947.1,NM_005834.3	,	2098,1411,1511,551,931	GG,GA,G,AA,A		46.4328,8.3464,32.6075	,	126/223,76/173	48751471	7118,3444	2202	4300	6502	SO:0001819	synonymous_variant	10245	exon6			ACAGTCAATGGTG	AF034790	CCDS14308.1, CCDS55411.1	Xp11.23	2008-02-05			ENSG00000126768	ENSG00000126768			17310	protein-coding gene	gene with protein product		300249				10339406	Standard	NM_001167947		Approved	DXS9822, JM3	uc004dla.2	O60830	OTTHUMG00000034498	ENST00000376582.3:c.228T>C	X.37:g.48751471A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001167947	A8K2E2|J3KPV3|Q9UJV0	Silent	SNP	ENST00000376582.3	37	CCDS14308.1																																																																																			A|0.307;G|0.693	0.693	strong		0.587	TIMM17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083411.2	NM_005834	
PIK3CG	5294	hgsc.bcm.edu	37	7	106509331	106509331	+	Missense_Mutation	SNP	C	C	A	rs17847825	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:106509331C>A	ENST00000359195.3	+	2	1635	c.1325C>A	c.(1324-1326)tCc>tAc	p.S442Y	PIK3CG_ENST00000496166.1_Missense_Mutation_p.S442Y|PIK3CG_ENST00000440650.2_Missense_Mutation_p.S442Y	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	442	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						CCAGCACTGTCCAGCAAGGCC	0.507													C|||	581	0.116014	0.0068	0.0476	5008	,	,		20166	0.1925		0.1103	False		,,,				2504	0.2393				p.S442Y		Atlas-SNP	.											.	PIK3CG	279	.	0			c.C1325A						PASS	.	C	TYR/SER	113,4293	86.8+/-125.4	1,111,2091	63.0	66.0	65.0		1325	5.5	0.4	7	dbSNP_123	65	923,7677	205.2+/-247.7	46,831,3423	yes	missense	PIK3CG	NM_002649.2	144	47,942,5514	AA,AC,CC		10.7326,2.5647,7.9656	possibly-damaging	442/1103	106509331	1036,11970	2203	4300	6503	SO:0001583	missense	5294	exon2			CACTGTCCAGCAA		CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.1325C>A	7.37:g.106509331C>A	ENSP00000352121:p.Ser442Tyr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	234	0.10714285714285714	5	0.01016260162601626	25	0.06906077348066299	119	0.20804195804195805	85	0.11213720316622691	C	10.63	1.403953	0.25291	0.025647	0.107326	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.77750	-1.12;-1.12;-1.12	5.51	5.51	0.81932	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (2);	0.433331	0.27302	N	0.019989	T	0.00241	0.0007	L	0.44542	1.39	0.20975	P	0.999812377	D	0.58970	0.984	P	0.54174	0.744	T	0.00918	-1.1515	9	0.62326	D	0.03	-15.0241	19.4208	0.94720	0.0:1.0:0.0:0.0	rs17847825	442	P48736	PK3CG_HUMAN	Y	442	ENSP00000392258:S442Y;ENSP00000419260:S442Y;ENSP00000352121:S442Y	ENSP00000352121:S442Y	S	+	2	0	PIK3CG	106296567	0.997000	0.39634	0.389000	0.26208	0.075000	0.17131	5.486000	0.66856	2.593000	0.87608	0.655000	0.94253	TCC	C|0.912;A|0.088	0.088	strong		0.507	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
TOR3A	64222	hgsc.bcm.edu	37	1	179055020	179055020	+	Silent	SNP	C	C	T	rs2296376	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:179055020C>T	ENST00000367627.3	+	3	1383	c.631C>T	c.(631-633)Ctg>Ttg	p.L211L	TOR3A_ENST00000352445.6_Silent_p.L211L|TOR3A_ENST00000495145.1_3'UTR	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	211					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						ATATGTGGACCTGTACAAGGT	0.582													C|||	663	0.132388	0.1112	0.0663	5008	,	,		21673	0.255		0.1402	False		,,,				2504	0.0736				p.L211L		Atlas-SNP	.											.	TOR3A	28	.	0			c.C631T						PASS	.	C		466,3940	217.8+/-236.0	21,424,1758	59.0	53.0	55.0		631	-0.4	0.6	1	dbSNP_100	55	1061,7539	220.1+/-257.9	61,939,3300	no	coding-synonymous	TOR3A	NM_022371.3		82,1363,5058	TT,TC,CC		12.3372,10.5765,11.7407		211/398	179055020	1527,11479	2203	4300	6503	SO:0001819	synonymous_variant	64222	exon3			GTGGACCTGTACA	BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"""ATP-dependant interferon responsive"""	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.631C>T	1.37:g.179055020C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	55	20	0.363636	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Silent	SNP	ENST00000367627.3	37	CCDS1329.1																																																																																			C|0.872;T|0.128	0.128	strong		0.582	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371	
CD33	945	hgsc.bcm.edu	37	19	51728641	51728641	+	Missense_Mutation	SNP	A	A	G	rs2455069	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51728641A>G	ENST00000262262.4	+	2	226	c.205A>G	c.(205-207)Agg>Ggg	p.R69G	CD33_ENST00000436584.2_Intron|CD33_ENST00000391796.3_Missense_Mutation_p.R69G|CD33_ENST00000421133.2_Intron	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	69	Ig-like V-type.		R -> G (in dbSNP:rs2455069). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3139766}.		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.R69G(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	CATTATATCCAGGGACTCTCC	0.537													N|||	1678	0.335064	0.5318	0.2983	5008	,	,		19238	0.1042		0.4483	False		,,,				2504	0.2168				p.R69G		Atlas-SNP	.											CD33,NS,carcinoma,0,1	CD33	55	1	1	Substitution - Missense(1)	stomach(1)	c.A205G						PASS	.	G	,GLY/ARG,GLY/ARG	2210,2196		567,1076,560	80.0	81.0	81.0		,205,205	-7.0	0.0	19	dbSNP_100	81	3698,4902		800,2098,1402	yes	intron,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	,125,125	1367,3174,1962	GG,GA,AA		43.0,49.8411,45.4252	,benign,benign	,69/311,69/365	51728641	5908,7098	2203	4300	6503	SO:0001583	missense	945	exon2			ATATCCAGGGACT	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.205A>G	19.37:g.51728641A>G	ENSP00000262262:p.Arg69Gly	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	126	54	0.428571	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	762	0.3489010989010989	246	0.5	118	0.3259668508287293	53	0.09265734265734266	345	0.4551451187335092	.	5.312	0.242838	0.10077	0.501589	0.43	ENSG00000105383	ENST00000262262;ENST00000391796	T;T	0.45276	0.9;0.9	3.49	-6.98	0.01611	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	8.617480	0.00763	N	0.001149	T	0.00012	0.0000	L	0.36672	1.1	0.54753	P	1.2000000000012001E-5	B;B	0.06786	0.0;0.001	B;B	0.13407	0.003;0.009	T	0.36114	-0.9761	9	0.25751	T	0.34	.	1.204	0.01891	0.4573:0.1499:0.1144:0.2784	rs2455069;rs17659491;rs17856792;rs56575195;rs59927365;rs2455069	69;69	F8WAL2;P20138	.;CD33_HUMAN	G	69	ENSP00000262262:R69G;ENSP00000375673:R69G	ENSP00000262262:R69G	R	+	1	2	CD33	56420453	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.931000	0.00688	-1.842000	0.01181	-4.293000	0.00008	AGG	A|0.596;G|0.404	0.404	strong		0.537	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
CCDC50	152137	hgsc.bcm.edu	37	3	191093175	191093175	+	Intron	SNP	T	T	A	rs2028574	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:191093175T>A	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Missense_Mutation_p.I258N	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		GAGACTAAGATTAACCATCAG	0.488													A|||	2512	0.501597	0.7231	0.4683	5008	,	,		23143	0.4702		0.4105	False		,,,				2504	0.3517				p.I258N		Atlas-SNP	.											.	CCDC50	39	.	0			c.T773A						PASS	.	A	,ASN/ILE	2955,1451	470.4+/-355.7	985,985,233	92.0	85.0	87.0		,773	-3.5	0.0	3	dbSNP_94	87	3404,5196	640.0+/-399.5	674,2056,1570	yes	intron,missense	CCDC50	NM_174908.3,NM_178335.2	,149	1659,3041,1803	AA,AT,TT		39.5814,32.9324,48.8928	,benign	,258/483	191093175	6359,6647	2203	4300	6503	SO:0001627	intron_variant	152137	exon6			CTAAGATTAACCA	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4773T>A	3.37:g.191093175T>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_178335	Q86VH7	Missense_Mutation	SNP	ENST00000392455.3	37	CCDS33913.1	1090	0.4990842490842491	356	0.7235772357723578	165	0.4558011049723757	254	0.44405594405594406	315	0.4155672823218997	A	0.005	-2.181485	0.00308	0.670676	0.395814	ENSG00000152492	ENST00000392456	T	0.27557	1.66	5.48	-3.51	0.04696	.	1.680560	0.03069	N	0.156876	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	8	0.08599	T	0.76	.	0.2695	0.00229	0.3492:0.2346:0.1778:0.2384	rs2028574;rs52816502;rs2028574	258	Q8IVM0-2	.	N	258	ENSP00000376250:I258N	ENSP00000376250:I258N	I	+	2	0	CCDC50	192575869	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.452000	0.06787	-0.512000	0.06505	-0.839000	0.03059	ATT	A|0.494;N|0.000	0.494	strong		0.488	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
OR2L8	391190	hgsc.bcm.edu	37	1	248112794	248112794	+	Missense_Mutation	SNP	G	G	C	rs200574966		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248112794G>C	ENST00000357191.3	+	1	635	c.635G>C	c.(634-636)gGt>gCt	p.G212A	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.G212A(2)		endometrium(1)|kidney(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			CCCTTCATTGGTATTTCATGT	0.498																																					p.G212A		Atlas-SNP	.											OR2L8,NS,carcinoma,0,2	OR2L8	92	2	2	Substitution - Missense(2)	prostate(1)|skin(1)	c.G635C						scavenged	.						176.0	87.0	117.0					1																	248112794		2203	4300	6503	SO:0001583	missense	391190	exon1			TCATTGGTATTTC	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.635G>C	1.37:g.248112794G>C	ENSP00000349719:p.Gly212Ala	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	168	8	0.047619	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	0.010	-1.747988	0.00669	.	.	ENSG00000196936	ENST00000357191	T	0.35973	1.28	1.8	-3.61	0.04556	GPCR, rhodopsin-like superfamily (1);	0.592578	0.12695	U	0.446818	T	0.14657	0.0354	N	0.05012	-0.13	0.09310	N	1	B	0.06786	0.001	B	0.18263	0.021	T	0.11817	-1.0572	10	0.46703	T	0.11	.	5.6462	0.17590	0.0:0.2703:0.1902:0.5394	.	212	Q8NGY9	OR2L8_HUMAN	A	212	ENSP00000349719:G212A	ENSP00000349719:G212A	G	+	2	0	OR2L8	246179417	0.000000	0.05858	0.006000	0.13384	0.165000	0.22458	-1.473000	0.02339	-1.273000	0.02424	-0.515000	0.04445	GGT	.	.	weak		0.498	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
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 GAIIx	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_ENST00000480277.2_3'UTR|NAA15_ENST00000398947.1_Missense_Mutation_p.R148K	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	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	128	40	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	
KLHL22	84861	hgsc.bcm.edu	37	22	20800835	20800835	+	Silent	SNP	A	A	G	rs8748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:20800835A>G	ENST00000328879.4	-	6	1590	c.1434T>C	c.(1432-1434)gaT>gaC	p.D478D	KLHL22_ENST00000440659.2_Silent_p.D335D	NM_032775.3	NP_116164.2	Q53GT1	KLH22_HUMAN	kelch-like family member 22	478					cell division (GO:0051301)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein monoubiquitination (GO:0006513)	centrosome (GO:0005813)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|polar microtubule (GO:0005827)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|skin(2)|upper_aerodigestive_tract(1)	20	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GCACAGGCCCATCAGCCAGTG	0.597													A|||	916	0.182907	0.1619	0.0605	5008	,	,		19611	0.4544		0.0547	False		,,,				2504	0.1503				p.D478D		Atlas-SNP	.											.	KLHL22	52	.	0			c.T1434C						PASS	.	A		719,3687	298.7+/-285.4	54,611,1538	193.0	149.0	164.0		1434	-8.7	0.1	22	dbSNP_52	164	530,8070	147.3+/-202.7	11,508,3781	no	coding-synonymous	KLHL22	NM_032775.3		65,1119,5319	GG,GA,AA		6.1628,16.3187,9.6033		478/635	20800835	1249,11757	2203	4300	6503	SO:0001819	synonymous_variant	84861	exon6			AGGCCCATCAGCC		CCDS13780.1	22q11.21	2013-01-30	2013-01-30		ENSG00000099910	ENSG00000099910		"""Kelch-like"", ""BTB/POZ domain containing"""	25888	protein-coding gene	gene with protein product			"""kelch-like 22 (Drosophila)"""			12477932	Standard	NM_032775		Approved	FLJ14360, KELCHL	uc002zsl.2	Q53GT1	OTTHUMG00000150778	ENST00000328879.4:c.1434T>C	22.37:g.20800835A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_032775	A8K3Q4|A8MTV3|B7Z2G1|D3DX30|Q96B68|Q96KC6	Silent	SNP	ENST00000328879.4	37	CCDS13780.1																																																																																			A|0.853;G|0.147	0.147	strong		0.597	KLHL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320045.2	NM_032775	
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 GAIIx	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_ENST00000320078.7_Missense_Mutation_p.A303V|PSG11_ENST00000403486.1_Missense_Mutation_p.A181V|PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000306322.7_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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	102	49	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	
QPCT	25797	hgsc.bcm.edu	37	2	37599963	37599963	+	Missense_Mutation	SNP	A	A	C	rs4670696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:37599963A>C	ENST00000338415.3	+	7	1237	c.1079A>C	c.(1078-1080)cAt>cCt	p.H360P	QPCT_ENST00000537448.1_Missense_Mutation_p.H311P	NM_012413.3	NP_036545.1	Q16769	QPCT_HUMAN	glutaminyl-peptide cyclotransferase	360			H -> P (in dbSNP:rs4670696). {ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)|peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	extracellular vesicular exosome (GO:0070062)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)	p.H360R(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|stomach(2)	17		Ovarian(717;0.051)|all_hematologic(82;0.21)				GAATATCTTCATTTGTAATAC	0.318													A|||	672	0.134185	0.0023	0.2219	5008	,	,		19761	0.3839		0.0368	False		,,,				2504	0.093				p.H360P		Atlas-SNP	.											QPCT,colon,carcinoma,0,1	QPCT	34	1	1	Substitution - Missense(1)	large_intestine(1)	c.A1079C						PASS	.	A	PRO/HIS	59,4347	57.4+/-93.9	1,57,2145	70.0	66.0	67.0		1079	6.0	1.0	2	dbSNP_111	67	260,8340	100.3+/-161.8	2,256,4042	yes	missense	QPCT	NM_012413.3	77	3,313,6187	CC,CA,AA		3.0233,1.3391,2.4527	benign	360/362	37599963	319,12687	2203	4300	6503	SO:0001583	missense	25797	exon7			ATCTTCATTTGTA	X71125	CCDS1790.1	2p22	2008-07-31	2008-07-31		ENSG00000115828	ENSG00000115828	2.3.2.5		9753	protein-coding gene	gene with protein product	"""glutaminyl cyclase"""	607065				7999256	Standard	NM_012413		Approved	QC, GCT	uc002rqg.3	Q16769	OTTHUMG00000100963	ENST00000338415.3:c.1079A>C	2.37:g.37599963A>C	ENSP00000344829:p.His360Pro	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_012413	Q16770|Q3KRG6|Q53TR4	Missense_Mutation	SNP	ENST00000338415.3	37	CCDS1790.1	307	0.14056776556776557	3	0.006097560975609756	71	0.19613259668508287	208	0.36363636363636365	25	0.032981530343007916	A	19.26	3.794008	0.70452	0.013391	0.030233	ENSG00000115828	ENST00000338415;ENST00000537448	T;T	0.30182	2.26;1.54	5.96	5.96	0.96718	.	0.093684	0.64402	D	0.000001	T	0.00012	0.0000	L	0.49350	1.555	0.23780	P	0.99686459	D;P	0.56287	0.975;0.925	P;B	0.52424	0.698;0.406	T	0.39961	-0.9588	9	0.45353	T	0.12	0.5586	16.1181	0.81324	1.0:0.0:0.0:0.0	rs4670696;rs52824678;rs57682818;rs4670696	311;360	Q16769-2;Q16769	.;QPCT_HUMAN	P	360;311	ENSP00000344829:H360P;ENSP00000441606:H311P	ENSP00000344829:H360P	H	+	2	0	QPCT	37453467	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	3.941000	0.56607	2.284000	0.76573	0.528000	0.53228	CAT	A|0.925;C|0.075	0.075	strong		0.318	QPCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218572.2		
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387503	46387503	+	Silent	SNP	T	T	C	rs3745926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46387503T>C	ENST00000302165.3	-	1	1873	c.1530A>G	c.(1528-1530)ctA>ctG	p.L510L		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	510	Cys-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		GGGTGTCTTCTAGCCGCTCCC	0.701													C|||	1610	0.321486	0.5764	0.3127	5008	,	,		13341	0.3125		0.169	False		,,,				2504	0.1493				p.L510L		Atlas-SNP	.											.	IRF2BP1	23	.	0			c.A1530G						PASS	.	C		2131,2247		538,1055,596	18.0	18.0	18.0		1530	1.3	1.0	19	dbSNP_107	18	1602,6944		164,1274,2835	no	coding-synonymous	IRF2BP1	NM_015649.1		702,2329,3431	CC,CT,TT		18.7456,48.6752,28.8842		510/585	46387503	3733,9191	2189	4273	6462	SO:0001819	synonymous_variant	26145	exon1			GTCTTCTAGCCGC	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1530A>G	19.37:g.46387503T>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	20	8	0.4	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Silent	SNP	ENST00000302165.3	37	CCDS12678.1																																																																																			T|0.681;C|0.319	0.319	strong		0.701	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649	
SORBS1	10580	hgsc.bcm.edu	37	10	97106165	97106165	+	Silent	SNP	T	T	C	rs726176	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:97106165T>C	ENST00000361941.3	-	24	2453	c.2427A>G	c.(2425-2427)ctA>ctG	p.L809L	SORBS1_ENST00000371227.4_Silent_p.L763L|SORBS1_ENST00000306402.6_Silent_p.L556L|SORBS1_ENST00000354106.3_Silent_p.L779L|SORBS1_ENST00000371245.3_Silent_p.L660L|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000607232.1_Silent_p.L1069L|SORBS1_ENST00000371247.2_Silent_p.L809L|SORBS1_ENST00000393949.1_Silent_p.L779L|SORBS1_ENST00000371241.1_Silent_p.L459L|SORBS1_ENST00000277982.5_Silent_p.L831L|SORBS1_ENST00000371246.2_Silent_p.L831L|SORBS1_ENST00000347291.4_Silent_p.L621L|SORBS1_ENST00000371239.1_Silent_p.L586L|SORBS1_ENST00000371249.2_Silent_p.L591L|SORBS1_ENST00000353505.5_Silent_p.L660L	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		GCACTTACTTTAGTGTCTGAG	0.343													T|||	2043	0.407947	0.205	0.451	5008	,	,		19496	0.6696		0.3241	False		,,,				2504	0.4683				p.L831L		Atlas-SNP	.											.	SORBS1	185	.	0			c.A2493G						PASS	.	T	,,,,,,	915,3491	351.6+/-311.3	95,725,1383	85.0	85.0	85.0		2427,2493,1980,1545,1377,1773,1668	2.1	1.0	10	dbSNP_86	85	2392,6208	398.1+/-346.0	331,1730,2239	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	426,2455,3622	CC,CT,TT		27.814,20.7671,25.4267	,,,,,,	809/1293,831/1152,660/906,515/741,459/685,591/817,556/782	97106165	3307,9699	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon24			TTACTTTAGTGTC	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.2427A>G	10.37:g.97106165T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	41	25	0.609756	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			A|0.002;C|0.320	0.320	strong		0.343	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
SLC39A8	64116	hgsc.bcm.edu	37	4	103188709	103188709	+	Missense_Mutation	SNP	C	C	T	rs13107325	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:103188709C>T	ENST00000394833.2	-	7	1647	c.1171G>A	c.(1171-1173)Gct>Act	p.A391T	SLC39A8_ENST00000356736.4_Missense_Mutation_p.A391T|SLC39A8_ENST00000424970.2_Missense_Mutation_p.A391T	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	391			A -> T (in dbSNP:rs13107325).		transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		ATATTTGGAGCGAAATTGTTG	0.388													C|||	118	0.0235623	0.0023	0.0504	5008	,	,		18547	0.0		0.0795	False		,,,				2504	0.0				p.A391T		Atlas-SNP	.											.	SLC39A8	24	.	0			c.G1171A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	68,4338	61.1+/-98.1	1,66,2136	76.0	74.0	74.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1171,1171,970,1171	4.4	1.0	4	dbSNP_121	74	651,7949	166.8+/-218.7	25,601,3674	yes	missense,missense,missense,missense	SLC39A8	NM_001135146.1,NM_001135147.1,NM_001135148.1,NM_022154.5	58,58,58,58	26,667,5810	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	7.5698,1.5433,5.5282	benign,benign,benign,benign	391/461,391/445,324/394,391/461	103188709	719,12287	2203	4300	6503	SO:0001583	missense	64116	exon7			TTGGAGCGAAATT		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"""Solute carriers"""	20862	protein-coding gene	gene with protein product		608732	"""solute carrier family 39 (metal ion transporter), member 8"""			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.1171G>A	4.37:g.103188709C>T	ENSP00000378310:p.Ala391Thr	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	173	87	0.50289	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Missense_Mutation	SNP	ENST00000394833.2	37	CCDS3656.1	75	0.034340659340659344	1	0.0020325203252032522	15	0.04143646408839779	0	0.0	59	0.07783641160949868	C	18.44	3.624463	0.66901	0.015433	0.075698	ENSG00000138821	ENST00000424970;ENST00000356736;ENST00000394833	T;T;T	0.44482	0.92;0.92;0.92	5.28	4.43	0.53597	.	0.107964	0.64402	D	0.000005	T	0.03783	0.0107	L	0.50333	1.59	0.53688	D	0.999973	P;P;P	0.46987	0.888;0.589;0.72	P;B;B	0.51777	0.679;0.313;0.111	T	0.00232	-1.1895	10	0.40728	T	0.16	-5.1873	12.3948	0.55378	0.0:0.9192:0.0:0.0808	rs13107325;rs17225587;rs52796265;rs60329194;rs13107325	391;391;324	B4E2H3;Q9C0K1;Q9C0K1-2	.;S39A8_HUMAN;.	T	391	ENSP00000394548:A391T;ENSP00000349174:A391T;ENSP00000378310:A391T	ENSP00000349174:A391T	A	-	1	0	SLC39A8	103407732	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.769000	0.38522	2.483000	0.83821	0.655000	0.94253	GCT	C|0.945;T|0.055	0.055	strong		0.388	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
SBF2	81846	hgsc.bcm.edu	37	11	9853777	9853777	+	Missense_Mutation	SNP	G	G	C	rs12574508	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:9853777G>C	ENST00000256190.8	-	27	3783	c.3646C>G	c.(3646-3648)Cag>Gag	p.Q1216E		NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	1216	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.		Q -> E (in dbSNP:rs12574508). {ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		TTACCGGCCTGAGGGGAGTTC	0.448													G|||	412	0.0822684	0.0129	0.0908	5008	,	,		18045	0.1319		0.1044	False		,,,				2504	0.0961				p.Q1216E		Atlas-SNP	.											.	SBF2	146	.	0			c.C3646G						PASS	.	G	GLU/GLN	124,4278	92.0+/-130.7	2,120,2079	73.0	73.0	73.0		3646	3.8	1.0	11	dbSNP_120	73	945,7643	208.4+/-249.9	46,853,3395	yes	missense	SBF2	NM_030962.3	29	48,973,5474	CC,CG,GG		11.0037,2.8169,8.2294	benign	1216/1850	9853777	1069,11921	2201	4294	6495	SO:0001583	missense	81846	exon27			CGGCCTGAGGGGA	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	2135	protein-coding gene	gene with protein product	"""myotubularin related 13"""	607697	"""Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)"", ""DENN/MADD domain containing 7B"""	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.3646C>G	11.37:g.9853777G>C	ENSP00000256190:p.Gln1216Glu	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Missense_Mutation	SNP	ENST00000256190.8	37	CCDS31427.1	225	0.10302197802197802	8	0.016260162601626018	37	0.10220994475138122	93	0.16258741258741258	87	0.11477572559366754	G	2.604	-0.292350	0.05568	0.028169	0.110037	ENSG00000133812	ENST00000256190	D	0.92348	-3.02	5.76	3.78	0.43462	Myotubularin phosphatase domain (1);	0.239117	0.42172	D	0.000744	T	0.00936	0.0031	N	0.08118	0	0.37636	P	0.07812600000000003	B	0.14805	0.011	B	0.19148	0.024	T	0.46331	-0.9199	9	0.06236	T	0.91	.	9.0325	0.36267	0.0782:0.0:0.6632:0.2586	rs12574508;rs52834006;rs12574508	1216	Q86WG5	MTMRD_HUMAN	E	1216	ENSP00000256190:Q1216E	ENSP00000256190:Q1216E	Q	-	1	0	SBF2	9810353	0.686000	0.27661	1.000000	0.80357	0.954000	0.61252	1.045000	0.30341	2.882000	0.98803	0.655000	0.94253	CAG	G|0.910;C|0.090	0.090	strong		0.448	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962	
XIRP2	129446	hgsc.bcm.edu	37	2	168101142	168101142	+	Silent	SNP	T	T	G	rs61748633	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:168101142T>G	ENST00000409195.1	+	9	3329	c.3240T>G	c.(3238-3240)acT>acG	p.T1080T	XIRP2_ENST00000409273.1_Silent_p.T858T|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000295237.9_Silent_p.T1080T|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	905					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAAGTAAAACTGAACAAACTA	0.343													T|||	420	0.0838658	0.0923	0.0735	5008	,	,		18551	0.1121		0.0408	False		,,,				2504	0.0951				p.T1080T		Atlas-SNP	.											XIRP2,NS,carcinoma,+1,1	XIRP2	914	1	0			c.T3240G						PASS	.	T	,,,,	316,3308		13,290,1509	31.0	29.0	30.0		,,2574,,3240	-1.0	0.8	2	dbSNP_129	30	354,7796		7,340,3728	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	20,630,5237	GG,GT,TT		4.3436,8.7196,5.6905	,,,,	,,858/3328,,1080/3550	168101142	670,11104	1812	4075	5887	SO:0001819	synonymous_variant	129446	exon9			TAAAACTGAACAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.3240T>G	2.37:g.168101142T>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			T|0.933;G|0.067	0.067	strong		0.343	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
MXRA5	25878	hgsc.bcm.edu	37	X	3241791	3241791	+	Silent	SNP	G	G	A	rs1635250	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:3241791G>A	ENST00000217939.6	-	5	2089	c.1935C>T	c.(1933-1935)gaC>gaT	p.D645D		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	645	Ig-like C2-type 2.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				AGTAACCACTGTCACTGACTT	0.443													A|||	1750	0.463576	0.298	0.3991	3775	,	,		16554	0.2728		0.4573	False		,,,				2504	0.3517				p.D645D		Atlas-SNP	.											.	MXRA5	815	.	0			c.C1935T						PASS	.	A		1535,2300		246,806,237,580,334	109.0	96.0	101.0		1935	-1.8	0.0	X	dbSNP_89	101	3837,2891		791,1190,1065,447,807	no	coding-synonymous	MXRA5	NM_015419.3		1037,1996,1302,1027,1141	AA,AG,A,GG,G		42.9697,40.0261,49.1432		645/2829	3241791	5372,5191	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			ACCACTGTCACTG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.1935C>T	X.37:g.3241791G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			0|0.003;A|0.487	0.487	strong		0.443	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610445	32610445	+	Silent	SNP	G	G	A	rs1048381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32610445G>A	ENST00000343139.5	+	4	774	c.672G>A	c.(670-672)ggG>ggA	p.G224G	HLA-DQA1_ENST00000374949.2_Silent_p.G224G|HLA-DQA1_ENST00000395363.1_Silent_p.G224G	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	223					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GTGCCCTGGGGTTGTCTGTGG	0.547													.|||	828	0.165335	0.1619	0.2075	5008	,	,		14512	0.1617		0.167	False		,,,				2504	0.1421				p.G224G		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.G672A						PASS	.	G		454,2566		61,332,1117	139.0	117.0	125.0		672	-4.3	0.4	6	dbSNP_86	125	685,4729		72,541,2094	no	coding-synonymous	HLA-DQA1	NM_002122.3		133,873,3211	AA,AG,GG		12.6524,15.0331,13.5049		224/256	32610445	1139,7295	1510	2707	4217	SO:0001819	synonymous_variant	3117	exon4			CCTGGGGTTGTCT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.672G>A	6.37:g.32610445G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	145	85	0.586207	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1																																																																																			G|0.851;A|0.149	0.149	strong		0.547	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
EFCAB13	124989	hgsc.bcm.edu	37	17	45425287	45425287	+	Nonsense_Mutation	SNP	C	C	T	rs71377306	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:45425287C>T	ENST00000331493.2	+	9	1042	c.631C>T	c.(631-633)Cga>Tga	p.R211*	EFCAB13_ENST00000517484.1_Intron	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	211						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TTTAGAAATGCGACAGGCACT	0.299													C|||	459	0.0916534	0.0023	0.0331	5008	,	,		16292	0.2252		0.0835	False		,,,				2504	0.1247				p.R211X		Atlas-SNP	.											.	.	.	.	0			c.C631T						PASS	.	C	,stop/ARG	59,4347	58.7+/-95.3	1,57,2145	70.0	69.0	69.0		,631	2.4	0.9	17	dbSNP_130	69	458,8134	135.9+/-193.0	15,428,3853	yes	intron,stop-gained	C17orf57	NM_001195192.1,NM_152347.4	,	16,485,5998	TT,TC,CC		5.3305,1.3391,3.9775	,	,211/974	45425287	517,12481	2203	4296	6499	SO:0001587	stop_gained	124989	exon9			GAAATGCGACAGG	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.631C>T	17.37:g.45425287C>T	ENSP00000332111:p.Arg211*	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_152347	G3V128|Q49AG9	Nonsense_Mutation	SNP	ENST00000331493.2	37	CCDS11512.1	193	0.08836996336996338	0	0.0	11	0.03038674033149171	114	0.1993006993006993	68	0.08970976253298153	C	37	6.586646	0.97684	0.013391	0.053305	ENSG00000178852	ENST00000331493	.	.	.	4.57	2.38	0.29361	.	0.000000	0.27826	N	0.017688	.	.	.	.	.	.	0.40293	P	0.021479000000000026	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.6487	8.9246	0.35632	0.4056:0.5944:0.0:0.0	.	.	.	.	X	211	.	ENSP00000332111:R211X	R	+	1	2	C17orf57	42780286	0.796000	0.28864	0.861000	0.33841	0.678000	0.39670	1.225000	0.32551	0.870000	0.35726	0.650000	0.86243	CGA	C|0.948;T|0.052	0.052	strong		0.299	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
PLXNA4	91584	hgsc.bcm.edu	37	7	132192295	132192295	+	Silent	SNP	G	G	A	rs156961|rs200081174	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:132192295G>A	ENST00000359827.3	-	2	2120	c.1158C>T	c.(1156-1158)ctC>ctT	p.L386L	PLXNA4_ENST00000378539.5_Silent_p.L386L|PLXNA4_ENST00000423507.2_Silent_p.L386L|PLXNA4_ENST00000321063.4_Silent_p.L386L			Q9HCM2	PLXA4_HUMAN	plexin A4	386	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CCTTCACCTTGAGCCAGGCCA	0.612													G|||	1969	0.393171	0.5159	0.3588	5008	,	,		20224	0.2708		0.3917	False		,,,				2504	0.3793				p.L386L		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C1158T						PASS	.	G	,,	2111,2295	547.2+/-377.2	509,1093,601	56.0	45.0	49.0		1158,1158,1158	3.2	1.0	7	dbSNP_79	49	3347,5253	468.8+/-367.4	641,2065,1594	no	coding-synonymous,coding-synonymous,coding-synonymous	PLXNA4	NM_001105543.1,NM_020911.1,NM_181775.3	,,	1150,3158,2195	AA,AG,GG		38.9186,47.9119,41.9652	,,	386/493,386/1895,386/523	132192295	5458,7548	2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			CACCTTGAGCCAG	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.1158C>T	7.37:g.132192295G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	70	31	0.442857	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			G|0.594;A|0.406	0.406	strong		0.612	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
HSPG2	3339	hgsc.bcm.edu	37	1	22181895	22181895	+	Missense_Mutation	SNP	C	C	T	rs2229475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22181895C>T	ENST00000374695.3	-	47	5978	c.5899G>A	c.(5899-5901)Gtc>Atc	p.V1967I	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1967	Ig-like C2-type 5.		V -> I (in dbSNP:rs2229475).		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CCTGCGTGGACCTGGGTCCTC	0.682													C|||	174	0.0347444	0.0015	0.0245	5008	,	,		14432	0.0		0.0497	False		,,,				2504	0.1074				p.V1967I		Atlas-SNP	.											.	HSPG2	311	.	0			c.G5899A						PASS	.	C	ILE/VAL	41,4365	43.1+/-76.7	0,41,2162	39.0	38.0	38.0		5899	5.1	1.0	1	dbSNP_98	38	486,8114	138.4+/-195.2	16,454,3830	yes	missense	HSPG2	NM_005529.5	29	16,495,5992	TT,TC,CC		5.6512,0.9305,4.052	possibly-damaging	1967/4392	22181895	527,12479	2203	4300	6503	SO:0001583	missense	3339	exon47			CGTGGACCTGGGT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.5899G>A	1.37:g.22181895C>T	ENSP00000363827:p.Val1967Ile	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	140	77	0.55	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	49	0.022435897435897436	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	36	0.047493403693931395	C	16.52	3.146828	0.57151	0.009305	0.056512	ENSG00000142798	ENST00000374695	T	0.70282	-0.47	5.12	5.12	0.69794	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.36066	N	0.002812	T	0.34424	0.0897	L	0.42008	1.315	0.42799	D	0.993925	D	0.71674	0.998	D	0.81914	0.995	T	0.64542	-0.6383	10	0.45353	T	0.12	.	16.0425	0.80695	0.0:1.0:0.0:0.0	rs2229475	1967	P98160	PGBM_HUMAN	I	1967	ENSP00000363827:V1967I	ENSP00000363827:V1967I	V	-	1	0	HSPG2	22054482	0.996000	0.38824	0.993000	0.49108	0.434000	0.31775	1.829000	0.39121	2.399000	0.81585	0.462000	0.41574	GTC	C|0.966;T|0.034	0.034	strong		0.682	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
C17orf82	388407	hgsc.bcm.edu	37	17	59489707	59489707	+	Missense_Mutation	SNP	C	C	T	rs77617620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:59489707C>T	ENST00000335108.2	+	1	596	c.371C>T	c.(370-372)gCa>gTa	p.A124V	RP11-332H18.4_ENST00000592009.1_RNA	NM_203425.1	NP_982249	Q86X59	CQ082_HUMAN	chromosome 17 open reading frame 82	124										cervix(1)|lung(1)	2						TCCGGAGGCGCATATCTGTTC	0.657											OREG0024630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	121	0.0241613	0.0023	0.0259	5008	,	,		13984	0.001		0.0487	False		,,,				2504	0.0511				p.A124V		Atlas-SNP	.											C17orf82_ENST00000335108,NS,carcinoma,0,2	C17orf82	16	2	0			c.C371T						scavenged	.	C	VAL/ALA	39,4343		1,37,2153	18.0	23.0	21.0		371	0.7	0.0	17	dbSNP_131	21	412,8144		13,386,3879	yes	missense	C17orf82	NM_203425.1	64	14,423,6032	TT,TC,CC		4.8153,0.89,3.4859	probably-damaging	124/252	59489707	451,12487	2191	4278	6469	SO:0001583	missense	388407	exon1			GAGGCGCATATCT	BC046200	CCDS11628.1	17q23.2	2012-10-23			ENSG00000187013	ENSG00000187013			32699	protein-coding gene	gene with protein product							Standard	NM_203425		Approved		uc002izh.1	Q86X59	OTTHUMG00000180077	ENST00000335108.2:c.371C>T	17.37:g.59489707C>T	ENSP00000335229:p.Ala124Val	Somatic	70	1	0.0142857	1038	WXS	Illumina HiSeq	Phase_I	56	33	0.589286	NM_203425		Missense_Mutation	SNP	ENST00000335108.2	37	CCDS11628.1	51	0.023351648351648352	2	0.0040650406504065045	13	0.03591160220994475	1	0.0017482517482517483	35	0.04617414248021108	C	12.92	2.082359	0.36758	0.0089	0.048153	ENSG00000187013	ENST00000335108	T	0.54866	0.55	2.87	0.696	0.18075	.	.	.	.	.	T	0.10766	0.0263	N	0.08118	0	0.09310	N	1	D	0.65815	0.995	P	0.58721	0.844	T	0.15752	-1.0426	9	0.87932	D	0	.	8.8236	0.35041	0.4014:0.5986:0.0:0.0	.	124	Q86X59	CQ082_HUMAN	V	124	ENSP00000335229:A124V	ENSP00000335229:A124V	A	+	2	0	C17orf82	56844489	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.243000	0.08915	0.220000	0.20860	0.297000	0.19635	GCA	C|0.968;T|0.032	0.032	strong		0.657	C17orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449646.1	NM_203425	
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 GAIIx	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	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	77	14	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	
TOP1MT	116447	hgsc.bcm.edu	37	8	144403449	144403449	+	Silent	SNP	G	G	A	rs61631623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144403449G>A	ENST00000329245.4	-	8	1102	c.1068C>T	c.(1066-1068)ggC>ggT	p.G356G	TOP1MT_ENST00000521193.1_Silent_p.G258G|TOP1MT_ENST00000519148.1_Silent_p.G258G|TOP1MT_ENST00000523676.1_Silent_p.G258G	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	356					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	CGTGTTGGCAGCCATCGGCCT	0.637													G|||	602	0.120208	0.236	0.0807	5008	,	,		15373	0.0893		0.0905	False		,,,				2504	0.0542				p.G356G		Atlas-SNP	.											.	TOP1MT	63	.	0			c.C1068T						PASS	.	G		844,3560	330.2+/-301.4	68,708,1426	80.0	75.0	77.0		1068	-0.7	0.0	8	dbSNP_129	77	952,7648	208.3+/-249.8	52,848,3400	no	coding-synonymous	TOP1MT	NM_052963.1		120,1556,4826	AA,AG,GG		11.0698,19.1644,13.8111		356/602	144403449	1796,11208	2202	4300	6502	SO:0001819	synonymous_variant	116447	exon8			TTGGCAGCCATCG	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1068C>T	8.37:g.144403449G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Silent	SNP	ENST00000329245.4	37	CCDS6400.1																																																																																			G|0.866;A|0.134	0.134	strong		0.637	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
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 GAIIx	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	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	47	22	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 GAIIx	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_ENST00000359918.4_Missense_Mutation_p.A272V|ART5_ENST00000397067.3_Missense_Mutation_p.A204V	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	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	73	33	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	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377424	49377424	+	Missense_Mutation	SNP	G	G	A	rs11541192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49377424G>A	ENST00000200453.5	+	2	1203	c.934G>A	c.(934-936)Ggt>Agt	p.G312S		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	312	Glu-rich.		G -> S (in dbSNP:rs11541192). {ECO:0000269|PubMed:14702039}.		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		TGAAGAGGAGGGTGAGGTCAA	0.612													G|||	765	0.152756	0.2474	0.1023	5008	,	,		18553	0.0179		0.1849	False		,,,				2504	0.1667				p.G312S		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G934A						PASS	.	G	SER/GLY	1136,3270	402.4+/-332.3	149,838,1216	68.0	74.0	72.0		934	4.3	0.0	19	dbSNP_120	72	1651,6949	302.0+/-305.7	153,1345,2802	yes	missense	PPP1R15A	NM_014330.3	56	302,2183,4018	AA,AG,GG		19.1977,25.783,21.4286	possibly-damaging	312/675	49377424	2787,10219	2203	4300	6503	SO:0001583	missense	23645	exon2			GAGGAGGGTGAGG	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.934G>A	19.37:g.49377424G>A	ENSP00000200453:p.Gly312Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	295	0.13507326007326007	105	0.21341463414634146	40	0.11049723756906077	12	0.02097902097902098	138	0.1820580474934037	G	15.27	2.783964	0.49891	0.25783	0.191977	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05139	3.49	4.26	4.26	0.50523	.	1.634130	0.03436	N	0.208525	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	P	0.34662	0.462	B	0.30855	0.121	T	0.38993	-0.9635	9	0.12103	T	0.63	0.3771	12.5678	0.56320	0.0:0.0:1.0:0.0	rs11541192;rs52818639	312	O75807	PR15A_HUMAN	S	312;152;270	ENSP00000200453:G312S	ENSP00000200453:G312S	G	+	1	0	PPP1R15A	54069236	0.001000	0.12720	0.002000	0.10522	0.007000	0.05969	0.442000	0.21628	2.078000	0.62432	0.650000	0.86243	GGT	G|0.811;A|0.189	0.189	strong		0.612	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
ZNF544	27300	hgsc.bcm.edu	37	19	58774094	58774094	+	Missense_Mutation	SNP	C	C	T	rs34914886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58774094C>T	ENST00000596652.1	+	6	2356	c.2122C>T	c.(2122-2124)Cgg>Tgg	p.R708W	ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000600220.1_Missense_Mutation_p.R680W|ZNF544_ENST00000599953.1_Missense_Mutation_p.R566W|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000415203.2_Missense_Mutation_p.R680W|ZNF544_ENST00000600044.1_Missense_Mutation_p.R680W|ZNF544_ENST00000269829.4_Missense_Mutation_p.R708W|CTD-3138B18.5_ENST00000597230.1_RNA|CTD-3138B18.4_ENST00000600029.1_Intron			Q6NX49	ZN544_HUMAN	zinc finger protein 544	708					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(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|skin(1)|urinary_tract(1)	18		all_cancers(17;4.17e-12)|all_epithelial(17;1.25e-08)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.17)|GBM - Glioblastoma multiforme(193;0.018)		AGTGCATCGGCGGACACATAC	0.498													C|||	28	0.00559105	0.0008	0.0043	5008	,	,		21265	0.0		0.0209	False		,,,				2504	0.0031				p.R708W		Atlas-SNP	.											.	ZNF544	57	.	0			c.C2122T						PASS	.	C	TRP/ARG	9,4397	14.3+/-33.2	0,9,2194	128.0	131.0	130.0		2122	-4.5	0.0	19	dbSNP_126	130	152,8448	74.2+/-136.8	2,148,4150	yes	missense	ZNF544	NM_014480.2	101	2,157,6344	TT,TC,CC		1.7674,0.2043,1.2379	probably-damaging	708/716	58774094	161,12845	2203	4300	6503	SO:0001583	missense	27300	exon7			CATCGGCGGACAC	AF020591	CCDS12973.1	19q13.43	2013-01-08				ENSG00000198131		"""Zinc fingers, C2H2-type"", ""-"""	16759	protein-coding gene	gene with protein product	"""zinc finger protein AF020591"""						Standard	NM_014480		Approved	AF020591	uc010euo.3	Q6NX49		ENST00000596652.1:c.2122C>T	19.37:g.58774094C>T	ENSP00000469635:p.Arg708Trp	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	37	CCDS12973.1	20	0.009157509157509158	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	C	15.70	2.910460	0.52439	0.002043	0.017674	ENSG00000198131	ENST00000269829;ENST00000415203;ENST00000441758	T;T	0.36520	1.25;1.25	3.36	-4.51	0.03483	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39708	0.1088	M	0.91354	3.2	0.09310	N	0.999999	P;D;D	0.89917	0.559;1.0;1.0	B;D;D	0.73708	0.019;0.981;0.981	T	0.48625	-0.9019	9	0.87932	D	0	.	1.5063	0.02487	0.484:0.2002:0.1223:0.1935	rs34914886	680;680;708	B7ZAY1;B4DL50;Q6NX49	.;.;ZN544_HUMAN	W	708;680;260	ENSP00000269829:R708W;ENSP00000394341:R680W	ENSP00000269829:R708W	R	+	1	2	ZNF544	63465906	0.000000	0.05858	0.007000	0.13788	0.886000	0.51366	-3.023000	0.00641	-0.426000	0.07360	0.563000	0.77884	CGG	C|0.989;T|0.011	0.011	strong		0.498	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480	
COL6A3	1293	hgsc.bcm.edu	37	2	238249630	238249630	+	Silent	SNP	C	C	T	rs4433949	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238249630C>T	ENST00000295550.4	-	38	8381	c.7929G>A	c.(7927-7929)gcG>gcA	p.A2643A	COL6A3_ENST00000472056.1_Silent_p.A2036A|COL6A3_ENST00000353578.4_Silent_p.A2437A|COL6A3_ENST00000346358.4_Silent_p.A2443A|COL6A3_ENST00000347401.3_Silent_p.A2442A|COL6A3_ENST00000409809.1_Silent_p.A2437A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2643	Nonhelical region.|VWFA 12. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGACCAGGTACGCTATGTACT	0.567													C|||	1715	0.342452	0.2133	0.3329	5008	,	,		21379	0.4802		0.4284	False		,,,				2504	0.2935				p.A2643A		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7929A						PASS	.	C	,,	1138,3268	405.1+/-333.4	155,828,1220	158.0	146.0	150.0		7929,6108,7311	-5.4	0.0	2	dbSNP_111	150	3646,4954	524.7+/-380.6	769,2108,1423	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	924,2936,2643	TT,TC,CC		42.3953,25.8284,36.783	,,	2643/3178,2036/2571,2437/2972	238249630	4784,8222	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			CAGGTACGCTATG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7929G>A	2.37:g.238249630C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	151	150	0.993378	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.625;T|0.375	0.375	strong		0.567	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
PSG5	5673	hgsc.bcm.edu	37	19	43680269	43680269	+	Missense_Mutation	SNP	G	G	C	rs1058259	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43680269G>C	ENST00000366175.3	-	3	592	c.462C>G	c.(460-462)aaC>aaG	p.N154K	PSG5_ENST00000342951.6_Missense_Mutation_p.N154K|PSG5_ENST00000599812.1_Missense_Mutation_p.N247K|PSG5_ENST00000404580.1_Missense_Mutation_p.N154K|PSG5_ENST00000407356.1_Missense_Mutation_p.N154K|PSG5_ENST00000407568.1_Intron			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	154	Ig-like C2-type 1.		N -> K (in dbSNP:rs1058259). {ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2735907}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				GTTTTGAGTTGTTGATGGTGA	0.478													G|||	622	0.124201	0.1702	0.1369	5008	,	,		21803	0.0		0.2614	False		,,,				2504	0.0399				p.N154K		Atlas-SNP	.											.	PSG5	58	.	0			c.C462G						PASS	.	G	LYS/ASN,LYS/ASN	850,3554	333.9+/-303.2	100,650,1452	242.0	225.0	231.0		462,462	1.2	0.0	19	dbSNP_86	231	2225,6365	378.1+/-338.8	338,1549,2408	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	94,94	438,2199,3860	CC,CG,GG		25.9022,19.3006,23.6648	probably-damaging,probably-damaging	154/336,154/336	43680269	3075,9919	2202	4295	6497	SO:0001583	missense	5673	exon3			TGAGTTGTTGATG		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.462C>G	19.37:g.43680269G>C	ENSP00000382334:p.Asn154Lys	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	332	0.152014652014652	78	0.15853658536585366	51	0.1408839779005525	0	0.0	203	0.2678100263852243	g	8.010	0.757313	0.15846	0.193006	0.259022	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951;ENST00000404580	T;T;T;T	0.12147	2.71;2.71;2.71;2.71	1.23	1.23	0.21249	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.91920	3.255	0.58432	P	5.999999999950489E-6	B;B	0.27765	0.002;0.188	B;B	0.44108	0.064;0.441	T	0.12041	-1.0563	8	0.66056	D	0.02	.	5.7748	0.18273	0.0:0.0:1.0:0.0	rs1058259;rs1962165;rs3174797;rs4387696;rs11549988;rs1058259	247;154	Q15228;Q15238	.;PSG5_HUMAN	K	154	ENSP00000382334:N154K;ENSP00000386008:N154K;ENSP00000344413:N154K;ENSP00000385250:N154K	ENSP00000344413:N154K	N	-	3	2	PSG5	48372109	0.164000	0.22935	0.030000	0.17652	0.014000	0.08584	1.323000	0.33701	0.630000	0.30394	0.184000	0.17185	AAC	.	.	weak		0.478	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
CEP152	22995	hgsc.bcm.edu	37	15	49048705	49048705	+	Missense_Mutation	SNP	G	G	C	rs16961560	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:49048705G>C	ENST00000380950.2	-	20	2927	c.2740C>G	c.(2740-2742)Ctt>Gtt	p.L914V	CEP152_ENST00000325747.5_Missense_Mutation_p.L821V|CEP152_ENST00000399334.3_Missense_Mutation_p.L914V	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	914			L -> V (in dbSNP:rs16961560).		cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)			breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		ATATTTTCAAGCTCACTCTTC	0.353													G|||	253	0.0505192	0.0053	0.0476	5008	,	,		17356	0.0724		0.0815	False		,,,				2504	0.0593				p.L914V		Atlas-SNP	.											.	CEP152	145	.	0			c.C2740G						PASS	.	G	VAL/LEU,VAL/LEU	50,3578		0,50,1764	42.0	40.0	41.0		2740,2740	0.3	0.9	15	dbSNP_123	41	603,7539		16,571,3484	yes	missense,missense	CEP152	NM_001194998.1,NM_014985.3	32,32	16,621,5248	CC,CG,GG		7.406,1.3782,5.548	benign,benign	914/1711,914/1655	49048705	653,11117	1814	4071	5885	SO:0001583	missense	22995	exon20			TTTCAAGCTCACT	AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.2740C>G	15.37:g.49048705G>C	ENSP00000370337:p.Leu914Val	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_014985	E7ER66|Q17RV1|Q6NTA0	Missense_Mutation	SNP	ENST00000380950.2	37	CCDS58361.1	130	0.05952380952380952	3	0.006097560975609756	12	0.03314917127071823	47	0.08216783216783216	68	0.08970976253298153	G	7.966	0.748128	0.15710	0.013782	0.07406	ENSG00000103995	ENST00000380950;ENST00000325747;ENST00000399334	T;T;T	0.54866	0.55;0.58;0.57	5.68	0.317	0.15861	.	0.691841	0.14451	N	0.318785	T	0.01287	0.0042	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.12013	0.001;0.005;0.005	B;B;B	0.12156	0.003;0.007;0.004	T	0.08513	-1.0718	9	0.17369	T	0.5	-0.3226	1.1175	0.01718	0.1777:0.1994:0.2942:0.3287	rs16961560;rs16961560	821;914;914	O94986-1;E7ER66;O94986	.;.;CE152_HUMAN	V	914;821;914	ENSP00000370337:L914V;ENSP00000321000:L821V;ENSP00000382271:L914V	ENSP00000321000:L821V	L	-	1	0	CEP152	46835997	0.606000	0.26949	0.894000	0.35097	0.974000	0.67602	0.785000	0.26830	-0.108000	0.12066	-0.229000	0.12294	CTT	G|0.933;C|0.067	0.067	strong		0.353	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	
PPP6R2	9701	hgsc.bcm.edu	37	22	50882338	50882338	+	Missense_Mutation	SNP	G	G	A	rs56269507	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50882338G>A	ENST00000216061.5	+	24	3014	c.2644G>A	c.(2644-2646)Gcg>Acg	p.A882T	PPP6R2_ENST00000359139.3_Missense_Mutation_p.A849T|PPP6R2_ENST00000395741.3_Missense_Mutation_p.A849T|PPP6R2_ENST00000395744.3_Missense_Mutation_p.A848T			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	882						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						TGCCTGCCCCGCGCCAAAGGA	0.677													G|||	48	0.00958466	0.0015	0.0216	5008	,	,		15844	0.0		0.0268	False		,,,				2504	0.0041				p.A875T		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G2623A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	19,4361		0,19,2171	17.0	16.0	16.0		2623,2545,2545,2542	1.0	0.0	22	dbSNP_129	16	236,8352		2,232,4060	yes	missense,missense,missense,missense	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	58,58,58,58	2,251,6231	AA,AG,GG		2.748,0.4338,1.9664	probably-damaging,probably-damaging,probably-damaging,probably-damaging	875/960,849/934,849/928,848/933	50882338	255,12713	2190	4294	6484	SO:0001583	missense	9701	exon23			TGCCCCGCGCCAA	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.2644G>A	22.37:g.50882338G>A	ENSP00000216061:p.Ala882Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	37		31	0.014194139194139194	0	0.0	9	0.024861878453038673	0	0.0	22	0.029023746701846966	G	10.73	1.433223	0.25813	0.004338	0.02748	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.35973	1.38;1.28;1.28;1.33	4.25	0.997	0.19851	.	5.374370	0.00397	N	0.000043	T	0.07954	0.0199	N	0.22421	0.69	0.09310	N	1	B;P;B;P;P;B	0.43287	0.342;0.472;0.342;0.802;0.695;0.023	B;B;B;B;B;B	0.31191	0.033;0.072;0.054;0.125;0.125;0.008	T	0.19353	-1.0308	10	0.42905	T	0.14	-2.4774	6.757	0.23520	0.2973:0.0:0.7027:0.0	rs56269507	408;875;882;849;848;849	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	T	849;849;848;882	ENSP00000352051:A849T;ENSP00000379090:A849T;ENSP00000379093:A848T;ENSP00000216061:A882T	ENSP00000216061:A882T	A	+	1	0	PPP6R2	49229204	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.436000	0.06922	0.204000	0.20548	-1.717000	0.00709	GCG	G|0.984;A|0.016	0.016	strong		0.677	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	
OR4L1	122742	hgsc.bcm.edu	37	14	20529019	20529019	+	Silent	SNP	C	C	T	rs1959629	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20529019C>T	ENST00000315683.1	+	1	816	c.816C>T	c.(814-816)gcC>gcT	p.A272A		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		AAACTCTTGCCGTATTTTATA	0.373													T|||	2161	0.43151	0.3729	0.3948	5008	,	,		18831	0.5357		0.3221	False		,,,				2504	0.5419				p.A272A		Atlas-SNP	.											.	OR4L1	98	.	0			c.C816T						PASS	.	T		1649,2757		312,1025,866	95.0	93.0	93.0		816	2.0	0.9	14	dbSNP_92	93	2782,5818		491,1800,2009	no	coding-synonymous	OR4L1	NM_001004717.1		803,2825,2875	TT,TC,CC		32.3488,37.4262,34.0689		272/313	20529019	4431,8575	2203	4300	6503	SO:0001819	synonymous_variant	122742	exon1			TCTTGCCGTATTT		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.816C>T	14.37:g.20529019C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_001004717	Q6IEZ5	Silent	SNP	ENST00000315683.1	37	CCDS32029.1																																																																																			C|0.617;T|0.383	0.383	strong		0.373	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
SAMD11	148398	hgsc.bcm.edu	37	1	878314	878314	+	Silent	SNP	G	G	C	rs142558220	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:878314G>C	ENST00000342066.3	+	11	1523	c.1440G>C	c.(1438-1440)ggG>ggC	p.G480G		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	480					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)		p.G480G(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	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;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		CAGCTGTTGGGTGCAGGGGGC	0.682													g|||	216	0.043131	0.0083	0.0778	5008	,	,		12009	0.0		0.1193	False		,,,				2504	0.0317				p.G480G		Atlas-SNP	.											SAMD11,NS,carcinoma,0,1	SAMD11	34	1	1	Substitution - coding silent(1)	breast(1)	c.G1440C						PASS	.	G		56,4108		0,56,2026	4.0	5.0	5.0		1440	0.1	0.0	1	dbSNP_134	5	550,7674		11,528,3573	no	coding-synonymous	SAMD11	NM_152486.2		11,584,5599	CC,CG,GG		6.6877,1.3449,4.8918		480/682	878314	606,11782	2082	4112	6194	SO:0001819	synonymous_variant	148398	exon11			TGTTGGGTGCAGG	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.1440G>C	1.37:g.878314G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Silent	SNP	ENST00000342066.3	37	CCDS2.2	105	0.04807692307692308	7	0.014227642276422764	23	0.06353591160220995	0	0.0	75	0.09894459102902374	G	0.091	-1.166837	0.01660	0.013449	0.066877	ENSG00000187634	ENST00000341065;ENST00000455979	.	.	.	4.44	0.115	0.14643	.	0.199096	0.43110	D	0.000620	T	0.00524	0.0017	.	.	.	0.18873	N	0.999987	.	.	.	.	.	.	T	0.07290	-1.0780	6	0.25751	T	0.34	-7.5702	2.372	0.04333	0.174:0.1478:0.526:0.1522	.	.	.	.	A	388;307	.	ENSP00000349216:G388A	G	+	2	0	SAMD11	868177	0.006000	0.16342	0.000000	0.03702	0.078000	0.17371	-0.015000	0.12634	-0.159000	0.11021	-0.708000	0.03648	GGT	G|0.952;C|0.048	0.048	strong		0.682	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486	
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 GAIIx	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		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	105	53	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	
MRPS34	65993	hgsc.bcm.edu	37	16	1823024	1823024	+	Missense_Mutation	SNP	G	G	T	rs11552431	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1823024G>T	ENST00000397375.2	-	1	132	c.97C>A	c.(97-99)Ctc>Atc	p.L33I	EME2_ENST00000568449.1_5'Flank|NME3_ENST00000219302.3_5'Flank|MRPS34_ENST00000177742.3_Missense_Mutation_p.L33I|EME2_ENST00000307394.7_5'Flank|NME3_ENST00000563498.1_5'Flank	NM_023936.1	NP_076425.1	P82930	RT34_HUMAN	mitochondrial ribosomal protein S34	33			L -> I (in dbSNP:rs11552431).			mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|skin(2)	3						ACCGCGTAGAGCTGGGAGTCG	0.736													G|||	731	0.145966	0.0393	0.0908	5008	,	,		11499	0.254		0.1342	False		,,,				2504	0.2301				p.L33I		Atlas-SNP	.											.	MRPS34	7	.	0			c.C97A						PASS	.	G	ILE/LEU	96,3250		0,96,1577	2.0	3.0	3.0		97	3.7	1.0	16	dbSNP_120	3	609,6405		16,577,2914	yes	missense	MRPS34	NM_023936.1	5	16,673,4491	TT,TG,GG		8.6826,2.8691,6.805	benign	33/219	1823024	705,9655	1673	3507	5180	SO:0001583	missense	65993	exon1			CGTAGAGCTGGGA	BC001182	CCDS10444.1, CCDS73805.1	16p13.3	2012-09-13			ENSG00000074071	ENSG00000074071		"""Mitochondrial ribosomal proteins / small subunits"""	16618	protein-coding gene	gene with protein product		611994					Standard	NM_023936		Approved	MRP-S12, MGC2616	uc002cmo.3	P82930	OTTHUMG00000128636	ENST00000397375.2:c.97C>A	16.37:g.1823024G>T	ENSP00000380531:p.Leu33Ile	Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	13	5	0.384615	NM_023936	Q9BVI7	Missense_Mutation	SNP	ENST00000397375.2	37	CCDS10444.1	335	0.1533882783882784	27	0.054878048780487805	41	0.1132596685082873	163	0.28496503496503495	104	0.13720316622691292	G	13.61	2.288846	0.40494	0.028691	0.086826	ENSG00000074071	ENST00000397375;ENST00000177742	T;T	0.44083	0.93;0.93	3.72	3.72	0.42706	.	0.322809	0.27214	N	0.020387	T	0.00012	0.0000	N	0.08118	0	0.37712	P	0.075407	B;B	0.29716	0.255;0.118	B;B	0.22601	0.04;0.04	T	0.22661	-1.0210	9	0.56958	D	0.05	-0.4229	9.7711	0.40589	0.0:0.0:0.7937:0.2063	rs11552431;rs11552431	33;33	C9JJ19;P82930	.;RT34_HUMAN	I	33	ENSP00000380531:L33I;ENSP00000177742:L33I	ENSP00000177742:L33I	L	-	1	0	MRPS34	1763025	1.000000	0.71417	0.998000	0.56505	0.151000	0.21798	4.143000	0.58051	1.891000	0.54761	0.591000	0.81541	CTC	G|0.846;T|0.154	0.154	strong		0.736	MRPS34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250506.1	NM_023936	
XRRA1	143570	hgsc.bcm.edu	37	11	74559446	74559446	+	Missense_Mutation	SNP	G	G	C	rs4944960	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:74559446G>C	ENST00000340360.6	-	15	1749	c.1418C>G	c.(1417-1419)aCg>aGg	p.T473R	XRRA1_ENST00000527087.1_Missense_Mutation_p.T386R|RN7SL239P_ENST00000490061.2_RNA|XRRA1_ENST00000321448.8_Missense_Mutation_p.T198R	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						CTTGGTTGTCGTCATGCGCGG	0.527													G|||	1417	0.282947	0.1452	0.4885	5008	,	,		20319	0.5089		0.2843	False		,,,				2504	0.089				p.T473R		Atlas-SNP	.											.	XRRA1	46	.	0			c.C1418G						PASS	.	G	ARG/THR	663,3461		68,527,1467	53.0	58.0	57.0		1418	-4.1	0.0	11	dbSNP_111	57	2197,6165		288,1621,2272	yes	missense	XRRA1	NM_182969.1	71	356,2148,3739	CC,CG,GG		26.2736,16.0766,22.9057	benign	473/793	74559446	2860,9626	2062	4181	6243	SO:0001583	missense	143570	exon15			GTTGTCGTCATGC	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1418C>G	11.37:g.74559446G>C	ENSP00000339918:p.Thr473Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_182969		Missense_Mutation	SNP	ENST00000340360.6	37	CCDS44680.1	748	0.3424908424908425	67	0.13617886178861788	161	0.4447513812154696	301	0.5262237762237763	219	0.28891820580474936	G	13.66	2.302324	0.40694	0.160766	0.262736	ENSG00000166435	ENST00000340360;ENST00000321448;ENST00000344880;ENST00000398418;ENST00000527087	T;T;T	0.50813	0.76;1.48;0.73	3.91	-4.08	0.03963	.	1.344830	0.04736	N	0.421977	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	P;D;P;P;P	0.59357	0.691;0.985;0.897;0.772;0.772	B;P;B;B;B	0.55999	0.171;0.789;0.417;0.424;0.424	T	0.44544	-0.9321	9	0.12103	T	0.63	-0.0273	0.2488	0.00202	0.3433:0.1407:0.2311:0.2849	rs4944960;rs52834190;rs57640924;rs4944960	473;29;386;417;459	Q6P2D8;E9PP69;Q6P2D8-2;Q6P2D8-4;Q6P2D8-3	XRRA1_HUMAN;.;.;.;.	R	473;198;459;417;386	ENSP00000339918:T473R;ENSP00000319303:T198R;ENSP00000435838:T386R	ENSP00000319303:T198R	T	-	2	0	XRRA1	74237094	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.008000	0.12788	-0.876000	0.04017	0.591000	0.81541	ACG	G|0.659;C|0.341	0.341	strong		0.527	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
DLX3	1747	hgsc.bcm.edu	37	17	48070878	48070878	+	Silent	SNP	C	C	T	rs2303466	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48070878C>T	ENST00000434704.2	-	2	627	c.402G>A	c.(400-402)acG>acA	p.T134T	DLX3_ENST00000512495.2_Silent_p.T14T	NM_005220.2	NP_005211.1	O60479	DLX3_HUMAN	distal-less homeobox 3	134					blood vessel development (GO:0001568)|odontoblast differentiation (GO:0071895)|odontogenesis of dentin-containing tooth (GO:0042475)|placenta development (GO:0001890)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	12						TGGAGTAGATCGTACGCGGCT	0.687													C|||	1134	0.226438	0.1483	0.134	5008	,	,		11687	0.4722		0.1909	False		,,,				2504	0.181				p.T134T		Atlas-SNP	.											.	DLX3	28	.	0			c.G402A						PASS	.	C		650,3756	276.0+/-272.9	51,548,1604	73.0	64.0	67.0		402	-1.6	1.0	17	dbSNP_100	67	1492,7108	279.4+/-293.9	127,1238,2935	no	coding-synonymous	DLX3	NM_005220.2		178,1786,4539	TT,TC,CC		17.3488,14.7526,16.4693		134/288	48070878	2142,10864	2203	4300	6503	SO:0001819	synonymous_variant	1747	exon2			GTAGATCGTACGC		CCDS11556.1	17q21.33	2011-06-20	2005-12-22			ENSG00000064195		"""Homeoboxes / ANTP class : NKL subclass"""	2916	protein-coding gene	gene with protein product		600525	"""distal-less homeo box 3"""			7613049	Standard	NM_005220		Approved		uc002ipy.3	O60479		ENST00000434704.2:c.402G>A	17.37:g.48070878C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_005220	B3KQL6	Silent	SNP	ENST00000434704.2	37	CCDS11556.1																																																																																			C|0.804;T|0.196	0.196	strong		0.687	DLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366307.1		
MUC2	4583	hgsc.bcm.edu	37	11	1080391	1080391	+	Missense_Mutation	SNP	G	G	A	rs41521547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1080391G>A	ENST00000441003.2	+	8	1138	c.1111G>A	c.(1111-1113)Gag>Aag	p.E371K	MUC2_ENST00000359061.5_Missense_Mutation_p.E371K	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	371					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)	CAATGACTGCGAGCAGTGGTG	0.662													G|||	242	0.0483227	0.0333	0.0461	5008	,	,		16331	0.0496		0.0915	False		,,,				2504	0.0245				p.E371K		Atlas-SNP	.											.	MUC2	614	.	0			c.G1111A						PASS	.	G	LYS/GLU	155,4047		4,147,1950	21.0	25.0	24.0		1111	0.8	0.0	11	dbSNP_127	24	746,7658		36,674,3492	yes	missense	MUC2	NM_002457.2	56	40,821,5442	AA,AG,GG		8.8767,3.6887,7.1474	benign	371/2813	1080391	901,11705	2101	4202	6303	SO:0001583	missense	4583	exon8			GACTGCGAGCAGT	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.1111G>A	11.37:g.1080391G>A	ENSP00000415183:p.Glu371Lys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		115	0.052655677655677656	14	0.028455284552845527	10	0.027624309392265192	25	0.043706293706293704	66	0.0870712401055409	G	13.29	2.193112	0.38707	0.036887	0.088767	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.64991	-0.13;-0.13	3.85	0.768	0.18487	.	0.340707	0.21166	U	0.079072	T	0.01627	0.0052	N	0.17800	0.525	0.80722	P	0.0	B	0.29646	0.253	B	0.27608	0.081	T	0.11084	-1.0602	9	0.13108	T	0.6	.	7.7094	0.28669	0.3541:0.0:0.6459:0.0	rs41521547;rs61732151	371	E7EUV1	.	K	371	ENSP00000415183:E371K;ENSP00000351956:E371K	ENSP00000351956:E371K	E	+	1	0	MUC2	1070391	0.207000	0.23482	0.040000	0.18447	0.145000	0.21501	2.397000	0.44477	0.296000	0.22592	0.491000	0.48974	GAG	G|0.947;A|0.053	0.053	strong		0.662	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
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 GAIIx	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	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	46	23	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	
FAM83F	113828	hgsc.bcm.edu	37	22	40417780	40417780	+	Silent	SNP	C	C	T	rs5995793	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:40417780C>T	ENST00000333407.6	+	4	1360	c.1266C>T	c.(1264-1266)aaC>aaT	p.N422N	FAM83F_ENST00000473717.1_Silent_p.N254N	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	422										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						CCAGCCGAAACGGCATGGGAG	0.667													T|||	1443	0.288139	0.3979	0.1628	5008	,	,		15282	0.0853		0.2873	False		,,,				2504	0.4387				p.N422N		Atlas-SNP	.											.	FAM83F	29	.	0			c.C1266T						PASS	.	T		1481,2919		256,969,975	21.0	20.0	21.0		1266	-6.0	0.1	22	dbSNP_114	21	2483,6113		342,1799,2157	no	coding-synonymous	FAM83F	NM_138435.2		598,2768,3132	TT,TC,CC		28.8855,33.6591,30.5017		422/501	40417780	3964,9032	2200	4298	6498	SO:0001819	synonymous_variant	113828	exon4			CCGAAACGGCATG		CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.1266C>T	22.37:g.40417780C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_138435	Q96FD6	Silent	SNP	ENST00000333407.6	37	CCDS14000.2																																																																																			C|0.719;T|0.281	0.281	strong		0.667	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
HYOU1	10525	hgsc.bcm.edu	37	11	118919206	118919206	+	Silent	SNP	T	T	C	rs568922	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:118919206T>C	ENST00000404233.3	-	19	2359	c.2235A>G	c.(2233-2235)gcA>gcG	p.A745A	HYOU1_ENST00000529972.1_Silent_p.A683A|HYOU1_ENST00000525859.1_Silent_p.A683A|HYOU1_ENST00000543287.1_3'UTR	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	745					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		CAAATATGAATGCTTCCAAGC	0.582													C|||	4026	0.803914	0.6694	0.6196	5008	,	,		20653	0.9454		0.841	False		,,,				2504	0.9325				p.A745A		Atlas-SNP	.											HYOU1,caecum,carcinoma,-1,1	HYOU1	88	1	0			c.A2235G						PASS	.	C	,	2981,1419	464.0+/-353.7	1011,959,230	110.0	92.0	98.0		2235,2235	-8.7	0.5	11	dbSNP_83	98	7341,1249	251.2+/-277.8	3142,1057,96	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	4153,2016,326	CC,CT,TT		14.5402,32.25,20.5389	,	745/1000,745/1000	118919206	10322,2668	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon19			TATGAATGCTTCC	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.2235A>G	11.37:g.118919206T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	42	0.75	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	37	CCDS8408.1																																																																																			T|0.207;C|0.793	0.793	strong		0.582	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
FCRL1	115350	hgsc.bcm.edu	37	1	157771880	157771880	+	Silent	SNP	C	C	T	rs4971154	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:157771880C>T	ENST00000368176.3	-	5	778	c.711G>A	c.(709-711)ccG>ccA	p.P237P	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000491942.1_Silent_p.P237P|FCRL1_ENST00000358292.3_Silent_p.P237P	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	237	Ig-like C2-type 3.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGTACAGGATCGGAGGAGAGC	0.597													C|||	1951	0.389577	0.0643	0.5072	5008	,	,		19272	0.5238		0.493	False		,,,				2504	0.501				p.P237P	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											FCRL1,NS,carcinoma,-1,1	FCRL1	164	1	0			c.G711A						PASS	.	C	,,	595,3811	261.3+/-264.2	42,511,1650	43.0	44.0	44.0		711,711,711	-9.9	0.0	1	dbSNP_111	44	4426,4174	585.6+/-391.9	1118,2190,992	no	coding-synonymous,coding-synonymous,coding-synonymous	FCRL1	NM_001159397.1,NM_001159398.1,NM_052938.4	,,	1160,2701,2642	TT,TC,CC		48.5349,13.5043,38.6053	,,	237/367,237/429,237/430	157771880	5021,7985	2203	4300	6503	SO:0001819	synonymous_variant	115350	exon5			CAGGATCGGAGGA	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.711G>A	1.37:g.157771880C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			C|0.596;T|0.404	0.404	strong		0.597	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244725	11244725	+	Missense_Mutation	SNP	C	C	G	rs68157013	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11244725C>G	ENST00000531678.1	-	1	187	c.104G>C	c.(103-105)tGg>tCg	p.W35S	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	35				W -> S (in Ref. 1; AAM19328, 3; AAU21145 and 5; AAI17424). {ECO:0000305}.	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)		TCTCTTGAACCACTCAATGGA	0.383													.|||	3113	0.621605	0.0976	0.7118	5008	,	,		11851	0.9425		0.7525	False		,,,				2504	0.8006				p.W35S		Atlas-SNP	.											TAS2R46_ENST00000422992,NS,carcinoma,0,4	TAS2R43	19	4	0			c.G104C						PASS	.						45.0	39.0	41.0					12																	11244725		1858	3572	5430	SO:0001583	missense	259289	exon1			TTGAACCACTCAA	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.104G>C	12.37:g.11244725C>G	ENSP00000431719:p.Trp35Ser	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	116	108	0.931035	NM_176884	P59546|Q645X4	Missense_Mutation	SNP	ENST00000531678.1	37	CCDS53749.1	926	0.423992673992674	31	0.06300813008130081	161	0.4447513812154696	418	0.7307692307692307	316	0.41688654353562005	-	1.291	-0.607724	0.03717	.	.	ENSG00000255374	ENST00000531678	T	0.01113	5.32	1.97	0.939	0.19506	.	.	.	.	.	T	0.00012	0.0000	H	0.97051	3.93	0.30802	P	0.739796	.	.	.	.	.	.	T	0.26573	-1.0099	6	0.72032	D	0.01	.	5.2922	0.15733	0.3385:0.6615:0.0:0.0	.	.	.	.	S	35	ENSP00000431719:W35S	ENSP00000431719:W35S	W	-	2	0	TAS2R43	11135992	0.155000	0.22806	0.246000	0.24233	0.092000	0.18411	1.065000	0.30592	0.107000	0.17824	0.184000	0.17185	TGG	C|0.597;G|0.403	0.403	strong		0.383	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
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 GAIIx	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		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	230	45	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	
TRIM31	11074	hgsc.bcm.edu	37	6	30078330	30078330	+	Silent	SNP	C	C	T	rs2239529	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30078330C>T	ENST00000376734.3	-	4	764	c.639G>A	c.(637-639)gcG>gcA	p.A213A	TRIM31_ENST00000485864.1_5'UTR|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Silent_p.A213A	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	213					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						AGTGTTTCCCCGCTTCCGTTC	0.512													C|||	317	0.0632987	0.0121	0.1138	5008	,	,		19102	0.0486		0.1193	False		,,,				2504	0.0542				p.A213A		Atlas-SNP	.											TRIM31,trunk,malignant_melanoma,-2,2	TRIM31	40	2	0			c.G639A						PASS	.	C		161,4245	107.3+/-145.7	5,151,2047	192.0	172.0	179.0		639	-2.6	0.0	6	dbSNP_98	179	1207,7393	243.9+/-273.3	75,1057,3168	yes	coding-synonymous	TRIM31	NM_007028.3		80,1208,5215	TT,TC,CC		14.0349,3.6541,10.5182		213/426	30078330	1368,11638	2203	4300	6503	SO:0001819	synonymous_variant	11074	exon4			TTTCCCCGCTTCC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.639G>A	6.37:g.30078330C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	127	98	0.771654	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			C|0.907;T|0.093	0.093	strong		0.512	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
FUCA2	2519	hgsc.bcm.edu	37	6	143825104	143825104	+	Missense_Mutation	SNP	G	G	T	rs11155297	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:143825104G>T	ENST00000002165.6	-	3	753	c.698C>A	c.(697-699)gCa>gAa	p.A233E	RP1-20N2.6_ENST00000589489.1_RNA|FUCA2_ENST00000438118.2_Intron|RP1-20N2.6_ENST00000593045.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA|RP1-20N2.6_ENST00000590703.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000415586.1_RNA|RP1-20N2.6_ENST00000591189.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000593175.1_RNA|FUCA2_ENST00000367585.1_Intron	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	233			A -> E (in dbSNP:rs11155297).		fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		TTGATCCGGTGCTCCTCCGTC	0.458													G|||	446	0.0890575	0.0144	0.1268	5008	,	,		18466	0.002		0.2724	False		,,,				2504	0.0644				p.A233E		Atlas-SNP	.											FUCA2,colon,carcinoma,0,1	FUCA2	28	1	0			c.C698A						PASS	.	G	GLU/ALA	209,4197	126.6+/-163.6	8,193,2002	82.0	75.0	77.0		698	3.8	0.0	6	dbSNP_120	77	2282,6318	384.5+/-341.1	278,1726,2296	yes	missense	FUCA2	NM_032020.4	107	286,1919,4298	TT,TG,GG		26.5349,4.7435,19.1527	benign	233/468	143825104	2491,10515	2203	4300	6503	SO:0001583	missense	2519	exon3			TCCGGTGCTCCTC	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.698C>A	6.37:g.143825104G>T	ENSP00000002165:p.Ala233Glu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	130	65	0.5	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	280	0.1282051282051282	10	0.02032520325203252	58	0.16022099447513813	2	0.0034965034965034965	210	0.2770448548812665	G	14.98	2.698181	0.48307	0.047435	0.265349	ENSG00000001036	ENST00000002165	T	0.56275	0.47	5.62	3.81	0.43845	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.58935	0.2157	M	0.81112	2.525	0.09310	P	1.0	D	0.76494	0.999	D	0.81914	0.995	T	0.61739	-0.7001	9	0.17369	T	0.5	-20.7489	11.8248	0.52261	0.0674:0.1219:0.8107:0.0	rs11155297;rs17286188;rs61663154;rs11155297	233	Q9BTY2	FUCO2_HUMAN	E	233	ENSP00000002165:A233E	ENSP00000002165:A233E	A	-	2	0	FUCA2	143866797	1.000000	0.71417	0.012000	0.15200	0.002000	0.02628	7.638000	0.83328	1.346000	0.45694	0.650000	0.86243	GCA	G|0.844;T|0.156	0.156	strong		0.458	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
CDH23	64072	hgsc.bcm.edu	37	10	73434906	73434906	+	Missense_Mutation	SNP	G	G	A	rs10999947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73434906G>A	ENST00000224721.6	+	14	1507	c.1502G>A	c.(1501-1503)aGc>aAc	p.S501N	CDH23_ENST00000299366.7_Missense_Mutation_p.S541N	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	496	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GGGGAAGTCAGCTACTTCTTC	0.577													A|||	1264	0.252396	0.2315	0.2738	5008	,	,		21316	0.2619		0.2555	False		,,,				2504	0.2526				p.S496N		Atlas-SNP	.											.	CDH23	365	.	0			c.G1487A						PASS	.	A	ASN/SER,ASN/SER,ASN/SER	963,3217		115,733,1242	94.0	97.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1487,1487,1487	-0.6	1.0	10	dbSNP_120	96	2193,6257		271,1651,2303	yes	missense,missense,missense	CDH23	NM_022124.5,NM_001171931.1,NM_001171930.1	46,46,46	386,2384,3545	AA,AG,GG		25.9527,23.0383,24.9881	benign,benign,benign	496/3355,496/1062,496/1382	73434906	3156,9474	2090	4225	6315	SO:0001583	missense	64072	exon14			AAGTCAGCTACTT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.1502G>A	10.37:g.73434906G>A	ENSP00000224721:p.Ser501Asn	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		587	0.26877289377289376	125	0.2540650406504065	107	0.2955801104972376	160	0.27972027972027974	195	0.25725593667546176	A	6.694	0.496660	0.12762	0.230383	0.259527	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.72	-0.614	0.11590	Cadherin (4);Cadherin-like (1);	0.362307	0.27754	N	0.017987	T	0.00012	0.0000	L	0.33339	1.005	0.09310	P	0.9999999899995	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.005;0.0;0.001	T	0.33137	-0.9880	8	0.12430	T	0.62	.	13.7661	0.62995	0.3039:0.0:0.6961:0.0	rs10999947;rs61259887;rs10999947	496;499;496	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	N	501;496;496;499;499;13	.	ENSP00000224721:S501N	S	+	2	0	CDH23	73104912	0.961000	0.32948	0.991000	0.47740	0.813000	0.45954	0.400000	0.20932	-0.381000	0.07882	-1.213000	0.01624	AGC	G|0.725;A|0.275	0.275	strong		0.577	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
DNAH12	201625	hgsc.bcm.edu	37	3	57528503	57528503	+	Missense_Mutation	SNP	A	A	G	rs9311651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:57528503A>G	ENST00000351747.2	-	2	275	c.95T>C	c.(94-96)gTt>gCt	p.V32A	DNAH12_ENST00000389536.4_Missense_Mutation_p.V32A|DNAH12_ENST00000311202.6_Missense_Mutation_p.V32A	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	32	Stem. {ECO:0000250}.		V -> A (in dbSNP:rs9311651). {ECO:0000269|PubMed:14702039}.		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(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						TGGTGTATCAACGCCTATGTT	0.398													A|||	1084	0.216454	0.5477	0.1715	5008	,	,		17572	0.003		0.1461	False		,,,				2504	0.093				p.V32A		Atlas-SNP	.											.	DNAH12	182	.	0			c.T95C						PASS	.	A	ALA/VAL,ALA/VAL	2164,2242	585.5+/-386.3	531,1102,570	147.0	138.0	141.0		95,95	-2.9	0.2	3	dbSNP_119	141	1302,7298	257.9+/-281.7	102,1098,3100	yes	missense,missense	DNAH12	NM_178504.4,NM_198564.3	64,64	633,2200,3670	GG,GA,AA		15.1395,49.1148,26.6492	possibly-damaging,possibly-damaging	32/3093,32/458	57528503	3466,9540	2203	4300	6503	SO:0001583	missense	201625	exon2			GTATCAACGCCTA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.95T>C	3.37:g.57528503A>G	ENSP00000295937:p.Val32Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_198564	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		453	0.20741758241758243	273	0.5548780487804879	72	0.19889502762430938	1	0.0017482517482517483	107	0.14116094986807387	A	1.215	-0.628672	0.03610	0.491148	0.151395	ENSG00000174844	ENST00000351747;ENST00000495027;ENST00000389536;ENST00000311202	T;T;T;T	0.20200	2.24;2.09;3.76;3.21	5.75	-2.94	0.05581	.	0.438335	0.19737	N	0.107210	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.47548	-0.9109	9	0.09338	T	0.73	.	3.9621	0.09415	0.3715:0.0:0.3074:0.3211	rs9311651;rs52837959;rs9311651	32;32	Q6ZR08-4;Q6ZR08	.;DYH12_HUMAN	A	32	ENSP00000295937:V32A;ENSP00000418137:V32A;ENSP00000374187:V32A;ENSP00000312554:V32A	ENSP00000312554:V32A	V	-	2	0	DNAH12	57503543	0.002000	0.14202	0.229000	0.23960	0.644000	0.38419	0.065000	0.14466	-0.116000	0.11893	-0.274000	0.10170	GTT	A|0.760;G|0.240	0.240	strong		0.398	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
WISP1	8840	hgsc.bcm.edu	37	8	134239770	134239770	+	Silent	SNP	T	T	C	rs3739261	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:134239770T>C	ENST00000250160.6	+	5	1027	c.921T>C	c.(919-921)aaT>aaC	p.N307N	WISP1_ENST00000220856.6_Silent_p.N220N|WISP1_ENST00000517423.1_Nonstop_Mutation_p.*156Q|WISP1-UT1_ENST00000602893.1_RNA|WISP1_ENST00000377863.2_Silent_p.N135N|WISP1_ENST00000519433.1_Silent_p.N62N	NM_003882.3	NP_003873.1	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	307	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21	all_epithelial(106;5.39e-23)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			GCATGGACAATAGGTGCTGCA	0.532													C|||	1396	0.278754	0.3502	0.4035	5008	,	,		21193	0.0665		0.3559	False		,,,				2504	0.2331				p.X156Q		Atlas-SNP	.											.	WISP1	64	.	0			c.T466C						PASS	.	C	GLN/stop,,,	1501,2905	676.1+/-403.2	240,1021,942	203.0	160.0	175.0		466,186,921,660	3.8	0.4	8	dbSNP_107	175	3013,5587	664.4+/-402.2	527,1959,1814	yes	stop-lost,coding-synonymous,coding-synonymous,coding-synonymous	WISP1	NM_001204869.1,NM_001204870.1,NM_003882.3,NM_080838.2	,,,	767,2980,2756	CC,CT,TT		35.0349,34.0672,34.7071	,,,	156/156,62/123,307/368,220/281	134239770	4514,8492	2203	4300	6503	SO:0001819	synonymous_variant	8840	exon3			GGACAATAGGTGC	AF100779	CCDS6371.1, CCDS6372.1, CCDS56555.1, CCDS56556.1	8q24.22	2007-05-14			ENSG00000104415	ENSG00000104415			12769	protein-coding gene	gene with protein product		603398				9843955	Standard	NM_003882		Approved	CCN4	uc003yub.3	O95388	OTTHUMG00000164440	ENST00000250160.6:c.921T>C	8.37:g.134239770T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	142	69	0.485915	NM_001204869	A8KAG6|E7EMM5|Q5JBS6|Q5JBS7|Q5JBS8|Q9HCS3	Missense_Mutation	SNP	ENST00000250160.6	37	CCDS6371.1	641	0.2934981684981685	181	0.3678861788617886	149	0.4116022099447514	39	0.06818181818181818	272	0.35883905013192613	C	12.85	2.061998	0.36373	0.340672	0.350349	ENSG00000104415	ENST00000517423	.	.	.	5.62	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999679082	.	.	.	.	.	.	.	.	.	.	.	.	.	-29.3152	10.7094	0.45973	0.0:0.7773:0.0:0.2227	rs3739261;rs17635410;rs3739261	.	.	.	Q	156	.	.	X	+	1	0	WISP1	134308952	0.442000	0.25633	0.398000	0.26321	0.575000	0.36095	0.047000	0.14056	0.838000	0.34948	-0.128000	0.14901	TAG	T|0.682;C|0.318	0.318	strong		0.532	WISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378794.2	NM_003882	
SCAMP4	113178	hgsc.bcm.edu	37	19	1918193	1918193	+	Silent	SNP	G	G	A	rs144595321	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1918193G>A	ENST00000316097.8	+	4	471	c.204G>A	c.(202-204)ggG>ggA	p.G68G	SCAMP4_ENST00000414057.2_3'UTR|SCAMP4_ENST00000409472.1_Silent_p.G68G	NM_079834.2	NP_524558.1	Q969E2	SCAM4_HUMAN	secretory carrier membrane protein 4	68					protein transport (GO:0015031)	integral component of membrane (GO:0016021)							Ovarian(11;2.11e-07)|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)		GAGGCTCGGGGACCAACTTCG	0.647													G|||	16	0.00319489	0.0	0.0043	5008	,	,		16624	0.0		0.0129	False		,,,				2504	0.0				p.G68G		Atlas-SNP	.											.	SCAMP4	7	.	0			c.G204A						PASS	.	G		6,4306		0,6,2150	44.0	53.0	50.0		204	-2.6	0.9	19	dbSNP_134	50	87,8369		2,83,4143	no	coding-synonymous	SCAMP4	NM_079834.2		2,89,6293	AA,AG,GG		1.0289,0.1391,0.7284		68/230	1918193	93,12675	2156	4228	6384	SO:0001819	synonymous_variant	113178	exon4			CTCGGGGACCAAC	AK091166	CCDS45903.1	19p13.3	2013-02-21			ENSG00000227500	ENSG00000227500		"""Secretory carrier membrane proteins"""	30385	protein-coding gene	gene with protein product		613764					Standard	NM_079834		Approved	FLJ33847	uc002luj.4	Q969E2	OTTHUMG00000154590	ENST00000316097.8:c.204G>A	19.37:g.1918193G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	154	66	0.428571	NM_079834	Q8N2N1|Q8NAV0	Silent	SNP	ENST00000316097.8	37	CCDS45903.1	15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	g	4.736	0.136798	0.09032	0.001391	0.010289	ENSG00000227500	ENST00000414057	.	.	.	4.77	-2.58	0.06228	.	.	.	.	.	T	0.24392	0.0591	.	.	.	0.45995	D	0.998802	.	.	.	.	.	.	T	0.22977	-1.0201	5	0.31617	T	0.26	-5.4836	1.499	0.02472	0.1905:0.224:0.3539:0.2316	.	.	.	.	E	78	.	ENSP00000387909:G78E	G	+	2	0	SCAMP4	1869193	0.000000	0.05858	0.870000	0.34147	0.309000	0.27889	-3.828000	0.00356	-1.045000	0.03250	-0.481000	0.04817	GGA	G|0.993;A|0.007	0.007	strong		0.647	SCAMP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336210.3	NM_079834	
DOCK2	1794	hgsc.bcm.edu	37	5	169504743	169504743	+	Silent	SNP	T	T	C	rs1045168	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:169504743T>C	ENST00000256935.8	+	48	4976	c.4896T>C	c.(4894-4896)cgT>cgC	p.R1632R	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Silent_p.R1124R|DOCK2_ENST00000540750.1_Silent_p.R693R	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1632					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.R1632R(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GAGTGGGCCGTCCCAGGTCTA	0.577													C|||	1458	0.291134	0.3782	0.2579	5008	,	,		15757	0.1071		0.334	False		,,,				2504	0.3425				p.R1632R		Atlas-SNP	.											DOCK2,NS,carcinoma,0,3	DOCK2	389	3	1	Substitution - coding silent(1)	stomach(1)	c.T4896C						scavenged	.	C		1660,2746	658.5+/-400.4	303,1054,846	132.0	119.0	124.0		4896	-5.4	0.9	5	dbSNP_86	124	2650,5950	685.7+/-404.1	414,1822,2064	no	coding-synonymous	DOCK2	NM_004946.2		717,2876,2910	CC,CT,TT		30.814,37.6759,33.1386		1632/1831	169504743	4310,8696	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon48			GGGCCGTCCCAGG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4896T>C	5.37:g.169504743T>C		Somatic	85	2	0.0235294		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			A|0.000;C|0.311;T|0.689	0.311	strong		0.577	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36628191	36628191	+	Missense_Mutation	SNP	G	G	A	rs199655106	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:36628191G>A	ENST00000431231.2	+	11	2130	c.2062G>A	c.(2062-2064)Gat>Aat	p.D688N	ARHGAP23_ENST00000443378.1_Missense_Mutation_p.D594N|ARHGAP23_ENST00000437668.3_Missense_Mutation_p.D688N	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	688	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						GACCTTCAGCGATATCAGGAG	0.522													G|||	55	0.0109824	0.0159	0.0072	5008	,	,		22272	0.0069		0.006	False		,,,				2504	0.0164				p.D688N		Atlas-SNP	.											ARHGAP23,NS,carcinoma,0,1	ARHGAP23	48	1	0			c.G2062A						scavenged	.						74.0	62.0	65.0					17																	36628191		692	1591	2283	SO:0001583	missense	57636	exon11			TTCAGCGATATCA	AB040934	CCDS56027.1	17q12	2014-05-06			ENSG00000225485	ENSG00000275832		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	29293	protein-coding gene	gene with protein product		610590				10819331, 15254754	Standard	NM_001199417		Approved	KIAA1501	uc021twd.1	Q9P227	OTTHUMG00000188547	ENST00000431231.2:c.2062G>A	17.37:g.36628191G>A	ENSP00000393539:p.Asp688Asn	Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	106	19	0.179245	NM_001199417		Missense_Mutation	SNP	ENST00000431231.2	37	CCDS56027.1	.	.	.	.	.	.	.	.	.	.	G	18.42	3.620931	0.66787	.	.	ENSG00000225485	ENST00000437668;ENST00000431231;ENST00000443378	T;T;T	0.18338	2.22;2.59;2.56	4.55	4.55	0.56014	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.195267	0.40908	D	0.000982	T	0.43986	0.1272	M	0.78223	2.4	0.41923	D	0.990523	P;D	0.89917	0.898;1.0	B;D	0.87578	0.355;0.998	T	0.47315	-0.9127	10	0.62326	D	0.03	.	16.2347	0.82365	0.0:0.0:1.0:0.0	.	688;688	Q9P227;Q9P227-2	RHG23_HUMAN;.	N	688;688;594	ENSP00000394153:D688N;ENSP00000393539:D688N;ENSP00000407333:D594N	ENSP00000393539:D688N	D	+	1	0	ARHGAP23	33881717	1.000000	0.71417	0.994000	0.49952	0.760000	0.43138	5.784000	0.68990	2.366000	0.80165	0.561000	0.74099	GAT	G|0.986;A|0.014	0.014	strong		0.522	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
GTF3C1	2975	hgsc.bcm.edu	37	16	27474910	27474910	+	Missense_Mutation	SNP	A	A	G	rs12919017	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:27474910A>G	ENST00000356183.4	-	35	5891	c.5876T>C	c.(5875-5877)tTc>tCc	p.F1959S	GTF3C1_ENST00000561623.1_Missense_Mutation_p.F1934S|GTF3C1_ENST00000567806.1_5'Flank	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1959			F -> S (in dbSNP:rs12919017).		5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						ACTCTCTGTGAACCCTGAGGG	0.602													A|||	344	0.0686901	0.0098	0.1844	5008	,	,		16004	0.001		0.161	False		,,,				2504	0.0409				p.F1959S		Atlas-SNP	.											.	GTF3C1	210	.	0			c.T5876C						PASS	.	A	SER/PHE	175,4219	114.2+/-152.2	1,173,2023	97.0	94.0	95.0		5876	-2.3	0.0	16	dbSNP_121	95	1311,7289	256.3+/-280.9	92,1127,3081	yes	missense	GTF3C1	NM_001520.3	155	93,1300,5104	GG,GA,AA		15.2442,3.9827,11.436	benign	1959/2110	27474910	1486,11508	2197	4300	6497	SO:0001583	missense	2975	exon35			TCTGTGAACCCTG	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.5876T>C	16.37:g.27474910A>G	ENSP00000348510:p.Phe1959Ser	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Missense_Mutation	SNP	ENST00000356183.4	37	CCDS32414.1	191	0.08745421245421245	6	0.012195121951219513	59	0.16298342541436464	0	0.0	126	0.1662269129287599	A	11.04	1.522915	0.27211	0.039827	0.152442	ENSG00000077235	ENST00000356183	T	0.20598	2.06	4.58	-2.26	0.06867	.	3.038090	0.00807	N	0.001467	T	0.00039	0.0001	L	0.36672	1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.23976	-1.0173	9	0.19147	T	0.46	-19.9669	5.7354	0.18063	0.3476:0.1927:0.4597:0.0	rs12919017;rs12919017	1959;1934	Q12789;Q12789-3	TF3C1_HUMAN;.	S	1959	ENSP00000348510:F1959S	ENSP00000348510:F1959S	F	-	2	0	GTF3C1	27382411	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.195000	0.17155	-0.496000	0.06650	0.459000	0.35465	TTC	A|0.904;G|0.096	0.096	strong		0.602	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
LHX3	8022	hgsc.bcm.edu	37	9	139092571	139092571	+	Silent	SNP	C	C	T	rs33998096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139092571C>T	ENST00000371748.5	-	2	204	c.108G>A	c.(106-108)caG>caA	p.Q36Q	LHX3_ENST00000371746.3_Silent_p.Q41Q	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	36	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		CCAGGATGTGCTGGTCACAGC	0.632													C|||	32	0.00638978	0.0068	0.0058	5008	,	,		19156	0.0		0.0189	False		,,,				2504	0.0				p.Q41Q		Atlas-SNP	.											.	LHX3	23	.	0			c.G123A						PASS	.	C	,	19,4387	26.2+/-53.5	0,19,2184	72.0	70.0	71.0		123,108	4.7	1.0	9	dbSNP_126	71	140,8460	69.0+/-131.5	2,136,4162	no	coding-synonymous,coding-synonymous	LHX3	NM_014564.3,NM_178138.4	,	2,155,6346	TT,TC,CC		1.6279,0.4312,1.2225	,	41/403,36/398	139092571	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	8022	exon2			GATGTGCTGGTCA	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"""Homeoboxes / LIM class"""	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.108G>A	9.37:g.139092571C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_014564	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Silent	SNP	ENST00000371748.5	37	CCDS6994.1																																																																																			C|0.990;T|0.010	0.010	strong		0.632	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3		
MRPS35	60488	hgsc.bcm.edu	37	12	27867727	27867727	+	Missense_Mutation	SNP	G	G	A	rs1127787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27867727G>A	ENST00000081029.3	+	2	198	c.127G>A	c.(127-129)Gga>Aga	p.G43R	MRPS35_ENST00000538315.1_Missense_Mutation_p.G43R	NM_021821.3	NP_068593.2	Q9Y2Q9	RT28_HUMAN	mitochondrial ribosomal protein S35	0						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	6	Lung SC(9;0.0873)					AAGAACACCCGGAAATGAAAG	0.348													G|||	598	0.119409	0.0068	0.1009	5008	,	,		18221	0.1944		0.173	False		,,,				2504	0.1524				p.G43R		Atlas-SNP	.											.	MRPS35	26	.	0			c.G127A						PASS	.	G	ARG/GLY,ARG/GLY	148,4258	103.4+/-141.9	1,146,2056	101.0	104.0	103.0		127,127	2.0	0.0	12	dbSNP_86	103	1372,7228	266.9+/-287.0	108,1156,3036	yes	missense,missense	MRPS35	NM_001190864.1,NM_021821.3	125,125	109,1302,5092	AA,AG,GG		15.9535,3.3591,11.6869	benign,benign	43/195,43/324	27867727	1520,11486	2203	4300	6503	SO:0001583	missense	60488	exon2			ACACCCGGAAATG	AF182422	CCDS8714.1, CCDS53769.1	12p11	2012-09-13			ENSG00000061794	ENSG00000061794		"""Mitochondrial ribosomal proteins / small subunits"""	16635	protein-coding gene	gene with protein product		611995				11279123	Standard	NM_021821		Approved	MRPS28, MDS023	uc001rih.3	P82673	OTTHUMG00000169215	ENST00000081029.3:c.127G>A	12.37:g.27867727G>A	ENSP00000081029:p.Gly43Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_001190864	B2RDZ7|Q96Q21	Missense_Mutation	SNP	ENST00000081029.3	37	CCDS8714.1	282	0.12912087912087913	7	0.014227642276422764	37	0.10220994475138122	106	0.1853146853146853	132	0.1741424802110818	G	0.077	-1.191671	0.01607	0.033591	0.159535	ENSG00000061794	ENST00000081029;ENST00000321446;ENST00000538315	T;T	0.41758	1.0;0.99	4.42	1.99	0.26369	.	0.456688	0.23123	N	0.051666	T	0.00012	0.0000	N	0.00152	-1.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26608	-1.0098	9	0.08599	T	0.76	-4.1139	4.4065	0.11411	0.6957:0.2013:0.103:0.0	rs1127787;rs1801373;rs3177168;rs3184093;rs11545242;rs17404577;rs52803578;rs3177168	43;43	P82673-2;P82673	.;RT35_HUMAN	R	43	ENSP00000081029:G43R;ENSP00000445390:G43R	ENSP00000081029:G43R	G	+	1	0	MRPS35	27758994	0.008000	0.16893	0.007000	0.13788	0.008000	0.06430	1.190000	0.32126	0.438000	0.26450	-0.238000	0.12139	GGA	G|0.873;A|0.127	0.127	strong		0.348	MRPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402897.1	NM_021821	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68995529	68995529	+	Splice_Site	SNP	C	C	T	rs10030708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:68995529C>T	ENST00000356291.2	-	1	69	c.10G>A	c.(10-12)Gca>Aca	p.A4T		NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	4			A -> T (in dbSNP:rs10030708).			extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						AATACTTACGCGTACATCATG	0.448													C|||	1647	0.328874	0.3238	0.2061	5008	,	,		15836	0.4593		0.2793	False		,,,				2504	0.3395				p.A4T		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.G10A						PASS	.	C	THR/ALA	1617,2789	498.3+/-364.1	269,1079,855	129.0	111.0	117.0		10	1.7	0.8	4	dbSNP_119	117	2388,6212	396.9+/-345.6	345,1698,2257	yes	missense-near-splice	TMPRSS11F	NM_207407.2	58	614,2777,3112	TT,TC,CC		27.7674,36.7,30.7935	benign	4/439	68995529	4005,9001	2203	4300	6503	SO:0001630	splice_region_variant	389208	exon1			CTTACGCGTACAT	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.11+1G>A	4.37:g.68995529C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	716	0.32783882783882784	145	0.29471544715447157	76	0.20994475138121546	276	0.4825174825174825	219	0.28891820580474936	C	11.04	1.521943	0.27211	0.367	0.277674	ENSG00000198092	ENST00000356291	D	0.88586	-2.4	5.24	1.66	0.24008	.	1.880980	0.02227	N	0.064593	T	0.00012	0.0000	N	0.08118	0	0.37347	P	0.08936500000000003	P	0.48089	0.905	B	0.33295	0.161	T	0.34453	-0.9828	9	0.30078	T	0.28	.	3.955	0.09385	0.1654:0.5739:0.0:0.2608	rs10030708;rs52796516;rs58602987;rs10030708	4	Q6ZWK6	TM11F_HUMAN	T	4	ENSP00000348639:A4T	ENSP00000348639:A4T	A	-	1	0	TMPRSS11F	68678124	0.830000	0.29337	0.836000	0.33094	0.334000	0.28698	0.109000	0.15417	0.102000	0.17638	-0.133000	0.14855	GCA	C|0.674;T|0.326	0.326	strong		0.448	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	Missense_Mutation
ZNF79	7633	hgsc.bcm.edu	37	9	130197414	130197414	+	Missense_Mutation	SNP	A	A	G	rs4504745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:130197414A>G	ENST00000342483.5	+	3	557	c.151A>G	c.(151-153)Agg>Ggg	p.R51G	ZNF79_ENST00000543471.1_Missense_Mutation_p.R27G	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		R -> G (in dbSNP:rs4504745). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						TGCACAGGAAAGGTGGAGGTG	0.493													G|||	2809	0.560903	0.6195	0.6513	5008	,	,		20698	0.4107		0.6342	False		,,,				2504	0.4969				p.R51G		Atlas-SNP	.											.	ZNF79	47	.	0			c.A151G						PASS	.	G	GLY/ARG	2851,1555	487.3+/-360.9	913,1025,265	141.0	136.0	137.0		151	2.5	0.0	9	dbSNP_111	137	5064,3536	514.8+/-378.5	1502,2060,738	yes	missense	ZNF79	NM_007135.2	125	2415,3085,1003	GG,GA,AA		41.1163,35.2928,39.1435	benign	51/499	130197414	7915,5091	2203	4300	6503	SO:0001583	missense	7633	exon3			CAGGAAAGGTGGA	X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"""Zinc fingers, C2H2-type"""	13153	protein-coding gene	gene with protein product		194552	"""zinc finger protein 79 (pT7)"""			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.151A>G	9.37:g.130197414A>G	ENSP00000362446:p.Arg51Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_007135	Q5VVW1|Q96NV1	Missense_Mutation	SNP	ENST00000342483.5	37	CCDS6871.1	1252	0.5732600732600732	307	0.6239837398373984	222	0.6132596685082873	237	0.4143356643356643	486	0.6411609498680739	G	9.998	1.232685	0.22626	0.647072	0.588837	ENSG00000196152	ENST00000342483;ENST00000543471	T;T	0.00784	5.7;5.7	3.42	2.5	0.30297	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07028	-1.0794	8	0.56958	D	0.05	.	5.0099	0.14308	0.122:0.2148:0.6632:0.0	rs4504745;rs17781813;rs17846591;rs17859672;rs52795524;rs61184710;rs4504745	51	Q15937	ZNF79_HUMAN	G	51;27	ENSP00000362446:R51G;ENSP00000438418:R27G	ENSP00000362446:R51G	R	+	1	2	ZNF79	129237235	0.073000	0.21202	0.012000	0.15200	0.027000	0.11550	0.620000	0.24403	0.263000	0.21812	-0.355000	0.07637	AGG	A|0.413;G|0.587	0.587	strong		0.493	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135	
TENM4	26011	hgsc.bcm.edu	37	11	78399121	78399121	+	Silent	SNP	G	G	A	rs1792148	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:78399121G>A	ENST00000278550.7	-	29	5700	c.5238C>T	c.(5236-5238)ggC>ggT	p.G1746G		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1746					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										TGTAGAAGGCGCCTGAGGCAG	0.542													A|||	662	0.132188	0.3222	0.1023	5008	,	,		18874	0.002		0.1342	False		,,,				2504	0.0286				p.G1746G		Atlas-SNP	.											ODZ4_ENST00000278550,colon,carcinoma,-2,1	.	.	1	0			c.C5238T						PASS	.	A		1085,3021		145,795,1113	159.0	163.0	162.0		5238	2.5	1.0	11	dbSNP_89	162	889,7415		45,799,3308	no	coding-synonymous	ODZ4	NM_001098816.2		190,1594,4421	AA,AG,GG		10.7057,26.4247,15.9065		1746/2770	78399121	1974,10436	2053	4152	6205	SO:0001819	synonymous_variant	26011	exon29			GAAGGCGCCTGAG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5238C>T	11.37:g.78399121G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	19	0.168142	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			G|0.864;A|0.136	0.136	strong		0.542	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
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 GAIIx	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_ENST00000518074.1_Missense_Mutation_p.L513Q|SPIDR_ENST00000541342.1_Missense_Mutation_p.L503Q|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000517693.1_Missense_Mutation_p.L48Q	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	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	103	10	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	
P2RY4	5030	hgsc.bcm.edu	37	X	69478942	69478942	+	Missense_Mutation	SNP	T	T	G	rs1152187	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:69478942T>G	ENST00000374519.2	-	1	712	c.533A>C	c.(532-534)aAc>aCc	p.N178T		NM_002565.3	NP_002556.1	P51582	P2RY4_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 4	178			N -> T (in dbSNP:rs1152187). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8537335}.		phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|transepithelial chloride transport (GO:0030321)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|uridine nucleotide receptor activity (GO:0015065)|UTP-activated nucleotide receptor activity (GO:0045030)			cervix(2)|endometrium(2)|large_intestine(8)|lung(6)	18						GGTCCCTTTGTTGCTGGTTGT	0.617													G|||	1584	0.419603	0.5318	0.1383	3775	,	,		15815	0.4127		0.1093	False		,,,				2504	0.2648				p.N178T		Atlas-SNP	.											.	P2RY4	39	.	0			c.A533C						PASS	.	G	THR/ASN	2457,1378		676,739,366,217,205	84.0	76.0	79.0		533	1.4	0.0	X	dbSNP_87	79	1014,5714		46,627,295,1755,1577	yes	missense	P2RY4	NM_002565.3	65	722,1366,661,1972,1782	GG,GT,G,TT,T		15.0713,35.9322,32.86	benign	178/366	69478942	3471,7092	2203	4300	6503	SO:0001583	missense	5030	exon1			CCTTTGTTGCTGG	X91852	CCDS14398.1	Xq13	2012-08-08			ENSG00000186912	ENSG00000186912		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8542	protein-coding gene	gene with protein product		300038				8537336	Standard	NM_002565		Approved	NRU, P2Y4, UNR, P2P	uc004dxz.1	P51582	OTTHUMG00000021769	ENST00000374519.2:c.533A>C	X.37:g.69478942T>G	ENSP00000363643:p.Asn178Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	105	81	0.771429	NM_002565	Q4VBB7|Q4VBB8|Q502W2|Q5JT22	Missense_Mutation	SNP	ENST00000374519.2	37	CCDS14398.1	588	0.35443037974683544	170	0.5	35	0.10736196319018405	143	0.325	50	0.07183908045977011	G	0.025	-1.379396	0.01204	0.640678	0.150713	ENSG00000186912	ENST00000374519	T	0.19938	2.11	4.29	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	0.584212	0.16362	N	0.217713	T	0.00012	0.0000	N	0.02192	-0.645	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31861	-0.9928	9	0.13470	T	0.59	.	2.8679	0.05607	0.1677:0.1381:0.5491:0.1451	rs1152187;rs3764747;rs17264895;rs58094732;rs1152187	178	P51582	P2RY4_HUMAN	T	178	ENSP00000363643:N178T	ENSP00000363643:N178T	N	-	2	0	P2RY4	69395667	0.021000	0.18746	0.008000	0.14137	0.362000	0.29581	0.507000	0.22675	-0.262000	0.09392	-0.269000	0.10298	AAC	0|0.003;G|0.369	0.369	strong		0.617	P2RY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057058.2	NM_002565	
PPP1R26	9858	hgsc.bcm.edu	37	9	138377433	138377433	+	Silent	SNP	G	G	A	rs3827827	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138377433G>A	ENST00000356818.2	+	4	1626	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	PPP1R26_ENST00000605286.1_Silent_p.A359A|PPP1R26_ENST00000605660.1_Silent_p.A359A|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000604351.1_Silent_p.A359A|PPP1R26_ENST00000401470.3_Silent_p.A359A	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	359					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CGTCCGAGGCGTCCGACTCCA	0.622													G|||	1001	0.19988	0.1717	0.2839	5008	,	,		18482	0.1141		0.175	False		,,,				2504	0.2924				p.A359A		Atlas-SNP	.											KIAA0649,NS,carcinoma,0,1	.	.	1	0			c.G1077A						PASS	.	G		660,3746	267.4+/-267.8	44,572,1587	51.0	59.0	57.0		1077	-10.7	0.0	9	dbSNP_107	57	1507,7093	274.3+/-291.2	141,1225,2934	no	coding-synonymous	KIAA0649	NM_014811.3		185,1797,4521	AA,AG,GG		17.5233,14.9796,16.6615		359/1210	138377433	2167,10839	2203	4300	6503	SO:0001819	synonymous_variant	9858	exon4			CGAGGCGTCCGAC	AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.1077G>A	9.37:g.138377433G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			G|0.824;A|0.176	0.176	strong		0.622	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
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 GAIIx	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	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	62	38	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	
DDIAS	220042	hgsc.bcm.edu	37	11	82643760	82643760	+	Missense_Mutation	SNP	G	G	T	rs7947780	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:82643760G>T	ENST00000533655.1	+	6	1592	c.1380G>T	c.(1378-1380)agG>agT	p.R460S	C11orf82_ENST00000430323.2_Missense_Mutation_p.R460S|C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000329143.3_Missense_Mutation_p.R159S	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		460			R -> S (in dbSNP:rs7947780). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						ACCACAGCAGGTTATCTGTGA	0.413													G|||	1540	0.307508	0.1793	0.4049	5008	,	,		22107	0.3244		0.3579	False		,,,				2504	0.3425				p.R460S		Atlas-SNP	.											.	C11orf82	71	.	0			c.G1380T						PASS	.	G	SER/ARG	984,3422	368.1+/-318.5	105,774,1324	77.0	76.0	76.0		1380	2.4	0.1	11	dbSNP_116	76	3028,5572	467.0+/-366.9	521,1986,1793	yes	missense	C11orf82	NM_145018.3	110	626,2760,3117	TT,TG,GG		35.2093,22.3332,30.8473	benign	460/999	82643760	4012,8994	2203	4300	6503	SO:0001583	missense	220042	exon6			CAGCAGGTTATCT																												ENST00000533655.1:c.1380G>T	11.37:g.82643760G>T	ENSP00000435421:p.Arg460Ser	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	29	23	0.793103	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	37	CCDS8263.1	665	0.30448717948717946	93	0.18902439024390244	128	0.35359116022099446	172	0.3006993006993007	272	0.35883905013192613	G	3.944	-0.013559	0.07727	0.223332	0.352093	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.38722	1.12;1.12;1.12	5.84	2.37	0.29283	.	0.621729	0.16187	N	0.225579	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.20780	0.048	B	0.15870	0.014	T	0.38265	-0.9669	8	.	.	.	.	5.6558	0.17642	0.2556:0.0:0.6159:0.1285	rs7947780;rs17571913;rs17857189;rs59924014;rs7947780	460	Q8IXT1	NOXIN_HUMAN	S	460;460;159	ENSP00000414687:R460S;ENSP00000435421:R460S;ENSP00000329930:R159S	.	R	+	3	2	C11orf82	82321408	0.001000	0.12720	0.089000	0.20774	0.053000	0.15095	0.093000	0.15086	0.534000	0.28695	0.655000	0.94253	AGG	G|0.697;N|0.000	.	strong		0.413	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1		
MRPL28	10573	hgsc.bcm.edu	37	16	419154	419154	+	Silent	SNP	G	G	A	rs1802752	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:419154G>A	ENST00000199706.8	-	3	390	c.355C>T	c.(355-357)Ctg>Ttg	p.L119L	MRPL28_ENST00000389675.2_Silent_p.L119L|MRPL28_ENST00000429738.1_Intron	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	119					translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				TTCTTGTCCAGGATCTCACTG	0.537													G|||	580	0.115815	0.0189	0.0865	5008	,	,		20657	0.1518		0.165	False		,,,				2504	0.18				p.L119L		Atlas-SNP	.											MRPL28,colon,carcinoma,0,1	MRPL28	15	1	0			c.C355T						PASS	.	G		179,4227	115.9+/-153.8	8,163,2032	202.0	154.0	170.0		355	1.0	1.0	16	dbSNP_89	170	1471,7129	281.6+/-295.1	114,1243,2943	no	coding-synonymous	MRPL28	NM_006428.4		122,1406,4975	AA,AG,GG		17.1047,4.0626,12.6865		119/257	419154	1650,11356	2203	4300	6503	SO:0001819	synonymous_variant	10573	exon3			TGTCCAGGATCTC	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.355C>T	16.37:g.419154G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Silent	SNP	ENST00000199706.8	37	CCDS32349.1																																																																																			G|0.881;A|0.119	0.119	strong		0.537	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
DPY19L3	147991	hgsc.bcm.edu	37	19	32973077	32973077	+	Silent	SNP	C	C	T	rs7253039	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:32973077C>T	ENST00000342179.5	+	19	2297	c.2082C>T	c.(2080-2082)taC>taT	p.Y694Y	DPY19L3_ENST00000586987.1_3'UTR|DPY19L3_ENST00000392250.2_Silent_p.Y694Y	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	694						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					TGCCTCCCTACGTGGCCTACT	0.468													C|||	897	0.179113	0.2474	0.1916	5008	,	,		18018	0.119		0.161	False		,,,				2504	0.1585				p.Y694Y		Atlas-SNP	.											.	DPY19L3	70	.	0			c.C2082T						PASS	.	C	,	1056,3350	386.8+/-326.2	127,802,1274	169.0	169.0	169.0		2082,2082	2.5	0.2	19	dbSNP_116	169	1415,7185	272.0+/-289.9	108,1199,2993	no	coding-synonymous,coding-synonymous	DPY19L3	NM_001172774.1,NM_207325.2	,	235,2001,4267	TT,TC,CC		16.4535,23.9673,18.9989	,	694/717,694/717	32973077	2471,10535	2203	4300	6503	SO:0001819	synonymous_variant	147991	exon19			TCCCTACGTGGCC		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.2082C>T	19.37:g.32973077C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	52	0.530612	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Silent	SNP	ENST00000342179.5	37	CCDS12422.1																																																																																			C|0.821;T|0.179	0.179	strong		0.468	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
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 GAIIx	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	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	79	36	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 GAIIx	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_ENST00000311129.5_Silent_p.P11P|PPP2R1B_ENST00000427203.2_5'UTR|PPP2R1B_ENST00000393055.2_Silent_p.P11P|PPP2R1B_ENST00000426998.2_Silent_p.P11P|RP11-108O10.2_ENST00000529841.1_lincRNA|PPP2R1B_ENST00000341980.6_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		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	17	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 GAIIx	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_ENST00000563542.1_5'UTR|MYO9A_ENST00000564571.1_Missense_Mutation_p.R1640H|MYO9A_ENST00000566885.1_Missense_Mutation_p.R1260H|MYO9A_ENST00000424560.1_Missense_Mutation_p.R1640H|MYO9A_ENST00000444904.1_Missense_Mutation_p.R1621H	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	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	192	52	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	
MFSD10	10227	hgsc.bcm.edu	37	4	2935527	2935527	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:2935527G>T	ENST00000329687.4	-	1	658	c.124C>A	c.(124-126)Ctg>Atg	p.L42M	NOP14-AS1_ENST00000505731.1_RNA|MFSD10_ENST00000507555.1_Missense_Mutation_p.L42M|MFSD10_ENST00000508221.1_Missense_Mutation_p.L42M|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000507999.1_RNA|MFSD10_ENST00000355443.4_Missense_Mutation_p.L42M|NOP14-AS1_ENST00000512712.2_RNA|MFSD10_ENST00000514800.1_Missense_Mutation_p.L42M	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	42					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)			breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		AGGGGCAGCAGCAGCGTGAAG	0.721																																					p.L42M		Atlas-SNP	.											.	MFSD10	22	.	0			c.C124A						PASS	.																																			SO:0001583	missense	10227	exon1			GCAGCAGCAGCGT	L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"""tetracycline transporter like protein"""	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.124C>A	4.37:g.2935527G>T	ENSP00000332646:p.Leu42Met	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	149	114	0.765101	NM_001120	Q07706	Missense_Mutation	SNP	ENST00000329687.4	37	CCDS3365.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.856860	0.51376	.	.	ENSG00000109736	ENST00000514800;ENST00000355443;ENST00000329687;ENST00000508221;ENST00000507555	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	3.35	-1.11	0.09840	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.074430	0.51477	D	0.000097	T	0.55369	0.1916	L	0.42245	1.32	0.32769	N	0.504055	D;D;D;D	0.59767	0.96;0.96;0.986;0.96	P;P;P;P	0.55455	0.776;0.776;0.776;0.776	T	0.60811	-0.7189	10	0.87932	D	0	-17.2753	0.5306	0.00628	0.2397:0.1257:0.2704:0.3642	.	42;42;42;42	D6RIZ4;D6RE79;D6RA47;Q14728	.;.;.;MFS10_HUMAN	M	42	ENSP00000426907:L42M;ENSP00000347619:L42M;ENSP00000332646:L42M;ENSP00000425757:L42M;ENSP00000423402:L42M	ENSP00000332646:L42M	L	-	1	2	MFSD10	2905325	1.000000	0.71417	0.973000	0.42090	0.232000	0.25224	2.998000	0.49465	-0.058000	0.13177	0.555000	0.69702	CTG	.	.	none		0.721	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2	NM_001120	
SMAD7	4092	hgsc.bcm.edu	37	18	46468946	46468946	+	Intron	SNP	G	G	A	rs3764482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:46468946G>A	ENST00000262158.2	-	3	954				SMAD7_ENST00000591805.1_Intron|SMAD7_ENST00000589634.1_Intron|SMAD7_ENST00000585986.1_Intron	NM_001190821.1|NM_005904.3	NP_001177750.1|NP_005895.1	O15105	SMAD7_HUMAN	SMAD family member 7						adherens junction assembly (GO:0034333)|artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|cellular protein complex localization (GO:0034629)|cellular response to transforming growth factor beta stimulus (GO:0071560)|gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of cardiac muscle contraction (GO:0055117)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|response to laminar fluid shear stress (GO:0034616)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activin binding (GO:0048185)|beta-catenin binding (GO:0008013)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	10	Colorectal(1;0.0518)					GAAAAGGGGAGAGAAAGAAAT	0.463													G|||	440	0.0878594	0.0159	0.1297	5008	,	,		20399	0.0665		0.1978	False		,,,				2504	0.0644				p.S28F		Atlas-SNP	.											.	SMAD7	22	.	0			c.C83T						PASS	.	G	,,PHE/SER,	177,4229	113.3+/-151.4	5,167,2031	56.0	62.0	60.0		,,83,	2.4	0.0	18	dbSNP_107	60	1653,6947	301.2+/-305.3	161,1331,2808	yes	intron,intron,missense,intron	SMAD7	NM_001190821.1,NM_001190822.1,NM_001190823.1,NM_005904.3	,,155,	166,1498,4839	AA,AG,GG		19.2209,4.0172,14.0704	,,,	,,28/239,	46468946	1830,11176	2203	4300	6503	SO:0001627	intron_variant	4092	exon1			AGGGGAGAGAAAG	AF010193	CCDS11936.1, CCDS54186.1, CCDS59317.1	18q21.1	2006-11-06	2006-11-06	2004-05-26	ENSG00000101665	ENSG00000101665		"""SMADs"""	6773	protein-coding gene	gene with protein product		602932	"""MAD, mothers against decapentaplegic homolog 7 (Drosophila)"", ""SMAD, mothers against DPP homolog 7 (Drosophila)"""	MADH8, MADH7		9256479, 9730599	Standard	NM_005904		Approved		uc002ldg.3	O15105	OTTHUMG00000132655	ENST00000262158.2:c.668-21C>T	18.37:g.46468946G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_001190823	B7Z773|K7EQ10|O14740|Q6DK23	Missense_Mutation	SNP	ENST00000262158.2	37	CCDS11936.1																																																																																			G|0.884;A|0.116	0.116	strong		0.463	SMAD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255906.1	NM_005904	
OR2T4	127074	hgsc.bcm.edu	37	1	248525060	248525060	+	Missense_Mutation	SNP	T	T	A	rs28491677	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248525060T>A	ENST00000366475.1	+	1	178	c.178T>A	c.(178-180)Tgt>Agt	p.C60S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	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)			AGCACTACTTTGTGTGGTCAT	0.488													t|||	1477	0.294928	0.2421	0.2709	5008	,	,		20455	0.4276		0.1809	False		,,,				2504	0.364				p.C60S		Atlas-SNP	.											OR2T4,NS,carcinoma,-1,1	OR2T4	126	1	0			c.T178A						scavenged	.						176.0	175.0	175.0					1																	248525060		2203	4300	6503	SO:0001583	missense	127074	exon1			CTACTTTGTGTGG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.178T>A	1.37:g.248525060T>A	ENSP00000355431:p.Cys60Ser	Somatic	559	0	0		WXS	Illumina HiSeq	Phase_I	533	11	0.0206379	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	500	0.22893772893772893	101	0.20528455284552846	72	0.19889502762430938	210	0.36713286713286714	117	0.15435356200527706	t	9.676	1.147970	0.21288	.	.	ENSG00000196944	ENST00000366475	T	0.02944	4.1	3.48	2.33	0.28932	.	0.441217	0.19340	N	0.116665	T	0.00012	0.0000	N	0.00746	-1.225	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.41574	-0.9501	9	0.59425	D	0.04	.	8.6683	0.34134	0.1713:0.0:0.0:0.8287	rs28491677;rs58960769	60	Q8NH00	OR2T4_HUMAN	S	60	ENSP00000355431:C60S	ENSP00000355431:C60S	C	+	1	0	OR2T4	246591683	0.044000	0.20184	0.001000	0.08648	0.025000	0.11179	2.832000	0.48152	0.248000	0.21435	-0.510000	0.04470	TGT	T|0.787;A|0.213	0.213	strong		0.488	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
PARVG	64098	hgsc.bcm.edu	37	22	44594584	44594584	+	Silent	SNP	C	C	G	rs139152	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44594584C>G	ENST00000444313.3	+	12	1279	c.795C>G	c.(793-795)ccC>ccG	p.P265P	PARVG_ENST00000422871.1_Silent_p.P265P|PARVG_ENST00000415224.1_Silent_p.P265P	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	265	CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				ACCTCACTCCCAACTCTCCTG	0.418													C|||	1022	0.204073	0.0545	0.2046	5008	,	,		15052	0.1954		0.3966	False		,,,				2504	0.2168				p.P265P		Atlas-SNP	.											.	PARVG	41	.	0			c.C795G						PASS	.	C	,,	455,3951	217.8+/-236.0	28,399,1776	189.0	177.0	181.0		795,795,795	3.9	1.0	22	dbSNP_78	181	3382,5218	500.6+/-375.3	639,2104,1557	no	coding-synonymous,coding-synonymous,coding-synonymous	PARVG	NM_001137605.1,NM_001137606.1,NM_022141.5	,,	667,2503,3333	GG,GC,CC		39.3256,10.3268,29.5018	,,	265/332,265/332,265/332	44594584	3837,9169	2203	4300	6503	SO:0001819	synonymous_variant	64098	exon12			CACTCCCAACTCT	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"""Parvins"""	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.795C>G	22.37:g.44594584C>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	134	72	0.537313	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Silent	SNP	ENST00000444313.3	37	CCDS14057.1																																																																																			C|0.712;G|0.288	0.288	strong		0.418	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141	
CHD2	1106	hgsc.bcm.edu	37	15	93536197	93536197	+	Silent	SNP	C	C	T	rs2272457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:93536197C>T	ENST00000394196.4	+	28	4632	c.3564C>T	c.(3562-3564)taC>taT	p.Y1188Y	CHD2_ENST00000557381.1_Silent_p.Y1188Y	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1188					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			TGCAGGAATACGAAGAGCAGC	0.507													C|||	969	0.19349	0.1702	0.2046	5008	,	,		21322	0.1319		0.2604	False		,,,				2504	0.2117				p.Y1188Y		Atlas-SNP	.											.	CHD2	280	.	0			c.C3564T						PASS	.	C		873,3521	340.5+/-306.2	85,703,1409	110.0	93.0	99.0		3564	-1.7	0.9	15	dbSNP_100	99	2355,6241	392.9+/-344.2	340,1675,2283	no	coding-synonymous	CHD2	NM_001271.3		425,2378,3692	TT,TC,CC		27.3965,19.868,24.8499		1188/1829	93536197	3228,9762	2197	4298	6495	SO:0001819	synonymous_variant	1106	exon28			GGAATACGAAGAG	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.3564C>T	15.37:g.93536197C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	40	0.930233	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	37	CCDS10374.2																																																																																			C|0.770;T|0.230	0.230	strong		0.507	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
PIGZ	80235	hgsc.bcm.edu	37	3	196674916	196674916	+	Silent	SNP	A	A	C	rs1147240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:196674916A>C	ENST00000412723.1	-	3	998	c.852T>G	c.(850-852)gcT>gcG	p.A284A		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	284					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		TCCTGGATGTAGCGGGGCTGG	0.607													A|||	2891	0.577276	0.6672	0.4568	5008	,	,		18756	0.7698		0.3976	False		,,,				2504	0.5276				p.A284A		Atlas-SNP	.											.	PIGZ	34	.	0			c.T852G						PASS	.	A		2723,1683	639.9+/-397.2	832,1059,312	104.0	110.0	108.0		852	-8.1	0.0	3	dbSNP_87	108	3228,5372	471.3+/-368.1	617,1994,1689	no	coding-synonymous	PIGZ	NM_025163.2		1449,3053,2001	CC,CA,AA		37.5349,38.1979,45.7558		284/580	196674916	5951,7055	2203	4300	6503	SO:0001819	synonymous_variant	80235	exon3			GGATGTAGCGGGG	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.852T>G	3.37:g.196674916A>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_025163	Q9H9G6	Silent	SNP	ENST00000412723.1	37	CCDS3324.1																																																																																			A|0.479;C|0.521	0.521	strong		0.607	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
TRIM69	140691	hgsc.bcm.edu	37	15	45048651	45048651	+	Missense_Mutation	SNP	C	C	T	rs3759880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:45048651C>T	ENST00000559390.1	+	4	1497	c.569C>T	c.(568-570)gCt>gTt	p.A190V	TRIM69_ENST00000338264.4_Missense_Mutation_p.A31V|TRIM69_ENST00000560442.1_5'UTR|TRIM69_ENST00000558173.1_5'UTR|TRIM69_ENST00000329464.4_Missense_Mutation_p.A190V|TRIM69_ENST00000561043.1_Missense_Mutation_p.A31V|TRIM69_ENST00000558329.1_5'UTR			Q86WT6	TRI69_HUMAN	tripartite motif containing 69	190			A -> V (in dbSNP:rs3759880).		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(9)|skin(1)	20		all_cancers(109;2.47e-13)|all_epithelial(112;2.84e-11)|Lung NSC(122;2.23e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;5.5e-19)|GBM - Glioblastoma multiforme(94;1.07e-06)|Colorectal(105;0.138)|COAD - Colon adenocarcinoma(120;0.141)		GAAGCTATTGCTGCTCACAAG	0.473													C|||	686	0.136981	0.2383	0.0764	5008	,	,		20191	0.0685		0.1123	False		,,,				2504	0.1391				p.A190V	Pancreas(84;519 1450 1802 20427 34706)	Atlas-SNP	.											.	TRIM69	47	.	0			c.C569T						PASS	.	C	VAL/ALA,VAL/ALA	703,3241		65,573,1334	41.0	33.0	36.0		92,569	0.1	1.0	15	dbSNP_107	36	694,6652		26,642,3005	yes	missense,missense	TRIM69	NM_080745.3,NM_182985.3	64,64	91,1215,4339	TT,TC,CC		9.4473,17.8245,12.3738	benign,benign	31/342,190/501	45048651	1397,9893	1972	3673	5645	SO:0001583	missense	140691	exon3			CTATTGCTGCTCA	AF302088	CCDS10114.1, CCDS32220.1, CCDS73719.1	15q15-q21	2013-01-09	2011-01-25	2006-09-26	ENSG00000185880	ENSG00000185880		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	17857	protein-coding gene	gene with protein product			"""ring finger protein 36"", ""tripartite motif-containing 69"""	RNF36			Standard	XM_005254162		Approved	Trif, TRIMLESS	uc001zug.1	Q86WT6	OTTHUMG00000131246	ENST00000559390.1:c.569C>T	15.37:g.45048651C>T	ENSP00000453177:p.Ala190Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	28	21	0.75	NM_182985	A8MX03|Q309B0|Q4G1A5|Q6W897|Q8IYY3|Q8WY16|Q8WY17	Missense_Mutation	SNP	ENST00000559390.1	37	CCDS32220.1	270	0.12362637362637363	119	0.241869918699187	32	0.08839779005524862	31	0.05419580419580419	88	0.11609498680738786	C	5.409	0.260660	0.10239	0.178245	0.094473	ENSG00000185880	ENST00000329464;ENST00000338264	T;T	0.56444	1.1;0.46	5.56	0.103	0.14526	.	0.669254	0.13224	N	0.404170	T	0.00012	0.0000	N	0.11106	0.095	0.50632	P	1.2000000000000899E-4	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.26087	-1.0113	9	0.23302	T	0.38	.	5.3173	0.15862	0.0:0.4436:0.2536:0.3028	rs3759880;rs17589120;rs59487609;rs3759880	31;190	Q86WT6-2;Q86WT6	.;TRI69_HUMAN	V	190;31	ENSP00000332284:A190V;ENSP00000342922:A31V	ENSP00000332284:A190V	A	+	2	0	TRIM69	42835943	0.999000	0.42202	0.995000	0.50966	0.061000	0.15899	0.335000	0.19806	0.110000	0.17919	-0.137000	0.14449	GCT	C|0.866;N|0.000	.	strong		0.473	TRIM69-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416171.1		
ANPEP	290	hgsc.bcm.edu	37	15	90335534	90335534	+	Silent	SNP	G	G	A	rs25652	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90335534G>A	ENST00000300060.6	-	18	2698	c.2385C>T	c.(2383-2385)acC>acT	p.T795T		NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	795	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	TGCAGTAGACGGTGGACCGCA	0.642													G|||	1263	0.252196	0.27	0.2075	5008	,	,		17265	0.1766		0.2584	False		,,,				2504	0.3313				p.T795T	NSCLC(30;827 977 2459 19669 26125)	Atlas-SNP	.											.	ANPEP	124	.	0			c.C2385T						PASS	.	G		1120,3280	402.2+/-332.3	147,826,1227	121.0	126.0	124.0		2385	-5.8	0.3	15	dbSNP_72	124	2288,6310	385.2+/-341.4	271,1746,2282	no	coding-synonymous	ANPEP	NM_001150.2		418,2572,3509	AA,AG,GG		26.6108,25.4545,26.2194		795/968	90335534	3408,9590	2200	4299	6499	SO:0001819	synonymous_variant	290	exon18			GTAGACGGTGGAC	M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.2385C>T	15.37:g.90335534G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	162	88	0.54321	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	37	CCDS10356.1																																																																																			T|0.000;G|0.749;A|0.251	0.251	strong		0.642	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
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 GAIIx	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		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	49	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	
SIRPG	55423	hgsc.bcm.edu	37	20	1610894	1610894	+	Silent	SNP	G	G	A	rs3746721	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:1610894G>A	ENST00000303415.3	-	5	1204	c.1140C>T	c.(1138-1140)taC>taT	p.Y380Y	SIRPG_ENST00000216927.4_Silent_p.Y269Y|SIRPG_ENST00000344103.4_Silent_p.Y163Y|SIRPG_ENST00000478145.2_5'UTR|SIRPG_ENST00000381583.2_Silent_p.Y269Y|SIRPG_ENST00000381580.1_Silent_p.Y347Y	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	380					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						TCCAGGGGACGTAGATGGGGC	0.582													g|||	1724	0.344249	0.1014	0.268	5008	,	,		18842	0.625		0.2594	False		,,,				2504	0.5245				p.Y380Y		Atlas-SNP	.											SIRPG,NS,carcinoma,0,1	SIRPG	61	1	0			c.C1140T						PASS	.	G	,,	502,3902		26,450,1726	63.0	50.0	54.0		807,1140,489	-4.2	0.0	20	dbSNP_107	54	2159,6433		279,1601,2416	no	coding-synonymous,coding-synonymous,coding-synonymous	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	305,2051,4142	AA,AG,GG		25.128,11.3987,20.4755	,,	269/277,380/388,163/171	1610894	2661,10335	2202	4296	6498	SO:0001819	synonymous_variant	55423	exon5			GGGGACGTAGATG	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.1140C>T	20.37:g.1610894G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_018556	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			G|0.742;A|0.258	0.258	strong		0.582	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
FSHR	2492	hgsc.bcm.edu	37	2	49189921	49189921	+	Missense_Mutation	SNP	C	C	T	rs6166	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:49189921C>T	ENST00000406846.2	-	10	2158	c.2039G>A	c.(2038-2040)aGt>aAt	p.S680N	FSHR_ENST00000304421.4_Missense_Mutation_p.S654N|FSHR_ENST00000346173.3_Missense_Mutation_p.S618N|FSHR_ENST00000541117.1_Missense_Mutation_p.S416N	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	680			N -> S (associated with longer menstrual cycles; dbSNP:rs6166). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12059813, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15815621, ECO:0000269|PubMed:1709010, ECO:0000269|PubMed:7916967, ECO:0000269|Ref.8}.		female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	AGTGGAACCACTGGTGACTCT	0.413									Gonadal Dysgenesis, 46 XX				T|||	2968	0.592652	0.5953	0.5778	5008	,	,		20407	0.6776		0.5507	False		,,,				2504	0.5552				p.S680N		Atlas-SNP	.											.	FSHR	164	.	0			c.G2039A	GRCh37	CM052876	FSHR	M	rs6166	PASS	.	T	ASN/SER,ASN/SER	2588,1818	533.3+/-373.7	768,1052,383	135.0	128.0	130.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2039,1961	1.5	0.1	2	dbSNP_52	130	4672,3928	548.0+/-385.3	1257,2158,885	yes	missense,missense	FSHR	NM_000145.3,NM_181446.2	46,46	2025,3210,1268	TT,TC,CC		45.6744,41.2619,44.1796	benign,benign	680/696,654/670	49189921	7260,5746	2203	4300	6503	SO:0001583	missense	2492	exon10	Familial Cancer Database		GAACCACTGGTGA		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"""GPCR / Class A : Gonadotropin and TSH receptors"""	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.2039G>A	2.37:g.49189921C>T	ENSP00000384708:p.Ser680Asn	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	37	CCDS1843.1	1307	0.5984432234432234	287	0.5833333333333334	212	0.585635359116022	394	0.6888111888111889	414	0.5461741424802111	T	0.015	-1.568847	0.00895	0.587381	0.543256	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000541117	T;T;T;T	0.72394	-0.48;-0.57;-0.47;-0.65	5.1	1.52	0.23074	.	0.214999	0.40728	N	0.001022	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.46076	-0.9217	7	.	.	.	.	9.0679	0.36475	0.0:0.3832:0.0:0.6168	rs6166;rs3181902;rs17487266;rs56532439;rs59607239;rs6166	654;618	Q05AH0;G5E967	.;.	N	680;618;654;416	ENSP00000384708:S680N;ENSP00000333908:S618N;ENSP00000306780:S654N;ENSP00000444172:S416N	.	S	-	2	0	FSHR	49043425	0.035000	0.19736	0.127000	0.21898	0.813000	0.45954	0.133000	0.15912	0.152000	0.19188	-0.254000	0.11334	AGT	C|0.421;T|0.579	0.579	strong		0.413	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2		
DIS3L	115752	hgsc.bcm.edu	37	15	66612965	66612965	+	Silent	SNP	T	T	C	rs17851970	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:66612965T>C	ENST00000319212.4	+	9	1271	c.1221T>C	c.(1219-1221)aaT>aaC	p.N407N	DIS3L_ENST00000441424.2_Missense_Mutation_p.W217R|DIS3L_ENST00000319194.5_Silent_p.N324N|RP11-352G18.2_ENST00000565993.1_RNA	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	407					RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						TGTATCCAAATGGACATTTTG	0.443													T|||	941	0.187899	0.0393	0.1686	5008	,	,		19029	0.1855		0.2614	False		,,,				2504	0.3292				p.N407N		Atlas-SNP	.											.	DIS3L	175	.	0			c.T1221C						PASS	.	T	,	353,4049	185.3+/-212.5	16,321,1864	163.0	150.0	155.0		1221,972	-4.5	0.8	15	dbSNP_123	155	2308,6290	387.7+/-342.3	306,1696,2297	no	coding-synonymous,coding-synonymous	DIS3L	NM_001143688.1,NM_133375.3	,	322,2017,4161	CC,CT,TT		26.8435,8.0191,20.4692	,	407/1055,324/972	66612965	2661,10339	2201	4299	6500	SO:0001819	synonymous_variant	115752	exon9			TCCAAATGGACAT		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"""DIS3 mitotic control homolog (S. cerevisiae)-like"""			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.1221T>C	15.37:g.66612965T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	118	69	0.584746	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Silent	SNP	ENST00000319212.4	37	CCDS45286.1	367	0.16804029304029305	17	0.034552845528455285	80	0.22099447513812154	76	0.13286713286713286	194	0.2559366754617414	T	14.64	2.594292	0.46214	0.080191	0.268435	ENSG00000166938	ENST00000441424	T	0.54279	0.58	5.11	-4.54	0.03452	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.40347	P	0.020901999999999976	.	.	.	.	.	.	T	0.26189	-1.0110	5	0.52906	T	0.07	-0.1593	8.8639	0.35274	0.1103:0.4874:0.0:0.4023	rs17851970;rs56437794;rs17851970	.	.	.	R	217	ENSP00000388980:W217R	ENSP00000388980:W217R	W	+	1	0	DIS3L	64400019	0.992000	0.36948	0.815000	0.32552	0.995000	0.86356	0.232000	0.17891	-0.986000	0.03498	0.459000	0.35465	TGG	T|0.806;C|0.194	0.194	strong		0.443	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
PHC1	1911	hgsc.bcm.edu	37	12	9086898	9086898	+	Missense_Mutation	SNP	A	A	G	rs1049925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9086898A>G	ENST00000543824.1	+	11	2409	c.2077A>G	c.(2077-2079)Act>Gct	p.T693A	PHC1_ENST00000433083.2_Missense_Mutation_p.T648A|PHC1_ENST00000544916.1_Missense_Mutation_p.T693A|PHC1_ENST00000536844.1_Missense_Mutation_p.T299A			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	693			T -> A (in dbSNP:rs1049925). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						GAATGCTAATACTCCAAGCAG	0.448													A|||	1770	0.353435	0.1551	0.3818	5008	,	,		-128	0.4107		0.4274	False		,,,				2504	0.4663				p.T693A		Atlas-SNP	.											.	PHC1	67	.	0			c.A2077G						PASS	.	A	ALA/THR	868,3538	335.2+/-303.8	82,704,1417	102.0	96.0	98.0		2077	0.9	0.1	12	dbSNP_86	98	3806,4794	524.3+/-380.5	784,2238,1278	yes	missense	PHC1	NM_004426.2	58	866,2942,2695	GG,GA,AA		44.2558,19.7004,35.9373	benign	693/1005	9086898	4674,8332	2203	4300	6503	SO:0001583	missense	1911	exon10			GCTAATACTCCAA	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"""Sterile alpha motif (SAM) domain containing"""	3182	protein-coding gene	gene with protein product		602978	"""early development regulator 1 (homolog of polyhomeotic 1)"", ""polyhomeotic-like 1 (Drosophila)"""	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.2077A>G	12.37:g.9086898A>G	ENSP00000440674:p.Thr693Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	55	16	0.290909	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	37	CCDS8597.1	803	0.3676739926739927	71	0.1443089430894309	135	0.3729281767955801	268	0.46853146853146854	329	0.4340369393139842	A	8.336	0.827685	0.16749	0.197004	0.442558	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844	T;T;T;T;T	0.36340	1.99;1.99;1.99;1.99;1.26	5.32	0.937	0.19494	.	0.365346	0.27008	N	0.021396	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47861	-0.9084	9	0.25106	T	0.35	-4.416	3.3522	0.07156	0.425:0.3732:0.0766:0.1252	rs1049925;rs12818486;rs16915798;rs17294227;rs17729971;rs52819214;rs59173968;rs1049925	693	P78364	PHC1_HUMAN	A	693;693;648;693;299	ENSP00000440674:T693A;ENSP00000251757:T693A;ENSP00000399194:T648A;ENSP00000437659:T693A;ENSP00000440488:T299A	ENSP00000251757:T693A	T	+	1	0	PHC1	8978165	0.000000	0.05858	0.105000	0.21289	0.907000	0.53573	-0.529000	0.06186	-0.009000	0.14296	0.533000	0.62120	ACT	A|0.630;G|0.370	0.370	strong		0.448	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.A57T|SGK1_ENST00000367857.5_Missense_Mutation_p.A33T|SGK1_ENST00000475719.2_Missense_Mutation_p.A43T|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367858.5_Missense_Mutation_p.A138T|SGK1_ENST00000528577.1_Missense_Mutation_p.A71T	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	Somatic	71	0	0	1611	WXS	Illumina HiSeq	Phase_I	45	7	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		
PCDHA12	56137	hgsc.bcm.edu	37	5	140255356	140255356	+	Missense_Mutation	SNP	C	C	T	rs182160950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140255356C>T	ENST00000398631.2	+	1	299	c.299C>T	c.(298-300)gCg>gTg	p.A100V	PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	100	Cadherin 1. {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(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCGGAGCGCGGAGTGCAGT	0.567													.|||	9	0.00179712	0.0	0.0086	5008	,	,		16883	0.0		0.003	False		,,,				2504	0.0				p.A100V	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,colon,carcinoma,0,1	PCDHA12	196	1	0			c.C299T						scavenged	.	C	,,,VAL/ALA,,,,,,,,,,,,VAL/ALA	5,4401	9.9+/-24.2	0,5,2198	116.0	132.0	126.0		,,,299,,,,,,,,,,,,299	0.4	0.0	5		126	35,8565	21.0+/-64.5	0,35,4265	no	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,64,,,,,,,,,,,,64	0,40,6463	TT,TC,CC		0.407,0.1135,0.3076	,,,,,,,,,,,,,,,	,,,100/942,,,,,,,,,,,,100/793	140255356	40,12966	2203	4300	6503	SO:0001583	missense	56137	exon1			GGAGCGCGGAGTG	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.299C>T	5.37:g.140255356C>T	ENSP00000381628:p.Ala100Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	9.540	1.113127	0.20795	0.001135	0.00407	ENSG00000251664	ENST00000398631	T	0.28069	1.63	5.28	0.447	0.16608	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.11623	0.0283	L	0.33668	1.02	0.09310	N	1	B;P	0.35077	0.295;0.483	B;B	0.15052	0.006;0.012	T	0.09207	-1.0685	9	0.44086	T	0.13	.	5.4992	0.16819	0.1235:0.5291:0.0:0.3474	.	100;100	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	V	100	ENSP00000381628:A100V	ENSP00000381628:A100V	A	+	2	0	PCDHA12	140235540	0.000000	0.05858	0.043000	0.18650	0.782000	0.44232	-4.183000	0.00278	-0.226000	0.09899	-0.229000	0.12294	GCG	C|0.998;T|0.002	0.002	strong		0.567	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
ADAM30	11085	hgsc.bcm.edu	37	1	120437718	120437718	+	Silent	SNP	G	G	A	rs2793823	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:120437718G>A	ENST00000369400.1	-	1	1400	c.1242C>T	c.(1240-1242)gaC>gaT	p.D414D		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	414	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		TGGAACCACAGTCACATTCCT	0.423													A|||	1656	0.330671	0.7171	0.2133	5008	,	,		22465	0.1052		0.1322	False		,,,				2504	0.3282				p.D414D		Atlas-SNP	.											.	ADAM30	88	.	0			c.C1242T						PASS	.	A		2579,1827	534.8+/-374.1	743,1093,367	174.0	167.0	170.0		1242	-5.5	0.7	1	dbSNP_100	170	1092,7508	769.0+/-407.6	74,944,3282	no	coding-synonymous	ADAM30	NM_021794.3		817,2037,3649	AA,AG,GG		12.6977,41.4662,28.2254		414/791	120437718	3671,9335	2203	4300	6503	SO:0001819	synonymous_variant	11085	exon1			ACCACAGTCACAT	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"""ADAM metallopeptidase domain containing"""	208	protein-coding gene	gene with protein product		604779	"""a disintegrin and metalloproteinase domain 30"""				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.1242C>T	1.37:g.120437718G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Silent	SNP	ENST00000369400.1	37	CCDS907.1																																																																																			G|0.719;A|0.280	0.280	strong		0.423	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794	
SCARF1	8578	hgsc.bcm.edu	37	17	1542153	1542153	+	Silent	SNP	G	G	A	rs2272012	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1542153G>A	ENST00000263071.4	-	8	1360	c.1311C>T	c.(1309-1311)ggC>ggT	p.G437G	SCARF1_ENST00000571272.1_Silent_p.G437G|SCARF1_ENST00000348987.3_Silent_p.G351G|SCARF1_ENST00000574545.1_5'Flank	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	437	Poly-Leu.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGCAGGCAAGGCCCAGGAAGA	0.667													G|||	3234	0.645767	0.4244	0.6902	5008	,	,		13734	0.877		0.6332	False		,,,				2504	0.6881				p.G437G		Atlas-SNP	.											.	SCARF1	46	.	0			c.C1311T						PASS	.	G	,,	2047,2357	547.5+/-377.3	490,1067,645	43.0	44.0	44.0		1311,1311,1053	4.5	0.9	17	dbSNP_100	44	5338,3262	637.9+/-399.3	1633,2072,595	no	coding-synonymous,coding-synonymous,coding-synonymous	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	,,	2123,3139,1240	AA,AG,GG		37.9302,46.4805,43.2098	,,	437/831,437/570,351/745	1542153	7385,5619	2202	4300	6502	SO:0001819	synonymous_variant	8578	exon8			GGCAAGGCCCAGG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1311C>T	17.37:g.1542153G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	148	66	0.445946	NM_145350	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Silent	SNP	ENST00000263071.4	37	CCDS11007.1																																																																																			G|0.403;A|0.597	0.597	strong		0.667	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
TMEM204	79652	hgsc.bcm.edu	37	16	1591962	1591962	+	Silent	SNP	G	G	A	rs2076443	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1591962G>A	ENST00000566264.1	+	2	1024	c.321G>A	c.(319-321)acG>acA	p.T107T	IFT140_ENST00000426508.2_Intron|TMEM204_ENST00000253934.5_Silent_p.T107T	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	107					lymph vessel development (GO:0001945)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to stress (GO:0006950)|smooth muscle cell differentiation (GO:0051145)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|cervix(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Hepatocellular(780;0.219)				TGGTGGCCACGGCCGCGCTCA	0.701													G|||	1534	0.30631	0.4228	0.1599	5008	,	,		18178	0.3423		0.1918	False		,,,				2504	0.3333				p.T107T		Atlas-SNP	.											TMEM204,NS,carcinoma,0,1	TMEM204	29	1	0			c.G321A						scavenged	.	G	,	1554,2760		288,978,891	30.0	37.0	35.0		,321	-11.5	0.2	16	dbSNP_96	35	1649,6841		166,1317,2762	no	intron,coding-synonymous	IFT140,TMEM204	NM_014714.3,NM_024600.4	,	454,2295,3653	AA,AG,GG		19.4229,36.0223,25.0156	,	,107/227	1591962	3203,9601	2157	4245	6402	SO:0001819	synonymous_variant	79652	exon2			GGCCACGGCCGCG		CCDS42098.1	16p13.3	2008-02-05	2008-01-08	2008-01-08		ENSG00000131634			14158	protein-coding gene	gene with protein product		611002	"""chromosome 16 open reading frame 30"""	C16orf30			Standard	NM_024600		Approved	FLJ20898	uc002cmc.3	Q9BSN7		ENST00000566264.1:c.321G>A	16.37:g.1591962G>A		Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_024600	D3DU76|Q3KRC1|Q9H7G5	Silent	SNP	ENST00000566264.1	37	CCDS42098.1																																																																																			G|0.746;A|0.254	0.254	strong		0.701	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600	
LAMC2	3918	hgsc.bcm.edu	37	1	183192304	183192304	+	Silent	SNP	T	T	G	rs1047980	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:183192304T>G	ENST00000264144.4	+	7	863	c.798T>G	c.(796-798)ggT>ggG	p.G266G	LAMC2_ENST00000493293.1_Silent_p.G266G	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	266	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)	p.G266G(1)		breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						TGAGCTATGGTCAAAGCCTGT	0.473													G|||	1778	0.355032	0.5477	0.3314	5008	,	,		22321	0.3363		0.159	False		,,,				2504	0.3323				p.G266G		Atlas-SNP	.											LAMC2,NS,carcinoma,0,1	LAMC2	113	1	1	Substitution - coding silent(1)	stomach(1)	c.T798G						PASS	.	G	,	2208,2198	587.3+/-386.7	578,1052,573	90.0	87.0	88.0		798,798	3.2	1.0	1	dbSNP_86	88	1526,7074	747.2+/-407.3	132,1262,2906	no	coding-synonymous,coding-synonymous	LAMC2	NM_005562.2,NM_018891.2	,	710,2314,3479	GG,GT,TT		17.7442,49.8865,28.7098	,	266/1194,266/1112	183192304	3734,9272	2203	4300	6503	SO:0001819	synonymous_variant	3918	exon7			CTATGGTCAAAGC	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.798T>G	1.37:g.183192304T>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	37	CCDS1352.1																																																																																			T|0.692;G|0.308	0.308	strong		0.473	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
ABCC4	10257	hgsc.bcm.edu	37	13	95858996	95858996	+	Silent	SNP	T	T	C	rs2274406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:95858996T>C	ENST00000376887.4	-	8	1065	c.951A>G	c.(949-951)agA>agG	p.R317R	ABCC4_ENST00000412704.1_Silent_p.R317R|ABCC4_ENST00000536256.1_Silent_p.R242R|ABCC4_ENST00000538287.1_3'UTR|ABCC4_ENST00000431522.1_Silent_p.R317R	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	317	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	p.R317R(1)		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)	AATTCATCCCTCTGAGGCAGG	0.468													T|||	2595	0.518171	0.3495	0.4957	5008	,	,		21994	0.5327		0.6193	False		,,,				2504	0.6431				p.R317R		Atlas-SNP	.											ABCC4_ENST00000376887,NS,carcinoma,0,1	ABCC4	248	1	1	Substitution - coding silent(1)	stomach(1)	c.A951G						PASS	.	T	,	1722,2684	512.2+/-368.0	368,986,849	158.0	156.0	157.0		951,951	3.2	1.0	13	dbSNP_100	157	5573,3027	662.7+/-402.0	1789,1995,516	no	coding-synonymous,coding-synonymous	ABCC4	NM_001105515.1,NM_005845.3	,	2157,2981,1365	CC,CT,TT		35.1977,39.0831,43.9105	,	317/860,317/1326	95858996	7295,5711	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon8			CATCCCTCTGAGG	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.951A>G	13.37:g.95858996T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			T|0.463;C|0.537	0.537	strong		0.468	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
HS1BP3	64342	hgsc.bcm.edu	37	2	20838318	20838318	+	Silent	SNP	G	G	A	rs3796064	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:20838318G>A	ENST00000304031.3	-	4	526	c.501C>T	c.(499-501)ttC>ttT	p.F167F	HS1BP3_ENST00000402541.1_Silent_p.F167F	NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	167							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAAAAGTCGAAAGCCTCTT	0.587													G|||	1798	0.359026	0.2292	0.3055	5008	,	,		19367	0.5565		0.2763	False		,,,				2504	0.454				p.F167F		Atlas-SNP	.											.	HS1BP3	33	.	0			c.C501T						PASS	.	G		985,3421	367.3+/-318.2	117,751,1335	155.0	141.0	146.0		501	-8.4	0.8	2	dbSNP_107	146	2254,6346	381.0+/-339.9	298,1658,2344	no	coding-synonymous	HS1BP3	NM_022460.3		415,2409,3679	AA,AG,GG		26.2093,22.3559,24.9039		167/393	20838318	3239,9767	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon4			AAAGTCGAAAGCC		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.501C>T	2.37:g.20838318G>A		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	235	118	0.502128	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1																																																																																			G|0.702;A|0.298	0.298	strong		0.587	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
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 GAIIx	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	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	59	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	
PRSS1	5644	hgsc.bcm.edu	37	7	142460313	142460313	+	Silent	SNP	T	T	C	rs6666	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:142460313T>C	ENST00000311737.7	+	4	492	c.486T>C	c.(484-486)gaT>gaC	p.D162D	PRSS1_ENST00000486171.1_Silent_p.D176D	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	162	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	AGTGCCTGGATGCTCCTGTGC	0.517													C|||	1986	0.396565	0.407	0.5288	5008	,	,		19819	0.2192		0.5835	False		,,,				2504	0.2791				p.D162D		Atlas-SNP	.											.	PRSS1	68	.	0			c.T486C	GRCh37	CM086253	PRSS1	M	rs6666	PASS	.						315.0	306.0	309.0					7																	142460313		2203	4300	6503	SO:0001819	synonymous_variant	5644	exon4			CCTGGATGCTCCT	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.486T>C	7.37:g.142460313T>C		Somatic	351	0	0		WXS	Illumina HiSeq	Phase_I	276	97	0.351449	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Silent	SNP	ENST00000311737.7	37	CCDS5872.1																																																																																			T|0.437;C|0.563	0.563	strong		0.517	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
MON1A	84315	hgsc.bcm.edu	37	3	49949071	49949071	+	Silent	SNP	A	A	G	rs868891	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49949071A>G	ENST00000417270.1	-	4	1218	c.525T>C	c.(523-525)ccT>ccC	p.P175P	MON1A_ENST00000455683.2_Intron|MON1A_ENST00000483022.1_5'UTR|MON1A_ENST00000296473.3_Silent_p.P264P|CTD-2330K9.3_ENST00000419183.1_Intron			Q86VX9	MON1A_HUMAN	MON1 secretory trafficking family member A	167										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GGGAGTACACAGGCTTCCCTG	0.612													A|||	1250	0.249601	0.2542	0.3012	5008	,	,		20663	0.122		0.4215	False		,,,				2504	0.1616				p.P264P		Atlas-SNP	.											MON1A,NS,carcinoma,0,1	MON1A	41	1	0			c.T792C						PASS	.	A	,	1209,3197	419.6+/-338.7	169,871,1163	91.0	79.0	83.0		,792	-10.2	0.6	3	dbSNP_86	83	3678,4922	527.8+/-381.2	763,2152,1385	yes	intron,coding-synonymous	MON1A	NM_001142501.1,NM_032355.3	,	932,3023,2548	GG,GA,AA		42.7674,27.4399,37.575	,	,264/653	49949071	4887,8119	2203	4300	6503	SO:0001819	synonymous_variant	84315	exon3			GTACACAGGCTTC	AK074404	CCDS2808.2, CCDS46830.1	3p21.31	2013-08-21	2013-08-21		ENSG00000164077	ENSG00000164077			28207	protein-coding gene	gene with protein product		611464	"""MON1 homolog A (yeast)"""			12477932	Standard	NM_032355		Approved	MGC13272, SAND1	uc003cxz.3	Q86VX9	OTTHUMG00000156737	ENST00000417270.1:c.525T>C	3.37:g.49949071A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_032355	B2RDQ1|G5E9N1|Q8NAV7|Q9BRF3	Silent	SNP	ENST00000417270.1	37																																																																																				A|0.671;G|0.329	0.329	strong		0.612	MON1A-005	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000345538.2	NM_032355	
CHIA	27159	hgsc.bcm.edu	37	1	111857951	111857951	+	Missense_Mutation	SNP	A	A	G	rs61756687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:111857951A>G	ENST00000369740.1	+	6	477	c.374A>G	c.(373-375)aAa>aGa	p.K125R	CHIA_ENST00000451398.2_5'UTR|CHIA_ENST00000343320.6_Missense_Mutation_p.K125R|CHIA_ENST00000430615.1_Missense_Mutation_p.K17R|RP5-1125M8.2_ENST00000426321.1_RNA|CHIA_ENST00000353665.6_Intron|CHIA_ENST00000483391.1_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	125			K -> R (in dbSNP:rs61756687). {ECO:0000269|PubMed:19435888}.		apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		TCAGTCATCAAATTCCTGCGC	0.542													A|||	331	0.0660942	0.0234	0.0677	5008	,	,		18683	0.0228		0.1382	False		,,,				2504	0.093				p.K125R		Atlas-SNP	.											.	CHIA	115	.	0			c.A374G						PASS	.	A	ARG/LYS,ARG/LYS	200,4206	124.9+/-162.1	3,194,2006	118.0	114.0	115.0		50,374	-0.8	1.0	1	dbSNP_129	115	1262,7338	251.4+/-277.9	82,1098,3120	yes	missense,missense	CHIA	NM_021797.2,NM_201653.2	26,26	85,1292,5126	GG,GA,AA		14.6744,4.5393,11.241	benign,benign	17/369,125/477	111857951	1462,11544	2203	4300	6503	SO:0001583	missense	27159	exon6			TCATCAAATTCCT	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.374A>G	1.37:g.111857951A>G	ENSP00000358755:p.Lys125Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	149	0.06822344322344322	13	0.026422764227642278	25	0.06906077348066299	3	0.005244755244755245	108	0.1424802110817942	A	11.51	1.659340	0.29515	0.045393	0.146744	ENSG00000134216	ENST00000422815;ENST00000369740;ENST00000343320;ENST00000430615	T;T;T;T	0.05717	3.4;3.4;3.4;3.4	4.72	-0.796	0.10912	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.144833	0.43579	N	0.000544	T	0.01489	0.0048	L	0.42529	1.33	0.09310	P	0.99999999764018	B	0.09022	0.002	B	0.15484	0.013	T	0.45425	-0.9262	9	0.29301	T	0.29	-10.7027	4.8	0.13292	0.5206:0.3028:0.1766:0.0	rs61756687	125	Q9BZP6	CHIA_HUMAN	R	69;125;125;17	ENSP00000387671:K69R;ENSP00000358755:K125R;ENSP00000341828:K125R;ENSP00000391132:K17R	ENSP00000341828:K125R	K	+	2	0	CHIA	111659474	0.921000	0.31238	0.991000	0.47740	0.748000	0.42578	0.251000	0.18257	-0.016000	0.14127	0.533000	0.62120	AAA	A|0.900;G|0.100	0.100	strong		0.542	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
USP34	9736	hgsc.bcm.edu	37	2	61647901	61647901	+	Silent	SNP	A	A	G	rs778155	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:61647901A>G	ENST00000398571.2	-	2	187	c.111T>C	c.(109-111)taT>taC	p.Y37Y		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	37					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			AGGAATTGATATAAGTAAATA	0.303													A|||	1680	0.335463	0.2375	0.4467	5008	,	,		17643	0.3284		0.3499	False		,,,				2504	0.3814				p.Y37Y		Atlas-SNP	.											USP34,colon,carcinoma,0,1	USP34	334	1	0			c.T111C						PASS	.	A		915,2803		116,683,1060	111.0	109.0	109.0		111	4.6	1.0	2	dbSNP_86	109	3058,5150		571,1916,1617	no	coding-synonymous	USP34	NM_014709.3		687,2599,2677	GG,GA,AA		37.2563,24.61,33.3138		37/3547	61647901	3973,7953	1859	4104	5963	SO:0001819	synonymous_variant	9736	exon2			ATTGATATAAGTA	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.111T>C	2.37:g.61647901A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1																																																																																			A|0.679;G|0.320	0.320	strong		0.303	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
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 GAIIx	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	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	138	67	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	
NLRC5	84166	hgsc.bcm.edu	37	16	57068107	57068107	+	Silent	SNP	C	C	T	rs3995817	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57068107C>T	ENST00000262510.6	+	13	2796	c.2571C>T	c.(2569-2571)caC>caT	p.H857H	NLRC5_ENST00000539144.1_Silent_p.H857H|NLRC5_ENST00000308149.7_Silent_p.H857H|NLRC5_ENST00000436936.1_Silent_p.H857H	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	857					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				TCCAGGTCCACGATGCGGAGG	0.622													C|||	1473	0.294129	0.2126	0.1988	5008	,	,		18273	0.5942		0.1292	False		,,,				2504	0.3323				p.H857H		Atlas-SNP	.											.	NLRC5	186	.	0			c.C2571T						PASS	.	C		913,3483	348.0+/-309.7	96,721,1381	54.0	45.0	48.0		2571	-7.8	0.0	16	dbSNP_108	48	901,7699	197.6+/-242.2	55,791,3454	no	coding-synonymous	NLRC5	NM_032206.3		151,1512,4835	TT,TC,CC		10.4767,20.7689,13.9581		857/1867	57068107	1814,11182	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon12			GGTCCACGATGCG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2571C>T	16.37:g.57068107C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	517	0.2367216117216117	93	0.18902439024390244	44	0.12154696132596685	287	0.5017482517482518	93	0.12269129287598944	C	3.826	-0.036769	0.07497	0.207689	0.104767	ENSG00000140853	ENST00000538805	.	.	.	4.82	-7.84	0.01196	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.6815	0.23123	0.1128:0.5634:0.1147:0.2092	rs3995817	.	.	.	X	610	.	.	R	+	1	2	NLRC5	55625608	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-1.739000	0.01840	-1.729000	0.01364	-0.379000	0.06801	CGA	C|0.834;T|0.166	0.166	strong		0.622	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
CCL23	6368	hgsc.bcm.edu	37	17	34341398	34341398	+	Silent	SNP	A	A	G	rs61737011	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:34341398A>G	ENST00000591423.1	-	2	176	c.112T>C	c.(112-114)Ttg>Ctg	p.L38L	CCL23_ENST00000293280.2_Silent_p.L38L|RP11-104J23.2_ENST00000590149.1_lincRNA|RP11-104J23.1_ENST00000588294.1_RNA	NM_145898.1	NP_665905.1	P55773	CCL23_HUMAN	chemokine (C-C motif) ligand 23	38				MLVTALGSQARVTKDAETEFMMSKLPLENPVLL -> HAFL LPLVPGPGHKRCRDRVHECQSFHWKIQYFW (in Ref. 1). {ECO:0000305}.	cell-cell signaling (GO:0007267)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|monocyte chemotaxis (GO:0002548)|negative regulation of C-C chemokine binding (GO:2001264)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)			large_intestine(2)|liver(1)|lung(2)|prostate(1)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		GGATTTTCCAATGGAAGCTTT	0.478													A|||	105	0.0209665	0.0083	0.0115	5008	,	,		21943	0.0496		0.0268	False		,,,				2504	0.0092				p.L38L		Atlas-SNP	.											.	CCL23	17	.	0			c.T112C						PASS	.	A	,	46,4360	48.2+/-83.0	0,46,2157	118.0	105.0	110.0		112,112	-5.9	0.0	17	dbSNP_129	110	231,8369	95.4+/-157.2	0,231,4069	no	coding-synonymous,coding-synonymous	CCL23	NM_005064.3,NM_145898.1	,	0,277,6226	GG,GA,AA		2.686,1.044,2.1298	,	38/138,38/121	34341398	277,12729	2203	4300	6503	SO:0001819	synonymous_variant	6368	exon2			TTTCCAATGGAAG	U58913	CCDS11305.1, CCDS59282.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000167236	ENSG00000274736		"""Chemokine ligands"", ""Endogenous ligands"""	10622	protein-coding gene	gene with protein product		602494	"""small inducible cytokine subfamily A (Cys-Cys), member 23"""	SCYA23		9104803, 10409433	Standard	XR_429910		Approved	Ckb-8, MPIF-1, MIP-3, CKb8	uc002hks.1	P55773	OTTHUMG00000188409	ENST00000591423.1:c.112T>C	17.37:g.34341398A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	130	76	0.584615	NM_005064	B7ZKQ3|O00174|O75950|Q52LD4	Silent	SNP	ENST00000591423.1	37	CCDS59282.1																																																																																			A|0.979;G|0.021	0.021	strong		0.478	CCL23-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450228.1	NM_005064, NM_145898	
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 GAIIx	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		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	66	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	
TEX38	374973	hgsc.bcm.edu	37	1	47139103	47139103	+	Missense_Mutation	SNP	C	C	T	rs1025806	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47139103C>T	ENST00000334122.4	+	2	703	c.596C>T	c.(595-597)gCc>gTc	p.A199V	ATPAF1_ENST00000525633.1_Intron|TEX38_ENST00000569393.1_Missense_Mutation_p.A253V|EFCAB14-AS1_ENST00000442839.1_RNA|TEX38_ENST00000564373.1_Missense_Mutation_p.A145V|EFCAB14-AS1_ENST00000418985.1_RNA|TEX38_ENST00000415500.1_Missense_Mutation_p.A123V|EFCAB14_ENST00000544071.1_Intron	NM_001145474.2	NP_001138946.1	Q6PEX7	TEX38_HUMAN	testis expressed 38	199			A -> V (in dbSNP:rs1025806). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)											AGCTTCAATGCCAAGCCTTTT	0.507													C|||	1333	0.266174	0.1785	0.3545	5008	,	,		20137	0.3353		0.2972	False		,,,				2504	0.2188				p.A199V		Atlas-SNP	.											ATPAF1-AS1_ENST00000569393,colon,carcinoma,0,2	.	.	2	0			c.C596T						PASS	.	C	VAL/ALA	258,1126		17,224,451	59.0	48.0	52.0		596	3.1	0.4	1	dbSNP_86	52	849,2333		97,655,839	yes	missense	ATPAF1-AS1	NM_001145474.2	64	114,879,1290	TT,TC,CC		26.6813,18.6416,24.2444	possibly-damaging	199/207	47139103	1107,3459	692	1591	2283	SO:0001583	missense	374973	exon2			TCAATGCCAAGCC		CCDS57999.1, CCDS72780.1, CCDS72781.1	1p33	2012-10-12	2012-10-12	2012-10-12	ENSG00000186118	ENSG00000186118			29589	protein-coding gene	gene with protein product	"""testis highly expressed protein 4"""		"""chromosome 1 open reading frame 223"", ""ATPAF1 antisense RNA 1 (non-protein coding)"", ""ATPAF1 antisense RNA 1"""	C1orf223, ATPAF1-AS1		12477932	Standard	XM_005270845		Approved	LOC374973, THEG4	uc001cqj.3	Q6PEX7	OTTHUMG00000007991	ENST00000334122.4:c.596C>T	1.37:g.47139103C>T	ENSP00000455854:p.Ala199Val	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_001145474	A1A4F8	Missense_Mutation	SNP	ENST00000334122.4	37	CCDS57999.1																																																																																			C|0.719;T|0.281	0.281	strong		0.507	TEX38-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000021929.2	NM_001145474	
BRINP2	57795	hgsc.bcm.edu	37	1	177247854	177247854	+	Missense_Mutation	SNP	C	C	G	rs3176443	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:177247854C>G	ENST00000361539.4	+	7	1480	c.1168C>G	c.(1168-1170)Cta>Gta	p.L390V	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	390			L -> V (in dbSNP:rs3176443).		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)	extracellular region (GO:0005576)											CCATCGGATCCTACGCCGGCT	0.612													G|||	1325	0.264577	0.4017	0.2061	5008	,	,		15428	0.2113		0.2187	False		,,,				2504	0.2229				p.L390V		Atlas-SNP	.											.	FAM5B	191	.	0			c.C1168G						PASS	.	G	VAL/LEU	1680,2726	654.9+/-399.8	289,1102,812	84.0	88.0	87.0		1168	3.2	0.6	1	dbSNP_105	87	1779,6821	734.2+/-406.9	199,1381,2720	yes	missense	FAM5B	NM_021165.2	32	488,2483,3532	GG,GC,CC		20.686,38.1298,26.5954	benign	390/784	177247854	3459,9547	2203	4300	6503	SO:0001583	missense	57795	exon7			CGGATCCTACGCC		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1168C>G	1.37:g.177247854C>G	ENSP00000354481:p.Leu390Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	576	0.26373626373626374	217	0.4410569105691057	72	0.19889502762430938	123	0.21503496503496503	164	0.21635883905013192	G	0.863	-0.734660	0.03111	0.381298	0.20686	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.11821	2.74	5.39	3.17	0.36434	.	0.246637	0.40064	N	0.001185	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.47573	-0.9107	9	0.02654	T	1	-19.594	8.7092	0.34374	0.1994:0.1281:0.6726:0.0	rs3176443;rs3736682;rs56601222;rs3176443	140;285;390	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	V	140;390	ENSP00000354481:L390V	ENSP00000354481:L390V	L	+	1	2	FAM5B	175514477	0.934000	0.31675	0.602000	0.28890	0.977000	0.68977	1.390000	0.34464	0.670000	0.31165	-0.120000	0.15030	CTA	C|0.730;G|0.270	0.270	strong		0.612	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
MED13L	23389	hgsc.bcm.edu	37	12	116446445	116446445	+	Silent	SNP	C	C	T	rs3741768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:116446445C>T	ENST00000281928.3	-	10	1979	c.1773G>A	c.(1771-1773)caG>caA	p.Q591Q		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	591						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		GAGTAGACAACTGCTGGAGTT	0.532													C|||	718	0.143371	0.0461	0.1268	5008	,	,		20760	0.1637		0.1869	False		,,,				2504	0.2209				p.Q591Q		Atlas-SNP	.											.	MED13L	193	.	0			c.G1773A						PASS	.	C		319,4087	171.2+/-201.5	4,311,1888	66.0	58.0	60.0		1773	-2.3	1.0	12	dbSNP_107	60	1530,7070	287.8+/-298.4	121,1288,2891	no	coding-synonymous	MED13L	NM_015335.4		125,1599,4779	TT,TC,CC		17.7907,7.2401,14.2165		591/2211	116446445	1849,11157	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon10			AGACAACTGCTGG	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.1773G>A	12.37:g.116446445C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	144	71	0.493056	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																			C|0.855;T|0.145	0.145	strong		0.532	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
TESK2	10420	hgsc.bcm.edu	37	1	45810923	45810923	+	Silent	SNP	G	G	A	rs3893383	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:45810923G>A	ENST00000372086.3	-	11	1705	c.1305C>T	c.(1303-1305)ccC>ccT	p.P435P	TESK2_ENST00000372084.1_Silent_p.P406P|TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000538496.1_Silent_p.P352P|TESK2_ENST00000341771.6_Silent_p.P406P	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	435					actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					GCATAGTTCCGGGCCCTGGTG	0.582													G|||	872	0.174121	0.2852	0.1095	5008	,	,		18447	0.1935		0.1044	False		,,,				2504	0.1217				p.P435P		Atlas-SNP	.											.	TESK2	60	.	0			c.C1305T						PASS	.	G		940,2854		108,724,1065	41.0	44.0	43.0		1305	-0.8	1.0	1	dbSNP_108	43	849,7353		42,765,3294	no	coding-synonymous	TESK2	NM_007170.2		150,1489,4359	AA,AG,GG		10.3511,24.776,14.9133		435/572	45810923	1789,10207	1897	4101	5998	SO:0001819	synonymous_variant	10420	exon11			AGTTCCGGGCCCT	AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.1305C>T	1.37:g.45810923G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Silent	SNP	ENST00000372086.3	37	CCDS41323.1																																																																																			G|0.838;A|0.161	0.161	strong		0.582	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170	
DOT1L	84444	hgsc.bcm.edu	37	19	2217023	2217023	+	Silent	SNP	C	C	T	rs141523228	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:2217023C>T	ENST00000398665.3	+	21	2514	c.2478C>T	c.(2476-2478)agC>agT	p.S826S	AC004490.1_ENST00000585593.1_RNA	NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	826					histone lysine methylation (GO:0034968)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription regulatory region DNA binding (GO:2000677)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(9)	42		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)		TGAAGCTGAGCCCTCAGGACC	0.662													C|||	68	0.0135783	0.0	0.0086	5008	,	,		18443	0.0		0.0378	False		,,,				2504	0.0245				p.S826S		Atlas-SNP	.											.	DOT1L	205	.	0			c.C2478T						PASS	.	C		10,4114		0,10,2052	34.0	37.0	36.0		2478	0.9	1.0	19	dbSNP_134	36	199,8199		4,191,4004	no	coding-synonymous	DOT1L	NM_032482.2		4,201,6056	TT,TC,CC		2.3696,0.2425,1.6691		826/1538	2217023	209,12313	2062	4199	6261	SO:0001819	synonymous_variant	84444	exon21			GCTGAGCCCTCAG	AF509504	CCDS42460.1	19p13.3	2013-05-21	2013-05-21		ENSG00000104885	ENSG00000104885	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"""	24948	protein-coding gene	gene with protein product	"""histone methyltransferase DOT1L"""	607375	"""DOT1-like, histone H3 methyltransferase (S. cerevisiae)"""			11347906, 12123582	Standard	NM_032482		Approved	KIAA1814, DOT1, KMT4	uc002lvb.4	Q8TEK3	OTTHUMG00000150431	ENST00000398665.3:c.2478C>T	19.37:g.2217023C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_032482	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	37	CCDS42460.1	32	0.014652014652014652	0	0.0	4	0.011049723756906077	0	0.0	28	0.036939313984168866	C	2.492	-0.317243	0.05386	0.002425	0.023696	ENSG00000104885	ENST00000440640	.	.	.	5.45	0.928	0.19443	.	.	.	.	.	T	0.26629	0.0651	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30504	-0.9976	4	.	.	.	-28.1148	10.812	0.46553	0.0:0.6388:0.0:0.3612	.	.	.	.	V	613	.	.	A	+	2	0	DOT1L	2168023	0.979000	0.34478	0.998000	0.56505	0.105000	0.19272	-0.038000	0.12144	0.029000	0.15352	-0.797000	0.03246	GCC	C|0.981;T|0.019	0.019	strong		0.662	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482	
ARHGEF18	23370	hgsc.bcm.edu	37	19	7524855	7524855	+	Silent	SNP	C	C	T	rs2287915	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:7524855C>T	ENST00000359920.6	+	10	2116	c.1863C>T	c.(1861-1863)cgC>cgT	p.R621R	CTD-2207O23.3_ENST00000593531.1_Missense_Mutation_p.A579V|ARHGEF18_ENST00000319670.9_Silent_p.R463R	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	621					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				TCGAGGCCCGCGCCACGAGAC	0.657													C|||	1137	0.227037	0.2133	0.219	5008	,	,		18144	0.2728		0.2455	False		,,,				2504	0.1851				p.R621R		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.C1863T						PASS	.	C	,	881,3507		88,705,1401	23.0	18.0	20.0		1863,1389	-9.7	0.0	19	dbSNP_100	20	1870,6720		205,1460,2630	no	coding-synonymous,coding-synonymous	ARHGEF18	NM_001130955.1,NM_015318.3	,	293,2165,4031	TT,TC,CC		21.7695,20.0775,21.1974	,	621/1174,463/1016	7524855	2751,10227	2194	4295	6489	SO:0001819	synonymous_variant	23370	exon10			GGCCCGCGCCACG	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.1863C>T	19.37:g.7524855C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	67	20	0.298507	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Silent	SNP	ENST00000359920.6	37	CCDS45946.1																																																																																			C|0.775;T|0.225	0.225	strong		0.657	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
ACTN4	81	hgsc.bcm.edu	37	19	39196736	39196736	+	Silent	SNP	G	G	A	rs11553600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39196736G>A	ENST00000252699.2	+	5	613	c.537G>A	c.(535-537)ccG>ccA	p.P179P	ACTN4_ENST00000390009.3_Intron|ACTN4_ENST00000424234.2_Intron	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	179	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.|Polyphosphoinositide (PIP2)-binding. {ECO:0000255}.				actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGACAGCCCCGTATAAGAACG	0.522													G|||	578	0.115415	0.0666	0.1527	5008	,	,		20772	0.0089		0.2266	False		,,,				2504	0.1503				p.P179P	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											ACTN4,NS,carcinoma,+1,1	ACTN4	69	1	0			c.G537A						PASS	.	G		371,4035	188.8+/-215.1	16,339,1848	119.0	102.0	108.0		537	-7.2	0.2	19	dbSNP_120	108	1621,6979	299.9+/-304.7	155,1311,2834	no	coding-synonymous	ACTN4	NM_004924.4		171,1650,4682	AA,AG,GG		18.8488,8.4203,15.316		179/912	39196736	1992,11014	2203	4300	6503	SO:0001819	synonymous_variant	81	exon5			AGCCCCGTATAAG	D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"""EF-hand domain containing"""	166	protein-coding gene	gene with protein product		604638	"""focal segmental glomerulosclerosis 1"""	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.537G>A	19.37:g.39196736G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	79	43	0.544304	NM_004924	A4K467|D6PXK4|O76048	Silent	SNP	ENST00000252699.2	37	CCDS12518.1																																																																																			G|0.852;A|0.148	0.148	strong		0.522	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1		
BSN	8927	hgsc.bcm.edu	37	3	49701298	49701298	+	Missense_Mutation	SNP	G	G	A	rs2005557	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49701298G>A	ENST00000296452.4	+	8	11701	c.11587G>A	c.(11587-11589)Gca>Aca	p.A3863T		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3863			A -> T (in dbSNP:rs2005557). {ECO:0000269|PubMed:10329005, ECO:0000269|PubMed:9455477, ECO:0000269|PubMed:9806829}.		synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GGCCCAGCCAGCACCAGGACC	0.592													A|||	3207	0.640375	0.4032	0.683	5008	,	,		19609	0.9325		0.5099	False		,,,				2504	0.7638				p.A3863T		Atlas-SNP	.											BSN,NS,adenoma,0,1	BSN	272	1	0			c.G11587A						PASS	.	A	THR/ALA	1903,2503	626.4+/-394.7	413,1077,713	108.0	94.0	99.0		11587	1.3	0.6	3	dbSNP_92	99	4443,4157	566.4+/-388.7	1166,2111,1023	yes	missense	BSN	NM_003458.3	58	1579,3188,1736	AA,AG,GG		48.3372,43.1911,48.7929	possibly-damaging	3863/3927	49701298	6346,6660	2203	4300	6503	SO:0001583	missense	8927	exon8			CAGCCAGCACCAG	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.11587G>A	3.37:g.49701298G>A	ENSP00000296452:p.Ala3863Thr	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	203	90	0.44335	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	1341	0.614010989010989	188	0.3821138211382114	229	0.6325966850828729	536	0.9370629370629371	388	0.5118733509234829	A	5.748	0.322360	0.10900	0.431911	0.516628	ENSG00000164061	ENST00000296452	T	0.17854	2.25	3.43	1.26	0.21427	.	0.977424	0.08377	N	0.955199	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41431	-0.9509	9	0.02654	T	1	-0.4728	1.03	0.01536	0.3322:0.2632:0.2701:0.1345	rs2005557;rs59206941;rs2005557	3863	Q9UPA5	BSN_HUMAN	T	3863	ENSP00000296452:A3863T	ENSP00000296452:A3863T	A	+	1	0	BSN	49676302	0.019000	0.18553	0.580000	0.28601	0.385000	0.30292	0.707000	0.25704	0.010000	0.14839	-0.521000	0.04368	GCA	G|0.472;A|0.528	0.528	strong		0.592	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
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 GAIIx	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_ENST00000535300.1_Missense_Mutation_p.E129D|RABGGTB_ENST00000496055.1_3'UTR|MSH4_ENST00000263187.3_5'Flank	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	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	20	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	
SWT1	54823	hgsc.bcm.edu	37	1	185143721	185143721	+	Missense_Mutation	SNP	A	A	G	rs10489579	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:185143721A>G	ENST00000367500.4	+	5	607	c.442A>G	c.(442-444)Att>Gtt	p.I148V	SWT1_ENST00000367501.3_Missense_Mutation_p.I148V	NM_017673.6	NP_060143.4	Q5T5J6	SWT1_HUMAN	SWT1 RNA endoribonuclease homolog (S. cerevisiae)	148			I -> V (in dbSNP:rs10489579). {ECO:0000269|PubMed:15489334}.							breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(16)|ovary(1)|prostate(1)|urinary_tract(1)	41						TGACCATGGAATTAAAAGCCT	0.368													A|||	2177	0.434704	0.6982	0.3487	5008	,	,		19153	0.2718		0.3439	False		,,,				2504	0.4008				p.I148V		Atlas-SNP	.											.	SWT1	88	.	0			c.A442G						PASS	.	A	VAL/ILE,VAL/ILE	2802,1604	659.4+/-400.6	907,988,308	53.0	53.0	53.0		442,442	0.9	0.0	1	dbSNP_119	53	3071,5529	467.9+/-367.2	556,1959,1785	yes	missense,missense	SWT1	NM_001105518.1,NM_017673.6	29,29	1463,2947,2093	GG,GA,AA		35.7093,36.4049,45.1561	benign,benign	148/901,148/901	185143721	5873,7133	2203	4300	6503	SO:0001583	missense	54823	exon5			CATGGAATTAAAA	AF288392	CCDS1367.1	1q25	2013-08-29	2011-01-24	2011-01-24	ENSG00000116668	ENSG00000116668			16785	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 26"""	C1orf26		11318611, 19127978, 23768067	Standard	NM_017673		Approved	FLJ20121, HsSwt1	uc001grg.4	Q5T5J6	OTTHUMG00000035390	ENST00000367500.4:c.442A>G	1.37:g.185143721A>G	ENSP00000356470:p.Ile148Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_017673	Q8NEK9|Q9BZQ7|Q9NXQ0	Missense_Mutation	SNP	ENST00000367500.4	37	CCDS1367.1	914	0.4184981684981685	350	0.7113821138211383	119	0.3287292817679558	187	0.3269230769230769	258	0.3403693931398417	A	0.583	-0.836082	0.02713	0.635951	0.357093	ENSG00000116668	ENST00000367501;ENST00000367500;ENST00000450350	T;T;T	0.37915	1.17;1.17;1.17	5.35	0.918	0.19386	.	1.040850	0.07571	N	0.918619	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.45687	-0.9244	9	0.11794	T	0.64	.	1.757	0.02984	0.2943:0.2806:0.308:0.1171	rs10489579;rs17845931;rs17858910;rs58368482;rs10489579	148	Q5T5J6	SWT1_HUMAN	V	148	ENSP00000356471:I148V;ENSP00000356470:I148V;ENSP00000401413:I148V	ENSP00000356470:I148V	I	+	1	0	SWT1	183410344	0.955000	0.32602	0.002000	0.10522	0.559000	0.35586	0.566000	0.23593	-0.149000	0.11215	0.455000	0.32223	ATT	G|0.396;N|0.000	0.396	strong		0.368	SWT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085790.1	NM_017673	
MUC2	4583	hgsc.bcm.edu	37	11	1081141	1081141	+	Splice_Site	SNP	C	C	T	rs41375149	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1081141C>T	ENST00000441003.2	+	11	1464	c.1437C>T	c.(1435-1437)acC>acT	p.T479T	MUC2_ENST00000359061.5_Splice_Site_p.T479T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	479	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	CCCACGTGACCGGTGAGTTGT	0.657													C|||	283	0.0565096	0.0408	0.0461	5008	,	,		16341	0.0506		0.0934	False		,,,				2504	0.0532				p.T479T		Atlas-SNP	.											.	MUC2	614	.	0			c.C1437T						PASS	.	C		167,3805		4,159,1823	31.0	37.0	35.0		1437	-7.3	0.6	11	dbSNP_127	35	744,7582		33,678,3452	yes	coding-synonymous-near-splice	MUC2	NM_002457.2		37,837,5275	TT,TC,CC		8.9359,4.2044,7.4077		479/2813	1081141	911,11387	1986	4163	6149	SO:0001630	splice_region_variant	4583	exon11			CGTGACCGGTGAG	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.1438+1C>T	11.37:g.1081141C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.939;T|0.061	0.061	strong		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	Silent
UBQLNL	143630	hgsc.bcm.edu	37	11	5537045	5537045	+	Silent	SNP	T	T	G	rs872751	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5537045T>G	ENST00000380184.1	-	1	890	c.627A>C	c.(625-627)ccA>ccC	p.P209P	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	209										endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		GGGAAACTTCTGGGTTCTGCT	0.468													T|||	1608	0.321086	0.3472	0.3487	5008	,	,		21098	0.375		0.2644	False		,,,				2504	0.2689				p.P209P		Atlas-SNP	.											.	UBQLNL	74	.	0			c.A627C						PASS	.	T		1484,2918	476.3+/-357.6	258,968,975	129.0	131.0	130.0		627	1.2	1.0	11	dbSNP_86	130	2364,6230	394.6+/-344.7	338,1688,2271	no	coding-synonymous	UBQLNL	NM_145053.4		596,2656,3246	GG,GT,TT		27.5076,33.7119,29.6091		209/476	5537045	3848,9148	2201	4297	6498	SO:0001819	synonymous_variant	143630	exon1			AACTTCTGGGTTC	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.627A>C	11.37:g.5537045T>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	104	66	0.634615	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	37	CCDS31385.1																																																																																			T|0.688;G|0.312	0.312	strong		0.468	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
ZNF30	90075	hgsc.bcm.edu	37	19	35434448	35434448	+	Missense_Mutation	SNP	A	A	G	rs62122088	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35434448A>G	ENST00000601142.1	+	5	815	c.578A>G	c.(577-579)aAg>aGg	p.K193R	ZNF30_ENST00000426813.2_Missense_Mutation_p.K112R|ZNF30_ENST00000303586.7_Missense_Mutation_p.K194R|ZNF30_ENST00000439785.1_Missense_Mutation_p.K194R|ZNF30_ENST00000601957.1_3'UTR			P17039	ZNF30_HUMAN	zinc finger protein 30	193				K -> R (in Ref. 2; CAE45802). {ECO:0000305}.	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)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		GCCTTTGTTAAGCATGGGAGA	0.398													A|||	427	0.0852636	0.0628	0.0403	5008	,	,		19724	0.0635		0.1551	False		,,,				2504	0.0982				p.K194R		Atlas-SNP	.											.	ZNF30	44	.	0			c.A581G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	309,3769		11,287,1741	39.0	42.0	41.0		581,581,578	-0.0	0.0	19	dbSNP_129	41	1266,7172		91,1084,3044	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	26,26,26	102,1371,4785	GG,GA,AA		15.0036,7.5772,12.5839	benign,benign,benign	194/625,194/625,193/624	35434448	1575,10941	2039	4219	6258	SO:0001583	missense	90075	exon5			TTGTTAAGCATGG	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.578A>G	19.37:g.35434448A>G	ENSP00000469954:p.Lys193Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	198	0.09065934065934066	30	0.06097560975609756	18	0.049723756906077346	30	0.05244755244755245	120	0.158311345646438	A	0.019	-1.464275	0.01053	0.075772	0.150036	ENSG00000168661	ENST00000439785;ENST00000303586;ENST00000426813	T;T	0.13657	2.57;2.57	2.4	-0.0256	0.13934	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04373	-0.215	0.80722	P	0.0	B;B	0.15473	0.005;0.013	B;B	0.13407	0.009;0.007	T	0.44651	-0.9314	8	0.10377	T	0.69	.	2.7105	0.05174	0.5563:0.2742:0.1695:0.0	rs62122088	194;193	P17039-2;P17039	.;ZNF30_HUMAN	R	194;193;112	ENSP00000403441:K194R;ENSP00000416457:K112R	ENSP00000303889:K193R	K	+	2	0	ZNF30	40126288	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.896000	0.00706	-0.220000	0.09988	-0.487000	0.04747	AAG	A|0.892;G|0.108	0.108	strong		0.398	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
MUC4	4585	hgsc.bcm.edu	37	3	195510011	195510011	+	Missense_Mutation	SNP	C	C	T	rs28375716		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195510011C>T	ENST00000463781.3	-	2	8899	c.8440G>A	c.(8440-8442)Gcc>Acc	p.A2814T	MUC4_ENST00000475231.1_Missense_Mutation_p.A2814T|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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)		AGAGAGGTGGCGTGACCTGTG	0.587																																					p.A2814T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G8440A						PASS	.						70.0	44.0	52.0					3																	195510011		685	1518	2203	SO:0001583	missense	4585	exon2			AGGTGGCGTGACC	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.8440G>A	3.37:g.195510011C>T	ENSP00000417498:p.Ala2814Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	6	0.0909091	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	.	.	.	.	.	.	.	.	.	.	-	8.082	0.772585	0.16051	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34472	1.37;1.36	.	.	.	.	.	.	.	.	T	0.23330	0.0564	N	0.19112	0.55	0.09310	N	0.999993	D	0.53312	0.959	P	0.45971	0.499	T	0.13575	-1.0504	7	.	.	.	.	5.8178	0.18506	0.0:0.999:0.0:0.001	.	2686	E7ESK3	.	T	2814	ENSP00000417498:A2814T;ENSP00000420243:A2814T	.	A	-	1	0	MUC4	196994790	0.001000	0.12720	0.022000	0.16811	0.020000	0.10135	-2.830000	0.00744	-0.000000	0.14550	0.000000	0.15137	GCC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CD163L1	283316	hgsc.bcm.edu	37	12	7528471	7528471	+	Silent	SNP	G	G	A	rs7306824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:7528471G>A	ENST00000313599.3	-	10	2568	c.2511C>T	c.(2509-2511)aaC>aaT	p.N837N	CD163L1_ENST00000396630.1_Silent_p.N837N|CD163L1_ENST00000416109.2_Silent_p.N847N|CD163L1_ENST00000544331.1_5'UTR			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	837	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CATCTCCACAGTTTAATTCTC	0.468													A|||	2323	0.463858	0.6331	0.4841	5008	,	,		-128	0.4752		0.2714	False		,,,				2504	0.407				p.N837N		Atlas-SNP	.											CD163L1,colon,carcinoma,0,2	CD163L1	238	2	0			c.C2511T						PASS	.	A		2474,1932	549.1+/-377.7	698,1078,427	99.0	99.0	99.0		2511	-5.5	0.0	12	dbSNP_116	99	2144,6456	714.9+/-406.0	281,1582,2437	no	coding-synonymous	CD163L1	NM_174941.4		979,2660,2864	AA,AG,GG		24.9302,43.8493,35.5067		837/1454	7528471	4618,8388	2203	4300	6503	SO:0001819	synonymous_variant	283316	exon10			TCCACAGTTTAAT	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.2511C>T	12.37:g.7528471G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	CCDS8577.1																																																																																			G|0.601;A|0.399	0.399	strong		0.468	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
FHAD1	114827	hgsc.bcm.edu	37	1	15708540	15708540	+	Missense_Mutation	SNP	A	A	G	rs1010294	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:15708540A>G	ENST00000375998.4	+	29	3973	c.3973A>G	c.(3973-3975)Att>Gtt	p.I1325V	FHAD1_ENST00000314740.8_Missense_Mutation_p.I578V|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000417793.1_Missense_Mutation_p.I1289V|FHAD1_ENST00000375999.3_Missense_Mutation_p.I1325V|FHAD1_ENST00000358897.4_Missense_Mutation_p.I1325V			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1325										skin(1)|stomach(1)	2						CAAAGTGTCCATTGAGATGTA	0.532													G|||	2114	0.422125	0.77	0.3055	5008	,	,		22117	0.2589		0.2624	False		,,,				2504	0.3671				p.I1325V		Atlas-SNP	.											.	FHAD1	78	.	0			c.A3973G						PASS	.	G	VAL/ILE	961,423		341,279,72	65.0	67.0	66.0		3973	-4.3	0.0	1	dbSNP_86	66	836,2346		102,632,857	yes	missense	FHAD1	NM_052929.1	29	443,911,929	GG,GA,AA		26.2728,30.5636,39.3561	benign	1325/1413	15708540	1797,2769	692	1591	2283	SO:0001583	missense	114827	exon30			GTGTCCATTGAGA	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.3973A>G	1.37:g.15708540A>G	ENSP00000365166:p.Ile1325Val	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	209	100	0.478469	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		834	0.38186813186813184	369	0.75	125	0.3453038674033149	141	0.2465034965034965	199	0.262532981530343	G	0.006	-2.038631	0.00402	0.694364	0.262728	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375999;ENST00000375998;ENST00000529606;ENST00000314740;ENST00000314668	T;T;T;T;T;T;T	0.39406	1.17;1.17;1.08;1.17;1.08;1.09;1.14	5.95	-4.31	0.03698	.	.	.	.	.	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38908	-0.9639	8	0.15952	T	0.53	-6.224	7.5924	0.28029	0.5737:0.2316:0.1946:0.0	rs1010294;rs3765368;rs52824203;rs61149895;rs1010294	578;1325	B7WPP2;B1AJZ9	.;FHAD1_HUMAN	V	1325;1289;1325;1325;596;578;560	ENSP00000351770:I1325V;ENSP00000407615:I1289V;ENSP00000365167:I1325V;ENSP00000365166:I1325V;ENSP00000434909:I596V;ENSP00000322979:I578V;ENSP00000318812:I560V	ENSP00000318812:I560V	I	+	1	0	FHAD1	15581127	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-1.470000	0.02346	-0.699000	0.05077	-0.716000	0.03619	ATT	T|0.004;G|0.400	0.400	strong		0.532	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
ZNF83	55769	hgsc.bcm.edu	37	19	53116940	53116940	+	Missense_Mutation	SNP	T	T	A	rs75857698	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:53116940T>A	ENST00000597597.1	-	2	3131	c.878A>T	c.(877-879)gAg>gTg	p.E293V	ZNF83_ENST00000544146.1_Missense_Mutation_p.E293V|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000536937.1_Missense_Mutation_p.E293V|ZNF83_ENST00000545872.1_Missense_Mutation_p.E293V|ZNF83_ENST00000391789.4_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000541777.2_Missense_Mutation_p.E293V|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000301096.3_Missense_Mutation_p.E293V			P51522	ZNF83_HUMAN	zinc finger protein 83	293					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)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		CTTGCCACACTCATTACATTT	0.408													T|||	1368	0.273163	0.1641	0.4294	5008	,	,		2446	0.499		0.2137	False		,,,				2504	0.138				p.E293V		Atlas-SNP	.											.	ZNF83	73	.	0			c.A878T						PASS	.						84.0	84.0	84.0					19																	53116940		2201	4300	6501	SO:0001583	missense	55769	exon3			CCACACTCATTAC	M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.878A>T	19.37:g.53116940T>A	ENSP00000472619:p.Glu293Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	33	10	0.30303	NM_018300	A8MT75|Q3ZCX0|Q6PI08	Missense_Mutation	SNP	ENST00000597597.1	37	CCDS12854.1	290	0.13278388278388278	19	0.03861788617886179	64	0.17679558011049723	135	0.23601398601398602	72	0.09498680738786279	t	5.390	0.257247	0.10239	.	.	ENSG00000167766	ENST00000536937;ENST00000301096;ENST00000544146;ENST00000545872;ENST00000541777	T;T;T;T;T	0.05580	3.42;3.42;3.42;3.42;3.42	1.63	-0.789	0.10935	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.05280	-0.08	0.09310	N	0.999996	B	0.10296	0.003	B	0.12837	0.008	T	0.49428	-0.8941	9	0.46703	T	0.11	.	6.1439	0.20275	0.4016:0.0:0.0:0.5984	.	293	P51522	ZNF83_HUMAN	V	293	ENSP00000445993:E293V;ENSP00000301096:E293V;ENSP00000445470:E293V;ENSP00000440713:E293V;ENSP00000439681:E293V	ENSP00000301096:E293V	E	-	2	0	ZNF83	57808752	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.740000	0.04861	-0.327000	0.08551	-0.820000	0.03113	GAG	T|0.867;A|0.133	0.133	strong		0.408	ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
DDX4	54514	hgsc.bcm.edu	37	5	55082474	55082474	+	Silent	SNP	C	C	T	rs957459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:55082474C>T	ENST00000505374.1	+	14	1085	c.993C>T	c.(991-993)tgC>tgT	p.C331C	DDX4_ENST00000511853.1_Silent_p.C182C|DDX4_ENST00000354991.5_Silent_p.C297C|DDX4_ENST00000514278.2_Silent_p.C311C|DDX4_ENST00000353507.5_Silent_p.C297C	NM_024415.2	NP_077726.1	Q9NQI0	DDX4_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 4	331	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				male meiosis I (GO:0007141)|multicellular organismal development (GO:0007275)|regulation of protein localization (GO:0032880)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pi-body (GO:0071546)|piP-body (GO:0071547)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	24		Lung NSC(810;6.93e-05)|all_neural(839;0.00409)|Prostate(74;0.0107)|Breast(144;0.0544)|Ovarian(174;0.223)				TGATGGCTTGCGCTCAAACAG	0.403													T|||	2329	0.465056	0.6339	0.5519	5008	,	,		18821	0.497		0.3091	False		,,,				2504	0.3027				p.C331C		Atlas-SNP	.											.	DDX4	194	.	0			c.C993T						PASS	.	T	,,,	2583,1823	532.6+/-373.5	754,1075,374	112.0	106.0	108.0		891,933,546,993	3.9	1.0	5	dbSNP_86	108	2721,5879	680.3+/-403.6	430,1861,2009	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DDX4	NM_001142549.1,NM_001166533.1,NM_001166534.1,NM_024415.2	,,,	1184,2936,2383	TT,TC,CC		31.6395,41.3754,40.7812	,,,	297/691,311/705,182/576,331/725	55082474	5304,7702	2203	4300	6503	SO:0001819	synonymous_variant	54514	exon14			GGCTTGCGCTCAA	AF262962	CCDS3969.1, CCDS47208.1, CCDS54854.1, CCDS54855.1	5p15.2-p13.1	2008-02-05	2003-06-13		ENSG00000152670	ENSG00000152670		"""DEAD-boxes"""	18700	protein-coding gene	gene with protein product		605281	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 4"""			10920202, 11850529	Standard	NM_001142549		Approved	VASA	uc003jqg.4	Q9NQI0	OTTHUMG00000097044	ENST00000505374.1:c.993C>T	5.37:g.55082474C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	NM_024415	A8K8Q2|B3KSF4|D6RDK4|E9PCD8|Q5M7Z3|Q86VX0|Q9NT92|Q9NYB1	Silent	SNP	ENST00000505374.1	37	CCDS3969.1																																																																																			C|0.565;T|0.435	0.435	strong		0.403	DDX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214147.2	NM_024415	
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 GAIIx	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	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	43	7	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		
TRPM1	4308	hgsc.bcm.edu	37	15	31330313	31330313	+	Silent	SNP	A	A	G	rs12913672	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:31330313A>G	ENST00000256552.6	-	19	2520	c.2373T>C	c.(2371-2373)taT>taC	p.Y791Y	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Silent_p.Y769Y|TRPM1_ENST00000542188.1_Silent_p.Y808Y|RP11-348B17.1_ENST00000558755.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AGAAATCATCATATGTGCGAA	0.388													A|||	914	0.182508	0.2678	0.2219	5008	,	,		18787	0.0079		0.2913	False		,,,				2504	0.1074				p.Y808Y		Atlas-SNP	.											.	TRPM1	183	.	0			c.T2424C						PASS	.	A		919,2787		113,693,1047	97.0	88.0	91.0		2307	-2.7	0.1	15	dbSNP_121	91	2128,6046		278,1572,2237	no	coding-synonymous	TRPM1	NM_002420.4		391,2265,3284	GG,GA,AA		26.0338,24.7976,25.6481		769/1604	31330313	3047,8833	1853	4087	5940	SO:0001819	synonymous_variant	4308	exon18			ATCATCATATGTG	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2373T>C	15.37:g.31330313A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			A|0.799;G|0.201	0.201	strong		0.388	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
DNAJC30	84277	hgsc.bcm.edu	37	7	73097654	73097654	+	Missense_Mutation	SNP	C	C	T	rs1128349	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:73097654C>T	ENST00000395176.2	-	1	129	c.100G>A	c.(100-102)Gga>Aga	p.G34R	WBSCR22_ENST00000265758.2_5'Flank|WBSCR22_ENST00000464615.1_3'UTR|WBSCR22_ENST00000423166.2_5'Flank|WBSCR22_ENST00000423497.1_5'Flank	NM_032317.2	NP_115693.2	Q96LL9	DJC30_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 30	34			G -> R (in dbSNP:rs1128349). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)				kidney(1)|large_intestine(2)|lung(1)	4						GTCCTCGCTCCTAGGCCCAGG	0.627													C|||	1516	0.302716	0.1967	0.268	5008	,	,		13139	0.3204		0.4463	False		,,,				2504	0.3047				p.G34R		Atlas-SNP	.											.	DNAJC30	12	.	0			c.G100A						PASS	.	C	ARG/GLY	923,3461		122,679,1391	63.0	74.0	70.0		100	-1.8	0.0	7	dbSNP_86	70	3837,4737		888,2061,1338	yes	missense	DNAJC30	NM_032317.2	125	1010,2740,2729	TT,TC,CC		44.7516,21.0538,36.7341	benign	34/227	73097654	4760,8198	2192	4287	6479	SO:0001583	missense	84277	exon1			TCGCTCCTAGGCC	AF412025	CCDS5556.1	7q11.23	2011-09-02	2008-06-17	2008-06-17	ENSG00000176410	ENSG00000176410		"""Heat shock proteins / DNAJ (HSP40)"""	16410	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 18"""	WBSCR18		12073013	Standard	NM_032317		Approved		uc003tys.1	Q96LL9	OTTHUMG00000023290	ENST00000395176.2:c.100G>A	7.37:g.73097654C>T	ENSP00000378605:p.Gly34Arg	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_032317	Q9BSG8	Missense_Mutation	SNP	ENST00000395176.2	37	CCDS5556.1	753	0.3447802197802198	105	0.21341463414634146	108	0.2983425414364641	201	0.3513986013986014	339	0.4472295514511873	C	10.84	1.464115	0.26335	0.210538	0.447516	ENSG00000176410	ENST00000395176;ENST00000539255	T	0.57436	0.4	4.87	-1.84	0.07809	Heat shock protein DnaJ, N-terminal (1);	1.599000	0.03889	N	0.278387	T	0.00012	0.0000	N	0.04508	-0.205	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.37174	-0.9717	9	0.13470	T	0.59	-9.3373	1.673	0.02816	0.1192:0.267:0.339:0.2748	rs1128349;rs11541498;rs17553400;rs17845038;rs17857811;rs58147772;rs1128349	34	Q96LL9	DJC30_HUMAN	R	34;31	ENSP00000378605:G34R	ENSP00000378605:G34R	G	-	1	0	DNAJC30	72735590	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.498000	0.06420	-0.483000	0.06772	0.591000	0.81541	GGA	C|0.641;T|0.359	0.359	strong		0.627	DNAJC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252304.2		
PADI6	353238	hgsc.bcm.edu	37	1	17715015	17715015	+	RNA	SNP	C	C	G	rs200922673		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17715015C>G	ENST00000434762.2	+	0	869							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)	p.I273I(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	CAGGCCTCATCTCCTACTCTG	0.537													C|||	1	0.000199681	0.0	0.0	5008	,	,		20167	0.0		0.0	False		,,,				2504	0.001				p.I273M		Atlas-SNP	.											PADI6,colon,carcinoma,0,1	PADI6	51	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C819G						PASS	.	C	MET/ILE	0,3850		0,0,1925	45.0	43.0	43.0		819	-3.2	1.0	1		43	10,8280		0,10,4135	yes	missense	PADI6	NM_207421.3	10	0,10,6060	GG,GC,CC		0.1206,0.0,0.0824	probably-damaging	273/695	17715015	10,12130	1925	4145	6070			353238	exon7			CCTCATCTCCTAC	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"""Peptidyl arginine deiminases"""	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17715015C>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_207421	Q330K5|Q70SX3	Missense_Mutation	SNP	ENST00000434762.2	37																																																																																				.	.	weak		0.537	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421	
SLC6A12	6539	hgsc.bcm.edu	37	12	319111	319111	+	Silent	SNP	T	T	C	rs526690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:319111T>C	ENST00000428720.1	-	3	785	c.42A>G	c.(40-42)gcA>gcG	p.A14A	SLC6A12_ENST00000536824.1_Silent_p.A14A|SLC6A12_ENST00000397296.2_Silent_p.A14A|SLC6A12_ENST00000424061.2_Silent_p.A14A|SLC6A12_ENST00000359674.4_Silent_p.A14A	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	14					amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	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:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			CCCAGGAGACTGCAGGAGGCC	0.617													C|||	2650	0.529153	0.7284	0.4366	5008	,	,		17247	0.3075		0.5268	False		,,,				2504	0.5562				p.A14A		Atlas-SNP	.											.	SLC6A12	60	.	0			c.A42G						PASS	.	C	,,,	3130,1276	435.9+/-344.5	1113,904,186	96.0	84.0	88.0		42,42,42,42	1.2	0.2	12	dbSNP_83	88	4598,4002	554.1+/-386.4	1219,2160,921	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC6A12	NM_001122847.2,NM_001122848.2,NM_001206931.1,NM_003044.4	,,,	2332,3064,1107	CC,CT,TT		46.5349,28.9605,40.5813	,,,	14/615,14/615,14/615,14/615	319111	7728,5278	2203	4300	6503	SO:0001819	synonymous_variant	6539	exon3			GGAGACTGCAGGA	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.42A>G	12.37:g.319111T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001122848	A0AV52|B2R992|D3DUN8	Silent	SNP	ENST00000428720.1	37	CCDS8501.1																																																																																			T|0.434;C|0.566	0.566	strong		0.617	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
WDR44	54521	hgsc.bcm.edu	37	X	117521338	117521338	+	Silent	SNP	G	G	A	rs17318100	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:117521338G>A	ENST00000254029.3	+	3	542	c.147G>A	c.(145-147)gaG>gaA	p.E49E	WDR44_ENST00000493448.1_3'UTR|WDR44_ENST00000371822.5_Intron|MIR1277_ENST00000408536.1_RNA|WDR44_ENST00000371825.3_Silent_p.E49E	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	49	Binding activity.					endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						TTGGAAATGAGTCCCCTGTAC	0.294													G|||	620	0.164238	0.0772	0.2464	3775	,	,		11903	0.127		0.0964	False		,,,				2504	0.1247				p.E49E		Atlas-SNP	.											.	WDR44	188	.	0			c.G147A						PASS	.	G	,,	420,3415		20,317,63,1295,508	92.0	88.0	90.0		147,,147	2.1	1.0	X	dbSNP_123	90	858,5868		31,542,254,1855,1616	no	coding-synonymous,intron,coding-synonymous	WDR44	NM_001184965.1,NM_001184966.1,NM_019045.4	,,	51,859,317,3150,2124	AA,AG,A,GG,G		12.7565,10.9518,12.1011	,,	49/906,,49/914	117521338	1278,9283	2203	4298	6501	SO:0001819	synonymous_variant	54521	exon3			AAATGAGTCCCCT	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"""WD repeat domain containing"""	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.147G>A	X.37:g.117521338G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	223	144	0.64574	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Silent	SNP	ENST00000254029.3	37	CCDS14572.1																																																																																			0|0.003;A|0.146	0.146	strong		0.294	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045	
GEMIN4	50628	hgsc.bcm.edu	37	17	649232	649232	+	Missense_Mutation	SNP	C	C	T	rs3744741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:649232C>T	ENST00000319004.5	-	2	2169	c.2051G>A	c.(2050-2052)cGa>cAa	p.R684Q	GEMIN4_ENST00000576778.1_Missense_Mutation_p.R673Q	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	684			R -> Q (in dbSNP:rs3744741).		gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GTATTCCTCTCGGCACGCGTT	0.527													C|||	1387	0.276957	0.3449	0.3055	5008	,	,		19971	0.3571		0.1412	False		,,,				2504	0.2219				p.R684Q		Atlas-SNP	.											.	GEMIN4	116	.	0			c.G2051A						PASS	.	C	GLN/ARG	1197,2743		208,781,981	36.0	38.0	37.0		2051	0.4	0.0	17	dbSNP_107	37	1049,7247		71,907,3170	yes	missense	GEMIN4	NM_015721.2	43	279,1688,4151	TT,TC,CC		12.6446,30.3807,18.3557	benign	684/1059	649232	2246,9990	1970	4148	6118	SO:0001583	missense	50628	exon2			TCCTCTCGGCACG	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2051G>A	17.37:g.649232C>T	ENSP00000321706:p.Arg684Gln	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	26	20	0.769231	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	540	0.24725274725274726	162	0.32926829268292684	97	0.26795580110497236	171	0.29895104895104896	110	0.14511873350923482	C	0.022	-1.409509	0.01155	0.303807	0.126446	ENSG00000179409	ENST00000319004	T	0.05258	3.47	5.57	0.423	0.16463	.	0.981010	0.08322	N	0.963658	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.32425	0.371	B	0.23419	0.046	T	0.45833	-0.9234	9	0.14252	T	0.57	-1.6698	1.934	0.03333	0.4363:0.3151:0.1026:0.1461	rs3744741;rs56482056;rs59343482;rs3744741	684	P57678	GEMI4_HUMAN	Q	684	ENSP00000321706:R684Q	ENSP00000321706:R684Q	R	-	2	0	GEMIN4	595982	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	0.224000	0.17738	0.402000	0.25451	-1.114000	0.02060	CGA	C|0.765;T|0.235	0.235	strong		0.527	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
OR5B17	219965	hgsc.bcm.edu	37	11	58126305	58126305	+	Missense_Mutation	SNP	A	A	T	rs4939208	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:58126305A>T	ENST00000357377.3	-	1	237	c.238T>A	c.(238-240)Tta>Ata	p.L80I		NM_001005489.1	NP_001005489.1	Q8NGF7	OR5BH_HUMAN	olfactory receptor, family 5, subfamily B, member 17	80			L -> I (in dbSNP:rs4939208).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AACCCAGTTAAAACCTTTGGA	0.453													a|||	3589	0.716653	0.6793	0.7305	5008	,	,		21559	0.8552		0.6312	False		,,,				2504	0.7025				p.L80I		Atlas-SNP	.											.	OR5B17	64	.	0			c.T238A						PASS	.	A	ILE/LEU	3073,1329	694.4+/-405.8	1068,937,196	81.0	77.0	79.0		238	-7.2	0.0	11	dbSNP_111	79	5445,3145	655.2+/-401.2	1714,2017,564	yes	missense	OR5B17	NM_001005489.1	5	2782,2954,760	TT,TA,AA		36.6123,30.1908,34.4366	benign	80/315	58126305	8518,4474	2201	4295	6496	SO:0001583	missense	219965	exon1			CAGTTAAAACCTT	AB065849	CCDS31548.1	11q12.1	2012-08-09			ENSG00000197786	ENSG00000197786		"""GPCR / Class A : Olfactory receptors"""	15267	protein-coding gene	gene with protein product				OR5B20P			Standard	NM_001005489		Approved		uc010rke.2	Q8NGF7	OTTHUMG00000167465	ENST00000357377.3:c.238T>A	11.37:g.58126305A>T	ENSP00000349945:p.Leu80Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_001005489	Q6IEX1	Missense_Mutation	SNP	ENST00000357377.3	37	CCDS31548.1	1546	0.7078754578754579	318	0.6463414634146342	273	0.7541436464088398	477	0.833916083916084	478	0.6306068601583114	a	3.995	-0.003650	0.07773	0.698092	0.633877	ENSG00000197786	ENST00000357377	T	0.00364	7.81	3.6	-7.19	0.01500	GPCR, rhodopsin-like superfamily (1);	0.977620	0.08297	N	0.967588	T	0.00012	0.0000	M	0.69358	2.11	0.80722	P	0.0	B	0.11235	0.004	B	0.12837	0.008	T	0.32666	-0.9898	9	0.45353	T	0.12	-0.5836	2.7067	0.05164	0.2337:0.0927:0.0991:0.5745	rs4939208;rs60870694;rs4939208	80	Q8NGF7	OR5BH_HUMAN	I	80	ENSP00000349945:L80I	ENSP00000349945:L80I	L	-	1	2	OR5B17	57882881	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.480000	0.00457	-1.830000	0.01199	-1.094000	0.02160	TTA	A|0.322;T|0.678	0.678	strong		0.453	OR5B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394708.2	NM_001005489	
SAGE1	55511	hgsc.bcm.edu	37	X	134978425	134978425	+	Silent	SNP	G	G	A	rs5930805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:134978425G>A	ENST00000370709.3	+	1	24	c.24G>A	c.(22-24)acG>acA	p.T8T	SAGE1_ENST00000535938.1_Silent_p.T8T|SAGE1_ENST00000537770.1_Silent_p.T8T|SAGE1_ENST00000324447.3_Silent_p.T8T			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	8						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					CACTTCAAACGAGTCAACCAA	0.403													g|||	611	0.161854	0.0673	0.1614	3775	,	,		11604	0.1012		0.2058	False		,,,				2504	0.1033				p.T8T		Atlas-SNP	.											.	SAGE1	160	.	0			c.G24A						PASS	.	G		545,3290		29,416,71,1187,500	108.0	88.0	95.0		24	0.8	0.0	X	dbSNP_114	95	1753,4975		188,923,454,1317,1418	no	coding-synonymous	SAGE1	NM_018666.2		217,1339,525,2504,1918	AA,AG,A,GG,G		26.0553,14.2112,21.7552		8/905	134978425	2298,8265	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon2			TCAAACGAGTCAA	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.24G>A	X.37:g.134978425G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	253	70	0.27668	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			G|0.792;A|0.208	0.208	strong		0.403	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
CATSPERD	257062	hgsc.bcm.edu	37	19	5778517	5778517	+	Missense_Mutation	SNP	A	A	T	rs2305925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5778517A>T	ENST00000381624.3	+	22	2288	c.2227A>T	c.(2227-2229)Acc>Tcc	p.T743S	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	743			T -> S (in dbSNP:rs2305925).		multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											GGCCTACAAGACCCCCAAGCT	0.592													A|||	1473	0.294129	0.2587	0.1859	5008	,	,		16971	0.5506		0.165	False		,,,				2504	0.2873				p.T743S		Atlas-SNP	.											.	.	.	.	0			c.A2227T						PASS	.	A	SER/THR	978,3170		107,764,1203	53.0	57.0	56.0		2227	-0.1	0.0	19	dbSNP_100	56	1303,7125		84,1135,2995	yes	missense	TMEM146	NM_152784.3	58	191,1899,4198	TT,TA,AA		15.4604,23.5776,18.1377	benign	743/799	5778517	2281,10295	2074	4214	6288	SO:0001583	missense	257062	exon22			TACAAGACCCCCA	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.2227A>T	19.37:g.5778517A>T	ENSP00000371037:p.Thr743Ser	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	165	77	0.466667	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	612	0.2802197802197802	124	0.25203252032520324	74	0.20441988950276244	287	0.5017482517482518	127	0.16754617414248021	A	11.15	1.554602	0.27739	0.235776	0.154604	ENSG00000174898	ENST00000381624;ENST00000381613	T	0.22945	1.93	3.45	-0.0986	0.13627	.	0.698912	0.12306	N	0.480693	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.30033	0.266	B	0.28553	0.091	T	0.45483	-0.9258	9	0.56958	D	0.05	-14.6815	4.2378	0.10634	0.4544:0.423:0.1226:0.0	rs2305925;rs2305925	743	Q86XM0	TM146_HUMAN	S	743;412	ENSP00000371037:T743S	ENSP00000371026:T412S	T	+	1	0	TMEM146	5729517	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-1.367000	0.02583	-0.200000	0.10300	0.454000	0.30748	ACC	A|0.755;T|0.245	0.245	strong		0.592	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
IL25	64806	hgsc.bcm.edu	37	14	23844979	23844979	+	Silent	SNP	C	C	A	rs79877597	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:23844979C>A	ENST00000329715.2	+	2	682	c.424C>A	c.(424-426)Cgg>Agg	p.R142R	CMTM5_ENST00000339180.4_5'Flank|CMTM5_ENST00000397227.3_5'Flank|CMTM5_ENST00000382809.2_5'Flank|CMTM5_ENST00000342473.4_5'Flank|IL25_ENST00000397242.2_Silent_p.R126R|CMTM5_ENST00000359320.3_5'Flank|CMTM5_ENST00000555731.1_5'Flank	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN	interleukin 25	142					eosinophil differentiation (GO:0030222)|inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to fungus (GO:0009620)|response to nematode (GO:0009624)	extracellular space (GO:0005615)	interleukin-17E receptor binding (GO:0030380)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)		TGTCTTCTACCGGCGGCCATG	0.637													C|||	1337	0.266973	0.3873	0.1974	5008	,	,		16724	0.2639		0.2157	False		,,,				2504	0.2096				p.R142R		Atlas-SNP	.											IL25,NS,carcinoma,0,1	IL25	21	1	0			c.C424A						PASS	.	C	,	1620,2786	500.0+/-364.6	290,1040,873	87.0	80.0	83.0		424,376	3.6	1.0	14	dbSNP_131	83	1820,6780	324.2+/-316.4	192,1436,2672	no	coding-synonymous,coding-synonymous	IL25	NM_022789.3,NM_172314.1	,	482,2476,3545	AA,AC,CC		21.1628,36.768,26.4493	,	142/178,126/162	23844979	3440,9566	2203	4300	6503	SO:0001819	synonymous_variant	64806	exon2			TTCTACCGGCGGC	AF305200	CCDS9597.1, CCDS45086.1	14q11.2	2008-01-07	2006-05-17	2006-05-17	ENSG00000166090	ENSG00000166090		"""Interleukins and interleukin receptors"""	13765	protein-coding gene	gene with protein product		605658	"""interleukin 17E"""	IL17E		11058597, 11754819	Standard	NM_172314		Approved	IL-25, IL-17E	uc001wjq.3	Q9H293	OTTHUMG00000028749	ENST00000329715.2:c.424C>A	14.37:g.23844979C>A		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	175	71	0.405714	NM_022789	Q2M3F0|Q8IZV3|Q8WXB0	Silent	SNP	ENST00000329715.2	37	CCDS9597.1																																																																																			A|0.271;C|0.727;T|0.002	0.271	strong		0.637	IL25-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071789.2		
PRSS55	203074	hgsc.bcm.edu	37	8	10396054	10396054	+	Silent	SNP	A	A	C	rs6601483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:10396054A>C	ENST00000328655.3	+	5	850	c.810A>C	c.(808-810)atA>atC	p.I270I	PRSS55_ENST00000522210.1_Intron|PRSS51_ENST00000523024.1_RNA	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	270	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)	31						TGGGCATCATAAGCTGGGGAA	0.572													C|||	3353	0.669529	0.6399	0.6902	5008	,	,		17515	0.7639		0.5964	False		,,,				2504	0.6728				p.I270I		Atlas-SNP	.											.	PRSS55	67	.	0			c.A810C						PASS	.	C	,	2745,1661	506.9+/-366.5	832,1081,290	89.0	96.0	93.0		,810	4.2	1.0	8	dbSNP_116	93	5422,3178	481.2+/-370.6	1702,2018,580	no	intron,coding-synonymous	PRSS55	NM_001197020.1,NM_198464.3	,	2534,3099,870	CC,CA,AA		36.9535,37.6986,37.2059	,	,270/353	10396054	8167,4839	2203	4300	6503	SO:0001819	synonymous_variant	203074	exon5			CATCATAAGCTGG	AY358867	CCDS5976.1, CCDS56523.1	8p23.1	2014-01-21			ENSG00000184647	ENSG00000184647		"""Serine peptidases / Serine peptidases"""	30824	protein-coding gene	gene with protein product		615144				12975309, 18844450	Standard	NM_198464		Approved	T-SP1, UNQ9391, CT153	uc003wta.3	Q6UWB4	OTTHUMG00000129345	ENST00000328655.3:c.810A>C	8.37:g.10396054A>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	139	137	0.985611	NM_198464	E5RJX5	Silent	SNP	ENST00000328655.3	37	CCDS5976.1																																																																																			A|0.358;C|0.642	0.642	strong		0.572	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
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 GAIIx	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	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000292896.2_Silent_p.N109N|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		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	6	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	
MIPEP	4285	hgsc.bcm.edu	37	13	24436475	24436475	+	Missense_Mutation	SNP	C	C	T	rs11551114	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:24436475C>T	ENST00000382172.3	-	9	1117	c.1019G>A	c.(1018-1020)cGa>cAa	p.R340Q		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	340			R -> Q (in dbSNP:rs11551114).		protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		TTTCATCCCTCGTATCATCTC	0.279													C|||	328	0.0654952	0.0582	0.072	5008	,	,		18310	0.001		0.1312	False		,,,				2504	0.0695				p.R340Q		Atlas-SNP	.											MIPEP,colon,carcinoma,-1,1	MIPEP	53	1	0			c.G1019A						scavenged	.	C	GLN/ARG	272,4120		10,252,1934	50.0	47.0	48.0		1019	1.5	0.0	13	dbSNP_120	48	1126,7454		73,980,3237	yes	missense	MIPEP	NM_005932.3	43	83,1232,5171	TT,TC,CC		13.1235,6.1931,10.7771	benign	340/714	24436475	1398,11574	2196	4290	6486	SO:0001583	missense	4285	exon9			ATCCCTCGTATCA		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.1019G>A	13.37:g.24436475C>T	ENSP00000371607:p.Arg340Gln	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	181	95	0.524862	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	147	0.0673076923076923	32	0.06504065040650407	19	0.052486187845303865	1	0.0017482517482517483	95	0.12532981530343007	C	6.085	0.383896	0.11524	0.061931	0.131235	ENSG00000027001	ENST00000382172	T	0.07114	3.22	4.79	1.51	0.23008	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.374324	0.28583	N	0.014834	T	0.00073	0.0002	L	0.31664	0.95	0.80722	P	0.0	B	0.19200	0.034	B	0.13407	0.009	T	0.38045	-0.9679	9	0.27785	T	0.31	.	4.5291	0.11995	0.0:0.3188:0.2723:0.4089	rs11551114;rs17424158;rs56587494;rs11551114	340	Q99797	MIPEP_HUMAN	Q	340	ENSP00000371607:R340Q	ENSP00000371607:R340Q	R	-	2	0	MIPEP	23334475	0.010000	0.17322	0.028000	0.17463	0.696000	0.40369	0.276000	0.18716	0.473000	0.27368	-0.150000	0.13652	CGA	C|0.909;T|0.091	0.091	strong		0.279	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
TXLNG	55787	hgsc.bcm.edu	37	X	16847765	16847765	+	Missense_Mutation	SNP	A	A	G	rs5969783	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:16847765A>G	ENST00000380122.5	+	5	797	c.736A>G	c.(736-738)Att>Gtt	p.I246V	TXLNG_ENST00000398155.4_Missense_Mutation_p.I114V	NM_018360.2	NP_060830.2	Q9NUQ3	TXLNG_HUMAN	taxilin gamma	246			I -> V (in dbSNP:rs5969783).		cell cycle (GO:0007049)|regulation of bone mineralization (GO:0030500)|regulation of cell cycle (GO:0051726)|regulation of cell cycle process (GO:0010564)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)	protein heterodimerization activity (GO:0046982)			breast(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	15						ACATTTCCAGATTACCTTAAA	0.418													A|||	44	0.0116556	0.0015	0.0058	3775	,	,		14754	0.0		0.0328	False		,,,				2504	0.0051				p.I246V		Atlas-SNP	.											.	TXLNG	40	.	0			c.A736G						PASS	.	A	VAL/ILE,VAL/ILE	21,3814		0,18,3,1614,568	84.0	74.0	78.0		340,736	3.3	0.4	X	dbSNP_114	78	193,6535		2,135,54,2291,1818	yes	missense,missense	TXLNG	NM_001168683.1,NM_018360.2	29,29	2,153,57,3905,2386	GG,GA,G,AA,A		2.8686,0.5476,2.0259	benign,benign	114/397,246/529	16847765	214,10349	2203	4300	6503	SO:0001583	missense	55787	exon5			TTCCAGATTACCT	AK002071	CCDS14178.1, CCDS55373.1	Xp22.2	2014-05-07	2010-04-20	2010-04-20	ENSG00000086712	ENSG00000086712			18578	protein-coding gene	gene with protein product	"""lipopolysaccharide specific response-5 protein"", ""factor inhibiting activating transcription factor 4 (ATF4)-mediated transcription"""	300677	"""chromosome X open reading frame 15"""	CXorf15		15911876, 15184072, 16831913	Standard	NM_018360		Approved	FLJ11209, LSR5, FIAT, MGC126621, MGC126625, TXLNGX	uc004cxq.2	Q9NUQ3	OTTHUMG00000021196	ENST00000380122.5:c.736A>G	X.37:g.16847765A>G	ENSP00000369465:p.Ile246Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	24	0.214286	NM_018360	Q2KQ75|Q5JNZ7|Q9P0X1	Missense_Mutation	SNP	ENST00000380122.5	37	CCDS14178.1	35	0.02109704641350211	1	0.0020408163265306124	2	0.0055248618784530384	0	0.0	30	0.04	A	8.080	0.772102	0.16051	0.005476	0.028686	ENSG00000086712	ENST00000380122;ENST00000398155	T;T	0.27890	1.64;1.64	5.63	3.28	0.37604	.	0.503618	0.23537	N	0.047106	T	0.02380	0.0073	N	0.02296	-0.605	0.34824	D	0.738991	B;B	0.10296	0.001;0.003	B;B	0.15052	0.004;0.012	T	0.16247	-1.0409	10	0.26408	T	0.33	0.0016	7.5565	0.27827	0.7634:0.0:0.2366:0.0	rs5969783;rs52800251;rs56577667;rs59582379;rs5969783	114;246	Q9NUQ3-2;Q9NUQ3	.;TXLNG_HUMAN	V	246;114	ENSP00000369465:I246V;ENSP00000381222:I114V	ENSP00000369465:I246V	I	+	1	0	TXLNG	16757686	0.998000	0.40836	0.355000	0.25773	0.789000	0.44602	1.372000	0.34261	0.293000	0.22520	0.486000	0.48141	ATT	A|0.979;G|0.021	0.021	strong		0.418	TXLNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055912.1	NM_018360	
HMHB1	57824	hgsc.bcm.edu	37	5	143200053	143200053	+	Missense_Mutation	SNP	C	C	T	rs161557	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:143200053C>T	ENST00000289448.2	+	2	153	c.46C>T	c.(46-48)Cat>Tat	p.H16Y	CTB-57H20.1_ENST00000503323.1_RNA	NM_021182.1	NP_067005	O97980	HMHB1_HUMAN	histocompatibility (minor) HB-1	16	Loss of recognition by cytotoxic T lymphocyte (CTL).		H -> Y (in allele HB-1Y; loss of CTL recognition for epitope HB-1. No influence on HLA-B/HLA-B44 binding, nor on the processing by the proteasome; dbSNP:rs161557). {ECO:0000269|PubMed:9892612}.		immune system process (GO:0002376)								Acute lymphoblastic leukemia(2;0.0236)|all_hematologic(2;0.041)	KIRC - Kidney renal clear cell carcinoma(527;0.00111)|Kidney(363;0.00176)			AGGTTCTCTGCATGTTTGGAA	0.393													C|||	1464	0.292332	0.295	0.3343	5008	,	,		16673	0.3889		0.2227	False		,,,				2504	0.2311				p.H16Y		Atlas-SNP	.											.	HMHB1	3	.	0			c.C46T						PASS	.	C	TYR/HIS	950,2776		114,722,1027	257.0	232.0	239.0		46	-2.3	0.0	5	dbSNP_79	239	1797,6417		203,1391,2513	yes	missense	HMHB1	NM_021182.1	83	317,2113,3540	TT,TC,CC		21.8773,25.4965,23.0067	benign	16/42	143200053	2747,9193	1863	4107	5970	SO:0001583	missense	57824	exon2			TCTCTGCATGTTT	AF103884	CCDS43376.1	5q32	2006-07-20			ENSG00000158497	ENSG00000158497			29677	protein-coding gene	gene with protein product		609961				9892612	Standard	NM_021182		Approved	HB-1	uc003lnj.3	O97980	OTTHUMG00000163173	ENST00000289448.2:c.46C>T	5.37:g.143200053C>T	ENSP00000289448:p.His16Tyr	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	119	118	0.991597	NM_021182	Q9MY25	Missense_Mutation	SNP	ENST00000289448.2	37	CCDS43376.1	610	0.2793040293040293	133	0.2703252032520325	93	0.2569060773480663	228	0.3986013986013986	156	0.20580474934036938	C	8.763	0.924004	0.18056	0.254965	0.218773	ENSG00000158497	ENST00000289448	T	0.62498	0.02	5.38	-2.32	0.06745	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25166	P	0.990314	B	0.17268	0.021	B	0.12156	0.007	T	0.39860	-0.9593	7	0.87932	D	0	.	0.1886	0.00131	0.3003:0.2066:0.1481:0.345	rs161557;rs52812230;rs61290874;rs161557	16	O97980	HMHB1_HUMAN	Y	16	ENSP00000289448:H16Y	ENSP00000289448:H16Y	H	+	1	0	HMHB1	143180246	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.312000	0.08113	-0.226000	0.09899	0.563000	0.77884	CAT	C|0.720;T|0.280	0.280	strong		0.393	HMHB1-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371899.1	NM_021182	
HUNK	30811	hgsc.bcm.edu	37	21	33371123	33371123	+	Missense_Mutation	SNP	C	C	T	rs10775648	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:33371123C>T	ENST00000270112.2	+	11	2131	c.1771C>T	c.(1771-1773)Cgc>Tgc	p.R591C		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	591			R -> C (in dbSNP:rs10775648). {ECO:0000269|PubMed:17344846}.		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						CAGCTTGGCTCGCAGAAATTC	0.567													C|||	1051	0.209864	0.0431	0.2378	5008	,	,		17721	0.2897		0.2256	False		,,,				2504	0.317				p.R591C		Atlas-SNP	.											.	HUNK	74	.	0			c.C1771T						PASS	.	C	CYS/ARG	351,4055	182.9+/-210.6	12,327,1864	56.0	48.0	51.0		1771	3.5	0.0	21	dbSNP_120	51	1960,6640	345.9+/-325.9	234,1492,2574	yes	missense	HUNK	NM_014586.1	180	246,1819,4438	TT,TC,CC		22.7907,7.9664,17.7687	probably-damaging	591/715	33371123	2311,10695	2203	4300	6503	SO:0001583	missense	30811	exon11			TTGGCTCGCAGAA	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.1771C>T	21.37:g.33371123C>T	ENSP00000270112:p.Arg591Cys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	111	67	0.603604	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	458	0.2097069597069597	21	0.042682926829268296	81	0.22375690607734808	195	0.3409090909090909	161	0.21240105540897097	C	15.63	2.890611	0.52014	0.079664	0.227907	ENSG00000142149	ENST00000270112	T	0.70869	-0.52	4.39	3.5	0.40072	.	0.236050	0.33772	N	0.004580	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	D	0.62365	0.991	P	0.47528	0.549	T	0.15723	-1.0427	9	0.62326	D	0.03	-14.5311	8.5968	0.33721	0.0:0.7514:0.157:0.0916	rs10775648;rs58214837;rs10775648	591	P57058	HUNK_HUMAN	C	591	ENSP00000270112:R591C	ENSP00000270112:R591C	R	+	1	0	HUNK	32292994	0.165000	0.22948	0.001000	0.08648	0.901000	0.52897	3.127000	0.50484	1.050000	0.40346	0.491000	0.48974	CGC	C|0.807;T|0.193	0.193	strong		0.567	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586	
FAM222B	55731	hgsc.bcm.edu	37	17	27085564	27085564	+	Silent	SNP	A	A	G	rs2043031	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27085564A>G	ENST00000341217.5	-	3	1628	c.1413T>C	c.(1411-1413)ctT>ctC	p.L471L	FAM222B_ENST00000581407.1_Silent_p.L471L|FAM222B_ENST00000582266.1_3'UTR|FAM222B_ENST00000452648.3_Silent_p.L471L	NM_018182.2	NP_060652.2	Q8WU58	F222B_HUMAN	family with sequence similarity 222, member B	471			L -> S (in dbSNP:rs2043031).														ACGGCATGGCAAGGTCCTGAG	0.657													G|||	1064	0.21246	0.1422	0.2349	5008	,	,		17804	0.1786		0.1938	False		,,,				2504	0.3456				p.L471L		Atlas-SNP	.											.	.	.	.	0			c.T1413C						PASS	.	G	,	557,3407		54,449,1479	40.0	41.0	41.0		1413,1413	0.7	0.3	17	dbSNP_94	41	1603,6699		152,1299,2700	no	coding-synonymous,coding-synonymous	C17orf63	NM_001077498.1,NM_018182.2	,	206,1748,4179	GG,GA,AA		19.3086,14.0515,17.6097	,	471/563,471/563	27085564	2160,10106	1982	4151	6133	SO:0001819	synonymous_variant	55731	exon4			CATGGCAAGGTCC	AK001562	CCDS45637.1, CCDS74022.1	17q11.2	2012-04-27	2012-04-27	2012-04-27	ENSG00000173065	ENSG00000173065			25563	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 63"""	C17orf63			Standard	NM_001288631		Approved	FLJ10700	uc010way.1	Q8WU58		ENST00000341217.5:c.1413T>C	17.37:g.27085564A>G		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_018182	Q9H6F3|Q9NVJ4|Q9NXN6	Silent	SNP	ENST00000341217.5	37	CCDS45637.1																																																																																			A|0.808;G|0.192	0.192	strong		0.657	FAM222B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446703.1	NM_018182	
LYZL2	119180	hgsc.bcm.edu	37	10	30901756	30901756	+	Silent	SNP	G	G	A	rs9954	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:30901756G>A	ENST00000375318.2	-	4	566	c.510C>T	c.(508-510)aaC>aaT	p.N170N		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	124					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				CTTACCAATAGTTCATTCCTT	0.423													G|||	1841	0.367612	0.3464	0.4063	5008	,	,		21212	0.2639		0.5527	False		,,,				2504	0.2853				p.N170N		Atlas-SNP	.											LYZL2,NS,carcinoma,-2,1	LYZL2	33	1	0			c.C510T						PASS	.	G		1813,2593	531.9+/-373.3	366,1081,756	119.0	100.0	106.0		510	2.2	0.4	10	dbSNP_52	106	4814,3786	614.0+/-396.2	1329,2156,815	no	coding-synonymous	LYZL2	NM_183058.2		1695,3237,1571	AA,AG,GG		44.0233,41.1484,49.0466		170/195	30901756	6627,6379	2203	4300	6503	SO:0001819	synonymous_variant	119180	exon4			CCAATAGTTCATT	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.510C>T	10.37:g.30901756G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	135	47	0.348148	NM_183058	Q6NZ69	Silent	SNP	ENST00000375318.2	37	CCDS7167.2																																																																																			G|0.517;A|0.483	0.483	strong		0.423	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058	
DPH1	1801	hgsc.bcm.edu	37	17	1943888	1943888	+	Silent	SNP	T	T	C	rs2236375	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1943888T>C	ENST00000263083.6	+	9	1056	c.1011T>C	c.(1009-1011)ccT>ccC	p.P337P	RP11-667K14.4_ENST00000572404.1_RNA|DPH1_ENST00000570477.1_Silent_p.P257P|OVCA2_ENST00000572195.1_5'Flank|RP11-667K14.3_ENST00000572790.1_lincRNA	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	337					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						GCCTACTTCCTGAGGTGGATG	0.537													C|||	4090	0.816693	0.8321	0.8761	5008	,	,		22382	0.9306		0.7575	False		,,,				2504	0.6973				p.P337P		Atlas-SNP	.											.	DPH1	32	.	0			c.T1011C						PASS	.	C		3267,747		1330,607,70	92.0	85.0	87.0		1011	-10.7	0.1	17	dbSNP_98	87	6472,1854		2503,1466,194	no	coding-synonymous	DPH1	NM_001383.3		3833,2073,264	CC,CT,TT		22.2676,18.6099,21.0778		337/444	1943888	9739,2601	2007	4163	6170	SO:0001819	synonymous_variant	1801	exon9			ACTTCCTGAGGTG	S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"""ovarian tumor suppressor candidate 1"""	603527	"""diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)"", ""DPH-like 1 (S. cerevisiae)"", ""DPH1 homolog (S. cerevisiae)"""	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.1011T>C	17.37:g.1943888T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Silent	SNP	ENST00000263083.6	37	CCDS42228.1																																																																																			T|0.175;C|0.825	0.825	strong		0.537	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383	
DUS3L	56931	hgsc.bcm.edu	37	19	5786815	5786815	+	Silent	SNP	G	G	A	rs10811	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5786815G>A	ENST00000309061.7	-	9	1527	c.1431C>T	c.(1429-1431)gcC>gcT	p.A477A	DUS3L_ENST00000320699.8_Silent_p.A235A|CTB-54O9.9_ENST00000586012.1_5'Flank|DUS3L_ENST00000590681.1_5'Flank|PRR22_ENST00000419421.2_5'Flank	NM_020175.2	NP_064560.2	Q96G46	DUS3L_HUMAN	dihydrouridine synthase 3-like (S. cerevisiae)	477							flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA dihydrouridine synthase activity (GO:0017150)			endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(2)	14						ACTGCCAGTCGGCTAGCTTGG	0.667													g|||	1567	0.312899	0.3298	0.1873	5008	,	,		17449	0.5437		0.165	False		,,,				2504	0.2935				p.A477A		Atlas-SNP	.											.	DUS3L	42	.	0			c.C1431T						PASS	.	A	,	1339,3057	427.6+/-341.6	205,929,1064	34.0	39.0	37.0		705,1431	-2.8	1.0	19	dbSNP_52	37	1348,7242	256.3+/-280.9	86,1176,3033	no	coding-synonymous,coding-synonymous	DUS3L	NM_001161619.1,NM_020175.2	,	291,2105,4097	AA,AG,GG		15.6927,30.4595,20.6915	,	235/409,477/651	5786815	2687,10299	2198	4295	6493	SO:0001819	synonymous_variant	56931	exon9			CCAGTCGGCTAGC		CCDS32880.1, CCDS54202.1	19p13.3	2014-02-12			ENSG00000141994	ENSG00000141994			26920	protein-coding gene	gene with protein product						12477932	Standard	NM_020175		Approved	DUS3, FLJ13896	uc002mdc.3	Q96G46	OTTHUMG00000162311	ENST00000309061.7:c.1431C>T	19.37:g.5786815G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_020175	Q96HM5|Q9BSU4|Q9H877|Q9NPR1	Silent	SNP	ENST00000309061.7	37	CCDS32880.1																																																																																			G|0.770;A|0.230	0.230	strong		0.667	DUS3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451870.2	NM_020175	
PNMAL1	55228	hgsc.bcm.edu	37	19	46973981	46973981	+	Silent	SNP	G	G	A	rs4803960	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46973981G>A	ENST00000313683.10	-	2	617	c.312C>T	c.(310-312)gcC>gcT	p.A104A	PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Silent_p.A104A	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	104										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		ttaaaaactcggcatcctggg	0.562													A|||	1183	0.236222	0.3313	0.2089	5008	,	,		18155	0.1796		0.2485	False		,,,				2504	0.1728				p.A104A		Atlas-SNP	.											.	PNMAL1	87	.	0			c.C312T						PASS	.	A	,	1536,2870	670.9+/-402.4	268,1000,935	43.0	44.0	43.0		312,312	-6.2	0.3	19	dbSNP_111	43	2106,6494	713.3+/-405.9	283,1540,2477	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	551,2540,3412	AA,AG,GG		24.4884,34.8616,28.0025	,	104/379,104/440	46973981	3642,9364	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			AAACTCGGCATCC	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.312C>T	19.37:g.46973981G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	51	30	0.588235	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			G|0.732;A|0.268	0.268	strong		0.562	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
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 GAIIx	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		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	110	30	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	
TPCN2	219931	hgsc.bcm.edu	37	11	68840160	68840160	+	Missense_Mutation	SNP	A	A	G	rs3750965	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:68840160A>G	ENST00000294309.3	+	12	1228	c.1127A>G	c.(1126-1128)aAa>aGa	p.K376R	TPCN2_ENST00000442692.2_Intron|TPCN2_ENST00000542467.1_Missense_Mutation_p.K376R	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	376			K -> R (in dbSNP:rs3750965).		calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|release of sequestered calcium ion into cytosol (GO:0051209)|smooth muscle contraction (GO:0006939)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|NAADP-sensitive calcium-release channel activity (GO:0072345)|protein kinase binding (GO:0019901)|voltage-gated calcium channel activity (GO:0005245)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	32			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			AGCTCCCACAAACAGGCCATG	0.632													A|||	1456	0.290735	0.2322	0.1945	5008	,	,		15326	0.2063		0.3032	False		,,,				2504	0.5123				p.K376R		Atlas-SNP	.											TPCN2,colon,carcinoma,0,1	TPCN2	63	1	0			c.A1127G						scavenged	.	A	ARG/LYS	1078,3322	387.7+/-326.6	133,812,1255	51.0	49.0	50.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1127	2.6	0.0	11	dbSNP_107	50	2710,5878	429.7+/-356.3	408,1894,1992	yes	missense	TPCN2	NM_139075.3	26	541,2706,3247	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	31.5557,24.5,29.1654	benign	376/753	68840160	3788,9200	2200	4294	6494	SO:0001583	missense	219931	exon12			CCCACAAACAGGC	AK023366	CCDS8189.1	11q13.1	2011-07-05			ENSG00000162341	ENSG00000162341		"""Voltage-gated ion channels / Two-pore channels"""	20820	protein-coding gene	gene with protein product		612163				16382101	Standard	NM_139075		Approved	TPC2	uc001oos.2	Q8NHX9	OTTHUMG00000167898	ENST00000294309.3:c.1127A>G	11.37:g.68840160A>G	ENSP00000294309:p.Lys376Arg	Somatic	105	2	0.0190476		WXS	Illumina HiSeq	Phase_I	104	79	0.759615	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	37	CCDS8189.1	558	0.2554945054945055	104	0.21138211382113822	83	0.2292817679558011	135	0.23601398601398602	236	0.3113456464379947	A	0.628	-0.818239	0.02776	0.245	0.315557	ENSG00000162341	ENST00000294309;ENST00000535009;ENST00000542467	D;D	0.96913	-4.16;-4.17	4.94	2.61	0.31194	.	0.188884	0.44688	N	0.000427	T	0.00039	0.0001	M	0.64997	1.995	0.33812	P	0.37205200000000005	B;B;B	0.33379	0.287;0.287;0.41	B;B;B	0.29524	0.048;0.048;0.103	T	0.00862	-1.1536	9	0.25106	T	0.35	-5.9663	6.5291	0.22316	0.8026:0.0:0.1974:0.0	rs3750965;rs57180849;rs3750965	376;376;291	E7ETX0;Q8NHX9;F5H1G5	.;TPC2_HUMAN;.	R	376;291;376	ENSP00000294309:K376R;ENSP00000445551:K376R	ENSP00000294309:K376R	K	+	2	0	TPCN2	68596736	0.057000	0.20700	0.030000	0.17652	0.117000	0.20001	0.272000	0.18644	0.327000	0.23409	0.459000	0.35465	AAA	A|0.718;G|0.282	0.282	strong		0.632	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
SRP72	6731	hgsc.bcm.edu	37	4	57333822	57333822	+	Silent	SNP	G	G	T	rs12513091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57333822G>T	ENST00000342756.5	+	1	742	c.21G>T	c.(19-21)ggG>ggT	p.G7G	SRP72_ENST00000510663.1_Silent_p.G7G|SRP72_ENST00000504757.1_Silent_p.G7G	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	7					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(7)|ovary(2)	22	Glioma(25;0.08)|all_neural(26;0.101)					GCGGCAGCGGGGGGGTGTCAG	0.642													G|||	1156	0.230831	0.1036	0.4092	5008	,	,		14542	0.2282		0.2127	False		,,,				2504	0.2975				p.G7G		Atlas-SNP	.											SRP72,NS,carcinoma,0,1	SRP72	59	1	0			c.G21T						PASS	.	G		515,3883		23,469,1707	15.0	17.0	16.0		21	1.5	1.0	4	dbSNP_120	16	1547,7047		120,1307,2870	no	coding-synonymous	SRP72	NM_006947.3		143,1776,4577	TT,TG,GG		18.0009,11.7099,15.8713		7/672	57333822	2062,10930	2199	4297	6496	SO:0001819	synonymous_variant	6731	exon1			CAGCGGGGGGGTG	AF069765	CCDS3506.1, CCDS58898.1	4q11	2013-01-10	2002-08-29		ENSG00000174780	ENSG00000174780		"""Tetratricopeptide (TTC) repeat domain containing"""	11303	protein-coding gene	gene with protein product		602122	"""signal recognition particle 72kD"""			9224693, 9857079	Standard	NM_006947		Approved		uc003hbv.3	O76094	OTTHUMG00000128843	ENST00000342756.5:c.21G>T	4.37:g.57333822G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_006947	G5E9Z8|Q7Z3C0	Silent	SNP	ENST00000342756.5	37	CCDS3506.1																																																																																			A|0.000;C|0.000;G|0.800;T|0.199	0.199	strong		0.642	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7		
TRIM31	11074	hgsc.bcm.edu	37	6	30080496	30080496	+	Silent	SNP	G	G	A	rs2844793	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30080496G>A	ENST00000376734.3	-	2	212	c.87C>T	c.(85-87)atC>atT	p.I29I	TRIM31_ENST00000485864.1_5'Flank|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Silent_p.I29I	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	29					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						GCCCACAGTCGATGGTGACAG	0.478													G|||	381	0.0760783	0.0567	0.1182	5008	,	,		21211	0.0486		0.1213	False		,,,				2504	0.0542				p.I29I		Atlas-SNP	.											.	TRIM31	40	.	0			c.C87T						PASS	.	G		200,2820		8,184,1318	107.0	110.0	109.0		87	-5.1	0.0	6	dbSNP_100	109	760,4658		46,668,1995	yes	coding-synonymous	TRIM31	NM_007028.3		54,852,3313	AA,AG,GG		14.0273,6.6225,11.3771		29/426	30080496	960,7478	1510	2709	4219	SO:0001819	synonymous_variant	11074	exon2			ACAGTCGATGGTG	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.87C>T	6.37:g.30080496G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	104	87	0.836538	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			G|0.893;A|0.107	0.107	strong		0.478	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
MRO	83876	hgsc.bcm.edu	37	18	48331524	48331524	+	Splice_Site	SNP	G	G	A	rs2586776|rs17852712	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:48331524G>A	ENST00000428869.2	-	6	687	c.429C>T	c.(427-429)gaC>gaT	p.D143D	MRO_ENST00000436348.2_Splice_Site_p.D157D|MRO_ENST00000431965.2_Splice_Site_p.D157D|MRO_ENST00000588444.1_Splice_Site_p.D143D|MRO_ENST00000587291.1_5'UTR|MRO_ENST00000256425.2_Splice_Site_p.D143D|MRO_ENST00000398439.3_Splice_Site_p.D143D			Q9BYG7	MSTRO_HUMAN	maestro	143						nucleolus (GO:0005730)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		ATTTACTTACGTCATCTAATA	0.453													A|||	2268	0.452875	0.4448	0.4193	5008	,	,		18644	0.3363		0.4801	False		,,,				2504	0.5798				p.D157D		Atlas-SNP	.											MRO_ENST00000436348,colon,carcinoma,0,2	MRO	36	2	0			c.C471T						scavenged	.	A	,,,	2010,2396	614.6+/-392.4	460,1090,653	82.0	78.0	79.0		429,471,471,429	-5.7	0.7	18	dbSNP_100	79	4081,4519	593.7+/-393.2	974,2133,1193	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	MRO	NM_001127174.1,NM_001127175.1,NM_001127176.1,NM_031939.3	,,,	1434,3223,1846	AA,AG,GG		47.4535,45.6196,46.8322	,,,	143/197,157/211,157/263,143/249	48331524	6091,6915	2203	4300	6503	SO:0001630	splice_region_variant	83876	exon4			ACTTACGTCATCT	AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.429+1C>T	18.37:g.48331524G>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_001127175	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Silent	SNP	ENST00000428869.2	37	CCDS11947.1																																																																																			G|0.541;A|0.459	0.459	strong		0.453	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2	NM_031939	Silent
KBTBD8	84541	hgsc.bcm.edu	37	3	67054649	67054649	+	Missense_Mutation	SNP	T	T	C	rs13096789	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:67054649T>C	ENST00000417314.2	+	3	1307	c.1258T>C	c.(1258-1260)Tgt>Cgt	p.C420R	KBTBD8_ENST00000295568.4_Missense_Mutation_p.C394R|KBTBD8_ENST00000460576.1_Intron			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	420			C -> R (in dbSNP:rs13096789).			cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		TAGAGAGAATTGTTGGACGAC	0.423													T|||	468	0.0934505	0.0522	0.2305	5008	,	,		20779	0.0179		0.1352	False		,,,				2504	0.0869				p.C420R		Atlas-SNP	.											.	KBTBD8	101	.	0			c.T1258C						PASS	.	T	ARG/CYS	270,4136	149.5+/-183.7	11,248,1944	193.0	180.0	184.0		1258	2.7	0.9	3	dbSNP_121	184	1167,7433	236.4+/-268.6	69,1029,3202	yes	missense	KBTBD8	NM_032505.2	180	80,1277,5146	CC,CT,TT		13.5698,6.128,11.0487	probably-damaging	420/602	67054649	1437,11569	2203	4300	6503	SO:0001583	missense	84541	exon3			GAGAATTGTTGGA	AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"""BTB/POZ domain containing"""	30691	protein-coding gene	gene with protein product	"""T-cell activation kelch repeat protein"""					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.1258T>C	3.37:g.67054649T>C	ENSP00000401878:p.Cys420Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_032505	B4DTW6|Q96JI5	Missense_Mutation	SNP	ENST00000417314.2	37	CCDS2906.2	208	0.09523809523809523	24	0.04878048780487805	68	0.1878453038674033	12	0.02097902097902098	104	0.13720316622691292	T	10.04	1.242106	0.22796	0.06128	0.135698	ENSG00000163376	ENST00000295568;ENST00000417314	T;T	0.76839	-1.05;-1.05	5.07	2.69	0.31865	Kelch-type beta propeller (1);	0.084638	0.85682	N	0.000000	T	0.00109	0.0003	N	0.05306	-0.075	0.09310	P	0.99999999876442	B	0.10296	0.003	B	0.10450	0.005	T	0.02625	-1.1132	8	.	.	.	.	9.3807	0.38311	0.0:0.145:0.0:0.855	rs13096789;rs17798278;rs52819173;rs58414813;rs13096789	420	Q8NFY9	KBTB8_HUMAN	R	394;420	ENSP00000295568:C394R;ENSP00000401878:C420R	.	C	+	1	0	KBTBD8	67137339	1.000000	0.71417	0.863000	0.33907	0.731000	0.41821	4.094000	0.57721	0.369000	0.24510	0.455000	0.32223	TGT	C|0.097;N|0.000	0.097	strong		0.423	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505	
C10orf11	83938	hgsc.bcm.edu	37	10	77807027	77807027	+	Silent	SNP	T	T	C	rs1898071	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:77807027T>C	ENST00000372499.1	+	3	495	c.280T>C	c.(280-282)Ttg>Ctg	p.L94L	C10orf11_ENST00000593699.1_3'UTR	NM_032024.3	NP_114413.1	Q9H2I8	CJ011_HUMAN	chromosome 10 open reading frame 11	94					melanocyte differentiation (GO:0030318)					endometrium(1)|large_intestine(4)|lung(4)|stomach(1)	10	Prostate(51;0.0095)|all_epithelial(25;0.0221)					GCTGGTCAGCTTGGAAAAGGA	0.502													T|||	1488	0.297125	0.4266	0.3055	5008	,	,		21008	0.0119		0.4384	False		,,,				2504	0.2648				p.L94L		Atlas-SNP	.											.	C10orf11	19	.	0			c.T280C						PASS	.	T		1905,2501	545.5+/-376.8	409,1087,707	88.0	81.0	83.0		280	2.6	1.0	10	dbSNP_92	83	3950,4650	547.6+/-385.2	907,2136,1257	no	coding-synonymous	C10orf11	NM_032024.3		1316,3223,1964	CC,CT,TT		45.9302,43.2365,45.0177		94/199	77807027	5855,7151	2203	4300	6503	SO:0001819	synonymous_variant	83938	exon3			GTCAGCTTGGAAA	AF267860	CCDS7351.1	10q22.3	2013-08-22			ENSG00000148655	ENSG00000148655			23405	protein-coding gene	gene with protein product	"""oculocutaneous albinism 7, autosomal recessive"""	614537				23395477	Standard	NM_032024		Approved	CDA017, OCA7	uc001jxi.3	Q9H2I8	OTTHUMG00000018532	ENST00000372499.1:c.280T>C	10.37:g.77807027T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_032024	B1AVW6	Silent	SNP	ENST00000372499.1	37	CCDS7351.1																																																																																			T|0.608;C|0.392	0.392	strong		0.502	C10orf11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048839.1	NM_032024	
POLRMT	5442	hgsc.bcm.edu	37	19	621070	621070	+	Silent	SNP	G	G	A	rs77809401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:621070G>A	ENST00000588649.2	-	10	2712	c.2628C>T	c.(2626-2628)gaC>gaT	p.D876D	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	876	Mediates interaction with TEFM.				gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		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)		TCAAGGGTTGGTCCGCGGAGT	0.746													G|||	1026	0.204872	0.1225	0.1441	5008	,	,		5027	0.25		0.171	False		,,,				2504	0.3476				p.D876D		Atlas-SNP	.											.	POLRMT	91	.	0			c.C2628T						PASS	.	G		582,3810		35,512,1649	19.0	22.0	21.0		2628	2.3	0.1	19	dbSNP_131	21	1532,7062		130,1272,2895	no	coding-synonymous	POLRMT	NM_005035.3		165,1784,4544	AA,AG,GG		17.8264,13.2514,16.2791		876/1231	621070	2114,10872	2196	4297	6493	SO:0001819	synonymous_variant	5442	exon10			GGGTTGGTCCGCG		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.2628C>T	19.37:g.621070G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.849;A|0.151	0.151	strong		0.746	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
ST13	6767	hgsc.bcm.edu	37	22	41223190	41223190	+	Missense_Mutation	SNP	C	C	T	rs710193	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:41223190C>T	ENST00000216218.3	-	11	1372	c.891G>A	c.(889-891)atG>atA	p.M297I		NM_003932.3	NP_003923.2	P50502	F10A1_HUMAN	suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting protein)	297	Gly/Met/Pro-rich.		M -> I (in dbSNP:rs710193).		chaperone cofactor-dependent protein refolding (GO:0070389)|negative regulation of protein refolding (GO:0061084)|protein folding (GO:0006457)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	dATP binding (GO:0032564)|protein binding, bridging (GO:0030674)			cervix(1)|large_intestine(1)|lung(3)|skin(1)	6						CCATTCCAGGCATTCCTCCGG	0.458													C|||	161	0.0321486	0.0053	0.0519	5008	,	,		16740	0.0		0.0934	False		,,,				2504	0.0245				p.M297I		Atlas-SNP	.											.	ST13	16	.	0			c.G891A						PASS	.	C	ILE/MET	80,4326	65.3+/-102.7	1,78,2124	53.0	58.0	56.0		891	5.0	1.0	22	dbSNP_86	56	853,7743	185.5+/-233.2	36,781,3481	no	missense	ST13	NM_003932.3	10	37,859,5605	TT,TC,CC		9.9232,1.8157,7.1758	benign	297/370	41223190	933,12069	2203	4298	6501	SO:0001583	missense	6767	exon11			TCCAGGCATTCCT		CCDS14006.1	22q13.2	2013-01-10	2001-11-29		ENSG00000100380	ENSG00000100380		"""Tetratricopeptide (TTC) repeat domain containing"""	11343	protein-coding gene	gene with protein product	"""progesterone receptor-associated p48 protein"""	606796	"""suppression of tumorigenicity 13 (colon carcinoma) (Hsp70-interacting protein)"""			9925927, 8721986	Standard	NM_003932		Approved	SNC6, HSPABP1, HIP, P48, FAM10A1	uc003aze.3	P50502	OTTHUMG00000151201	ENST00000216218.3:c.891G>A	22.37:g.41223190C>T	ENSP00000216218:p.Met297Ile	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_003932	O14999|Q2TU77	Missense_Mutation	SNP	ENST00000216218.3	37	CCDS14006.1	101	0.04624542124542125	3	0.006097560975609756	22	0.06077348066298342	0	0.0	76	0.10026385224274406	C	12.22	1.873034	0.33069	0.018157	0.099232	ENSG00000100380	ENST00000216218	D	0.84730	-1.89	5.01	5.01	0.66863	.	0.135171	0.64402	D	0.000003	T	0.16981	0.0408	M	0.80746	2.51	0.23920	P	0.99646228	B;B	0.27765	0.188;0.188	B;B	0.31101	0.124;0.124	T	0.67593	-0.5631	9	0.26408	T	0.33	.	13.9913	0.64369	0.1521:0.8479:0.0:0.0	rs710193;rs3194821;rs710193	287;297	B4E0U6;P50502	.;F10A1_HUMAN	I	297	ENSP00000216218:M297I	ENSP00000216218:M297I	M	-	3	0	ST13	39553136	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.292000	0.51772	2.340000	0.79590	0.555000	0.69702	ATG	C|0.940;T|0.060	0.060	strong		0.458	ST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321759.1	NM_003932	
EFCAB7	84455	hgsc.bcm.edu	37	1	63997633	63997633	+	Silent	SNP	A	A	T	rs9804078	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:63997633A>T	ENST00000371088.4	+	3	576	c.330A>T	c.(328-330)tcA>tcT	p.S110S	RN7SL488P_ENST00000585186.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	110	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.						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						TACTAAAATCATTTAAGCAAT	0.294													A|||	983	0.196286	0.2738	0.1715	5008	,	,		17546	0.1855		0.1441	False		,,,				2504	0.1738				p.S110S		Atlas-SNP	.											EFCAB7,colon,carcinoma,+1,1	EFCAB7	45	1	0			c.A330T						PASS	.	A		997,3409	346.2+/-308.9	114,769,1320	47.0	50.0	49.0		330	4.1	1.0	1	dbSNP_119	49	1324,7266	252.8+/-278.7	92,1140,3063	no	coding-synonymous	EFCAB7	NM_032437.2		206,1909,4383	TT,TA,AA		15.4133,22.6282,17.8593		110/630	63997633	2321,10675	2203	4295	6498	SO:0001819	synonymous_variant	84455	exon3			AAAATCATTTAAG	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.330A>T	1.37:g.63997633A>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	130	50	0.384615	NM_032437	Q658P0|Q96B95|Q96JM6	Silent	SNP	ENST00000371088.4	37	CCDS30737.1																																																																																			A|0.815;T|0.185	0.185	strong		0.294	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
OR10K2	391107	hgsc.bcm.edu	37	1	158390501	158390501	+	Silent	SNP	G	G	A	rs34616883	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158390501G>A	ENST00000314902.2	-	1	155	c.156C>T	c.(154-156)gaC>gaT	p.D52D		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	52						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)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					GAAGGGCCCTGTCCAGGACAA	0.512													G|||	1405	0.280551	0.2186	0.2695	5008	,	,		22238	0.1687		0.4592	False		,,,				2504	0.3037				p.D52D		Atlas-SNP	.											OR10K2,NS,carcinoma,0,1	OR10K2	69	1	0			c.C156T						PASS	.	G		1068,3338	389.1+/-327.2	134,800,1269	170.0	141.0	151.0		156	1.1	1.0	1	dbSNP_126	151	3769,4831	534.6+/-382.6	807,2155,1338	no	coding-synonymous	OR10K2	NM_001004476.1		941,2955,2607	AA,AG,GG		43.8256,24.2397,37.1905		52/313	158390501	4837,8169	2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			GGCCCTGTCCAGG	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"""GPCR / Class A : Olfactory receptors"""	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.156C>T	1.37:g.158390501G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	193	91	0.471503	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			G|0.643;A|0.357	0.357	strong		0.512	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476	
NSL1	25936	hgsc.bcm.edu	37	1	212965095	212965095	+	Missense_Mutation	SNP	G	G	A	rs17856201	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:212965095G>A	ENST00000366977.3	-	1	29	c.11C>T	c.(10-12)tCt>tTt	p.S4F	TATDN3_ENST00000526641.1_5'Flank|NSL1_ENST00000473995.1_5'Flank|NSL1_ENST00000366978.1_5'Flank|TATDN3_ENST00000366973.4_5'Flank|TATDN3_ENST00000531963.1_5'Flank|NSL1_ENST00000366975.6_Missense_Mutation_p.S4F|TATDN3_ENST00000532324.1_5'Flank|TATDN3_ENST00000366974.4_5'Flank|NSL1_ENST00000422588.2_Missense_Mutation_p.S4F|NSL1_ENST00000366976.1_Missense_Mutation_p.S4F|TATDN3_ENST00000526997.1_5'Flank|TATDN3_ENST00000530441.1_5'Flank	NM_015471.3	NP_056286.3	Q96IY1	NSL1_HUMAN	NSL1, MIS12 kinetochore complex component	4			S -> F (in dbSNP:rs17856201). {ECO:0000269|PubMed:15489334}.		chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|MIS12/MIND type complex (GO:0000444)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00597)|all cancers(67;0.00893)|GBM - Glioblastoma multiforme(131;0.0514)|Epithelial(68;0.102)		CAACTCAGGAGACCCCGCCAT	0.617													G|||	938	0.1873	0.2943	0.1081	5008	,	,		17447	0.1429		0.1441	False		,,,				2504	0.1892				p.S4F		Atlas-SNP	.											.	NSL1	24	.	0			c.C11T						PASS	.	G	PHE/SER,PHE/SER	1177,3229		168,841,1194	14.0	18.0	17.0		11,11	-0.6	0.0	1	dbSNP_123	17	1158,7426		71,1016,3205	yes	missense,missense	NSL1	NM_001042549.1,NM_015471.3	155,155	239,1857,4399	AA,AG,GG		13.4902,26.7136,17.9754	possibly-damaging,possibly-damaging	4/214,4/282	212965095	2335,10655	2203	4292	6495	SO:0001583	missense	25936	exon1			TCAGGAGACCCCG	AF255793	CCDS1509.1, CCDS73025.1	1q41	2013-07-03	2013-07-03	2006-11-07	ENSG00000117697	ENSG00000117697			24548	protein-coding gene	gene with protein product		609174	"""chromosome 1 open reading frame 48"", ""NSL1, MIND kinetochore complex component, homolog (S. cerevisiae)"""	C1orf48		20819937	Standard	NM_015471		Approved	DC8, DKFZP566O1646, MIS14	uc001hjn.3	Q96IY1	OTTHUMG00000036806	ENST00000366977.3:c.11C>T	1.37:g.212965095G>A	ENSP00000355944:p.Ser4Phe	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_015471	E7ETD5|Q5SY75|Q9H2M5|Q9NRN8|Q9Y415	Missense_Mutation	SNP	ENST00000366977.3	37	CCDS1509.1	398	0.18223443223443223	163	0.3313008130081301	46	0.1270718232044199	80	0.13986013986013987	109	0.1437994722955145	G	11.77	1.737654	0.30774	0.267136	0.134902	ENSG00000117697	ENST00000366977;ENST00000422588;ENST00000366975;ENST00000366976	T;T;T;T	0.50813	1.44;0.73;1.45;0.84	5.13	-0.561	0.11785	.	0.958527	0.08627	N	0.917615	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.40117	-0.9580	8	.	.	.	4.0511	4.2163	0.10537	0.3203:0.3257:0.354:0.0	rs17856201	4;4;4	B4E071;Q96IY1;E7ETD5	.;NSL1_HUMAN;.	F	4	ENSP00000355944:S4F;ENSP00000388406:S4F;ENSP00000355942:S4F;ENSP00000355943:S4F	.	S	-	2	0	NSL1	211031718	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.776000	0.04674	-0.262000	0.09392	-0.237000	0.12165	TCT	G|0.841;A|0.159	0.159	strong		0.617	NSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089398.2	NM_015471	
BCL2A1	597	hgsc.bcm.edu	37	15	80260014	80260014	+	Intron	SNP	T	T	C	rs8026803	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:80260014T>C	ENST00000267953.3	-	1	747				BCL2A1_ENST00000335661.6_Silent_p.T147T	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1						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)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						CCAGCATAGGTGTGTGATTGT	0.358													C|||	1950	0.389377	0.3956	0.2925	5008	,	,		18762	0.5288		0.2584	False		,,,				2504	0.4407				p.T147T		Atlas-SNP	.											.	BCL2A1	28	.	0			c.A441G						PASS	.	C	,	1147,1989		199,749,620	101.0	84.0	89.0		441,	-0.0	0.0	15	dbSNP_116	89	1841,5323		211,1419,1952	no	coding-synonymous,intron	BCL2A1	NM_001114735.1,NM_004049.3	,	410,2168,2572	CC,CT,TT		25.6979,36.5753,29.0097	,	147/164,	80260014	2988,7312	1568	3582	5150	SO:0001627	intron_variant	597	exon2			CATAGGTGTGTGA		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.420+3027A>G	15.37:g.80260014T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	71	26	0.366197	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Silent	SNP	ENST00000267953.3	37	CCDS10312.1																																																																																			T|0.622;C|0.378	0.378	strong		0.358	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
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 GAIIx	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	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	105	6	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		
NUDT16	131870	hgsc.bcm.edu	37	3	131102053	131102053	+	Silent	SNP	A	A	G	rs11549806	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:131102053A>G	ENST00000521288.1	+	3	487	c.456A>G	c.(454-456)gtA>gtG	p.V152V	NUDT16_ENST00000502852.1_3'UTR|RP11-933H2.4_ENST00000502521.1_RNA|NUDT16_ENST00000537561.1_Silent_p.V106V|NUDT16_ENST00000359850.3_Silent_p.V119V			Q96DE0	NUD16_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 16	152	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				adenosine to inosine editing (GO:0006382)|dephosphorylation (GO:0016311)|dITP catabolic process (GO:0035863)|IDP catabolic process (GO:0046709)|mRNA catabolic process (GO:0006402)|negative regulation of rRNA processing (GO:2000233)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of cell cycle process (GO:0090068)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|snoRNA catabolic process (GO:0016077)|XDP catabolic process (GO:1901639)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cobalt ion binding (GO:0050897)|dIDP diphosphatase activity (GO:0097383)|dITP diphosphatase activity (GO:0035870)|GTP binding (GO:0005525)|inosine-diphosphatase activity (GO:0090450)|ITP binding (GO:1901641)|m7G(5')pppN diphosphatase activity (GO:0050072)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)|mRNA binding (GO:0003729)|nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|protein homodimerization activity (GO:0042803)|snoRNA binding (GO:0030515)|XTP binding (GO:1901640)			large_intestine(1)|lung(6)	7						GGGATGGTGTAGGAGGCCTGC	0.577													G|||	360	0.071885	0.0325	0.1297	5008	,	,		18434	0.1667		0.0318	False		,,,				2504	0.0276				p.V152V		Atlas-SNP	.											.	NUDT16	10	.	0			c.A456G						PASS	.	G	,	123,4283	815.3+/-416.2	1,121,2081	128.0	117.0	121.0		318,456	3.0	1.0	3	dbSNP_120	121	273,8327	807.2+/-407.2	5,263,4032	no	coding-synonymous,coding-synonymous	NUDT16	NM_001171905.1,NM_152395.2	,	6,384,6113	GG,GA,AA		3.1744,2.7916,3.0447	,	106/160,152/196	131102053	396,12610	2203	4300	6503	SO:0001819	synonymous_variant	131870	exon3			TGGTGTAGGAGGC	AK055827	CCDS3070.1, CCDS3070.2, CCDS54640.1, CCDS54641.1	3q21.3	2005-01-25						"""Nudix motif containing"""	26442	protein-coding gene	gene with protein product						12477932	Standard	NM_152395		Approved	FLJ31265	uc021xec.1	Q96DE0		ENST00000521288.1:c.456A>G	3.37:g.131102053A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	75	45	0.6	NM_152395	B4E3B4|E9PED4|F5GYJ1|Q96N82	Silent	SNP	ENST00000521288.1	37	CCDS3070.2																																																																																			A|0.956;G|0.044	0.044	strong		0.577	NUDT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356537.9	NM_152395	
ZNF853	54753	hgsc.bcm.edu	37	7	6656897	6656897	+	Missense_Mutation	SNP	A	A	G	rs1806552	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6656897A>G	ENST00000457543.3	+	2	647	c.89A>G	c.(88-90)cAa>cGa	p.Q30R		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	30			Q -> R (in dbSNP:rs1806552). {ECO:0000269|Ref.2}.				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						CTGGAACTTCAATGTCTTGAG	0.622													G|||	3865	0.771765	0.9274	0.6931	5008	,	,		18650	0.7609		0.5437	False		,,,				2504	0.863				p.Q30R		Atlas-SNP	.											ZNF853_ENST00000457543,NS,carcinoma,+1,2	ZNF853	32	2	0			c.A89G						PASS	.						39.0	46.0	44.0					7																	6656897		692	1591	2283	SO:0001583	missense	54753	exon2			AACTTCAATGTCT	AL133055	CCDS59048.1	7p22.1	2013-01-08				ENSG00000236609		"""Zinc fingers, C2H2-type"""	21767	protein-coding gene	gene with protein product							Standard	NM_017560		Approved	DKFZp434J1015	uc011jwz.2	P0CG23		ENST00000457543.3:c.89A>G	7.37:g.6656897A>G	ENSP00000455585:p.Gln30Arg	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	29	12	0.413793	NM_017560		Missense_Mutation	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			A|0.289;G|0.711	0.711	strong		0.622	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
MMP10	4319	hgsc.bcm.edu	37	11	102650246	102650246	+	Silent	SNP	G	G	A	rs17860949	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102650246G>A	ENST00000279441.4	-	2	372	c.336C>T	c.(334-336)caC>caT	p.H112H		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	112					collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|regulation of cell migration (GO:0030334)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|liver(2)|lung(6)	22	all_epithelial(12;0.00961)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0303)|Lung(13;0.0828)|all cancers(10;0.116)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0145)	Marimastat(DB00786)	TGTATGTAAGGTGGGTTTTCC	0.418													G|||	598	0.119409	0.1475	0.0836	5008	,	,		19880	0.0952		0.1312	False		,,,				2504	0.1196				p.H112H		Atlas-SNP	.											.	MMP10	44	.	0			c.C336T						PASS	.	G		634,3772	272.8+/-271.0	46,542,1615	82.0	72.0	75.0		336	1.1	0.5	11	dbSNP_123	75	1075,7523	226.8+/-262.4	65,945,3289	no	coding-synonymous	MMP10	NM_002425.2		111,1487,4904	AA,AG,GG		12.5029,14.3895,13.1421		112/477	102650246	1709,11295	2203	4299	6502	SO:0001819	synonymous_variant	4319	exon2			TGTAAGGTGGGTT	X07820	CCDS8321.1	11q22.3	2008-02-05	2005-08-08		ENSG00000166670	ENSG00000166670	3.4.24.22		7156	protein-coding gene	gene with protein product		185260	"""matrix metalloproteinase 10 (stromelysin 2)"""	STMY2			Standard	NM_002425		Approved		uc001phg.2	P09238	OTTHUMG00000168083	ENST00000279441.4:c.336C>T	11.37:g.102650246G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	89	60	0.674157	NM_002425	B2R9X9|Q53HH9	Silent	SNP	ENST00000279441.4	37	CCDS8321.1																																																																																			G|0.872;A|0.128	0.128	strong		0.418	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
MARVELD3	91862	hgsc.bcm.edu	37	16	71674882	71674882	+	Silent	SNP	C	C	G	rs2303225	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:71674882C>G	ENST00000299952.4	+	3	1228	c.1185C>G	c.(1183-1185)ccC>ccG	p.P395P	PHLPP2_ENST00000540628.1_3'UTR|MARVELD3_ENST00000561682.1_Intron|MARVELD3_ENST00000565261.1_3'UTR	NM_001017967.3|NM_001271329.1	NP_001017967.2|NP_001258258.1	Q96A59	MALD3_HUMAN	MARVEL domain containing 3	0					cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|tight junction (GO:0005923)				NS(1)|endometrium(3)|large_intestine(5)|lung(6)|skin(2)	17		Ovarian(137;0.125)				GAGAACAGCCCGGAAGTTACA	0.517													C|||	2021	0.403554	0.2549	0.5274	5008	,	,		20414	0.6835		0.325	False		,,,				2504	0.3088				p.P395P		Atlas-SNP	.											.	MARVELD3	63	.	0			c.C1185G						PASS	.	C		1174,3222		167,840,1191	50.0	42.0	45.0		1185	1.4	0.0	16	dbSNP_100	45	2866,5734		483,1900,1917	no	coding-synonymous	MARVELD3	NM_001017967.2		650,2740,3108	GG,GC,CC		33.3256,26.7061,31.0865		395/411	71674882	4040,8956	2198	4300	6498	SO:0001819	synonymous_variant	91862	exon3			ACAGCCCGGAAGT	BC013376	CCDS10904.1, CCDS32478.1, CCDS59270.1	16q22.2	2008-02-05	2004-07-12	2004-07-14	ENSG00000140832	ENSG00000140832			30525	protein-coding gene	gene with protein product		614094	"""MARVEL (membrane-associating) domain containing 3"""	MRVLDC3			Standard	NM_001017967		Approved		uc002fat.4	Q96A59	OTTHUMG00000137591	ENST00000299952.4:c.1185C>G	16.37:g.71674882C>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	173	90	0.520231	NM_001017967	A8K820|H3BQM5|Q96MJ4	Silent	SNP	ENST00000299952.4	37	CCDS32478.1	917	0.4198717948717949	133	0.2703252032520325	166	0.4585635359116022	380	0.6643356643356644	238	0.31398416886543534	C	13.55	2.270000	0.40194	0.267061	0.333256	ENSG00000040199	ENST00000299971	.	.	.	5.67	1.4	0.22301	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44757	-0.9307	4	0.46703	T	0.11	-14.0177	9.1148	0.36750	0.0:0.4539:0.4643:0.0818	rs2303225;rs2303225	.	.	.	P	767	.	ENSP00000299971:R767P	R	-	2	0	PHLPP2	70232383	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.022000	0.13511	0.041000	0.15688	0.655000	0.94253	CGG	C|0.647;G|0.353	0.353	strong		0.517	MARVELD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268990.1	NM_052858	
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 GAIIx	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_ENST00000340052.3_5'Flank|DLEU2L_ENST00000371086.2_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	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	170	75	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	
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 GAIIx	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_ENST00000370549.1_Missense_Mutation_p.A241T|HPSE2_ENST00000370546.1_Missense_Mutation_p.A299T|HPSE2_ENST00000404542.1_Missense_Mutation_p.A187T	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	52	21	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	
STOML1	9399	hgsc.bcm.edu	37	15	74277666	74277666	+	Silent	SNP	C	C	T	rs34353835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:74277666C>T	ENST00000316900.5	-	5	907	c.783G>A	c.(781-783)ccG>ccA	p.P261P	STOML1_ENST00000316911.6_Silent_p.P211P|STOML1_ENST00000359750.4_Silent_p.P261P|STOML1_ENST00000561656.1_Silent_p.P174P|STOML1_ENST00000564777.1_Silent_p.P211P|STOML1_ENST00000541638.1_Silent_p.P219P	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	261						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						CACCTGGCCCCGGGGACGGGG	0.637													c|||	40	0.00798722	0.0008	0.0086	5008	,	,		17752	0.0		0.0298	False		,,,				2504	0.0031				p.P261P		Atlas-SNP	.											.	STOML1	22	.	0			c.G783A						PASS	.	T		31,4345		0,31,2157	14.0	15.0	15.0		783	-10.7	0.0	15	dbSNP_126	15	318,8242		8,302,3970	no	coding-synonymous	STOML1	NM_004809.3		8,333,6127	TT,TC,CC		3.715,0.7084,2.6979		261/399	74277666	349,12587	2188	4280	6468	SO:0001819	synonymous_variant	9399	exon5			TGGCCCCGGGGAC	Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"""stomatin-like 1"", ""stomatin (EBP72)-like 1"""	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.783G>A	15.37:g.74277666C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_001256672	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Silent	SNP	ENST00000316900.5	37	CCDS10254.1																																																																																			C|0.980;T|0.020	0.020	strong		0.637	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809	
SNX29	92017	hgsc.bcm.edu	37	16	12662420	12662420	+	Silent	SNP	C	C	T	rs2288423	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:12662420C>T	ENST00000566228.1	+	21	2445	c.2376C>T	c.(2374-2376)ttC>ttT	p.F792F	SNX29_ENST00000306030.3_Silent_p.F407F|CTD-3037G24.3_ENST00000564505.1_RNA	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	792						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						CTTCCCGCTTCCCCAAACTGT	0.642													C|||	1634	0.326278	0.41	0.2017	5008	,	,		15444	0.4524		0.2306	False		,,,				2504	0.2699				p.F792F		Atlas-SNP	.											.	SNX29	60	.	0			c.C2376T						PASS	.	C		1327,2603		227,873,865	31.0	39.0	36.0		1221	5.1	1.0	16	dbSNP_100	36	1854,6514		196,1462,2526	no	coding-synonymous	SNX29	NM_001080530.2		423,2335,3391	TT,TC,CC		22.1558,33.7659,25.866		407/429	12662420	3181,9117	1965	4184	6149	SO:0001819	synonymous_variant	92017	exon21			CCGCTTCCCCAAA	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.2376C>T	16.37:g.12662420C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Silent	SNP	ENST00000566228.1	37	CCDS10553.2																																																																																			C|0.684;T|0.316	0.316	strong		0.642	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
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 GAIIx	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		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	43	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		
COL2A1	1280	hgsc.bcm.edu	37	12	48379731	48379731	+	Silent	SNP	G	G	T	rs41317925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48379731G>T	ENST00000380518.3	-	24	1709	c.1545C>A	c.(1543-1545)cgC>cgA	p.R515R	COL2A1_ENST00000493991.1_5'UTR|COL2A1_ENST00000337299.6_Silent_p.R446R	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	515	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)	CTGGGAAACCGCGGTTGCCGG	0.627													G|||	28	0.00559105	0.0008	0.013	5008	,	,		17619	0.0		0.0179	False		,,,				2504	0.0				p.R515R		Atlas-SNP	.											COL2A1_ENST00000380518,colon,carcinoma,-1,2	COL2A1	368	2	0			c.C1545A						PASS	.	G	,	18,4038		0,18,2010	37.0	37.0	37.0		1545,1338	-2.0	1.0	12	dbSNP_127	37	135,7769		0,135,3817	no	coding-synonymous,coding-synonymous	COL2A1	NM_001844.4,NM_033150.2	,	0,153,5827	TT,TG,GG		1.708,0.4438,1.2793	,	515/1488,446/1419	48379731	153,11807	2028	3952	5980	SO:0001819	synonymous_variant	1280	exon24			GAAACCGCGGTTG	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.1545C>A	12.37:g.48379731G>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	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|0.990;T|0.010	0.010	strong		0.627	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923934	43923934	+	Silent	SNP	T	T	C	rs11079725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43923934T>C	ENST00000329196.5	+	1	1679	c.1662T>C	c.(1660-1662)gaT>gaC	p.D554D	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	554						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										GCGCAGCAGATGCCCACACAG	0.597													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		17960	0.001		0.2396	False		,,,				2504	0.0613				p.D554D		Atlas-SNP	.											.	.	.	.	0			c.T1662C						PASS	.	C		201,4205	806.3+/-415.8	5,191,2007	49.0	48.0	48.0		1662	-9.4	0.0	17	dbSNP_120	48	1926,6674	725.4+/-406.5	221,1484,2595	no	coding-synonymous	IMP5	NM_175882.2		226,1675,4602	CC,CT,TT		22.3953,4.562,16.354		554/685	43923934	2127,10879	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			AGCAGATGCCCAC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1662T>C	17.37:g.43923934T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			T|0.854;C|0.146	0.146	strong		0.597	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
CSNK2A3	283106	hgsc.bcm.edu	37	11	11374269	11374269	+	Missense_Mutation	SNP	A	A	G	rs2071460	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:11374269A>G	ENST00000528848.2	-	1	635	c.398T>C	c.(397-399)aTt>aCt	p.I133T	GALNT18_ENST00000227756.4_Intron|RP11-567I13.1_ENST00000526867.1_RNA	NM_001256686.1	NP_001243615.1	Q8NEV1	CSK23_HUMAN	casein kinase 2, alpha 3 polypeptide	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> T (in a lung carcinoma sample; somatic mutation; shows greater kinase activity, provides a cell growth advantage and increases its interaction with the PML tumor suppressor protein and PML degradation). {ECO:0000269|PubMed:20625391}.		positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)										GTAAAATCGAATATCATAGTC	0.408													-|||	2106	0.420527	0.1906	0.4553	5008	,	,		19710	0.5248		0.4791	False		,,,				2504	0.5389				p.I133T		Atlas-SNP	.											.	.	.	.	0			c.T398C						PASS	.																																			SO:0001583	missense	283106	exon1			AATCGAATATCAT	X64692	CCDS59224.1	11p15.3	2013-01-18	2013-01-17	2013-01-17	ENSG00000254598	ENSG00000254598			2458	protein-coding gene	gene with protein product			"""casein kinase 2, alpha 1 polypeptide pseudogene"""	CSNK2A1P		12102635, 1610905, 20625391	Standard	NM_001256686		Approved		uc001mjp.4	Q8NEV1	OTTHUMG00000165708	ENST00000528848.2:c.398T>C	11.37:g.11374269A>G	ENSP00000473553:p.Ile133Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_001256686		Missense_Mutation	SNP	ENST00000528848.2	37	CCDS59224.1																																																																																			A|0.875;G|0.125	0.125	weak		0.408	CSNK2A3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385850.3	NM_001256686	
CARD8	22900	hgsc.bcm.edu	37	19	48737764	48737764	+	5'UTR	SNP	A	A	G	rs2288876	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48737764A>G	ENST00000359009.4	-	0	284				CARD8_ENST00000391898.3_Silent_p.L82L|CARD8_ENST00000520753.1_Silent_p.L82L|CARD8_ENST00000447740.2_Silent_p.L32L|CARD8_ENST00000520153.1_Silent_p.L32L|CARD8_ENST00000520015.1_Silent_p.L82L|CARD8_ENST00000357778.5_5'UTR|CARD8_ENST00000521613.1_Silent_p.L32L|CARD8_ENST00000519940.1_Silent_p.L82L|ZNF114_ENST00000597695.1_Intron			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		AGATGTCACAAAGGGTCTCAG	0.438													A|||	1349	0.269369	0.1959	0.3674	5008	,	,		19111	0.1944		0.2932	False		,,,				2504	0.3517				p.L82L		Atlas-SNP	.											.	CARD8	53	.	0			c.T246C						PASS	.	A	,,,,	953,3453	357.1+/-313.8	98,757,1348	99.0	83.0	88.0		246,96,246,246,96	-0.1	0.0	19	dbSNP_100	88	2819,5781	442.7+/-360.2	486,1847,1967	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	,,,,	584,2604,3315	GG,GA,AA		32.7791,21.6296,29.002	,,,,	82/538,32/488,82/393,82/393,32/488	48737764	3772,9234	2203	4300	6503	SO:0001623	5_prime_UTR_variant	22900	exon3			GTCACAAAGGGTC	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.-29T>C	19.37:g.48737764A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Silent	SNP	ENST00000359009.4	37																																																																																				A|0.758;G|0.242	0.242	strong		0.438	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
LCAT	3931	hgsc.bcm.edu	37	16	67976320	67976320	+	Missense_Mutation	SNP	A	A	T	rs4986970	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:67976320A>T	ENST00000264005.5	-	5	723	c.694T>A	c.(694-696)Tct>Act	p.S232T	CTC-479C5.17_ENST00000590594.1_lincRNA	NM_000229.1	NP_000220.1	P04180	LCAT_HUMAN	lecithin-cholesterol acyltransferase	232			S -> T (in dbSNP:rs4986970). {ECO:0000269|PubMed:12957688, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:16874701}.		cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|high-density lipoprotein particle remodeling (GO:0034375)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein metabolic process (GO:0042157)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of high-density lipoprotein particle assembly (GO:0090107)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	apolipoprotein A-I binding (GO:0034186)|phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607)			cervix(4)|endometrium(4)|large_intestine(1)|lung(6)|ovary(1)	16		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00418)|Epithelial(162;0.0183)|all cancers(182;0.12)		GCCCCAAGAGAGATGAAGCCA	0.582													A|||	42	0.00838658	0.0015	0.0072	5008	,	,		19113	0.0		0.0268	False		,,,				2504	0.0082				p.S232T		Atlas-SNP	.											.	LCAT	31	.	0			c.T694A						PASS	.	A	THR/SER	29,4367	35.2+/-66.4	0,29,2169	58.0	63.0	61.0		694	3.8	1.0	16	dbSNP_111	61	263,8337	102.1+/-163.3	3,257,4040	yes	missense	LCAT	NM_000229.1	58	3,286,6209	TT,TA,AA		3.0581,0.6597,2.2468	possibly-damaging	232/441	67976320	292,12704	2198	4300	6498	SO:0001583	missense	3931	exon5			CAAGAGAGATGAA		CCDS10854.1	16q22.1	2012-10-02			ENSG00000213398	ENSG00000213398	2.3.1.43		6522	protein-coding gene	gene with protein product		606967					Standard	NM_000229		Approved		uc002euy.1	P04180	OTTHUMG00000137551	ENST00000264005.5:c.694T>A	16.37:g.67976320A>T	ENSP00000264005:p.Ser232Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_000229	Q53XQ3	Missense_Mutation	SNP	ENST00000264005.5	37	CCDS10854.1	25	0.011446886446886446	0	0.0	0	0.0	0	0.0	25	0.032981530343007916	A	15.28	2.786126	0.49997	0.006597	0.030581	ENSG00000213398	ENST00000264005	D	0.94897	-3.55	4.99	3.84	0.44239	.	0.068697	0.64402	U	0.000013	D	0.85071	0.5613	L	0.49699	1.58	0.44316	D	0.997195	D	0.56746	0.977	P	0.51453	0.67	D	0.85493	0.1186	10	0.32370	T	0.25	-15.1565	10.2821	0.43545	0.8354:0.1646:0.0:0.0	rs4986970;rs17687753;rs52824740;rs4986970	232	P04180	LCAT_HUMAN	T	232	ENSP00000264005:S232T	ENSP00000264005:S232T	S	-	1	0	LCAT	66533821	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.785000	0.68998	2.094000	0.63399	0.459000	0.35465	TCT	A|0.983;T|0.017	0.017	strong		0.582	LCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268885.3		
OR2L2	26246	hgsc.bcm.edu	37	1	248202344	248202344	+	Missense_Mutation	SNP	G	G	C	rs6658141	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248202344G>C	ENST00000366479.2	+	1	871	c.775G>C	c.(775-777)Gta>Cta	p.V259L	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	259			V -> L (in dbSNP:rs6658141).			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)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	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)			TTATACCTATGTACGTCCAAG	0.507													N|||	1728	0.345048	0.7799	0.1484	5008	,	,		20898	0.3036		0.1551	False		,,,				2504	0.135				p.V259L		Atlas-SNP	.											.	OR2L2	115	.	0			c.G775C						PASS	.	C	LEU/VAL,	3005,1401		1027,951,225	157.0	141.0	146.0		775,	1.9	0.0	1	dbSNP_116	146	1249,7351		91,1067,3142	no	missense,intron	OR2L2,OR2L13	NM_001004686.2,NM_175911.2	32,	1118,2018,3367	CC,CG,GG		14.5233,31.7975,32.708	benign,	259/313,	248202344	4254,8752	2203	4300	6503	SO:0001583	missense	26246	exon1			ACCTATGTACGTC	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"""GPCR / Class A : Olfactory receptors"""	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.775G>C	1.37:g.248202344G>C	ENSP00000355435:p.Val259Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	751	0.34386446886446886	381	0.774390243902439	58	0.16022099447513813	201	0.3513986013986014	111	0.14643799472295516	.	0.161	-1.081535	0.01888	0.682025	0.145233	ENSG00000203663	ENST00000366479	T	0.33654	1.4	1.9	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.000000	0.26055	N	0.026610	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32771	-0.9894	8	0.12103	T	0.63	.	3.3465	0.07137	0.0:0.5:0.2296:0.2703	rs6658141;rs6658141	259	Q8NH16	OR2L2_HUMAN	L	259	ENSP00000355435:V259L	ENSP00000355435:V259L	V	+	1	0	OR2L2	246268967	0.000000	0.05858	0.007000	0.13788	0.132000	0.20833	-3.472000	0.00459	0.046000	0.15833	-1.041000	0.02371	GTA	G|0.650;C|0.350	0.350	strong		0.507	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686	
MUC5B	727897	hgsc.bcm.edu	37	11	1264940	1264940	+	Missense_Mutation	SNP	C	C	G	rs71469858		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1264940C>G	ENST00000529681.1	+	31	6888	c.6830C>G	c.(6829-6831)aCg>aGg	p.T2277R	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T2280R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2277	7 X Cys-rich subdomain repeats.|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)		GGCCACACCACGGCCACCTCC	0.682																																					p.T2277R		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C6830G						scavenged	.						100.0	138.0	126.0					11																	1264940		2139	4228	6367	SO:0001583	missense	727897	exon31			ACACCACGGCCAC	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.6830C>G	11.37:g.1264940C>G	ENSP00000436812:p.Thr2277Arg	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	298	16	0.0536913	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	12.50	1.958043	0.34565	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.28895	1.59;1.79	2.99	-0.755	0.11061	.	.	.	.	.	T	0.30665	0.0772	L	0.50333	1.59	0.09310	N	1	B;B	0.25390	0.125;0.125	B;B	0.30179	0.064;0.112	T	0.43893	-0.9363	9	0.87932	D	0	.	13.3415	0.60547	0.0:0.5468:0.4532:0.0	.	2915;2280	A7Y9J9;E9PBJ0	.;.	R	2277;2280;2278;2292	ENSP00000436812:T2277R;ENSP00000415793:T2280R	ENSP00000343037:T2278R	T	+	2	0	MUC5B	1221516	0.000000	0.05858	0.001000	0.08648	0.188000	0.23474	-0.839000	0.04368	0.081000	0.16988	0.305000	0.20034	ACG	C|0.500;G|0.500	0.500	weak		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
RALGDS	5900	hgsc.bcm.edu	37	9	135985796	135985796	+	Silent	SNP	C	C	T	rs3761824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135985796C>T	ENST00000372050.3	-	3	396	c.375G>A	c.(373-375)gtG>gtA	p.V125V	RALGDS_ENST00000372062.3_Silent_p.V108V|RALGDS_ENST00000469972.1_5'Flank|RALGDS_ENST00000393160.3_Silent_p.V70V|RALGDS_ENST00000372047.3_Silent_p.V125V|RALGDS_ENST00000393157.3_Silent_p.V124V|RALGDS_ENST00000542690.1_Silent_p.V196V	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	125	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		CCAGGTGCTCCACCAGCTTCT	0.592			T	CIITA	"""PMBL, Hodgkin Lymphona, """								C|||	1245	0.248602	0.1278	0.2161	5008	,	,		18066	0.3204		0.2704	False		,,,				2504	0.3384				p.V125V	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.G375A						PASS	.	C	,	687,3717	288.1+/-279.7	48,591,1563	93.0	81.0	85.0		210,375	4.1	1.0	9	dbSNP_107	85	2649,5951	427.2+/-355.5	405,1839,2056	no	coding-synonymous,coding-synonymous	RALGDS	NM_001042368.1,NM_006266.2	,	453,2430,3619	TT,TC,CC		30.8023,15.5995,25.6536	,	70/860,125/915	135985796	3336,9668	2202	4300	6502	SO:0001819	synonymous_variant	5900	exon3			GTGCTCCACCAGC	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.375G>A	9.37:g.135985796C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																			C|0.754;T|0.246	0.246	strong		0.592	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
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 GAIIx	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-TK_ENST00000387421.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank			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*	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	ENST00000362079	Q14Y83	Silent	SNP	ENST00000362079.2	37																																																																																				.	.	none		0.383	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
GNPAT	8443	hgsc.bcm.edu	37	1	231376806	231376806	+	5'Flank	SNP	G	G	C	rs2274067	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:231376806G>C	ENST00000366647.4	+	0	0				C1orf131_ENST00000366651.3_Missense_Mutation_p.L28V|C1orf131_ENST00000471936.1_5'UTR|C1orf131_ENST00000318906.2_Missense_Mutation_p.L28V|C1orf131_ENST00000366649.2_Missense_Mutation_p.L28V|GNPAT_ENST00000366646.3_5'Flank	NM_014236.3	NP_055051.1	O15228	GNPAT_HUMAN	glyceronephosphate O-acyltransferase						cellular lipid metabolic process (GO:0044255)|cerebellum morphogenesis (GO:0021587)|ether lipid biosynthetic process (GO:0008611)|glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|paranodal junction assembly (GO:0030913)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to fatty acid (GO:0070542)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)|synapse assembly (GO:0007416)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	glycerone-phosphate O-acyltransferase activity (GO:0016287)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	23	Breast(184;0.0871)	all_cancers(173;0.2)|Prostate(94;0.183)				GCGTCAAGAAGTGTCGGAGAA	0.607													G|||	441	0.0880591	0.0356	0.2003	5008	,	,		15558	0.0863		0.0616	False		,,,				2504	0.1084				p.L28V		Atlas-SNP	.											.	C1orf131	30	.	0			c.C82G						PASS	.	G	VAL/LEU	210,4196	129.4+/-166.1	4,202,1997	112.0	113.0	113.0		82	3.1	0.0	1	dbSNP_100	113	888,7712	199.7+/-243.7	52,784,3464	yes	missense	C1orf131	NM_152379.2	32	56,986,5461	CC,CG,GG		10.3256,4.7662,8.4423	probably-damaging	28/294	231376806	1098,11908	2203	4300	6503	SO:0001631	upstream_gene_variant	128061	exon1			CAAGAAGTGTCGG	AF043937	CCDS1592.1	1q42	2008-02-05			ENSG00000116906	ENSG00000116906	2.3.1.42		4416	protein-coding gene	gene with protein product		602744				9459311, 9536089	Standard	NM_014236		Approved	DHAPAT, DAPAT, DAP-AT	uc001hup.4	O15228	OTTHUMG00000038024		1.37:g.231376806G>C	Exception_encountered	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_152379	B4DNM9|Q5TBH7|Q9BWC2	Missense_Mutation	SNP	ENST00000366647.4	37	CCDS1592.1	175	0.08012820512820513	31	0.06300813008130081	47	0.1298342541436464	50	0.08741258741258741	47	0.06200527704485488	G	16.78	3.218801	0.58560	0.047662	0.103256	ENSG00000143633	ENST00000366649;ENST00000318906;ENST00000366651;ENST00000366648;ENST00000451322	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.06	3.14	0.36123	.	0.295055	0.27266	N	0.020149	T	0.00328	0.0010	M	0.68952	2.095	0.80722	P	0.0	D;D;D;D;D	0.71674	0.998;0.997;0.998;0.998;0.998	D;D;D;D;D	0.83275	0.996;0.932;0.996;0.996;0.996	T	0.02668	-1.1126	9	0.62326	D	0.03	-13.3122	7.914	0.29808	0.0877:0.1623:0.75:0.0	rs2274067;rs17800413;rs17846596;rs17859678;rs56447138;rs2274067	28;28;28;28;28	B4E0F7;Q8NDD1-4;Q8NDD1;Q8NDD1-3;Q8NDD1-2	.;.;CA131_HUMAN;.;.	V	28;28;28;18;11	ENSP00000355609:L28V;ENSP00000321341:L28V;ENSP00000355611:L28V;ENSP00000401677:L11V	ENSP00000321341:L28V	L	-	1	0	C1orf131	229443429	0.517000	0.26226	0.003000	0.11579	0.012000	0.07955	3.041000	0.49807	0.689000	0.31550	0.650000	0.86243	CTT	G|0.919;C|0.081	0.081	strong		0.607	GNPAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092871.1		
LIPK	643414	hgsc.bcm.edu	37	10	90503075	90503075	+	Silent	SNP	T	T	C	rs390152	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:90503075T>C	ENST00000404190.1	+	8	957	c.957T>C	c.(955-957)caT>caC	p.H319H		NM_001080518.1	NP_001073987.1	Q5VXJ0	LIPK_HUMAN	lipase, family member K	319					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	12		Colorectal(252;0.0381)		Colorectal(12;7.03e-05)|COAD - Colon adenocarcinoma(12;8.33e-05)		TGCACTTCCATCAGGTACAAA	0.363													C|||	1291	0.257788	0.1959	0.2911	5008	,	,		17658	0.3502		0.2207	False		,,,				2504	0.2607				p.H319H		Atlas-SNP	.											LIPK_ENST00000404190,colon,carcinoma,0,2	LIPK	50	2	0			c.T957C						scavenged	.	C		767,2963		81,605,1179	76.0	71.0	72.0		957	-3.8	0.0	10	dbSNP_80	72	1837,6373		244,1349,2512	no	coding-synonymous	LIPK	NM_001080518.1		325,1954,3691	CC,CT,TT		22.3752,20.563,21.809		319/400	90503075	2604,9336	1865	4105	5970	SO:0001819	synonymous_variant	643414	exon8			CTTCCATCAGGTA		CCDS44455.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000204021	ENSG00000204021			23444	protein-coding gene	gene with protein product		613922	"""lipase-like, ab-hydrolase domain containing 2"""	LIPL2			Standard	NM_001080518		Approved	bA186O14.2	uc010qmv.2	Q5VXJ0	OTTHUMG00000018693	ENST00000404190.1:c.957T>C	10.37:g.90503075T>C		Somatic	62	1	0.016129		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_001080518	A7KIH8	Silent	SNP	ENST00000404190.1	37	CCDS44455.1																																																																																			T|0.754;C|0.246	0.246	strong		0.363	LIPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049253.2	XM_061222	
SLC4A9	83697	hgsc.bcm.edu	37	5	139745154	139745154	+	Silent	SNP	T	T	C	rs6860077	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139745154T>C	ENST00000230993.6	+	12	1808	c.1773T>C	c.(1771-1773)atT>atC	p.I591I	SLC4A9_ENST00000507527.1_Silent_p.I591I|SLC4A9_ENST00000506545.1_Silent_p.I567I|SLC4A9_ENST00000432095.2_Splice_Site_p.I556I|SLC4A9_ENST00000506757.2_Silent_p.I567I	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	591	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGACGACATTGTAAGCATGG	0.507													C|||	3553	0.709465	0.5651	0.7493	5008	,	,		22618	0.8353		0.7177	False		,,,				2504	0.7382				p.I591I		Atlas-SNP	.											.	SLC4A9	125	.	0			c.T1773C						PASS	.	C		2435,1519		741,953,283	81.0	88.0	86.0		1701	1.5	0.0	5	dbSNP_116	86	5872,2448		2077,1718,365	no	coding-synonymous	SLC4A9	NM_031467.2		2818,2671,648	CC,CT,TT		29.4231,38.4168,32.3204		567/960	139745154	8307,3967	1977	4160	6137	SO:0001819	synonymous_variant	83697	exon12			CGACATTGTAAGC	AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"""Solute carriers"""	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.1773T>C	5.37:g.139745154T>C		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	242	241	0.995868	NM_001258428	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Silent	SNP	ENST00000230993.6	37	CCDS58973.1																																																																																			T|0.282;C|0.718	0.718	strong		0.507	SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467	
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 GAIIx	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	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	36	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 GAIIx	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_ENST00000375946.4_Silent_p.Q712Q|MASTL_ENST00000477034.1_3'UTR|MASTL_ENST00000342386.6_Silent_p.Q712Q			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		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	66	31	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	
DMGDH	29958	hgsc.bcm.edu	37	5	78324352	78324352	+	Missense_Mutation	SNP	A	A	G	rs1805074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:78324352A>G	ENST00000255189.3	-	12	1964	c.1936T>C	c.(1936-1938)Tct>Cct	p.S646P	DMGDH_ENST00000540686.1_Missense_Mutation_p.S266P|DMGDH_ENST00000380311.4_Missense_Mutation_p.S445P	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	646			S -> P (in dbSNP:rs1805074). {ECO:0000269|PubMed:11231903}.		amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		AGATCTTCAGAGGTCAGTTTC	0.388													A|||	1523	0.304113	0.4917	0.1974	5008	,	,		17388	0.1399		0.2962	False		,,,				2504	0.3037				p.S646P		Atlas-SNP	.											.	DMGDH	88	.	0			c.T1936C						PASS	.	A	PRO/SER	2003,2403	560.9+/-380.6	448,1107,648	163.0	166.0	165.0		1936	2.1	1.0	5	dbSNP_89	165	2466,6134	407.0+/-349.0	377,1712,2211	yes	missense	DMGDH	NM_013391.2	74	825,2819,2859	GG,GA,AA		28.6744,45.4607,34.3611	benign	646/867	78324352	4469,8537	2203	4300	6503	SO:0001583	missense	29958	exon12			CTTCAGAGGTCAG	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1936T>C	5.37:g.78324352A>G	ENSP00000255189:p.Ser646Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	645	0.29532967032967034	260	0.5284552845528455	72	0.19889502762430938	90	0.15734265734265734	223	0.2941952506596306	A	11.97	1.798049	0.31777	0.454607	0.286744	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000540686;ENST00000539598	D;D;D;D	0.82803	-1.65;-1.65;-1.65;-1.65	5.92	2.11	0.27256	Glycine cleavage T-protein, N-terminal (1);	0.630757	0.18152	N	0.150067	T	0.00012	0.0000	L	0.31664	0.95	0.46279	P	0.0010350000000000081	B;B;B;B	0.14805	0.002;0.011;0.0;0.0	B;B;B;B	0.18871	0.023;0.019;0.003;0.002	T	0.41360	-0.9513	9	0.30854	T	0.27	.	1.5466	0.02566	0.344:0.3424:0.1351:0.1784	rs1805074;rs52819841;rs60117353;rs1805074	266;445;496;646	B4E1J9;F8W6P8;F5H1C7;Q9UI17	.;.;.;M2GD_HUMAN	P	646;485;445;266;496	ENSP00000255189:S646P;ENSP00000430972:S485P;ENSP00000369667:S445P;ENSP00000439478:S266P	ENSP00000255189:S646P	S	-	1	0	DMGDH	78360108	0.027000	0.19231	0.991000	0.47740	0.996000	0.88848	0.087000	0.14958	0.121000	0.18284	0.533000	0.62120	TCT	A|0.674;G|0.326	0.326	strong		0.388	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629963	32629963	+	Missense_Mutation	SNP	C	C	T	rs1049100	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32629963C>T	ENST00000399082.3	-	2	216	c.172G>A	c.(172-174)Gtc>Atc	p.V58I	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.V148I|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.V148I|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.V148I|HLA-DQB1-AS1_ENST00000419852.1_RNA|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.V148I			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	148	Beta-1.		Y -> G (in allele DQB1*03:05, allele DQB1*03:17, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05 and allele DQB1*06:23; requires 2 nucleotide substitutions).|Y -> L (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:12, allele DQB1*03:15, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	ACCGAGCAGACCAGCAGGTTG	0.552									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1067	0.213059	0.2284	0.1527	5008	,	,		12092	0.244		0.2008	False		,,,				2504	0.2157				p.V148I	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G442A						PASS	.	C	ILE/VAL	766,3122		97,572,1275	26.0	24.0	25.0		442	3.6	1.0	6	dbSNP_86	25	1351,6891		155,1041,2925	no	missense	HLA-DQB1	NM_002123.4	29	252,1613,4200	TT,TC,CC		16.3917,19.7016,17.4526	benign	148/262	32629963	2117,10013	1944	4121	6065	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AGCAGACCAGCAG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.172G>A	6.37:g.32629963C>T	ENSP00000382032:p.Val58Ile	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		444	0.2032967032967033	119	0.241869918699187	69	0.19060773480662985	90	0.15734265734265734	166	0.21899736147757257	.	13.20	2.166325	0.38217	0.197016	0.163917	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.02974	4.09;4.09;4.09;4.09;4.09	4.52	3.64	0.41730	.	0.322278	0.29653	N	0.011558	T	0.01421	0.0046	L	0.49256	1.55	0.37850	P	0.07064300000000001	B;B;B;B	0.18310	0.006;0.003;0.002;0.027	B;B;B;B	0.24701	0.02;0.02;0.02;0.055	T	0.29243	-1.0018	9	0.87932	D	0	.	6.057	0.19816	0.0:0.7833:0.0:0.2166	rs1049100;rs3189191;rs16870489	148;113;148;148	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	I	58;148;148;148;148;84	ENSP00000382032:V58I;ENSP00000382029:V148I;ENSP00000364080:V148I;ENSP00000407332:V148I;ENSP00000382034:V148I	ENSP00000364080:V148I	V	-	1	0	HLA-DQB1	32737941	0.967000	0.33354	1.000000	0.80357	0.683000	0.39861	0.196000	0.17176	2.065000	0.61736	0.313000	0.20887	GTC	C|0.816;T|0.184	0.184	strong		0.552	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
MAEL	84944	hgsc.bcm.edu	37	1	166958710	166958710	+	Missense_Mutation	SNP	T	T	G	rs11578336	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:166958710T>G	ENST00000367872.4	+	1	365	c.121T>G	c.(121-123)Tca>Gca	p.S41A	MAEL_ENST00000367870.2_Missense_Mutation_p.S41A	NM_032858.1	NP_116247.1	Q96JY0	MAEL_HUMAN	maelstrom spermatogenic transposon silencer	41			S -> A (in dbSNP:rs11578336).		cell differentiation (GO:0030154)|cell morphogenesis (GO:0000902)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|piRNA metabolic process (GO:0034587)|regulation of organ growth (GO:0046620)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	autosome (GO:0030849)|chromatin (GO:0000785)|chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|perinuclear region of cytoplasm (GO:0048471)|piP-body (GO:0071547)|XY body (GO:0001741)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(12)|skin(4)	28						TTACTGCTCCTCAGACTGGGC	0.632													G|||	1245	0.248602	0.3661	0.1513	5008	,	,		14443	0.248		0.2256	False		,,,				2504	0.183				p.S41A		Atlas-SNP	.											MAEL,NS,carcinoma,0,1	MAEL	95	1	0			c.T121G						PASS	.	G	ALA/SER	1568,2832		281,1006,913	35.0	31.0	33.0		121	2.5	0.0	1	dbSNP_120	33	2107,6485		254,1599,2443	yes	missense	MAEL	NM_032858.1	99	535,2605,3356	GG,GT,TT		24.5228,35.6364,28.2866	benign	41/435	166958710	3675,9317	2200	4296	6496	SO:0001583	missense	84944	exon1			TGCTCCTCAGACT	AK027810, DQ076156	CCDS1257.1, CCDS65712.1, CCDS72975.1	1q24.1	2013-10-11	2012-12-18		ENSG00000143194	ENSG00000143194			25929	protein-coding gene	gene with protein product	"""cancer/testis antigen 128"", ""spermatogenesis associated 35"""	611368	"""maelstrom homolog (Drosophila)"""			19693694, 18694567	Standard	NM_001286378		Approved	FLJ14904, CT128, SPATA35	uc001gdy.1	Q96JY0	OTTHUMG00000034432	ENST00000367872.4:c.121T>G	1.37:g.166958710T>G	ENSP00000356846:p.Ser41Ala	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_032858	B4DY43|E9JVC3|Q49AP9|Q5VZP8|Q9UIW6	Missense_Mutation	SNP	ENST00000367872.4	37	CCDS1257.1	556	0.25457875457875456	176	0.35772357723577236	58	0.16022099447513813	159	0.27797202797202797	163	0.21503957783641162	G	0.004	-2.240398	0.00274	0.356364	0.245228	ENSG00000143194	ENST00000367872;ENST00000367870;ENST00000447624	T;T;T	0.40756	1.02;2.53;2.53	5.49	2.46	0.29980	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);Domain of unknown function DUF1898 (1);	0.462954	0.20595	N	0.089278	T	0.04815	0.0130	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37911	-0.9685	9	0.07644	T	0.81	.	9.1724	0.37091	0.0672:0.0:0.5427:0.3901	rs11578336;rs17552415;rs57781349;rs11578336	41;41	E9JVC3;Q96JY0	.;MAEL_HUMAN	A	41	ENSP00000356846:S41A;ENSP00000356844:S41A;ENSP00000402143:S41A	ENSP00000356844:S41A	S	+	1	0	MAEL	165225334	0.000000	0.05858	0.011000	0.14972	0.016000	0.09150	-0.371000	0.07513	0.429000	0.26202	-2.444000	0.00210	TCA	T|0.743;G|0.257	0.257	strong		0.632	MAEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083239.1	NM_032858	
LAMC2	3918	hgsc.bcm.edu	37	1	183206573	183206573	+	Silent	SNP	G	G	A	rs1047981	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:183206573G>A	ENST00000264144.4	+	18	2753	c.2688G>A	c.(2686-2688)caG>caA	p.Q896Q	LAMC2_ENST00000493293.1_Silent_p.Q896Q	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	896	Domain II and I.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						AGCGTACACAGAAGAATCTGG	0.418													A|||	1765	0.352436	0.5401	0.3314	5008	,	,		21193	0.3333		0.1581	False		,,,				2504	0.3333				p.Q896Q		Atlas-SNP	.											LAMC2,NS,carcinoma,+2,1	LAMC2	113	1	0			c.G2688A						scavenged	.	A	,	2198,2208	588.8+/-387.0	573,1052,578	99.0	104.0	102.0		2688,2688	-7.6	0.0	1	dbSNP_86	102	1527,7073	747.3+/-407.3	132,1263,2905	no	coding-synonymous,coding-synonymous	LAMC2	NM_005562.2,NM_018891.2	,	705,2315,3483	AA,AG,GG		17.7558,49.8865,28.6406	,	896/1194,896/1112	183206573	3725,9281	2203	4300	6503	SO:0001819	synonymous_variant	3918	exon18			TACACAGAAGAAT	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.2688G>A	1.37:g.183206573G>A		Somatic	272	2	0.00735294		WXS	Illumina HiSeq	Phase_I	235	121	0.514894	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Silent	SNP	ENST00000264144.4	37	CCDS1352.1																																																																																			G|0.694;A|0.306	0.306	strong		0.418	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
DNMBP	23268	hgsc.bcm.edu	37	10	101645498	101645498	+	Silent	SNP	T	T	C	rs2490763	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101645498T>C	ENST00000324109.4	-	14	3835	c.3744A>G	c.(3742-3744)ccA>ccG	p.P1248P	DNMBP_ENST00000472036.1_5'Flank|DNMBP_ENST00000540316.1_Silent_p.P184P|DNMBP_ENST00000342239.3_Silent_p.P1272P|DNMBP_ENST00000543621.1_Silent_p.P494P	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1248					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		TCCTCTCAAATGGCTTCTTGG	0.542													C|||	2397	0.478634	0.587	0.4827	5008	,	,		16751	0.2698		0.5388	False		,,,				2504	0.4826				p.P1248P		Atlas-SNP	.											.	DNMBP	173	.	0			c.A3744G						PASS	.			2570,1836		765,1040,398	33.0	29.0	30.0		3744	-10.9	0.0	10	dbSNP_100	30	4502,4098		1188,2126,986	no	coding-synonymous	DNMBP	NM_015221.2		1953,3166,1384	CC,CT,TT		47.6512,41.6704,45.6251		1248/1578	101645498	7072,5934	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon14			CTCAAATGGCTTC	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.3744A>G	10.37:g.101645498T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	142	140	0.985915	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			T|0.492;C|0.508	0.508	strong		0.542	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
TSR1	55720	hgsc.bcm.edu	37	17	2238675	2238675	+	Silent	SNP	A	A	G	rs61743762	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2238675A>G	ENST00000301364.5	-	4	1514	c.435T>C	c.(433-435)gtT>gtC	p.V145V	SGSM2_ENST00000574563.1_5'Flank|TSR1_ENST00000576112.2_Silent_p.V145V|SGSM2_ENST00000268989.3_5'Flank|SGSM2_ENST00000426855.2_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	145	Bms1-type G.				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						TGTCTAACACAACGTGCAGAT	0.433													A|||	56	0.0111821	0.0023	0.0346	5008	,	,		18399	0.0		0.0249	False		,,,				2504	0.0041				p.V145V		Atlas-SNP	.											.	TSR1	57	.	0			c.T435C						PASS	.	A		23,4383	30.8+/-60.4	0,23,2180	99.0	87.0	91.0		435	-1.0	0.9	17	dbSNP_129	91	339,8261	116.5+/-176.2	5,329,3966	no	coding-synonymous	TSR1	NM_018128.4		5,352,6146	GG,GA,AA		3.9419,0.522,2.7833		145/805	2238675	362,12644	2203	4300	6503	SO:0001819	synonymous_variant	55720	exon4			TAACACAACGTGC	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.435T>C	17.37:g.2238675A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Silent	SNP	ENST00000301364.5	37	CCDS32525.1																																																																																			A|0.974;G|0.026	0.026	strong		0.433	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128	
SETX	23064	hgsc.bcm.edu	37	9	135205006	135205006	+	Missense_Mutation	SNP	G	G	C	rs882709	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135205006G>C	ENST00000224140.5	-	10	2161	c.1979C>G	c.(1978-1980)gCa>gGa	p.A660G	SETX_ENST00000372169.2_Missense_Mutation_p.A660G|SETX_ENST00000393220.1_Missense_Mutation_p.A660G	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	660			A -> G (in dbSNP:rs882709).		cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		AGTGTTATCTGCTTTGATCAA	0.378													G|||	1070	0.213658	0.2738	0.0908	5008	,	,		21088	0.4117		0.0606	False		,,,				2504	0.1728				p.A660G		Atlas-SNP	.											.	SETX	234	.	0			c.C1979G						PASS	.	G	GLY/ALA	982,3424	369.1+/-318.9	113,756,1334	97.0	93.0	95.0		1979	2.1	0.0	9	dbSNP_86	95	498,8100	143.4+/-199.5	16,466,3817	yes	missense	SETX	NM_015046.5	60	129,1222,5151	CC,CG,GG		5.792,22.2878,11.3811	benign	660/2678	135205006	1480,11524	2203	4299	6502	SO:0001583	missense	23064	exon10			TTATCTGCTTTGA	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.1979C>G	9.37:g.135205006G>C	ENSP00000224140:p.Ala660Gly	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	117	35	0.299145	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	458	0.2097069597069597	131	0.266260162601626	34	0.09392265193370165	243	0.42482517482517484	50	0.06596306068601583	G	11.41	1.629456	0.28978	0.222878	0.05792	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.87571	-2.18;-2.27;-1.88	5.37	2.12	0.27331	.	1.813340	0.03700	U	0.248429	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P;B;P	0.40731	0.728;0.421;0.728	B;B;B	0.41764	0.366;0.154;0.366	T	0.04153	-1.0973	9	0.35671	T	0.21	.	6.9477	0.24528	0.1947:0.1851:0.6202:0.0	rs882709;rs60311424;rs882709	660;660;660	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	G	660	ENSP00000224140:A660G;ENSP00000361242:A660G;ENSP00000376913:A660G	ENSP00000224140:A660G	A	-	2	0	SETX	134194827	0.001000	0.12720	0.003000	0.11579	0.048000	0.14542	0.949000	0.29109	0.575000	0.29434	0.555000	0.69702	GCA	G|0.828;C|0.172	0.172	strong		0.378	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
SLC7A4	6545	hgsc.bcm.edu	37	22	21385843	21385843	+	Silent	SNP	G	G	A	rs2072549	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:21385843G>A	ENST00000382932.2	-	2	326	c.259C>T	c.(259-261)Cta>Tta	p.L87L	MIR649_ENST00000384843.1_RNA|SLC7A4_ENST00000403586.1_Silent_p.L87L|AC002472.11_ENST00000450652.1_RNA	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	87					basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GCATAGCATAGGGCTGCCAGC	0.637													G|||	1045	0.208666	0.1566	0.2853	5008	,	,		17782	0.3294		0.2097	False		,,,				2504	0.0992				p.L87L		Atlas-SNP	.											.	SLC7A4	50	.	0			c.C259T						PASS	.	G		759,3647	304.6+/-288.6	63,633,1507	66.0	49.0	55.0		259	5.4	0.6	22	dbSNP_96	55	1693,6907	305.3+/-307.4	174,1345,2781	no	coding-synonymous	SLC7A4	NM_004173.2		237,1978,4288	AA,AG,GG		19.686,17.2265,18.8528		87/636	21385843	2452,10554	2203	4300	6503	SO:0001819	synonymous_variant	6545	exon2			AGCATAGGGCTGC	AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"""Solute carriers"""	11062	protein-coding gene	gene with protein product		603752	"""solute carrier family 7 (cationic amino acid transporter, y+ system), member 4"", ""solute carrier family 7 (orphan transporter), member 4"""			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.259C>T	22.37:g.21385843G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Silent	SNP	ENST00000382932.2	37	CCDS33608.1																																																																																			G|0.789;A|0.211	0.211	strong		0.637	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173	
BCL10	8915	hgsc.bcm.edu	37	1	85742012	85742012	+	Silent	SNP	G	G	C	rs11576939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:85742012G>C	ENST00000370580.1	-	1	761	c.24C>G	c.(22-24)ctC>ctG	p.L8L	RP11-131L23.1_ENST00000427819.1_RNA|RP11-131L23.1_ENST00000426125.1_RNA	NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	8					adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		CCTCCTCGGTGAGGGACGGTG	0.716			T	IGH@	MALT								G|||	1143	0.228235	0.2663	0.2032	5008	,	,		15363	0.0744		0.3111	False		,,,				2504	0.2679				p.L8L	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.C24G	GRCh37	CM062460	BCL10	M	rs11576939	PASS	.	G		1093,3313	394.7+/-329.4	144,805,1254	66.0	60.0	62.0		24	2.2	1.0	1	dbSNP_120	62	2637,5963	422.6+/-354.1	399,1839,2062	no	coding-synonymous	BCL10	NM_003921.4		543,2644,3316	CC,CG,GG		30.6628,24.8071,28.6791		8/234	85742012	3730,9276	2203	4300	6503	SO:0001819	synonymous_variant	8915	exon1			CTCGGTGAGGGAC	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.24C>G	1.37:g.85742012G>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_003921	Q5VUF1	Silent	SNP	ENST00000370580.1	37	CCDS704.1																																																																																			G|0.735;C|0.265	0.265	strong		0.716	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
MMP20	9313	hgsc.bcm.edu	37	11	102477377	102477377	+	Missense_Mutation	SNP	G	G	T	rs1784424	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:102477377G>T	ENST00000260228.2	-	6	854	c.842C>A	c.(841-843)aCt>aAt	p.T281N	MMP20_ENST00000544938.1_5'UTR|RP11-817J15.2_ENST00000542119.1_RNA|RP11-817J15.2_ENST00000544115.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	300					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ATGGGGCAGAGTGGGCTTCCC	0.532													G|||	2103	0.419928	0.2625	0.4424	5008	,	,		20032	0.4325		0.4364	False		,,,				2504	0.5869				p.T281N		Atlas-SNP	.											.	MMP20	52	.	0			c.C842A						PASS	.	G	ASN/THR	1360,3046	451.8+/-349.8	204,952,1047	113.0	109.0	110.0		842	2.3	0.2	11	dbSNP_89	110	3926,4672	547.7+/-385.2	867,2192,1240	yes	missense	MMP20	NM_004771.3	65	1071,3144,2287	TT,TG,GG		45.6618,30.867,40.649	benign	281/484	102477377	5286,7718	2203	4299	6502	SO:0001583	missense	9313	exon6			GGCAGAGTGGGCT	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.842C>A	11.37:g.102477377G>T	ENSP00000260228:p.Thr281Asn	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	131	21	0.160305	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	876	0.4010989010989011	129	0.2621951219512195	170	0.4696132596685083	248	0.43356643356643354	329	0.4340369393139842	G	0.027	-1.362562	0.01235	0.30867	0.456618	ENSG00000137674	ENST00000260228	T	0.14516	2.5	5.45	2.3	0.28687	.	0.506134	0.22203	N	0.063204	T	0.00012	0.0000	L	0.34521	1.04	0.53688	P	2.599999999997049E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46317	-0.9200	9	0.16420	T	0.52	.	8.1778	0.31292	0.1424:0.0:0.6217:0.2359	rs1784424;rs52816330;rs1784424	281	O60882	MMP20_HUMAN	N	281	ENSP00000260228:T281N	ENSP00000260228:T281N	T	-	2	0	MMP20	101982587	0.576000	0.26700	0.164000	0.22755	0.001000	0.01503	0.646000	0.24797	0.417000	0.25871	-0.813000	0.03139	ACT	G|0.598;T|0.402	0.402	strong		0.532	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
HTT	3064	hgsc.bcm.edu	37	4	3215835	3215835	+	Missense_Mutation	SNP	T	T	C	rs362331	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:3215835T>C	ENST00000355072.5	+	50	7070	c.6925T>C	c.(6925-6927)Tac>Cac	p.Y2309H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2309			Y -> H (in dbSNP:rs362331).		anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CTCCCTCATCTACTGTGTGCA	0.582													C|||	2210	0.441294	0.5862	0.4294	5008	,	,		19331	0.3859		0.4334	False		,,,				2504	0.319				p.Y2309H		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	1	0			c.T6925C						PASS	.	C	HIS/TYR	2355,1813		681,993,410	34.0	38.0	36.0		6925	5.7	1.0	4	dbSNP_79	36	3533,4873		764,2005,1434	yes	missense	HTT	NM_002111.6	83	1445,2998,1844	CC,CT,TT		42.0295,43.4981,46.8268	benign	2309/3143	3215835	5888,6686	2084	4203	6287	SO:0001583	missense	3064	exon50			CTCATCTACTGTG	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.6925T>C	4.37:g.3215835T>C	ENSP00000347184:p.Tyr2309His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	66	23	0.348485	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	995	0.4555860805860806	281	0.5711382113821138	161	0.4447513812154696	220	0.38461538461538464	333	0.4393139841688654	C	9.562	1.118641	0.20877	0.565019	0.420295	ENSG00000197386	ENST00000355072	T	0.04603	3.59	5.7	5.7	0.88788	.	0.117131	0.64402	N	0.000015	T	0.00012	0.0000	N	0.00583	-1.355	0.47065	P	6.969999999999477E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.21518	-1.0243	9	0.13853	T	0.58	.	8.2136	0.31499	0.2523:0.6699:0.0:0.0778	rs362331;rs878244;rs2229983;rs3821970;rs17793687;rs52791365;rs58994081;rs362331	2309	P42858	HD_HUMAN	H	2309	ENSP00000347184:Y2309H	ENSP00000347184:Y2309H	Y	+	1	0	HTT	3185633	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.175000	0.50855	1.427000	0.47276	-0.119000	0.15052	TAC	C|0.453;N|0.000	0.453	strong		0.582	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
MAN2A2	4122	hgsc.bcm.edu	37	15	91459475	91459475	+	Missense_Mutation	SNP	G	G	A	rs12909056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:91459475G>A	ENST00000559717.1	+	20	3442	c.2983G>A	c.(2983-2985)Gtg>Atg	p.V995M	MAN2A2_ENST00000431652.2_Missense_Mutation_p.V503M|MAN2A2_ENST00000558538.1_3'UTR|MAN2A2_ENST00000430376.2_Missense_Mutation_p.V185M|MAN2A2_ENST00000360468.3_Missense_Mutation_p.V995M			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	995					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GCGGCGAACCGTGGGCAGTGA	0.662													G|||	694	0.138578	0.3139	0.0548	5008	,	,		17889	0.0		0.0785	False		,,,				2504	0.1656				p.V995M		Atlas-SNP	.											.	MAN2A2	99	.	0			c.G2983A						PASS	.	G	MET/VAL	1244,3152	427.6+/-341.6	156,932,1110	77.0	74.0	75.0		2983	-8.3	0.0	15	dbSNP_121	75	707,7889	174.8+/-225.0	32,643,3623	yes	missense	MAN2A2	NM_006122.2	21	188,1575,4733	AA,AG,GG		8.2248,28.2985,15.0169	benign	995/1151	91459475	1951,11041	2198	4298	6496	SO:0001583	missense	4122	exon19			CGAACCGTGGGCA	L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.2983G>A	15.37:g.91459475G>A	ENSP00000452948:p.Val995Met	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_006122	A6NH12|A8K1E8|Q13754	Missense_Mutation	SNP	ENST00000559717.1	37	CCDS32332.1	243	0.11126373626373626	164	0.3333333333333333	20	0.055248618784530384	0	0.0	59	0.07783641160949868	G	10.16	1.272704	0.23221	0.282985	0.082248	ENSG00000196547	ENST00000360468;ENST00000431652;ENST00000430376	T;T;T	0.81078	-1.45;-1.45;-1.45	4.95	-8.26	0.01021	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	2.325910	0.02126	N	0.056002	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.21309	0.054;0.001;0.001	B;B;B	0.20184	0.028;0.017;0.01	T	0.04203	-1.0969	9	0.54805	T	0.06	0.6357	0.1226	0.00066	0.3297:0.1887:0.1754:0.3062	rs12909056;rs59142436;rs12909056	503;623;995	B4DEU9;B4DIK4;P49641	.;.;MA2A2_HUMAN	M	995;503;185	ENSP00000353655:V995M;ENSP00000388221:V503M;ENSP00000394372:V185M	ENSP00000353655:V995M	V	+	1	0	MAN2A2	89260479	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.904000	0.04080	-1.207000	0.02637	-1.894000	0.00533	GTG	G|0.859;A|0.141	0.141	strong		0.662	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122	
PDILT	204474	hgsc.bcm.edu	37	16	20410547	20410547	+	Missense_Mutation	SNP	C	C	T	rs9926580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20410547C>T	ENST00000302451.4	-	2	324	c.76G>A	c.(76-78)Gcc>Acc	p.A26T		NM_174924.1	NP_777584.1	Q8N807	PDILT_HUMAN	protein disulfide isomerase-like, testis expressed	26			A -> T (in dbSNP:rs9926580).		cell migration (GO:0016477)|cell redox homeostasis (GO:0045454)|multicellular organismal development (GO:0007275)|protein folding (GO:0006457)|spermatid development (GO:0007286)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|liver(1)|lung(33)|prostate(3)|skin(1)|urinary_tract(1)	61						GAAACACCGGCGTTAACCTCT	0.602													C|||	1712	0.341853	0.4637	0.3876	5008	,	,		18196	0.1508		0.3091	False		,,,				2504	0.3753				p.A26T		Atlas-SNP	.											.	PDILT	120	.	0			c.G76A						PASS	.	C	THR/ALA	1871,2535	540.4+/-375.5	373,1125,705	142.0	129.0	133.0		76	-2.3	0.0	16	dbSNP_119	133	2463,6137	405.5+/-348.5	325,1813,2162	yes	missense	PDILT	NM_174924.1	58	698,2938,2867	TT,TC,CC		28.6395,42.4648,33.3231	benign	26/585	20410547	4334,8672	2203	4300	6503	SO:0001583	missense	204474	exon2			CACCGGCGTTAAC		CCDS10584.1	16p12.3	2011-11-10	2009-02-23		ENSG00000169340	ENSG00000169340		"""Protein disulfide isomerases"""	27338	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 7"", ""protein disulfide isomerase-like protein of the testis"""					15475357	Standard	NM_174924		Approved	PDIA7	uc002dhc.1	Q8N807	OTTHUMG00000131487	ENST00000302451.4:c.76G>A	16.37:g.20410547C>T	ENSP00000305465:p.Ala26Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_174924	Q8IVQ5	Missense_Mutation	SNP	ENST00000302451.4	37	CCDS10584.1	677	0.309981684981685	211	0.42886178861788615	143	0.39502762430939226	90	0.15734265734265734	233	0.3073878627968338	C	5.611	0.297465	0.10622	0.424648	0.286395	ENSG00000169340	ENST00000302451	T	0.03004	4.08	3.62	-2.28	0.06826	.	1.496790	0.04333	N	0.352700	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.44757	-0.9307	9	0.11182	T	0.66	.	3.8175	0.08821	0.4809:0.3247:0.0:0.1944	rs9926580;rs9926580	26	Q8N807	PDILT_HUMAN	T	26	ENSP00000305465:A26T	ENSP00000305465:A26T	A	-	1	0	PDILT	20318048	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.759000	0.00100	-0.397000	0.07691	-0.469000	0.05056	GCC	C|0.673;T|0.327	0.327	strong		0.602	PDILT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254332.1	NM_174924	
ERCC6	2074	hgsc.bcm.edu	37	10	50740876	50740876	+	Silent	SNP	G	G	C	rs2228524	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50740876G>C	ENST00000355832.5	-	2	213	c.135C>G	c.(133-135)ctC>ctG	p.L45L	ERCC6-PGBD3_ENST00000515869.1_Silent_p.L45L|PGBD3_ENST00000603152.1_Silent_p.L45L|ERCC6-PGBD3_ENST00000447839.2_Silent_p.L45L	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	45					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AACGAAAGGAGAGGTACTCCT	0.552								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	2959	0.590855	0.3336	0.6657	5008	,	,		19189	0.5079		0.7346	False		,,,				2504	0.8231				p.T45T		Atlas-SNP	.											.	ERCC6	162	.	0			c.G135G						PASS	.	C		1782,2624	643.7+/-397.9	374,1034,795	153.0	130.0	138.0		135	-1.4	0.0	10	dbSNP_98	138	6380,2220	377.4+/-338.5	2379,1622,299	no	coding-synonymous	ERCC6	NM_000124.2		2753,2656,1094	CC,CG,GG		25.814,40.4448,37.2443		45/1494	50740876	8162,4844	2203	4300	6503	SO:0001819	synonymous_variant	2074	exon2			AAAGGAGAGGTAC	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.135C>G	10.37:g.50740876G>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			G|0.381;C|0.619	0.619	strong		0.552	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
ZSCAN12	9753	hgsc.bcm.edu	37	6	28366151	28366151	+	Missense_Mutation	SNP	A	A	G	rs2232423	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:28366151A>G	ENST00000361028.1	-	2	177	c.32T>C	c.(31-33)aTg>aCg	p.M11T	ZSCAN12_ENST00000396827.3_Missense_Mutation_p.M11T			O43309	ZSC12_HUMAN	zinc finger and SCAN domain containing 12	11					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(2)|endometrium(3)|urinary_tract(1)	6						ATCCTGGTCCATGTGGGCCTG	0.468													A|||	116	0.0231629	0.0242	0.0216	5008	,	,		18098	0.0		0.0686	False		,,,				2504	0.0				p.M11T		Atlas-SNP	.											.	ZSCAN12	35	.	0			c.T32C						PASS	.	A	THR/MET	58,1326		2,54,636	184.0	161.0	168.0		32	-0.9	0.0	6	dbSNP_98	168	306,2876		11,284,1296	yes	missense	ZSCAN12	NM_001163391.1	81	13,338,1932	GG,GA,AA		9.6166,4.1908,7.972	benign	11/612	28366151	364,4202	692	1591	2283	SO:0001583	missense	9753	exon2			TGGTCCATGTGGG	AB007886		6p21	2013-01-08	2007-02-20	2007-02-20	ENSG00000158691	ENSG00000158691		"""-"", ""Zinc fingers, C2H2-type"""	13172	protein-coding gene	gene with protein product		603978	"""zinc finger protein 305"", ""zinc finger protein 96"""	ZNF305, ZNF96		9244436	Standard	NM_001163391		Approved	KIAA0426, ZNF29K1, ZFP96, dJ29K1.2	uc011dlh.2	O43309	OTTHUMG00000014522	ENST00000361028.1:c.32T>C	6.37:g.28366151A>G	ENSP00000354305:p.Met11Thr	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	208	158	0.759615	NM_001163391	O43724	Missense_Mutation	SNP	ENST00000361028.1	37		76	0.0347985347985348	11	0.022357723577235773	8	0.022099447513812154	0	0.0	57	0.07519788918205805	A	3.426	-0.117064	0.06838	0.041908	0.096166	ENSG00000158691	ENST00000361028;ENST00000396827	T;T	0.06068	3.35;3.35	3.26	-0.902	0.10537	.	0.992491	0.08160	N	0.988573	T	0.00754	0.0025	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48896	-0.8994	10	0.27785	T	0.31	.	0.7463	0.00982	0.2025:0.1214:0.1994:0.4767	rs2232423;rs52816048;rs2232423	11;11	A8K187;O43309	.;ZSC12_HUMAN	T	11	ENSP00000354305:M11T;ENSP00000380039:M11T	ENSP00000354305:M11T	M	-	2	0	ZSCAN12	28474130	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.260000	0.02858	-0.281000	0.09141	-0.418000	0.06021	ATG	A|0.959;G|0.041	0.041	strong		0.468	ZSCAN12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040190.1	NM_014724	
NCKAP5	344148	hgsc.bcm.edu	37	2	133489601	133489601	+	Silent	SNP	A	A	G	rs56284623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:133489601A>G	ENST00000409261.1	-	17	5525	c.5152T>C	c.(5152-5154)Ttg>Ctg	p.L1718L	NCKAP5_ENST00000409213.1_Silent_p.L399L|NCKAP5_ENST00000473859.1_5'UTR|NCKAP5_ENST00000405974.3_Silent_p.L399L|NCKAP5_ENST00000317721.6_Silent_p.L1718L	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1718										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						CCACTGTCCAATGTTCTCATC	0.502													A|||	784	0.15655	0.0492	0.1499	5008	,	,		19816	0.1002		0.2634	False		,,,				2504	0.2546				p.L1718L		Atlas-SNP	.											.	NCKAP5	322	.	0			c.T5152C						PASS	.	A	,	316,3612		15,286,1663	51.0	53.0	52.0		5152,1195	-2.9	0.0	2	dbSNP_129	52	2221,6087		298,1625,2231	no	coding-synonymous,coding-synonymous	NCKAP5	NM_207363.2,NM_207481.3	,	313,1911,3894	GG,GA,AA		26.7333,8.0448,20.7339	,	1718/1910,399/591	133489601	2537,9699	1964	4154	6118	SO:0001819	synonymous_variant	344148	exon17			TGTCCAATGTTCT	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.5152T>C	2.37:g.133489601A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			A|0.822;G|0.178	0.178	strong		0.502	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
MS4A14	84689	hgsc.bcm.edu	37	11	60184191	60184191	+	Missense_Mutation	SNP	G	G	A	rs3825020	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:60184191G>A	ENST00000300187.6	+	5	2027	c.1750G>A	c.(1750-1752)Gga>Aga	p.G584R	MS4A14_ENST00000531783.1_Missense_Mutation_p.G617R|MS4A14_ENST00000395005.2_Missense_Mutation_p.G567R|MS4A14_ENST00000531787.1_Missense_Mutation_p.G472R	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	584	Gln-rich.		G -> R (in dbSNP:rs3825020). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						ATCTAAAGATGGACAAGTTAA	0.458													G|||	2495	0.498203	0.5182	0.6513	5008	,	,		21541	0.3433		0.6262	False		,,,				2504	0.3906				p.G617R		Atlas-SNP	.											.	MS4A14	120	.	0			c.G1849A						PASS	.	G	ARG/GLY,ARG/GLY	2155,2251	581.2+/-385.3	521,1113,569	72.0	62.0	65.0		1699,1750	-1.4	0.0	11	dbSNP_107	65	5324,3276	645.7+/-400.2	1639,2046,615	yes	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	125,125	2160,3159,1184	AA,AG,GG		38.093,48.9106,42.4958	benign,benign	567/663,584/680	60184191	7479,5527	2203	4300	6503	SO:0001583	missense	84689	exon6			AAAGATGGACAAG	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"""membrane-spanning 4-domains, subfamily A, member 16"""	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.1750G>A	11.37:g.60184191G>A	ENSP00000300187:p.Gly584Arg	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	1179	0.5398351648351648	254	0.516260162601626	226	0.6243093922651933	228	0.3986013986013986	471	0.6213720316622692	G	5.096	0.203398	0.09704	0.489106	0.61907	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.30981	1.51;2.73;1.52;3.1	4.31	-1.43	0.08884	.	4.009310	0.00541	N	0.000226	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.13145	0.007;0.004	B;B	0.08055	0.003;0.001	T	0.45948	-0.9226	9	0.15499	T	0.54	4.9183	3.2257	0.06731	0.3862:0.0:0.3485:0.2652	rs3825020;rs52806143;rs60869380;rs3825020	567;584	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	R	472;584;567;617	ENSP00000437222:G472R;ENSP00000300187:G584R;ENSP00000378453:G567R;ENSP00000433761:G617R	ENSP00000300187:G584R	G	+	1	0	MS4A14	59940767	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.859000	0.04277	-0.031000	0.13781	0.655000	0.94253	GGA	G|0.445;A|0.555	0.555	strong		0.458	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
RPA4	29935	hgsc.bcm.edu	37	X	96139406	96139406	+	Missense_Mutation	SNP	G	G	A	rs2642219	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:96139406G>A	ENST00000373040.3	+	1	500	c.97G>A	c.(97-99)Gct>Act	p.A33T	DIAPH2_ENST00000373054.4_Intron|DIAPH2_ENST00000324765.8_Intron|DIAPH2_ENST00000373049.4_Intron|DIAPH2_ENST00000355827.4_Intron|DIAPH2_ENST00000373061.3_Intron	NM_013347.4	NP_037479.1	Q13156	RFA4_HUMAN	replication protein A4, 30kDa	33			A -> T (in dbSNP:rs2642219). {ECO:0000269|Ref.3}.		DNA damage checkpoint (GO:0000077)|DNA recombination (GO:0006310)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)	DNA replication factor A complex (GO:0005662)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	13						TGCAACTCCTGCTATTAAGAC	0.493								Other identified genes with known or suspected DNA repair function					G|||	1517	0.401854	0.5076	0.2896	3775	,	,		14948	0.2837		0.2087	False		,,,				2504	0.1524				p.A33T		Atlas-SNP	.											.	RPA4	29	.	0			c.G97A	GRCh37	CM076485	RPA4	M	rs2642219	PASS	.	G	,,THR/ALA	2440,1395		657,774,352,201,219	141.0	113.0	122.0		,,97	1.3	0.0	X	dbSNP_100	122	2002,4726		212,1019,559,1197,1313	yes	intron,intron,missense	DIAPH2,RPA4	NM_006729.4,NM_007309.3,NM_013347.4	,,58	869,1793,911,1398,1532	AA,AG,A,GG,G		29.7562,36.3755,42.0524	,,benign	,,33/262	96139406	4442,6121	2203	4300	6503	SO:0001583	missense	29935	exon1			ACTCCTGCTATTA	U24186	CCDS35345.1	Xq21	2010-04-09	2010-04-09		ENSG00000204086	ENSG00000204086			30305	protein-coding gene	gene with protein product		300767	"""replication protein A4, 34kDa"""			7760808	Standard	NM_013347		Approved	HSU24186	uc004efv.4	Q13156	OTTHUMG00000021987	ENST00000373040.3:c.97G>A	X.37:g.96139406G>A	ENSP00000362131:p.Ala33Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	82	22	0.268293	NM_013347	Q3SY03	Missense_Mutation	SNP	ENST00000373040.3	37	CCDS35345.1	723	0.4358047016274864	183	0.5319767441860465	70	0.2517985611510791	123	0.2942583732057416	105	0.1590909090909091	G	5.102	0.204401	0.09704	0.636245	0.297562	ENSG00000204086	ENST00000373040	T	0.18502	2.21	3.17	1.31	0.21738	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.27498	0.18	B	0.21546	0.035	T	0.28427	-1.0044	8	0.62326	D	0.03	-14.3524	3.8015	0.08760	0.1496:0.2501:0.6003:0.0	rs2642219;rs3747348;rs17328529;rs52816515;rs57433190;rs2642219	33	Q13156	RFA4_HUMAN	T	33	ENSP00000362131:A33T	ENSP00000362131:A33T	A	+	1	0	RPA4	96026062	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.878000	0.28126	0.213000	0.20722	-0.191000	0.12829	GCT	G|0.556;0|0.014	.	strong		0.493	RPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057464.1	NM_013347	
OR4L1	122742	hgsc.bcm.edu	37	14	20528362	20528362	+	Silent	SNP	A	A	G	rs200624036|rs1958717	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20528362A>G	ENST00000315683.1	+	1	159	c.159A>G	c.(157-159)tcA>tcG	p.S53S		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		CATGTAGGTCAACCCTTCATT	0.418													N|||	2697	0.538538	0.4962	0.5576	5008	,	,		19901	0.5734		0.3857	False		,,,				2504	0.7035				p.S53S		Atlas-SNP	.											.	OR4L1	98	.	0			c.A159G						PASS	.			2211,2195		554,1103,546	179.0	185.0	183.0		159	-4.9	0.0	14	dbSNP_92	183	3472,5128		735,2002,1563	no	coding-synonymous	OR4L1	NM_001004717.1		1289,3105,2109	GG,GA,AA		40.3721,49.8184,43.6952		53/313	20528362	5683,7323	2203	4300	6503	SO:0001819	synonymous_variant	122742	exon1			TAGGTCAACCCTT		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.159A>G	14.37:g.20528362A>G		Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	303	129	0.425743	NM_001004717	Q6IEZ5	Silent	SNP	ENST00000315683.1	37	CCDS32029.1																																																																																			A|0.530;G|0.470	0.470	strong		0.418	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
MUC4	4585	hgsc.bcm.edu	37	3	195495916	195495916	+	Missense_Mutation	SNP	G	G	C	rs2550240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195495916G>C	ENST00000346145.4	-	6	837	c.798C>G	c.(796-798)aaC>aaG	p.N266K	MUC4_ENST00000475231.1_Missense_Mutation_p.N4450K|MUC4_ENST00000349607.4_Missense_Mutation_p.N215K|MUC4_ENST00000463781.3_Missense_Mutation_p.N4502K	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1259					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)		TGAGCACCGGGTTGCCTGAGC	0.622													.|||	2147	0.428714	0.1581	0.438	5008	,	,		19055	0.7659		0.4423	False		,,,				2504	0.4264				p.N4502K		Atlas-SNP	.											.	MUC4	1505	.	0			c.C13506G						PASS	.	G	LYS/ASN,LYS/ASN,LYS/ASN	922,3484		91,740,1372	67.0	54.0	59.0		798,13506,645	3.4	0.1	3	dbSNP_100	59	3745,4855		840,2065,1395	no	missense,missense,missense	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	94,94,94	931,2805,2767	CC,CG,GG		43.5465,20.926,35.8834	possibly-damaging,possibly-damaging,possibly-damaging	266/1177,4502/5413,215/1126	195495916	4667,8339	2203	4300	6503	SO:0001583	missense	4585	exon7			CACCGGGTTGCCT	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	ENST00000346145.4:c.798C>G	3.37:g.195495916G>C	ENSP00000304207:p.Asn266Lys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	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	ENST00000346145.4	37	CCDS3310.1	977	0.44734432234432236	78	0.15853658536585366	152	0.4198895027624309	412	0.7202797202797203	335	0.4419525065963061	.	6.319	0.426881	0.11987	0.20926	0.435465	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62	5.5	3.37	0.38596	Nidogen, extracellular domain (3);	0.550562	0.17475	N	0.172932	T	0.00012	0.0000	M	0.73598	2.24	0.80722	P	0.0	P;B;B;B	0.51791	0.948;0.082;0.079;0.037	P;B;B;B	0.57911	0.829;0.081;0.033;0.033	T	0.48151	-0.9060	9	0.12430	T	0.62	-29.412	9.3513	0.38140	0.1583:0.1257:0.716:0.0	rs2550240;rs3749332;rs60021717;rs2550240	4374;1259;215;266	E7ESK3;Q99102;Q99102-12;Q99102-13	.;MUC4_HUMAN;.;.	K	215;266;4502;4450;1228	ENSP00000338109:N215K;ENSP00000304207:N266K;ENSP00000417498:N4502K;ENSP00000420243:N4450K	ENSP00000304207:N266K	N	-	3	2	MUC4	196981550	0.001000	0.12720	0.130000	0.21974	0.019000	0.09904	0.759000	0.26461	1.349000	0.45751	0.540000	0.68198	AAC	G|0.607;C|0.393	0.393	strong		0.622	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
NEFH	4744	hgsc.bcm.edu	37	22	29885473	29885473	+	Missense_Mutation	SNP	C	C	T	rs5763269	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:29885473C>T	ENST00000310624.6	+	4	1877	c.1844C>T	c.(1843-1845)cCg>cTg	p.P615L		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	615	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.		P -> L (in dbSNP:rs5763269).		axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						gcaaagtcaccggctgagGCC	0.557													C|||	754	0.150559	0.1346	0.232	5008	,	,		22581	0.0744		0.2306	False		,,,				2504	0.1104				p.P615L		Atlas-SNP	.											.	NEFH	178	.	0			c.C1844T						PASS	.	C	LEU/PRO	752,3654	305.2+/-288.9	68,616,1519	65.0	64.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1844	4.6	0.1	22	dbSNP_114	64	1862,6738	326.0+/-317.2	200,1462,2638	no	missense	NEFH	NM_021076.3	98	268,2078,4157	TT,TC,CC		21.6512,17.0676,20.0984	possibly-damaging	615/1021	29885473	2614,10392	2203	4300	6503	SO:0001583	missense	4744	exon4			AGTCACCGGCTGA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1844C>T	22.37:g.29885473C>T	ENSP00000311997:p.Pro615Leu	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	371	0.16987179487179488	77	0.1565040650406504	69	0.19060773480662985	53	0.09265734265734266	172	0.22691292875989447	C	8.422	0.846715	0.16963	0.170676	0.216512	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.99586	-6.23	4.6	4.6	0.57074	.	0.000000	0.49916	D	0.000133	T	0.02571	0.0078	M	0.72894	2.215	0.48975	P	2.6199999999998447E-4	P	0.39404	0.672	B	0.28011	0.085	T	0.00000	-1.2872	9	0.87932	D	0	.	17.564	0.87914	0.0:1.0:0.0:0.0	rs5763269;rs52807263;rs58303921;rs5763269	615	P12036	NFH_HUMAN	L	615	ENSP00000311997:P615L	ENSP00000311997:P615L	P	+	2	0	NEFH	28215473	0.853000	0.29707	0.055000	0.19348	0.005000	0.04900	2.462000	0.45049	2.568000	0.86640	0.650000	0.86243	CCG	C|0.815;T|0.185	0.185	strong		0.557	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
SLC51A	200931	hgsc.bcm.edu	37	3	195956827	195956827	+	Silent	SNP	T	T	C	rs17852687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195956827T>C	ENST00000296327.5	+	7	884	c.675T>C	c.(673-675)ctT>ctC	p.L225L	PCYT1A_ENST00000419333.1_3'UTR	NM_152672.5	NP_689885.4	Q86UW1	OSTA_HUMAN	solute carrier family 51, alpha subunit	225					bile acid and bile salt transport (GO:0015721)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transporter activity (GO:0005215)									Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)	ACACTTTCCTTGGCGTGTCCA	0.537													C|||	2492	0.497604	0.3222	0.4914	5008	,	,		17557	0.7897		0.4394	False		,,,				2504	0.498				p.L225L		Atlas-SNP	.											.	.	.	.	0			c.T675C						PASS	.	C		1527,2879	674.0+/-402.9	244,1039,920	120.0	106.0	111.0		675	-11.7	0.0	3	dbSNP_123	111	3818,4782	612.9+/-396.0	870,2078,1352	no	coding-synonymous	OSTalpha	NM_152672.5		1114,3117,2272	CC,CT,TT		44.3953,34.6573,41.0964		225/341	195956827	5345,7661	2203	4300	6503	SO:0001819	synonymous_variant	200931	exon7			TTTCCTTGGCGTG		CCDS3314.1	3q29	2013-05-22			ENSG00000163959	ENSG00000163959		"""Solute carriers"""	29955	protein-coding gene	gene with protein product	"""organic solute transporter, alpha subunit"""	612084				12719432, 20538072	Standard	NM_152672		Approved	OSTalpha	uc003fwd.3	Q86UW1	OTTHUMG00000155684	ENST00000296327.5:c.675T>C	3.37:g.195956827T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_152672	Q6ZMC7	Silent	SNP	ENST00000296327.5	37	CCDS3314.1																																																																																			T|0.544;C|0.456	0.456	strong		0.537	SLC51A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341253.1	NM_152672	
C11orf24	53838	hgsc.bcm.edu	37	11	68030173	68030173	+	Missense_Mutation	SNP	C	C	A	rs3802746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:68030173C>A	ENST00000304271.6	-	4	692	c.290G>T	c.(289-291)gGt>gTt	p.G97V	C11orf24_ENST00000533310.1_Intron|C11orf24_ENST00000530166.1_5'UTR	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	97			G -> V (in dbSNP:rs3802746). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874}.			Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						ATCAGCTGCACCTCCTGAAGT	0.567													C|||	1920	0.383387	0.1309	0.513	5008	,	,		18929	0.4752		0.3062	False		,,,				2504	0.6176				p.G97V	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.G290T						PASS	.	C	VAL/GLY	690,3710	289.2+/-280.3	56,578,1566	133.0	98.0	110.0		290	1.5	0.0	11	dbSNP_107	110	2633,5955	425.0+/-354.8	428,1777,2089	yes	missense	C11orf24	NM_022338.3	109	484,2355,3655	AA,AC,CC		30.6591,15.6818,25.5852	probably-damaging	97/450	68030173	3323,9665	2200	4294	6494	SO:0001583	missense	53838	exon4			GCTGCACCTCCTG	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.290G>T	11.37:g.68030173C>A	ENSP00000307264:p.Gly97Val	Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	161	159	0.987578	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	37	CCDS8180.1	737	0.3374542124542125	56	0.11382113821138211	179	0.494475138121547	264	0.46153846153846156	238	0.31398416886543534	C	12.00	1.806515	0.31961	0.156818	0.306591	ENSG00000171067	ENST00000304271	T	0.55052	0.54	3.37	1.45	0.22620	.	.	.	.	.	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	D	0.65815	0.995	D	0.63877	0.919	T	0.45833	-0.9234	8	0.26408	T	0.33	3.0E-4	6.6072	0.22731	0.0:0.7456:0.0:0.2544	rs3802746;rs17855426;rs60804736;rs3802746	97	Q96F05	CK024_HUMAN	V	97	ENSP00000307264:G97V	ENSP00000307264:G97V	G	-	2	0	C11orf24	67786749	0.001000	0.12720	0.005000	0.12908	0.443000	0.32047	0.759000	0.26461	0.746000	0.32786	0.305000	0.20034	GGT	T|0.000;C|0.709;A|0.291	0.291	strong		0.567	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338	
TCHP	84260	hgsc.bcm.edu	37	12	110340852	110340852	+	Silent	SNP	G	G	A	rs11539159	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:110340852G>A	ENST00000312777.5	+	2	235	c.21G>A	c.(19-21)ccG>ccA	p.P7P	TCHP_ENST00000405876.4_Silent_p.P7P	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding											NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						CGACGCTGCCGTCCTACTGGT	0.607													G|||	520	0.103834	0.2156	0.0893	5008	,	,		17136	0.0		0.1044	False		,,,				2504	0.0695				p.P7P		Atlas-SNP	.											.	TCHP	45	.	0			c.G21A						PASS	.	G	,	882,3524	337.8+/-305.0	87,708,1408	49.0	51.0	50.0		21,21	-0.6	0.9	12	dbSNP_120	50	805,7795	184.7+/-232.6	29,747,3524	no	coding-synonymous,coding-synonymous	TCHP	NM_001143852.1,NM_032300.4	,	116,1455,4932	AA,AG,GG		9.3605,20.0182,12.9709	,	7/499,7/499	110340852	1687,11319	2203	4300	6503	SO:0001819	synonymous_variant	84260	exon2			GCTGCCGTCCTAC	AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.21G>A	12.37:g.110340852G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_001143852		Silent	SNP	ENST00000312777.5	37	CCDS9137.1																																																																																			G|0.883;A|0.117	0.117	strong		0.607	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
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 GAIIx	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	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	150	101	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 GAIIx	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	GDF9_ENST00000296875.2_Missense_Mutation_p.S76A|UQCRQ_ENST00000378667.1_5'Flank|UQCRQ_ENST00000378665.1_5'Flank|GDF9_ENST00000464378.1_5'UTR|UQCRQ_ENST00000378670.3_5'Flank			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	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	13	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	
APOL5	80831	hgsc.bcm.edu	37	22	36122517	36122517	+	Silent	SNP	T	T	C	rs17723764	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36122517T>C	ENST00000249044.2	+	3	402	c.402T>C	c.(400-402)ctT>ctC	p.L134L		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	134					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						ACGAGTTGCTTACCAAGACCA	0.507													C|||	1080	0.215655	0.115	0.2565	5008	,	,		19182	0.1389		0.3419	False		,,,				2504	0.272				p.L134L		Atlas-SNP	.											.	APOL5	45	.	0			c.T402C						PASS	.	C		632,3774	768.3+/-413.6	42,548,1613	73.0	74.0	74.0		402	-0.1	0.0	22	dbSNP_123	74	2924,5676	669.4+/-402.7	504,1916,1880	no	coding-synonymous	APOL5	NM_030642.1		546,2464,3493	CC,CT,TT		34.0,14.3441,27.3412		134/434	36122517	3556,9450	2203	4300	6503	SO:0001819	synonymous_variant	80831	exon3			GTTGCTTACCAAG	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"""Apolipoproteins"""	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.402T>C	22.37:g.36122517T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_030642	Q5TFL9|Q9UGW5	Silent	SNP	ENST00000249044.2	37	CCDS13920.1																																																																																			C|0.262;N|0.000	0.262	strong		0.507	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642	
HIST1H2BF	8343	hgsc.bcm.edu	37	6	26200083	26200083	+	Silent	SNP	A	A	G	rs1059486	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26200083A>G	ENST00000359985.1	+	1	336	c.297A>G	c.(295-297)gtA>gtG	p.V99V	HIST1H3D_ENST00000356476.2_5'Flank|HIST1H2AD_ENST00000341023.1_5'Flank|HIST1H3D_ENST00000377831.5_5'Flank	NM_003522.3	NP_003513.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bf	99					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(7)|upper_aerodigestive_tract(3)	17		all_hematologic(11;0.196)				AGACGGCCGTACGCCTGCTGC	0.592													G|||	3253	0.649561	0.5325	0.6066	5008	,	,		18860	0.9187		0.5089	False		,,,				2504	0.7055				p.V99V		Atlas-SNP	.											.	HIST1H2BF	25	.	0			c.A297G						PASS	.	G		2217,2189		554,1109,540	72.0	78.0	76.0		297	3.8	1.0	6	dbSNP_86	76	4149,4451		1020,2109,1171	no	coding-synonymous	HIST1H2BF	NM_003522.3		1574,3218,1711	GG,GA,AA		48.2442,49.6823,48.9466		99/127	26200083	6366,6640	2203	4300	6503	SO:0001819	synonymous_variant	8343	exon1			GGCCGTACGCCTG	Z80779	CCDS4592.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197846	ENSG00000277224		"""Histones / Replication-dependent"""	4752	protein-coding gene	gene with protein product		602804	"""H2B histone family, member G"", ""histone 1, H2bf"""	H2BFG		9119399, 12408966	Standard	NM_003522		Approved	H2B/g	uc003ngx.3	P62807	OTTHUMG00000014445	ENST00000359985.1:c.297A>G	6.37:g.26200083A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	45	36	0.8	NM_003522	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000359985.1	37	CCDS4592.1																																																																																			A|0.469;G|0.531	0.531	strong		0.592	HIST1H2BF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040108.1	NM_003522	
YME1L1	10730	hgsc.bcm.edu	37	10	27436566	27436566	+	Missense_Mutation	SNP	T	T	C	rs62622019	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27436566T>C	ENST00000326799.3	-	3	348	c.200A>G	c.(199-201)aAc>aGc	p.N67S	YME1L1_ENST00000375972.3_Intron|YME1L1_ENST00000376016.3_Intron|YME1L1_ENST00000477432.1_Missense_Mutation_p.N67S	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	67					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						tgaaacaatgttaagcttcgt	0.423													T|||	197	0.0393371	0.0666	0.0274	5008	,	,		22002	0.004		0.0527	False		,,,				2504	0.0337				p.N67S		Atlas-SNP	.											.	YME1L1	71	.	0			c.A200G						PASS	.	T	,SER/ASN	277,4029		8,261,1884	118.0	100.0	106.0		,200	0.8	0.0	10	dbSNP_129	106	387,7989		4,379,3805	yes	intron,missense	YME1L1	NM_014263.2,NM_139312.1	,46	12,640,5689	CC,CT,TT		4.6203,6.4329,5.2358	,	,67/774	27436566	664,12018	2153	4188	6341	SO:0001583	missense	10730	exon3			ACAATGTTAAGCT	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"""ATPases / AAA-type"""	12843	protein-coding gene	gene with protein product		607472	"""YME1 (S.cerevisiae)-like 1"", ""YME1-like 1 (S. cerevisiae)"""			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.200A>G	10.37:g.27436566T>C	ENSP00000318480:p.Asn67Ser	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	262	129	0.492366	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Missense_Mutation	SNP	ENST00000326799.3	37	CCDS7152.1	81	0.03708791208791209	26	0.052845528455284556	14	0.03867403314917127	2	0.0034965034965034965	39	0.051451187335092345	T	4.478	0.088539	0.08583	0.064329	0.046203	ENSG00000136758	ENST00000326799;ENST00000375969	D	0.92199	-2.99	1.96	0.803	0.18691	Peptidase M41, FtsH (1);	6.475830	0.00990	U	0.003505	T	0.41096	0.1144	N	0.08118	0	0.09310	N	1	B;B	0.23854	0.092;0.0	B;B	0.24269	0.052;0.0	T	0.66073	-0.6014	10	0.27082	T	0.32	.	3.7054	0.08398	0.0:0.1991:0.0:0.8009	rs62622019	67;67	Q6PJ89;Q96TA2	.;YMEL1_HUMAN	S	67	ENSP00000318480:N67S	ENSP00000318480:N67S	N	-	2	0	YME1L1	27476572	0.001000	0.12720	0.001000	0.08648	0.027000	0.11550	-0.164000	0.09983	0.222000	0.20900	0.377000	0.23210	AAC	T|0.948;C|0.052	0.052	strong		0.423	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312	
SPARCL1	8404	hgsc.bcm.edu	37	4	88416223	88416223	+	Silent	SNP	A	A	G	rs8342	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88416223A>G	ENST00000282470.6	-	3	581	c.111T>C	c.(109-111)ccT>ccC	p.P37P	SPARCL1_ENST00000418378.1_Silent_p.P37P|SPARCL1_ENST00000503414.1_5'UTR	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	37					signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		CAGTGTTGTCAGGTGCTACCG	0.378													G|||	3763	0.751398	0.9153	0.7939	5008	,	,		17361	0.631		0.5984	False		,,,				2504	0.7812				p.P37P		Atlas-SNP	.											.	SPARCL1	59	.	0			c.T111C						PASS	.	G	,	3805,601	263.4+/-265.5	1643,519,41	163.0	172.0	169.0		111,111	-7.4	0.0	4	dbSNP_52	169	5234,3366	500.1+/-375.1	1585,2064,651	no	coding-synonymous,coding-synonymous	SPARCL1	NM_001128310.1,NM_004684.4	,	3228,2583,692	GG,GA,AA		39.1395,13.6405,30.5013	,	37/665,37/665	88416223	9039,3967	2203	4300	6503	SO:0001819	synonymous_variant	8404	exon3			GTTGTCAGGTGCT	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.111T>C	4.37:g.88416223A>G		Somatic	264	1	0.00378788		WXS	Illumina HiSeq	Phase_I	243	109	0.44856	NM_004684	B4E2Z0|E7ESU2|Q14800	Silent	SNP	ENST00000282470.6	37	CCDS3622.1																																																																																			A|0.308;G|0.692	0.692	strong		0.378	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
CDRT1	374286	hgsc.bcm.edu	37	17	15510888	15510888	+	Splice_Site	SNP	G	G	A	rs62070401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:15510888G>A	ENST00000395906.3	-	6	1231	c.1232C>T	c.(1231-1233)aCg>aTg	p.T411M	RP11-385D13.1_ENST00000455584.2_Splice_Site_p.T721M	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	411										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		CAGTACCTACGTGTCAGAGAG	0.493													G|||	1466	0.292732	0.264	0.2767	5008	,	,		18548	0.4514		0.1511	False		,,,				2504	0.3252				p.T411M		Atlas-SNP	.											.	CDRT1	83	.	0			c.C1232T						PASS	.	G	MET/THR	1085,3321	390.3+/-327.6	143,799,1261	68.0	65.0	66.0		1232	-4.1	0.8	17	dbSNP_129	66	1459,7141	275.3+/-291.7	127,1205,2968	no	missense-near-splice	CDRT1	NM_006382.3	81	270,2004,4229	AA,AG,GG		16.9651,24.6255,19.5602	possibly-damaging	411/753	15510888	2544,10462	2203	4300	6503	SO:0001630	splice_region_variant	374286	exon6			ACCTACGTGTCAG	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1232+1C>T	17.37:g.15510888G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	157	76	0.484076	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	570|570	0.260989010989011|0.260989010989011	100|100	0.2032520325203252|0.2032520325203252	86|86	0.23756906077348067|0.23756906077348067	256|256	0.44755244755244755|0.44755244755244755	128|128	0.16886543535620052|0.16886543535620052	G|G	9.414|9.414	1.081185|1.081185	0.20309|0.20309	0.246255|0.246255	0.169651|0.169651	ENSG00000251537|ENSG00000251537	ENST00000455584|ENST00000261644;ENST00000395906	.|T	.|0.58940	.|0.3	4.99|4.99	-4.14|-4.14	0.03892|0.03892	.|WD40 repeat-like-containing domain (1);	.|0.395907	.|0.18373	.|U	.|0.143193	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.51422|0.51422	1.61|1.61	0.09310|0.09310	P|P	0.99999999077601|0.99999999077601	.|D;B	.|0.56521	.|0.976;0.203	.|B;B	.|0.42959	.|0.403;0.029	T|T	0.32955|0.32955	-0.9887|-0.9887	4|8	.|.	.|.	.|.	.|.	6.6345|6.6345	0.22875|0.22875	0.5699:0.138:0.2921:0.0|0.5699:0.138:0.2921:0.0	rs62070401|rs62070401	.|411;735	.|O95170;Q59EB2	.|CDRT1_HUMAN;.	C|M	736|441;411	.|ENSP00000379242:T411M	.|.	R|T	-|-	1|2	0|0	RP11-385D13.1|RP11-385D13.1	15451613|15451613	0.231000|0.231000	0.23751|0.23751	0.832000|0.832000	0.32986|0.32986	0.010000|0.010000	0.07245|0.07245	-0.782000|-0.782000	0.04643|0.04643	-0.694000|-0.694000	0.05113|0.05113	-1.259000|-1.259000	0.01468|0.01468	CGT|ACG	G|0.754;A|0.246	0.246	strong		0.493	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	Missense_Mutation
PROSER3	148137	hgsc.bcm.edu	37	19	36258721	36258721	+	Missense_Mutation	SNP	C	C	T	rs73592448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36258721C>T	ENST00000544099.1	+	9	1037	c.974C>T	c.(973-975)gCc>gTc	p.A325V	C19orf55_ENST00000396908.4_Missense_Mutation_p.A325V|AC002398.13_ENST00000589397.1_RNA			Q2NL68	PRSR3_HUMAN		325										cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TCTCTGAAAGCCAAGGCCTTG	0.627													C|||	445	0.0888578	0.059	0.0922	5008	,	,		13002	0.0744		0.1064	False		,,,				2504	0.1237				p.A325V		Atlas-SNP	.											.	C19orf55	39	.	0			c.C974T						PASS	.	C	VAL/ALA	249,3507		6,237,1635	21.0	24.0	23.0		974	-0.5	0.0	19	dbSNP_130	23	747,7433		27,693,3370	yes	missense	C19orf55	NM_001039887.2	64	33,930,5005	TT,TC,CC		9.132,6.6294,8.3445	probably-damaging	325/481	36258721	996,10940	1878	4090	5968	SO:0001583	missense	148137	exon9			TGAAAGCCAAGGC																												ENST00000544099.1:c.974C>T	19.37:g.36258721C>T	ENSP00000467267:p.Ala325Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000544099.1	37		184	0.08424908424908426	30	0.06097560975609756	34	0.09392265193370165	38	0.06643356643356643	82	0.10817941952506596	C	11.71	1.720944	0.30503	0.066294	0.09132	ENSG00000167595	ENST00000396908	T	0.32515	1.45	3.04	-0.484	0.12071	.	.	.	.	.	T	0.00412	0.0013	L	0.51422	1.61	0.80722	P	0.0	B	0.19331	0.035	B	0.14023	0.01	T	0.14254	-1.0479	8	0.56958	D	0.05	-0.5768	3.3343	0.07096	0.0:0.4894:0.2358:0.2748	.	325	E5RFB9	.	V	325	ENSP00000380116:A325V	ENSP00000380116:A325V	A	+	2	0	C19orf55	40950561	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	0.452000	0.21795	0.008000	0.14787	-0.490000	0.04691	GCC	C|0.916;T|0.084	0.084	strong		0.627	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		
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 GAIIx	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_ENST00000446172.2_Silent_p.T97T|DNAJA4_ENST00000394855.3_Silent_p.T153T|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		Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	255	113	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	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907762	12907762	+	Silent	SNP	T	T	C	rs57026768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907762T>C	ENST00000317869.6	-	2	606	c.381A>G	c.(379-381)ccA>ccG	p.P127P		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	127						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						GTACACGTGCTGGGAAACTGT	0.507																																					p.P127P		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,0,2	HNRNPCL1	68	2	0			c.A381G						PASS	.						87.0	85.0	86.0					1																	12907762		2203	4299	6502	SO:0001819	synonymous_variant	343069	exon2			ACGTGCTGGGAAA	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.381A>G	1.37:g.12907762T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	188	35	0.18617	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	37	CCDS30591.1																																																																																			T|0.966;C|0.034	0.034	strong		0.507	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
OR2T33	391195	hgsc.bcm.edu	37	1	248436721	248436721	+	Silent	SNP	A	A	G	rs74363422		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248436721A>G	ENST00000318021.2	-	1	417	c.396T>C	c.(394-396)acT>acC	p.T132T		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|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;0.0245)			AGCTCATGAGAGTGGGATATC	0.592																																					p.T132T		Atlas-SNP	.											OR2T33,NS,carcinoma,-1,1	OR2T33	133	1	0			c.T396C						scavenged	.						78.0	77.0	78.0					1																	248436721		2203	4299	6502	SO:0001819	synonymous_variant	391195	exon1			CATGAGAGTGGGA		CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"""GPCR / Class A : Olfactory receptors"""	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.396T>C	1.37:g.248436721A>G		Somatic	609	4	0.00656814		WXS	Illumina HiSeq	Phase_I	770	89	0.115584	NM_001004695	B2RNN0	Silent	SNP	ENST00000318021.2	37	CCDS31109.1																																																																																			A|0.999;G|0.001	0.001	weak		0.592	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695	
CASS4	57091	hgsc.bcm.edu	37	20	55012318	55012318	+	Silent	SNP	G	G	A	rs911159	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:55012318G>A	ENST00000360314.3	+	3	360	c.135G>A	c.(133-135)gtG>gtA	p.V45V	CASS4_ENST00000434344.1_Silent_p.V45V|CASS4_ENST00000371336.3_Silent_p.V45V	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	45	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AGCAACACGTGCCAGAAAGCG	0.602													G|||	678	0.135383	0.0817	0.1628	5008	,	,		19017	0.1508		0.1501	False		,,,				2504	0.1575				p.V45V		Atlas-SNP	.											.	CASS4	121	.	0			c.G135A						PASS	.	G	,,,	450,3956	215.8+/-234.7	21,408,1774	71.0	66.0	68.0		135,135,135,135	1.0	0.7	20	dbSNP_86	68	1240,7360	249.4+/-276.7	88,1064,3148	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	,,,	109,1472,4922	AA,AG,GG		14.4186,10.2133,12.994	,,,	45/733,45/350,45/787,45/787	55012318	1690,11316	2203	4300	6503	SO:0001819	synonymous_variant	57091	exon2			ACACGTGCCAGAA	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.135G>A	20.37:g.55012318G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	75	26	0.346667	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Silent	SNP	ENST00000360314.3	37	CCDS33492.1																																																																																			G|0.864;A|0.136	0.136	strong		0.602	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31088145	31088145	+	Intron	SNP	T	T	A	rs546626089	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31088145T>A	ENST00000259881.9	+	2	61				CDSN_ENST00000376288.2_Missense_Mutation_p.M18L	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						AGCAGTGCCATCATCCCGTGC	0.687													T|||	510	0.101837	0.1172	0.0778	5008	,	,		15043	0.0625		0.1819	False		,,,				2504	0.0562				p.M18L		Atlas-SNP	.											CDSN,NS,carcinoma,0,1	CDSN	48	1	0			c.A52T						PASS	.	T	LEU/MET,	615,3769		33,549,1610	36.0	30.0	32.0		52,	0.5	0.0	6	dbSNP_103	32	1831,6765		210,1411,2677	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	15,	243,1960,4287	AA,AT,TT		21.3006,14.0283,18.8444	benign,	18/530,	31088145	2446,10534	2192	4298	6490	SO:0001627	intron_variant	1041	exon1			GTGCCATCATCCC	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-228-5308T>A	6.37:g.31088145T>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	149	116	0.778524	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	256	0.11721611721611722	55	0.11178861788617886	29	0.08011049723756906	29	0.050699300699300696	143	0.18865435356200527	T	4.791	0.147084	0.09134	0.140283	0.213006	ENSG00000204539	ENST00000376288	T	0.05855	3.38	4.35	0.505	0.16953	.	0.370723	0.19751	N	0.106888	T	0.00695	0.0023	N	0.25201	0.72	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45920	-0.9228	9	0.02654	T	1	0.1892	0.8311	0.01130	0.1927:0.1215:0.1999:0.4859	rs3095318;rs9263680;rs17855560	18	Q15517	CDSN_HUMAN	L	18	ENSP00000365465:M18L	ENSP00000365465:M18L	M	-	1	0	CDSN	31196124	0.005000	0.15991	0.002000	0.10522	0.557000	0.35523	-0.033000	0.12246	-0.059000	0.13154	0.519000	0.50382	ATG	T|0.831;A|0.169	0.169	strong		0.687	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
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 GAIIx	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_ENST00000481323.1_Silent_p.L7L|SNX5_ENST00000377759.4_Silent_p.L7L|SNX5_ENST00000606557.1_Silent_p.L7L|MGME1_ENST00000377709.1_5'Flank|SNX5_ENST00000486039.1_Silent_p.L7L|MGME1_ENST00000377704.4_5'Flank|SNX5_ENST00000606602.1_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		Somatic	114	2	0.0175439		WXS	Illumina HiSeq	Phase_I	63	16	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		
MUC16	94025	hgsc.bcm.edu	37	19	9056989	9056989	+	Missense_Mutation	SNP	C	C	G	rs4804381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9056989C>G	ENST00000397910.4	-	3	30660	c.30457G>C	c.(30457-30459)Gag>Cag	p.E10153Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10155	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCTGTGGTCTCAAAATTAGCA	0.463													C|||	932	0.186102	0.0666	0.281	5008	,	,		22984	0.3313		0.167	False		,,,				2504	0.1503				p.E10153Q		Atlas-SNP	.											.	MUC16	4315	.	0			c.G30457C						PASS	.	C	GLN/GLU	314,3536		14,286,1625	76.0	73.0	74.0		30457	-0.7	0.0	19	dbSNP_111	74	1506,6768		136,1234,2767	yes	missense	MUC16	NM_024690.2	29	150,1520,4392	GG,GC,CC		18.2016,8.1558,15.0115	possibly-damaging	10153/14508	9056989	1820,10304	1925	4137	6062	SO:0001583	missense	94025	exon3			TGGTCTCAAAATT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30457G>C	19.37:g.9056989C>G	ENSP00000381008:p.Glu10153Gln	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	462	0.21153846153846154	35	0.07113821138211382	93	0.2569060773480663	208	0.36363636363636365	126	0.1662269129287599	c	4.952	0.176786	0.09443	0.081558	0.182016	ENSG00000181143	ENST00000397910	T	0.40756	1.02	2.85	-0.7	0.11273	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	.	.	.	P	0.41041	0.736	B	0.40636	0.335	T	0.37596	-0.9699	8	0.87932	D	0	.	4.9506	0.14011	0.0:0.4393:0.4299:0.1308	rs4804381;rs4804381	10153	B5ME49	.	Q	10153	ENSP00000381008:E10153Q	ENSP00000381008:E10153Q	E	-	1	0	MUC16	8917989	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.107000	0.10873	-0.044000	0.13491	-0.300000	0.09419	GAG	C|0.780;G|0.220	0.220	strong		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
BBS12	166379	hgsc.bcm.edu	37	4	123664427	123664427	+	Silent	SNP	G	G	C	rs13135766	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:123664427G>C	ENST00000314218.3	+	2	1573	c.1380G>C	c.(1378-1380)gtG>gtC	p.V460V	BBS12_ENST00000542236.1_Silent_p.V460V	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	460					cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TTACACAAGTGAATGAAGATT	0.478									Bardet-Biedl syndrome				G|||	474	0.0946486	0.0484	0.1081	5008	,	,		19718	0.0		0.2177	False		,,,				2504	0.1186				p.V460V		Atlas-SNP	.											.	BBS12	63	.	0			c.G1380C						PASS	.	G	,	294,4112	161.4+/-193.6	15,264,1924	79.0	79.0	79.0		1380,1380	3.0	0.2	4	dbSNP_121	79	1981,6619	347.3+/-326.5	241,1499,2560	no	coding-synonymous,coding-synonymous	BBS12	NM_001178007.1,NM_152618.2	,	256,1763,4484	CC,CG,GG		23.0349,6.6727,17.4919	,	460/711,460/711	123664427	2275,10731	2203	4300	6503	SO:0001819	synonymous_variant	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	ACAAGTGAATGAA	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1380G>C	4.37:g.123664427G>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Silent	SNP	ENST00000314218.3	37	CCDS3728.1																																																																																			G|0.853;C|0.147	0.147	strong		0.478	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
MUC16	94025	hgsc.bcm.edu	37	19	9049339	9049339	+	Silent	SNP	C	C	G	rs11883220	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9049339C>G	ENST00000397910.4	-	5	32495	c.32292G>C	c.(32290-32292)acG>acC	p.T10764T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10766	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						ATGAGGCTATCGTCTTTGGTT	0.478													G|||	1982	0.395767	0.2973	0.5533	5008	,	,		22256	0.3621		0.4493	False		,,,				2504	0.3967				p.T10764T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G32292C						PASS	.			1189,2691		192,805,943	139.0	128.0	131.0		32292	-1.0	0.0	19	dbSNP_120	131	4049,4225		1003,2043,1091	no	coding-synonymous	MUC16	NM_024690.2		1195,2848,2034	GG,GC,CC		48.9364,30.6443,43.0969		10764/14508	9049339	5238,6916	1940	4137	6077	SO:0001819	synonymous_variant	94025	exon5			GGCTATCGTCTTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.32292G>C	19.37:g.9049339C>G		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.572;G|0.428;T|0.001	0.428	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TNRC6C	57690	hgsc.bcm.edu	37	17	76093866	76093866	+	Intron	SNP	T	T	C	rs2290906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:76093866T>C	ENST00000588061.1	+	19	5033				TNRC6C_ENST00000301624.4_Intron|TNRC6C_ENST00000541771.1_Intron|TNRC6C_ENST00000588847.1_Silent_p.S1446S|TNRC6C_ENST00000335749.4_Silent_p.S1446S|TNRC6C_ENST00000544502.1_Silent_p.S1446S			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C						embryonic hemopoiesis (GO:0035162)|endoderm formation (GO:0001706)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of gene silencing by miRNA (GO:0060964)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CGCTGCCTTCTTCGAGTGCCT	0.587													C|||	1470	0.29353	0.4107	0.2666	5008	,	,		19861	0.2976		0.1252	False		,,,				2504	0.3231				p.S1446S		Atlas-SNP	.											.	TNRC6C	173	.	0			c.T4338C						PASS	.	C	,	489,895		86,317,289	43.0	40.0	41.0		4338,	2.6	1.0	17	dbSNP_100	41	468,2714		31,406,1154	no	coding-synonymous,intron	TNRC6C	NM_001142640.1,NM_018996.3	,	117,723,1443	CC,CT,TT		14.7077,35.3324,20.9593	,	1446/1727,	76093866	957,3609	692	1591	2283	SO:0001627	intron_variant	57690	exon18			GCCTTCTTCGAGT	AL834429	CCDS45798.1, CCDS45799.1	17q25.3	2012-10-04			ENSG00000078687	ENSG00000078687		"""Trinucleotide (CAG) repeat containing"""	29318	protein-coding gene	gene with protein product		610741					Standard	NM_018996		Approved	KIAA1582, FLJ20015	uc002juf.2	Q9HCJ0	OTTHUMG00000132642	ENST00000588061.1:c.4307-558T>C	17.37:g.76093866T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_001142640	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	37	CCDS45798.1																																																																																			T|0.737;C|0.263	0.263	strong		0.587	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996	
VWDE	221806	hgsc.bcm.edu	37	7	12433390	12433390	+	Missense_Mutation	SNP	G	G	A	rs139605380	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:12433390G>A	ENST00000275358.3	-	2	261	c.73C>T	c.(73-75)Cct>Tct	p.P25S		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	25						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TGTCCCCCAGGAGAGCACTCC	0.428													G|||	21	0.00419329	0.0023	0.0072	5008	,	,		18055	0.0		0.008	False		,,,				2504	0.0051				p.P25S		Atlas-SNP	.											.	VWDE	123	.	0			c.C73T						PASS	.	G	SER/PRO	9,1375		0,9,683	48.0	46.0	47.0		73	4.0	1.0	7	dbSNP_134	47	36,3146		2,32,1557	yes	missense	VWDE	NM_001135924.1	74	2,41,2240	AA,AG,GG		1.1314,0.6503,0.9855	benign	25/1591	12433390	45,4521	692	1591	2283	SO:0001583	missense	221806	exon2			CCCCAGGAGAGCA		CCDS47544.1	7p21.3	2008-09-23			ENSG00000146530	ENSG00000146530			21897	protein-coding gene	gene with protein product						14702039, 16303743	Standard	NM_001135924		Approved	FLJ14712	uc003ssj.2	Q8N2E2	OTTHUMG00000152315	ENST00000275358.3:c.73C>T	7.37:g.12433390G>A	ENSP00000275358:p.Pro25Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	16.46	3.130091	0.56721	0.006503	0.011314	ENSG00000146530	ENST00000275358;ENST00000541006	T	0.63913	-0.07	4.87	3.97	0.46021	.	0.308786	0.36101	N	0.002798	T	0.45316	0.1336	L	0.50333	1.59	0.29333	N	0.866531	P	0.50617	0.937	B	0.43754	0.43	T	0.51741	-0.8667	10	0.39692	T	0.17	.	6.3258	0.21242	0.1553:0.1577:0.687:0.0	.	25	Q8N2E2	VWDE_HUMAN	S	25	ENSP00000275358:P25S	ENSP00000275358:P25S	P	-	1	0	VWDE	12399915	1.000000	0.71417	0.993000	0.49108	0.773000	0.43773	5.133000	0.64764	1.263000	0.44181	0.655000	0.94253	CCT	G|0.993;A|0.007	0.007	strong		0.428	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
CPO	130749	hgsc.bcm.edu	37	2	207825656	207825656	+	Silent	SNP	A	A	T	rs13397039	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:207825656A>T	ENST00000272852.3	+	6	610	c.564A>T	c.(562-564)gcA>gcT	p.A188A		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	188						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		ATTTCAATGCATCTTGGTGTA	0.358													A|||	1918	0.382987	0.3707	0.2579	5008	,	,		21629	0.4058		0.4573	False		,,,				2504	0.3885				p.A188A		Atlas-SNP	.											.	CPO	42	.	0			c.A564T						PASS	.	A		1662,2744	507.6+/-366.7	329,1004,870	194.0	175.0	181.0		564	-1.9	0.3	2	dbSNP_121	181	4088,4512	560.3+/-387.6	976,2136,1188	no	coding-synonymous	CPO	NM_173077.2		1305,3140,2058	TT,TA,AA		47.5349,37.7213,44.2104		188/375	207825656	5750,7256	2203	4300	6503	SO:0001819	synonymous_variant	130749	exon6			CAATGCATCTTGG		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.564A>T	2.37:g.207825656A>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	101	56	0.554455	NM_173077	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																			A|0.570;T|0.430	0.430	strong		0.358	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
LCE1F	353137	hgsc.bcm.edu	37	1	152749091	152749091	+	Missense_Mutation	SNP	C	C	T	rs41268480	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152749091C>T	ENST00000334371.2	+	1	244	c.244C>T	c.(244-246)Cgg>Tgg	p.R82W		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	82	Poly-Arg.				keratinization (GO:0031424)					kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCACCACAGACGGCGTAGGTC	0.706													.|||	455	0.0908546	0.0053	0.1311	5008	,	,		13505	0.0278		0.2117	False		,,,				2504	0.1186				p.R82W		Atlas-SNP	.											LCE1F,right_lower_lobe,carcinoma,-1,1	LCE1F	42	1	0			c.C244T						PASS	.	C	TRP/ARG	161,4241		5,151,2045	22.0	26.0	25.0		244	4.4	1.0	1	dbSNP_127	25	1846,6746		213,1420,2663	no	missense	LCE1F	NM_178354.2	101	218,1571,4708	TT,TC,CC		21.4851,3.6574,15.4456	probably-damaging	82/119	152749091	2007,10987	2201	4296	6497	SO:0001583	missense	353137	exon1			CACAGACGGCGTA		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"""Late cornified envelopes"""	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.244C>T	1.37:g.152749091C>T	ENSP00000334187:p.Arg82Trp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_178354		Missense_Mutation	SNP	ENST00000334371.2	37	CCDS1023.1	229	0.10485347985347986	3	0.006097560975609756	43	0.11878453038674033	14	0.024475524475524476	169	0.22295514511873352	C	10.38	1.333655	0.24167	0.036574	0.214851	ENSG00000240386	ENST00000334371	T	0.03831	3.79	4.45	4.45	0.53987	.	.	.	.	.	T	0.03011	0.0089	L	0.50333	1.59	0.40610	P	0.01833600000000002	D	0.54772	0.968	B	0.40636	0.335	T	0.35176	-0.9799	8	0.87932	D	0	.	12.7727	0.57429	0.0:1.0:0.0:0.0	rs41268480	82	Q5T754	LCE1F_HUMAN	W	82	ENSP00000334187:R82W	ENSP00000334187:R82W	R	+	1	2	LCE1F	151015715	0.032000	0.19561	0.964000	0.40570	0.487000	0.33371	0.406000	0.21032	2.445000	0.82738	0.557000	0.71058	CGG	C|0.867;T|0.133	0.133	strong		0.706	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354	
PSG5	5673	hgsc.bcm.edu	37	19	43690506	43690506	+	Missense_Mutation	SNP	G	G	C	rs8107936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43690506G>C	ENST00000366175.3	-	1	182	c.52C>G	c.(52-54)Ctc>Gtc	p.L18V	PSG5_ENST00000342951.6_Missense_Mutation_p.L18V|PSG5_ENST00000599812.1_Missense_Mutation_p.L18V|PSG5_ENST00000401992.1_5'UTR|PSG5_ENST00000404580.1_Missense_Mutation_p.L18V|PSG5_ENST00000407356.1_Missense_Mutation_p.L18V|PSG5_ENST00000407568.1_Missense_Mutation_p.L18V			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	18			L -> V (in dbSNP:rs8107936). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2735907, ECO:0000269|PubMed:2789512}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				GTGAGCAGGAGCCCCTTCCAG	0.582													G|||	3659	0.730631	0.7481	0.5749	5008	,	,		18212	0.9762		0.6123	False		,,,				2504	0.6861				p.L18V		Atlas-SNP	.											PSG5,rectum,carcinoma,0,1	PSG5	58	1	0			c.C52G						PASS	.	G	VAL/LEU,VAL/LEU	3185,1221		1179,827,197	91.0	91.0	91.0		52,52	0.3	0.0	19	dbSNP_116	91	5160,3426		1603,1954,736	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	32,32	2782,2781,933	CC,CG,GG		39.9022,27.7122,35.7682	benign,benign	18/336,18/336	43690506	8345,4647	2203	4293	6496	SO:0001583	missense	5673	exon1			GCAGGAGCCCCTT		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.52C>G	19.37:g.43690506G>C	ENSP00000382334:p.Leu18Val	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	1393	0.6378205128205128	289	0.5873983739837398	177	0.4889502762430939	518	0.9055944055944056	409	0.5395778364116095	N	3.655	-0.070693	0.07228	0.722878	0.600978	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000407568;ENST00000342951;ENST00000404580;ENST00000401992	T;T;T;T;T	0.01665	5.01;5.01;4.7;5.01;4.99	1.41	0.325	0.15903	.	.	.	.	.	T	0.00012	0.0000	L	0.33753	1.03	0.80722	P	0.0	B;B	0.29671	0.254;0.14	B;B	0.43575	0.424;0.35	T	0.02639	-1.1130	8	0.49607	T	0.09	.	3.7117	0.08423	0.2559:0.0:0.7441:0.0	rs8107936;rs11549987;rs17856401;rs59769041	18;18	E9PC55;Q15238	.;PSG5_HUMAN	V	18	ENSP00000382334:L18V;ENSP00000386008:L18V;ENSP00000386053:L18V;ENSP00000344413:L18V;ENSP00000385250:L18V	ENSP00000344413:L18V	L	-	1	0	PSG5	48382346	0.117000	0.22190	0.003000	0.11579	0.030000	0.12068	0.008000	0.13197	0.166000	0.19597	0.184000	0.17185	CTC	G|0.373;C|0.627	0.627	strong		0.582	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
CARD8	22900	hgsc.bcm.edu	37	19	48715153	48715153	+	Silent	SNP	T	T	C	rs3745718	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48715153T>C	ENST00000359009.4	-	10	1422	c.1110A>G	c.(1108-1110)caA>caG	p.Q370Q	CARD8_ENST00000391898.3_Silent_p.Q476Q|CARD8_ENST00000520753.1_3'UTR|CARD8_ENST00000447740.2_Silent_p.Q426Q|CARD8_ENST00000520153.1_Silent_p.Q426Q|CARD8_ENST00000520015.1_3'UTR|CARD8_ENST00000357778.5_Intron|CARD8_ENST00000521613.1_Silent_p.Q426Q|CTC-453G23.8_ENST00000595201.1_RNA|CARD8_ENST00000519940.1_Silent_p.Q476Q|ZNF114_ENST00000597695.1_Intron			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	370	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		CCTCATTGTCTTGGAGATCAT	0.532													T|||	1948	0.388978	0.2186	0.5533	5008	,	,		20355	0.2282		0.5199	False		,,,				2504	0.5337				p.Q476Q		Atlas-SNP	.											CARD8_ENST00000391898,colon,carcinoma,0,1	CARD8	53	1	0			c.A1428G						PASS	.	T	,,,,	1188,3218	415.0+/-337.0	160,868,1175	185.0	173.0	177.0		1428,1278,,,1278	0.9	0.2	19	dbSNP_107	177	4800,3800	612.6+/-396.0	1370,2060,870	no	coding-synonymous,coding-synonymous,utr-3,utr-3,coding-synonymous	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	,,,,	1530,2928,2045	CC,CT,TT		44.186,26.9632,46.0403	,,,,	476/538,426/488,,,426/488	48715153	5988,7018	2203	4300	6503	SO:0001819	synonymous_variant	22900	exon11			ATTGTCTTGGAGA	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.1110A>G	19.37:g.48715153T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	162	90	0.555556	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Silent	SNP	ENST00000359009.4	37																																																																																				T|0.588;C|0.412	0.412	strong		0.532	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
IFT74	80173	hgsc.bcm.edu	37	9	27062721	27062721	+	Missense_Mutation	SNP	C	C	T	rs3429	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:27062721C>T	ENST00000443698.1	+	20	1961	c.1790C>T	c.(1789-1791)aCc>aTc	p.T597I	IFT74_ENST00000433700.1_Missense_Mutation_p.T597I|IFT74_ENST00000380062.5_Missense_Mutation_p.T597I	NM_001099222.1	NP_001092692.1	Q96LB3	IFT74_HUMAN	intraflagellar transport 74	597			T -> I (in dbSNP:rs3429). {ECO:0000269|PubMed:14702039}.		cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|keratinocyte development (GO:0003334)|negative regulation of epithelial cell proliferation (GO:0050680)|Notch signaling pathway (GO:0007219)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|nucleus (GO:0005634)	beta-tubulin binding (GO:0048487)|chromatin binding (GO:0003682)			endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	6		all_neural(11;2.36e-10)		Lung(218;1.4e-05)|LUSC - Lung squamous cell carcinoma(38;0.000114)		TTACATAGCACCAGCGGAAAC	0.393													C|||	527	0.105232	0.0408	0.0706	5008	,	,		15575	0.0308		0.1441	False		,,,				2504	0.2536				p.T597I		Atlas-SNP	.											.	IFT74	46	.	0			c.C1790T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	192,3546		5,182,1682	96.0	88.0	90.0		1790,1790,1790	3.9	0.0	9	dbSNP_36	90	1046,7146		67,912,3117	yes	missense,missense,missense	IFT74	NM_001099222.1,NM_001099223.1,NM_025103.2	89,89,89	72,1094,4799	TT,TC,CC		12.7686,5.1364,10.3772	benign,benign,benign	597/601,597/601,597/601	27062721	1238,10692	1869	4096	5965	SO:0001583	missense	80173	exon20			ATAGCACCAGCGG	AK023707	CCDS43793.1, CCDS47955.1	9p21.1	2014-07-03	2014-07-03	2005-11-02	ENSG00000096872	ENSG00000096872		"""Intraflagellar transport homologs"""	21424	protein-coding gene	gene with protein product	"""capillary morphogenesis protein 1"""	608040	"""coiled-coil domain containing 2"", ""intraflagellar transport 74 homolog (Chlamydomonas)"""	CCDC2		11683410	Standard	NM_001099223		Approved	CMG1, CMG-1, FLJ22621	uc003zqg.4	Q96LB3	OTTHUMG00000021028	ENST00000443698.1:c.1790C>T	9.37:g.27062721C>T	ENSP00000404122:p.Thr597Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_001099222	Q3B789|Q5VY34|Q6PGQ8|Q9H643|Q9H8G7	Missense_Mutation	SNP	ENST00000443698.1	37	CCDS43793.1	172	0.07875457875457875	21	0.042682926829268296	29	0.08011049723756906	18	0.03146853146853147	104	0.13720316622691292	C	11.59	1.684685	0.29872	0.051364	0.127686	ENSG00000096872	ENST00000433700;ENST00000443698;ENST00000380062	T;T;T	0.12039	2.72;2.72;2.72	5.9	3.87	0.44632	.	0.421653	0.24162	N	0.040969	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.22983	0.078	B	0.29785	0.107	T	0.26292	-1.0107	9	0.52906	T	0.07	-0.7514	8.2372	0.31634	0.0:0.6095:0.3013:0.0893	rs3429;rs3739543;rs17641379;rs52824285;rs3429	597	Q96LB3	IFT74_HUMAN	I	597	ENSP00000389224:T597I;ENSP00000404122:T597I;ENSP00000369402:T597I	ENSP00000369402:T597I	T	+	2	0	IFT74	27052721	0.902000	0.30710	0.026000	0.17262	0.675000	0.39556	1.796000	0.38794	0.641000	0.30601	0.650000	0.86243	ACC	C|0.900;T|0.100	0.100	strong		0.393	IFT74-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055476.2	NM_025103	
RSL1D1	26156	hgsc.bcm.edu	37	16	11933666	11933666	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11933666C>T	ENST00000571133.1	-	8	1104	c.1032G>A	c.(1030-1032)ggG>ggA	p.G344G	RSL1D1_ENST00000542106.1_Silent_p.G124G	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	344					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.G344G(1)		NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						GTTTTTTCTTCCCATGCTCTG	0.438																																					p.G344G		Atlas-SNP	.											RSL1D1,NS,NS,0,1	RSL1D1	40	1	1	Substitution - coding silent(1)	NS(1)	c.G1032A						scavenged	.						287.0	251.0	263.0					16																	11933666		2197	4300	6497	SO:0001819	synonymous_variant	26156	exon8			TTTCTTCCCATGC	AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.1032G>A	16.37:g.11933666C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	173	3	0.017341	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Silent	SNP	ENST00000571133.1	37	CCDS10551.1																																																																																			.	.	none		0.438	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659	
KRT28	162605	hgsc.bcm.edu	37	17	38950272	38950272	+	Silent	SNP	T	T	C	rs2250671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38950272T>C	ENST00000306658.7	-	6	1070	c.1005A>G	c.(1003-1005)acA>acG	p.T335T		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				TCTCGGTCTCTGTCAAGGAGC	0.552													C|||	3097	0.618411	0.8116	0.5259	5008	,	,		18684	0.4196		0.6213	False		,,,				2504	0.6247				p.T335T	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.A1005G						PASS	.	C		3393,1013	378.0+/-322.7	1305,783,115	109.0	113.0	111.0		1005	-11.4	0.0	17	dbSNP_100	111	5012,3588	520.0+/-379.6	1437,2138,725	no	coding-synonymous	KRT28	NM_181535.3		2742,2921,840	CC,CT,TT		41.7209,22.9914,35.376		335/465	38950272	8405,4601	2203	4300	6503	SO:0001819	synonymous_variant	162605	exon6			GGTCTCTGTCAAG	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30842	protein-coding gene	gene with protein product			"""keratin 25D"""	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.1005A>G	17.37:g.38950272T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_181535		Silent	SNP	ENST00000306658.7	37	CCDS11376.1																																																																																			T|0.373;C|0.627	0.627	strong		0.552	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
LRRC55	219527	hgsc.bcm.edu	37	11	56954846	56954846	+	Silent	SNP	C	C	T	rs716745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:56954846C>T	ENST00000497933.1	+	2	1065	c.918C>T	c.(916-918)ttC>ttT	p.F306F		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	276					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						TCATTGCGTTCGTGGGCTTCG	0.587													C|||	1211	0.241813	0.1422	0.255	5008	,	,		20458	0.1925		0.3817	False		,,,				2504	0.274				p.F306F		Atlas-SNP	.											.	LRRC55	52	.	0			c.C918T						PASS	.	C		790,3612	319.3+/-296.1	69,652,1480	172.0	116.0	135.0		918	-7.3	0.2	11	dbSNP_86	135	3263,5329	490.4+/-372.8	658,1947,1691	no	coding-synonymous	LRRC55	NM_001005210.2		727,2599,3171	TT,TC,CC		37.9772,17.9464,31.1913		306/342	56954846	4053,8941	2201	4296	6497	SO:0001819	synonymous_variant	219527	exon2			TGCGTTCGTGGGC		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.918C>T	11.37:g.56954846C>T		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_001005210	A7E2U7|B2RN81	Silent	SNP	ENST00000497933.1	37	CCDS31539.1																																																																																			C|0.718;T|0.282	0.282	strong		0.587	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
FAM86C1	55199	hgsc.bcm.edu	37	11	71507205	71507205	+	Missense_Mutation	SNP	C	C	T	rs57679800	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:71507205C>T	ENST00000359244.4	+	4	427	c.404C>T	c.(403-405)cCg>cTg	p.P135L	FAM86C1_ENST00000426628.2_Missense_Mutation_p.P128L|FAM86C1_ENST00000346333.6_Missense_Mutation_p.P101L	NM_018172.2	NP_060642.2	Q9NVL1	FA86C_HUMAN	family with sequence similarity 86, member C1	135			P -> L (in dbSNP:rs57679800).							lung(1)	1						TGTTCACCACCGAGCTATGTG	0.637													.|||	414	0.0826677	0.2247	0.036	5008	,	,		17898	0.0159		0.0278	False		,,,				2504	0.0491				p.P135L		Atlas-SNP	.											FAM86C1_ENST00000426628,NS,carcinoma,0,2	FAM86C1	27	2	0			c.C404T						scavenged	.	C	LEU/PRO,LEU/PRO,LEU/PRO	749,3651		38,673,1489	109.0	120.0	116.0		383,404,302	-3.0	0.0	11	dbSNP_129	116	108,8478		0,108,4185	yes	missense,missense,missense	FAM86C1	NM_001099653.1,NM_018172.2,NM_152563.2	98,98,98	38,781,5674	TT,TC,CC		1.2579,17.0227,6.5994	benign,benign,benign	128/159,135/166,101/132	71507205	857,12129	2200	4293	6493	SO:0001583	missense	55199	exon4			CACCACCGAGCTA	AK130709	CCDS8202.1, CCDS41686.1, CCDS44664.1	11q13.4	2011-07-07	2011-07-07	2011-07-07	ENSG00000158483	ENSG00000158483			25561	protein-coding gene	gene with protein product			"""family with sequence similarity 86, member C"""	FAM86C		12477932	Standard	NM_152563		Approved	FLJ10661, FLJ27199	uc001oqv.4	Q9NVL1	OTTHUMG00000160552	ENST00000359244.4:c.404C>T	11.37:g.71507205C>T	ENSP00000352182:p.Pro135Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	133	13	0.0977444	NM_018172	Q8N5D3	Missense_Mutation	SNP	ENST00000359244.4	37	CCDS41686.1	142	0.06501831501831502	94	0.1910569105691057	16	0.04419889502762431	7	0.012237762237762238	25	0.032981530343007916	.	7.137	0.580963	0.13686	0.170227	0.012579	ENSG00000158483	ENST00000346333;ENST00000359244;ENST00000426628;ENST00000528685	T;T;T;T	0.16597	2.38;2.62;2.39;2.33	1.49	-2.98	0.05513	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	N	0.999999	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.26430	-1.0103	8	0.02654	T	1	.	1.3057	0.02087	0.2011:0.2321:0.4001:0.1667	rs57679800;rs61889009	128;101;135	G3V0F7;Q9NVL1-2;Q9NVL1	.;.;FA86C_HUMAN	L	101;135;128;101	ENSP00000325662:P101L;ENSP00000352182:P135L;ENSP00000391329:P128L;ENSP00000436598:P101L	ENSP00000325662:P101L	P	+	2	0	FAM86C1	71184853	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-1.873000	0.01637	-1.543000	0.01723	-1.238000	0.01547	CCG	C|0.500;T|0.500	0.500	weak		0.637	FAM86C1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361120.1	NM_152563	
MATN2	4147	hgsc.bcm.edu	37	8	98954108	98954108	+	Silent	SNP	G	G	T	rs35407519	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:98954108G>T	ENST00000520016.1	+	3	940	c.816G>T	c.(814-816)tcG>tcT	p.S272S	MATN2_ENST00000521689.1_Silent_p.S272S|MATN2_ENST00000254898.5_Silent_p.S272S|MATN2_ENST00000524308.1_Silent_p.S272S|MATN2_ENST00000522025.2_5'UTR			O00339	MATN2_HUMAN	matrilin 2	272	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TTCTCAACTCGGATCAGACGA	0.463													G|||	557	0.111222	0.0098	0.2493	5008	,	,		22830	0.1042		0.0915	False		,,,				2504	0.1779				p.S272S		Atlas-SNP	.											.	MATN2	165	.	0			c.G816T						PASS	.	G	,	112,4018		3,106,1956	116.0	116.0	116.0		816,816	-1.0	0.9	8	dbSNP_126	116	884,7548		61,762,3393	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	64,868,5349	TT,TG,GG		10.4839,2.7119,7.9287	,	272/957,272/938	98954108	996,11566	2065	4216	6281	SO:0001819	synonymous_variant	4147	exon4			CAACTCGGATCAG	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.816G>T	8.37:g.98954108G>T		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	250	108	0.432	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	209	0.09569597069597069	6	0.012195121951219513	64	0.17679558011049723	60	0.1048951048951049	79	0.10422163588390501	G	7.339	0.620463	0.14193	0.027119	0.104839	ENSG00000132561	ENST00000518154	.	.	.	5.24	-0.969	0.10310	.	.	.	.	.	.	.	.	.	.	.	0.20638	P	0.999873685	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.3583	3.0914	0.06295	0.3844:0.1066:0.4007:0.1083	rs35407519	.	.	.	X	96	.	.	G	+	1	0	MATN2	99023284	0.797000	0.28877	0.927000	0.36925	0.908000	0.53690	0.050000	0.14120	-0.244000	0.09639	-1.134000	0.01955	GGA	G|0.905;T|0.095	0.095	strong		0.463	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
DOCK10	55619	hgsc.bcm.edu	37	2	225750861	225750861	+	Silent	SNP	C	C	T	rs2304336	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:225750861C>T	ENST00000258390.7	-	6	598	c.531G>A	c.(529-531)gcG>gcA	p.A177A	DOCK10_ENST00000409592.3_Silent_p.A171A	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	177					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		CAGTTCCTCCCGCTCCTCCAC	0.502													c|||	1123	0.224241	0.5272	0.0937	5008	,	,		17262	0.0556		0.1412	False		,,,				2504	0.1667				p.A177A		Atlas-SNP	.											DOCK10,colon,carcinoma,-1,1	DOCK10	308	1	0			c.G531A						PASS	.	T		1820,2040		428,964,538	115.0	117.0	116.0		531	-11.2	0.1	2	dbSNP_100	116	1240,6986		95,1050,2968	no	coding-synonymous	DOCK10	NM_014689.2		523,2014,3506	TT,TC,CC		15.0742,47.1503,25.3186		177/2187	225750861	3060,9026	1930	4113	6043	SO:0001819	synonymous_variant	55619	exon6			TCCTCCCGCTCCT	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.531G>A	2.37:g.225750861C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	74	27	0.364865	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																			C|0.784;T|0.216	0.216	strong		0.502	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
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 GAIIx	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		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	43	9	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		
UAP1L1	91373	hgsc.bcm.edu	37	9	139972672	139972672	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139972672G>A	ENST00000409858.3	+	2	492	c.460G>A	c.(460-462)Ggt>Agt	p.G154S	UAP1L1_ENST00000476184.1_Intron|UAP1L1_ENST00000360271.3_De_novo_Start_InFrame	NM_207309.2	NP_997192.2	Q3KQV9	UAP1L_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1 like 1	154							uridylyltransferase activity (GO:0070569)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		GCAGCTGGCCGGTGAGCGCCA	0.711																																					p.G154S		Atlas-SNP	.											.	UAP1L1	46	.	0			c.G460A						PASS	.						8.0	14.0	12.0					9																	139972672		686	1576	2262	SO:0001583	missense	91373	exon2			CTGGCCGGTGAGC	AK022632	CCDS7028.2	9q34.3	2014-07-31	2014-07-31		ENSG00000197355	ENSG00000197355			28082	protein-coding gene	gene with protein product							Standard	NM_207309		Approved		uc010ncb.3	Q3KQV9	OTTHUMG00000020962	ENST00000409858.3:c.460G>A	9.37:g.139972672G>A	ENSP00000386935:p.Gly154Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_207309	A2AMJ8|Q5SPZ2|Q69YQ3|Q6ZR38	Missense_Mutation	SNP	ENST00000409858.3	37	CCDS7028.2	.	.	.	.	.	.	.	.	.	.	G	11.19	1.564600	0.27915	.	.	ENSG00000197355	ENST00000409858	T	0.15952	2.38	4.92	3.09	0.35607	.	.	.	.	.	T	0.11153	0.0272	L	0.31120	0.905	0.31117	N	0.709254	B	0.24258	0.1	B	0.20184	0.028	T	0.26360	-1.0105	9	0.17369	T	0.5	.	8.1425	0.31091	0.2497:0.0:0.7503:0.0	.	154	Q3KQV9	UAP1L_HUMAN	S	154	ENSP00000386935:G154S	ENSP00000386935:G154S	G	+	1	0	UAP1L1	139092493	0.504000	0.26123	0.031000	0.17742	0.913000	0.54294	1.091000	0.30915	0.500000	0.27991	-0.306000	0.09157	GGT	.	.	none		0.711	UAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055216.2	XM_038063	
SOS2	6655	hgsc.bcm.edu	37	14	50616878	50616878	+	Silent	SNP	G	G	A	rs2229869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:50616878G>A	ENST00000216373.5	-	14	2506	c.2232C>T	c.(2230-2232)aaC>aaT	p.N744N	SOS2_ENST00000543680.1_Silent_p.N711N	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	744					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					GGCTTACTCCGTTTGCCTGAG	0.393													g|||	2596	0.518371	0.4024	0.647	5008	,	,		20617	0.4276		0.67	False		,,,				2504	0.5215				p.N744N		Atlas-SNP	.											.	SOS2	195	.	0			c.C2232T						PASS	.	A		2018,2388	562.1+/-380.9	463,1092,648	291.0	247.0	262.0		2232	1.7	1.0	14	dbSNP_98	262	5889,2711	682.4+/-403.8	2013,1863,424	no	coding-synonymous	SOS2	NM_006939.2		2476,2955,1072	AA,AG,GG		31.5233,45.8012,39.205		744/1333	50616878	7907,5099	2203	4300	6503	SO:0001819	synonymous_variant	6655	exon14			TACTCCGTTTGCC	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.2232C>T	14.37:g.50616878G>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	170	81	0.476471	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Silent	SNP	ENST00000216373.5	37	CCDS9697.1																																																																																			G|0.426;A|0.574	0.574	strong		0.393	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
OR10K1	391109	hgsc.bcm.edu	37	1	158435928	158435928	+	Missense_Mutation	SNP	G	G	A	rs41273489	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158435928G>A	ENST00000289451.2	+	1	657	c.577G>A	c.(577-579)Ggc>Agc	p.G193S		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	193						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)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					TCAGCACTCCGGCTTCAGTCA	0.493													G|||	182	0.0363419	0.0053	0.0576	5008	,	,		23947	0.0		0.0954	False		,,,				2504	0.0399				p.G193S		Atlas-SNP	.											.	OR10K1	80	.	0			c.G577A						PASS	.	G	SER/GLY	75,4331	67.0+/-104.6	1,73,2129	175.0	175.0	175.0		577	1.2	0.0	1	dbSNP_127	175	814,7786	188.9+/-235.7	31,752,3517	yes	missense	OR10K1	NM_001004473.1	56	32,825,5646	AA,AG,GG		9.4651,1.7022,6.8353	benign	193/314	158435928	889,12117	2203	4300	6503	SO:0001583	missense	391109	exon1			CACTCCGGCTTCA	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"""GPCR / Class A : Olfactory receptors"""	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.577G>A	1.37:g.158435928G>A	ENSP00000289451:p.Gly193Ser	Somatic	275	1	0.00363636		WXS	Illumina HiSeq	Phase_I	274	147	0.536496	NM_001004473	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	37	CCDS30897.1	101	0.04624542124542125	5	0.01016260162601626	22	0.06077348066298342	0	0.0	74	0.09762532981530343	g	0.026	-1.367623	0.01225	0.017022	0.094651	ENSG00000173285	ENST00000289451	T	0.00039	8.85	4.24	1.23	0.21249	GPCR, rhodopsin-like superfamily (1);	0.928471	0.08920	N	0.874611	T	0.00012	0.0000	N	0.00608	-1.33	0.80722	P	0.0	B	0.14012	0.009	B	0.08055	0.003	T	0.08249	-1.0731	9	0.08837	T	0.75	.	4.1017	0.10017	0.0:0.3947:0.2123:0.393	rs41273489	193	Q8NGX5	O10K1_HUMAN	S	193	ENSP00000289451:G193S	ENSP00000289451:G193S	G	+	1	0	OR10K1	156702552	0.000000	0.05858	0.001000	0.08648	0.313000	0.28021	-1.198000	0.03035	0.055000	0.16094	-0.310000	0.09108	GGC	G|0.931;A|0.069	0.069	strong		0.493	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1		
WDR66	144406	hgsc.bcm.edu	37	12	122405912	122405912	+	Splice_Site	SNP	G	G	T	rs1169081	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:122405912G>T	ENST00000288912.4	+	17	3462	c.2608G>T	c.(2608-2610)Gtg>Ttg	p.V870L	WDR66_ENST00000397454.2_Splice_Site_p.V870L|WDR66_ENST00000545752.1_3'UTR	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	870				V -> L (in Ref. 2; AAH28421 and 4; CAD38786). {ECO:0000305}.			calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		TCCTTTCTAGGTGGGACTTCA	0.527													G|||	1474	0.294329	0.0877	0.3631	5008	,	,		21223	0.4702		0.3121	False		,,,				2504	0.3252				p.V870L	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.G2608T						PASS	.	G	LEU/VAL,LEU/VAL	429,3459		32,365,1547	101.0	99.0	100.0		2608,2608	5.2	1.0	12	dbSNP_87	100	2488,5778		383,1722,2028	yes	missense-near-splice,missense-near-splice	WDR66	NM_001178003.1,NM_144668.5	32,32	415,2087,3575	TT,TG,GG		30.0992,11.034,24.0003	possibly-damaging,possibly-damaging	870/942,870/1150	122405912	2917,9237	1944	4133	6077	SO:0001630	splice_region_variant	144406	exon17			TTCTAGGTGGGAC	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2608-1G>T	12.37:g.122405912G>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	686	0.3141025641025641	46	0.09349593495934959	123	0.3397790055248619	277	0.48426573426573427	240	0.316622691292876	G	17.08	3.298504	0.60195	0.11034	0.300992	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.54479	0.57;1.31	5.19	5.19	0.71726	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.139333	0.47455	D	0.000222	T	0.00012	0.0000	L	0.55743	1.74	0.20703	P	0.999862575	P	0.35745	0.518	B	0.37091	0.241	T	0.47484	-0.9114	8	.	.	.	.	18.7082	0.91646	0.0:0.0:1.0:0.0	rs1169081;rs1720054;rs17298029;rs60986192;rs1169081	870	Q8TBY9	WDR66_HUMAN	L	870	ENSP00000288912:V870L;ENSP00000380595:V870L	.	V	+	1	0	WDR66	120890295	1.000000	0.71417	1.000000	0.80357	0.345000	0.29048	5.134000	0.64770	2.420000	0.82092	0.561000	0.74099	GTG	G|0.708;T|0.292	0.292	strong		0.527	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	Missense_Mutation
SEPT12	124404	hgsc.bcm.edu	37	16	4833970	4833970	+	Silent	SNP	C	C	T	rs759991	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4833970C>T	ENST00000268231.8	-	5	737	c.474G>A	c.(472-474)gtG>gtA	p.V158V	SEPT12_ENST00000591861.1_5'Flank|SEPT12_ENST00000396693.5_Intron	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	158	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.V158V(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						CGCAGCAGTGCACCCGGGTGT	0.642													C|||	1568	0.313099	0.1989	0.3559	5008	,	,		16641	0.2966		0.3131	False		,,,				2504	0.454				p.V158V		Atlas-SNP	.											SEPT12,NS,carcinoma,0,1	SEPT12	40	1	1	Substitution - coding silent(1)	stomach(1)	c.G474A						PASS	.	C	,	899,3495	346.9+/-309.2	95,709,1393	136.0	124.0	128.0		,474	1.4	1.0	16	dbSNP_86	128	2295,6305	385.5+/-341.5	307,1681,2312	no	intron,coding-synonymous	SEPT12	NM_001154458.2,NM_144605.4	,	402,2390,3705	TT,TC,CC		26.686,20.4597,24.5806	,	,158/359	4833970	3194,9800	2197	4300	6497	SO:0001819	synonymous_variant	124404	exon5			GCAGTGCACCCGG	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.474G>A	16.37:g.4833970C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	84	80	0.952381	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	CCDS10522.1																																																																																			C|0.728;T|0.272	0.272	strong		0.642	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
ACAP1	9744	hgsc.bcm.edu	37	17	7254315	7254315	+	Missense_Mutation	SNP	G	G	A	rs35985803	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7254315G>A	ENST00000158762.3	+	21	2325	c.2119G>A	c.(2119-2121)Gca>Aca	p.A707T	RP11-542C16.1_ENST00000572417.1_RNA|ACAP1_ENST00000570504.1_Missense_Mutation_p.A11T|ACAP1_ENST00000574499.1_Missense_Mutation_p.A32T|KCTD11_ENST00000333751.3_5'Flank|ACAP1_ENST00000575415.1_Missense_Mutation_p.A11T|ACAP1_ENST00000571471.1_Missense_Mutation_p.A11T	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	707	Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						CCAGGGGCAGGCAGGTAAAGA	0.587													g|||	214	0.0427316	0.0151	0.0389	5008	,	,		14235	0.0357		0.0716	False		,,,				2504	0.0603				p.A707T		Atlas-SNP	.											.	ACAP1	66	.	0			c.G2119A						PASS	.		THR/ALA	119,4287	90.2+/-128.9	3,113,2087	81.0	80.0	80.0		2119	0.2	1.0	17	dbSNP_126	80	728,7872	176.6+/-226.4	25,678,3597	yes	missense	ACAP1	NM_014716.3	58	28,791,5684	AA,AG,GG		8.4651,2.7009,6.5124	benign	707/741	7254315	847,12159	2203	4300	6503	SO:0001583	missense	9744	exon21			GGGCAGGCAGGTA	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.2119G>A	17.37:g.7254315G>A	ENSP00000158762:p.Ala707Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_014716	Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	37	CCDS11101.1	97	0.044413919413919416	12	0.024390243902439025	20	0.055248618784530384	13	0.022727272727272728	52	0.06860158311345646	g	12.55	1.972076	0.34754	0.027009	0.084651	ENSG00000072818	ENST00000158762	T	0.73152	-0.72	4.53	0.24	0.15489	.	0.666605	0.15127	N	0.279041	T	0.03520	0.0101	N	0.12746	0.255	0.28933	N	0.891457	B	0.02656	0.0	B	0.04013	0.001	T	0.03000	-1.1084	10	0.23891	T	0.37	.	7.096	0.25309	0.3837:0.0:0.6163:0.0	rs35985803;rs35985803	707	Q15027	ACAP1_HUMAN	T	707	ENSP00000158762:A707T	ENSP00000158762:A707T	A	+	1	0	ACAP1	7195039	1.000000	0.71417	0.996000	0.52242	0.310000	0.27922	0.407000	0.21049	-0.061000	0.13110	-0.461000	0.05368	GCA	G|0.944;A|0.056	0.056	strong		0.587	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
VCAN	1462	hgsc.bcm.edu	37	5	82815408	82815408	+	Missense_Mutation	SNP	G	G	A	rs2287926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:82815408G>A	ENST00000265077.3	+	7	1848	c.1283G>A	c.(1282-1284)gGc>gAc	p.G428D	VCAN_ENST00000342785.4_Missense_Mutation_p.G428D|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000512590.2_Missense_Mutation_p.G380D|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	428	GAG-alpha (glucosaminoglycan attachment domain).		G -> D (in dbSNP:rs2287926).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|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 organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ACACCTACTGGCAGTACCAAG	0.463													G|||	1066	0.212859	0.3275	0.1412	5008	,	,		20371	0.1796		0.1173	False		,,,				2504	0.2413				p.G428D		Atlas-SNP	.											.	VCAN	498	.	0			c.G1283A						PASS	.	G	,,ASP/GLY,ASP/GLY	1229,3177	414.4+/-336.8	175,879,1149	82.0	84.0	83.0		,,1283,1283	0.9	0.0	5	dbSNP_100	83	984,7616	211.3+/-251.9	55,874,3371	yes	intron,intron,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,94,94	230,1753,4520	AA,AG,GG		11.4419,27.8938,17.0152	,,probably-damaging,probably-damaging	,,428/1643,428/3397	82815408	2213,10793	2203	4300	6503	SO:0001583	missense	1462	exon7			CTACTGGCAGTAC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.1283G>A	5.37:g.82815408G>A	ENSP00000265077:p.Gly428Asp	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	137	78	0.569343	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	407	0.18635531135531136	163	0.3313008130081301	51	0.1408839779005525	103	0.18006993006993008	90	0.11873350923482849	G	6.902	0.535981	0.13188	0.278938	0.114419	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	D;D;D	0.85702	-1.91;-1.99;-2.02	5.92	0.918	0.19386	.	0.421595	0.22627	N	0.057628	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	P;D	0.61697	0.939;0.99	P;P	0.54889	0.66;0.763	T	0.09530	-1.0670	9	0.35671	T	0.21	.	1.2917	0.02061	0.2548:0.2651:0.3444:0.1357	rs2287926;rs52819906;rs57562090;rs2287926	428;428	P13611-3;P13611	.;CSPG2_HUMAN	D	428;428;380	ENSP00000265077:G428D;ENSP00000342768:G428D;ENSP00000425959:G380D	ENSP00000265077:G428D	G	+	2	0	VCAN	82851164	0.049000	0.20398	0.000000	0.03702	0.025000	0.11179	0.632000	0.24583	-0.114000	0.11936	-0.175000	0.13238	GGC	G|0.819;A|0.181	0.181	strong		0.463	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
IKBKAP	8518	hgsc.bcm.edu	37	9	111668652	111668652	+	Missense_Mutation	SNP	C	C	T	rs838827	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:111668652C>T	ENST00000374647.5	-	14	1881	c.1574G>A	c.(1573-1575)cGg>cAg	p.R525Q	IKBKAP_ENST00000537196.1_Missense_Mutation_p.R176Q	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	525			R -> Q (in dbSNP:rs838827).		chromatin organization (GO:0006325)|immune response (GO:0006955)|positive regulation of cell migration (GO:0030335)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)	phosphorylase kinase regulator activity (GO:0008607)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						AATGACAGACCGGGGGCTGAA	0.463													C|||	286	0.0571086	0.1324	0.0346	5008	,	,		19194	0.0		0.0686	False		,,,				2504	0.0184				p.R525Q		Atlas-SNP	.											.	IKBKAP	122	.	0			c.G1574A						PASS	.	C	GLN/ARG	500,3906	232.3+/-245.9	26,448,1729	137.0	121.0	126.0		1574	0.3	0.3	9	dbSNP_86	126	547,8053	150.9+/-205.7	18,511,3771	yes	missense	IKBKAP	NM_003640.3	43	44,959,5500	TT,TC,CC		6.3605,11.3482,8.0501	benign	525/1333	111668652	1047,11959	2203	4300	6503	SO:0001583	missense	8518	exon14			ACAGACCGGGGGC	AF044195	CCDS6773.1	9q31	2014-09-17	2003-12-02		ENSG00000070061	ENSG00000070061		"""Elongator acetyltransferase complex subunits"""	5959	protein-coding gene	gene with protein product	"""elongator acetyltransferase complex subunit 1"""	603722	"""dysautonomia (Riley-Day syndrome, hereditary sensory autonomic neuropathy type III)"""	DYS		9751059, 11179008	Standard	NM_003640		Approved	IKAP, TOT1, ELP1, IKI3	uc004bdm.4	O95163	OTTHUMG00000020465	ENST00000374647.5:c.1574G>A	9.37:g.111668652C>T	ENSP00000363779:p.Arg525Gln	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_003640	Q5JSV2|Q9H327|Q9UG87	Missense_Mutation	SNP	ENST00000374647.5	37	CCDS6773.1	125	0.05723443223443223	67	0.13617886178861788	11	0.03038674033149171	0	0.0	47	0.06200527704485488	C	1.540	-0.542007	0.04053	0.113482	0.063605	ENSG00000070061	ENST00000374647;ENST00000537196	T;T	0.26067	2.14;1.76	5.6	0.32	0.15878	.	0.690799	0.14980	N	0.287310	T	0.00039	0.0001	N	0.00446	-1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39981	-0.9587	9	0.10902	T	0.67	-0.7265	8.2551	0.31751	0.0:0.343:0.0:0.657	rs838827;rs1556536;rs1772034;rs2230790;rs52818078;rs59641501;rs838827	525	O95163	ELP1_HUMAN	Q	525;176	ENSP00000363779:R525Q;ENSP00000439367:R176Q	ENSP00000363779:R525Q	R	-	2	0	IKBKAP	110708473	0.964000	0.33143	0.343000	0.25615	0.003000	0.03518	0.340000	0.19892	0.149000	0.19098	-0.321000	0.08615	CGG	C|0.924;T|0.076	0.076	strong		0.463	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1		
NPHP4	261734	hgsc.bcm.edu	37	1	5965381	5965381	+	Silent	SNP	C	C	T	rs12120967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:5965381C>T	ENST00000378156.4	-	15	2191	c.1926G>A	c.(1924-1926)gaG>gaA	p.E642E	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	642					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)		GTAGCACCATCTCGTTGCTTT	0.448													C|||	421	0.0840655	0.0083	0.1095	5008	,	,		22481	0.0823		0.1561	False		,,,				2504	0.0961				p.E642E		Atlas-SNP	.											.	NPHP4	119	.	0			c.G1926A						PASS	.	C		118,3862		4,110,1876	163.0	164.0	164.0		1926	-4.3	0.0	1	dbSNP_120	164	1466,6838		142,1182,2828	no	coding-synonymous	NPHP4	NM_015102.3		146,1292,4704	TT,TC,CC		17.6541,2.9648,12.8948		642/1427	5965381	1584,10700	1990	4152	6142	SO:0001819	synonymous_variant	261734	exon15			CACCATCTCGTTG	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.1926G>A	1.37:g.5965381C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			C|0.908;T|0.092	0.092	strong		0.448	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
APBB3	10307	hgsc.bcm.edu	37	5	139936760	139936760	+	IGR	SNP	G	G	T	rs250426	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139936760G>T	ENST00000357560.4	-	0	2218				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Silent_p.V53V	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGTGCGGCGACCCTCTTGG	0.672													G|||	3165	0.631989	0.292	0.7248	5008	,	,		11754	0.8254		0.7167	False		,,,				2504	0.7393				p.S93X		Atlas-SNP	.											.	SRA1	24	.	0			c.C278A						PASS	.	G		1616,2784		306,1004,890	40.0	49.0	46.0		159	-4.0	1.0	5	dbSNP_79	46	5988,2602		2111,1766,418	no	coding-synonymous	SRA1	NM_001035235.2		2417,2770,1308	TT,TG,GG		30.291,36.7273,41.4627		53/237	139936760	7604,5386	2200	4295	6495	SO:0001628	intergenic_variant	10011	exon1			TGCGGCGACCCTC	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504		5.37:g.139936760G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	96	0.932039	NM_001253764	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Nonsense_Mutation	SNP	ENST00000357560.4	37	CCDS4229.1																																																																																			A|0.000;G|0.374;T|0.626	0.626	strong		0.672	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
SUSD5	26032	hgsc.bcm.edu	37	3	33195309	33195309	+	Missense_Mutation	SNP	A	A	G	rs61743461	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:33195309A>G	ENST00000309558.3	-	5	1232	c.815T>C	c.(814-816)tTg>tCg	p.L272S		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	272				L -> S (in Ref. 1; BAA25453). {ECO:0000305}.	cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						AGCACCAGGCAAGCCTGTGGT	0.562													A|||	1006	0.200879	0.2239	0.1902	5008	,	,		19136	0.1925		0.1551	False		,,,				2504	0.2331				p.L272S		Atlas-SNP	.											.	SUSD5	53	.	0			c.T815C						PASS	.	A	SER/LEU	755,3049		80,595,1227	51.0	51.0	51.0		815	-3.0	0.0	3	dbSNP_129	51	1322,6924		105,1112,2906	yes	missense	SUSD5	NM_015551.1	145	185,1707,4133	GG,GA,AA		16.032,19.8475,17.2365	benign	272/630	33195309	2077,9973	1902	4123	6025	SO:0001583	missense	26032	exon5			CCAGGCAAGCCTG	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.815T>C	3.37:g.33195309A>G	ENSP00000308727:p.Leu272Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_015551		Missense_Mutation	SNP	ENST00000309558.3	37	CCDS46787.1	415|415	0.190018315018315|0.190018315018315	117|117	0.23780487804878048|0.23780487804878048	67|67	0.1850828729281768|0.1850828729281768	117|117	0.20454545454545456|0.20454545454545456	114|114	0.1503957783641161|0.1503957783641161	A|A	5.226|5.226	0.227208|0.227208	0.09916|0.09916	0.198475|0.198475	0.16032|0.16032	ENSG00000173705|ENSG00000173705	ENST00000412539|ENST00000309558	.|T	.|0.06687	.|3.27	6.02|6.02	-2.95|-2.95	0.05564|0.05564	.|.	.|1.433320	.|0.04002	.|N	.|0.296634	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.24721	.|0.11	.|B	.|0.16722	.|0.016	T|T	0.43814|0.43814	-0.9368|-0.9368	4|9	.|0.19147	.|T	.|0.46	-1.7866|-1.7866	6.6702|6.6702	0.23064|0.23064	0.3956:0.2344:0.3699:0.0|0.3956:0.2344:0.3699:0.0	.|.	.|272	.|O60279	.|SUSD5_HUMAN	R|S	208|272	.|ENSP00000308727:L272S	.|ENSP00000308727:L272S	C|L	-|-	1|2	0|0	SUSD5|SUSD5	33170313|33170313	0.073000|0.073000	0.21202|0.21202	0.008000|0.008000	0.14137|0.14137	0.110000|0.110000	0.19582|0.19582	-0.086000|-0.086000	0.11233|0.11233	-0.713000|-0.713000	0.04981|0.04981	0.533000|0.533000	0.62120|0.62120	TGC|TTG	A|0.820;G|0.180	0.180	strong		0.562	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054	
FAM135B	51059	hgsc.bcm.edu	37	8	139144914	139144914	+	Silent	SNP	G	G	A	rs2280848	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:139144914G>A	ENST00000395297.1	-	20	4313	c.4143C>T	c.(4141-4143)gcC>gcT	p.A1381A		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1381										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)			CGATGTGAGCGGCTCGGCCGA	0.547										HNSCC(54;0.14)			G|||	374	0.0746805	0.0204	0.0764	5008	,	,		17920	0.2073		0.0408	False		,,,				2504	0.045				p.A1381A		Atlas-SNP	.											.	FAM135B	423	.	0			c.C4143T						PASS	.	G		87,3859		0,87,1886	197.0	209.0	205.0		4143	-11.5	0.0	8	dbSNP_100	205	210,8094		1,208,3943	no	coding-synonymous	FAM135B	NM_015912.3		1,295,5829	AA,AG,GG		2.5289,2.2048,2.4245		1381/1407	139144914	297,11953	1973	4152	6125	SO:0001819	synonymous_variant	51059	exon20			GTGAGCGGCTCGG	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.4143C>T	8.37:g.139144914G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	152	87	0.572368	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			G|0.930;A|0.070	0.070	strong		0.547	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
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 GAIIx	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	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	226	69	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	
MON2	23041	hgsc.bcm.edu	37	12	62928633	62928633	+	Missense_Mutation	SNP	G	G	A	rs10219555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:62928633G>A	ENST00000393632.2	+	13	2033	c.1642G>A	c.(1642-1644)Gct>Act	p.A548T	MON2_ENST00000552115.1_Missense_Mutation_p.A548T|MON2_ENST00000552738.1_Missense_Mutation_p.A548T|MON2_ENST00000393630.3_Missense_Mutation_p.A548T|MON2_ENST00000546600.1_Missense_Mutation_p.A548T|MON2_ENST00000280379.6_Missense_Mutation_p.A548T|MON2_ENST00000393629.2_Missense_Mutation_p.A548T	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	548			A -> T (in dbSNP:rs10219555). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1}.		actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		AGTTAGTAGGGCTGTTTGGGA	0.318													G|||	1740	0.347444	0.3661	0.2954	5008	,	,		10912	0.3423		0.3549	False		,,,				2504	0.3569				p.A548T		Atlas-SNP	.											.	MON2	160	.	0			c.G1642A						PASS	.	G	THR/ALA	1631,2775	502.4+/-365.2	305,1021,877	163.0	147.0	153.0		1642	4.9	1.0	12	dbSNP_119	153	3132,5468	474.5+/-368.9	574,1984,1742	yes	missense	MON2	NM_015026.2	58	879,3005,2619	AA,AG,GG		36.4186,37.0177,36.6216	benign	548/1718	62928633	4763,8243	2203	4300	6503	SO:0001583	missense	23041	exon13			AGTAGGGCTGTTT		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.1642G>A	12.37:g.62928633G>A	ENSP00000377252:p.Ala548Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	36	11	0.305556	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	782	0.35805860805860806	178	0.3617886178861789	115	0.31767955801104975	213	0.3723776223776224	276	0.3641160949868074	G	15.77	2.931028	0.52866	0.370177	0.364186	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000261188;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.55930	0.5;0.5;0.5;0.5;0.49;0.5;0.52	4.93	4.93	0.64822	.	0.309163	0.33382	N	0.004973	T	0.00012	0.0000	L	0.43152	1.355	0.26511	P	0.9746054	B;B;B;B	0.28055	0.015;0.076;0.043;0.199	B;B;B;B	0.26969	0.009;0.047;0.062;0.075	T	0.34601	-0.9822	8	.	.	.	-16.9989	11.9437	0.52915	0.0805:0.0:0.9195:0.0	rs10219555;rs52796214;rs56695552;rs10219555	548;548;548;548	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	T	548;548;548;548;476;548;548;548	ENSP00000377252:A548T;ENSP00000377250:A548T;ENSP00000280379:A548T;ENSP00000447407:A548T;ENSP00000449215:A548T;ENSP00000377249:A548T;ENSP00000446635:A548T	.	A	+	1	0	MON2	61214900	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	3.775000	0.55349	2.435000	0.82474	0.555000	0.69702	GCT	G|0.641;A|0.359	0.359	strong		0.318	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
PTPRB	5787	hgsc.bcm.edu	37	12	70990054	70990054	+	Missense_Mutation	SNP	T	T	C	rs2465811	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:70990054T>C	ENST00000261266.5	-	3	408	c.379A>G	c.(379-381)Agc>Ggc	p.S127G	PTPRB_ENST00000550358.1_Missense_Mutation_p.S345G|PTPRB_ENST00000538708.1_Missense_Mutation_p.S127G|PTPRB_ENST00000551525.1_Missense_Mutation_p.S344G|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550857.1_Missense_Mutation_p.S127G|PTPRB_ENST00000334414.6_Missense_Mutation_p.S345G|PTPRB_ENST00000451516.2_Missense_Mutation_p.S127G	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	127	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> G (in dbSNP:rs2465811). {ECO:0000269|PubMed:2170109}.		angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			ACATGCAAGCTGGTTGAAGTC	0.393													T|||	1603	0.320088	0.4402	0.2363	5008	,	,		15448	0.3026		0.2604	False		,,,				2504	0.2965				p.S345G		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1033G	GRCh37	CM086290	PTPRB	M	rs2465811	PASS	.	T	GLY/SER,GLY/SER,GLY/SER,GLY/SER	1481,2253		289,903,675	61.0	59.0	60.0		1033,379,379,379	5.8	0.8	12	dbSNP_100	60	2290,5936		310,1670,2133	yes	missense,missense,missense,missense	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	56,56,56,56	599,2573,2808	CC,CT,TT		27.8386,39.6626,31.5301	benign,benign,benign,benign	345/2216,127/1908,127/1908,127/1998	70990054	3771,8189	1867	4113	5980	SO:0001583	missense	5787	exon5			GCAAGCTGGTTGA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.379A>G	12.37:g.70990054T>C	ENSP00000261266:p.Ser127Gly	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	58	29	0.5	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	669	0.30631868131868134	209	0.4247967479674797	90	0.24861878453038674	175	0.30594405594405594	195	0.25725593667546176	T	10.86	1.471193	0.26423	0.396626	0.278386	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.089006	0.85682	D	0.000000	T	0.00012	0.0000	M	0.70275	2.135	0.25955	P	0.9827042	B;B;B;B;B;B;B;B	0.30482	0.001;0.001;0.008;0.281;0.008;0.007;0.003;0.007	B;B;B;B;B;B;B;B	0.35688	0.008;0.008;0.052;0.208;0.013;0.026;0.03;0.026	T	0.30119	-0.9989	9	0.59425	D	0.04	.	16.1596	0.81693	0.0:0.0:0.0:1.0	rs2465811;rs52801085;rs59164378;rs2465811	127;127;224;345;344;345;127;345	P23467-2;F5H3G6;Q6ZR19;Q6ZTX7;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;.;PTPRB_HUMAN;.	G	345;127;345;345;127;127;127;344;224	ENSP00000334928:S345G;ENSP00000393028:S127G;ENSP00000448058:S345G;ENSP00000438927:S127G;ENSP00000447302:S127G;ENSP00000261266:S127G;ENSP00000448349:S344G;ENSP00000446982:S224G	ENSP00000261266:S127G	S	-	1	0	PTPRB	69276321	1.000000	0.71417	0.821000	0.32701	0.029000	0.11900	4.003000	0.57061	2.216000	0.71823	0.533000	0.62120	AGC	C|0.325;N|0.000	0.325	strong		0.393	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
UMODL1	89766	hgsc.bcm.edu	37	21	43543193	43543193	+	Missense_Mutation	SNP	G	G	A	rs150611312	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43543193G>A	ENST00000408910.2	+	17	3080	c.3080G>A	c.(3079-3081)aGc>aAc	p.S1027N	UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400424.2_Missense_Mutation_p.S955N|UMODL1_ENST00000408989.2_Missense_Mutation_p.S1155N|UMODL1_ENST00000400427.1_Missense_Mutation_p.S1083N	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1027	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		S -> N (in dbSNP:rs150611312). {ECO:0000269|PubMed:16026467}.		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						TGCAACGTGAGCCACAGCAAT	0.607													G|||	19	0.00379393	0.0	0.0029	5008	,	,		21514	0.0		0.0149	False		,,,				2504	0.002				p.S1155N	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											UMODL1_ENST00000408989,NS,haematopoietic_neoplasm,0,2	UMODL1	186	2	0			c.G3464A						scavenged	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER	7,4317		0,7,2155	64.0	67.0	66.0		3080,3248,2864,3464	3.1	0.9	21	dbSNP_134	66	114,8362		1,112,4125	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	46,46,46,46	1,119,6280	AA,AG,GG		1.345,0.1619,0.9453	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1027/1319,1083/1375,955/1247,1155/1447	43543193	121,12679	2162	4238	6400	SO:0001583	missense	89766	exon16			ACGTGAGCCACAG		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.3080G>A	21.37:g.43543193G>A	ENSP00000386147:p.Ser1027Asn	Somatic	51	1	0.0196078		WXS	Illumina HiSeq	Phase_I	75	22	0.293333	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	G	17.79	3.475678	0.63737	0.001619	0.01345	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62	3.13	3.13	0.36017	Zona pellucida sperm-binding protein (3);	0.116173	0.37304	N	0.002159	D	0.83450	0.5257	L	0.50919	1.6	0.37860	D	0.929673	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.972	D	0.86025	0.1509	9	.	.	.	-19.0186	13.6342	0.62213	0.0:0.0:1.0:0.0	.	1155;1027	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	N	1083;955;1155;1027	ENSP00000383279:S1083N;ENSP00000383276:S955N;ENSP00000386126:S1155N;ENSP00000386147:S1027N	.	S	+	2	0	UMODL1	42416262	1.000000	0.71417	0.901000	0.35422	0.724000	0.41520	3.829000	0.55760	2.060000	0.61445	0.313000	0.20887	AGC	G|0.993;A|0.007	0.007	strong		0.607	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.A107V|SGK1_ENST00000367857.5_Missense_Mutation_p.A83V|SGK1_ENST00000475719.2_Missense_Mutation_p.A93V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367858.5_Missense_Mutation_p.A188V|SGK1_ENST00000528577.1_Missense_Mutation_p.A121V	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	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	85	16	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		
RGS12	6002	hgsc.bcm.edu	37	4	3417845	3417845	+	Silent	SNP	G	G	C	rs3213507	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:3417845G>C	ENST00000344733.5	+	7	3328	c.2424G>C	c.(2422-2424)ctG>ctC	p.L808L	RGS12_ENST00000338806.4_Silent_p.L160L|RGS12_ENST00000543385.1_3'UTR|RGS12_ENST00000382788.3_Silent_p.L808L|RGS12_ENST00000306648.7_Silent_p.L206L|RGS12_ENST00000336727.3_Silent_p.L808L|RGS12_ENST00000508158.1_3'UTR|RGS12_ENST00000538395.1_Silent_p.L150L	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	808	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|regulation of catalytic activity (GO:0050790)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|GTPase regulator activity (GO:0030695)|receptor signaling protein activity (GO:0005057)			autonomic_ganglia(1)|breast(4)|endometrium(3)|kidney(2)|large_intestine(9)|lung(16)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		AGCAGCAGCTGCAGGTAACCG	0.622													C|||	1881	0.375599	0.4395	0.4323	5008	,	,		17760	0.4851		0.2714	False		,,,				2504	0.2434				p.L808L		Atlas-SNP	.											.	RGS12	128	.	0			c.G2424C						PASS	.	C	,,	1650,2756	655.0+/-399.8	297,1056,850	49.0	45.0	46.0		2424,480,2424	-7.1	0.7	4	dbSNP_106	46	2412,6188	696.4+/-404.9	339,1734,2227	no	coding-synonymous,coding-synonymous,coding-synonymous	RGS12	NM_002926.3,NM_198227.1,NM_198229.2	,,	636,2790,3077	CC,CG,GG		28.0465,37.4489,31.2317	,,	808/1377,160/800,808/1448	3417845	4062,8944	2203	4300	6503	SO:0001819	synonymous_variant	6002	exon7			GCAGCTGCAGGTA	AF035152	CCDS3366.1, CCDS3367.1, CCDS3368.1	4p16.3	2008-02-05	2007-08-14		ENSG00000159788	ENSG00000159788		"""Regulators of G-protein signaling"""	9994	protein-coding gene	gene with protein product		602512	"""regulator of G-protein signalling 12"""			9651375	Standard	NM_198229		Approved		uc003ggw.3	O14924	OTTHUMG00000090277	ENST00000344733.5:c.2424G>C	4.37:g.3417845G>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	73	20	0.273973	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Silent	SNP	ENST00000344733.5	37	CCDS3366.1																																																																																			G|0.669;C|0.331	0.331	strong		0.622	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926	
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 GAIIx	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	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	64	33	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	
MAML1	9794	hgsc.bcm.edu	37	5	179201847	179201847	+	Missense_Mutation	SNP	G	G	A	rs6895902	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:179201847G>A	ENST00000292599.3	+	5	3283	c.3020G>A	c.(3019-3021)aGt>aAt	p.S1007N	MAML1_ENST00000503050.1_Intron	NM_014757.4	NP_055572.1			mastermind-like 1 (Drosophila)											central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(16)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	36	all_cancers(89;0.000197)|all_epithelial(37;6.7e-05)|Renal(175;0.000159)|Lung NSC(126;0.00121)|all_lung(126;0.00218)	all_cancers(40;0.0308)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGTGGATGAGTGATTTGGAC	0.463													A|||	1146	0.228834	0.1967	0.2594	5008	,	,		19614	0.1518		0.3579	False		,,,				2504	0.1973				p.S1007N		Atlas-SNP	.											MAML1,brain,glioma,0,1	MAML1	118	1	0			c.G3020A						PASS	.	A	ASN/SER	977,3427	707.4+/-407.5	109,759,1334	123.0	114.0	117.0		3020	1.6	0.6	5	dbSNP_116	117	2925,5675	643.1+/-399.9	503,1919,1878	yes	missense	MAML1	NM_014757.4	46	612,2678,3212	AA,AG,GG		34.0116,22.1844,30.0062	benign	1007/1017	179201847	3902,9102	2202	4300	6502	SO:0001583	missense	9794	exon5			GGATGAGTGATTT	D83785	CCDS34315.1	5q35	2008-07-18	2001-11-28			ENSG00000161021			13632	protein-coding gene	gene with protein product	"""mastermind homolog"""	605424	"""mastermind (drosophila)-like 1"""			11101851, 11390662	Standard	NM_014757		Approved	KIAA0200, Mam-1	uc003mkm.3	Q92585		ENST00000292599.3:c.3020G>A	5.37:g.179201847G>A	ENSP00000292599:p.Ser1007Asn	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	64	22	0.34375	NM_014757		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	551	0.2522893772893773	96	0.1951219512195122	97	0.26795580110497236	77	0.1346153846153846	281	0.370712401055409	A	0.840	-0.742301	0.03088	0.221844	0.340116	ENSG00000161021	ENST00000292599	T	0.21734	1.99	5.28	1.61	0.23674	.	0.198509	0.44285	N	0.000479	T	0.00012	0.0000	N	0.00392	-1.555	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48091	-0.9065	9	0.02654	T	1	-2.2874	9.1608	0.37021	0.7206:0.0:0.2794:0.0	rs6895902;rs57675371;rs6895902	1007	Q92585	MAML1_HUMAN	N	1007	ENSP00000292599:S1007N	ENSP00000292599:S1007N	S	+	2	0	MAML1	179134453	0.882000	0.30256	0.579000	0.28588	0.991000	0.79684	1.053000	0.30442	-0.182000	0.10602	-0.361000	0.07541	AGT	G|0.733;A|0.267	0.267	strong		0.463	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757	
IL1RN	3557	hgsc.bcm.edu	37	2	113890304	113890304	+	Silent	SNP	T	T	C	rs315952	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:113890304T>C	ENST00000409930.3	+	4	454	c.390T>C	c.(388-390)agT>agC	p.S130S	IL1RN_ENST00000354115.2_Silent_p.S112S|IL1RN_ENST00000409052.1_Silent_p.S96S|IL1RN_ENST00000361779.3_Silent_p.S96S|IL1RN_ENST00000259206.5_Silent_p.S133S	NM_173842.2	NP_776214.1	P18510	IL1RA_HUMAN	interleukin 1 receptor antagonist	130					acute-phase response (GO:0006953)|carboxylic acid metabolic process (GO:0019752)|chronic inflammatory response to antigenic stimulus (GO:0002439)|female pregnancy (GO:0007565)|fever generation (GO:0001660)|immune response (GO:0006955)|insulin secretion (GO:0030073)|lipid metabolic process (GO:0006629)|memory (GO:0007613)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of glutamate secretion (GO:0014050)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-1-mediated signaling pathway (GO:2000660)|negative regulation of membrane potential (GO:0045837)|positive regulation of JUN kinase activity (GO:0043507)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to interleukin-4 (GO:0070670)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	interleukin-1 receptor antagonist activity (GO:0005152)|interleukin-1 receptor binding (GO:0005149)|interleukin-1 Type I receptor antagonist activity (GO:0045352)|interleukin-1 Type II receptor antagonist activity (GO:0045353)|interleukin-1, Type I receptor binding (GO:0005150)|interleukin-1, Type II receptor binding (GO:0005151)			breast(1)|large_intestine(2)|lung(4)|ovary(1)|skin(2)	10					Rilonacept(DB06372)	GCTCAGACAGTGGCCCCACCA	0.572									Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	1753	0.35004	0.466	0.2147	5008	,	,		18651	0.5556		0.2803	False		,,,				2504	0.1493				p.S133S		Atlas-SNP	.											.	IL1RN	30	.	0			c.T399C						PASS	.	C	,,,	1921,2485	626.0+/-394.6	423,1075,705	94.0	94.0	94.0		336,399,390,288	-10.8	0.0	2	dbSNP_79	94	2412,6188	699.1+/-405.1	342,1728,2230	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL1RN	NM_000577.4,NM_173841.2,NM_173842.2,NM_173843.2	,,,	765,2803,2935	CC,CT,TT		28.0465,43.5996,33.3154	,,,	112/160,133/181,130/178,96/144	113890304	4333,8673	2203	4300	6503	SO:0001819	synonymous_variant	3557	exon6	Familial Cancer Database	Lichen Sclerosis, Familial	AGACAGTGGCCCC	M55646	CCDS2113.1, CCDS2114.1, CCDS2115.1, CCDS46396.1	2q14.2	2014-09-17			ENSG00000136689	ENSG00000136689		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	6000	protein-coding gene	gene with protein product	"""interleukin-1 receptor antagonist protein"", ""intracellular interleukin-1 receptor antagonist"""	147679				1386337, 8432529	Standard	NM_000577		Approved	IL1RA, ICIL-1RA, IL1F3, IRAP, IL-1RN, MGC10430	uc002tjb.3	P18510	OTTHUMG00000131341	ENST00000409930.3:c.390T>C	2.37:g.113890304T>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	81	49	0.604938	NM_173841	A8K4G1|Q14628|Q53SC2|Q7RTZ4|Q96GD6|Q9UPC0	Silent	SNP	ENST00000409930.3	37	CCDS46396.1																																																																																			T|0.641;C|0.359	0.359	strong		0.572	IL1RN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330802.1	NM_173841	
STAG3	10734	hgsc.bcm.edu	37	7	99796146	99796146	+	Silent	SNP	A	A	C	rs3735241	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99796146A>C	ENST00000426455.1	+	13	1700	c.1293A>C	c.(1291-1293)ccA>ccC	p.P431P	STAG3_ENST00000440830.1_3'UTR|STAG3_ENST00000317296.5_Silent_p.P431P|STAG3_ENST00000394018.2_Silent_p.P373P|GATS_ENST00000543273.1_RNA	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	431					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCGTCTACCCAGTTGTGTATG	0.522													C|||	2504	0.5	0.3654	0.6254	5008	,	,		19600	0.6815		0.498	False		,,,				2504	0.408				p.P431P		Atlas-SNP	.											.	STAG3	121	.	0			c.A1293C						PASS	.	C		1816,2590		363,1090,750	142.0	123.0	130.0		1293	-6.2	0.1	7	dbSNP_107	130	4281,4319		1082,2117,1101	no	coding-synonymous	STAG3	NM_012447.2		1445,3207,1851	CC,CA,AA		49.7791,41.2165,46.8784		431/1226	99796146	6097,6909	2203	4300	6503	SO:0001819	synonymous_variant	10734	exon13			CTACCCAGTTGTG	AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	ENST00000426455.1:c.1293A>C	7.37:g.99796146A>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	252	128	0.507937	NM_012447	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	37	CCDS34703.1																																																																																			C|0.482;N|0.000	0.482	strong		0.522	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2	NM_012447	
APOC4	346	hgsc.bcm.edu	37	19	45448465	45448465	+	Missense_Mutation	SNP	T	T	G	rs5167	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:45448465T>G	ENST00000592954.1	+	3	327	c.287T>G	c.(286-288)cTc>cGc	p.L96R	APOC2_ENST00000590360.1_5'Flank|APOC4_ENST00000419266.2_Missense_Mutation_p.L96R|APOC4-APOC2_ENST00000589057.1_Intron|APOC2_ENST00000591597.1_5'Flank|APOC2_ENST00000592257.1_5'Flank|APOC2_ENST00000252490.4_5'Flank	NM_001646.2	NP_001637.1	P55056	APOC4_HUMAN	apolipoprotein C-IV	96			L -> R (in dbSNP:rs5167). {ECO:0000269|PubMed:10996355}.		lipid metabolic process (GO:0006629)|positive regulation of sequestering of triglyceride (GO:0010890)|triglyceride homeostasis (GO:0070328)	high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|lung(2)	4	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00334)|Epithelial(262;0.178)		CTGGGTCCGCTCACCAAGGCC	0.587													G|||	2200	0.439297	0.4569	0.4553	5008	,	,		16354	0.5724		0.3668	False		,,,				2504	0.3415				p.L96R		Atlas-SNP	.											.	APOC4	6	.	0			c.T287G	GRCh37	CM065970	APOC4	M	rs5167	PASS	.	G	ARG/LEU	2023,2383	612.3+/-391.9	476,1071,656	179.0	177.0	177.0		287	2.1	0.0	19	dbSNP_52	177	3080,5520	659.3+/-401.7	558,1964,1778	yes	missense	APOC4	NM_001646.2	102	1034,3035,2434	GG,GT,TT		35.814,45.9147,39.2357	benign	96/128	45448465	5103,7903	2203	4300	6503	SO:0001583	missense	346	exon3			GTCCGCTCACCAA	U32576	CCDS12649.1	19q13.2	2013-09-30			ENSG00000267467	ENSG00000267467		"""Apolipoproteins"""	611	protein-coding gene	gene with protein product		600745				8530039	Standard	NM_001646		Approved			P55056	OTTHUMG00000180845	ENST00000592954.1:c.287T>G	19.37:g.45448465T>G	ENSP00000468236:p.Leu96Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001646	B3KWY6|Q53YY8	Missense_Mutation	SNP	ENST00000592954.1	37	CCDS12649.1	1033	0.47298534798534797	253	0.5142276422764228	170	0.4696132596685083	330	0.5769230769230769	280	0.36939313984168864	G	0.003	-2.515632	0.00151	0.459147	0.35814	ENSG00000224916	ENST00000419266;ENST00000436871	T;T	0.18174	2.23;2.23	4.26	2.07	0.26955	.	0.168114	0.28821	N	0.014031	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	0.41980	-0.9478	9	0.02654	T	1	-18.197	4.6363	0.12527	0.195:0.0:0.6327:0.1723	rs5167;rs17257587;rs17257887;rs52812385;rs56784720;rs5167	96	P55056	APOC4_HUMAN	R	96	ENSP00000406381:L96R;ENSP00000412935:L96R	ENSP00000406381:L96R	L	+	2	0	APOC4	50140305	0.042000	0.20092	0.006000	0.13384	0.060000	0.15804	1.155000	0.31700	0.176000	0.19873	-0.702000	0.03669	CTC	G|0.427;N|0.000	0.427	strong		0.587	APOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453255.1	NM_001646	
PSD4	23550	hgsc.bcm.edu	37	2	113940681	113940681	+	Silent	SNP	T	T	C	rs3748914	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:113940681T>C	ENST00000245796.6	+	2	843	c.648T>C	c.(646-648)agT>agC	p.S216S	PSD4_ENST00000441564.3_Silent_p.S216S	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	216					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AAGACAGCAGTGAGCCTGAGG	0.637													C|||	2881	0.57528	0.7375	0.5173	5008	,	,		17550	0.6042		0.4423	False		,,,				2504	0.5041				p.S216S		Atlas-SNP	.											PSD4,NS,carcinoma,0,1	PSD4	74	1	0			c.T648C						PASS	.	C		3023,1383	456.3+/-351.3	1046,931,226	61.0	65.0	63.0		648	-9.4	0.0	2	dbSNP_107	63	3513,5087	632.4+/-398.6	732,2049,1519	no	coding-synonymous	PSD4	NM_012455.2		1778,2980,1745	CC,CT,TT		40.8488,31.389,49.7463		216/1057	113940681	6536,6470	2203	4300	6503	SO:0001819	synonymous_variant	23550	exon2			CAGCAGTGAGCCT	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.648T>C	2.37:g.113940681T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	48	47	0.979167	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	37	CCDS33276.1																																																																																			C|0.529;N|0.000	0.529	strong		0.637	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
CCDC168	643677	hgsc.bcm.edu	37	13	103391634	103391634	+	5'Flank	SNP	C	C	T	rs7322112	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103391634C>T	ENST00000322527.2	-	0	0					NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168																		AGGCCCATTACATCTTTCACA	0.313													T|||	3504	0.699681	0.562	0.7478	5008	,	,		21243	0.5913		0.826	False		,,,				2504	0.8333				p.V3805I		Atlas-SNP	.											.	.	.	.	0			c.G11413A						PASS	.	T	ILE/VAL	787,597		225,337,130	72.0	53.0	59.0		11413	2.5	0.0	13	dbSNP_116	59	2540,636		1022,496,70	yes	missense	CCDC168	NM_001146197.1	29	1247,833,200	TT,TC,CC		20.0252,43.1358,27.0395		3805/7082	103391634	3327,1233	692	1588	2280	SO:0001631	upstream_gene_variant	643677	exon4			CCATTACATCTTT		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		13.37:g.103391634C>T	Exception_encountered	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37																																																																																				C|0.324;T|0.676	0.676	strong		0.313	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
TTN	7273	hgsc.bcm.edu	37	2	179650701	179650701	+	Silent	SNP	C	C	T	rs6715406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179650701C>T	ENST00000591111.1	-	14	2468	c.2244G>A	c.(2242-2244)gaG>gaA	p.E748E	TTN_ENST00000360870.5_Silent_p.E748E|TTN_ENST00000589042.1_Silent_p.E748E|TTN_ENST00000342175.6_Silent_p.E702E|TTN_ENST00000359218.5_Silent_p.E702E|TTN_ENST00000460472.2_Silent_p.E702E|TTN_ENST00000342992.6_Silent_p.E748E			Q8WZ42	TITIN_HUMAN	titin	33589					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTGGGGAGGCTCAGCTACCT	0.517													C|||	1025	0.204673	0.1445	0.1916	5008	,	,		20748	0.0685		0.4135	False		,,,				2504	0.2209				p.E748E		Atlas-SNP	.											.	TTN	18412	.	0			c.G2244A						PASS	.	C	,,,,	881,3525	342.5+/-307.2	91,699,1413	97.0	88.0	91.0		2106,2244,2244,2106,2106	5.9	1.0	2	dbSNP_116	91	3489,5111	510.8+/-377.6	733,2023,1544	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	824,2722,2957	TT,TC,CC		40.5698,19.9955,33.5999	,,,,	702/26927,748/33424,748/5605,702/27052,702/27119	179650701	4370,8636	2203	4300	6503	SO:0001819	synonymous_variant	7273	exon14			GGGAGGCTCAGCT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2244G>A	2.37:g.179650701C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.722;T|0.278	0.278	strong		0.517	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KLB	152831	hgsc.bcm.edu	37	4	39448586	39448586	+	Missense_Mutation	SNP	C	C	T	rs35372803	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:39448586C>T	ENST00000257408.4	+	4	2337	c.2240C>T	c.(2239-2241)gCg>gTg	p.A747V		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	747	Glycosyl hydrolase-1 2.		A -> V (in dbSNP:rs35372803).		carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						GCGGACTGGGCGGAACCCGCC	0.701													C|||	79	0.0157748	0.0023	0.0144	5008	,	,		15100	0.0		0.0457	False		,,,				2504	0.0204				p.A747V		Atlas-SNP	.											.	KLB	95	.	0			c.C2240T						PASS	.	C	VAL/ALA	25,4359		0,25,2167	21.0	23.0	22.0		2240	4.4	0.9	4	dbSNP_126	22	445,8115		12,421,3847	yes	missense	KLB	NM_175737.3	64	12,446,6014	TT,TC,CC		5.1986,0.5703,3.631	probably-damaging	747/1045	39448586	470,12474	2192	4280	6472	SO:0001583	missense	152831	exon4			ACTGGGCGGAACC	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.2240C>T	4.37:g.39448586C>T	ENSP00000257408:p.Ala747Val	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	37	CCDS3451.1	39	0.017857142857142856	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	34	0.044854881266490766	C	14.93	2.681692	0.47991	0.005703	0.051986	ENSG00000134962	ENST00000257408	T	0.28895	1.59	5.23	4.39	0.52855	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.105878	0.64402	N	0.000006	T	0.06690	0.0171	L	0.42744	1.35	0.39530	D	0.968646	D;D	0.53312	0.959;0.959	P;P	0.50378	0.547;0.639	T	0.01215	-1.1416	10	0.21540	T	0.41	-11.584	13.5181	0.61551	0.0:0.9243:0.0:0.0757	rs35372803	738;747	B7ZL50;Q86Z14	.;KLOTB_HUMAN	V	747	ENSP00000257408:A747V	ENSP00000257408:A747V	A	+	2	0	KLB	39124981	0.896000	0.30565	0.919000	0.36401	0.840000	0.47671	1.811000	0.38942	1.199000	0.43173	0.313000	0.20887	GCG	C|0.969;T|0.031	0.031	strong		0.701	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737	
GRIN3B	116444	hgsc.bcm.edu	37	19	1004740	1004740	+	Missense_Mutation	SNP	T	T	C	rs2240157	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1004740T>C	ENST00000234389.3	+	3	1259	c.1240T>C	c.(1240-1242)Tgg>Cgg	p.W414R	GRIN3B_ENST00000588335.1_Intron|AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	414			W -> R (in dbSNP:rs2240157).		ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGCCCAGGTCTGGCCCAAGCT	0.692													N|||	3413	0.68151	0.8048	0.5403	5008	,	,		12051	0.501		0.7157	False		,,,				2504	0.7658				p.W414R		Atlas-SNP	.											.	GRIN3B	46	.	0			c.T1240C						PASS	.	C	ARG/TRP	3447,941		1354,739,101	28.0	29.0	29.0		1240	3.3	0.0	19	dbSNP_98	29	6108,2472		2186,1736,368	yes	missense	GRIN3B	NM_138690.1	101	3540,2475,469	CC,CT,TT		28.8112,21.4448,26.3186	benign	414/1044	1004740	9555,3413	2194	4290	6484	SO:0001583	missense	116444	exon3			CAGGTCTGGCCCA		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1240T>C	19.37:g.1004740T>C	ENSP00000234389:p.Trp414Arg	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	1417	0.6488095238095238	390	0.7926829268292683	217	0.5994475138121547	273	0.4772727272727273	537	0.7084432717678101	C	0.103	-1.149021	0.01714	0.785552	0.711888	ENSG00000116032	ENST00000234389	T	0.46063	0.88	4.41	3.35	0.38373	.	0.406531	0.26492	N	0.024067	T	0.00012	0.0000	N	0.00092	-2.175	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33266	-0.9875	9	0.15066	T	0.55	.	9.8165	0.40856	0.0:0.8221:0.0:0.1779	rs2240157	414	O60391	NMD3B_HUMAN	R	414	ENSP00000234389:W414R	ENSP00000234389:W414R	W	+	1	0	GRIN3B	955740	0.047000	0.20315	0.002000	0.10522	0.005000	0.04900	0.585000	0.23879	0.880000	0.35969	-0.354000	0.07668	TGG	T|0.304;C|0.696	0.696	strong		0.692	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
KRT14	3861	hgsc.bcm.edu	37	17	39742718	39742718	+	Silent	SNP	A	A	G	rs3826549	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39742718A>G	ENST00000167586.6	-	1	455	c.369T>C	c.(367-369)aaT>aaC	p.N123N		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	123	Coil 1A.|Rod.		N -> K (in DM-EBS; dbSNP:rs3826549). {ECO:0000269|PubMed:14987259, ECO:0000269|PubMed:16786515}.|N -> S (in DM-EBS; dbSNP:rs60171927). {ECO:0000269|PubMed:9989794}.		aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				CCAGGCGGTCATTGAGGTTCT	0.617													G|||	3408	0.680511	0.4788	0.7233	5008	,	,		17169	0.9425		0.5855	False		,,,				2504	0.7505				p.N123N		Atlas-SNP	.											.	KRT14	65	.	0			c.T369C	GRCh37	CM044651	KRT14	M	rs3826549	PASS	.						141.0	148.0	145.0					17																	39742718		2203	4297	6500	SO:0001819	synonymous_variant	3861	exon1			GCGGTCATTGAGG	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.369T>C	17.37:g.39742718A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Silent	SNP	ENST00000167586.6	37	CCDS11400.1																																																																																			A|0.554;G|0.446	0.446	strong		0.617	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
CD101	9398	hgsc.bcm.edu	37	1	117560818	117560818	+	Silent	SNP	A	A	G	rs3736908	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117560818A>G	ENST00000256652.4	+	6	1711	c.1653A>G	c.(1651-1653)caA>caG	p.Q551Q	CD101_ENST00000369470.1_Silent_p.Q551Q	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	551	Ig-like C2-type 5.				cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GTCAGCCGCAAGTGATGTTAA	0.438													A|||	1725	0.344449	0.0408	0.4438	5008	,	,		19499	0.6181		0.2813	False		,,,				2504	0.4673				p.Q551Q		Atlas-SNP	.											.	CD101	95	.	0			c.A1653G						PASS	.	A		367,4039	185.3+/-212.5	18,331,1854	106.0	82.0	90.0		1653	1.6	1.0	1	dbSNP_107	90	2365,6235	390.0+/-343.1	324,1717,2259	no	coding-synonymous	CD101	NM_004258.3		342,2048,4113	GG,GA,AA		27.5,8.3296,21.0057		551/1022	117560818	2732,10274	2203	4300	6503	SO:0001819	synonymous_variant	9398	exon6			GCCGCAAGTGATG	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.1653A>G	1.37:g.117560818A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001256109	Q15856	Silent	SNP	ENST00000256652.4	37	CCDS891.1																																																																																			A|0.738;G|0.262	0.262	strong		0.438	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
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 GAIIx	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_ENST00000515768.1_Splice_Site_p.Q119L|CSNK1A1_ENST00000504676.1_Splice_Site_p.Q30L|CSNK1A1_ENST00000261798.5_Splice_Site_p.Q119L|CSNK1A1_ENST00000515435.1_Splice_Site_p.Q30L	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		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	261	18	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
OR2AG2	338755	hgsc.bcm.edu	37	11	6790028	6790028	+	Missense_Mutation	SNP	C	C	G	rs10839616	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6790028C>G	ENST00000338569.2	-	1	258	c.161G>C	c.(160-162)cGg>cCg	p.R54P		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, member 2	54			R -> P (in dbSNP:rs10839616).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATGTGGAGCCGGGCTTCTAT	0.542													c|||	1445	0.288538	0.3654	0.1671	5008	,	,		21247	0.2143		0.2157	False		,,,				2504	0.4223				p.R54P		Atlas-SNP	.											OR2AG2,right_upper_lobe,carcinoma,-1,1	OR2AG2	55	1	0			c.G161C						scavenged	.	T	PRO/ARG	1501,2901	479.0+/-358.4	246,1009,946	140.0	127.0	132.0		161	0.4	0.0	11	dbSNP_120	132	1890,6702	334.9+/-321.2	231,1428,2637	yes	missense	OR2AG2	NM_001004490.1	103	477,2437,3583	GG,GC,CC		21.9972,34.0981,26.0967	probably-damaging	54/317	6790028	3391,9603	2201	4296	6497	SO:0001583	missense	338755	exon1			TGGAGCCGGGCTT	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"""GPCR / Class A : Olfactory receptors"""	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.161G>C	11.37:g.6790028C>G	ENSP00000342697:p.Arg54Pro	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	512	0.23443223443223443	162	0.32926829268292684	74	0.20441988950276244	109	0.19055944055944055	167	0.22031662269129287	c	7.698	0.692473	0.15039	0.340981	0.219972	ENSG00000188124	ENST00000338569	T	0.00449	7.37	4.28	0.401	0.16338	GPCR, rhodopsin-like superfamily (1);	0.497698	0.17054	N	0.188819	T	0.00012	0.0000	M	0.78049	2.395	0.80722	P	0.0	P	0.51147	0.942	P	0.53954	0.738	T	0.49041	-0.8980	9	0.72032	D	0.01	.	8.3017	0.32019	0.0:0.6516:0.0:0.3484	rs10839616;rs52830974;rs10839616	54	A6NM03	O2AG2_HUMAN	P	54	ENSP00000342697:R54P	ENSP00000342697:R54P	R	-	2	0	OR2AG2	6746604	0.000000	0.05858	0.006000	0.13384	0.004000	0.04260	-0.918000	0.04021	0.087000	0.17167	-1.594000	0.00841	CGG	C|0.737;G|0.263	0.263	strong		0.542	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490	
TMEM17	200728	hgsc.bcm.edu	37	2	62729653	62729653	+	Silent	SNP	A	A	G	rs6713096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:62729653A>G	ENST00000335390.5	-	3	448	c.237T>C	c.(235-237)atT>atC	p.I79I		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	79					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			CAGTGATCACAATGAATTTGT	0.333													A|||	349	0.0696885	0.1225	0.0418	5008	,	,		19818	0.0079		0.0676	False		,,,				2504	0.0838				p.I79I		Atlas-SNP	.											.	TMEM17	19	.	0			c.T237C						PASS	.	A		524,3882	238.0+/-249.6	36,452,1715	93.0	92.0	92.0		237	3.6	1.0	2	dbSNP_116	92	713,7887	175.0+/-225.2	34,645,3621	no	coding-synonymous	TMEM17	NM_198276.2		70,1097,5336	GG,GA,AA		8.2907,11.8929,9.511		79/199	62729653	1237,11769	2203	4300	6503	SO:0001819	synonymous_variant	200728	exon3			GATCACAATGAAT		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.237T>C	2.37:g.62729653A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_198276	Q53QP7|Q53R98	Silent	SNP	ENST00000335390.5	37	CCDS1871.1																																																																																			A|0.922;G|0.078	0.078	strong		0.333	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
BIN3	55909	hgsc.bcm.edu	37	8	22526559	22526559	+	Silent	SNP	G	G	A	rs11550509	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:22526559G>A	ENST00000276416.6	-	1	74	c.6C>T	c.(4-6)agC>agT	p.S2S	BIN3_ENST00000522268.1_Silent_p.S2S|BIN3_ENST00000519513.1_5'UTR|BIN3_ENST00000519335.1_5'UTR|BIN3_ENST00000520292.1_Silent_p.S2S	NM_018688.4	NP_061158.1	Q9NQY0	BIN3_HUMAN	bridging integrator 3	2					actin filament organization (GO:0007015)|barrier septum assembly (GO:0000917)|cytokinesis (GO:0000910)|myoblast migration involved in skeletal muscle regeneration (GO:0014839)|protein localization (GO:0008104)|regulation of lamellipodium assembly (GO:0010591)|skeletal muscle fiber development (GO:0048741)|unidimensional cell growth (GO:0009826)	actin filament (GO:0005884)|cytoplasm (GO:0005737)	cytoskeletal adaptor activity (GO:0008093)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	9		Prostate(55;0.0424)|Breast(100;0.102)|all_epithelial(46;0.143)		BRCA - Breast invasive adenocarcinoma(99;0.00664)|Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		TCACTCACCAGCTCATGGTCC	0.682													G|||	495	0.0988419	0.0106	0.1614	5008	,	,		13749	0.0069		0.2555	False		,,,				2504	0.1074				p.S2S		Atlas-SNP	.											.	BIN3	16	.	0			c.C6T						PASS	.	G		220,3746		6,208,1769	14.0	21.0	19.0		6	0.7	1.0	8	dbSNP_123	19	2085,6159		267,1551,2304	no	coding-synonymous	BIN3	NM_018688.4		273,1759,4073	AA,AG,GG		25.2911,5.5472,18.878		2/254	22526559	2305,9905	1983	4122	6105	SO:0001819	synonymous_variant	55909	exon1			TCACCAGCTCATG		CCDS47825.1	8p21.2	2008-07-04			ENSG00000147439	ENSG00000147439			1054	protein-coding gene	gene with protein product		606396				16524918	Standard	NM_018688		Approved		uc003xcl.3	Q9NQY0	OTTHUMG00000163844	ENST00000276416.6:c.6C>T	8.37:g.22526559G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	67	33	0.492537	NM_018688	Q9BVG2|Q9NVY9	Silent	SNP	ENST00000276416.6	37	CCDS47825.1																																																																																			G|0.877;A|0.123	0.123	strong		0.682	BIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375895.1		
COL4A4	1286	hgsc.bcm.edu	37	2	227872182	227872182	+	Silent	SNP	G	G	A	rs2228557	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:227872182G>A	ENST00000396625.3	-	48	5139	c.4932C>T	c.(4930-4932)ttC>ttT	p.F1644F	COL4A4_ENST00000329662.7_Silent_p.F1641F	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1644	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		ACTTATTTGCGAAAAAGTGGC	0.537													A|||	2576	0.514377	0.6369	0.4741	5008	,	,		19939	0.4048		0.4205	False		,,,				2504	0.5869				p.F1644F		Atlas-SNP	.											.	COL4A4	215	.	0			c.C4932T						PASS	.	A		2238,1660		642,954,353	187.0	197.0	193.0		4932	1.8	1.0	2	dbSNP_98	193	3379,4923		687,2005,1459	no	coding-synonymous	COL4A4	NM_000092.4		1329,2959,1812	AA,AG,GG		40.701,42.5859,46.041		1644/1691	227872182	5617,6583	1949	4151	6100	SO:0001819	synonymous_variant	1286	exon48			ATTTGCGAAAAAG		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4932C>T	2.37:g.227872182G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			G|0.540;A|0.460	0.460	strong		0.537	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
PLEC	5339	hgsc.bcm.edu	37	8	144994212	144994212	+	Silent	SNP	A	A	T	rs34644439	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144994212A>T	ENST00000322810.4	-	32	10357	c.10188T>A	c.(10186-10188)tcT>tcA	p.S3396S	PLEC_ENST00000354589.3_Silent_p.S3259S|PLEC_ENST00000357649.2_Silent_p.S3263S|PLEC_ENST00000436759.2_Silent_p.S3286S|PLEC_ENST00000354958.2_Silent_p.S3237S|PLEC_ENST00000527096.1_Silent_p.S3282S|PLEC_ENST00000345136.3_Silent_p.S3259S|PLEC_ENST00000356346.3_Silent_p.S3245S|PLEC_ENST00000398774.2_Silent_p.S3227S	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3396	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TGAAGTACTCAGAGCTGATGA	0.597													A|||	548	0.109425	0.3911	0.0418	5008	,	,		18443	0.0		0.002	False		,,,				2504	0.0				p.S3396S		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	0			c.T10188A						PASS	.	A	,,,,,,,	1236,3088		173,890,1099	56.0	63.0	60.0		9858,9735,9711,10188,9681,9777,9789,9777	-6.7	0.1	8	dbSNP_126	60	24,8478		0,24,4227	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	173,914,5326	TT,TA,AA		0.2823,28.5846,9.8238	,,,,,,,	3286/4575,3245/4534,3237/4526,3396/4685,3227/4516,3259/4548,3263/4552,3259/4548	144994212	1260,11566	2162	4251	6413	SO:0001819	synonymous_variant	5339	exon32			GTACTCAGAGCTG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.10188T>A	8.37:g.144994212A>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	54	32	0.592593	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			A|0.938;T|0.062	0.062	strong		0.597	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
SENP6	26054	hgsc.bcm.edu	37	6	76344431	76344431	+	Missense_Mutation	SNP	C	C	T	rs17414086	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:76344431C>T	ENST00000447266.2	+	5	840	c.362C>T	c.(361-363)aCg>aTg	p.T121M	SENP6_ENST00000327284.8_Missense_Mutation_p.T121M|SENP6_ENST00000370014.3_Missense_Mutation_p.T121M|SENP6_ENST00000370010.2_Missense_Mutation_p.T121M	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	121			T -> M (in dbSNP:rs17414086). {ECO:0000269|PubMed:10799485, ECO:0000269|PubMed:9872452}.		protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				AGTGAAAATACGCAAAATACG	0.318													C|||	779	0.155551	0.0121	0.1931	5008	,	,		17545	0.0595		0.327	False		,,,				2504	0.2454				p.T121M		Atlas-SNP	.											.	SENP6	189	.	0			c.C362T						PASS	.	C	MET/THR,MET/THR	224,3478		13,198,1640	96.0	85.0	89.0		362,362	3.7	1.0	6	dbSNP_123	89	2915,5255		523,1869,1693	yes	missense,missense	SENP6	NM_001100409.1,NM_015571.2	81,81	536,2067,3333	TT,TC,CC		35.6793,6.0508,26.4404	possibly-damaging,possibly-damaging	121/1106,121/1113	76344431	3139,8733	1851	4085	5936	SO:0001583	missense	26054	exon5			AAAATACGCAAAA		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.362C>T	6.37:g.76344431C>T	ENSP00000402527:p.Thr121Met	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	50	48	0.96	NM_001100409	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	37	CCDS47454.1	362	0.16575091575091574	5	0.01016260162601626	80	0.22099447513812154	29	0.050699300699300696	248	0.32717678100263853	C	9.316	1.056883	0.19907	0.060508	0.356793	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000538088;ENST00000327284;ENST00000447266;ENST00000483859;ENST00000424947	T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83	5.5	3.73	0.42828	.	0.529195	0.21759	N	0.069557	T	0.28101	0.0693	L	0.36672	1.1	0.09310	P	0.99999999882185	D;P;D	0.52996	0.957;0.927;0.957	B;B;P	0.47981	0.439;0.255;0.563	T	0.10613	-1.0622	9	0.52906	T	0.07	-7.6876	10.3397	0.43870	0.0:0.7846:0.0:0.2154	rs17414086;rs52797714;rs17414086	121;121;121	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	M	121;121;121;121;121;12;11	ENSP00000359027:T121M;ENSP00000359031:T121M;ENSP00000321820:T121M;ENSP00000402527:T121M;ENSP00000426480:T12M;ENSP00000391426:T11M	ENSP00000321820:T121M	T	+	2	0	SENP6	76401151	0.864000	0.29904	0.993000	0.49108	0.048000	0.14542	0.928000	0.28831	0.710000	0.31997	-0.203000	0.12734	ACG	C|0.803;N|0.000	.	strong		0.318	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
ARL11	115761	hgsc.bcm.edu	37	13	50205025	50205025	+	Missense_Mutation	SNP	T	T	C	rs3803185	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:50205025T>C	ENST00000282026.1	+	2	777	c.442T>C	c.(442-444)Tgc>Cgc	p.C148R	ARL11_ENST00000490932.1_Intron	NM_138450.5	NP_612459.1	Q969Q4	ARL11_HUMAN	ADP-ribosylation factor-like 11	148			C -> R (in dbSNP:rs3803185). {ECO:0000269|PubMed:15843669}.		hematopoietic progenitor cell differentiation (GO:0002244)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			kidney(1)|large_intestine(4)|ovary(1)	6		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.119)|Kidney(9;0.169)	GBM - Glioblastoma multiforme(99;1.67e-09)		CCAGGACCACTGCTGGGAGCT	0.612													T|||	1271	0.253794	0.0666	0.4006	5008	,	,		16728	0.1865		0.496	False		,,,				2504	0.2229				p.C148R		Atlas-SNP	.											.	ARL11	26	.	0			c.T442C	GRCh37	CM062430	ARL11	M	rs3803185	PASS	.	T	ARG/CYS	643,3763	265.0+/-266.4	50,543,1610	36.0	35.0	36.0		442	-10.8	0.0	13	dbSNP_107	36	4418,4178	553.7+/-386.3	1153,2112,1033	yes	missense	ARL11	NM_138450.5	180	1203,2655,2643	CC,CT,TT		48.604,14.5937,38.9248	benign	148/197	50205025	5061,7941	2203	4298	6501	SO:0001583	missense	115761	exon2			GACCACTGCTGGG	AF441378	CCDS9419.1	13q14.12	2014-05-09			ENSG00000152213	ENSG00000152213		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	24046	protein-coding gene	gene with protein product		609351				12477932	Standard	NM_138450		Approved	ARLTS1, FLJ33930	uc001vdf.2	Q969Q4	OTTHUMG00000016919	ENST00000282026.1:c.442T>C	13.37:g.50205025T>C	ENSP00000282026:p.Cys148Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	107	66	0.616822	NM_138450		Missense_Mutation	SNP	ENST00000282026.1	37	CCDS9419.1	673	0.30815018315018317	36	0.07317073170731707	146	0.40331491712707185	97	0.16958041958041958	394	0.5197889182058048	T	0.113	-1.135197	0.01742	0.145937	0.51396	ENSG00000152213	ENST00000282026	T	0.81330	-1.48	5.42	-10.8	0.00216	.	0.790281	0.12116	N	0.498086	T	0.00012	0.0000	N	0.04724	-0.175	0.58432	P	4.000000000004E-6	B	0.06786	0.001	B	0.08055	0.003	T	0.16364	-1.0405	9	0.32370	T	0.25	-17.1507	5.6024	0.17361	0.4664:0.3524:0.0788:0.1023	rs3803185;rs3803185	148	Q969Q4	ARL11_HUMAN	R	148	ENSP00000282026:C148R	ENSP00000282026:C148R	C	+	1	0	ARL11	49103026	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.348000	0.02629	-2.504000	0.00508	-1.140000	0.01884	TGC	T|0.660;C|0.340	0.340	strong		0.612	ARL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044929.2	NM_138450	
COBL	23242	hgsc.bcm.edu	37	7	51094269	51094269	+	Missense_Mutation	SNP	G	G	A	rs61737954	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:51094269G>A	ENST00000265136.7	-	11	3643	c.3478C>T	c.(3478-3480)Cac>Tac	p.H1160Y	COBL_ENST00000395542.2_Missense_Mutation_p.H1242Y	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1160	WH2 2. {ECO:0000255|PROSITE- ProRule:PRU00406}.				actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					GTGCCGCTGTGCCCGCGGATA	0.632													G|||	157	0.0313498	0.003	0.0245	5008	,	,		19629	0.001		0.0606	False		,,,				2504	0.0757				p.H1160Y	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C3478T						PASS	.	G	TYR/HIS	67,4339	62.3+/-99.4	0,67,2136	91.0	79.0	83.0		3478	5.0	0.9	7	dbSNP_129	83	681,7919	168.7+/-220.2	28,625,3647	yes	missense	COBL	NM_015198.3	83	28,692,5783	AA,AG,GG		7.9186,1.5207,5.7512	probably-damaging	1160/1262	51094269	748,12258	2203	4300	6503	SO:0001583	missense	23242	exon11			CGCTGTGCCCGCG	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3478C>T	7.37:g.51094269G>A	ENSP00000265136:p.His1160Tyr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	69	0.03159340659340659	3	0.006097560975609756	10	0.027624309392265192	1	0.0017482517482517483	55	0.07255936675461741	G	15.29	2.788493	0.49997	0.015207	0.079186	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.0	5.0	0.66597	Actin-binding WH2 (3);	0.000000	0.43747	D	0.000526	T	0.05135	0.0137	L	0.34521	1.04	0.38943	D	0.958182	D;D;D;D;D	0.89917	0.998;0.998;0.999;0.998;1.0	D;D;D;D;D	0.91635	0.994;0.994;0.984;0.994;0.999	T	0.08597	-1.0714	10	0.45353	T	0.12	.	15.0181	0.71605	0.0:0.0:1.0:0.0	.	1160;1217;1160;1242;702	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	Y	1160;1052;1045;1242	ENSP00000265136:H1160Y;ENSP00000401204:H1052Y;ENSP00000413498:H1045Y;ENSP00000378912:H1242Y	ENSP00000265136:H1160Y	H	-	1	0	COBL	51061763	1.000000	0.71417	0.891000	0.34965	0.033000	0.12548	7.524000	0.81866	2.294000	0.77228	0.563000	0.77884	CAC	G|0.947;A|0.053	0.053	strong		0.632	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
SYT2	127833	hgsc.bcm.edu	37	1	202565948	202565948	+	Silent	SNP	G	G	A	rs504261	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:202565948G>A	ENST00000367267.1	-	9	1389	c.1197C>T	c.(1195-1197)atC>atT	p.I399I	SYT2_ENST00000367268.4_Silent_p.I399I	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	399					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	GCCACTGGGCGATGGGCCTCC	0.627													G|||	1542	0.307907	0.3033	0.2594	5008	,	,		18163	0.2927		0.3509	False		,,,				2504	0.32				p.I399I		Atlas-SNP	.											.	SYT2	51	.	0			c.C1197T						PASS	.	G	,	1381,3025	456.9+/-351.5	215,951,1037	69.0	62.0	64.0		1197,1197	-3.9	0.9	1	dbSNP_83	64	3318,5282	495.3+/-374.0	623,2072,1605	no	coding-synonymous,coding-synonymous	SYT2	NM_001136504.1,NM_177402.4	,	838,3023,2642	AA,AG,GG		38.5814,31.3436,36.1295	,	399/420,399/420	202565948	4699,8307	2203	4300	6503	SO:0001819	synonymous_variant	127833	exon9			CTGGGCGATGGGC	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"""Synaptotagmins"""	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.1197C>T	1.37:g.202565948G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	37	CCDS1427.1																																																																																			G|0.655;A|0.345	0.345	strong		0.627	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402	
ZCCHC9	84240	hgsc.bcm.edu	37	5	80600619	80600619	+	Missense_Mutation	SNP	C	C	G	rs16878594	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:80600619C>G	ENST00000254037.2	+	1	3198	c.43C>G	c.(43-45)Ccc>Gcc	p.P15A	ZCCHC9_ENST00000438268.2_Missense_Mutation_p.P15A|ZCCHC9_ENST00000380199.5_Missense_Mutation_p.P15A|ZCCHC9_ENST00000506458.1_Intron|ZCCHC9_ENST00000407610.3_Missense_Mutation_p.P15A			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	15			P -> A (in dbSNP:rs16878594). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		TAACAAGAGACCCTTGCCTGC	0.443													C|||	328	0.0654952	0.0605	0.0692	5008	,	,		16766	0.0069		0.1123	False		,,,				2504	0.0818				p.P15A		Atlas-SNP	.											.	ZCCHC9	26	.	0			c.C43G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	284,4122	159.2+/-191.8	8,268,1927	110.0	103.0	105.0		43,43,43	4.6	0.5	5	dbSNP_123	105	864,7736	196.3+/-241.3	40,784,3476	yes	missense,missense,missense	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	27,27,27	48,1052,5403	GG,GC,CC		10.0465,6.4458,8.8267	benign,benign,benign	15/272,15/272,15/272	80600619	1148,11858	2203	4300	6503	SO:0001583	missense	84240	exon2			AAGAGACCCTTGC	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"""Zinc fingers, CCHC domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25424	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 41"""					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.43C>G	5.37:g.80600619C>G	ENSP00000254037:p.Pro15Ala	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	108	64	0.592593	NM_001131036	B2RAE7|Q9H027	Missense_Mutation	SNP	ENST00000254037.2	37	CCDS4054.1	134	0.06135531135531135	27	0.054878048780487805	29	0.08011049723756906	2	0.0034965034965034965	76	0.10026385224274406	C	7.999	0.754886	0.15846	0.064458	0.100465	ENSG00000131732	ENST00000254037;ENST00000407610;ENST00000380199;ENST00000438268	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.47	4.59	0.56863	.	0.164580	0.52532	D	0.000068	T	0.00552	0.0018	N	0.12569	0.235	0.38236	D	0.941193	B	0.09022	0.002	B	0.06405	0.002	T	0.03566	-1.1024	10	0.05959	T	0.93	-11.6587	12.4682	0.55771	0.0:0.6027:0.3973:0.0	rs16878594;rs17853086;rs52817728;rs16878594	15	Q8N567	ZCHC9_HUMAN	A	15	ENSP00000254037:P15A;ENSP00000385047:P15A;ENSP00000369546:P15A;ENSP00000412637:P15A	ENSP00000254037:P15A	P	+	1	0	ZCCHC9	80636375	1.000000	0.71417	0.458000	0.27068	0.616000	0.37450	2.765000	0.47621	2.559000	0.86315	0.655000	0.94253	CCC	C|0.916;G|0.084	0.084	strong		0.443	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	
LPIN3	64900	hgsc.bcm.edu	37	20	39986085	39986085	+	Missense_Mutation	SNP	A	A	C	rs12625565	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:39986085A>C	ENST00000373257.3	+	16	2128	c.2037A>C	c.(2035-2037)caA>caC	p.Q679H		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	679	C-LIP.		Q -> H (in dbSNP:rs12625565).		fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				ACAAAATCCAACTGTGAGTGC	0.602													C|||	1816	0.36262	0.4561	0.3501	5008	,	,		20475	0.5754		0.2346	False		,,,				2504	0.1575				p.Q679H		Atlas-SNP	.											.	LPIN3	69	.	0			c.A2037C						PASS	.	C	HIS/GLN	1934,2472	621.7+/-393.8	428,1078,697	60.0	53.0	55.0		2037	4.2	1.0	20	dbSNP_120	55	1882,6718	727.0+/-406.6	225,1432,2643	yes	missense	LPIN3	NM_022896.1	24	653,2510,3340	CC,CA,AA		21.8837,43.8947,29.3403	benign	679/852	39986085	3816,9190	2203	4300	6503	SO:0001583	missense	64900	exon16			AATCCAACTGTGA	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.2037A>C	20.37:g.39986085A>C	ENSP00000362354:p.Gln679His	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Missense_Mutation	SNP	ENST00000373257.3	37	CCDS33469.1	837|837	0.38324175824175827|0.38324175824175827	216|216	0.43902439024390244|0.43902439024390244	112|112	0.30939226519337015|0.30939226519337015	321|321	0.5611888111888111|0.5611888111888111	188|188	0.24802110817941952|0.24802110817941952	C|C	5.601|5.601	0.295673|0.295673	0.10622|0.10622	0.438947|0.438947	0.218837|0.218837	ENSG00000132793|ENSG00000132793	ENST00000445975|ENST00000373257;ENST00000373259	.|T	.|0.76709	.|-1.04	5.2|5.2	4.24|4.24	0.50183|0.50183	.|HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	.|0.000000	.|0.85682	.|N	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00471|0.00471	-1.455|-1.455	0.47308|0.47308	P|P	6.110000000000282E-4|6.110000000000282E-4	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.45731|0.45731	-0.9241|-0.9241	4|8	.|.	.|.	.|.	-15.3171|-15.3171	6.8264|6.8264	0.23885|0.23885	0.1436:0.7034:0.0:0.153|0.1436:0.7034:0.0:0.153	rs12625565;rs52822966;rs57276596;rs12625565|rs12625565;rs52822966;rs57276596;rs12625565	.|680;679	.|Q9BQK8-2;Q9BQK8	.|.;LPIN3_HUMAN	T|H	169|679;312	.|ENSP00000362354:Q679H	.|.	N|Q	+|+	2|3	0|2	LPIN3|LPIN3	39419499|39419499	0.854000|0.854000	0.29725|0.29725	1.000000|1.000000	0.80357|0.80357	0.941000|0.941000	0.58515|0.58515	0.392000|0.392000	0.20801|0.20801	0.572000|0.572000	0.29383|0.29383	-0.215000|-0.215000	0.12644|0.12644	AAC|CAA	A|0.667;C|0.333	0.333	strong		0.602	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896	
PSG6	5675	hgsc.bcm.edu	37	19	43420451	43420451	+	Missense_Mutation	SNP	G	G	C	rs386809477|rs3198831	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43420451G>C	ENST00000292125.2	-	2	297	c.253C>G	c.(253-255)Cac>Gac	p.H85D	PSG6_ENST00000402603.4_Missense_Mutation_p.H85D|PSG6_ENST00000601833.1_Missense_Mutation_p.H14D|PSG6_ENST00000187910.2_Missense_Mutation_p.H85D	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	85	Ig-like V-type.		H -> D (in dbSNP:rs3198831). {ECO:0000269|PubMed:2271648, ECO:0000269|PubMed:2346748}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				ATTTGACCGTGTACTACATAT	0.443													.|||	2271	0.453474	0.5991	0.4265	5008	,	,		21337	0.4325		0.2525	False		,,,				2504	0.5041				p.H85D		Atlas-SNP	.											.	PSG6	89	.	0			c.C253G						PASS	.	C	ASP/HIS,ASP/HIS	2533,1869		767,999,435	312.0	293.0	300.0		253,253	-4.2	0.0	19	dbSNP_105	300	2232,6366		347,1538,2414	yes	missense,missense	PSG6	NM_001031850.2,NM_002782.3	81,81	1114,2537,2849	CC,CG,GG		25.9595,42.458,36.6538	,	85/425,85/436	43420451	4765,8235	2201	4299	6500	SO:0001583	missense	5675	exon2			GACCGTGTACTAC		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.253C>G	19.37:g.43420451G>C	ENSP00000292125:p.His85Asp	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	850	0.3891941391941392	293	0.5955284552845529	130	0.35911602209944754	231	0.40384615384615385	196	0.25857519788918204	N	0.005	-2.167004	0.00318	0.57542	0.259595	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.63744	-0.06;-0.06;-0.06	2.24	-4.23	0.03789	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00033	-2.575	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34153	-0.9840	8	0.02654	T	1	.	5.3567	0.16065	0.2634:0.2385:0.4981:0.0	rs3198831;rs52810447;rs3198831	85;85;85	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	D	85	ENSP00000187910:H85D;ENSP00000385736:H85D;ENSP00000292125:H85D	ENSP00000187910:H85D	H	-	1	0	PSG6	48112291	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.739000	0.01840	-1.078000	0.03117	-1.041000	0.02371	CAC	G|0.625;C|0.375	0.375	strong		0.443	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
CCDC157	550631	hgsc.bcm.edu	37	22	30766698	30766698	+	Silent	SNP	G	G	A	rs141091935	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30766698G>A	ENST00000405659.1	+	5	1513	c.804G>A	c.(802-804)ccG>ccA	p.P268P	CCDC157_ENST00000338306.3_Silent_p.P268P			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	268										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						GGCCACTGCCGGCTGCCACCG	0.647													G|||	6	0.00119808	0.0	0.0043	5008	,	,		18880	0.0		0.003	False		,,,				2504	0.0				p.P268P		Atlas-SNP	.											.	CCDC157	86	.	0			c.G804A						PASS	.	G		5,4393	8.1+/-20.4	0,5,2194	38.0	35.0	36.0		804	-8.2	0.8	22	dbSNP_134	36	58,8540	34.8+/-89.0	0,58,4241	no	coding-synonymous	CCDC157	NM_001017437.2		0,63,6435	AA,AG,GG		0.6746,0.1137,0.4848		268/753	30766698	63,12933	2199	4299	6498	SO:0001819	synonymous_variant	550631	exon5			ACTGCCGGCTGCC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.804G>A	22.37:g.30766698G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			G|0.996;A|0.004	0.004	strong		0.647	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
MLPH	79083	hgsc.bcm.edu	37	2	238449007	238449007	+	Missense_Mutation	SNP	T	T	C	rs3817362	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238449007T>C	ENST00000264605.3	+	10	1415	c.1121T>C	c.(1120-1122)gTg>gCg	p.V374A	MLPH_ENST00000338530.4_Missense_Mutation_p.V346A|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Missense_Mutation_p.V374A|MLPH_ENST00000409373.1_Missense_Mutation_p.V306A|MLPH_ENST00000410032.1_Missense_Mutation_p.V231A	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	374			V -> A (in dbSNP:rs3817362). {ECO:0000269|PubMed:14702039}.		melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		GGTGCTGGAGTGCGCACGGAG	0.622													T|||	2161	0.43151	0.8071	0.3026	5008	,	,		18892	0.3899		0.1193	False		,,,				2504	0.3793				p.V374A		Atlas-SNP	.											.	MLPH	41	.	0			c.T1121C						PASS	.	T	ALA/VAL,ALA/VAL	3125,1281	690.5+/-405.3	1116,893,194	64.0	61.0	62.0		1037,1121	0.1	0.0	2	dbSNP_107	62	1187,7413	240.1+/-271.0	73,1041,3186	yes	missense,missense	MLPH	NM_001042467.1,NM_024101.5	64,64	1189,1934,3380	CC,CT,TT		13.8023,29.074,33.1539	benign,benign	346/573,374/601	238449007	4312,8694	2203	4300	6503	SO:0001583	missense	79083	exon10			CTGGAGTGCGCAC	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1121T>C	2.37:g.238449007T>C	ENSP00000264605:p.Val374Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	788|788	0.3608058608058608|0.3608058608058608	388|388	0.7886178861788617|0.7886178861788617	96|96	0.26519337016574585|0.26519337016574585	221|221	0.38636363636363635|0.38636363636363635	83|83	0.10949868073878628|0.10949868073878628	T|T	0.772|0.772	-0.765435|-0.765435	0.02996|0.02996	0.70926|0.70926	0.138023|0.138023	ENSG00000115648|ENSG00000115648	ENST00000436965|ENST00000410032;ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373;ENST00000437893	.|T;T;T;T;T;T	.|0.25250	.|2.05;2.17;2.05;2.02;1.81;1.93	4.66|4.66	0.0828|0.0828	0.14430|0.14430	.|.	.|6.460240	.|0.01732	.|N	.|0.028890	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B;B;B;B	.|0.17465	.|0.001;0.002;0.013;0.013;0.005;0.022;0.007;0.001	.|B;B;B;B;B;B;B;B	.|0.16289	.|0.001;0.001;0.01;0.007;0.002;0.015;0.002;0.001	T|T	0.39563|0.39563	-0.9608|-0.9608	4|9	.|0.08837	.|T	.|0.75	-8.0E-4|-8.0E-4	3.5252|3.5252	0.07757|0.07757	0.3479:0.3383:0.0:0.3138|0.3479:0.3383:0.0:0.3138	rs3817362;rs56654643;rs3817362|rs3817362;rs56654643;rs3817362	.|35;374;230;346;306;346;374;231	.|Q53QV8;B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36;G5E9G5	.|.;.;.;.;.;.;MELPH_HUMAN;.	R|A	95|231;374;374;346;306;134	.|ENSP00000386338:V231A;ENSP00000264605:V374A;ENSP00000414849:V374A;ENSP00000341845:V346A;ENSP00000386780:V306A;ENSP00000412438:V134A	.|ENSP00000264605:V374A	C|V	+|+	1|2	0|0	MLPH|MLPH	238113746|238113746	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.086000|-1.086000	0.03386|0.03386	-0.239000|-0.239000	0.09710|0.09710	-1.117000|-1.117000	0.02048|0.02048	TGC|GTG	T|0.643;C|0.357	0.357	strong		0.622	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
ZDHHC11	79844	hgsc.bcm.edu	37	5	825286	825286	+	Missense_Mutation	SNP	G	G	T	rs2335585	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:825286G>T	ENST00000283441.8	-	8	1399	c.1016C>A	c.(1015-1017)aCg>aAg	p.T339K	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.T339K	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	339						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			TACCCGTGCCGTCGAATCCCC	0.547																																					p.T339K		Atlas-SNP	.											ZDHHC11_ENST00000424784,NS,carcinoma,0,2	ZDHHC11	97	2	0			c.C1016A						PASS	.	G	LYS/THR	49,4357		0,49,2154	175.0	127.0	143.0		1016	0.1	0.0	5	dbSNP_100	143	124,8468		2,120,4174	yes	missense	ZDHHC11	NM_024786.2	78	2,169,6328	TT,TG,GG		1.4432,1.1121,1.331	benign	339/413	825286	173,12825	2203	4296	6499	SO:0001583	missense	79844	exon8			CGTGCCGTCGAAT	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1016C>A	5.37:g.825286G>T	ENSP00000283441:p.Thr339Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	129	14	0.108527	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	.	.	.	.	.	.	.	.	.	.	N	1.645	-0.515441	0.04200	0.011121	0.014432	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.27104	1.69;1.69	0.131	0.131	0.14755	.	.	.	.	.	T	0.06462	0.0166	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36841	-0.9731	8	0.06099	T	0.92	.	.	.	.	rs2335585;rs16900451;rs52807118;rs59749811;rs2335585	339	Q9H8X9	ZDH11_HUMAN	K	339	ENSP00000397719:T339K;ENSP00000283441:T339K	ENSP00000283441:T339K	T	-	2	0	ZDHHC11	878286	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.529000	0.23019	0.171000	0.19730	0.174000	0.16983	ACG	G|0.985;T|0.015	0.015	strong		0.547	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
CYP2C9	1559	hgsc.bcm.edu	37	10	96702047	96702047	+	Missense_Mutation	SNP	C	C	T	rs1799853	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96702047C>T	ENST00000260682.6	+	3	442	c.430C>T	c.(430-432)Cgt>Tgt	p.R144C	CYP2C9_ENST00000461906.1_3'UTR	NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	144			R -> C (in allele CYP2C9*2; dbSNP:rs1799853). {ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2827463, ECO:0000269|PubMed:3697070, ECO:0000269|PubMed:8946475, ECO:0000269|PubMed:9110362, ECO:0000269|Ref.3}.		arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	CATTGAGGACCGTGTTCAAGA	0.498													C|||	240	0.0479233	0.0083	0.0994	5008	,	,		20423	0.001		0.1243	False		,,,				2504	0.0348				p.R144C	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											.	CYP2C9	82	.	0			c.C430T	GRCh37	CM994193	CYP2C9	M	rs1799853	PASS	.	C	CYS/ARG	118,4288		4,110,2089	154.0	146.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	430	1.4	0.1	10	dbSNP_89	149	1124,7470		75,974,3248	yes	missense	CYP2C9	NM_000771.3	180	79,1084,5337	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	13.0789,2.6782,9.5538	probably-damaging	144/491	96702047	1242,11758	2203	4297	6500	SO:0001583	missense	1559	exon3			GAGGACCGTGTTC	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"""Cytochrome P450s"""	2623	protein-coding gene	gene with protein product		601130	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"""	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.430C>T	10.37:g.96702047C>T	ENSP00000260682:p.Arg144Cys	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	131	59	0.450382	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	149	0.06822344322344322	9	0.018292682926829267	45	0.12430939226519337	2	0.0034965034965034965	93	0.12269129287598944	.	16.06	3.014845	0.54468	0.026782	0.130789	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.69926	-0.44	3.54	1.42	0.22433	.	0.089345	0.47093	U	0.000246	T	0.02418	0.0074	M	0.74647	2.275	0.23144	P	0.99822706	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.989;0.989;0.995	T	0.51810	-0.8658	9	0.72032	D	0.01	.	5.9087	0.19016	0.4066:0.4141:0.1794:0.0	rs1799853;rs17110268;rs60690363;rs1799853	144;144;144	Q5VX92;P11712;Q8WW80	.;CP2C9_HUMAN;.	C	144	ENSP00000260682:R144C	ENSP00000260682:R144C	R	+	1	0	CYP2C9	96692037	0.000000	0.05858	0.125000	0.21846	0.884000	0.51177	-0.307000	0.08167	0.194000	0.20326	0.484000	0.47621	CGT	C|1.000;|0.000	.	weak		0.498	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771	
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 GAIIx	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_ENST00000366206.2_5'Flank|STRN3_ENST00000355683.5_Silent_p.A289A	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		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	80	37	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	
BBOX1	8424	hgsc.bcm.edu	37	11	27114788	27114788	+	Silent	SNP	C	C	T	rs3183973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:27114788C>T	ENST00000529202.1	+	4	747	c.408C>T	c.(406-408)caC>caT	p.H136H	BBOX1_ENST00000527505.1_Intron|RP11-1L12.3_ENST00000530430.1_RNA|RP11-1L12.3_ENST00000526061.1_RNA|BBOX1_ENST00000525090.1_Silent_p.H136H|BBOX1_ENST00000263182.3_Silent_p.H136H|RP11-1L12.3_ENST00000525302.1_RNA|BBOX1_ENST00000528583.1_Silent_p.H136H			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	136					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)	p.H136H(1)		breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	ATGATGAACACGCATACAAGT	0.423													T|||	1463	0.292133	0.68	0.1686	5008	,	,		19165	0.0516		0.2237	False		,,,				2504	0.1738				p.H136H		Atlas-SNP	.											BBOX1,NS,carcinoma,0,1	BBOX1	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C408T						PASS	.	T		2551,1853	535.6+/-374.3	734,1083,385	93.0	92.0	92.0		408	0.5	0.2	11	dbSNP_105	92	2022,6574	720.2+/-406.3	229,1564,2505	no	coding-synonymous	BBOX1	NM_003986.2		963,2647,2890	TT,TC,CC		23.5226,42.0754,35.1769		136/388	27114788	4573,8427	2202	4298	6500	SO:0001819	synonymous_variant	8424	exon5			TGAACACGCATAC	AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.408C>T	11.37:g.27114788C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Silent	SNP	ENST00000529202.1	37	CCDS7862.1																																																																																			C|0.675;T|0.325	0.325	strong		0.423	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986	
CCDC18	343099	hgsc.bcm.edu	37	1	93672688	93672688	+	Silent	SNP	C	C	T	rs2783499	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:93672688C>T	ENST00000343253.7	+	9	1444	c.942C>T	c.(940-942)aaC>aaT	p.N314N	CCDC18_ENST00000334652.5_5'UTR|CCDC18_ENST00000557479.1_Silent_p.N432N|CCDC18_ENST00000338949.4_Silent_p.N113N|CCDC18_ENST00000401026.3_Silent_p.N314N			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	314										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AAAATAACAACGGAAAAGAAA	0.274													C|||	1163	0.232228	0.1974	0.2392	5008	,	,		16376	0.3175		0.1511	False		,,,				2504	0.2699				p.N314N		Atlas-SNP	.											.	CCDC18	93	.	0			c.C942T						PASS	.	C		664,2932		60,544,1194	37.0	32.0	33.0		942	0.9	1.0	1	dbSNP_100	33	1326,6790		128,1070,2860	no	coding-synonymous	CCDC18	NM_206886.3		188,1614,4054	TT,TC,CC		16.3381,18.465,16.9911		314/1300	93672688	1990,9722	1798	4058	5856	SO:0001819	synonymous_variant	343099	exon9			TAACAACGGAAAA			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.942C>T	1.37:g.93672688C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_206886	Q6ZU17	Silent	SNP	ENST00000343253.7	37		469	0.21474358974358973	91	0.18495934959349594	84	0.23204419889502761	174	0.3041958041958042	120	0.158311345646438	C	5.368	0.253238	0.10185	0.18465	0.163381	ENSG00000122483	ENST00000370276	.	.	.	5.83	0.948	0.19561	.	.	.	.	.	T	0.32194	0.0821	.	.	.	0.09310	P	0.999999999729022	.	.	.	.	.	.	T	0.11867	-1.0570	3	.	.	.	.	9.6036	0.39619	0.0:0.3783:0.0:0.6217	rs2783499;rs57879641;rs2783499	.	.	.	M	368	.	.	T	+	2	0	CCDC18	93445276	0.315000	0.24571	0.976000	0.42696	0.868000	0.49771	0.374000	0.20501	-0.076000	0.12775	-1.300000	0.01332	ACG	C|0.794;T|0.206	0.206	strong		0.274	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
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 GAIIx	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	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	71	40	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	
ZNF292	23036	hgsc.bcm.edu	37	6	87969480	87969480	+	Missense_Mutation	SNP	G	G	A	rs6910541	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:87969480G>A	ENST00000369577.3	+	8	6176	c.6133G>A	c.(6133-6135)Gta>Ata	p.V2045I	ZNF292_ENST00000339907.4_Missense_Mutation_p.V2040I	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	2045			V -> I (in dbSNP:rs6910541). {ECO:0000269|PubMed:9628581}.			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 positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		AAAACAACTTGTAGAAAAAAA	0.358													G|||	563	0.11242	0.1112	0.1527	5008	,	,		18764	0.0972		0.1064	False		,,,				2504	0.1074				p.V2045I		Atlas-SNP	.											.	ZNF292	479	.	0			c.G6133A						PASS	.	G	ILE/VAL	437,3161		24,389,1386	28.0	25.0	26.0		6133	-9.9	0.0	6	dbSNP_116	26	846,7270		37,772,3249	yes	missense	ZNF292	NM_015021.1	29	61,1161,4635	AA,AG,GG		10.4239,12.1456,10.9527	benign	2045/2724	87969480	1283,10431	1799	4058	5857	SO:0001583	missense	23036	exon8			CAACTTGTAGAAA	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.6133G>A	6.37:g.87969480G>A	ENSP00000358590:p.Val2045Ile	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	148	59	0.398649	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	275	0.1259157509157509	71	0.1443089430894309	61	0.1685082872928177	63	0.11013986013986014	80	0.10554089709762533	G	4.208	0.037399	0.08148	0.121456	0.104239	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.07114	3.22;3.23	5.87	-9.85	0.00476	.	1.934300	0.01884	N	0.038072	T	0.00608	0.0020	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40627	-0.9553	9	0.19147	T	0.46	.	6.9653	0.24619	0.1398:0.3551:0.4245:0.0806	rs6910541;rs52830459;rs61648684;rs6910541	2045	O60281	ZN292_HUMAN	I	2045;2040	ENSP00000358590:V2045I;ENSP00000342847:V2040I	ENSP00000342847:V2040I	V	+	1	0	ZNF292	88026199	0.000000	0.05858	0.000000	0.03702	0.445000	0.32107	-0.649000	0.05384	-1.686000	0.01439	-0.345000	0.07892	GTA	G|0.875;A|0.125	0.125	strong		0.358	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
CCDC65	85478	hgsc.bcm.edu	37	12	49312593	49312593	+	Silent	SNP	A	A	G	rs10875893	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49312593A>G	ENST00000320516.4	+	6	1121	c.933A>G	c.(931-933)agA>agG	p.R311R	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Silent_p.R311R	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	311										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						AGGCCCAAAGAACTCAGGCCC	0.473													G|||	1541	0.307708	0.1021	0.4942	5008	,	,		17380	0.4415		0.4095	False		,,,				2504	0.2106				p.R311R		Atlas-SNP	.											.	CCDC65	41	.	0			c.A933G						PASS	.	G		696,3710	761.9+/-413.1	72,552,1579	87.0	84.0	85.0		933	1.9	0.8	12	dbSNP_120	85	3288,5312	646.8+/-400.3	618,2052,1630	no	coding-synonymous	CCDC65	NM_033124.4		690,2604,3209	GG,GA,AA		38.2326,15.7966,30.632		311/485	49312593	3984,9022	2203	4300	6503	SO:0001819	synonymous_variant	85478	exon6			CCAAAGAACTCAG		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.933A>G	12.37:g.49312593A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	125	67	0.536	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Silent	SNP	ENST00000320516.4	37	CCDS8772.1																																																																																			A|0.678;G|0.322	0.322	strong		0.473	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
ZNF831	128611	hgsc.bcm.edu	37	20	57768399	57768399	+	Silent	SNP	T	T	C	rs442091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:57768399T>C	ENST00000371030.2	+	1	2325	c.2325T>C	c.(2323-2325)gcT>gcC	p.A775A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	775							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)					ATGTAGAGGCTCCCAGGCCAG	0.652													.|||	1808	0.361022	0.5643	0.3141	5008	,	,		16119	0.372		0.2356	False		,,,				2504	0.2372				p.A775A		Atlas-SNP	.											ZNF831,NS,carcinoma,+2,1	ZNF831	287	1	0			c.T2325C						scavenged	.	C		1847,1895		445,957,469	22.0	29.0	27.0		2325	-1.1	0.0	20	dbSNP_80	27	1835,6361		198,1439,2461	yes	coding-synonymous	ZNF831	NM_178457.1		643,2396,2930	CC,CT,TT		22.389,49.3586,30.8427		775/1678	57768399	3682,8256	1871	4098	5969	SO:0001819	synonymous_variant	128611	exon1			AGAGGCTCCCAGG	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.2325T>C	20.37:g.57768399T>C		Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	49	31	0.632653	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																			T|0.666;C|0.334	0.334	strong		0.652	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
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 GAIIx	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	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	154	64	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		
ABHD12	26090	hgsc.bcm.edu	37	20	25282944	25282944	+	Silent	SNP	A	A	G	rs10966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:25282944A>G	ENST00000339157.5	-	12	1340	c.1068T>C	c.(1066-1068)gaT>gaC	p.D356D	ABHD12_ENST00000376542.3_Silent_p.D356D	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	356					adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						GAACTTTGAAATCTCGGAAGC	0.547													G|||	2712	0.541534	0.4629	0.3516	5008	,	,		19604	0.9107		0.4374	False		,,,				2504	0.5092				p.D356D		Atlas-SNP	.											.	ABHD12	46	.	0			c.T1068C						PASS	.	G	,	1987,2419	617.9+/-393.1	434,1119,650	126.0	112.0	117.0		1068,1068	5.0	1.0	20	dbSNP_52	117	3754,4846	616.2+/-396.5	809,2136,1355	no	coding-synonymous,coding-synonymous	ABHD12	NM_001042472.2,NM_015600.4	,	1243,3255,2005	GG,GA,AA		43.6512,45.0976,44.1412	,	356/399,356/405	25282944	5741,7265	2203	4300	6503	SO:0001819	synonymous_variant	26090	exon12			TTTGAAATCTCGG	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"""Abhydrolase domain containing"""	15868	protein-coding gene	gene with protein product		613599	"""chromosome 20 open reading frame 22"""	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.1068T>C	20.37:g.25282944A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Silent	SNP	ENST00000339157.5	37	CCDS42857.1																																																																																			A|0.530;G|0.470	0.470	strong		0.547	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600	
PITPNM3	83394	hgsc.bcm.edu	37	17	6386947	6386947	+	Silent	SNP	G	G	A	rs34897053	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6386947G>A	ENST00000262483.8	-	6	564	c.477C>T	c.(475-477)tcC>tcT	p.S159S	PITPNM3_ENST00000421306.3_Silent_p.S123S	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	159					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		TCTCCAGCACGGAGCTGAAGG	0.617													G|||	333	0.0664936	0.0053	0.111	5008	,	,		19629	0.0645		0.0298	False		,,,				2504	0.1575				p.S159S		Atlas-SNP	.											.	PITPNM3	91	.	0			c.C477T						PASS	.	G	,	36,4370	40.8+/-73.8	0,36,2167	143.0	97.0	112.0		369,477	-8.4	0.8	17	dbSNP_126	112	191,8409	84.2+/-146.7	3,185,4112	no	coding-synonymous,coding-synonymous	PITPNM3	NM_001165966.1,NM_031220.3	,	3,221,6279	AA,AG,GG		2.2209,0.8171,1.7453	,	123/939,159/975	6386947	227,12779	2203	4300	6503	SO:0001819	synonymous_variant	83394	exon6			CAGCACGGAGCTG	AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.477C>T	17.37:g.6386947G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	37	CCDS11076.1																																																																																			G|0.973;A|0.027	0.027	strong		0.617	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
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 GAIIx	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	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	168	72	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	
OR10H5	284433	hgsc.bcm.edu	37	19	15905431	15905431	+	Silent	SNP	T	T	C	rs4808381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15905431T>C	ENST00000308940.8	+	1	671	c.573T>C	c.(571-573)gaT>gaC	p.D191D		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						CCTGTGGAGATGATGTGCTGG	0.572													.|||	2284	0.45607	0.3359	0.4784	5008	,	,		22330	0.7897		0.3052	False		,,,				2504	0.4141				p.D191D		Atlas-SNP	.											.	OR10H5	49	.	0			c.T573C						PASS	.	T		1488,2918		260,968,975	165.0	130.0	142.0		573	-5.6	0.0	19	dbSNP_111	142	2843,5757		509,1825,1966	no	coding-synonymous	OR10H5	NM_001004466.1		769,2793,2941	CC,CT,TT		33.0581,33.7721,33.3		191/316	15905431	4331,8675	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			TGGAGATGATGTG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.573T>C	19.37:g.15905431T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	216	103	0.476852	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			T|0.623;C|0.377	0.377	strong		0.572	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
MGAT5B	146664	hgsc.bcm.edu	37	17	74942478	74942478	+	Silent	SNP	C	C	T	rs8067984	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74942478C>T	ENST00000569840.2	+	16	2443	c.1869C>T	c.(1867-1869)taC>taT	p.Y623Y	MGAT5B_ENST00000428789.2_Silent_p.Y632Y|MGAT5B_ENST00000301618.4_Silent_p.Y621Y	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	623					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ACCTACCCTACGAGTACACCT	0.657													C|||	1784	0.35623	0.2451	0.2651	5008	,	,		16241	0.5357		0.4026	False		,,,				2504	0.3384				p.Y632Y		Atlas-SNP	.											.	MGAT5B	98	.	0			c.C1896T						PASS	.	C	,,	1210,3196	419.6+/-338.7	176,858,1169	88.0	62.0	70.0		1869,1863,1896	-3.6	1.0	17	dbSNP_116	70	3312,5288	493.4+/-373.6	641,2030,1629	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	817,2888,2798	TT,TC,CC		38.5116,27.4626,34.7686	,,	623/793,621/791,632/802	74942478	4522,8484	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon14			ACCCTACGAGTAC	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1869C>T	17.37:g.74942478C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			C|0.639;T|0.361	0.361	strong		0.657	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
ASB5	140458	hgsc.bcm.edu	37	4	177137988	177137988	+	Silent	SNP	C	C	T	rs6827525	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:177137988C>T	ENST00000296525.3	-	6	956	c.843G>A	c.(841-843)agG>agA	p.R281R	ASB5_ENST00000512254.1_Silent_p.R228R	NM_080874.3	NP_543150.1	Q8WWX0	ASB5_HUMAN	ankyrin repeat and SOCS box containing 5	281	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					endometrium(2)|kidney(1)|large_intestine(9)|lung(18)|prostate(2)|skin(2)	34		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.13e-20)|Epithelial(43;9.94e-18)|OV - Ovarian serous cystadenocarcinoma(60;2e-09)|GBM - Glioblastoma multiforme(59;0.000254)|STAD - Stomach adenocarcinoma(60;0.000653)|LUSC - Lung squamous cell carcinoma(193;0.0393)		GAAGCAATATCCTTTCCACCA	0.348													T|||	2582	0.515575	0.5219	0.5533	5008	,	,		19224	0.5675		0.4751	False		,,,				2504	0.4683				p.R281R		Atlas-SNP	.											.	ASB5	88	.	0			c.G843A						PASS	.	T		2190,2216	591.1+/-387.5	534,1122,547	155.0	147.0	150.0		843	1.4	0.1	4	dbSNP_116	150	4095,4505	592.8+/-393.0	973,2149,1178	no	coding-synonymous	ASB5	NM_080874.3		1507,3271,1725	TT,TC,CC		47.6163,49.7049,48.3239		281/330	177137988	6285,6721	2203	4300	6503	SO:0001819	synonymous_variant	140458	exon6			CAATATCCTTTCC	AY057053	CCDS3827.1	4q34.1	2013-01-10	2011-01-25		ENSG00000164122	ENSG00000164122		"""Ankyrin repeat domain containing"""	17180	protein-coding gene	gene with protein product		615050	"""ankyrin repeat and SOCS box-containing 5"""				Standard	NM_080874		Approved		uc003iuq.2	Q8WWX0	OTTHUMG00000160793	ENST00000296525.3:c.843G>A	4.37:g.177137988C>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	159	80	0.503145	NM_080874	Q8N7B5	Silent	SNP	ENST00000296525.3	37	CCDS3827.1																																																																																			C|0.504;T|0.496	0.496	strong		0.348	ASB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362344.1		
RAB3B	5865	hgsc.bcm.edu	37	1	52399021	52399021	+	Silent	SNP	A	A	G	rs2230325	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:52399021A>G	ENST00000371655.3	-	4	653	c.441T>C	c.(439-441)acT>acC	p.T147T		NM_002867.3	NP_002858.2	P20337	RAB3B_HUMAN	RAB3B, member RAS oncogene family	147					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of vesicle size (GO:0097494)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	9						GGCCCTTCTCAGTGGGAACAA	0.483													A|||	295	0.0589058	0.1717	0.0216	5008	,	,		20129	0.001		0.0209	False		,,,				2504	0.0317				p.T147T		Atlas-SNP	.											.	RAB3B	22	.	0			c.T441C						PASS	.	A		682,3724	288.9+/-280.1	49,584,1570	191.0	146.0	161.0		441	0.1	1.0	1	dbSNP_123	161	243,8357	96.3+/-158.1	7,229,4064	no	coding-synonymous	RAB3B	NM_002867.3		56,813,5634	GG,GA,AA		2.8256,15.4789,7.1121		147/220	52399021	925,12081	2203	4300	6503	SO:0001819	synonymous_variant	5865	exon4			CTTCTCAGTGGGA	BC005035	CCDS560.1	1p32-p31	2008-02-05			ENSG00000169213	ENSG00000169213		"""RAB, member RAS oncogene"""	9778	protein-coding gene	gene with protein product		179510					Standard	NM_002867		Approved		uc001cth.3	P20337	OTTHUMG00000008627	ENST00000371655.3:c.441T>C	1.37:g.52399021A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_002867	Q5VUL2|Q9BSI1	Silent	SNP	ENST00000371655.3	37	CCDS560.1																																																																																			A|0.931;G|0.069	0.069	strong		0.483	RAB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023816.1	NM_002867	
EFCAB5	374786	hgsc.bcm.edu	37	17	28296327	28296327	+	Missense_Mutation	SNP	T	T	G	rs9897794	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:28296327T>G	ENST00000394835.3	+	4	901	c.709T>G	c.(709-711)Ttg>Gtg	p.L237V	EFCAB5_ENST00000536908.2_Missense_Mutation_p.L181V|EFCAB5_ENST00000320856.5_Missense_Mutation_p.L237V|EFCAB5_ENST00000541045.1_Intron|EFCAB5_ENST00000378738.3_Missense_Mutation_p.L237V|EFCAB5_ENST00000394832.2_Missense_Mutation_p.L237V|EFCAB5_ENST00000534836.2_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	237			L -> V (in dbSNP:rs9897794). {ECO:0000269|PubMed:14702039}.				calcium ion binding (GO:0005509)			breast(7)|endometrium(2)|kidney(4)|large_intestine(11)|lung(14)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TTACCAGAGGTTGATGAAAGA	0.363													G|||	2716	0.542332	0.444	0.5677	5008	,	,		17724	0.7133		0.4622	False		,,,				2504	0.5634				p.L237V		Atlas-SNP	.											EFCAB5,NS,carcinoma,-2,1	EFCAB5	122	1	0			c.T709G						scavenged	.	G	VAL/LEU,VAL/LEU	1561,2119		322,917,601	30.0	31.0	31.0		541,709	5.3	1.0	17	dbSNP_119	31	3994,4168		989,2016,1076	yes	missense,missense	EFCAB5	NM_001145053.1,NM_198529.3	32,32	1311,2933,1677	GG,GT,TT		48.9341,42.4185,46.9093	benign,benign	181/857,237/1504	28296327	5555,6287	1840	4081	5921	SO:0001583	missense	374786	exon4			CAGAGGTTGATGA	AL833911	CCDS11254.2, CCDS54103.1	17q11.2	2013-01-10			ENSG00000176927	ENSG00000176927		"""EF-hand domain containing"""	24801	protein-coding gene	gene with protein product							Standard	NM_198529		Approved	FLJ46247	uc002het.3	A4FU69	OTTHUMG00000132753	ENST00000394835.3:c.709T>G	17.37:g.28296327T>G	ENSP00000378312:p.Leu237Val	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	152	63	0.414474	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	1199	0.548992673992674	229	0.4654471544715447	200	0.5524861878453039	410	0.7167832167832168	360	0.47493403693931396	G	5.176	0.218080	0.09810	0.424185	0.489341	ENSG00000176927	ENST00000536908;ENST00000394835;ENST00000320856;ENST00000394832;ENST00000378738;ENST00000423598;ENST00000419434	T;T;T;T;T;T	0.21031	2.03;3.04;3.05;2.37;2.04;3.04	5.32	5.32	0.75619	.	0.302373	0.23275	N	0.049963	T	0.00012	0.0000	N	0.00289	-1.7	0.09310	P	0.9999999999999422	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.23084	-1.0198	9	0.13108	T	0.6	-6.0022	13.3301	0.60480	0.0:0.0:0.8418:0.1582	rs9897794;rs61407133;rs9897794	181;237;237;237	F5GYL2;B5MEA3;E7EVS9;A4FU69	.;.;.;EFCB5_HUMAN	V	181;237;237;237;237;181;43	ENSP00000440619:L181V;ENSP00000378312:L237V;ENSP00000322003:L237V;ENSP00000378309:L237V;ENSP00000368012:L237V;ENSP00000417009:L43V	ENSP00000322003:L237V	L	+	1	2	EFCAB5	25320453	1.000000	0.71417	0.999000	0.59377	0.914000	0.54420	3.577000	0.53885	1.390000	0.46547	-0.217000	0.12591	TTG	T|0.452;G|0.548	0.548	strong		0.363	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529	
DMXL2	23312	hgsc.bcm.edu	37	15	51829812	51829812	+	Missense_Mutation	SNP	G	G	A	rs17524906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:51829812G>A	ENST00000251076.5	-	11	1777	c.1490C>T	c.(1489-1491)aCg>aTg	p.T497M	DMXL2_ENST00000543779.2_Missense_Mutation_p.T497M|DMXL2_ENST00000449909.3_Missense_Mutation_p.T497M	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	497			T -> M (in dbSNP:rs17524906).			cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		AGTTAGCAGCGTTTCAATCTT	0.408													g|||	643	0.128395	0.1233	0.1758	5008	,	,		16597	0.0069		0.2197	False		,,,				2504	0.1329				p.T497M		Atlas-SNP	.											DMXL2,colon,carcinoma,0,1	DMXL2	262	1	0			c.C1490T						PASS	.	A	MET/THR,MET/THR,MET/THR	628,3762	271.3+/-270.1	43,542,1610	214.0	184.0	194.0		1490,1490,1490	-1.7	1.0	15	dbSNP_123	194	2097,6489	361.6+/-332.4	282,1533,2478	yes	missense,missense,missense	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	81,81,81	325,2075,4088	AA,AG,GG		24.4235,14.3052,21.0003	benign,benign,benign	497/3038,497/2401,497/3037	51829812	2725,10251	2195	4293	6488	SO:0001583	missense	23312	exon11			AGCAGCGTTTCAA	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.1490C>T	15.37:g.51829812G>A	ENSP00000251076:p.Thr497Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	141	71	0.503546	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	291	0.13324175824175824	56	0.11382113821138211	71	0.19613259668508287	4	0.006993006993006993	160	0.21108179419525067	g	11.20	1.568214	0.28003	0.143052	0.244235	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.11385	2.78;2.78;2.78	4.88	-1.66	0.08265	.	0.444359	0.27618	N	0.018574	T	0.00012	0.0000	N	0.19112	0.55	0.52501	P	4.999999999999449E-5	B;B;B	0.10296	0.002;0.0;0.003	B;B;B	0.06405	0.002;0.001;0.001	T	0.48502	-0.9030	9	0.23302	T	0.38	.	7.1983	0.25866	0.5027:0.1213:0.376:0.0	rs17524906;rs52793467;rs17524906	497;497;497	F5GWF1;B2RTR3;Q8TDJ6	.;.;DMXL2_HUMAN	M	497	ENSP00000251076:T497M;ENSP00000441858:T497M;ENSP00000400855:T497M	ENSP00000251076:T497M	T	-	2	0	DMXL2	49617104	0.980000	0.34600	0.995000	0.50966	0.985000	0.73830	0.516000	0.22817	-0.308000	0.08792	-1.128000	0.01989	ACG	G|0.825;A|0.175	0.175	strong		0.408	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
ZNF710	374655	hgsc.bcm.edu	37	15	90610807	90610807	+	Silent	SNP	C	C	A	rs74038806	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90610807C>A	ENST00000268154.4	+	2	689	c.438C>A	c.(436-438)ggC>ggA	p.G146G		NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	146					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(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			CCAGTGGCGGCTGCGACGCCC	0.682													C|||	435	0.086861	0.1286	0.0764	5008	,	,		12810	0.0		0.1093	False		,,,				2504	0.1043				p.G146G		Atlas-SNP	.											.	ZNF710	50	.	0			c.C438A						PASS	.	C		509,3863		39,431,1716	35.0	40.0	38.0		438	3.9	1.0	15	dbSNP_130	38	933,7649		51,831,3409	no	coding-synonymous	ZNF710	NM_198526.2		90,1262,5125	AA,AC,CC		10.8716,11.6423,11.1317		146/665	90610807	1442,11512	2186	4291	6477	SO:0001819	synonymous_variant	374655	exon2			TGGCGGCTGCGAC	AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"""Zinc fingers, C2H2-type"""	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.438C>A	15.37:g.90610807C>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	37	36	0.972973	NM_198526	A0AVS3|Q6ZMK9|Q8NDU0	Silent	SNP	ENST00000268154.4	37	CCDS10358.1																																																																																			C|0.923;A|0.077	0.077	strong		0.682	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526	
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 GAIIx	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		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	13	7	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 GAIIx	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_ENST00000354560.6_5'Flank|CRIP1_ENST00000392531.3_Missense_Mutation_p.C52F|C14orf80_ENST00000329886.7_5'Flank|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000392527.1_5'Flank|CRIP1_ENST00000409393.2_Missense_Mutation_p.C52F|C14orf80_ENST00000392523.4_5'Flank|CRIP1_ENST00000551180.1_Silent_p.L20L|C14orf80_ENST00000334656.7_5'Flank			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	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	110	57	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	
CCNT1	904	hgsc.bcm.edu	37	12	49087325	49087325	+	Missense_Mutation	SNP	T	T	C	rs61751603	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49087325T>C	ENST00000261900.3	-	9	1894	c.1672A>G	c.(1672-1674)Acc>Gcc	p.T558A		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	558	Ser-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						AAGCTATAGGTTTTATGTGCT	0.458													T|||	50	0.00998403	0.0008	0.013	5008	,	,		19991	0.0		0.0348	False		,,,				2504	0.0051				p.T558A		Atlas-SNP	.											.	CCNT1	55	.	0			c.A1672G						PASS	.	T	ALA/THR	21,4385	27.2+/-55.0	0,21,2182	137.0	138.0	138.0		1672	-1.5	1.0	12	dbSNP_129	138	204,8396	88.1+/-150.5	1,202,4097	yes	missense	CCNT1	NM_001240.2	58	1,223,6279	CC,CT,TT		2.3721,0.4766,1.73	benign	558/727	49087325	225,12781	2203	4300	6503	SO:0001583	missense	904	exon9			TATAGGTTTTATG	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1672A>G	12.37:g.49087325T>C	ENSP00000261900:p.Thr558Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001240	A9XU13|E7EX76|O60581	Missense_Mutation	SNP	ENST00000261900.3	37	CCDS8766.1	29	0.013278388278388278	0	0.0	4	0.011049723756906077	0	0.0	25	0.032981530343007916	T	3.209	-0.162057	0.06502	0.004766	0.023721	ENSG00000129315	ENST00000261900	T	0.17054	2.3	4.77	-1.5	0.08691	.	0.856083	0.10144	N	0.710481	T	0.01800	0.0057	N	0.08118	0	0.25020	N	0.991346	B	0.02656	0.0	B	0.01281	0.0	T	0.40720	-0.9548	10	0.06625	T	0.88	0.1159	5.8234	0.18540	0.0:0.5057:0.1918:0.3025	rs61751603	558	O60563	CCNT1_HUMAN	A	558	ENSP00000261900:T558A	ENSP00000261900:T558A	T	-	1	0	CCNT1	47373592	0.011000	0.17503	0.996000	0.52242	0.993000	0.82548	-0.383000	0.07398	-0.229000	0.09854	0.459000	0.35465	ACC	T|0.984;C|0.016	0.016	strong		0.458	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240	
STAB2	55576	hgsc.bcm.edu	37	12	104100617	104100617	+	Silent	SNP	C	C	T	rs697212	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:104100617C>T	ENST00000388887.2	+	38	4248	c.4044C>T	c.(4042-4044)tgC>tgT	p.C1348C		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GCCAGCCCTGCCCAGGGAATG	0.547													C|||	2158	0.430911	0.1203	0.3256	5008	,	,		20375	0.747		0.504	False		,,,				2504	0.5245				p.C1348C		Atlas-SNP	.											.	STAB2	370	.	0			c.C4044T						PASS	.	C		862,3544	338.1+/-305.1	88,686,1429	126.0	117.0	120.0		4044	3.5	1.0	12	dbSNP_86	120	4234,4366	573.2+/-389.8	1044,2146,1110	no	coding-synonymous	STAB2	NM_017564.9		1132,2832,2539	TT,TC,CC		49.2326,19.5642,39.1819		1348/2552	104100617	5096,7910	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon38			GCCCTGCCCAGGG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.4044C>T	12.37:g.104100617C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	151	148	0.980132	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			T|0.403;G|0.003	0.403	strong		0.547	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
CCDC105	126402	hgsc.bcm.edu	37	19	15133787	15133787	+	Silent	SNP	C	C	A	rs10424547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15133787C>A	ENST00000292574.3	+	7	1438	c.1356C>A	c.(1354-1356)atC>atA	p.I452I		NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	452						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						GCAAGAACATCGGGCATGAGG	0.637													c|||	1610	0.321486	0.1203	0.4323	5008	,	,		15747	0.5208		0.2346	False		,,,				2504	0.3988				p.I452I		Atlas-SNP	.											.	CCDC105	53	.	0			c.C1356A						PASS	.			739,3667	291.5+/-281.6	62,615,1526	55.0	40.0	45.0		1356	-6.5	0.0	19	dbSNP_119	45	2035,6563	339.6+/-323.3	227,1581,2491	no	coding-synonymous	CCDC105	NM_173482.2		289,2196,4017	AA,AC,CC		23.6683,16.7726,21.3319		452/500	15133787	2774,10230	2203	4299	6502	SO:0001819	synonymous_variant	126402	exon7			GAACATCGGGCAT	AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.1356C>A	19.37:g.15133787C>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_173482	Q8N7T5|Q8NDL5	Silent	SNP	ENST00000292574.3	37	CCDS12322.1																																																																																			C|0.749;A|0.251	0.251	strong		0.637	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482	
ESPNL	339768	hgsc.bcm.edu	37	2	239040218	239040218	+	Missense_Mutation	SNP	G	G	A	rs73102309	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:239040218G>A	ENST00000343063.3	+	9	3126	c.2863G>A	c.(2863-2865)Gcc>Acc	p.A955T	ESPNL_ENST00000409169.1_Missense_Mutation_p.A911T|ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.A587T	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	955				A -> T (in Ref. 1; BAC85884). {ECO:0000305}.						endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GCCTCACGCCGCCGTCCCCTG	0.687													G|||	670	0.133786	0.2368	0.0908	5008	,	,		14386	0.0546		0.1173	False		,,,				2504	0.1237				p.A955T		Atlas-SNP	.											.	ESPNL	63	.	0			c.G2863A						PASS	.	G	THR/ALA	921,3467		109,703,1382	16.0	18.0	17.0		2863	-8.3	0.0	2	dbSNP_130	17	1011,7585		55,901,3342	no	missense	ESPNL	NM_194312.2	58	164,1604,4724	AA,AG,GG		11.7613,20.9891,14.8799	benign	955/1006	239040218	1932,11052	2194	4298	6492	SO:0001583	missense	339768	exon9			CACGCCGCCGTCC	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2863G>A	2.37:g.239040218G>A	ENSP00000339115:p.Ala955Thr	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	256	0.11721611721611722	95	0.19308943089430894	35	0.09668508287292818	41	0.07167832167832168	85	0.11213720316622691	G	5.082	0.200731	0.09652	0.209891	0.117613	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.63744	-0.06;1.04;0.64	4.16	-8.28	0.01013	.	0.795116	0.10989	N	0.611773	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.15549	-1.0433	9	0.15499	T	0.54	-0.9499	0.4266	0.00464	0.3016:0.1957:0.2867:0.216	.	911;955	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	T	955;911;587	ENSP00000339115:A955T;ENSP00000386577:A911T;ENSP00000386579:A587T	ENSP00000339115:A955T	A	+	1	0	ESPNL	238704957	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-1.492000	0.02300	-1.336000	0.02238	-0.378000	0.06908	GCC	G|0.865;A|0.135	0.135	strong		0.687	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964510	88964510	+	Silent	SNP	T	T	C	rs62469518	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:88964510T>C	ENST00000333190.4	+	4	2823	c.2214T>C	c.(2212-2214)aaT>aaC	p.N738N		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	738							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GCAGAGGTAATTTGCTCTGCT	0.393										HNSCC(36;0.09)			T|||	171	0.0341454	0.0113	0.0605	5008	,	,		20637	0.0		0.0785	False		,,,				2504	0.0358				p.N738N		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T2214C						PASS	.	T		90,4316	73.1+/-111.1	1,88,2114	93.0	88.0	90.0		2214	-1.9	0.0	7	dbSNP_129	90	730,7870	177.5+/-227.1	30,670,3600	no	coding-synonymous	ZNF804B	NM_181646.2		31,758,5714	CC,CT,TT		8.4884,2.0427,6.3048		738/1350	88964510	820,12186	2203	4300	6503	SO:0001819	synonymous_variant	219578	exon4			AGGTAATTTGCTC	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2214T>C	7.37:g.88964510T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																			T|0.939;C|0.061	0.061	strong		0.393	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
PRB4	5545	hgsc.bcm.edu	37	12	11461154	11461154	+	Splice_Site	SNP	C	C	G	rs7297795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11461154C>G	ENST00000279575.1	-	3	796		c.e3+1		PRB4_ENST00000535904.1_Intron	NM_001261399.1|NM_002723.4	NP_001248328.1|NP_002714.2	P10163	PRB4_HUMAN	proline-rich protein BstNI subfamily 4							extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|skin(4)|upper_aerodigestive_tract(3)	30						TGGAATCATACCTGTCATTGA	0.483										HNSCC(22;0.051)			C|||	28	0.00559105	0.0	0.0058	5008	,	,		18676	0.0		0.0219	False		,,,				2504	0.002				.		Atlas-SNP	.											.	PRB4	59	.	0			c.762+1G>C	GRCh37	CS961669	PRB4	S	rs7297795	PASS	.	C		19,4387		0,19,2184	97.0	106.0	103.0			1.1	0.0	12	dbSNP_116	103	145,8455		3,139,4158	yes	splice-5	PRB4	NM_002723.3		3,158,6342	GG,GC,CC		1.686,0.4312,1.261			11461154	164,12842	2203	4300	6503	SO:0001630	splice_region_variant	5545	exon4			ATCATACCTGTCA		CCDS8641.1, CCDS58208.1	12p13.2	2012-10-02			ENSG00000230657	ENSG00000230657			9340	protein-coding gene	gene with protein product		180990					Standard	NM_002723		Approved		uc001qzt.4	P10163	OTTHUMG00000169116	ENST00000279575.1:c.741+1G>C	12.37:g.11461154C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_002723	A1L439|O00600|P02813|P10161|P10162|P81489	Splice_Site	SNP	ENST00000279575.1	37	CCDS8641.1																																																																																			C|0.988;G|0.012	0.012	strong		0.483	PRB4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_002723	Intron
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 GAIIx	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_ENST00000581619.1_Silent_p.L30L|CLUL1_ENST00000579494.1_Silent_p.L5L|CLUL1_ENST00000580436.1_3'UTR|CLUL1_ENST00000540035.1_Silent_p.L57L|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		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	91	30	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		
MRGPRE	116534	hgsc.bcm.edu	37	11	3249829	3249829	+	Silent	SNP	G	G	A	rs11026040	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:3249829G>A	ENST00000389832.5	-	2	507	c.201C>T	c.(199-201)tgC>tgT	p.C67C	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Silent_p.C66C			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	67						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)		TGAGATCCGCGCAGGCCACGT	0.637													G|||	1131	0.225839	0.2776	0.3213	5008	,	,		18071	0.13		0.1431	False		,,,				2504	0.272				p.C67C		Atlas-SNP	.											.	MRGPRE	35	.	0			c.C201T						PASS	.	G		1085,3169		138,809,1180	79.0	97.0	91.0		198	-7.0	0.0	11	dbSNP_120	91	1029,7463		57,915,3274	no	coding-synonymous	MRGPRE	NM_001039165.2		195,1724,4454	AA,AG,GG		12.1173,25.5054,16.5856		66/312	3249829	2114,10632	2127	4246	6373	SO:0001819	synonymous_variant	116534	exon2			ATCCGCGCAGGCC	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.201C>T	11.37:g.3249829G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_001039165	Q2M1V7	Silent	SNP	ENST00000389832.5	37																																																																																				A|0.172;G|0.828	0.172	strong		0.637	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
IL9	3578	hgsc.bcm.edu	37	5	135228165	135228165	+	Missense_Mutation	SNP	G	G	A	rs2069885	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:135228165G>A	ENST00000274520.1	-	5	360	c.350C>T	c.(349-351)aCg>aTg	p.T117M		NM_000590.1	NP_000581.1	P15248	IL9_HUMAN	interleukin 9	117			T -> M (in dbSNP:rs2069885). {ECO:0000269|Ref.5}.		immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-5 biosynthetic process (GO:0045407)	extracellular space (GO:0005615)				large_intestine(3)|lung(2)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GTTGCCTGCCGTGGTTTGGTT	0.433													G|||	472	0.0942492	0.1286	0.0865	5008	,	,		15259	0.002		0.1282	False		,,,				2504	0.1135				p.T117M		Atlas-SNP	.											.	IL9	14	.	0			c.C350T	GRCh37	CM084882	IL9	M	rs2069885	PASS	.	G	MET/THR	570,3836	251.8+/-258.4	39,492,1672	74.0	82.0	79.0		350	-1.6	0.0	5	dbSNP_96	79	1171,7429	238.5+/-269.9	79,1013,3208	yes	missense	IL9	NM_000590.1	81	118,1505,4880	AA,AG,GG		13.6163,12.9369,13.3861	benign	117/145	135228165	1741,11265	2203	4300	6503	SO:0001583	missense	3578	exon5			CCTGCCGTGGTTT	S63356	CCDS4189.1	5q31-q35	2008-07-18			ENSG00000145839	ENSG00000145839		"""Interleukins and interleukin receptors"""	6029	protein-coding gene	gene with protein product	"""p40 T-cell and mast cell growth factor"", ""T-cell growth factor p40"", ""p40 cytokine"", ""homolog of mouse T cell and mast cell growth factor 40"""	146931				8379467	Standard	NM_000590		Approved	IL-9, HP40, P40	uc003lbb.1	P15248	OTTHUMG00000129147	ENST00000274520.1:c.350C>T	5.37:g.135228165G>A	ENSP00000274520:p.Thr117Met	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	124	66	0.532258	NM_000590		Missense_Mutation	SNP	ENST00000274520.1	37	CCDS4189.1	187	0.08562271062271062	46	0.09349593495934959	35	0.09668508287292818	0	0.0	106	0.13984168865435356	G	8.970	0.972757	0.18736	0.129369	0.136163	ENSG00000145839	ENST00000274520	T	0.45276	0.9	5.48	-1.62	0.08372	.	0.477737	0.19059	N	0.123837	T	0.00144	0.0004	N	0.24115	0.695	0.80722	P	0.0	B	0.31548	0.328	B	0.30401	0.115	T	0.08249	-1.0731	9	0.39692	T	0.17	-17.9061	4.3352	0.11083	0.2657:0.0:0.4671:0.2672	rs2069885;rs17519717;rs60288032;rs2069885	117	P15248	IL9_HUMAN	M	117	ENSP00000274520:T117M	ENSP00000274520:T117M	T	-	2	0	IL9	135256064	0.000000	0.05858	0.022000	0.16811	0.101000	0.19017	-0.044000	0.12023	-0.000000	0.14550	-0.940000	0.02684	ACG	G|0.890;A|0.110	0.110	strong		0.433	IL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251210.1	NM_000590	
NRAP	4892	hgsc.bcm.edu	37	10	115392919	115392919	+	Missense_Mutation	SNP	T	T	A	rs2270182	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:115392919T>A	ENST00000359988.3	-	16	1800	c.1556A>T	c.(1555-1557)aAt>aTt	p.N519I	NRAP_ENST00000360478.3_Missense_Mutation_p.N484I|NRAP_ENST00000369358.4_Missense_Mutation_p.N519I|NRAP_ENST00000369360.3_Missense_Mutation_p.N484I	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		ATTCAACTTATTTTTCTCATA	0.423													T|||	1296	0.258786	0.3336	0.2248	5008	,	,		19373	0.1915		0.2714	False		,,,				2504	0.2382				p.N519I		Atlas-SNP	.											.	NRAP	208	.	0			c.A1556T						PASS	.	T	ILE/ASN,ILE/ASN	1556,2850	488.5+/-361.2	276,1004,923	139.0	118.0	125.0		1451,1556	5.7	1.0	10	dbSNP_100	125	2383,6217	394.7+/-344.8	332,1719,2249	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	149,149	608,2723,3172	AA,AT,TT		27.7093,35.3155,30.286	benign,benign	484/1696,519/1731	115392919	3939,9067	2203	4300	6503	SO:0001583	missense	4892	exon16			AACTTATTTTTCT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.1556A>T	10.37:g.115392919T>A	ENSP00000353078:p.Asn519Ile	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	166	71	0.427711	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	561	0.25686813186813184	152	0.3089430894308943	75	0.20718232044198895	117	0.20454545454545456	217	0.2862796833773087	T	17.26	3.344359	0.61073	0.353155	0.277093	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.67	5.67	0.87782	.	0.097718	0.64402	D	0.000002	T	0.00012	0.0000	N	0.17082	0.46	0.32215	P	0.576051	D;P;D	0.53151	0.958;0.889;0.958	P;P;P	0.55749	0.783;0.578;0.783	T	0.38542	-0.9656	9	0.37606	T	0.19	.	11.4347	0.50062	0.0:0.0:0.2723:0.7277	rs2270182;rs60908683;rs2270182	519;484;519	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	I	519;484;519;484;248;248	ENSP00000358365:N519I;ENSP00000358367:N484I;ENSP00000353078:N519I;ENSP00000353666:N484I	ENSP00000353078:N519I	N	-	2	0	NRAP	115382909	1.000000	0.71417	0.959000	0.39883	0.989000	0.77384	2.477000	0.45180	2.159000	0.67721	0.455000	0.32223	AAT	T|0.718;A|0.282	0.282	strong		0.423	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
PIP4K2B	8396	hgsc.bcm.edu	37	17	36926731	36926731	+	Silent	SNP	T	T	G	rs228289	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:36926731T>G	ENST00000269554.3	-	9	1608	c.1128A>C	c.(1126-1128)acA>acC	p.T376T		NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	376	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						CTTTCTTCTTTGTATCGTATG	0.542													C|||	2013	0.401957	0.5068	0.3559	5008	,	,		17056	0.3591		0.2306	False		,,,				2504	0.5133				p.T376T		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.A1128C						PASS	.	C		1964,2442		433,1098,672	240.0	213.0	222.0		1128	-4.9	0.1	17	dbSNP_79	222	2018,6582		250,1518,2532	no	coding-synonymous	PIP4K2B	NM_003559.4		683,2616,3204	GG,GT,TT		23.4651,44.5756,30.6166		376/417	36926731	3982,9024	2203	4300	6503	SO:0001819	synonymous_variant	8396	exon9			CTTCTTTGTATCG	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"""phosphatidylinositol-4-phosphate 5-kinase, type II, beta"""	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.1128A>C	17.37:g.36926731T>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	179	90	0.502793	NM_003559	Q5U0E8|Q8TBP2	Silent	SNP	ENST00000269554.3	37	CCDS11329.1																																																																																			T|0.663;G|0.337	0.337	strong		0.542	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559	
ABHD11	83451	hgsc.bcm.edu	37	7	73151644	73151644	+	Silent	SNP	A	A	G	rs112580831|rs6460052|rs386714666	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:73151644A>G	ENST00000222800.3	-	4	609	c.540T>C	c.(538-540)taT>taC	p.Y180Y	ABHD11_ENST00000437775.2_Silent_p.Y173Y|ABHD11_ENST00000468998.1_5'Flank|ABHD11_ENST00000395147.4_Intron|LINC00035_ENST00000427153.1_RNA|ABHD11_ENST00000458339.1_Intron	NM_148912.2	NP_683710.1	Q8NFV4	ABHDB_HUMAN	abhydrolase domain containing 11	180						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Lung NSC(55;0.0908)|all_lung(88;0.198)				TGGCTGCCACATAGGTTGCAA	0.562													G|||	3028	0.604633	0.8298	0.5389	5008	,	,		21322	0.5218		0.4891	False		,,,				2504	0.5511				p.Y180Y		Atlas-SNP	.											.	ABHD11	11	.	0			c.T540C						PASS	.	G	,,	3384,1022	367.6+/-318.3	1317,750,136	91.0	74.0	80.0		,540,519	2.6	0.0	7	dbSNP_116	80	4230,4370	582.9+/-391.5	1054,2122,1124	no	intron,coding-synonymous,coding-synonymous	ABHD11	NM_001145364.1,NM_148912.2,NM_148913.2	,,	2371,2872,1260	GG,GA,AA		49.186,23.1956,41.4578	,,	,180/316,173/309	73151644	7614,5392	2203	4300	6503	SO:0001819	synonymous_variant	83451	exon4			TGCCACATAGGTT	AF217971	CCDS5558.1, CCDS47607.1, CCDS47608.1, CCDS75615.1	7q11.23	2010-08-05	2005-01-24	2005-01-27	ENSG00000106077	ENSG00000106077		"""Abhydrolase domain containing"""	16407	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 21"""	WBSCR21		12073013	Standard	NR_026910		Approved	PP1226	uc003tzb.3	Q8NFV4	OTTHUMG00000130029	ENST00000222800.3:c.540T>C	7.37:g.73151644A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_148912	H7BYM8|Q6PJU0|Q8N722|Q8N723|Q8NFV2|Q8NFV3|Q9HBS8	Silent	SNP	ENST00000222800.3	37	CCDS5558.1																																																																																			A|0.410;G|0.590	0.590	strong		0.562	ABHD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252306.1		
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 GAIIx	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		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	48	27	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		
RBL2	5934	hgsc.bcm.edu	37	16	53481010	53481010	+	Missense_Mutation	SNP	A	A	G	rs17800727	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:53481010A>G	ENST00000262133.6	+	4	766	c.629A>G	c.(628-630)tAt>tGt	p.Y210C	RBL2_ENST00000379935.4_3'UTR|RP11-44F14.5_ENST00000565073.1_RNA|RBL2_ENST00000544545.1_5'Flank	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	210			Y -> C (in dbSNP:rs17800727).		chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CTTTTTATATATGCAAAAGGT	0.299													A|||	541	0.108027	0.0189	0.2075	5008	,	,		15260	0.001		0.2883	False		,,,				2504	0.0828				p.Y210C		Atlas-SNP	.											.	RBL2	115	.	0			c.A629G						PASS	.	A	CYS/TYR	233,4161	128.2+/-165.1	6,221,1970	50.0	51.0	50.0		629	5.4	1.0	16	dbSNP_123	50	2647,5953	419.1+/-353.0	407,1833,2060	yes	missense	RBL2	NM_005611.3	194	413,2054,4030	GG,GA,AA		30.7791,5.3027,22.1641	benign	210/1140	53481010	2880,10114	2197	4300	6497	SO:0001583	missense	5934	exon4			TTATATATGCAAA	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.629A>G	16.37:g.53481010A>G	ENSP00000262133:p.Tyr210Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Missense_Mutation	SNP	ENST00000262133.6	37	CCDS10748.1	308	0.14102564102564102	14	0.028455284552845527	81	0.22375690607734808	1	0.0017482517482517483	212	0.2796833773087071	A	17.05	3.289226	0.59976	0.053027	0.307791	ENSG00000103479	ENST00000262133;ENST00000544405	T;T	0.73047	-0.71;-0.71	5.38	5.38	0.77491	Domain of unknown function DUF3452, retinoblastoma-associated (1);	0.055127	0.64402	D	0.000001	T	0.00012	0.0000	N	0.11698	0.16	0.09310	P	1.0	B;D	0.69078	0.368;0.997	B;P	0.60173	0.271;0.87	T	0.11665	-1.0578	9	0.37606	T	0.19	-15.9424	15.3883	0.74723	1.0:0.0:0.0:0.0	rs17800727;rs52799983;rs17800727	210;210	Q8NE70;Q08999	.;RBL2_HUMAN	C	210;136	ENSP00000262133:Y210C;ENSP00000443744:Y136C	ENSP00000262133:Y210C	Y	+	2	0	RBL2	52038511	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.903000	0.69877	2.047000	0.60756	0.482000	0.46254	TAT	A|0.828;G|0.172	0.172	strong		0.299	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
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 GAIIx	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	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	135	71	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	
FAM71F1	84691	hgsc.bcm.edu	37	7	128359133	128359133	+	Missense_Mutation	SNP	C	C	T	rs6949056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128359133C>T	ENST00000315184.5	+	3	736	c.683C>T	c.(682-684)tCg>tTg	p.S228L	FAM71F1_ENST00000469348.1_3'UTR|FAM71F1_ENST00000485070.1_Missense_Mutation_p.S129L	NM_001282788.1|NM_032599.2	NP_001269717.1|NP_115988.1	Q96KD3	F71F1_HUMAN	family with sequence similarity 71, member F1	228			S -> L (in dbSNP:rs6949056).							NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						TCAGGAGATTCGAAGGTAAGT	0.527													C|||	1258	0.251198	0.1604	0.2651	5008	,	,		15529	0.4077		0.2376	False		,,,				2504	0.2168				p.S228L		Atlas-SNP	.											.	FAM71F1	42	.	0			c.C683T						PASS	.	C	LEU/SER	698,3708	293.0+/-282.3	51,596,1556	93.0	86.0	88.0		683	2.8	0.0	7	dbSNP_116	88	1978,6622	344.9+/-325.5	233,1512,2555	yes	missense	FAM71F1	NM_032599.2	145	284,2108,4111	TT,TC,CC		23.0,15.842,20.5751	benign	228/345	128359133	2676,10330	2203	4300	6503	SO:0001583	missense	84691	exon3			GAGATTCGAAGGT	AF367470	CCDS5804.1, CCDS64763.1	7q32.1	2007-11-20	2007-11-20	2007-11-20	ENSG00000135248	ENSG00000135248			30704	protein-coding gene	gene with protein product			"""family with sequence similarity 137, member A"""	FAM137A		12477932	Standard	XM_005250645		Approved	NYD-SP18	uc003vno.1	Q96KD3	OTTHUMG00000158276	ENST00000315184.5:c.683C>T	7.37:g.128359133C>T	ENSP00000326652:p.Ser228Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_032599	Q8IY75|Q8NA48	Missense_Mutation	SNP	ENST00000315184.5	37	CCDS5804.1	576	0.26373626373626374	91	0.18495934959349594	90	0.24861878453038674	213	0.3723776223776224	182	0.24010554089709762	C	13.48	2.248810	0.39797	0.15842	0.23	ENSG00000135248	ENST00000485070;ENST00000315184;ENST00000466842	T;T;T	0.25085	1.82;3.2;1.88	4.69	2.82	0.32997	.	1.292180	0.05116	N	0.489775	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P;P;P;P;D	0.59357	0.918;0.863;0.733;0.772;0.985	B;B;B;B;B	0.40702	0.288;0.176;0.187;0.122;0.338	T	0.39781	-0.9597	9	0.46703	T	0.11	-0.2479	5.5328	0.16995	0.1967:0.7013:0.0:0.102	rs6949056;rs52814344;rs59123459;rs6949056	120;228;228;228;129	B4DY15;F8WC62;Q96KD3-2;Q96KD3;Q8NA48	.;.;.;F71F1_HUMAN;.	L	129;228;84	ENSP00000418192:S129L;ENSP00000326652:S228L;ENSP00000417930:S84L	ENSP00000326652:S228L	S	+	2	0	FAM71F1	128146369	0.001000	0.12720	0.005000	0.12908	0.129000	0.20672	0.676000	0.25247	0.666000	0.31087	0.591000	0.81541	TCG	C|0.765;N|0.000	.	strong		0.527	FAM71F1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350544.2	NM_032599	
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 GAIIx	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_ENST00000392782.1_Missense_Mutation_p.N1964S|BAZ2B_ENST00000343439.5_Missense_Mutation_p.N1900S|BAZ2B_ENST00000355831.2_Missense_Mutation_p.N1966S	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	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	103	20	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 GAIIx	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	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	82	44	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	
ATP13A5	344905	hgsc.bcm.edu	37	3	193031875	193031875	+	Missense_Mutation	SNP	C	C	T	rs78188075	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193031875C>T	ENST00000342358.4	-	19	2383	c.2266G>A	c.(2266-2268)Gcc>Acc	p.A756T	ATP13A5-AS1_ENST00000414634.1_RNA|ATP13A5_ENST00000495496.1_5'Flank	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	756						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		GTCACAGAGGCAGGAACAAAT	0.502													C|||	87	0.0173722	0.0015	0.0159	5008	,	,		20077	0.001		0.0517	False		,,,				2504	0.0215				p.A756T		Atlas-SNP	.											.	ATP13A5	171	.	0			c.G2266A						PASS	.	C	THR/ALA	40,4366	42.3+/-75.8	0,40,2163	134.0	131.0	132.0		2266	5.7	1.0	3	dbSNP_131	132	382,8218	123.9+/-182.7	10,362,3928	yes	missense	ATP13A5	NM_198505.2	58	10,402,6091	TT,TC,CC		4.4419,0.9079,3.2447	probably-damaging	756/1219	193031875	422,12584	2203	4300	6503	SO:0001583	missense	344905	exon19			CAGAGGCAGGAAC	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.2266G>A	3.37:g.193031875C>T	ENSP00000341942:p.Ala756Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	135	55	0.407407	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	40	0.018315018315018316	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	33	0.04353562005277045	C	33	5.211118	0.95069	0.009079	0.044419	ENSG00000187527	ENST00000342358	D	0.85339	-1.97	5.72	5.72	0.89469	HAD-like domain (1);	0.000000	0.64402	D	0.000002	T	0.77212	0.4097	M	0.71581	2.175	0.47341	D	0.99939	D	0.89917	1.0	D	0.91635	0.999	T	0.82348	-0.0502	10	0.32370	T	0.25	-15.0961	17.3806	0.87403	0.0:1.0:0.0:0.0	.	756	Q4VNC0	AT135_HUMAN	T	756	ENSP00000341942:A756T	ENSP00000341942:A756T	A	-	1	0	ATP13A5	194514569	1.000000	0.71417	0.954000	0.39281	0.995000	0.86356	5.702000	0.68332	2.709000	0.92574	0.655000	0.94253	GCC	C|0.971;T|0.029	0.029	strong		0.502	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
EXTL1	2134	hgsc.bcm.edu	37	1	26357656	26357656	+	Missense_Mutation	SNP	C	C	A	rs2736831	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26357656C>A	ENST00000374280.3	+	5	2002	c.1135C>A	c.(1135-1137)Cac>Aac	p.H379N	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	379			H -> N (in dbSNP:rs2736831). {ECO:0000269|PubMed:10480354, ECO:0000269|PubMed:10575224, ECO:0000269|PubMed:9037597}.		protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		AACATCAGCTCACCCCTCACT	0.567													C|||	2976	0.594249	0.2027	0.732	5008	,	,		18516	0.75		0.6978	False		,,,				2504	0.7587				p.H379N		Atlas-SNP	.											.	EXTL1	61	.	0			c.C1135A						PASS	.	C	ASN/HIS	1276,3130	433.7+/-343.7	198,880,1125	118.0	112.0	114.0		1135	4.7	0.0	1	dbSNP_100	114	5833,2767	679.2+/-403.5	1980,1873,447	yes	missense	EXTL1	NM_004455.2	68	2178,2753,1572	AA,AC,CC		32.1744,28.9605,45.3406	possibly-damaging	379/677	26357656	7109,5897	2203	4300	6503	SO:0001583	missense	2134	exon5			TCAGCTCACCCCT	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"""Exostosin glycosyltransferase family"""	3515	protein-coding gene	gene with protein product	"""glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""alpha-N-acetylglucosaminyltransferase II"", ""glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase"", ""exostosin-L"""	601738	"""exostoses (multiple)-like 1"""			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.1135C>A	1.37:g.26357656C>A	ENSP00000363398:p.His379Asn	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_004455	Q6GSC1	Missense_Mutation	SNP	ENST00000374280.3	37	CCDS271.1	1339	0.6130952380952381	115	0.23373983739837398	259	0.7154696132596685	419	0.7325174825174825	546	0.7203166226912929	C	22.0	4.233153	0.79688	0.289605	0.678256	ENSG00000158008	ENST00000374280	D	0.94862	-3.54	4.7	4.7	0.59300	.	0.331675	0.27500	N	0.019092	T	0.00012	0.0000	L	0.47716	1.5	0.33240	P	0.44294900000000004	B	0.18610	0.029	B	0.14023	0.01	T	0.48525	-0.9028	9	0.30854	T	0.27	-12.1318	16.6014	0.84816	0.0:1.0:0.0:0.0	rs2736831;rs11247847;rs58001292;rs11247847	379	Q92935	EXTL1_HUMAN	N	379	ENSP00000363398:H379N	ENSP00000363398:H379N	H	+	1	0	EXTL1	26230243	0.003000	0.15002	0.038000	0.18304	0.975000	0.68041	1.294000	0.33365	2.453000	0.82957	0.561000	0.74099	CAC	C|0.442;A|0.558	0.558	strong		0.567	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455	
RYR1	6261	hgsc.bcm.edu	37	19	38996990	38996990	+	Silent	SNP	T	T	C	rs2229146	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38996990T>C	ENST00000359596.3	+	55	8589	c.8589T>C	c.(8587-8589)agT>agC	p.S2863S	RYR1_ENST00000360985.3_Silent_p.S2863S|RYR1_ENST00000355481.4_Silent_p.S2863S			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2863	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.S2863S(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCGACCTTAGTGCTGTTACCC	0.597													C|||	2044	0.408147	0.4856	0.3674	5008	,	,		14713	0.3532		0.3072	False		,,,				2504	0.4928				p.S2863S		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	1	1	Substitution - coding silent(1)	stomach(1)	c.T8589C						PASS	.	C	,	1893,2513	628.6+/-395.1	398,1097,708	59.0	58.0	58.0		8589,8589	-0.1	1.0	19	dbSNP_98	58	2186,6414	712.0+/-405.9	298,1590,2412	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	696,2687,3120	CC,CT,TT		25.4186,42.9641,31.3624	,	2863/5039,2863/5034	38996990	4079,8927	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon55			CCTTAGTGCTGTT	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.8589T>C	19.37:g.38996990T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			T|0.663;C|0.337	0.337	strong		0.597	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
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 GAIIx	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	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	94	43	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	
KIAA1551	55196	hgsc.bcm.edu	37	12	32138410	32138410	+	Silent	SNP	A	A	G	rs12827942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:32138410A>G	ENST00000312561.4	+	4	4935	c.4521A>G	c.(4519-4521)gaA>gaG	p.E1507E	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1507																	CCTCTAAAGAATCATTAAATG	0.393													A|||	259	0.0517173	0.0371	0.0879	5008	,	,		17744	0.0149		0.0984	False		,,,				2504	0.0358				p.E1507E		Atlas-SNP	.											.	.	.	.	0			c.A4521G						PASS	.	A		224,4180	130.2+/-166.9	5,214,1983	48.0	50.0	49.0		4521	0.1	0.0	12	dbSNP_121	49	1021,7579	213.4+/-253.3	56,909,3335	no	coding-synonymous	C12orf35	NM_018169.3		61,1123,5318	GG,GA,AA		11.8721,5.0863,9.574		1507/1748	32138410	1245,11759	2202	4300	6502	SO:0001819	synonymous_variant	55196	exon4			TAAAGAATCATTA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.4521A>G	12.37:g.32138410A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	CCDS8725.2																																																																																			A|0.921;G|0.079	0.079	strong		0.393	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
SH3TC1	54436	hgsc.bcm.edu	37	4	8242499	8242499	+	Silent	SNP	G	G	A	rs1048506	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:8242499G>A	ENST00000245105.3	+	18	3895	c.3828G>A	c.(3826-3828)caG>caA	p.Q1276Q	SH3TC1_ENST00000539824.1_Silent_p.Q1200Q	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	1276										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						AGAAGGCACAGCTGAAGATCT	0.607													G|||	117	0.0233626	0.0008	0.0216	5008	,	,		12669	0.0		0.0378	False		,,,				2504	0.0644				p.Q1276Q	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.G3828A						PASS	.	G		53,4353	52.9+/-88.7	1,51,2151	82.0	85.0	84.0		3828	4.2	1.0	4	dbSNP_86	84	438,8162	134.7+/-192.1	12,414,3874	no	coding-synonymous	SH3TC1	NM_018986.3		13,465,6025	AA,AG,GG		5.093,1.2029,3.7752		1276/1337	8242499	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	54436	exon18			GGCACAGCTGAAG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.3828G>A	4.37:g.8242499G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	52	37	0.711538	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			G|0.967;A|0.033	0.033	strong		0.607	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
TEX264	51368	hgsc.bcm.edu	37	3	51737965	51737965	+	Missense_Mutation	SNP	G	G	A	rs11553574	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:51737965G>A	ENST00000415259.1	+	5	1956	c.875G>A	c.(874-876)gGg>gAg	p.G292E	TEX264_ENST00000416589.1_Missense_Mutation_p.G292E|TEX264_ENST00000463857.1_3'UTR|TEX264_ENST00000457573.1_Missense_Mutation_p.G292E|TEX264_ENST00000341333.5_Missense_Mutation_p.G292E|TEX264_ENST00000395057.1_Missense_Mutation_p.G292E			Q9Y6I9	TX264_HUMAN	testis expressed 264	292			G -> E (in dbSNP:rs11553574).			extracellular vesicular exosome (GO:0070062)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(193;8.53e-05)|Kidney(197;0.000594)|KIRC - Kidney renal clear cell carcinoma(197;0.000759)		CTGGACCCTGGGACTGAGCCC	0.647													A|||	941	0.187899	0.2519	0.2622	5008	,	,		16102	0.3542		0.0209	False		,,,				2504	0.0491				p.G292E		Atlas-SNP	.											.	TEX264	18	.	0			c.G875A						PASS	.	A	GLU/GLY,GLU/GLY	936,3468		92,752,1358	16.0	19.0	18.0		875,875	4.3	0.4	3	dbSNP_120	18	184,8408		2,180,4114	yes	missense,missense	TEX264	NM_001129884.1,NM_015926.4	98,98	94,932,5472	AA,AG,GG		2.1415,21.2534,8.618	benign,benign	292/314,292/314	51737965	1120,11876	2202	4296	6498	SO:0001583	missense	51368	exon5			ACCCTGGGACTGA	AF072733	CCDS2833.1, CCDS74945.1	3p21	2007-03-13	2007-03-13		ENSG00000164081	ENSG00000164081			30247	protein-coding gene	gene with protein product			"""testis expressed gene 264"", ""testis expressed sequence 264"""			12975309	Standard	NM_001243725		Approved	ZSIG11, FLJ13935	uc003dbm.4	Q9Y6I9	OTTHUMG00000156901	ENST00000415259.1:c.875G>A	3.37:g.51737965G>A	ENSP00000396628:p.Gly292Glu	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_001243726	B3KN87|Q9UKD7	Missense_Mutation	SNP	ENST00000415259.1	37	CCDS2833.1	422	0.19322344322344323	132	0.2682926829268293	84	0.23204419889502761	191	0.3339160839160839	15	0.01978891820580475	A	0.005	-2.235816	0.00277	0.212534	0.021415	ENSG00000164081	ENST00000457573;ENST00000341333;ENST00000415259;ENST00000395057;ENST00000416589	T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13	4.27	4.27	0.50696	.	0.285254	0.32655	N	0.005817	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39881	-0.9592	9	0.02654	T	1	-15.3894	5.969	0.19340	0.6911:0.0:0.3089:0.0	rs11553574	292;292	Q53GI2;Q9Y6I9	.;TX264_HUMAN	E	292	ENSP00000408186:G292E;ENSP00000340969:G292E;ENSP00000396628:G292E;ENSP00000378497:G292E;ENSP00000398802:G292E	ENSP00000340969:G292E	G	+	2	0	TEX264	51713005	0.843000	0.29541	0.408000	0.26446	0.112000	0.19704	2.276000	0.43408	0.614000	0.30107	-0.817000	0.03123	GGG	G|0.875;A|0.125	0.125	strong		0.647	TEX264-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346530.1	NM_015926	
ADCK5	203054	hgsc.bcm.edu	37	8	145603114	145603114	+	Missense_Mutation	SNP	A	A	C	rs6599528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145603114A>C	ENST00000308860.6	+	2	95	c.51A>C	c.(49-51)agA>agC	p.R17S	ADCK5_ENST00000526231.2_3'UTR|ADCK5_ENST00000532190.1_Missense_Mutation_p.R17S	NM_174922.3	NP_777582.4	Q3MIX3	ADCK5_HUMAN	aarF domain containing kinase 5	17			R -> S (in dbSNP:rs6599528). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	protein serine/threonine kinase activity (GO:0004674)	p.R17S(1)		endometrium(1)|lung(2)|prostate(2)|skin(1)|stomach(2)	8	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;8.96e-41)|Epithelial(56;4.08e-40)|all cancers(56;4.51e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TGCTGCACAGAAGGCAGAAGC	0.602													C|||	3167	0.632388	0.8101	0.5648	5008	,	,		20220	0.6577		0.4314	False		,,,				2504	0.6207				p.R17S		Atlas-SNP	.											ADCK5,rectum,carcinoma,0,3	ADCK5	36	3	1	Substitution - Missense(1)	stomach(1)	c.A51C						PASS	.	C	SER/ARG	3290,1114	391.2+/-328.0	1218,854,130	64.0	54.0	57.0		51	3.7	0.0	8	dbSNP_116	57	3755,4845	613.8+/-396.1	826,2103,1371	yes	missense	ADCK5	NM_174922.3	110	2044,2957,1501	CC,CA,AA		43.6628,25.2952,45.8244	benign	17/581	145603114	7045,5959	2202	4300	6502	SO:0001583	missense	203054	exon2			GCACAGAAGGCAG	BC032402	CCDS34965.1, CCDS34965.2	8q24.3	2004-07-06			ENSG00000173137	ENSG00000173137			21738	protein-coding gene	gene with protein product							Standard	NM_174922		Approved	FLJ35454	uc003zch.3	Q3MIX3	OTTHUMG00000165190	ENST00000308860.6:c.51A>C	8.37:g.145603114A>C	ENSP00000310547:p.Arg17Ser	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	175	173	0.988571	NM_174922	B3KS46|Q5U4P1|Q6P2S4|Q8N5V3	Missense_Mutation	SNP	ENST00000308860.6	37	CCDS34965.1	1275	0.5837912087912088	387	0.7865853658536586	201	0.5552486187845304	369	0.6451048951048951	318	0.41952506596306066	C	0.157	-1.085760	0.01873	0.747048	0.436628	ENSG00000173137	ENST00000308860;ENST00000532190	T;T	0.74421	-0.84;0.92	4.55	3.68	0.42216	.	0.917523	0.09037	N	0.857810	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42582	-0.9443	9	0.07175	T	0.84	-5.5209	5.77	0.18247	0.1918:0.7078:0.0:0.1004	rs6599528;rs61015944;rs6599528	17	Q3MIX3	ADCK5_HUMAN	S	17	ENSP00000310547:R17S;ENSP00000435155:R17S	ENSP00000310547:R17S	R	+	3	2	ADCK5	145573922	0.127000	0.22367	0.001000	0.08648	0.279000	0.26890	2.275000	0.43399	0.389000	0.25086	-0.975000	0.02590	AGA	A|0.433;C|0.567	0.567	strong		0.602	ADCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382556.2	NM_174922	
TMEM99	147184	hgsc.bcm.edu	37	17	38991052	38991052	+	Missense_Mutation	SNP	T	T	G	rs1044806|rs386796999	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38991052T>G	ENST00000301665.3	+	3	588	c.284T>G	c.(283-285)cTt>cGt	p.L95R		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	95			L -> R (in dbSNP:rs1044806). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				AGAGAAGGACTTCTTCTTCCT	0.468													T|||	544	0.108626	0.1248	0.1182	5008	,	,		19701	0.004		0.1928	False		,,,				2504	0.1012				p.L95R		Atlas-SNP	.											.	TMEM99	21	.	0			c.T284G						PASS	.	T	ARG/LEU,ARG/LEU,ARG/LEU	429,3453		27,375,1539	202.0	199.0	200.0		284,284,284	0.2	0.1	17	dbSNP_86	200	1612,6682		151,1310,2686	yes	missense,missense,missense	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	102,102,102	178,1685,4225	GG,GT,TT		19.4357,11.051,16.7625	possibly-damaging,possibly-damaging,possibly-damaging	95/259,95/259,95/259	38991052	2041,10135	1941	4147	6088	SO:0001583	missense	147184	exon3			AAGGACTTCTTCT	AK097454	CCDS42319.1	17q21.2	2008-11-06			ENSG00000167920	ENSG00000167920			28305	protein-coding gene	gene with protein product						12477932	Standard	NM_001195386		Approved	MGC21518	uc021txc.1	Q8N816	OTTHUMG00000133579	ENST00000301665.3:c.284T>G	17.37:g.38991052T>G	ENSP00000301665:p.Leu95Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_001195386	B4DQ34|Q96BP9	Missense_Mutation	SNP	ENST00000301665.3	37	CCDS42319.1	190	0.08699633699633699	48	0.0975609756097561	39	0.10773480662983426	0	0.0	103	0.1358839050131926	T	7.070	0.568095	0.13560	0.11051	0.194357	ENSG00000167920	ENST00000436612;ENST00000301665	T;T	0.33654	1.4;1.4	0.158	0.158	0.14942	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	D	0.54397	0.966	P	0.61070	0.883	T	0.17623	-1.0363	7	0.87932	D	0	.	.	.	.	rs1044806;rs3169916;rs1044806	95	Q8N816	TMM99_HUMAN	R	95	ENSP00000390036:L95R;ENSP00000301665:L95R	ENSP00000301665:L95R	L	+	2	0	TMEM99	36244578	0.051000	0.20477	0.089000	0.20774	0.090000	0.18270	0.215000	0.17562	0.175000	0.19841	0.172000	0.16884	CTT	T|0.907;G|0.093	0.093	strong		0.468	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
UNC45A	55898	hgsc.bcm.edu	37	15	91489919	91489919	+	Silent	SNP	A	A	G	rs12911432	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:91489919A>G	ENST00000418476.2	+	10	1315	c.1275A>G	c.(1273-1275)ccA>ccG	p.P425P	UNC45A_ENST00000394275.2_Silent_p.P410P	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	425					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.P425P(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			TGCAGGGCCCATGTGACGCTG	0.657													A|||	274	0.0547125	0.0038	0.0317	5008	,	,		19077	0.001		0.0746	False		,,,				2504	0.1748				p.P425P		Atlas-SNP	.											UNC45A,NS,carcinoma,0,1	UNC45A	57	1	1	Substitution - coding silent(1)	lung(1)	c.A1275G						PASS	.	A	,	72,4324	64.7+/-102.0	0,72,2126	55.0	50.0	52.0		1230,1275	-10.3	0.0	15	dbSNP_121	52	677,7919	170.0+/-221.2	26,625,3647	no	coding-synonymous,coding-synonymous	UNC45A	NM_001039675.1,NM_018671.3	,	26,697,5773	GG,GA,AA		7.8758,1.6379,5.7651	,	410/930,425/945	91489919	749,12243	2198	4298	6496	SO:0001819	synonymous_variant	55898	exon10			GGGCCCATGTGAC		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.1275A>G	15.37:g.91489919A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Silent	SNP	ENST00000418476.2	37	CCDS10367.1																																																																																			A|0.952;G|0.048	0.048	strong		0.657	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
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 GAIIx	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	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	17	10	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 GAIIx	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	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	31	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		
DUSP12	11266	hgsc.bcm.edu	37	1	161722204	161722204	+	Silent	SNP	C	C	T	rs1063179	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161722204C>T	ENST00000367943.4	+	4	656	c.624C>T	c.(622-624)acC>acT	p.T208T		NM_007240.1	NP_009171.1	Q9UNI6	DUS12_HUMAN	dual specificity phosphatase 12	208					cellular protein modification process (GO:0006464)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of glucokinase activity (GO:0033133)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|lung(1)	5	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			ACCCAACTACCGTTTCACAAG	0.323													C|||	855	0.170727	0.3865	0.0648	5008	,	,		16390	0.2192		0.0507	False		,,,				2504	0.0276				p.T208T		Atlas-SNP	.											.	DUSP12	20	.	0			c.C624T						PASS	.	C		1462,2944	464.2+/-353.8	248,966,989	108.0	123.0	118.0		624	-1.0	0.0	1	dbSNP_86	118	391,8207	125.5+/-184.1	10,371,3918	no	coding-synonymous	DUSP12	NM_007240.1		258,1337,4907	TT,TC,CC		4.5476,33.182,14.2495		208/341	161722204	1853,11151	2203	4299	6502	SO:0001819	synonymous_variant	11266	exon4			AACTACCGTTTCA	AF119226	CCDS1234.1	1q21-q22	2011-06-09			ENSG00000081721	ENSG00000081721		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3067	protein-coding gene	gene with protein product	"""serine/threonine specific protein phosphatase"", ""YVH1 protein-tyrosine phosphatase (S. cerevisiae) ortholog"""	604835				10446167	Standard	XM_005244862		Approved	YVH1, DUSP1	uc001gbo.3	Q9UNI6	OTTHUMG00000034540	ENST00000367943.4:c.624C>T	1.37:g.161722204C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	223	102	0.457399	NM_007240	Q5VXA8	Silent	SNP	ENST00000367943.4	37	CCDS1234.1																																																																																			C|0.848;T|0.152	0.152	strong		0.323	DUSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083588.1	NM_007240	
IZUMO2	126123	hgsc.bcm.edu	37	19	50666389	50666389	+	Silent	SNP	G	G	A	rs61742305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50666389G>A	ENST00000293405.3	-	1	63	c.63C>T	c.(61-63)tgC>tgT	p.C21C		NM_152358.2	NP_689571.2	Q6UXV1	IZUM2_HUMAN	IZUMO family member 2	21						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						CGCACTGCAGGCAGCCCCAGC	0.706													G|||	587	0.117212	0.0159	0.1643	5008	,	,		12810	0.0625		0.2485	False		,,,				2504	0.1421				p.C21C		Atlas-SNP	.											IZUMO2,NS,carcinoma,0,1	IZUMO2	26	1	0			c.C63T						PASS	.	G		174,3710		4,166,1772	10.0	14.0	13.0		63	2.4	1.0	19	dbSNP_129	13	1851,6415		214,1423,2496	no	coding-synonymous	IZUMO2	NM_152358.2		218,1589,4268	AA,AG,GG		22.3929,4.4799,16.6667		21/222	50666389	2025,10125	1942	4133	6075	SO:0001819	synonymous_variant	126123	exon1			CTGCAGGCAGCCC	AY358196	CCDS12792.2	19q13.33	2014-02-17	2010-07-29	2010-07-29	ENSG00000161652	ENSG00000161652		"""-"""	28518	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 41"""	C19orf41		19658160, 22957301	Standard	XM_006723007		Approved	MGC33947, SCRL	uc002prp.1	Q6UXV1	OTTHUMG00000074063	ENST00000293405.3:c.63C>T	19.37:g.50666389G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_152358	Q5GRG3|Q5GRG4|Q6ZNM5|Q8NHR8	Silent	SNP	ENST00000293405.3	37	CCDS12792.2																																																																																			G|0.859;A|0.141	0.141	strong		0.706	IZUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157232.1	NM_152358	
CARD10	29775	hgsc.bcm.edu	37	22	37906262	37906262	+	Missense_Mutation	SNP	C	C	T	rs9610775	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:37906262C>T	ENST00000403299.1	-	5	1082	c.866G>A	c.(865-867)cGg>cAg	p.R289Q	CARD10_ENST00000251973.5_Missense_Mutation_p.R289Q|CARD10_ENST00000494166.1_5'UTR|CARD10_ENST00000406271.3_5'Flank			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	289			R -> Q (in dbSNP:rs9610775). {ECO:0000269|PubMed:11259443, ECO:0000269|PubMed:11356195}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					CGCCGTCAGCCGCTGGTTCTC	0.662													C|||	1085	0.216653	0.2579	0.1282	5008	,	,		14625	0.1915		0.1948	False		,,,				2504	0.272				p.R289Q		Atlas-SNP	.											.	CARD10	55	.	0			c.G866A						PASS	.	C	GLN/ARG	1053,3353	366.6+/-317.9	134,785,1284	38.0	38.0	38.0		866	4.9	1.0	22	dbSNP_119	38	1557,7039	278.4+/-293.4	166,1225,2907	yes	missense	CARD10	NM_014550.3	43	300,2010,4191	TT,TC,CC		18.1131,23.8992,20.0738	probably-damaging	289/1033	37906262	2610,10392	2203	4298	6501	SO:0001583	missense	29775	exon4			GTCAGCCGCTGGT	AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.866G>A	22.37:g.37906262C>T	ENSP00000384570:p.Arg289Gln	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	392	0.1794871794871795	94	0.1910569105691057	46	0.1270718232044199	104	0.18181818181818182	148	0.19525065963060687	C	15.72	2.915945	0.52546	0.238992	0.181131	ENSG00000100065	ENST00000403299;ENST00000251973	T;T	0.34472	1.36;1.36	4.86	4.86	0.63082	.	0.252547	0.31909	N	0.006875	T	0.00012	0.0000	L	0.60455	1.87	0.35512	P	0.199303	D	0.67145	0.996	P	0.45829	0.494	T	0.20739	-1.0266	9	0.19590	T	0.45	-16.9506	18.0032	0.89203	0.0:1.0:0.0:0.0	rs9610775;rs9610775	289	Q9BWT7	CAR10_HUMAN	Q	289	ENSP00000384570:R289Q;ENSP00000251973:R289Q	ENSP00000251973:R289Q	R	-	2	0	CARD10	36236208	1.000000	0.71417	1.000000	0.80357	0.676000	0.39594	4.785000	0.62418	2.250000	0.74265	0.655000	0.94253	CGG	C|0.806;T|0.194	0.194	strong		0.662	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206905043	206905043	+	Silent	SNP	C	C	T	rs4073250	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:206905043C>T	ENST00000367103.3	+	8	1144	c.951C>T	c.(949-951)acC>acT	p.T317T	MAPKAPK2_ENST00000294981.4_Silent_p.T317T|MAPKAPK2_ENST00000479009.1_3'UTR	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	317	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			TGACCATCACCGAGTTTATGA	0.562													C|||	979	0.195487	0.1838	0.1729	5008	,	,		18715	0.0526		0.2137	False		,,,				2504	0.3558				p.T317T		Atlas-SNP	.											.	MAPKAPK2	45	.	0			c.C951T						PASS	.	C	,	847,3559	334.9+/-303.7	95,657,1451	132.0	131.0	131.0		951,951	-10.2	0.0	1	dbSNP_108	131	1652,6948	305.2+/-307.3	168,1316,2816	no	coding-synonymous,coding-synonymous	MAPKAPK2	NM_004759.4,NM_032960.3	,	263,1973,4267	TT,TC,CC		19.2093,19.2238,19.2142	,	317/371,317/401	206905043	2499,10507	2203	4300	6503	SO:0001819	synonymous_variant	9261	exon8			CATCACCGAGTTT	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.951C>T	1.37:g.206905043C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	166	93	0.560241	NM_004759	Q5SY30|Q5SY41|Q8IYD6	Silent	SNP	ENST00000367103.3	37	CCDS31001.1																																																																																			C|0.820;T|0.180	0.180	strong		0.562	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759	
NPLOC4	55666	hgsc.bcm.edu	37	17	79564304	79564304	+	Silent	SNP	G	G	T	rs62074671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79564304G>T	ENST00000331134.6	-	10	1175	c.960C>A	c.(958-960)acC>acA	p.T320T	NPLOC4_ENST00000539314.1_Silent_p.T159T|NPLOC4_ENST00000374747.5_Silent_p.T320T	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	320					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			TACCCTTTCGGGTATCTTCTG	0.483													G|||	345	0.0688898	0.0938	0.0648	5008	,	,		17001	0.001		0.1262	False		,,,				2504	0.0491				p.T320T		Atlas-SNP	.											.	NPLOC4	27	.	0			c.C960A						PASS	.	G		387,3609		20,347,1631	121.0	120.0	120.0		960	2.5	1.0	17	dbSNP_129	120	900,7438		57,786,3326	yes	coding-synonymous	NPLOC4	NM_017921.2		77,1133,4957	TT,TG,GG		10.794,9.6847,10.4346		320/609	79564304	1287,11047	1998	4169	6167	SO:0001819	synonymous_variant	55666	exon10			CTTTCGGGTATCT	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.960C>A	17.37:g.79564304G>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	56	17	0.303571	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Silent	SNP	ENST00000331134.6	37	CCDS45812.1																																																																																			G|0.918;T|0.082	0.082	strong		0.483	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
ANKS3	124401	hgsc.bcm.edu	37	16	4751045	4751045	+	Missense_Mutation	SNP	C	C	T	rs863980	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4751045C>T	ENST00000304283.4	-	11	1504	c.1210G>A	c.(1210-1212)Gct>Act	p.A404T	ANKS3_ENST00000585773.1_Missense_Mutation_p.A331T|ANKS3_ENST00000450067.2_Missense_Mutation_p.A198T|ANKS3_ENST00000446014.2_Missense_Mutation_p.A275T	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	404			A -> T (in dbSNP:rs863980). {ECO:0000269|PubMed:14702039}.					p.A404T(1)		endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						TCAGTTGCAGCGCGGGGAGGC	0.562													T|||	2566	0.51238	0.447	0.5216	5008	,	,		17676	0.626		0.5398	False		,,,				2504	0.4489				p.A404T		Atlas-SNP	.											ANKS3,caecum,carcinoma,0,2	ANKS3	44	2	1	Substitution - Missense(1)	stomach(1)	c.G1210A						PASS	.	T	THR/ALA,THR/ALA	2169,2225	591.6+/-387.6	524,1121,552	145.0	154.0	151.0		889,1210	-4.5	0.0	16	dbSNP_86	151	4752,3848	541.5+/-384.0	1314,2124,862	yes	missense,missense	ANKS3	NM_001242929.1,NM_133450.3	58,58	1838,3245,1414	TT,TC,CC		44.7442,49.3628,46.737	benign,benign	297/550,404/657	4751045	6921,6073	2197	4300	6497	SO:0001583	missense	124401	exon11			TTGCAGCGCGGGG	AK057329	CCDS10520.1, CCDS73820.1	16p13.3	2013-01-10			ENSG00000168096	ENSG00000168096		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	29422	protein-coding gene	gene with protein product						11853319	Standard	NM_133450		Approved	KIAA1977, FLJ32345, FLJ32767	uc002cxj.2	Q6ZW76	OTTHUMG00000129478	ENST00000304283.4:c.1210G>A	16.37:g.4751045C>T	ENSP00000304586:p.Ala404Thr	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	146	143	0.979452	NM_133450	B4DWU4|D3DUE2|Q8TF25	Missense_Mutation	SNP	ENST00000304283.4	37	CCDS10520.1	1228	0.5622710622710623	245	0.49796747967479676	190	0.5248618784530387	384	0.6713286713286714	409	0.5395778364116095	T	2.107	-0.404636	0.04832	0.493628	0.552558	ENSG00000168096	ENST00000304283;ENST00000446014;ENST00000450067	T;T;T	0.43688	1.44;3.19;0.94	5.71	-4.46	0.03536	.	0.911266	0.09508	N	0.792789	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.18013	0.025;0.0	B;B	0.09377	0.004;0.0	T	0.39542	-0.9609	9	0.02654	T	1	-9.9624	3.5825	0.07958	0.1013:0.2578:0.4154:0.2255	rs863980;rs17857380;rs863980	198;404	Q6ZWA7;Q6ZW76	.;ANKS3_HUMAN	T	404;275;198	ENSP00000304586:A404T;ENSP00000406796:A275T;ENSP00000388270:A198T	ENSP00000304586:A404T	A	-	1	0	ANKS3	4691046	0.031000	0.19500	0.000000	0.03702	0.001000	0.01503	-0.174000	0.09839	-1.797000	0.01252	-1.533000	0.00918	GCT	C|0.457;T|0.543	0.543	strong		0.562	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450	
OR1E1	8387	hgsc.bcm.edu	37	17	3301549	3301549	+	Silent	SNP	G	G	A	rs150988	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3301549G>A	ENST00000322608.2	-	1	155	c.156C>T	c.(154-156)gaC>gaT	p.D52D		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	52					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(3)|large_intestine(2)|lung(5)	10						GGAGATGGGAGTCCAGTCGAA	0.498													G|||	2235	0.446286	0.3464	0.5663	5008	,	,		20648	0.4315		0.4016	False		,,,				2504	0.5573				p.D52D		Atlas-SNP	.											.	OR1E1	37	.	0			c.C156T						PASS	.	G		1631,2775	501.5+/-365.0	309,1013,881	127.0	119.0	122.0		156	3.3	1.0	17	dbSNP_79	122	3357,5243	498.3+/-374.7	651,2055,1594	no	coding-synonymous	OR1E1	NM_003553.2		960,3068,2475	AA,AG,GG		39.0349,37.0177,38.3515		52/315	3301549	4988,8018	2203	4300	6503	SO:0001819	synonymous_variant	8387	exon1			ATGGGAGTCCAGT	U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"""GPCR / Class A : Olfactory receptors"""	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.156C>T	17.37:g.3301549G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	240	103	0.429167	NM_003553	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Silent	SNP	ENST00000322608.2	37	CCDS11024.1																																																																																			G|0.602;A|0.398	0.398	strong		0.498	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553	
SNAPC4	6621	hgsc.bcm.edu	37	9	139275294	139275294	+	Missense_Mutation	SNP	G	G	C	rs3812571	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139275294G>C	ENST00000298532.2	-	19	2765	c.2397C>G	c.(2395-2397)caC>caG	p.H799Q		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		CAGTATCGATGTGGAACAGCT	0.637													C|||	2034	0.40615	0.3631	0.6066	5008	,	,		19093	0.3224		0.4155	False		,,,				2504	0.3988				p.H799Q		Atlas-SNP	.											SNAPC4,NS,carcinoma,0,2	SNAPC4	82	2	0			c.C2397G						PASS	.	C	GLN/HIS	1604,2798	656.1+/-400.0	287,1030,884	49.0	45.0	47.0		2397	4.2	1.0	9	dbSNP_107	47	3805,4791	609.2+/-395.5	844,2117,1337	yes	missense	SNAPC4	NM_003086.2	24	1131,3147,2221	CC,CG,GG		44.2648,36.438,41.6141	benign	799/1470	139275294	5409,7589	2201	4298	6499	SO:0001583	missense	6621	exon19			ATCGATGTGGAAC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.2397C>G	9.37:g.139275294G>C	ENSP00000298532:p.His799Gln	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	870	0.3983516483516483	184	0.37398373983739835	190	0.5248618784530387	177	0.3094405594405594	319	0.420844327176781	C	0.022	-1.406691	0.01155	0.36438	0.442648	ENSG00000165684	ENST00000298532	T	0.24538	1.85	4.15	4.15	0.48705	.	0.206990	0.35708	N	0.003030	T	0.00012	0.0000	N	0.00260	-1.75	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47142	-0.9140	9	0.02654	T	1	-18.3209	11.0145	0.47681	0.0:0.634:0.366:0.0	rs3812571;rs13298729;rs17602983;rs3812571	799	Q5SXM2	SNPC4_HUMAN	Q	799	ENSP00000298532:H799Q	ENSP00000298532:H799Q	H	-	3	2	SNAPC4	138395115	0.967000	0.33354	0.979000	0.43373	0.337000	0.28794	0.133000	0.15912	0.877000	0.35895	-0.120000	0.15030	CAC	G|0.591;C|0.409	0.409	strong		0.637	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
STX16	8675	hgsc.bcm.edu	37	20	57244396	57244396	+	Missense_Mutation	SNP	G	G	A	rs41276950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:57244396G>A	ENST00000371141.4	+	5	1167	c.443G>A	c.(442-444)cGg>cAg	p.R148Q	STX16_ENST00000496003.1_Intron|STX16_ENST00000355957.5_Missense_Mutation_p.R131Q|STX16_ENST00000361770.5_Missense_Mutation_p.R131Q|STX16-NPEPL1_ENST00000530122.1_Missense_Mutation_p.R148Q|STX16_ENST00000361830.3_Missense_Mutation_p.R148Q|STX16_ENST00000371132.4_Missense_Mutation_p.R127Q|STX16_ENST00000358029.4_Missense_Mutation_p.R144Q|STX16_ENST00000359617.4_Missense_Mutation_p.R95Q	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	148					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			AGCCGGGCCCGGGCCTGCTCC	0.692													G|||	72	0.014377	0.0023	0.0159	5008	,	,		14505	0.0		0.0537	False		,,,				2504	0.0041				p.R148Q		Atlas-SNP	.											.	STX16	36	.	0			c.G443A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	43,4275		0,43,2116	17.0	22.0	20.0		443,431,392,284,380	4.9	1.0	20	dbSNP_127	20	359,8095		10,339,3878	no	missense,missense,missense,missense,missense	STX16	NM_001001433.2,NM_001134772.2,NM_001134773.2,NM_001204868.1,NM_003763.5	43,43,43,43,43	10,382,5994	AA,AG,GG		4.2465,0.9958,3.1475	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	148/326,144/322,131/309,95/273,127/305	57244396	402,12370	2159	4227	6386	SO:0001583	missense	8675	exon5			GGGCCCGGGCCTG	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.443G>A	20.37:g.57244396G>A	ENSP00000360183:p.Arg148Gln	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Missense_Mutation	SNP	ENST00000371141.4	37	CCDS13468.1	49	0.022435897435897436	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	41	0.05408970976253298	G	23.1	4.371512	0.82573	0.009958	0.042465	ENSG00000124222	ENST00000458280;ENST00000355957;ENST00000361770;ENST00000312283;ENST00000412911;ENST00000359617;ENST00000371141;ENST00000371138;ENST00000371132;ENST00000358029;ENST00000361830;ENST00000438253	T;T;T;T;T;T;T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41;2.41	5.87	4.92	0.64577	t-SNARE (1);Syntaxin, N-terminal (1);	0.236192	0.36268	U	0.002693	T	0.02727	0.0082	L	0.55743	1.74	0.80722	D	1	B;B;B;B	0.25235	0.086;0.121;0.018;0.11	B;B;B;B	0.28305	0.088;0.016;0.01;0.067	T	0.04708	-1.0932	10	0.15952	T	0.53	.	13.8388	0.63426	0.0727:0.0:0.9273:0.0	rs41276950	144;131;127;148	Q6GMS8;O14662-4;O14662-2;O14662	.;.;.;STX16_HUMAN	Q	95;131;131;95;95;95;148;95;127;144;148;90	ENSP00000388348:R95Q;ENSP00000348229:R131Q;ENSP00000355408:R131Q;ENSP00000312086:R95Q;ENSP00000416852:R95Q;ENSP00000352634:R95Q;ENSP00000360183:R148Q;ENSP00000360173:R127Q;ENSP00000350723:R144Q;ENSP00000354445:R148Q;ENSP00000401801:R90Q	ENSP00000360180:R95Q	R	+	2	0	STX16	56677802	0.992000	0.36948	0.989000	0.46669	0.981000	0.71138	6.292000	0.72725	1.491000	0.48482	0.655000	0.94253	CGG	G|0.972;A|0.028	0.028	strong		0.692	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	
CLDN12	9069	hgsc.bcm.edu	37	7	90042176	90042176	+	Silent	SNP	C	C	T	rs17862175	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:90042176C>T	ENST00000287916.4	+	3	473	c.186C>T	c.(184-186)gaC>gaT	p.D62D	CTB-13L3.1_ENST00000480135.1_RNA|CLDN12_ENST00000535571.1_Silent_p.D62D|CLDN12_ENST00000394605.2_Silent_p.D62D	NM_001185073.2|NM_012129.4	NP_001172002.1|NP_036261.1	P56749	CLD12_HUMAN	claudin 12	62					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			breast(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)	15						CCCGGTATGACGGGAGCAGTG	0.507													c|||	61	0.0121805	0.0136	0.0101	5008	,	,		23361	0.0		0.0328	False		,,,				2504	0.0031				p.D62D		Atlas-SNP	.											.	CLDN12	32	.	0			c.C186T						PASS	.	T	,,	53,4353	52.9+/-88.7	0,53,2150	165.0	139.0	148.0		186,186,186	-9.2	0.0	7	dbSNP_123	148	229,8371	93.1+/-155.1	4,221,4075	no	coding-synonymous,coding-synonymous,coding-synonymous	CLDN12	NM_001185072.2,NM_001185073.2,NM_012129.4	,,	4,274,6225	TT,TC,CC		2.6628,1.2029,2.1682	,,	62/245,62/245,62/245	90042176	282,12724	2203	4300	6503	SO:0001819	synonymous_variant	9069	exon3			GTATGACGGGAGC	AJ250713	CCDS5618.1	7q21	2008-07-18			ENSG00000157224	ENSG00000157224		"""Claudins"""	2034	protein-coding gene	gene with protein product		611232					Standard	NM_001185072		Approved		uc003ukr.3	P56749	OTTHUMG00000156612	ENST00000287916.4:c.186C>T	7.37:g.90042176C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_012129	D6W5Q4|Q7LDZ0	Silent	SNP	ENST00000287916.4	37	CCDS5618.1																																																																																			C|0.981;T|0.019	0.019	strong		0.507	CLDN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059221.1	NM_012129	
D2HGDH	728294	hgsc.bcm.edu	37	2	242674803	242674803	+	Missense_Mutation	SNP	G	G	A	rs77940364	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242674803G>A	ENST00000321264.4	+	2	373	c.164G>A	c.(163-165)cGg>cAg	p.R55Q	D2HGDH_ENST00000342518.6_Missense_Mutation_p.R55Q|D2HGDH_ENST00000537090.1_Missense_Mutation_p.R55Q|D2HGDH_ENST00000403782.1_Intron|AC114730.8_ENST00000400768.2_RNA	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	55				R -> Q (in Ref. 3; AAH36604). {ECO:0000305}.	2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular protein metabolic process (GO:0044267)|response to cobalt ion (GO:0032025)|response to manganese ion (GO:0010042)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	(R)-2-hydroxyglutarate dehydrogenase activity (GO:0051990)|flavin adenine dinucleotide binding (GO:0050660)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(1)|endometrium(3)|lung(10)|skin(1)|urinary_tract(1)	16		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;4.59e-33)|all cancers(36;9.89e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.89e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0833)		TACCCCGTGCGGCGCTTGCCG	0.741													G|||	1134	0.226438	0.1914	0.2017	5008	,	,		13600	0.1617		0.3191	False		,,,				2504	0.2628				p.R55Q		Atlas-SNP	.											.	D2HGDH	39	.	0			c.G164A						PASS	.	G	GLN/ARG	788,3316		84,620,1348	7.0	9.0	9.0		164	-6.4	0.4	2	dbSNP_131	9	2638,5780		471,1696,2042	yes	missense	D2HGDH	NM_152783.3	43	555,2316,3390	AA,AG,GG		31.3376,19.2008,27.3598	benign	55/522	242674803	3426,9096	2052	4209	6261	SO:0001583	missense	728294	exon2			CCGTGCGGCGCTT	AK091725	CCDS33426.1, CCDS74684.1	2p25.3	2010-05-11			ENSG00000180902	ENSG00000180902	1.1.99.-		28358	protein-coding gene	gene with protein product		609186				15070399, 15609246	Standard	NM_152783		Approved	MGC25181, D2HGD, FLJ42195	uc002wce.1	Q8N465	OTTHUMG00000151474	ENST00000321264.4:c.164G>A	2.37:g.242674803G>A	ENSP00000315351:p.Arg55Gln	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	37	CCDS33426.1	474	0.21703296703296704	84	0.17073170731707318	74	0.20441988950276244	77	0.1346153846153846	239	0.3153034300791557	G	11.38	1.622085	0.28889	0.192008	0.313376	ENSG00000180902	ENST00000537090;ENST00000321264;ENST00000342518	D;D;D	0.88277	-2.36;-1.97;-2.36	4.13	-6.41	0.01938	.	0.966165	0.08381	N	0.954463	T	0.00012	0.0000	N	0.25992	0.78	0.80722	P	0.0	B	0.18968	0.032	B	0.19148	0.024	T	0.03524	-1.1028	9	0.15952	T	0.53	.	13.5346	0.61641	0.7652:0.0:0.2348:0.0	.	55	Q8N465	D2HDH_HUMAN	Q	55	ENSP00000442796:R55Q;ENSP00000315351:R55Q;ENSP00000339536:R55Q	ENSP00000315351:R55Q	R	+	2	0	D2HGDH	242323476	0.045000	0.20229	0.395000	0.26283	0.607000	0.37147	-0.267000	0.08619	-1.798000	0.01250	0.297000	0.19635	CGG	G|0.785;A|0.215	0.215	strong		0.741	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
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 GAIIx	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	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	23	2	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	
DLGAP5	9787	hgsc.bcm.edu	37	14	55619311	55619311	+	Silent	SNP	A	A	G	rs15870	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:55619311A>G	ENST00000247191.2	-	16	2334	c.2118T>C	c.(2116-2118)aaT>aaC	p.N706N	DLGAP5_ENST00000395425.2_Silent_p.N706N	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	706					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TACTTACATGATTTTCTTCAA	0.338													G|||	1693	0.338059	0.4145	0.2911	5008	,	,		21438	0.1895		0.4085	False		,,,				2504	0.3487				p.N706N		Atlas-SNP	.											.	DLGAP5	84	.	0			c.T2118C						PASS	.	G	,	1849,2557	630.4+/-395.5	390,1069,744	104.0	103.0	104.0		2118,2118	-1.9	0.0	14	dbSNP_52	104	3465,5135	631.3+/-398.5	727,2011,1562	no	coding-synonymous,coding-synonymous	DLGAP5	NM_001146015.1,NM_014750.4	,	1117,3080,2306	GG,GA,AA		40.2907,41.9655,40.8581	,	706/843,706/847	55619311	5314,7692	2203	4300	6503	SO:0001819	synonymous_variant	9787	exon16			TACATGATTTTCT	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.2118T>C	14.37:g.55619311A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_014750	A8MTM6|B4DRM8|Q86T11|Q8NG58	Silent	SNP	ENST00000247191.2	37	CCDS9723.1																																																																																			A|0.621;G|0.379	0.379	strong		0.338	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
VPS13C	54832	hgsc.bcm.edu	37	15	62214607	62214607	+	Missense_Mutation	SNP	C	C	T	rs12907567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62214607C>T	ENST00000261517.5	-	54	7037	c.6964G>A	c.(6964-6966)Gtg>Atg	p.V2322M	VPS13C_ENST00000395896.4_Missense_Mutation_p.V2322M|VPS13C_ENST00000395898.3_Missense_Mutation_p.V2279M|VPS13C_ENST00000249837.3_Missense_Mutation_p.V2279M	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.V2322M(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TGTAGTGTCACGTCAGCAACA	0.393													C|||	227	0.0453275	0.0159	0.0403	5008	,	,		16987	0.0367		0.0736	False		,,,				2504	0.0685				p.V2322M		Atlas-SNP	.											VPS13C,NS,carcinoma,0,1	VPS13C	506	1	1	Substitution - Missense(1)	stomach(1)	c.G6964A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	112,4294	85.8+/-124.5	0,112,2091	80.0	82.0	82.0		6964,6835,6835,6964	0.4	1.0	15	dbSNP_121	82	686,7914	170.3+/-221.5	32,622,3646	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	21,21,21,21	32,734,5737	TT,TC,CC		7.9767,2.542,6.1356	benign,benign,benign,benign	2322/3629,2279/3711,2279/3586,2322/3754	62214607	798,12208	2203	4300	6503	SO:0001583	missense	54832	exon54			GTGTCACGTCAGC	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6964G>A	15.37:g.62214607C>T	ENSP00000261517:p.Val2322Met	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	96	0.04395604395604396	6	0.012195121951219513	16	0.04419889502762431	26	0.045454545454545456	48	0.0633245382585752	C	0.672	-0.801742	0.02841	0.02542	0.079767	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.40476	1.03;1.03;1.03	5.31	0.355	0.16069	.	0.209777	0.56097	N	0.000022	T	0.00524	0.0017	N	0.00788	-1.185	0.29574	N	0.849682	B;B;B;B	0.14012	0.003;0.009;0.003;0.005	B;B;B;B	0.12156	0.004;0.007;0.004;0.003	T	0.27872	-1.0061	10	0.02654	T	1	.	7.498	0.27500	0.1099:0.1304:0.0:0.7597	rs12907567;rs17238196;rs52823611;rs59641802;rs12907567	2279;2322;2279;2322	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	M	2279;2322;2322;2322	ENSP00000249837:V2279M;ENSP00000261517:V2322M;ENSP00000379233:V2322M	ENSP00000249837:V2279M	V	-	1	0	VPS13C	60001899	1.000000	0.71417	0.989000	0.46669	0.001000	0.01503	0.720000	0.25896	-0.125000	0.11703	-2.241000	0.00287	GTG	C|0.946;T|0.054	0.054	strong		0.393	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
POTEC	388468	hgsc.bcm.edu	37	18	14537949	14537949	+	Missense_Mutation	SNP	A	A	G	rs7505568	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:14537949A>G	ENST00000358970.5	-	3	660	c.661T>C	c.(661-663)Tgt>Cgt	p.C221R	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	221			C -> R (in dbSNP:rs7505568).							NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						ATTAACACACATTCATCTTCC	0.368																																					p.C221R		Atlas-SNP	.											.	POTEC	129	.	0			c.T661C						PASS	.	A	ARG/CYS	197,1187		13,171,508	333.0	264.0	285.0		661	1.4	0.1	18	dbSNP_116	285	445,2737		32,381,1178	no	missense	POTEC	NM_001137671.1	180	45,552,1686	GG,GA,AA		13.9849,14.2341,14.0604	probably-damaging	221/543	14537949	642,3924	692	1591	2283	SO:0001583	missense	388468	exon3			ACACACATTCATC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.661T>C	18.37:g.14537949A>G	ENSP00000351856:p.Cys221Arg	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	224	90	0.401786	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	540	0.24725274725274726	66	0.13414634146341464	92	0.2541436464088398	268	0.46853146853146854	114	0.1503957783641161	A	12.33	1.905479	0.33628	0.142341	0.139849	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.64991	-0.13	1.4	1.4	0.22301	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.00012	0.0000	M	0.80982	2.52	0.19575	P	0.9999604921	D	0.67145	0.996	D	0.83275	0.996	T	0.32322	-0.9911	8	0.87932	D	0	.	4.9723	0.14123	1.0:0.0:0.0:0.0	rs7505568;rs59218795;rs7505568	221	B2RU33	POTEC_HUMAN	R	221	ENSP00000351856:C221R	ENSP00000351856:C221R	C	-	1	0	POTEC	14527949	1.000000	0.71417	0.085000	0.20634	0.013000	0.08279	5.428000	0.66489	0.898000	0.36418	0.163000	0.16589	TGT	A|0.792;G|0.208	0.208	strong		0.368	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
PINK1	65018	hgsc.bcm.edu	37	1	20977000	20977000	+	Missense_Mutation	SNP	A	A	C	rs1043424	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:20977000A>C	ENST00000321556.4	+	8	1656	c.1562A>C	c.(1561-1563)aAt>aCt	p.N521T	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	521			N -> T (in dbSNP:rs1043424). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15349860, ECO:0000269|PubMed:15596610, ECO:0000269|PubMed:16009891, ECO:0000269|PubMed:16257123, ECO:0000269|PubMed:16482571, ECO:0000269|PubMed:17344846}.		activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCCCTGAAGAATCTGAAGTTA	0.498													A|||	1505	0.300519	0.2458	0.1931	5008	,	,		21372	0.3571		0.2922	False		,,,				2504	0.4008				p.N521T	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.A1562C						PASS	.	A	THR/ASN	1179,3227	413.9+/-336.6	167,845,1191	74.0	66.0	69.0		1562	1.5	0.2	1	dbSNP_86	69	2333,6267	390.2+/-343.2	309,1715,2276	yes	missense	PINK1	NM_032409.2	65	476,2560,3467	CC,CA,AA		27.1279,26.759,27.0029	benign	521/582	20977000	3512,9494	2203	4300	6503	SO:0001583	missense	65018	exon8			TGAAGAATCTGAA	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.1562A>C	1.37:g.20977000A>C	ENSP00000364204:p.Asn521Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	37	CCDS211.1	614	0.28113553113553114	109	0.22154471544715448	80	0.22099447513812154	208	0.36363636363636365	217	0.2862796833773087	A	13.74	2.327369	0.41197	0.26759	0.271279	ENSG00000158828	ENST00000321556	T	0.74106	-0.81	5.83	1.55	0.23275	.	0.653207	0.17574	N	0.169362	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.17465	0.004;0.022	B;B	0.11329	0.005;0.006	T	0.18681	-1.0329	9	0.33141	T	0.24	-7.6155	7.3998	0.26956	0.6411:0.0:0.3589:0.0	rs1043424;rs60071348;rs1043424	214;521	Q9BXM7-2;Q9BXM7	.;PINK1_HUMAN	T	521	ENSP00000364204:N521T	ENSP00000364204:N521T	N	+	2	0	PINK1	20849587	0.208000	0.23494	0.242000	0.24170	0.980000	0.70556	0.601000	0.24119	0.382000	0.24878	0.402000	0.26972	AAT	A|0.725;C|0.275	0.275	strong		0.498	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
GPSM1	26086	hgsc.bcm.edu	37	9	139235606	139235606	+	Intron	SNP	G	G	C	rs78403475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139235606G>C	ENST00000440944.1	+	9	1427				GPSM1_ENST00000392945.3_Missense_Mutation_p.A455P	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		CTCAGGGACAGCACAGGCCTG	0.657													G|||	467	0.0932508	0.0567	0.1009	5008	,	,		16606	0.1508		0.0805	False		,,,				2504	0.091				p.A455P		Atlas-SNP	.											GPSM1_ENST00000392945,caecum,carcinoma,-1,1	GPSM1	50	1	0			c.G1363C						PASS	.						15.0	19.0	18.0					9																	139235606		691	1590	2281	SO:0001627	intron_variant	26086	exon9			GGGACAGCACAGG	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1207+156G>C	9.37:g.139235606G>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_015597	A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Missense_Mutation	SNP	ENST00000440944.1	37	CCDS48055.1	217	0.09935897435897435	35	0.07113821138211382	31	0.0856353591160221	86	0.15034965034965034	65	0.08575197889182058	G	4.405	0.074756	0.08485	.	.	ENSG00000160360	ENST00000392945	D	0.91996	-2.95	1.44	0.511	0.16989	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.80722	P	0.0	P	0.34977	0.478	B	0.21151	0.033	T	0.48364	-0.9042	7	0.87932	D	0	.	3.8124	0.08802	0.2453:0.0:0.7547:0.0	.	455	Q86YR5-3	.	P	455	ENSP00000376674:A455P	ENSP00000376674:A455P	A	+	1	0	GPSM1	138355427	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	-0.389000	0.07342	0.176000	0.19873	-0.379000	0.06801	GCA	G|0.900;C|0.100	0.100	strong		0.657	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597	
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 GAIIx	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	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	9	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		
MC1R	4157	hgsc.bcm.edu	37	16	89985844	89985844	+	Missense_Mutation	SNP	G	G	T	rs1805005	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89985844G>T	ENST00000555147.1	+	1	1558	c.178G>T	c.(178-180)Gtg>Ttg	p.V60L	TUBB3_ENST00000556922.1_Missense_Mutation_p.V60L|TUBB3_ENST00000554444.1_5'Flank|MC1R_ENST00000555427.1_Missense_Mutation_p.V60L|RP11-566K11.7_ENST00000570217.1_RNA|RP11-566K11.4_ENST00000554623.1_RNA	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	60			V -> L (associated with a risk for developing melanoma; unable to stimulate cAMP production as strongly as the wild type receptor in response to alpha- melanocyte-stimulating hormone stimulation; dbSNP:rs1805005). {ECO:0000269|PubMed:17434924, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:9302268, ECO:0000269|Ref.12}.		G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		CGCGCTGGTGGTGGCCACCAT	0.637									Melanoma, Familial Clustering of				G|||	177	0.0353435	0.0053	0.072	5008	,	,		19038	0.0		0.1123	False		,,,				2504	0.0072				p.V60L		Atlas-SNP	.											.	MC1R	20	.	0			c.G178T	GRCh37	CM973294	MC1R	M	rs1805005	PASS	.	G	LEU/VAL	98,4236		1,96,2070	57.0	69.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	178	4.9	1.0	16	dbSNP_89	65	1137,7385		79,979,3203	yes	missense	MC1R	NM_002386.3	32	80,1075,5273	TT,TG,GG		13.3419,2.2612,9.6064		60/318	89985844	1235,11621	2167	4261	6428	SO:0001583	missense	4157	exon1	Familial Cancer Database		CTGGTGGTGGCCA		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"""GPCR / Class A : Melanocortin receptors"""	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.178G>T	16.37:g.89985844G>T	ENSP00000451605:p.Val60Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Missense_Mutation	SNP	ENST00000555147.1	37	CCDS56011.1	111	0.050824175824175824	3	0.006097560975609756	27	0.07458563535911603	0	0.0	81	0.10686015831134564	G	14.85	2.658140	0.47467	0.022612	0.133419	ENSG00000258947;ENSG00000258947;ENSG00000258839	ENST00000555427;ENST00000556922;ENST00000555147	T;T;T	0.70631	-0.5;-0.5;-0.5	4.86	4.86	0.63082	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34178	U	0.004187	T	0.02649	0.0080	L	0.41415	1.275	0.24989	P	0.99154802	D	0.60575	0.988	D	0.67382	0.951	T	0.32587	-0.9901	8	.	.	.	.	16.9746	0.86309	0.0:0.0:1.0:0.0	rs1805005;rs1805005	60	Q01726	MSHR_HUMAN	L	60	ENSP00000451760:V60L;ENSP00000451560:V60L;ENSP00000451605:V60L	.	V	+	1	0	MC1R;RP11-566K11.2	88513345	1.000000	0.71417	0.995000	0.50966	0.082000	0.17680	2.424000	0.44714	2.255000	0.74692	0.455000	0.32223	GTG	G|0.944;T|0.056	0.056	strong		0.637	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
GAB4	128954	hgsc.bcm.edu	37	22	17446991	17446991	+	Splice_Site	SNP	C	C	T	rs4819925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:17446991C>T	ENST00000400588.1	-	6	1394	c.1287G>A	c.(1285-1287)aaG>aaA	p.K429K	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	429										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				AAGACTTACCCTTCTGGTTAG	0.532													T|||	4133	0.82528	0.9773	0.8444	5008	,	,		21489	0.8353		0.7396	False		,,,				2504	0.684				p.K429K		Atlas-SNP	.											GAB4,NS,carcinoma,0,1	GAB4	95	1	0			c.G1287A						PASS	.	T		3849,227		1820,209,9	94.0	102.0	99.0		1287	1.2	1.0	22	dbSNP_111	99	6337,2071		2412,1513,279	yes	coding-synonymous-near-splice	GAB4	NM_001037814.1		4232,1722,288	TT,TC,CC		24.6313,5.5692,18.4076		429/575	17446991	10186,2298	2038	4204	6242	SO:0001630	splice_region_variant	128954	exon6			CTTACCCTTCTGG	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.1288+1G>A	22.37:g.17446991C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	36	0.382979	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			C|0.190;T|0.810	0.810	strong		0.532	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	Silent
MMP17	4326	hgsc.bcm.edu	37	12	132326298	132326298	+	Missense_Mutation	SNP	G	G	A	rs35466884	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132326298G>A	ENST00000360564.1	+	5	938	c.836G>A	c.(835-837)cGc>cAc	p.R279H	MMP17_ENST00000535291.1_Missense_Mutation_p.R195H|MMP17_ENST00000535182.1_3'UTR	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	279					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	GACCCGCTGCGCTACGGGCTC	0.647													G|||	1264	0.252396	0.3177	0.1599	5008	,	,		16971	0.1657		0.1869	False		,,,				2504	0.3865				p.R279H		Atlas-SNP	.											.	MMP17	77	.	0			c.G836A						PASS	.	G	HIS/ARG	1424,2982	453.2+/-350.3	234,956,1013	53.0	45.0	48.0		836	-1.4	1.0	12	dbSNP_126	48	1431,7169	267.9+/-287.5	125,1181,2994	yes	missense	MMP17	NM_016155.4	29	359,2137,4007	AA,AG,GG		16.6395,32.3196,21.9514	benign	279/604	132326298	2855,10151	2203	4300	6503	SO:0001583	missense	4326	exon5			CGCTGCGCTACGG	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.836G>A	12.37:g.132326298G>A	ENSP00000353767:p.Arg279His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_016155	Q14850	Missense_Mutation	SNP	ENST00000360564.1	37	CCDS31927.1	439	0.20100732600732601	165	0.3353658536585366	45	0.12430939226519337	96	0.16783216783216784	133	0.17546174142480211	G	9.571	1.121060	0.20877	0.323196	0.166395	ENSG00000198598	ENST00000360564;ENST00000535291;ENST00000534865	T;T;T	0.17054	2.3;2.3;2.51	4.15	-1.36	0.09085	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.933443	0.08804	N	0.891295	T	0.00012	0.0000	N	0.11892	0.195	0.09310	P	0.99999999683036	B	0.11235	0.004	B	0.09377	0.004	T	0.47586	-0.9106	9	0.51188	T	0.08	.	5.4444	0.16527	0.6075:0.1672:0.2252:0.0	rs35466884;rs61942396	279	Q9ULZ9	MMP17_HUMAN	H	279;195;120	ENSP00000353767:R279H;ENSP00000441106:R195H;ENSP00000442104:R120H	ENSP00000353767:R279H	R	+	2	0	MMP17	130892251	1.000000	0.71417	0.989000	0.46669	0.024000	0.10985	2.944000	0.49034	-0.146000	0.11274	-0.233000	0.12211	CGC	G|0.780;A|0.220	0.220	strong		0.647	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
SUN2	25777	hgsc.bcm.edu	37	22	39147235	39147235	+	Missense_Mutation	SNP	A	A	C	rs35496634	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39147235A>C	ENST00000405510.1	-	4	624	c.266T>G	c.(265-267)cTg>cGg	p.L89R	SUN2_ENST00000411587.2_Missense_Mutation_p.L124R|SUN2_ENST00000216064.4_Missense_Mutation_p.L89R|RP3-508I15.14_ENST00000416406.1_RNA|SUN2_ENST00000406622.1_Missense_Mutation_p.L89R|SUN2_ENST00000405018.1_Missense_Mutation_p.L89R	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	89	LMNA-binding. {ECO:0000250}.|Ser-rich.		L -> R (in dbSNP:rs35496634). {ECO:0000269|PubMed:15489334}.		centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						GTCACCATGCAGTTCCTCCAG	0.647													A|||	174	0.0347444	0.0061	0.0461	5008	,	,		18485	0.0		0.1243	False		,,,				2504	0.0092				p.L89R		Atlas-SNP	.											.	SUN2	59	.	0			c.T266G						PASS	.	A	ARG/LEU,ARG/LEU,ARG/LEU	91,4315	74.1+/-112.3	3,85,2115	85.0	93.0	90.0		266,266,266	4.0	0.5	22	dbSNP_126	90	957,7643	210.5+/-251.4	54,849,3397	yes	missense,missense,missense	SUN2	NM_001199579.1,NM_001199580.1,NM_015374.2	102,102,102	57,934,5512	CC,CA,AA		11.1279,2.0654,8.0578	possibly-damaging,possibly-damaging,possibly-damaging	89/739,89/718,89/718	39147235	1048,11958	2203	4300	6503	SO:0001583	missense	25777	exon4			CCATGCAGTTCCT	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"""unc-84 homolog B (C. elegans)"""	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.266T>G	22.37:g.39147235A>C	ENSP00000385740:p.Leu89Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001199580	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Missense_Mutation	SNP	ENST00000405510.1	37	CCDS13978.1	128	0.05860805860805861	4	0.008130081300813009	21	0.058011049723756904	0	0.0	103	0.1358839050131926	A	8.085	0.773188	0.16051	0.020654	0.111279	ENSG00000100242	ENST00000405510;ENST00000216064;ENST00000405018;ENST00000406622;ENST00000411587;ENST00000438058;ENST00000456894;ENST00000420859;ENST00000452294;ENST00000433561;ENST00000417332;ENST00000439339	T;T;T;T;T;T;T;T;T;T;T;T	0.54866	2.38;2.38;2.2;2.38;2.49;1.32;0.95;1.26;0.55;1.04;1.13;0.81	5.11	4.01	0.46588	.	3.288000	0.00904	N	0.002383	T	0.00524	0.0017	N	0.24115	0.695	0.40157	P	0.022989999999999955	P;P;P;P;P	0.52316	0.933;0.952;0.952;0.952;0.875	P;B;B;B;B	0.49012	0.598;0.438;0.438;0.307;0.307	T	0.14504	-1.0470	9	0.59425	D	0.04	-13.6442	9.5706	0.39425	0.8438:0.0:0.0:0.1562	rs35496634	124;124;89;89;89	B4DIU6;B4E2A6;Q2T9F7;B0QY62;Q9UH99	.;.;.;.;SUN2_HUMAN	R	89;89;89;89;124;89;89;89;89;89;89;89	ENSP00000385740:L89R;ENSP00000216064:L89R;ENSP00000385616:L89R;ENSP00000383992:L89R;ENSP00000395601:L124R;ENSP00000406941:L89R;ENSP00000415588:L89R;ENSP00000408834:L89R;ENSP00000414950:L89R;ENSP00000411615:L89R;ENSP00000412928:L89R;ENSP00000393271:L89R	ENSP00000216064:L89R	L	-	2	0	SUN2	37477181	1.000000	0.71417	0.517000	0.27799	0.090000	0.18270	2.683000	0.46943	1.917000	0.55516	0.460000	0.39030	CTG	A|0.927;C|0.073	0.073	strong		0.647	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332	
KIAA1804	84451	hgsc.bcm.edu	37	1	233515102	233515102	+	Missense_Mutation	SNP	T	T	G	rs963981	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:233515102T>G	ENST00000366624.3	+	9	2611	c.2350T>G	c.(2350-2352)Tgt>Ggt	p.C784G	MLK4_ENST00000366622.1_Missense_Mutation_p.C230G	NM_032435.2	NP_115811.2																					GCCATCCACCTGTGGGGAGGC	0.602													G|||	1384	0.276358	0.2405	0.3444	5008	,	,		17780	0.3433		0.173	False		,,,				2504	0.3139				p.C784G		Atlas-SNP	.											.	KIAA1804	129	.	0			c.T2350G						PASS	.	G	GLY/CYS	995,3411	729.8+/-410.1	105,785,1313	53.0	57.0	55.0		2350	1.2	0.0	1	dbSNP_86	55	1571,7029	743.5+/-407.2	147,1277,2876	yes	missense	KIAA1804	NM_032435.2	159	252,2062,4189	GG,GT,TT		18.2674,22.5828,19.7294	benign	784/1037	233515102	2566,10440	2203	4300	6503	SO:0001583	missense	0	exon9			TCCACCTGTGGGG																												ENST00000366624.3:c.2350T>G	1.37:g.233515102T>G	ENSP00000355583:p.Cys784Gly	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	551	0.2522893772893773	130	0.26422764227642276	98	0.27071823204419887	194	0.33916083916083917	129	0.17018469656992086	G	2.556	-0.302961	0.05495	0.225828	0.182674	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.73363	-0.74;3.34	4.49	1.18	0.20946	.	0.962447	0.08551	N	0.929050	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15093	-1.0449	9	0.12766	T	0.61	.	0.6602	0.00841	0.4483:0.1853:0.1819:0.1844	rs963981;rs3795372;rs52838398;rs963981	231;784	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	G	784;230	ENSP00000355583:C784G;ENSP00000355581:C230G	ENSP00000355581:C230G	C	+	1	0	RP5-862P8.2	231581725	0.030000	0.19436	0.000000	0.03702	0.001000	0.01503	0.411000	0.21115	-0.164000	0.10927	-0.764000	0.03450	TGT	T|0.771;G|0.223	0.223	strong		0.602	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
GCKR	2646	hgsc.bcm.edu	37	2	27730940	27730940	+	Splice_Site	SNP	T	T	C	rs1260326	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27730940T>C	ENST00000264717.2	+	15	1400	c.1337T>C	c.(1336-1338)cTg>cCg	p.L446P	GCKR_ENST00000424318.2_Splice_Site_p.L256P	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	446	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.		P -> L (associated with high triglyceride levels and low fasting plasma glucose levels; associated with a reduced risk for type 2 diabetes; the mutant protein is less efficiently regulated by physiological concentrations of fructose- 6 phosphate; dbSNP:rs1260326). {ECO:0000269|PubMed:15815621, ECO:0000269|PubMed:18556336, ECO:0000269|PubMed:18678614, ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					CAGACCTTGCTGGTGAGAGTC	0.582													C|||	3539	0.706669	0.9062	0.6383	5008	,	,		17520	0.5188		0.5895	False		,,,				2504	0.7996				p.L446P		Atlas-SNP	.											.	GCKR	73	.	0			c.T1337C	GRCh37	CM083701	GCKR	M	rs1260326	PASS	.	C	PRO/LEU	3776,630	270.1+/-269.4	1614,548,41	69.0	63.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1337	3.0	1.0	2	dbSNP_87	65	5015,3585	519.5+/-379.5	1454,2107,739	yes	missense-near-splice	GCKR	NM_001486.3	98	3068,2655,780	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	41.686,14.2987,32.4081	probably-damaging	446/626	27730940	8791,4215	2203	4300	6503	SO:0001630	splice_region_variant	2646	exon15			CCTTGCTGGTGAG	Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"""glucokinase (hexokinase 4) regulatory protein"""			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.1338+1T>C	2.37:g.27730940T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	153	79	0.51634	NM_001486	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	ENST00000264717.2	37	CCDS1757.1	1345|1345	0.6158424908424909|0.6158424908424909	433|433	0.8800813008130082|0.8800813008130082	215|215	0.5939226519337016|0.5939226519337016	252|252	0.4405594405594406|0.4405594405594406	445|445	0.5870712401055409|0.5870712401055409	C|C	0.004|0.004	-2.287046|-2.287046	0.00248|0.00248	0.857013|0.857013	0.58314|0.58314	ENSG00000084734|ENSG00000084734	ENST00000264717;ENST00000424318|ENST00000411584	T;T|.	0.21734|.	2.31;1.99|.	3.83|3.83	2.95|2.95	0.34219|0.34219	.|.	0.455576|.	0.21275|.	N|.	0.077250|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.30867|0.30867	P|P	0.732871|0.732871	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|.	0.14008|.	-1.0488|.	8|.	0.02654|.	T|.	1|.	-3.9783|-3.9783	6.3237|6.3237	0.21232|0.21232	0.0:0.768:0.0:0.232|0.0:0.768:0.0:0.232	rs1260326;rs17705011;rs58226775;rs1260326|rs1260326;rs17705011;rs58226775;rs1260326	256|.	F5H1P6|.	.|.	P|R	446;256|147	ENSP00000264717:L446P;ENSP00000409109:L256P|.	ENSP00000264717:L446P|.	L|X	+|+	2|1	0|0	GCKR|GCKR	27584444|27584444	0.996000|0.996000	0.38824|0.38824	0.994000|0.994000	0.49952|0.49952	0.015000|0.015000	0.08874|0.08874	0.075000|0.075000	0.14686|0.14686	0.409000|0.409000	0.25649|0.25649	-0.726000|-0.726000	0.03593|0.03593	CTG|TGA	A|0.003;C|0.649	0.649	strong		0.582	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486	Missense_Mutation
EXOSC8	11340	hgsc.bcm.edu	37	13	37580139	37580139	+	Silent	SNP	G	G	A	rs1127446	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:37580139G>A	ENST00000389704.3	+	6	586	c.321G>A	c.(319-321)caG>caA	p.Q107Q	EXOSC8_ENST00000489088.1_3'UTR	NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	107					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)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)			biliary_tract(1)|breast(1)|kidney(2)|pancreas(1)|prostate(1)|skin(1)	7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		TGGCTAGCCAGTTCATTGCAG	0.413													G|||	2071	0.413538	0.0817	0.4236	5008	,	,		14507	0.7232		0.3797	False		,,,				2504	0.5706				p.Q107Q		Atlas-SNP	.											.	EXOSC8	16	.	0			c.G321A						PASS	.	G		624,3782	268.6+/-268.5	47,530,1626	92.0	87.0	89.0		321	4.2	1.0	13	dbSNP_86	89	3428,5172	505.0+/-376.3	692,2044,1564	no	coding-synonymous	EXOSC8	NM_181503.2		739,2574,3190	AA,AG,GG		39.8605,14.1625,31.1549		107/277	37580139	4052,8954	2203	4300	6503	SO:0001819	synonymous_variant	11340	exon6			TAGCCAGTTCATT	AF025438	CCDS31958.1	13q13.1	2010-05-07			ENSG00000120699	ENSG00000120699	3.1.13.-		17035	protein-coding gene	gene with protein product	"""CBP-interacting protein 3"", ""Opa interacting protein 2"""	606019				9466265, 11929972	Standard	NM_181503		Approved	OIP2, RRP43, bA421P11.3, Rrp43p, EAP2, p9, CIP3	uc001uwa.3	Q96B26	OTTHUMG00000016742	ENST00000389704.3:c.321G>A	13.37:g.37580139G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	121	66	0.545455	NM_181503	O43480|Q5TBA5	Silent	SNP	ENST00000389704.3	37	CCDS31958.1																																																																																			G|0.659;A|0.341	0.341	strong		0.413	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503	
CNTN5	53942	hgsc.bcm.edu	37	11	100226883	100226883	+	Missense_Mutation	SNP	T	T	A	rs1216183	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:100226883T>A	ENST00000524871.1	+	25	3525	c.3235T>A	c.(3235-3237)Tct>Act	p.S1079T	CNTN5_ENST00000279463.3_Missense_Mutation_p.S1079T|CNTN5_ENST00000418526.2_Missense_Mutation_p.S1005T|CNTN5_ENST00000528682.1_Missense_Mutation_p.S1079T|CNTN5_ENST00000524560.1_3'UTR	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	1079			S -> T (in dbSNP:rs1216183). {ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		GACCCTTCACTCTCTCTCCAC	0.413													A|||	1638	0.327077	0.531	0.2896	5008	,	,		19676	0.3313		0.1193	False		,,,				2504	0.2873				p.S1079T		Atlas-SNP	.											CNTN5_ENST00000524871,colon,carcinoma,-2,2	CNTN5	324	2	0			c.T3235A						PASS	.	A	THR/SER,THR/SER	1708,2280		366,976,652	137.0	133.0	134.0		3235,3013	1.5	0.1	11	dbSNP_87	134	886,7448		52,782,3333	yes	missense,missense	CNTN5	NM_014361.3,NM_175566.2	58,58	418,1758,3985	AA,AT,TT		10.6311,42.8285,21.0518	benign,benign	1079/1101,1005/1027	100226883	2594,9728	1994	4167	6161	SO:0001583	missense	53942	exon24			CTTCACTCTCTCT	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.3235T>A	11.37:g.100226883T>A	ENSP00000435637:p.Ser1079Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	91	9	0.0989011	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	636	0.29120879120879123	254	0.516260162601626	95	0.26243093922651933	193	0.3374125874125874	94	0.12401055408970976	A	0.081	-1.183514	0.01620	0.428285	0.106311	ENSG00000149972	ENST00000528682;ENST00000524871;ENST00000418526;ENST00000279463	T;T;T;T	0.54479	0.58;0.58;0.57;0.58	5.4	1.5	0.22942	.	0.581661	0.18924	N	0.127412	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46748	-0.9169	8	.	.	.	.	0.953	0.01379	0.3979:0.1191:0.1366:0.3463	rs1216183;rs17094898;rs52792685;rs1216183	1005;1079	O94779-2;O94779	.;CNTN5_HUMAN	T	1079;1079;1005;1079	ENSP00000436185:S1079T;ENSP00000435637:S1079T;ENSP00000393229:S1005T;ENSP00000279463:S1079T	.	S	+	1	0	CNTN5	99732093	0.000000	0.05858	0.057000	0.19452	0.209000	0.24338	-0.013000	0.12678	-0.254000	0.09500	-0.364000	0.07487	TCT	T|0.706;A|0.294	0.294	strong		0.413	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
ERCC6	2074	hgsc.bcm.edu	37	10	50678369	50678369	+	Missense_Mutation	SNP	T	T	C	rs2228527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50678369T>C	ENST00000355832.5	-	18	3715	c.3637A>G	c.(3637-3639)Aga>Gga	p.R1213G	ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000542458.1_Missense_Mutation_p.R583G	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1213			R -> G (in dbSNP:rs2228527). {ECO:0000269|PubMed:19894250, ECO:0000269|PubMed:9443879, ECO:0000269|Ref.3}.		activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						TTGGCGTCTCTGCAATGCTTA	0.443								Direct reversal of damage;Nucleotide excision repair (NER)					T|||	925	0.184704	0.1452	0.2104	5008	,	,		19648	0.0437		0.2087	False		,,,				2504	0.3405				p.L1213V		Atlas-SNP	.											.	ERCC6	162	.	0			c.C3637G	GRCh37	CM980633	ERCC6	M	rs2228527	PASS	.	T	GLY/ARG	688,3718	288.1+/-279.7	70,548,1585	337.0	321.0	326.0		3637	1.9	0.0	10	dbSNP_98	326	1870,6730	333.3+/-320.5	198,1474,2628	yes	missense	ERCC6	NM_000124.2	125	268,2022,4213	CC,CT,TT		21.7442,15.6151,19.6678	possibly-damaging	1213/1494	50678369	2558,10448	2203	4300	6503	SO:0001583	missense	2074	exon18			CGTCTCTGCAATG	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.3637A>G	10.37:g.50678369T>C	ENSP00000348089:p.Arg1213Gly	Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	365	165	0.452055	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	356	0.163003663003663	75	0.1524390243902439	83	0.2292817679558011	30	0.05244755244755245	168	0.22163588390501318	T	11.21	1.572105	0.28092	0.156151	0.217442	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.83591	-1.74;-1.48	5.65	1.87	0.25490	.	.	.	.	.	T	0.00109	0.0003	M	0.72118	2.19	0.80722	P	0.0	P	0.38922	0.651	B	0.32677	0.15	T	0.01071	-1.1461	8	0.27785	T	0.31	-8.3756	8.6269	0.33895	0.0:0.0653:0.3698:0.5649	rs2228527;rs17702436;rs56512951;rs60642826;rs2228527	1213	Q03468	ERCC6_HUMAN	G	1213;590;583	ENSP00000348089:R1213G;ENSP00000445134:R583G	ENSP00000348089:R1213G	R	-	1	2	ERCC6	50348375	0.572000	0.26668	0.042000	0.18584	0.716000	0.41182	1.716000	0.37981	0.122000	0.18314	-0.316000	0.08728	AGA	T|0.820;C|0.180	0.180	strong		0.443	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
THUMPD3	25917	hgsc.bcm.edu	37	3	9406836	9406836	+	Silent	SNP	T	T	C	rs1054975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9406836T>C	ENST00000345094.3	+	2	418	c.84T>C	c.(82-84)agT>agC	p.S28S	RP11-380O24.1_ENST00000517846.1_RNA|THUMPD3_ENST00000515662.2_Silent_p.S28S|RP11-380O24.1_ENST00000518331.1_RNA|SETD5-AS1_ENST00000468186.1_RNA|RP11-380O24.1_ENST00000517687.1_RNA|THUMPD3_ENST00000452837.2_Silent_p.S28S|RP11-380O24.1_ENST00000491930.2_RNA|RP11-380O24.1_ENST00000466431.2_RNA	NM_001114092.1|NM_015453.2	NP_001107564.1|NP_056268.2	Q9BV44	THUM3_HUMAN	THUMP domain containing 3	28						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	19	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.101)		TGACAGAAAGTGACCTCGGAA	0.458													T|||	3101	0.619209	0.5454	0.5922	5008	,	,		17587	0.5813		0.6034	False		,,,				2504	0.7935				p.S28S		Atlas-SNP	.											.	THUMPD3	46	.	0			c.T84C						PASS	.	T	,	2456,1950	622.4+/-393.9	694,1068,441	98.0	98.0	98.0		84,84	1.5	0.0	3	dbSNP_86	98	5223,3377	640.6+/-399.6	1592,2039,669	no	coding-synonymous,coding-synonymous	THUMPD3	NM_001114092.1,NM_015453.2	,	2286,3107,1110	CC,CT,TT		39.2674,44.2578,40.958	,	28/508,28/508	9406836	7679,5327	2203	4300	6503	SO:0001819	synonymous_variant	25917	exon2			AGAAAGTGACCTC	AL117483	CCDS2573.1	3p25.3	2004-06-04			ENSG00000134077	ENSG00000134077			24493	protein-coding gene	gene with protein product						12477932	Standard	NM_015453		Approved	DKFZP434F091	uc003brn.4	Q9BV44	OTTHUMG00000097031	ENST00000345094.3:c.84T>C	3.37:g.9406836T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	154	152	0.987013	NM_001114092	Q9H8V6|Q9NVC1|Q9UFS3	Silent	SNP	ENST00000345094.3	37	CCDS2573.1																																																																																			T|0.410;C|0.590	0.590	strong		0.458	THUMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214127.1	NM_015453	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994488	45994488	+	Missense_Mutation	SNP	G	G	T	rs396912	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45994488G>T	ENST00000400374.3	+	1	883	c.853G>T	c.(853-855)Ggc>Tgc	p.G285C	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	285	36 X 5 AA repeats of C-C-X(3).		G -> C (in dbSNP:rs396912).			keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAAGCCTGTCGGCTCTGTGCC	0.642													.|||	931	0.185903	0.3812	0.0937	5008	,	,		22814	0.2054		0.0368	False		,,,				2504	0.1207				p.G285C		Atlas-SNP	.											KRTAP10-4,colon,carcinoma,-1,1	KRTAP10-4	44	1	0			c.G853T						scavenged	.	T	,CYS/GLY	1527,2879	669.8+/-402.2	259,1009,935	115.0	120.0	118.0		,853	1.9	0.0	21	dbSNP_80	118	266,8334	803.6+/-407.3	4,258,4038	no	intron,missense	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,159	263,1267,4973	TT,TG,GG		3.093,34.6573,13.7859	,benign	,285/402	45994488	1793,11213	2203	4300	6503	SO:0001583	missense	386672	exon1			CCTGTCGGCTCTG	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.853G>T	21.37:g.45994488G>T	ENSP00000383225:p.Gly285Cys	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	156	102	0.653846	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	365|365	0.1671245421245421|0.1671245421245421	181|181	0.3678861788617886|0.3678861788617886	33|33	0.09116022099447514|0.09116022099447514	130|130	0.22727272727272727|0.22727272727272727	21|21	0.027704485488126648|0.027704485488126648	T|t	0.403|0.403	-0.917088|-0.917088	0.02415|0.02415	0.346573|0.346573	0.03093|0.03093	ENSG00000215454|ENSG00000215454	ENST00000334871|ENST00000400374	.|T	.|0.00686	.|5.85	4.38|4.38	1.89|1.89	0.25635|0.25635	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	N|N	0.00019|0.00019	-2.79|-2.79	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	.|T	.|0.41698	.|-0.9494	.|8	.|0.02654	.|T	.|1	.|.	1.2795|1.2795	0.02037|0.02037	0.299:0.0913:0.154:0.4556|0.299:0.0913:0.154:0.4556	rs396912;rs396912|rs396912;rs396912	.|285	.|P60372	.|KR104_HUMAN	.|C	-1|285	.|ENSP00000383225:G285C	.|ENSP00000383225:G285C	.|G	+|+	.|1	.|0	KRTAP10-4|KRTAP10-4	44818916|44818916	0.040000|0.040000	0.19996|0.19996	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.499000|-0.499000	0.06413|0.06413	0.160000|0.160000	0.19432|0.19432	-0.320000|-0.320000	0.08662|0.08662	.|GGC	G|0.785;T|0.215	0.215	strong		0.642	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
SEMA4A	64218	hgsc.bcm.edu	37	1	156146689	156146689	+	Silent	SNP	G	G	A	rs41265019	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156146689G>A	ENST00000368285.3	+	15	2454	c.2187G>A	c.(2185-2187)ccG>ccA	p.P729P	SEMA4A_ENST00000368284.1_Silent_p.P597P|SEMA4A_ENST00000368286.2_Silent_p.P597P|SEMA4A_ENST00000355014.2_Silent_p.P729P|SEMA4A_ENST00000368282.1_Silent_p.P729P	NM_001193300.1|NM_022367.3	NP_001180229.1|NP_071762.2	Q9H3S1	SEM4A_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4A	729					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|regulation of cell shape (GO:0008360)|regulation of endothelial cell migration (GO:0010594)|semaphorin-plexin signaling pathway (GO:0071526)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|ovary(2)|skin(2)	5	Hepatocellular(266;0.158)					AGAAGGCCCCGTTAAGCAGAG	0.602													g|||	34	0.00678914	0.0008	0.0086	5008	,	,		20372	0.0		0.0209	False		,,,				2504	0.0061				p.P729P		Atlas-SNP	.											.	SEMA4A	75	.	0			c.G2187A						PASS	.		,,,	9,4397	16.8+/-37.8	0,9,2194	59.0	56.0	57.0		2187,2187,1791,2187	-10.4	0.0	1	dbSNP_127	57	198,8402	86.3+/-148.7	2,194,4104	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEMA4A	NM_001193300.1,NM_001193301.1,NM_001193302.1,NM_022367.3	,,,	2,203,6298	AA,AG,GG		2.3023,0.2043,1.5916	,,,	729/762,729/762,597/630,729/762	156146689	207,12799	2203	4300	6503	SO:0001819	synonymous_variant	64218	exon15			GGCCCCGTTAAGC	AK022416	CCDS1132.1, CCDS53378.1	1q22	2014-01-28			ENSG00000196189	ENSG00000196189		"""Semaphorins"""	10729	protein-coding gene	gene with protein product		607292		SEMAB		7748561	Standard	NM_022367		Approved	SemB, FLJ12287, CORD10	uc009wrq.3	Q9H3S1	OTTHUMG00000014042	ENST00000368285.3:c.2187G>A	1.37:g.156146689G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_001193300	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Silent	SNP	ENST00000368285.3	37	CCDS1132.1																																																																																			G|0.987;A|0.013	0.013	strong		0.602	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039484.2	NM_022367	
KCNH3	23416	hgsc.bcm.edu	37	12	49951232	49951232	+	Silent	SNP	T	T	C	rs2241418	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49951232T>C	ENST00000257981.6	+	15	3008	c.2748T>C	c.(2746-2748)ggT>ggC	p.G916G	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	916					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						ACAGGGAGGGTCCGTGCCCTC	0.662													C|||	1036	0.206869	0.5151	0.1081	5008	,	,		16526	0.0833		0.1054	False		,,,				2504	0.092				p.G916G		Atlas-SNP	.											.	KCNH3	88	.	0			c.T2748C						PASS	.	C		1914,2490	586.8+/-386.5	429,1056,717	24.0	27.0	26.0		2748	2.4	0.5	12	dbSNP_98	26	900,7698	752.9+/-407.4	56,788,3455	no	coding-synonymous	KCNH3	NM_012284.1		485,1844,4172	CC,CT,TT		10.4676,43.4605,21.6428		916/1084	49951232	2814,10188	2202	4299	6501	SO:0001819	synonymous_variant	23416	exon15			GGAGGGTCCGTGC	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2748T>C	12.37:g.49951232T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_012284	Q9UQ06	Silent	SNP	ENST00000257981.6	37	CCDS8786.1																																																																																			T|0.792;C|0.208	0.208	strong		0.662	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
KRT6C	286887	hgsc.bcm.edu	37	12	52865918	52865918	+	Silent	SNP	G	G	C	rs425073		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52865918G>C	ENST00000252250.6	-	2	734	c.687C>G	c.(685-687)gtC>gtG	p.V229V		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	229	Coil 1B.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		CCCGTTCCCCGACGATGCTGT	0.592																																					p.V229V		Atlas-SNP	.											.	KRT6C	55	.	0			c.C687G						PASS	.	C		29,4375		9,11,2182	140.0	93.0	109.0		687	-5.8	0.0	12	dbSNP_80	109	996,7490		394,208,3641	no	coding-synonymous	KRT6C	NM_173086.4		403,219,5823	CC,CG,GG		11.737,0.6585,7.9519		229/565	52865918	1025,11865	2202	4243	6445	SO:0001819	synonymous_variant	286887	exon2			TTCCCCGACGATG	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.687C>G	12.37:g.52865918G>C		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	153	49	0.320261	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			G|0.750;C|0.250	0.250	weak		0.592	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
VAMP8	8673	hgsc.bcm.edu	37	2	85808737	85808737	+	Silent	SNP	A	A	G	rs1009	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85808737A>G	ENST00000263864.5	+	3	357	c.201A>G	c.(199-201)cgA>cgG	p.R67R	VAMP5_ENST00000306384.4_5'Flank|VAMP8_ENST00000432071.1_Silent_p.R41R|VAMP8_ENST00000409760.1_3'UTR	NM_003761.4	NP_003752.2	Q9BV40	VAMP8_HUMAN	vesicle-associated membrane protein 8	67	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				autophagic vacuole fusion (GO:0000046)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule membrane (GO:0030667)|SNARE complex (GO:0031201)		p.R67R(1)		breast(1)|endometrium(2)|large_intestine(1)|stomach(2)	6						AGGTGGCTCGAAAATTCTGGT	0.468													G|||	2201	0.439497	0.5976	0.3473	5008	,	,		21409	0.3859		0.4314	False		,,,				2504	0.3548				p.R67R		Atlas-SNP	.											VAMP8,NS,carcinoma,0,1	VAMP8	10	1	1	Substitution - coding silent(1)	stomach(1)	c.A201G						PASS	.	G		2423,1983	557.4+/-379.7	672,1079,452	378.0	321.0	340.0		201	0.4	1.0	2	dbSNP_36	340	3554,5046	629.9+/-398.3	734,2086,1480	no	coding-synonymous	VAMP8	NM_003761.4		1406,3165,1932	GG,GA,AA		41.3256,45.0068,45.9557		67/101	85808737	5977,7029	2203	4300	6503	SO:0001819	synonymous_variant	8673	exon3			GGCTCGAAAATTC	AF053233	CCDS1979.1	2p12-p11.2	2013-02-13	2012-10-17		ENSG00000118640	ENSG00000118640		"""Vesicle-associated membrane proteins"""	12647	protein-coding gene	gene with protein product	"""endobrevin"""	603177				9878266, 9614193	Standard	NM_003761		Approved	EDB	uc002spt.4	Q9BV40	OTTHUMG00000130180	ENST00000263864.5:c.201A>G	2.37:g.85808737A>G		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	158	108	0.683544	NM_003761	O60625|Q53SP9|Q6IB09	Silent	SNP	ENST00000263864.5	37	CCDS1979.1																																																																																			A|0.547;G|0.453	0.453	strong		0.468	VAMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252498.3	NM_003761	
KIAA0753	9851	hgsc.bcm.edu	37	17	6493198	6493198	+	Missense_Mutation	SNP	T	T	C	rs386794938|rs1443417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6493198T>C	ENST00000361413.3	-	18	3045	c.2687A>G	c.(2686-2688)cAg>cGg	p.Q896R	KIAA0753_ENST00000572370.1_Missense_Mutation_p.Q597R|KIAA0753_ENST00000575027.1_5'UTR|KIAA0753_ENST00000589033.1_Missense_Mutation_p.Q352R|KIAA0753_ENST00000542606.1_Missense_Mutation_p.Q597R	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	896			Q -> R (in dbSNP:rs1443417). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		GATGCTGTGCTGCATACCCGG	0.527													C|||	3450	0.688898	0.8253	0.6787	5008	,	,		18401	0.7093		0.5477	False		,,,				2504	0.636				p.Q896R		Atlas-SNP	.											.	KIAA0753	63	.	0			c.A2687G						PASS	.	C	ARG/GLN	2960,840		1155,650,95	102.0	102.0	102.0		2687	2.4	0.9	17	dbSNP_88	102	4733,3513		1360,2013,750	yes	missense	KIAA0753	NM_014804.2	43	2515,2663,845	CC,CT,TT		42.6025,22.1053,36.1365	benign	896/968	6493198	7693,4353	1900	4123	6023	SO:0001583	missense	9851	exon18			CTGTGCTGCATAC		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.2687A>G	17.37:g.6493198T>C	ENSP00000355250:p.Gln896Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	1437	0.657967032967033	402	0.8170731707317073	243	0.6712707182320442	390	0.6818181818181818	402	0.5303430079155673	C	0.533	-0.857067	0.02630	0.778947	0.573975	ENSG00000198920	ENST00000361413;ENST00000542606;ENST00000542826	T;T	0.40756	1.02;1.02	5.64	2.43	0.29744	.	0.425305	0.24465	N	0.038289	T	0.00012	0.0000	N	0.00419	-1.52	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.23904	-1.0175	9	0.21014	T	0.42	-1.7375	5.4199	0.16394	0.5144:0.3093:0.0:0.1764	rs1443417;rs17804140;rs52825594;rs60861383;rs1443417	896	Q2KHM9	K0753_HUMAN	R	896;597;352	ENSP00000355250:Q896R;ENSP00000444634:Q597R	ENSP00000355250:Q896R	Q	-	2	0	KIAA0753	6433922	0.796000	0.28864	0.892000	0.35008	0.127000	0.20565	1.060000	0.30530	0.088000	0.17205	-0.119000	0.15052	CAG	T|0.340;C|0.660	0.660	strong		0.527	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:17527386A>G	ENST00000318024.4	-	16	1393				USH1C_ENST00000527020.1_Intron|USH1C_ENST00000005226.7_Silent_p.S708S|USH1C_ENST00000529563.1_Intron|USH1C_ENST00000527720.1_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		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	80	41	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	
ARPP21	10777	hgsc.bcm.edu	37	3	35725250	35725250	+	Silent	SNP	C	C	T	rs969818	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:35725250C>T	ENST00000187397.4	+	5	660	c.204C>T	c.(202-204)agC>agT	p.S68S	ARPP21_ENST00000438071.1_Silent_p.S68S|ARPP21_ENST00000412048.1_Silent_p.S68S|ARPP21_ENST00000337271.5_Silent_p.S68S|ARPP21_ENST00000396481.2_Silent_p.S68S|ARPP21_ENST00000417925.1_Silent_p.S68S|ARPP21_ENST00000444190.1_Silent_p.S68S|ARPP21_ENST00000436702.1_Silent_p.S68S|ARPP21_ENST00000427542.1_Silent_p.S68S|ARPP21_ENST00000396482.2_Silent_p.S68S|ARPP21_ENST00000441454.1_Silent_p.S68S|ARPP21_ENST00000428373.1_Silent_p.S68S|ARPP21_ENST00000474696.1_Silent_p.S68S|ARPP21_ENST00000458225.1_Silent_p.S68S|ARPP21_ENST00000432682.1_Silent_p.S68S	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	68					cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						TGACTCGCAGCCTTGCTGTCT	0.453													T|||	3605	0.719848	0.8737	0.562	5008	,	,		16773	0.6508		0.6243	False		,,,				2504	0.7935				p.S68S		Atlas-SNP	.											.	ARPP21	153	.	0			c.C204T						PASS	.	T	,,,	3693,711	294.4+/-283.1	1550,593,59	63.0	56.0	58.0		204,204,204,204	-3.4	1.0	3	dbSNP_86	58	5574,3026	463.9+/-366.1	1828,1918,554	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARPP21	NM_001025068.1,NM_001025069.1,NM_016300.4,NM_198399.1	,,,	3378,2511,613	TT,TC,CC		35.186,16.1444,28.7373	,,,	68/90,68/90,68/813,68/90	35725250	9267,3737	2202	4300	6502	SO:0001819	synonymous_variant	10777	exon4			TCGCAGCCTTGCT	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"""R3H domain containing 3"""	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.204C>T	3.37:g.35725250C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_001267618	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Silent	SNP	ENST00000187397.4	37	CCDS2661.1																																																																																			T|0.701;C|0.299;A|0.000	0.701	strong		0.453	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399	
ZNF138	7697	hgsc.bcm.edu	37	7	64291405	64291405	+	Intron	SNP	G	G	A	rs118016824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:64291405G>A	ENST00000359735.3	+	4	384				ZNF138_ENST00000397136.2_Intron|ZNF138_ENST00000430838.2_Intron|ZNF138_ENST00000494380.1_Missense_Mutation_p.G99E|ZNF138_ENST00000440155.2_Intron|ZNF138_ENST00000307355.7_Intron|ZNF138_ENST00000437743.1_Intron|ZNF138_ENST00000440598.1_Intron	NM_001271637.1|NM_001271639.1	NP_001258566.1|NP_001258568.1	P52744	ZN138_HUMAN	zinc finger protein 138						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)			kidney(1)|large_intestine(3)|lung(2)|stomach(1)	7		Lung NSC(55;0.0795)|all_lung(88;0.18)				TATGTCATGGGAAACAGAAAC	0.383													G|||	101	0.0201677	0.0008	0.0893	5008	,	,		18729	0.0		0.007	False		,,,				2504	0.0317				p.G99E		Atlas-SNP	.											.	ZNF138	43	.	0			c.G296A						PASS	.	G	GLU/GLY,	2,1382		0,2,690	112.0	84.0	92.0		296,	0.2	0.0	7	dbSNP_132	92	25,3157		0,25,1566	yes	missense,intron	ZNF138	NM_001160183.1,NM_006524.2	98,	0,27,2256	AA,AG,GG		0.7857,0.1445,0.5913	,	99/127,	64291405	27,4539	692	1591	2283	SO:0001627	intron_variant	7697	exon4			TCATGGGAAACAG	U09847	CCDS34645.1, CCDS34645.2, CCDS55115.1, CCDS64659.1, CCDS64660.1, CCDS64661.1, CCDS75607.1	7q11.21	2013-01-08	2005-07-11		ENSG00000197008	ENSG00000197008		"""Zinc fingers, C2H2-type"", ""-"""	12922	protein-coding gene	gene with protein product		604080	"""zinc finger protein 138 (clone pHZ-32)"""				Standard	NM_006524		Approved	pHZ-32	uc031sxl.1	P52744	OTTHUMG00000156603	ENST00000359735.3:c.38-424G>A	7.37:g.64291405G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_001160183	B4DFX2|B4DP87|E9PHI7|E9PHK7	Missense_Mutation	SNP	ENST00000359735.3	37		36	0.016483516483516484	0	0.0	30	0.08287292817679558	0	0.0	6	0.0079155672823219	.	5.910	0.352006	0.11182	0.001445	0.007857	ENSG00000197008	ENST00000494380	T	0.01113	5.32	0.225	0.225	0.15325	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.09310	N	0.999997	D	0.59357	0.985	P	0.47827	0.558	T	0.58457	-0.7633	9	0.37606	T	0.19	.	6.2336	0.20750	3.0E-4:0.0:0.9997:0.0	.	99	E9PHK7	.	E	99	ENSP00000419197:G99E	ENSP00000419197:G99E	G	+	2	0	ZNF138	63928840	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.215000	0.17562	0.300000	0.22699	0.305000	0.20034	GGA	G|0.987;A|0.013	0.013	strong		0.383	ZNF138-201	KNOWN	basic	protein_coding	protein_coding		NM_006524	
TLK1	9874	hgsc.bcm.edu	37	2	171910313	171910313	+	Silent	SNP	C	C	T	rs11553951	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:171910313C>T	ENST00000431350.2	-	8	1094	c.690G>A	c.(688-690)caG>caA	p.Q230Q	TLK1_ENST00000486857.1_5'UTR|TLK1_ENST00000360843.3_Silent_p.Q251Q|TLK1_ENST00000434911.2_Silent_p.Q134Q|TLK1_ENST00000521943.1_Silent_p.Q182Q|TLK1_ENST00000442919.2_Silent_p.Q182Q			Q9UKI8	TLK1_HUMAN	tousled-like kinase 1	230				Q -> L (in Ref. 1; BAA20562). {ECO:0000305}.	cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of chromatin assembly or disassembly (GO:0001672)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|liver(3)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	33						TTTCCAGGTCCTGGATTTTAT	0.313													C|||	563	0.11242	0.0189	0.1484	5008	,	,		18239	0.0437		0.2783	False		,,,				2504	0.1135				p.Q230Q		Atlas-SNP	.											.	TLK1	134	.	0			c.G690A						PASS	.	C	,,	241,4163	141.9+/-177.2	1,239,1962	162.0	174.0	170.0		546,402,690	-0.4	1.0	2	dbSNP_120	170	2326,6274	388.4+/-342.6	311,1704,2285	no	coding-synonymous,coding-synonymous,coding-synonymous	TLK1	NM_001136554.1,NM_001136555.1,NM_012290.4	,,	312,1943,4247	TT,TC,CC		27.0465,5.4723,19.7401	,,	182/719,134/671,230/767	171910313	2567,10437	2202	4300	6502	SO:0001819	synonymous_variant	9874	exon8			CAGGTCCTGGATT	AB004885	CCDS2241.1, CCDS46447.1, CCDS46448.1	2q31.1	2010-04-19			ENSG00000198586	ENSG00000198586			11841	protein-coding gene	gene with protein product		608438				9427565, 12660173	Standard	NM_012290		Approved	KIAA0137, PKU-BETA	uc002ugp.2	Q9UKI8	OTTHUMG00000132243	ENST00000431350.2:c.690G>A	2.37:g.171910313C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	33	0.362637	NM_012290	B3KR15|B4DX87|Q14150|Q8N591|Q9NYH2|Q9Y4F6	Silent	SNP	ENST00000431350.2	37	CCDS2241.1																																																																																			C|0.814;T|0.186	0.186	strong		0.313	TLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255314.1	NM_012290	
QRICH2	84074	hgsc.bcm.edu	37	17	74289500	74289500	+	Silent	SNP	G	G	A	rs3803737	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74289500G>A	ENST00000262765.5	-	4	989	c.810C>T	c.(808-810)gtC>gtT	p.V270V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	270										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						GCTCATCCACGACAAATGGTA	0.517													G|||	2351	0.469449	0.7073	0.3098	5008	,	,		26072	0.5724		0.2753	False		,,,				2504	0.3548				p.V270V		Atlas-SNP	.											.	QRICH2	143	.	0			c.C810T						PASS	.	G		2925,1481	679.3+/-403.7	976,973,254	138.0	115.0	122.0		810	0.2	0.0	17	dbSNP_107	122	2483,6117	406.9+/-349.0	347,1789,2164	no	coding-synonymous	QRICH2	NM_032134.1		1323,2762,2418	AA,AG,GG		28.8721,33.6133,41.5808		270/1664	74289500	5408,7598	2203	4300	6503	SO:0001819	synonymous_variant	84074	exon4			ATCCACGACAAAT	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.810C>T	17.37:g.74289500G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			G|0.557;A|0.443	0.443	strong		0.517	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
DPCD	25911	hgsc.bcm.edu	37	10	103361088	103361088	+	Silent	SNP	C	C	T	rs7874	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:103361088C>T	ENST00000370151.4	+	4	448	c.399C>T	c.(397-399)aaC>aaT	p.N133N	MIR3158-1_ENST00000583596.1_RNA|DPCD_ENST00000370148.2_Silent_p.N133N|DPCD_ENST00000370147.1_Silent_p.N133N	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	133					determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|lateral ventricle development (GO:0021670)|left/right pattern formation (GO:0060972)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)	nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5						GAACAACCAACAAGAAGTGAG	0.517													c|||	500	0.0998403	0.0408	0.1369	5008	,	,		13063	0.0347		0.2217	False		,,,				2504	0.0951				p.N133N		Atlas-SNP	.											.	DPCD	15	.	0			c.C399T						PASS	.			329,4077	174.4+/-204.0	14,301,1888	152.0	130.0	137.0		399	5.9	1.0	10	dbSNP_52	137	1968,6632	346.9+/-326.4	236,1496,2568	no	coding-synonymous	DPCD	NM_015448.1		250,1797,4456	TT,TC,CC		22.8837,7.4671,17.6611		133/204	103361088	2297,10709	2203	4300	6503	SO:0001819	synonymous_variant	25911	exon4			AACCAACAAGAAG		CCDS7514.1	10q24.32	2012-05-03			ENSG00000166171	ENSG00000166171			24542	protein-coding gene	gene with protein product						14630615	Standard	NM_015448		Approved	DKFZP566F084, RP11-529I10.4	uc001ktn.3	Q9BVM2	OTTHUMG00000018934	ENST00000370151.4:c.399C>T	10.37:g.103361088C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_015448	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Silent	SNP	ENST00000370151.4	37	CCDS7514.1																																																																																			C|0.854;T|0.146	0.146	strong		0.517	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049958.2		
IL7R	3575	hgsc.bcm.edu	37	5	35874575	35874575	+	Missense_Mutation	SNP	C	C	T	rs6897932	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:35874575C>T	ENST00000303115.3	+	6	860	c.731C>T	c.(730-732)aCc>aTc	p.T244I	IL7R_ENST00000343305.4_Intron|IL7R_ENST00000506850.1_Intron	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	244			T -> I (in dbSNP:rs6897932). {ECO:0000269|PubMed:17660817, ECO:0000269|PubMed:9843216, ECO:0000269|Ref.5}.		B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)	p.T244_I245insPPVCSVT(2)|p.T244I(2)|p.T244>NECS(1)|p.T244>KKCTN(1)|p.L243_T244insMCP(1)|p.T244_I245insRPCG(1)|p.P240_T244>RFCPH(1)|p.T244_I245insCPT(1)|p.L243_T244insMPEQDCP(1)|p.T244_I245insLPCVY(1)|p.L243_T244>PIYRCVL(1)|p.L242_S246>PQGGC(1)|p.P240_S246>LKC(1)|p.L242_T243>CGIREI(1)|p.L243_T244>PCPL(1)|p.P240_S246>LQSC(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			ATCTTACTAACCATCAGCATT	0.443			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						C|||	864	0.172524	0.0658	0.183	5008	,	,		20099	0.1687		0.2714	False		,,,				2504	0.2117				p.T244I		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	IL7R,NS,carcinoma,-1,3	IL7R	200	3	18	Insertion - In frame(7)|Complex - insertion inframe(5)|Substitution - Missense(2)|Complex - deletion inframe(2)|Complex - compound substitution(2)	haematopoietic_and_lymphoid_tissue(17)|stomach(1)	c.C731T	GRCh37	CM074279	IL7R	M	rs6897932	PASS	.	C	ILE/THR	484,3922	227.5+/-242.7	28,428,1747	251.0	218.0	229.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	731	-2.5	0.0	5	dbSNP_116	229	2300,6300	386.4+/-341.8	296,1708,2296	yes	missense	IL7R	NM_002185.2	89	324,2136,4043	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	26.7442,10.985,21.4055	benign	244/460	35874575	2784,10222	2203	4300	6503	SO:0001583	missense	3575	exon6			TACTAACCATCAG	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.731C>T	5.37:g.35874575C>T	ENSP00000306157:p.Thr244Ile	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	297	137	0.461279	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	417	0.19093406593406592	32	0.06504065040650407	72	0.19889502762430938	102	0.17832167832167833	211	0.2783641160949868	C	7.247	0.602421	0.13939	0.10985	0.267442	ENSG00000168685	ENST00000303115	D	0.96104	-3.91	5.97	-2.49	0.06403	.	1.508970	0.03292	N	0.187788	T	0.00039	0.0001	N	0.20766	0.605	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.55964	-0.8057	9	0.06757	T	0.87	-26.1859	7.3691	0.26792	0.0:0.3863:0.1198:0.4939	rs6897932;rs57894527;rs6897932	244	P16871	IL7RA_HUMAN	I	244	ENSP00000306157:T244I	ENSP00000306157:T244I	T	+	2	0	IL7R	35910332	0.000000	0.05858	0.000000	0.03702	0.889000	0.51656	-0.450000	0.06803	-0.378000	0.07918	0.655000	0.94253	ACC	C|0.810;T|0.190	0.190	strong		0.443	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
NXPE1	120400	hgsc.bcm.edu	37	11	114393652	114393652	+	Missense_Mutation	SNP	C	C	T	rs10891692	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:114393652C>T	ENST00000424269.1	-	4	1056	c.1057G>A	c.(1057-1059)Gga>Aga	p.G353R	NXPE1_ENST00000251921.2_Missense_Mutation_p.G211R|NXPE1_ENST00000536271.1_Missense_Mutation_p.G69R			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	353			G -> R (in dbSNP:rs10891692).			extracellular region (GO:0005576)											GTAGAGTCTCCCAGGAGGTAA	0.358													C|||	1864	0.372204	0.2534	0.3069	5008	,	,		18462	0.6687		0.337	False		,,,				2504	0.3098				p.G211R		Atlas-SNP	.											FAM55A,NS,adenoma,0,1	NXPE1	8	1	0			c.G631A						PASS	.	C	ARG/GLY	1194,3208	416.5+/-337.6	159,876,1166	97.0	85.0	89.0		631	4.5	1.0	11	dbSNP_120	89	2963,5629	459.2+/-364.8	496,1971,1829	yes	missense	FAM55A	NM_152315.2	125	655,2847,2995	TT,TC,CC		34.4856,27.124,31.9917	probably-damaging	211/406	114393652	4157,8837	2201	4296	6497	SO:0001583	missense	120400	exon5			AGTCTCCCAGGAG	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.1057G>A	11.37:g.114393652C>T	ENSP00000411690:p.Gly353Arg	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		864	0.3956043956043956	121	0.2459349593495935	110	0.30386740331491713	380	0.6643356643356644	253	0.3337730870712401	C	22.8	4.332185	0.81801	0.27124	0.344856	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.73258	-0.73;-0.73;-0.73	4.46	4.46	0.54185	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	M	0.93594	3.435	0.23784	P	0.99685252	D	0.89917	1.0	D	0.97110	1.0	T	0.52503	-0.8567	9	0.87932	D	0	.	15.4186	0.74991	0.0:1.0:0.0:0.0	rs10891692;rs57749610;rs10891692	353	Q8N323	FA55A_HUMAN	R	69;211;353	ENSP00000445200:G69R;ENSP00000251921:G211R;ENSP00000411690:G353R	ENSP00000251921:G211R	G	-	1	0	FAM55A	113898862	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.585000	0.67497	2.408000	0.81797	0.650000	0.86243	GGA	C|0.645;T|0.355	0.355	strong		0.358	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
HSD17B11	51170	hgsc.bcm.edu	37	4	88293887	88293887	+	Silent	SNP	G	G	A	rs6531985	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88293887G>A	ENST00000358290.4	-	4	846	c.531C>T	c.(529-531)gtC>gtT	p.V177V	HSD17B11_ENST00000507518.1_5'UTR|HSD17B11_ENST00000507286.1_Silent_p.V133V	NM_016245.3	NP_057329.2	Q8NBQ5	DHB11_HUMAN	hydroxysteroid (17-beta) dehydrogenase 11	177					androgen catabolic process (GO:0006710)|steroid biosynthetic process (GO:0006694)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|lipid particle (GO:0005811)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|steroid dehydrogenase activity (GO:0016229)			cervix(1)|endometrium(4)|kidney(2)|lung(2)|ovary(2)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)		AGGGGACCGAGACATGTCCAG	0.413													A|||	1429	0.285343	0.5764	0.2882	5008	,	,		14982	0.005		0.327	False		,,,				2504	0.136				p.V177V		Atlas-SNP	.											.	HSD17B11	28	.	0			c.C531T						PASS	.	A		2371,2035	564.7+/-381.5	634,1103,466	159.0	130.0	140.0		531	-8.2	0.0	4	dbSNP_116	140	2700,5900	682.1+/-403.8	406,1888,2006	no	coding-synonymous	HSD17B11	NM_016245.3		1040,2991,2472	AA,AG,GG		31.3953,46.187,38.9897		177/301	88293887	5071,7935	2203	4300	6503	SO:0001819	synonymous_variant	51170	exon4			GACCGAGACATGT	AF126780	CCDS3619.1	4q22.1	2011-09-20	2006-11-22	2006-11-22	ENSG00000198189	ENSG00000198189	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	22960	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 2"", ""short chain dehydrogenase/reductase family 16C, member 2"""	612831	"""dehydrogenase/reductase (SDR family) member 8"""	DHRS8		11165019, 12697717, 19027726	Standard	XM_006714232		Approved	RetSDR2, 17-BETA-HSD11, 17-BETA-HSDXI, PAN1B, SDR16C2	uc003hqp.2	Q8NBQ5	OTTHUMG00000130594	ENST00000358290.4:c.531C>T	4.37:g.88293887G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_016245	Q96HF6|Q9UKU4	Silent	SNP	ENST00000358290.4	37	CCDS3619.1																																																																																			G|0.645;A|0.355	0.355	strong		0.413	HSD17B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253041.1	NM_016245	
PRDM9	56979	hgsc.bcm.edu	37	5	23527324	23527324	+	Silent	SNP	T	T	A	rs200723191	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:23527324T>A	ENST00000296682.3	+	11	2309	c.2127T>A	c.(2125-2127)acT>acA	p.T709T		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	709					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						TCCTCCTCACTCACCAGAGGA	0.582										HNSCC(3;0.000094)			T|||	492	0.0982428	0.2398	0.0893	5008	,	,		20918	0.0387		0.0298	False		,,,				2504	0.045				p.T709T		Atlas-SNP	.											PRDM9,NS,carcinoma,+1,1	PRDM9	344	1	0			c.T2127A						PASS	.						16.0	15.0	15.0					5																	23527324		1813	3616	5429	SO:0001819	synonymous_variant	56979	exon11			CCTCACTCACCAG	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.2127T>A	5.37:g.23527324T>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	14	0.191781	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																			T|0.988;A|0.012	0.012	strong		0.582	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
CNNM1	26507	hgsc.bcm.edu	37	10	101147720	101147720	+	Silent	SNP	C	C	T	rs17490682	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101147720C>T	ENST00000356713.4	+	8	2773	c.2484C>T	c.(2482-2484)gaC>gaT	p.D828D	CNNM1_ENST00000370534.4_Silent_p.D484D|CNNM1_ENST00000370528.3_Silent_p.D757D|CNNM1_ENST00000446890.1_Silent_p.D757D	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	828					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		CTAAGGATGACCCCGCCATCA	0.637													C|||	73	0.0145767	0.0008	0.0159	5008	,	,		18692	0.001		0.0457	False		,,,				2504	0.0143				p.D828D		Atlas-SNP	.											.	CNNM1	101	.	0			c.C2484T						PASS	.	C		34,4372	36.8+/-68.6	0,34,2169	38.0	42.0	41.0		2484	3.1	1.0	10	dbSNP_123	41	360,8240	118.3+/-177.8	4,352,3944	yes	coding-synonymous	CNNM1	NM_020348.2		4,386,6113	TT,TC,CC		4.186,0.7717,3.0294		828/952	101147720	394,12612	2203	4300	6503	SO:0001819	synonymous_variant	26507	exon8			GGATGACCCCGCC	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2484C>T	10.37:g.101147720C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	37	CCDS7478.2																																																																																			C|0.972;T|0.028	0.028	strong		0.637	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
NCOA3	8202	hgsc.bcm.edu	37	20	46279827	46279827	+	Silent	SNP	G	G	A	rs6018623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:46279827G>A	ENST00000371998.3	+	20	3944	c.3753G>A	c.(3751-3753)caG>caA	p.Q1251Q	NCOA3_ENST00000341724.6_Silent_p.Q1177Q|NCOA3_ENST00000372004.3_Silent_p.Q1247Q|NCOA3_ENST00000371997.3_Silent_p.Q1242Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1251	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcagcagcagcagcaac	0.552													G|||	876	0.17492	0.1906	0.1571	5008	,	,		14950	0.1617		0.1928	False		,,,				2504	0.1616				p.Q1251Q		Atlas-SNP	.											.	NCOA3	156	.	0			c.G3753A						PASS	.	G	,,,	850,3556	326.4+/-299.6	85,680,1438	49.0	55.0	53.0		3750,3726,3741,3753	4.4	1.0	20	dbSNP_114	53	959,7641	191.8+/-238.0	90,779,3431	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	175,1459,4869	AA,AG,GG		11.1512,19.2919,13.909	,,,	1250/1424,1242/1416,1247/1421,1251/1425	46279827	1809,11197	2203	4300	6503	SO:0001819	synonymous_variant	8202	exon20			GCAGCAGCAGCAG	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3753G>A	20.37:g.46279827G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			G|0.861;A|0.139	0.139	strong		0.552	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
PRTN3	5657	hgsc.bcm.edu	37	19	844020	844020	+	Missense_Mutation	SNP	G	G	A	rs351111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:844020G>A	ENST00000234347.5	+	3	401	c.355G>A	c.(355-357)Gtt>Att	p.V119I	PRTN3_ENST00000544537.2_Missense_Mutation_p.V78I	NM_002777.3	NP_002768.3	P24158	PRTN3_HUMAN	proteinase 3	119	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		V -> I (in dbSNP:rs351111). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1681549, ECO:0000269|PubMed:2377228, ECO:0000269|PubMed:2598267, ECO:0000269|PubMed:7539799, ECO:0000269|PubMed:9924693, ECO:0000269|Ref.3}.		collagen catabolic process (GO:0030574)|mature dendritic cell differentiation (GO:0097029)|negative regulation of phagocytosis (GO:0050765)|positive regulation of cell proliferation (GO:0008284)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|ovary(2)|urinary_tract(1)	4		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		ACTGAACGACGTTCTCCTCAT	0.647													g|||	2223	0.44389	0.5333	0.4971	5008	,	,		9006	0.3512		0.4006	False		,,,				2504	0.4254				p.V119I		Atlas-SNP	.											.	PRTN3	9	.	0			c.G355A						PASS	.		ILE/VAL	2319,2083		616,1087,498	33.0	34.0	34.0		355	-3.6	0.0	19	dbSNP_79	34	3531,5067		711,2109,1479	yes	missense	PRTN3	NM_002777.3	29	1327,3196,1977	AA,AG,GG		41.0677,47.3194,45.0	benign	119/257	844020	5850,7150	2201	4299	6500	SO:0001583	missense	5657	exon3			AACGACGTTCTCC		CCDS32860.1	19p13.3	2008-07-31	2008-07-31			ENSG00000196415			9495	protein-coding gene	gene with protein product	"""myeloblastin"", ""serine proteinase, neutrophil"", ""Wegener granulomatosis autoantigen"""	177020				2258701	Standard	NM_002777		Approved	PR-3, ACPA, C-ANCA, AGP7, MBT, P29	uc002lqa.1	P24158		ENST00000234347.5:c.355G>A	19.37:g.844020G>A	ENSP00000234347:p.Val119Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_002777	P15637|P18078|Q4VB08|Q4VB09|Q6LBM7|Q6LBN2|Q9UD25|Q9UQD8	Missense_Mutation	SNP	ENST00000234347.5	37	CCDS32860.1	964	0.4413919413919414	250	0.508130081300813	185	0.511049723756906	213	0.3723776223776224	316	0.41688654353562005	g	0.118	-1.128857	0.01756	0.526806	0.410677	ENSG00000196415	ENST00000234347;ENST00000544537	T	0.49139	0.79	2.73	-3.59	0.04583	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.00473	-1.45	0.80722	P	0.0	B	0.30406	0.278	B	0.28139	0.086	T	0.31475	-0.9942	8	0.02654	T	1	.	7.6584	0.28389	0.6738:0.0:0.3262:0.0	rs351111;rs600071;rs1126597;rs3181721;rs17366042;rs17400579;rs58626854;rs351111	119	P24158	PRTN3_HUMAN	I	119;78	ENSP00000234347:V119I	ENSP00000234347:V119I	V	+	1	0	PRTN3	795020	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.066000	0.03454	-0.588000	0.05882	-0.348000	0.07805	GTT	G|0.546;A|0.454	0.454	strong		0.647	PRTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457888.2	NM_002777	
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 GAIIx	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		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	37	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	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923266	43923266	+	Missense_Mutation	SNP	G	G	A	rs62054815	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43923266G>A	ENST00000329196.5	+	1	1011	c.994G>A	c.(994-996)Gca>Aca	p.A332T	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	332						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										GAGCCTGTGCGCAACCGTGAT	0.652													A|||	431	0.0860623	0.0151	0.1571	5008	,	,		19554	0.001		0.2396	False		,,,				2504	0.0613				p.A332T		Atlas-SNP	.											.	.	.	.	0			c.G994A						PASS	.	A	THR/ALA	203,4203	805.8+/-415.8	5,193,2005	57.0	50.0	52.0		994	-10.4	0.0	17	dbSNP_129	52	1928,6672	725.8+/-406.6	221,1486,2593	yes	missense	IMP5	NM_175882.2	58	226,1679,4598	AA,AG,GG		22.4186,4.6074,16.3847	benign	332/685	43923266	2131,10875	2203	4300	6503	SO:0001583	missense	162540	exon1			CTGTGCGCAACCG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.994G>A	17.37:g.43923266G>A	ENSP00000332488:p.Ala332Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	254	0.1163003663003663	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	175	0.23087071240105542	A	0.550	-0.850026	0.02651	0.046074	0.224186	ENSG00000185294	ENST00000329196	T	0.16743	2.32	5.18	-10.4	0.00318	.	1.578760	0.03901	N	0.280320	T	0.00012	0.0000	N	0.16166	0.38	0.80722	P	0.0	B	0.24483	0.104	B	0.21708	0.036	T	0.37957	-0.9683	9	0.33141	T	0.24	-8.7503	15.2695	0.73689	0.7025:0.1361:0.1614:0.0	rs62054815	332	Q8IUH8	IMP5_HUMAN	T	332	ENSP00000332488:A332T	ENSP00000332488:A332T	A	+	1	0	AC217771.1	41279046	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.159000	0.01280	-4.847000	0.00029	-3.352000	0.00042	GCA	A|0.120;C|0.240	0.120	strong		0.652	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
SEC14L5	9717	hgsc.bcm.edu	37	16	5050897	5050897	+	Silent	SNP	G	G	C	rs2286966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:5050897G>C	ENST00000251170.7	+	10	1281	c.1101G>C	c.(1099-1101)ggG>ggC	p.G367G		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	367	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						GGTGTGAGGGGAGCACAAGGC	0.612													G|||	1990	0.397364	0.413	0.4885	5008	,	,		17758	0.2609		0.4742	False		,,,				2504	0.3732				p.G367G		Atlas-SNP	.											.	SEC14L5	79	.	0			c.G1101C						PASS	.	G		1707,2497		362,983,757	25.0	29.0	27.0		1101	-0.4	1.0	16	dbSNP_100	27	4018,4450		963,2092,1179	no	coding-synonymous	SEC14L5	NM_014692.1		1325,3075,1936	CC,CG,GG		47.4492,40.6042,45.1783		367/697	5050897	5725,6947	2102	4234	6336	SO:0001819	synonymous_variant	9717	exon10			TGAGGGGAGCACA	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1101G>C	16.37:g.5050897G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	50	29	0.58	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			G|0.589;C|0.411	0.411	strong		0.612	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
OLFM3	118427	hgsc.bcm.edu	37	1	102296279	102296279	+	Silent	SNP	T	T	C	rs10493973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:102296279T>C	ENST00000338858.5	-	3	380	c.381A>G	c.(379-381)aaA>aaG	p.K127K	OLFM3_ENST00000359814.3_Silent_p.K127K|OLFM3_ENST00000536598.1_Silent_p.K32K|OLFM3_ENST00000370103.4_Silent_p.K107K|OLFM3_ENST00000462354.1_5'UTR			Q96PB7	NOE3_HUMAN	olfactomedin 3	127					eye photoreceptor cell development (GO:0042462)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(24)|ovary(3)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	43		all_epithelial(167;1.87e-06)|all_lung(203;8.12e-05)|Lung NSC(277;0.000189)		all cancers(265;0.0843)|Epithelial(280;0.0921)|COAD - Colon adenocarcinoma(174;0.145)		TCTGCCGAAATTTTGCCTTCA	0.383													C|||	736	0.146965	0.2852	0.1081	5008	,	,		18517	0.0079		0.1779	False		,,,				2504	0.0992				p.K107K		Atlas-SNP	.											.	OLFM3	178	.	0			c.A321G						PASS	.	C		1055,3351	724.9+/-409.6	132,791,1280	207.0	199.0	202.0		321	2.5	1.0	1	dbSNP_119	202	1546,7054	746.1+/-407.3	148,1250,2902	no	coding-synonymous	OLFM3	NM_058170.2		280,2041,4182	CC,CT,TT		17.9767,23.9446,19.9985		107/459	102296279	2601,10405	2203	4300	6503	SO:0001819	synonymous_variant	118427	exon3			CCGAAATTTTGCC	AF397392	CCDS30781.1, CCDS72832.1	1p22	2008-05-23			ENSG00000118733	ENSG00000118733			17990	protein-coding gene	gene with protein product	"""optimedin"""	607567				12019210, 16115881	Standard	NM_001288821		Approved	NOE3	uc001dug.2	Q96PB7	OTTHUMG00000010941	ENST00000338858.5:c.381A>G	1.37:g.102296279T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_058170	Q5T3V6|Q6IMI7|Q6IMI8|Q6IMI9|Q6IMJ1|Q8TBG1|Q96PB2|Q96PB3|Q96PB4|Q96PB5|Q96PB6	Silent	SNP	ENST00000338858.5	37																																																																																				T|0.824;C|0.176	0.176	strong		0.383	OLFM3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000030142.1		
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 GAIIx	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_ENST00000422508.2_Missense_Mutation_p.P493L|CD109_ENST00000437994.2_Missense_Mutation_p.P570L			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	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	43	23	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	
UNC13C	440279	hgsc.bcm.edu	37	15	54847677	54847677	+	Silent	SNP	C	C	T	rs11639005	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:54847677C>T	ENST00000260323.11	+	28	5925	c.5925C>T	c.(5923-5925)tgC>tgT	p.C1975C	UNC13C_ENST00000545554.1_Silent_p.C1975C|UNC13C_ENST00000537900.1_Silent_p.C1973C	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1975	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		CAAGACAATGCGCTATAATGG	0.453													C|||	2050	0.409345	0.1233	0.464	5008	,	,		18348	0.5427		0.4423	False		,,,				2504	0.5859				p.C1975C		Atlas-SNP	.											.	UNC13C	674	.	0			c.C5925T						PASS	.	C		680,3214		57,566,1324	80.0	77.0	78.0		5925	-4.4	0.0	15	dbSNP_120	78	3562,4696		787,1988,1354	no	coding-synonymous	UNC13C	NM_001080534.1		844,2554,2678	TT,TC,CC		43.1339,17.4628,34.9078		1975/2215	54847677	4242,7910	1947	4129	6076	SO:0001819	synonymous_variant	440279	exon27			ACAATGCGCTATA	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5925C>T	15.37:g.54847677C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	77	0.987179	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																			C|0.625;T|0.375	0.375	strong		0.453	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
PTX3	5806	hgsc.bcm.edu	37	3	157155314	157155314	+	Missense_Mutation	SNP	C	C	A	rs3816527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:157155314C>A	ENST00000295927.3	+	2	288	c.143C>A	c.(142-144)gCc>gAc	p.A48D	VEPH1_ENST00000392832.2_Intron|VEPH1_ENST00000392833.2_Intron|VEPH1_ENST00000543418.1_Intron|VEPH1_ENST00000362010.2_Intron	NM_002852.3	NP_002843.2	P26022	PTX3_HUMAN	pentraxin 3, long	48			A -> D (in dbSNP:rs3816527). {ECO:0000269|PubMed:1429570, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7679696, ECO:0000269|PubMed:8131794}.		inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of viral entry into host cell (GO:0046597)|opsonization (GO:0008228)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phagocytosis (GO:0050766)|response to yeast (GO:0001878)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	(1->3)-beta-D-glucan binding (GO:0001872)|complement component C1q binding (GO:0001849)|virion binding (GO:0046790)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)	10			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			ACGCCGTGCGCCTGCGGTCAG	0.602													A|||	3579	0.714657	0.7436	0.7176	5008	,	,		17859	0.7569		0.6024	False		,,,				2504	0.7454				p.A48D		Atlas-SNP	.											.	PTX3	27	.	0			c.C143A						PASS	.	A	,,ASP/ALA,	3146,1122		1188,770,176	12.0	11.0	11.0		,,143,	3.5	1.0	3	dbSNP_107	11	4869,3543		1514,1841,851	yes	intron,intron,missense,intron	PTX3,VEPH1	NM_001167911.1,NM_001167912.1,NM_002852.3,NM_024621.2	,,126,	2702,2611,1027	AA,AC,CC		42.1184,26.2887,36.7902	,,benign,	,,48/382,	157155314	8015,4665	2134	4206	6340	SO:0001583	missense	5806	exon2			CGTGCGCCTGCGG	X63613	CCDS3180.1	3q25	2010-03-11	2010-03-11		ENSG00000163661	ENSG00000163661			9692	protein-coding gene	gene with protein product		602492	"""pentaxin-related gene, rapidly induced by IL-1 beta"", ""tumor necrosis factor, alpha-induced protein 5"", ""pentraxin-related gene, rapidly induced by IL-1 beta"""	TNFAIP5		1429570	Standard	NM_002852		Approved	TSG-14	uc003fbl.4	P26022	OTTHUMG00000158750	ENST00000295927.3:c.143C>A	3.37:g.157155314C>A	ENSP00000295927:p.Ala48Asp	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_002852	B2R6T6|Q38M82	Missense_Mutation	SNP	ENST00000295927.3	37	CCDS3180.1	1515	0.6936813186813187	364	0.7398373983739838	245	0.6767955801104972	456	0.7972027972027972	450	0.5936675461741425	A	0.566	-0.843373	0.02671	0.737113	0.578816	ENSG00000163661	ENST00000295927	T	0.06768	3.26	4.66	3.48	0.39840	.	0.693410	0.13134	N	0.411169	T	0.00012	0.0000	N	0.00170	-1.935	0.48830	P	2.8399999999995096E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.33033	-0.9884	9	0.02654	T	1	-8.9853	11.4409	0.50096	0.7121:0.2879:0.0:0.0	rs3816527;rs17857200;rs61677924	48	P26022	PTX3_HUMAN	D	48	ENSP00000295927:A48D	ENSP00000295927:A48D	A	+	2	0	PTX3	158638008	1.000000	0.71417	0.998000	0.56505	0.330000	0.28571	3.669000	0.54561	0.166000	0.19597	-0.363000	0.07495	GCC	C|0.346;A|0.654	0.654	strong		0.602	PTX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352028.1	NM_002852	
AOC1	26	hgsc.bcm.edu	37	7	150557665	150557665	+	Missense_Mutation	SNP	C	C	G	rs1049793	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150557665C>G	ENST00000493429.1	+	6	2517	c.1933C>G	c.(1933-1935)Cac>Gac	p.H645D	AOC1_ENST00000467291.1_Missense_Mutation_p.H645D|AOC1_ENST00000360937.4_Missense_Mutation_p.H645D|AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000416793.2_Missense_Mutation_p.H664D			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	645			H -> D (in dbSNP:rs1049793). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2217167, ECO:0000269|PubMed:8595053, ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)	p.H645D(1)								Amiloride(DB00594)	CGACCCCTGGCACCCGCCCGT	0.617													G|||	2270	0.453275	0.5446	0.3991	5008	,	,		18854	0.4792		0.2694	False		,,,				2504	0.5307				p.H664D		Atlas-SNP	.											ABP1,NS,carcinoma,0,1	ABP1	92	1	1	Substitution - Missense(1)	stomach(1)	c.C1990G	GRCh37	CM073993	ABP1	M	rs1049793	PASS	.	G	ASP/HIS	1945,2241		479,987,627	95.0	109.0	105.0		1933	3.1	1.0	7	dbSNP_86	105	2531,5897		402,1727,2085	yes	missense	ABP1	NM_001091.2	81	881,2714,2712	GG,GC,CC		30.0308,46.4644,35.4844	benign	645/752	150557665	4476,8138	2093	4214	6307	SO:0001583	missense	26	exon4			CCCTGGCACCCGC	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1933C>G	7.37:g.150557665C>G	ENSP00000418614:p.His645Asp	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	20	0.327869	NM_001272072	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	CCDS43679.1	922	0.42216117216117216	267	0.5426829268292683	148	0.4088397790055249	291	0.5087412587412588	216	0.2849604221635884	G	1.200	-0.632801	0.03584	0.464644	0.300308	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000360937;ENST00000487631;ENST00000416793;ENST00000437714	T;T;T;T	0.02916	4.11;4.11;4.11;4.11	5.05	3.07	0.35406	Copper amine oxidase, C-terminal (3);	0.101712	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00042	-2.48	0.40518	P	0.01919800000000005	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.42899	-0.9424	9	0.02654	T	1	-7.9873	13.8505	0.63494	0.0:0.4414:0.5586:0.0	rs1049793;rs3177802;rs17416505;rs17845408;rs17858269;rs1049793	664;645	C9J690;P19801	.;ABP1_HUMAN	D	645;645;645;171;664;521	ENSP00000418614:H645D;ENSP00000418328:H645D;ENSP00000354193:H645D;ENSP00000411613:H664D	ENSP00000354193:H645D	H	+	1	0	ABP1	150188598	0.141000	0.22595	1.000000	0.80357	0.567000	0.35839	0.377000	0.20552	0.521000	0.28445	-0.322000	0.08575	CAC	C|0.600;G|0.400	0.400	strong		0.617	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
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 GAIIx	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_ENST00000274562.9_Silent_p.E593E|LARS_ENST00000510191.1_Silent_p.E566E	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		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	88	45	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	
TAF10	6881	hgsc.bcm.edu	37	11	6636106	6636106	+	5'Flank	SNP	T	T	A	rs1128396	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6636106T>A	ENST00000299424.4	-	0	0				TAF10_ENST00000531760.1_5'Flank|TPP1_ENST00000533371.1_Silent_p.G271G|TPP1_ENST00000299427.6_Silent_p.G514G|TPP1_ENST00000534644.1_5'Flank	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa						chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|perinuclear region of cytoplasm (GO:0048471)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|RNA polymerase binding (GO:0070063)|transcription coactivator activity (GO:0003713)						Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.0481)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CATCAAAGAGTCCTGCCCCAT	0.537													T|||	1158	0.23123	0.23	0.2075	5008	,	,		18533	0.3512		0.161	False		,,,				2504	0.1984				p.G514G		Atlas-SNP	.											.	TPP1	71	.	0			c.A1542T						PASS	.	T		978,3424	367.1+/-318.1	111,756,1334	244.0	266.0	259.0		1542	3.8	1.0	11	dbSNP_86	259	1431,7161	275.0+/-291.5	129,1173,2994	no	coding-synonymous	TPP1	NM_000391.3		240,1929,4328	AA,AT,TT		16.655,22.2172,18.5393		514/564	6636106	2409,10585	2201	4296	6497	SO:0001631	upstream_gene_variant	1200	exon12			AAAGAGTCCTGCC	U13991, U25816	CCDS7769.1	11p15.5-p15.2	2006-11-14	2002-08-29	2001-12-07	ENSG00000166337	ENSG00000166337			11543	protein-coding gene	gene with protein product		600475	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, H, 30kD"""	TAF2H, TAF2A		7923369	Standard	NM_006284		Approved	TAFII30	uc001mej.2	Q12962	OTTHUMG00000133402		11.37:g.6636106T>A	Exception_encountered	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	40	0.606061	NM_000391	O00703|Q13175|Q6FH13	Silent	SNP	ENST00000299424.4	37	CCDS7769.1																																																																																			T|0.785;A|0.215	0.215	strong		0.537	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284	
IL17RA	23765	hgsc.bcm.edu	37	22	17590269	17590269	+	Silent	SNP	C	C	T	rs4819555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:17590269C>T	ENST00000319363.6	+	13	2293	c.2160C>T	c.(2158-2160)ccC>ccT	p.P720P		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	720					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		TCTTCCTCCCCGTGGACCCCG	0.701													T|||	1215	0.242612	0.3767	0.2723	5008	,	,		13793	0.0962		0.2505	False		,,,				2504	0.183				p.P720P		Atlas-SNP	.											.	IL17RA	62	.	0			c.C2160T						PASS	.	T		1441,2959		257,927,1016	20.0	20.0	20.0		2160	-5.0	0.0	22	dbSNP_111	20	2030,6556		256,1518,2519	no	coding-synonymous	IL17RA	NM_014339.5		513,2445,3535	TT,TC,CC		23.6431,32.75,26.7288		720/867	17590269	3471,9515	2200	4293	6493	SO:0001819	synonymous_variant	23765	exon13			CCTCCCCGTGGAC	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"""Interleukins and interleukin receptors"", ""CD molecules"""	5985	protein-coding gene	gene with protein product		605461	"""interleukin 17 receptor"""	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.2160C>T	22.37:g.17590269C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_014339	O43844|Q20WK1	Silent	SNP	ENST00000319363.6	37	CCDS13739.1																																																																																			C|0.753;T|0.247	0.247	strong		0.701	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339	
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 GAIIx	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_ENST00000344227.2_Missense_Mutation_p.S200N|CARD14_ENST00000392434.2_5'Flank|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	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	73	34	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		
IGSF8	93185	hgsc.bcm.edu	37	1	160062727	160062727	+	Silent	SNP	A	A	G	rs2295621	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:160062727A>G	ENST00000368086.1	-	4	1515	c.1299T>C	c.(1297-1299)caT>caC	p.H433H	IGSF8_ENST00000460351.1_5'Flank|IGSF8_ENST00000314485.7_Silent_p.H433H			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	433	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CCTCCCGCACATGTACAGGGA	0.632													G|||	800	0.159744	0.0287	0.2522	5008	,	,		19269	0.2232		0.1879	False		,,,				2504	0.1769				p.H433H		Atlas-SNP	.											.	IGSF8	59	.	0			c.T1299C						PASS	.	G	,	244,4162	772.5+/-413.9	10,224,1969	32.0	37.0	35.0		1299,1299	-0.9	1.0	1	dbSNP_100	35	1826,6774	713.9+/-406.0	189,1448,2663	no	coding-synonymous,coding-synonymous	IGSF8	NM_001206665.2,NM_052868.4	,	199,1672,4632	GG,GA,AA		21.2326,5.5379,15.9157	,	433/614,433/614	160062727	2070,10936	2203	4300	6503	SO:0001819	synonymous_variant	93185	exon4			CCGCACATGTACA	AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.1299T>C	1.37:g.160062727A>G		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Silent	SNP	ENST00000368086.1	37	CCDS1195.1																																																																																			A|0.840;G|0.160	0.160	strong		0.632	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868	
ZBTB44	29068	hgsc.bcm.edu	37	11	130130758	130130758	+	Silent	SNP	G	G	A	rs202193079		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:130130758G>A	ENST00000357899.4	-	2	1283	c.1011C>T	c.(1009-1011)tcC>tcT	p.S337S	ZBTB44_ENST00000530205.1_Silent_p.S337S|ZBTB44_ENST00000525842.1_Silent_p.S337S|ZBTB44_ENST00000397753.1_Silent_p.S337S			Q8NCP5	ZBT44_HUMAN	zinc finger and BTB domain containing 44	337					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)	15	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0192)|Lung(977;0.235)		TACCTATAGAGGAAGACTGTG	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		19065	0.0		0.0	False		,,,				2504	0.001				p.S337S		Atlas-SNP	.											.	ZBTB44	41	.	0			c.C1011T						PASS	.	G		2,3764		0,2,1881	86.0	81.0	83.0		1011	2.6	1.0	11		83	13,8199		0,13,4093	no	coding-synonymous	ZBTB44	NM_014155.4		0,15,5974	AA,AG,GG		0.1583,0.0531,0.1252		337/454	130130758	15,11963	1883	4106	5989	SO:0001819	synonymous_variant	29068	exon2			TATAGAGGAAGAC	AK024659	CCDS44776.1, CCDS73414.1, CCDS73415.1	11q24.3	2013-01-08	2006-09-19	2006-09-19		ENSG00000196323		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	25001	protein-coding gene	gene with protein product			"""BTB (POZ) domain containing 15"""	BTBD15		11042152	Standard	NM_014155		Approved	HSPC063, ZNF851	uc001qgb.4	Q8NCP5		ENST00000357899.4:c.1011C>T	11.37:g.130130758G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	28	0.8	NM_014155	Q6IPT8|Q86VJ7|Q86XX5	Silent	SNP	ENST00000357899.4	37		3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	G|G	4.778|4.778	0.144713|0.144713	0.09134|0.09134	5.31E-4|5.31E-4	0.001583|0.001583	ENSG00000196323|ENSG00000196323	ENST00000527478|ENST00000529982	.|.	.|.	.|.	5.47|5.47	2.57|2.57	0.30868|0.30868	.|.	.|.	.|.	.|.	.|.	T|T	0.52549|0.52549	0.1741|0.1741	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43130|0.43130	-0.9410|-0.9410	4|4	.|.	.|.	.|.	.|.	5.436|5.436	0.16482|0.16482	0.3403:0.0:0.534:0.1257|0.3403:0.0:0.534:0.1257	.|.	.|.	.|.	.|.	F|L	334|191	.|.	.|.	L|P	-|-	1|2	0|0	ZBTB44|ZBTB44	129635968|129635968	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	1.416000|1.416000	0.34759|0.34759	0.688000|0.688000	0.31529|0.31529	-0.251000|-0.251000	0.11542|0.11542	CTC|CCT	G|0.999;A|0.001	0.001	strong		0.413	ZBTB44-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000386126.1	NM_014155	
MED24	9862	hgsc.bcm.edu	37	17	38175866	38175866	+	Silent	SNP	G	G	A	rs11555254	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38175866G>A	ENST00000394128.2	-	26	2967	c.2886C>T	c.(2884-2886)tcC>tcT	p.S962S	MED24_ENST00000394126.1_Silent_p.S987S|MED24_ENST00000394127.2_Silent_p.S949S|MED24_ENST00000356271.3_Silent_p.S949S|MED24_ENST00000501516.3_Silent_p.S981S	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	962					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CCTTGGGGCTGGACATGGCTG	0.647													G|||	557	0.111222	0.1762	0.1225	5008	,	,		17624	0.006		0.162	False		,,,				2504	0.0716				p.S962S		Atlas-SNP	.											.	MED24	89	.	0			c.C2886T						PASS	.	G	,	798,3608	316.9+/-294.8	72,654,1477	71.0	61.0	64.0		2847,2886	4.1	1.0	17	dbSNP_120	64	1405,7195	268.7+/-288.0	114,1177,3009	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	186,1831,4486	AA,AG,GG		16.3372,18.1117,16.9383	,	949/977,962/990	38175866	2203,10803	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon26			GGGGCTGGACATG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2886C>T	17.37:g.38175866G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1	272	0.12454212454212454	91	0.18495934959349594	48	0.13259668508287292	3	0.005244755244755245	130	0.17150395778364116	G	10.91	1.484460	0.26598	0.181117	0.163372	ENSG00000008838	ENST00000422942	.	.	.	5.08	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.2844	14.4219	0.67190	0.0753:0.0:0.9247:0.0	rs11555254;rs17850738;rs11555254	.	.	.	X	260	.	.	Q	-	1	0	MED24	35429392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.006000	0.49529	2.506000	0.84524	0.650000	0.86243	CAG	G|0.850;A|0.150	0.150	strong		0.647	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
SNX18	112574	hgsc.bcm.edu	37	5	53813830	53813830	+	Silent	SNP	A	A	C	rs76854460	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:53813830A>C	ENST00000326277.3	+	1	238	c.48A>C	c.(46-48)ccA>ccC	p.P16P	SNX18_ENST00000381410.4_Silent_p.P16P|SNX18_ENST00000343017.6_Silent_p.P16P	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	16	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.P16P(3)		endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				CGGAGAACCCAGGAGAGATCT	0.731													a|||	1180	0.235623	0.1142	0.2622	5008	,	,		8124	0.1746		0.4046	False		,,,				2504	0.2699				p.P16P		Atlas-SNP	.											SNX18_ENST00000381410,NS,carcinoma,0,2	SNX18	102	2	3	Substitution - coding silent(3)	prostate(3)	c.A48C						PASS	.	A	,,	536,3750		43,450,1650	6.0	7.0	7.0		48,48,48	-3.6	0.9	5	dbSNP_131	7	2782,5576		482,1818,1879	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX18	NM_001102575.1,NM_001145427.1,NM_052870.2	,,	525,2268,3529	CC,CA,AA		33.2855,12.5058,26.2417	,,	16/625,16/592,16/629	53813830	3318,9326	2143	4179	6322	SO:0001819	synonymous_variant	112574	exon1			GAACCCAGGAGAG	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.48A>C	5.37:g.53813830A>C		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	7	6	0.857143	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Silent	SNP	ENST00000326277.3	37	CCDS3962.1																																																																																			A|0.733;C|0.267	0.267	strong		0.731	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
DSEL	92126	hgsc.bcm.edu	37	18	65179829	65179829	+	Missense_Mutation	SNP	G	G	A	rs2279269	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:65179829G>A	ENST00000310045.7	-	2	3520	c.2047C>T	c.(2047-2049)Ccc>Tcc	p.P683S	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	673					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				GTGATTGTGGGTTCCATCTGA	0.388													A|||	2181	0.435503	0.3041	0.4294	5008	,	,		18126	0.498		0.5686	False		,,,				2504	0.4162				p.P683S		Atlas-SNP	.											.	DSEL	196	.	0			c.C2047T						PASS	.	A	SER/PRO	1427,2979	682.4+/-404.1	245,937,1021	77.0	80.0	79.0		2047	2.9	1.0	18	dbSNP_100	79	4444,4156	566.2+/-388.6	1167,2110,1023	yes	missense	DSEL	NM_032160.2	74	1412,3047,2044	AA,AG,GG		48.3256,32.3877,45.1407	benign	683/1223	65179829	5871,7135	2203	4300	6503	SO:0001583	missense	92126	exon2			TTGTGGGTTCCAT	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.2047C>T	18.37:g.65179829G>A	ENSP00000310565:p.Pro683Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	156	152	0.974359	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	1025	0.4693223443223443	132	0.2682926829268293	166	0.4585635359116022	294	0.513986013986014	433	0.5712401055408971	A	6.141	0.394297	0.11638	0.323877	0.516744	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.15139	2.45	5.4	2.92	0.33932	.	0.380247	0.25094	N	0.033200	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44802	-0.9304	9	0.02654	T	1	.	1.1721	0.01827	0.4319:0.244:0.0915:0.2326	rs2279269;rs52806269;rs56523437;rs58927058;rs2279269	673	Q8IZU8	DSEL_HUMAN	S	683;673	ENSP00000310565:P683S	ENSP00000310565:P683S	P	-	1	0	DSEL	63330809	0.888000	0.30383	0.987000	0.45799	0.671000	0.39405	1.602000	0.36783	0.905000	0.36596	-0.521000	0.04368	CCC	G|0.545;A|0.455	0.455	strong		0.388	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
RABEP1	9135	hgsc.bcm.edu	37	17	5284770	5284770	+	Silent	SNP	G	G	A	rs1065483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5284770G>A	ENST00000546142.2	+	17	2644	c.2457G>A	c.(2455-2457)agG>agA	p.R819R	RABEP1_ENST00000262477.6_Silent_p.R819R|RABEP1_ENST00000408982.2_Silent_p.R786R|RABEP1_ENST00000537505.1_Silent_p.R776R|RABEP1_ENST00000341923.6_Silent_p.R786R|NUP88_ENST00000573169.1_Intron			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	819					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						AAGTCCAGAGGGATTTTGTAA	0.443													A|||	3393	0.677516	0.6301	0.5187	5008	,	,		20225	0.9623		0.4553	False		,,,				2504	0.7894				p.R819R		Atlas-SNP	.											.	RABEP1	59	.	0			c.G2457A						PASS	.	A	,	2224,1532		648,928,302	86.0	88.0	87.0		2358,2457	1.3	1.0	17	dbSNP_86	87	3360,4856		684,1992,1432	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	1332,2920,1734	AA,AG,GG		40.8958,40.7881,46.6422	,	786/830,819/863	5284770	5584,6388	1878	4108	5986	SO:0001819	synonymous_variant	9135	exon17			CCAGAGGGATTTT	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2457G>A	17.37:g.5284770G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			G|0.390;A|0.610	0.610	strong		0.443	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
CCL4	6351	hgsc.bcm.edu	37	17	34432664	34432664	+	Missense_Mutation	SNP	T	T	A	rs1719152|rs386796798	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:34432664T>A	ENST00000250151.4	+	3	554	c.238T>A	c.(238-240)Tcc>Acc	p.S80T	CCL4_ENST00000394495.1_Missense_Mutation_p.N41K	NM_002984.2	NP_002975.1	P13236	CCL4_HUMAN	chemokine (C-C motif) ligand 4	80			S -> T (in dbSNP:rs1719152). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2809212}.		cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|establishment or maintenance of cell polarity (GO:0007163)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation by host of viral transcription (GO:0043922)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of natural killer cell chemotaxis (GO:2000503)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR1 chemokine receptor binding (GO:0031726)|CCR5 chemokine receptor binding (GO:0031730)|chemokine activity (GO:0008009)|cytokine activity (GO:0005125)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(1)|lung(2)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TCCCAGTGAATCCTGGGTCCA	0.498													A|||	898	0.179313	0.0492	0.1182	5008	,	,		21017	0.2758		0.2485	False		,,,				2504	0.228				p.S80T	Colon(139;824 1752 21188 21615 24765)	Atlas-SNP	.											.	CCL4	14	.	0			c.T238A						PASS	.	A	THR/SER	14,4392		3,8,2192	199.0	183.0	188.0		238	-10.1	0.7	17	dbSNP_89	188	113,8487		33,47,4220	no	missense	CCL4	NM_002984.2	58	36,55,6412	AA,AT,TT		1.314,0.3177,0.9765	benign	80/93	34432664	127,12879	2203	4300	6503	SO:0001583	missense	6351	exon3			AGTGAATCCTGGG	M23502	CCDS11308.1	17q21-q23	2014-05-06	2002-08-22	2002-08-23	ENSG00000129277	ENSG00000275302		"""Chemokine ligands"", ""Endogenous ligands"""	10630	protein-coding gene	gene with protein product		182284	"""small inducible cytokine A4 (homologous to mouse Mip-1b)"""	LAG1, SCYA4		1972563	Standard	NM_002984		Approved	MIP-1-beta, Act-2, AT744.1	uc002hkw.1	P13236	OTTHUMG00000188414	ENST00000250151.4:c.238T>A	17.37:g.34432664T>A	ENSP00000250151:p.Ser80Thr	Somatic	292	0	0		WXS	Illumina HiSeq	Phase_I	378	371	0.981481	NM_002984	P22617|Q13704|Q3SXL8|Q6FGI8	Missense_Mutation	SNP	ENST00000250151.4	37	CCDS11308.1	314|314	0.14377289377289376|0.14377289377289376	13|13	0.026422764227642278|0.026422764227642278	43|43	0.11878453038674033|0.11878453038674033	122|122	0.21328671328671328|0.21328671328671328	136|136	0.17941952506596306|0.17941952506596306	.|.	0.132|0.132	-1.112281|-1.112281	0.01799|0.01799	0.003177|0.003177	0.01314|0.01314	ENSG00000129277|ENSG00000129277	ENST00000394495|ENST00000250151	T|T	0.71698|0.04551	-0.59|3.6	5.03|5.03	-10.1|-10.1	0.00402|0.00402	.|Chemokine interleukin-8-like domain (3);	.|0.947069	.|0.08503	.|N	.|0.936124	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.50813|0.50813	P|P	1.020000000000465E-4|1.020000000000465E-4	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.40098|0.40098	-0.9581|-0.9581	5|8	0.87932|0.20519	D|T	0|0.43	.|.	2.6529|2.6529	0.05003|0.05003	0.1602:0.1173:0.3049:0.4176|0.1602:0.1173:0.3049:0.4176	rs1719152;rs52821607;rs1719152|rs1719152;rs52821607;rs1719152	.|80	.|P13236	.|CCL4_HUMAN	K|T	41|80	ENSP00000378004:N41K|ENSP00000250151:S80T	ENSP00000378004:N41K|ENSP00000250151:S80T	N|S	+|+	3|1	2|0	CCL4|CCL4	31456777|31456777	0.000000|0.000000	0.05858|0.05858	0.651000|0.651000	0.29564|0.29564	0.096000|0.096000	0.18686|0.18686	-6.619000|-6.619000	0.00059|0.00059	-3.661000|-3.661000	0.00124|0.00124	-2.948000|-2.948000	0.00085|0.00085	AAT|TCC	T|0.845;A|0.155	0.155	strong		0.498	CCL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256592.2	NM_002984	
OR2L8	391190	hgsc.bcm.edu	37	1	248112754	248112754	+	Missense_Mutation	SNP	T	T	C	rs201126494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248112754T>C	ENST00000357191.3	+	1	595	c.595T>C	c.(595-597)Ttt>Ctt	p.F199L	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	199						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(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			GGGCACAGTGTTTTTGAGTGC	0.483																																					p.F199L		Atlas-SNP	.											.	OR2L8	92	.	0			c.T595C						PASS	.						145.0	45.0	79.0					1																	248112754		2203	4297	6500	SO:0001583	missense	391190	exon1			ACAGTGTTTTTGA	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.595T>C	1.37:g.248112754T>C	ENSP00000349719:p.Phe199Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	160	38	0.2375	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	7.762	0.705616	0.15172	.	.	ENSG00000196936	ENST00000357191	T	0.00042	8.84	1.79	0.313	0.15842	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33732	U	0.004607	T	0.00144	0.0004	N	0.13235	0.315	0.09310	N	1	D	0.58970	0.984	P	0.59948	0.866	T	0.52230	-0.8603	10	0.51188	T	0.08	.	2.0669	0.03605	0.463:0.2458:0.0:0.2912	.	199	Q8NGY9	OR2L8_HUMAN	L	199	ENSP00000349719:F199L	ENSP00000349719:F199L	F	+	1	0	OR2L8	246179377	0.000000	0.05858	0.788000	0.31933	0.689000	0.40095	-0.139000	0.10358	0.833000	0.34828	0.392000	0.25879	TTT	T|0.945;C|0.055	0.055	strong		0.483	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
TROAP	10024	hgsc.bcm.edu	37	12	49723963	49723963	+	Silent	SNP	A	A	G	rs4243545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49723963A>G	ENST00000257909.3	+	13	1411	c.1335A>G	c.(1333-1335)gaA>gaG	p.E445E	TROAP_ENST00000547923.1_Silent_p.E153E|TROAP_ENST00000551245.1_Silent_p.E445E	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	445					cell adhesion (GO:0007155)	cytoplasm (GO:0005737)		p.E445E(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						TGAGACAGGAAGTAGAGGGGC	0.532													G|||	972	0.194089	0.4123	0.1138	5008	,	,		19065	0.0407		0.1531	False		,,,				2504	0.1564				p.E445E		Atlas-SNP	.											TROAP,NS,carcinoma,0,1	TROAP	80	1	1	Substitution - coding silent(1)	stomach(1)	c.A1335G						scavenged	.	G		1686,2720	629.2+/-395.2	314,1058,831	105.0	110.0	108.0		1335	1.6	0.8	12	dbSNP_111	108	1408,7188	725.2+/-406.5	122,1164,3012	no	coding-synonymous	TROAP	NM_005480.3		436,2222,3843	GG,GA,AA		16.3797,38.266,23.7963		445/779	49723963	3094,9908	2203	4298	6501	SO:0001819	synonymous_variant	10024	exon13			ACAGGAAGTAGAG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.1335A>G	12.37:g.49723963A>G		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	169	79	0.467456	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Silent	SNP	ENST00000257909.3	37	CCDS8784.1																																																																																			A|0.789;G|0.211	0.211	strong		0.532	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
DCAF10	79269	hgsc.bcm.edu	37	9	37860058	37860058	+	Silent	SNP	A	A	G	rs118047034	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:37860058A>G	ENST00000377724.3	+	6	1544	c.1179A>G	c.(1177-1179)cgA>cgG	p.R393R	RP11-613M10.9_ENST00000540557.1_Intron|DCAF10_ENST00000242323.7_Silent_p.R356R|DCAF10_ENST00000483167.1_3'UTR	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	393					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	12						TTTCACCACGAAATAGTCTTG	0.443													A|||	42	0.00838658	0.0	0.0072	5008	,	,		21846	0.0		0.0288	False		,,,				2504	0.0082				p.R393R		Atlas-SNP	.											DCAF10,rectum,carcinoma,+1,1	DCAF10	31	1	0			c.A1179G						PASS	.	A		13,4393	20.2+/-43.8	0,13,2190	113.0	100.0	104.0		1179	1.8	1.0	9	dbSNP_132	104	249,8351	96.6+/-158.3	4,241,4055	no	coding-synonymous	DCAF10	NM_024345.3		4,254,6245	GG,GA,AA		2.8953,0.2951,2.0145		393/560	37860058	262,12744	2203	4300	6503	SO:0001819	synonymous_variant	79269	exon6			ACCACGAAATAGT	BC003520	CCDS6613.2, CCDS75835.1	9p13.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000122741	ENSG00000122741		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	23686	protein-coding gene	gene with protein product			"""WD repeat domain 32"""	WDR32			Standard	NM_001286810		Approved	MGC10765, FLJ23201	uc004aao.3	Q5QP82	OTTHUMG00000019934	ENST00000377724.3:c.1179A>G	9.37:g.37860058A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_024345	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Silent	SNP	ENST00000377724.3	37	CCDS6613.2																																																																																			A|0.984;G|0.016	0.016	strong		0.443	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345	
CFI	3426	hgsc.bcm.edu	37	4	110681505	110681505	+	Silent	SNP	C	C	T	rs2298749	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:110681505C>T	ENST00000394634.2	-	6	1011	c.804G>A	c.(802-804)tcG>tcA	p.S268S	CFI_ENST00000512148.1_Silent_p.S268S|CFI_ENST00000394635.3_Silent_p.S268S	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	268	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		TGCAAACACCCGATTTGCAAT	0.428													C|||	1563	0.312101	0.357	0.4395	5008	,	,		19434	0.3095		0.2455	False		,,,				2504	0.2321				p.S268S		Atlas-SNP	.											.	CFI	59	.	0			c.G804A						PASS	.	C		1631,2775	501.2+/-364.9	314,1003,886	143.0	129.0	134.0		804	-2.0	0.9	4	dbSNP_100	134	2195,6405	374.3+/-337.3	293,1609,2398	no	coding-synonymous	CFI	NM_000204.3		607,2612,3284	TT,TC,CC		25.5233,37.0177,29.4172		268/584	110681505	3826,9180	2203	4300	6503	SO:0001819	synonymous_variant	3426	exon6			AACACCCGATTTG	J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"""Complement system"""	5394	protein-coding gene	gene with protein product	"""Konglutinogen-activating factor"", ""C3b-inactivator"""	217030	"""I factor (complement)"""	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.804G>A	4.37:g.110681505C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_000204	O60442	Silent	SNP	ENST00000394634.2	37	CCDS34049.1																																																																																			C|0.702;T|0.298	0.298	strong		0.428	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204	
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 GAIIx	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	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	178	43	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	
ZFPM1	161882	hgsc.bcm.edu	37	16	88599023	88599023	+	Splice_Site	SNP	A	A	G	rs56041036	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88599023A>G	ENST00000319555.3	+	8	1270	c.948A>G	c.(946-948)ggA>ggG	p.G316G	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	316					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	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)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GTGTTCCAGGAGAGCGGCCCT	0.662													a|||	741	0.147963	0.0741	0.1484	5008	,	,		16600	0.3591		0.0974	False		,,,				2504	0.0818				p.G316G	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											ZFPM1,NS,carcinoma,0,1	ZFPM1	32	1	0			c.A948G						scavenged	.	A		345,4013		17,311,1851	29.0	27.0	28.0		948	0.6	1.0	16	dbSNP_129	28	652,7914		21,610,3652	yes	coding-synonymous-near-splice	ZFPM1	NM_153813.2		38,921,5503	GG,GA,AA		7.6115,7.9165,7.7143		316/1007	88599023	997,11927	2179	4283	6462	SO:0001630	splice_region_variant	161882	exon8			TCCAGGAGAGCGG	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.947-1A>G	16.37:g.88599023A>G		Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_153813		Silent	SNP	ENST00000319555.3	37	CCDS32502.1																																																																																			A|0.879;G|0.121	0.121	strong		0.662	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		Silent
POTEC	388468	hgsc.bcm.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	C	T	rs201788045		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:14513764C>T	ENST00000358970.5	-	10	1429	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q		NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	477								p.R477Q(12)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						AAGTTGTTTCCGGGTATCATT	0.358																																					p.R477Q		Atlas-SNP	.											POTEC,NS,carcinoma,0,17	POTEC	129	17	12	Substitution - Missense(12)	endometrium(4)|kidney(3)|urinary_tract(2)|prostate(2)|soft_tissue(1)	c.G1430A						scavenged	.						13.0	9.0	10.0					18																	14513764		683	1543	2226	SO:0001583	missense	388468	exon10			TGTTTCCGGGTAT	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.1430G>A	18.37:g.14513764C>T	ENSP00000351856:p.Arg477Gln	Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	282	6	0.0212766	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	492	0.22527472527472528	61	0.12398373983739837	82	0.2265193370165746	187	0.3269230769230769	162	0.21372031662269128	c	0.001	-3.539655	0.00009	.	.	ENSG00000183206	ENST00000358970	T	0.20881	2.04	1.34	0.0657	0.14358	.	.	.	.	.	T	0.00012	0.0000	N	0.00116	-2.08	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42430	-0.9452	9	0.06757	T	0.87	.	3.4153	0.07373	0.0:0.2473:0.0:0.7527	.	477	B2RU33	POTEC_HUMAN	Q	477	ENSP00000351856:R477Q	ENSP00000351856:R477Q	R	-	2	0	POTEC	14503764	0.885000	0.30320	0.063000	0.19743	0.005000	0.04900	1.581000	0.36558	0.005000	0.14708	-1.615000	0.00797	CGG	.	.	weak		0.358	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
FBXO10	26267	hgsc.bcm.edu	37	9	37537557	37537557	+	Silent	SNP	G	G	A	rs7044153	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:37537557G>A	ENST00000432825.2	-	3	1017	c.969C>T	c.(967-969)gcC>gcT	p.A323A	RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Intron|FBXO10_ENST00000543968.1_5'Flank	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	323					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		GGGAGCTAGAGGCTGGGCTGG	0.607													G|||	2757	0.550519	0.3116	0.5447	5008	,	,		20557	0.6984		0.6571	False		,,,				2504	0.6155				p.A323A		Atlas-SNP	.											.	FBXO10	75	.	0			c.C969T						PASS	.	G		1554,2422		316,922,750	20.0	24.0	23.0		969	0.9	1.0	9	dbSNP_116	23	5312,3004		1693,1926,539	no	coding-synonymous	FBXO10	NM_012166.2		2009,2848,1289	AA,AG,GG		36.1231,39.0845,44.1425		323/957	37537557	6866,5426	1988	4158	6146	SO:0001819	synonymous_variant	26267	exon3			GCTAGAGGCTGGG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.969C>T	9.37:g.37537557G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Silent	SNP	ENST00000432825.2	37	CCDS47966.1																																																																																			G|0.429;A|0.571	0.571	strong		0.607	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
KLF17	128209	hgsc.bcm.edu	37	1	44595047	44595047	+	Missense_Mutation	SNP	T	T	A	rs11210969	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:44595047T>A	ENST00000372299.3	+	2	162	c.104T>A	c.(103-105)aTc>aAc	p.I35N	KLF17_ENST00000476802.1_3'UTR	NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	35			I -> N (in dbSNP:rs11210969). {ECO:0000269|PubMed:14702039}.		gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.I35N(1)		NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					TCAGCGCCCATCTTGAACATG	0.498													T|||	1089	0.217452	0.121	0.255	5008	,	,		18875	0.2044		0.2962	False		,,,				2504	0.2536				p.I35N		Atlas-SNP	.											KLF17,NS,carcinoma,0,1	KLF17	92	1	1	Substitution - Missense(1)	stomach(1)	c.T104A						PASS	.	T	ASN/ILE	645,3761	276.0+/-272.9	56,533,1614	126.0	118.0	120.0		104	1.2	0.0	1	dbSNP_120	120	2509,6091	411.2+/-350.4	361,1787,2152	yes	missense	KLF17	NM_173484.3	149	417,2320,3766	AA,AT,TT		29.1744,14.6391,24.2503	benign	35/390	44595047	3154,9852	2203	4300	6503	SO:0001583	missense	128209	exon2			CGCCCATCTTGAA	BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.104T>A	1.37:g.44595047T>A	ENSP00000361373:p.Ile35Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_173484	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	502	0.22985347985347984	60	0.12195121951219512	91	0.2513812154696133	125	0.21853146853146854	226	0.29815303430079154	T	8.842	0.942534	0.18281	0.146391	0.291744	ENSG00000171872	ENST00000372299	T	0.13420	2.59	4.78	1.18	0.20946	.	1.018550	0.07854	N	0.965188	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.45902	0.868	B	0.42851	0.4	T	0.45600	-0.9250	9	0.54805	T	0.06	.	3.9088	0.09194	0.0:0.1891:0.1838:0.6271	rs11210969;rs17381026;rs52807679;rs56504303;rs11210969	35	Q5JT82	KLF17_HUMAN	N	35	ENSP00000361373:I35N	ENSP00000361373:I35N	I	+	2	0	KLF17	44367634	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.624000	0.24462	0.189000	0.20188	-0.263000	0.10527	ATC	T|0.767;A|0.233	0.233	strong		0.498	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1	NM_173484	
NXPE4	54827	hgsc.bcm.edu	37	11	114442103	114442103	+	Missense_Mutation	SNP	A	A	G	rs550897	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:114442103A>G	ENST00000375478.3	-	6	1372	c.1192T>C	c.(1192-1194)Tat>Cat	p.Y398H	NXPE4_ENST00000424261.2_Missense_Mutation_p.Y114H	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	398			Y -> H (in dbSNP:rs550897). {ECO:0000269|PubMed:15375555}.			extracellular vesicular exosome (GO:0070062)											GGATAACAATATTTTTGCCAC	0.423													G|||	3275	0.653954	0.9054	0.5605	5008	,	,		19012	0.6746		0.4682	False		,,,				2504	0.5501				p.Y398H		Atlas-SNP	.											.	.	.	.	0			c.T1192C						PASS	.	G	HIS/TYR,HIS/TYR	3195,621		1345,505,58	212.0	190.0	197.0		1192,340	4.5	0.2	11	dbSNP_83	197	4029,4229		963,2103,1063	yes	missense,missense	FAM55D	NM_001077639.1,NM_017678.2	83,83	2308,2608,1121	GG,GA,AA		48.7891,16.2736,40.169	benign,benign	398/545,114/261	114442103	7224,4850	1908	4129	6037	SO:0001583	missense	54827	exon6			AACAATATTTTTG	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1192T>C	11.37:g.114442103A>G	ENSP00000364627:p.Tyr398His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	1352	0.6190476190476191	436	0.8861788617886179	191	0.5276243093922652	381	0.666083916083916	344	0.45382585751978893	G	1.074	-0.668989	0.03403	0.837264	0.487891	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.10960	2.82;2.82	5.44	4.54	0.55810	.	0.000000	0.64402	N	0.000005	T	0.00012	0.0000	N	0.00003	-3.415	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35798	-0.9774	9	0.02654	T	1	.	11.2986	0.49292	0.1497:0.0:0.8503:0.0	rs550897;rs52827494;rs58118885;rs550897	398	Q6UWF7	FA55D_HUMAN	H	114;398	ENSP00000401503:Y114H;ENSP00000364627:Y398H	ENSP00000364627:Y398H	Y	-	1	0	FAM55D	113947313	0.999000	0.42202	0.201000	0.23476	0.807000	0.45602	4.178000	0.58284	0.804000	0.34136	-0.166000	0.13349	TAT	T|0.007;G|0.608	0.608	strong		0.423	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
VAMP5	10791	hgsc.bcm.edu	37	2	85818886	85818886	+	Silent	SNP	C	C	T	rs14976	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85818886C>T	ENST00000306384.4	+	2	125	c.42C>T	c.(40-42)aaC>aaT	p.N14N		NM_006634.2	NP_006625.1	O95183	VAMP5_HUMAN	vesicle-associated membrane protein 5	14	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				cell differentiation (GO:0030154)|Golgi to plasma membrane protein transport (GO:0043001)|muscle organ development (GO:0007517)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|large_intestine(3)|lung(1)	5						AGCAGGCGAACGAGGTGACGG	0.607													C|||	963	0.192292	0.152	0.2003	5008	,	,		18936	0.0883		0.2813	False		,,,				2504	0.2566				p.N14N		Atlas-SNP	.											.	VAMP5	13	.	0			c.C42T						PASS	.	C		692,3714	290.7+/-281.1	51,590,1562	132.0	113.0	119.0		42	-3.7	0.5	2	dbSNP_52	119	2410,6190	401.2+/-347.1	335,1740,2225	no	coding-synonymous	VAMP5	NM_006634.2		386,2330,3787	TT,TC,CC		28.0233,15.7059,23.8505		14/117	85818886	3102,9904	2203	4300	6503	SO:0001819	synonymous_variant	10791	exon2			GGCGAACGAGGTG	AF054825	CCDS1980.1	2p11.2	2013-02-13	2012-10-17		ENSG00000168899	ENSG00000168899		"""Vesicle-associated membrane proteins"""	12646	protein-coding gene	gene with protein product	"""myobrevin"""	607029				9725904	Standard	NM_006634		Approved		uc002spu.1	O95183	OTTHUMG00000130169	ENST00000306384.4:c.42C>T	2.37:g.85818886C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_006634	Q9P0T2	Silent	SNP	ENST00000306384.4	37	CCDS1980.1																																																																																			C|0.797;T|0.203	0.203	strong		0.607	VAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252484.2	NM_006634	
GDPD4	220032	hgsc.bcm.edu	37	11	76954812	76954812	+	Missense_Mutation	SNP	T	T	C	rs11237145	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:76954812T>C	ENST00000376217.2	-	12	1418	c.1168A>G	c.(1168-1170)Att>Gtt	p.I390V	GDPD4_ENST00000315938.4_Missense_Mutation_p.I390V			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	390	GP-PDE.		I -> V (in dbSNP:rs11237145).		glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						AGGGTTTCAATGGATACTAAA	0.413													C|||	1274	0.254393	0.0514	0.1916	5008	,	,		16179	0.256		0.3738	False		,,,				2504	0.4489				p.I390V		Atlas-SNP	.											.	GDPD4	49	.	0			c.A1168G						PASS	.	C	VAL/ILE	458,3942	784.3+/-414.7	30,398,1772	117.0	108.0	111.0		1168	-8.5	0.0	11	dbSNP_120	111	3083,5501	658.5+/-401.6	536,2011,1745	yes	missense	GDPD4	NM_182833.1	29	566,2409,3517	CC,CT,TT		35.9157,10.4091,27.272	benign	390/521	76954812	3541,9443	2200	4292	6492	SO:0001583	missense	220032	exon12			TTTCAATGGATAC	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1168A>G	11.37:g.76954812T>C	ENSP00000365390:p.Ile390Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	91	15	0.164835	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	37		501	0.22939560439560439	25	0.0508130081300813	76	0.20994475138121546	130	0.22727272727272727	270	0.3562005277044855	C	0.016	-1.522396	0.00967	0.104091	0.359157	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.10763	2.84;2.84	4.27	-8.54	0.00912	.	0.708347	0.13925	N	0.353264	T	0.00012	0.0000	N	0.05351	-0.065	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.32955	-0.9887	9	0.06099	T	0.92	-2.8135	3.1474	0.06477	0.0959:0.3517:0.1943:0.3581	rs11237145;rs17824220;rs52820078;rs11237145	390	Q6W3E5-2	.	V	390	ENSP00000365390:I390V;ENSP00000320815:I390V	ENSP00000320815:I390V	I	-	1	0	GDPD4	76632460	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.063000	0.00622	-2.006000	0.00958	-1.874000	0.00550	ATT	C|0.254;N|0.000	0.254	strong		0.413	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
CDH23	64072	hgsc.bcm.edu	37	10	73537614	73537614	+	Missense_Mutation	SNP	G	G	A	rs17712523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73537614G>A	ENST00000224721.6	+	38	5043	c.5038G>A	c.(5038-5040)Gtc>Atc	p.V1680I		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1675	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.V1680I(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CTATGCCATCGTCGCAGGCAA	0.582													G|||	662	0.132188	0.0083	0.1225	5008	,	,		22375	0.1518		0.2177	False		,,,				2504	0.1984				p.V1675I		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - Missense(1)	stomach(1)	c.G5023A						PASS	.	G	ILE/VAL	171,4215	98.9+/-137.6	7,157,2029	87.0	80.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5023	-1.2	0.0	10	dbSNP_123	82	1654,6906	296.7+/-303.1	168,1318,2794	yes	missense	CDH23	NM_022124.5	29	175,1475,4823	AA,AG,GG		19.3224,3.8988,14.097	benign	1675/3355	73537614	1825,11121	2193	4280	6473	SO:0001583	missense	64072	exon37			GCCATCGTCGCAG	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.5038G>A	10.37:g.73537614G>A	ENSP00000224721:p.Val1680Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		318	0.14560439560439561	8	0.016260162601626018	52	0.143646408839779	79	0.1381118881118881	179	0.23614775725593667	G	11.11	1.542382	0.27563	0.038988	0.193224	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.76	-1.2	0.09554	Cadherin (4);Cadherin-like (1);	0.734425	0.13151	N	0.409894	T	0.00012	0.0000	N	0.20845	0.615	0.41555	P	0.01140399999999997	B	0.06786	0.001	B	0.06405	0.002	T	0.26710	-1.0095	8	0.27785	T	0.31	.	6.2351	0.20758	0.6383:0.0:0.2126:0.1492	rs17712523;rs52808163;rs56502918;rs17712523	1675	Q9H251	CAD23_HUMAN	I	1680;1675;1678	.	ENSP00000224721:V1680I	V	+	1	0	CDH23	73207620	0.003000	0.15002	0.028000	0.17463	0.800000	0.45204	0.102000	0.15272	-0.097000	0.12307	-0.140000	0.14226	GTC	G|0.857;A|0.143	0.143	strong		0.582	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
SMG8	55181	hgsc.bcm.edu	37	17	57290383	57290383	+	Silent	SNP	G	G	A	rs3744383	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:57290383G>A	ENST00000543872.2	+	4	2463	c.2199G>A	c.(2197-2199)agG>agA	p.R733R	SMG8_ENST00000300917.5_Silent_p.R733R|SMG8_ENST00000580498.1_3'UTR|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	733					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						CTGAGAAGAGGCCAAACTTCG	0.468													A|||	2445	0.488219	0.7375	0.3646	5008	,	,		19687	0.4415		0.2942	False		,,,				2504	0.4867				p.R733R		Atlas-SNP	.											.	SMG8	79	.	0			c.G2199A						PASS	.	A		2915,1491	474.6+/-357.0	962,991,250	111.0	111.0	111.0		2199	1.0	1.0	17	dbSNP_107	111	2683,5917	684.6+/-404.0	413,1857,2030	no	coding-synonymous	SMG8	NM_018149.6		1375,2848,2280	AA,AG,GG		31.1977,33.8402,43.0417		733/992	57290383	5598,7408	2203	4300	6503	SO:0001819	synonymous_variant	55181	exon3			GAAGAGGCCAAAC	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"""chromosome 17 open reading frame 71"", ""smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.2199G>A	17.37:g.57290383G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Silent	SNP	ENST00000543872.2	37	CCDS11615.1																																																																																			G|0.551;A|0.449	0.449	strong		0.468	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149	
RNF152	220441	hgsc.bcm.edu	37	18	59483310	59483310	+	Silent	SNP	G	G	A	rs4362478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:59483310G>A	ENST00000312828.3	-	2	1486	c.387C>T	c.(385-387)tcC>tcT	p.S129S		NM_173557.2	NP_775828.1	Q8N8N0	RN152_HUMAN	ring finger protein 152	129					apoptotic process (GO:0006915)|protein K48-linked ubiquitination (GO:0070936)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(10)|skin(1)	17		Colorectal(73;0.186)				CCACGGTGACGGACTTCTGCT	0.672													G|||	112	0.0223642	0.0106	0.0187	5008	,	,		16311	0.0		0.0746	False		,,,				2504	0.0102				p.S129S		Atlas-SNP	.											RNF152,NS,carcinoma,0,1	RNF152	37	1	0			c.C387T						PASS	.	G		112,4294	85.3+/-124.0	0,112,2091	51.0	56.0	54.0		387	-9.6	0.2	18	dbSNP_111	54	546,8054	148.9+/-204.1	19,508,3773	no	coding-synonymous	RNF152	NM_173557.2		19,620,5864	AA,AG,GG		6.3488,2.542,5.0592		129/204	59483310	658,12348	2203	4300	6503	SO:0001819	synonymous_variant	220441	exon2			GGTGACGGACTTC	AK096495	CCDS11978.1	18q21.33	2013-01-09			ENSG00000176641	ENSG00000176641		"""RING-type (C3HC4) zinc fingers"""	26811	protein-coding gene	gene with protein product							Standard	XM_005266650		Approved	FLJ39176	uc002lih.1	Q8N8N0	OTTHUMG00000132774	ENST00000312828.3:c.387C>T	18.37:g.59483310G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_173557	B3KV99|Q52LA4	Silent	SNP	ENST00000312828.3	37	CCDS11978.1																																																																																			G|0.959;A|0.041	0.041	strong		0.672	RNF152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256180.1	NM_173557	
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 GAIIx	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	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	4	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 GAIIx	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		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	233	116	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	
PLCXD1	55344	hgsc.bcm.edu	37	X	200860	200860	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:200860T>C	ENST00000381657.2	+	2	520	c.6T>C	c.(4-6)ggT>ggC	p.G2G	PLCXD1_ENST00000399012.1_Silent_p.G2G|PLCXD1_ENST00000484611.2_3'UTR|PLCXD1_ENST00000381663.3_Silent_p.G2G	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	2					lipid metabolic process (GO:0006629)		phosphoric diester hydrolase activity (GO:0008081)			endometrium(3)|large_intestine(1)|lung(7)	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)				CTCTGATGGGTGGGCAGGTGA	0.587													.|||	3792	0.757188	0.9569	0.6542	5008	,	,		17891	0.7788		0.7485	False		,,,				2504	0.547				p.G2G		Atlas-SNP	.											.	PLCXD1	18	.	0			c.T6C						PASS	.			4036,370		1850,336,17	124.0	130.0	128.0		6	-1.6	0.0	X	dbSNP_134	128	6348,2244		2361,1626,309	no	coding-synonymous	PLCXD1	NM_018390.3		4211,1962,326	CC,CT,TT		26.1173,8.3976,20.1108		2/324	200860	10384,2614	2203	4296	6499	SO:0001819	synonymous_variant	55344	exon2			GATGGGTGGGCAG	AK002185	CCDS14103.1	Xp22.33 and Yp11.32	2010-07-28			ENSG00000182378	ENSG00000182378		"""Pseudoautosomal regions / PAR1"""	23148	protein-coding gene	gene with protein product							Standard	NM_018390		Approved	FLJ11323	uc004cpc.3	Q9NUJ7	OTTHUMG00000022693	ENST00000381657.2:c.6T>C	X.37:g.200860T>C		Somatic	268	2	0.00746269		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_018390	A2BH51|A2BH52	Silent	SNP	ENST00000381657.2	37	CCDS14103.1																																																																																			T|0.204;C|0.796	0.796	strong		0.587	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390	
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 GAIIx	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	DPCR1_ENST00000304311.2_Missense_Mutation_p.K28T|HCG21_ENST00000419481.1_RNA			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	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	45	16	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 GAIIx	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	KTN1_ENST00000554507.1_Missense_Mutation_p.A210T|KTN1_ENST00000395309.3_Missense_Mutation_p.A915T|KTN1_ENST00000413890.2_Missense_Mutation_p.A892T|KTN1_ENST00000395308.1_Missense_Mutation_p.A892T|Y_RNA_ENST00000363872.1_RNA|KTN1_ENST00000438792.2_Missense_Mutation_p.A915T|KTN1_ENST00000395311.1_Missense_Mutation_p.A892T|KTN1_ENST00000416613.1_Missense_Mutation_p.A915T	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	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	163	75	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		
IL31RA	133396	hgsc.bcm.edu	37	5	55210702	55210702	+	Silent	SNP	C	C	T	rs17701253	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:55210702C>T	ENST00000447346.2	+	14	1829	c.1764C>T	c.(1762-1764)acC>acT	p.T588T	IL31RA_ENST00000359040.5_Silent_p.T588T|IL31RA_ENST00000396834.1_Silent_p.T569T|IL31RA_ENST00000490985.1_Silent_p.T446T|IL31RA_ENST00000354961.4_Silent_p.T569T	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	556					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GTTGGCCCACCGTTCCCAACC	0.418													C|||	147	0.029353	0.0038	0.0706	5008	,	,		22559	0.006		0.0497	False		,,,				2504	0.0378				p.T588T		Atlas-SNP	.											.	IL31RA	84	.	0			c.C1764T						PASS	.	C	,,,,	61,4345	58.1+/-94.6	0,61,2142	120.0	106.0	111.0		1707,1764,1707,1338,1764	-5.7	0.0	5	dbSNP_123	111	513,8087	145.3+/-201.0	15,483,3802	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL31RA	NM_001242636.1,NM_001242637.1,NM_001242638.1,NM_001242639.1,NM_139017.5	,,,,	15,544,5944	TT,TC,CC		5.9651,1.3845,4.4133	,,,,	569/746,588/682,569/663,446/623,588/765	55210702	574,12432	2203	4300	6503	SO:0001819	synonymous_variant	133396	exon14			GCCCACCGTTCCC	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1764C>T	5.37:g.55210702C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	202	101	0.5	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Silent	SNP	ENST00000447346.2	37	CCDS3970.2																																																																																			C|0.962;T|0.038	0.038	strong		0.418	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
MTHFD1	4522	hgsc.bcm.edu	37	14	64882380	64882380	+	Missense_Mutation	SNP	A	A	G	rs1950902	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:64882380A>G	ENST00000545908.1	+	6	798	c.569A>G	c.(568-570)aAa>aGa	p.K190R	MTHFD1_ENST00000216605.8_Missense_Mutation_p.K134R			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	134	Methylenetetrahydrofolate dehydrogenase and cyclohydrolase.				folic acid metabolic process (GO:0046655)|folic acid-containing compound biosynthetic process (GO:0009396)|histidine biosynthetic process (GO:0000105)|methionine biosynthetic process (GO:0009086)|one-carbon metabolic process (GO:0006730)|purine nucleotide biosynthetic process (GO:0006164)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|methenyltetrahydrofolate cyclohydrolase activity (GO:0004477)|methylenetetrahydrofolate dehydrogenase (NADP+) activity (GO:0004488)|methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity (GO:0004486)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	30				OV - Ovarian serous cystadenocarcinoma(108;8.7e-12)|all cancers(60;3.29e-11)|BRCA - Breast invasive adenocarcinoma(234;0.0488)	Tetrahydrofolic acid(DB00116)	aatgctgggaaacttgctaga	0.363													A|||	4124	0.823482	0.8616	0.9107	5008	,	,		22898	0.6448		0.7962	False		,,,				2504	0.9223				p.K134R	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											MTHFD1,tonsil,carcinoma,0,1	MTHFD1	61	1	0			c.A401G	GRCh37	CM065321	MTHFD1	M	rs1950902	PASS	.	A	ARG/LYS	3728,678	763.1+/-413.2	1567,594,42	80.0	73.0	75.0		401	5.1	1.0	14	dbSNP_92	75	7087,1513	747.6+/-407.3	2928,1231,141	yes	missense	MTHFD1	NM_005956.3	26	4495,1825,183	GG,GA,AA		17.593,15.3881,16.8461	benign	134/936	64882380	10815,2191	2203	4300	6503	SO:0001583	missense	4522	exon6			CTGGGAAACTTGC	J04031	CCDS9763.1	14q24	2004-12-13			ENSG00000100714	ENSG00000100714	1.5.1.15, 3.5.4.-		7432	protein-coding gene	gene with protein product		172460		MTHFC, MTHFD		3053686, 2786332	Standard	NM_005956		Approved		uc001xhb.3	P11586	OTTHUMG00000141309	ENST00000545908.1:c.569A>G	14.37:g.64882380A>G	ENSP00000438588:p.Lys190Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Missense_Mutation	SNP	ENST00000545908.1	37		1768	0.8095238095238095	420	0.8536585365853658	326	0.9005524861878453	416	0.7272727272727273	606	0.7994722955145118	A	12.12	1.841279	0.32513	0.846119	0.82407	ENSG00000100714	ENST00000545908;ENST00000555709;ENST00000216605;ENST00000555252	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999360405	B;B	0.14012	0.003;0.009	B;B	0.17098	0.009;0.017	T	0.28396	-1.0045	8	0.08599	T	0.76	-21.4612	15.1283	0.72500	1.0:0.0:0.0:0.0	rs1950902;rs2070262;rs17854633;rs17858060;rs52808281;rs57359350;rs1950902	190;134	F5H2F4;G3V2B8	.;.	R	190;134;190;114	ENSP00000438588:K190R;ENSP00000450560:K134R;ENSP00000216605:K190R;ENSP00000451309:K114R	ENSP00000216605:K134R	K	+	2	0	MTHFD1	63952133	1.000000	0.71417	1.000000	0.80357	0.556000	0.35491	8.820000	0.92003	2.032000	0.59987	0.374000	0.22700	AAA	G|0.827;N|0.000	0.827	strong		0.363	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1		
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 GAIIx	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_ENST00000503538.1_3'UTR|AGGF1_ENST00000506806.1_Missense_Mutation_p.E133K	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	Somatic	208	2	0.00961538		WXS	Illumina HiSeq	Phase_I	244	105	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	
BBS12	166379	hgsc.bcm.edu	37	4	123664446	123664446	+	Missense_Mutation	SNP	G	G	A	rs13135778	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:123664446G>A	ENST00000314218.3	+	2	1592	c.1399G>A	c.(1399-1401)Gac>Aac	p.D467N	BBS12_ENST00000542236.1_Missense_Mutation_p.D467N	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	467			D -> N (in dbSNP:rs13135778). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TTGTGTGGGCGACGGGGTCTG	0.468									Bardet-Biedl syndrome				A|||	464	0.0926518	0.0514	0.1052	5008	,	,		19474	0.0		0.2127	False		,,,				2504	0.1115				p.D467N		Atlas-SNP	.											.	BBS12	63	.	0			c.G1399A						PASS	.	A	ASN/ASP,ASN/ASP	304,4102	798.2+/-415.5	15,274,1914	80.0	79.0	79.0		1399,1399	1.9	0.0	4	dbSNP_121	79	1941,6659	725.5+/-406.6	230,1481,2589	yes	missense,missense	BBS12	NM_001178007.1,NM_152618.2	23,23	245,1755,4503	AA,AG,GG		22.5698,6.8997,17.2613	benign,benign	467/711,467/711	123664446	2245,10761	2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GTGGGCGACGGGG	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1399G>A	4.37:g.123664446G>A	ENSP00000319062:p.Asp467Asn	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	86	84	0.976744	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	238	0.10897435897435898	32	0.06504065040650407	42	0.11602209944751381	0	0.0	164	0.21635883905013192	A	0.015	-1.552873	0.00918	0.068997	0.225698	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.78246	-1.16;-1.16	5.69	1.9	0.25705	.	1.320260	0.04713	N	0.418035	T	0.00039	0.0001	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05099	-1.0906	9	0.07813	T	0.8	-38.0042	9.6017	0.39607	0.7363:0.0:0.2637:0.0	rs13135778;rs17857450;rs13135778	467	Q6ZW61	BBS12_HUMAN	N	467	ENSP00000319062:D467N;ENSP00000438273:D467N	ENSP00000319062:D467N	D	+	1	0	BBS12	123883896	0.000000	0.05858	0.033000	0.17914	0.138000	0.21146	0.602000	0.24134	-0.117000	0.11872	-0.269000	0.10298	GAC	G|0.857;A|0.143	0.143	strong		0.468	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
CD44	960	hgsc.bcm.edu	37	11	35201842	35201842	+	Silent	SNP	C	C	T	rs1071695	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:35201842C>T	ENST00000428726.2	+	3	378	c.255C>T	c.(253-255)caC>caT	p.H85H	CD44_ENST00000263398.6_Silent_p.H85H|CD44_ENST00000433354.2_Silent_p.H85H|CD44_ENST00000278386.6_Intron|CD44_ENST00000415148.2_Silent_p.H85H|CD44_ENST00000360158.4_Silent_p.H85H|CD44_ENST00000437706.2_Silent_p.H85H|CD44_ENST00000449691.2_Silent_p.H85H|CD44_ENST00000352818.4_Silent_p.H85H|CD44_ENST00000434472.2_Silent_p.H85H|CD44_ENST00000526669.2_Silent_p.H85H|CD44_ENST00000433892.2_Silent_p.H85H	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	85	Link. {ECO:0000255|PROSITE- ProRule:PRU00323}.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	TAGAAGGGCACGTGGTGATTC	0.438													C|||	698	0.139377	0.149	0.2205	5008	,	,		19558	0.0714		0.173	False		,,,				2504	0.1043				p.H85H		Atlas-SNP	.											CD44,colon,carcinoma,0,1	CD44	48	1	0			c.C255T	GRCh37	CM076085	CD44	M	rs1071695	PASS	.	C	,,,,,,,	712,3692	296.7+/-284.4	54,604,1544	168.0	140.0	150.0		255,255,255,255,,255,255,255	-8.2	0.3	11	dbSNP_86	150	1477,7119	280.8+/-294.7	123,1231,2944	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	CD44	NM_000610.3,NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1,NM_001202555.1,NM_001202556.1,NM_001202557.1	,,,,,,,	177,1835,4488	TT,TC,CC		17.1824,16.1671,16.8385	,,,,,,,	85/743,85/700,85/494,85/362,,85/430,85/341,85/295	35201842	2189,10811	2202	4298	6500	SO:0001819	synonymous_variant	960	exon3			AGGGCACGTGGTG	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.255C>T	11.37:g.35201842C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	153	57	0.372549	NM_001001391	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	37	CCDS7897.1	333|333	0.15247252747252749|0.15247252747252749	75|75	0.1524390243902439|0.1524390243902439	79|79	0.21823204419889503|0.21823204419889503	47|47	0.08216783216783216|0.08216783216783216	132|132	0.1741424802110818|0.1741424802110818	C|C	4.473|4.473	0.087625|0.087625	0.08583|0.08583	0.161671|0.161671	0.171824|0.171824	ENSG00000026508|ENSG00000026508	ENST00000442151;ENST00000528455|ENST00000527889;ENST00000531873	.|.	.|.	.|.	5.86|5.86	-8.16|-8.16	0.01061|0.01061	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999831683|0.999999831683	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18366|0.18366	-1.0339|-1.0339	3|3	.|.	.|.	.|.	-5.8315|-5.8315	17.4346|17.4346	0.87548|0.87548	0.0:0.1989:0.0:0.8011|0.0:0.1989:0.0:0.8011	rs1071695;rs3198437;rs3198804;rs11542696;rs17423178;rs17849845;rs1071695|rs1071695;rs3198437;rs3198804;rs11542696;rs17423178;rs17849845;rs1071695	.|.	.|.	.|.	C|M	85;22|41;6	.|.	.|.	R|T	+|+	1|2	0|0	CD44|CD44	35158418|35158418	0.001000|0.001000	0.12720|0.12720	0.296000|0.296000	0.24974|0.24974	0.509000|0.509000	0.34042|0.34042	-3.037000|-3.037000	0.00634|0.00634	-1.565000|-1.565000	0.01676|0.01676	-0.806000|-0.806000	0.03193|0.03193	CGT|ACG	C|0.835;T|0.165	0.165	strong		0.438	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
CDH11	1009	hgsc.bcm.edu	37	16	65022114	65022114	+	Silent	SNP	C	C	T	rs28216	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:65022114C>T	ENST00000268603.4	-	7	1560	c.945G>A	c.(943-945)tcG>tcA	p.S315S	CDH11_ENST00000394156.3_Silent_p.S315S|CDH11_ENST00000566827.1_Silent_p.S189S	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	315	Cadherin 3. {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)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TGATTTCAAACGATTCCATAC	0.443			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			C|||	1120	0.223642	0.0734	0.255	5008	,	,		19686	0.2054		0.4066	False		,,,				2504	0.2352				p.S315S		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	CDH11_ENST00000394156,NS,carcinoma,-1,2	CDH11	260	2	0			c.G945A						PASS	.	C		530,3876	241.2+/-251.7	31,468,1704	368.0	309.0	329.0		945	5.7	1.0	16	dbSNP_76	329	3660,4940	527.1+/-381.1	774,2112,1414	no	coding-synonymous	CDH11	NM_001797.2		805,2580,3118	TT,TC,CC		42.5581,12.0291,32.2159		315/797	65022114	4190,8816	2203	4300	6503	SO:0001819	synonymous_variant	1009	exon7			TTCAAACGATTCC	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.945G>A	16.37:g.65022114C>T		Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	232	117	0.50431	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																			C|0.715;T|0.285	0.285	strong		0.443	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
SORCS3	22986	hgsc.bcm.edu	37	10	106917003	106917003	+	Silent	SNP	G	G	A	rs150165918	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:106917003G>A	ENST00000369701.3	+	10	1817	c.1590G>A	c.(1588-1590)ccG>ccA	p.P530P		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	530					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGCAAGCTCCGGATGTGGACC	0.547													G|||	30	0.00599042	0.0015	0.0101	5008	,	,		19428	0.0		0.0149	False		,,,				2504	0.0061				p.P530P	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.G1590A						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	94.0	84.0	87.0		1590	-4.3	0.8	10	dbSNP_134	87	163,8437	76.3+/-139.0	2,159,4139	no	coding-synonymous	SORCS3	NM_014978.1		2,172,6329	AA,AG,GG		1.8953,0.2951,1.3532		530/1223	106917003	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	22986	exon10			AGCTCCGGATGTG	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1590G>A	10.37:g.106917003G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_014978	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																			G|0.987;A|0.013	0.013	strong		0.547	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
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 GAIIx	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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	140	60	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	
BTN3A3	10384	hgsc.bcm.edu	37	6	26443853	26443853	+	Silent	SNP	C	C	A	rs17611438	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26443853C>A	ENST00000244519.2	+	3	294	c.51C>A	c.(49-51)tcC>tcA	p.S17S	BTN3A3_ENST00000339789.4_Intron|BTN3A3_ENST00000361232.3_Intron	NM_006994.4	NP_008925.1	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3	17					T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30						TTCATGTCTCCCTCTTCTTGG	0.438													C|||	725	0.144768	0.1634	0.1772	5008	,	,		17327	0.0308		0.165	False		,,,				2504	0.1933				p.S17S		Atlas-SNP	.											.	BTN3A3	56	.	0			c.C51A						PASS	.	C	,,	788,3618	318.8+/-295.8	65,658,1480	295.0	238.0	257.0		,51,	0.1	0.0	6	dbSNP_129	257	1450,7150	279.1+/-293.8	125,1200,2975	no	intron,coding-synonymous,intron	BTN3A3	NM_001242803.1,NM_006994.4,NM_197974.2	,,	190,1858,4455	AA,AC,CC		16.8605,17.8847,17.2074	,,	,17/585,	26443853	2238,10768	2203	4300	6503	SO:0001819	synonymous_variant	10384	exon3			TGTCTCCCTCTTC	U90548	CCDS4611.1, CCDS4612.1, CCDS4612.2	6p22.1	2014-01-14			ENSG00000111801	ENSG00000111801		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1140	protein-coding gene	gene with protein product		613595				10354554, 9149941	Standard	NM_006994		Approved	BTF3, BTN3.3	uc003nhz.3	O00478	OTTHUMG00000014451	ENST00000244519.2:c.51C>A	6.37:g.26443853C>A		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	268	53	0.197761	NM_006994	B4DWI7|E9PCP5	Silent	SNP	ENST00000244519.2	37	CCDS4611.1																																																																																			C|0.836;A|0.164	0.164	strong		0.438	BTN3A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040116.2	NM_006994	
FRMD6	122786	hgsc.bcm.edu	37	14	52186972	52186972	+	Silent	SNP	A	A	G	rs2277494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:52186972A>G	ENST00000344768.5	+	11	1420	c.1224A>G	c.(1222-1224)ccA>ccG	p.P408P	FRMD6_ENST00000553556.1_Silent_p.P50P|FRMD6_ENST00000395718.2_Silent_p.P400P|FRMD6_ENST00000554167.1_Silent_p.P331P|FRMD6_ENST00000356218.4_Silent_p.P400P			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	408					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					ACACGGGGCCAGAAGACAGCT	0.617													A|||	1692	0.337859	0.388	0.33	5008	,	,		17787	0.3552		0.2525	False		,,,				2504	0.3456				p.P408P		Atlas-SNP	.											.	FRMD6	100	.	0			c.A1224G						PASS	.	A	,	1572,2834	482.3+/-359.4	278,1016,909	62.0	60.0	61.0		1200,1200	-12.0	0.0	14	dbSNP_100	61	1942,6658	337.6+/-322.4	230,1482,2588	no	coding-synonymous,coding-synonymous	FRMD6	NM_001042481.1,NM_152330.3	,	508,2498,3497	GG,GA,AA		22.5814,35.6786,27.0183	,	400/615,400/615	52186972	3514,9492	2203	4300	6503	SO:0001819	synonymous_variant	122786	exon11			GGGGCCAGAAGAC	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"""expanded homolog"""	614555	"""chromosome 14 open reading frame 31"""	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.1224A>G	14.37:g.52186972A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_001267046	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	37	CCDS58318.1																																																																																			A|0.700;G|0.300	0.300	strong		0.617	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189184	11189184	+	Missense_Mutation	SNP	C	C	T	rs115295428	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11189184C>T	ENST00000382435.4	+	1	788	c.569C>T	c.(568-570)aCc>aTc	p.T190I		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	190						integral component of membrane (GO:0016021)		p.T190I(1)									GTCTACACCACCCTGGGCTAT	0.587																																					p.T190I		Atlas-SNP	.											AMAC1L2,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.C569T						scavenged	.						145.0	143.0	143.0					8																	11189184		2203	4300	6503	SO:0001583	missense	83650	exon1			ACACCACCCTGGG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.569C>T	8.37:g.11189184C>T	ENSP00000371872:p.Thr190Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	99	16	0.161616	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	C	6.076	0.382330	0.11524	.	.	ENSG00000177710	ENST00000382435	T	0.24151	1.87	.	.	.	.	0.138504	0.32287	N	0.006302	T	0.10937	0.0267	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28106	-1.0054	8	0.18276	T	0.48	-0.7964	.	.	.	.	190	Q96KT7	S35G5_HUMAN	I	190	ENSP00000371872:T190I	ENSP00000371872:T190I	T	+	2	0	SLC35G5	11226594	0.778000	0.28640	0.080000	0.20451	0.075000	0.17131	0.362000	0.20284	0.088000	0.17205	0.089000	0.15464	ACC	C|0.978;T|0.022	0.022	strong		0.587	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
TAP1	6890	hgsc.bcm.edu	37	6	32814942	32814942	+	Missense_Mutation	SNP	C	C	T	rs1057149	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32814942C>T	ENST00000354258.4	-	10	2284	c.2123G>A	c.(2122-2124)cGa>cAa	p.R708Q	TAPSAR1_ENST00000453426.1_lincRNA|PSMB8_ENST00000374881.2_5'Flank|PSMB9_ENST00000395330.1_Intron|TAP1_ENST00000425148.2_Missense_Mutation_p.R447Q	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	708	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> Q (in allele TAP1*04:01; dbSNP:rs1057149). {ECO:0000269|PubMed:11250043, ECO:0000269|PubMed:12878362, ECO:0000269|PubMed:8168860, ECO:0000269|PubMed:8248212}.		antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|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)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	CACTGCCTGTCGCTGACCCCC	0.572													C|||	296	0.0591054	0.171	0.049	5008	,	,		19876	0.001		0.0338	False		,,,				2504	0.001				p.R708Q		Atlas-SNP	.											.	TAP1	39	.	0			c.G2123A						PASS	.	C	GLN/ARG	373,2649		21,331,1159	99.0	83.0	89.0		2123	4.6	1.0	6	dbSNP_86	89	158,5260		2,154,2553	yes	missense	TAP1	NM_000593.5	43	23,485,3712	TT,TC,CC		2.9162,12.3428,6.2915	probably-damaging	708/809	32814942	531,7909	1511	2709	4220	SO:0001583	missense	6890	exon10			GCCTGTCGCTGAC		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.2123G>A	6.37:g.32814942C>T	ENSP00000346206:p.Arg708Gln	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	42	6	0.142857	NM_000593	Q16149|Q96CP4	Missense_Mutation	SNP	ENST00000354258.4	37	CCDS4758.1	132	0.06043956043956044	95	0.19308943089430894	16	0.04419889502762431	1	0.0017482517482517483	20	0.026385224274406333	C	26.8	4.772874	0.90108	0.123428	0.029162	ENSG00000168394	ENST00000354258;ENST00000425148	D;D	0.94138	-3.36;-3.36	5.43	4.56	0.56223	ABC transporter, conserved site (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.39146	N	0.001454	D	0.93465	0.7915	L	0.56124	1.755	0.29257	P	0.871604	D	0.89917	1.0	D	0.71870	0.975	D	0.93820	0.7118	9	0.72032	D	0.01	1.8168	8.8967	0.35470	0.0:0.8297:0.0:0.1703	rs1057149;rs17883085;rs45470196;rs52792188;rs59175449;rs1057149	708	Q03518	TAP1_HUMAN	Q	708;447	ENSP00000346206:R708Q;ENSP00000401919:R447Q	ENSP00000346206:R708Q	R	-	2	0	TAP1	32922920	0.979000	0.34478	1.000000	0.80357	0.997000	0.91878	1.782000	0.38654	2.552000	0.86080	0.643000	0.83706	CGA	.	.	weak		0.572	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
FAAH2	158584	hgsc.bcm.edu	37	X	57475132	57475132	+	Silent	SNP	T	T	C	rs1367830	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:57475132T>C	ENST00000374900.4	+	10	1524	c.1404T>C	c.(1402-1404)ccT>ccC	p.P468P	FAAH2_ENST00000491179.1_3'UTR	NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	468						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						TAACACGGCCTTTCAACTTTG	0.398										HNSCC(52;0.14)			T|||	1777	0.470728	0.0295	0.402	3775	,	,		9355	0.4663		0.5457	False		,,,				2504	0.4499				p.P468P		Atlas-SNP	.											.	FAAH2	66	.	0			c.T1404C						PASS	.	T		451,3384		30,328,63,1274,508	202.0	146.0	165.0		1404	1.3	1.0	X	dbSNP_88	165	4917,1811		1311,944,1351,173,521	no	coding-synonymous	FAAH2	NM_174912.3		1341,1272,1414,1447,1029	CC,CT,C,TT,T		26.9174,11.7601,49.1811		468/533	57475132	5368,5195	2203	4300	6503	SO:0001819	synonymous_variant	158584	exon10			ACGGCCTTTCAAC	AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"""amidase domain containing"""	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.1404T>C	X.37:g.57475132T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_174912	Q86VT2|Q96N98	Silent	SNP	ENST00000374900.4	37	CCDS14375.1																																																																																			T|0.496;0|0.015	.	strong		0.398	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912	
NEDD9	4739	hgsc.bcm.edu	37	6	11185533	11185533	+	Silent	SNP	G	G	A	rs1050775	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:11185533G>A	ENST00000379446.5	-	7	2533	c.2367C>T	c.(2365-2367)acC>acT	p.T789T	NEDD9_ENST00000504387.1_Silent_p.T789T|RP3-510L9.1_ENST00000500636.2_RNA	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	789					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)		p.T789T(1)		endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			CCATGACTATGGTCTTGAGCT	0.557													A|||	2464	0.492013	0.6452	0.4236	5008	,	,		17248	0.3492		0.5477	False		,,,				2504	0.4233				p.T789T		Atlas-SNP	.											NEDD9_ENST00000379446,NS,carcinoma,0,1	NEDD9	191	1	1	Substitution - coding silent(1)	stomach(1)	c.C2367T						scavenged	.	A	,	2778,1628	500.5+/-364.7	870,1038,295	193.0	170.0	178.0		2367,2367	-11.6	0.0	6	dbSNP_86	178	4595,4005	554.3+/-386.5	1241,2113,946	no	coding-synonymous,coding-synonymous	NEDD9	NM_001142393.1,NM_006403.3	,	2111,3151,1241	AA,AG,GG		46.5698,36.9496,43.3108	,	789/835,789/835	11185533	7373,5633	2203	4300	6503	SO:0001819	synonymous_variant	4739	exon8			GACTATGGTCTTG	L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	7733	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.2367C>T	6.37:g.11185533G>A		Somatic	160	2	0.0125		WXS	Illumina HiSeq	Phase_I	157	154	0.980892	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Silent	SNP	ENST00000379446.5	37	CCDS4520.1																																																																																			G|0.457;A|0.543	0.543	strong		0.557	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
SLC25A32	81034	hgsc.bcm.edu	37	8	104427578	104427578	+	5'Flank	SNP	T	T	C	rs3134297	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:104427578T>C	ENST00000297578.4	-	0	0				DCAF13_ENST00000297579.5_Silent_p.S120S|DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|SLC25A32_ENST00000543107.1_5'Flank	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TGACTGGAAGTAGTCTGGGAA	0.632													T|||	1270	0.253594	0.202	0.268	5008	,	,		18261	0.3333		0.2306	False		,,,				2504	0.2546				p.S120S		Atlas-SNP	.											DCAF13,NS,carcinoma,0,1	DCAF13	66	1	0			c.T360C						PASS	.	T		949,3453		103,743,1355	37.0	45.0	43.0		360	1.9	0.7	8	dbSNP_103	43	1809,6783		189,1431,2676	no	coding-synonymous	DCAF13	NM_015420.6		292,2174,4031	CC,CT,TT		21.0545,21.5584,21.2252		120/598	104427578	2758,10236	2201	4296	6497	SO:0001631	upstream_gene_variant	25879	exon1			TGGAAGTAGTCTG	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		8.37:g.104427578T>C	Exception_encountered	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_015420	Q96JZ6|Q96SU7	Silent	SNP	ENST00000297578.4	37	CCDS6300.1																																																																																			T|0.764;C|0.236	0.236	strong		0.632	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
PSMD9	5715	hgsc.bcm.edu	37	12	122353796	122353796	+	Missense_Mutation	SNP	A	A	G	rs14259	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:122353796A>G	ENST00000541212.1	+	5	716	c.590A>G	c.(589-591)gAa>gGa	p.E197G	PSMD9_ENST00000261817.2_Missense_Mutation_p.E196G|WDR66_ENST00000397454.2_5'Flank|RP11-87C12.2_ENST00000546333.1_Intron|PSMD9_ENST00000542602.1_Missense_Mutation_p.E92G|WDR66_ENST00000288912.4_5'Flank			O00233	PSMD9_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 9	197			E -> G (in dbSNP:rs14259).		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)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion (GO:0046676)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome regulatory particle assembly (GO:0070682)|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)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome regulatory particle (GO:0005838)	bHLH transcription factor binding (GO:0043425)|transcription coactivator activity (GO:0003713)			endometrium(1)|large_intestine(1)|lung(1)	3	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000117)|Epithelial(86;0.000415)|BRCA - Breast invasive adenocarcinoma(302;0.231)		CGCAGGGGGGAAAAACACCAG	0.468													A|||	1429	0.285343	0.0454	0.3602	5008	,	,		20405	0.4812		0.3131	False		,,,				2504	0.3262				p.E197G		Atlas-SNP	.											.	PSMD9	8	.	0			c.A590G						PASS	.	A	GLY/GLU	327,4079		16,295,1892	52.0	50.0	51.0		590	5.3	1.0	12	dbSNP_52	51	2448,6152		399,1650,2251	yes	missense	PSMD9	NM_002813.4	98	415,1945,4143	GG,GA,AA		28.4651,7.4217,21.3363	benign	197/224	122353796	2775,10231	2203	4300	6503	SO:0001583	missense	5715	exon5			GGGGGGAAAAACA	AB003177	CCDS9225.1, CCDS58284.1	12q24.31-q24.32	2008-05-22			ENSG00000110801	ENSG00000110801		"""Proteasome (prosome, macropain) subunits"""	9567	protein-coding gene	gene with protein product		603146				9653651	Standard	NM_002813		Approved	p27, Rpn4	uc001ubl.4	O00233	OTTHUMG00000168945	ENST00000541212.1:c.590A>G	12.37:g.122353796A>G	ENSP00000440485:p.Glu197Gly	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_002813	B2RD35|G3V1Q6|Q9BQ42	Missense_Mutation	SNP	ENST00000541212.1	37	CCDS9225.1	672	0.3076923076923077	23	0.046747967479674794	123	0.3397790055248619	286	0.5	240	0.316622691292876	A	16.62	3.174136	0.57692	0.074217	0.284651	ENSG00000110801;ENSG00000110801;ENSG00000110801;ENSG00000256950	ENST00000541212;ENST00000261817;ENST00000544724;ENST00000542602	T;T;T;T	0.73575	-0.76;2.24;-0.76;2.24	5.31	5.31	0.75309	PDZ/DHR/GLGF (1);	0.224065	0.47455	D	0.000232	T	0.00012	0.0000	L	0.47078	1.49	0.09310	P	1.0	P	0.37594	0.601	B	0.39876	0.312	T	0.48422	-0.9037	9	0.40728	T	0.16	-32.2127	12.676	0.56895	1.0:0.0:0.0:0.0	rs14259;rs1043307;rs3182873;rs52803200;rs1043307	197	O00233	PSMD9_HUMAN	G	197;196;108;92	ENSP00000440485:E197G;ENSP00000261817:E196G;ENSP00000443929:E108G;ENSP00000443772:E92G	ENSP00000261817:E196G	E	+	2	0	RP11-87C12.2;PSMD9	120838179	0.999000	0.42202	0.996000	0.52242	0.275000	0.26752	2.324000	0.43831	2.012000	0.59069	0.533000	0.62120	GAA	A|0.747;G|0.253	0.253	strong		0.468	PSMD9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401686.1	NM_002813	
OSBP2	23762	hgsc.bcm.edu	37	22	31266546	31266546	+	Silent	SNP	T	T	C	rs2301816	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:31266546T>C	ENST00000332585.6	+	3	1088	c.984T>C	c.(982-984)gcT>gcC	p.A328A	OSBP2_ENST00000401475.1_5'UTR|OSBP2_ENST00000446658.2_Silent_p.A328A|OSBP2_ENST00000437268.2_Silent_p.A70A|OSBP2_ENST00000382310.3_Silent_p.A328A|OSBP2_ENST00000403222.3_Silent_p.A163A|OSBP2_ENST00000407373.1_Silent_p.A155A	NM_001282739.1|NM_001282740.1|NM_001282741.1|NM_001282742.1|NM_030758.3	NP_001269668.1|NP_001269669.1|NP_001269670.1|NP_001269671.1|NP_110385.1	Q969R2	OSBP2_HUMAN	oxysterol binding protein 2	328					lipid transport (GO:0006869)	membrane (GO:0016020)	cholesterol binding (GO:0015485)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(6)|ovary(1)|skin(3)|urinary_tract(1)	19						AGCACGGCGCTGCACTCCAGC	0.597													C|||	3539	0.706669	0.7383	0.6686	5008	,	,		18461	0.8234		0.6252	False		,,,				2504	0.6544				p.A328A		Atlas-SNP	.											.	OSBP2	52	.	0			c.T984C						PASS	.	C		3146,1174		1162,822,176	67.0	73.0	71.0		984	-8.7	0.0	22	dbSNP_100	71	5265,3227		1664,1937,645	no	coding-synonymous	OSBP2	NM_030758.3		2826,2759,821	CC,CT,TT		38.0005,27.1759,34.3506		328/917	31266546	8411,4401	2160	4246	6406	SO:0001819	synonymous_variant	23762	exon3			CGGCGCTGCACTC		CCDS43002.1, CCDS63448.1, CCDS63449.1, CCDS63450.1, CCDS63451.1	22q12.2	2013-01-10			ENSG00000184792	ENSG00000184792		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	8504	protein-coding gene	gene with protein product		606729		OSBPL1		10591208, 11278871, 11802775	Standard	NM_001282738		Approved	KIAA1664, ORP-4, ORP4	uc003aiy.1	Q969R2	OTTHUMG00000151153	ENST00000332585.6:c.984T>C	22.37:g.31266546T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_030758	B0QYG1|B4DK24|B4DKE4|B4DTR3|F5H2A3|O60396|Q0VF99|Q8NA37|Q9BY96|Q9BZF0	Silent	SNP	ENST00000332585.6	37	CCDS43002.1																																																																																			T|0.307;C|0.693	0.693	strong		0.597	OSBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321547.2	NM_030758	
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 GAIIx	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	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	60	28	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	
EXPH5	23086	hgsc.bcm.edu	37	11	108384207	108384207	+	Missense_Mutation	SNP	C	C	T	rs2846412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:108384207C>T	ENST00000265843.4	-	6	2137	c.2027G>A	c.(2026-2028)aGc>aAc	p.S676N	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Missense_Mutation_p.S600N|EXPH5_ENST00000525344.1_Missense_Mutation_p.S669N|EXPH5_ENST00000443411.1_Missense_Mutation_p.S488N	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	676			S -> N (in dbSNP:rs2846412). {ECO:0000269|PubMed:12062444, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TGAATTGCTGCTGGTCACAGT	0.413													T|||	3211	0.641174	0.6982	0.5533	5008	,	,		20113	0.8542		0.4384	False		,,,				2504	0.6155				p.S676N		Atlas-SNP	.											.	EXPH5	193	.	0			c.G2027A						PASS	.	T	ASN/SER	2893,1509	479.2+/-358.4	976,941,284	119.0	114.0	116.0		2027	1.1	0.0	11	dbSNP_100	116	3627,4969	624.4+/-397.6	786,2055,1457	yes	missense	EXPH5	NM_015065.2	46	1762,2996,1741	TT,TC,CC		42.194,34.2799,49.8384	benign	676/1990	108384207	6520,6478	2201	4298	6499	SO:0001583	missense	23086	exon6			TTGCTGCTGGTCA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.2027G>A	11.37:g.108384207C>T	ENSP00000265843:p.Ser676Asn	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	1351	0.6185897435897436	333	0.676829268292683	176	0.4861878453038674	506	0.8846153846153846	336	0.44327176781002636	T	0.006	-2.111572	0.00353	0.657201	0.42194	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03831	4.38;4.3;4.15;4.38;4.23;3.79	6.03	1.14	0.20703	.	0.625758	0.16479	N	0.212613	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22661	-1.0210	9	0.02654	T	1	-0.745	9.5688	0.39416	0.0:0.3732:0.0:0.6268	rs2846412;rs3824986;rs52806719;rs59043239;rs2846412	676	Q8NEV8	EXPH5_HUMAN	N	676;600;488;669;520;600;488	ENSP00000265843:S676N;ENSP00000391966:S600N;ENSP00000411390:S488N;ENSP00000432546:S669N;ENSP00000432683:S600N;ENSP00000446434:S488N	ENSP00000265843:S676N	S	-	2	0	EXPH5	107889417	0.006000	0.16342	0.000000	0.03702	0.004000	0.04260	0.673000	0.25203	-0.041000	0.13558	-1.396000	0.01147	AGC	C|0.440;T|0.560	0.560	strong		0.413	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
LAMA1	284217	hgsc.bcm.edu	37	18	7012123	7012123	+	Silent	SNP	A	A	G	rs9946794	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:7012123A>G	ENST00000389658.3	-	24	3471	c.3378T>C	c.(3376-3378)ggT>ggC	p.G1126G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1126	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				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)				TGCACTGAGGACCAAAGACAT	0.512													G|||	2104	0.420128	0.851	0.3833	5008	,	,		15427	0.0536		0.3648	False		,,,				2504	0.2986				p.G1126G		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	1	0			c.T3378C						PASS	.	G		3346,1060	383.0+/-324.7	1264,818,121	42.0	42.0	42.0		3378	-0.9	0.8	18	dbSNP_119	42	3349,5251	640.8+/-399.6	663,2023,1614	no	coding-synonymous	LAMA1	NM_005559.3		1927,2841,1735	GG,GA,AA		38.9419,24.0581,48.5238		1126/3076	7012123	6695,6311	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon24			CTGAGGACCAAAG	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.3378T>C	18.37:g.7012123A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			A|0.528;G|0.472	0.472	strong		0.512	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
DPCR1	135656	hgsc.bcm.edu	37	6	30920124	30920124	+	Missense_Mutation	SNP	G	G	A	rs3132580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30920124G>A	ENST00000462446.1	+	2	3911	c.3883G>A	c.(3883-3885)Gag>Aag	p.E1295K	DPCR1_ENST00000304311.2_Missense_Mutation_p.E137K|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	419						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CACAGGAAACGAGAGCCATCC	0.443													G|||	192	0.0383387	0.0378	0.0288	5008	,	,		20858	0.0159		0.0964	False		,,,				2504	0.0092				p.E1295K		Atlas-SNP	.											.	DPCR1	99	.	0			c.G3883A						PASS	.	G	LYS/GLU	308,4098	166.2+/-197.5	7,294,1902	95.0	90.0	92.0		3883	-7.2	0.0	6	dbSNP_103	92	1135,7465	234.0+/-267.1	72,991,3237	yes	missense	DPCR1	NM_080870.3	56	79,1285,5139	AA,AG,GG		13.1977,6.9905,11.0949	benign	1295/1394	30920124	1443,11563	2203	4300	6503	SO:0001583	missense	135656	exon2			GGAAACGAGAGCC	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.3883G>A	6.37:g.30920124G>A	ENSP00000417182:p.Glu1295Lys	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	178	140	0.786517	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	134	0.06135531135531135	30	0.06097560975609756	11	0.03038674033149171	14	0.024475524475524476	79	0.10422163588390501	G	7.300	0.612780	0.14066	0.069905	0.131977	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.24350	1.86;1.97	3.61	-7.22	0.01485	.	.	.	.	.	T	0.01661	0.0053	N	0.04508	-0.205	0.80722	P	0.0	B	0.18968	0.032	B	0.13407	0.009	T	0.36553	-0.9743	8	0.10111	T	0.7	0.1331	3.183	0.06590	0.193:0.4849:0.1963:0.1259	rs3132580;rs52797861;rs59423268;rs3132580	1295	E9PEI6	.	K	1295;419;137	ENSP00000417182:E1295K;ENSP00000305948:E137K	ENSP00000305948:E137K	E	+	1	0	DPCR1	31028103	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.956000	0.03865	-2.176000	0.00770	-0.499000	0.04595	GAG	G|0.913;A|0.087	0.087	strong		0.443	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
NAV2	89797	hgsc.bcm.edu	37	11	20117232	20117232	+	Silent	SNP	T	T	C	rs2289566	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:20117232T>C	ENST00000396087.3	+	33	6207	c.6108T>C	c.(6106-6108)caT>caC	p.H2036H	NAV2_ENST00000533917.1_Silent_p.H1041H|NAV2_ENST00000540292.1_Silent_p.H1967H|NAV2_ENST00000360655.4_Silent_p.H1913H|NAV2_ENST00000396085.1_Silent_p.H1980H|NAV2_ENST00000311043.8_Silent_p.H1041H|NAV2_ENST00000349880.4_Silent_p.H1977H|NAV2_ENST00000527559.2_Silent_p.H1965H	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2036					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CCAGACCACATCTCTTTCTTA	0.458													C|||	2271	0.453474	0.2239	0.438	5008	,	,		20775	0.8899		0.3012	False		,,,				2504	0.4816				p.H2036H		Atlas-SNP	.											.	NAV2	255	.	0			c.T6108C						PASS	.	C	,,,	973,3433	732.5+/-410.4	107,759,1337	243.0	219.0	227.0		5739,3123,5931,5940	2.7	0.9	11	dbSNP_100	227	2371,6229	701.9+/-405.2	335,1701,2264	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	442,2460,3601	CC,CT,TT		27.5698,22.0835,25.7112	,,,	1913/2366,1041/1494,1977/2430,1980/2433	20117232	3344,9662	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon32			ACCACATCTCTTT	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.6108T>C	11.37:g.20117232T>C		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	167	90	0.538922	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			T|0.656;C|0.344	0.344	strong		0.458	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
MRPS24	64951	hgsc.bcm.edu	37	7	43906513	43906513	+	Missense_Mutation	SNP	A	A	G	rs670573	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:43906513A>G	ENST00000317534.5	-	4	350	c.289T>C	c.(289-291)Tgg>Cgg	p.W97R	MRPS24_ENST00000467084.1_5'UTR|URGCP-MRPS24_ENST00000603700.1_3'UTR	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	97			W -> R (in dbSNP:rs670573).		translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						AAGGTACCCCACATGAACTTG	0.552													A|||	492	0.0982428	0.1445	0.0865	5008	,	,		17920	0.1379		0.0865	False		,,,				2504	0.0153				p.W97R		Atlas-SNP	.											.	MRPS24	9	.	0			c.T289C						PASS	.	A	,ARG/TRP	541,3865	244.3+/-253.7	32,477,1694	73.0	67.0	69.0		,289	-5.2	0.6	7	dbSNP_83	69	614,7986	160.7+/-213.8	23,568,3709	yes	utr-3,missense	MRPS24,URGCP-MRPS24	NM_001204871.1,NM_032014.2	,101	55,1045,5403	GG,GA,AA		7.1395,12.2787,8.8805	,benign	,97/168	43906513	1155,11851	2203	4300	6503	SO:0001583	missense	64951	exon4			TACCCCACATGAA	AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"""Mitochondrial ribosomal proteins / small subunits"""	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.289T>C	7.37:g.43906513A>G	ENSP00000318158:p.Trp97Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	44	35	0.795455	NM_032014	A4D1U9|P82668|Q96Q23|Q9P047	Missense_Mutation	SNP	ENST00000317534.5	37	CCDS5473.1	280	0.1282051282051282	91	0.18495934959349594	33	0.09116022099447514	94	0.16433566433566432	62	0.08179419525065963	A	9.445	1.089135	0.20390	0.122787	0.071395	ENSG00000062582	ENST00000317534	T	0.39056	1.1	5.24	-5.21	0.02815	.	0.555420	0.19142	N	0.121667	T	0.00039	0.0001	N	0.01352	-0.895	0.46222	P	0.0010639999999999539	B	0.14438	0.01	B	0.18871	0.023	T	0.24440	-1.0160	9	0.25106	T	0.35	.	4.527	0.11986	0.3699:0.0:0.2779:0.3522	rs670573;rs1058812;rs3199453;rs3735265;rs11549686;rs52789329;rs58986208;rs670573	97	Q96EL2	RT24_HUMAN	R	97	ENSP00000318158:W97R	ENSP00000318158:W97R	W	-	1	0	MRPS24	43873038	0.990000	0.36364	0.587000	0.28692	0.609000	0.37215	0.834000	0.27518	-0.925000	0.03775	-0.242000	0.12053	TGG	T|0.000;G|0.102;N|0.000;A|0.898	0.102	strong		0.552	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014	
TMEM86A	144110	hgsc.bcm.edu	37	11	18727448	18727448	+	IGR	SNP	T	T	C	rs1867877	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18727448T>C	ENST00000280734.2	+	0	3595				IGSF22_ENST00000510673.1_5'UTR|IGSF22_ENST00000513874.1_Missense_Mutation_p.T1276A|RP11-1081L13.4_ENST00000527285.1_RNA	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A							integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						TCCTTGAGCGTGCAGGTGGGG	0.632													T|||	110	0.0219649	0.0242	0.0346	5008	,	,		16793	0.0		0.0507	False		,,,				2504	0.0031				p.T1276A		Atlas-SNP	.											.	IGSF22	211	.	0			c.A3826G						PASS	.	T	ALA/THR	35,1349		0,35,657	50.0	46.0	47.0		3826	3.5	0.8	11	dbSNP_92	47	158,3024		3,152,1436	yes	missense	IGSF22	NM_173588.3	58	3,187,2093	CC,CT,TT		4.9654,2.5289,4.2269	possibly-damaging	1276/1327	18727448	193,4373	692	1591	2283	SO:0001628	intergenic_variant	283284	exon22			TGAGCGTGCAGGT	BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4			11.37:g.18727448T>C		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_173588	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	68	0.031135531135531136	11	0.022357723577235773	14	0.03867403314917127	0	0.0	43	0.05672823218997362	T	18.51	3.640639	0.67244	0.025289	0.049654	ENSG00000179057	ENST00000513874	T	0.66995	-0.24	5.28	3.48	0.39840	.	.	.	.	.	T	0.14227	0.0344	L	0.53249	1.67	0.20703	N	0.999865	B	0.25007	0.116	B	0.32393	0.145	T	0.19811	-1.0294	9	0.16420	T	0.52	.	7.3562	0.26721	0.0:0.1563:0.0:0.8437	rs1867877;rs4509732;rs16935667;rs1867877	1276	D6RGV7	.	A	1276	ENSP00000421191:T1276A	ENSP00000421191:T1276A	T	-	1	0	IGSF22	18684024	0.367000	0.25023	0.834000	0.33040	0.994000	0.84299	0.444000	0.21661	0.467000	0.27218	0.528000	0.53228	ACG	T|0.970;C|0.030	0.030	strong		0.632	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
ACE	1636	hgsc.bcm.edu	37	17	61559923	61559923	+	Silent	SNP	C	C	T	rs4309	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:61559923C>T	ENST00000290866.4	+	8	1239	c.1215C>T	c.(1213-1215)ccC>ccT	p.P405P	ACE_ENST00000290863.6_5'Flank|ACE_ENST00000428043.1_Silent_p.P405P|ACE_ENST00000577647.1_5'Flank|ACE_ENST00000538928.1_Silent_p.P405P|ACE_ENST00000584529.1_3'UTR|ACE_ENST00000421982.2_5'Flank|ACE_ENST00000490216.2_5'Flank|ACE_ENST00000413513.3_5'Flank	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	405	Peptidase M2 1.				angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|arachidonic acid secretion (GO:0050482)|blood vessel remodeling (GO:0001974)|cellular protein metabolic process (GO:0044267)|hematopoietic stem cell differentiation (GO:0060218)|hormone catabolic process (GO:0042447)|kidney development (GO:0001822)|mononuclear cell proliferation (GO:0032943)|peptide catabolic process (GO:0043171)|regulation of blood pressure (GO:0008217)|regulation of renal output by angiotensin (GO:0002019)|regulation of smooth muscle cell migration (GO:0014910)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|bradykinin receptor binding (GO:0031711)|carboxypeptidase activity (GO:0004180)|chloride ion binding (GO:0031404)|drug binding (GO:0008144)|endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|peptidyl-dipeptidase activity (GO:0008241)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(3)|lung(22)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	51					Benazepril(DB00542)|Candoxatril(DB00616)|Captopril(DB01197)|Cilazapril(DB01340)|Enalapril(DB00584)|Fosinopril(DB00492)|Lisinopril(DB00722)|Moexipril(DB00691)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Rescinnamine(DB01180)|Spirapril(DB01348)|Trandolapril(DB00519)	AGGATCTGCCCGTCTCCCTGC	0.602													C|||	2121	0.423522	0.1104	0.5519	5008	,	,		17804	0.6468		0.3877	False		,,,				2504	0.5624				p.P405P		Atlas-SNP	.											.	ACE	187	.	0			c.C1215T						PASS	.	C		779,3627	312.5+/-292.6	66,647,1490	121.0	98.0	106.0		1215	-6.1	0.9	17	dbSNP_36	106	3587,5013	519.6+/-379.5	748,2091,1461	no	coding-synonymous	ACE	NM_000789.3		814,2738,2951	TT,TC,CC		41.7093,17.6804,33.5691		405/1307	61559923	4366,8640	2203	4300	6503	SO:0001819	synonymous_variant	1636	exon8			TCTGCCCGTCTCC	J04144	CCDS11637.1, CCDS45755.1, CCDS54155.1	17q23.3	2013-06-12	2013-06-12		ENSG00000159640	ENSG00000159640	3.4.15.1	"""CD molecules"""	2707	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	106180	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 1"""	DCP1		2554286, 10319862	Standard	NM_001178057		Approved	ACE1, CD143	uc002jau.2	P12821	OTTHUMG00000154927	ENST00000290866.4:c.1215C>T	17.37:g.61559923C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Silent	SNP	ENST00000290866.4	37	CCDS11637.1																																																																																			C|0.639;T|0.361	0.361	strong		0.602	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2		
ZNF100	163227	hgsc.bcm.edu	37	19	21910451	21910451	+	Silent	SNP	A	A	C	rs35587380	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:21910451A>C	ENST00000358296.6	-	5	861	c.663T>G	c.(661-663)acT>acG	p.T221T	ZNF100_ENST00000305570.6_Silent_p.T157T	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	221					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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						TTTTATGTTGAGTTAGGTGTA	0.318													N|||	514	0.102636	0.1369	0.0533	5008	,	,		19858	0.0218		0.0596	False		,,,				2504	0.2188				p.T221T		Atlas-SNP	.											.	ZNF100	62	.	0			c.T663G						PASS	.	A		621,3465		51,519,1473	53.0	55.0	55.0		663	1.0	0.0	19	dbSNP_126	55	631,7821		23,585,3618	no	coding-synonymous	ZNF100	NM_173531.3		74,1104,5091	CC,CA,AA		7.4657,15.1982,9.9856		221/543	21910451	1252,11286	2043	4226	6269	SO:0001819	synonymous_variant	163227	exon5			ATGTTGAGTTAGG	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"""Zinc fingers, C2H2-type"", ""-"""	12880	protein-coding gene	gene with protein product		603982	"""zinc finger protein 100 (Y1)"""			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.663T>G	19.37:g.21910451A>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			.	.	weak		0.318	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
PCDH8	5100	hgsc.bcm.edu	37	13	53422553	53422553	+	Missense_Mutation	SNP	A	A	G	rs3742301	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:53422553A>G	ENST00000377942.3	-	1	222	c.19T>C	c.(19-21)Tgg>Cgg	p.W7R	PCDH8_ENST00000338862.4_Missense_Mutation_p.W7R	NM_002590.3	NP_002581.2	O95206	PCDH8_HUMAN	protocadherin 8	7			W -> R (in dbSNP:rs3742301). {ECO:0000269|PubMed:12884975}.		cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|morphogenesis of embryonic epithelium (GO:0016331)|somitogenesis (GO:0001756)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(23)|ovary(1)|skin(1)|urinary_tract(1)	36		Lung NSC(96;0.0019)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.19e-08)		GGGCTGCCCCAACGCCTCACA	0.592													A|||	1425	0.284545	0.1876	0.2579	5008	,	,		16382	0.5119		0.2048	False		,,,				2504	0.2822				p.W7R	GBM(36;25 841 9273 49207)	Atlas-SNP	.											.	PCDH8	95	.	0			c.T19C						PASS	.	A	ARG/TRP,ARG/TRP	881,3523		103,675,1424	36.0	35.0	35.0		19,19	-0.2	0.5	13	dbSNP_107	35	1620,6978		145,1330,2824	yes	missense,missense	PCDH8	NM_002590.3,NM_032949.2	101,101	248,2005,4248	GG,GA,AA		18.8416,20.0045,19.2355	benign,benign	7/1071,7/974	53422553	2501,10501	2202	4299	6501	SO:0001583	missense	5100	exon1			TGCCCCAACGCCT	AF061573	CCDS9438.1, CCDS9439.1	13q21.1	2010-02-22			ENSG00000136099	ENSG00000136099		"""Cadherins / Protocadherins : Non-clustered"""	8660	protein-coding gene	gene with protein product		603580				9787079, 9315676	Standard	NM_002590		Approved	PAPC, ARCADLIN	uc001vhi.3	O95206	OTTHUMG00000016979	ENST00000377942.3:c.19T>C	13.37:g.53422553A>G	ENSP00000367177:p.Trp7Arg	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_002590	B4DMV7|Q5TAN1|Q5TAN2|Q8IYE9|Q96SF1	Missense_Mutation	SNP	ENST00000377942.3	37	CCDS9438.1	608	0.2783882783882784	89	0.18089430894308944	64	0.17679558011049723	293	0.5122377622377622	162	0.21372031662269128	A	5.090	0.202283	0.09652	0.200045	0.188416	ENSG00000136099	ENST00000377942;ENST00000338862;ENST00000418407;ENST00000448969	T;T	0.51817	0.72;0.69	5.3	-0.221	0.13126	.	0.164261	0.28841	N	0.013964	T	0.00012	0.0000	N	0.08118	0	0.51012	P	9.40000000000385E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46176	-0.9210	9	0.25751	T	0.34	.	2.1402	0.03772	0.3347:0.3898:0.0967:0.1789	rs3742301;rs3742301	7;7	O95206-2;O95206	.;PCDH8_HUMAN	R	7	ENSP00000367177:W7R;ENSP00000341350:W7R	ENSP00000341350:W7R	W	-	1	0	PCDH8	52320554	0.032000	0.19561	0.455000	0.27031	0.390000	0.30446	0.115000	0.15540	-0.415000	0.07484	0.460000	0.39030	TGG	A|0.769;G|0.231	0.231	strong		0.592	PCDH8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045108.2	NM_002590	
CHAD	1101	hgsc.bcm.edu	37	17	48543154	48543154	+	Silent	SNP	G	G	A	rs2231507	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48543154G>A	ENST00000508540.1	-	2	1004	c.852C>T	c.(850-852)ccC>ccT	p.P284P	CHAD_ENST00000258969.4_Silent_p.P284P|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000427954.2_Intron|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000504392.1_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	284					bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGAAGTTGGAGGGTAGCTGGT	0.577													G|||	121	0.0241613	0.0015	0.0202	5008	,	,		16822	0.0		0.0527	False		,,,				2504	0.0532				p.P284P		Atlas-SNP	.											CHAD,upper_leg,malignant_melanoma,-2,1	CHAD	36	1	0			c.C852T						PASS	.	G	,	35,4371	40.0+/-72.8	0,35,2168	206.0	176.0	186.0		852,	-3.4	0.7	17	dbSNP_98	186	406,8194	128.2+/-186.4	13,380,3907	no	coding-synonymous,intron	CHAD,ACSF2	NM_001267.2,NM_025149.4	,	13,415,6075	AA,AG,GG		4.7209,0.7944,3.3907	,	284/360,	48543154	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	1101	exon2			GTTGGAGGGTAGC	U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1909	protein-coding gene	gene with protein product	"""chondroadherin proteoglycan"""	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.852C>T	17.37:g.48543154G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001267	A8K812|Q6GTU0|Q96RJ5	Silent	SNP	ENST00000508540.1	37	CCDS11568.1																																																																																			G|0.964;A|0.036	0.036	strong		0.577	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267	
TUBA3E	112714	hgsc.bcm.edu	37	2	130949491	130949491	+	Silent	SNP	G	G	A	rs60154251	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:130949491G>A	ENST00000312988.7	-	5	1366	c.1266C>T	c.(1264-1266)cgC>cgT	p.R422R		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	422					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					CCAGGTCCTCGCGGGCCTCAG	0.582																																					p.R422R		Atlas-SNP	.											TUBA3E,colon,carcinoma,-2,1	TUBA3E	73	1	0			c.C1266T						PASS	.	G		1579,2827	492.0+/-362.3	286,1007,910	126.0	130.0	129.0		1266	-5.0	0.8	2	dbSNP_129	129	3354,5246	497.4+/-374.5	654,2046,1600	no	coding-synonymous	TUBA3E	NM_207312.2		940,3053,2510	AA,AG,GG		39.0,35.8375,37.9286		422/451	130949491	4933,8073	2203	4300	6503	SO:0001819	synonymous_variant	112714	exon5			GTCCTCGCGGGCC	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.1266C>T	2.37:g.130949491G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	127	32	0.251969	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			G|0.612;A|0.388	0.388	strong		0.582	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
INPP4B	8821	hgsc.bcm.edu	37	4	143324094	143324094	+	Silent	SNP	G	G	A	rs1982966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:143324094G>A	ENST00000513000.1	-	8	802	c.369C>T	c.(367-369)gaC>gaT	p.D123D	INPP4B_ENST00000308502.4_Silent_p.D123D|INPP4B_ENST00000509777.1_Silent_p.D123D|INPP4B_ENST00000508116.1_Silent_p.D123D|INPP4B_ENST00000506217.1_Silent_p.D123D|INPP4B_ENST00000262992.4_Silent_p.D123D	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	123	C2.				cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.D123D(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					TACTTACGGTGTCATGAGACT	0.363													G|||	1265	0.252596	0.0318	0.2378	5008	,	,		20821	0.2907		0.3489	False		,,,				2504	0.4233				p.D123D		Atlas-SNP	.											INPP4B,NS,carcinoma,0,1	INPP4B	132	1	1	Substitution - coding silent(1)	stomach(1)	c.C369T						PASS	.	G	,	374,4032	188.1+/-214.6	16,342,1845	164.0	129.0	141.0		369,369	2.8	1.0	4	dbSNP_92	141	2980,5620	462.6+/-365.7	489,2002,1809	no	coding-synonymous,coding-synonymous	INPP4B	NM_001101669.1,NM_003866.2	,	505,2344,3654	AA,AG,GG		34.6512,8.4884,25.7881	,	123/925,123/925	143324094	3354,9652	2203	4300	6503	SO:0001819	synonymous_variant	8821	exon8			TACGGTGTCATGA	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.369C>T	4.37:g.143324094G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			G|0.743;A|0.257	0.257	strong		0.363	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	
DPT	1805	hgsc.bcm.edu	37	1	168683476	168683476	+	Silent	SNP	C	C	T	rs35449613	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:168683476C>T	ENST00000367817.3	-	2	503	c.414G>A	c.(412-414)agG>agA	p.R138R		NM_001937.4	NP_001928.2	Q07507	DERM_HUMAN	dermatopontin	138	2 X 53-55 AA tandem repeats.|3 X 6 AA repeats of D-R-[EQ]-W-[NQK]- [FY].				cell adhesion (GO:0007155)|collagen fibril organization (GO:0030199)|negative regulation of cell proliferation (GO:0008285)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)	12	all_hematologic(923;0.208)					AATATGGGCACCTCTTGCTGT	0.567													C|||	149	0.0297524	0.0023	0.0245	5008	,	,		16666	0.001		0.0596	False		,,,				2504	0.0695				p.R138R		Atlas-SNP	.											.	DPT	29	.	0			c.G414A						PASS	.	C		53,4353	53.6+/-89.4	1,51,2151	83.0	74.0	77.0		414	-1.8	1.0	1	dbSNP_126	77	536,8064	148.3+/-203.6	18,500,3782	no	coding-synonymous	DPT	NM_001937.4		19,551,5933	TT,TC,CC		6.2326,1.2029,4.5287		138/202	168683476	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	1805	exon2			TGGGCACCTCTTG	BC033736	CCDS1275.1	1q12-q23	2008-02-05			ENSG00000143196	ENSG00000143196			3011	protein-coding gene	gene with protein product		125597				8104875	Standard	NM_001937		Approved		uc001gfp.3	Q07507	OTTHUMG00000034554	ENST00000367817.3:c.414G>A	1.37:g.168683476C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	NM_001937	A8K981|Q8N4R2|Q9UIX8	Silent	SNP	ENST00000367817.3	37	CCDS1275.1																																																																																			C|0.957;G|0.000;T|0.043	0.043	strong		0.567	DPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083618.1	NM_001937	
ATP2A3	489	hgsc.bcm.edu	37	17	3845927	3845927	+	Silent	SNP	A	A	G	rs17846889	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3845927A>G	ENST00000352011.3	-	12	1572	c.1518T>C	c.(1516-1518)acT>acC	p.T506T	ATP2A3_ENST00000397043.3_Silent_p.T506T|ATP2A3_ENST00000359983.3_Silent_p.T506T|ATP2A3_ENST00000397035.3_Silent_p.T506T|ATP2A3_ENST00000397041.3_Silent_p.T506T|ATP2A3_ENST00000309890.7_Silent_p.T506T|ATP2A3_ENST00000397039.1_5'UTR			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	506					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		TGCCCTGGCCAGTAGGGTGAG	0.642													a|||	1927	0.384784	0.584	0.4712	5008	,	,		16766	0.0873		0.4553	False		,,,				2504	0.2883				p.T506T	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T1518C						PASS	.	G	,,,,,,	2512,1894	629.2+/-395.2	714,1084,405	78.0	68.0	72.0		1518,1518,1518,1518,1518,1518,1518	-7.9	0.0	17	dbSNP_123	72	3954,4646	550.0+/-385.7	933,2088,1279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	1647,3172,1684	GG,GA,AA		45.9767,42.9868,49.7155	,,,,,,	506/1000,506/1053,506/1045,506/1044,506/1030,506/999,506/1030	3845927	6466,6540	2203	4300	6503	SO:0001819	synonymous_variant	489	exon12			CTGGCCAGTAGGG		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1518T>C	17.37:g.3845927A>G		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	46	24	0.521739	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			G|0.461;C|0.000;A|0.539	0.461	strong		0.642	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
LGR4	55366	hgsc.bcm.edu	37	11	27389739	27389739	+	Missense_Mutation	SNP	T	T	C	rs34804482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:27389739T>C	ENST00000379214.4	-	18	2974	c.2531A>G	c.(2530-2532)gAc>gGc	p.D844G	LGR4_ENST00000389858.4_Missense_Mutation_p.D820G	NM_018490.2	NP_060960.2	Q9BXB1	LGR4_HUMAN	leucine-rich repeat containing G protein-coupled receptor 4	844			D -> G (in dbSNP:rs34804482).		bone mineralization (GO:0030282)|bone remodeling (GO:0046849)|canonical Wnt signaling pathway involved in metanephric kidney development (GO:0061290)|cell differentiation involved in metanephros development (GO:0072202)|epithelial cell proliferation (GO:0050673)|innate immune response (GO:0045087)|male genitalia development (GO:0030539)|metanephric glomerulus development (GO:0072224)|metanephric nephron tubule morphogenesis (GO:0072282)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast differentiation (GO:0001649)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(10)|ovary(1)	32						CATGCCACAGTCGTAGTAGAA	0.438													T|||	33	0.00658946	0.0	0.0159	5008	,	,		20498	0.0		0.0219	False		,,,				2504	0.0				p.D844G		Atlas-SNP	.											LGR4,right_upper_lobe,carcinoma,-1,1	LGR4	87	1	0			c.A2531G						PASS	.	T	GLY/ASP	27,4377	33.5+/-64.1	0,27,2175	160.0	153.0	156.0		2531	5.4	1.0	11	dbSNP_126	156	187,8411	84.5+/-147.0	3,181,4115	yes	missense	LGR4	NM_018490.2	94	3,208,6290	CC,CT,TT		2.1749,0.6131,1.6459	probably-damaging	844/952	27389739	214,12788	2202	4299	6501	SO:0001583	missense	55366	exon18			CCACAGTCGTAGT	AF257182	CCDS31449.1	11p14-p13	2012-08-21	2011-01-25	2004-11-12	ENSG00000205213	ENSG00000205213		"""GPCR / Class A : Orphans"""	13299	protein-coding gene	gene with protein product		606666	"""G protein-coupled receptor 48"", ""leucine-rich repeat-containing G protein-coupled receptor 4"""	GPR48		10894923	Standard	NM_018490		Approved		uc001mrj.4	Q9BXB1	OTTHUMG00000133508	ENST00000379214.4:c.2531A>G	11.37:g.27389739T>C	ENSP00000368516:p.Asp844Gly	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	61	37	0.606557	NM_018490	A6NCH3|G5E9B3|Q8N537|Q9NYD1	Missense_Mutation	SNP	ENST00000379214.4	37	CCDS31449.1	27	0.012362637362637362	0	0.0	9	0.024861878453038673	0	0.0	18	0.023746701846965697	T	18.54	3.645483	0.67358	0.006131	0.021749	ENSG00000205213	ENST00000379214;ENST00000389858	T;T	0.62105	0.05;0.15	5.39	5.39	0.77823	.	0.094876	0.64402	D	0.000001	T	0.53932	0.1827	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	0.986;1.0	P;D	0.83275	0.84;0.996	T	0.68349	-0.5432	10	0.62326	D	0.03	.	15.4105	0.74914	0.0:0.0:0.0:1.0	rs34804482	820;844	G5E9B3;Q9BXB1	.;LGR4_HUMAN	G	844;820	ENSP00000368516:D844G;ENSP00000374508:D820G	ENSP00000368516:D844G	D	-	2	0	LGR4	27346315	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	6.000000	0.70678	2.062000	0.61559	0.454000	0.30748	GAC	T|0.983;C|0.017	0.017	strong		0.438	LGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257467.1	NM_018490	
APOBEC3H	164668	hgsc.bcm.edu	37	22	39497454	39497454	+	Missense_Mutation	SNP	G	G	C	rs139299	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39497454G>C	ENST00000401756.1	+	3	439	c.363G>C	c.(361-363)aaG>aaC	p.K121N	APOBEC3H_ENST00000348946.4_Missense_Mutation_p.K121N|APOBEC3H_ENST00000421988.2_Missense_Mutation_p.K121N|APOBEC3H_ENST00000442487.3_Missense_Mutation_p.K121N	NM_001166003.1	NP_001159475.1	Q6NTF7	ABC3H_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3H	121			K -> E (in allele A3H-Var; haplotype 2; allele presenting a higher expression and more effective in retrotransposons and HIV-1 restriction; dbSNP:rs139298).|K -> N (in dbSNP:rs139299).	K -> D (in Ref. 2; CAG30367). {ECO:0000305}.	cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral process (GO:0048525)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(8)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15	Melanoma(58;0.04)					CCCAGCAGAAGGGGCTGCGGC	0.597													G|||	2653	0.529752	0.8752	0.3876	5008	,	,		6362	0.3155		0.4771	False		,,,				2504	0.4387				p.K121N		Atlas-SNP	.											.	APOBEC3H	28	.	0			c.G363C						PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	3564,842		1465,634,104	51.0	49.0	50.0		363,363,363,363	1.3	0.4	22	dbSNP_78	50	3932,4668		898,2136,1266	yes	missense,missense,missense,missense	APOBEC3H	NM_001166002.1,NM_001166003.1,NM_001166004.1,NM_181773.3	94,94,94,94	2363,2770,1370	CC,CG,GG		45.7209,19.1103,42.3651	benign,benign,benign,benign	121/183,121/201,121/155,121/184	39497454	7496,5510	2203	4300	6503	SO:0001583	missense	164668	exon3			GCAGAAGGGGCTG	BC069023	CCDS13985.1, CCDS54530.1, CCDS54531.1, CCDS54532.1	22q13.1	2007-02-01			ENSG00000100298	ENSG00000100298		"""Apolipoprotein B mRNA editing enzymes"""	24100	protein-coding gene	gene with protein product		610976				16571802	Standard	NM_001166003		Approved	ARP10	uc021wpt.1	Q6NTF7	OTTHUMG00000151082	ENST00000401756.1:c.363G>C	22.37:g.39497454G>C	ENSP00000385741:p.Lys121Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001166003	B0QYP0|B0QYP1|B7TQM5|E9PF38|Q5JYL9|Q6IC87	Missense_Mutation	SNP	ENST00000401756.1	37	CCDS54530.1	1098	0.5027472527472527	427	0.8678861788617886	129	0.356353591160221	172	0.3006993006993007	370	0.48812664907651715	.	11.64	1.698131	0.30142	0.808897	0.457209	ENSG00000100298	ENST00000348946;ENST00000442487;ENST00000421988;ENST00000401756	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	3.33	1.26	0.21427	.	.	.	.	.	T	0.00012	0.0000	L	0.59436	1.845	0.58432	P	1.0000000000287557E-6	B	0.26602	0.154	B	0.36719	0.231	T	0.18209	-1.0344	8	0.72032	D	0.01	-5.078	5.5224	0.16939	0.2545:0.0:0.7455:0.0	rs139299;rs60075609	121	B7TQM3	.	N	121	ENSP00000216123:K121N;ENSP00000411754:K121N;ENSP00000393520:K121N;ENSP00000385741:K121N	ENSP00000216123:K121N	K	+	3	2	APOBEC3H	37827400	0.860000	0.29831	0.436000	0.26797	0.010000	0.07245	1.033000	0.30191	0.441000	0.26529	0.460000	0.39030	AAG	G|0.453;C|0.547	0.547	strong		0.597	APOBEC3H-002	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321230.1	NM_181773	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180701	57180701	+	Missense_Mutation	SNP	A	A	G	rs181288707	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57180701A>G	ENST00000504228.1	+	6	1138	c.1033A>G	c.(1033-1035)Agg>Ggg	p.R345G	KIAA1211_ENST00000541073.1_Missense_Mutation_p.R338G|KIAA1211_ENST00000264229.6_Missense_Mutation_p.R345G			Q6ZU35	K1211_HUMAN	KIAA1211	345	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GGAGGAGCggaggcggcagga	0.692													A|||	34	0.00678914	0.0008	0.0159	5008	,	,		12439	0.0		0.0149	False		,,,				2504	0.0072				p.R345G		Atlas-SNP	.											KIAA1211,NS,carcinoma,-2,1	KIAA1211	178	1	0			c.A1033G						scavenged	.	A	GLY/ARG	1,3909		0,1,1954	5.0	6.0	6.0		1033	1.2	0.0	4		6	38,7718		0,38,3840	yes	missense	KIAA1211	NM_020722.1	125	0,39,5794	GG,GA,AA		0.4899,0.0256,0.3343	probably-damaging	345/1234	57180701	39,11627	1955	3878	5833	SO:0001583	missense	57482	exon8			GAGCGGAGGCGGC	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.1033A>G	4.37:g.57180701A>G	ENSP00000423366:p.Arg345Gly	Somatic	16	2	0.125		WXS	Illumina HiSeq	Phase_I	12	9	0.75	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	24	0.01098901098901099	6	0.012195121951219513	6	0.016574585635359115	0	0.0	12	0.0158311345646438	A	13.06	2.125450	0.37533	2.56E-4	0.004899	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.01981	4.52;4.52;4.52	4.97	1.2	0.21068	.	.	.	.	.	T	0.01421	0.0046	N	0.24115	0.695	0.09310	N	1	P;D;D	0.53462	0.873;0.96;0.96	P;P;P	0.50537	0.544;0.643;0.643	T	0.50285	-0.8846	9	0.66056	D	0.02	-6.5533	8.6736	0.34165	0.7855:0.0:0.2145:0.0	.	338;338;345	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	G	345;345;338;255	ENSP00000264229:R345G;ENSP00000423366:R345G;ENSP00000444006:R338G	ENSP00000264229:R345G	R	+	1	2	KIAA1211	56875458	0.000000	0.05858	0.000000	0.03702	0.307000	0.27823	0.488000	0.22371	-0.012000	0.14223	0.379000	0.24179	AGG	A|0.989;G|0.011	0.011	strong		0.692	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
CD276	80381	hgsc.bcm.edu	37	15	73996590	73996590	+	Silent	SNP	G	G	A	rs143255170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:73996590G>A	ENST00000318443.5	+	6	1448	c.1146G>A	c.(1144-1146)acG>acA	p.T382T	CD276_ENST00000537340.2_Silent_p.T236T|CD276_ENST00000318424.5_Silent_p.T164T|CD276_ENST00000561213.1_Silent_p.T382T|CD276_ENST00000564751.1_Silent_p.T164T	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	382	Ig-like C2-type 2.				cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						TGACCATCACGTGCTCCAGCT	0.647													G|||	56	0.0111821	0.0045	0.0101	5008	,	,		20817	0.001		0.0358	False		,,,				2504	0.0061				p.T382T		Atlas-SNP	.											.	CD276	29	.	0			c.G1146A						PASS	.	G	,	37,4359	39.2+/-71.8	0,37,2161	84.0	76.0	79.0		1146,492	2.2	1.0	15	dbSNP_134	79	376,8218	123.8+/-182.6	9,358,3930	no	coding-synonymous,coding-synonymous	CD276	NM_001024736.1,NM_025240.2	,	9,395,6091	AA,AG,GG		4.3751,0.8417,3.1794	,	382/535,164/317	73996590	413,12577	2198	4297	6495	SO:0001819	synonymous_variant	80381	exon6			CATCACGTGCTCC	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.1146G>A	15.37:g.73996590G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	138	73	0.528986	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Silent	SNP	ENST00000318443.5	37	CCDS32288.1																																																																																			G|0.974;A|0.026	0.026	strong		0.647	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
MTMR2	8898	hgsc.bcm.edu	37	11	95580926	95580926	+	Silent	SNP	G	G	A	rs566204	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:95580926G>A	ENST00000346299.5	-	10	1471	c.1131C>T	c.(1129-1131)acC>acT	p.T377T	MTMR2_ENST00000393223.3_Silent_p.T305T|MTMR2_ENST00000484818.1_5'Flank|MTMR2_ENST00000409459.1_Silent_p.T305T|MTMR2_ENST00000352297.7_Silent_p.T305T	NM_016156.5	NP_057240.3	Q13614	MTMR2_HUMAN	myotubularin related protein 2	377	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				cell death (GO:0008219)|dendritic spine maintenance (GO:0097062)|inositol phosphate dephosphorylation (GO:0046855)|myelin assembly (GO:0032288)|negative regulation of endocytosis (GO:0045806)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of myelination (GO:0031642)|negative regulation of receptor catabolic process (GO:2000645)|negative regulation of receptor internalization (GO:0002091)|neuron development (GO:0048666)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of early endosome to late endosome transport (GO:2000643)|protein dephosphorylation (GO:0006470)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endosome (GO:0005768)|neuronal postsynaptic density (GO:0097481)|nucleus (GO:0005634)|synaptic membrane (GO:0097060)|synaptic vesicle (GO:0008021)|vacuolar membrane (GO:0005774)	phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	19		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				ACAACCAGTGGGTTTCCTCAA	0.378													A|||	1048	0.209265	0.0923	0.2378	5008	,	,		19645	0.253		0.3708	False		,,,				2504	0.136				p.T377T		Atlas-SNP	.											.	MTMR2	79	.	0			c.C1131T						PASS	.	A	,,	585,3817	771.7+/-413.8	43,499,1659	140.0	139.0	139.0		1131,915,915	-9.1	0.6	11	dbSNP_83	139	3289,5307	646.7+/-400.3	598,2093,1607	no	coding-synonymous,coding-synonymous,coding-synonymous	MTMR2	NM_016156.5,NM_201278.2,NM_201281.2	,,	641,2592,3266	AA,AG,GG		38.262,13.2894,29.8046	,,	377/644,305/572,305/572	95580926	3874,9124	2201	4298	6499	SO:0001819	synonymous_variant	8898	exon10			CCAGTGGGTTTCC	U58033	CCDS8305.1, CCDS8306.1	11q22	2014-09-17			ENSG00000087053	ENSG00000087053		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7450	protein-coding gene	gene with protein product		603557		CMT4B		8640223, 9736772	Standard	NM_016156		Approved	KIAA1073	uc001pfu.3	Q13614	OTTHUMG00000153837	ENST00000346299.5:c.1131C>T	11.37:g.95580926G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	234	37	0.15812	NM_016156	A6NN98|Q9UPS9	Silent	SNP	ENST00000346299.5	37	CCDS8305.1																																																																																			G|0.715;A|0.285	0.285	strong		0.378	MTMR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332620.1	NM_016156	
LILRB5	10990	hgsc.bcm.edu	37	19	54759361	54759361	+	Missense_Mutation	SNP	T	T	C	rs12975366	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54759361T>C	ENST00000316219.5	-	5	847	c.740A>G	c.(739-741)gAt>gGt	p.D247G	LILRB5_ENST00000449561.2_Missense_Mutation_p.D247G|LILRB5_ENST00000450632.1_Missense_Mutation_p.D238G|LILRB5_ENST00000345866.6_Missense_Mutation_p.D147G	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	247	Ig-like C2-type 3.		D -> G (in dbSNP:rs12975366).		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ATAGCCGACATCAGAGCGACA	0.632													.|||	1356	0.270767	0.1483	0.3213	5008	,	,		15944	0.125		0.4344	False		,,,				2504	0.3824				p.D247G		Atlas-SNP	.											LILRB5_ENST00000450632,colon,carcinoma,0,4	LILRB5	176	4	0			c.A740G						scavenged	.	T	GLY/ASP,GLY/ASP,GLY/ASP	790,3616	317.7+/-295.3	61,668,1474	52.0	49.0	50.0		740,440,740	1.5	0.1	19	dbSNP_121	50	3529,5071	512.5+/-378.0	735,2059,1506	yes	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	94,94,94	796,2727,2980	CC,CT,TT		41.0349,17.9301,33.2078	probably-damaging,probably-damaging,probably-damaging	247/592,147/492,247/591	54759361	4319,8687	2203	4300	6503	SO:0001583	missense	10990	exon5			CCGACATCAGAGC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.740A>G	19.37:g.54759361T>C	ENSP00000320390:p.Asp247Gly	Somatic	170	2	0.0117647		WXS	Illumina HiSeq	Phase_I	156	75	0.480769	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	582	0.2664835164835165	91	0.18495934959349594	135	0.3729281767955801	44	0.07692307692307693	312	0.41160949868073876	T	13.84	2.356397	0.41700	0.179301	0.410349	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	2.62	1.52	0.23074	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.931743	0.08893	N	0.878354	T	0.00012	0.0000	M	0.78285	2.405	0.80722	P	0.0	D;D;D;D;D	0.89917	0.998;0.999;0.998;0.982;1.0	D;D;D;P;D	0.78314	0.988;0.959;0.961;0.9;0.991	T	0.39820	-0.9595	9	0.66056	D	0.02	.	5.5585	0.17129	0.0:0.0:0.2868:0.7132	rs12975366	238;138;147;247;247	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	G	247;238;247;147	ENSP00000320390:D247G;ENSP00000414225:D238G;ENSP00000406478:D247G;ENSP00000263430:D147G	ENSP00000320390:D247G	D	-	2	0	LILRB5	59451173	0.000000	0.05858	0.055000	0.19348	0.130000	0.20726	0.165000	0.16564	0.372000	0.24591	0.366000	0.22137	GAT	T|0.679;C|0.321	0.321	strong		0.632	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
MCM10	55388	hgsc.bcm.edu	37	10	13214753	13214753	+	Missense_Mutation	SNP	G	G	C	rs34630110	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:13214753G>C	ENST00000484800.2	+	5	686	c.583G>C	c.(583-585)Gct>Cct	p.A195P	MCM10_ENST00000378714.3_Missense_Mutation_p.A194P|MCM10_ENST00000378694.1_Missense_Mutation_p.A194P			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	195			A -> P (in dbSNP:rs34630110). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039}.		cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						AACACCAAAGGCTTCACCTCC	0.502													G|||	206	0.0411342	0.0166	0.0447	5008	,	,		17884	0.0149		0.1163	False		,,,				2504	0.0215				p.A195P		Atlas-SNP	.											.	MCM10	76	.	0			c.G583C						PASS	.	G	PRO/ALA,PRO/ALA	177,4229	113.8+/-151.8	1,175,2027	90.0	77.0	82.0		580,583	-6.1	0.0	10	dbSNP_126	82	1027,7573	218.4+/-256.8	53,921,3326	yes	missense,missense	MCM10	NM_018518.4,NM_182751.2	27,27	54,1096,5353	CC,CG,GG		11.9419,4.0172,9.2573	benign,benign	194/875,195/876	13214753	1204,11802	2203	4300	6503	SO:0001583	missense	55388	exon5			CCAAAGGCTTCAC	AB042719	CCDS7095.1, CCDS7096.1	10p13	2008-08-01	2007-04-04		ENSG00000065328	ENSG00000065328			18043	protein-coding gene	gene with protein product		609357	"""MCM10 minichromosome maintenance deficient 10 (S. cerevisiae)"""			11095689, 17699597	Standard	NM_018518		Approved	PRO2249, CNA43, DNA43	uc001ima.3	Q7L590	OTTHUMG00000017694	ENST00000484800.2:c.583G>C	10.37:g.13214753G>C	ENSP00000418268:p.Ala195Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	137	0.06272893772893773	10	0.02032520325203252	23	0.06353591160220995	13	0.022727272727272728	91	0.12005277044854881	G	10.32	1.317398	0.23908	0.040172	0.119419	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.14516	2.5;2.5;2.5	5.23	-6.07	0.02158	.	0.992219	0.08198	N	0.982792	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.41413	-0.9510	9	0.28530	T	0.3	-13.661	7.3141	0.26491	0.3368:0.4113:0.2519:0.0	rs34630110	194;194;195	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	P	194;195;195;194	ENSP00000367986:A194P;ENSP00000418268:A195P;ENSP00000367966:A194P	ENSP00000354945:A195P	A	+	1	0	MCM10	13254759	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.322000	0.02695	-1.167000	0.02779	-0.175000	0.13238	GCT	G|0.912;C|0.088	0.088	strong		0.502	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
DLG5	9231	hgsc.bcm.edu	37	10	79570873	79570873	+	Missense_Mutation	SNP	G	G	T	rs2289310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:79570873G>T	ENST00000372391.2	-	23	4447	c.4442C>A	c.(4441-4443)cCa>cAa	p.P1481Q	DLG5_ENST00000372388.2_Missense_Mutation_p.P1141Q|DLG5_ENST00000459739.1_5'UTR	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1481			P -> Q (in dbSNP:rs2289310). {ECO:0000269|PubMed:15489334}.		apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			CTGCTTGGCTGGGGGGGTGCT	0.647													G|||	338	0.067492	0.0371	0.0447	5008	,	,		18071	0.1716		0.0338	False		,,,				2504	0.0521				p.P1481Q		Atlas-SNP	.											.	DLG5	154	.	0			c.C4442A	GRCh37	CM066561	DLG5	M	rs2289310	PASS	.	G	GLN/PRO	134,4272	96.2+/-134.9	2,130,2071	65.0	66.0	66.0		4442	0.4	0.0	10	dbSNP_100	66	363,8237	118.5+/-177.9	7,349,3944	yes	missense	DLG5	NM_004747.3	76	9,479,6015	TT,TG,GG		4.2209,3.0413,3.8213	benign	1481/1920	79570873	497,12509	2203	4300	6503	SO:0001583	missense	9231	exon23			TTGGCTGGGGGGG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.4442C>A	10.37:g.79570873G>T	ENSP00000361467:p.Pro1481Gln	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	177	0.08104395604395605	19	0.03861788617886179	18	0.049723756906077346	118	0.2062937062937063	22	0.029023746701846966	G	11.97	1.797217	0.31777	0.030413	0.042209	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.05513	3.66;3.43;3.67	5.44	0.391	0.16282	PDZ/DHR/GLGF (1);	0.634763	0.13153	N	0.409694	T	0.00012	0.0000	N	0.11255	0.115	0.30320	P	0.787655	B;B	0.31680	0.0;0.335	B;B	0.24541	0.001;0.054	T	0.49890	-0.8891	9	0.15066	T	0.55	.	6.6646	0.23032	0.2518:0.0:0.6338:0.1144	rs2289310;rs2289310	1481;1141	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	Q	1481;442;1141	ENSP00000361467:P1481Q;ENSP00000394797:P442Q;ENSP00000361464:P1141Q	ENSP00000361464:P1141Q	P	-	2	0	DLG5	79240879	1.000000	0.71417	0.040000	0.18447	0.575000	0.36095	3.891000	0.56227	-0.112000	0.11979	-0.812000	0.03155	CCA	G|0.944;T|0.056	0.056	strong		0.647	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
FANCM	57697	hgsc.bcm.edu	37	14	45658449	45658449	+	Missense_Mutation	SNP	A	A	G	rs143662421	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:45658449A>G	ENST00000267430.5	+	20	5309	c.5224A>G	c.(5224-5226)Att>Gtt	p.I1742V	FANCM_ENST00000542564.2_Missense_Mutation_p.I1716V	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1742	Interaction with FAAP24 and EME1.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAAGGATACAATTTCCGAAGT	0.423								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				A|||	19	0.00379393	0.0	0.0086	5008	,	,		16827	0.0		0.0119	False		,,,				2504	0.001				p.I1742V		Atlas-SNP	.											.	FANCM	225	.	0			c.A5224G						PASS	.	A	VAL/ILE	18,4388	25.3+/-52.1	0,18,2185	125.0	129.0	127.0		5224	-2.3	0.0	14	dbSNP_134	127	121,8479	63.9+/-126.0	2,117,4181	yes	missense	FANCM	NM_020937.2	29	2,135,6366	GG,GA,AA		1.407,0.4085,1.0687	benign	1742/2049	45658449	139,12867	2203	4300	6503	SO:0001583	missense	57697	exon20	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GATACAATTTCCG	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5224A>G	14.37:g.45658449A>G	ENSP00000267430:p.Ile1742Val	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	113	45	0.39823	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	A|A	0.102|0.102	-1.150801|-1.150801	0.01700|0.01700	0.004085|0.004085	0.01407|0.01407	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.76709|.	-1.04;-1.04;-1.04|.	5.26|5.26	-2.26|-2.26	0.06867|0.06867	.|.	2.866430|.	0.01021|.	N|.	0.003992|.	T|T	0.04497|0.04497	0.0123|0.0123	N|N	0.00841|0.00841	-1.15|-1.15	0.09310|0.09310	N|N	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|T	0.29305|0.29305	-1.0016|-1.0016	10|5	0.02654|.	T|.	1|.	.|.	1.4104|1.4104	0.02290|0.02290	0.2872:0.1195:0.4341:0.1592|0.2872:0.1195:0.4341:0.1592	.|.	1716;1742|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	V|S	1742;1716;1258|674	ENSP00000267430:I1742V;ENSP00000442493:I1716V;ENSP00000452033:I1258V|.	ENSP00000267430:I1742V|.	I|N	+|+	1|2	0|0	FANCM|FANCM	44728199|44728199	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.006000|0.006000	0.05464|0.05464	-0.518000|-0.518000	0.06267|0.06267	-0.703000|-0.703000	0.05049|0.05049	-0.256000|-0.256000	0.11100|0.11100	ATT|AAT	A|0.992;G|0.008	0.008	strong		0.423	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
CDH17	1015	hgsc.bcm.edu	37	8	95186382	95186382	+	Silent	SNP	G	G	A	rs3214050	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:95186382G>A	ENST00000027335.3	-	6	655	c.531C>T	c.(529-531)gtC>gtT	p.V177V	CDH17_ENST00000450165.2_Silent_p.V177V|CDH17_ENST00000441892.2_Intron	NM_004063.3	NP_004054.3	Q12864	CAD17_HUMAN	cadherin 17, LI cadherin (liver-intestine)	177	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|oligopeptide transmembrane transport (GO:0035672)|oligopeptide transport (GO:0006857)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)|transporter activity (GO:0005215)	p.V177V(1)		NS(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(4)|stomach(2)	52	Breast(36;4.65e-06)		BRCA - Breast invasive adenocarcinoma(8;0.00691)			GAAAGTACATGACATTGTTGA	0.488													G|||	1732	0.345847	0.2307	0.281	5008	,	,		17966	0.3165		0.4384	False		,,,				2504	0.4826				p.V177V		Atlas-SNP	.											CDH17,NS,carcinoma,0,1	CDH17	119	1	1	Substitution - coding silent(1)	stomach(1)	c.C531T						PASS	.	G	,	1045,3361	384.2+/-325.2	103,839,1261	179.0	172.0	174.0		531,531	-2.8	0.5	8	dbSNP_106	174	4029,4571	555.7+/-386.7	933,2163,1204	no	coding-synonymous,coding-synonymous	CDH17	NM_001144663.1,NM_004063.3	,	1036,3002,2465	AA,AG,GG		46.8488,23.7177,39.0128	,	177/833,177/833	95186382	5074,7932	2203	4300	6503	SO:0001819	synonymous_variant	1015	exon6			GTACATGACATTG	X83228	CCDS6260.1	8q22.1	2010-01-26			ENSG00000079112	ENSG00000079112		"""Cadherins / Major cadherins"""	1756	protein-coding gene	gene with protein product		603017				9615235, 10191097	Standard	NM_004063		Approved	HPT-1, cadherin	uc003ygh.2	Q12864	OTTHUMG00000164391	ENST00000027335.3:c.531C>T	8.37:g.95186382G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_004063	Q15336|Q2M2E0	Silent	SNP	ENST00000027335.3	37	CCDS6260.1																																																																																			G|0.634;A|0.366	0.366	strong		0.488	CDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378560.1	NM_004063	
PEPD	5184	hgsc.bcm.edu	37	19	33882222	33882222	+	Silent	SNP	G	G	A	rs17569	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:33882222G>A	ENST00000244137.7	-	13	1164	c.1131C>T	c.(1129-1131)caC>caT	p.H377H	PEPD_ENST00000591968.1_5'UTR|PEPD_ENST00000397032.4_Silent_p.H336H|PEPD_ENST00000436370.3_Silent_p.H313H	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	377					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					CTCCCACGTCGTGCACGTCAA	0.667													G|||	493	0.0984425	0.0068	0.0562	5008	,	,		17793	0.2192		0.1392	False		,,,				2504	0.0859				p.H377H		Atlas-SNP	.											.	PEPD	48	.	0			c.C1131T						PASS	.	G	,,	96,4118		1,94,2012	26.0	31.0	29.0		1131,1008,939	-1.8	1.0	19	dbSNP_63	29	1242,7202		88,1066,3068	no	coding-synonymous,coding-synonymous,coding-synonymous	PEPD	NM_000285.3,NM_001166056.1,NM_001166057.1	,,	89,1160,5080	AA,AG,GG		14.7087,2.2781,10.5704	,,	377/494,336/453,313/430	33882222	1338,11320	2107	4222	6329	SO:0001819	synonymous_variant	5184	exon13			CACGTCGTGCACG	BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"""prolidase"""	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.1131C>T	19.37:g.33882222G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Silent	SNP	ENST00000244137.7	37	CCDS42544.1																																																																																			T|0.045;G|0.545;C|0.327;A|0.083	0.083	strong		0.667	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285	
POM121	9883	hgsc.bcm.edu	37	7	72418992	72418992	+	IGR	SNP	C	C	T	rs9955	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:72418992C>T	ENST00000434423.2	+	0	3750				NSUN5P2_ENST00000388955.4_RNA|POM121_ENST00000446813.1_Missense_Mutation_p.P995S|POM121_ENST00000395270.1_Missense_Mutation_p.P995S			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.G269G(1)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				ATCTTCCTTTCCCACCAGGAA	0.587													.|||	723	0.144369	0.0234	0.2118	5008	,	,		17517	0.2768		0.1282	False		,,,				2504	0.1401				p.P995S		Atlas-SNP	.											NSUN5P2,NS,carcinoma,0,1	POM121	131	1	1	Substitution - coding silent(1)	stomach(1)	c.C2983T						PASS	.	C		207,4189	127.0+/-164.0	17,173,2008	82.0	94.0	90.0			-4.5	0.0	7	dbSNP_52	90	1162,7438	238.3+/-269.8	78,1006,3216	no	near-gene-3				95,1179,5224	TT,TC,CC		13.5116,4.7088,10.534			72418992	1369,11627	2198	4300	6498	SO:0001628	intergenic_variant	9883	exon16			TCCTTTCCCACCA	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527		7.37:g.72418992C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_001257190	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		326	0.14926739926739926	16	0.032520325203252036	49	0.13535911602209943	169	0.29545454545454547	92	0.12137203166226913	C	3.853	-0.031491	0.07543	0.047088	0.135116	ENSG00000196313	ENST00000446813;ENST00000395270	T;T	0.05786	3.39;3.39	2.23	-4.46	0.03536	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.19706	0.038	B	0.10450	0.005	T	0.47873	-0.9083	7	0.87932	D	0	.	4.9717	0.14119	0.0:0.1933:0.3082:0.4985	rs9955;rs3176073;rs11555377;rs59369353	995	A8MXF9	.	S	995	ENSP00000393020:P995S;ENSP00000378687:P995S	ENSP00000378687:P995S	P	+	1	0	POM121	72056928	0.001000	0.12720	0.000000	0.03702	0.063000	0.16089	0.048000	0.14078	-1.254000	0.02485	0.162000	0.16502	CCC	C|0.882;T|0.118	0.118	strong		0.587	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
CNPPD1	27013	hgsc.bcm.edu	37	2	220037666	220037666	+	Missense_Mutation	SNP	A	A	G	rs1127102	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:220037666A>G	ENST00000409789.1	-	9	1302	c.875T>C	c.(874-876)cTc>cCc	p.L292P	SLC23A3_ENST00000396775.3_5'Flank|SLC23A3_ENST00000409878.3_5'Flank|CNPPD1_ENST00000360507.5_Missense_Mutation_p.L292P|SLC23A3_ENST00000455516.2_5'Flank|SLC23A3_ENST00000295738.7_5'Flank			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	292			L -> P (in dbSNP:rs1127102). {ECO:0000269|PubMed:10810093, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	integral component of membrane (GO:0016021)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	12						GACATTAGCGAGAGACGGCAG	0.627													G|||	2013	0.401957	0.2421	0.402	5008	,	,		15637	0.2302		0.6163	False		,,,				2504	0.5746				p.L292P		Atlas-SNP	.											.	CNPPD1	22	.	0			c.T875C						PASS	.	G	PRO/LEU	1277,3129	676.9+/-403.3	199,879,1125	98.0	84.0	89.0		875	2.2	0.0	2	dbSNP_86	89	5167,3433	476.2+/-369.3	1545,2077,678	yes	missense	CNPPD1	NM_015680.4	98	1744,2956,1803	GG,GA,AA		39.9186,28.9832,49.5464	benign	292/411	220037666	6444,6562	2203	4300	6503	SO:0001583	missense	27013	exon8			TTAGCGAGAGACG	AF070638	CCDS2433.1	2q36	2011-03-23	2011-03-23	2011-03-23	ENSG00000115649	ENSG00000115649			25220	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 24"""	C2orf24		8619474, 9110174	Standard	NM_015680		Approved	CGI-57	uc002vju.4	Q9BV87	OTTHUMG00000133132	ENST00000409789.1:c.875T>C	2.37:g.220037666A>G	ENSP00000386277:p.Leu292Pro	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_015680	B2RC77|O75548|Q9H4N0|Q9UQN0	Missense_Mutation	SNP	ENST00000409789.1	37	CCDS2433.1	921	0.4217032967032967	133	0.2703252032520325	162	0.44751381215469616	146	0.25524475524475526	480	0.633245382585752	G	0.589	-0.833693	0.02713	0.289832	0.600814	ENSG00000115649	ENST00000360507;ENST00000409789;ENST00000453038	T;T;T	0.31769	2.43;2.43;1.48	4.11	2.22	0.28083	.	0.929335	0.09138	N	0.843386	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39333	-0.9619	9	0.34782	T	0.22	-10.9143	1.2749	0.02028	0.1975:0.1742:0.4488:0.1795	rs1127102;rs3182634;rs16859617;rs17844906;rs17856406;rs17857627;rs60431309;rs1127102	292	Q9BV87	CNPD1_HUMAN	P	292	ENSP00000353698:L292P;ENSP00000386277:L292P;ENSP00000410109:L292P	ENSP00000353698:L292P	L	-	2	0	CNPPD1	219745910	0.666000	0.27475	0.003000	0.11579	0.033000	0.12548	0.941000	0.29005	0.045000	0.15804	-0.119000	0.15052	CTC	A|0.553;G|0.447	0.447	strong		0.627	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189215	11189215	+	Silent	SNP	C	C	A	rs151245433	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11189215C>A	ENST00000382435.4	+	1	819	c.600C>A	c.(598-600)ggC>ggA	p.G200G		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	200						integral component of membrane (GO:0016021)		p.G200G(1)									TCCTGGGAGGCCTGGCGCTGT	0.592																																					p.G200G		Atlas-SNP	.											AMAC1L2,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C600A						scavenged	.						106.0	112.0	110.0					8																	11189215		2203	4300	6503	SO:0001819	synonymous_variant	83650	exon1			GGGAGGCCTGGCG	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.600C>A	8.37:g.11189215C>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	13	0.139785	NM_054028	A2RRL6	Silent	SNP	ENST00000382435.4	37	CCDS5980.1																																																																																			C|0.988;A|0.011	0.011	strong		0.592	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
MUC16	94025	hgsc.bcm.edu	37	19	9072221	9072221	+	Silent	SNP	G	G	A	rs66498329	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9072221G>A	ENST00000397910.4	-	3	15428	c.15225C>T	c.(15223-15225)ggC>ggT	p.G5075G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5077	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCTTCACTAGGCCAGAGGTGA	0.468													G|||	1007	0.201078	0.0946	0.2824	5008	,	,		21007	0.3254		0.167	False		,,,				2504	0.1943				p.G5075G		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	0			c.C15225T						scavenged	.			401,3443		18,365,1539	153.0	138.0	143.0		15225	-3.4	0.0	19	dbSNP_130	143	1503,6757		136,1231,2763	no	coding-synonymous	MUC16	NM_024690.2		154,1596,4302	AA,AG,GG		18.1961,10.4318,15.7303		5075/14508	9072221	1904,10200	1922	4130	6052	SO:0001819	synonymous_variant	94025	exon3			CACTAGGCCAGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.15225C>T	19.37:g.9072221G>A		Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.787;A|0.213	0.213	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
BAI2	576	hgsc.bcm.edu	37	1	32221913	32221913	+	Silent	SNP	G	G	A	rs4949223	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:32221913G>A	ENST00000373658.3	-	4	866	c.525C>T	c.(523-525)ccC>ccT	p.P175P	BAI2_ENST00000257070.4_Silent_p.P175P|BAI2_ENST00000398547.1_Silent_p.P163P|BAI2_ENST00000398556.3_Silent_p.P178P|MIR4254_ENST00000581063.1_RNA|BAI2_ENST00000398538.1_Silent_p.P163P|BAI2_ENST00000373655.2_Silent_p.P175P|BAI2_ENST00000527361.1_Silent_p.P175P|BAI2_ENST00000398542.1_Silent_p.P163P	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	175					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(2)|endometrium(1)|large_intestine(7)|liver(2)|lung(24)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	55		Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0606)|all_neural(195;0.0837)|Breast(348;0.174)		STAD - Stomach adenocarcinoma(196;0.0557)		CTAGGGCAGCGGGCGCCAGCA	0.617													G|||	683	0.136382	0.0333	0.1715	5008	,	,		15990	0.1121		0.1133	False		,,,				2504	0.2996				p.P175P		Atlas-SNP	.											.	BAI2	128	.	0			c.C525T						PASS	.	G		202,4204		2,198,2003	28.0	35.0	33.0		525	-3.1	0.0	1	dbSNP_111	33	1104,7492		73,958,3267	no	coding-synonymous	BAI2	NM_001703.2		75,1156,5270	AA,AG,GG		12.8432,4.5847,10.0446		175/1586	32221913	1306,11696	2203	4298	6501	SO:0001819	synonymous_variant	576	exon4			GGCAGCGGGCGCC	AB005298	CCDS72746.1, CCDS72747.1	1p35	2014-08-08			ENSG00000121753	ENSG00000121753		"""-"", ""GPCR / Class B : Orphans"""	944	protein-coding gene	gene with protein product		602683				9533023	Standard	XM_006710783		Approved		uc001btn.3	O60241	OTTHUMG00000003885	ENST00000373658.3:c.525C>T	1.37:g.32221913G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Silent	SNP	ENST00000373658.3	37	CCDS346.2																																																																																			G|0.896;A|0.104	0.104	strong		0.617	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703	
TEX15	56154	hgsc.bcm.edu	37	8	30706224	30706224	+	Missense_Mutation	SNP	A	A	G	rs323347	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:30706224A>G	ENST00000256246.2	-	1	384	c.310T>C	c.(310-312)Tgt>Cgt	p.C104R	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	104			C -> R (in dbSNP:rs323347). {ECO:0000269|PubMed:11279525}.		fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AGAACAGCACAATCACCAGGG	0.398													G|||	1987	0.396765	0.851	0.3761	5008	,	,		21494	0.1131		0.165	False		,,,				2504	0.3282				p.C104R		Atlas-SNP	.											.	TEX15	350	.	0			c.T310C						PASS	.	G	ARG/CYS	3261,1145	405.1+/-333.4	1208,845,150	123.0	120.0	121.0		310	-1.4	0.0	8	dbSNP_79	121	1470,7130	750.2+/-407.4	127,1216,2957	yes	missense	TEX15	NM_031271.3	180	1335,2061,3107	GG,GA,AA		17.093,25.9873,36.3755	benign	104/2790	30706224	4731,8275	2203	4300	6503	SO:0001583	missense	56154	exon1			CAGCACAATCACC	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.310T>C	8.37:g.30706224A>G	ENSP00000256246:p.Cys104Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	722	0.3305860805860806	414	0.8414634146341463	130	0.35911602209944754	58	0.10139860139860139	120	0.158311345646438	G	0.043	-1.277378	0.01410	0.740127	0.17093	ENSG00000133863	ENST00000256246	T	0.09538	2.97	4.04	-1.36	0.09085	.	1.737400	0.02770	N	0.119591	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42189	-0.9466	9	0.87932	D	0	.	6.0942	0.20010	0.4081:0.2279:0.364:0.0	rs323347;rs52816425;rs58331847;rs323347	104	Q9BXT5	TEX15_HUMAN	R	104	ENSP00000256246:C104R	ENSP00000256246:C104R	C	-	1	0	TEX15	30825766	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.456000	0.06754	-0.937000	0.03719	-2.946000	0.00085	TGT	A|0.651;G|0.349	0.349	strong		0.398	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
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 GAIIx	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	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	150	59	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	
CAPG	822	hgsc.bcm.edu	37	2	85628983	85628983	+	Missense_Mutation	SNP	C	C	T	rs2229668	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85628983C>T	ENST00000409921.1	-	3	187	c.121G>A	c.(121-123)Gtc>Atc	p.V41I	CAPG_ENST00000263867.4_Missense_Mutation_p.V41I|CAPG_ENST00000483659.1_5'Flank|CAPG_ENST00000409670.1_Missense_Mutation_p.V41I|CAPG_ENST00000409724.1_Missense_Mutation_p.V41I			Q9BPX3	CND3_HUMAN	capping protein (actin filament), gelsolin-like	0					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(6)	11						GAGAAGAAGACGCCCTGGTTC	0.602													C|||	461	0.0920527	0.0832	0.0807	5008	,	,		15851	0.0764		0.1233	False		,,,				2504	0.0961				p.V41I		Atlas-SNP	.											.	CAPG	32	.	0			c.G121A						PASS	.	C	ILE/VAL	427,3979	206.8+/-228.3	17,393,1793	115.0	112.0	113.0		121	-9.8	0.1	2	dbSNP_98	113	1217,7383	245.3+/-274.2	79,1059,3162	yes	missense	CAPG	NM_001747.2	29	96,1452,4955	TT,TC,CC		14.1512,9.6913,12.6403	benign	41/349	85628983	1644,11362	2203	4300	6503	SO:0001583	missense	822	exon3			AGAAGACGCCCTG	M94345	CCDS1974.1, CCDS58715.1	2p11.2	2008-06-04			ENSG00000042493	ENSG00000042493			1474	protein-coding gene	gene with protein product	"""macrophage capping protein"""	153615		AFCP		1322908, 12754261	Standard	NM_001747		Approved	MCP	uc010fgi.2	P40121	OTTHUMG00000130183	ENST00000409921.1:c.121G>A	2.37:g.85628983C>T	ENSP00000387063:p.Val41Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	71	51	0.71831	NM_001256140	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000409921.1	37	CCDS58715.1	208	0.09523809523809523	45	0.09146341463414634	31	0.0856353591160221	44	0.07692307692307693	88	0.11609498680738786	C	6.620	0.482844	0.12581	0.096913	0.141512	ENSG00000042493	ENST00000542681;ENST00000263867;ENST00000409921;ENST00000409670;ENST00000409724;ENST00000439385;ENST00000449030;ENST00000447219;ENST00000409275	T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	5.55	-9.84	0.00479	Gelsolin domain (1);	0.945727	0.09027	N	0.859253	T	0.00210	0.0006	N	0.10685	0.025	0.54753	P	1.0999999999983245E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09509	-1.0671	9	0.34782	T	0.22	.	17.0438	0.86496	0.0:0.2888:0.0:0.7112	rs2229668;rs11539102;rs17765052;rs2229668	41;41	B8ZZS7;P40121	.;CAPG_HUMAN	I	41	ENSP00000263867:V41I;ENSP00000387063:V41I;ENSP00000386315:V41I;ENSP00000386965:V41I;ENSP00000391923:V41I;ENSP00000403330:V41I;ENSP00000398232:V41I;ENSP00000386596:V41I	ENSP00000263867:V41I	V	-	1	0	CAPG	85482494	0.000000	0.05858	0.054000	0.19295	0.324000	0.28378	-5.140000	0.00147	-2.182000	0.00764	-0.964000	0.02622	GTC	C|0.890;T|0.110	0.110	strong		0.602	CAPG-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329383.1	NM_001747	
ZNF469	84627	hgsc.bcm.edu	37	16	88501971	88501971	+	Missense_Mutation	SNP	T	T	A	rs3812956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88501971T>A	ENST00000437464.1	+	2	8009	c.8009T>A	c.(8008-8010)cTg>cAg	p.L2670Q	ZNF469_ENST00000565624.1_Missense_Mutation_p.L2698Q	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2670			L -> Q (in dbSNP:rs3812956). {ECO:0000269|PubMed:11347906}.		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						TTGGCCACTCTGGGACCTGGG	0.657													T|||	1474	0.294329	0.1815	0.3473	5008	,	,		15665	0.4028		0.3728	False		,,,				2504	0.2168				p.L2670Q		Atlas-SNP	.											.	ZNF469	121	.	0			c.T8009A						PASS	.	T	GLN/LEU	301,1083		33,235,424	18.0	21.0	20.0		8009	-6.5	0.0	16	dbSNP_107	20	1243,1937		247,749,594	yes	missense	ZNF469	NM_001127464.1	113	280,984,1018	AA,AT,TT		39.0881,21.7486,33.83	benign	2670/3926	88501971	1544,3020	692	1590	2282	SO:0001583	missense	84627	exon2			CCACTCTGGGACC	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.8009T>A	16.37:g.88501971T>A	ENSP00000402343:p.Leu2670Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	695	0.3182234432234432	92	0.18699186991869918	110	0.30386740331491713	209	0.36538461538461536	284	0.37467018469656993	T	4.345	0.063439	0.08388	0.217486	0.390881	ENSG00000225614	ENST00000437464	T	0.05382	3.45	3.23	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48514	-0.9029	8	0.27785	T	0.31	.	0.6077	0.00755	0.1968:0.1814:0.3023:0.3196	rs3812956;rs60168268	2670	Q96JG9	ZN469_HUMAN	Q	2670	ENSP00000402343:L2670Q	ENSP00000402343:L2670Q	L	+	2	0	ZNF469	87029472	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.057000	0.03486	-2.507000	0.00506	-1.156000	0.01807	CTG	T|0.680;A|0.320	0.320	strong		0.657	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
SV2C	22987	hgsc.bcm.edu	37	5	75594743	75594743	+	Missense_Mutation	SNP	G	G	A	rs31244	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:75594743G>A	ENST00000502798.2	+	10	2069	c.1627G>A	c.(1627-1629)Gac>Aac	p.D543N	SV2C_ENST00000322285.7_Missense_Mutation_p.D543N|RP11-466P24.6_ENST00000502589.1_RNA	NM_014979.1	NP_055794.1	Q496J9	SV2C_HUMAN	synaptic vesicle glycoprotein 2C	543			D -> N (in dbSNP:rs31244).		neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_lung(232;0.007)|Lung NSC(167;0.0148)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;1.16e-50)|all cancers(79;7.25e-40)		CACTGTTTTTGACAACACAGG	0.438													G|||	493	0.0984425	0.1551	0.1427	5008	,	,		19622	0.0863		0.0785	False		,,,				2504	0.0235				p.D543N		Atlas-SNP	.											.	SV2C	97	.	0			c.G1627A						PASS	.	G	ASN/ASP	528,3276		35,458,1409	136.0	123.0	127.0		1627	4.7	1.0	5	dbSNP_76	127	606,7616		15,576,3520	yes	missense	SV2C	NM_014979.1	23	50,1034,4929	AA,AG,GG		7.3705,13.8801,9.4296	benign	543/728	75594743	1134,10892	1902	4111	6013	SO:0001583	missense	22987	exon10			GTTTTTGACAACA	AB028977	CCDS43331.1, CCDS75261.1	5q13	2008-02-05			ENSG00000122012	ENSG00000122012			30670	protein-coding gene	gene with protein product		610291				10470851, 9801366	Standard	XM_005248470		Approved		uc003kei.1	Q496J9	OTTHUMG00000162384	ENST00000502798.2:c.1627G>A	5.37:g.75594743G>A	ENSP00000423541:p.Asp543Asn	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_014979	Q496K1|Q9UPU8	Missense_Mutation	SNP	ENST00000502798.2	37	CCDS43331.1	251	0.11492673992673992	91	0.18495934959349594	47	0.1298342541436464	59	0.10314685314685315	54	0.0712401055408971	G	15.50	2.851171	0.51270	0.138801	0.073705	ENSG00000122012	ENST00000502798;ENST00000322285	T;T	0.43688	0.94;0.94	5.61	4.72	0.59763	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.405907	0.27084	N	0.021013	T	0.00039	0.0001	N	0.01352	-0.895	0.37291	P	0.09171499999999999	B	0.02656	0.0	B	0.04013	0.001	T	0.10776	-1.0615	9	0.29301	T	0.29	-17.6025	8.4266	0.32733	0.0842:0.0:0.7243:0.1915	rs31244;rs58027942;rs31244	543	Q496J9	SV2C_HUMAN	N	543	ENSP00000423541:D543N;ENSP00000316983:D543N	ENSP00000316983:D543N	D	+	1	0	SV2C	75630499	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	3.199000	0.51043	1.330000	0.45394	0.650000	0.86243	GAC	G|0.892;A|0.108	0.108	strong		0.438	SV2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368700.4		
ABCD2	225	hgsc.bcm.edu	37	12	40013392	40013392	+	Missense_Mutation	SNP	G	G	C	rs117275340	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:40013392G>C	ENST00000308666.3	-	1	161	c.26C>G	c.(25-27)gCt>gGt	p.A9G		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	9	Interaction with PEX19.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						CACTCGATCAGCTGCTGCATT	0.473													G|||	72	0.014377	0.0023	0.0231	5008	,	,		19811	0.0208		0.0189	False		,,,				2504	0.0133				p.A9G		Atlas-SNP	.											.	ABCD2	127	.	0			c.C26G						PASS	.	G	GLY/ALA	15,4391	21.2+/-45.6	0,15,2188	48.0	39.0	42.0		26	3.7	1.0	12	dbSNP_132	42	177,8423	75.4+/-138.0	3,171,4126	yes	missense	ABCD2	NM_005164.3	60	3,186,6314	CC,CG,GG		2.0581,0.3404,1.4762	possibly-damaging	9/741	40013392	192,12814	2203	4300	6503	SO:0001583	missense	225	exon1			CGATCAGCTGCTG	U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"""ATP binding cassette transporters / subfamily D"""	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.26C>G	12.37:g.40013392G>C	ENSP00000310688:p.Ala9Gly	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_005164	B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	37	CCDS8734.1	36	0.016483516483516484	2	0.0040650406504065045	7	0.019337016574585635	12	0.02097902097902098	15	0.01978891820580475	G	13.29	2.193118	0.38707	0.003404	0.020581	ENSG00000173208	ENST00000308666	D	0.94862	-3.54	4.54	3.65	0.41850	.	0.187019	0.46442	D	0.000294	T	0.76126	0.3944	N	0.08118	0	0.37908	D	0.931263	B	0.20550	0.046	B	0.20384	0.029	T	0.76219	-0.3039	9	.	.	.	-5.9902	9.8908	0.41290	0.0936:0.0:0.9064:0.0	.	9	Q9UBJ2	ABCD2_HUMAN	G	9	ENSP00000310688:A9G	.	A	-	2	0	ABCD2	38299659	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.291000	0.65667	1.142000	0.42291	0.655000	0.94253	GCT	G|0.986;C|0.014	0.014	strong		0.473	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1	NM_005164	
FAM46C	54855	hgsc.bcm.edu	37	1	118165691	118165691	+	Missense_Mutation	SNP	C	C	G	rs1630312	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:118165691C>G	ENST00000369448.3	+	2	448	c.201C>G	c.(199-201)caC>caG	p.H67Q		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	67			H -> Q (in dbSNP:rs1630312).							endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		TCAAAGTGCACGACGTCCGGC	0.557			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			G|||	635	0.126797	0.2617	0.085	5008	,	,		22050	0.122		0.0626	False		,,,				2504	0.045				p.H67Q		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C201G						PASS	.						87.0	84.0	85.0					1																	118165691		2203	4300	6503	SO:0001583	missense	54855	exon2			AGTGCACGACGTC	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.201C>G	1.37:g.118165691C>G	ENSP00000358458:p.His67Gln	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Missense_Mutation	SNP	ENST00000369448.3	37	CCDS896.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.383795	0.25031	.	.	ENSG00000183508	ENST00000369448	T	0.20598	2.06	5.75	5.75	0.90469	Domain of unknown function DUF1693 (1);	0.361437	0.26331	N	0.024995	T	0.05135	0.0137	N	0.17082	0.46	0.22989	N	0.998469	B	0.02656	0.0	B	0.04013	0.001	T	0.23332	-1.0191	10	0.41790	T	0.15	-3.2272	10.9521	0.47336	0.0:0.3738:0.4948:0.1313	rs1630312;rs3738417;rs17853647	67	Q5VWP2	FA46C_HUMAN	Q	67	ENSP00000358458:H67Q	ENSP00000358458:H67Q	H	+	3	2	FAM46C	117967214	0.998000	0.40836	1.000000	0.80357	0.976000	0.68499	0.413000	0.21148	1.446000	0.47643	-0.120000	0.15030	CAC	T|0.288;G|0.015;C|0.697	0.015	strong		0.557	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
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 GAIIx	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		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	157	73	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 GAIIx	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_ENST00000295897.4_Silent_p.R361R|ALB_ENST00000509063.1_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		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	125	30	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 GAIIx	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	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	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	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	156	44	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		
PRDM9	56979	hgsc.bcm.edu	37	5	23527471	23527471	+	Silent	SNP	C	C	A	rs183034145	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:23527471C>A	ENST00000296682.3	+	11	2456	c.2274C>A	c.(2272-2274)cgC>cgA	p.R758R		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	758					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						GGGGCTTTCGCGATAAGTCAC	0.577										HNSCC(3;0.000094)			C|||	153	0.0305511	0.0832	0.0216	5008	,	,		9161	0.0079		0.003	False		,,,				2504	0.0174				p.R758R		Atlas-SNP	.											PRDM9,NS,carcinoma,+1,2	PRDM9	344	2	0			c.C2274A						scavenged	.						62.0	87.0	79.0					5																	23527471		2122	4294	6416	SO:0001819	synonymous_variant	56979	exon11			CTTTCGCGATAAG	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.2274C>A	5.37:g.23527471C>A		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	43	9	0.209302	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																			C|0.981;A|0.019	0.019	strong		0.577	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
ADCY3	109	hgsc.bcm.edu	37	2	25064193	25064193	+	Silent	SNP	G	G	A	rs2241759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:25064193G>A	ENST00000260600.5	-	5	1982	c.1131C>T	c.(1129-1131)ccC>ccT	p.P377P	ADCY3_ENST00000405392.1_5'UTR	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	377					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					CCCGGTAGTCGGGCAAGCCGC	0.632													A|||	2557	0.510583	0.3555	0.4438	5008	,	,		17167	0.7421		0.4791	False		,,,				2504	0.5613				p.P377P		Atlas-SNP	.											.	ADCY3	114	.	0			c.C1131T						PASS	.	A		1609,2793		304,1001,896	36.0	36.0	36.0		1131	-7.6	0.9	2	dbSNP_98	36	4197,4399		1066,2065,1167	yes	coding-synonymous	ADCY3	NM_004036.3		1370,3066,2063	AA,AG,GG		48.825,36.5516,44.6684		377/1145	25064193	5806,7192	2201	4298	6499	SO:0001819	synonymous_variant	109	exon5			GTAGTCGGGCAAG	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.1131C>T	2.37:g.25064193G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_004036	B3KT86|Q53T54|Q9UDB1	Silent	SNP	ENST00000260600.5	37	CCDS1715.1																																																																																			G|0.520;A|0.480	0.480	strong		0.632	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
ANXA9	8416	hgsc.bcm.edu	37	1	150960593	150960593	+	Missense_Mutation	SNP	G	G	A	rs149528939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:150960593G>A	ENST00000368947.4	+	11	1200	c.724G>A	c.(724-726)Ggg>Agg	p.G242R		NM_003568.2	NP_003559.2	O76027	ANXA9_HUMAN	annexin A9	242					single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	acetylcholine receptor activity (GO:0015464)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylserine binding (GO:0001786)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(4)|skin(2)	8	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GCGGAGCACTGGGCAAGAGCT	0.542													G|||	9	0.00179712	0.0	0.0043	5008	,	,		21771	0.0		0.006	False		,,,				2504	0.0				p.G242R		Atlas-SNP	.											.	ANXA9	28	.	0			c.G724A						PASS	.	G	ARG/GLY	8,4398	14.3+/-33.2	0,8,2195	112.0	114.0	113.0		724	5.3	0.2	1	dbSNP_134	113	75,8525	44.9+/-103.4	1,73,4226	yes	missense	ANXA9	NM_003568.2	125	1,81,6421	AA,AG,GG		0.8721,0.1816,0.6382	probably-damaging	242/346	150960593	83,12923	2203	4300	6503	SO:0001583	missense	8416	exon11			AGCACTGGGCAAG	AJ009985	CCDS975.2	1q21.2	2008-02-05			ENSG00000143412	ENSG00000143412		"""Annexins"""	547	protein-coding gene	gene with protein product		603319		ANX31		9742942, 9931420	Standard	NM_003568		Approved		uc001ewa.2	O76027	OTTHUMG00000035063	ENST00000368947.4:c.724G>A	1.37:g.150960593G>A	ENSP00000357943:p.Gly242Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	150	81	0.54	NM_003568	Q5SZF1|Q6FI55|Q9BS00|Q9HBJ6	Missense_Mutation	SNP	ENST00000368947.4	37	CCDS975.2	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	15.62	2.886965	0.52014	0.001816	0.008721	ENSG00000143412	ENST00000368947	T	0.05258	3.47	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.17577	0.0422	M	0.79123	2.44	0.58432	D	0.999992	D	0.76494	0.999	D	0.72982	0.979	T	0.00239	-1.1888	10	0.72032	D	0.01	.	14.4694	0.67506	0.0:0.0:1.0:0.0	.	242	O76027	ANXA9_HUMAN	R	242	ENSP00000357943:G242R	ENSP00000357943:G242R	G	+	1	0	ANXA9	149227217	0.998000	0.40836	0.227000	0.23927	0.421000	0.31385	4.639000	0.61361	2.495000	0.84180	0.655000	0.94253	GGG	G|0.994;A|0.006	0.006	strong		0.542	ANXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084895.2	NM_003568	
QSER1	79832	hgsc.bcm.edu	37	11	32956492	32956492	+	Missense_Mutation	SNP	C	C	T	rs62618693	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:32956492C>T	ENST00000399302.2	+	4	3636	c.3301C>T	c.(3301-3303)Cgc>Tgc	p.R1101C	QSER1_ENST00000527788.1_Missense_Mutation_p.R862C	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1101										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					CCAAGGCAAACGCCAGAATCC	0.408													C|||	53	0.0105831	0.0015	0.0159	5008	,	,		20451	0.0		0.0338	False		,,,				2504	0.0061				p.R1101C		Atlas-SNP	.											.	QSER1	153	.	0			c.C3301T						PASS	.	C	CYS/ARG	26,3752		1,24,1864	108.0	106.0	106.0		3301	5.7	1.0	11	dbSNP_129	106	317,7911		4,309,3801	yes	missense	QSER1	NM_001076786.1	180	5,333,5665	TT,TC,CC		3.8527,0.6882,2.8569	probably-damaging	1101/1736	32956492	343,11663	1889	4114	6003	SO:0001583	missense	79832	exon4			GGCAAACGCCAGA	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.3301C>T	11.37:g.32956492C>T	ENSP00000382241:p.Arg1101Cys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	123	68	0.552846	NM_001076786	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	37	CCDS41631.1	38	0.0173992673992674	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	31	0.040897097625329816	C	16.86	3.238498	0.58886	0.006882	0.038527	ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788	T;T	0.26810	2.04;1.71	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000003	T	0.19525	0.0469	M	0.72118	2.19	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	T	0.16070	-1.0415	10	0.72032	D	0.01	.	14.6476	0.68772	0.1454:0.8546:0.0:0.0	rs62618693	862;862;1101	C9JJ88;Q2KHR3-2;Q2KHR3	.;.;QSER1_HUMAN	C	1101;862;862	ENSP00000382241:R1101C;ENSP00000432766:R862C	ENSP00000078652:R862C	R	+	1	0	QSER1	32913068	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.455000	0.60075	2.687000	0.91594	0.563000	0.77884	CGC	C|0.977;T|0.023	0.023	strong		0.408	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774	
MUC16	94025	hgsc.bcm.edu	37	19	9056941	9056941	+	Missense_Mutation	SNP	A	A	G	rs10410136	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9056941A>G	ENST00000397910.4	-	3	30708	c.30505T>C	c.(30505-30507)Ttt>Ctt	p.F10169L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10171	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTCTTCCTAAATCCAGAAGTC	0.453													A|||	970	0.19369	0.1762	0.2666	5008	,	,		22681	0.0258		0.2823	False		,,,				2504	0.2474				p.F10169L		Atlas-SNP	.											.	MUC16	4315	.	0			c.T30505C						PASS	.	A	LEU/PHE	711,3201		59,593,1304	112.0	109.0	110.0		30505	-0.5	0.0	19	dbSNP_119	110	2507,5789		400,1707,2041	yes	missense	MUC16	NM_024690.2	22	459,2300,3345	GG,GA,AA		30.2194,18.1748,26.3598	benign	10169/14508	9056941	3218,8990	1956	4148	6104	SO:0001583	missense	94025	exon3			TCCTAAATCCAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.30505T>C	19.37:g.9056941A>G	ENSP00000381008:p.Phe10169Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	51	0.548387	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	413	0.1891025641025641	91	0.18495934959349594	93	0.2569060773480663	11	0.019230769230769232	218	0.287598944591029	a	8.852	0.944925	0.18356	0.181748	0.302194	ENSG00000181143	ENST00000397910	T	0.02446	4.29	3.07	-0.497	0.12023	.	.	.	.	.	T	0.00012	0.0000	N	0.01168	-0.975	.	.	.	B	0.12630	0.006	B	0.06405	0.002	T	0.44877	-0.9299	8	0.87932	D	0	.	5.5872	0.17281	0.6046:0.0:0.3954:0.0	rs10410136;rs56575663;rs60219599;rs10410136	10169	B5ME49	.	L	10169	ENSP00000381008:F10169L	ENSP00000381008:F10169L	F	-	1	0	MUC16	8917941	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.150000	0.16263	-0.091000	0.12440	0.383000	0.25322	TTT	A|0.797;G|0.203	0.203	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
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 GAIIx	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|CDKN1C_ENST00000414822.3_5'Flank|SLC22A18AS_ENST00000526203.1_Missense_Mutation_p.T97I|CDKN1C_ENST00000430149.2_5'Flank|CDKN1C_ENST00000313407.6_5'Flank|CDKN1C_ENST00000380725.1_5'Flank|SLC22A18AS_ENST00000455942.2_Missense_Mutation_p.T97I	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	Somatic	60	0	0	607	WXS	Illumina HiSeq	Phase_I	64	33	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	
HSPG2	3339	hgsc.bcm.edu	37	1	22159774	22159774	+	Silent	SNP	G	G	A	rs2229486	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22159774G>A	ENST00000374695.3	-	80	11161	c.11082C>T	c.(11080-11082)ccC>ccT	p.P3694P	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3694	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CGGCTGAGTCGGGCCGGAAGG	0.607													G|||	430	0.0858626	0.1672	0.0519	5008	,	,		20816	0.0		0.0676	False		,,,				2504	0.1074				p.P3694P		Atlas-SNP	.											.	HSPG2	311	.	0			c.C11082T						PASS	.	G		762,3644	310.2+/-291.5	67,628,1508	67.0	59.0	62.0		11082	-9.6	0.8	1	dbSNP_98	62	660,7940	165.9+/-218.0	26,608,3666	no	coding-synonymous	HSPG2	NM_005529.5		93,1236,5174	AA,AG,GG		7.6744,17.2946,10.9334		3694/4392	22159774	1422,11584	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon80			TGAGTCGGGCCGG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.11082C>T	1.37:g.22159774G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			T|0.000;G|0.907;C|0.000;A|0.093	0.093	strong		0.607	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
PTCRA	171558	hgsc.bcm.edu	37	6	42893121	42893121	+	Missense_Mutation	SNP	G	G	A	rs36111725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42893121G>A	ENST00000304672.1	+	4	628	c.547G>A	c.(547-549)Gca>Aca	p.A183T	PTCRA_ENST00000446507.1_Missense_Mutation_p.A76T|PTCRA_ENST00000441198.1_Missense_Mutation_p.A158T	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	183			A -> T (in dbSNP:rs36111725).		negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			GCCTTCCCCCGCAACCACCAC	0.711													G|||	256	0.0511182	0.152	0.0331	5008	,	,		13302	0.001		0.0179	False		,,,				2504	0.0133				p.A198T		Atlas-SNP	.											.	PTCRA	24	.	0			c.G592A						PASS	.	G	THR/ALA	460,3744		27,406,1669	12.0	9.0	10.0		547	-3.2	0.0	6	dbSNP_126	10	223,7975		5,213,3881	no	missense	PTCRA	NM_138296.2	58	32,619,5550	AA,AG,GG		2.7202,10.942,5.5072	possibly-damaging	183/282	42893121	683,11719	2102	4099	6201	SO:0001583	missense	171558	exon4			TCCCCCGCAACCA	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.547G>A	6.37:g.42893121G>A	ENSP00000304447:p.Ala183Thr	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_001243168	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	86	0.039377289377289376	57	0.11585365853658537	14	0.03867403314917127	0	0.0	15	0.01978891820580475	G	9.163	1.019306	0.19355	0.10942	0.027202	ENSG00000171611	ENST00000304672;ENST00000441198;ENST00000446507	T;T;T	0.52526	1.31;1.29;0.66	3.95	-3.18	0.05186	.	.	.	.	.	T	0.06280	0.0162	N	0.08118	0	0.80722	P	0.0	B;B;B	0.23490	0.022;0.086;0.027	B;B;B	0.14578	0.011;0.005;0.005	T	0.25222	-1.0138	8	0.30854	T	0.27	-0.3583	1.1502	0.01784	0.2686:0.2711:0.3219:0.1384	rs36111725;rs59437443	76;158;183	Q6ISU1-2;Q6ISU1-3;Q6ISU1	.;.;PTCRA_HUMAN	T	183;158;76	ENSP00000304447:A183T;ENSP00000409550:A158T;ENSP00000392288:A76T	ENSP00000304447:A183T	A	+	1	0	PTCRA	43001099	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.769000	0.04710	-0.916000	0.03818	-0.899000	0.02877	GCA	G|0.960;A|0.040	0.040	strong		0.711	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296	
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 GAIIx	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	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	123	91	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	
PLCB1	23236	hgsc.bcm.edu	37	20	8737734	8737734	+	Silent	SNP	G	G	A	rs2076413	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:8737734G>A	ENST00000338037.6	+	24	2592	c.2565G>A	c.(2563-2565)gcG>gcA	p.A855A	PLCB1_ENST00000378641.3_Silent_p.A855A|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Silent_p.A855A	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	855					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						CAAGTGAAGCGAGAACGACTC	0.473													G|||	1063	0.21226	0.1104	0.2219	5008	,	,		17943	0.13		0.3022	False		,,,				2504	0.3354				p.P855P		Atlas-SNP	.											.	PLCB1	394	.	0			c.T2565A						PASS	.	G	,	588,3818	257.0+/-261.6	43,502,1658	71.0	74.0	73.0		2565,2565	-1.6	0.8	20	dbSNP_96	73	2688,5912	430.6+/-356.6	451,1786,2063	no	coding-synonymous,coding-synonymous	PLCB1	NM_015192.2,NM_182734.1	,	494,2288,3721	AA,AG,GG		31.2558,13.3454,25.1884	,	855/1217,855/1174	8737734	3276,9730	2203	4300	6503	SO:0001819	synonymous_variant	23236	exon24			TGAAGCGAGAACG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2565G>A	20.37:g.8737734G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	57	20	0.350877	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			G|0.773;A|0.227	0.227	strong		0.473	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
KIF16B	55614	hgsc.bcm.edu	37	20	16486698	16486698	+	Silent	SNP	G	G	A	rs2295115	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:16486698G>A	ENST00000354981.2	-	8	994	c.837C>T	c.(835-837)ctC>ctT	p.L279L	KIF16B_ENST00000355755.3_Silent_p.L279L|KIF16B_ENST00000408042.1_Silent_p.L279L|KIF16B_ENST00000378003.2_5'UTR	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	279	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CCAGAGTCACGAGGGACTTGT	0.512													G|||	1206	0.240815	0.0582	0.2839	5008	,	,		16869	0.38		0.2843	False		,,,				2504	0.2689				p.L279L		Atlas-SNP	.											.	KIF16B	305	.	0			c.C837T						PASS	.	G	,,	458,3948	218.1+/-236.3	28,402,1773	114.0	106.0	109.0		837,837,837	-1.3	1.0	20	dbSNP_100	109	2639,5961	425.5+/-355.0	384,1871,2045	no	coding-synonymous,coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	,,	412,2273,3818	AA,AG,GG		30.686,10.3949,23.8121	,,	279/1267,279/1393,279/1318	16486698	3097,9909	2203	4300	6503	SO:0001819	synonymous_variant	55614	exon8			AGTCACGAGGGAC	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.837C>T	20.37:g.16486698G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			G|0.760;A|0.240	0.240	strong		0.512	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
C3orf67	200844	hgsc.bcm.edu	37	3	58849343	58849343	+	Missense_Mutation	SNP	C	C	T	rs34631714	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:58849343C>T	ENST00000482387.1	-	8	1255	c.1159G>A	c.(1159-1161)Gtg>Atg	p.V387M	RP11-147N17.1_ENST00000482372.1_RNA|RP11-147N17.1_ENST00000463703.1_RNA|RP11-147N17.1_ENST00000492031.1_RNA|C3orf67_ENST00000295966.7_Missense_Mutation_p.V387M|C3orf67_ENST00000472469.1_Missense_Mutation_p.V294M|RP11-147N17.1_ENST00000493123.1_RNA			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	387			V -> M (in dbSNP:rs34631714).							endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(3)|prostate(2)|skin(1)	19		all_cancers(2;0.000156)|all_epithelial(2;0.000493)|Breast(2;0.00446)|all_lung(2;0.074)|Lung NSC(2;0.248)		BRCA - Breast invasive adenocarcinoma(55;5.93e-06)|Kidney(10;0.00155)|KIRC - Kidney renal clear cell carcinoma(10;0.00172)|OV - Ovarian serous cystadenocarcinoma(275;0.23)		CTGCTTGTCACACTGTTATCC	0.448													C|||	3	0.000599042	0.0	0.0014	5008	,	,		19443	0.0		0.002	False		,,,				2504	0.0				p.V387M		Atlas-SNP	.											.	C3orf67	45	.	0			c.G1159A						PASS	.	C	MET/VAL	3,4403	6.2+/-15.9	0,3,2200	96.0	88.0	91.0		1159	0.6	0.0	3	dbSNP_126	91	25,8575	17.3+/-56.4	0,25,4275	yes	missense	C3orf67	NM_198463.2	21	0,28,6475	TT,TC,CC		0.2907,0.0681,0.2153	benign	387/564	58849343	28,12978	2203	4300	6503	SO:0001583	missense	200844	exon12			TTGTCACACTGTT	AK124920	CCDS33776.1	3p14.2	2011-01-25			ENSG00000163689	ENSG00000163689			24763	protein-coding gene	gene with protein product							Standard	NM_198463		Approved	FLJ42117, FLJ42930	uc003dkt.1	Q6ZVT6	OTTHUMG00000159151	ENST00000482387.1:c.1159G>A	3.37:g.58849343C>T	ENSP00000417122:p.Val387Met	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_198463	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	9.130	1.011164	0.19277	6.81E-4	0.002907	ENSG00000163689	ENST00000295966;ENST00000482387;ENST00000394474;ENST00000472469	T;T;T	0.18960	2.23;2.23;2.18	5.41	0.55	0.17219	.	1.359750	0.04580	N	0.394744	T	0.15392	0.0371	L	0.31664	0.95	0.09310	N	1	B;B;B	0.24920	0.053;0.006;0.114	B;B;B	0.20955	0.032;0.009;0.022	T	0.28554	-1.0040	10	0.33141	T	0.24	0.4302	5.7954	0.18383	0.0:0.5162:0.1257:0.3581	rs34631714	294;387;387	C9J3M8;Q6ZVT6-2;Q6ZVT6	.;.;CC067_HUMAN	M	387;387;92;294	ENSP00000295966:V387M;ENSP00000417122:V387M;ENSP00000417271:V294M	ENSP00000295966:V387M	V	-	1	0	C3orf67	58824383	0.000000	0.05858	0.004000	0.12327	0.921000	0.55340	-0.680000	0.05197	0.084000	0.17077	0.655000	0.94253	GTG	C|0.998;T|0.002	0.002	strong		0.448	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463	
HS1BP3	64342	hgsc.bcm.edu	37	2	20824559	20824559	+	Silent	SNP	C	C	T	rs2305457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:20824559C>T	ENST00000304031.3	-	5	742	c.717G>A	c.(715-717)gaG>gaA	p.E239E		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	239							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAGAGCCCCTCATCAGGGT	0.612													C|||	1380	0.275559	0.0333	0.366	5008	,	,		18239	0.4881		0.2614	False		,,,				2504	0.3344				p.E239E		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G717A						PASS	.	C		325,4081	170.1+/-200.6	9,307,1887	74.0	81.0	79.0		717	0.7	0.3	2	dbSNP_100	79	2227,6373	378.2+/-338.8	303,1621,2376	no	coding-synonymous	HS1BP3	NM_022460.3		312,1928,4263	TT,TC,CC		25.8953,7.3763,19.6217		239/393	20824559	2552,10454	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon5			GAGCCCCTCATCA		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.717G>A	2.37:g.20824559C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1	629	0.288003663003663	21	0.042682926829268296	125	0.3453038674033149	284	0.4965034965034965	199	0.262532981530343	C	0.179	-1.064030	0.01934	0.073763	0.258953	ENSG00000118960	ENST00000445102	.	.	.	4.7	0.696	0.18075	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.47661	-0.9100	3	.	.	.	-5.486	3.0218	0.06078	0.172:0.3953:0.3349:0.0978	rs2305457;rs2305457	.	.	.	R	32	.	.	G	-	1	0	HS1BP3	20688040	0.000000	0.05858	0.278000	0.24718	0.003000	0.03518	-0.441000	0.06879	0.580000	0.29522	-0.176000	0.13171	GGG	C|0.772;T|0.228	0.228	strong		0.612	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
ACACB	32	hgsc.bcm.edu	37	12	109623516	109623516	+	Missense_Mutation	SNP	G	G	A	rs2300455	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:109623516G>A	ENST00000338432.7	+	12	2070	c.1951G>A	c.(1951-1953)Gcc>Acc	p.A651T	ACACB_ENST00000377848.3_Missense_Mutation_p.A651T|ACACB_ENST00000377854.5_Missense_Mutation_p.A651T			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	651	Biotin carboxylation.		A -> T (in dbSNP:rs2300455).		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)	CGTCATTGCCGCCAGAATCAC	0.572													G|||	799	0.159545	0.0159	0.1571	5008	,	,		14912	0.2639		0.1581	False		,,,				2504	0.2495				p.A651T		Atlas-SNP	.											ACACB,colon,carcinoma,0,1	ACACB	330	1	0			c.G1951A						PASS	.	G	THR/ALA	198,4208	122.5+/-159.9	7,184,2012	47.0	44.0	45.0		1951	4.4	1.0	12	dbSNP_100	45	1704,6896	311.2+/-310.2	176,1352,2772	yes	missense	ACACB	NM_001093.3	58	183,1536,4784	AA,AG,GG		19.814,4.4939,14.624	probably-damaging	651/2459	109623516	1902,11104	2203	4300	6503	SO:0001583	missense	32	exon11			ATTGCCGCCAGAA	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.1951G>A	12.37:g.109623516G>A	ENSP00000341044:p.Ala651Thr	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	359	0.16437728937728938	10	0.02032520325203252	68	0.1878453038674033	159	0.27797202797202797	122	0.16094986807387862	G	22.2	4.264058	0.80358	0.044939	0.19814	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.82984	-1.67;-1.67;-1.67	5.33	4.44	0.53790	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.099413	0.64402	N	0.000002	T	0.00039	0.0001	L	0.58302	1.8	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00004	-1.2561	9	0.52906	T	0.07	.	14.2525	0.66028	0.073:0.0:0.927:0.0	rs2300455;rs52806590;rs61539340;rs2300455	651	O00763	ACACB_HUMAN	T	651	ENSP00000341044:A651T;ENSP00000367079:A651T;ENSP00000367085:A651T	ENSP00000341044:A651T	A	+	1	0	ACACB	108107899	1.000000	0.71417	0.964000	0.40570	0.597000	0.36814	8.003000	0.88520	1.402000	0.46780	-0.224000	0.12420	GCC	G|0.846;A|0.154	0.154	strong		0.572	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
CPSF1	29894	hgsc.bcm.edu	37	8	145623963	145623963	+	Silent	SNP	G	G	A	rs4317614	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145623963G>A	ENST00000349769.3	-	18	1798	c.1704C>T	c.(1702-1704)gaC>gaT	p.D568D	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	568					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GTCTGCGGCCGTCGTCGTCTG	0.677													G|||	2299	0.459065	0.2383	0.5	5008	,	,		13266	0.6597		0.3668	False		,,,				2504	0.6166				p.D568D	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C1704T						PASS	.	G		1169,3237	411.3+/-335.7	163,843,1197	105.0	105.0	105.0		1704	-10.4	0.0	8	dbSNP_111	105	3073,5527	468.6+/-367.3	566,1941,1793	no	coding-synonymous	CPSF1	NM_013291.2		729,2784,2990	AA,AG,GG		35.7326,26.532,32.6157		568/1444	145623963	4242,8764	2203	4300	6503	SO:0001819	synonymous_variant	29894	exon18			GCGGCCGTCGTCG	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1704C>T	8.37:g.145623963G>A		Somatic	252	1	0.00396825		WXS	Illumina HiSeq	Phase_I	199	197	0.98995	NM_013291	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																			G|0.629;A|0.371	0.371	strong		0.677	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
MAGEB3	4114	hgsc.bcm.edu	37	X	30254530	30254530	+	Silent	SNP	A	A	G	rs2071310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:30254530A>G	ENST00000361644.2	+	5	1226	c.489A>G	c.(487-489)gtA>gtG	p.V163V		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	163	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.V163V(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						TGGAGGTGGTATTTGGTGTTG	0.408													A|||	1761	0.46649	0.2474	0.3746	3775	,	,		15794	0.4008		0.3648	False		,,,				2504	0.4121				p.V163V		Atlas-SNP	.											.	MAGEB3	54	.	1	Substitution - coding silent(1)	prostate(1)	c.A489G						PASS	.	A		1297,2536		173,753,198,705,373	92.0	85.0	88.0		489	-7.2	0.1	X	dbSNP_96	88	3010,3718		470,1217,853,741,1019	no	coding-synonymous	MAGEB3	NM_002365.4		643,1970,1051,1446,1392	GG,GA,G,AA,A		44.7384,33.8377,40.7821		163/347	30254530	4307,6254	2202	4300	6502	SO:0001819	synonymous_variant	4114	exon5			GGTGGTATTTGGT	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.489A>G	X.37:g.30254530A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	212	152	0.716981	NM_002365	A0AVE4|B3KQ52|O75861	Silent	SNP	ENST00000361644.2	37	CCDS14220.1																																																																																			A|0.567;0|0.003	.	strong		0.408	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365	
KIAA1755	85449	hgsc.bcm.edu	37	20	36850940	36850940	+	Silent	SNP	G	G	C	rs41310010	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:36850940G>C	ENST00000279024.4	-	10	2599	c.2328C>G	c.(2326-2328)ccC>ccG	p.P776P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	776										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CCAGTAGGCCGGGGTCCCTCA	0.657											OREG0025921	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	546	0.109026	0.1649	0.0461	5008	,	,		18609	0.0992		0.0696	False		,,,				2504	0.1288				p.P776P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C2328G						PASS	.	C		680,3726	759.2+/-412.9	65,550,1588	50.0	47.0	48.0		2328	-9.9	0.5	20	dbSNP_127	48	582,8018	790.4+/-407.6	23,536,3741	no	coding-synonymous	KIAA1755	NM_001029864.1		88,1086,5329	CC,CG,GG		6.7674,15.4335,9.7032		776/1201	36850940	1262,11744	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon10			TAGGCCGGGGTCC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2328C>G	20.37:g.36850940G>C		Somatic	32	0	0	866	WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.891;C|0.109	0.109	strong		0.657	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
TNK2	10188	hgsc.bcm.edu	37	3	195615376	195615376	+	Silent	SNP	A	A	G	rs3747669	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195615376A>G	ENST00000333602.6	-	2	701	c.84T>C	c.(82-84)gaT>gaC	p.D28D	TNK2_ENST00000468819.1_5'UTR|TNK2_ENST00000392400.1_Silent_p.D28D|TNK2_ENST00000428187.1_Silent_p.D60D|TNK2_ENST00000316664.3_Silent_p.D28D|TNK2_ENST00000381916.2_Silent_p.D91D	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	28	SAM-like domain.				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)	CGTTGAGGTCATCTCGGAGCC	0.622													G|||	2217	0.442692	0.6694	0.4164	5008	,	,		15605	0.4583		0.2922	False		,,,				2504	0.2935				p.D91D		Atlas-SNP	.											.	TNK2	246	.	0			c.T273C						PASS	.	G	,	2615,1791	640.8+/-397.4	792,1031,380	109.0	96.0	101.0		273,84	-6.0	0.4	3	dbSNP_107	101	2462,6138	404.7+/-348.2	362,1738,2200	no	coding-synonymous,coding-synonymous	TNK2	NM_001010938.1,NM_005781.4	,	1154,2769,2580	GG,GA,AA		28.6279,40.6491,39.0358	,	91/1087,28/1039	195615376	5077,7929	2203	4300	6503	SO:0001819	synonymous_variant	10188	exon2			GAGGTCATCTCGG	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.84T>C	3.37:g.195615376A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Silent	SNP	ENST00000333602.6	37	CCDS33928.1	919	0.4207875457875458	325	0.6605691056910569	130	0.35911602209944754	246	0.43006993006993005	218	0.287598944591029	a	0.697	-0.792193	0.02884	0.593509	0.286279	ENSG00000061938	ENST00000438207	.	.	.	5.21	-5.99	0.02213	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999974593	.	.	.	.	.	.	T	0.04454	-1.0950	3	.	.	.	.	16.0289	0.80564	0.4693:0.0:0.5307:0.0	rs3747669;rs17852507;rs60556678;rs3747669	.	.	.	T	27	.	.	M	-	2	0	TNK2	197099773	0.055000	0.20627	0.417000	0.26559	0.012000	0.07955	-0.816000	0.04477	-1.458000	0.01916	-3.185000	0.00055	ATG	A|0.584;G|0.416	0.416	strong		0.622	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
DNASE2B	58511	hgsc.bcm.edu	37	1	84878228	84878228	+	Splice_Site	SNP	C	C	T	rs7511984	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:84878228C>T	ENST00000370665.3	+	5	777	c.744C>T	c.(742-744)gaC>gaT	p.D248D	DNASE2B_ENST00000370662.3_Splice_Site_p.D40D	NM_021233.2	NP_067056.2	Q8WZ79	DNS2B_HUMAN	deoxyribonuclease II beta	248					apoptotic DNA fragmentation (GO:0006309)	extracellular region (GO:0005576)|intracellular (GO:0005622)|lysosome (GO:0005764)	deoxyribonuclease II activity (GO:0004531)			endometrium(1)|lung(4)|skin(1)	6				all cancers(265;0.00303)|Epithelial(280;0.0112)|OV - Ovarian serous cystadenocarcinoma(397;0.0808)		CTTTTCTTGACGGTATGAAAG	0.438													C|||	679	0.135583	0.2012	0.0937	5008	,	,		18374	0.0119		0.1889	False		,,,				2504	0.1493				p.D248D	Pancreas(54;788 1175 11852 16034 30034)	Atlas-SNP	.											.	DNASE2B	40	.	0			c.C744T						PASS	.	C	,	889,3517	342.3+/-307.1	96,697,1410	71.0	71.0	71.0		744,120	-10.2	0.5	1	dbSNP_116	71	1518,7082	285.5+/-297.2	135,1248,2917	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	DNASE2B	NM_021233.2,NM_058248.1	,	231,1945,4327	TT,TC,CC		17.6512,20.177,18.5068	,	248/362,40/154	84878228	2407,10599	2203	4300	6503	SO:0001630	splice_region_variant	58511	exon5			TCTTGACGGTATG	AF274571	CCDS694.1, CCDS44167.1	1p22.3	2008-02-05			ENSG00000137976	ENSG00000137976			28875	protein-coding gene	gene with protein product		608057				12594037, 11376952	Standard	NM_021233		Approved	DLAD	uc001djt.1	Q8WZ79	OTTHUMG00000009860	ENST00000370665.3:c.745+1C>T	1.37:g.84878228C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_021233	Q5VXD0|Q5VXD1|Q8WZ80|Q9NQW3	Silent	SNP	ENST00000370665.3	37	CCDS44167.1																																																																																			C|0.841;T|0.159	0.159	strong		0.438	DNASE2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027248.1	NM_021233	Silent
RSPH10B	222967	hgsc.bcm.edu	37	7	5983063	5983063	+	Missense_Mutation	SNP	C	C	T	rs148485394	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:5983063C>T	ENST00000405415.1	-	14	2036	c.1650G>A	c.(1648-1650)atG>atA	p.M550I	RSPH10B_ENST00000404406.1_Missense_Mutation_p.M550I|RSPH10B_ENST00000337579.3_Missense_Mutation_p.M550I|RSPH10B_ENST00000539903.1_3'UTR|RSPH10B_ENST00000441023.2_Missense_Mutation_p.M550I|RSPH10B_ENST00000535104.1_5'UTR			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	550										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		TCATGTAACTCATAGAGTAGA	0.428																																					p.M550I		Atlas-SNP	.											RSPH10B,NS,carcinoma,-1,2	RSPH10B	28	2	0			c.G1650A						PASS	.						30.0	29.0	29.0					7																	5983063		2164	4268	6432	SO:0001583	missense	222967	exon15			GTAACTCATAGAG		CCDS34598.1	7p22.2	2008-07-04			ENSG00000155026	ENSG00000155026			27362	protein-coding gene	gene with protein product						16507594	Standard	NM_173565		Approved		uc003sph.1	P0C881	OTTHUMG00000152378	ENST00000405415.1:c.1650G>A	7.37:g.5983063C>T	ENSP00000385443:p.Met550Ile	Somatic	607	1	0.00164745		WXS	Illumina HiSeq	Phase_I	785	313	0.398726	NM_173565	A6NMW7|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000405415.1	37	CCDS34598.1	420	0.19230769230769232	86	0.17479674796747968	87	0.24033149171270718	42	0.07342657342657342	205	0.2704485488126649	C	2.557	-0.302794	0.05495	.	.	ENSG00000155026	ENST00000405415;ENST00000404406;ENST00000337579;ENST00000354951;ENST00000441023	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	3.38	2.48	0.30137	.	0.193985	0.44285	D	0.000471	T	0.00012	0.0000	L	0.60455	1.87	0.09310	P	0.99999528627	B;B;B	0.33288	0.406;0.068;0.112	B;B;B	0.28232	0.087;0.013;0.04	T	0.15378	-1.0439	9	0.40728	T	0.16	.	5.6003	0.17349	0.1944:0.6963:0.0:0.1094	.	251;550;409	B7Z298;P0C881;F5GXE3	.;R10B1_HUMAN;.	I	550;550;550;409;550	ENSP00000385443:M550I;ENSP00000384097:M550I;ENSP00000338556:M550I;ENSP00000400988:M550I	ENSP00000338556:M550I	M	-	3	0	RSPH10B	5949589	0.985000	0.35326	0.060000	0.19600	0.014000	0.08584	0.436000	0.21526	0.734000	0.32515	0.551000	0.68910	ATG	.	.	weak		0.428	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325465.2	NM_173565	
STK17A	9263	hgsc.bcm.edu	37	7	43664280	43664280	+	Missense_Mutation	SNP	A	A	G	rs1044141	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:43664280A>G	ENST00000319357.5	+	7	1263	c.1084A>G	c.(1084-1086)Aag>Gag	p.K362E		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	362			K -> E (in dbSNP:rs1044141). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9786912, ECO:0000269|Ref.4}.		apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						ATCAGAAACCAAGGAATCCAT	0.403													G|||	4111	0.820887	0.9622	0.8516	5008	,	,		19120	0.6746		0.7465	False		,,,				2504	0.8354				p.K362E		Atlas-SNP	.											.	STK17A	31	.	0			c.A1084G						PASS	.	G	GLU/LYS	4101,305	165.8+/-197.2	1907,287,9	97.0	91.0	93.0		1084	1.0	0.0	7	dbSNP_86	93	6580,2020	353.5+/-329.1	2541,1498,261	yes	missense	STK17A	NM_004760.2	56	4448,1785,270	GG,GA,AA		23.4884,6.9224,17.8764	benign	362/415	43664280	10681,2325	2203	4300	6503	SO:0001583	missense	9263	exon7			GAAACCAAGGAAT	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 1"""	604726	"""serine/threonine kinase 17a (apoptosis-inducing)"""			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.1084A>G	7.37:g.43664280A>G	ENSP00000319192:p.Lys362Glu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_004760	A4D1V6|Q8IVC8	Missense_Mutation	SNP	ENST00000319357.5	37	CCDS5470.1	1729	0.7916666666666666	473	0.9613821138211383	304	0.8397790055248618	387	0.6765734265734266	565	0.7453825857519789	G	0.008	-1.883960	0.00532	0.930776	0.765116	ENSG00000164543	ENST00000319357	T	0.65732	-0.17	4.86	1.04	0.20106	.	0.000000	0.47852	N	0.000220	T	0.00012	0.0000	N	0.01168	-0.975	0.45439	P	0.0015889999999999516	B	0.02656	0.0	B	0.01281	0.0	T	0.43228	-0.9404	9	0.02654	T	1	.	9.6298	0.39772	0.3507:0.0:0.6493:0.0	rs1044141;rs3183813;rs10341701;rs11555023;rs17846412;rs17856689;rs17859456;rs57186046;rs1044141	362	Q9UEE5	ST17A_HUMAN	E	362	ENSP00000319192:K362E	ENSP00000319192:K362E	K	+	1	0	STK17A	43630805	0.859000	0.29813	0.001000	0.08648	0.145000	0.21501	1.079000	0.30766	-0.362000	0.08113	-0.981000	0.02577	AAG	A|0.185;G|0.815	0.815	strong		0.403	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760	
MINK1	50488	hgsc.bcm.edu	37	17	4796274	4796274	+	Splice_Site	SNP	T	T	C	rs397843893|rs11556634	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4796274T>C	ENST00000355280.6	+	20	2508	c.2312T>C	c.(2311-2313)gTc>gCc	p.V771A	MINK1_ENST00000453408.3_Splice_Site_p.V751A|MINK1_ENST00000347992.7_Splice_Site_p.V734A	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						TGCCGTCCAGTCTCCTCCAAA	0.632													C|||	3539	0.706669	0.8548	0.5562	5008	,	,		17876	0.9266		0.4264	False		,,,				2504	0.6748				p.V771A		Atlas-SNP	.											.	MINK1	110	.	0			c.T2312C						PASS	.	C	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	3232,882		1301,630,126	21.0	27.0	25.0		2252,2201,2312,2201	3.9	1.0	17	dbSNP_120	25	3365,4989		723,1919,1535	yes	missense-near-splice,missense-near-splice,missense-near-splice,missense-near-splice	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	64,64,64,64	2024,2549,1661	CC,CT,TT		40.2801,21.439,47.0885	benign,benign,benign,benign	751/1313,734/1296,771/1333,734/1304	4796274	6597,5871	2057	4177	6234	SO:0001630	splice_region_variant	50488	exon20			GTCCAGTCTCCTC	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.2312-1T>C	17.37:g.4796274T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_153827		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	1462	0.6694139194139194	435	0.8841463414634146	187	0.5165745856353591	528	0.9230769230769231	312	0.41160949868073876	C	4.663	0.123176	0.08931	0.78561	0.402801	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.72167	-0.63;-0.62;-0.58	4.91	3.93	0.45458	.	0.282714	0.35615	N	0.003100	T	0.00012	0.0000	N	0.00182	-1.905	0.34067	P	0.34206099999999995	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.38351	-0.9665	8	.	.	.	.	9.6596	0.39947	0.0:0.8272:0.0:0.1728	rs11556634;rs12944582	734;751;771;734	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	A	771;751;734	ENSP00000347427:V771A;ENSP00000406487:V751A;ENSP00000269296:V734A	.	V	+	2	0	MINK1	4737050	0.603000	0.26924	0.993000	0.49108	0.799000	0.45148	0.356000	0.20181	0.675000	0.31264	-0.119000	0.15052	GTC	A|0.000;C|0.651;G|0.000;T|0.348	0.651	strong		0.632	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	Missense_Mutation
CTAGE5	4253	hgsc.bcm.edu	37	14	39818028	39818028	+	Missense_Mutation	SNP	A	A	G	rs1140952	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39818028A>G	ENST00000280083.3	+	23	2409	c.2095A>G	c.(2095-2097)Atc>Gtc	p.I699V	CTAGE5_ENST00000348007.3_Missense_Mutation_p.I656V|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.I670V|CTAGE5_ENST00000396158.2_Missense_Mutation_p.I704V|CTAGE5_ENST00000556148.1_Missense_Mutation_p.I624V|CTAGE5_ENST00000341502.5_Missense_Mutation_p.I699V|CTAGE5_ENST00000341749.3_Missense_Mutation_p.I687V|CTAGE5_ENST00000553352.1_Missense_Mutation_p.I670V|CTAGE5_ENST00000557038.1_Missense_Mutation_p.I619V|CTAGE5_ENST00000396165.4_Missense_Mutation_p.I670V|CTAGE5_ENST00000553383.1_3'UTR|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.I1234V			O15320	CTGE5_HUMAN	CTAGE family, member 5	699	Pro-rich.		I -> V (in dbSNP:rs1140952). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9356211}.		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)		TCTTGCTCCAATCAGAGGTCC	0.493													A|||	1926	0.384585	0.2519	0.3415	5008	,	,		16436	0.5923		0.4115	False		,,,				2504	0.3528				p.I704V		Atlas-SNP	.											CTAGE5,rectum,carcinoma,0,1	CTAGE5	75	1	0			c.A2110G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1173,3233	412.2+/-336.0	151,871,1181	191.0	199.0	196.0		2095,2059,1966,2008	-2.0	0.0	14	dbSNP_86	196	3395,5205	500.7+/-375.3	671,2053,1576	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	29,29,29,29	822,2924,2757	GG,GA,AA		39.4767,26.6228,35.1223	benign,benign,benign,benign	699/805,687/793,656/762,670/776	39818028	4568,8438	2203	4300	6503	SO:0001583	missense	4253	exon23			GCTCCAATCAGAG	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.2095A>G	14.37:g.39818028A>G	ENSP00000280083:p.Ile699Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	121	63	0.520661	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	937	0.429029304029304	131	0.266260162601626	136	0.3756906077348066	359	0.6276223776223776	311	0.4102902374670185	A	0.004	-2.297832	0.00243	0.266228	0.394767	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	0.06528	3.49;3.33;3.33;3.29;3.55;3.58;3.58;3.33;3.83;3.29	5.41	-2.01	0.07410	.	1.206650	0.06423	N	0.722732	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.002;0.004;0.002;0.004;0.002	T	0.32241	-0.9914	8	.	.	.	.	8.1094	0.30905	0.1281:0.1851:0.6868:0.0	rs1140952;rs3204972;rs17846661;rs17859758;rs1140952	704;656;699;627;687	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	V	1234;687;619;670;699;704;699;624;656;670	ENSP00000452252:I1234V;ENSP00000343897:I687V;ENSP00000450869:I619V;ENSP00000379468:I670V;ENSP00000339286:I699V;ENSP00000379462:I704V;ENSP00000280083:I699V;ENSP00000452562:I624V;ENSP00000343912:I656V;ENSP00000450449:I670V	.	I	+	1	0	CTAGE5;RP11-407N17.3	38887779	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-1.436000	0.02421	-0.792000	0.04480	-0.316000	0.08728	ATC	A|0.632;G|0.368	0.368	strong		0.493	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
NPFFR1	64106	hgsc.bcm.edu	37	10	72015409	72015409	+	Silent	SNP	C	C	A	rs10999212	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72015409C>A	ENST00000277942.6	-	4	596	c.597G>T	c.(595-597)ccG>ccT	p.P199P		NM_022146.4	NP_071429.1	Q9GZQ6	NPFF1_HUMAN	neuropeptide FF receptor 1	199					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			endometrium(2)|lung(1)	3						AGGAGTAGAGCGGGTAGGAGC	0.667													C|||	798	0.159345	0.0666	0.1671	5008	,	,		16808	0.004		0.2982	False		,,,				2504	0.2965				p.P199P		Atlas-SNP	.											.	NPFFR1	21	.	0			c.G597T						PASS	.	C		409,3929		20,369,1780	13.0	16.0	15.0		597	-0.3	1.0	10	dbSNP_120	15	2307,6231		334,1639,2296	no	coding-synonymous	NPFFR1	NM_022146.4		354,2008,4076	AA,AC,CC		27.0204,9.4283,21.0935		199/431	72015409	2716,10160	2169	4269	6438	SO:0001819	synonymous_variant	64106	exon4			GTAGAGCGGGTAG	AB040104	CCDS53539.1	10q21-q22	2012-08-10	2006-02-15	2006-02-15	ENSG00000148734	ENSG00000148734		"""GPCR / Class A :  Neuropeptide receptors : FF/AF"", ""GPCR / Class A : RF amide peptide receptors"""	17425	protein-coding gene	gene with protein product	"""neuropeptide FF 1"""	607448	"""G protein-coupled receptor 147"""	GPR147		11024015	Standard	NM_022146		Approved	OT7T022, NPFF1R1	uc021psj.1	Q9GZQ6	OTTHUMG00000018404	ENST00000277942.6:c.597G>T	10.37:g.72015409C>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_022146	A2RRF0|Q8NGR0|Q96RN3	Silent	SNP	ENST00000277942.6	37	CCDS53539.1																																																																																			C|0.843;A|0.157	0.157	strong		0.667	NPFFR1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048504.2	NM_022146	
TLR3	7098	hgsc.bcm.edu	37	4	187004217	187004217	+	Silent	SNP	C	C	T	rs3775290	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187004217C>T	ENST00000296795.3	+	4	1481	c.1377C>T	c.(1375-1377)ttC>ttT	p.F459F	TLR3_ENST00000504367.1_Silent_p.F182F	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	459					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)		AAAATATTTTCGAAATCTATC	0.478													C|||	1363	0.272165	0.1861	0.2738	5008	,	,		19762	0.3363		0.2734	False		,,,				2504	0.32				p.F459F		Atlas-SNP	.											TLR3,caecum,carcinoma,0,1	TLR3	83	1	0			c.C1377T						PASS	.	C		869,3537	325.6+/-299.2	91,687,1425	61.0	61.0	61.0		1377	0.3	0.5	4	dbSNP_107	61	2661,5939	415.9+/-351.9	396,1869,2035	yes	coding-synonymous	TLR3	NM_003265.2		487,2556,3460	TT,TC,CC		30.9419,19.7231,27.1413		459/905	187004217	3530,9476	2203	4300	6503	SO:0001819	synonymous_variant	7098	exon4			TATTTTCGAAATC	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.1377C>T	4.37:g.187004217C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	139	64	0.460432	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Silent	SNP	ENST00000296795.3	37	CCDS3846.1																																																																																			C|0.727;T|0.273	0.273	strong		0.478	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4		
GIP	2695	hgsc.bcm.edu	37	17	47041771	47041771	+	Missense_Mutation	SNP	G	G	A	rs367741847		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:47041771G>A	ENST00000357424.2	-	3	258	c.158C>T	c.(157-159)gCg>gTg	p.A53V		NM_004123.2	NP_004114.1	P09681	GIP_HUMAN	gastric inhibitory polypeptide	53					adult locomotory behavior (GO:0008344)|cellular protein metabolic process (GO:0044267)|digestive system development (GO:0055123)|endocrine pancreas development (GO:0031018)|exploration behavior (GO:0035640)|female pregnancy (GO:0007565)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of glucagon secretion (GO:0070094)|positive regulation of glucose transport (GO:0010828)|positive regulation of insulin secretion (GO:0032024)|regulation of insulin secretion (GO:0050796)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to lipid (GO:0033993)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|response to selenium ion (GO:0010269)|response to starvation (GO:0042594)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|secretory granule lumen (GO:0034774)	hormone activity (GO:0005179)			lung(2)|skin(1)|stomach(1)	4						AGTCCCTTCCGCGTACCTGGG	0.552																																					p.A53V		Atlas-SNP	.											.	GIP	15	.	0			c.C158T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	150.0	129.0	136.0		158	5.3	0.6	17		136	1,8599	1.2+/-3.3	0,1,4299	no	missense	GIP	NM_004123.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	53/154	47041771	1,13005	2203	4300	6503	SO:0001583	missense	2695	exon3			CCTTCCGCGTACC		CCDS11542.1	17q21.3-q22	2013-02-26			ENSG00000159224	ENSG00000159224		"""Endogenous ligands"""	4270	protein-coding gene	gene with protein product	"""glucose-dependent insulinotropic polypeptide"""	137240				2739653	Standard	NM_004123		Approved		uc002iol.1	P09681	OTTHUMG00000161171	ENST00000357424.2:c.158C>T	17.37:g.47041771G>A	ENSP00000350005:p.Ala53Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	67	0.614679	NM_004123	Q4VB42|Q6NTD3	Missense_Mutation	SNP	ENST00000357424.2	37	CCDS11542.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.048167	0.93740	0.0	1.16E-4	ENSG00000159224	ENST00000357424	T	0.55234	0.53	5.32	5.32	0.75619	Glucagon/GIP/secretin/VIP (3);	0.109714	0.41097	D	0.000945	T	0.72479	0.3465	M	0.78344	2.41	0.36540	D	0.871212	D	0.89917	1.0	D	0.91635	0.999	T	0.79205	-0.1899	10	0.72032	D	0.01	-13.4303	14.357	0.66745	0.0:0.0:1.0:0.0	.	53	P09681	GIP_HUMAN	V	53	ENSP00000350005:A53V	ENSP00000350005:A53V	A	-	2	0	GIP	44396770	0.714000	0.27936	0.596000	0.28811	0.500000	0.33767	4.738000	0.62073	2.769000	0.95229	0.563000	0.77884	GCG	.	.	weak		0.552	GIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364044.1	NM_004123	
ICOSLG	23308	hgsc.bcm.edu	37	21	45656774	45656774	+	Missense_Mutation	SNP	C	C	T	rs11558819	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45656774C>T	ENST00000407780.3	-	3	509	c.382G>A	c.(382-384)Gtt>Att	p.V128I	ICOSLG_ENST00000400377.3_Intron|ICOSLG_ENST00000400379.3_Missense_Mutation_p.V128I|ICOSLG_ENST00000344330.4_Missense_Mutation_p.V128I	NM_001283052.1	NP_001269981.1	O75144	ICOSL_HUMAN	inducible T-cell co-stimulator ligand	128	Ig-like V-type.		V -> I (in dbSNP:rs11558819).		B cell activation (GO:0042113)|defense response (GO:0006952)|hyperosmotic response (GO:0006972)|positive regulation of activated T cell proliferation (GO:0042104)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.V128I(1)		endometrium(2)|lung(1)|stomach(1)|urinary_tract(1)	5				Colorectal(79;0.0163)|READ - Rectum adenocarcinoma(84;0.0772)		GTAACCTCAACGCTCAAAACC	0.572													c|||	1348	0.269169	0.3427	0.3271	5008	,	,		18992	0.1438		0.2873	False		,,,				2504	0.2393				p.V128I		Atlas-SNP	.											ICOSLG,NS,carcinoma,0,1	ICOSLG	20	1	1	Substitution - Missense(1)	stomach(1)	c.G382A						PASS	.	T	ILE/VAL	1318,2860		210,898,981	101.0	113.0	109.0		382	1.0	0.0	21	dbSNP_120	109	2320,6132		329,1662,2235	yes	missense	ICOSLG	NM_015259.4	29	539,2560,3216	TT,TC,CC		27.4491,31.5462,28.8044	possibly-damaging	128/303	45656774	3638,8992	2089	4226	6315	SO:0001583	missense	23308	exon3			CCTCAACGCTCAA	AB014553	CCDS42952.1, CCDS63377.1, CCDS63379.1	21q22.3	2014-01-30		2005-01-12	ENSG00000160223	ENSG00000160223		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Endogenous ligands"""	17087	protein-coding gene	gene with protein product	"""B7-related protein 1"", ""B7 homologue 2"", ""B7 homolog 2"""	605717		ICOSL		9734811, 11007762	Standard	NM_001283050		Approved	KIAA0653, GL50, B7-H2, B7RP-1, B7H2, B7RP1, ICOS-L, CD275	uc002zee.3	O75144	OTTHUMG00000086920	ENST00000407780.3:c.382G>A	21.37:g.45656774C>T	ENSP00000384432:p.Val128Ile	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_015259	A8MUZ1|Q9HD18|Q9NRQ1	Missense_Mutation	SNP	ENST00000407780.3	37	CCDS42952.1	547	0.25045787545787546	150	0.3048780487804878	105	0.2900552486187845	77	0.1346153846153846	215	0.2836411609498681	c	8.707	0.911038	0.17833	0.315462	0.274491	ENSG00000160223	ENST00000344330;ENST00000407780;ENST00000400379	T;T;T	0.27557	1.66;1.66;1.66	5.01	1.05	0.20165	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.262160	0.05654	N	0.585727	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	P;P	0.39903	0.694;0.694	B;B	0.37550	0.253;0.253	T	0.32079	-0.9920	9	0.24483	T	0.36	.	4.0371	0.09735	0.0:0.5387:0.1755:0.2858	rs11558819;rs11575872	128;128	A0N0L8;O75144	.;ICOSL_HUMAN	I	128	ENSP00000339477:V128I;ENSP00000384432:V128I;ENSP00000383230:V128I	ENSP00000339477:V128I	V	-	1	0	ICOSLG	44481202	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.355000	0.07671	0.332000	0.23536	-0.766000	0.03442	GTT	C|0.738;T|0.262	0.262	strong		0.572	ICOSLG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195838.1	NM_015259	
ZNF700	90592	hgsc.bcm.edu	37	19	12059645	12059645	+	Missense_Mutation	SNP	A	A	G	rs12327617	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:12059645A>G	ENST00000254321.5	+	4	949	c.806A>G	c.(805-807)gAa>gGa	p.E269G	CTD-2006C1.12_ENST00000586394.1_RNA|ZNF700_ENST00000482090.1_Missense_Mutation_p.E251G|ZNF763_ENST00000590798.1_Intron|ZNF763_ENST00000591944.1_Intron|ZNF763_ENST00000538752.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	269			E -> G (in dbSNP:rs12327617).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)		ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						CAAATACATGAAAGAACTCAC	0.358													a|||	181	0.0361422	0.0045	0.0591	5008	,	,		20641	0.0		0.0964	False		,,,				2504	0.0378				p.E272G		Atlas-SNP	.											.	ZNF700	81	.	0			c.A815G						PASS	.	A	GLY/GLU	95,4311	74.1+/-112.3	1,93,2109	46.0	45.0	45.0		806	0.7	0.6	19	dbSNP_120	45	823,7777	184.6+/-232.5	42,739,3519	yes	missense	ZNF700	NM_144566.1	98	43,832,5628	GG,GA,AA		9.5698,2.1562,7.0583	probably-damaging	269/743	12059645	918,12088	2203	4300	6503	SO:0001583	missense	90592	exon4			TACATGAAAGAAC	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"""Zinc fingers, C2H2-type"", ""-"""	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.806A>G	19.37:g.12059645A>G	ENSP00000254321:p.Glu269Gly	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_001271848	B9EGU4	Missense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	92	0.04212454212454213	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	70	0.09234828496042216	a	17.26	3.344785	0.61073	0.021562	0.095698	ENSG00000196757	ENST00000254321	T	0.07444	3.19	0.672	0.672	0.17935	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00356	0.0011	L	0.38531	1.155	0.24211	N	0.995479	D	0.53462	0.96	P	0.61722	0.893	T	0.24728	-1.0152	9	0.66056	D	0.02	.	6.9083	0.24321	1.0:0.0:0.0:0.0	rs12327617;rs52820867;rs12327617	269	Q9H0M5	ZN700_HUMAN	G	269	ENSP00000254321:E269G	ENSP00000254321:E269G	E	+	2	0	ZNF700	11920645	0.000000	0.05858	0.631000	0.29282	0.972000	0.66771	-0.911000	0.04050	0.524000	0.28502	0.254000	0.18369	GAA	A|0.938;G|0.062	0.062	strong		0.358	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566	
RYR1	6261	hgsc.bcm.edu	37	19	38995438	38995438	+	Silent	SNP	T	T	C	rs2960340	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38995438T>C	ENST00000359596.3	+	51	8118	c.8118T>C	c.(8116-8118)atT>atC	p.I2706I	RYR1_ENST00000360985.3_Silent_p.I2706I|RYR1_ENST00000355481.4_Silent_p.I2706I			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2706	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.I2706I(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGTGCGCCATTGCCGGGGCTC	0.572													C|||	2079	0.415136	0.5182	0.3689	5008	,	,		16810	0.3532		0.2992	False		,,,				2504	0.4918				p.I2706I		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	1	1	Substitution - coding silent(1)	stomach(1)	c.T8118C						PASS	.	C	,	2016,2390	612.3+/-391.9	458,1100,645	59.0	56.0	57.0		8118,8118	0.2	1.0	19	dbSNP_101	57	2143,6457	713.9+/-406.0	289,1565,2446	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	747,2665,3091	CC,CT,TT		24.9186,45.7558,31.9775	,	2706/5039,2706/5034	38995438	4159,8847	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon51			CGCCATTGCCGGG	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.8118T>C	19.37:g.38995438T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			T|0.657;C|0.343	0.343	strong		0.572	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
SPTBN1	6711	hgsc.bcm.edu	37	2	54858511	54858511	+	Silent	SNP	C	C	T	rs1052788	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54858511C>T	ENST00000356805.4	+	16	3608	c.3327C>T	c.(3325-3327)aaC>aaT	p.N1109N	SPTBN1_ENST00000333896.5_Silent_p.N1096N	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1109					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)	p.N1109N(1)		NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ACATCAAGAACGAGATCGACA	0.587													C|||	1204	0.240415	0.0431	0.3343	5008	,	,		23981	0.2788		0.336	False		,,,				2504	0.3027				p.N1109N		Atlas-SNP	.											SPTBN1,NS,carcinoma,0,1	SPTBN1	378	1	1	Substitution - coding silent(1)	stomach(1)	c.C3327T						PASS	.	C	,	392,4014	195.3+/-220.0	13,366,1824	173.0	142.0	152.0		3327,3288	-5.8	0.9	2	dbSNP_86	152	2617,5983	424.3+/-354.6	360,1897,2043	no	coding-synonymous,coding-synonymous	SPTBN1	NM_003128.2,NM_178313.2	,	373,2263,3867	TT,TC,CC		30.4302,8.897,23.1355	,	1109/2365,1096/2156	54858511	3009,9997	2203	4300	6503	SO:0001819	synonymous_variant	6711	exon16			CAAGAACGAGATC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3327C>T	2.37:g.54858511C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.759;T|0.241	0.241	strong		0.587	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
SERPINB7	8710	hgsc.bcm.edu	37	18	61471523	61471523	+	Missense_Mutation	SNP	G	G	A	rs17782413	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61471523G>A	ENST00000398019.2	+	8	1122	c.797G>A	c.(796-798)cGa>cAa	p.R266Q	SERPINB7_ENST00000336429.2_Missense_Mutation_p.R266Q|SERPINB7_ENST00000540675.1_Missense_Mutation_p.R249Q|SERPINB7_ENST00000546027.1_Missense_Mutation_p.R266Q	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	266			R -> Q (in dbSNP:rs17782413).		negative regulation of endopeptidase activity (GO:0010951)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	27		Esophageal squamous(42;0.129)				AATCCAAGGCGAATGACCTCT	0.333													G|||	791	0.157947	0.0787	0.2277	5008	,	,		20230	0.1071		0.2247	False		,,,				2504	0.1994				p.R266Q		Atlas-SNP	.											.	SERPINB7	66	.	0			c.G797A						PASS	.	G	GLN/ARG,GLN/ARG	519,3887	233.6+/-246.7	27,465,1711	46.0	45.0	45.0		797,797	1.9	1.0	18	dbSNP_123	45	1992,6608	341.3+/-324.0	225,1542,2533	yes	missense,missense	SERPINB7	NM_001040147.1,NM_003784.2	43,43	252,2007,4244	AA,AG,GG		23.1628,11.7794,19.3065	possibly-damaging,possibly-damaging	266/381,266/381	61471523	2511,10495	2203	4300	6503	SO:0001583	missense	8710	exon8			CAAGGCGAATGAC	AF027866	CCDS11988.1, CCDS58633.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166396	ENSG00000166396		"""Serine (or cysteine) peptidase inhibitors"""	13902	protein-coding gene	gene with protein product		603357	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7"""			24172014	Standard	NM_003784		Approved	MEGSIN	uc002ljl.4	O75635	OTTHUMG00000060591	ENST00000398019.2:c.797G>A	18.37:g.61471523G>A	ENSP00000381101:p.Arg266Gln	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	20	11	0.55	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Missense_Mutation	SNP	ENST00000398019.2	37	CCDS11988.1	346	0.15842490842490842	48	0.0975609756097561	79	0.21823204419889503	56	0.0979020979020979	163	0.21503957783641162	G	13.79	2.343575	0.41498	0.117794	0.231628	ENSG00000166396	ENST00000336429;ENST00000398019;ENST00000540675;ENST00000546027	D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84	5.92	1.9	0.25705	Serpin domain (3);	0.423452	0.22978	N	0.053345	T	0.00073	0.0002	L	0.31578	0.945	0.80722	P	0.0	P;P	0.41524	0.709;0.753	B;B	0.32533	0.091;0.147	T	0.03268	-1.1054	9	0.38643	T	0.18	.	4.6409	0.12548	0.4709:0.0:0.3723:0.1567	rs17782413;rs52800605;rs17782413	249;266	F5GZC0;O75635	.;SPB7_HUMAN	Q	266;266;249;266	ENSP00000337212:R266Q;ENSP00000381101:R266Q;ENSP00000444572:R249Q;ENSP00000444861:R266Q	ENSP00000337212:R266Q	R	+	2	0	SERPINB7	59622503	0.000000	0.05858	0.975000	0.42487	0.866000	0.49608	-0.195000	0.09546	0.495000	0.27882	-0.302000	0.09304	CGA	G|0.824;A|0.176	0.176	strong		0.333	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784	
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 GAIIx	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	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	106	29	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		
CNPY3	10695	hgsc.bcm.edu	37	6	42906384	42906384	+	Missense_Mutation	SNP	G	G	T	rs9471969	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42906384G>T	ENST00000372836.4	+	6	1063	c.692G>T	c.(691-693)aGc>aTc	p.S231I	CNPY3_ENST00000394142.3_3'UTR|RP3-475N16.1_ENST00000450671.1_RNA	NM_006586.3	NP_006577.2	Q9BT09	CNPY3_HUMAN	canopy FGF signaling regulator 3	231	Saposin B-type.		S -> I (in dbSNP:rs9471969).		innate immune response (GO:0045087)|toll-like receptor signaling pathway (GO:0002224)	endoplasmic reticulum lumen (GO:0005788)				central_nervous_system(1)|endometrium(1)|lung(3)|ovary(1)	6	Colorectal(47;0.196)		all cancers(41;0.000954)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			AAGAAGAGCAGCAGGGCCAAG	0.622													G|||	1071	0.213858	0.3328	0.2075	5008	,	,		19202	0.0149		0.2744	False		,,,				2504	0.2004				p.S231I		Atlas-SNP	.											.	CNPY3	25	.	0			c.G692T						PASS	.	G	ILE/SER	1419,2987	449.8+/-349.2	230,959,1014	79.0	80.0	80.0		692	5.0	0.6	6	dbSNP_119	80	2199,6399	362.9+/-332.9	263,1673,2363	yes	missense	CNPY3	NM_006586.3	142	493,2632,3377	TT,TG,GG		25.5757,32.2061,27.8222	benign	231/279	42906384	3618,9386	2203	4299	6502	SO:0001583	missense	10695	exon6			AGAGCAGCAGGGC	U80744	CCDS4875.1	6p21.1	2013-09-19	2013-07-23	2007-10-22	ENSG00000137161	ENSG00000137161		"""Trinucleotide (CAG) repeat containing"""	11968	protein-coding gene	gene with protein product		610774	"""trinucleotide repeat containing 5"", ""canopy 3 homolog (zebrafish)"""	TNRC5		9225980	Standard	NM_006586		Approved	CAG4A	uc003ota.4	Q9BT09	OTTHUMG00000014708	ENST00000372836.4:c.692G>T	6.37:g.42906384G>T	ENSP00000361926:p.Ser231Ile	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_006586	O15412|Q0P6I2|Q8NF54|Q8WTU8|Q9P0F2	Missense_Mutation	SNP	ENST00000372836.4	37	CCDS4875.1	463	0.211996336996337	158	0.32113821138211385	81	0.22375690607734808	13	0.022727272727272728	211	0.2783641160949868	G	16.53	3.149626	0.57151	0.322061	0.255757	ENSG00000137161	ENST00000372836	T	0.24723	1.84	5.02	5.02	0.67125	.	0.433550	0.25747	N	0.028570	T	0.06690	0.0171	N	0.08118	0	0.09310	P	1.0	B	0.32693	0.38	B	0.28011	0.085	T	0.15607	-1.0431	9	0.39692	T	0.17	-13.8584	15.6126	0.76737	0.0:0.0:1.0:0.0	rs9471969;rs52835372;rs58234738;rs9471969	231	Q9BT09	CNPY3_HUMAN	I	231	ENSP00000361926:S231I	ENSP00000361926:S231I	S	+	2	0	CNPY3	43014362	1.000000	0.71417	0.631000	0.29282	0.974000	0.67602	4.641000	0.61375	2.504000	0.84457	0.462000	0.41574	AGC	G|0.754;T|0.246	0.246	strong		0.622	CNPY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040564.1	NM_006586	
CTNNA1	1495	hgsc.bcm.edu	37	5	138266552	138266552	+	Silent	SNP	C	C	G	rs11552052	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:138266552C>G	ENST00000302763.7	+	16	2316	c.2226C>G	c.(2224-2226)gtC>gtG	p.V742V	CTNNA1_ENST00000518825.1_Silent_p.V742V|CTNNA1_ENST00000540387.1_Silent_p.V372V|CTNNA1_ENST00000355078.5_Silent_p.V639V	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	742					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CATCGGATGTCATCAGTGCTG	0.473													C|||	46	0.0091853	0.0008	0.0202	5008	,	,		20074	0.0		0.0288	False		,,,				2504	0.002				p.V742V		Atlas-SNP	.											.	CTNNA1	114	.	0			c.C2226G						PASS	.	C		25,4381	31.7+/-61.6	0,25,2178	86.0	88.0	87.0		2226	2.3	1.0	5	dbSNP_120	87	259,8341	101.0+/-162.3	1,257,4042	no	coding-synonymous	CTNNA1	NM_001903.2		1,282,6220	GG,GC,CC		3.0116,0.5674,2.1836		742/907	138266552	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	1495	exon16			GGATGTCATCAGT	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"""catenin (cadherin-associated protein), alpha 1 (102kD)"""			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2226C>G	5.37:g.138266552C>G		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_001903	Q12795|Q8N1C0	Silent	SNP	ENST00000302763.7	37	CCDS34243.1																																																																																			C|0.983;G|0.017	0.017	strong		0.473	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
HLA-A	3105	hgsc.bcm.edu	37	6	29910725	29910725	+	Missense_Mutation	SNP	C	C	G	rs281864737|rs199474430	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29910725C>G	ENST00000396634.1	+	4	606	c.265C>G	c.(265-267)Cgg>Ggg	p.R89G	HLA-A_ENST00000376806.5_Missense_Mutation_p.R89G|HLA-A_ENST00000376802.2_Missense_Mutation_p.R89G|HLA-A_ENST00000376809.5_Missense_Mutation_p.R89G			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	89	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CCAGGAGACACGGAATGTGAA	0.682									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	761	0.151957	0.1241	0.1758	5008	,	,		11022	0.2014		0.1103	False		,,,				2504	0.1646				p.R89G		Atlas-SNP	.											.	HLA-A	89	.	0			c.C265G						PASS	.						78.0	83.0	81.0					6																	29910725		2202	4288	6490	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGACACGGAATG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.265C>G	6.37:g.29910725C>G	ENSP00000379873:p.Arg89Gly	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	156	14	0.0897436	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.670	0.902510	0.17760	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00010	9.45;9.45;9.45;9.45	3.57	-0.156	0.13391	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	1.962500	0.04109	U	0.314318	T	0.00039	0.0001	M	0.77712	2.385	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.001;0.001	T	0.41502	-0.9505	9	0.45353	T	0.12	.	6.4473	0.21883	0.0:0.4033:0.4832:0.1135	rs1059459;rs2230993;rs3179182;rs3200133;rs16867779;rs16896284;rs41545216	89;89;89;89;89	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	G	89	ENSP00000379873:R89G;ENSP00000366002:R89G;ENSP00000366005:R89G;ENSP00000365998:R89G	ENSP00000348012:R89G	R	+	1	2	HLA-A	30018704	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.167000	0.03126	-0.108000	0.12066	0.478000	0.44815	CGG	C|0.921;G|0.080	0.080	strong		0.682	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144671955C>T	ENST00000529272.1	-	2	397				EEF1D_ENST00000528610.1_Intron|EEF1D_ENST00000317198.6_Intron|EEF1D_ENST00000524624.1_Intron|EEF1D_ENST00000532741.1_Silent_p.A149A|EEF1D_ENST00000395119.3_Intron|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000419152.2_Intron|EEF1D_ENST00000531770.1_5'Flank|EEF1D_ENST00000442189.2_Silent_p.A99A|EEF1D_ENST00000423316.2_Silent_p.A99A|EEF1D_ENST00000531621.1_Intron|EEF1D_ENST00000532400.1_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		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	29	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 GAIIx	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_ENST00000536376.1_Silent_p.G96G|ATP2A1_ENST00000395503.4_Silent_p.G221G	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		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	69	39	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 GAIIx	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_ENST00000366796.3_Intron|DACT2_ENST00000610183.1_Missense_Mutation_p.A417P	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	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	41	8	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		
ESPL1	9700	hgsc.bcm.edu	37	12	53670545	53670545	+	Missense_Mutation	SNP	C	C	A	rs1318648	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53670545C>A	ENST00000257934.4	+	8	1933	c.1842C>A	c.(1840-1842)agC>agA	p.S614R	ESPL1_ENST00000552462.1_Missense_Mutation_p.S614R	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	614			S -> R (in dbSNP:rs1318648).		apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TGGAGCTGAGCCCCGAGGAGA	0.637													C|||	3171	0.633187	0.4024	0.5994	5008	,	,		19167	0.8194		0.6372	False		,,,				2504	0.773				p.S614R	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C1842A						PASS	.	C	ARG/SER	1887,2519		394,1099,710	50.0	54.0	53.0		1842	1.2	1.0	12	dbSNP_88	53	5491,3105		1770,1951,577	yes	missense	ESPL1	NM_012291.4	110	2164,3050,1287	AA,AC,CC		36.1215,42.828,43.2549	probably-damaging	614/2121	53670545	7378,5624	2203	4298	6501	SO:0001583	missense	9700	exon8			GCTGAGCCCCGAG	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.1842C>A	12.37:g.53670545C>A	ENSP00000257934:p.Ser614Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	49	43	0.877551	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	1355	0.6204212454212454	203	0.41260162601626016	221	0.6104972375690608	462	0.8076923076923077	469	0.6187335092348285	C	16.80	3.223939	0.58668	0.42828	0.638785	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.14144	2.53;2.53	5.11	1.25	0.21368	.	0.144838	0.64402	D	0.000007	T	0.00012	0.0000	M	0.68317	2.08	0.38397	P	0.054444999999999966	D	0.71674	0.998	P	0.61940	0.896	T	0.10567	-1.0624	9	0.46703	T	0.11	.	8.7053	0.34351	0.0:0.6008:0.0:0.3992	rs1318648;rs3817539;rs52811463;rs59896279;rs1318648	614	Q14674	ESPL1_HUMAN	R	614;289;614	ENSP00000257934:S614R;ENSP00000449831:S614R	ENSP00000257934:S614R	S	+	3	2	ESPL1	51956812	0.553000	0.26513	0.996000	0.52242	0.994000	0.84299	-0.161000	0.10026	0.341000	0.23771	0.650000	0.86243	AGC	C|0.400;N|0.000	.	strong		0.637	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
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 GAIIx	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_ENST00000354453.4_5'Flank|SPNS1_ENST00000323081.8_Silent_p.G402G|LAT_ENST00000360872.5_5'Flank|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000566177.1_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000395461.3_5'Flank|SPNS1_ENST00000565975.1_Silent_p.G520G|SPNS1_ENST00000334536.8_Silent_p.G423G|SPNS1_ENST00000352260.7_Silent_p.G401G	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		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	24	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	
BZRAP1	9256	hgsc.bcm.edu	37	17	56393840	56393840	+	Missense_Mutation	SNP	G	G	C	rs61739511	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:56393840G>C	ENST00000343736.4	-	15	2097	c.1934C>G	c.(1933-1935)gCg>gGg	p.A645G	BZRAP1_ENST00000355701.3_Missense_Mutation_p.A645G|BZRAP1_ENST00000268893.6_Missense_Mutation_p.A585G			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	645						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GCCCTCTGGCGCAGCTGGGAG	0.632													G|||	185	0.0369409	0.0174	0.0274	5008	,	,		17472	0.001		0.0567	False		,,,				2504	0.0869				p.A645G		Atlas-SNP	.											.	BZRAP1	287	.	0			c.C1934G						PASS	.	G	GLY/ALA,GLY/ALA	100,4306	79.9+/-118.3	1,98,2104	48.0	44.0	45.0		1934,1754	-0.7	0.0	17	dbSNP_129	45	485,8115	135.9+/-193.0	16,453,3831	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	60,60	17,551,5935	CC,CG,GG		5.6395,2.2696,4.4979	probably-damaging,probably-damaging	645/1858,585/1798	56393840	585,12421	2203	4300	6503	SO:0001583	missense	9256	exon15			TCTGGCGCAGCTG	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.1934C>G	17.37:g.56393840G>C	ENSP00000345824:p.Ala645Gly	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	57	0.0260989010989011	3	0.006097560975609756	9	0.024861878453038673	1	0.0017482517482517483	44	0.05804749340369393	G	5.714	0.316210	0.10789	0.022696	0.056395	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04758	3.56;3.56;3.57	5.3	-0.687	0.11320	Src homology-3 domain (1);	0.490311	0.22357	N	0.061133	T	0.00784	0.0026	L	0.29908	0.895	0.09310	N	1	D;B	0.76494	0.999;0.142	D;B	0.70935	0.971;0.051	T	0.32640	-0.9899	10	0.18710	T	0.47	.	8.1183	0.30957	0.497:0.0:0.503:0.0	rs61739511	585;645	O95153-2;O95153	.;RIMB1_HUMAN	G	645;645;585	ENSP00000347929:A645G;ENSP00000345824:A645G;ENSP00000268893:A585G	ENSP00000268893:A585G	A	-	2	0	BZRAP1	53748839	0.000000	0.05858	0.017000	0.16124	0.080000	0.17528	-0.290000	0.08354	-0.251000	0.09542	-0.126000	0.14955	GCG	G|0.952;C|0.048	0.048	strong		0.632	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
COL7A1	1294	hgsc.bcm.edu	37	3	48628014	48628014	+	Missense_Mutation	SNP	G	G	A	rs2228561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:48628014G>A	ENST00000328333.8	-	14	1891	c.1784C>T	c.(1783-1785)cCg>cTg	p.P595L	COL7A1_ENST00000454817.1_Missense_Mutation_p.P595L	NM_000094.3	NP_000085.1	Q02388	CO7A1_HUMAN	collagen, type VII, alpha 1	595	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region (NC1).		P -> L (in RDEB; dbSNP:rs2228561).		cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen type VII trimer (GO:0005590)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(3)|breast(8)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(57)|ovary(7)|prostate(5)|skin(9)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	137				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGGAGTTTCCGGCTCTAGGAG	0.607													G|||	496	0.0990415	0.0303	0.0735	5008	,	,		17827	0.0357		0.1233	False		,,,				2504	0.2505				p.P595L		Atlas-SNP	.											.	COL7A1	320	.	0			c.C1784T						PASS	.	G	LEU/PRO	237,4169	140.4+/-175.9	6,225,1972	53.0	54.0	54.0		1784	-3.0	0.0	3	dbSNP_98	54	1093,7507	229.7+/-264.3	70,953,3277	yes	missense	COL7A1	NM_000094.3	98	76,1178,5249	AA,AG,GG		12.7093,5.379,10.226	benign	595/2945	48628014	1330,11676	2203	4300	6503	SO:0001583	missense	1294	exon14			GTTTCCGGCTCTA	L02870	CCDS2773.1	3p21.1	2014-09-17	2008-08-01		ENSG00000114270	ENSG00000114270		"""Collagens"", ""Fibronectin type III domain containing"""	2214	protein-coding gene	gene with protein product	"""collagen VII, alpha-1 polypeptide"", ""LC collagen"""	120120	"""epidermolysis bullosa, dystrophic, dominant and recessive"""	EBDCT, EBD1, EBR1		1871109	Standard	NM_000094		Approved		uc003ctz.2	Q02388	OTTHUMG00000133541	ENST00000328333.8:c.1784C>T	3.37:g.48628014G>A	ENSP00000332371:p.Pro595Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	128	75	0.585938	NM_000094	Q14054|Q16507	Missense_Mutation	SNP	ENST00000328333.8	37	CCDS2773.1	158	0.07234432234432235	18	0.036585365853658534	25	0.06906077348066299	21	0.03671328671328671	94	0.12401055408970976	G	2.955	-0.215871	0.06101	0.05379	0.127093	ENSG00000114270	ENST00000328333;ENST00000454817	D;D	0.87650	-2.27;-2.28	5.01	-2.98	0.05513	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.471958	0.17545	N	0.170387	T	0.01765	0.0056	N	0.25647	0.755	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.14144	-1.0483	9	0.20519	T	0.43	.	3.7128	0.08427	0.3101:0.0:0.3156:0.3743	rs2228561;rs2532887;rs17257060;rs52826985;rs58208609;rs2228561	595	Q02388	CO7A1_HUMAN	L	595	ENSP00000332371:P595L;ENSP00000412569:P595L	ENSP00000332371:P595L	P	-	2	0	COL7A1	48603018	0.000000	0.05858	0.002000	0.10522	0.081000	0.17604	-1.148000	0.03185	-0.751000	0.04734	-0.143000	0.13931	CCG	G|0.914;A|0.086	0.086	strong		0.607	COL7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257519.1	NM_000094	
ASAH1	427	hgsc.bcm.edu	37	8	17927327	17927327	+	Missense_Mutation	SNP	T	T	C	rs1049874	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17927327T>C	ENST00000262097.6	-	4	588	c.277A>G	c.(277-279)Att>Gtt	p.I93V	ASAH1_ENST00000314146.10_Intron|ASAH1_ENST00000520051.1_5'Flank|ASAH1_ENST00000520781.1_Missense_Mutation_p.I93V|ASAH1_ENST00000381733.4_Missense_Mutation_p.I109V|ASAH1_ENST00000417108.2_Missense_Mutation_p.I28V	NM_177924.3	NP_808592.2	Q13510	ASAH1_HUMAN	N-acylsphingosine amidohydrolase (acid ceramidase) 1	93			I -> V (in dbSNP:rs1049874). {ECO:0000269|PubMed:10993717, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8955159, ECO:0000269|Ref.2}.		cell death (GO:0008219)|ceramide metabolic process (GO:0006672)|glycosphingolipid metabolic process (GO:0006687)|lung development (GO:0030324)|response to organic substance (GO:0010033)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	catalytic activity (GO:0003824)|ceramidase activity (GO:0017040)			breast(1)|endometrium(2)|large_intestine(4)|lung(2)	9				Colorectal(111;0.0646)|COAD - Colon adenocarcinoma(73;0.228)		ACCTGCATAATTTTTCCACTT	0.279													T|||	2106	0.420527	0.2496	0.5735	5008	,	,		17684	0.372		0.4771	False		,,,				2504	0.5348				p.I109V		Atlas-SNP	.											.	ASAH1	71	.	0			c.A325G						PASS	.	T	,VAL/ILE,VAL/ILE	1253,3151	420.8+/-339.2	194,865,1143	92.0	88.0	89.0		,325,277	-10.5	0.0	8	dbSNP_86	89	4229,4369	566.5+/-388.7	1034,2161,1104	yes	intron,missense,missense	ASAH1	NM_001127505.1,NM_004315.4,NM_177924.3	,29,29	1228,3026,2247	CC,CT,TT		49.1859,28.4514,42.1627	,benign,benign	,109/412,93/396	17927327	5482,7520	2202	4299	6501	SO:0001583	missense	427	exon4			GCATAATTTTTCC	U70063	CCDS6005.1, CCDS6006.1, CCDS47813.1	8p22	2007-03-27	2002-09-11	2002-09-13	ENSG00000104763	ENSG00000104763			735	protein-coding gene	gene with protein product		613468	"""N-acylsphingosine amidohydrolase (acid ceramidase)"""	ASAH		8955159, 10610716	Standard	NM_004315		Approved	AC, PHP32, FLJ21558	uc003wyn.2	Q13510	OTTHUMG00000096997	ENST00000262097.6:c.277A>G	8.37:g.17927327T>C	ENSP00000262097:p.Ile93Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_004315	E9PDS0|Q6W898|Q96AS2	Missense_Mutation	SNP	ENST00000262097.6	37	CCDS6006.1	927	0.42445054945054944	148	0.3008130081300813	219	0.6049723756906077	204	0.35664335664335667	356	0.46965699208443273	T	0.084	-1.179147	0.01633	0.284514	0.491859	ENSG00000104763	ENST00000262097;ENST00000381733;ENST00000520781;ENST00000417108	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.23	-10.5	0.00291	.	0.816289	0.11418	N	0.566080	T	0.00012	0.0000	N	0.16307	0.4	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.26155	-1.0111	9	0.12766	T	0.61	-4.3637	4.1802	0.10370	0.0758:0.3291:0.3039:0.2912	rs1049874;rs1049881;rs1804721;rs3174002;rs17416580;rs17856504;rs52833760;rs59209829;rs1049874	109;93;93	Q13510-2;E7EMM4;Q13510	.;.;ASAH1_HUMAN	V	93;109;93;28	ENSP00000262097:I93V;ENSP00000371152:I109V;ENSP00000427751:I93V;ENSP00000394125:I28V	ENSP00000262097:I93V	I	-	1	0	ASAH1	17971607	0.001000	0.12720	0.002000	0.10522	0.310000	0.27922	-1.936000	0.01549	-3.229000	0.00210	-0.804000	0.03201	ATT	T|0.579;C|0.421	0.421	strong		0.279	ASAH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214077.2	NM_004315	
UBASH3A	53347	hgsc.bcm.edu	37	21	43824123	43824123	+	Silent	SNP	G	G	C	rs2277799	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43824123G>C	ENST00000319294.6	+	1	100	c.69G>C	c.(67-69)tcG>tcC	p.S23S	UBASH3A_ENST00000450356.1_Silent_p.S23S|UBASH3A_ENST00000291535.6_Silent_p.S23S|UBASH3A_ENST00000398367.1_Silent_p.S23S	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	23	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						GCAGCCCCTCGCTCCTGGAGC	0.667													G|||	2002	0.39976	0.4228	0.3415	5008	,	,		14549	0.4593		0.3688	False		,,,				2504	0.3804				p.S23S		Atlas-SNP	.											.	UBASH3A	72	.	0			c.G69C						PASS	.	G	,	1640,2638		357,926,856	19.0	17.0	18.0		69,69	-5.3	0.3	21	dbSNP_100	18	3233,5075		710,1813,1631	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	1067,2739,2487	CC,CG,GG		38.9143,38.3357,38.7176	,	23/624,23/662	43824123	4873,7713	2139	4154	6293	SO:0001819	synonymous_variant	53347	exon1			CCCCTCGCTCCTG	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.69G>C	21.37:g.43824123G>C		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	150	150	1	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			G|0.601;C|0.399	0.399	strong		0.667	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
SLC39A4	55630	hgsc.bcm.edu	37	8	145639681	145639681	+	Missense_Mutation	SNP	G	G	C	rs1871534	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145639681G>C	ENST00000301305.3	-	6	1219	c.1114C>G	c.(1114-1116)Ctc>Gtc	p.L372V	SLC39A4_ENST00000276833.5_Missense_Mutation_p.L347V|SLC39A4_ENST00000531013.1_5'Flank	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	372			L -> P (in AEZ). {ECO:0000269|PubMed:12032886}.|L -> V (in dbSNP:rs1871534).		cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			TCCCCAGTGAGTGCACCCACT	0.667													G|||	1268	0.253195	0.9145	0.0735	5008	,	,		15930	0.0		0.007	False		,,,				2504	0.001				p.L372V		Atlas-SNP	.											.	SLC39A4	54	.	0			c.C1114G						PASS	.	G	VAL/LEU,VAL/LEU	3399,989		1341,717,136	55.0	50.0	51.0		1039,1114	4.1	0.2	8	dbSNP_92	51	53,8541		0,53,4244	yes	missense,missense	SLC39A4	NM_017767.2,NM_130849.2	32,32	1341,770,4380	CC,CG,GG		0.6167,22.5387,26.5907	probably-damaging,probably-damaging	347/623,372/648	145639681	3452,9530	2194	4297	6491	SO:0001583	missense	55630	exon6			CAGTGAGTGCACC	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.1114C>G	8.37:g.145639681G>C	ENSP00000301305:p.Leu372Val	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	212	102	0.481132	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	467	0.21382783882783882	436	0.8861788617886179	29	0.08011049723756906	0	0.0	2	0.002638522427440633	G	17.34	3.364066	0.61513	0.774613	0.006167	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.61510	0.1;0.1	5.03	4.12	0.48240	.	0.164767	0.38720	N	0.001590	T	0.00012	0.0000	M	0.91612	3.225	0.22446	P	0.999095413	D;D	0.89917	0.991;1.0	P;D	0.85130	0.883;0.997	T	0.15492	-1.0435	9	0.87932	D	0	-23.7231	12.8953	0.58095	0.0:0.1654:0.8346:0.0	rs1871534;rs2928379;rs1871534	372;347	Q6P5W5;A6NDY5	S39A4_HUMAN;.	V	347;372	ENSP00000276833:L347V;ENSP00000301305:L372V	ENSP00000276833:L347V	L	-	1	0	SLC39A4	145610489	1.000000	0.71417	0.172000	0.22920	0.396000	0.30629	6.389000	0.73199	1.087000	0.41251	0.573000	0.79308	CTC	G|0.744;C|0.256	0.256	strong		0.667	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
C14orf37	145407	hgsc.bcm.edu	37	14	58604850	58604850	+	Silent	SNP	A	A	C	rs11626667	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:58604850A>C	ENST00000267485.7	-	2	1421	c.1227T>G	c.(1225-1227)gtT>gtG	p.V409V	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	409						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TCACAATGGAAACTTTCATGT	0.463													A|||	127	0.0253594	0.0257	0.0231	5008	,	,		19684	0.002		0.0398	False		,,,				2504	0.0358				p.V409V		Atlas-SNP	.											.	C14orf37	87	.	0			c.T1227G						PASS	.	A		160,4246	108.2+/-146.6	5,150,2048	90.0	86.0	87.0		1227	-3.9	0.0	14	dbSNP_120	87	344,8256	118.3+/-177.8	7,330,3963	no	coding-synonymous	C14orf37	NM_001001872.2		12,480,6011	CC,CA,AA		4.0,3.6314,3.8751		409/775	58604850	504,12502	2203	4300	6503	SO:0001819	synonymous_variant	145407	exon2			AATGGAAACTTTC		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1227T>G	14.37:g.58604850A>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																			A|0.965;C|0.035	0.035	strong		0.463	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
ZSWIM8	23053	hgsc.bcm.edu	37	10	75559077	75559077	+	Silent	SNP	G	G	A	rs11000780	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:75559077G>A	ENST00000605216.1	+	21	4696	c.4479G>A	c.(4477-4479)ccG>ccA	p.P1493P	ZSWIM8_ENST00000604729.1_Silent_p.P1498P|ZSWIM8_ENST00000604524.1_Intron|ZSWIM8_ENST00000398706.2_Silent_p.P1498P|ZSWIM8-AS1_ENST00000456638.2_RNA|RP11-574K11.31_ENST00000603027.1_Intron|ZSWIM8_ENST00000603114.1_Silent_p.P1460P	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	1493	Pro-rich.						zinc ion binding (GO:0008270)										GTTTATACCCGGGTCCAGGAC	0.642													G|||	611	0.122005	0.0764	0.0994	5008	,	,		16406	0.1181		0.1342	False		,,,				2504	0.1912				p.P1498P		Atlas-SNP	.											.	.	.	.	0			c.G4494A						PASS	.	G	,,	330,3768		17,296,1736	37.0	46.0	43.0		4479,4479,4494	-8.8	0.6	10	dbSNP_120	43	1171,7215		77,1017,3099	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA0913	NM_001242487.1,NM_001242488.1,NM_015037.3	,,	94,1313,4835	AA,AG,GG		13.9637,8.0527,12.0234	,,	1493/1838,1493/1893,1498/1843	75559077	1501,10983	2049	4193	6242	SO:0001819	synonymous_variant	23053	exon21			ATACCCGGGTCCA	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"""Zinc fingers, SWIM-type"""	23528	protein-coding gene	gene with protein product			"""KIAA0913"""	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.4479G>A	10.37:g.75559077G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_015037	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Silent	SNP	ENST00000605216.1	37		254|254	0.1163003663003663|0.1163003663003663	44|44	0.08943089430894309|0.08943089430894309	38|38	0.10497237569060773|0.10497237569060773	66|66	0.11538461538461539|0.11538461538461539	106|106	0.13984168865435356|0.13984168865435356	G|G	5.453|5.453	0.268757|0.268757	0.10349|0.10349	0.080527|0.080527	0.139637|0.139637	ENSG00000214655|ENSG00000214655	ENST00000433366|ENST00000412198	.|.	.|.	.|.	5.07|5.07	-8.78|-8.78	0.00824|0.00824	.|.	.|.	.|.	.|.	.|.	T|T	0.00496|0.00496	0.0016|0.0016	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39461|0.39461	-0.9613|-0.9613	3|3	.|.	.|.	.|.	-6.0714|-6.0714	17.4382|17.4382	0.87558|0.87558	0.9178:0.0:0.0822:0.0|0.9178:0.0:0.0822:0.0	rs11000780;rs11000780|rs11000780;rs11000780	.|.	.|.	.|.	R|Q	1209|768	.|.	.|.	G|R	+|+	1|2	0|0	KIAA0913|KIAA0913	75229083|75229083	0.008000|0.008000	0.16893|0.16893	0.575000|0.575000	0.28536|0.28536	0.697000|0.697000	0.40408|0.40408	-0.957000|-0.957000	0.03861|0.03861	-1.852000|-1.852000	0.01166|0.01166	-1.303000|-1.303000	0.01326|0.01326	GGG|CGG	G|0.880;A|0.120	0.120	strong		0.642	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487	
C21orf2	755	hgsc.bcm.edu	37	21	45750346	45750346	+	Intron	SNP	C	C	A	rs2070573	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45750346C>A	ENST00000339818.4	-	7	850				C21orf2_ENST00000325223.7_Intron|C21orf2_ENST00000496321.1_Intron|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000397956.3_Splice_Site_p.P333P|AP001062.8_ENST00000422357.1_RNA	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2						cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		AGTGACTGACCGGCACACTCG	0.697													c|||	1322	0.263978	0.298	0.2089	5008	,	,		14117	0.3591		0.2107	False		,,,				2504	0.2137				p.P333P		Atlas-SNP	.											.	C21orf2	10	.	0			c.G999T						PASS	.																																			SO:0001627	intron_variant	755	exon6			ACTGACCGGCACA	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.643-137G>T	21.37:g.45750346C>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_001271441	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	37	CCDS13709.1																																																																																			C|0.728;A|0.272	0.272	strong		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
WDFY4	57705	hgsc.bcm.edu	37	10	50038800	50038800	+	Silent	SNP	A	A	G	rs3747874	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50038800A>G	ENST00000325239.5	+	37	6423	c.6396A>G	c.(6394-6396)caA>caG	p.Q2132Q	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2132						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						TGGTGGCACAAAGGCAGCAGA	0.547													G|||	3256	0.65016	0.7216	0.5331	5008	,	,		21862	0.8115		0.5149	False		,,,				2504	0.6094				p.Q2132Q		Atlas-SNP	.											.	WDFY4	205	.	0			c.A6396G						PASS	.	G		986,398		357,272,63	69.0	68.0	68.0		6396	5.9	1.0	10	dbSNP_107	68	1614,1568		395,824,372	no	coding-synonymous	WDFY4	NM_020945.1		752,1096,435	GG,GA,AA		49.2772,28.7572,43.0574		2132/3185	50038800	2600,1966	692	1591	2283	SO:0001819	synonymous_variant	57705	exon38			GGCACAAAGGCAG	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.6396A>G	10.37:g.50038800A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	222	108	0.486486	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	1404|1404	0.6428571428571429|0.6428571428571429	347|347	0.7052845528455285|0.7052845528455285	202|202	0.5580110497237569|0.5580110497237569	467|467	0.8164335664335665|0.8164335664335665	388|388	0.5118733509234829|0.5118733509234829	G|G	1.008|1.008	-0.688822|-0.688822	0.03328|0.03328	0.712428|0.712428	0.507228|0.507228	ENSG00000128815|ENSG00000128815	ENST00000312002|ENST00000265453	.|.	.|.	.|.	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.27502|0.27502	-1.0072|-1.0072	3|3	.|.	.|.	.|.	.|.	9.5838|9.5838	0.39504|0.39504	0.0708:0.0:0.7887:0.1405|0.0708:0.0:0.7887:0.1405	rs3747874;rs17449924;rs3747874|rs3747874;rs17449924;rs3747874	.|.	.|.	.|.	E|R	1223|219	.|.	.|.	K|K	+|+	1|2	0|0	WDFY4|WDFY4	49708806|49708806	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.063000|0.063000	0.16089|0.16089	2.819000|2.819000	0.48049|0.48049	1.644000|1.644000	0.50603|0.50603	-0.119000|-0.119000	0.15052|0.15052	AAG|AAA	A|0.353;G|0.647	0.647	strong		0.547	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
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 GAIIx	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_ENST00000402951.1_Missense_Mutation_p.D166Y|TREX2_ENST00000370232.1_Missense_Mutation_p.D166Y|TREX2_ENST00000414588.1_Missense_Mutation_p.D165Y|TREX2_ENST00000370231.2_Missense_Mutation_p.D123Y|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000338525.2_Missense_Mutation_p.D123Y|TREX2_ENST00000330912.2_Missense_Mutation_p.D123Y|TREX2_ENST00000393862.2_Missense_Mutation_p.D123Y			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	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	20	7	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 GAIIx	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	Somatic	262	1	0.00381679		WXS	Illumina HiSeq	Phase_I	220	92	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		
GPSM2	29899	hgsc.bcm.edu	37	1	109440215	109440215	+	Missense_Mutation	SNP	G	G	A	rs41279678	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109440215G>A	ENST00000406462.2	+	5	1153	c.380G>A	c.(379-381)cGa>cAa	p.R127Q	AKNAD1_ENST00000357393.4_Intron|GPSM2_ENST00000264126.3_Missense_Mutation_p.R127Q			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	127					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		TGTTGTCAGCGACACCTAGAT	0.408													G|||	345	0.0688898	0.1218	0.0447	5008	,	,		12988	0.002		0.0984	False		,,,				2504	0.0532				p.R127Q		Atlas-SNP	.											.	GPSM2	56	.	0			c.G380A						PASS	.	G	GLN/ARG	431,3975	208.5+/-229.5	23,385,1795	97.0	97.0	97.0		380	5.0	1.0	1	dbSNP_127	97	844,7756	192.8+/-238.7	54,736,3510	yes	missense	GPSM2	NM_013296.4	43	77,1121,5305	AA,AG,GG		9.814,9.7821,9.8032	probably-damaging	127/685	109440215	1275,11731	2203	4300	6503	SO:0001583	missense	29899	exon4			GTCAGCGACACCT	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.380G>A	1.37:g.109440215G>A	ENSP00000385510:p.Arg127Gln	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	168	0.07692307692307693	71	0.1443089430894309	20	0.055248618784530384	1	0.0017482517482517483	76	0.10026385224274406	G	25.1	4.603107	0.87157	0.097821	0.09814	ENSG00000121957	ENST00000406462;ENST00000435987;ENST00000264126	D;D;D	0.94092	-3.35;-3.35;-3.35	5.93	5.01	0.66863	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.063176	0.64402	D	0.000002	D	0.86138	0.5861	L	0.60012	1.86	0.20307	P	0.9999151039	P	0.50272	0.933	B	0.37144	0.242	D	0.85224	0.1028	9	0.22109	T	0.4	-14.5614	16.5133	0.84292	0.0:0.0:0.8681:0.1319	rs41279678;rs57325583;rs61749054	127	P81274	GPSM2_HUMAN	Q	127	ENSP00000385510:R127Q;ENSP00000408664:R127Q;ENSP00000264126:R127Q	ENSP00000264126:R127Q	R	+	2	0	GPSM2	109241738	1.000000	0.71417	1.000000	0.80357	0.493000	0.33554	8.031000	0.88826	1.489000	0.48450	-0.182000	0.12963	CGA	G|0.908;A|0.092	0.092	strong		0.408	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296	
NPY4R	5540	hgsc.bcm.edu	37	10	47087078	47087078	+	Missense_Mutation	SNP	G	G	T	rs2229967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:47087078G>T	ENST00000395716.1	+	2	380	c.295G>T	c.(295-297)Gcc>Tcc	p.A99S	NPY4R_ENST00000374312.1_Missense_Mutation_p.A99S			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	99			A -> S (in dbSNP:rs2229967). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8643460, ECO:0000269|Ref.4}.		blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										GCCGCTGACCGCCGTCTACAC	0.567																																					p.A99S		Atlas-SNP	.											PPYR1,colon,carcinoma,0,1	PPYR1	54	1	0			c.G295T						PASS	.	G	SER/ALA	1235,3171		0,1235,968	166.0	157.0	160.0		295	3.9	0.5	10	dbSNP_98	160	2329,6271		0,2329,1971	yes	missense	PPYR1	NM_005972.4	99	0,3564,2939	TT,TG,GG		27.0814,28.03,27.4027	benign	99/376	47087078	3564,9442	2203	4300	6503	SO:0001583	missense	5540	exon3			CTGACCGCCGTCT		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.295G>T	10.37:g.47087078G>T	ENSP00000379066:p.Ala99Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	112	32	0.285714	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	37	CCDS31193.1	588	0.2692307692307692	134	0.27235772357723576	121	0.3342541436464088	131	0.229020979020979	202	0.26649076517150394	G	12.08	1.829727	0.32329	0.2803	0.270814	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.38401	1.14;1.14	4.85	3.89	0.44902	GPCR, rhodopsin-like superfamily (1);	0.357409	0.28659	N	0.014578	T	0.00012	0.0000	L	0.46670	1.46	0.21445	N	0.999686	P	0.39759	0.687	P	0.49853	0.624	T	0.00967	-1.1497	10	0.66056	D	0.02	.	13.6434	0.62265	0.0:0.1565:0.8435:0.0	rs2229967;rs52836873;rs2229967	99	P50391	NPY4R_HUMAN	S	99	ENSP00000363431:A99S;ENSP00000379066:A99S	ENSP00000363431:A99S	A	+	1	0	PPYR1	46507084	0.241000	0.23857	0.465000	0.27155	0.017000	0.09413	1.524000	0.35942	2.418000	0.82041	0.655000	0.94253	GCC	G|0.725;T|0.275	0.275	strong		0.567	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
PTPRD	5789	hgsc.bcm.edu	37	9	8389364	8389364	+	Silent	SNP	C	C	G	rs2279776	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:8389364C>G	ENST00000381196.4	-	34	4797	c.4254G>C	c.(4252-4254)ggG>ggC	p.G1418G	PTPRD_ENST00000356435.5_Silent_p.G1418G|PTPRD_ENST00000397611.3_Silent_p.G1008G|PTPRD_ENST00000358503.5_Silent_p.G1396G|PTPRD_ENST00000537002.1_Silent_p.G1008G|PTPRD_ENST00000360074.4_Silent_p.G1405G|PTPRD_ENST00000486161.1_Silent_p.G1011G|PTPRD_ENST00000397617.3_Silent_p.G1011G|PTPRD_ENST00000397606.3_Silent_p.G1011G|PTPRD_ENST00000540109.1_Silent_p.G1418G|PTPRD_ENST00000355233.5_Silent_p.G1012G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1418	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)		GCTTCCTATACCCATCTATGT	0.458										TSP Lung(15;0.13)			G|||	2786	0.55631	0.6195	0.451	5008	,	,		18503	0.6329		0.4354	False		,,,				2504	0.591				p.G1418G		Atlas-SNP	.											.	PTPRD	1348	.	0			c.G4254C						PASS	.	G	,,,,,	2547,1859	540.5+/-375.5	733,1081,389	184.0	172.0	176.0		3024,3033,4254,3033,3036,3006	-0.9	0.9	9	dbSNP_100	176	3757,4843	616.4+/-396.5	832,2093,1375	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRD	NM_001040712.2,NM_001171025.1,NM_002839.3,NM_130391.3,NM_130392.3,NM_130393.3	,,,,,	1565,3174,1764	GG,GC,CC		43.686,42.1925,48.4699	,,,,,	1008/1503,1011/1506,1418/1913,1011/1506,1012/1507,1002/1497	8389364	6304,6702	2203	4300	6503	SO:0001819	synonymous_variant	5789	exon37			CCTATACCCATCT	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.4254G>C	9.37:g.8389364C>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	105	52	0.495238	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	37	CCDS43786.1																																																																																			C|0.506;G|0.494	0.494	strong		0.458	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
ZC3H12D	340152	hgsc.bcm.edu	37	6	149795522	149795522	+	Missense_Mutation	SNP	G	G	A	rs7747948	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:149795522G>A	ENST00000409806.3	-	2	476	c.158C>T	c.(157-159)cCg>cTg	p.P53L	ZC3H12D_ENST00000416573.2_Missense_Mutation_p.P53L|ZC3H12D_ENST00000409948.1_Missense_Mutation_p.P53L|ZC3H12D_ENST00000542614.1_Missense_Mutation_p.P53L|ZC3H12D_ENST00000389942.5_Missense_Mutation_p.P53L			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	53			P -> L (in dbSNP:rs7747948). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:19531561}.		negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		GGGTGCAGCCGGGTGCTCCAG	0.716													G|||	903	0.180312	0.2965	0.1902	5008	,	,		14767	0.0169		0.2465	False		,,,				2504	0.1166				p.P53L		Atlas-SNP	.											.	ZC3H12D	21	.	0			c.C158T						PASS	.	G	LEU/PRO	1027,2693		158,711,991	17.0	19.0	18.0		158	-0.3	0.0	6	dbSNP_116	18	2191,5983		305,1581,2201	no	missense	ZC3H12D	NM_207360.2	98	463,2292,3192	AA,AG,GG		26.8045,27.6075,27.0557	benign	53/528	149795522	3218,8676	1860	4087	5947	SO:0001583	missense	340152	exon2			GCAGCCGGGTGCT			6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199		"""Zinc fingers, CCCH-type domain containing"""	21175	protein-coding gene	gene with protein product	"""MCP induced protein 4"""	611106	"""chromosome 6 open reading frame 95"""	C6orf95		18178554	Standard	NM_207360		Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409806.3:c.158C>T	6.37:g.149795522G>A	ENSP00000386616:p.Pro53Leu	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	32	20	0.625	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Missense_Mutation	SNP	ENST00000409806.3	37		450	0.20604395604395603	175	0.3556910569105691	72	0.19889502762430938	11	0.019230769230769232	192	0.2532981530343008	G	8.967	0.971885	0.18736	0.276075	0.268045	ENSG00000178199	ENST00000389942;ENST00000416573;ENST00000409806;ENST00000542614;ENST00000409948	T;T;T;T;T	0.43688	1.49;1.53;1.49;1.54;0.94	4.46	-0.297	0.12820	.	.	.	.	.	T	0.09642	0.0237	L	0.39898	1.24	0.80722	P	0.0	B;P	0.36535	0.176;0.557	B;B	0.22880	0.012;0.042	T	0.11591	-1.0581	8	0.32370	T	0.25	-0.1115	5.0201	0.14356	0.0:0.2903:0.3337:0.376	rs7747948;rs17417830	53;53	A2A288;B7WNU7	ZC12D_HUMAN;.	L	53	ENSP00000374592:P53L;ENSP00000408686:P53L;ENSP00000386616:P53L;ENSP00000440813:P53L;ENSP00000387062:P53L	ENSP00000374592:P53L	P	-	2	0	ZC3H12D	149837215	0.000000	0.05858	0.001000	0.08648	0.046000	0.14306	-0.044000	0.12023	0.027000	0.15297	-0.457000	0.05445	CCG	G|0.788;A|0.212	0.212	strong		0.716	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360	
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 GAIIx	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	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	21	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	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33048686	33048686	+	Missense_Mutation	SNP	G	G	A	rs1042169	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33048686G>A	ENST00000418931.2	+	2	454	c.338G>A	c.(337-339)gGc>gAc	p.G113D	HLA-DPB1_ENST00000535465.1_Missense_Mutation_p.G113D|HLA-DPA1_ENST00000419277.1_5'Flank|HLA-DPB1_ENST00000471184.1_3'UTR	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	113	Beta-1.		G -> D (in allele DPB1*01:01, allele DPB1*03:01, allele DPB1*03:02, allele DPB1*04:03, allele DPB1*05:01, allele DPB1*05:02, allele DPB1*06:01, allele DPB1*08:01, allele DPB1*08:02, allele DPB1*09:01, allele DPB1*09:02, allele DPB1*10:01, allele DPB1*11:01, allele DPB1*11:01, allele DPB1*13:01, allele DPB1*13:02, allele DPB1*13:02, allele DPB1*14:01, allele DPB1*14:02, allele DPB1*16:01, allele DPB1*17:01, allele DPB1*17:02, allele DPB1*19:01, allele DPB1*21:01, allele DPB1*21:01, allele DPB1*21:02, allele DPB1*21:02, allele DPB1*20:01, allele DPB1*22:01, allele DPB1*25:01, allele DPB1*25:02, allele DPB1*26:01, allele DPB1*27:01, allele DPB1*29:01, allele DPB1*30:01, allele DPB1*31:01, allele DPB1*35:01, allele DPB1*36:01, allele DPB1*37:01, allele DPB1*38:01, allele DPB1*44:01, allele DPB1*45:01, allele DPB1*50:01, allele DPB1*52:01, allele DPB1*54:01, allele DPB1*55:01, allele DPB1*56:01, allele DPB1*57:01, allele DPB1*58:01, allele DPB1*63:01, allele DPB1*65:01, allele DPB1*67:01, allele DPB1*68:01, allele DPB1*69:01, allele DPB1*70:01, allele DPB1*76:01, allele DPB1*78:01, allele DPB1*79:01, allele DPB1*84:01, allele DPB1*85:01, allele DPB1*87:01, allele DPB1*88:01, allele DPB1*89:01, allele DPB1*90:01, allele DPB1*91:01, allele DPB1*92:01, allele DPB1*93:01, allele DPB1*97:01 and allele DPB1*98:01; dbSNP:rs1042169). {ECO:0000269|PubMed:6330724}.|G -> N (in allele DPB1*22:02; requires 2 nucleotide substitutions).|G -> V (in allele DPB1*15:01, allele DPB1*18:01, allele DPB1*28:01, allele DPB1*34:01, allele DPB1*40:01, allele DPB1*53:01, allele DPB1*62:01 and allele DPB1*74:01; dbSNP:rs1042169).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						TACGAGCTGGGCGGGCCCATG	0.711													.|||	2405	0.480232	0.6324	0.3573	5008	,	,		13258	0.63		0.328	False		,,,				2504	0.364				p.G113D		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.G338A						PASS	.						19.0	22.0	21.0					6																	33048686		1500	2703	4203	SO:0001583	missense	3115	exon2			AGCTGGGCGGGCC		CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.338G>A	6.37:g.33048686G>A	ENSP00000408146:p.Gly113Asp	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	20	4	0.2	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Missense_Mutation	SNP	ENST00000418931.2	37	CCDS4765.1	996|996	0.45604395604395603|0.45604395604395603	312|312	0.6341463414634146|0.6341463414634146	115|115	0.31767955801104975|0.31767955801104975	338|338	0.5909090909090909|0.5909090909090909	231|231	0.30474934036939316|0.30474934036939316	A|A	0.854|0.854	-0.737728|-0.737728	0.03111|0.03111	.|.	.|.	ENSG00000223865|ENSG00000223865	ENST00000416804|ENST00000418931;ENST00000535465;ENST00000411942;ENST00000428835	.|T;T;T	.|0.00245	.|8.45;8.45;8.45	3.94|3.94	-7.08|-7.08	0.01558|0.01558	.|MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (2);MHC classes I/II-like antigen recognition protein (1);	.|2.725850	.|0.01611	.|N	.|0.022533	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.12502|0.12502	0.225|0.225	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.24541	.|0.033;0.054;0.017	T|T	0.12400|0.12400	-1.0549|-1.0549	4|9	.|0.26408	.|T	.|0.33	.|.	0.3193|0.3193	0.00301|0.00301	0.2892:0.2279:0.2568:0.226|0.2892:0.2279:0.2568:0.226	rs1042169;rs2567286;rs3176946;rs9277353;rs17214755|rs1042169;rs2567286;rs3176946;rs9277353;rs17214755	.|79;123;113	.|A2ALJ6;Q59GY1;P04440	.|.;.;DPB1_HUMAN	T|D	80|113;113;113;90	.|ENSP00000408146:G113D;ENSP00000439674:G113D;ENSP00000412654:G90D	.|ENSP00000389210:G113D	A|G	+|+	1|2	0|0	HLA-DPB1|HLA-DPB1	33156664|33156664	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-2.975000|-2.975000	0.00666|0.00666	-1.442000|-1.442000	0.01955|0.01955	-1.101000|-1.101000	0.02118|0.02118	GCG|GGC	A|0.392;G|0.603;T|0.005	0.392	strong		0.711	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
TLE6	79816	hgsc.bcm.edu	37	19	2994903	2994903	+	Silent	SNP	T	T	C	rs34831575	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:2994903T>C	ENST00000246112.4	+	17	1821	c.1620T>C	c.(1618-1620)ccT>ccC	p.P540P	TLE6_ENST00000452088.1_Silent_p.P417P	NM_001143986.1	NP_001137458.1	Q9H808	TLE6_HUMAN	transducin-like enhancer of split 6	540					regulation of transcription, DNA-templated (GO:0006355)	cell cortex (GO:0005938)|nucleus (GO:0005634)|protein complex (GO:0043234)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|urinary_tract(1)	10				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)		TCCAGGTGCCTGAGATGTCTC	0.597													t|||	1588	0.317093	0.4077	0.3919	5008	,	,		11958	0.3353		0.2356	False		,,,				2504	0.2065				p.P540P		Atlas-SNP	.											.	TLE6	68	.	0			c.T1620C						PASS	.	C	,	1572,2832		304,964,934	63.0	42.0	49.0		1620,1251	-3.0	0.0	19	dbSNP_126	49	1893,6705		207,1479,2613	no	coding-synonymous,coding-synonymous	TLE6	NM_001143986.1,NM_024760.2	,	511,2443,3547	CC,CT,TT		22.0167,35.6948,26.6497	,	540/573,417/450	2994903	3465,9537	2202	4299	6501	SO:0001819	synonymous_variant	79816	exon17			GGTGCCTGAGATG	AK024071	CCDS12100.1, CCDS45910.1	19p13.3	2014-03-07	2014-03-07		ENSG00000104953	ENSG00000104953		"""WD repeat domain containing"""	30788	protein-coding gene	gene with protein product		612399	"""transducin-like enhancer of split 6 (E(sp1) homolog, Drosophila)"""			11486032	Standard	NM_024760		Approved	FLJ14009, GRG6	uc002lwt.2	Q9H808	OTTHUMG00000156793	ENST00000246112.4:c.1620T>C	19.37:g.2994903T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	21	0.466667	NM_001143986	J3KMZ1	Silent	SNP	ENST00000246112.4	37	CCDS45910.1	704	0.32234432234432236	186	0.3780487804878049	125	0.3453038674033149	206	0.36013986013986016	187	0.24670184696569922	t	4.589	0.109429	0.08780	0.356948	0.220167	ENSG00000104953	ENST00000441927	.	.	.	3.37	-3.05	0.05396	.	.	.	.	.	.	.	.	.	.	.	0.23496	P	0.99755694	.	.	.	.	.	.	.	.	.	.	.	.	.	-8.3614	5.1751	0.15131	0.0:0.3401:0.1554:0.5044	rs34831575	.	.	.	R	417	.	.	X	+	1	0	TLE6	2945903	.	.	0.008000	0.14137	0.003000	0.03518	.	.	-0.787000	0.04510	-0.946000	0.02672	TGA	T|0.715;C|0.285	0.285	strong		0.597	TLE6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345996.3	NM_024760	
CTC1	80169	hgsc.bcm.edu	37	17	8139463	8139463	+	Silent	SNP	G	G	A	rs74506939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:8139463G>A	ENST00000315684.8	-	6	997	c.990C>T	c.(988-990)gaC>gaT	p.D330D	CTC1_ENST00000581671.1_5'Flank	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	330					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						GTGGCTTGGGGTCAGCCTCTA	0.542													g|||	451	0.0900559	0.0182	0.1196	5008	,	,		17659	0.0337		0.2207	False		,,,				2504	0.09				p.D330D		Atlas-SNP	.											.	CTC1	75	.	0			c.C990T						PASS	.			185,3817		1,183,1817	78.0	85.0	82.0		990	-2.7	0.0	17	dbSNP_131	82	1931,6427		217,1497,2465	no	coding-synonymous	CTC1	NM_025099.5		218,1680,4282	AA,AG,GG		23.1036,4.6227,17.1197		330/1218	8139463	2116,10244	2001	4179	6180	SO:0001819	synonymous_variant	80169	exon6			CTTGGGGTCAGCC	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.990C>T	17.37:g.8139463G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			G|0.849;A|0.151	0.151	strong		0.542	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
ALPP	250	hgsc.bcm.edu	37	2	233245026	233245026	+	Missense_Mutation	SNP	G	G	A	rs2853378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233245026G>A	ENST00000392027.2	+	6	1057	c.788G>A	c.(787-789)cGc>cAc	p.R263H	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	263			R -> H (in dbSNP:rs2853378). {ECO:0000269|PubMed:3461452}.		dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		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;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		CTGGCGAAGCGCCAGGTGATG	0.662													A|||	501	0.10004	0.0507	0.0605	5008	,	,		10859	0.2242		0.1004	False		,,,				2504	0.0665				p.R263H		Atlas-SNP	.											ALPP,NS,carcinoma,+1,1	ALPP	53	1	0			c.G788A						scavenged	.						69.0	73.0	71.0					2																	233245026		2203	4300	6503	SO:0001583	missense	250	exon6			CGAAGCGCCAGGT	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.788G>A	2.37:g.233245026G>A	ENSP00000375881:p.Arg263His	Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	287	9	0.0313589	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	224	0.10256410256410256	21	0.042682926829268296	22	0.06077348066298342	111	0.19405594405594406	70	0.09234828496042216	.	0.012	-1.655324	0.00779	.	.	ENSG00000163283	ENST00000392027	D	0.96522	-4.04	2.31	-0.177	0.13307	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	1.003840	0.08014	N	0.990937	T	0.00608	0.0020	N	0.02685	-0.53	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.54549	-0.8277	9	0.05959	T	0.93	.	7.1392	0.25546	0.6554:0.0:0.3446:0.0	rs2853378;rs12617638;rs17838624	263	P05187	PPB1_HUMAN	H	263	ENSP00000375881:R263H	ENSP00000375881:R263H	R	+	2	0	ALPP	232953270	0.000000	0.05858	0.964000	0.40570	0.162000	0.22319	0.146000	0.16180	0.135000	0.18707	-1.054000	0.02325	CGC	G|0.500;A|0.500	0.500	weak		0.662	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
TNIP2	79155	hgsc.bcm.edu	37	4	2744087	2744087	+	Missense_Mutation	SNP	G	G	A	rs2269495	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:2744087G>A	ENST00000315423.7	-	6	1273	c.1187C>T	c.(1186-1188)gCc>gTc	p.A396V	TNIP2_ENST00000505186.1_5'UTR|TNIP2_ENST00000510267.1_Missense_Mutation_p.A289V|TNIP2_ENST00000503235.1_Missense_Mutation_p.A313V	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCCTCTCTGGGCCGCGCCAGG	0.667													G|||	1717	0.342851	0.0651	0.5663	5008	,	,		16508	0.3879		0.4165	False		,,,				2504	0.4376				p.A396V		Atlas-SNP	.											TNIP2,NS,carcinoma,0,1	TNIP2	28	1	0			c.C1187T						PASS	.	G	VAL/ALA,VAL/ALA	628,3778	265.0+/-266.4	47,534,1622	31.0	34.0	33.0		866,1187	2.0	0.0	4	dbSNP_100	33	3674,4926	513.9+/-378.3	792,2090,1418	no	missense,missense	TNIP2	NM_001161527.1,NM_024309.3	64,64	839,2624,3040	AA,AG,GG		42.7209,14.2533,33.077	benign,benign	289/323,396/430	2744087	4302,8704	2203	4300	6503	SO:0001583	missense	79155	exon6			CTCTGGGCCGCGC	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.1187C>T	4.37:g.2744087G>A	ENSP00000321203:p.Ala396Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	82	26	0.317073	NM_024309		Missense_Mutation	SNP	ENST00000315423.7	37	CCDS3362.1	795	0.364010989010989	42	0.08536585365853659	189	0.5220994475138122	232	0.40559440559440557	332	0.43799472295514513	G	17.98	3.520625	0.64747	0.142533	0.427209	ENSG00000168884	ENST00000510267;ENST00000315423;ENST00000503235	T;T;T	0.38722	1.12;1.12;1.12	5.11	1.99	0.26369	.	0.969853	0.08459	N	0.942635	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	P;P	0.38078	0.617;0.483	B;B	0.33960	0.173;0.163	T	0.45396	-0.9264	9	0.54805	T	0.06	-3.312	12.8156	0.57663	0.0:0.0:0.4836:0.5164	rs2269495;rs17849661;rs2269495	313;396	D6RGJ2;Q8NFZ5	.;TNIP2_HUMAN	V	289;396;313	ENSP00000427613:A289V;ENSP00000321203:A396V;ENSP00000426314:A313V	ENSP00000321203:A396V	A	-	2	0	TNIP2	2713885	0.002000	0.14202	0.001000	0.08648	0.006000	0.05464	0.476000	0.22180	0.536000	0.28733	0.561000	0.74099	GCC	G|0.671;N|0.001	.	strong		0.667	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309	
C9orf156	51531	hgsc.bcm.edu	37	9	100684719	100684719	+	Silent	SNP	A	A	C	rs3183928	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:100684719A>C	ENST00000375119.3	-	1	133	c.57T>G	c.(55-57)gtT>gtG	p.V19V	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	19					viral process (GO:0016032)		hydrolase activity (GO:0016787)	p.V19V(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				GAGCCGGCTTAACGCAGCCGC	0.637											OREG0019350	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1328	0.265176	0.1959	0.3401	5008	,	,		16982	0.2113		0.4115	False		,,,				2504	0.2106				p.V19V		Atlas-SNP	.											C9orf156,NS,carcinoma,0,1	C9orf156	35	1	1	Substitution - coding silent(1)	prostate(1)	c.T57G						PASS	.	C		956,3442		116,724,1359	31.0	28.0	29.0		57	-0.1	0.9	9	dbSNP_105	29	3028,5558		557,1914,1822	no	coding-synonymous	C9orf156	NM_016481.3		673,2638,3181	CC,CA,AA		35.2667,21.7372,30.6839		19/442	100684719	3984,9000	2199	4293	6492	SO:0001819	synonymous_variant	51531	exon1			CGGCTTAACGCAG	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"""Nef (lentivirus myristoylated factor) associated protein 1"""						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.57T>G	9.37:g.100684719A>C		Somatic	46	0	0	1353	WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Silent	SNP	ENST00000375119.3	37	CCDS6730.1																																																																																			T|0.181;G|0.063	.	strong		0.637	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
KIAA1731	85459	hgsc.bcm.edu	37	11	93400796	93400796	+	Silent	SNP	C	C	T	rs67112133	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:93400796C>T	ENST00000325212.6	+	3	294	c.132C>T	c.(130-132)atC>atT	p.I44I	KIAA1731_ENST00000411936.1_Silent_p.I44I|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	44						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.I44I(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				AAAGAGATATCGCCTTACAGA	0.358													C|||	685	0.136781	0.1044	0.0749	5008	,	,		18829	0.2718		0.0974	False		,,,				2504	0.1258				p.I44I		Atlas-SNP	.											KIAA1731_ENST00000325212,NS,carcinoma,0,1	KIAA1731	173	1	1	Substitution - coding silent(1)	stomach(1)	c.C132T						PASS	.	C		150,1234		6,138,548	50.0	41.0	44.0		132	-8.8	0.1	11	dbSNP_130	44	273,2909		9,255,1327	no	coding-synonymous	KIAA1731	NM_033395.1		15,393,1875	TT,TC,CC		8.5795,10.8382,9.2641		44/2602	93400796	423,4143	692	1591	2283	SO:0001819	synonymous_variant	85459	exon3			AGATATCGCCTTA	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.132C>T	11.37:g.93400796C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	110	78	0.709091	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Silent	SNP	ENST00000325212.6	37	CCDS44708.1																																																																																			C|0.864;T|0.136	0.136	strong		0.358	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
CCT6A	908	hgsc.bcm.edu	37	7	56129511	56129511	+	Silent	SNP	A	A	G	rs4927	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:56129511A>G	ENST00000275603.4	+	12	1638	c.1419A>G	c.(1417-1419)tcA>tcG	p.S473S	SUMF2_ENST00000275607.9_5'Flank|SUMF2_ENST00000437307.2_5'Flank|SUMF2_ENST00000395435.2_5'Flank|SUMF2_ENST00000342190.6_5'Flank|SUMF2_ENST00000395436.2_5'Flank|CCT6A_ENST00000335503.3_Silent_p.S428S|CCT6A_ENST00000540286.1_Silent_p.S442S|SNORA15_ENST00000384439.1_RNA|SUMF2_ENST00000413756.1_5'Flank|CCT6A_ENST00000462133.1_3'UTR|SUMF2_ENST00000434526.2_5'Flank	NM_001762.3	NP_001753.1	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A (zeta 1)	473					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|cervix(2)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)	15	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			ATTCAGAATCAGGTCAGCTTG	0.383													A|||	464	0.0926518	0.2352	0.0375	5008	,	,		15193	0.0159		0.0517	False		,,,				2504	0.0603				p.S473S		Atlas-SNP	.											.	CCT6A	44	.	0			c.A1419G						PASS	.	A	,	961,3445	362.4+/-316.1	113,735,1355	51.0	48.0	49.0		1284,1419	-7.7	0.8	7	dbSNP_52	49	480,8120	138.9+/-195.6	12,456,3832	no	coding-synonymous,coding-synonymous	CCT6A	NM_001009186.1,NM_001762.3	,	125,1191,5187	GG,GA,AA		5.5814,21.8112,11.0795	,	428/487,473/532	56129511	1441,11565	2203	4300	6503	SO:0001819	synonymous_variant	908	exon12			AGAATCAGGTCAG	M94083	CCDS5523.1, CCDS34640.1	7p11.2	2011-09-02			ENSG00000146731	ENSG00000146731		"""Heat Shock Proteins / Chaperonins"""	1620	protein-coding gene	gene with protein product		104613		CCT6		1352881, 8034610	Standard	NM_001762		Approved	TTCP20, TCPZ, Cctz, HTR3, TCP20	uc003trl.1	P40227	OTTHUMG00000022842	ENST00000275603.4:c.1419A>G	7.37:g.56129511A>G		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	224	109	0.486607	NM_001762	A6NCD2|Q3KP28|Q75LP4|Q96S46	Silent	SNP	ENST00000275603.4	37	CCDS5523.1																																																																																			A|0.904;G|0.096	0.096	strong		0.383	CCT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251526.2	NM_001762	
PTPLA	9200	hgsc.bcm.edu	37	10	17636309	17636309	+	Missense_Mutation	SNP	G	G	A	rs1053926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:17636309G>A	ENST00000361271.3	-	6	716	c.679C>T	c.(679-681)Cat>Tat	p.H227Y		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	227			H -> Y (in dbSNP:rs1053926). {ECO:0000269|PubMed:10644438, ECO:0000269|PubMed:11054553}.		fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						TTCTTCACATGCGGCAAGGCA	0.323													A|||	994	0.198482	0.2542	0.1744	5008	,	,		15516	0.0685		0.3022	False		,,,				2504	0.1677				p.H227Y		Atlas-SNP	.											.	PTPLA	34	.	0			c.C679T						PASS	.	A	TYR/HIS	1118,3288	711.7+/-408.0	151,816,1236	68.0	69.0	69.0		679	5.7	0.6	10	dbSNP_86	69	2405,6183	696.0+/-404.8	358,1689,2247	yes	missense	PTPLA	NM_014241.3	83	509,2505,3483	AA,AG,GG		28.0042,25.3745,27.1125	benign	227/289	17636309	3523,9471	2203	4294	6497	SO:0001583	missense	9200	exon6			TCACATGCGGCAA	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"""cementum attachment protein"""	610467	"""protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"""			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.679C>T	10.37:g.17636309G>A	ENSP00000355308:p.His227Tyr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	172	87	0.505814	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Missense_Mutation	SNP	ENST00000361271.3	37	CCDS7121.1	435	0.19917582417582416	123	0.25	72	0.19889502762430938	26	0.045454545454545456	214	0.28232189973614774	A	0.881	-0.728885	0.03135	0.253745	0.280042	ENSG00000165996	ENST00000361271	T	0.28666	1.6	5.72	5.72	0.89469	.	0.165083	0.56097	N	0.000036	T	0.00012	0.0000	N	0.01410	-0.885	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	9	0.02654	T	1	-17.2091	9.2783	0.37714	0.8614:0.0:0.1386:0.0	rs1053926;rs3167994;rs52791621;rs1053926	227	B0YJ81	HACD1_HUMAN	Y	227	ENSP00000355308:H227Y	ENSP00000355308:H227Y	H	-	1	0	PTPLA	17676315	0.996000	0.38824	0.583000	0.28640	0.543000	0.35085	3.798000	0.55522	1.099000	0.41499	-0.269000	0.10298	CAT	G|0.764;A|0.236	0.236	strong		0.323	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241	
FUT6	2528	hgsc.bcm.edu	37	19	5831672	5831672	+	Missense_Mutation	SNP	G	G	C	rs61147939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5831672G>C	ENST00000318336.4	-	3	2101	c.907C>G	c.(907-909)Cgg>Ggg	p.R303G	FUT6_ENST00000592563.1_Missense_Mutation_p.R303G|FUT6_ENST00000286955.5_Missense_Mutation_p.R303G|FUT6_ENST00000524754.1_Missense_Mutation_p.R303G|FUT6_ENST00000527106.1_Missense_Mutation_p.R303G	NM_000150.2	NP_000141.1	P51993	FUT6_HUMAN	fucosyltransferase 6 (alpha (1,3) fucosyltransferase)	303			R -> G (found in alpha(1,3)- fucosyltransferase-deficient individuals; complete enzyme inactivation when associated with S-124 and V-244; dbSNP:rs61147939). {ECO:0000269|PubMed:11102976}.		fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			endometrium(2)|kidney(1)|large_intestine(1)|lung(2)	6						TGCAGGTACCGGGCCAGGTCC	0.657													G|||	945	0.188698	0.0734	0.2954	5008	,	,		19862	0.4484		0.0736	False		,,,				2504	0.1196				p.R303G		Atlas-SNP	.											.	FUT6	30	.	0			c.C907G	GRCh37	CM002971	FUT6	M	rs61147939	PASS	.						27.0	31.0	30.0					19																	5831672		2200	4279	6479	SO:0001583	missense	2528	exon3			GGTACCGGGCCAG		CCDS12152.1	19p13.3	2013-02-26			ENSG00000156413	ENSG00000156413	2.4.1.65	"""Fucosyltransferases"""	4017	protein-coding gene	gene with protein product	"""alpha-(1,3)-fucosyltransferase"", ""galactoside 3-L-fucosyltransferase"""	136836				1520296, 7782074	Standard	NM_001040701		Approved	FT1A, FCT3A, FucT-VI, FLJ40754	uc002mdh.1	P51993	OTTHUMG00000167335	ENST00000318336.4:c.907C>G	19.37:g.5831672G>C	ENSP00000313398:p.Arg303Gly	Somatic	566	0	0		WXS	Illumina HiSeq	Phase_I	518	155	0.299228	NM_000150	A6NEX0|D6W637|Q9UND8	Missense_Mutation	SNP	ENST00000318336.4	37	CCDS12152.1	460	0.21062271062271062	38	0.07723577235772358	96	0.26519337016574585	273	0.4772727272727273	53	0.06992084432717678	G	4.807	0.150075	0.09185	.	.	ENSG00000156413	ENST00000524754;ENST00000527106;ENST00000318336;ENST00000286955;ENST00000341530	T;T;T;T	0.25912	1.77;1.77;1.77;1.77	3.03	3.03	0.35002	.	1.347070	0.05003	N	0.469400	T	0.00012	0.0000	M	0.66939	2.045	0.80722	P	0.0	B;B	0.23442	0.085;0.049	B;B	0.39152	0.292;0.232	T	0.46512	-0.9186	9	0.27785	T	0.31	.	8.6736	0.34165	0.0:0.2378:0.7622:0.0	rs61147939	303;303	C9J8A2;P51993	.;FUT6_HUMAN	G	303	ENSP00000431708:R303G;ENSP00000432954:R303G;ENSP00000313398:R303G;ENSP00000286955:R303G	ENSP00000286955:R303G	R	-	1	2	FUT6	5782672	0.000000	0.05858	0.080000	0.20451	0.111000	0.19643	0.461000	0.21940	1.628000	0.50416	0.436000	0.28706	CGG	G|0.090;C|0.910	0.910	strong		0.657	FUT6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394218.2	NM_000150	
TAS2R60	338398	hgsc.bcm.edu	37	7	143141475	143141475	+	Silent	SNP	T	T	C	rs4595035	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143141475T>C	ENST00000332690.1	+	1	930	c.930T>C	c.(928-930)cgT>cgC	p.R310R	EPHA1-AS1_ENST00000429289.1_RNA	NM_177437.1	NP_803186.1	P59551	T2R60_HUMAN	taste receptor, type 2, member 60	310					sensory perception of bitter taste (GO:0050913)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(1)|large_intestine(2)|lung(17)|prostate(1)|skin(7)|urinary_tract(2)	31	Melanoma(164;0.172)					TGAAGAGTCGTCGTTCCTCAA	0.498													C|||	3542	0.707268	0.5061	0.7853	5008	,	,		19685	0.8889		0.66	False		,,,				2504	0.7853				p.R310R		Atlas-SNP	.											TAS2R60,colon,carcinoma,+1,1	TAS2R60	55	1	0			c.T930C						PASS	.	C		2358,2046	556.1+/-379.4	654,1050,498	95.0	90.0	92.0		930	-5.4	0.0	7	dbSNP_111	92	5748,2850	432.4+/-357.1	1957,1834,508	no	coding-synonymous	TAS2R60	NM_177437.1		2611,2884,1006	CC,CT,TT		33.1472,46.4578,37.6557		310/319	143141475	8106,4896	2202	4299	6501	SO:0001819	synonymous_variant	338398	exon1			GAGTCGTCGTTCC	AY114094	CCDS5885.1	7q35	2014-07-10			ENSG00000185899	ENSG00000185899		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	20639	protein-coding gene	gene with protein product		613968				12584440	Standard	NM_177437		Approved	T2R60	uc011ktg.2	P59551	OTTHUMG00000154891	ENST00000332690.1:c.930T>C	7.37:g.143141475T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_177437	A4D2G8|Q645W8|Q7RTR7	Silent	SNP	ENST00000332690.1	37	CCDS5885.1																																																																																			T|0.360;C|0.640	0.640	strong		0.498	TAS2R60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337541.1		
HLA-G	3135	hgsc.bcm.edu	37	6	29796376	29796376	+	Missense_Mutation	SNP	C	C	A	rs12722477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29796376C>A	ENST00000360323.6	+	3	424	c.400C>A	c.(400-402)Ctc>Atc	p.L134I	HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376818.3_Intron|HLA-G_ENST00000376828.2_Missense_Mutation_p.L139I|HLA-G_ENST00000428701.1_Missense_Mutation_p.L134I			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	134	Alpha-2.				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 peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cytokine-mediated signaling pathway (GO:0019221)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						CGGACGCCTCCTCCGCGGGTA	0.667													c|||	1015	0.202676	0.2398	0.17	5008	,	,		14748	0.2857		0.0924	False		,,,				2504	0.2035				p.L134I		Atlas-SNP	.											.	HLA-G	90	.	0			c.C400A						PASS	.	C	ILE/LEU	660,2360		76,508,926	107.0	109.0	108.0		400	0.6	0.1	6	dbSNP_126	108	473,4945		23,427,2259	yes	missense	HLA-G	NM_002127.5	5	99,935,3185	AA,AC,CC		8.7302,21.8543,13.4274	benign	134/339	29796376	1133,7305	1510	2709	4219	SO:0001583	missense	3135	exon4			CGCCTCCTCCGCG		CCDS4668.1	6p21.3	2013-01-11	2007-12-12		ENSG00000204632	ENSG00000204632		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4964	protein-coding gene	gene with protein product	"""b2 microglobulin"""	142871	"""HLA-G histocompatibility antigen, class I, G"""				Standard	NM_002127		Approved		uc003nnw.2	P17693	OTTHUMG00000031157	ENST00000360323.6:c.400C>A	6.37:g.29796376C>A	ENSP00000353472:p.Leu134Ile	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	126	15	0.119048	NM_002127		Missense_Mutation	SNP	ENST00000360323.6	37	CCDS4668.1	424	0.19413919413919414	95	0.19308943089430894	71	0.19613259668508287	192	0.3356643356643357	66	0.0870712401055409	.	12.81	2.050353	0.36181	0.218543	0.087302	ENSG00000204632	ENST00000376828;ENST00000428701;ENST00000360323	T;T;T	0.00010	9.42;9.42;9.42	1.72	0.563	0.17296	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	6.445200	0.02343	U	0.075118	T	0.00178	0.0005	M	0.89414	3.03	0.80722	P	0.0	B;D	0.58620	0.284;0.983	P;D	0.83275	0.475;0.996	T	0.50642	-0.8804	9	0.87932	D	0	.	5.3	0.15773	0.5224:0.4776:0.0:0.0	rs12722477;rs17225116;rs59771878	139;134	Q5RJ85;P17693	.;HLAG_HUMAN	I	139;134;134	ENSP00000366024:L139I;ENSP00000412927:L134I;ENSP00000353472:L134I	ENSP00000353472:L134I	L	+	1	0	HLA-G	29904355	0.000000	0.05858	0.062000	0.19696	0.038000	0.13279	-0.975000	0.03790	0.952000	0.37798	0.298000	0.19748	CTC	C|0.838;A|0.162	0.162	strong		0.667	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127	
FAM26F	441168	hgsc.bcm.edu	37	6	116783330	116783330	+	Missense_Mutation	SNP	G	G	A	rs1057192	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:116783330G>A	ENST00000368605.1	+	2	333	c.238G>A	c.(238-240)Gga>Aga	p.G80R	FAM26F_ENST00000368606.3_Intron|RP1-93H18.6_ENST00000476099.1_RNA	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	80			G -> R (in dbSNP:rs1057192).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(1)	3				GBM - Glioblastoma multiforme(226;0.0402)|all cancers(137;0.0627)|OV - Ovarian serous cystadenocarcinoma(136;0.0655)|Epithelial(106;0.231)		CCTGCTCACCGGATGCTGCTC	0.721													G|||	1200	0.239617	0.0628	0.17	5008	,	,		13100	0.3651		0.2485	False		,,,				2504	0.3896				p.E80K		Atlas-SNP	.											.	FAM26F	12	.	0			c.G238A						PASS	.	G	ARG/GLY	285,3437		11,263,1587	4.0	4.0	4.0		238	4.2	1.0	6	dbSNP_86	4	1331,5787		122,1087,2350	yes	missense	FAM26F	NM_001010919.1	125	133,1350,3937	AA,AG,GG		18.6991,7.6572,14.9077	probably-damaging	80/316	116783330	1616,9224	1861	3559	5420	SO:0001583	missense	441168	exon2			CTCACCGGATGCT	AF086130	CCDS34519.1, CCDS64506.1	6q22.1	2007-06-20			ENSG00000188820	ENSG00000188820			33391	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 187"""	C6orf187			Standard	NM_001010919		Approved	RP1-93H18.5, OTTHUMP00000017061, OTTHUMP00000017062, dJ93H18.5	uc003pwv.4	Q5R3K3	OTTHUMG00000015438	ENST00000368605.1:c.238G>A	6.37:g.116783330G>A	ENSP00000357594:p.Gly80Arg	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	492	0.22527472527472528	23	0.046747967479674794	64	0.17679558011049723	209	0.36538461538461536	196	0.25857519788918204	G	19.26	3.793370	0.70452	0.076572	0.186991	ENSG00000188820	ENST00000368605	T	0.24908	1.83	5.1	4.22	0.49857	.	0.060943	0.64402	D	0.000004	T	0.45498	0.1345	M	0.83223	2.63	0.09310	P	0.999999384292	D	0.89917	1.0	D	0.79784	0.993	T	0.59150	-0.7508	9	0.87932	D	0	-20.7189	15.7243	0.77743	0.0:0.137:0.863:0.0	rs1057192;rs3173147	80	Q5R3K3	FA26F_HUMAN	R	80	ENSP00000357594:G80R	ENSP00000357594:G80R	G	+	1	0	FAM26F	116890023	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	4.925000	0.63425	1.372000	0.46190	0.491000	0.48974	GGA	.	.	weak		0.721	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919	
RAD23B	5887	hgsc.bcm.edu	37	9	110084328	110084328	+	Missense_Mutation	SNP	C	C	T	rs1805329	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:110084328C>T	ENST00000358015.3	+	7	1097	c.746C>T	c.(745-747)gCt>gTt	p.A249V	RAD23B_ENST00000416373.2_Missense_Mutation_p.A177V	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	249			A -> V (in dbSNP:rs1805329). {ECO:0000269|PubMed:15064313, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AGTACTGGGGCTCCTCAGTCT	0.502								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	765	0.152756	0.0076	0.3055	5008	,	,		14900	0.2014		0.1789	False		,,,				2504	0.1636				p.A249V		Atlas-SNP	.											.	RAD23B	31	.	0			c.C746T	GRCh37	CM057926	RAD23B	M	rs1805329	PASS	.	C	VAL/ALA	216,4190	130.6+/-167.2	7,202,1994	53.0	54.0	54.0		746	5.3	0.9	9	dbSNP_98	54	1577,7023	295.9+/-302.6	159,1259,2882	yes	missense	RAD23B	NM_002874.4	64	166,1461,4876	TT,TC,CC		18.3372,4.9024,13.7859	benign	249/410	110084328	1793,11213	2203	4300	6503	SO:0001583	missense	5887	exon7			CTGGGGCTCCTCA		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"""XP-C repair complementing protein"", ""XP-C repair complementing complex 58 kDa"""	600062	"""RAD23 (S. cerevisiae) homolog B"""			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.746C>T	9.37:g.110084328C>T	ENSP00000350708:p.Ala249Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	37	CCDS6769.1	365	0.1671245421245421	8	0.016260162601626018	88	0.2430939226519337	109	0.19055944055944055	160	0.21108179419525067	C	17.70	3.455281	0.63401	0.049024	0.183372	ENSG00000119318	ENST00000358015;ENST00000416373	T;T	0.20598	2.08;2.06	5.28	5.28	0.74379	.	0.710413	0.14969	N	0.287917	T	0.00012	0.0000	N	0.24115	0.695	0.38373	P	0.05508299999999999	B;B;B	0.30889	0.005;0.073;0.299	B;B;B	0.28553	0.015;0.011;0.091	T	0.47249	-0.9132	9	0.30078	T	0.28	-9.4451	19.2797	0.94048	0.0:1.0:0.0:0.0	rs1805329;rs2227991;rs2266668;rs4134750;rs4987013;rs17845630;rs17858561;rs52825339;rs1805329	228;249;249	B7Z4W4;B4DEA3;P54727	.;.;RD23B_HUMAN	V	249;177	ENSP00000350708:A249V;ENSP00000405623:A177V	ENSP00000350708:A249V	A	+	2	0	RAD23B	109124149	0.872000	0.30054	0.858000	0.33744	0.972000	0.66771	3.697000	0.54764	2.626000	0.88956	0.555000	0.69702	GCT	C|0.850;T|0.150	0.150	strong		0.502	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874	
F5	2153	hgsc.bcm.edu	37	1	169510233	169510233	+	Silent	SNP	G	G	A	rs9332607	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:169510233G>A	ENST00000367797.3	-	13	4296	c.4095C>T	c.(4093-4095)acC>acT	p.T1365T	F5_ENST00000367796.3_Silent_p.T1370T	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	1365	35 X 9 AA approximate tandem repeats of [TNP]-L-S-P-D-L-S-Q-T.|B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	CTAGAGAAAGGGTTGTATGGC	0.522													N|||	912	0.182109	0.1513	0.2017	5008	,	,		21282	0.001		0.4095	False		,,,				2504	0.1626				p.T1365T		Atlas-SNP	.											.	F5	301	.	0			c.C4095T						PASS	.	G		809,3597		78,653,1472	168.0	186.0	180.0		4095	-3.8	0.0	1	dbSNP_119	180	3471,5129		660,2151,1489	no	coding-synonymous	F5	NM_000130.4		738,2804,2961	AA,AG,GG		40.3605,18.3613,32.9079		1365/2225	169510233	4280,8726	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			AGAAAGGGTTGTA	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.4095C>T	1.37:g.169510233G>A		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	228	218	0.95614	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.698;A|0.302	0.302	strong		0.522	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
MUC16	94025	hgsc.bcm.edu	37	19	9048170	9048170	+	Missense_Mutation	SNP	G	G	A	rs10417600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9048170G>A	ENST00000397910.4	-	5	33664	c.33461C>T	c.(33460-33462)tCt>tTt	p.S11154F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11156	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGTGACCAGAGAGGTCACCAT	0.478													G|||	948	0.189297	0.1982	0.1988	5008	,	,		23687	0.0258		0.2813	False		,,,				2504	0.2444				p.S11154F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C33461T						PASS	.		PHE/SER	749,3069		69,611,1229	86.0	79.0	81.0		33461	2.4	0.0	19	dbSNP_119	81	2497,5763		399,1699,2032	yes	missense	MUC16	NM_024690.2	155	468,2310,3261	AA,AG,GG		30.23,19.6176,26.8753	probably-damaging	11154/14508	9048170	3246,8832	1909	4130	6039	SO:0001583	missense	94025	exon5			ACCAGAGAGGTCA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.33461C>T	19.37:g.9048170G>A	ENSP00000381008:p.Ser11154Phe	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	406	0.1858974358974359	103	0.20934959349593496	76	0.20994475138121546	11	0.019230769230769232	216	0.2849604221635884	g	6.853	0.526597	0.13066	0.196176	0.3023	ENSG00000181143	ENST00000397910	T	0.02737	4.18	3.43	2.39	0.29439	.	.	.	.	.	T	0.00012	0.0000	L	0.55481	1.735	.	.	.	D	0.76494	0.999	D	0.78314	0.991	T	0.48843	-0.8999	8	0.87932	D	0	.	6.5891	0.22636	0.1311:0.0:0.8689:0.0	rs10417600;rs52818682;rs10417600	11154	B5ME49	.	F	11154	ENSP00000381008:S11154F	ENSP00000381008:S11154F	S	-	2	0	MUC16	8909170	0.001000	0.12720	0.002000	0.10522	0.011000	0.07611	0.463000	0.21972	0.994000	0.38892	0.550000	0.68814	TCT	G|0.796;A|0.204	0.204	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
BANF2	140836	hgsc.bcm.edu	37	20	17716416	17716416	+	Missense_Mutation	SNP	C	C	G	rs1053993	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:17716416C>G	ENST00000246090.5	+	4	495	c.233C>G	c.(232-234)aCt>aGt	p.T78S	BANF2_ENST00000377805.3_Missense_Mutation_p.T78S|BANF2_ENST00000467330.1_3'UTR|BANF2_ENST00000545418.2_Missense_Mutation_p.T85S	NM_178477.4	NP_848572.3	Q9H503	BAFL_HUMAN	barrier to autointegration factor 2	78			T -> S (in dbSNP:rs1053993).			cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(1)|prostate(3)|skin(1)	6						GCCCAGCAGACTTCTCACTGC	0.537													G|||	1965	0.392372	0.5212	0.2536	5008	,	,		17148	0.4861		0.2604	False		,,,				2504	0.3558				p.T85S		Atlas-SNP	.											.	BANF2	12	.	0			c.C254G						PASS	.	G	SER/THR,SER/THR,SER/THR	2165,2241	593.8+/-388.1	540,1085,578	178.0	148.0	158.0		233,254,233	3.4	0.1	20	dbSNP_86	158	2368,6232	703.0+/-405.3	324,1720,2256	yes	missense,missense,missense	BANF2	NM_178477.4,NM_001159495.1,NM_001014977.3	58,58,58	864,2805,2834	GG,GC,CC		27.5349,49.1375,34.8531	benign,benign,benign	78/91,85/98,78/91	17716416	4533,8473	2203	4300	6503	SO:0001583	missense	140836	exon3			AGCAGACTTCTCA	BC054871	CCDS13129.1, CCDS54449.1	20p12.1	2007-12-17	2007-12-17	2007-12-17	ENSG00000125888	ENSG00000125888			16172	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 179"""	C20orf179			Standard	NM_178477		Approved	dJ803K15.1, BAF-L, BAFL, BAF2	uc010zrs.1	Q9H503	OTTHUMG00000031949	ENST00000246090.5:c.233C>G	20.37:g.17716416C>G	ENSP00000246090:p.Thr78Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001159495	D3DW25|F5H3F6|Q7Z4M6	Missense_Mutation	SNP	ENST00000246090.5	37	CCDS13129.1	817	0.3740842490842491	240	0.4878048780487805	105	0.2900552486187845	282	0.493006993006993	190	0.25065963060686014	G	10.90	1.481913	0.26598	0.491375	0.275349	ENSG00000125888	ENST00000545418;ENST00000377805;ENST00000246090	T;T;T	0.53640	0.61;0.61;0.61	5.43	3.36	0.38483	.	0.234635	0.35615	N	0.003098	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45920	-0.9228	8	0.33940	T	0.23	.	7.6537	0.28363	0.0:0.316:0.4986:0.1855	rs1053993;rs3194554;rs1053993	85;78	F5H3F6;Q9H503	.;BAFL_HUMAN	S	85;78;78	ENSP00000439128:T85S;ENSP00000367036:T78S;ENSP00000246090:T78S	ENSP00000246090:T78S	T	+	2	0	BANF2	17664416	0.537000	0.26386	0.107000	0.21349	0.973000	0.67179	0.676000	0.25247	1.305000	0.44909	-0.216000	0.12614	ACT	C|0.647;G|0.353	0.353	strong		0.537	BANF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102261.2	NM_178477	
ZNF134	7693	hgsc.bcm.edu	37	19	58132106	58132106	+	Missense_Mutation	SNP	A	A	C	rs34034473	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58132106A>C	ENST00000396161.5	+	3	929	c.619A>C	c.(619-621)Agc>Cgc	p.S207R		NM_003435.3	NP_003426.3	P52741	ZN134_HUMAN	zinc finger protein 134	207			S -> R (in dbSNP:rs34034473).		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)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(3)|prostate(1)	11		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		TTATGAGTGCAGCGAATGTGG	0.468													A|||	303	0.0605032	0.0076	0.0735	5008	,	,		21039	0.0923		0.1004	False		,,,				2504	0.0491				p.S207R		Atlas-SNP	.											ZNF134,caecum,carcinoma,0,1	ZNF134	34	1	0			c.A619C						PASS	.	A	ARG/SER	69,4337	57.4+/-93.9	1,67,2135	57.0	63.0	61.0		619	-1.5	0.0	19	dbSNP_126	61	783,7815	180.9+/-229.7	32,719,3548	yes	missense	ZNF134	NM_003435.3	110	33,786,5683	CC,CA,AA		9.1068,1.566,6.5518	benign	207/428	58132106	852,12152	2203	4299	6502	SO:0001583	missense	7693	exon3			GAGTGCAGCGAAT	U09412	CCDS42638.1	19q13.4	2013-01-08	2006-06-13			ENSG00000213762		"""Zinc fingers, C2H2-type"""	12918	protein-coding gene	gene with protein product		604076	"""zinc finger protein 134 (clone pHZ-15)"""			7557990	Standard	NM_003435		Approved	pHZ-15	uc002qpn.2	P52741		ENST00000396161.5:c.619A>C	19.37:g.58132106A>C	ENSP00000379464:p.Ser207Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_003435	Q9Y4B2	Missense_Mutation	SNP	ENST00000396161.5	37	CCDS42638.1	164	0.07509157509157509	7	0.014227642276422764	28	0.07734806629834254	56	0.0979020979020979	73	0.09630606860158311	A	9.906	1.208160	0.22205	0.01566	0.091068	ENSG00000213762	ENST00000418193;ENST00000541849;ENST00000396161	T	0.18960	2.18	4.09	-1.55	0.08558	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00384	0.0012	N	0.22421	0.69	0.80722	P	0.0	B	0.28850	0.225	B	0.37346	0.247	T	0.34850	-0.9812	8	0.52906	T	0.07	.	5.7765	0.18281	0.5166:0.1396:0.3438:0.0	rs34034473	207	P52741	ZN134_HUMAN	R	274;127;207	ENSP00000379464:S207R	ENSP00000379464:S207R	S	+	1	0	ZNF134	62823918	0.000000	0.05858	0.002000	0.10522	0.024000	0.10985	-1.585000	0.02112	-0.345000	0.08325	-0.375000	0.07067	AGC	A|0.917;C|0.083	0.083	strong		0.468	ZNF134-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466808.1	NM_003435	
MAGEB4	4115	hgsc.bcm.edu	37	X	30261002	30261002	+	Silent	SNP	A	A	G	rs2071311	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:30261002A>G	ENST00000378982.2	+	1	946	c.750A>G	c.(748-750)gtA>gtG	p.V250V	MAGEB1_ENST00000397550.1_5'Flank|MAGEB1_ENST00000378981.3_5'Flank	NM_002367.3	NP_002358.1	O15481	MAGB4_HUMAN	melanoma antigen family B, 4	250	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.V250V(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27						AAGATCTGGTACAGGAAAAAT	0.483													G|||	3042	0.805828	0.6815	0.6744	3775	,	,		14881	0.4276		0.6829	False		,,,				2504	0.5675				p.V250V		Atlas-SNP	.											.	MAGEB4	75	.	1	Substitution - coding silent(1)	prostate(1)	c.A750G						PASS	.	G		3431,402		1305,305,516,21,55	63.0	60.0	61.0		750	0.3	0.0	X	dbSNP_96	61	6035,693		1961,444,1669,23,203	no	coding-synonymous	MAGEB4	NM_002367.3		3266,749,2185,44,258	GG,GA,G,AA,A		10.3002,10.4879,10.3683		250/347	30261002	9466,1095	2202	4300	6502	SO:0001819	synonymous_variant	4115	exon1			TCTGGTACAGGAA		CCDS14221.1	Xp21.3	2009-03-17			ENSG00000120289	ENSG00000120289			6811	protein-coding gene	gene with protein product	"""melanoma-associated antigen B4"", ""cancer/testis antigen family 3, member 6"""	300153				9441743	Standard	NM_002367		Approved	MGC33144, CT3.6	uc004dcb.3	O15481	OTTHUMG00000021321	ENST00000378982.2:c.750A>G	X.37:g.30261002A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_002367	B2R9G0|Q6FHH4|Q8IZ00	Silent	SNP	ENST00000378982.2	37	CCDS14221.1																																																																																			A|0.120;G|0.880	0.880	strong		0.483	MAGEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056159.1	NM_002367	
ZFYVE28	57732	hgsc.bcm.edu	37	4	2275835	2275835	+	Silent	SNP	G	G	A	rs2051561	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:2275835G>A	ENST00000290974.2	-	9	2499	c.2160C>T	c.(2158-2160)ttC>ttT	p.F720F	ZFYVE28_ENST00000508471.1_Silent_p.F25F|ZFYVE28_ENST00000511071.1_Silent_p.F690F|ZFYVE28_ENST00000515312.1_Silent_p.F650F	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	720					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						GGCTGCCGTGGAACCTGGACC	0.642													G|||	1784	0.35623	0.3623	0.513	5008	,	,		14371	0.12		0.5427	False		,,,				2504	0.2883				p.F720F		Atlas-SNP	.											.	ZFYVE28	79	.	0			c.C2160T						PASS	.	G	,,	1557,2849	487.6+/-361.0	256,1045,902	136.0	119.0	125.0		2070,1950,2160	2.8	1.0	4	dbSNP_94	125	4616,3984	599.4+/-394.1	1260,2096,944	no	coding-synonymous,coding-synonymous,coding-synonymous	ZFYVE28	NM_001172656.1,NM_001172659.1,NM_020972.2	,,	1516,3141,1846	AA,AG,GG		46.3256,35.3382,47.4627	,,	690/858,650/818,720/888	2275835	6173,6833	2203	4300	6503	SO:0001819	synonymous_variant	57732	exon9			GCCGTGGAACCTG	AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"""Zinc fingers, FYVE domain containing"""	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.2160C>T	4.37:g.2275835G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_020972	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Silent	SNP	ENST00000290974.2	37	CCDS33942.1																																																																																			G|0.575;A|0.425	0.425	strong		0.642	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
PIGQ	9091	hgsc.bcm.edu	37	16	632283	632283	+	Intron	SNP	G	G	A	rs7187227	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:632283G>A	ENST00000026218.5	+	10	1619				PIGQ_ENST00000321878.5_Missense_Mutation_p.G523S|PIGQ_ENST00000409527.2_Missense_Mutation_p.G523S	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q						C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GCACGAGGCCGGCAGGCCCCT	0.692													G|||	696	0.138978	0.1377	0.0793	5008	,	,		17264	0.0248		0.1799	False		,,,				2504	0.2587				p.G523S		Atlas-SNP	.											.	PIGQ	43	.	0			c.G1567A						PASS	.	G	SER/GLY,	675,3717		50,575,1571	25.0	26.0	26.0		1567,	5.1	1.0	16	dbSNP_116	26	1560,7032		144,1272,2880	yes	missense,intron	PIGQ	NM_004204.3,NM_148920.1	56,	194,1847,4451	AA,AG,GG		18.1564,15.3689,17.2135	,	523/582,	632283	2235,10749	2196	4296	6492	SO:0001627	intron_variant	9091	exon10			GAGGCCGGCAGGC	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.1532-600G>A	16.37:g.632283G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_004204	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	268	0.1227106227106227	73	0.1483739837398374	32	0.08839779005524862	18	0.03146853146853147	145	0.19129287598944592	G	22.4	4.284826	0.80803	0.153689	0.181564	ENSG00000007541	ENST00000409527;ENST00000321878;ENST00000540241	T;T	0.44482	0.92;0.92	5.08	5.08	0.68730	.	.	.	.	.	T	0.00178	0.0005	M	0.73598	2.24	0.09310	P	1.0	D	0.89917	1.0	D	0.76575	0.988	T	0.08743	-1.0707	8	0.10636	T	0.68	.	17.4349	0.87548	0.0:0.0:1.0:0.0	rs7187227	523	Q9BRB3-2	.	S	523;523;81	ENSP00000386760:G523S;ENSP00000326674:G523S	ENSP00000326674:G523S	G	+	1	0	PIGQ	572284	1.000000	0.71417	0.995000	0.50966	0.430000	0.31655	5.884000	0.69729	2.361000	0.80049	0.561000	0.74099	GGC	G|0.853;A|0.147	0.147	strong		0.692	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
CDH23	64072	hgsc.bcm.edu	37	10	73550969	73550969	+	Missense_Mutation	SNP	G	G	A	rs10466026	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73550969G>A	ENST00000224721.6	+	46	6150	c.6145G>A	c.(6145-6147)Gag>Aag	p.E2049K		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2044	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.E2049K(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						GCTGCTGGCTGAGGACATCGG	0.627													G|||	1666	0.332668	0.261	0.3473	5008	,	,		20132	0.5288		0.2763	False		,,,				2504	0.2751				p.E2044K		Atlas-SNP	.											CDH23,colon,carcinoma,0,2	CDH23	365	2	1	Substitution - Missense(1)	stomach(1)	c.G6130A						PASS	.	G	LYS/GLU	1189,3207		151,887,1160	51.0	58.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6130	5.9	1.0	10	dbSNP_119	55	2258,6330		313,1632,2349	yes	missense	CDH23	NM_022124.5	56	464,2519,3509	AA,AG,GG		26.2925,27.0473,26.5481	possibly-damaging	2044/3355	73550969	3447,9537	2198	4294	6492	SO:0001583	missense	64072	exon45			CTGGCTGAGGACA	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.6145G>A	10.37:g.73550969G>A	ENSP00000224721:p.Glu2049Lys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		760	0.34798534798534797	145	0.29471544715447157	108	0.2983425414364641	299	0.5227272727272727	208	0.27440633245382584	G	21.3	4.130608	0.77549	0.270473	0.262925	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.91	5.91	0.95273	Cadherin (3);Cadherin-like (1);	0.213542	0.38605	N	0.001630	T	0.00012	0.0000	N	0.02142	-0.665	0.09310	P	1.0	P	0.38535	0.635	B	0.40134	0.32	T	0.18840	-1.0324	8	0.08179	T	0.78	.	11.4841	0.50344	0.0683:0.1272:0.8045:0.0	rs10466026;rs58573365;rs10466026	2044	Q9H251	CAD23_HUMAN	K	2049;2044;2047	.	ENSP00000224721:E2049K	E	+	1	0	CDH23	73220975	0.996000	0.38824	1.000000	0.80357	0.837000	0.47467	2.222000	0.42926	2.793000	0.96121	0.655000	0.94253	GAG	G|0.661;A|0.339	0.339	strong		0.627	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
ANKRD13A	88455	hgsc.bcm.edu	37	12	110456175	110456175	+	Silent	SNP	A	A	G	rs2302689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:110456175A>G	ENST00000261739.4	+	5	592	c.426A>G	c.(424-426)ccA>ccG	p.P142P	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	142						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						GAATATGCCCAAATGATGTCT	0.463													G|||	1560	0.311502	0.6717	0.183	5008	,	,		19584	0.1448		0.1769	False		,,,				2504	0.226				p.P142P		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.A426G						PASS	.	G		2675,1731	518.3+/-369.7	814,1047,342	103.0	98.0	100.0		426	-11.2	0.1	12	dbSNP_100	100	1375,7225	755.3+/-407.5	102,1171,3027	no	coding-synonymous	ANKRD13A	NM_033121.1		916,2218,3369	GG,GA,AA		15.9884,39.2873,31.1395		142/591	110456175	4050,8956	2203	4300	6503	SO:0001819	synonymous_variant	88455	exon5			ATGCCCAAATGAT	AF064604	CCDS9140.1	12q24.12	2013-01-10	2006-06-30	2006-06-30		ENSG00000076513		"""Ankyrin repeat domain containing"""	21268	protein-coding gene	gene with protein product		615123	"""ankyrin repeat domain 13"""	ANKRD13		10508479	Standard	NM_033121		Approved	NY-REN-25	uc001tpx.3	Q8IZ07	OTTHUMG00000169314	ENST00000261739.4:c.426A>G	12.37:g.110456175A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	235	136	0.578723	NM_033121	O60736	Silent	SNP	ENST00000261739.4	37	CCDS9140.1																																																																																			A|0.706;G|0.294	0.294	strong		0.463	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121	
MUC16	94025	hgsc.bcm.edu	37	19	9072875	9072875	+	Silent	SNP	G	G	A	rs73009098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9072875G>A	ENST00000397910.4	-	3	14774	c.14571C>T	c.(14569-14571)gtC>gtT	p.V4857V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4859	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTGGAGATGTGACTTTAGATG	0.438													G|||	935	0.186701	0.0923	0.2536	5008	,	,		24451	0.3254		0.1322	False		,,,				2504	0.18				p.V4857V		Atlas-SNP	.											.	MUC16	4315	.	0			c.C14571T						PASS	.			389,3697		16,357,1670	186.0	175.0	179.0		14571	-1.3	0.0	19	dbSNP_130	179	1160,7216		73,1014,3101	no	coding-synonymous	MUC16	NM_024690.2		89,1371,4771	AA,AG,GG		13.8491,9.5203,12.4298		4857/14508	9072875	1549,10913	2043	4188	6231	SO:0001819	synonymous_variant	94025	exon3			AGATGTGACTTTA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.14571C>T	19.37:g.9072875G>A		Somatic	414	0	0		WXS	Illumina HiSeq	Phase_I	439	193	0.439636	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.809;A|0.191	0.191	strong		0.438	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
HYDIN	54768	hgsc.bcm.edu	37	16	71015329	71015329	+	Missense_Mutation	SNP	G	G	T	rs78763837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:71015329G>T	ENST00000393567.2	-	29	4625	c.4475C>A	c.(4474-4476)cCc>cAc	p.P1492H		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1492					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)				GCAGATTTGGGGAAAGATTCC	0.483													G|||	2340	0.467252	0.4455	0.5591	5008	,	,		18143	0.5645		0.328	False		,,,				2504	0.4744				p.P1492H		Atlas-SNP	.											LOC652153,NS,haematopoietic_neoplasm,0,2	HYDIN	788	2	0			c.C4475A						PASS	.						66.0	66.0	66.0					16																	71015329		1844	4072	5916	SO:0001583	missense	54768	exon29			ATTTGGGGAAAGA	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.4475C>A	16.37:g.71015329G>T	ENSP00000377197:p.Pro1492His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	127	47	0.370079	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	964	0.4413919413919414	233	0.4735772357723577	184	0.5082872928176796	312	0.5454545454545454	235	0.3100263852242744	G	24.0	4.480970	0.84747	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01221	5.15	4.26	4.26	0.50523	.	0.000000	0.33023	U	0.005376	T	0.00012	0.0000	M	0.80183	2.485	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.45056	-0.9287	9	0.49607	T	0.09	.	16.6224	0.84934	0.0:0.0:1.0:0.0	.	1491	F8WD23	.	H	1492;1491	ENSP00000377197:P1492H	ENSP00000313052:P1491H	P	-	2	0	HYDIN	69572830	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.105000	0.94246	2.083000	0.62718	0.603000	0.83216	CCC	.	.	weak		0.483	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
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 GAIIx	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	ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000389651.4_5'Flank|LCMT2_ENST00000567039.1_3'UTR|LCMT2_ENST00000544735.1_5'UTR|ADAL_ENST00000422466.2_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	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	63	45	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	
SLC39A14	23516	hgsc.bcm.edu	37	8	22262321	22262321	+	Missense_Mutation	SNP	T	T	C	rs896378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:22262321T>C	ENST00000381237.1	+	2	217	c.98T>C	c.(97-99)cTg>cCg	p.L33P	SLC39A14_ENST00000240095.6_Missense_Mutation_p.L33P|SLC39A14_ENST00000289952.5_Missense_Mutation_p.L33P|SLC39A14_ENST00000359741.5_Missense_Mutation_p.L33P	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	33			L -> P (in dbSNP:rs896378). {ECO:0000269|PubMed:15489334}.		cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		GCTTCATCCCTGGGTGCACCA	0.602													C|||	3150	0.628994	0.7617	0.5288	5008	,	,		18688	0.6974		0.504	False		,,,				2504	0.5787				p.L33P		Atlas-SNP	.											.	SLC39A14	59	.	0			c.T98C						PASS	.	C	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	3134,1272	430.8+/-342.7	1107,920,176	93.0	94.0	94.0		98,98,98,98	-2.4	0.0	8	dbSNP_86	94	4056,4544	593.0+/-393.1	952,2152,1196	yes	missense,missense,missense,missense	SLC39A14	NM_001128431.2,NM_001135153.1,NM_001135154.1,NM_015359.4	98,98,98,98	2059,3072,1372	CC,CT,TT		47.1628,28.8697,44.7178	benign,benign,benign,benign	33/493,33/493,33/482,33/493	22262321	7190,5816	2203	4300	6503	SO:0001583	missense	23516	exon2			CATCCCTGGGTGC	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.98T>C	8.37:g.22262321T>C	ENSP00000370635:p.Leu33Pro	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Missense_Mutation	SNP	ENST00000381237.1	37	CCDS47823.1	1361	0.6231684981684982	364	0.7398373983739838	199	0.5497237569060773	414	0.7237762237762237	384	0.5065963060686016	C	9.809	1.182733	0.21870	0.711303	0.471628	ENSG00000104635	ENST00000359741;ENST00000520644;ENST00000240095;ENST00000381237;ENST00000289952;ENST00000524285;ENST00000520832;ENST00000519960;ENST00000522881;ENST00000517552	T;T;T;T;T;T;T;T;T;T	0.68025	-0.28;0.87;-0.3;-0.28;-0.28;0.87;0.73;0.78;0.78;0.79	5.48	-2.43	0.06522	.	1.717850	0.02385	N	0.079140	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42999	-0.9418	9	0.23891	T	0.37	0.4749	2.1354	0.03760	0.1041:0.3154:0.2047:0.3758	rs896378;rs17263733;rs17856493;rs896378	33;33;33	Q15043-2;Q15043;B6EU88	.;S39AE_HUMAN;.	P	33	ENSP00000352779:L33P;ENSP00000428789:L33P;ENSP00000240095:L33P;ENSP00000370635:L33P;ENSP00000289952:L33P;ENSP00000430315:L33P;ENSP00000428905:L33P;ENSP00000430629:L33P;ENSP00000429328:L33P;ENSP00000430564:L33P	ENSP00000240095:L33P	L	+	2	0	SLC39A14	22318266	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.407000	0.02488	-0.359000	0.08150	-0.355000	0.07637	CTG	C|0.584;N|0.000	0.584	strong		0.602	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
TRIM31	11074	hgsc.bcm.edu	37	6	30080274	30080274	+	Silent	SNP	G	G	A	rs2517598	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30080274G>A	ENST00000376734.3	-	2	434	c.309C>T	c.(307-309)caC>caT	p.H103H	TRIM31_ENST00000485864.1_5'Flank|TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Silent_p.H103H	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	103					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						CGCAGAAATAGTGGAACATCT	0.493													A|||	606	0.121006	0.093	0.1297	5008	,	,		21287	0.0873		0.1252	False		,,,				2504	0.183				p.H103H		Atlas-SNP	.											.	TRIM31	40	.	0			c.C309T						PASS	.	A		306,2716		16,274,1221	138.0	122.0	127.0		309	-3.8	0.0	6	dbSNP_100	127	785,4633		51,683,1975	no	coding-synonymous	TRIM31	NM_007028.3		67,957,3196	AA,AG,GG		14.4887,10.1257,12.9265		103/426	30080274	1091,7349	1511	2709	4220	SO:0001819	synonymous_variant	11074	exon2			GAAATAGTGGAAC	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.309C>T	6.37:g.30080274G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	121	96	0.793388	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			G|0.878;A|0.122	0.122	strong		0.493	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
ADAMTS14	140766	hgsc.bcm.edu	37	10	72517830	72517830	+	Missense_Mutation	SNP	G	G	A	rs10999516	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72517830G>A	ENST00000373207.1	+	20	3050	c.3050G>A	c.(3049-3051)aGc>aAc	p.S1017N	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.S1020N	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1017	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.		S -> N (in dbSNP:rs10999516).		collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CAGGTCTGCAGCCTGCCCGCC	0.622													G|||	1069	0.213458	0.1543	0.2262	5008	,	,		18477	0.37		0.1849	False		,,,				2504	0.1524				p.S1020N		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.G3059A						PASS	.	G	ASN/SER,ASN/SER	769,3637	307.5+/-290.0	67,635,1501	40.0	38.0	38.0		3050,3059	3.4	1.0	10	dbSNP_120	38	1384,7216	264.8+/-285.7	113,1158,3029	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	46,46	180,1793,4530	AA,AG,GG		16.093,17.4535,16.5539	benign,benign	1017/1224,1020/1227	72517830	2153,10853	2203	4300	6503	SO:0001583	missense	140766	exon20			TCTGCAGCCTGCC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3050G>A	10.37:g.72517830G>A	ENSP00000362303:p.Ser1017Asn	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	500	0.22893772893772893	75	0.1524390243902439	69	0.19060773480662985	213	0.3723776223776224	143	0.18865435356200527	G	11.65	1.702981	0.30232	0.174535	0.16093	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.52754	0.65;0.65	4.34	3.39	0.38822	.	0.482320	0.22699	N	0.056718	T	0.00012	0.0000	N	0.01640	-0.785	0.38674	P	0.047624	B;P	0.34699	0.019;0.464	B;B	0.39027	0.044;0.288	T	0.35773	-0.9775	9	0.10111	T	0.7	.	5.8642	0.18765	0.1314:0.0:0.6843:0.1842	rs10999516;rs57370271	1017;1020	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	N	1020;1017	ENSP00000362304:S1020N;ENSP00000362303:S1017N	ENSP00000362303:S1017N	S	+	2	0	ADAMTS14	72187836	0.998000	0.40836	1.000000	0.80357	0.945000	0.59286	2.373000	0.44266	2.250000	0.74265	0.561000	0.74099	AGC	G|0.824;A|0.176	0.176	strong		0.622	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
MED11	400569	hgsc.bcm.edu	37	17	4638737	4638737	+	IGR	SNP	A	A	G	rs1050998	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4638737A>G	ENST00000293777.5	+	0	833				CXCL16_ENST00000293778.6_Missense_Mutation_p.I142T|CXCL16_ENST00000576153.1_5'UTR|CXCL16_ENST00000574412.1_Missense_Mutation_p.I142T	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.I142T(1)		lung(2)|ovary(2)	4						GGCCTGAGAAATTGGGGGGCT	0.547													A|||	2320	0.463259	0.2958	0.4813	5008	,	,		15653	0.5883		0.4394	False		,,,				2504	0.5726				p.I142T		Atlas-SNP	.											CXCL16_ENST00000293778,NS,carcinoma,0,1	CXCL16	30	1	1	Substitution - Missense(1)	stomach(1)	c.T425C						PASS	.	A	THR/ILE,THR/ILE	1377,3029	442.7+/-346.8	219,939,1045	40.0	46.0	44.0		425,425	-10.8	0.0	17	dbSNP_86	44	3757,4843	524.7+/-380.6	837,2083,1380	yes	missense,missense	CXCL16	NM_022059.2,NM_001100812.1	89,89	1056,3022,2425	GG,GA,AA		43.686,31.2528,39.4741	benign,benign	142/274,142/274	4638737	5134,7872	2203	4300	6503	SO:0001628	intergenic_variant	58191	exon4			TGAGAAATTGGGG	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086			17.37:g.4638737A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_022059	Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	CCDS32533.1	988	0.4523809523809524	149	0.30284552845528456	162	0.44751381215469616	342	0.5979020979020979	335	0.4419525065963061	A	7.511	0.654588	0.14580	0.312528	0.43686	ENSG00000161921	ENST00000293778	T	0.37058	1.22	5.39	-10.8	0.00216	.	1.751720	0.03251	N	0.181791	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.31641	-0.9936	9	0.20519	T	0.43	-0.0524	11.7582	0.51888	0.1525:0.3809:0.4666:0.0	rs1050998;rs3191367;rs17824101;rs17846369;rs17859405;rs52827810;rs57321128;rs1050998	123	Q9H2A7	CXL16_HUMAN	T	142	ENSP00000293778:I142T	ENSP00000293778:I142T	I	-	2	0	CXCL16	4585486	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.475000	0.06599	-2.302000	0.00657	-1.759000	0.00671	ATT	G|0.428;N|0.001	0.428	strong		0.547	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
LTF	4057	hgsc.bcm.edu	37	3	46501213	46501213	+	Missense_Mutation	SNP	T	T	C	rs1126478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46501213T>C	ENST00000231751.4	-	2	435	c.140A>G	c.(139-141)aAa>aGa	p.K47R	LTF_ENST00000426532.2_Missense_Mutation_p.K3R|LTF_ENST00000417439.1_Missense_Mutation_p.K47R	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	47	Bactericidal and antifungal activity.|Interaction with lipopolysaccharide.|Involved in glycosaminoglycan binding.|Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.		K -> R (decreased antibacterial activity against Gram-positive bacteria; seems to reduce susceptibility to localized juvenile periodontitis; associated with increased plasma lactoferrin concentrations and possibly with susceptibility to coronary artery stenosis; dbSNP:rs1126478). {ECO:0000269|PubMed:11702692, ECO:0000269|PubMed:14573629, ECO:0000269|PubMed:22406253, ECO:0000269|PubMed:22900286, ECO:0000269|PubMed:9873069, ECO:0000269|Ref.11, ECO:0000269|Ref.8, ECO:0000269|Ref.9}.		antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		GCCACGCACTTTTCTCATATT	0.562													C|||	3142	0.627396	0.9644	0.487	5008	,	,		17963	0.6498		0.3489	False		,,,				2504	0.5348				p.K47R		Atlas-SNP	.											.	LTF	98	.	0			c.A140G						PASS	.	C	ARG/LYS,ARG/LYS	3783,623	270.4+/-269.6	1637,509,57	149.0	133.0	139.0		8,140	-9.7	0.0	3	dbSNP_86	139	2720,5880	682.3+/-403.8	441,1838,2021	yes	missense,missense	LTF	NM_001199149.1,NM_002343.3	26,26	2078,2347,2078	CC,CT,TT		31.6279,14.1398,50.0	benign,benign	3/667,47/711	46501213	6503,6503	2203	4300	6503	SO:0001583	missense	4057	exon2			CGCACTTTTCTCA		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.140A>G	3.37:g.46501213T>C	ENSP00000231751:p.Lys47Arg	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	170	79	0.464706	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	37	CCDS33747.1	1278	0.5851648351648352	472	0.959349593495935	169	0.46685082872928174	371	0.6486013986013986	266	0.35092348284960423	C	9.497	1.102132	0.20632	0.858602	0.316279	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496;ENST00000443743;ENST00000431944;ENST00000415180	T;T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32;1.32	4.83	-9.66	0.00534	.	0.832641	0.10628	N	0.652479	T	0.00012	0.0000	N	0.25380	0.74	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.002	T	0.10823	-1.0613	9	0.15952	T	0.53	-0.6452	6.3207	0.21217	0.0921:0.4621:0.0936:0.3522	rs1126478;rs3181525;rs17220161;rs52823440;rs60725703;rs1126478	47;34;47	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	R	47;3;47;34;47;58;3	ENSP00000231751:K47R;ENSP00000405719:K3R;ENSP00000405546:K47R;ENSP00000397427:K34R;ENSP00000395234:K58R;ENSP00000400254:K3R	ENSP00000231751:K47R	K	-	2	0	LTF	46476217	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.120000	0.01323	-2.970000	0.00286	-1.929000	0.00512	AAA	T|0.446;C|0.554	0.554	strong		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
ETNK1	55500	hgsc.bcm.edu	37	12	22814036	22814036	+	Silent	SNP	A	A	G	rs4963793	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:22814036A>G	ENST00000266517.4	+	4	953	c.864A>G	c.(862-864)gaA>gaG	p.E288E		NM_018638.4	NP_061108.2	Q9HBU6	EKI1_HUMAN	ethanolamine kinase 1	288					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16						TTCTCCAGGAAGAGATGACTT	0.363													A|||	1282	0.25599	0.0794	0.196	5008	,	,		14489	0.6925		0.1292	False		,,,				2504	0.2178				p.E288E	Esophageal Squamous(42;87 913 3224 6226 43339)	Atlas-SNP	.											.	ETNK1	61	.	0			c.A864G						PASS	.	A		393,4013	197.1+/-221.3	20,353,1830	111.0	108.0	109.0		864	1.1	1.0	12	dbSNP_111	109	997,7603	215.0+/-254.5	51,895,3354	no	coding-synonymous	ETNK1	NM_018638.4		71,1248,5184	GG,GA,AA		11.593,8.9197,10.6874		288/453	22814036	1390,11616	2203	4300	6503	SO:0001819	synonymous_variant	55500	exon4			CCAGGAAGAGATG	BC006111	CCDS8698.1, CCDS41760.1	12p12.2	2004-07-09			ENSG00000139163	ENSG00000139163			24649	protein-coding gene	gene with protein product		609858				11912161, 11044454	Standard	XM_005253420		Approved	EKI1, EKI	uc001rft.3	Q9HBU6	OTTHUMG00000169008	ENST00000266517.4:c.864A>G	12.37:g.22814036A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_018638	G5E969	Silent	SNP	ENST00000266517.4	37	CCDS8698.1	616	0.28205128205128205	42	0.08536585365853659	77	0.212707182320442	398	0.6958041958041958	99	0.13060686015831136	A	8.711	0.912067	0.17907	0.089197	0.11593	ENSG00000139163	ENST00000538218	.	.	.	4.75	1.08	0.20341	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.37641	-0.9697	3	.	.	.	-5.9551	8.0978	0.30840	0.7262:0.0:0.2738:0.0	rs4963793;rs58477815;rs4963793	.	.	.	R	279	.	.	K	+	2	0	ETNK1	22705303	0.971000	0.33674	1.000000	0.80357	0.993000	0.82548	0.154000	0.16343	0.338000	0.23692	0.482000	0.46254	AAG	A|0.810;G|0.190	0.190	strong		0.363	ETNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401926.2	NM_018638	
TMEM200A	114801	hgsc.bcm.edu	37	6	130761867	130761867	+	Silent	SNP	T	T	C	rs12207253	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:130761867T>C	ENST00000296978.3	+	3	1171	c.300T>C	c.(298-300)aaT>aaC	p.N100N	TMEM200A_ENST00000392429.1_Silent_p.N100N|TMEM200A_ENST00000545622.1_Silent_p.N100N	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	100						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TGTCAACAAATGAAACTCAGG	0.428													T|||	66	0.0131789	0.0189	0.0159	5008	,	,		20525	0.0		0.0298	False		,,,				2504	0.0				p.N100N		Atlas-SNP	.											.	TMEM200A	108	.	0			c.T300C						PASS	.	T		115,4291	87.8+/-126.4	1,113,2089	105.0	94.0	98.0		300	-2.7	1.0	6	dbSNP_120	98	322,8278	113.9+/-173.9	5,312,3983	no	coding-synonymous	TMEM200A	NM_052913.2		6,425,6072	CC,CT,TT		3.7442,2.6101,3.36		100/492	130761867	437,12569	2203	4300	6503	SO:0001819	synonymous_variant	114801	exon3			AACAAATGAAACT	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.300T>C	6.37:g.130761867T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_001258277	Q96PX5	Silent	SNP	ENST00000296978.3	37	CCDS5140.1																																																																																			T|0.971;C|0.029	0.029	strong		0.428	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
FECH	2235	hgsc.bcm.edu	37	18	55226383	55226383	+	Silent	SNP	G	G	C	rs536765	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:55226383G>C	ENST00000262093.5	-	7	949	c.798C>G	c.(796-798)ccC>ccG	p.P266P	FECH_ENST00000382873.3_Silent_p.P272P	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	266					cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				TTACAGACATGGGCAGTGAGT	0.413													C|||	3754	0.749601	0.9758	0.6902	5008	,	,		17556	0.6081		0.6421	False		,,,				2504	0.7423				p.P272P		Atlas-SNP	.											.	FECH	42	.	0			c.C816G						PASS	.	C	,	4051,355	181.9+/-209.8	1862,327,14	105.0	96.0	99.0		798,816	-9.6	0.0	18	dbSNP_83	99	5881,2719	434.3+/-357.7	2016,1849,435	no	coding-synonymous,coding-synonymous	FECH	NM_000140.3,NM_001012515.2	,	3878,2176,449	CC,CG,GG		31.6163,8.0572,23.6352	,	266/424,272/430	55226383	9932,3074	2203	4300	6503	SO:0001819	synonymous_variant	2235	exon7			AGACATGGGCAGT	D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"""protoporphyria"""	612386	"""ferrochelatase (protoporphyria)"""			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.798C>G	18.37:g.55226383G>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001012515	A8KA72|Q8IXN1|Q8NAN0	Silent	SNP	ENST00000262093.5	37	CCDS11964.1																																																																																			G|0.249;C|0.751	0.751	strong		0.413	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1		
QRICH2	84074	hgsc.bcm.edu	37	17	74289875	74289875	+	Silent	SNP	C	C	T	rs6501882	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74289875C>T	ENST00000262765.5	-	4	614	c.435G>A	c.(433-435)ggG>ggA	p.G145G		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	145										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						GCTGCTGTCTCCCAGTACCAG	0.562													C|||	2351	0.469449	0.7073	0.3098	5008	,	,		19445	0.5724		0.2753	False		,,,				2504	0.3548				p.G145G		Atlas-SNP	.											.	QRICH2	143	.	0			c.G435A						PASS	.	C		2925,1481	678.2+/-403.5	977,971,255	57.0	59.0	58.0		435	-5.1	0.0	17	dbSNP_116	58	2485,6115	405.8+/-348.6	347,1791,2162	no	coding-synonymous	QRICH2	NM_032134.1		1324,2762,2417	TT,TC,CC		28.8953,33.6133,41.5962		145/1664	74289875	5410,7596	2203	4300	6503	SO:0001819	synonymous_variant	84074	exon4			CTGTCTCCCAGTA	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.435G>A	17.37:g.74289875C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	104	43	0.413462	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																			C|0.558;T|0.442	0.442	strong		0.562	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
LSM5	23658	hgsc.bcm.edu	37	7	32529936	32529936	+	Silent	SNP	G	G	C	rs1584614	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:32529936G>C	ENST00000450169.2	-	1	94	c.42C>G	c.(40-42)ccC>ccG	p.P14P	LSM5_ENST00000409782.1_5'UTR|LSM5_ENST00000409952.3_Intron|LSM5_ENST00000409909.3_Intron|LSM5_ENST00000410044.1_5'UTR|LSM5_ENST00000409987.1_Silent_p.P14P|LSM5_ENST00000409292.1_5'Flank	NM_001130710.1|NM_012322.2	NP_001124182.1|NP_036454.1	Q9Y4Y9	LSM5_HUMAN	LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae)	14					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)	p.P14P(1)		breast(1)|cervix(1)|large_intestine(1)|lung(1)|stomach(1)	5			GBM - Glioblastoma multiforme(11;0.152)			GATTACCTAAGGGCAGCAGCT	0.622													C|||	3761	0.750998	0.6808	0.804	5008	,	,		19253	0.8651		0.8052	False		,,,				2504	0.635				p.P14P		Atlas-SNP	.											LSM5,NS,carcinoma,0,1	LSM5	9	1	1	Substitution - coding silent(1)	stomach(1)	c.C42G						PASS	.	C	,,	2914,1492	475.7+/-357.4	977,960,266	88.0	70.0	76.0		,,42	-1.6	0.6	7	dbSNP_88	76	6947,1653	302.4+/-305.9	2818,1311,171	no	intron,intron,coding-synonymous	LSM5	NM_001130710.1,NM_001139499.1,NM_012322.2	,,	3795,2271,437	CC,CG,GG		19.2209,33.8629,24.1811	,,	,,14/92	32529936	9861,3145	2203	4300	6503	SO:0001819	synonymous_variant	23658	exon1			ACCTAAGGGCAGC	AF182291	CCDS5438.1, CCDS47571.1	7p14.3	2003-02-17			ENSG00000106355	ENSG00000106355			17162	protein-coding gene	gene with protein product		607285				10369684, 12515382	Standard	NM_001130710		Approved	YER146W	uc003tct.2	Q9Y4Y9	OTTHUMG00000022913	ENST00000450169.2:c.42C>G	7.37:g.32529936G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_012322		Silent	SNP	ENST00000450169.2	37	CCDS5438.1																																																																																			G|0.237;C|0.763	0.763	strong		0.622	LSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215102.2		
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 GAIIx	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	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	135	34	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	
GCDH	2639	hgsc.bcm.edu	37	19	13008607	13008607	+	Silent	SNP	G	G	T	rs1060218	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:13008607G>T	ENST00000222214.5	+	11	1384	c.1173G>T	c.(1171-1173)ggG>ggT	p.G391G	GCDH_ENST00000422947.2_Silent_p.G347G|GCDH_ENST00000457854.1_Silent_p.G391G|GCDH_ENST00000591470.1_Silent_p.G391G			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase	391					cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	TGCTGGGGGGGAATGGGATTT	0.602													G|||	1254	0.250399	0.171	0.4308	5008	,	,		19457	0.1438		0.325	False		,,,				2504	0.2628				p.S391S	GBM(123;875 1636 7726 16444 26754)	Atlas-SNP	.											GCDH_ENST00000457854,NS,carcinoma,+2,2	GCDH	76	2	0			c.C1173T	GRCh37	CD962014	GCDH	D	rs1060218	PASS	.	G	,	913,3493	345.7+/-308.6	82,749,1372	64.0	69.0	67.0		1173,1173	-11.2	0.2	19	dbSNP_86	67	3081,5519	465.6+/-366.6	539,2003,1758	no	coding-synonymous,coding-synonymous	GCDH	NM_000159.2,NM_013976.2	,	621,2752,3130	TT,TG,GG		35.8256,20.7217,30.7089	,	391/439,391/429	13008607	3994,9012	2203	4300	6503	SO:0001819	synonymous_variant	2639	exon11			GGGGGGGAATGGG	AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"""glutaryl-Coenzyme A dehydrogenase"""			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.1173G>T	19.37:g.13008607G>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	56	53	0.946429	NM_013976	A8K2Z2|O14719	Silent	SNP	ENST00000222214.5	37	CCDS12286.1																																																																																			G|0.732;T|0.268	0.268	strong		0.602	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1		
ATP13A4	84239	hgsc.bcm.edu	37	3	193180592	193180592	+	Silent	SNP	G	G	A	rs59451116	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193180592G>A	ENST00000342695.4	-	13	1804	c.1482C>T	c.(1480-1482)gaC>gaT	p.D494D	ATP13A4_ENST00000392443.3_Silent_p.D475D|ATP13A4_ENST00000295548.3_Silent_p.D494D	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	494						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)		GGTCCAAGCCGTCCCTTGTTA	0.488													A|||	1477	0.294928	0.2905	0.3141	5008	,	,		17830	0.3046		0.1918	False		,,,				2504	0.3834				p.D494D		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C1482T						PASS	.	A		1191,3215	710.1+/-407.8	142,907,1154	111.0	99.0	103.0		1482	2.0	1.0	3	dbSNP_129	103	1706,6894	737.6+/-407.0	169,1368,2763	no	coding-synonymous	ATP13A4	NM_032279.2		311,2275,3917	AA,AG,GG		19.8372,27.0313,22.2743		494/1197	193180592	2897,10109	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon13			CAAGCCGTCCCTT	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.1482C>T	3.37:g.193180592G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			G|0.762;A|0.238	0.238	strong		0.488	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
CPN1	1369	hgsc.bcm.edu	37	10	101802262	101802262	+	Silent	SNP	G	G	A	rs61733667	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101802262G>A	ENST00000370418.3	-	9	1550	c.1299C>T	c.(1297-1299)caC>caT	p.H433H		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	433					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		CTCTGACTCCGTGCCTTCTGC	0.542													G|||	113	0.0225639	0.0023	0.0663	5008	,	,		16811	0.0238		0.0338	False		,,,				2504	0.0061				p.H433H		Atlas-SNP	.											.	CPN1	62	.	0			c.C1299T						PASS	.			34,4372	39.2+/-71.8	0,34,2169	99.0	85.0	90.0		1299	-9.1	0.0	10	dbSNP_129	90	327,8273	114.2+/-174.2	5,317,3978	no	coding-synonymous	CPN1	NM_001308.2		5,351,6147	AA,AG,GG		3.8023,0.7717,2.7756		433/459	101802262	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	1369	exon9			GACTCCGTGCCTT	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1299C>T	10.37:g.101802262G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	37	CCDS7486.1																																																																																			G|0.971;A|0.029	0.029	strong		0.542	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
SPAG17	200162	hgsc.bcm.edu	37	1	118644430	118644430	+	Silent	SNP	A	A	G	rs10754367	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:118644430A>G	ENST00000336338.5	-	5	632	c.567T>C	c.(565-567)aaT>aaC	p.N189N		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	189	Lys-rich.					cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TCACTGGTGCATTTGCCTCAG	0.498													G|||	2824	0.563898	0.6906	0.5072	5008	,	,		18672	0.4534		0.5477	False		,,,				2504	0.5634				p.N189N		Atlas-SNP	.											.	SPAG17	263	.	0			c.T567C						PASS	.	G		3023,1383	456.9+/-351.5	1051,921,231	312.0	267.0	282.0		567	-0.1	0.0	1	dbSNP_120	282	4844,3756	534.2+/-382.6	1369,2106,825	yes	coding-synonymous	SPAG17	NM_206996.2		2420,3027,1056	GG,GA,AA		43.6744,31.389,39.5125		189/2224	118644430	7867,5139	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon5			TGGTGCATTTGCC		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.567T>C	1.37:g.118644430A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	145	60	0.413793	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			A|0.430;G|0.570	0.570	strong		0.498	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
CFHR3	10878	hgsc.bcm.edu	37	1	196757392	196757392	+	Silent	SNP	C	C	T	rs400344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196757392C>T	ENST00000367425.4	+	4	569	c.477C>T	c.(475-477)tcC>tcT	p.S159S	CFHR3_ENST00000471440.2_Silent_p.S159S|CFHR3_ENST00000391985.3_Intron	NM_021023.5	NP_066303.2	Q02985	FHR3_HUMAN	complement factor H-related 3	159	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						GATTCATTTCCGAATCTTCCT	0.254													-|||	3252	0.649361	0.646	0.6657	5008	,	,		9863	0.9484		0.501	False		,,,				2504	0.4867				p.S159S		Atlas-SNP	.											CFHR3,NS,carcinoma,0,1	CFHR3	52	1	0			c.C477T						PASS	.						9.0	15.0	13.0					1																	196757392		1478	3842	5320	SO:0001819	synonymous_variant	10878	exon4			CATTTCCGAATCT	X68679	CCDS30958.1, CCDS53453.1	1q32	2014-09-17		2006-02-28	ENSG00000116785	ENSG00000116785		"""Complement system"""	16980	protein-coding gene	gene with protein product	"""complement factor H related 3"""	605336		CFHL3		8428964, 10380701	Standard	NM_021023		Approved	FHR-3, HLF4, FHR3, DOWN16	uc001gtl.3	Q02985	OTTHUMG00000035929	ENST00000367425.4:c.477C>T	1.37:g.196757392C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_021023	B4DPR0|Q9UJ16	Silent	SNP	ENST00000367425.4	37	CCDS30958.1																																																																																			C|0.379;T|0.621	0.621	strong		0.254	CFHR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087505.2	NM_021023	
DMKN	93099	hgsc.bcm.edu	37	19	35998362	35998362	+	Intron	SNP	T	T	G	rs4254439	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35998362T>G	ENST00000339686.3	-	8	1215				DMKN_ENST00000392206.2_Intron|DMKN_ENST00000424570.2_Intron|DMKN_ENST00000492341.2_Intron|DMKN_ENST00000402589.2_Intron|DMKN_ENST00000474928.1_Intron|DMKN_ENST00000436012.1_Intron|DMKN_ENST00000480502.1_Intron|DMKN_ENST00000602781.1_Intron|DMKN_ENST00000461300.1_Intron|DMKN_ENST00000458071.1_Intron|DMKN_ENST00000467637.1_Intron|DMKN_ENST00000440396.1_Silent_p.R376R|DMKN_ENST00000451297.2_Intron|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000419602.1_Silent_p.R315R|DMKN_ENST00000414866.2_Intron|DMKN_ENST00000472252.2_Intron|DMKN_ENST00000488892.1_Intron|DMKN_ENST00000447113.2_Silent_p.R376R|DMKN_ENST00000443640.1_Silent_p.R89R|DMKN_ENST00000418261.1_Intron|DMKN_ENST00000462126.1_Intron	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine							extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGGCTCACCCTATAATTGTCT	0.507													G|||	1927	0.384784	0.4455	0.3184	5008	,	,		18711	0.4425		0.3022	False		,,,				2504	0.3753				p.R376R		Atlas-SNP	.											.	DMKN	116	.	0			c.A1126C						PASS	.						94.0	84.0	87.0					19																	35998362		692	1591	2283	SO:0001627	intron_variant	93099	exon9			TCACCCTATAATT	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.1039-1474A>C	19.37:g.35998362T>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_001190348	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1	837	0.38324175824175827	224	0.45528455284552843	108	0.2983425414364641	269	0.47027972027972026	236	0.3113456464379947	G	8.948	0.967522	0.18659	.	.	ENSG00000161249	ENST00000434389	.	.	.	3.66	3.66	0.41972	.	.	.	.	.	.	.	.	.	.	.	0.20074	P	0.9999308811	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.7274	0.34478	0.0:0.0:0.7736:0.2264	rs4254439;rs59459723	.	.	.	S	56	.	.	X	-	2	0	DMKN	40690202	0.932000	0.31603	0.543000	0.28128	0.000000	0.00434	1.913000	0.39956	1.133000	0.42147	-0.121000	0.15023	TAG	G|0.367;N|0.002	0.367	strong		0.507	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
SYT17	51760	hgsc.bcm.edu	37	16	19195130	19195130	+	Silent	SNP	C	C	T	rs11541511	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:19195130C>T	ENST00000355377.2	+	5	1010	c.612C>T	c.(610-612)cgC>cgT	p.R204R	SYT17_ENST00000562034.1_Silent_p.R143R|SYT17_ENST00000562711.2_Silent_p.R200R|SYT17_ENST00000568115.1_Silent_p.R143R	NM_016524.2	NP_057608.2	Q9BSW7	SYT17_HUMAN	synaptotagmin XVII	204	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)	membrane (GO:0016020)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	17						TCACCGTGCGCGTGATCGAGG	0.612													c|||	441	0.0880591	0.0613	0.0836	5008	,	,		19368	0.0169		0.162	False		,,,				2504	0.1247				p.R204R		Atlas-SNP	.											SYT17,colon,carcinoma,+1,1	SYT17	51	1	0			c.C612T						scavenged	.			372,4022	189.2+/-215.4	21,330,1846	127.0	111.0	116.0		612	-3.1	0.5	16	dbSNP_120	116	1373,7227	267.4+/-287.2	119,1135,3046	no	coding-synonymous	SYT17	NM_016524.2		140,1465,4892	TT,TC,CC		15.9651,8.4661,13.4293		204/475	19195130	1745,11249	2197	4300	6497	SO:0001819	synonymous_variant	51760	exon5			CGTGCGCGTGATC		CCDS10575.1	16p12.3	2013-01-21			ENSG00000103528	ENSG00000103528		"""Synaptotagmins"""	24119	protein-coding gene	gene with protein product	"""B/K protein"""					10493829	Standard	NM_016524		Approved		uc002dfw.3	Q9BSW7	OTTHUMG00000131461	ENST00000355377.2:c.612C>T	16.37:g.19195130C>T		Somatic	62	2	0.0322581		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_016524	O43330|Q9NZ18	Silent	SNP	ENST00000355377.2	37	CCDS10575.1																																																																																			C|0.887;T|0.113	0.113	strong		0.612	SYT17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254286.2	NM_016524	
TEX15	56154	hgsc.bcm.edu	37	8	30703431	30703431	+	Missense_Mutation	SNP	T	T	C	rs323346	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:30703431T>C	ENST00000256246.2	-	1	3177	c.3103A>G	c.(3103-3105)Ata>Gta	p.I1035V	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1035			I -> V (in dbSNP:rs323346). {ECO:0000269|PubMed:11279525}.		fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TTGCATATTATTGCATATGAT	0.318													T|||	1911	0.381589	0.7965	0.3703	5008	,	,		18250	0.1131		0.165	False		,,,				2504	0.3282				p.I1035V		Atlas-SNP	.											.	TEX15	350	.	0			c.A3103G						PASS	.	T	VAL/ILE	3058,1348	655.8+/-400.0	1053,952,198	77.0	83.0	81.0		3103	0.2	1.0	8	dbSNP_79	81	1470,7122	272.0+/-289.9	129,1212,2955	yes	missense	TEX15	NM_031271.3	29	1182,2164,3153	CC,CT,TT		17.1089,30.5946,34.8361	benign	1035/2790	30703431	4528,8470	2203	4296	6499	SO:0001583	missense	56154	exon1			ATATTATTGCATA	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3103A>G	8.37:g.30703431T>C	ENSP00000256246:p.Ile1035Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	70	0.514706	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	694	0.31776556776556775	389	0.790650406504065	127	0.35082872928176795	58	0.10139860139860139	120	0.158311345646438	T	8.240	0.806712	0.16467	0.694054	0.171089	ENSG00000133863	ENST00000256246	T	0.09445	2.98	5.71	0.22	0.15279	.	0.397123	0.24341	N	0.039372	T	0.00012	0.0000	L	0.27053	0.805	0.47547	P	5.429999999999602E-4	B	0.19583	0.037	B	0.18561	0.022	T	0.08534	-1.0717	9	0.87932	D	0	.	8.8903	0.35429	0.0:0.4309:0.0:0.5691	rs323346;rs3802157;rs57880876;rs323346	1035	Q9BXT5	TEX15_HUMAN	V	1035	ENSP00000256246:I1035V	ENSP00000256246:I1035V	I	-	1	0	TEX15	30822973	0.994000	0.37717	0.994000	0.49952	0.953000	0.61014	0.094000	0.15107	0.054000	0.16065	0.383000	0.25322	ATA	A|0.004;C|0.320	0.320	strong		0.318	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
NBPF10	100132406	hgsc.bcm.edu	37	1	145296478	145296478	+	Missense_Mutation	SNP	G	G	T	rs6663523	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145296478G>T	ENST00000342960.5	+	3	435	c.400G>T	c.(400-402)Gat>Tat	p.D134Y	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	134						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CCTCACTCCGGATGAGCCGGA	0.587																																					p.D134Y		Atlas-SNP	.											.	NBPF10	221	.	0			c.G400T						PASS	.																																			SO:0001583	missense	100132406	exon3			ACTCCGGATGAGC	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.400G>T	1.37:g.145296478G>T	ENSP00000345684:p.Asp134Tyr	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	51	29	0.568627	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	8.335	0.827301	0.16749	.	.	ENSG00000163386	ENST00000369339;ENST00000448873;ENST00000342960	T	0.03272	3.99	1.15	-2.3	0.06785	.	.	.	.	.	T	0.02342	0.0072	M	0.73962	2.25	0.09310	N	1	.	.	.	.	.	.	T	0.25502	-1.0130	7	0.72032	D	0.01	.	3.5681	0.07907	0.288:0.4976:0.2144:0.0	rs6663523	.	.	.	Y	134;59;134	ENSP00000345684:D134Y	ENSP00000345684:D134Y	D	+	1	0	NBPF10	144007835	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.738000	0.04871	-1.517000	0.01780	0.121000	0.15741	GAT	G|0.500;T|0.500	0.500	strong		0.587	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
ASGR2	433	hgsc.bcm.edu	37	17	7012079	7012079	+	Missense_Mutation	SNP	C	C	T	rs2304978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7012079C>T	ENST00000380952.2	-	3	517	c.253G>A	c.(253-255)Ggg>Agg	p.G85R	ASGR2_ENST00000355035.5_Missense_Mutation_p.G85R|ASGR2_ENST00000446679.2_Missense_Mutation_p.G66R|ASGR2_ENST00000254850.7_Intron	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	85			G -> R (in dbSNP:rs2304978). {ECO:0000269|PubMed:1371982, ECO:0000269|PubMed:3863106, ECO:0000269|Ref.4}.		bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)	p.G85R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	TGCTGGCCCCCGTGACCCTCA	0.637													T|||	1277	0.254992	0.0703	0.3689	5008	,	,		14768	0.2887		0.2724	False		,,,				2504	0.3712				p.G85R		Atlas-SNP	.											ASGR2,NS,carcinoma,0,2	ASGR2	38	2	1	Substitution - Missense(1)	stomach(1)	c.G253A						PASS	.	T	ARG/GLY,,ARG/GLY,,ARG/GLY	476,3930	778.9+/-414.3	30,416,1757	67.0	59.0	62.0		253,,253,,196	0.4	0.0	17	dbSNP_100	62	2435,6165	692.5+/-404.6	362,1711,2227	yes	missense,intron,missense,intron,missense	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	125,,125,,125	392,2127,3984	TT,TC,CC		28.314,10.8034,22.382	benign,,benign,,benign	85/312,,85/312,,66/293	7012079	2911,10095	2203	4300	6503	SO:0001583	missense	433	exon3			GGCCCCCGTGACC	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.253G>A	17.37:g.7012079C>T	ENSP00000370339:p.Gly85Arg	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	135	62	0.459259	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Missense_Mutation	SNP	ENST00000380952.2	37	CCDS32544.1	519	0.23763736263736263	30	0.06097560975609756	125	0.3453038674033149	155	0.270979020979021	209	0.2757255936675462	T	0.718	-0.784581	0.02907	0.108034	0.28314	ENSG00000161944	ENST00000355035;ENST00000380952;ENST00000446679	T;T;T	0.00776	5.71;5.71;5.74	1.92	0.39	0.16275	Hepatic lectin, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17258	-1.0375	8	0.15066	T	0.55	.	1.9813	0.03427	0.3715:0.1682:0.0:0.4603	rs2304978	85;66	P07307;P07307-2	ASGR2_HUMAN;.	R	85;85;66	ENSP00000347140:G85R;ENSP00000370339:G85R;ENSP00000405844:G66R	ENSP00000347140:G85R	G	-	1	0	ASGR2	6952803	0.000000	0.05858	0.001000	0.08648	0.543000	0.35085	-0.348000	0.07740	-0.404000	0.07610	-0.326000	0.08463	GGG	C|0.777;T|0.223	0.223	strong		0.637	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	
ENPP3	5169	hgsc.bcm.edu	37	6	132061420	132061420	+	Missense_Mutation	SNP	G	G	A	rs17601580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:132061420G>A	ENST00000414305.1	+	25	2685	c.2357G>A	c.(2356-2358)aGt>aAt	p.S786N	ENPP3_ENST00000358229.5_3'UTR|ENPP3_ENST00000357639.3_Missense_Mutation_p.S786N			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	786	Nuclease.		S -> N (in dbSNP:rs17601580).		immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		GTGCTGACCAGTTGTAAAAAC	0.443													G|||	447	0.0892572	0.0106	0.0879	5008	,	,		15569	0.0129		0.1998	False		,,,				2504	0.1616				p.S786N		Atlas-SNP	.											.	ENPP3	117	.	0			c.G2357A						PASS	.	G	ASN/SER	126,4280	92.0+/-130.7	1,124,2078	111.0	97.0	102.0		2357	5.4	0.3	6	dbSNP_123	102	1403,7197	270.4+/-288.9	106,1191,3003	yes	missense	ENPP3	NM_005021.3	46	107,1315,5081	AA,AG,GG		16.314,2.8597,11.7561	possibly-damaging	786/876	132061420	1529,11477	2203	4300	6503	SO:0001583	missense	5169	exon24			TGACCAGTTGTAA	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2357G>A	6.37:g.132061420G>A	ENSP00000406261:p.Ser786Asn	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	37	CCDS5148.1	213	0.09752747252747253	8	0.016260162601626018	40	0.11049723756906077	5	0.008741258741258742	160	0.21108179419525067	G	24.4	4.527897	0.85706	0.028597	0.16314	ENSG00000154269	ENST00000414305;ENST00000357639	T;T	0.70399	-0.48;-0.48	5.45	5.45	0.79879	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.061286	0.64402	D	0.000002	T	0.81264	0.4786	M	0.82823	2.61	0.09310	P	1.0	D	0.54207	0.965	P	0.57371	0.819	T	0.82874	-0.0241	9	0.62326	D	0.03	-22.9283	19.6632	0.95882	0.0:0.0:1.0:0.0	rs17601580;rs52796056;rs58865025;rs17601580	786	O14638	ENPP3_HUMAN	N	786	ENSP00000406261:S786N;ENSP00000350265:S786N	ENSP00000350265:S786N	S	+	2	0	ENPP3	132103113	1.000000	0.71417	0.332000	0.25469	0.987000	0.75469	8.015000	0.88690	2.716000	0.92895	0.655000	0.94253	AGT	G|0.897;A|0.103	0.103	strong		0.443	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		
SHROOM3	57619	hgsc.bcm.edu	37	4	77631425	77631425	+	Missense_Mutation	SNP	T	T	A	rs3821979	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:77631425T>A	ENST00000296043.6	+	3	1393	c.440T>A	c.(439-441)cTt>cAt	p.L147H	SHROOM3_ENST00000473602.1_3'UTR	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	147			L -> H (in dbSNP:rs3821979).		actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			GGGGTTAAACTTCGGCTGAAG	0.577													T|||	1097	0.21905	0.1611	0.2032	5008	,	,		18546	0.3363		0.1093	False		,,,				2504	0.3006				p.L147H		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T440A	GRCh37	CM063143	SHROOM3	M	rs3821979	PASS	.	T	HIS/LEU	760,3646	310.0+/-291.3	62,636,1505	85.0	73.0	77.0		440	3.8	1.0	4	dbSNP_107	77	1131,7469	233.3+/-266.6	83,965,3252	yes	missense	SHROOM3	NM_020859.3	99	145,1601,4757	AA,AT,TT		13.1512,17.2492,14.5394	probably-damaging	147/1997	77631425	1891,11115	2203	4300	6503	SO:0001583	missense	57619	exon3			TTAAACTTCGGCT	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.440T>A	4.37:g.77631425T>A	ENSP00000296043:p.Leu147His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	404	0.184981684981685	80	0.16260162601626016	70	0.19337016574585636	173	0.30244755244755245	81	0.10686015831134564	T	15.60	2.882384	0.51908	0.172492	0.131512	ENSG00000138771	ENST00000296043	T	0.34472	1.36	4.96	3.78	0.43462	.	0.000000	0.36101	N	0.002789	T	0.00012	0.0000	M	0.62723	1.935	0.31241	P	0.695171	D	0.71674	0.998	P	0.60789	0.879	T	0.15896	-1.0421	9	0.87932	D	0	-2.793	7.8964	0.29708	0.0:0.0961:0.0:0.9039	rs3821979;rs52831344;rs3821979	147	Q8TF72	SHRM3_HUMAN	H	147	ENSP00000296043:L147H	ENSP00000296043:L147H	L	+	2	0	SHROOM3	77850449	0.921000	0.31238	1.000000	0.80357	0.879000	0.50718	0.142000	0.16096	1.002000	0.39104	0.482000	0.46254	CTT	T|0.843;A|0.157	0.157	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
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 GAIIx	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_ENST00000392657.3_Silent_p.P903P|ARHGAP32_ENST00000527272.1_Silent_p.P903P|ARHGAP32_ENST00000524655.1_3'UTR	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		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	137	40	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 GAIIx	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	ABLIM3_ENST00000519549.1_3'UTR|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000508983.1_Missense_Mutation_p.S357F|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000309868.7_Missense_Mutation_p.S357F|ABLIM3_ENST00000504238.1_Intron|ABLIM3_ENST00000326685.7_Intron|RP11-331K21.1_ENST00000522685.1_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	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	179	85	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	
ZNF74	7625	hgsc.bcm.edu	37	22	20761063	20761063	+	Silent	SNP	G	G	A	rs2228236	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:20761063G>A	ENST00000400451.2	+	5	2254	c.1740G>A	c.(1738-1740)gaG>gaA	p.E580E	ZNF74_ENST00000403682.3_3'UTR|ZNF74_ENST00000405993.1_Silent_p.E548E|ZNF74_ENST00000357502.5_3'UTR|ZNF74_ENST00000356671.5_Silent_p.E580E	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	580					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			TGCACAGCGAGGGGAAGCCCT	0.572													G|||	547	0.109225	0.1899	0.1066	5008	,	,		20956	0.002		0.164	False		,,,				2504	0.0562				p.E580E		Atlas-SNP	.											.	ZNF74	54	.	0			c.G1740A						PASS	.	G		751,3543		63,625,1459	49.0	55.0	53.0		1740	-8.5	0.0	22	dbSNP_98	53	1315,7225		102,1111,3057	no	coding-synonymous	ZNF74	NM_003426.2		165,1736,4516	AA,AG,GG		15.3981,17.4895,16.0979		580/645	20761063	2066,10768	2147	4270	6417	SO:0001819	synonymous_variant	7625	exon5			CAGCGAGGGGAAG	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"""Zinc fingers, C2H2-type"", ""-"""	13144	protein-coding gene	gene with protein product		194548	"""zinc finger protein 74 (Cos52)"""			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.1740G>A	22.37:g.20761063G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Silent	SNP	ENST00000400451.2	37	CCDS42982.1																																																																																			G|0.859;A|0.141	0.141	strong		0.572	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426	
TSNARE1	203062	hgsc.bcm.edu	37	8	143436034	143436034	+	Missense_Mutation	SNP	A	A	G	rs7814359	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143436034A>G	ENST00000307180.3	-	2	169	c.52T>C	c.(52-54)Ttc>Ctc	p.F18L	TSNARE1_ENST00000524325.1_Missense_Mutation_p.F18L|TSNARE1_ENST00000520166.1_Missense_Mutation_p.F18L|TSNARE1_ENST00000519651.1_Missense_Mutation_p.F18L	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	18			F -> L (in dbSNP:rs7814359). {ECO:0000269|PubMed:14702039}.		intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GGTCCCCCGAAAGGGCCACGG	0.607													A|||	1782	0.355831	0.6278	0.2896	5008	,	,		14925	0.3472		0.1978	False		,,,				2504	0.2065				p.F18L		Atlas-SNP	.											.	TSNARE1	59	.	0			c.T52C						PASS	.	A	LEU/PHE	2416,1990	606.1+/-390.7	674,1068,461	50.0	45.0	47.0		52	2.3	0.0	8	dbSNP_116	47	1803,6797	321.2+/-315.0	183,1437,2680	yes	missense	TSNARE1	NM_145003.3	22	857,2505,3141	GG,GA,AA		20.9651,45.1657,32.4389	benign	18/514	143436034	4219,8787	2203	4300	6503	SO:0001583	missense	203062	exon2			CCCCGAAAGGGCC			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.52T>C	8.37:g.143436034A>G	ENSP00000303437:p.Phe18Leu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	723	0.33104395604395603	275	0.5589430894308943	96	0.26519337016574585	214	0.3741258741258741	138	0.1820580474934037	A	11.01	1.512251	0.27036	0.548343	0.209651	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651;ENST00000520462;ENST00000518720	T;T;T;T;T;T	0.37584	1.33;1.3;1.33;1.52;1.26;1.19	3.47	2.26	0.28386	.	0.000000	0.34025	U	0.004330	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B	0.30914	0.3;0.043;0.3;0.3	B;B;B;B	0.26202	0.067;0.016;0.067;0.067	T	0.44757	-0.9307	9	0.48119	T	0.1	-0.2963	7.1576	0.25647	0.7708:0.2292:0.0:0.0	rs7814359;rs61501797;rs7814359	18;18;18;18	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	L	18;18;18;18;18;34	ENSP00000428763:F18L;ENSP00000303437:F18L;ENSP00000427770:F18L;ENSP00000429679:F18L;ENSP00000429626:F18L;ENSP00000430789:F34L	ENSP00000303437:F18L	F	-	1	0	TSNARE1	143433941	0.197000	0.23362	0.001000	0.08648	0.491000	0.33493	2.089000	0.41672	0.461000	0.27071	-0.418000	0.06021	TTC	A|0.674;G|0.326	0.326	strong		0.607	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
SAGE1	55511	hgsc.bcm.edu	37	X	134986700	134986700	+	Silent	SNP	T	T	C	rs12014884	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:134986700T>C	ENST00000370709.3	+	3	285	c.285T>C	c.(283-285)aaT>aaC	p.N95N	SAGE1_ENST00000535938.1_Silent_p.N95N|SAGE1_ENST00000537770.1_Silent_p.N95N|SAGE1_ENST00000324447.3_Silent_p.N95N			Q9NXZ1	SAGE1_HUMAN	sarcoma antigen 1	95						nucleus (GO:0005634)				breast(5)|endometrium(5)|large_intestine(10)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	55	Acute lymphoblastic leukemia(192;0.000127)					TAGCTGATAATGTCTTGTCAA	0.423													N|||	610	0.161589	0.0673	0.1614	3775	,	,		15712	0.1002		0.2058	False		,,,				2504	0.1033				p.N95N		Atlas-SNP	.											.	SAGE1	160	.	0			c.T285C						PASS	.	C		557,3278		30,426,71,1176,500	167.0	132.0	144.0		285	1.4	0.0	X	dbSNP_120	144	1755,4973		188,924,455,1316,1417	no	coding-synonymous	SAGE1	NM_018666.2		218,1350,526,2492,1917	CC,CT,C,TT,T		26.085,14.5241,21.8877		95/905	134986700	2312,8251	2203	4300	6503	SO:0001819	synonymous_variant	55511	exon4			TGATAATGTCTTG	AJ278111	CCDS14652.1	Xq26	2009-03-25			ENSG00000181433	ENSG00000181433			30369	protein-coding gene	gene with protein product	"""cancer/testis antigen 14"""	300359				10919659	Standard	NM_018666		Approved	SAGE, CT14	uc004ezh.3	Q9NXZ1	OTTHUMG00000022496	ENST00000370709.3:c.285T>C	X.37:g.134986700T>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	257	54	0.210117	NM_018666	Q5JNW0	Silent	SNP	ENST00000370709.3	37	CCDS14652.1																																																																																			T|0.806;C|0.194	0.194	strong		0.423	SAGE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058448.1	NM_018666	
METTL22	79091	hgsc.bcm.edu	37	16	8722629	8722629	+	Missense_Mutation	SNP	G	G	C	rs2270286	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:8722629G>C	ENST00000381920.3	+	3	434	c.176G>C	c.(175-177)tGg>tCg	p.W59S	METTL22_ENST00000561758.1_Missense_Mutation_p.W59S	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	59			W -> S (in dbSNP:rs2270286).			nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						CAAGACTCTTGGACAGATTCA	0.488													G|||	880	0.175719	0.0076	0.2061	5008	,	,		20032	0.3105		0.1889	False		,,,				2504	0.229				p.W59S		Atlas-SNP	.											.	METTL22	23	.	0			c.G176C						PASS	.	G	SER/TRP	160,3688		2,156,1766	57.0	59.0	58.0		176	-2.2	0.0	16	dbSNP_100	58	1560,6748		154,1252,2748	yes	missense	METTL22	NM_024109.2	177	156,1408,4514	CC,CG,GG		18.7771,4.158,14.1494	benign	59/405	8722629	1720,10436	1924	4154	6078	SO:0001583	missense	79091	exon3			ACTCTTGGACAGA	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"""chromosome 16 open reading frame 68"""	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.176G>C	16.37:g.8722629G>C	ENSP00000371345:p.Trp59Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	89	47	0.52809	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	37	CCDS10533.2	405	0.18543956043956045	8	0.016260162601626018	69	0.19060773480662985	176	0.3076923076923077	152	0.20052770448548812	G	6.561	0.471814	0.12461	0.04158	0.187771	ENSG00000067365	ENST00000381920;ENST00000163678	T;T	0.41758	2.37;0.99	5.0	-2.18	0.07037	.	1.766790	0.03076	N	0.157894	T	0.00012	0.0000	L	0.40543	1.245	0.33131	P	0.45687999999999995	B	0.14438	0.01	B	0.09377	0.004	T	0.23297	-1.0192	9	0.11485	T	0.65	-12.35	5.5293	0.16974	0.5345:0.0:0.3172:0.1483	rs2270286;rs17746596;rs52824520;rs2270286	59	Q9BUU2	MET22_HUMAN	S	59	ENSP00000371345:W59S;ENSP00000163678:W59S	ENSP00000163678:W59S	W	+	2	0	METTL22	8630130	0.000000	0.05858	0.009000	0.14445	0.639000	0.38242	-0.392000	0.07314	-0.770000	0.04614	0.561000	0.74099	TGG	G|0.810;C|0.190	0.190	strong		0.488	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109	
MOV10	4343	hgsc.bcm.edu	37	1	113237171	113237171	+	Silent	SNP	A	A	G	rs883593	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:113237171A>G	ENST00000413052.2	+	9	1782	c.1392A>G	c.(1390-1392)acA>acG	p.T464T	MOV10_ENST00000369645.1_Silent_p.T464T|RP11-426L16.3_ENST00000421943.1_RNA|MOV10_ENST00000357443.2_Silent_p.T464T|MOV10_ENST00000369644.1_Silent_p.T408T|MOV10_ENST00000468624.1_3'UTR	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	464					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		TGGAGCTGACAGGGCGCTGGC	0.617													G|||	1426	0.284744	0.1672	0.2911	5008	,	,		17708	0.5427		0.2346	False		,,,				2504	0.2249				p.T464T		Atlas-SNP	.											MOV10,NS,carcinoma,0,1	MOV10	74	1	0			c.A1392G						PASS	.	G	,	803,3603	743.3+/-411.4	83,637,1483	39.0	38.0	38.0		1392,1392	-10.2	0.3	1	dbSNP_86	38	1763,6837	726.8+/-406.6	180,1403,2717	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	263,2040,4200	GG,GA,AA		20.5,18.2251,19.7294	,	464/1004,464/1004	113237171	2566,10440	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon9			GCTGACAGGGCGC	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.1392A>G	1.37:g.113237171A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	54	0.613636	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			A|0.765;G|0.235	0.235	strong		0.617	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
ZNF577	84765	hgsc.bcm.edu	37	19	52376952	52376952	+	Silent	SNP	T	T	A	rs8107969	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52376952T>A	ENST00000301399.5	-	7	656	c.291A>T	c.(289-291)gtA>gtT	p.V97V	ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000451628.2_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000485702.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	97					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)		TACTCTGGATTACAAAACCTA	0.353													A|||	2536	0.50639	0.68	0.4553	5008	,	,		20806	0.3026		0.3897	False		,,,				2504	0.638				p.V97V		Atlas-SNP	.											.	ZNF577	63	.	0			c.A291T						PASS	.	A	,	2797,1609		908,981,314	39.0	36.0	37.0		,291	0.5	0.0	19	dbSNP_116	37	3324,5274		639,2046,1614	no	intron,coding-synonymous	ZNF577	NM_001135590.1,NM_032679.2	,	1547,3027,1928	AA,AT,TT		38.6602,36.5184,47.0701	,	,97/486	52376952	6121,6883	2203	4299	6502	SO:0001819	synonymous_variant	84765	exon7			CTGGATTACAAAA	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.291A>T	19.37:g.52376952T>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			T|0.527;A|0.473	0.473	strong		0.353	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
KIF27	55582	hgsc.bcm.edu	37	9	86465131	86465131	+	Missense_Mutation	SNP	T	T	C	rs58077086	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:86465131T>C	ENST00000297814.2	-	16	3582	c.3439A>G	c.(3439-3441)Atg>Gtg	p.M1147V	RP11-575L7.4_ENST00000590813.1_RNA|KIF27_ENST00000413982.1_Missense_Mutation_p.M1081V|RP11-575L7.4_ENST00000590368.1_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.M1050V|RP11-575L7.4_ENST00000608866.1_RNA|RP11-575L7.4_ENST00000591217.1_RNA|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000586206.1_RNA	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	1147					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						TCACGAACCATATTATCCCGT	0.393													T|||	659	0.131589	0.034	0.1729	5008	,	,		19611	0.1052		0.2356	False		,,,				2504	0.1544				p.M1147V		Atlas-SNP	.											.	KIF27	103	.	0			c.A3439G						PASS	.	T	VAL/MET	248,4158	142.7+/-177.9	10,228,1965	98.0	91.0	93.0		3439	-0.8	0.3	9	dbSNP_129	93	2071,6525	357.4+/-330.7	266,1539,2493	no	missense	KIF27	NM_017576.1	21	276,1767,4458	CC,CT,TT		24.0926,5.6287,17.8357	benign	1147/1402	86465131	2319,10683	2203	4298	6501	SO:0001583	missense	55582	exon16			GAACCATATTATC	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.3439A>G	9.37:g.86465131T>C	ENSP00000297814:p.Met1147Val	Somatic	429	0	0		WXS	Illumina HiSeq	Phase_I	441	194	0.439909	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	337	0.1543040293040293	23	0.046747967479674794	60	0.16574585635359115	76	0.13286713286713286	178	0.23482849604221637	T	10.42	1.344925	0.24426	0.056287	0.240926	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.68624	-0.33;-0.34;-0.23	4.58	-0.817	0.10836	.	0.340347	0.27245	N	0.020250	T	0.00039	0.0001	L	0.42245	1.32	0.58432	P	5.999999999950489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.06427	-1.0827	9	0.41790	T	0.15	.	8.8801	0.35370	0.0:0.3374:0.0:0.6626	rs58077086;rs62561946	1050;1081;1147	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	V	1147;1081;1050	ENSP00000297814:M1147V;ENSP00000401688:M1081V;ENSP00000333928:M1050V	ENSP00000297814:M1147V	M	-	1	0	KIF27	85654951	0.027000	0.19231	0.307000	0.25127	0.982000	0.71751	-0.115000	0.10741	-0.311000	0.08754	0.358000	0.22013	ATG	.	.	weak		0.393	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
DAGLA	747	hgsc.bcm.edu	37	11	61505168	61505168	+	Silent	SNP	G	G	A	rs198444	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:61505168G>A	ENST00000257215.5	+	15	1640	c.1524G>A	c.(1522-1524)gcG>gcA	p.A508A		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	508					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)		GTGAGGATGCGATGGAGTATT	0.622													G|||	2461	0.491414	0.3631	0.4986	5008	,	,		15387	0.7986		0.4284	False		,,,				2504	0.408				p.A508A		Atlas-SNP	.											DAGLA,NS,carcinoma,+1,1	DAGLA	109	1	0			c.G1524A						PASS	.	G		1586,2818	492.9+/-362.5	275,1036,891	160.0	131.0	141.0		1524	-3.4	1.0	11	dbSNP_79	141	3767,4831	535.2+/-382.8	819,2129,1351	no	coding-synonymous	DAGLA	NM_006133.2		1094,3165,2242	AA,AG,GG		43.8125,36.0127,41.1706		508/1043	61505168	5353,7649	2202	4299	6501	SO:0001819	synonymous_variant	747	exon15			GGATGCGATGGAG	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.1524G>A	11.37:g.61505168G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.536;A|0.464	0.464	strong		0.622	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
TAS2R30	259293	hgsc.bcm.edu	37	12	11286214	11286214	+	Missense_Mutation	SNP	C	C	G	rs200082783	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11286214C>G	ENST00000539585.1	-	1	1029	c.630G>C	c.(628-630)caG>caC	p.Q210H	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	210					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						TGCCATGGAGCTGCATCTTCT	0.428																																					p.Q210H		Atlas-SNP	.											TAS2R30,NS,carcinoma,0,1	TAS2R30	28	1	0			c.G630C						scavenged	.						214.0	229.0	224.0					12																	11286214		2203	4300	6503	SO:0001583	missense	259293	exon1			ATGGAGCTGCATC	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19112	protein-coding gene	gene with protein product		613963	"""taste receptor, type 2, member 47"""	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.630G>C	12.37:g.11286214C>G	ENSP00000444736:p.Gln210His	Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	140	11	0.0785714	NM_001097643	Q645X7	Missense_Mutation	SNP	ENST00000539585.1	37	CCDS53750.1	.	.	.	.	.	.	.	.	.	.	-	5.367	0.253041	0.10185	.	.	ENSG00000256188	ENST00000539585	T	0.00966	5.49	2.6	-0.678	0.11353	.	.	.	.	.	T	0.02012	0.0063	M	0.84846	2.72	0.09310	N	1	B	0.20887	0.049	B	0.33254	0.16	T	0.41305	-0.9516	9	0.66056	D	0.02	.	2.6486	0.04992	0.2226:0.4927:0.0:0.2847	.	210	P59541	T2R30_HUMAN	H	210	ENSP00000444736:Q210H	ENSP00000444736:Q210H	Q	-	3	2	TAS2R30	11177481	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	-1.414000	0.02471	-0.324000	0.08589	-0.823000	0.03104	CAG	C|0.944;G|0.055	0.055	strong		0.428	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643	
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 GAIIx	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_ENST00000553030.1_Missense_Mutation_p.T277I|BEST2_ENST00000042931.1_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	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	147	21	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	
OR10H5	284433	hgsc.bcm.edu	37	19	15905002	15905002	+	Silent	SNP	T	T	C	rs4808379	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15905002T>C	ENST00000308940.8	+	1	242	c.144T>C	c.(142-144)acT>acC	p.T48T		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	48						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						TCATGGCCACTGTCTGGAGCG	0.597													.|||	2431	0.485423	0.4433	0.4841	5008	,	,		19819	0.7907		0.3052	False		,,,				2504	0.4141				p.T48T		Atlas-SNP	.											.	OR10H5	49	.	0			c.T144C						PASS	.	C		1909,2497		406,1097,700	205.0	166.0	179.0		144	-6.8	0.0	19	dbSNP_111	179	2918,5682		510,1898,1892	no	coding-synonymous	OR10H5	NM_001004466.1		916,2995,2592	CC,CT,TT		33.9302,43.3273,37.1136		48/316	15905002	4827,8179	2203	4300	6503	SO:0001819	synonymous_variant	284433	exon1			GGCCACTGTCTGG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.144T>C	19.37:g.15905002T>C		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	156	70	0.448718	NM_001004466	Q6IFJ0|Q96R60	Silent	SNP	ENST00000308940.8	37	CCDS32940.1																																																																																			.	.	weak		0.597	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
ARHGAP32	9743	hgsc.bcm.edu	37	11	128842873	128842873	+	Silent	SNP	T	T	C	rs581258	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:128842873T>C	ENST00000310343.9	-	21	3485	c.3486A>G	c.(3484-3486)gaA>gaG	p.E1162E	ARHGAP32_ENST00000392657.3_Silent_p.E813E|ARHGAP32_ENST00000527272.1_Silent_p.E813E|ARHGAP32_ENST00000524655.1_3'UTR	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1162					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						TTCTGGCCTTTTCTGGGTCCC	0.448													T|||	999	0.199481	0.2625	0.2219	5008	,	,		20466	0.1746		0.1332	False		,,,				2504	0.1922				p.E1162E		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.A3486G						PASS	.	T	,	1165,3237	411.5+/-335.8	156,853,1192	165.0	158.0	160.0		3486,2439	-2.8	0.9	11	dbSNP_83	160	1266,7328	253.3+/-279.0	110,1046,3141	no	coding-synonymous,coding-synonymous	ARHGAP32	NM_001142685.1,NM_014715.3	,	266,1899,4333	CC,CT,TT		14.7312,26.4652,18.7058	,	1162/2088,813/1739	128842873	2431,10565	2201	4297	6498	SO:0001819	synonymous_variant	9743	exon21			GGCCTTTTCTGGG	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.3486A>G	11.37:g.128842873T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	133	114	0.857143	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			T|0.809;G|0.002	.	strong		0.448	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
CNPPD1	27013	hgsc.bcm.edu	37	2	220037756	220037756	+	Missense_Mutation	SNP	A	A	G	rs1043160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:220037756A>G	ENST00000409789.1	-	9	1212	c.785T>C	c.(784-786)aTc>aCc	p.I262T	SLC23A3_ENST00000396775.3_5'Flank|CNPPD1_ENST00000360507.5_Missense_Mutation_p.I262T|SLC23A3_ENST00000295738.7_5'Flank			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	262			I -> T (in dbSNP:rs1043160). {ECO:0000269|PubMed:10810093, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)	integral component of membrane (GO:0016021)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)	12						AGGTGTAGGGATGCAGGACAG	0.592													G|||	2055	0.410343	0.2655	0.4063	5008	,	,		16187	0.2302		0.6223	False		,,,				2504	0.5767				p.I262T		Atlas-SNP	.											.	CNPPD1	22	.	0			c.T785C						PASS	.	G	THR/ILE	1370,3036	678.4+/-403.5	223,924,1056	90.0	72.0	78.0		785	2.2	0.9	2	dbSNP_86	78	5239,3359	481.4+/-370.6	1589,2061,649	yes	missense	CNPPD1	NM_015680.4	89	1812,2985,1705	GG,GA,AA		39.0672,31.094,49.1772	benign	262/411	220037756	6609,6395	2203	4299	6502	SO:0001583	missense	27013	exon8			GTAGGGATGCAGG	AF070638	CCDS2433.1	2q36	2011-03-23	2011-03-23	2011-03-23	ENSG00000115649	ENSG00000115649			25220	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 24"""	C2orf24		8619474, 9110174	Standard	NM_015680		Approved	CGI-57	uc002vju.4	Q9BV87	OTTHUMG00000133132	ENST00000409789.1:c.785T>C	2.37:g.220037756A>G	ENSP00000386277:p.Ile262Thr	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_015680	B2RC77|O75548|Q9H4N0|Q9UQN0	Missense_Mutation	SNP	ENST00000409789.1	37	CCDS2433.1	942	0.43131868131868134	146	0.2967479674796748	164	0.4530386740331492	146	0.25524475524475526	486	0.6411609498680739	G	0.011	-1.736839	0.00681	0.31094	0.609328	ENSG00000115649	ENST00000360507;ENST00000409789;ENST00000453038	T;T;T	0.30981	2.47;2.47;1.51	5.18	2.24	0.28232	.	0.538553	0.22230	N	0.062831	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35871	-0.9771	9	0.18710	T	0.47	-1.3659	11.9911	0.53176	0.1128:0.5008:0.3864:0.0	rs1043160;rs3182633;rs17844905;rs17857626;rs17858205;rs52831722;rs58409827;rs1043160	262	Q9BV87	CNPD1_HUMAN	T	262	ENSP00000353698:I262T;ENSP00000386277:I262T;ENSP00000410109:I262T	ENSP00000353698:I262T	I	-	2	0	CNPPD1	219746000	0.984000	0.35163	0.936000	0.37596	0.359000	0.29487	0.652000	0.24888	0.345000	0.23873	-0.821000	0.03111	ATC	A|0.545;G|0.455	0.455	strong		0.592	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680	
ZNF256	10172	hgsc.bcm.edu	37	19	58453342	58453342	+	Silent	SNP	T	T	C	rs959231	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58453342T>C	ENST00000282308.3	-	3	1030	c.834A>G	c.(832-834)caA>caG	p.Q278Q	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	278					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		GGCTAGAGCTTTGCCTATAGG	0.393													T|||	1336	0.266773	0.1596	0.3112	5008	,	,		24363	0.3145		0.3002	False		,,,				2504	0.2965				p.Q278Q	NSCLC(55;1313 1552 8040 11996)	Atlas-SNP	.											.	ZNF256	117	.	0			c.A834G						PASS	.	T		767,3639		72,623,1508	114.0	108.0	110.0		834	0.9	0.0	19	dbSNP_86	110	2549,6051		369,1811,2120	no	coding-synonymous	ZNF256	NM_005773.2		441,2434,3628	CC,CT,TT		29.6395,17.4081,25.4959		278/628	58453342	3316,9690	2203	4300	6503	SO:0001819	synonymous_variant	10172	exon3			AGAGCTTTGCCTA	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"""Zinc fingers, C2H2-type"", ""-"""	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.834A>G	19.37:g.58453342T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_005773	B2RA92|Q53Y85|Q9BV71	Silent	SNP	ENST00000282308.3	37	CCDS12966.1																																																																																			T|0.741;C|0.259	0.259	strong		0.393	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1		
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 GAIIx	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_ENST00000441551.2_Missense_Mutation_p.L577R|LOXHD1_ENST00000536736.1_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	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	154	74	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	
CSMD2	114784	hgsc.bcm.edu	37	1	34038214	34038214	+	Missense_Mutation	SNP	T	T	C	rs2641962	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:34038214T>C	ENST00000373381.4	-	50	7830	c.7654A>G	c.(7654-7656)Atg>Gtg	p.M2552V		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2554	Sushi 15. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CAGCTGTACATGGCCTTGGTT	0.552													C|||	2554	0.509984	0.5424	0.6542	5008	,	,		17034	0.4087		0.494	False		,,,				2504	0.4847				p.M2554V		Atlas-SNP	.											.	CSMD2	946	.	0			c.A7660G						PASS	.	C	VAL/MET	2281,2125	578.8+/-384.8	606,1069,528	144.0	122.0	130.0		7660	1.7	0.8	1	dbSNP_100	130	4026,4574	596.6+/-393.6	938,2150,1212	yes	missense	CSMD2	NM_052896.3	21	1544,3219,1740	CC,CT,TT		46.814,48.2297,48.493	benign	2554/3488	34038214	6307,6699	2203	4300	6503	SO:0001583	missense	114784	exon51			TGTACATGGCCTT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.7654A>G	1.37:g.34038214T>C	ENSP00000362479:p.Met2552Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373381.4	37		1094	0.5009157509157509	281	0.5711382113821138	218	0.6022099447513812	229	0.40034965034965037	366	0.48284960422163586	C	0.024	-1.389467	0.01185	0.517703	0.46814	ENSG00000121904	ENST00000373381	T	0.62788	-0.0	5.65	1.67	0.24075	Complement control module (2);Sushi/SCR/CCP (3);	0.437433	0.24698	N	0.036329	T	0.00012	0.0000	N	0.00149	-1.99	0.26660	P	0.9719208	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44345	-0.9334	9	0.10636	T	0.68	.	6.1601	0.20360	0.1202:0.5973:0.0:0.2824	rs2641962;rs52795195;rs58510459;rs2641962	2554;2552	Q7Z408;E7EUA6	CSMD2_HUMAN;.	V	2552	ENSP00000362479:M2552V	ENSP00000241312:M2554V	M	-	1	0	CSMD2	33810801	0.095000	0.21747	0.819000	0.32651	0.299000	0.27559	0.282000	0.18829	-0.127000	0.11661	-1.886000	0.00541	ATG	C|0.495;N|0.000	0.495	strong		0.552	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319399	21319399	+	Missense_Mutation	SNP	A	A	G	rs4985866	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:21319399A>G	ENST00000583088.1	+	3	1640	c.745A>G	c.(745-747)Atc>Gtc	p.I249V	KCNJ12_ENST00000331718.5_Missense_Mutation_p.I249V	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	249			I -> V (in dbSNP:rs4985866).		muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GCTGGACCAGATCGACATCGA	0.622										Prostate(3;0.18)																											p.I249V		Atlas-SNP	.											KCNJ12,NS,neuroblastoma,0,1	.	.	1	0			c.A745G						scavenged	.	A	VAL/ILE	964,3442		0,964,1239	127.0	92.0	104.0		745	4.3	1.0	17	dbSNP_111	104	2315,6285		0,2315,1985	yes	missense	KCNJ12	NM_021012.4	29	0,3279,3224	GG,GA,AA		26.9186,21.8793,25.2114	benign	249/434	21319399	3279,9727	2203	4300	6503	SO:0001583	missense	100134444	exon3			GACCAGATCGACA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.745A>G	17.37:g.21319399A>G	ENSP00000463778:p.Ile249Val	Somatic	154	2	0.012987		WXS	Illumina HiSeq	Phase_I	156	46	0.294872	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	816	0.37362637362637363	160	0.3252032520325203	129	0.356353591160221	276	0.4825174825174825	251	0.3311345646437995	A	6.561	0.471839	0.12461	0.218793	0.269186	ENSG00000184185	ENST00000331718	D	0.91180	-2.8	5.43	4.33	0.51752	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.052254	0.85682	D	0.000000	T	0.00012	0.0000	N	0.05124	-0.11	0.23735	P	0.99698559	B	0.06786	0.001	B	0.04013	0.001	T	0.24548	-1.0157	9	0.14656	T	0.56	.	12.5199	0.56054	0.8604:0.1396:0.0:0.0	rs4985866;rs4985866	249	Q14500	IRK12_HUMAN	V	249	ENSP00000328150:I249V	ENSP00000328150:I249V	I	+	1	0	KCNJ12	21259992	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	5.809000	0.69172	0.873000	0.35799	0.533000	0.62120	ATC	A|0.625;G|0.375	0.375	strong		0.622	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
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 GAIIx	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	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	107	53	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	
COLGALT2	23127	hgsc.bcm.edu	37	1	183909717	183909717	+	Silent	SNP	G	G	A	rs2296713	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:183909717G>A	ENST00000361927.4	-	11	1973	c.1602C>T	c.(1600-1602)ccC>ccT	p.P534P	COLGALT2_ENST00000486375.1_5'UTR|COLGALT2_ENST00000546159.1_Silent_p.P534P|COLGALT2_ENST00000367521.1_Silent_p.P142P|COLGALT2_ENST00000367520.3_Silent_p.P271P	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	534					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										AGACTCACACGGGATGCTTGT	0.478													A|||	863	0.172324	0.0726	0.245	5008	,	,		22211	0.1776		0.1978	False		,,,				2504	0.2239				p.P534P		Atlas-SNP	.											.	.	.	.	0			c.C1602T						PASS	.	A		416,3990	788.5+/-414.9	28,360,1815	174.0	152.0	159.0		1602	-2.7	1.0	1	dbSNP_100	159	1634,6966	741.6+/-407.2	140,1354,2806	no	coding-synonymous	GLT25D2	NM_015101.2		168,1714,4621	AA,AG,GG		19.0,9.4417,15.762		534/627	183909717	2050,10956	2203	4300	6503	SO:0001819	synonymous_variant	23127	exon11			TCACACGGGATGC	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 17"", ""glycosyltransferase 25 domain containing 2"""	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.1602C>T	1.37:g.183909717G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_015101	O60327|Q9BZR0	Silent	SNP	ENST00000361927.4	37	CCDS1360.1																																																																																			G|0.828;A|0.172	0.172	strong		0.478	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101	
OBSCN	84033	hgsc.bcm.edu	37	1	228434467	228434467	+	Silent	SNP	T	T	C	rs7517108	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228434467T>C	ENST00000422127.1	+	13	4040	c.3996T>C	c.(3994-3996)gcT>gcC	p.A1332A	OBSCN_ENST00000570156.2_Silent_p.A1424A|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.A1332A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1332	Ig-like 13.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CCTGTGAGGCTGGGGGCCAGC	0.592													t|||	3318	0.66254	0.848	0.6902	5008	,	,		19733	0.6151		0.6421	False		,,,				2504	0.4622				p.A1424A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T4272C						PASS	.	T	,	3317,691		1369,579,56	71.0	79.0	77.0		3996,3996	-7.1	0.8	1	dbSNP_116	77	5702,2654		1978,1746,454	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	3347,2325,510	CC,CT,TT		31.7616,17.2405,27.0544	,	1332/7969,1332/6621	228434467	9019,3345	2004	4178	6182	SO:0001819	synonymous_variant	84033	exon14			TGAGGCTGGGGGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.3996T>C	1.37:g.228434467T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	114	42	0.368421	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			T|0.327;C|0.673	0.673	strong		0.592	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
TAS2R20	259295	hgsc.bcm.edu	37	12	11149769	11149769	+	Missense_Mutation	SNP	T	T	C	rs10845281	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11149769T>C	ENST00000538986.1	-	1	705	c.706A>G	c.(706-708)Ata>Gta	p.I236V	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	236			I -> V (in dbSNP:rs10845281). {ECO:0000269|PubMed:15496549}.		sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						GCAAGTAATATGAGGAAGGAG	0.393													T|||	2118	0.422923	0.0651	0.3847	5008	,	,		20724	0.755		0.3817	False		,,,				2504	0.6339				p.I236V		Atlas-SNP	.											.	TAS2R20	17	.	0			c.A706G						PASS	.	T	VAL/ILE	442,3964	212.2+/-232.1	18,406,1779	154.0	152.0	152.0		706	-1.6	0.0	12	dbSNP_120	152	3016,5584	465.5+/-366.5	544,1928,1828	yes	missense	TAS2R20	NM_176889.2	29	562,2334,3607	CC,CT,TT		35.0698,10.0318,26.5877	benign	236/310	11149769	3458,9548	2203	4300	6503	SO:0001583	missense	259295	exon1			GTAATATGAGGAA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.706A>G	12.37:g.11149769T>C	ENSP00000441624:p.Ile236Val	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	898	0.41117216117216115	33	0.06707317073170732	155	0.4281767955801105	426	0.7447552447552448	284	0.37467018469656993	T	4.775	0.144169	0.09134	0.100318	0.350698	ENSG00000255837	ENST00000538986	T	0.00864	5.6	2.66	-1.57	0.08506	.	1.555360	0.04751	U	0.424564	T	0.00012	0.0000	L	0.31476	0.935	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.08166	-1.0735	9	0.62326	D	0.03	.	0.4216	0.00457	0.3201:0.1817:0.1247:0.3734	rs10845281;rs52830191;rs10845281	236	P59543	T2R20_HUMAN	V	236	ENSP00000441624:I236V	ENSP00000441624:I236V	I	-	1	0	TAS2R20	11041036	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.139000	0.16036	-0.493000	0.06678	-2.198000	0.00308	ATA	T|0.675;C|0.325	0.325	strong		0.393	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
PPT1	5538	hgsc.bcm.edu	37	1	40535913	40535913	+	IGR	SNP	C	C	T	rs550460068		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:40535913C>T	ENST00000433473.3	-	0	2740				CAP1_ENST00000372797.3_Missense_Mutation_p.T359M|CAP1_ENST00000372792.2_Missense_Mutation_p.T359M|CAP1_ENST00000372805.3_Missense_Mutation_p.T359M|CAP1_ENST00000372802.1_Missense_Mutation_p.T358M|CAP1_ENST00000372798.1_Missense_Mutation_p.T358M|CAP1_ENST00000479759.1_3'UTR|CAP1_ENST00000340450.3_Missense_Mutation_p.T358M	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1						adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TGTGTCAACACGACATTGCAA	0.473																																					p.T359M		Atlas-SNP	.											CAP1,NS,carcinoma,-1,1	CAP1	38	1	0			c.C1076T						scavenged	.						86.0	82.0	83.0					1																	40535913		2028	4175	6203	SO:0001628	intergenic_variant	10487	exon10			TCAACACGACATT	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 1, infantile"""	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495		1.37:g.40535913C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	127	2	0.015748	NM_006367	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	37	CCDS447.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072401	0.76415	.	.	ENSG00000131236	ENST00000372797;ENST00000372802;ENST00000372792;ENST00000538246;ENST00000372798;ENST00000340450;ENST00000372805	T;T;T;T;T;T	0.09350	2.99;2.99;2.99;2.99;2.99;2.99	5.34	4.37	0.52481	CARP motif (1);Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal (1);Adenylate cyclase-associated CAP, C-terminal (2);C-CAP/cofactor C-like domain (1);	0.121407	0.85682	D	0.000000	T	0.29749	0.0743	M	0.70275	2.135	0.45962	D	0.998789	D;D	0.76494	0.999;0.999	D;D	0.71656	0.974;0.962	T	0.01545	-1.1328	10	0.87932	D	0	-8.4741	12.5502	0.56222	0.0:0.6705:0.3295:0.0	.	306;359	E7ENY9;Q01518	.;CAP1_HUMAN	M	359;358;359;336;358;358;359	ENSP00000361883:T359M;ENSP00000361888:T358M;ENSP00000361878:T359M;ENSP00000361884:T358M;ENSP00000344832:T358M;ENSP00000361891:T359M	ENSP00000344832:T358M	T	+	2	0	CAP1	40308500	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.639000	0.67868	2.466000	0.83321	0.650000	0.86243	ACG	.	.	none		0.473	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310	
WNK2	65268	hgsc.bcm.edu	37	9	95993326	95993326	+	Silent	SNP	T	T	C	rs11787888	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:95993326T>C	ENST00000297954.4	+	3	1011	c.1011T>C	c.(1009-1011)tcT>tcC	p.S337S	WNK2_ENST00000349097.3_5'UTR|WNK2_ENST00000395475.2_Silent_p.S323S|WNK2_ENST00000427277.2_5'UTR|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395477.2_Silent_p.S337S	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	337	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						CAACTGGGTCTGTGAAGATTG	0.537													T|||	744	0.148562	0.0983	0.111	5008	,	,		20051	0.0843		0.1541	False		,,,				2504	0.3037				p.S337S		Atlas-SNP	.											WNK2_ENST00000297954,NS,carcinoma,+1,2	WNK2	277	2	0			c.T1011C						PASS	.	T		467,3939	221.0+/-238.3	15,437,1751	184.0	183.0	184.0		1011	-6.7	0.5	9	dbSNP_120	184	1181,7419	242.1+/-272.2	87,1007,3206	no	coding-synonymous	WNK2	NM_006648.3		102,1444,4957	CC,CT,TT		13.7326,10.5992,12.6711		337/2218	95993326	1648,11358	2203	4300	6503	SO:0001819	synonymous_variant	65268	exon3			TGGGTCTGTGAAG	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.1011T>C	9.37:g.95993326T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	162	70	0.432099	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		247	0.1130952380952381	49	0.09959349593495935	42	0.11602209944751381	38	0.06643356643356643	118	0.15567282321899736	T	10.56	1.385337	0.25031	0.105992	0.137326	ENSG00000165238	ENST00000432730	.	.	.	5.52	-6.68	0.01778	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.18840	-1.0324	3	.	.	.	.	3.2884	0.06940	0.1033:0.3687:0.2131:0.315	rs11787888;rs11787888	.	.	.	P	333	.	.	L	+	2	0	WNK2	95033147	0.000000	0.05858	0.535000	0.28026	0.976000	0.68499	-1.965000	0.01511	-1.726000	0.01370	0.533000	0.62120	CTG	T|0.881;C|0.119	0.119	strong		0.537	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
TPO	7173	hgsc.bcm.edu	37	2	1460004	1460004	+	Missense_Mutation	SNP	G	G	T	rs4927611	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:1460004G>T	ENST00000345913.4	+	7	860	c.769G>T	c.(769-771)Gct>Tct	p.A257S	TPO_ENST00000329066.4_Missense_Mutation_p.A257S|TPO_ENST00000349624.3_Missense_Mutation_p.A257S|TPO_ENST00000382198.1_Missense_Mutation_p.A257S|TPO_ENST00000346956.3_Missense_Mutation_p.A257S|TPO_ENST00000337415.3_Missense_Mutation_p.A257S|TPO_ENST00000497517.2_Intron|TPO_ENST00000382201.3_Missense_Mutation_p.A257S	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	257			A -> S (in dbSNP:rs4927611). {ECO:0000269|PubMed:7550241, ECO:0000269|Ref.5, ECO:0000269|Ref.6}.		cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CGGGGGAGGGGCTGACTGCCA	0.468													G|||	1830	0.365415	0.3918	0.3674	5008	,	,		20988	0.1825		0.3668	False		,,,				2504	0.5153				p.A257S		Atlas-SNP	.											.	TPO	224	.	0			c.G769T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA,SER/ALA,SER/ALA,SER/ALA	1657,2749	501.8+/-365.1	312,1033,858	82.0	73.0	76.0		769,769,769,769,769,769	0.5	0.0	2	dbSNP_111	76	3302,5298	493.1+/-373.5	620,2062,1618	yes	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	99,99,99,99,99,99	932,3095,2476	TT,TG,GG		38.3953,37.6078,38.1286	benign,benign,benign,benign,benign,benign	257/934,257/934,257/877,257/877,257/890,257/761	1460004	4959,8047	2203	4300	6503	SO:0001583	missense	7173	exon7			GGAGGGGCTGACT		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.769G>T	2.37:g.1460004G>T	ENSP00000318820:p.Ala257Ser	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	718	0.32875457875457875	203	0.41260162601626016	133	0.3674033149171271	104	0.18181818181818182	278	0.36675461741424803	G	6.803	0.517173	0.13005	0.376078	0.383953	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T	0.73152	-0.72;-0.72;-0.72;-0.72;-0.72;-0.72;-0.72;-0.72	4.81	0.493	0.16878	.	1.146100	0.06111	N	0.667134	T	0.00012	0.0000	L	0.39467	1.215	0.80722	P	0.0	P;P;B;B	0.40398	0.716;0.617;0.045;0.056	B;B;B;B	0.43082	0.407;0.173;0.026;0.065	T	0.17531	-1.0366	9	0.51188	T	0.08	-4.4593	9.7845	0.40668	0.4302:0.0:0.5698:0.0	rs4927611;rs52835610;rs57959348;rs4927611	257;257;257;257	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	S	257;257;257;257;257;257;257;186	ENSP00000337263:A257S;ENSP00000318820:A257S;ENSP00000263886:A257S;ENSP00000332044:A257S;ENSP00000329869:A257S;ENSP00000371636:A257S;ENSP00000371633:A257S;ENSP00000405788:A186S	ENSP00000329869:A257S	A	+	1	0	TPO	1439011	0.001000	0.12720	0.000000	0.03702	0.072000	0.16883	1.055000	0.30467	0.121000	0.18284	0.563000	0.77884	GCT	G|0.632;T|0.368	0.368	strong		0.468	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
WDR18	57418	hgsc.bcm.edu	37	19	991968	991968	+	Silent	SNP	T	T	C	rs1127043	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:991968T>C	ENST00000251289.5	+	8	968	c.945T>C	c.(943-945)aaT>aaC	p.N315N	WDR18_ENST00000587001.2_Silent_p.N315N	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	315					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		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)		CAGTCACCAATGCCGCCATCC	0.706													N|||	1975	0.394369	0.4758	0.2738	5008	,	,		7631	0.4107		0.2962	False		,,,				2504	0.454				p.N315N		Atlas-SNP	.											.	WDR18	20	.	0			c.T945C						PASS	.	C		1912,2278		470,972,653	8.0	9.0	9.0		945	-0.6	0.9	19	dbSNP_86	9	2388,5854		417,1554,2150	no	coding-synonymous	WDR18	NM_024100.3		887,2526,2803	CC,CT,TT		28.9736,45.6325,34.5882		315/433	991968	4300,8132	2095	4121	6216	SO:0001819	synonymous_variant	57418	exon8			CACCAATGCCGCC		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.945T>C	19.37:g.991968T>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			T|0.651;C|0.349	0.349	strong		0.706	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
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 GAIIx	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_ENST00000446119.2_Missense_Mutation_p.R45W|MRC2_ENST00000580916.1_3'UTR	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	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	118	35	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		
DSPP	1834	hgsc.bcm.edu	37	4	88536551	88536551	+	Missense_Mutation	SNP	G	G	A	rs111456637	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88536551G>A	ENST00000282478.7	+	4	2770	c.2737G>A	c.(2737-2739)Gac>Aac	p.D913N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D913N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	913	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		caacagcagtgacagcagtga	0.483																																					p.D913N		Atlas-SNP	.											DSPP,NS,carcinoma,-2,3	DSPP	174	3	0			c.G2737A						PASS	.						64.0	91.0	82.0					4																	88536551		1607	2973	4580	SO:0001583	missense	1834	exon5			AGCAGTGACAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2737G>A	4.37:g.88536551G>A	ENSP00000282478:p.Asp913Asn	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	69	8	0.115942	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	2.328	-0.354162	0.05173	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88277	-2.36;-2.36	1.47	1.47	0.22746	.	.	.	.	.	T	0.78717	0.4327	N	0.12961	0.28	0.23542	N	0.997454	D	0.61080	0.989	P	0.45406	0.479	T	0.68712	-0.5336	9	0.32370	T	0.25	0.4114	6.3882	0.21572	0.0:0.0:1.0:0.0	.	913	Q9NZW4	DSPP_HUMAN	N	913	ENSP00000382213:D913N;ENSP00000282478:D913N	ENSP00000282478:D913N	D	+	1	0	DSPP	88755575	0.004000	0.15560	0.895000	0.35142	0.015000	0.08874	0.755000	0.26405	1.138000	0.42230	0.187000	0.17357	GAC	.	.	none		0.483	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
SYNE1	23345	hgsc.bcm.edu	37	6	152443744	152443744	+	Missense_Mutation	SNP	G	G	T	rs2295190	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152443744G>T	ENST00000367255.5	-	146	26822	c.26221C>A	c.(26221-26223)Ctg>Atg	p.L8741M	SYNE1_ENST00000423061.1_Missense_Mutation_p.L8693M|SYNE1_ENST00000354674.4_Missense_Mutation_p.L919M|SYNE1_ENST00000539504.1_Missense_Mutation_p.L896M|SYNE1_ENST00000265368.4_Missense_Mutation_p.L8741M|SYNE1_ENST00000448038.1_Missense_Mutation_p.L8693M|SYNE1_ENST00000347037.5_5'UTR|ESR1_ENST00000427531.2_Intron|SYNE1_ENST00000356820.4_Missense_Mutation_p.L3265M|SYNE1_ENST00000341594.5_Missense_Mutation_p.L8353M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8741	KASH. {ECO:0000255|PROSITE- ProRule:PRU00385}.		L -> M (in dbSNP:rs2295190).		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)		ACTCTGAACAGGAAGCCGCGG	0.557										HNSCC(10;0.0054)			G|||	385	0.076877	0.0204	0.0533	5008	,	,		19383	0.0675		0.1491	False		,,,				2504	0.1053				p.L8741M		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C26221A						PASS	.	G	MET/LEU,MET/LEU	152,4254	105.6+/-144.1	2,148,2053	94.0	97.0	96.0		26077,26221	0.6	0.8	6	dbSNP_100	96	1202,7398	243.8+/-273.2	74,1054,3172	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	15,15	76,1202,5225	TT,TG,GG		13.9767,3.4498,10.4106	possibly-damaging,possibly-damaging	8693/8750,8741/8798	152443744	1354,11652	2203	4300	6503	SO:0001583	missense	23345	exon146			TGAACAGGAAGCC	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.26221C>A	6.37:g.152443744G>T	ENSP00000356224:p.Leu8741Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	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	202	0.0924908424908425	18	0.036585365853658534	21	0.058011049723756904	42	0.07342657342657342	121	0.15963060686015831	G	17.90	3.503200	0.64298	0.034498	0.139767	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000354674	T;T;T;T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75	5.56	0.627	0.17675	Klarsicht/ANC-1/syne-1 homology (2);	0.330699	0.21571	N	0.072401	T	0.36166	0.0957	M	0.84433	2.695	0.31636	P	0.648409	D;D;D	0.64830	0.994;0.994;0.993	D;D;D	0.69824	0.966;0.966;0.943	T	0.34378	-0.9831	9	0.72032	D	0.01	.	8.7024	0.34334	0.5975:0.0:0.4025:0.0	rs2295190;rs2295190	8741;8741;8693	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	M	8741;896;8693;8741;8693;8353;3265;926;921;919	ENSP00000356224:L8741M;ENSP00000441052:L896M;ENSP00000396024:L8693M;ENSP00000265368:L8741M;ENSP00000390975:L8693M;ENSP00000341887:L8353M;ENSP00000349276:L3265M;ENSP00000346701:L919M	ENSP00000265368:L8741M	L	-	1	2	SYNE1	152485437	1.000000	0.71417	0.840000	0.33206	0.821000	0.46438	1.590000	0.36654	0.025000	0.15241	0.655000	0.94253	CTG	G|0.898;T|0.102	0.102	strong		0.557	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TENM4	26011	hgsc.bcm.edu	37	11	78380199	78380199	+	Silent	SNP	C	C	T	rs61745709	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:78380199C>T	ENST00000278550.7	-	32	7653	c.7191G>A	c.(7189-7191)caG>caA	p.Q2397Q		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2397					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CTATGATGATCTGAAAGTTGG	0.517													C|||	136	0.0271565	0.0189	0.0418	5008	,	,		18377	0.0		0.0696	False		,,,				2504	0.0123				p.Q2397Q		Atlas-SNP	.											.	.	.	.	0			c.G7191A						PASS	.	C		76,3822		1,74,1874	57.0	57.0	57.0		7191	5.7	1.0	11	dbSNP_129	57	482,7810		15,452,3679	no	coding-synonymous	ODZ4	NM_001098816.2		16,526,5553	TT,TC,CC		5.8128,1.9497,4.5775		2397/2770	78380199	558,11632	1949	4146	6095	SO:0001819	synonymous_variant	26011	exon32			GATGATCTGAAAG	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.7191G>A	11.37:g.78380199C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	183	20	0.10929	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			C|0.950;T|0.050	0.050	strong		0.517	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
CA5A	763	hgsc.bcm.edu	37	16	87921846	87921846	+	Silent	SNP	T	T	A	rs72816311	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:87921846T>A	ENST00000309893.2	-	7	872	c.807A>T	c.(805-807)gcA>gcT	p.A269A		NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	269					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	CTTCACCAAGTGCAGAAAACA	0.547													T|||	864	0.172524	0.1263	0.134	5008	,	,		20689	0.1567		0.1829	False		,,,				2504	0.2679				p.A269A		Atlas-SNP	.											.	CA5A	32	.	0			c.A807T						PASS	.	T		609,3787	262.8+/-265.1	39,531,1628	54.0	49.0	50.0		807	-9.5	0.0	16	dbSNP_131	50	1789,6811	322.8+/-315.7	197,1395,2708	no	coding-synonymous	CA5A	NM_001739.1		236,1926,4336	AA,AT,TT		20.8023,13.8535,18.4518		269/306	87921846	2398,10598	2198	4300	6498	SO:0001819	synonymous_variant	763	exon7			ACCAAGTGCAGAA	L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	4.2.1.1	"""Carbonic anhydrases"""	1377	protein-coding gene	gene with protein product		114761		CA5		8356065, 7490083	Standard	NM_001739		Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.807A>T	16.37:g.87921846T>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	163	85	0.521472	NM_001739	B2RPF2	Silent	SNP	ENST00000309893.2	37	CCDS10965.1																																																																																			T|0.825;A|0.175	0.175	strong		0.547	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269164.1	NM_001739	
HDC	3067	hgsc.bcm.edu	37	15	50544871	50544871	+	Silent	SNP	G	G	A	rs34406040	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:50544871G>A	ENST00000267845.3	-	8	1290	c.888C>T	c.(886-888)gcC>gcT	p.A296A	HDC_ENST00000543581.1_Silent_p.A296A	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TGAAGGAGTCGGCATACTCAA	0.572													G|||	37	0.00738818	0.003	0.0115	5008	,	,		21047	0.0		0.0209	False		,,,				2504	0.0041				p.A296A	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.C888T						PASS	.	G		17,4375	26.2+/-53.5	0,17,2179	81.0	80.0	80.0		888	-4.3	0.9	15	dbSNP_126	80	234,8356	95.2+/-157.0	2,230,4063	no	coding-synonymous	HDC	NM_002112.3		2,247,6242	AA,AG,GG		2.7241,0.3871,1.9334		296/663	50544871	251,12731	2196	4295	6491	SO:0001819	synonymous_variant	3067	exon8			GGAGTCGGCATAC		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.888C>T	15.37:g.50544871G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_002112		Silent	SNP	ENST00000267845.3	37	CCDS10134.1																																																																																			G|0.983;A|0.017	0.017	strong		0.572	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
IL31RA	133396	hgsc.bcm.edu	37	5	55206444	55206444	+	Missense_Mutation	SNP	G	G	A	rs161704	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:55206444G>A	ENST00000447346.2	+	12	1651	c.1586G>A	c.(1585-1587)aGc>aAc	p.S529N	IL31RA_ENST00000359040.5_Missense_Mutation_p.S529N|IL31RA_ENST00000396834.1_Missense_Mutation_p.S510N|IL31RA_ENST00000490985.1_Missense_Mutation_p.S387N|IL31RA_ENST00000354961.4_Missense_Mutation_p.S510N	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	497					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GTCATGGCCAGCACCAGTGCT	0.468													G|||	1552	0.309904	0.3321	0.2176	5008	,	,		22564	0.3254		0.2962	False		,,,				2504	0.3436				p.S529N		Atlas-SNP	.											.	IL31RA	84	.	0			c.G1586A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER,ASN/SER	1511,2895	480.3+/-358.8	262,987,954	163.0	141.0	148.0		1529,1586,1529,1160,1586	3.3	1.0	5	dbSNP_79	148	2503,6097	410.3+/-350.1	354,1795,2151	yes	missense,missense,missense,missense,missense	IL31RA	NM_001242636.1,NM_001242637.1,NM_001242638.1,NM_001242639.1,NM_139017.5	46,46,46,46,46	616,2782,3105	AA,AG,GG		29.1047,34.2941,30.8627	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	510/746,529/682,510/663,387/623,529/765	55206444	4014,8992	2203	4300	6503	SO:0001583	missense	133396	exon12			TGGCCAGCACCAG	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.1586G>A	5.37:g.55206444G>A	ENSP00000415900:p.Ser529Asn	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	148	87	0.587838	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	669	0.30631868131868134	147	0.29878048780487804	82	0.2265193370165746	205	0.3583916083916084	235	0.3100263852242744	G	3.877	-0.026766	0.07589	0.342941	0.291047	ENSG00000164509	ENST00000396834;ENST00000447346;ENST00000359040;ENST00000490985;ENST00000354961	T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41	5.11	3.33	0.38152	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.372887	0.31685	N	0.007222	T	0.00012	0.0000	M	0.71871	2.18	0.09310	P	0.9999999999994192	B;B;B;B	0.27166	0.17;0.037;0.141;0.141	B;B;B;B	0.26310	0.068;0.028;0.041;0.041	T	0.31861	-0.9928	9	0.25751	T	0.34	-19.8536	6.2045	0.20595	0.2609:0.0:0.7391:0.0	rs161704;rs327251;rs52803246;rs58671636;rs161704	497;529;510;529	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2	IL31R_HUMAN;.;.;.	N	510;529;529;387;510	ENSP00000380046:S510N;ENSP00000415900:S529N;ENSP00000351935:S529N;ENSP00000427533:S387N;ENSP00000347047:S510N	ENSP00000347047:S510N	S	+	2	0	IL31RA	55242201	0.982000	0.34865	1.000000	0.80357	0.987000	0.75469	0.168000	0.16622	1.521000	0.48983	0.557000	0.71058	AGC	G|0.694;N|0.000	.	strong		0.468	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
XPO5	57510	hgsc.bcm.edu	37	6	43492578	43492578	+	Silent	SNP	G	G	A	rs2257082	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:43492578G>A	ENST00000265351.7	-	30	3513	c.3303C>T	c.(3301-3303)taC>taT	p.Y1101Y	POLR1C_ENST00000304004.3_Intron	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	1101					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			CCAGTGCCTCGTATATCTGGA	0.557													G|||	1627	0.32488	0.1611	0.2983	5008	,	,		21459	0.62		0.2853	False		,,,				2504	0.3016				p.Y1101Y		Atlas-SNP	.											.	XPO5	79	.	0			c.C3303T						PASS	.	G		720,3440		72,576,1432	57.0	61.0	60.0		3303	-6.1	0.9	6	dbSNP_100	60	2173,6235		274,1625,2305	no	coding-synonymous	XPO5	NM_020750.2		346,2201,3737	AA,AG,GG		25.8444,17.3077,23.0188		1101/1205	43492578	2893,9675	2080	4204	6284	SO:0001819	synonymous_variant	57510	exon30			TGCCTCGTATATC	AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.3303C>T	6.37:g.43492578G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	21	0.28	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1	766	0.3507326007326007	90	0.18292682926829268	105	0.2900552486187845	351	0.6136363636363636	220	0.29023746701846964	G	3.527	-0.096513	0.07010	0.173077	0.258444	ENSG00000124571	ENST00000455285	.	.	.	6.08	-6.07	0.02158	.	.	.	.	.	T	0.47544	0.1451	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.57353	-0.7826	3	.	.	.	-16.2365	19.3651	0.94459	0.255:0.0:0.745:0.0	rs2257082;rs3198268;rs11544381;rs13212498;rs17287943;rs17846608;rs17859692;rs61216486;rs2257082	.	.	.	M	216	.	.	T	-	2	0	XPO5	43600556	0.233000	0.23772	0.921000	0.36526	0.496000	0.33645	-0.282000	0.08445	-0.948000	0.03668	-0.948000	0.02665	ACG	G|0.652;N|0.002	.	strong		0.557	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807953	18807953	+	Missense_Mutation	SNP	C	C	A	rs11261022	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:18807953C>A	ENST00000400664.1	+	1	530	c.478C>A	c.(478-480)Cgc>Agc	p.R160S		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	160			R -> S (in dbSNP:rs11261022).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CCATTTCCCCCGCTTGGGCAG	0.642													C|||	1400	0.279553	0.2534	0.3401	5008	,	,		17782	0.2321		0.3628	False		,,,				2504	0.2352				p.R160S		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.C478A						PASS	.	C	SER/ARG	1039,3127		137,765,1181	32.0	37.0	35.0		478	-4.0	0.0	1	dbSNP_120	35	2972,5484		509,1954,1765	yes	missense	KLHDC7A	NM_152375.2	110	646,2719,2946	AA,AC,CC		35.1466,24.94,31.7778	benign	160/778	18807953	4011,8611	2083	4228	6311	SO:0001583	missense	127707	exon1			TTCCCCCGCTTGG	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.478C>A	1.37:g.18807953C>A	ENSP00000383505:p.Arg160Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	17	0.354167	NM_152375	Q8N8W6	Missense_Mutation	SNP	ENST00000400664.1	37	CCDS185.2	670	0.3067765567765568	140	0.2845528455284553	105	0.2900552486187845	139	0.243006993006993	286	0.37730870712401055	C	11.86	1.764864	0.31228	0.2494	0.351466	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.72051	-0.62	4.65	-3.99	0.04069	.	3.517270	0.05457	U	0.550465	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18166	0.026	B	0.12837	0.008	T	0.13926	-1.0491	9	0.12430	T	0.62	.	2.446	0.04506	0.1147:0.3232:0.3378:0.2243	rs11261022	160	Q5VTJ3	KLD7A_HUMAN	S	160;97	ENSP00000383505:R160S	ENSP00000383505:R160S	R	+	1	0	KLHDC7A	18680540	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-4.138000	0.00287	-0.507000	0.06549	-0.216000	0.12614	CGC	C|0.671;A|0.329	0.329	strong		0.642	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
TFDP2	7029	hgsc.bcm.edu	37	3	141724328	141724328	+	Silent	SNP	T	T	C	rs7627056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:141724328T>C	ENST00000489671.1	-	4	571	c.141A>G	c.(139-141)ttA>ttG	p.L47L	TFDP2_ENST00000317104.7_5'UTR|TFDP2_ENST00000477292.1_Intron|TFDP2_ENST00000499676.2_5'UTR|TFDP2_ENST00000486111.1_5'UTR|TFDP2_ENST00000464782.1_5'UTR|TFDP2_ENST00000467072.1_5'UTR|TFDP2_ENST00000310282.6_5'UTR|TFDP2_ENST00000479040.1_5'Flank|TFDP2_ENST00000495310.1_5'UTR			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	47					gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|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)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.L47L(1)		kidney(1)|upper_aerodigestive_tract(2)	3						AGGTTTTTGGTAAAATCTTTG	0.318													T|||	207	0.0413339	0.0477	0.0259	5008	,	,		17613	0.003		0.0527	False		,,,				2504	0.0716				p.L47L		Atlas-SNP	.											TFDP2_ENST00000489671,NS,carcinoma,0,1	TFDP2	44	1	1	Substitution - coding silent(1)	endometrium(1)	c.A141G						scavenged	.	T	,,,,	132,3490		1,130,1680	121.0	109.0	113.0		,141,,,	4.7	1.0	3	dbSNP_116	113	449,7701		11,427,3637	no	utr-5,coding-synonymous,utr-5,intron,utr-5	TFDP2	NM_001178138.1,NM_001178139.1,NM_001178141.1,NM_001178142.1,NM_006286.4	,,,,	12,557,5317	CC,CT,TT		5.5092,3.6444,4.9354	,,,,	,47/447,,,	141724328	581,11191	1811	4075	5886	SO:0001819	synonymous_variant	7029	exon4			TTTTGGTAAAATC	U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.141A>G	3.37:g.141724328T>C		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	99	57	0.575758	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Silent	SNP	ENST00000489671.1	37	CCDS54650.1																																																																																			T|0.967;C|0.033	0.033	strong		0.318	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286	
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 GAIIx	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	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	207	46	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 GAIIx	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	PYGL_ENST00000544180.2_Missense_Mutation_p.D600H|PYGL_ENST00000532462.1_Missense_Mutation_p.D634H|RP11-218E20.5_ENST00000557343.1_RNA	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	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	164	81	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	
LRP1B	53353	hgsc.bcm.edu	37	2	141260668	141260668	+	Silent	SNP	A	A	G	rs4444457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:141260668A>G	ENST00000389484.3	-	54	9497	c.8526T>C	c.(8524-8526)taT>taC	p.Y2842Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2842					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CACACTGTCGATATCCTAGAG	0.398										TSP Lung(27;0.18)			G|||	2720	0.543131	0.466	0.451	5008	,	,		17484	0.7222		0.5388	False		,,,				2504	0.5327				p.Y2842Y	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T8526C						PASS	.	G		2201,2205	587.3+/-386.7	557,1087,559	118.0	110.0	113.0		8526	1.6	1.0	2	dbSNP_111	113	4728,3872	543.0+/-384.3	1306,2116,878	no	coding-synonymous	LRP1B	NM_018557.2		1863,3203,1437	GG,GA,AA		45.0233,49.9546,46.7246		2842/4600	141260668	6929,6077	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon54			CTGTCGATATCCT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8526T>C	2.37:g.141260668A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			A|0.460;G|0.540	0.540	strong		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
LILRB1	10859	hgsc.bcm.edu	37	19	55145454	55145454	+	Missense_Mutation	SNP	G	G	A	rs1138736	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55145454G>A	ENST00000396331.1	+	10	1699	c.1342G>A	c.(1342-1344)Ggg>Agg	p.G448R	LILRB1_ENST00000396315.1_Missense_Mutation_p.G449R|LILRB1_ENST00000396332.4_Missense_Mutation_p.G448R|LILRB1_ENST00000324602.7_Missense_Mutation_p.G449R|LILRB1_ENST00000418536.2_Missense_Mutation_p.G432R|LILRB1_ENST00000427581.2_Missense_Mutation_p.G485R|LILRB1_ENST00000448689.1_Missense_Mutation_p.G448R|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000396321.2_Missense_Mutation_p.G448R|LILRB1_ENST00000396327.3_Missense_Mutation_p.G449R|LILRB1_ENST00000396317.1_Missense_Mutation_p.G432R|LILRB1_ENST00000434867.2_Missense_Mutation_p.G448R	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	448					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CACCCCCACCGGGTCGGATCC	0.697										HNSCC(37;0.09)			g|||	527	0.105232	0.2012	0.0576	5008	,	,		13562	0.0139		0.1163	False		,,,				2504	0.092				p.G449R		Atlas-SNP	.											.	LILRB1	140	.	0			c.G1345A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	854,3536		90,674,1431	19.0	23.0	22.0		1345,1345,1342,1342	0.6	0.0	19	dbSNP_86	22	1009,7581		50,909,3336	no	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	125,125,125,125	140,1583,4767	AA,AG,GG		11.7462,19.4533,14.3529	benign,benign,benign,benign	449/653,449/652,448/652,448/651	55145454	1863,11117	2195	4295	6490	SO:0001583	missense	10859	exon9			CCCACCGGGTCGG	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1342G>A	19.37:g.55145454G>A	ENSP00000379622:p.Gly448Arg	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	183	88	0.480874	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	234	0.10714285714285714	121	0.2459349593495935	19	0.052486187845303865	9	0.015734265734265736	85	0.11213720316622691	g	0.071	-1.202897	0.01581	0.194533	0.117462	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.00492	7.14;7.06;7.01;7.14;7.09;7.08;7.14;7.14;7.08;7.06;7.08	1.66	0.586	0.17434	.	.	.	.	.	T	0.00012	0.0000	M	0.80183	2.485	0.80722	P	0.0	B;B;B;B;B;B	0.28512	0.023;0.017;0.101;0.11;0.171;0.214	B;B;B;B;B;B	0.21546	0.009;0.004;0.034;0.023;0.035;0.023	T	0.18681	-1.0329	8	0.10636	T	0.68	.	4.2958	0.10901	0.2166:0.0:0.7834:0.0	rs1138736;rs3202773	432;448;449;448;449;448	A8MVE2;D9IDM5;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;.;LIRB1_HUMAN	R	448;432;448;448;449;449;448;448;485;432;449	ENSP00000379614:G448R;ENSP00000391514:G432R;ENSP00000409968:G448R;ENSP00000379622:G448R;ENSP00000379618:G449R;ENSP00000315997:G449R;ENSP00000405243:G448R;ENSP00000379623:G448R;ENSP00000395004:G485R;ENSP00000379610:G432R;ENSP00000379608:G449R	ENSP00000315997:G449R	G	+	1	0	LILRB1	59837266	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.139000	0.10358	0.276000	0.22118	-1.051000	0.02340	GGG	G|0.895;A|0.105	0.105	strong		0.697	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
CAGE1	285782	hgsc.bcm.edu	37	6	7387236	7387236	+	Silent	SNP	G	G	A	rs9406026	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:7387236G>A	ENST00000512086.1	-	2	373	c.171C>T	c.(169-171)acC>acT	p.T57T	CAGE1_ENST00000338150.4_Silent_p.T57T|CAGE1_ENST00000296742.7_Intron|CAGE1_ENST00000509324.1_5'UTR|CAGE1_ENST00000379918.4_Silent_p.T57T|CAGE1_ENST00000502583.1_Silent_p.T57T|RIOK1_ENST00000379834.2_5'Flank			Q8TC20	CAGE1_HUMAN	cancer antigen 1	57										breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					AAGTGGTGCCGGTGGTTTCCA	0.403													G|||	1871	0.373602	0.3079	0.4337	5008	,	,		19276	0.4504		0.3638	False		,,,				2504	0.3507				p.T57T		Atlas-SNP	.											.	CAGE1	165	.	0			c.C171T						PASS	.						197.0	178.0	184.0					6																	7387236		692	1591	2283	SO:0001819	synonymous_variant	285782	exon2			GGTGCCGGTGGTT	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"""cancer/testis antigen 95"""	608304	"""cancer/testis antigen 3"""	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.171C>T	6.37:g.7387236G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	83	62	0.746988	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Silent	SNP	ENST00000512086.1	37																																																																																				G|0.618;A|0.382	0.382	strong		0.403	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745	
EXPH5	23086	hgsc.bcm.edu	37	11	108385251	108385251	+	Missense_Mutation	SNP	C	C	T	rs11212684	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:108385251C>T	ENST00000265843.4	-	6	1093	c.983G>A	c.(982-984)cGg>cAg	p.R328Q	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Missense_Mutation_p.R252Q|EXPH5_ENST00000525344.1_Missense_Mutation_p.R321Q|EXPH5_ENST00000443411.1_Missense_Mutation_p.R140Q	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	328			R -> Q (in dbSNP:rs11212684).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TAAGGCCGACCGTTGCCTGCT	0.463													C|||	101	0.0201677	0.0083	0.0245	5008	,	,		18894	0.0149		0.0378	False		,,,				2504	0.0204				p.R328Q		Atlas-SNP	.											.	EXPH5	193	.	0			c.G983A						PASS	.	C	GLN/ARG	47,4355	48.9+/-83.8	0,47,2154	70.0	62.0	65.0		983	-1.7	0.2	11	dbSNP_120	65	342,8254	117.0+/-176.6	9,324,3965	yes	missense	EXPH5	NM_015065.2	43	9,371,6119	TT,TC,CC		3.9786,1.0677,2.9928	benign	328/1990	108385251	389,12609	2201	4298	6499	SO:0001583	missense	23086	exon6			GCCGACCGTTGCC		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.983G>A	11.37:g.108385251C>T	ENSP00000265843:p.Arg328Gln	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	185	148	0.8	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	48	0.02197802197802198	5	0.01016260162601626	11	0.03038674033149171	5	0.008741258741258742	27	0.03562005277044855	C	11.57	1.678413	0.29783	0.010677	0.039786	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04603	4.18;4.1;3.96;4.18;4.02;3.59	5.44	-1.72	0.08107	.	0.455884	0.18584	N	0.136955	T	0.00666	0.0022	N	0.25426	0.745	0.09310	N	1	B	0.31817	0.341	B	0.26517	0.07	T	0.44787	-0.9305	10	0.34782	T	0.22	-0.2183	7.6046	0.28095	0.0:0.5356:0.1138:0.3506	rs11212684;rs52821178;rs11212684	328	Q8NEV8	EXPH5_HUMAN	Q	328;252;140;321;172;252;140	ENSP00000265843:R328Q;ENSP00000391966:R252Q;ENSP00000411390:R140Q;ENSP00000432546:R321Q;ENSP00000432683:R252Q;ENSP00000446434:R140Q	ENSP00000265843:R328Q	R	-	2	0	EXPH5	107890461	0.000000	0.05858	0.196000	0.23383	0.603000	0.37013	-1.994000	0.01474	-0.181000	0.10619	0.491000	0.48974	CGG	C|0.973;T|0.027	0.027	strong		0.463	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
SFI1	9814	hgsc.bcm.edu	37	22	31971351	31971351	+	Missense_Mutation	SNP	C	C	T	rs78295829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:31971351C>T	ENST00000400288.2	+	10	1162	c.1057C>T	c.(1057-1059)Cgg>Tgg	p.R353W	SFI1_ENST00000443326.1_Missense_Mutation_p.R271W|SFI1_ENST00000540643.1_Missense_Mutation_p.R329W|SFI1_ENST00000414585.1_Missense_Mutation_p.R200W|SFI1_ENST00000432498.1_Missense_Mutation_p.R353W|SFI1_ENST00000400289.1_Missense_Mutation_p.R271W|SFI1_ENST00000443011.1_Missense_Mutation_p.R200W	NM_001007467.2	NP_001007468.1	A8K8P3	SFI1_HUMAN	Sfi1 homolog, spindle assembly associated (yeast)	353				R -> W (in Ref. 5; AAI10815). {ECO:0000305}.	G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(2)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)	38						GATGGCCCTGCGGCGCGCCTT	0.562													C|||	74	0.0147764	0.0008	0.013	5008	,	,		15635	0.0		0.0249	False		,,,				2504	0.0399				p.R353W		Atlas-SNP	.											.	SFI1	78	.	0			c.C1057T						PASS	.	C	TRP/ARG,TRP/ARG	10,4038		0,10,2014	70.0	75.0	73.0		1057,1057	2.2	0.8	22	dbSNP_131	73	137,8235		0,137,4049	yes	missense,missense	SFI1	NM_001007467.1,NM_014775.2	101,101	0,147,6063	TT,TC,CC		1.6364,0.247,1.1836	benign,benign	353/1243,353/1212	31971351	147,12273	2024	4186	6210	SO:0001583	missense	9814	exon10			GCCCTGCGGCGCG	AB011114	CCDS43004.1, CCDS43005.1, CCDS58803.1, CCDS58804.1	22q12.2	2014-06-13			ENSG00000198089	ENSG00000198089			29064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 139"""	612765				14504268	Standard	NM_001007467		Approved	KIAA0542, PISD, PPP1R139	uc003ale.4	A8K8P3	OTTHUMG00000030249	ENST00000400288.2:c.1057C>T	22.37:g.31971351C>T	ENSP00000383145:p.Arg353Trp	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	90	48	0.533333	NM_001007467	A1L373|A1L387|A2A2L2|B1AKL9|B5MDB7|B7Z1V6|B7Z8G3|B7ZBE2|B7ZBE3|O60289|Q2TAN8|Q5W1B5|Q86TK0|Q8N4U8|Q8N8C1|Q8WU14	Missense_Mutation	SNP	ENST00000400288.2	37	CCDS43004.1	31	0.014194139194139194	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	23	0.030343007915567283	C	8.721	0.914260	0.17907	0.00247	0.016364	ENSG00000198089	ENST00000432498;ENST00000540643;ENST00000443326;ENST00000421060;ENST00000414585;ENST00000443011;ENST00000400289;ENST00000400288	T;T;T;T;T;T;T	0.61627	2.8;2.81;0.09;0.09;0.09;0.09;0.09	5.49	2.24	0.28232	.	0.145914	0.45606	N	0.000347	T	0.20414	0.0491	N	0.08118	0	0.40823	D	0.983521	B;B;D;B;B;B	0.71674	0.233;0.048;0.998;0.099;0.007;0.024	B;B;P;B;B;B	0.53861	0.048;0.016;0.736;0.022;0.005;0.022	T	0.28004	-1.0057	10	0.62326	D	0.03	.	6.5643	0.22503	0.3192:0.5974:0.0:0.0834	.	329;271;271;353;353;329	A8K8P3-9;A8K8P3-10;A8K8P3-3;A8K8P3-2;A8K8P3;A8K8P3-5	.;.;.;.;SFI1_HUMAN;.	W	353;329;271;329;200;200;271;353	ENSP00000402679:R353W;ENSP00000443025:R329W;ENSP00000416469:R271W;ENSP00000397148:R200W;ENSP00000401199:R200W;ENSP00000383146:R271W;ENSP00000383145:R353W	ENSP00000383145:R353W	R	+	1	2	SFI1	30301351	0.776000	0.28616	0.797000	0.32132	0.016000	0.09150	-0.230000	0.09083	0.281000	0.22233	-0.152000	0.13540	CGG	C|0.983;T|0.017	0.017	strong		0.562	SFI1-023	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337180.3	NM_014775	
TRIM26	7726	hgsc.bcm.edu	37	6	30154199	30154199	+	Silent	SNP	T	T	C	rs2074473	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30154199T>C	ENST00000454678.2	-	10	1510	c.1074A>G	c.(1072-1074)ctA>ctG	p.L358L	TRIM26_ENST00000453195.1_Silent_p.L358L|TRIM26_ENST00000437089.1_Silent_p.L358L	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	358	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						CCTTGCTGCCTAGCACCCCAG	0.592													C|||	1911	0.381589	0.4788	0.4827	5008	,	,		17250	0.2837		0.4334	False		,,,				2504	0.226				p.L358L		Atlas-SNP	.											.	TRIM26	74	.	0			c.A1074G						PASS	.	C	,	1315,1705		282,751,477	104.0	94.0	98.0		1074,1074	1.9	1.0	6	dbSNP_96	98	2393,3025		537,1319,853	no	coding-synonymous,coding-synonymous	TRIM26	NM_001242783.1,NM_003449.4	,	819,2070,1330	CC,CT,TT		44.1676,43.543,43.9441	,	358/540,358/540	30154199	3708,4730	1510	2709	4219	SO:0001819	synonymous_variant	7726	exon9			GCTGCCTAGCACC	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.1074A>G	6.37:g.30154199T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	65	51	0.784615	NM_001242783	A6NG96|Q5SRL2	Silent	SNP	ENST00000454678.2	37	CCDS4678.1																																																																																			T|0.583;C|0.417	0.417	strong		0.592	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	
OR2L2	26246	hgsc.bcm.edu	37	1	248202474	248202474	+	Missense_Mutation	SNP	A	A	G	rs144950416	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248202474A>G	ENST00000366479.2	+	1	1001	c.905A>G	c.(904-906)cAa>cGa	p.Q302R	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	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)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	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)			GCCCTGACACAAGTGATTCAG	0.453																																					p.Q302R		Atlas-SNP	.											.	OR2L2	115	.	0			c.A905G						PASS	.						72.0	71.0	71.0					1																	248202474		2203	4300	6503	SO:0001583	missense	26246	exon1			TGACACAAGTGAT	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"""GPCR / Class A : Olfactory receptors"""	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.905A>G	1.37:g.248202474A>G	ENSP00000355435:p.Gln302Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	168	38	0.22619	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	0.033	-1.322520	0.01320	.	.	ENSG00000203663	ENST00000366479	T	0.34072	1.38	1.9	1.9	0.25705	.	.	.	.	.	T	0.18551	0.0445	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31752	-0.9932	8	0.12766	T	0.61	.	7.897	0.29712	0.1358:0.0:0.8642:0.0	.	302	Q8NH16	OR2L2_HUMAN	R	302	ENSP00000355435:Q302R	ENSP00000355435:Q302R	Q	+	2	0	OR2L2	246269097	0.000000	0.05858	0.016000	0.15963	0.416000	0.31233	-0.713000	0.05007	0.047000	0.15862	-1.032000	0.02404	CAA	A|0.990;G|0.010	0.010	strong		0.453	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686	
ASXL3	80816	hgsc.bcm.edu	37	18	31320229	31320229	+	Missense_Mutation	SNP	A	A	G	rs2282632	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:31320229A>G	ENST00000269197.5	+	11	2861	c.2861A>G	c.(2860-2862)aAt>aGt	p.N954S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	954			N -> S (in dbSNP:rs2282632). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:17974005}.		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						GGGATAAGAAATGAAAGTAGA	0.403													A|||	3522	0.703275	0.8094	0.6916	5008	,	,		18519	0.8988		0.5249	False		,,,				2504	0.5501				p.N954S		Atlas-SNP	.											.	ASXL3	405	.	0			c.A2861G						PASS	.	A	SER/ASN	2900,796		1133,634,81	58.0	55.0	56.0		2861	0.4	0.9	18	dbSNP_100	56	4246,3954		1084,2078,938	yes	missense	ASXL3	NM_030632.1	46	2217,2712,1019	GG,GA,AA		48.2195,21.5368,39.9294	benign	954/2249	31320229	7146,4750	1848	4100	5948	SO:0001583	missense	80816	exon11			TAAGAAATGAAAG	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.2861A>G	18.37:g.31320229A>G	ENSP00000269197:p.Asn954Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	1533	0.7019230769230769	385	0.782520325203252	239	0.6602209944751382	516	0.9020979020979021	393	0.5184696569920845	A	9.879	1.200986	0.22121	0.784632	0.517805	ENSG00000141431	ENST00000269197	T	0.48522	0.81	5.72	0.361	0.16107	.	1.491830	0.03855	N	0.272982	T	0.00012	0.0000	L	0.29908	0.895	0.44352	P	0.0027599999999999847	B	0.10296	0.003	B	0.06405	0.002	T	0.35475	-0.9787	9	0.07813	T	0.8	.	5.8836	0.18868	0.4169:0.3758:0.2073:0.0	rs2282632;rs17746901;rs60259995;rs2282632	954	Q9C0F0	ASXL3_HUMAN	S	954	ENSP00000269197:N954S	ENSP00000269197:N954S	N	+	2	0	ASXL3	29574227	0.996000	0.38824	0.907000	0.35723	0.870000	0.49936	0.405000	0.21015	0.109000	0.17891	0.533000	0.62120	AAT	G|0.767;N|0.000	0.767	strong		0.403	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
ARHGEF4	50649	hgsc.bcm.edu	37	2	131688587	131688587	+	Silent	SNP	G	G	A	rs6718816	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:131688587G>A	ENST00000326016.5	+	3	576	c.57G>A	c.(55-57)gcG>gcA	p.A19A	ARHGEF4_ENST00000409359.1_Silent_p.A875A|ARHGEF4_ENST00000428230.2_Silent_p.A19A|SCARNA4_ENST00000517020.2_RNA|ARHGEF4_ENST00000409303.1_Silent_p.A19A|ARHGEF4_ENST00000525839.1_Silent_p.A19A|ARHGEF4_ENST00000392953.3_Silent_p.A19A	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	19					apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		GTCAGAAGGCGTTCCACATGG	0.592													G|||	1289	0.257388	0.4047	0.1297	5008	,	,		18326	0.1607		0.1829	False		,,,				2504	0.3252				p.A19A		Atlas-SNP	.											ARHGEF4,NS,carcinoma,+2,1	ARHGEF4	89	1	0			c.G57A						scavenged	.	G	,	1702,2704	513.2+/-368.3	327,1048,828	70.0	64.0	66.0		57,57	-2.4	0.0	2	dbSNP_116	66	1523,7077	287.8+/-298.4	131,1261,2908	no	coding-synonymous,coding-synonymous	ARHGEF4	NM_015320.2,NM_032995.1	,	458,2309,3736	AA,AG,GG		17.7093,38.6291,24.7962	,	19/691,19/671	131688587	3225,9781	2203	4300	6503	SO:0001819	synonymous_variant	50649	exon3			GAAGGCGTTCCAC	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.57G>A	2.37:g.131688587G>A		Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	42	7	0.166667	NM_032995	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	37	CCDS2165.1																																																																																			G|0.748;A|0.252	0.252	strong		0.592	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
SALL3	27164	hgsc.bcm.edu	37	18	76754549	76754549	+	Missense_Mutation	SNP	T	T	C	rs35578880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:76754549T>C	ENST00000537592.2	+	2	2558	c.2558T>C	c.(2557-2559)gTc>gCc	p.V853A	SALL3_ENST00000536229.3_Missense_Mutation_p.V720A|SALL3_ENST00000575389.2_Missense_Mutation_p.V853A	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	853					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|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(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		ATCGACTCGGTCATGAGCTGC	0.662													T|||	127	0.0253594	0.0015	0.0692	5008	,	,		12886	0.004		0.0557	False		,,,				2504	0.0174				p.V853A		Atlas-SNP	.											SALL3,NS,carcinoma,-1,1	SALL3	162	1	0			c.T2558C						scavenged	.	T	ALA/VAL	44,4360		0,44,2158	43.0	45.0	44.0		2558	1.9	0.9	18	dbSNP_126	44	427,8171		7,413,3879	yes	missense	SALL3	NM_171999.2	64	7,457,6037	CC,CT,TT		4.9663,0.9991,3.6225	possibly-damaging	853/1301	76754549	471,12531	2202	4299	6501	SO:0001583	missense	27164	exon2			ACTCGGTCATGAG	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.2558T>C	18.37:g.76754549T>C	ENSP00000441823:p.Val853Ala	Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	73	0.033424908424908424	2	0.0040650406504065045	22	0.06077348066298342	1	0.0017482517482517483	48	0.0633245382585752	T	10.03	1.239741	0.22711	0.009991	0.049663	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.08102	3.13	5.49	1.85	0.25348	.	0.119337	0.35870	N	0.002934	T	0.00524	0.0017	N	0.25485	0.75	0.34251	D	0.678814	B;B	0.22276	0.007;0.067	B;B	0.14023	0.01;0.008	T	0.43410	-0.9393	10	0.08179	T	0.78	-51.7539	9.0484	0.36360	0.0:0.2084:0.0:0.7916	rs35578880	585;853	F5GXY4;Q9BXA9	.;SALL3_HUMAN	A	853;853;585	ENSP00000441823:V853A	ENSP00000299466:V853A	V	+	2	0	SALL3	74855537	1.000000	0.71417	0.893000	0.35052	0.929000	0.56500	2.298000	0.43602	0.085000	0.17107	0.459000	0.35465	GTC	T|0.963;C|0.037	0.037	strong		0.662	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
KDM4C	23081	hgsc.bcm.edu	37	9	6984236	6984236	+	Missense_Mutation	SNP	G	G	A	rs2296067	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6984236G>A	ENST00000381309.3	+	10	1751	c.1186G>A	c.(1186-1188)Gat>Aat	p.D396N	KDM4C_ENST00000428870.2_Missense_Mutation_p.D83N|KDM4C_ENST00000543771.1_Missense_Mutation_p.D396N|KDM4C_ENST00000381306.3_Missense_Mutation_p.D396N|KDM4C_ENST00000535193.1_Missense_Mutation_p.D418N|KDM4C_ENST00000442236.2_Missense_Mutation_p.D215N|KDM4C_ENST00000536108.1_Missense_Mutation_p.D215N	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	396			D -> N (in dbSNP:rs2296067).		histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						AGATGAAGTCGATGGGGCAGA	0.512													G|||	1639	0.327276	0.205	0.3213	5008	,	,		19889	0.4286		0.2227	False		,,,				2504	0.5				p.D418N		Atlas-SNP	.											KDM4C_ENST00000381306,NS,carcinoma,0,4	KDM4C	186	4	0			c.G1252A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	937,3469	357.6+/-314.0	103,731,1369	94.0	84.0	87.0		1186,1186,1252,1186	-0.9	0.0	9	dbSNP_100	87	1886,6714	334.9+/-321.2	200,1486,2614	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	23,23,23,23	303,2217,3983	AA,AG,GG		21.9302,21.2665,21.7054	benign,benign,benign,benign	396/1048,396/814,418/836,396/1057	6984236	2823,10183	2203	4300	6503	SO:0001583	missense	23081	exon10			GAAGTCGATGGGG	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.1186G>A	9.37:g.6984236G>A	ENSP00000370710:p.Asp396Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	620	0.2838827838827839	92	0.18699186991869918	111	0.30662983425414364	236	0.4125874125874126	181	0.23878627968337732	G	10.61	1.398802	0.25291	0.212665	0.219302	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.17370	2.39;2.39;2.56;2.47;2.77;2.28;3.53	5.24	-0.93	0.10441	.	2.473570	0.00904	N	0.002391	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B	0.15719	0.0;0.003;0.008;0.005;0.014	B;B;B;B;B	0.10450	0.0;0.002;0.001;0.003;0.005	T	0.46133	-0.9213	9	0.17369	T	0.5	-29.4604	11.5707	0.50832	0.4732:0.0:0.5268:0.0	rs2296067;rs52808244;rs60515857;rs2296067	215;396;418;396;396	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	N	418;396;396;396;215;215;83	ENSP00000442382:D418N;ENSP00000445427:D396N;ENSP00000370710:D396N;ENSP00000370707:D396N;ENSP00000409353:D215N;ENSP00000440656:D215N;ENSP00000405739:D83N	ENSP00000370707:D396N	D	+	1	0	KDM4C	6974236	0.004000	0.15560	0.000000	0.03702	0.021000	0.10359	0.744000	0.26245	-0.118000	0.11851	-0.137000	0.14449	GAT	G|0.743;A|0.257	0.257	strong		0.512	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
HCFC1	3054	hgsc.bcm.edu	37	X	153215839	153215839	+	Silent	SNP	G	G	A	rs3027875		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153215839G>A	ENST00000310441.7	-	24	6825	c.5859C>T	c.(5857-5859)tgC>tgT	p.C1953C	HCFC1_ENST00000354233.3_Silent_p.C1884C|HCFC1_ENST00000369984.4_Silent_p.C1998C	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1953	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)					GGCTGGGCCCGCAGTACACCC	0.652													G|||	722	0.191258	0.0197	0.1816	3775	,	,		11049	0.002		0.4821	False		,,,				2504	0.0849				p.C1953C		Atlas-SNP	.											.	HCFC1	284	.	0			c.C5859T						PASS	.	G		298,3211		22,216,38,1232,531	41.0	47.0	45.0		5859	-5.3	0.9	X	dbSNP_102	45	4106,2410		924,1122,1136,313,662	no	coding-synonymous	HCFC1	NM_005334.2		946,1338,1174,1545,1193	AA,AG,A,GG,G		36.9859,8.4924,43.9302		1953/2036	153215839	4404,5621	2039	4157	6196	SO:0001819	synonymous_variant	3054	exon24			GGGCCCGCAGTAC		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.5859C>T	X.37:g.153215839G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	71	67	0.943662	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1	475	0.2863170584689572	17	0.035269709543568464	46	0.15333333333333332	2	0.0034965034965034965	261	0.4943181818181818	G	10.91	1.485602	0.26686	0.084924	0.630141	ENSG00000172534	ENST00000444191	.	.	.	5.42	-5.26	0.02772	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11108	-1.0601	3	.	.	.	.	15.8112	0.78565	0.7732:0.0:0.2268:0.0	rs3027875	.	.	.	W	529	.	.	R	-	1	2	HCFC1	152869033	0.009000	0.17119	0.935000	0.37517	0.942000	0.58702	-0.600000	0.05693	-1.195000	0.02680	-0.411000	0.06167	CGG	G|0.712;A|0.288	0.288	strong		0.652	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
SLC45A4	57210	hgsc.bcm.edu	37	8	142228909	142228909	+	Missense_Mutation	SNP	G	G	A	rs753778	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:142228909G>A	ENST00000024061.3	-	4	984	c.677C>T	c.(676-678)cCg>cTg	p.P226L	SLC45A4_ENST00000517878.1_Missense_Mutation_p.P277L|SLC45A4_ENST00000433583.2_Missense_Mutation_p.P219L|SLC45A4_ENST00000519067.1_Missense_Mutation_p.P226L	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			GACGCCGTGCGGCTCGCCCCC	0.682													G|||	1880	0.375399	0.3737	0.366	5008	,	,		15297	0.4038		0.2942	False		,,,				2504	0.4387				p.P226L		Atlas-SNP	.											.	SLC45A4	71	.	0			c.C677T						PASS	.	G	LEU/PRO	1732,2674	500.5+/-364.7	345,1042,816	64.0	69.0	68.0		677	-10.6	0.0	8	dbSNP_86	68	2448,6150	391.5+/-343.7	352,1744,2203	yes	missense	SLC45A4	NM_001080431.1	98	697,2786,3019	AA,AG,GG		28.4717,39.31,32.144	benign	226/799	142228909	4180,8824	2203	4299	6502	SO:0001583	missense	57210	exon4			CCGTGCGGCTCGC	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"""Solute carriers"""	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.677C>T	8.37:g.142228909G>A	ENSP00000024061:p.Pro226Leu	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	87	55	0.632184	NM_001080431	Q6ZRI2|Q9ULU3	Missense_Mutation	SNP	ENST00000024061.3	37	CCDS34948.1	766	0.3507326007326007	194	0.3943089430894309	136	0.3756906077348066	220	0.38461538461538464	216	0.2849604221635884	G	6.417	0.445021	0.12164	0.3931	0.284717	ENSG00000022567	ENST00000519067;ENST00000517878;ENST00000433583;ENST00000024061;ENST00000520137	T;T;T;T;T	0.42513	2.47;2.46;2.47;2.44;0.97	5.3	-10.6	0.00265	.	1.534320	0.03423	N	0.206591	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B;B;B	0.13594	0.004;0.008;0.001	B;B;B	0.09377	0.002;0.002;0.004	T	0.15549	-1.0433	9	0.36615	T	0.2	-4.4495	9.9976	0.41909	0.2636:0.0:0.5968:0.1396	rs753778;rs57687708;rs753778	277;226;226	E7EV90;Q5BKX6-3;Q5BKX6-2	.;.;.	L	226;277;219;226;84	ENSP00000429059:P226L;ENSP00000428137:P277L;ENSP00000400799:P219L;ENSP00000024061:P226L;ENSP00000429033:P84L	ENSP00000024061:P226L	P	-	2	0	SLC45A4	142298091	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	0.059000	0.14322	-1.756000	0.01318	-2.934000	0.00087	CCG	G|0.657;A|0.343	0.343	strong		0.682	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
SLC22A5	6584	hgsc.bcm.edu	37	5	131721174	131721174	+	Silent	SNP	A	A	G	rs274558	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131721174A>G	ENST00000245407.3	+	4	1028	c.807A>G	c.(805-807)ctA>ctG	p.L269L	SLC22A5_ENST00000435065.2_Silent_p.L293L	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	269					carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	CGGGGGTGCTATGCGTGGCAC	0.557											OREG0016766	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2435	0.486222	0.3434	0.33	5008	,	,		16426	0.6736		0.4145	False		,,,				2504	0.6708				p.L269L		Atlas-SNP	.											.	SLC22A5	34	.	0			c.A807G						PASS	.	G		1555,2851	668.4+/-402.0	264,1027,912	113.0	100.0	104.0		807	-0.8	1.0	5	dbSNP_79	104	3365,5235	642.5+/-399.8	674,2017,1609	no	coding-synonymous	SLC22A5	NM_003060.3		938,3044,2521	GG,GA,AA		39.1279,35.2928,37.8287		269/558	131721174	4920,8086	2203	4300	6503	SO:0001819	synonymous_variant	6584	exon4			GGTGCTATGCGTG	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"""Solute carriers"""	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.807A>G	5.37:g.131721174A>G		Somatic	108	0	0	1589	WXS	Illumina HiSeq	Phase_I	113	67	0.59292	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Silent	SNP	ENST00000245407.3	37	CCDS4154.1																																																																																			A|0.579;G|0.421	0.421	strong		0.557	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	
APOA4	337	hgsc.bcm.edu	37	11	116692324	116692324	+	Silent	SNP	G	G	A	rs2234668	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:116692324G>A	ENST00000357780.3	-	3	564	c.450C>T	c.(448-450)gcC>gcT	p.A150A		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	150	13 X 22 AA approximate tandem repeats.				cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		GCAGCTGCTCGGCCTGCGTGC	0.692													G|||	125	0.0249601	0.0053	0.0231	5008	,	,		17935	0.0		0.0427	False		,,,				2504	0.0603				p.A150A		Atlas-SNP	.											.	APOA4	51	.	0			c.C450T						PASS	.	G		42,4358	44.6+/-78.6	0,42,2158	43.0	41.0	42.0		450	-10.0	0.0	11	dbSNP_98	42	434,8156	131.7+/-189.4	11,412,3872	no	coding-synonymous	APOA4	NM_000482.3		11,454,6030	AA,AG,GG		5.0524,0.9545,3.6644		150/397	116692324	476,12514	2200	4295	6495	SO:0001819	synonymous_variant	337	exon3			CTGCTCGGCCTGC		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.450C>T	11.37:g.116692324G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	7	0.194444	NM_000482	A8MSL6|Q14CW8|Q6Q787	Silent	SNP	ENST00000357780.3	37	CCDS31681.1																																																																																			G|0.971;A|0.029	0.029	strong		0.692	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
RTFDC1	51507	hgsc.bcm.edu	37	20	55088404	55088404	+	Missense_Mutation	SNP	A	A	G	rs1059768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:55088404A>G	ENST00000023939.4	+	6	618	c.511A>G	c.(511-513)Atg>Gtg	p.M171V	RTFDC1_ENST00000395881.3_Missense_Mutation_p.M171V|RTFDC1_ENST00000357348.5_Missense_Mutation_p.M201V|GCNT7_ENST00000243913.4_Intron	NM_001283035.1|NM_001283036.1|NM_016407.3	NP_001269964.1|NP_001269965.1|NP_057491.2	Q9BY42	RTF2_HUMAN	replication termination factor 2 domain containing 1	171			M -> V (in dbSNP:rs1059768). {ECO:0000269|PubMed:10931946, ECO:0000269|PubMed:11042152, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.														TGATGTCATCATGCTCAATGG	0.547													G|||	4333	0.865216	0.8699	0.8631	5008	,	,		19666	0.9911		0.8002	False		,,,				2504	0.7975				p.M171V		Atlas-SNP	.											.	.	.	.	0			c.A511G						PASS	.	G	VAL/MET,	3783,623	260.7+/-263.8	1625,533,45	142.0	87.0	106.0		511,	4.7	0.7	20	dbSNP_86	106	6744,1856	321.7+/-315.2	2659,1426,215	yes	missense,intron	C20orf43,GCNT7	NM_016407.3,NM_080615.1	21,	4284,1959,260	GG,GA,AA		21.5814,14.1398,19.0604	benign,	171/307,	55088404	10527,2479	2203	4300	6503	SO:0001583	missense	51507	exon6			GTCATCATGCTCA	AF161513	CCDS13453.1, CCDS63316.1, CCDS63317.1	20q13	2012-10-29	2012-10-29	2012-10-29	ENSG00000022277	ENSG00000022277			15890	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 43"""	C20orf43			Standard	NM_001283035		Approved	HSPC164, CDAO5	uc002xxt.2	Q9BY42	OTTHUMG00000032801	ENST00000023939.4:c.511A>G	20.37:g.55088404A>G	ENSP00000023939:p.Met171Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_016407	E1P5Z9|Q9BYL7|Q9HCV9|Q9NX29|Q9NZZ8|Q9P002|Q9UHW3	Missense_Mutation	SNP	ENST00000023939.4	37	CCDS13453.1	1891	0.8658424908424909	426	0.8658536585365854	299	0.8259668508287292	568	0.993006993006993	598	0.7889182058047494	G	2.589	-0.295598	0.05532	0.858602	0.784186	ENSG00000022277	ENST00000023939;ENST00000395881;ENST00000357348;ENST00000449062	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.62	4.67	0.58626	.	0.120651	0.56097	N	0.000028	T	0.00012	0.0000	N	0.00170	-1.935	0.09310	P	1.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.35549	-0.9784	9	0.06757	T	0.87	-14.7738	7.6233	0.28197	0.1452:0.135:0.7198:0.0	rs1059768;rs3171191;rs17380207;rs17856084;rs57309016;rs1059768	201;171;171	A8MSH5;A2A2L6;Q9BY42	.;.;CT043_HUMAN	V	171;171;201;201	ENSP00000023939:M171V;ENSP00000379220:M171V;ENSP00000349906:M201V;ENSP00000400322:M201V	ENSP00000023939:M171V	M	+	1	0	C20orf43	54521811	0.992000	0.36948	0.675000	0.29917	0.927000	0.56198	1.467000	0.35321	0.740000	0.32651	-0.119000	0.15052	ATG	A|0.172;G|0.828	0.828	strong		0.547	RTFDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079817.2	NM_016407	
TJP2	9414	hgsc.bcm.edu	37	9	71862975	71862975	+	Silent	SNP	C	C	T	rs2282336	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:71862975C>T	ENST00000377245.4	+	19	2923	c.2715C>T	c.(2713-2715)acC>acT	p.T905T	TJP2_ENST00000498204.1_3'UTR|TJP2_ENST00000453658.2_Silent_p.T882T|TJP2_ENST00000348208.4_Silent_p.T905T|TJP2_ENST00000265384.7_Silent_p.T905T|TJP2_ENST00000539225.1_Silent_p.T936T|TJP2_ENST00000535702.1_Silent_p.T909T	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	905					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						CCTACTTAACCGCCATGGGCG	0.557													C|||	1423	0.284145	0.1664	0.451	5008	,	,		18768	0.4514		0.2197	False		,,,				2504	0.2188				p.T936T		Atlas-SNP	.											.	TJP2	120	.	0			c.C2808T						PASS	.	C	,,,,,	754,3652	307.5+/-290.0	78,598,1527	94.0	84.0	87.0		2646,2727,2808,2715,2715,2715	-3.0	1.0	9	dbSNP_100	87	1815,6785	323.8+/-316.2	197,1421,2682	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,,,,	275,2019,4209	TT,TC,CC		21.1047,17.113,19.7524	,,,,,	882/1021,909/1158,936/1222,905/994,905/1191,905/1044	71862975	2569,10437	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon19			CTTAACCGCCATG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.2715C>T	9.37:g.71862975C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			C|0.770;T|0.230	0.230	strong		0.557	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
SYCE1	93426	hgsc.bcm.edu	37	10	135369532	135369532	+	Missense_Mutation	SNP	T	T	C	rs3747881	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135369532T>C	ENST00000343131.5	-	9	652	c.548A>G	c.(547-549)aAg>aGg	p.K183R	SYCE1_ENST00000432597.2_Missense_Mutation_p.K147R|SYCE1_ENST00000368517.3_Missense_Mutation_p.K147R|SPRN_ENST00000541506.1_Intron	NM_001143764.1	NP_001137236.1	Q8N0S2	SYCE1_HUMAN	synaptonemal complex central element protein 1	183			K -> R (in dbSNP:rs3747881). {ECO:0000269|PubMed:15489334}.		synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(2)|stomach(3)|urinary_tract(1)	19		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		ACAAATCTCCTTTGCCAGCCG	0.552													C|||	988	0.197284	0.1997	0.1844	5008	,	,		21691	0.2698		0.1093	False		,,,				2504	0.2188				p.K183R		Atlas-SNP	.											.	SYCE1	81	.	0			c.A548G						PASS	.	C	ARG/LYS,ARG/LYS,ARG/LYS	722,3684	748.4+/-411.9	41,640,1522	99.0	87.0	91.0		548,548,440	-3.9	0.0	10	dbSNP_107	91	807,7793	779.6+/-407.7	45,717,3538	yes	missense,missense,missense	SYCE1	NM_001143763.1,NM_001143764.1,NM_130784.2	26,26,26	86,1357,5060	CC,CT,TT		9.3837,16.3867,11.7561	benign,benign,benign	183/319,183/352,147/283	135369532	1529,11477	2203	4300	6503	SO:0001583	missense	93426	exon9			ATCTCCTTTGCCA	AY027808	CCDS7687.1, CCDS44500.1, CCDS44501.1	10q26.3	2009-03-12	2005-09-27	2005-09-27	ENSG00000171772	ENSG00000171772			28852	protein-coding gene	gene with protein product	"""cancer/testis antigen 76"""	611486	"""chromosome 10 open reading frame 94"""	C10orf94		11829491	Standard	NM_130784		Approved	bA108K14.6, CT76	uc001lno.2	Q8N0S2	OTTHUMG00000019321	ENST00000343131.5:c.548A>G	10.37:g.135369532T>C	ENSP00000341282:p.Lys183Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_001143763	B2RC80|Q9BWU3|Q9BWU4	Missense_Mutation	SNP	ENST00000343131.5	37	CCDS44501.1	404	0.184981684981685	93	0.18902439024390244	68	0.1878453038674033	153	0.2674825174825175	90	0.11873350923482849	C	0.855	-0.737129	0.03111	0.163867	0.093837	ENSG00000171772	ENST00000303903;ENST00000432597;ENST00000368517;ENST00000343131	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	4.38	-3.92	0.04155	.	0.864322	0.10196	N	0.704037	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.28996	-1.0026	9	0.05959	T	0.93	-9.816	7.6589	0.28392	0.133:0.1995:0.0:0.6675	rs3747881;rs17857025;rs52827544;rs60545805;rs3747881	55;183;147	Q8N0S2-3;Q8N0S2;Q8N0S2-2	.;SYCE1_HUMAN;.	R	183;147;147;183	ENSP00000303978:K183R;ENSP00000411779:K147R;ENSP00000357503:K147R;ENSP00000341282:K183R	ENSP00000303978:K183R	K	-	2	0	SYCE1	135219522	0.001000	0.12720	0.005000	0.12908	0.017000	0.09413	-1.544000	0.02192	-1.244000	0.02516	-0.119000	0.15052	AAG	T|0.851;C|0.149	0.149	strong		0.552	SYCE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_201564	
EXT1	2131	hgsc.bcm.edu	37	8	118832020	118832020	+	Silent	SNP	G	G	A	rs17439693	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:118832020G>A	ENST00000378204.2	-	6	2237	c.1431C>T	c.(1429-1431)ccC>ccT	p.P477P		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	477					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			TGAATTTGGAGGGGGGCTTTA	0.517			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Langer-Giedion syndrome;Hereditary Multiple Exostoses				G|||	602	0.120208	0.0787	0.1772	5008	,	,		18267	0.0308		0.2445	False		,,,				2504	0.1002				p.P477P		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.C1431T						PASS	.	G		467,3939	217.4+/-235.8	21,425,1757	69.0	78.0	75.0		1431	-3.1	1.0	8	dbSNP_123	75	1670,6930	302.0+/-305.7	181,1308,2811	no	coding-synonymous	EXT1	NM_000127.2		202,1733,4568	AA,AG,GG		19.4186,10.5992,16.4309		477/747	118832020	2137,10869	2203	4300	6503	SO:0001819	synonymous_variant	2131	exon6	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	TTTGGAGGGGGGC	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3512	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608177	"""Langer-Giedion syndrome chromosome region"", ""exostoses (multiple) 1"", ""exostosin 1"""	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1431C>T	8.37:g.118832020G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	123	122	0.99187	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	37	CCDS6324.1																																																																																			G|0.849;A|0.151	0.151	strong		0.517	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127	
PAAF1	80227	hgsc.bcm.edu	37	11	73620537	73620537	+	Missense_Mutation	SNP	C	C	G	rs3741138	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:73620537C>G	ENST00000310571.3	+	7	679	c.626C>G	c.(625-627)gCc>gGc	p.A209G	PAAF1_ENST00000376384.5_Missense_Mutation_p.A192G|PAAF1_ENST00000541951.1_Missense_Mutation_p.A94G|PAAF1_ENST00000536003.1_Missense_Mutation_p.A192G|PAAF1_ENST00000544909.1_Missense_Mutation_p.A210G|PAAF1_ENST00000544552.1_Missense_Mutation_p.A192G|PAAF1_ENST00000535604.1_Missense_Mutation_p.A94G	NM_025155.2	NP_079431.1	Q9BRP4	PAAF1_HUMAN	proteasomal ATPase-associated factor 1	209			A -> G (in dbSNP:rs3741138). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		viral process (GO:0016032)	proteasome complex (GO:0000502)				breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	Breast(11;7.42e-05)					GGGCGCTCAGCCTGCTTGGGA	0.552													C|||	610	0.121805	0.1188	0.0778	5008	,	,		19099	0.1716		0.0984	False		,,,				2504	0.1299				p.A209G		Atlas-SNP	.											.	PAAF1	39	.	0			c.C626G						PASS	.	C	GLY/ALA	448,3952	216.8+/-235.3	18,412,1770	200.0	169.0	179.0		626	4.2	1.0	11	dbSNP_107	179	841,7745	194.2+/-239.7	43,755,3495	yes	missense	PAAF1	NM_025155.1	60	61,1167,5265	GG,GC,CC		9.795,10.1818,9.9261	benign	209/393	73620537	1289,11697	2200	4293	6493	SO:0001583	missense	80227	exon7			GCTCAGCCTGCTT	BC006142	CCDS8226.1, CCDS58157.1, CCDS58158.1	11q13.4	2013-05-21	2007-08-16	2007-08-16	ENSG00000175575	ENSG00000175575		"""WD repeat domain containing"""	25687	protein-coding gene	gene with protein product			"""WD repeat domain 71"""	WDR71		15831487, 17317272, 17289585	Standard	NM_001267803		Approved	FLJ11848, Rpn14	uc001ouk.2	Q9BRP4	OTTHUMG00000168062	ENST00000310571.3:c.626C>G	11.37:g.73620537C>G	ENSP00000311665:p.Ala209Gly	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	195	159	0.815385	NM_025155	A6NDR5|B4DPB0|B7ZAS9|Q4G165|Q53HS9|Q7Z500|Q8TBU6|Q9HAB6	Missense_Mutation	SNP	ENST00000310571.3	37	CCDS8226.1	265|265	0.12133699633699634|0.12133699633699634	52|52	0.10569105691056911|0.10569105691056911	39|39	0.10773480662983426|0.10773480662983426	103|103	0.18006993006993008|0.18006993006993008	71|71	0.09366754617414248|0.09366754617414248	C|C	11.82|11.82	1.753587|1.753587	0.31046|0.31046	0.101818|0.101818	0.09795|0.09795	ENSG00000175575|ENSG00000175575	ENST00000541951;ENST00000310571;ENST00000504441;ENST00000543814;ENST00000535604;ENST00000542293;ENST00000536003;ENST00000544552;ENST00000546039;ENST00000376384;ENST00000544909|ENST00000540659	T;T;T;T;T;T;T;T;T;T;T|T	0.81415|0.80909	2.21;2.21;-1.49;-1.49;2.21;-1.49;2.21;2.21;2.21;2.21;2.21|-1.43	5.06|5.06	4.15|4.15	0.48705|0.48705	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.166885|.	0.40728|.	N|.	0.001026|.	T|T	0.00695|0.00695	0.0023|0.0023	L|L	0.54323|0.54323	1.7|1.7	0.27539|0.27539	P|P	0.9508404|0.9508404	B;B|.	0.22800|.	0.002;0.075|.	B;B|.	0.19946|.	0.005;0.027|.	T|T	0.22382|0.22382	-1.0218|-1.0218	9|6	0.35671|0.66056	T|D	0.21|0.02	-6.468|-6.468	14.292|14.292	0.66284|0.66284	0.0:0.8501:0.1499:0.0|0.0:0.8501:0.1499:0.0	rs3741138;rs17845650;rs17858583;rs52834465;rs3741138|rs3741138;rs17845650;rs17858583;rs52834465;rs3741138	192;209|.	Q9BRP4-2;Q9BRP4|.	.;PAAF1_HUMAN|.	G|R	94;209;192;192;94;94;192;192;73;192;210|49	ENSP00000441333:A94G;ENSP00000311665:A209G;ENSP00000439747:A192G;ENSP00000438894:A192G;ENSP00000438789:A94G;ENSP00000439143:A94G;ENSP00000438124:A192G;ENSP00000441494:A192G;ENSP00000439877:A73G;ENSP00000365564:A192G;ENSP00000438071:A210G|ENSP00000442434:S49R	ENSP00000311665:A209G|ENSP00000442434:S49R	A|S	+|+	2|3	0|2	PAAF1|PAAF1	73298185|73298185	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.746000|0.746000	0.42486|0.42486	2.779000|2.779000	0.47734|0.47734	1.135000|1.135000	0.42183|0.42183	-0.304000|-0.304000	0.09214|0.09214	GCC|AGC	C|0.891;G|0.109	0.109	strong		0.552	PAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397885.1	NM_025155	
ZNF438	220929	hgsc.bcm.edu	37	10	31138817	31138817	+	Missense_Mutation	SNP	G	G	A	rs10160116	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:31138817G>A	ENST00000361310.3	-	6	846	c.517C>T	c.(517-519)Ccc>Tcc	p.P173S	ZNF438_ENST00000442986.1_Missense_Mutation_p.P173S|ZNF438_ENST00000452305.1_Missense_Mutation_p.P163S|ZNF438_ENST00000331737.6_Missense_Mutation_p.P163S|ZNF438_ENST00000538351.2_Missense_Mutation_p.P124S|ZNF438_ENST00000413025.1_Missense_Mutation_p.P173S|ZNF438_ENST00000375311.1_Intron|ZNF438_ENST00000444692.2_Missense_Mutation_p.P163S|ZNF438_ENST00000436087.2_Missense_Mutation_p.P173S			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	173			P -> S (in dbSNP:rs10160116). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		negative regulation of transcription, DNA-templated (GO:0045892)|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(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				AATGGACTGGGTTTGTACAGG	0.537													G|||	1880	0.375399	0.326	0.4308	5008	,	,		19303	0.3978		0.3479	False		,,,				2504	0.408				p.P173S		Atlas-SNP	.											.	ZNF438	90	.	0			c.C517T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	1464,2942	472.4+/-356.4	257,950,996	184.0	180.0	181.0		517,517,517,370,487,487,517	1.2	0.0	10	dbSNP_119	181	3242,5358	487.8+/-372.2	607,2028,1665	yes	missense,missense,missense,missense,missense,missense,missense	ZNF438	NM_001143766.1,NM_001143767.1,NM_001143768.1,NM_001143769.1,NM_001143770.1,NM_001143771.1,NM_182755.2	74,74,74,74,74,74,74	864,2978,2661	AA,AG,GG		37.6977,33.2274,36.1833	benign,benign,benign,benign,benign,benign,benign	173/829,173/829,173/829,124/780,163/819,163/819,173/829	31138817	4706,8300	2203	4300	6503	SO:0001583	missense	220929	exon7			GACTGGGTTTGTA	AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"""Zinc fingers, C2H2-type"""	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.517C>T	10.37:g.31138817G>A	ENSP00000354663:p.Pro173Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	37	CCDS7168.1	831	0.3804945054945055	159	0.3231707317073171	164	0.4530386740331492	232	0.40559440559440557	276	0.3641160949868074	G	4.324	0.059571	0.08339	0.332274	0.376977	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351	T;T;T;T;T;T;T;T	0.09073	3.02;3.03;3.03;3.03;3.03;3.02;3.02;3.03	5.63	1.18	0.20946	.	0.795778	0.12376	N	0.474327	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B;B	0.21225	0.031;0.053	B;B	0.17722	0.009;0.019	T	0.45848	-0.9233	9	0.06757	T	0.87	-9.3051	2.5867	0.04832	0.0921:0.3113:0.2257:0.3709	rs10160116;rs59589778;rs10160116	173;163	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	S	163;173;173;173;173;163;163;124	ENSP00000333571:P163S;ENSP00000354663:P173S;ENSP00000406934:P173S;ENSP00000412363:P173S;ENSP00000387546:P173S;ENSP00000413060:P163S;ENSP00000410898:P163S;ENSP00000445461:P124S	ENSP00000333571:P163S	P	-	1	0	ZNF438	31178823	0.000000	0.05858	0.001000	0.08648	0.285000	0.27093	0.165000	0.16564	0.010000	0.14839	0.655000	0.94253	CCC	G|0.641;A|0.359	0.359	strong		0.537	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755	
SCARF1	8578	hgsc.bcm.edu	37	17	1542190	1542190	+	Missense_Mutation	SNP	G	G	A	rs2272011	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1542190G>A	ENST00000263071.4	-	8	1323	c.1274C>T	c.(1273-1275)gCg>gTg	p.A425V	SCARF1_ENST00000571272.1_Missense_Mutation_p.A425V|SCARF1_ENST00000348987.3_Missense_Mutation_p.A339V|SCARF1_ENST00000574545.1_5'Flank	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	425			A -> V (in dbSNP:rs2272011). {ECO:0000269|PubMed:11978792, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8590280, ECO:0000269|PubMed:9395444, ECO:0000269|Ref.5}.		cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AAGGCTGCCCGCGATGAGGGC	0.622													A|||	3339	0.666733	0.5197	0.6916	5008	,	,		14491	0.878		0.6133	False		,,,				2504	0.6851				p.A425V		Atlas-SNP	.											SCARF1,caecum,carcinoma,0,2	SCARF1	46	2	0			c.C1274T						PASS	.	A	VAL/ALA,VAL/ALA,VAL/ALA	2357,2049	552.0+/-378.4	649,1059,495	46.0	48.0	47.0		1274,1274,1016	-3.5	0.0	17	dbSNP_100	47	5140,3460	500.8+/-375.3	1511,2118,671	yes	missense,missense,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	64,64,64	2160,3177,1166	AA,AG,GG		40.2326,46.5048,42.3574	benign,benign,benign	425/831,425/570,339/745	1542190	7497,5509	2203	4300	6503	SO:0001583	missense	8578	exon8			CTGCCCGCGATGA	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1274C>T	17.37:g.1542190G>A	ENSP00000263071:p.Ala425Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_145350	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	1485	0.679945054945055	270	0.5487804878048781	246	0.6795580110497238	508	0.8881118881118881	461	0.6081794195250659	A	12.18	1.859897	0.32884	0.534952	0.597674	ENSG00000074660	ENST00000263071;ENST00000348987;ENST00000434376	T;T	0.39592	1.07;1.07	5.51	-3.51	0.04696	.	0.481912	0.17375	N	0.176501	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B;B;B	0.24258	0.007;0.1;0.082	B;B;B	0.17722	0.003;0.019;0.016	T	0.18304	-1.0341	9	0.32370	T	0.25	-2.7866	8.8818	0.35378	0.4624:0.0977:0.4398:0.0	rs2272011;rs58871060;rs2272011	339;425;425	Q14162-2;Q14162;Q14162-3	.;SREC_HUMAN;.	V	425;339;425	ENSP00000263071:A425V;ENSP00000323964:A339V	ENSP00000263071:A425V	A	-	2	0	SCARF1	1488940	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.070000	0.11523	-1.023000	0.03342	-3.352000	0.00042	GCG	G|0.385;A|0.615	0.615	strong		0.622	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
RRAGC	64121	hgsc.bcm.edu	37	1	39311617	39311617	+	Silent	SNP	T	T	G	rs11549874	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:39311617T>G	ENST00000373001.3	-	6	1218	c.1042A>C	c.(1042-1044)Aga>Cga	p.R348R	RRAGC_ENST00000474456.1_5'UTR	NM_022157.2	NP_071440.1			Ras-related GTP binding C											endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)	10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				TTACCTTTTCTTTCAAAGCTT	0.308													G|||	216	0.043131	0.0484	0.0274	5008	,	,		18881	0.001		0.0716	False		,,,				2504	0.0613				p.R348R		Atlas-SNP	.											.	RRAGC	28	.	0			c.A1042C						PASS	.	G		185,4219	805.8+/-415.8	4,177,2021	70.0	70.0	70.0		1042	3.6	1.0	1	dbSNP_132	70	515,8079	794.2+/-407.5	18,479,3800	no	coding-synonymous	RRAGC	NM_022157.2		22,656,5821	GG,GT,TT		5.9926,4.2007,5.3854		348/400	39311617	700,12298	2202	4297	6499	SO:0001819	synonymous_variant	64121	exon6			CTTTTCTTTCAAA	AF323609	CCDS430.1	1p34	2008-02-05			ENSG00000116954	ENSG00000116954			19902	protein-coding gene	gene with protein product		608267				11073942	Standard	NM_022157		Approved	GTR2, FLJ13311	uc001ccq.3	Q9HB90	OTTHUMG00000000490	ENST00000373001.3:c.1042A>C	1.37:g.39311617T>G		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	209	104	0.497608	NM_022157		Silent	SNP	ENST00000373001.3	37	CCDS430.1																																																																																			T|0.948;G|0.052	0.052	strong		0.308	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157	
DENND2D	79961	hgsc.bcm.edu	37	1	111730901	111730901	+	Silent	SNP	C	C	T	rs608881	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:111730901C>T	ENST00000357640.4	-	11	1420	c.1191G>A	c.(1189-1191)gaG>gaA	p.E397E	DENND2D_ENST00000369752.5_Silent_p.E394E	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	397	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		GCCCATTTGCCTCCCGCTTGA	0.488													C|||	736	0.146965	0.1536	0.1628	5008	,	,		19612	0.002		0.2286	False		,,,				2504	0.1922				p.E397E		Atlas-SNP	.											.	DENND2D	50	.	0			c.G1191A						PASS	.	C		733,3673	303.0+/-287.7	58,617,1528	88.0	91.0	90.0		1191	-1.1	1.0	1	dbSNP_83	90	1911,6689	337.7+/-322.4	218,1475,2607	no	coding-synonymous	DENND2D	NM_024901.3		276,2092,4135	TT,TC,CC		22.2209,16.6364,20.3291		397/472	111730901	2644,10362	2203	4300	6503	SO:0001819	synonymous_variant	79961	exon11			ATTTGCCTCCCGC		CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"""DENN/MADD domain containing"""	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.1191G>A	1.37:g.111730901C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	99	36	0.363636	NM_024901	Q5T5V6|Q9BSU0	Silent	SNP	ENST00000357640.4	37	CCDS831.1																																																																																			T|0.178;G|0.008	0.178	strong		0.488	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901	
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 GAIIx	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_ENST00000377848.3_Missense_Mutation_p.R1033W|ACACB_ENST00000377854.5_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	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	115	51	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	
ANKRD18A	253650	hgsc.bcm.edu	37	9	38595886	38595886	+	Missense_Mutation	SNP	T	T	C	rs2996347	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:38595886T>C	ENST00000399703.5	-	9	1825	c.1451A>G	c.(1450-1452)aAt>aGt	p.N484S		NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	484			N -> S (in dbSNP:rs2996347).					p.N484S(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						TTTTAAGGTATTGAACTTCAC	0.413													.|||	1662	0.331869	0.4826	0.317	5008	,	,		20583	0.4603		0.2187	False		,,,				2504	0.1227				p.N484S		Atlas-SNP	.											ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	1	Substitution - Missense(1)	stomach(1)	c.A1451G						PASS	.	T	SER/ASN	628,756		136,356,200	95.0	67.0	75.0		1451	1.4	0.0	9	dbSNP_101	75	651,2529		66,519,1005	no	missense	ANKRD18A	NM_147195.2	46	202,875,1205	CC,CT,TT		20.4717,45.3757,28.0237	possibly-damaging	484/993	38595886	1279,3285	692	1590	2282	SO:0001583	missense	253650	exon9			AAGGTATTGAACT	AB095935	CCDS55311.1	9p13.1	2013-01-10			ENSG00000180071	ENSG00000180071		"""Ankyrin repeat domain containing"""	23643	protein-coding gene	gene with protein product							Standard	NM_147195		Approved	KIAA2015, FLJ35740	uc004abg.4	Q8IVF6	OTTHUMG00000019950	ENST00000399703.5:c.1451A>G	9.37:g.38595886T>C	ENSP00000382610:p.Asn484Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_147195	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Missense_Mutation	SNP	ENST00000399703.5	37	CCDS55311.1	745	0.3411172161172161	249	0.5060975609756098	99	0.27348066298342544	224	0.3916083916083916	173	0.22823218997361477	T	5.964	0.361918	0.11296	0.453757	0.204717	ENSG00000180071	ENST00000399703	T	0.17370	2.28	1.35	1.35	0.21983	.	.	.	.	.	T	0.00012	0.0000	N	0.25286	0.73	0.29173	P	0.877008	B	0.12013	0.005	B	0.01281	0.0	T	0.44314	-0.9336	8	0.35671	T	0.21	.	6.8814	0.24174	0.0:0.0:0.0:1.0	rs2996347;rs7036857;rs59857660;rs2996347	484	Q8IVF6	AN18A_HUMAN	S	484	ENSP00000382610:N484S	ENSP00000382610:N484S	N	-	2	0	ANKRD18A	38585886	0.234000	0.23783	0.009000	0.14445	0.065000	0.16274	0.494000	0.22467	0.892000	0.36259	0.113000	0.15668	AAT	T|0.680;C|0.320	0.320	strong		0.413	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052506.3		
KLK1	3816	hgsc.bcm.edu	37	19	51323232	51323232	+	Missense_Mutation	SNP	T	T	C	rs5517	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51323232T>C	ENST00000301420.2	-	4	591	c.556A>G	c.(556-558)Aaa>Gaa	p.K186E	KLK1_ENST00000448701.2_Missense_Mutation_p.K84E|CTD-2568A17.5_ENST00000326989.5_lincRNA	NM_002257.2	NP_002248.1	P06870	KLK1_HUMAN	kallikrein 1	186	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		K -> E (in dbSNP:rs5517). {ECO:0000269|PubMed:3004571, ECO:0000269|PubMed:3853975, ECO:0000269|Ref.7}.			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(4)|lung(7)|urinary_tract(1)	13		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00399)	Aprotinin(DB06692)	TGGGCTTTTTTGCACTCATCA	0.557													t|||	1700	0.339457	0.1815	0.4568	5008	,	,		19193	0.5972		0.2674	False		,,,				2504	0.2781				p.K186E		Atlas-SNP	.											.	KLK1	27	.	0			c.A556G	GRCh37	CM074309	KLK1	M	rs5517	PASS	.		GLU/LYS	865,3541		80,705,1418	109.0	86.0	94.0		556	-0.6	0.0	19	dbSNP_52	94	2310,6290		313,1684,2303	yes	missense	KLK1	NM_002257.2	56	393,2389,3721	CC,CT,TT		26.8605,19.6323,24.4118	benign	186/263	51323232	3175,9831	2203	4300	6503	SO:0001583	missense	3816	exon4			CTTTTTTGCACTC	L10038	CCDS12804.1	19q13.3	2008-02-05	2006-10-27			ENSG00000167748	3.4.21.35	"""Kallikreins"""	6357	protein-coding gene	gene with protein product		147910	"""kallikrein 1, renal/pancreas/salivary"""			1684954, 16800724, 16800723	Standard	NM_002257		Approved	Klk6	uc002ptk.1	P06870		ENST00000301420.2:c.556A>G	19.37:g.51323232T>C	ENSP00000301420:p.Lys186Glu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	178	87	0.488764	NM_002257	Q66US9|Q86U61|Q8TCV8|Q9BS53|Q9NQU4|Q9UD19|Q9UMJ1	Missense_Mutation	SNP	ENST00000301420.2	37	CCDS12804.1	791	0.36217948717948717	94	0.1910569105691057	151	0.4171270718232044	336	0.5874125874125874	210	0.2770448548812665	N	0.052	-1.247545	0.01469	0.196323	0.268605	ENSG00000167748	ENST00000301420;ENST00000448701	D;D	0.88664	-2.41;-2.41	2.89	-0.553	0.11815	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B	0.14805	0.011	B	0.19391	0.025	T	0.26503	-1.0101	8	0.02654	T	1	.	6.4041	0.21654	0.0:0.5048:0.0:0.4952	rs5517;rs3195245;rs3819318;rs17800555;rs61327587;rs5517	186	P06870	KLK1_HUMAN	E	186;84	ENSP00000301420:K186E;ENSP00000400994:K84E	ENSP00000301420:K186E	K	-	1	0	KLK1	56015044	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.665000	0.01965	-0.281000	0.09141	-0.747000	0.03512	AAA	T|0.707;C|0.293	0.293	strong		0.557	KLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464135.2	NM_002257	
PLEKHA6	22874	hgsc.bcm.edu	37	1	204226896	204226896	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:204226896C>T	ENST00000272203.3	-	9	1425	c.1109G>A	c.(1108-1110)cGg>cAg	p.R370Q	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.R390Q	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	370	Pro-rich.									breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			GCTCTCCGGCCGCACTCCTGG	0.627																																					p.R370Q		Atlas-SNP	.											PLEKHA6,colon,carcinoma,0,1	PLEKHA6	115	1	0			c.G1109A						scavenged	.						34.0	35.0	35.0					1																	204226896		2203	4300	6503	SO:0001583	missense	22874	exon9			TCCGGCCGCACTC	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.1109G>A	1.37:g.204226896C>T	ENSP00000272203:p.Arg370Gln	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	95	2	0.0210526	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.664688	0.88251	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.14022	2.54;3.02	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.36331	0.0963	L	0.61387	1.9	0.80722	D	1	D	0.71674	0.998	D	0.66602	0.945	T	0.01287	-1.1395	10	0.62326	D	0.03	-28.423	19.7263	0.96165	0.0:1.0:0.0:0.0	.	370	Q9Y2H5	PKHA6_HUMAN	Q	370;390	ENSP00000272203:R370Q;ENSP00000402046:R390Q	ENSP00000272203:R370Q	R	-	2	0	PLEKHA6	202493519	1.000000	0.71417	1.000000	0.80357	0.423000	0.31445	6.763000	0.74955	2.837000	0.97791	0.655000	0.94253	CGG	.	.	none		0.627	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
OR13C5	138799	hgsc.bcm.edu	37	9	107360851	107360851	+	Missense_Mutation	SNP	T	T	C	rs1523678	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107360851T>C	ENST00000374779.2	-	1	937	c.844A>G	c.(844-846)Ata>Gta	p.I282V		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	282			I -> V (in dbSNP:rs1523678).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTGTAGAATATGAATATAAGT	0.393													T|||	2184	0.436102	0.6475	0.2277	5008	,	,		19814	0.5754		0.1789	False		,,,				2504	0.4192				p.I282V		Atlas-SNP	.											.	OR13C5	60	.	0			c.A844G						PASS	.	T	VAL/ILE	2577,1829	638.3+/-396.9	762,1053,388	123.0	118.0	120.0		844	-7.7	0.0	9	dbSNP_88	120	1669,6931	308.1+/-308.7	183,1303,2814	yes	missense	OR13C5	NM_001004482.1	29	945,2356,3202	CC,CT,TT		19.407,41.5116,32.6465	benign	282/319	107360851	4246,8760	2203	4300	6503	SO:0001583	missense	138799	exon1			AGAATATGAATAT		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.844A>G	9.37:g.107360851T>C	ENSP00000363911:p.Ile282Val	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	839	0.3841575091575092	297	0.6036585365853658	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	T	6.399	0.441735	0.12164	0.584884	0.19407	ENSG00000255800	ENST00000374779	T	0.00019	9.06	3.85	-7.7	0.01259	GPCR, rhodopsin-like superfamily (1);	0.893919	0.09140	N	0.843087	T	0.00012	0.0000	N	0.00879	-1.12	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40421	-0.9564	9	0.51188	T	0.08	.	3.554	0.07857	0.3832:0.0767:0.4015:0.1386	rs1523678;rs52800382;rs58776918;rs1523678	282	Q8NGS8	O13C5_HUMAN	V	282	ENSP00000363911:I282V	ENSP00000363911:I282V	I	-	1	0	OR13C5	106400672	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-6.926000	0.00049	-2.857000	0.00329	0.347000	0.21830	ATA	T|0.634;C|0.366	0.366	strong		0.393	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
GAK	2580	hgsc.bcm.edu	37	4	844781	844781	+	Silent	SNP	G	G	A	rs75072999	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:844781G>A	ENST00000314167.4	-	26	3710	c.3600C>T	c.(3598-3600)acC>acT	p.T1200T	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Silent_p.T1121T	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1200					cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T1200T(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		TCTCTGCAATGGTCTTTGGCC	0.522													G|||	134	0.0267572	0.0015	0.036	5008	,	,		16676	0.0		0.0835	False		,,,				2504	0.0235				p.T1200T		Atlas-SNP	.											GAK,rectum,carcinoma,0,1	GAK	104	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C3600T						PASS	.	G		92,4314	74.1+/-112.3	2,88,2113	213.0	192.0	199.0		3600	2.3	1.0	4	dbSNP_132	199	802,7798	187.4+/-234.7	48,706,3546	no	coding-synonymous	GAK	NM_005255.2		50,794,5659	AA,AG,GG		9.3256,2.0881,6.8738		1200/1312	844781	894,12112	2203	4300	6503	SO:0001819	synonymous_variant	2580	exon26			TGCAATGGTCTTT	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3600C>T	4.37:g.844781G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	70	0.03205128205128205	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	55	0.07255936675461741	G	12.15	1.852878	0.32699	0.020881	0.093256	ENSG00000178950	ENST00000511980	.	.	.	5.41	2.33	0.28932	.	.	.	.	.	T	0.08447	0.0210	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41627	-0.9498	5	0.87932	D	0	-52.9883	11.0372	0.47808	0.0:0.2378:0.6265:0.1357	.	.	.	.	L	356	.	ENSP00000424553:P66L	P	-	2	0	GAK	834781	1.000000	0.71417	0.998000	0.56505	0.856000	0.48823	0.666000	0.25097	0.625000	0.30304	0.655000	0.94253	CCA	G|0.939;A|0.061	0.061	strong		0.522	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
ABCA13	154664	hgsc.bcm.edu	37	7	48336844	48336844	+	Silent	SNP	C	C	T	rs6583546	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48336844C>T	ENST00000435803.1	+	22	9159	c.9135C>T	c.(9133-9135)ctC>ctT	p.L3045L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3045					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						CCAAAAGCCTCGAGGAAACTT	0.393													C|||	3851	0.76897	0.7035	0.7781	5008	,	,		19963	0.9881		0.5934	False		,,,				2504	0.8057				p.L3045L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C9135T						PASS	.	C		2517,1165		861,795,185	66.0	63.0	64.0		9135	-10.0	0.0	7	dbSNP_116	64	5199,3009		1647,1905,552	no	coding-synonymous	ABCA13	NM_152701.3		2508,2700,737	TT,TC,CC		36.6594,31.6404,35.1051		3045/5059	48336844	7716,4174	1841	4104	5945	SO:0001819	synonymous_variant	154664	exon22			AAGCCTCGAGGAA	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.9135C>T	7.37:g.48336844C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			C|0.254;T|0.746	0.746	strong		0.393	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
FCGBP	8857	hgsc.bcm.edu	37	19	40399385	40399385	+	Missense_Mutation	SNP	C	C	T	rs201168964		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40399385C>T	ENST00000221347.6	-	13	6317	c.6310G>A	c.(6310-6312)Gga>Aga	p.G2104R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2104	VWFD 5. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AAGGGTGGTCCGTGGCAGGGT	0.597																																					p.G2104R		Atlas-SNP	.											FCGBP,NS,carcinoma,0,2	FCGBP	416	2	0			c.G6310A						scavenged	.						9.0	12.0	11.0					19																	40399385		1085	2084	3169	SO:0001583	missense	8857	exon13			GTGGTCCGTGGCA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6310G>A	19.37:g.40399385C>T	ENSP00000221347:p.Gly2104Arg	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	183	44	0.240437	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	0.241	-1.013596	0.02095	.	.	ENSG00000090920	ENST00000221347	T	0.59083	0.29	3.01	0.723	0.18231	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.43389	0.1245	L	0.43923	1.385	0.09310	N	1	B	0.19445	0.036	B	0.10450	0.005	T	0.26780	-1.0093	9	0.28530	T	0.3	.	5.6999	0.17877	0.0:0.5011:0.0:0.4989	.	2104	Q9Y6R7	FCGBP_HUMAN	R	2104	ENSP00000221347:G2104R	ENSP00000221347:G2104R	G	-	1	0	FCGBP	45091225	0.000000	0.05858	0.002000	0.10522	0.254000	0.26022	-2.133000	0.01308	0.480000	0.27534	0.298000	0.19748	GGA	C|0.500;T|0.500	0.500	strong		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
C7orf57	136288	hgsc.bcm.edu	37	7	48081095	48081095	+	Missense_Mutation	SNP	G	G	T	rs10951942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48081095G>T	ENST00000348904.3	+	3	432	c.220G>T	c.(220-222)Gcg>Tcg	p.A74S	C7orf57_ENST00000435376.1_5'UTR|C7orf57_ENST00000539619.1_Missense_Mutation_p.A74S|C7orf57_ENST00000420324.1_Missense_Mutation_p.A119S|C7orf57_ENST00000430738.1_Missense_Mutation_p.A119S	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	74			A -> S (in dbSNP:rs10951942).							breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						TGTGAAGCTCGCGAAACAAGG	0.557													G|||	1790	0.357428	0.2383	0.3559	5008	,	,		16754	0.3294		0.4513	False		,,,				2504	0.4519				p.A74S		Atlas-SNP	.											C7orf57_ENST00000348904,colon,carcinoma,-1,2	C7orf57	59	2	0			c.G220T						PASS	.	G	SER/ALA	878,2922		94,690,1116	30.0	34.0	33.0		220	5.7	0.5	7	dbSNP_120	33	3534,4720		734,2066,1327	yes	missense	C7orf57	NM_001100159.1	99	828,2756,2443	TT,TG,GG		42.8156,23.1053,36.602	probably-damaging	74/296	48081095	4412,7642	1900	4127	6027	SO:0001583	missense	136288	exon3			AAGCTCGCGAAAC	BC031107	CCDS47583.1, CCDS59054.1, CCDS75594.1	7p12.3	2011-11-25			ENSG00000164746	ENSG00000164746			22247	protein-coding gene	gene with protein product							Standard	NM_001100159		Approved		uc003toh.5	Q8NEG2	OTTHUMG00000155808	ENST00000348904.3:c.220G>T	7.37:g.48081095G>T	ENSP00000335500:p.Ala74Ser	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	17	4	0.235294	NM_001100159	C9JBJ8	Missense_Mutation	SNP	ENST00000348904.3	37	CCDS47583.1	796	0.36446886446886445	123	0.25	128	0.35359116022099446	213	0.3723776223776224	332	0.43799472295514513	G	18.43	3.621309	0.66787	0.231053	0.428156	ENSG00000164746	ENST00000420324;ENST00000430738;ENST00000348904;ENST00000539619	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.76002	2.32	0.20074	P	0.9999323842	D	0.61080	0.989	D	0.69142	0.962	T	0.35968	-0.9767	9	0.87932	D	0	-24.527	17.2972	0.87173	0.0:0.0:1.0:0.0	rs10951942;rs12702410;rs17547034;rs52805538;rs56638263;rs10951942	74	Q8NEG2	CG057_HUMAN	S	119;119;74;74	ENSP00000394648:A119S;ENSP00000410944:A119S;ENSP00000335500:A74S;ENSP00000442474:A74S	ENSP00000335500:A74S	A	+	1	0	C7orf57	48047620	1.000000	0.71417	0.501000	0.27601	0.148000	0.21650	6.127000	0.71642	2.670000	0.90874	0.563000	0.77884	GCG	G|0.632;T|0.368	0.368	strong		0.557	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159	
SEC63	11231	hgsc.bcm.edu	37	6	108214694	108214694	+	Missense_Mutation	SNP	C	C	T	rs17854547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:108214694C>T	ENST00000369002.4	-	16	1845	c.1666G>A	c.(1666-1668)Gtt>Att	p.V556I		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	556			V -> I (in dbSNP:rs17854547). {ECO:0000269|PubMed:14574404}.		liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		ACATTCCCAACGACTCCATTT	0.299													C|||	116	0.0231629	0.003	0.0259	5008	,	,		18017	0.002		0.0378	False		,,,				2504	0.0552				p.V556I		Atlas-SNP	.											.	SEC63	79	.	0			c.G1666A						PASS	.	C	ILE/VAL	45,4361	47.5+/-82.1	0,45,2158	116.0	114.0	115.0		1666	1.3	0.3	6	dbSNP_123	115	382,8218	124.1+/-182.9	10,362,3928	yes	missense	SEC63	NM_007214.4	29	10,407,6086	TT,TC,CC		4.4419,1.0213,3.2831	benign	556/761	108214694	427,12579	2203	4300	6503	SO:0001583	missense	11231	exon16			TCCCAACGACTCC	BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"""Heat shock proteins / DNAJ (HSP40)"""	21082	protein-coding gene	gene with protein product		608648	"""SEC63-like (S. cerevisiae)"""			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.1666G>A	6.37:g.108214694C>T	ENSP00000357998:p.Val556Ile	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	38	0.426966	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	Missense_Mutation	SNP	ENST00000369002.4	37	CCDS5061.1	43|43	0.019688644688644688|0.019688644688644688	3|3	0.006097560975609756|0.006097560975609756	11|11	0.03038674033149171|0.03038674033149171	0|0	0.0|0.0	29|29	0.03825857519788918|0.03825857519788918	C|C	12.53|12.53	1.966057|1.966057	0.34659|0.34659	0.010213|0.010213	0.044419|0.044419	ENSG00000025796|ENSG00000025796	ENST00000423697|ENST00000369002;ENST00000437345	.|T	.|0.70164	.|-0.46	5.38|5.38	1.29|1.29	0.21616|0.21616	.|Sec63 domain (2);	.|0.292991	.|0.38058	.|N	.|0.001827	T|T	0.25717|0.25717	0.0626|0.0626	L|L	0.29908|0.29908	0.895|0.895	0.25285|0.25285	N|N	0.989404|0.989404	.|B;B	.|0.28208	.|0.146;0.203	.|B;B	.|0.15052	.|0.011;0.012	T|T	0.12578|0.12578	-1.0542|-1.0542	6|10	0.87932|0.36615	D|T	0|0.2	-3.4703|-3.4703	6.7599|6.7599	0.23534|0.23534	0.0:0.6487:0.1248:0.2265|0.0:0.6487:0.1248:0.2265	rs17854547|rs17854547	.|556;556	.|Q9UGP8;B3KQF0	.|SEC63_HUMAN;.	H|I	415|556;207	.|ENSP00000357998:V556I	ENSP00000394572:R415H|ENSP00000357998:V556I	R|V	-|-	2|1	0|0	SEC63|SEC63	108321387|108321387	0.020000|0.020000	0.18652|0.18652	0.343000|0.343000	0.25615|0.25615	0.807000|0.807000	0.45602|0.45602	0.108000|0.108000	0.15396|0.15396	0.007000|0.007000	0.14760|0.14760	0.563000|0.563000	0.77884|0.77884	CGT|GTT	C|0.969;T|0.031	0.031	strong		0.299	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214	
DOCK10	55619	hgsc.bcm.edu	37	2	225670901	225670901	+	Missense_Mutation	SNP	G	G	C	rs4674941	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:225670901G>C	ENST00000258390.7	-	34	3823	c.3756C>G	c.(3754-3756)atC>atG	p.I1252M	DOCK10_ENST00000409592.3_Missense_Mutation_p.I1246M	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1252					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TTGCATGTTTGATAGCTGTCT	0.353													C|||	1248	0.249201	0.6634	0.1196	5008	,	,		19929	0.0228		0.1501	False		,,,				2504	0.1166				p.I1252M		Atlas-SNP	.											.	DOCK10	308	.	0			c.C3756G						PASS	.	C	MET/ILE	2089,1635		577,935,350	141.0	142.0	142.0		3756	6.0	1.0	2	dbSNP_111	142	1093,7089		80,933,3078	yes	missense	DOCK10	NM_014689.2	10	657,1868,3428	CC,CG,GG		13.3586,43.9044,26.726	benign	1252/2187	225670901	3182,8724	1862	4091	5953	SO:0001583	missense	55619	exon34			ATGTTTGATAGCT	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3756C>G	2.37:g.225670901G>C	ENSP00000258390:p.Ile1252Met	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	478|478	0.21886446886446886|0.21886446886446886	301|301	0.6117886178861789|0.6117886178861789	48|48	0.13259668508287292|0.13259668508287292	16|16	0.027972027972027972|0.027972027972027972	113|113	0.14907651715039577|0.14907651715039577	C|C	1.091|1.091	-0.664100|-0.664100	0.03428|0.03428	0.560956|0.560956	0.133586|0.133586	ENSG00000135905|ENSG00000135905	ENST00000409592;ENST00000258390|ENST00000422684	T;T|.	0.21734|.	1.99;1.99|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.088261|.	0.85682|.	N|.	0.000000|.	T|.	0.00012|.	0.0000|.	N|N	0.00347|0.00347	-1.61|-1.61	0.49915|0.49915	P|P	1.64000000000053E-4|1.64000000000053E-4	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.01281|.	0.0;0.0;0.0|.	T|.	0.29243|.	-1.0018|.	9|.	0.08179|.	T|.	0.78|.	.|.	17.4358|17.4358	0.87552|0.87552	0.0:0.8755:0.1245:0.0|0.0:0.8755:0.1245:0.0	rs4674941;rs52829997;rs60007997;rs4674941|rs4674941;rs52829997;rs60007997;rs4674941	1252;115;1246|.	Q96BY6;B4DF07;B3FL70|.	DOC10_HUMAN;.;.|.	M|X	1246;1252|143	ENSP00000386694:I1246M;ENSP00000258390:I1252M|.	ENSP00000258390:I1252M|.	I|S	-|-	3|2	3|0	DOCK10|DOCK10	225379145|225379145	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.932000|0.932000	0.56968|0.56968	2.565000|2.565000	0.45939|0.45939	1.544000|1.544000	0.49359|0.49359	-0.120000|-0.120000	0.15030|0.15030	ATC|TCA	G|0.790;C|0.209	0.209	strong		0.353	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
OR2L8	391190	hgsc.bcm.edu	37	1	248112546	248112546	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248112546C>T	ENST00000357191.3	+	1	387	c.387C>T	c.(385-387)ctC>ctT	p.L129L	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	129						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(3)|large_intestine(3)|lung(30)|ovary(1)|prostate(1)|skin(3)	42	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			GCTTTCCTCTCCACTATCTCA	0.443																																					p.L129L		Atlas-SNP	.											OR2L8,NS,carcinoma,0,1	OR2L8	92	1	0			c.C387T						scavenged	.						298.0	260.0	273.0					1																	248112546		2203	4300	6503	SO:0001819	synonymous_variant	391190	exon1			TCCTCTCCACTAT	BK004459	CCDS31101.1	1q44	2013-10-10	2013-10-10		ENSG00000196936	ENSG00000196936		"""GPCR / Class A : Olfactory receptors"""	15014	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily L, member 8"""				Standard	NM_001001963		Approved		uc001idt.1	Q8NGY9	OTTHUMG00000040196	ENST00000357191.3:c.387C>T	1.37:g.248112546C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	172	21	0.122093	NM_001001963	Q6IF03	Silent	SNP	ENST00000357191.3	37	CCDS31101.1																																																																																			.	.	none		0.443	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2		
AKAP1	8165	hgsc.bcm.edu	37	17	55183813	55183813	+	Missense_Mutation	SNP	A	A	G	rs34535433	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:55183813A>G	ENST00000337714.3	+	2	1221	c.988A>G	c.(988-990)Agc>Ggc	p.S330G	AKAP1_ENST00000571629.1_Missense_Mutation_p.S330G|AKAP1_ENST00000314126.3_Missense_Mutation_p.S330G|AKAP1_ENST00000572557.1_Missense_Mutation_p.S330G|AKAP1_ENST00000539273.1_Missense_Mutation_p.S330G	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	330					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					AAATGAGGAGAGCTTGGATAG	0.488													A|||	373	0.0744808	0.1142	0.0504	5008	,	,		17826	0.006		0.1123	False		,,,				2504	0.0695				p.S330G		Atlas-SNP	.											.	AKAP1	73	.	0			c.A988G						PASS	.						99.0	107.0	104.0					17																	55183813		2203	4300	6503	SO:0001583	missense	8165	exon3			GAGGAGAGCTTGG	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.988A>G	17.37:g.55183813A>G	ENSP00000337736:p.Ser330Gly	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	42	0.666667	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	119	0.05448717948717949	41	0.08333333333333333	11	0.03038674033149171	5	0.008741258741258742	62	0.08179419525065963	A	4.183	0.032588	0.08101	.	.	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.17370	2.63;2.28;2.63	2.59	-2.24	0.06909	.	.	.	.	.	T	0.00356	0.0011	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45469	-0.9259	8	0.11485	T	0.65	.	7.4748	0.27369	0.7577:0.0:0.2423:0.0	rs34535433	330	Q92667	AKAP1_HUMAN	G	330;330;372;330	ENSP00000337736:S330G;ENSP00000314075:S330G;ENSP00000443139:S330G	ENSP00000314075:S330G	S	+	1	0	AKAP1	52538812	0.459000	0.25768	0.002000	0.10522	0.420000	0.31355	0.675000	0.25232	-0.573000	0.05998	-1.216000	0.01612	AGC	A|0.944;G|0.056	0.056	strong		0.488	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1		
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971109	45971109	+	Missense_Mutation	SNP	G	G	A	rs200984587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45971109G>A	ENST00000391621.1	-	1	279	c.233C>T	c.(232-234)tCg>tTg	p.S78L	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	78	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CTGGCAGCACGAGGGCGTGCA	0.687																																					p.S78L		Atlas-SNP	.											KRTAP10-2,caecum,carcinoma,0,1	KRTAP10-2	21	1	0			c.C233T						scavenged	.																																			SO:0001583	missense	386679	exon1			CAGCACGAGGGCG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.233C>T	21.37:g.45971109G>A	ENSP00000375479:p.Ser78Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	76	7	0.0921053	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	g	5.987	0.366047	0.11352	.	.	ENSG00000205445	ENST00000391621	T	0.01572	4.76	3.44	1.48	0.22813	.	.	.	.	.	T	0.03305	0.0096	M	0.87682	2.9	0.09310	N	1	B	0.22683	0.073	B	0.16289	0.015	T	0.40384	-0.9566	9	0.51188	T	0.08	.	2.1189	0.03721	0.1176:0.1948:0.4883:0.1993	.	78	P60368	KR102_HUMAN	L	78	ENSP00000375479:S78L	ENSP00000375479:S78L	S	-	2	0	KRTAP10-2	44795537	0.060000	0.20803	0.001000	0.08648	0.073000	0.16967	1.997000	0.40786	0.133000	0.18654	0.456000	0.33151	TCG	.	.	weak		0.687	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
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 GAIIx	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_ENST00000336740.6_Missense_Mutation_p.E570D|EGFLAM_ENST00000397202.2_Missense_Mutation_p.E170D|EGFLAM_ENST00000322350.5_Missense_Mutation_p.E804D	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	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	54	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	
IGSF10	285313	hgsc.bcm.edu	37	3	151155620	151155620	+	Silent	SNP	G	G	A	rs6781302	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:151155620G>A	ENST00000282466.3	-	6	6728	c.6729C>T	c.(6727-6729)aaC>aaT	p.N2243N	IGSF10_ENST00000495443.1_5'UTR	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	2243	Ig-like C2-type 9.			N -> S (in Ref. 3; AAH31063). {ECO:0000305}.	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)			TAACAGTTCTGTTTGTATACA	0.438													G|||	2964	0.591853	0.5015	0.5937	5008	,	,		22139	0.5169		0.7565	False		,,,				2504	0.6207				p.N2243N		Atlas-SNP	.											.	IGSF10	279	.	0			c.C6729T						PASS	.	G	,,	2340,2066	605.2+/-390.5	628,1084,491	110.0	98.0	102.0		810,666,6729	3.7	0.1	3	dbSNP_116	102	6549,2051	720.2+/-406.3	2496,1557,247	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	3124,2641,738	AA,AG,GG		23.8488,46.8906,31.6546	,,	270/651,222/603,2243/2624	151155620	8889,4117	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			AGTTCTGTTTGTA	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.6729C>T	3.37:g.151155620G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			G|0.352;A|0.648	0.648	strong		0.438	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
FAM170B	170370	hgsc.bcm.edu	37	10	50340304	50340304	+	Missense_Mutation	SNP	C	C	A	rs17773851	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50340304C>A	ENST00000311787.5	-	2	295	c.206G>T	c.(205-207)cGg>cTg	p.R69L	FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	69			R -> L (in dbSNP:rs17773851).							central_nervous_system(1)|endometrium(1)|skin(1)	3						GCTCCAGTCCCGCATCCCCCG	0.632													A|||	1228	0.245208	0.118	0.3444	5008	,	,		17030	0.3075		0.2684	False		,,,				2504	0.2587				p.R69L		Atlas-SNP	.											.	FAM170B	20	.	0			c.G206T						PASS	.	A	LEU/ARG	223,1161		20,183,489	38.0	43.0	42.0		206	3.9	1.0	10	dbSNP_123	42	922,2260		148,626,817	yes	missense	FAM170B	NM_001164484.1	102	168,809,1306	AA,AC,CC		28.9755,16.1127,25.0767	benign	69/284	50340304	1145,3421	692	1591	2283	SO:0001583	missense	170370	exon2			CAGTCCCGCATCC		CCDS53536.1	10q11.23	2008-11-06	2008-06-12	2008-06-12	ENSG00000172538	ENSG00000172538			19736	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 73"""	C10orf73			Standard	NM_001164484		Approved	Em:AC084727.4	uc001jhj.3	A6NMN3	OTTHUMG00000018187	ENST00000311787.5:c.206G>T	10.37:g.50340304C>A	ENSP00000308292:p.Arg69Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_001164484	Q86WY6|Q8N6K8	Missense_Mutation	SNP	ENST00000311787.5	37	CCDS53536.1	527	0.2413003663003663	61	0.12398373983739837	117	0.32320441988950277	148	0.25874125874125875	201	0.26517150395778366	A	0.262	-0.998912	0.02128	0.161127	0.289755	ENSG00000172538	ENST00000311787	T	0.27557	1.66	5.12	3.93	0.45458	.	0.372809	0.19801	N	0.105742	T	0.00012	0.0000	N	0.00237	-1.79	0.48830	P	2.889999999999837E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41520	-0.9504	9	0.16896	T	0.51	-16.088	5.9475	0.19227	0.6642:0.1716:0.0:0.1642	rs17773851;rs52836194;rs17773851	69	A6NMN3	F170B_HUMAN	L	69	ENSP00000308292:R69L	ENSP00000308292:R69L	R	-	2	0	FAM170B	50010310	0.838000	0.29461	0.986000	0.45419	0.043000	0.13939	1.760000	0.38430	0.970000	0.38263	-0.262000	0.10625	CGG	C|0.765;A|0.235	0.235	strong		0.632	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
PLEC	5339	hgsc.bcm.edu	37	8	144997671	144997671	+	Silent	SNP	G	G	A	rs200062782	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144997671G>A	ENST00000322810.4	-	31	7006	c.6837C>T	c.(6835-6837)gcC>gcT	p.A2279A	PLEC_ENST00000354589.3_Silent_p.A2142A|PLEC_ENST00000357649.2_Silent_p.A2146A|PLEC_ENST00000436759.2_Silent_p.A2169A|PLEC_ENST00000354958.2_Silent_p.A2120A|PLEC_ENST00000527096.1_Silent_p.A2165A|PLEC_ENST00000345136.3_Silent_p.A2142A|PLEC_ENST00000356346.3_Silent_p.A2128A|PLEC_ENST00000398774.2_Silent_p.A2110A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2279	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCTCTTGCTCGGCCTCCTTGC	0.692													g|||	4	0.000798722	0.0023	0.0	5008	,	,		11676	0.0		0.001	False		,,,				2504	0.0				p.A2279A		Atlas-SNP	.											.	PLEC	1144	.	0			c.C6837T						PASS	.	A	,,,,,,,	0,3958		0,0,1979	8.0	10.0	9.0		6507,6384,6360,6837,6330,6426,6438,6426	-9.9	0.1	8		9	5,8105		0,5,4050	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	0,5,6029	AA,AG,GG		0.0617,0.0,0.0414	,,,,,,,	2169/4575,2128/4534,2120/4526,2279/4685,2110/4516,2142/4548,2146/4552,2142/4548	144997671	5,12063	1979	4055	6034	SO:0001819	synonymous_variant	5339	exon31			TTGCTCGGCCTCC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.6837C>T	8.37:g.144997671G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	12	9	0.75	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.998;A|0.002	0.002	weak		0.692	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
EYS	346007	hgsc.bcm.edu	37	6	65300640	65300640	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:65300640T>C	ENST00000370621.3	-	26	5646	c.5120A>G	c.(5119-5121)tAt>tGt	p.Y1707C	EYS_ENST00000503581.1_Missense_Mutation_p.Y1707C|EYS_ENST00000370616.2_Missense_Mutation_p.Y1707C			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1707					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGTTATGCCATATTGTCTTAT	0.338																																					p.Y1707C		Atlas-SNP	.											EYS_ENST00000370621,NS,carcinoma,+1,1	EYS	527	1	0			c.A5120G						scavenged	.						31.0	28.0	29.0					6																	65300640		692	1589	2281	SO:0001583	missense	346007	exon26			ATGCCATATTGTC		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.5120A>G	6.37:g.65300640T>C	ENSP00000359655:p.Tyr1707Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	176	2	0.0113636	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	T	9.716	1.158468	0.21454	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84873	-1.91;-1.88;-1.88	5.06	1.21	0.21127	.	.	.	.	.	T	0.54143	0.1840	N	0.08118	0	0.09310	N	1	P;P	0.40332	0.713;0.59	B;B	0.39562	0.303;0.159	T	0.50346	-0.8839	9	0.87932	D	0	.	8.5212	0.33277	0.0:0.2217:0.0:0.7783	.	1707;1707	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	C	1707	ENSP00000424243:Y1707C;ENSP00000359655:Y1707C;ENSP00000359650:Y1707C	ENSP00000359650:Y1707C	Y	-	2	0	EYS	65357361	0.000000	0.05858	0.000000	0.03702	0.483000	0.33249	0.587000	0.23909	0.113000	0.18004	0.482000	0.46254	TAT	.	.	none		0.338	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
SIGLEC15	284266	hgsc.bcm.edu	37	18	43420177	43420177	+	Splice_Site	SNP	G	G	A	rs61104666	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:43420177G>A	ENST00000389474.3	+	5	1093	c.876G>A	c.(874-876)gaG>gaA	p.E292E	SIGLEC15_ENST00000602118.2_3'UTR|SIGLEC15_ENST00000546268.1_Splice_Site_p.E138E|SIGLEC15_ENST00000587418.1_Splice_Site_p.S62N	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	292					cellular response to lipoprotein particle stimulus (GO:0071402)|innate immune response (GO:0045087)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of bone resorption (GO:0045124)|regulation of osteoclast development (GO:2001204)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	4						CTCCCACAGAGCATCTGGACA	0.652													G|||	1267	0.252995	0.1536	0.3689	5008	,	,		14636	0.371		0.1322	False		,,,				2504	0.3078				p.E292E		Atlas-SNP	.											.	SIGLEC15	10	.	0			c.G876A						PASS	.	G		674,3732	284.3+/-277.5	54,566,1583	129.0	101.0	110.0		876	1.0	0.9	18	dbSNP_129	110	974,7626	210.7+/-251.5	54,866,3380	yes	coding-synonymous-near-splice	SIGLEC15	NM_213602.2		108,1432,4963	AA,AG,GG		11.3256,15.2973,12.6711		292/329	43420177	1648,11358	2203	4300	6503	SO:0001630	splice_region_variant	284266	exon5			CACAGAGCATCTG	AK095432	CCDS32819.1	18q21.1	2014-01-28	2007-05-31	2007-05-31	ENSG00000197046	ENSG00000197046		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27596	protein-coding gene	gene with protein product			"""CD33 antigen-like 3"", ""CD33 molecule-like 3"""	CD33L3		17483134	Standard	NM_213602		Approved	HsT1361	uc002lbl.1	Q6ZMC9		ENST00000389474.3:c.875-1G>A	18.37:g.43420177G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_213602	A8K2Y5|B4DVQ9	Silent	SNP	ENST00000389474.3	37	CCDS32819.1																																																																																			G|0.844;A|0.156	0.156	strong		0.652	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602	Silent
USP6	9098	hgsc.bcm.edu	37	17	5042894	5042894	+	Missense_Mutation	SNP	T	T	C	rs8073787	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5042894T>C	ENST00000574788.1	+	22	3653	c.1423T>C	c.(1423-1425)Tgg>Cgg	p.W475R	USP6_ENST00000250066.6_Missense_Mutation_p.W475R|USP6_ENST00000332776.4_Missense_Mutation_p.W475R|USP6_ENST00000304328.5_Missense_Mutation_p.W158R			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	475			W -> R (in dbSNP:rs8073787). {ECO:0000269|PubMed:1565468}.		cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TGATTTTGAATGGAGCTGCTG	0.587			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								T|||	3881	0.77496	0.8805	0.5735	5008	,	,		18430	0.9087		0.5626	False		,,,				2504	0.8558				p.W475R		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6_ENST00000250066,NS,carcinoma,-1,2	USP6	213	2	0			c.T1423C						PASS	.	T	ARG/TRP	3571,835	741.1+/-411.2	1441,689,73	46.0	52.0	50.0		1423	-0.5	0.0	17	dbSNP_116	50	4723,3877	605.6+/-395.0	1312,2099,889	yes	missense	USP6	NM_004505.2	101	2753,2788,962	CC,CT,TT		45.0814,18.9514,36.2294	benign	475/1407	5042894	8294,4712	2203	4300	6503	SO:0001583	missense	9098	exon14			TTTGAATGGAGCT	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1423T>C	17.37:g.5042894T>C	ENSP00000460380:p.Trp475Arg	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	19	0.542857	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	1584	0.7252747252747253	425	0.8638211382113821	205	0.5662983425414365	523	0.9143356643356644	431	0.5686015831134564	T	4.806	0.149914	0.09185	0.810486	0.549186	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.13089	2.62;3.11;2.7	0.266	-0.532	0.11890	.	0.115600	0.85682	D	0.000000	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12630	0.003;0.006	B;B	0.04013	0.001;0.001	T	0.09997	-1.0649	8	0.19147	T	0.46	.	.	.	.	rs8073787;rs52828858;rs59236784;rs8073787	158;475	P35125-2;P35125	.;UBP6_HUMAN	R	475;475;158	ENSP00000328010:W475R;ENSP00000250066:W475R;ENSP00000305473:W158R	ENSP00000250066:W475R	W	+	1	0	USP6	4983618	0.074000	0.21230	0.001000	0.08648	0.001000	0.01503	-0.049000	0.11924	-1.209000	0.02631	-1.203000	0.01651	TGG	T|0.322;C|0.678	0.678	strong		0.587	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
LRRC18	474354	hgsc.bcm.edu	37	10	50121454	50121454	+	Silent	SNP	G	G	A	rs41302987	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50121454G>A	ENST00000374160.3	-	1	823	c.747C>T	c.(745-747)gaC>gaT	p.D249D	RP11-523O18.7_ENST00000430438.1_RNA|WDFY4_ENST00000413659.2_Intron|WDFY4_ENST00000325239.5_Intron|LRRC18_ENST00000298124.3_Silent_p.D249D	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	249						cytoplasm (GO:0005737)				NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						CTTCCCAGGAGTCCTTGGCCA	0.547													G|||	140	0.0279553	0.0159	0.0375	5008	,	,		20260	0.001		0.0696	False		,,,				2504	0.0225				p.D249D		Atlas-SNP	.											.	LRRC18	52	.	0			c.C747T						PASS	.	G	,	141,4265	100.3+/-138.9	3,135,2065	185.0	187.0	187.0		747,	-11.9	0.0	10	dbSNP_127	187	508,8092	144.5+/-200.4	10,488,3802	no	coding-synonymous,intron	WDFY4,LRRC18	NM_001006939.3,NM_020945.1	,	13,623,5867	AA,AG,GG		5.907,3.2002,4.99	,	249/262,	50121454	649,12357	2203	4300	6503	SO:0001819	synonymous_variant	474354	exon1			CCAGGAGTCCTTG	AY358137	CCDS31197.1	10q11.23	2011-02-10			ENSG00000165383	ENSG00000165383			23199	protein-coding gene	gene with protein product							Standard	NM_001006939		Approved	UNQ933, MGC34773, UNQ9338, VKGE9338	uc001jhd.3	Q8N456	OTTHUMG00000018182	ENST00000374160.3:c.747C>T	10.37:g.50121454G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	187	94	0.502674	NM_001006939	Q6UY02	Silent	SNP	ENST00000374160.3	37	CCDS31197.1																																																																																			G|0.956;A|0.044	0.044	strong		0.547	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939	
MGAT5B	146664	hgsc.bcm.edu	37	17	74922706	74922706	+	Silent	SNP	C	C	T	rs33966966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74922706C>T	ENST00000569840.2	+	10	1759	c.1185C>T	c.(1183-1185)ttC>ttT	p.F395F	MGAT5B_ENST00000428789.2_Silent_p.F406F|MGAT5B_ENST00000301618.4_Silent_p.F395F	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	395					protein N-linked glycosylation (GO:0006487)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(15)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCGACACCTTCGGGACGGAAC	0.637													C|||	1220	0.24361	0.1271	0.2032	5008	,	,		20909	0.4117		0.2038	False		,,,				2504	0.2975				p.F406F		Atlas-SNP	.											.	MGAT5B	98	.	0			c.C1218T						PASS	.	C	,,	625,3777	267.7+/-268.0	44,537,1620	83.0	68.0	73.0		1185,1185,1218	-2.9	1.0	17	dbSNP_126	73	1469,7121	280.2+/-294.4	140,1189,2966	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	184,1726,4586	TT,TC,CC		17.1013,14.1981,16.1176	,,	395/793,395/791,406/802	74922706	2094,10898	2201	4295	6496	SO:0001819	synonymous_variant	146664	exon9			CACCTTCGGGACG	AB109185	CCDS11751.1, CCDS45788.1, CCDS59299.1	17q25.3	2013-02-25	2005-11-16		ENSG00000167889	ENSG00000167889		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	24140	protein-coding gene	gene with protein product		612441	"""mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isoenzyme B"""			14617637, 14623122	Standard	NM_001199172		Approved	GnT-IX, FLJ25132, GnT-VB	uc002jth.3	Q3V5L5	OTTHUMG00000177278	ENST00000569840.2:c.1185C>T	17.37:g.74922706C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			C|0.816;T|0.184	0.184	strong		0.637	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
MDN1	23195	hgsc.bcm.edu	37	6	90402482	90402482	+	Missense_Mutation	SNP	G	G	A	rs9294445	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90402482G>A	ENST00000369393.3	-	63	10382	c.10267C>T	c.(10267-10269)Cac>Tac	p.H3423Y	MDN1_ENST00000428876.1_Missense_Mutation_p.H3423Y			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3423			H -> Y (in dbSNP:rs9294445).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ATACTGCTGTGGAGTGAGGTG	0.582													G|||	3027	0.604433	0.5998	0.6988	5008	,	,		19282	0.9077		0.4602	False		,,,				2504	0.3793				p.H3423Y		Atlas-SNP	.											.	MDN1	478	.	0			c.C10267T						PASS	.	G	TYR/HIS	2654,1752	644.8+/-398.1	810,1034,359	59.0	62.0	61.0		10267	3.3	0.3	6	dbSNP_119	61	4016,4584	553.7+/-386.4	961,2094,1245	yes	missense	MDN1	NM_014611.1	83	1771,3128,1604	AA,AG,GG		46.6977,39.764,48.716	possibly-damaging	3423/5597	90402482	6670,6336	2203	4300	6503	SO:0001583	missense	23195	exon63			TGCTGTGGAGTGA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.10267C>T	6.37:g.90402482G>A	ENSP00000358400:p.His3423Tyr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	71	26	0.366197	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	1432	0.6556776556776557	305	0.6199186991869918	242	0.6685082872928176	524	0.916083916083916	361	0.4762532981530343	G	0.053	-1.243550	0.01481	0.60236	0.466977	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.02974	4.09;4.09	5.1	3.31	0.37934	.	0.259259	0.33610	N	0.004723	T	0.01222	0.0040	M	0.62723	1.935	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.46679	-0.9174	9	0.22706	T	0.39	.	7.6737	0.28473	0.1373:0.0:0.6393:0.2234	rs9294445;rs52802793;rs60191675;rs9294445	3423	Q9NU22	MDN1_HUMAN	Y	3423	ENSP00000358400:H3423Y;ENSP00000413970:H3423Y	ENSP00000358400:H3423Y	H	-	1	0	MDN1	90459203	0.961000	0.32948	0.279000	0.24732	0.004000	0.04260	1.635000	0.37134	0.280000	0.22209	-1.579000	0.00862	CAC	G|0.429;A|0.571	0.571	strong		0.582	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ECHDC3	79746	hgsc.bcm.edu	37	10	11805339	11805339	+	Silent	SNP	C	C	T	rs17850531	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:11805339C>T	ENST00000379215.4	+	5	919	c.708C>T	c.(706-708)atC>atT	p.I236I	ECHDC3_ENST00000496136.1_3'UTR	NM_024693.4	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl CoA hydratase domain containing 3	236						mitochondrion (GO:0005739)	catalytic activity (GO:0003824)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)	4						CCATGCGGATCGCTAGGAAGA	0.622													C|||	987	0.197085	0.0197	0.2435	5008	,	,		19195	0.3075		0.2107	False		,,,				2504	0.2761				p.I236I		Atlas-SNP	.											.	ECHDC3	12	.	0			c.C708T						PASS	.	C		239,4167	140.0+/-175.5	9,221,1973	90.0	74.0	79.0		708	-11.5	0.0	10	dbSNP_123	79	1777,6823	318.6+/-313.7	173,1431,2696	no	coding-synonymous	ECHDC3	NM_024693.4		182,1652,4669	TT,TC,CC		20.6628,5.4244,15.5005		236/304	11805339	2016,10990	2203	4300	6503	SO:0001819	synonymous_variant	79746	exon5			GCGGATCGCTAGG	AF275677	CCDS7084.1	10p14	2010-04-30	2010-04-30		ENSG00000134463	ENSG00000134463			23489	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 3"""			12477932	Standard	NM_024693		Approved	FLJ20909	uc001ikw.4	Q96DC8	OTTHUMG00000017675	ENST00000379215.4:c.708C>T	10.37:g.11805339C>T		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_024693	Q53HR9|Q5W0J7|Q8WYY8|Q9BVL8|Q9H7G4	Silent	SNP	ENST00000379215.4	37	CCDS7084.1																																																																																			C|0.831;T|0.169	0.169	strong		0.622	ECHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046771.1	NM_024693	
CIITA	4261	hgsc.bcm.edu	37	16	11016045	11016045	+	Silent	SNP	C	C	T	rs2229322	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11016045C>T	ENST00000324288.8	+	17	3304	c.3171C>T	c.(3169-3171)tgC>tgT	p.C1057C	CIITA_ENST00000381835.5_Silent_p.C473C	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	1057					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)	p.C1057C(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						ACTGCATCTGCGACGTGGGAG	0.612			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								C|||	525	0.104832	0.0787	0.1081	5008	,	,		17922	0.1865		0.0994	False		,,,				2504	0.0593				p.C1057C		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	CIITA,NS,carcinoma,0,1	CIITA	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C3171T						PASS	.	C		342,4052	179.7+/-208.2	8,326,1863	150.0	143.0	145.0		3171	-6.7	0.3	16	dbSNP_98	145	932,7668	205.1+/-247.6	49,834,3417	no	coding-synonymous	CIITA	NM_000246.3		57,1160,5280	TT,TC,CC		10.8372,7.7833,9.8045		1057/1131	11016045	1274,11720	2197	4300	6497	SO:0001819	synonymous_variant	4261	exon17			CATCTGCGACGTG	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.3171C>T	16.37:g.11016045C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			C|0.893;T|0.107	0.107	strong		0.612	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
STK17B	9262	hgsc.bcm.edu	37	2	197004439	197004439	+	Silent	SNP	A	A	G	rs1054537	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:197004439A>G	ENST00000263955.4	-	7	1027	c.741T>C	c.(739-741)atT>atC	p.I247I	STK17B_ENST00000409228.1_Silent_p.I247I	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	247	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)			TAACTTGAGAAATATTGAGGT	0.338													A|||	3521	0.703075	0.5794	0.7305	5008	,	,		13926	0.9028		0.6481	False		,,,				2504	0.7014				p.I247I		Atlas-SNP	.											.	STK17B	28	.	0			c.T741C						PASS	.	A		2569,1837	634.2+/-396.2	724,1121,358	106.0	108.0	107.0		741	4.0	1.0	2	dbSNP_86	107	5350,3242	647.5+/-400.4	1662,2026,608	no	coding-synonymous	STK17B	NM_004226.3		2386,3147,966	GG,GA,AA		37.7328,41.6931,39.0752		247/373	197004439	7919,5079	2203	4296	6499	SO:0001819	synonymous_variant	9262	exon7			TTGAGAAATATTG	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.741T>C	2.37:g.197004439A>G		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	123	70	0.569106	NM_004226		Silent	SNP	ENST00000263955.4	37	CCDS2315.1																																																																																			A|0.349;G|0.651	0.651	strong		0.338	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2		
PSG1	5669	hgsc.bcm.edu	37	19	43372386	43372386	+	Silent	SNP	T	T	C	rs1064491	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43372386T>C	ENST00000436291.2	-	5	1226	c.1110A>G	c.(1108-1110)gaA>gaG	p.E370E	PSG1_ENST00000312439.6_Silent_p.E370E|PSG1_ENST00000403380.3_Silent_p.E277E|PSG1_ENST00000595124.1_Silent_p.E277E|PSG1_ENST00000244296.2_Silent_p.E370E|PSG1_ENST00000595356.1_Silent_p.E370E	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	370	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				GCTGAAACTTTTCATTAATTG	0.453													.|||	1436	0.286741	0.3139	0.1945	5008	,	,		19460	0.4167		0.1014	False		,,,				2504	0.3722				p.E370E		Atlas-SNP	.											.	PSG1	196	.	0			c.A1110G						PASS	.	C	,,	1266,3136		213,840,1148	167.0	177.0	174.0		1110,1110,1110	0.5	0.0	19	dbSNP_86	174	936,7660		68,800,3430	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	,,	281,1640,4578	CC,CT,TT		10.8888,28.7597,16.9411	,,	370/420,370/418,370/427	43372386	2202,10796	2201	4298	6499	SO:0001819	synonymous_variant	5669	exon5			AAACTTTTCATTA		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.1110A>G	19.37:g.43372386T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	114	49	0.429825	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	37	CCDS54275.1																																																																																			T|0.797;C|0.203	0.203	strong		0.453	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
TYRO3	7301	hgsc.bcm.edu	37	15	41860490	41860490	+	Missense_Mutation	SNP	T	T	A	rs12148316	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:41860490T>A	ENST00000263798.3	+	8	1261	c.1037T>A	c.(1036-1038)aTc>aAc	p.I346N	TYRO3_ENST00000559066.1_Missense_Mutation_p.I301N	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	346	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> N (in dbSNP:rs12148316).		apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GAAGAAGTGATCCCCGAGGCC	0.577													T|||	775	0.154752	0.0946	0.1671	5008	,	,		17669	0.0109		0.2922	False		,,,				2504	0.2342				p.I346N		Atlas-SNP	.											TYRO3_ENST00000263798,colon,carcinoma,0,2	TYRO3	169	2	0			c.T1037A						PASS	.	T	ASN/ILE	542,3864	245.9+/-254.7	32,478,1693	60.0	58.0	59.0		1037	4.0	1.0	15	dbSNP_120	59	2512,6088	408.4+/-349.5	324,1864,2112	no	missense	TYRO3	NM_006293.3	149	356,2342,3805	AA,AT,TT		29.2093,12.3014,23.4815	benign	346/891	41860490	3054,9952	2203	4300	6503	SO:0001583	missense	7301	exon8			AAGTGATCCCCGA	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1037T>A	15.37:g.41860490T>A	ENSP00000263798:p.Ile346Asn	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	106	17	0.160377	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	341	0.15613553113553114	45	0.09146341463414634	65	0.17955801104972377	5	0.008741258741258742	226	0.29815303430079154	T	11.51	1.659473	0.29515	0.123014	0.292093	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.72615	-0.67	5.09	3.95	0.45737	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.194192	0.25839	N	0.027971	T	0.00012	0.0000	L	0.44542	1.39	0.29829	P	0.8302080000000001	B	0.33318	0.408	B	0.31614	0.133	T	0.13229	-1.0517	9	0.20519	T	0.43	-5.0066	8.7958	0.34878	0.3005:0.0:0.0:0.6995	rs12148316	346	Q06418	TYRO3_HUMAN	N	278;346	ENSP00000263798:I346N	ENSP00000263798:I346N	I	+	2	0	TYRO3	39647782	0.370000	0.25047	0.999000	0.59377	0.998000	0.95712	0.484000	0.22308	0.938000	0.37419	0.533000	0.62120	ATC	T|0.803;A|0.197	0.197	strong		0.577	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		
GPR112	139378	hgsc.bcm.edu	37	X	135426968	135426968	+	Missense_Mutation	SNP	C	C	A	rs5930931	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135426968C>A	ENST00000394143.1	+	6	1394	c.1103C>A	c.(1102-1104)cCt>cAt	p.P368H	GPR112_ENST00000394141.1_Missense_Mutation_p.P163H|GPR112_ENST00000370652.1_Missense_Mutation_p.P368H|GPR112_ENST00000287534.4_Missense_Mutation_p.P305H|GPR112_ENST00000412101.1_Missense_Mutation_p.P163H	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	368			P -> H (in dbSNP:rs5930931). {ECO:0000269|Ref.2}.		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)	p.P368L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTTCAACCACCTACACCTTCT	0.368													c|||	1700	0.450331	0.4213	0.3545	3775	,	,		16744	0.2024		0.3738	False		,,,				2504	0.3241				p.P368H		Atlas-SNP	.											.	GPR112	459	.	1	Substitution - Missense(1)	prostate(1)	c.C1103A						PASS	.		HIS/PRO	2081,1754		479,816,307,337,264	84.0	78.0	80.0		1103	2.1	0.0	X	dbSNP_114	80	3200,3528		554,1184,908,690,964	yes	missense	GPR112	NM_153834.3	77	1033,2000,1215,1027,1228	AA,AC,A,CC,C		47.5624,45.7366,49.9953	possibly-damaging	368/3081	135426968	5281,5282	2203	4300	6503	SO:0001583	missense	139378	exon6			AACCACCTACACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1103C>A	X.37:g.135426968C>A	ENSP00000377699:p.Pro368His	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	53	36	0.679245	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	706	0.4255575647980711	138	0.3689839572192513	80	0.27972027972027974	76	0.15702479338842976	186	0.3174061433447099	c	2.747	-0.260836	0.05791	0.542634	0.475624	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.29397	1.61;1.61;1.57;1.71;1.57	3.95	2.08	0.27032	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P	0.55605	0.972;0.924;0.875	P;P;B	0.49047	0.599;0.46;0.271	T	0.44544	-0.9321	8	0.66056	D	0.02	.	8.6564	0.34066	0.3924:0.6076:0.0:0.0	rs5930931;rs58573078;rs5930931	305;163;368	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	H	368;368;163;305;163	ENSP00000377699:P368H;ENSP00000359686:P368H;ENSP00000416526:P163H;ENSP00000287534:P305H;ENSP00000377697:P163H	ENSP00000287534:P305H	P	+	2	0	GPR112	135254634	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.303000	0.19210	0.238000	0.21222	-0.519000	0.04390	CCT	0|0.025;A|0.455	0.455	strong		0.368	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
EVPL	2125	hgsc.bcm.edu	37	17	74017579	74017579	+	Silent	SNP	G	G	C	rs138421545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74017579G>C	ENST00000301607.3	-	9	1234	c.981C>G	c.(979-981)acC>acG	p.T327T	EVPL_ENST00000586740.1_Silent_p.T327T	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	327	Globular 1.				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						GCTGCAGCTGGGTCTCCTGGC	0.711													G|||	9	0.00179712	0.0	0.0058	5008	,	,		8246	0.0		0.003	False		,,,				2504	0.002				p.T327T		Atlas-SNP	.											EVPL,NS,carcinoma,0,1	EVPL	155	1	0			c.C981G						PASS	.	G		8,4394		0,8,2193	30.0	27.0	28.0		981	1.3	1.0	17	dbSNP_134	28	75,8523		0,75,4224	no	coding-synonymous	EVPL	NM_001988.2		0,83,6417	CC,CG,GG		0.8723,0.1817,0.6385		327/2034	74017579	83,12917	2201	4299	6500	SO:0001819	synonymous_variant	2125	exon9			CAGCTGGGTCTCC	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.981C>G	17.37:g.74017579G>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	42	0.355932	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.995;C|0.005	0.005	strong		0.711	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
MUC4	4585	hgsc.bcm.edu	37	3	195505774	195505774	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195505774G>T	ENST00000463781.3	-	2	13136	c.12677C>A	c.(12676-12678)cCt>cAt	p.P4226H	MUC4_ENST00000475231.1_Missense_Mutation_p.P4226H|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	983					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.P4226H(1)		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)		GCTGGTGACAGGAAGAGGGGT	0.587																																					p.P4226H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.C12677A						scavenged	.						35.0	35.0	35.0					3																	195505774		2091	4190	6281	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	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.12677C>A	3.37:g.195505774G>T	ENSP00000417498:p.Pro4226His	Somatic	87	2	0.0229885		WXS	Illumina HiSeq	Phase_I	69	7	0.101449	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	10.38	1.335266	0.24253	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.43294	1.33;0.95	1.57	1.57	0.23409	.	.	.	.	.	T	0.40448	0.1117	N	0.14661	0.345	0.26065	N	0.981307	D	0.89917	1.0	D	0.72982	0.979	T	0.18840	-1.0324	8	.	.	.	.	6.711	0.23276	0.0:0.0:1.0:0.0	.	4098	E7ESK3	.	H	4226	ENSP00000417498:P4226H;ENSP00000420243:P4226H	.	P	-	2	0	MUC4	196990553	0.000000	0.05858	0.040000	0.18447	0.017000	0.09413	-0.298000	0.08265	1.213000	0.43380	0.484000	0.47621	CCT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC44A5	204962	hgsc.bcm.edu	37	1	75699771	75699771	+	Silent	SNP	A	A	G	rs10493565	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:75699771A>G	ENST00000370855.5	-	12	866	c.753T>C	c.(751-753)atT>atC	p.I251I	SLC44A5_ENST00000535611.1_Silent_p.I121I|SLC44A5_ENST00000370859.3_Silent_p.I251I	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	251					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)		p.I251I(1)		kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						GGACCATGGCAATCGTCAGGC	0.383													G|||	1170	0.233626	0.3654	0.2291	5008	,	,		15755	0.0486		0.2694	False		,,,				2504	0.2127				p.I251I		Atlas-SNP	.											SLC44A5,NS,carcinoma,0,1	SLC44A5	231	1	1	Substitution - coding silent(1)	stomach(1)	c.T753C						PASS	.	G	,	1558,2848	667.0+/-401.8	290,978,935	99.0	98.0	98.0		753,753	-2.6	0.0	1	dbSNP_119	98	2301,6299	704.1+/-405.4	315,1671,2314	no	coding-synonymous,coding-synonymous	SLC44A5	NM_001130058.1,NM_152697.4	,	605,2649,3249	GG,GA,AA		26.7558,35.3609,29.6709	,	251/718,251/720	75699771	3859,9147	2203	4300	6503	SO:0001819	synonymous_variant	204962	exon12			CATGGCAATCGTC	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.753T>C	1.37:g.75699771A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	37	CCDS667.1																																																																																			A|0.766;G|0.234	0.234	strong		0.383	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697	
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 GAIIx	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	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	150	8	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	
TMEM2	23670	hgsc.bcm.edu	37	9	74344821	74344821	+	Silent	SNP	T	T	C	rs25693	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:74344821T>C	ENST00000377044.4	-	10	2528	c.1989A>G	c.(1987-1989)tcA>tcG	p.S663S	TMEM2_ENST00000377066.5_Silent_p.S600S	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	663					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		TCCAGAAAGTTGAAACAGCCC	0.383													C|||	407	0.08127	0.0393	0.0476	5008	,	,		16682	0.0198		0.0815	False		,,,				2504	0.2249				p.S663S		Atlas-SNP	.											.	TMEM2	112	.	0			c.A1989G						PASS	.	C	,	174,4232	808.3+/-415.9	6,162,2035	83.0	90.0	87.0		1800,1989	0.4	1.0	9	dbSNP_72	87	717,7883	786.6+/-407.6	31,655,3614	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	37,817,5649	CC,CT,TT		8.3372,3.9492,6.8507	,	600/1321,663/1384	74344821	891,12115	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon10			GAAAGTTGAAACA		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1989A>G	9.37:g.74344821T>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	113	65	0.575221	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			T|0.937;C|0.063	0.063	strong		0.383	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
CARD9	64170	hgsc.bcm.edu	37	9	139265870	139265870	+	Silent	SNP	G	G	A	rs11145769	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139265870G>A	ENST00000371732.5	-	3	393	c.228C>T	c.(226-228)taC>taT	p.Y76Y	CARD9_ENST00000371734.3_Silent_p.Y76Y|CARD9_ENST00000315908.7_Silent_p.Y76Y	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	76	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		GGAAGGCCACGTAGCCCTTGT	0.657													G|||	332	0.0662939	0.0598	0.0086	5008	,	,		12148	0.1339		0.0378	False		,,,				2504	0.0757				p.Y76Y		Atlas-SNP	.											CARD9,NS,carcinoma,0,1	CARD9	47	1	0			c.C228T						PASS	.	G	,	215,4147		9,197,1975	25.0	19.0	21.0		228,228	-3.2	1.0	9	dbSNP_120	21	271,8309		1,269,4020	no	coding-synonymous,coding-synonymous	CARD9	NM_052813.4,NM_052814.3	,	10,466,5995	AA,AG,GG		3.1585,4.9289,3.7552	,	76/537,76/493	139265870	486,12456	2181	4290	6471	SO:0001819	synonymous_variant	64170	exon3			GGCCACGTAGCCC	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.228C>T	9.37:g.139265870G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			G|0.955;A|0.045	0.045	strong		0.657	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135722264	135722264	+	Missense_Mutation	SNP	A	A	G	rs17197552	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:135722264A>G	ENST00000264977.3	+	2	2541	c.1924A>G	c.(1924-1926)Agt>Ggt	p.S642G	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	642			S -> G (in dbSNP:rs17197552).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGTCTGTAGAAGTCCTGTTGG	0.423													A|||	865	0.172724	0.1505	0.1412	5008	,	,		17582	0.0288		0.2783	False		,,,				2504	0.2648				p.S642G		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A1924G						PASS	.	A	,GLY/SER	770,3634	291.0+/-281.2	64,642,1496	82.0	77.0	79.0		,1924	3.5	1.0	3	dbSNP_123	79	2708,5892	418.8+/-352.9	415,1878,2007	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,56	479,2520,3503	GG,GA,AA		31.4884,17.4841,26.7456	,benign	,642/1151	135722264	3478,9526	2202	4300	6502	SO:0001583	missense	5523	exon2			TGTAGAAGTCCTG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.1924A>G	3.37:g.135722264A>G	ENSP00000264977:p.Ser642Gly	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	340	0.15567765567765568	66	0.13414634146341464	57	0.1574585635359116	13	0.022727272727272728	204	0.2691292875989446	A	9.126	1.010279	0.19277	0.174841	0.314884	ENSG00000073711	ENST00000264977	T	0.06218	3.33	5.83	3.47	0.39725	.	0.643751	0.17330	N	0.178150	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.999999999742355	B	0.02656	0.0	B	0.04013	0.001	T	0.47636	-0.9102	9	0.44086	T	0.13	.	8.2194	0.31532	0.8457:0.0:0.1543:0.0	rs17197552;rs52827295;rs17197552	642	Q06190	P2R3A_HUMAN	G	642	ENSP00000264977:S642G	ENSP00000264977:S642G	S	+	1	0	PPP2R3A	137204954	0.878000	0.30173	0.996000	0.52242	0.962000	0.63368	1.520000	0.35899	0.481000	0.27557	0.460000	0.39030	AGT	A|0.779;G|0.221	0.221	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
TTN	7273	hgsc.bcm.edu	37	2	179579093	179579093	+	Missense_Mutation	SNP	T	T	C	rs12693164	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179579093T>C	ENST00000591111.1	-	89	25681	c.25457A>G	c.(25456-25458)aAt>aGt	p.N8486S	TTN_ENST00000589042.1_Missense_Mutation_p.N8803S|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N7559S			Q8WZ42	TITIN_HUMAN	titin	12654	Ig-like 67.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTTCCAGCATTGGCTGGTTC	0.393													T|||	1237	0.247005	0.1936	0.1859	5008	,	,		21117	0.4365		0.1561	False		,,,				2504	0.2607				p.N8803S		Atlas-SNP	.											TTN_ENST00000342992,colon,carcinoma,0,1	TTN	18412	1	0			c.A26408G						PASS	.	T	,,,SER/ASN	595,3173		45,505,1334	116.0	113.0	114.0		,,,22676	2.2	1.0	2	dbSNP_121	114	1240,6996		96,1048,2974	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,46	141,1553,4308	CC,CT,TT		15.0559,15.7909,15.2866	,,,benign	,,,7559/33424	179579093	1835,10169	1884	4118	6002	SO:0001583	missense	7273	exon91			CCAGCATTGGCTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.25457A>G	2.37:g.179579093T>C	ENSP00000465570:p.Asn8486Ser	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	187	71	0.379679	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		512	0.23443223443223443	98	0.1991869918699187	55	0.15193370165745856	243	0.42482517482517484	116	0.15303430079155672	T	7.990	0.752982	0.15778	0.157909	0.150559	ENSG00000155657	ENST00000342992	T	0.68025	-0.3	5.96	2.25	0.28309	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.999999999999746	B	0.16603	0.018	B	0.09377	0.004	T	0.32025	-0.9922	8	0.87932	D	0	.	12.1749	0.54180	0.0:0.1656:0.0:0.8344	rs12693164;rs52822704;rs58566262;rs12693164	8486	Q8WZ42	TITIN_HUMAN	S	7559	ENSP00000343764:N7559S	ENSP00000343764:N7559S	N	-	2	0	TTN	179287338	1.000000	0.71417	0.983000	0.44433	0.345000	0.29048	0.818000	0.27295	-0.075000	0.12798	-2.240000	0.00288	AAT	T|0.765;C|0.235	0.235	strong		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CRABP2	1382	hgsc.bcm.edu	37	1	156670344	156670344	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156670344T>C	ENST00000368222.3	-	3	510	c.356A>G	c.(355-357)gAa>gGa	p.E119G	CRABP2_ENST00000368221.1_Missense_Mutation_p.E119G	NM_001199723.1|NM_001878.3	NP_001186652.1|NP_001869.1	P29373	RABP2_HUMAN	cellular retinoic acid binding protein 2	119					epidermis development (GO:0008544)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(2)|lung(3)|upper_aerodigestive_tract(1)	6	all_hematologic(923;0.088)|Hepatocellular(266;0.158)				Alitretinoin(DB00523)|Tretinoin(DB00755)	CAGGATCAGTTCCCCATCGTT	0.537																																					p.E119G		Atlas-SNP	.											CRABP2,NS,carcinoma,-1,1	CRABP2	13	1	0			c.A356G						scavenged	.						121.0	108.0	112.0					1																	156670344		2203	4300	6503	SO:0001583	missense	1382	exon4			ATCAGTTCCCCAT	BC001109	CCDS1152.1	1q21.3	2013-03-01	2001-11-28		ENSG00000143320	ENSG00000143320		"""Fatty acid binding protein family"""	2339	protein-coding gene	gene with protein product		180231	"""cellular retinoic acid-binding protein 2"""			1654334	Standard	NM_001878		Approved	CRABP-II	uc001fpr.3	P29373	OTTHUMG00000041300	ENST00000368222.3:c.356A>G	1.37:g.156670344T>C	ENSP00000357205:p.Glu119Gly	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	175	3	0.0171429	NM_001199723	B2R4Z8|D3DVC5|F1T098|Q6ICN6	Missense_Mutation	SNP	ENST00000368222.3	37	CCDS1152.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.730886	0.89390	.	.	ENSG00000143320	ENST00000368222;ENST00000368221	T;T	0.10860	2.83;2.83	4.98	4.98	0.66077	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.108139	0.64402	D	0.000007	T	0.13372	0.0324	L	0.47716	1.5	0.58432	D	0.999997	D	0.61697	0.99	P	0.58970	0.849	T	0.00880	-1.1529	10	0.72032	D	0.01	.	12.6382	0.56694	0.0:0.0:0.0:1.0	.	119	P29373	RABP2_HUMAN	G	119	ENSP00000357205:E119G;ENSP00000357204:E119G	ENSP00000357204:E119G	E	-	2	0	CRABP2	154936968	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.613000	0.82986	1.880000	0.54463	0.459000	0.35465	GAA	.	.	none		0.537	CRABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098966.1	NM_001878	
ACACB	32	hgsc.bcm.edu	37	12	109693982	109693982	+	Silent	SNP	C	C	T	rs3742023	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:109693982C>T	ENST00000338432.7	+	45	6323	c.6204C>T	c.(6202-6204)caC>caT	p.H2068H	ACACB_ENST00000377848.3_Silent_p.H2068H|ACACB_ENST00000377854.5_Silent_p.H1998H|ACACB_ENST00000543201.1_Silent_p.H734H			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2068	Carboxyltransferase.				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)	TCTTTGACCACGGCAGTTTCA	0.607													C|||	1278	0.255192	0.1241	0.2709	5008	,	,		17499	0.2817		0.3777	False		,,,				2504	0.2679				p.H2068H		Atlas-SNP	.											.	ACACB	330	.	0			c.C6204T						PASS	.	C		675,3731	284.9+/-277.9	58,559,1586	72.0	66.0	68.0		6204	-3.5	0.9	12	dbSNP_107	68	3088,5512	473.1+/-368.5	550,1988,1762	no	coding-synonymous	ACACB	NM_001093.3		608,2547,3348	TT,TC,CC		35.907,15.32,28.9328		2068/2459	109693982	3763,9243	2203	4300	6503	SO:0001819	synonymous_variant	32	exon44			TGACCACGGCAGT	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.6204C>T	12.37:g.109693982C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	125	71	0.568	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.719;T|0.281	0.281	strong		0.607	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
CNTN6	27255	hgsc.bcm.edu	37	3	1424850	1424850	+	Silent	SNP	T	T	G	rs2291100	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:1424850T>G	ENST00000446702.2	+	18	3018	c.2391T>G	c.(2389-2391)tcT>tcG	p.S797S	CNTN6_ENST00000539053.1_Silent_p.S725S|CNTN6_ENST00000350110.2_Silent_p.S797S			Q9UQ52	CNTN6_HUMAN	contactin 6	797	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		TTGTCTACTCTGGGGAAGATG	0.418													T|||	1325	0.264577	0.0386	0.2781	5008	,	,		20256	0.3452		0.3877	False		,,,				2504	0.3507				p.S797S		Atlas-SNP	.											.	CNTN6	245	.	0			c.T2391G						PASS	.	T		404,4002	200.8+/-224.0	17,370,1816	123.0	109.0	114.0		2391	-12.2	0.2	3	dbSNP_100	114	3216,5384	485.5+/-371.6	597,2022,1681	no	coding-synonymous	CNTN6	NM_014461.2		614,2392,3497	GG,GT,TT		37.3953,9.1693,27.8333		797/1029	1424850	3620,9386	2203	4300	6503	SO:0001819	synonymous_variant	27255	exon18			CTACTCTGGGGAA	AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2391T>G	3.37:g.1424850T>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	157	157	1	NM_014461	Q2KHM2	Silent	SNP	ENST00000446702.2	37	CCDS2557.1																																																																																			T|0.724;G|0.276	0.276	strong		0.418	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
PROKR1	10887	hgsc.bcm.edu	37	2	68882468	68882468	+	Silent	SNP	T	T	C	rs6722313	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:68882468T>C	ENST00000303786.3	+	3	1362	c.942T>C	c.(940-942)ttT>ttC	p.F314F	PROKR1_ENST00000394342.2_Silent_p.F314F			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	314					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCACCGTGTTTGTGAAGGAGA	0.562													C|||	2265	0.452276	0.6823	0.3055	5008	,	,		22858	0.3919		0.3171	False		,,,				2504	0.4468				p.F314F		Atlas-SNP	.											.	PROKR1	69	.	0			c.T942C						PASS	.	C		2684,1722	516.3+/-369.1	817,1050,336	180.0	130.0	147.0		942	0.8	1.0	2	dbSNP_116	147	2415,6185	699.9+/-405.1	333,1749,2218	no	coding-synonymous	PROKR1	NM_138964.2		1150,2799,2554	CC,CT,TT		28.0814,39.0831,39.205		314/394	68882468	5099,7907	2203	4300	6503	SO:0001819	synonymous_variant	10887	exon2			CGTGTTTGTGAAG	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.942T>C	2.37:g.68882468T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	95	66	0.694737	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Silent	SNP	ENST00000303786.3	37	CCDS1889.1																																																																																			T|0.606;C|0.394	0.394	strong		0.562	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2		
NBPF10	100132406	hgsc.bcm.edu	37	1	145302775	145302775	+	Missense_Mutation	SNP	T	T	G	rs376014420		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145302775T>G	ENST00000369339.3	+	5	653	c.400T>G	c.(400-402)Tat>Gat	p.Y134D	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000342960.5_Missense_Mutation_p.Y405D|NBPF10_ENST00000369338.1_Missense_Mutation_p.Y134D			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	405						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CCTCACTCCGTATGAGCCGGA	0.577																																					p.Y405D		Atlas-SNP	.											NBPF10_ENST00000369338,NS,carcinoma,0,2	NBPF10	221	2	0			c.T1213G						scavenged	.																																			SO:0001583	missense	100132406	exon8			ACTCCGTATGAGC	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.400T>G	1.37:g.145302775T>G	ENSP00000358345:p.Tyr134Asp	Somatic	48	7	0.145833		WXS	Illumina HiSeq	Phase_I	63	12	0.190476	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	0	-2.664813	0.00107	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.46063	0.88;4.33	0.712	-0.91	0.10511	.	.	.	.	.	T	0.03390	0.0098	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33189	-0.9878	7	0.02654	T	1	.	.	.	.	.	134	A8MQ30	.	D	330;134;134;405	ENSP00000358344:Y134D;ENSP00000345684:Y405D	ENSP00000345684:Y405D	Y	+	1	0	NBPF10	144014132	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.464000	0.06688	-1.158000	0.02811	-1.371000	0.01190	TAT	T|0.500;G|0.500	0.500	weak		0.577	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
MRC2	9902	hgsc.bcm.edu	37	17	60741917	60741917	+	Missense_Mutation	SNP	G	G	A	rs2014055	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:60741917G>A	ENST00000303375.5	+	2	529	c.127G>A	c.(127-129)Gtc>Atc	p.V43I	Y_RNA_ENST00000384652.1_RNA	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	43	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		V -> I (in dbSNP:rs2014055). {ECO:0000269|PubMed:10683150}.		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						AGAACCCAACGTCTTCCTCAT	0.632													G|||	416	0.0830671	0.0091	0.098	5008	,	,		18061	0.0437		0.1839	False		,,,				2504	0.1094				p.V43I		Atlas-SNP	.											.	MRC2	126	.	0			c.G127A						PASS	.	G	ILE/VAL	164,4242	106.9+/-145.3	3,158,2042	111.0	113.0	113.0		127	2.7	0.7	17	dbSNP_92	113	1499,7101	272.2+/-289.9	118,1263,2919	yes	missense	MRC2	NM_006039.3	29	121,1421,4961	AA,AG,GG		17.4302,3.7222,12.7864	possibly-damaging	43/1480	60741917	1663,11343	2203	4300	6503	SO:0001583	missense	9902	exon2			CCCAACGTCTTCC	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.127G>A	17.37:g.60741917G>A	ENSP00000307513:p.Val43Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	202	0.0924908424908425	5	0.01016260162601626	37	0.10220994475138122	22	0.038461538461538464	138	0.1820580474934037	G	4.078	0.012468	0.07912	0.037222	0.174302	ENSG00000011028	ENST00000303375	T	0.28666	1.6	4.7	2.71	0.32032	Ricin B-related lectin (1);Ricin B lectin (1);	0.292600	0.32769	N	0.005677	T	0.00039	0.0001	L	0.31065	0.9	0.09310	P	0.999999999999957	B	0.16396	0.017	B	0.06405	0.002	T	0.28650	-1.0037	9	0.13853	T	0.58	-35.3953	8.395	0.32550	0.2394:0.0:0.7606:0.0	rs2014055;rs17547249;rs52798705;rs58922856;rs2014055	43	Q9UBG0	MRC2_HUMAN	I	43	ENSP00000307513:V43I	ENSP00000307513:V43I	V	+	1	0	MRC2	58095649	0.999000	0.42202	0.724000	0.30704	0.990000	0.78478	2.991000	0.49409	0.603000	0.29913	0.561000	0.74099	GTC	G|0.890;A|0.110	0.110	strong		0.632	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
XPC	7508	hgsc.bcm.edu	37	3	14199887	14199887	+	Missense_Mutation	SNP	G	G	A	rs2228000	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:14199887G>A	ENST00000285021.7	-	9	1710	c.1496C>T	c.(1495-1497)gCg>gTg	p.A499V	XPC_ENST00000449060.2_Missense_Mutation_p.A462V	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	499	Interaction with RAD23B.		A -> V (in dbSNP:rs2228000). {ECO:0000269|PubMed:12177305, ECO:0000269|PubMed:8168482, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGAGGATGCCGCTGGCAAGCT	0.537			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	1167	0.233027	0.093	0.245	5008	,	,		20742	0.4127		0.2584	False		,,,				2504	0.2025				p.A499V		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	XPC,caecum,carcinoma,+1,1	XPC	60	1	0			c.C1496T	GRCh37	CM057944	XPC	M	rs2228000	PASS	.	G	VAL/ALA,VAL/ALA	288,2848		18,252,1298	71.0	64.0	66.0		1385,1496	-1.0	0.0	3	dbSNP_98	66	1778,5386		219,1340,2023	yes	missense,missense	XPC	NM_001145769.1,NM_004628.4	64,64	237,1592,3321	AA,AG,GG		24.8185,9.1837,20.0583	benign,benign	462/904,499/941	14199887	2066,8234	1568	3582	5150	SO:0001583	missense	7508	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GATGCCGCTGGCA		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.1496C>T	3.37:g.14199887G>A	ENSP00000285021:p.Ala499Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	541	0.24771062271062272	39	0.07926829268292683	93	0.2569060773480663	210	0.36713286713286714	199	0.262532981530343	G	9.045	0.990686	0.18966	0.091837	0.248185	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.36699	1.24;1.26	5.34	-1.03	0.10102	.	0.809781	0.11805	N	0.527757	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.23185	0.081;0.004	B;B	0.19946	0.027;0.004	T	0.45745	-0.9240	9	0.30854	T	0.27	0.064	4.6128	0.12411	0.1193:0.0886:0.4136:0.3785	rs2228000;rs3729586;rs52792520;rs2228000	462;499	E9PH69;Q01831	.;XPC_HUMAN	V	499;462	ENSP00000285021:A499V;ENSP00000404002:A462V	ENSP00000285021:A499V	A	-	2	0	XPC	14174889	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-0.927000	0.03766	-0.797000	0.03246	GCG	G|0.772;A|0.228	0.228	strong		0.537	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
SMC1B	27127	hgsc.bcm.edu	37	22	45767421	45767421	+	Missense_Mutation	SNP	C	C	T	rs56174639	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:45767421C>T	ENST00000357450.4	-	14	2242	c.2243G>A	c.(2242-2244)tGt>tAt	p.C748Y	SMC1B_ENST00000404354.3_Missense_Mutation_p.C748Y	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	748					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		CAACATAATACATTGAGACTC	0.279													C|||	434	0.0866613	0.0908	0.0908	5008	,	,		18743	0.003		0.1889	False		,,,				2504	0.0593				p.C748Y		Atlas-SNP	.											.	SMC1B	215	.	0			c.G2243A						PASS	.	C	TYR/CYS	313,3313		11,291,1511	95.0	85.0	88.0		2243	3.3	0.4	22	dbSNP_129	88	1329,6801		115,1099,2851	yes	missense	SMC1B	NM_148674.3	194	126,1390,4362	TT,TC,CC		16.3469,8.6321,13.9673	benign	748/1236	45767421	1642,10114	1813	4065	5878	SO:0001583	missense	27127	exon14			ATAATACATTGAG	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.2243G>A	22.37:g.45767421C>T	ENSP00000350036:p.Cys748Tyr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	145	55	0.37931	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	243	0.11126373626373626	49	0.09959349593495935	39	0.10773480662983426	3	0.005244755244755245	152	0.20052770448548812	C	4.996	0.184893	0.09495	0.086321	0.163469	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.78003	-1.14;-0.97	5.66	3.35	0.38373	RecF/RecN/SMC (1);	0.372163	0.24518	N	0.037825	T	0.00073	0.0002	N	0.01729	-0.75	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.03443	-1.1036	9	0.18710	T	0.47	.	6.1198	0.20148	0.1837:0.6861:0.0:0.1302	rs56174639;rs61748561	748;748;748	Q8NDV3;Q8NDV3-2;Q8NDV3-3	SMC1B_HUMAN;.;.	Y	748	ENSP00000350036:C748Y;ENSP00000385902:C748Y	ENSP00000350036:C748Y	C	-	2	0	SMC1B	44146085	0.022000	0.18835	0.436000	0.26797	0.345000	0.29048	0.560000	0.23500	2.669000	0.90835	0.655000	0.94253	TGT	C|0.874;T|0.126	0.126	strong		0.279	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
PPFIA4	8497	hgsc.bcm.edu	37	1	203024767	203024767	+	Silent	SNP	C	C	T	rs3736314	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203024767C>T	ENST00000447715.2	+	21	2412	c.1971C>T	c.(1969-1971)gcC>gcT	p.A657A	PPFIA4_ENST00000295706.4_Silent_p.A173A|PPFIA4_ENST00000599966.1_Silent_p.A173A|PPFIA4_ENST00000272198.6_Silent_p.A173A|PPFIA4_ENST00000367240.2_Silent_p.A658A|PPFIA4_ENST00000414050.2_Silent_p.A386A			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	657					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						GCAGTGCTGCCCAGGACCTGG	0.662													c|||	774	0.154553	0.2216	0.1138	5008	,	,		18276	0.128		0.1541	False		,,,				2504	0.1207				p.A173A		Atlas-SNP	.											.	PPFIA4	139	.	0			c.C519T						PASS	.			951,3315		102,747,1284	46.0	53.0	50.0		519	2.7	1.0	1	dbSNP_107	50	1333,7131		98,1137,2997	no	coding-synonymous	PPFIA4	NM_015053.1		200,1884,4281	TT,TC,CC		15.7491,22.2925,17.9419		173/702	203024767	2284,10446	2133	4232	6365	SO:0001819	synonymous_variant	8497	exon3			TGCTGCCCAGGAC	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.1971C>T	1.37:g.203024767C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	189	188	0.994709	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Silent	SNP	ENST00000447715.2	37																																																																																				C|0.848;T|0.152	0.152	strong		0.662	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
C11orf84	144097	hgsc.bcm.edu	37	11	63585804	63585804	+	Silent	SNP	C	C	A	rs643634	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:63585804C>A	ENST00000294244.4	+	3	873	c.574C>A	c.(574-576)Cgg>Agg	p.R192R		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	192	Pro-rich.									endometrium(3)|kidney(1)|lung(3)|skin(1)	8						TAAAAGGAGCCGGCCCAGGGG	0.612													C|||	1966	0.392572	0.0734	0.6354	5008	,	,		14644	0.6944		0.4225	False		,,,				2504	0.3098				p.R192R		Atlas-SNP	.											.	C11orf84	33	.	0			c.C574A						PASS	.	C		609,3793	263.8+/-265.7	46,517,1638	51.0	62.0	58.0		574	5.5	1.0	11	dbSNP_83	58	4008,4588	554.1+/-386.4	935,2138,1225	no	coding-synonymous	C11orf84	NM_138471.1		981,2655,2863	AA,AC,CC		46.6263,13.8346,35.5208		192/382	63585804	4617,8381	2201	4298	6499	SO:0001819	synonymous_variant	144097	exon3			AGGAGCCGGCCCA	BC007540	CCDS31594.1	11q13.1	2014-02-10			ENSG00000168005	ENSG00000168005			25115	protein-coding gene	gene with protein product						12477932	Standard	NM_138471		Approved		uc001nxt.3	Q9BUA3	OTTHUMG00000167746	ENST00000294244.4:c.574C>A	11.37:g.63585804C>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Silent	SNP	ENST00000294244.4	37	CCDS31594.1																																																																																			C|0.623;A|0.377	0.377	strong		0.612	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471	
KIAA1244	57221	hgsc.bcm.edu	37	6	138584685	138584685	+	Missense_Mutation	SNP	T	T	G	rs7764091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:138584685T>G	ENST00000251691.4	+	12	2231	c.2065T>G	c.(2065-2067)Tct>Gct	p.S689A		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		TCGGCTCCTGTCTCTCTCCAA	0.527													G|||	1487	0.296925	0.5749	0.2233	5008	,	,		19009	0.371		0.0895	False		,,,				2504	0.1104				p.S689A		Atlas-SNP	.											.	KIAA1244	236	.	0			c.T2065G						PASS	.	G	ALA/SER	2151,2245		544,1063,591	46.0	51.0	50.0		2065	5.2	1.0	6	dbSNP_116	50	739,7859		35,669,3595	yes	missense	KIAA1244	NM_020340.4	99	579,1732,4186	GG,GT,TT		8.595,48.9308,22.241	benign	689/2178	138584685	2890,10104	2198	4299	6497	SO:0001583	missense	57221	exon12			CTCCTGTCTCTCT	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.2065T>G	6.37:g.138584685T>G	ENSP00000251691:p.Ser689Ala	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	629	0.288003663003663	270	0.5487804878048781	71	0.19613259668508287	221	0.38636363636363635	67	0.08839050131926121	G	0.018	-1.468445	0.01053	0.489308	0.08595	ENSG00000112379	ENST00000251691	T	0.40476	1.03	5.17	5.17	0.71159	SEC7-like (1);	253.487000	0.00166	N	0.000000	T	0.06735	0.0172	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30031	-0.9992	9	0.02654	T	1	-32.0037	9.0639	0.36451	0.0735:0.0:0.7781:0.1483	rs7764091;rs52831040;rs58555015;rs7764091	689	Q5TH69	BIG3_HUMAN	A	689	ENSP00000251691:S689A	ENSP00000251691:S689A	S	+	1	0	KIAA1244	138626378	1.000000	0.71417	0.991000	0.47740	0.075000	0.17131	2.458000	0.45014	1.326000	0.45319	-0.121000	0.15023	TCT	T|0.728;G|0.272	0.272	strong		0.527	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
LHX2	9355	hgsc.bcm.edu	37	9	126776410	126776410	+	Silent	SNP	C	C	T	rs144291200	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:126776410C>T	ENST00000373615.4	+	2	1030	c.291C>T	c.(289-291)gaC>gaT	p.D97D		NM_004789.3	NP_004780.3	P50458	LHX2_HUMAN	LIM homeobox 2	97	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				axon extension (GO:0048675)|axon guidance (GO:0007411)|cerebral cortex development (GO:0021987)|dorsal/ventral pattern formation (GO:0009953)|mesoderm development (GO:0007498)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural tube closure (GO:0001843)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|retina development in camera-type eye (GO:0060041)|telencephalon regionalization (GO:0021978)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)	10						TCAGCAAGGACGGTAGCATCT	0.587													C|||	5	0.000998403	0.0008	0.0	5008	,	,		12257	0.0		0.004	False		,,,				2504	0.0				p.D97D		Atlas-SNP	.											.	LHX2	30	.	0			c.C291T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	79.0	68.0	72.0		291	-1.3	1.0	9	dbSNP_134	72	39,8561	26.3+/-74.7	0,39,4261	no	coding-synonymous	LHX2	NM_004789.3		0,43,6460	TT,TC,CC		0.4535,0.0908,0.3306		97/407	126776410	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	9355	exon2			CAAGGACGGTAGC	U11701	CCDS6853.1	9q33.3	2011-06-20			ENSG00000106689	ENSG00000106689		"""Homeoboxes / LIM class"""	6594	protein-coding gene	gene with protein product		603759				8649822, 10051612	Standard	NM_004789		Approved	LH-2, hLhx2	uc004boe.1	P50458	OTTHUMG00000020647	ENST00000373615.4:c.291C>T	9.37:g.126776410C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	183	83	0.453552	NM_004789	O95860|Q52M57|Q8N1Z3	Silent	SNP	ENST00000373615.4	37	CCDS6853.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	10.20	1.283529	0.23392	9.08E-4	0.004535	ENSG00000106689	ENST00000446480	.	.	.	5.91	-1.26	0.09376	.	.	.	.	.	T	0.55146	0.1902	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55698	-0.8100	4	.	.	.	.	12.4537	0.55691	0.0:0.7269:0.0:0.2731	.	.	.	.	W	95	.	.	R	+	1	2	LHX2	125816231	0.856000	0.29760	0.976000	0.42696	0.933000	0.57130	0.027000	0.13621	-0.575000	0.05982	-0.880000	0.02959	CGG	C|0.996;T|0.004	0.004	strong		0.587	LHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054010.2		
CCDC94	55702	hgsc.bcm.edu	37	19	4254375	4254375	+	Silent	SNP	C	C	T	rs11085068	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4254375C>T	ENST00000262962.7	+	4	362	c.294C>T	c.(292-294)taC>taT	p.Y98Y		NM_018074.4	NP_060544.2	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94	98								p.Y98Y(1)		NS(1)|endometrium(1)|lung(2)|ovary(1)|stomach(2)	7				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0348)|STAD - Stomach adenocarcinoma(1328;0.183)		ACACAGACTACACCATGGAGC	0.547													C|||	2092	0.417732	0.5083	0.2695	5008	,	,		19031	0.4435		0.3091	False		,,,				2504	0.4857				p.Y98Y		Atlas-SNP	.											CCDC94,NS,carcinoma,0,1	CCDC94	28	1	1	Substitution - coding silent(1)	stomach(1)	c.C294T						PASS	.			2162,2244	583.2+/-385.8	528,1106,569	117.0	105.0	109.0		294	3.1	1.0	19	dbSNP_120	109	2482,6118	407.3+/-349.1	381,1720,2199	no	coding-synonymous	CCDC94	NM_018074.4		909,2826,2768	TT,TC,CC		28.8605,49.0695,35.7066		98/324	4254375	4644,8362	2203	4300	6503	SO:0001819	synonymous_variant	55702	exon4			AGACTACACCATG	AK001236	CCDS12124.1	19p13.3	2008-02-05				ENSG00000105248			25518	protein-coding gene	gene with protein product						12477932	Standard	NM_018074		Approved	FLJ10374	uc002lzv.4	Q9BW85		ENST00000262962.7:c.294C>T	19.37:g.4254375C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	107	62	0.579439	NM_018074	O75270|Q9H862|Q9NW16	Silent	SNP	ENST00000262962.7	37	CCDS12124.1																																																																																			C|0.632;T|0.368	0.368	strong		0.547	CCDC94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458007.2	NM_018074	
PLIN4	729359	hgsc.bcm.edu	37	19	4511680	4511680	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4511680A>G	ENST00000301286.3	-	3	2249	c.2250T>C	c.(2248-2250)gaT>gaC	p.D750D		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	750	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TGGACACAGCATCTTTAGTGC	0.577																																					p.D750D		Atlas-SNP	.											PLIN4_ENST00000301286,right_lower_lobe,carcinoma,0,2	PLIN4	191	2	0			c.T2250C						scavenged	.						120.0	88.0	98.0					19																	4511680		2000	4144	6144	SO:0001819	synonymous_variant	729359	exon3			CACAGCATCTTTA	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2250T>C	19.37:g.4511680A>G		Somatic	68	9	0.132353		WXS	Illumina HiSeq	Phase_I	76	17	0.223684	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			.	.	none		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
JARID2	3720	hgsc.bcm.edu	37	6	15513482	15513482	+	Silent	SNP	G	G	A	rs2235258	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:15513482G>A	ENST00000341776.2	+	16	3523	c.3279G>A	c.(3277-3279)ctG>ctA	p.L1093L	JARID2_ENST00000397311.3_Silent_p.L921L	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1093					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				ATACAGAGCTGCGGCAGCGCA	0.667													G|||	2929	0.584864	0.3003	0.6513	5008	,	,		16258	0.6667		0.7465	False		,,,				2504	0.6718				p.L1093L		Atlas-SNP	.											JARID2,NS,carcinoma,0,1	JARID2	135	1	0			c.G3279A						PASS	.	G		1670,2696		354,962,867	16.0	15.0	15.0		3279	2.5	1.0	6	dbSNP_98	15	6569,1975		2569,1431,272	no	coding-synonymous	JARID2	NM_004973.2		2923,2393,1139	AA,AG,GG		23.1156,38.2501,36.1813		1093/1247	15513482	8239,4671	2183	4272	6455	SO:0001819	synonymous_variant	3720	exon16			AGAGCTGCGGCAG	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.3279G>A	6.37:g.15513482G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																			G|0.410;A|0.590	0.590	strong		0.667	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
TNS3	64759	hgsc.bcm.edu	37	7	47436497	47436497	+	Silent	SNP	G	G	A	rs17544028	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:47436497G>A	ENST00000398879.1	-	16	1290	c.924C>T	c.(922-924)tcC>tcT	p.S308S	TNS3_ENST00000355730.3_Intron|TNS3_ENST00000311160.9_Silent_p.S308S			Q68CZ2	TENS3_HUMAN	tensin 3	308					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						ACAAGTGTTCGGACCCTGCAC	0.532													G|||	555	0.110823	0.034	0.1513	5008	,	,		20266	0.0764		0.159	False		,,,				2504	0.1718				p.S308S		Atlas-SNP	.											.	TNS3	140	.	0			c.C924T						PASS	.	G		201,4137		7,187,1975	146.0	158.0	154.0		924	0.4	0.1	7	dbSNP_123	154	1325,7203		93,1139,3032	no	coding-synonymous	TNS3	NM_022748.11		100,1326,5007	AA,AG,GG		15.5371,4.6335,11.8607		308/1446	47436497	1526,11340	2169	4264	6433	SO:0001819	synonymous_variant	64759	exon16			GTGTTCGGACCCT	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"""SH2 domain containing"""	21616	protein-coding gene	gene with protein product	"""tumor endothelial marker 6"""	606825	"""tensin-like SH2 domain-containing 1"""	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.924C>T	7.37:g.47436497G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	21	5	0.238095	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Silent	SNP	ENST00000398879.1	37	CCDS5506.2																																																																																			G|0.892;A|0.108	0.108	strong		0.532	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748	
OBSCN	84033	hgsc.bcm.edu	37	1	228402508	228402508	+	Silent	SNP	C	C	T	rs2776853	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228402508C>T	ENST00000422127.1	+	5	1581	c.1537C>T	c.(1537-1539)Ctg>Ttg	p.L513L	C1orf145_ENST00000295012.5_5'Flank|OBSCN_ENST00000570156.2_Silent_p.L513L|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.L513L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	513					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GAAGCCTCCCCTGCAACCCCC	0.612													C|||	1381	0.275759	0.3086	0.353	5008	,	,		17070	0.1706		0.3618	False		,,,				2504	0.1963				p.L513L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C1537T						PASS	.	C	,	1272,2538		201,870,834	35.0	39.0	38.0		1537,1537	3.6	0.0	1	dbSNP_100	38	3213,5025		632,1949,1538	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	833,2819,2372	TT,TC,CC		39.0022,33.3858,37.2261	,	513/7969,513/6621	228402508	4485,7563	1905	4119	6024	SO:0001819	synonymous_variant	84033	exon5			CCTCCCCTGCAAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.1537C>T	1.37:g.228402508C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.687;T|0.313	0.313	strong		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
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 GAIIx	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_ENST00000409098.1_5'Flank|MIR5001_ENST00000580185.1_RNA|EIF4E2_ENST00000409495.1_5'Flank|EIF4E2_ENST00000409514.1_5'Flank|EIF4E2_ENST00000409322.1_5'Flank|EIF4E2_ENST00000409167.3_5'Flank|EIF4E2_ENST00000409394.1_5'Flank|EIF4E2_ENST00000258416.3_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		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	4	4	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	
C1orf101	257044	hgsc.bcm.edu	37	1	244724092	244724092	+	Silent	SNP	G	G	A	rs7544794	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:244724092G>A	ENST00000366534.4	+	10	1206	c.1152G>A	c.(1150-1152)tcG>tcA	p.S384S	C1orf101_ENST00000473875.1_3'UTR|C1orf101_ENST00000366533.4_Silent_p.S384S|C1orf101_ENST00000366531.3_Silent_p.S233S	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	384						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)			TAAGTCTATCGGTGACTGCTA	0.398													A|||	1368	0.273163	0.4334	0.2435	5008	,	,		15481	0.376		0.0775	False		,,,				2504	0.1728				p.S384S		Atlas-SNP	.											.	C1orf101	158	.	0			c.G1152A						PASS	.	A	,,	1680,2726	654.5+/-399.8	318,1044,841	109.0	113.0	111.0		1152,699,1152	-5.6	0.0	1	dbSNP_116	111	764,7836	785.0+/-407.6	26,712,3562	no	coding-synonymous,coding-synonymous,coding-synonymous	C1orf101	NM_001130957.1,NM_001242340.1,NM_173807.4	,,	344,1756,4403	AA,AG,GG		8.8837,38.1298,18.7913	,,	384/952,233/801,384/833	244724092	2444,10562	2203	4300	6503	SO:0001819	synonymous_variant	257044	exon10			TCTATCGGTGACT	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.1152G>A	1.37:g.244724092G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	139	65	0.467626	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																			G|0.779;A|0.221	0.221	strong		0.398	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807	
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 GAIIx	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_ENST00000447897.2_Silent_p.K809K|TMEM257_ENST00000408967.2_5'Flank|SLITRK2_ENST00000434188.2_Silent_p.K809K|SLITRK2_ENST00000413937.2_Silent_p.K809K|SLITRK2_ENST00000428560.2_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		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	174	122	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	
ADRB2	154	hgsc.bcm.edu	37	5	148206917	148206917	+	Silent	SNP	C	C	A	rs1042718	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148206917C>A	ENST00000305988.4	+	1	762	c.523C>A	c.(523-525)Cgg>Agg	p.R175R		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	175					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	GCACTGGTACCGGGCCACCCA	0.537													C|||	1491	0.297724	0.3381	0.2882	5008	,	,		19720	0.369		0.169	False		,,,				2504	0.3088				p.R175R		Atlas-SNP	.											.	ADRB2	42	.	0			c.C523A						PASS	.	C		1419,2987	464.3+/-353.8	230,959,1014	196.0	174.0	181.0		523	2.9	1.0	5	dbSNP_86	181	1462,7138	280.5+/-294.5	119,1224,2957	no	coding-synonymous	ADRB2	NM_000024.5		349,2183,3971	AA,AC,CC		17.0,32.2061,22.1513		175/414	148206917	2881,10125	2203	4300	6503	SO:0001819	synonymous_variant	154	exon1			TGGTACCGGGCCA	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.523C>A	5.37:g.148206917C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Silent	SNP	ENST00000305988.4	37	CCDS4292.1																																																																																			C|0.747;A|0.253	0.253	strong		0.537	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
PIDD1	55367	hgsc.bcm.edu	37	11	804212	804212	+	Silent	SNP	C	C	A	rs7104785	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:804212C>A	ENST00000347755.5	-	2	318	c.177G>T	c.(175-177)ctG>ctT	p.L59L	PIDD_ENST00000411829.2_Silent_p.L59L|PIDD_ENST00000534649.1_5'UTR	NM_145886.3|NM_145887.3	NP_665893.2|NP_665894.2																					GCAGCAGCTGCAGAGGCTGCT	0.672													A|||	1757	0.350839	0.292	0.6354	5008	,	,		16607	0.2728		0.493	False		,,,				2504	0.1626				p.L59L		Atlas-SNP	.											.	PIDD	76	.	0			c.G177T						PASS	.	A	,	1396,3010	648.5+/-398.7	216,964,1023	29.0	29.0	29.0		177,177	-7.2	0.0	11	dbSNP_116	29	4402,4196	537.7+/-383.3	1138,2126,1035	no	coding-synonymous,coding-synonymous	PIDD	NM_145886.3,NM_145887.3	,	1354,3090,2058	AA,AC,CC		48.802,31.6841,44.5863	,	59/911,59/894	804212	5798,7206	2203	4299	6502	SO:0001819	synonymous_variant	55367	exon2			CAGCTGCAGAGGC																												ENST00000347755.5:c.177G>T	11.37:g.804212C>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_145887		Silent	SNP	ENST00000347755.5	37	CCDS7716.1																																																																																			C|0.567;A|0.433	0.433	strong		0.672	PIDD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257103.1		
NXPE4	54827	hgsc.bcm.edu	37	11	114441943	114441943	+	Missense_Mutation	SNP	G	G	A	rs10891705	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:114441943G>A	ENST00000375478.3	-	6	1532	c.1352C>T	c.(1351-1353)gCc>gTc	p.A451V	NXPE4_ENST00000424261.2_Missense_Mutation_p.A167V	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	451			A -> V (in dbSNP:rs10891705). {ECO:0000269|PubMed:15375555}.			extracellular vesicular exosome (GO:0070062)											GACATTGAGGGCCCTTCGGAT	0.438													G|||	1803	0.360024	0.2118	0.2968	5008	,	,		17837	0.6746		0.332	False		,,,				2504	0.3098				p.A451V		Atlas-SNP	.											.	.	.	.	0			c.C1352T						PASS	.	G	VAL/ALA,VAL/ALA	889,2877		91,707,1085	136.0	125.0	129.0		1352,500	-0.9	1.0	11	dbSNP_120	129	2795,5417		460,1875,1771	yes	missense,missense	FAM55D	NM_001077639.1,NM_017678.2	64,64	551,2582,2856	AA,AG,GG		34.0356,23.6059,30.7564	benign,benign	451/545,167/261	114441943	3684,8294	1883	4106	5989	SO:0001583	missense	54827	exon6			TTGAGGGCCCTTC	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1352C>T	11.37:g.114441943G>A	ENSP00000364627:p.Ala451Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	844	0.38644688644688646	110	0.22357723577235772	105	0.2900552486187845	381	0.666083916083916	248	0.32717678100263853	G	11.30	1.599017	0.28534	0.236059	0.340356	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.20598	2.06;2.06	5.51	-0.856	0.10697	.	0.586195	0.16084	N	0.230369	T	0.00012	0.0000	L	0.45285	1.41	0.40129	P	0.023301000000000016	B	0.27316	0.175	B	0.37304	0.246	T	0.30851	-0.9964	9	0.14656	T	0.56	.	6.3911	0.21587	0.5261:0.0:0.3512:0.1227	rs10891705;rs61407553;rs10891705	451	Q6UWF7	FA55D_HUMAN	V	167;451	ENSP00000401503:A167V;ENSP00000364627:A451V	ENSP00000364627:A451V	A	-	2	0	FAM55D	113947153	0.038000	0.19896	0.967000	0.41034	0.984000	0.73092	0.241000	0.18065	-0.347000	0.08299	-1.074000	0.02243	GCC	G|0.639;A|0.361	0.361	strong		0.438	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
HECTD1	25831	hgsc.bcm.edu	37	14	31619392	31619392	+	Silent	SNP	T	T	C	rs11620816	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:31619392T>C	ENST00000399332.1	-	13	2456	c.1968A>G	c.(1966-1968)caA>caG	p.Q656Q	HECTD1_ENST00000553700.1_Silent_p.Q656Q	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	656			Q -> H (in dbSNP:rs11620816).		neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		GTTTACCTTGTTGCAATTCTT	0.338													C|||	1468	0.293131	0.5053	0.1585	5008	,	,		17711	0.2907		0.1074	False		,,,				2504	0.2955				p.Q656Q		Atlas-SNP	.											.	HECTD1	159	.	0			c.A1968G						PASS	.	C		1599,2143		354,891,626	250.0	232.0	238.0		1968	6.0	1.0	14	dbSNP_120	238	1060,7164		60,940,3112	no	coding-synonymous	HECTD1	NM_015382.2		414,1831,3738	CC,CT,TT		12.8891,42.7312,22.2213		656/2611	31619392	2659,9307	1871	4112	5983	SO:0001819	synonymous_variant	25831	exon13			ACCTTGTTGCAAT	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.1968A>G	14.37:g.31619392T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	163	70	0.429448	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1																																																																																			C|0.246;T|0.754	0.246	strong		0.338	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
ZHX2	22882	hgsc.bcm.edu	37	8	123964953	123964953	+	Silent	SNP	C	C	T	rs3808600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:123964953C>T	ENST00000314393.4	+	3	2038	c.1203C>T	c.(1201-1203)acC>acT	p.T401T		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	401	Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CAGGAGTCACCAACCATGGCC	0.632													C|||	1161	0.231829	0.0136	0.3314	5008	,	,		16083	0.131		0.3579	False		,,,				2504	0.4305				p.T401T	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.C1203T						PASS	.	C		308,4098	164.7+/-196.3	10,288,1905	50.0	57.0	55.0		1203	4.0	1.0	8	dbSNP_107	55	2985,5615	460.5+/-365.2	509,1967,1824	no	coding-synonymous	ZHX2	NM_014943.3		519,2255,3729	TT,TC,CC		34.7093,6.9905,25.3191		401/838	123964953	3293,9713	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			AGTCACCAACCAT	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1203C>T	8.37:g.123964953C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			C|0.762;T|0.238	0.238	strong		0.632	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
MYH4	4622	hgsc.bcm.edu	37	17	10355763	10355763	+	Missense_Mutation	SNP	T	T	C	rs917361	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:10355763T>C	ENST00000255381.2	-	26	3428	c.3318A>G	c.(3316-3318)atA>atG	p.I1106M	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1106			I -> M (in dbSNP:rs917361). {ECO:0000269|PubMed:10388558}.		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						TTTGTAGCTGTATTGCAAGGG	0.353													C|||	2674	0.533946	0.3442	0.5187	5008	,	,		18291	0.8631		0.3698	False		,,,				2504	0.6309				p.I1106M		Atlas-SNP	.											.	MYH4	349	.	0			c.A3318G						PASS	.	C	MET/ILE	1585,2821	666.0+/-401.6	281,1023,899	150.0	138.0	142.0		3318	4.6	1.0	17	dbSNP_86	142	3577,5023	628.0+/-398.0	760,2057,1483	yes	missense	MYH4	NM_017533.2	10	1041,3080,2382	CC,CT,TT		41.593,35.9737,39.6894	benign	1106/1940	10355763	5162,7844	2203	4300	6503	SO:0001583	missense	4622	exon26			TAGCTGTATTGCA		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.3318A>G	17.37:g.10355763T>C	ENSP00000255381:p.Ile1106Met	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	155	66	0.425806	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	1125	0.5151098901098901	162	0.32926829268292684	181	0.5	498	0.8706293706293706	284	0.37467018469656993	C	7.093	0.572480	0.13623	0.359737	0.41593	ENSG00000141048	ENST00000255381	D	0.82984	-1.67	5.6	4.63	0.57726	Myosin tail (1);	0.000000	0.45361	N	0.000374	T	0.00012	0.0000	N	0.03050	-0.425	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.08055	0.003	T	0.38950	-0.9637	9	0.34782	T	0.22	.	4.1163	0.10083	0.1302:0.6059:0.126:0.1378	rs917361;rs3744556;rs17811136;rs52820909;rs58019198;rs917361	1106	Q9Y623	MYH4_HUMAN	M	1106	ENSP00000255381:I1106M	ENSP00000255381:I1106M	I	-	3	3	MYH4	10296488	0.004000	0.15560	0.998000	0.56505	0.963000	0.63663	-0.314000	0.08092	0.854000	0.35336	-0.119000	0.15052	ATA	C|0.466;N|0.000	0.466	strong		0.353	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
CDH22	64405	hgsc.bcm.edu	37	20	44806643	44806643	+	Silent	SNP	G	G	A	rs34603854	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44806643G>A	ENST00000372262.3	-	10	2257	c.1857C>T	c.(1855-1857)gcC>gcT	p.A619A	CDH22_ENST00000537909.1_Silent_p.A619A	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	619					brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				TGAGGGAGGCGGCCATGACAA	0.657													G|||	280	0.0559105	0.031	0.0764	5008	,	,		17343	0.0129		0.1024	False		,,,				2504	0.0716				p.A619A		Atlas-SNP	.											.	CDH22	112	.	0			c.C1857T						PASS	.	G		238,4168	139.2+/-174.8	7,224,1972	82.0	64.0	70.0		1857	-8.9	0.1	20	dbSNP_126	70	1070,7530	224.8+/-261.1	72,926,3302	no	coding-synonymous	CDH22	NM_021248.1		79,1150,5274	AA,AG,GG		12.4419,5.4017,10.0569		619/829	44806643	1308,11698	2203	4300	6503	SO:0001819	synonymous_variant	64405	exon11			GGAGGCGGCCATG	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"""Cadherins / Major cadherins"""	13251	protein-coding gene	gene with protein product		609920	"""cadherin-like 22"""	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1857C>T	20.37:g.44806643G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_021248	B9EGK7|O43205	Silent	SNP	ENST00000372262.3	37	CCDS13395.1																																																																																			G|0.916;A|0.084	0.084	strong		0.657	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248	
MTX1	4580	hgsc.bcm.edu	37	1	155178782	155178782	+	Missense_Mutation	SNP	A	A	T	rs760077	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:155178782A>T	ENST00000368376.3	+	1	293	c.187A>T	c.(187-189)Act>Tct	p.T63S	THBS3_ENST00000541990.1_5'Flank|THBS3_ENST00000486260.1_5'UTR|MTX1_ENST00000316721.4_Missense_Mutation_p.T63S|THBS3_ENST00000457183.2_5'Flank|RP11-263K19.6_ENST00000455788.1_RNA|THBS3_ENST00000368378.3_5'Flank|MTX1_ENST00000609421.1_5'Flank	NM_002455.3	NP_002446.2	Q13505	MTX1_HUMAN	metaxin 1	63			T -> S (in dbSNP:rs760077). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)				breast(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)	7	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GCGCCGTGACACTCCGAGGCG	0.761													T|||	3339	0.666733	0.6331	0.7608	5008	,	,		8727	0.7738		0.6054	False		,,,				2504	0.5982				p.T63S		Atlas-SNP	.											.	MTX1	17	.	0			c.A187T						PASS	.	T	SER/THR,SER/THR	2914,1394		1026,862,266	7.0	11.0	10.0		187,187	-2.4	0.0	1	dbSNP_86	10	5140,3348		1612,1916,716	yes	missense,missense	MTX1	NM_002455.3,NM_198883.2	58,58	2638,2778,982	TT,TA,AA		39.4439,32.3584,37.0585	benign,benign	63/467,63/436	155178782	8054,4742	2154	4244	6398	SO:0001583	missense	4580	exon1			CGTGACACTCCGA		CCDS1100.1, CCDS1101.1	1q21	2008-07-18			ENSG00000173171	ENSG00000173171			7504	protein-coding gene	gene with protein product		600605		MTX		7753840	Standard	XM_006711338		Approved	MTXN	uc001fjb.3	Q13505	OTTHUMG00000035708	ENST00000368376.3:c.187A>T	1.37:g.155178782A>T	ENSP00000357360:p.Thr63Ser	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_198883	B1AVR9|B1AVS0|B2R9P4|Q9BUU3	Missense_Mutation	SNP	ENST00000368376.3	37	CCDS1100.1	1515	0.6936813186813187	314	0.6382113821138211	252	0.6961325966850829	474	0.8286713286713286	475	0.6266490765171504	T	10.85	1.466570	0.26335	0.676416	0.605561	ENSG00000173171	ENST00000368376;ENST00000316721	T;T	0.27890	1.64;1.64	4.25	-2.39	0.06602	.	0.398228	0.18519	N	0.138831	T	0.01320	0.0043	N	0.01168	-0.975	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22591	-1.0212	9	0.02654	T	1	-7.2218	0.3438	0.00338	0.2917:0.2744:0.1499:0.2841	rs760077;rs57404131	63;63	Q13505-2;Q13505	.;MTX1_HUMAN	S	63	ENSP00000357360:T63S;ENSP00000317106:T63S	ENSP00000317106:T63S	T	+	1	0	MTX1	153445406	0.001000	0.12720	0.000000	0.03702	0.015000	0.08874	-0.293000	0.08320	-0.656000	0.05380	-0.257000	0.10917	ACT	A|0.304;T|0.696	0.696	strong		0.761	MTX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086844.1	NM_198883	
TBCD	6904	hgsc.bcm.edu	37	17	80899281	80899281	+	Silent	SNP	G	G	A	rs9390	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:80899281G>A	ENST00000355528.4	+	38	3616	c.3486G>A	c.(3484-3486)gcG>gcA	p.A1162A	TBCD_ENST00000576691.1_3'UTR|TBCD_ENST00000539345.2_Silent_p.A1200A	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1162					'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			ACAGGGACGCGGAGCTTGCAG	0.647													G|||	2153	0.429912	0.1997	0.4798	5008	,	,		18481	0.5486		0.5507	False		,,,				2504	0.4591				p.A1162A		Atlas-SNP	.											.	TBCD	94	.	0			c.G3486A						PASS	.	G		964,3292		125,714,1289	37.0	48.0	44.0		3486	-9.6	0.0	17	dbSNP_52	44	4091,4383		988,2115,1134	no	coding-synonymous	TBCD	NM_005993.4		1113,2829,2423	AA,AG,GG		48.2771,22.6504,39.7093		1162/1193	80899281	5055,7675	2128	4237	6365	SO:0001819	synonymous_variant	6904	exon38			GGACGCGGAGCTT	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.3486G>A	17.37:g.80899281G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Silent	SNP	ENST00000355528.4	37	CCDS45818.1																																																																																			A|0.453;C|0.000;G|0.546;T|0.000	0.453	strong		0.647	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
SLC9C1	285335	hgsc.bcm.edu	37	3	111921116	111921116	+	Missense_Mutation	SNP	C	C	A	rs9288938	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111921116C>A	ENST00000305815.5	-	18	2555	c.2303G>T	c.(2302-2304)aGt>aTt	p.S768I	SLC9C1_ENST00000487372.1_Missense_Mutation_p.S720I	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	768			S -> I (in dbSNP:rs9288938). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CTGTTTAGAACTTGTAATCTG	0.353													C|||	1680	0.335463	0.3699	0.4049	5008	,	,		17677	0.3393		0.2376	False		,,,				2504	0.3364				p.S768I		Atlas-SNP	.											.	.	.	.	0			c.G2303T						PASS	.	C	ILE/SER	1601,2805	495.5+/-363.3	302,997,904	116.0	119.0	118.0		2303	2.0	1.0	3	dbSNP_119	118	2330,6268	388.5+/-342.6	322,1686,2291	yes	missense	SLC9A10	NM_183061.1	142	624,2683,3195	AA,AC,CC		27.0993,36.3368,30.2292	benign	768/1178	111921116	3931,9073	2203	4299	6502	SO:0001583	missense	285335	exon18			TTAGAACTTGTAA	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2303G>T	3.37:g.111921116C>A	ENSP00000306627:p.Ser768Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	689	0.31547619047619047	181	0.3678861788617886	138	0.3812154696132597	185	0.32342657342657344	185	0.24406332453825857	C	15.44	2.835271	0.50951	0.363368	0.270993	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.78364	-1.17;-1.17	5.78	1.96	0.26148	.	0.273276	0.33127	N	0.005256	T	0.00012	0.0000	M	0.62723	1.935	0.43076	P	0.005272000000000054	P;P	0.48162	0.906;0.893	P;B	0.54270	0.747;0.387	T	0.12400	-1.0549	9	0.32370	T	0.25	.	6.0804	0.19938	0.0:0.5468:0.2926:0.1606	rs9288938;rs61474261;rs9288938	720;768	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	I	768;720	ENSP00000306627:S768I;ENSP00000420688:S720I	ENSP00000306627:S768I	S	-	2	0	SLC9A10	113403806	0.996000	0.38824	0.998000	0.56505	0.760000	0.43138	0.167000	0.16602	0.072000	0.16694	0.609000	0.83330	AGT	C|0.676;A|0.324	0.324	strong		0.353	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
EHF	26298	hgsc.bcm.edu	37	11	34668143	34668143	+	Silent	SNP	C	C	T	rs2281910	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:34668143C>T	ENST00000533754.1	+	3	472	c.255C>T	c.(253-255)ctC>ctT	p.L85L	EHF_ENST00000531794.1_Silent_p.L107L|EHF_ENST00000450654.2_Silent_p.L85L|EHF_ENST00000257831.3_Silent_p.L85L|EHF_ENST00000531728.1_Silent_p.L85L|EHF_ENST00000527935.1_Silent_p.L85L|EHF_ENST00000530286.1_Silent_p.L85L					ets homologous factor										NFIA/EHF(2)	autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|lung(8)|upper_aerodigestive_tract(1)	17		all_hematologic(20;0.117)	Epithelial(1;0.055)|all cancers(1;0.137)|STAD - Stomach adenocarcinoma(6;0.235)			GCGAGCACCTCTGCAGCATGA	0.582													C|||	1158	0.23123	0.1558	0.3213	5008	,	,		21223	0.38		0.1948	False		,,,				2504	0.1534				p.L107L		Atlas-SNP	.											.	EHF	38	.	0			c.C321T						PASS	.	C	,,	688,3716	289.8+/-280.6	48,592,1562	124.0	119.0	120.0		255,321,255	-3.2	1.0	11	dbSNP_100	120	1762,6834	318.4+/-313.7	178,1406,2714	no	coding-synonymous,coding-synonymous,coding-synonymous	EHF	NM_001206615.1,NM_001206616.1,NM_012153.5	,,	226,1998,4276	TT,TC,CC		20.4979,15.6222,18.8462	,,	85/278,107/323,85/301	34668143	2450,10550	2202	4298	6500	SO:0001819	synonymous_variant	26298	exon3			GCACCTCTGCAGC	AF170583	CCDS7894.1, CCDS55752.1, CCDS55753.1	11p12	2008-07-18				ENSG00000135373			3246	protein-coding gene	gene with protein product	"""epithelium-specific ets factor 3"", ""ESE3 transcription factor"""	605439				10527851	Standard	NM_012153		Approved	ESE3, ESEJ	uc021qfu.1	Q9NZC4		ENST00000533754.1:c.255C>T	11.37:g.34668143C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_001206616		Silent	SNP	ENST00000533754.1	37	CCDS7894.1																																																																																			C|0.792;T|0.208	0.208	strong		0.582	EHF-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389855.1	NM_012153	
SETX	23064	hgsc.bcm.edu	37	9	135203530	135203530	+	Missense_Mutation	SNP	A	A	C	rs3739922	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135203530A>C	ENST00000224140.5	-	10	3637	c.3455T>G	c.(3454-3456)tTt>tGt	p.F1152C	SETX_ENST00000372169.2_Missense_Mutation_p.F1152C|SETX_ENST00000393220.1_Missense_Mutation_p.F1152C	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1152			F -> C (in dbSNP:rs3739922). {ECO:0000269|PubMed:14770181}.		cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		AATTTCACAAAATTCTTCAAC	0.398													A|||	449	0.0896565	0.0492	0.062	5008	,	,		18778	0.2371		0.0328	False		,,,				2504	0.0706				p.F1152C		Atlas-SNP	.											.	SETX	234	.	0			c.T3455G						PASS	.	A	CYS/PHE	211,4195	128.6+/-165.4	0,211,1992	90.0	93.0	92.0		3455	1.8	0.0	9	dbSNP_107	92	289,8311	107.6+/-168.3	5,279,4016	yes	missense	SETX	NM_015046.5	205	5,490,6008	CC,CA,AA		3.3605,4.7889,3.8444	benign	1152/2678	135203530	500,12506	2203	4300	6503	SO:0001583	missense	23064	exon10			TCACAAAATTCTT	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.3455T>G	9.37:g.135203530A>C	ENSP00000224140:p.Phe1152Cys	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	151	78	0.516556	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	216	0.0989010989010989	19	0.03861788617886179	20	0.055248618784530384	149	0.26048951048951047	28	0.036939313984168866	A	11.34	1.608425	0.28623	0.047889	0.033605	ENSG00000107290	ENST00000224140;ENST00000372169;ENST00000393220	D;D;D	0.86769	-2.08;-2.17;-1.79	5.62	1.75	0.24633	.	4.607390	0.00166	N	0.000006	T	0.00039	0.0001	L	0.34521	1.04	0.80722	P	0.0	B;B;B	0.14438	0.01;0.003;0.01	B;B;B	0.14023	0.01;0.002;0.01	T	0.13469	-1.0508	9	0.46703	T	0.11	.	5.0594	0.14550	0.5409:0.2953:0.1637:0.0	rs3739922;rs52804863;rs3739922	1152;1152;1152	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	C	1152	ENSP00000224140:F1152C;ENSP00000361242:F1152C;ENSP00000376913:F1152C	ENSP00000224140:F1152C	F	-	2	0	SETX	134193351	0.007000	0.16637	0.004000	0.12327	0.207000	0.24258	1.533000	0.36040	0.401000	0.25424	0.528000	0.53228	TTT	A|0.931;C|0.069	0.069	strong		0.398	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
CPA4	51200	hgsc.bcm.edu	37	7	129962414	129962414	+	Silent	SNP	C	C	T	rs2306848	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:129962414C>T	ENST00000222482.4	+	11	1192	c.1164C>T	c.(1162-1164)acC>acT	p.T388T	CPA4_ENST00000445470.2_Silent_p.T355T|CPA4_ENST00000493259.1_Silent_p.T284T	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	388					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					ATACCGGGACCTATGGCTTCC	0.537													C|||	222	0.0443291	0.0613	0.0591	5008	,	,		21653	0.0139		0.0636	False		,,,				2504	0.0225				p.T388T		Atlas-SNP	.											.	CPA4	47	.	0			c.C1164T						PASS	.	C	,	269,4137	151.8+/-185.6	10,249,1944	179.0	160.0	166.0		1065,1164	2.9	0.1	7	dbSNP_100	166	658,7942	167.7+/-219.4	23,612,3665	no	coding-synonymous,coding-synonymous	CPA4	NM_001163446.1,NM_016352.3	,	33,861,5609	TT,TC,CC		7.6512,6.1053,7.1275	,	355/389,388/422	129962414	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	51200	exon11			CGGGACCTATGGC	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.1164C>T	7.37:g.129962414C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_016352	B7Z576|Q86UY9	Silent	SNP	ENST00000222482.4	37	CCDS5818.1																																																																																			C|0.941;T|0.059	0.059	strong		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
POTEC	388468	hgsc.bcm.edu	37	18	14543057	14543057	+	Missense_Mutation	SNP	T	T	G	rs532182918|rs9807633	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:14543057T>G	ENST00000358970.5	-	1	88	c.89A>C	c.(88-90)cAc>cCc	p.H30P	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	30			H -> P (in dbSNP:rs9807633).							NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GGGGAAGCGGTGGTGAAACCA	0.537													.|||	1443	0.288139	0.2776	0.2565	5008	,	,		19800	0.4544		0.1521	False		,,,				2504	0.2935				p.H30P		Atlas-SNP	.											.	POTEC	129	.	0			c.A89C						PASS	.						127.0	109.0	114.0					18																	14543057		692	1591	2283	SO:0001583	missense	388468	exon1			AAGCGGTGGTGAA	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.89A>C	18.37:g.14543057T>G	ENSP00000351856:p.His30Pro	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	201	80	0.39801	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	630	0.28846153846153844	139	0.28252032520325204	94	0.2596685082872928	279	0.48776223776223776	118	0.15567282321899736	t	9.187	1.025066	0.19433	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.30182	1.54	0.722	-1.44	0.08856	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	D	0.57899	0.981	B	0.44044	0.439	T	0.45614	-0.9249	7	0.72032	D	0.01	.	.	.	.	rs9807633;rs57776886;rs9807633	30	B2RU33	POTEC_HUMAN	P	30	ENSP00000351856:H30P	ENSP00000351856:H30P	H	-	2	0	POTEC	14533057	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.584000	0.05800	-0.528000	0.06366	0.156000	0.16432	CAC	T|0.701;G|0.299	0.299	strong		0.537	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
KIAA1211	57482	hgsc.bcm.edu	37	4	57182647	57182647	+	Silent	SNP	G	G	A	rs3822003	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57182647G>A	ENST00000504228.1	+	6	3084	c.2979G>A	c.(2977-2979)gcG>gcA	p.A993A	KIAA1211_ENST00000541073.1_Silent_p.A986A|KIAA1211_ENST00000264229.6_Silent_p.A993A			Q6ZU35	K1211_HUMAN	KIAA1211	993	Pro-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CTCGCCGAGCGGGGAGGCCGG	0.667													G|||	949	0.189497	0.0174	0.2061	5008	,	,		13721	0.253		0.339	False		,,,				2504	0.1912				p.A993A		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G2979A						PASS	.	G		297,3731		13,271,1730	34.0	43.0	40.0		2979	-10.1	0.0	4	dbSNP_107	40	2817,5535		481,1855,1840	no	coding-synonymous	KIAA1211	NM_020722.1		494,2126,3570	AA,AG,GG		33.7284,7.3734,25.1535		993/1234	57182647	3114,9266	2014	4176	6190	SO:0001819	synonymous_variant	57482	exon8			CCGAGCGGGGAGG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.2979G>A	4.37:g.57182647G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			G|0.773;A|0.227	0.227	strong		0.667	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
USP51	158880	hgsc.bcm.edu	37	X	55514818	55514818	+	Silent	SNP	C	C	T	rs3126255	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:55514818C>T	ENST00000500968.3	-	2	637	c.555G>A	c.(553-555)gaG>gaA	p.E185E	USP51_ENST00000586165.1_Intron	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	185					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						CAAACTCGACCTCCAGCAACC	0.587													.|||	1754	0.464636	0.0507	0.3501	3775	,	,		7246	0.4712		0.5149	False		,,,				2504	0.4611				p.E185E		Atlas-SNP	.											.	USP51	71	.	0			c.G555A						PASS	.	C		500,3335		30,369,71,1233,500	35.0	30.0	32.0		555	2.9	1.0	X	dbSNP_103	32	4634,2094		1149,1055,1281,224,591	no	coding-synonymous	USP51	NM_201286.3		1179,1424,1352,1457,1091	TT,TC,T,CC,C		31.1237,13.0378,48.6036		185/712	55514818	5134,5429	2203	4300	6503	SO:0001819	synonymous_variant	158880	exon2			CTCGACCTCCAGC	BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.555G>A	X.37:g.55514818C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_201286	Q8IWJ8	Silent	SNP	ENST00000500968.3	37	CCDS14370.1																																																																																			C|0.528;T|0.472	0.472	strong		0.587	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2	NM_201286	
IDO2	169355	hgsc.bcm.edu	37	8	39872935	39872935	+	Nonsense_Mutation	SNP	T	T	A	rs4503083	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:39872935T>A	ENST00000389060.4	+	10	1038	c.1038T>A	c.(1036-1038)taT>taA	p.Y346*	IDO2_ENST00000343295.4_3'UTR|IDO2_ENST00000502986.2_Nonsense_Mutation_p.Y359*			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	346					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						TGCGGAGCTATCACATCACCA	0.542													T|||	1151	0.229832	0.112	0.317	5008	,	,		19406	0.3601		0.2107	False		,,,				2504	0.2127				p.Y359X		Atlas-SNP	.											.	IDO2	78	.	0			c.T1077A						PASS	.	T	stop/TYR	458,3716		22,414,1651	80.0	79.0	79.0		1077	-2.2	1.0	8	dbSNP_111	79	1743,6659		175,1393,2633	yes	stop-gained	IDO2	NM_194294.2		197,1807,4284	AA,AT,TT		20.7451,10.9727,17.5016		359/421	39872935	2201,10375	2087	4201	6288	SO:0001587	stop_gained	169355	exon11			GAGCTATCACATC	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.1038T>A	8.37:g.39872935T>A	ENSP00000426447:p.Tyr346*	Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_194294	A4UD41	Nonsense_Mutation	SNP	ENST00000389060.4	37		540	0.24725274725274726	46	0.09349593495934959	106	0.292817679558011	228	0.3986013986013986	160	0.21108179419525067	T	18.77	3.694799	0.68386	0.109727	0.207451	ENSG00000188676	ENST00000502986;ENST00000389060	.	.	.	5.74	-2.22	0.06952	.	0.257128	0.39210	N	0.001422	.	.	.	.	.	.	0.09310	P	0.9999999999991586	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0548	0.71904	0.0:0.7555:0.0:0.2445	rs4503083;rs56452642;rs4503083	.	.	.	X	359;346	.	.	Y	+	3	2	IDO2	39992092	0.996000	0.38824	0.988000	0.46212	0.680000	0.39746	0.394000	0.20834	-0.380000	0.07894	-0.256000	0.11100	TAT	T|0.758;A|0.242	0.242	strong		0.542	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
LRRC2	79442	hgsc.bcm.edu	37	3	46592987	46592987	+	Missense_Mutation	SNP	A	A	G	rs28687398	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46592987A>G	ENST00000395905.3	-	2	487	c.95T>C	c.(94-96)gTg>gCg	p.V32A	LRRC2_ENST00000296144.3_Missense_Mutation_p.V32A|LRRC2_ENST00000496388.1_Intron|AC104304.2_ENST00000583198.1_RNA	NM_024512.4	NP_078788.2	Q9BYS8	LRRC2_HUMAN	leucine rich repeat containing 2	32			V -> A (in dbSNP:rs28687398). {ECO:0000269|PubMed:14702039}.							breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	17		Ovarian(412;0.0563)		OV - Ovarian serous cystadenocarcinoma(275;6.37e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00133)|KIRC - Kidney renal clear cell carcinoma(197;0.0214)|Kidney(197;0.0254)		AAGCCTTTCCACCTCCTTCTT	0.463													G|||	630	0.125799	0.0946	0.1037	5008	,	,		18319	0.1687		0.0875	False		,,,				2504	0.1789				p.V32A		Atlas-SNP	.											.	LRRC2	37	.	0			c.T95C						PASS	.	G	ALA/VAL	425,3981	786.5+/-414.8	23,379,1801	140.0	139.0	139.0		95	1.8	0.1	3	dbSNP_125	139	664,7936	789.4+/-407.6	22,620,3658	yes	missense	LRRC2	NM_024512.4	64	45,999,5459	GG,GA,AA		7.7209,9.6459,8.3731	benign	32/372	46592987	1089,11917	2203	4300	6503	SO:0001583	missense	79442	exon2			CTTTCCACCTCCT	AJ308569	CCDS2741.1	3p21.3	2014-07-30	2003-11-19		ENSG00000163827	ENSG00000163827			14676	protein-coding gene	gene with protein product		607180	"""leucine-rich repeat-containing 2"""			11896456	Standard	NM_024512		Approved		uc010hji.3	Q9BYS8	OTTHUMG00000133479	ENST00000395905.3:c.95T>C	3.37:g.46592987A>G	ENSP00000379241:p.Val32Ala	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_024512	B2RDQ7|Q96LT5	Missense_Mutation	SNP	ENST00000395905.3	37	CCDS2741.1	268	0.1227106227106227	54	0.10975609756097561	39	0.10773480662983426	106	0.1853146853146853	69	0.09102902374670185	G	0.150	-1.092052	0.01858	0.096459	0.077209	ENSG00000163827	ENST00000395905;ENST00000296144	T;T	0.15718	2.4;2.4	4.73	1.81	0.25067	.	0.442822	0.20534	N	0.090455	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44452	-0.9327	9	0.10902	T	0.67	.	7.6676	0.28441	0.0811:0.0:0.3235:0.5954	rs28687398;rs58155764	32	Q9BYS8	LRRC2_HUMAN	A	32	ENSP00000379241:V32A;ENSP00000296144:V32A	ENSP00000296144:V32A	V	-	2	0	LRRC2	46567991	0.025000	0.19082	0.143000	0.22291	0.502000	0.33828	0.186000	0.16978	0.019000	0.15079	-1.096000	0.02151	GTG	A|0.904;G|0.096	0.096	strong		0.463	LRRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257375.2		
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 GAIIx	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_ENST00000517885.1_Missense_Mutation_p.E324D|MYBL1_ENST00000522419.1_Intron|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	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	123	70	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	
HLA-A	3105	hgsc.bcm.edu	37	6	29912386	29912386	+	Missense_Mutation	SNP	G	G	C	rs1137160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29912386G>C	ENST00000396634.1	+	7	1346	c.1005G>C	c.(1003-1005)aaG>aaC	p.K335N	HLA-A_ENST00000376806.5_Missense_Mutation_p.K335N|HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Missense_Mutation_p.K335N			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	335					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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GGAGGAGGAAGAGCTCAGGTG	0.577									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	772	0.154153	0.1286	0.1758	5008	,	,		18081	0.2034		0.1153	False		,,,				2504	0.1626				p.K335N		Atlas-SNP	.											HLA-A,colon,carcinoma,0,1	HLA-A	89	1	0			c.G1005C						PASS	.	G	ASN/LYS	435,2585		58,319,1133	98.0	96.0	96.0		1005	1.2	0.0	6	dbSNP_86	96	608,4800		61,486,2157	no	missense	HLA-A	NM_002116.7	94	119,805,3290	CC,CG,GG		11.2426,14.404,12.3754	benign	335/366	29912386	1043,7385	1510	2704	4214	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGGAAGAGCTCA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.1005G>C	6.37:g.29912386G>C	ENSP00000379873:p.Lys335Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	196	48	0.244898	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	341	0.15613553113553114	48	0.0975609756097561	72	0.19889502762430938	143	0.25	78	0.10290237467018469	.	9.448	1.089767	0.20390	0.14404	0.112426	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00792	5.71;5.69;5.71	3.69	1.25	0.21368	.	0.329884	0.20907	U	0.083532	T	0.00468	0.0015	M	0.70108	2.13	0.80722	P	0.0	B;B;B;B;B	0.23058	0.079;0.0;0.0;0.0;0.0	B;B;B;B;B	0.23716	0.048;0.003;0.002;0.001;0.001	T	0.40664	-0.9551	9	0.87932	D	0	.	6.8963	0.24257	0.2254:0.0:0.7746:0.0	rs1137160;rs2157680;rs2231116;rs3179297;rs41562615	214;335;335;335;335	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	N	335	ENSP00000379873:K335N;ENSP00000366002:K335N;ENSP00000366005:K335N	ENSP00000366002:K335N	K	+	3	2	HLA-A	30020365	0.004000	0.15560	0.001000	0.08648	0.642000	0.38348	0.648000	0.24828	0.132000	0.18615	0.485000	0.47835	AAG	G|0.868;C|0.132	0.132	strong		0.577	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
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 GAIIx	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	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	84	32	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	
CDH11	1009	hgsc.bcm.edu	37	16	65038674	65038674	+	Silent	SNP	G	G	A	rs35182	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:65038674G>A	ENST00000268603.4	-	3	714	c.99C>T	c.(97-99)ccC>ccT	p.P33P	CDH11_ENST00000569624.1_5'UTR|CDH11_ENST00000394156.3_Silent_p.P33P|CDH11_ENST00000566827.1_Intron	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	33					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		CATGGAAGGAGGGCCGCAGGT	0.607			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)			G|||	313	0.0625	0.0061	0.0865	5008	,	,		14916	0.0675		0.1054	False		,,,				2504	0.0726				p.P33P		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	CDH11	260	.	0			c.C99T						PASS	.	G		87,4317	69.2+/-107.0	2,83,2117	29.0	26.0	27.0		99	2.2	1.0	16	dbSNP_76	27	969,7631	198.5+/-242.8	56,857,3387	no	coding-synonymous	CDH11	NM_001797.2		58,940,5504	AA,AG,GG		11.2674,1.9755,8.1206		33/797	65038674	1056,11948	2202	4300	6502	SO:0001819	synonymous_variant	1009	exon3			GAAGGAGGGCCGC	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.99C>T	16.37:g.65038674G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	100	56	0.56	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Silent	SNP	ENST00000268603.4	37	CCDS10803.1																																																																																			G|0.923;A|0.077	0.077	strong		0.607	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
GALNT18	374378	hgsc.bcm.edu	37	11	11354346	11354346	+	Silent	SNP	T	T	C	rs901553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:11354346T>C	ENST00000227756.4	-	8	1722	c.1311A>G	c.(1309-1311)gcA>gcG	p.A437A		NM_198516.2	NP_940918.2	Q6P9A2	GLT18_HUMAN	polypeptide N-acetylgalactosaminyltransferase 18	437					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)										GAGCCTTCCTTGCAGTGATGT	0.532													T|||	2177	0.434704	0.3381	0.4452	5008	,	,		19093	0.5764		0.3559	False		,,,				2504	0.4928				p.A437A		Atlas-SNP	.											GALNTL4,NS,carcinoma,0,1	.	.	1	0			c.A1311G						PASS	.	T		1503,2899	481.4+/-359.1	272,959,970	127.0	100.0	109.0		1311	-4.5	0.7	11	dbSNP_86	109	3272,5316	491.0+/-373.0	615,2042,1637	no	coding-synonymous	GALNTL4	NM_198516.2		887,3001,2607	CC,CT,TT		38.0997,34.1436,36.759		437/608	11354346	4775,8215	2201	4294	6495	SO:0001819	synonymous_variant	374378	exon8			CTTCCTTGCAGTG	AK055111	CCDS7807.1	11p15	2014-03-13	2014-03-13	2013-01-25	ENSG00000110328	ENSG00000110328	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	30488	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 18"""	615136	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 4"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 18"""	GALNTL4		22186971	Standard	NM_198516		Approved	MGC71806, GALNT15, GalNAc-T18	uc001mjo.2	Q6P9A2	OTTHUMG00000165707	ENST00000227756.4:c.1311A>G	11.37:g.11354346T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_198516	O95903|Q8NDY9	Silent	SNP	ENST00000227756.4	37	CCDS7807.1																																																																																			C|0.397;N|0.000	0.397	strong		0.532	GALNT18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385848.1	NM_198516	
DOCK6	57572	hgsc.bcm.edu	37	19	11326504	11326504	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:11326504G>A	ENST00000294618.7	-	31	4005	c.3994C>T	c.(3994-3996)Cga>Tga	p.R1332*	CTC-510F12.2_ENST00000588634.1_RNA|DOCK6_ENST00000319867.7_Nonsense_Mutation_p.R671*	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1332					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.R1332*(1)		breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						ATTTCTTGTCGAGCTCCGATG	0.537																																					p.R1332X		Atlas-SNP	.											DOCK6,NS,carcinoma,0,1	DOCK6	104	1	1	Substitution - Nonsense(1)	lung(1)	c.C3994T						scavenged	.						118.0	114.0	115.0					19																	11326504		1976	4153	6129	SO:0001587	stop_gained	57572	exon31			CTTGTCGAGCTCC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.3994C>T	19.37:g.11326504G>A	ENSP00000294618:p.Arg1332*	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	129	4	0.0310078	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Nonsense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	41	8.761828	0.98943	.	.	ENSG00000130158	ENST00000294618;ENST00000319867	.	.	.	5.29	3.09	0.35607	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0306	13.3368	0.60522	0.0:0.0:0.712:0.288	.	.	.	.	X	1332;671	.	ENSP00000294618:R1332X	R	-	1	2	DOCK6	11187504	0.978000	0.34361	0.039000	0.18376	0.620000	0.37586	1.740000	0.38228	0.754000	0.32968	0.591000	0.81541	CGA	.	.	none		0.537	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
SMTNL2	342527	hgsc.bcm.edu	37	17	4495740	4495740	+	Missense_Mutation	SNP	G	G	A	rs12449695	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4495740G>A	ENST00000389313.4	+	2	551	c.484G>A	c.(484-486)Gca>Aca	p.A162T	SMTNL2_ENST00000338859.4_Missense_Mutation_p.A18T	NM_001114974.1	NP_001108446.1	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2	162			A -> T (in dbSNP:rs12449695). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|endometrium(9)|kidney(1)|lung(1)|skin(1)	13				READ - Rectum adenocarcinoma(115;0.0325)		CCAGCCGGGGGCAGGTAGGGC	0.567													G|||	1662	0.331869	0.1067	0.4467	5008	,	,		14261	0.5813		0.3131	False		,,,				2504	0.317				p.A162T		Atlas-SNP	.											.	SMTNL2	57	.	0			c.G484A						PASS	.	G	THR/ALA,THR/ALA	580,3826	258.3+/-262.4	29,522,1652	55.0	57.0	57.0		484,52	-1.4	0.1	17	dbSNP_120	57	2623,5977	422.8+/-354.1	402,1819,2079	yes	missense,missense	SMTNL2	NM_001114974.1,NM_198501.2	58,58	431,2341,3731	AA,AG,GG		30.5,13.1639,24.6271	benign,benign	162/462,18/318	4495740	3203,9803	2203	4300	6503	SO:0001583	missense	342527	exon2			CCGGGGGCAGGTA	AK124452	CCDS11048.1, CCDS45583.1	17p13.2	2006-04-26			ENSG00000188176	ENSG00000188176			24764	protein-coding gene	gene with protein product							Standard	NM_001114974		Approved	FLJ42461	uc002fyf.1	Q2TAL5	OTTHUMG00000132938	ENST00000389313.4:c.484G>A	17.37:g.4495740G>A	ENSP00000373964:p.Ala162Thr	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001114974	Q6ZVK6	Missense_Mutation	SNP	ENST00000389313.4	37	CCDS45583.1	776	0.3553113553113553	49	0.09959349593495935	149	0.4116022099447514	340	0.5944055944055944	238	0.31398416886543534	G	11.19	1.566285	0.27915	0.131639	0.305	ENSG00000188176	ENST00000338859;ENST00000389313	D;T	0.81579	-1.51;-1.41	4.85	-1.36	0.09085	.	.	.	.	.	T	0.00012	0.0000	L	0.38175	1.15	0.53005	P	3.2999999999949736E-5	B	0.19706	0.038	B	0.11329	0.006	T	0.44251	-0.9340	8	0.27785	T	0.31	-0.0062	1.0384	0.01553	0.3536:0.1476:0.3476:0.1511	rs12449695;rs59472147;rs12449695	162	Q2TAL5	SMTL2_HUMAN	T	18;162	ENSP00000345143:A18T;ENSP00000373964:A162T	ENSP00000345143:A18T	A	+	1	0	SMTNL2	4442489	0.175000	0.23083	0.112000	0.21494	0.603000	0.37013	0.375000	0.20518	-0.051000	0.13334	0.655000	0.94253	GCA	G|0.713;A|0.287	0.287	strong		0.567	SMTNL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439129.1	NM_198501	
PARVB	29780	hgsc.bcm.edu	37	22	44395451	44395451	+	Missense_Mutation	SNP	T	T	C	rs1007863	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44395451T>C	ENST00000406477.3	+	2	239	c.109T>C	c.(109-111)Tgg>Cgg	p.W37R		NM_001003828.2	NP_001003828.1	Q9HBI1	PARVB_HUMAN	parvin, beta	0					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)		p.W37R(1)		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)				ttcctgcagctggggcctgtg	0.517													t|||	2664	0.531949	0.674	0.5014	5008	,	,		16851	0.4623		0.4344	False		,,,				2504	0.5337				p.W37R		Atlas-SNP	.											PARVB,NS,carcinoma,0,1	PARVB	44	1	1	Substitution - Missense(1)	stomach(1)	c.T109C						PASS	.	C	ARG/TRP	2375,1695		712,951,372	91.0	98.0	96.0		109	-3.8	0.0	22	dbSNP_86	96	3171,5173		631,1909,1632	yes	missense	PARVB	NM_001003828.2	101	1343,2860,2004	CC,CT,TT		38.0034,41.6462,44.6754		37/398	44395451	5546,6868	2035	4172	6207	SO:0001583	missense	29780	exon2			TGCAGCTGGGGCC	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	ENST00000406477.3:c.109T>C	22.37:g.44395451T>C	ENSP00000384515:p.Trp37Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000406477.3	37	CCDS46724.1	1113	0.5096153846153846	313	0.6361788617886179	178	0.49171270718232046	291	0.5087412587412588	331	0.4366754617414248	C	0.014	-1.586745	0.00872	0.583538	0.380034	ENSG00000188677	ENST00000406477	T	0.35048	1.33	1.91	-3.83	0.04269	.	1.001040	0.08064	N	0.998800	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.41520	-0.9504	9	0.06891	T	0.86	-4.2361	7.888	0.29661	0.0:0.5695:0.0:0.4305	rs1007863;rs52789429;rs1007863	37	Q9HBI1-2	.	R	37	ENSP00000384515:W37R	ENSP00000384515:W37R	W	+	1	0	PARVB	42726784	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.505000	0.00963	-1.311000	0.02309	-1.645000	0.00762	TGG	T|0.506;C|0.494	0.494	strong		0.517	PARVB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319517.1	NM_001003828	
MAPKBP1	23005	hgsc.bcm.edu	37	15	42105918	42105918	+	Missense_Mutation	SNP	C	C	G	rs1201689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42105918C>G	ENST00000456763.2	+	10	1133	c.937C>G	c.(937-939)Ctt>Gtt	p.L313V	MAPKBP1_ENST00000514566.1_Missense_Mutation_p.L307V|MAPKBP1_ENST00000221214.6_Intron|MAPKBP1_ENST00000260357.7_Missense_Mutation_p.L195V|MAPKBP1_ENST00000457542.2_Missense_Mutation_p.L307V	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	313			L -> V (in dbSNP:rs1201689).							breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		CCTGCACTTCCTTAGCACCTT	0.582													c|||	1528	0.305112	0.3585	0.232	5008	,	,		21640	0.2073		0.3907	False		,,,				2504	0.2975				p.L313V		Atlas-SNP	.											.	MAPKBP1	120	.	0			c.C937G						PASS	.	C	VAL/LEU,VAL/LEU	1483,2923	476.1+/-357.5	265,953,985	196.0	179.0	185.0		937,919	4.7	1.0	15	dbSNP_87	185	3367,5233	500.6+/-375.3	675,2017,1608	yes	missense,missense	MAPKBP1	NM_001128608.1,NM_014994.2	32,32	940,2970,2593	GG,GC,CC		39.1512,33.6586,37.2905	benign,benign	313/1515,307/1509	42105918	4850,8156	2203	4300	6503	SO:0001583	missense	23005	exon10			CACTTCCTTAGCA	AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.937C>G	15.37:g.42105918C>G	ENSP00000393099:p.Leu313Val	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	118	35	0.29661	NM_001128608	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	616	0.28205128205128205	170	0.34552845528455284	89	0.24585635359116023	82	0.14335664335664336	275	0.3627968337730871	c	11.80	1.745410	0.30955	0.336586	0.391512	ENSG00000137802	ENST00000457542;ENST00000260357;ENST00000456763;ENST00000514566	T;T;T;T	0.55413	5.03;0.52;5.02;5.02	5.64	4.72	0.59763	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.319926	0.32401	N	0.006154	T	0.00012	0.0000	L	0.27053	0.805	0.27420	P	0.9543032	B;B;B;B	0.28350	0.208;0.007;0.0;0.019	B;B;B;B	0.22152	0.038;0.013;0.003;0.018	T	0.42649	-0.9439	9	0.22706	T	0.39	-12.0447	10.5005	0.44802	0.0:0.7534:0.1714:0.0752	rs1201689;rs1201689	195;307;313;307	F8WC21;O60336-2;O60336;O60336-6	.;.;MABP1_HUMAN;.	V	307;195;313;307	ENSP00000397570:L307V;ENSP00000260357:L195V;ENSP00000393099:L313V;ENSP00000426154:L307V	ENSP00000260357:L195V	L	+	1	0	MAPKBP1	39893210	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.438000	0.35002	1.374000	0.46228	0.651000	0.88453	CTT	C|0.662;G|0.338	0.338	strong		0.582	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994	
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 GAIIx	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	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	128	14	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		
PIP4K2C	79837	hgsc.bcm.edu	37	12	57985204	57985204	+	Silent	SNP	C	C	T	rs11537654	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:57985204C>T	ENST00000354947.5	+	1	148	c.132C>T	c.(130-132)gcC>gcT	p.A44A	PIP4K2C_ENST00000422156.3_Silent_p.A44A|PIP4K2C_ENST00000540759.2_Silent_p.A44A|PIP4K2C_ENST00000550465.1_Silent_p.A44A			Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	44	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(13)|pancreas(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Melanoma(17;0.122)					TCCGGGCGGCCGACCCGCTGG	0.662													C|||	1561	0.311701	0.0204	0.4078	5008	,	,		14182	0.5337		0.2535	False		,,,				2504	0.4683				p.A44A		Atlas-SNP	.											.	PIP4K2C	50	.	0			c.C132T						PASS	.	C	,,,	282,4124	158.9+/-191.5	6,270,1927	100.0	108.0	105.0		132,132,132,132	-1.2	1.0	12	dbSNP_120	105	2148,6452	368.8+/-335.2	279,1590,2431	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PIP4K2C	NM_001146258.1,NM_001146259.1,NM_001146260.1,NM_024779.4	,,,	285,1860,4358	TT,TC,CC		24.9767,6.4004,18.6837	,,,	44/422,44/404,44/374,44/422	57985204	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	79837	exon1			GGCGGCCGACCCG	AK125526	CCDS8946.1, CCDS53808.1, CCDS55839.1	12q13.3	2014-09-04	2007-08-14	2007-08-14	ENSG00000166908	ENSG00000166908			23786	protein-coding gene	gene with protein product			"""phosphatidylinositol-4-phosphate 5-kinase, type II, gamma"""	PIP5K2C		9367159	Standard	NM_024779		Approved	FLJ22055	uc001sot.3	Q8TBX8	OTTHUMG00000170144	ENST00000354947.5:c.132C>T	12.37:g.57985204C>T		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	172	170	0.988372	NM_001146258	B2RDL3|B4DM11|B4DY44|Q9H6N2	Silent	SNP	ENST00000354947.5	37	CCDS8946.1																																																																																			C|0.763;T|0.237	0.237	strong		0.662	PIP4K2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407644.1	NM_024779	
SAG	6295	hgsc.bcm.edu	37	2	234255547	234255547	+	Missense_Mutation	SNP	G	G	A	rs1046974	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:234255547G>A	ENST00000409110.1	+	16	1437	c.1207G>A	c.(1207-1209)Gtt>Att	p.V403I		NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	403			V -> A (in dbSNP:rs1046976). {ECO:0000269|PubMed:3164688, ECO:0000269|PubMed:9020843}.|V -> I (in dbSNP:rs1046974).		cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		CAAGAATGACGTTGATGAGTG	0.453													A|||	1517	0.302915	0.0545	0.245	5008	,	,		20836	0.3988		0.4344	False		,,,				2504	0.4458				p.V403I		Atlas-SNP	.											.	SAG	77	.	0			c.G1207A						PASS	.	A	ILE/VAL	462,3554		25,412,1571	91.0	96.0	95.0		1207	-2.7	0.0	2	dbSNP_86	95	3350,5002		661,2028,1487	yes	missense	SAG	NM_000541.4	29	686,2440,3058	AA,AG,GG		40.1102,11.504,30.8215	benign	403/406	234255547	3812,8556	2008	4176	6184	SO:0001583	missense	6295	exon16			AATGACGTTGATG		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.1207G>A	2.37:g.234255547G>A	ENSP00000386444:p.Val403Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_000541	A0FDN6|Q53SV3|Q99858	Missense_Mutation	SNP	ENST00000409110.1	37	CCDS46545.1	683	0.31272893772893773	31	0.06300813008130081	104	0.287292817679558	224	0.3916083916083916	324	0.42744063324538256	g	4.826	0.153569	0.09185	0.11504	0.401102	ENSG00000130561	ENST00000252857;ENST00000409110	T	0.06849	3.25	4.39	-2.67	0.06059	.	2.199560	0.02549	N	0.095496	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.48234	-0.9053	9	0.36615	T	0.2	6.8364	6.9618	0.24601	0.5946:0.0:0.2798:0.1255	rs1046974;rs3172176;rs52832638;rs57908936;rs1046974	403	P10523	ARRS_HUMAN	I	403	ENSP00000386444:V403I	ENSP00000252857:V403I	V	+	1	0	SAG	233920286	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.089000	0.15002	-0.720000	0.04935	-0.934000	0.02701	GTT	G|0.696;A|0.304	0.304	strong		0.453	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541	
ATP7B	540	hgsc.bcm.edu	37	13	52544805	52544805	+	Missense_Mutation	SNP	C	C	G	rs1801244	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:52544805C>G	ENST00000242839.4	-	3	1522	c.1366G>C	c.(1366-1368)Gtg>Ctg	p.V456L	ATP7B_ENST00000482841.1_5'UTR|ATP7B_ENST00000418097.2_Missense_Mutation_p.V456L|ATP7B_ENST00000400366.3_Missense_Mutation_p.V345L|ATP7B_ENST00000542656.1_Missense_Mutation_p.V424L|ATP7B_ENST00000400370.3_Intron|ATP7B_ENST00000344297.5_Missense_Mutation_p.V456L|ATP7B_ENST00000448424.2_Missense_Mutation_p.V456L	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	456			V -> L (in dbSNP:rs1801244). {ECO:0000269|PubMed:10721669, ECO:0000269|PubMed:10790207, ECO:0000269|PubMed:11690702, ECO:0000269|PubMed:14986826, ECO:0000269|PubMed:15952988, ECO:0000269|PubMed:15967699, ECO:0000269|PubMed:18373411, ECO:0000269|PubMed:9887381, ECO:0000269|Ref.2}.		cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ACTTCCTGCACAGATGTAGGT	0.512									Wilson disease				C|||	1888	0.376997	0.1868	0.389	5008	,	,		18719	0.4841		0.5258	False		,,,				2504	0.362				p.V456L		Atlas-SNP	.											.	ATP7B	123	.	0			c.G1366C						PASS	.	C	LEU/VAL,LEU/VAL	887,3065		90,707,1179	126.0	121.0	123.0		1366,1366	-0.2	0.0	13	dbSNP_89	123	4068,4208		1013,2042,1083	yes	missense,missense	ATP7B	NM_000053.3,NM_001005918.2	32,32	1103,2749,2262	GG,GC,CC		49.1542,22.4443,40.5218	benign,benign	456/1466,456/1259	52544805	4955,7273	1976	4138	6114	SO:0001583	missense	540	exon3	Familial Cancer Database		CCTGCACAGATGT	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.1366G>C	13.37:g.52544805C>G	ENSP00000242839:p.Val456Leu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	183	183	1	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	907	0.4152930402930403	99	0.20121951219512196	152	0.4198895027624309	264	0.46153846153846156	392	0.5171503957783641	C	11.11	1.543605	0.27563	0.224443	0.491542	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000448424;ENST00000418097;ENST00000542656	D;D;D;D;D;D	0.96168	-3.8;-3.8;-3.93;-3.74;-3.82;-1.94	5.17	-0.181	0.13291	.	0.905138	0.09744	N	0.761497	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B;B;B;B;B;B	0.20164	0.009;0.004;0.0;0.023;0.003;0.042;0.001	B;B;B;B;B;B;B	0.22386	0.02;0.009;0.0;0.039;0.018;0.032;0.002	T	0.28073	-1.0055	9	0.09843	T	0.71	-10.9119	2.1644	0.03833	0.1161:0.3756:0.2808:0.2275	rs1801244;rs3742287;rs17401228;rs52819705;rs58218043;rs1801244	424;456;456;456;345;456;456	F6XIH0;E7ET55;B7ZLR4;F5H748;P35670-3;P35670-2;P35670	.;.;.;.;.;.;ATP7B_HUMAN	L	456;345;456;456;456;424	ENSP00000242839:V456L;ENSP00000383217:V345L;ENSP00000342559:V456L;ENSP00000416738:V456L;ENSP00000393343:V456L;ENSP00000443128:V424L	ENSP00000242839:V456L	V	-	1	0	ATP7B	51442806	0.000000	0.05858	0.001000	0.08648	0.631000	0.37964	-1.004000	0.03678	0.214000	0.20742	0.655000	0.94253	GTG	C|0.579;G|0.421	0.421	strong		0.512	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053	
ANGPTL4	51129	hgsc.bcm.edu	37	19	8438716	8438716	+	Silent	SNP	G	G	A	rs11672433	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8438716G>A	ENST00000301455.2	+	7	1338	c.1167G>A	c.(1165-1167)ccG>ccA	p.P389P	RAB11B-AS1_ENST00000597785.1_RNA|RAB11B-AS1_ENST00000593581.1_RNA|RAB11B-AS1_ENST00000597407.1_RNA|ANGPTL4_ENST00000541807.1_Silent_p.P222P|ANGPTL4_ENST00000393962.2_Silent_p.P351P	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	389	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.			P -> S (in Ref. 1; AAF62868). {ECO:0000305}.	angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						GCTACTACCCGCTGCAGGCCA	0.617													G|||	278	0.0555112	0.0061	0.072	5008	,	,		16313	0.001		0.1441	False		,,,				2504	0.0757				p.P389P		Atlas-SNP	.											ANGPTL4,NS,carcinoma,0,1	ANGPTL4	21	1	0			c.G1167A						PASS	.	G	,	122,4284	86.8+/-125.4	4,114,2085	68.0	76.0	73.0		1053,1167	-11.2	0.1	19	dbSNP_120	73	1221,7379	237.8+/-269.5	72,1077,3151	no	coding-synonymous,coding-synonymous	ANGPTL4	NM_001039667.1,NM_139314.1	,	76,1191,5236	AA,AG,GG		14.1977,2.769,10.326	,	351/369,389/407	8438716	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	51129	exon7			CTACCCGCTGCAG	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"""Fibrinogen C domain containing"""	16039	protein-coding gene	gene with protein product	"""fasting-induced adipose factor"", ""hepatic angiopoietin-related protein"", ""PPARG angiopoietin related protein"", ""hepatic fibrinogen/angiopoietin-related protein"", ""peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein"", ""angiopoietin-related protein 4"""	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.1167G>A	19.37:g.8438716G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_139314	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Silent	SNP	ENST00000301455.2	37	CCDS12200.1																																																																																			G|0.911;A|0.089	0.089	strong		0.617	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314	
TSEN54	283989	hgsc.bcm.edu	37	17	73513289	73513289	+	Silent	SNP	C	C	G	rs6501818	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73513289C>G	ENST00000333213.6	+	4	369	c.333C>G	c.(331-333)cgC>cgG	p.R111R	CASKIN2_ENST00000581870.1_5'Flank|CASKIN2_ENST00000321617.3_5'Flank|TSEN54_ENST00000580013.1_3'UTR	NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	111					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;4.57e-07)|Epithelial(20;2.92e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCCGGCAGCGCCTTCACCCGG	0.612													G|||	817	0.163139	0.351	0.1066	5008	,	,		15203	0.0298		0.1421	False		,,,				2504	0.1084				p.R111R		Atlas-SNP	.											.	TSEN54	27	.	0			c.C333G						PASS	.	G		1452,2942		260,932,1005	20.0	23.0	22.0		333	2.0	1.0	17	dbSNP_116	22	1130,7468		70,990,3239	no	coding-synonymous	TSEN54	NM_207346.2		330,1922,4244	GG,GC,CC		13.1426,33.0451,19.8738		111/527	73513289	2582,10410	2197	4299	6496	SO:0001819	synonymous_variant	283989	exon4			GCAGCGCCTTCAC	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"""tRNA splicing endonuclease subunits"""	27561	protein-coding gene	gene with protein product		608755	"""tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)"", ""tRNA splicing endonuclease 54 homolog (S. cerevisiae)"""			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.333C>G	17.37:g.73513289C>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Silent	SNP	ENST00000333213.6	37	CCDS11724.1																																																																																			C|0.822;G|0.178	0.178	strong		0.612	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346	
APEH	327	hgsc.bcm.edu	37	3	49723784	49723784	+	IGR	SNP	C	C	A	rs9713651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49723784C>A	ENST00000296456.5	+	0	3220				AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_Silent_p.P251P|MST1_ENST00000449682.2_Silent_p.P326P|MST1_ENST00000545762.1_3'UTR	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGTGCTGATGCGGGATTTGCG	0.647																																					p.P326P		Atlas-SNP	.											.	MST1	84	.	0			c.G978T						PASS	.	C		1307,3095		67,1173,961	22.0	21.0	22.0		978	-2.8	0.9	3	dbSNP_119	22	3605,4981		373,2859,1061	no	coding-synonymous	MST1	NM_020998.3		440,4032,2022	AA,AC,CC		41.987,29.691,37.8195		326/726	49723784	4912,8076	2201	4293	6494	SO:0001628	intergenic_variant	4485	exon8			CTGATGCGGGATT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723784C>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	165	68	0.412121	NM_020998	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1																																																																																			C|0.562;A|0.438	0.438	strong		0.647	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
BPIFB2	80341	hgsc.bcm.edu	37	20	31609581	31609581	+	Silent	SNP	C	C	T	rs17124003	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:31609581C>T	ENST00000170150.3	+	15	1506	c.1311C>T	c.(1309-1311)gtC>gtT	p.V437V		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	437						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)	p.V437V(1)									TCCACTATGTCGCCCCTGAGA	0.582													C|||	1604	0.320288	0.4773	0.2118	5008	,	,		18493	0.1964		0.326	False		,,,				2504	0.3067				p.V437V		Atlas-SNP	.											BPIL1,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C1311T						scavenged	.	C		1934,2472	551.7+/-378.3	428,1078,697	159.0	144.0	149.0		1311	1.5	0.0	20	dbSNP_123	149	2459,6141	405.5+/-348.5	372,1715,2213	no	coding-synonymous	BPIFB2	NM_025227.1		800,2793,2910	TT,TC,CC		28.593,43.8947,33.7767		437/459	31609581	4393,8613	2203	4300	6503	SO:0001819	synonymous_variant	80341	exon15			CTATGTCGCCCCT	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.1311C>T	20.37:g.31609581C>T		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Silent	SNP	ENST00000170150.3	37	CCDS13210.1																																																																																			C|0.672;N|0.000	.	strong		0.582	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
PCDHA9	9752	hgsc.bcm.edu	37	5	140228413	140228413	+	Missense_Mutation	SNP	C	C	A	rs17844323	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140228413C>A	ENST00000532602.1	+	1	1366	c.333C>A	c.(331-333)gaC>gaA	p.D111E	PCDHA9_ENST00000378122.3_Missense_Mutation_p.D111E|PCDHA7_ENST00000525929.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	111	Cadherin 1. {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(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGATCGTAGACAGGCCGCTGC	0.547													.|||	1014	0.202476	0.0272	0.2954	5008	,	,		15362	0.1339		0.3012	False		,,,				2504	0.3425				p.D111E	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											PCDHA9_ENST00000532602,bladder,carcinoma,+2,2	PCDHA9	373	2	0			c.C333A						scavenged	.	C	GLU/ASP,,,,,,,,,,,GLU/ASP	36,4310		9,18,2146	111.0	87.0	95.0		333,,,,,,,,,,,333	1.1	0.7	5	dbSNP_123	95	891,7347		303,285,3531	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1	45,,,,,,,,,,,45	312,303,5677	AA,AC,CC		10.8157,0.8283,7.3665	,,,,,,,,,,,	111/843,,,,,,,,,,,111/951	140228413	927,11657	2173	4119	6292	SO:0001583	missense	9752	exon1			CGTAGACAGGCCG	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.333C>A	5.37:g.140228413C>A	ENSP00000436042:p.Asp111Glu	Somatic	221	2	0.00904977		WXS	Illumina HiSeq	Phase_I	148	38	0.256757	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	393	0.17994505494505494	19	0.03861788617886179	113	0.31215469613259667	63	0.11013986013986014	198	0.2612137203166227	C	9.157	1.017662	0.19355	0.008283	0.108157	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.21031	2.03;2.03	4.13	1.1	0.20463	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.275715	0.18390	N	0.142694	T	0.00012	0.0000	N	0.11341	0.13	0.51767	P	6.099999999997774E-5	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.44298	-0.9337	9	0.54805	T	0.06	.	8.9368	0.35704	0.0:0.3062:0.5482:0.1455	rs17844323	111;111	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	E	111	ENSP00000436042:D111E;ENSP00000367362:D111E	ENSP00000367362:D111E	D	+	3	2	PCDHA9	140208597	0.000000	0.05858	0.746000	0.31095	0.806000	0.45545	-2.220000	0.01217	0.080000	0.16959	-0.274000	0.10170	GAC	C|0.819;A|0.181	0.181	strong		0.547	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
MKI67	4288	hgsc.bcm.edu	37	10	129904917	129904917	+	Silent	SNP	G	G	A	rs1894410	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:129904917G>A	ENST00000368654.3	-	13	5562	c.5187C>T	c.(5185-5187)aaC>aaT	p.N1729N	MKI67_ENST00000368653.3_Silent_p.N1369N	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1729	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TAGTTTTTTCGTTAGTCATTG	0.498													G|||	697	0.139177	0.1505	0.1556	5008	,	,		18802	0.0813		0.1451	False		,,,				2504	0.1656				p.N1729N		Atlas-SNP	.											.	MKI67	363	.	0			c.C5187T						PASS	.	G	,	711,3695	296.7+/-284.4	60,591,1552	152.0	134.0	140.0		4107,5187	-3.2	0.0	10	dbSNP_92	140	1364,7236	265.8+/-286.4	104,1156,3040	no	coding-synonymous,coding-synonymous	MKI67	NM_001145966.1,NM_002417.4	,	164,1747,4592	AA,AG,GG		15.8605,16.1371,15.9542	,	1369/2897,1729/3257	129904917	2075,10931	2203	4300	6503	SO:0001819	synonymous_variant	4288	exon13			TTTTTCGTTAGTC	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.5187C>T	10.37:g.129904917G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_002417	Q5VWH2	Silent	SNP	ENST00000368654.3	37	CCDS7659.1																																																																																			G|0.863;N|0.000	.	strong		0.498	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
SYT6	148281	hgsc.bcm.edu	37	1	114680540	114680540	+	Silent	SNP	C	C	T	rs17032441	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:114680540C>T	ENST00000610222.1	-	3	794	c.648G>A	c.(646-648)tcG>tcA	p.S216S	SYT6_ENST00000609117.1_Silent_p.S131S|SYT6_ENST00000393296.1_Silent_p.S216S|SYT6_ENST00000607941.1_Silent_p.S131S|SYT6_ENST00000369547.1_Silent_p.S131S			Q5T7P8	SYT6_HUMAN	synaptotagmin VI	216					acrosomal vesicle exocytosis (GO:0060478)	cell junction (GO:0030054)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	clathrin binding (GO:0030276)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)|transporter activity (GO:0005215)	p.S131S(1)		central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37	Lung SC(450;0.184)	all_cancers(81;4.41e-08)|all_epithelial(167;5.18e-08)|all_lung(203;1.58e-05)|Lung NSC(69;2.82e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CCCCATCCACCGACTTCTGCT	0.557													c|||	1040	0.207668	0.2247	0.1628	5008	,	,		21878	0.2579		0.2078	False		,,,				2504	0.1646				p.S131S		Atlas-SNP	.											SYT6,NS,carcinoma,0,1	SYT6	66	1	1	Substitution - coding silent(1)	stomach(1)	c.G393A						PASS	.	T		836,3570	331.5+/-302.0	74,688,1441	116.0	101.0	106.0		393	-10.8	0.4	1	dbSNP_123	106	1817,6783	327.6+/-317.9	191,1435,2674	no	coding-synonymous	SYT6	NM_205848.2		265,2123,4115	TT,TC,CC		21.1279,18.9741,20.3983		131/426	114680540	2653,10353	2203	4300	6503	SO:0001819	synonymous_variant	148281	exon3			ATCCACCGACTTC		CCDS871.1	1p13.1	2013-01-21			ENSG00000134207	ENSG00000134207		"""Synaptotagmins"""	18638	protein-coding gene	gene with protein product		607718				11543631	Standard	NM_205848		Approved		uc021orz.1	Q5T7P8	OTTHUMG00000011755	ENST00000610222.1:c.648G>A	1.37:g.114680540C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	234	122	0.521368	NM_205848	B1AMB8|B3KPK1	Silent	SNP	ENST00000610222.1	37																																																																																				.	.	alt		0.557	SYT6-004	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000314819.2	NM_205848	
PRR34	55267	hgsc.bcm.edu	37	22	46447714	46447714	+	Missense_Mutation	SNP	T	T	C	rs59929908	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:46447714T>C	ENST00000396008.2	-	2	460	c.410A>G	c.(409-411)cAg>cGg	p.Q137R	RP6-109B7.5_ENST00000608644.1_RNA|C22orf26_ENST00000333761.1_Missense_Mutation_p.Q137R|RP6-109B7.3_ENST00000451166.1_RNA|RP6-109B7.3_ENST00000416202.1_RNA|FLJ27365_ENST00000381051.2_5'Flank			Q9NV39	PRR34_HUMAN		137			Q -> R (in dbSNP:rs59929908).										Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.0784)|LUAD - Lung adenocarcinoma(64;0.247)		agctcatacctgtaattccag	0.512													T|||	443	0.0884585	0.062	0.0908	5008	,	,		19210	0.1419		0.1004	False		,,,				2504	0.0552				p.Q137R		Atlas-SNP	.											.	C22orf26	1	.	0			c.A410G						PASS	.	T	ARG/GLN	135,1881		3,129,876	112.0	134.0	127.0		410	-0.3	0.0	22	dbSNP_129	127	432,3788		19,394,1697	yes	missense	C22orf26	NM_018280.2	43	22,523,2573	CC,CT,TT		10.237,6.6964,9.0924	possibly-damaging	137/139	46447714	567,5669	1008	2110	3118	SO:0001583	missense	55267	exon2			CATACCTGTAATT																												ENST00000396008.2:c.410A>G	22.37:g.46447714T>C	ENSP00000379329:p.Gln137Arg	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_018280	B0QZ24	Missense_Mutation	SNP	ENST00000396008.2	37	CCDS14071.1	224	0.10256410256410256	30	0.06097560975609756	40	0.11049723756906077	83	0.1451048951048951	71	0.09366754617414248	T	1.623	-0.521060	0.04171	0.066964	0.10237	ENSG00000182257	ENST00000396008;ENST00000333761	T;T	0.38560	1.13;1.13	0.772	-0.328	0.12690	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	P	0.42039	0.769	P	0.49332	0.607	T	0.09100	-1.0690	8	0.87932	D	0	.	2.7796	0.05357	0.0:0.3573:0.0:0.6427	rs59929908	137	Q9NV39	CV026_HUMAN	R	137	ENSP00000379329:Q137R;ENSP00000327764:Q137R	ENSP00000327764:Q137R	Q	-	2	0	C22orf26	44826378	.	.	0.003000	0.11579	0.024000	0.10985	.	.	-0.184000	0.10567	0.460000	0.39030	CAG	T|0.897;C|0.103	0.103	strong		0.512	C22orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317994.1		
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 GAIIx	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_ENST00000432564.1_Missense_Mutation_p.L241F|HCAR1_ENST00000356987.2_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	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	70	36	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 GAIIx	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	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	27	2	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		
PAQR9	344838	hgsc.bcm.edu	37	3	142681249	142681249	+	Silent	SNP	G	G	A	rs62276870	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:142681249G>A	ENST00000340634.3	-	1	929	c.930C>T	c.(928-930)agC>agT	p.S310S	RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	310						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						AGAGCTGGTGGCTGTGGCCGA	0.607													G|||	144	0.028754	0.0053	0.0389	5008	,	,		17580	0.0		0.0895	False		,,,				2504	0.0204				p.S310S		Atlas-SNP	.											.	PAQR9	57	.	0			c.C930T						PASS	.	G		60,4346	56.8+/-93.2	1,58,2144	69.0	73.0	71.0		930	2.9	1.0	3	dbSNP_129	71	679,7921	170.4+/-221.6	29,621,3650	no	coding-synonymous	PAQR9	NM_198504.2		30,679,5794	AA,AG,GG		7.8953,1.3618,5.682		310/378	142681249	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	344838	exon1			CTGGTGGCTGTGG	AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.930C>T	3.37:g.142681249G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_198504	Q147T6	Silent	SNP	ENST00000340634.3	37	CCDS3128.1	93	0.042582417582417584	4	0.008130081300813009	17	0.04696132596685083	0	0.0	72	0.09498680738786279	G	7.505	0.653518	0.14580	0.013618	0.078953	ENSG00000188582	ENST00000492509	.	.	.	5.62	2.88	0.33553	.	.	.	.	.	T	0.05502	0.0145	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.42682	-0.9437	3	.	.	.	-29.595	13.4878	0.61377	0.1896:0.0:0.8104:0.0	rs62276870	.	.	.	S	51	.	.	P	-	1	0	PAQR9	144163939	1.000000	0.71417	0.999000	0.59377	0.984000	0.73092	2.840000	0.48215	0.075000	0.16796	-0.813000	0.03139	CCA	G|0.946;A|0.054	0.054	strong		0.607	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504	
HLA-A	3105	hgsc.bcm.edu	37	6	29911951	29911951	+	Silent	SNP	C	C	T	rs1059570	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29911951C>T	ENST00000396634.1	+	6	1013	c.672C>T	c.(670-672)acC>acT	p.T224T	HLA-A_ENST00000376806.5_Silent_p.T224T|HLA-A_ENST00000376802.2_Silent_p.T224T|HLA-A_ENST00000376809.5_Silent_p.T224T			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	224	Alpha-3.|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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ATGAGGCCACCCTGAGGTGCT	0.597									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	793	0.158347	0.1377	0.1801	5008	,	,		19929	0.2093		0.1123	False		,,,				2504	0.1656				p.T224T		Atlas-SNP	.											.	HLA-A	89	.	0			c.C672T						PASS	.	C		447,2569		62,323,1123	79.0	103.0	94.0		672	1.7	1.0	6	dbSNP_86	94	602,4812		54,494,2159	no	coding-synonymous	HLA-A	NM_002116.7		116,817,3282	TT,TC,CC		11.1193,14.821,12.4437		224/366	29911951	1049,7381	1508	2707	4215	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGCCACCCTGAGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.672C>T	6.37:g.29911951C>T		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	290	30	0.103448	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	weak		0.597	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
TTLL6	284076	hgsc.bcm.edu	37	17	46877063	46877063	+	Missense_Mutation	SNP	G	G	A	rs61739953	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:46877063G>A	ENST00000393382.3	-	6	812	c.671C>T	c.(670-672)cCg>cTg	p.P224L		NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						GCCCGAATCCGGCTTACAAAT	0.453													G|||	391	0.0780751	0.0439	0.0375	5008	,	,		19751	0.0952		0.0447	False		,,,				2504	0.1697				p.P224L		Atlas-SNP	.											.	TTLL6	113	.	0			c.C671T						PASS	.	G	LEU/PRO	62,1322		1,60,631	121.0	97.0	104.0		671	5.4	1.0	17	dbSNP_129	104	100,3082		2,96,1493	yes	missense	TTLL6	NM_001130918.1	98	3,156,2124	AA,AG,GG		3.1427,4.4798,3.548		224/892	46877063	162,4404	692	1591	2283	SO:0001583	missense	284076	exon6			GAATCCGGCTTAC	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"""Tubulin tyrosine ligase-like family"""	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.671C>T	17.37:g.46877063G>A	ENSP00000377043:p.Pro224Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_001130918		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	111	0.050824175824175824	26	0.052845528455284556	14	0.03867403314917127	40	0.06993006993006994	31	0.040897097625329816	G	29.7	5.029883	0.93575	0.044798	0.031427	ENSG00000170703	ENST00000440941;ENST00000393382	.	.	.	5.45	5.45	0.79879	.	0.000000	0.64402	U	0.000007	T	0.51787	0.1695	H	0.97415	4	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81769	-0.0781	9	0.72032	D	0.01	.	18.0737	0.89421	0.0:0.0:1.0:0.0	rs61739953	176	Q8N841	TTLL6_HUMAN	L	224;176	.	ENSP00000377043:P176L	P	-	2	0	TTLL6	44232062	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.615000	0.83006	2.555000	0.86185	0.655000	0.94253	CCG	G|0.953;A|0.047	0.047	strong		0.453	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623	
SSH3	54961	hgsc.bcm.edu	37	11	67072382	67072382	+	Silent	SNP	C	C	T	rs61731786	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67072382C>T	ENST00000308127.4	+	3	421	c.243C>T	c.(241-243)ttC>ttT	p.F81F	SSH3_ENST00000308298.7_Silent_p.F81F|SSH3_ENST00000376757.5_Silent_p.F81F|SSH3_ENST00000532181.1_3'UTR	NM_017857.3	NP_060327.3	Q8TE77	SSH3_HUMAN	slingshot protein phosphatase 3	81					protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|DNA binding (GO:0003677)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			AGACAGACTTCGGGCAAGGAT	0.612													C|||	331	0.0660942	0.0855	0.2651	5008	,	,		17130	0.0298		0.004	False		,,,				2504	0.0				p.F81F		Atlas-SNP	.											.	SSH3	54	.	0			c.C243T						PASS	.	C		282,4116	155.2+/-188.4	8,266,1925	50.0	51.0	51.0		243	-8.4	0.0	11	dbSNP_129	51	37,8553	21.6+/-65.8	1,35,4259	no	coding-synonymous	SSH3	NM_017857.3		9,301,6184	TT,TC,CC		0.4307,6.412,2.4561		81/660	67072382	319,12669	2199	4295	6494	SO:0001819	synonymous_variant	54961	exon3			AGACTTCGGGCAA	AF085851	CCDS8157.1	11q13	2013-03-05	2013-03-05		ENSG00000172830	ENSG00000172830		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30581	protein-coding gene	gene with protein product		606780	"""slingshot homolog 3 (Drosophila)"""			11832213	Standard	NM_017857		Approved	FLJ20515, FLJ10928	uc001okj.3	Q8TE77	OTTHUMG00000167105	ENST00000308127.4:c.243C>T	11.37:g.67072382C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	172	29	0.168605	NM_017857	Q6PK42|Q76I75|Q8N9L8|Q8WYL0|Q9NV45|Q9NWZ7	Silent	SNP	ENST00000308127.4	37	CCDS8157.1																																																																																			C|0.964;T|0.036	0.036	strong		0.612	SSH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393167.1	NM_018276	
Unknown	0	hgsc.bcm.edu	37	X	71379881	71379881	+	IGR	SNP	G	G	A	rs6624600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:71379881G>A								BX119917.1 (7617 upstream) : PIN4 (21644 downstream)																							CAAAGGTACCGAAAGCACAGT	0.453													G|||	1652	0.437616	0.1747	0.3112	3775	,	,		16157	0.7143		0.1769	False		,,,				2504	0.3139				p.E68K		Atlas-SNP	.											.	FLJ44635	13	.	0			c.G202A						PASS	.	G	LYS/GLU	926,2909		93,592,148,947,423	102.0	87.0	92.0		202	0.5	0.5	X	dbSNP_116	92	1509,5219		122,838,427,1468,1445	no	missense	FLJ44635	NM_207422.2	56	215,1430,575,2415,1868	AA,AG,A,GG,G		22.4287,24.146,23.0522	benign	68/141	71379881	2435,8128	2203	4300	6503	SO:0001628	intergenic_variant	0	exon2			GGTACCGAAAGCA																													X.37:g.71379881G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	149	45	0.302013	NM_207422		Missense_Mutation	SNP		37																																																																																				G|0.566;A|0.434	0.434	strong	0	0.453								
NCF2	4688	hgsc.bcm.edu	37	1	183542387	183542387	+	Missense_Mutation	SNP	T	T	C	rs2274064	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:183542387T>C	ENST00000367535.3	-	5	793	c.542A>G	c.(541-543)aAg>aGg	p.K181R	NCF2_ENST00000418089.1_Intron|NCF2_ENST00000367536.1_Missense_Mutation_p.K181R|NCF2_ENST00000413720.1_Missense_Mutation_p.K136R	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	181			K -> R (in dbSNP:rs2274064). {ECO:0000269|PubMed:10498624, ECO:0000269|PubMed:10598813, ECO:0000269|PubMed:12207919, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.		aging (GO:0007568)|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)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	TCGAAACAGCTTGCCCACAGG	0.512													C|||	2462	0.491613	0.3306	0.598	5008	,	,		21080	0.621		0.4672	False		,,,				2504	0.5256				p.K181R		Atlas-SNP	.											.	NCF2	69	.	0			c.A542G						PASS	.	C	ARG/LYS,ARG/LYS,,ARG/LYS	1581,2825	667.0+/-401.8	294,993,916	203.0	185.0	191.0		542,542,,407	1.3	1.0	1	dbSNP_100	191	4012,4588	597.2+/-393.7	952,2108,1240	yes	missense,missense,intron,missense	NCF2	NM_000433.3,NM_001127651.2,NM_001190789.1,NM_001190794.1	26,26,,26	1246,3101,2156	CC,CT,TT		46.6512,35.8829,43.0032	benign,benign,,benign	181/527,181/527,,136/482	183542387	5593,7413	2203	4300	6503	SO:0001583	missense	4688	exon6			AACAGCTTGCCCA	BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"""Tetratricopeptide (TTC) repeat domain containing"""	7661	protein-coding gene	gene with protein product	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	608515	"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.542A>G	1.37:g.183542387T>C	ENSP00000356505:p.Lys181Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001127651	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Missense_Mutation	SNP	ENST00000367535.3	37	CCDS1356.1	1097	0.5022893772893773	176	0.35772357723577236	198	0.5469613259668509	369	0.6451048951048951	354	0.46701846965699206	C	5.163	0.215651	0.09810	0.358829	0.466512	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000367535	T;T;T	0.65732	-0.17;-0.1;-0.17	5.08	1.27	0.21489	.	0.555420	0.21403	N	0.075117	T	0.00012	0.0000	N	0.04043	-0.29	0.09310	P	0.999999999854424	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44467	-0.9326	9	0.06891	T	0.86	-10.3885	9.9264	0.41494	0.0:0.53:0.0:0.47	rs2274064;rs12691462;rs17434977;rs17844914;rs17857636;rs34730753;rs58356110;rs2274064	136;181	E9PHX3;P19878	.;NCF2_HUMAN	R	181;209;136;181	ENSP00000356506:K181R;ENSP00000399294:K136R;ENSP00000356505:K181R	ENSP00000356505:K181R	K	-	2	0	NCF2	181809010	0.992000	0.36948	0.998000	0.56505	0.968000	0.65278	0.583000	0.23849	0.100000	0.17581	-0.962000	0.02626	AAG	T|0.538;C|0.462	0.462	strong		0.512	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433	
CST1	1469	hgsc.bcm.edu	37	20	23731426	23731426	+	Silent	SNP	C	C	T	rs13045477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:23731426C>T	ENST00000304749.2	-	1	148	c.78G>A	c.(76-78)gaG>gaA	p.E26E	CST1_ENST00000398402.1_Silent_p.E26E	NM_001898.2	NP_001889.2	P01037	CYTN_HUMAN	cystatin SN	26					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.E26E(1)		kidney(1)|large_intestine(1)|lung(8)|ovary(1)|stomach(1)|urinary_tract(1)	13	Lung NSC(19;0.0676)|all_lung(19;0.148)					TTATCCTATCCTCCTCCTTGG	0.582													.|||	1837	0.366813	0.5779	0.3343	5008	,	,		14402	0.2123		0.2465	False		,,,				2504	0.3875				p.E26E		Atlas-SNP	.											CST1,NS,carcinoma,0,1	CST1	37	1	1	Substitution - coding silent(1)	stomach(1)	c.G78A						PASS	.	C		2206,2200	589.8+/-387.2	566,1074,563	93.0	82.0	86.0		78	-0.9	0.0	20	dbSNP_121	86	2140,6460	365.2+/-333.8	274,1592,2434	no	coding-synonymous	CST1	NM_001898.2		840,2666,2997	TT,TC,CC		24.8837,49.9319,33.4153		26/142	23731426	4346,8660	2203	4300	6503	SO:0001819	synonymous_variant	1469	exon1			CCTATCCTCCTCC	M19169	CCDS13160.1	20p11.2	2008-04-15			ENSG00000170373	ENSG00000170373			2473	protein-coding gene	gene with protein product		123855					Standard	NM_001898		Approved		uc002wtp.3	P01037	OTTHUMG00000032085	ENST00000304749.2:c.78G>A	20.37:g.23731426C>T		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_001898	Q96LE6|Q9UCQ6	Silent	SNP	ENST00000304749.2	37	CCDS13160.1																																																																																			C|0.665;T|0.335	0.335	strong		0.582	CST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078351.2	NM_001898	
MTR	4548	hgsc.bcm.edu	37	1	237048500	237048500	+	Missense_Mutation	SNP	A	A	G	rs1805087	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:237048500A>G	ENST00000366577.5	+	26	3150	c.2756A>G	c.(2755-2757)gAc>gGc	p.D919G	MTR_ENST00000535889.1_Missense_Mutation_p.D868G	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	919			D -> G (may be associated with susceptibility to FS-NTD; dbSNP:rs1805087). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9013615}.		cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|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)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	ATTAGACAGGACCATTATGAG	0.318													A|||	1093	0.218251	0.2844	0.1772	5008	,	,		20140	0.1052		0.173	False		,,,				2504	0.3211				p.D919G		Atlas-SNP	.											MTR,rectum,carcinoma,+1,1	MTR	127	1	0			c.A2756G	GRCh37	CM983303	MTR	M	rs1805087	scavenged	.	A	GLY/ASP	1164,3242	407.1+/-334.1	154,856,1193	91.0	95.0	94.0		2756	6.0	1.0	1	dbSNP_89	94	1702,6898	309.6+/-309.4	177,1348,2775	yes	missense	MTR	NM_000254.2	94	331,2204,3968	GG,GA,AA		19.7907,26.4185,22.036	benign	919/1266	237048500	2866,10140	2203	4300	6503	SO:0001583	missense	4548	exon26			GACAGGACCATTA	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2756A>G	1.37:g.237048500A>G	ENSP00000355536:p.Asp919Gly	Somatic	52	2	0.0384615		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Missense_Mutation	SNP	ENST00000366577.5	37	CCDS1614.1	421	0.19276556776556777	154	0.3130081300813008	67	0.1850828729281768	74	0.12937062937062938	126	0.1662269129287599	A	14.35	2.510220	0.44660	0.264185	0.197907	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000535889;ENST00000366576	T;T;T	0.72051	-0.62;-0.62;-0.62	5.99	5.99	0.97316	Cobalamin (vitamin B12)-binding (2);	0.149441	0.64402	D	0.000017	T	0.00012	0.0000	L	0.28694	0.88	0.20196	P	0.9999212773	B;P;B	0.37176	0.159;0.586;0.159	B;B;B	0.35770	0.161;0.21;0.161	T	0.07046	-1.0793	9	0.59425	D	0.04	-19.2895	16.4943	0.84223	1.0:0.0:0.0:0.0	rs1805087;rs17658739;rs56618494;rs61036243;rs1805087	919;868;919	B7ZLW8;B7ZLW7;Q99707	.;.;METH_HUMAN	G	773;919;868;473	ENSP00000355536:D919G;ENSP00000441845:D868G;ENSP00000355535:D473G	ENSP00000355535:D473G	D	+	2	0	MTR	235115123	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.545000	0.90657	2.291000	0.77112	0.533000	0.62120	GAC	A|0.786;G|0.214	0.214	strong		0.318	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	
TNK2	10188	hgsc.bcm.edu	37	3	195595054	195595054	+	Silent	SNP	C	C	T	rs7516	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195595054C>T	ENST00000333602.6	-	12	2687	c.2070G>A	c.(2068-2070)ccG>ccA	p.P690P	TNK2_ENST00000392400.1_Silent_p.P690P|TNK2_ENST00000428187.1_Silent_p.P722P|TNK2_ENST00000381916.2_Silent_p.P768P	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	690	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)	CACCCTGGGGCGGGAGGAACA	0.711													c|||	416	0.0830671	0.0998	0.0519	5008	,	,		11446	0.0278		0.1163	False		,,,				2504	0.1053				p.P768P		Atlas-SNP	.											TNK2_ENST00000381916,NS,carcinoma,0,3	TNK2	246	3	0			c.G2304A						PASS	.		,	401,3965		21,359,1803	10.0	12.0	11.0		2304,2070	-10.6	0.0	3	dbSNP_52	11	981,7557		42,897,3330	no	coding-synonymous,coding-synonymous	TNK2	NM_001010938.1,NM_005781.4	,	63,1256,5133	TT,TC,CC		11.4898,9.1846,10.7099	,	768/1087,690/1039	195595054	1382,11522	2183	4269	6452	SO:0001819	synonymous_variant	10188	exon13			CTGGGGCGGGAGG	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.2070G>A	3.37:g.195595054C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Silent	SNP	ENST00000333602.6	37	CCDS33928.1																																																																																			C|0.921;T|0.079	0.079	strong		0.711	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
OR2Z1	284383	hgsc.bcm.edu	37	19	8841588	8841588	+	Silent	SNP	C	C	G	rs147384704	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8841588C>G	ENST00000324060.2	+	1	273	c.198C>G	c.(196-198)ctC>ctG	p.L66L		NM_001004699.1	NP_001004699.1	Q8NG97	OR2Z1_HUMAN	olfactory receptor, family 2, subfamily Z, member 1	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCAGCCAGCTCTCCCTGTTTG	0.552													C|||	38	0.00758786	0.0008	0.0086	5008	,	,		21028	0.001		0.0229	False		,,,				2504	0.0072				p.L66L		Atlas-SNP	.											OR2Z1,NS,carcinoma,0,1	OR2Z1	53	1	0			c.C198G						PASS	.	C		37,4369	41.6+/-74.8	0,37,2166	148.0	131.0	137.0		198	0.6	0.9	19	dbSNP_134	137	244,8356	98.1+/-159.7	5,234,4061	no	coding-synonymous	OR2Z1	NM_001004699.1		5,271,6227	GG,GC,CC		2.8372,0.8398,2.1605		66/315	8841588	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	284383	exon1			CCAGCTCTCCCTG	AC008753	CCDS32895.1	19p13.2	2013-09-20	2002-11-13		ENSG00000181733	ENSG00000181733		"""GPCR / Class A : Olfactory receptors"""	15391	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily Z, member 2"""	OR2Z2			Standard	NM_001004699		Approved		uc010xkg.2	Q8NG97	OTTHUMG00000182195	ENST00000324060.2:c.198C>G	19.37:g.8841588C>G		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	136	72	0.529412	NM_001004699	B9EH50|Q6IFK0|Q96R25	Silent	SNP	ENST00000324060.2	37	CCDS32895.1																																																																																			C|0.981;G|0.019	0.019	strong		0.552	OR2Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459954.1		
MCM3	4172	hgsc.bcm.edu	37	6	52144221	52144221	+	Silent	SNP	C	C	T	rs2307331	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:52144221C>T	ENST00000229854.7	-	5	784	c.708G>A	c.(706-708)caG>caA	p.Q236Q	MCM3_ENST00000476448.1_5'UTR|MCM3_ENST00000596288.1_Silent_p.Q281Q|MCM3_ENST00000419835.2_Silent_p.Q190Q			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	236					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					TTCCCACCACCTGAACCCGGT	0.562													C|||	132	0.0263578	0.0023	0.0274	5008	,	,		18999	0.0		0.0616	False		,,,				2504	0.0491				p.Q281Q		Atlas-SNP	.											.	MCM3	63	.	0			c.G843A						PASS	.	C		64,4342	59.3+/-96.0	0,64,2139	75.0	76.0	76.0		708	4.3	1.0	6	dbSNP_100	76	681,7919	171.0+/-222.0	27,627,3646	no	coding-synonymous	MCM3	NM_002388.3		27,691,5785	TT,TC,CC		7.9186,1.4526,5.7281		236/809	52144221	745,12261	2203	4300	6503	SO:0001819	synonymous_variant	4172	exon5			CACCACCTGAACC	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"""minichromosome maintenance deficient (S. cerevisiae) 3"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"""			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.708G>A	6.37:g.52144221C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Silent	SNP	ENST00000229854.7	37																																																																																				C|0.954;T|0.046	0.046	strong		0.562	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1		
DNAH7	56171	hgsc.bcm.edu	37	2	196791276	196791276	+	Silent	SNP	T	T	G	rs1489802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:196791276T>G	ENST00000312428.6	-	22	3586	c.3486A>C	c.(3484-3486)gcA>gcC	p.A1162A		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1162	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						AGGCAAAAGTTGCATCTCCAG	0.333													T|||	2404	0.480032	0.093	0.5764	5008	,	,		16510	0.5635		0.6471	False		,,,				2504	0.6769				p.A1162A		Atlas-SNP	.											.	DNAH7	512	.	0			c.A3486C						PASS	.	T		663,2965		71,521,1222	112.0	100.0	104.0		3486	-10.2	0.0	2	dbSNP_88	104	5083,3075		1569,1945,565	no	coding-synonymous	DNAH7	NM_018897.2		1640,2466,1787	GG,GT,TT		37.6931,18.2745,48.7528		1162/4025	196791276	5746,6040	1814	4079	5893	SO:0001819	synonymous_variant	56171	exon22			AAAAGTTGCATCT	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.3486A>C	2.37:g.196791276T>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			T|0.505;G|0.495	0.495	strong		0.333	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
SIRPG	55423	hgsc.bcm.edu	37	20	1617069	1617069	+	Silent	SNP	A	A	G	rs2277761	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:1617069A>G	ENST00000303415.3	-	3	577	c.513T>C	c.(511-513)caT>caC	p.H171H	SIRPG_ENST00000216927.4_Silent_p.H171H|RP11-77C3.3_ENST00000456177.1_RNA|SIRPG_ENST00000344103.4_Intron|RP11-77C3.3_ENST00000437384.1_RNA|SIRPG_ENST00000381583.2_Silent_p.H171H|SIRPG_ENST00000381580.1_Silent_p.H138H	NM_018556.3	NP_061026.2	Q9P1W8	SIRPG_HUMAN	signal-regulatory protein gamma	171	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell activation (GO:0050870)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|stomach(1)	27						GAGAGAAGCCATGGGACTCAC	0.557													a|||	1148	0.229233	0.1619	0.366	5008	,	,		19683	0.2103		0.2376	False		,,,				2504	0.2342				p.H171H		Atlas-SNP	.											SIRPG,NS,carcinoma,-1,1	SIRPG	61	1	0			c.T513C						PASS	.	A	,,	726,3680		54,618,1531	149.0	133.0	138.0		513,513,	-4.2	0.0	20	dbSNP_100	138	2134,6466		266,1602,2432	no	coding-synonymous,coding-synonymous,intron	SIRPG	NM_001039508.1,NM_018556.3,NM_080816.2	,,	320,2220,3963	GG,GA,AA		24.814,16.4775,21.9899	,,	171/277,171/388,	1617069	2860,10146	2203	4300	6503	SO:0001819	synonymous_variant	55423	exon3			GAAGCCATGGGAC	AB042624	CCDS13020.2, CCDS13021.2, CCDS33434.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000089012	ENSG00000089012		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15757	protein-coding gene	gene with protein product		605466	"""signal-regulatory protein beta 2"""	SIRPB2		11185750, 16339511	Standard	XM_005260749		Approved	bA77C3.1, SIRP-B2, SIRPgamma, CD172g	uc002wfm.1	Q9P1W8	OTTHUMG00000031680	ENST00000303415.3:c.513T>C	20.37:g.1617069A>G		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	277	147	0.530686	NM_001039508	B1AKP6|Q5D051|Q5JV25|Q5MKL4|Q8WWA5|Q9NQK8	Silent	SNP	ENST00000303415.3	37	CCDS13020.2																																																																																			A|0.776;G|0.224	0.224	strong		0.557	SIRPG-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077566.2	NM_018556	
SEC16B	89866	hgsc.bcm.edu	37	1	177908852	177908852	+	Missense_Mutation	SNP	C	C	T	rs943762	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:177908852C>T	ENST00000308284.6	-	18	2277	c.2188G>A	c.(2188-2190)Gga>Aga	p.G730R	RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	730			G -> R (in dbSNP:rs943762). {ECO:0000269|PubMed:11605020}.		COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						GTTGTTCCTCCGGCTCCCGAA	0.408													T|||	809	0.161542	0.0545	0.1844	5008	,	,		20386	0.3294		0.1233	False		,,,				2504	0.1564				p.G730R		Atlas-SNP	.											.	SEC16B	92	.	0			c.G2188A						PASS	.	T	ARG/GLY	242,3554		9,224,1665	97.0	98.0	97.0		2188	-1.9	0.1	1	dbSNP_86	97	920,7326		46,828,3249	yes	missense	SEC16B	NM_033127.2	125	55,1052,4914	TT,TC,CC		11.1569,6.3751,9.6496	benign	730/1061	177908852	1162,10880	1898	4123	6021	SO:0001583	missense	89866	exon18			TTCCTCCGGCTCC	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2188G>A	1.37:g.177908852C>T	ENSP00000308339:p.Gly730Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	370	0.16941391941391942	20	0.04065040650406504	65	0.17955801104972377	191	0.3339160839160839	94	0.12401055408970976	T	0.443	-0.897738	0.02472	0.063751	0.111569	ENSG00000120341	ENST00000308284;ENST00000414025;ENST00000239472	T	0.12879	2.64	5.07	-1.94	0.07571	.	0.842615	0.10735	N	0.640198	T	0.00012	0.0000	N	0.00368	-1.59	0.49299	P	2.2999999999995246E-4	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.44283	-0.9338	9	0.15499	T	0.54	0.0027	5.3097	0.15823	0.0:0.3262:0.2809:0.3929	rs943762;rs52829735;rs59850561;rs943762	285;731;730;427	B1AM07;B1AM08;Q96JE7;Q96PW0	.;.;SC16B_HUMAN;.	R	730;414;445	ENSP00000308339:G730R	ENSP00000239472:G445R	G	-	1	0	AL359075.1	176175475	0.008000	0.16893	0.064000	0.19789	0.013000	0.08279	-0.582000	0.05814	-0.915000	0.03823	-0.982000	0.02568	GGA	C|0.838;T|0.162	0.162	strong		0.408	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
OBSCN	84033	hgsc.bcm.edu	37	1	228465346	228465346	+	Intron	SNP	A	A	G	rs493945	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228465346A>G	ENST00000422127.1	+	25	6798				OBSCN_ENST00000284548.11_Intron|OBSCN_ENST00000359599.6_Intron|RP5-1139B12.3_ENST00000602529.1_RNA|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000570156.2_Missense_Mutation_p.N2674D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCCCACTGACAACGTGCGCAT	0.647													A|||	1653	0.330072	0.3585	0.3617	5008	,	,		15447	0.378		0.3638	False		,,,				2504	0.1851				p.N2674D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A8020G						PASS	.																																			SO:0001627	intron_variant	84033	exon29			ACTGACAACGTGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.6755-109A>G	1.37:g.228465346A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			A|0.659;G|0.341	0.341	strong		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
GLTPD2	388323	hgsc.bcm.edu	37	17	4693054	4693054	+	Splice_Site	SNP	G	G	A	rs12951761	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4693054G>A	ENST00000331264.7	+	4	392	c.339G>A	c.(337-339)gaG>gaA	p.E113E		NM_001014985.2	NP_001014985	A6NH11	GLTD2_HUMAN	glycolipid transfer protein domain containing 2	113						cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4						TCGCCCGCAGGTTCCTGACTC	0.682													G|||	2567	0.51258	0.7557	0.5216	5008	,	,		14032	0.4494		0.4722	False		,,,				2504	0.2843				p.E113E		Atlas-SNP	.											.	GLTPD2	15	.	0			c.G339A						PASS	.	G		3050,1318		1085,880,219	22.0	22.0	22.0		339	0.3	1.0	17	dbSNP_121	22	4087,4467		995,2097,1185	no	coding-synonymous-near-splice	GLTPD2	NM_001014985.2		2080,2977,1404	AA,AG,GG		47.7788,30.174,44.7686		113/292	4693054	7137,5785	2184	4277	6461	SO:0001630	splice_region_variant	388323	exon4			CCGCAGGTTCCTG	BC029290	CCDS32534.1	17p13.2	2007-12-19				ENSG00000182327			33756	protein-coding gene	gene with protein product							Standard	NM_001014985		Approved		uc002fza.2	A6NH11		ENST00000331264.7:c.339-1G>A	17.37:g.4693054G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_001014985	A7E2T2	Silent	SNP	ENST00000331264.7	37	CCDS32534.1																																																																																			G|0.443;A|0.557	0.557	strong		0.682	GLTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439781.1	NM_001014985	Silent
DZIP3	9666	hgsc.bcm.edu	37	3	108381023	108381023	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:108381023A>C	ENST00000361582.3	+	21	2572	c.2342A>C	c.(2341-2343)aAc>aCc	p.N781T	DZIP3_ENST00000463306.1_Missense_Mutation_p.N781T	NM_014648.3	NP_055463.1	Q86Y13	DZIP3_HUMAN	DAZ interacting zinc finger protein 3	781					protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|poly(A) RNA binding (GO:0044822)|polyubiquitin binding (GO:0031593)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(9)|lung(21)|ovary(1)|pancreas(1)|prostate(5)|skin(1)	45						TGGCAAGAAAACCAAATGCAG	0.303																																					p.N781T		Atlas-SNP	.											DZIP3,NS,neuroblastoma,-1,1	DZIP3	111	1	0			c.A2342C						scavenged	.						56.0	57.0	56.0					3																	108381023		2203	4300	6503	SO:0001583	missense	9666	exon21			AAGAAAACCAAAT	AF279370	CCDS2952.1	3q13.13	2013-05-22	2013-05-22		ENSG00000198919	ENSG00000198919		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30938	protein-coding gene	gene with protein product	"""human RNA-binding ubiquitin ligase of 138 kDa"", ""protein phosphatase 1, regulatory subunit 66"""	608672	"""DAZ interacting protein 3, zinc finger"""			9734811, 12538761	Standard	NM_014648		Approved	hRUL138, PPP1R66	uc003dxd.3	Q86Y13	OTTHUMG00000159232	ENST00000361582.3:c.2342A>C	3.37:g.108381023A>C	ENSP00000355028:p.Asn781Thr	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	170	6	0.0352941	NM_014648	B3KN01|O75162|Q6P3R9|Q6PH82|Q86Y14|Q86Y15|Q86Y16|Q8IWI0|Q96RS9	Missense_Mutation	SNP	ENST00000361582.3	37	CCDS2952.1	.	.	.	.	.	.	.	.	.	.	A	17.70	3.454893	0.63290	.	.	ENSG00000198919	ENST00000361582;ENST00000463306	D;D	0.83837	-1.77;-1.77	5.09	5.09	0.68999	.	0.104471	0.42821	D	0.000653	T	0.82111	0.4966	L	0.44542	1.39	0.37460	D	0.915173	D;P	0.55172	0.97;0.956	P;P	0.51833	0.681;0.549	D	0.84122	0.0407	10	0.44086	T	0.13	-17.428	11.185	0.48650	1.0:0.0:0.0:0.0	.	399;781	D3DN61;Q86Y13	.;DZIP3_HUMAN	T	781	ENSP00000355028:N781T;ENSP00000419981:N781T	ENSP00000355028:N781T	N	+	2	0	DZIP3	109863713	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.571000	0.45990	2.136000	0.66102	0.460000	0.39030	AAC	.	.	none		0.303	DZIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353968.1	NM_014648	
LRP2BP	55805	hgsc.bcm.edu	37	4	186299260	186299260	+	Silent	SNP	A	A	G	rs2030802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:186299260A>G	ENST00000328559.7	-	1	892	c.81T>C	c.(79-81)ttT>ttC	p.F27F	LRP2BP_ENST00000505916.1_Silent_p.F27F|LRP2BP_ENST00000510776.1_5'UTR|LRP2BP_ENST00000362004.3_Silent_p.F27F|RP11-714G18.1_ENST00000514884.1_RNA	NM_018409.3	NP_060879.2	Q9P2M1	LR2BP_HUMAN	LRP2 binding protein	27						cytoplasm (GO:0005737)		p.F27F(1)		breast(1)|endometrium(2)|large_intestine(6)|lung(3)|prostate(1)|skin(2)	15		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;2.14e-25)|Epithelial(43;1.55e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-11)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000766)|Colorectal(24;0.00116)|LUSC - Lung squamous cell carcinoma(40;0.00904)|COAD - Colon adenocarcinoma(29;0.0101)|READ - Rectum adenocarcinoma(43;0.161)		TCCACTGGAAAAATTTTTGGT	0.378													G|||	1855	0.370407	0.612	0.3199	5008	,	,		19885	0.247		0.2624	False		,,,				2504	0.318				p.F27F		Atlas-SNP	.											LRP2BP,NS,carcinoma,0,1	LRP2BP	34	1	1	Substitution - coding silent(1)	prostate(1)	c.T81C						PASS	.	G		2369,2037	565.8+/-381.8	633,1103,467	135.0	137.0	137.0		81	2.9	0.3	4	dbSNP_94	137	2197,6403	712.0+/-405.9	273,1651,2376	no	coding-synonymous	LRP2BP	NM_018409.3		906,2754,2843	GG,GA,AA		25.5465,46.2324,35.1069		27/348	186299260	4566,8440	2203	4300	6503	SO:0001819	synonymous_variant	55805	exon1			CTGGAAAAATTTT	AB037746	CCDS3840.1	4q35.1	2011-05-03			ENSG00000109771	ENSG00000109771			25434	protein-coding gene	gene with protein product						10718198, 12508107	Standard	NM_018409		Approved	DKFZp761O0113	uc003ixj.2	Q9P2M1	OTTHUMG00000160460	ENST00000328559.7:c.81T>C	4.37:g.186299260A>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	115	63	0.547826	NM_018409	A6NJR7|A7E219|B3KX83|Q9NSN6	Silent	SNP	ENST00000328559.7	37	CCDS3840.1																																																																																			A|0.641;G|0.359	0.359	strong		0.378	LRP2BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360679.2	NM_018409	
FAM120A	23196	hgsc.bcm.edu	37	9	96238578	96238578	+	Silent	SNP	C	C	T	rs10821135	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:96238578C>T	ENST00000277165.6	+	3	956	c.762C>T	c.(760-762)caC>caT	p.H254H	FAM120A_ENST00000340893.4_Silent_p.H254H|FAM120A_ENST00000375389.3_Silent_p.H254H|FAM120A_ENST00000333936.5_Silent_p.H254H	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	254						cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.H254H(1)		endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CTTCCTTTCACTGGAGTTTAC	0.348													T|||	2627	0.524561	0.6838	0.5591	5008	,	,		19963	0.5972		0.498	False		,,,				2504	0.2372				p.H254H		Atlas-SNP	.											FAM120A,NS,carcinoma,+2,2	FAM120A	105	2	1	Substitution - coding silent(1)	stomach(1)	c.C762T						PASS	.	T		2905,1501	478.8+/-358.3	955,995,253	138.0	125.0	129.0		762	-1.4	1.0	9	dbSNP_120	129	4248,4352	581.2+/-391.2	1041,2166,1093	no	coding-synonymous	FAM120A	NM_014612.3		1996,3161,1346	TT,TC,CC		49.3953,34.0672,45.0023		254/1119	96238578	7153,5853	2203	4300	6503	SO:0001819	synonymous_variant	23196	exon3			CTTTCACTGGAGT	AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"""DNA polymerase-transactivated protein 1"", ""oxidative stess-associated Src activator"""	612265	"""chromosome 9 open reading frame 10"""	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.762C>T	9.37:g.96238578C>T		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Silent	SNP	ENST00000277165.6	37	CCDS6706.1	1279	0.5856227106227107	330	0.6707317073170732	212	0.585635359116022	357	0.6241258741258742	380	0.5013192612137203	T	9.458	1.092407	0.20471	0.659328	0.493953	ENSG00000048828	ENST00000446420	.	.	.	5.52	-1.38	0.09027	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39881	-0.9592	3	.	.	.	-15.061	11.9011	0.52685	0.0:0.4902:0.0:0.5098	rs10821135;rs57788214;rs10821135	.	.	.	I	97	.	.	T	+	2	0	FAM120A	95278399	1.000000	0.71417	0.968000	0.41197	0.993000	0.82548	1.012000	0.29924	-0.707000	0.05022	-0.360000	0.07572	ACT	C|0.447;T|0.553	0.553	strong		0.348	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612	
WDR11	55717	hgsc.bcm.edu	37	10	122663585	122663585	+	Silent	SNP	G	G	A	rs1652727	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:122663585G>A	ENST00000263461.6	+	24	3204	c.2958G>A	c.(2956-2958)ctG>ctA	p.L986L	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|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)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						GGGTTAATCTGCAGGAAGTGA	0.328													A|||	3388	0.676518	0.8752	0.6657	5008	,	,		16683	0.5179		0.6511	False		,,,				2504	0.6053				p.L986L		Atlas-SNP	.											.	WDR11	95	.	0			c.G2958A						PASS	.	A		3786,620	270.1+/-269.4	1634,518,51	97.0	98.0	98.0		2958	-11.7	0.2	10	dbSNP_89	98	5628,2972	459.8+/-365.0	1853,1922,525	no	coding-synonymous	WDR11	NM_018117.11		3487,2440,576	AA,AG,GG		34.5581,14.0717,27.618		986/1225	122663585	9414,3592	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon24			TAATCTGCAGGAA	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2958G>A	10.37:g.122663585G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	42	24	0.571429	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			G|0.301;A|0.699	0.699	strong		0.328	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
RMND5A	64795	hgsc.bcm.edu	37	2	86979093	86979093	+	Silent	SNP	G	G	A	rs10186663	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:86979093G>A	ENST00000283632.4	+	3	855	c.360G>A	c.(358-360)gaG>gaA	p.E120E		NM_022780.3	NP_073617.1	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog A (S. cerevisiae)	120	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.									kidney(1)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	17						TTCTCAATGAGGTGATGGTGG	0.468													G|||	3454	0.689696	0.615	0.696	5008	,	,		16063	0.9058		0.664	False		,,,				2504	0.59				p.E120E		Atlas-SNP	.											.	RMND5A	33	.	0			c.G360A						PASS	.	G		2898,1508	674.7+/-403.0	959,980,264	77.0	71.0	73.0		360	4.4	1.0	2	dbSNP_119	73	5592,3008	664.5+/-402.2	1799,1994,507	no	coding-synonymous	RMND5A	NM_022780.3		2758,2974,771	AA,AG,GG		34.9767,34.2261,34.7224		120/392	86979093	8490,4516	2203	4300	6503	SO:0001819	synonymous_variant	64795	exon3			CAATGAGGTGATG	BC012165	CCDS1991.1	2p11.2	2012-07-20			ENSG00000153561	ENSG00000153561			25850	protein-coding gene	gene with protein product	"""GID complex subunit 2 homolog A"""					12477932	Standard	NM_022780		Approved	FLJ13910, RMD5, GID2, GID2A	uc002srs.4	Q9H871	OTTHUMG00000130262	ENST00000283632.4:c.360G>A	2.37:g.86979093G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	125	15	0.12	NM_022780	D6W5M6|Q6NTF0|Q9H6W5|Q9H9H2	Silent	SNP	ENST00000283632.4	37	CCDS1991.1																																																																																			G|0.330;A|0.670	0.670	strong		0.468	RMND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252591.2	NM_022780	
VWA3B	200403	hgsc.bcm.edu	37	2	98844674	98844674	+	Missense_Mutation	SNP	C	C	G	rs7601049	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:98844674C>G	ENST00000477737.1	+	15	2233	c.2029C>G	c.(2029-2031)Ctg>Gtg	p.L677V		NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	677	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		L -> V (in dbSNP:rs7601049). {ECO:0000269|PubMed:17974005}.							NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						GAATGAAGATCTGACTCTTTT	0.373													C|||	3451	0.689097	0.6346	0.5331	5008	,	,		20042	0.7986		0.6034	False		,,,				2504	0.8487				p.L677V		Atlas-SNP	.											.	VWA3B	138	.	0			c.C2029G						PASS	.	C	VAL/LEU	2444,1386		774,896,245	100.0	98.0	99.0		2029	-5.1	0.0	2	dbSNP_116	99	5055,3197		1546,1963,617	yes	missense	VWA3B	NM_144992.4	32	2320,2859,862	GG,GC,CC		38.7421,36.188,37.9325	benign	677/1295	98844674	7499,4583	1915	4126	6041	SO:0001583	missense	200403	exon15			GAAGATCTGACTC	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.2029C>G	2.37:g.98844674C>G	ENSP00000417955:p.Leu677Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	1395|1395	0.6387362637362637|0.6387362637362637	314|314	0.6382113821138211|0.6382113821138211	198|198	0.5469613259668509|0.5469613259668509	439|439	0.7674825174825175|0.7674825174825175	444|444	0.5857519788918206|0.5857519788918206	C|C	9.203|9.203	1.029089|1.029089	0.19512|0.19512	0.63812|0.63812	0.612579|0.612579	ENSG00000168658|ENSG00000168658	ENST00000477737|ENST00000473149	T|.	0.05717|.	3.4|.	5.8|5.8	-5.07|-5.07	0.02938|0.02938	von Willebrand factor, type A (1);|.	0.945622|.	0.08741|.	N|.	0.900507|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.25890|0.25890	0.77|0.77	0.44816|0.44816	P|P	0.0021769999999999845|0.0021769999999999845	B;B;B;B|.	0.31318|.	0.319;0.064;0.023;0.141|.	B;B;B;B|.	0.22753|.	0.041;0.015;0.015;0.041|.	T|T	0.36432|0.36432	-0.9748|-0.9748	9|4	0.07030|.	T|.	0.85|.	.|.	3.0445|3.0445	0.06149|0.06149	0.1981:0.2596:0.3913:0.151|0.1981:0.2596:0.3913:0.151	rs7601049;rs52808975;rs58638435;rs7601049|rs7601049;rs52808975;rs58638435;rs7601049	69;677;677;677|.	Q502W6-5;Q502W6;Q502W6-8;Q502W6-6|.	.;VWA3B_HUMAN;.;.|.	V|C	677|87	ENSP00000417955:L677V|.	ENSP00000417955:L677V|.	L|S	+|+	1|2	2|0	VWA3B|VWA3B	98211106|98211106	0.001000|0.001000	0.12720|0.12720	0.033000|0.033000	0.17914|0.17914	0.874000|0.874000	0.50279|0.50279	-1.794000|-1.794000	0.01753|0.01753	-0.468000|-0.468000	0.06922|0.06922	0.467000|0.467000	0.42956|0.42956	CTG|TCT	C|0.354;G|0.646	0.646	strong		0.373	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
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 GAIIx	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_ENST00000344576.2_Missense_Mutation_p.R521K|EGFR_ENST00000455089.1_Missense_Mutation_p.R476K|EGFR_ENST00000442591.1_Missense_Mutation_p.R521K|EGFR_ENST00000342916.3_Missense_Mutation_p.R521K|EGFR_ENST00000454757.2_Missense_Mutation_p.R468K	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	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	44	25	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	
SGCG	6445	hgsc.bcm.edu	37	13	23824783	23824783	+	Silent	SNP	T	T	G	rs1800351	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:23824783T>G	ENST00000218867.3	+	4	436	c.312T>G	c.(310-312)ctT>ctG	p.L104L	SGCG_ENST00000537476.1_Silent_p.L104L|SGCG_ENST00000545013.1_Silent_p.L104L	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	104					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		CATCTCTGCTTCTACAATCAA	0.368													T|||	2628	0.52476	0.7035	0.4236	5008	,	,		15922	0.7014		0.333	False		,,,				2504	0.3701				p.L104L		Atlas-SNP	.											.	SGCG	64	.	0			c.T312G						PASS	.	T		2958,1448	681.6+/-404.0	996,966,241	95.0	83.0	87.0		312	0.1	0.8	13	dbSNP_89	87	3170,5430	480.1+/-370.3	584,2002,1714	no	coding-synonymous	SGCG	NM_000231.2		1580,2968,1955	GG,GT,TT		36.8605,32.8643,47.1167		104/292	23824783	6128,6878	2203	4300	6503	SO:0001819	synonymous_variant	6445	exon4			TCTGCTTCTACAA	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.312T>G	13.37:g.23824783T>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	37	CCDS9299.1																																																																																			T|0.510;G|0.490	0.490	strong		0.368	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
ERAP2	64167	hgsc.bcm.edu	37	5	96215680	96215680	+	Silent	SNP	C	C	T	rs41506651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:96215680C>T	ENST00000437043.3	+	2	1002	c.291C>T	c.(289-291)atC>atT	p.I97I	ERAP2_ENST00000379904.4_Silent_p.I97I|ERAP2_ENST00000510309.1_Silent_p.I97I|CTD-2260A17.2_ENST00000501338.1_Intron	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	97					antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		CTGAGAAGATCGAAGTCTTGG	0.473													C|||	244	0.048722	0.0061	0.0663	5008	,	,		22981	0.003		0.1004	False		,,,				2504	0.0879				p.I97I		Atlas-SNP	.											.	ERAP2	77	.	0			c.C291T						PASS	.	C	,	112,4294	87.3+/-125.9	1,110,2092	82.0	71.0	75.0		291,291	-4.0	0.5	5	dbSNP_127	75	924,7676	205.4+/-247.8	45,834,3421	no	coding-synonymous,coding-synonymous	ERAP2	NM_001130140.1,NM_022350.3	,	46,944,5513	TT,TC,CC		10.7442,2.542,7.9656	,	97/961,97/961	96215680	1036,11970	2203	4300	6503	SO:0001819	synonymous_variant	64167	exon2			GAAGATCGAAGTC	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.291C>T	5.37:g.96215680C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Silent	SNP	ENST00000437043.3	37	CCDS4086.1																																																																																			C|0.928;T|0.072	0.072	strong		0.473	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
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 GAIIx	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	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	43	10	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	
FAM160B1	57700	hgsc.bcm.edu	37	10	116615045	116615045	+	Silent	SNP	T	T	C	rs3180654	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:116615045T>C	ENST00000369248.4	+	14	2228	c.1893T>C	c.(1891-1893)ttT>ttC	p.F631F	FAM160B1_ENST00000369250.3_Silent_p.F631F	NM_020940.3	NP_065991.3	Q5W0V3	F16B1_HUMAN	family with sequence similarity 160, member B1	631			F -> L (in dbSNP:rs3180654).							NS(1)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|lung(13)	25						CTGCTTTCTTTGAAGGTCATT	0.373													T|||	1275	0.254593	0.2322	0.2032	5008	,	,		17980	0.0357		0.3777	False		,,,				2504	0.4202				p.F631F		Atlas-SNP	.											.	FAM160B1	107	.	0			c.T1893C						PASS	.	T	,	1128,3278	402.8+/-332.5	138,852,1213	92.0	93.0	92.0		1893,1893	4.5	1.0	10	dbSNP_105	92	3324,5276	493.8+/-373.7	635,2054,1611	no	coding-synonymous,coding-synonymous	FAM160B1	NM_001135051.1,NM_020940.3	,	773,2906,2824	CC,CT,TT		38.6512,25.6015,34.2304	,	631/739,631/766	116615045	4452,8554	2203	4300	6503	SO:0001819	synonymous_variant	57700	exon14			TTTCTTTGAAGGT	AB046820	CCDS31290.1, CCDS44480.1	10q26.11	2008-06-05	2008-06-05	2008-06-05	ENSG00000151553	ENSG00000151553			29320	protein-coding gene	gene with protein product			"""KIAA1600"""	KIAA1600		10997877	Standard	NM_020940		Approved	bA106M7.3	uc001lcb.3	Q5W0V3	OTTHUMG00000019092	ENST00000369248.4:c.1893T>C	10.37:g.116615045T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_020940	Q5H9P7|Q5W0V2|Q8IY76|Q9HCH2	Silent	SNP	ENST00000369248.4	37	CCDS31290.1																																																																																			C|0.312;T|0.688	0.312	strong		0.373	FAM160B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050499.1	XM_049351	
NAGPA	51172	hgsc.bcm.edu	37	16	5075542	5075542	+	Silent	SNP	G	G	A	rs887854	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:5075542G>A	ENST00000312251.3	-	10	1504	c.1485C>T	c.(1483-1485)aaC>aaT	p.N495N	RP11-165E7.1_ENST00000588778.1_RNA|NAGPA_ENST00000381955.3_Silent_p.N461N	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	495					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|lysosome organization (GO:0007040)|protein glycosylation (GO:0006486)|protein targeting to lysosome (GO:0006622)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity (GO:0003944)			endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1)	12					N-Acetyl-D-glucosamine(DB00141)	GAGGCTCCCCGTTCATCTCCT	0.632													g|||	3969	0.792532	0.8941	0.6988	5008	,	,		17272	0.8224		0.6581	False		,,,				2504	0.8292				p.N495N		Atlas-SNP	.											.	NAGPA	30	.	0			c.C1485T						PASS	.	A		3735,659	758.7+/-412.8	1582,571,44	79.0	89.0	86.0		1485	-7.3	0.6	16	dbSNP_86	86	5585,3015	659.3+/-401.7	1821,1943,536	no	coding-synonymous	NAGPA	NM_016256.3		3403,2514,580	AA,AG,GG		35.0581,14.9977,28.2746		495/516	5075542	9320,3674	2197	4300	6497	SO:0001819	synonymous_variant	51172	exon10			CTCCCCGTTCATC	AF187072	CCDS10527.1	16p13.3	2008-02-05			ENSG00000103174	ENSG00000103174	3.1.4.45		17378	protein-coding gene	gene with protein product		607985				10551838, 12058031	Standard	NM_016256		Approved	APAA, UCE	uc002cyg.3	Q9UK23	OTTHUMG00000090515	ENST00000312251.3:c.1485C>T	16.37:g.5075542G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	138	70	0.507246	NM_016256	B2RAS1|Q96EJ8	Silent	SNP	ENST00000312251.3	37	CCDS10527.1																																																																																			G|0.253;N|0.000	.	strong		0.632	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207003.1	NM_016256	
PMP2	5375	hgsc.bcm.edu	37	8	82357112	82357112	+	Silent	SNP	T	T	C	rs2229015	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:82357112T>C	ENST00000256103.2	-	2	322	c.186A>G	c.(184-186)gaA>gaG	p.E62E	PMP2_ENST00000519260.1_Intron|RP11-157I4.4_ENST00000524085.2_RNA	NM_002677.3	NP_002668.1	P02689	MYP2_HUMAN	peripheral myelin protein 2	62					membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	cholesterol binding (GO:0015485)|fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			Epithelial(68;0.186)			TGAAGGAGATTTCTGTATTTT	0.398													C|||	1760	0.351438	0.357	0.3285	5008	,	,		19779	0.748		0.1412	False		,,,				2504	0.1677				p.E62E		Atlas-SNP	.											.	PMP2	21	.	0			c.A186G						PASS	.	C		1469,2937	678.9+/-403.6	258,953,992	142.0	140.0	141.0		186	4.6	1.0	8	dbSNP_98	141	1449,7151	750.6+/-407.4	131,1187,2982	no	coding-synonymous	PMP2	NM_002677.3		389,2140,3974	CC,CT,TT		16.8488,33.3409,22.4358		62/133	82357112	2918,10088	2203	4300	6503	SO:0001819	synonymous_variant	5375	exon2			GGAGATTTCTGTA	X62167	CCDS6229.1	8q21.3-q22.1	2013-03-01			ENSG00000147588	ENSG00000147588		"""Fatty acid binding protein family"""	9117	protein-coding gene	gene with protein product		170715				1720307, 8288226	Standard	NM_002677		Approved	MP2, FABP8, M-FABP	uc003ycb.1	P02689	OTTHUMG00000164600	ENST00000256103.2:c.186A>G	8.37:g.82357112T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_002677	Q6FHL4	Silent	SNP	ENST00000256103.2	37	CCDS6229.1																																																																																			T|0.706;C|0.294	0.294	strong		0.398	PMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379365.1	NM_002677	
ATP9B	374868	hgsc.bcm.edu	37	18	76870397	76870397	+	Silent	SNP	G	G	A	rs492657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:76870397G>A	ENST00000426216.2	+	3	353	c.336G>A	c.(334-336)gaG>gaA	p.E112E	ATP9B_ENST00000586722.1_Silent_p.E112E|ATP9B_ENST00000591464.1_Intron|ATP9B_ENST00000307671.7_Silent_p.E112E|ATP9B_ENST00000458297.2_Silent_p.E60E	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	112					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		GAAAGAAAGAGCTGAAAGCTC	0.318													A|||	578	0.115415	0.2882	0.0749	5008	,	,		18999	0.0228		0.1034	False		,,,				2504	0.0184				p.E112E		Atlas-SNP	.											.	ATP9B	96	.	0			c.G336A						PASS	.	A		1196,3210	705.1+/-407.2	143,910,1150	70.0	76.0	74.0		336	-1.9	0.9	18	dbSNP_83	74	809,7791	781.8+/-407.6	43,723,3534	no	coding-synonymous	ATP9B	NM_198531.3		186,1633,4684	AA,AG,GG		9.407,27.1448,15.416		112/1148	76870397	2005,11001	2203	4300	6503	SO:0001819	synonymous_variant	374868	exon3			GAAAGAGCTGAAA	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.336G>A	18.37:g.76870397G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_198531	O60872|Q08AD8|Q08AD9	Silent	SNP	ENST00000426216.2	37	CCDS12014.1																																																																																			G|0.862;A|0.138	0.138	strong		0.318	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
ADAM30	11085	hgsc.bcm.edu	37	1	120437884	120437884	+	Missense_Mutation	SNP	A	A	G	rs2641348	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:120437884A>G	ENST00000369400.1	-	1	1234	c.1076T>C	c.(1075-1077)cTt>cCt	p.L359P		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	359	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.		L -> P (in dbSNP:rs2641348). {ECO:0000269|PubMed:10512762, ECO:0000269|PubMed:14702039}.		binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		GATGCAATTAAGCCTACCCCT	0.428													A|||	981	0.195887	0.3805	0.1196	5008	,	,		21438	0.0466		0.1143	False		,,,				2504	0.2382				p.L359P		Atlas-SNP	.											.	ADAM30	88	.	0			c.T1076C						PASS	.	A	PRO/LEU	1431,2975	465.1+/-354.1	237,957,1009	142.0	132.0	135.0		1076	-9.3	0.0	1	dbSNP_100	135	896,7704	200.6+/-244.3	53,790,3457	yes	missense	ADAM30	NM_021794.3	98	290,1747,4466	GG,GA,AA		10.4186,32.4784,17.8917	benign	359/791	120437884	2327,10679	2203	4300	6503	SO:0001583	missense	11085	exon1			CAATTAAGCCTAC	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"""ADAM metallopeptidase domain containing"""	208	protein-coding gene	gene with protein product		604779	"""a disintegrin and metalloproteinase domain 30"""				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.1076T>C	1.37:g.120437884A>G	ENSP00000358407:p.Leu359Pro	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	147	67	0.455782	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Missense_Mutation	SNP	ENST00000369400.1	37	CCDS907.1	337	0.1543040293040293	192	0.3902439024390244	42	0.11602209944751381	17	0.02972027972027972	86	0.11345646437994723	A	8.303	0.820393	0.16678	0.324784	0.104186	ENSG00000134249	ENST00000369400;ENST00000543066	T	0.62941	-0.01	4.63	-9.26	0.00662	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	3.500000	0.01102	N	0.005395	T	0.12263	0.0298	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.04128	-1.0975	9	0.30078	T	0.28	.	3.1426	0.06461	0.1031:0.4271:0.2496:0.2202	rs2641348;rs52793885;rs59741634;rs2641348	359	Q9UKF2	ADA30_HUMAN	P	359	ENSP00000358407:L359P	ENSP00000358407:L359P	L	-	2	0	ADAM30	120239407	0.000000	0.05858	0.000000	0.03702	0.293000	0.27360	-4.390000	0.00242	-2.444000	0.00548	0.460000	0.39030	CTT	A|0.830;G|0.170	0.170	strong		0.428	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794	
PTX4	390667	hgsc.bcm.edu	37	16	1536372	1536372	+	Silent	SNP	G	G	A	rs28444604	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1536372G>A	ENST00000447419.2	-	3	1030	c.1005C>T	c.(1003-1005)ccC>ccT	p.P335P	PTX4_ENST00000440447.2_Missense_Mutation_p.P187L|PTX4_ENST00000293922.1_Silent_p.P330P			Q96A99	PTX4_HUMAN	pentraxin 4, long	335	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GGATGGATCCGGGCAGCAGGG	0.667													G|||	854	0.170527	0.0446	0.0937	5008	,	,		16676	0.4544		0.0964	False		,,,				2504	0.1789				p.P330P		Atlas-SNP	.											.	PTX4	46	.	0			c.C990T						PASS	.	G		207,4191	127.8+/-164.7	5,197,1997	47.0	56.0	53.0		990	-11.2	0.0	16	dbSNP_125	53	763,7837	179.2+/-228.4	31,701,3568	no	coding-synonymous	PTX4	NM_001013658.1		36,898,5565	AA,AG,GG		8.8721,4.7067,7.4627		330/474	1536372	970,12028	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GGATCCGGGCAGC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1005C>T	16.37:g.1536372G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				G|0.895;A|0.105	0.105	strong		0.667	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
SMC1B	27127	hgsc.bcm.edu	37	22	45782903	45782903	+	Silent	SNP	T	T	C	rs6007010	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:45782903T>C	ENST00000357450.4	-	11	1754	c.1755A>G	c.(1753-1755)ctA>ctG	p.L585L	SMC1B_ENST00000404354.3_Silent_p.L585L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	585	Flexible hinge.				meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		TAAGCTCCCTTAGTCTTTCAT	0.323													T|||	2837	0.566494	0.9054	0.3977	5008	,	,		21535	0.5268		0.3728	False		,,,				2504	0.4683				p.L585L		Atlas-SNP	.											SMC1B_ENST00000357450,NS,carcinoma,-1,4	SMC1B	215	4	0			c.A1755G						scavenged	.	T		3069,633		1281,507,63	148.0	139.0	142.0		1755	-6.2	0.2	22	dbSNP_114	142	2935,5279		530,1875,1702	no	coding-synonymous	SMC1B	NM_148674.3		1811,2382,1765	CC,CT,TT		35.7317,17.0989,49.614		585/1236	45782903	6004,5912	1851	4107	5958	SO:0001819	synonymous_variant	27127	exon11			CTCCCTTAGTCTT	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.1755A>G	22.37:g.45782903T>C		Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			T|0.518;C|0.482	0.482	strong		0.323	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
HTR5A	3361	hgsc.bcm.edu	37	7	154862621	154862621	+	Silent	SNP	T	T	A	rs6320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:154862621T>A	ENST00000287907.2	+	1	588	c.12T>A	c.(10-12)ccT>ccA	p.P4P	HTR5A-AS1_ENST00000493904.1_Intron|HTR5A-AS1_ENST00000543018.1_Intron|HTR5A-AS1_ENST00000395731.2_Intron	NM_024012.3	NP_076917.1	P47898	5HT5A_HUMAN	5-hydroxytryptamine (serotonin) receptor 5A, G protein-coupled	4					cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hippocampus development (GO:0021766)|response to estradiol (GO:0032355)|serotonin receptor signaling pathway (GO:0007210)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	serotonin receptor activity (GO:0004993)	p.P4P(1)		NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(3)|stomach(1)	48	all_neural(206;0.119)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.0238)	UCEC - Uterine corpus endometrioid carcinoma (81;0.171)	Asenapine(DB06216)|Loxapine(DB00408)|Olanzapine(DB00334)	TGGATTTACCTGTGAACCTAA	0.612													T|||	1287	0.256989	0.211	0.2075	5008	,	,		17998	0.3492		0.2734	False		,,,				2504	0.2423				p.P4P		Atlas-SNP	.											HTR5A,NS,carcinoma,+1,2	HTR5A	114	2	1	Substitution - coding silent(1)	stomach(1)	c.T12A						PASS	.	T		922,3484	353.1+/-312.0	99,724,1380	115.0	124.0	121.0		12	-2.8	0.0	7	dbSNP_52	121	2429,6171	402.8+/-347.6	358,1713,2229	no	coding-synonymous	HTR5A	NM_024012.2		457,2437,3609	AA,AT,TT		28.2442,20.926,25.765		4/358	154862621	3351,9655	2203	4300	6503	SO:0001819	synonymous_variant	3361	exon1			TTTACCTGTGAAC		CCDS5936.1	7q36.1	2012-08-08	2012-02-03		ENSG00000157219	ENSG00000157219		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5300	protein-coding gene	gene with protein product		601305	"""5-hydroxytryptamine (serotonin) receptor 5A"""			7988681	Standard	NM_024012		Approved	5-HT5A	uc003wlu.2	P47898	OTTHUMG00000151327	ENST00000287907.2:c.12T>A	7.37:g.154862621T>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	29	17	0.586207	NM_024012	Q2M2D2	Silent	SNP	ENST00000287907.2	37	CCDS5936.1																																																																																			T|0.726;A|0.274	0.274	strong		0.612	HTR5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322240.1	NM_024012	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026146	176026146	+	Silent	SNP	C	C	T	rs79403503|rs386695335	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176026146C>T	ENST00000303991.4	-	2	867	c.690G>A	c.(688-690)ccG>ccA	p.P230P		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	230					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCTCCTTCCTCGGTGACACTG	0.498																																					p.P230P		Atlas-SNP	.											.	GPRIN1	77	.	0			c.G690A						PASS	.						98.0	99.0	99.0					5																	176026146		2203	4299	6502	SO:0001819	synonymous_variant	114787	exon2			CTTCCTCGGTGAC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.690G>A	5.37:g.176026146C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	96	32	0.333333	NM_052899	C9JM70|Q8ND74|Q96PZ4	Silent	SNP	ENST00000303991.4	37	CCDS4405.1																																																																																			C|0.779;T|0.221	0.221	strong		0.498	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
PIGM	93183	hgsc.bcm.edu	37	1	160000435	160000435	+	Missense_Mutation	SNP	A	A	T	rs12409352	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:160000435A>T	ENST00000368090.2	-	1	1348	c.1095T>A	c.(1093-1095)ttT>ttA	p.F365L		NM_145167.2	NP_660150.1	Q9H3S5	PIGM_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class M	365			F -> L (in dbSNP:rs12409352).		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			kidney(1)|large_intestine(4)|lung(9)|ovary(2)|skin(1)	17	all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CCTGCCCTATAAACCATAACA	0.438													A|||	341	0.0680911	0.0091	0.1182	5008	,	,		21320	0.0357		0.1292	False		,,,				2504	0.0828				p.F365L		Atlas-SNP	.											.	PIGM	27	.	0			c.T1095A						PASS	.	A	LEU/PHE	155,4251	106.0+/-144.5	5,145,2053	134.0	143.0	140.0		1095	-0.8	0.1	1	dbSNP_120	140	1528,7072	289.2+/-299.1	138,1252,2910	yes	missense	PIGM	NM_145167.2	22	143,1397,4963	TT,TA,AA		17.7674,3.5179,12.9402	possibly-damaging	365/424	160000435	1683,11323	2203	4300	6503	SO:0001583	missense	93183	exon1			CCCTATAAACCAT	AB028127	CCDS1192.1	1q23.2	2013-02-26	2006-06-28		ENSG00000143315	ENSG00000143315		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	18858	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 1"", ""DPM:GlcN-(acyl-)PI mannosyltransferase"", ""dol-P-Man dependent GPI mannosyltransferase"""	610273	"""phosphatidylinositol glycan, class M"""			11226175	Standard	NM_145167		Approved	GPI-MT-I	uc001fuv.1	Q9H3S5	OTTHUMG00000024081	ENST00000368090.2:c.1095T>A	1.37:g.160000435A>T	ENSP00000357069:p.Phe365Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	107	58	0.542056	NM_145167		Missense_Mutation	SNP	ENST00000368090.2	37	CCDS1192.1	184	0.08424908424908426	10	0.02032520325203252	44	0.12154696132596685	28	0.04895104895104895	102	0.1345646437994723	A	11.34	1.609087	0.28623	0.035179	0.177674	ENSG00000143315	ENST00000368090	T	0.38722	1.12	5.4	-0.827	0.10802	.	0.058196	0.64402	D	0.000001	T	0.11196	0.0273	N	0.25647	0.755	0.29209	P	0.87474	B	0.24618	0.107	B	0.27262	0.078	T	0.20505	-1.0273	8	.	.	.	-21.1888	10.5406	0.45031	0.3832:0.0:0.6168:0.0	rs12409352;rs12409352	365	Q9H3S5	PIGM_HUMAN	L	365	ENSP00000357069:F365L	.	F	-	3	2	PIGM	158267059	0.000000	0.05858	0.067000	0.19924	0.986000	0.74619	-0.710000	0.05024	-0.155000	0.11098	0.379000	0.24179	TTT	A|0.892;T|0.108	0.108	strong		0.438	PIGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060643.2	NM_145167	
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 GAIIx	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		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	93	37	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	
RNF207	388591	hgsc.bcm.edu	37	1	6278414	6278414	+	Missense_Mutation	SNP	A	A	G	rs709209	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:6278414A>G	ENST00000377939.4	+	17	1845	c.1718A>G	c.(1717-1719)aAc>aGc	p.N573S	RNF207_ENST00000483336.1_3'UTR|RNF207_ENST00000377948.2_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	573			N -> S (in dbSNP:rs709209). {ECO:0000269|PubMed:19305409}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		AGCAGGAACAACGCGGCCTCA	0.567													G|||	2189	0.437101	0.7405	0.2939	5008	,	,		19938	0.2639		0.3469	False		,,,				2504	0.3998				p.N573S		Atlas-SNP	.											.	RNF207	45	.	0			c.A1718G						PASS	.	G	SER/ASN	2908,1368		1019,870,249	65.0	77.0	73.0		1718	-1.3	0.0	1	dbSNP_86	73	2857,5645		495,1867,1889	yes	missense	RNF207	NM_207396.2	46	1514,2737,2138	GG,GA,AA		33.6039,31.9925,45.1166	benign	573/635	6278414	5765,7013	2138	4251	6389	SO:0001583	missense	388591	exon17			GGAACAACGCGGC	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1718A>G	1.37:g.6278414A>G	ENSP00000367173:p.Asn573Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	53	0.569892	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	864	0.3956043956043956	346	0.7032520325203252	116	0.32044198895027626	153	0.2674825174825175	249	0.32849604221635886	G	0.509	-0.867304	0.02590	0.680075	0.336039	ENSG00000158286	ENST00000377939	T	0.16196	2.36	4.71	-1.29	0.09288	.	2.289780	0.03153	N	0.168212	T	0.00012	0.0000	N	0.00707	-1.245	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41502	-0.9505	9	0.06625	T	0.88	-28.6057	1.1273	0.01738	0.2717:0.2697:0.3211:0.1375	rs709209;rs9435252;rs56791368;rs709209	573	Q6ZRF8	RN207_HUMAN	S	573	ENSP00000367173:N573S	ENSP00000367173:N573S	N	+	2	0	RNF207	6201001	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.296000	0.08287	-0.582000	0.05929	-0.213000	0.12676	AAC	A|0.586;G|0.414	0.414	strong		0.567	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
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 GAIIx	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	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	85	14	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		
CHEK2	11200	hgsc.bcm.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000404276.1_Silent_p.S372S|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000544772.1_Silent_p.S151S			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.S415S		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	CHEK2,bladder,carcinoma,0,38	CHEK2	438	38	8	Substitution - coding silent(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	c.C1245T						scavenged	.						43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200	exon12			AATCTTGGAGTGC	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	101	7	0.0693069	NM_001005735	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA	.	.	weak		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735	
VPS13D	55187	hgsc.bcm.edu	37	1	12342990	12342990	+	Missense_Mutation	SNP	G	G	A	rs41279452	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12342990G>A	ENST00000358136.3	+	21	4961	c.4831G>A	c.(4831-4833)Gaa>Aaa	p.E1611K	VPS13D_ENST00000356315.4_Missense_Mutation_p.E1611K	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		GTCAGTGAAGGAAGTCAAATC	0.458													G|||	11	0.00219649	0.0	0.0043	5008	,	,		20499	0.0		0.008	False		,,,				2504	0.0				p.E1611K		Atlas-SNP	.											.	VPS13D	316	.	0			c.G4831A						PASS	.	G	LYS/GLU,LYS/GLU	10,4396	15.5+/-35.6	0,10,2193	101.0	103.0	103.0		4831,4831	5.8	1.0	1	dbSNP_127	103	105,8495	57.5+/-118.9	2,101,4197	yes	missense,missense	VPS13D	NM_015378.2,NM_018156.2	56,56	2,111,6390	AA,AG,GG		1.2209,0.227,0.8842	benign,benign	1611/4389,1611/4364	12342990	115,12891	2203	4300	6503	SO:0001583	missense	55187	exon21			GTGAAGGAAGTCA	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.4831G>A	1.37:g.12342990G>A	ENSP00000350854:p.Glu1611Lys	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	135	50	0.37037	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	14.82	2.649755	0.47362	0.00227	0.012209	ENSG00000048707	ENST00000356315;ENST00000358136	T;T	0.54071	0.59;0.59	5.82	5.82	0.92795	.	0.313930	0.34700	N	0.003753	T	0.27967	0.0689	N	0.14661	0.345	0.80722	D	1	B;B	0.33171	0.4;0.278	B;B	0.30855	0.121;0.057	T	0.13335	-1.0513	10	0.26408	T	0.33	.	15.5604	0.76240	0.0:0.1372:0.8628:0.0	rs41279452	1611;1611	Q5THJ4-2;Q5THJ4	.;VP13D_HUMAN	K	1611	ENSP00000348666:E1611K;ENSP00000350854:E1611K	ENSP00000348666:E1611K	E	+	1	0	VPS13D	12265577	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.743000	0.55104	2.756000	0.94617	0.561000	0.74099	GAA	G|0.993;A|0.007	0.007	strong		0.458	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
MARC2	54996	hgsc.bcm.edu	37	1	220928376	220928376	+	Silent	SNP	T	T	C	rs371348	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:220928376T>C	ENST00000366913.3	+	2	558	c.360T>C	c.(358-360)aaT>aaC	p.N120N	MARC2_ENST00000359316.2_Silent_p.N120N	NM_017898.3	NP_060368.2	Q969Z3	MARC2_HUMAN	mitochondrial amidoxime reducing component 2	120					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										TTTATGAGAATAACTGCCTGA	0.517													C|||	308	0.0615016	0.1339	0.0072	5008	,	,		19391	0.0625		0.0099	False		,,,				2504	0.0542				p.N120N		Atlas-SNP	.											.	.	.	.	0			c.T360C						PASS	.	C		502,3904	780.1+/-414.4	31,440,1732	165.0	156.0	159.0		360	-2.7	0.0	1	dbSNP_80	159	51,8549	817.1+/-406.9	0,51,4249	no	coding-synonymous	MOSC2	NM_017898.3		31,491,5981	CC,CT,TT		0.593,11.3936,4.2519		120/336	220928376	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	54996	exon2			TGAGAATAACTGC		CCDS1525.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000117791	ENSG00000117791			26064	protein-coding gene	gene with protein product		614127	"""MOCO sulphurase C-terminal domain containing 2"""	MOSC2		11886751	Standard	NM_017898		Approved	FLJ20605	uc001hmq.3	Q969Z3	OTTHUMG00000037354	ENST00000366913.3:c.360T>C	1.37:g.220928376T>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	132	62	0.469697	NM_017898	B2D0R5|D3DTB3|Q0JSK7|Q5VT67|Q5VXC7|Q7L317|Q9H066|Q9NWU0	Silent	SNP	ENST00000366913.3	37	CCDS1525.1																																																																																			T|0.947;C|0.053	0.053	strong		0.517	MARC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090911.1	NM_017898	
BANK1	55024	hgsc.bcm.edu	37	4	102839287	102839287	+	Missense_Mutation	SNP	G	G	A	rs3733197	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:102839287G>A	ENST00000322953.4	+	7	1421	c.1147G>A	c.(1147-1149)Gca>Aca	p.A383T	BANK1_ENST00000428908.1_Missense_Mutation_p.A250T|BANK1_ENST00000504592.1_Missense_Mutation_p.A368T|BANK1_ENST00000444316.2_Missense_Mutation_p.A353T|BANK1_ENST00000508653.1_Missense_Mutation_p.A250T	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	383			A -> T (influences susceptibility to SLE; dbSNP:rs3733197). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18204447}.		B cell activation (GO:0042113)					NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|liver(2)|lung(16)|ovary(2)|skin(2)|urinary_tract(1)	44		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)		TTCAGACCCCGCACATATTGC	0.363													G|||	1136	0.226837	0.1498	0.219	5008	,	,		15219	0.254		0.3489	False		,,,				2504	0.183				p.A383T		Atlas-SNP	.											.	BANK1	95	.	0			c.G1147A	GRCh37	CM080096	BANK1	M	rs3733197	PASS	.	G	THR/ALA,THR/ALA,THR/ALA	812,3592	310.0+/-291.3	85,642,1475	63.0	66.0	65.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1057,748,1147	1.9	0.1	4	dbSNP_107	65	3053,5547	465.6+/-366.6	542,1969,1789	yes	missense,missense,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	58,58,58	627,2611,3264	AA,AG,GG		35.5,18.4378,29.7216	benign,benign,benign	353/756,250/653,383/786	102839287	3865,9139	2202	4300	6502	SO:0001583	missense	55024	exon7			GACCCCGCACATA	AB063170	CCDS34038.1, CCDS47115.1, CCDS47116.1	4q23	2013-01-11						"""Ankyrin repeat domain containing"""	18233	protein-coding gene	gene with protein product		610292				11782428, 21208380, 21480188	Standard	NM_017935		Approved	BANK, FLJ20706	uc003hvy.4	Q8NDB2		ENST00000322953.4:c.1147G>A	4.37:g.102839287G>A	ENSP00000320509:p.Ala383Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	547	0.25045787545787546	70	0.14227642276422764	83	0.2292817679558011	125	0.21853146853146854	269	0.3548812664907652	G	4.252	0.045840	0.08196	0.184378	0.355	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	4.55	1.85	0.25348	Ankyrin repeat-containing domain (1);	0.537909	0.15287	N	0.270369	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	D;D;D	0.76494	0.999;0.983;0.983	P;P;P	0.59357	0.856;0.608;0.608	T	0.29671	-1.0004	9	0.08381	T	0.77	.	4.0106	0.09621	0.2958:0.1862:0.518:0.0	rs3733197;rs52823400;rs3733197	250;383;368	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	T	368;383;250;250;353	ENSP00000421443:A368T;ENSP00000320509:A383T;ENSP00000412748:A250T;ENSP00000422314:A250T;ENSP00000388817:A353T	ENSP00000320509:A383T	A	+	1	0	BANK1	103058310	0.059000	0.20769	0.056000	0.19401	0.127000	0.20565	0.723000	0.25939	0.163000	0.19507	-0.126000	0.14955	GCA	G|0.725;A|0.275	0.275	strong		0.363	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
ZFP36L2	678	hgsc.bcm.edu	37	2	43452618	43452618	+	Missense_Mutation	SNP	C	C	T	rs11675632	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:43452618C>T	ENST00000282388.3	-	2	618	c.325G>A	c.(325-327)Ggc>Agc	p.G109S	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	109	Poly-Gly.				cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				AGGGCTGTGCCGCCGCCCCCC	0.687													C|||	354	0.0706869	0.0552	0.036	5008	,	,		12872	0.003		0.0676	False		,,,				2504	0.1892				p.G109S		Atlas-SNP	.											.	ZFP36L2	56	.	0			c.G325A						PASS	.	C	SER/GLY	213,4173		3,207,1983	18.0	23.0	21.0		325	3.2	1.0	2	dbSNP_120	21	596,8002		22,552,3725	yes	missense	ZFP36L2	NM_006887.4	56	25,759,5708	TT,TC,CC		6.9318,4.8564,6.2307	benign	109/495	43452618	809,12175	2193	4299	6492	SO:0001583	missense	678	exon2			CTGTGCCGCCGCC	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"""RING-type (C3HC4) zinc fingers"""	1108	protein-coding gene	gene with protein product		612053	"""zinc finger protein 36, C3H type-like 1"", ""zinc finger protein 36, C3H type-like 2"""	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.325G>A	2.37:g.43452618C>T	ENSP00000282388:p.Gly109Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	26	13	0.5	NM_006887	Q53TB4|Q9BSJ3	Missense_Mutation	SNP	ENST00000282388.3	37	CCDS1811.1	100	0.045787545787545784	33	0.06707317073170732	14	0.03867403314917127	3	0.005244755244755245	50	0.06596306068601583	C	20.5	4.009224	0.75046	0.048564	0.069318	ENSG00000152518	ENST00000282388	T	0.45668	0.89	5.04	3.24	0.37175	Tis11B-like protein, N-terminal (1);	0.000000	0.43579	D	0.000544	T	0.01558	0.0050	N	0.20530	0.585	0.80722	D	1	B	0.20671	0.047	B	0.15484	0.013	T	0.04930	-1.0917	10	0.09843	T	0.71	-15.7329	6.861	0.24067	0.0:0.715:0.0:0.2849	rs11675632	109	P47974	TISD_HUMAN	S	109	ENSP00000282388:G109S	ENSP00000282388:G109S	G	-	1	0	ZFP36L2	43306122	0.000000	0.05858	1.000000	0.80357	0.989000	0.77384	-0.959000	0.03853	0.527000	0.28560	0.561000	0.74099	GGC	C|0.947;T|0.053	0.053	strong		0.687	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887	
LTBP2	4053	hgsc.bcm.edu	37	14	75052587	75052587	+	Missense_Mutation	SNP	G	G	A	rs149952751	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:75052587G>A	ENST00000261978.4	-	3	1186	c.800C>T	c.(799-801)tCg>tTg	p.S267L	LTBP2_ENST00000556690.1_Missense_Mutation_p.S267L|LTBP2_ENST00000557425.1_Intron	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	267					protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.S267L(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		TGCGGGCGGCGACTGTGGTGC	0.662													G|||	2	0.000399361	0.0	0.0014	5008	,	,		14970	0.0		0.001	False		,,,				2504	0.0				p.S267L		Atlas-SNP	.											LTBP2,NS,carcinoma,0,1	LTBP2	158	1	1	Substitution - Missense(1)	lung(1)	c.C800T						PASS	.	G	LEU/SER	3,4403	6.2+/-15.9	0,3,2200	45.0	56.0	52.0		800	0.2	0.1	14	dbSNP_134	52	13,8587	10.5+/-38.8	0,13,4287	yes	missense	LTBP2	NM_000428.2	145	0,16,6487	AA,AG,GG		0.1512,0.0681,0.123	benign	267/1822	75052587	16,12990	2203	4300	6503	SO:0001583	missense	4053	exon3			GGCGGCGACTGTG		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.800C>T	14.37:g.75052587G>A	ENSP00000261978:p.Ser267Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	37	CCDS9831.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	2.461	-0.324095	0.05350	6.81E-4	0.001512	ENSG00000119681	ENST00000261978;ENST00000556690	T;T	0.78481	-1.17;-1.18	0.158	0.158	0.14942	.	2.239770	0.02540	N	0.094513	T	0.50051	0.1593	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44742	-0.9308	9	0.25751	T	0.34	.	.	.	.	.	267	Q14767	LTBP2_HUMAN	L	267	ENSP00000261978:S267L;ENSP00000451477:S267L	ENSP00000261978:S267L	S	-	2	0	LTBP2	74122340	0.521000	0.26258	0.145000	0.22337	0.048000	0.14542	0.251000	0.18257	0.202000	0.20498	0.205000	0.17691	TCG	G|0.998;A|0.002	0.002	strong		0.662	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	
GRM6	2916	hgsc.bcm.edu	37	5	178415937	178415937	+	Splice_Site	SNP	A	A	G	rs2067011	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178415937A>G	ENST00000517717.1	-	7	1391	c.1353T>C	c.(1351-1353)aaT>aaC	p.N451N	GRM6_ENST00000231188.5_Splice_Site_p.N451N|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	451					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)		CCCACTCACCATTGAAGCGGA	0.637													A|||	2539	0.506989	0.388	0.5317	5008	,	,		13198	0.5913		0.5547	False		,,,				2504	0.5143				p.N451N		Atlas-SNP	.											.	GRM6	149	.	0			c.T1353C						PASS	.	A		1806,2600	523.5+/-371.1	382,1042,779	38.0	37.0	38.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1353	-4.4	1.0	5	dbSNP_96	38	4625,3975	592.2+/-392.9	1195,2235,870	yes	coding-synonymous-near-splice	GRM6	NM_000843.3		1577,3277,1649	GG,GA,AA		46.2209,40.9896,49.4464		451/878	178415937	6431,6575	2203	4300	6503	SO:0001630	splice_region_variant	2916	exon6			CTCACCATTGAAG	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.1354+1T>C	5.37:g.178415937A>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1	1153	0.5279304029304029	219	0.4451219512195122	180	0.4972375690607735	336	0.5874125874125874	418	0.5514511873350924	A	11.88	1.769401	0.31320	0.409896	0.537791	ENSG00000113262	ENST00000319065	.	.	.	5.29	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46020	-0.9221	4	0.87932	D	0	.	15.2442	0.73493	0.2527:0.0:0.7473:0.0	rs2067011;rs17839799;rs52803732;rs61390692;rs2067011	.	.	.	R	491	.	ENSP00000325675:W491R	W	-	1	0	GRM6	178348543	0.002000	0.14202	0.973000	0.42090	0.937000	0.57800	-1.561000	0.02158	-0.676000	0.05238	0.459000	0.35465	TGG	A|0.500;G|0.500	0.500	strong		0.637	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		Silent
ELTD1	64123	hgsc.bcm.edu	37	1	79411968	79411968	+	Missense_Mutation	SNP	C	C	A	rs41313381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:79411968C>A	ENST00000370742.3	-	3	379	c.316G>T	c.(316-318)Gtc>Ttc	p.V106F		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	106	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		CCTATACAGACGGTTCCATCA	0.363													C|||	51	0.0101837	0.0008	0.0101	5008	,	,		16659	0.001		0.0278	False		,,,				2504	0.0143				p.V106F		Atlas-SNP	.											.	ELTD1	143	.	0			c.G316T						PASS	.	C	PHE/VAL	19,3713		0,19,1847	92.0	87.0	88.0		316	-6.5	0.3	1	dbSNP_127	88	227,7987		2,223,3882	yes	missense	ELTD1	NM_022159.3	50	2,242,5729	AA,AC,CC		2.7636,0.5091,2.0593	benign	106/691	79411968	246,11700	1866	4107	5973	SO:0001583	missense	64123	exon3			TACAGACGGTTCC	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.316G>T	1.37:g.79411968C>A	ENSP00000359778:p.Val106Phe	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	26	0.011904761904761904	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	3.579	-0.085996	0.07097	0.005091	0.027636	ENSG00000162618	ENST00000370742	T	0.37058	1.22	5.03	-6.52	0.01872	EGF-like calcium-binding (1);	1.218660	0.05368	N	0.534935	T	0.02455	0.0075	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23797	-1.0178	9	.	.	.	.	1.7478	0.02966	0.4211:0.2728:0.0918:0.2144	rs41313381	106	Q9HBW9	ELTD1_HUMAN	F	106	ENSP00000359778:V106F	.	V	-	1	0	ELTD1	79184556	0.002000	0.14202	0.277000	0.24703	0.877000	0.50540	0.026000	0.13599	-1.673000	0.01462	-2.143000	0.00337	GTC	C|0.981;A|0.019	0.019	strong		0.363	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
ANKK1	255239	hgsc.bcm.edu	37	11	113270828	113270828	+	Missense_Mutation	SNP	G	G	A	rs1800497	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:113270828G>A	ENST00000303941.3	+	8	2231	c.2137G>A	c.(2137-2139)Gag>Aag	p.E713K		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	713			E -> K (in dbSNP:rs1800497). {ECO:0000269|PubMed:14741327, ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		AGTGCTGGTCGAGGCAGGCGC	0.637													A|||	1631	0.325679	0.385	0.3112	5008	,	,		20348	0.4058		0.1879	False		,,,				2504	0.3149				p.E713K		Atlas-SNP	.											.	ANKK1	83	.	0			c.G2137A	GRCh37	CM041241	ANKK1	M	rs1800497	PASS	.	A	LYS/GLU	1351,2783		230,891,946	21.0	26.0	24.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2137	2.0	0.1	11	dbSNP_89	24	1598,6796		160,1278,2759	yes	missense	ANKK1	NM_178510.1	56	390,2169,3705	AA,AG,GG		19.0374,32.6802,23.5393	benign	713/766	113270828	2949,9579	2067	4197	6264	SO:0001583	missense	255239	exon8			CTGGTCGAGGCAG	AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.2137G>A	11.37:g.113270828G>A	ENSP00000306678:p.Glu713Lys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	144	119	0.826389	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	647	0.29624542124542125	188	0.3821138211382114	100	0.27624309392265195	222	0.3881118881118881	137	0.18073878627968337	A	0.006	-2.089378	0.00367	0.326802	0.190374	ENSG00000170209	ENST00000303941	T	0.65732	-0.17	4.42	1.98	0.26296	Ankyrin repeat-containing domain (3);	0.914415	0.09102	N	0.848445	T	0.00012	0.0000	N	0.17800	0.525	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33137	-0.9880	9	0.05833	T	0.94	-2.6564	1.1851	0.01854	0.5313:0.1533:0.1676:0.1478	rs1800497;rs4134623;rs4245144;rs59538675;rs1800497	713	Q8NFD2	ANKK1_HUMAN	K	713	ENSP00000306678:E713K	ENSP00000306678:E713K	E	+	1	0	ANKK1	112776038	0.001000	0.12720	0.054000	0.19295	0.051000	0.14879	0.411000	0.21115	-0.053000	0.13289	-0.439000	0.05793	GAG	G|0.703;A|0.297	0.297	strong		0.637	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
ZNF774	342132	hgsc.bcm.edu	37	15	90903311	90903311	+	Missense_Mutation	SNP	A	A	G	rs2589957|rs386786344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:90903311A>G	ENST00000354377.3	+	4	434	c.248A>G	c.(247-249)aAt>aGt	p.N83S	ZNF774_ENST00000558115.1_3'UTR|ZNF774_ENST00000379090.5_Intron	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	83			N -> S (in dbSNP:rs2589957). {ECO:0000269|PubMed:15489334}.		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)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			AATCAGGACAATTCTGAAACA	0.393													G|||	3443	0.6875	0.8177	0.6873	5008	,	,		21296	0.8393		0.4513	False		,,,				2504	0.5982				p.N83S		Atlas-SNP	.											.	ZNF774	35	.	0			c.A248G						PASS	.	G	SER/ASN	3280,1118	400.6+/-331.6	1203,874,122	70.0	70.0	70.0		248	1.7	0.5	15	dbSNP_100	70	4079,4517	593.2+/-393.1	961,2157,1180	yes	missense	ZNF774	NM_001004309.2	46	2164,3031,1302	GG,GA,AA		47.4523,25.4206,43.3662	benign	83/484	90903311	7359,5635	2199	4298	6497	SO:0001583	missense	342132	exon4			AGGACAATTCTGA	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"""Zinc fingers, C2H2-type"""	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.248A>G	15.37:g.90903311A>G	ENSP00000346348:p.Asn83Ser	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_001004309	A8K020	Missense_Mutation	SNP	ENST00000354377.3	37	CCDS32330.1	1456	0.6666666666666666	394	0.8008130081300813	224	0.6187845303867403	490	0.8566433566433567	348	0.45910290237467016	G	3.219	-0.159861	0.06502	0.745794	0.474523	ENSG00000196391	ENST00000354377	T	0.25749	1.78	5.22	1.71	0.24356	.	0.708846	0.11560	N	0.551823	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.19516	-1.0303	9	0.12430	T	0.62	.	1.5984	0.02669	0.1391:0.1581:0.1464:0.5564	rs2589957;rs17175377;rs52799004;rs61016263;rs2589957	83	Q6NX45	ZN774_HUMAN	S	83	ENSP00000346348:N83S	ENSP00000346348:N83S	N	+	2	0	ZNF774	88704315	0.001000	0.12720	0.495000	0.27527	0.676000	0.39594	0.019000	0.13444	0.024000	0.15214	-2.026000	0.00426	AAT	A|0.386;G|0.614	0.614	strong		0.393	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309	
TTN	7273	hgsc.bcm.edu	37	2	179430997	179430997	+	Missense_Mutation	SNP	G	G	A	rs3731746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179430997G>A	ENST00000591111.1	-	276	75163	c.74939C>T	c.(74938-74940)aCg>aTg	p.T24980M	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T26621M|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T17748M|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T17681M|TTN_ENST00000460472.2_Missense_Mutation_p.T17556M|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T24053M			Q8WZ42	TITIN_HUMAN	titin	24980	Ig-like 123.		T -> M. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GATCTCAGGCGTTGGACGACC	0.418													G|||	1714	0.342252	0.3442	0.2061	5008	,	,		22404	0.629		0.171	False		,,,				2504	0.317				p.T26621M		Atlas-SNP	.											.	TTN	18412	.	0			c.C79862T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	1257,2583		208,841,871	161.0	155.0	157.0		52667,72158,53042,53243	5.0	1.0	2	dbSNP_107	157	1385,6915		116,1153,2881	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	81,81,81,81	324,1994,3752	AA,AG,GG		16.6867,32.7344,21.7628	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	17556/26927,24053/33424,17681/27052,17748/27119	179430997	2642,9498	1920	4150	6070	SO:0001583	missense	7273	exon326			TCAGGCGTTGGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.74939C>T	2.37:g.179430997G>A	ENSP00000465570:p.Thr24980Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	130	63	0.484615	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		693	0.3173076923076923	157	0.31910569105691056	68	0.1878453038674033	341	0.5961538461538461	127	0.16754617414248021	G	9.152	1.016420	0.19355	0.327344	0.166867	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68624	-0.34;-0.34;-0.34;-0.34	5.91	5.03	0.67393	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.80183	2.485	0.25672	P	0.9858806	P;P;P;P	0.48694	0.914;0.914;0.914;0.914	P;P;P;P	0.50270	0.636;0.636;0.636;0.636	T	0.50338	-0.8840	8	0.87932	D	0	.	11.7884	0.52055	0.1854:0.0:0.8146:0.0	rs3731746;rs52794037;rs56683294;rs3731746	17556;17681;17748;24980	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	M	24053;17556;17748;17681;17554	ENSP00000343764:T24053M;ENSP00000434586:T17556M;ENSP00000340554:T17748M;ENSP00000352154:T17681M	ENSP00000340554:T17748M	T	-	2	0	TTN	179139243	1.000000	0.71417	0.980000	0.43619	0.991000	0.79684	2.938000	0.48987	1.485000	0.48380	0.555000	0.69702	ACG	T|0.000;G|0.681;N|0.000;A|0.318	0.318	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NALCN	259232	hgsc.bcm.edu	37	13	101736075	101736075	+	Silent	SNP	A	A	G	rs686141	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:101736075A>G	ENST00000251127.6	-	31	3651	c.3570T>C	c.(3568-3570)ctT>ctC	p.L1190L		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1190					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GGCGAGGCGGAAGATGAAGAG	0.473													G|||	3629	0.724641	0.882	0.5418	5008	,	,		16362	0.622		0.7117	False		,,,				2504	0.7607				p.L1190L		Atlas-SNP	.											.	NALCN	431	.	0			c.T3570C						PASS	.	G		3712,694	288.9+/-280.1	1563,586,54	64.0	66.0	65.0		3570	2.5	1.0	13	dbSNP_83	65	6185,2415	400.2+/-346.7	2210,1765,325	no	coding-synonymous	NALCN	NM_052867.2		3773,2351,379	GG,GA,AA		28.0814,15.7512,23.9044		1190/1739	101736075	9897,3109	2203	4300	6503	SO:0001819	synonymous_variant	259232	exon31			AGGCGGAAGATGA	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.3570T>C	13.37:g.101736075A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			A|0.256;G|0.744	0.744	strong		0.473	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610529	32610529	+	Silent	SNP	A	A	G	rs13379	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32610529A>G	ENST00000343139.5	+	4	858	c.756A>G	c.(754-756)caA>caG	p.Q252Q	HLA-DQA1_ENST00000374949.2_Silent_p.Q252Q|HLA-DQA1_ENST00000395363.1_Silent_p.Q252Q	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	251					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CCAGACACCAAGGGCCATTGT	0.542													.|||	104	0.0207668	0.0477	0.0389	5008	,	,		13127	0.001		0.0119	False		,,,				2504	0.001				p.Q252Q		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.A756G						PASS	.	A		138,2880		25,88,1396	128.0	102.0	112.0		756	2.9	0.4	6	dbSNP_52	112	88,5324		21,46,2639	no	coding-synonymous	HLA-DQA1	NM_002122.3		46,134,4035	GG,GA,AA		1.626,4.5726,2.6809		252/256	32610529	226,8204	1509	2706	4215	SO:0001819	synonymous_variant	3117	exon4			ACACCAAGGGCCA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.756A>G	6.37:g.32610529A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	157	64	0.407643	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1																																																																																			A|0.973;G|0.027	0.027	strong		0.542	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
VSIG10L	147645	hgsc.bcm.edu	37	19	51844978	51844978	+	Silent	SNP	G	G	T	rs8105710	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51844978G>T	ENST00000335624.4	-	2	323	c.324C>A	c.(322-324)tcC>tcA	p.S108S	CTD-2616J11.16_ENST00000594311.1_RNA|CTD-2616J11.16_ENST00000601148.1_RNA	NM_001163922.1	NP_001157394.1	Q86VR7	VS10L_HUMAN	V-set and immunoglobulin domain containing 10 like	108	Ser-rich.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)	4						CAGAGAAGGGGGAAACCGGGC	0.507													G|||	3188	0.636581	0.6687	0.5086	5008	,	,		16773	0.619		0.5795	False		,,,				2504	0.7607				p.S108S		Atlas-SNP	.											.	VSIG10L	40	.	0			c.C324A						PASS	.	G		876,508		283,310,99	61.0	63.0	62.0		324	0.7	0.0	19	dbSNP_116	62	1913,1269		576,761,254	no	coding-synonymous	VSIG10L	NM_001163922.1		859,1071,353	TT,TG,GG		39.8806,36.7052,38.9181		108/868	51844978	2789,1777	692	1591	2283	SO:0001819	synonymous_variant	147645	exon2			GAAGGGGGAAACC		CCDS54300.1	19q13.41	2013-01-11				ENSG00000186806		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27111	protein-coding gene	gene with protein product						12477932	Standard	NM_001163922		Approved		uc002pwf.3	Q86VR7		ENST00000335624.4:c.324C>A	19.37:g.51844978G>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	61	34	0.557377	NM_001163922		Silent	SNP	ENST00000335624.4	37	CCDS54300.1																																																																																			G|0.400;T|0.600	0.600	strong		0.507	VSIG10L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464535.1	NM_001163922	
H2BFWT	158983	hgsc.bcm.edu	37	X	103267865	103267865	+	Missense_Mutation	SNP	C	C	T	rs553509	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:103267865C>T	ENST00000217926.5	-	1	394	c.368G>A	c.(367-369)cGc>cAc	p.R123H	H2BFM_ENST00000243297.5_5'Flank	NM_001002916.3	NP_001002916.3	Q7Z2G1	H2BWT_HUMAN	H2B histone family, member W, testis-specific	123			R -> H (in dbSNP:rs553509). {ECO:0000269|PubMed:15475252, ECO:0000269|PubMed:15489334}.			membrane (GO:0016020)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	16						GCGGGCCAGGCGACCAGCCTC	0.647													.|||	2193	0.580927	0.438	0.3098	3775	,	,		13169	0.4603		0.5089	False		,,,				2504	0.4325				p.R123H		Atlas-SNP	.											.	H2BFWT	33	.	0			c.G368A						PASS	.	C	HIS/ARG	2258,1577		574,775,335,283,236	36.0	33.0	34.0		368	-2.7	0.0	X	dbSNP_83	34	4476,2251		1080,1091,1225,257,646	yes	missense	H2BFWT	NM_001002916.3	29	1654,1866,1560,540,882	TT,TC,T,CC,C		33.4622,41.1213,36.2431	benign	123/176	103267865	6734,3828	2203	4299	6502	SO:0001583	missense	158983	exon1			GCCAGGCGACCAG	BC038109	CCDS35362.1	Xq22.2	2011-01-27			ENSG00000123569	ENSG00000123569		"""Histones / Replication-independent"""	27252	protein-coding gene	gene with protein product		300507				12477932	Standard	NM_001002916		Approved		uc004elr.3	Q7Z2G1	OTTHUMG00000022120	ENST00000217926.5:c.368G>A	X.37:g.103267865C>T	ENSP00000354723:p.Arg123His	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	97	93	0.958763	NM_001002916	B1AK72|Q147W3	Missense_Mutation	SNP	ENST00000217926.5	37	CCDS35362.1	968	0.5834840265220012	141	0.375	88	0.32116788321167883	170	0.4146341463414634	271	0.5132575757575758	.	9.810	1.182830	0.21870	0.588787	0.665378	ENSG00000123569	ENST00000217926	T	0.27890	1.64	2.84	-2.67	0.06059	Histone-fold (2);Histone core (1);	1.333640	0.06752	U	0.780175	T	0.00012	0.0000	L	0.43598	1.365	0.80722	P	0.0	B	0.16166	0.016	B	0.17098	0.017	T	0.44143	-0.9347	9	0.62326	D	0.03	.	3.36	0.07182	0.3156:0.366:0.0:0.3184	rs553509;rs17340491;rs58833763	123	Q7Z2G1	H2BWT_HUMAN	H	123	ENSP00000354723:R123H	ENSP00000354723:R123H	R	-	2	0	H2BFWT	103154521	0.994000	0.37717	0.000000	0.03702	0.000000	0.00434	0.783000	0.26802	-0.944000	0.03686	-0.849000	0.03036	CGC	C|0.378;0|0.003	.	strong		0.647	H2BFWT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057756.2	NM_001002916	
PTX4	390667	hgsc.bcm.edu	37	16	1537839	1537839	+	Missense_Mutation	SNP	G	G	A	rs2745101	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1537839G>A	ENST00000447419.2	-	2	299	c.274C>T	c.(274-276)Cgg>Tgg	p.R92W	PTX4_ENST00000440447.2_Missense_Mutation_p.R92W|PTX4_ENST00000293922.1_Missense_Mutation_p.R87W			Q96A99	PTX4_HUMAN	pentraxin 4, long	92			R -> W (in dbSNP:rs2745101).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GCCTGTGACCGGTTGACTGCC	0.652													G|||	1333	0.266174	0.1679	0.1945	5008	,	,		16731	0.5079		0.2316	False		,,,				2504	0.2362				p.R87W		Atlas-SNP	.											.	PTX4	46	.	0			c.C259T						PASS	.	G	TRP/ARG	697,3701		57,583,1559	76.0	79.0	78.0		259	-0.6	0.0	16	dbSNP_100	78	2102,6492		238,1626,2433	yes	missense	PTX4	NM_001013658.1	101	295,2209,3992	AA,AG,GG		24.4589,15.8481,21.544	probably-damaging	87/474	1537839	2799,10193	2199	4297	6496	SO:0001583	missense	390667	exon2			GTGACCGGTTGAC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.274C>T	16.37:g.1537839G>A	ENSP00000445277:p.Arg92Trp	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	66	39	0.590909	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		645	0.29532967032967034	74	0.15040650406504066	67	0.1850828729281768	315	0.5506993006993007	189	0.24934036939313983	G	10.43	1.346709	0.24426	0.158481	0.244589	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.05382	3.6;3.45	5.78	-0.593	0.11667	.	2.089320	0.01936	N	0.041576	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.13145	0.007	B	0.08055	0.003	T	0.47497	-0.9113	9	0.72032	D	0.01	.	2.2422	0.04023	0.179:0.1478:0.523:0.1502	rs2745101;rs2745101	87	Q96A99-2	.	W	92;87	ENSP00000445277:R92W;ENSP00000293922:R87W	ENSP00000293922:R87W	R	-	1	2	PTX4	1477840	0.000000	0.05858	0.002000	0.10522	0.000000	0.00434	0.282000	0.18829	-0.015000	0.14150	-0.251000	0.11542	CGG	G|0.753;A|0.247	0.247	strong		0.652	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
PRKG2	5593	hgsc.bcm.edu	37	4	82126121	82126121	+	Silent	SNP	C	C	G	rs17484474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:82126121C>G	ENST00000395578.1	-	2	197	c.81G>C	c.(79-81)cgG>cgC	p.R27R	PRKG2_ENST00000418486.2_Silent_p.R27R|PRKG2_ENST00000264399.1_Silent_p.R27R			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	27					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						TCACCTTGTTCCGCAGAGCAT	0.527													C|||	75	0.014976	0.003	0.0317	5008	,	,		19484	0.0		0.0388	False		,,,				2504	0.0102				p.R27R		Atlas-SNP	.											PRKG2_ENST00000395578,bladder,carcinoma,-2,6	PRKG2	195	6	0			c.G81C						PASS	.	C		39,4367	44.6+/-78.6	0,39,2164	89.0	83.0	85.0		81	4.2	1.0	4	dbSNP_123	85	323,8277	112.7+/-172.9	3,317,3980	no	coding-synonymous	PRKG2	NM_006259.1		3,356,6144	GG,GC,CC		3.7558,0.8852,2.7833		27/763	82126121	362,12644	2203	4300	6503	SO:0001819	synonymous_variant	5593	exon1			CTTGTTCCGCAGA	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.81G>C	4.37:g.82126121C>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	130	70	0.538462	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	37	CCDS3589.1																																																																																			C|0.973;G|0.027	0.027	strong		0.527	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259	
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 GAIIx	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_ENST00000392912.2_Missense_Mutation_p.R880H|HLTF_ENST00000494055.1_Missense_Mutation_p.R880H|HLTF_ENST00000465259.1_Missense_Mutation_p.R879H	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	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	22	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		
TRPA1	8989	hgsc.bcm.edu	37	8	72984041	72984041	+	Missense_Mutation	SNP	C	C	G	rs16937976	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:72984041C>G	ENST00000262209.4	-	2	380	c.173G>C	c.(172-174)aGa>aCa	p.R58T		NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	58			R -> T (in dbSNP:rs16937976). {ECO:0000269|PubMed:10066796}.		calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ATCGTCACATCTTTTTAATTT	0.363													C|||	509	0.101637	0.0847	0.0749	5008	,	,		18505	0.0565		0.173	False		,,,				2504	0.1166				p.R58T		Atlas-SNP	.											TRPA1,right_upper_lobe,carcinoma,+1,2	TRPA1	256	2	0			c.G173C						PASS	.	C	THR/ARG	368,4038	187.4+/-214.1	14,340,1849	143.0	127.0	132.0		173	-4.1	0.0	8	dbSNP_123	132	1443,7157	277.2+/-292.7	119,1205,2976	yes	missense	TRPA1	NM_007332.2	71	133,1545,4825	GG,GC,CC		16.7791,8.3522,13.9243	benign	58/1120	72984041	1811,11195	2203	4300	6503	SO:0001583	missense	8989	exon2			TCACATCTTTTTA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.173G>C	8.37:g.72984041C>G	ENSP00000262209:p.Arg58Thr	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	37	CCDS34908.1	224	0.10256410256410256	26	0.052845528455284556	29	0.08011049723756906	40	0.06993006993006994	129	0.17018469656992086	C	5.574	0.290729	0.10567	0.083522	0.167791	ENSG00000104321	ENST00000262209	T	0.39056	1.1	5.08	-4.1	0.03940	.	1.264600	0.05255	N	0.514708	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.16158	-1.0412	9	0.16896	T	0.51	-0.2071	6.303	0.21123	0.0:0.2639:0.3009:0.4352	rs16937976;rs57019352;rs16937976	58	O75762	TRPA1_HUMAN	T	58	ENSP00000262209:R58T	ENSP00000262209:R58T	R	-	2	0	TRPA1	73146595	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.077000	0.11394	-0.237000	0.09739	-0.251000	0.11542	AGA	C|0.874;G|0.126	0.126	strong		0.363	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
CELF4	56853	hgsc.bcm.edu	37	18	34846518	34846518	+	Silent	SNP	G	G	A	rs145042940	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:34846518G>A	ENST00000591282.1	-	9	1142	c.1143C>T	c.(1141-1143)gcC>gcT	p.A381A	CELF4_ENST00000361795.5_Silent_p.A379A|CELF4_ENST00000420428.2_Silent_p.A381A|CELF4_ENST00000591287.1_Silent_p.A380A|CELF4_ENST00000588597.1_Silent_p.A370A|CELF4_ENST00000603232.1_Silent_p.A380A|CELF4_ENST00000601019.1_Silent_p.A379A|CELF4_ENST00000334919.5_Silent_p.A371A|CELF4_ENST00000412753.1_Silent_p.A380A			Q9BZC1	CELF4_HUMAN	CUGBP, Elav-like family member 4	381					alternative mRNA splicing, via spliceosome (GO:0000380)|embryo development (GO:0009790)|germ cell development (GO:0007281)|mRNA splice site selection (GO:0006376)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of translation (GO:0017148)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	BRE binding (GO:0042835)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	44						GCTGCACTCCGGCGTAGGCCT	0.652													G|||	5	0.000998403	0.0	0.0029	5008	,	,		18360	0.0		0.003	False		,,,				2504	0.0				p.A381A		Atlas-SNP	.											.	CELF4	90	.	0			c.C1143T						PASS	.	G	,,,	2,4400		0,2,2199	62.0	52.0	55.0		1140,1137,1113,1143	-9.3	0.6	18	dbSNP_134	55	34,8560		0,34,4263	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CELF4	NM_001025087.1,NM_001025088.1,NM_001025089.1,NM_020180.3	,,,	0,36,6462	AA,AG,GG		0.3956,0.0454,0.277	,,,	380/486,379/485,371/449,381/487	34846518	36,12960	2201	4297	6498	SO:0001819	synonymous_variant	56853	exon9			CACTCCGGCGTAG	AF248651	CCDS32818.1, CCDS45857.1, CCDS45858.1	18q12	2013-02-12	2010-02-19	2010-02-19				"""RNA binding motif (RRM) containing"""	14015	protein-coding gene	gene with protein product		612679	"""Bruno (Drosophila) -like 4, RNA binding protein"", ""bruno-like 4, RNA binding protein (Drosophila)"""	BRUNOL4		10893231	Standard	NM_020180		Approved		uc002lae.2	Q9BZC1		ENST00000591282.1:c.1143C>T	18.37:g.34846518G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_020180	Q59EN7|Q86XB9|Q8N2M6|Q9BQ96|Q9NR84|Q9NR85	Silent	SNP	ENST00000591282.1	37	CCDS32818.1																																																																																			G|0.999;A|0.001	0.001	strong		0.652	CELF4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440892.1	NM_020180	
TRIM52	84851	hgsc.bcm.edu	37	5	180687212	180687212	+	Silent	SNP	C	C	T	rs918388	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180687212C>T	ENST00000327767.4	-	1	907	c.603G>A	c.(601-603)ctG>ctA	p.L201L	TRIM52_ENST00000514805.1_5'UTR|TRIM52-AS1_ENST00000507434.1_RNA|CTC-338M12.4_ENST00000505151.1_RNA|TRIM52-AS1_ENST00000514146.1_RNA|TRIM52-AS1_ENST00000509252.1_RNA|CTC-338M12.4_ENST00000511331.1_RNA|CTC-338M12.4_ENST00000417281.2_RNA|CTC-338M12.4_ENST00000506340.1_RNA	NM_032765.2	NP_116154.1	Q96A61	TRI52_HUMAN	tripartite motif containing 52	201					positive regulation of NF-kappaB transcription factor activity (GO:0051092)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.0106)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.0588)|all_lung(500;0.149)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.232)		CCATGTTGGCCAGCTGCAAGT	0.562													.|||	988	0.197284	0.3003	0.1859	5008	,	,		20159	0.0665		0.2256	False		,,,				2504	0.1718				p.L201L		Atlas-SNP	.											.	TRIM52	20	.	0			c.G603A						PASS	.	C		1247,3159	428.7+/-342.0	180,887,1136	104.0	98.0	100.0		603	1.6	1.0	5	dbSNP_87	100	1949,6651	344.0+/-325.1	218,1513,2569	no	coding-synonymous	TRIM52	NM_032765.2		398,2400,3705	TT,TC,CC		22.6628,28.3023,24.5733		201/298	180687212	3196,9810	2203	4300	6503	SO:0001819	synonymous_variant	84851	exon1			GTTGGCCAGCTGC		CCDS4467.1	5q35.3	2013-01-09	2011-01-25		ENSG00000183718	ENSG00000183718		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19024	protein-coding gene	gene with protein product			"""tripartite motif-containing 52"""				Standard	NM_032765		Approved	RNF102	uc003mnp.3	Q96A61	OTTHUMG00000130964	ENST00000327767.4:c.603G>A	5.37:g.180687212C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_032765		Silent	SNP	ENST00000327767.4	37	CCDS4467.1																																																																																			C|0.784;T|0.216	0.216	strong		0.562	TRIM52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253572.3	NM_032765	
TSNARE1	203062	hgsc.bcm.edu	37	8	143425720	143425720	+	Missense_Mutation	SNP	T	T	C	rs10100935	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143425720T>C	ENST00000307180.3	-	4	469	c.352A>G	c.(352-354)Act>Gct	p.T118A	TSNARE1_ENST00000524325.1_Missense_Mutation_p.T118A|TSNARE1_ENST00000520166.1_Missense_Mutation_p.T118A|TSNARE1_ENST00000519651.1_Intron	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	118			T -> A (in dbSNP:rs10100935). {ECO:0000269|PubMed:14702039}.		intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					GCCCGGGTAGTGCTGGGCCCC	0.672													C|||	2935	0.586062	0.8608	0.4841	5008	,	,		11765	0.631		0.336	False		,,,				2504	0.498				p.T118A		Atlas-SNP	.											.	TSNARE1	59	.	0			c.A352G						PASS	.	C	ALA/THR	3302,1088		1263,776,156	15.0	18.0	17.0		352	2.2	0.0	8	dbSNP_119	17	2903,5675		516,1871,1902	yes	missense	TSNARE1	NM_145003.3	58	1779,2647,2058	CC,CT,TT		33.8424,24.7836,47.8486	benign	118/514	143425720	6205,6763	2195	4289	6484	SO:0001583	missense	203062	exon4			GGGTAGTGCTGGG			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.352A>G	8.37:g.143425720T>C	ENSP00000303437:p.Thr118Ala	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	1186	0.543040293040293	415	0.8434959349593496	163	0.45027624309392267	362	0.6328671328671329	246	0.3245382585751979	C	0.003	-2.526480	0.00147	0.752164	0.338424	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000520462;ENST00000518720	T;T;T;T;T	0.28895	2.74;2.74;2.74;1.85;1.59	3.54	2.2	0.27929	.	0.222341	0.22278	N	0.062164	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38585	-0.9654	9	0.02654	T	1	-8.4321	5.7206	0.17985	0.0:0.6452:0.0:0.3548	rs10100935;rs59914660;rs10100935	118;118;118	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	A	118;118;118;118;134	ENSP00000428763:T118A;ENSP00000303437:T118A;ENSP00000427770:T118A;ENSP00000429626:T118A;ENSP00000430789:T134A	ENSP00000303437:T118A	T	-	1	0	TSNARE1	143423627	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.656000	0.05342	-0.050000	0.13356	-0.166000	0.13349	ACT	T|0.418;C|0.582	0.582	strong		0.672	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
CDH5	1003	hgsc.bcm.edu	37	16	66420885	66420885	+	Silent	SNP	C	C	T	rs1130844	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:66420885C>T	ENST00000341529.3	+	3	532	c.384C>T	c.(382-384)ggC>ggT	p.G128G	CDH5_ENST00000563425.2_Silent_p.G128G	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	128	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|blood vessel maturation (GO:0001955)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|negative regulation of cell proliferation (GO:0008285)|regulation of establishment of cell polarity (GO:2000114)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(18)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54		Ovarian(137;0.0955)		OV - Ovarian serous cystadenocarcinoma(108;0.107)	Lenalidomide(DB00480)	AGGACACTGGCGAAAACCTGG	0.532													C|||	3116	0.622204	0.5582	0.7017	5008	,	,		22132	0.8175		0.5119	False		,,,				2504	0.5644				p.G128G		Atlas-SNP	.											.	CDH5	111	.	0			c.C384T						PASS	.	C		2481,1923	625.4+/-394.5	689,1103,410	126.0	103.0	111.0		384	-2.0	0.0	16	dbSNP_86	111	4551,4049	595.1+/-393.4	1185,2181,934	no	coding-synonymous	CDH5	NM_001795.3		1874,3284,1344	TT,TC,CC		47.0814,43.6649,45.9243		128/785	66420885	7032,5972	2202	4300	6502	SO:0001819	synonymous_variant	1003	exon3			CACTGGCGAAAAC	X79981	CCDS10804.1	16q22.1	2010-01-26	2008-07-25		ENSG00000179776	ENSG00000179776		"""CD molecules"", ""Cadherins / Major cadherins"""	1764	protein-coding gene	gene with protein product	"""VE-cadherin"""	601120	"""cadherin 5, type 2, VE-cadherin (vascular epithelium)"""			2059658	Standard	NM_001795		Approved	7B4, CD144	uc002eom.4	P33151	OTTHUMG00000137495	ENST00000341529.3:c.384C>T	16.37:g.66420885C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_001795	Q4VAI5|Q4VAI6	Silent	SNP	ENST00000341529.3	37	CCDS10804.1																																																																																			C|0.420;N|0.001	.	strong		0.532	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795	
BEST1	7439	hgsc.bcm.edu	37	11	61730234	61730234	+	Silent	SNP	T	T	C	rs1800009	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:61730234T>C	ENST00000378043.4	+	10	2251	c.1608T>C	c.(1606-1608)acT>acC	p.T536T	FTH1_ENST00000529191.1_Intron|BEST1_ENST00000449131.2_Silent_p.T476T|BEST1_ENST00000301774.9_Silent_p.T164T|FTH1_ENST00000529631.1_Intron|BEST1_ENST00000534553.1_3'UTR|BEST1_ENST00000378042.3_Silent_p.T449T	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	536					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						GGAGGAAAACTGTGGAGTTTA	0.463													C|||	2962	0.591454	0.5348	0.4899	5008	,	,		21553	0.8552		0.3539	False		,,,				2504	0.7127				p.T536T		Atlas-SNP	.											.	BEST1	85	.	0			c.T1608C						PASS	.	C	,	2166,2238	593.3+/-388.0	530,1106,566	109.0	111.0	110.0		1428,1608	-4.6	0.8	11	dbSNP_89	110	3026,5572	663.5+/-402.1	553,1920,1826	no	coding-synonymous,coding-synonymous	BEST1	NM_001139443.1,NM_004183.3	,	1083,3026,2392	CC,CT,TT		35.1942,49.1826,39.9323	,	476/605,536/586	61730234	5192,7810	2202	4299	6501	SO:0001819	synonymous_variant	7439	exon10			GAAAACTGTGGAG	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1608T>C	11.37:g.61730234T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.406;N|0.000	0.406	strong		0.463	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
MUC16	94025	hgsc.bcm.edu	37	19	9084216	9084216	+	Silent	SNP	T	T	C	rs1609459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9084216T>C	ENST00000397910.4	-	1	7802	c.7599A>G	c.(7597-7599)gcA>gcG	p.A2533A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2533	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAATAGTTGATGCTAGAAGTG	0.522													T|||	1134	0.226438	0.27	0.2983	5008	,	,		18135	0.0228		0.3111	False		,,,				2504	0.2393				p.A2533A		Atlas-SNP	.											.	MUC16	4315	.	0			c.A7599G						PASS	.	T		1097,3141		155,787,1177	85.0	87.0	86.0		7599	0.2	0.5	19	dbSNP_88	86	2785,5723		476,1833,1945	yes	coding-synonymous	MUC16	NM_024690.2		631,2620,3122	CC,CT,TT		32.7339,25.8849,30.4566		2533/14508	9084216	3882,8864	2119	4254	6373	SO:0001819	synonymous_variant	94025	exon1			AGTTGATGCTAGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7599A>G	19.37:g.9084216T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.767;C|0.233	0.233	strong		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DEK	7913	hgsc.bcm.edu	37	6	18237661	18237661	+	Silent	SNP	C	C	T	rs1013062	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:18237661C>T	ENST00000397239.3	-	8	1296	c.849G>A	c.(847-849)aaG>aaA	p.K283K	DEK_ENST00000244776.7_Silent_p.K249K	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	283					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			TATCTGCTTTCTTAACATTGG	0.313			T	NUP214	AML								C|||	823	0.164337	0.0295	0.1124	5008	,	,		18170	0.247		0.2087	False		,,,				2504	0.2526				p.K283K		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.G849A						PASS	.	C	,	280,4124	155.9+/-189.0	6,268,1928	218.0	189.0	199.0		747,849	4.0	1.0	6	dbSNP_86	199	1791,6809	322.2+/-315.5	196,1399,2705	no	coding-synonymous,coding-synonymous	DEK	NM_001134709.1,NM_003472.3	,	202,1667,4633	TT,TC,CC		20.8256,6.3579,15.9259	,	249/342,283/376	18237661	2071,10933	2202	4300	6502	SO:0001819	synonymous_variant	7913	exon8			TGCTTTCTTAACA	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.849G>A	6.37:g.18237661C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	204	48	0.235294	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																			C|0.837;T|0.163	0.163	strong		0.313	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
SPATA21	374955	hgsc.bcm.edu	37	1	16736132	16736132	+	Missense_Mutation	SNP	T	T	C	rs4661746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:16736132T>C	ENST00000335496.1	-	6	1033	c.551A>G	c.(550-552)cAg>cGg	p.Q184R	SPATA21_ENST00000540400.1_Missense_Mutation_p.Q161R|SPATA21_ENST00000466212.1_5'UTR	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	184			Q -> R (in dbSNP:rs4661746).				calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		CTCGCTGCTCTGGTGCAAGAG	0.682													t|||	765	0.152756	0.0159	0.1686	5008	,	,		14091	0.1726		0.3161	False		,,,				2504	0.138				p.Q184R		Atlas-SNP	.											.	SPATA21	47	.	0			c.A551G						PASS	.		ARG/GLN	282,4124	149.2+/-183.4	9,264,1930	27.0	27.0	27.0		551	-1.8	0.0	1	dbSNP_111	27	2822,5778	425.0+/-354.8	512,1798,1990	yes	missense	SPATA21	NM_198546.1	43	521,2062,3920	CC,CT,TT		32.814,6.4004,23.8659	benign	184/470	16736132	3104,9902	2203	4300	6503	SO:0001583	missense	374955	exon6			CTGCTCTGGTGCA		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.551A>G	1.37:g.16736132T>C	ENSP00000335612:p.Gln184Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_198546	B9EK40|F5GXP5	Missense_Mutation	SNP	ENST00000335496.1	37	CCDS172.1	436	0.19963369963369965	14	0.028455284552845527	72	0.19889502762430938	115	0.20104895104895104	235	0.3100263852242744	t	8.622	0.891646	0.17613	0.064004	0.32814	ENSG00000187144	ENST00000335496;ENST00000540400	T;T	0.65732	-0.17;-0.15	4.03	-1.76	0.08006	.	1.538070	0.03919	N	0.283261	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.26195	0.144;0.037	B;B	0.18871	0.023;0.01	T	0.15321	-1.0441	9	0.38643	T	0.18	0.1062	2.3344	0.04243	0.3824:0.2539:0.0:0.3636	rs4661746;rs17453182;rs52812478;rs58066662;rs4661746	161;184	F5GXP5;Q7Z572	.;SPT21_HUMAN	R	184;161	ENSP00000335612:Q184R;ENSP00000440046:Q161R	ENSP00000335612:Q184R	Q	-	2	0	SPATA21	16608719	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-0.374000	0.07484	-0.066000	0.12998	0.358000	0.22013	CAG	T|0.794;C|0.206	0.206	strong		0.682	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33893987	33893987	+	Missense_Mutation	SNP	A	A	G	rs9813017	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:33893987A>G	ENST00000307296.3	+	13	2026	c.1649A>G	c.(1648-1650)aAt>aGt	p.N550S	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.N555S			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	550	Interaction with EIAV p9.|Self-association.		N -> S (in dbSNP:rs9813017). {ECO:0000269|PubMed:10718198, ECO:0000269|PubMed:11683497}.		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						TAGGTTGTAAATGTCTTAAAA	0.313													A|||	413	0.0824681	0.1362	0.0922	5008	,	,		13897	0.0218		0.0994	False		,,,				2504	0.0481				p.N555S		Atlas-SNP	.											.	PDCD6IP	62	.	0			c.A1664G						PASS	.	A	SER/ASN,SER/ASN	610,3788		41,528,1630	30.0	31.0	31.0		1664,1649	4.2	1.0	3	dbSNP_119	31	955,7641		56,843,3399	no	missense,missense	PDCD6IP	NM_001162429.1,NM_013374.4	46,46	97,1371,5029	GG,GA,AA		11.1098,13.8699,12.044	benign,benign	555/874,550/869	33893987	1565,11429	2199	4298	6497	SO:0001583	missense	10015	exon13			TTGTAAATGTCTT	BC020066	CCDS2660.1, CCDS54561.1	3p22.3	2012-08-30	2001-11-29		ENSG00000170248	ENSG00000170248			8766	protein-coding gene	gene with protein product	"""ALG-2 interacting protein X"""	608074	"""programmed cell death 6-interacting protein"""			9880530	Standard	NM_001162429		Approved	Alix, AIP1, Hp95	uc003cfy.4	Q8WUM4	OTTHUMG00000130751	ENST00000307296.3:c.1649A>G	3.37:g.33893987A>G	ENSP00000307387:p.Asn550Ser	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	156	61	0.391026	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	170	0.07783882783882784	66	0.13414634146341464	34	0.09392265193370165	8	0.013986013986013986	62	0.08179419525065963	A	6.915	0.538385	0.13250	0.138699	0.111098	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.27256	1.68;1.68	5.33	4.17	0.49024	.	0.191499	0.56097	N	0.000039	T	0.00109	0.0003	L	0.28274	0.84	0.23361	P	0.99783538	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.0;0.002;0.002	T	0.22941	-1.0202	9	0.07644	T	0.81	-8.7419	8.1568	0.31173	0.8446:0.0:0.1554:0.0	rs9813017;rs52832450;rs9813017	331;555;550	B7Z5C1;E9PFU1;Q8WUM4	.;.;PDC6I_HUMAN	S	550;555	ENSP00000307387:N550S;ENSP00000411825:N555S	ENSP00000307387:N550S	N	+	2	0	PDCD6IP	33868991	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.475000	0.45162	0.858000	0.35431	0.383000	0.25322	AAT	A|0.901;G|0.099	0.099	strong		0.313	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
CCDC86	79080	hgsc.bcm.edu	37	11	60610065	60610065	+	Silent	SNP	G	G	A	rs141728952|rs2074420	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:60610065G>A	ENST00000227520.5	+	1	522	c.468G>A	c.(466-468)ccG>ccA	p.P156P	RP11-804A23.4_ENST00000538705.1_RNA|RP11-804A23.2_ENST00000539897.1_RNA	NM_024098.3	NP_077003.1	Q9H6F5	CCD86_HUMAN	coiled-coil domain containing 86	156	Pro-rich.				viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|liver(2)|lung(2)|urinary_tract(3)	10						AGCTACCGCCGGTCCCAGGAT	0.662													G|||	1707	0.340855	0.1664	0.2752	5008	,	,		14318	0.6806		0.1899	False		,,,				2504	0.4284				p.P156P		Atlas-SNP	.											CCDC86,NS,carcinoma,0,1	CCDC86	24	1	0			c.G468A						scavenged	.						25.0	31.0	29.0					11																	60610065		2196	4289	6485	SO:0001819	synonymous_variant	79080	exon1			ACCGCCGGTCCCA	AK025974	CCDS7993.1	11q12.2	2006-03-16			ENSG00000110104	ENSG00000110104			28359	protein-coding gene	gene with protein product		611293					Standard	NM_024098		Approved	MGC2574	uc001nqa.2	Q9H6F5	OTTHUMG00000167706	ENST00000227520.5:c.468G>A	11.37:g.60610065G>A		Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_024098	B4DY99	Silent	SNP	ENST00000227520.5	37	CCDS7993.1																																																																																			G|0.725;A|0.275	0.275	strong		0.662	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098	
VPS13C	54832	hgsc.bcm.edu	37	15	62165577	62165577	+	Silent	SNP	G	G	A	rs17303894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62165577G>A	ENST00000261517.5	-	78	10519	c.10446C>T	c.(10444-10446)acC>acT	p.T3482T	VPS13C_ENST00000558919.1_5'Flank|VPS13C_ENST00000395896.4_Silent_p.T3482T|VPS13C_ENST00000395898.3_Silent_p.T3439T|VPS13C_ENST00000249837.3_Silent_p.T3439T	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)									p.T3482T(1)		NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						CAACAGAACCGGTGATTCGAG	0.408													A|||	292	0.0583067	0.062	0.0403	5008	,	,		17066	0.0397		0.0746	False		,,,				2504	0.0685				p.T3482T		Atlas-SNP	.											VPS13C,NS,carcinoma,0,1	VPS13C	506	1	1	Substitution - coding silent(1)	stomach(1)	c.C10446T						PASS	.	A	,,,	303,4103	798.9+/-415.5	10,283,1910	173.0	169.0	170.0		10446,10317,10317,10446	-11.8	0.5	15	dbSNP_123	170	684,7916	788.1+/-407.6	32,620,3648	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	,,,	42,903,5558	AA,AG,GG		7.9535,6.877,7.5888	,,,	3482/3629,3439/3711,3439/3586,3482/3754	62165577	987,12019	2203	4300	6503	SO:0001819	synonymous_variant	54832	exon78			AGAACCGGTGATT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.10446C>T	15.37:g.62165577G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	165	59	0.357576	NM_020821		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																			G|0.932;A|0.068	0.068	strong		0.408	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
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 GAIIx	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_ENST00000380567.1_Silent_p.D849D|OFD1_ENST00000490265.1_3'UTR|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		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	211	48	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	
TMEM2	23670	hgsc.bcm.edu	37	9	74345158	74345158	+	Silent	SNP	G	G	A	rs25694	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:74345158G>A	ENST00000377044.4	-	9	2324	c.1785C>T	c.(1783-1785)acC>acT	p.T595T	TMEM2_ENST00000377066.5_Silent_p.T532T	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	595					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		CAAACCCAATGGTGTCTTTTA	0.383													G|||	407	0.08127	0.0393	0.0476	5008	,	,		18302	0.0198		0.0815	False		,,,				2504	0.2249				p.T595T		Atlas-SNP	.											.	TMEM2	112	.	0			c.C1785T						PASS	.	G	,	174,4232	113.8+/-151.8	6,162,2035	74.0	71.0	72.0		1596,1785	2.3	1.0	9	dbSNP_72	72	717,7883	175.0+/-225.2	30,657,3613	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	36,819,5648	AA,AG,GG		8.3372,3.9492,6.8507	,	532/1321,595/1384	74345158	891,12115	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon9			CCCAATGGTGTCT		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1785C>T	9.37:g.74345158G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			G|0.935;A|0.065	0.065	strong		0.383	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209609	84209609	+	Missense_Mutation	SNP	C	C	T	rs34777958	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84209609C>T	ENST00000378553.5	+	11	1893	c.1769C>T	c.(1768-1770)aCg>aTg	p.T590M	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	590					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						CTGGACTACACGTCACTCCCT	0.473											OREG0023983	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	40	0.00798722	0.0008	0.0216	5008	,	,		19436	0.0		0.0239	False		,,,				2504	0.0				p.T590M		Atlas-SNP	.											DNAAF1,NS,carcinoma,-1,1	DNAAF1	81	1	0			c.C1769T						PASS	.	C	MET/THR	12,4388	19.1+/-41.9	0,12,2188	95.0	85.0	88.0		1769	-1.8	0.0	16	dbSNP_126	88	138,8462	68.7+/-131.2	2,134,4164	yes	missense	DNAAF1	NM_178452.4	81	2,146,6352	TT,TC,CC		1.6047,0.2727,1.1538	possibly-damaging	590/726	84209609	150,12850	2200	4300	6500	SO:0001583	missense	123872	exon11			ACTACACGTCACT	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1769C>T	16.37:g.84209609C>T	ENSP00000367815:p.Thr590Met	Somatic	95	0	0	1227	WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	21	0.009615384615384616	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	11	0.014511873350923483	C	11.12	1.546089	0.27652	0.002727	0.016047	ENSG00000154099	ENST00000378553	T	0.27557	1.66	4.35	-1.82	0.07857	.	1.214380	0.05915	N	0.632346	T	0.12135	0.0295	L	0.46157	1.445	0.09310	N	0.999999	B;B	0.32893	0.389;0.109	B;B	0.21546	0.035;0.023	T	0.19386	-1.0307	10	0.48119	T	0.1	-1.788	8.1146	0.30935	0.0:0.3621:0.0:0.6379	rs34777958	354;590	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	M	590	ENSP00000367815:T590M	ENSP00000367815:T590M	T	+	2	0	DNAAF1	82767110	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.099000	0.03343	-0.425000	0.07371	-0.965000	0.02619	ACG	C|0.988;T|0.012	0.012	strong		0.473	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
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 GAIIx	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_ENST00000475231.1_Missense_Mutation_p.H3485D|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	86	21	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 GAIIx	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		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	241	118	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	
IKZF1	10320	hgsc.bcm.edu	37	7	50467767	50467767	+	Silent	SNP	C	C	A	rs61731355	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:50467767C>A	ENST00000331340.3	+	8	1157	c.1002C>A	c.(1000-1002)ccC>ccA	p.P334P	IKZF1_ENST00000343574.5_Silent_p.P247P|IKZF1_ENST00000346667.4_Silent_p.P104P|IKZF1_ENST00000439701.1_Silent_p.P292P|IKZF1_ENST00000359197.5_Silent_p.P292P|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000438033.1_Silent_p.P247P|IKZF1_ENST00000349824.4_Silent_p.P191P|IKZF1_ENST00000357364.4_Silent_p.P247P	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	334					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				TGCAGACGCCCCCGGGCGGTT	0.657			"""D,T"""	BCL6	"""ALL, DLBCL"""								C|||	746	0.148962	0.0908	0.196	5008	,	,		14198	0.0546		0.2296	False		,,,				2504	0.2086				p.P334P		Atlas-SNP	.		"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	IKZF1_ENST00000331340,NS,carcinoma,0,1	IKZF1	613	1	28	Unknown(28)	haematopoietic_and_lymphoid_tissue(28)	c.C1002A						PASS	.	C	,,,,,,,,,,,,	401,3625		19,363,1631	13.0	16.0	15.0		716,581,551,581,455,425,413,155,424,394,292,262,842	-2.3	0.6	7	dbSNP_129	15	1538,6786		155,1228,2779	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IKZF1	NM_001220765.1,NM_001220766.1,NM_001220767.1,NM_001220768.1,NM_001220769.1,NM_001220770.1,NM_001220771.1,NM_001220772.1,NM_001220773.1,NM_001220774.1,NM_001220775.1,NM_001220776.1,NM_006060.4	,,,,,,,,,,,,	174,1591,4410	AA,AC,CC		18.4767,9.9603,15.7004	,,,,,,,,,,,,	292/478,247/433,237/423,247/433,205/391,195/381,191/377,64/250,151/337,141/327,109/295,99/285,334/520	50467767	1939,10411	2013	4162	6175	SO:0001819	synonymous_variant	10320	exon8			GACGCCCCCGGGC	U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.1002C>A	7.37:g.50467767C>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	23	17	0.73913	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	37																																																																																				C|0.852;A|0.148	0.148	strong		0.657	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
PLCB3	5331	hgsc.bcm.edu	37	11	64026639	64026639	+	Missense_Mutation	SNP	G	G	A	rs12146487	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64026639G>A	ENST00000540288.1	+	13	1551	c.1448G>A	c.(1447-1449)cGc>cAc	p.R483H	PLCB3_ENST00000325234.5_Missense_Mutation_p.R416H|PLCB3_ENST00000279230.6_Missense_Mutation_p.R483H	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	483			R -> H (in dbSNP:rs12146487).		inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						AGCGCCGGGCGCAAGCGGCCC	0.721													G|||	385	0.076877	0.0272	0.0836	5008	,	,		13593	0.0565		0.1551	False		,,,				2504	0.0798				p.R483H		Atlas-SNP	.											.	PLCB3	103	.	0			c.G1448A						PASS	.	G	HIS/ARG,HIS/ARG	243,4133		10,223,1955	12.0	16.0	15.0		1448,1247	4.6	1.0	11	dbSNP_120	15	1352,7226		108,1136,3045	yes	missense,missense	PLCB3	NM_000932.2,NM_001184883.1	29,29	118,1359,5000	AA,AG,GG		15.7612,5.553,12.3128	possibly-damaging,possibly-damaging	483/1235,416/1168	64026639	1595,11359	2188	4289	6477	SO:0001583	missense	5331	exon13			CCGGGCGCAAGCG	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.1448G>A	11.37:g.64026639G>A	ENSP00000443631:p.Arg483His	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	NM_000932	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	37	CCDS8064.1	209	0.09569597069597069	14	0.028455284552845527	34	0.09392265193370165	41	0.07167832167832168	120	0.158311345646438	G	21.0	4.074922	0.76415	0.05553	0.157612	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.53423	0.62;0.62;0.62	4.61	4.61	0.57282	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	12.047800	0.00802	N	0.001420	T	0.00356	0.0011	L	0.40543	1.245	0.21675	P	0.99959836	D;D	0.58620	0.983;0.971	P;B	0.55713	0.782;0.24	T	0.03840	-1.0999	9	0.42905	T	0.14	.	9.9773	0.41791	0.0962:0.0:0.9038:0.0	rs12146487	416;483	G5E960;Q01970	.;PLCB3_HUMAN	H	483;483;416	ENSP00000279230:R483H;ENSP00000443631:R483H;ENSP00000324660:R416H	ENSP00000279230:R483H	R	+	2	0	PLCB3	63783215	1.000000	0.71417	1.000000	0.80357	0.744000	0.42396	3.459000	0.53021	2.112000	0.64535	0.561000	0.74099	CGC	G|0.903;A|0.097	0.097	strong		0.721	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
SPRR3	6707	hgsc.bcm.edu	37	1	152975941	152975941	+	Missense_Mutation	SNP	C	C	G	rs1055935	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152975941C>G	ENST00000295367.4	+	2	487	c.445C>G	c.(445-447)Cta>Gta	p.L149V	SPRR3_ENST00000542696.1_Missense_Mutation_p.L141V|SPRR3_ENST00000331860.3_Missense_Mutation_p.L149V	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	149	14 X 8 AA approximate tandem repeats.		L -> V (in dbSNP:rs1055935). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20599699, ECO:0000269|Ref.6}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTACACAAAGCTACCAGAGCC	0.522													G|||	2922	0.583466	0.7133	0.4496	5008	,	,		19882	0.6319		0.5328	False		,,,				2504	0.5051				p.L149V		Atlas-SNP	.											.	SPRR3	45	.	0			c.C445G						PASS	.	G	VAL/LEU,VAL/LEU	3017,1389	456.3+/-351.3	1020,977,206	81.0	74.0	76.0		445,445	-0.2	0.0	1	dbSNP_86	76	4681,3919	547.5+/-385.2	1284,2113,903	yes	missense,missense	SPRR3	NM_001097589.1,NM_005416.2	32,32	2304,3090,1109	GG,GC,CC		45.5698,31.5252,40.8119	benign,benign	149/170,149/170	152975941	7698,5308	2203	4300	6503	SO:0001583	missense	6707	exon2			ACAAAGCTACCAG	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.445C>G	1.37:g.152975941C>G	ENSP00000295367:p.Leu149Val	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	152	65	0.427632	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Missense_Mutation	SNP	ENST00000295367.4	37	CCDS1033.1	1315	0.6021062271062271	357	0.725609756097561	176	0.4861878453038674	377	0.6590909090909091	405	0.5343007915567283	G	0.013	-1.623696	0.00820	0.684748	0.544302	ENSG00000163209	ENST00000331860;ENST00000443178;ENST00000295367;ENST00000542696	T;T;T;T	0.07688	3.17;3.17;3.17;3.17	4.27	-0.145	0.13436	.	.	.	.	.	T	0.00608	0.0020	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.001	T	0.46303	-0.9201	8	0.23302	T	0.38	.	1.562	0.02596	0.178:0.1369:0.4058:0.2793	rs1055935;rs17681096;rs1055935	141;149	F5GZ12;Q9UBC9	.;SPRR3_HUMAN	V	149;149;149;141	ENSP00000330391:L149V;ENSP00000402016:L149V;ENSP00000295367:L149V;ENSP00000441477:L141V	ENSP00000295367:L149V	L	+	1	2	SPRR3	151242565	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.505000	0.22642	0.064000	0.16427	-0.990000	0.02549	CTA	C|0.409;G|0.590	0.590	strong		0.522	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
DDX60L	91351	hgsc.bcm.edu	37	4	169362557	169362557	+	Missense_Mutation	SNP	C	C	G	rs13151700	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:169362557C>G	ENST00000511577.1	-	10	1472	c.1225G>C	c.(1225-1227)Gtt>Ctt	p.V409L	DDX60L_ENST00000260184.7_Missense_Mutation_p.V409L|DDX60L_ENST00000505890.1_Missense_Mutation_p.V409L			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	409			V -> L (in dbSNP:rs13151700).				ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		GACTTTCCAACGTTAAATTCT	0.358													C|||	1674	0.334265	0.0469	0.5159	5008	,	,		17538	0.6141		0.3439	False		,,,				2504	0.2955				p.V409L		Atlas-SNP	.											.	DDX60L	116	.	0			c.G1225C						PASS	.	C	LEU/VAL	351,3307		31,289,1509	109.0	104.0	106.0		1225	3.1	0.8	4	dbSNP_121	106	2714,5446		435,1844,1801	yes	missense	DDX60L	NM_001012967.1	32	466,2133,3310	GG,GC,CC		33.2598,9.5954,25.935	benign	409/1707	169362557	3065,8753	1829	4080	5909	SO:0001583	missense	91351	exon10			TTCCAACGTTAAA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.1225G>C	4.37:g.169362557C>G	ENSP00000422423:p.Val409Leu	Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		817	0.3740842490842491	27	0.054878048780487805	171	0.4723756906077348	365	0.6381118881118881	254	0.33509234828496043	C	11.22	1.574833	0.28092	0.095954	0.332598	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.18502	2.22;2.22;2.21;2.86	3.1	3.1	0.35709	.	0.263396	0.19176	U	0.120809	T	0.00012	0.0000	M	0.65975	2.015	0.46631	P	8.650000000000047E-4	B;B;B	0.32620	0.378;0.336;0.378	B;B;B	0.25987	0.065;0.048;0.065	T	0.20974	-1.0259	9	0.09084	T	0.74	.	9.9765	0.41786	0.0:1.0:0.0:0.0	rs13151700;rs17706604;rs52823633;rs13151700	409;409;409	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	L	409;409;409;137	ENSP00000260184:V409L;ENSP00000422423:V409L;ENSP00000422202:V409L;ENSP00000421026:V137L	ENSP00000260184:V409L	V	-	1	0	DDX60L	169599132	0.993000	0.37304	0.808000	0.32385	0.024000	0.10985	3.471000	0.53107	1.411000	0.46957	0.313000	0.20887	GTT	C|0.615;G|0.385	0.385	strong		0.358	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
POLRMT	5442	hgsc.bcm.edu	37	19	629846	629846	+	Silent	SNP	G	G	A	rs11550305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:629846G>A	ENST00000588649.2	-	3	600	c.516C>T	c.(514-516)gcC>gcT	p.A172A		NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	172					gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)	p.A172A(1)		cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		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)		CCAGGCACCCGGCCATCTGCT	0.697													G|||	492	0.0982428	0.0325	0.1081	5008	,	,		15486	0.006		0.174	False		,,,				2504	0.1973				p.A172A		Atlas-SNP	.											POLRMT,NS,NS,0,1	POLRMT	91	1	1	Substitution - coding silent(1)	pancreas(1)	c.C516T						PASS	.	G		265,4139		6,253,1943	13.0	14.0	14.0		516	-8.1	0.0	19	dbSNP_120	14	1525,7057		134,1257,2900	no	coding-synonymous	POLRMT	NM_005035.3		140,1510,4843	AA,AG,GG		17.7698,6.0173,13.7841		172/1231	629846	1790,11196	2202	4291	6493	SO:0001819	synonymous_variant	5442	exon3			GCACCCGGCCATC		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.516C>T	19.37:g.629846G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.500;A|0.500	0.500	weak		0.697	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
FERMT3	83706	hgsc.bcm.edu	37	11	63988045	63988045	+	Silent	SNP	G	G	A	rs3802932	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:63988045G>A	ENST00000279227.5	+	12	1556	c.1461G>A	c.(1459-1461)ccG>ccA	p.P487P	FERMT3_ENST00000345728.5_Silent_p.P483P	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	487	FERM.				integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						GTGGGGGCCCGGGCAACCACC	0.682													G|||	828	0.165335	0.1172	0.147	5008	,	,		15893	0.4762		0.0726	False		,,,				2504	0.0184				p.P487P		Atlas-SNP	.											URP2,NS,carcinoma,0,2	FERMT3	51	2	0			c.G1461A						PASS	.	G	,	431,3951		29,373,1789	11.0	13.0	12.0		1449,1461	-8.6	0.0	11	dbSNP_107	12	480,8084		24,432,3826	no	coding-synonymous,coding-synonymous	FERMT3	NM_031471.5,NM_178443.2	,	53,805,5615	AA,AG,GG		5.6049,9.8357,7.0369	,	483/664,487/668	63988045	911,12035	2191	4282	6473	SO:0001819	synonymous_variant	83706	exon12			GGGCCCGGGCAAC	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	23151	protein-coding gene	gene with protein product	"""kindlin-3"""	607901	"""fermitin family homolog 3 (Drosophila)"""				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.1461G>A	11.37:g.63988045G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_178443	Q8IUA1|Q8N207|Q9BT48	Silent	SNP	ENST00000279227.5	37	CCDS8060.1	432	0.1978021978021978	65	0.13211382113821138	45	0.12430939226519337	271	0.4737762237762238	51	0.06728232189973615	G	0.006	-2.020701	0.00418	0.098357	0.056049	ENSG00000149781	ENST00000545896	T	0.56611	0.45	4.31	-8.61	0.00885	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25357	P	0.9888111	.	.	.	.	.	.	T	0.11767	-1.0574	5	0.38643	T	0.18	-6.5345	0.571	0.00695	0.3445:0.2066:0.2388:0.21	rs3802932	.	.	.	Q	46	ENSP00000440209:R46Q	ENSP00000440209:R46Q	R	+	2	0	FERMT3	63744621	0.000000	0.05858	0.024000	0.17045	0.006000	0.05464	-1.539000	0.02202	-3.948000	0.00088	-2.961000	0.00082	CGG	G|0.808;A|0.192	0.192	strong		0.682	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	
CCDC15	80071	hgsc.bcm.edu	37	11	124857708	124857708	+	Missense_Mutation	SNP	G	G	A	rs4936966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124857708G>A	ENST00000344762.5	+	8	1845	c.1586G>A	c.(1585-1587)gGc>gAc	p.G529D	CCDC15_ENST00000529051.1_Missense_Mutation_p.G529D	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	529			G -> D (in dbSNP:rs4936966).			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)		AAATATCAAGGCCAGGATTTT	0.398													A|||	1437	0.286941	0.4705	0.1801	5008	,	,		18812	0.1935		0.1958	False		,,,				2504	0.3047				p.G529D		Atlas-SNP	.											CCDC15_ENST00000344762,colon,carcinoma,0,7	CCDC15	134	7	0			c.G1586A						scavenged	.	A	ASP/GLY	1566,2052		356,854,599	175.0	168.0	170.0		1586	-3.0	0.0	11	dbSNP_111	170	1647,6511		173,1301,2605	yes	missense	CCDC15	NM_025004.2	94	529,2155,3204	AA,AG,GG		20.1888,43.2836,27.2843	benign	529/952	124857708	3213,8563	1809	4079	5888	SO:0001583	missense	80071	exon8			ATCAAGGCCAGGA	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.1586G>A	11.37:g.124857708G>A	ENSP00000341684:p.Gly529Asp	Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	103	82	0.796117	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	578	0.26465201465201466	242	0.491869918699187	71	0.19613259668508287	114	0.1993006993006993	151	0.19920844327176782	A	5.456	0.269138	0.10349	0.432836	0.201888	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.28454	1.61;1.66	4.23	-2.98	0.05513	.	2.421730	0.01604	N	0.022219	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41538	-0.9503	9	0.06365	T	0.9	.	0.3885	0.00406	0.2229:0.2635:0.2557:0.2578	rs4936966;rs52818517;rs60858036;rs4936966	529	Q0P6D6	CCD15_HUMAN	D	529	ENSP00000435403:G529D;ENSP00000341684:G529D	ENSP00000341684:G529D	G	+	2	0	CCDC15	124362918	0.002000	0.14202	0.000000	0.03702	0.157000	0.22087	0.082000	0.14847	-0.801000	0.04427	-0.451000	0.05528	GGC	G|0.721;A|0.279	0.279	strong		0.398	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
PDXDC1	23042	hgsc.bcm.edu	37	16	15129940	15129940	+	Silent	SNP	C	C	T	rs3198697	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:15129940C>T	ENST00000396410.4	+	23	2272	c.2175C>T	c.(2173-2175)caC>caT	p.H725H	PDXDC1_ENST00000325823.7_Silent_p.H710H|PDXDC1_ENST00000563679.1_Silent_p.H743H|PDXDC1_ENST00000450288.2_Silent_p.H697H|PDXDC1_ENST00000569715.1_Silent_p.H698H|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000447912.2_Silent_p.H634H	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	725					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CAGTCAGTCACATTGAAGACT	0.567													C|||	813	0.16234	0.0227	0.2133	5008	,	,		18967	0.003		0.3976	False		,,,				2504	0.2372				p.H725H		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C2175T						PASS	.	C		378,4016	190.2+/-216.2	20,338,1839	138.0	134.0	135.0		2175	1.3	0.8	16	dbSNP_105	135	3603,4997	521.2+/-379.8	748,2107,1445	no	coding-synonymous	PDXDC1	NM_015027.2		768,2445,3284	TT,TC,CC		41.8953,8.6026,30.6372		725/789	15129940	3981,9013	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon23			CAGTCACATTGAA	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.2175C>T	16.37:g.15129940C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	14	0.325581	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			C|0.746;T|0.254	0.254	strong		0.567	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116073801	116073801	+	Silent	SNP	T	T	C	rs621375	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:116073801T>C	ENST00000304129.4	-	7	650	c.621A>G	c.(619-621)aaA>aaG	p.K207K	AFAP1L2_ENST00000369271.3_Silent_p.K207K|AFAP1L2_ENST00000545353.1_Silent_p.K260K			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	207	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		CCTTGGAGGATTTGTAGCACT	0.567													T|||	1775	0.354433	0.7322	0.1671	5008	,	,		20693	0.1071		0.2097	False		,,,				2504	0.3804				p.K207K		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.A621G						PASS	.	T	,	2790,1616	662.7+/-401.1	899,992,312	116.0	88.0	98.0		621,621	1.2	1.0	10	dbSNP_83	98	1672,6928	306.4+/-307.9	163,1346,2791	no	coding-synonymous,coding-synonymous	AFAP1L2	NM_001001936.1,NM_032550.2	,	1062,2338,3103	CC,CT,TT		19.4419,36.6773,34.3072	,	207/819,207/815	116073801	4462,8544	2203	4300	6503	SO:0001819	synonymous_variant	84632	exon7			GGAGGATTTGTAG	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.621A>G	10.37:g.116073801T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	101	42	0.415842	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			C|0.337;N|0.000	0.337	strong		0.567	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
VWA5B2	90113	hgsc.bcm.edu	37	3	183955109	183955109	+	Silent	SNP	C	C	T	rs843334	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183955109C>T	ENST00000426955.2	+	11	1729	c.1629C>T	c.(1627-1629)ccC>ccT	p.P543P	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Silent_p.P324P	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	554										breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						TGCTGACCCCCCGGGAGATCC	0.622													C|||	996	0.198882	0.1377	0.1844	5008	,	,		16035	0.2351		0.2256	False		,,,				2504	0.227				p.P543P		Atlas-SNP	.											.	VWA5B2	47	.	0			c.C1629T						PASS	.	C		207,1177		17,173,502	42.0	43.0	43.0		1629	1.4	1.0	3	dbSNP_86	43	660,2522		69,522,1000	no	coding-synonymous	VWA5B2	NM_138345.1		86,695,1502	TT,TC,CC		20.7417,14.9566,18.9882		543/1243	183955109	867,3699	692	1591	2283	SO:0001819	synonymous_variant	90113	exon11			GACCCCCCGGGAG		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.1629C>T	3.37:g.183955109C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	99	33	0.333333	NM_138345	B9EGN7	Silent	SNP	ENST00000426955.2	37	CCDS54686.1																																																																																			C|0.817;T|0.183	0.183	strong		0.622	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
HEY2	23493	hgsc.bcm.edu	37	6	126080522	126080522	+	Silent	SNP	G	G	C	rs61737181	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:126080522G>C	ENST00000368364.3	+	5	785	c.588G>C	c.(586-588)ctG>ctC	p.L196L	HEY2_ENST00000368365.1_Silent_p.L150L	NM_012259.2	NP_036391.1	Q9UBP5	HEY2_HUMAN	hes-related family bHLH transcription factor with YRPW motif 2	196					anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|ascending aorta morphogenesis (GO:0035910)|atrial septum morphogenesis (GO:0060413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate commitment (GO:0045165)|cochlea development (GO:0090102)|coronary vasculature morphogenesis (GO:0060977)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|mesenchymal cell development (GO:0014031)|muscular septum morphogenesis (GO:0003150)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cardiac vascular smooth muscle cell differentiation (GO:2000723)|negative regulation of gene expression (GO:0010629)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription initiation from RNA polymerase II promoter (GO:0060633)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of heart rate (GO:0010460)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of auditory receptor cell differentiation (GO:0045607)|regulation of vasculogenesis (GO:2001212)|smooth muscle cell differentiation (GO:0051145)|tricuspid valve formation (GO:0003195)|tricuspid valve morphogenesis (GO:0003186)|umbilical cord morphogenesis (GO:0036304)|vascular smooth muscle cell development (GO:0097084)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	histone deacetylase binding (GO:0042826)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|large_intestine(7)|lung(5)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		CCGCAGCCCTGCTCCAGCCCA	0.672													G|||	211	0.0421326	0.0038	0.0605	5008	,	,		17235	0.003		0.1183	False		,,,				2504	0.0429				p.L196L		Atlas-SNP	.											.	HEY2	44	.	0			c.G588C						PASS	.	G		79,4327		0,79,2124	109.0	113.0	112.0		588	4.7	1.0	6	dbSNP_129	112	1006,7592		63,880,3356	no	coding-synonymous	HEY2	NM_012259.2		63,959,5480	CC,CG,GG		11.7004,1.793,8.3436		196/338	126080522	1085,11919	2203	4299	6502	SO:0001819	synonymous_variant	23493	exon5			AGCCCTGCTCCAG	AJ249545	CCDS5131.1	6q	2013-10-17	2013-10-17		ENSG00000135547	ENSG00000135547		"""Basic helix-loop-helix proteins"""	4881	protein-coding gene	gene with protein product		604674	"""hairy/enhancer-of-split related with YRPW motif 2"""			10415358	Standard	NM_012259		Approved	bHLHb32, HERP1, HESR2	uc003qad.3	Q9UBP5	OTTHUMG00000015512	ENST00000368364.3:c.588G>C	6.37:g.126080522G>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_012259		Silent	SNP	ENST00000368364.3	37	CCDS5131.1																																																																																			G|0.925;C|0.075	0.075	strong		0.672	HEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042077.1		
ATP13A2	23400	hgsc.bcm.edu	37	1	17313654	17313654	+	Silent	SNP	C	C	T	rs761421	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17313654C>T	ENST00000326735.8	-	26	3003	c.2970G>A	c.(2968-2970)gtG>gtA	p.V990V	ATP13A2_ENST00000341676.5_Silent_p.V946V|ATP13A2_ENST00000452699.1_Silent_p.V985V|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	990					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		CCGGTGGCCGCACCCGTCCCA	0.687													C|||	1734	0.346246	0.171	0.4582	5008	,	,		13199	0.252		0.508	False		,,,				2504	0.4346				p.V990V		Atlas-SNP	.											.	ATP13A2	85	.	0			c.G2970A						PASS	.	C	,,	1046,3360	380.6+/-323.8	133,780,1290	46.0	43.0	44.0		2955,2838,2970	-5.5	0.9	1	dbSNP_86	44	4488,4110	583.2+/-391.5	1155,2178,966	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	1288,2958,2256	TT,TC,CC		47.8018,23.7404,42.5561	,,	985/1176,946/1159,990/1181	17313654	5534,7470	2203	4299	6502	SO:0001819	synonymous_variant	23400	exon26			TGGCCGCACCCGT	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2970G>A	1.37:g.17313654C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	39	28	0.717949	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			C|0.600;T|0.400	0.400	strong		0.687	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68029313	68029313	+	Missense_Mutation	SNP	G	G	A	rs2236235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:68029313G>A	ENST00000329153.5	+	7	1097	c.965G>A	c.(964-966)cGg>cAg	p.R322Q		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	322			R -> Q (in dbSNP:rs2236235).			cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		GGCACCCCGCGGGACAGCATC	0.632													G|||	867	0.173123	0.0136	0.1758	5008	,	,		18193	0.2887		0.2207	False		,,,				2504	0.2188				p.R322Q		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G965A						PASS	.	G	GLN/ARG	154,3814		4,146,1834	21.0	24.0	23.0		965	2.3	0.0	14	dbSNP_98	23	1779,6509		180,1419,2545	yes	missense	PLEKHH1	NM_020715.2	43	184,1565,4379	AA,AG,GG		21.4648,3.881,15.7719	probably-damaging	322/1365	68029313	1933,10323	1984	4144	6128	SO:0001583	missense	57475	exon7			CCCCGCGGGACAG	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.965G>A	14.37:g.68029313G>A	ENSP00000330278:p.Arg322Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	404	0.184981684981685	6	0.012195121951219513	62	0.1712707182320442	170	0.2972027972027972	166	0.21899736147757257	G	8.718	0.913728	0.17907	0.03881	0.214648	ENSG00000054690	ENST00000329153	T	0.22134	1.97	5.08	2.26	0.28386	.	0.279487	0.38548	N	0.001647	T	0.00012	0.0000	M	0.64997	1.995	0.09310	P	0.99999495267	B	0.16166	0.016	B	0.09377	0.004	T	0.41998	-0.9477	9	0.18710	T	0.47	.	8.094	0.30818	0.2591:0.0:0.7409:0.0	rs2236235;rs17782308;rs59522386;rs2236235	322	Q9ULM0	PKHH1_HUMAN	Q	322	ENSP00000330278:R322Q	ENSP00000330278:R322Q	R	+	2	0	PLEKHH1	67099066	0.997000	0.39634	0.016000	0.15963	0.052000	0.14988	2.565000	0.45939	0.310000	0.22990	0.491000	0.48974	CGG	G|0.809;N|0.000	.	strong		0.632	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
SLC4A7	9497	hgsc.bcm.edu	37	3	27490194	27490194	+	Silent	SNP	T	T	C	rs13096477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:27490194T>C	ENST00000295736.5	-	3	280	c.210A>G	c.(208-210)agA>agG	p.R70R	SLC4A7_ENST00000446700.1_Silent_p.R75R|SLC4A7_ENST00000454389.1_Silent_p.R79R|SLC4A7_ENST00000428386.1_Silent_p.R70R|SLC4A7_ENST00000435667.2_Silent_p.R79R|SLC4A7_ENST00000425128.2_Silent_p.R75R|SLC4A7_ENST00000388777.4_5'UTR|SLC4A7_ENST00000437179.1_Silent_p.R75R|SLC4A7_ENST00000445684.1_Silent_p.R79R|SLC4A7_ENST00000440156.1_Silent_p.R79R|SLC4A7_ENST00000455077.1_Silent_p.R75R	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	70					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	TATCTTTTCTTCTCCGGTGGT	0.403													T|||	605	0.120807	0.034	0.1527	5008	,	,		14346	0.0565		0.2107	False		,,,				2504	0.1892				p.R75R		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A225G						PASS	.	T		300,4106	162.9+/-194.8	7,286,1910	238.0	214.0	222.0		210	0.6	1.0	3	dbSNP_121	222	1989,6611	347.9+/-326.8	221,1547,2532	no	coding-synonymous	SLC4A7	NM_003615.3		228,1833,4442	CC,CT,TT		23.1279,6.8089,17.5996		70/1215	27490194	2289,10717	2203	4300	6503	SO:0001819	synonymous_variant	9497	exon3			TTTTCTTCTCCGG	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.210A>G	3.37:g.27490194T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	173	75	0.433526	NM_001258379	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Silent	SNP	ENST00000295736.5	37	CCDS33721.1																																																																																			T|0.851;C|0.149	0.149	strong		0.403	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
DNAH3	55567	hgsc.bcm.edu	37	16	20959918	20959918	+	Missense_Mutation	SNP	G	G	A	rs2301620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20959918G>A	ENST00000261383.3	-	57	11229	c.11230C>T	c.(11230-11232)Cgg>Tgg	p.R3744W	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3744			R -> W (in dbSNP:rs2301620).		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)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		AGGAGACGCCGGTCTTTGTCA	0.517													G|||	500	0.0998403	0.0862	0.0663	5008	,	,		18879	0.1806		0.0447	False		,,,				2504	0.1155				p.R3744W		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C11230T						PASS	.	G	TRP/ARG	294,4108	160.7+/-193.0	11,272,1918	101.0	90.0	94.0		11230	2.3	1.0	16	dbSNP_100	94	460,8140	137.9+/-194.8	12,436,3852	yes	missense	DNAH3	NM_017539.1	101	23,708,5770	AA,AG,GG		5.3488,6.6788,5.7991	probably-damaging	3744/4117	20959918	754,12248	2201	4300	6501	SO:0001583	missense	55567	exon57			GACGCCGGTCTTT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.11230C>T	16.37:g.20959918G>A	ENSP00000261383:p.Arg3744Trp	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	179	0.08195970695970696	42	0.08536585365853659	17	0.04696132596685083	82	0.14335664335664336	38	0.05013192612137203	G	20.1	3.937606	0.73557	0.066788	0.053488	ENSG00000158486	ENST00000261383	T	0.11385	2.78	5.9	2.33	0.28932	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.00468	0.0015	H	0.98314	4.2	0.09310	P	1.0	D	0.89917	1.0	D	0.97110	1.0	T	0.48525	-0.9028	9	0.87932	D	0	.	13.6452	0.62277	0.0:0.0:0.3842:0.6158	rs2301620;rs57956717;rs2301620	3744	Q8TD57	DYH3_HUMAN	W	3744	ENSP00000261383:R3744W	ENSP00000261383:R3744W	R	-	1	2	DNAH3	20867419	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	1.259000	0.32956	0.117000	0.18138	-0.271000	0.10264	CGG	G|0.929;A|0.071	0.071	strong		0.517	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ACAN	176	hgsc.bcm.edu	37	15	89415247	89415247	+	Missense_Mutation	SNP	C	C	G	rs3817428	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89415247C>G	ENST00000561243.1	+	14	7119	c.7119C>G	c.(7117-7119)gaC>gaG	p.D2373E	ACAN_ENST00000559004.1_Missense_Mutation_p.D2335E|ACAN_ENST00000439576.2_Missense_Mutation_p.D2373E|ACAN_ENST00000352105.7_Missense_Mutation_p.D2335E			P16112	PGCA_HUMAN	aggrecan	2258	G3.|Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)	p.D2259E(1)		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)			ATGCCCAAGACTACCAGTGGA	0.592													C|||	572	0.114217	0.0477	0.1268	5008	,	,		22065	0.123		0.2445	False		,,,				2504	0.0521				p.D2373E		Atlas-SNP	.											ACAN,NS,carcinoma,0,1	ACAN	220	1	1	Substitution - Missense(1)	stomach(1)	c.C7119G						PASS	.	C	GLU/ASP,GLU/ASP	307,4045	151.4+/-185.3	15,277,1884	110.0	114.0	112.0		7119,7005	3.9	1.0	15	dbSNP_107	112	2308,6282	380.0+/-339.5	298,1712,2285	yes	missense,missense	ACAN	NM_013227.3,NM_001135.3	45,45	313,1989,4169	GG,GC,CC		26.8685,7.0542,20.2055	benign,benign	2373/2531,2335/2432	89415247	2615,10327	2176	4295	6471	SO:0001583	missense	176	exon15			CCAAGACTACCAG	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.7119C>G	15.37:g.89415247C>G	ENSP00000453342:p.Asp2373Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_013227	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	342	0.1565934065934066	25	0.0508130081300813	57	0.1574585635359116	63	0.11013986013986014	197	0.2598944591029024	C	13.69	2.311104	0.40895	0.070542	0.268685	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.18338	2.22;2.22	5.76	3.89	0.44902	.	0.000000	0.34386	N	0.004011	T	0.00012	0.0000	N	0.04705	-0.18	0.38965	P	0.04137299999999999	P;B	0.35493	0.505;0.286	B;B	0.35607	0.161;0.206	T	0.50389	-0.8834	9	0.23891	T	0.37	-28.3785	11.615	0.51083	0.0:0.8564:0.0:0.1436	rs3817428;rs17201667;rs52795578;rs3817428	2335;2373	E7ENV9;E7EX88	.;.	E	2373;2335;2259	ENSP00000387356:D2373E;ENSP00000341615:D2335E	ENSP00000268134:D2259E	D	+	3	2	ACAN	87216251	0.991000	0.36638	1.000000	0.80357	0.979000	0.70002	0.384000	0.20668	0.796000	0.33947	-0.192000	0.12808	GAC	C|0.854;G|0.146	0.146	strong		0.592	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
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 GAIIx	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	PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_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	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	101	48	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	
ADPGK	83440	hgsc.bcm.edu	37	15	73052845	73052845	+	Silent	SNP	A	A	G	rs8023358	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:73052845A>G	ENST00000311669.8	-	4	639	c.546T>C	c.(544-546)ggT>ggC	p.G182G	ADPGK_ENST00000567733.1_5'UTR	NM_031284.4	NP_112574.3	Q9BRR6	ADPGK_HUMAN	ADP-dependent glucokinase	182	ADPK. {ECO:0000255|PROSITE- ProRule:PRU00584}.				glycolytic process (GO:0006096)	extracellular region (GO:0005576)|membrane (GO:0016020)	ADP-specific glucokinase activity (GO:0043843)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|skin(1)	7						GTAGCTTTGGACCAACTGGAC	0.498													A|||	980	0.195687	0.3003	0.1657	5008	,	,		19483	0.2252		0.1441	False		,,,				2504	0.0982				p.G182G		Atlas-SNP	.											.	ADPGK	19	.	0			c.T546C						PASS	.	A		1027,2957		135,757,1100	123.0	125.0	124.0		546	-3.2	1.0	15	dbSNP_116	124	1113,7187		72,969,3109	no	coding-synonymous	ADPGK	NM_031284.4		207,1726,4209	GG,GA,AA		13.4096,25.7781,17.421		182/497	73052845	2140,10144	1992	4150	6142	SO:0001819	synonymous_variant	83440	exon4			CTTTGGACCAACT	AL136873	CCDS42057.1	15q24.1	2012-07-02			ENSG00000159322	ENSG00000159322			25250	protein-coding gene	gene with protein product		611861				11230166	Standard	NM_031284		Approved	DKFZp434B195, ADP-GK	uc002avf.4	Q9BRR6	OTTHUMG00000172777	ENST00000311669.8:c.546T>C	15.37:g.73052845A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_031284	Q49AU7|Q8NBI1|Q8WZ90|Q96NF8|Q9H0A7	Silent	SNP	ENST00000311669.8	37	CCDS42057.1																																																																																			A|0.822;G|0.178	0.178	strong		0.498	ADPGK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420434.1	NM_031284	
ZNF880	400713	hgsc.bcm.edu	37	19	52887427	52887427	+	Missense_Mutation	SNP	A	A	C	rs8104808	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52887427A>C	ENST00000422689.2	+	4	609	c.594A>C	c.(592-594)agA>agC	p.R198S		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	198					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						TGTCTTCAAGACTTGCTAACA	0.373													C|||	1900	0.379393	0.2428	0.379	5008	,	,		20891	0.3462		0.4205	False		,,,				2504	0.5562				p.R198S		Atlas-SNP	.											.	ZNF880	45	.	0			c.A594C						PASS	.	C	SER/ARG	394,990		53,288,351	51.0	50.0	50.0		594	-2.1	0.0	19	dbSNP_116	50	1214,1968		222,770,599	yes	missense	ZNF880	NM_001145434.1	110	275,1058,950	CC,CA,AA		38.1521,28.4682,35.2168	benign	198/578	52887427	1608,2958	692	1591	2283	SO:0001583	missense	400713	exon4			TTCAAGACTTGCT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.594A>C	19.37:g.52887427A>C	ENSP00000406318:p.Arg198Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	746	0.3415750915750916	120	0.24390243902439024	138	0.3812154696132597	177	0.3094405594405594	311	0.4102902374670185	C	1.585	-0.530539	0.04112	0.284682	0.381521	ENSG00000221923	ENST00000422689	T	0.26660	1.72	1.84	-2.1	0.07210	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00408	-1.53	0.80722	P	0.0	B	0.18741	0.03	B	0.04013	0.001	T	0.42932	-0.9422	7	.	.	.	.	3.0674	0.06219	0.3498:0.3892:0.0:0.261	rs8104808;rs17736357;rs52798557;rs8104808	198	Q6PDB4	ZN880_HUMAN	S	198	ENSP00000406318:R198S	.	R	+	3	2	ZNF880	57579239	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.885000	0.01620	-0.814000	0.04352	-1.140000	0.01884	AGA	A|0.652;C|0.348	0.348	strong		0.373	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ELTD1	64123	hgsc.bcm.edu	37	1	79358827	79358827	+	Missense_Mutation	SNP	G	G	T	rs1968956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:79358827G>T	ENST00000370742.3	-	13	1860	c.1797C>A	c.(1795-1797)caC>caA	p.H599Q		NM_022159.3	NP_071442.2	Q9HBW9	ELTD1_HUMAN	EGF, latrophilin and seven transmembrane domain containing 1	599			H -> Q (in dbSNP:rs1968956).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(45)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	69				COAD - Colon adenocarcinoma(225;0.0905)|Colorectal(170;0.103)|all cancers(265;0.105)|Epithelial(280;0.148)		ACCCTGCAGTGTGACGAAAAA	0.299													G|||	66	0.0131789	0.0015	0.0101	5008	,	,		15308	0.002		0.0368	False		,,,				2504	0.0184				p.H599Q		Atlas-SNP	.											.	ELTD1	143	.	0			c.C1797A						PASS	.	G	GLN/HIS	31,3613		0,31,1791	71.0	66.0	68.0		1797	3.6	1.0	1	dbSNP_92	68	308,7830		5,298,3766	yes	missense	ELTD1	NM_022159.3	24	5,329,5557	TT,TG,GG		3.7847,0.8507,2.8773	probably-damaging	599/691	79358827	339,11443	1822	4069	5891	SO:0001583	missense	64123	exon13			TGCAGTGTGACGA	AF192403	CCDS41352.1	1p33-p32	2014-08-08			ENSG00000162618	ENSG00000162618		"""-"", ""GPCR / Class B : Orphans"""	20822	protein-coding gene	gene with protein product						11050079	Standard	NM_022159		Approved	ETL	uc001diq.4	Q9HBW9	OTTHUMG00000009738	ENST00000370742.3:c.1797C>A	1.37:g.79358827G>T	ENSP00000359778:p.His599Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	32	8	0.25	NM_022159	B1AR71|Q5KU34	Missense_Mutation	SNP	ENST00000370742.3	37	CCDS41352.1	32	0.014652014652014652	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	27	0.03562005277044855	G	18.96	3.733399	0.69189	0.008507	0.037847	ENSG00000162618	ENST00000370742;ENST00000401034	T;T	0.42131	0.98;0.98	5.55	3.56	0.40772	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.30792	0.0776	M	0.67569	2.06	0.48975	D	0.999739	B	0.27997	0.197	B	0.42163	0.378	T	0.20974	-1.0259	9	.	.	.	.	6.5758	0.22564	0.1642:0.0:0.6933:0.1425	rs1968956;rs52802033;rs58909799;rs1968956	599	Q9HBW9	ELTD1_HUMAN	Q	599;57	ENSP00000359778:H599Q;ENSP00000383813:H57Q	.	H	-	3	2	ELTD1	79131415	0.991000	0.36638	1.000000	0.80357	0.996000	0.88848	0.222000	0.17699	1.211000	0.43351	0.655000	0.94253	CAC	G|0.980;T|0.020	0.020	strong		0.299	ELTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026859.1	NM_022159	
PRG4	10216	hgsc.bcm.edu	37	1	186273994	186273994	+	Missense_Mutation	SNP	C	C	T	rs2273779	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186273994C>T	ENST00000445192.2	+	6	583	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W	PRG4_ENST00000367484.3_Missense_Mutation_p.R139W|PRG4_ENST00000367485.4_Intron|PRG4_ENST00000367486.3_Intron|PRG4_ENST00000367483.4_Missense_Mutation_p.R139W	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	180	Ser-rich.		R -> W (in dbSNP:rs2273779). {ECO:0000269|Ref.1}.		cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ttcAACAATTCGGAAAATCAA	0.358													C|||	1160	0.231629	0.149	0.4063	5008	,	,		16449	0.129		0.33	False		,,,				2504	0.2239				p.R180W		Atlas-SNP	.											.	PRG4	259	.	0			c.C538T						PASS	.	C	TRP/ARG,TRP/ARG,,	822,3576	293.6+/-282.7	79,664,1456	41.0	44.0	43.0		415,538,,	4.3	1.0	1	dbSNP_100	43	3031,5567	451.4+/-362.6	537,1957,1805	yes	missense,missense,intron,intron	PRG4	NM_001127708.1,NM_005807.3,NM_001127709.1,NM_001127710.1	101,101,,	616,2621,3261	TT,TC,CC		35.2524,18.6903,29.6476	possibly-damaging,possibly-damaging,,	139/1364,180/1405,,	186273994	3853,9143	2199	4299	6498	SO:0001583	missense	10216	exon6			ACAATTCGGAAAA	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.538C>T	1.37:g.186273994C>T	ENSP00000399679:p.Arg180Trp	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	168	168	1	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	550	0.2518315018315018	65	0.13211382113821138	145	0.4005524861878453	77	0.1346153846153846	263	0.3469656992084433	C	18.69	3.677565	0.68042	0.186903	0.352524	ENSG00000116690	ENST00000367484;ENST00000533951;ENST00000367483;ENST00000445192	T;T;T;T	0.50548	2.96;0.74;2.87;2.92	5.17	4.26	0.50523	.	0.199396	0.25081	U	0.033299	T	0.00012	0.0000	N	0.19112	0.55	0.41286	P	0.013051999999999953	P;D	0.55172	0.949;0.97	B;P	0.46850	0.329;0.529	T	0.42085	-0.9472	9	0.62326	D	0.03	-4.2039	9.7397	0.40411	0.0:0.9046:0.0:0.0954	rs2273779;rs52813784;rs58219930;rs2273779	180;139	Q92954;Q92954-2	PRG4_HUMAN;.	W	139;89;139;180	ENSP00000356454:R139W;ENSP00000431330:R89W;ENSP00000356453:R139W;ENSP00000399679:R180W	ENSP00000356453:R139W	R	+	1	2	PRG4	184540617	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.402000	0.34600	1.188000	0.43014	0.650000	0.86243	CGG	C|0.726;T|0.274	0.274	strong		0.358	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
ADCK3	56997	hgsc.bcm.edu	37	1	227149203	227149203	+	Silent	SNP	G	G	A	rs11549708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:227149203G>A	ENST00000366779.1	+	7	2888	c.117G>A	c.(115-117)gcG>gcA	p.A39A	ADCK3_ENST00000478406.1_Intron|ADCK3_ENST00000458507.2_Intron|ADCK3_ENST00000366778.1_Intron|ADCK3_ENST00000366777.3_Silent_p.A39A			Q8NI60	ADCK3_HUMAN	aarF domain containing kinase 3	39					cell death (GO:0008219)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|kidney(2)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	9						TGATCATGGCGGCCAGGGCCC	0.632													G|||	404	0.0806709	0.031	0.111	5008	,	,		18320	0.001		0.2187	False		,,,				2504	0.0665				p.A39A		Atlas-SNP	.											.	ADCK3	77	.	0			c.G117A						PASS	.	G		245,4161	137.3+/-173.1	5,235,1963	39.0	40.0	40.0		117	-11.2	0.3	1	dbSNP_120	40	2055,6543	339.2+/-323.1	251,1553,2495	no	coding-synonymous	ADCK3	NM_020247.4		256,1788,4458	AA,AG,GG		23.9009,5.5606,17.6869		39/648	227149203	2300,10704	2203	4299	6502	SO:0001819	synonymous_variant	56997	exon2			CATGGCGGCCAGG	AJ278126	CCDS1557.1	1q42.11	2011-05-03	2010-10-01	2010-10-01	ENSG00000163050	ENSG00000163050			16812	protein-coding gene	gene with protein product	"""coenzyme Q8 homolog (yeast)"""	606980	"""chaperone-ABC1 (activity of bc1 complex, S.pombe)-like"", ""chaperone, ABC1 activity of bc1 complex like (S. pombe)"", ""chaperone, ABC1 activity of bc1 complex homolog (S. pombe)"""	CABC1			Standard	NM_020247		Approved	COQ8, SCAR9	uc001hqn.1	Q8NI60	OTTHUMG00000037621	ENST00000366779.1:c.117G>A	1.37:g.227149203G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	189	90	0.47619	NM_020247	Q5T7A5|Q63HK0|Q8NCJ6|Q9HBQ1|Q9NQ67	Silent	SNP	ENST00000366779.1	37	CCDS1557.1																																																																																			G|0.849;A|0.151	0.151	strong		0.632	ADCK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091712.1	NM_020247	
OR2T34	127068	hgsc.bcm.edu	37	1	248737348	248737348	+	Silent	SNP	G	G	A	rs61833442	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248737348G>A	ENST00000328782.2	-	1	732	c.711C>T	c.(709-711)gcC>gcT	p.A237A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	237						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)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	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)			TCCTGCGGCCGGCGGCAGAAT	0.567													g|||	1625	0.324481	0.5098	0.2349	5008	,	,		20077	0.251		0.2107	False		,,,				2504	0.3303				p.A237A		Atlas-SNP	.											OR2T34,NS,carcinoma,-2,1	OR2T34	72	1	0			c.C711T						PASS	.						110.0	124.0	119.0					1																	248737348		2176	4300	6476	SO:0001819	synonymous_variant	127068	exon1			GCGGCCGGCGGCA	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.711C>T	1.37:g.248737348G>A		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	365	95	0.260274	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Silent	SNP	ENST00000328782.2	37	CCDS31120.1																																																																																			G|0.787;A|0.213	0.213	strong		0.567	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
NALCN	259232	hgsc.bcm.edu	37	13	101720300	101720300	+	Silent	SNP	T	T	G	rs1289556	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:101720300T>G	ENST00000251127.6	-	39	4497	c.4416A>C	c.(4414-4416)atA>atC	p.I1472I		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1472					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TGTTCCATATTATTTGAAAGT	0.363													G|||	2018	0.402955	0.7519	0.2752	5008	,	,		19628	0.1171		0.3608	False		,,,				2504	0.3599				p.I1472I		Atlas-SNP	.											.	NALCN	431	.	0			c.A4416C						PASS	.	G		3159,1247	428.3+/-341.8	1136,887,180	123.0	119.0	120.0		4416	5.9	1.0	13	dbSNP_87	120	3118,5482	657.8+/-401.5	580,1958,1762	no	coding-synonymous	NALCN	NM_052867.2		1716,2845,1942	GG,GT,TT		36.2558,28.3023,48.2623		1472/1739	101720300	6277,6729	2203	4300	6503	SO:0001819	synonymous_variant	259232	exon39			CCATATTATTTGA	AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4416A>C	13.37:g.101720300T>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			T|0.558;G|0.442	0.442	strong		0.363	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
COL6A2	1292	hgsc.bcm.edu	37	21	47552385	47552385	+	Silent	SNP	C	C	T	rs6652	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:47552385C>T	ENST00000300527.4	+	28	3083	c.2979C>T	c.(2977-2979)cgC>cgT	p.R993R		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	993	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGGGTGACCGCGCCGCCGTGT	0.682													C|||	463	0.0924521	0.0893	0.0749	5008	,	,		15128	0.0288		0.1978	False		,,,				2504	0.0665				p.R993R		Atlas-SNP	.											.	COL6A2	351	.	0			c.C2979T						PASS	.	C		497,3905	215.8+/-234.7	29,439,1733	54.0	45.0	49.0		2979	1.4	1.0	21	dbSNP_52	49	1678,6920	297.1+/-303.3	145,1388,2766	no	coding-synonymous	COL6A2	NM_001849.3		174,1827,4499	TT,TC,CC		19.5162,11.2903,16.7308		993/1020	47552385	2175,10825	2201	4299	6500	SO:0001819	synonymous_variant	1292	exon28			TGACCGCGCCGCC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2979C>T	21.37:g.47552385C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	84	52	0.619048	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			C|0.863;T|0.137	0.137	strong		0.682	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
SENP6	26054	hgsc.bcm.edu	37	6	76376552	76376552	+	Silent	SNP	G	G	A	rs17414687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:76376552G>A	ENST00000447266.2	+	10	1597	c.1119G>A	c.(1117-1119)gcG>gcA	p.A373A	SENP6_ENST00000327284.8_Silent_p.A366A|SENP6_ENST00000541192.1_5'Flank|SENP6_ENST00000370014.3_Silent_p.A373A|SENP6_ENST00000370010.2_Silent_p.A366A	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	373					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TAGAAGCAGCGCTAAATGAAA	0.428													G|||	893	0.178315	0.1014	0.2046	5008	,	,		12943	0.0466		0.329	False		,,,				2504	0.2444				p.A373A		Atlas-SNP	.											SENP6_ENST00000447266,NS,carcinoma,0,2	SENP6	189	2	0			c.G1119A						PASS	.	G	,	491,3351		35,421,1465	125.0	121.0	122.0		1098,1119	-1.7	1.0	6	dbSNP_123	122	2944,5302		525,1894,1704	no	coding-synonymous,coding-synonymous	SENP6	NM_001100409.1,NM_015571.2	,	560,2315,3169	AA,AG,GG		35.7022,12.7798,28.4166	,	366/1106,373/1113	76376552	3435,8653	1921	4123	6044	SO:0001819	synonymous_variant	26054	exon10			AGCAGCGCTAAAT		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.1119G>A	6.37:g.76376552G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Silent	SNP	ENST00000447266.2	37	CCDS47454.1																																																																																			G|0.773;A|0.227	0.227	strong		0.428	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
OR3A1	4994	hgsc.bcm.edu	37	17	3195503	3195503	+	Missense_Mutation	SNP	C	C	T	rs703903	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3195503C>T	ENST00000323404.1	-	1	373	c.374G>A	c.(373-375)cGa>cAa	p.R125Q	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	125			R -> Q (in dbSNP:rs703903). {ECO:0000269|PubMed:10673334, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8004088, ECO:0000269|PubMed:8647456}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	20						GGCCAGGAATCGGTCATAGGC	0.592													.|||	2755	0.55012	0.2451	0.5447	5008	,	,		20550	0.9266		0.5427	False		,,,				2504	0.5859				p.R125Q	GBM(20;287 516 18743 28660 36594)	Atlas-SNP	.											.	OR3A1	46	.	0			c.G374A						PASS	.	C	GLN/ARG	1357,3049	440.6+/-346.1	189,979,1035	94.0	87.0	90.0		374	5.3	1.0	17	dbSNP_86	90	4620,3980	601.1+/-394.3	1237,2146,917	yes	missense	OR3A1	NM_002550.2	43	1426,3125,1952	TT,TC,CC		46.2791,30.7989,45.9557	probably-damaging	125/316	3195503	5977,7029	2203	4300	6503	SO:0001583	missense	4994	exon1			AGGAATCGGTCAT	X80391	CCDS11023.1	17p13.3	2012-08-09			ENSG00000180090	ENSG00000180090		"""GPCR / Class A : Olfactory receptors"""	8282	protein-coding gene	gene with protein product						8921386, 8647456	Standard	NM_002550		Approved	OLFRA03, OR40, OR17-40	uc002fvh.1	P47881	OTTHUMG00000090642	ENST00000323404.1:c.374G>A	17.37:g.3195503C>T	ENSP00000313803:p.Arg125Gln	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	162	70	0.432099	NM_002550	Q4VB06|Q6IFM4	Missense_Mutation	SNP	ENST00000323404.1	37	CCDS11023.1	1287	0.5892857142857143	125	0.2540650406504065	207	0.5718232044198895	548	0.958041958041958	407	0.5369393139841688	C	35	5.417656	0.96092	0.307989	0.537209	ENSG00000180090	ENST00000323404	T	0.76968	-1.06	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	D	0.000626	T	0.00012	0.0000	M	0.90977	3.165	0.21933	P	0.99946813	D	0.89917	1.0	D	0.71870	0.975	T	0.38436	-0.9661	9	0.87932	D	0	-14.5448	17.7101	0.88319	0.0:1.0:0.0:0.0	rs703903;rs61014652;rs703903	125	P47881	OR3A1_HUMAN	Q	125	ENSP00000313803:R125Q	ENSP00000313803:R125Q	R	-	2	0	OR3A1	3142253	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	4.592000	0.61027	2.753000	0.94483	0.650000	0.86243	CGA	A|0.000;C|0.493;T|0.507	0.507	strong		0.592	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2		
TBC1D17	79735	hgsc.bcm.edu	37	19	50387729	50387729	+	Silent	SNP	C	C	T	rs35681527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50387729C>T	ENST00000221543.5	+	12	1556	c.1257C>T	c.(1255-1257)ggC>ggT	p.G419G	TBC1D17_ENST00000535102.2_Silent_p.G386G	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	419	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		ACGTCCAGGGCATGAGTGATC	0.642													C|||	536	0.107029	0.1876	0.0749	5008	,	,		15216	0.0		0.1163	False		,,,				2504	0.1217				p.G419G		Atlas-SNP	.											.	TBC1D17	39	.	0			c.C1257T						PASS	.	C	,	789,3617	316.3+/-294.6	67,655,1481	179.0	169.0	172.0		1158,1257	0.2	1.0	19	dbSNP_126	172	1031,7569	220.5+/-258.2	70,891,3339	no	coding-synonymous,coding-synonymous	TBC1D17	NM_001168222.1,NM_024682.2	,	137,1546,4820	TT,TC,CC		11.9884,17.9074,13.9935	,	386/616,419/649	50387729	1820,11186	2203	4300	6503	SO:0001819	synonymous_variant	79735	exon12			CCAGGGCATGAGT	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.1257C>T	19.37:g.50387729C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	154	74	0.480519	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	37	CCDS12785.1																																																																																			C|0.873;G|0.000;T|0.127	0.127	strong		0.642	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
SEPT12	124404	hgsc.bcm.edu	37	16	4837545	4837545	+	Silent	SNP	A	A	G	rs9673735	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4837545A>G	ENST00000268231.8	-	2	365	c.102T>C	c.(100-102)gcT>gcC	p.A34A	SMIM22_ENST00000589721.1_5'Flank|SEPT12_ENST00000591861.1_5'UTR|SMIM22_ENST00000589327.1_5'Flank|SEPT12_ENST00000396693.5_Silent_p.A34A	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	34					cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.A34A(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						GGTCCAGCACAGCCTCAATGC	0.627													A|||	1520	0.303514	0.1536	0.3458	5008	,	,		18187	0.3026		0.328	False		,,,				2504	0.4519				p.A34A		Atlas-SNP	.											SEPT12,colon,carcinoma,0,2	SEPT12	40	2	1	Substitution - coding silent(1)	stomach(1)	c.T102C						PASS	.	A	,	704,3690	293.6+/-282.7	56,592,1549	200.0	146.0	164.0		102,102	-9.9	0.5	16	dbSNP_119	164	2371,6229	394.7+/-344.8	340,1691,2269	no	coding-synonymous,coding-synonymous	SEPT12	NM_001154458.2,NM_144605.4	,	396,2283,3818	GG,GA,AA		27.5698,16.0218,23.6648	,	34/313,34/359	4837545	3075,9919	2197	4300	6497	SO:0001819	synonymous_variant	124404	exon2			CAGCACAGCCTCA	AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.102T>C	16.37:g.4837545A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	CCDS10522.1																																																																																			A|0.743;G|0.257	0.257	strong		0.627	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
DSPP	1834	hgsc.bcm.edu	37	4	88536457	88536457	+	Silent	SNP	T	T	C	rs141186173|rs111205177|rs199994008	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88536457T>C	ENST00000282478.7	+	4	2676	c.2643T>C	c.(2641-2643)gaT>gaC	p.D881D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D881D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	881	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D881_S882insSSD(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgatagcagtgaca	0.498																																					p.D881D		Atlas-SNP	.											.	DSPP	174	.	1	Insertion - In frame(1)	ovary(1)	c.T2643C						PASS	.						73.0	87.0	82.0					4																	88536457		1618	2922	4540	SO:0001819	synonymous_variant	1834	exon5			CAGTGATAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2643T>C	4.37:g.88536457T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	76	11	0.144737	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
GRIA3	2892	hgsc.bcm.edu	37	X	122537277	122537277	+	Silent	SNP	T	T	C	rs502434	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:122537277T>C	ENST00000371251.1	+	9	1252	c.1200T>C	c.(1198-1200)aaT>aaC	p.N400N	GRIA3_ENST00000264357.5_Silent_p.N400N|GRIA3_ENST00000542149.1_Silent_p.N400N|GRIA3_ENST00000371256.5_Silent_p.N400N|GRIA3_ENST00000541091.1_Silent_p.N384N			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	400					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	GCTACTGGAATGAGTATGAAA	0.423													T|||	1997	0.529007	0.3003	0.4308	3775	,	,		13991	0.5208		0.4682	False		,,,				2504	0.3119				p.N400N		Atlas-SNP	.											.	GRIA3	386	.	0			c.T1200C						PASS	.	T	,	1647,2188		290,803,264,539,307	210.0	194.0	199.0		1200,1200	2.2	1.0	X	dbSNP_83	199	4115,2613		895,1165,1160,368,712	no	coding-synonymous,coding-synonymous	GRIA3	NM_000828.4,NM_007325.4	,	1185,1968,1424,907,1019	CC,CT,C,TT,T		38.8377,42.9465,45.4511	,	400/895,400/895	122537277	5762,4801	2203	4300	6503	SO:0001819	synonymous_variant	2892	exon9			CTGGAATGAGTAT	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.1200T>C	X.37:g.122537277T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_000828	D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Silent	SNP	ENST00000371251.1	37	CCDS14604.1																																																																																			T|0.440;0|0.004	.	strong		0.423	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
HBP1	26959	hgsc.bcm.edu	37	7	106826381	106826381	+	Silent	SNP	C	C	T	rs201145168|rs7794598	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:106826381C>T	ENST00000222574.4	+	4	720	c.534C>T	c.(532-534)caC>caT	p.H178H	HBP1_ENST00000468410.1_Silent_p.H178H|HBP1_ENST00000485846.1_Silent_p.H178H	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	178					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						CAGTAAGACACGAAAGGGTAA	0.413														792	0.158147	0.1483	0.1282	5008	,	,		18826	0.124		0.2018	False		,,,				2504	0.183				p.H188H		Atlas-SNP	.											.	HBP1	31	.	0			c.C564T						PASS	.	T		637,3769	767.1+/-413.5	61,515,1627	96.0	88.0	91.0		534	-0.4	1.0	7	dbSNP_116	91	1850,6750	730.1+/-406.7	206,1438,2656	no	coding-synonymous	HBP1	NM_012257.3		267,1953,4283	TT,TC,CC		21.5116,14.4576,19.1219		178/515	106826381	2487,10519	2203	4300	6503	SO:0001819	synonymous_variant	26959	exon4			AAGACACGAAAGG	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.534C>T	7.37:g.106826381C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	37	CCDS5741.1																																																																																			C|0.818;T|0.182	0.182	strong		0.413	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257	
HSPG2	3339	hgsc.bcm.edu	37	1	22179244	22179244	+	Missense_Mutation	SNP	C	C	T	rs35669711	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22179244C>T	ENST00000374695.3	-	52	6752	c.6673G>A	c.(6673-6675)Ggc>Agc	p.G2225S	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2225	Ig-like C2-type 7.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TCTAGGGGGCCGGAGGTGCCC	0.642													c|||	174	0.0347444	0.0023	0.0245	5008	,	,		15891	0.0		0.0487	False		,,,				2504	0.1074				p.G2225S		Atlas-SNP	.											.	HSPG2	311	.	0			c.G6673A						PASS	.	C	SER/GLY	42,4364	44.6+/-78.6	0,42,2161	62.0	68.0	66.0		6673	1.6	0.0	1	dbSNP_126	66	491,8109	139.2+/-195.9	16,459,3825	yes	missense	HSPG2	NM_005529.5	56	16,501,5986	TT,TC,CC		5.7093,0.9532,4.0981	benign	2225/4392	22179244	533,12473	2203	4300	6503	SO:0001583	missense	3339	exon52			GGGGGCCGGAGGT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.6673G>A	1.37:g.22179244C>T	ENSP00000363827:p.Gly2225Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	49	0.022435897435897436	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	36	0.047493403693931395	C	9.963	1.223344	0.22457	0.009532	0.057093	ENSG00000142798	ENST00000374695	T	0.74315	-0.83	5.84	1.57	0.23409	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.135700	0.06909	N	0.807399	T	0.29028	0.0721	M	0.72576	2.205	0.09310	N	1	B;B	0.30889	0.299;0.088	B;B	0.36567	0.228;0.066	T	0.52208	-0.8606	10	0.52906	T	0.07	.	8.045	0.30545	0.0:0.6409:0.1285:0.2306	rs35669711	165;2225	Q59EG0;P98160	.;PGBM_HUMAN	S	2225	ENSP00000363827:G2225S	ENSP00000363827:G2225S	G	-	1	0	HSPG2	22051831	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.182000	0.09726	0.394000	0.25230	0.561000	0.74099	GGC	C|0.965;T|0.035	0.035	strong		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45993727	45993727	+	Missense_Mutation	SNP	A	A	C	rs148418343	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45993727A>C	ENST00000400374.3	+	1	122	c.92A>C	c.(91-93)gAc>gCc	p.D31A	TSPEAR_ENST00000397916.1_5'Flank|TSPEAR_ENST00000323084.4_Intron	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	31						keratin filament (GO:0045095)		p.D31A(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAGGTGGACGACTGCCCAGAG	0.687													.|||	308	0.0615016	0.0484	0.0288	5008	,	,		14764	0.1329		0.0249	False		,,,				2504	0.0665				p.D31A		Atlas-SNP	.											KRTAP10-4,NS,carcinoma,0,1	KRTAP10-4	44	1	1	Substitution - Missense(1)	pancreas(1)	c.A92C						PASS	.	A	,ALA/ASP	231,3929		1,229,1850	60.0	65.0	64.0		,92	3.5	1.0	21	dbSNP_134	64	165,8221		1,163,4029	no	intron,missense	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,126	2,392,5879	CC,CA,AA		1.9676,5.5529,3.1564	,probably-damaging	,31/402	45993727	396,12150	2080	4193	6273	SO:0001583	missense	386672	exon1			TGGACGACTGCCC	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.92A>C	21.37:g.45993727A>C	ENSP00000383225:p.Asp31Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	106	0.048534798534798536	13	0.026422764227642278	12	0.03314917127071823	70	0.12237762237762238	11	0.014511873350923483	N	13.44	2.238867	0.39598	0.055529	0.019676	ENSG00000215454	ENST00000400374;ENST00000334871	T	0.14893	2.47	4.69	3.52	0.40303	.	.	.	.	.	T	0.00440	0.0014	M	0.63843	1.955	0.40243	P	0.022011000000000003	D	0.67145	0.996	P	0.62740	0.906	T	0.04281	-1.0963	8	0.33141	T	0.24	.	7.9837	0.30198	0.8999:0.0:0.1001:0.0	.	31	P60372	KR104_HUMAN	A	31;20	ENSP00000383225:D31A	ENSP00000333987:D20A	D	+	2	0	KRTAP10-4	44818155	0.911000	0.30947	0.997000	0.53966	0.226000	0.24999	1.128000	0.31369	1.863000	0.54032	0.397000	0.26171	GAC	.	.	weak		0.687	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
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 GAIIx	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		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	88	41	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		
GRIN2B	2904	hgsc.bcm.edu	37	12	14018777	14018777	+	Silent	SNP	G	G	C	rs7301328	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:14018777G>C	ENST00000609686.1	-	2	575	c.366C>G	c.(364-366)ccC>ccG	p.P122P		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	122					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TGCCCAGGATGGGGGTGAGAG	0.547													G|||	2211	0.441494	0.4955	0.3112	5008	,	,		17048	0.4931		0.3618	False		,,,				2504	0.4898				p.P122P		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C366G	GRCh37	CM014358	GRIN2B	M	rs7301328	PASS	.	G		2171,2235	582.9+/-385.7	558,1055,590	111.0	122.0	118.0		366	1.6	1.0	12	dbSNP_116	118	3435,5165	505.3+/-376.3	700,2035,1565	no	coding-synonymous	GRIN2B	NM_000834.3		1258,3090,2155	CC,CG,GG		39.9419,49.2737,43.1032		122/1485	14018777	5606,7400	2203	4300	6503	SO:0001819	synonymous_variant	2904	exon2			CAGGATGGGGGTG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.366C>G	12.37:g.14018777G>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	114	66	0.578947	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			G|0.580;C|0.420	0.420	strong		0.547	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
FECH	2235	hgsc.bcm.edu	37	18	55221648	55221648	+	Silent	SNP	T	T	C	rs536560	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:55221648T>C	ENST00000262093.5	-	9	1072	c.921A>G	c.(919-921)ccA>ccG	p.P307P	FECH_ENST00000382873.3_Silent_p.P313P	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	307					cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)	p.P313P(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				ACCAGGGCATTGGACCAACCT	0.527													T|||	3794	0.757588	0.9735	0.6945	5008	,	,		18971	0.628		0.6441	False		,,,				2504	0.7607				p.P313P		Atlas-SNP	.											FECH,NS,carcinoma,0,1	FECH	42	1	1	Substitution - coding silent(1)	prostate(1)	c.A939G						PASS	.	T	,	4044,362	793.7+/-415.2	1856,332,15	129.0	115.0	120.0		921,939	-12.3	0.1	18	dbSNP_83	120	5901,2699	683.2+/-403.9	2029,1843,428	no	coding-synonymous,coding-synonymous	FECH	NM_000140.3,NM_001012515.2	,	3885,2175,443	CC,CT,TT		31.3837,8.2161,23.5353	,	307/424,313/430	55221648	9945,3061	2203	4300	6503	SO:0001819	synonymous_variant	2235	exon9			GGGCATTGGACCA	D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"""protoporphyria"""	612386	"""ferrochelatase (protoporphyria)"""			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.921A>G	18.37:g.55221648T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001012515	A8KA72|Q8IXN1|Q8NAN0	Silent	SNP	ENST00000262093.5	37	CCDS11964.1																																																																																			T|0.244;C|0.756	0.756	strong		0.527	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1		
CELF5	60680	hgsc.bcm.edu	37	19	3224896	3224896	+	Silent	SNP	G	G	C	rs17852497	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:3224896G>C	ENST00000292672.2	+	1	196	c.159G>C	c.(157-159)ccG>ccC	p.P53P	CELF5_ENST00000541430.2_Silent_p.P53P	NM_021938.3	NP_068757.2	Q8N6W0	CELF5_HUMAN	CUGBP, Elav-like family member 5	53	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)	13						GCCAGATCCCGCGGCACCTGG	0.677													G|||	873	0.174321	0.1104	0.1671	5008	,	,		3684	0.1984		0.2256	False		,,,				2504	0.1881				p.P53P		Atlas-SNP	.											CELF5,NS,carcinoma,0,1	CELF5	32	1	0			c.G159C						PASS	.	G	,	632,3772		46,540,1616	21.0	20.0	20.0		159,159	-0.6	0.9	19	dbSNP_123	20	1751,6843		186,1379,2732	no	coding-synonymous,coding-synonymous	CELF5	NM_001172673.1,NM_021938.3	,	232,1919,4348	CC,CG,GG		20.3747,14.3506,18.3336	,	53/410,53/486	3224896	2383,10615	2202	4297	6499	SO:0001819	synonymous_variant	60680	exon1			GATCCCGCGGCAC	AF248649	CCDS12106.1, CCDS54197.1	19p13	2013-02-12	2010-02-19	2010-02-19		ENSG00000161082		"""RNA binding motif (RRM) containing"""	14058	protein-coding gene	gene with protein product		612680	"""Bruno (Drosophila) -like 5, RNA binding protein"", ""bruno-like 5, RNA binding protein (Drosophila)"""	BRUNOL5		10893231	Standard	NM_001172673		Approved		uc002lxm.3	Q8N6W0		ENST00000292672.2:c.159G>C	19.37:g.3224896G>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_021938	D6W614|O75253|Q59GP2|Q86VW6|Q9BZC0|Q9NR86	Silent	SNP	ENST00000292672.2	37	CCDS12106.1																																																																																			G|0.815;C|0.185	0.185	strong		0.677	CELF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452574.1	NM_021938	
SLC28A3	64078	hgsc.bcm.edu	37	9	86917301	86917301	+	Missense_Mutation	SNP	T	T	C	rs10868138	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:86917301T>C	ENST00000376238.4	-	5	387	c.338A>G	c.(337-339)tAt>tGt	p.Y113C	SLC28A3_ENST00000495823.1_5'Flank|SLC28A3_ENST00000537648.1_Missense_Mutation_p.Y44C	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	113			Y -> C (in dbSNP:rs10868138). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15738947}.		pyrimidine nucleoside transport (GO:0015864)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|purine-specific nucleoside:sodium symporter activity (GO:0015390)|pyrimidine- and adenine-specific:sodium symporter activity (GO:0015389)			endometrium(2)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31					Adenosine(DB00640)|Cladribine(DB00242)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Ribavirin(DB00811)	CATAACCAGATAACCTGTCCA	0.512													T|||	563	0.11242	0.1906	0.0663	5008	,	,		18622	0.0823		0.0954	False		,,,				2504	0.0879				p.Y113C	Ovarian(106;425 1539 34835 42413 43572)	Atlas-SNP	.											.	SLC28A3	72	.	0			c.A338G						PASS	.	T	CYS/TYR,CYS/TYR	766,3640	309.7+/-291.2	60,646,1497	65.0	51.0	56.0		338,338	2.8	0.9	9	dbSNP_120	56	660,7940	166.5+/-218.5	20,620,3660	yes	missense,missense	SLC28A3	NM_001199633.1,NM_022127.2	194,194	80,1266,5157	CC,CT,TT		7.6744,17.3854,10.9642	probably-damaging,probably-damaging	113/692,113/692	86917301	1426,11580	2203	4300	6503	SO:0001583	missense	64078	exon5			ACCAGATAACCTG	AF305210	CCDS6670.1	9q21.33	2013-07-17	2013-07-17		ENSG00000197506	ENSG00000197506		"""Solute carriers"""	16484	protein-coding gene	gene with protein product		608269	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 3"""			11032837	Standard	NM_001199633		Approved	CNT3	uc010mpz.3	Q9HAS3	OTTHUMG00000020117	ENST00000376238.4:c.338A>G	9.37:g.86917301T>C	ENSP00000365413:p.Tyr113Cys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_001199633	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Missense_Mutation	SNP	ENST00000376238.4	37	CCDS6670.1	229	0.10485347985347986	93	0.18902439024390244	24	0.06629834254143646	43	0.07517482517482517	69	0.09102902374670185	T	13.18	2.158981	0.38119	0.173854	0.076744	ENSG00000197506	ENST00000376238;ENST00000537648	D;D	0.83250	-1.7;-1.7	5.33	2.8	0.32819	.	0.125588	0.53938	D	0.000044	T	0.00524	0.0017	M	0.69823	2.125	0.36591	P	0.125884	B;B	0.33964	0.105;0.434	B;B	0.43783	0.114;0.431	T	0.42015	-0.9476	9	0.66056	D	0.02	-2.286	9.2725	0.37679	0.4193:0.0:0.0:0.5807	rs10868138;rs52792697;rs56686947;rs10868138	44;113	B4E2S8;Q9HAS3	.;S28A3_HUMAN	C	113;44	ENSP00000365413:Y113C;ENSP00000446438:Y44C	ENSP00000365413:Y113C	Y	-	2	0	SLC28A3	86107121	0.999000	0.42202	0.887000	0.34795	0.925000	0.55904	1.300000	0.33436	1.000000	0.39049	0.533000	0.62120	TAT	T|0.894;C|0.106	0.106	strong		0.512	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127	
NUP88	4927	hgsc.bcm.edu	37	17	5326145	5326145	+	5'Flank	SNP	C	C	G	rs12761	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5326145C>G	ENST00000573584.1	-	0	0				RPAIN_ENST00000381208.5_Missense_Mutation_p.N103K|RPAIN_ENST00000536255.2_Missense_Mutation_p.N103K|RPAIN_ENST00000405578.4_Missense_Mutation_p.N103K|RPAIN_ENST00000381209.3_Missense_Mutation_p.N103K|RPAIN_ENST00000327154.6_Missense_Mutation_p.N103K|CTC-524C5.2_ENST00000575890.1_RNA|RPAIN_ENST00000574003.1_Missense_Mutation_p.N103K	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						AGCTGATCAACCAAGGTAACC	0.448													C|||	2234	0.446086	0.1899	0.4193	5008	,	,		21124	0.7946		0.3052	False		,,,				2504	0.5971				p.N103K		Atlas-SNP	.											.	RPAIN	24	.	0			c.C309G						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN,LYS/ASN	966,3440	364.4+/-316.9	87,792,1324	121.0	113.0	115.0		309,309,309,309,309,309	-6.5	0.0	17	dbSNP_52	115	2363,6237	395.6+/-345.1	300,1763,2237	yes	missense,missense,missense,missense,missense,missense	RPAIN	NM_001033002.3,NM_001160243.1,NM_001160244.1,NM_001160246.1,NM_001160266.1,NM_001160267.1	94,94,94,94,94,94	387,2555,3561	GG,GC,CC		27.4767,21.9246,25.5959	benign,benign,benign,benign,benign,benign	103/220,103/232,103/173,103/107,103/149,103/107	5326145	3329,9677	2203	4300	6503	SO:0001631	upstream_gene_variant	84268	exon3			GATCAACCAAGGT	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453		17.37:g.5326145C>G	Exception_encountered	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_001160246	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	944	0.43223443223443225	104	0.21138211382113822	138	0.3812154696132597	463	0.8094405594405595	239	0.3153034300791557	C	0.013	-1.639801	0.00799	0.219246	0.274767	ENSG00000129197	ENST00000381209;ENST00000381208;ENST00000539417;ENST00000536255;ENST00000405578;ENST00000540734;ENST00000327154	T;T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06;1.06	5.52	-6.47	0.01902	.	1.010540	0.07896	N	0.971857	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B;B;B	0.19817	0.002;0.002;0.039;0.022	B;B;B;B	0.18871	0.01;0.008;0.023;0.023	T	0.40813	-0.9543	8	0.07030	T	0.85	-7.9814	1.9952	0.03455	0.2026:0.1488:0.4018:0.2468	rs12761;rs1131190;rs2189335;rs11549501;rs17343146;rs17357256;rs17636530;rs17854726;rs59730384;rs2189335	103;103;103;103	F5GYE1;F5H3Q7;E9PES3;E9PDG9	.;.;.;.	K	103	ENSP00000370606:N103K;ENSP00000370605:N103K;ENSP00000446453:N103K;ENSP00000439939:N103K;ENSP00000385814:N103K;ENSP00000315069:N103K	ENSP00000315069:N103K	N	+	3	2	RPAIN	5266869	0.000000	0.05858	0.015000	0.15790	0.058000	0.15608	-1.251000	0.02882	-0.952000	0.03649	-1.253000	0.01494	AAC	C|0.669;G|0.330	0.330	strong		0.448	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047857	46047857	+	Missense_Mutation	SNP	C	C	T	rs9980129	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46047857C>T	ENST00000397911.3	+	1	818	c.769C>T	c.(769-771)Cgc>Tgc	p.R257C	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	257			R -> C (in dbSNP:rs9980129). {ECO:0000269|PubMed:14962103, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CACCTCCTCCCGCCAGCCCAG	0.692													T|||	3138	0.626597	0.5076	0.6744	5008	,	,		18439	0.6488		0.7068	False		,,,				2504	0.6483				p.R257C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.C769T						PASS	.	T	,CYS/ARG	2317,2085	528.4+/-372.4	626,1065,510	61.0	78.0	72.0		,769	1.2	1.0	21	dbSNP_119	72	5788,2798	430.3+/-356.5	1953,1882,458	yes	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,180	2579,2947,968	TT,TC,CC		32.5879,47.3648,37.5962	,benign	,257/293	46047857	8105,4883	2201	4293	6494	SO:0001583	missense	386676	exon1			TCCTCCCGCCAGC	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.769C>T	21.37:g.46047857C>T	ENSP00000381009:p.Arg257Cys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	121	50	0.413223	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	1384	0.6336996336996337	252	0.5121951219512195	245	0.6767955801104972	353	0.6171328671328671	534	0.7044854881266491	t	0.033	-1.322386	0.01320	0.526352	0.674121	ENSG00000221837	ENST00000397911	T	0.00635	6.06	2.6	1.24	0.21308	.	.	.	.	.	T	0.00012	0.0000	N	0.00043	-2.465	0.36089	P	0.15666400000000003	B	0.20052	0.041	B	0.18871	0.023	T	0.06935	-1.0799	7	.	.	.	.	3.9932	0.09546	0.0:0.1389:0.2108:0.6503	rs9980129	257	P60411	KR109_HUMAN	C	257	ENSP00000381009:R257C	.	R	+	1	0	KRTAP10-9	44872285	0.190000	0.23276	0.997000	0.53966	0.734000	0.41952	0.165000	0.16564	0.229000	0.21039	-0.360000	0.07572	CGC	C|0.352;T|0.648	0.648	strong		0.692	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
TRABD2A	129293	hgsc.bcm.edu	37	2	85051122	85051122	+	Missense_Mutation	SNP	G	G	A	rs1649292	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85051122G>A	ENST00000409520.2	-	6	1331	c.1289C>T	c.(1288-1290)cCg>cTg	p.P430L	TRABD2A_ENST00000335459.5_Missense_Mutation_p.P381L|TRABD2A_ENST00000479944.1_5'UTR	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	430			P -> L (in dbSNP:rs1649292).		head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										CCGGAGTCGCGGCCTCCGCTG	0.652													g|||	778	0.155351	0.2103	0.2032	5008	,	,		16920	0.1141		0.1352	False		,,,				2504	0.1104				p.R381L		Atlas-SNP	.											.	.	.	.	0			c.G1142T						PASS	.		LEU/PRO	966,3438	332.0+/-302.3	117,732,1353	36.0	42.0	40.0		1142	2.4	0.0	2	dbSNP_89	40	1245,7355	239.9+/-270.8	82,1081,3137	yes	missense	C2orf89	NM_001080824.1	98	199,1813,4490	AA,AG,GG		14.4767,21.9346,17.0025	benign	381/457	85051122	2211,10793	2202	4300	6502	SO:0001583	missense	129293	exon5			AGTCGCGGCCTCC	BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"""chromosome 2 open reading frame 89"""	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.1289C>T	2.37:g.85051122G>A	ENSP00000387075:p.Pro430Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	70	54	0.771429	NM_001080824	B4DKK8|I6UMB9	Missense_Mutation	SNP	ENST00000409520.2	37		348	0.15934065934065933	100	0.2032520325203252	66	0.18232044198895028	72	0.1258741258741259	110	0.14511873350923482	g	11.01	1.511788	0.27036	0.219346	0.144767	ENSG00000186854	ENST00000335459;ENST00000409520	T;T	0.23348	1.91;1.95	3.6	2.37	0.29283	.	1.238030	0.06061	N	0.658445	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.20988	0.05;0.043	B;B	0.14023	0.003;0.01	T	0.27297	-1.0078	8	0.56958	D	0.05	.	7.8423	0.29406	0.0:0.0:0.42:0.58	rs1649292;rs57067301;rs1649292	430;381	Q86V40;Q86V40-2	CB089_HUMAN;.	L	381;430	ENSP00000335004:P381L;ENSP00000387075:P430L	ENSP00000335004:P381L	P	-	2	0	C2orf89	84904633	0.005000	0.15991	0.001000	0.08648	0.193000	0.23685	0.081000	0.14823	0.098000	0.17522	-1.316000	0.01300	CCG	G|0.843;A|0.157	0.157	strong		0.652	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824	
NKX1-2	390010	hgsc.bcm.edu	37	10	126136112	126136112	+	Silent	SNP	A	A	G	rs7075981|rs386748536	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:126136112A>G	ENST00000451024.3	-	2	1059	c.819T>C	c.(817-819)aaT>aaC	p.N273N	RP13-238F13.5_ENST00000602332.1_lincRNA|NKX1-2_ENST00000440536.2_Silent_p.N295N|RP13-238F13.3_ENST00000604581.1_RNA	NM_001146340.1	NP_001139812.1	Q9UD57	NKX12_HUMAN	NK1 homeobox 2	273					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)										GGAAGAGGACATTGGCCGCGG	0.741													G|||	937	0.187101	0.3154	0.1167	5008	,	,		9188	0.1012		0.173	False		,,,				2504	0.1667				p.N273N		Atlas-SNP	.											NKX1-2_ENST00000440536,NS,carcinoma,0,2	NKX1-2	6	2	0			c.T819C						PASS	.	G		385,999		58,269,365	42.0	66.0	59.0		819	2.1	1.0	10	dbSNP_116	59	438,2744		33,372,1186	no	coding-synonymous	NKX1-2	NM_001146340.1		91,641,1551	GG,GA,AA		13.7649,27.8179,18.0245		273/311	126136112	823,3743	692	1591	2283	SO:0001819	synonymous_variant	390010	exon2			GAGGACATTGGCC	CN285329	CCDS59221.1	10q26.13	2012-03-09	2007-07-09	2006-06-29		ENSG00000229544		"""Homeoboxes / ANTP class : NKL subclass"""	31652	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 121"", ""NK1 transcription factor related, locus 2 (Drosophila)"""	C10orf121		10681422	Standard	NM_001146340		Approved	bB238F13.2	uc010quf.2	Q9UD57		ENST00000451024.3:c.819T>C	10.37:g.126136112A>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_001146340		Silent	SNP	ENST00000451024.3	37	CCDS59221.1																																																																																			A|0.824;G|0.176	0.176	strong		0.741	NKX1-2-001	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050861.3	XM_372331	
SP140L	93349	hgsc.bcm.edu	37	2	231222675	231222675	+	Missense_Mutation	SNP	T	T	C	rs4973318	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:231222675T>C	ENST00000415673.2	+	3	349	c.263T>C	c.(262-264)aTg>aCg	p.M88T	SP140L_ENST00000243810.6_Missense_Mutation_p.M88T|SP140L_ENST00000444636.1_Missense_Mutation_p.M88T|SP140L_ENST00000458341.1_Start_Codon_SNP_p.M1T|SP140_ENST00000486687.2_3'UTR|SP140L_ENST00000396563.4_Missense_Mutation_p.M88T	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	88	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.		M -> T (in dbSNP:rs4973318).			nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						ACAAATAAAATGTTTGAAGTA	0.363													T|||	414	0.0826677	0.0098	0.121	5008	,	,		20932	0.1042		0.1252	False		,,,				2504	0.0879				p.M88T		Atlas-SNP	.											.	SP140L	68	.	0			c.T263C						PASS	.	T	THR/MET	96,4192		0,96,2048	117.0	126.0	123.0		263	2.2	0.4	2	dbSNP_111	123	1016,7550		64,888,3331	yes	missense	SP140L	NM_138402.4	81	64,984,5379	CC,CT,TT		11.8608,2.2388,8.651	possibly-damaging	88/581	231222675	1112,11742	2144	4283	6427	SO:0001583	missense	93349	exon3			ATAAAATGTTTGA	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.263T>C	2.37:g.231222675T>C	ENSP00000397911:p.Met88Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	199	0.09111721611721611	6	0.012195121951219513	45	0.12430939226519337	61	0.10664335664335664	87	0.11477572559366754	T	8.718	0.913676	0.17907	0.022388	0.118608	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563;ENST00000458341	D;D;D;D;D	0.94793	-3.52;-3.52;-3.52;-3.52;-3.52	3.36	2.19	0.27852	.	.	.	.	.	T	0.29321	0.0730	M	0.79926	2.475	0.58432	P	1.0000000000287557E-6	P;B	0.45011	0.848;0.123	P;B	0.50231	0.635;0.026	T	0.70124	-0.4958	8	0.62326	D	0.03	.	5.4578	0.16600	0.0:0.1412:0.0:0.8588	rs4973318;rs52807436;rs59203650;rs4973318	1;88	Q9H930-3;Q9H930-4	.;.	T	88;88;88;88;1	ENSP00000395195:M88T;ENSP00000397911:M88T;ENSP00000243810:M88T;ENSP00000379811:M88T;ENSP00000395223:M1T	ENSP00000243810:M88T	M	+	2	0	SP140L	230930919	0.339000	0.24784	0.403000	0.26384	0.260000	0.26232	1.100000	0.31025	0.460000	0.27045	0.397000	0.26171	ATG	T|0.905;C|0.095	0.095	strong		0.363	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
AQP5	362	hgsc.bcm.edu	37	12	50358888	50358888	+	Silent	SNP	G	G	A	rs41308104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:50358888G>A	ENST00000293599.6	+	4	874	c.726G>A	c.(724-726)acG>acA	p.T242T	RP11-469H8.6_ENST00000550530.1_RNA|RP11-469H8.6_ENST00000550214.1_RNA|AQP6_ENST00000551733.1_5'Flank|RP11-469H8.6_ENST00000552379.1_RNA	NM_001651.2	NP_001642.1	P55064	AQP5_HUMAN	aquaporin 5	242					camera-type eye morphogenesis (GO:0048593)|carbon dioxide transport (GO:0015670)|excretion (GO:0007588)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)			large_intestine(1)|lung(3)	4						TCAAAGGCACGTATGAGCCTG	0.627													G|||	25	0.00499201	0.0015	0.0086	5008	,	,		15752	0.0		0.0169	False		,,,				2504	0.0				p.T242T		Atlas-SNP	.											.	AQP5	19	.	0			c.G726A						PASS	.	G		20,4386	28.1+/-56.4	0,20,2183	98.0	82.0	87.0		726	-10.5	0.6	12	dbSNP_127	87	156,8444	75.4+/-138.0	1,154,4145	no	coding-synonymous	AQP5	NM_001651.2		1,174,6328	AA,AG,GG		1.814,0.4539,1.3532		242/266	50358888	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	362	exon4			AGGCACGTATGAG	U46569	CCDS8793.1	12q13	2013-09-10				ENSG00000161798		"""Ion channels / Aquaporins"""	638	protein-coding gene	gene with protein product		600442				8621489, 23830519	Standard	NM_001651		Approved		uc001rvo.3	P55064	OTTHUMG00000169710	ENST00000293599.6:c.726G>A	12.37:g.50358888G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_001651	Q6FGW8	Silent	SNP	ENST00000293599.6	37	CCDS8793.1																																																																																			G|0.988;A|0.012	0.012	strong		0.627	AQP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405542.2	NM_001651	
PLCB1	23236	hgsc.bcm.edu	37	20	8717713	8717713	+	Silent	SNP	G	G	A	rs3761170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:8717713G>A	ENST00000338037.6	+	20	2109	c.2082G>A	c.(2080-2082)ggG>ggA	p.G694G	PLCB1_ENST00000378641.3_Silent_p.G694G|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Silent_p.G694G	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	694	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						AGAAAGTTGGGACTTACGTGG	0.358													G|||	497	0.0992412	0.0371	0.0821	5008	,	,		17801	0.1349		0.0765	False		,,,				2504	0.182				p.Q694Q		Atlas-SNP	.											.	PLCB1	394	.	0			c.G2082A						PASS	.	G	,	168,4238	111.6+/-149.8	2,164,2037	113.0	110.0	111.0		2082,2082	-0.4	1.0	20	dbSNP_107	111	578,8022	154.0+/-208.3	15,548,3737	no	coding-synonymous,coding-synonymous	PLCB1	NM_015192.2,NM_182734.1	,	17,712,5774	AA,AG,GG		6.7209,3.813,5.7358	,	694/1217,694/1174	8717713	746,12260	2203	4300	6503	SO:0001819	synonymous_variant	23236	exon20			AGTTGGGACTTAC	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2082G>A	20.37:g.8717713G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			G|0.932;A|0.068	0.068	strong		0.358	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
SOCS7	30837	hgsc.bcm.edu	37	17	36552190	36552190	+	Missense_Mutation	SNP	A	A	G	rs55687042	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:36552190A>G	ENST00000577233.1	+	9	1715	c.1715A>G	c.(1714-1716)aAa>aGa	p.K572R	SOCS7_ENST00000331159.5_Missense_Mutation_p.K538R	NM_014598.2	NP_055413.1	O14512	SOCS7_HUMAN	suppressor of cytokine signaling 7	572					fat cell differentiation (GO:0045444)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of signal transduction (GO:0009968)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	SH3 domain binding (GO:0017124)			central_nervous_system(1)|endometrium(1)|kidney(1)|prostate(1)|skin(5)	9	Breast(7;3.47e-17)					CTCATTTCCAAACAGAAGCAA	0.502													A|||	66	0.0131789	0.0008	0.0159	5008	,	,		18836	0.001		0.0348	False		,,,				2504	0.0184				p.K572R		Atlas-SNP	.											.	SOCS7	22	.	0			c.A1715G						PASS	.	A	ARG/LYS	37,4369	40.8+/-73.8	0,37,2166	61.0	59.0	60.0		1715	5.9	1.0	17	dbSNP_129	60	381,8219	124.3+/-183.0	6,369,3925	yes	missense	SOCS7	NM_014598.2	26	6,406,6091	GG,GA,AA		4.4302,0.8398,3.2139	benign	572/582	36552190	418,12588	2203	4300	6503	SO:0001583	missense	30837	exon9			TTTCCAAACAGAA	AB005216	CCDS32637.1	17q12	2014-08-12			ENSG00000274211	ENSG00000274211		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	29846	protein-coding gene	gene with protein product	"""Nck, Ash and phospholipase C binding protein"", ""NCK-associated protein 4"""	608788				9344857, 12076535	Standard	XM_005257264		Approved	NAP4, NCKAP4	uc002hqa.3	O14512	OTTHUMG00000188546	ENST00000577233.1:c.1715A>G	17.37:g.36552190A>G	ENSP00000464034:p.Lys572Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_014598	A2VCU2|Q0IJ63	Missense_Mutation	SNP	ENST00000577233.1	37	CCDS32637.1	38	0.0173992673992674	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	29	0.03825857519788918	A	13.56	2.274571	0.40194	0.008398	0.044302	ENSG00000174111	ENST00000331159	.	.	.	5.93	5.93	0.95920	.	0.208574	0.41396	D	0.000884	T	0.06142	0.0159	N	0.14661	0.345	0.32131	N	0.586711	P;P	0.44734	0.842;0.842	B;B	0.34536	0.185;0.185	T	0.07986	-1.0744	9	0.31617	T	0.26	-8.9747	15.3769	0.74615	1.0:0.0:0.0:0.0	rs55687042;rs61746210	288;572	B5MDS8;O14512	.;SOCS7_HUMAN	R	572	.	ENSP00000330659:K572R	K	+	2	0	SOCS7	33805716	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.180000	0.50895	2.281000	0.76405	0.533000	0.62120	AAA	A|0.971;G|0.029	0.029	strong		0.502	SOCS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440486.4	XM_371052	
TCOF1	6949	hgsc.bcm.edu	37	5	149755340	149755340	+	Silent	SNP	G	G	T	rs7701163	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149755340G>T	ENST00000504761.2	+	12	1761	c.1761G>T	c.(1759-1761)ggG>ggT	p.G587G	TCOF1_ENST00000377797.3_Silent_p.G587G|TCOF1_ENST00000513346.1_Silent_p.G587G|TCOF1_ENST00000394269.3_Silent_p.G587G|TCOF1_ENST00000451292.1_Silent_p.G587G|TCOF1_ENST00000445265.2_Silent_p.G510G|TCOF1_ENST00000439160.2_Silent_p.G587G|TCOF1_ENST00000323668.7_Silent_p.G510G			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	587					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGCCAAGGGGCCCCCTCAGA	0.612													G|||	363	0.072484	0.1415	0.0548	5008	,	,		18897	0.0228		0.0636	False		,,,				2504	0.0521				p.G587G		Atlas-SNP	.											.	TCOF1	154	.	0			c.G1761T						PASS	.	G	,,,,,	654,3752	271.9+/-270.5	48,558,1597	86.0	98.0	94.0		1530,1761,1761,1761,1530,1761	-9.9	0.0	5	dbSNP_116	94	658,7942	163.5+/-216.0	18,622,3660	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	,,,,,	66,1180,5257	TT,TG,GG		7.6512,14.8434,10.0877	,,,,,	510/1412,587/959,587/1489,587/1452,510/1413,587/1451	149755340	1312,11694	2203	4300	6503	SO:0001819	synonymous_variant	6949	exon12			CAAGGGGCCCCCT		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.1761G>T	5.37:g.149755340G>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Silent	SNP	ENST00000504761.2	37	CCDS54936.1																																																																																			G|0.910;T|0.090	0.090	strong		0.612	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
SMC6	79677	hgsc.bcm.edu	37	2	17884495	17884495	+	Missense_Mutation	SNP	C	C	T	rs1065381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:17884495C>T	ENST00000448223.2	-	19	2340	c.2071G>A	c.(2071-2073)Gcc>Acc	p.A691T	SMC6_ENST00000402989.1_Missense_Mutation_p.A691T|SMC6_ENST00000351948.4_Missense_Mutation_p.A691T|SMC6_ENST00000381272.4_Missense_Mutation_p.A717T	NM_001142286.1	NP_001135758.1	Q96SB8	SMC6_HUMAN	structural maintenance of chromosomes 6	691			A -> T (in dbSNP:rs1065381). {ECO:0000269|PubMed:11408570, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular senescence (GO:0090398)|double-strand break repair via homologous recombination (GO:0000724)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|intracellular (GO:0005622)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|Smc5-Smc6 complex (GO:0030915)	ATP binding (GO:0005524)			NS(1)|biliary_tract(1)|breast(6)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TTTTCAAGGGCAGATAAATGT	0.299													C|||	1034	0.20647	0.3548	0.2161	5008	,	,		14389	0.0119		0.3241	False		,,,				2504	0.0787				p.A691T		Atlas-SNP	.											.	SMC6	102	.	0			c.G2071A						PASS	.	C	THR/ALA,THR/ALA	1395,3009	438.0+/-345.2	215,965,1022	78.0	82.0	81.0		2071,2071	1.5	1.0	2	dbSNP_86	81	2866,5730	447.2+/-361.5	471,1924,1903	yes	missense,missense	SMC6	NM_001142286.1,NM_024624.5	58,58	686,2889,2925	TT,TC,CC		33.3411,31.6757,32.7769	benign,benign	691/1092,691/1092	17884495	4261,8739	2202	4298	6500	SO:0001583	missense	79677	exon19			CAAGGGCAGATAA	AJ310551	CCDS1690.1	2p24.3	2008-02-05	2006-07-06	2006-07-06	ENSG00000163029	ENSG00000163029		"""Structural maintenance of chromosomes proteins"""	20466	protein-coding gene	gene with protein product		609387	"""SMC6 structural maintenance of chromosomes 6-like 1 (yeast)"""	SMC6L1		11230166	Standard	NM_024624		Approved	FLJ22116	uc002rcn.3	Q96SB8	OTTHUMG00000090675	ENST00000448223.2:c.2071G>A	2.37:g.17884495C>T	ENSP00000404092:p.Ala691Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_001142286	A8K8Q6|D6W518|Q05BV4|Q9H0X3|Q9H6M0	Missense_Mutation	SNP	ENST00000448223.2	37	CCDS1690.1	492	0.22527472527472528	153	0.31097560975609756	89	0.24585635359116023	12	0.02097902097902098	238	0.31398416886543534	C	9.006	0.981245	0.18812	0.316757	0.333411	ENSG00000163029	ENST00000448223;ENST00000351948;ENST00000381272;ENST00000402989;ENST00000446852	T;T;T;T;T	0.31769	1.57;1.57;1.57;1.57;1.48	5.75	1.55	0.23275	RecF/RecN/SMC (1);	0.528124	0.23204	N	0.050752	T	0.00012	0.0000	N	0.08118	0	0.39475	P	0.032214999999999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.002;0.003;0.002	T	0.46830	-0.9163	9	0.16420	T	0.52	.	4.2671	0.10768	0.2883:0.4449:0.0:0.2668	rs1065381;rs52791607;rs57702280;rs1065381	717;717;691	C9JMN1;Q96SB8-2;Q96SB8	.;.;SMC6_HUMAN	T	691;691;717;691;717	ENSP00000404092:A691T;ENSP00000323439:A691T;ENSP00000370672:A717T;ENSP00000384539:A691T;ENSP00000408644:A717T	ENSP00000323439:A691T	A	-	1	0	SMC6	17747976	1.000000	0.71417	0.990000	0.47175	0.186000	0.23388	0.736000	0.26130	0.371000	0.24564	0.579000	0.79373	GCC	C|0.738;T|0.262	0.262	strong		0.299	SMC6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207359.1	NM_024624	
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 GAIIx	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_ENST00000492028.1_5'UTR|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.V713I|ARHGAP12_ENST00000396144.4_Missense_Mutation_p.V760I|ARHGAP12_ENST00000375245.4_Missense_Mutation_p.V713I|ARHGAP12_ENST00000375250.5_Missense_Mutation_p.V735I	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	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	31	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		
ZNF750	79755	hgsc.bcm.edu	37	17	80788492	80788492	+	Silent	SNP	A	A	G	rs12948179	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:80788492A>G	ENST00000269394.3	-	3	2531	c.1698T>C	c.(1696-1698)ccT>ccC	p.P566P	TBCD_ENST00000355528.4_Intron|TBCD_ENST00000397466.2_Intron|ZNF750_ENST00000572562.1_Silent_p.P167P|TBCD_ENST00000539345.2_Intron	NM_024702.2	NP_078978.2	Q32MQ0	ZN750_HUMAN	zinc finger protein 750	566					cell differentiation (GO:0030154)|epidermis development (GO:0008544)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	31	Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0514)|all_epithelial(8;0.0748)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.149)			CGGGGAAGGCAGGCCTCGGAG	0.622													A|||	1848	0.36901	0.4009	0.3343	5008	,	,		15937	0.3512		0.4205	False		,,,				2504	0.316				p.P566P		Atlas-SNP	.											.	ZNF750	60	.	0			c.T1698C						PASS	.	A	,	1774,2632	517.3+/-369.4	367,1040,796	61.0	66.0	64.0		,1698	-9.3	0.0	17	dbSNP_121	64	3535,5065	508.2+/-377.0	715,2105,1480	no	intron,coding-synonymous	TBCD,ZNF750	NM_005993.4,NM_024702.2	,	1082,3145,2276	GG,GA,AA		41.1047,40.2633,40.8196	,	,566/724	80788492	5309,7697	2203	4300	6503	SO:0001819	synonymous_variant	79755	exon3			GAAGGCAGGCCTC	AK023903	CCDS11819.1	17q25.3	2008-05-02				ENSG00000141579			25843	protein-coding gene	gene with protein product		610226				16751772	Standard	NM_024702		Approved	FLJ13841, Zfp750	uc002kga.3	Q32MQ0		ENST00000269394.3:c.1698T>C	17.37:g.80788492A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_024702	Q9H899	Silent	SNP	ENST00000269394.3	37	CCDS11819.1																																																																																			A|0.595;G|0.405	0.405	strong		0.622	ZNF750-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439074.2	NM_024702	
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 GAIIx	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	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	158	64	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	
ITPR3	3710	hgsc.bcm.edu	37	6	33648144	33648144	+	Silent	SNP	C	C	T	rs11967839	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33648144C>T	ENST00000374316.5	+	33	5323	c.4263C>T	c.(4261-4263)taC>taT	p.Y1421Y	ITPR3_ENST00000605930.1_Silent_p.Y1421Y			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1421					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	ACCACTGCTACGTGGACACGG	0.607													C|||	572	0.114217	0.2958	0.0375	5008	,	,		16528	0.0585		0.0447	False		,,,				2504	0.0521				p.Y1421Y		Atlas-SNP	.											.	ITPR3	409	.	0			c.C4263T						PASS	.	C		1037,3369	382.3+/-324.4	121,795,1287	63.0	57.0	59.0		4263	-4.0	0.9	6	dbSNP_120	59	392,8208	126.5+/-185.0	11,370,3919	no	coding-synonymous	ITPR3	NM_002224.3		132,1165,5206	TT,TC,CC		4.5581,23.5361,10.9872		1421/2672	33648144	1429,11577	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon32			CTGCTACGTGGAC	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.4263C>T	6.37:g.33648144C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	63	16	0.253968	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.890;T|0.110	0.110	strong		0.607	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
HOXB13	10481	hgsc.bcm.edu	37	17	46805590	46805590	+	Silent	SNP	G	G	A	rs8556	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:46805590G>A	ENST00000290295.7	-	1	950	c.366C>T	c.(364-366)agC>agT	p.S122S	PRAC2_ENST00000422730.2_RNA	NM_006361.5	NP_006352.2	Q92826	HXB13_HUMAN	homeobox B13	122					angiogenesis (GO:0001525)|epidermis development (GO:0008544)|epithelial cell maturation involved in prostate gland development (GO:0060743)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|response to testosterone (GO:0033574)|response to wounding (GO:0009611)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|lung(6)|prostate(1)	11						CAGTGGGGCGGCTGGGGTACT	0.657													G|||	879	0.175519	0.3139	0.0908	5008	,	,		14940	0.0327		0.1262	False		,,,				2504	0.2464				p.S122S		Atlas-SNP	.											.	HOXB13	28	.	0			c.C366T						PASS	.	G		1156,3250	408.4+/-334.6	162,832,1209	80.0	92.0	88.0		366	1.5	1.0	17	dbSNP_52	88	1136,7464	233.6+/-266.8	76,984,3240	no	coding-synonymous	HOXB13	NM_006361.5		238,1816,4449	AA,AG,GG		13.2093,26.2369,17.6226		122/285	46805590	2292,10714	2203	4300	6503	SO:0001819	synonymous_variant	10481	exon1			GGGGCGGCTGGGG	U57052	CCDS11536.1	17q21.32	2014-09-17	2005-12-22		ENSG00000159184	ENSG00000159184		"""Homeoboxes / ANTP class : HOXL subclass"""	5112	protein-coding gene	gene with protein product		604607	"""homeo box B13"""			8756292, 9665387	Standard	NM_006361		Approved		uc002ioa.3	Q92826	OTTHUMG00000159900	ENST00000290295.7:c.366C>T	17.37:g.46805590G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_006361	B2R878|Q96QM4|Q99810	Silent	SNP	ENST00000290295.7	37	CCDS11536.1																																																																																			G|0.835;A|0.165	0.165	strong		0.657	HOXB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358087.3	NM_006361	
DDX18	8886	hgsc.bcm.edu	37	2	118575215	118575215	+	Missense_Mutation	SNP	C	C	G	rs1052637	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:118575215C>G	ENST00000263239.2	+	2	409	c.281C>G	c.(280-282)aCc>aGc	p.T94S	DDX18_ENST00000474694.1_3'UTR	NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	94			T -> S (in dbSNP:rs1052637). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ACTGTATTAACCAATGGAGAA	0.373													C|||	2138	0.426917	0.6263	0.3602	5008	,	,		17432	0.2282		0.3688	False		,,,				2504	0.4693				p.T94S		Atlas-SNP	.											.	DDX18	79	.	0			c.C281G						PASS	.	C	SER/THR	2550,1854	590.2+/-387.3	739,1072,391	87.0	100.0	95.0		281	2.2	0.8	2	dbSNP_86	95	3143,5457	463.4+/-366.0	574,1995,1731	yes	missense	DDX18	NM_006773.3	58	1313,3067,2122	GG,GC,CC		36.5465,42.0981,43.7788	benign	94/671	118575215	5693,7311	2202	4300	6502	SO:0001583	missense	8886	exon2			TATTAACCAATGG	X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"""DEAD-boxes"""	2741	protein-coding gene	gene with protein product		606355	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"""			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.281C>G	2.37:g.118575215C>G	ENSP00000263239:p.Thr94Ser	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_006773	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Missense_Mutation	SNP	ENST00000263239.2	37	CCDS2120.1	829	0.37957875457875456	299	0.6077235772357723	126	0.34806629834254144	123	0.21503496503496503	281	0.370712401055409	C	5.931	0.355794	0.11239	0.579019	0.365465	ENSG00000088205	ENST00000263239	T	0.21031	2.03	4.01	2.2	0.27929	.	2.399920	0.01794	N	0.032491	T	0.00012	0.0000	L	0.56769	1.78	0.44539	P	0.002507000000000037	B	0.17038	0.02	B	0.11329	0.006	T	0.47873	-0.9083	9	0.05959	T	0.93	-3.7378	6.2096	0.20621	0.0:0.7687:0.0:0.2313	rs1052637;rs1583331;rs2070147;rs3171830;rs16897521;rs17852239;rs17857615;rs17857732;rs52829447;rs60628909;rs1052637	94	Q9NVP1	DDX18_HUMAN	S	94	ENSP00000263239:T94S	ENSP00000263239:T94S	T	+	2	0	DDX18	118291685	0.055000	0.20627	0.842000	0.33263	0.713000	0.41058	0.094000	0.15107	0.480000	0.27534	0.655000	0.94253	ACC	C|0.601;G|0.399	0.399	strong		0.373	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773	
CTXN3	613212	hgsc.bcm.edu	37	5	126993263	126993263	+	Missense_Mutation	SNP	A	A	T	rs248709|rs386692235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:126993263A>T	ENST00000379445.3	+	3	601	c.50A>T	c.(49-51)gAa>gTa	p.E17V	CTC-548H10.2_ENST00000512352.1_RNA|CTXN3_ENST00000395322.3_Missense_Mutation_p.E17V	NM_001048252.2	NP_001041717.1	Q4LDR2	CTXN3_HUMAN	cortexin 3	17			E -> V (in dbSNP:rs248709). {ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		CTTGGGAACGAATCAGCAGAT	0.483													T|||	3272	0.653355	0.7678	0.6037	5008	,	,		21019	0.6141		0.6551	False		,,,				2504	0.5726				p.E17V		Atlas-SNP	.											.	CTXN3	19	.	0			c.A50T						PASS	.	T	VAL/GLU,VAL/GLU	3389,1017	377.3+/-322.4	1310,769,124	129.0	111.0	117.0		50,50	-4.2	0.0	5	dbSNP_79	117	5785,2815	446.0+/-361.1	1929,1927,444	yes	missense,missense	CTXN3	NM_001048252.2,NM_001127385.1	121,121	3239,2696,568	TT,TA,AA		32.7326,23.0822,29.4633	benign,benign	17/82,17/82	126993263	9174,3832	2203	4300	6503	SO:0001583	missense	613212	exon3			GGAACGAATCAGC	AB219764	CCDS34221.1	5q23.2	2006-09-21				ENSG00000205279			31110	protein-coding gene	gene with protein product							Standard	NM_001048252		Approved		uc003kum.4	Q4LDR2		ENST00000379445.3:c.50A>T	5.37:g.126993263A>T	ENSP00000368758:p.Glu17Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_001048252	B2RV32|D3DQ82	Missense_Mutation	SNP	ENST00000379445.3	37	CCDS34221.1	1437	0.657967032967033	372	0.7560975609756098	230	0.6353591160220995	347	0.6066433566433567	488	0.6437994722955145	T	9.693	1.152390	0.21371	0.769178	0.672674	ENSG00000205279	ENST00000379445;ENST00000395322	T;T	0.31510	1.49;1.49	4.52	-4.23	0.03789	.	1.776230	0.02356	N	0.076391	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34875	-0.9811	8	0.25106	T	0.35	0.374	5.0489	0.14497	0.1027:0.4831:0.1095:0.3047	rs248709;rs56900329;rs248709	17	Q4LDR2	CTXN3_HUMAN	V	17	ENSP00000368758:E17V;ENSP00000378732:E17V	ENSP00000368758:E17V	E	+	2	0	CTXN3	127021162	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.449000	0.06812	-1.231000	0.02557	-0.257000	0.10917	GAA	A|0.308;T|0.692	0.692	strong		0.483	CTXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372467.1	XM_932841	
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 GAIIx	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		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	124	13	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	
PDIA2	64714	hgsc.bcm.edu	37	16	334580	334580	+	Silent	SNP	G	G	C	rs432925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:334580G>C	ENST00000219406.6	+	2	411	c.393G>C	c.(391-393)ccG>ccC	p.P131P	PDIA2_ENST00000404312.1_Silent_p.P131P	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	131	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				GCACGCACCCGGAGGAGTACA	0.677													g|||	1234	0.246406	0.32	0.2089	5008	,	,		15702	0.119		0.2913	False		,,,				2504	0.2587				p.P131P		Atlas-SNP	.											.	PDIA2	51	.	0			c.G393C						PASS	.	G		1233,3005		191,851,1077	34.0	40.0	38.0		393	-8.9	0.4	16	dbSNP_80	38	2417,6025		353,1711,2157	no	coding-synonymous	PDIA2	NM_006849.2		544,2562,3234	CC,CG,GG		28.6307,29.0939,28.7855		131/526	334580	3650,9030	2119	4221	6340	SO:0001819	synonymous_variant	64714	exon2			GCACCCGGAGGAG	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"""Protein disulfide isomerases"""	14180	protein-coding gene	gene with protein product		608012	"""protein disulfide isomerase, pancreatic"", ""protein disulfide isomerase-associated 2"""	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.393G>C	16.37:g.334580G>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Silent	SNP	ENST00000219406.6	37	CCDS42089.1	508	0.2326007326007326	142	0.2886178861788618	81	0.22375690607734808	69	0.12062937062937062	216	0.2849604221635884	g	0.088	-1.171117	0.01660	0.290939	0.286307	ENSG00000185615	ENST00000456379	.	.	.	4.47	-8.93	0.00771	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999673342	.	.	.	.	.	.	T	0.20840	-1.0263	3	.	.	.	.	2.4162	0.04437	0.1433:0.1924:0.3952:0.2691	rs432925	.	.	.	P	128	.	.	R	+	2	0	PDIA2	274581	0.000000	0.05858	0.433000	0.26760	0.013000	0.08279	-1.350000	0.02624	-2.615000	0.00443	-1.077000	0.02231	CGG	G|0.756;C|0.244	0.244	strong		0.677	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
ESPNL	339768	hgsc.bcm.edu	37	2	239040343	239040343	+	Silent	SNP	G	G	A	rs73102311	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:239040343G>A	ENST00000343063.3	+	9	3251	c.2988G>A	c.(2986-2988)aaG>aaA	p.K996K	ESPNL_ENST00000409169.1_Silent_p.K952K|ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Silent_p.K628K	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	996										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGAAGGAGAAGGAAGCTGAGA	0.547													G|||	429	0.0856629	0.0923	0.062	5008	,	,		19468	0.0546		0.0915	False		,,,				2504	0.1196				p.K996K		Atlas-SNP	.											.	ESPNL	63	.	0			c.G2988A						PASS	.	G		379,4025	183.3+/-210.9	17,345,1840	70.0	75.0	74.0		2988	-4.2	0.9	2	dbSNP_130	74	763,7837	181.0+/-229.8	35,693,3572	no	coding-synonymous	ESPNL	NM_194312.2		52,1038,5412	AA,AG,GG		8.8721,8.6058,8.7819		996/1006	239040343	1142,11862	2202	4300	6502	SO:0001819	synonymous_variant	339768	exon9			GGAGAAGGAAGCT	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2988G>A	2.37:g.239040343G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			G|0.914;A|0.086	0.086	strong		0.547	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
HPS3	84343	hgsc.bcm.edu	37	3	148881673	148881673	+	Silent	SNP	C	C	T	rs3732557	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:148881673C>T	ENST00000296051.2	+	14	2666	c.2526C>T	c.(2524-2526)caC>caT	p.H842H	HPS3_ENST00000460120.1_Silent_p.H677H	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	842					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CATGGGTTCACGTCGTAATAT	0.279									Hermansky-Pudlak syndrome				C|||	778	0.155351	0.0136	0.1441	5008	,	,		17878	0.2738		0.1799	False		,,,				2504	0.2076				p.H842H		Atlas-SNP	.											.	HPS3	104	.	0			c.C2526T						PASS	.	C		201,4203	120.4+/-158.0	4,193,2005	79.0	78.0	78.0		2526	-2.1	0.1	3	dbSNP_107	78	1627,6969	298.1+/-303.7	162,1303,2833	no	coding-synonymous	HPS3	NM_032383.3		166,1496,4838	TT,TC,CC		18.9274,4.564,14.0615		842/1005	148881673	1828,11172	2202	4298	6500	SO:0001819	synonymous_variant	84343	exon14	Familial Cancer Database	HPS, HPS1-8	GGTTCACGTCGTA	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2526C>T	3.37:g.148881673C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	37	CCDS3140.1																																																																																			C|0.849;T|0.151	0.151	strong		0.279	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
CRTAC1	55118	hgsc.bcm.edu	37	10	99625319	99625319	+	Missense_Mutation	SNP	C	C	T	rs56007204	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:99625319C>T	ENST00000370597.3	-	15	2327	c.1972G>A	c.(1972-1974)Gag>Aag	p.E658K	GOLGA7B_ENST00000596005.1_5'Flank|GOLGA7B_ENST00000370602.1_Intron|CRTAC1_ENST00000298819.4_3'UTR	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	658			E -> K (in dbSNP:rs56007204).			extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		CAGCTGGGCTCGCAGCTCTCC	0.622													C|||	396	0.0790735	0.0129	0.1484	5008	,	,		16528	0.0		0.2316	False		,,,				2504	0.044				p.E658K		Atlas-SNP	.											CRTAC1,NS,adenoma,0,2	CRTAC1	86	2	0			c.G1972A						scavenged	.	C	,LYS/GLU	213,4193	130.6+/-167.2	7,199,1997	38.0	39.0	39.0		,1972	-1.5	0.0	10	dbSNP_129	39	1892,6708	334.9+/-321.2	199,1494,2607	yes	intron,missense	CRTAC1,GOLGA7B	NM_001010917.2,NM_018058.6	,56	206,1693,4604	TT,TC,CC		22.0,4.8343,16.1848	,benign	,658/662	99625319	2105,10901	2203	4300	6503	SO:0001583	missense	55118	exon15			TGGGCTCGCAGCT	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.1972G>A	10.37:g.99625319C>T	ENSP00000359629:p.Glu658Lys	Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	78	34	0.435897	NM_018058	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	37	CCDS31266.1	241	0.11034798534798534	10	0.02032520325203252	69	0.19060773480662985	0	0.0	162	0.21372031662269128	C	17.52	3.410848	0.62399	0.048343	0.22	ENSG00000095713	ENST00000370597	T	0.74209	-0.82	3.19	-1.52	0.08637	.	1.841770	0.03457	N	0.211645	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.08638	-1.0712	9	0.87932	D	0	.	7.4764	0.27378	0.0:0.5166:0.0:0.4834	rs56007204;rs61874778	658	Q9NQ79	CRAC1_HUMAN	K	658	ENSP00000359629:E658K	ENSP00000359629:E658K	E	-	1	0	CRTAC1	99615309	0.004000	0.15560	0.000000	0.03702	0.840000	0.47671	-0.670000	0.05256	-0.329000	0.08527	0.462000	0.41574	GAG	C|0.846;T|0.154	0.154	strong		0.622	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
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 GAIIx	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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	150	59	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	
THSD7A	221981	hgsc.bcm.edu	37	7	11581121	11581121	+	Missense_Mutation	SNP	T	T	C	rs47	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:11581121T>C	ENST00000423059.4	-	6	1998	c.1747A>G	c.(1747-1749)Aac>Gac	p.N583D		NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	583			N -> H (in dbSNP:rs47).	N -> D (in Ref. 3; BAA76804). {ECO:0000305}.	angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		GGCTCGCAGTTTCCCAGTCTC	0.507										HNSCC(18;0.044)			C|||	4153	0.829273	0.9864	0.8703	5008	,	,		18193	0.7649		0.7674	False		,,,				2504	0.7178				p.N583D		Atlas-SNP	.											.	THSD7A	219	.	0			c.A1747G						PASS	.	C	ASP/ASN	3803,189		1812,179,5	100.0	100.0	100.0		1747	4.7	1.0	7	dbSNP_36	100	6332,1992		2384,1564,214	yes	missense	THSD7A	NM_015204.2	23	4196,1743,219	CC,CT,TT		23.9308,4.7345,17.7087	benign	583/1658	11581121	10135,2181	1996	4162	6158	SO:0001583	missense	221981	exon6			CGCAGTTTCCCAG		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1747A>G	7.37:g.11581121T>C	ENSP00000406482:p.Asn583Asp	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	184	184	1	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	1803	0.8255494505494505	480	0.975609756097561	311	0.8591160220994475	433	0.756993006993007	579	0.7638522427440633	C	12.56	1.975602	0.34848	0.952655	0.760692	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.57595	0.39	5.63	4.7	0.59300	.	0.136762	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00729	-1.24	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38693	-0.9649	9	0.12103	T	0.63	.	11.4606	0.50208	0.0:0.8064:0.1255:0.0681	rs47;rs10368694;rs11509150;rs17572612;rs61561821;rs47	583	Q9UPZ6	THS7A_HUMAN	D	583	ENSP00000406482:N583D	ENSP00000262042:N583D	N	-	1	0	THSD7A	11547646	0.953000	0.32496	1.000000	0.80357	0.917000	0.54804	1.496000	0.35638	1.521000	0.48983	-0.119000	0.15052	AAC	T|0.170;C|0.827	0.827	strong		0.507	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
MBD3L3	653657	hgsc.bcm.edu	37	19	7056553	7056553	+	Missense_Mutation	SNP	C	C	T	rs199680919	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:7056553C>T	ENST00000333843.4	-	2	441	c.407G>A	c.(406-408)cGc>cAc	p.R136H		NM_001164425.1	NP_001157897.1	A6NE82	MB3L3_HUMAN	methyl-CpG binding domain protein 3-like 3	136					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					central_nervous_system(1)|lung(5)|stomach(1)	7						AAGCGGGCTGCGCACACGCTC	0.632																																					p.R136H		Atlas-SNP	.											MBD3L3,NS,haematopoietic_neoplasm,0,1	MBD3L3	12	1	0			c.G407A						scavenged	.						36.0	45.0	42.0					19																	7056553		692	1591	2283	SO:0001583	missense	653657	exon2			GGGCTGCGCACAC		CCDS45944.1	19p13.2	2014-04-01			ENSG00000182315	ENSG00000182315			37205	protein-coding gene	gene with protein product							Standard	NM_001164425		Approved		uc021uns.1	A6NE82	OTTHUMG00000181976	ENST00000333843.4:c.407G>A	19.37:g.7056553C>T	ENSP00000333183:p.Arg136His	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	157	65	0.414013	NM_001164425		Missense_Mutation	SNP	ENST00000333843.4	37	CCDS45944.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.031306	0.00410	.	.	ENSG00000182315	ENST00000333843	.	.	.	0.742	0.742	0.18341	.	1.821020	0.03465	N	0.212818	T	0.07279	0.0184	N	0.00413	-1.525	0.09310	N	1	.	.	.	.	.	.	T	0.35992	-0.9766	7	0.02654	T	1	-3.5374	3.0013	0.06015	0.0:0.3185:0.0:0.6815	.	.	.	.	H	136	.	ENSP00000333183:R136H	R	-	2	0	MBD3L3	7007553	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-1.532000	0.02217	-0.239000	0.09710	-0.981000	0.02577	CGC	C|0.881;T|0.119	0.119	strong		0.632	MBD3L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458500.1	NM_001164425	
DFNB31	25861	hgsc.bcm.edu	37	9	117166311	117166311	+	Silent	SNP	G	G	A	rs34963246	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:117166311G>A	ENST00000362057.3	-	10	2451	c.2283C>T	c.(2281-2283)agC>agT	p.S761S	DFNB31_ENST00000265134.6_Silent_p.S378S|DFNB31_ENST00000374059.3_Silent_p.S410S	NM_001173425.1|NM_015404.3	NP_001166896.1|NP_056219	Q9P202	WHRN_HUMAN	deafness, autosomal recessive 31	761					inner ear receptor stereocilium organization (GO:0060122)|retina homeostasis (GO:0001895)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	actin filament (GO:0005884)|cilium (GO:0005929)|cytoplasm (GO:0005737)|stereocilia ankle link complex (GO:0002142)|stereocilium (GO:0032420)				central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|ovary(5)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CACTGTCCTCGCTTAGAGTCT	0.622													G|||	463	0.0924521	0.1921	0.147	5008	,	,		19778	0.001		0.0905	False		,,,				2504	0.0153				p.S761S		Atlas-SNP	.											.	DFNB31	100	.	0			c.C2283T						PASS	.	G	,,	849,3557	329.9+/-301.2	82,685,1436	58.0	53.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1134,2280,2283	-4.2	0.3	9	dbSNP_126	55	755,7845	179.9+/-228.9	31,693,3576	no	coding-synonymous,coding-synonymous,coding-synonymous	DFNB31	NM_001083885.2,NM_001173425.1,NM_015404.3	,,	113,1378,5012	AA,AG,GG		8.7791,19.2692,12.3328	,,	378/525,760/907,761/908	117166311	1604,11402	2203	4300	6503	SO:0001819	synonymous_variant	25861	exon10			GTCCTCGCTTAGA	AK056190	CCDS6806.1, CCDS43870.1	9q32	2013-06-19			ENSG00000095397	ENSG00000095397			16361	protein-coding gene	gene with protein product	"""whirlin"""	607928				12833159, 17171570	Standard	NM_015404		Approved	CIP98, WHRN, USH2D, PDZD7B	uc004biz.4	Q9P202	OTTHUMG00000020539	ENST00000362057.3:c.2283C>T	9.37:g.117166311G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_015404	A5PKU1|A5PKZ9|Q5TAU9|Q5TAV0|Q5TAV1|Q5TAV2|Q96MZ9|Q9H9F4|Q9UFZ3	Silent	SNP	ENST00000362057.3	37	CCDS6806.1																																																																																			A|0.112;G|0.887;T|0.000	0.112	strong		0.622	DFNB31-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053776.2	NM_015404	
PRKCDBP	112464	hgsc.bcm.edu	37	11	6340525	6340525	+	Silent	SNP	A	A	T	rs12570	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6340525A>T	ENST00000303927.3	-	2	824	c.654T>A	c.(652-654)gcT>gcA	p.A218A	PRKCDBP_ENST00000530979.1_Silent_p.A250A	NM_145040.2	NP_659477.2	Q969G5	PRDBP_HUMAN	protein kinase C, delta binding protein	218					cortical actin cytoskeleton organization (GO:0030866)|negative regulation of fermentation (GO:1901003)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	caveola (GO:0005901)|protein complex (GO:0043234)				large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCTGGGCTTCAGCGCTCCGGC	0.721													A|||	3279	0.654752	0.5537	0.5937	5008	,	,		14486	0.7341		0.7097	False		,,,				2504	0.6963				p.A218A		Atlas-SNP	.											PRKCDBP,NS,carcinoma,0,1	PRKCDBP	19	1	0			c.T654A						PASS	.	A		2461,1937		689,1083,427	33.0	40.0	38.0		654	-2.9	0.0	11	dbSNP_52	38	5896,2690		2025,1846,422	no	coding-synonymous	PRKCDBP	NM_145040.2		2714,2929,849	TT,TA,AA		31.3301,44.0427,35.6362		218/262	6340525	8357,4627	2199	4293	6492	SO:0001819	synonymous_variant	112464	exon2			GGCTTCAGCGCTC	AF339881	CCDS7762.1	11p15.4	2011-04-20			ENSG00000170955	ENSG00000170955			9400	protein-coding gene	gene with protein product	"""sdr-related gene product that binds to c-kinase"""					9054438	Standard	NM_145040		Approved	SRBC, HSRBC, MGC20400, cavin-3, CAVIN3	uc001mcu.1	Q969G5	OTTHUMG00000133378	ENST00000303927.3:c.654T>A	11.37:g.6340525A>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_145040		Silent	SNP	ENST00000303927.3	37	CCDS7762.1																																																																																			A|0.354;T|0.646	0.646	strong		0.721	PRKCDBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257228.2	NM_145040	
PRDM16	63976	hgsc.bcm.edu	37	1	3301721	3301721	+	Silent	SNP	C	C	T	rs2282198	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3301721C>T	ENST00000270722.5	+	4	493	c.444C>T	c.(442-444)tcC>tcT	p.S148S	PRDM16_ENST00000378398.3_Silent_p.S148S|PRDM16_ENST00000441472.2_Silent_p.S148S|PRDM16_ENST00000514189.1_Silent_p.S149S|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000442529.2_Silent_p.S148S|PRDM16_ENST00000511072.1_Silent_p.S149S|PRDM16_ENST00000378391.2_Silent_p.S148S			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	148	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AGCAGATCTCCGAAGACCTGG	0.607			T	EVI1	"""MDS, AML"""								C|||	1705	0.340455	0.0386	0.3285	5008	,	,		18269	0.622		0.2684	False		,,,				2504	0.5409				p.S148S		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C444T						PASS	.	C	,	351,3947		22,307,1820	75.0	85.0	82.0		444,444	-9.1	0.5	1	dbSNP_100	82	2281,6267		290,1701,2283	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	312,2008,4103	TT,TC,CC		26.6846,8.1666,20.4889	,	148/1277,148/1258	3301721	2632,10214	2149	4274	6423	SO:0001819	synonymous_variant	63976	exon4			GATCTCCGAAGAC	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.444C>T	1.37:g.3301721C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			C|0.713;T|0.287	0.287	strong		0.607	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
KCNH3	23416	hgsc.bcm.edu	37	12	49951377	49951377	+	Missense_Mutation	SNP	C	C	T	rs59261129	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49951377C>T	ENST00000257981.6	+	15	3153	c.2893C>T	c.(2893-2895)Cgt>Tgt	p.R965C	MCRS1_ENST00000547182.1_5'Flank	NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	965	Pro-rich.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						GCCCCACCCTCGTCCGGGGCC	0.682													C|||	367	0.0732827	0.149	0.0533	5008	,	,		16519	0.0238		0.0686	False		,,,				2504	0.0409				p.R965C		Atlas-SNP	.											.	KCNH3	88	.	0			c.C2893T						PASS	.	C	CYS/ARG	558,3848	250.0+/-257.2	37,484,1682	48.0	48.0	48.0		2893	5.1	0.9	12	dbSNP_129	48	615,7985	158.8+/-212.2	21,573,3706	yes	missense	KCNH3	NM_012284.1	180	58,1057,5388	TT,TC,CC		7.1512,12.6645,9.0189	probably-damaging	965/1084	49951377	1173,11833	2203	4300	6503	SO:0001583	missense	23416	exon15			CACCCTCGTCCGG	AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.2893C>T	12.37:g.49951377C>T	ENSP00000257981:p.Arg965Cys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	37	CCDS8786.1	156	0.07142857142857142	73	0.1483739837398374	25	0.06906077348066299	7	0.012237762237762238	51	0.06728232189973615	C	14.56	2.571254	0.45798	0.126645	0.071512	ENSG00000135519	ENST00000257981	D	0.98978	-5.29	5.09	5.09	0.68999	.	0.174710	0.28082	N	0.016664	T	0.09730	0.0239	N	0.08118	0	0.09310	P	1.0	D	0.56968	0.978	B	0.30782	0.12	T	0.70494	-0.4856	9	0.36615	T	0.2	.	13.8582	0.63542	0.0:1.0:0.0:0.0	rs59261129;rs61745869	965	Q9ULD8	KCNH3_HUMAN	C	965	ENSP00000257981:R965C	ENSP00000257981:R965C	R	+	1	0	KCNH3	48237644	0.668000	0.27493	0.935000	0.37517	0.960000	0.62799	1.494000	0.35616	2.650000	0.89964	0.561000	0.74099	CGT	C|0.914;T|0.086	0.086	strong		0.682	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
CASC5	57082	hgsc.bcm.edu	37	15	40916801	40916801	+	Missense_Mutation	SNP	A	A	G	rs16970911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:40916801A>G	ENST00000346991.5	+	11	4807	c.4417A>G	c.(4417-4419)Acc>Gcc	p.T1473A	CASC5_ENST00000399668.2_Missense_Mutation_p.T1447A			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1473			T -> A (in dbSNP:rs16970911). {ECO:0000269|PubMed:10980622}.		acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TCATTTCTCAACCGACCAACC	0.318													A|||	155	0.0309505	0.0023	0.049	5008	,	,		21576	0.0		0.0934	False		,,,				2504	0.0245				p.T1473A		Atlas-SNP	.											.	CASC5	269	.	0			c.A4417G						PASS	.	A	ALA/THR,ALA/THR	72,3612		0,72,1770	81.0	76.0	78.0		4339,4417	1.5	0.0	15	dbSNP_123	78	724,7464		36,652,3406	yes	missense,missense	CASC5	NM_144508.3,NM_170589.3	58,58	36,724,5176	GG,GA,AA		8.8422,1.9544,6.7049	benign,benign	1447/2317,1473/2343	40916801	796,11076	1842	4094	5936	SO:0001583	missense	57082	exon11			TTCTCAACCGACC	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.4417A>G	15.37:g.40916801A>G	ENSP00000335463:p.Thr1473Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	34	10	0.294118	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Missense_Mutation	SNP	ENST00000346991.5	37	CCDS42023.1	105	0.04807692307692308	2	0.0040650406504065045	25	0.06906077348066299	0	0.0	78	0.10290237467018469	A	1.921	-0.448317	0.04572	0.019544	0.088422	ENSG00000137812	ENST00000346991;ENST00000260369;ENST00000399668	T;T	0.04706	3.57;3.57	5.12	1.48	0.22813	.	0.641069	0.14008	N	0.347669	T	0.00109	0.0003	L	0.27053	0.805	0.09310	N	1	B;B;B	0.31705	0.04;0.04;0.336	B;B;B	0.23150	0.028;0.028;0.044	T	0.48625	-0.9019	10	0.10636	T	0.68	.	8.2843	0.31920	0.664:0.0:0.336:0.0	rs16970911;rs52817506;rs60813014;rs16970911	1447;1473;1447	Q8NG31-2;Q8NG31;Q8NG31-4	.;CASC5_HUMAN;.	A	1473;1447;1447	ENSP00000335463:T1473A;ENSP00000382576:T1447A	ENSP00000260369:T1447A	T	+	1	0	CASC5	38704093	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.292000	0.19011	0.056000	0.16144	0.491000	0.48974	ACC	A|0.945;G|0.055	0.055	strong		0.318	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
EPS8L2	64787	hgsc.bcm.edu	37	11	721570	721570	+	Silent	SNP	C	C	T	rs7635	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:721570C>T	ENST00000533256.1	+	11	1149	c.774C>T	c.(772-774)atC>atT	p.I258I	EPS8L2_ENST00000526198.1_Silent_p.I274I|EPS8L2_ENST00000318562.8_Silent_p.I258I|EPS8L2_ENST00000530636.1_Silent_p.I258I|AP006621.9_ENST00000527021.2_RNA			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	258					positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	actin binding (GO:0003779)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|pancreas(1)|prostate(2)|soft_tissue(1)|urinary_tract(1)	13		all_cancers(49;1.24e-08)|all_epithelial(84;1.87e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.106)|all_lung(207;0.136)		all cancers(45;4.37e-27)|Epithelial(43;2.81e-26)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-20)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCAGCAAATCCTCAACTGCG	0.637													c|||	1401	0.279752	0.1884	0.5648	5008	,	,		14025	0.1746		0.4155	False		,,,				2504	0.1697				p.I258I		Atlas-SNP	.											EPS8L2,colon,carcinoma,0,1	EPS8L2	42	1	0			c.C774T						scavenged	.			970,3408		127,716,1346	22.0	27.0	26.0		774	3.8	1.0	11	dbSNP_52	26	3854,4700		888,2078,1311	no	coding-synonymous	EPS8L2	NM_022772.3		1015,2794,2657	TT,TC,CC		45.0549,22.1562,37.3028		258/716	721570	4824,8108	2189	4277	6466	SO:0001819	synonymous_variant	64787	exon10			GCAAATCCTCAAC	AF318331	CCDS31328.1	11p15.5	2008-02-05				ENSG00000177106			21296	protein-coding gene	gene with protein product		614988				12620401	Standard	NM_022772		Approved	FLJ21935, FLJ22171, MGC3088	uc001lqt.3	Q9H6S3		ENST00000533256.1:c.774C>T	11.37:g.721570C>T		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			C|0.687;T|0.313	0.313	strong		0.637	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
MYO15A	51168	hgsc.bcm.edu	37	17	18041507	18041507	+	Silent	SNP	C	C	T	rs2280777	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18041507C>T	ENST00000205890.5	+	17	5292	c.4954C>T	c.(4954-4956)Ctg>Ttg	p.L1652L		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1652	Myosin motor.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					CCTCATCTCACTGAAGCCTTA	0.562													C|||	2397	0.478634	0.4047	0.5735	5008	,	,		15838	0.5933		0.5209	False		,,,				2504	0.3497				p.L1652L		Atlas-SNP	.											.	MYO15A	268	.	0			c.C4954T						PASS	.	C		1901,2475	491.5+/-362.1	428,1045,715	109.0	111.0	111.0		4954	2.5	0.7	17	dbSNP_100	111	4595,3985	580.7+/-391.1	1247,2101,942	yes	coding-synonymous	MYO15A	NM_016239.3		1675,3146,1657	TT,TC,CC		46.4452,43.4415,49.8611		1652/3531	18041507	6496,6460	2188	4290	6478	SO:0001819	synonymous_variant	51168	exon16			ATCTCACTGAAGC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.4954C>T	17.37:g.18041507C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																			C|0.501;N|0.000	.	strong		0.562	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
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 GAIIx	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_ENST00000425117.2_Intron|UTP14A_ENST00000371042.3_5'Flank|UTP14A_ENST00000371051.5_Missense_Mutation_p.R98Q|RP4-537K23.4_ENST00000432062.1_RNA	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	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	17	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 GAIIx	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_ENST00000513970.1_Missense_Mutation_p.P218A|CDC25C_ENST00000357274.3_Missense_Mutation_p.P175A|CDC25C_ENST00000356505.3_Missense_Mutation_p.P188A|CDC25C_ENST00000348983.3_Missense_Mutation_p.P145A|CDC25C_ENST00000415130.2_Missense_Mutation_p.P145A|CDC25C_ENST00000514555.1_Missense_Mutation_p.P188A	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	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	32	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		
SDK2	54549	hgsc.bcm.edu	37	17	71426670	71426670	+	Silent	SNP	G	G	A	rs1105354	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:71426670G>A	ENST00000392650.3	-	12	1563	c.1563C>T	c.(1561-1563)caC>caT	p.H521H	SDK2_ENST00000388726.3_Silent_p.H521H	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	521	Ig-like C2-type 6.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CTCGGGGGTCGTGGGTCACTC	0.612													G|||	664	0.132588	0.0431	0.1974	5008	,	,		15367	0.0655		0.2903	False		,,,				2504	0.1145				p.H521H		Atlas-SNP	.											.	SDK2	219	.	0			c.C1563T						PASS	.	G		369,4037	185.0+/-212.2	15,339,1849	51.0	39.0	43.0		1563	-5.9	0.9	17	dbSNP_86	43	2311,6289	373.2+/-336.9	316,1679,2305	no	coding-synonymous	SDK2	NM_001144952.1		331,2018,4154	AA,AG,GG		26.8721,8.3749,20.6059		521/2173	71426670	2680,10326	2203	4300	6503	SO:0001819	synonymous_variant	54549	exon12			GGGGTCGTGGGTC	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.1563C>T	17.37:g.71426670G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1	370	0.16941391941391942	27	0.054878048780487805	74	0.20441988950276244	42	0.07342657342657342	227	0.2994722955145119	G	1.692	-0.503757	0.04261	0.083749	0.268721	ENSG00000069188	ENST00000416616	.	.	.	4.08	-5.92	0.02261	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999142	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5169	0.61545	0.6916:0.0:0.3084:0.0	rs1105354;rs17782278;rs1105354	.	.	.	X	426	.	.	R	-	1	2	SDK2	68938265	0.099000	0.21834	0.945000	0.38365	0.171000	0.22731	-0.479000	0.06567	-1.056000	0.03205	-0.369000	0.07265	CGA	G|0.818;A|0.182	0.182	strong		0.612	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
GZMM	3004	hgsc.bcm.edu	37	19	549080	549080	+	Silent	SNP	A	A	G	rs59771750	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:549080A>G	ENST00000264553.3	+	4	545	c.507A>G	c.(505-507)caA>caG	p.Q169Q		NM_001258351.1|NM_005317.3	NP_001245280.1|NP_005308	P51124	GRAM_HUMAN	granzyme M (lymphocyte met-ase 1)	169	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(1)|prostate(1)	3		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|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)		TGGACCTCCAAGTGCTGGACA	0.697													a|||	184	0.0367412	0.0068	0.0533	5008	,	,		6240	0.0298		0.0686	False		,,,				2504	0.0399				p.Q169Q		Atlas-SNP	.											.	GZMM	11	.	0			c.A507G						PASS	.			60,4314		2,56,2129	16.0	13.0	14.0		507	-5.7	0.0	19	dbSNP_129	14	527,8005		20,487,3759	no	coding-synonymous	GZMM	NM_005317.2		22,543,5888	GG,GA,AA		6.1767,1.3717,4.5483		169/258	549080	587,12319	2187	4266	6453	SO:0001819	synonymous_variant	3004	exon4			CCTCCAAGTGCTG		CCDS12031.1, CCDS74240.1	19p13.3	2008-07-16				ENSG00000197540			4712	protein-coding gene	gene with protein product	"""lymphocyte met-ase 1"""	600311				8119738	Standard	NM_005317		Approved	MET1, LMET1	uc002low.2	P51124		ENST00000264553.3:c.507A>G	19.37:g.549080A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_005317		Silent	SNP	ENST00000264553.3	37	CCDS12031.1																																																																																			A|0.953;G|0.047	0.047	strong		0.697	GZMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451895.2	NM_005317	
RABEP1	9135	hgsc.bcm.edu	37	17	5280440	5280440	+	Silent	SNP	T	T	C	rs3026101	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5280440T>C	ENST00000546142.2	+	14	2242	c.2055T>C	c.(2053-2055)cgT>cgC	p.R685R	RABEP1_ENST00000262477.6_Silent_p.R685R|RABEP1_ENST00000408982.2_Silent_p.R685R|RABEP1_ENST00000537505.1_Silent_p.R642R|RABEP1_ENST00000341923.6_Silent_p.R685R|NUP88_ENST00000573169.1_Intron			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	685					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						TAAAATACCGTGAGGACATCA	0.408													T|||	1963	0.391973	0.2315	0.3573	5008	,	,		18412	0.6012		0.3479	False		,,,				2504	0.4632				p.R685R		Atlas-SNP	.											RABEP1,NS,haematopoietic_neoplasm,+1,1	RABEP1	59	1	0			c.T2055C						PASS	.	T	,	907,2861		102,703,1079	141.0	135.0	137.0		2055,2055	-10.0	0.2	17	dbSNP_102	137	2497,5717		364,1769,1974	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	466,2472,3053	CC,CT,TT		30.3993,24.0711,28.4093	,	685/830,685/863	5280440	3404,8578	1884	4107	5991	SO:0001819	synonymous_variant	9135	exon14			ATACCGTGAGGAC	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2055T>C	17.37:g.5280440T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			T|0.635;C|0.365	0.365	strong		0.408	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
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 GAIIx	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	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	40	27	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1263234	1263234	+	Silent	SNP	A	A	G	rs56117556	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1263234A>G	ENST00000529681.1	+	31	5182	c.5124A>G	c.(5122-5124)acA>acG	p.T1708T	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.T1711T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1708	7 X Cys-rich subdomain repeats.|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)		GCTTGGGCACATGGCGCCCCT	0.662													a|||	241	0.048123	0.0688	0.0403	5008	,	,		16319	0.0089		0.0388	False		,,,				2504	0.0757				p.T1708T		Atlas-SNP	.											.	MUC5B	473	.	0			c.A5124G						PASS	.			275,3985		7,261,1862	19.0	27.0	24.0		5124	-2.0	0.0	11	dbSNP_129	24	276,8176		6,264,3956	no	coding-synonymous	MUC5B	NM_002458.2		13,525,5818	GG,GA,AA		3.2655,6.4554,4.3345		1708/5763	1263234	551,12161	2130	4226	6356	SO:0001819	synonymous_variant	727897	exon31			GGGCACATGGCGC	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.5124A>G	11.37:g.1263234A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			A|0.960;G|0.040	0.040	strong		0.662	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
RYR1	6261	hgsc.bcm.edu	37	19	39010023	39010023	+	Silent	SNP	C	C	T	rs2229145	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39010023C>T	ENST00000359596.3	+	67	10188	c.10188C>T	c.(10186-10188)gaC>gaT	p.D3396D	RYR1_ENST00000360985.3_Silent_p.D3396D|RYR1_ENST00000355481.4_Silent_p.D3396D			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3396					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	TGGTGCGGGACGAGTTCTCTG	0.692													C|||	149	0.0297524	0.0129	0.0432	5008	,	,		15234	0.0		0.0746	False		,,,				2504	0.0276				p.D3396D		Atlas-SNP	.											.	RYR1	708	.	0			c.C10188T						PASS	.	C	,	61,4337		0,61,2138	60.0	45.0	50.0		10188,10188	-7.2	0.9	19	dbSNP_98	50	424,8176		9,406,3885	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	9,467,6023	TT,TC,CC		4.9302,1.387,3.7313	,	3396/5039,3396/5034	39010023	485,12513	2199	4300	6499	SO:0001819	synonymous_variant	6261	exon67			GCGGGACGAGTTC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.10188C>T	19.37:g.39010023C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.961;T|0.039	0.039	strong		0.692	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
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 GAIIx	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_ENST00000539668.1_5'UTR|SLC6A13_ENST00000445055.2_Missense_Mutation_p.R319H	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	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	5	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	
ARRB2	409	hgsc.bcm.edu	37	17	4622638	4622638	+	Silent	SNP	C	C	T	rs1045280	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4622638C>T	ENST00000269260.2	+	11	1073	c.840C>T	c.(838-840)agC>agT	p.S280S	ARRB2_ENST00000575877.1_Intron|ARRB2_ENST00000574954.1_Silent_p.S88S|ARRB2_ENST00000572457.1_Silent_p.S88S|ARRB2_ENST00000412477.3_Silent_p.S301S|ARRB2_ENST00000571206.1_Silent_p.S88S|ARRB2_ENST00000346341.2_Silent_p.S265S|ARRB2_ENST00000381488.6_Silent_p.S265S	NM_001257328.1|NM_001257330.1|NM_004313.3	NP_001244257.1|NP_001244259.1|NP_004304.1	P32121	ARRB2_HUMAN	arrestin, beta 2	280	Interaction with TRAF6.				adult walking behavior (GO:0007628)|apoptotic DNA fragmentation (GO:0006309)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell chemotaxis (GO:0060326)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor internalization (GO:0002031)|negative regulation of GTPase activity (GO:0034260)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|Notch signaling pathway (GO:0007219)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of receptor internalization (GO:0002092)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|receptor internalization (GO:0031623)|regulation of androgen receptor signaling pathway (GO:0060765)|transcription from RNA polymerase II promoter (GO:0006366)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	angiotensin receptor binding (GO:0031701)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|ubiquitin protein ligase binding (GO:0031625)			large_intestine(1)|liver(2)|lung(3)|prostate(1)	7						CACTGCTCAGCGACAACCGGG	0.602													C|||	3353	0.669529	0.4047	0.7205	5008	,	,		15652	0.8254		0.6879	False		,,,				2504	0.8119				p.S301S		Atlas-SNP	.											.	ARRB2	30	.	0			c.C903T						PASS	.	C	,	1982,2424	557.6+/-379.8	433,1116,654	95.0	87.0	90.0		840,795	-4.6	0.5	17	dbSNP_86	90	5815,2785	678.1+/-403.4	1973,1869,458	no	coding-synonymous,coding-synonymous	ARRB2	NM_004313.3,NM_199004.1	,	2406,2985,1112	TT,TC,CC		32.3837,44.9841,40.0507	,	280/410,265/395	4622638	7797,5209	2203	4300	6503	SO:0001819	synonymous_variant	409	exon11			GCTCAGCGACAAC		CCDS11050.1, CCDS11051.1, CCDS58504.1, CCDS58505.1, CCDS59276.1	17p13	2008-12-11			ENSG00000141480	ENSG00000141480			712	protein-coding gene	gene with protein product	"""arrestin 3"""	107941		ARR2		7695743	Standard	NM_001257329		Approved	BARR2, DKFZp686L0365	uc002fyl.3	P32121	OTTHUMG00000090759	ENST00000269260.2:c.840C>T	17.37:g.4622638C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	98	36	0.367347	NM_001257328	B4DLW0|B5B0C0|B7WPL3|D3DTK2|H0Y688|Q0Z8D3|Q2PP19|Q6ICT3|Q8N7Y2|Q9UEQ6	Silent	SNP	ENST00000269260.2	37	CCDS11050.1																																																																																			C|0.376;T|0.624	0.624	strong		0.602	ARRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439552.1	NM_004313	
TPR	7175	hgsc.bcm.edu	37	1	186321242	186321242	+	Splice_Site	SNP	C	C	T	rs61744267	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186321242C>T	ENST00000367478.4	-	19	2631	c.2335G>A	c.(2335-2337)Gta>Ata	p.V779I	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	779				V -> I (in Ref. 3; AAB48030). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.V780I(2)|p.V779I(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		TCTGCTCTTACCTAAACATAA	0.303			T	NTRK1	papillary thyroid								C|||	436	0.0870607	0.0234	0.121	5008	,	,		14946	0.0714		0.1849	False		,,,				2504	0.0644				p.V779I		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	TPR_ENST00000367478,NS,carcinoma,0,3	TPR	441	3	3	Substitution - Missense(3)	pancreas(2)|stomach(1)	c.G2335A						PASS	.	C	ILE/VAL	189,3415		5,179,1618	73.0	68.0	70.0		2335	5.8	1.0	1	dbSNP_129	70	1469,6669		123,1223,2723	yes	missense-near-splice	TPR	NM_003292.2	29	128,1402,4341	TT,TC,CC		18.0511,5.2442,14.1203	probably-damaging	779/2364	186321242	1658,10084	1802	4069	5871	SO:0001630	splice_region_variant	7175	exon19			CTCTTACCTAAAC	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.2335-1G>A	1.37:g.186321242C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	31	9	0.290323	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	239	0.10943223443223443	7	0.014227642276422764	45	0.12430939226519337	36	0.06293706293706294	151	0.19920844327176782	C	23.5	4.421789	0.83559	0.052442	0.180511	ENSG00000047410	ENST00000367478	T	0.24908	1.83	5.75	5.75	0.90469	.	0.242826	0.41194	D	0.000931	T	0.00039	0.0001	L	0.54323	1.7	0.20703	P	0.999866087	D	0.59357	0.985	B	0.43950	0.437	T	0.15037	-1.0451	9	0.21540	T	0.41	.	19.5445	0.95285	0.0:1.0:0.0:0.0	.	779	P12270	TPR_HUMAN	I	779	ENSP00000356448:V779I	ENSP00000356448:V779I	V	-	1	0	TPR	184587865	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	4.876000	0.63079	2.711000	0.92665	0.563000	0.77884	GTA	C|0.871;T|0.129	0.129	strong		0.303	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	Missense_Mutation
RBMXL3	139804	hgsc.bcm.edu	37	X	114424148	114424148	+	Silent	SNP	G	G	A	rs62601525		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:114424148G>A	ENST00000424776.3	+	1	186	c.144G>A	c.(142-144)tcG>tcA	p.S48S	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	48	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						CCAACAAGTCGAGGGGCTTCG	0.532													G|||	221	0.058543	0.0038	0.0533	3775	,	,		13320	0.002		0.1133	False		,,,				2504	0.0644				p.S48S		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G144A						PASS	.	G	,	34,1175		1,25,7,491,168	84.0	77.0	79.0		144,	-0.4	0.0	X	dbSNP_129	79	391,2000		18,215,140,567,651	no	coding-synonymous,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	,	19,240,147,1058,819	AA,AG,A,GG,G		16.353,2.8122,11.8056	,	48/1068,	114424148	425,3175	692	1591	2283	SO:0001819	synonymous_variant	139804	exon1			CAAGTCGAGGGGC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.144G>A	X.37:g.114424148G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	120	23	0.191667	NM_001145346	B4DXC0	Silent	SNP	ENST00000424776.3	37	CCDS55478.1																																																																																			G|0.929;A|0.071	0.071	strong		0.532	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
GFM1	85476	hgsc.bcm.edu	37	3	158366900	158366900	+	Missense_Mutation	SNP	G	G	A	rs2303909	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:158366900G>A	ENST00000486715.1	+	5	1000	c.643G>A	c.(643-645)Gta>Ata	p.V215I	GFM1_ENST00000478576.1_Missense_Mutation_p.V215I|GFM1_ENST00000264263.5_Missense_Mutation_p.V215I	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TAAAGGTATTGTAGATCTTAT	0.294													A|||	2921	0.583267	0.7708	0.5303	5008	,	,		16604	0.3849		0.5437	False		,,,				2504	0.6125				p.V215I		Atlas-SNP	.											.	GFM1	83	.	0			c.G643A						PASS	.	A	ILE/VAL	3149,1257	428.7+/-342.0	1121,907,175	147.0	162.0	157.0		643	3.7	0.6	3	dbSNP_100	157	4634,3966	550.0+/-385.7	1237,2160,903	yes	missense	GFM1	NM_024996.5	29	2358,3067,1078	AA,AG,GG		46.1163,28.5293,40.1584	benign	215/752	158366900	7783,5223	2203	4300	6503	SO:0001583	missense	85476	exon5			GGTATTGTAGATC	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"""G translation elongation factor, mitochondrial"""			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.643G>A	3.37:g.158366900G>A	ENSP00000419038:p.Val215Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	37	CCDS33885.1	1205	0.5517399267399268	376	0.7642276422764228	191	0.5276243093922652	215	0.3758741258741259	423	0.558047493403694	A	11.36	1.614309	0.28712	0.714707	0.538837	ENSG00000168827	ENST00000486715;ENST00000478576;ENST00000264263	T;T;T	0.73681	-0.77;-0.77;-0.77	6.06	3.69	0.42338	Small GTP-binding protein domain (1);Protein synthesis factor, GTP-binding (1);	0.091294	0.64402	N	0.000001	T	0.00012	0.0000	N	0.21508	0.67	0.09310	P	1.0	B;B;B	0.12630	0.002;0.002;0.006	B;B;B	0.26864	0.013;0.013;0.074	T	0.44050	-0.9353	9	0.05721	T	0.95	-8.8081	9.7227	0.40313	0.8059:0.0:0.1941:0.0	rs2303909;rs17559776;rs52829419;rs60262155;rs2303909	215;215;215	Q96RP9-2;Q96RP9;C9IZ01	.;EFGM_HUMAN;.	I	215	ENSP00000419038:V215I;ENSP00000418755:V215I;ENSP00000264263:V215I	ENSP00000264263:V215I	V	+	1	0	GFM1	159849594	1.000000	0.71417	0.563000	0.28383	0.978000	0.69477	3.315000	0.51951	0.188000	0.20168	-0.254000	0.11334	GTA	G|0.424;N|0.000	.	strong		0.294	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996	
MLLT10	8028	hgsc.bcm.edu	37	10	21827796	21827796	+	Silent	SNP	G	G	A	rs1802669	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:21827796G>A	ENST00000307729.7	+	3	373	c.195G>A	c.(193-195)ccG>ccA	p.P65P	MLLT10_ENST00000446906.2_Silent_p.P65P|MLLT10_ENST00000495130.1_3'UTR|MLLT10_ENST00000377100.3_Silent_p.P65P|MLLT10_ENST00000377059.3_Silent_p.P65P|MLLT10_ENST00000377091.2_Silent_p.P65P|MLLT10_ENST00000377072.3_Silent_p.P65P			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	65					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						CCACTGGACCGTGGTTTTGCA	0.368			T	"""MLL, PICALM, CDK6"""	AL								A|||	1389	0.277356	0.4327	0.2277	5008	,	,		19521	0.0546		0.3579	False		,,,				2504	0.2495				p.P65P		Atlas-SNP	.		Dom	yes		10	10p12	8028	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"""		L	.	MLLT10	183	.	0			c.G195A						PASS	.	A	,,,,	1741,2665	648.1+/-398.7	366,1009,828	108.0	104.0	105.0		195,195,195,195,195	0.2	1.0	10	dbSNP_89	105	3025,5575	663.6+/-402.1	527,1971,1802	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MLLT10	NM_001195626.1,NM_001195627.1,NM_001195628.1,NM_001195630.1,NM_004641.3	,,,,	893,2980,2630	AA,AG,GG		35.1744,39.5143,36.6446	,,,,	65/1069,65/127,65/180,65/180,65/1028	21827796	4766,8240	2203	4300	6503	SO:0001819	synonymous_variant	8028	exon2			TGGACCGTGGTTT	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"""Zinc fingers, PHD-type"""	16063	protein-coding gene	gene with protein product		602409	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"""			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.195G>A	10.37:g.21827796G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Silent	SNP	ENST00000307729.7	37	CCDS55708.1	604	0.2765567765567766	227	0.4613821138211382	92	0.2541436464088398	16	0.027972027972027972	269	0.3548812664907652	A	9.769	1.172082	0.21704	0.395143	0.351744	ENSG00000078403	ENST00000430455	.	.	.	5.64	0.171	0.15026	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.46091	-0.9216	3	.	.	.	.	0.7844	0.01046	0.2486:0.194:0.3192:0.2382	rs1802669;rs57900300	.	.	.	M	31	.	.	V	+	1	0	MLLT10	21867802	0.224000	0.23674	0.997000	0.53966	0.986000	0.74619	-0.310000	0.08135	-0.145000	0.11294	-1.087000	0.02190	GTG	A|0.343;G|0.657;T|0.000	0.343	strong		0.368	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		
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 GAIIx	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	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	24	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	
CAND2	23066	hgsc.bcm.edu	37	3	12848822	12848822	+	Missense_Mutation	SNP	T	T	C	rs11718898	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:12848822T>C	ENST00000456430.2	+	3	271	c.230T>C	c.(229-231)gTc>gCc	p.V77A	CAND2_ENST00000295989.5_Intron|CAND2_ENST00000466558.1_3'UTR	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	77					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCTCTGGTGGTCAAAGTGAAG	0.582													C|||	3002	0.599441	0.9735	0.5115	5008	,	,		19788	0.2907		0.7008	False		,,,				2504	0.3701				p.V77A	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.T230C						PASS	.	C	ALA/VAL,	1281,103		591,99,2	89.0	89.0	89.0		230,	3.8	1.0	3	dbSNP_120	89	2100,1082		695,710,186	yes	missense,intron	CAND2	NM_001162499.1,NM_012298.2	64,	1286,809,188	CC,CT,TT		34.0038,7.4422,25.9527	benign,	77/1237,	12848822	3381,1185	692	1591	2283	SO:0001583	missense	23066	exon3			TGGTGGTCAAAGT		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.230T>C	3.37:g.12848822T>C	ENSP00000387641:p.Val77Ala	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	109	106	0.972477	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1330	0.6089743589743589	471	0.9573170731707317	185	0.511049723756906	150	0.26223776223776224	524	0.6912928759894459	C	13.80	2.345690	0.41498	0.925578	0.659962	ENSG00000144712	ENST00000456430	T	0.64438	-0.1	5.63	3.85	0.44370	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999999998	B	0.02656	0.0	B	0.01281	0.0	T	0.34875	-0.9811	8	0.09843	T	0.71	-6.7597	5.7286	0.18026	0.0764:0.1413:0.6371:0.1452	rs11718898;rs17773733;rs56779280;rs11718898	77	O75155	CAND2_HUMAN	A	77	ENSP00000387641:V77A	ENSP00000387641:V77A	V	+	2	0	CAND2	12823822	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	5.661000	0.68025	0.763000	0.33175	-0.936000	0.02699	GTC	C|0.622;N|0.000	0.622	strong		0.582	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
GCDH	2639	hgsc.bcm.edu	37	19	13010520	13010520	+	3'UTR	SNP	A	A	G	rs8012	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:13010520A>G	ENST00000222214.5	+	0	1693				GCDH_ENST00000422947.2_3'UTR|GCDH_ENST00000457854.1_Missense_Mutation_p.Q417R|GCDH_ENST00000588242.2_3'UTR|GCDH_ENST00000591470.1_3'UTR|SYCE2_ENST00000293695.7_Intron			Q92947	GCDH_HUMAN	glutaryl-CoA dehydrogenase						cellular nitrogen compound metabolic process (GO:0034641)|fatty acid oxidation (GO:0019395)|fatty-acyl-CoA biosynthetic process (GO:0046949)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan metabolic process (GO:0006568)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|glutaryl-CoA dehydrogenase activity (GO:0004361)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)	19					Flavin adenine dinucleotide(DB03147)	GAAGTCGTTCAGATGTGTTCC	0.438													G|||	3608	0.720447	0.8563	0.6988	5008	,	,		16551	0.7768		0.5219	False		,,,				2504	0.6984				p.L417R	GBM(123;875 1636 7726 16444 26754)	Atlas-SNP	.											GCDH_ENST00000457854,NS,carcinoma,+1,1	GCDH	76	1	0			c.T1250G						PASS	.	G	,,ARG/GLN	3530,752		1455,620,66	73.0	87.0	83.0		,,1250	-1.4	0.0	19	dbSNP_52	83	4635,3863		1306,2023,920	yes	utr-3,intron,missense	GCDH,SYCE2	NM_000159.2,NM_001105578.1,NM_013976.2	,,43	2761,2643,986	GG,GA,AA		45.4578,17.5619,36.1111	,,	,,417/429	13010520	8165,4615	2141	4249	6390	SO:0001624	3_prime_UTR_variant	2639	exon12			TCGTTCAGATGTG	AF012342	CCDS12286.1	19p13.2	2010-04-30	2010-04-30			ENSG00000105607	1.3.99.7		4189	protein-coding gene	gene with protein product		608801	"""glutaryl-Coenzyme A dehydrogenase"""			1438360, 8088809	Standard	NM_000159		Approved	ACAD5	uc002mvq.4	Q92947		ENST00000222214.5:c.*165A>G	19.37:g.13010520A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_013976	A8K2Z2|O14719	Missense_Mutation	SNP	ENST00000222214.5	37	CCDS12286.1	1499	0.6863553113553114	416	0.8455284552845529	242	0.6685082872928176	461	0.8059440559440559	380	0.5013192612137203	G	0.525	-0.860606	0.02610	0.824381	0.545422	ENSG00000105607	ENST00000457854	D	0.97455	-4.39	4.81	-1.41	0.08941	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42882	-0.9425	7	0.62326	D	0.03	.	6.9724	0.24656	0.5991:0.2464:0.1545:0.0	rs8012;rs3170319;rs17639268;rs60041561;rs8012	417	Q92947-2	.	R	417	ENSP00000394872:Q417R	ENSP00000394872:Q417R	Q	+	2	0	GCDH	12871520	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.326000	0.19646	-0.796000	0.04456	-4.229000	0.00009	CAG	A|0.293;G|0.706	0.706	strong		0.438	GCDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451897.1		
MMRN1	22915	hgsc.bcm.edu	37	4	90857479	90857479	+	Missense_Mutation	SNP	G	G	A	rs12646270	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:90857479G>A	ENST00000394980.1	+	7	2967	c.2648G>A	c.(2647-2649)gGc>gAc	p.G883D	MMRN1_ENST00000264790.2_Missense_Mutation_p.G883D|MMRN1_ENST00000508372.1_Missense_Mutation_p.G625D|MMRN1_ENST00000394981.1_Intron			Q13201	MMRN1_HUMAN	multimerin 1	883			G -> D (in dbSNP:rs12646270).		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)		p.G883D(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GTTAAAAAAGGCAGTGTAGTT	0.348													G|||	434	0.0866613	0.0008	0.0115	5008	,	,		18484	0.2728		0.0477	False		,,,				2504	0.1043				p.G883D		Atlas-SNP	.											MMRN1,NS,carcinoma,0,2	MMRN1	174	2	1	Substitution - Missense(1)	stomach(1)	c.G2648A						PASS	.	G	ASP/GLY	49,4345	39.2+/-71.8	0,49,2148	46.0	49.0	48.0		2648	-0.5	0.0	4	dbSNP_120	48	372,8216	121.7+/-180.7	7,358,3929	yes	missense	MMRN1	NM_007351.2	94	7,407,6077	AA,AG,GG		4.3316,1.1152,3.243	benign	883/1229	90857479	421,12561	2197	4294	6491	SO:0001583	missense	22915	exon6			AAAAAGGCAGTGT	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2648G>A	4.37:g.90857479G>A	ENSP00000378431:p.Gly883Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	97	55	0.56701	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	212	0.09706959706959707	0	0.0	5	0.013812154696132596	167	0.291958041958042	40	0.052770448548812667	G	1.871	-0.460202	0.04508	0.011152	0.043316	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.64438	0.25;0.25;-0.1	5.3	-0.489	0.12052	.	0.759983	0.12411	N	0.471241	T	0.00012	0.0000	L	0.28740	0.885	0.80722	P	0.0	B	0.15141	0.012	B	0.13407	0.009	T	0.19289	-1.0310	9	0.11485	T	0.65	.	2.1337	0.03756	0.3386:0.2176:0.3419:0.1019	rs12646270;rs52807437;rs12646270	883	Q13201	MMRN1_HUMAN	D	883;883;625	ENSP00000378431:G883D;ENSP00000264790:G883D;ENSP00000426461:G625D	ENSP00000264790:G883D	G	+	2	0	MMRN1	91076502	0.011000	0.17503	0.004000	0.12327	0.477000	0.33069	-0.077000	0.11394	-0.054000	0.13266	-0.140000	0.14226	GGC	G|0.939;A|0.061	0.061	strong		0.348	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351	
TLR5	7100	hgsc.bcm.edu	37	1	223285200	223285200	+	Nonsense_Mutation	SNP	G	G	A	rs5744168	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:223285200G>A	ENST00000540964.1	-	4	1635	c.1174C>T	c.(1174-1176)Cga>Tga	p.R392*	TLR5_ENST00000342210.6_Nonsense_Mutation_p.R392*			O60602	TLR5_HUMAN	toll-like receptor 5	392			Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		GCATTGTCTCGGAGATCCAAG	0.373													G|||	252	0.0503195	0.0227	0.0303	5008	,	,		20662	0.0387		0.0606	False		,,,				2504	0.1033				p.R392X		Atlas-SNP	.											TLR5,NS,carcinoma,+1,1	TLR5	86	1	0			c.C1174T	GRCh37	CM034621	TLR5	M	rs5744168	scavenged	.	G	stop/ARG	106,4300	82.4+/-120.9	2,102,2099	103.0	102.0	103.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1174	4.7	0.9	1	dbSNP_114	103	470,8130	138.7+/-195.5	15,440,3845	yes	stop-gained	TLR5	NM_003268.5		17,542,5944	AA,AG,GG		5.4651,2.4058,4.4287		392/859	223285200	576,12430	2203	4300	6503	SO:0001587	stop_gained	7100	exon6			TGTCTCGGAGATC		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"""Toll/interleukin-1 receptor-like protein 3"""	603031	"""systemic lupus erythematosus susceptibility 1"""	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1174C>T	1.37:g.223285200G>A	ENSP00000440643:p.Arg392*	Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Nonsense_Mutation	SNP	ENST00000540964.1	37	CCDS31033.1	87	0.03983516483516483	17	0.034552845528455285	13	0.03591160220994475	15	0.026223776223776224	42	0.055408970976253295	G	39	7.367396	0.98238	0.024058	0.054651	ENSG00000187554	ENST00000540964;ENST00000366881;ENST00000342210	.	.	.	5.59	4.67	0.58626	.	0.554792	0.18536	N	0.138357	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.0789	0.42377	0.0:0.1327:0.5963:0.271	rs5744168	.	.	.	X	392	.	ENSP00000340089:R392X	R	-	1	2	TLR5	221351823	0.997000	0.39634	0.949000	0.38748	0.732000	0.41865	1.885000	0.39678	1.330000	0.45394	0.650000	0.86243	CGA	.	.	none		0.373	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268	
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 GAIIx	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	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	180	73	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	
TMEM2	23670	hgsc.bcm.edu	37	9	74360096	74360096	+	Missense_Mutation	SNP	C	C	T	rs25689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:74360096C>T	ENST00000377044.4	-	4	1411	c.872G>A	c.(871-873)cGc>cAc	p.R291H	TMEM2_ENST00000377066.5_Missense_Mutation_p.R291H	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	291			R -> H (in dbSNP:rs25689).|R -> L (in dbSNP:rs25689).|R -> P (in dbSNP:rs25689).		multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GCTCTCATTGCGGTATTCATG	0.483													T|||	1423	0.284145	0.3608	0.2752	5008	,	,		19539	0.1766		0.2187	False		,,,				2504	0.365				p.R291H		Atlas-SNP	.											.	TMEM2	112	.	0			c.G872A						PASS	.	T	HIS/ARG,HIS/ARG	1447,2959	681.5+/-404.0	239,969,995	100.0	98.0	99.0		872,872	6.0	1.0	9	dbSNP_72	99	1817,6783	732.2+/-406.8	187,1443,2670	yes	missense,missense	TMEM2	NM_001135820.1,NM_013390.2	29,29	426,2412,3665	TT,TC,CC		21.1279,32.8416,25.0961	benign,benign	291/1321,291/1384	74360096	3264,9742	2203	4300	6503	SO:0001583	missense	23670	exon4			TCATTGCGGTATT		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.872G>A	9.37:g.74360096C>T	ENSP00000366243:p.Arg291His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	513	0.2348901098901099	169	0.3434959349593496	81	0.22375690607734808	102	0.17832167832167833	161	0.21240105540897097	T	10.08	1.251990	0.22880	0.328416	0.211279	ENSG00000135048	ENST00000377044;ENST00000377066	T;T	0.73152	-0.72;-0.66	6.03	6.03	0.97812	.	0.486723	0.25836	N	0.027997	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.999999999999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18147	-1.0346	9	0.33940	T	0.23	.	9.0014	0.36083	0.0:0.0672:0.134:0.7989	rs25689;rs3739782;rs59504885;rs25689	291;291	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	H	291	ENSP00000366243:R291H;ENSP00000366266:R291H	ENSP00000366243:R291H	R	-	2	0	TMEM2	73549916	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	1.925000	0.40074	1.106000	0.41623	-0.254000	0.11334	CGC	T|0.248;C|0.752	0.248	strong		0.483	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
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 GAIIx	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	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	209	151	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	
IMPDH1	3614	hgsc.bcm.edu	37	7	128038555	128038555	+	Silent	SNP	C	C	G	rs2288550	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:128038555C>G	ENST00000480861.1	-	7	794	c.717G>C	c.(715-717)ctG>ctC	p.L239L	IMPDH1_ENST00000338791.6_Silent_p.L329L|IMPDH1_ENST00000470772.1_Silent_p.L243L|IMPDH1_ENST00000348127.6_Silent_p.L293L|IMPDH1_ENST00000378717.4_Silent_p.L260L|IMPDH1_ENST00000496200.1_Silent_p.L219L|IMPDH1_ENST00000419067.2_Silent_p.L296L|IMPDH1_ENST00000354269.5_Silent_p.L319L|IMPDH1_ENST00000343214.4_Silent_p.L219L	NM_001142574.1	NP_001136046.1			IMP (inosine 5'-monophosphate) dehydrogenase 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)	22						CCCCACAGAGCAGCTGCTTCT	0.607											OREG0018292	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	652	0.130192	0.0537	0.1023	5008	,	,		18094	0.121		0.1789	False		,,,				2504	0.2127				p.L329L		Atlas-SNP	.											.	IMPDH1	38	.	0			c.G987C						PASS	.	C	,,,,,,	337,4069	171.6+/-201.8	11,315,1877	57.0	63.0	61.0		987,957,732,717,657,888,879	3.5	1.0	7	dbSNP_100	61	1469,7131	266.4+/-286.7	115,1239,2946	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IMPDH1	NM_000883.3,NM_001102605.1,NM_001142573.1,NM_001142574.1,NM_001142575.1,NM_001142576.1,NM_183243.2	,,,,,,	126,1554,4823	GG,GC,CC		17.0814,7.6487,13.8859	,,,,,,	329/600,319/590,244/515,239/510,219/490,296/567,293/564	128038555	1806,11200	2203	4300	6503	SO:0001819	synonymous_variant	3614	exon10			ACAGAGCAGCTGC		CCDS34748.1, CCDS34749.1, CCDS43643.1, CCDS47699.1, CCDS47700.1, CCDS55161.1	7q31.3-q32	2013-01-08	2010-04-29		ENSG00000106348	ENSG00000106348	1.1.1.205		6052	protein-coding gene	gene with protein product		146690	"""retinitis pigmentosa 10 (autosomal dominant)"", ""IMP (inosine monophosphate) dehydrogenase 1"""	RP10		1969416, 11875049, 11875050	Standard	NM_000883		Approved	sWSS2608, LCA11	uc003vmu.2	P20839	OTTHUMG00000157713	ENST00000480861.1:c.717G>C	7.37:g.128038555C>G		Somatic	92	0	0	1561	WXS	Illumina HiSeq	Phase_I	97	97	1	NM_000883		Silent	SNP	ENST00000480861.1	37	CCDS55161.1																																																																																			C|0.868;G|0.132	0.132	strong		0.607	IMPDH1-009	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000349462.1	NM_000883	
CHUK	1147	hgsc.bcm.edu	37	10	101977883	101977883	+	Missense_Mutation	SNP	C	C	T	rs2230804	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101977883C>T	ENST00000370397.7	-	9	888	c.802G>A	c.(802-804)Gta>Ata	p.V268I		NM_001278.3	NP_001269.3	O15111	IKKA_HUMAN	conserved helix-loop-helix ubiquitous kinase	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in dbSNP:rs2230804). {ECO:0000269|PubMed:15164054, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8777433, ECO:0000269|PubMed:9244310, ECO:0000269|PubMed:9252186, ECO:0000269|PubMed:9813230}.		anatomical structure morphogenesis (GO:0009653)|cellular response to tumor necrosis factor (GO:0071356)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|morphogenesis of an epithelial sheet (GO:0002011)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein phosphorylation (GO:0006468)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to hydroperoxide (GO:0033194)|response to lipopolysaccharide (GO:0032496)|response to toxic substance (GO:0009636)|response to virus (GO:0009615)|Rho protein signal transduction (GO:0007266)|skeletal muscle contraction (GO:0003009)|striated muscle cell differentiation (GO:0051146)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|scaffold protein binding (GO:0097110)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)	27		Colorectal(252;0.117)		Epithelial(162;2.05e-10)|all cancers(201;1.91e-08)	Acetylcysteine(DB06151)|Aminosalicylic Acid(DB00233)|Mesalazine(DB00244)|Sulfasalazine(DB00795)	GGTTCTACTACTAAACTAGAA	0.378													T|||	2733	0.545727	0.7965	0.4294	5008	,	,		18558	0.5109		0.5179	False		,,,				2504	0.3538				p.V268I	Ovarian(159;52 1904 10536 35305 37148)	Atlas-SNP	.											.	CHUK	71	.	0			c.G802A						PASS	.	T	ILE/VAL	3274,1132	402.6+/-332.4	1210,854,139	71.0	67.0	68.0		802	4.9	1.0	10	dbSNP_98	68	4309,4291	575.8+/-390.3	1091,2127,1082	yes	missense	CHUK	NM_001278.3	29	2301,2981,1221	TT,TC,CC		49.8953,25.6922,41.6961	benign	268/746	101977883	7583,5423	2203	4300	6503	SO:0001583	missense	1147	exon9			CTACTACTAAACT	AF009225	CCDS7488.1	10q24-q25	2008-08-01			ENSG00000213341	ENSG00000213341			1974	protein-coding gene	gene with protein product		600664		TCF16		7558004, 16902410	Standard	XR_246062		Approved	IKK1, IKK-alpha, IkBKA, NFKBIKA, IKKA	uc001kqp.3	O15111	OTTHUMG00000018899	ENST00000370397.7:c.802G>A	10.37:g.101977883C>T	ENSP00000359424:p.Val268Ile	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_001278	O14666|Q13132|Q5W0I4|Q92467	Missense_Mutation	SNP	ENST00000370397.7	37	CCDS7488.1	1228	0.5622710622710623	372	0.7560975609756098	176	0.4861878453038674	288	0.5034965034965035	392	0.5171503957783641	T	12.31	1.899988	0.33535	0.743078	0.501047	ENSG00000213341	ENST00000370397	T	0.70986	-0.53	6.05	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.099835	0.64402	N	0.000002	T	0.00012	0.0000	N	0.16368	0.405	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.41592	-0.9500	9	0.31617	T	0.26	-10.1519	9.0067	0.36115	0.0:0.1499:0.0:0.8501	rs2230804;rs2274177;rs7903344;rs17883804;rs52829928;rs60143964;rs2230804	268	O15111	IKKA_HUMAN	I	268	ENSP00000359424:V268I	ENSP00000359424:V268I	V	-	1	0	CHUK	101967873	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.572000	0.45999	0.543000	0.28864	-0.269000	0.10298	GTA	C|0.431;T|0.569	0.569	strong		0.378	CHUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049836.1	NM_001278	
ATP6V1C2	245973	hgsc.bcm.edu	37	2	10908893	10908893	+	Missense_Mutation	SNP	A	A	G	rs1198849	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:10908893A>G	ENST00000272238.4	+	6	536	c.427A>G	c.(427-429)Aac>Gac	p.N143D	ATP6V1C2_ENST00000381661.3_Missense_Mutation_p.N143D|RP11-791G15.2_ENST00000606907.1_lincRNA	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	143			N -> D (in dbSNP:rs1198849). {ECO:0000269|PubMed:15489334}.		ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|protein dimerization activity (GO:0046983)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		GGCCGCCTACAACACTCTGAA	0.557													A|||	2266	0.452476	0.3434	0.438	5008	,	,		17633	0.6597		0.3648	False		,,,				2504	0.4867				p.N143D	NSCLC(188;1042 2136 10807 16813 47705)	Atlas-SNP	.											.	ATP6V1C2	73	.	0			c.A427G						PASS	.	A	ASP/ASN,ASP/ASN	1463,2943	470.0+/-355.6	248,967,988	68.0	75.0	73.0		427,427	4.5	0.6	2	dbSNP_87	73	3186,5414	481.3+/-370.6	596,1994,1710	yes	missense,missense	ATP6V1C2	NM_001039362.1,NM_144583.3	23,23	844,2961,2698	GG,GA,AA		37.0465,33.2047,35.745	benign,benign	143/428,143/382	10908893	4649,8357	2203	4300	6503	SO:0001583	missense	245973	exon6			GCCTACAACACTC	AY039759	CCDS1674.1, CCDS42653.1	2p25.1	2010-04-21	2006-01-13		ENSG00000143882	ENSG00000143882		"""ATPases / V-type"""	18264	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 42kD, V1 subunit C isoform 2"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2"""			12384298	Standard	XR_426949		Approved	VMA5, ATP6C2	uc002ras.3	Q8NEY4	OTTHUMG00000090459	ENST00000272238.4:c.427A>G	2.37:g.10908893A>G	ENSP00000272238:p.Asn143Asp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_001039362	Q96EL8	Missense_Mutation	SNP	ENST00000272238.4	37	CCDS42653.1	967	0.44276556776556775	166	0.33739837398373984	158	0.43646408839779005	356	0.6223776223776224	287	0.3786279683377309	A	14.76	2.630472	0.46944	0.332047	0.370465	ENSG00000143882	ENST00000272238;ENST00000381661	T;T	0.53857	0.6;0.6	5.65	4.48	0.54585	.	0.096395	0.64402	D	0.000001	T	0.00012	0.0000	M	0.92026	3.265	0.22754	P	0.99877951	B;B	0.24823	0.112;0.036	B;B	0.38156	0.266;0.163	T	0.44174	-0.9345	9	0.72032	D	0.01	-2.7858	10.7183	0.46026	0.8398:0.1602:0.0:0.0	rs1198849;rs1734463;rs17364715;rs17850878;rs61181462;rs1198849	143;143	Q8NEY4-2;Q8NEY4	.;VATC2_HUMAN	D	143	ENSP00000272238:N143D;ENSP00000371077:N143D	ENSP00000272238:N143D	N	+	1	0	ATP6V1C2	10826344	1.000000	0.71417	0.636000	0.29352	0.338000	0.28826	5.384000	0.66225	0.951000	0.37770	-0.313000	0.08912	AAC	A|0.600;G|0.400	0.400	strong		0.557	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583	
USP40	55230	hgsc.bcm.edu	37	2	234394569	234394569	+	Silent	SNP	A	A	G	rs386656355|rs2603547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:234394569A>G	ENST00000427112.2	-	28	3284	c.3249T>C	c.(3247-3249)taT>taC	p.Y1083Y	USP40_ENST00000496298.1_5'UTR|USP40_ENST00000251722.6_Silent_p.Y1083Y|USP40_ENST00000450966.1_Silent_p.Y1095Y			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1083					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		GGGCAGGGGCATAGGTCCTCT	0.597													G|||	1286	0.256789	0.5053	0.1542	5008	,	,		16483	0.1458		0.2455	False		,,,				2504	0.1196				p.Y1095Y		Atlas-SNP	.											.	USP40	174	.	0			c.T3285C						PASS	.	G		1637,2333		357,923,705	14.0	16.0	15.0		3285	2.0	0.0	2	dbSNP_100	15	1735,6567		188,1359,2604	no	coding-synonymous	USP40	NM_018218.2		545,2282,3309	GG,GA,AA		20.8986,41.2343,27.4772		1095/1248	234394569	3372,8900	1985	4151	6136	SO:0001819	synonymous_variant	55230	exon28			AGGGGCATAGGTC	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3249T>C	2.37:g.234394569A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_018218	Q6NX38|Q70EL0	Silent	SNP	ENST00000427112.2	37	CCDS46547.1	520	0.23809523809523808	222	0.45121951219512196	56	0.15469613259668508	67	0.11713286713286714	175	0.23087071240105542	G	0.033	-1.324183	0.01309	0.412343	0.208986	ENSG00000085982	ENST00000454354	.	.	.	5.75	2.03	0.26663	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25277	P	0.9894669	.	.	.	.	.	.	T	0.46176	-0.9210	3	.	.	.	.	10.1403	0.42732	0.4526:0.0:0.5474:0.0	rs2603547;rs3738932;rs17668948;rs56738620;rs2603547	.	.	.	T	51	.	.	M	-	2	0	USP40	234059308	0.026000	0.19158	0.004000	0.12327	0.003000	0.03518	0.191000	0.17076	-0.094000	0.12374	-1.702000	0.00720	ATG	A|0.749;G|0.251	0.251	strong		0.597	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047633	46047633	+	Missense_Mutation	SNP	A	A	G	rs8127342	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46047633A>G	ENST00000397911.3	+	1	594	c.545A>G	c.(544-546)tAc>tGc	p.Y182C	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	182	25 X 5 AA repeats of C-C-X(3).		Y -> C (in dbSNP:rs8127342). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						CAGCAGTCCTACTGTGTGCCT	0.592													G|||	3191	0.637181	0.5219	0.6772	5008	,	,		22988	0.6667		0.7167	False		,,,				2504	0.6524				p.Y182C		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.A545G						PASS	.	G	,CYS/TYR	2344,2062	568.0+/-382.3	633,1078,492	248.0	264.0	259.0		,545	1.3	0.0	21	dbSNP_116	259	5810,2790	442.8+/-360.2	1958,1894,448	no	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,194	2591,2972,940	GG,GA,AA		32.4419,46.7998,37.3059	,benign	,182/293	46047633	8154,4852	2203	4300	6503	SO:0001583	missense	386676	exon1			AGTCCTACTGTGT	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.545A>G	21.37:g.46047633A>G	ENSP00000381009:p.Tyr182Cys	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	1408	0.6446886446886447	259	0.5264227642276422	245	0.6767955801104972	364	0.6363636363636364	540	0.712401055408971	g	0	-2.837910	0.00069	0.532002	0.675581	ENSG00000221837	ENST00000397911	T	0.00768	5.72	3.45	1.28	0.21552	.	.	.	.	.	T	0.00012	0.0000	N	0.00000	-4.235	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35425	-0.9789	7	.	.	.	.	6.7087	0.23264	0.1159:0.5079:0.3762:0.0	rs8127342	182	P60411	KR109_HUMAN	C	182	ENSP00000381009:Y182C	.	Y	+	2	0	KRTAP10-9	44872061	0.001000	0.12720	0.004000	0.12327	0.010000	0.07245	0.351000	0.20096	0.092000	0.17331	-0.176000	0.13171	TAC	A|0.343;G|0.657	0.657	strong		0.592	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
CACNA1A	773	hgsc.bcm.edu	37	19	13409390	13409390	+	Silent	SNP	C	C	T	rs16025	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:13409390C>T	ENST00000360228.5	-	19	3056	c.3057G>A	c.(3055-3057)agG>agA	p.R1019R	CACNA1A_ENST00000573710.2_Silent_p.R1020R	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1020					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CCTTGTCCTCCCTCCGCGCGT	0.652													C|||	620	0.123802	0.1203	0.1369	5008	,	,		9654	0.1171		0.1501	False		,,,				2504	0.0992				p.R1020R		Atlas-SNP	.											CACNA1A_ENST00000360228,NS,carcinoma,0,4	CACNA1A	715	4	0			c.G3060A						scavenged	.	C	,,,,	371,2877		22,327,1275	22.0	23.0	23.0		3069,3060,3057,3060,3069	2.0	1.0	19	dbSNP_54	23	798,5418		47,704,2357	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	69,1031,3632	TT,TC,CC		12.8378,11.4224,12.3521	,,,,	1023/2267,1020/2262,1019/2507,1020/2264,1023/2513	13409390	1169,8295	1624	3108	4732	SO:0001819	synonymous_variant	773	exon19			GTCCTCCCTCCGC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3057G>A	19.37:g.13409390C>T		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	143	84	0.587413	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.871;T|0.129	0.129	strong		0.652	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
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 GAIIx	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		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	143	29	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	
CCDC88B	283234	hgsc.bcm.edu	37	11	64109118	64109118	+	Missense_Mutation	SNP	T	T	G	rs647152	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64109118T>G	ENST00000356786.5	+	7	623	c.579T>G	c.(577-579)gaT>gaG	p.D193E	CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	193			D -> E (in dbSNP:rs647152).			membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTGGGCCAGATCCTGGGGAGC	0.697													G|||	1768	0.353035	0.3502	0.3991	5008	,	,		12964	0.2401		0.3708	False		,,,				2504	0.4223				p.D193E		Atlas-SNP	.											CCDC88B,NS,carcinoma,0,1	CCDC88B	89	1	0			c.T579G						scavenged	.	G	GLU/ASP	1526,2870		283,960,955	18.0	21.0	20.0		579	2.1	0.9	11	dbSNP_83	20	3090,5492		563,1964,1764	yes	missense	CCDC88B	NM_032251.5	45	846,2924,2719	GG,GT,TT		36.0056,34.7134,35.5679	benign	193/1477	64109118	4616,8362	2198	4291	6489	SO:0001583	missense	283234	exon7			GCCAGATCCTGGG	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.579T>G	11.37:g.64109118T>G	ENSP00000349238:p.Asp193Glu	Somatic	157	2	0.0127389		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	37	CCDS8072.2	760	0.34798534798534797	185	0.37601626016260165	134	0.3701657458563536	147	0.256993006993007	294	0.38786279683377306	.	1.011	-0.687781	0.03328	0.347134	0.360056	ENSG00000168071	ENST00000377638;ENST00000356786	T	0.26223	1.75	4.09	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	N	0.00652	-1.29	0.09310	P	0.99999999176656	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45056	-0.9287	8	0.02654	T	1	.	2.3045	0.04171	0.112:0.1937:0.4945:0.1997	rs647152;rs1201767;rs647152	193;193	B2RTU8;A6NC98	.;CC88B_HUMAN	E	193	ENSP00000349238:D193E	ENSP00000349238:D193E	D	+	3	2	CCDC88B	63865694	0.285000	0.24296	0.937000	0.37676	0.408000	0.30992	0.044000	0.13992	0.129000	0.18514	-0.383000	0.06682	GAT	T|0.649;G|0.351	0.351	strong		0.697	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
PSRC1	84722	hgsc.bcm.edu	37	1	109824250	109824250	+	Silent	SNP	G	G	A	rs35358959	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109824250G>A	ENST00000438534.2	-	4	648	c.510C>T	c.(508-510)aaC>aaT	p.N170N	PSRC1_ENST00000369907.3_Silent_p.N170N|PSRC1_ENST00000369909.2_Silent_p.N170N|PSRC1_ENST00000409267.1_Silent_p.N170N|PSRC1_ENST00000409138.2_Silent_p.N170N|PSRC1_ENST00000369904.3_Silent_p.N170N|PSRC1_ENST00000369903.2_Silent_p.N170N	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	170	4 X 4 AA repeats of P-X-X-P.				microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		CCCTCTTCATGTTGGAGGGCC	0.557													G|||	214	0.0427316	0.0166	0.0303	5008	,	,		18881	0.0308		0.0835	False		,,,				2504	0.0573				p.N170N		Atlas-SNP	.											.	PSRC1	12	.	0			c.C510T						PASS	.	G	,,	115,4291		0,115,2088	74.0	75.0	75.0		510,510,510	-2.6	0.0	1	dbSNP_126	75	633,7965		20,593,3686	no	coding-synonymous,coding-synonymous,coding-synonymous	PSRC1	NM_001005290.3,NM_001032291.2,NM_032636.7	,,	20,708,5774	AA,AG,GG		7.3622,2.6101,5.7521	,,	170/311,170/334,170/334	109824250	748,12256	2203	4299	6502	SO:0001819	synonymous_variant	84722	exon4			CTTCATGTTGGAG		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"""differential display and activated by p53"""	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.510C>T	1.37:g.109824250G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	138	66	0.478261	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Silent	SNP	ENST00000438534.2	37																																																																																				G|0.944;A|0.056	0.056	strong		0.557	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636	
Unknown	0	hgsc.bcm.edu	37	17	17326605	17326605	+	IGR	SNP	A	A	G	rs370938128|rs7225831	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:17326605A>G								NT5M (75630 upstream) : Y_RNA (37152 downstream)																							ATGATGGGGCAAATGCCAGAG	0.478													G|||	2121	0.423522	0.798	0.268	5008	,	,		23339	0.1915		0.3221	False		,,,				2504	0.3712				p.A140A		Atlas-SNP	.											.	.	.	.	0			c.A420G						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			TGGGGCAAATGCC																													17.37:g.17326605A>G		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	16	11	0.6875	NM_001243312		Silent	SNP		37																																																																																				A|0.600;G|0.400	0.400	strong	0	0.478								
ATP2C2	9914	hgsc.bcm.edu	37	16	84449161	84449161	+	Silent	SNP	C	C	T	rs3743651	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84449161C>T	ENST00000262429.4	+	7	677	c.588C>T	c.(586-588)atC>atT	p.I196I	ATP2C2_ENST00000416219.2_Silent_p.I196I|ATP2C2_ENST00000420010.2_3'UTR	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	196					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						CTCTCTCGATCGGAGACCGGA	0.498													C|||	465	0.0928514	0.0575	0.1009	5008	,	,		20453	0.121		0.0736	False		,,,				2504	0.1258				p.I196I		Atlas-SNP	.											.	ATP2C2	75	.	0			c.C588T						PASS	.	C		154,3728		4,146,1791	107.0	102.0	104.0		588	-4.8	0.0	16	dbSNP_107	104	550,7748		17,516,3616	no	coding-synonymous	ATP2C2	NM_014861.2		21,662,5407	TT,TC,CC		6.6281,3.967,5.78		196/947	84449161	704,11476	1941	4149	6090	SO:0001819	synonymous_variant	9914	exon7			CTCGATCGGAGAC	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.588C>T	16.37:g.84449161C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Silent	SNP	ENST00000262429.4	37	CCDS42207.1																																																																																			C|0.917;T|0.083	0.083	strong		0.498	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
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 GAIIx	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	FASTKD2_ENST00000403094.3_Silent_p.H237H|MDH1B_ENST00000454776.2_5'Flank|MDH1B_ENST00000449792.1_5'Flank|MDH1B_ENST00000374412.3_5'Flank|FASTKD2_ENST00000402774.3_Silent_p.H237H|MDH1B_ENST00000392214.2_5'Flank	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		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	25	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	
MUC16	94025	hgsc.bcm.edu	37	19	9084299	9084299	+	Missense_Mutation	SNP	T	T	C	rs1609458	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9084299T>C	ENST00000397910.4	-	1	7719	c.7516A>G	c.(7516-7518)Acc>Gcc	p.T2506A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2506	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CCTACACTGGTCCATGTACCT	0.498											OREG0006612	type=TRANSCRIPTION FACTOR BINDING SITE|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	T|||	2087	0.416733	0.3411	0.5692	5008	,	,		21424	0.3264		0.4841	False		,,,				2504	0.4346				p.T2506A		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	2	0			c.A7516G						PASS	.	T	ALA/THR	1492,2872		282,928,972	72.0	74.0	74.0		7516	0.2	0.0	19	dbSNP_88	74	4373,4211		1142,2089,1061	yes	missense	MUC16	NM_024690.2	58	1424,3017,2033	CC,CT,TT		49.0564,34.1888,45.2966	possibly-damaging	2506/14508	9084299	5865,7083	2182	4292	6474	SO:0001583	missense	94025	exon1			CACTGGTCCATGT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7516A>G	19.37:g.9084299T>C	ENSP00000381008:p.Thr2506Ala	Somatic	119	0	0	654	WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	940	0.43040293040293043	164	0.3333333333333333	200	0.5524861878453039	207	0.3618881118881119	369	0.4868073878627968	t	1.720	-0.496774	0.04291	0.341888	0.509436	ENSG00000181143	ENST00000397910	T	0.01538	4.79	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	P	0.49696	0.927	P	0.56563	0.801	T	0.39683	-0.9602	6	0.87932	D	0	.	.	.	.	rs1609458;rs52827802;rs1609458	2506	B5ME49	.	A	2506	ENSP00000381008:T2506A	ENSP00000381008:T2506A	T	-	1	0	MUC16	8945299	0.002000	0.14202	0.044000	0.18714	0.045000	0.14185	0.793000	0.26944	0.257000	0.21650	0.254000	0.18369	ACC	T|0.562;C|0.438	0.438	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TSPYL4	23270	hgsc.bcm.edu	37	6	116575083	116575083	+	Missense_Mutation	SNP	C	C	A	rs2232470	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:116575083C>A	ENST00000420283.1	-	1	178	c.89G>T	c.(88-90)cGa>cTa	p.R30L	RP3-486I3.7_ENST00000448740.2_lincRNA|DSE_ENST00000540275.1_5'Flank	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	30			R -> L (in dbSNP:rs2232470).		nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(2)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.045)|OV - Ovarian serous cystadenocarcinoma(136;0.0666)|GBM - Glioblastoma multiforme(226;0.095)|Epithelial(106;0.125)		GCACTGGTCTCGGTCCGGATC	0.647													A|||	4423	0.883187	0.9629	0.7896	5008	,	,		16553	0.998		0.661	False		,,,				2504	0.9519				p.R30L		Atlas-SNP	.											.	TSPYL4	18	.	0			c.G89T						PASS	.	A	LEU/ARG	3632,348		1662,308,20	28.0	32.0	31.0		89	-4.1	0.0	6	dbSNP_98	31	5351,2991		1710,1931,530	yes	missense	TSPYL4	NM_021648.4	102	3372,2239,550	AA,AC,CC		35.8547,8.7437,27.0979	benign	30/415	116575083	8983,3339	1990	4171	6161	SO:0001583	missense	23270	exon1			TGGTCTCGGTCCG		CCDS5106.1	6q22.1	2010-05-12			ENSG00000187189	ENSG00000187189			21559	protein-coding gene	gene with protein product							Standard	NM_021648		Approved	dJ486I3.2, KIAA0721	uc003pwn.3	Q9UJ04	OTTHUMG00000015429	ENST00000420283.1:c.89G>T	6.37:g.116575083C>A	ENSP00000410943:p.Arg30Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_021648	B4DYQ2|O94828|Q96GW8	Missense_Mutation	SNP	ENST00000420283.1	37	CCDS5106.1	1825	0.8356227106227107	474	0.9634146341463414	270	0.7458563535911602	570	0.9965034965034965	511	0.6741424802110818	A	6.640	0.486619	0.12641	0.912563	0.641453	ENSG00000187189	ENST00000420283	T	0.25250	1.81	4.3	-4.12	0.03916	.	.	.	.	.	T	0.01627	0.0052	N	0.03115	-0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39542	-0.9609	8	0.07482	T	0.82	6.606	2.2909	0.04138	0.2164:0.2736:0.376:0.1339	rs2232470;rs17582841;rs52798477;rs59116838;rs2232470	30	Q9UJ04	TSYL4_HUMAN	L	30	ENSP00000410943:R30L	ENSP00000410943:R30L	R	-	2	0	TSPYL4	116681776	0.000000	0.05858	0.000000	0.03702	0.502000	0.33828	-0.926000	0.03988	-1.168000	0.02776	-0.525000	0.04345	CGA	C|0.176;A|0.824	0.824	strong		0.647	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2		
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 GAIIx	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	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	150	38	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	
SBNO2	22904	hgsc.bcm.edu	37	19	1127720	1127720	+	Silent	SNP	G	G	A	rs2074916	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1127720G>A	ENST00000361757.3	-	5	561	c.324C>T	c.(322-324)tcC>tcT	p.S108S	SBNO2_ENST00000438103.2_Silent_p.S51S|SBNO2_ENST00000587024.1_Silent_p.S108S	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	108					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)		CCACGGACGAGGAGAAGATGG	0.612													G|||	874	0.174521	0.0136	0.304	5008	,	,		18510	0.1865		0.1958	False		,,,				2504	0.2658				p.S108S		Atlas-SNP	.											SBNO2_ENST00000250872,NS,carcinoma,0,2	SBNO2	112	2	0			c.C324T						PASS	.	G	,	194,4044		3,188,1928	104.0	113.0	110.0		153,324	1.0	0.5	19	dbSNP_96	110	1781,6681		185,1411,2635	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	188,1599,4563	AA,AG,GG		21.047,4.5776,15.5512	,	51/1310,108/1367	1127720	1975,10725	2119	4231	6350	SO:0001819	synonymous_variant	22904	exon5			GGACGAGGAGAAG	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.324C>T	19.37:g.1127720G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			G|0.833;A|0.167	0.167	strong		0.612	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
BCAM	4059	hgsc.bcm.edu	37	19	45322744	45322744	+	Missense_Mutation	SNP	A	A	G	rs1135062	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:45322744A>G	ENST00000270233.6	+	12	1637	c.1615A>G	c.(1615-1617)Acc>Gcc	p.T539A	BCAM_ENST00000589651.1_Missense_Mutation_p.T539A	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	539	Ig-like C2-type 3.		T -> A (in dbSNP:rs1135062). {ECO:0000269|PubMed:7777537, ECO:0000269|PubMed:7954395, ECO:0000269|Ref.7}.		cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				CCACTTCGGCACCGGTGAGTG	0.642													a|||	1354	0.270367	0.4349	0.2305	5008	,	,		15269	0.1131		0.3002	False		,,,				2504	0.2076				p.T539A		Atlas-SNP	.											BCAM,NS,adenoma,0,1	BCAM	53	1	0			c.A1615G	GRCh37	CM973377	BCAM	M	rs1135062	PASS	.		ALA/THR,ALA/THR	1803,2603		376,1051,776	55.0	61.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1615,1615	-8.3	0.0	19	dbSNP_86	59	2588,6012		384,1820,2096	yes	missense,missense	BCAM	NM_001013257.1,NM_005581.3	58,58	760,2871,2872	GG,GA,AA		30.093,40.9215,33.7613	benign,benign	539/589,539/629	45322744	4391,8615	2203	4300	6503	SO:0001583	missense	4059	exon12			TTCGGCACCGGTG	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.1615A>G	19.37:g.45322744A>G	ENSP00000270233:p.Thr539Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	579	0.2651098901098901	205	0.4166666666666667	88	0.2430939226519337	55	0.09615384615384616	231	0.30474934036939316	.	5.337	0.247523	0.10130	0.409215	0.30093	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.59364	0.27;0.29	4.24	-8.33	0.00992	Immunoglobulin subtype (1);Immunoglobulin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29731	-1.0002	8	0.05620	T	0.96	0.1002	1.2179	0.01918	0.1523:0.2382:0.3376:0.2719	rs1135062;rs11548861;rs11880954;rs16979448;rs58063257;rs1135062	539	P50895	BCAM_HUMAN	A	539	ENSP00000270233:T539A;ENSP00000375817:T539A	ENSP00000270233:T539A	T	+	1	0	BCAM	50014584	0.000000	0.05858	0.001000	0.08648	0.187000	0.23431	-0.967000	0.03821	-1.683000	0.01444	0.434000	0.28630	ACC	A|0.703;G|0.297	0.297	strong		0.642	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
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 GAIIx	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	Somatic	145	0	0	1526	WXS	Illumina HiSeq	Phase_I	177	82	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	
SACS	26278	hgsc.bcm.edu	37	13	23929095	23929095	+	Silent	SNP	T	T	C	rs1536365	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:23929095T>C	ENST00000382292.3	-	7	1929	c.1656A>G	c.(1654-1656)ctA>ctG	p.L552L	SACS_ENST00000382298.3_Silent_p.L552L|SACS_ENST00000402364.1_5'UTR|SACS_ENST00000476776.1_5'Flank			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	552					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GCTCGCTGAATAGAGGCTCTA	0.448													T|||	434	0.0866613	0.0068	0.0922	5008	,	,		20446	0.121		0.1302	False		,,,				2504	0.1104				p.L552L		Atlas-SNP	.											.	SACS	871	.	0			c.A1656G						PASS	.	T		103,4303	79.9+/-118.3	2,99,2102	92.0	90.0	91.0		1656	3.0	0.8	13	dbSNP_88	91	1000,7600	214.9+/-254.4	49,902,3349	no	coding-synonymous	SACS	NM_014363.4		51,1001,5451	CC,CT,TT		11.6279,2.3377,8.4807		552/4580	23929095	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	26278	exon8			GCTGAATAGAGGC	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.1656A>G	13.37:g.23929095T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	82	30	0.365854	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2	209	0.09569597069597069	2	0.0040650406504065045	32	0.08839779005524862	74	0.12937062937062938	101	0.13324538258575197	T	6.072	0.381670	0.11524	0.023377	0.116279	ENSG00000151835	ENST00000455470	.	.	.	5.74	2.98	0.34508	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.12243	-1.0555	3	.	.	.	.	1.3758	0.02220	0.237:0.4256:0.1283:0.2092	rs1536365;rs17378673;rs1536365	.	.	.	V	452	.	.	I	-	1	0	SACS	22827095	0.449000	0.25689	0.846000	0.33378	0.721000	0.41392	-0.234000	0.09028	0.451000	0.26802	-1.239000	0.01543	ATT	T|0.909;C|0.091	0.091	strong		0.448	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
KIAA1377	57562	hgsc.bcm.edu	37	11	101829006	101829006	+	Missense_Mutation	SNP	G	G	A	rs61743062	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:101829006G>A	ENST00000263468.8	+	5	884	c.614G>A	c.(613-615)aGg>aAg	p.R205K	KIAA1377_ENST00000537689.1_Missense_Mutation_p.R6K	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	205										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		GAAAACATGAGGGCAACCTTG	0.378													G|||	69	0.013778	0.0318	0.0058	5008	,	,		17783	0.0		0.0129	False		,,,				2504	0.0102				p.R205K		Atlas-SNP	.											.	KIAA1377	111	.	0			c.G614A						PASS	.	G	LYS/ARG	118,4288	88.2+/-126.9	1,116,2086	156.0	167.0	163.0		614	-5.8	0.0	11	dbSNP_129	163	174,8424	78.9+/-141.6	1,172,4126	yes	missense	KIAA1377	NM_020802.2	26	2,288,6212	AA,AG,GG		2.0237,2.6782,2.2455	benign	205/1118	101829006	292,12712	2203	4299	6502	SO:0001583	missense	57562	exon5			ACATGAGGGCAAC	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.614G>A	11.37:g.101829006G>A	ENSP00000263468:p.Arg205Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	99	84	0.848485	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	21	0.009615384615384616	6	0.012195121951219513	4	0.011049723756906077	0	0.0	11	0.014511873350923483	G	0.653	-0.808792	0.02819	0.026782	0.020237	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.06849	3.25;3.25	5.68	-5.78	0.02362	.	0.438298	0.23596	N	0.046498	T	0.00724	0.0024	N	0.12569	0.235	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38628	-0.9652	10	0.02654	T	1	0.0771	0.7288	0.00953	0.4017:0.1676:0.2139:0.2169	rs61743062	205	Q9P2H0	K1377_HUMAN	K	205;6	ENSP00000263468:R205K;ENSP00000443184:R6K	ENSP00000263468:R205K	R	+	2	0	KIAA1377	101334216	0.000000	0.05858	0.020000	0.16555	0.094000	0.18550	0.063000	0.14410	-0.928000	0.03761	-0.808000	0.03180	AGG	G|0.981;A|0.019	0.019	strong		0.378	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
NT5DC3	51559	hgsc.bcm.edu	37	12	104208868	104208868	+	Silent	SNP	C	C	T	rs10861107	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:104208868C>T	ENST00000392876.3	-	2	280	c.240G>A	c.(238-240)ttG>ttA	p.L80L		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	80						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						CATCTGGATTCAACAAGTTGC	0.318													C|||	611	0.122005	0.1263	0.1412	5008	,	,		18667	0.0833		0.2326	False		,,,				2504	0.0286				p.L80L		Atlas-SNP	.											.	NT5DC3	113	.	0			c.G240A						PASS	.	C		597,3809	261.9+/-264.6	36,525,1642	71.0	66.0	67.0		240	5.0	1.0	12	dbSNP_120	67	1856,6744	331.4+/-319.6	187,1482,2631	no	coding-synonymous	NT5DC3	NM_001031701.2		223,2007,4273	TT,TC,CC		21.5814,13.5497,18.8605		80/549	104208868	2453,10553	2203	4300	6503	SO:0001819	synonymous_variant	51559	exon2			TGGATTCAACAAG	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.240G>A	12.37:g.104208868C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Silent	SNP	ENST00000392876.3	37	CCDS41824.1																																																																																			C|0.828;T|0.172	0.172	strong		0.318	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575	
RYR1	6261	hgsc.bcm.edu	37	19	38995975	38995975	+	Silent	SNP	G	G	A	rs2915952	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38995975G>A	ENST00000359596.3	+	53	8337	c.8337G>A	c.(8335-8337)gaG>gaA	p.E2779E	RYR1_ENST00000360985.3_Silent_p.E2779E|RYR1_ENST00000355481.4_Silent_p.E2779E			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2779	6 X approximate repeats.		E -> K (in dbSNP:rs2915952).		calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.E2779E(1)		NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	CCTATGGAGAGAACATAGACG	0.592													G|||	2033	0.40595	0.4856	0.366	5008	,	,		16453	0.3532		0.2982	False		,,,				2504	0.4918				p.E2779E		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	1	1	Substitution - coding silent(1)	stomach(1)	c.G8337A						PASS	.	G	,	1879,2525	527.6+/-372.2	394,1091,717	44.0	36.0	39.0		8337,8337	1.9	1.0	19	dbSNP_101	39	2129,6471	351.7+/-328.4	286,1557,2457	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	680,2648,3174	AA,AG,GG		24.7558,42.6658,30.8213	,	2779/5039,2779/5034	38995975	4008,8996	2202	4300	6502	SO:0001819	synonymous_variant	6261	exon53			TGGAGAGAACATA	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.8337G>A	19.37:g.38995975G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			G|0.684;A|0.316	0.316	strong		0.592	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
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 GAIIx	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_ENST00000478285.1_5'Flank|TDP2_ENST00000341060.3_Silent_p.L187L|TDP2_ENST00000545995.1_Silent_p.L275L			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		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	74	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 GAIIx	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_ENST00000348007.3_Missense_Mutation_p.R672G|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000396158.2_Missense_Mutation_p.R720G|CTAGE5_ENST00000556148.1_Missense_Mutation_p.R640G|CTAGE5_ENST00000341502.5_Missense_Mutation_p.R715G|CTAGE5_ENST00000341749.3_Missense_Mutation_p.R703G|CTAGE5_ENST00000553352.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000557038.1_Missense_Mutation_p.R635G|CTAGE5_ENST00000396165.4_Missense_Mutation_p.R686G|CTAGE5_ENST00000553383.1_3'UTR|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.R1250G			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	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	129	61	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	
ADAM9	8754	hgsc.bcm.edu	37	8	38854660	38854660	+	Silent	SNP	C	C	A	rs148707472	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:38854660C>A	ENST00000487273.2	+	1	156	c.78C>A	c.(76-78)gtC>gtA	p.V26V	ADAM9_ENST00000466936.1_Silent_p.V26V|TM2D2_ENST00000397070.2_5'Flank|ADAM9_ENST00000481513.1_Silent_p.V26V|TM2D2_ENST00000456845.2_5'Flank|TM2D2_ENST00000456397.2_5'Flank|TM2D2_ENST00000412303.1_5'Flank|TM2D2_ENST00000522434.1_5'Flank	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	26				Missing (in Ref. 2; no nucleotide entry). {ECO:0000305}.	activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			TGGGCCCAGTCCTCGGTGCGG	0.706													C|||	110	0.0219649	0.0038	0.049	5008	,	,		11618	0.0		0.0666	False		,,,				2504	0.0041				p.V26V		Atlas-SNP	.											.	ADAM9	66	.	0			c.C78A						PASS	.	C		54,4348	52.9+/-88.7	1,52,2148	50.0	44.0	46.0		78	0.9	1.0	8	dbSNP_134	46	452,8146	131.2+/-189.0	9,434,3856	no	coding-synonymous	ADAM9	NM_003816.2		10,486,6004	AA,AC,CC		5.257,1.2267,3.8923		26/820	38854660	506,12494	2201	4299	6500	SO:0001819	synonymous_variant	8754	exon1			CCCAGTCCTCGGT	U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"""ADAM metallopeptidase domain containing"""	216	protein-coding gene	gene with protein product	"""meltrin gamma"""	602713	"""a disintegrin and metalloproteinase domain 9 (meltrin gamma)"", ""cone rod dystrophy 9"""	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.78C>A	8.37:g.38854660C>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_003816	B7ZLN7|Q10718|Q8NFM6	Silent	SNP	ENST00000487273.2	37	CCDS6112.1																																																																																			C|0.964;A|0.036	0.036	strong		0.706	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2		
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2930339	2930339	+	Silent	SNP	G	G	A	rs4790115	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2930339G>A	ENST00000254695.8	+	22	2172	c.2082G>A	c.(2080-2082)ccG>ccA	p.P694P	RAP1GAP2_ENST00000542807.1_Silent_p.P694P|RAP1GAP2_ENST00000366401.4_Silent_p.P679P|RAP1GAP2_ENST00000540393.2_Silent_p.P675P	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	694	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CTGCCACCCCGATCATCATGA	0.657													G|||	2140	0.427316	0.2428	0.4942	5008	,	,		17712	0.5486		0.4066	False		,,,				2504	0.5256				p.P694P		Atlas-SNP	.											RAP1GAP2_ENST00000254695,colon,carcinoma,0,2	RAP1GAP2	90	2	0			c.G2082A						PASS	.	G	,	1208,3184		180,848,1168	22.0	27.0	25.0		2037,2082	-1.5	1.0	17	dbSNP_111	25	3488,5074		722,2044,1515	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	902,2892,2683	AA,AG,GG		40.7381,27.5046,36.2514	,	679/716,694/731	2930339	4696,8258	2196	4281	6477	SO:0001819	synonymous_variant	23108	exon22			CACCCCGATCATC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.2082G>A	17.37:g.2930339G>A		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	217	100	0.460829	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			G|0.567;A|0.433	0.433	strong		0.657	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
SYT9	143425	hgsc.bcm.edu	37	11	7324584	7324584	+	Missense_Mutation	SNP	G	G	A	rs78477754	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7324584G>A	ENST00000318881.6	+	2	697	c.460G>A	c.(460-462)Gtg>Atg	p.V154M	SYT9_ENST00000396716.2_Missense_Mutation_p.V122M	NM_175733.3	NP_783860.1	Q86SS6	SYT9_HUMAN	synaptotagmin IX	154			V -> M (in dbSNP:rs78477754). {ECO:0000269|PubMed:21220648}.		positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of insulin secretion (GO:0050796)	cell junction (GO:0030054)|dense core granule (GO:0031045)|integral component of membrane (GO:0016021)|secretory granule membrane (GO:0030667)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	38				Epithelial(150;1.34e-07)|LUSC - Lung squamous cell carcinoma(625;0.0949)		TGGCGTCCGCGTGCAGCGCCA	0.612													G|||	70	0.0139776	0.0151	0.0288	5008	,	,		17439	0.0		0.0288	False		,,,				2504	0.001				p.V154M		Atlas-SNP	.											.	SYT9	91	.	0			c.G460A						PASS	.	G	MET/VAL	75,4327	66.4+/-103.9	2,71,2128	50.0	43.0	45.0		460	1.3	0.0	11	dbSNP_131	45	276,8316	105.2+/-166.2	6,264,4026	yes	missense	SYT9	NM_175733.3	21	8,335,6154	AA,AG,GG		3.2123,1.7038,2.7012	benign	154/492	7324584	351,12643	2201	4296	6497	SO:0001583	missense	143425	exon2			GTCCGCGTGCAGC	AK055003	CCDS7778.1	11p15.4	2013-01-21			ENSG00000170743	ENSG00000170743		"""Synaptotagmins"""	19265	protein-coding gene	gene with protein product		613528				11543631	Standard	NM_175733		Approved		uc001mfe.3	Q86SS6	OTTHUMG00000165499	ENST00000318881.6:c.460G>A	11.37:g.7324584G>A	ENSP00000324419:p.Val154Met	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_175733		Missense_Mutation	SNP	ENST00000318881.6	37	CCDS7778.1	37	0.01694139194139194	5	0.01016260162601626	13	0.03591160220994475	0	0.0	19	0.025065963060686015	G	4.269	0.049097	0.08243	0.017038	0.032123	ENSG00000170743	ENST00000396716;ENST00000318881	T;T	0.55760	0.5;0.53	5.73	1.29	0.21616	.	0.265273	0.32655	N	0.005811	T	0.06234	0.0161	N	0.03154	-0.405	0.09310	N	0.999996	B	0.12630	0.006	B	0.12156	0.007	T	0.09684	-1.0663	10	0.33940	T	0.23	.	8.3136	0.32086	0.4328:0.0:0.5672:0.0	.	154	Q86SS6	SYT9_HUMAN	M	122;154	ENSP00000379944:V122M;ENSP00000324419:V154M	ENSP00000324419:V154M	V	+	1	0	SYT9	7281160	0.957000	0.32711	0.009000	0.14445	0.461000	0.32589	2.068000	0.41471	0.368000	0.24481	-0.136000	0.14681	GTG	G|0.974;A|0.026	0.026	strong		0.612	SYT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384483.1	NM_175733	
KCNJ11	3767	hgsc.bcm.edu	37	11	17408496	17408496	+	Silent	SNP	C	C	T	rs8175351	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:17408496C>T	ENST00000339994.4	-	1	1710	c.1143G>A	c.(1141-1143)aaG>aaA	p.K381K	KCNJ11_ENST00000528731.1_Silent_p.K294K|KCNJ11_ENST00000526747.1_5'Flank	NM_000525.3	NP_000516.3	Q14654	KCJ11_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 11	381					cellular response to glucose stimulus (GO:0071333)|cellular response to nicotine (GO:0071316)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|negative regulation of insulin secretion (GO:0046676)|neurological system process (GO:0050877)|positive regulation of cation channel activity (GO:2001259)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ischemia (GO:0002931)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	ATP-sensitive potassium channel complex (GO:0008282)|axolemma (GO:0030673)|cell body fiber (GO:0070852)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|ion channel binding (GO:0044325)|potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(3)|skin(2)	16				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)	Diazoxide(DB01119)|Glimepiride(DB00222)|Glyburide(DB01016)|Ibutilide(DB00308)|Levosimendan(DB00922)|Thiamylal(DB01154)|Verapamil(DB00661)|Yohimbine(DB01392)	AGATGCTGAACTTGGGCTTGG	0.647											OREG0020810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	22	0.00439297	0.0023	0.0072	5008	,	,		18714	0.001		0.0099	False		,,,				2504	0.0031				p.K381K		Atlas-SNP	.											.	KCNJ11	39	.	0			c.G1143A						PASS	.	C	,	19,4381	26.2+/-53.5	0,19,2181	46.0	43.0	44.0		1143,882	4.3	1.0	11	dbSNP_117	44	184,8402	82.6+/-145.2	3,178,4112	yes	coding-synonymous,coding-synonymous	KCNJ11	NM_000525.3,NM_001166290.1	,	3,197,6293	TT,TC,CC		2.143,0.4318,1.5632	,	381/391,294/304	17408496	203,12783	2200	4293	6493	SO:0001819	synonymous_variant	3767	exon1			GCTGAACTTGGGC	D50582	CCDS31436.1, CCDS53606.1	11p15.1	2011-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6257	protein-coding gene	gene with protein product		600937				7502040, 16382105	Standard	NM_001166290		Approved	Kir6.2, BIR	uc001mna.3	Q14654		ENST00000339994.4:c.1143G>A	11.37:g.17408496C>T		Somatic	88	0	0	717	WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_000525	B4DWI4|E9PNK0|Q2M1H7|Q58EX3|Q8IW96	Silent	SNP	ENST00000339994.4	37	CCDS31436.1																																																																																			C|0.986;T|0.014	0.014	strong		0.647	KCNJ11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387037.1	NM_000525	
MUC16	94025	hgsc.bcm.edu	37	19	9090531	9090531	+	Silent	SNP	T	T	C	rs12976721	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9090531T>C	ENST00000397910.4	-	1	1487	c.1284A>G	c.(1282-1284)gaA>gaG	p.E428E		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	428	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.E428E(2)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCCTTCTGTTTCCTTTCCAC	0.502													T|||	1082	0.216054	0.27	0.2248	5008	,	,		21630	0.0228		0.3091	False		,,,				2504	0.2403				p.E428E		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	2	Substitution - coding silent(2)	prostate(2)	c.A1284G						PASS	.	T		1019,2945		145,729,1108	152.0	141.0	145.0		1284	-2.8	0.0	19	dbSNP_121	145	2733,5603		459,1815,1894	no	coding-synonymous	MUC16	NM_024690.2		604,2544,3002	CC,CT,TT		32.7855,25.7064,30.5041		428/14508	9090531	3752,8548	1982	4168	6150	SO:0001819	synonymous_variant	94025	exon1			TTCTGTTTCCTTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.1284A>G	19.37:g.9090531T>C		Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	245	108	0.440816	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			T|0.772;C|0.228	0.228	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
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 GAIIx	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	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	184	47	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	
DND1	373863	hgsc.bcm.edu	37	5	140050940	140050940	+	Missense_Mutation	SNP	C	C	T	rs77880328	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140050940C>T	ENST00000542735.1	-	4	1043	c.1000G>A	c.(1000-1002)Gag>Aag	p.E334K	WDR55_ENST00000358337.5_3'UTR|WDR55_ENST00000520764.1_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	334					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of gene silencing by miRNA (GO:0060965)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)			central_nervous_system(1)|prostate(4)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCCCAGACTCACTGAGTGCC	0.592																																					p.E334K		Atlas-SNP	.											DND1,NS,carcinoma,0,1	DND1	15	1	0			c.G1000A						scavenged	.						67.0	61.0	63.0					5																	140050940		2008	4046	6054	SO:0001583	missense	373863	exon4			CAGACTCACTGAG	AY321065	CCDS4236.1	5q31.3	2013-07-31	2013-07-31		ENSG00000256453	ENSG00000256453		"""RNA binding motif (RRM) containing"""	23799	protein-coding gene	gene with protein product		609385	"""dead end homolog 1 (zebrafish)"""			12932328	Standard	NM_194249		Approved	MGC34750, RBMS4	uc003lgt.3	Q8IYX4	OTTHUMG00000129499	ENST00000542735.1:c.1000G>A	5.37:g.140050940C>T	ENSP00000445366:p.Glu334Lys	Somatic	322	0	0		WXS	Illumina HiSeq	Phase_I	761	127	0.166886	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	C	12.59	1.984700	0.35036	.	.	ENSG00000256453	ENST00000542735	T	0.32988	1.43	5.3	3.53	0.40419	.	0.429652	0.22940	N	0.053797	T	0.16769	0.0403	L	0.27053	0.805	0.27535	N	0.950973	B	0.02656	0.0	B	0.06405	0.002	T	0.29792	-1.0000	10	0.05620	T	0.96	-17.9422	9.0835	0.36567	0.0:0.7627:0.0:0.2373	.	334	Q8IYX4	DND1_HUMAN	K	334	ENSP00000445366:E334K	ENSP00000445366:E334K	E	-	1	0	DND1	140031124	0.995000	0.38212	0.998000	0.56505	0.721000	0.41392	1.914000	0.39966	0.821000	0.34540	0.551000	0.68910	GAG	A|0.029;G|0.971	.	alt		0.592	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
NRF1	4899	hgsc.bcm.edu	37	7	129297332	129297332	+	Silent	SNP	T	T	G	rs1882094	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:129297332T>G	ENST00000393232.1	+	2	258	c.141T>G	c.(139-141)tcT>tcG	p.S47S	NRF1_ENST00000353868.4_Silent_p.S47S|NRF1_ENST00000393231.3_Silent_p.S47S|NRF1_ENST00000539636.1_5'UTR|NRF1_ENST00000393230.2_Silent_p.S47S|NRF1_ENST00000311967.2_Silent_p.S47S|NRF1_ENST00000223190.4_Silent_p.S47S	NM_005011.3	NP_005002.3	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	47	Asp/Glu-rich (acidic).|Dimerization.				cellular lipid metabolic process (GO:0044255)|generation of precursor metabolites and energy (GO:0006091)|mitochondrion organization (GO:0007005)|organ regeneration (GO:0031100)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	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(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	24						CGCCTTCTTCTCCCGAGGACA	0.512																																					p.S47S		Atlas-SNP	.											NRF1,NS,adenoma,0,1	NRF1	40	1	0			c.T141G						PASS	.	T	,	2992,1414	686.2+/-404.7	1016,960,227	127.0	108.0	114.0		141,141	-0.5	1.0	7	dbSNP_92	114	2533,6067	412.5+/-350.8	383,1767,2150	no	coding-synonymous,coding-synonymous	NRF1	NM_001040110.1,NM_005011.3	,	1399,2727,2377	GG,GT,TT		29.4535,32.0926,42.4804	,	47/504,47/504	129297332	5525,7481	2203	4300	6503	SO:0001819	synonymous_variant	4899	exon2			TTCTTCTCCCGAG	L22454	CCDS5813.2	7q32	2008-07-18			ENSG00000106459	ENSG00000106459			7996	protein-coding gene	gene with protein product	"""alpha palindromic-binding protein"""	600879				2584221	Standard	NM_005011		Approved	EWG, ALPHA-PAL	uc003voz.3	Q16656	OTTHUMG00000143736	ENST00000393232.1:c.141T>G	7.37:g.129297332T>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_005011	A8K4C6|B4DDV6|Q15305|Q96AN2	Silent	SNP	ENST00000393232.1	37	CCDS5813.2																																																																																			T|0.531;G|0.469	0.469	strong		0.512	NRF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289813.1	NM_001040110	
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 GAIIx	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	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	136	40	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	
NANOG	79923	hgsc.bcm.edu	37	12	7945757	7945757	+	Silent	SNP	C	C	T	rs4438116	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:7945757C>T	ENST00000229307.4	+	2	582	c.363C>T	c.(361-363)agC>agT	p.S121S	NANOG_ENST00000526286.1_Silent_p.S121S	NM_024865.2	NP_079141.2	Q9H9S0	NANOG_HUMAN	Nanog homeobox	121					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|embryo development (GO:0009790)|embryonic pattern specification (GO:0009880)|endodermal cell fate specification (GO:0001714)|gonad development (GO:0008406)|mesodermal cell fate commitment (GO:0001710)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell differentiation (GO:0045595)|regulation of gene expression (GO:0010468)|regulation of transcription, DNA-templated (GO:0006355)|response to retinoic acid (GO:0032526)|somatic stem cell maintenance (GO:0035019)|stem cell division (GO:0017145)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	14				Kidney(36;0.0872)		AATACCTCAGCCTCCAGCAGA	0.438													C|||	804	0.160543	0.1384	0.1787	5008	,	,		-128	0.006		0.3151	False		,,,				2504	0.1779				p.S121S		Atlas-SNP	.											.	NANOG	30	.	0			c.C363T						PASS	.	C		705,3665		61,583,1541	26.0	24.0	24.0		363	-1.3	1.0	12	dbSNP_111	24	2295,6121		325,1645,2238	no	coding-synonymous	NANOG	NM_024865.2		386,2228,3779	TT,TC,CC		27.2695,16.1327,23.4632		121/306	7945757	3000,9786	2185	4208	6393	SO:0001819	synonymous_variant	79923	exon2			CCTCAGCCTCCAG	AB093576	CCDS31736.1, CCDS73436.1	12p13.31	2011-06-20			ENSG00000111704	ENSG00000111704		"""Homeoboxes / ANTP class : NKL subclass"""	20857	protein-coding gene	gene with protein product		607937				12787505, 12787504	Standard	XM_005253484		Approved	FLJ12581, FLJ40451	uc009zfy.1	Q9H9S0		ENST00000229307.4:c.363C>T	12.37:g.7945757C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	106	0.938053	NM_024865	D3DUU4|Q2TTG0|Q6JZS5	Silent	SNP	ENST00000229307.4	37	CCDS31736.1																																																																																			.	.	weak		0.438	NANOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387480.2	NM_024865	
KIF4A	24137	hgsc.bcm.edu	37	X	69561780	69561780	+	Splice_Site	SNP	T	T	G	rs1199457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:69561780T>G	ENST00000374403.3	+	11	1347	c.1265T>G	c.(1264-1266)tTg>tGg	p.L422W	KIF4A_ENST00000374388.3_Splice_Site_p.L422W	NM_012310.4	NP_036442.3	O95239	KIF4A_HUMAN	kinesin family member 4A	422			L -> W (in dbSNP:rs1199457). {ECO:0000269|PubMed:10978527, ECO:0000269|PubMed:15489334}.		anterograde axon cargo transport (GO:0008089)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle organization (GO:0006996)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(6)|endometrium(9)|kidney(3)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	51						AGGATCATTTTGGTAAGCCCC	0.403													T|||	451	0.11947	0.2799	0.0375	3775	,	,		12134	0.0		0.0398	False		,,,				2504	0.0153				p.L422W		Atlas-SNP	.											.	KIF4A	118	.	0			c.T1265G						PASS	.	T	TRP/LEU	1333,2502		212,708,201,712,370	95.0	95.0	95.0		1265	4.8	1.0	X	dbSNP_87	95	323,6405		3,227,90,2198,1782	yes	missense-near-splice	KIF4A	NM_012310.4	61	215,935,291,2910,2152	GG,GT,G,TT,T		4.8008,34.7588,15.6774	possibly-damaging	422/1233	69561780	1656,8907	2203	4300	6503	SO:0001630	splice_region_variant	24137	exon11			TCATTTTGGTAAG	AF179308	CCDS14401.1	Xq13.1	2008-08-11			ENSG00000090889	ENSG00000090889		"""Kinesins"""	13339	protein-coding gene	gene with protein product	"""chromokinesin"""	300521				10773663	Standard	NM_012310		Approved	KIF4-G1, KIF4, HSA271784, FLJ12530, FLJ12655, FLJ14204, FLJ20631	uc004dyg.3	O95239	OTTHUMG00000021775	ENST00000374403.3:c.1266+1T>G	X.37:g.69561780T>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	175	125	0.714286	NM_012310	B2R7V5|D3DVU4|Q86TN3|Q86XX7|Q9NNY6|Q9NY24|Q9UMW3	Missense_Mutation	SNP	ENST00000374403.3	37	CCDS14401.1	160	0.09644364074743822	73	0.17464114832535885	13	0.03672316384180791	0	0.0	20	0.0273224043715847	T	18.31	3.595877	0.66332	0.347588	0.048008	ENSG00000090889	ENST00000374388;ENST00000374403	T;T	0.52983	0.64;0.64	4.77	4.77	0.60923	.	0.151044	0.31167	N	0.008127	T	0.00012	0.0000	L	0.27053	0.805	0.20307	P	0.9999110836	D;D	0.67145	0.995;0.996	P;D	0.63703	0.844;0.917	T	0.31861	-0.9928	9	0.72032	D	0.01	.	12.2319	0.54492	0.0:0.0:0.0:1.0	rs1199457;rs52827837;rs1199457	422;422	O95239;O95239-2	KIF4A_HUMAN;.	W	422	ENSP00000363509:L422W;ENSP00000363524:L422W	ENSP00000363509:L422W	L	+	2	0	KIF4A	69478505	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	3.976000	0.56867	1.765000	0.52091	0.345000	0.21793	TTG	T|0.841;0|0.015	.	strong		0.403	KIF4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057068.1	NM_012310	Missense_Mutation
MUC16	94025	hgsc.bcm.edu	37	19	9086123	9086123	+	Missense_Mutation	SNP	A	A	C	rs10402812	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9086123A>C	ENST00000397910.4	-	1	5895	c.5692T>G	c.(5692-5694)Tac>Gac	p.Y1898D		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1898	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TTCTCTGTGTAAGTCATGGAA	0.493													A|||	1134	0.226438	0.27	0.2983	5008	,	,		21776	0.0228		0.3111	False		,,,				2504	0.2393				p.Y1898D		Atlas-SNP	.											.	MUC16	4315	.	0			c.T5692G						PASS	.	A	ASP/TYR	1034,2846		147,740,1053	90.0	84.0	86.0		5692	0.2	0.0	19	dbSNP_119	86	2740,5574		461,1818,1878	yes	missense	MUC16	NM_024690.2	160	608,2558,2931	CC,CA,AA		32.9565,26.6495,30.9496	probably-damaging	1898/14508	9086123	3774,8420	1940	4157	6097	SO:0001583	missense	94025	exon1			CTGTGTAAGTCAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.5692T>G	19.37:g.9086123A>C	ENSP00000381008:p.Tyr1898Asp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	490	0.22435897435897437	127	0.258130081300813	111	0.30662983425414364	14	0.024475524475524476	238	0.31398416886543534	a	0.462	-0.888737	0.02511	0.266495	0.329565	ENSG00000181143	ENST00000397910	T	0.01560	4.77	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	D	0.62365	0.991	D	0.68039	0.955	T	0.50171	-0.8859	6	0.87932	D	0	.	.	.	.	rs10402812;rs58531423;rs10402812	1898	B5ME49	.	D	1898	ENSP00000381008:Y1898D	ENSP00000381008:Y1898D	Y	-	1	0	MUC16	8947123	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-1.057000	0.03486	0.257000	0.21650	0.254000	0.18369	TAC	A|0.765;C|0.235	0.235	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MAGEB18	286514	hgsc.bcm.edu	37	X	26157792	26157792	+	Silent	SNP	C	C	T	rs5944318	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:26157792C>T	ENST00000325250.1	+	2	877	c.690C>T	c.(688-690)gcC>gcT	p.A230A		NM_173699.3	NP_775970	Q96M61	MAGBI_HUMAN	melanoma antigen family B, 18	230	Interaction with LNX1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					cytoplasm (GO:0005737)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(17)|skin(2)|stomach(1)|urinary_tract(2)	33						GTGTATATGCCGATAGGAAGC	0.498													T|||	2795	0.740397	0.6339	0.5519	3775	,	,		15061	0.6935		0.3151	False		,,,				2504	0.5706				p.A230A		Atlas-SNP	.											.	MAGEB18	67	.	0			c.C690T						PASS	.	T		3040,793		1012,548,468,71,103	47.0	41.0	43.0		690	-0.7	0.1	X	dbSNP_114	43	2837,3891		443,1165,786,820,1086	no	coding-synonymous	MAGEB18	NM_173699.3		1455,1713,1254,891,1189	TT,TC,T,CC,C		42.1671,20.6888,44.3519		230/344	26157792	5877,4684	2202	4300	6502	SO:0001819	synonymous_variant	286514	exon2			ATATGCCGATAGG	AK057361	CCDS14216.1	Xp21.3	2008-02-05			ENSG00000176774	ENSG00000176774			28515	protein-coding gene	gene with protein product							Standard	NM_173699		Approved	MGC33889	uc004dbq.2	Q96M61	OTTHUMG00000021282	ENST00000325250.1:c.690C>T	X.37:g.26157792C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	38	0.372549	NM_173699		Silent	SNP	ENST00000325250.1	37	CCDS14216.1																																																																																			C|0.368;T|0.632	0.632	strong		0.498	MAGEB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056120.1	NM_173699	
SSTR4	6754	hgsc.bcm.edu	37	20	23017017	23017017	+	Silent	SNP	T	T	C	rs2567609	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:23017017T>C	ENST00000255008.3	+	1	961	c.897T>C	c.(895-897)ctT>ctC	p.L299L	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	299					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					CCCTTATCCTTAGCTATGCCA	0.572													C|||	2415	0.482228	0.4107	0.4669	5008	,	,		18691	0.5258		0.4294	False		,,,				2504	0.5992				p.L299L	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,colon,carcinoma,0,2	SSTR4	83	2	0			c.T897C						PASS	.	C		1770,2636	625.8+/-394.6	379,1012,812	199.0	197.0	197.0		897	2.4	1.0	20	dbSNP_100	197	3925,4675	598.8+/-394.0	922,2081,1297	no	coding-synonymous	SSTR4	NM_001052.2		1301,3093,2109	CC,CT,TT		45.6395,40.1725,43.7875		299/389	23017017	5695,7311	2203	4300	6503	SO:0001819	synonymous_variant	6754	exon1			TATCCTTAGCTAT		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.897T>C	20.37:g.23017017T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Silent	SNP	ENST00000255008.3	37	CCDS42856.1																																																																																			T|0.514;C|0.486	0.486	strong		0.572	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
MICALL2	79778	hgsc.bcm.edu	37	7	1482101	1482101	+	Missense_Mutation	SNP	C	C	G	rs12540098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:1482101C>G	ENST00000297508.7	-	7	1613	c.1438G>C	c.(1438-1440)Gct>Cct	p.A480P	MICALL2_ENST00000405088.4_Missense_Mutation_p.A268P	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	480	Mediates targeting to the cell plasma membrane. {ECO:0000250}.		A -> P (in dbSNP:rs12540098).		actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CTGGGAACAGCGGCAGTGGCT	0.627													G|||	1035	0.206669	0.4486	0.2925	5008	,	,		14067	0.0397		0.1054	False		,,,				2504	0.0951				p.A480P		Atlas-SNP	.											.	MICALL2	63	.	0			c.G1438C						PASS	.		PRO/ALA	1640,2766	655.8+/-400.0	302,1036,865	163.0	174.0	170.0		1438	0.4	0.0	7	dbSNP_120	170	797,7803	781.8+/-407.6	32,733,3535	yes	missense	MICALL2	NM_182924.3	27	334,1769,4400	GG,GC,CC		9.2674,37.222,18.7375	benign	480/905	1482101	2437,10569	2203	4300	6503	SO:0001583	missense	79778	exon7			GAACAGCGGCAGT	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.1438G>C	7.37:g.1482101C>G	ENSP00000297508:p.Ala480Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	107	38	0.35514	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	449	0.20558608058608058	232	0.4715447154471545	99	0.27348066298342544	35	0.06118881118881119	83	0.10949868073878628	G	0.011	-1.716954	0.00706	0.37222	0.092674	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.68765	2.53;-0.35	3.69	0.38	0.16222	.	1.188450	0.06575	N	0.749296	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34850	-0.9812	9	0.30078	T	0.28	.	3.7085	0.08410	0.4146:0.1886:0.3968:0.0	rs12540098;rs12540098	480	Q8IY33	MILK2_HUMAN	P	268;480	ENSP00000385928:A268P;ENSP00000297508:A480P	ENSP00000297508:A480P	A	-	1	0	MICALL2	1448627	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.597000	0.05713	-0.513000	0.06496	-0.978000	0.02582	GCT	C|0.807;G|0.193	0.193	strong		0.627	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
NOX3	50508	hgsc.bcm.edu	37	6	155774608	155774608	+	Silent	SNP	C	C	T	rs34960420	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:155774608C>T	ENST00000159060.2	-	4	372	c.270G>A	c.(268-270)ccG>ccA	p.P90P		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	90	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)			cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GCCTCCTCCACGGTCCTCTGC	0.378													C|||	638	0.127396	0.1059	0.2291	5008	,	,		19963	0.1121		0.1044	False		,,,				2504	0.1237				p.P90P		Atlas-SNP	.											.	NOX3	93	.	0			c.G270A						PASS	.	C		471,3935	221.7+/-238.7	29,413,1761	203.0	209.0	207.0		270	-5.3	0.8	6	dbSNP_126	207	968,7632	210.8+/-251.6	57,854,3389	no	coding-synonymous	NOX3	NM_015718.2		86,1267,5150	TT,TC,CC		11.2558,10.69,11.0641		90/569	155774608	1439,11567	2203	4300	6503	SO:0001819	synonymous_variant	50508	exon4			CCTCCACGGTCCT	AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.270G>A	6.37:g.155774608C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	172	64	0.372093	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	37	CCDS5250.1																																																																																			C|0.888;T|0.112	0.112	strong		0.378	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
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 GAIIx	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_ENST00000535572.1_Missense_Mutation_p.S289P|WNK1_ENST00000447667.2_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	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	67	31	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	
SAMD9	54809	hgsc.bcm.edu	37	7	92734451	92734451	+	Silent	SNP	A	A	G	rs6965201	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92734451A>G	ENST00000379958.2	-	3	1229	c.960T>C	c.(958-960)taT>taC	p.Y320Y		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	320						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TAATCTGGAAATAATCATATT	0.338													A|||	2610	0.521166	0.8359	0.4971	5008	,	,		19412	0.5188		0.2873	False		,,,				2504	0.3558				p.Y320Y		Atlas-SNP	.											.	SAMD9	239	.	0			c.T960C						PASS	.	A	,	3224,1182	707.0+/-407.4	1179,866,158	89.0	85.0	86.0		960,960	3.2	1.0	7	dbSNP_116	86	2470,6130	404.2+/-348.1	365,1740,2195	no	coding-synonymous,coding-synonymous	SAMD9	NM_001193307.1,NM_017654.3	,	1544,2606,2353	GG,GA,AA		28.7209,26.8271,43.7798	,	320/1590,320/1590	92734451	5694,7312	2203	4300	6503	SO:0001819	synonymous_variant	54809	exon2			CTGGAAATAATCA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.960T>C	7.37:g.92734451A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	113	113	1	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																			A|0.525;G|0.475	0.475	strong		0.338	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55324635	55324635	+	Intron	SNP	T	T	C	rs649216	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55324635T>C	ENST00000538269.1	+	2	61				KIR2DL4_ENST00000357494.4_Intron|KIR2DL4_ENST00000345540.5_Intron|KIR2DL4_ENST00000359085.4_Silent_p.F254F|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Silent_p.F252F|KIR2DL4_ENST00000396293.1_Intron|KIR2DL4_ENST00000463062.1_3'UTR|KIR2DL4_ENST00000346587.4_Intron|KIR3DL1_ENST00000541392.1_Intron			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)	p.F254F(2)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TCATCCTCTTTACCATCCTTC	0.502													c|||	2958	0.590655	0.6528	0.5605	5008	,	,		6076	0.8056		0.4871	False		,,,				2504	0.4131				p.F254F		Atlas-SNP	.											KIR2DL4,NS,carcinoma,0,2	KIR2DL4	62	2	2	Substitution - coding silent(2)	prostate(2)	c.C762C						PASS	.						121.0	187.0	166.0					19																	55324635		1991	4152	6143	SO:0001627	intron_variant	3805	exon6			CCTCTTTACCATC	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-4354T>C	19.37:g.55324635T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	68	11	0.161765	NM_001080772	O43473|Q14946|Q16541	Silent	SNP	ENST00000538269.1	37																																																																																				T|0.315;C|0.685	0.685	strong		0.502	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289	
POLL	27343	hgsc.bcm.edu	37	10	103340144	103340144	+	Silent	SNP	A	A	G	rs3730476	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:103340144A>G	ENST00000370162.3	-	8	1718	c.1224T>C	c.(1222-1224)tcT>tcC	p.S408S	DPCD_ENST00000470165.1_Intron|POLL_ENST00000463515.1_5'UTR|POLL_ENST00000456836.2_Silent_p.S145S|POLL_ENST00000339310.3_Silent_p.S131S|POLL_ENST00000370172.1_Silent_p.S320S|DPCD_ENST00000416979.2_Intron|POLL_ENST00000370168.3_Silent_p.S81S|POLL_ENST00000370158.3_Silent_p.S133S|POLL_ENST00000370169.1_Silent_p.S408S|POLL_ENST00000299206.4_Silent_p.S408S	NM_001174084.1|NM_001174085.1|NM_013274.3	NP_001167555.1|NP_001167556.1|NP_037406.1	Q9UGP5	DPOLL_HUMAN	polymerase (DNA directed), lambda	408					DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|nucleotide-excision repair (GO:0006289)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		ACAGCAGCCCAGAGTTAAAGG	0.622								DNA polymerases (catalytic subunits)					G|||	817	0.163139	0.1649	0.183	5008	,	,		18428	0.0377		0.2982	False		,,,				2504	0.137				p.S408S		Atlas-SNP	.											.	POLL	43	.	0			c.T1224C						PASS	.	G	,,	835,3571	746.4+/-411.7	83,669,1451	68.0	70.0	70.0		1224,948,1224	-5.8	0.8	10	dbSNP_107	70	2617,5983	686.6+/-404.1	410,1797,2093	no	coding-synonymous,coding-synonymous,coding-synonymous	POLL	NM_001174084.1,NM_001174085.1,NM_013274.3	,,	493,2466,3544	GG,GA,AA		30.4302,18.9514,26.5416	,,	408/576,316/484,408/576	103340144	3452,9554	2203	4300	6503	SO:0001819	synonymous_variant	27343	exon8			CAGCCCAGAGTTA	AF161019	CCDS7513.1	10q23	2012-05-18			ENSG00000166169	ENSG00000166169		"""DNA polymerases"""	9184	protein-coding gene	gene with protein product		606343				17686665	Standard	NM_001174084		Approved		uc001kti.2	Q9UGP5	OTTHUMG00000018933	ENST00000370162.3:c.1224T>C	10.37:g.103340144A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_013274	D3DR76|Q5JQP5|Q6NUM2|Q9BTN8|Q9HA10|Q9HB35	Silent	SNP	ENST00000370162.3	37	CCDS7513.1																																																																																			A|0.771;G|0.229	0.229	strong		0.622	POLL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049946.1	NM_013274	
SLC9A3	6550	hgsc.bcm.edu	37	5	476353	476353	+	Silent	SNP	C	C	T	rs2230437	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:476353C>T	ENST00000264938.3	-	13	2040	c.2031G>A	c.(2029-2031)gcG>gcA	p.A677A	CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA|CTD-2228K2.7_ENST00000606319.1_RNA|SLC9A3_ENST00000514375.1_Silent_p.A668A|CTD-2228K2.7_ENST00000607286.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	677					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)	p.A677A(1)		NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			ACAGCTTGGCCGCCTTCTTGT	0.642													C|||	1062	0.212061	0.1377	0.3112	5008	,	,		16387	0.0347		0.4115	False		,,,				2504	0.2198				p.A677A		Atlas-SNP	.											SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	1	Substitution - coding silent(1)	prostate(1)	c.G2031A						PASS	.	C		788,3616	316.3+/-294.6	73,642,1487	61.0	60.0	61.0		2031	-9.5	0.0	5	dbSNP_98	61	3384,5216	499.2+/-374.9	689,2006,1605	no	coding-synonymous	SLC9A3	NM_004174.2		762,2648,3092	TT,TC,CC		39.3488,17.8928,32.0824		677/835	476353	4172,8832	2202	4300	6502	SO:0001819	synonymous_variant	6550	exon13			CTTGGCCGCCTTC		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2031G>A	5.37:g.476353C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			C|0.706;T|0.294	0.294	strong		0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
HABP2	3026	hgsc.bcm.edu	37	10	115334124	115334124	+	Silent	SNP	C	C	T	rs3740530	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:115334124C>T	ENST00000351270.3	+	3	279	c.183C>T	c.(181-183)caC>caT	p.H61H	HABP2_ENST00000537906.1_Missense_Mutation_p.T50M|HABP2_ENST00000541666.1_Silent_p.H61H|HABP2_ENST00000542051.1_Silent_p.H35H	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	61					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	CACTTACCCACGCTGAGAATC	0.502													C|||	2677	0.534545	0.2965	0.6354	5008	,	,		19524	0.6042		0.6183	False		,,,				2504	0.6268				p.H61H		Atlas-SNP	.											.	HABP2	52	.	0			c.C183T						PASS	.	C	,	1585,2821	493.4+/-362.7	292,1001,910	151.0	124.0	133.0		105,183	2.4	0.0	10	dbSNP_107	133	5491,3109	658.1+/-401.5	1777,1937,586	no	coding-synonymous,coding-synonymous	HABP2	NM_001177660.1,NM_004132.3	,	2069,2938,1496	TT,TC,CC		36.1512,35.9737,45.5943	,	35/535,61/561	115334124	7076,5930	2203	4300	6503	SO:0001819	synonymous_variant	3026	exon3			TACCCACGCTGAG		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.183C>T	10.37:g.115334124C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_004132	A8K467|B7Z8U5|F5H5M6|O00663	Silent	SNP	ENST00000351270.3	37	CCDS7577.1	1187	0.5434981684981685	132	0.2682926829268293	233	0.643646408839779	353	0.6171328671328671	469	0.6187335092348285	C	4.611	0.113538	0.08831	0.359737	0.638488	ENSG00000148702	ENST00000537906	.	.	.	4.31	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	D	0.61697	0.99	P	0.48627	0.584	T	0.43180	-0.9407	6	0.87932	D	0	.	6.0471	0.19766	0.1873:0.7092:0.0:0.1035	rs3740530;rs17698474;rs59251586;rs3740530	50	F5H475	.	M	50	.	ENSP00000446135:T50M	T	+	2	0	HABP2	115324114	0.001000	0.12720	0.002000	0.10522	0.013000	0.08279	0.639000	0.24690	0.729000	0.32403	-0.261000	0.10672	ACG	C|0.467;T|0.533	0.533	strong		0.502	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
RC3H2	54542	hgsc.bcm.edu	37	9	125652757	125652757	+	Silent	SNP	G	G	A	rs10818759	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:125652757G>A	ENST00000373670.1	-	3	1017	c.417C>T	c.(415-417)aaC>aaT	p.N139N	RC3H2_ENST00000423239.2_Silent_p.N139N|RC3H2_ENST00000357244.2_Silent_p.N139N|RC3H2_ENST00000335387.5_Silent_p.N139N|RC3H2_ENST00000373665.2_Silent_p.N139N|RC3H2_ENST00000471874.2_Silent_p.N139N|RC3H2_ENST00000478216.1_5'UTR			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	139					B cell homeostasis (GO:0001782)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymph node development (GO:0048535)|multicellular organism growth (GO:0035264)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|post-embryonic development (GO:0009791)|posttranscriptional regulation of gene expression (GO:0010608)|protein polyubiquitination (GO:0000209)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)|T follicular helper cell differentiation (GO:0061470)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|large_intestine(4)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33						CCAGTTGACAGTTTACAAGTG	0.473													G|||	1630	0.325479	0.3903	0.3617	5008	,	,		17647	0.6419		0.1233	False		,,,				2504	0.0941				p.N139N		Atlas-SNP	.											.	RC3H2	150	.	0			c.C417T						PASS	.	G	,	1180,2702		178,824,939	99.0	99.0	99.0		417,417	1.2	1.0	9	dbSNP_120	99	925,7385		46,833,3276	no	coding-synonymous,coding-synonymous	RC3H2	NM_001100588.1,NM_018835.2	,	224,1657,4215	AA,AG,GG		11.1312,30.3967,17.2654	,	139/1192,139/1065	125652757	2105,10087	1941	4155	6096	SO:0001819	synonymous_variant	54542	exon4			TTGACAGTTTACA	AK000308	CCDS43874.1, CCDS48014.1	9q34	2013-01-18	2010-09-15	2007-02-06	ENSG00000056586	ENSG00000056586		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCCH-type domain containing"""	21461	protein-coding gene	gene with protein product		615231	"""membrane associated DNA binding protein"", ""ring finger and CCCH-type zinc finger domains 2"""	MNAB		10938276	Standard	NM_001100588		Approved	FLJ20301, FLJ20713, RNF164	uc010mwc.1	Q9HBD1	OTTHUMG00000020632	ENST00000373670.1:c.417C>T	9.37:g.125652757G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Silent	SNP	ENST00000373670.1	37	CCDS43874.1																																																																																			G|0.685;A|0.315	0.315	strong		0.473	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835	
INPP5B	3633	hgsc.bcm.edu	37	1	38348506	38348506	+	Silent	SNP	G	G	A	rs41307896	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:38348506G>A	ENST00000373026.1	-	13	1644	c.1644C>T	c.(1642-1644)gaC>gaT	p.D548D	RNU6-584P_ENST00000410350.1_RNA|SNORA63_ENST00000516639.1_RNA|INPP5B_ENST00000467066.1_5'Flank|INPP5B_ENST00000373023.2_Silent_p.D548D|INPP5B_ENST00000373024.3_Silent_p.D468D|INPP5B_ENST00000373027.1_Silent_p.D304D|INPP5B_ENST00000458109.2_Missense_Mutation_p.L169F			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	548	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)				GCATTTGAAAGTCCTTCTCTT	0.502													G|||	390	0.0778754	0.0166	0.0893	5008	,	,		20591	0.003		0.164	False		,,,				2504	0.1411				p.D468D		Atlas-SNP	.											.	INPP5B	76	.	0			c.C1404T						PASS	.	G		131,3793		2,127,1833	169.0	158.0	161.0		1404	4.6	1.0	1	dbSNP_127	161	1188,7134		77,1034,3050	no	coding-synonymous	INPP5B	NM_005540.2		79,1161,4883	AA,AG,GG		14.2754,3.3384,10.7709		468/914	38348506	1319,10927	1962	4161	6123	SO:0001819	synonymous_variant	3633	exon14			TTGAAAGTCCTTC	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.1644C>T	1.37:g.38348506G>A		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	284	124	0.43662	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	37		160	0.07326007326007326	11	0.022357723577235773	39	0.10773480662983426	0	0.0	110	0.14511873350923482	G	14.37	2.516326	0.44763	0.033384	0.142754	ENSG00000204084	ENST00000458109	D	0.97161	-4.27	5.58	4.6	0.57074	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.43745	P	0.003758999999999957	.	.	.	.	.	.	T	0.69446	-0.5143	5	0.02654	T	1	.	8.4959	0.33127	0.0869:0.0:0.703:0.2101	rs41307896;rs61742717	.	.	.	F	169	ENSP00000397748:L169F	ENSP00000397748:L169F	L	-	1	0	INPP5B	38121093	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.545000	0.23268	2.645000	0.89757	0.655000	0.94253	CTT	G|0.897;A|0.103	0.103	strong		0.502	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
MFSD10	10227	hgsc.bcm.edu	37	4	2935528	2935528	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:2935528C>A	ENST00000329687.4	-	1	657	c.123G>T	c.(121-123)ctG>ctT	p.L41L	NOP14-AS1_ENST00000505731.1_RNA|MFSD10_ENST00000507555.1_Silent_p.L41L|MFSD10_ENST00000508221.1_Silent_p.L41L|NOP14-AS1_ENST00000515194.1_RNA|NOP14-AS1_ENST00000507999.1_RNA|MFSD10_ENST00000355443.4_Silent_p.L41L|NOP14-AS1_ENST00000512712.2_RNA|MFSD10_ENST00000514800.1_Silent_p.L41L	NM_001120.4	NP_001111.3	Q14728	MFS10_HUMAN	major facilitator superfamily domain containing 10	41					apoptotic process (GO:0006915)|tetracycline transport (GO:0015904)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)	tetracycline transporter activity (GO:0008493)			breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GGGGCAGCAGCAGCGTGAAGG	0.726																																					p.L41L		Atlas-SNP	.											.	MFSD10	22	.	0			c.G123T						PASS	.																																			SO:0001819	synonymous_variant	10227	exon1			CAGCAGCAGCGTG	L11669	CCDS3365.1	4p16.3	2008-03-03			ENSG00000109736	ENSG00000109736			16894	protein-coding gene	gene with protein product	"""tetracycline transporter like protein"""	610977				8353488, 17362938	Standard	NM_001120		Approved	TETRAN, IT10C3	uc003gfz.3	Q14728	OTTHUMG00000122081	ENST00000329687.4:c.123G>T	4.37:g.2935528C>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	149	115	0.771812	NM_001120	Q07706	Silent	SNP	ENST00000329687.4	37	CCDS3365.1																																																																																			.	.	none		0.726	MFSD10-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358072.2	NM_001120	
PSG5	5673	hgsc.bcm.edu	37	19	43680051	43680051	+	Missense_Mutation	SNP	C	C	T	rs1058285	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43680051C>T	ENST00000366175.3	-	3	810	c.680G>A	c.(679-681)cGc>cAc	p.R227H	PSG5_ENST00000342951.6_Missense_Mutation_p.R227H|PSG5_ENST00000599812.1_Missense_Mutation_p.R320H|PSG5_ENST00000404580.1_Missense_Mutation_p.R227H|PSG5_ENST00000407356.1_Missense_Mutation_p.R227H|PSG5_ENST00000407568.1_Intron			Q15238	PSG5_HUMAN	pregnancy specific beta-1-glycoprotein 5	227	Ig-like C2-type 1.		R -> H (in dbSNP:rs1058285). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1922019, ECO:0000269|PubMed:2735907, ECO:0000269|PubMed:2789512}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(18)|prostate(1)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(69;0.00899)				TGGGTCACTGCGCATGCCACC	0.493													C|||	3818	0.76238	0.8245	0.5821	5008	,	,		20297	0.9851		0.6123	False		,,,				2504	0.7311				p.R227H		Atlas-SNP	.											PSG5,NS,carcinoma,+1,1	PSG5	58	1	0			c.G680A						PASS	.	C	HIS/ARG,HIS/ARG	3465,937	737.2+/-410.9	1384,697,120	163.0	157.0	159.0		680,680	-0.6	0.0	19	dbSNP_86	159	5169,3421	638.3+/-399.3	1609,1951,735	no	missense,missense	PSG5	NM_001130014.1,NM_002781.3	29,29	2993,2648,855	TT,TC,CC		39.8254,21.2858,33.5437	benign,benign	227/336,227/336	43680051	8634,4358	2201	4295	6496	SO:0001583	missense	5673	exon3			TCACTGCGCATGC		CCDS12617.1	19q13.2	2013-01-29			ENSG00000204941	ENSG00000204941		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9522	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta 1 glycoprotein"""	176394				2735907	Standard	NM_002781		Approved	FL-NCA-3, PSG	uc002ovx.3	Q15238	OTTHUMG00000151539	ENST00000366175.3:c.680G>A	19.37:g.43680051C>T	ENSP00000382334:p.Arg227His	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	13	12	0.923077	NM_002781	Q15239|Q96QJ1|Q9UQ75	Missense_Mutation	SNP	ENST00000366175.3	37	CCDS12617.1	1650	0.7554945054945055	415	0.8434959349593496	207	0.5718232044198895	567	0.9912587412587412	461	0.6081794195250659	c	2.454	-0.325779	0.05350	0.787142	0.601746	ENSG00000204941	ENST00000366175;ENST00000407356;ENST00000342951;ENST00000404580	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	1.08	-0.623	0.11556	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.69823	2.125	0.80722	P	0.0	B	0.18610	0.029	B	0.25140	0.058	T	0.14868	-1.0457	8	0.42905	T	0.14	.	5.5781	0.17235	0.0:0.6701:0.3299:0.0	rs1058285;rs3179036;rs3198896;rs17845347;rs17858192;rs58622191;rs1058285	227	Q15238	PSG5_HUMAN	H	227	ENSP00000382334:R227H;ENSP00000386008:R227H;ENSP00000344413:R227H;ENSP00000385250:R227H	ENSP00000344413:R227H	R	-	2	0	PSG5	48371891	0.000000	0.05858	0.016000	0.15963	0.006000	0.05464	-0.267000	0.08619	-1.394000	0.02077	-1.271000	0.01417	CGC	C|0.311;T|0.689	0.689	strong		0.493	PSG5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323055.1	NM_002781	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035301	110035301	+	Silent	SNP	A	A	G	rs1026607	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:110035301A>G	ENST00000278590.3	+	6	1542	c.1491A>G	c.(1489-1491)acA>acG	p.T497T	ZC3H12C_ENST00000453089.2_Silent_p.T466T|ZC3H12C_ENST00000528673.1_Silent_p.T498T	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	497							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GCATAAGGACACAAGTCTACC	0.448													G|||	1222	0.24401	0.3041	0.2248	5008	,	,		23059	0.2004		0.2724	False		,,,				2504	0.1922				p.T497T		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A1491G						PASS	.	G		1098,2738		170,758,990	108.0	105.0	106.0		1491	-1.1	0.9	11	dbSNP_86	106	2086,6162		248,1590,2286	no	coding-synonymous	ZC3H12C	NM_033390.1		418,2348,3276	GG,GA,AA		25.291,28.6236,26.3489		497/884	110035301	3184,8900	1918	4124	6042	SO:0001819	synonymous_variant	85463	exon6			AAGGACACAAGTC		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1491A>G	11.37:g.110035301A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	81	13	0.160494	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			A|0.729;G|0.271	0.271	strong		0.448	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
PLEC	5339	hgsc.bcm.edu	37	8	144992103	144992103	+	Silent	SNP	T	T	C	rs6558406	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144992103T>C	ENST00000322810.4	-	32	12466	c.12297A>G	c.(12295-12297)acA>acG	p.T4099T	PLEC_ENST00000354589.3_Silent_p.T3962T|PLEC_ENST00000357649.2_Silent_p.T3966T|PLEC_ENST00000436759.2_Silent_p.T3989T|PLEC_ENST00000354958.2_Silent_p.T3940T|PLEC_ENST00000527096.1_Silent_p.T3985T|PLEC_ENST00000345136.3_Silent_p.T3962T|PLEC_ENST00000356346.3_Silent_p.T3948T|PLEC_ENST00000398774.2_Silent_p.T3930T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4099	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GCTCAAAGGCTGTGCCGGGGC	0.627													C|||	2456	0.490415	0.916	0.3775	5008	,	,		18721	0.1538		0.4563	False		,,,				2504	0.3773				p.T4099T		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,3	PLEC	1144	3	0			c.A12297G						PASS	.	C	,,,,,,,	3615,601		1558,499,51	28.0	34.0	32.0		11967,11844,11820,12297,11790,11886,11898,11886	-8.6	0.4	8	dbSNP_116	32	3834,4614		903,2028,1293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	2461,2527,1344	CC,CT,TT		45.3835,14.2552,41.1797	,,,,,,,	3989/4575,3948/4534,3940/4526,4099/4685,3930/4516,3962/4548,3966/4552,3962/4548	144992103	7449,5215	2108	4224	6332	SO:0001819	synonymous_variant	5339	exon32			AAAGGCTGTGCCG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.12297A>G	8.37:g.144992103T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			T|0.520;C|0.480	0.480	strong		0.627	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
OR13D1	286365	hgsc.bcm.edu	37	9	107457725	107457725	+	Silent	SNP	G	G	A	rs12338899	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107457725G>A	ENST00000318763.5	+	1	1066	c.1023G>A	c.(1021-1023)ctG>ctA	p.L341L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	341						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(4)|lung(10)|ovary(1)|prostate(2)|skin(2)	19						GCAGACATCTGCATTTATTGA	0.408													G|||	1353	0.270168	0.1657	0.183	5008	,	,		19813	0.4821		0.1909	False		,,,				2504	0.3364				p.L341L		Atlas-SNP	.											.	OR13D1	42	.	0			c.G1023A						PASS	.	G		789,3617	314.4+/-293.6	75,639,1489	58.0	59.0	59.0		1023	-6.9	0.0	9	dbSNP_120	59	1824,6776	323.0+/-315.8	224,1376,2700	yes	coding-synonymous	OR13D1	NM_001004484.1		299,2015,4189	AA,AG,GG		21.2093,17.9074,20.0907		341/347	107457725	2613,10393	2203	4300	6503	SO:0001819	synonymous_variant	286365	exon1			ACATCTGCATTTA		CCDS35094.1	9q31.1	2013-09-24			ENSG00000179055	ENSG00000179055		"""GPCR / Class A : Olfactory receptors"""	14695	protein-coding gene	gene with protein product							Standard	NM_001004484		Approved		uc011lvs.2	Q8NGV5	OTTHUMG00000020412	ENST00000318763.5:c.1023G>A	9.37:g.107457725G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_001004484	B9EIS1|Q6IFL1	Silent	SNP	ENST00000318763.5	37	CCDS35094.1																																																																																			G|0.786;A|0.214	0.214	strong		0.408	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
ZNF236	7776	hgsc.bcm.edu	37	18	74637167	74637167	+	Silent	SNP	C	C	T	rs61739891	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:74637167C>T	ENST00000253159.8	+	22	3876	c.3678C>T	c.(3676-3678)caC>caT	p.H1226H	ZNF236_ENST00000320610.9_Silent_p.H1228H	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1226					cellular response to glucose stimulus (GO:0071333)|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(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		TCAGCTGTCACGTCTGCAGCA	0.582													C|||	108	0.0215655	0.0008	0.0317	5008	,	,		18973	0.002		0.0457	False		,,,				2504	0.0378				p.H1226H		Atlas-SNP	.											.	ZNF236	325	.	0			c.C3678T						PASS	.	C		35,4119		0,35,2042	82.0	83.0	83.0		3678	-7.2	0.8	18	dbSNP_129	83	343,8115		6,331,3892	no	coding-synonymous	ZNF236	NM_007345.3		6,366,5934	TT,TC,CC		4.0553,0.8426,2.9971		1226/1846	74637167	378,12234	2077	4229	6306	SO:0001819	synonymous_variant	7776	exon22			CTGTCACGTCTGC	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.3678C>T	18.37:g.74637167C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_007345	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	CCDS42447.1																																																																																			C|0.973;T|0.027	0.027	strong		0.582	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
RELL2	285613	hgsc.bcm.edu	37	5	141019110	141019110	+	Missense_Mutation	SNP	C	C	A	rs14251	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:141019110C>A	ENST00000297164.3	+	4	1597	c.397C>A	c.(397-399)Ctc>Atc	p.L133I	RELL2_ENST00000521367.1_Missense_Mutation_p.L67I|FCHSD1_ENST00000523856.1_5'UTR|HDAC3_ENST00000305264.3_5'Flank|FCHSD1_ENST00000435817.2_3'UTR|RELL2_ENST00000518025.1_3'UTR|RELL2_ENST00000518856.1_Missense_Mutation_p.L67I|RELL2_ENST00000444782.1_Missense_Mutation_p.L133I	NM_173828.4	NP_776189.3	Q8NC24	RELL2_HUMAN	RELT-like 2	133			L -> I (in dbSNP:rs14251). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334}.		positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCCCTTGCCTCCATTGCAG	0.642													A|||	1991	0.397564	0.5772	0.379	5008	,	,		14976	0.1637		0.3807	False		,,,				2504	0.4264				p.L133I		Atlas-SNP	.											.	RELL2	24	.	0			c.C397A						PASS	.	A	ILE/LEU,,ILE/LEU	2265,2141	571.5+/-383.1	599,1067,537	43.0	45.0	44.0		397,,397	5.7	1.0	5	dbSNP_52	44	3593,5007	617.7+/-396.7	771,2051,1478	yes	missense,utr-3,missense	FCHSD1,RELL2	NM_001130029.1,NM_033449.2,NM_173828.4	5,,5	1370,3118,2015	AA,AC,CC		41.7791,48.5928,45.0408	benign,,benign	133/304,,133/304	141019110	5858,7148	2203	4300	6503	SO:0001583	missense	285613	exon4			CCTTGCCTCCATT	AK054889	CCDS4265.1	5q31.3	2011-10-11	2007-06-15	2007-06-15	ENSG00000164620	ENSG00000164620			26902	protein-coding gene	gene with protein product		611213	"""chromosome 5 open reading frame 16"""	C5orf16		12975309, 16389068	Standard	NM_173828		Approved	FLJ90583	uc003lli.3	Q8NC24	OTTHUMG00000129612	ENST00000297164.3:c.397C>A	5.37:g.141019110C>A	ENSP00000297164:p.Leu133Ile	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_173828	D3DQE2|Q6P4E7|Q6UXY2	Missense_Mutation	SNP	ENST00000297164.3	37	CCDS4265.1	817	0.3740842490842491	295	0.5995934959349594	144	0.39779005524861877	89	0.1555944055944056	289	0.3812664907651715	A	5.924	0.354549	0.11239	0.514072	0.417791	ENSG00000164620	ENST00000444782;ENST00000521367;ENST00000297164;ENST00000518856	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.7	5.7	0.88788	.	0.064449	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00436	-1.5	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44787	-0.9305	9	0.02654	T	1	-5.8058	12.8604	0.57910	0.8636:0.1364:0.0:0.0	rs14251;rs251179;rs3191867;rs17855846;rs14251	67;133	E5RHA7;Q8NC24	.;RELL2_HUMAN	I	133;67;133;67	ENSP00000409443:L133I;ENSP00000430948:L67I;ENSP00000297164:L133I;ENSP00000427992:L67I	ENSP00000297164:L133I	L	+	1	0	RELL2	140999294	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.514000	0.53422	0.990000	0.38787	-0.256000	0.11100	CTC	C|0.567;A|0.433	0.433	strong		0.642	RELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251807.2	NM_173828	
CD19	930	hgsc.bcm.edu	37	16	28944396	28944396	+	Missense_Mutation	SNP	C	C	G	rs2904880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28944396C>G	ENST00000324662.3	+	3	564	c.520C>G	c.(520-522)Ctc>Gtc	p.L174V	CD19_ENST00000538922.1_Missense_Mutation_p.L174V|CD19_ENST00000567541.1_Missense_Mutation_p.L174V			P15391	CD19_HUMAN	CD19 molecule	174			L -> V (in dbSNP:rs2904880). {ECO:0000269|PubMed:12215898, ECO:0000269|PubMed:1370948, ECO:0000269|PubMed:1375324, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2459292, ECO:0000269|PubMed:2472450, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		B cell receptor signaling pathway (GO:0050853)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(4)|urinary_tract(1)	29						GCCTCCGTGTCTCCCACCGAG	0.642													G|||	4158	0.830272	0.9909	0.5504	5008	,	,		16529	0.9018		0.7276	False		,,,				2504	0.8436				p.L174V		Atlas-SNP	.											.	CD19	65	.	0			c.C520G						PASS	.	G	VAL/LEU,VAL/LEU	4084,310	160.3+/-192.7	1900,284,13	39.0	34.0	36.0		520,520	2.8	0.0	16	dbSNP_101	36	5913,2687	401.7+/-347.2	2044,1825,431	yes	missense,missense	CD19	NM_001178098.1,NM_001770.5	32,32	3944,2109,444	GG,GC,CC		31.2442,7.0551,23.0645	benign,benign	174/558,174/557	28944396	9997,2997	2197	4300	6497	SO:0001583	missense	930	exon3			CCGTGTCTCCCAC		CCDS10644.1, CCDS53998.1	16p11.2	2014-09-17	2006-03-28		ENSG00000177455	ENSG00000177455		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1633	protein-coding gene	gene with protein product		107265	"""CD19 antigen"""				Standard	NM_001770		Approved		uc010byo.2	P15391	OTTHUMG00000097049	ENST00000324662.3:c.520C>G	16.37:g.28944396C>G	ENSP00000313419:p.Leu174Val	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	14	8	0.571429	NM_001178098	A0N0P9|F5H635|Q96S68|Q9BRD6	Missense_Mutation	SNP	ENST00000324662.3	37	CCDS10644.1	1785	0.8173076923076923	487	0.9898373983739838	236	0.6519337016574586	510	0.8916083916083916	552	0.7282321899736148	G	10.71	1.427882	0.25726	0.929449	0.687558	ENSG00000177455	ENST00000538922;ENST00000324662;ENST00000537306	T;T	0.34667	1.35;1.35	5.16	2.82	0.32997	.	0.832156	0.10532	N	0.663709	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24941	-1.0146	9	0.41790	T	0.15	-0.0091	5.7621	0.18207	0.2024:0.1664:0.6312:0.0	rs2904880;rs2904880	174;174	F5H635;P15391	.;CD19_HUMAN	V	174;174;23	ENSP00000437940:L174V;ENSP00000313419:L174V	ENSP00000313419:L174V	L	+	1	0	CD19	28851897	0.014000	0.17966	0.045000	0.18777	0.001000	0.01503	0.092000	0.15066	0.572000	0.29383	-0.371000	0.07208	CTC	C|0.215;G|0.785	0.785	strong		0.642	CD19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214152.2		
PDCD11	22984	hgsc.bcm.edu	37	10	105174869	105174869	+	Silent	SNP	G	G	A	rs2271750	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:105174869G>A	ENST00000369797.3	+	12	1573	c.1479G>A	c.(1477-1479)ccG>ccA	p.P493P		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	493	S1 motif 5. {ECO:0000255|PROSITE- ProRule:PRU00180}.				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)		TGAAGAATCCGGAGAAGAAGT	0.537													G|||	628	0.125399	0.1407	0.098	5008	,	,		21118	0.0933		0.1392	False		,,,				2504	0.1431				p.P493P		Atlas-SNP	.											.	PDCD11	160	.	0			c.G1479A						PASS	.	G		658,3748	280.8+/-275.6	52,554,1597	87.0	79.0	82.0		1479	-5.0	1.0	10	dbSNP_100	82	1081,7519	227.2+/-262.7	70,941,3289	no	coding-synonymous	PDCD11	NM_014976.1		122,1495,4886	AA,AG,GG		12.5698,14.9342,13.3708		493/1872	105174869	1739,11267	2203	4300	6503	SO:0001819	synonymous_variant	22984	exon12			GAATCCGGAGAAG	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.1479G>A	10.37:g.105174869G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	37	CCDS31276.1																																																																																			G|0.863;A|0.137	0.137	strong		0.537	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1		
RAD21L1	642636	hgsc.bcm.edu	37	20	1210647	1210647	+	Missense_Mutation	SNP	T	T	C	rs450739	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:1210647T>C	ENST00000409241.1	+	3	361	c.268T>C	c.(268-270)Tgc>Cgc	p.C90R	RAD21L1_ENST00000402452.1_Missense_Mutation_p.C90R|RAD21L1_ENST00000381882.2_Missense_Mutation_p.C90R	NM_001136566.2	NP_001130038.2	Q9H4I0	RD21L_HUMAN	RAD21-like 1 (S. pombe)	90			C -> R (in dbSNP:rs450739). {ECO:0000269|PubMed:15489334}.		attachment of telomeric heterochromatin to nuclear envelope (GO:0070197)|chromosome segregation (GO:0007059)|double-strand break repair via homologous recombination (GO:0000724)|fertilization (GO:0009566)|linear element assembly (GO:0030999)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)	chromosome (GO:0005694)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleus (GO:0005634)				NS(1)|breast(1)|large_intestine(1)|lung(2)|skin(1)|stomach(1)	7						GATGACATTTTGCCCAGGTAT	0.373													C|||	2474	0.49401	0.7542	0.428	5008	,	,		17544	0.2202		0.5378	False		,,,				2504	0.4264				p.C90R		Atlas-SNP	.											.	RAD21L1	51	.	0			c.T268C						PASS	.						158.0	132.0	140.0					20																	1210647		692	1591	2283	SO:0001583	missense	642636	exon3			ACATTTTGCCCAG	AL031665	CCDS46568.1	20p13	2011-08-12			ENSG00000244588	ENSG00000244588			16271	protein-coding gene	gene with protein product							Standard	NM_001136566		Approved	dJ545L17.2, RAD21L	uc010gab.1	Q9H4I0	OTTHUMG00000031664	ENST00000409241.1:c.268T>C	20.37:g.1210647T>C	ENSP00000386414:p.Cys90Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_001136566	B2RXL0|B7ZBB1|B7ZW76|Q5W0X5	Missense_Mutation	SNP	ENST00000409241.1	37	CCDS46568.1	1057	0.483974358974359	373	0.758130081300813	175	0.48342541436464087	113	0.19755244755244755	396	0.5224274406332454	C	3.037	-0.198432	0.06219	.	.	ENSG00000244588	ENST00000402452;ENST00000409241;ENST00000381882	T;T;T	0.25912	1.77;1.77;1.77	5.16	5.16	0.70880	Rad21/Rec8-like protein, N-terminal (1);	0.000000	0.64402	N	0.000007	T	0.00012	0.0000	N	0.00009	-3.09	0.22330	P	0.999196335	B	0.02656	0.0	B	0.01281	0.0	T	0.43130	-0.9410	9	0.02654	T	1	.	14.0293	0.64606	0.0:0.9264:0.0:0.0736	rs450739;rs52795523;rs59077672;rs450739	90	Q9H4I0	RD21L_HUMAN	R	90	ENSP00000385925:C90R;ENSP00000386414:C90R;ENSP00000371306:C90R	ENSP00000371306:C90R	C	+	1	0	RAD21L1	1158647	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.090000	0.50191	1.555000	0.49500	-0.186000	0.12905	TGC	T|0.506;C|0.494	0.494	strong		0.373	RAD21L1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334022.1		
GOLGA3	2802	hgsc.bcm.edu	37	12	133389998	133389998	+	Silent	SNP	T	T	C	rs7134809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:133389998T>C	ENST00000450791.2	-	3	597	c.414A>G	c.(412-414)acA>acG	p.T138T	GOLGA3_ENST00000456883.2_Silent_p.T138T|GOLGA3_ENST00000204726.3_Silent_p.T138T|GOLGA3_ENST00000545875.1_Silent_p.T138T|GOLGA3_ENST00000537452.1_Silent_p.T138T			Q08378	GOGA3_HUMAN	golgin A3	138	Interaction with GOPC.				intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GGGGAGAATCTGTAGAGCCTG	0.507													T|||	363	0.072484	0.0106	0.0735	5008	,	,		19223	0.0446		0.171	False		,,,				2504	0.0828				p.T138T		Atlas-SNP	.											.	GOLGA3	234	.	0			c.A414G						PASS	.	T	,	129,4277	95.7+/-134.4	3,123,2077	48.0	44.0	45.0		414,414	-2.5	0.0	12	dbSNP_116	45	1437,7163	275.0+/-291.5	134,1169,2997	no	coding-synonymous,coding-synonymous	GOLGA3	NM_001172557.1,NM_005895.3	,	137,1292,5074	CC,CT,TT		16.7093,2.9278,12.0406	,	138/1135,138/1499	133389998	1566,11440	2203	4300	6503	SO:0001819	synonymous_variant	2802	exon4			AGAATCTGTAGAG	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.414A>G	12.37:g.133389998T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Silent	SNP	ENST00000450791.2	37	CCDS9281.1																																																																																			T|0.897;C|0.103	0.103	strong		0.507	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
KRTAP9-4	85280	hgsc.bcm.edu	37	17	39406002	39406002	+	Silent	SNP	G	G	A	rs12952568	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39406002G>A	ENST00000334109.2	+	1	64	c.30G>A	c.(28-30)caG>caA	p.Q10Q		NM_033191.2	NP_149461.2	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4	10	15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].					keratin filament (GO:0045095)				breast(1)|large_intestine(1)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTTGCTGTCAGCCTACATGCT	0.597													.|||	238	0.047524	0.003	0.0677	5008	,	,		20391	0.0		0.1113	False		,,,				2504	0.0767				p.Q10Q		Atlas-SNP	.											.	KRTAP9-4	30	.	0			c.G30A						PASS	.	G		81,4325		0,81,2122	148.0	122.0	131.0		30	2.5	1.0	17	dbSNP_121	131	727,7869		18,691,3589	no	coding-synonymous	KRTAP9-4	NM_033191.2		18,772,5711	AA,AG,GG		8.4574,1.8384,6.2144		10/155	39406002	808,12194	2203	4298	6501	SO:0001819	synonymous_variant	85280	exon1			CTGTCAGCCTACA	AJ406948	CCDS11386.1	17q21.2	2013-06-25			ENSG00000241595	ENSG00000241595		"""Keratin associated proteins"""	18902	protein-coding gene	gene with protein product						11279113	Standard	NM_033191		Approved	KAP9.4	uc002hwi.3	Q9BYQ2	OTTHUMG00000133438	ENST00000334109.2:c.30G>A	17.37:g.39406002G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_033191	Q0VAE3	Silent	SNP	ENST00000334109.2	37	CCDS11386.1																																																																																			G|0.941;A|0.059	0.059	strong		0.597	KRTAP9-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257306.1		
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 GAIIx	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	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	172	50	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	
DSC3	1825	hgsc.bcm.edu	37	18	28610988	28610988	+	Missense_Mutation	SNP	C	C	T	rs276938	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:28610988C>T	ENST00000360428.4	-	3	385	c.305G>A	c.(304-306)aGg>aAg	p.R102K	DSC3_ENST00000434452.1_Missense_Mutation_p.R102K	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	102			R -> K (in dbSNP:rs276938).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			TGTCTGTTTCCTTTTGTCAGA	0.363													C|||	2181	0.435503	0.32	0.3401	5008	,	,		15601	0.6776		0.3549	False		,,,				2504	0.4928				p.R102K		Atlas-SNP	.											.	DSC3	225	.	0			c.G305A						PASS	.	C	LYS/ARG,LYS/ARG	1498,2908	474.4+/-357.0	253,992,958	102.0	92.0	95.0		305,305	1.6	0.0	18	dbSNP_79	95	2760,5840	437.2+/-358.5	443,1874,1983	yes	missense,missense	DSC3	NM_001941.3,NM_024423.2	26,26	696,2866,2941	TT,TC,CC		32.093,33.9991,32.7387	benign,benign	102/897,102/840	28610988	4258,8748	2203	4300	6503	SO:0001583	missense	1825	exon3			TGTTTCCTTTTGT	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.305G>A	18.37:g.28610988C>T	ENSP00000353608:p.Arg102Lys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_024423	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	941	0.4308608058608059	161	0.32723577235772355	127	0.35082872928176795	393	0.6870629370629371	260	0.34300791556728233	C	2.166	-0.391109	0.04932	0.339991	0.32093	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.60299	0.2;0.2	5.28	1.64	0.23874	Cadherin prodomain-like (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.01800	-0.715	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.38564	-0.9655	8	0.32370	T	0.25	.	5.0997	0.14753	0.0:0.1586:0.2902:0.5512	rs276938;rs1098250;rs1303279;rs52831455;rs58484203;rs276938	102;102	Q14574;Q14574-2	DSC3_HUMAN;.	K	102	ENSP00000353608:R102K;ENSP00000392068:R102K	ENSP00000353608:R102K	R	-	2	0	DSC3	26864986	0.013000	0.17824	0.014000	0.15608	0.005000	0.04900	1.229000	0.32600	0.134000	0.18681	-1.224000	0.01588	AGG	T|0.384;G|0.001	0.384	strong		0.363	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
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 GAIIx	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		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	154	50	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 GAIIx	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	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	77	4	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 GAIIx	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_ENST00000535299.1_Intron|NTF3_ENST00000423158.3_Silent_p.T241T	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		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	37	19	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 GAIIx	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		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	16	7	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	
RSPH10B2	728194	hgsc.bcm.edu	37	7	6798735	6798735	+	Missense_Mutation	SNP	G	G	A	rs199536223		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6798735G>A	ENST00000403107.1	+	3	662	c.275G>A	c.(274-276)cGt>cAt	p.R92H	RSPH10B2_ENST00000359718.3_5'UTR|RSPH10B2_ENST00000297186.3_Missense_Mutation_p.R92H|RSPH10B2_ENST00000404077.1_Missense_Mutation_p.R92H|RSPH10B2_ENST00000433859.2_Missense_Mutation_p.R92H			B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B2 (Chlamydomonas)	92										breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|skin(2)	15						GAAAAGGTTCGTGGGCTGTAT	0.438																																					p.R92H		Atlas-SNP	.											RSPH10B2,NS,carcinoma,0,2	RSPH10B	28	2	0			c.G275A						scavenged	.	G	HIS/ARG	8,3516		0,8,1754	5.0	5.0	5.0		275	1.3	0.9	7		5	125,7477		0,125,3676	no	missense	RSPH10B2	NM_001099697.1	29	0,133,5430	AA,AG,GG		1.6443,0.227,1.1954	benign	92/871	6798735	133,10993	1762	3801	5563	SO:0001583	missense	222967	exon4			AGGTTCGTGGGCT		CCDS43552.1	7p22.1	2008-07-04			ENSG00000169402	ENSG00000169402			34385	protein-coding gene	gene with protein product							Standard	NM_001099697		Approved		uc003sqw.1	B2RC85	OTTHUMG00000151856	ENST00000403107.1:c.275G>A	7.37:g.6798735G>A	ENSP00000384766:p.Arg92His	Somatic	1021	1	0.000979432		WXS	Illumina HiSeq	Phase_I	1243	540	0.434433	NM_173565	A6NMW7|B2RXI4|B2RXJ0|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000403107.1	37	CCDS43552.1	.	.	.	.	.	.	.	.	.	.	G	4.629	0.116979	0.08881	0.00227	0.016443	ENSG00000169402	ENST00000403107;ENST00000404077;ENST00000297186;ENST00000433859	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	3.21	1.33	0.21861	.	0.588391	0.17861	N	0.159518	T	0.12902	0.0313	N	0.21583	0.68	0.24340	N	0.994965	B	0.23316	0.083	B	0.22386	0.039	T	0.10823	-1.0613	10	0.45353	T	0.12	.	5.6641	0.17684	0.3696:0.0:0.6304:0.0	.	92	B2RC85	R10B2_HUMAN	H	92	ENSP00000384766:R92H;ENSP00000386102:R92H;ENSP00000297186:R92H;ENSP00000416710:R92H	ENSP00000297186:R92H	R	+	2	0	RSPH10B2	6765260	0.097000	0.21791	0.863000	0.33907	0.273000	0.26683	0.336000	0.19823	0.198000	0.20407	0.398000	0.26397	CGT	G|0.994;A|0.006	0.006	weak		0.438	RSPH10B2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324184.4	NM_001099697	
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 GAIIx	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_ENST00000399201.1_Splice_Site_p.K75T|SETD4_ENST00000399212.1_Splice_Site_p.K75T|SETD4_ENST00000399208.2_Splice_Site_p.K99T|SETD4_ENST00000481477.1_Intron|SETD4_ENST00000399207.1_Splice_Site_p.K99T|SETD4_ENST00000332131.4_Splice_Site_p.K99T|SETD4_ENST00000399205.1_Splice_Site_p.K75T			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		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	71	15	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
NUP214	8021	hgsc.bcm.edu	37	9	134020092	134020092	+	Missense_Mutation	SNP	C	C	T	rs103612	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:134020092C>T	ENST00000359428.5	+	12	1864	c.1720C>T	c.(1720-1722)Ccc>Tcc	p.P574S	RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000586290.1_RNA|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000587408.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.P574S|NUP214_ENST00000451030.1_Missense_Mutation_p.P574S|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|RP11-544A12.4_ENST00000588378.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	574	11 X 5 AA approximate repeats.		P -> S (in dbSNP:rs103612). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1549122}.		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		AGCAATGAAGCCCTCCTTCCC	0.443			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""								C|||	3215	0.641973	0.6626	0.7522	5008	,	,		17540	0.627		0.6779	False		,,,				2504	0.5143				p.P574S	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.C1720T						PASS	.	C	SER/PRO	2944,1462	679.2+/-403.7	990,964,249	63.0	57.0	59.0		1720	1.8	1.0	9	dbSNP_79	59	5753,2847	673.1+/-403.0	1927,1899,474	yes	missense	NUP214	NM_005085.2	74	2917,2863,723	TT,TC,CC		33.1047,33.182,33.1309	possibly-damaging	574/2091	134020092	8697,4309	2203	4300	6503	SO:0001583	missense	8021	exon12			ATGAAGCCCTCCT	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.1720C>T	9.37:g.134020092C>T	ENSP00000352400:p.Pro574Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	1454|1454	0.6657509157509157|0.6657509157509157	312|312	0.6341463414634146|0.6341463414634146	268|268	0.7403314917127072|0.7403314917127072	359|359	0.6276223776223776|0.6276223776223776	515|515	0.679419525065963|0.679419525065963	C|C	9.078|9.078	0.998540|0.998540	0.19121|0.19121	0.66818|0.66818	0.668953|0.668953	ENSG00000126883|ENSG00000126883	ENST00000530863|ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	.|T;T;T	.|0.31769	.|1.51;1.48;1.51	6.07|6.07	1.78|1.78	0.24846|0.24846	.|.	.|0.705821	.|0.12317	.|N	.|0.479602	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.35292|0.35292	P|P	0.21768500000000002|0.21768500000000002	.|B;B;B	.|0.15473	.|0.002;0.002;0.013	.|B;B;B	.|0.12156	.|0.007;0.005;0.007	T|T	0.30880|0.30880	-0.9963|-0.9963	4|9	.|0.14252	.|T	.|0.57	-7.3578|-7.3578	5.3463|5.3463	0.16010|0.16010	0.1512:0.5573:0.0:0.2915|0.1512:0.5573:0.0:0.2915	rs103612;rs755806;rs818061;rs17526738;rs52837203;rs60032848;rs103612|rs103612;rs755806;rs818061;rs17526738;rs52837203;rs60032848;rs103612	.|167;574;574	.|Q5JUP9;P35658-4;P35658	.|.;.;NU214_HUMAN	V|S	149|574;574;574;574;167;3	.|ENSP00000352400:P574S;ENSP00000396576:P574S;ENSP00000405014:P574S	.|ENSP00000352400:P574S	A|P	+|+	2|1	0|0	NUP214|NUP214	133009913|133009913	0.145000|0.145000	0.22656|0.22656	0.954000|0.954000	0.39281|0.39281	0.478000|0.478000	0.33099|0.33099	-0.048000|-0.048000	0.11944|0.11944	0.816000|0.816000	0.34421|0.34421	0.655000|0.655000	0.94253|0.94253	GCC|CCC	C|0.333;N|0.001	.	strong		0.443	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
FAM83E	54854	hgsc.bcm.edu	37	19	49116438	49116438	+	Silent	SNP	A	A	G	rs376524	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49116438A>G	ENST00000263266.3	-	1	381	c.192T>C	c.(190-192)gtT>gtC	p.V64V	FAM83E_ENST00000595110.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	64										NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CCAAGCCCTGAACCTCATCCG	0.677													G|||	1674	0.334265	0.3298	0.4251	5008	,	,		15077	0.4702		0.2147	False		,,,				2504	0.2587				p.V64V		Atlas-SNP	.											FAM83E,colon,carcinoma,0,1	FAM83E	34	1	0			c.T192C						scavenged	.	G		1189,3091		181,827,1132	25.0	32.0	30.0		192	1.9	0.2	19	dbSNP_80	30	1730,6790		188,1354,2718	no	coding-synonymous	FAM83E	NM_017708.3		369,2181,3850	GG,GA,AA		20.3052,27.7804,22.8047		64/479	49116438	2919,9881	2140	4260	6400	SO:0001819	synonymous_variant	54854	exon1			GCCCTGAACCTCA	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.192T>C	19.37:g.49116438A>G		Somatic	118	2	0.0169492		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_017708	Q9NXK1	Silent	SNP	ENST00000263266.3	37	CCDS42587.1																																																																																			A|0.708;G|0.292	0.292	strong		0.677	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
BCAN	63827	hgsc.bcm.edu	37	1	156622252	156622252	+	Missense_Mutation	SNP	G	G	A	rs1056695	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156622252G>A	ENST00000329117.5	+	8	1846	c.1510G>A	c.(1510-1512)Gag>Aag	p.E504K	BCAN_ENST00000361588.5_Missense_Mutation_p.E504K|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	504			E -> K (in dbSNP:rs1056695). {ECO:0000269|PubMed:12975309}.		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)					AGCCCAGGAGGAGTCACTCTC	0.652													G|||	1874	0.374201	0.2595	0.3718	5008	,	,		17190	0.3532		0.3926	False		,,,				2504	0.5337				p.E504K		Atlas-SNP	.											.	BCAN	174	.	0			c.G1510A						PASS	.	G	LYS/GLU,LYS/GLU	1167,3235		171,825,1205	14.0	14.0	14.0		1510,1510	2.8	0.7	1	dbSNP_86	14	3236,5352		650,1936,1708	yes	missense,missense	BCAN	NM_021948.4,NM_198427.1	56,56	821,2761,2913	AA,AG,GG		37.6805,26.5107,33.8953	benign,benign	504/912,504/672	156622252	4403,8587	2201	4294	6495	SO:0001583	missense	63827	exon8			CAGGAGGAGTCAC	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.1510G>A	1.37:g.156622252G>A	ENSP00000331210:p.Glu504Lys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	721	0.3301282051282051	114	0.23170731707317074	119	0.3287292817679558	193	0.3374125874125874	295	0.3891820580474934	G	7.441	0.640635	0.14386	0.265107	0.376805	ENSG00000132692	ENST00000255029;ENST00000329117;ENST00000361588	T;T	0.14766	2.48;3.16	4.72	2.81	0.32909	.	3.147680	0.01292	N	0.010040	T	0.03136	0.0092	L	0.29908	0.895	0.41919	P	0.009492999999999974	B;B	0.28933	0.172;0.228	B;B	0.27796	0.039;0.083	T	0.36456	-0.9747	9	0.18276	T	0.48	-3.1566	5.9979	0.19505	0.1053:0.2031:0.6916:0.0	rs1056695;rs3197287;rs3748573;rs17845205;rs17858017;rs17858799;rs56988326;rs1056695	504;504	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	K	443;504;504	ENSP00000331210:E504K;ENSP00000354925:E504K	ENSP00000255029:E443K	E	+	1	0	BCAN	154888876	0.997000	0.39634	0.738000	0.30950	0.048000	0.14542	1.020000	0.30027	0.569000	0.29329	0.555000	0.69702	GAG	G|0.678;A|0.322	0.322	strong		0.652	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
DGKG	1608	hgsc.bcm.edu	37	3	186006566	186006566	+	Silent	SNP	T	T	C	rs710443	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:186006566T>C	ENST00000265022.3	-	6	1016	c.477A>G	c.(475-477)gtA>gtG	p.V159V	DGKG_ENST00000344484.4_Silent_p.V159V|DGKG_ENST00000382164.4_Silent_p.V159V|DGKG_ENST00000544847.1_Silent_p.V159V	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	159					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	CCTTCAGGTATACCACTGGGG	0.577													C|||	3485	0.695887	0.6936	0.6974	5008	,	,		16536	0.7103		0.6978	False		,,,				2504	0.681				p.V159V		Atlas-SNP	.											.	DGKG	98	.	0			c.A477G						PASS	.	C	,,	3039,1367	452.8+/-350.1	1054,931,218	129.0	139.0	136.0		477,477,477	0.8	1.0	3	dbSNP_86	136	5916,2684	430.4+/-356.5	2023,1870,407	no	coding-synonymous,coding-synonymous,coding-synonymous	DGKG	NM_001080744.1,NM_001080745.1,NM_001346.2	,,	3077,2801,625	CC,CT,TT		31.2093,31.0259,31.1472	,,	159/767,159/753,159/792	186006566	8955,4051	2203	4300	6503	SO:0001819	synonymous_variant	1608	exon6			CAGGTATACCACT	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"""EF-hand domain containing"""	2853	protein-coding gene	gene with protein product		601854	"""diacylglycerol kinase, gamma (90kD)"""	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.477A>G	3.37:g.186006566T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Silent	SNP	ENST00000265022.3	37	CCDS3274.1																																																																																			T|0.313;C|0.687	0.687	strong		0.577	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3		
HLA-DMA	3108	hgsc.bcm.edu	37	6	32917544	32917544	+	Missense_Mutation	SNP	C	C	T	rs1063478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32917544C>T	ENST00000374843.4	-	3	581	c.496G>A	c.(496-498)Gtc>Atc	p.V166I	HLA-DMA_ENST00000464392.1_5'UTR|HLA-DMA_ENST00000395305.3_Missense_Mutation_p.V71I|HLA-DMA_ENST00000395303.3_Missense_Mutation_p.V132I|XXbac-BPG181M17.5_ENST00000429234.1_Intron	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	166	Alpha-2.|Ig-like C1-type.		V -> I (in allele DMA*01:02 and allele DMA*01:04; dbSNP:rs1063478).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						TCCACAGGGACGGAATGATGC	0.498													c|||	870	0.173722	0.0915	0.1974	5008	,	,		20678	0.2391		0.1292	False		,,,				2504	0.2464				p.V166I		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G496A						PASS	.	T	ILE/VAL	283,2739		13,257,1241	78.0	71.0	73.0		496	1.5	0.0	6	dbSNP_86	73	696,4722		34,628,2047	yes	missense	HLA-DMA	NM_006120.3	29	47,885,3288	TT,TC,CC		12.8461,9.3647,11.5995	benign	166/262	32917544	979,7461	1511	2709	4220	SO:0001583	missense	3108	exon3			CAGGGACGGAATG		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.496G>A	6.37:g.32917544C>T	ENSP00000363976:p.Val166Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	84	11	0.130952	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	37	CCDS4761.1	328	0.15018315018315018	50	0.1016260162601626	55	0.15193370165745856	129	0.22552447552447552	94	0.12401055408970976	c	2.325	-0.354828	0.05138	0.093647	0.128461	ENSG00000204257	ENST00000395305;ENST00000395303;ENST00000374843;ENST00000456800;ENST00000422832	T;T;T;T;T	0.03004	4.08;4.08;4.08;4.08;4.08	5.28	1.54	0.23209	.	1.512590	0.03389	N	0.201603	T	0.00784	0.0026	N	0.16130	0.375	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46830	-0.9163	9	0.33141	T	0.24	.	4.0461	0.09773	0.1635:0.5772:0.0:0.2594	rs1063478;rs13209997;rs17214050;rs17617501;rs17882348;rs45482294;rs52831176;rs1063478	166	Q31604	.	I	71;132;166;196;133	ENSP00000378716:V71I;ENSP00000378714:V132I;ENSP00000363976:V166I;ENSP00000409668:V196I;ENSP00000403122:V133I	ENSP00000363976:V166I	V	-	1	0	HLA-DMA	33025522	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.119000	0.10676	0.095000	0.17434	-0.131000	0.14894	GTC	.	.	weak		0.498	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120	
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 GAIIx	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	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	147	8	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	
TTN	7273	hgsc.bcm.edu	37	2	179605180	179605180	+	Silent	SNP	C	C	T	rs746578	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179605180C>T	ENST00000591111.1	-	46	12053	c.11829G>A	c.(11827-11829)gcG>gcA	p.A3943A	TTN_ENST00000589042.1_Silent_p.A4260A|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000342175.6_Silent_p.A4089A|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Silent_p.A4022A|TTN_ENST00000460472.2_Silent_p.A3897A|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCAAGATGAGCGCACTTTGTG	0.483													C|||	1196	0.238818	0.1846	0.1585	5008	,	,		20859	0.4702		0.1382	False		,,,				2504	0.2342				p.A4260A		Atlas-SNP	.											TTN_ENST00000359218,colon,carcinoma,-1,1	TTN	18412	1	0			c.G12780A						PASS	.	C	,,,	585,3313		44,497,1408	106.0	99.0	101.0		11691,,12066,12267	-1.9	0.0	2	dbSNP_86	101	1064,7228		80,904,3162	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	124,1401,4570	TT,TC,CC		12.8316,15.0077,13.5275	,,,	3897/26927,,4022/27052,4089/27119	179605180	1649,10541	1949	4146	6095	SO:0001819	synonymous_variant	7273	exon48			GATGAGCGCACTT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.11829G>A	2.37:g.179605180C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.233;C|0.757;A|0.010	0.233	strong		0.483	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KCNQ1	3784	hgsc.bcm.edu	37	11	2797237	2797237	+	Silent	SNP	G	G	A	rs1057128|rs4151646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:2797237G>A	ENST00000155840.5	+	13	1746	c.1638G>A	c.(1636-1638)tcG>tcA	p.S546S	KCNQ1_ENST00000335475.5_Silent_p.S419S	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	546			S -> L (in LQT1). {ECO:0000269|PubMed:15840476}.		atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	AGCAGTACTCGCAGGGCCACC	0.642													G|||	906	0.180911	0.0106	0.33	5008	,	,		18625	0.2927		0.1978	False		,,,				2504	0.1728				p.S546S		Atlas-SNP	.											KCNQ1,NS,carcinoma,0,1	KCNQ1	60	1	0			c.G1638A						PASS	.	G	,	204,4188		2,200,1994	82.0	62.0	69.0		1638,1257	-5.7	0.9	11	dbSNP_86	69	1657,6919		168,1321,2799	no	coding-synonymous,coding-synonymous	KCNQ1	NM_000218.2,NM_181798.1	,	170,1521,4793	AA,AG,GG		19.3214,4.6448,14.3507	,	546/677,419/550	2797237	1861,11107	2196	4288	6484	SO:0001819	synonymous_variant	3784	exon13			GTACTCGCAGGGC	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6294	protein-coding gene	gene with protein product	"""Jervell and Lange-Nielsen syndrome 1"""	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1638G>A	11.37:g.2797237G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			G|0.838;A|0.162	0.162	strong		0.642	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
ASB10	136371	hgsc.bcm.edu	37	7	150878332	150878332	+	Silent	SNP	G	G	A	rs61743170	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150878332G>A	ENST00000420175.2	-	3	822	c.798C>T	c.(796-798)gcC>gcT	p.A266A	ASB10_ENST00000422024.1_Silent_p.A311A|ASB10_ENST00000377867.3_Silent_p.A251A|ASB10_ENST00000275838.1_Silent_p.A266A|ASB10_ENST00000434669.1_Silent_p.A311A			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	266					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGTGGCCTCGGCATCGGTGA	0.657													G|||	453	0.0904553	0.1573	0.085	5008	,	,		16735	0.0823		0.0686	False		,,,				2504	0.0348				p.A266A		Atlas-SNP	.											.	ASB10	99	.	0			c.C798T						PASS	.	G	,,	621,3785		37,547,1619	31.0	33.0	32.0		798,798,753	-10.5	0.0	7	dbSNP_129	32	415,8181		8,399,3891	no	coding-synonymous,coding-synonymous,coding-synonymous	ASB10	NM_001142459.1,NM_001142460.1,NM_080871.3	,,	45,946,5510	AA,AG,GG		4.8278,14.0944,7.968	,,	266/468,266/430,251/453	150878332	1036,11966	2203	4298	6501	SO:0001819	synonymous_variant	136371	exon3			GGCCTCGGCATCG	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"""Ankyrin repeat domain containing"""	17185	protein-coding gene	gene with protein product		615054	"""ankyrin repeat and SOCS box-containing 10"", ""glaucoma 1, open angle, F (adult-onset)"""	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.798C>T	7.37:g.150878332G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_001142459	A0AVH0|Q6ZUL6	Silent	SNP	ENST00000420175.2	37	CCDS47750.2																																																																																			G|0.914;A|0.086	0.086	strong		0.657	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871	
C2CD4A	145741	hgsc.bcm.edu	37	15	62359914	62359914	+	Silent	SNP	C	C	T	rs12911068	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62359914C>T	ENST00000355522.5	+	2	243	c.102C>T	c.(100-102)acC>acT	p.T34T		NM_207322.2	NP_997205.2	Q8NCU7	C2C4A_HUMAN	C2 calcium-dependent domain containing 4A	34				T -> I (in Ref. 1; AAM28197). {ECO:0000305}.		nucleus (GO:0005634)											CTCGCACCACCGCCGCGTGCG	0.682													C|||	179	0.0357428	0.0182	0.0403	5008	,	,		11915	0.0069		0.0676	False		,,,				2504	0.0532				p.T34T		Atlas-SNP	.											.	C2CD4A	3	.	0			c.C102T						PASS	.	C		107,4295		1,105,2095	21.0	24.0	23.0		102	3.4	0.1	15	dbSNP_121	23	681,7913		34,613,3650	no	coding-synonymous	C2CD4A	NM_207322.2		35,718,5745	TT,TC,CC		7.9241,2.4307,6.0634		34/370	62359914	788,12208	2201	4297	6498	SO:0001819	synonymous_variant	145741	exon2			CACCACCGCCGCG	AF504646	CCDS32258.1	15q22.2	2009-09-28	2009-09-28	2009-09-28		ENSG00000198535			33627	protein-coding gene	gene with protein product	"""nuclear localized factor 1"""	610343	"""family with sequence similarity 148, member A"""	FAM148A			Standard	NM_207322		Approved	NLF1	uc002ahf.4	Q8NCU7		ENST00000355522.5:c.102C>T	15.37:g.62359914C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_207322		Silent	SNP	ENST00000355522.5	37	CCDS32258.1																																																																																			C|0.949;T|0.051	0.051	strong		0.682	C2CD4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416008.2	NM_207322	
ZDHHC11	79844	hgsc.bcm.edu	37	5	825297	825297	+	Silent	SNP	A	A	G	rs1808545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:825297A>G	ENST00000283441.8	-	8	1388	c.1005T>C	c.(1003-1005)gaT>gaC	p.D335D	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Silent_p.D335D	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	335						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			TCGAATCCCCATCCTGGTTTA	0.547																																					p.D335D		Atlas-SNP	.											.	ZDHHC11	97	.	0			c.T1005C						PASS	.						191.0	137.0	155.0					5																	825297		2203	4296	6499	SO:0001819	synonymous_variant	79844	exon8			ATCCCCATCCTGG	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1005T>C	5.37:g.825297A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	138	15	0.108696	NM_024786	Q6UWR9	Silent	SNP	ENST00000283441.8	37	CCDS3857.1																																																																																			A|0.977;G|0.023	0.023	strong		0.547	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
ZBTB46	140685	hgsc.bcm.edu	37	20	62378349	62378349	+	Silent	SNP	C	C	T	rs5019252	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62378349C>T	ENST00000245663.4	-	5	1854	c.1704G>A	c.(1702-1704)gaG>gaA	p.E568E	RP4-583P15.10_ENST00000433905.2_RNA|RP4-583P15.10_ENST00000447343.2_RNA|ZBTB46_ENST00000395104.1_Silent_p.E568E|ZBTB46_ENST00000302995.2_Silent_p.E568E	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	568					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GCGAGTCTTCCTCATCCTTGT	0.726													c|||	1350	0.269569	0.1498	0.379	5008	,	,		10337	0.3472		0.336	False		,,,				2504	0.2055				p.E568E		Atlas-SNP	.											ZBTB46,rectum,carcinoma,0,1	ZBTB46	72	1	0			c.G1704A						PASS	.	T		770,3626		79,612,1507	25.0	24.0	25.0		1704	-7.5	0.0	20	dbSNP_113	25	2820,5768		445,1930,1919	no	coding-synonymous	ZBTB46	NM_025224.3		524,2542,3426	TT,TC,CC		32.8365,17.5159,27.6494		568/590	62378349	3590,9394	2198	4294	6492	SO:0001819	synonymous_variant	140685	exon5			GTCTTCCTCATCC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1704G>A	20.37:g.62378349C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.724;T|0.276	0.276	strong		0.726	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
ALPK3	57538	hgsc.bcm.edu	37	15	85383145	85383145	+	Missense_Mutation	SNP	C	C	G	rs3803403	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:85383145C>G	ENST00000258888.5	+	5	1408	c.1241C>G	c.(1240-1242)aCt>aGt	p.T414S		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	414			T -> S (in dbSNP:rs3803403). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GAGGTCGACACTCTGCGCAAG	0.677													C|||	683	0.136382	0.0159	0.1628	5008	,	,		16453	0.1329		0.2575	False		,,,				2504	0.1595				p.T414S		Atlas-SNP	.											.	ALPK3	289	.	0			c.C1241G						PASS	.	C	SER/THR	247,4159	141.1+/-176.5	10,227,1966	38.0	40.0	40.0		1241	3.0	0.0	15	dbSNP_107	40	2334,6264	387.5+/-342.2	314,1706,2279	yes	missense	ALPK3	NM_020778.4	58	324,1933,4245	GG,GC,CC		27.1458,5.606,19.8477	benign	414/1908	85383145	2581,10423	2203	4299	6502	SO:0001583	missense	57538	exon5			TCGACACTCTGCG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.1241C>G	15.37:g.85383145C>G	ENSP00000258888:p.Thr414Ser	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	359	0.16437728937728938	7	0.014227642276422764	72	0.19889502762430938	81	0.14160839160839161	199	0.262532981530343	C	2.744	-0.261585	0.05791	0.05606	0.271458	ENSG00000136383	ENST00000258888	T	0.59502	0.26	4.95	2.95	0.34219	.	0.880280	0.09710	N	0.765881	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.26318	0.146	B	0.24974	0.057	T	0.21042	-1.0257	9	0.22109	T	0.4	-2.83	4.2817	0.10836	0.1755:0.6128:0.0:0.2117	rs3803403;rs60827617;rs3803403	414	Q96L96	ALPK3_HUMAN	S	414	ENSP00000258888:T414S	ENSP00000258888:T414S	T	+	2	0	ALPK3	83184149	0.001000	0.12720	0.003000	0.11579	0.126000	0.20510	0.517000	0.22832	0.981000	0.38548	0.563000	0.77884	ACT	C|0.808;G|0.192	0.192	strong		0.677	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
ACSS1	84532	hgsc.bcm.edu	37	20	24994289	24994289	+	Missense_Mutation	SNP	C	C	T	rs6050249	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:24994289C>T	ENST00000323482.4	-	10	1541	c.1462G>A	c.(1462-1464)Gtg>Atg	p.V488M	ACSS1_ENST00000432802.2_Missense_Mutation_p.V488M|ACSS1_ENST00000484396.1_5'Flank|ACSS1_ENST00000542618.1_Missense_Mutation_p.V367M|ACSS1_ENST00000537502.1_Missense_Mutation_p.V405M	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	488			V -> M (in dbSNP:rs6050249). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CTGCCCTCCACGACGCTGCCC	0.627													C|||	821	0.163938	0.3064	0.1513	5008	,	,		19085	0.0595		0.167	False		,,,				2504	0.0849				p.V488M		Atlas-SNP	.											ACSS1,colon,carcinoma,0,2	ACSS1	46	2	0			c.G1462A						PASS	.	C	MET/VAL	1378,3028	440.6+/-346.1	210,958,1035	35.0	34.0	34.0		1462	-10.6	0.0	20	dbSNP_114	34	1562,7038	286.3+/-297.7	137,1288,2875	no	missense	ACSS1	NM_032501.2	21	347,2246,3910	TT,TC,CC		18.1628,31.2755,22.605	benign	488/690	24994289	2940,10066	2203	4300	6503	SO:0001583	missense	84532	exon10			CCTCCACGACGCT		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"""Acyl-CoA synthetase family"""	16091	protein-coding gene	gene with protein product		614355	"""acetyl-Coenzyme A synthetase 2 (AMP forming)-like"""	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.1462G>A	20.37:g.24994289C>T	ENSP00000316924:p.Val488Met	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Missense_Mutation	SNP	ENST00000323482.4	37	CCDS13167.1	397	0.18177655677655677	165	0.3353658536585366	74	0.20441988950276244	42	0.07342657342657342	116	0.15303430079155672	C	12.75	2.031940	0.35893	0.312755	0.181628	ENSG00000154930	ENST00000323482;ENST00000376727;ENST00000537502;ENST00000432802;ENST00000542618	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.28	-10.6	0.00265	AMP-dependent synthetase/ligase (1);	0.931963	0.09151	N	0.841609	T	0.00012	0.0000	L	0.52266	1.64	0.53688	P	2.5000000000052758E-5	B;B;B;B	0.27823	0.095;0.158;0.19;0.153	B;B;B;B	0.27715	0.009;0.049;0.082;0.056	T	0.16988	-1.0384	9	0.62326	D	0.03	-35.3763	2.2329	0.04001	0.182:0.1005:0.2864:0.431	rs6050249;rs8115396;rs17853908;rs17854324;rs17854886;rs52790525;rs6050249	283;486;488;405	E9PC79;Q9NUB1-2;Q9NUB1;Q6ZV30	.;.;ACS2L_HUMAN;.	M	488;283;405;488;367	ENSP00000316924:V488M;ENSP00000439304:V405M;ENSP00000388793:V488M;ENSP00000437657:V367M	ENSP00000316924:V488M	V	-	1	0	ACSS1	24942289	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.494000	0.00972	-1.951000	0.01029	-0.137000	0.14449	GTG	C|0.785;T|0.215	0.215	strong		0.627	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
PRAMEF10	343071	hgsc.bcm.edu	37	1	12954921	12954921	+	Missense_Mutation	SNP	A	A	G	rs199792484	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12954921A>G	ENST00000235347.4	-	3	441	c.362T>C	c.(361-363)gTc>gCc	p.V121A		NM_001039361.3	NP_001034450.2	O60809	PRA10_HUMAN	PRAME family member 10	121					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)					NS(2)|breast(1)|large_intestine(2)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	12	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGGAGAGGACCCTGGCTCC	0.532																																					p.V121A		Atlas-SNP	.											PRAMEF10,NS,carcinoma,0,1	PRAMEF10	35	1	0			c.T362C						scavenged	.						16.0	16.0	16.0					1																	12954921		1209	2747	3956	SO:0001583	missense	343071	exon3			GAGAGGACCCTGG	AL049682	CCDS41255.1	1p36.21	2013-01-17			ENSG00000187545	ENSG00000187545		"""-"""	27997	protein-coding gene	gene with protein product							Standard	NM_001039361		Approved		uc001auo.3	O60809	OTTHUMG00000001981	ENST00000235347.4:c.362T>C	1.37:g.12954921A>G	ENSP00000235347:p.Val121Ala	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	127	17	0.133858	NM_001039361	Q2M1V2	Missense_Mutation	SNP	ENST00000235347.4	37	CCDS41255.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.989193	0.00046	.	.	ENSG00000187545	ENST00000235347	T	0.04706	3.57	1.65	-3.3	0.05003	.	2.600110	0.01694	N	0.026836	T	0.01287	0.0042	N	0.00642	-1.3	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35101	-0.9802	10	0.02654	T	1	.	2.8919	0.05679	0.4191:0.0:0.2344:0.3465	.	121	O60809	PRA10_HUMAN	A	121	ENSP00000235347:V121A	ENSP00000235347:V121A	V	-	2	0	PRAMEF10	12877508	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.380000	0.00491	-2.367000	0.00605	-1.140000	0.01884	GTC	A|0.930;G|0.070	0.070	strong		0.532	PRAMEF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005512.2	XM_496342	
SLC15A4	121260	hgsc.bcm.edu	37	12	129278864	129278864	+	Silent	SNP	A	A	G	rs1059312	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:129278864A>G	ENST00000266771.5	-	8	1650	c.1611T>C	c.(1609-1611)ttT>ttC	p.F537F	SLC15A4_ENST00000544112.1_Silent_p.F200F|SLC15A4_ENST00000545031.1_Silent_p.F54F	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	537					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		CAGCCAGAAGAAAAAAGTAAT	0.423													A|||	2331	0.465455	0.4803	0.5389	5008	,	,		18523	0.4266		0.4195	False		,,,				2504	0.4806				p.F537F		Atlas-SNP	.											.	SLC15A4	41	.	0			c.T1611C						PASS	.	A		2103,2303	562.9+/-381.1	492,1119,592	74.0	86.0	82.0		1611	-0.8	0.7	12	dbSNP_86	82	3275,5325	484.3+/-371.4	628,2019,1653	no	coding-synonymous	SLC15A4	NM_145648.3		1120,3138,2245	GG,GA,AA		38.0814,47.7304,41.3501		537/578	129278864	5378,7628	2203	4300	6503	SO:0001819	synonymous_variant	121260	exon8			CAGAAGAAAAAAG	AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"""Solute carriers"""	23090	protein-coding gene	gene with protein product		615806	"""solute carrier family 15, member 4"""			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1611T>C	12.37:g.129278864A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	85	0.955056	NM_145648	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Silent	SNP	ENST00000266771.5	37	CCDS9264.1																																																																																			A|0.574;G|0.426	0.426	strong		0.423	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648	
PON3	5446	hgsc.bcm.edu	37	7	95001555	95001555	+	Silent	SNP	C	C	T	rs1053275	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:95001555C>T	ENST00000265627.5	-	4	307	c.297G>A	c.(295-297)gcG>gcA	p.A99A	PON1_ENST00000542556.1_Intron|PON3_ENST00000427422.1_Silent_p.A99A|PON3_ENST00000451904.1_Silent_p.A99A	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	99					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	TGATTTCTAGCGCTTGTGCCC	0.398													T|||	3308	0.660543	0.6422	0.6772	5008	,	,		17161	0.7788		0.501	False		,,,				2504	0.7157				p.A99A		Atlas-SNP	.											.	PON3	59	.	0			c.G297A						PASS	.	T		2501,1905	544.8+/-376.6	708,1085,410	156.0	147.0	150.0		297	-0.6	0.0	7	dbSNP_86	150	3933,4667	604.0+/-394.7	906,2121,1273	no	coding-synonymous	PON3	NM_000940.2		1614,3206,1683	TT,TC,CC		45.7326,43.2365,49.4695		99/355	95001555	6434,6572	2203	4300	6503	SO:0001819	synonymous_variant	5446	exon4			TTCTAGCGCTTGT	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.297G>A	7.37:g.95001555C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	193	193	1	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																			C|0.417;T|0.583	0.583	strong		0.398	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
OCA2	4948	hgsc.bcm.edu	37	15	28090173	28090173	+	Silent	SNP	C	C	T	rs12592307	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:28090173C>T	ENST00000354638.3	-	23	2519	c.2364G>A	c.(2362-2364)tcG>tcA	p.S788S	OCA2_ENST00000353809.5_Silent_p.S764S	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	788					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.S788S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		CGACGTTTGCCGACGCGCCAA	0.388									Oculocutaneous Albinism				C|||	1416	0.282748	0.0802	0.3559	5008	,	,		16618	0.5635		0.2008	False		,,,				2504	0.2996				p.S788S		Atlas-SNP	.											OCA2,NS,carcinoma,0,1	OCA2	173	1	1	Substitution - coding silent(1)	stomach(1)	c.G2364A						PASS	.	C		505,3901	232.3+/-245.9	25,455,1723	61.0	61.0	61.0		2364	-5.0	0.7	15	dbSNP_120	61	1767,6833	320.4+/-314.6	181,1405,2714	no	coding-synonymous	OCA2	NM_000275.2		206,1860,4437	TT,TC,CC		20.5465,11.4616,17.4689		788/839	28090173	2272,10734	2203	4300	6503	SO:0001819	synonymous_variant	4948	exon23	Familial Cancer Database		GTTTGCCGACGCG		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.2364G>A	15.37:g.28090173C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	144	82	0.569444	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																			C|0.769;T|0.231	0.231	strong		0.388	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
LDHAL6B	92483	hgsc.bcm.edu	37	15	59499274	59499274	+	Silent	SNP	C	C	A	rs3809528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:59499274C>A	ENST00000307144.4	+	1	233	c.135C>A	c.(133-135)acC>acA	p.T45T	MYO1E_ENST00000288235.4_Intron	NM_033195.2	NP_149972.1	Q9BYZ2	LDH6B_HUMAN	lactate dehydrogenase A-like 6B	45					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	L-lactate dehydrogenase activity (GO:0004459)			endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|stomach(1)	10						GGCTCTTCACCCCCGTGAGCA	0.562													C|||	2509	0.500998	0.5113	0.4409	5008	,	,		20835	0.6131		0.34	False		,,,				2504	0.5798				p.T45T		Atlas-SNP	.											.	LDHAL6B	30	.	0			c.C135A						PASS	.	C	,	2053,2329	567.5+/-382.2	502,1049,640	78.0	70.0	72.0		,135	-0.3	0.0	15	dbSNP_107	72	2754,5826	439.4+/-359.2	437,1880,1973	no	intron,coding-synonymous	MYO1E,LDHAL6B	NM_004998.2,NM_033195.1	,	939,2929,2613	AA,AC,CC		32.0979,46.8508,37.0853	,	,45/382	59499274	4807,8155	2191	4290	6481	SO:0001819	synonymous_variant	92483	exon1			CTTCACCCCCGTG	AY009108	CCDS10171.1	15q21.3	2011-01-27	2004-07-27	2004-07-28	ENSG00000171989	ENSG00000171989			21481	protein-coding gene	gene with protein product			"""lactate dehydrogenase A-like 6"""	LDHAL6		15870898	Standard	NM_033195		Approved	LDHL, LDH6B	uc002agb.4	Q9BYZ2	OTTHUMG00000132714	ENST00000307144.4:c.135C>A	15.37:g.59499274C>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_033195	Q6DUY4|Q96LI2	Silent	SNP	ENST00000307144.4	37	CCDS10171.1																																																																																			C|0.586;A|0.414	0.414	strong		0.562	LDHAL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256015.1	NM_033195	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274415	39274415	+	Silent	SNP	C	C	T	rs425487		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39274415C>T	ENST00000391413.2	-	1	191	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	51	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)		p.R51R(6)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGCACTGGGGCCTGCAGCAGC	0.667																																					p.R51R		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,-1,11	KRTAP4-11	94	11	6	Substitution - coding silent(6)	endometrium(3)|kidney(2)|lung(1)	c.G153A						scavenged	.						9.0	15.0	13.0					17																	39274415		682	1579	2261	SO:0001819	synonymous_variant	653240	exon1			CTGGGGCCTGCAG	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.153G>A	17.37:g.39274415C>T		Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	72	3	0.0416667	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	weak		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
METTL11B	149281	hgsc.bcm.edu	37	1	170135765	170135765	+	Silent	SNP	T	T	C	rs6669514	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:170135765T>C	ENST00000439373.2	+	3	560	c.453T>C	c.(451-453)ttT>ttC	p.F151F	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	151						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						TGGAATCCTTTCTCCTTGAAG	0.512													T|||	1330	0.265575	0.4758	0.2219	5008	,	,		18181	0.1349		0.2207	False		,,,				2504	0.1933				p.F151F		Atlas-SNP	.											.	METTL11B	18	.	0			c.T453C						PASS	.	T		599,785		131,337,224	111.0	101.0	104.0		453	2.3	1.0	1	dbSNP_116	104	752,2430		97,558,936	no	coding-synonymous	METTL11B	NM_001136107.1		228,895,1160	CC,CT,TT		23.6329,43.2803,29.5883		151/284	170135765	1351,3215	692	1591	2283	SO:0001819	synonymous_variant	149281	exon3			ATCCTTTCTCCTT	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.453T>C	1.37:g.170135765T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	67	0.598214	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			T|0.746;C|0.254	0.254	strong		0.512	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
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 GAIIx	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		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	49	25	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	
SYNE3	161176	hgsc.bcm.edu	37	14	95910933	95910933	+	Silent	SNP	T	T	C	rs9919918	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:95910933T>C	ENST00000334258.5	-	9	1679	c.1665A>G	c.(1663-1665)gcA>gcG	p.A555A	SYNE3_ENST00000557275.1_Silent_p.A555A|SYNE3_ENST00000554873.1_Silent_p.A312A|SYNE3_ENST00000553340.1_Silent_p.A555A	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	555					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)	p.A555A(1)		breast(1)|endometrium(2)|lung(25)	28						GCTCAAAAGCTGCTCCAAAGT	0.577													C|||	1410	0.28155	0.3427	0.4035	5008	,	,		19740	0.3155		0.2078	False		,,,				2504	0.1534				p.A555A		Atlas-SNP	.											C14orf49,NS,carcinoma,0,1	SYNE3	130	1	1	Substitution - coding silent(1)	stomach(1)	c.A1665G						PASS	.	C		1436,2970	682.6+/-404.1	244,948,1011	52.0	51.0	51.0		1665	-10.8	0.0	14	dbSNP_119	51	1620,6980	742.8+/-407.2	171,1278,2851	no	coding-synonymous	C14orf49	NM_152592.3		415,2226,3862	CC,CT,TT		18.8372,32.5919,23.4968		555/976	95910933	3056,9950	2203	4300	6503	SO:0001819	synonymous_variant	161176	exon9			AAAAGCTGCTCCA	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.1665A>G	14.37:g.95910933T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	CCDS9935.1																																																																																			C|0.242;N|0.000	0.242	strong		0.577	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
ATP2A3	489	hgsc.bcm.edu	37	17	3848013	3848013	+	Silent	SNP	A	A	C	rs1800911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3848013A>C	ENST00000352011.3	-	10	1326	c.1272T>G	c.(1270-1272)gcT>gcG	p.A424A	ATP2A3_ENST00000397043.3_Silent_p.A424A|ATP2A3_ENST00000359983.3_Silent_p.A424A|ATP2A3_ENST00000397035.3_Silent_p.A424A|ATP2A3_ENST00000397041.3_Silent_p.A424A|ATP2A3_ENST00000309890.7_Silent_p.A424A|ATP2A3_ENST00000397039.1_5'UTR			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	424					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		TGTAGTCCAGAGCCGAGTCGT	0.657													C|||	1684	0.336262	0.4062	0.4597	5008	,	,		11878	0.0843		0.4573	False		,,,				2504	0.2894				p.A424A	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T1272G						PASS	.	C	,,,,,,	1739,2667	636.6+/-396.6	349,1041,813	51.0	42.0	45.0		1272,1272,1272,1272,1272,1272,1272	-4.1	0.5	17	dbSNP_89	45	3945,4651	593.9+/-393.2	927,2091,1280	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	1276,3132,2093	CC,CA,AA		45.8934,39.4689,43.7164	,,,,,,	424/1000,424/1053,424/1045,424/1044,424/1030,424/999,424/1030	3848013	5684,7318	2203	4298	6501	SO:0001819	synonymous_variant	489	exon10			GTCCAGAGCCGAG		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1272T>G	17.37:g.3848013A>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	128	54	0.421875	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.610;C|0.390	0.390	strong		0.657	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
PCDHB15	56121	hgsc.bcm.edu	37	5	140627020	140627020	+	Missense_Mutation	SNP	G	G	T	rs77506821	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140627020G>T	ENST00000231173.3	+	1	1874	c.1874G>T	c.(1873-1875)cGc>cTc	p.R625L		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	625	Cadherin 6. {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(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCGAGGTGCGCACCGCCAGG	0.701													G|||	280	0.0559105	0.1793	0.0447	5008	,	,		15490	0.0		0.0119	False		,,,				2504	0.0				p.R625L		Atlas-SNP	.											.	PCDHB15	138	.	0			c.G1874T						PASS	.	G	LEU/ARG	605,3647		37,531,1558	30.0	33.0	32.0		1874	4.3	1.0	5	dbSNP_131	32	110,8226		0,110,4058	no	missense	PCDHB15	NM_018935.2	102	37,641,5616	TT,TG,GG		1.3196,14.2286,5.68	probably-damaging	625/788	140627020	715,11873	2126	4168	6294	SO:0001583	missense	56121	exon1			AGGTGCGCACCGC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1874G>T	5.37:g.140627020G>T	ENSP00000231173:p.Arg625Leu	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	118	0.05402930402930403	93	0.18902439024390244	17	0.04696132596685083	0	0.0	8	0.010554089709762533	G	19.41	3.822720	0.71028	0.142286	0.013196	ENSG00000113248	ENST00000231173	T	0.52754	0.65	4.28	4.28	0.50868	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00210	0.0006	M	0.83483	2.645	0.30124	P	0.805412	D	0.89917	1.0	D	0.85130	0.997	T	0.19321	-1.0309	8	0.87932	D	0	.	11.4524	0.50160	0.0906:0.0:0.9094:0.0	.	625	Q9Y5E8	PCDBF_HUMAN	L	625	ENSP00000231173:R625L	ENSP00000231173:R625L	R	+	2	0	PCDHB15	140607204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.958000	0.76025	2.117000	0.64856	0.549000	0.68633	CGC	G|0.941;T|0.059	0.059	strong		0.701	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
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 GAIIx	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_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Silent_p.K613K	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		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	24	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	
TTN	7273	hgsc.bcm.edu	37	2	179398823	179398823	+	Silent	SNP	G	G	A	rs2857265	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179398823G>A	ENST00000591111.1	-	308	97820	c.97596C>T	c.(97594-97596)ggC>ggT	p.G32532G	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000589042.1_Silent_p.G34173G|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342175.6_Silent_p.G25300G|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Silent_p.G25233G|TTN_ENST00000460472.2_Silent_p.G25108G|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.G31605G|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588257.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32532	Ig-like 143.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCTGTCGGACGCCAAAGTACC	0.418													G|||	1162	0.232029	0.1483	0.1571	5008	,	,		23498	0.4514		0.1392	False		,,,				2504	0.2679				p.G34173G		Atlas-SNP	.											.	TTN	18412	.	0			c.C102519T						PASS	.	G	,,,	552,3352		40,472,1440	114.0	112.0	113.0		75324,94815,75699,75900	-10.3	0.8	2	dbSNP_100	113	1214,7072		92,1030,3021	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	132,1502,4461	AA,AG,GG		14.6512,14.1393,14.4873	,,,	25108/26927,31605/33424,25233/27052,25300/27119	179398823	1766,10424	1952	4143	6095	SO:0001819	synonymous_variant	7273	exon358			TCGGACGCCAAAG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.97596C>T	2.37:g.179398823G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.802;A|0.198	0.198	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OR5P2	120065	hgsc.bcm.edu	37	11	7817959	7817959	+	Silent	SNP	G	G	A	rs73406603	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7817959G>A	ENST00000329434.2	-	1	561	c.531C>T	c.(529-531)ttC>ttT	p.F177F	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GTAAGGGAGCGAAATCACAGA	0.388													G|||	1185	0.236621	0.3472	0.2911	5008	,	,		20101	0.128		0.2763	False		,,,				2504	0.1196				p.F177F		Atlas-SNP	.											OR5P2,brain,glioma,0,1	OR5P2	68	1	0			c.C531T						PASS	.	G		1366,2838		399,568,1135	69.0	81.0	77.0		531	3.2	1.0	11	dbSNP_130	77	2424,6160		392,1640,2260	no	coding-synonymous	OR5P2	NM_153444.1		791,2208,3395	AA,AG,GG		28.2386,32.4929,29.6372		177/323	7817959	3790,8998	2102	4292	6394	SO:0001819	synonymous_variant	120065	exon1			GGGAGCGAAATCA	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.531C>T	11.37:g.7817959G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			G|0.739;A|0.261	0.261	strong		0.388	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
KCNH2	3757	hgsc.bcm.edu	37	7	150648789	150648789	+	Silent	SNP	T	T	C	rs1805121	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150648789T>C	ENST00000262186.5	-	7	2093	c.1692A>G	c.(1690-1692)ctA>ctG	p.L564L	KCNH2_ENST00000430723.3_Silent_p.L564L|KCNH2_ENST00000392968.2_Silent_p.L468L|KCNH2_ENST00000330883.4_Silent_p.L224L	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	564			L -> P (in LQT2).		cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	AGATGCAGGCTAGCCAGTGCG	0.622													C|||	3047	0.608427	0.82	0.4625	5008	,	,		17035	0.8343		0.3608	False		,,,				2504	0.4479				p.L564L	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											KCNH2_ENST00000430723,NS,carcinoma,0,2	KCNH2	157	2	0			c.A1692G						scavenged	.	C	,,,	3268,1138	406.2+/-333.8	1230,808,165	75.0	61.0	65.0		1692,672,1692,672	3.5	1.0	7	dbSNP_89	65	3097,5503	658.0+/-401.5	588,1921,1791	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNH2	NM_000238.3,NM_001204798.1,NM_172056.2,NM_172057.2	,,,	1818,2729,1956	CC,CT,TT		36.0116,25.8284,48.939	,,,	564/1160,224/549,564/889,224/820	150648789	6365,6641	2203	4300	6503	SO:0001819	synonymous_variant	3757	exon7			GCAGGCTAGCCAG	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.1692A>G	7.37:g.150648789T>C		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	141	79	0.560284	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Silent	SNP	ENST00000262186.5	37	CCDS5910.1																																																																																			T|0.477;C|0.523	0.523	strong		0.622	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:12967127C>T	ENST00000358007.3	+	2	172	c.150C>T	c.(148-150)atC>atT	p.I50I	DDX47_ENST00000352940.4_Silent_p.I50I	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	50					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		CCACCAAGATCCAGATTGAAG	0.398													C|||	1937	0.386781	0.2511	0.4121	5008	,	,		23125	0.5992		0.2734	False		,,,				2504	0.4499				p.I50I		Atlas-SNP	.											.	DDX47	37	.	0			c.C150T						PASS	.	C	,	1166,3240	412.4+/-336.1	168,830,1205	308.0	290.0	296.0		150,150	5.3	1.0	12	dbSNP_86	296	2385,6215	397.3+/-345.7	330,1725,2245	yes	coding-synonymous,coding-synonymous	DDX47	NM_016355.3,NM_201224.1	,	498,2555,3450	TT,TC,CC		27.7326,26.4639,27.3028	,	50/456,50/407	12967127	3551,9455	2203	4300	6503	SO:0001819	synonymous_variant	51202	exon2			CAAGATCCAGATT	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.150C>T	12.37:g.12967127C>T		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	148	69	0.466216	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Silent	SNP	ENST00000358007.3	37	CCDS8655.1																																																																																			C|0.686;T|0.314	0.314	strong		0.398	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
MUC16	94025	hgsc.bcm.edu	37	19	9088330	9088330	+	Missense_Mutation	SNP	G	G	A	rs17000947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9088330G>A	ENST00000397910.4	-	1	3688	c.3485C>T	c.(3484-3486)aCt>aTt	p.T1162I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1162	Thr-rich.		T -> I (in dbSNP:rs17000947).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GACTTTGGGAGTAGGAGAAGA	0.483													G|||	951	0.189896	0.0711	0.2709	5008	,	,		22315	0.3036		0.172	False		,,,				2504	0.1943				p.T1162I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C3485T						PASS	.	G	ILE/THR	299,3929		5,289,1820	148.0	142.0	144.0		3485	-0.7	0.0	19	dbSNP_123	144	1504,6954		128,1248,2853	yes	missense	MUC16	NM_024690.2	89	133,1537,4673	AA,AG,GG		17.782,7.0719,14.2125	benign	1162/14508	9088330	1803,10883	2114	4229	6343	SO:0001583	missense	94025	exon1			TTGGGAGTAGGAG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.3485C>T	19.37:g.9088330G>A	ENSP00000381008:p.Thr1162Ile	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	133	66	0.496241	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	g	2.677	-0.276221	0.05679	0.070719	0.17782	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.09	-0.731	0.11151	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.19817	0.039	B	0.11329	0.006	T	0.47058	-0.9146	8	0.87932	D	0	.	3.4331	0.07436	0.4447:0.0:0.5553:0.0	rs17000947;rs17000947	1162	B5ME49	.	I	1162	ENSP00000381008:T1162I	ENSP00000381008:T1162I	T	-	2	0	MUC16	8949330	0.000000	0.05858	0.000000	0.03702	0.250000	0.25880	-0.783000	0.04638	-0.176000	0.10707	0.305000	0.20034	ACT	G|0.811;A|0.189	0.189	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
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 GAIIx	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	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	18	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	
BBS2	583	hgsc.bcm.edu	37	16	56545175	56545175	+	Missense_Mutation	SNP	T	T	C	rs11373	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:56545175T>C	ENST00000245157.5	-	3	787	c.367A>G	c.(367-369)Att>Gtt	p.I123V	BBS2_ENST00000561951.1_5'UTR|BBS2_ENST00000568104.1_Missense_Mutation_p.I123V	NM_031885.3	NP_114091	Q9BXC9	BBS2_HUMAN	Bardet-Biedl syndrome 2	123			I -> V (polymorphism in linkage disequilibrium with G-75 in a Bedouin kindred; dbSNP:rs11373). {ECO:0000269|PubMed:11285252, ECO:0000269|PubMed:15666242, ECO:0000269|PubMed:15770229}.		adult behavior (GO:0030534)|artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|cilium morphogenesis (GO:0060271)|fat cell differentiation (GO:0045444)|Golgi to plasma membrane protein transport (GO:0043001)|hippocampus development (GO:0021766)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of gene expression (GO:0010629)|negative regulation of multicellular organism growth (GO:0040015)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|positive regulation of multicellular organism growth (GO:0040018)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sperm axoneme assembly (GO:0007288)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)	26						CCCAGCACAATTGCATTTGCC	0.413									Bardet-Biedl syndrome				T|||	1320	0.263578	0.2458	0.2767	5008	,	,		18413	0.4127		0.1789	False		,,,				2504	0.2117				p.I123V		Atlas-SNP	.											.	BBS2	67	.	0			c.A367G						PASS	.	T	VAL/ILE	994,3402	372.5+/-320.4	102,790,1306	116.0	98.0	104.0		367	0.5	1.0	16	dbSNP_52	104	1546,7054	290.9+/-300.1	138,1270,2892	yes	missense	BBS2	NM_031885.3	29	240,2060,4198	CC,CT,TT		17.9767,22.6115,19.5445	benign	123/722	56545175	2540,10456	2198	4300	6498	SO:0001583	missense	583	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GCACAATTGCATT	AF342736	CCDS32451.1	16q21	2013-01-08				ENSG00000125124			967	protein-coding gene	gene with protein product		606151		BBS		11285252	Standard	NM_031885		Approved		uc002ejd.2	Q9BXC9		ENST00000245157.5:c.367A>G	16.37:g.56545175T>C	ENSP00000245157:p.Ile123Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_031885	Q96CM0|Q96SN9	Missense_Mutation	SNP	ENST00000245157.5	37	CCDS32451.1	578	0.26465201465201466	110	0.22357723577235772	93	0.2569060773480663	236	0.4125874125874126	139	0.18337730870712401	T	5.499	0.277020	0.10403	0.226115	0.179767	ENSG00000125124	ENST00000245157	D	0.82167	-1.58	5.9	0.542	0.17174	WD40 repeat-like-containing domain (1);	0.376395	0.31976	N	0.006774	T	0.00012	0.0000	N	0.16307	0.4	0.34697	P	0.273659	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.25117	-1.0141	9	0.14656	T	0.56	-3.2293	5.865	0.18771	0.0:0.3239:0.1315:0.5446	rs11373;rs1129878;rs3177663;rs3188184;rs11555777;rs17295965;rs17354402;rs17845410;rs17858274;rs52799276;rs57383601;rs11373	123;123	A8K0N9;Q9BXC9	.;BBS2_HUMAN	V	123	ENSP00000245157:I123V	ENSP00000245157:I123V	I	-	1	0	BBS2	55102676	0.997000	0.39634	0.994000	0.49952	0.608000	0.37181	0.402000	0.20965	-0.180000	0.10637	-0.276000	0.10085	ATT	T|0.778;C|0.222	0.222	strong		0.413	BBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434386.2	NM_031885	
SLC2A6	11182	hgsc.bcm.edu	37	9	136337168	136337168	+	Missense_Mutation	SNP	G	G	A	rs3094378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136337168G>A	ENST00000371899.4	-	10	1576	c.1499C>T	c.(1498-1500)aCg>aTg	p.T500M	SLC2A6_ENST00000485978.1_5'UTR|SLC2A6_ENST00000371897.4_Missense_Mutation_p.T438M	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	500			T -> M (in dbSNP:rs3094378). {ECO:0000269|PubMed:10970791, ECO:0000269|Ref.2}.		glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		CCTTCTCCCCGTGCGGAAGAA	0.632													G|||	167	0.0333466	0.0121	0.0562	5008	,	,		19068	0.002		0.0924	False		,,,				2504	0.0174				p.T500M		Atlas-SNP	.											.	SLC2A6	31	.	0			c.C1499T						PASS	.	G	MET/THR,MET/THR	69,4337	63.5+/-100.7	2,65,2136	101.0	87.0	92.0		1313,1499	1.8	0.0	9	dbSNP_103	92	779,7821	183.0+/-231.3	38,703,3559	yes	missense,missense	SLC2A6	NM_001145099.1,NM_017585.3	81,81	40,768,5695	AA,AG,GG		9.0581,1.566,6.5201	probably-damaging,probably-damaging	438/446,500/508	136337168	848,12158	2203	4300	6503	SO:0001583	missense	11182	exon10			CTCCCCGTGCGGA	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"""Solute carriers"""	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.1499C>T	9.37:g.136337168G>A	ENSP00000360966:p.Thr500Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	37	CCDS6975.1	104	0.047619047619047616	9	0.018292682926829267	24	0.06629834254143646	0	0.0	71	0.09366754617414248	G	10.78	1.447376	0.25987	0.01566	0.090581	ENSG00000160326	ENST00000371897;ENST00000371899	D;D	0.82344	-1.53;-1.6	4.78	1.84	0.25277	.	0.208551	0.49305	D	0.000157	T	0.19967	0.0480	N	0.17764	0.52	0.28480	N	0.914992	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.914	T	0.63409	-0.6644	10	0.62326	D	0.03	.	13.8686	0.63603	0.0:0.4442:0.5558:0.0	rs3094378;rs52832403;rs57165600;rs3094378	438;500	Q9UGQ3-2;Q9UGQ3	.;GTR6_HUMAN	M	438;500	ENSP00000360964:T438M;ENSP00000360966:T500M	ENSP00000360964:T438M	T	-	2	0	SLC2A6	135326989	1.000000	0.71417	0.011000	0.14972	0.011000	0.07611	3.728000	0.54991	0.224000	0.20940	-0.182000	0.12963	ACG	G|0.943;A|0.057	0.057	strong		0.632	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585	
SLC7A3	84889	hgsc.bcm.edu	37	X	70146398	70146398	+	Silent	SNP	A	A	G	rs4360450	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:70146398A>G	ENST00000374299.3	-	10	1743	c.1599T>C	c.(1597-1599)agT>agC	p.S533S	SLC7A3_ENST00000298085.4_Silent_p.S533S			Q8WY07	CTR3_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 3	533					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)|L-lysine transmembrane transporter activity (GO:0015189)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|liver(1)|lung(9)|ovary(1)|urinary_tract(1)	31	Renal(35;0.156)				L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	GGGGAGTGGAACTCTGTGGCT	0.468													G|||	3066	0.812185	0.5658	0.6081	3775	,	,		14725	0.754		0.4791	False		,,,				2504	0.6687				p.S533S		Atlas-SNP	.											.	SLC7A3	76	.	0			c.T1599C						PASS	.	G	,	2907,924		934,598,441,99,128	47.0	39.0	42.0		1599,1599	1.1	0.1	X	dbSNP_111	42	4337,2385		992,1138,1215,297,653	no	coding-synonymous,coding-synonymous	SLC7A3	NM_001048164.2,NM_032803.5	,	1926,1736,1656,396,781	GG,GA,G,AA,A		35.4805,24.119,31.356	,	533/620,533/620	70146398	7244,3309	2200	4295	6495	SO:0001819	synonymous_variant	84889	exon10			AGTGGAACTCTGT	AF320612	CCDS14404.1	Xq12	2013-05-22			ENSG00000165349	ENSG00000165349		"""Solute carriers"""	11061	protein-coding gene	gene with protein product		300443				11591158	Standard	NM_001048164		Approved	CAT-3, ATRC3, FLJ14541	uc004dyn.3	Q8WY07	OTTHUMG00000021780	ENST00000374299.3:c.1599T>C	X.37:g.70146398A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_032803	D3DVU7|Q5JQR2|Q8N185|Q8NCA7|Q96SZ7	Silent	SNP	ENST00000374299.3	37	CCDS14404.1																																																																																			A|0.284;G|0.716	0.716	strong		0.468	SLC7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057080.1	NM_032803	
RIN3	79890	hgsc.bcm.edu	37	14	93118692	93118692	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:93118692G>A	ENST00000216487.7	+	6	1457	c.1298G>A	c.(1297-1299)gGc>gAc	p.G433D	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	433	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				ACGGAGCAAGGCCAGGACACA	0.657																																					p.G433D		Atlas-SNP	.											RIN3,NS,carcinoma,+1,1	RIN3	81	1	0			c.G1298A						scavenged	.						79.0	90.0	87.0					14																	93118692		2203	4300	6503	SO:0001583	missense	79890	exon6			AGCAAGGCCAGGA	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1298G>A	14.37:g.93118692G>A	ENSP00000216487:p.Gly433Asp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	98	2	0.0204082	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	.	.	.	.	.	.	.	.	.	.	G	1.525	-0.545975	0.04024	.	.	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.06768	3.26	4.22	0.865	0.19074	.	0.669254	0.13448	N	0.387102	T	0.07007	0.0178	L	0.57536	1.79	0.19300	N	0.999972	B;B;B;B	0.31931	0.347;0.005;0.002;0.067	B;B;B;B	0.31751	0.135;0.003;0.003;0.038	T	0.34030	-0.9845	10	0.12430	T	0.62	-14.06	3.2523	0.06819	0.3348:0.0:0.407:0.2582	.	433;479;358;433	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	D	433;357	ENSP00000216487:G433D	ENSP00000216487:G433D	G	+	2	0	RIN3	92188445	0.000000	0.05858	0.986000	0.45419	0.350000	0.29205	-0.208000	0.09371	0.757000	0.33036	0.313000	0.20887	GGC	.	.	none		0.657	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
DNAJB8	165721	hgsc.bcm.edu	37	3	128181777	128181777	+	Silent	SNP	A	A	G	rs2659690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:128181777A>G	ENST00000469083.1	-	2	2869	c.312T>C	c.(310-312)ttT>ttC	p.F104F	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Silent_p.F104F			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	104					chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CCAGGCCACCAAAAAACTCCC	0.637													G|||	2374	0.474042	0.388	0.5389	5008	,	,		17408	0.4058		0.6352	False		,,,				2504	0.4489				p.F104F		Atlas-SNP	.											.	DNAJB8	34	.	0			c.T312C						PASS	.	G		1820,2586	637.5+/-396.8	383,1054,766	71.0	72.0	72.0		312	-5.8	0.0	3	dbSNP_100	72	5341,3259	490.0+/-372.7	1644,2053,603	no	coding-synonymous	DNAJB8	NM_153330.2		2027,3107,1369	GG,GA,AA		37.8953,41.3073,44.9408		104/233	128181777	7161,5845	2203	4300	6503	SO:0001819	synonymous_variant	165721	exon3			GCCACCAAAAAAC		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"""Heat shock proteins / DNAJ (HSP40)"""	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.312T>C	3.37:g.128181777A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_153330	B3KWV7	Silent	SNP	ENST00000469083.1	37	CCDS3048.1																																																																																			G|0.508;N|0.000	0.508	strong		0.637	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
WDR44	54521	hgsc.bcm.edu	37	X	117528056	117528056	+	Missense_Mutation	SNP	G	G	A	rs17271416	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:117528056G>A	ENST00000254029.3	+	5	1260	c.865G>A	c.(865-867)Gca>Aca	p.A289T	WDR44_ENST00000371822.5_Missense_Mutation_p.A264T|WDR44_ENST00000371825.3_Missense_Mutation_p.A289T	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	289			A -> T (in dbSNP:rs17271416). {ECO:0000269|PubMed:17974005}.			endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						TCTCCTAACCGCAAGCATGGC	0.398													G|||	615	0.162914	0.0772	0.2464	3775	,	,		15457	0.127		0.0974	False		,,,				2504	0.1186				p.A289T		Atlas-SNP	.											.	WDR44	188	.	0			c.G865A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	421,3414		20,318,63,1294,508	127.0	114.0	119.0		865,790,865	-1.2	0.3	X	dbSNP_123	119	864,5864		31,545,257,1852,1615	yes	missense,missense,missense	WDR44	NM_001184965.1,NM_001184966.1,NM_019045.4	58,58,58	51,863,320,3146,2123	AA,AG,A,GG,G		12.8419,10.9778,12.1651	benign,benign,benign	289/906,264/825,289/914	117528056	1285,9278	2203	4300	6503	SO:0001583	missense	54521	exon5			CTAACCGCAAGCA	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"""WD repeat domain containing"""	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.865G>A	X.37:g.117528056G>A	ENSP00000254029:p.Ala289Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	196	138	0.704082	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Missense_Mutation	SNP	ENST00000254029.3	37	CCDS14572.1	283|283	0.17058468957203135|0.17058468957203135	31|31	0.06595744680851064|0.06595744680851064	58|58	0.1870967741935484|0.1870967741935484	49|49	0.09645669291338582|0.09645669291338582	58|58	0.08033240997229917|0.08033240997229917	G|G	1.922|1.922	-0.448083|-0.448083	0.04572|0.04572	0.109778|0.109778	0.128419|0.128419	ENSG00000131725|ENSG00000131725	ENST00000371822;ENST00000254029;ENST00000371825|ENST00000371848	T;T;T|.	0.72167|.	-0.63;-0.04;0.08|.	5.43|5.43	-1.2|-1.2	0.09554|0.09554	.|.	0.215756|.	0.49305|.	N|.	0.000159|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.06786|.	0.001;0.0;0.0|.	B;B;B|.	0.04013|.	0.001;0.001;0.0|.	T|T	0.36335|0.36335	-0.9752|-0.9752	9|4	0.07175|.	T|.	0.84|.	-11.5679|-11.5679	0.8417|0.8417	0.01151|0.01151	0.234:0.3109:0.2598:0.1953|0.234:0.3109:0.2598:0.1953	rs17271416;rs52837890;rs17271416|rs17271416;rs52837890;rs17271416	264;289;289|.	F8W913;Q5JSH3-2;Q5JSH3|.	.;.;WDR44_HUMAN|.	T|H	264;289;289|188	ENSP00000360887:A264T;ENSP00000254029:A289T;ENSP00000360890:A289T|.	ENSP00000254029:A289T|.	A|R	+|+	1|2	0|0	WDR44|WDR44	117412084|117412084	0.005000|0.005000	0.15991|0.15991	0.264000|0.264000	0.24511|0.24511	0.274000|0.274000	0.26718|0.26718	-0.002000|-0.002000	0.12924|0.12924	-0.044000|-0.044000	0.13491|0.13491	-1.113000|-1.113000	0.02065|0.02065	GCA|CGC	0|0.015;A|0.144	0.144	strong		0.398	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045	
SERTAD1	29950	hgsc.bcm.edu	37	19	40928944	40928944	+	Silent	SNP	A	A	G	rs4150992	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40928944A>G	ENST00000357949.4	-	2	668	c.510T>C	c.(508-510)ctT>ctC	p.L170L		NM_013376.3	NP_037508.2	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	170					positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription, DNA-templated (GO:0006351)					endometrium(2)|lung(1)|prostate(1)|skin(1)	5			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			ACAGGCCCTCAAGCCCATCGT	0.627													G|||	1390	0.277556	0.6346	0.2406	5008	,	,		17754	0.0595		0.1382	False		,,,				2504	0.1892				p.L170L		Atlas-SNP	.											.	SERTAD1	18	.	0			c.T510C						PASS	.	G		2493,1887		743,1007,440	18.0	16.0	17.0		510	-10.2	0.3	19	dbSNP_110	17	1038,7550		73,892,3329	no	coding-synonymous	SERTAD1	NM_013376.3		816,1899,3769	GG,GA,AA		12.0866,43.0822,27.2286		170/237	40928944	3531,9437	2190	4294	6484	SO:0001819	synonymous_variant	29950	exon2			GCCCTCAAGCCCA	AF117959	CCDS12557.1	19q13.1-q13.2	2008-02-05				ENSG00000197019			17932	protein-coding gene	gene with protein product	"""CDK4-binding protein p34SEI"", ""transcriptional regulator interacting with the PHD-bromodomain 1"""					6434876, 10580009	Standard	NM_013376		Approved	SEI1, TRIP-Br1	uc002ont.4	Q9UHV2		ENST00000357949.4:c.510T>C	19.37:g.40928944A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	99	43	0.434343	NM_013376	Q9BUE7	Silent	SNP	ENST00000357949.4	37	CCDS12557.1																																																																																			A|0.715;G|0.285	0.285	strong		0.627	SERTAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462571.1	NM_013376	
ERAL1	26284	hgsc.bcm.edu	37	17	27185814	27185814	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27185814T>C	ENST00000254928.5	+	7	1029	c.932T>C	c.(931-933)cTa>cCa	p.L311P	MIR144_ENST00000581873.1_lincRNA|MIR144_ENST00000385059.1_lincRNA|MIR144_ENST00000384886.1_lincRNA	NM_005702.2	NP_005693.1	O75616	ERAL1_HUMAN	Era-like 12S mitochondrial rRNA chaperone 1	311	Era-type G.				ribosomal small subunit assembly (GO:0000028)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			TTGTCAGCCCTAAGCCAGGAG	0.512																																					p.L311P		Atlas-SNP	.											ERAL1,colon,carcinoma,+1,1	ERAL1	28	1	0			c.T932C						scavenged	.						134.0	136.0	135.0					17																	27185814		2203	4300	6503	SO:0001583	missense	26284	exon7			CAGCCCTAAGCCA	AF082657	CCDS11244.1	17q11.2	2013-05-22	2013-05-22		ENSG00000132591	ENSG00000132591			3424	protein-coding gene	gene with protein product		607435	"""Era (E. coli G-protein homolog)-like 1"", ""Era G-protein-like 1 (E. coli)"""			10945472, 20604745	Standard	NM_005702		Approved	HERA-B	uc002hcy.1	O75616	OTTHUMG00000132675	ENST00000254928.5:c.932T>C	17.37:g.27185814T>C	ENSP00000254928:p.Leu311Pro	Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	87	2	0.0229885	NM_005702	B3KN21|C9JEC6|O75617|Q8WUY4|Q96LE2|Q96TC0	Missense_Mutation	SNP	ENST00000254928.5	37	CCDS11244.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.521294	0.85600	.	.	ENSG00000132591	ENST00000254928	D	0.96200	-3.94	6.08	6.08	0.98989	.	0.225469	0.40728	N	0.001039	D	0.98105	0.9375	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.98956	1.0796	10	0.72032	D	0.01	-4.1933	15.4678	0.75416	0.0:0.0:0.0:1.0	.	311	O75616	ERAL1_HUMAN	P	311	ENSP00000254928:L311P	ENSP00000254928:L311P	L	+	2	0	ERAL1	24209940	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.318000	0.65829	2.333000	0.79357	0.533000	0.62120	CTA	.	.	none		0.512	ERAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255937.2		
OR5A2	219981	hgsc.bcm.edu	37	11	59189912	59189912	+	Missense_Mutation	SNP	G	G	A	rs1453547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:59189912G>A	ENST00000302040.4	-	1	537	c.515C>T	c.(514-516)cCc>cTc	p.P172L		NM_001001954.1	NP_001001954.1	Q8NGI9	OR5A2_HUMAN	olfactory receptor, family 5, subfamily A, member 2	172			P -> L (in dbSNP:rs1453547).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	21						GATCATATAGGGCCCACAGAA	0.463													G|||	631	0.125998	0.0242	0.1311	5008	,	,		22596	0.1121		0.2515	False		,,,				2504	0.1452				p.P172L		Atlas-SNP	.											.	OR5A2	35	.	0			c.C515T						PASS	.	G	LEU/PRO	256,4146	148.8+/-183.1	10,236,1955	95.0	88.0	91.0		515	4.6	0.3	11	dbSNP_88	91	2258,6332	382.8+/-340.5	282,1694,2319	yes	missense	OR5A2	NM_001001954.1	98	292,1930,4274	AA,AG,GG		26.2864,5.8155,19.3504	probably-damaging	172/325	59189912	2514,10478	2201	4295	6496	SO:0001583	missense	219981	exon1			ATATAGGGCCCAC	AB065805	CCDS31560.1	11q12.1	2012-08-09			ENSG00000172324	ENSG00000172324		"""GPCR / Class A : Olfactory receptors"""	15249	protein-coding gene	gene with protein product							Standard	NM_001001954		Approved		uc010rkt.2	Q8NGI9	OTTHUMG00000167419	ENST00000302040.4:c.515C>T	11.37:g.59189912G>A	ENSP00000303834:p.Pro172Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_001001954	B9EH21|Q6IFF4|Q96RB0	Missense_Mutation	SNP	ENST00000302040.4	37	CCDS31560.1	349	0.15979853479853479	19	0.03861788617886179	59	0.16298342541436464	71	0.12412587412587413	200	0.2638522427440633	G	19.64	3.865680	0.71949	0.058155	0.262864	ENSG00000172324	ENST00000302040	T	0.00076	8.76	5.47	4.55	0.56014	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34932	U	0.003564	T	0.00012	0.0000	M	0.79343	2.45	0.30789	P	0.741141	D	0.69078	0.997	D	0.79784	0.993	T	0.68070	-0.5506	9	0.72032	D	0.01	.	13.8893	0.63729	0.0:0.0:0.8469:0.1531	rs1453547;rs17499129;rs57323320;rs1453547	172	Q8NGI9	OR5A2_HUMAN	L	172	ENSP00000303834:P172L	ENSP00000303834:P172L	P	-	2	0	OR5A2	58946488	0.328000	0.24687	0.276000	0.24689	0.826000	0.46750	3.157000	0.50716	1.428000	0.47296	0.585000	0.79938	CCC	G|0.820;A|0.180	0.180	strong		0.463	OR5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394552.1	NM_001001954	
DNAH9	1770	hgsc.bcm.edu	37	17	11650958	11650958	+	Missense_Mutation	SNP	G	G	A	rs61743635	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:11650958G>A	ENST00000262442.4	+	32	6553	c.6485G>A	c.(6484-6486)aGg>aAg	p.R2162K	DNAH9_ENST00000454412.2_Missense_Mutation_p.R2162K	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2162	AAA 2. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CAGGTGCTGAGGTCCTTGCAC	0.557													G|||	430	0.0858626	0.0363	0.0562	5008	,	,		17386	0.1696		0.0895	False		,,,				2504	0.0838				p.R2162K		Atlas-SNP	.											.	DNAH9	695	.	0			c.G6485A						PASS	.	G	LYS/ARG	246,4160	143.5+/-178.5	6,234,1963	90.0	82.0	85.0		6485	2.4	1.0	17	dbSNP_129	85	798,7802	188.1+/-235.2	35,728,3537	yes	missense	DNAH9	NM_001372.3	26	41,962,5500	AA,AG,GG		9.2791,5.5833,8.0271	benign	2162/4487	11650958	1044,11962	2203	4300	6503	SO:0001583	missense	1770	exon32			TGCTGAGGTCCTT	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.6485G>A	17.37:g.11650958G>A	ENSP00000262442:p.Arg2162Lys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	178	0.0815018315018315	16	0.032520325203252036	23	0.06353591160220995	76	0.13286713286713286	63	0.08311345646437995	G	2.495	-0.316623	0.05422	0.055833	0.092791	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.39406	1.08;1.08	4.5	2.41	0.29592	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.177992	0.48286	N	0.000193	T	0.00144	0.0004	N	0.04203	-0.255	0.09310	P	0.9999999999766689	B	0.02656	0.0	B	0.12837	0.008	T	0.23404	-1.0189	9	0.02654	T	1	.	7.5211	0.27629	0.3555:0.0:0.6445:0.0	rs61743635	2162	Q9NYC9	DYH9_HUMAN	K	2162;2162;744	ENSP00000262442:R2162K;ENSP00000414874:R2162K	ENSP00000262442:R2162K	R	+	2	0	DNAH9	11591683	0.992000	0.36948	0.999000	0.59377	0.774000	0.43823	1.256000	0.32921	0.463000	0.27118	0.557000	0.71058	AGG	G|0.922;A|0.078	0.078	strong		0.557	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
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 GAIIx	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		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	82	29	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	
MON1B	22879	hgsc.bcm.edu	37	16	77228866	77228866	+	Silent	SNP	T	T	C	rs2232504	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:77228866T>C	ENST00000248248.3	+	4	1460	c.1110T>C	c.(1108-1110)gtT>gtC	p.V370V	MON1B_ENST00000320859.6_Intron|MON1B_ENST00000439557.2_Silent_p.V261V|MON1B_ENST00000545553.1_Silent_p.V224V	NM_014940.2	NP_055755.1	Q7L1V2	MON1B_HUMAN	MON1 secretory trafficking family member B	370										breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	17						GGCGCCTGGTTGAAGATGGGA	0.637													C|||	3900	0.778754	0.9107	0.755	5008	,	,		17923	0.8651		0.5835	False		,,,				2504	0.729				p.V370V		Atlas-SNP	.											MON1B,NS,carcinoma,+2,1	MON1B	55	1	0			c.T1110C						PASS	.	C		3803,593	258.9+/-262.7	1645,513,40	60.0	57.0	58.0		1110	-9.6	0.1	16	dbSNP_98	58	5138,3462	505.9+/-376.5	1524,2090,686	no	coding-synonymous	MON1B	NM_014940.2		3169,2603,726	CC,CT,TT		40.2558,13.4895,31.2019		370/548	77228866	8941,4055	2198	4300	6498	SO:0001819	synonymous_variant	22879	exon4			CCTGGTTGAAGAT	BC024277	CCDS10925.1, CCDS67082.1, CCDS67083.1	16q23.1	2013-08-21	2013-08-21		ENSG00000103111	ENSG00000103111			25020	protein-coding gene	gene with protein product		608954	"""MON1 homolog B (yeast)"""			10048485	Standard	NM_014940		Approved	SAND2, HSRG1, KIAA0872	uc002fez.3	Q7L1V2	OTTHUMG00000137618	ENST00000248248.3:c.1110T>C	16.37:g.77228866T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	92	42	0.456522	NM_014940	B4DDZ0|O94949	Silent	SNP	ENST00000248248.3	37	CCDS10925.1																																																																																			T|0.276;C|0.724	0.724	strong		0.637	MON1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269036.2	NM_014940	
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 GAIIx	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		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	30	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
PRAMEF11	440560	hgsc.bcm.edu	37	1	12884981	12884981	+	Missense_Mutation	SNP	T	T	C	rs4989318	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12884981T>C	ENST00000535591.1	-	4	1325	c.1130A>G	c.(1129-1131)cAg>cGg	p.Q377R	RP5-845O24.8_ENST00000438401.1_lincRNA	NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	377					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)					NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						ATAACTTTCCTGCGGGGCAGG	0.507													.|||	76	0.0151757	0.0008	0.0231	5008	,	,		22853	0.003		0.0507	False		,,,				2504	0.0051				p.Q377R		Atlas-SNP	.											.	PRAMEF11	72	.	0			c.A1130G						PASS	.	C	ARG/GLN	9,1375		0,9,683	96.0	71.0	78.0		1130	-1.2	0.0	1	dbSNP_113	78	165,3015		10,145,1435	no	missense	PRAMEF11	NM_001146344.1	43	10,154,2118	CC,CT,TT		5.1887,0.6503,3.8124	benign	377/437	12884981	174,4390	692	1590	2282	SO:0001583	missense	440560	exon4			CTTTCCTGCGGGG	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"""-"""	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.1130A>G	1.37:g.12884981T>C	ENSP00000439551:p.Gln377Arg	Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	349	173	0.495702	NM_001146344		Missense_Mutation	SNP	ENST00000535591.1	37	CCDS53268.1	61	0.027930402930402932	1	0.0020325203252032522	12	0.03314917127071823	5	0.008741258741258742	43	0.05672823218997362	.	1.215	-0.628591	0.03610	0.006503	0.051887	ENSG00000204513	ENST00000535591;ENST00000331684;ENST00000437584	T;T	0.56103	0.48;0.48	1.76	-1.18	0.09617	.	0.329023	0.24884	N	0.034831	T	0.02230	0.0069	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.05616	-1.0874	10	0.21540	T	0.41	.	2.7367	0.05242	0.308:0.2838:0.0:0.4082	rs4989318	377	O60813	PRA11_HUMAN	R	377;418;377	ENSP00000439551:Q377R;ENSP00000391839:Q377R	ENSP00000328783:Q418R	Q	-	2	0	PRAMEF11	12807568	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	-1.124000	0.03260	-1.008000	0.03404	-0.479000	0.04858	CAG	T|0.500;C|0.500	0.500	weak		0.507	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
DUSP13	51207	hgsc.bcm.edu	37	10	76855412	76855412	+	Silent	SNP	G	G	A	rs3740317	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:76855412G>A	ENST00000472493.2	-	3	393	c.315C>T	c.(313-315)gaC>gaT	p.D105D	DUSP13_ENST00000607009.1_5'Flank|DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000491677.2_Silent_p.D234D|DUSP13_ENST00000464872.1_Intron|DUSP13_ENST00000372700.3_Silent_p.D155D|DUSP13_ENST00000605915.1_Silent_p.D127D|DUSP13_ENST00000478873.2_Silent_p.D241D|DUSP13_ENST00000607131.1_Silent_p.D198D	NM_016364.3	NP_057448.3	Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	105					meiotic nuclear division (GO:0007126)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.D234D(1)		large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	8	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					AGGGGTTGTCGTCCGCCTCGA	0.552													A|||	2110	0.421326	0.4289	0.4424	5008	,	,		21230	0.6379		0.2773	False		,,,				2504	0.3211				p.D198D	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											DUSP13_ENST00000356369,NS,carcinoma,0,1	DUSP13	82	1	1	Substitution - coding silent(1)	stomach(1)	c.C594T						PASS	.	A	,,,	1849,2557	634.9+/-396.3	383,1083,737	263.0	210.0	228.0		,465,594,315	2.7	1.0	10	dbSNP_107	228	2298,6302	705.7+/-405.5	303,1692,2305	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1,NM_016364.3	,,,	686,2775,3042	AA,AG,GG		26.7209,41.9655,31.8853	,,,	,155/249,198/292,105/199	76855412	4147,8859	2203	4300	6503	SO:0001819	synonymous_variant	51207	exon5			GTTGTCGTCCGCC	AB027004	CCDS7346.1, CCDS31224.1, CCDS53542.1	10q23.1	2013-10-25			ENSG00000079393	ENSG00000079393		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	19681	protein-coding gene	gene with protein product		613191				10585869	Standard	XM_005269883		Approved	BEDP, TMDP, FLJ32450, DUSP13A, DUSP13B	uc001jwu.3	Q6B8I1	OTTHUMG00000018516	ENST00000472493.2:c.315C>T	10.37:g.76855412G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	102	57	0.558824	NM_001007273	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Silent	SNP	ENST00000472493.2	37	CCDS7346.1																																																																																			G|0.642;A|0.358	0.358	strong		0.552	DUSP13-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048786.3		
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919267	51919267	+	Silent	SNP	A	A	G	rs7258638	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51919267A>G	ENST00000339313.5	-	5	1025	c.909T>C	c.(907-909)ccT>ccC	p.P303P	SIGLEC10_ENST00000439889.2_Silent_p.P245P|SIGLEC10_ENST00000436984.2_Silent_p.P255P|SIGLEC10_ENST00000353836.5_Silent_p.P303P|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000432469.2_Silent_p.P220P|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.P303P|SIGLEC10_ENST00000441969.3_Silent_p.P245P|CTD-2616J11.2_ENST00000532688.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	303	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CCAGGGGTCTAGGGCCCCAGG	0.677																																					p.P303P		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T909C						PASS	.						26.0	30.0	29.0					19																	51919267		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			GGGTCTAGGGCCC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.909T>C	19.37:g.51919267A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	125	21	0.168	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			A|0.996;G|0.004	0.004	strong		0.677	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
PACSIN2	11252	hgsc.bcm.edu	37	22	43289473	43289473	+	Silent	SNP	G	G	A	rs5759013	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:43289473G>A	ENST00000263246.3	-	3	408	c.207C>T	c.(205-207)ctC>ctT	p.L69L	PACSIN2_ENST00000402229.1_Silent_p.L69L|PACSIN2_ENST00000337959.4_Silent_p.L69L|PACSIN2_ENST00000407585.1_Silent_p.L69L|PACSIN2_ENST00000403744.3_Silent_p.L69L	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	69	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				CTTTCTCCACGAGCTGCCTCC	0.667													G|||	1374	0.274361	0.1581	0.3573	5008	,	,		16356	0.0933		0.4304	False		,,,				2504	0.3988				p.L69L		Atlas-SNP	.											PACSIN2,NS,carcinoma,-2,1	PACSIN2	48	1	0			c.C207T						PASS	.	G	,,	867,3281		110,647,1317	27.0	31.0	29.0		207,207,207	-9.0	0.1	22	dbSNP_114	29	3811,4661		904,2003,1329	no	coding-synonymous,coding-synonymous,coding-synonymous	PACSIN2	NM_001184970.1,NM_001184971.1,NM_007229.3	,,	1014,2650,2646	AA,AG,GG		44.9835,20.9016,37.0681	,,	69/487,69/446,69/487	43289473	4678,7942	2074	4236	6310	SO:0001819	synonymous_variant	11252	exon3			CTCCACGAGCTGC	AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"""syndapin II"""	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.207C>T	22.37:g.43289473G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_007229	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Silent	SNP	ENST00000263246.3	37	CCDS43023.1																																																																																			G|0.724;A|0.276	0.276	strong		0.667	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229	
RIN2	54453	hgsc.bcm.edu	37	20	19951534	19951534	+	Missense_Mutation	SNP	T	T	A	rs3803981	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:19951534T>A	ENST00000255006.6	+	7	885	c.736T>A	c.(736-738)Tcg>Acg	p.S246T	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	197					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						AACAGCCAAGTCGGAGGCTCA	0.438													T|||	798	0.159345	0.1679	0.1614	5008	,	,		20069	0.2431		0.1392	False		,,,				2504	0.0808				p.S246T		Atlas-SNP	.											RIN2_ENST00000255006,NS,carcinoma,0,3	RIN2	126	3	0			c.T736A						PASS	.	T	THR/SER,THR/SER	547,3323		39,469,1427	71.0	72.0	72.0		736,589	4.6	1.0	20	dbSNP_107	72	1255,6999		94,1067,2966	yes	missense,missense	RIN2	NM_001242581.1,NM_018993.3	58,58	133,1536,4393	AA,AT,TT		15.2047,14.1344,14.8631	benign,benign	246/945,197/896	19951534	1802,10322	1935	4127	6062	SO:0001583	missense	54453	exon7			GCCAAGTCGGAGG	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.736T>A	20.37:g.19951534T>A	ENSP00000255006:p.Ser246Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	395	0.18086080586080586	95	0.19308943089430894	54	0.14917127071823205	143	0.25	103	0.1358839050131926	T	6.996	0.553871	0.13374	0.141344	0.152047	ENSG00000132669	ENST00000255006	T	0.49139	0.79	5.66	4.56	0.56223	.	0.049002	0.85682	N	0.000000	T	0.00012	0.0000	N	0.01152	-0.98	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20042	-1.0287	8	.	.	.	-15.9515	11.5874	0.50927	0.8613:0.0:0.0:0.1387	rs3803981;rs60446832;rs3803981	197	Q8WYP3	RIN2_HUMAN	T	246	ENSP00000255006:S246T	.	S	+	1	0	RIN2	19899534	1.000000	0.71417	0.994000	0.49952	0.971000	0.66376	6.837000	0.75354	0.960000	0.38005	-0.624000	0.04008	TCG	T|0.818;A|0.182	0.182	strong		0.438	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
NINL	22981	hgsc.bcm.edu	37	20	25456888	25456888	+	Silent	SNP	A	A	G	rs437635	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:25456888A>G	ENST00000278886.6	-	17	3112	c.3039T>C	c.(3037-3039)agT>agC	p.S1013S	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1013					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CAACCTCCACACTGTGCTTGT	0.682													G|||	2795	0.558107	0.5356	0.3559	5008	,	,		14219	0.9067		0.4304	False		,,,				2504	0.5041				p.S1013S		Atlas-SNP	.											.	NINL	148	.	0			c.T3039C						PASS	.	G		2241,2165	583.5+/-385.8	552,1137,514	58.0	62.0	60.0		3039	0.2	0.0	20	dbSNP_80	60	3727,4873	615.9+/-396.4	794,2139,1367	no	coding-synonymous	NINL	NM_025176.4		1346,3276,1881	GG,GA,AA		43.3372,49.1375,45.8865		1013/1383	25456888	5968,7038	2203	4300	6503	SO:0001819	synonymous_variant	22981	exon17			CTCCACACTGTGC		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3039T>C	20.37:g.25456888A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Silent	SNP	ENST00000278886.6	37	CCDS33452.1																																																																																			A|0.506;G|0.494	0.494	strong		0.682	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
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 GAIIx	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	83	22	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	
THSD7A	221981	hgsc.bcm.edu	37	7	11676377	11676377	+	Silent	SNP	G	G	A	rs2074598	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:11676377G>A	ENST00000423059.4	-	2	653	c.402C>T	c.(400-402)ccC>ccT	p.P134P	THSD7A_ENST00000480061.1_5'UTR	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	134					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TTGAAATCACGGGCTGACACT	0.468										HNSCC(18;0.044)			A|||	1335	0.266573	0.1649	0.33	5008	,	,		18947	0.2837		0.2535	False		,,,				2504	0.3548				p.P134P		Atlas-SNP	.											.	THSD7A	219	.	0			c.C402T						PASS	.	A		564,3316		48,468,1424	81.0	80.0	80.0		402	-11.4	0.1	7	dbSNP_96	80	2112,6180		261,1590,2295	no	coding-synonymous	THSD7A	NM_015204.2		309,2058,3719	AA,AG,GG		25.4703,14.5361,21.9849		134/1658	11676377	2676,9496	1940	4146	6086	SO:0001819	synonymous_variant	221981	exon2			AATCACGGGCTGA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.402C>T	7.37:g.11676377G>A		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			G|0.745;N|0.000	.	strong		0.468	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
HLA-A	3105	hgsc.bcm.edu	37	6	29912281	29912281	+	Silent	SNP	G	G	A	rs1136917|rs35946537	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29912281G>A	ENST00000396634.1	+	7	1241	c.900G>A	c.(898-900)ctG>ctA	p.L300L	HLA-A_ENST00000376806.5_Silent_p.L300L|HLA-A_ENST00000376802.2_Intron|HLA-A_ENST00000376809.5_Silent_p.L300L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	300	Connecting peptide.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TCCCAGAGCTGTCTTCCCAGC	0.592									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	780	0.155751	0.1377	0.1772	5008	,	,		18959	0.2004		0.1133	False		,,,				2504	0.1626				p.L300L		Atlas-SNP	.											.	HLA-A	89	.	0			c.G900A						PASS	.	G		345,2677		28,289,1194	81.0	76.0	78.0		900	-6.7	0.0	6	dbSNP_86	78	520,4898		36,448,2225	no	coding-synonymous	HLA-A	NM_002116.7		64,737,3419	AA,AG,GG		9.5976,11.4163,10.2488		300/366	29912281	865,7575	1511	2709	4220	SO:0001819	synonymous_variant	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGAGCTGTCTTCC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.900G>A	6.37:g.29912281G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	140	32	0.228571	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.872;A|0.128	0.128	strong		0.592	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
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 GAIIx	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	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	5	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	
MON2	23041	hgsc.bcm.edu	37	12	62926398	62926398	+	Silent	SNP	G	G	A	rs7957417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:62926398G>A	ENST00000393632.2	+	12	1972	c.1581G>A	c.(1579-1581)tcG>tcA	p.S527S	MON2_ENST00000552115.1_Silent_p.S527S|MON2_ENST00000552738.1_Silent_p.S527S|MON2_ENST00000393630.3_Silent_p.S527S|MON2_ENST00000546600.1_Silent_p.S527S|MON2_ENST00000280379.6_Silent_p.S527S|MON2_ENST00000393629.2_Silent_p.S527S	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	527					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		CAACACAGTCGACAGAACAGC	0.368													G|||	1769	0.353235	0.3828	0.3055	5008	,	,		17654	0.3423		0.3549	False		,,,				2504	0.3569				p.S527S		Atlas-SNP	.											.	MON2	160	.	0			c.G1581A						PASS	.	G		1735,2671	521.7+/-370.6	347,1041,815	140.0	128.0	132.0		1581	-10.8	0.7	12	dbSNP_116	132	3132,5468	475.3+/-369.1	575,1982,1743	no	coding-synonymous	MON2	NM_015026.2		922,3023,2558	AA,AG,GG		36.4186,39.3781,37.4212		527/1718	62926398	4867,8139	2203	4300	6503	SO:0001819	synonymous_variant	23041	exon12			ACAGTCGACAGAA		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.1581G>A	12.37:g.62926398G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Silent	SNP	ENST00000393632.2	37	CCDS31849.1																																																																																			G|0.636;A|0.364	0.364	strong		0.368	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
TNC	3371	hgsc.bcm.edu	37	9	117797597	117797597	+	Silent	SNP	T	T	C	rs12347433	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:117797597T>C	ENST00000350763.4	-	22	6084	c.5673A>G	c.(5671-5673)agA>agG	p.R1891R	TNC_ENST00000537320.1_Silent_p.R1254R|TNC_ENST00000345230.3_Silent_p.R1254R|TNC_ENST00000346706.3_Silent_p.R1345R|TNC_ENST00000341037.4_Silent_p.R1709R|TNC_ENST00000535648.1_Silent_p.R1436R|TNC_ENST00000542877.1_Silent_p.R1528R|TNC_ENST00000340094.3_Silent_p.R1527R|TNC_ENST00000423613.2_Silent_p.R1618R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1891	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.R1891R(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						CAGTCAAGTCTCTTGGAGAAT	0.512													T|||	773	0.154353	0.0666	0.1484	5008	,	,		19335	0.129		0.2793	False		,,,				2504	0.1748				p.R1891R		Atlas-SNP	.											TNC,NS,carcinoma,0,1	TNC	282	1	1	Substitution - coding silent(1)	stomach(1)	c.A5673G						PASS	.	T		404,4002	199.4+/-223.0	21,362,1820	72.0	72.0	72.0		5673	6.0	1.0	9	dbSNP_120	72	2313,6287	389.1+/-342.8	320,1673,2307	no	coding-synonymous	TNC	NM_002160.3		341,2035,4127	CC,CT,TT		26.8953,9.1693,20.8904		1891/2202	117797597	2717,10289	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon22			CAAGTCTCTTGGA		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.5673A>G	9.37:g.117797597T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	28	10	0.357143	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	383	0.17536630036630035	40	0.08130081300813008	46	0.1270718232044199	85	0.1486013986013986	212	0.2796833773087071	T	10.49	1.365894	0.24684	0.091693	0.268953	ENSG00000041982	ENST00000544972	T	0.57436	0.4	5.97	5.97	0.96955	.	0.206129	0.51477	D	0.000084	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22034	-1.0228	6	0.48119	T	0.1	.	10.4647	0.44600	0.0:0.1145:0.0:0.8855	rs12347433;rs17240303;rs12347433	.	.	.	G	454	ENSP00000445380:R454G	ENSP00000445380:R454G	R	-	1	2	TNC	116837418	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.042000	0.49815	2.274000	0.75844	0.533000	0.62120	AGA	T|0.813;C|0.187	0.187	strong		0.512	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
MUC2	4583	hgsc.bcm.edu	37	11	1093364	1093364	+	Missense_Mutation	SNP	C	C	G	rs113138128		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1093364C>G	ENST00000441003.2	+	30	5210	c.5183C>G	c.(5182-5184)aCt>aGt	p.T1728S	MUC2_ENST00000333592.6_Missense_Mutation_p.T16S|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1695S	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				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)		p.T1695S(2)|p.T1728S(2)		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)	tccaccaccactacggtgacc	0.652																																					p.T1728S		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,6	MUC2	614	6	4	Substitution - Missense(4)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(2)	c.C5183G						scavenged	.						184.0	230.0	214.0					11																	1093364		1968	3805	5773	SO:0001583	missense	4583	exon30			CCACCACTACGGT	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.5183C>G	11.37:g.1093364C>G	ENSP00000415183:p.Thr1728Ser	Somatic	40	1	0.025		WXS	Illumina HiSeq	Phase_I	49	10	0.204082	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	1.152	-0.646415	0.03531	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.11604	2.76;2.85;2.86	1.47	-2.95	0.05564	.	0.396535	0.13252	N	0.402004	T	0.03136	0.0092	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42207	-0.9465	9	0.06236	T	0.91	.	4.7261	0.12941	0.0:0.4234:0.393:0.1837	.	1728	E7EUV1	.	S	1728;1695;16	ENSP00000415183:T1728S;ENSP00000351956:T1695S;ENSP00000331373:T16S	ENSP00000331373:T16S	T	+	2	0	MUC2	1083364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.577000	0.05847	-0.762000	0.04664	-1.112000	0.02068	ACT	C|0.500;G|0.500	0.500	weak		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919934	12919934	+	Missense_Mutation	SNP	A	A	G	rs3204805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12919934A>G	ENST00000240189.2	+	3	761	c.674A>G	c.(673-675)tAt>tGt	p.Y225C		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	225			Y -> C (in dbSNP:rs3204805).		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)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAAGCTTTATTGTTACCTG	0.383													.|||	849	0.169529	0.1437	0.1095	5008	,	,		22588	0.3125		0.1352	False		,,,				2504	0.135				p.Y225C		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.A674G						PASS	.	G	CYS/TYR	714,3690	758.0+/-412.8	77,560,1565	101.0	106.0	104.0		674	-1.7	0.0	1	dbSNP_105	104	1254,7330	756.9+/-407.5	112,1030,3150	no	missense	PRAMEF2	NM_023014.1	194	189,1590,4715	GG,GA,AA		14.6086,16.2125,15.1524	benign	225/475	12919934	1968,11020	2202	4292	6494	SO:0001583	missense	65122	exon3			AGCTTTATTGTTA		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.674A>G	1.37:g.12919934A>G	ENSP00000240189:p.Tyr225Cys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	154	55	0.357143	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	372	0.17032967032967034	50	0.1016260162601626	46	0.1270718232044199	165	0.28846153846153844	111	0.14643799472295516	G	1.447	-0.566127	0.03910	0.162125	0.146086	ENSG00000120952	ENST00000240189	T	0.14766	2.48	0.842	-1.68	0.08212	.	0.335847	0.28688	N	0.014461	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.17465	0.022	B	0.26202	0.067	T	0.48103	-0.9064	9	0.66056	D	0.02	.	3.4172	0.07380	0.4582:0.2964:0.2453:0.0	rs3204805;rs17038687;rs52806752;rs3204805	225	O60811	PRAM2_HUMAN	C	225	ENSP00000240189:Y225C	ENSP00000240189:Y225C	Y	+	2	0	PRAMEF2	12842521	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.549000	0.02182	-2.688000	0.00405	-2.828000	0.00107	TAT	A|0.846;G|0.154	0.154	strong		0.383	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
FMN2	56776	hgsc.bcm.edu	37	1	240370934	240370934	+	Missense_Mutation	SNP	G	G	C	rs71170718|rs4997328|rs562038978	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:240370934G>C	ENST00000319653.9	+	5	3052	c.2822G>C	c.(2821-2823)gGa>gCa	p.G941A		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	941	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCCGGAGCGGGAATACCTCCT	0.706													G|||	1385	0.276558	0.3616	0.1902	5008	,	,		7542	0.3115		0.2276	False		,,,				2504	0.2372				p.G941A		Atlas-SNP	.											FMN2,NS,carcinoma,0,3	FMN2	451	3	0			c.G2822C						scavenged	.						25.0	31.0	29.0					1																	240370934		2135	4205	6340	SO:0001583	missense	56776	exon5			GAGCGGGAATACC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2822G>C	1.37:g.240370934G>C	ENSP00000318884:p.Gly941Ala	Somatic	121	1	0.00826446		WXS	Illumina HiSeq	Phase_I	66	13	0.19697	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	510	0.23351648351648352	149	0.30284552845528456	59	0.16298342541436464	154	0.2692307692307692	148	0.19525065963060687	G	6.179	0.401283	0.11696	.	.	ENSG00000155816	ENST00000319653	T	0.51574	0.7	3.52	2.6	0.31112	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.28291	0.206	B	0.31869	0.137	T	0.28618	-1.0038	7	.	.	.	.	8.7591	0.34663	0.0:0.2724:0.5786:0.149	rs4997328	941	Q9NZ56	FMN2_HUMAN	A	941	ENSP00000318884:G941A	.	G	+	2	0	FMN2	238437557	0.024000	0.19004	0.019000	0.16419	0.001000	0.01503	0.529000	0.23019	1.071000	0.40834	-0.415000	0.06103	GGA	G|0.781;C|0.219	0.219	strong		0.706	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138418910	138418910	+	Silent	SNP	G	G	A	rs1026435	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:138418910G>A	ENST00000310018.2	-	16	1944	c.1662C>T	c.(1660-1662)ttC>ttT	p.F554F	ATP6V0A4_ENST00000393054.1_Silent_p.F554F|ATP6V0A4_ENST00000353492.4_Silent_p.F554F	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	554			F -> L (in dbSNP:rs1026435).		ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GGATGACACCGAAAACCATCT	0.438													G|||	3589	0.716653	0.6074	0.7709	5008	,	,		19455	0.8403		0.7147	False		,,,				2504	0.7004				p.F554F		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.C1662T						PASS	.	G	,,	2681,1725	649.7+/-398.9	815,1051,337	167.0	138.0	148.0		1662,1662,1662	-11.0	0.0	7	dbSNP_86	148	6205,2395	700.8+/-405.2	2232,1741,327	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	,,	3047,2792,664	AA,AG,GG		27.8488,39.1512,31.6777	,,	554/841,554/841,554/841	138418910	8886,4120	2203	4300	6503	SO:0001819	synonymous_variant	50617	exon15			GACACCGAAAACC	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1662C>T	7.37:g.138418910G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_130841	A4D1R4|A8KA80|Q32M47	Silent	SNP	ENST00000310018.2	37	CCDS5849.1																																																																																			G|0.304;A|0.696	0.696	strong		0.438	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
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 GAIIx	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		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	34	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	
HELLS	3070	hgsc.bcm.edu	37	10	96313960	96313960	+	Silent	SNP	A	A	C	rs11188019	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96313960A>C	ENST00000348459.5	+	3	336	c.231A>C	c.(229-231)atA>atC	p.I77I	HELLS_ENST00000394044.1_Silent_p.I77I|HELLS_ENST00000239026.6_Silent_p.I77I|HELLS_ENST00000462057.1_3'UTR|HELLS_ENST00000394045.1_Silent_p.I77I|HELLS_ENST00000394036.1_Silent_p.I77I|HELLS_ENST00000371332.4_Silent_p.I77I	NM_018063.3	NP_060533.2			helicase, lymphoid-specific											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		Colorectal(252;0.0429)		all cancers(201;2.13e-05)		AAAGCAATATATACTCCAAAT	0.328													C|||	2657	0.530551	0.469	0.3228	5008	,	,		16049	0.746		0.4404	False		,,,				2504	0.6319				p.I77I		Atlas-SNP	.											.	HELLS	63	.	0			c.A231C						PASS	.	C		2107,2299	590.4+/-387.4	518,1071,614	73.0	81.0	78.0		231	1.3	1.0	10	dbSNP_120	78	3807,4793	609.2+/-395.5	809,2189,1302	no	coding-synonymous	HELLS	NM_018063.3		1327,3260,1916	CC,CA,AA		44.2674,47.8212,45.4713		77/839	96313960	5914,7092	2203	4300	6503	SO:0001819	synonymous_variant	3070	exon3			CAATATATACTCC	AF155827	CCDS7434.1, CCDS73162.1, CCDS73163.1, CCDS73164.1, CCDS73165.1	10q24.2	2008-08-01			ENSG00000119969	ENSG00000119969			4861	protein-coding gene	gene with protein product	"""SWI/SNF2-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member 6"", ""proliferation-associated SNF2-like protein"""	603946				9878251, 10910076	Standard	NM_018063		Approved	PASG, SMARCA6, LSH, Nbla10143	uc001kjt.3	Q9NRZ9	OTTHUMG00000018793	ENST00000348459.5:c.231A>C	10.37:g.96313960A>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	175	86	0.491429	NM_018063		Silent	SNP	ENST00000348459.5	37	CCDS7434.1																																																																																			A|0.531;C|0.469	0.469	strong		0.328	HELLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049475.1	NM_018063	
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 GAIIx	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	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	43	21	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	
KANSL1	284058	hgsc.bcm.edu	37	17	44248769	44248769	+	Silent	SNP	T	T	C	rs566672630	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44248769T>C	ENST00000262419.6	-	2	1211	c.741A>G	c.(739-741)agA>agG	p.R247R	KANSL1_ENST00000575318.1_Silent_p.R247R|KANSL1_ENST00000432791.1_Silent_p.R247R|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Silent_p.R247R|KANSL1_ENST00000572904.1_Silent_p.R247R|KANSL1_ENST00000576248.1_5'Flank	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	247					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CAGGTGATAATCTACTGCTTC	0.438													C|||	437	0.0872604	0.0182	0.1571	5008	,	,		24930	0.001		0.2406	False		,,,				2504	0.0624				p.R247R		Atlas-SNP	.											.	.	.	.	0			c.A741G						PASS	.	C	,,	226,4180	805.7+/-415.8	6,214,1983	92.0	118.0	109.0		741,741,741	5.0	1.0	17	dbSNP_92	109	1936,6664	725.7+/-406.6	220,1496,2584	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	226,1710,4567	CC,CT,TT		22.5116,5.1294,16.6231	,,	247/1105,247/1106,247/1106	44248769	2162,10844	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon2			TGATAATCTACTG	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.741A>G	17.37:g.44248769T>C		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	384	382	0.994792	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			T|0.841;C|0.159	0.159	strong		0.438	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
FYCO1	79443	hgsc.bcm.edu	37	3	46010007	46010007	+	Silent	SNP	T	T	C	rs13071283	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46010007T>C	ENST00000296137.2	-	8	1024	c.819A>G	c.(817-819)caA>caG	p.Q273Q	FYCO1_ENST00000535325.1_Silent_p.Q273Q	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	273					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)		CTGTCTGCAGTTGCTCCCCTT	0.627													T|||	551	0.110024	0.0197	0.0634	5008	,	,		19918	0.004		0.1243	False		,,,				2504	0.3599				p.Q273Q		Atlas-SNP	.											.	FYCO1	115	.	0			c.A819G						PASS	.	T		138,4268	98.5+/-137.1	1,136,2066	94.0	82.0	86.0		819	0.5	1.0	3	dbSNP_121	86	963,7637	210.5+/-251.4	51,861,3388	no	coding-synonymous	FYCO1	NM_024513.2		52,997,5454	CC,CT,TT		11.1977,3.1321,8.4653		273/1479	46010007	1101,11905	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			CTGCAGTTGCTCC	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.819A>G	3.37:g.46010007T>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			T|0.917;C|0.083	0.083	strong		0.627	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
KLHL12	59349	hgsc.bcm.edu	37	1	202888947	202888947	+	Silent	SNP	T	T	C	rs3182429	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:202888947T>C	ENST00000367261.3	-	3	503	c.285A>G	c.(283-285)acA>acG	p.T95T	KLHL12_ENST00000435533.3_Silent_p.T133T	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	95	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			TCACATGTACTGTTTCTGTGT	0.398													T|||	1461	0.291733	0.0681	0.3271	5008	,	,		18036	0.5208		0.2326	False		,,,				2504	0.3937				p.T95T		Atlas-SNP	.											.	KLHL12	50	.	0			c.A285G						PASS	.	T		508,3898	233.0+/-246.3	35,438,1730	96.0	85.0	88.0		285	-6.0	0.5	1	dbSNP_105	88	1950,6650	344.7+/-325.5	234,1482,2584	no	coding-synonymous	KLHL12	NM_021633.2		269,1920,4314	CC,CT,TT		22.6744,11.5297,18.899		95/569	202888947	2458,10548	2203	4300	6503	SO:0001819	synonymous_variant	59349	exon3			ATGTACTGTTTCT	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"""Kelch-like"", ""BTB/POZ domain containing"""	19360	protein-coding gene	gene with protein product		614522	"""kelch-like 12 (Drosophila)"""			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.285A>G	1.37:g.202888947T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	126	61	0.484127	NM_021633	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	37	CCDS1429.1																																																																																			T|0.778;C|0.222	0.222	strong		0.398	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633	
SEC23B	10483	hgsc.bcm.edu	37	20	18505200	18505200	+	Missense_Mutation	SNP	G	G	T	rs36023150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:18505200G>T	ENST00000336714.3	+	5	922	c.490G>T	c.(490-492)Gtg>Ttg	p.V164L	SEC23B_ENST00000377465.1_Missense_Mutation_p.V164L|SEC23B_ENST00000262544.2_Missense_Mutation_p.V164L|SEC23B_ENST00000377475.3_Missense_Mutation_p.V164L	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	164					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						AGATGCTCTGGTGGGTCTGAT	0.483													G|||	44	0.00878594	0.0	0.0029	5008	,	,		18479	0.0		0.0089	False		,,,				2504	0.0337				p.V164L		Atlas-SNP	.											SEC23B,NS,carcinoma,0,1	SEC23B	70	1	0			c.G490T						PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	12,4394	19.1+/-41.9	0,12,2191	136.0	120.0	126.0		490,436,490,490,490	4.9	1.0	20	dbSNP_126	126	85,8515	48.9+/-108.6	1,83,4216	yes	missense,missense,missense,missense,missense	SEC23B	NM_001172745.1,NM_001172746.1,NM_006363.4,NM_032985.4,NM_032986.3	32,32,32,32,32	1,95,6407	TT,TG,GG		0.9884,0.2724,0.7458	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	164/768,146/750,164/768,164/768,164/768	18505200	97,12909	2203	4300	6503	SO:0001583	missense	10483	exon5			GCTCTGGTGGGTC	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"""Sec23 (S. cerevisiae) homolog B"", ""congenital dyserythropoietic anemia, type II"""	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.490G>T	20.37:g.18505200G>T	ENSP00000338844:p.Val164Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	37	CCDS13137.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	33	5.246578	0.95305	0.002724	0.009884	ENSG00000101310	ENST00000450074;ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74	4.91	4.91	0.64330	Sec23/Sec24, trunk domain (1);	0.056124	0.64402	D	0.000001	D	0.89829	0.6828	M	0.91663	3.23	0.80722	D	1	D;P	0.64830	0.994;0.87	P;P	0.62382	0.901;0.718	D	0.92153	0.5730	10	0.72032	D	0.01	-21.6049	17.2703	0.87099	0.0:0.0:1.0:0.0	rs36023150	146;164	B4DJW8;Q15437	.;SC23B_HUMAN	L	164	ENSP00000403971:V164L;ENSP00000338844:V164L;ENSP00000262544:V164L;ENSP00000366695:V164L;ENSP00000366685:V164L	ENSP00000262544:V164L	V	+	1	0	SEC23B	18453200	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.787000	0.85759	2.560000	0.86352	0.591000	0.81541	GTG	G|0.992;T|0.008	0.008	strong		0.483	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5		
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 GAIIx	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_ENST00000449184.3_Missense_Mutation_p.D282N|B4GALNT1_ENST00000550943.1_5'Flank|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	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	69	26	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	
TEX26	122046	hgsc.bcm.edu	37	13	31543095	31543095	+	Silent	SNP	C	C	T	rs2274869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:31543095C>T	ENST00000380473.3	+	6	733	c.720C>T	c.(718-720)taC>taT	p.Y240Y	TEX26_ENST00000530916.1_Intron	NM_152325.1	NP_689538.1	Q8N6G2	TEX26_HUMAN	testis expressed 26	240																	AAAGTGACTACGACAAAACCT	0.428													C|||	965	0.192692	0.0726	0.317	5008	,	,		20151	0.126		0.2445	False		,,,				2504	0.2822				p.Y240Y		Atlas-SNP	.											.	.	.	.	0			c.C720T						PASS	.	C		458,3948	220.7+/-238.1	27,404,1772	177.0	173.0	174.0		720	-4.5	0.2	13	dbSNP_100	174	2265,6335	382.8+/-340.5	322,1621,2357	no	coding-synonymous	C13orf26	NM_152325.1		349,2025,4129	TT,TC,CC		26.3372,10.3949,20.9365		240/290	31543095	2723,10283	2203	4300	6503	SO:0001819	synonymous_variant	122046	exon6			TGACTACGACAAA	BC030277	CCDS9339.1	13q12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000175664	ENSG00000175664			28622	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 26"""	C13orf26		12477932	Standard	NM_152325		Approved	MGC40178	uc001uti.3	Q8N6G2	OTTHUMG00000016682	ENST00000380473.3:c.720C>T	13.37:g.31543095C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_152325		Silent	SNP	ENST00000380473.3	37	CCDS9339.1																																																																																			C|0.784;T|0.216	0.216	strong		0.428	TEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044380.2	NM_152325	
LYPD5	284348	hgsc.bcm.edu	37	19	44303066	44303066	+	Missense_Mutation	SNP	C	C	G	rs11547806	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:44303066C>G	ENST00000377950.3	-	3	348	c.268G>C	c.(268-270)Gcg>Ccg	p.A90P	LYPD5_ENST00000594013.1_Missense_Mutation_p.A47P|LYPD5_ENST00000414615.2_Missense_Mutation_p.A47P	NM_001031749.2	NP_001026919.2	Q6UWN5	LYPD5_HUMAN	LY6/PLAUR domain containing 5	90			A -> P (in dbSNP:rs11547806). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039}.			anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.A47P(1)		breast(3)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	8		Prostate(69;0.0352)				AGCGCGTCCGCGTTCGATTGC	0.687													c|||	3112	0.621406	0.5772	0.634	5008	,	,		14726	0.5437		0.5765	False		,,,				2504	0.7986				p.A90P		Atlas-SNP	.											LYPD5,NS,carcinoma,0,1	LYPD5	22	1	1	Substitution - Missense(1)	prostate(1)	c.G268C						PASS	.		PRO/ALA,PRO/ALA	2618,1784		797,1024,380	22.0	20.0	21.0		268,139	-4.2	0.0	19	dbSNP_120	21	5027,3569		1477,2073,748	no	missense,missense	LYPD5	NM_001031749.2,NM_182573.2	27,27	2274,3097,1128	GG,GC,CC		41.5193,40.527,41.1833	benign,benign	90/252,47/209	44303066	7645,5353	2201	4298	6499	SO:0001583	missense	284348	exon3			CGTCCGCGTTCGA	AK055031	CCDS12631.1, CCDS46096.1	19q13.31	2008-02-05				ENSG00000159871			26397	protein-coding gene	gene with protein product						12477932	Standard	NM_182573		Approved	FLJ30469	uc002oxm.4	Q6UWN5		ENST00000377950.3:c.268G>C	19.37:g.44303066C>G	ENSP00000367185:p.Ala90Pro	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_001031749	Q6PEX9|Q96DR2	Missense_Mutation	SNP	ENST00000377950.3	37	CCDS46096.1	1248	0.5714285714285714	276	0.5609756097560976	240	0.6629834254143646	304	0.5314685314685315	428	0.5646437994722955	c	9.759	1.169584	0.21621	0.59473	0.584807	ENSG00000159871	ENST00000377950;ENST00000414615	T;D	0.98493	3.22;-4.96	3.3	-4.2	0.03823	.	2.677820	0.02015	N	0.047340	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.48559	-0.9025	9	0.19590	T	0.45	-0.3627	2.7515	0.05282	0.1087:0.4392:0.2049:0.2471	rs11547806;rs17798417;rs60214634;rs11547806	90	Q6UWN5	LYPD5_HUMAN	P	90;47	ENSP00000367185:A90P;ENSP00000408433:A47P	ENSP00000367185:A90P	A	-	1	0	LYPD5	48994906	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.157000	0.10085	-0.792000	0.04480	-1.579000	0.00862	GCG	C|0.420;G|0.580	0.580	strong		0.687	LYPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463611.1	NM_182573	
CLCNKB	1188	hgsc.bcm.edu	37	1	16378739	16378739	+	Silent	SNP	G	G	A	rs34652156	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:16378739G>A	ENST00000375679.4	+	15	1566	c.1455G>A	c.(1453-1455)gcG>gcA	p.A485A	CLCNKB_ENST00000375667.3_Silent_p.A316A	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	485					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)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		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)		TCTCCACGGCGCTGCTGGCCT	0.657													A|||	151	0.0301518	0.0749	0.013	5008	,	,		20068	0.002		0.0258	False		,,,				2504	0.0153				p.A485A		Atlas-SNP	.											.	CLCNKB	50	.	0			c.G1455A						PASS	.	A	,	252,4154	796.5+/-415.4	8,236,1959	61.0	59.0	60.0		1455,948	-8.6	0.1	1	dbSNP_126	60	259,8339	802.0+/-407.4	6,247,4046	no	coding-synonymous,coding-synonymous	CLCNKB	NM_000085.3,NM_001165945.1	,	14,483,6005	AA,AG,GG		3.0123,5.7195,3.9296	,	485/688,316/519	16378739	511,12493	2203	4299	6502	SO:0001819	synonymous_variant	1188	exon15			CACGGCGCTGCTG	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1455G>A	1.37:g.16378739G>A		Somatic	395	0	0		WXS	Illumina HiSeq	Phase_I	318	314	0.987421	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Silent	SNP	ENST00000375679.4	37	CCDS168.1																																																																																			G|0.967;A|0.033	0.033	strong		0.657	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
PCSK1	5122	hgsc.bcm.edu	37	5	95733112	95733112	+	Silent	SNP	A	A	G	rs6233	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:95733112A>G	ENST00000311106.3	-	12	1887	c.1650T>C	c.(1648-1650)aaT>aaC	p.N550N	PCSK1_ENST00000513085.1_5'UTR|PCSK1_ENST00000508626.1_Silent_p.N503N|CTD-2337A12.1_ENST00000502645.2_RNA	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	550					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TGAAGTCCCAATTCTTAAAGC	0.398													A|||	1717	0.342851	0.4092	0.4078	5008	,	,		18310	0.2401		0.3678	False		,,,				2504	0.2873				p.N550N		Atlas-SNP	.											.	PCSK1	93	.	0			c.T1650C						PASS	.	A	,,	1822,2584	533.9+/-373.8	356,1110,737	118.0	103.0	108.0		1650,1509,720	-6.4	0.9	5	dbSNP_52	108	3230,5370	485.6+/-371.7	590,2050,1660	no	coding-synonymous,coding-synonymous,coding-synonymous	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	,,	946,3160,2397	GG,GA,AA		37.5581,41.3527,38.8436	,,	550/754,503/707,240/444	95733112	5052,7954	2203	4300	6503	SO:0001819	synonymous_variant	5122	exon12			GTCCCAATTCTTA		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1650T>C	5.37:g.95733112A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Silent	SNP	ENST00000311106.3	37	CCDS4081.1																																																																																			A|0.628;G|0.372	0.372	strong		0.398	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
ENDOG	2021	hgsc.bcm.edu	37	9	131584631	131584631	+	Silent	SNP	C	C	T	rs2280844	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131584631C>T	ENST00000372642.4	+	3	847	c.636C>T	c.(634-636)taC>taT	p.Y212Y	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	212					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										GGAAATCCTACGTAAAGTACC	0.592													C|||	417	0.0832668	0.1346	0.0432	5008	,	,		19734	0.0933		0.0408	False		,,,				2504	0.0757				p.Y212Y		Atlas-SNP	.											.	ENDOG	8	.	0			c.C636T						PASS	.	C	,	503,3903	228.5+/-243.3	35,433,1735	80.0	72.0	75.0		636,	-10.4	0.4	9	dbSNP_100	75	337,8263	115.2+/-175.0	6,325,3969	no	coding-synonymous,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	,	41,758,5704	TT,TC,CC		3.9186,11.4163,6.4586	,	212/298,	131584631	840,12166	2203	4300	6503	SO:0001819	synonymous_variant	2021	exon3			ATCCTACGTAAAG	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.636C>T	9.37:g.131584631C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	90	48	0.533333	NM_004435	Q5T281|Q9BSP2	Silent	SNP	ENST00000372642.4	37	CCDS6912.1																																																																																			C|0.923;T|0.077	0.077	strong		0.592	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435	
EVA1A	84141	hgsc.bcm.edu	37	2	75720664	75720664	+	Silent	SNP	G	G	A	rs6741778	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:75720664G>A	ENST00000233712.1	-	4	594	c.157C>T	c.(157-159)Ctg>Ttg	p.L53L	EVA1A_ENST00000490746.1_Intron|EVA1A_ENST00000393913.3_Silent_p.L53L|EVA1A_ENST00000410071.1_Silent_p.L53L|EVA1A_ENST00000410113.1_Silent_p.L53L|EVA1A_ENST00000410010.1_Silent_p.L41L	NM_032181.2	NP_115557.1	Q9H8M9	EVA1A_HUMAN	eva-1 homolog A (C. elegans)	53	Necessary for the localization and biological activity.				apoptotic process (GO:0006915)|autophagy (GO:0006914)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|plasma membrane (GO:0005886)											CTTATCACCAGAGCAGCCAGG	0.572													A|||	1155	0.230631	0.4576	0.1599	5008	,	,		17088	0.0298		0.2078	False		,,,				2504	0.2045				p.L53L		Atlas-SNP	.											.	.	.	.	0			c.C157T						PASS	.	A	,	1810,2596	638.3+/-396.9	376,1058,769	41.0	39.0	40.0		157,157	-8.4	0.0	2	dbSNP_116	40	1801,6799	732.1+/-406.8	198,1405,2697	no	coding-synonymous,coding-synonymous	FAM176A	NM_001135032.1,NM_032181.2	,	574,2463,3466	AA,AG,GG		20.9419,41.0803,27.7641	,	53/153,53/153	75720664	3611,9395	2203	4300	6503	SO:0001819	synonymous_variant	84141	exon4			TCACCAGAGCAGC	BC016157	CCDS1959.1	2p12	2012-11-05	2012-11-05	2012-11-05	ENSG00000115363	ENSG00000115363			25816	protein-coding gene	gene with protein product			"""transmembrane protein 166"", ""family with sequence similarity 176, member A"""	TMEM166, FAM176A		12477932	Standard	NM_001135032		Approved	FLJ13391	uc002sni.2	Q9H8M9	OTTHUMG00000129991	ENST00000233712.1:c.157C>T	2.37:g.75720664G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	32	10	0.3125	NM_032181	D6W5J3|Q9HC41	Silent	SNP	ENST00000233712.1	37	CCDS1959.1																																																																																			G|0.745;A|0.255	0.255	strong		0.572	EVA1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328707.1	NM_032181	
SAMM50	25813	hgsc.bcm.edu	37	22	44368204	44368204	+	Silent	SNP	A	A	G	rs3177036	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44368204A>G	ENST00000350028.4	+	5	568	c.411A>G	c.(409-411)ggA>ggG	p.G137G	SAMM50_ENST00000396202.3_Intron|SAMM50_ENST00000493161.1_3'UTR	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	137					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)				endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				CCATGGTTGGAAACAATGAAG	0.368													A|||	3483	0.695487	0.7496	0.5692	5008	,	,		18461	0.8185		0.5477	False		,,,				2504	0.7372				p.G137G		Atlas-SNP	.											.	SAMM50	30	.	0			c.A411G						PASS	.	A		3090,1316	694.3+/-405.8	1093,904,206	127.0	117.0	120.0		411	-5.5	1.0	22	dbSNP_105	120	4254,4346	568.0+/-388.9	1058,2138,1104	no	coding-synonymous	SAMM50	NM_015380.4		2151,3042,1310	GG,GA,AA		49.4651,29.8684,43.5338		137/470	44368204	7344,5662	2203	4300	6503	SO:0001819	synonymous_variant	25813	exon5			GGTTGGAAACAAT	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.411A>G	22.37:g.44368204A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Silent	SNP	ENST00000350028.4	37	CCDS14055.1																																																																																			A|0.383;G|0.617	0.617	strong		0.368	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
TATDN3	128387	hgsc.bcm.edu	37	1	212965284	212965284	+	Silent	SNP	C	C	G	rs61736926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:212965284C>G	ENST00000366974.4	+	1	115	c.21C>G	c.(19-21)ggC>ggG	p.G7G	TATDN3_ENST00000526641.1_Silent_p.G7G|NSL1_ENST00000473995.1_5'Flank|NSL1_ENST00000366978.1_5'Flank|TATDN3_ENST00000366973.4_Silent_p.G7G|TATDN3_ENST00000531963.1_Silent_p.G7G|NSL1_ENST00000366975.6_5'Flank|TATDN3_ENST00000532324.1_Silent_p.G7G|NSL1_ENST00000366977.3_5'Flank|NSL1_ENST00000422588.2_5'Flank|NSL1_ENST00000366976.1_5'Flank|TATDN3_ENST00000526997.1_Silent_p.G7G|TATDN3_ENST00000530441.1_Silent_p.G7G	NM_001042552.2|NM_001042553.2|NM_001146169.1|NM_001146171.1	NP_001036017.1|NP_001036018.1|NP_001139641.1|NP_001139643.1	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3	7					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)		CTGGCGTAGGCTTGGTGGACT	0.672													G|||	1141	0.227835	0.3986	0.1196	5008	,	,		12998	0.1538		0.1541	False		,,,				2504	0.226				p.G7G		Atlas-SNP	.											TATDN3,NS,carcinoma,0,1	TATDN3	23	1	0			c.C21G						scavenged	.	G	,,,,	1595,2809	626.1+/-394.7	296,1003,903	25.0	31.0	29.0		21,21,21,21,21	-3.6	0.0	1	dbSNP_129	29	1321,7279	727.2+/-406.6	101,1119,3080	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TATDN3	NM_001042552.2,NM_001042553.2,NM_001146169.1,NM_001146170.1,NM_001146171.1	,,,,	397,2122,3983	GG,GC,CC		15.3605,36.2171,22.4239	,,,,	7/275,7/274,7/241,7/254,7/282	212965284	2916,10088	2202	4300	6502	SO:0001819	synonymous_variant	128387	exon1			CGTAGGCTTGGTG	AL832248	CCDS31019.1, CCDS41465.1, CCDS53475.1, CCDS53476.1, CCDS53477.1	1q32.3	2008-02-05			ENSG00000203705	ENSG00000203705			27010	protein-coding gene	gene with protein product							Standard	NM_001042552		Approved		uc001hjo.2	Q17R31	OTTHUMG00000036805	ENST00000366974.4:c.21C>G	1.37:g.212965284C>G		Somatic	140	7	0.05		WXS	Illumina HiSeq	Phase_I	147	74	0.503401	NM_001146170	A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Silent	SNP	ENST00000366974.4	37	CCDS31019.1	469	0.21474358974358973	216	0.43902439024390244	48	0.13259668508287292	89	0.1555944055944056	116	0.15303430079155672	G	7.215	0.596217	0.13875	0.362171	0.153605	ENSG00000203705	ENST00000488246	.	.	.	5.24	-3.62	0.04543	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.199999999998649E-5	.	.	.	.	.	.	T	0.42548	-0.9445	3	.	.	.	-9.0778	9.1104	0.36723	0.064:0.5664:0.1779:0.1917	rs61736926	.	.	.	V	7	.	.	L	+	1	0	TATDN3	211031907	0.029000	0.19370	0.004000	0.12327	0.043000	0.13939	-0.132000	0.10467	-0.757000	0.04697	-2.997000	0.00077	CTT	C|0.772;G|0.228	0.228	strong		0.672	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2	XM_375838	
CDON	50937	hgsc.bcm.edu	37	11	125830970	125830970	+	Missense_Mutation	SNP	A	A	T	rs684535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:125830970A>T	ENST00000392693.3	-	20	3858	c.3731T>A	c.(3730-3732)aTc>aAc	p.I1244N	CDON_ENST00000263577.7_Missense_Mutation_p.I1221N|RP11-680F20.12_ENST00000582823.1_RNA|CDON_ENST00000531738.1_Missense_Mutation_p.I598N	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1244				I -> N (in Ref. 3; AAH98583). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		TACAATGTTGATCTCTGTTTC	0.458																																					p.I1244N		Atlas-SNP	.											.	CDON	137	.	0			c.T3731A						PASS	.	T	ASN/ILE	3635,767	312.5+/-292.6	1497,641,63	97.0	95.0	96.0		3662	4.3	0.6	11	dbSNP_83	96	5855,2743	437.2+/-358.5	2002,1851,446	yes	missense	CDON	NM_016952.4	149	3499,2492,509	TT,TA,AA		31.9028,17.4239,27.0	benign	1221/1265	125830970	9490,3510	2201	4299	6500	SO:0001583	missense	50937	exon20			ATGTTGATCTCTG	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.3731T>A	11.37:g.125830970A>T	ENSP00000376458:p.Ile1244Asn	Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	162	162	1	NM_001243597	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	1747	0.799908424908425	419	0.8516260162601627	298	0.8232044198895028	523	0.9143356643356644	507	0.6688654353562006	T	0.007	-1.989020	0.00439	0.825761	0.680972	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	T;T;T	0.66099	-0.03;0.56;-0.19	5.46	4.34	0.51931	.	0.483674	0.17406	N	0.175374	T	0.00012	0.0000	N	0.00289	-1.7	0.58432	P	1.0000000000287557E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41556	-0.9502	9	0.02654	T	1	-10.0522	3.1381	0.06446	0.1398:0.0756:0.146:0.6386	rs684535;rs17723591;rs52838362;rs59963094;rs684535	1244;1221;598	Q4KMG0;Q4KMG0-2;E9PN78	CDON_HUMAN;.;.	N	1244;598;1221	ENSP00000376458:I1244N;ENSP00000432901:I598N;ENSP00000263577:I1221N	ENSP00000263577:I1221N	I	-	2	0	CDON	125336180	0.664000	0.27457	0.581000	0.28614	0.003000	0.03518	0.438000	0.21559	0.515000	0.28320	-0.257000	0.10917	ATC	A|0.238;T|0.762	0.762	strong		0.458	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
ZNF99	7652	hgsc.bcm.edu	37	19	22942325	22942325	+	Missense_Mutation	SNP	G	G	C	rs7255780	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:22942325G>C	ENST00000596209.1	-	4	476	c.386C>G	c.(385-387)gCt>gGt	p.A129G	ZNF99_ENST00000397104.3_Missense_Mutation_p.A150G	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	129			A -> G (in dbSNP:rs7255780).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				TTTATTATAAGCTTCTTCGTG	0.299													C|||	1840	0.367412	0.5386	0.3256	5008	,	,		16402	0.3462		0.2783	False		,,,				2504	0.2791				p.A129G		Atlas-SNP	.											.	ZNF99	273	.	0			c.C386G						PASS	.	C	GLY/ALA	1869,1871		455,959,456	101.0	98.0	99.0		449	-0.8	0.0	19	dbSNP_116	99	2332,5862		324,1684,2089	yes	missense	ZNF99	NM_001080409.2	60	779,2643,2545	CC,CG,GG		28.4598,49.9733,35.2019	benign	150/912	22942325	4201,7733	1870	4097	5967	SO:0001583	missense	7652	exon4			TTATAAGCTTCTT	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.386C>G	19.37:g.22942325G>C	ENSP00000472969:p.Ala129Gly	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	37	CCDS59369.1	802	0.36721611721611724	266	0.540650406504065	120	0.3314917127071823	207	0.3618881118881119	209	0.2757255936675462	N	0.175	-1.068074	0.01934	0.499733	0.284598	ENSG00000213973	ENST00000397104	T	0.06294	3.32	1.18	-0.806	0.10875	.	.	.	.	.	T	0.00012	0.0000	N	0.00057	-2.36	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	8	0.02654	T	1	.	4.3885	0.11328	0.2323:0.3046:0.4631:0.0	rs7255780;rs57975939;rs7255780	150	A8MXY4	ZNF99_HUMAN	G	150	ENSP00000380293:A150G	ENSP00000380293:A150G	A	-	2	0	ZNF99	22734165	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.658000	0.05329	-1.903000	0.01093	-1.120000	0.02017	GCT	G|0.635;C|0.364	0.364	strong		0.299	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
ANKMY2	57037	hgsc.bcm.edu	37	7	16655387	16655387	+	Silent	SNP	C	C	T	rs11540037	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:16655387C>T	ENST00000306999.2	-	5	756	c.513G>A	c.(511-513)acG>acA	p.T171T		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	171						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GATGAAGATTCGTTGTGGTGA	0.413													C|||	883	0.176318	0.0681	0.1657	5008	,	,		16455	0.2173		0.1948	False		,,,				2504	0.2689				p.T171T		Atlas-SNP	.											.	ANKMY2	46	.	0			c.G513A						PASS	.	C		420,3986	203.5+/-225.9	16,388,1799	95.0	92.0	93.0		513	-1.6	1.0	7	dbSNP_120	93	1795,6805	323.0+/-315.8	178,1439,2683	no	coding-synonymous	ANKMY2	NM_020319.2		194,1827,4482	TT,TC,CC		20.8721,9.5325,17.0306		171/442	16655387	2215,10791	2203	4300	6503	SO:0001819	synonymous_variant	57037	exon5			AAGATTCGTTGTG	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.513G>A	7.37:g.16655387C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	77	14	0.181818	NM_020319	A4D124|Q659G1|Q96BL3	Silent	SNP	ENST00000306999.2	37	CCDS5361.1																																																																																			T|0.144;G|0.146;C|0.687;A|0.024	0.144	strong		0.413	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319	
VPS13C	54832	hgsc.bcm.edu	37	15	62174894	62174894	+	Silent	SNP	A	A	G	rs17303915	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62174894A>G	ENST00000261517.5	-	69	9598	c.9525T>C	c.(9523-9525)atT>atC	p.I3175I	VPS13C_ENST00000558919.1_5'Flank|VPS13C_ENST00000395896.4_Silent_p.I3175I|VPS13C_ENST00000395898.3_Silent_p.I3132I|VPS13C_ENST00000249837.3_Silent_p.I3132I	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						TAGGGCTACGAATAGGGAGGC	0.388													A|||	233	0.0465256	0.0166	0.0418	5008	,	,		16084	0.0397		0.0746	False		,,,				2504	0.0685				p.I3175I		Atlas-SNP	.											.	VPS13C	506	.	0			c.T9525C						PASS	.	A	,,,	119,4287	89.2+/-127.9	1,117,2085	103.0	102.0	103.0		9525,9396,9396,9525	-3.1	0.0	15	dbSNP_123	103	684,7916	169.7+/-221.0	31,622,3647	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	,,,	32,739,5732	GG,GA,AA		7.9535,2.7009,6.1741	,,,	3175/3629,3132/3711,3132/3586,3175/3754	62174894	803,12203	2203	4300	6503	SO:0001819	synonymous_variant	54832	exon69			GCTACGAATAGGG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.9525T>C	15.37:g.62174894A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_020821		Silent	SNP	ENST00000261517.5	37	CCDS32257.1																																																																																			A|0.943;G|0.057	0.057	strong		0.388	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
ACIN1	22985	hgsc.bcm.edu	37	14	23549380	23549380	+	Silent	SNP	G	G	A	rs1885098|rs386775580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:23549380G>A	ENST00000262710.1	-	6	1665	c.1338C>T	c.(1336-1338)ccC>ccT	p.P446P	ACIN1_ENST00000555053.1_Silent_p.P446P|ACIN1_ENST00000605057.1_Silent_p.P388P|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000457657.1_Silent_p.P406P	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	446					apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		TGAGGACAGCGGGGGCTGGGC	0.502													G|||	527	0.105232	0.0877	0.1239	5008	,	,		19104	0.004		0.1561	False		,,,				2504	0.1677				p.P446P		Atlas-SNP	.											.	ACIN1	147	.	0			c.C1338T						PASS	.	G	,,	5,4401		1,3,2199	61.0	65.0	64.0		1338,1218,1338	-2.6	1.0	14	dbSNP_92	64	31,8569		4,23,4273	no	coding-synonymous,coding-synonymous,coding-synonymous	ACIN1	NM_001164814.1,NM_001164815.1,NM_014977.3	,,	5,26,6472	AA,AG,GG		0.3605,0.1135,0.2768	,,	446/1329,406/1302,446/1342	23549380	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	22985	exon6			GACAGCGGGGGCT	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1338C>T	14.37:g.23549380G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	149	70	0.469799	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	37	CCDS9587.1																																																																																			G|0.871;A|0.129	0.129	strong		0.502	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
PDE6A	5145	hgsc.bcm.edu	37	5	149323772	149323772	+	Silent	SNP	G	G	A	rs2277926	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149323772G>A	ENST00000255266.5	-	1	584	c.465C>T	c.(463-465)aaC>aaT	p.N155N		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	155	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)	p.N155N(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CCTCCTCTGTGTTGGGGACGT	0.557													G|||	1247	0.249002	0.2761	0.2305	5008	,	,		17039	0.246		0.166	False		,,,				2504	0.3139				p.N155N		Atlas-SNP	.											PDE6A,NS,carcinoma,0,1	PDE6A	98	1	1	Substitution - coding silent(1)	stomach(1)	c.C465T						PASS	.	G		1052,3354	386.1+/-326.0	110,832,1261	151.0	129.0	136.0		465	4.5	1.0	5	dbSNP_100	136	1230,7370	247.2+/-275.4	103,1024,3173	no	coding-synonymous	PDE6A	NM_000440.2		213,1856,4434	AA,AG,GG		14.3023,23.8765,17.5457		155/861	149323772	2282,10724	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			CTCTGTGTTGGGG		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.465C>T	5.37:g.149323772G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|0.807;A|0.193	0.193	strong		0.557	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
AKR7A3	22977	hgsc.bcm.edu	37	1	19611227	19611227	+	Silent	SNP	G	G	A	rs1065658	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19611227G>A	ENST00000361640.4	-	5	1197	c.657C>T	c.(655-657)ccC>ccT	p.P219P		NM_012067.2	NP_036199.2	O95154	ARK73_HUMAN	aldo-keto reductase family 7, member A3 (aflatoxin aldehyde reductase)	219					cellular aldehyde metabolic process (GO:0006081)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|electron carrier activity (GO:0009055)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|stomach(2)	13		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;1.78e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00276)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AGCGGCCCACGGGCTGTTTCC	0.587													G|||	735	0.146765	0.1293	0.1383	5008	,	,		16948	0.0258		0.1789	False		,,,				2504	0.2679				p.P219P		Atlas-SNP	.											.	AKR7A3	30	.	0			c.C657T						PASS	.	G		566,3832		49,468,1682	122.0	132.0	129.0		657	-6.0	0.2	1	dbSNP_86	129	1590,7010		158,1274,2868	no	coding-synonymous	AKR7A3	NM_012067.2		207,1742,4550	AA,AG,GG		18.4884,12.8695,16.5872		219/332	19611227	2156,10842	2199	4300	6499	SO:0001819	synonymous_variant	22977	exon5			GCCCACGGGCTGT	AF040639	CCDS193.1	1p36.13	2008-05-14			ENSG00000162482	ENSG00000162482		"""Aldo-keto reductases"""	390	protein-coding gene	gene with protein product		608477				10383892	Standard	NM_012067		Approved		uc001bbv.1	O95154	OTTHUMG00000002523	ENST00000361640.4:c.657C>T	1.37:g.19611227G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_012067	Q86SR4|Q8IVN6|Q8N5V6|Q8TAX1|Q9NUC3	Silent	SNP	ENST00000361640.4	37	CCDS193.1																																																																																			G|0.842;A|0.158	0.158	strong		0.587	AKR7A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007166.1	NM_012067	
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 GAIIx	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	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	134	58	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	
NEK11	79858	hgsc.bcm.edu	37	3	130992385	130992385	+	Missense_Mutation	SNP	T	T	C	rs16836266	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:130992385T>C	ENST00000510769.1	+	13	1623	c.1370T>C	c.(1369-1371)gTg>gCg	p.V457A	NEK11_ENST00000429253.2_Missense_Mutation_p.V562A|NEK11_ENST00000508196.1_Missense_Mutation_p.V562A|NEK11_ENST00000412440.2_Missense_Mutation_p.V378A|NEK11_ENST00000510688.1_Intron|NEK11_ENST00000383366.4_Missense_Mutation_p.V562A					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						TTCAACAGTGTGATGGCCAGG	0.483													C|||	948	0.189297	0.3139	0.1844	5008	,	,		20541	0.2837		0.0537	False		,,,				2504	0.0665				p.V562A		Atlas-SNP	.											.	NEK11	76	.	0			c.T1685C						PASS	.	C	,ALA/VAL	1179,3227	711.2+/-408.0	161,857,1185	157.0	118.0	131.0		,1685	1.7	0.0	3	dbSNP_123	131	513,8087	796.5+/-407.5	11,491,3798	yes	intron,missense	NEK11	NM_001146003.1,NM_024800.4	,64	172,1348,4983	CC,CT,TT		5.9651,26.759,13.0094	,benign	,562/646	130992385	1692,11314	2203	4300	6503	SO:0001583	missense	79858	exon17			ACAGTGTGATGGC	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.1370T>C	3.37:g.130992385T>C	ENSP00000421549:p.Val457Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_024800		Missense_Mutation	SNP	ENST00000510769.1	37		413	0.1891025641025641	146	0.2967479674796748	62	0.1712707182320442	172	0.3006993006993007	33	0.04353562005277045	C	0.010	-1.758049	0.00657	0.26759	0.059651	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000383366;ENST00000412440;ENST00000508196	T;T;T;T;T	0.70986	-0.42;-0.2;-0.2;-0.53;-0.2	5.73	1.66	0.24008	.	0.537726	0.15484	N	0.259948	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.16305	-1.0407	9	0.16420	T	0.52	.	12.1749	0.54180	0.0:0.7575:0.0:0.2425	rs16836266;rs52793822;rs59585289;rs16836266	457;378;562	E9PHI8;B4DDN2;Q8NG66	.;.;NEK11_HUMAN	A	457;562;562;378;562	ENSP00000421549:V457A;ENSP00000397180:V562A;ENSP00000372857:V562A;ENSP00000411888:V378A;ENSP00000421851:V562A	ENSP00000372857:V562A	V	+	2	0	NEK11	132475075	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	0.378000	0.20569	0.059000	0.16252	-1.246000	0.01523	GTG	C|0.166;N|0.000	0.166	strong		0.483	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800	
EML5	161436	hgsc.bcm.edu	37	14	89206861	89206861	+	Missense_Mutation	SNP	G	G	A	rs139652502	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:89206861G>A	ENST00000380664.5	-	5	580	c.581C>T	c.(580-582)aCg>aTg	p.T194M	EML5_ENST00000554922.1_Missense_Mutation_p.T194M|EML5_ENST00000352093.5_Missense_Mutation_p.T194M			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	194						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AAGGTCACCCGTCTTACCAAA	0.378													G|||	17	0.00339457	0.0015	0.0014	5008	,	,		16789	0.0		0.0119	False		,,,				2504	0.002				p.T194M		Atlas-SNP	.											EML5,colon,NS,+1,1	EML5	141	1	0			c.C581T						PASS	.	G	MET/THR	11,3737		0,11,1863	154.0	145.0	148.0		581	5.2	1.0	14	dbSNP_134	148	112,8122		0,112,4005	yes	missense	EML5	NM_183387.2	81	0,123,5868	AA,AG,GG		1.3602,0.2935,1.0265	benign	194/1978	89206861	123,11859	1874	4117	5991	SO:0001583	missense	161436	exon5			TCACCCGTCTTAC	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.581C>T	14.37:g.89206861G>A	ENSP00000370039:p.Thr194Met	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	8	0.003663003663003663	1	0.0020325203252032522	0	0.0	0	0.0	7	0.009234828496042216	G	15.13	2.742905	0.49151	0.002935	0.013602	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.22134	1.97;1.97;1.97	5.21	5.21	0.72293	WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.195228	0.43919	D	0.000501	T	0.18173	0.0436	L	0.49640	1.575	0.54753	D	0.999982	B	0.24368	0.102	B	0.24394	0.053	T	0.02208	-1.1195	10	0.46703	T	0.11	-17.6021	18.7549	0.91828	0.0:0.0:1.0:0.0	.	194	Q05BV3	EMAL5_HUMAN	M	194	ENSP00000451998:T194M;ENSP00000298315:T194M;ENSP00000370039:T194M	ENSP00000298315:T194M	T	-	2	0	EML5	88276614	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.542000	0.82095	2.417000	0.82017	0.591000	0.81541	ACG	G|0.994;A|0.006	0.006	strong		0.378	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
MAGIX	79917	hgsc.bcm.edu	37	X	49021052	49021052	+	Silent	SNP	C	C	T	rs12843494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49021052C>T	ENST00000412696.2	+	3	204	c.204C>T	c.(202-204)agC>agT	p.S68S	MAGIX_ENST00000425661.2_Silent_p.S68S|MAGIX_ENST00000376339.1_5'UTR|MAGIX_ENST00000376338.3_5'UTR|MAGIX_ENST00000498742.1_3'UTR	NM_024859.2	NP_079135.3	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked	68																	CAGCTGTTAGCGTGCTGGACT	0.537													C|||	386	0.102252	0.0121	0.0375	3775	,	,		14079	0.0486		0.0805	False		,,,				2504	0.2188				p.S68S		Atlas-SNP	.											.	MAGIX	25	.	0			c.C204T						PASS	.	C	,,,	81,3515		0,63,18,1450,552	153.0	154.0	153.0		48,204,204,204	-7.9	0.0	X	dbSNP_121	153	684,5879		25,439,195,1914,1612	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAGIX	NM_001099680.1,NM_001099681.1,NM_001099682.1,NM_024859.2	,,,	25,502,213,3364,2164	TT,TC,T,CC,C		10.4221,2.2525,7.5303	,,,	16/263,68/259,68/254,68/335	49021052	765,9394	2083	4185	6268	SO:0001819	synonymous_variant	79917	exon3			TGTTAGCGTGCTG	AK025340	CCDS48106.1, CCDS48107.1, CCDS75976.1	Xp11.23	2014-05-06			ENSG00000017621	ENSG00000269313			30006	protein-coding gene	gene with protein product							Standard	XM_005278065		Approved	PDZX, JM10, FLJ21687	uc010nin.1	Q9H6Y5	OTTHUMG00000188218	ENST00000412696.2:c.204C>T	X.37:g.49021052C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	117	83	0.709402	NM_001099681	A6XND4|A8MSX9|B7WP26|Q14C81	Silent	SNP	ENST00000412696.2	37	CCDS48106.1	107|107	0.0644966847498493|0.0644966847498493	6|6	0.012345679012345678|0.012345679012345678	8|8	0.022598870056497175|0.022598870056497175	16|16	0.028985507246376812|0.028985507246376812	38|38	0.05337078651685393|0.05337078651685393	.|.	7.167|7.167	0.586807|0.586807	0.13749|0.13749	0.022525|0.022525	0.104221|0.104221	ENSG00000017621|ENSG00000017621	ENST00000415364|ENST00000458388	.|.	.|.	.|.	3.95|3.95	-7.9|-7.9	0.01169|0.01169	.|.	.|.	.|.	.|.	.|.	T|T	0.00412|0.00412	0.0013|0.0013	.|.	.|.	.|.	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.13845|0.13845	-1.0494|-1.0494	3|3	.|.	.|.	.|.	-11.4604|-11.4604	2.5019|2.5019	0.04636|0.04636	0.1162:0.2925:0.1152:0.4761|0.1162:0.2925:0.1152:0.4761	rs12843494;rs17328035|rs12843494;rs17328035	.|.	.|.	.|.	V|C	52|74	.|.	.|.	A|R	+|+	2|1	0|0	MAGIX|MAGIX	48907996|48907996	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.111000|0.111000	0.19643|0.19643	-1.449000|-1.449000	0.02392|0.02392	-2.019000|-2.019000	0.00942|0.00942	-0.711000|-0.711000	0.03637|0.03637	GCG|CGT	C|0.926;0|0.013	.	strong		0.537	MAGIX-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378832.1	NM_024859	
AKR1B15	441282	hgsc.bcm.edu	37	7	134264286	134264286	+	Silent	SNP	C	C	T	rs6467538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:134264286C>T	ENST00000457545.2	+	12	1280	c.1020C>T	c.(1018-1020)ttC>ttT	p.F340F	AKR1B15_ENST00000423958.1_Silent_p.F312F	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	340							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						ACTTTCCCTTCGATGCAGAAT	0.408													C|||	1681	0.335663	0.559	0.3084	5008	,	,		20009	0.1438		0.339	False		,,,				2504	0.2474				p.F340F		Atlas-SNP	.											.	AKR1B15	105	.	0			c.C1020T						PASS	.	C		2235,2169	554.5+/-379.0	576,1083,543	87.0	88.0	87.0		1020	-1.6	0.0	7	dbSNP_116	87	2959,5641	449.5+/-362.1	520,1919,1861	no	coding-synonymous	AKR1B15	NM_001080538.2		1096,3002,2404	TT,TC,CC		34.407,49.2507,39.9416		340/345	134264286	5194,7810	2202	4300	6502	SO:0001819	synonymous_variant	441282	exon12			TCCCTTCGATGCA		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"""Aldo-keto reductases"""	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.1020C>T	7.37:g.134264286C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_001080538	C9J3V2	Silent	SNP	ENST00000457545.2	37	CCDS47715.2																																																																																			C|0.651;T|0.349	0.349	strong		0.408	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2		
ATAD2B	54454	hgsc.bcm.edu	37	2	24046426	24046426	+	Silent	SNP	G	G	A	rs75866363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:24046426G>A	ENST00000238789.5	-	16	2176	c.1833C>T	c.(1831-1833)gcC>gcT	p.A611A	ATAD2B_ENST00000474583.1_5'UTR	NM_001242338.1|NM_017552.2	NP_001229267.1|NP_060022.1	Q9ULI0	ATD2B_HUMAN	ATPase family, AAA domain containing 2B	611						nucleus (GO:0005634)	ATP binding (GO:0005524)|lysine-acetylated histone binding (GO:0070577)			central_nervous_system(1)	1	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCTTGATATCGGCTCCACAGT	0.448													G|||	105	0.0209665	0.0008	0.0317	5008	,	,		18800	0.0		0.0596	False		,,,				2504	0.0225				p.A611A		Atlas-SNP	.											ATAD2B_ENST00000238789,colon,carcinoma,0,1	ATAD2B	110	1	0			c.C1833T						PASS	.	G	,	54,3846		0,54,1896	64.0	62.0	63.0		1833,1833	-2.2	1.0	2	dbSNP_132	63	604,7662		22,560,3551	no	coding-synonymous,coding-synonymous	ATAD2B	NM_001242338.1,NM_017552.2	,	22,614,5447	AA,AG,GG		7.307,1.3846,5.4085	,	611/1454,611/1459	24046426	658,11508	1950	4133	6083	SO:0001819	synonymous_variant	54454	exon16			GATATCGGCTCCA	AB033066	CCDS46227.1	2p24.1-p23.3	2010-04-21		2007-02-08	ENSG00000119778	ENSG00000119778		"""ATPases / AAA-type"""	29230	protein-coding gene	gene with protein product		615347					Standard	XM_005264372		Approved	KIAA1240	uc002rek.4	Q9ULI0	OTTHUMG00000151902	ENST00000238789.5:c.1833C>T	2.37:g.24046426G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_001242338	B9ZVQ5|Q6ZNA6|Q8N9E7	Silent	SNP	ENST00000238789.5	37	CCDS46227.1																																																																																			G|0.968;A|0.032	0.032	strong		0.448	ATAD2B-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324333.1	NM_017552	
LAMC3	10319	hgsc.bcm.edu	37	9	133911706	133911706	+	Silent	SNP	C	C	T	rs2275131	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:133911706C>T	ENST00000361069.4	+	4	1096	c.963C>T	c.(961-963)gcC>gcT	p.A321A	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	321	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		CCGAGGCTGCCCACGAGTGTC	0.677													C|||	1995	0.398363	0.1641	0.4885	5008	,	,		14573	0.6647		0.4791	False		,,,				2504	0.2935				p.A321A		Atlas-SNP	.											LAMC3,NS,carcinoma,0,1	LAMC3	167	1	0			c.C963T						PASS	.	C		951,3433		125,701,1366	18.0	21.0	20.0		963	4.1	0.8	9	dbSNP_100	20	4190,4386		1066,2058,1164	no	coding-synonymous	LAMC3	NM_006059.3		1191,2759,2530	TT,TC,CC		48.8573,21.6925,39.6682		321/1576	133911706	5141,7819	2192	4288	6480	SO:0001819	synonymous_variant	10319	exon4			GGCTGCCCACGAG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.963C>T	9.37:g.133911706C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			C|0.579;T|0.421	0.421	strong		0.677	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
C4orf47	441054	hgsc.bcm.edu	37	4	186366181	186366181	+	Missense_Mutation	SNP	G	G	A	rs74560263	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:186366181G>A	ENST00000378850.4	+	6	800	c.778G>A	c.(778-780)Gct>Act	p.A260T		NM_001114357.1	NP_001107829.1	A7E2U8	CD047_HUMAN	chromosome 4 open reading frame 47	260										breast(2)|endometrium(1)	3						CCCTTATGTGGCTAAATTGGC	0.403													G|||	349	0.0696885	0.0363	0.0908	5008	,	,		17154	0.0109		0.1034	False		,,,				2504	0.1258				p.A260T		Atlas-SNP	.											.	C4orf47	13	.	0			c.G778A						PASS	.	G	THR/ALA	54,1330		2,50,640	149.0	125.0	132.0		778	-1.6	0.0	4	dbSNP_131	132	291,2891		13,265,1313	yes	missense	C4orf47	NM_001114357.1	58	15,315,1953	AA,AG,GG		9.1452,3.9017,7.5558	benign	260/310	186366181	345,4221	692	1591	2283	SO:0001583	missense	441054	exon6			TATGTGGCTAAAT	AY947525, BC127739, BC141967	CCDS47169.1	4q35.1	2008-07-18			ENSG00000205129	ENSG00000205129			34346	protein-coding gene	gene with protein product						12477932	Standard	NM_001114357		Approved	LOC441054	uc003ixt.2	A7E2U8	OTTHUMG00000160458	ENST00000378850.4:c.778G>A	4.37:g.186366181G>A	ENSP00000368127:p.Ala260Thr	Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	237	96	0.405063	NM_001114357	Q5BLP7	Missense_Mutation	SNP	ENST00000378850.4	37	CCDS47169.1	132	0.06043956043956044	12	0.024390243902439025	34	0.09392265193370165	4	0.006993006993006993	82	0.10817941952506596	G	0.152	-1.090902	0.01858	0.039017	0.091452	ENSG00000205129	ENST00000378850	.	.	.	5.68	-1.63	0.08345	.	.	.	.	.	T	0.00210	0.0006	N	0.02916	-0.46	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.30416	-0.9979	7	0.10377	T	0.69	-0.0288	3.3421	0.07122	0.3937:0.105:0.3953:0.106	.	260	A7E2U8	CD047_HUMAN	T	260	.	ENSP00000368127:A260T	A	+	1	0	C4orf47	186603175	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.285000	0.18883	-0.250000	0.09555	-1.012000	0.02466	GCT	G|0.938;A|0.062	0.062	strong		0.403	C4orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360667.1	NM_001114357	
NUP107	57122	hgsc.bcm.edu	37	12	69115698	69115698	+	Silent	SNP	G	G	A	rs17851475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:69115698G>A	ENST00000229179.4	+	16	1721	c.1389G>A	c.(1387-1389)caG>caA	p.Q463Q	NUP107_ENST00000378905.2_Silent_p.Q312Q|NUP107_ENST00000539906.1_Silent_p.Q434Q	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	463					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TGGTAGAACAGGAGATCCAGA	0.468													G|||	1101	0.219848	0.059	0.2968	5008	,	,		16799	0.2996		0.2922	False		,,,				2504	0.226				p.Q463Q		Atlas-SNP	.											.	NUP107	88	.	0			c.G1389A						PASS	.	G		404,4002	200.8+/-224.0	20,364,1819	115.0	114.0	115.0		1389	2.1	1.0	12	dbSNP_123	115	2348,6252	393.9+/-344.5	319,1710,2271	no	coding-synonymous	NUP107	NM_020401.2		339,2074,4090	AA,AG,GG		27.3023,9.1693,21.1595		463/926	69115698	2752,10254	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon16			AGAACAGGAGATC	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.1389G>A	12.37:g.69115698G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			G|0.782;A|0.218	0.218	strong		0.468	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
CDHR1	92211	hgsc.bcm.edu	37	10	85972043	85972043	+	Silent	SNP	A	A	G	rs10749482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:85972043A>G	ENST00000372117.3	+	15	1765	c.1662A>G	c.(1660-1662)gaA>gaG	p.E554E	CDHR1_ENST00000332904.3_Silent_p.E554E|CDHR1_ENST00000440770.2_Silent_p.E258E	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	554	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						AGGACATGGAAGGCAAGTACA	0.542													G|||	2149	0.429113	0.7542	0.3876	5008	,	,		20639	0.2619		0.2853	False		,,,				2504	0.3395				p.E554E		Atlas-SNP	.											.	CDHR1	122	.	0			c.A1662G						PASS	.	G	,	2938,1468	472.6+/-356.4	990,958,255	172.0	152.0	159.0		1662,1662	0.6	1.0	10	dbSNP_120	159	2503,6097	694.5+/-404.7	376,1751,2173	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	1366,2709,2428	GG,GA,AA		29.1047,33.3182,41.8345	,	554/746,554/860	85972043	5441,7565	2203	4300	6503	SO:0001819	synonymous_variant	92211	exon15			CATGGAAGGCAAG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.1662A>G	10.37:g.85972043A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			A|0.585;G|0.415	0.415	strong		0.542	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98469507	98469507	+	Missense_Mutation	SNP	C	C	A	rs3748229	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:98469507C>A	ENST00000339364.5	-	2	366	c.247G>T	c.(247-249)Gcc>Tcc	p.A83S		NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	83	Necessary and sufficent to mediate inhibition of NF-kappa-B downstream of activated TLRs; may mediate interaction with MYD88 and TIRAP. {ECO:0000250}.		A -> S (in dbSNP:rs3748229). {ECO:0000269|PubMed:17974005}.		negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		GGCAGCAAGGCGGGCTTGTGG	0.642													C|||	2116	0.422524	0.5439	0.4092	5008	,	,		19812	0.3095		0.3191	False		,,,				2504	0.4908				p.A83S		Atlas-SNP	.											PIK3AP1,caecum,carcinoma,+2,1	PIK3AP1	111	1	0			c.G247T						scavenged	.	C	SER/ALA	2222,2184	585.1+/-386.2	566,1090,547	53.0	54.0	53.0		247	2.0	0.0	10	dbSNP_107	53	2710,5890	430.9+/-356.6	463,1784,2053	yes	missense	PIK3AP1	NM_152309.2	99	1029,2874,2600	AA,AC,CC		31.5116,49.5688,37.921	benign	83/806	98469507	4932,8074	2203	4300	6503	SO:0001583	missense	118788	exon2			GCAAGGCGGGCTT	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.247G>T	10.37:g.98469507C>A	ENSP00000339826:p.Ala83Ser	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	37	CCDS31259.1	795	0.364010989010989	264	0.5365853658536586	139	0.3839779005524862	146	0.25524475524475526	246	0.3245382585751979	C	4.397	0.073314	0.08485	0.504312	0.315116	ENSG00000155629	ENST00000339364	T	0.09255	3.0	5.01	2.01	0.26516	.	0.850864	0.10569	N	0.659363	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.43278	-0.9401	9	0.07325	T	0.83	-2.6884	2.6317	0.04946	0.143:0.5239:0.1577:0.1754	rs3748229;rs52814694;rs60576678;rs3748229	83	Q6ZUJ8	BCAP_HUMAN	S	83	ENSP00000339826:A83S	ENSP00000339826:A83S	A	-	1	0	PIK3AP1	98459497	0.000000	0.05858	0.002000	0.10522	0.864000	0.49448	0.168000	0.16622	0.588000	0.29660	0.655000	0.94253	GCC	C|0.621;A|0.379	0.379	strong		0.642	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
ADRB2	154	hgsc.bcm.edu	37	5	148206646	148206646	+	Silent	SNP	G	G	A	rs113509650|rs1042717	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148206646G>A	ENST00000305988.4	+	1	491	c.252G>A	c.(250-252)ctG>ctA	p.L84L		NM_000024.5	NP_000015	P07550	ADRB2_HUMAN	adrenoceptor beta 2, surface	84					activation of adenylate cyclase activity (GO:0007190)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|bone resorption (GO:0045453)|brown fat cell differentiation (GO:0050873)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway by arrestin (GO:0002032)|diet induced thermogenesis (GO:0002024)|endosome to lysosome transport (GO:0008333)|heat generation (GO:0031649)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor-mediated endocytosis (GO:0006898)|regulation of sodium ion transport (GO:0002028)|regulation of vasodilation (GO:0042312)|response to cold (GO:0009409)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	beta2-adrenergic receptor activity (GO:0004941)|norepinephrine binding (GO:0051380)|potassium channel regulator activity (GO:0015459)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|lung(8)|ovary(1)|prostate(3)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Acebutolol(DB01193)|Alprenolol(DB00866)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Arformoterol(DB01274)|Asenapine(DB06216)|Atenolol(DB00335)|Bambuterol(DB01408)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dipivefrin(DB00449)|Dobutamine(DB00841)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Fenoterol(DB01288)|Formoterol(DB00983)|Indacaterol(DB05039)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Orciprenaline(DB00816)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenoxybenzamine(DB00925)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Procaterol(DB01366)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Ritodrine(DB00867)|Salbutamol(DB01001)|Salmeterol(DB00938)|Sotalol(DB00489)|Terbutaline(DB00871)|Timolol(DB00373)|Trimipramine(DB00726)	TCATGGGCCTGGCAGTGGTGC	0.522													G|||	1576	0.314696	0.3404	0.2997	5008	,	,		19280	0.3641		0.1988	False		,,,				2504	0.3589				p.L84L		Atlas-SNP	.											.	ADRB2	42	.	0			c.G252A						PASS	.	G		1442,2964	468.5+/-355.1	242,958,1003	89.0	84.0	85.0		252	1.8	1.0	5	dbSNP_86	85	1702,6898	312.6+/-310.9	162,1378,2760	no	coding-synonymous	ADRB2	NM_000024.5		404,2336,3763	AA,AG,GG		19.7907,32.7281,24.1735		84/414	148206646	3144,9862	2203	4300	6503	SO:0001819	synonymous_variant	154	exon1			GGGCCTGGCAGTG	AF022953	CCDS4292.1	5q31-q32	2012-08-08	2012-05-09		ENSG00000169252	ENSG00000169252		"""GPCR / Class A : Adrenoceptors : beta"""	286	protein-coding gene	gene with protein product		109690	"""adrenergic, beta-2-, receptor, surface"""	ADRB2R			Standard	NM_000024		Approved	ADRBR, BAR, B2AR	uc003lpr.2	P07550	OTTHUMG00000129933	ENST00000305988.4:c.252G>A	5.37:g.148206646G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	147	65	0.442177	NM_000024	B0LPE4|B2R7X2|O14823|O14824|O14825|O14826|Q4JG18|Q53GA6|Q6GMT4|Q6P4D8|Q8NEQ9|Q96EC3|Q9UCZ0|Q9UCZ1|Q9UCZ2|Q9UCZ3|Q9UH95|Q9UHA1|Q9UMZ5	Silent	SNP	ENST00000305988.4	37	CCDS4292.1																																																																																			G|0.772;A|0.228	0.228	strong		0.522	ADRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252189.1	NM_000024	
PSG2	5670	hgsc.bcm.edu	37	19	43585334	43585334	+	Silent	SNP	T	T	G	rs79582550	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43585334T>G	ENST00000406487.1	-	2	227	c.129A>C	c.(127-129)ccA>ccC	p.P43P	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	43	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.P43P(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CGGAAACTTTTGGTGGCTGGG	0.488																																					p.P43P		Atlas-SNP	.											PSG2,NS,carcinoma,-1,2	PSG2	84	2	2	Substitution - coding silent(2)	lung(2)	c.A129C						scavenged	.						171.0	168.0	169.0					19																	43585334		2203	4299	6502	SO:0001819	synonymous_variant	5670	exon2			AACTTTTGGTGGC		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.129A>C	19.37:g.43585334T>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	152	13	0.0855263	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			T|0.944;G|0.056	0.056	strong		0.488	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
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 GAIIx	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		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	223	110	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	
GRK7	131890	hgsc.bcm.edu	37	3	141497150	141497150	+	Silent	SNP	C	C	T	rs1533501	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:141497150C>T	ENST00000264952.2	+	1	161	c.24C>T	c.(22-24)gaC>gaT	p.D8D		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	8					protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)|rhodopsin kinase activity (GO:0050254)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(14)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	26						GGGCCCTGGACAACCTGATCG	0.692													C|||	254	0.0507188	0.0537	0.0274	5008	,	,		16572	0.0179		0.0517	False		,,,				2504	0.0961				p.D8D		Atlas-SNP	.											.	GRK7	65	.	0			c.C24T						PASS	.	C		277,4119		7,263,1928	47.0	57.0	53.0		24	4.3	1.0	3	dbSNP_88	53	333,8267		8,317,3975	no	coding-synonymous	GRK7	NM_139209.2		15,580,5903	TT,TC,CC		3.8721,6.3012,4.6938		8/554	141497150	610,12386	2198	4300	6498	SO:0001819	synonymous_variant	131890	exon1			CCTGGACAACCTG		CCDS3120.1	3q24	2004-02-04	2004-02-04	2004-02-04	ENSG00000114124	ENSG00000114124			17031	protein-coding gene	gene with protein product		606987		GPRK7		11717351, 11754336	Standard	NM_139209		Approved		uc011bnd.2	Q8WTQ7	OTTHUMG00000159068	ENST00000264952.2:c.24C>T	3.37:g.141497150C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_139209		Silent	SNP	ENST00000264952.2	37	CCDS3120.1																																																																																			C|0.953;T|0.047	0.047	strong		0.692	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209	
TTC9C	283237	hgsc.bcm.edu	37	11	62505764	62505764	+	Silent	SNP	C	C	T	rs6675	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:62505764C>T	ENST00000316461.4	+	3	736	c.426C>T	c.(424-426)gcC>gcT	p.A142A	TTC9C_ENST00000532583.1_Silent_p.A142A	NM_173810.3	NP_776171.1	Q8N5M4	TTC9C_HUMAN	tetratricopeptide repeat domain 9C	142										breast(1)|endometrium(1)|lung(2)|ovary(1)|pancreas(1)	6						TCCAAGATGCCAACGTCCGGC	0.448													C|||	688	0.13738	0.0968	0.1542	5008	,	,		14964	0.0853		0.1938	False		,,,				2504	0.1759				p.A142A		Atlas-SNP	.											.	TTC9C	12	.	0			c.C426T						PASS	.	C		531,3873	241.2+/-251.7	33,465,1704	58.0	51.0	53.0		426	5.2	1.0	11	dbSNP_52	53	1897,6701	330.2+/-319.1	219,1459,2621	no	coding-synonymous	TTC9C	NM_173810.3		252,1924,4325	TT,TC,CC		22.0633,12.0572,18.6741		142/172	62505764	2428,10574	2202	4299	6501	SO:0001819	synonymous_variant	283237	exon3			AGATGCCAACGTC	BC032123	CCDS8033.1	11q12.3	2013-01-10			ENSG00000162222	ENSG00000162222		"""Tetratricopeptide (TTC) repeat domain containing"""	28432	protein-coding gene	gene with protein product							Standard	NM_173810		Approved	MGC29649	uc001nuy.3	Q8N5M4	OTTHUMG00000167607	ENST00000316461.4:c.426C>T	11.37:g.62505764C>T		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_173810	Q8WYY7	Silent	SNP	ENST00000316461.4	37	CCDS8033.1																																																																																			T|0.143;G|0.159;C|0.672;A|0.026	0.143	strong		0.448	TTC9C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395338.1	NM_173810	
ESX1	80712	hgsc.bcm.edu	37	X	103495552	103495552	+	Missense_Mutation	SNP	T	T	C	rs41305431	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:103495552T>C	ENST00000372588.4	-	4	661	c.578A>G	c.(577-579)aAg>aGg	p.K193R		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	193					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						TCGTTTCCACTTGGCTCTTCT	0.418													T|||	69	0.0182781	0.0015	0.0173	3775	,	,		13325	0.0		0.0507	False		,,,				2504	0.0041				p.K193R	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.A578G						PASS	.	T	ARG/LYS	47,3788		0,42,5,1590,566	134.0	115.0	121.0		578	5.0	1.0	X	dbSNP_127	121	588,6140		24,384,156,2020,1716	yes	missense	ESX1	NM_153448.3	26	24,426,161,3610,2282	CC,CT,C,TT,T		8.7396,1.2256,6.0115	benign	193/407	103495552	635,9928	2203	4300	6503	SO:0001583	missense	80712	exon4			TTCCACTTGGCTC	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.578A>G	X.37:g.103495552T>C	ENSP00000361669:p.Lys193Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	36	25	0.694444	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	44	0.02652200120554551	3	0.006097560975609756	4	0.011111111111111112	0	0.0	28	0.03783783783783784	T	16.03	3.007318	0.54361	0.012256	0.087396	ENSG00000123576	ENST00000372588	D	0.97256	-4.31	4.96	4.96	0.65561	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	.	.	.	.	T	0.59905	0.2228	N	0.16066	0.365	0.29263	P	0.871183	D	0.89917	1.0	D	0.79784	0.993	T	0.81564	-0.0875	8	0.62326	D	0.03	-40.3685	8.6024	0.33754	0.1738:0.0:0.0:0.8262	rs41305431	193	Q8N693	ESX1_HUMAN	R	193	ENSP00000361669:K193R	ENSP00000361669:K193R	K	-	2	0	ESX1	103382208	1.000000	0.71417	0.999000	0.59377	0.200000	0.23975	2.488000	0.45276	1.902000	0.55061	0.486000	0.48141	AAG	T|0.951;C|0.049	0.049	strong		0.418	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448	
VMAC	400673	hgsc.bcm.edu	37	19	5908969	5908969	+	Missense_Mutation	SNP	G	G	A	rs10404195	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5908969G>A	ENST00000339485.3	+	2	359	c.326G>A	c.(325-327)cGc>cAc	p.R109H	AC104532.2_ENST00000588891.1_Intron|AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000588776.1_5'Flank	NM_001017921.3	NP_001017921.1	Q2NL98	VMAC_HUMAN	vimentin-type intermediate filament associated coiled-coil protein	109						cytoplasm (GO:0005737)				lung(1)	1						GACATCTGCCGCCGCCGGCCA	0.721													G|||	525	0.104832	0.149	0.1311	5008	,	,		11910	0.0119		0.1302	False		,,,				2504	0.0961				p.R109H		Atlas-SNP	.											VMAC,NS,carcinoma,0,1	VMAC	5	1	0			c.G326A						scavenged	.	G	HIS/ARG	599,3805		47,505,1650	21.0	22.0	22.0		326	-0.9	0.1	19	dbSNP_119	22	1242,7356		95,1052,3152	yes	missense	VMAC	NM_001017921.3	29	142,1557,4802	AA,AG,GG		14.4452,13.6013,14.1594	benign	109/170	5908969	1841,11161	2202	4299	6501	SO:0001583	missense	400673	exon2			TCTGCCGCCGCCG	BC110802	CCDS32881.1	19p13.3	2012-04-23			ENSG00000187650	ENSG00000187650			33803	protein-coding gene	gene with protein product						14985129	Standard	NM_001017921		Approved		uc002mds.4	Q2NL98		ENST00000339485.3:c.326G>A	19.37:g.5908969G>A	ENSP00000343348:p.Arg109His	Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_001017921	B3KW55	Missense_Mutation	SNP	ENST00000339485.3	37	CCDS32881.1	236	0.10805860805860806	72	0.14634146341463414	60	0.16574585635359115	8	0.013986013986013986	96	0.1266490765171504	G	3.845	-0.033031	0.07543	0.136013	0.144452	ENSG00000187650	ENST00000339485	.	.	.	4.4	-0.847	0.10730	.	0.602001	0.15669	N	0.250469	T	0.00073	0.0002	L	0.29908	0.895	0.58432	P	5.000000000032756E-6	B	0.12630	0.006	B	0.08055	0.003	T	0.10451	-1.0629	8	0.33141	T	0.24	-4.2626	7.651	0.28348	0.4534:0.0:0.5466:0.0	rs10404195	109	Q2NL98	VMAC_HUMAN	H	109	.	ENSP00000343348:R109H	R	+	2	0	VMAC	5859969	0.010000	0.17322	0.050000	0.19076	0.091000	0.18340	0.105000	0.15333	0.032000	0.15435	-0.448000	0.05591	CGC	G|0.872;A|0.128	0.128	strong		0.721	VMAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452220.2	NM_001017921	
PPP1CC	5501	hgsc.bcm.edu	37	12	111160003	111160003	+	Silent	SNP	G	G	A	rs1973505	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:111160003G>A	ENST00000335007.5	-	6	1009	c.819C>T	c.(817-819)tgC>tgT	p.C273C	PPP1CC_ENST00000550991.1_Silent_p.C273C|PPP1CC_ENST00000340766.5_Silent_p.C273C|PPP1CC_ENST00000551676.1_3'UTR|PPP1CC_ENST00000546933.1_Silent_p.C282C	NM_002710.3	NP_002701.1	P36873	PP1G_HUMAN	protein phosphatase 1, catalytic subunit, gamma isozyme	273		Inhibition by microcystin toxin binding.			cell division (GO:0051301)|circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|glycogen metabolic process (GO:0005977)|mitotic cell cycle (GO:0000278)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|protein dephosphorylation (GO:0006470)|regulation of circadian rhythm (GO:0042752)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)|triglyceride catabolic process (GO:0019433)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|focal adhesion (GO:0005925)|kinetochore (GO:0000776)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleolus (GO:0005730)|nucleus (GO:0005634)|protein complex (GO:0043234)|PTW/PP1 phosphatase complex (GO:0072357)	metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|large_intestine(2)|lung(3)	6						CAAACTCTCCGCAATAATTGG	0.368													A|||	1176	0.234824	0.5303	0.121	5008	,	,		19020	0.0635		0.164	False		,,,				2504	0.1656				p.C273C		Atlas-SNP	.											.	PPP1CC	22	.	0			c.C819T						PASS	.	A		2158,2248	595.9+/-388.5	534,1090,579	109.0	104.0	105.0		819	4.6	1.0	12	dbSNP_92	105	1182,7418	764.6+/-407.6	84,1014,3202	no	coding-synonymous	PPP1CC	NM_002710.3		618,2104,3781	AA,AG,GG		13.7442,48.9787,25.6805		273/324	111160003	3340,9666	2203	4300	6503	SO:0001819	synonymous_variant	5501	exon6			CTCTCCGCAATAA		CCDS9150.1, CCDS58279.1	12q24.1-q24.2	2013-01-17	2010-03-05		ENSG00000186298	ENSG00000186298	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9283	protein-coding gene	gene with protein product		176914	"""protein phosphatase 1, catalytic subunit, gamma isoform"""				Standard	NM_002710		Approved	PP1C, PP1gamma	uc021rdx.1	P36873	OTTHUMG00000169531	ENST00000335007.5:c.819C>T	12.37:g.111160003G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_002710		Silent	SNP	ENST00000335007.5	37	CCDS9150.1																																																																																			G|0.770;A|0.230	0.230	strong		0.368	PPP1CC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404659.1		
SGK223	157285	hgsc.bcm.edu	37	8	8234714	8234714	+	Missense_Mutation	SNP	C	C	T	rs3896980	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:8234714C>T	ENST00000520004.1	-	3	1469	c.1205G>A	c.(1204-1206)cGg>cAg	p.R402Q	SGK223_ENST00000330777.4_Missense_Mutation_p.R402Q			Q86YV5	SG223_HUMAN		404							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TGTAGCCTCCCGGGGGTGGGC	0.642													C|||	2283	0.455871	0.3903	0.4366	5008	,	,		16058	0.6409		0.3052	False		,,,				2504	0.5225				p.R402Q	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G1205A						PASS	.	C	GLN/ARG	1363,2447		257,849,799	28.0	32.0	31.0		1205	1.0	0.0	8	dbSNP_108	31	2494,5700		391,1712,1994	yes	missense	SGK223	NM_001080826.1	43	648,2561,2793	TT,TC,CC		30.4369,35.7743,32.131	probably-damaging	402/1403	8234714	3857,8147	1905	4097	6002	SO:0001583	missense	0	exon2			GCCTCCCGGGGGT																												ENST00000520004.1:c.1205G>A	8.37:g.8234714C>T	ENSP00000428054:p.Arg402Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	961	0.440018315018315	202	0.4105691056910569	144	0.39779005524861877	392	0.6853146853146853	223	0.2941952506596306	C	8.815	0.936192	0.18206	0.357743	0.304369	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.57595	0.39;0.39	5.02	1.03	0.20045	.	0.467819	0.18850	N	0.129440	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P	0.40398	0.716	B	0.22880	0.042	T	0.45862	-0.9232	9	0.35671	T	0.21	.	0.8844	0.01241	0.1558:0.3864:0.1731:0.2847	rs3896980;rs60739349	402	Q86YV5	SG223_HUMAN	Q	402	ENSP00000330930:R402Q;ENSP00000428054:R402Q	ENSP00000330930:R402Q	R	-	2	0	AC068353.1	8272124	0.000000	0.05858	0.016000	0.15963	0.307000	0.27823	0.001000	0.13038	0.644000	0.30656	-0.136000	0.14681	CGG	C|0.612;T|0.388	0.388	strong		0.642	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
ZNF692	55657	hgsc.bcm.edu	37	1	249150116	249150116	+	Missense_Mutation	SNP	G	G	C	rs13313088	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:249150116G>C	ENST00000306601.4	-	7	855	c.689C>G	c.(688-690)cCt>cGt	p.P230R	ZNF692_ENST00000427146.1_Missense_Mutation_p.P185R|ZNF692_ENST00000468455.1_5'UTR|ZNF692_ENST00000451251.1_Missense_Mutation_p.P235R|ZNF692_ENST00000366469.5_Missense_Mutation_p.P229R|ZNF692_ENST00000366471.3_Missense_Mutation_p.P185R	NM_017865.3	NP_060335.2	Q9BU19	ZN692_HUMAN	zinc finger protein 692	230			P -> R (in dbSNP:rs13313088). {ECO:0000269|PubMed:14702039}.		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(3)|large_intestine(6)|lung(7)|stomach(1)	17	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			GACAGGGGAAGGCAGTAGTCT	0.577													G|||	1043	0.208267	0.3669	0.1513	5008	,	,		17702	0.1925		0.0457	False		,,,				2504	0.2178				p.P235R		Atlas-SNP	.											.	ZNF692	41	.	0			c.C704G						PASS	.	G	ARG/PRO,ARG/PRO,ARG/PRO	1383,3023	452.6+/-350.1	221,941,1041	46.0	48.0	47.0		704,554,689	3.6	0.0	1	dbSNP_121	47	380,8220	123.6+/-182.4	6,368,3926	yes	missense,missense,missense	ZNF692	NM_001136036.2,NM_001193328.1,NM_017865.3	103,103,103	227,1309,4967	CC,CG,GG		4.4186,31.389,13.5553	benign,benign,benign	235/525,185/475,230/520	249150116	1763,11243	2203	4300	6503	SO:0001583	missense	55657	exon7			GGGGAAGGCAGTA	BC002948	CCDS31127.1, CCDS44348.1, CCDS53487.1	1q44	2013-01-08			ENSG00000171163	ENSG00000171163		"""Zinc fingers, C2H2-type"""	26049	protein-coding gene	gene with protein product						12477932	Standard	NM_001136036		Approved	FLJ20531, Zfp692	uc001ifc.2	Q9BU19	OTTHUMG00000040423	ENST00000306601.4:c.689C>G	1.37:g.249150116G>C	ENSP00000305483:p.Pro230Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_001136036	B4DXZ0|Q5SRA5|Q5SRA6|Q9HBC9|Q9NW93|Q9NWY6|Q9UF97	Missense_Mutation	SNP	ENST00000306601.4	37	CCDS31127.1	363	0.1662087912087912	165	0.3353658536585366	55	0.15193370165745856	111	0.19405594405594406	32	0.04221635883905013	G	11.13	1.548200	0.27652	0.31389	0.044186	ENSG00000171163	ENST00000306601;ENST00000427146;ENST00000366471;ENST00000366469;ENST00000451251	T;T;T;T;T	0.08720	3.09;3.2;3.2;3.06;3.08	4.55	3.61	0.41365	.	0.254375	0.27782	N	0.017870	T	0.00012	0.0000	L	0.36672	1.1	0.40421	P	0.020151999999999948	B;B;B	0.27932	0.123;0.194;0.123	B;B;B	0.29785	0.03;0.107;0.03	T	0.50783	-0.8787	9	0.26408	T	0.33	-2.4426	10.5729	0.45211	0.0:0.1956:0.8044:0.0	rs13313088;rs52823877;rs13313088	235;185;230	B4DXZ0;Q9BU19-2;Q9BU19	.;.;ZN692_HUMAN	R	230;185;185;229;235	ENSP00000305483:P230R;ENSP00000390044:P185R;ENSP00000355427:P185R;ENSP00000355425:P229R;ENSP00000391200:P235R	ENSP00000305483:P230R	P	-	2	0	ZNF692	247116739	0.449000	0.25689	0.005000	0.12908	0.138000	0.21146	1.732000	0.38146	1.239000	0.43787	0.462000	0.41574	CCT	G|0.850;C|0.150	0.150	strong		0.577	ZNF692-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000097298.1	NM_017865	
SLITRK2	84631	hgsc.bcm.edu	37	X	144904252	144904252	+	Silent	SNP	G	G	A	rs3810704	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:144904252G>A	ENST00000370490.1	+	1	4564	c.309G>A	c.(307-309)acG>acA	p.T103T	SLITRK2_ENST00000447897.2_Silent_p.T103T|SLITRK2_ENST00000434188.2_Silent_p.T103T|SLITRK2_ENST00000413937.2_Silent_p.T103T|SLITRK2_ENST00000428560.2_Silent_p.T103T			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	103					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)					AGATCCGAACGGGGGCATTCA	0.483													G|||	592	0.156821	0.1407	0.0591	3775	,	,		14738	0.0407		0.1412	False		,,,				2504	0.1861				p.T103T		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G309A						PASS	.	G	,,,,,,,	719,3116		63,494,99,1075,472	72.0	63.0	66.0		309,309,309,309,309,309,309,309	-9.8	0.0	X	dbSNP_107	66	1124,5604		56,670,342,1702,1530	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	,,,,,,,	119,1164,441,2777,2002	AA,AG,A,GG,G		16.7063,18.7484,17.4477	,,,,,,,	103/846,103/846,103/846,103/846,103/846,103/846,103/846,103/846	144904252	1843,8720	2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			CCGAACGGGGGCA	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.309G>A	X.37:g.144904252G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	125	82	0.656	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																			G|0.836;A|0.164	0.164	strong		0.483	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
GPD1	2819	hgsc.bcm.edu	37	12	50503269	50503269	+	Silent	SNP	C	C	T	rs836180	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:50503269C>T	ENST00000301149.3	+	8	1249	c.1017C>T	c.(1015-1017)atC>atT	p.I339I	GPD1_ENST00000548814.1_Silent_p.I316I|COX14_ENST00000550487.1_5'Flank|COX14_ENST00000548985.1_5'Flank|RP4-605O3.4_ENST00000552815.1_RNA|COX14_ENST00000550654.1_5'Flank|COX14_ENST00000317943.2_5'Flank	NM_001257199.1|NM_005276.3	NP_001244128.1|NP_005267.2	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	339					cellular lipid metabolic process (GO:0044255)|cellular response to cAMP (GO:0071320)|cellular response to tumor necrosis factor (GO:0071356)|gluconeogenesis (GO:0006094)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophosphate shuttle (GO:0006127)|glycerophospholipid biosynthetic process (GO:0046474)|NADH oxidation (GO:0006116)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrion (GO:0005739)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|NAD binding (GO:0051287)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GTGAATTCATCCACTGCCTGC	0.567													C|||	1030	0.205671	0.0983	0.2968	5008	,	,		19272	0.0962		0.3956	False		,,,				2504	0.2035				p.I339I	NSCLC(141;1402 1905 9497 13391 44868)	Atlas-SNP	.											.	GPD1	23	.	0			c.C1017T						PASS	.	C		616,3790	267.4+/-267.8	44,528,1631	118.0	98.0	105.0		1017	2.1	0.4	12	dbSNP_86	105	3237,5363	487.5+/-372.1	633,1971,1696	no	coding-synonymous	GPD1	NM_005276.2		677,2499,3327	TT,TC,CC		37.6395,13.9809,29.6248		339/350	50503269	3853,9153	2203	4300	6503	SO:0001819	synonymous_variant	2819	exon8			ATTCATCCACTGC		CCDS8799.1, CCDS58229.1	12q13.12	2013-09-20			ENSG00000167588	ENSG00000167588	1.1.1.8		4455	protein-coding gene	gene with protein product		138420					Standard	NM_005276		Approved		uc001rvz.4	P21695	OTTHUMG00000169813	ENST00000301149.3:c.1017C>T	12.37:g.50503269C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	89	33	0.370787	NM_005276	F8W1L5|Q8N1B0	Silent	SNP	ENST00000301149.3	37	CCDS8799.1																																																																																			C|0.726;T|0.274	0.274	strong		0.567	GPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406018.1		
CA5A	763	hgsc.bcm.edu	37	16	87938398	87938398	+	Silent	SNP	G	G	A	rs7186698	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:87938398G>A	ENST00000309893.2	-	3	518	c.453C>T	c.(451-453)ccC>ccT	p.P151P		NM_001739.1	NP_001730.1	P35218	CAH5A_HUMAN	carbonic anhydrase VA, mitochondrial	151					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(4)|lung(8)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(80;0.0513)	Brinzolamide(DB01194)|Zonisamide(DB00909)	AAACCTCTGCGGGGTACGCGT	0.577													G|||	837	0.167133	0.0772	0.1354	5008	,	,		19267	0.1677		0.1958	False		,,,				2504	0.2812				p.P151P		Atlas-SNP	.											.	CA5A	32	.	0			c.C453T						PASS	.	G		420,3976	202.8+/-225.5	21,378,1799	100.0	90.0	93.0		453	-8.4	0.1	16	dbSNP_116	93	1751,6849	317.6+/-313.3	191,1369,2740	no	coding-synonymous	CA5A	NM_001739.1		212,1747,4539	AA,AG,GG		20.3605,9.5541,16.7051		151/306	87938398	2171,10825	2198	4300	6498	SO:0001819	synonymous_variant	763	exon3			CTCTGCGGGGTAC	L19297	CCDS10965.1	16q24.2	2012-08-21			ENSG00000174990	ENSG00000174990	4.2.1.1	"""Carbonic anhydrases"""	1377	protein-coding gene	gene with protein product		114761		CA5		8356065, 7490083	Standard	NM_001739		Approved	CAV, CAVA	uc002fkn.1	P35218	OTTHUMG00000137677	ENST00000309893.2:c.453C>T	16.37:g.87938398G>A		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	230	109	0.473913	NM_001739	B2RPF2	Silent	SNP	ENST00000309893.2	37	CCDS10965.1																																																																																			G|0.840;A|0.160	0.160	strong		0.577	CA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269164.1	NM_001739	
ZSCAN4	201516	hgsc.bcm.edu	37	19	58189287	58189287	+	Silent	SNP	C	C	T	rs9676604	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58189287C>T	ENST00000318203.5	+	4	1099	c.402C>T	c.(400-402)caC>caT	p.H134H		NM_152677.2	NP_689890.1	Q8NAM6	ZSCA4_HUMAN	zinc finger and SCAN domain containing 4	134					telomere maintenance via telomere lengthening (GO:0010833)|transcription, DNA-templated (GO:0006351)	nuclear chromosome, telomeric region (GO:0000784)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H134H(1)		endometrium(3)|large_intestine(5)|liver(2)|lung(17)|ovary(1)|skin(1)|stomach(1)	30		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TACAGGTCCACGTCCACATGC	0.443													C|||	798	0.159345	0.1664	0.134	5008	,	,		20895	0.2629		0.164	False		,,,				2504	0.0562				p.H134H		Atlas-SNP	.											ZSCAN4,NS,carcinoma,0,1	ZSCAN4	72	1	1	Substitution - coding silent(1)	stomach(1)	c.C402T						PASS	.	C		694,3712	289.5+/-280.5	48,598,1557	119.0	104.0	109.0		402	-8.0	0.0	19	dbSNP_119	109	1414,7186	272.2+/-289.9	117,1180,3003	no	coding-synonymous	ZSCAN4	NM_152677.2		165,1778,4560	TT,TC,CC		16.4419,15.7512,16.2079		134/434	58189287	2108,10898	2203	4300	6503	SO:0001819	synonymous_variant	201516	exon4			GGTCCACGTCCAC	AK092424	CCDS12958.1	19q13.43	2013-01-08	2004-11-01	2004-11-02		ENSG00000180532		"""-"", ""Zinc fingers, C2H2-type"""	23709	protein-coding gene	gene with protein product		613419	"""zinc finger protein 494"""	ZNF494			Standard	NM_152677		Approved	FLJ35105	uc002qpu.3	Q8NAM6		ENST00000318203.5:c.402C>T	19.37:g.58189287C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_152677	Q3MIQ2	Silent	SNP	ENST00000318203.5	37	CCDS12958.1																																																																																			C|0.827;T|0.173	0.173	strong		0.443	ZSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466812.1	NM_152677	
PRG4	10216	hgsc.bcm.edu	37	1	186277989	186277989	+	Silent	SNP	A	A	G	rs3737940	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186277989A>G	ENST00000445192.2	+	7	3183	c.3138A>G	c.(3136-3138)ccA>ccG	p.P1046P	PRG4_ENST00000367484.3_Silent_p.P575P|PRG4_ENST00000367485.4_Silent_p.P953P|PRG4_ENST00000367486.3_Silent_p.P1003P|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367483.4_Silent_p.P1005P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1046					cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TGAGAAAACCAAAGACGACAC	0.448													A|||	1108	0.221246	0.1142	0.402	5008	,	,		21201	0.125		0.33	False		,,,				2504	0.2249				p.P1046P		Atlas-SNP	.											.	PRG4	259	.	0			c.A3138G						PASS	.	A	,,,	658,3748	281.4+/-275.9	53,552,1598	164.0	175.0	171.0		3015,2859,2736,3138	-2.0	0.3	1	dbSNP_107	171	3044,5556	467.6+/-367.1	543,1958,1799	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRG4	NM_001127708.1,NM_001127709.1,NM_001127710.1,NM_005807.3	,,,	596,2510,3397	GG,GA,AA		35.3953,14.9342,28.4638	,,,	1005/1364,953/1312,912/1271,1046/1405	186277989	3702,9304	2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			AAAACCAAAGACG	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.3138A>G	1.37:g.186277989A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			A|0.735;G|0.265	0.265	strong		0.448	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
PLCG1	5335	hgsc.bcm.edu	37	20	39797465	39797465	+	Missense_Mutation	SNP	T	T	C	rs753381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:39797465T>C	ENST00000373271.1	+	21	2843	c.2438T>C	c.(2437-2439)aTc>aCc	p.I813T	PLCG1_ENST00000373272.2_Missense_Mutation_p.I813T|PLCG1_ENST00000244007.3_Missense_Mutation_p.I813T	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	813	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.		I -> T (in dbSNP:rs753381). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phospholipid catabolic process (GO:0009395)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cell projection (GO:0042995)|cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|protein kinase binding (GO:0019901)|receptor signaling protein activity (GO:0005057)			breast(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(16)|skin(6)|urinary_tract(2)	46		Myeloproliferative disorder(115;0.00878)				CTGACCTTCATCAAGAGCGCC	0.587													C|||	3670	0.732827	0.9818	0.6398	5008	,	,		20643	0.8075		0.5398	False		,,,				2504	0.5838				p.I813T		Atlas-SNP	.											PLCG1,NS,malignant_melanoma,-1,1	PLCG1	111	1	0			c.T2438C						scavenged	.	C	THR/ILE,THR/ILE	4043,363	185.3+/-212.5	1856,331,16	66.0	57.0	60.0		2438,2438	5.8	1.0	20	dbSNP_86	60	4662,3938	548.2+/-385.3	1272,2118,910	yes	missense,missense	PLCG1	NM_002660.2,NM_182811.1	89,89	3128,2449,926	CC,CT,TT		45.7907,8.2388,33.0694	benign,benign	813/1292,813/1291	39797465	8705,4301	2203	4300	6503	SO:0001583	missense	5335	exon21			CCTTCATCAAGAG	M34667	CCDS13313.1, CCDS13314.1	20q12-q13.1	2013-02-14	2004-01-29		ENSG00000124181	ENSG00000124181	3.1.4.11	"""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"", ""SH2 domain containing"""	9065	protein-coding gene	gene with protein product		172420	"""phospholipase C, gamma 1 (formerly subtype 148)"""	PLC1		2167438, 3254788	Standard	NM_182811		Approved	PLC148, PLC-II, PLCgamma1, NCKAP3	uc002xjo.1	P19174	OTTHUMG00000033082	ENST00000373271.1:c.2438T>C	20.37:g.39797465T>C	ENSP00000362368:p.Ile813Thr	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	149	59	0.395973	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Missense_Mutation	SNP	ENST00000373271.1	37	CCDS13314.1	1556	0.7124542124542125	478	0.9715447154471545	205	0.5662983425414365	461	0.8059440559440559	412	0.5435356200527705	C	10.38	1.335060	0.24253	0.917612	0.542093	ENSG00000124181	ENST00000244007;ENST00000373271;ENST00000373272	T;T;T	0.44881	0.91;0.91;0.91	5.82	5.82	0.92795	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);Src homology-3 domain (4);Pleckstrin homology domain (1);	0.094169	0.64402	N	0.000001	T	0.00012	0.0000	N	0.01522	-0.82	0.47341	P	6.040000000000489E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43572	-0.9383	9	0.02654	T	1	.	15.181	0.72960	0.0:0.9325:0.0:0.0675	rs753381;rs1042402;rs2228245;rs3171217;rs17179876;rs57258770;rs753381	813;813;813	P19174-2;P19174;A2A284	.;PLCG1_HUMAN;.	T	813	ENSP00000244007:I813T;ENSP00000362368:I813T;ENSP00000362369:I813T	ENSP00000244007:I813T	I	+	2	0	PLCG1	39230879	0.708000	0.27876	1.000000	0.80357	0.982000	0.71751	1.012000	0.29924	1.486000	0.48398	-0.119000	0.15052	ATC	T|0.302;C|0.698	0.698	strong		0.587	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811	
CD276	80381	hgsc.bcm.edu	37	15	74002006	74002006	+	Missense_Mutation	SNP	G	G	A	rs3825859	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:74002006G>A	ENST00000318443.5	+	8	1824	c.1522G>A	c.(1522-1524)Ggg>Agg	p.G508R	CD276_ENST00000537340.2_Missense_Mutation_p.G362R|CD276_ENST00000318424.5_Missense_Mutation_p.G290R|CD276_ENST00000561213.1_Missense_Mutation_p.G508R|CD276_ENST00000564751.1_Missense_Mutation_p.G290R	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	508					cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GGACCAGGATGGGGAGGGAGA	0.522													G|||	335	0.066893	0.0461	0.0533	5008	,	,		19630	0.1081		0.0388	False		,,,				2504	0.091				p.G508R		Atlas-SNP	.											.	CD276	29	.	0			c.G1522A						PASS	.	G	ARG/GLY,ARG/GLY	186,4210	116.7+/-154.6	7,172,2019	93.0	100.0	98.0		1522,868	4.3	1.0	15	dbSNP_107	98	390,8204	126.0+/-184.5	11,368,3918	yes	missense,missense	CD276	NM_001024736.1,NM_025240.2	125,125	18,540,5937	AA,AG,GG		4.538,4.2311,4.4342	benign,benign	508/535,290/317	74002006	576,12414	2198	4297	6495	SO:0001583	missense	80381	exon8			CAGGATGGGGAGG	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.1522G>A	15.37:g.74002006G>A	ENSP00000320084:p.Gly508Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	128	0.05860805860805861	17	0.034552845528455285	20	0.055248618784530384	59	0.10314685314685315	32	0.04221635883905013	G	15.31	2.794853	0.50102	0.042311	0.04538	ENSG00000103855	ENST00000318424;ENST00000318443;ENST00000537340	T;T;T	0.18657	2.2;2.39;2.36	4.34	4.34	0.51931	.	0.523272	0.17016	N	0.190287	T	0.00384	0.0012	N	0.14661	0.345	0.28652	N	0.906585	P;D;B;D	0.53745	0.937;0.962;0.265;0.962	B;P;B;P	0.49276	0.307;0.605;0.229;0.504	T	0.05386	-1.0888	10	0.17832	T	0.49	-5.8479	8.3574	0.32338	0.1096:0.0:0.8904:0.0	rs3825859;rs11552771;rs17358183;rs3825859	454;290;508;508	B4DK26;Q5ZPR3-2;Q5ZPR3;Q5ZPR3-4	.;.;CD276_HUMAN;.	R	290;508;362	ENSP00000320058:G290R;ENSP00000320084:G508R;ENSP00000441087:G362R	ENSP00000320058:G290R	G	+	1	0	CD276	71789059	0.983000	0.35010	1.000000	0.80357	0.975000	0.68041	2.985000	0.49362	1.954000	0.56735	0.462000	0.41574	GGG	G|0.949;A|0.051	0.051	strong		0.522	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
UBQLNL	143630	hgsc.bcm.edu	37	11	5536852	5536852	+	Missense_Mutation	SNP	A	A	G	rs2017434	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5536852A>G	ENST00000380184.1	-	1	1083	c.820T>C	c.(820-822)Tat>Cat	p.Y274H	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	274			Y -> H (in dbSNP:rs2017434). {ECO:0000269|PubMed:15489334}.					p.Y274D(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		ATATCAGCATAGTTCTGACCC	0.468													A|||	1607	0.320887	0.3472	0.3487	5008	,	,		22946	0.375		0.2644	False		,,,				2504	0.2679				p.Y274H		Atlas-SNP	.											UBQLNL,colon,carcinoma,0,1	UBQLNL	74	1	1	Substitution - Missense(1)	large_intestine(1)	c.T820C						PASS	.	A	HIS/TYR	1480,2922	475.9+/-357.4	256,968,977	94.0	87.0	90.0		820	3.9	0.0	11	dbSNP_92	90	2366,6228	394.9+/-344.9	339,1688,2270	yes	missense	UBQLNL	NM_145053.4	83	595,2656,3247	GG,GA,AA		27.5308,33.6211,29.5937	probably-damaging	274/476	5536852	3846,9150	2201	4297	6498	SO:0001583	missense	143630	exon1			CAGCATAGTTCTG	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.820T>C	11.37:g.5536852A>G	ENSP00000369531:p.Tyr274His	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Missense_Mutation	SNP	ENST00000380184.1	37	CCDS31385.1	742	0.33974358974358976	181	0.3678861788617886	112	0.30939226519337015	237	0.4143356643356643	212	0.2796833773087071	A	7.494	0.651206	0.14516	0.336211	0.275308	ENSG00000175518	ENST00000380184	T	0.59906	0.23	5.09	3.94	0.45596	.	0.465067	0.18305	N	0.145300	T	0.00012	0.0000	M	0.85373	2.75	0.80722	P	0.0	P	0.43094	0.799	B	0.43623	0.425	T	0.27123	-1.0083	9	0.72032	D	0.01	-17.5765	8.8448	0.35164	0.8102:0.1898:0.0:0.0	rs2017434;rs3802975;rs17853351;rs57070605;rs2017434	274	Q8IYU4	UBQLN_HUMAN	H	274	ENSP00000369531:Y274H	ENSP00000369531:Y274H	Y	-	1	0	UBQLNL	5493428	0.002000	0.14202	0.003000	0.11579	0.002000	0.02628	1.024000	0.30077	0.925000	0.37094	-0.313000	0.08912	TAT	A|0.689;G|0.311	0.311	strong		0.468	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
IL10RA	3587	hgsc.bcm.edu	37	11	117864047	117864047	+	Silent	SNP	A	A	G	rs2256111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:117864047A>G	ENST00000227752.3	+	4	579	c.459A>G	c.(457-459)gcA>gcG	p.A153A	IL10RA_ENST00000545409.1_Silent_p.A4A|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Silent_p.A133A	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	153					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)		TGGCCCCCGCAAATGACACAT	0.522													A|||	2588	0.516773	0.4569	0.5663	5008	,	,		19299	0.5536		0.506	False		,,,				2504	0.5358				p.A153A		Atlas-SNP	.											.	IL10RA	46	.	0			c.A459G						PASS	.	A		2059,2341	568.5+/-382.4	474,1111,615	92.0	82.0	85.0		459	3.5	0.0	11	dbSNP_100	85	4455,4137	589.5+/-392.5	1133,2189,974	no	coding-synonymous	IL10RA	NM_001558.3		1607,3300,1589	GG,GA,AA		48.1494,46.7955,49.8615		153/579	117864047	6514,6478	2200	4296	6496	SO:0001819	synonymous_variant	3587	exon4			CCCCGCAAATGAC	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.459A>G	11.37:g.117864047A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	98	81	0.826531	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	37	CCDS8388.1																																																																																			A|0.496;G|0.504	0.504	strong		0.522	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
PCDHB11	56125	hgsc.bcm.edu	37	5	140579834	140579834	+	Missense_Mutation	SNP	G	G	A	rs61743184	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140579834G>A	ENST00000354757.3	+	1	487	c.487G>A	c.(487-489)Gga>Aga	p.G163R	PCDHB11_ENST00000536699.1_Intron	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	163	Cadherin 2. {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)			TTTAGATGTAGGAATCAATGC	0.408													G|||	37	0.00738818	0.0068	0.0231	5008	,	,		19884	0.0		0.0119	False		,,,				2504	0.0				p.G163R		Atlas-SNP	.											.	PCDHB11	162	.	0			c.G487A						PASS	.	G	ARG/GLY	25,4381	30.8+/-60.4	0,25,2178	88.0	95.0	92.0		487	2.8	0.5	5	dbSNP_129	92	115,8485	61.0+/-122.8	0,115,4185	yes	missense	PCDHB11	NM_018931.2	125	0,140,6363	AA,AG,GG		1.3372,0.5674,1.0764	probably-damaging	163/798	140579834	140,12866	2203	4300	6503	SO:0001583	missense	56125	exon1			GATGTAGGAATCA	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.487G>A	5.37:g.140579834G>A	ENSP00000346802:p.Gly163Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	22	0.010073260073260074	3	0.006097560975609756	11	0.03038674033149171	0	0.0	8	0.010554089709762533	G	32	5.188961	0.94923	0.005674	0.013372	ENSG00000197479	ENST00000354757	T	0.27890	1.64	2.8	2.8	0.32819	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.43545	0.1252	H	0.97023	3.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74328	-0.3701	9	0.87932	D	0	.	13.6368	0.62227	0.0:0.0:1.0:0.0	rs61743184	163	Q9Y5F2	PCDBB_HUMAN	R	163	ENSP00000346802:G163R	ENSP00000346802:G163R	G	+	1	0	PCDHB11	140560018	1.000000	0.71417	0.516000	0.27786	0.969000	0.65631	7.385000	0.79763	1.558000	0.49541	0.467000	0.42956	GGA	G|0.988;A|0.012	0.012	strong		0.408	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
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 GAIIx	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	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	18	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	
GORAB	92344	hgsc.bcm.edu	37	1	170521376	170521376	+	Missense_Mutation	SNP	G	G	A	rs913257	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:170521376G>A	ENST00000367763.3	+	5	978	c.958G>A	c.(958-960)Gaa>Aaa	p.E320K		NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	320	Necessary for interaction with RCHY1.		E -> K (in dbSNP:rs913257). {ECO:0000269|PubMed:14702039}.			cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						ATTGCTACACGAACAAGAAGT	0.463													G|||	2968	0.592652	0.5257	0.5865	5008	,	,		20225	0.877		0.4692	False		,,,				2504	0.5215				p.E320K		Atlas-SNP	.											.	GORAB	41	.	0			c.G958A						PASS	.	G	LYS/GLU	2340,2066	607.5+/-391.0	620,1100,483	104.0	93.0	96.0		958	2.7	0.6	1	dbSNP_86	96	3979,4621	553.3+/-386.3	914,2151,1235	yes	missense	GORAB	NM_152281.2	56	1534,3251,1718	AA,AG,GG		46.2674,46.8906,48.5853	possibly-damaging	320/395	170521376	6319,6687	2203	4300	6503	SO:0001583	missense	92344	exon5			CTACACGAACAAG	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"""gerodermia osteodysplastica"""	607983	"""SCY1-like 1 binding protein 1"""	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.958G>A	1.37:g.170521376G>A	ENSP00000356737:p.Glu320Lys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_152281	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Missense_Mutation	SNP	ENST00000367763.3	37	CCDS1289.1	1334	0.6108058608058609	262	0.532520325203252	186	0.5138121546961326	518	0.9055944055944056	368	0.48548812664907653	G	12.55	1.971203	0.34754	0.531094	0.462674	ENSG00000120370	ENST00000367763	T	0.62941	-0.01	5.63	2.65	0.31530	.	0.191109	0.45606	D	0.000353	T	0.33089	0.0851	L	0.57536	1.79	0.19300	P	0.9999718336	P	0.42357	0.777	B	0.30179	0.112	T	0.18335	-1.0340	9	0.49607	T	0.09	-3.2992	9.7822	0.40656	0.0881:0.5253:0.3866:0.0	rs913257;rs52837440;rs56596330;rs59554694;rs913257	320	Q5T7V8	GORAB_HUMAN	K	320	ENSP00000356737:E320K	ENSP00000356737:E320K	E	+	1	0	GORAB	168788000	0.999000	0.42202	0.640000	0.29408	0.012000	0.07955	2.566000	0.45948	0.737000	0.32582	0.655000	0.94253	GAA	G|0.448;A|0.552	0.552	strong		0.463	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106685448	106685448	+	Silent	SNP	G	G	T	rs75385144	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:106685448G>T	ENST00000265717.4	+	1	355	c.96G>T	c.(94-96)gcG>gcT	p.A32A		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	32	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TGGAGTTCGCGCTGCAGCACT	0.701													G|||	1434	0.286342	0.0197	0.4164	5008	,	,		6544	0.3433		0.3579	False		,,,				2504	0.4223				p.A32A		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G96T						PASS	.	G		271,3937		14,243,1847	6.0	8.0	7.0		96	2.0	1.0	7	dbSNP_131	7	2493,5831		437,1619,2106	no	coding-synonymous	PRKAR2B	NM_002736.2		451,1862,3953	TT,TG,GG		29.9495,6.4401,22.0555		32/419	106685448	2764,9768	2104	4162	6266	SO:0001819	synonymous_variant	5577	exon1			GTTCGCGCTGCAG		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.96G>T	7.37:g.106685448G>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.707;T|0.293	0.293	strong		0.701	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
CPNE7	27132	hgsc.bcm.edu	37	16	89644001	89644001	+	Missense_Mutation	SNP	T	T	C	rs455527	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89644001T>C	ENST00000268720.5	+	2	359	c.229T>C	c.(229-231)Ttc>Ctc	p.F77L	CPNE7_ENST00000319518.8_Missense_Mutation_p.F77L	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	77	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.		F -> L (in dbSNP:rs455527).		lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		CTCCAAGGTCTTCACGGTGGA	0.617													T|||	466	0.0930511	0.0038	0.1441	5008	,	,		18717	0.2143		0.0785	False		,,,				2504	0.0675				p.F77L		Atlas-SNP	.											.	CPNE7	56	.	0			c.T229C						PASS	.	T	LEU/PHE,LEU/PHE	54,4312		0,54,2129	132.0	80.0	98.0		229,229	4.5	1.0	16	dbSNP_80	98	445,8125		18,409,3858	yes	missense,missense	CPNE7	NM_014427.4,NM_153636.2	22,22	18,463,5987	CC,CT,TT		5.1925,1.2368,3.8575	benign,benign	77/634,77/559	89644001	499,12437	2183	4285	6468	SO:0001583	missense	27132	exon2			AAGGTCTTCACGG	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.229T>C	16.37:g.89644001T>C	ENSP00000268720:p.Phe77Leu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	130	64	0.492308	NM_153636		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	269	0.12316849816849818	3	0.006097560975609756	53	0.1464088397790055	141	0.2465034965034965	72	0.09498680738786279	T	12.18	1.860949	0.32884	0.012368	0.051925	ENSG00000178773	ENST00000319518;ENST00000268720	T;T	0.76060	-0.99;-0.99	4.48	4.48	0.54585	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.052687	0.85682	D	0.000000	T	0.00039	0.0001	L	0.31926	0.97	0.26930	P	0.9664978	B;B	0.21606	0.058;0.012	B;B	0.25987	0.065;0.012	T	0.05599	-1.0875	9	0.41790	T	0.15	-21.3714	12.7544	0.57325	0.0:0.0:0.0:1.0	rs455527;rs58958112;rs455527	77;77	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	L	77	ENSP00000317374:F77L;ENSP00000268720:F77L	ENSP00000268720:F77L	F	+	1	0	CPNE7	88171502	1.000000	0.71417	1.000000	0.80357	0.230000	0.25150	5.789000	0.69029	1.632000	0.50472	0.459000	0.35465	TTC	T|0.915;C|0.085	0.085	strong		0.617	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
HELB	92797	hgsc.bcm.edu	37	12	66698895	66698895	+	Missense_Mutation	SNP	T	T	C	rs4430553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:66698895T>C	ENST00000247815.4	+	2	631	c.572T>C	c.(571-573)cTa>cCa	p.L191P		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	191			L -> P (in dbSNP:rs4430553). {ECO:0000269|PubMed:14702039}.		DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GAGTTGTTCCTAGACAATGAG	0.353													C|||	2495	0.498203	0.68	0.3761	5008	,	,		19279	0.3304		0.5358	False		,,,				2504	0.4734				p.L191P		Atlas-SNP	.											.	HELB	90	.	0			c.T572C						PASS	.	C	PRO/LEU	2782,1624	497.6+/-363.9	869,1044,290	70.0	67.0	68.0		572	2.0	0.0	12	dbSNP_111	68	4712,3888	540.4+/-383.8	1308,2096,896	yes	missense	HELB	NM_033647.2	98	2177,3140,1186	CC,CT,TT		45.2093,36.8588,42.3804	benign	191/1088	66698895	7494,5512	2203	4300	6503	SO:0001583	missense	92797	exon2			TGTTCCTAGACAA	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.572T>C	12.37:g.66698895T>C	ENSP00000247815:p.Leu191Pro	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	1023	0.4684065934065934	301	0.6117886178861789	142	0.39226519337016574	182	0.3181818181818182	398	0.525065963060686	C	9.200	1.028122	0.19512	0.631412	0.547907	ENSG00000127311	ENST00000247815	T	0.12984	2.63	5.07	1.97	0.26223	.	0.736219	0.11733	N	0.534734	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28713	-1.0035	8	.	.	.	0.0517	3.6302	0.08128	0.1307:0.5712:0.1352:0.163	rs4430553;rs17180588;rs52812202;rs57492101;rs4430553	191	Q8NG08	HELB_HUMAN	P	191	ENSP00000247815:L191P	.	L	+	2	0	HELB	64985162	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.143000	0.16115	0.238000	0.21222	-0.227000	0.12334	CTA	T|0.468;C|0.532	0.532	strong		0.353	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
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 GAIIx	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|ACTG1_ENST00000573283.1_Missense_Mutation_p.I64N|ACTG1_ENST00000575087.1_Missense_Mutation_p.I64N|AC139149.1_ENST00000584254.1_RNA|RP13-766D20.2_ENST00000430912.1_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	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	37	10	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	
C4orf17	84103	hgsc.bcm.edu	37	4	100443784	100443784	+	Silent	SNP	C	C	G	rs200176388|rs36110345|rs386677740|rs61732380	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:100443784C>G	ENST00000326581.4	+	3	617	c.255C>G	c.(253-255)tcC>tcG	p.S85S	C4orf17_ENST00000514652.1_Silent_p.S85S|C4orf17_ENST00000503257.1_3'UTR	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	85			S -> P (in dbSNP:rs13119384). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		GTTACCCCTCCAGCACTGCAG	0.498													C|||	1057	0.211062	0.202	0.1888	5008	,	,		16686	0.1161		0.2744	False		,,,				2504	0.272				p.S85S		Atlas-SNP	.											.	C4orf17	42	.	0			c.C255G						PASS	.	C		90,4316		28,34,2141	112.0	104.0	107.0		255	1.6	0.1	4	dbSNP_129	107	186,8414		49,88,4163	no	coding-synonymous	C4orf17	NM_032149.2		77,122,6304	GG,GC,CC		2.1628,2.0427,2.1221		85/360	100443784	276,12730	2203	4300	6503	SO:0001819	synonymous_variant	84103	exon3			CCCCTCCAGCACT	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.255C>G	4.37:g.100443784C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	Silent	SNP	ENST00000326581.4	37	CCDS3649.1																																																																																			C|0.769;G|0.231	0.231	strong		0.498	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	
ELAC2	60528	hgsc.bcm.edu	37	17	12899963	12899963	+	Silent	SNP	T	T	C	rs11545302	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:12899963T>C	ENST00000338034.4	-	17	1799	c.1560A>G	c.(1558-1560)acA>acG	p.T520T	ELAC2_ENST00000395962.2_Silent_p.T501T|ELAC2_ENST00000426905.3_Silent_p.T480T	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	520			T -> I (in COXPD17). {ECO:0000269|PubMed:23849775}.		mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						GCTGCCCAAATGTGCCCTCAC	0.592													C|||	1038	0.207268	0.2057	0.2406	5008	,	,		17696	0.0347		0.3151	False		,,,				2504	0.2526				p.T520T		Atlas-SNP	.											.	ELAC2	48	.	0			c.A1560G						PASS	.	C	,,	957,3449	733.1+/-410.4	96,765,1342	71.0	56.0	61.0		1440,1560,1557	-7.5	0.7	17	dbSNP_120	61	2553,6047	690.6+/-404.4	392,1769,2139	no	coding-synonymous,coding-synonymous,coding-synonymous	ELAC2	NM_001165962.1,NM_018127.6,NM_173717.1	,,	488,2534,3481	CC,CT,TT		29.686,21.7204,26.9875	,,	480/787,520/827,519/826	12899963	3510,9496	2203	4300	6503	SO:0001819	synonymous_variant	60528	exon17			CCCAAATGTGCCC	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"""tRNase Z (long form)"""	605367	"""elaC (E. coli) homolog 2"", ""elaC homolog 2 (E. coli)"""			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1560A>G	17.37:g.12899963T>C		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	37	CCDS11164.1																																																																																			T|0.745;C|0.255;A|0.000	0.255	strong		0.592	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		
OR2A2	442361	hgsc.bcm.edu	37	7	143807304	143807304	+	Missense_Mutation	SNP	T	T	C	rs10252253	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143807304T>C	ENST00000408979.2	+	1	698	c.629T>C	c.(628-630)cTt>cCt	p.L210P		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	210			L -> P (in dbSNP:rs10252253).			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(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4)	22	Melanoma(164;0.0783)					GTCGGGCCTCTTTCCTTGATT	0.522													.|||	802	0.160144	0.4039	0.1311	5008	,	,		20164	0.0		0.166	False		,,,				2504	0.0102				p.L210P		Atlas-SNP	.											OR2A2,colon,carcinoma,0,1	OR2A2	48	1	0			c.T629C						PASS	.	T	PRO/LEU	1470,2502		249,972,765	129.0	134.0	132.0		629	3.5	0.0	7	dbSNP_119	132	1680,6688		159,1362,2663	yes	missense	OR2A2	NM_001005480.2	98	408,2334,3428	CC,CT,TT		20.0765,37.0091,25.5267	benign	210/319	143807304	3150,9190	1986	4184	6170	SO:0001583	missense	442361	exon1			GGCCTCTTTCCTT		CCDS43671.1	7q35	2013-09-20		2004-03-10	ENSG00000221989	ENSG00000221989		"""GPCR / Class A : Olfactory receptors"""	8230	protein-coding gene	gene with protein product				OR2A2P, OR2A17P			Standard	NM_001005480		Approved	OST008	uc011ktz.2	Q6IF42	OTTHUMG00000158001	ENST00000408979.2:c.629T>C	7.37:g.143807304T>C	ENSP00000386209:p.Leu210Pro	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_001005480	B2RN85|Q8NGT6	Missense_Mutation	SNP	ENST00000408979.2	37	CCDS43671.1	372	0.17032967032967034	200	0.4065040650406504	52	0.143646408839779	0	0.0	120	0.158311345646438	T	9.379	1.072517	0.20147	0.370091	0.200765	ENSG00000221989	ENST00000408979	T	0.49432	0.78	3.47	3.47	0.39725	GPCR, rhodopsin-like superfamily (1);	0.293273	0.18405	U	0.142236	T	0.00012	0.0000	M	0.87900	2.915	0.38232	P	0.05894100000000002	B	0.31383	0.321	B	0.43728	0.429	T	0.40496	-0.9560	9	0.59425	D	0.04	-12.3573	10.1929	0.43037	0.0:0.0:0.0:1.0	rs10252253;rs59481350;rs10252253	210	Q6IF42	OR2A2_HUMAN	P	210	ENSP00000386209:L210P	ENSP00000386209:L210P	L	+	2	0	OR2A2	143438237	0.001000	0.12720	0.044000	0.18714	0.012000	0.07955	1.019000	0.30014	1.576000	0.49790	0.418000	0.28097	CTT	T|0.806;C|0.194	0.194	strong		0.522	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1		
CEP192	55125	hgsc.bcm.edu	37	18	13068132	13068132	+	Missense_Mutation	SNP	T	T	C	rs578208	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:13068132T>C	ENST00000325971.8	+	21	4459	c.2866T>C	c.(2866-2868)Tcc>Ccc	p.S956P	CEP192_ENST00000506447.1_Missense_Mutation_p.S1552P|CEP192_ENST00000430049.2_Missense_Mutation_p.S1077P			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	956			S -> P (in dbSNP:rs578208). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12693554, ECO:0000269|PubMed:15498874}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TTCCAAGGAATCCGTCCGAGC	0.488													C|||	3742	0.747204	0.8669	0.6354	5008	,	,		17132	0.8105		0.6203	False		,,,				2504	0.7301				p.S1552P		Atlas-SNP	.											.	CEP192	340	.	0			c.T4654C						PASS	.	C	PRO/SER	3568,838	328.0+/-300.3	1451,666,86	97.0	103.0	101.0		4654	5.4	0.8	18	dbSNP_83	101	5325,3275	489.6+/-372.6	1662,2001,637	yes	missense	CEP192	NM_032142.3	74	3113,2667,723	CC,CT,TT		38.0814,19.0195,31.6239	benign	1552/2538	13068132	8893,4113	2203	4300	6503	SO:0001583	missense	55125	exon23			AAGGAATCCGTCC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.2866T>C	18.37:g.13068132T>C	ENSP00000317156:p.Ser956Pro	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1607	0.7358058608058609	435	0.8841463414634146	236	0.6519337016574586	464	0.8111888111888111	472	0.6226912928759895	C	6.879	0.531696	0.13127	0.809805	0.619186	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.24350	1.86;1.86;1.86	5.37	5.37	0.77165	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00082	-2.215	0.42656	P	0.006533000000000011	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39354	-0.9618	9	0.02654	T	1	-8.0771	14.6427	0.68737	0.0:0.9298:0.0:0.0702	rs578208;rs1787012;rs17660892;rs52836713;rs60741171;rs578208	1077;1552	C9JT09;E9PF99	.;.	P	1552;956;956;1077	ENSP00000427550:S1552P;ENSP00000317156:S956P;ENSP00000389190:S1077P	ENSP00000317156:S956P	S	+	1	0	CEP192	13058132	1.000000	0.71417	0.796000	0.32109	0.247000	0.25773	4.296000	0.59055	1.415000	0.47037	-0.119000	0.15052	TCC	A|0.001;C|0.718	0.718	strong		0.488	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
THRAP3	9967	hgsc.bcm.edu	37	1	36752152	36752152	+	Silent	SNP	C	C	T	rs2242428	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:36752152C>T	ENST00000354618.5	+	4	545	c.321C>T	c.(319-321)taC>taT	p.Y107Y	THRAP3_ENST00000469141.2_Silent_p.Y107Y	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	107	Arg-rich.|Required for mRNA splicing activation.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.Y107Y(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				ATGGAAACTACCGCTCAAATT	0.522			T	USP6	aneurysmal bone cysts								C|||	1240	0.247604	0.1036	0.2219	5008	,	,		17948	0.0754		0.4205	False		,,,				2504	0.4601				p.Y107Y	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	THRAP3,NS,carcinoma,+1,2	THRAP3	93	2	1	Substitution - coding silent(1)	stomach(1)	c.C321T						PASS	.	C		615,3791	268.3+/-268.4	54,507,1642	116.0	117.0	116.0		321	3.9	1.0	1	dbSNP_98	116	3300,5300	493.9+/-373.7	624,2052,1624	no	coding-synonymous	THRAP3	NM_005119.3		678,2559,3266	TT,TC,CC		38.3721,13.9582,30.1015		107/956	36752152	3915,9091	2203	4300	6503	SO:0001819	synonymous_variant	9967	exon4			AAACTACCGCTCA	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.321C>T	1.37:g.36752152C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_005119	D3DPS5|Q5VTK6	Silent	SNP	ENST00000354618.5	37	CCDS405.1																																																																																			C|0.710;T|0.290	0.290	strong		0.522	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119	
PITRM1	10531	hgsc.bcm.edu	37	10	3214942	3214942	+	Missense_Mutation	SNP	T	T	C	rs11818724	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:3214942T>C	ENST00000224949.4	-	1	57	c.23A>G	c.(22-24)cAg>cGg	p.Q8R	PITRM1_ENST00000380989.2_Missense_Mutation_p.Q8R|PITRM1_ENST00000451104.2_Silent_p.A10A			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	8			Q -> R (in dbSNP:rs11818724). {ECO:0000269|PubMed:15489334}.		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						ACACAGGCCCTGCCGCCCGCC	0.746													T|||	247	0.0493211	0.0416	0.0793	5008	,	,		8780	0.0		0.1004	False		,,,				2504	0.0368				p.Q8R		Atlas-SNP	.											.	PITRM1	109	.	0			c.A23G						PASS	.	T	ARG/GLN,,ARG/GLN	69,3643		2,65,1789	4.0	7.0	6.0		23,30,23	-5.3	0.0	10	dbSNP_120	6	355,7157		7,341,3408	no	missense,coding-synonymous,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	43,,43	9,406,5197	CC,CT,TT		4.7258,1.8588,3.7776	benign,,benign	8/1039,10/940,8/1038	3214942	424,10800	1856	3756	5612	SO:0001583	missense	10531	exon1			AGGCCCTGCCGCC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.23A>G	10.37:g.3214942T>C	ENSP00000224949:p.Gln8Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	26	8	0.307692	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	133	0.060897435897435896	13	0.026422764227642278	36	0.09944751381215469	6	0.01048951048951049	78	0.10290237467018469	T	2.957	-0.215562	0.06101	0.018588	0.047258	ENSG00000107959	ENST00000224949;ENST00000380989	T;T	0.03635	3.86;3.86	2.65	-5.29	0.02747	.	1.236170	0.05795	N	0.611110	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48514	-0.9029	8	0.11485	T	0.65	.	5.5752	0.17218	0.0:0.5019:0.2589:0.2392	rs11818724;rs17356065	8;8	Q5JRX3-2;Q5JRX3	.;PREP_HUMAN	R	8	ENSP00000224949:Q8R;ENSP00000370377:Q8R	ENSP00000224949:Q8R	Q	-	2	0	PITRM1	3204942	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.684000	0.05173	-1.341000	0.02225	-2.324000	0.00251	CAG	T|0.938;C|0.062	0.062	strong		0.746	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
XYLT1	64131	hgsc.bcm.edu	37	16	17202801	17202801	+	Silent	SNP	G	G	A	rs34511974	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:17202801G>A	ENST00000261381.6	-	12	2715	c.2631C>T	c.(2629-2631)ccC>ccT	p.P877P		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	877					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGCTGAGGACGGGGTTTAGGC	0.617													G|||	514	0.102636	0.0045	0.2478	5008	,	,		18519	0.002		0.1491	False		,,,				2504	0.1881				p.P877P		Atlas-SNP	.											XYLT1,colon,carcinoma,0,1	XYLT1	147	1	0			c.C2631T						PASS	.	G		154,4240	105.6+/-144.1	3,148,2046	100.0	100.0	100.0		2631	-11.6	0.1	16	dbSNP_126	100	1342,7258	261.9+/-284.1	96,1150,3054	no	coding-synonymous	XYLT1	NM_022166.3		99,1298,5100	AA,AG,GG		15.6047,3.5048,11.513		877/960	17202801	1496,11498	2197	4300	6497	SO:0001819	synonymous_variant	64131	exon12			GAGGACGGGGTTT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.2631C>T	16.37:g.17202801G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	114	58	0.508772	NM_022166	Q9H1B6	Silent	SNP	ENST00000261381.6	37	CCDS10569.1																																																																																			G|0.888;A|0.112	0.112	strong		0.617	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
FYCO1	79443	hgsc.bcm.edu	37	3	46007823	46007823	+	Missense_Mutation	SNP	G	G	T	rs13079478|rs71622515|rs199842602	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46007823G>T	ENST00000296137.2	-	8	3208	c.3003C>A	c.(3001-3003)aaC>aaA	p.N1001K	FYCO1_ENST00000535325.1_Missense_Mutation_p.N1001K	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1001			N -> D (in dbSNP:rs13059238).		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)		ACTTGAGGGTGTTGAGCTCCT	0.612													G|||	527	0.105232	0.0053	0.0591	5008	,	,		19406	0.004		0.1223	False		,,,				2504	0.3599				p.N1001K		Atlas-SNP	.											.	FYCO1	115	.	0			c.C3003A						PASS	.	G	LYS/ASN	0,4406		0,0,2203	97.0	84.0	89.0		3003	1.4	0.3	3	dbSNP_121	89	12,8588		1,10,4289	yes	missense	FYCO1	NM_024513.2	94	1,10,6492	TT,TG,GG		0.1395,0.0,0.0923	benign	1001/1479	46007823	12,12994	2203	4300	6503	SO:0001583	missense	79443	exon8			GAGGGTGTTGAGC	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.3003C>A	3.37:g.46007823G>T	ENSP00000296137:p.Asn1001Lys	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	158	64	0.405063	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	129	0.059065934065934064	3	0.006097560975609756	19	0.052486187845303865	0	0.0	107	0.14116094986807387	G	9.521	1.108394	0.20714	0.0	0.001395	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.79940	-1.32;-1.32	5.49	1.44	0.22558	.	0.437095	0.25572	N	0.029755	T	0.00580	0.0019	N	0.14661	0.345	0.80722	P	0.0	B;B	0.15719	0.014;0.008	B;B	0.15484	0.013;0.008	T	0.03534	-1.1027	9	0.06891	T	0.86	-17.5834	3.5326	0.07782	0.4252:0.0:0.4016:0.1732	rs13079478	1001;1001	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	K	1001	ENSP00000296137:N1001K;ENSP00000441178:N1001K	ENSP00000296137:N1001K	N	-	3	2	FYCO1	45982827	0.033000	0.19621	0.300000	0.25030	0.997000	0.91878	0.297000	0.19101	0.281000	0.22233	0.655000	0.94253	AAC	GTT|0.500;TTC|0.500	.	alt		0.612	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
EXO1	9156	hgsc.bcm.edu	37	1	242030151	242030151	+	Missense_Mutation	SNP	A	A	G	rs735943	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:242030151A>G	ENST00000366548.3	+	11	1654	c.1061A>G	c.(1060-1062)cAt>cGt	p.H354R	EXO1_ENST00000348581.5_Missense_Mutation_p.H354R|EXO1_ENST00000518483.1_Missense_Mutation_p.H354R	NM_130398.3	NP_569082.2	Q9UQ84	EXO1_HUMAN	exonuclease 1	354	Interaction with MSH3.		H -> R (in dbSNP:rs735943). {ECO:0000269|PubMed:10364235, ECO:0000269|PubMed:9685493, ECO:0000269|PubMed:9788596, ECO:0000269|PubMed:9823303, ECO:0000269|Ref.5}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	5'-3' exodeoxyribonuclease activity (GO:0035312)|5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|double-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0051908)|exonuclease activity (GO:0004527)|flap endonuclease activity (GO:0048256)|metal ion binding (GO:0046872)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)|structure-specific DNA binding (GO:0043566)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(3)|lung(29)|ovary(2)|skin(1)|stomach(2)|urinary_tract(2)	45	Ovarian(103;0.103)	all_cancers(173;0.0555)	OV - Ovarian serous cystadenocarcinoma(106;0.0107)			TCAAGAAGTCATAGTTGGGAT	0.358								Editing and processing nucleases					G|||	3190	0.636981	0.615	0.6902	5008	,	,		18299	0.7956		0.5716	False		,,,				2504	0.5327				p.H354R		Atlas-SNP	.											.	EXO1	103	.	0			c.A1061G						PASS	.	G	ARG/HIS,ARG/HIS,ARG/HIS	2739,1667	506.6+/-366.4	838,1063,302	107.0	101.0	103.0		1061,1061,1061	-0.8	0.8	1	dbSNP_86	103	4641,3959	550.5+/-385.8	1275,2091,934	yes	missense,missense,missense	EXO1	NM_003686.4,NM_006027.4,NM_130398.3	29,29,29	2113,3154,1236	GG,GA,AA		46.0349,37.8348,43.257	benign,benign,benign	354/804,354/847,354/847	242030151	7380,5626	2203	4300	6503	SO:0001583	missense	9156	exon9			GAAGTCATAGTTG	AF042282	CCDS1620.1, CCDS44336.1	1q42-q43	2008-07-18			ENSG00000174371	ENSG00000174371			3511	protein-coding gene	gene with protein product	"""rad2 nuclease family member, homolog of S. cerevisiae exonuclease 1"""	606063				9685493, 9788596	Standard	NM_003686		Approved	HEX1, hExoI	uc001hzh.3	Q9UQ84	OTTHUMG00000039965	ENST00000366548.3:c.1061A>G	1.37:g.242030151A>G	ENSP00000355506:p.His354Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_006027	O60545|O75214|O75466|Q5T396|Q96IJ1|Q9UG38|Q9UNW0	Missense_Mutation	SNP	ENST00000366548.3	37	CCDS1620.1	1423	0.6515567765567766	294	0.5975609756097561	244	0.6740331491712708	448	0.7832167832167832	437	0.5765171503957783	G	0.007	-1.936856	0.00484	0.621652	0.539651	ENSG00000174371	ENST00000366548;ENST00000348581;ENST00000518483	T;T;T	0.34667	1.41;1.41;1.35	5.75	-0.821	0.10822	-3&apos (1); exonuclease, C-terminal domain (1);5&apos (1);	0.693627	0.15870	N	0.240566	T	0.00012	0.0000	L	0.32530	0.975	0.49798	P	1.7699999999998273E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.32666	-0.9898	9	0.12430	T	0.62	-1.583	11.7251	0.51704	0.5927:0.0:0.4073:0.0	rs735943;rs17391620;rs52795383;rs59790129;rs735943	354;354	Q9UQ84-4;Q9UQ84	.;EXO1_HUMAN	R	354	ENSP00000355506:H354R;ENSP00000311873:H354R;ENSP00000430251:H354R	ENSP00000311873:H354R	H	+	2	0	EXO1	240096774	0.989000	0.36119	0.815000	0.32552	0.291000	0.27294	0.382000	0.20635	-0.369000	0.08028	-1.088000	0.02184	CAT	T|0.001;G|0.609	0.609	strong		0.358	EXO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096405.1	NM_006027	
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 GAIIx	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	EPB41L4A_ENST00000507810.1_5'UTR|CTC-459M5.2_ENST00000515563.1_RNA|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		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	77	37	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		
WDFY4	57705	hgsc.bcm.edu	37	10	49998824	49998824	+	Silent	SNP	C	C	T	rs10857644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:49998824C>T	ENST00000325239.5	+	22	4146	c.4119C>T	c.(4117-4119)ggC>ggT	p.G1373G	WDFY4_ENST00000413659.2_Intron	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1373						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						ACTTCATTGGCGGGCCTGCCA	0.547													C|||	849	0.169529	0.3147	0.0922	5008	,	,		21863	0.1577		0.0924	False		,,,				2504	0.1196				p.G1373G		Atlas-SNP	.											WDFY4,colon,carcinoma,0,1	WDFY4	205	1	0			c.C4119T						PASS	.						72.0	62.0	65.0					10																	49998824		692	1591	2283	SO:0001819	synonymous_variant	57705	exon23			CATTGGCGGGCCT	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.4119C>T	10.37:g.49998824C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	142	79	0.556338	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	364	0.16666666666666666	153	0.31097560975609756	40	0.11049723756906077	95	0.1660839160839161	76	0.10026385224274406	C	9.198	1.027641	0.19512	.	.	ENSG00000128815	ENST00000312002	.	.	.	5.18	-8.28	0.01013	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999985119	.	.	.	.	.	.	T	0.20605	-1.0270	3	.	.	.	.	7.56	0.27845	0.275:0.1759:0.0:0.5492	rs10857644;rs56445870;rs10857644	.	.	.	W	464	.	.	R	+	1	2	WDFY4	49668830	0.000000	0.05858	0.272000	0.24630	0.996000	0.88848	-2.359000	0.01085	-1.729000	0.01364	0.557000	0.71058	CGG	C|0.834;T|0.166	0.166	strong		0.547	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
CCT6B	10693	hgsc.bcm.edu	37	17	33269648	33269648	+	Missense_Mutation	SNP	C	C	G	rs2230553	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33269648C>G	ENST00000314144.5	-	7	855	c.740G>C	c.(739-741)gGt>gCt	p.G247A	CCT6B_ENST00000436961.3_Missense_Mutation_p.G202A|CCT6B_ENST00000421975.3_Missense_Mutation_p.G210A	NM_006584.3	NP_006575.2	Q92526	TCPW_HUMAN	chaperonin containing TCP1, subunit 6B (zeta 2)	247			G -> A (in dbSNP:rs2230553). {ECO:0000269|PubMed:8812458}.		chaperone-mediated protein complex assembly (GO:0051131)|protein folding (GO:0006457)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)	chaperonin-containing T-complex (GO:0005832)	ATP binding (GO:0005524)|protein transporter activity (GO:0008565)|unfolded protein binding (GO:0051082)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)	20		Ovarian(249;0.17)				ATAAAAGAAACCAGAGTTCAC	0.328													C|||	1218	0.243211	0.149	0.1859	5008	,	,		14931	0.2639		0.3728	False		,,,				2504	0.2566				p.G247A		Atlas-SNP	.											.	CCT6B	63	.	0			c.G740C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	765,3635	276.0+/-272.9	73,619,1508	48.0	47.0	48.0		629,605,740	4.1	1.0	17	dbSNP_98	48	3152,5434	452.4+/-362.9	585,1982,1726	yes	missense,missense,missense	CCT6B	NM_001193529.1,NM_001193530.1,NM_006584.3	60,60,60	658,2601,3234	GG,GC,CC		36.7109,17.3864,30.1633	possibly-damaging,possibly-damaging,possibly-damaging	210/494,202/486,247/531	33269648	3917,9069	2200	4293	6493	SO:0001583	missense	10693	exon7			AAGAAACCAGAGT	D78333	CCDS32617.1, CCDS54105.1, CCDS54106.1	17q	2011-09-02			ENSG00000132141	ENSG00000132141		"""Heat Shock Proteins / Chaperonins"""	1621	protein-coding gene	gene with protein product		610730				8812458, 9013858	Standard	NM_006584		Approved	Cctz2, TSA303	uc002hig.3	Q92526		ENST00000314144.5:c.740G>C	17.37:g.33269648C>G	ENSP00000327191:p.Gly247Ala	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_006584	B4DX20|B4DYB0|Q8TC34	Missense_Mutation	SNP	ENST00000314144.5	37	CCDS32617.1	582	0.2664835164835165	87	0.17682926829268292	75	0.20718232044198895	131	0.229020979020979	289	0.3812664907651715	C	16.88	3.244978	0.59103	0.173864	0.367109	ENSG00000132141	ENST00000421975;ENST00000314144;ENST00000436961	T;T;T	0.67523	-0.27;-0.27;-0.27	4.06	4.06	0.47325	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.91920	3.255	0.09310	P	0.9999999860995	B;B;P	0.37233	0.155;0.248;0.588	B;B;P	0.44696	0.276;0.303;0.458	T	0.08006	-1.0743	9	0.62326	D	0.03	-9.8571	14.0935	0.65006	0.0:1.0:0.0:0.0	rs2230553;rs16970466;rs52825862;rs2230553	202;210;247	B4DYB0;B4DX20;Q92526	.;.;TCPW_HUMAN	A	210;247;202	ENSP00000398044:G210A;ENSP00000327191:G247A;ENSP00000400917:G202A	ENSP00000327191:G247A	G	-	2	0	CCT6B	30293761	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	7.019000	0.76412	2.220000	0.72140	0.591000	0.81541	GGT	C|0.717;G|0.283	0.283	strong		0.328	CCT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448014.1	NM_006584	
TMIGD2	126259	hgsc.bcm.edu	37	19	4294807	4294807	+	Missense_Mutation	SNP	G	G	A	rs78320454	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4294807G>A	ENST00000301272.2	-	3	458	c.413C>T	c.(412-414)cCc>cTc	p.P138L	TMIGD2_ENST00000600114.1_Missense_Mutation_p.P18L|TMIGD2_ENST00000595645.1_Missense_Mutation_p.P138L|TMIGD2_ENST00000600349.1_Intron	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	138					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		GTTCTGTGTGGGGTCATCTGC	0.602													G|||	555	0.110823	0.0068	0.1513	5008	,	,		15935	0.0754		0.1561	False		,,,				2504	0.2127				p.P138L		Atlas-SNP	.											.	TMIGD2	38	.	0			c.C413T						PASS	.	G	LEU/PRO,LEU/PRO	149,4257	100.7+/-139.4	6,137,2060	107.0	105.0	106.0		413,413	-5.0	0.0	19	dbSNP_131	106	1350,7250	262.1+/-284.2	113,1124,3063	yes	missense,missense	TMIGD2	NM_001169126.1,NM_144615.2	98,98	119,1261,5123	AA,AG,GG		15.6977,3.3818,11.5254	probably-damaging,probably-damaging	138/279,138/283	4294807	1499,11507	2203	4300	6503	SO:0001583	missense	126259	exon3			TGTGTGGGGTCAT	BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.413C>T	19.37:g.4294807G>A	ENSP00000301272:p.Pro138Leu	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_144615	Q6UW59	Missense_Mutation	SNP	ENST00000301272.2	37	CCDS12126.1	227	0.10393772893772894	5	0.01016260162601626	57	0.1574585635359116	58	0.10139860139860139	107	0.14116094986807387	G	5.801	0.332096	0.10956	0.033818	0.156977	ENSG00000167664	ENST00000301272	T	0.28255	1.62	2.49	-4.98	0.03019	.	.	.	.	.	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B;B	0.18968	0.032;0.019	B;B	0.16289	0.015;0.007	T	0.30851	-0.9964	8	0.33141	T	0.24	.	0.9883	0.01451	0.2356:0.3097:0.2959:0.1588	.	138;138	Q96BF3-2;Q96BF3	.;TMIG2_HUMAN	L	138	ENSP00000301272:P138L	ENSP00000301272:P138L	P	-	2	0	TMIGD2	4245807	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-0.461000	0.06712	-1.024000	0.03338	0.549000	0.68633	CCC	G|0.889;A|0.111	0.111	strong		0.602	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615	
SPHK1	8877	hgsc.bcm.edu	37	17	74383475	74383475	+	Silent	SNP	T	T	C	rs3744037	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74383475T>C	ENST00000545180.1	+	8	1772	c.963T>C	c.(961-963)taT>taC	p.Y321Y	SPHK1_ENST00000323374.4_Silent_p.Y407Y|SPHK1_ENST00000592299.1_Silent_p.Y321Y|SPHK1_ENST00000590959.1_Silent_p.Y335Y|SPHK1_ENST00000392496.3_Silent_p.Y321Y			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	321					'de novo' posttranslational protein folding (GO:0051084)|blood vessel development (GO:0001568)|brain development (GO:0007420)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|female pregnancy (GO:0007565)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of neuron projection development (GO:0010976)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of smooth muscle contraction (GO:0045987)|protein folding (GO:0006457)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of interleukin-1 beta production (GO:0032651)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|response to amine (GO:0014075)|response to ATP (GO:0033198)|response to interleukin-1 (GO:0070555)|response to magnesium ion (GO:0032026)|response to progesterone (GO:0032570)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingoid catabolic process (GO:0046521)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|NAD+ kinase activity (GO:0003951)|protein phosphatase 2A binding (GO:0051721)|sphinganine kinase activity (GO:0008481)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)	11					Fingolimod(DB08868)	ACTTGGTATATGTGCCCGTGG	0.597													T|||	1073	0.214257	0.2057	0.1715	5008	,	,		20914	0.4028		0.1392	False		,,,				2504	0.1391				p.Y407Y	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.T1221C						PASS	.	T	,,,	932,3474	352.3+/-311.7	92,748,1363	88.0	80.0	83.0		963,963,1005,1221	-8.2	0.0	17	dbSNP_107	83	1416,7184	272.7+/-290.2	104,1208,2988	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK1	NM_001142601.1,NM_001142602.1,NM_021972.3,NM_182965.2	,,,	196,1956,4351	CC,CT,TT		16.4651,21.153,18.0532	,,,	321/385,321/385,335/399,407/471	74383475	2348,10658	2203	4300	6503	SO:0001819	synonymous_variant	8877	exon6			GGTATATGTGCCC	BC030553	CCDS11744.1, CCDS45785.1, CCDS59297.1	17q25.2	2004-02-18				ENSG00000176170			11240	protein-coding gene	gene with protein product		603730				9726979	Standard	NM_182965		Approved	SPHK	uc002jrj.2	Q9NYA1		ENST00000545180.1:c.963T>C	17.37:g.74383475T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Silent	SNP	ENST00000545180.1	37	CCDS45785.1																																																																																			T|0.796;C|0.204	0.204	strong		0.597	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
FXYD4	53828	hgsc.bcm.edu	37	10	43869097	43869097	+	5'UTR	SNP	C	C	A	rs10899795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:43869097C>A	ENST00000476166.1	+	0	237				FXYD4_ENST00000480834.1_Intron	NM_173160.2	NP_775183.1	P59646	FXYD4_HUMAN	FXYD domain containing ion transport regulator 4						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ion channel activity (GO:0005216)			NS(1)|large_intestine(1)|lung(3)	5						TGCCTCCTCTCGCTGACCAAT	0.612													A|||	1900	0.379393	0.5492	0.255	5008	,	,		16681	0.4256		0.2197	False		,,,				2504	0.3548				.	GBM(173;880 2047 13035 42390 49655)	Atlas-SNP	.											.	FXYD4	9	.	0			.						PASS	.																																			SO:0001623	5_prime_UTR_variant	53828	.			TCCTCTCGCTGAC		CCDS7203.1	10q11.21	2008-02-01	2002-01-14		ENSG00000150201	ENSG00000150201			4028	protein-coding gene	gene with protein product			"""FXYD domain-containing ion transport regulator 4"""			10950925, 12763854	Standard	NM_001184963		Approved	CHIF	uc001jaq.1	P59646	OTTHUMG00000018027	ENST00000476166.1:c.-98C>A	10.37:g.43869097C>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	25	14	0.56	.	Q6UWZ1|Q7Z4M5	Splice_Site	SNP	ENST00000476166.1	37	CCDS7203.1																																																																																			C|0.603;A|0.397	0.397	strong		0.612	FXYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047698.2	NM_173160	
KEAP1	9817	hgsc.bcm.edu	37	19	10600442	10600442	+	Silent	SNP	G	G	C	rs1048290	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10600442G>C	ENST00000171111.5	-	4	1960	c.1413C>G	c.(1411-1413)ctC>ctG	p.L471L	CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Silent_p.L471L	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	471					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)		p.L471L(1)		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)	CGGCATAAAGGAGACGATTGA	0.562													C|||	2545	0.508187	0.7534	0.2983	5008	,	,		14922	0.5337		0.3549	False		,,,				2504	0.4571				p.L471L		Atlas-SNP	.											KEAP1,NS,carcinoma,0,1	KEAP1	182	1	1	Substitution - coding silent(1)	stomach(1)	c.C1413G						PASS	.	C	,	3017,1389	455.9+/-351.1	1037,943,223	77.0	63.0	68.0		1413,1413	0.6	1.0	19	dbSNP_86	68	3200,5400	653.2+/-401.0	612,1976,1712	no	coding-synonymous,coding-synonymous	KEAP1	NM_012289.3,NM_203500.1	,	1649,2919,1935	CC,CG,GG		37.2093,31.5252,47.801	,	471/625,471/625	10600442	6217,6789	2203	4300	6503	SO:0001819	synonymous_variant	9817	exon4			ATAAAGGAGACGA	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.1413C>G	19.37:g.10600442G>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Silent	SNP	ENST00000171111.5	37	CCDS12239.1																																																																																			G|0.511;C|0.489	0.489	strong		0.562	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
KANSL1	284058	hgsc.bcm.edu	37	17	44248837	44248837	+	Missense_Mutation	SNP	T	T	C	rs553586616	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44248837T>C	ENST00000262419.6	-	2	1143	c.673A>G	c.(673-675)Aat>Gat	p.N225D	KANSL1_ENST00000575318.1_Missense_Mutation_p.N225D|KANSL1_ENST00000432791.1_Missense_Mutation_p.N225D|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000574590.1_Missense_Mutation_p.N225D|KANSL1_ENST00000572904.1_Missense_Mutation_p.N225D|KANSL1_ENST00000576248.1_5'Flank	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	225			N -> D (in dbSNP:rs35643216).		chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GTGCTATTATTGCTATACAAA	0.443													T|||	364	0.0726837	0.0113	0.1398	5008	,	,		24410	0.001		0.1998	False		,,,				2504	0.0511				p.N225D		Atlas-SNP	.											.	.	.	.	0			c.A673G						PASS	.	T	ASP/ASN,ASP/ASN,ASP/ASN	167,4239		0,167,2036	132.0	164.0	154.0		673,673,673	5.0	1.0	17	dbSNP_126	154	1565,7035		0,1565,2735	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	23,23,23	0,1732,4771	CC,CT,TT		18.1977,3.7903,13.3169	benign,benign,benign	225/1105,225/1106,225/1106	44248837	1732,11274	2203	4300	6503	SO:0001583	missense	284058	exon2			TATTATTGCTATA	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.673A>G	17.37:g.44248837T>C	ENSP00000262419:p.Asn225Asp	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	315	164	0.520635	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	215	0.09844322344322344	10	0.02032520325203252	58	0.16022099447513813	1	0.0017482517482517483	146	0.19261213720316622	T	12.33	1.907105	0.33628	0.037903	0.181977	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.10668	2.85;2.85	6.04	4.97	0.65823	.	0.224065	0.47455	D	0.000233	T	0.00012	0.0000	N	0.12182	0.205	0.80722	D	1	B;B	0.33637	0.011;0.42	B;B	0.31337	0.007;0.128	T	0.61222	-0.7106	10	0.44086	T	0.13	-16.177	9.254	0.37573	0.0:0.0809:0.0:0.9191	rs35643216	225;225	C9JHY2;Q7Z3B3	.;K1267_HUMAN	D	225	ENSP00000262419:N225D;ENSP00000387393:N225D	ENSP00000262419:N225D	N	-	1	0	KIAA1267	41604614	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.265000	0.51561	2.317000	0.78254	0.459000	0.35465	AAT	T|0.857;C|0.143	0.143	strong		0.443	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
MRO	83876	hgsc.bcm.edu	37	18	48333203	48333203	+	Missense_Mutation	SNP	C	C	G	rs4940019	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:48333203C>G	ENST00000428869.2	-	5	375	c.117G>C	c.(115-117)agG>agC	p.R39S	MRO_ENST00000436348.2_Missense_Mutation_p.R53S|MRO_ENST00000431965.2_Missense_Mutation_p.R53S|MRO_ENST00000588444.1_Missense_Mutation_p.R39S|MRO_ENST00000587291.1_Intron|MRO_ENST00000256425.2_Missense_Mutation_p.R39S|MRO_ENST00000398439.3_Missense_Mutation_p.R39S			Q9BYG7	MSTRO_HUMAN	maestro	39			R -> S (in dbSNP:rs4940019). {ECO:0000269|PubMed:14702039}.			nucleolus (GO:0005730)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)|skin(2)	10		Colorectal(6;0.0596)		Colorectal(21;0.082)		GCTTCTGGAACCTCAGTTTCC	0.463													C|||	2319	0.463059	0.1929	0.6816	5008	,	,		19022	0.4673		0.496	False		,,,				2504	0.635				p.R53S		Atlas-SNP	.											.	MRO	36	.	0			c.G159C						PASS	.	C	SER/ARG,SER/ARG,SER/ARG,SER/ARG	1065,3341	387.7+/-326.6	111,843,1249	84.0	87.0	86.0		117,159,159,117	2.6	0.1	18	dbSNP_111	86	4146,4454	565.6+/-388.5	1008,2130,1162	yes	missense,missense,missense,missense	MRO	NM_001127174.1,NM_001127175.1,NM_001127176.1,NM_031939.3	110,110,110,110	1119,2973,2411	GG,GC,CC		48.2093,24.1716,40.0661	benign,benign,benign,benign	39/197,53/211,53/263,39/249	48333203	5211,7795	2203	4300	6503	SO:0001583	missense	83876	exon3			CTGGAACCTCAGT	AK054702	CCDS11947.1, CCDS45867.1, CCDS45868.1, CCDS45869.1	18q21	2012-12-19	2004-06-15		ENSG00000134042	ENSG00000134042		"""maestro heat-like repeat containing"""	24121	protein-coding gene	gene with protein product	"""B29 protein"", ""beside the Ma29 deletion"""	608080	"""chromosome 18 open reading frame 3"""	C18orf3		11401430	Standard	NM_031939		Approved	B29, FLJ30140	uc010dpa.3	Q9BYG7	OTTHUMG00000132692	ENST00000428869.2:c.117G>C	18.37:g.48333203C>G	ENSP00000409509:p.Arg39Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_001127175	B7Z2I5|B7Z3B2|E9PAT5|E9PBI3|K7EKJ8|Q8N6K5	Missense_Mutation	SNP	ENST00000428869.2	37	CCDS11947.1	980	0.44871794871794873	94	0.1910569105691057	230	0.6353591160220995	288	0.5034965034965035	368	0.48548812664907653	C	7.049	0.564038	0.13498	0.241716	0.482093	ENSG00000134042	ENST00000436348;ENST00000431965;ENST00000428869;ENST00000398439;ENST00000256425	T;T;T;T;T	0.31247	2.38;1.98;1.5;1.5;1.5	5.39	2.63	0.31362	Armadillo-type fold (1);	2.863360	0.00855	N	0.001864	T	0.00012	0.0000	M	0.72479	2.2	0.80722	P	0.0	B;P;B;B	0.35774	0.016;0.519;0.024;0.002	B;B;B;B	0.37480	0.006;0.251;0.02;0.007	T	0.47573	-0.9107	9	0.09590	T	0.72	-20.4336	5.1639	0.15075	0.1637:0.6627:0.0:0.1736	rs4940019;rs52818026;rs57216618;rs4940019	39;53;53;39	E9PFU2;E9PBI3;E9PAT5;Q9BYG7	.;.;.;MSTRO_HUMAN	S	53;53;39;39;39	ENSP00000397900:R53S;ENSP00000392614:R53S;ENSP00000409509:R39S;ENSP00000381465:R39S;ENSP00000256425:R39S	ENSP00000256425:R39S	R	-	3	2	MRO	46587201	0.019000	0.18553	0.094000	0.20943	0.732000	0.41865	0.590000	0.23954	0.271000	0.22005	-0.300000	0.09419	AGG	C|0.579;G|0.421	0.421	strong		0.463	MRO-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449478.2	NM_031939	
KLRG1	10219	hgsc.bcm.edu	37	12	9142297	9142297	+	Silent	SNP	T	T	C	rs1805723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:9142297T>C	ENST00000266551.4	+	1	81	c.66T>C	c.(64-66)taT>taC	p.Y22Y	KLRG1_ENST00000356986.3_Silent_p.Y22Y|KLRG1_ENST00000538029.1_Intron|RP11-259O18.4_ENST00000545706.1_RNA	NM_005810.3	NP_005801.3	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G, member 1	22					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8						AGAATGACTATGGACCACAGC	0.428													t|||	1731	0.345647	0.1377	0.3775	5008	,	,		-128	0.3998		0.4334	False		,,,				2504	0.4581				p.Y22Y		Atlas-SNP	.											.	KLRG1	16	.	0			c.T66C						PASS	.	C		761,3645	310.5+/-291.6	63,635,1505	92.0	88.0	89.0		66	-0.1	0.0	12	dbSNP_92	89	3836,4764	541.4+/-384.0	852,2132,1316	no	coding-synonymous	KLRG1	NM_005810.3		915,2767,2821	CC,CT,TT		44.6047,17.2719,35.3452		22/190	9142297	4597,8409	2203	4300	6503	SO:0001819	synonymous_variant	10219	exon1			TGACTATGGACCA	AF097358	CCDS8599.1	12p13.31	2011-08-30			ENSG00000139187	ENSG00000139187		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	6380	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member A"""	604874				9862378, 9842918, 16461340, 16140789	Standard	NM_005810		Approved	MAFA, 2F1, MAFA-L, CLEC15A	uc001qvg.3	Q96E93		ENST00000266551.4:c.66T>C	12.37:g.9142297T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_005810	B7ZAM2|O43198|O75613	Silent	SNP	ENST00000266551.4	37																																																																																				T|0.639;C|0.361	0.361	strong		0.428	KLRG1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399145.1	NM_005810	
SMCR8	140775	hgsc.bcm.edu	37	17	18220674	18220674	+	Missense_Mutation	SNP	C	C	T	rs8080966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18220674C>T	ENST00000406438.3	+	1	2051	c.1571C>T	c.(1570-1572)cCc>cTc	p.P524L	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	524			P -> L (in dbSNP:rs8080966). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						AGTACCTGCCCCTCTGAGGCC	0.537													C|||	894	0.178514	0.1604	0.2421	5008	,	,		20664	0.0605		0.3062	False		,,,				2504	0.1483				p.P524L		Atlas-SNP	.											.	SMCR8	62	.	0			c.C1571T						PASS	.	C	LEU/PRO	916,3490	349.3+/-310.3	87,742,1374	90.0	89.0	90.0		1571	5.9	1.0	17	dbSNP_116	90	2594,6006	418.1+/-352.7	382,1830,2088	yes	missense	SMCR8	NM_144775.2	98	469,2572,3462	TT,TC,CC		30.1628,20.7898,26.9875	probably-damaging	524/938	18220674	3510,9496	2203	4300	6503	SO:0001583	missense	140775	exon1			CCTGCCCCTCTGA	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1571C>T	17.37:g.18220674C>T	ENSP00000385025:p.Pro524Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	440	0.20146520146520147	79	0.16056910569105692	91	0.2513812154696133	33	0.057692307692307696	237	0.31266490765171506	C	9.135	1.012468	0.19277	0.207898	0.301628	ENSG00000176994	ENST00000406438	T	0.71934	-0.61	5.91	5.91	0.95273	.	0.151452	0.46442	D	0.000294	T	0.00012	0.0000	L	0.32530	0.975	0.09310	P	0.99999898358	D	0.89917	1.0	D	0.85130	0.997	T	0.06935	-1.0799	9	0.14656	T	0.56	-56.313	20.2983	0.98569	0.0:1.0:0.0:0.0	rs8080966;rs52799159;rs59228353;rs8080966	524	Q8TEV9	SMCR8_HUMAN	L	524	ENSP00000385025:P524L	ENSP00000385025:P524L	P	+	2	0	SMCR8	18161399	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.311000	0.65786	2.802000	0.96397	0.655000	0.94253	CCC	C|0.770;T|0.230	0.230	strong		0.537	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
FAM83E	54854	hgsc.bcm.edu	37	19	49116359	49116359	+	Missense_Mutation	SNP	T	T	C	rs447802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49116359T>C	ENST00000263266.3	-	1	460	c.271A>G	c.(271-273)Acc>Gcc	p.T91A	FAM83E_ENST00000595110.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	91			T -> A (in dbSNP:rs447802). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TCCACATCGGTGGTGGTGGCT	0.682													C|||	2759	0.550919	0.7277	0.4986	5008	,	,		12886	0.7431		0.2614	False		,,,				2504	0.4489				p.T91A		Atlas-SNP	.											FAM83E,NS,carcinoma,0,2	FAM83E	34	2	0			c.A271G						PASS	.						12.0	21.0	18.0					19																	49116359		2090	4216	6306	SO:0001583	missense	54854	exon1			CATCGGTGGTGGT	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.271A>G	19.37:g.49116359T>C	ENSP00000263266:p.Thr91Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	105	42	0.4	NM_017708	Q9NXK1	Missense_Mutation	SNP	ENST00000263266.3	37	CCDS42587.1	1077	0.49313186813186816	343	0.6971544715447154	160	0.4419889502762431	389	0.6800699300699301	185	0.24406332453825857	C	2.961	-0.214627	0.06101	.	.	ENSG00000105523	ENST00000263266	T	0.10668	2.85	3.79	-5.7	0.02421	.	1.732010	0.03225	N	0.178172	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.42565	-0.9444	9	0.02654	T	1	-0.2116	10.3255	0.43790	0.0:0.5744:0.1163:0.3093	rs447802;rs52796733;rs447802	91	Q2M2I3	FA83E_HUMAN	A	91	ENSP00000263266:T91A	ENSP00000263266:T91A	T	-	1	0	FAM83E	53808171	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.799000	0.01746	-1.443000	0.01953	-1.874000	0.00550	ACC	T|0.521;C|0.479	0.479	strong		0.682	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
GRM6	2916	hgsc.bcm.edu	37	5	178416063	178416063	+	Silent	SNP	G	G	A	rs2645339	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178416063G>A	ENST00000517717.1	-	7	1265	c.1227C>T	c.(1225-1227)taC>taT	p.Y409Y	GRM6_ENST00000231188.5_Silent_p.Y409Y|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	409					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)		GGGCAATGGCGTACACCGCAT	0.637																																					p.Y409Y		Atlas-SNP	.											GRM6,NS,adenoma,0,1	GRM6	149	1	0			c.C1227T	GRCh37	CM061056	GRM6	M	rs2645339	PASS	.	G		1757,2649	523.5+/-371.1	361,1035,807	143.0	123.0	129.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1227	-0.9	1.0	5	dbSNP_100	129	4593,4007	596.8+/-393.7	1177,2239,884	no	coding-synonymous	GRM6	NM_000843.3		1538,3274,1691	AA,AG,GG		46.593,39.8774,48.8236		409/878	178416063	6350,6656	2203	4300	6503	SO:0001819	synonymous_variant	2916	exon6			AATGGCGTACACC	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.1227C>T	5.37:g.178416063G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																			G|0.502;A|0.498	0.498	strong		0.637	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
ABCC1	4363	hgsc.bcm.edu	37	16	16139714	16139714	+	Silent	SNP	T	T	C	rs35587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:16139714T>C	ENST00000399410.3	+	9	1237	c.1062T>C	c.(1060-1062)aaT>aaC	p.N354N	ABCC1_ENST00000349029.5_Silent_p.N354N|ABCC1_ENST00000345148.5_Silent_p.N354N|ABCC1_ENST00000346370.5_Silent_p.N354N|ABCC1_ENST00000399408.2_Silent_p.N354N|ABCC1_ENST00000351154.5_Silent_p.N354N	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	354	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	AGTTCGTGAATGACACGAAGG	0.562											OREG0023639	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	2118	0.422923	0.711	0.3573	5008	,	,		21507	0.4415		0.3131	False		,,,				2504	0.1738				p.N354N		Atlas-SNP	.											.	ABCC1	156	.	0			c.T1062C						PASS	.	C	,,,,	2564,1580		821,922,329	47.0	51.0	50.0		1062,1062,1062,1062,1062	-6.0	0.2	16	dbSNP_76	50	2447,5985		348,1751,2117	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	1169,2673,2446	CC,CT,TT		29.0204,38.1274,39.8457	,,,,	354/1532,354/1473,354/1476,354/1417,354/1467	16139714	5011,7565	2072	4216	6288	SO:0001819	synonymous_variant	4363	exon9			CGTGAATGACACG	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.1062T>C	16.37:g.16139714T>C		Somatic	68	0	0	708	WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			T|0.576;C|0.424	0.424	strong		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
ANKRD6	22881	hgsc.bcm.edu	37	6	90338863	90338863	+	Silent	SNP	C	C	T	rs9353687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90338863C>T	ENST00000522441.1	+	15	2159	c.1518C>T	c.(1516-1518)tgC>tgT	p.C506C	ANKRD6_ENST00000339746.4_Silent_p.C506C|ANKRD6_ENST00000520793.1_Silent_p.C447C|LYRM2_ENST00000520441.1_Intron|ANKRD6_ENST00000369408.5_Silent_p.C471C|ANKRD6_ENST00000447838.2_Silent_p.C506C	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	506					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		AAACCTGGTGCATGTTAAAGA	0.378													C|||	841	0.167931	0.1876	0.1398	5008	,	,		18179	0.2222		0.1809	False		,,,				2504	0.092				p.C506C		Atlas-SNP	.											.	ANKRD6	51	.	0			c.C1518T						PASS	.	C	,,,,	705,2943		73,559,1192	82.0	81.0	81.0		1518,1518,1413,1341,1518	4.0	1.0	6	dbSNP_119	81	1461,6697		132,1197,2750	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANKRD6	NM_001242809.1,NM_001242811.1,NM_001242813.1,NM_001242814.1,NM_014942.4	,,,,	205,1756,3942	TT,TC,CC		17.9088,19.3257,18.3466	,,,,	506/728,506/728,471/693,447/664,506/723	90338863	2166,9640	1824	4079	5903	SO:0001819	synonymous_variant	22881	exon15			CTGGTGCATGTTA	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1518C>T	6.37:g.90338863C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Silent	SNP	ENST00000522441.1	37	CCDS56441.1	419	0.19184981684981686	99	0.20121951219512196	46	0.1270718232044199	131	0.229020979020979	143	0.18865435356200527	C	9.377	1.071923	0.20147	0.193257	0.179088	ENSG00000135299	ENST00000492158	.	.	.	6.07	3.97	0.46021	.	.	.	.	.	T	0.53222	0.1783	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.56245	-0.8011	3	.	.	.	-6.6477	14.3358	0.66589	0.0:0.8596:0.0:0.1404	rs9353687	.	.	.	Y	80	.	.	H	+	1	0	ANKRD6	90395584	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.526000	0.45607	1.550000	0.49438	0.655000	0.94253	CAT	C|0.815;T|0.185	0.185	strong		0.378	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
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 GAIIx	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_ENST00000490844.1_5'UTR|OGDHL_ENST00000432695.1_Missense_Mutation_p.A668S|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	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	63	28	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 GAIIx	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	C12orf79_ENST00000551563.2_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|RP11-796E2.4_ENST00000499685.2_RNA	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		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	106	30	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		
COG6	57511	hgsc.bcm.edu	37	13	40293428	40293428	+	Missense_Mutation	SNP	T	T	C	rs41286961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:40293428T>C	ENST00000455146.3	+	14	1390	c.1340T>C	c.(1339-1341)aTg>aCg	p.M447T	COG6_ENST00000416691.1_Missense_Mutation_p.M447T	NM_020751.2	NP_065802.1	Q9Y2V7	COG6_HUMAN	component of oligomeric golgi complex 6	447			M -> T (in dbSNP:rs41286961).		glycosylation (GO:0070085)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				NS(1)|kidney(2)|large_intestine(5)|lung(4)|skin(1)	13		Lung NSC(96;0.000124)|Breast(139;0.0199)|Prostate(109;0.0233)|Lung SC(185;0.0367)		all cancers(112;6.03e-09)|Epithelial(112;7e-07)|OV - Ovarian serous cystadenocarcinoma(117;0.00015)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.0168)		CAGACACTCATGTTGCTGCGT	0.378													T|||	237	0.0473243	0.0363	0.0346	5008	,	,		16926	0.0159		0.0716	False		,,,				2504	0.0787				p.M447T		Atlas-SNP	.											.	COG6	49	.	0			c.T1340C						PASS	.	T	THR/MET,THR/MET	186,4220	118.8+/-156.5	2,182,2019	129.0	114.0	119.0		1340,1340	-1.5	0.0	13	dbSNP_127	119	485,8115	140.6+/-197.1	22,441,3837	yes	missense,missense	COG6	NM_001145079.1,NM_020751.2	81,81	24,623,5856	CC,CT,TT		5.6395,4.2215,5.1592	benign,benign	447/616,447/658	40293428	671,12335	2203	4300	6503	SO:0001583	missense	57511	exon14			CACTCATGTTGCT	AK026638	CCDS9370.1, CCDS45042.1	13q13.2	2011-08-01			ENSG00000133103	ENSG00000133103		"""Components of oligomeric golgi complex"""	18621	protein-coding gene	gene with protein product		606977				11980916	Standard	NM_020751		Approved	COD2, KIAA1134	uc001uxh.2	Q9Y2V7	OTTHUMG00000016768	ENST00000455146.3:c.1340T>C	13.37:g.40293428T>C	ENSP00000397441:p.Met447Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	162	106	0.654321	NM_001145079	Q5T0U1|Q6AI19|Q86V49|Q9ULT5	Missense_Mutation	SNP	ENST00000455146.3	37	CCDS9370.1	104	0.047619047619047616	27	0.054878048780487805	16	0.04419889502762431	5	0.008741258741258742	56	0.07387862796833773	T	0.021	-1.418662	0.01136	0.042215	0.056395	ENSG00000133103	ENST00000416691;ENST00000255468;ENST00000455146	T;T	0.53423	0.62;0.62	5.71	-1.52	0.08637	.	1.132670	0.06385	N	0.715901	T	0.01353	0.0044	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.11518	-1.0584	10	0.23302	T	0.38	-5.3306	9.5221	0.39143	0.2525:0.614:0.0:0.1335	rs41286961;rs61732703	468;447	Q5T0U2;Q9Y2V7	.;COG6_HUMAN	T	447;478;447	ENSP00000403733:M447T;ENSP00000397441:M447T	ENSP00000255468:M478T	M	+	2	0	COG6	39191428	0.000000	0.05858	0.000000	0.03702	0.274000	0.26718	0.246000	0.18160	-0.689000	0.05149	0.533000	0.62120	ATG	T|0.946;C|0.054	0.054	strong		0.378	COG6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044622.3		
MED14	9282	hgsc.bcm.edu	37	X	40573157	40573157	+	Silent	SNP	G	G	A	rs6520683	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:40573157G>A	ENST00000324817.1	-	5	643	c.525C>T	c.(523-525)gaC>gaT	p.D175D		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	175					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GAATAATTTTGTCCTGCAAAA	0.338													A|||	1136	0.300927	0.4584	0.1124	3775	,	,		12488	0.1538		0.1352	False		,,,				2504	0.1646				p.D175D		Atlas-SNP	.											.	MED14	108	.	0			c.C525T						PASS	.	A		1994,1841		442,809,301,381,270	122.0	122.0	122.0		525	3.2	1.0	X	dbSNP_116	122	1203,5525		74,735,320,1619,1552	no	coding-synonymous	MED14	NM_004229.3		516,1544,621,2000,1822	AA,AG,A,GG,G		17.8805,48.0052,30.266		175/1455	40573157	3197,7366	2203	4300	6503	SO:0001819	synonymous_variant	9282	exon5			AATTTTGTCCTGC	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.525C>T	X.37:g.40573157G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	97	57	0.587629	NM_004229	Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	37	CCDS14254.1																																																																																			G|0.693;A|0.307	0.307	strong		0.338	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	
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 GAIIx	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		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	57	40	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	
DNAH5	1767	hgsc.bcm.edu	37	5	13762972	13762972	+	Silent	SNP	T	T	C	rs6554812	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:13762972T>C	ENST00000265104.4	-	60	10244	c.10140A>G	c.(10138-10140)gaA>gaG	p.E3380E	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3380	Stalk. {ECO:0000250}.				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)					GACTCAAAAATTCTATCACCT	0.373									Kartagener syndrome				C|||	1554	0.310304	0.3722	0.2709	5008	,	,		21726	0.1052		0.3012	False		,,,				2504	0.4755				p.E3380E		Atlas-SNP	.											DNAH5,NS,carcinoma,-2,1	DNAH5	868	1	0			c.A10140G						PASS	.	C		1601,2805	665.6+/-401.6	294,1013,896	77.0	74.0	75.0		10140	-5.2	0.7	5	dbSNP_116	75	2272,6328	707.4+/-405.6	306,1660,2334	no	coding-synonymous	DNAH5	NM_001369.2		600,2673,3230	CC,CT,TT		26.4186,36.3368,29.7786		3380/4625	13762972	3873,9133	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon60	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAAAAATTCTATC	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.10140A>G	5.37:g.13762972T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.714;C|0.286	0.286	strong		0.373	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
DUSP4	1846	hgsc.bcm.edu	37	8	29197672	29197672	+	Silent	SNP	A	A	G	rs583034	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:29197672A>G	ENST00000240100.2	-	2	911	c.522T>C	c.(520-522)agT>agC	p.S174S	DUSP4_ENST00000240101.2_Silent_p.S83S	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	174					endoderm formation (GO:0001706)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein dephosphorylation (GO:0006470)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleoplasm (GO:0005654)|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)			endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		GCTCTGTGGCACTGGGGGGAA	0.617											OREG0018686	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3117	0.622404	0.8147	0.6455	5008	,	,		14166	0.6617		0.4533	False		,,,				2504	0.4796				p.S174S		Atlas-SNP	.											.	DUSP4	58	.	0			c.T522C						PASS	.	G	,	3306,1098		1252,802,148	16.0	21.0	19.0		522,249	-2.5	0.0	8	dbSNP_83	19	3636,4962		755,2126,1418	no	coding-synonymous,coding-synonymous	DUSP4	NM_001394.6,NM_057158.3	,	2007,2928,1566	GG,GA,AA		42.2889,24.9319,46.6082	,	174/395,83/304	29197672	6942,6060	2202	4299	6501	SO:0001819	synonymous_variant	1846	exon2			TGTGGCACTGGGG	U21108	CCDS6072.1, CCDS6073.1	8p12-p11	2011-06-09			ENSG00000120875	ENSG00000120875		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3070	protein-coding gene	gene with protein product	"""VH1 homologous phosphatase 2"", ""MAP kinase phosphatase 2"""	602747				7535768, 9205128	Standard	NM_001394		Approved	HVH2, MKP-2, TYP	uc003xhm.3	Q13115	OTTHUMG00000133395	ENST00000240100.2:c.522T>C	8.37:g.29197672A>G		Somatic	25	0	0	807	WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Silent	SNP	ENST00000240100.2	37	CCDS6072.1																																																																																			A|0.447;G|0.553	0.553	strong		0.617	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394	
RTN4IP1	84816	hgsc.bcm.edu	37	6	107076783	107076783	+	Silent	SNP	A	A	T	rs1987623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:107076783A>T	ENST00000369063.3	-	1	579	c.114T>A	c.(112-114)ccT>ccA	p.P38P	QRSL1_ENST00000369046.4_5'Flank|QRSL1_ENST00000369044.1_5'Flank|RTN4IP1_ENST00000539449.1_Silent_p.P38P	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	38						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		CAGTGCTCCTAGGAGAGGTAG	0.423													T|||	2340	0.467252	0.6074	0.5029	5008	,	,		19829	0.622		0.3181	False		,,,				2504	0.2464				p.P38P		Atlas-SNP	.											.	RTN4IP1	31	.	0			c.T114A						PASS	.	T		2533,1873	539.8+/-375.3	731,1071,401	126.0	116.0	119.0		114	-5.1	0.9	6	dbSNP_92	119	2365,6235	701.5+/-405.2	313,1739,2248	no	coding-synonymous	RTN4IP1	NM_032730.4		1044,2810,2649	TT,TA,AA		27.5,42.5102,37.6595		38/397	107076783	4898,8108	2203	4300	6503	SO:0001819	synonymous_variant	84816	exon1			GCTCCTAGGAGAG	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.114T>A	6.37:g.107076783A>T		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Silent	SNP	ENST00000369063.3	37	CCDS5056.1																																																																																			A|0.608;T|0.392	0.392	strong		0.423	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1		
SOGA3	387104	hgsc.bcm.edu	37	6	127797179	127797179	+	Silent	SNP	G	G	A	rs3734448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:127797179G>A	ENST00000525778.1	-	6	2737	c.1992C>T	c.(1990-1992)gcC>gcT	p.A664A	SOGA3_ENST00000556132.1_Silent_p.A664A|SOGA3_ENST00000465909.2_Silent_p.A664A|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000481848.2_Silent_p.A664A|SOGA3_ENST00000368268.2_Silent_p.A664A			Q5TF21	SOGA3_HUMAN	SOGA family member 3	664					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CCTCCAGGTCGGCCACGTTCC	0.642													G|||	1875	0.374401	0.2035	0.4467	5008	,	,		17874	0.7351		0.2406	False		,,,				2504	0.32				p.A664A		Atlas-SNP	.											.	.	.	.	0			c.C1992T						PASS	.	G		931,3445	314.4+/-293.6	115,701,1372	55.0	60.0	58.0		1992	-3.4	1.0	6	dbSNP_107	58	2110,6462	351.3+/-328.2	278,1554,2454	no	coding-synonymous	C6orf174	NM_001012279.2		393,2255,3826	AA,AG,GG		24.615,21.2751,23.4863		664/948	127797179	3041,9907	2188	4286	6474	SO:0001819	synonymous_variant	387104	exon6			CAGGTCGGCCACG	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1992C>T	6.37:g.127797179G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																			G|0.657;A|0.343	0.343	strong		0.642	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
XRRA1	143570	hgsc.bcm.edu	37	11	74563077	74563077	+	Silent	SNP	G	G	A	rs2304683	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:74563077G>A	ENST00000340360.6	-	13	1528	c.1197C>T	c.(1195-1197)tgC>tgT	p.C399C	XRRA1_ENST00000527087.1_Intron|XRRA1_ENST00000321448.8_Silent_p.C124C	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						AGACGAACTCGCAGAGAGATG	0.542													G|||	1340	0.267572	0.093	0.4827	5008	,	,		21900	0.506		0.2833	False		,,,				2504	0.089				p.C399C		Atlas-SNP	.											.	XRRA1	46	.	0			c.C1197T						PASS	.	G		507,3555		40,427,1564	139.0	141.0	140.0		1197	-6.4	0.7	11	dbSNP_100	140	2189,6181		286,1617,2282	no	coding-synonymous	XRRA1	NM_182969.1		326,2044,3846	AA,AG,GG		26.1529,12.4815,21.686		399/793	74563077	2696,9736	2031	4185	6216	SO:0001819	synonymous_variant	143570	exon13			GAACTCGCAGAGA	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1197C>T	11.37:g.74563077G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_182969		Silent	SNP	ENST00000340360.6	37	CCDS44680.1																																																																																			G|0.689;A|0.311	0.311	strong		0.542	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
TRIM67	440730	hgsc.bcm.edu	37	1	231335983	231335983	+	Silent	SNP	C	C	T	rs139376072	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:231335983C>T	ENST00000366653.5	+	4	1353	c.1353C>T	c.(1351-1353)aaC>aaT	p.N451N	TRIM67_ENST00000366652.2_Silent_p.N451N|TRIM67_ENST00000444294.3_Silent_p.N451N|TRIM67_ENST00000449018.3_Silent_p.N389N			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	451	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				TCAAGGAGAACGACCCCTCCG	0.542													C|||	49	0.00978435	0.0008	0.0072	5008	,	,		20173	0.0		0.0099	False		,,,				2504	0.0337				p.N451N		Atlas-SNP	.											.	TRIM67	160	.	0			c.C1353T						PASS	.	C		13,3939		0,13,1963	117.0	118.0	118.0		1353	-2.2	0.8	1	dbSNP_134	118	129,8187		1,127,4030	no	coding-synonymous	TRIM67	NM_001004342.3		1,140,5993	TT,TC,CC		1.5512,0.3289,1.1575		451/784	231335983	142,12126	1976	4158	6134	SO:0001819	synonymous_variant	440730	exon4			GGAGAACGACCCC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.1353C>T	1.37:g.231335983C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	57	22	0.385965	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																			C|0.992;T|0.008	0.008	strong		0.542	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
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 GAIIx	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		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	63	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	
C1orf177	163747	hgsc.bcm.edu	37	1	55273580	55273580	+	Missense_Mutation	SNP	G	G	T	rs9782980	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:55273580G>T	ENST00000371273.3	+	4	391	c.376G>T	c.(376-378)Ggc>Tgc	p.G126C	C1orf177_ENST00000358193.3_Missense_Mutation_p.G126C	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	126			G -> C (in dbSNP:rs9782980). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						GCTGGGCCCCGGCTCCTACAA	0.547													G|||	2494	0.498003	0.5023	0.4568	5008	,	,		18603	0.2708		0.5905	False		,,,				2504	0.6605				p.G126C		Atlas-SNP	.											.	C1orf177	36	.	0			c.G376T						PASS	.	G	CYS/GLY,CYS/GLY	2245,2161	593.5+/-388.0	582,1081,540	72.0	83.0	79.0		376,376	4.4	1.0	1	dbSNP_119	79	5145,3455	636.4+/-399.1	1550,2045,705	yes	missense,missense	C1orf177	NM_001110533.1,NM_152607.2	159,159	2132,3126,1245	TT,TG,GG		40.1744,49.0468,43.1801	probably-damaging,probably-damaging	126/419,126/415	55273580	7390,5616	2203	4300	6503	SO:0001583	missense	163747	exon4			GGCCCCGGCTCCT	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.376G>T	1.37:g.55273580G>T	ENSP00000360320:p.Gly126Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001110533	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	1040	0.47619047619047616	257	0.5223577235772358	175	0.48342541436464087	159	0.27797202797202797	449	0.5923482849604221	G	14.62	2.589442	0.46214	0.509532	0.598256	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.26067	1.76;1.76	5.37	4.45	0.53987	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	M	0.70275	2.135	0.21147	P	0.99977731	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.48525	-0.9028	9	0.87932	D	0	-6.5581	9.0072	0.36120	0.0986:0.0:0.9014:0.0	rs9782980;rs17855891;rs60697485;rs9782980	126;126	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	C	126	ENSP00000350924:G126C;ENSP00000360320:G126C	ENSP00000350924:G126C	G	+	1	0	C1orf177	55046168	0.998000	0.40836	0.987000	0.45799	0.343000	0.28985	3.474000	0.53129	2.531000	0.85337	0.561000	0.74099	GGC	G|0.474;T|0.526	0.526	strong		0.547	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
SEC16B	89866	hgsc.bcm.edu	37	1	177902388	177902388	+	Silent	SNP	G	G	A	rs3813647	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:177902388G>A	ENST00000308284.6	-	22	2873	c.2784C>T	c.(2782-2784)ccC>ccT	p.P928P	SEC16B_ENST00000495165.1_5'UTR|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	928					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CGTCTCCAGCGGGGGATGCGT	0.592													G|||	464	0.0926518	0.093	0.111	5008	,	,		17865	0.0268		0.172	False		,,,				2504	0.0654				p.P928P		Atlas-SNP	.											.	SEC16B	92	.	0			c.C2784T						PASS	.	G		434,3510		25,384,1563	29.0	36.0	34.0		2784	1.8	0.2	1	dbSNP_107	34	1498,6858		129,1240,2809	no	coding-synonymous	SEC16B	NM_033127.2		154,1624,4372	AA,AG,GG		17.9272,11.0041,15.7073		928/1061	177902388	1932,10368	1972	4178	6150	SO:0001819	synonymous_variant	89866	exon22			TCCAGCGGGGGAT	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2784C>T	1.37:g.177902388G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			G|0.878;A|0.122	0.122	strong		0.592	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
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 GAIIx	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	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	288	20	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		
VCPIP1	80124	hgsc.bcm.edu	37	8	67577670	67577670	+	Silent	SNP	G	G	A	rs3808602	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:67577670G>A	ENST00000310421.4	-	1	1782	c.1524C>T	c.(1522-1524)taC>taT	p.Y508Y	C8orf44-SGK3_ENST00000519289.1_5'Flank|C8orf44_ENST00000519561.1_5'Flank|C8orf44_ENST00000521889.1_5'Flank	NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	508					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)			breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			AGGGAAAGCTGTAATTTTTGT	0.418													A|||	725	0.144768	0.4319	0.0562	5008	,	,		22571	0.0218		0.0318	False		,,,				2504	0.0624				p.Y508Y	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.C1524T						PASS	.	A		1619,2787	661.7+/-400.9	298,1023,882	163.0	173.0	169.0		1524	-1.3	1.0	8	dbSNP_107	169	194,8406	810.8+/-407.1	1,192,4107	no	coding-synonymous	VCPIP1	NM_025054.4		299,1215,4989	AA,AG,GG		2.2558,36.7453,13.9397		508/1223	67577670	1813,11193	2203	4300	6503	SO:0001819	synonymous_variant	80124	exon1			AAAGCTGTAATTT	AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"""OTU domain containing"""	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.1524C>T	8.37:g.67577670G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	238	110	0.462185	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Silent	SNP	ENST00000310421.4	37	CCDS6192.1																																																																																			G|0.858;A|0.142	0.142	strong		0.418	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1		
POLL	27343	hgsc.bcm.edu	37	10	103340056	103340056	+	Missense_Mutation	SNP	G	G	A	rs3730477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:103340056G>A	ENST00000370162.3	-	8	1806	c.1312C>T	c.(1312-1314)Cgg>Tgg	p.R438W	DPCD_ENST00000470165.1_3'UTR|POLL_ENST00000463515.1_5'UTR|POLL_ENST00000456836.2_Missense_Mutation_p.R175W|POLL_ENST00000339310.3_Missense_Mutation_p.R161W|POLL_ENST00000370172.1_Missense_Mutation_p.R350W|DPCD_ENST00000416979.2_5'UTR|POLL_ENST00000370168.3_Missense_Mutation_p.R111W|POLL_ENST00000370158.3_Missense_Mutation_p.R163W|POLL_ENST00000370169.1_Missense_Mutation_p.R438W|POLL_ENST00000299206.4_Missense_Mutation_p.R438W	NM_001174084.1|NM_001174085.1|NM_013274.3	NP_001167555.1|NP_001167556.1|NP_037406.1	Q9UGP5	DPOLL_HUMAN	polymerase (DNA directed), lambda	438			R -> W (in dbSNP:rs3730477). {ECO:0000269|Ref.4}.		DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|nucleotide-excision repair (GO:0006289)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|lyase activity (GO:0016829)|metal ion binding (GO:0046872)			biliary_tract(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(2)	19		Colorectal(252;0.234)		Epithelial(162;1.55e-08)|all cancers(201;6.64e-07)		CGGTGGGACCGGCCATCTGGG	0.587								DNA polymerases (catalytic subunits)					G|||	500	0.0998403	0.0408	0.1369	5008	,	,		17978	0.0347		0.2207	False		,,,				2504	0.0961				p.R438W		Atlas-SNP	.											.	POLL	43	.	0			c.C1312T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	327,4079	173.7+/-203.5	15,297,1891	81.0	78.0	79.0		1312,1036,1312	1.7	1.0	10	dbSNP_107	79	1964,6636	346.5+/-326.2	238,1488,2574	yes	missense,missense,missense	POLL	NM_001174084.1,NM_001174085.1,NM_013274.3	101,101,101	253,1785,4465	AA,AG,GG		22.8372,7.4217,17.6149	probably-damaging,probably-damaging,probably-damaging	438/576,346/484,438/576	103340056	2291,10715	2203	4300	6503	SO:0001583	missense	27343	exon8			GGGACCGGCCATC	AF161019	CCDS7513.1	10q23	2012-05-18			ENSG00000166169	ENSG00000166169		"""DNA polymerases"""	9184	protein-coding gene	gene with protein product		606343				17686665	Standard	NM_001174084		Approved		uc001kti.2	Q9UGP5	OTTHUMG00000018933	ENST00000370162.3:c.1312C>T	10.37:g.103340056G>A	ENSP00000359181:p.Arg438Trp	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_013274	D3DR76|Q5JQP5|Q6NUM2|Q9BTN8|Q9HA10|Q9HB35	Missense_Mutation	SNP	ENST00000370162.3	37	CCDS7513.1	255	0.11675824175824176	22	0.044715447154471545	58	0.16022099447513813	12	0.02097902097902098	163	0.21503957783641162	G	13.54	2.267434	0.40095	0.074217	0.228372	ENSG00000166169	ENST00000299206;ENST00000370174;ENST00000370169;ENST00000339310;ENST00000370172;ENST00000370168;ENST00000370162;ENST00000370158;ENST00000370157;ENST00000456836;ENST00000415897;ENST00000429502	T;T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	5.63	1.68	0.24146	DNA-directed DNA polymerase X (1);	0.339697	0.31963	N	0.006799	T	0.00039	0.0001	M	0.77103	2.36	0.09310	P	0.9999999998503	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;1.0;1.0;1.0	P;P;P;P;P;P	0.58172	0.714;0.834;0.693;0.834;0.757;0.757	T	0.04268	-1.0964	9	0.66056	D	0.02	-14.6362	4.8301	0.13435	0.2031:0.0:0.5395:0.2574	rs3730477;rs17690382;rs52826958;rs59816638;rs3730477	161;175;163;438;346;111	Q5JQP4;B4DEF5;Q9BTN8;Q9UGP5;A8K860;Q9HBN3	.;.;.;DPOLL_HUMAN;.;.	W	438;438;438;161;350;111;438;163;438;175;346;161	ENSP00000299206:R438W;ENSP00000359188:R438W;ENSP00000343102:R161W;ENSP00000359191:R350W;ENSP00000359187:R111W;ENSP00000359181:R438W;ENSP00000359177:R163W;ENSP00000390810:R175W;ENSP00000400676:R346W;ENSP00000406791:R161W	ENSP00000299206:R438W	R	-	1	2	POLL	103330046	0.967000	0.33354	0.991000	0.47740	0.595000	0.36748	1.670000	0.37502	0.050000	0.15949	-0.253000	0.11424	CGG	G|0.858;A|0.142	0.142	strong		0.587	POLL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049946.1	NM_013274	
FAM86B1	85002	hgsc.bcm.edu	37	8	12044042	12044042	+	Silent	SNP	G	G	A	rs148527538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:12044042G>A	ENST00000448228.2	-	5	508	c.459C>T	c.(457-459)agC>agT	p.S153S	FAM86B1_ENST00000321602.8_Intron|FAM86B1_ENST00000533513.1_3'UTR|FAM86B1_ENST00000534520.1_Intron|FAM86B1_ENST00000533852.2_Silent_p.S187S	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	153								p.S187S(1)		kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		TGTGAGGGTCGCTGAAGATGT	0.612																																					p.S153S		Atlas-SNP	.											FAM86B1,NS,carcinoma,0,1	FAM86B1	7	1	1	Substitution - coding silent(1)	stomach(1)	c.C459T						scavenged	.						32.0	36.0	35.0					8																	12044042		1480	2621	4101	SO:0001819	synonymous_variant	85002	exon5			AGGGTCGCTGAAG	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.459C>T	8.37:g.12044042G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	160	25	0.15625	NM_001083537		Silent	SNP	ENST00000448228.2	37	CCDS59512.1																																																																																			G|0.500;A|0.500	0.500	strong		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
ZC3H4	23211	hgsc.bcm.edu	37	19	47585517	47585517	+	Silent	SNP	G	G	C	rs7250850	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47585517G>C	ENST00000253048.5	-	10	1291	c.1254C>G	c.(1252-1254)ctC>ctG	p.L418L	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	418							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		GCTTCTTTGGGAGTTCGATGT	0.463													G|||	1876	0.374601	0.1006	0.5403	5008	,	,		21577	0.2758		0.6869	False		,,,				2504	0.408				p.L418L		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C1254G						PASS	.	G		954,2974		123,708,1133	175.0	156.0	162.0		1254	-3.1	1.0	19	dbSNP_116	162	5827,2503		2038,1751,376	no	coding-synonymous	ZC3H4	NM_015168.1		2161,2459,1509	CC,CG,GG		30.048,24.2872,44.681		418/1304	47585517	6781,5477	1964	4165	6129	SO:0001819	synonymous_variant	23211	exon10			CTTTGGGAGTTCG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1254C>G	19.37:g.47585517G>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	186	185	0.994624	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			G|0.552;C|0.448	0.448	strong		0.463	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
YAE1D1	57002	hgsc.bcm.edu	37	7	39606107	39606107	+	Silent	SNP	G	G	A	rs1051162	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:39606107G>A	ENST00000223273.2	+	1	133	c.90G>A	c.(88-90)gcG>gcA	p.A30A	YAE1D1_ENST00000432096.2_Silent_p.A30A|AC011290.4_ENST00000439751.2_RNA|YAE1D1_ENST00000448268.1_Silent_p.A30A	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	30								p.A30A(1)									CGCTCCTGGCGCAGCGGGAAT	0.587													G|||	778	0.155351	0.298	0.072	5008	,	,		17313	0.1131		0.0984	False		,,,				2504	0.1237				p.A30A		Atlas-SNP	.											C7orf36,NS,carcinoma,0,1	YAE1D1	2	1	1	Substitution - coding silent(1)	stomach(1)	c.G90A						PASS	.	G		1033,3373	380.6+/-323.8	125,783,1295	87.0	78.0	81.0		90	-0.0	0.7	7	dbSNP_86	81	806,7794	188.4+/-235.4	30,746,3524	no	coding-synonymous	C7orf36	NM_020192.3		155,1529,4819	AA,AG,GG		9.3721,23.4453,14.1396		30/227	39606107	1839,11167	2203	4300	6503	SO:0001819	synonymous_variant	57002	exon1			CCTGGCGCAGCGG	AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 36"""	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.90G>A	7.37:g.39606107G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_020192	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Silent	SNP	ENST00000223273.2	37	CCDS5459.1																																																																																			G|0.842;A|0.158	0.158	strong		0.587	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250586.1	NM_020192	
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 GAIIx	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_ENST00000422110.2_Missense_Mutation_p.D162Y|GORASP1_ENST00000479927.1_Missense_Mutation_p.D222Y|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	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	131	58	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 GAIIx	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_ENST00000354673.2_5'Flank|IGSF11_ENST00000441144.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000425327.2_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	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	47	22	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	
CCDC39	339829	hgsc.bcm.edu	37	3	180377529	180377529	+	Missense_Mutation	SNP	G	G	C	rs112738198	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:180377529G>C	ENST00000442201.2	-	5	664	c.545C>G	c.(544-546)aCt>aGt	p.T182S	CCDC39_ENST00000273654.4_Missense_Mutation_p.T266S	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	182					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			ACATTCCAAAGTTAGTCTTTC	0.279													G|||	42	0.00838658	0.0008	0.0115	5008	,	,		16142	0.0		0.0298	False		,,,				2504	0.0031				p.T182S		Atlas-SNP	.											.	CCDC39	242	.	0			c.C545G						PASS	.	G	SER/THR	34,3598		1,32,1783	140.0	131.0	134.0		545	4.0	0.9	3	dbSNP_132	134	263,7891		3,257,3817	yes	missense	CCDC39	NM_181426.1	58	4,289,5600	CC,CG,GG		3.2254,0.9361,2.5199	probably-damaging	182/942	180377529	297,11489	1816	4077	5893	SO:0001583	missense	339829	exon5			TCCAAAGTTAGTC	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.545C>G	3.37:g.180377529G>C	ENSP00000405708:p.Thr182Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	37	CCDS46964.1	35	0.016025641025641024	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	26	0.03430079155672823	G	14.75	2.629547	0.46944	0.009361	0.032254	ENSG00000145075	ENST00000273654;ENST00000442201	T;T	0.22134	1.97;1.97	5.87	4.04	0.47022	.	0.317484	0.36101	N	0.002791	T	0.12817	0.0311	L	0.58583	1.82	0.38838	D	0.956009	D	0.57257	0.979	P	0.56563	0.801	T	0.01945	-1.1242	10	0.26408	T	0.33	-11.6697	10.6107	0.45421	0.0681:0.0:0.7983:0.1337	.	182	Q9UFE4	CCD39_HUMAN	S	266;182	ENSP00000273654:T266S;ENSP00000405708:T182S	ENSP00000273654:T266S	T	-	2	0	CCDC39	181860223	1.000000	0.71417	0.905000	0.35620	0.089000	0.18198	5.472000	0.66768	0.781000	0.33589	0.585000	0.79938	ACT	G|0.983;C|0.017	0.017	strong		0.279	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
MUC5B	727897	hgsc.bcm.edu	37	11	1265831	1265831	+	Missense_Mutation	SNP	T	T	C	rs200031789	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1265831T>C	ENST00000529681.1	+	31	7779	c.7721T>C	c.(7720-7722)gTc>gCc	p.V2574A	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.V2577A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2574	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.|V -> A (in Ref. 4; CAA96577). {ECO:0000305}.	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)		p.V2577A(1)		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)		CCAGAGACTGTCCACACCTCC	0.652													T|||	62	0.0123802	0.0076	0.0115	5008	,	,		19571	0.001		0.0348	False		,,,				2504	0.0082				p.V2574A		Atlas-SNP	.											MUC5AC,NS,carcinoma,0,1	MUC5B	473	1	1	Substitution - Missense(1)	ovary(1)	c.T7721C						scavenged	.						115.0	137.0	130.0					11																	1265831		2072	4188	6260	SO:0001583	missense	727897	exon31			AGACTGTCCACAC	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.7721T>C	11.37:g.1265831T>C	ENSP00000436812:p.Val2574Ala	Somatic	256	5	0.0195312		WXS	Illumina HiSeq	Phase_I	306	39	0.127451	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.871|3.871	-0.027898|-0.027898	0.07589|0.07589	.|.	.|.	ENSG00000117983|ENSG00000117983	ENST00000537836|ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	.|T;T	.|0.20881	.|2.04;2.23	2.44|2.44	-1.37|-1.37	0.09056|0.09056	.|.	.|.	.|.	.|.	.|.	T|T	0.09905|0.09905	0.0243|0.0243	N|N	0.13098|0.13098	0.295|0.295	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.31052|0.31052	-0.9957|-0.9957	6|9	0.66056|0.87932	D|D	0.02|0	.|.	2.2601|2.2601	0.04065|0.04065	0.2406:0.4351:0.0:0.3243|0.2406:0.4351:0.0:0.3243	.|.	.|3212;2577	.|A7Y9J9;E9PBJ0	.|.;.	P|A	118|2574;2577;2546;2589	.|ENSP00000436812:V2574A;ENSP00000415793:V2577A	ENSP00000440615:S118P|ENSP00000343037:V2546A	S|V	+|+	1|2	0|0	MUC5B|MUC5B	1222407|1222407	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-2.187000|-2.187000	0.01250|0.01250	-0.039000|-0.039000	0.13602|0.13602	-1.232000|-1.232000	0.01568|0.01568	TCC|GTC	T|0.998;C|0.002	0.002	weak		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MUC5B	727897	hgsc.bcm.edu	37	11	1270965	1270965	+	Silent	SNP	G	G	A	rs114687104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1270965G>A	ENST00000529681.1	+	31	12913	c.12855G>A	c.(12853-12855)ccG>ccA	p.P4285P	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.P4288P	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4285	23 X approximate tandem repeats, Ser/Thr- rich.|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)		TGACCAGCCCGGCCACCACAC	0.617													-|||	253	0.0505192	0.0825	0.0418	5008	,	,		16226	0.002		0.0388	False		,,,				2504	0.0757				p.P4285P		Atlas-SNP	.											MUC5B,NS,haematopoietic_neoplasm,0,2	MUC5B	473	2	0			c.G12855A						PASS	.	G		385,3823		22,341,1741	119.0	140.0	133.0		12855	-3.8	0.0	11	dbSNP_132	133	295,8125		14,267,3929	no	coding-synonymous	MUC5B	NM_002458.2		36,608,5670	AA,AG,GG		3.5036,9.1492,5.3849		4285/5763	1270965	680,11948	2104	4210	6314	SO:0001819	synonymous_variant	727897	exon31			CAGCCCGGCCACC	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.12855G>A	11.37:g.1270965G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	167	63	0.377246	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.958;A|0.042	0.042	strong		0.617	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
APOB	338	hgsc.bcm.edu	37	2	21238367	21238367	+	Missense_Mutation	SNP	C	C	T	rs12713843	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:21238367C>T	ENST00000233242.1	-	22	3510	c.3383G>A	c.(3382-3384)cGt>cAt	p.R1128H		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1128			R -> H (in dbSNP:rs12713843). {ECO:0000269|PubMed:14732481}.		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTTGCAAACGGGGTATGGA	0.448													C|||	14	0.00279553	0.0	0.0043	5008	,	,		19671	0.001		0.004	False		,,,				2504	0.0061				p.R1128H		Atlas-SNP	.											APOB,NS,carcinoma,0,1	APOB	761	1	0			c.G3383A	GRCh37	CM040371	APOB	M	rs12713843	PASS	.	C	HIS/ARG	1,4405		0,1,2202	134.0	126.0	129.0		3383	3.5	0.9	2	dbSNP_126	129	41,8559	26.8+/-75.7	1,39,4260	yes	missense	APOB	NM_000384.2	29	1,40,6462	TT,TC,CC		0.4767,0.0227,0.3229	probably-damaging	1128/4564	21238367	42,12964	2203	4300	6503	SO:0001583	missense	338	exon22			TGCAAACGGGGTA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.3383G>A	2.37:g.21238367C>T	ENSP00000233242:p.Arg1128His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	18.75	3.691170	0.68271	2.27E-4	0.004767	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00824	5.65	5.43	3.52	0.40303	.	0.096408	0.46442	N	0.000295	T	0.00967	0.0032	M	0.69823	2.125	0.80722	D	1	B	0.33135	0.399	B	0.23275	0.045	T	0.58222	-0.7674	10	0.66056	D	0.02	.	9.9257	0.41492	0.136:0.7906:0.0:0.0735	rs12713843;rs17240848;rs52795763;rs57267700;rs12713843	1128	P04114	APOB_HUMAN	H	1128	ENSP00000233242:R1128H	ENSP00000233242:R1128H	R	-	2	0	APOB	21091872	0.764000	0.28473	0.931000	0.37212	0.995000	0.86356	0.128000	0.15810	1.432000	0.47375	0.655000	0.94253	CGT	C|0.997;T|0.003	0.003	strong		0.448	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
KCNMA1	3778	hgsc.bcm.edu	37	10	78944590	78944590	+	Silent	SNP	G	G	A	rs1131824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:78944590G>A	ENST00000286628.8	-	4	686	c.687C>T	c.(685-687)ttC>ttT	p.F229F	KCNMA1_ENST00000404771.3_Silent_p.F229F|KCNMA1_ENST00000404857.1_Silent_p.F229F|KCNMA1_ENST00000354353.5_Silent_p.F229F|KCNMA1_ENST00000286627.5_Silent_p.F229F|KCNMA1_ENST00000406533.3_Silent_p.F229F|KCNMA1_ENST00000372440.1_Silent_p.F229F|KCNMA1_ENST00000372443.1_Silent_p.F229F	NM_001161352.1	NP_001154824.1	Q12791	KCMA1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, alpha member 1	229					blood coagulation (GO:0007596)|cellular potassium ion homeostasis (GO:0030007)|micturition (GO:0060073)|negative regulation of cell volume (GO:0045794)|positive regulation of apoptotic process (GO:0043065)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|response to calcium ion (GO:0051592)|response to carbon monoxide (GO:0034465)|response to hypoxia (GO:0001666)|response to osmotic stress (GO:0006970)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	actin binding (GO:0003779)|calcium-activated potassium channel activity (GO:0015269)|large conductance calcium-activated potassium channel activity (GO:0060072)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(17)|lung(23)|ovary(2)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	68	all_cancers(46;0.203)|all_epithelial(25;0.00604)|Prostate(51;0.0198)		OV - Ovarian serous cystadenocarcinoma(4;0.0586)|Epithelial(14;0.081)|all cancers(16;0.183)		Bendroflumethiazide(DB00436)|Chlorzoxazone(DB00356)|Cromoglicic acid(DB01003)|Diazoxide(DB01119)|Halothane(DB01159)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Miconazole(DB01110)|Procaine(DB00721)	CCCGCAAGCCGAAGTAGAGAA	0.468													A|||	2033	0.40595	0.705	0.2695	5008	,	,		18937	0.249		0.335	False		,,,				2504	0.3333				p.F229F		Atlas-SNP	.											.	KCNMA1	370	.	0			c.C687T						PASS	.	A	,,,	2735,1671	508.4+/-367.0	857,1021,325	155.0	140.0	145.0		687,687,687,687	5.3	1.0	10	dbSNP_86	145	3109,5491	658.9+/-401.6	549,2011,1740	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNMA1	NM_001014797.2,NM_001161352.1,NM_001161353.1,NM_002247.3	,,,	1406,3032,2065	AA,AG,GG		36.1512,37.9256,44.9331	,,,	229/1183,229/1237,229/1220,229/1179	78944590	5844,7162	2203	4300	6503	SO:0001819	synonymous_variant	3778	exon4			CAAGCCGAAGTAG	U11717	CCDS7352.1, CCDS60569.1, CCDS60571.1, CCDS60572.1, CCDS73156.1	10q22	2012-07-05			ENSG00000156113	ENSG00000156113		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6284	protein-coding gene	gene with protein product	"""BK channel alpha subunit"""	600150		SLO		7987297, 16382103	Standard	NM_002247		Approved	KCa1.1, mSLO1	uc001jxn.3	Q12791	OTTHUMG00000018543	ENST00000286628.8:c.687C>T	10.37:g.78944590G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_001161352	F8WA96|Q12886|Q12917|Q12921|Q12960|Q13150|Q5JQ23|Q5SQR9|Q96LG8|Q9UBB0|Q9UCX0|Q9UQK6	Silent	SNP	ENST00000286628.8	37		835|835	0.3823260073260073|0.3823260073260073	335|335	0.6808943089430894|0.6808943089430894	108|108	0.2983425414364641|0.2983425414364641	138|138	0.24125874125874125|0.24125874125874125	254|254	0.33509234828496043|0.33509234828496043	A|A	6.974|6.974	0.549742|0.549742	0.13374|0.13374	0.620744|0.620744	0.361512|0.361512	ENSG00000156113|ENSG00000156113	ENST00000372421|ENST00000372403	.|.	.|.	.|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45366|0.45366	-0.9266|-0.9266	3|3	.|.	.|.	.|.	-11.1608|-11.1608	10.553|10.553	0.45101|0.45101	0.8628:0.0:0.1372:0.0|0.8628:0.0:0.1372:0.0	rs1131824;rs2227912;rs2296678;rs3192016;rs7098260;rs17414082;rs17482985;rs41318619;rs57078861;rs1131824|rs1131824;rs2227912;rs2296678;rs3192016;rs7098260;rs17414082;rs17482985;rs41318619;rs57078861;rs1131824	.|.	.|.	.|.	W|L	218|180	.|.	.|.	R|S	-|-	1|2	2|0	KCNMA1|KCNMA1	78614596|78614596	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	1.408000|1.408000	0.34668|0.34668	1.101000|1.101000	0.41535|0.41535	-0.254000|-0.254000	0.11334|0.11334	CGG|TCG	G|0.579;A|0.421	0.421	strong		0.468	KCNMA1-009	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000048885.3	NM_002247	
CXorf21	80231	hgsc.bcm.edu	37	X	30577846	30577846	+	Silent	SNP	A	A	C	rs887369	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:30577846A>C	ENST00000378962.3	-	3	949	c.627T>G	c.(625-627)gtT>gtG	p.V209V		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21	209										kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						ACTCATTCAGAACTGCATTAG	0.423													C|||	3387	0.897219	0.7012	0.6916	3775	,	,		15942	0.7103		0.5815	False		,,,				2504	0.6943				p.V209V		Atlas-SNP	.											.	CXorf21	42	.	0			c.T627G						PASS	.	C		3451,382		1318,298,517,15,54	156.0	139.0	145.0		627	2.2	0.9	X	dbSNP_86	145	5043,1685		1352,929,1410,147,462	no	coding-synonymous	CXorf21	NM_025159.2		2670,1227,1927,162,516	CC,CA,C,AA,A		25.0446,9.9661,19.572		209/302	30577846	8494,2067	2202	4300	6502	SO:0001819	synonymous_variant	80231	exon3			ATTCAGAACTGCA	BC020611	CCDS14224.1	Xp21.3	2006-04-12			ENSG00000120280	ENSG00000120280			25667	protein-coding gene	gene with protein product						12477932	Standard	NM_025159		Approved	FLJ11577	uc004dcg.2	Q9HAI6	OTTHUMG00000021325	ENST00000378962.3:c.627T>G	X.37:g.30577846A>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	130	34	0.261538	NM_025159		Silent	SNP	ENST00000378962.3	37	CCDS14224.1																																																																																			A|0.160;0|0.002	.	strong		0.423	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1	NM_025159	
COX11	1353	hgsc.bcm.edu	37	17	53038654	53038654	+	3'UTR	SNP	A	A	C	rs1802212	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:53038654A>C	ENST00000299335.3	-	0	2409				TOM1L1_ENST00000572158.1_3'UTR|COX11_ENST00000573912.1_5'Flank|TOM1L1_ENST00000348161.4_3'UTR|TOM1L1_ENST00000540336.1_3'UTR|TOM1L1_ENST00000575882.1_3'UTR|TOM1L1_ENST00000536554.1_3'UTR|TOM1L1_ENST00000445275.2_3'UTR	NM_004375.3	NP_004366.1	Q9Y6N1	COX11_HUMAN	cytochrome c oxidase assembly homolog 11 (yeast)						hydrogen ion transmembrane transport (GO:1902600)|negative regulation of glucokinase activity (GO:0033132)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|prostate(1)	9						TAAAACGTAGACTCTGTGCAG	0.398													A|||	759	0.151558	0.0605	0.1585	5008	,	,		20632	0.129		0.2714	False		,,,				2504	0.1697				p.S228A		Atlas-SNP	.											.	COX11	16	.	0			c.T682G						PASS	.						93.0	76.0	81.0					17																	53038654		692	1591	2283	SO:0001624	3_prime_UTR_variant	1353	exon4			ACGTAGACTCTGT	AF044321	CCDS11583.1, CCDS58579.1	17q22	2012-10-15	2012-10-15			ENSG00000166260		"""Mitochondrial respiratory chain complex assembly factors"""	2261	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit 11"", ""cytochrome c oxidase assembly protein COX11"""	603648	"""COX11 (yeast) homolog, cytochrome c oxidase assembly protein"", ""COX11 cytochrome c oxidase assembly homolog (yeast)"""			9878253	Standard	NM_004375		Approved	COX11P	uc010wng.1	Q9Y6N1		ENST00000299335.3:c.*1440T>G	17.37:g.53038654A>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_001162861	D3DTY5|I3L220|Q6FHB7|Q9BRX0|Q9UME8	Missense_Mutation	SNP	ENST00000299335.3	37	CCDS11583.1																																																																																			A|0.835;C|0.165	0.165	strong		0.398	COX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439182.1	NM_004375	
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 GAIIx	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	RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000544413.1_Missense_Mutation_p.S487N|HNF1A_ENST00000541395.1_Missense_Mutation_p.S487N|HNF1A_ENST00000400024.2_Missense_Mutation_p.S487N|HNF1A_ENST00000538626.1_Missense_Mutation_p.S69N			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	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	127	124	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	
TNXB	7148	hgsc.bcm.edu	37	6	32064726	32064726	+	Missense_Mutation	SNP	T	T	C	rs1150752	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32064726T>C	ENST00000479795.1	-	3	1044	c.904A>G	c.(904-906)Act>Gct	p.T302A	TNXB_ENST00000375244.3_Missense_Mutation_p.T302A|TNXB_ENST00000375247.2_Missense_Mutation_p.T302A			P22105	TENX_HUMAN	tenascin XB	302	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> A (in dbSNP:rs1150752). {ECO:0000269|PubMed:14574404}.		actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						TCCTCGCCAGTGTAGCCGGGG	0.677													T|||	94	0.01877	0.0023	0.0216	5008	,	,		16586	0.0		0.0755	False		,,,				2504	0.0				p.T302A		Atlas-SNP	.											.	TNXB	553	.	0			c.A904G						PASS	.	T	ALA/THR	94,4262		2,90,2086	32.0	38.0	36.0		904	-2.2	0.4	6	dbSNP_87	36	900,7614		48,804,3405	yes	missense	TNXB	NM_019105.6	58	50,894,5491	CC,CT,TT		10.5708,2.1579,7.7234	benign	302/4243	32064726	994,11876	2178	4257	6435	SO:0001583	missense	7148	exon3			CGCCAGTGTAGCC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.904A>G	6.37:g.32064726T>C	ENSP00000418248:p.Thr302Ala	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	233	178	0.763949	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000479795.1	37		67	0.030677655677655676	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	57	0.07519788918205805	T	5.247	0.230987	0.09969	0.021579	0.105708	ENSG00000168477	ENST00000375244;ENST00000375247;ENST00000479795	T;T;T	0.62788	0.0;0.0;0.0	4.13	-2.19	0.07015	.	0.846146	0.10066	N	0.720316	T	0.26048	0.0635	L	0.53671	1.685	0.20703	N	0.999867	B	0.16603	0.018	B	0.16722	0.016	T	0.17198	-1.0377	10	0.23302	T	0.38	.	3.0831	0.06269	0.3851:0.1996:0.0:0.4153	rs1150752;rs57909093;rs1150752	302	P22105-3	.	A	302	ENSP00000364393:T302A;ENSP00000364396:T302A;ENSP00000418248:T302A	ENSP00000364393:T302A	T	-	1	0	TNXB	32172704	0.000000	0.05858	0.376000	0.26042	0.237000	0.25408	-0.203000	0.09438	-0.427000	0.07350	-0.468000	0.05107	ACT	T|0.967;C|0.033	0.033	strong		0.677	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105	
LAMA1	284217	hgsc.bcm.edu	37	18	7011413	7011413	+	Silent	SNP	G	G	A	rs619106	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:7011413G>A	ENST00000389658.3	-	25	3666	c.3573C>T	c.(3571-3573)acC>acT	p.T1191T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1191	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				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)	p.T1191T(1)		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)				AAACCCCCTCGGTCGTGCCCC	0.597													G|||	1826	0.364617	0.7027	0.3401	5008	,	,		13451	0.12		0.2823	False		,,,				2504	0.2618				p.T1191T		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	1	1	Substitution - coding silent(1)	stomach(1)	c.C3573T						PASS	.	G		2787,1619	628.7+/-395.1	893,1001,309	29.0	29.0	29.0		3573	-11.4	0.0	18	dbSNP_83	29	2564,6034	394.7+/-344.8	380,1804,2115	no	coding-synonymous	LAMA1	NM_005559.3		1273,2805,2424	AA,AG,GG		29.8209,36.7453,41.1489		1191/3076	7011413	5351,7653	2203	4299	6502	SO:0001819	synonymous_variant	284217	exon25			CCCCTCGGTCGTG	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.3573C>T	18.37:g.7011413G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.609;A|0.391	0.391	strong		0.597	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
VWA5B2	90113	hgsc.bcm.edu	37	3	183951431	183951431	+	Missense_Mutation	SNP	C	C	T	rs902417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183951431C>T	ENST00000426955.2	+	4	698	c.598C>T	c.(598-600)Cct>Tct	p.P200S	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_5'UTR	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	211								p.P200S(1)		breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						GCTGGCTGCCCCTCGGGACGT	0.662													C|||	1088	0.217252	0.177	0.2075	5008	,	,		16546	0.2351		0.2485	False		,,,				2504	0.228				p.P200S		Atlas-SNP	.											VWA5B2,NS,carcinoma,0,1	VWA5B2	47	1	1	Substitution - Missense(1)	kidney(1)	c.C598T						PASS	.	C	SER/PRO	241,1143		25,191,476	30.0	37.0	35.0		598	2.0	1.0	3	dbSNP_92	35	724,2458		83,558,950	yes	missense	VWA5B2	NM_138345.1	74	108,749,1426	TT,TC,CC		22.753,17.4133,21.1345	benign	200/1243	183951431	965,3601	692	1591	2283	SO:0001583	missense	90113	exon4			GCTGCCCCTCGGG		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.598C>T	3.37:g.183951431C>T	ENSP00000398688:p.Pro200Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_138345	B9EGN7	Missense_Mutation	SNP	ENST00000426955.2	37	CCDS54686.1	444	0.2032967032967033	88	0.17886178861788618	74	0.20441988950276244	94	0.16433566433566432	188	0.24802110817941952	C	1.623	-0.521080	0.04171	0.174133	0.22753	ENSG00000145198	ENST00000426955	T	0.60424	0.19	3.84	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999633179	B;B	0.27823	0.19;0.004	B;B	0.29267	0.1;0.006	T	0.19160	-1.0314	8	0.33141	T	0.24	-0.1148	4.7979	0.13281	0.2103:0.6742:0.0:0.1154	rs902417;rs1687244;rs3882317;rs59041042;rs902417	200;211	B9EGN7;C9JW99	.;.	S	200	ENSP00000398688:P200S	ENSP00000398688:P200S	P	+	1	0	VWA5B2	185434125	0.999000	0.42202	0.982000	0.44146	0.641000	0.38312	1.678000	0.37586	0.384000	0.24942	0.462000	0.41574	CCT	C|0.788;T|0.212	0.212	strong		0.662	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
NLRC5	84166	hgsc.bcm.edu	37	16	57101340	57101340	+	Missense_Mutation	SNP	T	T	C	rs7190199	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57101340T>C	ENST00000262510.6	+	35	4589	c.4364T>C	c.(4363-4365)gTc>gCc	p.V1455A	NLRC5_ENST00000539144.1_Missense_Mutation_p.V1426A|NLRC5_ENST00000308149.7_Missense_Mutation_p.V1426A|NLRC5_ENST00000436936.1_Missense_Mutation_p.V1455A	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1455			V -> A (in dbSNP:rs7190199).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AGCCTTCTTGTCGGGCAGCTG	0.567													T|||	450	0.0898562	0.146	0.0893	5008	,	,		19926	0.1181		0.0646	False		,,,				2504	0.0112				p.V1455A		Atlas-SNP	.											.	NLRC5	186	.	0			c.T4364C						PASS	.	T	ALA/VAL	562,3834	251.8+/-258.4	36,490,1672	126.0	117.0	120.0		4364	-2.2	0.0	16	dbSNP_116	120	445,8155	134.9+/-192.2	16,413,3871	yes	missense	NLRC5	NM_032206.3	64	52,903,5543	CC,CT,TT		5.1744,12.7843,7.7485	benign	1455/1867	57101340	1007,11989	2198	4300	6498	SO:0001583	missense	84166	exon34			TTCTTGTCGGGCA	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.4364T>C	16.37:g.57101340T>C	ENSP00000262510:p.Val1455Ala	Somatic	187	1	0.00534759		WXS	Illumina HiSeq	Phase_I	193	107	0.554404	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	213	0.09752747252747253	56	0.11382113821138211	30	0.08287292817679558	80	0.13986013986013987	47	0.06200527704485488	T	6.600	0.478986	0.12581	0.127843	0.051744	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	T;T;T;T	0.54479	2.14;2.14;0.57;2.14	4.64	-2.22	0.06952	.	.	.	.	.	T	0.00178	0.0005	N	0.03253	-0.375	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.07558	-1.0766	8	0.49607	T	0.09	.	4.5154	0.11932	0.154:0.3836:0.0:0.4624	rs7190199;rs7190199	1455	Q86WI3	NLRC5_HUMAN	A	1455;1426;1455;1426	ENSP00000262510:V1455A;ENSP00000308886:V1426A;ENSP00000389739:V1455A;ENSP00000441727:V1426A	ENSP00000262510:V1455A	V	+	2	0	NLRC5	55658841	0.000000	0.05858	0.000000	0.03702	0.258000	0.26162	-0.273000	0.08548	-0.545000	0.06224	0.450000	0.29827	GTC	T|0.912;C|0.088	0.088	strong		0.567	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
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 GAIIx	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	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	71	31	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 GAIIx	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_ENST00000538608.1_Missense_Mutation_p.V163L|PARVA_ENST00000539723.1_Missense_Mutation_p.V216L|PARVA_ENST00000334956.8_Missense_Mutation_p.V256L			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	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	131	63	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	
NPAP1	23742	hgsc.bcm.edu	37	15	24922230	24922230	+	Missense_Mutation	SNP	C	C	G	rs3742950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:24922230C>G	ENST00000329468.2	+	1	1690	c.1216C>G	c.(1216-1218)Cag>Gag	p.Q406E		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	406	Pro-rich.		Q -> E (in dbSNP:rs3742950).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCAACCTGTGCAGACCACAGA	0.537													G|||	2633	0.525759	0.8865	0.353	5008	,	,		17165	0.4742		0.3559	False		,,,				2504	0.3885				p.Q406E		Atlas-SNP	.											.	.	.	.	0			c.C1216G						PASS	.	G	GLU/GLN	3483,923		1379,725,99	73.0	74.0	74.0		1216	-0.4	0.0	15	dbSNP_107	74	2879,5721		469,1941,1890	yes	missense	C15orf2	NM_018958.2	29	1848,2666,1989	GG,GC,CC		33.4767,20.9487,48.9159	benign	406/1157	24922230	6362,6644	2203	4300	6503	SO:0001583	missense	23742	exon1			CCTGTGCAGACCA	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.1216C>G	15.37:g.24922230C>G	ENSP00000333735:p.Gln406Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	1102	0.5045787545787546	433	0.8800813008130082	126	0.34806629834254144	255	0.4458041958041958	288	0.37994722955145116	.	0.004	-2.281677	0.00251	0.790513	0.334767	ENSG00000185823	ENST00000329468	T	0.05025	3.51	1.78	-0.437	0.12272	.	2.469220	0.01831	N	0.034702	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24977	-1.0145	9	0.11182	T	0.66	.	9.397	0.38408	0.0:0.6466:0.3534:0.0	rs3742950;rs58788820;rs3742950	406	Q9NZP6	CO002_HUMAN	E	406	ENSP00000333735:Q406E	ENSP00000333735:Q406E	Q	+	1	0	C15orf2	22473323	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.565000	0.05929	-0.475000	0.06852	-0.647000	0.03941	CAG	C|0.509;G|0.491	0.491	strong		0.537	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
SETD9	133383	hgsc.bcm.edu	37	5	56209735	56209735	+	Missense_Mutation	SNP	A	A	G	rs40497	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:56209735A>G	ENST00000285947.2	+	4	1011	c.625A>G	c.(625-627)Aaa>Gaa	p.K209E	SETD9_ENST00000475908.1_3'UTR|SETD9_ENST00000541720.1_Missense_Mutation_p.K209E	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	209	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		K -> E (in dbSNP:rs40497).				methyltransferase activity (GO:0008168)										CGGCCCTTTAAAAATGAGTGA	0.403													A|||	715	0.142772	0.0794	0.1772	5008	,	,		16227	0.0308		0.335	False		,,,				2504	0.1217				p.K209E		Atlas-SNP	.											.	.	.	.	0			c.A625G						PASS	.	A	GLU/LYS,GLU/LYS	529,3877	240.9+/-251.5	39,451,1713	101.0	97.0	98.0		625,625	3.3	1.0	5	dbSNP_76	98	2909,5691	455.3+/-363.7	481,1947,1872	yes	missense,missense	C5orf35	NM_001171990.1,NM_153706.3	56,56	520,2398,3585	GG,GA,AA		33.8256,12.0064,26.434	benign,benign	209/272,209/300	56209735	3438,9568	2203	4300	6503	SO:0001583	missense	133383	exon4			CCTTTAAAAATGA	BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542			28508	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 35"""	C5orf35		20930037	Standard	NM_153706		Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.625A>G	5.37:g.56209735A>G	ENSP00000285947:p.Lys209Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_153706	F5H713	Missense_Mutation	SNP	ENST00000285947.2	37	CCDS3972.1	369	0.16895604395604397	40	0.08130081300813008	73	0.20165745856353592	15	0.026223776223776224	241	0.3179419525065963	A	13.40	2.227366	0.39399	0.120064	0.338256	ENSG00000155542	ENST00000285947;ENST00000541720	T;T	0.31769	1.49;1.48	5.73	3.33	0.38152	.	0.322809	0.35870	N	0.002937	T	0.00012	0.0000	L	0.60455	1.87	0.58432	P	2.9999999999752447E-6	B	0.24533	0.105	B	0.13407	0.009	T	0.38243	-0.9670	9	0.07990	T	0.79	-8.8601	7.1006	0.25336	0.7288:0.1317:0.1395:0.0	rs40497;rs17662843;rs60847384;rs40497	209	Q8NE22	CE035_HUMAN	E	209	ENSP00000285947:K209E;ENSP00000442886:K209E	ENSP00000285947:K209E	K	+	1	0	C5orf35	56245492	0.084000	0.21492	0.980000	0.43619	0.975000	0.68041	0.552000	0.23376	1.008000	0.39264	0.528000	0.53228	AAA	A|0.788;G|0.212	0.212	strong		0.403	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706	
ADCK1	57143	hgsc.bcm.edu	37	14	78392115	78392115	+	Silent	SNP	G	G	A	rs55721310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:78392115G>A	ENST00000238561.5	+	9	1116	c.1017G>A	c.(1015-1017)acG>acA	p.T339T	ADCK1_ENST00000341211.5_Silent_p.T271T|ADCK1_ENST00000556560.1_3'UTR	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	346	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		AGATGCTCACGGAAGAATTCC	0.582													G|||	19	0.00379393	0.0008	0.0043	5008	,	,		19027	0.0		0.0129	False		,,,				2504	0.002				p.T339T		Atlas-SNP	.											.	ADCK1	81	.	0			c.G1017A						PASS	.	G	,	17,4389	24.3+/-50.5	0,17,2186	60.0	62.0	61.0		813,1017	-7.3	0.3	14	dbSNP_129	61	98,8502	54.4+/-115.2	0,98,4202	no	coding-synonymous,coding-synonymous	ADCK1	NM_001142545.1,NM_020421.3	,	0,115,6388	AA,AG,GG		1.1395,0.3858,0.8842	,	271/456,339/524	78392115	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	57143	exon9			GCTCACGGAAGAA	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.1017G>A	14.37:g.78392115G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Silent	SNP	ENST00000238561.5	37	CCDS9869.1																																																																																			G|0.991;A|0.009	0.009	strong		0.582	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
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 GAIIx	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	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	63	24	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		
PTGFRN	5738	hgsc.bcm.edu	37	1	117529458	117529458	+	Missense_Mutation	SNP	G	G	A	rs10801922	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117529458G>A	ENST00000393203.2	+	9	2656	c.2509G>A	c.(2509-2511)Gtc>Atc	p.V837I		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	837			V -> I (in dbSNP:rs10801922).		lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GCTGATCGGCGTCGGTCTGTC	0.617													G|||	2494	0.498003	0.3018	0.5951	5008	,	,		18613	0.6597		0.4364	False		,,,				2504	0.591				p.V837I		Atlas-SNP	.											PTGFRN,NS,carcinoma,-2,1	PTGFRN	91	1	0			c.G2509A						PASS	.	G	ILE/VAL	1378,3028	454.4+/-350.6	235,908,1060	111.0	96.0	101.0		2509	0.1	0.7	1	dbSNP_120	101	3825,4775	539.9+/-383.7	853,2119,1328	yes	missense	PTGFRN	NM_020440.2	29	1088,3027,2388	AA,AG,GG		44.4767,31.2755,40.0046	benign	837/880	117529458	5203,7803	2203	4300	6503	SO:0001583	missense	5738	exon9			ATCGGCGTCGGTC	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9601	protein-coding gene	gene with protein product		601204	"""prostaglandin F2 receptor negative regulator"""			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.2509G>A	1.37:g.117529458G>A	ENSP00000376899:p.Val837Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_020440	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	1078	0.4935897435897436	159	0.3231707317073171	190	0.5248618784530387	382	0.6678321678321678	347	0.4577836411609499	G	8.889	0.953437	0.18431	0.312755	0.444767	ENSG00000134247	ENST00000393203;ENST00000544471	T	0.04360	3.64	6.17	0.122	0.14702	.	0.456264	0.23245	N	0.050303	T	0.00552	0.0018	N	0.02539	-0.55	0.58432	P	5.000000000032756E-6	B	0.12013	0.005	B	0.08055	0.003	T	0.44436	-0.9328	9	0.07175	T	0.84	-16.8037	11.6594	0.51337	0.3447:0.0:0.6553:0.0	rs10801922;rs17579898;rs52822596;rs61548861;rs10801922	837	Q9P2B2	FPRP_HUMAN	I	837;696	ENSP00000376899:V837I	ENSP00000376899:V837I	V	+	1	0	PTGFRN	117330981	0.796000	0.28864	0.726000	0.30738	0.976000	0.68499	0.593000	0.23999	0.115000	0.18071	-0.137000	0.14449	GTC	G|0.560;A|0.440	0.440	strong		0.617	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
OVOL2	58495	hgsc.bcm.edu	37	20	18022362	18022362	+	Silent	SNP	G	G	T	rs6111803	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:18022362G>T	ENST00000278780.6	-	3	569	c.327C>A	c.(325-327)acC>acA	p.T109T	OVOL2_ENST00000483661.1_5'UTR	NM_021220.2	NP_067043.2	Q9BRP0	OVOL2_HUMAN	ovo-like zinc finger 2	109					angiogenesis (GO:0001525)|dorsal/ventral pattern formation (GO:0009953)|embryonic digestive tract morphogenesis (GO:0048557)|endocardium formation (GO:0060214)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|neural fold formation (GO:0001842)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of keratinocyte proliferation (GO:0010837)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)	6						ACGTGCCTGTGGTGAACTGGG	0.627													G|||	202	0.0403355	0.0726	0.0173	5008	,	,		15700	0.004		0.0636	False		,,,				2504	0.0266				p.T109T		Atlas-SNP	.											.	OVOL2	18	.	0			c.C327A						PASS	.	G		316,4090	169.4+/-200.1	11,294,1898	54.0	42.0	46.0		327	0.9	1.0	20	dbSNP_114	46	594,8006	156.1+/-210.0	23,548,3729	no	coding-synonymous	OVOL2	NM_021220.2		34,842,5627	TT,TG,GG		6.907,7.172,6.9968		109/276	18022362	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	58495	exon3			GCCTGTGGTGAAC	AK022284	CCDS13132.1	20p11.23	2013-10-17	2013-10-17	2005-05-31	ENSG00000125850	ENSG00000125850		"""Zinc fingers, C2H2-type"""	15804	protein-coding gene	gene with protein product			"""zinc finger protein 339"", ""ovo-like 2 (Drosophila)"""	ZNF339			Standard	NM_021220		Approved	bA504H3.3, HOVO2	uc002wqi.1	Q9BRP0	OTTHUMG00000031960	ENST00000278780.6:c.327C>A	20.37:g.18022362G>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_021220	Q5T8B4|Q9BX22|Q9HA54|Q9Y4M0	Silent	SNP	ENST00000278780.6	37	CCDS13132.1																																																																																			G|0.945;T|0.055	0.055	strong		0.627	OVOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078148.5	NM_021220	
PACSIN2	11252	hgsc.bcm.edu	37	22	43278220	43278220	+	Silent	SNP	C	C	T	rs2899365	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:43278220C>T	ENST00000263246.3	-	7	1077	c.876G>A	c.(874-876)ccG>ccA	p.P292P	PACSIN2_ENST00000402229.1_Silent_p.P292P|PACSIN2_ENST00000337959.4_Silent_p.P292P|PACSIN2_ENST00000407585.1_Silent_p.P292P|PACSIN2_ENST00000403744.3_Silent_p.P292P	NM_001184970.1	NP_001171899.1	Q9UNF0	PACN2_HUMAN	protein kinase C and casein kinase substrate in neurons 2	292	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cell projection morphogenesis (GO:0048858)|membrane tubulation (GO:0097320)|negative regulation of endocytosis (GO:0045806)|protein localization to endosome (GO:0036010)	caveola (GO:0005901)|cell projection (GO:0042995)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	19		Glioma(61;0.222)				TGGCCATGCCCGGCCCGTGAT	0.562													C|||	1707	0.340855	0.3631	0.3761	5008	,	,		20424	0.0933		0.4622	False		,,,				2504	0.4162				p.P292P		Atlas-SNP	.											.	PACSIN2	48	.	0			c.G876A						PASS	.	C	,,	1711,2415		376,959,728	66.0	71.0	69.0		876,876,876	-10.8	0.0	22	dbSNP_101	69	4023,4431		994,2035,1198	no	coding-synonymous,coding-synonymous,coding-synonymous	PACSIN2	NM_001184970.1,NM_001184971.1,NM_007229.3	,,	1370,2994,1926	TT,TC,CC		47.5869,41.4687,45.5803	,,	292/487,292/446,292/487	43278220	5734,6846	2063	4227	6290	SO:0001819	synonymous_variant	11252	exon7			CATGCCCGGCCCG	AF128536	CCDS43023.1, CCDS54536.1	22q13.2-q13.33	2009-05-08			ENSG00000100266	ENSG00000100266			8571	protein-coding gene	gene with protein product	"""syndapin II"""	604960				10431838, 11082044	Standard	NM_007229		Approved	SDPII	uc003bdg.4	Q9UNF0	OTTHUMG00000150701	ENST00000263246.3:c.876G>A	22.37:g.43278220C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	74	71	0.959459	NM_007229	O95921|Q96HV9|Q9H0D3|Q9NPN1|Q9Y4V2	Silent	SNP	ENST00000263246.3	37	CCDS43023.1																																																																																			C|0.642;T|0.358	0.358	strong		0.562	PACSIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319665.1	NM_007229	
MUC2	4583	hgsc.bcm.edu	37	11	1093272	1093272	+	Silent	SNP	A	A	C	rs56230143		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1093272A>C	ENST00000441003.2	+	30	5118	c.5091A>C	c.(5089-5091)acA>acC	p.T1697T	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1664T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				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)		p.T1664T(2)|p.T1697T(2)		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)	agaccccaacatcgacaccca	0.637																																					p.T1697T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	4	Substitution - coding silent(4)	kidney(2)|endometrium(2)	c.A5091C						scavenged	.						128.0	167.0	153.0					11																	1093272		1845	3351	5196	SO:0001819	synonymous_variant	4583	exon30			CCCAACATCGACA	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.5091A>C	11.37:g.1093272A>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	6	0.162162	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FSHR	2492	hgsc.bcm.edu	37	2	49191041	49191041	+	Missense_Mutation	SNP	C	C	T	rs6165	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:49191041C>T	ENST00000406846.2	-	10	1038	c.919G>A	c.(919-921)Gct>Act	p.A307T	FSHR_ENST00000304421.4_Missense_Mutation_p.A281T|FSHR_ENST00000346173.3_Missense_Mutation_p.A245T|FSHR_ENST00000541117.1_Missense_Mutation_p.A43T	NM_000145.3	NP_000136.2	P23945	FSHR_HUMAN	follicle stimulating hormone receptor	307			A -> T (in dbSNP:rs6165). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:12059813, ECO:0000269|PubMed:1301382, ECO:0000269|PubMed:1322283, ECO:0000269|PubMed:1359889, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7916967, ECO:0000269|Ref.5}.		female gamete generation (GO:0007292)|female gonad development (GO:0008585)|follicle-stimulating hormone signaling pathway (GO:0042699)|G-protein coupled receptor signaling pathway (GO:0007186)|gonad development (GO:0008406)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	follicle-stimulating hormone receptor activity (GO:0004963)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(10)|liver(1)|lung(45)|ovary(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	73		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.181)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Choriogonadotropin alfa(DB00097)|Follitropin beta(DB00066)|Menotropins(DB00032)|Suramin(DB04786)|Urofollitropin(DB00094)	TGACCCCTAGCCTGAGTCATA	0.388									Gonadal Dysgenesis, 46 XX				C|||	2465	0.492212	0.2375	0.5793	5008	,	,		21707	0.6597		0.5487	False		,,,				2504	0.544				p.A307T		Atlas-SNP	.											.	FSHR	164	.	0			c.G919A	GRCh37	CM062747	FSHR	M	rs6165	PASS	.	C	THR/ALA,THR/ALA	1256,3150	431.2+/-342.8	188,880,1135	188.0	174.0	179.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	919,841	1.8	1.0	2	dbSNP_52	179	4657,3943	603.7+/-394.7	1247,2163,890	yes	missense,missense	FSHR	NM_000145.3,NM_181446.2	58,58	1435,3043,2025	TT,TC,CC		45.8488,28.5066,45.4636	benign,benign	307/696,281/670	49191041	5913,7093	2203	4300	6503	SO:0001583	missense	2492	exon10	Familial Cancer Database		CCCTAGCCTGAGT		CCDS1843.1, CCDS1844.1, CCDS1844.2	2p21-p16	2014-09-17			ENSG00000170820	ENSG00000170820		"""GPCR / Class A : Gonadotropin and TSH receptors"""	3969	protein-coding gene	gene with protein product		136435		ODG1		8230163, 8855829	Standard	NM_000145		Approved	FSHRO, LGR1	uc002rww.3	P23945	OTTHUMG00000129259	ENST00000406846.2:c.919G>A	2.37:g.49191041C>T	ENSP00000384708:p.Ala307Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	90	0.967742	NM_000145	A8K947|G5CBS7|G5E967|J3KQ00|Q05AH0|Q16225|Q4QRJ3|Q4ZFZ2|Q53RW2	Missense_Mutation	SNP	ENST00000406846.2	37	CCDS1843.1	1123	0.5141941391941391	120	0.24390243902439024	209	0.5773480662983426	382	0.6678321678321678	412	0.5435356200527705	C	5.128	0.209238	0.09757	0.285066	0.541512	ENSG00000170820	ENST00000406846;ENST00000346173;ENST00000304421;ENST00000541117;ENST00000454032	T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06	5.53	1.76	0.24704	Gonadotropin hormone receptor, transmembrane domain (1);	1.030830	0.07635	N	0.929398	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.11329	0.006;0.004;0.006	T	0.45396	-0.9264	8	.	.	.	.	4.4676	0.11696	0.0:0.4356:0.1575:0.4068	rs6165;rs17434419;rs52810983;rs60724827;rs6165	281;245;307	Q05AH0;G5E967;P23945	.;.;FSHR_HUMAN	T	307;245;281;43;245	ENSP00000384708:A307T;ENSP00000333908:A245T;ENSP00000306780:A281T;ENSP00000444172:A43T;ENSP00000415504:A245T	.	A	-	1	0	FSHR	49044545	0.000000	0.05858	0.989000	0.46669	0.977000	0.68977	-0.110000	0.10824	0.150000	0.19136	-0.136000	0.14681	GCT	C|0.525;T|0.475	0.475	strong		0.388	FSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251367.2		
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 GAIIx	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	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	46	25	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		
RNF215	200312	hgsc.bcm.edu	37	22	30782089	30782089	+	Silent	SNP	A	A	G	rs5997629	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30782089A>G	ENST00000382363.3	-	3	545	c.471T>C	c.(469-471)ctT>ctC	p.L157L		NM_001017981.1	NP_001017981.1	Q9Y6U7	RN215_HUMAN	ring finger protein 215	157						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)	6						TCAGGATGAGAAGAAGCAGGG	0.607													G|||	1763	0.352037	0.3222	0.353	5008	,	,		17396	0.3929		0.3111	False		,,,				2504	0.3916				p.L157L		Atlas-SNP	.											.	RNF215	19	.	0			c.T471C						PASS	.	G		1435,2969	658.4+/-400.4	254,927,1021	43.0	40.0	41.0		471	-0.1	1.0	22	dbSNP_114	41	2543,6057	662.9+/-402.0	361,1821,2118	no	coding-synonymous	RNF215	NM_001017981.1		615,2748,3139	GG,GA,AA		29.5698,32.584,30.5906		157/378	30782089	3978,9026	2202	4300	6502	SO:0001819	synonymous_variant	200312	exon3			GATGAGAAGAAGC		CCDS33633.1	22q12.2	2013-01-09			ENSG00000099999	ENSG00000099999		"""RING-type (C3HC4) zinc fingers"""	33434	protein-coding gene	gene with protein product							Standard	NM_001017981		Approved		uc003ahp.3	Q9Y6U7	OTTHUMG00000151016	ENST00000382363.3:c.471T>C	22.37:g.30782089A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_001017981	A6NEL1	Silent	SNP	ENST00000382363.3	37	CCDS33633.1	752	0.3443223443223443	176	0.35772357723577236	114	0.3149171270718232	223	0.38986013986013984	239	0.3153034300791557	G	10.87	1.473926	0.26423	0.32584	0.295698	ENSG00000099999	ENST00000215798	.	.	.	4.61	-0.0468	0.13846	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45396	-0.9264	3	.	.	.	-17.5385	5.1726	0.15118	0.3224:0.1381:0.5396:0.0	rs5997629;rs7288193;rs56627483;rs5997629	.	.	.	P	95	.	.	S	-	1	0	RNF215	29112089	1.000000	0.71417	0.956000	0.39512	0.996000	0.88848	0.733000	0.26087	-0.472000	0.06881	-0.124000	0.14976	TCT	A|0.674;G|0.326	0.326	strong		0.607	RNF215-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320960.1	NM_001017981	
DAGLA	747	hgsc.bcm.edu	37	11	61487690	61487690	+	Silent	SNP	G	G	A	rs198430	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:61487690G>A	ENST00000257215.5	+	2	179	c.63G>A	c.(61-63)ccG>ccA	p.P21P		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	21					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)		TCGTCCTACCGGCCATCTTCC	0.642													G|||	1503	0.30012	0.2269	0.3213	5008	,	,		18461	0.4643		0.2416	False		,,,				2504	0.2751				p.P21P		Atlas-SNP	.											DAGLA,NS,carcinoma,0,1	DAGLA	109	1	0			c.G63A						PASS	.	G		991,3413	368.3+/-318.6	107,777,1318	113.0	101.0	105.0		63	-6.5	1.0	11	dbSNP_79	105	2179,6419	372.6+/-336.7	266,1647,2386	no	coding-synonymous	DAGLA	NM_006133.2		373,2424,3704	AA,AG,GG		25.3431,22.5023,24.3809		21/1043	61487690	3170,9832	2202	4299	6501	SO:0001819	synonymous_variant	747	exon2			CCTACCGGCCATC	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.63G>A	11.37:g.61487690G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.742;A|0.258	0.258	strong		0.642	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
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 GAIIx	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_ENST00000279035.9_Silent_p.V123V|PIGT_ENST00000341555.5_Intron|PIGT_ENST00000545755.1_5'UTR|PIGT_ENST00000543458.2_Silent_p.V169V|PIGT_ENST00000535404.1_Silent_p.V70V|PIGT_ENST00000372689.5_Silent_p.V225V	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		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	88	35	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 GAIIx	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		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	254	119	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	
TMCC2	9911	hgsc.bcm.edu	37	1	205238275	205238275	+	Silent	SNP	A	A	G	rs1768586	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205238275A>G	ENST00000358024.3	+	3	1334	c.945A>G	c.(943-945)gcA>gcG	p.A315A	TMCC2_ENST00000329800.7_Silent_p.A75A|TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000330675.7_Silent_p.A90A|TMCC2_ENST00000545499.1_Silent_p.A237A	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	315						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			ACAATGTGGCAGAGTATCTGA	0.562													a|||	750	0.14976	0.1036	0.1902	5008	,	,		18858	0.0516		0.3549	False		,,,				2504	0.0736				p.A315A		Atlas-SNP	.											.	TMCC2	89	.	0			c.A945G						PASS	.	G	,	655,3751	280.2+/-275.2	54,547,1602	76.0	62.0	67.0		711,945	-11.4	0.0	1	dbSNP_89	67	3051,5549	469.6+/-367.6	543,1965,1792	no	coding-synonymous,coding-synonymous	TMCC2	NM_001242925.1,NM_014858.3	,	597,2512,3394	GG,GA,AA		35.4767,14.8661,28.4945	,	237/632,315/710	205238275	3706,9300	2203	4300	6503	SO:0001819	synonymous_variant	9911	exon3			TGTGGCAGAGTAT	AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"""Transmembrane and coiled-coil domain containing"""	24239	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 2"""			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.945A>G	1.37:g.205238275A>G		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	197	99	0.502538	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Silent	SNP	ENST00000358024.3	37	CCDS30984.1																																																																																			A|0.748;G|0.252	0.252	strong		0.562	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858	
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 GAIIx	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	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	152	50	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	
ETV3L	440695	hgsc.bcm.edu	37	1	157069154	157069154	+	Silent	SNP	A	A	G	rs16838075	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:157069154A>G	ENST00000454449.2	-	2	359	c.75T>C	c.(73-75)gaT>gaC	p.D25D		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	25					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				TGTAGGCCCAATCAGGGAAGG	0.647													G|||	1480	0.295527	0.5575	0.2666	5008	,	,		16899	0.2202		0.1312	False		,,,				2504	0.2086				p.D25D		Atlas-SNP	.											.	ETV3L	73	.	0			c.T75C						PASS	.	G		2197,2209	588.8+/-387.0	550,1097,556	42.0	44.0	43.0		75	4.0	1.0	1	dbSNP_123	43	1207,7393	762.1+/-407.6	98,1011,3191	no	coding-synonymous	ETV3L	NM_001004341.2		648,2108,3747	GG,GA,AA		14.0349,49.8638,26.1725		25/362	157069154	3404,9602	2203	4300	6503	SO:0001819	synonymous_variant	440695	exon2			GGCCCAATCAGGG	AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"""ets variant gene 3-like"""				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.75T>C	1.37:g.157069154A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_001004341		Silent	SNP	ENST00000454449.2	37	CCDS30893.1																																																																																			A|0.729;G|0.271	0.271	strong		0.647	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341	
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 GAIIx	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-AS2_ENST00000411616.1_RNA|MAGI2_ENST00000522391.1_Missense_Mutation_p.L114V	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	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	74	25	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	
MUC2	4583	hgsc.bcm.edu	37	11	1081112	1081112	+	Missense_Mutation	SNP	G	G	C	rs41345745	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1081112G>C	ENST00000441003.2	+	11	1435	c.1408G>C	c.(1408-1410)Gag>Cag	p.E470Q	MUC2_ENST00000359061.5_Missense_Mutation_p.E470Q	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	470	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	ACTGCTCAACGAGCTGCAGGT	0.667													G|||	1814	0.36222	0.4198	0.3617	5008	,	,		16214	0.376		0.2197	False		,,,				2504	0.4172				p.E470Q		Atlas-SNP	.											.	MUC2	614	.	0			c.G1408C						PASS	.	G	GLN/GLU	1542,2438		310,922,758	37.0	42.0	40.0		1408	2.8	0.7	11	dbSNP_127	40	1691,6641		178,1335,2653	yes	missense	MUC2	NM_002457.2	29	488,2257,3411	CC,CG,GG		20.2952,38.7437,26.2589	benign	470/2813	1081112	3233,9079	1990	4166	6156	SO:0001583	missense	4583	exon11			CTCAACGAGCTGC	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.1408G>C	11.37:g.1081112G>C	ENSP00000415183:p.Glu470Gln	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		677	0.309981684981685	185	0.37601626016260165	106	0.292817679558011	224	0.3916083916083916	162	0.21372031662269128	G	8.980	0.975023	0.18736	0.387437	0.202952	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.59502	0.26;0.26	3.8	2.82	0.32997	.	0.659591	0.13673	N	0.370764	T	0.00012	0.0000	.	.	.	0.48632	P	3.1400000000003647E-4	B	0.31241	0.315	B	0.42163	0.378	T	0.40059	-0.9583	8	0.16420	T	0.52	.	12.3415	0.55097	0.0:0.1706:0.8294:0.0	rs41345745;rs61738285	470	E7EUV1	.	Q	470	ENSP00000415183:E470Q;ENSP00000351956:E470Q	ENSP00000351956:E470Q	E	+	1	0	MUC2	1071112	0.990000	0.36364	0.722000	0.30670	0.123000	0.20343	2.410000	0.44592	1.958000	0.56883	0.491000	0.48974	GAG	G|0.716;C|0.284	0.284	strong		0.667	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
OR2T3	343173	hgsc.bcm.edu	37	1	248637391	248637391	+	Missense_Mutation	SNP	C	C	T	rs150934113	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248637391C>T	ENST00000359594.2	+	1	765	c.740C>T	c.(739-741)tCc>tTc	p.S247F		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	247						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(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	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)			GCCACCTGCTCCTCCCACATG	0.562																																					p.S247F		Atlas-SNP	.											OR2T3,colon,carcinoma,0,1	OR2T3	79	1	0			c.C740T						scavenged	.						208.0	180.0	190.0					1																	248637391		2203	4300	6503	SO:0001583	missense	343173	exon1			CCTGCTCCTCCCA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.740C>T	1.37:g.248637391C>T	ENSP00000352604:p.Ser247Phe	Somatic	478	1	0.00209205		WXS	Illumina HiSeq	Phase_I	413	44	0.106538	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	133	0.060897435897435896	67	0.13617886178861788	13	0.03591160220994475	22	0.038461538461538464	31	0.040897097625329816	c	12.69	2.015045	0.35511	.	.	ENSG00000196539	ENST00000359594	T	0.37058	1.22	2.37	-0.0991	0.13625	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00637	0.0021	M	0.93197	3.39	0.09310	N	1	P	0.46912	0.886	P	0.55087	0.768	T	0.01018	-1.1479	9	0.72032	D	0.01	.	5.0305	0.14407	0.0:0.4862:0.3582:0.1556	.	247	Q8NH03	OR2T3_HUMAN	F	247	ENSP00000352604:S247F	ENSP00000352604:S247F	S	+	2	0	OR2T3	246704014	0.000000	0.05858	0.014000	0.15608	0.232000	0.25224	-0.547000	0.06055	0.112000	0.17975	0.186000	0.17326	TCC	C|0.956;T|0.044	0.044	strong		0.562	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
SLC52A3	113278	hgsc.bcm.edu	37	20	746098	746098	+	Silent	SNP	G	G	A	rs3746808	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:746098G>A	ENST00000217254.7	-	2	562	c.321C>T	c.(319-321)gcC>gcT	p.A107A	SLC52A3_ENST00000381944.3_Silent_p.A107A|SLC52A3_ENST00000473664.1_5'UTR	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	107					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										GGACCAAGAAGGCGATGCTGT	0.592													G|||	1284	0.25639	0.1362	0.3401	5008	,	,		19825	0.2014		0.3082	False		,,,				2504	0.363				p.A107A		Atlas-SNP	.											.	.	.	.	0			c.C321T						PASS	.	G		692,3714	275.4+/-272.5	54,584,1565	62.0	48.0	53.0		321	3.7	0.7	20	dbSNP_107	53	2633,5967	403.1+/-347.7	420,1793,2087	no	coding-synonymous	C20orf54	NM_033409.3		474,2377,3652	AA,AG,GG		30.6163,15.7059,25.5651		107/470	746098	3325,9681	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon2			CAAGAAGGCGATG	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.321C>T	20.37:g.746098G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.754;A|0.246	0.246	strong		0.592	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
HDAC10	83933	hgsc.bcm.edu	37	22	50686830	50686830	+	Silent	SNP	G	G	A	rs35820251	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50686830G>A	ENST00000216271.5	-	11	1330	c.978C>T	c.(976-978)gcC>gcT	p.A326A	MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000448072.1_Silent_p.A276A|HDAC10_ENST00000349505.4_Silent_p.A306A|HDAC10_ENST00000498366.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	326					chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		ACAGGGGTGGGGCCGGGTCAC	0.657													G|||	188	0.0375399	0.0008	0.0317	5008	,	,		16824	0.0833		0.0288	False		,,,				2504	0.0532				p.A326A		Atlas-SNP	.											.	HDAC10	29	.	0			c.C978T						PASS	.	G	,	18,4384	24.3+/-50.5	0,18,2183	38.0	40.0	39.0		918,978	-8.2	0.0	22	dbSNP_126	39	195,8403	84.0+/-146.5	1,193,4105	no	coding-synonymous,coding-synonymous	HDAC10	NM_001159286.1,NM_032019.5	,	1,211,6288	AA,AG,GG		2.268,0.4089,1.6385	,	306/650,326/670	50686830	213,12787	2201	4299	6500	SO:0001819	synonymous_variant	83933	exon11			GGGTGGGGCCGGG	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.978C>T	22.37:g.50686830G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	36	18	0.5	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Silent	SNP	ENST00000216271.5	37	CCDS14088.1																																																																																			A|0.024;C|0.000;G|0.976	0.024	strong		0.657	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	
TUFT1	7286	hgsc.bcm.edu	37	1	151512895	151512895	+	Missense_Mutation	SNP	A	A	G	rs3828054	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:151512895A>G	ENST00000368849.3	+	1	115	c.53A>G	c.(52-54)cAg>cGg	p.Q18R	TUFT1_ENST00000353024.3_Missense_Mutation_p.Q18R|TUFT1_ENST00000392712.3_Missense_Mutation_p.Q18R|TUFT1_ENST00000538902.1_5'UTR|TUFT1_ENST00000368848.2_Missense_Mutation_p.Q18R|RP11-74C1.4_ENST00000434112.1_RNA	NM_020127.2	NP_064512.1	Q9NNX1	TUFT1_HUMAN	tuftelin 1	18			Q -> R (in dbSNP:rs3828054).		bone mineralization (GO:0030282)|odontogenesis (GO:0042476)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	structural constituent of tooth enamel (GO:0030345)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)	13	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			CCAGAGGACCAGGCGGCGGTA	0.617													A|||	560	0.111821	0.1641	0.098	5008	,	,		15997	0.0526		0.1133	False		,,,				2504	0.1104				p.Q18R		Atlas-SNP	.											TUFT1,NS,carcinoma,0,1	TUFT1	32	1	0			c.A53G						PASS	.	A	ARG/GLN,ARG/GLN	678,3728	285.5+/-278.2	57,564,1582	156.0	144.0	148.0		53,53	2.5	0.3	1	dbSNP_107	148	1069,7531	224.4+/-260.8	64,941,3295	yes	missense,missense	TUFT1	NM_001126337.1,NM_020127.2	43,43	121,1505,4877	GG,GA,AA		12.4302,15.3881,13.4323	benign,benign	18/366,18/391	151512895	1747,11259	2203	4300	6503	SO:0001583	missense	7286	exon1			AGGACCAGGCGGC	AF254260	CCDS1000.1, CCDS44223.1	1q21	2008-02-05			ENSG00000143367	ENSG00000143367			12422	protein-coding gene	gene with protein product		600087				7919663	Standard	NM_020127		Approved		uc001eyl.3	Q9NNX1	OTTHUMG00000012536	ENST00000368849.3:c.53A>G	1.37:g.151512895A>G	ENSP00000357842:p.Gln18Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_020127	B2RD57|D3DV21|D3DV22|Q5T384|Q5T385|Q9BU28|Q9H5L1	Missense_Mutation	SNP	ENST00000368849.3	37	CCDS1000.1	229	0.10485347985347986	84	0.17073170731707318	37	0.10220994475138122	20	0.03496503496503497	88	0.11609498680738786	A	14.77	2.634094	0.47049	0.153881	0.124302	ENSG00000143367	ENST00000368849;ENST00000392712;ENST00000353024;ENST00000368848;ENST00000544350;ENST00000507671	T;T;T;T	0.32272	2.28;1.53;1.96;1.46	4.96	2.54	0.30619	.	0.620936	0.16645	N	0.205446	T	0.09818	0.0241	L	0.57536	1.79	0.09310	P	0.999999609933	P;P	0.39782	0.634;0.688	B;B	0.36134	0.167;0.218	T	0.14699	-1.0463	9	0.08381	T	0.77	-8.2208	9.0122	0.36148	0.6337:0.3663:0.0:0.0	rs3828054;rs52810023;rs59912521;rs3828054	18;18	Q9NNX1-2;Q9NNX1	.;TUFT1_HUMAN	R	18	ENSP00000357842:Q18R;ENSP00000376476:Q18R;ENSP00000343781:Q18R;ENSP00000357841:Q18R	ENSP00000343781:Q18R	Q	+	2	0	TUFT1	149779519	0.288000	0.24324	0.350000	0.25708	0.928000	0.56348	1.688000	0.37690	0.335000	0.23614	0.459000	0.35465	CAG	A|0.885;G|0.115	0.115	strong		0.617	TUFT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035022.1	NM_020127	
PM20D1	148811	hgsc.bcm.edu	37	1	205819104	205819104	+	Missense_Mutation	SNP	G	G	A	rs11540014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205819104G>A	ENST00000367136.4	-	1	141	c.97C>T	c.(97-99)Cat>Tat	p.H33Y	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	33			H -> Y (in dbSNP:rs11540014). {ECO:0000269|PubMed:15489334}.		negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			GCCCTTTGATGCTCCCCGCTC	0.602													G|||	806	0.160942	0.053	0.0605	5008	,	,		18337	0.4266		0.0974	False		,,,				2504	0.1697				p.H33Y		Atlas-SNP	.											.	PM20D1	56	.	0			c.C97T						PASS	.	G	TYR/HIS	266,4140	150.7+/-184.7	8,250,1945	85.0	86.0	85.0		97	-1.6	0.0	1	dbSNP_120	85	648,7952	165.9+/-218.0	20,608,3672	yes	missense	PM20D1	NM_152491.4	83	28,858,5617	AA,AG,GG		7.5349,6.0372,7.0275	benign	33/503	205819104	914,12092	2203	4300	6503	SO:0001583	missense	148811	exon1			TTTGATGCTCCCC		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.97C>T	1.37:g.205819104G>A	ENSP00000356104:p.His33Tyr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	139	77	0.553957	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	361	0.1652930402930403	23	0.046747967479674794	23	0.06353591160220995	241	0.42132867132867136	74	0.09762532981530343	G	1.008	-0.688948	0.03328	0.060372	0.075349	ENSG00000162877	ENST00000367136	T	0.06528	3.29	5.17	-1.59	0.08453	.	1.185250	0.05391	N	0.539060	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45411	-0.9263	9	0.02654	T	1	.	0.572	0.00697	0.2463:0.1352:0.3419:0.2767	rs11540014;rs61022628;rs11540014	33	Q6GTS8	P20D1_HUMAN	Y	33	ENSP00000356104:H33Y	ENSP00000356104:H33Y	H	-	1	0	PM20D1	204085727	0.001000	0.12720	0.000000	0.03702	0.029000	0.11900	0.390000	0.20768	-0.492000	0.06687	0.655000	0.94253	CAT	G|0.889;A|0.111	0.111	strong		0.602	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
CARD14	79092	hgsc.bcm.edu	37	17	78166385	78166385	+	Silent	SNP	C	C	T	rs11658460	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78166385C>T	ENST00000573882.1	+	11	1859	c.1323C>T	c.(1321-1323)gaC>gaT	p.D441D	CARD14_ENST00000344227.2_Silent_p.D441D|CARD14_ENST00000573754.1_3'UTR|CARD14_ENST00000392434.2_Silent_p.D204D|CARD14_ENST00000570421.1_Silent_p.D441D			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	441					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)			GCCCCAGAGACGACAGCGACT	0.667													C|||	608	0.121406	0.115	0.0533	5008	,	,		13764	0.1696		0.1054	False		,,,				2504	0.1452				p.D441D		Atlas-SNP	.											CARD14_ENST00000309710,NS,carcinoma,0,2	CARD14	98	2	0			c.C1323T						PASS	.	C	,	529,3877	238.4+/-249.8	32,465,1706	52.0	52.0	52.0		1323,612	-7.2	0.0	17	dbSNP_120	52	798,7802	183.9+/-232.0	45,708,3547	no	coding-synonymous,coding-synonymous	CARD14	NM_024110.3,NM_052819.2	,	77,1173,5253	TT,TC,CC		9.2791,12.0064,10.203	,	441/1005,204/435	78166385	1327,11679	2203	4300	6503	SO:0001819	synonymous_variant	79092	exon9			CAGAGACGACAGC	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.1323C>T	17.37:g.78166385C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	166	65	0.391566	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			C|0.895;T|0.105	0.105	strong		0.667	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
ARHGEF4	50649	hgsc.bcm.edu	37	2	131688783	131688783	+	Missense_Mutation	SNP	G	G	A	rs61750360	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:131688783G>A	ENST00000326016.5	+	3	772	c.253G>A	c.(253-255)Gtc>Atc	p.V85I	ARHGEF4_ENST00000409359.1_Missense_Mutation_p.V941I|ARHGEF4_ENST00000428230.2_Missense_Mutation_p.V85I|SCARNA4_ENST00000517020.2_RNA|ARHGEF4_ENST00000409303.1_Missense_Mutation_p.V85I|ARHGEF4_ENST00000525839.1_Missense_Mutation_p.V85I|ARHGEF4_ENST00000392953.3_Missense_Mutation_p.V85I	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	85	ABR (APC-binding region) domain.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		GCAGGCCCACGTCGAAAGGAG	0.577													G|||	700	0.139776	0.0378	0.0951	5008	,	,		20620	0.1319		0.175	False		,,,				2504	0.2812				p.V85I		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.G253A						PASS	.	G	ILE/VAL,ILE/VAL	260,4146		14,232,1957	34.0	28.0	30.0		253,253	-6.6	0.0	2	dbSNP_129	30	1482,7118		125,1232,2943	yes	missense,missense	ARHGEF4	NM_032995.1,NM_015320.2	29,29	139,1464,4900	AA,AG,GG		17.2326,5.901,13.3938	benign,benign	85/671,85/691	131688783	1742,11264	2203	4300	6503	SO:0001583	missense	50649	exon3			GCCCACGTCGAAA	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.253G>A	2.37:g.131688783G>A	ENSP00000316845:p.Val85Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	54	11	0.203704	NM_032995	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	37	CCDS2165.1	265	0.12133699633699634	17	0.034552845528455285	41	0.1132596685082873	60	0.1048951048951049	147	0.19393139841688653	G	12.77	2.037539	0.35989	0.05901	0.172326	ENSG00000136002	ENST00000409359;ENST00000326016;ENST00000392953;ENST00000438985;ENST00000428230;ENST00000525839;ENST00000409303	T;T;T;T;T;T;T	0.70164	0.95;-0.18;-0.29;0.95;0.96;-0.29;-0.46	4.72	-6.62	0.01813	.	.	.	.	.	T	0.00073	0.0002	L	0.27053	0.805	0.80722	P	0.0	B;B;B;B	0.28470	0.001;0.213;0.001;0.001	B;B;B;B	0.16722	0.0;0.016;0.001;0.0	T	0.06215	-1.0839	8	0.34782	T	0.22	.	0.0491	0.00011	0.2661:0.2247:0.2034:0.3058	rs61750360	85;941;85;85	E9PEM0;E7EV07;Q9NR80-4;Q9NR80	.;.;.;ARHG4_HUMAN	I	941;85;85;265;85;85;85	ENSP00000386794:V941I;ENSP00000316845:V85I;ENSP00000376680:V85I;ENSP00000389661:V265I;ENSP00000398455:V85I;ENSP00000432267:V85I;ENSP00000387285:V85I	ENSP00000316845:V85I	V	+	1	0	ARHGEF4	131405253	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-1.771000	0.01789	-1.009000	0.03400	0.467000	0.42956	GTC	G|0.866;A|0.134	0.134	strong		0.577	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
MLX	6945	hgsc.bcm.edu	37	17	40722029	40722029	+	Missense_Mutation	SNP	A	A	G	rs665268	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40722029A>G	ENST00000246912.4	+	7	721	c.668A>G	c.(667-669)cAg>cGg	p.Q223R	MLX_ENST00000346833.4_Missense_Mutation_p.Q139R|MLX_ENST00000435881.2_Missense_Mutation_p.Q169R	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	223			Q -> R (in dbSNP:rs665268).		energy reserve metabolic process (GO:0006112)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|positive regulation of cellular metabolic process (GO:0031325)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(3)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	10		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		AAGGCACACCAGGACAACCCC	0.547													A|||	1610	0.321486	0.1952	0.2075	5008	,	,		22617	0.4355		0.2654	False		,,,				2504	0.5133				p.Q223R	GBM(121;657 1601 4665 24731 34640)	Atlas-SNP	.											.	MLX	17	.	0			c.A668G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN	877,3529	341.8+/-306.9	88,701,1414	118.0	101.0	107.0		668,506,416	4.7	1.0	17	dbSNP_83	107	2350,6250	393.6+/-344.4	318,1714,2268	yes	missense,missense,missense	MLX	NM_170607.2,NM_198204.1,NM_198205.1	43,43,43	406,2415,3682	GG,GA,AA		27.3256,19.9047,24.8116	probably-damaging,probably-damaging,probably-damaging	223/299,169/245,139/215	40722029	3227,9779	2203	4300	6503	SO:0001583	missense	6945	exon7			CACACCAGGACAA	AF213668	CCDS11430.1, CCDS42341.1, CCDS45687.1	17q21.1	2013-05-21	2012-11-15	2005-02-11		ENSG00000108788		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	11645	protein-coding gene	gene with protein product		602976	"""transcription factor-like 4"", ""MAX-like protein X"""	TCFL4		8973301	Standard	NM_170607		Approved	MAD7, MXD7, bHLHd13	uc002iag.3	Q9UH92		ENST00000246912.4:c.668A>G	17.37:g.40722029A>G	ENSP00000246912:p.Gln223Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_170607	A8K2J3|B2RAV8|B2RD73|Q53XM6|Q96FL2|Q9H2V0|Q9H2V1|Q9H2V2|Q9NXN3	Missense_Mutation	SNP	ENST00000246912.4	37	CCDS11430.1	634	0.2902930402930403	110	0.22357723577235772	71	0.19613259668508287	242	0.4230769230769231	211	0.2783641160949868	A	15.08	2.727690	0.48833	0.199047	0.273256	ENSG00000108788	ENST00000346833;ENST00000246912;ENST00000435881	T;T;T	0.80738	-1.08;-1.41;-1.12	5.72	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.09310	P	0.99999999486047	D;B;B	0.89917	1.0;0.005;0.011	D;B;B	0.74023	0.982;0.006;0.029	T	0.14531	-1.0469	9	0.25106	T	0.35	-16.5052	11.4367	0.50072	0.9298:0.0:0.0702:0.0	rs665268;rs665268	139;223;169	Q9UH92-2;Q9UH92;Q9UH92-3	.;MLX_HUMAN;.	R	139;223;169	ENSP00000320913:Q139R;ENSP00000246912:Q223R;ENSP00000416627:Q169R	ENSP00000246912:Q223R	Q	+	2	0	MLX	37975555	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.525000	0.81892	1.014000	0.39417	0.459000	0.35465	CAG	A|0.732;G|0.268	0.268	strong		0.547	MLX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450415.1	NM_170607	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751544	19751544	+	Silent	SNP	C	C	T	rs2297224	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:19751544C>T	ENST00000400113.3	-	4	683	c.579G>A	c.(577-579)acG>acA	p.T193T		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	193					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		GTTCCAGGGTCGTGTGGGTGG	0.552													C|||	1446	0.288738	0.2171	0.2824	5008	,	,		20432	0.3671		0.2674	False		,,,				2504	0.3313				p.T193T		Atlas-SNP	.											.	TUBA3C	166	.	0			c.G579A						PASS	.	C		895,3511	345.7+/-308.6	108,679,1416	149.0	146.0	147.0		579	-1.0	1.0	13	dbSNP_100	147	2078,6518	360.1+/-331.8	261,1556,2481	no	coding-synonymous	TUBA3C	NM_006001.2		369,2235,3897	TT,TC,CC		24.174,20.3132,22.8657		193/451	19751544	2973,10029	2203	4298	6501	SO:0001819	synonymous_variant	7278	exon4			CAGGGTCGTGTGG	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.579G>A	13.37:g.19751544C>T		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	275	129	0.469091	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			C|0.737;T|0.263	0.263	strong		0.552	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
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 GAIIx	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		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	90	36	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	
SOGA1	140710	hgsc.bcm.edu	37	20	35414905	35414905	+	Missense_Mutation	SNP	G	G	T	rs73109216	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:35414905G>T	ENST00000357779.3	-	15	4581	c.4255C>A	c.(4255-4257)Ctc>Atc	p.L1419I	SOGA1_ENST00000237536.4_Missense_Mutation_p.L1657I|SOGA1_ENST00000456801.2_Missense_Mutation_p.L1260I|SOGA1_ENST00000279034.6_Intron			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	1419					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						CTGGGGGGGAGTGCCCTCTCC	0.662													G|||	261	0.0521166	0.003	0.1412	5008	,	,		17075	0.0		0.0825	False		,,,				2504	0.0777				p.L1657I		Atlas-SNP	.											.	SOGA1	136	.	0			c.C4969A						PASS	.						38.0	44.0	42.0					20																	35414905		692	1591	2283	SO:0001583	missense	140710	exon15			GGGGGAGTGCCCT	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.4255C>A	20.37:g.35414905G>T	ENSP00000350424:p.Leu1419Ile	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	16	10	0.625	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		109	0.04990842490842491	3	0.006097560975609756	44	0.12154696132596685	0	0.0	62	0.08179419525065963	G	10.85	1.467932	0.26335	.	.	ENSG00000149639	ENST00000237536;ENST00000456801;ENST00000357779	T;T;T	0.17213	2.29;2.3;2.3	4.72	2.72	0.32119	.	1.008940	0.07937	N	0.978596	T	0.00178	0.0005	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.43360	-0.9396	8	0.62326	D	0.03	-0.4527	11.4719	0.50275	0.0:0.6416:0.3584:0.0	.	.	.	.	I	1657;1260;1419	ENSP00000237536:L1657I;ENSP00000413886:L1260I;ENSP00000350424:L1419I	ENSP00000237536:L1657I	L	-	1	0	KIAA0889	34848319	0.100000	0.21855	0.005000	0.12908	0.474000	0.32979	3.383000	0.52471	0.704000	0.31869	-0.539000	0.04255	CTC	G|0.950;T|0.050	0.050	strong		0.662	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181	
GGT1	2678	hgsc.bcm.edu	37	22	25023419	25023419	+	Silent	SNP	C	C	T	rs202087650	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:25023419C>T	ENST00000400382.1	+	12	1796	c.1041C>T	c.(1039-1041)tcC>tcT	p.S347S	GGT1_ENST00000400383.1_Silent_p.S347S|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404920.1_Silent_p.S3S|GGT1_ENST00000401885.1_Silent_p.S3S|GGT1_ENST00000406383.2_Silent_p.S347S|GGT1_ENST00000400380.1_Silent_p.S347S|GGT1_ENST00000403838.1_Silent_p.S3S|GGT1_ENST00000404532.1_Silent_p.S3S|GGT1_ENST00000248923.4_Silent_p.S347S|GGT1_ENST00000404223.1_Silent_p.S3S			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	347					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	ACATGACCTCCGAGTTCTTCG	0.647																																					p.S347S		Atlas-SNP	.											GGT1,NS,carcinoma,0,2	GGT1	68	2	0			c.C1041T						scavenged	.						53.0	54.0	54.0					22																	25023419		2201	4297	6498	SO:0001819	synonymous_variant	2678	exon12			GACCTCCGAGTTC	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1041C>T	22.37:g.25023419C>T		Somatic	228	4	0.0175439		WXS	Illumina HiSeq	Phase_I	292	34	0.116438	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			C|0.989;T|0.011	0.011	strong		0.647	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72503344	72503344	+	Silent	SNP	G	G	A	rs10999502	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72503344G>A	ENST00000373207.1	+	13	1965	c.1965G>A	c.(1963-1965)acG>acA	p.T655T	ADAMTS14_ENST00000373208.1_Silent_p.T658T	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	655	Cys-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CGGCGGACACGGGGGACGTGG	0.622													G|||	1560	0.311502	0.1641	0.2089	5008	,	,		19688	0.5387		0.2167	False		,,,				2504	0.4468				p.T658T		Atlas-SNP	.											ADAMTS14,NS,adenoma,0,1	ADAMTS14	148	1	0			c.G1974A						PASS	.	G	,	760,3646	308.0+/-290.3	51,658,1494	95.0	76.0	82.0		1965,1974	-10.0	0.4	10	dbSNP_120	82	1824,6776	328.1+/-318.2	192,1440,2668	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	243,2098,4162	AA,AG,GG		21.2093,17.2492,19.8678	,	655/1224,658/1227	72503344	2584,10422	2203	4300	6503	SO:0001819	synonymous_variant	140766	exon13			GGACACGGGGGAC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.1965G>A	10.37:g.72503344G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	127	69	0.543307	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			G|0.768;A|0.232	0.232	strong		0.622	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
TERT	7015	hgsc.bcm.edu	37	5	1294086	1294086	+	Silent	SNP	C	C	T	rs2736098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:1294086C>T	ENST00000310581.5	-	2	972	c.915G>A	c.(913-915)gcG>gcA	p.A305A	TERT_ENST00000508104.2_Silent_p.A305A|TERT_ENST00000296820.5_Silent_p.A305A|TERT_ENST00000522877.1_5'Flank|TERT_ENST00000334602.6_Silent_p.A305A	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	305	Linker.|Required for oligomerization.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	ATGGGGGGCCCGCGTGGTGCT	0.682									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis				C|||	1330	0.265575	0.0658	0.2032	5008	,	,		15213	0.371		0.2346	False		,,,				2504	0.5031				p.A305A		Atlas-SNP	.											.	TERT	2594	.	0			c.G915A						PASS	.	C	,	454,3864		27,400,1732	16.0	16.0	16.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	915,915	-4.8	0.0	5	dbSNP_100	16	2202,6278		319,1564,2357	no	coding-synonymous,coding-synonymous	TERT	NM_001193376.1,NM_198253.2	,	346,1964,4089	TT,TC,CC		25.967,10.5141,20.7532	,	305/1070,305/1133	1294086	2656,10142	2159	4240	6399	SO:0001819	synonymous_variant	7015	exon2	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	GGGGCCCGCGTGG	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.915G>A	5.37:g.1294086C>T		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_001193376	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	37	CCDS3861.2																																																																																			C|0.792;T|0.208	0.208	strong		0.682	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2		
LRP1B	53353	hgsc.bcm.edu	37	2	141773397	141773397	+	Silent	SNP	C	C	A	rs78806080	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:141773397C>A	ENST00000389484.3	-	13	3029	c.2058G>T	c.(2056-2058)cgG>cgT	p.R686R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	686					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CAAAAATCTGCCGATTGAATC	0.423										TSP Lung(27;0.18)			C|||	170	0.0339457	0.0	0.0274	5008	,	,		17062	0.002		0.0736	False		,,,				2504	0.0767				p.R686R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.G2058T						PASS	.	C		53,4353	52.3+/-87.9	1,51,2151	152.0	148.0	149.0		2058	2.9	1.0	2	dbSNP_132	149	546,8054	150.1+/-205.1	14,518,3768	no	coding-synonymous	LRP1B	NM_018557.2		15,569,5919	AA,AC,CC		6.3488,1.2029,4.6056		686/4600	141773397	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon13			AATCTGCCGATTG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.2058G>T	2.37:g.141773397C>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	104	20	0.192308	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			C|0.957;A|0.043	0.043	strong		0.423	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
HLA-A	3105	hgsc.bcm.edu	37	6	29910761	29910761	+	Missense_Mutation	SNP	G	G	A	rs1136688	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29910761G>A	ENST00000396634.1	+	4	642	c.301G>A	c.(301-303)Gac>Aac	p.D101N	HLA-A_ENST00000376806.5_Missense_Mutation_p.D101N|HLA-A_ENST00000376802.2_Missense_Mutation_p.D101N|HLA-A_ENST00000376809.5_Missense_Mutation_p.D101N			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	101	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TGACCGAGTGGACCTGGGGAC	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	1928	0.384984	0.3812	0.3963	5008	,	,		10355	0.3115		0.3936	False		,,,				2504	0.4489				p.D101N		Atlas-SNP	.											.	HLA-A	89	.	0			c.G301A						PASS	.	A	ASN/ASP	1178,3210		254,670,1270	60.0	64.0	62.0		301	-7.2	0.0	6	dbSNP_86	62	2688,5880		672,1344,2268	no	missense	HLA-A	NM_002116.7	23	926,2014,3538	AA,AG,GG		31.3725,26.8459,29.8395	benign	101/366	29910761	3866,9090	2194	4284	6478	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGAGTGGACCTGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.301G>A	6.37:g.29910761G>A	ENSP00000379873:p.Asp101Asn	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	118	118	1	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	631	0.2889194139194139	145	0.29471544715447157	127	0.35082872928176795	124	0.21678321678321677	235	0.3100263852242744	.	6.812	0.518999	0.13005	0.268459	0.313725	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00682	5.86;5.86;5.86;5.86	3.57	-7.15	0.01521	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	2.561180	0.02614	N	0.102464	T	0.00073	0.0002	N	0.00670	-1.27	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.12156	0.002;0.007;0.002;0.003;0.002	T	0.43540	-0.9385	9	0.07325	T	0.83	.	9.8047	0.40786	0.1773:0.0:0.5959:0.2268	rs1136688;rs2231003;rs3179183;rs3200156;rs9260135;rs16896601;rs17423978;rs41563415	101;101;101;101;101	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	N	101	ENSP00000379873:D101N;ENSP00000366002:D101N;ENSP00000366005:D101N;ENSP00000365998:D101N	ENSP00000348012:D101N	D	+	1	0	HLA-A	30018740	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.635000	0.00108	-3.195000	0.00218	-4.015000	0.00013	GAC	A|0.386;G|0.614	0.386	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SSPO	23145	hgsc.bcm.edu	37	7	149503834	149503834	+	RNA	SNP	G	G	T	rs141503732	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:149503834G>T	ENST00000378016.2	+	0	8662							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)			CCAGTGCCCAGAGAACATGTT	0.612													G|||	10	0.00199681	0.0	0.0029	5008	,	,		18927	0.0		0.008	False		,,,				2504	0.0				p.E2888X		Atlas-SNP	.											.	.	.	.	0			c.G8662T						PASS	.	G		6,3894		0,6,1944	27.0	32.0	30.0		8666	3.2	0.0	7	dbSNP_134	30	18,8110		0,18,4046	yes	coding-notMod3	SSPO	NM_198455.2		0,24,5990	TT,TG,GG		0.2215,0.1538,0.1995			149503834	24,12004	1950	4064	6014			23145	exon59			TGCCCAGAGAACA	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.149503834G>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	161	87	0.540373	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.996;T|0.004	0.004	strong		0.612	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
PSPC1	55269	hgsc.bcm.edu	37	13	20279879	20279879	+	Missense_Mutation	SNP	T	T	C	rs200516102	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:20279879T>C	ENST00000338910.4	-	8	1468	c.1309A>G	c.(1309-1311)Atg>Gtg	p.M437V		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	437	Gly-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		CCAGGACCCATTGGTGGGCCA	0.473																																					p.M437V		Atlas-SNP	.											PSPC1,NS,haematopoietic_neoplasm,0,1	PSPC1	61	1	0			c.A1309G						scavenged	.						49.0	55.0	53.0					13																	20279879		1832	4086	5918	SO:0001583	missense	55269	exon9			GACCCATTGGTGG	AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"""RNA binding motif (RRM) containing"""	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.1309A>G	13.37:g.20279879T>C	ENSP00000343966:p.Met437Val	Somatic	566	4	0.00706714		WXS	Illumina HiSeq	Phase_I	452	140	0.309735	NM_001042414	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	T	7.585	0.669496	0.14776	.	.	ENSG00000121390	ENST00000338910;ENST00000422828	T	0.13420	2.59	5.29	2.98	0.34508	.	0.178534	0.56097	D	0.000021	T	0.08044	0.0201	N	0.22421	0.69	0.30474	N	0.772982	B	0.15141	0.012	B	0.12156	0.007	T	0.25847	-1.0120	10	0.14252	T	0.57	-7.4851	9.0578	0.36416	0.0:0.0762:0.1546:0.7692	.	437	Q8WXF1	PSPC1_HUMAN	V	437;377	ENSP00000343966:M437V	ENSP00000343966:M437V	M	-	1	0	PSPC1	19177879	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	0.910000	0.28571	0.844000	0.35094	0.402000	0.26972	ATG	T|0.998;C|0.002	0.002	strong		0.473	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2		
PLEKHH3	79990	hgsc.bcm.edu	37	17	40822678	40822678	+	Silent	SNP	C	C	T	rs2277618	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40822678C>T	ENST00000591022.1	-	10	1854	c.1467G>A	c.(1465-1467)ggG>ggA	p.G489G	PLEKHH3_ENST00000456950.2_5'UTR|PLEKHH3_ENST00000293349.6_Silent_p.G486G|PLEKHH3_ENST00000412503.1_Silent_p.G486G	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	489	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		ATAGTCTCCACCCGGAGTCGG	0.647													C|||	1066	0.212859	0.0098	0.2378	5008	,	,		11351	0.5347		0.1421	False		,,,				2504	0.2106				p.G489G		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.G1467A						PASS	.	C		140,4266	98.9+/-137.6	0,140,2063	48.0	47.0	47.0		1467	-1.6	0.9	17	dbSNP_100	47	1083,7517	224.1+/-260.6	59,965,3276	no	coding-synonymous	PLEKHH3	NM_024927.4		59,1105,5339	TT,TC,CC		12.593,3.1775,9.4034		489/794	40822678	1223,11783	2203	4300	6503	SO:0001819	synonymous_variant	79990	exon10			TCTCCACCCGGAG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1467G>A	17.37:g.40822678C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Silent	SNP	ENST00000591022.1	37	CCDS11434.1																																																																																			C|0.843;T|0.157	0.157	strong		0.647	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
PDHB	5162	hgsc.bcm.edu	37	3	58410554	58410554	+	IGR	SNP	C	C	T	rs34579268	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:58410554C>T	ENST00000302746.6	-	0	1527				PXK_ENST00000479241.1_Silent_p.G528G|PXK_ENST00000536660.1_Missense_Mutation_p.A398V|PXK_ENST00000383716.3_Missense_Mutation_p.A502V|PXK_ENST00000463280.1_3'UTR|PXK_ENST00000302779.5_Missense_Mutation_p.A518V|PXK_ENST00000356151.2_Missense_Mutation_p.A535V	NM_000925.3|NM_001173468.1	NP_000916.2|NP_001166939.1	P11177	ODPB_HUMAN	pyruvate dehydrogenase (lipoamide) beta						acetyl-CoA biosynthetic process from pyruvate (GO:0006086)|cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|pyruvate dehydrogenase complex (GO:0045254)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)|pyruvate dehydrogenase activity (GO:0004738)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)	9				BRCA - Breast invasive adenocarcinoma(55;0.000179)|Kidney(10;0.00231)|KIRC - Kidney renal clear cell carcinoma(10;0.00258)|OV - Ovarian serous cystadenocarcinoma(275;0.187)	Pyruvic acid(DB00119)	AGCACCGAGGCACCTGCCCAG	0.567													C|||	1029	0.205471	0.2141	0.2839	5008	,	,		17867	0.001		0.3777	False		,,,				2504	0.1718				p.A535V		Atlas-SNP	.											PXK_ENST00000356151,brain,glioma,0,1	PXK	89	1	0			c.C1604T						PASS	.	C	VAL/ALA	952,3454	360.4+/-315.2	97,758,1348	61.0	48.0	53.0		1604	-5.2	0.0	3	dbSNP_126	53	3205,5395	482.5+/-370.9	615,1975,1710	yes	missense	PXK	NM_017771.3	64	712,2733,3058	TT,TC,CC		37.2674,21.6069,31.9622	benign	535/579	58410554	4157,8849	2203	4300	6503	SO:0001628	intergenic_variant	54899	exon18			CCGAGGCACCTGC		CCDS2890.1, CCDS54602.1	3p21.1-p14.2	1995-12-20			ENSG00000168291	ENSG00000168291	1.2.4.1		8808	protein-coding gene	gene with protein product		179060					Standard	NR_033384		Approved		uc003dkf.4	P11177	OTTHUMG00000159157		3.37:g.58410554C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	150	79	0.526667	NM_017771	B2R7L0|B4DDD7|Q6FH45|Q9BQ27|Q9UFK3	Missense_Mutation	SNP	ENST00000302746.6	37	CCDS2890.1	521|521	0.23855311355311357|0.23855311355311357	131|131	0.266260162601626|0.266260162601626	111|111	0.30662983425414364|0.30662983425414364	2|2	0.0034965034965034965|0.0034965034965034965	277|277	0.3654353562005277|0.3654353562005277	C|C	8.525|8.525	0.869609|0.869609	0.17322|0.17322	0.216069|0.216069	0.372674|0.372674	ENSG00000168297|ENSG00000168297	ENST00000356151;ENST00000302779;ENST00000383716;ENST00000536660|ENST00000479134	T;T;T;T|.	0.19250|.	2.16;2.16;2.17;2.17|.	6.03|6.03	-5.16|-5.16	0.02857|0.02857	.|.	1.260030|.	0.05066|.	N|.	0.480815|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.16478|0.16478	0.41|0.41	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.35301|0.35301	-0.9794|-0.9794	9|4	0.37606|.	T|.	0.19|.	2.213|2.213	11.2739|11.2739	0.49155|0.49155	0.0:0.2675:0.0935:0.639|0.0:0.2675:0.0935:0.639	rs34579268;rs58363342|rs34579268;rs58363342	502;535|.	Q7Z7A4-6;Q7Z7A4|.	.;PXK_HUMAN|.	V|Y	535;518;502;398|269	ENSP00000348472:A535V;ENSP00000305045:A518V;ENSP00000373222:A502V;ENSP00000438356:A398V|.	ENSP00000305045:A518V|.	A|H	+|+	2|1	0|0	PXK|PXK	58385594|58385594	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.334000|0.334000	0.28698|0.28698	-1.086000|-1.086000	0.03386|0.03386	-0.924000|-0.924000	0.03780|0.03780	-0.140000|-0.140000	0.14226|0.14226	GCA|CAC	C|0.691;T|0.309	0.309	strong		0.567	PDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353558.1		
LRRC47	57470	hgsc.bcm.edu	37	1	3712513	3712513	+	Silent	SNP	G	G	C	rs148481344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:3712513G>C	ENST00000378251.1	-	1	555	c.528C>G	c.(526-528)ggC>ggG	p.G176G		NM_020710.2	NP_065761.1	Q8N1G4	LRC47_HUMAN	leucine rich repeat containing 47	176							phenylalanine-tRNA ligase activity (GO:0004826)|poly(A) RNA binding (GO:0044822)	p.G176G(1)		central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17	all_cancers(77;0.0375)|Ovarian(185;0.0634)|all_lung(157;0.208)|Lung NSC(156;0.21)	all_epithelial(116;1.34e-16)|all_lung(118;2.53e-06)|Lung NSC(185;0.00028)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.0743)|Ovarian(437;0.127)		Epithelial(90;5.49e-39)|OV - Ovarian serous cystadenocarcinoma(86;1.43e-22)|GBM - Glioblastoma multiforme(42;3.69e-16)|Colorectal(212;1.21e-05)|COAD - Colon adenocarcinoma(227;5.87e-05)|Kidney(185;0.000367)|BRCA - Breast invasive adenocarcinoma(365;0.000704)|KIRC - Kidney renal clear cell carcinoma(229;0.00567)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.124)		GGGGCAGCGCGCCGGGGCGAA	0.692													G|||	36	0.0071885	0.0	0.0115	5008	,	,		11015	0.001		0.0249	False		,,,				2504	0.002				p.G176G		Atlas-SNP	.											LRRC47,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	LRRC47	42	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C528G						scavenged	.	G		8,4354		0,8,2173	12.0	12.0	12.0		528	-6.6	0.1	1	dbSNP_134	12	105,8427		2,101,4163	no	coding-synonymous	LRRC47	NM_020710.2		2,109,6336	CC,CG,GG		1.2307,0.1834,0.8764		176/584	3712513	113,12781	2181	4266	6447	SO:0001819	synonymous_variant	57470	exon1			CAGCGCGCCGGGG	AB033011	CCDS51.1	1p36.32	2008-02-05			ENSG00000130764	ENSG00000130764			29207	protein-coding gene	gene with protein product						10574461	Standard	NM_020710		Approved	KIAA1185, RP1-286D6.3	uc001akx.1	Q8N1G4	OTTHUMG00000003506	ENST00000378251.1:c.528C>G	1.37:g.3712513G>C		Somatic	80	2	0.025		WXS	Illumina HiSeq	Phase_I	59	34	0.576271	NM_020710	Q9ULN5	Silent	SNP	ENST00000378251.1	37	CCDS51.1																																																																																			G|0.985;C|0.015	0.015	strong		0.692	LRRC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009744.1	NM_020710	
BAIAP2L1	55971	hgsc.bcm.edu	37	7	97922875	97922875	+	Silent	SNP	G	G	A	rs13008	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:97922875G>A	ENST00000005260.8	-	14	1709	c.1494C>T	c.(1492-1494)cgC>cgT	p.R498R		NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	498	Binds F-actin.				filopodium assembly (GO:0046847)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of actin filament polymerization (GO:0030838)|response to bacterium (GO:0009617)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)			NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)	23	all_cancers(62;4.34e-10)|all_epithelial(64;5e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0113)|all_lung(186;0.0126)		STAD - Stomach adenocarcinoma(171;0.215)			TCACAGTCGGGCGGAGTTTCA	0.537													G|||	739	0.147564	0.0144	0.2637	5008	,	,		16327	0.001		0.4284	False		,,,				2504	0.1074				p.R498R		Atlas-SNP	.											.	BAIAP2L1	61	.	0			c.C1494T						PASS	.	G		433,3973	208.5+/-229.5	21,391,1791	129.0	127.0	128.0		1494	-4.7	0.0	7	dbSNP_52	128	4026,4574	556.9+/-386.9	945,2136,1219	no	coding-synonymous	BAIAP2L1	NM_018842.4		966,2527,3010	AA,AG,GG		46.814,9.8275,34.2842		498/512	97922875	4459,8547	2203	4300	6503	SO:0001819	synonymous_variant	55971	exon14			AGTCGGGCGGAGT	AF119666	CCDS34687.1	7q22.1	2012-10-04			ENSG00000006453	ENSG00000006453			21649	protein-coding gene	gene with protein product		611877					Standard	NM_018842		Approved	IRTKS	uc003upj.3	Q9UHR4	OTTHUMG00000165117	ENST00000005260.8:c.1494C>T	7.37:g.97922875G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	95	93	0.978947	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Silent	SNP	ENST00000005260.8	37	CCDS34687.1																																																																																			G|0.717;A|0.283	0.283	strong		0.537	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842	
TM9SF1	10548	hgsc.bcm.edu	37	14	24662177	24662177	+	Missense_Mutation	SNP	C	C	T	rs10583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24662177C>T	ENST00000261789.4	-	3	1002	c.644G>A	c.(643-645)cGt>cAt	p.R215H	TM9SF1_ENST00000556387.1_Missense_Mutation_p.R424H|TM9SF1_ENST00000528669.1_Missense_Mutation_p.R215H|TM9SF1_ENST00000396854.4_Missense_Mutation_p.R215H|TM9SF1_ENST00000530611.1_Missense_Mutation_p.R424H|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000524835.1_Missense_Mutation_p.R128H	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	215			R -> H (in dbSNP:rs10583).		autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		GTCACTCCGACGCTCCACTGA	0.537													C|||	274	0.0547125	0.0053	0.1066	5008	,	,		20922	0.003		0.1421	False		,,,				2504	0.0481				p.R215H		Atlas-SNP	.											.	TM9SF1	58	.	0			c.G644A						PASS	.	C	HIS/ARG,HIS/ARG	137,4269	97.1+/-135.8	2,133,2068	93.0	83.0	87.0		644,644	-3.8	0.0	14	dbSNP_52	87	1332,7268	261.4+/-283.8	97,1138,3065	yes	missense,missense	TM9SF1	NM_001014842.1,NM_006405.5	29,29	99,1271,5133	TT,TC,CC		15.4884,3.1094,11.2948	benign,benign	215/490,215/607	24662177	1469,11537	2203	4300	6503	SO:0001583	missense	10548	exon3			CTCCGACGCTCCA	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.644G>A	14.37:g.24662177C>T	ENSP00000261789:p.Arg215His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	156	0.07142857142857142	5	0.01016260162601626	43	0.11878453038674033	3	0.005244755244755245	105	0.13852242744063326	C	5.187	0.220125	0.09863	0.031094	0.154884	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000528895;ENST00000530563;ENST00000530468;ENST00000525592;ENST00000530611	T;T;T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	5.1	-3.78	0.04333	.	0.469726	0.22557	N	0.058512	T	0.00073	0.0002	N	0.01352	-0.895	0.45354	P	0.0016540000000000443	B;B;B	0.16166	0.016;0.006;0.0	B;B;B	0.06405	0.002;0.001;0.0	T	0.20042	-1.0287	9	0.35671	T	0.21	0.0262	11.9113	0.52741	0.0:0.3895:0.0:0.6105	rs10583;rs17794740;rs59496657;rs10583	215;215;215	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	H	215;215;424;128;215;215;128;215;215;424	ENSP00000261789:R215H;ENSP00000432997:R215H;ENSP00000451949:R424H;ENSP00000434387:R128H;ENSP00000380063:R215H;ENSP00000431447:R215H;ENSP00000437127:R128H;ENSP00000435857:R215H;ENSP00000432435:R215H;ENSP00000433967:R424H	ENSP00000433967:R424H	R	-	2	0	TM9SF1;RP11-468E2.1	23732017	0.175000	0.23083	0.008000	0.14137	0.719000	0.41307	0.594000	0.24014	-1.011000	0.03391	-0.140000	0.14226	CGT	C|0.908;T|0.092	0.092	strong		0.537	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377873	49377873	+	Silent	SNP	G	G	A	rs35023389	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49377873G>A	ENST00000200453.5	+	2	1652	c.1383G>A	c.(1381-1383)ttG>ttA	p.L461L		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	461	4 X 34 AA approximate repeats.|Glu-rich.|Interaction with SMAD7.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		AAGCAGCCTTGGGAGAAGCTG	0.562													G|||	419	0.0836661	0.0877	0.0793	5008	,	,		18197	0.003		0.164	False		,,,				2504	0.0818				p.L461L		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G1383A						PASS	.	G		576,3830	255.2+/-260.5	35,506,1662	73.0	74.0	73.0		1383	0.6	0.0	19	dbSNP_126	73	1549,7051	290.4+/-299.8	128,1293,2879	no	coding-synonymous	PPP1R15A	NM_014330.3		163,1799,4541	AA,AG,GG		18.0116,13.0731,16.3386		461/675	49377873	2125,10881	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon2			AGCCTTGGGAGAA	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.1383G>A	19.37:g.49377873G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			G|0.860;A|0.140	0.140	strong		0.562	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
IL2RB	3560	hgsc.bcm.edu	37	22	37524619	37524619	+	Missense_Mutation	SNP	G	G	T	rs228942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:37524619G>T	ENST00000216223.5	-	10	1371	c.1173C>A	c.(1171-1173)gaC>gaA	p.D391E		NM_000878.3	NP_000869.1	P14784	IL2RB_HUMAN	interleukin 2 receptor, beta	391			D -> E (in dbSNP:rs228942). {ECO:0000269|Ref.3}.		cytokine-mediated signaling pathway (GO:0019221)|interleukin-2-mediated signaling pathway (GO:0038110)|negative regulation of apoptotic process (GO:0043066)|protein complex assembly (GO:0006461)|signal transduction (GO:0007165)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-2 binding (GO:0019976)|interleukin-2 receptor activity (GO:0004911)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(5)	23					Aldesleukin(DB00041)|Basiliximab(DB00074)|Daclizumab(DB00111)|Denileukin diftitox(DB00004)	CCTCATCAGGGTCTTCCTCTG	0.612													G|||	903	0.180312	0.0764	0.3098	5008	,	,		17234	0.2341		0.1839	False		,,,				2504	0.1697				p.D391E		Atlas-SNP	.											.	IL2RB	44	.	0			c.C1173A						PASS	.	G	GLU/ASP	406,4000	200.8+/-224.0	16,374,1813	59.0	60.0	59.0		1173	2.2	0.2	22	dbSNP_79	59	1585,7015	295.4+/-302.4	158,1269,2873	yes	missense	IL2RB	NM_000878.2	45	174,1643,4686	TT,TG,GG		18.4302,9.2147,15.3083	benign	391/552	37524619	1991,11015	2203	4300	6503	SO:0001583	missense	3560	exon10			ATCAGGGTCTTCC	M26062	CCDS13942.1	22q13	2011-02-15			ENSG00000100385	ENSG00000100385		"""Interleukins and interleukin receptors"", ""CD molecules"""	6009	protein-coding gene	gene with protein product		146710	"""interleukin 15 receptor, beta"""	IL15RB			Standard	NM_000878		Approved	CD122	uc003aqv.1	P14784	OTTHUMG00000150534	ENST00000216223.5:c.1173C>A	22.37:g.37524619G>T	ENSP00000216223:p.Asp391Glu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_000878	B2R765	Missense_Mutation	SNP	ENST00000216223.5	37	CCDS13942.1	438	0.20054945054945056	40	0.08130081300813008	110	0.30386740331491713	144	0.2517482517482518	144	0.18997361477572558	G	0.759	-0.769881	0.02974	0.092147	0.184302	ENSG00000100385	ENST00000216223	T	0.06849	3.25	4.28	2.16	0.27623	.	1.830200	0.02534	N	0.093949	T	0.00012	0.0000	N	0.02539	-0.55	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40156	-0.9578	9	0.02654	T	1	-6.2193	7.4522	0.27244	0.0:0.738:0.1698:0.0922	rs228942;rs57366109;rs228942	391	P14784	IL2RB_HUMAN	E	391	ENSP00000216223:D391E	ENSP00000216223:D391E	D	-	3	2	IL2RB	35854565	0.000000	0.05858	0.226000	0.23910	0.001000	0.01503	-2.511000	0.00958	0.543000	0.28864	-0.766000	0.03442	GAC	G|0.839;T|0.161	0.161	strong		0.612	IL2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318792.1		
FAM220A	84792	hgsc.bcm.edu	37	7	6370305	6370305	+	Missense_Mutation	SNP	C	C	G	rs3750039	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6370305C>G	ENST00000313324.4	-	2	948	c.481G>C	c.(481-483)Gtg>Ctg	p.V161L	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	161			V -> L (in dbSNP:rs3750039). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			nucleus (GO:0005634)											ATTTCCGGCACTTTTTGATGG	0.607													G|||	3618	0.722444	0.8631	0.6571	5008	,	,		17127	0.8829		0.4573	False		,,,				2504	0.6861				p.V161L		Atlas-SNP	.											.	.	.	.	0			c.G481C						PASS	.	G	LEU/VAL	3576,830	313.8+/-293.3	1475,626,102	47.0	57.0	54.0		481	-3.8	0.0	7	dbSNP_107	54	4101,4497	587.6+/-392.2	972,2157,1170	no	missense	C7orf70	NM_001037163.1	32	2447,2783,1272	GG,GC,CC		47.6971,18.8379,40.9643	benign	161/260	6370305	7677,5327	2203	4299	6502	SO:0001583	missense	84792	exon2			CCGGCACTTTTTG	BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"""STAT3-interacting protein as a repressor"""		"""chromosome 7 open reading frame 70"""	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.481G>C	7.37:g.6370305C>G	ENSP00000317289:p.Val161Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	Missense_Mutation	SNP	ENST00000313324.4	37	CCDS34599.1	1477	0.6762820512820513	408	0.8292682926829268	227	0.6270718232044199	503	0.8793706293706294	339	0.4472295514511873	G	2.298	-0.360916	0.05103	0.811621	0.476971	ENSG00000178397	ENST00000313324	T	0.05580	3.42	4.91	-3.78	0.04333	.	0.864271	0.09333	N	0.816637	T	0.00012	0.0000	N	0.00926	-1.1	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.29852	-0.9998	9	0.02654	T	1	5.7759	3.879	0.09069	0.1259:0.3907:0.2838:0.1995	rs3750039;rs6952329;rs10304730;rs52835924;rs58918211;rs3750039	161	Q7Z4H9	SIPAR_HUMAN	L	161	ENSP00000317289:V161L	ENSP00000317289:V161L	V	-	1	0	C7orf70	6336830	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-0.039000	0.12124	-0.771000	0.04608	-0.120000	0.15030	GTG	C|0.397;G|0.603	0.603	strong		0.607	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163	
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 GAIIx	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	FAM83G_ENST00000585154.2_Missense_Mutation_p.Q458H|FAM83G_ENST00000345041.4_Missense_Mutation_p.Q458H|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395645.3_Intron			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	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	119	72	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		
TGFBR3	7049	hgsc.bcm.edu	37	1	92262874	92262874	+	Silent	SNP	T	T	C	rs2810904|rs1805111	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:92262874T>C	ENST00000525962.1	-	2	277	c.216A>G	c.(214-216)gcA>gcG	p.A72A	TGFBR3_ENST00000370399.2_Silent_p.A72A|TGFBR3_ENST00000212355.4_Silent_p.A72A			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	72					blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		GCCCCTGGCCTGCAGTGCGGA	0.582													C|||	3582	0.715256	0.7761	0.7176	5008	,	,		17523	0.7748		0.6322	False		,,,				2504	0.6554				p.A72A		Atlas-SNP	.											.	TGFBR3	103	.	0			c.A216G						PASS	.	C	,,	3308,1098	390.3+/-327.6	1236,836,131	129.0	136.0	134.0		216,216,216	-8.5	0.0	1	dbSNP_100	134	5518,3082	460.9+/-365.3	1760,1998,542	no	coding-synonymous,coding-synonymous,coding-synonymous	TGFBR3	NM_001195683.1,NM_001195684.1,NM_003243.4	,,	2996,2834,673	CC,CT,TT		35.8372,24.9206,32.139	,,	72/851,72/851,72/852	92262874	8826,4180	2203	4300	6503	SO:0001819	synonymous_variant	7049	exon4			CTGGCCTGCAGTG	L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"""Proteoglycans / Cell surface : Other"""	11774	protein-coding gene	gene with protein product	"""betaglycan proteoglycan"""	600742	"""transforming growth factor, beta receptor III (betaglycan, 300kDa)"""			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.216A>G	1.37:g.92262874T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	163	162	0.993865	NM_001195684	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Silent	SNP	ENST00000525962.1	37	CCDS30770.1																																																																																			.	.	none		0.582	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243	
RNF213	57674	hgsc.bcm.edu	37	17	78363847	78363847	+	Silent	SNP	G	G	A	rs3185057	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78363847G>A	ENST00000582970.1	+	67	15464	c.15321G>A	c.(15319-15321)gcG>gcA	p.A5107A	CTD-2047H16.4_ENST00000573394.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Silent_p.A3180A|RNF213_ENST00000508628.2_Silent_p.A5156A|CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000427003.3_3'UTR	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	5107					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GGTACAAAGCGGATCTGAGCC	0.493													G|||	386	0.0770767	0.087	0.0504	5008	,	,		20421	0.0367		0.0905	False		,,,				2504	0.1104				p.A5107A		Atlas-SNP	.											RNF213_ENST00000411702,caecum,carcinoma,0,2	RNF213	766	2	0			c.G15321A						PASS	.	G		357,4049	183.3+/-210.9	10,337,1856	99.0	102.0	101.0		15468	-11.3	0.0	17	dbSNP_105	101	750,7850	180.0+/-229.1	39,672,3589	no	coding-synonymous	RNF213	NM_020914.4		49,1009,5445	AA,AG,GG		8.7209,8.1026,8.5115		5156/5257	78363847	1107,11899	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon67			CAAAGCGGATCTG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.15321G>A	17.37:g.78363847G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			G|0.916;A|0.084	0.084	strong		0.493	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
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 GAIIx	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_ENST00000588077.1_Missense_Mutation_p.D852N|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.D916N|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.D891N|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.D852N|CACNA2D4_ENST00000538027.2_Missense_Mutation_p.D61N|CACNA2D4_ENST00000538450.1_Missense_Mutation_p.D46N	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	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	61	32	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 GAIIx	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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	179	42	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	
TRIM65	201292	hgsc.bcm.edu	37	17	73886888	73886888	+	Missense_Mutation	SNP	A	A	G	rs3760128	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73886888A>G	ENST00000269383.3	-	6	1591	c.1526T>C	c.(1525-1527)cTg>cCg	p.L509P		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	509			L -> P (in dbSNP:rs3760128). {ECO:0000269|PubMed:15489334}.			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CTGGGGCCCCAGAGGGAACAC	0.627													G|||	2328	0.464856	0.9032	0.3141	5008	,	,		17564	0.2222		0.3499	False		,,,				2504	0.3476				p.L509P		Atlas-SNP	.											TRIM65,NS,carcinoma,0,1	TRIM65	23	1	0			c.T1526C						PASS	.	G	PRO/LEU	3605,787		1492,621,83	19.0	19.0	19.0		1526	3.7	0.0	17	dbSNP_107	19	2944,5646		541,1862,1892	yes	missense	TRIM65	NM_173547.2	98	2033,2483,1975	GG,GA,AA		34.2724,17.9189,49.5532	benign	509/518	73886888	6549,6433	2196	4295	6491	SO:0001583	missense	201292	exon6			GGCCCCAGAGGGA	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.1526T>C	17.37:g.73886888A>G	ENSP00000269383:p.Leu509Pro	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	37	CCDS11732.1	961	0.440018315018315	441	0.8963414634146342	128	0.35359116022099446	147	0.256993006993007	245	0.3232189973614776	G	0	-2.811358	0.00073	0.820811	0.342724	ENSG00000141569	ENST00000269383	T	0.57595	0.39	4.69	3.69	0.42338	Concanavalin A-like lectin/glucanase (1);	0.337845	0.21595	N	0.072024	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32481	-0.9905	9	0.11182	T	0.66	.	5.6825	0.17784	0.079:0.1377:0.6412:0.1422	rs3760128;rs57250342;rs3760128	509	Q6PJ69	TRI65_HUMAN	P	509	ENSP00000269383:L509P	ENSP00000269383:L509P	L	-	2	0	TRIM65	71398483	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	1.022000	0.30052	0.395000	0.25257	-0.215000	0.12644	CTG	A|0.500;G|0.500	0.500	strong		0.627	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
DOCK1	1793	hgsc.bcm.edu	37	10	129245684	129245684	+	Missense_Mutation	SNP	G	G	A	rs869801	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:129245684G>A	ENST00000280333.6	+	51	5486	c.5377G>A	c.(5377-5379)Gcg>Acg	p.A1793T		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1793	Interaction with NCK2 second and third SH3 domain (minor).		A -> T (in dbSNP:rs869801).		apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.A1793T(1)		NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CATGACGGGGGCGGACGTGGC	0.592													G|||	1025	0.204673	0.211	0.2233	5008	,	,		17616	0.12		0.2584	False		,,,				2504	0.2147				p.A1793T		Atlas-SNP	.											DOCK1,NS,carcinoma,0,1	DOCK1	188	1	1	Substitution - Missense(1)	stomach(1)	c.G5377A						PASS	.	G	THR/ALA	769,3209		69,631,1289	32.0	36.0	35.0		5332	-10.4	0.0	10	dbSNP_86	35	2153,6171		278,1597,2287	yes	missense	DOCK1	NM_001380.3	58	347,2228,3576	AA,AG,GG		25.865,19.3313,23.7522	benign	1778/1851	129245684	2922,9380	1989	4162	6151	SO:0001583	missense	1793	exon51			ACGGGGGCGGACG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5377G>A	10.37:g.129245684G>A	ENSP00000280333:p.Ala1793Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	37	0.493333	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		458	0.2097069597069597	99	0.20121951219512196	91	0.2513812154696133	69	0.12062937062937062	199	0.262532981530343	G	6.324	0.427794	0.11987	0.193313	0.25865	ENSG00000150760	ENST00000280333	T	0.03663	3.85	5.22	-10.4	0.00318	.	1.639210	0.04650	U	0.407008	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48536	-0.9027	9	0.21014	T	0.42	.	0.4032	0.00429	0.3463:0.1465:0.2334:0.2738	rs869801;rs2229602;rs17777746;rs869801	1793;1793	B2RUU3;Q14185	.;DOCK1_HUMAN	T	1793	ENSP00000280333:A1793T	ENSP00000280333:A1793T	A	+	1	0	DOCK1	129135674	0.000000	0.05858	0.000000	0.03702	0.340000	0.28889	-0.958000	0.03857	-1.651000	0.01504	0.655000	0.94253	GCG	G|0.786;A|0.214	0.214	strong		0.592	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
SLC2A2	6514	hgsc.bcm.edu	37	3	170732300	170732300	+	Missense_Mutation	SNP	G	G	A	rs5400	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:170732300G>A	ENST00000314251.3	-	3	408	c.329C>T	c.(328-330)aCt>aTt	p.T110I	SLC2A2_ENST00000382808.4_Intron	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	110			T -> I (in dbSNP:rs5400). {ECO:0000269|PubMed:7593414, ECO:0000269|PubMed:8063045}.		carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	GAATGATGCAGTCATTCCACC	0.448													A|||	1078	0.215256	0.4894	0.1715	5008	,	,		18629	0.0159		0.1352	False		,,,				2504	0.1636				p.T110I		Atlas-SNP	.											.	SLC2A2	71	.	0			c.C329T	GRCh37	CM941277	SLC2A2	M	rs5400	PASS	.	A	ILE/THR	1970,2436	620.0+/-393.5	446,1078,679	175.0	160.0	165.0		329	6.1	1.0	3	dbSNP_52	165	1147,7453	766.6+/-407.6	71,1005,3224	yes	missense	SLC2A2	NM_000340.1	89	517,2083,3903	AA,AG,GG		13.3372,44.7118,23.9659	benign	110/525	170732300	3117,9889	2203	4300	6503	SO:0001583	missense	6514	exon3			GATGCAGTCATTC	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.329C>T	3.37:g.170732300G>A	ENSP00000323568:p.Thr110Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	110	44	0.4	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Missense_Mutation	SNP	ENST00000314251.3	37	CCDS3215.1	411	0.18818681318681318	228	0.4634146341463415	70	0.19337016574585636	9	0.015734265734265736	104	0.13720316622691292	A	8.575	0.880856	0.17467	0.447118	0.133372	ENSG00000163581	ENST00000314251	T	0.70399	-0.48	6.08	6.08	0.98989	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.399027	0.29218	N	0.012794	T	0.00012	0.0000	N	0.00016	-2.86	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41945	-0.9480	9	0.02654	T	1	.	12.1128	0.53848	0.9328:0.0:0.0672:0.0	rs5400;rs52828515;rs61638260;rs5400	110	P11168	GTR2_HUMAN	I	110	ENSP00000323568:T110I	ENSP00000323568:T110I	T	-	2	0	SLC2A2	172214994	0.955000	0.32602	0.981000	0.43875	0.991000	0.79684	7.036000	0.76524	1.126000	0.42016	-0.254000	0.11334	ACT	G|0.776;A|0.224	0.224	strong		0.448	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
ERICH3	127254	hgsc.bcm.edu	37	1	75097426	75097426	+	Missense_Mutation	SNP	G	G	C	rs11210490	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:75097426G>C	ENST00000326665.5	-	7	1008	c.790C>G	c.(790-792)Cca>Gca	p.P264A	C1orf173_ENST00000420661.2_Missense_Mutation_p.P67A	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		264			P -> A (in dbSNP:rs11210490). {ECO:0000269|PubMed:14702039}.							NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						AAGCCATTTGGAGCAGTGGTT	0.368													G|||	1607	0.320887	0.2284	0.4741	5008	,	,		18825	0.1141		0.5268	False		,,,				2504	0.3384				p.P264A		Atlas-SNP	.											.	C1orf173	380	.	0			c.C790G						PASS	.	G	ALA/PRO	1399,3007	458.8+/-352.1	224,951,1028	171.0	154.0	160.0		790	3.5	1.0	1	dbSNP_120	160	4519,4081	592.4+/-393.0	1211,2097,992	yes	missense	C1orf173	NM_001002912.4	27	1435,3048,2020	CC,CG,GG		47.4535,31.7522,45.5021	probably-damaging	264/1531	75097426	5918,7088	2203	4300	6503	SO:0001583	missense	127254	exon7			CATTTGGAGCAGT																												ENST00000326665.5:c.790C>G	1.37:g.75097426G>C	ENSP00000322609:p.Pro264Ala	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	246	245	0.995935	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	741	0.3392857142857143	116	0.23577235772357724	178	0.49171270718232046	62	0.10839160839160839	385	0.5079155672823219	G	9.911	1.209431	0.22289	0.317522	0.525465	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.21932	2.43;1.98	5.39	3.49	0.39957	.	.	.	.	.	T	0.27169	0.0666	M	0.73598	2.24	0.27326	P	0.9569008	P;D	0.65815	0.944;0.995	P;P	0.61722	0.572;0.893	T	0.12268	-1.0554	8	0.54805	T	0.06	-7.5504	9.8566	0.41090	0.0729:0.0:0.7875:0.1396	rs11210490;rs11210490	67;264	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	A	264;67	ENSP00000322609:P264A;ENSP00000398581:P67A	ENSP00000322609:P264A	P	-	1	0	C1orf173	74870014	1.000000	0.71417	0.977000	0.42913	0.089000	0.18198	2.431000	0.44775	0.640000	0.30582	-0.142000	0.14014	CCA	G|0.588;C|0.412	0.412	strong		0.368	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
DAGLB	221955	hgsc.bcm.edu	37	7	6449496	6449496	+	Missense_Mutation	SNP	T	T	C	rs2303361	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6449496T>C	ENST00000297056.6	-	15	2160	c.1991A>G	c.(1990-1992)cAa>cGa	p.Q664R	DAGLB_ENST00000436575.1_Missense_Mutation_p.Q623R|DAGLB_ENST00000425398.2_Missense_Mutation_p.Q535R	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	664			Q -> R (in dbSNP:rs2303361). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GGAGACCCCTTGTGCTGGACA	0.587													T|||	816	0.162939	0.0545	0.1816	5008	,	,		17814	0.2669		0.2107	False		,,,				2504	0.1401				p.Q664R		Atlas-SNP	.											.	DAGLB	74	.	0			c.A1991G						PASS	.	T	ARG/GLN,ARG/GLN	414,3992		20,374,1809	62.0	59.0	60.0		1604,1991	-1.7	0.0	7	dbSNP_100	60	1889,6711		231,1427,2642	yes	missense,missense	DAGLB	NM_001142936.1,NM_139179.3	43,43	251,1801,4451	CC,CT,TT		21.9651,9.3963,17.7072	benign,benign	535/544,664/673	6449496	2303,10703	2203	4300	6503	SO:0001583	missense	221955	exon15			ACCCCTTGTGCTG	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1991A>G	7.37:g.6449496T>C	ENSP00000297056:p.Gln664Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	122	70	0.57377	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	37	CCDS5350.1	388	0.17765567765567766	30	0.06097560975609756	71	0.19613259668508287	124	0.21678321678321677	163	0.21503957783641162	.	5.573	0.290535	0.10567	0.093963	0.219651	ENSG00000164535	ENST00000297056;ENST00000425398;ENST00000436575	T;T;T	0.44083	0.94;0.93;0.94	5.79	-1.66	0.08265	.	1.121680	0.06392	N	0.717245	T	0.00012	0.0000	L	0.51422	1.61	0.58432	P	1.999999999946489E-6	B;B;B;B	0.13145	0.007;0.0;0.003;0.0	B;B;B;B	0.08055	0.003;0.001;0.001;0.0	T	0.25012	-1.0144	9	0.11182	T	0.66	-17.9873	6.5442	0.22397	0.0:0.2794:0.3284:0.3923	rs2303361;rs57945063;rs2303361	535;478;664;361	B4DQU0;B4DQQ6;Q8NCG7;B3KRA0	.;.;DGLB_HUMAN;.	R	664;535;623	ENSP00000297056:Q664R;ENSP00000391171:Q535R;ENSP00000404785:Q623R	ENSP00000297056:Q664R	Q	-	2	0	DAGLB	6416021	0.003000	0.15002	0.000000	0.03702	0.274000	0.26718	0.453000	0.21811	-0.549000	0.06191	-0.280000	0.10049	CAA	T|0.832;C|0.168	0.168	strong		0.587	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
GPR112	139378	hgsc.bcm.edu	37	X	135430483	135430483	+	Missense_Mutation	SNP	T	T	C	rs912002	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135430483T>C	ENST00000394143.1	+	6	4909	c.4618T>C	c.(4618-4620)Tct>Cct	p.S1540P	GPR112_ENST00000394141.1_Missense_Mutation_p.S1335P|GPR112_ENST00000370652.1_Missense_Mutation_p.S1540P|GPR112_ENST00000287534.4_Missense_Mutation_p.S1477P|GPR112_ENST00000412101.1_Missense_Mutation_p.S1335P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1540			S -> P (in dbSNP:rs912002).		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(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					AACTAAATCTTCTAAAACAAT	0.418													t|||	1764	0.467285	0.4251	0.3573	3775	,	,		14599	0.255		0.3797	False		,,,				2504	0.3221				p.S1540P		Atlas-SNP	.											.	GPR112	459	.	0			c.T4618C						PASS	.		PRO/SER	2110,1725		493,813,311,326,260	96.0	94.0	95.0		4618	1.7	0.1	X	dbSNP_86	95	3223,3505		567,1177,912,684,960	yes	missense	GPR112	NM_153834.3	74	1060,1990,1223,1010,1220	CC,CT,C,TT,T		47.9043,44.9804,49.5124	probably-damaging	1540/3081	135430483	5333,5230	2203	4300	6503	SO:0001583	missense	139378	exon6			AAATCTTCTAAAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4618T>C	X.37:g.135430483T>C	ENSP00000377699:p.Ser1540Pro	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	84	56	0.666667	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	754	0.45449065702230257	137	0.37027027027027026	83	0.2902097902097902	103	0.22391304347826088	190	0.3242320819112628	t	14.52	2.560180	0.45590	0.550196	0.479043	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.40756	1.06;1.06;1.02;1.13;1.02	3.02	1.66	0.24008	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.80764	0.986;0.994;0.987	T	0.44483	-0.9325	8	0.87932	D	0	.	4.2365	0.10628	0.3093:0.0:0.0:0.6907	rs912002;rs52799687;rs61339577;rs912002	1477;1335;1540	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	P	1540;1540;1335;1477;1335	ENSP00000377699:S1540P;ENSP00000359686:S1540P;ENSP00000416526:S1335P;ENSP00000287534:S1477P;ENSP00000377697:S1335P	ENSP00000287534:S1477P	S	+	1	0	GPR112	135258149	0.316000	0.24580	0.086000	0.20670	0.250000	0.25880	0.927000	0.28818	1.195000	0.43115	0.378000	0.23410	TCT	0|0.015;C|0.478	0.478	strong		0.418	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
PGPEP1L	145814	hgsc.bcm.edu	37	15	99511793	99511793	+	Missense_Mutation	SNP	C	C	G	rs1521484	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:99511793C>G	ENST00000378919.6	-	5	710	c.505G>C	c.(505-507)Gaa>Caa	p.E169Q	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_Missense_Mutation_p.E115Q	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	169			E -> Q (in dbSNP:rs1521484).				cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						TCCAGCATTTCCTGGATGATG	0.587													C|||	2220	0.443291	0.1581	0.4914	5008	,	,		17547	0.4841		0.5726	False		,,,				2504	0.6196				p.E169Q		Atlas-SNP	.											.	PGPEP1L	26	.	0			c.G505C						PASS	.	C	GLN/GLU,GLN/GLU	811,3067		85,641,1213	46.0	45.0	45.0		505,343	2.5	0.2	15	dbSNP_88	45	4275,3985		1098,2079,953	yes	missense,missense	PGPEP1L	NM_001102612.2,NM_001167902.1	29,29	1183,2720,2166	GG,GC,CC		48.2446,20.9128,41.9015	probably-damaging,probably-damaging	169/197,115/143	99511793	5086,7052	1939	4130	6069	SO:0001583	missense	145814	exon5			GCATTTCCTGGAT		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.505G>C	15.37:g.99511793C>G	ENSP00000368199:p.Glu169Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	968	0.4432234432234432	83	0.16869918699186992	181	0.5	281	0.49125874125874125	423	0.558047493403694	C	13.24	2.178331	0.38511	0.209128	0.517554	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.30981	1.51	5.39	2.51	0.30379	.	0.377447	0.26704	N	0.022923	T	0.00012	0.0000	N	0.19112	0.55	0.51482	P	7.599999999996498E-5	P	0.39665	0.682	B	0.40199	0.322	T	0.38845	-0.9642	9	0.19147	T	0.46	-10.9564	10.1423	0.42742	0.0:0.786:0.0:0.214	rs1521484;rs1521484	169	A6NFU8	PGPIL_HUMAN	Q	169;162	ENSP00000368199:E169Q	ENSP00000368199:E169Q	E	-	1	0	PGPEP1L	97329316	0.022000	0.18835	0.213000	0.23690	0.357000	0.29423	1.000000	0.29770	0.273000	0.22049	-0.140000	0.14226	GAA	C|0.537;G|0.463	0.463	strong		0.587	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
RPA1	6117	hgsc.bcm.edu	37	17	1795180	1795180	+	Silent	SNP	T	T	C	rs2230931	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1795180T>C	ENST00000254719.5	+	15	1715	c.1605T>C	c.(1603-1605)tcT>tcC	p.S535S		NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	535					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of cell proliferation (GO:0008284)|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)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|DNA replication factor A complex (GO:0005662)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|single-stranded DNA binding (GO:0003697)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						TCCAGGAGTCTGCTGAAGCTA	0.323								Nucleotide excision repair (NER)					T|||	1472	0.29393	0.3654	0.304	5008	,	,		17399	0.252		0.1799	False		,,,				2504	0.3507				p.S535S		Atlas-SNP	.											.	RPA1	48	.	0			c.T1605C	GRCh37	CM995272	RPA1	M	rs2230931	PASS	.	T		1567,2839	490.8+/-361.9	273,1021,909	86.0	89.0	88.0		1605	2.2	1.0	17	dbSNP_98	88	1533,7067	288.6+/-298.9	135,1263,2902	no	coding-synonymous	RPA1	NM_002945.3		408,2284,3811	CC,CT,TT		17.8256,35.5651,23.8352		535/617	1795180	3100,9906	2203	4300	6503	SO:0001819	synonymous_variant	6117	exon15			GGAGTCTGCTGAA	M63488	CCDS11014.1	17p13.3	2008-02-05	2002-08-29		ENSG00000132383	ENSG00000132383			10289	protein-coding gene	gene with protein product		179835	"""replication protein A1 (70kD)"""			8454588	Standard	NM_002945		Approved	REPA1, RPA70, HSSB, RF-A, RP-A	uc002fto.2	P27694	OTTHUMG00000090579	ENST00000254719.5:c.1605T>C	17.37:g.1795180T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_002945	A8K0Y9|Q59ES9	Silent	SNP	ENST00000254719.5	37	CCDS11014.1																																																																																			T|0.751;C|0.249	0.249	strong		0.323	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207118.2	NM_002945	
FHIT	2272	hgsc.bcm.edu	37	3	59997112	59997112	+	Silent	SNP	G	G	A	rs1130972	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:59997112G>A	ENST00000468189.1	-	7	634	c.264C>T	c.(262-264)gcC>gcT	p.A88A	FHIT_ENST00000492590.1_Silent_p.A88A|FHIT_ENST00000476844.1_Silent_p.A88A|FHIT_ENST00000466788.1_5'UTR|FHIT_ENST00000341848.4_Silent_p.A88A			P49789	FHIT_HUMAN	fragile histidine triad	88	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)		CAGTCTGTCCGGCTTCGGGGC	0.378			T	HMGA2	pleomorphic salivary gland adenoma				Renal Cell Cancer associated with constitutional translocation of chromosome 3				g|||	411	0.0820687	0.0681	0.1571	5008	,	,		19215	0.0		0.1491	False		,,,				2504	0.0634				p.A88A		Atlas-SNP	.		Dom	yes		3	3p14.2	2272	fragile histidine triad gene		E	.	FHIT	44	.	0			c.C264T						PASS	.	A	,	337,4069	175.5+/-204.9	14,309,1880	76.0	81.0	79.0		264,264	-11.1	0.4	3	dbSNP_123	79	1371,7229	266.3+/-286.6	115,1141,3044	no	coding-synonymous,coding-synonymous	FHIT	NM_001166243.1,NM_002012.2	,	129,1450,4924	AA,AG,GG		15.9419,7.6487,13.1324	,	88/148,88/148	59997112	1708,11298	2203	4300	6503	SO:0001819	synonymous_variant	2272	exon7	Familial Cancer Database		CTGTCCGGCTTCG	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.264C>T	3.37:g.59997112G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_002012	A2IAS9|A2IAT0|A2IAT6|A8K1A9|Q45QG9|Q6IU12	Silent	SNP	ENST00000468189.1	37	CCDS2894.1																																																																																			G|0.893;A|0.107	0.107	strong		0.378	FHIT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351648.1	NM_002012	
FAM135B	51059	hgsc.bcm.edu	37	8	139165068	139165068	+	Silent	SNP	C	C	T	rs3763590	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:139165068C>T	ENST00000395297.1	-	13	1820	c.1650G>A	c.(1648-1650)gtG>gtA	p.V550V		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	550										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)			TGTAGGTCAGCACTGGGGCCT	0.502										HNSCC(54;0.14)			C|||	1825	0.364417	0.1566	0.4135	5008	,	,		17906	0.5298		0.3757	False		,,,				2504	0.4284				p.V550V		Atlas-SNP	.											.	FAM135B	423	.	0			c.G1650A						PASS	.	C		741,3163		75,591,1286	83.0	82.0	82.0		1650	-9.9	0.0	8	dbSNP_107	82	2847,5445		498,1851,1797	no	coding-synonymous	FAM135B	NM_015912.3		573,2442,3083	TT,TC,CC		34.3343,18.9805,29.4195		550/1407	139165068	3588,8608	1952	4146	6098	SO:0001819	synonymous_variant	51059	exon13			GGTCAGCACTGGG	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.1650G>A	8.37:g.139165068C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			C|0.632;T|0.368	0.368	strong		0.502	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
ACAT1	38	hgsc.bcm.edu	37	11	107992346	107992346	+	Missense_Mutation	SNP	G	G	C	rs11540420|rs3741056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:107992346G>C	ENST00000265838.4	+	1	104	c.13G>C	c.(13-15)Gcg>Ccg	p.A5P	ACAT1_ENST00000299355.6_Missense_Mutation_p.A5P|RP11-144G7.2_ENST00000525548.1_RNA	NM_000019.3	NP_000010.1	P24752	THIL_HUMAN	acetyl-CoA acetyltransferase 1	5			A -> P (in dbSNP:rs3741056).		adipose tissue development (GO:0060612)|brain development (GO:0007420)|branched-chain amino acid catabolic process (GO:0009083)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular nitrogen compound metabolic process (GO:0034641)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|metanephric proximal convoluted tubule development (GO:0072229)|protein homooligomerization (GO:0051260)|response to hormone (GO:0009725)|response to organic cyclic compound (GO:0014070)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acetyl-CoA C-acetyltransferase activity (GO:0003985)|coenzyme binding (GO:0050662)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|prostate(2)	10		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	GGCTGTGCTGGCGGCACTTCT	0.726													G|||	1662	0.331869	0.1293	0.4222	5008	,	,		13418	0.3601		0.3419	False		,,,				2504	0.502				p.A5P		Atlas-SNP	.											.	ACAT1	35	.	0			c.G13C						PASS	.	G	PRO/ALA	498,3570		40,418,1576	7.0	7.0	7.0		13	0.2	0.0	11	dbSNP_107	7	2021,5923		259,1503,2210	yes	missense	ACAT1	NM_000019.3	27	299,1921,3786	CC,CG,GG		25.4406,12.2419,20.9707	possibly-damaging	5/428	107992346	2519,9493	2034	3972	6006	SO:0001583	missense	38	exon1			GTGCTGGCGGCAC	D90228	CCDS8339.1	11q22.3	2010-04-30	2010-04-30		ENSG00000075239	ENSG00000075239	2.3.1.9		93	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	607809	"""acetyl-Coenzyme A acetyltransferase 1"""	ACAT		1979337	Standard	NM_000019		Approved	THIL	uc001pjy.3	P24752	OTTHUMG00000166381	ENST00000265838.4:c.13G>C	11.37:g.107992346G>C	ENSP00000265838:p.Ala5Pro	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	58	51	0.87931	NM_000019	B2R6H1|G3XAB4|Q96FG8	Missense_Mutation	SNP	ENST00000265838.4	37	CCDS8339.1	677	0.309981684981685	73	0.1483739837398374	142	0.39226519337016574	210	0.36713286713286714	252	0.3324538258575198	G	16.39	3.111218	0.56398	0.122419	0.254406	ENSG00000075239	ENST00000265838;ENST00000299355	D;D	0.93906	-3.13;-3.31	3.31	0.195	0.15151	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P	0.37864	0.61;0.514	B;B	0.35688	0.103;0.208	T	0.11792	-1.0573	8	0.66056	D	0.02	-1.264	2.6303	0.04942	0.2756:0.0:0.4998:0.2246	rs3741056;rs17800684;rs17845275;rs17858107;rs3741056	5;5	P24752;G3XAB4	THIL_HUMAN;.	P	5	ENSP00000265838:A5P;ENSP00000299355:A5P	ENSP00000265838:A5P	A	+	1	0	ACAT1	107497556	0.001000	0.12720	0.002000	0.10522	0.760000	0.43138	-0.118000	0.10692	0.050000	0.15949	-0.475000	0.04921	GCG	G|0.710;C|0.290	0.290	strong		0.726	ACAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389474.1	NM_000019	
LMTK2	22853	hgsc.bcm.edu	37	7	97822210	97822210	+	Silent	SNP	G	G	A	rs3801294	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:97822210G>A	ENST00000297293.5	+	11	2726	c.2433G>A	c.(2431-2433)ccG>ccA	p.P811P		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	811					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					AGTCTTCCCCGGAAGTGCAGG	0.537													G|||	1121	0.223842	0.0356	0.3156	5008	,	,		19064	0.1528		0.5119	False		,,,				2504	0.1902				p.P811P		Atlas-SNP	.											.	LMTK2	228	.	0			c.G2433A						PASS	.	G		551,3855	247.2+/-255.5	34,483,1686	94.0	99.0	97.0		2433	-10.8	0.0	7	dbSNP_107	97	4709,3891	607.7+/-395.3	1299,2111,890	no	coding-synonymous	LMTK2	NM_014916.3		1333,2594,2576	AA,AG,GG		45.2442,12.5057,40.4429		811/1504	97822210	5260,7746	2203	4300	6503	SO:0001819	synonymous_variant	22853	exon11			TTCCCCGGAAGTG	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.2433G>A	7.37:g.97822210G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_014916	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	37	CCDS5654.1																																																																																			G|0.650;A|0.350	0.350	strong		0.537	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
UNC13C	440279	hgsc.bcm.edu	37	15	54841874	54841874	+	Silent	SNP	A	A	G	rs9302181	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:54841874A>G	ENST00000260323.11	+	27	5862	c.5862A>G	c.(5860-5862)caA>caG	p.Q1954Q	UNC13C_ENST00000545554.1_Silent_p.Q1954Q|UNC13C_ENST00000537900.1_Silent_p.Q1952Q	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1954	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		ATCTTGGACAATTATCCAAAC	0.343													A|||	1822	0.363818	0.1346	0.2853	5008	,	,		17350	0.5258		0.3887	False		,,,				2504	0.5368				p.Q1954Q		Atlas-SNP	.											.	UNC13C	674	.	0			c.A5862G						PASS	.	A		639,2961		52,535,1213	135.0	126.0	129.0		5862	-3.7	1.0	15	dbSNP_119	129	3092,5036		595,1902,1567	no	coding-synonymous	UNC13C	NM_001080534.1		647,2437,2780	GG,GA,AA		38.0413,17.75,31.8128		1954/2215	54841874	3731,7997	1800	4064	5864	SO:0001819	synonymous_variant	440279	exon26			TGGACAATTATCC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5862A>G	15.37:g.54841874A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	33	32	0.969697	NM_001080534	Q0P613|Q8ND48|Q96NP3	Silent	SNP	ENST00000260323.11	37	CCDS45264.1																																																																																			A|0.596;G|0.404	0.404	strong		0.343	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
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 GAIIx	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_ENST00000439576.2_Missense_Mutation_p.V2211I|ACAN_ENST00000352105.7_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	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	100	47	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	
ZNF853	54753	hgsc.bcm.edu	37	7	6660790	6660790	+	Silent	SNP	G	G	A	rs940873	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6660790G>A	ENST00000457543.3	+	3	726	c.168G>A	c.(166-168)gaG>gaA	p.E56E		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	56							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						AGGAGGAAGAGCCTCAGGAGA	0.607													G|||	2052	0.409744	0.4395	0.2651	5008	,	,		16821	0.5208		0.2147	False		,,,				2504	0.5583				p.E56E		Atlas-SNP	.											.	ZNF853	32	.	0			c.G168A						PASS	.	G		609,775		136,337,219	24.0	27.0	26.0		168	2.6	1.0	7	dbSNP_86	26	763,2419		88,587,916	no	coding-synonymous	ZNF853	NM_017560.1		224,924,1135	AA,AG,GG		23.9786,44.0029,30.0482		56/660	6660790	1372,3194	692	1591	2283	SO:0001819	synonymous_variant	54753	exon3			GGAAGAGCCTCAG	AL133055	CCDS59048.1	7p22.1	2013-01-08				ENSG00000236609		"""Zinc fingers, C2H2-type"""	21767	protein-coding gene	gene with protein product							Standard	NM_017560		Approved	DKFZp434J1015	uc011jwz.2	P0CG23		ENST00000457543.3:c.168G>A	7.37:g.6660790G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_017560		Silent	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			G|0.644;A|0.356	0.356	strong		0.607	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
ARHGAP33	115703	hgsc.bcm.edu	37	19	36278470	36278470	+	Silent	SNP	C	C	G	rs231235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36278470C>G	ENST00000007510.4	+	21	3147	c.3003C>G	c.(3001-3003)gcC>gcG	p.A1001A	ARHGAP33_ENST00000314737.5_Silent_p.A840A|ARHGAP33_ENST00000378944.5_Intron|AC002398.5_ENST00000433059.1_lincRNA			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	1001					protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						AGGTCAGTGCCCAGCTCAGGG	0.662													C|||	2678	0.534744	0.6551	0.5879	5008	,	,		13735	0.627		0.3688	False		,,,				2504	0.41				p.A840A		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.C2520G						PASS	.	C	,	2644,1732		812,1020,356	16.0	20.0	19.0		,2520	2.6	1.0	19	dbSNP_79	19	3095,5441		619,1857,1792	no	intron,coding-synonymous	ARHGAP33	NM_001172630.1,NM_052948.3	,	1431,2877,2148	GG,GC,CC		36.2582,39.5795,44.447	,	,840/1127	36278470	5739,7173	2188	4268	6456	SO:0001819	synonymous_variant	115703	exon21			CAGTGCCCAGCTC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.3003C>G	19.37:g.36278470C>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Silent	SNP	ENST00000007510.4	37																																																																																				C|0.531;G|0.469	0.469	strong		0.662	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
DDX60L	91351	hgsc.bcm.edu	37	4	169325233	169325233	+	Missense_Mutation	SNP	T	T	A	rs17540213	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:169325233T>A	ENST00000511577.1	-	25	3485	c.3238A>T	c.(3238-3240)Agt>Tgt	p.S1080C	DDX60L_ENST00000260184.7_Missense_Mutation_p.S1080C|DDX60L_ENST00000505890.1_Missense_Mutation_p.S1080C			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1080			S -> C (in dbSNP:rs17540213).				ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		GAATCCGGACTAAGGTTCTTC	0.284													T|||	117	0.0233626	0.0045	0.036	5008	,	,		11306	0.0		0.0616	False		,,,				2504	0.0245				p.S1080C		Atlas-SNP	.											.	DDX60L	116	.	0			c.A3238T						PASS	.	T	CYS/SER	46,3494		0,46,1724	36.0	30.0	32.0		3238	2.2	0.0	4	dbSNP_123	32	528,7514		15,498,3508	yes	missense	DDX60L	NM_001012967.1	112	15,544,5232	AA,AT,TT		6.5655,1.2994,4.956	benign	1080/1707	169325233	574,11008	1770	4021	5791	SO:0001583	missense	91351	exon25			CCGGACTAAGGTT	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.3238A>T	4.37:g.169325233T>A	ENSP00000422423:p.Ser1080Cys	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		69	0.03159340659340659	3	0.006097560975609756	15	0.04143646408839779	0	0.0	51	0.06728232189973615	T	8.896	0.955101	0.18507	0.012994	0.065655	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.19532	2.14;2.14;2.16;2.8	3.53	2.23	0.28157	.	0.497453	0.14877	U	0.293180	T	0.01156	0.0038	L	0.43152	1.355	0.09310	N	1	B;B;B	0.25272	0.122;0.058;0.122	B;B;B	0.22601	0.04;0.027;0.04	T	0.11891	-1.0569	10	0.56958	D	0.05	.	7.7384	0.28827	0.0:0.0:0.4075:0.5925	rs17540213;rs52820957;rs17540213	1080;1080;1080	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	C	1080;1080;1080;776	ENSP00000260184:S1080C;ENSP00000422423:S1080C;ENSP00000422202:S1080C;ENSP00000421026:S776C	ENSP00000260184:S1080C	S	-	1	0	DDX60L	169561808	0.001000	0.12720	0.007000	0.13788	0.028000	0.11728	0.236000	0.17967	1.246000	0.43901	0.383000	0.25322	AGT	T|0.950;A|0.050	0.050	strong		0.284	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
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 GAIIx	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		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	40	20	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 GAIIx	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	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	137	65	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	
PABPN1L	390748	hgsc.bcm.edu	37	16	88931274	88931274	+	Missense_Mutation	SNP	C	C	T	rs76267236	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88931274C>T	ENST00000419291.2	-	5	652	c.641G>A	c.(640-642)gGc>gAc	p.G214D	PABPN1L_ENST00000411789.2_Intron|PABPN1L_ENST00000427766.1_Silent_p.G178G|PABPN1L_ENST00000378358.4_Missense_Mutation_p.G214D	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	214	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.					cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						GATGACCCGGCCCCGGAAGAG	0.682													.|||	103	0.0205671	0.0038	0.0187	5008	,	,		14223	0.001		0.0726	False		,,,				2504	0.0112				p.G214D		Atlas-SNP	.											PABPN1L_ENST00000419291,colon,carcinoma,0,2	PABPN1L	25	2	0			c.G641A						PASS	.	C	ASP/GLY	56,3896		0,56,1920	14.0	19.0	17.0		641	4.5	0.5	16	dbSNP_131	17	588,7688		18,552,3568	yes	missense	PABPN1L	NM_001080487.2	94	18,608,5488	TT,TC,CC		7.1049,1.417,5.2666	possibly-damaging	214/279	88931274	644,11584	1976	4138	6114	SO:0001583	missense	390748	exon5			ACCCGGCCCCGGA		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"""RNA binding motif (RRM) containing"""	37237	protein-coding gene	gene with protein product	"""embryonic poly(A) binding protein 2"""					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.641G>A	16.37:g.88931274C>T	ENSP00000408598:p.Gly214Asp	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	165	81	0.490909	NM_001080487	A1L3B3|A2VDI2	Missense_Mutation	SNP	ENST00000419291.2	37	CCDS45547.2	70	0.03205128205128205	0	0.0	8	0.022099447513812154	0	0.0	62	0.08179419525065963	C	20.9	4.063480	0.76187	0.01417	0.071049	ENSG00000205022	ENST00000378358;ENST00000419291	D;D	0.81821	-1.54;-1.54	5.41	4.46	0.54185	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.099305	0.64402	N	0.000001	T	0.39600	0.1084	M	0.85373	2.75	0.80722	D	1	D;P	0.60160	0.987;0.622	D;B	0.66351	0.943;0.097	T	0.70691	-0.4802	10	0.54805	T	0.06	4.3894	11.22	0.48848	0.0:0.8482:0.0:0.1518	.	214;214	A6NDY0;A6NDY0-4	EPAB2_HUMAN;.	D	214	ENSP00000367609:G214D;ENSP00000408598:G214D	ENSP00000367609:G214D	G	-	2	0	PABPN1L	87458775	1.000000	0.71417	0.538000	0.28064	0.814000	0.46013	3.555000	0.53727	1.273000	0.44346	0.511000	0.50034	GGC	C|0.965;T|0.035	0.035	strong		0.682	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	
SUGP1	57794	hgsc.bcm.edu	37	19	19390185	19390185	+	Silent	SNP	G	G	A	rs11555053	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:19390185G>A	ENST00000247001.5	-	10	1712	c.1365C>T	c.(1363-1365)taC>taT	p.Y455Y		NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	455	Gln/Met-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						TGATCATGTCGTACATCTGCT	0.642													G|||	747	0.149161	0.295	0.1268	5008	,	,		19295	0.0		0.167	False		,,,				2504	0.1033				p.Y455Y		Atlas-SNP	.											SUGP1,NS,carcinoma,0,1	SUGP1	63	1	0			c.C1365T						PASS	.	G		1242,3162	411.7+/-335.8	171,900,1131	67.0	44.0	52.0		1365	-2.3	1.0	19	dbSNP_120	52	1363,7237	257.9+/-281.7	106,1151,3043	no	coding-synonymous	SUGP1	NM_172231.3		277,2051,4174	AA,AG,GG		15.8488,28.2016,20.0323		455/646	19390185	2605,10399	2202	4300	6502	SO:0001819	synonymous_variant	57794	exon10			CATGTCGTACATC	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"""G patch domain containing"""	18643	protein-coding gene	gene with protein product		607992	"""splicing factor 4"""	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.1365C>T	19.37:g.19390185G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	46	28	0.608696	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Silent	SNP	ENST00000247001.5	37	CCDS12399.1																																																																																			G|0.805;A|0.195	0.195	strong		0.642	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	
BSPRY	54836	hgsc.bcm.edu	37	9	116132334	116132334	+	Missense_Mutation	SNP	C	C	T	rs3088235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:116132334C>T	ENST00000374183.4	+	6	1160	c.1121C>T	c.(1120-1122)aCa>aTa	p.T374I	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	374	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		T -> I (in dbSNP:rs3088235). {ECO:0000269|PubMed:10978534, ECO:0000269|PubMed:14702039}.		calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						GCCTCCGGCACAGTGCTCTGT	0.632													C|||	630	0.125799	0.0068	0.0893	5008	,	,		18166	0.1448		0.1799	False		,,,				2504	0.2372				p.T374I		Atlas-SNP	.											.	BSPRY	21	.	0			c.C1121T						PASS	.	C	ILE/THR	147,3783		3,141,1821	45.0	49.0	47.0		1121	3.9	0.0	9	dbSNP_102	47	1606,6686		153,1300,2693	yes	missense	BSPRY	NM_017688.2	89	156,1441,4514	TT,TC,CC		19.3681,3.7405,14.343	benign	374/403	116132334	1753,10469	1965	4146	6111	SO:0001583	missense	54836	exon6			CCGGCACAGTGCT	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.1121C>T	9.37:g.116132334C>T	ENSP00000363298:p.Thr374Ile	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	37	CCDS43868.1	264	0.12087912087912088	4	0.008130081300813009	42	0.11602209944751381	73	0.12762237762237763	145	0.19129287598944592	C	1.512	-0.549115	0.04024	0.037405	0.193681	ENSG00000119411	ENST00000374183	T	0.70164	-0.46	5.69	3.86	0.44501	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.221215	0.49916	D	0.000124	T	0.00144	0.0004	L	0.58583	1.82	0.58432	P	1.0000000000287557E-6	P	0.40360	0.714	B	0.40782	0.34	T	0.09122	-1.0689	9	0.16420	T	0.52	-4.634	8.9651	0.35872	0.0:0.7749:0.0:0.2251	rs3088235;rs3750528;rs52790594;rs61234611;rs3088235	374	Q5W0U4	BSPRY_HUMAN	I	374	ENSP00000363298:T374I	ENSP00000363298:T374I	T	+	2	0	BSPRY	115172155	0.029000	0.19370	0.019000	0.16419	0.174000	0.22865	2.875000	0.48491	0.767000	0.33267	0.561000	0.74099	ACA	C|0.852;T|0.148	0.148	strong		0.632	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
CAND2	23066	hgsc.bcm.edu	37	3	12856856	12856856	+	Missense_Mutation	SNP	A	A	G	rs2305398	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:12856856A>G	ENST00000456430.2	+	8	1264	c.1223A>G	c.(1222-1224)cAg>cGg	p.Q408R	CAND2_ENST00000295989.5_Missense_Mutation_p.Q315R	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	408			Q -> R (in dbSNP:rs2305398). {ECO:0000269|PubMed:9734811}.		positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CGGCAAACACAGCCCCCGAAG	0.617													G|||	2887	0.576478	0.972	0.4986	5008	,	,		20497	0.2907		0.6551	False		,,,				2504	0.3108				p.Q408R	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.A1223G						PASS	.	G	ARG/GLN,ARG/GLN	3844,376		1752,340,18	46.0	54.0	51.0		1223,944	3.8	1.0	3	dbSNP_100	51	5225,3213		1621,1983,615	yes	missense,missense	CAND2	NM_001162499.1,NM_012298.2	43,43	3373,2323,633	GG,GA,AA		38.0777,8.91,28.3536	benign,benign	408/1237,315/1120	12856856	9069,3589	2110	4219	6329	SO:0001583	missense	23066	exon8			AAACACAGCCCCC		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1223A>G	3.37:g.12856856A>G	ENSP00000387641:p.Gln408Arg	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	37	CCDS54554.1	1283	0.5874542124542125	469	0.9532520325203252	180	0.4972375690607735	150	0.26223776223776224	484	0.6385224274406333	G	0.066	-1.213618	0.01555	0.9109	0.619223	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.64991	-0.13;-0.13	4.86	3.85	0.44370	Armadillo-like helical (1);Armadillo-type fold (1);	0.296572	0.26016	N	0.026849	T	0.00012	0.0000	N	0.00399	-1.545	0.09310	P	0.999996978	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36504	-0.9745	9	0.07482	T	0.82	-22.8675	7.173	0.25728	0.2702:0.0:0.7298:0.0	rs2305398;rs17824975;rs59611646;rs2305398	408;315	O75155;O75155-2	CAND2_HUMAN;.	R	315;408	ENSP00000295989:Q315R;ENSP00000387641:Q408R	ENSP00000295989:Q315R	Q	+	2	0	CAND2	12831856	0.994000	0.37717	0.955000	0.39395	0.098000	0.18820	0.601000	0.24119	1.046000	0.40249	-0.215000	0.12644	CAG	G|0.597;N|0.001	0.597	strong		0.617	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
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 GAIIx	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	ACAA1_ENST00000480865.1_5'UTR|ACAA1_ENST00000450296.1_Missense_Mutation_p.V346A|Y_RNA_ENST00000365095.1_RNA|ACAA1_ENST00000301810.7_Missense_Mutation_p.V294A	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	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	100	46	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	
ANKRD26	22852	hgsc.bcm.edu	37	10	27317840	27317840	+	Missense_Mutation	SNP	C	C	T	rs10829163	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27317840C>T	ENST00000376087.4	-	27	4078	c.3913G>A	c.(3913-3915)Gtc>Atc	p.V1305I	ANKRD26_ENST00000436985.2_Missense_Mutation_p.V1321I|ANKRD26_ENST00000376070.3_Missense_Mutation_p.V862I	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1304					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TGCTTTTTGACTGTAACTTTT	0.279													T|||	1589	0.317292	0.2352	0.1758	5008	,	,		14382	0.5516		0.1928	False		,,,				2504	0.4151				p.V1305I		Atlas-SNP	.											.	ANKRD26	179	.	0			c.G3913A						PASS	.	T	ILE/VAL	839,2761		96,647,1057	121.0	110.0	114.0		3913	-4.4	0.0	10	dbSNP_120	114	1180,6940		77,1026,2957	yes	missense	ANKRD26	NM_014915.2	29	173,1673,4014	TT,TC,CC		14.532,23.3056,17.227	benign	1305/1711	27317840	2019,9701	1800	4060	5860	SO:0001583	missense	22852	exon27			TTTTGACTGTAAC	AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.3913G>A	10.37:g.27317840C>T	ENSP00000365255:p.Val1305Ile	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	660	0.3021978021978022	109	0.22154471544715448	63	0.17403314917127072	340	0.5944055944055944	148	0.19525065963060687	T	0.013	-1.644536	0.00792	0.233056	0.14532	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.75050	-0.9;-0.9;-0.9	4.9	-4.39	0.03611	.	0.729179	0.11831	N	0.525220	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.24261	-1.0165	9	0.02654	T	1	.	8.0976	0.30837	0.0:0.4553:0.1065:0.4382	rs10829163;rs52823343;rs58305733;rs10829163	1305;1304;1321	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	I	862;1305;1321	ENSP00000365238:V862I;ENSP00000365255:V1305I;ENSP00000405112:V1321I	ENSP00000365238:V862I	V	-	1	0	ANKRD26	27357846	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-1.827000	0.01704	-1.176000	0.02747	-0.308000	0.09152	GTC	C|0.724;T|0.276	0.276	strong		0.279	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		
NSDHL	50814	hgsc.bcm.edu	37	X	152018832	152018832	+	Silent	SNP	T	T	G	rs5969919	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:152018832T>G	ENST00000370274.3	+	3	326	c.132T>G	c.(130-132)ggT>ggG	p.G44G	NSDHL_ENST00000440023.1_Silent_p.G44G	NM_015922.2	NP_057006.1	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	44					cholesterol biosynthetic process (GO:0006695)|hair follicle development (GO:0001942)|labyrinthine layer blood vessel development (GO:0060716)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity (GO:0047012)			NS(1)|breast(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(5)	15	Acute lymphoblastic leukemia(192;6.56e-05)					CAGTGATCGGTGGCTCTGGAT	0.512													g|||	3252	0.861457	0.5446	0.7089	3775	,	,		14434	0.6915		0.661	False		,,,				2504	0.6933				p.G44G		Atlas-SNP	.											.	NSDHL	33	.	0			c.T132G						PASS	.		,	2857,978		905,617,430,110,141	171.0	150.0	158.0		132,132	-3.7	0.7	X	dbSNP_114	158	5812,916		1812,560,1628,56,244	no	coding-synonymous,coding-synonymous	NSDHL	NM_001129765.1,NM_015922.2	,	2717,1177,2058,166,385	GG,GT,G,TT,T		13.6147,25.502,17.9305	,	44/374,44/374	152018832	8669,1894	2203	4300	6503	SO:0001819	synonymous_variant	50814	exon3			GATCGGTGGCTCT	X96621	CCDS14717.1	Xq28	2011-09-14			ENSG00000147383	ENSG00000147383	1.1.1.170	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	13398	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 31E, member 1"""	300275				10710235, 12837764, 19027726	Standard	NM_015922		Approved	XAP104, H105e3, SDR31E1	uc004fgs.1	Q15738	OTTHUMG00000024185	ENST00000370274.3:c.132T>G	X.37:g.152018832T>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	127	90	0.708661	NM_015922	D3DWT6|O00344	Silent	SNP	ENST00000370274.3	37	CCDS14717.1																																																																																			0|0.015;G|0.819	0.819	strong		0.512	NSDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060927.1	NM_015922	
WDR11	55717	hgsc.bcm.edu	37	10	122665459	122665459	+	Silent	SNP	C	C	G	rs3740307	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:122665459C>G	ENST00000263461.6	+	27	3609	c.3363C>G	c.(3361-3363)gtC>gtG	p.V1121V	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|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)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.V1121V(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						CTCCACAAGTCAATCAGAAAT	0.498													C|||	777	0.155152	0.0129	0.2305	5008	,	,		16030	0.3373		0.1093	False		,,,				2504	0.1534				p.V1121V		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.C3363G						PASS	.	C		144,4262	102.1+/-140.7	1,142,2060	131.0	119.0	123.0		3363	1.7	1.0	10	dbSNP_107	123	1110,7490	230.4+/-264.8	70,970,3260	no	coding-synonymous	WDR11	NM_018117.11		71,1112,5320	GG,GC,CC		12.907,3.2683,9.6417		1121/1225	122665459	1254,11752	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon27			ACAAGTCAATCAG	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.3363C>G	10.37:g.122665459C>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			C|0.885;G|0.115	0.115	strong		0.498	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
CYP4A22	284541	hgsc.bcm.edu	37	1	47607851	47607851	+	Missense_Mutation	SNP	A	A	T	rs2056899	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47607851A>T	ENST00000371891.3	+	4	485	c.454A>T	c.(454-456)Aat>Tat	p.N152Y	CYP4A22_ENST00000294337.3_Missense_Mutation_p.N152Y|CYP4A22_ENST00000371890.3_Missense_Mutation_p.N152Y|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000485117.1_3'UTR	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	152			N -> Y (in allele CYP4A22*2, allele CYP4A22*3, allele CYP4A22*4, allele CYP4A22*5, allele CYP4A22*6, allele CYP4A22*7, allele CYP4A22*8, allele CYP4A22*9, allele CYP4A22*10, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs2056899). {ECO:0000269|PubMed:15611369, ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGCCTTCCACAATGACATCCT	0.542													T|||	3660	0.730831	0.944	0.5072	5008	,	,		20966	0.9802		0.4036	False		,,,				2504	0.681				p.N152Y	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.A454T						PASS	.	T	TYR/ASN	3737,669	282.8+/-276.7	1591,555,57	115.0	99.0	104.0		454	0.2	1.0	1	dbSNP_94	104	3324,5276	644.4+/-400.0	634,2056,1610	no	missense	CYP4A22	NM_001010969.2	143	2225,2611,1667	TT,TA,AA		38.6512,15.1838,45.7097	benign	152/520	47607851	7061,5945	2203	4300	6503	SO:0001583	missense	284541	exon4			TTCCACAATGACA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.454A>T	1.37:g.47607851A>T	ENSP00000360958:p.Asn152Tyr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	133	73	0.548872	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	1483	0.6790293040293041	447	0.9085365853658537	168	0.46408839779005523	568	0.993006993006993	300	0.39577836411609496	t	0.006	-2.066875	0.00382	0.848162	0.386512	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.68903	-0.36;-0.36;-0.36	1.7	0.248	0.15526	.	0.070255	0.64402	N	0.000015	T	0.00012	0.0000	N	0.00016	-2.85	0.58432	P	5.999999999950489E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38714	-0.9648	9	0.02654	T	1	.	6.7756	0.23619	0.365:0.0:0.0:0.635	rs2056899;rs52810631;rs56721463;rs2056899	152;152	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	Y	152	ENSP00000360957:N152Y;ENSP00000360958:N152Y;ENSP00000294337:N152Y	ENSP00000294337:N152Y	N	+	1	0	CYP4A22	47380438	0.997000	0.39634	0.957000	0.39632	0.243000	0.25628	2.912000	0.48782	-0.032000	0.13758	-1.247000	0.01520	AAT	.	.	weak		0.542	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
PHLDB1	23187	hgsc.bcm.edu	37	11	118509668	118509668	+	Silent	SNP	A	A	G	rs483598	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:118509668A>G	ENST00000361417.2	+	12	3006	c.2595A>G	c.(2593-2595)gaA>gaG	p.E865E	AP002954.3_ENST00000530198.1_RNA|PHLDB1_ENST00000527898.1_5'UTR|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000356063.5_Silent_p.E865E|PHLDB1_ENST00000524713.1_5'Flank	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	865										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CCGTGCAGGAATCAGAACGCC	0.612													G|||	2868	0.572684	0.4773	0.7089	5008	,	,		18170	0.6558		0.5368	False		,,,				2504	0.5562				p.E865E		Atlas-SNP	.											.	PHLDB1	103	.	0			c.A2595G						PASS	.	G	,,	2087,2311	593.3+/-388.0	490,1107,602	38.0	36.0	37.0		2595,2595,2595	-1.5	0.7	11	dbSNP_83	37	4742,3848	531.7+/-382.0	1319,2104,872	no	coding-synonymous,coding-synonymous,coding-synonymous	PHLDB1	NM_001144758.1,NM_001144759.1,NM_015157.2	,,	1809,3211,1474	GG,GA,AA		44.7963,47.4534,47.4207	,,	865/1378,865/1320,865/1378	118509668	6829,6159	2199	4295	6494	SO:0001819	synonymous_variant	23187	exon11			GCAGGAATCAGAA		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.2595A>G	11.37:g.118509668A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Silent	SNP	ENST00000361417.2	37	CCDS8401.1																																																																																			A|0.454;G|0.546	0.546	strong		0.612	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157	
NOC3L	64318	hgsc.bcm.edu	37	10	96100094	96100094	+	Silent	SNP	C	C	A	rs140939496	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96100094C>A	ENST00000371361.3	-	16	1819	c.1719G>T	c.(1717-1719)ctG>ctT	p.L573L	NOC3L_ENST00000543788.1_Silent_p.L311L|NOC3L_ENST00000371350.1_Silent_p.L573L	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	573					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				GATCAATATTCAGAACATCAC	0.289													C|||	40	0.00798722	0.0	0.0159	5008	,	,		19426	0.0		0.0239	False		,,,				2504	0.0051				p.L573L		Atlas-SNP	.											.	NOC3L	67	.	0			c.G1719T						PASS	.	C		23,4383	29.9+/-59.1	0,23,2180	112.0	107.0	109.0		1719	1.8	1.0	10	dbSNP_134	109	280,8316	104.4+/-165.4	6,268,4024	no	coding-synonymous	NOC3L	NM_022451.9		6,291,6204	AA,AC,CC		3.2573,0.522,2.3304		573/801	96100094	303,12699	2203	4298	6501	SO:0001819	synonymous_variant	64318	exon16			AATATTCAGAACA	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"""chromosome 10 open reading frame 117"""	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.1719G>T	10.37:g.96100094C>A		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	213	89	0.41784	NM_022451	Q9H5M6|Q9H9D8	Silent	SNP	ENST00000371361.3	37	CCDS7433.1																																																																																			C|0.979;A|0.021	0.021	strong		0.289	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	
HLA-A	3105	hgsc.bcm.edu	37	6	29911222	29911222	+	Missense_Mutation	SNP	C	C	T	rs1059535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29911222C>T	ENST00000396634.1	+	5	862	c.521C>T	c.(520-522)gCc>gTc	p.A174V	HLA-A_ENST00000376806.5_Missense_Mutation_p.A174V|HLA-A_ENST00000376802.2_Missense_Mutation_p.A174V|HLA-A_ENST00000376809.5_Missense_Mutation_p.A174V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	174	Alpha-2.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TGGGAGGCGGCCCATGAGGCG	0.647									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	435	0.086861	0.0817	0.0461	5008	,	,		12539	0.0188		0.1233	False		,,,				2504	0.1554				p.A174V		Atlas-SNP	.											.	HLA-A	89	.	0			c.C521T						PASS	.						37.0	28.0	31.0					6																	29911222		1507	2706	4213	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGCGGCCCATGA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.521C>T	6.37:g.29911222C>T	ENSP00000379873:p.Ala174Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	110	70	0.636364	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	154|154	0.07051282051282051|0.07051282051282051	36|36	0.07317073170731707|0.07317073170731707	14|14	0.03867403314917127|0.03867403314917127	9|9	0.015734265734265736|0.015734265734265736	95|95	0.12532981530343007|0.12532981530343007	.|.	9.119|9.119	1.008386|1.008386	0.19199|0.19199	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802|ENST00000355767	T;T;T;T|.	0.00832|.	5.64;5.64;5.64;5.64|.	3.78|3.78	-6.55|-6.55	0.01854|0.01854	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);|.	13.981400|.	0.02424|.	N|.	0.082844|.	T|T	0.47911|0.47911	0.1471|0.1471	M|M	0.90082|0.90082	3.085|3.085	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.12013|.	0.005;0.003;0.002;0.003;0.002;0.003|.	B;B;B;B;B;B|.	0.14578|.	0.002;0.011;0.006;0.005;0.003;0.005|.	T|T	0.56135|0.56135	-0.8029|-0.8029	9|5	0.72032|0.87932	D|D	0.01|0	.|.	5.5436|5.5436	0.17051|0.17051	0.5823:0.1603:0.0:0.2574|0.5823:0.1603:0.0:0.2574	rs1059535;rs2231055;rs3200233;rs9260154;rs16868223;rs41548615|rs1059535;rs2231055;rs3200233;rs9260154;rs16868223;rs41548615	53;174;174;174;174;174|.	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P04439|.	.;1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN|.	V|S	174|149	ENSP00000379873:A174V;ENSP00000366002:A174V;ENSP00000366005:A174V;ENSP00000365998:A174V|.	ENSP00000365998:A174V|ENSP00000348012:P149S	A|P	+|+	2|1	0|0	HLA-A|HLA-A	30019201|30019201	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.007000|0.007000	0.05969|0.05969	-6.247000|-6.247000	0.00074|0.00074	-1.123000|-1.123000	0.02940|0.02940	-1.504000|-1.504000	0.00955|0.00955	GCC|CCC	C|0.912;T|0.088	0.088	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
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 GAIIx	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	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	31	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	
ENGASE	64772	hgsc.bcm.edu	37	17	77075667	77075667	+	Silent	SNP	T	T	C	rs3744183	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77075667T>C	ENST00000579016.1	+	4	513	c.513T>C	c.(511-513)atT>atC	p.I171I	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	171						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						CCGTCACCATTCCCCCAGTGG	0.587													C|||	2085	0.416334	0.6316	0.4063	5008	,	,		19718	0.38		0.173	False		,,,				2504	0.4202				p.I171I		Atlas-SNP	.											ENGASE,caecum,adenoma,0,1	ENGASE	55	1	0			c.T513C						scavenged	.						103.0	128.0	120.0					17																	77075667		2115	4220	6335	SO:0001819	synonymous_variant	64772	exon4			CACCATTCCCCCA	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.513T>C	17.37:g.77075667T>C		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	48	16	0.333333	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			T|0.737;C|0.263	0.263	strong		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
HNRNPUL1	11100	hgsc.bcm.edu	37	19	41809995	41809995	+	Silent	SNP	A	A	G	rs1056854	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41809995A>G	ENST00000392006.3	+	13	2264	c.2091A>G	c.(2089-2091)ccA>ccG	p.P697P	HNRNPUL1_ENST00000352456.3_Silent_p.P597P|HNRNPUL1_ENST00000595018.1_Silent_p.P597P|HNRNPUL1_ENST00000593587.1_Silent_p.P597P|HNRNPUL1_ENST00000263367.3_Silent_p.P608P|HNRNPUL1_ENST00000378215.4_Silent_p.P583P|HNRNPUL1_ENST00000602130.1_Silent_p.P697P	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	697	Necessary for interaction with TP53.|Pro-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						AACAgccgccaccacagcagc	0.632													A|||	625	0.1248	0.0673	0.1311	5008	,	,		12076	0.2034		0.171	False		,,,				2504	0.0695				p.P697P		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.A2091G						PASS	.	A	,	388,4018	187.1+/-213.8	22,344,1837	57.0	62.0	60.0		2091,1791	-2.1	0.6	19	dbSNP_86	60	1334,7262	253.0+/-278.9	106,1122,3070	no	coding-synonymous,coding-synonymous	HNRNPUL1	NM_007040.3,NM_144732.2	,	128,1466,4907	GG,GA,AA		15.5188,8.8062,13.2441	,	697/857,597/757	41809995	1722,11280	2203	4298	6501	SO:0001819	synonymous_variant	11100	exon13			GCCGCCACCACAG	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.2091A>G	19.37:g.41809995A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Silent	SNP	ENST00000392006.3	37	CCDS12576.1																																																																																			A|0.867;G|0.133	0.133	strong		0.632	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
WDR44	54521	hgsc.bcm.edu	37	X	117528142	117528142	+	Silent	SNP	C	C	T	rs6603401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:117528142C>T	ENST00000254029.3	+	5	1346	c.951C>T	c.(949-951)acC>acT	p.T317T	WDR44_ENST00000371822.5_Silent_p.T292T|WDR44_ENST00000371825.3_Silent_p.T317T	NM_019045.4	NP_061918.3	Q5JSH3	WDR44_HUMAN	WD repeat domain 44	317						endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)		p.T317T(2)		breast(4)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	33						AAATAGTTACCGCCCAGGTTG	0.433													T|||	2177	0.576689	0.7156	0.451	3775	,	,		14217	0.4395		0.1581	False		,,,				2504	0.3231				p.T317T		Atlas-SNP	.											.	WDR44	188	.	2	Substitution - coding silent(2)	stomach(2)	c.C951T						PASS	.	T	,,	3246,589		1172,407,495,53,76	121.0	120.0	121.0		951,876,951	2.9	1.0	X	dbSNP_116	121	1413,5315		101,797,414,1530,1458	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR44	NM_001184965.1,NM_001184966.1,NM_019045.4	,,	1273,1204,909,1583,1534	TT,TC,T,CC,C		21.0018,15.3585,44.1068	,,	317/906,292/825,317/914	117528142	4659,5904	2203	4300	6503	SO:0001819	synonymous_variant	54521	exon5			AGTTACCGCCCAG	AK001978	CCDS14572.1, CCDS55482.1, CCDS55483.1	Xq24	2013-01-09			ENSG00000131725	ENSG00000131725		"""WD repeat domain containing"""	30512	protein-coding gene	gene with protein product						12477932	Standard	NM_019045		Approved	DKFZp686L20145, RPH11, RAB11BP	uc004eqn.3	Q5JSH3	OTTHUMG00000022254	ENST00000254029.3:c.951C>T	X.37:g.117528142C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	84	0.666667	NM_001184965	B4DSE9|F8W913|Q0JS52|Q0JTF3|Q5JSH2|Q6ZSC1|Q7Z365|Q7Z3P6|Q8NAU8|Q8NHU5|Q9NUV4	Silent	SNP	ENST00000254029.3	37	CCDS14572.1	875	0.5274261603375527	238	0.8561151079136691	99	0.38671875	172	0.42574257425742573	90	0.12968299711815562	T	10.12	1.263062	0.23051	0.846415	0.210018	ENSG00000131725	ENST00000371848	.	.	.	5.51	2.9	0.33743	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14420	-1.0473	3	.	.	.	-13.3646	2.8866	0.05663	0.1348:0.0751:0.2745:0.5156	rs6603401;rs57593030;rs6603401	.	.	.	C	217	.	.	R	+	1	0	WDR44	117412170	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.982000	0.29539	0.220000	0.20860	-0.314000	0.08810	CGC	C|0.475;T|0.525	0.525	strong		0.433	WDR44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058001.1	NM_019045	
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145273431	145273431	+	Silent	SNP	A	A	G	rs17421312	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145273431A>G	ENST00000369340.3	+	4	729	c.285A>G	c.(283-285)caA>caG	p.Q95Q	NOTCH2NL_ENST00000362074.6_Silent_p.Q95Q|RP11-458D21.5_ENST00000468030.1_Silent_p.Q95Q|NOTCH2NL_ENST00000344859.3_Silent_p.Q95Q			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	95	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						GCACCTGTCAAGTCGGGTTTA	0.478																																					p.Q95Q		Atlas-SNP	.											.	NOTCH2NL	100	.	0			c.A285G						PASS	.						296.0	303.0	301.0					1																	145273431		2203	4300	6503	SO:0001819	synonymous_variant	388677	exon3			CTGTCAAGTCGGG		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.285A>G	1.37:g.145273431A>G		Somatic	1048	0	0		WXS	Illumina HiSeq	Phase_I	1054	127	0.120493	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Silent	SNP	ENST00000369340.3	37	CCDS909.1																																																																																			A|0.962;G|0.038	0.038	strong		0.478	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458	
VSIG10L	147645	hgsc.bcm.edu	37	19	51841417	51841417	+	Missense_Mutation	SNP	C	C	T	rs34380065	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51841417C>T	ENST00000335624.4	-	6	1774	c.1775G>A	c.(1774-1776)cGg>cAg	p.R592Q	CTD-2616J11.16_ENST00000594311.1_RNA|CTD-2616J11.16_ENST00000601148.1_RNA	NM_001163922.1	NP_001157394.1	Q86VR7	VS10L_HUMAN	V-set and immunoglobulin domain containing 10 like	592			R -> Q (in dbSNP:rs34380065). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)	4						CTCCCCCAACCGTGTCTCTGC	0.652													C|||	2851	0.569289	0.4644	0.4654	5008	,	,		13538	0.6151		0.5636	False		,,,				2504	0.7434				p.R592Q		Atlas-SNP	.											.	VSIG10L	40	.	0			c.G1775A						PASS	.	C	GLN/ARG	659,717		171,317,200	6.0	7.0	7.0		1775	-8.4	0.0	19	dbSNP_126	7	1876,1278		588,700,289	yes	missense	VSIG10L	NM_001163922.1	43	759,1017,489	TT,TC,CC		40.52,47.8924,44.0397	benign	592/868	51841417	2535,1995	688	1577	2265	SO:0001583	missense	147645	exon6			CCCAACCGTGTCT		CCDS54300.1	19q13.41	2013-01-11				ENSG00000186806		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	27111	protein-coding gene	gene with protein product						12477932	Standard	NM_001163922		Approved		uc002pwf.3	Q86VR7		ENST00000335624.4:c.1775G>A	19.37:g.51841417C>T	ENSP00000335623:p.Arg592Gln	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_001163922		Missense_Mutation	SNP	ENST00000335624.4	37	CCDS54300.1	1153	0.5279304029304029	224	0.45528455284552843	162	0.44751381215469616	352	0.6153846153846154	415	0.5474934036939314	C	8.276	0.814392	0.16607	0.478924	0.5948	ENSG00000186806	ENST00000335624	T	0.27890	1.64	5.12	-8.41	0.00961	.	0.956791	0.08552	N	0.928865	T	0.00012	0.0000	L	0.41027	1.25	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.49341	-0.8950	9	0.13853	T	0.58	-4.3012	2.0607	0.03592	0.1109:0.2745:0.1805:0.4341	rs34380065;rs58868085	592	Q86VR7	VS10L_HUMAN	Q	592	ENSP00000335623:R592Q	ENSP00000335623:R592Q	R	-	2	0	VSIG10L	56533229	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.742000	0.01835	-0.736000	0.04831	-0.367000	0.07326	CGG	C|0.464;T|0.536	0.536	strong		0.652	VSIG10L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464535.1	NM_001163922	
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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.P105L|SGK1_ENST00000367857.5_Missense_Mutation_p.P81L|SGK1_ENST00000475719.2_Missense_Mutation_p.P91L|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367858.5_Missense_Mutation_p.P186L|SGK1_ENST00000528577.1_Missense_Mutation_p.P119L	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	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	23	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		
CCDC15	80071	hgsc.bcm.edu	37	11	124863136	124863136	+	Silent	SNP	C	C	A	rs7951202	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124863136C>A	ENST00000344762.5	+	11	2470	c.2211C>A	c.(2209-2211)ccC>ccA	p.P737P	CCDC15_ENST00000529051.1_Silent_p.P737P	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	737						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)		CTGGAGTGCCCTTGGTATGTT	0.358													A|||	1437	0.286941	0.4705	0.1801	5008	,	,		21131	0.1935		0.1958	False		,,,				2504	0.3047				p.P737P		Atlas-SNP	.											.	CCDC15	134	.	0			c.C2211A						PASS	.	A		1594,2086		362,870,608	69.0	64.0	65.0		2211	-7.2	0.0	11	dbSNP_116	65	1643,6523		170,1303,2610	no	coding-synonymous	CCDC15	NM_025004.2		532,2173,3218	AA,AC,CC		20.12,43.3152,27.3257		737/952	124863136	3237,8609	1840	4083	5923	SO:0001819	synonymous_variant	80071	exon11			AGTGCCCTTGGTA	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.2211C>A	11.37:g.124863136C>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	43	35	0.813953	NM_025004	Q9H8U7	Silent	SNP	ENST00000344762.5	37	CCDS44756.1																																																																																			C|0.719;A|0.281	0.281	strong		0.358	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
KIAA1614	57710	hgsc.bcm.edu	37	1	180897569	180897569	+	Silent	SNP	C	C	T	rs3747958	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:180897569C>T	ENST00000367588.4	+	4	1120	c.1065C>T	c.(1063-1065)acC>acT	p.T355T	KIAA1614_ENST00000367587.1_5'UTR	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	355										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						GCTGCAGGACCGTTGGTCCCA	0.637													C|||	1953	0.389976	0.2731	0.4063	5008	,	,		16840	0.5516		0.4135	False		,,,				2504	0.3456				p.T355T		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C1065T						PASS	.	C		1136,2920		167,802,1059	111.0	116.0	114.0		1065	5.4	1.0	1	dbSNP_107	114	3433,4953		709,2015,1469	no	coding-synonymous	KIAA1614	NM_020950.1		876,2817,2528	TT,TC,CC		40.9373,28.0079,36.7224		355/1191	180897569	4569,7873	2028	4193	6221	SO:0001819	synonymous_variant	57710	exon4			CAGGACCGTTGGT	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.1065C>T	1.37:g.180897569C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	129	68	0.527132	NM_020950	Q5VZ45|Q9HCF8	Silent	SNP	ENST00000367588.4	37	CCDS41442.1																																																																																			C|0.600;T|0.400	0.400	strong		0.637	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
WDFY4	57705	hgsc.bcm.edu	37	10	50038878	50038878	+	Missense_Mutation	SNP	G	G	C	rs41283281	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50038878G>C	ENST00000325239.5	+	37	6501	c.6474G>C	c.(6472-6474)gaG>gaC	p.E2158D	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2158						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						AGATTGAAGAGGTCACACCGC	0.557													G|||	169	0.033746	0.0212	0.0461	5008	,	,		21721	0.001		0.0855	False		,,,				2504	0.0225				p.E2158D		Atlas-SNP	.											.	WDFY4	205	.	0			c.G6474C						PASS	.	G	ASP/GLU	48,1336		0,48,644	90.0	89.0	89.0		6474	-1.9	1.0	10	dbSNP_127	89	210,2972		4,202,1385	yes	missense	WDFY4	NM_020945.1	45	4,250,2029	CC,CG,GG		6.5996,3.4682,5.6505	benign	2158/3185	50038878	258,4308	692	1591	2283	SO:0001583	missense	57705	exon38			TGAAGAGGTCACA	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.6474G>C	10.37:g.50038878G>C	ENSP00000320563:p.Glu2158Asp	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	194	103	0.530928	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	92|92|92	0.04212454212454213|0.04212454212454213|0.04212454212454213	8|8|8	0.016260162601626018|0.016260162601626018|0.016260162601626018	18|18|18	0.049723756906077346|0.049723756906077346|0.049723756906077346	0|0|0	0.0|0.0|0.0	66|66|66	0.0870712401055409|0.0870712401055409|0.0870712401055409	G|G|G	8.766|8.766|8.766	0.924841|0.924841|0.924841	0.18056|0.18056|0.18056	0.034682|0.034682|0.034682	0.065996|0.065996|0.065996	ENSG00000128815|ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000312002|ENST00000265453	T|.|.	0.55588|.|.	0.51|.|.	5.87|5.87|5.87	-1.88|-1.88|-1.88	0.07713|0.07713|0.07713	.|.|.	0.190175|.|.	0.45126|.|.	D|.|.	0.000400|.|.	T|T|T	0.02047|0.02047|0.02047	0.0064|0.0064|0.0064	L|L|L	0.46157|0.46157|0.46157	1.445|1.445|1.445	0.80722|0.80722|0.80722	D|D|D	1|1|1	B|.|.	0.12013|.|.	0.005|.|.	B|.|.	0.11329|.|.	0.006|.|.	T|T|T	0.12502|0.12502|0.12502	-1.0545|-1.0545|-1.0545	9|5|5	.|.|.	.|.|.	.|.|.	.|.|.	2.7635|2.7635|2.7635	0.05314|0.05314|0.05314	0.3072:0.1891:0.4076:0.0962|0.3072:0.1891:0.4076:0.0962|0.3072:0.1891:0.4076:0.0962	rs41283281;rs61733235|rs41283281;rs61733235|rs41283281;rs61733235	2158|.|.	Q6ZS81|.|.	WDFY4_HUMAN|.|.	D|R|T	2158|1249|245	ENSP00000320563:E2158D|.|.	.|.|.	E|G|R	+|+|+	3|1|2	2|0|0	WDFY4|WDFY4|WDFY4	49708884|49708884|49708884	0.971000|0.971000|0.971000	0.33674|0.33674|0.33674	0.953000|0.953000|0.953000	0.39169|0.39169|0.39169	0.979000|0.979000|0.979000	0.70002|0.70002|0.70002	0.057000|0.057000|0.057000	0.14279|0.14279|0.14279	-0.020000|-0.020000|-0.020000	0.14032|0.14032|0.14032	-0.175000|-0.175000|-0.175000	0.13238|0.13238|0.13238	GAG|GGT|AGG	G|0.954;C|0.046	0.046	strong		0.557	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
DNAL4	10126	hgsc.bcm.edu	37	22	39178701	39178701	+	Silent	SNP	A	A	G	rs760482	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39178701A>G	ENST00000216068.4	-	2	280	c.36T>C	c.(34-36)gaT>gaC	p.D12D	DNAL4_ENST00000406199.3_Silent_p.D12D|SUN2_ENST00000406622.1_Intron|DNAL4_ENST00000486019.1_Intron	NM_005740.2	NP_005731.1	O96015	DNAL4_HUMAN	dynein, axonemal, light chain 4	12					microtubule-based process (GO:0007017)|neurotrophin TRK receptor signaling pathway (GO:0048011)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	motor activity (GO:0003774)			lung(1)|skin(1)	2	Melanoma(58;0.04)					GTCGCTTATAATCAGCCTCAT	0.587													A|||	2066	0.41254	0.4206	0.245	5008	,	,		18303	0.6925		0.2734	False		,,,				2504	0.3753				p.D12D		Atlas-SNP	.											.	DNAL4	5	.	0			c.T36C						PASS	.	A		1658,2748	505.9+/-366.3	328,1002,873	230.0	170.0	191.0		36	-2.4	1.0	22	dbSNP_86	191	2591,6009	419.8+/-353.2	381,1829,2090	yes	coding-synonymous	DNAL4	NM_005740.2		709,2831,2963	GG,GA,AA		30.1279,37.6305,32.6695		12/106	39178701	4249,8757	2203	4300	6503	SO:0001819	synonymous_variant	10126	exon2			CTTATAATCAGCC	AL035366	CCDS13979.1	22q13.1	2008-06-10	2006-09-04		ENSG00000100246	ENSG00000100246		"""Axonemal dyneins"""	2955	protein-coding gene	gene with protein product		610565	"""dynein, axonemal, light polypeptide 4"", ""dynein, axonemal, light 4"""			10591208	Standard	NM_005740		Approved	dJ327J16, PIG27	uc003awj.3	O96015	OTTHUMG00000151025	ENST00000216068.4:c.36T>C	22.37:g.39178701A>G		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	179	179	1	NM_005740	Q6FGB2|Q6FGD0	Silent	SNP	ENST00000216068.4	37	CCDS13979.1																																																																																			A|0.627;G|0.373	0.373	strong		0.587	DNAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321032.1	NM_005740	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340835	55340835	+	Silent	SNP	C	C	T	rs45459293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55340835C>T	ENST00000391728.4	+	7	1053	c.1020C>T	c.(1018-1020)caC>caT	p.H340H	KIR3DL1_ENST00000358178.4_Silent_p.H245H|KIR3DL1_ENST00000326542.7_Silent_p.H323H|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000538269.1_Silent_p.H340H|KIR3DL1_ENST00000541392.1_Silent_p.H323H	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	340					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		GACACCTGCACATTCTGATTG	0.448													c|||	526	0.105032	0.0938	0.1427	5008	,	,		16236	0.001		0.2475	False		,,,				2504	0.0542				p.H340H		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.C1020T						PASS	.	C		157,4191		77,3,2094	273.0	207.0	230.0		1020	-1.5	0.0	19	dbSNP_127	230	730,7570		355,20,3775	no	coding-synonymous	KIR3DL1	NM_013289.2		432,23,5869	TT,TC,CC		8.7952,3.6109,7.013		340/445	55340835	887,11761	2174	4150	6324	SO:0001819	synonymous_variant	3811	exon7			CCTGCACATTCTG	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1020C>T	19.37:g.55340835C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	10	10	1	NM_013289	O43473|Q14946|Q16541	Silent	SNP	ENST00000391728.4	37	CCDS42621.1																																																																																			C|0.913;T|0.087	0.087	strong		0.448	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
CEP19	84984	hgsc.bcm.edu	37	3	196435534	196435534	+	Missense_Mutation	SNP	T	T	C	rs6776064	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:196435534T>C	ENST00000409690.3	-	2	429	c.7A>G	c.(7-9)Atg>Gtg	p.M3V	RNU6-646P_ENST00000364571.1_RNA|CEP19_ENST00000399942.4_Intron	NM_032898.3	NP_116287.2	Q96LK0	CEP19_HUMAN	centrosomal protein 19kDa	0						centriole (GO:0005814)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				NS(1)|breast(2)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	10						ATCATTCCCATGTACATGTCC	0.408													C|||	2194	0.438099	0.4319	0.3184	5008	,	,		19510	0.5952		0.3459	False		,,,				2504	0.4642				p.M3V		Atlas-SNP	.											.	CEP19	22	.	0			c.A7G						PASS	.	C	VAL/MET	1516,2322		306,904,709	95.0	88.0	90.0		7	2.9	0.0	3	dbSNP_116	90	2935,5349		493,1949,1700	yes	missense	CEP19	NM_032898.3	21	799,2853,2409	CC,CT,TT		35.4297,39.4997,36.7184		3/168	196435534	4451,7671	1919	4142	6061	SO:0001583	missense	84984	exon2			TTCCCATGTACAT	BC007827	CCDS43193.2	3q29	2014-02-20	2011-05-06	2011-05-06	ENSG00000174007	ENSG00000174007			28209	protein-coding gene	gene with protein product		615586	"""chromosome 3 open reading frame 34"""	C3orf34		21399614	Standard	XM_005269370		Approved	MGC14126	uc011btw.2	Q96LK0	OTTHUMG00000153933	ENST00000409690.3:c.7A>G	3.37:g.196435534T>C	ENSP00000387209:p.Met3Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_032898	B2RA74|Q96I48	Missense_Mutation	SNP	ENST00000409690.3	37	CCDS43193.2	950	0.434981684981685	217	0.4410569105691057	115	0.31767955801104975	347	0.6066433566433567	271	0.3575197889182058	C	0.005	-2.165644	0.00318	0.394997	0.354297	ENSG00000174007	ENST00000409690	.	.	.	4.99	2.89	0.33648	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.44128	-0.9348	4	0.05525	T	0.97	.	7.3183	0.26513	0.0:0.5696:0.0:0.4304	rs6776064;rs56846764;rs6776064	.	.	.	V	3	.	ENSP00000387209:M3V	M	-	1	0	CEP19	197919931	0.000000	0.05858	0.007000	0.13788	0.318000	0.28184	-0.082000	0.11304	0.535000	0.28714	-0.128000	0.14901	ATG	T|0.571;C|0.429	0.429	strong		0.408	CEP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333080.2	NM_032898	
FCGBP	8857	hgsc.bcm.edu	37	19	40392496	40392496	+	Missense_Mutation	SNP	C	C	T	rs143680639	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40392496C>T	ENST00000221347.6	-	16	8015	c.8008G>A	c.(8008-8010)Ggg>Agg	p.G2670R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2670	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.G2670R(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GACAGTGGCCCTGTGGGGCTG	0.597																																					p.G2670R		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	large_intestine(1)	c.G8008A						PASS	.						36.0	38.0	37.0					19																	40392496		2171	4287	6458	SO:0001583	missense	8857	exon16			GTGGCCCTGTGGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8008G>A	19.37:g.40392496C>T	ENSP00000221347:p.Gly2670Arg	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	176	47	0.267045	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.401441	0.42613	.	.	ENSG00000090920	ENST00000221347	T	0.24908	1.83	2.66	2.66	0.31614	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.000000	0.85682	D	0.000000	T	0.57533	0.2060	M	0.92784	3.345	0.42617	D	0.993336	D	0.89917	1.0	D	0.97110	1.0	T	0.70223	-0.4931	10	0.87932	D	0	.	12.5273	0.56093	0.0:1.0:0.0:0.0	.	2670	Q9Y6R7	FCGBP_HUMAN	R	2670	ENSP00000221347:G2670R	ENSP00000221347:G2670R	G	-	1	0	FCGBP	45084336	1.000000	0.71417	0.382000	0.26119	0.147000	0.21601	5.593000	0.67550	1.495000	0.48549	0.298000	0.19748	GGG	C|0.970;T|0.030	0.030	strong		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
TMEM200C	645369	hgsc.bcm.edu	37	18	5891637	5891637	+	Silent	SNP	C	C	A	rs28656885	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:5891637C>A	ENST00000581347.2	-	3	1071	c.426G>T	c.(424-426)ccG>ccT	p.P142P	RP11-945C19.4_ENST00000580845.1_RNA|TMEM200C_ENST00000383490.2_Silent_p.P142P|RP11-945C19.4_ENST00000577694.1_RNA|RP11-945C19.4_ENST00000582939.1_RNA			A6NKL6	T200C_HUMAN	transmembrane protein 200C	142						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)	12						AGGAGGAGGACGGGGAGGCGG	0.652													A|||	1704	0.340256	0.4319	0.3444	5008	,	,		13431	0.2986		0.3598	False		,,,				2504	0.2362				p.P142P		Atlas-SNP	.											.	TMEM200C	30	.	0			c.G426T						PASS	.	A		1809,2421		391,1027,697	58.0	71.0	67.0		426	-8.4	0.0	18	dbSNP_125	67	3219,5213		630,1959,1627	no	coding-synonymous	TMEM200C	NM_001080209.1		1021,2986,2324	AA,AC,CC		38.176,42.766,39.7094		142/622	5891637	5028,7634	2115	4216	6331	SO:0001819	synonymous_variant	645369	exon1			GGAGGACGGGGAG		CCDS45825.1	18p11.31	2009-09-08			ENSG00000206432	ENSG00000206432			37208	protein-coding gene	gene with protein product						15722956	Standard	NM_001080209		Approved	TTMA	uc002kmx.1	A6NKL6		ENST00000581347.2:c.426G>T	18.37:g.5891637C>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	42	26	0.619048	NM_001080209		Silent	SNP	ENST00000581347.2	37	CCDS45825.1																																																																																			C|0.642;A|0.358	0.358	strong		0.652	TMEM200C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441917.4	NM_001080209	
SMYD4	114826	hgsc.bcm.edu	37	17	1703156	1703156	+	Missense_Mutation	SNP	T	T	C	rs61753098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1703156T>C	ENST00000305513.7	-	5	1699	c.1532A>G	c.(1531-1533)cAc>cGc	p.H511R		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	511	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.			H -> R (in Ref. 1; BAC04538). {ECO:0000305}.			metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						CTTACCTGTGTGTTGTATGGT	0.448													T|||	72	0.014377	0.0	0.0086	5008	,	,		22501	0.0		0.0229	False		,,,				2504	0.044				p.H511R		Atlas-SNP	.											.	SMYD4	50	.	0			c.A1532G						PASS	.	T	ARG/HIS	11,4395	16.8+/-37.8	0,11,2192	62.0	54.0	57.0		1532	6.0	0.0	17	dbSNP_129	57	175,8425	80.6+/-143.3	2,171,4127	yes	missense	SMYD4	NM_052928.2	29	2,182,6319	CC,CT,TT		2.0349,0.2497,1.4301	benign	511/805	1703156	186,12820	2203	4300	6503	SO:0001583	missense	114826	exon5			CCTGTGTGTTGTA	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.1532A>G	17.37:g.1703156T>C	ENSP00000304360:p.His511Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	T	10.25	1.299119	0.23650	0.002497	0.020349	ENSG00000186532	ENST00000305513	T	0.81163	-1.46	6.03	6.03	0.97812	SET domain (2);	0.828083	0.11555	N	0.552372	T	0.51432	0.1674	L	0.36672	1.1	0.09310	N	0.999997	B	0.24920	0.114	B	0.28553	0.091	T	0.53739	-0.8396	10	0.17369	T	0.5	0.4719	12.2015	0.54328	0.1276:0.0:0.0:0.8724	rs61753098	511	Q8IYR2	SMYD4_HUMAN	R	511	ENSP00000304360:H511R	ENSP00000304360:H511R	H	-	2	0	SMYD4	1649906	0.950000	0.32346	0.019000	0.16419	0.157000	0.22087	2.001000	0.40825	2.308000	0.77769	0.533000	0.62120	CAC	T|0.985;C|0.015	0.015	strong		0.448	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
LENG9	94059	hgsc.bcm.edu	37	19	54973307	54973307	+	Missense_Mutation	SNP	C	C	T	rs115799049	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54973307C>T	ENST00000333834.4	-	1	1587	c.1469G>A	c.(1468-1470)gGg>gAg	p.G490E		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	490							catalytic activity (GO:0003824)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)	11	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.134)		CTGGAAAGGCCCCCCTGTCCT	0.622													C|||	80	0.0159744	0.003	0.0274	5008	,	,		15399	0.001		0.0457	False		,,,				2504	0.0102				p.G490E		Atlas-SNP	.											.	LENG9	46	.	0			c.G1469A						PASS	.	C	GLU/GLY	32,4374	39.2+/-71.8	0,32,2171	51.0	59.0	57.0		1469	-5.9	0.0	19	dbSNP_132	57	309,8291	107.4+/-168.2	1,307,3992	yes	missense	LENG9	NM_198988.1	98	1,339,6163	TT,TC,CC		3.593,0.7263,2.6219	benign	490/502	54973307	341,12665	2203	4300	6503	SO:0001583	missense	94059	exon1			AAAGGCCCCCCTG	AF211976		19q13.4	2014-05-06			ENSG00000182909	ENSG00000275183			16306	protein-coding gene	gene with protein product						10941842	Standard	NM_198988		Approved		uc010yez.2	Q96B70	OTTHUMG00000188273	ENST00000333834.4:c.1469G>A	19.37:g.54973307C>T	ENSP00000331647:p.Gly490Glu	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_198988	B2VAM3	Missense_Mutation	SNP	ENST00000333834.4	37	CCDS12895.2	41	0.018772893772893772	2	0.0040650406504065045	11	0.03038674033149171	1	0.0017482517482517483	27	0.03562005277044855	C	11.54	1.669688	0.29693	0.007263	0.03593	ENSG00000182909	ENST00000333834	T	0.46451	0.87	4.98	-5.94	0.02247	RNA ligase/cyclic nucleotide phosphodiesterase (1);	0.274738	0.33916	U	0.004426	T	0.07369	0.0186	L	0.50333	1.59	0.09310	N	1	B	0.20052	0.041	B	0.25614	0.062	T	0.12041	-1.0563	10	0.33141	T	0.24	-0.0382	7.5113	0.27575	0.0:0.2166:0.1344:0.649	.	490	Q96B70	LENG9_HUMAN	E	490	ENSP00000331647:G490E	ENSP00000331647:G490E	G	-	2	0	LENG9	59665119	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.447000	0.02396	-0.793000	0.04475	0.655000	0.94253	GGG	C|0.977;T|0.023	0.023	strong		0.622	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988	
PLA2G4B	100137049	hgsc.bcm.edu	37	15	42138456	42138456	+	Silent	SNP	G	G	A	rs1197669	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42138456G>A	ENST00000452633.1	+	18	2008	c.1656G>A	c.(1654-1656)agG>agA	p.R552R	JMJD7-PLA2G4B_ENST00000382448.4_Silent_p.R783R|PLA2G4B_ENST00000458483.1_Silent_p.R552R|PLA2G4B_ENST00000542534.2_Silent_p.R783R|JMJD7-PLA2G4B_ENST00000342159.4_Silent_p.R783R			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	552	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		CAGCCGGCAGGATAGCTGAGT	0.537													G|||	1189	0.23742	0.3321	0.2061	5008	,	,		19172	0.0179		0.331	False		,,,				2504	0.2618				p.R783R		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.G2349A						PASS	.	G	,,	1419,2987		231,957,1015	101.0	105.0	104.0		1656,2349,2349	3.5	0.6	15	dbSNP_87	104	2775,5825		464,1847,1989	no	coding-synonymous,coding-synonymous,coding-synonymous	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	,,	695,2804,3004	AA,AG,GG		32.2674,32.2061,32.2467	,,	552/782,783/894,783/1013	42138456	4194,8812	2203	4300	6503	SO:0001819	synonymous_variant	8681	exon22			CGGCAGGATAGCT	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.1656G>A	15.37:g.42138456G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Silent	SNP	ENST00000452633.1	37	CCDS45241.1																																																																																			G|0.725;A|0.275	0.275	strong		0.537	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633	
KIF2B	84643	hgsc.bcm.edu	37	17	51900729	51900729	+	Missense_Mutation	SNP	C	C	T	rs3803824	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:51900729C>T	ENST00000268919.4	+	1	491	c.335C>T	c.(334-336)gCc>gTc	p.A112V		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	112			A -> V (in dbSNP:rs3803824). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						CAGCGTACCGCCACGAAATGG	0.597													C|||	1053	0.210264	0.025	0.268	5008	,	,		15495	0.2034		0.3847	False		,,,				2504	0.2474				p.A112V		Atlas-SNP	.											KIF2B,NS,carcinoma,+1,3	KIF2B	254	3	0			c.C335T						scavenged	.	C	VAL/ALA	377,4029	190.5+/-216.4	18,341,1844	77.0	83.0	81.0		335	4.0	0.0	17	dbSNP_107	81	3525,5075	513.5+/-378.2	730,2065,1505	yes	missense	KIF2B	NM_032559.4	64	748,2406,3349	TT,TC,CC		40.9884,8.5565,30.0015	benign	112/674	51900729	3902,9104	2203	4300	6503	SO:0001583	missense	84643	exon1			GTACCGCCACGAA	AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.335C>T	17.37:g.51900729C>T	ENSP00000268919:p.Ala112Val	Somatic	44	1	0.0227273		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	520	0.23809523809523808	16	0.032520325203252036	104	0.287292817679558	96	0.16783216783216784	304	0.40105540897097625	C	1.990	-0.432000	0.04669	0.085565	0.409884	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.75154	-0.91	4.99	4.02	0.46733	.	0.344162	0.20835	N	0.084805	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.12630	0.006	B	0.14023	0.01	T	0.30851	-0.9964	9	0.18276	T	0.48	.	7.5842	0.27982	0.0:0.811:0.0:0.189	rs3803824;rs17654285;rs52812737;rs61204455;rs3803824	112	Q8N4N8	KIF2B_HUMAN	V	112;35	ENSP00000268919:A112V	ENSP00000268919:A112V	A	+	2	0	KIF2B	49255728	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	0.532000	0.23067	1.446000	0.47643	0.655000	0.94253	GCC	C|0.741;T|0.259	0.259	strong		0.597	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
MS4A3	932	hgsc.bcm.edu	37	11	59837097	59837097	+	Silent	SNP	C	C	T	rs528823	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:59837097C>T	ENST00000278865.3	+	6	637	c.564C>T	c.(562-564)acC>acT	p.T188T	MS4A3_ENST00000358152.2_Silent_p.T142T|MS4A3_ENST00000534744.1_Silent_p.T142T|MS4A3_ENST00000395032.2_Silent_p.T65T	NM_006138.4	NP_006129.4	Q96HJ5	MS4A3_HUMAN	membrane-spanning 4-domains, subfamily A, member 3 (hematopoietic cell-specific)	188						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(4)|kidney(2)|lung(9)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		all_epithelial(135;0.245)				TATGCGTAACCATCTCTACCA	0.433													C|||	1506	0.300719	0.2859	0.1844	5008	,	,		20032	0.2272		0.2724	False		,,,				2504	0.5082				p.T188T		Atlas-SNP	.											.	MS4A3	47	.	0			c.C564T						PASS	.	C	,,	1101,3301	397.0+/-330.2	153,795,1253	277.0	256.0	263.0		195,426,564	-0.4	0.0	11	dbSNP_83	263	2392,6198	399.8+/-346.6	343,1706,2246	no	coding-synonymous,coding-synonymous,coding-synonymous	MS4A3	NM_001031666.1,NM_001031809.1,NM_006138.4	,,	496,2501,3499	TT,TC,CC		27.8463,25.0114,26.8858	,,	65/92,142/169,188/215	59837097	3493,9499	2201	4295	6496	SO:0001819	synonymous_variant	932	exon6			CGTAACCATCTCT	L35848	CCDS31567.1, CCDS31568.1, CCDS41651.1	11q12-q13.1	2008-03-25				ENSG00000149516			7317	protein-coding gene	gene with protein product		606498		CD20L		7524084	Standard	NM_006138		Approved	HTM4	uc001nom.3	Q96HJ5		ENST00000278865.3:c.564C>T	11.37:g.59837097C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	160	84	0.525	NM_006138	A8MTP8|Q8NHW2	Silent	SNP	ENST00000278865.3	37	CCDS31567.1																																																																																			C|0.734;T|0.266	0.266	strong		0.433	MS4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394417.1		
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 GAIIx	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_ENST00000396592.3_Silent_p.L556L|MCMDC2_ENST00000313616.5_Silent_p.L556L|MCMDC2_ENST00000541540.1_Silent_p.L493L	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		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	171	65	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	
TSNARE1	203062	hgsc.bcm.edu	37	8	143396446	143396446	+	Missense_Mutation	SNP	C	C	T	rs62000450	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143396446C>T	ENST00000307180.3	-	8	1109	c.992G>A	c.(991-993)cGt>cAt	p.R331H	TSNARE1_ENST00000518928.1_5'UTR|TSNARE1_ENST00000524325.1_Missense_Mutation_p.R330H|TSNARE1_ENST00000520166.1_Missense_Mutation_p.R330H|TSNARE1_ENST00000519651.1_Missense_Mutation_p.R111H	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	331					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CTGCTGCAGACGCTCCTGCTG	0.642													C|||	190	0.0379393	0.028	0.0865	5008	,	,		17241	0.0794		0.0089	False		,,,				2504	0.0041				p.R331H		Atlas-SNP	.											.	TSNARE1	59	.	0			c.G992A						PASS	.	C	HIS/ARG	125,4281	93.9+/-132.6	5,115,2083	85.0	62.0	70.0		992	-3.2	0.0	8	dbSNP_129	70	95,8505	53.1+/-113.8	0,95,4205	yes	missense	TSNARE1	NM_145003.3	29	5,210,6288	TT,TC,CC		1.1047,2.837,1.6915	benign	331/514	143396446	220,12786	2203	4300	6503	SO:0001583	missense	203062	exon8			TGCAGACGCTCCT			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.992G>A	8.37:g.143396446C>T	ENSP00000303437:p.Arg331His	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	129	69	0.534884	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	104	0.047619047619047616	18	0.036585365853658534	35	0.09668508287292818	42	0.07342657342657342	9	0.011873350923482849	C	9.131	1.011305	0.19277	0.02837	0.011047	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.29655	1.97;1.56;1.97;1.97	2.51	-3.19	0.05171	t-SNARE (1);	.	.	.	.	T	0.00271	0.0008	N	0.08118	0	0.09310	N	1	B;P;B;B	0.40534	0.156;0.72;0.156;0.156	B;B;B;B	0.26864	0.043;0.074;0.043;0.043	T	0.17471	-1.0368	9	0.35671	T	0.21	.	7.4502	0.27234	0.0:0.2344:0.0:0.7656	.	330;111;331;331	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	H	330;331;330;111	ENSP00000428763:R330H;ENSP00000303437:R331H;ENSP00000427770:R330H;ENSP00000429679:R111H	ENSP00000303437:R331H	R	-	2	0	TSNARE1	143394353	0.002000	0.14202	0.003000	0.11579	0.020000	0.10135	-1.948000	0.01533	-0.727000	0.04888	-0.143000	0.13931	CGT	C|0.975;T|0.025	0.025	strong		0.642	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
PARP4	143	hgsc.bcm.edu	37	13	25058867	25058867	+	Missense_Mutation	SNP	C	C	T	rs143070451	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25058867C>T	ENST00000381989.3	-	12	1477	c.1372G>A	c.(1372-1374)Gta>Ata	p.V458I		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	458	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCTTCCACTACTTTGGGTAAA	0.453																																					p.V458I		Atlas-SNP	.											PARP4,NS,carcinoma,0,5	PARP4	142	5	0			c.G1372A						scavenged	.						136.0	138.0	137.0					13																	25058867		2203	4297	6500	SO:0001583	missense	143	exon12			CCACTACTTTGGG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1372G>A	13.37:g.25058867C>T	ENSP00000371419:p.Val458Ile	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	101	16	0.158416	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	47	0.02152014652014652	23	0.046747967479674794	2	0.0055248618784530384	7	0.012237762237762238	15	0.01978891820580475	C	16.65	3.183039	0.57800	.	.	ENSG00000102699	ENST00000381989	T	0.13901	2.55	4.35	3.4	0.38934	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.162995	0.39985	N	0.001218	T	0.01523	0.0049	L	0.41906	1.305	0.26728	N	0.970657	P	0.37708	0.606	B	0.39904	0.313	T	0.12528	-1.0544	10	0.42905	T	0.14	-16.8693	5.0719	0.14611	0.0:0.7642:0.0:0.2358	.	458	Q9UKK3	PARP4_HUMAN	I	458	ENSP00000371419:V458I	ENSP00000371419:V458I	V	-	1	0	PARP4	23956867	0.210000	0.23517	0.999000	0.59377	0.973000	0.67179	0.932000	0.28884	2.229000	0.72834	0.650000	0.86243	GTA	.	.	weak		0.453	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
FAT2	2196	hgsc.bcm.edu	37	5	150948016	150948016	+	Silent	SNP	C	C	T	rs3734062	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150948016C>T	ENST00000261800.5	-	1	489	c.477G>A	c.(475-477)gaG>gaA	p.E159E		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	159	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGGGCATGTCCTCAGAGATGG	0.517													C|||	256	0.0511182	0.003	0.062	5008	,	,		23257	0.0774		0.0865	False		,,,				2504	0.045				p.E159E		Atlas-SNP	.											.	FAT2	465	.	0			c.G477A						PASS	.	C		66,4340	62.3+/-99.4	0,66,2137	138.0	126.0	130.0		477	2.5	1.0	5	dbSNP_107	130	571,8029	154.2+/-208.4	15,541,3744	no	coding-synonymous	FAT2	NM_001447.2		15,607,5881	TT,TC,CC		6.6395,1.498,4.8977		159/4350	150948016	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			CATGTCCTCAGAG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.477G>A	5.37:g.150948016C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	180	99	0.55	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.944;T|0.056	0.056	strong		0.517	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
SLC4A5	57835	hgsc.bcm.edu	37	2	74466594	74466594	+	Silent	SNP	G	G	A	rs4853018	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:74466594G>A	ENST00000377634.4	-	21	2586	c.2187C>T	c.(2185-2187)ggC>ggT	p.G729G	SLC4A5_ENST00000359484.4_Silent_p.G665G|SLC4A5_ENST00000358683.4_Silent_p.G665G|RP11-287D1.3_ENST00000451608.2_3'UTR|SLC4A5_ENST00000377632.1_Silent_p.G729G|SLC4A5_ENST00000357822.5_Silent_p.G729G|SLC4A5_ENST00000423644.1_Silent_p.G729G|SLC4A5_ENST00000346834.4_Silent_p.G729G|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000394019.2_Silent_p.G729G					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						GCAGGCGCCCGCCGTAGCTCA	0.537													G|||	1135	0.226637	0.1384	0.2291	5008	,	,		19259	0.1954		0.4304	False		,,,				2504	0.1667				p.G729G		Atlas-SNP	.											SLC4A5_ENST00000377634,colon,carcinoma,0,2	SLC4A5	215	2	0			c.C2187T						PASS	.	G	,	876,3530	340.7+/-306.4	71,734,1398	75.0	74.0	74.0		2187,2187	-9.0	0.7	2	dbSNP_111	74	3620,4980	522.4+/-380.1	757,2106,1437	yes	coding-synonymous,coding-synonymous	SLC4A5	NM_021196.3,NM_133478.2	,	828,2840,2835	AA,AG,GG		42.093,19.882,34.5687	,	729/1138,729/1122	74466594	4496,8510	2203	4300	6503	SO:0001819	synonymous_variant	57835	exon16			GCGCCCGCCGTAG	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.2187C>T	2.37:g.74466594G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	62	60	0.967742	NM_021196		Silent	SNP	ENST00000377634.4	37	CCDS1936.1																																																																																			G|0.694;A|0.306	0.306	strong		0.537	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3		
SERPINB2	5055	hgsc.bcm.edu	37	18	61564394	61564394	+	Missense_Mutation	SNP	A	A	G	rs6098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61564394A>G	ENST00000299502.4	+	4	438	c.358A>G	c.(358-360)Aat>Gat	p.N120D	SERPINB2_ENST00000482254.1_3'UTR|SERPINB2_ENST00000457692.1_Missense_Mutation_p.N120D	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	120			N -> D (in dbSNP:rs6098). {ECO:0000269|PubMed:10391209}.		blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	ATCCACAGGGAATTATTTACT	0.408													G|||	1748	0.349042	0.3661	0.3559	5008	,	,		18272	0.499		0.2296	False		,,,				2504	0.2894				p.N120D		Atlas-SNP	.											.	SERPINB2	63	.	0			c.A358G						PASS	.	G	ASP/ASN,ASP/ASN	1626,2780	661.1+/-400.8	294,1038,871	108.0	107.0	108.0		358,358	4.1	0.1	18	dbSNP_52	108	1878,6722	728.6+/-406.7	206,1466,2628	yes	missense,missense	SERPINB2	NM_001143818.1,NM_002575.2	23,23	500,2504,3499	GG,GA,AA		21.8372,36.9042,26.9414	benign,benign	120/416,120/416	61564394	3504,9502	2203	4300	6503	SO:0001583	missense	5055	exon4			ACAGGGAATTATT	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.358A>G	18.37:g.61564394A>G	ENSP00000299502:p.Asn120Asp	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_002575	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	37	CCDS11989.1	720	0.32967032967032966	172	0.34959349593495936	118	0.3259668508287293	261	0.4562937062937063	169	0.22295514511873352	G	9.952	1.220485	0.22457	0.369042	0.218372	ENSG00000197632	ENST00000299502;ENST00000457692;ENST00000413956;ENST00000443281	T;T;D;D	0.83914	2.85;2.85;-1.53;-1.78	5.93	4.13	0.48395	Serpin domain (3);	0.896348	0.09903	N	0.740770	T	0.00012	0.0000	N	0.01197	-0.965	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36504	-0.9745	8	.	.	.	.	6.7175	0.23312	0.2126:0.1262:0.6612:0.0	rs6098;rs3169981;rs52838286;rs59526530;rs6098	120	P05120	PAI2_HUMAN	D	120	ENSP00000299502:N120D;ENSP00000401645:N120D;ENSP00000402386:N120D;ENSP00000397096:N120D	.	N	+	1	0	SERPINB2	59715374	0.000000	0.05858	0.121000	0.21740	0.697000	0.40408	0.618000	0.24373	0.865000	0.35603	-0.119000	0.15052	AAT	A|0.695;C|0.002	.	strong		0.408	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
OR10A4	283297	hgsc.bcm.edu	37	11	6898758	6898758	+	Silent	SNP	A	A	C	rs7102808	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6898758A>C	ENST00000379829.2	+	1	903	c.880A>C	c.(880-882)Agg>Cgg	p.R294R		NM_207186.2	NP_997069.2	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A, member 4	294					axon guidance (GO:0007411)	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(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CTACAGCTCAAGGAATAAAGA	0.493													A|||	737	0.147165	0.0333	0.2666	5008	,	,		19061	0.1419		0.1889	False		,,,				2504	0.1789				p.R294R		Atlas-SNP	.											.	OR10A4	65	.	0			c.A880C						PASS	.			275,4127	153.3+/-186.9	10,255,1936	110.0	108.0	109.0		880	3.9	1.0	11	dbSNP_116	109	1958,6634	344.4+/-325.3	246,1466,2584	no	coding-synonymous	OR10A4	NM_207186.2		256,1721,4520	CC,CA,AA		22.7886,6.2472,17.1849		294/316	6898758	2233,10761	2201	4296	6497	SO:0001819	synonymous_variant	283297	exon1			AGCTCAAGGAATA	AF209506	CCDS7774.1	11p15.4	2012-08-09	2002-11-13	2004-03-10	ENSG00000170782	ENSG00000170782		"""GPCR / Class A : Olfactory receptors"""	15130	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily A, member 4 pseudogene"""	OR10A4P			Standard	NM_207186		Approved		uc010rat.2	Q9H209	OTTHUMG00000165740	ENST00000379829.2:c.880A>C	11.37:g.6898758A>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_207186	B2RNP5|B9EH36|Q96R20	Silent	SNP	ENST00000379829.2	37	CCDS7774.1																																																																																			A|0.839;C|0.161	0.161	strong		0.493	OR10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385985.1	NM_207186	
VPS13A	23230	hgsc.bcm.edu	37	9	79946961	79946961	+	Silent	SNP	C	C	T	rs17424026	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:79946961C>T	ENST00000360280.3	+	46	6287	c.6027C>T	c.(6025-6027)taC>taT	p.Y2009Y	VPS13A_ENST00000376634.4_Silent_p.Y2009Y|VPS13A_ENST00000357409.5_Silent_p.Y2009Y|VPS13A_ENST00000376636.3_Silent_p.Y1970Y	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2009					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TGTCTGTTTACGAAGGGGATA	0.303													C|||	345	0.0688898	0.0325	0.0576	5008	,	,		13748	0.1091		0.0954	False		,,,				2504	0.0573				p.Y2009Y		Atlas-SNP	.											.	VPS13A	735	.	0			c.C6027T						PASS	.	C	,,,	241,4165	140.8+/-176.2	10,221,1972	144.0	145.0	145.0		5910,6027,6027,6027	1.8	1.0	9	dbSNP_123	145	782,7816	184.0+/-232.1	42,698,3559	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	52,919,5531	TT,TC,CC		9.0951,5.4698,7.8668	,,,	1970/3136,2009/3070,2009/3096,2009/3175	79946961	1023,11981	2203	4299	6502	SO:0001819	synonymous_variant	23230	exon46			TGTTTACGAAGGG	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.6027C>T	9.37:g.79946961C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	161	93	0.57764	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1	182	0.08333333333333333	24	0.04878048780487805	18	0.049723756906077346	62	0.10839160839160839	78	0.10290237467018469	C	7.668	0.686428	0.14973	0.054698	0.090951	ENSG00000197969	ENST00000419472	.	.	.	5.65	1.82	0.25136	.	.	.	.	.	T	0.01320	0.0043	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17837	-1.0356	3	.	.	.	.	9.6039	0.39622	0.0:0.2021:0.0:0.7979	rs17424026;rs52828794;rs61371354;rs17424026	.	.	.	M	262	.	.	T	+	2	0	VPS13A	79136781	1.000000	0.71417	0.994000	0.49952	0.959000	0.62525	1.220000	0.32491	0.150000	0.19136	-0.440000	0.05779	ACG	C|0.918;T|0.082	0.082	strong		0.303	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
SEMA4D	10507	hgsc.bcm.edu	37	9	92003679	92003679	+	Missense_Mutation	SNP	C	C	T	rs11526468	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:92003679C>T	ENST00000450295.1	-	11	1755	c.979G>A	c.(979-981)Gcc>Acc	p.A327T	SEMA4D_ENST00000339861.4_Missense_Mutation_p.A327T|SEMA4D_ENST00000343780.4_Missense_Mutation_p.A327T|SEMA4D_ENST00000356444.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000420987.1_Missense_Mutation_p.A327T|SEMA4D_ENST00000455551.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000422704.2_Missense_Mutation_p.A327T|SEMA4D_ENST00000438547.2_Missense_Mutation_p.A327T			Q92854	SEM4D_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D	327	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.		A -> T (in dbSNP:rs11526468).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|immune response (GO:0006955)|leukocyte aggregation (GO:0070486)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell adhesion (GO:0007162)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ossification involved in bone maturation (GO:0043931)|positive regulation of cell migration (GO:0030335)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell projection organization (GO:0031344)|regulation of cell shape (GO:0008360)|regulation of dendrite morphogenesis (GO:0048814)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in bone trabecula morphogenesis (GO:1900220)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)|semaphorin receptor binding (GO:0030215)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(8)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34						AGGTTGTAGGCGCACACTGCC	0.627													C|||	1128	0.22524	0.0174	0.2723	5008	,	,		19441	0.3294		0.3072	False		,,,				2504	0.2812				p.A327T		Atlas-SNP	.											.	SEMA4D	81	.	0			c.G979A						PASS	.	C	THR/ALA,THR/ALA	278,4128	153.7+/-187.2	11,256,1936	76.0	61.0	66.0		979,979	4.0	1.0	9	dbSNP_120	66	2486,6114	407.8+/-349.3	349,1788,2163	yes	missense,missense	SEMA4D	NM_001142287.1,NM_006378.3	58,58	360,2044,4099	TT,TC,CC		28.907,6.3096,21.2517	probably-damaging,probably-damaging	327/739,327/863	92003679	2764,10242	2203	4300	6503	SO:0001583	missense	10507	exon13			TGTAGGCGCACAC	U60800	CCDS6685.1, CCDS47991.1	9q22-q31	2013-01-11			ENSG00000187764	ENSG00000187764		"""Semaphorins"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10732	protein-coding gene	gene with protein product	"""M-sema G"""	601866	"""chromosome 9 open reading frame 164"""	SEMAJ, C9orf164		8876214, 8969198	Standard	NM_006378		Approved	CD100, coll-4, FLJ39737	uc004aqo.1	Q92854	OTTHUMG00000020185	ENST00000450295.1:c.979G>A	9.37:g.92003679C>T	ENSP00000416523:p.Ala327Thr	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_006378	B2RPM6|Q7Z5S4|Q8N8B0	Missense_Mutation	SNP	ENST00000450295.1	37	CCDS6685.1	573	0.2623626373626374	13	0.026422764227642278	107	0.2955801104972376	218	0.3811188811188811	235	0.3100263852242744	C	25.8	4.678510	0.88542	0.063096	0.28907	ENSG00000187764	ENST00000339861;ENST00000420987;ENST00000455551;ENST00000343780;ENST00000450295;ENST00000438547;ENST00000356444;ENST00000422704	T;T;T;T;T;T;T;T	0.14266	2.52;2.52;2.52;2.52;2.52;2.52;2.52;2.52	4.96	4.03	0.46877	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.092834	0.85682	D	0.000000	T	0.00012	0.0000	H	0.94886	3.595	0.09310	P	0.999991156	D;D	0.89917	0.997;1.0	P;D	0.73380	0.871;0.98	T	0.33854	-0.9852	9	0.41790	T	0.15	.	14.4731	0.67529	0.1481:0.8519:0.0:0.0	rs11526468	327;327	Q92854-2;Q92854	.;SEM4D_HUMAN	T	327	ENSP00000344923:A327T;ENSP00000391733:A327T;ENSP00000411981:A327T;ENSP00000343418:A327T;ENSP00000416523:A327T;ENSP00000405102:A327T;ENSP00000348822:A327T;ENSP00000388768:A327T	ENSP00000344923:A327T	A	-	1	0	SEMA4D	91193499	1.000000	0.71417	0.985000	0.45067	0.882000	0.50991	5.521000	0.67086	1.250000	0.43966	0.561000	0.74099	GCC	C|0.774;T|0.226	0.226	strong		0.627	SEMA4D-018	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342411.1	NM_006378	
MUC4	4585	hgsc.bcm.edu	37	3	195505763	195505763	+	Missense_Mutation	SNP	G	G	A	rs534260673	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195505763G>A	ENST00000463781.3	-	2	13147	c.12688C>T	c.(12688-12690)Ctt>Ttt	p.L4230F	MUC4_ENST00000475231.1_Missense_Mutation_p.L4230F|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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)		ACTGAGGAAAGGCTGGTGACA	0.582																																					p.L4230F		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	2	Substitution - Missense(2)	kidney(2)	c.C12688T						scavenged	.						42.0	42.0	42.0					3																	195505763		2092	4200	6292	SO:0001583	missense	4585	exon2			AGGAAAGGCTGGT	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.12688C>T	3.37:g.195505763G>A	ENSP00000417498:p.Leu4230Phe	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	58	4	0.0689655	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	.	.	.	.	.	.	.	.	.	.	N	10.21	1.286628	0.23478	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.48;1.49	1.78	0.849	0.18972	.	.	.	.	.	T	0.13756	0.0333	N	0.19112	0.55	0.09310	N	1	P	0.35139	0.486	B	0.19946	0.027	T	0.16276	-1.0408	8	.	.	.	.	6.3726	0.21489	0.0:0.3086:0.6914:0.0	.	4102	E7ESK3	.	F	4230	ENSP00000417498:L4230F;ENSP00000420243:L4230F	.	L	-	1	0	MUC4	196990542	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.092000	0.11129	0.347000	0.23924	-0.229000	0.12294	CTT	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAM131C	348487	hgsc.bcm.edu	37	1	16386065	16386065	+	Silent	SNP	T	T	A	rs61769893	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:16386065T>A	ENST00000375662.4	-	6	669	c.486A>T	c.(484-486)acA>acT	p.T162T	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	162								p.T162T(1)		large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		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;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AAGCGCTCAGTGTGGCCTCTG	0.662																																					p.T162T		Atlas-SNP	.											FAM131C,caecum,carcinoma,0,1	FAM131C	21	1	1	Substitution - coding silent(1)	large_intestine(1)	c.A486T						scavenged	.						24.0	23.0	24.0					1																	16386065		1844	4061	5905	SO:0001819	synonymous_variant	348487	exon6			GCTCAGTGTGGCC		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.486A>T	1.37:g.16386065T>A		Somatic	174	18	0.103448		WXS	Illumina HiSeq	Phase_I	271	40	0.147601	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			T|0.958;A|0.042	0.042	strong		0.662	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
TTN	7273	hgsc.bcm.edu	37	2	179396354	179396354	+	Silent	SNP	G	G	A	rs3829748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179396354G>A	ENST00000591111.1	-	308	100289	c.100065C>T	c.(100063-100065)gtC>gtT	p.V33355V	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000589042.1_Silent_p.V34996V|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342175.6_Silent_p.V26123V|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Silent_p.V26056V|TTN_ENST00000460472.2_Silent_p.V25931V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.V32428V|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588257.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33355	Ig-like 146.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CCAGGGTGAGGACTCCACTCG	0.473													G|||	1161	0.231829	0.1483	0.1571	5008	,	,		20197	0.4504		0.1392	False		,,,				2504	0.2679				p.V34996V		Atlas-SNP	.											.	TTN	18412	.	0			c.C104988T						PASS	.	G	,,,	540,3446		39,462,1492	128.0	126.0	127.0		77793,97284,78168,78369	-1.9	1.0	2	dbSNP_107	127	1213,7149		92,1029,3060	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	131,1491,4552	AA,AG,GG		14.5061,13.5474,14.1966	,,,	25931/26927,32428/33424,26056/27052,26123/27119	179396354	1753,10595	1993	4181	6174	SO:0001819	synonymous_variant	7273	exon358			GGTGAGGACTCCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.100065C>T	2.37:g.179396354G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	48	0.440367	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.790;A|0.210	0.210	strong		0.473	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
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 GAIIx	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	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	34	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	
CAD	790	hgsc.bcm.edu	37	2	27462076	27462076	+	Silent	SNP	C	C	T	rs3739092	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27462076C>T	ENST00000403525.1	+	31	5184	c.5040C>T	c.(5038-5040)ccC>ccT	p.P1680P	CAD_ENST00000264705.4_Silent_p.P1743P			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCACCTGCCCCCGCAGGAGG	0.627													C|||	1330	0.265575	0.2716	0.3689	5008	,	,		20316	0.1488		0.2237	False		,,,				2504	0.3476				p.P1743P		Atlas-SNP	.											.	CAD	199	.	0			c.C5229T						PASS	.	C		1049,3357	373.9+/-321.0	127,795,1281	37.0	38.0	38.0		5229	-5.3	0.0	2	dbSNP_107	38	1995,6605	341.3+/-324.0	238,1519,2543	no	coding-synonymous	CAD	NM_004341.3		365,2314,3824	TT,TC,CC		23.1977,23.8084,23.4046		1743/2226	27462076	3044,9962	2203	4300	6503	SO:0001819	synonymous_variant	790	exon32			CCTGCCCCCGCAG	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.5040C>T	2.37:g.27462076C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37		495	0.22664835164835165	149	0.30284552845528456	112	0.30939226519337015	63	0.11013986013986014	171	0.22559366754617413	C	6.980	0.550843	0.13374	0.238084	0.231977	ENSG00000084774	ENST00000456311	.	.	.	5.16	-5.32	0.02722	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999995955	.	.	.	.	.	.	T	0.20405	-1.0276	5	0.42905	T	0.14	0.856	4.5504	0.12108	0.0831:0.2532:0.4063:0.2573	rs3739092;rs17855323;rs3739092	.	.	.	S	31	.	ENSP00000388740:P31S	P	+	1	0	CAD	27315580	0.000000	0.05858	0.001000	0.08648	0.902000	0.53008	-3.104000	0.00603	-2.352000	0.00616	-1.943000	0.00494	CCC	C|0.773;T|0.227	0.227	strong		0.627	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
DMWD	1762	hgsc.bcm.edu	37	19	46289509	46289509	+	Silent	SNP	G	G	A	rs11545326	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46289509G>A	ENST00000270223.6	-	3	1290	c.1245C>T	c.(1243-1245)ggC>ggT	p.G415G	DMWD_ENST00000377735.3_Silent_p.G415G|DMWD_ENST00000601370.1_5'Flank|AC011530.4_ENST00000593999.1_5'Flank	NM_004943.1	NP_004934.1	Q09019	DMWD_HUMAN	dystrophia myotonica, WD repeat containing	415										central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	16		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00604)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.236)		AGAGCGGGGCGCCCCCGGCCG	0.701													G|||	412	0.0822684	0.0045	0.111	5008	,	,		12595	0.0407		0.162	False		,,,				2504	0.1278				p.G415G		Atlas-SNP	.											.	DMWD	46	.	0			c.C1245T						PASS	.	G		95,4227		1,93,2067	15.0	18.0	17.0		1245	-7.3	0.0	19	dbSNP_120	17	1083,7415		69,945,3235	no	coding-synonymous	DMWD	NM_004943.1		70,1038,5302	AA,AG,GG		12.7442,2.1981,9.1888		415/675	46289509	1178,11642	2161	4249	6410	SO:0001819	synonymous_variant	1762	exon3			CGGGGCGCCCCCG	L19267	CCDS33054.1	19q13.32	2013-01-09	2007-02-20		ENSG00000185800	ENSG00000185800		"""WD repeat domain containing"""	2936	protein-coding gene	gene with protein product		609857	"""dystrophia myotonica-containing WD repeat motif"""			1302022	Standard	NM_004943		Approved	DMR-N9, gene59, D19S593E	uc021uwc.1	Q09019	OTTHUMG00000169044	ENST00000270223.6:c.1245C>T	19.37:g.46289509G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_004943		Silent	SNP	ENST00000270223.6	37	CCDS33054.1																																																																																			G|0.917;A|0.083	0.083	strong		0.701	DMWD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402063.1	NM_004943	
BSCL2	26580	hgsc.bcm.edu	37	11	62458275	62458275	+	Silent	SNP	T	T	C	rs6856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:62458275T>C	ENST00000403550.1	-	9	1368	c.945A>G	c.(943-945)gaA>gaG	p.E315E	BSCL2_ENST00000405837.1_Silent_p.E381E|BSCL2_ENST00000433053.1_Silent_p.E379E|HNRNPUL2-BSCL2_ENST00000403734.2_3'UTR|BSCL2_ENST00000360796.5_Silent_p.E379E|BSCL2_ENST00000407022.3_Silent_p.E315E|BSCL2_ENST00000278893.7_Missense_Mutation_p.K268R|LRRN4CL_ENST00000317449.4_5'Flank|BSCL2_ENST00000421906.1_Silent_p.E315E			Q96G97	BSCL2_HUMAN	Berardinelli-Seip congenital lipodystrophy 2 (seipin)	315					cell death (GO:0008219)|fat cell differentiation (GO:0045444)|lipid catabolic process (GO:0016042)|lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|negative regulation of lipid catabolic process (GO:0050995)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	12						CTGAGGGATCTTCAGGGCTCT	0.567													T|||	676	0.134984	0.084	0.1556	5008	,	,		19992	0.0853		0.1928	False		,,,				2504	0.181				p.K268R		Atlas-SNP	.											.	BSCL2	35	.	0			c.A803G						PASS	.	T	,ARG/LYS,	492,3912	231.0+/-245.0	29,434,1739	90.0	81.0	84.0		1137,803,945	-3.9	0.0	11	dbSNP_52	84	1891,6707	336.3+/-321.8	215,1461,2623	yes	coding-synonymous,missense,coding-synonymous	BSCL2	NM_001122955.3,NM_001130702.2,NM_032667.6	,26,	244,1895,4362	CC,CT,TT		21.9935,11.1717,18.3279	,,	379/463,268/288,315/399	62458275	2383,10619	2202	4299	6501	SO:0001819	synonymous_variant	26580	exon8			GGGATCTTCAGGG		CCDS8031.1, CCDS44627.1, CCDS55769.1	11q13	2014-09-17	2009-07-30		ENSG00000168000	ENSG00000168000			15832	protein-coding gene	gene with protein product		606158	"""spastic paraplegia 17 (Silver syndrome)"""	GNG3LG, SPG17		11479539, 14981520	Standard	NM_001122955		Approved		uc001nur.4	Q96G97	OTTHUMG00000150624	ENST00000403550.1:c.945A>G	11.37:g.62458275T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001130702	G3XAE4|Q567S1|Q96SV1|Q9BSQ0	Missense_Mutation	SNP	ENST00000403550.1	37	CCDS8031.1	321	0.14697802197802198	52	0.10569105691056911	70	0.19337016574585636	50	0.08741258741258741	149	0.19656992084432717	T	18.17	3.563743	0.65651	0.111717	0.219935	ENSG00000168000	ENST00000278893	D	0.90324	-2.65	4.96	-3.94	0.04130	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13495	-1.0507	7	0.56958	D	0.05	-3.8108	6.2679	0.20939	0.1468:0.4889:0.0:0.3643	rs6856;rs1128631;rs3185757;rs11558434;rs17294661;rs17353223;rs17848888;rs17849878;rs52801011	268	Q96G97-3	.	R	268	ENSP00000278893:K268R	ENSP00000278893:K268R	K	-	2	0	BSCL2	62214851	0.017000	0.18338	0.005000	0.12908	0.974000	0.67602	-0.325000	0.07976	-0.967000	0.03582	0.459000	0.35465	AAG	T|0.825;C|0.175	0.175	strong		0.567	BSCL2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319185.1	NM_032667	
RPL36	25873	hgsc.bcm.edu	37	19	5693616	5693616	+	IGR	SNP	C	C	T	rs35804229	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5693616C>T	ENST00000577222.1	+	0	874				LONP1_ENST00000585374.1_Missense_Mutation_p.A715T|LONP1_ENST00000593119.1_Missense_Mutation_p.A765T|LONP1_ENST00000360614.3_Missense_Mutation_p.A829T|LONP1_ENST00000540670.2_Missense_Mutation_p.A633T|LONP1_ENST00000590729.1_Missense_Mutation_p.A699T			Q9Y3U8	RL36_HUMAN	ribosomal protein L36						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.A829T(1)		breast(1)|upper_aerodigestive_tract(1)	2						TTGGCGGGGGCGTGCTGCATG	0.657													C|||	31	0.0061901	0.0008	0.0058	5008	,	,		17440	0.0		0.0189	False		,,,				2504	0.0072				p.I829I		Atlas-SNP	.											LONP1,colon,carcinoma,0,1	LONP1	66	1	1	Substitution - Missense(1)	large_intestine(1)	c.A2485A						PASS	.	C	THR/ALA	9,4397	16.8+/-37.8	0,9,2194	145.0	108.0	120.0		2485	4.3	0.8	19	dbSNP_126	120	148,8452	72.3+/-134.9	2,144,4154	yes	missense	LONP1	NM_004793.2	58	2,153,6348	TT,TC,CC		1.7209,0.2043,1.2071	benign	829/960	5693616	157,12849	2203	4300	6503	SO:0001628	intergenic_variant	9361	exon16			CGGGGGCGTGCTG		CCDS12147.1	19p13.2	2011-04-06				ENSG00000130255		"""L ribosomal proteins"""	13631	protein-coding gene	gene with protein product							Standard	NM_033643		Approved	DKFZp566B023, L36	uc002mcv.3	Q9Y3U8			19.37:g.5693616C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	151	44	0.291391	NM_004793	B2R4Y1|D6W634|Q6FIG1|Q9UQF6	Silent	SNP	ENST00000577222.1	37	CCDS12147.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	C	8.530	0.870892	0.17322	0.002043	0.017209	ENSG00000196365	ENST00000360614;ENST00000358403;ENST00000540670	T;T	0.30448	1.53;1.53	4.33	4.33	0.51752	Ribosomal protein S5 domain 2-type fold (1);Peptidase S16, Lon C-terminal (1);	0.499176	0.22251	N	0.062555	T	0.10208	0.0250	L	0.27975	0.815	0.22378	N	0.999159	B;B;B	0.25105	0.118;0.118;0.118	B;B;B	0.25291	0.059;0.059;0.059	T	0.11665	-1.0578	10	0.19590	T	0.45	-37.6726	10.4234	0.44363	0.0:0.8007:0.1993:0.0	rs35804229;rs35804229	829;765;829	E5KMH8;Q8N8K8;P36776	.;.;LONM_HUMAN	T	829;793;633	ENSP00000353826:A829T;ENSP00000441523:A633T	ENSP00000351177:A793T	A	-	1	0	LONP1	5644616	0.832000	0.29368	0.832000	0.32986	0.596000	0.36781	1.696000	0.37773	1.922000	0.55676	0.549000	0.68633	GCC	C|0.988;T|0.012	0.012	strong		0.657	RPL36-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442561.1	NM_015414	
SAMD9L	219285	hgsc.bcm.edu	37	7	92760738	92760738	+	Missense_Mutation	SNP	T	T	G	rs10282508	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92760738T>G	ENST00000318238.4	-	5	5763	c.4547A>C	c.(4546-4548)aAt>aCt	p.N1516T	SAMD9L_ENST00000411955.1_Missense_Mutation_p.N1516T|SAMD9L_ENST00000437805.1_Missense_Mutation_p.N1516T	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1516			N -> T (in dbSNP:rs10282508).		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)			TTTGACTTCATTTTTTTTCCA	0.393													T|||	534	0.106629	0.2247	0.0461	5008	,	,		19427	0.1369		0.0467	False		,,,				2504	0.0204				p.N1516T		Atlas-SNP	.											.	SAMD9L	227	.	0			c.A4547C						PASS	.	T	THR/ASN	859,3547	337.6+/-304.9	86,687,1430	128.0	127.0	127.0		4547	-1.9	0.1	7	dbSNP_119	127	438,8162	132.6+/-190.3	22,394,3884	yes	missense	SAMD9L	NM_152703.2	65	108,1081,5314	GG,GT,TT		5.093,19.4961,9.9723	benign	1516/1585	92760738	1297,11709	2203	4300	6503	SO:0001583	missense	219285	exon5			ACTTCATTTTTTT	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.4547A>C	7.37:g.92760738T>G	ENSP00000326247:p.Asn1516Thr	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	167	102	0.610778	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	267	0.12225274725274725	122	0.24796747967479674	16	0.04419889502762431	95	0.1660839160839161	34	0.044854881266490766	T	2.359	-0.347034	0.05208	0.194961	0.05093	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.21543	2.0;2.0;2.0	4.77	-1.89	0.07689	.	0.928117	0.09002	N	0.862767	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.43294	-0.9400	9	0.48119	T	0.1	0.0887	5.8963	0.18941	0.0:0.3078:0.1296:0.5625	rs10282508;rs10282508	1516	Q8IVG5	SAM9L_HUMAN	T	1516;1516;1516;338	ENSP00000326247:N1516T;ENSP00000405760:N1516T;ENSP00000408796:N1516T	ENSP00000326247:N1516T	N	-	2	0	SAMD9L	92598674	0.000000	0.05858	0.098000	0.21074	0.437000	0.31866	0.047000	0.14056	-0.193000	0.10415	0.383000	0.25322	AAT	T|0.887;G|0.113	0.113	strong		0.393	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
ZNF749	388567	hgsc.bcm.edu	37	19	57955244	57955244	+	Missense_Mutation	SNP	A	A	G	rs12986235	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57955244A>G	ENST00000334181.4	+	3	978	c.728A>G	c.(727-729)cAg>cGg	p.Q243R	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	243			Q -> R (in dbSNP:rs12986235).		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)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		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;0.0264)|Lung(386;0.177)		ATTAAATATCAGCAAAATCAT	0.413													A|||	998	0.199281	0.2428	0.1931	5008	,	,		21163	0.0913		0.2883	False		,,,				2504	0.1646				p.Q243R		Atlas-SNP	.											.	ZNF749	75	.	0			c.A728G						PASS	.	A	ARG/GLN	1078,3328	384.2+/-325.2	123,832,1248	57.0	57.0	57.0		728	-0.1	0.0	19	dbSNP_121	57	2297,6303	379.7+/-339.4	306,1685,2309	yes	missense	ZNF749	NM_001023561.2	43	429,2517,3557	GG,GA,AA		26.7093,24.4666,25.9496	probably-damaging	243/779	57955244	3375,9631	2203	4300	6503	SO:0001583	missense	388567	exon3			AATATCAGCAAAA	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"""Zinc fingers, C2H2-type"", ""-"""	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.728A>G	19.37:g.57955244A>G	ENSP00000333980:p.Gln243Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_001023561		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	449	0.20558608058608058	109	0.22154471544715448	90	0.24861878453038674	38	0.06643356643356643	212	0.2796833773087071	A	13.76	2.333168	0.41297	0.244666	0.267093	ENSG00000186230	ENST00000334181	T	0.16196	2.36	2.27	-0.122	0.13531	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.54863	1.705	0.80722	P	0.0	B	0.21225	0.053	B	0.15052	0.012	T	0.39683	-0.9602	8	0.38643	T	0.18	.	2.7912	0.05388	0.6341:0.0:0.1448:0.2211	rs12986235;rs52824955;rs60657301;rs12986235	243	O43361	ZN749_HUMAN	R	243	ENSP00000333980:Q243R	ENSP00000333980:Q243R	Q	+	2	0	ZNF749	62647056	0.000000	0.05858	0.012000	0.15200	0.338000	0.28826	-0.861000	0.04268	-0.268000	0.09312	0.254000	0.18369	CAG	A|0.771;G|0.229	0.229	strong		0.413	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
HYDIN	54768	hgsc.bcm.edu	37	16	71025245	71025245	+	Silent	SNP	C	C	T	rs1774516	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:71025245C>T	ENST00000393567.2	-	25	3990	c.3840G>A	c.(3838-3840)acG>acA	p.T1280T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1280					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)				TGGAAGCTTTCGTTTTTCTTA	0.463																																					p.T1280T		Atlas-SNP	.											LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	0			c.G3840A						scavenged	.						130.0	119.0	122.0					16																	71025245		1909	4145	6054	SO:0001819	synonymous_variant	54768	exon25			AGCTTTCGTTTTT	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.3840G>A	16.37:g.71025245C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	130	15	0.115385	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
MDN1	23195	hgsc.bcm.edu	37	6	90371202	90371202	+	Silent	SNP	G	G	A	rs9444701	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90371202G>A	ENST00000369393.3	-	88	14776	c.14661C>T	c.(14659-14661)ctC>ctT	p.L4887L	MDN1_ENST00000428876.1_Silent_p.L4887L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4887					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTTCACTGTCGAGGTTCAAGT	0.473													G|||	3633	0.725439	0.7163	0.7824	5008	,	,		17383	0.9167		0.6501	False		,,,				2504	0.5777				p.L4887L		Atlas-SNP	.											.	MDN1	478	.	0			c.C14661T						PASS	.	G		3139,1267	701.9+/-406.8	1130,879,194	182.0	172.0	176.0		14661	-8.6	0.8	6	dbSNP_119	176	5601,2999	665.5+/-402.3	1879,1843,578	no	coding-synonymous	MDN1	NM_014611.1		3009,2722,772	AA,AG,GG		34.8721,28.7562,32.8002		4887/5597	90371202	8740,4266	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon88			ACTGTCGAGGTTC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14661C>T	6.37:g.90371202G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	183	182	0.994536	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			G|0.286;A|0.714	0.714	strong		0.473	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ALMS1	7840	hgsc.bcm.edu	37	2	73679990	73679990	+	Missense_Mutation	SNP	T	T	A	rs6724782	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73679990T>A	ENST00000264448.6	+	8	6444	c.6333T>A	c.(6331-6333)agT>agA	p.S2111R	ALMS1_ENST00000409009.1_Missense_Mutation_p.S2069R|ALMS1_ENST00000377715.1_Missense_Mutation_p.S2111R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2111	34 X 47 AA approximate tandem repeat.		S -> R (in dbSNP:rs6724782). {ECO:0000269|PubMed:11941370}.		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						TGCCAGGTAGTCATGTAACTG	0.403													A|||	1822	0.363818	0.8775	0.3919	5008	,	,		20591	0.0089		0.2276	False		,,,				2504	0.1554				p.S2111R		Atlas-SNP	.											.	ALMS1	384	.	0			c.T6333A						PASS	.	A	ARG/SER	2748,966		1032,684,141	37.0	36.0	36.0		6333	-5.1	0.0	2	dbSNP_116	36	1956,6228		226,1504,2362	yes	missense	ALMS1	NM_015120.4	110	1258,2188,2503	AA,AT,TT		23.9003,26.0097,39.5361	benign	2111/4168	73679990	4704,7194	1857	4092	5949	SO:0001583	missense	7840	exon8			AGGTAGTCATGTA	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.6333T>A	2.37:g.73679990T>A	ENSP00000264448:p.Ser2111Arg	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	43	0.704918	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	737	0.3374542124542125	425	0.8638211382113821	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	A	0.003	-2.434460	0.00182	0.739903	0.239003	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.12774	3.53;3.53;2.65	3.99	-5.06	0.02946	.	1.049810	0.07584	N	0.920720	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.39292	-0.9621	9	0.02654	T	1	.	0.5589	0.00676	0.257:0.124:0.2356:0.3834	rs6724782;rs17349573;rs17848883;rs52820401;rs56921282;rs6724782	2111;2069;2111	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	R	2069;2111;2111	ENSP00000386627:S2069R;ENSP00000264448:S2111R;ENSP00000366944:S2111R	ENSP00000264448:S2111R	S	+	3	2	ALMS1	73533498	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-0.204000	0.09425	-1.484000	0.01856	-0.375000	0.07067	AGT	T|0.691;A|0.309	0.309	strong		0.403	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
TRIM3	10612	hgsc.bcm.edu	37	11	6478619	6478619	+	Silent	SNP	G	G	A	rs16913748	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6478619G>A	ENST00000525074.1	-	5	997	c.603C>T	c.(601-603)atC>atT	p.I201I	TRIM3_ENST00000529058.1_5'UTR|TRIM3_ENST00000345851.3_Silent_p.I201I|TRIM3_ENST00000359518.3_Silent_p.I201I|TRIM3_ENST00000536344.1_Silent_p.I82I|TRIM3_ENST00000537602.1_Silent_p.I201I	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	201					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACGCTGCACTGATCTGGGCCA	0.617													G|||	938	0.1873	0.2973	0.1772	5008	,	,		20774	0.0188		0.1849	False		,,,				2504	0.2219				p.I201I	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.C603T						PASS	.	G	,	1271,3131	434.1+/-343.8	178,915,1108	95.0	87.0	90.0		603,603	2.1	1.0	11	dbSNP_123	90	1764,6828	318.4+/-313.7	189,1386,2721	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	367,2301,3829	AA,AG,GG		20.5307,28.8732,23.3569	,	201/745,201/745	6478619	3035,9959	2201	4296	6497	SO:0001819	synonymous_variant	10612	exon5			TGCACTGATCTGG	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.603C>T	11.37:g.6478619G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			G|0.791;A|0.209	0.209	strong		0.617	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52132668	52132668	+	Missense_Mutation	SNP	T	T	C	rs34553740		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52132668T>C	ENST00000534261.2	-	4	1042	c.643A>G	c.(643-645)Atg>Gtg	p.M215V	SIGLEC5_ENST00000570106.2_Missense_Mutation_p.M215V|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.M215V|SIGLEC5_ENST00000222107.4_Missense_Mutation_p.M215V|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.M215V			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	215	Ig-like C2-type 1.		M -> V (in dbSNP:rs1807124).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.M215V(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGGCGTTTCATCTGACAGGTG	0.637																																					p.M215V		Atlas-SNP	.											SIGLEC5,NS,carcinoma,0,1	SIGLEC5	67	1	1	Substitution - Missense(1)	prostate(1)	c.A643G						scavenged	.						122.0	109.0	113.0					19																	52132668		2203	4300	6503	SO:0001583	missense	8778	exon3			GTTTCATCTGACA	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.643A>G	19.37:g.52132668T>C	ENSP00000473238:p.Met215Val	Somatic	541	2	0.00369686		WXS	Illumina HiSeq	Phase_I	570	8	0.0140351	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.691237	0.00731	.	.	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.02050	4.48;4.48	3.69	2.65	0.31530	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.42682	N	0.000676	T	0.00412	0.0013	N	0.00023	-2.71	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44651	-0.9314	10	0.02654	T	1	.	6.1979	0.20559	0.0:0.7599:0.0:0.2401	rs34553740	215	O15389	SIGL5_HUMAN	V	215	ENSP00000222107:M215V;ENSP00000415200:M215V	ENSP00000222107:M215V	M	-	1	0	SIGLEC5	56824480	0.020000	0.18652	0.004000	0.12327	0.034000	0.12701	1.066000	0.30604	0.367000	0.24454	-0.320000	0.08662	ATG	.	.	weak		0.637	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
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 GAIIx	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	PCDHA13_ENST00000289272.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.Q149H|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_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	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	71	15	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	
NMI	9111	hgsc.bcm.edu	37	2	152132130	152132130	+	Silent	SNP	A	A	G	rs289834	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:152132130A>G	ENST00000243346.5	-	6	972	c.502T>C	c.(502-504)Ttg>Ctg	p.L168L		NM_004688.2	NP_004679.2	Q13287	NMI_HUMAN	N-myc (and STAT) interactor	168					inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription cofactor activity (GO:0003712)			endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				BRCA - Breast invasive adenocarcinoma(221;0.0571)		TCTTCACGCAATGTGTCAGGA	0.413													A|||	837	0.167133	0.3162	0.1182	5008	,	,		18489	0.0516		0.1203	False		,,,				2504	0.1677				p.L168L		Atlas-SNP	.											.	NMI	21	.	0			c.T502C						PASS	.	A		1165,3241	412.2+/-336.0	161,843,1199	95.0	98.0	97.0		502	-9.2	0.0	2	dbSNP_79	97	1086,7514	227.6+/-262.9	73,940,3287	no	coding-synonymous	NMI	NM_004688.2		234,1783,4486	GG,GA,AA		12.6279,26.4412,17.3074		168/308	152132130	2251,10755	2203	4300	6503	SO:0001819	synonymous_variant	9111	exon6			CACGCAATGTGTC	U32849	CCDS2192.1	2q23	2008-05-23			ENSG00000123609	ENSG00000123609			7854	protein-coding gene	gene with protein product		603525				8668343, 9989503	Standard	NM_004688		Approved		uc002txi.2	Q13287	OTTHUMG00000131867	ENST00000243346.5:c.502T>C	2.37:g.152132130A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	114	25	0.219298	NM_004688	B5BU69|Q53TI8|Q9BVE5	Silent	SNP	ENST00000243346.5	37	CCDS2192.1																																																																																			A|0.833;G|0.167	0.167	strong		0.413	NMI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254817.2	NM_004688	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580931	140580931	+	Missense_Mutation	SNP	C	C	G	rs34415020|rs799834	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140580931C>G	ENST00000354757.3	+	1	1584	c.1584C>G	c.(1582-1584)gaC>gaG	p.D528E	PCDHB11_ENST00000536699.1_Missense_Mutation_p.D163E	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		D -> E (in dbSNP:rs799834).		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)			AGGCTTTCGACTTCCGCGTGG	0.677													G|||	2793	0.557708	0.7648	0.5576	5008	,	,		16257	0.5694		0.4105	False		,,,				2504	0.4172				p.D528E		Atlas-SNP	.											PCDHB11,NS,carcinoma,+2,1	PCDHB11	162	1	0			c.C1584G						PASS	.	G	GLU/ASP	3038,1366		1027,984,191	58.0	76.0	70.0		1584	1.6	0.0	5	dbSNP_86	70	3520,5080		757,2006,1537	no	missense	PCDHB11	NM_018931.2	45	1784,2990,1728	GG,GC,CC		40.9302,31.0173,49.5694	benign	528/798	140580931	6558,6446	2202	4300	6502	SO:0001583	missense	56125	exon1			TTTCGACTTCCGC	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.1584C>G	5.37:g.140580931C>G	ENSP00000346802:p.Asp528Glu	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	197	100	0.507614	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	1096	0.5018315018315018	329	0.6686991869918699	165	0.4558011049723757	320	0.5594405594405595	282	0.3720316622691293	N	0.046	-1.265433	0.01433	0.689827	0.409302	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.01705	4.68;4.68	2.51	1.61	0.23674	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.18461	-1.0336	8	0.02654	T	1	.	3.8674	0.09022	0.3311:0.1861:0.4828:0.0	rs799834;rs61497114	528	Q9Y5F2	PCDBB_HUMAN	E	163;528	ENSP00000440344:D163E;ENSP00000346802:D528E	ENSP00000346802:D528E	D	+	3	2	PCDHB11	140561115	0.001000	0.12720	0.010000	0.14722	0.076000	0.17211	0.179000	0.16840	0.005000	0.14708	-0.702000	0.03669	GAC	C|0.497;G|0.503	0.503	strong		0.677	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
GGA3	23163	hgsc.bcm.edu	37	17	73239557	73239557	+	Missense_Mutation	SNP	T	T	C	rs117805695	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73239557T>C	ENST00000245541.6	-	5	611	c.395A>G	c.(394-396)aAa>aGa	p.K132R	GGA3_ENST00000582717.1_Missense_Mutation_p.K60R|GGA3_ENST00000351904.7_Missense_Mutation_p.K99R|GGA3_ENST00000537686.1_Missense_Mutation_p.K132R|GGA3_ENST00000582486.1_Missense_Mutation_p.K60R|GGA3_ENST00000578348.1_Missense_Mutation_p.K10R|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000538886.1_Missense_Mutation_p.K10R	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	132	Binds to ARF1 (in long isoform).|VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			GTAGGCGTCTTTGATCTTTGC	0.572													T|||	5	0.000998403	0.0	0.0	5008	,	,		23430	0.0		0.005	False		,,,				2504	0.0				p.K132R		Atlas-SNP	.											.	GGA3	54	.	0			c.A395G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	2,4404	4.2+/-10.8	0,2,2201	229.0	186.0	201.0		179,29,296,395	5.3	1.0	17	dbSNP_132	201	32,8568	22.2+/-67.0	0,32,4268	yes	missense,missense,missense,missense	GGA3	NM_001172703.1,NM_001172704.1,NM_014001.3,NM_138619.2	26,26,26,26	0,34,6469	CC,CT,TT		0.3721,0.0454,0.2614	benign,benign,benign,benign	60/652,10/593,99/691,132/724	73239557	34,12972	2203	4300	6503	SO:0001583	missense	23163	exon5			GCGTCTTTGATCT	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.395A>G	17.37:g.73239557T>C	ENSP00000245541:p.Lys132Arg	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	156	82	0.525641	NM_138619	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Missense_Mutation	SNP	ENST00000245541.6	37	CCDS11717.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	13.11	2.140695	0.37825	4.54E-4	0.003721	ENSG00000125447	ENST00000245541;ENST00000351904;ENST00000537584;ENST00000538886;ENST00000537686	T;T;T	0.21543	2.0;2.0;2.0	5.27	5.27	0.74061	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.365028	0.34314	N	0.004061	T	0.15003	0.0362	N	0.04959	-0.14	0.50632	D	0.999887	B;D;B;B	0.57257	0.009;0.979;0.018;0.148	B;P;B;B	0.52554	0.018;0.702;0.113;0.064	T	0.04229	-1.0967	10	0.02654	T	1	-5.7368	15.3726	0.74577	0.0:0.0:0.0:1.0	.	99;10;99;132	B7Z9A2;B7Z7E2;Q9NZ52-2;Q9NZ52	.;.;.;GGA3_HUMAN	R	132;99;60;10;132	ENSP00000245541:K132R;ENSP00000326575:K99R;ENSP00000438085:K132R	ENSP00000245541:K132R	K	-	2	0	GGA3	70751152	0.998000	0.40836	1.000000	0.80357	0.858000	0.48976	1.939000	0.40213	2.209000	0.71365	0.533000	0.62120	AAA	T|0.998;C|0.002	0.002	strong		0.572	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619	
MXD3	83463	hgsc.bcm.edu	37	5	176734855	176734855	+	Silent	SNP	G	G	C	rs4568379	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176734855G>C	ENST00000439742.2	-	5	910	c.432C>G	c.(430-432)gcC>gcG	p.A144A	MXD3_ENST00000423571.2_Silent_p.A144A|MXD3_ENST00000427908.2_Silent_p.A144A|MXD3_ENST00000513063.1_Silent_p.A144A	NM_031300.3	NP_112590.1	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3	144					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)			GCTCCCGCTCGGCCGCCCCTG	0.697													G|||	1039	0.207468	0.3555	0.1686	5008	,	,		11663	0.0258		0.2276	False		,,,				2504	0.2014				p.A144A		Atlas-SNP	.											.	MXD3	13	.	0			c.C432G						PASS	.	G	,	1112,2786		174,764,1011	8.0	10.0	10.0		432,432	-8.5	0.0	5	dbSNP_111	10	1622,6156		180,1262,2447	no	coding-synonymous,coding-synonymous	MXD3	NM_001142935.1,NM_031300.3	,	354,2026,3458	CC,CG,GG		20.8537,28.5274,23.4156	,	144/194,144/207	176734855	2734,8942	1949	3889	5838	SO:0001819	synonymous_variant	83463	exon5			CCGCTCGGCCGCC	BC000745	CCDS4416.1, CCDS47347.1	5q35.3	2013-03-20			ENSG00000213347	ENSG00000213347		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	14008	protein-coding gene	gene with protein product		609450					Standard	NM_031300		Approved	MAD3, bHLHc13	uc003mgb.2	Q9BW11	OTTHUMG00000130854	ENST00000439742.2:c.432C>G	5.37:g.176734855G>C		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	NM_001142935	B4E0J1|Q53HK1|Q7Z4Y0|Q8NDJ7|Q96ME3	Silent	SNP	ENST00000439742.2	37	CCDS4416.1																																																																																			G|0.800;C|0.200	0.200	strong		0.697	MXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253427.1		
ARL17B	100506084	hgsc.bcm.edu	37	17	44430254	44430254	+	Missense_Mutation	SNP	G	G	C	rs35595570	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44430254G>C	ENST00000450673.3	-	3	296	c.191C>G	c.(190-192)gCt>gGt	p.A64G	ARL17B_ENST00000575698.1_Missense_Mutation_p.A64G|ARL17B_ENST00000434041.2_Missense_Mutation_p.A64G|ARL17B_ENST00000571246.1_Missense_Mutation_p.A64G|ARL17B_ENST00000575960.1_Missense_Mutation_p.A64G|ARL17B_ENST00000570618.1_Missense_Mutation_p.A64G	NM_001039083.3	NP_001034172.3	Q8IVW1	ARL17_HUMAN	ADP-ribosylation factor-like 17B	64					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)	GTP binding (GO:0005525)	p.A64G(1)		pancreas(1)	1						ATCCCAGACAGCGAAGGTGTT	0.378																																					p.A64G		Atlas-SNP	.											ARL17B,NS,other,0,1	ARL17B	3	1	1	Substitution - Missense(1)	pancreas(1)	c.C191G						scavenged	.						3.0	3.0	3.0					17																	44430254		1275	3002	4277	SO:0001583	missense	100506084	exon3			CAGACAGCGAAGG	AF493886	CCDS54137.1, CCDS58557.1	17q21.31	2014-05-09	2009-11-17	2009-11-17	ENSG00000228696	ENSG00000228696		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	32387	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 17"""	ARL17			Standard	NM_001039083		Approved			Q8IVW1	OTTHUMG00000178031	ENST00000450673.3:c.191C>G	17.37:g.44430254G>C	ENSP00000404247:p.Ala64Gly	Somatic	396	0	0		WXS	Illumina HiSeq	Phase_I	532	322	0.605263	NM_001039083	B0AZR6|Q59FW5|Q8N6E2|Q8TD73|Q8WW54|Q9NZD5|Q9P158	Missense_Mutation	SNP	ENST00000450673.3	37	CCDS58557.1	.	.	.	.	.	.	.	.	.	.	g	4.858	0.159467	0.09236	.	.	ENSG00000228696	ENST00000434041;ENST00000450673	T;T	0.63744	-0.06;-0.06	2.89	2.89	0.33648	.	.	.	.	.	T	0.51736	0.1692	.	.	.	0.29739	N	0.837233	B;B;B	0.31817	0.164;0.054;0.341	B;B;B	0.31686	0.134;0.038;0.08	T	0.55768	-0.8089	8	0.52906	T	0.07	.	11.9465	0.52930	0.0:0.0:1.0:0.0	.	64;64;64	Q8IVW1;Q8IVW1-2;F8VZA5	ARL17_HUMAN;.;.	G	64	ENSP00000391751:A64G;ENSP00000404247:A64G	ENSP00000391751:A64G	A	-	2	0	ARL17B	41786010	1.000000	0.71417	0.999000	0.59377	0.006000	0.05464	8.736000	0.91554	1.898000	0.54952	0.393000	0.25936	GCT	G|0.905;C|0.095	0.095	strong		0.378	ARL17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440297.1	NM_001039083	
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 GAIIx	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	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	70	14	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	
SMCO4	56935	hgsc.bcm.edu	37	11	93212245	93212245	+	Silent	SNP	C	C	T	rs3207348	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:93212245C>T	ENST00000298966.2	-	3	496	c.111G>A	c.(109-111)acG>acA	p.T37T	SMCO4_ENST00000527149.1_Silent_p.T37T|SMCO4_ENST00000525141.1_Silent_p.T37T	NM_020179.2	NP_064564.1	Q9NRQ5	SMCO4_HUMAN	single-pass membrane protein with coiled-coil domains 4	37						integral component of membrane (GO:0016021)											CCACGGCCAGCGTGGGCAGCA	0.637													c|||	390	0.0778754	0.0113	0.0764	5008	,	,		14773	0.0397		0.159	False		,,,				2504	0.1247				p.T37T		Atlas-SNP	.											.	.	.	.	0			c.G111A						PASS	.	T		157,4245	106.0+/-144.5	1,155,2045	100.0	84.0	90.0		111	-3.5	1.0	11	dbSNP_105	90	1373,7223	267.4+/-287.2	114,1145,3039	no	coding-synonymous	C11orf75	NM_020179.2		115,1300,5084	TT,TC,CC		15.9725,3.5666,11.771		37/60	93212245	1530,11468	2201	4298	6499	SO:0001819	synonymous_variant	0	exon3			GGCCAGCGTGGGC	BC031564	CCDS8292.1	11q21	2013-03-11	2013-03-11	2013-03-11	ENSG00000166002	ENSG00000166002			24810	protein-coding gene	gene with protein product		609477	"""chromosome 11 open reading frame 75"""	C11orf75		10863097	Standard	NM_020179		Approved	FN5	uc001pds.4	Q9NRQ5	OTTHUMG00000167442	ENST00000298966.2:c.111G>A	11.37:g.93212245C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_020179		Silent	SNP	ENST00000298966.2	37	CCDS8292.1																																																																																			C|0.891;T|0.109	0.109	strong		0.637	SMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394630.1	NM_020179	
NRAP	4892	hgsc.bcm.edu	37	10	115409840	115409840	+	Missense_Mutation	SNP	C	C	T	rs2275799	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:115409840C>T	ENST00000359988.3	-	9	1088	c.844G>A	c.(844-846)Gct>Act	p.A282T	NRAP_ENST00000360478.3_Missense_Mutation_p.A282T|NRAP_ENST00000369358.4_Missense_Mutation_p.A282T|NRAP_ENST00000369360.3_Missense_Mutation_p.A282T	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		ATGCCCTCAGCTCCAATGGCT	0.458													C|||	1341	0.267772	0.3419	0.2248	5008	,	,		18853	0.2173		0.2684	False		,,,				2504	0.2495				p.A282T		Atlas-SNP	.											.	NRAP	208	.	0			c.G844A						PASS	.	C	THR/ALA,THR/ALA	1595,2811	497.7+/-363.9	294,1007,902	184.0	168.0	174.0		844,844	5.2	1.0	10	dbSNP_100	174	2389,6211	397.6+/-345.8	334,1721,2245	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	58,58	628,2728,3147	TT,TC,CC		27.7791,36.2006,30.632	benign,benign	282/1696,282/1731	115409840	3984,9022	2203	4300	6503	SO:0001583	missense	4892	exon9			CCTCAGCTCCAAT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.844G>A	10.37:g.115409840C>T	ENSP00000353078:p.Ala282Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	584	0.2673992673992674	159	0.3231707317073171	75	0.20718232044198895	134	0.23426573426573427	216	0.2849604221635884	C	9.493	1.101124	0.20552	0.362006	0.277791	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350;ENST00000369343	T;T;T;T	0.16743	2.51;2.54;2.44;2.32	6.06	5.15	0.70609	.	0.150870	0.64402	D	0.000011	T	0.00012	0.0000	N	0.14661	0.345	0.35895	P	0.17004300000000006	B;B;B	0.27656	0.184;0.036;0.038	B;B;B	0.27262	0.078;0.06;0.02	T	0.49341	-0.8950	9	0.19590	T	0.45	.	10.3614	0.43996	0.0:0.8583:0.0:0.1417	rs2275799;rs52833940;rs60271628;rs2275799	282;282;282	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	T	282;282;282;282;11;11	ENSP00000358365:A282T;ENSP00000358367:A282T;ENSP00000353078:A282T;ENSP00000353666:A282T	ENSP00000353078:A282T	A	-	1	0	NRAP	115399830	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	1.080000	0.30779	2.876000	0.98609	0.655000	0.94253	GCT	C|0.708;T|0.292	0.292	strong		0.458	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
ATG16L1	55054	hgsc.bcm.edu	37	2	234183368	234183368	+	Missense_Mutation	SNP	A	A	G	rs2241880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:234183368A>G	ENST00000392017.4	+	9	1155	c.898A>G	c.(898-900)Act>Gct	p.T300A	SCARNA5_ENST00000516201.1_RNA|ATG16L1_ENST00000392020.4_Missense_Mutation_p.T281A|ATG16L1_ENST00000373525.5_Missense_Mutation_p.T156A|ATG16L1_ENST00000498620.1_3'UTR|ATG16L1_ENST00000347464.5_Missense_Mutation_p.T137A|ATG16L1_ENST00000392018.1_Missense_Mutation_p.T317A	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	300			T -> A (associated with susceptibility to IBD10; has no effect on the stability of the protein; enhances the cleavage and the degradation mediated by activated CASP3; results in reduced autophagy and defective clearance of intestinal pathogens; dbSNP:rs2241880). {ECO:0000269|PubMed:15620219}.		autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CAATGTGGATACTCATCCTGG	0.473													A|||	1983	0.395966	0.3101	0.3213	5008	,	,		21225	0.3224		0.5368	False		,,,				2504	0.4959				p.T300A		Atlas-SNP	.											.	ATG16L1	83	.	0			c.A898G	GRCh37	CM070026	ATG16L1	M	rs2241880	PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	1428,2978	465.9+/-354.3	234,960,1009	181.0	149.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	646,550,841,898,409	-11.4	0.0	2	dbSNP_98	160	4506,4094	592.4+/-393.0	1198,2110,992	yes	missense,missense,missense,missense,missense	ATG16L1	NM_001190266.1,NM_001190267.1,NM_017974.3,NM_030803.6,NM_198890.2	58,58,58,58,58	1432,3070,2001	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	47.6047,32.4103,45.6251	benign,benign,benign,benign,benign	216/524,184/492,281/589,300/608,137/445	234183368	5934,7072	2203	4300	6503	SO:0001583	missense	55054	exon9			GTGGATACTCATC	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"""WD repeat domain containing"""	21498	protein-coding gene	gene with protein product		610767	"""APG16 autophagy 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like 1 (S. cerevisiae)"""	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.898A>G	2.37:g.234183368A>G	ENSP00000375872:p.Thr300Ala	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_030803	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Missense_Mutation	SNP	ENST00000392017.4	37	CCDS2503.2	851	0.38965201465201466	123	0.25	136	0.3756906077348066	190	0.3321678321678322	402	0.5303430079155673	A	10.98	1.504884	0.26949	0.324103	0.523953	ENSG00000085978	ENST00000392017;ENST00000347464;ENST00000444735;ENST00000373525;ENST00000419681;ENST00000392020;ENST00000392018	T;T;T;T;T;T;T	0.48522	0.88;0.92;1.09;0.99;1.71;0.81;0.91	5.71	-11.4	0.00090	WD40 repeat-like-containing domain (1);	1.946940	0.02287	N	0.069914	T	0.00012	0.0000	N	0.04203	-0.255	0.47341	P	6.049999999999667E-4	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.0;0.001;0.005;0.0;0.001	T	0.27536	-1.0071	9	0.14252	T	0.57	.	12.6604	0.56811	0.1798:0.4806:0.3396:0.0	rs2241880;rs17607702;rs52836811;rs57853061;rs2241880	254;281;156;300;137	B7ZLM5;Q676U5-2;Q676U5-4;Q676U5;A3EXL0	.;.;.;A16L1_HUMAN;.	A	300;137;173;156;137;281;317	ENSP00000375872:T300A;ENSP00000318259:T137A;ENSP00000409215:T173A;ENSP00000362625:T156A;ENSP00000398773:T137A;ENSP00000375875:T281A;ENSP00000375873:T317A	ENSP00000318259:T137A	T	+	1	0	ATG16L1	233848107	0.000000	0.05858	0.001000	0.08648	0.985000	0.73830	-0.395000	0.07287	-1.999000	0.00967	0.528000	0.53228	ACT	G|0.422;N|0.000	0.422	strong		0.473	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974	
ANKLE1	126549	hgsc.bcm.edu	37	19	17397244	17397244	+	Silent	SNP	C	C	T	rs10425939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17397244C>T	ENST00000394458.3	+	9	2007	c.1731C>T	c.(1729-1731)ggC>ggT	p.G577G	ANKLE1_ENST00000594072.1_Silent_p.G540G|ANKLE1_ENST00000404085.1_Silent_p.G573G|ANKLE1_ENST00000598347.1_Missense_Mutation_p.A505V|ANKLE1_ENST00000433424.2_3'UTR	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	577										large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						TGGTGGCAGGCTGGCCACCTG	0.637													C|||	494	0.0986422	0.1354	0.0908	5008	,	,		15259	0.001		0.163	False		,,,				2504	0.089				p.G577G		Atlas-SNP	.											.	ANKLE1	27	.	0			c.C1731T						PASS	.	C		639,3765	258.6+/-262.5	48,543,1611	37.0	33.0	35.0		1731	2.0	0.5	19	dbSNP_119	35	1581,7013	278.7+/-293.6	156,1269,2872	no	coding-synonymous	ANKLE1	NM_152363.4		204,1812,4483	TT,TC,CC		18.3966,14.5095,17.0796		577/616	17397244	2220,10778	2202	4297	6499	SO:0001819	synonymous_variant	126549	exon9			GGCAGGCTGGCCA	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"""Ankyrin repeat domain containing"""	26812	protein-coding gene	gene with protein product	"""LEM domain containing 6"""		"""ankyrin repeat domain 41"""	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.1731C>T	19.37:g.17397244C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	65	0.613208	NM_152363	A8VU82|Q8N8J8	Silent	SNP	ENST00000394458.3	37	CCDS12354.2	221	0.10119047619047619	60	0.12195121951219512	35	0.09668508287292818	1	0.0017482517482517483	125	0.16490765171503957	C	10.12	1.261737	0.23051	0.145095	0.183966	ENSG00000160117	ENST00000438921	.	.	.	5.42	2.04	0.26737	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999999992	B	0.27823	0.19	B	0.22386	0.039	T	0.07404	-1.0774	6	0.62326	D	0.03	.	4.6632	0.12652	0.0:0.5771:0.1644:0.2584	rs10425939	505	E7ETZ9	.	V	505	.	ENSP00000415429:A505V	A	+	2	0	ANKLE1	17258244	0.040000	0.19996	0.452000	0.26994	0.978000	0.69477	0.390000	0.20768	0.227000	0.20999	0.491000	0.48974	GCT	C|0.850;T|0.150	0.150	strong		0.637	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363	
KCNAB1	7881	hgsc.bcm.edu	37	3	156249214	156249214	+	Silent	SNP	T	T	C	rs2280031	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:156249214T>C	ENST00000490337.1	+	13	1162	c.1098T>C	c.(1096-1098)aaT>aaC	p.N366N	KCNAB1_ENST00000389636.5_Silent_p.N337N|KCNAB1_ENST00000389634.5_Silent_p.N319N|KCNAB1_ENST00000302490.8_Silent_p.N348N|KCNAB1_ENST00000497291.1_3'UTR|KCNAB1_ENST00000471742.1_Silent_p.N355N	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	366					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GCCTGAGAAATGAAGGTGTGA	0.478													t|||	1300	0.259585	0.2171	0.268	5008	,	,		22188	0.3175		0.2435	False		,,,				2504	0.2679				p.N366N		Atlas-SNP	.											.	KCNAB1	176	.	0			c.T1098C						PASS	.		,,	963,3443	364.1+/-316.8	102,759,1342	247.0	214.0	225.0		1065,1044,1098	-4.5	0.9	3	dbSNP_100	225	2027,6573	354.0+/-329.3	244,1539,2517	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNAB1	NM_003471.3,NM_172159.3,NM_172160.2	,,	346,2298,3859	CC,CT,TT		23.5698,21.8566,22.9894	,,	355/409,348/402,366/420	156249214	2990,10016	2203	4300	6503	SO:0001819	synonymous_variant	7881	exon13			GAGAAATGAAGGT	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.1098T>C	3.37:g.156249214T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Silent	SNP	ENST00000490337.1	37	CCDS3174.1																																																																																			T|0.756;C|0.244	0.244	strong		0.478	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
ELANE	1991	hgsc.bcm.edu	37	19	855966	855966	+	Silent	SNP	C	C	A	rs17216649|rs587780934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:855966C>A	ENST00000590230.1	+	6	747	c.606C>A	c.(604-606)tcC>tcA	p.S202S	ELANE_ENST00000263621.1_Silent_p.S202S			P08246	ELNE_HUMAN	elastase, neutrophil expressed	202	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute inflammatory response to antigenic stimulus (GO:0002438)|cellular calcium ion homeostasis (GO:0006874)|collagen catabolic process (GO:0030574)|defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of chemotaxis (GO:0050922)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neutrophil mediated killing of fungus (GO:0070947)|phagocytosis (GO:0006909)|positive regulation of immune response (GO:0050778)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)|response to UV (GO:0009411)|response to yeast (GO:0001878)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|transcriptional repressor complex (GO:0017053)	cytokine binding (GO:0019955)|endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|RNA polymerase II transcription corepressor activity (GO:0001106)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(1)|lung(4)|pancreas(1)	13					Alpha-1-proteinase inhibitor(DB00058)|Filgrastim(DB00099)|Pegfilgrastim(DB00019)	AGGGGGACTCCGGCAGCCCCT	0.677													C|||	243	0.0485224	0.0053	0.0648	5008	,	,		15201	0.002		0.169	False		,,,				2504	0.0194				p.S202S		Atlas-SNP	.											ELANE,NS,carcinoma,0,1	ELANE	27	1	0			c.C606A						PASS	.	C		161,4245	105.6+/-144.1	4,153,2046	34.0	39.0	37.0		606	-5.4	0.9	19	dbSNP_123	37	1548,7050	277.5+/-292.9	126,1296,2877	no	coding-synonymous	ELANE	NM_001972.2		130,1449,4923	AA,AC,CC		18.0042,3.6541,13.1421		202/268	855966	1709,11295	2203	4299	6502	SO:0001819	synonymous_variant	1991	exon5			GGACTCCGGCAGC		CCDS12045.1	19p13.3	2014-09-17	2009-05-05	2009-05-05	ENSG00000197561	ENSG00000197561	3.4.21.37		3309	protein-coding gene	gene with protein product	"""neutrophil elastase"", ""leukocyte elastase"", ""medullasin"""	130130	"""elastase 2, neutrophil"""	ELA2		2902087	Standard	XM_005259517		Approved	NE, HNE, HLE	uc002lqb.3	P08246		ENST00000590230.1:c.606C>A	19.37:g.855966C>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	34	17	0.5	NM_001972	P09649|Q6B0D9|Q6LDP5	Silent	SNP	ENST00000590230.1	37	CCDS12045.1																																																																																			A|0.114;C|0.886;T|0.000	0.114	strong		0.677	ELANE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457890.2	NM_001972	
FFAR3	2865	hgsc.bcm.edu	37	19	35849926	35849926	+	Missense_Mutation	SNP	G	G	A	rs62109581	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35849926G>A	ENST00000327809.4	+	2	335	c.134G>A	c.(133-135)cGc>cAc	p.R45H	FFAR3_ENST00000594310.1_Missense_Mutation_p.R45H	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	45			R -> C (in dbSNP:rs423385). {ECO:0000269|PubMed:19630535}.		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.R45H(1)		endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			AAGCTGCAGCGCCGCCCGGTG	0.647																																					p.R45H	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											FFAR3,NS,carcinoma,0,1	FFAR3	40	1	1	Substitution - Missense(1)	stomach(1)	c.G134A						PASS	.	G	HIS/ARG	631,3767		14,603,1582	188.0	172.0	178.0		134	0.4	0.6	19	dbSNP_131	178	1976,6614		53,1870,2372	no	missense	FFAR3	NM_005304.3	29	67,2473,3954	AA,AG,GG		23.0035,14.3474,20.0724	probably-damaging	45/347	35849926	2607,10381	2199	4295	6494	SO:0001583	missense	2865	exon2			TGCAGCGCCGCCC	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"""GPCR / Class A : Fatty acid receptors"""	4499	protein-coding gene	gene with protein product		603821	"""G protein-coupled receptor 41"""	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.134G>A	19.37:g.35849926G>A	ENSP00000328230:p.Arg45His	Somatic	506	0	0		WXS	Illumina HiSeq	Phase_I	521	161	0.309021	NM_005304	B2RWM8|Q14CM7	Missense_Mutation	SNP	ENST00000327809.4	37	CCDS12459.1	404	0.184981684981685	58	0.11788617886178862	62	0.1712707182320442	119	0.20804195804195805	165	0.21767810026385223	G	11.81	1.750715	0.31046	0.143474	0.230035	ENSG00000185897	ENST00000327809	T	0.39406	1.08	4.99	0.408	0.16377	GPCR, rhodopsin-like superfamily (1);	0.283555	0.33610	U	0.004728	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.6000000000016E-5	B	0.32425	0.371	B	0.28553	0.091	T	0.28902	-1.0029	9	0.45353	T	0.12	-13.598	4.4639	0.11680	0.3446:0.1552:0.5002:0.0	.	45	O14843	FFAR3_HUMAN	H	45	ENSP00000328230:R45H	ENSP00000328230:R45H	R	+	2	0	FFAR3	40541766	0.000000	0.05858	0.608000	0.28969	0.840000	0.47671	-0.177000	0.09796	0.033000	0.15463	0.455000	0.32223	CGC	G|0.800;A|0.200	0.200	strong		0.647	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304	
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 GAIIx	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	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	73	30	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	
ECE1	1889	hgsc.bcm.edu	37	1	21573722	21573722	+	Silent	SNP	G	G	A	rs2229450	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:21573722G>A	ENST00000374893.6	-	9	1229	c.1155C>T	c.(1153-1155)acC>acT	p.T385T	ECE1_ENST00000436918.2_Silent_p.T385T|ECE1_ENST00000264205.6_Silent_p.T382T|ECE1_ENST00000357071.4_Silent_p.T373T|ECE1_ENST00000528294.1_5'UTR|ECE1_ENST00000415912.2_Silent_p.T369T	NM_001397.2	NP_001388.1	P42892	ECE1_HUMAN	endothelin converting enzyme 1	385					bradykinin catabolic process (GO:0010815)|calcitonin catabolic process (GO:0010816)|ear development (GO:0043583)|embryonic digit morphogenesis (GO:0042733)|endothelin maturation (GO:0034959)|heart development (GO:0007507)|hormone catabolic process (GO:0042447)|peptide hormone processing (GO:0016486)|pharyngeal system development (GO:0060037)|positive regulation of receptor recycling (GO:0001921)|protein processing (GO:0016485)|regulation of systemic arterial blood pressure by endothelin (GO:0003100)|regulation of vasoconstriction (GO:0019229)|substance P catabolic process (GO:0010814)	early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intrinsic component of endosome membrane (GO:0031302)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|vesicle (GO:0031982)|Weibel-Palade body (GO:0033093)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)			endometrium(5)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)	25		Lung NSC(340;1.14e-05)|all_lung(284;1.23e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00147)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0183)|OV - Ovarian serous cystadenocarcinoma(117;4.83e-27)|COAD - Colon adenocarcinoma(152;1.36e-06)|GBM - Glioblastoma multiforme(114;1.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000162)|STAD - Stomach adenocarcinoma(196;0.00326)|KIRC - Kidney renal clear cell carcinoma(1967;0.00755)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.206)		ACCATCTGTCGGTGGTGTTGA	0.552													G|||	735	0.146765	0.0144	0.2709	5008	,	,		17950	0.128		0.2535	False		,,,				2504	0.1472				p.T385T		Atlas-SNP	.											.	ECE1	76	.	0			c.C1155T						PASS	.	G	,,,	253,4153	145.7+/-180.5	10,233,1960	157.0	127.0	137.0		1119,1107,1146,1155	-11.0	0.0	1	dbSNP_98	137	2309,6291	387.6+/-342.3	286,1737,2277	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ECE1	NM_001113347.1,NM_001113348.1,NM_001113349.1,NM_001397.2	,,,	296,1970,4237	AA,AG,GG		26.8488,5.7422,19.6986	,,,	373/759,369/755,382/768,385/771	21573722	2562,10444	2203	4300	6503	SO:0001819	synonymous_variant	1889	exon9			TCTGTCGGTGGTG	D49471	CCDS215.1, CCDS44081.1, CCDS44082.1, CCDS44083.1	1p36.1	2008-02-05			ENSG00000117298	ENSG00000117298			3146	protein-coding gene	gene with protein product		600423		ECE		7805846, 7864876, 17592116	Standard	NM_001397		Approved		uc001bei.2	P42892	OTTHUMG00000002625	ENST00000374893.6:c.1155C>T	1.37:g.21573722G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	125	50	0.4	NM_001397	A8K3P1|B4E291|Q14217|Q17RN5|Q2Z2K8|Q58GE7|Q5THM5|Q5THM7|Q5THM8|Q9UJQ6|Q9UPF4|Q9UPM4|Q9Y501	Silent	SNP	ENST00000374893.6	37	CCDS215.1																																																																																			G|0.817;N|0.000;A|0.183	0.183	strong		0.552	ECE1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007470.2	NM_001397	
MYOM1	8736	hgsc.bcm.edu	37	18	3188976	3188976	+	Missense_Mutation	SNP	A	A	G	rs1962519	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:3188976A>G	ENST00000356443.4	-	4	874	c.541T>C	c.(541-543)Tct>Cct	p.S181P	MYOM1_ENST00000261606.7_Missense_Mutation_p.S181P|MYOM1_ENST00000400569.3_Missense_Mutation_p.S181P|RP13-270P17.2_ENST00000580139.1_RNA	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	181			S -> P (in dbSNP:rs1962519). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505783}.		muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GACTGTTTAGATGTTGTGATT	0.488													A|||	2220	0.443291	0.1641	0.402	5008	,	,		17012	0.8363		0.4026	False		,,,				2504	0.4867				p.S181P		Atlas-SNP	.											.	MYOM1	192	.	0			c.T541C						PASS	.	A	PRO/SER,PRO/SER	747,3251		72,603,1324	325.0	297.0	306.0		541,541	1.3	0.6	18	dbSNP_92	306	3467,4881		745,1977,1452	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	74,74	817,2580,2776	GG,GA,AA		41.5309,18.6843,34.1325	benign,benign	181/1686,181/1590	3188976	4214,8132	1999	4174	6173	SO:0001583	missense	8736	exon4			GTTTAGATGTTGT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.541T>C	18.37:g.3188976A>G	ENSP00000348821:p.Ser181Pro	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	67	39	0.58209	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	1011	0.46291208791208793	85	0.17276422764227642	139	0.3839779005524862	477	0.833916083916084	310	0.40897097625329815	A	12.33	1.904802	0.33628	0.186843	0.415309	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.54479	0.73;0.74;0.57	4.27	1.27	0.21489	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	6.999999999979245E-6	D;P	0.56968	0.978;0.856	P;B	0.53146	0.719;0.312	T	0.31806	-0.9930	8	0.27082	T	0.32	.	7.6383	0.28280	0.5186:0.0:0.0:0.4814	rs1962519;rs17531602;rs60425523;rs1962519	181;181	P52179-2;P52179	.;MYOM1_HUMAN	P	181	ENSP00000348821:S181P;ENSP00000383413:S181P;ENSP00000261606:S181P	ENSP00000261606:S181P	S	-	1	0	MYOM1	3178976	0.077000	0.21312	0.612000	0.29024	0.571000	0.35966	-0.165000	0.09968	0.370000	0.24538	0.491000	0.48974	TCT	A|0.536;G|0.464	0.464	strong		0.488	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
ATP13A4	84239	hgsc.bcm.edu	37	3	193183817	193183817	+	Silent	SNP	A	A	G	rs3796181	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193183817A>G	ENST00000342695.4	-	11	1591	c.1269T>C	c.(1267-1269)agT>agC	p.S423S	ATP13A4_ENST00000392443.3_Intron|ATP13A4_ENST00000295548.3_Silent_p.S423S	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	423						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)		AGCTTACCCCACTAAGCACAT	0.423													G|||	2775	0.554113	0.6838	0.5288	5008	,	,		16612	0.5387		0.4503	False		,,,				2504	0.5194				p.S423S		Atlas-SNP	.											.	ATP13A4	154	.	0			c.T1269C						PASS	.	G		2811,1595	496.0+/-363.4	883,1045,275	169.0	152.0	158.0		1269	-2.9	0.9	3	dbSNP_107	158	3828,4772	611.5+/-395.8	876,2076,1348	no	coding-synonymous	ATP13A4	NM_032279.2		1759,3121,1623	GG,GA,AA		44.5116,36.2006,48.9543		423/1197	193183817	6639,6367	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon11			TACCCCACTAAGC	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.1269T>C	3.37:g.193183817A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			A|0.474;G|0.526	0.526	strong		0.423	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
WDFY4	57705	hgsc.bcm.edu	37	10	50034833	50034833	+	Missense_Mutation	SNP	G	G	A	rs6537579	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50034833G>A	ENST00000325239.5	+	35	6127	c.6100G>A	c.(6100-6102)Ggc>Agc	p.G2034S	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2034						integral component of membrane (GO:0016021)		p.G2034S(1)		NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CGAATGCCTCGGCCTTCTCAG	0.488													A|||	1005	0.200679	0.4039	0.1729	5008	,	,		20229	0.1012		0.1243	False		,,,				2504	0.1268				p.G2034S		Atlas-SNP	.											WDFY4,NS,carcinoma,0,1	WDFY4	205	1	1	Substitution - Missense(1)	stomach(1)	c.G6100A						PASS	.	A	SER/GLY	522,862		96,330,266	112.0	93.0	99.0		6100	-4.3	0.3	10	dbSNP_116	99	342,2840		19,304,1268	yes	missense	WDFY4	NM_020945.1	56	115,634,1534	AA,AG,GG		10.748,37.7168,18.9225	benign	2034/3185	50034833	864,3702	692	1591	2283	SO:0001583	missense	57705	exon36			TGCCTCGGCCTTC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.6100G>A	10.37:g.50034833G>A	ENSP00000320563:p.Gly2034Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	171	94	0.549708	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	394|394	0.1804029304029304|0.1804029304029304	177|177	0.3597560975609756|0.3597560975609756	55|55	0.15193370165745856|0.15193370165745856	70|70	0.12237762237762238|0.12237762237762238	92|92	0.12137203166226913|0.12137203166226913	A|A	3.158|3.158	-0.172780|-0.172780	0.06421|0.06421	0.377168|0.377168	0.10748|0.10748	ENSG00000128815|ENSG00000128815	ENST00000426033;ENST00000325239|ENST00000312002	T|.	0.51071|.	0.72|.	5.62|5.62	-4.33|-4.33	0.03677|0.03677	.|.	0.801903|.	0.11711|.	N|.	0.536877|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02315|0.02315	-0.6|-0.6	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.32981|0.32981	-0.9886|-0.9886	8|4	.|.	.|.	.|.	.|.	15.8609|15.8609	0.79019|0.79019	0.4631:0.0:0.5369:0.0|0.4631:0.0:0.5369:0.0	rs6537579;rs52795837;rs61660295;rs6537579|rs6537579;rs52795837;rs61660295;rs6537579	2034|.	Q6ZS81|.	WDFY4_HUMAN|.	S|Q	2034|1124	ENSP00000320563:G2034S|.	.|.	G|R	+|+	1|2	0|0	WDFY4|WDFY4	49704839|49704839	0.000000|0.000000	0.05858|0.05858	0.266000|0.266000	0.24541|0.24541	0.867000|0.867000	0.49689|0.49689	0.486000|0.486000	0.22340|0.22340	-1.105000|-1.105000	0.03011|0.03011	-1.062000|-1.062000	0.02293|0.02293	GGC|CGG	G|0.801;A|0.199	0.199	strong		0.488	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
NSUN2	54888	hgsc.bcm.edu	37	5	6600150	6600150	+	Silent	SNP	G	G	A	rs3822434	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:6600150G>A	ENST00000264670.6	-	19	2504	c.2193C>T	c.(2191-2193)gaC>gaT	p.D731D	NSUN2_ENST00000539938.1_Silent_p.D495D|NSUN2_ENST00000506139.1_Silent_p.D696D	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	731					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CCTCAGTCACGTCATTGTCTG	0.572													C|||	869	0.173522	0.0825	0.2507	5008	,	,		18174	0.2321		0.1402	False		,,,				2504	0.2157				p.D731D		Atlas-SNP	.											NSUN2,colon,carcinoma,0,1	NSUN2	82	1	0			c.C2193T						PASS	.	C	,	411,3995		17,377,1809	182.0	144.0	157.0		2088,2193	-0.6	0.0	5	dbSNP_107	157	1279,7321		105,1069,3126	no	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	122,1446,4935	AA,AG,GG		14.8721,9.3282,12.994	,	696/733,731/768	6600150	1690,11316	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon19			AGTCACGTCATTG	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.2193C>T	5.37:g.6600150G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	91	52	0.571429	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			G|0.862;C|0.000;A|0.138	0.138	strong		0.572	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
ZNF638	27332	hgsc.bcm.edu	37	2	71633389	71633389	+	Silent	SNP	C	C	T	rs6714975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71633389C>T	ENST00000409544.1	+	19	3762	c.3132C>T	c.(3130-3132)aaC>aaT	p.N1044N	ZNF638_ENST00000355812.3_Silent_p.N1044N|ZNF638_ENST00000409407.1_5'Flank|ZNF638_ENST00000264447.4_Silent_p.N1044N	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1044					regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						GTAATAGAAACAAGGTAACAA	0.353													C|||	2127	0.42472	0.2201	0.6225	5008	,	,		18856	0.2927		0.5527	False		,,,				2504	0.5654				p.N1044N		Atlas-SNP	.											.	ZNF638	179	.	0			c.C3132T						PASS	.	C	,	1193,3211	414.6+/-336.9	160,873,1169	118.0	107.0	111.0		3132,3132	3.6	1.0	2	dbSNP_116	111	4982,3618	625.1+/-397.7	1437,2108,755	yes	coding-synonymous,coding-synonymous	ZNF638	NM_001014972.1,NM_014497.3	,	1597,2981,1924	TT,TC,CC		42.0698,27.089,47.4854	,	1044/1979,1044/1979	71633389	6175,6829	2202	4300	6502	SO:0001819	synonymous_variant	27332	exon19			TAGAAACAAGGTA	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.3132C>T	2.37:g.71633389C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Silent	SNP	ENST00000409544.1	37	CCDS1917.1																																																																																			C|0.545;T|0.455	0.455	strong		0.353	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
NGEF	25791	hgsc.bcm.edu	37	2	233750074	233750074	+	Silent	SNP	C	C	T	rs2292725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233750074C>T	ENST00000264051.3	-	10	1631	c.1353G>A	c.(1351-1353)gtG>gtA	p.V451V	NGEF_ENST00000539537.1_Silent_p.V174V|NGEF_ENST00000373552.4_Silent_p.V359V	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	451	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|ephrin receptor signaling pathway (GO:0048013)|negative regulation of dendritic spine morphogenesis (GO:0061002)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(4)|endometrium(8)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|skin(4)	35		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.00793)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;8.65e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(119;0.00984)|GBM - Glioblastoma multiforme(43;0.0604)		TGCATGCCTTCACCACCTGGG	0.577													C|||	773	0.154353	0.1861	0.1427	5008	,	,		19749	0.0992		0.2465	False		,,,				2504	0.0818				p.V451V		Atlas-SNP	.											.	NGEF	198	.	0			c.G1353A						PASS	.	C	,	803,3603	322.9+/-297.8	59,685,1459	199.0	167.0	178.0		1077,1353	-2.5	1.0	2	dbSNP_100	178	1937,6663	342.6+/-324.5	214,1509,2577	no	coding-synonymous,coding-synonymous	NGEF	NM_001114090.1,NM_019850.2	,	273,2194,4036	TT,TC,CC		22.5233,18.2251,21.0672	,	359/619,451/711	233750074	2740,10266	2203	4300	6503	SO:0001819	synonymous_variant	25791	exon10			TGCCTTCACCACC	AJ238899	CCDS2500.1, CCDS46544.1	2q37	2012-07-24			ENSG00000066248	ENSG00000066248		"""Rho guanine nucleotide exchange factors"""	7807	protein-coding gene	gene with protein product	"""ephexin"""	605991				10777665	Standard	NM_019850		Approved	ARHGEF27	uc002vts.2	Q8N5V2	OTTHUMG00000133272	ENST00000264051.3:c.1353G>A	2.37:g.233750074C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Silent	SNP	ENST00000264051.3	37	CCDS2500.1																																																																																			C|0.798;T|0.202	0.202	strong		0.577	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799	
PAK6	56924	hgsc.bcm.edu	37	15	40564576	40564576	+	Missense_Mutation	SNP	C	C	T	rs3743137	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:40564576C>T	ENST00000542403.2	+	4	1121	c.1010C>T	c.(1009-1011)cCg>cTg	p.P337L	PAK6_ENST00000455577.2_Missense_Mutation_p.P337L|PAK6_ENST00000260404.4_Missense_Mutation_p.P337L|RP11-133K1.2_ENST00000558658.1_3'UTR|PAK6_ENST00000453867.1_Missense_Mutation_p.P337L|PAK6_ENST00000560346.1_Missense_Mutation_p.P337L|PAK6_ENST00000441369.1_Missense_Mutation_p.P337L	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	337	Linker.		P -> L (in dbSNP:rs3743137). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		CGCACAGCCCCGGCCACAGGC	0.697													C|||	471	0.0940495	0.0348	0.0663	5008	,	,		15740	0.119		0.1252	False		,,,				2504	0.136				p.P337L		Atlas-SNP	.											.	PAK6	49	.	0			c.C1010T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	206,4200	128.2+/-165.1	5,196,2002	44.0	51.0	49.0		1010,1010,1010	3.0	0.1	15	dbSNP_107	49	960,7640	205.9+/-248.2	47,866,3387	yes	missense,missense,missense	PAK6	NM_001128628.1,NM_001128629.1,NM_020168.4	98,98,98	52,1062,5389	TT,TC,CC		11.1628,4.6754,8.9651	benign,benign,benign	337/682,337/682,337/682	40564576	1166,11840	2203	4300	6503	SO:0001583	missense	56924	exon5			CAGCCCCGGCCAC	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"""p21(CDKN1A)-activated kinase 6"""			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.1010C>T	15.37:g.40564576C>T	ENSP00000439597:p.Pro337Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	55	13	0.236364	NM_001128629	A8K2G2|B3KYB0|G5E9R2	Missense_Mutation	SNP	ENST00000542403.2	37	CCDS10054.1	238	0.10897435897435898	32	0.06504065040650407	31	0.0856353591160221	70	0.12237762237762238	105	0.13852242744063326	C	10.65	1.408476	0.25378	0.046754	0.111628	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	T;T;T;T;T	0.76448	-0.92;-0.92;-1.02;-0.92;-0.92	3.97	3.04	0.35103	.	0.411806	0.28393	N	0.015516	T	0.00754	0.0025	L	0.27053	0.805	0.20074	P	0.9999341805	P;P	0.39920	0.569;0.695	B;B	0.32928	0.074;0.155	T	0.20538	-1.0272	9	0.25106	T	0.35	.	13.2801	0.60210	0.1596:0.8404:0.0:0.0	rs3743137;rs3743137	337;337	Q9NQU5;G5E9R2	PAK6_HUMAN;.	L	337	ENSP00000406873:P337L;ENSP00000401153:P337L;ENSP00000409465:P337L;ENSP00000260404:P337L;ENSP00000439597:P337L	ENSP00000260404:P337L	P	+	2	0	PAK6	38351868	0.368000	0.25031	0.132000	0.22025	0.036000	0.12997	2.667000	0.46808	0.996000	0.38943	0.555000	0.69702	CCG	C|0.904;T|0.096	0.096	strong		0.697	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1		
ZNF880	400713	hgsc.bcm.edu	37	19	52888210	52888210	+	Silent	SNP	T	T	C	rs56151179	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52888210T>C	ENST00000422689.2	+	4	1392	c.1377T>C	c.(1375-1377)acT>acC	p.T459T		NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	459					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						GATTTCATACTGGAGAGAAAC	0.388																																					p.T459T		Atlas-SNP	.											.	ZNF880	45	.	0			c.T1377C						PASS	.	T		529,855		102,325,265	74.0	70.0	71.0		1377	2.0	0.9	19	dbSNP_129	71	1217,1965		222,773,596	no	coding-synonymous	ZNF880	NM_001145434.1		324,1098,861	CC,CT,TT		38.2464,38.2225,38.2392		459/578	52888210	1746,2820	692	1591	2283	SO:0001819	synonymous_variant	400713	exon4			TCATACTGGAGAG	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.1377T>C	19.37:g.52888210T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	38	35	0.921053	NM_001145434	B4DNA6	Silent	SNP	ENST00000422689.2	37	CCDS46164.1																																																																																			T|0.633;C|0.367	0.367	strong		0.388	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
ZNF587B	100293516	hgsc.bcm.edu	37	19	58353003	58353003	+	Missense_Mutation	SNP	G	G	A	rs34871842	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58353003G>A	ENST00000442832.4	+	3	1195	c.961G>A	c.(961-963)Gct>Act	p.A321T	ZNF587B_ENST00000594901.1_Missense_Mutation_p.A321T|ZNF587B_ENST00000316462.4_Intron|CTD-2583A14.10_ENST00000598031.1_Intron	NM_001204818.1	NP_001191747.1	E7ETH6	Z587B_HUMAN	zinc finger protein 587B	321					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AAAAGTTCACGCTGGAAAAGG	0.418													.|||	148	0.0295527	0.0068	0.049	5008	,	,		20383	0.001		0.0885	False		,,,				2504	0.0153				p.A321T		Atlas-SNP	.											.	.	.	.	0			c.G961A						PASS	.																																			SO:0001583	missense	100293516	exon3			GTTCACGCTGGAA	AK299091	CCDS56109.1	19q13.43	2013-01-08				ENSG00000269343		"""Zinc fingers, C2H2-type"", ""-"""	37142	protein-coding gene	gene with protein product							Standard	NM_001204818		Approved		uc021vcp.1	E7ETH6		ENST00000442832.4:c.961G>A	19.37:g.58353003G>A	ENSP00000392410:p.Ala321Thr	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	8	4	0.5	NM_001204818	B4DR41	Missense_Mutation	SNP	ENST00000442832.4	37	CCDS56109.1	90	0.04120879120879121	3	0.006097560975609756	20	0.055248618784530384	0	0.0	67	0.08839050131926121	.	0.011	-1.719340	0.00700	.	.	ENSG00000198466	ENST00000442832	T	0.11277	2.79	1.95	-0.711	0.11230	.	.	.	.	.	T	0.00178	0.0005	N	0.02391	-0.57	.	.	.	B;B	0.11235	0.004;0.0	B;B	0.06405	0.002;0.0	T	0.47497	-0.9113	7	.	.	.	.	8.043	0.30532	0.8648:0.0:0.1352:0.0	rs34871842;rs34871842	321;270	E7ETH6;Q92967	.;.	T	321	ENSP00000392410:A321T	.	A	+	1	0	ZNF587	63044815	0.000000	0.05858	0.012000	0.15200	0.001000	0.01503	-0.072000	0.11486	-0.455000	0.07054	-1.873000	0.00551	GCT	G|0.956;A|0.044	0.044	strong		0.418	ZNF587B-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466834.2	NM_001204818	
KIAA0825	285600	hgsc.bcm.edu	37	5	93722050	93722050	+	Silent	SNP	G	G	T	rs29913	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:93722050G>T	ENST00000513200.3	-	18	3588	c.3516C>A	c.(3514-3516)atC>atA	p.I1172I	KIAA0825_ENST00000427991.2_Silent_p.I1172I	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	1172										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTAAAGGTCGGATGGGTAATG	0.388													G|||	581	0.116014	0.1157	0.1066	5008	,	,		17135	0.004		0.1471	False		,,,				2504	0.2065				p.I1172I		Atlas-SNP	.											.	KIAA0825	172	.	0			c.C3516A						PASS	.						157.0	136.0	142.0					5																	93722050		692	1591	2283	SO:0001819	synonymous_variant	285600	exon19			AGGTCGGATGGGT	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.3516C>A	5.37:g.93722050G>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_001145678	O94914|Q6ZNN2	Silent	SNP	ENST00000513200.3	37																																																																																				G|0.892;T|0.108	0.108	strong		0.388	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665	
TAF1C	9013	hgsc.bcm.edu	37	16	84215867	84215867	+	Missense_Mutation	SNP	C	C	T	rs79432776	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84215867C>T	ENST00000567759.1	-	7	844	c.662G>A	c.(661-663)gGa>gAa	p.G221E	TAF1C_ENST00000378541.4_Missense_Mutation_p.G221E|TAF1C_ENST00000341690.6_Missense_Mutation_p.G154E|TAF1C_ENST00000541676.1_Missense_Mutation_p.G154E|TAF1C_ENST00000565544.1_5'Flank|TAF1C_ENST00000570117.1_5'UTR|TAF1C_ENST00000566732.1_Missense_Mutation_p.G221E	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	221					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						GGGTGTCCTTCCAGGAACCCA	0.662													C|||	40	0.00798722	0.0008	0.0216	5008	,	,		16212	0.0		0.0239	False		,,,				2504	0.0				p.G221E		Atlas-SNP	.											.	TAF1C	60	.	0			c.G662A						PASS	.	C	GLU/GLY,GLU/GLY	12,4386		0,12,2187	25.0	28.0	27.0		662,461	4.8	0.2	16	dbSNP_131	27	132,8458		2,128,4165	yes	missense,missense	TAF1C	NM_005679.3,NM_139353.2	98,98	2,140,6352	TT,TC,CC		1.5367,0.2729,1.1087	probably-damaging,probably-damaging	221/870,154/776	84215867	144,12844	2199	4295	6494	SO:0001583	missense	9013	exon7			GTCCTTCCAGGAA	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.662G>A	16.37:g.84215867C>T	ENSP00000455265:p.Gly221Glu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_001243156	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	37	CCDS32496.1	21	0.009615384615384616	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	11	0.014511873350923483	C	15.12	2.739328	0.49045	0.002729	0.015367	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000537450	T;T;T	0.02737	4.18;4.18;4.18	4.78	4.78	0.61160	.	0.231190	0.26272	N	0.025334	T	0.05593	0.0147	M	0.68317	2.08	0.44531	D	0.99748	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.19745	-1.0296	10	0.22109	T	0.4	-13.5696	13.7107	0.62667	0.0:1.0:0.0:0.0	.	221;221;221;154	F5H7W6;Q15572-6;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	E	221;154;154;221	ENSP00000367802:G221E;ENSP00000437900:G154E;ENSP00000345305:G154E	ENSP00000345305:G154E	G	-	2	0	TAF1C	82773368	0.236000	0.23804	0.157000	0.22605	0.162000	0.22319	2.001000	0.40825	2.388000	0.81334	0.655000	0.94253	GGA	C|0.989;T|0.011	0.011	strong		0.662	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
ATP10A	57194	hgsc.bcm.edu	37	15	25924539	25924539	+	Silent	SNP	T	T	C	rs1047700	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:25924539T>C	ENST00000356865.6	-	21	4560	c.4449A>G	c.(4447-4449)caA>caG	p.Q1483Q		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1483					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GGTCTGGCCCTTGAAGTCCTG	0.473													C|||	1334	0.266374	0.4153	0.3386	5008	,	,		13468	0.2748		0.1382	False		,,,				2504	0.137				p.Q1483Q		Atlas-SNP	.											.	ATP10A	270	.	0			c.A4449G						PASS	.	C		1631,2775	643.7+/-397.9	298,1035,870	58.0	63.0	61.0		4449	-4.4	0.0	15	dbSNP_86	61	1339,7261	749.9+/-407.4	99,1141,3060	no	coding-synonymous	ATP10A	NM_024490.3		397,2176,3930	CC,CT,TT		15.5698,37.0177,22.8356		1483/1500	25924539	2970,10036	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon21			TGGCCCTTGAAGT	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.4449A>G	15.37:g.25924539T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			T|0.749;C|0.251	0.251	strong		0.473	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
SMTNL2	342527	hgsc.bcm.edu	37	17	4497160	4497160	+	Silent	SNP	T	T	C	rs8080130	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4497160T>C	ENST00000389313.4	+	4	841	c.774T>C	c.(772-774)taT>taC	p.Y258Y	SMTNL2_ENST00000338859.4_Silent_p.Y114Y	NM_001114974.1	NP_001108446.1	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2	258										breast(1)|endometrium(9)|kidney(1)|lung(1)|skin(1)	13				READ - Rectum adenocarcinoma(115;0.0325)		GCTCTGGCTATGGGGCAGTGA	0.582													C|||	3419	0.682708	0.5257	0.7709	5008	,	,		19667	0.8462		0.6441	False		,,,				2504	0.7035				p.Y258Y		Atlas-SNP	.											.	SMTNL2	57	.	0			c.T774C						PASS	.	C	,	2439,1967	552.7+/-378.6	668,1103,432	81.0	73.0	76.0		774,342	-5.6	0.2	17	dbSNP_116	76	5622,2978	461.5+/-365.4	1833,1956,511	no	coding-synonymous,coding-synonymous	SMTNL2	NM_001114974.1,NM_198501.2	,	2501,3059,943	CC,CT,TT		34.6279,44.6437,38.0209	,	258/462,114/318	4497160	8061,4945	2203	4300	6503	SO:0001819	synonymous_variant	342527	exon4			TGGCTATGGGGCA	AK124452	CCDS11048.1, CCDS45583.1	17p13.2	2006-04-26			ENSG00000188176	ENSG00000188176			24764	protein-coding gene	gene with protein product							Standard	NM_001114974		Approved	FLJ42461	uc002fyf.1	Q2TAL5	OTTHUMG00000132938	ENST00000389313.4:c.774T>C	17.37:g.4497160T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001114974	Q6ZVK6	Silent	SNP	ENST00000389313.4	37	CCDS45583.1																																																																																			T|0.350;C|0.650	0.650	strong		0.582	SMTNL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439129.1	NM_198501	
STK17A	9263	hgsc.bcm.edu	37	7	43664198	43664198	+	Silent	SNP	A	A	G	rs10233697	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:43664198A>G	ENST00000319357.5	+	7	1181	c.1002A>G	c.(1000-1002)gaA>gaG	p.E334E		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	334					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						TCAGGATGGAAAAGGCACTAG	0.433													A|||	467	0.0932508	0.0174	0.1354	5008	,	,		19180	0.0119		0.2157	False		,,,				2504	0.1237				p.E334E		Atlas-SNP	.											.	STK17A	31	.	0			c.A1002G						PASS	.	A		191,4215	120.8+/-158.4	6,179,2018	86.0	76.0	79.0		1002	2.3	0.5	7	dbSNP_119	79	1820,6780	325.8+/-317.1	195,1430,2675	no	coding-synonymous	STK17A	NM_004760.2		201,1609,4693	GG,GA,AA		21.1628,4.335,15.4621		334/415	43664198	2011,10995	2203	4300	6503	SO:0001819	synonymous_variant	9263	exon7			GATGGAAAAGGCA	AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 1"""	604726	"""serine/threonine kinase 17a (apoptosis-inducing)"""			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.1002A>G	7.37:g.43664198A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	31	22	0.709677	NM_004760	A4D1V6|Q8IVC8	Silent	SNP	ENST00000319357.5	37	CCDS5470.1																																																																																			A|0.868;G|0.132	0.132	strong		0.433	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760	
YME1L1	10730	hgsc.bcm.edu	37	10	27434483	27434483	+	Silent	SNP	G	G	A	rs2274634	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27434483G>A	ENST00000326799.3	-	4	524	c.376C>T	c.(376-378)Cta>Tta	p.L126L	YME1L1_ENST00000375972.3_Silent_p.L69L|YME1L1_ENST00000376016.3_Silent_p.L69L|YME1L1_ENST00000477432.1_3'UTR	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	126					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						CCAATTTTTAGTTCAGATAAT	0.368													A|||	1747	0.348842	0.3132	0.1873	5008	,	,		14029	0.5506		0.2247	False		,,,				2504	0.4315				p.L126L		Atlas-SNP	.											.	YME1L1	71	.	0			c.C376T						PASS	.	A	,	1366,3040	686.8+/-404.8	197,972,1034	94.0	100.0	98.0		205,376	4.6	1.0	10	dbSNP_100	98	1532,7066	745.8+/-407.3	131,1270,2898	no	coding-synonymous,coding-synonymous	YME1L1	NM_014263.2,NM_139312.1	,	328,2242,3932	AA,AG,GG		17.8181,31.0032,22.2855	,	69/717,126/774	27434483	2898,10106	2203	4299	6502	SO:0001819	synonymous_variant	10730	exon4			TTTTTAGTTCAGA	AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"""ATPases / AAA-type"""	12843	protein-coding gene	gene with protein product		607472	"""YME1 (S.cerevisiae)-like 1"", ""YME1-like 1 (S. cerevisiae)"""			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.376C>T	10.37:g.27434483G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_139312	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Silent	SNP	ENST00000326799.3	37	CCDS7152.1																																																																																			G|0.727;A|0.273	0.273	strong		0.368	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312	
R3HCC1L	27291	hgsc.bcm.edu	37	10	99969475	99969475	+	Missense_Mutation	SNP	A	A	C	rs34494334	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:99969475A>C	ENST00000298999.3	+	5	1907	c.1604A>C	c.(1603-1605)gAc>gCc	p.D535A	R3HCC1L_ENST00000314594.5_5'UTR|R3HCC1L_ENST00000370586.2_Intron|R3HCC1L_ENST00000370584.3_Missense_Mutation_p.D535A	NM_014472.4	NP_055287	Q7Z5L2	R3HCL_HUMAN	R3H domain and coiled-coil containing 1-like	535			D -> A (in dbSNP:rs34494334).				nucleotide binding (GO:0000166)										GAGCAAGATGACTCAGGGAGT	0.438													A|||	680	0.135783	0.1664	0.1499	5008	,	,		20094	0.0298		0.2217	False		,,,				2504	0.1053				p.D535A		Atlas-SNP	.											.	R3HCC1L	3	.	0			c.A1604C						PASS	.	A	ALA/ASP	806,3600	320.4+/-296.6	84,638,1481	133.0	124.0	127.0		1604	-0.5	1.0	10	dbSNP_126	127	1857,6743	332.1+/-320.0	195,1467,2638	yes	missense	C10orf28	NM_014472.4	126	279,2105,4119	CC,CA,AA		21.593,18.2932,20.4752	benign	535/779	99969475	2663,10343	2203	4300	6503	SO:0001583	missense	27291	exon4			AAGATGACTCAGG	AF525304	CCDS31267.1, CCDS58093.1, CCDS73178.1	10q24.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166024	ENSG00000166024			23512	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 28"""	C10orf28			Standard	NM_014472		Approved	GIDRP86, PSORT	uc001kox.4	Q7Z5L2	OTTHUMG00000018873	ENST00000298999.3:c.1604A>C	10.37:g.99969475A>C	ENSP00000298999:p.Asp535Ala	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_001256620	O60598|Q5W0B4|Q5W0B5|Q86VT9|Q8N9H0	Missense_Mutation	SNP	ENST00000298999.3	37	CCDS31267.1	353	0.16163003663003664	104	0.21138211382113822	63	0.17403314917127072	19	0.033216783216783216	167	0.22031662269129287	A	5.598	0.295168	0.10622	0.182932	0.21593	ENSG00000166024	ENST00000370584;ENST00000298999	T;T	0.07216	3.21;3.21	5.15	-0.501	0.12008	.	0.693696	0.13424	N	0.388881	T	0.00012	0.0000	L	0.38838	1.175	0.09310	P	0.999999999439986	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.003	T	0.45338	-0.9268	8	.	.	.	0.4892	4.5381	0.12043	0.4801:0.0:0.0844:0.4355	rs34494334	535;535	Q7Z5L2;Q7Z5L2-2	GIDRP_HUMAN;.	A	535	ENSP00000359616:D535A;ENSP00000298999:D535A	.	D	+	2	0	C10orf28	99959465	0.992000	0.36948	0.987000	0.45799	0.581000	0.36288	0.319000	0.19522	-0.020000	0.14032	-0.501000	0.04562	GAC	A|0.813;C|0.187	0.187	strong		0.438	R3HCC1L-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049764.1	NM_014472	
ITGA11	22801	hgsc.bcm.edu	37	15	68649587	68649587	+	Silent	SNP	G	G	A	rs12907890	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:68649587G>A	ENST00000315757.7	-	7	737	c.651C>T	c.(649-651)aaC>aaT	p.N217N	ITGA11_ENST00000562826.1_5'UTR|ITGA11_ENST00000423218.2_Silent_p.N217N	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	217	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						ACCTGTAGTCGTTGAGGTGAA	0.512													A|||	4396	0.877796	0.913	0.8357	5008	,	,		17353	1.0		0.7475	False		,,,				2504	0.8681				p.N217N		Atlas-SNP	.											.	ITGA11	110	.	0			c.C651T						PASS	.	A		3542,546		1533,476,35	89.0	90.0	90.0		651	1.3	1.0	15	dbSNP_121	90	6314,2056		2374,1566,245	no	coding-synonymous	ITGA11	NM_001004439.1		3907,2042,280	AA,AG,GG		24.5639,13.3562,20.8862		217/1189	68649587	9856,2602	2044	4185	6229	SO:0001819	synonymous_variant	22801	exon7			GTAGTCGTTGAGG	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.651C>T	15.37:g.68649587G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	45	15	0.333333	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.148;A|0.852	0.852	strong		0.512	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
XIRP2	129446	hgsc.bcm.edu	37	2	168115325	168115325	+	Missense_Mutation	SNP	A	A	G	rs3749005	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:168115325A>G	ENST00000409728.1	+	11	2457	c.2368A>G	c.(2368-2370)Aga>Gga	p.R790G	XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409605.1_Missense_Mutation_p.R535G|XIRP2_ENST00000420519.1_Missense_Mutation_p.R790G|XIRP2_ENST00000409756.2_Missense_Mutation_p.R757G|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409043.1_Missense_Mutation_p.R757G	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAATACATCTAGAATCTCAGA	0.358													A|||	400	0.0798722	0.0787	0.0735	5008	,	,		18335	0.1111		0.0408	False		,,,				2504	0.0941				p.R790G		Atlas-SNP	.											.	XIRP2	914	.	0			c.A2368G						PASS	.	A	GLY/ARG,GLY/ARG,,GLY/ARG,	282,3390		11,260,1565	44.0	44.0	44.0		2269,2368,,1603,	5.7	1.0	2	dbSNP_107	44	350,7802		8,334,3734	yes	missense,missense,utr-3,missense,utr-3	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	125,125,,125,	19,594,5299	GG,GA,AA		4.2934,7.6797,5.3451	,,,,	757/939,790/972,,535/717,	168115325	632,11192	1836	4076	5912	SO:0001583	missense	129446	exon11			ACATCTAGAATCT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2368A>G	2.37:g.168115325A>G	ENSP00000386619:p.Arg790Gly	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	168	0.07692307692307693	37	0.07520325203252033	30	0.08287292817679558	69	0.12062937062937062	32	0.04221635883905013	A	6.461	0.453253	0.12283	0.076797	0.042934	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.79554	-1.27;-1.27;-1.27;-1.27;-1.28	5.67	5.67	0.87782	.	.	.	.	.	T	0.02230	0.0069	.	.	.	0.09310	P	0.9999999999998913	B;B	0.26081	0.141;0.141	B;B	0.26770	0.073;0.073	T	0.45848	-0.9233	7	0.25751	T	0.34	.	7.9518	0.30019	0.9048:0.0:0.0952:0.0	rs3749005;rs52833883;rs61286377;rs3749005	757;790	A4UGR9-4;A4UGR9-6	.;.	G	757;790;757;790;535	ENSP00000386454:R757G;ENSP00000386619:R790G;ENSP00000386724:R757G;ENSP00000415541:R790G;ENSP00000386981:R535G	ENSP00000386454:R757G	R	+	1	2	XIRP2	167823571	1.000000	0.71417	0.958000	0.39756	0.360000	0.29518	3.270000	0.51600	2.165000	0.68154	0.459000	0.35465	AGA	A|0.928;G|0.072	0.072	strong		0.358	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
NUP88	4927	hgsc.bcm.edu	37	17	5326089	5326089	+	5'Flank	SNP	C	C	T	rs1071648	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5326089C>T	ENST00000573584.1	-	0	0				RPAIN_ENST00000381208.5_Splice_Site_p.L85L|RPAIN_ENST00000536255.2_Splice_Site_p.L85L|RPAIN_ENST00000405578.4_Splice_Site_p.L85L|RPAIN_ENST00000381209.3_Splice_Site_p.L85L|RPAIN_ENST00000327154.6_Splice_Site_p.L85L|CTC-524C5.2_ENST00000575890.1_RNA|RPAIN_ENST00000574003.1_Splice_Site_p.L85L	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						TCTCTTCCAGCTGGAGGAGCT	0.473													T|||	2233	0.445887	0.1899	0.4193	5008	,	,		20883	0.7937		0.3052	False		,,,				2504	0.5971				p.L85L		Atlas-SNP	.											.	RPAIN	24	.	0			c.C253T						PASS	.	T	,,,,,	966,3440	734.1+/-410.5	87,792,1324	110.0	102.0	104.0		253,253,253,253,253,253	3.3	1.0	17	dbSNP_86	104	2362,6238	701.7+/-405.2	300,1762,2238	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	RPAIN	NM_001033002.3,NM_001160243.1,NM_001160244.1,NM_001160246.1,NM_001160266.1,NM_001160267.1	,,,,,	387,2554,3562	TT,TC,CC		27.4651,21.9246,25.5882	,,,,,	85/220,85/232,85/173,85/107,85/149,85/107	5326089	3328,9678	2203	4300	6503	SO:0001631	upstream_gene_variant	84268	exon3			TTCCAGCTGGAGG	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453		17.37:g.5326089C>T	Exception_encountered	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	158	63	0.398734	NM_001160246	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			C|0.689;T|0.311	0.311	strong		0.473	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
DMP1	1758	hgsc.bcm.edu	37	4	88583135	88583135	+	Missense_Mutation	SNP	A	A	T	rs10019009	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88583135A>T	ENST00000339673.6	+	6	304	c.205A>T	c.(205-207)Agc>Tgc	p.S69C	RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA|DMP1_ENST00000282479.7_Missense_Mutation_p.S53C|RP11-742B18.1_ENST00000506480.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	69			S -> C (in dbSNP:rs10019009). {ECO:0000269|PubMed:17033625, ECO:0000269|Ref.2}.		biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		CCCCAGTGACAGCACTCAGTC	0.463													A|||	1447	0.288938	0.2625	0.3285	5008	,	,		18623	0.4256		0.2326	False		,,,				2504	0.2137				p.S69C		Atlas-SNP	.											.	DMP1	72	.	0			c.A205T						PASS	.	A	CYS/SER,CYS/SER	1302,3104	439.4+/-345.7	180,942,1081	54.0	57.0	56.0		157,205	4.1	1.0	4	dbSNP_119	56	2289,6311	386.9+/-342.0	285,1719,2296	yes	missense,missense	DMP1	NM_001079911.2,NM_004407.3	112,112	465,2661,3377	TT,TA,AA		26.6163,29.5506,27.6103	possibly-damaging,possibly-damaging	53/498,69/514	88583135	3591,9415	2203	4300	6503	SO:0001583	missense	1758	exon6			AGTGACAGCACTC	U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"""dentin matrix acidic phosphoprotein"""			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.205A>T	4.37:g.88583135A>T	ENSP00000340935:p.Ser69Cys	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	168	79	0.470238	NM_004407	A1L4L3|O43265	Missense_Mutation	SNP	ENST00000339673.6	37	CCDS3623.1	679	0.3108974358974359	132	0.2682926829268293	126	0.34806629834254144	238	0.4160839160839161	183	0.24142480211081793	A	13.09	2.132536	0.37630	0.295506	0.266163	ENSG00000152592	ENST00000339673;ENST00000282479	T;T	0.57907	0.37;0.37	5.37	4.14	0.48551	.	0.083812	0.51477	D	0.000086	T	0.00012	0.0000	L	0.54323	1.7	0.36906	P	0.10935499999999998	D;D	0.89917	1.0;1.0	D;D	0.69824	0.943;0.966	T	0.41378	-0.9512	9	0.87932	D	0	-13.8218	9.4666	0.38817	0.8231:0.1769:0.0:0.0	rs10019009;rs10019009	53;69	Q13316-2;Q13316	.;DMP1_HUMAN	C	69;53	ENSP00000340935:S69C;ENSP00000282479:S53C	ENSP00000282479:S53C	S	+	1	0	DMP1	88802159	0.716000	0.27956	0.954000	0.39281	0.027000	0.11550	2.418000	0.44662	2.045000	0.60652	0.454000	0.30748	AGC	A|0.719;T|0.281	0.281	strong		0.463	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1		
UBD	10537	hgsc.bcm.edu	37	6	29523957	29523957	+	Silent	SNP	A	A	G	rs404240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29523957A>G	ENST00000377050.4	-	2	421	c.198T>C	c.(196-198)taT>taC	p.Y66Y	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	66	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.				aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TGTCAATGCCATAAGATGAGA	0.498													A|||	90	0.0179712	0.0023	0.0187	5008	,	,		21228	0.0		0.0736	False		,,,				2504	0.0				p.Y66Y		Atlas-SNP	.											.	UBD	13	.	0			c.T198C						PASS	.	A		61,2961		0,61,1450	62.0	62.0	62.0		198	-3.2	0.3	6	dbSNP_80	62	501,4917		26,449,2234	no	coding-synonymous	UBD	NM_006398.3		26,510,3684	GG,GA,AA		9.247,2.0185,6.6588		66/166	29523957	562,7878	1511	2709	4220	SO:0001819	synonymous_variant	10537	exon2			AATGCCATAAGAT	Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.198T>C	6.37:g.29523957A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	158	129	0.816456	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Silent	SNP	ENST00000377050.4	37	CCDS4662.1																																																																																			A|0.947;G|0.053	0.053	strong		0.498	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3		
MT-ND2	4536	hgsc.bcm.edu	37	M	5442	5442	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrM:5442T>C	ENST00000361453.3	+	1	973	c.973T>C	c.(973-975)Ttc>Ctc	p.F325L	MT-TK_ENST00000387421.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TM_ENST00000387377.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TL1_ENST00000386347.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-TW_ENST00000387382.1_RNA|MT-TQ_ENST00000387372.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2	325			F -> L. {ECO:0000269|PubMed:7530363}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|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)|lung(1)	3						AACCCACCCCATTCCTCCCCA	0.403																																					p.F325L		Atlas-SNP	.											.	.	.	.	0			c.T973C						PASS	.																																			SO:0001583	missense	0	exon1			ACCCCATTCCTCC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891		ENST00000361453.3:c.973T>C	M.37:g.5442T>C	ENSP00000355046:p.Phe325Leu	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	ENST00000361453	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	Missense_Mutation	SNP	ENST00000361453.3	37																																																																																				.	.	none		0.403	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024027	
KLK3	354	hgsc.bcm.edu	37	19	51362803	51362803	+	Intron	SNP	C	C	T	rs35192866	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51362803C>T	ENST00000326003.2	+	5	671				KLK3_ENST00000595952.1_Intron|KLK3_ENST00000360617.3_Silent_p.T216T|KLK3_ENST00000597483.1_Silent_p.T173T	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3						cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		TTCTGATCACCGAACTGACCA	0.612													c|||	359	0.0716853	0.0893	0.0807	5008	,	,		17561	0.0665		0.0944	False		,,,				2504	0.0235				p.T216T	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.C648T						PASS	.	T	,,	379,4027	191.6+/-217.2	19,341,1843	117.0	94.0	102.0		648,,	-3.3	0.0	19	dbSNP_126	102	743,7857	178.5+/-227.8	28,687,3585	no	coding-synonymous,intron,intron	KLK3	NM_001030047.1,NM_001030048.1,NM_001648.2	,,	47,1028,5428	TT,TC,CC		8.6395,8.6019,8.6268	,,	216/239,,	51362803	1122,11884	2203	4300	6503	SO:0001627	intron_variant	354	exon5			GATCACCGAACTG	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.631-425C>T	19.37:g.51362803C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_001030047	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			C|0.912;T|0.088	0.088	strong		0.612	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
P2RY2	5029	hgsc.bcm.edu	37	11	72946140	72946140	+	Missense_Mutation	SNP	G	G	C	rs3741156	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:72946140G>C	ENST00000311131.2	+	3	1403	c.936G>C	c.(934-936)agG>agC	p.R312S	P2RY2_ENST00000393596.2_Missense_Mutation_p.R312S|P2RY2_ENST00000393597.2_Missense_Mutation_p.R312S	NM_002564.2|NM_176072.1	NP_002555|NP_788086	P41231	P2RY2_HUMAN	purinergic receptor P2Y, G-protein coupled, 2	312			R -> S (in dbSNP:rs3741156). {ECO:0000269|PubMed:15489334}.		cellular ion homeostasis (GO:0006873)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of mucus secretion (GO:0070257)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25					Suramin(DB04786)	CTGGGCAGAGGCTCGTACGCT	0.647													G|||	1364	0.272364	0.0121	0.4107	5008	,	,		17319	0.5397		0.2266	False		,,,				2504	0.2975				p.R312S		Atlas-SNP	.											.	P2RY2	54	.	0			c.G936C						PASS	.	G	SER/ARG,SER/ARG,SER/ARG	261,4139	143.5+/-178.5	3,255,1942	64.0	54.0	57.0		936,936,936	2.2	1.0	11	dbSNP_107	57	2036,6550	346.9+/-326.4	248,1540,2505	yes	missense,missense,missense	P2RY2	NM_002564.2,NM_176071.1,NM_176072.1	110,110,110	251,1795,4447	CC,CG,GG		23.713,5.9318,17.6883	benign,benign,benign	312/378,312/378,312/378	72946140	2297,10689	2200	4293	6493	SO:0001583	missense	5029	exon3			GCAGAGGCTCGTA	U07225	CCDS8219.1	11q13.5-q14.1	2012-08-08				ENSG00000175591		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8541	protein-coding gene	gene with protein product		600041				8159738, 9286708	Standard	NM_002564		Approved	P2U	uc001otj.4	P41231		ENST00000311131.2:c.936G>C	11.37:g.72946140G>C	ENSP00000310305:p.Arg312Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	45	6	0.133333	NM_176071	B2R9W3|Q96EM8	Missense_Mutation	SNP	ENST00000311131.2	37	CCDS8219.1	625	0.28617216117216115	6	0.012195121951219513	132	0.36464088397790057	312	0.5454545454545454	175	0.23087071240105542	G	5.105	0.205055	0.09704	0.059318	0.23713	ENSG00000175591	ENST00000393597;ENST00000311131;ENST00000393596	T;T;T	0.27720	1.65;1.65;1.65	4.09	2.16	0.27623	.	0.464574	0.23797	N	0.044477	T	0.00012	0.0000	N	0.21448	0.665	0.34061	P	0.34272100000000005	B	0.15930	0.015	B	0.12837	0.008	T	0.46289	-0.9202	9	0.15066	T	0.55	.	6.0799	0.19935	0.3699:0.0:0.6301:0.0	rs3741156;rs17850859	312	P41231	P2RY2_HUMAN	S	312	ENSP00000377222:R312S;ENSP00000310305:R312S;ENSP00000377221:R312S	ENSP00000310305:R312S	R	+	3	2	P2RY2	72623788	1.000000	0.71417	0.983000	0.44433	0.022000	0.10575	1.609000	0.36858	0.305000	0.22832	-0.254000	0.11334	AGG	C|0.211;G|0.789	0.211	strong		0.647	P2RY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397336.1	NM_176072	
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 GAIIx	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	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	32	16	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	
CYP4A22	284541	hgsc.bcm.edu	37	1	47608983	47608983	+	Missense_Mutation	SNP	G	G	T	rs113777592	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47608983G>T	ENST00000371891.3	+	5	584	c.553G>T	c.(553-555)Gtc>Ttc	p.V185F	CYP4A22_ENST00000294337.3_Missense_Mutation_p.V185F|CYP4A22_ENST00000371890.3_Missense_Mutation_p.V185F|CYP4A22-AS1_ENST00000444042.2_lincRNA|CYP4A22_ENST00000485117.1_3'UTR	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	185			V -> F (in allele CYP4A22*10, allele CYP4A22*11, allele CYP4A22*12, allele CYP4A22*13, allele CYP4A22*14 and allele CYP4A22*15; dbSNP:rs113777592). {ECO:0000269|PubMed:16806293}.			endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCCTCTGGAGGTCTTTCAGCA	0.542													G|||	1681	0.335663	0.2057	0.232	5008	,	,		19651	0.5536		0.1928	False		,,,				2504	0.5072				p.V185F	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											CYP4A22,colon,carcinoma,-2,1	CYP4A22	60	1	0			c.G553T						PASS	.	G	PHE/VAL	1006,3400	372.0+/-320.2	107,792,1304	70.0	64.0	66.0		553	-1.9	0.0	1	dbSNP_132	66	1731,6865	315.9+/-312.5	184,1363,2751	no	missense	CYP4A22	NM_001010969.2	50	291,2155,4055	TT,TG,GG		20.1373,22.8325,21.0506	possibly-damaging	185/520	47608983	2737,10265	2203	4298	6501	SO:0001583	missense	284541	exon5			CTGGAGGTCTTTC		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.553G>T	1.37:g.47608983G>T	ENSP00000360958:p.Val185Phe	Somatic	489	0	0		WXS	Illumina HiSeq	Phase_I	516	209	0.405039	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	613	0.2806776556776557	95	0.19308943089430894	83	0.2292817679558011	298	0.5209790209790209	137	0.18073878627968337	g	12.99	2.104200	0.37145	0.228325	0.201373	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.70516	-0.45;-0.49;-0.49	1.44	-1.89	0.07689	.	0.621999	0.16471	N	0.212985	T	0.00012	0.0000	M	0.63843	1.955	0.45567	P	0.0014880000000000448	P;P	0.46064	0.846;0.872	B;P	0.49597	0.264;0.616	T	0.37478	-0.9704	9	0.62326	D	0.03	.	5.0373	0.14441	0.5021:0.2748:0.2231:0.0	.	185;185	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	F	185	ENSP00000360957:V185F;ENSP00000360958:V185F;ENSP00000294337:V185F	ENSP00000294337:V185F	V	+	1	0	CYP4A22	47381570	0.001000	0.12720	0.002000	0.10522	0.478000	0.33099	-1.183000	0.03079	-0.551000	0.06175	0.194000	0.17425	GTC	G|0.849;T|0.151	0.151	strong		0.542	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
SAMD9	54809	hgsc.bcm.edu	37	7	92733766	92733766	+	Missense_Mutation	SNP	C	C	A	rs10279499	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92733766C>A	ENST00000379958.2	-	3	1914	c.1645G>T	c.(1645-1647)Gtg>Ttg	p.V549L		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	549			V -> L (in dbSNP:rs10279499).			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			GGGTCATCCACAGAGGACAGT	0.403													C|||	485	0.096845	0.1195	0.0994	5008	,	,		19903	0.1359		0.0974	False		,,,				2504	0.0235				p.V549L		Atlas-SNP	.											.	SAMD9	239	.	0			c.G1645T						PASS	.	C	LEU/VAL,LEU/VAL	581,3825	245.6+/-254.5	41,499,1663	87.0	90.0	89.0		1645,1645	3.4	0.5	7	dbSNP_119	89	879,7719	194.8+/-240.1	50,779,3470	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	32,32	91,1278,5133	AA,AC,CC		10.2233,13.1866,11.2273	possibly-damaging,possibly-damaging	549/1590,549/1590	92733766	1460,11544	2203	4299	6502	SO:0001583	missense	54809	exon2			CATCCACAGAGGA	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1645G>T	7.37:g.92733766C>A	ENSP00000369292:p.Val549Leu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	256	0.11721611721611722	55	0.11178861788617886	38	0.10497237569060773	94	0.16433566433566432	69	0.09102902374670185	C	9.680	1.148940	0.21288	0.131866	0.102233	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.17213	2.29;2.29	4.25	3.37	0.38596	.	0.000000	0.51477	U	0.000083	T	0.00109	0.0003	M	0.76002	2.32	0.30847	P	0.7349859999999999	D	0.58268	0.982	P	0.45660	0.489	T	0.11518	-1.0584	9	0.72032	D	0.01	.	11.0892	0.48106	0.0:0.9068:0.0:0.0932	rs10279499;rs10279499	549	Q5K651	SAMD9_HUMAN	L	549	ENSP00000369292:V549L;ENSP00000414529:V549L	ENSP00000369292:V549L	V	-	1	0	SAMD9	92571702	0.999000	0.42202	0.539000	0.28077	0.069000	0.16628	3.695000	0.54749	1.147000	0.42369	0.603000	0.83216	GTG	C|0.882;A|0.118	0.118	strong		0.403	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
IL17RA	23765	hgsc.bcm.edu	37	22	17589209	17589209	+	Missense_Mutation	SNP	C	C	T	rs879577	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:17589209C>T	ENST00000319363.6	+	13	1233	c.1100C>T	c.(1099-1101)gCg>gTg	p.A367V		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	367			A -> V (in dbSNP:rs879577). {ECO:0000269|PubMed:15489334}.		cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)	p.A367V(1)		endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		GGCCTGCCTGCGGCTGACCTG	0.642													C|||	1360	0.271565	0.4682	0.2767	5008	,	,		16084	0.0942		0.2624	False		,,,				2504	0.1943				p.A367V		Atlas-SNP	.											IL17RA,NS,carcinoma,0,1	IL17RA	62	1	1	Substitution - Missense(1)	stomach(1)	c.C1100T						PASS	.	C	VAL/ALA	1884,2520	541.6+/-375.8	412,1060,730	57.0	60.0	59.0		1100	-1.4	0.0	22	dbSNP_86	59	2115,6485	363.2+/-333.1	275,1565,2460	yes	missense	IL17RA	NM_014339.5	64	687,2625,3190	TT,TC,CC		24.593,42.7793,30.7521	benign	367/867	17589209	3999,9005	2202	4300	6502	SO:0001583	missense	23765	exon13			TGCCTGCGGCTGA	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"""Interleukins and interleukin receptors"", ""CD molecules"""	5985	protein-coding gene	gene with protein product		605461	"""interleukin 17 receptor"""	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1100C>T	22.37:g.17589209C>T	ENSP00000320936:p.Ala367Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	107	105	0.981308	NM_014339	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	37	CCDS13739.1	590	0.27014652014652013	243	0.49390243902439024	98	0.27071823204419887	51	0.08916083916083917	198	0.2612137203166227	C	8.859	0.946477	0.18356	0.427793	0.24593	ENSG00000177663	ENST00000425985;ENST00000319363	T	0.05925	3.37	5.06	-1.44	0.08856	.	2.983420	0.00892	N	0.002247	T	0.00012	0.0000	L	0.31294	0.92	0.80722	P	0.0	B;B	0.21688	0.059;0.026	B;B	0.08055	0.003;0.003	T	0.47573	-0.9107	9	0.27082	T	0.32	0.9002	0.6191	0.00775	0.1809:0.2631:0.1607:0.3952	rs879577;rs2228076;rs17856361;rs59969560;rs879577	315;367	D3YTB4;Q96F46	.;I17RA_HUMAN	V	315;367	ENSP00000320936:A367V	ENSP00000320936:A367V	A	+	2	0	IL17RA	15969209	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-2.423000	0.01030	-0.308000	0.08792	-0.234000	0.12200	GCG	C|0.709;T|0.291	0.291	strong		0.642	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339	
CTSH	1512	hgsc.bcm.edu	37	15	79224747	79224747	+	Silent	SNP	C	C	T	rs13345	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:79224747C>T	ENST00000220166.5	-	6	568	c.459G>A	c.(457-459)gcG>gcA	p.A153A	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	153					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						CGATGGCGATCGCAGACTCCA	0.637													C|||	1517	0.302915	0.5166	0.2219	5008	,	,		17877	0.3214		0.1909	False		,,,				2504	0.1677				p.A153A		Atlas-SNP	.											CTSH,NS,carcinoma,0,1	CTSH	23	1	0			c.G459A						PASS	.	C		1976,2416	557.6+/-379.8	458,1060,678	70.0	71.0	71.0		459	-9.4	0.0	15	dbSNP_52	71	1635,6951	303.4+/-306.4	157,1321,2815	no	coding-synonymous	CTSH	NM_004390.3		615,2381,3493	TT,TC,CC		19.0426,44.9909,27.824		153/336	79224747	3611,9367	2196	4293	6489	SO:0001819	synonymous_variant	1512	exon6			GGCGATCGCAGAC	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.459G>A	15.37:g.79224747C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Silent	SNP	ENST00000220166.5	37	CCDS10308.1																																																																																			C|0.720;T|0.280	0.280	strong		0.637	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
TCP10L	140290	hgsc.bcm.edu	37	21	33951068	33951068	+	Missense_Mutation	SNP	T	T	C	rs9622	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:33951068T>C	ENST00000300258.3	-	4	547	c.434A>G	c.(433-435)cAc>cGc	p.H145R	TCP10L_ENST00000472557.1_Missense_Mutation_p.H59R|LINC00846_ENST00000334165.4_lincRNA	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	145			H -> R (in dbSNP:rs9622). {ECO:0000269|PubMed:10830953, ECO:0000269|Ref.3}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						CTGATTCTTGTGGCCAGCGTA	0.433													C|||	1093	0.218251	0.2012	0.2133	5008	,	,		18820	0.2599		0.1928	False		,,,				2504	0.228				p.H145R		Atlas-SNP	.											.	TCP10L	24	.	0			c.A434G						PASS	.	C	ARG/HIS	886,3520	741.7+/-411.3	79,728,1396	179.0	154.0	163.0		434	0.5	0.0	21	dbSNP_52	163	1564,7036	745.3+/-407.3	142,1280,2878	yes	missense	TCP10L	NM_144659.5	29	221,2008,4274	CC,CT,TT		18.186,20.1089,18.8375		145/216	33951068	2450,10556	2203	4300	6503	SO:0001583	missense	140290	exon4			TTCTTGTGGCCAG	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"""t-complex 10 (a murine tcp homolog)-like"", ""t-complex 10 (mouse)-like"""			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.434A>G	21.37:g.33951068T>C	ENSP00000300258:p.His145Arg	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	350	233	0.665714	NM_144659	Q53EW0|Q96LN5	Missense_Mutation	SNP	ENST00000300258.3	37	CCDS13616.1	484	0.2216117216117216	97	0.19715447154471544	76	0.20994475138121546	159	0.27797202797202797	152	0.20052770448548812	C	1.066	-0.671530	0.03403	0.201089	0.18186	ENSG00000242220	ENST00000300258	T	0.22743	1.94	0.459	0.459	0.16678	.	.	.	.	.	T	0.00012	0.0000	N	0.01188	-0.97	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	7	0.02654	T	1	.	.	.	.	rs9622;rs2246107;rs6517105;rs17353914;rs9622	145	Q8TDR4	TCP1L_HUMAN	R	145	ENSP00000300258:H145R	ENSP00000300258:H145R	H	-	2	0	TCP10L	32872939	0.037000	0.19845	0.010000	0.14722	0.046000	0.14306	-0.931000	0.03967	-0.405000	0.07599	-1.063000	0.02288	CAC	T|0.791;C|0.209	0.209	strong		0.433	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659	
KIAA1551	55196	hgsc.bcm.edu	37	12	32135938	32135938	+	Silent	SNP	A	A	G	rs11051718	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:32135938A>G	ENST00000312561.4	+	4	2463	c.2049A>G	c.(2047-2049)caA>caG	p.Q683Q	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	683																	GGAAAAAGCAACCTTCAGATA	0.428													A|||	260	0.0519169	0.0371	0.0893	5008	,	,		21768	0.0149		0.0984	False		,,,				2504	0.0358				p.Q683Q		Atlas-SNP	.											.	.	.	.	0			c.A2049G						PASS	.	A		224,4182	133.7+/-170.0	5,214,1984	63.0	58.0	60.0		2049	-3.3	0.0	12	dbSNP_120	60	1025,7573	219.4+/-257.5	55,915,3329	no	coding-synonymous	C12orf35	NM_018169.3		60,1129,5313	GG,GA,AA		11.9214,5.084,9.6047		683/1748	32135938	1249,11755	2203	4299	6502	SO:0001819	synonymous_variant	55196	exon4			AAAGCAACCTTCA	AK001514	CCDS8725.2	12p11.21	2012-08-14	2012-08-14	2012-08-14	ENSG00000174718	ENSG00000174718			25559	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 35"""	C12orf35		10997877	Standard	NM_018169		Approved	FLJ20696, FLJ10652	uc001rks.3	Q9HCM1	OTTHUMG00000128501	ENST00000312561.4:c.2049A>G	12.37:g.32135938A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Silent	SNP	ENST00000312561.4	37	CCDS8725.2																																																																																			A|0.920;G|0.080	0.080	strong		0.428	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
CCDC63	160762	hgsc.bcm.edu	37	12	111342558	111342558	+	Silent	SNP	G	G	T	rs34300256	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:111342558G>T	ENST00000308208.5	+	11	1751	c.1509G>T	c.(1507-1509)gtG>gtT	p.V503V	CCDC63_ENST00000545036.1_Silent_p.V463V|CCDC63_ENST00000552694.1_Silent_p.V424V	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	503										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						TCCCCCCAGTGCTGGGGGCTG	0.592													G|||	758	0.151358	0.1271	0.3516	5008	,	,		19331	0.002		0.2555	False		,,,				2504	0.089				p.V503V		Atlas-SNP	.											.	CCDC63	89	.	0			c.G1509T						PASS	.	G		640,3766	269.2+/-268.9	49,542,1612	58.0	58.0	58.0		1509	-0.4	0.0	12	dbSNP_126	58	2108,6492	352.9+/-328.9	260,1588,2452	no	coding-synonymous	CCDC63	NM_152591.1		309,2130,4064	TT,TG,GG		24.5116,14.5256,21.1287		503/564	111342558	2748,10258	2203	4300	6503	SO:0001819	synonymous_variant	160762	exon11			CCCAGTGCTGGGG	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"""outer row dynein assembly 5 homolog (Chlamydomonas)"""						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1509G>T	12.37:g.111342558G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_152591	B4DY03|Q0P603|Q6P2E1	Silent	SNP	ENST00000308208.5	37	CCDS9151.1																																																																																			G|0.810;T|0.190	0.190	strong		0.592	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591	
MUC4	4585	hgsc.bcm.edu	37	3	195515304	195515304	+	Silent	SNP	T	T	A	rs202019266		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195515304T>A	ENST00000463781.3	-	2	3606	c.3147A>T	c.(3145-3147)gcA>gcT	p.A1049A	MUC4_ENST00000475231.1_Silent_p.A1049A|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	479					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.A1049A(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)		CACCTGTGGATGCTGAGGAAA	0.562																																					p.A1049A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - coding silent(2)	kidney(1)|endometrium(1)	c.A3147T						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			TGTGGATGCTGAG	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.3147A>T	3.37:g.195515304T>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	45	2	0.0444444	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																																																																																			.	.	weak		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TMEM60	85025	hgsc.bcm.edu	37	7	77423574	77423574	+	Silent	SNP	G	G	A	rs7953	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:77423574G>A	ENST00000257663.3	-	2	493	c.117C>T	c.(115-117)ttC>ttT	p.F39F		NM_032936.3	NP_116325.1	Q9H2L4	TMM60_HUMAN	transmembrane protein 60	39						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)	4						AGACTGGAATGAATATGAGGA	0.448													A|||	2838	0.566693	0.8646	0.4424	5008	,	,		20016	0.3165		0.508	False		,,,				2504	0.5706				p.F39F		Atlas-SNP	.											.	TMEM60	24	.	0			c.C117T						PASS	.	A		3494,912	348.2+/-309.8	1386,722,95	76.0	76.0	76.0		117	3.8	1.0	7	dbSNP_52	76	4227,4373	583.0+/-391.5	1081,2065,1154	no	coding-synonymous	TMEM60	NM_032936.3		2467,2787,1249	AA,AG,GG		49.1512,20.699,40.6351		39/134	77423574	7721,5285	2203	4300	6503	SO:0001819	synonymous_variant	85025	exon2			TGGAATGAATATG	AF260336	CCDS5593.1	7q11.23	2005-07-25	2005-07-25	2005-07-25	ENSG00000135211	ENSG00000135211			21754	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 35"""	C7orf35			Standard	NM_032936		Approved	DC32	uc003ugn.3	Q9H2L4	OTTHUMG00000130689	ENST00000257663.3:c.117C>T	7.37:g.77423574G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_032936	A4D1C3|Q86UM0	Silent	SNP	ENST00000257663.3	37	CCDS5593.1																																																																																			G|0.424;A|0.576	0.576	strong		0.448	TMEM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253185.2	NM_032936	
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 GAIIx	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*	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	53	4	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		
LILRB1	10859	hgsc.bcm.edu	37	19	55148031	55148031	+	Silent	SNP	T	T	C	rs41308746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55148031T>C	ENST00000396331.1	+	15	2091	c.1734T>C	c.(1732-1734)ccT>ccC	p.P578P	LILRB1_ENST00000396315.1_Silent_p.P580P|LILRB1_ENST00000396332.4_Silent_p.P579P|LILRB1_ENST00000324602.7_Silent_p.P580P|LILRB1_ENST00000418536.2_Silent_p.P562P|LILRB1_ENST00000427581.2_Silent_p.P629P|LILRB1_ENST00000448689.1_3'UTR|AC009892.10_ENST00000456337.1_Intron|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000396321.2_Silent_p.P578P|LILRB1_ENST00000396327.3_Silent_p.P579P|LILRB1_ENST00000396317.1_Silent_p.P562P|LILRB1_ENST00000434867.2_Silent_p.P578P	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	578					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CCTCTCCTCCTTCCCCACTGT	0.582										HNSCC(37;0.09)			t|||	554	0.110623	0.1785	0.0893	5008	,	,		16680	0.0139		0.1491	False		,,,				2504	0.0941				p.P580P		Atlas-SNP	.											LILRB1,NS,carcinoma,+2,1	LILRB1	140	1	0			c.T1740C						scavenged	.						111.0	95.0	100.0					19																	55148031		2200	4295	6495	SO:0001819	synonymous_variant	10859	exon14			TCCTCCTTCCCCA	AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1734T>C	19.37:g.55148031T>C		Somatic	247	2	0.00809717		WXS	Illumina HiSeq	Phase_I	154	28	0.181818	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			.	.	weak		0.582	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
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 GAIIx	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	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	60	20	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 GAIIx	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_ENST00000368601.1_Missense_Mutation_p.S152A|CREB3L4_ENST00000368603.1_Missense_Mutation_p.S152A|CREB3L4_ENST00000271889.4_Missense_Mutation_p.S152A|SLC39A1_ENST00000310483.6_5'Flank|RP11-422P24.10_ENST00000608147.1_RNA|CREB3L4_ENST00000405694.3_Missense_Mutation_p.S5A|CREB3L4_ENST00000368600.3_Missense_Mutation_p.S132A	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	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	119	62	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	
SMG5	23381	hgsc.bcm.edu	37	1	156233189	156233189	+	Silent	SNP	C	C	T	rs2273833	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156233189C>T	ENST00000361813.5	-	13	2172	c.2028G>A	c.(2026-2028)gcG>gcA	p.A676A	SMG5_ENST00000489907.2_5'Flank|SMG5_ENST00000368267.5_Intron	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	676					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					GACACACCTGCGCACACACGA	0.607													C|||	966	0.192891	0.0582	0.2666	5008	,	,		18271	0.2242		0.2644	False		,,,				2504	0.2168				p.A676A		Atlas-SNP	.											.	SMG5	98	.	0			c.G2028A						PASS	.	C		402,4004	201.8+/-224.7	19,364,1820	104.0	91.0	95.0		2028	-10.4	0.1	1	dbSNP_100	95	2463,6137	405.6+/-348.5	364,1735,2201	no	coding-synonymous	SMG5	NM_015327.2		383,2099,4021	TT,TC,CC		28.6395,9.1239,22.0283		676/1017	156233189	2865,10141	2203	4300	6503	SO:0001819	synonymous_variant	23381	exon13			CACCTGCGCACAC	AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog B (S. cerevisiae)"""	610962	"""smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"""			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.2028G>A	1.37:g.156233189C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	147	61	0.414966	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Silent	SNP	ENST00000361813.5	37	CCDS1137.1																																																																																			C|0.798;T|0.202	0.202	strong		0.607	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327	
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 GAIIx	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	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	210	105	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	
STXBP5L	9515	hgsc.bcm.edu	37	3	121100283	121100283	+	Missense_Mutation	SNP	G	G	A	rs17740066	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:121100283G>A	ENST00000273666.6	+	23	2834	c.2563G>A	c.(2563-2565)Gtt>Att	p.V855I	STXBP5L_ENST00000471454.1_Missense_Mutation_p.V831I|STXBP5L_ENST00000472879.1_Missense_Mutation_p.V831I|STXBP5L_ENST00000492541.1_Missense_Mutation_p.V855I|STXBP5L_ENST00000497029.1_Missense_Mutation_p.V829I	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	855			V -> I (in dbSNP:rs17740066).		exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V855F(1)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		TTGTCTGTTCGTTGGAACCAG	0.413													G|||	337	0.0672923	0.0091	0.147	5008	,	,		17412	0.0675		0.0984	False		,,,				2504	0.0573				p.V855I		Atlas-SNP	.											.	STXBP5L	159	.	1	Substitution - Missense(1)	lung(1)	c.G2563A						PASS	.	G	ILE/VAL	79,3713		1,77,1818	189.0	177.0	180.0		2563	5.1	1.0	3	dbSNP_123	180	890,7358		58,774,3292	yes	missense	STXBP5L	NM_014980.2	29	59,851,5110	AA,AG,GG		10.7905,2.0833,8.0482	benign	855/1187	121100283	969,11071	1896	4124	6020	SO:0001583	missense	9515	exon23			CTGTTCGTTGGAA	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"""WD repeat domain containing"""	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.2563G>A	3.37:g.121100283G>A	ENSP00000273666:p.Val855Ile	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_014980	Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	CCDS43137.1	154	0.07051282051282051	8	0.016260162601626018	49	0.13535911602209943	19	0.033216783216783216	78	0.10290237467018469	G	16.65	3.183023	0.57800	0.020833	0.107905	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37;1.37	5.1	5.1	0.69264	Lethal giant larvae (Lgl)-like, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00524	0.0017	L	0.60904	1.88	0.09310	P	0.99999639701	D;D	0.89917	0.958;1.0	P;D	0.81914	0.582;0.995	T	0.02781	-1.1111	9	0.27082	T	0.32	-8.4264	12.0804	0.53667	0.0781:0.0:0.9219:0.0	rs17740066;rs52790800;rs56442849;rs56887239;rs17740066	831;855	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	I	855;831;831;829;855;798	ENSP00000273666:V855I;ENSP00000420019:V831I;ENSP00000419627:V831I;ENSP00000420287:V829I;ENSP00000420666:V855I;ENSP00000420167:V798I	ENSP00000273666:V855I	V	+	1	0	STXBP5L	122582973	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.584000	0.82572	2.660000	0.90430	0.650000	0.86243	GTT	G|0.930;A|0.070	0.070	strong		0.413	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34803947	34803947	+	Silent	SNP	C	C	T	rs4259246	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:34803947C>T	ENST00000192788.5	+	8	1026	c.855C>T	c.(853-855)gcC>gcT	p.A285A	UHRF1BP1_ENST00000452449.2_Silent_p.A285A	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	285							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						CTCCACCAGCCCCCAGTGCCC	0.537													T|||	2311	0.461462	0.7723	0.3069	5008	,	,		19389	0.4633		0.335	False		,,,				2504	0.2791				p.A285A		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C855T						PASS	.	T		2664,1394		881,902,246	133.0	151.0	145.0		855	2.2	1.0	6	dbSNP_111	145	2867,5545		491,1885,1830	no	coding-synonymous	UHRF1BP1	NM_017754.3		1372,2787,2076	TT,TC,CC		34.0823,34.3519,44.3545		285/1441	34803947	5531,6939	2029	4206	6235	SO:0001819	synonymous_variant	54887	exon8			ACCAGCCCCCAGT	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.855C>T	6.37:g.34803947C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	41	5	0.121951	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	37	CCDS43455.1																																																																																			C|0.564;T|0.436	0.436	strong		0.537	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
HECTD1	25831	hgsc.bcm.edu	37	14	31598248	31598248	+	Silent	SNP	A	A	G	rs17097743	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:31598248A>G	ENST00000399332.1	-	25	4817	c.4329T>C	c.(4327-4329)tcT>tcC	p.S1443S	HECTD1_ENST00000553700.1_Silent_p.S1443S	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1443	Ser-rich.				neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTGCACTGGAAGATGACCCTA	0.453													A|||	616	0.123003	0.0106	0.1066	5008	,	,		22845	0.1806		0.1064	False		,,,				2504	0.2444				p.S1443S		Atlas-SNP	.											.	HECTD1	159	.	0			c.T4329C						PASS	.	A		138,3778		2,134,1822	144.0	130.0	134.0		4329	0.6	1.0	14	dbSNP_123	134	1041,7257		58,925,3166	no	coding-synonymous	HECTD1	NM_015382.2		60,1059,4988	GG,GA,AA		12.5452,3.524,9.6529		1443/2611	31598248	1179,11035	1958	4149	6107	SO:0001819	synonymous_variant	25831	exon25			ACTGGAAGATGAC	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.4329T>C	14.37:g.31598248A>G		Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	238	116	0.487395	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1																																																																																			A|0.888;G|0.112	0.112	strong		0.453	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
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 GAIIx	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		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	41	12	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	
RFC2	5982	hgsc.bcm.edu	37	7	73663362	73663362	+	Silent	SNP	T	T	C	rs1805395	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:73663362T>C	ENST00000055077.3	-	4	372	c.312A>G	c.(310-312)gaA>gaG	p.E104E	RFC2_ENST00000352131.3_Silent_p.E104E	NM_181471.1	NP_852136.1	P35250	RFC2_HUMAN	replication factor C (activator 1) 2, 40kDa	104					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)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(3)	8						AAGCATTGAGTTCCAACATGG	0.537													T|||	59	0.0117812	0.0	0.0216	5008	,	,		16046	0.0		0.0368	False		,,,				2504	0.0072				p.E104E		Atlas-SNP	.											.	RFC2	27	.	0			c.A312G						PASS	.	T	,	43,4363	43.8+/-77.6	0,43,2160	93.0	100.0	98.0		312,312	-5.7	0.9	7	dbSNP_98	98	405,8195	128.2+/-186.4	10,385,3905	no	coding-synonymous,coding-synonymous	RFC2	NM_002914.3,NM_181471.1	,	10,428,6065	CC,CT,TT		4.7093,0.9759,3.4446	,	104/321,104/355	73663362	448,12558	2203	4300	6503	SO:0001819	synonymous_variant	5982	exon4			ATTGAGTTCCAAC		CCDS5567.1, CCDS5568.1, CCDS75618.1	7q11.23	2010-04-21	2002-08-29		ENSG00000049541	ENSG00000049541		"""ATPases / AAA-type"""	9970	protein-coding gene	gene with protein product	"""activator 1"""	600404	"""replication factor C (activator 1) 2 (40kD)"""			1313560, 7774928	Standard	NM_181471		Approved	A1, RFC40	uc003uaj.3	P35250	OTTHUMG00000023239	ENST00000055077.3:c.312A>G	7.37:g.73663362T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	30	12	0.4	NM_181471	B5BU07|D3DXG3|P32846|Q9BU93	Silent	SNP	ENST00000055077.3	37	CCDS5568.1																																																																																			T|0.971;C|0.029	0.029	strong		0.537	RFC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252459.2	NM_181471	
REG3A	5068	hgsc.bcm.edu	37	2	79385786	79385786	+	Silent	SNP	T	T	C	rs76653007	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:79385786T>C	ENST00000409839.3	-	3	222	c.186A>G	c.(184-186)acA>acG	p.T62T	REG3A_ENST00000305165.2_Silent_p.T62T|REG3A_ENST00000393878.1_Silent_p.T62T|AC011754.1_ENST00000415201.1_RNA	NM_002580.2|NM_138937.2	NP_002571.1|NP_620354.1	Q06141	REG3A_HUMAN	regenerating islet-derived 3 alpha	62	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|cell proliferation (GO:0008283)|heterophilic cell-cell adhesion (GO:0007157)|multicellular organismal development (GO:0007275)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)			breast(2)|large_intestine(4)|lung(41)|prostate(2)|skin(1)	50						CATCTGCATCTGTCCAGGATT	0.552																																					p.T62T		Atlas-SNP	.											.	REG3A	76	.	0			c.A186G						PASS	.						129.0	118.0	122.0					2																	79385786		2203	4300	6503	SO:0001819	synonymous_variant	5068	exon2			TGCATCTGTCCAG	S51768	CCDS1965.1	2p12	2008-02-05	2005-02-11	2005-02-11	ENSG00000172016	ENSG00000172016			8601	protein-coding gene	gene with protein product		167805	"""pancreatitis-associated protein"""	PAP		8188210	Standard	NM_002580		Approved	HIP, REG-III, REG3, PBCGF, PAP1	uc002sof.2	Q06141	OTTHUMG00000130017	ENST00000409839.3:c.186A>G	2.37:g.79385786T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	91	11	0.120879	NM_138938		Silent	SNP	ENST00000409839.3	37	CCDS1965.1																																																																																			T|0.894;C|0.106	0.106	strong		0.552	REG3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252290.2	NM_002580	
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 GAIIx	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	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	103	27	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	
GPR82	27197	hgsc.bcm.edu	37	X	41587218	41587218	+	Silent	SNP	T	T	C	rs587783365|rs1023065	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:41587218T>C	ENST00000302548.4	+	3	1179	c.939T>C	c.(937-939)gaT>gaC	p.D313D	CASK_ENST00000378154.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378163.1_Intron	NM_080817.4	NP_543007.1	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	313						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	10						TTTTATTAGATAAAACATTCA	0.318													T|||	3266	0.865166	0.6641	0.6787	3775	,	,		12785	0.7411		0.5388	False		,,,				2504	0.6421				p.D313D		Atlas-SNP	.											.	GPR82	52	.	0			c.T939C						PASS	.	T	,,,	3322,508		1230,374,488,26,82	23.0	23.0	23.0		,,,939	1.7	1.0	X	dbSNP_86	23	5170,1533		1448,838,1436,136,423	no	intron,intron,intron,coding-synonymous	CASK,GPR82	NM_001126054.2,NM_001126055.2,NM_003688.3,NM_080817.4	,,,	2678,1212,1924,162,505	CC,CT,C,TT,T		22.8704,13.2637,19.3772	,,,	,,,313/337	41587218	8492,2041	2200	4281	6481	SO:0001819	synonymous_variant	27197	exon3			ATTAGATAAAACA	AF411111	CCDS14259.1	Xp11.4	2012-08-21			ENSG00000171657	ENSG00000171657		"""GPCR / Class A : Orphans"""	4533	protein-coding gene	gene with protein product		300748				11574155	Standard	NM_080817		Approved		uc004dft.3	Q96P67	OTTHUMG00000021373	ENST00000302548.4:c.939T>C	X.37:g.41587218T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_080817	Q5VT13	Silent	SNP	ENST00000302548.4	37	CCDS14259.1																																																																																			T|0.167;C|0.833	0.833	strong		0.318	GPR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056261.1	NM_080817	
AKR1C3	8644	hgsc.bcm.edu	37	10	5138607	5138607	+	Silent	SNP	G	G	A	rs7741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:5138607G>A	ENST00000380554.3	+	2	742	c.90G>A	c.(88-90)ccG>ccA	p.P30P	AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000605149.1_Silent_p.P7P|U8_ENST00000459536.1_RNA|AKR1C3_ENST00000470862.2_3'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	30					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	TCCAGGTTCCGAGAAGTAAAG	0.438													G|||	1083	0.216254	0.3381	0.196	5008	,	,		20326	0.0		0.3648	False		,,,				2504	0.136				p.P30P		Atlas-SNP	.											.	AKR1C3	21	.	0			c.G90A						PASS	.	G		1485,2921	475.7+/-357.4	246,993,964	72.0	68.0	69.0		90	-3.2	0.0	10	dbSNP_52	69	3041,5557	468.9+/-367.4	544,1953,1802	no	coding-synonymous	AKR1C3	NM_003739.4		790,2946,2766	AA,AG,GG		35.3687,33.704,34.8047		30/324	5138607	4526,8478	2203	4299	6502	SO:0001819	synonymous_variant	8644	exon2			GGTTCCGAGAAGT	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.90G>A	10.37:g.5138607G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Silent	SNP	ENST00000380554.3	37	CCDS7063.1																																																																																			G|0.710;A|0.290	0.290	strong		0.438	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
PARVG	64098	hgsc.bcm.edu	37	22	44586522	44586522	+	Silent	SNP	C	C	T	rs2272942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44586522C>T	ENST00000444313.3	+	7	964	c.480C>T	c.(478-480)gtC>gtT	p.V160V	PARVG_ENST00000422871.1_Silent_p.V160V|PARVG_ENST00000415224.1_Silent_p.V160V	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	160					actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				CAACCAACGTCCAGGTGGAGG	0.602													C|||	875	0.17472	0.0696	0.1758	5008	,	,		19312	0.12		0.3618	False		,,,				2504	0.18				p.V160V		Atlas-SNP	.											.	PARVG	41	.	0			c.C480T						PASS	.	C	,,	439,3967	212.8+/-232.6	24,391,1788	86.0	68.0	74.0		480,480,480	-0.3	0.4	22	dbSNP_100	74	2938,5662	457.4+/-364.3	501,1936,1863	no	coding-synonymous,coding-synonymous,coding-synonymous	PARVG	NM_001137605.1,NM_001137606.1,NM_022141.5	,,	525,2327,3651	TT,TC,CC		34.1628,9.9637,25.9649	,,	160/332,160/332,160/332	44586522	3377,9629	2203	4300	6503	SO:0001819	synonymous_variant	64098	exon7			CAACGTCCAGGTG	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"""Parvins"""	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.480C>T	22.37:g.44586522C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Silent	SNP	ENST00000444313.3	37	CCDS14057.1																																																																																			C|0.747;T|0.253	0.253	strong		0.602	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141	
ENTPD1	953	hgsc.bcm.edu	37	10	97599537	97599537	+	Silent	SNP	G	G	C	rs61731067	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:97599537G>C	ENST00000371205.4	+	3	517	c.234G>C	c.(232-234)gtG>gtC	p.V78V	ENTPD1_ENST00000371203.5_5'UTR|ENTPD1_ENST00000371207.3_Silent_p.V90V|ENTPD1_ENST00000543964.1_5'UTR|ENTPD1_ENST00000490659.1_3'UTR|ENTPD1_ENST00000539125.1_Intron|ENTPD1_ENST00000453258.2_Silent_p.V85V|RP11-429G19.3_ENST00000433113.1_RNA|ENTPD1-AS1_ENST00000416301.1_RNA			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	78					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)		CAGGCGTGGTGCATCAAGTAG	0.473													G|||	260	0.0519169	0.0234	0.0663	5008	,	,		9998	0.0407		0.0596	False		,,,				2504	0.0838				p.V90V		Atlas-SNP	.											.	ENTPD1	44	.	0			c.G270C						PASS	.	G	,,,,,,	154,4252	105.6+/-144.1	3,148,2052	166.0	154.0	158.0		255,270,234,,,,234	1.5	0.4	10	dbSNP_129	158	554,8046	151.6+/-206.3	21,512,3767	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-5,utr-5,intron,coding-synonymous	ENTPD1	NM_001098175.1,NM_001164178.1,NM_001164179.1,NM_001164181.1,NM_001164182.1,NM_001164183.1,NM_001776.5	,,,,,,	24,660,5819	CC,CG,GG		6.4419,3.4952,5.4436	,,,,,,	85/518,90/523,78/470,,,,78/511	97599537	708,12298	2203	4300	6503	SO:0001819	synonymous_variant	953	exon3			CGTGGTGCATCAA	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	ENST00000371205.4:c.234G>C	10.37:g.97599537G>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_001164178	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Silent	SNP	ENST00000371205.4	37	CCDS7444.1																																																																																			G|0.945;C|0.055	0.055	strong		0.473	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776	
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 GAIIx	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	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	53	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		
MYOF	26509	hgsc.bcm.edu	37	10	95107428	95107428	+	Missense_Mutation	SNP	G	G	A	rs11187393	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:95107428G>A	ENST00000359263.4	-	37	4194	c.4195C>T	c.(4195-4197)Cgc>Tgc	p.R1399C	MYOF_ENST00000358334.5_Missense_Mutation_p.R1386C|MYOF_ENST00000371502.4_Missense_Mutation_p.R1399C|MYOF_ENST00000371501.4_Missense_Mutation_p.R1399C	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1399			R -> C (in dbSNP:rs11187393).		blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						CAGCGAAAGCGGTCCAGGCGC	0.547													G|||	113	0.0225639	0.0045	0.0403	5008	,	,		15768	0.0		0.0656	False		,,,				2504	0.0133				p.R1399C		Atlas-SNP	.											.	MYOF	177	.	0			c.C4195T						PASS	.	G	CYS/ARG,CYS/ARG	53,3885		0,53,1916	44.0	47.0	46.0		4195,4156	5.7	1.0	10	dbSNP_120	46	497,7795		13,471,3662	yes	missense,missense	MYOF	NM_013451.3,NM_133337.2	180,180	13,524,5578	AA,AG,GG		5.9937,1.3459,4.4971	possibly-damaging,possibly-damaging	1399/2062,1386/2049	95107428	550,11680	1969	4146	6115	SO:0001583	missense	26509	exon37			GAAAGCGGTCCAG	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4195C>T	10.37:g.95107428G>A	ENSP00000352208:p.Arg1399Cys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	37	CCDS41551.1	73	0.033424908424908424	4	0.008130081300813009	21	0.058011049723756904	0	0.0	48	0.0633245382585752	G	18.40	3.615468	0.66672	0.013459	0.059937	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.69	5.69	0.88448	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.364053	0.30732	N	0.008983	T	0.11410	0.0278	N	0.14661	0.345	0.42947	D	0.994363	D;D	0.62365	0.959;0.991	P;B	0.51229	0.663;0.394	T	0.42103	-0.9471	10	0.59425	D	0.04	-11.0812	5.1512	0.15011	0.0773:0.1355:0.628:0.1592	rs11187393;rs52820934;rs11187393	1386;1399	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	C	1386;1399;1399;1399	ENSP00000351094:R1386C;ENSP00000352208:R1399C;ENSP00000360556:R1399C;ENSP00000360557:R1399C	ENSP00000351094:R1386C	R	-	1	0	MYOF	95097418	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	1.330000	0.33781	2.691000	0.91804	0.561000	0.74099	CGC	G|0.960;A|0.040	0.040	strong		0.547	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
MOB3C	148932	hgsc.bcm.edu	37	1	47078637	47078637	+	Silent	SNP	T	T	C	rs4660947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47078637T>C	ENST00000319928.3	-	2	587	c.357A>G	c.(355-357)gcA>gcG	p.A119A	MOB3C_ENST00000477318.1_5'UTR|MOB3C_ENST00000271139.8_Silent_p.A171A|MKNK1_ENST00000545730.1_Intron|MOB3C_ENST00000371940.1_Silent_p.A142A	NM_201403.2	NP_958805.1	Q70IA8	MOB3C_HUMAN	MOB kinase activator 3C	119							metal ion binding (GO:0046872)										CCATGAGCAATGCCATATAGC	0.672													C|||	3371	0.673123	0.5779	0.5677	5008	,	,		14769	0.9583		0.5	False		,,,				2504	0.7607				p.A171A		Atlas-SNP	.											.	MOB3C	1	.	0			c.A513G						PASS	.	C	,	2521,1881	511.6+/-367.8	730,1061,410	40.0	45.0	44.0		513,357	-10.5	0.0	1	dbSNP_111	44	4126,4470	577.7+/-390.6	992,2142,1164	no	coding-synonymous,coding-synonymous	MOB3C	NM_145279.4,NM_201403.2	,	1722,3203,1574	CC,CT,TT		47.9991,42.7306,48.8614	,	171/269,119/217	47078637	6647,6351	2201	4298	6499	SO:0001819	synonymous_variant	148932	exon2			GAGCAATGCCATA	AK091808	CCDS539.1, CCDS540.1	1p34.1	2011-09-28	2011-09-28	2011-09-28	ENSG00000142961	ENSG00000142961		"""MOB kinase activators"""	29800	protein-coding gene	gene with protein product			"""MOB1, Mps One Binder kinase activator-like 2C (yeast)"""	MOBKL2C		12477932	Standard	NM_145279		Approved	MOB1E	uc001cqe.4	Q70IA8	OTTHUMG00000007989	ENST00000319928.3:c.357A>G	1.37:g.47078637T>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	42	14	0.333333	NM_145279	D3DQ22|Q0VA98|Q5TC10|Q5TC11|Q8NAZ2|Q8NF28	Silent	SNP	ENST00000319928.3	37	CCDS540.1																																																																																			T|0.452;C|0.548	0.548	strong		0.672	MOB3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_145279	
ACAT1	38	hgsc.bcm.edu	37	11	108009660	108009660	+	Silent	SNP	C	C	A	rs35188041	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:108009660C>A	ENST00000265838.4	+	6	562	c.471C>A	c.(469-471)tcC>tcA	p.S157S		NM_000019.3	NP_000010.1	P24752	THIL_HUMAN	acetyl-CoA acetyltransferase 1	157					adipose tissue development (GO:0060612)|brain development (GO:0007420)|branched-chain amino acid catabolic process (GO:0009083)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular nitrogen compound metabolic process (GO:0034641)|ketone body biosynthetic process (GO:0046951)|ketone body catabolic process (GO:0046952)|liver development (GO:0001889)|metanephric proximal convoluted tubule development (GO:0072229)|protein homooligomerization (GO:0051260)|response to hormone (GO:0009725)|response to organic cyclic compound (GO:0014070)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acetyl-CoA C-acetyltransferase activity (GO:0003985)|coenzyme binding (GO:0050662)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|prostate(2)	10		all_cancers(61;6.41e-10)|all_epithelial(67;2.83e-06)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;2.96e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.00108)|OV - Ovarian serous cystadenocarcinoma(223;0.192)	Sulfasalazine(DB00795)	AGAGCATGTCCAATGTTCCAT	0.408													C|||	636	0.126997	0.1929	0.0965	5008	,	,		19189	0.0198		0.1581	False		,,,				2504	0.138				p.S157S		Atlas-SNP	.											ACAT1,colon,carcinoma,0,1	ACAT1	35	1	0			c.C471A						PASS	.	C		862,3540	338.4+/-305.3	91,680,1430	218.0	191.0	200.0		471	1.8	1.0	11	dbSNP_126	200	1501,7095	284.4+/-296.6	127,1247,2924	no	coding-synonymous	ACAT1	NM_000019.3		218,1927,4354	AA,AC,CC		17.4616,19.582,18.1797		157/428	108009660	2363,10635	2201	4298	6499	SO:0001819	synonymous_variant	38	exon6			CATGTCCAATGTT	D90228	CCDS8339.1	11q22.3	2010-04-30	2010-04-30		ENSG00000075239	ENSG00000075239	2.3.1.9		93	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	607809	"""acetyl-Coenzyme A acetyltransferase 1"""	ACAT		1979337	Standard	NM_000019		Approved	THIL	uc001pjy.3	P24752	OTTHUMG00000166381	ENST00000265838.4:c.471C>A	11.37:g.108009660C>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	119	17	0.142857	NM_000019	B2R6H1|G3XAB4|Q96FG8	Silent	SNP	ENST00000265838.4	37	CCDS8339.1	273	0.125	94	0.1910569105691057	41	0.1132596685082873	13	0.022727272727272728	125	0.16490765171503957	C	15.57	2.873841	0.51695	0.19582	0.174616	ENSG00000075239	ENST00000528370	.	.	.	5.74	1.76	0.24704	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11616	-1.0580	3	.	.	.	-18.5574	7.7441	0.28858	0.1131:0.6655:0.0:0.2213	rs35188041	.	.	.	K	93	.	.	Q	+	1	0	ACAT1	107514870	0.977000	0.34250	0.993000	0.49108	0.960000	0.62799	0.158000	0.16422	0.775000	0.33450	0.603000	0.83216	CAA	A|0.168;C|0.832;G|0.000	0.168	strong		0.408	ACAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389474.1	NM_000019	
NLRP11	204801	hgsc.bcm.edu	37	19	56297019	56297019	+	Missense_Mutation	SNP	G	G	A	rs11671248	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56297019G>A	ENST00000589093.1	-	10	3167	c.3074C>T	c.(3073-3075)tCa>tTa	p.S1025L	NLRP11_ENST00000592953.1_Missense_Mutation_p.S926L|NLRP11_ENST00000589824.2_Missense_Mutation_p.S971L|NLRP11_ENST00000360133.3_Missense_Mutation_p.S971L|NLRP11_ENST00000443188.1_Missense_Mutation_p.S1025L			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	1025							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		TGCTGTATTTGACGTTCTCAT	0.378													G|||	12	0.00239617	0.0008	0.0058	5008	,	,		19715	0.0		0.007	False		,,,				2504	0.0				p.S1025L		Atlas-SNP	.											.	NLRP11	139	.	0			c.C3074T						PASS	.	G	LEU/SER	8,4398	12.9+/-30.5	0,8,2195	93.0	91.0	92.0		3074	-1.5	0.0	19	dbSNP_120	92	89,8511	51.1+/-111.2	0,89,4211	yes	missense	NLRP11	NM_145007.3	145	0,97,6406	AA,AG,GG		1.0349,0.1816,0.7458	benign	1025/1034	56297019	97,12909	2203	4300	6503	SO:0001583	missense	204801	exon12			GTATTTGACGTTC	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.3074C>T	19.37:g.56297019G>A	ENSP00000466285:p.Ser1025Leu	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	232	96	0.413793	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	8.884	0.952420	0.18431	0.001816	0.010349	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.75050	-0.9;-0.87	1.27	-1.46	0.08800	.	.	.	.	.	T	0.51890	0.1701	N	0.08118	0	0.09310	N	1	P;D	0.65815	0.949;0.995	B;P	0.51945	0.277;0.685	T	0.53443	-0.8438	9	0.87932	D	0	.	6.7227	0.23338	0.0:0.5889:0.4111:0.0	rs11671248;rs11671248	1025;971	P59045;P59045-2	NAL11_HUMAN;.	L	1025;971	ENSP00000409898:S1025L;ENSP00000353251:S971L	ENSP00000353251:S971L	S	-	2	0	NLRP11	60988831	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.022000	0.13511	-0.328000	0.08539	-0.300000	0.09419	TCA	G|0.992;A|0.008	0.008	strong		0.378	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
LMBRD2	92255	hgsc.bcm.edu	37	5	36143392	36143392	+	Silent	SNP	C	C	T	rs267766	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:36143392C>T	ENST00000296603.4	-	2	522	c.60G>A	c.(58-60)ctG>ctA	p.L20L		NM_001007527.1	NP_001007528.1	Q68DH5	LMBD2_HUMAN	LMBR1 domain containing 2	20						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.L20L(1)		breast(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(31;0.000146)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATCGATGAAGCAGAAATAATG	0.363													T|||	1681	0.335663	0.4425	0.2752	5008	,	,		16604	0.2192		0.4066	False		,,,				2504	0.2812				p.L20L		Atlas-SNP	.											LMBRD2,NS,carcinoma,0,1	LMBRD2	89	1	1	Substitution - coding silent(1)	stomach(1)	c.G60A						PASS	.	T		1885,2521	628.9+/-395.2	400,1085,718	117.0	109.0	111.0		60	-0.8	1.0	5	dbSNP_79	111	3502,5098	633.6+/-398.8	717,2068,1515	no	coding-synonymous	LMBRD2	NM_001007527.1		1117,3153,2233	TT,TC,CC		40.7209,42.7826,41.4193		20/696	36143392	5387,7619	2203	4300	6503	SO:0001819	synonymous_variant	92255	exon2			ATGAAGCAGAAAT		CCDS34145.1	5p13.2	2008-02-05			ENSG00000164187	ENSG00000164187			25287	protein-coding gene	gene with protein product							Standard	NM_001007527		Approved	DKFZp434H2226	uc003jkb.1	Q68DH5	OTTHUMG00000162150	ENST00000296603.4:c.60G>A	5.37:g.36143392C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	NM_001007527	B3KRB6|Q9NTC7	Silent	SNP	ENST00000296603.4	37	CCDS34145.1																																																																																			C|0.628;T|0.372	0.372	strong		0.363	LMBRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367552.1	NM_001007527	
LILRB3	11025	hgsc.bcm.edu	37	19	54723030	54723030	+	Missense_Mutation	SNP	C	C	A	rs61734493	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54723030C>A	ENST00000391750.1	-	9	1530	c.1394G>T	c.(1393-1395)cGa>cTa	p.R465L	LILRB3_ENST00000407860.2_Missense_Mutation_p.R482L|LILRA6_ENST00000440558.2_Missense_Mutation_p.R465L|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000245620.9_Missense_Mutation_p.R465L|LILRA6_ENST00000270464.5_Missense_Mutation_p.R465L|LILRB3_ENST00000346401.6_Missense_Mutation_p.R477L|LILRB3_ENST00000424807.1_Missense_Mutation_p.R465L|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.R465L			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	465					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACGCTGACGTCggaggaggag	0.607													.|||	102	0.0203674	0.0023	0.0259	5008	,	,		16344	0.0		0.0785	False		,,,				2504	0.002				p.R465L		Atlas-SNP	.											.	LILRB3	67	.	0			c.G1394T						PASS	.	C	LEU/ARG,LEU/ARG	55,4351		2,51,2150	165.0	119.0	134.0		1394,1394	0.7	0.0	19	dbSNP_129	134	515,8085		40,435,3825	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	102,102	42,486,5975	AA,AC,CC		5.9884,1.2483,4.3826	possibly-damaging,possibly-damaging	465/633,465/632	54723030	570,12436	2203	4300	6503	SO:0001583	missense	11025	exon8			TGACGTCGGAGGA	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1394G>T	19.37:g.54723030C>A	ENSP00000375630:p.Arg465Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	56	0.02564102564102564	0	0.0	10	0.027624309392265192	0	0.0	46	0.06068601583113457	C	10.70	1.424541	0.25639	0.012483	0.059884	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00498	7.04;7.04;6.97;7.04;6.99;7.02;7.02;7.04	2.82	0.67	0.17923	.	2586.710000	0.00166	N	0.000000	T	0.00109	0.0003	L	0.58428	1.81	0.09310	N	1	B;B;B;B;B;B;B	0.30179	0.271;0.107;0.031;0.017;0.052;0.207;0.032	B;B;B;B;B;B;B	0.31869	0.137;0.062;0.008;0.013;0.039;0.051;0.036	T	0.47086	-0.9144	10	0.38643	T	0.18	.	4.9124	0.13829	0.0:0.7061:0.0:0.2939	.	482;465;465;477;482;465;465	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	L	465;465;477;465;482;465;465;465	ENSP00000375630:R465L;ENSP00000412771:R465L;ENSP00000345184:R477L;ENSP00000245620:R465L;ENSP00000384274:R482L;ENSP00000390120:R465L;ENSP00000270464:R465L;ENSP00000411227:R465L	ENSP00000270464:R465L	R	-	2	0	LILRB3;LILRA6	59414842	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.092000	0.11129	0.294000	0.22547	-0.424000	0.05967	CGA	C|0.956;A|0.044	0.044	strong		0.607	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
CYP11B2	1585	hgsc.bcm.edu	37	8	143996539	143996539	+	Missense_Mutation	SNP	T	T	C	rs4539	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143996539T>C	ENST00000323110.2	-	3	520	c.518A>G	c.(517-519)aAg>aGg	p.K173R		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	173			K -> R (in dbSNP:rs4539). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:9931115}.		aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	CACCTTCTTCTTCAGGGCCTG	0.627									Familial Hyperaldosteronism type I				.|||	1735	0.346446	0.1876	0.4697	5008	,	,		19583	0.2867		0.4841	False		,,,				2504	0.3937				p.K173R		Atlas-SNP	.											.	CYP11B2	107	.	0			c.A518G	GRCh37	CM962423	CYP11B2	M	rs4539	PASS	.	C	ARG/LYS	1038,3368		127,784,1292	44.0	41.0	42.0		518	-4.2	0.0	8	dbSNP_52	42	3857,4735		877,2103,1316	no	missense	CYP11B2	NM_000498.3	26	1004,2887,2608	CC,CT,TT		44.8906,23.5588,37.6596	benign	173/504	143996539	4895,8103	2203	4296	6499	SO:0001583	missense	1585	exon3	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TTCTTCTTCAGGG	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"""Cytochrome P450s"""	2592	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	124080	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"""	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.518A>G	8.37:g.143996539T>C	ENSP00000325822:p.Lys173Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	125	50	0.4	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	37	CCDS6393.1	793	0.3630952380952381	93	0.18902439024390244	156	0.430939226519337	179	0.3129370629370629	365	0.4815303430079156	.	0.007	-1.971021	0.00457	0.235588	0.448906	ENSG00000179142	ENST00000323110	T	0.66995	-0.24	3.44	-4.17	0.03857	.	0.947674	0.08784	N	0.894271	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.30149	-0.9988	9	0.06365	T	0.9	.	6.5262	0.22303	0.1184:0.3843:0.0:0.4973	rs4539;rs61617752	173	P19099	C11B2_HUMAN	R	173	ENSP00000325822:K173R	ENSP00000325822:K173R	K	-	2	0	CYP11B2	143993541	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.668000	0.05268	-1.541000	0.01727	-2.253000	0.00282	AAG	T|0.648;C|0.352	0.352	strong		0.627	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
FYB	2533	hgsc.bcm.edu	37	5	39141240	39141240	+	Silent	SNP	G	G	A	rs3188386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:39141240G>A	ENST00000351578.6	-	4	1486	c.1296C>T	c.(1294-1296)agC>agT	p.S432S	FYB_ENST00000512982.1_Silent_p.S432S|FYB_ENST00000505428.1_Silent_p.S432S|FYB_ENST00000540520.1_Silent_p.S442S|FYB_ENST00000515010.1_Silent_p.S432S	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	432	Interaction with SKAP1.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			CATTGACAGGGCTTCTGAAAA	0.338													g|||	611	0.122005	0.1188	0.1369	5008	,	,		20305	0.001		0.2326	False		,,,				2504	0.1268				p.S442S		Atlas-SNP	.											.	FYB	354	.	0			c.C1326T						PASS	.		,	429,3339		29,371,1484	58.0	54.0	56.0		1296,1296	-5.2	0.0	5	dbSNP_126	56	1765,6487		179,1407,2540	no	coding-synonymous,coding-synonymous	FYB	NM_001465.4,NM_199335.3	,	208,1778,4024	AA,AG,GG		21.3888,11.3854,18.2529	,	432/830,432/784	39141240	2194,9826	1884	4126	6010	SO:0001819	synonymous_variant	2533	exon4			GACAGGGCTTCTG	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1296C>T	5.37:g.39141240G>A		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	168	74	0.440476	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	37	CCDS47200.1																																																																																			G|0.843;A|0.157	0.157	strong		0.338	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
ABCB4	5244	hgsc.bcm.edu	37	7	87092185	87092185	+	Silent	SNP	G	G	A	rs2302387	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:87092185G>A	ENST00000265723.4	-	4	286	c.175C>T	c.(175-177)Ctg>Ttg	p.L59L	ABCB4_ENST00000453593.1_Silent_p.L59L|ABCB4_ENST00000359206.3_Silent_p.L59L|ABCB4_ENST00000545634.1_Silent_p.L59L|ABCB4_ENST00000358400.3_Silent_p.L59L	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	59	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	ATGGTACCCAGCGACATAAAC	0.388													G|||	1264	0.252396	0.4939	0.1744	5008	,	,		15328	0.2024		0.1481	False		,,,				2504	0.1401				p.L59L		Atlas-SNP	.											.	ABCB4	177	.	0			c.C175T						PASS	.	G	,,	1884,2522	541.4+/-375.8	396,1092,715	93.0	83.0	86.0		175,175,175	1.5	0.5	7	dbSNP_100	86	1264,7336	251.8+/-278.1	82,1100,3118	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCB4	NM_000443.3,NM_018849.2,NM_018850.2	,,	478,2192,3833	AA,AG,GG		14.6977,42.7599,24.2042	,,	59/1280,59/1287,59/1233	87092185	3148,9858	2203	4300	6503	SO:0001819	synonymous_variant	5244	exon4			TACCCAGCGACAT	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.175C>T	7.37:g.87092185G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	125	66	0.528	NM_018850	A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	37	CCDS5606.1																																																																																			G|0.744;A|0.256	0.256	strong		0.388	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443	
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 GAIIx	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	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_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	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	77	42	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 GAIIx	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		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	190	34	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 GAIIx	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	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	50	6	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	
TTL	150465	hgsc.bcm.edu	37	2	113277949	113277949	+	Silent	SNP	T	T	C	rs62157538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:113277949T>C	ENST00000233336.6	+	6	1157	c.966T>C	c.(964-966)gaT>gaC	p.D322D		NM_153712.4	NP_714923.1	Q8NG68	TTL_HUMAN	tubulin tyrosine ligase	322	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)|microtubule cytoskeleton organization (GO:0000226)|regulation of axon extension (GO:0030516)		ATP binding (GO:0005524)|tubulin-tyrosine ligase activity (GO:0004835)			breast(1)|large_intestine(2)|ovary(1)	4		Ovarian(717;0.024)		BRCA - Breast invasive adenocarcinoma(221;6.17e-07)|STAD - Stomach adenocarcinoma(1183;0.00644)		TCATGGTCGATGAGGAGCTGA	0.537			T	ETV6	ALL								T|||	923	0.184305	0.1188	0.0937	5008	,	,		19479	0.2758		0.2068	False		,,,				2504	0.2198				p.D322D		Atlas-SNP	.		Dom	yes		2	2q13	150465	tubulin tyrosine ligase		L	TTL_ENST00000233336,colon,carcinoma,0,1	TTL	27	1	0			c.T966C						PASS	.	T		564,3842	252.1+/-258.6	40,484,1679	132.0	112.0	119.0		966	-9.1	0.5	2	dbSNP_129	119	1346,7254	263.8+/-285.2	115,1116,3069	no	coding-synonymous	TTL	NM_153712.4		155,1600,4748	CC,CT,TT		15.6512,12.8007,14.6855		322/378	113277949	1910,11096	2203	4300	6503	SO:0001819	synonymous_variant	150465	exon6			GGTCGATGAGGAG		CCDS2096.1	2q13	2010-04-21			ENSG00000114999	ENSG00000114999	6.3.2.25		21586	protein-coding gene	gene with protein product		608291				11431336	Standard	NM_153712		Approved	MGC46235	uc002thu.3	Q8NG68	OTTHUMG00000131316	ENST00000233336.6:c.966T>C	2.37:g.113277949T>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_153712	Q585T3|Q7Z302|Q8N426	Silent	SNP	ENST00000233336.6	37	CCDS2096.1																																																																																			T|0.838;C|0.162	0.162	strong		0.537	TTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254085.2	NM_153712	
PCDHA7	56141	hgsc.bcm.edu	37	5	140214361	140214361	+	Silent	SNP	G	G	A	rs17844307	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140214361G>A	ENST00000525929.1	+	1	393	c.393G>A	c.(391-393)ccG>ccA	p.P131P	PCDHA7_ENST00000378125.3_Silent_p.P131P|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	131	Cadherin 1. {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)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAACCCTCCGGTGTTCCCAG	0.582																																					p.P131P	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											PCDHA7_ENST00000525929,NS,carcinoma,+1,4	PCDHA7	367	4	0			c.G393A						PASS	.						111.0	108.0	109.0					5																	140214361		2203	4300	6503	SO:0001819	synonymous_variant	56141	exon1			CCCTCCGGTGTTC	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.393G>A	5.37:g.140214361G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	356	26	0.0730337	NM_031852	O75282	Silent	SNP	ENST00000525929.1	37	CCDS54918.1																																																																																			G|0.981;A|0.019	0.019	strong		0.582	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
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 GAIIx	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		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	17	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	
ERCC6L2	375748	hgsc.bcm.edu	37	9	98638288	98638288	+	Start_Codon_SNP	SNP	A	A	G	rs690528	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:98638288A>G	ENST00000288985.7	+	1	306	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	LINC00476_ENST00000429781.1_RNA	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	1					DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										CGGGTGTTACATGCAGCCGGG	0.726													G|||	1264	0.252396	0.1029	0.2896	5008	,	,		15448	0.3423		0.3082	False		,,,				2504	0.2781				p.M1V		Atlas-SNP	.											C9orf102,NS,carcinoma,0,2	.	.	2	0			c.A1G						PASS	.	G	VAL/MET	561,3725		45,471,1627	7.0	9.0	8.0		1	-3.7	0.0	9	dbSNP_83	8	2502,5908		422,1658,2125	no	missense	C9orf102	NM_001010895.2	21	467,2129,3752	GG,GA,AA		29.7503,13.0891,24.1257	benign	1/713	98638288	3063,9633	2143	4205	6348	SO:0001582	initiator_codon_variant	375748	exon1			TGTTACATGCAGC	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"""chromosome 9 open reading frame 102"", ""excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"""	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.1A>G	9.37:g.98638288A>G	ENSP00000288985:p.Met1Val	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	30	12	0.4	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	37	CCDS35072.1	608	0.2783882783882784	64	0.13008130081300814	111	0.30662983425414364	196	0.34265734265734266	237	0.31266490765171506	G	0.019	-1.460743	0.01062	0.130891	0.297503	ENSG00000182150	ENST00000288985	D	0.89050	-2.46	3.26	-3.74	0.04385	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06092	-1.0846	7	0.87932	D	0	.	6.0461	0.19760	0.473:0.1408:0.3862:0.0	rs690528;rs13301906;rs16910324;rs61146597	1	Q5T890	RAD26_HUMAN	V	1	ENSP00000288985:M1V	ENSP00000288985:M1V	M	+	1	0	C9orf102	97678109	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.059000	0.11731	-1.326000	0.02266	-1.988000	0.00451	ATG	A|0.717;G|0.283	0.283	strong		0.726	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895	Missense_Mutation
LILRB3	11025	hgsc.bcm.edu	37	19	54722250	54722250	+	Missense_Mutation	SNP	T	T	C	rs1132610	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54722250T>C	ENST00000391750.1	-	12	1709	c.1573A>G	c.(1573-1575)Agg>Ggg	p.R525G	LILRB3_ENST00000407860.2_Missense_Mutation_p.R542G|LILRA6_ENST00000440558.2_Missense_Mutation_p.R525G|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.R525G|LILRA6_ENST00000270464.5_Missense_Mutation_p.R525G|LILRB3_ENST00000346401.6_Missense_Mutation_p.R537G|LILRB3_ENST00000424807.1_Missense_Mutation_p.R525G|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.R525G			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	525				R -> G (in Ref. 2; AAB87667). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGCTCCACCCTGTCCTCAGAC	0.617													.|||	740	0.147764	0.3525	0.1354	5008	,	,		18421	0.002		0.1103	False		,,,				2504	0.0685				p.R525G		Atlas-SNP	.											LILRB3,colon,carcinoma,+2,1	LILRB3	67	1	0			c.A1573G						PASS	.	G	GLY/ARG,GLY/ARG	1383,3023		239,905,1059	119.0	102.0	108.0		1573,1573	-0.3	0.0	19	dbSNP_86	108	1039,7561		58,923,3319	yes	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	125,125	297,1828,4378	CC,CT,TT		12.0814,31.389,18.6222	benign,benign	525/633,525/632	54722250	2422,10584	2203	4300	6503	SO:0001583	missense	11025	exon11			CCACCCTGTCCTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1573A>G	19.37:g.54722250T>C	ENSP00000375630:p.Arg525Gly	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	294	0.1346153846153846	176	0.35772357723577236	42	0.11602209944751381	2	0.0034965034965034965	74	0.09762532981530343	G	0.006	-2.043597	0.00398	0.31389	0.120814	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00454	7.49;7.49;7.36;7.47;7.32;7.48;7.49;7.49	3.11	-0.331	0.12679	.	.	.	.	.	T	0.00012	0.0000	N	0.00221	-1.82	0.80722	P	0.0	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B;B	0.12156	0.0;0.001;0.0;0.007;0.003;0.001;0.001	T	0.25047	-1.0143	8	0.02654	T	1	.	4.2725	0.10794	0.0:0.4068:0.3677:0.2255	rs1132610;rs3193489;rs52834610;rs58789613	542;525;525;537;542;525;525	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	G	525;525;537;525;542;525;525;525	ENSP00000375630:R525G;ENSP00000412771:R525G;ENSP00000345184:R537G;ENSP00000245620:R525G;ENSP00000384274:R542G;ENSP00000390120:R525G;ENSP00000270464:R525G;ENSP00000411227:R525G	ENSP00000270464:R525G	R	-	1	2	LILRB3;LILRA6	59414062	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.023000	0.01438	-0.189000	0.10482	-3.810000	0.00019	AGG	T|0.826;C|0.174	0.174	strong		0.617	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
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 GAIIx	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	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	80	30	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	
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 GAIIx	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		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	94	29	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 GAIIx	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	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	101	20	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 GAIIx	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	53	30	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	
EYS	346007	hgsc.bcm.edu	37	6	66005857	66005857	+	Missense_Mutation	SNP	T	T	A	rs17411795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:66005857T>A	ENST00000370621.3	-	12	2448	c.1922A>T	c.(1921-1923)gAg>gTg	p.E641V	EYS_ENST00000503581.1_Missense_Mutation_p.E641V|EYS_ENST00000370616.2_Missense_Mutation_p.E641V			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	641			E -> V (in dbSNP:rs17411795). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.E641V(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGTATCTATCTCACAGATGTT	0.438													T|||	522	0.104233	0.0582	0.1585	5008	,	,		13592	0.0655		0.2018	False		,,,				2504	0.0675				p.E641V		Atlas-SNP	.											EYS_ENST00000370621,NS,carcinoma,0,1	EYS	527	1	1	Substitution - Missense(1)	kidney(1)	c.A1922T						PASS	.	T	VAL/GLU	114,1270		6,102,584	157.0	124.0	134.0		1922	0.4	0.4	6	dbSNP_123	134	666,2516		60,546,985	yes	missense	EYS	NM_001142800.1	121	66,648,1569	AA,AT,TT		20.9302,8.237,17.0828	probably-damaging	641/3145	66005857	780,3786	692	1591	2283	SO:0001583	missense	346007	exon12			TCTATCTCACAGA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1922A>T	6.37:g.66005857T>A	ENSP00000359655:p.Glu641Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		293	0.13415750915750915	34	0.06910569105691057	63	0.17403314917127072	38	0.06643356643356643	158	0.20844327176781002	.	12.97	2.098574	0.37048	0.08237	0.209302	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.80480	-1.38;-1.38;-1.38	5.48	0.452	0.16634	.	.	.	.	.	T	0.75213	0.3819	L	0.55481	1.735	0.09310	P	0.99999830371	D	0.55385	0.971	P	0.58454	0.839	T	0.70605	-0.4826	8	0.66056	D	0.02	.	7.9912	0.30242	0.0:0.3484:0.0:0.6516	rs17411795;rs17411795	641	Q5T1H1-1	.	V	641	ENSP00000424243:E641V;ENSP00000359655:E641V;ENSP00000359650:E641V	ENSP00000359650:E641V	E	-	2	0	EYS	66062578	0.526000	0.26298	0.371000	0.25978	0.109000	0.19521	0.278000	0.18753	0.091000	0.17302	0.482000	0.46254	GAG	A|0.141;N|0.000	0.141	strong		0.438	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
ZNF716	441234	hgsc.bcm.edu	37	7	57529392	57529392	+	Missense_Mutation	SNP	A	A	C	rs13235676	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:57529392A>C	ENST00000420713.1	+	4	1337	c.1225A>C	c.(1225-1227)Aaa>Caa	p.K409Q		NM_001159279.1	NP_001152751.1	A6NP11	ZN716_HUMAN	zinc finger protein 716	409					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(1)|lung(20)|ovary(2)	24						GAAACCCTACAAATGTGAAGA	0.403													a|||	2109	0.421126	0.3215	0.4798	5008	,	,		20228	0.5397		0.3797	False		,,,				2504	0.4346				p.K409Q		Atlas-SNP	.											.	ZNF716	207	.	0			c.A1225C						PASS	.	A	GLN/LYS	479,905		82,315,295	27.0	27.0	27.0		1225	0.2	0.2	7	dbSNP_121	27	1251,1931		247,757,587	no	missense	ZNF716	NM_001159279.1	53	329,1072,882	CC,CA,AA		39.3149,34.6098,37.8887	benign	409/496	57529392	1730,2836	692	1591	2283	SO:0001583	missense	441234	exon4			CCCTACAAATGTG	AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111		"""Zinc fingers, C2H2-type"", ""-"""	32458	protein-coding gene	gene with protein product							Standard	NM_001159279		Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	ENST00000420713.1:c.1225A>C	7.37:g.57529392A>C	ENSP00000394248:p.Lys409Gln	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_001159279		Missense_Mutation	SNP	ENST00000420713.1	37	CCDS55112.1	906	0.41483516483516486	162	0.32926829268292684	158	0.43646408839779005	307	0.5367132867132867	279	0.36807387862796836	A	7.864	0.726705	0.15439	0.346098	0.393149	ENSG00000182111	ENST00000420713;ENST00000418732	T	0.18810	2.19	0.195	0.195	0.15151	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.55743	1.74	0.52501	P	4.4000000000044004E-5	B	0.33299	0.407	B	0.30716	0.119	T	0.43750	-0.9372	8	0.49607	T	0.09	.	4.8229	0.13400	0.9998:0.0:2.0E-4:0.0	rs13235676	397	A6NP11	ZN716_HUMAN	Q	409;397	ENSP00000394248:K409Q	ENSP00000387687:K397Q	K	+	1	0	ZNF716	57533334	0.000000	0.05858	0.190000	0.23270	0.191000	0.23601	-2.138000	0.01303	0.257000	0.21650	0.254000	0.18369	AAA	A|0.591;C|0.409	0.409	strong		0.403	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345309.1	NM_001159279	
CCDC132	55610	hgsc.bcm.edu	37	7	92970847	92970847	+	Silent	SNP	C	C	T	rs2106432	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92970847C>T	ENST00000305866.5	+	23	2295	c.2167C>T	c.(2167-2169)Ctg>Ttg	p.L723L	CCDC132_ENST00000474412.1_3'UTR|CCDC132_ENST00000544910.1_Silent_p.L693L|CCDC132_ENST00000541136.1_Silent_p.L534L|CCDC132_ENST00000535481.1_Silent_p.L443L	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	723						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TGGGGATACGCTGTATGGGTT	0.443													T|||	3023	0.603634	0.9675	0.5144	5008	,	,		18323	0.5952		0.3807	False		,,,				2504	0.4131				p.L723L		Atlas-SNP	.											.	CCDC132	136	.	0			c.C2167T						PASS	.	T		3353,563		1448,457,53	132.0	141.0	138.0		2167	-1.3	0.1	7	dbSNP_96	138	3109,5219		579,1951,1634	no	coding-synonymous	CCDC132	NM_017667.2		2027,2408,1687	TT,TC,CC		37.3319,14.3769,47.2231		723/965	92970847	6462,5782	1958	4164	6122	SO:0001819	synonymous_variant	55610	exon23			GATACGCTGTATG	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.2167C>T	7.37:g.92970847C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Silent	SNP	ENST00000305866.5	37	CCDS43617.1																																																																																			C|0.433;T|0.567	0.567	strong		0.443	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
FRG1	2483	hgsc.bcm.edu	37	4	190878569	190878569	+	Missense_Mutation	SNP	T	T	C	rs575384276		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:190878569T>C	ENST00000226798.4	+	6	671	c.449T>C	c.(448-450)tTg>tCg	p.L150S	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	150					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.L150S(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ATGGCTTTGTTGGCCTCAAAT	0.358																																					p.L150S		Atlas-SNP	.											FRG1,NS,carcinoma,0,2	FRG1	76	2	1	Substitution - Missense(1)	prostate(1)	c.T449C						scavenged	.						13.0	18.0	16.0					4																	190878569		2139	4261	6400	SO:0001583	missense	2483	exon6			CTTTGTTGGCCTC	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.449T>C	4.37:g.190878569T>C	ENSP00000226798:p.Leu150Ser	Somatic	80	5	0.0625		WXS	Illumina HiSeq	Phase_I	105	5	0.047619	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	15.24	2.773472	0.49786	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.50813	1.86;0.73	4.19	4.19	0.49359	Actin cross-linking (1);	0.139630	0.48286	D	0.000199	T	0.55417	0.1919	M	0.78456	2.415	0.80722	D	1	B	0.31680	0.335	B	0.41299	0.353	T	0.60393	-0.7272	10	0.54805	T	0.06	-2.69	11.5749	0.50856	0.0:0.0:0.0:1.0	.	150	Q14331	FRG1_HUMAN	S	150;22;87	ENSP00000226798:L150S;ENSP00000435943:L87S	ENSP00000226798:L150S	L	+	2	0	FRG1	191115563	1.000000	0.71417	0.991000	0.47740	0.482000	0.33219	7.788000	0.85771	1.677000	0.50941	0.373000	0.22412	TTG	.	.	none		0.358	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
MSH4	4438	hgsc.bcm.edu	37	1	76345823	76345823	+	Missense_Mutation	SNP	A	A	G	rs5745459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:76345823A>G	ENST00000263187.3	+	13	1870	c.1766A>G	c.(1765-1767)tAt>tGt	p.Y589C		NM_002440.3	NP_002431.2	O15457	MSH4_HUMAN	mutS homolog 4	589			Y -> C (in dbSNP:rs5745459). {ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|female gamete generation (GO:0007292)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|ovarian follicle development (GO:0001541)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	47						AGAGAAATCTATCACATGACT	0.259								Mismatch excision repair (MMR)					A|||	21	0.00419329	0.0	0.0043	5008	,	,		16013	0.0		0.0139	False		,,,				2504	0.0041				p.Y589C		Atlas-SNP	.											.	MSH4	147	.	0			c.A1766G						PASS	.	A	CYS/TYR	7,4387	14.3+/-33.2	0,7,2190	44.0	44.0	44.0		1766	5.7	1.0	1	dbSNP_114	44	80,8458	43.6+/-101.6	0,80,4189	yes	missense	MSH4	NM_002440.3	194	0,87,6379	GG,GA,AA		0.937,0.1593,0.6727	probably-damaging	589/937	76345823	87,12845	2197	4269	6466	SO:0001583	missense	4438	exon13			AAATCTATCACAT	U89293	CCDS670.1	1p31	2013-09-12	2013-09-12		ENSG00000057468	ENSG00000057468			7327	protein-coding gene	gene with protein product		602105	"""mutS (E. coli) homolog 4"", ""mutS homolog 4 (E. coli)"""			9299235	Standard	NM_002440		Approved		uc001dhd.2	O15457	OTTHUMG00000009788	ENST00000263187.3:c.1766A>G	1.37:g.76345823A>G	ENSP00000263187:p.Tyr589Cys	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	221	115	0.520362	NM_002440	Q5T4U6|Q8NEB3|Q9UNP8	Missense_Mutation	SNP	ENST00000263187.3	37	CCDS670.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	A	17.41	3.383542	0.61845	0.001593	0.00937	ENSG00000057468	ENST00000263187	D	0.90385	-2.66	5.71	5.71	0.89125	DNA mismatch repair protein MutS, core (3);	0.122706	0.64402	D	0.000020	D	0.92609	0.7652	L	0.56199	1.76	0.44762	D	0.997762	D	0.69078	0.997	D	0.69142	0.962	D	0.93514	0.6855	10	0.66056	D	0.02	-21.5982	15.9836	0.80130	1.0:0.0:0.0:0.0	rs5745459;rs52835929;rs5745459	589	O15457	MSH4_HUMAN	C	589	ENSP00000263187:Y589C	ENSP00000263187:Y589C	Y	+	2	0	MSH4	76118411	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.450000	0.73477	2.185000	0.69588	0.528000	0.53228	TAT	A|0.993;G|0.007	0.007	strong		0.259	MSH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026983.1	NM_002440	
ZDHHC11	79844	hgsc.bcm.edu	37	5	825280	825280	+	Splice_Site	SNP	C	C	T	rs1809008	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:825280C>T	ENST00000283441.8	-	8	1405	c.1022G>A	c.(1021-1023)cGg>cAg	p.R341Q	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Splice_Site_p.R341Q	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	341			R -> Q (in dbSNP:rs1809008).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GCAACTTACCCGTGCCGTCGA	0.537													c|||	1874	0.374201	0.6422	0.3386	5008	,	,		27210	0.4127		0.1541	False		,,,				2504	0.2239				p.R341Q		Atlas-SNP	.											.	ZDHHC11	97	.	0			c.G1022A						PASS	.	C	GLN/ARG	2381,2025		580,1221,402	159.0	115.0	130.0		1022	-0.3	0.0	5	dbSNP_92	130	854,7732		60,734,3499	yes	missense-near-splice	ZDHHC11	NM_024786.2	43	640,1955,3901	TT,TC,CC		9.9464,45.9601,24.8999	benign	341/413	825280	3235,9757	2203	4293	6496	SO:0001630	splice_region_variant	79844	exon8			CTTACCCGTGCCG	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1023+1G>A	5.37:g.825280C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	118	9	0.0762712	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	688	0.315018315018315	298	0.6056910569105691	93	0.2569060773480663	234	0.4090909090909091	63	0.08311345646437995	N	1.075	-0.668841	0.03403	0.540399	0.099464	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.28069	1.63;1.63	0.131	-0.261	0.12963	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.43180	-0.9407	7	0.10902	T	0.67	.	.	.	.	rs1809008;rs61386472	341	Q9H8X9	ZDH11_HUMAN	Q	341	ENSP00000397719:R341Q;ENSP00000283441:R341Q	ENSP00000283441:R341Q	R	-	2	0	ZDHHC11	878280	0.003000	0.15002	0.002000	0.10522	0.002000	0.02628	-0.384000	0.07389	-1.204000	0.02648	-1.197000	0.01672	CGG	C|0.724;T|0.276	0.276	strong		0.537	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	Missense_Mutation
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 GAIIx	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	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	7	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	
NSUN4	387338	hgsc.bcm.edu	37	1	46827485	46827485	+	Silent	SNP	C	C	T	rs1053624	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46827485C>T	ENST00000474844.1	+	6	1772	c.1122C>T	c.(1120-1122)ccC>ccT	p.P374P	NSUN4_ENST00000537428.1_Silent_p.P325P|NSUN4_ENST00000498008.1_3'UTR|NSUN4_ENST00000536062.1_Silent_p.P325P	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	374					rRNA methylation (GO:0031167)	mitochondrial large ribosomal subunit (GO:0005762)	methyltransferase activity (GO:0008168)|rRNA binding (GO:0019843)			endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)	8	Acute lymphoblastic leukemia(166;0.155)					ATTTTGGCCCCATGTACTTCT	0.453																																					p.P374P		Atlas-SNP	.											.	NSUN4	26	.	0			c.C1122T						PASS	.	C		672,3734	284.6+/-277.7	58,556,1589	138.0	128.0	132.0		1122	-0.9	1.0	1	dbSNP_86	132	2493,6107	409.3+/-349.8	360,1773,2167	no	coding-synonymous	NSUN4	NM_199044.2		418,2329,3756	TT,TC,CC		28.9884,15.2519,24.3349		374/385	46827485	3165,9841	2203	4300	6503	SO:0001819	synonymous_variant	387338	exon6			TGGCCCCATGTAC	AK021577	CCDS534.1, CCDS57996.1	1p34	2012-02-24	2009-11-23		ENSG00000117481	ENSG00000117481		"""NOP2/Sun domain containing"""	31802	protein-coding gene	gene with protein product	"""sperm head and tail associated protein"""	615394	"""NOL1/NOP2/Sun domain family 4"", ""NOL1/NOP2/Sun domain family, member 4"""				Standard	NM_199044		Approved	MGC22960, SHTAP	uc001cpr.2	Q96CB9	OTTHUMG00000007808	ENST00000474844.1:c.1122C>T	1.37:g.46827485C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	218	91	0.417431	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Silent	SNP	ENST00000474844.1	37	CCDS534.1																																																																																			C|0.804;T|0.196	0.196	strong		0.453	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	
OR10A6	390093	hgsc.bcm.edu	37	11	7950024	7950024	+	Silent	SNP	A	A	G	rs12272735	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7950024A>G	ENST00000309838.2	-	1	185	c.186T>C	c.(184-186)ttT>ttC	p.F62F		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AGTTCAGGAGAAACAGGTACA	0.443													A|||	1669	0.333267	0.2617	0.4568	5008	,	,		17833	0.2698		0.3718	False		,,,				2504	0.3681				p.F62F		Atlas-SNP	.											.	OR10A6	49	.	0			c.T186C						PASS	.	A		1257,3145	430.8+/-342.7	187,883,1131	119.0	114.0	116.0		186	-3.1	0.9	11	dbSNP_120	116	3233,5359	486.1+/-371.8	643,1947,1706	no	coding-synonymous	OR10A6	NM_001004461.1		830,2830,2837	GG,GA,AA		37.628,28.5552,34.5544		62/315	7950024	4490,8504	2201	4296	6497	SO:0001819	synonymous_variant	390093	exon1			CAGGAGAAACAGG	AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"""GPCR / Class A : Olfactory receptors"""	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.186T>C	11.37:g.7950024A>G		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	215	107	0.497674	NM_001004461	Q6IF59	Silent	SNP	ENST00000309838.2	37	CCDS31420.1																																																																																			A|0.658;G|0.342	0.342	strong		0.443	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461	
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 GAIIx	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	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	41	32	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	
CCDC38	120935	hgsc.bcm.edu	37	12	96260947	96260947	+	Silent	SNP	A	A	G	rs7960706	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:96260947A>G	ENST00000344280.3	-	16	2156	c.1599T>C	c.(1597-1599)ttT>ttC	p.F533F	SNRPF_ENST00000552085.1_Intron|SNRPF_ENST00000553192.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	533										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GTTTTGAATGAAAGACAAGTC	0.289													A|||	1574	0.314297	0.2231	0.3112	5008	,	,		18523	0.2014		0.3767	False		,,,				2504	0.4918				p.F533F		Atlas-SNP	.											.	CCDC38	45	.	0			c.T1599C						PASS	.	A		1211,3193	389.1+/-327.2	172,867,1163	60.0	58.0	59.0		1599	-4.4	0.0	12	dbSNP_116	59	3520,5074	496.3+/-374.3	766,1988,1543	no	coding-synonymous	CCDC38	NM_182496.2		938,2855,2706	GG,GA,AA		40.9588,27.4977,36.3979		533/564	96260947	4731,8267	2202	4297	6499	SO:0001819	synonymous_variant	120935	exon16			TGAATGAAAGACA	AK097408	CCDS9056.1	12q23.1	2005-11-02				ENSG00000165972			26843	protein-coding gene	gene with protein product							Standard	NM_182496		Approved	FLJ40089	uc001tek.2	Q502W7	OTTHUMG00000170352	ENST00000344280.3:c.1599T>C	12.37:g.96260947A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	154	63	0.409091	NM_182496	Q8N835	Silent	SNP	ENST00000344280.3	37	CCDS9056.1																																																																																			A|0.677;G|0.323	0.323	strong		0.289	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
TPX2	22974	hgsc.bcm.edu	37	20	30381758	30381758	+	Silent	SNP	G	G	C	rs1062794	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:30381758G>C	ENST00000300403.6	+	14	2145	c.1617G>C	c.(1615-1617)tcG>tcC	p.S539S	TPX2_ENST00000340513.4_Silent_p.S575S	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	539					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			GCCCTTTCTCGTTTGATTCTC	0.438													C|||	1461	0.291733	0.6778	0.2435	5008	,	,		18940	0.001		0.3161	False		,,,				2504	0.0787				p.S539S		Atlas-SNP	.											.	TPX2	61	.	0			c.G1617C						PASS	.	C		2598,1808	531.2+/-373.1	757,1084,362	144.0	144.0	144.0		1617	3.8	1.0	20	dbSNP_86	144	2500,6100	694.3+/-404.7	358,1784,2158	no	coding-synonymous	TPX2	NM_012112.4		1115,2868,2520	CC,CG,GG		29.0698,41.035,39.1973		539/748	30381758	5098,7908	2203	4300	6503	SO:0001819	synonymous_variant	22974	exon14			TTTCTCGTTTGAT	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.1617G>C	20.37:g.30381758G>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	141	67	0.475177	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Silent	SNP	ENST00000300403.6	37	CCDS13190.1																																																																																			G|0.637;C|0.363	0.363	strong		0.438	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
RNF123	63891	hgsc.bcm.edu	37	3	49738945	49738945	+	Silent	SNP	C	C	T	rs6804655	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49738945C>T	ENST00000327697.6	+	16	1443	c.1299C>T	c.(1297-1299)gtC>gtT	p.V433V	RNF123_ENST00000432042.1_Silent_p.V287V	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	433					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)		TCCGCTCCGTCGTCTTCTTTT	0.632											OREG0015570	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1193	0.238219	0.2095	0.2017	5008	,	,		20644	0.1518		0.3091	False		,,,				2504	0.319				p.V433V		Atlas-SNP	.											.	RNF123	100	.	0			c.C1299T						PASS	.	C		913,3493	346.4+/-309.0	93,727,1383	52.0	56.0	55.0		1299	-11.4	0.0	3	dbSNP_116	55	2583,6017	415.0+/-351.6	390,1803,2107	no	coding-synonymous	RNF123	NM_022064.2		483,2530,3490	TT,TC,CC		30.0349,20.7217,26.8799		433/1315	49738945	3496,9510	2203	4300	6503	SO:0001819	synonymous_variant	63891	exon16			CTCCGTCGTCTTC	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.1299C>T	3.37:g.49738945C>T		Somatic	87	0	0	964	WXS	Illumina HiSeq	Phase_I	88	57	0.647727	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	CCDS33758.1																																																																																			C|0.749;N|0.001	.	strong		0.632	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
SERTAD1	29950	hgsc.bcm.edu	37	19	40929363	40929363	+	Missense_Mutation	SNP	T	T	C	rs268687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:40929363T>C	ENST00000357949.4	-	2	249	c.91A>G	c.(91-93)Aca>Gca	p.T31A		NM_013376.3	NP_037508.2	Q9UHV2	SRTD1_HUMAN	SERTA domain containing 1	31			T -> A (in dbSNP:rs268687). {ECO:0000269|PubMed:10580009, ECO:0000269|PubMed:11331592, ECO:0000269|Ref.3}.		positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription, DNA-templated (GO:0006351)					endometrium(2)|lung(1)|prostate(1)|skin(1)	5			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCCACCGCTGTGTGGCCAGGA	0.632													C|||	2714	0.541933	0.8797	0.4914	5008	,	,		14942	0.2411		0.503	False		,,,				2504	0.4714				p.T31A		Atlas-SNP	.											.	SERTAD1	18	.	0			c.A91G						PASS	.	C	ALA/THR	3613,759		1517,579,90	26.0	30.0	29.0		91	1.5	0.1	19	dbSNP_79	29	4441,4127		1193,2055,1036	yes	missense	SERTAD1	NM_013376.3	58	2710,2634,1126	CC,CT,TT		48.1676,17.3605,37.7589	benign	31/237	40929363	8054,4886	2186	4284	6470	SO:0001583	missense	29950	exon2			CCGCTGTGTGGCC	AF117959	CCDS12557.1	19q13.1-q13.2	2008-02-05				ENSG00000197019			17932	protein-coding gene	gene with protein product	"""CDK4-binding protein p34SEI"", ""transcriptional regulator interacting with the PHD-bromodomain 1"""					6434876, 10580009	Standard	NM_013376		Approved	SEI1, TRIP-Br1	uc002ont.4	Q9UHV2		ENST00000357949.4:c.91A>G	19.37:g.40929363T>C	ENSP00000350633:p.Thr31Ala	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_013376	Q9BUE7	Missense_Mutation	SNP	ENST00000357949.4	37	CCDS12557.1	1113	0.5096153846153846	411	0.8353658536585366	199	0.5497237569060773	129	0.22552447552447552	374	0.49340369393139843	C	0.011	-1.731682	0.00687	0.826395	0.518324	ENSG00000197019	ENST00000357949	T	0.42900	0.96	5.0	1.5	0.22942	.	0.180459	0.37761	N	0.001944	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	0.33059	-0.9883	9	0.08179	T	0.78	-5.4715	3.7036	0.08391	0.0896:0.1253:0.4702:0.3149	rs268687;rs17670026;rs268687	31	Q9UHV2	SRTD1_HUMAN	A	31	ENSP00000350633:T31A	ENSP00000350633:T31A	T	-	1	0	SERTAD1	45621203	0.923000	0.31300	0.074000	0.20217	0.048000	0.14542	0.243000	0.18106	0.173000	0.19788	-1.157000	0.01802	ACA	T|0.444;C|0.556	0.556	strong		0.632	SERTAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462571.1	NM_013376	
NCKAP5L	57701	hgsc.bcm.edu	37	12	50189807	50189807	+	Silent	SNP	C	C	A	rs2720298	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:50189807C>A	ENST00000335999.6	-	8	2037	c.1836G>T	c.(1834-1836)tcG>tcT	p.S612S		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	608	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CATAGGGGTACGATTCTGGGA	0.622													C|||	3026	0.604233	0.7277	0.598	5008	,	,		14259	0.6577		0.3638	False		,,,				2504	0.6339				p.S612S		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.G1836T						PASS	.	C		2483,1191		850,783,204	19.0	23.0	22.0		1836	-4.7	0.3	12	dbSNP_100	22	3147,5039		626,1895,1572	no	coding-synonymous	NCKAP5L	NM_001037806.3		1476,2678,1776	AA,AC,CC		38.4437,32.417,47.4705		612/1335	50189807	5630,6230	1837	4093	5930	SO:0001819	synonymous_variant	57701	exon8			GGGGTACGATTCT	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"""KIAA1602"""	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.1836G>T	12.37:g.50189807C>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	37	CCDS41781.2	1247	0.5709706959706959	369	0.75	207	0.5718232044198895	391	0.6835664335664335	280	0.36939313984168864	C	0.009	-1.815812	0.00595	0.67583	0.384437	ENSG00000167566	ENST00000433948	.	.	.	4.28	-4.74	0.03249	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	T	0.37798	-0.9690	3	.	.	.	-9.0909	1.8684	0.03203	0.4356:0.2543:0.1895:0.1206	rs2720298;rs3813527;rs60184917;rs2720298	.	.	.	L	327	.	.	V	-	1	0	NCKAP5L	48476074	0.084000	0.21492	0.283000	0.24790	0.160000	0.22226	-0.757000	0.04772	-0.729000	0.04875	-0.311000	0.09066	GTA	C|0.433;A|0.567	0.567	strong		0.622	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497	
NAV2	89797	hgsc.bcm.edu	37	11	20112417	20112417	+	Silent	SNP	A	A	C	rs2243624	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:20112417A>C	ENST00000396087.3	+	30	5781	c.5682A>C	c.(5680-5682)tcA>tcC	p.S1894S	NAV2_ENST00000533917.1_Silent_p.S899S|NAV2_ENST00000540292.1_Silent_p.S1825S|NAV2_ENST00000360655.4_Silent_p.S1771S|NAV2_ENST00000396085.1_Silent_p.S1838S|NAV2_ENST00000311043.8_Silent_p.S899S|NAV2_ENST00000349880.4_Silent_p.S1835S|NAV2_ENST00000527559.2_Silent_p.S1823S	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1894					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						CTAGAATTTCAGAATGCATGG	0.438													A|||	2038	0.406949	0.4592	0.4467	5008	,	,		19772	0.6349		0.3101	False		,,,				2504	0.1728				p.S1894S		Atlas-SNP	.											.	NAV2	255	.	0			c.A5682C						PASS	.	A	,,,	1805,2601	531.5+/-373.2	358,1089,756	85.0	70.0	75.0		5313,2697,5505,5514	-11.1	0.0	11	dbSNP_100	75	2748,5852	439.1+/-359.1	457,1834,2009	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	815,2923,2765	CC,CA,AA		31.9535,40.9669,35.0069	,,,	1771/2366,899/1494,1835/2430,1838/2433	20112417	4553,8453	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon29			AATTTCAGAATGC	AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.5682A>C	11.37:g.20112417A>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			A|0.618;C|0.382	0.382	strong		0.438	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
DMBX1	127343	hgsc.bcm.edu	37	1	46978076	46978076	+	Silent	SNP	C	C	A	rs11211298	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46978076C>A	ENST00000360032.3	+	4	1058	c.1044C>A	c.(1042-1044)acC>acA	p.T348T	DMBX1_ENST00000371956.4_Silent_p.T353T	NM_172225.1	NP_757379.1			diencephalon/mesencephalon homeobox 1											endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)					CATCAGCTACCCTGAACAGTA	0.642													C|||	284	0.0567093	0.1293	0.0447	5008	,	,		19133	0.0407		0.0179	False		,,,				2504	0.0235				p.T353T		Atlas-SNP	.											.	DMBX1	50	.	0			c.C1059A						PASS	.	C	,	561,3845	241.5+/-251.9	40,481,1682	56.0	60.0	59.0		1059,1044	3.3	1.0	1	dbSNP_120	59	185,8415	82.6+/-145.2	0,185,4115	no	coding-synonymous,coding-synonymous	DMBX1	NM_147192.2,NM_172225.1	,	40,666,5797	AA,AC,CC		2.1512,12.7326,5.7358	,	353/383,348/378	46978076	746,12260	2203	4300	6503	SO:0001819	synonymous_variant	127343	exon4			AGCTACCCTGAAC	AB037699	CCDS536.1	1p34.1	2011-06-20	2004-03-29	2004-03-30	ENSG00000197587	ENSG00000197587		"""Homeoboxes / PRD class"""	19026	protein-coding gene	gene with protein product		607410	"""orthodenticle homolog 3 (Drosophila)"""	OTX3			Standard	NM_147192		Approved	PAXB	uc001cpx.3	Q8NFW5	OTTHUMG00000007982	ENST00000360032.3:c.1044C>A	1.37:g.46978076C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_147192		Silent	SNP	ENST00000360032.3	37	CCDS536.1																																																																																			C|0.938;A|0.062	0.062	strong		0.642	DMBX1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021895.1		
OR2T34	127068	hgsc.bcm.edu	37	1	248737293	248737293	+	Missense_Mutation	SNP	G	G	A	rs200427293	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248737293G>A	ENST00000328782.2	-	1	787	c.766C>T	c.(766-768)Ctc>Ttc	p.L256F		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	256						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)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	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)			GCACCGAAGAGCAGCAGCACT	0.547													a|||	1515	0.302516	0.379	0.2536	5008	,	,		10823	0.3194		0.2018	False		,,,				2504	0.32				p.L256F		Atlas-SNP	.											.	OR2T34	72	.	0			c.C766T						PASS	.																																			SO:0001583	missense	127068	exon1			CGAAGAGCAGCAG	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.766C>T	1.37:g.248737293G>A	ENSP00000330904:p.Leu256Phe	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	262	70	0.267176	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-3.326158	0.00017	.	.	ENSG00000183310	ENST00000328782	T	0.00014	9.19	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00049	-2.42	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.44847	-0.9301	9	0.02654	T	1	.	3.1711	0.06552	0.6602:0.0:0.1333:0.2065	.	256	Q8NGX1	O2T34_HUMAN	F	256	ENSP00000330904:L256F	ENSP00000330904:L256F	L	-	1	0	OR2T34	246803916	0.042000	0.20092	0.004000	0.12327	0.033000	0.12548	2.616000	0.46376	0.081000	0.16988	-1.849000	0.00571	CTC	.	.	weak		0.547	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
PSG7	5676	hgsc.bcm.edu	37	19	43433805	43433805	+	RNA	SNP	A	A	G	rs1065178	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43433805A>G	ENST00000406070.2	-	0	594				PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				CACAGGTTAAAATCACAGCCT	0.527													.|||	2229	0.445088	0.5666	0.4294	5008	,	,		18641	0.4216		0.2704	False		,,,				2504	0.4959				p.I44I		Atlas-SNP	.											.	.	.	.	0			c.T132C						PASS	.	G	,	2464,1938		733,998,470	220.0	217.0	218.0		132,498	-2.7	0.0	19	dbSNP_86	218	2421,6179		400,1621,2279	no	coding-synonymous,coding-synonymous	PSG7	NM_001206650.1,NM_002783.2	,	1133,2619,2749	GG,GA,AA		28.1512,44.0254,37.5711	,	44/298,166/420	43433805	4885,8117	2201	4300	6501			5676	exon2			GGTTAAAATCACA			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9524	protein-coding gene	gene with protein product		176396	"""pregnancy specific beta-1-glycoprotein 7"""				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		19.37:g.43433805A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	98	58	0.591837	NM_001206650	Q15232	Silent	SNP	ENST00000406070.2	37																																																																																				A|0.622;G|0.378	0.378	strong		0.527	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	NM_001206650	
SUPT6H	6830	hgsc.bcm.edu	37	17	27014483	27014483	+	Silent	SNP	C	C	A	rs28588628	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27014483C>A	ENST00000314616.6	+	23	3283	c.3000C>A	c.(2998-3000)ctC>ctA	p.L1000L	SUPT6H_ENST00000347486.4_Silent_p.L1000L	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1000	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					GGACCCACCTCCTGAAGGTAG	0.458													C|||	558	0.111422	0.1445	0.0634	5008	,	,		21310	0.1062		0.0726	False		,,,				2504	0.1462				p.L1000L		Atlas-SNP	.											.	SUPT6H	165	.	0			c.C3000A						PASS	.	C		589,3817	259.5+/-263.1	44,501,1658	48.0	43.0	45.0		3000	-5.8	1.0	17	dbSNP_125	45	767,7833	181.9+/-230.5	32,703,3565	no	coding-synonymous	SUPT6H	NM_003170.3		76,1204,5223	AA,AC,CC		8.9186,13.3681,10.426		1000/1727	27014483	1356,11650	2203	4300	6503	SO:0001819	synonymous_variant	6830	exon23			CCACCTCCTGAAG	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.3000C>A	17.37:g.27014483C>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	28	16	0.571429	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																			C|0.897;A|0.103	0.103	strong		0.458	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
ARHGAP24	83478	hgsc.bcm.edu	37	4	86915848	86915848	+	Silent	SNP	T	T	C	rs10003909	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:86915848T>C	ENST00000395184.1	+	9	1507	c.1041T>C	c.(1039-1041)aaT>aaC	p.N347N	ARHGAP24_ENST00000264343.4_Silent_p.N254N|ARHGAP24_ENST00000395183.2_Silent_p.N252N	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	347					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		GCAACAACAATGAAATTCAGA	0.463													C|||	1775	0.354433	0.4697	0.3098	5008	,	,		19886	0.3145		0.2227	False		,,,				2504	0.407				p.N347N		Atlas-SNP	.											.	ARHGAP24	116	.	0			c.T1041C						PASS	.	C	,,	1965,2441	619.5+/-393.4	445,1075,683	129.0	124.0	126.0		1041,756,762	0.2	0.7	4	dbSNP_119	126	1925,6675	726.8+/-406.6	236,1453,2611	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP24	NM_001025616.2,NM_001042669.1,NM_031305.2	,,	681,2528,3294	CC,CT,TT		22.3837,44.5983,29.9093	,,	347/749,252/654,254/656	86915848	3890,9116	2203	4300	6503	SO:0001819	synonymous_variant	83478	exon9			CAACAATGAAATT	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1041T>C	4.37:g.86915848T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Silent	SNP	ENST00000395184.1	37	CCDS34025.1																																																																																			T|0.690;C|0.310	0.310	strong		0.463	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
WDR62	284403	hgsc.bcm.edu	37	19	36549684	36549684	+	Silent	SNP	G	G	A	rs61742664	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36549684G>A	ENST00000270301.7	+	2	180	c.180G>A	c.(178-180)gtG>gtA	p.V60V	WDR62_ENST00000388999.3_Silent_p.V60V|WDR62_ENST00000401500.2_Silent_p.V60V|WDR62_ENST00000378860.4_3'UTR			O43379	WDR62_HUMAN	WD repeat domain 62	60					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CTTTGCAGGTGTCACTCGAGA	0.582													G|||	568	0.113419	0.0189	0.0865	5008	,	,		19086	0.2173		0.0358	False		,,,				2504	0.2331				p.V60V		Atlas-SNP	.											.	WDR62	102	.	0			c.G180A						PASS	.	G	,	124,4282	91.6+/-130.3	0,124,2079	81.0	70.0	74.0		180,180	-0.4	1.0	19	dbSNP_129	74	346,8254	116.5+/-176.2	3,340,3957	no	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	3,464,6036	AA,AG,GG		4.0233,2.8143,3.6137	,	60/1524,60/1519	36549684	470,12536	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon2			GCAGGTGTCACTC	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.180G>A	19.37:g.36549684G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			G|0.947;A|0.053	0.053	strong		0.582	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
STAB2	55576	hgsc.bcm.edu	37	12	104153004	104153004	+	Missense_Mutation	SNP	C	C	G	rs2271637	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:104153004C>G	ENST00000388887.2	+	65	7405	c.7201C>G	c.(7201-7203)Ctg>Gtg	p.L2401V	RP11-341G23.4_ENST00000551299.1_RNA	NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GCAAACGAGGCTGGGAAGCAA	0.537													C|||	1629	0.32528	0.1286	0.317	5008	,	,		19970	0.5238		0.2535	False		,,,				2504	0.4663				p.L2401V		Atlas-SNP	.											.	STAB2	370	.	0			c.C7201G						PASS	.	C	VAL/LEU	641,3765	275.2+/-272.4	47,547,1609	123.0	100.0	108.0		7201	3.8	1.0	12	dbSNP_100	108	2301,6299	388.9+/-342.7	280,1741,2279	yes	missense	STAB2	NM_017564.9	32	327,2288,3888	GG,GC,CC		26.7558,14.5483,22.6203	benign	2401/2552	104153004	2942,10064	2203	4300	6503	SO:0001583	missense	55576	exon65			ACGAGGCTGGGAA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.7201C>G	12.37:g.104153004C>G	ENSP00000373539:p.Leu2401Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	637	0.2916666666666667	53	0.10772357723577236	109	0.3011049723756906	283	0.49475524475524474	192	0.2532981530343008	C	12.05	1.822038	0.32237	0.145483	0.267558	ENSG00000136011	ENST00000388887	D	0.90620	-2.7	4.77	3.8	0.43715	FAS1 domain (4);	0.273443	0.30093	N	0.010439	T	0.00012	0.0000	M	0.78916	2.43	0.28695	P	0.9043705	P	0.47604	0.898	P	0.45167	0.472	T	0.11717	-1.0576	9	0.31617	T	0.26	.	11.0836	0.48074	0.311:0.689:0.0:0.0	rs2271637;rs52828564;rs2271637	2401	Q8WWQ8	STAB2_HUMAN	V	2401	ENSP00000373539:L2401V	ENSP00000373539:L2401V	L	+	1	2	STAB2	102677134	1.000000	0.71417	0.992000	0.48379	0.390000	0.30446	2.061000	0.41403	2.340000	0.79590	0.655000	0.94253	CTG	C|0.734;G|0.266	0.266	strong		0.537	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
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 GAIIx	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	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	24	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	
OR2T2	401992	hgsc.bcm.edu	37	1	248616401	248616401	+	Silent	SNP	G	G	A	rs77680148	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248616401G>A	ENST00000342927.3	+	1	325	c.303G>A	c.(301-303)caG>caA	p.Q101Q		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	101						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(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	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)			GTGCAGTTCAGATCTTCCTCT	0.532																																					p.Q101Q		Atlas-SNP	.											.	OR2T2	73	.	0			c.G303A						PASS	.						303.0	339.0	327.0					1																	248616401		2203	4300	6503	SO:0001819	synonymous_variant	401992	exon1			AGTTCAGATCTTC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.303G>A	1.37:g.248616401G>A		Somatic	824	1	0.00121359		WXS	Illumina HiSeq	Phase_I	673	135	0.200594	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			G|0.913;A|0.087	0.087	strong		0.532	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
CAMKV	79012	hgsc.bcm.edu	37	3	49898273	49898273	+	Silent	SNP	A	A	G	rs2681781	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49898273A>G	ENST00000477224.1	-	8	1129	c.651T>C	c.(649-651)aaT>aaC	p.N217N	CAMKV_ENST00000466940.1_Silent_p.N174N|CAMKV_ENST00000467248.1_Silent_p.N142N|RN7SL217P_ENST00000584520.1_RNA|CAMKV_ENST00000296471.7_Silent_p.N189N|CAMKV_ENST00000498324.1_5'Flank|CAMKV_ENST00000463537.1_Silent_p.N217N|CAMKV_ENST00000488336.1_Silent_p.N217N			Q8NCB2	CAMKV_HUMAN	CaM kinase-like vesicle-associated	217	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)			central_nervous_system(1)|large_intestine(2)|lung(2)|ovary(2)	7				BRCA - Breast invasive adenocarcinoma(193;4.62e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		AGAAAGGTGGATTGCCTGAAA	0.507													G|||	2019	0.403155	0.6914	0.3703	5008	,	,		16605	0.1448		0.4911	False		,,,				2504	0.2127				p.N217N		Atlas-SNP	.											.	CAMKV	84	.	0			c.T651C						PASS	.	G		2797,1609	497.6+/-363.9	894,1009,300	154.0	157.0	156.0		651	0.7	1.0	3	dbSNP_100	156	4271,4329	579.4+/-390.9	1060,2151,1089	no	coding-synonymous	CAMKV	NM_024046.3		1954,3160,1389	GG,GA,AA		49.6628,36.5184,45.6559		217/502	49898273	7068,5938	2203	4300	6503	SO:0001819	synonymous_variant	79012	exon8			AGGTGGATTGCCT	BC017363	CCDS33762.1	3p21.31	2005-03-04			ENSG00000164076	ENSG00000164076			28788	protein-coding gene	gene with protein product		614993				12477932	Standard	XM_005265478		Approved	MGC8407, VACAMKL	uc003cxt.1	Q8NCB2	OTTHUMG00000158288	ENST00000477224.1:c.651T>C	3.37:g.49898273A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_024046	A6NFD4|Q6FIB8|Q8NBS8|Q8NC85|Q8NDU4|Q8WTT8|Q9BQC9|Q9H0Q5	Silent	SNP	ENST00000477224.1	37	CCDS33762.1																																																																																			A|0.515;G|0.485	0.485	strong		0.507	CAMKV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350584.4	NM_024046	
FAM71D	161142	hgsc.bcm.edu	37	14	67675021	67675021	+	3'UTR	SNP	C	C	T	rs35680137	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:67675021C>T	ENST00000556046.1	+	0	1556							Q8N9W8	FA71D_HUMAN	family with sequence similarity 71, member D							cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)	13		all_hematologic(31;0.0116)		all cancers(60;0.00107)|BRCA - Breast invasive adenocarcinoma(234;0.00993)|OV - Ovarian serous cystadenocarcinoma(108;0.012)		AAACATAACACTGACTTTTGA	0.353													C|||	53	0.0105831	0.0	0.0144	5008	,	,		20068	0.0		0.0258	False		,,,				2504	0.0174				p.L339L		Atlas-SNP	.											.	FAM71D	33	.	0			c.C1015T						PASS	.	C		22,4384	29.0+/-57.7	0,22,2181	102.0	92.0	95.0		1015	2.6	0.7	14	dbSNP_126	95	240,8360	95.9+/-157.7	3,234,4063	no	coding-synonymous	FAM71D	NM_173526.3		3,256,6244	TT,TC,CC		2.7907,0.4993,2.0145		339/423	67675021	262,12744	2203	4300	6503	SO:0001624	3_prime_UTR_variant	161142	exon6			ATAACACTGACTT		CCDS9778.1	14q23.3	2007-11-20	2007-11-20	2007-11-20		ENSG00000172717			20101	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 54"""	C14orf54			Standard	NM_173526		Approved		uc001xja.2	Q8N9W8		ENST00000556046.1:c.*1071C>T	14.37:g.67675021C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_173526	Q86VN4	Silent	SNP	ENST00000556046.1	37																																																																																				C|0.983;T|0.017	0.017	strong		0.353	FAM71D-009	KNOWN	not_organism_supported|basic|appris_candidate	nonsense_mediated_decay	protein_coding	OTTHUMT00000412390.1	NM_173526	
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 GAIIx	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	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	65	24	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 GAIIx	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		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	31	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	
OR1S1	219959	hgsc.bcm.edu	37	11	57982726	57982726	+	Silent	SNP	G	G	T	rs1993089	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57982726G>T	ENST00000309433.6	+	1	510	c.510G>T	c.(508-510)ctG>ctT	p.L170L		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	170						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L170L(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTATTGCTCTGACACACACCC	0.478													G|||	2620	0.523163	0.2844	0.5418	5008	,	,		18215	0.8036		0.4225	False		,,,				2504	0.6472				p.L170L		Atlas-SNP	.											OR1S1,NS,carcinoma,0,1	OR1S1	139	1	1	Substitution - coding silent(1)	stomach(1)	c.G510T						PASS	.	G		1158,3244		197,764,1240	214.0	189.0	197.0		510	1.2	1.0	11	dbSNP_92	197	3386,5206		781,1824,1691	no	coding-synonymous	OR1S1	NM_001004458.1		978,2588,2931	TT,TG,GG		39.4088,26.3062,34.97		170/326	57982726	4544,8450	2201	4296	6497	SO:0001819	synonymous_variant	219959	exon1			TGCTCTGACACAC	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.510G>T	11.37:g.57982726G>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_001004458	Q6IFG3	Silent	SNP	ENST00000309433.6	37	CCDS31546.1																																																																																			G|0.609;T|0.391	0.391	strong		0.478	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
OR2T8	343172	hgsc.bcm.edu	37	1	248084470	248084470	+	Missense_Mutation	SNP	C	C	T	rs140846339|rs547311711	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248084470C>T	ENST00000319968.4	+	1	151	c.151C>T	c.(151-153)Cac>Tac	p.H51Y		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H51D(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCACTGGGACCACCGGCTCCA	0.532													C|||	94	0.01877	0.0666	0.0014	5008	,	,		15432	0.002		0.001	False		,,,				2504	0.002				p.H51Y		Atlas-SNP	.											OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	1	Substitution - Missense(1)	large_intestine(1)	c.C151T						scavenged	.						61.0	60.0	60.0					1																	248084470		2201	4297	6498	SO:0001583	missense	343172	exon1			TGGGACCACCGGC		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.151C>T	1.37:g.248084470C>T	ENSP00000326225:p.His51Tyr	Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	417	49	0.117506	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	.	.	.	.	.	.	.	.	.	.	c	7.674	0.687584	0.14973	.	.	ENSG00000177462	ENST00000319968	T	0.00428	7.44	3.65	0.32	0.15878	GPCR, rhodopsin-like superfamily (1);	3.036110	0.01499	U	0.017405	T	0.00300	0.0009	L	0.31476	0.935	0.09310	N	1	B	0.09022	0.002	B	0.17098	0.017	T	0.45920	-0.9228	10	0.45353	T	0.12	.	2.7852	0.05372	0.0:0.3992:0.2448:0.3561	.	51	A6NH00	OR2T8_HUMAN	Y	51	ENSP00000326225:H51Y	ENSP00000326225:H51Y	H	+	1	0	OR2T8	246151093	0.118000	0.22208	0.005000	0.12908	0.016000	0.09150	-0.265000	0.08644	0.228000	0.21019	0.603000	0.83216	CAC	.	.	weak		0.532	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
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 GAIIx	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		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	47	29	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	
FRY	10129	hgsc.bcm.edu	37	13	32752503	32752503	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:32752503A>G	ENST00000380250.3	+	21	3107	c.2611A>G	c.(2611-2613)Aca>Gca	p.T871A		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	871						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GCACTGCCCCACAGCCCTCAG	0.562																																					p.T871A		Atlas-SNP	.											.	FRY	312	.	0			c.A2611G						PASS	.						100.0	111.0	108.0					13																	32752503		2202	4298	6500	SO:0001583	missense	10129	exon21			TGCCCCACAGCCC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.2611A>G	13.37:g.32752503A>G	ENSP00000369600:p.Thr871Ala	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.605951	0.46527	.	.	ENSG00000073910	ENST00000380250	T	0.23754	1.89	5.5	4.33	0.51752	.	0.052645	0.85682	D	0.000000	T	0.25232	0.0613	L	0.55743	1.74	0.80722	D	1	B	0.32731	0.382	B	0.35607	0.206	T	0.02639	-1.1130	10	0.20046	T	0.44	.	11.2749	0.49161	0.9289:0.0:0.0711:0.0	.	871	Q5TBA9	FRY_HUMAN	A	871	ENSP00000369600:T871A	ENSP00000369600:T871A	T	+	1	0	FRY	31650503	1.000000	0.71417	0.963000	0.40424	0.887000	0.51463	4.264000	0.58859	0.935000	0.37341	-0.256000	0.11100	ACA	.	.	none		0.562	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
ZNF792	126375	hgsc.bcm.edu	37	19	35449760	35449760	+	Silent	SNP	G	G	C	rs2651080	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35449760G>C	ENST00000404801.1	-	4	1385	c.999C>G	c.(997-999)acC>acG	p.T333T	ZNF792_ENST00000605484.1_Silent_p.T266T	NM_175872.4	NP_787068.3	Q3KQV3	ZN792_HUMAN	zinc finger protein 792	333					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(4)|kidney(1)|large_intestine(1)|lung(5)	12	all_lung(56;4.18e-08)|Lung NSC(56;6.62e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			GGCTTTCACCGGTGTGAACCC	0.478													G|||	1615	0.322484	0.4652	0.1844	5008	,	,		20270	0.2034		0.33	False		,,,				2504	0.3425				p.T333T	GBM(1;7 183 21053 22581 22847)	Atlas-SNP	.											ZNF792,NS,carcinoma,-1,2	ZNF792	46	2	0			c.C999G						PASS	.	G		1845,2561	530.8+/-373.0	370,1105,728	61.0	58.0	59.0		999	-4.1	0.3	19	dbSNP_100	59	2542,6058	407.7+/-349.2	384,1774,2142	no	coding-synonymous	ZNF792	NM_175872.4		754,2879,2870	CC,CG,GG		29.5581,41.8747,33.7306		333/633	35449760	4387,8619	2203	4300	6503	SO:0001819	synonymous_variant	126375	exon4			TTCACCGGTGTGA	AK095770	CCDS12440.2	19q13.11	2013-01-08			ENSG00000180884	ENSG00000180884		"""Zinc fingers, C2H2-type"", ""-"""	24751	protein-coding gene	gene with protein product						8889548	Standard	NM_175872		Approved	FLJ38451	uc002nxh.1	Q3KQV3	OTTHUMG00000150339	ENST00000404801.1:c.999C>G	19.37:g.35449760G>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_175872	B4E333|Q495L1|Q495L3|Q8N932	Silent	SNP	ENST00000404801.1	37	CCDS12440.2																																																																																			G|0.671;C|0.329	0.329	strong		0.478	ZNF792-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317673.1	NM_175872	
DOCK1	1793	hgsc.bcm.edu	37	10	129216658	129216658	+	Silent	SNP	T	T	C	rs2229600	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:129216658T>C	ENST00000280333.6	+	45	4591	c.4482T>C	c.(4480-4482)atT>atC	p.I1494I		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1494	DHR-2.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AGAATGCCATTGAGACCATGC	0.597													C|||	1597	0.31889	0.2247	0.4222	5008	,	,		15912	0.4296		0.2575	False		,,,				2504	0.3221				p.I1494I		Atlas-SNP	.											.	DOCK1	188	.	0			c.T4482C						PASS	.	C		1055,3329		158,739,1295	52.0	62.0	59.0		4437	-1.7	1.0	10	dbSNP_98	59	2232,6364		304,1624,2370	no	coding-synonymous	DOCK1	NM_001380.3		462,2363,3665	CC,CT,TT		25.9656,24.0648,25.3236		1479/1851	129216658	3287,9693	2192	4298	6490	SO:0001819	synonymous_variant	1793	exon45			TGCCATTGAGACC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.4482T>C	10.37:g.129216658T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				A|0.000;C|0.325;G|0.000;T|0.674	0.325	strong		0.597	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
NOSTRIN	115677	hgsc.bcm.edu	37	2	169681151	169681151	+	Silent	SNP	C	C	T	rs3732031	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:169681151C>T	ENST00000317647.7	+	3	350	c.121C>T	c.(121-123)Ctg>Ttg	p.L41L	NOSTRIN_ENST00000421711.2_Intron|NOSTRIN_ENST00000458381.2_Silent_p.L41L|NOSTRIN_ENST00000397206.2_5'UTR|NOSTRIN_ENST00000397209.2_Intron|NOSTRIN_ENST00000445023.2_5'UTR|NOSTRIN_ENST00000444448.2_Silent_p.L41L	NM_001039724.3	NP_001034813.2	Q8IVI9	NOSTN_HUMAN	nitric oxide synthase trafficking	41	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				endocytosis (GO:0006897)|negative regulation of transcription, DNA-templated (GO:0045892)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoskeleton (GO:0005856)|endocytic vesicle membrane (GO:0030666)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)	p.L41L(2)		kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	9						CAGGGCAAACCTGGAAATTAG	0.473													C|||	535	0.106829	0.0446	0.0576	5008	,	,		21300	0.2788		0.0308	False		,,,				2504	0.1268				p.L41L		Atlas-SNP	.											NOSTRIN_ENST00000444448,NS,carcinoma,0,2	NOSTRIN	68	2	2	Substitution - coding silent(2)	prostate(2)	c.C121T						PASS	.	C	,,,	140,3642		2,136,1753	82.0	77.0	79.0		121,121,,	3.2	1.0	2	dbSNP_107	79	273,7981		6,261,3860	no	coding-synonymous,coding-synonymous,intron,utr-5	NOSTRIN	NM_001039724.3,NM_001171631.1,NM_001171632.1,NM_052946.3	,,,	8,397,5613	TT,TC,CC		3.3075,3.7017,3.4314	,,,	41/507,41/564,,	169681151	413,11623	1891	4127	6018	SO:0001819	synonymous_variant	115677	exon3			GCAAACCTGGAAA	AJ532842	CCDS42771.1, CCDS42772.1, CCDS54415.1, CCDS54416.1	2q31.1	2013-08-05	2013-08-05		ENSG00000163072	ENSG00000163072			20203	protein-coding gene	gene with protein product		607496	"""nitric oxide synthase trafficker"""			12446846	Standard	NM_001171631		Approved	MGC20702	uc002ueg.3	Q8IVI9	OTTHUMG00000153990	ENST00000317647.7:c.121C>T	2.37:g.169681151C>T		Somatic	421	0	0		WXS	Illumina HiSeq	Phase_I	367	168	0.457766	NM_001039724	A8K2I9|B3KSF5|E7EPT9|Q27HG3|Q53S62|Q96CJ9	Silent	SNP	ENST00000317647.7	37	CCDS42771.1																																																																																			C|0.900;T|0.100	0.100	strong		0.473	NOSTRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333356.4	NM_052946	
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 GAIIx	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_ENST00000448430.2_Splice_Site_p.V91I|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Splice_Site_p.V91I|DYX1C1_ENST00000457155.2_Splice_Site_p.V91I|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		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	29	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
MADD	8567	hgsc.bcm.edu	37	11	47303275	47303275	+	Silent	SNP	T	T	C	rs326217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:47303275T>C	ENST00000311027.5	+	8	1605	c.1440T>C	c.(1438-1440)aaT>aaC	p.N480N	MADD_ENST00000407859.3_Silent_p.N480N|MADD_ENST00000402192.2_Silent_p.N480N|MADD_ENST00000342922.4_Silent_p.N480N|MADD_ENST00000395344.3_Silent_p.N480N|MADD_ENST00000406482.1_Silent_p.N480N|MADD_ENST00000349238.3_Silent_p.N480N|MADD_ENST00000489415.1_3'UTR|MADD_ENST00000395336.3_Silent_p.N480N|MADD_ENST00000402799.1_Silent_p.N480N	NM_003682.3	NP_003673.3			MAP-kinase activating death domain											breast(7)|central_nervous_system(2)|endometrium(9)|kidney(3)|large_intestine(19)|lung(26)|ovary(6)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	84				Lung(87;0.182)		TCTATGGCAATGATGTGGATT	0.468													T|||	1483	0.296126	0.2481	0.4352	5008	,	,		18300	0.252		0.3042	False		,,,				2504	0.2996				p.N480N		Atlas-SNP	.											.	MADD	172	.	0			c.T1440C						PASS	.	T	,,,,,,,,,	1066,3336	389.1+/-327.2	115,836,1250	80.0	75.0	77.0		1440,1440,1440,1440,1440,1440,1440,1440,1440,1440	-4.1	0.7	11	dbSNP_79	77	2635,5961	426.0+/-355.2	391,1853,2054	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MADD	NM_001135943.1,NM_001135944.1,NM_003682.3,NM_130470.2,NM_130471.2,NM_130472.2,NM_130473.2,NM_130474.2,NM_130475.2,NM_130476.2	,,,,,,,,,	506,2689,3304	CC,CT,TT		30.6538,24.2163,28.4736	,,,,,,,,,	480/1545,480/1542,480/1648,480/1589,480/1566,480/1546,480/1609,480/1480,480/1582,480/1588	47303275	3701,9297	2201	4298	6499	SO:0001819	synonymous_variant	8567	exon8			TGGCAATGATGTG	AB002356	CCDS7930.1, CCDS7931.1, CCDS7932.1, CCDS41642.1, CCDS44586.1, CCDS44587.1, CCDS44588.1, CCDS44589.1, CCDS44590.1	11p11.2	2012-10-04			ENSG00000110514	ENSG00000110514		"""DENN/MADD domain containing"""	6766	protein-coding gene	gene with protein product		603584				9115275, 9796103	Standard	NM_130476		Approved	DENN, KIAA0358, RAB3GEP	uc001ner.1	Q8WXG6	OTTHUMG00000150350	ENST00000311027.5:c.1440T>C	11.37:g.47303275T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_130474		Silent	SNP	ENST00000311027.5	37	CCDS7930.1																																																																																			T|0.698;C|0.302	0.302	strong		0.468	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
TSNARE1	203062	hgsc.bcm.edu	37	8	143427178	143427178	+	Missense_Mutation	SNP	C	C	G	rs33970858	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143427178C>G	ENST00000307180.3	-	3	281	c.164G>C	c.(163-165)cGc>cCc	p.R55P	TSNARE1_ENST00000524325.1_Missense_Mutation_p.R55P|TSNARE1_ENST00000520166.1_Missense_Mutation_p.R55P|TSNARE1_ENST00000519651.1_Intron	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	55			R -> P (in dbSNP:rs33970858). {ECO:0000269|PubMed:14702039}.		intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)	p.R55P(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCCACACAGCGGTTCTGCAG	0.607													G|||	1814	0.36222	0.652	0.2896	5008	,	,		21165	0.3472		0.1978	False		,,,				2504	0.2065				p.R55P		Atlas-SNP	.											TSNARE1,NS,carcinoma,0,1	TSNARE1	59	1	1	Substitution - Missense(1)	stomach(1)	c.G164C						scavenged	.	G	PRO/ARG	2522,1884	543.6+/-376.3	730,1062,411	111.0	92.0	99.0		164	-0.3	0.0	8	dbSNP_126	99	1806,6794	732.8+/-406.9	185,1436,2679	yes	missense	TSNARE1	NM_145003.3	103	915,2498,3090	GG,GC,CC		21.0,42.7599,33.2769	benign	55/514	143427178	4328,8678	2203	4300	6503	SO:0001583	missense	203062	exon3			ACACAGCGGTTCT			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.164G>C	8.37:g.143427178C>G	ENSP00000303437:p.Arg55Pro	Somatic	136	3	0.0220588		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	734	0.3360805860805861	284	0.5772357723577236	96	0.26519337016574585	216	0.3776223776223776	138	0.1820580474934037	G	0.008	-1.876825	0.00537	0.572401	0.21	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000520462;ENST00000518720	T;T;T;T;T	0.25414	2.68;2.67;2.68;1.82;1.8	2.62	-0.305	0.12784	.	0.698313	0.10997	N	0.610948	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43147	-0.9409	9	0.02654	T	1	.	3.8909	0.09119	0.258:0.3986:0.3434:0.0	rs33970858	55;55;55	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	P	55;55;55;55;71	ENSP00000428763:R55P;ENSP00000303437:R55P;ENSP00000427770:R55P;ENSP00000429626:R55P;ENSP00000430789:R71P	ENSP00000303437:R55P	R	-	2	0	TSNARE1	143425085	0.005000	0.15991	0.000000	0.03702	0.730000	0.41778	0.493000	0.22451	-0.386000	0.07821	-0.744000	0.03518	CGC	C|0.671;G|0.329	0.329	strong		0.607	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
DOK3	79930	hgsc.bcm.edu	37	5	176931594	176931594	+	Missense_Mutation	SNP	G	G	C	rs61749657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:176931594G>C	ENST00000357198.4	-	6	885	c.881C>G	c.(880-882)cCc>cGc	p.P294R	DOK3_ENST00000501403.2_Missense_Mutation_p.P238R|DOK3_ENST00000377112.4_Intron|RP11-1334A24.6_ENST00000506025.1_RNA|DOK3_ENST00000312943.6_Intron	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3	294	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				Ras protein signal transduction (GO:0007265)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|lung(7)	13	all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	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)|Epithelial(233;0.191)			AGGGGCACAGGGGGTGCTGAA	0.721													G|||	229	0.0457268	0.0333	0.0922	5008	,	,		15822	0.0149		0.0527	False		,,,				2504	0.0542				p.P294R		Atlas-SNP	.											.	DOK3	41	.	0			c.C881G						PASS	.	G	,,ARG/PRO	112,4246		1,110,2068	9.0	11.0	10.0		,,881	3.5	0.1	5	dbSNP_129	10	415,8115		8,399,3858	no	intron,intron,missense	DOK3	NM_001144875.1,NM_001144876.1,NM_024872.2	,,103	9,509,5926	CC,CG,GG		4.8652,2.57,4.0891	,,probably-damaging	,,294/497	176931594	527,12361	2179	4265	6444	SO:0001583	missense	79930	exon6			GCACAGGGGGTGC	AK026223	CCDS4426.1, CCDS47349.1, CCDS47350.1	5q35	2008-02-05			ENSG00000146094	ENSG00000146094			24583	protein-coding gene	gene with protein product		611435				10733577, 12595900	Standard	NM_024872		Approved	FLJ22570	uc003mhk.3	Q7L591	OTTHUMG00000130850	ENST00000357198.4:c.881C>G	5.37:g.176931594G>C	ENSP00000349727:p.Pro294Arg	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	14	6	0.428571	NM_024872	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	37	CCDS4426.1	79	0.036172161172161175	14	0.028455284552845527	23	0.06353591160220995	7	0.012237762237762238	35	0.04617414248021108	G	0.016	-1.529722	0.00951	0.0257	0.048652	ENSG00000146094	ENST00000357198;ENST00000501403	T;T	0.81330	-1.48;-1.48	3.55	3.55	0.40652	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (3);	1.308000	0.05370	N	0.535246	T	0.31451	0.0797	N	0.20881	0.62	0.09310	N	1	P	0.49307	0.922	P	0.52386	0.697	T	0.54529	-0.8280	10	0.02654	T	1	0.2479	13.0678	0.59043	0.0:0.0:1.0:0.0	rs61749657	294	Q7L591	DOK3_HUMAN	R	294;238	ENSP00000349727:P294R;ENSP00000421688:P238R	ENSP00000349727:P294R	P	-	2	0	DOK3	176864200	0.620000	0.27068	0.106000	0.21319	0.013000	0.08279	1.014000	0.29950	1.805000	0.52779	0.313000	0.20887	CCC	G|0.965;C|0.035	0.035	strong		0.721	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872	
ENTPD7	57089	hgsc.bcm.edu	37	10	101445591	101445591	+	Silent	SNP	A	A	C	rs3740078	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101445591A>C	ENST00000370489.4	+	6	769	c.591A>C	c.(589-591)ccA>ccC	p.P197P		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	197						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		AAGATTTACCACTGGAGTTTG	0.443													A|||	1260	0.251597	0.233	0.2277	5008	,	,		18818	0.2956		0.3082	False		,,,				2504	0.1902				p.P197P		Atlas-SNP	.											.	ENTPD7	44	.	0			c.A591C						PASS	.	A		1020,3386	379.0+/-323.1	114,792,1297	127.0	119.0	121.0		591	-11.0	0.2	10	dbSNP_107	121	2571,6029	419.2+/-353.0	391,1789,2120	no	coding-synonymous	ENTPD7	NM_020354.3		505,2581,3417	CC,CA,AA		29.8953,23.1502,27.6103		197/605	101445591	3591,9415	2203	4300	6503	SO:0001819	synonymous_variant	57089	exon6			TTTACCACTGGAG	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.591A>C	10.37:g.101445591A>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_020354	B2RB83|B3KP21|D3DR64	Silent	SNP	ENST00000370489.4	37	CCDS7480.1																																																																																			A|0.734;C|0.266	0.266	strong		0.443	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
PRR14L	253143	hgsc.bcm.edu	37	22	32110163	32110163	+	Missense_Mutation	SNP	G	G	A	rs140078	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:32110163G>A	ENST00000327423.6	-	4	3851	c.3662C>T	c.(3661-3663)tCg>tTg	p.S1221L	PRR14L_ENST00000434485.1_Missense_Mutation_p.S1221L|PRR14L_ENST00000461722.1_5'Flank|PRR14L_ENST00000397493.2_Missense_Mutation_p.S1221L	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1221			S -> L (in dbSNP:rs140078).							endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GCAAGACATCGACTCTTTTGA	0.373											OREG0003535	type=REGULATORY REGION|Gene=AK130944|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	A|||	1729	0.345248	0.5847	0.3055	5008	,	,		19890	0.1875		0.2048	False		,,,				2504	0.3569				p.S1221L		Atlas-SNP	.											.	PRR14L	198	.	0			c.C3662T						PASS	.	A	LEU/SER	729,655		195,339,158	210.0	155.0	172.0		3662	-0.9	0.0	22	dbSNP_78	172	680,2502		80,520,991	yes	missense	PRR14L	NM_173566.2	145	275,859,1149	AA,AG,GG		21.3702,47.3266,30.8585	benign	1221/2152	32110163	1409,3157	692	1591	2283	SO:0001583	missense	253143	exon4			GACATCGACTCTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.3662C>T	22.37:g.32110163G>A	ENSP00000331845:p.Ser1221Leu	Somatic	118	0	0	829	WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	649	0.29716117216117216	286	0.5813008130081301	104	0.287292817679558	105	0.18356643356643357	154	0.20316622691292877	A	0.005	-2.181697	0.00308	0.526734	0.213702	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.05649	3.41;3.42;3.42	5.53	-0.868	0.10652	.	0.739382	0.11730	N	0.535009	T	0.00012	0.0000	N	0.01297	-0.9	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.18555	-1.0333	8	.	.	.	0.8397	8.0433	0.30534	0.362:0.131:0.5069:0.0	rs140078;rs3804091;rs60386080;rs140078	1221;1221;1221	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	L	1221	ENSP00000380630:S1221L;ENSP00000331845:S1221L;ENSP00000388314:S1221L	.	S	-	2	0	PRR14L	30440163	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.533000	0.06157	-0.419000	0.07439	-1.242000	0.01536	TCG	G|0.689;A|0.311	0.311	strong		0.373	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
FANCI	55215	hgsc.bcm.edu	37	15	89836228	89836228	+	Missense_Mutation	SNP	G	G	C	rs2283432	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89836228G>C	ENST00000310775.7	+	22	2311	c.2225G>C	c.(2224-2226)tGt>tCt	p.C742S	FANCI_ENST00000300027.8_Missense_Mutation_p.C742S	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	742			C -> S (in dbSNP:rs2283432). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:14702039}.		cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					AATAATATCTGTGCTTTTCTT	0.313								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	1327	0.264976	0.0393	0.3473	5008	,	,		18777	0.3135		0.3837	False		,,,				2504	0.3395				p.C742S		Atlas-SNP	.											FANCI_ENST00000310775,NS,adenoma,0,2	FANCI	129	2	0			c.G2225C						PASS	.	G	SER/CYS,SER/CYS	419,3979	203.8+/-226.2	19,381,1799	118.0	119.0	119.0		2225,2225	4.9	1.0	15	dbSNP_100	119	3349,5249	495.5+/-374.1	653,2043,1603	yes	missense,missense	FANCI	NM_001113378.1,NM_018193.2	112,112	672,2424,3402	CC,CG,GG		38.9509,9.5271,28.9935	benign,benign	742/1329,742/1269	89836228	3768,9228	2199	4299	6498	SO:0001583	missense	55215	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	ATATCTGTGCTTT	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.2225G>C	15.37:g.89836228G>C	ENSP00000310842:p.Cys742Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Missense_Mutation	SNP	ENST00000310775.7	37	CCDS45346.1	635	0.2907509157509158	29	0.05894308943089431	121	0.3342541436464088	179	0.3129370629370629	306	0.40369393139841686	G	12.46	1.945389	0.34377	0.095271	0.389509	ENSG00000140525	ENST00000300027;ENST00000310775;ENST00000447611	T;T;T	0.28069	1.63;1.63;1.63	5.9	4.89	0.63831	.	0.102357	0.64402	N	0.000001	T	0.00012	0.0000	L	0.44542	1.39	0.09310	P	1.0	B;P;P	0.39131	0.007;0.46;0.661	B;B;B	0.31869	0.006;0.089;0.137	T	0.48768	-0.9006	9	0.22109	T	0.4	-6.0576	3.9069	0.09186	0.3188:0.0:0.6812:0.0	rs2283432;rs52810132;rs2283432	742;742;742	Q9NVI1;Q9NVI1-2;Q9NVI1-1	FANCI_HUMAN;.;.	S	742	ENSP00000300027:C742S;ENSP00000310842:C742S;ENSP00000413249:C742S	ENSP00000300027:C742S	C	+	2	0	FANCI	87637232	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	4.932000	0.63476	2.793000	0.96121	0.563000	0.77884	TGT	G|0.715;C|0.285	0.285	strong		0.313	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
ARSE	415	hgsc.bcm.edu	37	X	2856155	2856155	+	Missense_Mutation	SNP	C	C	T	rs35143646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:2856155C>T	ENST00000381134.3	-	9	1336	c.1270G>A	c.(1270-1272)Ggc>Agc	p.G424S	ARSE_ENST00000540563.1_Missense_Mutation_p.G379S|ARSE_ENST00000545496.1_Missense_Mutation_p.G449S	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	424			G -> S (in dbSNP:rs35143646). {ECO:0000269|Ref.2}.		cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		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)				GGCACCTCGCCGCCCGCCAGC	0.602													C|||	2169	0.57457	0.059	0.415	3775	,	,		11186	0.6786		0.5278	False		,,,				2504	0.6012				p.G424S		Atlas-SNP	.											.	ARSE	43	.	0			c.G1270A						PASS	.	C	SER/GLY	687,3144		65,474,83,1093,484	52.0	55.0	54.0		1270	3.5	0.0	X	dbSNP_126	54	4504,2211		1084,1066,1270,277,591	no	missense	ARSE	NM_000047.2	56	1149,1540,1353,1370,1075	TT,TC,T,CC,C		32.9263,17.9327,49.2225	benign	424/590	2856155	5191,5355	2199	4288	6487	SO:0001583	missense	415	exon9			CCTCGCCGCCCGC	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1270G>A	X.37:g.2856155C>T	ENSP00000370526:p.Gly424Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	176	47	0.267045	NM_000047	Q53FT2|Q53FU8	Missense_Mutation	SNP	ENST00000381134.3	37	CCDS14122.1	951	0.5732368896925859	22	0.046413502109704644	94	0.3671875	255	0.796875	275	0.5308880308880309	c	10.51	1.369388	0.24771	0.179327	0.670737	ENSG00000157399	ENST00000540563;ENST00000545496;ENST00000381134	D;D;D	0.93859	-3.3;-3.3;-3.3	3.46	3.46	0.39613	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.055865	0.64402	D	0.000001	T	0.00012	0.0000	L	0.56769	1.78	0.22424	P	0.999114817	P;P;P	0.50819	0.931;0.939;0.905	P;B;P	0.46299	0.511;0.41;0.49	T	0.48502	-0.9030	9	0.20519	T	0.43	.	14.3929	0.66991	0.0:1.0:0.0:0.0	rs35143646;rs60405351	379;449;424	F5H324;F5GYY5;P51690	.;.;ARSE_HUMAN	S	379;449;424	ENSP00000438198:G379S;ENSP00000441417:G449S;ENSP00000370526:G424S	ENSP00000370526:G424S	G	-	1	0	ARSE	2866155	1.000000	0.71417	0.017000	0.16124	0.005000	0.04900	6.335000	0.72949	1.355000	0.45865	0.540000	0.68198	GGC	C|0.503;T|0.497	0.497	strong		0.602	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
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 GAIIx	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	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	39	14	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		
TRPA1	8989	hgsc.bcm.edu	37	8	72948588	72948588	+	Silent	SNP	C	C	T	rs13280644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:72948588C>T	ENST00000262209.4	-	21	2697	c.2490G>A	c.(2488-2490)ctG>ctA	p.L830L	RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron|TRPA1_ENST00000519720.1_5'UTR|RP11-383H13.1_ENST00000524152.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	830					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	ATTGCCACTGCAGATGAGCTG	0.353													C|||	251	0.0501198	0.0045	0.0634	5008	,	,		17025	0.003		0.0924	False		,,,				2504	0.1074				p.L830L		Atlas-SNP	.											.	TRPA1	256	.	0			c.G2490A						PASS	.	C		78,4328	69.8+/-107.6	0,78,2125	67.0	66.0	67.0		2490	0.2	0.6	8	dbSNP_121	67	841,7759	193.7+/-239.3	46,749,3505	no	coding-synonymous	TRPA1	NM_007332.2		46,827,5630	TT,TC,CC		9.7791,1.7703,7.066		830/1120	72948588	919,12087	2203	4300	6503	SO:0001819	synonymous_variant	8989	exon21			CCACTGCAGATGA	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.2490G>A	8.37:g.72948588C>T		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	189	109	0.57672	NM_007332	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																			C|0.934;T|0.066	0.066	strong		0.353	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
BMS1	9790	hgsc.bcm.edu	37	10	43281089	43281089	+	Silent	SNP	T	T	C	rs7074877	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:43281089T>C	ENST00000374518.5	+	3	399	c.336T>C	c.(334-336)acT>acC	p.T112T		NM_014753.3	NP_055568.3	Q14692	BMS1_HUMAN	BMS1 ribosome biogenesis factor	112	Bms1-type G.				ribosome assembly (GO:0042255)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(23)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						AGAAGTTGACTGAGATCAGAG	0.512													C|||	2810	0.561102	0.6293	0.4899	5008	,	,		15419	0.6359		0.4185	False		,,,				2504	0.589				p.T112T		Atlas-SNP	.											.	BMS1	132	.	0			c.T336C						PASS	.	C		2628,1778		783,1062,358	136.0	140.0	139.0		336	-7.2	0.8	10	dbSNP_116	139	3363,5237		651,2061,1588	no	coding-synonymous	BMS1	NM_014753.3		1434,3123,1946	CC,CT,TT		39.1047,40.3541,46.0634		112/1283	43281089	5991,7015	2203	4300	6503	SO:0001819	synonymous_variant	9790	exon3			GTTGACTGAGATC	BC043345	CCDS7199.1	10q11.21	2013-05-01	2013-05-01	2007-03-20	ENSG00000165733	ENSG00000165733			23505	protein-coding gene	gene with protein product		611448	"""BMS1-like, ribosome assembly protein (yeast)"", ""BMS1 homolog, ribosome assembly protein (yeast)"""	BMS1L		11779832	Standard	NM_014753		Approved	KIAA0187	uc001jaj.3	Q14692	OTTHUMG00000018020	ENST00000374518.5:c.336T>C	10.37:g.43281089T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_014753	Q5QPT5|Q86XJ9	Silent	SNP	ENST00000374518.5	37	CCDS7199.1																																																																																			T|0.503;C|0.497	0.497	strong		0.512	BMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047690.2	NM_014753	
IPO4	79711	hgsc.bcm.edu	37	14	24653954	24653954	+	Missense_Mutation	SNP	G	G	A	rs7146310	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24653954G>A	ENST00000354464.6	-	16	1714	c.1538C>T	c.(1537-1539)gCc>gTc	p.A513V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	513			A -> V (in dbSNP:rs7146310). {ECO:0000269|PubMed:11823430, ECO:0000269|PubMed:14702039}.		DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		CAGCAGCGAGGCCTGGGCAGC	0.622													G|||	1592	0.317891	0.2163	0.2363	5008	,	,		18141	0.4206		0.2654	False		,,,				2504	0.4611				p.A513V		Atlas-SNP	.											IPO4,NS,carcinoma,+1,1	IPO4	74	1	0			c.C1538T						PASS	.	G	VAL/ALA	911,3223		105,701,1261	21.0	26.0	24.0		1538	3.3	1.0	14	dbSNP_116	24	2400,5978		321,1758,2110	yes	missense	IPO4	NM_024658.3	64	426,2459,3371	AA,AG,GG		28.6465,22.0368,26.4626	benign	513/1082	24653954	3311,9201	2067	4189	6256	SO:0001583	missense	79711	exon16			AGCGAGGCCTGGG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1538C>T	14.37:g.24653954G>A	ENSP00000346453:p.Ala513Val	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	190	114	0.6	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Missense_Mutation	SNP	ENST00000354464.6	37	CCDS9616.1	648	0.2967032967032967	106	0.21544715447154472	94	0.2596685082872928	249	0.4353146853146853	199	0.262532981530343	G	14.34	2.506634	0.44558	0.220368	0.286465	ENSG00000196497	ENST00000354464;ENST00000399536	T	0.04654	3.58	5.28	3.32	0.38043	Armadillo-like helical (1);Armadillo-type fold (1);	0.612691	0.17322	N	0.178468	T	0.00012	0.0000	N	0.17474	0.49	0.46317	P	0.0010149999999999881	B	0.09022	0.002	B	0.16722	0.016	T	0.43925	-0.9361	9	0.51188	T	0.08	-1.7252	7.6189	0.28173	0.0:0.1498:0.4235:0.4267	rs7146310;rs17256720;rs61234434;rs7146310	513	Q8TEX9	IPO4_HUMAN	V	513;189	ENSP00000346453:A513V	ENSP00000346453:A513V	A	-	2	0	IPO4	23723794	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	1.072000	0.30678	1.412000	0.46977	0.558000	0.71614	GCC	G|0.693;A|0.307	0.307	strong		0.622	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
TACC2	10579	hgsc.bcm.edu	37	10	123845897	123845897	+	Silent	SNP	G	G	C	rs1106992	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:123845897G>C	ENST00000369005.1	+	4	4222	c.3882G>C	c.(3880-3882)ctG>ctC	p.L1294L	TACC2_ENST00000334433.3_Silent_p.L1294L|TACC2_ENST00000515603.1_Silent_p.L1294L|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000453444.2_Silent_p.L1294L|TACC2_ENST00000515273.1_Silent_p.L1294L	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1294					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TCGCCCCCCTGTTGCAACCAG	0.607													C|||	1024	0.204473	0.2973	0.1916	5008	,	,		18740	0.1022		0.2167	False		,,,				2504	0.181				p.L1294L		Atlas-SNP	.											.	TACC2	271	.	0			c.G3882C						PASS	.	C	,	1462,2944	674.0+/-402.9	243,976,984	33.0	34.0	34.0		,3882	2.0	0.0	10	dbSNP_86	34	1971,6629	719.9+/-406.3	224,1523,2553	no	intron,coding-synonymous	TACC2	NM_206861.1,NM_206862.2	,	467,2499,3537	CC,CG,GG		22.9186,33.182,26.3955	,	,1294/2949	123845897	3433,9573	2203	4300	6503	SO:0001819	synonymous_variant	10579	exon4			CCCCCTGTTGCAA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.3882G>C	10.37:g.123845897G>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	43	18	0.418605	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			G|0.758;C|0.242	0.242	strong		0.607	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
NSFL1C	55968	hgsc.bcm.edu	37	20	1426393	1426393	+	Missense_Mutation	SNP	C	C	T	rs9575	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:1426393C>T	ENST00000216879.4	-	8	1735	c.868G>A	c.(868-870)Gac>Aac	p.D290N	NSFL1C_ENST00000350991.4_Missense_Mutation_p.D292N|NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000476071.1_Missense_Mutation_p.D292N|NSFL1C_ENST00000353088.2_Missense_Mutation_p.D259N|NSFL1C_ENST00000381658.4_Missense_Mutation_p.D179N	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	290			D -> N (in dbSNP:rs9575). {ECO:0000269|PubMed:11042152}.			chromosome (GO:0005694)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						TCTGATTCGTCGATTAAGATG	0.537													C|||	2336	0.466454	0.2534	0.5115	5008	,	,		19949	0.7887		0.4076	False		,,,				2504	0.4509				p.D290N		Atlas-SNP	.											NSFL1C,colon,carcinoma,+2,2	NSFL1C	38	2	0			c.G868A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	1221,3185	423.4+/-340.1	169,883,1151	200.0	195.0	197.0		874,868,775	-1.4	0.1	20	dbSNP_52	197	3519,5081	514.1+/-378.3	735,2049,1516	yes	missense,missense,missense	NSFL1C	NM_001206736.1,NM_016143.4,NM_018839.4	23,23,23	904,2932,2667	TT,TC,CC		40.9186,27.7122,36.4447	benign,benign,benign	292/373,290/371,259/340	1426393	4740,8266	2203	4300	6503	SO:0001583	missense	55968	exon8			ATTCGTCGATTAA	AF112211	CCDS13015.1, CCDS13016.1, CCDS56175.1	20p13	2011-06-28			ENSG00000088833	ENSG00000088833		"""UBX domain containing"""	15912	protein-coding gene	gene with protein product	"""SHP1 homolog (S. cerevisiae)"", ""UBX domain protein 2C"""	606610				11042152	Standard	NM_016143		Approved	dJ776F14.1, p47, UBXD10, UBX1, UBXN2C	uc002wfc.3	Q9UNZ2	OTTHUMG00000031665	ENST00000216879.4:c.868G>A	20.37:g.1426393C>T	ENSP00000216879:p.Asp290Asn	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	122	120	0.983607	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	37	CCDS13015.1	1054	0.4826007326007326	117	0.23780487804878048	172	0.47513812154696133	439	0.7674825174825175	326	0.43007915567282323	C	15.62	2.888671	0.52014	0.277122	0.409186	ENSG00000088833	ENST00000353088;ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91	4.53	-1.35	0.09114	UBX (1);	0.224720	0.44688	N	0.000435	T	0.00012	0.0000	L	0.52759	1.655	0.20403	P	0.9999006895	B;B;B	0.20671	0.027;0.047;0.013	B;B;B	0.17433	0.007;0.017;0.018	T	0.27468	-1.0073	9	0.49607	T	0.09	-3.2202	9.1604	0.37019	0.0:0.65:0.0:0.35	rs9575;rs3171294;rs17719623;rs9575	259;179;290	Q9UNZ2-4;Q9UNZ2-6;Q9UNZ2	.;.;NSF1C_HUMAN	N	259;292;290;179;292	ENSP00000338643:D259N;ENSP00000418529:D292N;ENSP00000216879:D290N;ENSP00000371074:D179N;ENSP00000202584:D292N	ENSP00000216879:D290N	D	-	1	0	NSFL1C	1374393	0.977000	0.34250	0.137000	0.22149	0.916000	0.54674	1.085000	0.30840	-0.271000	0.09272	-0.367000	0.07326	GAC	C|0.589;T|0.411	0.411	strong		0.537	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143	
GABRA6	2559	hgsc.bcm.edu	37	5	161119125	161119125	+	Silent	SNP	C	C	G	rs13184586	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:161119125C>G	ENST00000274545.5	+	8	1438	c.1005C>G	c.(1003-1005)gcC>gcG	p.A335A	GABRA6_ENST00000523217.1_Silent_p.A325A|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	335					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CACAGAAGGCCAAAAGGAAGG	0.433										TCGA Ovarian(5;0.080)			C|||	2009	0.401158	0.3351	0.3732	5008	,	,		19042	0.3185		0.5736	False		,,,				2504	0.4182				p.A335A		Atlas-SNP	.											.	GABRA6	139	.	0			c.C1005G						PASS	.	C		1564,2842	491.3+/-362.1	273,1018,912	161.0	139.0	146.0		1005	-1.1	1.0	5	dbSNP_121	146	4784,3816	613.0+/-396.0	1320,2144,836	no	coding-synonymous	GABRA6	NM_000811.2		1593,3162,1748	GG,GC,CC		44.3721,35.497,48.8082		335/454	161119125	6348,6658	2203	4300	6503	SO:0001819	synonymous_variant	2559	exon8			GAAGGCCAAAAGG		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.1005C>G	5.37:g.161119125C>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	99	53	0.535354	NM_000811	A8K096|Q4VAV2	Silent	SNP	ENST00000274545.5	37	CCDS4356.1																																																																																			C|0.535;G|0.465	0.465	strong		0.433	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
TET2	54790	hgsc.bcm.edu	37	4	106196829	106196829	+	Missense_Mutation	SNP	T	T	G	rs34402524	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106196829T>G	ENST00000540549.1	+	11	6022	c.5162T>G	c.(5161-5163)tTg>tGg	p.L1721W	TET2_ENST00000513237.1_Missense_Mutation_p.L1742W|TET2_ENST00000380013.4_Missense_Mutation_p.L1721W|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1721			L -> W (in dbSNP:rs34402524). {ECO:0000269|PubMed:19483684}.		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.L1721*(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)		GTAGGGAAATTGCCTCCTTAT	0.408			"""Mis N, F"""		MDS								T|||	459	0.0916534	0.0915	0.0893	5008	,	,		23039	0.0466		0.1402	False		,,,				2504	0.09				p.L1721W		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,haematopoietic_neoplasm,0,1	TET2	1762	1	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T5162G						PASS	.	T	TRP/LEU	134,1250		4,126,562	102.0	85.0	91.0		5162	5.2	0.1	4	dbSNP_126	91	429,2753		23,383,1185	yes	missense	TET2	NM_001127208.2	61	27,509,1747	GG,GT,TT		13.4821,9.6821,12.3303	possibly-damaging	1721/2003	106196829	563,4003	692	1591	2283	SO:0001583	missense	54790	exon11			GGAAATTGCCTCC	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.5162T>G	4.37:g.106196829T>G	ENSP00000442788:p.Leu1721Trp	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	137	71	0.518248	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	201	0.09203296703296704	33	0.06707317073170732	43	0.11878453038674033	22	0.038461538461538464	103	0.1358839050131926	T	10.42	1.344270	0.24339	0.096821	0.134821	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.02301	4.35;4.35;4.35	5.16	5.16	0.70880	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.37752	P	0.07400899999999999	P;P	0.42941	0.794;0.794	P;P	0.54499	0.754;0.478	T	0.65076	-0.6256	8	0.49607	T	0.09	-5.4358	13.5897	0.61953	0.0:0.0:0.0:1.0	rs34402524;rs56501389;rs34402524	1742;1721	E7EQS8;Q6N021	.;TET2_HUMAN	W	1721;1742;1721	ENSP00000442788:L1721W;ENSP00000425443:L1742W;ENSP00000369351:L1721W	ENSP00000369351:L1721W	L	+	2	0	TET2	106416278	0.980000	0.34600	0.053000	0.19242	0.139000	0.21198	3.357000	0.52277	1.937000	0.56155	0.383000	0.25322	TTG	T|0.903;G|0.097	0.097	strong		0.408	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
TRPM5	29850	hgsc.bcm.edu	37	11	2432666	2432666	+	Missense_Mutation	SNP	C	C	T	rs34364959	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:2432666C>T	ENST00000155858.6	-	18	2706	c.2698G>A	c.(2698-2700)Ggc>Agc	p.G900S	TRPM5_ENST00000452833.1_Missense_Mutation_p.G902S|TRPM5_ENST00000533060.1_Missense_Mutation_p.G900S|TRPM5_ENST00000528453.1_Missense_Mutation_p.G900S	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		TCCAGGCGGCCGTCATGGGGG	0.617													C|||	259	0.0517173	0.0356	0.062	5008	,	,		15018	0.0427		0.1133	False		,,,				2504	0.0123				p.G900S	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G2698A						PASS	.	C	SER/GLY	214,4188	124.9+/-162.1	5,204,1992	34.0	38.0	36.0		2698	-4.3	0.1	11	dbSNP_126	36	808,7780	181.9+/-230.5	43,722,3529	yes	missense	TRPM5	NM_014555.3	56	48,926,5521	TT,TC,CC		9.4085,4.8614,7.8676	benign	900/1166	2432666	1022,11968	2201	4294	6495	SO:0001583	missense	29850	exon18			GGCGGCCGTCATG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.2698G>A	11.37:g.2432666C>T	ENSP00000155858:p.Gly900Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	158	0.07234432234432235	29	0.05894308943089431	26	0.0718232044198895	23	0.04020979020979021	80	0.10554089709762533	C	4.086	0.013949	0.07959	0.048614	0.094085	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	3.89	-4.32	0.03688	Ion transport (1);	0.360410	0.28927	N	0.013686	T	0.00328	0.0010	N	0.00289	-1.7	0.38436	P	0.05342800000000003	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.24476	-1.0159	9	0.07482	T	0.82	-11.0608	11.7545	0.51868	0.0:0.1898:0.0:0.8102	rs34364959	900;902;900	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	S	894;900;902;900;900	ENSP00000434383:G894S;ENSP00000155858:G900S;ENSP00000387965:G902S;ENSP00000434121:G900S;ENSP00000436809:G900S	ENSP00000155858:G900S	G	-	1	0	TRPM5	2389242	0.018000	0.18449	0.072000	0.20136	0.715000	0.41141	-0.133000	0.10451	-0.724000	0.04908	-1.165000	0.01757	GGC	C|0.930;T|0.070	0.070	strong		0.617	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
DDX51	317781	hgsc.bcm.edu	37	12	132626425	132626425	+	Missense_Mutation	SNP	G	G	A	rs60927391	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132626425G>A	ENST00000397333.3	-	6	1003	c.965C>T	c.(964-966)gCc>gTc	p.A322V	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	322	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		A -> V (in dbSNP:rs60927391). {ECO:0000269|PubMed:14702039}.		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)		CTGCTCCTTGGCCAGAGACTT	0.572													G|||	1433	0.286142	0.5446	0.2017	5008	,	,		18216	0.1786		0.1809	False		,,,				2504	0.2157				p.A322V		Atlas-SNP	.											.	DDX51	33	.	0			c.C965T						PASS	.	G	VAL/ALA	1871,2029		446,979,525	63.0	64.0	64.0		965	3.1	1.0	12	dbSNP_129	64	1520,6764		168,1184,2790	yes	missense	DDX51	NM_175066.3	64	614,2163,3315	AA,AG,GG		18.3486,47.9744,27.8316	benign	322/667	132626425	3391,8793	1950	4142	6092	SO:0001583	missense	317781	exon6			TCCTTGGCCAGAG	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.965C>T	12.37:g.132626425G>A	ENSP00000380495:p.Ala322Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	573	0.2623626373626374	258	0.524390243902439	68	0.1878453038674033	110	0.19230769230769232	137	0.18073878627968337	G	12.78	2.039785	0.35989	0.479744	0.183486	ENSG00000185163	ENST00000397333	T	0.17528	2.27	4.95	3.06	0.35304	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.247526	0.40144	N	0.001173	T	0.00012	0.0000	N	0.13198	0.31	0.26266	P	0.9785098	B	0.24186	0.099	B	0.31751	0.135	T	0.42882	-0.9425	9	0.19590	T	0.45	-15.3121	6.5455	0.22404	0.3132:0.0:0.6868:0.0	rs60927391;rs61729148	322	Q8N8A6	DDX51_HUMAN	V	322	ENSP00000380495:A322V	ENSP00000380495:A322V	A	-	2	0	DDX51	131192378	1.000000	0.71417	0.997000	0.53966	0.764000	0.43329	3.027000	0.49697	0.445000	0.26639	0.491000	0.48974	GCC	G|0.765;A|0.235	0.235	strong		0.572	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
RBAK	57786	hgsc.bcm.edu	37	7	5105133	5105133	+	Silent	SNP	C	C	T	rs12334144	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:5105133C>T	ENST00000353796.3	+	6	2370	c.2046C>T	c.(2044-2046)aaC>aaT	p.N682N	RBAK_ENST00000396912.1_Silent_p.N682N|RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK-RBAKDN_ENST00000396904.2_Intron	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	682	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|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)			NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		ATGAATGTAACGAGTGTGGGA	0.383													T|||	2884	0.575879	0.7504	0.4193	5008	,	,		19541	0.5526		0.5129	False		,,,				2504	0.5399				p.N682N		Atlas-SNP	.											RBAK_ENST00000396912,colon,carcinoma,0,1	RBAK	82	1	0			c.C2046T						PASS	.	T	,,	3186,1220	420.2+/-338.9	1143,900,160	90.0	99.0	96.0		2046,,2046	-2.8	0.6	7	dbSNP_120	96	4257,4341	577.2+/-390.5	1066,2125,1108	no	coding-synonymous,intron,coding-synonymous	RBAK,RBAK-LOC389458	NM_001204456.1,NM_001204513.1,NM_021163.3	,,	2209,3025,1268	TT,TC,CC		49.5115,27.6895,42.7638	,,	682/715,,682/715	5105133	7443,5561	2203	4299	6502	SO:0001819	synonymous_variant	57786	exon6			ATGTAACGAGTGT	AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.2046C>T	7.37:g.5105133C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_001204456	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Silent	SNP	ENST00000353796.3	37	CCDS5337.1																																																																																			C|0.426;G|0.000;T|0.574	0.574	strong		0.383	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2	NM_021163	
TTN	7273	hgsc.bcm.edu	37	2	179634961	179634961	+	Missense_Mutation	SNP	C	C	A	rs33917087	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179634961C>A	ENST00000591111.1	-	36	8691	c.8467G>T	c.(8467-8469)Gtt>Ttt	p.V2823F	TTN_ENST00000360870.5_Missense_Mutation_p.V2823F|TTN_ENST00000589042.1_Missense_Mutation_p.V2823F|TTN_ENST00000342175.6_Missense_Mutation_p.V2777F|TTN_ENST00000359218.5_Missense_Mutation_p.V2777F|TTN_ENST00000460472.2_Missense_Mutation_p.V2777F|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V2823F|TTN-AS1_ENST00000584485.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13151			V -> F (in dbSNP:rs33917087). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTACTGGAACAGTGTCATGG	0.413													C|||	38	0.00758786	0.0008	0.0231	5008	,	,		21665	0.0		0.0179	False		,,,				2504	0.0031				p.V2823F		Atlas-SNP	.											.	TTN	18412	.	0			c.G8467T						PASS	.	C	PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL	12,4394	17.9+/-39.9	0,12,2191	171.0	164.0	166.0		8329,8467,8467,8329,8329	6.1	1.0	2	dbSNP_126	166	189,8411	84.0+/-146.5	3,183,4114	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	50,50,50,50,50	3,195,6305	AA,AC,CC		2.1977,0.2724,1.5454	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	2777/26927,2823/33424,2823/5605,2777/27052,2777/27119	179634961	201,12805	2203	4300	6503	SO:0001583	missense	7273	exon36			CTGGAACAGTGTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.8467G>T	2.37:g.179634961C>A	ENSP00000465570:p.Val2823Phe	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		18	0.008241758241758242	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	10	0.013192612137203167	C	12.92	2.081432	0.36758	0.002724	0.021977	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	6.06	6.06	0.98353	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72692	0.3492	M	0.76328	2.33	0.33914	D	0.640097	D;D;D;D;D	0.76494	0.998;0.998;0.998;0.997;0.999	D;D;D;D;D	0.77557	0.964;0.964;0.964;0.944;0.99	T	0.83239	-0.0059	9	0.87932	D	0	.	20.6282	0.99521	0.0:1.0:0.0:0.0	rs33917087	2777;2777;2777;2823;2823	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	F	2823;2777;2777;2777;2777;2823	ENSP00000343764:V2823F;ENSP00000434586:V2777F;ENSP00000340554:V2777F;ENSP00000352154:V2777F;ENSP00000354117:V2823F	ENSP00000340554:V2777F	V	-	1	0	TTN	179343206	0.961000	0.32948	0.970000	0.41538	0.891000	0.51852	2.129000	0.42055	2.871000	0.98454	0.655000	0.94253	GTT	C|0.985;A|0.015	0.015	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF578	147660	hgsc.bcm.edu	37	19	53014787	53014787	+	Missense_Mutation	SNP	A	A	G	rs35356792	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:53014787A>G	ENST00000421239.2	+	6	1397	c.1153A>G	c.(1153-1155)Acc>Gcc	p.T385A	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TCAAAATTCAACCCTTGTAAT	0.378													a|||	301	0.0601038	0.1362	0.0591	5008	,	,		25349	0.001		0.0636	False		,,,				2504	0.0153				p.T385A		Atlas-SNP	.											.	.	.	.	0			c.A1153G						PASS	.	A	ALA/THR	508,3898		38,432,1733	96.0	101.0	99.0		1153	-3.0	0.0	19	dbSNP_126	99	570,8028		14,542,3743	no	missense	ZNF578	NM_001099694.1	58	52,974,5476	GG,GA,AA		6.6294,11.5297,8.2898	possibly-damaging	385/591	53014787	1078,11926	2203	4299	6502	SO:0001583	missense	147660	exon6			AATTCAACCCTTG	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1153A>G	19.37:g.53014787A>G	ENSP00000459216:p.Thr385Ala	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	130	0.05952380952380952	67	0.13617886178861788	18	0.049723756906077346	1	0.0017482517482517483	44	0.05804749340369393	-	0.314	-0.965816	0.02249	0.115297	0.066294	ENSG00000258405	ENST00000553364	.	.	.	1.48	-2.97	0.05530	.	.	.	.	.	T	0.00073	0.0002	N	0.02685	-0.53	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.23013	-1.0200	6	.	.	.	.	0.5818	0.00713	0.4441:0.1578:0.131:0.2671	rs35356792;rs61746281	385	G3V4F6	.	A	385	.	.	T	+	1	0	ZNF578	57706599	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-13.157000	0.00001	-1.870000	0.01139	0.246000	0.17985	ACC	A|0.938;G|0.062	0.062	strong		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
SEC24D	9871	hgsc.bcm.edu	37	4	119736796	119736796	+	Silent	SNP	A	A	C	rs2389688	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:119736796A>C	ENST00000280551.6	-	5	721	c.483T>G	c.(481-483)ccT>ccG	p.P161P	SEC24D_ENST00000379735.5_Silent_p.P161P|SEC24D_ENST00000419654.2_5'UTR			O94855	SC24D_HUMAN	SEC24 family member D	161	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.P161P(1)		breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						GCAAAATGGAAGGCTGTGGAG	0.562													c|||	2188	0.436901	0.2436	0.5807	5008	,	,		18170	0.5506		0.4354	False		,,,				2504	0.4806				p.P161P		Atlas-SNP	.											SEC24D,NS,carcinoma,0,1	SEC24D	96	1	1	Substitution - coding silent(1)	prostate(1)	c.T483G						PASS	.	T		1283,3123	700.8+/-406.7	192,899,1112	238.0	212.0	221.0		483	-11.4	0.0	4	dbSNP_100	221	3875,4725	608.7+/-395.4	892,2091,1317	no	coding-synonymous	SEC24D	NM_014822.2		1084,2990,2429	CC,CA,AA		45.0581,29.1194,39.6586		161/1033	119736796	5158,7848	2203	4300	6503	SO:0001819	synonymous_variant	9871	exon5			AATGGAAGGCTGT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.483T>G	4.37:g.119736796A>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			T|0.108;G|0.070	.	strong		0.562	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
ALMS1	7840	hgsc.bcm.edu	37	2	73677898	73677898	+	Missense_Mutation	SNP	G	G	C	rs6546837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73677898G>C	ENST00000264448.6	+	8	4352	c.4241G>C	c.(4240-4242)gGt>gCt	p.G1414A	ALMS1_ENST00000409009.1_Missense_Mutation_p.G1372A|ALMS1_ENST00000377715.1_Missense_Mutation_p.G1414A	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1414	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						CCTGGACCAGGTGACCGGAAG	0.468													C|||	1821	0.363618	0.8782	0.3905	5008	,	,		20924	0.0089		0.2266	False		,,,				2504	0.1554				p.G1414A		Atlas-SNP	.											.	ALMS1	384	.	0			c.G4241C						PASS	.	C	ALA/GLY	2767,981		1033,701,140	115.0	117.0	116.0		4241	-0.2	0.0	2	dbSNP_116	116	1956,6266		223,1510,2378	yes	missense	ALMS1	NM_015120.4	60	1256,2211,2518	CC,CG,GG		23.7898,26.174,39.457	benign	1414/4168	73677898	4723,7247	1874	4111	5985	SO:0001583	missense	7840	exon8			GACCAGGTGACCG	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.4241G>C	2.37:g.73677898G>C	ENSP00000264448:p.Gly1414Ala	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	65	41	0.630769	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	738	0.33791208791208793	426	0.8658536585365854	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	C	0.017	-1.493229	0.01009	0.73826	0.237898	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.12774	3.55;3.55;2.65	4.01	-0.18	0.13295	.	1.040500	0.07585	N	0.920948	T	0.00012	0.0000	N	0.01729	-0.75	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.28650	-1.0037	9	0.02654	T	1	.	5.8903	0.18909	0.0:0.3401:0.4597:0.2002	rs6546837;rs41313208;rs52798677;rs6546837	1414;1372;1414	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	A	1372;1414;1414	ENSP00000386627:G1372A;ENSP00000264448:G1414A;ENSP00000366944:G1414A	ENSP00000264448:G1414A	G	+	2	0	ALMS1	73531406	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-2.366000	0.01078	-0.286000	0.09076	-0.248000	0.11899	GGT	G|0.697;C|0.303	0.303	strong		0.468	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
CARD14	79092	hgsc.bcm.edu	37	17	78157995	78157995	+	Silent	SNP	G	G	A	rs4889990	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78157995G>A	ENST00000573882.1	+	6	1169	c.633G>A	c.(631-633)gaG>gaA	p.E211E	CARD14_ENST00000344227.2_Silent_p.E211E|CARD14_ENST00000392434.2_5'UTR|CARD14_ENST00000570421.1_Silent_p.E211E			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	211					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)			CGCTGCAGGAGAAGGAGCTGG	0.652													G|||	1738	0.347045	0.4198	0.2939	5008	,	,		19510	0.2212		0.3618	False		,,,				2504	0.4008				p.E211E		Atlas-SNP	.											.	CARD14	98	.	0			c.G633A						PASS	.	G		1790,2568		388,1014,777	19.0	15.0	17.0		633	0.8	1.0	17	dbSNP_111	17	3203,5351		655,1893,1729	no	coding-synonymous	CARD14	NM_024110.3		1043,2907,2506	AA,AG,GG		37.4445,41.0739,38.6695		211/1005	78157995	4993,7919	2179	4277	6456	SO:0001819	synonymous_variant	79092	exon4			GCAGGAGAAGGAG	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.633G>A	17.37:g.78157995G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			G|0.641;A|0.359	0.359	strong		0.652	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
C2orf42	54980	hgsc.bcm.edu	37	2	70377653	70377653	+	Silent	SNP	G	G	A	rs12989348	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:70377653G>A	ENST00000264434.2	-	10	1939	c.1560C>T	c.(1558-1560)atC>atT	p.I520I	C2orf42_ENST00000420306.1_Silent_p.I520I	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	520										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						GGATCCACTCGATGATGAAAG	0.478													G|||	172	0.034345	0.0053	0.0447	5008	,	,		18358	0.001		0.1243	False		,,,				2504	0.0082				p.I520I		Atlas-SNP	.											.	C2orf42	30	.	0			c.C1560T						PASS	.	G		122,4284	92.5+/-131.2	1,120,2082	136.0	120.0	126.0		1560	-7.9	0.7	2	dbSNP_121	126	1151,7449	236.9+/-269.0	80,991,3229	no	coding-synonymous	C2orf42	NM_017880.1		81,1111,5311	AA,AG,GG		13.3837,2.769,9.7878		520/575	70377653	1273,11733	2203	4300	6503	SO:0001819	synonymous_variant	54980	exon10			CCACTCGATGATG	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.1560C>T	2.37:g.70377653G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	31	9	0.290323	NM_017880	D6W5G3|Q9H629	Silent	SNP	ENST00000264434.2	37	CCDS1899.1																																																																																			G|0.920;A|0.080	0.080	strong		0.478	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880	
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 GAIIx	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		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	51	23	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	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951949	130951949	+	Missense_Mutation	SNP	G	G	A	rs62165074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:130951949G>A	ENST00000312988.7	-	4	566	c.466C>T	c.(466-468)Cgg>Tgg	p.R156W		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	156					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					ACTGAGAGCCGCTCCATGAGC	0.577																																					p.R156W		Atlas-SNP	.											TUBA3E,NS,carcinoma,+2,1	TUBA3E	73	1	0			c.C466T						PASS	.	G	TRP/ARG	1567,2837	489.4+/-361.5	284,999,919	71.0	76.0	74.0		466	0.6	1.0	2	dbSNP_129	74	3350,5248	496.3+/-374.3	657,2036,1606	no	missense	TUBA3E	NM_207312.2	101	941,3035,2525	AA,AG,GG		38.9625,35.5813,37.8173	probably-damaging	156/451	130951949	4917,8085	2202	4299	6501	SO:0001583	missense	112714	exon4			AGAGCCGCTCCAT	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.466C>T	2.37:g.130951949G>A	ENSP00000318197:p.Arg156Trp	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	180	38	0.211111	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	874	0.4001831501831502	166	0.33739837398373984	163	0.45027624309392267	269	0.47027972027972026	276	0.3641160949868074	g	12.55	1.970279	0.34754	0.355813	0.389625	ENSG00000152086	ENST00000312988	T	0.71698	-0.59	2.71	0.549	0.17213	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.49916	U	0.000125	T	0.00012	0.0000	H	0.98487	4.245	0.23700	P	0.99707653	D	0.71674	0.998	P	0.62649	0.905	T	0.18116	-1.0347	9	0.87932	D	0	.	4.7171	0.12899	0.1389:0.0:0.649:0.212	rs62165074	156	Q6PEY2	TBA3E_HUMAN	W	156	ENSP00000318197:R156W	ENSP00000318197:R156W	R	-	1	2	TUBA3E	130668419	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.313000	0.33585	0.485000	0.27652	0.449000	0.29647	CGG	G|0.500;A|0.500	0.500	weak		0.577	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
ITK	3702	hgsc.bcm.edu	37	5	156671437	156671437	+	Silent	SNP	G	G	T	rs17595896	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:156671437G>T	ENST00000422843.3	+	13	1550	c.1398G>T	c.(1396-1398)gtG>gtT	p.V466V	ITK_ENST00000519749.1_3'UTR	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	466	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)			breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	GTCTGGATGTGTGTGAGGGCA	0.552			T	SYK	peripheral T-cell lymphoma								G|||	42	0.00838658	0.0	0.0086	5008	,	,		18420	0.001		0.006	False		,,,				2504	0.0297				p.V466V	Esophageal Squamous(70;1378 1469 8785 19883)	Atlas-SNP	.		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	.	ITK	136	.	0			c.G1398T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	96.0	92.0	94.0		1398	5.2	1.0	5	dbSNP_123	94	54,8546	33.3+/-86.6	0,54,4246	yes	coding-synonymous	ITK	NM_005546.3		0,55,6448	TT,TG,GG		0.6279,0.0227,0.4229		466/621	156671437	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	3702	exon13			GGATGTGTGTGAG	D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.1398G>T	5.37:g.156671437G>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	142	66	0.464789	NM_005546	B2R752|Q32ML7	Silent	SNP	ENST00000422843.3	37	CCDS4336.1																																																																																			G|0.994;T|0.006	0.006	strong		0.552	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2		
SIGLEC10	89790	hgsc.bcm.edu	37	19	51918112	51918112	+	Silent	SNP	A	A	G	rs3810099	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51918112A>G	ENST00000339313.5	-	8	1697	c.1581T>C	c.(1579-1581)caT>caC	p.H527H	SIGLEC10_ENST00000439889.2_Silent_p.H469H|SIGLEC10_ENST00000436984.2_Intron|SIGLEC10_ENST00000353836.5_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000432469.2_Intron|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.H527H|SIGLEC10_ENST00000441969.3_Intron|CTD-2616J11.2_ENST00000532688.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	527					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		TCTGGGCCCCATGGACGTTCC	0.662													a|||	1218	0.243211	0.3835	0.1974	5008	,	,		15844	0.2113		0.1501	False		,,,				2504	0.2147				p.H527H		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,-1,4	SIGLEC10	112	4	0			c.T1581C						PASS	.	A	,,,,,,	1516,2890		260,996,947	55.0	65.0	61.0		1407,,,,,,1581	-9.4	0.0	19	dbSNP_107	61	1291,7309		101,1089,3110	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	SIGLEC10	NM_001171156.1,NM_001171157.1,NM_001171158.1,NM_001171159.1,NM_001171160.1,NM_001171161.1,NM_033130.4	,,,,,,	361,2085,4057	GG,GA,AA		15.0116,34.4076,21.5823	,,,,,,	469/640,,,,,,527/698	51918112	2807,10199	2203	4300	6503	SO:0001819	synonymous_variant	89790	exon8			GGCCCCATGGACG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.1581T>C	19.37:g.51918112A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_033130	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			A|0.791;G|0.209	0.209	strong		0.662	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
SLC38A10	124565	hgsc.bcm.edu	37	17	79244802	79244802	+	Silent	SNP	T	T	C	rs2292184	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79244802T>C	ENST00000374759.3	-	10	1430	c.1047A>G	c.(1045-1047)acA>acG	p.T349T	SLC38A10_ENST00000288439.5_Silent_p.T349T|SLC38A10_ENST00000546352.1_5'UTR	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	349					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TGGTCGCTCCTGTGAGGCCCA	0.582													C|||	2149	0.429113	0.7837	0.4121	5008	,	,		16257	0.1825		0.4414	False		,,,				2504	0.2035				p.T349T		Atlas-SNP	.											SLC38A10_ENST00000374759,NS,carcinoma,0,2	SLC38A10	133	2	0			c.A1047G						PASS	.	C	,	3292,1114	397.4+/-330.4	1230,832,141	87.0	76.0	79.0		1047,1047	-5.6	0.4	17	dbSNP_100	79	3646,4954	623.5+/-397.5	807,2032,1461	no	coding-synonymous,coding-synonymous	SLC38A10	NM_001037984.1,NM_138570.2	,	2037,2864,1602	CC,CT,TT		42.3953,25.2837,46.6554	,	349/1120,349/781	79244802	6938,6068	2203	4300	6503	SO:0001819	synonymous_variant	124565	exon10			CGCTCCTGTGAGG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1047A>G	17.37:g.79244802T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	81	28	0.345679	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1																																																																																			T|0.518;C|0.482	0.482	strong		0.582	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
COL4A3	1285	hgsc.bcm.edu	37	2	228121101	228121101	+	Missense_Mutation	SNP	G	G	T	rs55703767	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:228121101G>T	ENST00000396578.3	+	17	1138	c.976G>T	c.(976-978)Gat>Tat	p.D326Y	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000606119.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000437673.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	326	Triple-helical region.		D -> Y (in dbSNP:rs55703767). {ECO:0000269|PubMed:11134255}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		AATGGGTGAAGATGGCATTAA	0.448													G|||	580	0.115815	0.0189	0.1542	5008	,	,		19808	0.129		0.2117	False		,,,				2504	0.1074				p.D326Y		Atlas-SNP	.											.	COL4A3	293	.	0			c.G976T						PASS	.	G	TYR/ASP	159,3543		0,159,1692	126.0	113.0	117.0		976	3.0	0.8	2	dbSNP_129	117	1814,6386		207,1400,2493	yes	missense	COL4A3	NM_000091.4	160	207,1559,4185	TT,TG,GG		22.122,4.295,16.577	probably-damaging	326/1671	228121101	1973,9929	1851	4100	5951	SO:0001583	missense	1285	exon17			GGTGAAGATGGCA		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.976G>T	2.37:g.228121101G>T	ENSP00000379823:p.Asp326Tyr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	37	14	0.378378	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	309	0.14148351648351648	8	0.016260162601626018	62	0.1712707182320442	65	0.11363636363636363	174	0.22955145118733508	G	9.616	1.132535	0.21041	0.04295	0.22122	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.93859	-3.3	5.87	3.01	0.34805	.	0.946366	0.08846	N	0.885103	T	0.00300	0.0009	L	0.56340	1.77	0.40599	P	0.01843499999999998	B;B;B;B	0.30634	0.244;0.244;0.244;0.288	B;B;B;B	0.33042	0.026;0.06;0.097;0.157	T	0.37798	-0.9690	9	0.59425	D	0.04	.	5.6832	0.17788	0.172:0.0:0.6504:0.1776	rs55703767;rs62277854	326;326;326;326	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	Y	326	ENSP00000379823:D326Y	ENSP00000323334:D326Y	D	+	1	0	COL4A3	227829345	0.695000	0.27747	0.788000	0.31933	0.349000	0.29174	0.499000	0.22546	0.898000	0.36418	-0.136000	0.14681	GAT	G|0.828;T|0.172	0.172	strong		0.448	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
PLEK2	26499	hgsc.bcm.edu	37	14	67862269	67862269	+	Missense_Mutation	SNP	G	G	A	rs34300264	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:67862269G>A	ENST00000216446.4	-	3	379	c.239C>T	c.(238-240)aCg>aTg	p.T80M	PLEK2_ENST00000557388.1_5'Flank	NM_016445.1	NP_057529.1	Q9NYT0	PLEK2_HUMAN	pleckstrin 2	80	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.		T -> M (in dbSNP:rs34300264).		actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	15				all cancers(60;0.000728)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.00953)		GAAGTACTCCGTGGATGTTTG	0.587													G|||	51	0.0101837	0.0	0.0144	5008	,	,		17392	0.0		0.0239	False		,,,				2504	0.0174				p.T80M		Atlas-SNP	.											.	PLEK2	23	.	0			c.C239T						PASS	.	G	MET/THR	23,4383	29.9+/-59.1	0,23,2180	79.0	80.0	79.0		239	5.3	0.9	14	dbSNP_126	79	242,8358	96.3+/-158.1	3,236,4061	yes	missense	PLEK2	NM_016445.1	81	3,259,6241	AA,AG,GG		2.814,0.522,2.0375	probably-damaging	80/354	67862269	265,12741	2203	4300	6503	SO:0001583	missense	26499	exon3			TACTCCGTGGATG	AF228603	CCDS9782.1	14q23.3	2014-08-12			ENSG00000100558	ENSG00000100558		"""Pleckstrin homology (PH) domain containing"""	19238	protein-coding gene	gene with protein product		608007				11911883, 17658464	Standard	NM_016445		Approved		uc001xjh.1	Q9NYT0	OTTHUMG00000171247	ENST00000216446.4:c.239C>T	14.37:g.67862269G>A	ENSP00000216446:p.Thr80Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_016445	Q96JT0	Missense_Mutation	SNP	ENST00000216446.4	37	CCDS9782.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	18	0.023746701846965697	G	13.02	2.113784	0.37339	0.00522	0.02814	ENSG00000100558	ENST00000216446;ENST00000554395	T;T	0.76060	-0.99;1.41	5.34	5.34	0.76211	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.309199	0.37669	N	0.001984	T	0.68595	0.3018	M	0.87900	2.915	0.37481	D	0.916015	P	0.52316	0.952	P	0.52957	0.714	T	0.82961	-0.0197	10	0.51188	T	0.08	-12.9714	17.2187	0.86951	0.0:0.0:1.0:0.0	rs34300264	80	Q9NYT0	PLEK2_HUMAN	M	80;14	ENSP00000216446:T80M;ENSP00000450892:T14M	ENSP00000216446:T80M	T	-	2	0	PLEK2	66932022	1.000000	0.71417	0.897000	0.35233	0.367000	0.29736	3.582000	0.53921	2.490000	0.84030	0.462000	0.41574	ACG	G|0.983;A|0.017	0.017	strong		0.587	PLEK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412547.2		
CTSL	1514	hgsc.bcm.edu	37	9	90343505	90343505	+	Silent	SNP	G	G	A	rs11541204	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:90343505G>A	ENST00000343150.5	+	5	1292	c.402G>A	c.(400-402)caG>caA	p.Q134Q	CTSL_ENST00000340342.6_Silent_p.Q134Q|CTSL_ENST00000342020.5_Silent_p.Q134Q|CTSL_ENST00000495822.1_Intron			P07711	CATL1_HUMAN	cathepsin L	134					adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|macrophage apoptotic process (GO:0071888)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|nucleus (GO:0005634)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|fibronectin binding (GO:0001968)|histone binding (GO:0042393)|proteoglycan binding (GO:0043394)										TTCAGGGTCAGTGTGGTTCTT	0.403													G|||	112	0.0223642	0.0045	0.0375	5008	,	,		19368	0.001		0.0477	False		,,,				2504	0.0317				p.Q134Q		Atlas-SNP	.											.	CTSL1	43	.	0			c.G402A						PASS	.	G	,	35,4371	36.8+/-68.6	0,35,2168	128.0	130.0	129.0		402,402	-5.9	0.0	9	dbSNP_120	129	414,8186	130.0+/-188.0	11,392,3897	no	coding-synonymous,coding-synonymous	CTSL1	NM_001912.4,NM_145918.2	,	11,427,6065	AA,AG,GG		4.814,0.7944,3.4523	,	134/334,134/334	90343505	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	1514	exon5			GGGTCAGTGTGGT	X12451	CCDS6675.1	9q21.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000135047	ENSG00000135047	3.4.22.15	"""Cathepsins"""	2537	protein-coding gene	gene with protein product		116880	"""cathepsin L1"""	CTSL1		8419312, 2835398	Standard	NM_145918		Approved	FLJ31037	uc004apk.4	P07711	OTTHUMG00000020149	ENST00000343150.5:c.402G>A	9.37:g.90343505G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_145918	Q6IAV1|Q96QJ0	Silent	SNP	ENST00000343150.5	37	CCDS6675.1																																																																																			G|0.968;A|0.032	0.032	strong		0.403	CTSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052936.1	NM_001912	
DYNC2LI1	51626	hgsc.bcm.edu	37	2	44021826	44021826	+	Intron	SNP	T	T	A	rs9309107	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44021826T>A	ENST00000260605.8	+	6	607				DYNC2LI1_ENST00000406852.3_Missense_Mutation_p.F184Y|DYNC2LI1_ENST00000489222.2_Intron|DYNC2LI1_ENST00000443170.3_Intron|DYNC2LI1_ENST00000605786.1_Intron|DYNC2LI1_ENST00000398823.2_3'UTR	NM_001193464.1|NM_016008.3	NP_001180393.1|NP_057092.2	Q8TCX1	DC2L1_HUMAN	dynein, cytoplasmic 2, light intermediate chain 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)	apical part of cell (GO:0045177)|axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|cytosol (GO:0005829)|intraciliary transport particle (GO:0030990)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|primary cilium (GO:0072372)	motor activity (GO:0003774)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|skin(1)	26		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TTAGTCCCATTTATAGTTAAT	0.343													A|||	2262	0.451677	0.7262	0.4654	5008	,	,		18661	0.1895		0.326	False		,,,				2504	0.4703				p.F184Y		Atlas-SNP	.											.	DYNC2LI1	46	.	0			c.T551A						PASS	.	A	,TYR/PHE,	2915,1491	456.1+/-351.2	990,935,278	92.0	99.0	96.0		,551,	0.9	0.0	2	dbSNP_119	96	2828,5772	675.0+/-403.2	471,1886,1943	yes	intron,missense,intron	DYNC2LI1	NM_001193464.1,NM_015522.3,NM_016008.3	,22,	1461,2821,2221	AA,AT,TT		32.8837,33.8402,44.1565	,,	,184/202,	44021826	5743,7263	2203	4300	6503	SO:0001627	intron_variant	51626	exon6			TCCCATTTATAGT		CCDS1813.1, CCDS46270.1, CCDS62903.1	2p25.1-p24.1	2008-02-05			ENSG00000138036	ENSG00000138036		"""Cytoplasmic dyneins"""	24595	protein-coding gene	gene with protein product						10810093, 11907264	Standard	NM_016008		Approved	D2LIC, LIC3, CGI-60, DKFZP564A033	uc002rtl.3	Q8TCX1	OTTHUMG00000128656	ENST00000260605.8:c.507+44T>A	2.37:g.44021826T>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	180	179	0.994444	NM_015522	A8MVJ5|Q53F57|Q6PDB2|Q8IWA3|Q96B03|Q96J00|Q9Y370|Q9Y3S9	Missense_Mutation	SNP	ENST00000260605.8	37	CCDS1813.1	884	0.40476190476190477	361	0.733739837398374	172	0.47513812154696133	108	0.1888111888111888	243	0.32058047493403696	A	4.001	-0.002468	0.07819	0.661598	0.328837	ENSG00000138036	ENST00000406852	T	0.32023	1.47	4.45	0.913	0.19354	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22591	-1.0212	7	0.87932	D	0	.	5.1073	0.14790	0.6522:0.0:0.2213:0.1265	rs9309107;rs52802708;rs59663186;rs9309107	184	Q8TCX1-4	.	Y	184	ENSP00000385738:F184Y	ENSP00000385738:F184Y	F	+	2	0	DYNC2LI1	43875330	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.411000	0.21115	0.048000	0.15891	-1.185000	0.01705	TTT	A|0.389;N|0.001	0.389	strong		0.343	DYNC2LI1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250536.2	NM_016008	
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 GAIIx	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_ENST00000376893.3_Missense_Mutation_p.R72H|SSX3_ENST00000376895.1_5'Flank	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	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	278	109	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	
NOTCH4	4855	hgsc.bcm.edu	37	6	32168996	32168996	+	Missense_Mutation	SNP	C	C	G	rs8192573	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32168996C>G	ENST00000375023.3	-	22	4175	c.4037G>C	c.(4036-4038)cGg>cCg	p.R1346P		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1346			R -> P (in dbSNP:rs8192573).		cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TTCTTCAGCCCGGGCCCCAGG	0.617													C|||	56	0.0111821	0.0129	0.0403	5008	,	,		16760	0.0		0.0099	False		,,,				2504	0.001				p.R1346P		Atlas-SNP	.											NOTCH4,right_upper_lobe,carcinoma,-1,1	NOTCH4	201	1	0			c.G4037C						PASS	.	C	PRO/ARG	59,2957		0,59,1449	58.0	67.0	64.0		4037	1.1	1.0	6	dbSNP_117	64	70,5344		1,68,2638	yes	missense	NOTCH4	NM_004557.3	103	1,127,4087	GG,GC,CC		1.2929,1.9562,1.5302	possibly-damaging	1346/2004	32168996	129,8301	1508	2707	4215	SO:0001583	missense	4855	exon22			TCAGCCCGGGCCC		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.4037G>C	6.37:g.32168996C>G	ENSP00000364163:p.Arg1346Pro	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	86	14	0.162791	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	32	0.014652014652014652	11	0.022357723577235773	15	0.04143646408839779	0	0.0	6	0.0079155672823219	C	12.75	2.031954	0.35893	0.019562	0.012929	ENSG00000204301	ENST00000375023	T	0.81247	-1.47	4.37	1.09	0.20402	.	0.581966	0.13081	N	0.415340	T	0.62429	0.2427	N	0.14661	0.345	0.80722	D	1	P;B	0.46578	0.88;0.165	P;B	0.56343	0.796;0.077	T	0.59663	-0.7412	10	0.41790	T	0.15	.	5.443	0.16519	0.0:0.4431:0.0:0.5569	rs8192573;rs8192573	1346;1345	Q99466;B0S882	NOTC4_HUMAN;.	P	1346	ENSP00000364163:R1346P	ENSP00000364163:R1346P	R	-	2	0	NOTCH4	32276974	0.999000	0.42202	0.990000	0.47175	0.931000	0.56810	1.224000	0.32539	0.052000	0.16007	0.456000	0.33151	CGG	C|0.984;G|0.016	0.016	strong		0.617	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
REP15	387849	hgsc.bcm.edu	37	12	27850113	27850113	+	Missense_Mutation	SNP	A	A	T	rs12819160	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27850113A>T	ENST00000310791.2	+	1	686	c.618A>T	c.(616-618)gaA>gaT	p.E206D	RP11-1060J15.4_ENST00000536922.1_RNA|RP11-1060J15.4_ENST00000542660.1_RNA|RP11-1060J15.4_ENST00000536317.1_RNA	NM_001029874.1	NP_001025045.1	Q6BDI9	REP15_HUMAN	RAB15 effector protein	206			E -> D (in dbSNP:rs12819160).		receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	endosome membrane (GO:0010008)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)				breast(1)|cervix(1)|large_intestine(2)|lung(4)|ovary(1)	9	Lung SC(9;0.0873)					TGGAAACTGAAGATTGTGTGT	0.483													A|||	451	0.0900559	0.0068	0.0994	5008	,	,		19167	0.0506		0.175	False		,,,				2504	0.1493				p.E206D		Atlas-SNP	.											.	REP15	13	.	0			c.A618T						PASS	.	A	ASP/GLU	169,4237	112.9+/-151.0	3,163,2037	99.0	100.0	100.0		618	1.3	0.0	12	dbSNP_121	100	1526,7074	287.8+/-298.4	125,1276,2899	yes	missense	REP15	NM_001029874.1	45	128,1439,4936	TT,TA,AA		17.7442,3.8357,13.0324	benign	206/237	27850113	1695,11311	2203	4300	6503	SO:0001583	missense	387849	exon1			AACTGAAGATTGT	BC140921	CCDS31762.1	12p11.22	2010-09-02			ENSG00000174236	ENSG00000174236			33748	protein-coding gene	gene with protein product		610848				16195351	Standard	NM_001029874		Approved	RAB15EP	uc001rig.1	Q6BDI9		ENST00000310791.2:c.618A>T	12.37:g.27850113A>T	ENSP00000310335:p.Glu206Asp	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	58	31	0.534483	NM_001029874	B2RU16	Missense_Mutation	SNP	ENST00000310791.2	37	CCDS31762.1	212	0.09706959706959707	7	0.014227642276422764	38	0.10497237569060773	34	0.05944055944055944	133	0.17546174142480211	A	4.863	0.160403	0.09287	0.038357	0.177442	ENSG00000174236	ENST00000310791	T	0.32753	1.44	4.91	1.3	0.21679	.	0.598204	0.16508	N	0.211344	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.27571	-1.0070	9	0.12766	T	0.61	-20.553	1.1719	0.01827	0.2933:0.2663:0.2981:0.1423	rs12819160;rs52834046;rs12819160	206	Q6BDI9	REP15_HUMAN	D	206	ENSP00000310335:E206D	ENSP00000310335:E206D	E	+	3	2	REP15	27741380	0.000000	0.05858	0.005000	0.12908	0.464000	0.32679	-0.146000	0.10250	0.387000	0.25024	0.533000	0.62120	GAA	A|0.877;T|0.123	0.123	strong		0.483	REP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402894.1	NM_001029874	
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 GAIIx	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		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	52	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	
OTOGL	283310	hgsc.bcm.edu	37	12	80750659	80750659	+	Missense_Mutation	SNP	G	G	A	rs11836060	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:80750659G>A	ENST00000547103.1	+	48	5927	c.5921G>A	c.(5920-5922)cGa>cAa	p.R1974Q	OTOGL_ENST00000546620.1_Missense_Mutation_p.R5Q|OTOGL_ENST00000458043.2_Missense_Mutation_p.R1986Q			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1974	Cys-rich.				L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						ATTCAAGTTCGACAGGAAGAA	0.348													A|||	859	0.171526	0.1838	0.2075	5008	,	,		13699	0.0506		0.1819	False		,,,				2504	0.2434				p.R1986Q		Atlas-SNP	.											.	OTOGL	235	.	0			c.G5957A						PASS	.	A	GLN/ARG	823,3583	747.6+/-411.9	74,675,1454	110.0	98.0	102.0		5957	4.1	1.0	12	dbSNP_120	102	1690,6910	738.1+/-407.0	170,1350,2780	yes	missense	OTOGL	NM_173591.3	43	244,2025,4234	AA,AG,GG		19.6512,18.6791,19.3219	benign	1986/2345	80750659	2513,10493	2203	4300	6503	SO:0001583	missense	283310	exon48			AAGTTCGACAGGA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.5921G>A	12.37:g.80750659G>A	ENSP00000447211:p.Arg1974Gln	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	109	62	0.568807	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		324|324	0.14835164835164835|0.14835164835164835	86|86	0.17479674796747968|0.17479674796747968	75|75	0.20718232044198895|0.20718232044198895	27|27	0.0472027972027972|0.0472027972027972	136|136	0.17941952506596306|0.17941952506596306	A|A	13.96|13.96	2.393127|2.393127	0.42410|0.42410	0.186791|0.186791	0.196512|0.196512	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182	.|T;T;T;T	.|0.28454	.|1.61;1.61;1.61;1.61	5.36|5.36	4.06|4.06	0.47325|0.47325	.|.	.|0.264710	.|0.30244	.|N	.|0.010074	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.13168|0.13168	0.305|0.305	0.48830|0.48830	P|P	2.9000000000001247E-4|2.9000000000001247E-4	.|B	.|0.06786	.|0.001	.|B	.|0.04013	.|0.001	T|T	0.37641|0.37641	-0.9697|-0.9697	4|9	.|0.15952	.|T	.|0.53	.|.	7.6258|7.6258	0.28212|0.28212	0.7196:0.0:0.2804:0.0|0.7196:0.0:0.2804:0.0	rs11836060;rs17309026;rs52804264;rs60470781;rs11836060|rs11836060;rs17309026;rs52804264;rs60470781;rs11836060	.|351	.|Q3ZCN5	.|OTOGL_HUMAN	N|Q	429|1974;1986;5;3	.|ENSP00000447211:R1974Q;ENSP00000400895:R1986Q;ENSP00000449094:R5Q;ENSP00000449641:R3Q	.|ENSP00000400895:R1986Q	D|R	+|+	1|2	0|0	OTOGL|OTOGL	79274790|79274790	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.988000|0.988000	0.76386|0.76386	3.251000|3.251000	0.51453|0.51453	0.253000|0.253000	0.21552|0.21552	-0.381000|-0.381000	0.06696|0.06696	GAC|CGA	G|0.823;A|0.177	0.177	strong		0.348	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
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 GAIIx	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	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	99	49	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	
CMTR2	55783	hgsc.bcm.edu	37	16	71318001	71318001	+	Missense_Mutation	SNP	G	G	T	rs3096381	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:71318001G>T	ENST00000338099.5	-	3	2159	c.1823C>A	c.(1822-1824)aCa>aAa	p.T608K	CMTR2_ENST00000434935.2_Missense_Mutation_p.T608K			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	608			T -> K (in dbSNP:rs3096381).		7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										GCTAAAAGTTGTGAGTTCAGC	0.423													G|||	566	0.113019	0.0651	0.1354	5008	,	,		19124	0.0288		0.1879	False		,,,				2504	0.1718				p.T608K		Atlas-SNP	.											.	FTSJD1	70	.	0			c.C1823A						PASS	.	G	LYS/THR,LYS/THR	346,4050	176.2+/-205.4	17,312,1869	52.0	51.0	52.0		1823,1823	2.7	0.1	16	dbSNP_103	52	1472,7128	277.2+/-292.7	133,1206,2961	yes	missense,missense	FTSJD1	NM_001099642.1,NM_018348.5	78,78	150,1518,4830	TT,TG,GG		17.1163,7.8708,13.9889	benign,benign	608/771,608/771	71318001	1818,11178	2198	4300	6498	SO:0001583	missense	55783	exon3			AAAGTTGTGAGTT	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1823C>A	16.37:g.71318001G>T	ENSP00000337512:p.Thr608Lys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	239	0.10943223443223443	36	0.07317073170731707	61	0.1685082872928177	17	0.02972027972027972	125	0.16490765171503957	G	1.669	-0.509532	0.04231	0.078708	0.171163	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.13778	2.56;2.56	6.04	2.66	0.31614	.	0.614618	0.17231	N	0.181921	T	0.00039	0.0001	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B	0.23735	0.09	B	0.15870	0.014	T	0.33954	-0.9848	9	0.45353	T	0.12	-12.7017	8.4422	0.32822	0.7783:0.0:0.2217:0.0	rs3096381;rs52829342;rs59344681;rs3096381	608	Q8IYT2	FTSJ1_HUMAN	K	608	ENSP00000337512:T608K;ENSP00000411148:T608K	ENSP00000337512:T608K	T	-	2	0	FTSJD1	69875502	0.506000	0.26139	0.080000	0.20451	0.220000	0.24768	1.210000	0.32370	0.204000	0.20548	-0.367000	0.07326	ACA	G|0.883;T|0.117	0.117	strong		0.423	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
TTN	7273	hgsc.bcm.edu	37	2	179397561	179397561	+	Missense_Mutation	SNP	C	C	T	rs3829747	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179397561C>T	ENST00000591111.1	-	308	99082	c.98858G>A	c.(98857-98859)cGc>cAc	p.R32953H	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R34594H|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R25721H|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R25654H|TTN_ENST00000460472.2_Missense_Mutation_p.R25529H|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R32026H|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000588257.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32953			R -> H. {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAGGCGGATGCGCTTGGGTCG	0.443													C|||	1045	0.208666	0.0666	0.1484	5008	,	,		22656	0.4484		0.1392	False		,,,				2504	0.2679				p.R34594H		Atlas-SNP	.											TTN_ENST00000359218,caecum,carcinoma,-1,7	TTN	18412	7	0			c.G103781A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	293,3679		10,273,1703	108.0	102.0	104.0		76586,96077,76961,77162	5.8	1.0	2	dbSNP_107	104	1201,7129		90,1021,3054	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,29,29,29	100,1294,4757	TT,TC,CC		14.4178,7.3766,12.1444	probably-damaging,probably-damaging,probably-damaging,probably-damaging	25529/26927,32026/33424,25654/27052,25721/27119	179397561	1494,10808	1986	4165	6151	SO:0001583	missense	7273	exon358			CGGATGCGCTTGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.98858G>A	2.37:g.179397561C>T	ENSP00000465570:p.Arg32953His	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	172	83	0.482558	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		414	0.18956043956043955	31	0.06300813008130081	43	0.11878453038674033	236	0.4125874125874126	104	0.13720316622691292	C	21.1	4.097774	0.76870	0.073766	0.144178	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.66460	-0.21;0.02;0.0;-0.01	5.81	5.81	0.92471	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	0.999999927113	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.39210	-0.9625	8	0.87932	D	0	.	19.6737	0.95921	0.0:1.0:0.0:0.0	rs3829747;rs59855847;rs3829747	25529;25654;25721;32953	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	32026;25529;25721;25654;25526	ENSP00000343764:R32026H;ENSP00000434586:R25529H;ENSP00000340554:R25721H;ENSP00000352154:R25654H	ENSP00000340554:R25721H	R	-	2	0	TTN	179105807	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.794000	0.85869	2.757000	0.94681	0.462000	0.41574	CGC	C|0.813;T|0.187	0.187	strong		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
OR13C9	286362	hgsc.bcm.edu	37	9	107380215	107380215	+	Missense_Mutation	SNP	T	T	A	rs993658	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107380215T>A	ENST00000259362.1	-	1	270	c.271A>T	c.(271-273)Acc>Tcc	p.T91S		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	91			T -> S (in dbSNP:rs993658).			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)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AAGGAAATGGTCTTTCTTTCT	0.502													T|||	1753	0.35004	0.351	0.2104	5008	,	,		20373	0.5645		0.1779	False		,,,				2504	0.4039				p.T91S		Atlas-SNP	.											OR13C9,colon,carcinoma,+2,1	OR13C9	42	1	0			c.A271T						PASS	.	T	SER/THR	1362,3044	451.8+/-349.8	223,916,1064	134.0	139.0	137.0		271	2.2	1.0	9	dbSNP_86	137	1654,6946	306.2+/-307.8	181,1292,2827	no	missense	OR13C9	NM_001001956.1	58	404,2208,3891	AA,AT,TT		19.2326,30.9124,23.1893	probably-damaging	91/319	107380215	3016,9990	2203	4300	6503	SO:0001583	missense	286362	exon1			AAATGGTCTTTCT		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.271A>T	9.37:g.107380215T>A	ENSP00000259362:p.Thr91Ser	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	296	138	0.466216	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	684	0.3131868131868132	156	0.3170731707317073	74	0.20441988950276244	322	0.5629370629370629	132	0.1741424802110818	T	11.45	1.641969	0.29157	0.309124	0.192326	ENSG00000136839	ENST00000259362	T	0.01422	4.91	4.78	2.2	0.27929	GPCR, rhodopsin-like superfamily (1);	0.282386	0.25256	N	0.031997	T	0.00012	0.0000	N	0.17764	0.52	0.54753	P	1.6000000000016E-5	B	0.06786	0.001	B	0.10450	0.005	T	0.09271	-1.0682	9	0.33141	T	0.24	.	8.3632	0.32372	0.3107:0.0:0.0:0.6893	rs993658;rs52822852;rs993658	91	Q8NGT0	O13C9_HUMAN	S	91	ENSP00000259362:T91S	ENSP00000259362:T91S	T	-	1	0	OR13C9	106420036	0.000000	0.05858	1.000000	0.80357	0.973000	0.67179	-0.033000	0.12246	0.809000	0.34255	0.519000	0.50382	ACC	T|0.743;A|0.257	0.257	strong		0.502	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
SPPL2C	162540	hgsc.bcm.edu	37	17	43924200	43924200	+	Missense_Mutation	SNP	C	C	G	rs12373142	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43924200C>G	ENST00000329196.5	+	1	1945	c.1928C>G	c.(1927-1929)cCg>cGg	p.P643R	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	643			P -> R (in dbSNP:rs12373142).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										CTGATGCCCCCGCCCTCAGAG	0.627													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		18729	0.001		0.2396	False		,,,				2504	0.0613				p.P643R		Atlas-SNP	.											.	.	.	.	0			c.C1928G						PASS	.	C	ARG/PRO	200,4206	121.3+/-158.8	5,190,2008	43.0	41.0	42.0		1928	-0.3	0.0	17	dbSNP_120	42	1916,6684	328.1+/-318.2	221,1474,2605	yes	missense	IMP5	NM_175882.2	103	226,1664,4613	GG,GC,CC		22.2791,4.5393,16.2694	possibly-damaging	643/685	43924200	2116,10890	2203	4300	6503	SO:0001583	missense	162540	exon1			TGCCCCCGCCCTC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.1928C>G	17.37:g.43924200C>G	ENSP00000332488:p.Pro643Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	253	0.11584249084249085	10	0.02032520325203252	68	0.1878453038674033	1	0.0017482517482517483	174	0.22955145118733508	C	0.238	-1.015902	0.02078	0.045393	0.222791	ENSG00000185294	ENST00000329196	T	0.04406	3.63	4.23	-0.281	0.12882	.	0.237510	0.22293	N	0.061965	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.21309	0.054	B	0.14023	0.01	T	0.48490	-0.9031	9	0.48119	T	0.1	-18.8908	2.3936	0.04384	0.382:0.3664:0.1536:0.098	rs12373142;rs12373142	643	Q8IUH8	IMP5_HUMAN	R	643	ENSP00000332488:P643R	ENSP00000332488:P643R	P	+	2	0	AC217771.1	41279980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.094000	0.11094	-0.001000	0.14495	-1.047000	0.02352	CCG	C|0.473;G|0.527	0.527	strong		0.627	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
ZNF462	58499	hgsc.bcm.edu	37	9	109687288	109687288	+	Silent	SNP	T	T	C	rs1000152	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:109687288T>C	ENST00000277225.5	+	3	1384	c.1095T>C	c.(1093-1095)taT>taC	p.Y365Y	ZNF462_ENST00000457913.1_Silent_p.Y365Y|ZNF462_ENST00000441147.2_5'Flank			Q96JM2	ZN462_HUMAN	zinc finger protein 462	365					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GATCCCGTTATGGAATGACTG	0.418													T|||	988	0.197284	0.4297	0.17	5008	,	,		23464	0.129		0.0895	False		,,,				2504	0.0838				p.Y365Y		Atlas-SNP	.											ZNF462,colon,carcinoma,0,1	ZNF462	322	1	0			c.T1095C						PASS	.	T		1634,2772	503.5+/-365.6	291,1052,860	73.0	69.0	70.0		1095	-6.4	0.9	9	dbSNP_86	70	806,7794	188.7+/-235.6	50,706,3544	no	coding-synonymous	ZNF462	NM_021224.4		341,1758,4404	CC,CT,TT		9.3721,37.0858,18.7606		365/2507	109687288	2440,10566	2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			CCGTTATGGAATG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.1095T>C	9.37:g.109687288T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			T|0.801;C|0.199	0.199	strong		0.418	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
SLC6A17	388662	hgsc.bcm.edu	37	1	110709720	110709720	+	Missense_Mutation	SNP	G	G	A	rs12737742|rs35600013	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:110709720G>A	ENST00000331565.4	+	2	654	c.169G>A	c.(169-171)Gca>Aca	p.A57T	RP5-1028L10.1_ENST00000443008.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA|RP5-1028L10.1_ENST00000430098.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	57			A -> T (in dbSNP:rs12737742). {ECO:0000269|PubMed:15489334}.		alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GGAGCTGGATGCAGAGGACCG	0.612													G|||	1253	0.2502	0.0333	0.2608	5008	,	,		14238	0.2143		0.4652	False		,,,				2504	0.3517				p.A57T		Atlas-SNP	.											.	SLC6A17	86	.	0			c.G169A						PASS	.	G	THR/ALA,	477,3929		30,417,1756	71.0	58.0	62.0		169,291	2.6	0.0	1	dbSNP_121	62	3831,4769		935,1961,1404	yes	missense,coding-synonymous	SLC6A17,LOC100130800	NM_001010898.2,XM_001719118.1	58,	965,2378,3160	AA,AG,GG		44.5465,10.8261,33.1232	benign,	57/728,97/154	110709720	4308,8698	2203	4300	6503	SO:0001583	missense	388662	exon2			CTGGATGCAGAGG		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.169G>A	1.37:g.110709720G>A	ENSP00000330199:p.Ala57Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	37	CCDS30799.1	500	0.22893772893772893	15	0.03048780487804878	100	0.27624309392265195	108	0.1888111888111888	277	0.3654353562005277	G	13.10	2.134875	0.37728	0.108261	0.445465	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.74209	-0.82	4.44	2.57	0.30868	.	0.616662	0.17593	N	0.168698	T	0.28830	0.0715	N	0.08118	0	0.80722	P	0.0	B	0.20887	0.049	B	0.23275	0.045	T	0.03325	-1.1048	9	0.22706	T	0.39	.	6.0414	0.19736	0.1679:0.1554:0.6768:0.0	rs12737742	57	Q9H1V8	S6A17_HUMAN	T	57	ENSP00000330199:A57T	ENSP00000330199:A57T	A	+	1	0	SLC6A17	110511243	0.000000	0.05858	0.042000	0.18584	0.914000	0.54420	0.538000	0.23160	0.504000	0.28082	0.655000	0.94253	GCA	A|0.305;C|0.000;G|0.695	0.305	strong		0.612	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
KRBA2	124751	hgsc.bcm.edu	37	17	8272767	8272767	+	Silent	SNP	G	G	A	rs2430949	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:8272767G>A	ENST00000331336.2	-	2	1169	c.1164C>T	c.(1162-1164)ctC>ctT	p.L388L	RP11-849F2.7_ENST00000582471.1_3'UTR|RP11-849F2.5_ENST00000583963.1_RNA|KRBA2_ENST00000396267.1_Silent_p.L306L|RP11-849F2.5_ENST00000580537.1_RNA	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	388	Integrase catalytic. {ECO:0000255|PROSITE-ProRule:PRU00457}.				DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)	p.L388L(1)		endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						GCATGAATCGGAGGCCTTTGG	0.483													G|||	800	0.159744	0.1762	0.0951	5008	,	,		22638	0.3264		0.1133	False		,,,				2504	0.0593				p.L388L		Atlas-SNP	.											KRBA2,NS,carcinoma,0,1	KRBA2	34	1	1	Substitution - coding silent(1)	stomach(1)	c.C1164T						PASS	.	G		716,3690	296.1+/-284.1	48,620,1535	107.0	98.0	101.0		1164	-3.8	0.0	17	dbSNP_100	101	1239,7361	249.0+/-276.5	95,1049,3156	no	coding-synonymous	KRBA2	NM_213597.2		143,1669,4691	AA,AG,GG		14.407,16.2506,15.0315		388/493	8272767	1955,11051	2203	4300	6503	SO:0001819	synonymous_variant	124751	exon2			GAATCGGAGGCCT	BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"""-"""	26989	protein-coding gene	gene with protein product			"""KRAB A domain containing 2"""			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.1164C>T	17.37:g.8272767G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_213597	Q8IYY0	Silent	SNP	ENST00000331336.2	37	CCDS11141.1																																																																																			G|0.834;A|0.166	0.166	strong		0.483	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597	
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 GAIIx	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	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	89	46	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	
EGFL8	80864	hgsc.bcm.edu	37	6	32134510	32134510	+	Missense_Mutation	SNP	G	G	A	rs3096697	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32134510G>A	ENST00000395512.1	+	4	362	c.257G>A	c.(256-258)aGg>aAg	p.R86K	PPT2-EGFL8_ENST00000422437.1_3'UTR|EGFL8_ENST00000333845.6_Missense_Mutation_p.R86K|AGPAT1_ENST00000490711.1_5'Flank			Q99944	EGFL8_HUMAN	EGF-like-domain, multiple 8	86	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.		R -> K (in dbSNP:rs3096697). {ECO:0000269|PubMed:14574404}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	10						CGGGAGGTGAGGCGGGAGGTT	0.652													G|||	777	0.155152	0.2095	0.1023	5008	,	,		15949	0.0367		0.2008	False		,,,				2504	0.1943				p.R86K		Atlas-SNP	.											.	EGFL8	15	.	0			c.G257A						PASS	.	G	LYS/ARG	825,3581	316.1+/-294.4	77,671,1455	45.0	54.0	51.0		257	3.4	1.0	6	dbSNP_103	51	1861,6739	322.8+/-315.7	197,1467,2636	yes	missense	EGFL8	NM_030652.3	26	274,2138,4091	AA,AG,GG		21.6395,18.7245,20.652	benign	86/294	32134510	2686,10320	2203	4300	6503	SO:0001583	missense	80864	exon4			AGGTGAGGCGGGA	U89336	CCDS4743.1	6p21	2010-06-25	2003-05-21	2003-05-23	ENSG00000241404	ENSG00000241404			13944	protein-coding gene	gene with protein product		609897	"""chromosome 6 open reading frame 8"""	C6orf8			Standard	NM_030652		Approved	NG3		Q99944	OTTHUMG00000031222	ENST00000395512.1:c.257G>A	6.37:g.32134510G>A	ENSP00000378888:p.Arg86Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	70	0.76087	NM_030652	B0S884|G5E9Q0|Q5JP23|Q5SSX3|Q8IV30	Missense_Mutation	SNP	ENST00000395512.1	37	CCDS4743.1	311	0.1423992673992674	105	0.21341463414634146	33	0.09116022099447514	23	0.04020979020979021	150	0.19788918205804748	G	9.290	1.050493	0.19827	0.187245	0.216395	ENSG00000241404	ENST00000333845;ENST00000395512;ENST00000432129	T;T;T	0.40225	1.04;1.04;1.04	6.08	3.38	0.38709	EMI domain (2);	.	.	.	.	T	0.08268	0.0206	N	0.11560	0.145	0.43421	P	0.004430000000000045	B	0.09022	0.002	B	0.08055	0.003	T	0.26780	-1.0093	8	0.19590	T	0.45	-9.8585	8.4318	0.32761	0.2396:0.0:0.7604:0.0	rs3096697;rs17421868;rs58410180;rs3096697	86	Q99944	EGFL8_HUMAN	K	86	ENSP00000333380:R86K;ENSP00000378888:R86K;ENSP00000401694:R86K	ENSP00000333380:R86K	R	+	2	0	EGFL8	32242488	0.002000	0.14202	0.990000	0.47175	0.990000	0.78478	0.683000	0.25349	0.474000	0.27392	-0.136000	0.14681	AGG	G|0.830;A|0.170	0.170	strong		0.652	EGFL8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076463.3	NM_030652	
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 GAIIx	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	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	72	4	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	
CLIC5	53405	hgsc.bcm.edu	37	6	45882076	45882076	+	Missense_Mutation	SNP	C	C	A	rs148377014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:45882076C>A	ENST00000185206.6	-	5	1106	c.954G>T	c.(952-954)gaG>gaT	p.E318D	CLIC5_ENST00000486570.1_5'UTR|CLIC5_ENST00000339561.6_Missense_Mutation_p.E159D|CLIC5_ENST00000544153.1_Missense_Mutation_p.E159D	NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	318	GST C-terminal.				auditory receptor cell stereocilium organization (GO:0060088)|chloride transport (GO:0006821)|diet induced thermogenesis (GO:0002024)|female pregnancy (GO:0007565)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|sensory perception of sound (GO:0007605)|transport (GO:0006810)	actin cytoskeleton (GO:0015629)|chloride channel complex (GO:0034707)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|stereocilium (GO:0032420)	voltage-gated chloride channel activity (GO:0005247)			endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	13						TGGCGTCAATCTCCTCTGGTA	0.522													C|||	2	0.000399361	0.0	0.0	5008	,	,		18968	0.0		0.002	False		,,,				2504	0.0				p.E318D		Atlas-SNP	.											.	CLIC5	48	.	0			c.G954T						PASS	.	C	ASP/GLU,ASP/GLU	0,4406		0,0,2203	135.0	133.0	134.0		954,477	3.1	1.0	6	dbSNP_134	134	18,8582	14.0+/-48.4	0,18,4282	yes	missense,missense	CLIC5	NM_001114086.1,NM_016929.3	45,45	0,18,6485	AA,AC,CC		0.2093,0.0,0.1384	probably-damaging,probably-damaging	318/411,159/252	45882076	18,12988	2203	4300	6503	SO:0001583	missense	53405	exon5			GTCAATCTCCTCT	AF216941	CCDS4914.1, CCDS47438.1, CCDS59022.1	6p12.3	2014-03-14			ENSG00000112782	ENSG00000112782		"""Ion channels / Chloride channels : Intracellular"""	13517	protein-coding gene	gene with protein product		607293				10793131	Standard	NM_001114086		Approved		uc003oxv.3	Q9NZA1	OTTHUMG00000014775	ENST00000185206.6:c.954G>T	6.37:g.45882076C>A	ENSP00000185206:p.Glu318Asp	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_001114086	B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Missense_Mutation	SNP	ENST00000185206.6	37	CCDS47438.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	24.5	4.535007	0.85812	0.0	0.002093	ENSG00000112782	ENST00000185206;ENST00000339561;ENST00000544153	D;D;D	0.93953	-3.32;-3.32;-3.32	5.84	3.1	0.35709	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);	0.089937	0.85682	D	0.000000	D	0.95516	0.8543	H	0.94734	3.575	0.53005	D	0.999961	D;P;P	0.58970	0.984;0.776;0.821	P;P;P	0.55667	0.555;0.513;0.781	D	0.95357	0.8452	10	0.87932	D	0	.	9.9085	0.41390	0.0:0.7314:0.0:0.2686	.	159;318;159	Q8NBY3;Q9NZA1;Q53G01	.;CLIC5_HUMAN;.	D	318;159;159	ENSP00000185206:E318D;ENSP00000344165:E159D;ENSP00000439195:E159D	ENSP00000185206:E318D	E	-	3	2	CLIC5	45990054	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	1.705000	0.37867	0.943000	0.37553	0.650000	0.86243	GAG	C|0.998;A|0.002	0.002	strong		0.522	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1		
TCEB3C	162699	hgsc.bcm.edu	37	18	44555147	44555147	+	Missense_Mutation	SNP	T	T	G	rs139717358	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44555147T>G	ENST00000330682.2	-	1	1302	c.1067A>C	c.(1066-1068)gAa>gCa	p.E356A	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron	NM_145653.3	NP_663628.2	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide 3C (elongin A3)	356	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(16)|skin(2)	30						GGGGACCCCTTCCACGTCGCC	0.647																																					p.E356A		Atlas-SNP	.											TCEB3C,NS,carcinoma,0,1	TCEB3C	49	1	0			c.A1067C						scavenged	.	T	,ALA/GLU	71,3171		0,71,1550	233.0	223.0	226.0		,1067	-1.6	0.0	18	dbSNP_134	226	595,6065		0,595,2735	no	intron,missense	KATNAL2,TCEB3C	NM_031303.2,NM_145653.3	,107	0,666,4285	GG,GT,TT		8.9339,2.19,6.7259	,benign	,356/547	44555147	666,9236	1621	3330	4951	SO:0001583	missense	162699	exon1			ACCCCTTCCACGT	AB076840	CCDS11931.1	18q21.1	2008-08-13			ENSG00000183791	ENSG00000183791			24617	protein-coding gene	gene with protein product	"""elongin A3"""					11932239, 11994304	Standard	NM_145653		Approved	HsT829, TCEB3L2	uc010xdb.2	Q8NG57	OTTHUMG00000132651	ENST00000330682.2:c.1067A>C	18.37:g.44555147T>G	ENSP00000328232:p.Glu356Ala	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	317	17	0.0536278	NM_145653		Missense_Mutation	SNP	ENST00000330682.2	37	CCDS11931.1	.	.	.	.	.	.	.	.	.	.	t	5.286	0.238258	0.10023	0.0219	0.089339	ENSG00000183791	ENST00000330682	T	0.29397	1.57	1.6	-1.61	0.08399	.	0.408249	0.20310	N	0.094854	T	0.00580	0.0019	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.10382	-1.0632	10	0.62326	D	0.03	-1.0576	6.2705	0.20951	0.0:0.6512:0.0:0.3488	.	356	Q8NG57	ELOA3_HUMAN	A	356	ENSP00000328232:E356A	ENSP00000328232:E356A	E	-	2	0	TCEB3C	42809145	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.045000	0.12003	-0.528000	0.06366	-1.744000	0.00683	GAA	T|0.924;G|0.076	0.076	strong		0.647	TCEB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255902.1	NM_145653	
LRIT2	340745	hgsc.bcm.edu	37	10	85981889	85981889	+	Silent	SNP	G	G	A	rs12218853	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:85981889G>A	ENST00000372113.4	-	3	1445	c.1440C>T	c.(1438-1440)ggC>ggT	p.G480G	LRIT2_ENST00000538192.1_Silent_p.G490G	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	480						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						AGGCATAGGCGCCCACAGGCA	0.642													g|||	932	0.186102	0.0514	0.232	5008	,	,		18674	0.2907		0.2316	False		,,,				2504	0.181				p.G480G		Atlas-SNP	.											.	LRIT2	81	.	0			c.C1440T						PASS	.	A		379,4027	188.8+/-215.1	12,355,1836	38.0	40.0	39.0		1440	-6.2	0.0	10	dbSNP_120	39	1906,6694	325.0+/-316.7	193,1520,2587	no	coding-synonymous	LRIT2	NM_001017924.2		205,1875,4423	AA,AG,GG		22.1628,8.6019,17.5688		480/551	85981889	2285,10721	2203	4300	6503	SO:0001819	synonymous_variant	340745	exon3			ATAGGCGCCCACA		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"""Immunoglobulin superfamily / I-set domain containing"""	23443	protein-coding gene	gene with protein product			"""leucine rich repeat containing 22"""	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.1440C>T	10.37:g.85981889G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_001017924	B7ZME6	Silent	SNP	ENST00000372113.4	37	CCDS31234.1																																																																																			G|0.817;A|0.183	0.183	strong		0.642	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
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 GAIIx	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		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	49	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		
DAGLB	221955	hgsc.bcm.edu	37	7	6456347	6456347	+	Silent	SNP	G	G	T	rs1055428	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6456347G>T	ENST00000297056.6	-	11	1507	c.1338C>A	c.(1336-1338)ggC>ggA	p.G446G	DAGLB_ENST00000421761.2_Silent_p.G190G|DAGLB_ENST00000436575.1_Silent_p.G405G|DAGLB_ENST00000425398.2_Silent_p.G317G|DAGLB_ENST00000428902.2_Silent_p.G319G	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	446					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		CGGCCGCCCCGCCCCCGAGGC	0.637													G|||	761	0.151957	0.0348	0.1744	5008	,	,		14012	0.245		0.2097	False		,,,				2504	0.1391				p.G446G		Atlas-SNP	.											.	DAGLB	74	.	0			c.C1338A						PASS	.	G	,	330,4076	166.9+/-198.0	12,306,1885	35.0	39.0	38.0		951,1338	-9.5	0.0	7	dbSNP_86	38	1860,6740	320.0+/-314.4	222,1416,2662	no	coding-synonymous,coding-synonymous	DAGLB	NM_001142936.1,NM_139179.3	,	234,1722,4547	TT,TG,GG		21.6279,7.4898,16.8384	,	317/544,446/673	6456347	2190,10816	2203	4300	6503	SO:0001819	synonymous_variant	221955	exon11			CGCCCCGCCCCCG	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1338C>A	7.37:g.6456347G>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	52	43	0.826923	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Silent	SNP	ENST00000297056.6	37	CCDS5350.1																																																																																			G|0.843;T|0.157	0.157	strong		0.637	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
MRPL35	51318	hgsc.bcm.edu	37	2	86433240	86433240	+	Missense_Mutation	SNP	C	C	T	rs10901	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:86433240C>T	ENST00000337109.4	+	2	89	c.55C>T	c.(55-57)Ccc>Tcc	p.P19S	MRPL35_ENST00000409180.1_Missense_Mutation_p.P19S|MRPL35_ENST00000605125.1_Missense_Mutation_p.P19S|MRPL35_ENST00000254644.8_Missense_Mutation_p.P19S	NM_016622.3	NP_057706.2	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35	19			P -> S (in dbSNP:rs12714176). {ECO:0000269|PubMed:15489334}.		translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)	p.P19S(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(2)	14						AATCCTACGGCCCCTGAATAT	0.378													C|||	1225	0.244609	0.0552	0.2781	5008	,	,		17596	0.121		0.4751	False		,,,				2504	0.3671				p.P19S		Atlas-SNP	.											MRPL35,NS,adenoma,0,2	MRPL35	23	2	1	Substitution - Missense(1)	stomach(1)	c.C55T						PASS	.	C	SER/PRO,SER/PRO	497,3909	231.0+/-245.0	30,437,1736	141.0	139.0	140.0		55,55	4.7	1.0	2	dbSNP_52	140	4343,4257	580.4+/-391.0	1090,2163,1047	yes	missense,missense	MRPL35	NM_016622.3,NM_145644.2	74,74	1120,2600,2783	TT,TC,CC		49.5,11.2801,37.2136	probably-damaging,probably-damaging	19/189,19/171	86433240	4840,8166	2203	4300	6503	SO:0001583	missense	51318	exon2			CTACGGCCCCTGA	AF208849	CCDS1987.1, CCDS1988.1	2p11.2	2012-09-13			ENSG00000132313	ENSG00000132313		"""Mitochondrial ribosomal proteins / large subunits"""	14489	protein-coding gene	gene with protein product		611841				11042152, 11551941	Standard	NM_016622		Approved		uc002srg.4	Q9NZE8	OTTHUMG00000037385	ENST00000337109.4:c.55C>T	2.37:g.86433240C>T	ENSP00000338389:p.Pro19Ser	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	205	204	0.995122	NM_016622	A6NKV6|B2RB93|Q658U7|Q8WWA2	Missense_Mutation	SNP	ENST00000337109.4	37	CCDS1988.1	571	0.26144688644688646	30	0.06097560975609756	121	0.3342541436464088	69	0.12062937062937062	351	0.4630606860158311	C	15.36	2.809597	0.50421	0.112801	0.505	ENSG00000132313	ENST00000254644;ENST00000337109;ENST00000409180	T;T;T	0.18174	2.24;2.65;2.23	5.62	4.74	0.60224	.	0.096882	0.64402	N	0.000001	T	0.00012	0.0000	M	0.75264	2.295	0.27111	P	0.9623878	B	0.27882	0.192	B	0.21151	0.033	T	0.43081	-0.9413	9	0.26408	T	0.33	-10.0043	10.6449	0.45615	0.0:0.912:0.0:0.088	rs12714176;rs17845611;rs17858541;rs52836017;rs57050204;rs12714176	19	Q9NZE8	RM35_HUMAN	S	19	ENSP00000254644:P19S;ENSP00000338389:P19S;ENSP00000386255:P19S	ENSP00000254644:P19S	P	+	1	0	MRPL35	86286751	0.330000	0.24705	0.987000	0.45799	0.922000	0.55478	2.399000	0.44495	1.527000	0.49086	0.650000	0.86243	CCC	T|0.269;G|0.143	0.269	strong		0.378	MRPL35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091002.2	NM_016622	
ZNF860	344787	hgsc.bcm.edu	37	3	32031024	32031024	+	Silent	SNP	C	C	T	rs4449357	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:32031024C>T	ENST00000360311.4	+	2	1002	c.453C>T	c.(451-453)atC>atT	p.I151I		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	151					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(3)|lung(4)|ovary(1)	8						ACAAGCCTATCAAAGATCAGC	0.398													T|||	2149	0.429113	0.7912	0.3573	5008	,	,		20480	0.3006		0.1928	False		,,,				2504	0.3661				p.I151I		Atlas-SNP	.											.	ZNF860	96	.	0			c.C453T						PASS	.	T		922,462		315,292,85	67.0	49.0	54.0		453	0.3	0.0	3	dbSNP_111	54	608,2574		58,492,1041	no	coding-synonymous	ZNF860	NM_001137674.2		373,784,1126	TT,TC,CC		19.1075,33.3815,33.5085		151/633	32031024	1530,3036	692	1591	2283	SO:0001819	synonymous_variant	344787	exon2			GCCTATCAAAGAT	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.453C>T	3.37:g.32031024C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_001137674	B4DFA4	Silent	SNP	ENST00000360311.4	37	CCDS46784.1																																																																																			C|0.655;T|0.345	0.345	strong		0.398	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
SLC5A8	160728	hgsc.bcm.edu	37	12	101573812	101573812	+	Silent	SNP	A	A	G	rs61738704	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:101573812A>G	ENST00000536262.2	-	10	1786	c.1228T>C	c.(1228-1230)Ttg>Ctg	p.L410L		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTCACCTGCAACAAAGCTCCC	0.443													A|||	73	0.0145767	0.0023	0.0115	5008	,	,		16968	0.0		0.0249	False		,,,				2504	0.0378				p.L410L	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.T1228C						PASS	.	A		27,4379	33.5+/-64.1	1,25,2177	163.0	162.0	162.0		1228	1.1	1.0	12	dbSNP_129	162	307,8293	111.0+/-171.3	8,291,4001	yes	coding-synonymous	SLC5A8	NM_145913.3		9,316,6178	GG,GA,AA		3.5698,0.6128,2.568		410/611	101573812	334,12672	2203	4300	6503	SO:0001819	synonymous_variant	160728	exon10			CCTGCAACAAAGC	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"""Solute carriers"""	19119	protein-coding gene	gene with protein product		608044	"""solute carrier family 5 (iodide transporter), member 8"""			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1228T>C	12.37:g.101573812A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_145913		Silent	SNP	ENST00000536262.2	37	CCDS9080.1																																																																																			A|0.978;G|0.022	0.022	strong		0.443	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913	
TRIM32	22954	hgsc.bcm.edu	37	9	119461275	119461275	+	Silent	SNP	G	G	A	rs1661300	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:119461275G>A	ENST00000450136.1	+	2	1415	c.1254G>A	c.(1252-1254)gtG>gtA	p.V418V	ASTN2_ENST00000361209.2_Intron|ASTN2_ENST00000313400.4_Intron|ASTN2_ENST00000361477.3_Intron|TRIM32_ENST00000373983.2_Silent_p.V418V|ASTN2_ENST00000373996.3_Intron	NM_001099679.1|NM_012210.3	NP_001093149.1|NP_036342.2	Q13049	TRI32_HUMAN	tripartite motif containing 32	418					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of proteolysis (GO:0045862)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of type I interferon production (GO:0032479)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|striated muscle myosin thick filament (GO:0005863)	ligase activity (GO:0016874)|myosin binding (GO:0017022)|protein self-association (GO:0043621)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|translation initiation factor binding (GO:0031369)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	26						ATAGCTTTGTGCTAAGCTTCC	0.507													G|||	519	0.103634	0.0802	0.0749	5008	,	,		19747	0.1548		0.1153	False		,,,				2504	0.091				p.V418V	Esophageal Squamous(92;212 1916 19711 26951)	Atlas-SNP	.											.	TRIM32	67	.	0			c.G1254A						PASS	.	G	,,	296,4110	162.2+/-194.2	5,286,1912	131.0	138.0	136.0		1254,1254,	3.6	1.0	9	dbSNP_89	136	1093,7507	225.8+/-261.7	82,929,3289	no	coding-synonymous,coding-synonymous,intron	TRIM32,ASTN2	NM_001099679.1,NM_012210.3,NM_014010.4	,,	87,1215,5201	AA,AG,GG		12.7093,6.7181,10.6797	,,	418/654,418/654,	119461275	1389,11617	2203	4300	6503	SO:0001819	synonymous_variant	22954	exon2			CTTTGTGCTAAGC	U18543	CCDS6817.1	9q33.1	2014-09-17	2011-01-25		ENSG00000119401	ENSG00000119401		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16380	protein-coding gene	gene with protein product		602290	"""limb girdle muscular dystrophy 2H (autosomal recessive)"", ""tripartite motif-containing 32"""	LGMD2H		11331580, 7778269, 16606853	Standard	NM_001099679		Approved	HT2A, TATIP, BBS11	uc004bjx.2	Q13049	OTTHUMG00000021026	ENST00000450136.1:c.1254G>A	9.37:g.119461275G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_012210	Q9NQP8	Silent	SNP	ENST00000450136.1	37	CCDS6817.1																																																																																			G|0.896;A|0.104	0.104	strong		0.507	TRIM32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055466.2	NM_012210	
KCNJ2	3759	hgsc.bcm.edu	37	17	68172326	68172326	+	Silent	SNP	C	C	T	rs173135	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:68172326C>T	ENST00000243457.3	+	2	1529	c.1146C>T	c.(1144-1146)ctC>ctT	p.L382L	KCNJ2_ENST00000535240.1_Silent_p.L382L	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	382					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)					AAGTTGCCCTCACAAGCAAAG	0.448													C|||	771	0.153954	0.1551	0.2392	5008	,	,		20815	0.131		0.1203	False		,,,				2504	0.1503				p.L382L		Atlas-SNP	.											.	KCNJ2	74	.	0			c.C1146T						PASS	.	C		574,3832	251.8+/-258.4	35,504,1664	121.0	123.0	122.0		1146	3.0	1.0	17	dbSNP_79	122	1020,7580	214.9+/-254.4	63,894,3343	no	coding-synonymous	KCNJ2	NM_000891.2		98,1398,5007	TT,TC,CC		11.8605,13.0277,12.2559		382/428	68172326	1594,11412	2203	4300	6503	SO:0001819	synonymous_variant	3759	exon2			TGCCCTCACAAGC	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.1146C>T	17.37:g.68172326C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_000891	O15110|P48049	Silent	SNP	ENST00000243457.3	37	CCDS11688.1																																																																																			C|0.867;T|0.133	0.133	strong		0.448	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891	
RSF1	51773	hgsc.bcm.edu	37	11	77378505	77378505	+	Silent	SNP	A	A	G	rs28930682	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77378505A>G	ENST00000308488.6	-	16	4085	c.3783T>C	c.(3781-3783)gaT>gaC	p.D1261D	RSF1_ENST00000360355.2_Silent_p.D1230D|RSF1_ENST00000480887.1_Silent_p.D1009D			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	1261					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			TAGCTAGCTCATCATCTTCAG	0.443													G|||	983	0.196286	0.329	0.2147	5008	,	,		19989	0.1736		0.0984	False		,,,				2504	0.1278				p.D1261D		Atlas-SNP	.											.	RSF1	105	.	0			c.T3783C						PASS	.	G		1327,3073		199,929,1072	57.0	59.0	58.0		3783	2.6	1.0	11	dbSNP_125	58	823,7761		36,751,3505	no	coding-synonymous	RSF1	NM_016578.3		235,1680,4577	GG,GA,AA		9.5876,30.1591,16.5588		1261/1442	77378505	2150,10834	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon16			TAGCTCATCATCT	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.3783T>C	11.37:g.77378505A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	51	43	0.843137	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1																																																																																			A|0.816;G|0.184	0.184	strong		0.443	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
TMEM2	23670	hgsc.bcm.edu	37	9	74349846	74349846	+	Missense_Mutation	SNP	A	A	T	rs25695	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:74349846A>T	ENST00000377044.4	-	6	1808	c.1269T>A	c.(1267-1269)gaT>gaA	p.D423E	TMEM2_ENST00000377066.5_Intron	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	423			D -> E (in dbSNP:rs25695).		multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		AACTACTAACATCATCTAGCA	0.408													A|||	406	0.0810703	0.0386	0.0476	5008	,	,		17399	0.0198		0.0815	False		,,,				2504	0.2249				p.D423E		Atlas-SNP	.											.	TMEM2	112	.	0			c.T1269A						PASS	.	A	,GLU/ASP	173,4233	113.3+/-151.4	6,161,2036	198.0	188.0	191.0		,1269	-7.4	0.7	9	dbSNP_72	191	724,7876	176.3+/-226.2	31,662,3607	yes	intron,missense	TMEM2	NM_001135820.1,NM_013390.2	,45	37,823,5643	TT,TA,AA		8.4186,3.9265,6.8968	,benign	,423/1384	74349846	897,12109	2203	4300	6503	SO:0001583	missense	23670	exon6			ACTAACATCATCT		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.1269T>A	9.37:g.74349846A>T	ENSP00000366243:p.Asp423Glu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	118	51	0.432203	NM_013390	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	123	0.05631868131868132	27	0.054878048780487805	21	0.058011049723756904	13	0.022727272727272728	62	0.08179419525065963	A	11.46	1.646357	0.29246	0.039265	0.084186	ENSG00000135048	ENST00000377044	T	0.80123	-1.34	6.08	-7.36	0.01417	Pectin lyase fold/virulence factor (1);	0.146554	0.64402	D	0.000012	T	0.17704	0.0425	M	0.81497	2.545	0.80722	D	1	B	0.32245	0.361	B	0.30029	0.11	T	0.54289	-0.8316	10	0.41790	T	0.15	.	18.5272	0.90976	0.4864:0.0:0.5136:0.0	rs25695;rs17476197;rs25695	423	Q9UHN6	TMEM2_HUMAN	E	423	ENSP00000366243:D423E	ENSP00000366243:D423E	D	-	3	2	TMEM2	73539666	0.011000	0.17503	0.663000	0.29738	0.318000	0.28184	-0.689000	0.05144	-1.738000	0.01348	-1.139000	0.01908	GAT	A|0.936;T|0.064	0.064	strong		0.408	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
SERPINF2	5345	hgsc.bcm.edu	37	17	1648502	1648502	+	Missense_Mutation	SNP	C	C	T	rs2070863	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1648502C>T	ENST00000324015.3	+	3	174	c.97C>T	c.(97-99)Cgg>Tgg	p.R33W	SERPINF2_ENST00000382061.4_Missense_Mutation_p.R33W|SERPINF2_ENST00000450523.2_Missense_Mutation_p.R33W	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	33			R -> W (in dbSNP:rs2070863). {ECO:0000269|PubMed:10583218}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	GCCCTTGGGCCGGCAGGTACT	0.672													C|||	1197	0.239018	0.2201	0.2089	5008	,	,		9905	0.1855		0.1988	False		,,,				2504	0.3824				p.R33W		Atlas-SNP	.											.	SERPINF2	33	.	0			c.C97T	GRCh37	CM073337	SERPINF2	M	rs2070863	PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	894,3468		90,714,1377	23.0	18.0	20.0		97,97,97	3.0	0.0	17	dbSNP_96	20	1705,6805		177,1351,2727	yes	missense,missense,missense	SERPINF2	NM_000934.3,NM_001165920.1,NM_001165921.1	101,101,101	267,2065,4104	TT,TC,CC		20.0353,20.4952,20.1911	probably-damaging,probably-damaging,probably-damaging	33/492,33/492,33/428	1648502	2599,10273	2181	4255	6436	SO:0001583	missense	5345	exon3			TTGGGCCGGCAGG	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"""Serine (or cysteine) peptidase inhibitors"""	9075	protein-coding gene	gene with protein product	"""alpha-2-plasmin inhibitor"", ""alpha-2-antiplasmin"""	613168	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"""	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.97C>T	17.37:g.1648502C>T	ENSP00000321853:p.Arg33Trp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Missense_Mutation	SNP	ENST00000324015.3	37	CCDS11011.1	419	0.19184981684981686	99	0.20121951219512196	71	0.19613259668508287	103	0.18006993006993008	146	0.19261213720316622	C	11.31	1.601548	0.28534	0.204952	0.200353	ENSG00000167711	ENST00000453066;ENST00000324015;ENST00000450523;ENST00000423861;ENST00000453723;ENST00000382061	D;D;D;D;D	0.87809	-2.3;-1.97;-2.03;-1.72;-1.97	4.98	2.96	0.34315	.	1.515610	0.03304	N	0.189536	T	0.00356	0.0011	L	0.29908	0.895	0.80722	P	0.0	D;P	0.55172	0.97;0.946	B;B	0.42087	0.375;0.12	T	0.32295	-0.9912	9	0.52906	T	0.07	.	10.6516	0.45651	0.0:0.8237:0.0:0.1763	rs2070863;rs2234833;rs61057008;rs2070863	33;33	B4E1B7;P08697	.;A2AP_HUMAN	W	33	ENSP00000402286:R33W;ENSP00000321853:R33W;ENSP00000403877:R33W;ENSP00000402056:R33W;ENSP00000371493:R33W	ENSP00000321853:R33W	R	+	1	2	SERPINF2	1595252	0.001000	0.12720	0.003000	0.11579	0.006000	0.05464	0.793000	0.26944	0.235000	0.21160	-1.626000	0.00786	CGG	C|0.794;T|0.206	0.206	strong		0.672	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934	
VPS33B	26276	hgsc.bcm.edu	37	15	91543761	91543761	+	Missense_Mutation	SNP	C	C	T	rs11073964	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:91543761C>T	ENST00000333371.3	-	20	1893	c.1540G>A	c.(1540-1542)Ggt>Agt	p.G514S	VPS33B_ENST00000535906.1_Missense_Mutation_p.G487S|VPS33B_ENST00000535843.1_Missense_Mutation_p.G423S	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	514			G -> S (in dbSNP:rs11073964). {ECO:0000269|PubMed:10894945, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					TAAGCACCACCGAAGACGTAA	0.493													T|||	3845	0.767772	0.9607	0.6686	5008	,	,		20263	0.996		0.3986	False		,,,				2504	0.7219				p.G514S		Atlas-SNP	.											.	VPS33B	42	.	0			c.G1540A						PASS	.	T	SER/GLY	3870,526	240.6+/-251.3	1709,452,37	118.0	96.0	104.0		1540	5.8	1.0	15	dbSNP_120	104	3422,5174	637.6+/-399.2	670,2082,1546	yes	missense	VPS33B	NM_018668.3	56	2379,2534,1583	TT,TC,CC		39.8092,11.9654,43.8732	benign	514/618	91543761	7292,5700	2198	4298	6496	SO:0001583	missense	26276	exon20			CACCACCGAAGAC	AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"""vacuolar protein sorting 33B (yeast homolog)"""			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.1540G>A	15.37:g.91543761C>T	ENSP00000327650:p.Gly514Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Missense_Mutation	SNP	ENST00000333371.3	37	CCDS10369.1	1573	0.7202380952380952	469	0.9532520325203252	218	0.6022099447513812	571	0.9982517482517482	315	0.4155672823218997	T	10.36	1.328511	0.24167	0.880346	0.398092	ENSG00000184056	ENST00000333371;ENST00000535906;ENST00000535843;ENST00000537510	T;T;T	0.74737	-0.87;-0.87;-0.87	5.83	5.83	0.93111	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00303	-1.675	0.39820	P	0.027178999999999953	B;B	0.12630	0.006;0.002	B;B	0.08055	0.002;0.003	T	0.44559	-0.9320	9	0.02654	T	1	-15.2107	11.7519	0.51853	0.0:0.0695:0.0:0.9305	rs11073964;rs17515382;rs17845495;rs17858380;rs57245246;rs11073964	487;514	F5H008;Q9H267	.;VP33B_HUMAN	S	514;487;423;469	ENSP00000327650:G514S;ENSP00000444053:G487S;ENSP00000446267:G423S	ENSP00000327650:G514S	G	-	1	0	VPS33B	89344765	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	4.267000	0.58877	1.028000	0.39785	-0.269000	0.10298	GGT	C|0.359;T|0.641	0.641	strong		0.493	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668	
IPO4	79711	hgsc.bcm.edu	37	14	24654489	24654489	+	Silent	SNP	T	T	C	rs2025258	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24654489T>C	ENST00000354464.6	-	14	1484	c.1308A>G	c.(1306-1308)gtA>gtG	p.V436V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	436					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		GCAGTGGCATTACCTCCCTTG	0.577													C|||	2312	0.461661	0.3782	0.2939	5008	,	,		19134	0.7897		0.339	False		,,,				2504	0.4816				p.V436V		Atlas-SNP	.											.	IPO4	74	.	0			c.A1308G						PASS	.	C		1560,2650		286,988,831	73.0	75.0	75.0		1308	5.1	1.0	14	dbSNP_94	75	2895,5573		485,1925,1824	no	coding-synonymous	IPO4	NM_024658.3		771,2913,2655	CC,CT,TT		34.1875,37.0546,35.1396		436/1082	24654489	4455,8223	2105	4234	6339	SO:0001819	synonymous_variant	79711	exon14			TGGCATTACCTCC	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.1308A>G	14.37:g.24654489T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																			T|0.551;C|0.448	0.448	strong		0.577	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244194	11244194	+	Missense_Mutation	SNP	T	T	C	rs71443637	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11244194T>C	ENST00000531678.1	-	1	718	c.635A>G	c.(634-636)cAt>cGt	p.H212R	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	212				H -> R (in Ref. 1; AAM19328, 3; AAU21145 and 5; AAI17424). {ECO:0000305}.	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)		TCCTTTACCATGGAGCTGCAT	0.408													.|||	3114	0.621805	0.0998	0.7104	5008	,	,		13446	0.9425		0.7525	False		,,,				2504	0.7996				p.H212R		Atlas-SNP	.											TAS2R43,NS,carcinoma,0,2	TAS2R43	19	2	0			c.A635G						PASS	.						123.0	99.0	107.0					12																	11244194		2155	4165	6320	SO:0001583	missense	259289	exon1			TTACCATGGAGCT	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.635A>G	12.37:g.11244194T>C	ENSP00000431719:p.His212Arg	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	103	87	0.84466	NM_176884	P59546|Q645X4	Missense_Mutation	SNP	ENST00000531678.1	37	CCDS53749.1	949	0.43452380952380953	28	0.056910569105691054	163	0.45027624309392267	439	0.7674825174825175	319	0.420844327176781	-	2.129	-0.399500	0.04865	.	.	ENSG00000255374	ENST00000531678	T	0.00737	5.76	1.45	-1.32	0.09201	.	.	.	.	.	T	0.00012	0.0000	M	0.86178	2.8	0.80722	P	0.0	.	.	.	.	.	.	T	0.07028	-1.0794	6	0.52906	T	0.07	.	4.3248	0.11034	0.0:0.4339:0.0:0.5661	.	.	.	.	R	212	ENSP00000431719:H212R	ENSP00000431719:H212R	H	-	2	0	TAS2R43	11135461	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.381000	0.07417	-0.374000	0.07967	-1.273000	0.01405	CAT	T|0.599;C|0.401	0.401	strong		0.408	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884	
PML	5371	hgsc.bcm.edu	37	15	74336633	74336633	+	Missense_Mutation	SNP	T	T	C	rs5742915	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:74336633T>C	ENST00000268058.3	+	9	2029	c.1933T>C	c.(1933-1935)Ttc>Ctc	p.F645L	PML_ENST00000565898.1_Missense_Mutation_p.F597L	NM_033238.2	NP_150241.2	P29590	PML_HUMAN	promyelocytic leukemia	645			F -> L (in dbSNP:rs5742915). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:1720570}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to interleukin-4 (GO:0071353)|cellular senescence (GO:0090398)|circadian regulation of gene expression (GO:0032922)|common-partner SMAD protein phosphorylation (GO:0007182)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|entrainment of circadian clock by photoperiod (GO:0043153)|extrinsic apoptotic signaling pathway (GO:0097191)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|maintenance of protein location in nucleus (GO:0051457)|myeloid cell differentiation (GO:0030099)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation in response to oxidative stress (GO:0032938)|negative regulation of viral release from host cell (GO:1902187)|PML body organization (GO:0030578)|positive regulation of apoptotic process involved in mammary gland involution (GO:0060058)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of histone deacetylation (GO:0031065)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)|regulation of calcium ion transport into cytosol (GO:0010522)|regulation of circadian rhythm (GO:0042752)|regulation of double-strand break repair (GO:2000779)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of protein phosphorylation (GO:0001932)|regulation of transcription, DNA-templated (GO:0006355)|response to cytokine (GO:0034097)|response to gamma radiation (GO:0010332)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|retinoic acid receptor signaling pathway (GO:0048384)|SMAD protein import into nucleus (GO:0007184)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of endoplasmic reticulum membrane (GO:0042406)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	cobalt ion binding (GO:0050897)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|SUMO binding (GO:0032183)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	31						GCCTGAAGCCTTCTTCAGCAT	0.602			T	"""RARA, PAX5"""	"""APL, ALL"""								T|||	963	0.192292	0.0454	0.2911	5008	,	,		18031	0.004		0.4384	False		,,,				2504	0.2618				p.F645L		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.T1933C						PASS	.	T	LEU/PHE	467,3929	221.7+/-238.7	25,417,1756	73.0	69.0	71.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1933	-3.3	0.0	15	dbSNP_114	71	3970,4624	549.1+/-385.5	921,2128,1248	yes	missense	PML	NM_033238.2	22	946,2545,3004	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	46.195,10.6233,34.157	benign	645/883	74336633	4437,8553	2198	4297	6495	SO:0001583	missense	5371	exon9			GAAGCCTTCTTCA	AB208950	CCDS10255.1, CCDS10256.1, CCDS10257.1, CCDS10258.1, CCDS45297.1, CCDS45298.1, CCDS45299.1, CCDS45300.1, CCDS58386.1	15q24.1	2011-04-21			ENSG00000140464	ENSG00000140464		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9113	protein-coding gene	gene with protein product		102578					Standard	NM_033244		Approved	MYL, TRIM19, RNF71	uc002awv.3	P29590	OTTHUMG00000137607	ENST00000268058.3:c.1933T>C	15.37:g.74336633T>C	ENSP00000268058:p.Phe645Leu	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_033238	E9PBR7|P29591|P29592|P29593|Q00755|Q15959|Q59FP9|Q8WUA0|Q96S41|Q9BPW2|Q9BWP7|Q9BZX6|Q9BZX7|Q9BZX8|Q9BZX9|Q9BZY0|Q9BZY2|Q9BZY3	Missense_Mutation	SNP	ENST00000268058.3	37	CCDS10255.1	494	0.2261904761904762	26	0.052845528455284556	129	0.356353591160221	2	0.0034965034965034965	337	0.4445910290237467	T	3.535	-0.094924	0.07010	0.106233	0.46195	ENSG00000140464	ENST00000268058;ENST00000417341;ENST00000418568	T	0.41065	1.01	3.24	-3.26	0.05064	.	2.331610	0.02379	U	0.078638	T	0.00012	0.0000	N	0.08118	0	0.38303	P	0.056952	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.35724	-0.9777	9	0.02654	T	1	-0.5428	5.6012	0.17355	0.0:0.18:0.6082:0.2118	rs5742915;rs59256395;rs5742915	645;597	P29590;P29590-11	PML_HUMAN;.	L	645;206;645	ENSP00000268058:F645L	ENSP00000268058:F645L	F	+	1	0	PML	72123686	0.000000	0.05858	0.047000	0.18901	0.665000	0.39181	-0.220000	0.09215	-0.543000	0.06240	0.482000	0.46254	TTC	T|0.714;C|0.286	0.286	strong		0.602	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
ZNF302	55900	hgsc.bcm.edu	37	19	35175749	35175749	+	Silent	SNP	C	C	G	rs10401309	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:35175749C>G	ENST00000446502.2	+	6	1147	c.939C>G	c.(937-939)ggC>ggG	p.G313G	ZNF302_ENST00000423823.2_Silent_p.G269G|ZNF302_ENST00000457781.2_Silent_p.G269G|ZNF302_ENST00000505242.1_Silent_p.G269G|ZNF302_ENST00000505365.2_3'UTR			Q9NR11	ZN302_HUMAN	zinc finger protein 302	348					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)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TTAGCCATGGCTCATCACTTA	0.443													C|||	421	0.0840655	0.0598	0.0807	5008	,	,		21702	0.006		0.1153	False		,,,				2504	0.1677				p.G269G		Atlas-SNP	.											.	ZNF302	27	.	0			c.C807G						PASS	.	C	,	327,4079	172.3+/-202.3	10,307,1886	94.0	93.0	93.0		807,807	-0.2	0.9	19	dbSNP_119	93	1015,7585	216.4+/-255.5	58,899,3343	no	coding-synonymous,coding-synonymous	ZNF302	NM_001012320.1,NM_018443.2	,	68,1206,5229	GG,GC,CC		11.8023,7.4217,10.3183	,	269/400,269/400	35175749	1342,11664	2203	4300	6503	SO:0001819	synonymous_variant	55900	exon5			CCATGGCTCATCA	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.939C>G	19.37:g.35175749C>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Silent	SNP	ENST00000446502.2	37																																																																																				C|0.915;G|0.085	0.085	strong		0.443	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
SAA1	6288	hgsc.bcm.edu	37	11	18291321	18291321	+	Silent	SNP	T	T	C	rs12218	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18291321T>C	ENST00000405158.2	+	4	472	c.288T>C	c.(286-288)gcT>gcC	p.A96A	SAA1_ENST00000356524.4_Silent_p.A96A|SAA1_ENST00000532858.1_Silent_p.A96A	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	96				ADQAAN -> SEATVK (in Ref. 9; AA sequence). {ECO:0000305}.	acute-phase response (GO:0006953)|innate immune response (GO:0045087)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of inflammatory response (GO:0050728)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of interleukin-1 secretion (GO:0050716)|regulation of protein secretion (GO:0050708)	endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)	p.A96A(1)		endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	ACTCGCTGGCTGATCAGGCTG	0.527													T|||	1490	0.297524	0.0303	0.4712	5008	,	,		18503	0.2748		0.4911	False		,,,				2504	0.3599				p.A96A		Atlas-SNP	.											SAA1,NS,carcinoma,0,1	SAA1	14	1	1	Substitution - coding silent(1)	stomach(1)	c.T288C						scavenged	.	T	,,	511,3887	233.0+/-246.3	29,453,1717	114.0	97.0	103.0		288,288,288	-5.6	0.0	11	dbSNP_52	103	4273,4313	575.0+/-390.2	1069,2135,1089	no	coding-synonymous,coding-synonymous,coding-synonymous	SAA1	NM_000331.4,NM_001178006.1,NM_199161.3	,,	1098,2588,2806	CC,CT,TT		49.7671,11.6189,36.8453	,,	96/123,96/123,96/123	18291321	4784,8200	2199	4293	6492	SO:0001819	synonymous_variant	6288	exon4			GCTGGCTGATCAG	M10906	CCDS7835.1	11p15.1	2014-01-30			ENSG00000173432	ENSG00000173432		"""Endogenous ligands"""	10513	protein-coding gene	gene with protein product		104750		SAA		2595451, 9305847	Standard	NM_199161		Approved	PIG4, TP53I4	uc021qeo.1	P0DJI8	OTTHUMG00000166147	ENST00000405158.2:c.288T>C	11.37:g.18291321T>C		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	174	79	0.454023	NM_199161	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Silent	SNP	ENST00000405158.2	37	CCDS7835.1																																																																																			T|0.648;C|0.352	0.352	strong		0.527	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161	
CCL14	6358	hgsc.bcm.edu	37	17	34313674	34313674	+	Silent	SNP	G	G	A	rs113937434	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:34313674G>A	ENST00000394509.4	-	1	120	c.12C>T	c.(10-12)tcC>tcT	p.S4S	CTB-186H2.3_ENST00000593057.1_3'UTR|CCL14_ENST00000536149.1_Silent_p.S4S|CCL14_ENST00000480944.2_5'UTR|CCL14_ENST00000586216.1_Silent_p.S4S|CCL14_ENST00000435911.2_Silent_p.S4S|CCL15-CCL14_ENST00000481427.2_3'UTR|CTB-186H2.3_ENST00000591669.1_Silent_p.T40T			Q16627	CCL14_HUMAN	chemokine (C-C motif) ligand 14	4					cell chemotaxis (GO:0060326)|cellular calcium ion homeostasis (GO:0006874)|immune response (GO:0006955)|positive regulation of cell proliferation (GO:0008284)	extracellular space (GO:0005615)				large_intestine(1)|lung(6)	7		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TGGCAGCCACGGAGATCTTCA	0.537													G|||	106	0.0211661	0.003	0.0144	5008	,	,		16096	0.0476		0.0358	False		,,,				2504	0.0082				p.S4S		Atlas-SNP	.											.	CCL14	22	.	0			c.C12T						PASS	.	G	,	46,4360	48.2+/-83.0	0,46,2157	194.0	137.0	157.0		12,12	0.2	0.0	17	dbSNP_132	157	252,8348	99.9+/-161.4	0,252,4048	no	coding-synonymous,coding-synonymous	CCL14	NM_032962.4,NM_032963.3	,	0,298,6205	AA,AG,GG		2.9302,1.044,2.2913	,	4/110,4/94	34313674	298,12708	2203	4300	6503	SO:0001819	synonymous_variant	6358	exon1			AGCCACGGAGATC	Z49270	CCDS32624.1, CCDS45652.1	17q11.2	2014-04-10	2002-08-22	2002-08-23	ENSG00000213494	ENSG00000276409		"""Chemokine ligands"", ""Endogenous ligands"""	10612	protein-coding gene	gene with protein product		601392	"""small inducible cytokine subfamily A (Cys-Cys), member 14"""	SCYA14		8661057	Standard	NM_032963		Approved	HCC-1, HCC-3, NCC-2, SCYL2, CKb1, MCIF	uc010wcq.1	Q16627	OTTHUMG00000188403	ENST00000394509.4:c.12C>T	17.37:g.34313674G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	111	59	0.531532	NM_032962	E1P649|E1P650|Q13954	Silent	SNP	ENST00000394509.4	37	CCDS32624.1																																																																																			G|0.977;A|0.023	0.023	strong		0.537	CCL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272892.2	NM_032962	
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 GAIIx	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		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	24	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	
SLC12A7	10723	hgsc.bcm.edu	37	5	1057615	1057615	+	Silent	SNP	A	A	G	rs2241606	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:1057615A>G	ENST00000264930.5	-	22	3040	c.2997T>C	c.(2995-2997)tcT>tcC	p.S999S		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	999					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CTTTGAAACCAGATAGGCTGG	0.602													a|||	2469	0.493011	0.2352	0.6282	5008	,	,		17436	0.4772		0.6372	False		,,,				2504	0.6135				p.S999S		Atlas-SNP	.											SLC12A7,NS,carcinoma,-1,1	SLC12A7	97	1	0			c.T2997C						PASS	.	G		1337,3069	447.5+/-348.4	216,905,1082	167.0	139.0	148.0		2997	-5.7	0.0	5	dbSNP_98	148	5619,2981	666.1+/-402.3	1832,1955,513	no	coding-synonymous	SLC12A7	NM_006598.2		2048,2860,1595	GG,GA,AA		34.6628,30.345,46.517		999/1084	1057615	6956,6050	2203	4300	6503	SO:0001819	synonymous_variant	10723	exon22			GAAACCAGATAGG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2997T>C	5.37:g.1057615A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1																																																																																			A|0.485;G|0.515	0.515	strong		0.602	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
SPTBN5	51332	hgsc.bcm.edu	37	15	42171462	42171462	+	Missense_Mutation	SNP	C	C	T	rs12708402	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42171462C>T	ENST00000320955.6	-	16	3405	c.3178G>A	c.(3178-3180)Gta>Ata	p.V1060I		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1060					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCGTACTTTACGACCACACTT	0.617													C|||	902	0.180112	0.1657	0.1888	5008	,	,		19056	0.0516		0.2684	False		,,,				2504	0.2352				p.V1025I		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G3073A						PASS	.	C	ILE/VAL	690,3428		66,558,1435	43.0	47.0	46.0		3073	-1.1	0.0	15	dbSNP_121	46	2192,6226		298,1596,2315	yes	missense	SPTBN5	NM_016642.2	29	364,2154,3750	TT,TC,CC		26.0394,16.7557,22.9898	benign	1025/3640	42171462	2882,9654	2059	4209	6268	SO:0001583	missense	51332	exon16			ACTTTACGACCAC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.3178G>A	15.37:g.42171462C>T	ENSP00000317790:p.Val1060Ile	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	39	24	0.615385	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		375	0.1717032967032967	79	0.16056910569105692	72	0.19889502762430938	19	0.033216783216783216	205	0.2704485488126649	.	11.20	1.568878	0.28003	0.167557	0.260394	ENSG00000137877	ENST00000320955	T	0.34667	1.35	4.26	-1.14	0.09741	.	2.753290	0.01702	N	0.027227	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26155	-1.0111	9	0.35671	T	0.21	.	4.4363	0.11552	0.0:0.3366:0.3577:0.3057	rs12708402;rs56456804;rs12708402	1060	Q9NRC6	SPTN5_HUMAN	I	1060	ENSP00000317790:V1060I	ENSP00000317790:V1060I	V	-	1	0	SPTBN5	39958754	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-1.257000	0.02866	-0.245000	0.09625	-0.752000	0.03492	GTA	C|0.800;T|0.200	0.200	strong		0.617	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
HECTD1	25831	hgsc.bcm.edu	37	14	31578762	31578762	+	Silent	SNP	C	C	T	rs17097735	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:31578762C>T	ENST00000399332.1	-	36	6809	c.6321G>A	c.(6319-6321)gaG>gaA	p.E2107E	HECTD1_ENST00000553700.1_Silent_p.E2107E	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	2107					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)			breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTCTCGTTCGCTCCACAGTGG	0.458													T|||	1463	0.292133	0.5038	0.1585	5008	,	,		17990	0.2897		0.1064	False		,,,				2504	0.2945				p.E2107E		Atlas-SNP	.											.	HECTD1	159	.	0			c.G6321A						PASS	.	T		1657,2387		359,939,724	90.0	90.0	90.0		6321	3.2	1.0	14	dbSNP_123	90	1068,7304		59,950,3177	no	coding-synonymous	HECTD1	NM_015382.2		418,1889,3901	TT,TC,CC		12.7568,40.9743,21.9475		2107/2611	31578762	2725,9691	2022	4186	6208	SO:0001819	synonymous_variant	25831	exon36			CGTTCGCTCCACA	AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.6321G>A	14.37:g.31578762C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1	535	0.24496336996336995	235	0.47764227642276424	59	0.16298342541436464	167	0.291958041958042	74	0.09762532981530343	T	9.054	0.992889	0.18966	0.409743	0.127568	ENSG00000092148	ENST00000554882	.	.	.	5.56	3.24	0.37175	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.48269	-0.9050	3	.	.	.	-14.6745	8.8967	0.35470	0.0:0.3664:0.0:0.6335	rs17097735;rs17097735	.	.	.	N	473	.	.	S	-	2	0	HECTD1	30648513	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	1.082000	0.30803	0.103000	0.17682	-0.550000	0.04213	AGC	C|0.750;T|0.250	0.250	strong		0.458	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
KHK	3795	hgsc.bcm.edu	37	2	27315252	27315252	+	Missense_Mutation	SNP	G	G	A	rs2304681	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27315252G>A	ENST00000260599.6	+	2	658	c.145G>A	c.(145-147)Gtt>Att	p.V49I	KHK_ENST00000490823.1_3'UTR|KHK_ENST00000260598.5_Missense_Mutation_p.V49I	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	49			V -> I (in dbSNP:rs2304681). {ECO:0000269|PubMed:7833921}.		carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCTGCACCGTTCTCTCCCT	0.632													G|||	1660	0.33147	0.3033	0.5043	5008	,	,		19742	0.2312		0.3767	False		,,,				2504	0.3037				p.V49I		Atlas-SNP	.											KHK_ENST00000260598,colon,carcinoma,0,2	KHK	60	2	0			c.G145A						PASS	.	G	ILE/VAL,ILE/VAL	1399,3007	459.0+/-352.1	230,939,1034	76.0	63.0	67.0		145,145	2.7	0.0	2	dbSNP_100	67	3231,5369	486.6+/-371.9	622,1987,1691	yes	missense,missense	KHK	NM_000221.2,NM_006488.2	29,29	852,2926,2725	AA,AG,GG		37.5698,31.7522,35.599	benign,benign	49/299,49/299	27315252	4630,8376	2203	4300	6503	SO:0001583	missense	3795	exon2			TGCACCGTTCTCT		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.145G>A	2.37:g.27315252G>A	ENSP00000260599:p.Val49Ile	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_006488	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	37	CCDS1734.1	745	0.3411172161172161	156	0.3170731707317073	172	0.47513812154696133	150	0.26223776223776224	267	0.35224274406332456	G	19.83	3.900193	0.72754	0.317522	0.375698	ENSG00000138030	ENST00000260599;ENST00000260598;ENST00000429697	T;T;T	0.77877	-1.13;-1.13;-1.13	5.5	2.71	0.32032	Carbohydrate/purine kinase (1);	0.183501	0.47852	N	0.000205	T	0.00012	0.0000	M	0.69185	2.1	0.24585	P	0.99385471	B;P;B	0.35821	0.045;0.523;0.045	B;B;B	0.32393	0.012;0.145;0.012	T	0.43734	-0.9373	9	0.18710	T	0.47	-18.5598	7.773	0.29019	0.336:0.0:0.664:0.0	rs2304681;rs13006404;rs17845083;rs17847238;rs17857867;rs57123139;rs2304681	49;49;49	Q6IBK2;P50053-2;P50053	.;.;KHK_HUMAN	I	49	ENSP00000260599:V49I;ENSP00000260598:V49I;ENSP00000404741:V49I	ENSP00000260598:V49I	V	+	1	0	KHK	27168756	1.000000	0.71417	0.013000	0.15412	0.966000	0.64601	4.090000	0.57693	0.701000	0.31803	0.462000	0.41574	GTT	G|0.649;A|0.351	0.351	strong		0.632	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1		
THUMPD1	55623	hgsc.bcm.edu	37	16	20748331	20748331	+	Missense_Mutation	SNP	C	C	A	rs11074471	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20748331C>A	ENST00000381337.2	-	4	1277	c.933G>T	c.(931-933)gaG>gaT	p.E311D	THUMPD1_ENST00000431224.2_Missense_Mutation_p.E397D|THUMPD1_ENST00000396083.2_Missense_Mutation_p.E311D	NM_017736.3	NP_060206.2	Q9NXG2	THUM1_HUMAN	THUMP domain containing 1	311			E -> D (in dbSNP:rs11074471).				poly(A) RNA binding (GO:0044822)			NS(2)|large_intestine(2)|lung(6)|pancreas(1)|urinary_tract(1)	12						CCTCAGTATTCTCTGGTACCT	0.463													C|||	734	0.146565	0.0961	0.0865	5008	,	,		18190	0.2212		0.1262	False		,,,				2504	0.2014				p.E311D		Atlas-SNP	.											.	THUMPD1	33	.	0			c.G933T						PASS	.	C	ASP/GLU	418,3984	204.1+/-226.4	31,356,1814	179.0	166.0	171.0		933	2.8	0.0	16	dbSNP_120	171	1234,7366	249.2+/-276.5	86,1062,3152	yes	missense	THUMPD1	NM_017736.3	45	117,1418,4966	AA,AC,CC		14.3488,9.4957,12.7057	benign	311/354	20748331	1652,11350	2201	4300	6501	SO:0001583	missense	55623	exon4			AGTATTCTCTGGT	BC000448	CCDS10588.1	16p13.11	2010-06-17			ENSG00000066654	ENSG00000066654			23807	protein-coding gene	gene with protein product							Standard	XM_005255422		Approved	FLJ20274	uc002dho.3	Q9NXG2	OTTHUMG00000131558	ENST00000381337.2:c.933G>T	16.37:g.20748331C>A	ENSP00000370741:p.Glu311Asp	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	228	129	0.565789	NM_017736	Q9BWC3	Missense_Mutation	SNP	ENST00000381337.2	37	CCDS10588.1	274	0.12545787545787546	36	0.07317073170731707	32	0.08839779005524862	102	0.17832167832167833	104	0.13720316622691292	C	7.688	0.690456	0.15039	0.094957	0.143488	ENSG00000066654	ENST00000381337;ENST00000431224;ENST00000396083	T;T;T	0.50001	0.84;0.76;0.84	5.92	2.77	0.32553	.	0.423294	0.26692	N	0.022994	T	0.00073	0.0002	L	0.54323	1.7	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09997	-1.0649	9	0.16420	T	0.52	.	5.0688	0.14596	0.0:0.5405:0.1705:0.289	rs11074471;rs61089332;rs11074471	311	Q9NXG2	THUM1_HUMAN	D	311;397;311	ENSP00000370741:E311D;ENSP00000392282:E397D;ENSP00000379392:E311D	ENSP00000370741:E311D	E	-	3	2	THUMPD1	20655832	0.000000	0.05858	0.004000	0.12327	0.026000	0.11368	-0.042000	0.12063	0.769000	0.33313	0.561000	0.74099	GAG	C|0.868;A|0.132	0.132	strong		0.463	THUMPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254420.1	NM_017736	
PSAPL1	768239	hgsc.bcm.edu	37	4	7436486	7436486	+	Missense_Mutation	SNP	C	C	A	rs11548325	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:7436486C>A	ENST00000319098.4	-	1	214	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	41	Saposin A-type 1. {ECO:0000255|PROSITE- ProRule:PRU00414}.		A -> S (in dbSNP:rs11548325).		sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						CCGCACCTGGCAGCTGTCTGC	0.677													C|||	1002	0.20008	0.1543	0.2795	5008	,	,		17157	0.2946		0.1252	False		,,,				2504	0.1851				p.A41S		Atlas-SNP	.											.	PSAPL1	51	.	0			c.G121T						PASS	.	C	SER/ALA,	573,3421		36,501,1460	21.0	25.0	24.0		121,	1.6	0.0	4	dbSNP_120	24	908,7426		45,818,3304	yes	missense,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	99,	81,1319,4764	AA,AC,CC		10.8951,14.3465,12.0133	benign,	41/522,	7436486	1481,10847	1997	4167	6164	SO:0001583	missense	768239	exon1			ACCTGGCAGCTGT	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.121G>T	4.37:g.7436486C>A	ENSP00000317445:p.Ala41Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_001085382	A0A184|Q8N7T4	Missense_Mutation	SNP	ENST00000319098.4	37	CCDS47009.1	401	0.18360805860805862	65	0.13211382113821138	88	0.2430939226519337	150	0.26223776223776224	98	0.12928759894459102	C	0.005	-2.189265	0.00302	0.143465	0.108951	ENSG00000178597	ENST00000319098	T	0.54866	0.55	2.67	1.63	0.23807	Saposin type A (3);	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.34181	0.44	B	0.32090	0.14	T	0.17501	-1.0367	8	0.09084	T	0.74	.	4.6842	0.12750	0.0:0.7638:0.0:0.2362	rs11548325	41	Q6NUJ1	SAPL1_HUMAN	S	41	ENSP00000317445:A41S	ENSP00000317445:A41S	A	-	1	0	PSAPL1	7487387	0.003000	0.15002	0.001000	0.08648	0.035000	0.12851	0.676000	0.25247	0.487000	0.27698	0.561000	0.74099	GCC	C|0.820;A|0.180	0.180	strong		0.677	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
HRNR	388697	hgsc.bcm.edu	37	1	152187588	152187588	+	Missense_Mutation	SNP	C	C	T	rs201071455	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152187588C>T	ENST00000368801.2	-	3	6592	c.6517G>A	c.(6517-6519)Ggc>Agc	p.G2173S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2173					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTTGTCGGCCGTGGCCCGAA	0.632																																					p.G2173S		Atlas-SNP	.											HRNR,NS,carcinoma,0,2	HRNR	403	2	0			c.G6517A						scavenged	.						105.0	129.0	121.0					1																	152187588		1574	3256	4830	SO:0001583	missense	388697	exon3			GTCGGCCGTGGCC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.6517G>A	1.37:g.152187588C>T	ENSP00000357791:p.Gly2173Ser	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	263	25	0.095057	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	9.554	1.116776	0.20795	.	.	ENSG00000197915	ENST00000368801	T	0.01527	4.8	3.22	-0.994	0.10225	.	.	.	.	.	T	0.00328	0.0010	N	0.16743	0.435	0.80722	P	0.0	B	0.27264	0.173	B	0.11329	0.006	T	0.35076	-0.9803	8	0.06494	T	0.89	.	7.4135	0.27032	0.0:0.5254:0.0:0.4746	.	2173	Q86YZ3	HORN_HUMAN	S	2173	ENSP00000357791:G2173S	ENSP00000357791:G2173S	G	-	1	0	HRNR	150454212	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.789000	0.00768	-0.075000	0.12798	-0.131000	0.14894	GGC	C|0.806;T|0.194	0.194	strong		0.632	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
C6orf15	29113	hgsc.bcm.edu	37	6	31080016	31080016	+	Missense_Mutation	SNP	C	C	G	rs2233974	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31080016C>G	ENST00000259870.3	-	2	123	c.120G>C	c.(118-120)ttG>ttC	p.L40F	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	40			L -> F (in dbSNP:rs2233974). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404}.		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						AGTTGGTCCCCAAGTTTTGGG	0.557													C|||	527	0.105232	0.1218	0.1066	5008	,	,		19205	0.0466		0.1461	False		,,,				2504	0.1002				p.L40F		Atlas-SNP	.											.	C6orf15	29	.	0			c.G120C						PASS	.	C	PHE/LEU	569,3753		41,487,1633	127.0	149.0	142.0		120	2.7	0.0	6	dbSNP_98	142	1529,6989		138,1253,2868	yes	missense	C6orf15	NM_014070.2	22	179,1740,4501	GG,GC,CC		17.9502,13.1652,16.3396	possibly-damaging	40/326	31080016	2098,10742	2161	4259	6420	SO:0001583	missense	29113	exon2			GGTCCCCAAGTTT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.120G>C	6.37:g.31080016C>G	ENSP00000259870:p.Leu40Phe	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	76	0.826087	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	246	0.11263736263736264	71	0.1443089430894309	45	0.12430939226519337	19	0.033216783216783216	111	0.14643799472295516	C	13.84	2.357554	0.41801	0.131652	0.179502	ENSG00000204542	ENST00000259870	T	0.07114	3.22	4.44	2.65	0.31530	.	1.477720	0.05072	N	0.481790	T	0.08626	0.0214	L	0.51422	1.61	0.80722	P	0.0	D	0.61697	0.99	P	0.59487	0.858	T	0.14671	-1.0464	9	0.44086	T	0.13	.	6.7339	0.23399	0.0:0.7832:0.0:0.2168	rs2233974;rs52811515;rs2233974	40	Q6UXA7	CF015_HUMAN	F	40	ENSP00000259870:L40F	ENSP00000259870:L40F	L	-	3	2	C6orf15	31187995	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.062000	0.11674	0.492000	0.27815	-0.275000	0.10095	TTG	C|0.832;G|0.168	0.168	strong		0.557	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
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 GAIIx	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_ENST00000418019.1_Silent_p.L433L|USP37_ENST00000415516.1_Silent_p.L361L	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		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	59	21	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	
RAMP1	10267	hgsc.bcm.edu	37	2	238820380	238820380	+	Silent	SNP	G	G	A	rs61752232	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238820380G>A	ENST00000254661.4	+	3	534	c.402G>A	c.(400-402)acG>acA	p.T134T	RAMP1_ENST00000403885.1_Silent_p.T112T|RAMP1_ENST00000409726.1_Silent_p.T112T|RAMP1_ENST00000404910.2_Silent_p.T112T	NM_005855.2	NP_005846.1	O60894	RAMP1_HUMAN	receptor (G protein-coupled) activity modifying protein 1	134					angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|intracellular protein transport (GO:0006886)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein glycosylation (GO:0060050)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcitonin receptor activity (GO:0004948)|calcitonin receptor binding (GO:0031716)|coreceptor activity (GO:0015026)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			kidney(1)|large_intestine(1)|lung(2)	4		Breast(86;0.000596)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;9.56e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.49e-11)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.49e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00013)|Lung(119;0.0119)|LUSC - Lung squamous cell carcinoma(224;0.0288)	Pramlintide(DB01278)	TGCTGGTGACGGCACTGGTGG	0.697													G|||	12	0.00239617	0.0015	0.0029	5008	,	,		17250	0.0		0.008	False		,,,				2504	0.0				p.T134T	NSCLC(177;211 2889 43936 50767)	Atlas-SNP	.											.	RAMP1	10	.	0			c.G402A						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	31.0	25.0	27.0		402	-7.4	0.0	2	dbSNP_129	27	123,8475	61.3+/-123.2	1,121,4177	no	coding-synonymous	RAMP1	NM_005855.2		1,130,6371	AA,AG,GG		1.4306,0.2043,1.0151		134/149	238820380	132,12872	2203	4299	6502	SO:0001819	synonymous_variant	10267	exon3			GGTGACGGCACTG	AJ001014	CCDS2522.1	2q36-q37.1	2008-02-05	2006-11-21		ENSG00000132329	ENSG00000132329		"""Receptor (G protein-coupled) activity modifying proteins"""	9843	protein-coding gene	gene with protein product		605153	"""receptor activity modifying protein 1"", ""receptor (calcitonin) activity modifying protein 1"""				Standard	NM_005855		Approved		uc002vxj.3	O60894	OTTHUMG00000133337	ENST00000254661.4:c.402G>A	2.37:g.238820380G>A		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	223	98	0.439462	NM_005855	Q6FGS5	Silent	SNP	ENST00000254661.4	37	CCDS2522.1																																																																																			G|0.994;A|0.006	0.006	strong		0.697	RAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257166.2	NM_005855	
SARDH	1757	hgsc.bcm.edu	37	9	136599146	136599146	+	Silent	SNP	C	C	T	rs573904	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136599146C>T	ENST00000371872.4	-	2	407	c.150G>A	c.(148-150)caG>caA	p.Q50Q	SARDH_ENST00000422262.2_Intron|SARDH_ENST00000298628.5_Silent_p.Q50Q|SARDH_ENST00000439388.1_Silent_p.Q50Q|SARDH_ENST00000371867.1_5'UTR	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	50					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CCGAGGTGCCCTGTCCCTCCT	0.677													T|||	1100	0.219649	0.084	0.2406	5008	,	,		17712	0.3056		0.2952	False		,,,				2504	0.2219				p.Q50Q		Atlas-SNP	.											.	SARDH	112	.	0			c.G150A						PASS	.	T	,	584,3816		38,508,1654	30.0	28.0	29.0		150,150	1.6	0.0	9	dbSNP_83	29	2497,6097		383,1731,2183	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	421,2239,3837	TT,TC,CC		29.0552,13.2727,23.7109	,	50/919,50/919	136599146	3081,9913	2200	4297	6497	SO:0001819	synonymous_variant	1757	exon2			GGTGCCCTGTCCC		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.150G>A	9.37:g.136599146C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			C|0.776;T|0.224	0.224	strong		0.677	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
RFC1	5981	hgsc.bcm.edu	37	4	39302029	39302029	+	Silent	SNP	T	T	C	rs2066786	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:39302029T>C	ENST00000381897.1	-	20	2677	c.2544A>G	c.(2542-2544)ccA>ccG	p.P848P	RFC1_ENST00000349703.2_Silent_p.P847P|RNU6-32P_ENST00000383948.1_RNA	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	848					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						CAACATCAAATGGGCCCTGAA	0.428													T|||	2330	0.465256	0.0552	0.6066	5008	,	,		20360	0.63		0.5477	False		,,,				2504	0.6646				p.P848P	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.A2544G						PASS	.	T	,	664,3742	276.6+/-273.2	59,546,1598	53.0	54.0	54.0		2544,2541	-5.6	0.9	4	dbSNP_94	54	4860,3740	616.4+/-396.5	1371,2118,811	no	coding-synonymous,coding-synonymous	RFC1	NM_001204747.1,NM_002913.4	,	1430,2664,2409	CC,CT,TT		43.4884,15.0704,42.4727	,	848/1149,847/1148	39302029	5524,7482	2203	4300	6503	SO:0001819	synonymous_variant	5981	exon20			ATCAAATGGGCCC	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.2544A>G	4.37:g.39302029T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_001204747	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	37	CCDS56329.1																																																																																			T|0.557;C|0.443	0.443	strong		0.428	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913	
ATP13A2	23400	hgsc.bcm.edu	37	1	17314702	17314702	+	Silent	SNP	C	C	T	rs3738815	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:17314702C>T	ENST00000326735.8	-	25	2823	c.2790G>A	c.(2788-2790)tcG>tcA	p.S930S	ATP13A2_ENST00000341676.5_Silent_p.S886S|ATP13A2_ENST00000452699.1_Silent_p.S925S|RP1-37C10.3_ENST00000446261.1_RNA			Q9NQ11	AT132_HUMAN	ATPase type 13A2	930					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGACGCTGAACGAAGTGTCAA	0.607													C|||	1457	0.290935	0.1369	0.3429	5008	,	,		21211	0.5774		0.2058	False		,,,				2504	0.2546				p.S930S		Atlas-SNP	.											ATP13A2,NS,carcinoma,-1,1	ATP13A2	85	1	0			c.G2790A						PASS	.	C	,,	659,3747	280.5+/-275.4	56,547,1600	142.0	127.0	132.0		2775,2658,2790	-11.0	0.0	1	dbSNP_107	132	1657,6943	305.7+/-307.6	145,1367,2788	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	201,1914,4388	TT,TC,CC		19.2674,14.9569,17.8072	,,	925/1176,886/1159,930/1181	17314702	2316,10690	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon25			GCTGAACGAAGTG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2790G>A	1.37:g.17314702C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	105	51	0.485714	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			C|0.770;T|0.230	0.230	strong		0.607	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
SLC1A6	6511	hgsc.bcm.edu	37	19	15083693	15083693	+	Silent	SNP	C	C	A	rs3746295	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15083693C>A	ENST00000221742.3	-	1	37	c.30G>T	c.(28-30)ctG>ctT	p.L10L	SLC1A6_ENST00000598504.1_Silent_p.L10L|SLC1A6_ENST00000430939.2_Missense_Mutation_p.A15S|SLC1A6_ENST00000544886.2_Silent_p.L10L|SLC1A6_ENST00000600144.1_Silent_p.L10L	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	10					aspartate transport (GO:0015810)|ion transport (GO:0006811)|L-glutamate transport (GO:0015813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|sodium:dicarboxylate symporter activity (GO:0017153)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(8)|liver(1)|lung(12)|ovary(3)|pancreas(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42						CGCTCTCCCGCAGGAACAGGC	0.682													C|||	2765	0.552117	0.5091	0.4697	5008	,	,		15275	0.6567		0.5199	False		,,,				2504	0.5941				p.L10L		Atlas-SNP	.											SLC1A6,NS,carcinoma,0,2	SLC1A6	111	2	0			c.G30T						PASS	.	C		2182,2006		634,914,546	6.0	7.0	7.0		30	4.4	1.0	19	dbSNP_107	7	4397,3857		1268,1861,998	no	coding-synonymous	SLC1A6	NM_005071.1		1902,2775,1544	AA,AC,CC		46.7289,47.8988,47.1226		10/565	15083693	6579,5863	2094	4127	6221	SO:0001819	synonymous_variant	6511	exon4			CTCCCGCAGGAAC		CCDS12321.1, CCDS62578.1	19p13.12	2013-07-15			ENSG00000105143	ENSG00000105143		"""Solute carriers"""	10944	protein-coding gene	gene with protein product		600637				7791878	Standard	NM_005071		Approved	EAAT4	uc002naa.2	P48664	OTTHUMG00000183351	ENST00000221742.3:c.30G>T	19.37:g.15083693C>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	49	15	0.306122	NM_001272087	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1	1207	0.5526556776556777	249	0.5060975609756098	186	0.5138121546961326	377	0.6590909090909091	395	0.521108179419525	C	13.75	2.329945	0.41297	0.521012	0.532711	ENSG00000105143	ENST00000430939	T	0.74002	-0.8	4.41	4.41	0.53225	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	B	0.16603	0.018	B	0.14578	0.011	T	0.48387	-0.9040	7	0.87932	D	0	-12.2133	12.3616	0.55207	0.0:1.0:0.0:0.0	rs3746295;rs57060104;rs3746295	15	E7EV13	.	S	15	ENSP00000409386:A15S	ENSP00000409386:A15S	A	-	1	0	SLC1A6	14944693	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.323000	0.33701	2.278000	0.76064	0.313000	0.20887	GCG	C|0.450;A|0.550	0.550	strong		0.682	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071	
TCTE3	6991	hgsc.bcm.edu	37	6	170144228	170144228	+	Missense_Mutation	SNP	C	C	A	rs2027063	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:170144228C>A	ENST00000366774.3	-	2	363	c.263G>T	c.(262-264)aGa>aTa	p.R88I		NM_174910.1	NP_777570.1	Q8IZS6	TC1D3_HUMAN	t-complex-associated-testis-expressed 3	88			R -> I (in dbSNP:rs2027063). {ECO:0000269|PubMed:12584439}.		transport (GO:0006810)	cytoplasm (GO:0005737)|dynein complex (GO:0030286)|membrane (GO:0016020)|microtubule (GO:0005874)	motor activity (GO:0003774)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|prostate(1)	4		Breast(66;0.000338)		OV - Ovarian serous cystadenocarcinoma(33;1.08e-21)|BRCA - Breast invasive adenocarcinoma(81;1.32e-07)|GBM - Glioblastoma multiforme(31;0.00157)		TGGCTCCATTCTATATGAATT	0.348													C|||	798	0.159345	0.3797	0.0663	5008	,	,		16740	0.0466		0.0229	False		,,,				2504	0.184				p.R88I		Atlas-SNP	.											.	TCTE3	13	.	0			c.G263T						PASS	.	C	ILE/ARG	1358,3046	447.7+/-348.4	221,916,1065	65.0	70.0	68.0		263	4.7	1.0	6	dbSNP_94	68	286,8312	105.6+/-166.5	6,274,4019	yes	missense	TCTE3	NM_174910.1	97	227,1190,5084	AA,AC,CC		3.3264,30.8356,12.6442	probably-damaging	88/199	170144228	1644,11358	2202	4299	6501	SO:0001583	missense	6991	exon2			TCCATTCTATATG	AF519569	CCDS5310.1	6q27	2014-06-03			ENSG00000184786	ENSG00000184786			11695	protein-coding gene	gene with protein product	"""Tctex1 domain containing 3"""	186977				1505969, 12584439	Standard	NM_174910		Approved	TCTEX1D3	uc003qxe.1	Q8IZS6	OTTHUMG00000016068	ENST00000366774.3:c.263G>T	6.37:g.170144228C>A	ENSP00000355736:p.Arg88Ile	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_174910		Missense_Mutation	SNP	ENST00000366774.3	37	CCDS5310.1	297	0.13598901098901098	212	0.43089430894308944	29	0.08011049723756906	38	0.06643356643356643	18	0.023746701846965697	C	18.66	3.671432	0.67814	0.308356	0.033264	ENSG00000184786	ENST00000366774	T	0.17213	2.29	5.53	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.20333	0.0489	L	0.36672	1.1	0.09310	P	0.99999808204	D	0.89917	1.0	D	0.75484	0.986	T	0.00923	-1.1513	9	0.56958	D	0.05	-0.0865	12.0566	0.53538	0.0:0.9163:0.0:0.0837	rs2027063;rs52823898;rs58724481;rs2027063	88	Q8IZS6	TC1D3_HUMAN	I	88	ENSP00000355736:R88I	ENSP00000355736:R88I	R	-	2	0	TCTE3	169886153	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.734000	0.38166	2.610000	0.88304	0.491000	0.48974	AGA	C|0.862;A|0.138	0.138	strong		0.348	TCTE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043243.1	NM_174910	
DNAH3	55567	hgsc.bcm.edu	37	16	20966362	20966362	+	Missense_Mutation	SNP	T	T	C	rs34051490	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:20966362T>C	ENST00000261383.3	-	55	10843	c.10844A>G	c.(10843-10845)tAt>tGt	p.Y3615C	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3615	AAA 6. {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)|microtubule motor activity (GO:0003777)	p.Y3615F(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTCTGATGGATAGCTGGTTAG	0.438													T|||	440	0.0878594	0.0204	0.0706	5008	,	,		16990	0.1716		0.0746	False		,,,				2504	0.1186				p.Y3615C		Atlas-SNP	.											.	DNAH3	1142	.	2	Substitution - Missense(2)	kidney(2)	c.A10844G						PASS	.	T	CYS/TYR	122,4280	90.2+/-128.9	3,116,2082	96.0	93.0	94.0		10844	5.4	1.0	16	dbSNP_126	94	715,7885	175.9+/-225.9	28,659,3613	yes	missense	DNAH3	NM_017539.1	194	31,775,5695	CC,CT,TT		8.314,2.7715,6.4375	probably-damaging	3615/4117	20966362	837,12165	2201	4300	6501	SO:0001583	missense	55567	exon55			GATGGATAGCTGG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.10844A>G	16.37:g.20966362T>C	ENSP00000261383:p.Tyr3615Cys	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	75	43	0.573333	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	183	0.08379120879120878	16	0.032520325203252036	19	0.052486187845303865	83	0.1451048951048951	65	0.08575197889182058	T	17.67	3.447041	0.63178	0.027715	0.08314	ENSG00000158486	ENST00000261383	T	0.08807	3.05	5.43	5.43	0.79202	Dynein heavy chain (1);	0.151822	0.44688	D	0.000424	T	0.00210	0.0006	M	0.90814	3.15	0.09310	P	0.9999999999999944	D	0.89917	1.0	D	0.77557	0.99	T	0.04495	-1.0947	9	0.54805	T	0.06	.	11.4825	0.50333	0.0:0.0:0.1501:0.8499	rs34051490;rs58030299	3615	Q8TD57	DYH3_HUMAN	C	3615	ENSP00000261383:Y3615C	ENSP00000261383:Y3615C	Y	-	2	0	DNAH3	20873863	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.910000	0.69931	2.058000	0.61347	0.533000	0.62120	TAT	T|0.927;C|0.073	0.073	strong		0.438	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
B4GALNT4	338707	hgsc.bcm.edu	37	11	372700	372700	+	Silent	SNP	G	G	C	rs35475866	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:372700G>C	ENST00000329962.6	+	3	294	c.294G>C	c.(292-294)ggG>ggC	p.G98G		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	98					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)		TTCCTGGGGGGGCTGGGAGGC	0.647													.|||	1656	0.330671	0.3253	0.2997	5008	,	,		10061	0.3839		0.2952	False		,,,				2504	0.3415				p.G98G		Atlas-SNP	.											B4GALNT4,rectum,carcinoma,0,1	B4GALNT4	83	1	0			c.G294C						PASS	.	G		1430,2946		245,940,1003	18.0	21.0	20.0		294	-1.3	0.0	11	dbSNP_126	20	2375,6187		331,1713,2237	no	coding-synonymous	B4GALNT4	NM_178537.4		576,2653,3240	CC,CG,GG		27.7388,32.6782,29.4095		98/1040	372700	3805,9133	2188	4281	6469	SO:0001819	synonymous_variant	338707	exon3			TGGGGGGGCTGGG	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.294G>C	11.37:g.372700G>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	59	57	0.966102	NM_178537	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																			G|0.714;C|0.286	0.286	strong		0.647	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
KRTAP3-1	83896	hgsc.bcm.edu	37	17	39165174	39165174	+	Silent	SNP	G	G	A	rs112432710	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39165174G>A	ENST00000391588.1	-	1	192	c.153C>T	c.(151-153)tgC>tgT	p.C51C	KRTAP3-1_ENST00000581033.1_5'UTR	NM_031958.1	NP_114164.1	Q9BYR8	KRA31_HUMAN	keratin associated protein 3-1	51	4 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	8		Breast(137;0.00043)				AGGGTGGGGGGCAGGTGTCAC	0.577													g|||	386	0.0770767	0.0386	0.0778	5008	,	,		18684	0.0288		0.1143	False		,,,				2504	0.1401				p.C51C		Atlas-SNP	.											.	KRTAP3-1	11	.	0			c.C153T						PASS	.	G		224,4182	135.7+/-171.8	6,212,1985	78.0	68.0	71.0		153	3.4	1.0	17	dbSNP_132	71	785,7807	185.6+/-233.3	40,705,3551	no	coding-synonymous	KRTAP3-1	NM_031958.1		46,917,5536	AA,AG,GG		9.1364,5.084,7.7627		51/99	39165174	1009,11989	2203	4296	6499	SO:0001819	synonymous_variant	83896	exon1			TGGGGGGCAGGTG	AJ406931	CCDS32645.1	17q21.2	2013-06-25			ENSG00000212901	ENSG00000212901		"""Keratin associated proteins"""	16778	protein-coding gene	gene with protein product						11279113	Standard	NM_031958		Approved	KAP3.1	uc002hvt.1	Q9BYR8	OTTHUMG00000133595	ENST00000391588.1:c.153C>T	17.37:g.39165174G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	161	75	0.465839	NM_031958	Q14DM4	Silent	SNP	ENST00000391588.1	37	CCDS32645.1																																																																																			G|0.925;A|0.075	0.075	strong		0.577	KRTAP3-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257699.1		
ZNF335	63925	hgsc.bcm.edu	37	20	44590732	44590732	+	Silent	SNP	G	G	A	rs16990964	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44590732G>A	ENST00000322927.2	-	10	1723	c.1623C>T	c.(1621-1623)caC>caT	p.H541H	ZNF335_ENST00000426788.1_Silent_p.H386H	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	541					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				GCACAGCGGCGTGCCGAATGA	0.632													G|||	244	0.048722	0.0825	0.013	5008	,	,		16329	0.0952		0.0129	False		,,,				2504	0.0174				p.H541H		Atlas-SNP	.											.	ZNF335	115	.	0			c.C1623T						PASS	.	G		373,4033	190.5+/-216.4	17,339,1847	152.0	120.0	131.0		1623	-4.5	0.4	20	dbSNP_123	131	91,8509	51.9+/-112.3	1,89,4210	no	coding-synonymous	ZNF335	NM_022095.3		18,428,6057	AA,AG,GG		1.0581,8.4657,3.5676		541/1343	44590732	464,12542	2203	4300	6503	SO:0001819	synonymous_variant	63925	exon10			AGCGGCGTGCCGA	AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1623C>T	20.37:g.44590732G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	35	0.406977	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																			G|0.963;A|0.037	0.037	strong		0.632	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
TSEN15	116461	hgsc.bcm.edu	37	1	184023529	184023529	+	Missense_Mutation	SNP	A	A	C	rs1046934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:184023529A>C	ENST00000361641.1	+	2	256	c.177A>C	c.(175-177)caA>caC	p.Q59H	TSEN15_ENST00000533373.1_Missense_Mutation_p.Q59H|TSEN15_ENST00000423085.2_Missense_Mutation_p.Q59H	NM_052965.2	NP_443197.1	Q8WW01	SEN15_HUMAN	TSEN15 tRNA splicing endonuclease subunit	59			Q -> H (in dbSNP:rs1046934).		mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)	tRNA-intron endonuclease activity (GO:0000213)			breast(1)|kidney(3)|large_intestine(2)|lung(2)	8						ATGCCACCCAAGTTTATGTAG	0.323													A|||	1517	0.302915	0.1233	0.3026	5008	,	,		16302	0.4504		0.327	False		,,,				2504	0.3691				p.Q59H		Atlas-SNP	.											.	TSEN15	19	.	0			c.A177C						PASS	.	A	HIS/GLN,HIS/GLN	717,3689	297.0+/-284.5	55,607,1541	177.0	173.0	174.0		177,177	1.6	1.0	1	dbSNP_86	174	2989,5611	462.2+/-365.6	491,2007,1802	yes	missense,missense	TSEN15	NM_001127394.2,NM_052965.2	24,24	546,2614,3343	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	34.7558,16.2733,28.4945	probably-damaging,probably-damaging	59/130,59/172	184023529	3706,9300	2203	4300	6503	SO:0001583	missense	116461	exon2			CACCCAAGTTTAT	AF288394	CCDS1361.1, CCDS44286.1, CCDS72993.1	1q25	2013-08-06	2013-08-06	2008-06-12	ENSG00000198860	ENSG00000198860		"""tRNA splicing endonuclease subunits"""	16791	protein-coding gene	gene with protein product		608756	"""chromosome 1 open reading frame 19"", ""tRNA splicing endonuclease 15 homolog (S. cerevisiae)"""	C1orf19		11318611, 17166513	Standard	XM_006711148		Approved		uc001gqt.4	Q8WW01	OTTHUMG00000035461	ENST00000361641.1:c.177A>C	1.37:g.184023529A>C	ENSP00000355299:p.Gln59His	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	77	45	0.584416	NM_001127394	B4DKP0|Q9BZQ5	Missense_Mutation	SNP	ENST00000361641.1	37	CCDS1361.1	703	0.3218864468864469	76	0.15447154471544716	112	0.30939226519337015	263	0.4597902097902098	252	0.3324538258575198	A	17.48	3.399957	0.62177	0.162733	0.347558	ENSG00000198860	ENST00000361641;ENST00000533373;ENST00000423085	T;T;T	0.49139	0.79;0.79;0.79	5.27	1.56	0.23342	tRNA-intron endonuclease, Sen15 domain (1);	0.053462	0.85682	N	0.000000	T	0.00012	0.0000	M	0.61703	1.905	0.21719	P	0.999571061	B;B	0.13145	0.007;0.002	B;B	0.18263	0.021;0.009	T	0.36016	-0.9765	9	0.72032	D	0.01	-14.3213	5.5494	0.17081	0.5737:0.3382:0.0881:0.0	rs1046934;rs3186920;rs3736959;rs17415534;rs52791391;rs58806237;rs1046934	59;59	B4DKP0;Q8WW01	.;SEN15_HUMAN	H	59	ENSP00000355299:Q59H;ENSP00000436996:Q59H;ENSP00000402002:Q59H	ENSP00000355299:Q59H	Q	+	3	2	TSEN15	182290152	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	1.476000	0.35420	0.094000	0.17404	0.528000	0.53228	CAA	A|0.705;C|0.295	0.295	strong		0.323	TSEN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086132.1		
TARBP1	6894	hgsc.bcm.edu	37	1	234564951	234564951	+	Missense_Mutation	SNP	A	A	T	rs12135427	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:234564951A>T	ENST00000040877.1	-	17	2990	c.2991T>A	c.(2989-2991)ttT>ttA	p.F997L		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	997			F -> L (in dbSNP:rs12135427).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			TATCAAAAACAAACTGAACAA	0.338													A|||	29	0.00579073	0.0	0.0043	5008	,	,		18345	0.0		0.0239	False		,,,				2504	0.002				p.F997L		Atlas-SNP	.											.	TARBP1	111	.	0			c.T2991A						PASS	.	A	LEU/PHE	12,4394	17.9+/-39.9	0,12,2191	68.0	71.0	70.0		2991	1.9	1.0	1	dbSNP_120	70	146,8454	71.0+/-133.6	1,144,4155	yes	missense	TARBP1	NM_005646.3	22	1,156,6346	TT,TA,AA		1.6977,0.2724,1.2148	benign	997/1622	234564951	158,12848	2203	4300	6503	SO:0001583	missense	6894	exon17			AAAAACAAACTGA		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"""tRNA methyltransferase 3 homolog (S. cerevisiae)"""	605052	"""Tar (HIV-1) RNA binding protein 1"""			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.2991T>A	1.37:g.234564951A>T	ENSP00000040877:p.Phe997Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_005646	Q9H581	Missense_Mutation	SNP	ENST00000040877.1	37	CCDS1601.1	22	0.010073260073260074	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	20	0.026385224274406333	A	11.08	1.534172	0.27475	0.002724	0.016977	ENSG00000059588	ENST00000040877	T	0.27402	1.67	5.58	1.93	0.25924	Armadillo-type fold (1);	0.146623	0.64402	N	0.000006	T	0.08313	0.0207	L	0.56769	1.78	0.41431	D	0.987869	B	0.29188	0.236	B	0.24848	0.056	T	0.04915	-1.0918	10	0.20046	T	0.44	-24.6981	6.0265	0.19658	0.6531:0.128:0.2189:0.0	rs12135427;rs52805781;rs12135427	997	Q13395	TARB1_HUMAN	L	997	ENSP00000040877:F997L	ENSP00000040877:F997L	F	-	3	2	TARBP1	232631574	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	1.950000	0.40323	0.131000	0.18576	0.533000	0.62120	TTT	A|0.988;T|0.012	0.012	strong		0.338	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
OBP2A	29991	hgsc.bcm.edu	37	9	138440641	138440641	+	Missense_Mutation	SNP	T	T	C	rs2853652	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138440641T>C	ENST00000539850.1	+	5	502	c.476T>C	c.(475-477)aTg>aCg	p.M159T	OBP2A_ENST00000371776.1_Missense_Mutation_p.M159T|OBP2A_ENST00000340780.3_Missense_Mutation_p.C181R|OBP2A_ENST00000342114.4_Missense_Mutation_p.M136T			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A	159			M -> T (in dbSNP:rs2853652). {ECO:0000269|PubMed:10607840}.		response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		GACATTTTCATGCCCCTGCAG	0.557													.|||	4220	0.842652	0.8177	0.8631	5008	,	,		14501	0.9901		0.7445	False		,,,				2504	0.8108				p.M159T		Atlas-SNP	.											.	OBP2A	21	.	0			c.T476C						PASS	.	C	THR/MET	3594,812	323.2+/-298.0	1473,648,82	116.0	106.0	109.0		476	-4.8	0.0	9	dbSNP_100	109	6400,2198	375.4+/-337.8	2388,1624,287	no	missense	OBP2A	NM_014582.2	81	3861,2272,369	CC,CT,TT		25.5641,18.4294,23.1467	benign	159/171	138440641	9994,3010	2203	4299	6502	SO:0001583	missense	29991	exon5			TTTTCATGCCCCT	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.476T>C	9.37:g.138440641T>C	ENSP00000441028:p.Met159Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_014582	Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	CCDS6992.1	1843|1843	0.8438644688644689|0.8438644688644689	418|418	0.8495934959349594|0.8495934959349594	308|308	0.850828729281768|0.850828729281768	564|564	0.986013986013986|0.986013986013986	553|553	0.7295514511873351|0.7295514511873351	c|c	0.005|0.005	-2.191828|-2.191828	0.00302|0.00302	0.815706|0.815706	0.744359|0.744359	ENSG00000122136|ENSG00000122136	ENST00000340780|ENST00000342114;ENST00000371776;ENST00000539850	T|T;T;T	0.32753|0.08634	1.44|3.07;3.24;3.24	2.39|2.39	-4.77|-4.77	0.03219|0.03219	.|Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.784800|.	0.03775|.	N|.	0.260443|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04636|0.04636	-0.2|-0.2	0.80722|0.80722	P|P	0.0|0.0	B|B;B	0.02656|0.02656	0.0|0.0;0.0	B|B;B	0.01281|0.01281	0.0|0.0;0.0	T|T	0.11518|0.11518	-1.0584|-1.0584	9|8	0.02654|0.13853	T|T	1|0.58	.|.	4.1979|4.1979	0.10452|0.10452	0.166:0.4005:0.0:0.4335|0.166:0.4005:0.0:0.4335	rs2853652;rs3178141;rs57299334|rs2853652;rs3178141;rs57299334	181|136;159	Q5T8A5|Q5T8A4;Q9NY56	.|.;OBP2A_HUMAN	R|T	181|136;159;159	ENSP00000342097:C181R|ENSP00000340950:M136T;ENSP00000360841:M159T;ENSP00000441028:M159T	ENSP00000342097:C181R|ENSP00000340950:M136T	C|M	+|+	1|2	0|0	OBP2A|OBP2A	137580462|137580462	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.869000|-1.869000	0.01643|0.01643	-1.501000|-1.501000	0.01817|0.01817	-1.774000|-1.774000	0.00658|0.00658	TGC|ATG	T|0.207;C|0.793	0.793	strong		0.557	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582	
TBC1D4	9882	hgsc.bcm.edu	37	13	76055820	76055820	+	Silent	SNP	G	G	C	rs7327548	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:76055820G>C	ENST00000377636.3	-	1	430	c.84C>G	c.(82-84)ccC>ccG	p.P28P	TBC1D4_ENST00000377625.2_Silent_p.P28P|TBC1D4_ENST00000431480.2_Silent_p.P28P|TBC1D4_ENST00000425511.1_5'UTR	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	28					cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		TTGGCTTCCCGGGGCCGGGCT	0.677													G|||	1784	0.35623	0.5492	0.3573	5008	,	,		11294	0.2153		0.3976	False		,,,				2504	0.1973				p.P28P		Atlas-SNP	.											.	TBC1D4	142	.	0			c.C84G						PASS	.	G		1931,1805		532,867,469	10.0	13.0	12.0		84	-2.1	0.0	13	dbSNP_116	12	3195,4929		685,1825,1552	no	coding-synonymous	TBC1D4	NM_014832.2		1217,2692,2021	CC,CG,GG		39.3279,48.3137,43.2209		28/1299	76055820	5126,6734	1868	4062	5930	SO:0001819	synonymous_variant	9882	exon1			CTTCCCGGGGCCG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.84C>G	13.37:g.76055820G>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	80	50	0.625	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	37	CCDS41901.1																																																																																			G|0.616;C|0.384	0.384	strong		0.677	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
DPF3	8110	hgsc.bcm.edu	37	14	73220020	73220020	+	Silent	SNP	A	A	G	rs3742836	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:73220020A>G	ENST00000556509.1	-	3	252	c.253T>C	c.(253-255)Ttg>Ctg	p.L85L	DPF3_ENST00000541685.1_Silent_p.L85L|DPF3_ENST00000546183.1_Silent_p.L95L	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	85					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		GGTGGGTGCAATCGTCTCTTC	0.562													A|||	1118	0.223243	0.0764	0.2205	5008	,	,		19283	0.2907		0.2744	False		,,,				2504	0.3016				p.L85L		Atlas-SNP	.											.	DPF3	117	.	0			c.T253C						PASS	.	A		401,3395		29,343,1526	58.0	59.0	59.0		253	3.2	1.0	14	dbSNP_107	59	2312,5912		328,1656,2128	yes	coding-synonymous	DPF3	NM_012074.3		357,1999,3654	GG,GA,AA		28.1128,10.5638,22.5707		85/358	73220020	2713,9307	1898	4112	6010	SO:0001819	synonymous_variant	8110	exon3			GGTGCAATCGTCT	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"""Zinc fingers, PHD-type"""	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.253T>C	14.37:g.73220020A>G		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	39	23	0.589744	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Silent	SNP	ENST00000556509.1	37																																																																																				A|0.773;G|0.227	0.227	strong		0.562	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2		
LRRC52	440699	hgsc.bcm.edu	37	1	165533005	165533005	+	Silent	SNP	C	C	A	rs453717	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:165533005C>A	ENST00000294818.1	+	2	1176	c.886C>A	c.(886-888)Cgg>Agg	p.R296R	RP11-280O1.2_ENST00000416424.1_RNA|RP11-280O1.2_ENST00000438275.1_RNA|RP11-280O1.2_ENST00000421273.1_RNA	NM_001005214.3	NP_001005214.2	Q8N7C0	LRC52_HUMAN	leucine rich repeat containing 52	296					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)	18	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					GGAAGTCAGCCGGCGGATTTT	0.572													A|||	1600	0.319489	0.3767	0.2954	5008	,	,		17171	0.2282		0.3052	False		,,,				2504	0.3681				p.R296R		Atlas-SNP	.											LRRC52,caecum,carcinoma,0,1	LRRC52	50	1	0			c.C886A						scavenged	.	A		1511,2895	673.6+/-402.8	261,989,953	62.0	68.0	66.0		886	-0.4	0.0	1	dbSNP_80	66	2460,6140	696.1+/-404.9	336,1788,2176	no	coding-synonymous	LRRC52	NM_001005214.3		597,2777,3129	AA,AC,CC		28.6047,34.2941,30.5321		296/314	165533005	3971,9035	2203	4300	6503	SO:0001819	synonymous_variant	440699	exon2			GTCAGCCGGCGGA	AK098677	CCDS30930.1	1q23.3	2008-02-05			ENSG00000162763	ENSG00000162763			32156	protein-coding gene	gene with protein product		615218					Standard	NM_001005214		Approved	FLJ25811	uc001gde.2	Q8N7C0	OTTHUMG00000034625	ENST00000294818.1:c.886C>A	1.37:g.165533005C>A		Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_001005214	A2RUN7|Q5T9K5	Silent	SNP	ENST00000294818.1	37	CCDS30930.1																																																																																			C|0.692;A|0.308	0.308	strong		0.572	LRRC52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083793.1	NM_001005214	
ATP9B	374868	hgsc.bcm.edu	37	18	77097360	77097360	+	Missense_Mutation	SNP	A	A	T	rs585033	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:77097360A>T	ENST00000426216.2	+	19	2211	c.2194A>T	c.(2194-2196)Atg>Ttg	p.M732L	ATP9B_ENST00000543761.1_Missense_Mutation_p.M53L|ATP9B_ENST00000307671.7_Missense_Mutation_p.M732L|RP11-800A18.4_ENST00000592906.1_RNA	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	732			M -> L (in dbSNP:rs585033).		establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		GGAGAGGGAGATGGAACTGCT	0.652													A|||	162	0.0323482	0.003	0.0562	5008	,	,		20784	0.001		0.1024	False		,,,				2504	0.0153				p.M732L		Atlas-SNP	.											.	ATP9B	96	.	0			c.A2194T						PASS	.	A	LEU/MET	99,4307	77.8+/-116.1	2,95,2106	120.0	100.0	107.0		2194	4.2	1.0	18	dbSNP_83	107	777,7823	184.2+/-232.2	44,689,3567	yes	missense	ATP9B	NM_198531.3	15	46,784,5673	TT,TA,AA		9.0349,2.2469,6.7354	benign	732/1148	77097360	876,12130	2203	4300	6503	SO:0001583	missense	374868	exon19			AGGGAGATGGAAC	R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.2194A>T	18.37:g.77097360A>T	ENSP00000398076:p.Met732Leu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_198531	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	97	0.044413919413919416	1	0.0020325203252032522	21	0.058011049723756904	1	0.0017482517482517483	74	0.09762532981530343	A	8.343	0.829243	0.16749	0.022469	0.090349	ENSG00000166377	ENST00000426216;ENST00000307671;ENST00000543761	T;T;D	0.98835	0.15;0.15;-5.17	5.36	4.18	0.49190	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.039059	0.85682	N	0.000000	T	0.37404	0.1002	N	0.03281	-0.365	0.54753	D	0.999984	B;B;B	0.16396	0.002;0.017;0.014	B;B;B	0.23716	0.012;0.048;0.028	T	0.77667	-0.2502	10	0.02654	T	1	.	11.587	0.50925	0.8662:0.0:0.0:0.1338	rs585033;rs585033	53;732;732	F5H8J1;O43861;O43861-2	.;ATP9B_HUMAN;.	L	732;732;53	ENSP00000398076:M732L;ENSP00000304500:M732L;ENSP00000442015:M53L	ENSP00000304500:M732L	M	+	1	0	ATP9B	75198348	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.809000	0.75211	0.850000	0.35239	0.533000	0.62120	ATG	A|0.943;T|0.057	0.057	strong		0.652	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
RSF1	51773	hgsc.bcm.edu	37	11	77409568	77409568	+	Silent	SNP	T	T	C	rs4945203	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77409568T>C	ENST00000308488.6	-	7	2981	c.2679A>G	c.(2677-2679)ccA>ccG	p.P893P	RSF1_ENST00000360355.2_Silent_p.P862P|RSF1_ENST00000480887.1_Silent_p.P641P			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	893					CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			ATTTTTTGCATGGTTCATCAT	0.433													C|||	986	0.196885	0.3298	0.2161	5008	,	,		17411	0.1736		0.0984	False		,,,				2504	0.1288				p.P893P		Atlas-SNP	.											.	RSF1	105	.	0			c.A2679G						PASS	.	C		1343,3057	693.4+/-405.7	208,927,1065	223.0	203.0	210.0		2679	-8.3	0.4	11	dbSNP_111	210	832,7752	780.7+/-407.7	36,760,3496	no	coding-synonymous	RSF1	NM_016578.3		244,1687,4561	CC,CT,TT		9.6925,30.5227,16.7514		893/1442	77409568	2175,10809	2200	4292	6492	SO:0001819	synonymous_variant	51773	exon7			TTTGCATGGTTCA	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.2679A>G	11.37:g.77409568T>C		Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	309	237	0.76699	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Silent	SNP	ENST00000308488.6	37	CCDS8253.1	421	0.19276556776556777	172	0.34959349593495936	67	0.1850828729281768	109	0.19055944055944055	73	0.09630606860158311	C	8.729	0.916226	0.17907	0.305227	0.096925	ENSG00000048649	ENST00000532556	.	.	.	4.68	-8.3	0.01005	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996607	.	.	.	.	.	.	T	0.33445	-0.9868	3	.	.	.	-7.7615	2.551	0.04749	0.1499:0.3493:0.2269:0.2739	rs4945203;rs4945203	.	.	.	R	147	.	.	H	-	2	0	RSF1	77087216	0.001000	0.12720	0.444000	0.26895	0.979000	0.70002	-1.814000	0.01723	-2.263000	0.00689	-0.930000	0.02707	CAT	T|0.813;C|0.187	0.187	strong		0.433	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
CR1	1378	hgsc.bcm.edu	37	1	207737312	207737312	+	Silent	SNP	T	T	C	rs56232421	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207737312T>C	ENST00000367049.4	+	22	3690	c.3690T>C	c.(3688-3690)taT>taC	p.Y1230Y	CR1_ENST00000367052.1_Intron|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367051.1_Silent_p.Y780Y|CR1_ENST00000367053.1_Silent_p.Y780Y|CR1_ENST00000400960.2_Silent_p.Y780Y	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	780	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.Y1230Y(1)|p.Y780Y(1)|p.Y785Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						AGCCCGGCTATGACCTCAGAG	0.577													-|||	995	0.198682	0.4675	0.0749	5008	,	,		10279	0.1508		0.0308	False		,,,				2504	0.1452				p.Y1230Y		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,0,2	CR1	354	2	3	Substitution - coding silent(3)	prostate(3)	c.T3690C						scavenged	.						60.0	128.0	112.0					1																	207737312		1285	4057	5342	SO:0001819	synonymous_variant	1378	exon22			CGGCTATGACCTC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.3690T>C	1.37:g.207737312T>C		Somatic	392	0	0		WXS	Illumina HiSeq	Phase_I	6	5	0.833333	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1																																																																																			C|1.000;|0.000	1.000	weak		0.577	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
HP	3240	hgsc.bcm.edu	37	16	72094348	72094348	+	Silent	SNP	G	G	A	rs5475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:72094348G>A	ENST00000355906.5	+	7	838	c.780G>A	c.(778-780)gaG>gaA	p.E260E	HP_ENST00000570083.1_Silent_p.E201E|HP_ENST00000562526.1_Intron|HP_ENST00000357763.4_Silent_p.E296E|HP_ENST00000565574.1_Silent_p.E201E|HP_ENST00000398131.2_Silent_p.E201E|HPR_ENST00000540303.2_5'Flank|HPR_ENST00000356967.5_Intron|HPR_ENST00000561690.1_5'Flank	NM_005143.3	NP_005134.1	P00738	HPT_HUMAN	haptoglobin	260	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				acute-phase response (GO:0006953)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|immune system process (GO:0002376)|negative regulation of hydrogen peroxide catabolic process (GO:2000296)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of cell death (GO:0010942)|response to hydrogen peroxide (GO:0042542)	blood microparticle (GO:0072562)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|haptoglobin-hemoglobin complex (GO:0031838)	antioxidant activity (GO:0016209)|hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|urinary_tract(1)	7		Renal(780;9.67e-05)|Ovarian(137;0.00327)|Hepatocellular(780;0.114)		BRCA - Breast invasive adenocarcinoma(221;0.00015)|Kidney(780;0.000529)		CTGTTAATGAGAGAGTGATGC	0.438													G|||	72	0.014377	0.0015	0.0331	5008	,	,		21745	0.0		0.0427	False		,,,				2504	0.0041				p.E260E		Atlas-SNP	.											.	HP	27	.	0			c.G780A						PASS	.	G	,	36,3832		0,36,1898	102.0	99.0	100.0		603,780	3.1	1.0	16	dbSNP_52	100	403,7885		15,373,3756	no	coding-synonymous,coding-synonymous	HP	NM_001126102.1,NM_005143.3	,	15,409,5654	AA,AG,GG		4.8625,0.9307,3.6114	,	201/348,260/407	72094348	439,11717	1934	4144	6078	SO:0001819	synonymous_variant	3240	exon7			TAATGAGAGAGTG		CCDS45524.1, CCDS45525.1	16q22.2	2012-10-02			ENSG00000257017	ENSG00000257017			5141	protein-coding gene	gene with protein product		140100				11109501, 9352226	Standard	NM_005143		Approved		uc002fbr.4	P00738		ENST00000355906.5:c.780G>A	16.37:g.72094348G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	NM_005143	B0AZL5|P00737|Q0VAC4|Q0VAC5|Q2PP15|Q3B7J0|Q6LBY9|Q9UC67	Silent	SNP	ENST00000355906.5	37	CCDS45524.1																																																																																			G|0.978;A|0.022	0.022	strong		0.438	HP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421680.1	NM_005143	
LAMA5	3911	hgsc.bcm.edu	37	20	60895697	60895697	+	Missense_Mutation	SNP	C	C	T	rs2297587	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60895697C>T	ENST00000252999.3	-	50	6743	c.6677G>A	c.(6676-6678)cGc>cAc	p.R2226H		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2226	Domain II and I.		R -> H (in dbSNP:rs2297587).		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)			CGTCTCATGGCGGGGGCCCAG	0.706													.|||	935	0.186701	0.152	0.219	5008	,	,		13119	0.1855		0.2376	False		,,,				2504	0.1595				p.R2226H		Atlas-SNP	.											.	LAMA5	268	.	0			c.G6677A						PASS	.		HIS/ARG	888,3386		124,640,1373	10.0	14.0	13.0		6677	-0.2	0.0	20	dbSNP_100	13	1876,6580		239,1398,2591	yes	missense	LAMA5	NM_005560.3	29	363,2038,3964	TT,TC,CC		22.1854,20.7768,21.7125	benign	2226/3696	60895697	2764,9966	2137	4228	6365	SO:0001583	missense	3911	exon50			TCATGGCGGGGGC	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.6677G>A	20.37:g.60895697C>T	ENSP00000252999:p.Arg2226His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	428	0.19597069597069597	80	0.16260162601626016	78	0.2154696132596685	101	0.17657342657342656	169	0.22295514511873352	-	12.18	1.859616	0.32884	0.207768	0.221854	ENSG00000130702	ENST00000252999	T	0.10005	2.92	4.23	-0.196	0.13232	Laminin I (1);	0.716055	0.13292	N	0.398926	T	0.00012	0.0000	L	0.29908	0.895	0.53688	P	2.8999999999945736E-5	B	0.18310	0.027	B	0.10450	0.005	T	0.47235	-0.9133	9	0.15952	T	0.53	.	5.2616	0.15576	0.0:0.5371:0.1381:0.3247	rs2297587;rs57072194;rs2297587	2226	O15230	LAMA5_HUMAN	H	2226	ENSP00000252999:R2226H	ENSP00000252999:R2226H	R	-	2	0	LAMA5	60329092	0.003000	0.15002	0.009000	0.14445	0.014000	0.08584	-0.041000	0.12084	-0.080000	0.12685	-0.330000	0.08379	CGC	C|0.805;T|0.195	0.195	strong		0.706	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
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 GAIIx	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	52	10	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	
METTL11B	149281	hgsc.bcm.edu	37	1	170135669	170135669	+	Silent	SNP	C	C	T	rs6427234	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:170135669C>T	ENST00000439373.2	+	3	464	c.357C>T	c.(355-357)tgC>tgT	p.C119C	METTL11B_ENST00000367764.3_3'UTR	NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	119						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						GAACAGACTGCGCCTTGGACT	0.542													C|||	1458	0.291134	0.5076	0.2421	5008	,	,		16699	0.1349		0.2724	False		,,,				2504	0.2137				p.C119C		Atlas-SNP	.											.	METTL11B	18	.	0			c.C357T						PASS	.	C		657,727		159,339,194	85.0	80.0	82.0		357	-7.7	0.7	1	dbSNP_116	82	885,2297		133,619,839	no	coding-synonymous	METTL11B	NM_001136107.1		292,958,1033	TT,TC,CC		27.8127,47.4711,33.7714		119/284	170135669	1542,3024	692	1591	2283	SO:0001819	synonymous_variant	149281	exon3			AGACTGCGCCTTG	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.357C>T	1.37:g.170135669C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			C|0.725;T|0.275	0.275	strong		0.542	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
ATP2A3	489	hgsc.bcm.edu	37	17	3846802	3846802	+	Silent	SNP	A	A	G	rs758641	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3846802A>G	ENST00000352011.3	-	11	1356	c.1302T>C	c.(1300-1302)taT>taC	p.Y434Y	ATP2A3_ENST00000397043.3_Silent_p.Y434Y|ATP2A3_ENST00000359983.3_Silent_p.Y434Y|ATP2A3_ENST00000397035.3_Silent_p.Y434Y|ATP2A3_ENST00000397041.3_Silent_p.Y434Y|ATP2A3_ENST00000309890.7_Silent_p.Y434Y|ATP2A3_ENST00000397039.1_5'UTR			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	434					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		CCACCTTCTCATACACACCCT	0.642													G|||	1669	0.333267	0.3956	0.4582	5008	,	,		16607	0.0843		0.4563	False		,,,				2504	0.2904				p.Y434Y	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T1302C						PASS	.	G	,,,,,,	1730,2676	648.5+/-398.7	344,1042,817	132.0	118.0	123.0		1302,1302,1302,1302,1302,1302,1302	-0.9	0.9	17	dbSNP_86	123	3981,4619	600.8+/-394.3	943,2095,1262	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	1287,3137,2079	GG,GA,AA		46.2907,39.2646,43.9105	,,,,,,	434/1000,434/1053,434/1045,434/1044,434/1030,434/999,434/1030	3846802	5711,7295	2203	4300	6503	SO:0001819	synonymous_variant	489	exon11			CTTCTCATACACA		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.1302T>C	17.37:g.3846802A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	83	31	0.373494	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.605;G|0.395	0.395	strong		0.642	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
LRRN1	57633	hgsc.bcm.edu	37	3	3887093	3887093	+	Silent	SNP	A	A	G	rs9844909	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:3887093A>G	ENST00000319331.3	+	2	1529	c.768A>G	c.(766-768)caA>caG	p.Q256Q	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	256						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		AAGTCCCTCAACTTGCCCTGC	0.393													A|||	1262	0.251997	0.1422	0.2032	5008	,	,		17992	0.3224		0.2525	False		,,,				2504	0.362				p.Q256Q		Atlas-SNP	.											.	LRRN1	82	.	0			c.A768G						PASS	.	A		602,3802	237.4+/-249.2	42,518,1642	77.0	85.0	82.0		768	-1.2	1.0	3	dbSNP_119	82	2011,6589	346.7+/-326.3	237,1537,2526	no	coding-synonymous	LRRN1	NM_020873.5		279,2055,4168	GG,GA,AA		23.3837,13.6694,20.0938		256/717	3887093	2613,10391	2202	4300	6502	SO:0001819	synonymous_variant	57633	exon2			CCCTCAACTTGCC	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.768A>G	3.37:g.3887093A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	31	0.607843	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			A|0.775;G|0.225	0.225	strong		0.393	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
TAP2	6891	hgsc.bcm.edu	37	6	32802938	32802938	+	Missense_Mutation	SNP	C	C	T	rs140654840	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32802938C>T	ENST00000452392.2	-	5	1111	c.938G>A	c.(937-939)cGc>cAc	p.R313H	TAP2_ENST00000374899.4_Missense_Mutation_p.R313H|TAP2_ENST00000485701.1_5'Flank|TAP2_ENST00000374897.2_Missense_Mutation_p.R313H			Q9UDX4	S14L3_HUMAN	transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)	0	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)									Vitamin E(DB00163)	CACCTGATGGCGGGTGTTGTA	0.537													C|||	54	0.0107827	0.0219	0.0245	5008	,	,		19257	0.0		0.007	False		,,,				2504	0.001				p.R313H		Atlas-SNP	.											.	TAP2	98	.	0			c.G938A						PASS	.	C	HIS/ARG,HIS/ARG	66,2952		0,66,1443	66.0	53.0	58.0		938,938	4.8	1.0	6	dbSNP_134	58	48,5370		0,48,2661	yes	missense,missense	TAP2	NM_000544.3,NM_018833.2	29,29	0,114,4104	TT,TC,CC		0.8859,2.1869,1.3514	probably-damaging,probably-damaging	313/704,313/654	32802938	114,8322	1509	2709	4218	SO:0001583	missense	6891	exon5			TGATGGCGGGTGT	M74447	CCDS4755.1	6p21.3	2014-09-17			ENSG00000204267	ENSG00000204267		"""ATP binding cassette transporters / subfamily B"""	44	protein-coding gene	gene with protein product		170261		ABCB3		1529427, 1946428, 16395595	Standard	NM_001290043		Approved	PSF2, RING11, D6S217E	uc003ocd.3	Q03519	OTTHUMG00000031068	ENST00000452392.2:c.938G>A	6.37:g.32802938C>T	ENSP00000391806:p.Arg313His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	143	26	0.181818	NM_018833	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000452392.2	37		23	0.010531135531135532	11	0.022357723577235773	9	0.024861878453038673	0	0.0	3	0.00395778364116095	C	12.64	1.997375	0.35226	0.021869	0.008859	ENSG00000204267;ENSG00000204267;ENSG00000204267;ENSG00000250264	ENST00000556934;ENST00000374899;ENST00000374897;ENST00000452392	D;D;D	0.90004	-2.6;-2.6;-2.6	4.8	4.8	0.61643	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.000000	0.48286	D	0.000191	D	0.90321	0.6972	M	0.63169	1.94	0.27461	N	0.953144	P;D;D;D	0.89917	0.784;1.0;1.0;1.0	B;D;D;D	0.97110	0.273;1.0;1.0;1.0	D	0.87818	0.2636	9	0.18276	T	0.48	-58.1812	13.7068	0.62644	0.0:1.0:0.0:0.0	.	313;314;313;313	E7ENX8;Q59H06;Q03519;Q9UP03	.;.;TAP2_HUMAN;.	H	313	ENSP00000364034:R313H;ENSP00000364032:R313H;ENSP00000391806:R313H	ENSP00000364032:R313H	R	-	2	0	XXbac-BPG246D15.9;TAP2	32910916	0.979000	0.34478	0.985000	0.45067	0.154000	0.21943	1.224000	0.32539	2.354000	0.79902	0.542000	0.68232	CGC	C|0.986;T|0.014	0.014	strong		0.537	TAP2-001	NOVEL	mRNA_end_NF|cds_end_NF|basic|appris_principal|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000361828.1	NM_000544	
HSPG2	3339	hgsc.bcm.edu	37	1	22174518	22174518	+	Silent	SNP	G	G	T	rs12737091	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22174518G>T	ENST00000374695.3	-	60	7885	c.7806C>A	c.(7804-7806)gtC>gtA	p.V2602V	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2602	Ig-like C2-type 11.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CACCGTTACTGACGTGACACA	0.642													G|||	174	0.0347444	0.0015	0.0245	5008	,	,		19204	0.0		0.0487	False		,,,				2504	0.1084				p.V2602V		Atlas-SNP	.											.	HSPG2	311	.	0			c.C7806A						PASS	.	G		41,4365	45.3+/-79.5	0,41,2162	79.0	65.0	70.0		7806	3.0	1.0	1	dbSNP_121	70	491,8109	141.7+/-198.0	16,459,3825	no	coding-synonymous	HSPG2	NM_005529.5		16,500,5987	TT,TG,GG		5.7093,0.9305,4.0904		2602/4392	22174518	532,12474	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon60			GTTACTGACGTGA	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.7806C>A	1.37:g.22174518G>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			G|0.964;T|0.036	0.036	strong		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
OR2M5	127059	hgsc.bcm.edu	37	1	248309356	248309356	+	Missense_Mutation	SNP	A	A	G	rs73141283	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248309356A>G	ENST00000366476.1	+	1	907	c.907A>G	c.(907-909)Aaa>Gaa	p.K303E		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	303						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(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	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;0.0388)			AGCACTCAGGAAAGTGTTAGG	0.453													a|||	273	0.0545128	0.0575	0.0187	5008	,	,		17595	0.0754		0.0646	False		,,,				2504	0.044				p.K303E		Atlas-SNP	.											.	OR2M5	117	.	0			c.A907G						PASS	.	A	GLU/LYS	248,4158	123.3+/-160.7	10,228,1965	61.0	57.0	58.0		907	2.7	0.1	1	dbSNP_130	58	457,8143	109.4+/-169.9	19,419,3862	yes	missense	OR2M5	NM_001004690.1	56	29,647,5827	GG,GA,AA		5.314,5.6287,5.4206	possibly-damaging	303/313	248309356	705,12301	2203	4300	6503	SO:0001583	missense	127059	exon1			CTCAGGAAAGTGT		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.907A>G	1.37:g.248309356A>G	ENSP00000355432:p.Lys303Glu	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	140	0.0641025641025641	30	0.06097560975609756	8	0.022099447513812154	57	0.09965034965034965	45	0.059366754617414245	a	12.30	1.896938	0.33535	0.056287	0.05314	ENSG00000162727	ENST00000366476	T	0.40476	1.03	2.65	2.65	0.31530	.	.	.	.	.	T	0.01558	0.0050	M	0.82923	2.615	0.80722	P	0.0	B	0.14805	0.011	B	0.18871	0.023	T	0.29119	-1.0022	8	0.87932	D	0	.	8.6949	0.34289	1.0:0.0:0.0:0.0	.	303	A3KFT3	OR2M5_HUMAN	E	303	ENSP00000355432:K303E	ENSP00000355432:K303E	K	+	1	0	OR2M5	246375979	0.003000	0.15002	0.066000	0.19879	0.030000	0.12068	1.499000	0.35671	0.948000	0.37687	0.317000	0.21355	AAA	A|0.942;G|0.058	0.058	strong		0.453	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
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 GAIIx	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_ENST00000420326.2_Silent_p.V301V|RECQL5_ENST00000340830.5_Silent_p.V301V|RECQL5_ENST00000584999.1_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		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	155	61	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	
OR10H4	126541	hgsc.bcm.edu	37	19	16059846	16059846	+	Missense_Mutation	SNP	C	C	G	rs117192411	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:16059846C>G	ENST00000322107.1	+	1	29	c.29C>G	c.(28-30)tCt>tGt	p.S10C		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	10						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)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						AGCATCATATCTGAATTTAAC	0.448													.|||	32	0.00638978	0.0008	0.0086	5008	,	,		22517	0.0		0.0219	False		,,,				2504	0.0031				p.S10C		Atlas-SNP	.											.	OR10H4	48	.	0			c.C29G						PASS	.	C	CYS/SER	24,4382	30.8+/-60.4	0,24,2179	236.0	205.0	216.0		29	1.5	0.0	19	dbSNP_132	216	222,8378	93.1+/-155.1	5,212,4083	yes	missense	OR10H4	NM_001004465.1	112	5,236,6262	GG,GC,CC		2.5814,0.5447,1.8914	possibly-damaging	10/317	16059846	246,12760	2203	4300	6503	SO:0001583	missense	126541	exon1			TCATATCTGAATT	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.29C>G	19.37:g.16059846C>G	ENSP00000318834:p.Ser10Cys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	79	32	0.405063	NM_001004465	Q6IFJ2|Q96R57	Missense_Mutation	SNP	ENST00000322107.1	37	CCDS32941.1	18	0.008241758241758242	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	16	0.021108179419525065	c	10.32	1.316726	0.23908	0.005447	0.025814	ENSG00000176231	ENST00000322107	T	0.00462	7.26	1.53	1.53	0.23141	.	0.385400	0.18832	U	0.129946	T	0.00356	0.0011	M	0.83852	2.665	0.09310	N	1	D	0.67145	0.996	P	0.60345	0.873	T	0.48043	-0.9069	10	0.72032	D	0.01	.	3.9006	0.09159	0.0:0.7617:0.0:0.2383	.	10	Q8NGA5	O10H4_HUMAN	C	10	ENSP00000318834:S10C	ENSP00000318834:S10C	S	+	2	0	OR10H4	15920846	0.582000	0.26749	0.016000	0.15963	0.013000	0.08279	0.451000	0.21779	0.828000	0.34709	0.471000	0.43371	TCT	C|0.982;G|0.018	0.018	strong		0.448	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
IPP	3652	hgsc.bcm.edu	37	1	46195375	46195375	+	Missense_Mutation	SNP	T	T	C	rs28375469	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46195375T>C	ENST00000396478.3	-	4	893	c.791A>G	c.(790-792)aAa>aGa	p.K264R		NM_005897.2	NP_005888.1	Q9Y573	IPP_HUMAN	intracisternal A particle-promoted polypeptide	264			K -> R (in dbSNP:rs28375469). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.			actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	actin binding (GO:0003779)	p.K264R(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|stomach(2)	20	Acute lymphoblastic leukemia(166;0.155)					TTTGGGAGATTTGCATACTTC	0.373													T|||	1577	0.314896	0.2504	0.3473	5008	,	,		15649	0.3135		0.2833	False		,,,				2504	0.4131				p.K264R		Atlas-SNP	.											IPP,NS,carcinoma,0,1	IPP	66	1	1	Substitution - Missense(1)	stomach(1)	c.A791G						PASS	.	T	ARG/LYS,ARG/LYS	1088,3318	393.7+/-329.0	138,812,1253	110.0	112.0	111.0		791,791	5.8	1.0	1	dbSNP_125	111	2546,6054	415.3+/-351.7	384,1778,2138	yes	missense,missense	IPP	NM_001145349.1,NM_005897.2	26,26	522,2590,3391	CC,CT,TT		29.6047,24.6936,27.941	benign,benign	264/583,264/585	46195375	3634,9372	2203	4300	6503	SO:0001583	missense	3652	exon4			GGAGATTTGCATA	BC032544	CCDS30702.1, CCDS44132.1	1p34-p32	2013-01-30			ENSG00000197429	ENSG00000197429		"""Kelch-like"", ""BTB/POZ domain containing"""	6108	protein-coding gene	gene with protein product	"""kelch-like family member 27"""	147485				1905535, 8432546	Standard	NM_005897		Approved	KLHL27	uc001cou.3	Q9Y573	OTTHUMG00000008004	ENST00000396478.3:c.791A>G	1.37:g.46195375T>C	ENSP00000379739:p.Lys264Arg	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_001145349	A2A6V4|D3DQ11|Q8N5C3	Missense_Mutation	SNP	ENST00000396478.3	37	CCDS30702.1	649	0.29716117216117216	130	0.26422764227642276	114	0.3149171270718232	182	0.3181818181818182	223	0.2941952506596306	T	16.43	3.121918	0.56613	0.246936	0.296047	ENSG00000197429	ENST00000359942;ENST00000396478	T;T	0.74106	-0.63;-0.81	5.81	5.81	0.92471	.	0.197772	0.52532	D	0.000068	T	0.00012	0.0000	N	0.08118	0	0.20873	P	0.999833586	B;B	0.12630	0.003;0.006	B;B	0.10450	0.002;0.005	T	0.05354	-1.0890	9	0.59425	D	0.04	.	16.1671	0.81777	0.0:0.0:0.0:1.0	rs28375469;rs28375469	264;264	Q9Y573;A2A6V3	IPP_HUMAN;.	R	264	ENSP00000353024:K264R;ENSP00000379739:K264R	ENSP00000353024:K264R	K	-	2	0	IPP	45967962	1.000000	0.71417	0.994000	0.49952	0.629000	0.37895	7.623000	0.83113	2.226000	0.72624	0.459000	0.35465	AAA	T|0.709;C|0.291	0.291	strong		0.373	IPP-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021974.3	NM_005897	
TMEM99	147184	hgsc.bcm.edu	37	17	38991053	38991053	+	Silent	SNP	T	T	A	rs3169915|rs386796999	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:38991053T>A	ENST00000301665.3	+	3	589	c.285T>A	c.(283-285)ctT>ctA	p.L95L		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	95			L -> R (in dbSNP:rs1044806). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				GAGAAGGACTTCTTCTTCCTT	0.468													T|||	544	0.108626	0.1248	0.1182	5008	,	,		19724	0.004		0.1928	False		,,,				2504	0.1012				p.L95L		Atlas-SNP	.											.	TMEM99	21	.	0			c.T285A						PASS	.	T	,,	427,3447		27,373,1537	201.0	197.0	199.0		285,285,285	0.2	0.1	17	dbSNP_105	199	1612,6680		151,1310,2685	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	,,	178,1683,4222	AA,AT,TT		19.4404,11.0222,16.7598	,,	95/259,95/259,95/259	38991053	2039,10127	1937	4146	6083	SO:0001819	synonymous_variant	147184	exon3			AGGACTTCTTCTT	AK097454	CCDS42319.1	17q21.2	2008-11-06			ENSG00000167920	ENSG00000167920			28305	protein-coding gene	gene with protein product						12477932	Standard	NM_001195386		Approved	MGC21518	uc021txc.1	Q8N816	OTTHUMG00000133579	ENST00000301665.3:c.285T>A	17.37:g.38991053T>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_001195386	B4DQ34|Q96BP9	Silent	SNP	ENST00000301665.3	37	CCDS42319.1																																																																																			T|0.873;A|0.127	0.127	strong		0.468	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
ANK3	288	hgsc.bcm.edu	37	10	61831744	61831744	+	Silent	SNP	A	A	G	rs10740006	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:61831744A>G	ENST00000280772.2	-	37	9086	c.8895T>C	c.(8893-8895)gcT>gcC	p.A2965A	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2965					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						TCCTCTCATCAGCAACTCTGA	0.463													A|||	631	0.125998	0.0204	0.2104	5008	,	,		18180	0.0347		0.2724	False		,,,				2504	0.1524				p.A2965A		Atlas-SNP	.											.	ANK3	703	.	0			c.T8895C						PASS	.	A	,,,	226,4180	133.7+/-170.0	8,210,1985	106.0	95.0	99.0		,,,8895	-10.9	0.0	10	dbSNP_120	99	2252,6348	381.3+/-340.0	300,1652,2348	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	308,1862,4333	GG,GA,AA		26.186,5.1294,19.0527	,,,	,,,2965/4378	61831744	2478,10528	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			CTCATCAGCAACT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8895T>C	10.37:g.61831744A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			A|0.834;G|0.166	0.166	strong		0.463	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
WDR11	55717	hgsc.bcm.edu	37	10	122624679	122624679	+	Silent	SNP	G	G	A	rs10886789	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:122624679G>A	ENST00000263461.6	+	6	1080	c.834G>A	c.(832-834)acG>acA	p.T278T		NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|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)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.T278T(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TGAATCAGACGGTGGGTGTGA	0.363													G|||	1617	0.322883	0.171	0.4063	5008	,	,		17443	0.4177		0.333	False		,,,				2504	0.3609				p.T278T		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.G834A						PASS	.	G		792,3614	320.2+/-296.5	74,644,1485	135.0	130.0	132.0		834	-2.8	1.0	10	dbSNP_120	132	2886,5714	452.3+/-362.9	468,1950,1882	no	coding-synonymous	WDR11	NM_018117.11		542,2594,3367	AA,AG,GG		33.5581,17.9755,28.2793		278/1225	122624679	3678,9328	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon6			TCAGACGGTGGGT	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.834G>A	10.37:g.122624679G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			G|0.708;A|0.292	0.292	strong		0.363	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
IL10RA	3587	hgsc.bcm.edu	37	11	117869670	117869670	+	Missense_Mutation	SNP	A	A	G	rs2229113	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:117869670A>G	ENST00000227752.3	+	7	1171	c.1051A>G	c.(1051-1053)Agg>Ggg	p.R351G	IL10RA_ENST00000545409.1_Missense_Mutation_p.R202G|IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Missense_Mutation_p.R331G	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	351			R -> G (in dbSNP:rs2229113). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8120391, ECO:0000269|Ref.2, ECO:0000269|Ref.6}.		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)		GCTGGGAAACAGGGAGCCCCC	0.637													G|||	4062	0.811102	0.8177	0.8141	5008	,	,		18853	0.9931		0.6829	False		,,,				2504	0.7444				p.R351G		Atlas-SNP	.											.	IL10RA	46	.	0			c.A1051G	GRCh37	CM035836	IL10RA	M	rs2229113	PASS	.	G	GLY/ARG	3556,844	331.2+/-301.9	1445,666,89	42.0	42.0	42.0		1051	1.1	0.0	11	dbSNP_98	42	5908,2684	427.5+/-355.6	2037,1834,425	yes	missense	IL10RA	NM_001558.3	125	3482,2500,514	GG,GA,AA		31.2384,19.1818,27.1552	benign	351/579	117869670	9464,3528	2200	4296	6496	SO:0001583	missense	3587	exon7			GGAAACAGGGAGC	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.1051A>G	11.37:g.117869670A>G	ENSP00000227752:p.Arg351Gly	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	46	0.884615	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	1770	0.8104395604395604	408	0.8292682926829268	281	0.7762430939226519	566	0.9895104895104895	515	0.679419525065963	G	7.318	0.616388	0.14129	0.808182	0.687616	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.25912	1.77;1.77;1.77	5.66	1.13	0.20643	.	1.744910	0.02362	N	0.077009	T	0.00012	0.0000	N	0.00621	-1.32	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29088	-1.0023	9	0.09843	T	0.71	-0.8429	5.621	0.17457	0.3457:0.1398:0.5145:0.0	rs2229113;rs17513512;rs17856786;rs60071346;rs2229113	331;351	F5GYV8;Q13651	.;I10R1_HUMAN	G	351;331;202;331	ENSP00000227752:R351G;ENSP00000441397:R331G;ENSP00000443019:R202G	ENSP00000227752:R351G	R	+	1	2	IL10RA	117374880	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.038000	0.13862	0.073000	0.16731	-0.213000	0.12676	AGG	A|0.247;G|0.753	0.753	strong		0.637	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
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 GAIIx	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	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	60	33	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	
FAM21A	387680	hgsc.bcm.edu	37	10	47915898	47915898	+	Silent	SNP	A	A	G	rs183064568		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:47915898A>G	ENST00000358474.5	+	15	1305	c.1305A>G	c.(1303-1305)aaA>aaG	p.K435K		NM_018232.1	NP_060702.1	Q5SNT6	FA21B_HUMAN		435					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.K435K(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						CTTCCAGCAAAAATCTCAAGC	0.408																																					p.K435K		Atlas-SNP	.											FAM21B_ENST00000358474,NS,carcinoma,0,1	FAM21B	31	1	1	Substitution - coding silent(1)	stomach(1)	c.A1305G						scavenged	.						20.0	29.0	26.0					10																	47915898		1759	4018	5777	SO:0001819	synonymous_variant	55747	exon15			CAGCAAAAATCTC																												ENST00000358474.5:c.1305A>G	10.37:g.47915898A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	605	68	0.112397	NM_018232		Silent	SNP	ENST00000358474.5	37	CCDS44379.1																																																																																			A|0.375;G|0.625	0.625	strong		0.408	FAM21B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047871.2		
KRT32	3882	hgsc.bcm.edu	37	17	39619115	39619115	+	Missense_Mutation	SNP	G	G	A	rs2071563	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39619115G>A	ENST00000225899.3	-	6	1287	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	395	Coil 2.|Rod.		T -> M (in dbSNP:rs2071563).		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GCTCCGGTACGTGTTGATCTC	0.632													G|||	1847	0.36881	0.4259	0.402	5008	,	,		16423	0.3363		0.4245	False		,,,				2504	0.2444				p.T395M		Atlas-SNP	.											.	KRT32	57	.	0			c.C1184T						PASS	.	G	MET/THR	1809,2597	530.3+/-372.9	371,1067,765	72.0	73.0	72.0		1184	5.1	1.0	17	dbSNP_96	72	3226,5374	483.7+/-371.2	622,1982,1696	no	missense	KRT32	NM_002278.3	81	993,3049,2461	AA,AG,GG		37.5116,41.0576,38.7129	probably-damaging	395/449	39619115	5035,7971	2203	4300	6503	SO:0001583	missense	3882	exon6			CGGTACGTGTTGA	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.1184C>T	17.37:g.39619115G>A	ENSP00000225899:p.Thr395Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	869	0.39789377289377287	213	0.4329268292682927	125	0.3453038674033149	208	0.36363636363636365	323	0.4261213720316623	G	17.48	3.400513	0.62177	0.410576	0.375116	ENSG00000108759	ENST00000225899	D	0.91996	-2.95	5.07	5.07	0.68467	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.40554	N	0.001074	T	0.00012	0.0000	H	0.95114	3.625	0.31049	P	0.715462	D	0.89917	1.0	D	0.97110	1.0	T	0.00000	-1.5298	9	0.72032	D	0.01	.	17.8011	0.88587	0.0:0.0:1.0:0.0	rs2071563;rs52800623;rs58844466;rs2071563	395	Q14532	K1H2_HUMAN	M	395	ENSP00000225899:T395M	ENSP00000225899:T395M	T	-	2	0	KRT32	36872641	0.563000	0.26594	0.969000	0.41365	0.720000	0.41350	2.380000	0.44327	2.493000	0.84123	0.561000	0.74099	ACG	G|0.611;A|0.389	0.389	strong		0.632	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
PDGFRB	5159	hgsc.bcm.edu	37	5	149499672	149499672	+	Silent	SNP	T	T	C	rs246395	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149499672T>C	ENST00000261799.4	-	19	3070	c.2601A>G	c.(2599-2601)ttA>ttG	p.L867L		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	867	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)	p.L867L(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCATCCACTTTAAAGGCAAAA	0.572			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""								C|||	1184	0.236422	0.1528	0.2997	5008	,	,		21447	0.1538		0.2903	False		,,,				2504	0.3344				p.L867L		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	1	Substitution - coding silent(1)	stomach(1)	c.A2601G						PASS	.	C		822,3584	748.8+/-412.0	78,666,1459	84.0	76.0	79.0		2601	2.7	1.0	5	dbSNP_79	79	2833,5767	673.2+/-403.0	457,1919,1924	no	coding-synonymous	PDGFRB	NM_002609.3		535,2585,3383	CC,CT,TT		32.9419,18.6564,28.1024		867/1107	149499672	3655,9351	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon19			CCACTTTAAAGGC	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.2601A>G	5.37:g.149499672T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			T|0.745;C|0.255	0.255	strong		0.572	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
SH2D4A	63898	hgsc.bcm.edu	37	8	19221700	19221700	+	Missense_Mutation	SNP	G	G	A	rs34608771	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:19221700G>A	ENST00000265807.3	+	7	1235	c.824G>A	c.(823-825)aGc>aAc	p.S275N	SH2D4A_ENST00000519207.1_Missense_Mutation_p.S275N|SH2D4A_ENST00000518040.1_Missense_Mutation_p.S230N	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	275			S -> N (in dbSNP:rs34608771). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AGGCTGCAAAGCCCCTTGCGT	0.527													G|||	891	0.177915	0.0946	0.2378	5008	,	,		14052	0.0595		0.3072	False		,,,				2504	0.2372				p.S275N		Atlas-SNP	.											.	SH2D4A	49	.	0			c.G824A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	556,3850	249.0+/-256.6	36,484,1683	81.0	82.0	81.0		824,689,824	3.9	0.0	8	dbSNP_126	81	2669,5931	427.8+/-355.7	416,1837,2047	yes	missense,missense,missense	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	46,46,46	452,2321,3730	AA,AG,GG		31.0349,12.6192,24.7962	benign,benign,benign	275/455,230/410,275/455	19221700	3225,9781	2203	4300	6503	SO:0001583	missense	63898	exon7			TGCAAAGCCCCTT	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.824G>A	8.37:g.19221700G>A	ENSP00000265807:p.Ser275Asn	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	401	0.18360805860805862	40	0.08130081300813008	95	0.26243093922651933	32	0.055944055944055944	234	0.3087071240105541	G	11.29	1.596322	0.28445	0.126192	0.310349	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207	T;D;T	0.94537	2.62;-3.45;2.62	5.75	3.94	0.45596	.	0.730267	0.13855	N	0.358071	T	0.00012	0.0000	L	0.28344	0.845	0.80722	P	0.0	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.07481	-1.0770	9	0.13853	T	0.58	.	7.9302	0.29897	0.1895:0.0:0.8105:0.0	rs34608771	230;275	B4DDR1;Q9H788	.;SH24A_HUMAN	N	275;230;275	ENSP00000265807:S275N;ENSP00000429482:S230N;ENSP00000428684:S275N	ENSP00000265807:S275N	S	+	2	0	SH2D4A	19265980	0.001000	0.12720	0.006000	0.13384	0.008000	0.06430	0.087000	0.14958	0.754000	0.32968	0.563000	0.77884	AGC	G|0.764;A|0.236	0.236	strong		0.527	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
ATP10A	57194	hgsc.bcm.edu	37	15	25926186	25926186	+	Silent	SNP	G	G	A	rs2076743	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:25926186G>A	ENST00000356865.6	-	18	3639	c.3528C>T	c.(3526-3528)gcC>gcT	p.A1176A		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1176					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		AGGCGGCGTCGGCCATGTTAA	0.512													G|||	3395	0.677915	0.8094	0.7147	5008	,	,		17707	0.6121		0.6123	False		,,,				2504	0.6094				p.A1176A		Atlas-SNP	.											.	ATP10A	270	.	0			c.C3528T						PASS	.	G		3525,881	742.5+/-411.4	1413,699,91	84.0	81.0	82.0		3528	-9.7	0.0	15	dbSNP_96	82	5320,3280	647.2+/-400.4	1655,2010,635	no	coding-synonymous	ATP10A	NM_024490.3		3068,2709,726	AA,AG,GG		38.1395,19.9955,31.9929		1176/1500	25926186	8845,4161	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon18			GGCGTCGGCCATG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3528C>T	15.37:g.25926186G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			G|0.329;A|0.671	0.671	strong		0.512	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
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 GAIIx	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		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	187	94	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	
XIRP2	129446	hgsc.bcm.edu	37	2	168099738	168099738	+	Silent	SNP	T	T	C	rs10497323	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:168099738T>C	ENST00000409195.1	+	9	1925	c.1836T>C	c.(1834-1836)ggT>ggC	p.G612G	XIRP2_ENST00000409273.1_Silent_p.G390G|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000295237.9_Silent_p.G612G|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	437					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGCTGGTGGTGATGTGAAAT	0.428													C|||	1763	0.352037	0.5719	0.255	5008	,	,		19983	0.3284		0.169	False		,,,				2504	0.3364				p.G612G		Atlas-SNP	.											.	XIRP2	914	.	0			c.T1836C						PASS	.	C	,,,,	1921,2051		459,1003,524	88.0	92.0	91.0		,,1170,,1836	-5.3	0.7	2	dbSNP_119	91	1298,6980		100,1098,2941	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	559,2101,3465	CC,CT,TT		15.6801,48.3635,26.2776	,,,,	,,390/3328,,612/3550	168099738	3219,9031	1986	4139	6125	SO:0001819	synonymous_variant	129446	exon9			TGGTGGTGATGTG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.1836T>C	2.37:g.168099738T>C		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	217	120	0.552995	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			T|0.689;C|0.311	0.311	strong		0.428	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
ARSB	411	hgsc.bcm.edu	37	5	78181477	78181477	+	Missense_Mutation	SNP	C	C	T	rs1065757	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:78181477C>T	ENST00000264914.4	-	5	1608	c.1072G>A	c.(1072-1074)Gtg>Atg	p.V358M	ARSB_ENST00000396151.3_Missense_Mutation_p.V358M|ARSB_ENST00000565165.1_Missense_Mutation_p.V358M|ARSB_ENST00000521800.1_5'UTR	NM_000046.3	NP_000037.2	P15848	ARSB_HUMAN	arylsulfatase B	358			V -> L (in dbSNP:rs1065757).|V -> M (in dbSNP:rs1065757). {ECO:0000269|PubMed:10036316, ECO:0000269|PubMed:11802522, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14974081, ECO:0000269|PubMed:7687847, ECO:0000269|PubMed:9582121}.		autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|lysosomal transport (GO:0007041)|lysosome organization (GO:0007040)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|rough endoplasmic reticulum (GO:0005791)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_lung(232;0.000637)|Lung NSC(167;0.00173)|Ovarian(174;0.0105)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;4.24e-44)|Epithelial(54;3.12e-39)|all cancers(79;3.02e-34)		GCCAGCTTCACGAGTGTTGGC	0.587													C|||	1430	0.285543	0.0371	0.4294	5008	,	,		14652	0.372		0.4662	False		,,,				2504	0.2444				p.V358M	Melanoma(169;563 1968 25780 26156 52266)	Atlas-SNP	.											.	ARSB	47	.	0			c.G1072A						PASS	.	C	MET/VAL,MET/VAL	504,3902	232.6+/-246.1	30,444,1729	109.0	100.0	103.0		1072,1072	5.5	0.4	5	dbSNP_86	103	3719,4881	531.8+/-382.1	819,2081,1400	yes	missense,missense	ARSB	NM_000046.3,NM_198709.2	21,21	849,2525,3129	TT,TC,CC		43.2442,11.4389,32.4696	possibly-damaging,possibly-damaging	358/534,358/414	78181477	4223,8783	2203	4300	6503	SO:0001583	missense	411	exon6			GCTTCACGAGTGT	M32373	CCDS4043.1, CCDS43334.1	5q14.1	2013-02-14			ENSG00000113273	ENSG00000113273	3.1.6.1	"""Arylsulfatase family"""	714	protein-coding gene	gene with protein product		611542				2303452	Standard	NM_000046		Approved		uc003kfq.3	P15848	OTTHUMG00000108129	ENST00000264914.4:c.1072G>A	5.37:g.78181477C>T	ENSP00000264914:p.Val358Met	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_198709	B2RC20|Q8N322|Q9UDI9	Missense_Mutation	SNP	ENST00000264914.4	37	CCDS4043.1	743	0.3402014652014652	21	0.042682926829268296	155	0.4281767955801105	225	0.39335664335664333	342	0.45118733509234826	C	21.3	4.121790	0.77436	0.114389	0.432442	ENSG00000113273	ENST00000264914;ENST00000396151	D;D	0.98493	-4.96;-4.96	5.46	5.46	0.80206	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.058789	0.64402	D	0.000002	T	0.00012	0.0000	L	0.49571	1.57	0.09310	P	0.99999737313	D;D	0.89917	1.0;0.997	D;D	0.80764	0.994;0.91	T	0.00000	-1.5423	9	0.44086	T	0.13	.	18.2841	0.90108	0.0:1.0:0.0:0.0	rs1065757;rs1801060;rs17819819;rs52799154;rs1065757	358;358	Q8N322;P15848	.;ARSB_HUMAN	M	358	ENSP00000264914:V358M;ENSP00000379455:V358M	ENSP00000264914:V358M	V	-	1	0	ARSB	78217233	0.997000	0.39634	0.410000	0.26471	0.986000	0.74619	3.985000	0.56930	2.555000	0.86185	0.561000	0.74099	GTG	T|0.311;C|0.689	0.311	strong		0.587	ARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226932.2	NM_000046	
TGIF2LX	90316	hgsc.bcm.edu	37	X	89177673	89177673	+	Missense_Mutation	SNP	G	G	A	rs2290380	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:89177673G>A	ENST00000561129.2	+	1	719	c.589G>A	c.(589-591)Gtc>Atc	p.V197I	TGIF2LX_ENST00000283891.5_Missense_Mutation_p.V197I			Q8IUE1	TF2LX_HUMAN	TGFB-induced factor homeobox 2-like, X-linked	197			V -> I (in dbSNP:rs2290380). {ECO:0000269|PubMed:12815422, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(29)|ovary(1)|skin(3)|urinary_tract(1)	40						CAAGGTTTCTGTCACATCCCC	0.557													A|||	2746	0.727417	0.7012	0.5994	3775	,	,		13445	0.5		0.496	False		,,,				2504	0.409				p.V197I		Atlas-SNP	.											.	TGIF2LX	84	.	0			c.G589A						PASS	.	A	ILE/VAL	3446,389		1309,307,521,16,50	75.0	80.0	78.0		589	0.4	0.0	X	dbSNP_100	78	4588,2140		1130,1048,1280,250,592	yes	missense	TGIF2LX	NM_138960.3	29	2439,1355,1801,266,642	AA,AG,A,GG,G		31.8074,10.1434,23.9421	benign	197/242	89177673	8034,2529	2203	4300	6503	SO:0001583	missense	90316	exon2			GTTTCTGTCACAT	AF497480	CCDS14459.1	Xq21.31	2014-05-14	2007-02-07		ENSG00000153779	ENSG00000153779		"""Homeoboxes / TALE class"""	18570	protein-coding gene	gene with protein product		300411	"""TGFB-induced factor 2-like, X-linked"""				Standard	NM_138960		Approved		uc004efe.3	Q8IUE1	OTTHUMG00000021954	ENST00000561129.2:c.589G>A	X.37:g.89177673G>A	ENSP00000453704:p.Val197Ile	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	207	150	0.724638	NM_138960	Q5JRM9|Q8TD48	Missense_Mutation	SNP	ENST00000561129.2	37	CCDS14459.1	1231	0.7420132610006027	234	0.823943661971831	152	0.672566371681416	187	0.5252808988764045	266	0.49812734082397003	A	7.084	0.570894	0.13623	0.898566	0.681926	ENSG00000153779	ENST00000283891	T	0.63580	-0.05	2.82	0.387	0.16259	.	3.568200	0.02202	N	0.062395	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35475	-0.9787	8	.	.	.	-31.1656	5.7356	0.18065	0.5447:0.0:0.4553:0.0	rs2290380;rs6423513;rs52796488;rs58435818;rs2290380	197	Q8IUE1	TF2LX_HUMAN	I	197	ENSP00000355119:V197I	.	V	+	1	0	TGIF2LX	89064329	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.495000	0.22483	-0.320000	0.08640	-0.631000	0.03989	GTC	G|0.234;A|0.766	0.766	strong		0.557	TGIF2LX-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417911.2	NM_138960	
ZNF138	7697	hgsc.bcm.edu	37	7	64291987	64291987	+	Missense_Mutation	SNP	G	G	A	rs35742014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:64291987G>A	ENST00000359735.3	+	4	543	c.196G>A	c.(196-198)Ggt>Agt	p.G66S	ZNF138_ENST00000397136.2_Missense_Mutation_p.G66S|ZNF138_ENST00000430838.2_3'UTR|ZNF138_ENST00000494380.1_3'UTR|ZNF138_ENST00000440155.2_Missense_Mutation_p.G97S|ZNF138_ENST00000307355.7_Missense_Mutation_p.G123S|ZNF138_ENST00000437743.1_Missense_Mutation_p.G91S|ZNF138_ENST00000440598.1_3'UTR	NM_001271637.1|NM_001271639.1	NP_001258566.1|NP_001258568.1	P52744	ZN138_HUMAN	zinc finger protein 138	66					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)			kidney(1)|large_intestine(3)|lung(2)|stomach(1)	7		Lung NSC(55;0.0795)|all_lung(88;0.18)				ACACCAAGGAGGTTTTAATGG	0.308													G|||	494	0.0986422	0.0083	0.1499	5008	,	,		17875	0.2609		0.0338	False		,,,				2504	0.0838				p.G123S		Atlas-SNP	.											.	ZNF138	43	.	0			c.G367A						PASS	.	G	,SER/GLY	89,4309		2,85,2112	71.0	71.0	71.0		,289	-1.7	0.0	7	dbSNP_126	71	260,8340		6,248,4046	no	utr-3,missense	ZNF138	NM_001160183.1,NM_006524.2	,56	8,333,6158	AA,AG,GG		3.0233,2.0236,2.685	,benign	,97/294	64291987	349,12649	2199	4300	6499	SO:0001583	missense	7697	exon4			CAAGGAGGTTTTA	U09847	CCDS34645.1, CCDS34645.2, CCDS55115.1, CCDS64659.1, CCDS64660.1, CCDS64661.1, CCDS75607.1	7q11.21	2013-01-08	2005-07-11		ENSG00000197008	ENSG00000197008		"""Zinc fingers, C2H2-type"", ""-"""	12922	protein-coding gene	gene with protein product		604080	"""zinc finger protein 138 (clone pHZ-32)"""				Standard	NM_006524		Approved	pHZ-32	uc031sxl.1	P52744	OTTHUMG00000156603	ENST00000359735.3:c.196G>A	7.37:g.64291987G>A	ENSP00000352770:p.Gly66Ser	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	65	24	0.369231	NM_001271639	B4DFX2|B4DP87|E9PHI7|E9PHK7	Missense_Mutation	SNP	ENST00000359735.3	37		227	0.10393772893772894	4	0.008130081300813009	54	0.14917127071823205	143	0.25	26	0.03430079155672823	.	2.013	-0.426608	0.04701	0.020236	0.030233	ENSG00000197008	ENST00000307355;ENST00000359735;ENST00000440155;ENST00000437743;ENST00000397136	T;T;T;T;T	0.05996	3.51;3.36;3.49;3.47;3.36	0.85	-1.7	0.08159	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P;B;D	0.62365	0.691;0.165;0.991	B;B;P	0.60949	0.259;0.066;0.881	T	0.36720	-0.9736	8	0.37606	T	0.19	.	2.1441	0.03782	0.3136:0.3484:0.338:0.0	rs35742014;rs61749534	97;91;66	E9PHI7;E7EWC5;P52744	.;.;ZN138_HUMAN	S	123;66;97;91;66	ENSP00000303533:G123S;ENSP00000352770:G66S;ENSP00000407262:G97S;ENSP00000399528:G91S;ENSP00000380325:G66S	ENSP00000303533:G123S	G	+	1	0	ZNF138	63929422	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.018000	0.12568	-1.051000	0.03226	-1.041000	0.02371	GGT	G|0.953;A|0.047	0.047	strong		0.308	ZNF138-201	KNOWN	basic	protein_coding	protein_coding		NM_006524	
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 GAIIx	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	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	199	37	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 GAIIx	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	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	66	34	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	
PM20D1	148811	hgsc.bcm.edu	37	1	205810947	205810947	+	Missense_Mutation	SNP	C	C	T	rs11240573	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205810947C>T	ENST00000367136.4	-	9	1080	c.1036G>A	c.(1036-1038)Ggg>Agg	p.G346R	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	346			G -> R (in dbSNP:rs11240573). {ECO:0000269|PubMed:15489334}.		negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			ACCTTGACCCCTGCTTTGAAT	0.468													C|||	592	0.118211	0.1339	0.0663	5008	,	,		21048	0.2113		0.0845	False		,,,				2504	0.0726				p.G346R		Atlas-SNP	.											.	PM20D1	56	.	0			c.G1036A						PASS	.	C	ARG/GLY	533,3873		34,465,1704	176.0	162.0	167.0		1036	5.4	0.9	1	dbSNP_120	167	490,8106		13,464,3821	yes	missense	PM20D1	NM_152491.4	125	47,929,5525	TT,TC,CC		5.7003,12.0971,7.868	probably-damaging	346/503	205810947	1023,11979	2203	4298	6501	SO:0001583	missense	148811	exon9			TGACCCCTGCTTT		CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.1036G>A	1.37:g.205810947C>T	ENSP00000356104:p.Gly346Arg	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	260	132	0.507692	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	245	0.11217948717948718	62	0.12601626016260162	26	0.0718232044198895	96	0.16783216783216784	61	0.08047493403693931	C	18.62	3.662890	0.67700	0.120971	0.057003	ENSG00000162877	ENST00000367136	T	0.73789	-0.78	5.4	5.4	0.78164	Peptidase M20, dimerisation (2);	0.000000	0.85682	D	0.000000	T	0.01730	0.0055	H	0.94698	3.57	0.09310	P	0.99999999824732	P	0.50443	0.935	P	0.57244	0.816	T	0.44329	-0.9335	9	0.59425	D	0.04	.	18.7848	0.91949	0.0:1.0:0.0:0.0	rs11240573;rs52836737;rs11240573	346	Q6GTS8	P20D1_HUMAN	R	346	ENSP00000356104:G346R	ENSP00000356104:G346R	G	-	1	0	PM20D1	204077570	1.000000	0.71417	0.926000	0.36857	0.191000	0.23601	6.856000	0.75450	2.548000	0.85928	0.655000	0.94253	GGG	C|0.906;T|0.094	0.094	strong		0.468	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
CNR1	1268	hgsc.bcm.edu	37	6	88853635	88853635	+	Silent	SNP	C	C	T	rs1049353	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:88853635C>T	ENST00000537554.1	-	2	4921	c.1359G>A	c.(1357-1359)acG>acA	p.T453T	CNR1_ENST00000428600.2_Silent_p.T453T|CNR1_ENST00000369501.2_Silent_p.T453T|CNR1_ENST00000549716.1_Silent_p.T392T|CNR1_ENST00000369499.2_Silent_p.T453T|CNR1_ENST00000549890.1_Silent_p.T453T|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000535130.1_Silent_p.T453T|CNR1_ENST00000468898.1_Silent_p.T420T	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	453					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	CAATCTTGACCGTGCTCTTGA	0.537													C|||	648	0.129393	0.0287	0.147	5008	,	,		20357	0.0764		0.2584	False		,,,				2504	0.1748				p.T453T		Atlas-SNP	.											CNR1,NS,carcinoma,-1,1	CNR1	91	1	0			c.G1359A	GRCh37	CM074755	CNR1	M	rs1049353	PASS	.	C	,,,,	314,4092	168.0+/-198.9	16,282,1905	226.0	204.0	212.0		1359,1359,1359,1359,1260	-7.6	0.6	6	dbSNP_86	212	2330,6270	390.2+/-343.2	338,1654,2308	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CNR1	NM_001160226.1,NM_001160258.1,NM_001160259.1,NM_016083.4,NM_033181.3	,,,,	354,1936,4213	TT,TC,CC		27.093,7.1266,20.3291	,,,,	453/473,453/473,453/473,453/473,420/440	88853635	2644,10362	2203	4300	6503	SO:0001819	synonymous_variant	1268	exon4			CTTGACCGTGCTC	AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"""GPCR / Class A : Cannabinoid receptors"""	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.1359G>A	6.37:g.88853635C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Silent	SNP	ENST00000537554.1	37	CCDS5015.1																																																																																			C|0.840;T|0.160	0.160	strong		0.537	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2		
GPR78	27201	hgsc.bcm.edu	37	4	8588950	8588950	+	Missense_Mutation	SNP	C	C	T	rs61746144	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:8588950C>T	ENST00000382487.4	+	3	1369	c.952C>T	c.(952-954)Cgc>Tgc	p.R318C	GPR78_ENST00000509216.1_3'UTR	NM_080819.4	NP_543009.2	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	318					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(4)|kidney(4)|large_intestine(1)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26						GAGAACCCCGCGCCCAGCATC	0.672													C|||	22	0.00439297	0.0023	0.0029	5008	,	,		16850	0.0		0.0159	False		,,,				2504	0.001				p.R318C		Atlas-SNP	.											.	GPR78	58	.	0			c.C952T						PASS	.	C	CYS/ARG	21,4385	26.2+/-53.5	0,21,2182	42.0	46.0	45.0		952	-2.8	0.0	4	dbSNP_129	45	173,8425	77.8+/-140.4	0,173,4126	yes	missense	GPR78	NM_080819.2	180	0,194,6308	TT,TC,CC		2.0121,0.4766,1.4918	possibly-damaging	318/364	8588950	194,12810	2203	4299	6502	SO:0001583	missense	27201	exon3			ACCCCGCGCCCAG	AF411107	CCDS3403.1	4p16.1	2012-08-21			ENSG00000155269	ENSG00000155269		"""GPCR / Class A : Orphans"""	4528	protein-coding gene	gene with protein product		606921				11574155	Standard	NM_080819		Approved		uc003glk.4	Q96P69	OTTHUMG00000128483	ENST00000382487.4:c.952C>T	4.37:g.8588950C>T	ENSP00000371927:p.Arg318Cys	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	136	79	0.580882	NM_080819	Q8NGV3	Missense_Mutation	SNP	ENST00000382487.4	37	CCDS3403.1	17	0.007783882783882784	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	C	5.506	0.278329	0.10403	0.004766	0.020121	ENSG00000155269	ENST00000382487	T	0.38887	1.11	2.09	-2.81	0.05805	.	0.196794	0.33610	U	0.004723	T	0.06781	0.0173	N	0.08118	0	0.26252	N	0.978707	D	0.54207	0.965	B	0.38156	0.266	T	0.36163	-0.9759	10	0.39692	T	0.17	.	3.0938	0.06302	0.2097:0.1443:0.0:0.646	rs61746144	318	Q96P69	GPR78_HUMAN	C	318	ENSP00000371927:R318C	ENSP00000371927:R318C	R	+	1	0	GPR78	8639850	1.000000	0.71417	0.006000	0.13384	0.105000	0.19272	3.454000	0.52986	-1.075000	0.03129	0.205000	0.17691	CGC	C|0.986;T|0.014	0.014	strong		0.672	GPR78-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359201.1		
FAM200B	285550	hgsc.bcm.edu	37	4	15689632	15689632	+	Silent	SNP	G	G	A	rs11729955	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:15689632G>A	ENST00000422728.2	+	2	1870	c.1032G>A	c.(1030-1032)gaG>gaA	p.E344E	FAM200B_ENST00000504137.1_Intron	NM_001145191.1	NP_001138663.1	P0CF97	F200B_HUMAN	family with sequence similarity 200, member B	344							nucleic acid binding (GO:0003676)	p.E344E(2)		endometrium(1)|kidney(1)	2						atctcatggaggtattgaaaa	0.328													A|||	1502	0.29992	0.3858	0.3098	5008	,	,		17540	0.1379		0.4056	False		,,,				2504	0.2352				p.E344E		Atlas-SNP	.											FAM200B_ENST00000422728,NS,carcinoma,0,2	FAM200B	56	2	2	Substitution - coding silent(2)	kidney(2)	c.G1032A						PASS	.	A		529,855		110,309,273	52.0	48.0	49.0		1032	2.6	1.0	4	dbSNP_120	49	1257,1925		249,759,583	no	coding-synonymous	FAM200B	NM_001145191.1		359,1068,856	AA,AG,GG		39.5035,38.2225,39.1152		344/658	15689632	1786,2780	692	1591	2283	SO:0001819	synonymous_variant	285550	exon2			CATGGAGGTATTG	BC048993	CCDS47028.1	4p15.32	2014-04-02			ENSG00000237765	ENSG00000237765			27740	protein-coding gene	gene with protein product	"""chromosome 4 open reading frame 53"""						Standard	NM_001145191		Approved	C4orf53	uc003gof.4	P0CF97	OTTHUMG00000160279	ENST00000422728.2:c.1032G>A	4.37:g.15689632G>A		Somatic	224	2	0.00892857		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_001145191		Silent	SNP	ENST00000422728.2	37	CCDS47028.1																																																																																			G|0.683;A|0.317	0.317	strong		0.328	FAM200B-005	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360100.1	NM_001145191	
THEM6	51337	hgsc.bcm.edu	37	8	143808951	143808951	+	Silent	SNP	C	C	T	rs2585138	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143808951C>T	ENST00000336138.3	+	1	331	c.187C>T	c.(187-189)Ctg>Ttg	p.L63L	CTD-2292P10.4_ENST00000520572.1_RNA|CTD-2292P10.2_ENST00000519782.1_RNA	NM_016647.2	NP_057731.1	Q8WUY1	THEM6_HUMAN	thioesterase superfamily member 6	63						extracellular region (GO:0005576)											GGACCTGCTGCTGCACATGAA	0.736													C|||	2445	0.488219	0.6369	0.4568	5008	,	,		13054	0.4206		0.4722	False		,,,				2504	0.3957				p.L63L		Atlas-SNP	.											.	.	.	.	0			c.C187T						PASS	.	C		2662,1646		889,884,381	8.0	9.0	9.0		187	0.7	1.0	8	dbSNP_100	9	4014,4460		1000,2014,1223	no	coding-synonymous	C8orf55	NM_016647.2		1889,2898,1604	TT,TC,CC		47.3684,38.208,47.7703		63/209	143808951	6676,6106	2154	4237	6391	SO:0001819	synonymous_variant	51337	exon1			CTGCTGCTGCACA	BC001311	CCDS6386.1	8q24.3	2012-05-03	2012-04-13	2012-04-13	ENSG00000130193	ENSG00000130193			29656	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 55"""	C8orf55		12477932	Standard	XM_005250955		Approved	DSCD75	uc003yww.1	Q8WUY1	OTTHUMG00000164673	ENST00000336138.3:c.187C>T	8.37:g.143808951C>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	8	7	0.875	NM_016647	B2RDN6|Q8NBN2|Q9NYI2	Silent	SNP	ENST00000336138.3	37	CCDS6386.1																																																																																			C|0.510;T|0.490	0.490	strong		0.736	THEM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379706.1	NM_016647	
AKNAD1	254268	hgsc.bcm.edu	37	1	109363232	109363232	+	Silent	SNP	T	T	C	rs1333130	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109363232T>C	ENST00000370001.3	-	14	2452	c.2184A>G	c.(2182-2184)aaA>aaG	p.K728K	AKNAD1_ENST00000477908.1_5'Flank	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	728						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						AACAGATCCGTTTGGGTTTTA	0.328													T|||	1935	0.386382	0.2617	0.3919	5008	,	,		5833	0.6974		0.2565	False		,,,				2504	0.364				p.K728K		Atlas-SNP	.											.	AKNAD1	83	.	0			c.A2184G						PASS	.	T		1216,3190	414.6+/-336.9	178,860,1165	89.0	93.0	92.0		2184	2.9	0.0	1	dbSNP_88	92	1983,6617	345.0+/-325.6	220,1543,2537	no	coding-synonymous	AKNAD1	NM_152763.3		398,2403,3702	CC,CT,TT		23.0581,27.5987,24.5963		728/837	109363232	3199,9807	2203	4300	6503	SO:0001819	synonymous_variant	254268	exon14			GATCCGTTTGGGT	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.2184A>G	1.37:g.109363232T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Silent	SNP	ENST00000370001.3	37	CCDS791.2																																																																																			T|0.694;C|0.306	0.306	strong		0.328	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
CCDC174	51244	hgsc.bcm.edu	37	3	14712473	14712473	+	Silent	SNP	G	G	A	rs1901	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:14712473G>A	ENST00000383794.3	+	11	1249	c.1176G>A	c.(1174-1176)ccG>ccA	p.P392P	CCDC174_ENST00000303688.7_Silent_p.P316P|CCDC174_ENST00000476763.1_3'UTR	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	392						cytoplasm (GO:0005737)|nucleus (GO:0005634)											AGTTTGCCCCGCCGTCAGATT	0.507													A|||	1730	0.345447	0.4614	0.4568	5008	,	,		16410	0.2262		0.3499	False		,,,				2504	0.228				p.P392P		Atlas-SNP	.											.	.	.	.	0			c.G1176A						PASS	.	A		2007,2399	614.5+/-392.4	465,1077,661	50.0	47.0	48.0		1176	1.4	1.0	3	dbSNP_36	48	2909,5691	670.3+/-402.7	460,1989,1851	no	coding-synonymous	C3orf19	NM_016474.4		925,3066,2512	AA,AG,GG		33.8256,45.5515,37.7979		392/468	14712473	4916,8090	2203	4300	6503	SO:0001819	synonymous_variant	51244	exon11			TGCCCCGCCGTCA	AF151046	CCDS2620.2	3p25.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000154781	ENSG00000154781			28033	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 19"""	C3orf19		11042152	Standard	NM_016474		Approved	FLJ33839	uc003byw.3	Q6PII3	OTTHUMG00000129837	ENST00000383794.3:c.1176G>A	3.37:g.14712473G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	143	57	0.398601	NM_016474	Q96CS5	Silent	SNP	ENST00000383794.3	37	CCDS2620.2																																																																																			G|0.630;A|0.370	0.370	strong		0.507	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474	
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 GAIIx	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_ENST00000458711.2_Missense_Mutation_p.V113L|CARKD_ENST00000470164.2_3'UTR|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	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	55	40	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	
ZNF671	79891	hgsc.bcm.edu	37	19	58233008	58233008	+	Missense_Mutation	SNP	G	G	A	rs3746207	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58233008G>A	ENST00000317398.6	-	4	541	c.446C>T	c.(445-447)gCa>gTa	p.A149V	AC003006.7_ENST00000594684.1_Intron|ZNF671_ENST00000594803.1_5'Flank|AC003006.7_ENST00000599221.1_Intron|ZNF671_ENST00000335820.3_Missense_Mutation_p.A51V	NM_024833.2	NP_079109.2	Q8TAW3	ZN671_HUMAN	zinc finger protein 671	149			A -> V (in dbSNP:rs3746207). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(6)|liver(1)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TGACACTCCTGCTACAAAAAT	0.453													G|||	767	0.153155	0.2814	0.111	5008	,	,		22236	0.0873		0.175	False		,,,				2504	0.0552				p.A149V		Atlas-SNP	.											.	ZNF671	55	.	0			c.C446T						PASS	.	G	VAL/ALA	1167,3239	410.9+/-335.5	145,877,1181	111.0	107.0	109.0		446	-0.6	0.0	19	dbSNP_107	109	1280,7320	254.4+/-279.7	90,1100,3110	yes	missense	ZNF671	NM_024833.2	64	235,1977,4291	AA,AG,GG		14.8837,26.4866,18.8144	possibly-damaging	149/535	58233008	2447,10559	2203	4300	6503	SO:0001583	missense	79891	exon4			ACTCCTGCTACAA		CCDS12961.1	19q13.43	2013-01-08				ENSG00000083814		"""Zinc fingers, C2H2-type"", ""-"""	26279	protein-coding gene	gene with protein product	"""hypothetical protein FLJ23506"""					12477932	Standard	NM_024833		Approved	FLJ23506	uc002qpz.4	Q8TAW3		ENST00000317398.6:c.446C>T	19.37:g.58233008G>A	ENSP00000321848:p.Ala149Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	137	58	0.423358	NM_024833	A6NF07|Q9H5E9	Missense_Mutation	SNP	ENST00000317398.6	37	CCDS12961.1	367	0.16804029304029305	126	0.25609756097560976	48	0.13259668508287292	57	0.09965034965034965	136	0.17941952506596306	G	9.713	1.157550	0.21454	0.264866	0.148837	ENSG00000083814	ENST00000317398;ENST00000335820	T;T	0.06142	3.46;3.34	1.66	-0.654	0.11443	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.399999999997849E-5	B	0.27192	0.171	B	0.15870	0.014	T	0.48875	-0.8996	8	0.32370	T	0.25	.	4.2045	0.10481	0.5669:0.0:0.4331:0.0	rs3746207;rs52832436;rs61034509;rs3746207	149	Q8TAW3	ZN671_HUMAN	V	149;51	ENSP00000321848:A149V;ENSP00000338670:A51V	ENSP00000321848:A149V	A	-	2	0	ZNF671	62924820	0.000000	0.05858	0.015000	0.15790	0.180000	0.23129	-2.628000	0.00873	-0.229000	0.09854	0.313000	0.20887	GCA	G|0.819;A|0.181	0.181	strong		0.453	ZNF671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466817.1	NM_024833	
PLA2G2A	5320	hgsc.bcm.edu	37	1	20304962	20304962	+	Silent	SNP	C	C	G	rs2236771	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:20304962C>G	ENST00000375111.3	-	4	367	c.96G>C	c.(94-96)acG>acC	p.T32T	PLA2G2A_ENST00000496748.1_5'UTR|PLA2G2A_ENST00000400520.3_Silent_p.T32T	NM_000300.3|NM_001161727.1	NP_000291.1|NP_001155199.1	P14555	PA2GA_HUMAN	phospholipase A2, group IIA (platelets, synovial fluid)	32					defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of epithelial cell proliferation (GO:0050680)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidic acid metabolic process (GO:0046473)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|small molecule metabolic process (GO:0044281)|somatic stem cell maintenance (GO:0035019)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|phospholipase A2 activity (GO:0004623)|phospholipid binding (GO:0005543)			central_nervous_system(1)|lung(6)|prostate(1)|stomach(1)	9		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00459)|Lung NSC(340;0.00475)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000138)|Kidney(64;0.000171)|GBM - Glioblastoma multiforme(114;0.00032)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Diclofenac(DB00586)|Ginkgo biloba(DB01381)|Indomethacin(DB00328)|Suramin(DB04786)	CCTTTCCTGTCGTCAACTTGA	0.557													C|||	486	0.0970447	0.0053	0.1009	5008	,	,		19229	0.2282		0.0775	False		,,,				2504	0.1033				p.T32T		Atlas-SNP	.											.	PLA2G2A	14	.	0			c.G96C						PASS	.	C	,,,	81,4325	69.2+/-107.0	1,79,2123	81.0	79.0	80.0		96,96,96,96	-4.2	0.0	1	dbSNP_98	80	794,7806	185.5+/-233.2	42,710,3548	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLA2G2A	NM_000300.3,NM_001161727.1,NM_001161728.1,NM_001161729.1	,,,	43,789,5671	GG,GC,CC		9.2326,1.8384,6.7277	,,,	32/145,32/145,32/145,32/145	20304962	875,12131	2203	4300	6503	SO:0001819	synonymous_variant	5320	exon3			TCCTGTCGTCAAC	BC005919	CCDS201.1	1p35	2008-09-19			ENSG00000188257	ENSG00000188257	3.1.1.4		9031	protein-coding gene	gene with protein product		172411		PLA2B, PLA2L		8838795	Standard	NM_000300		Approved		uc010odb.2	P14555	OTTHUMG00000002699	ENST00000375111.3:c.96G>C	1.37:g.20304962C>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_001161729	A8K5I7|Q6DN24|Q6IBD9|Q9UCD2	Silent	SNP	ENST00000375111.3	37	CCDS201.1																																																																																			C|0.904;G|0.096	0.096	strong		0.557	PLA2G2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007675.1	NM_000300	
OR6K3	391114	hgsc.bcm.edu	37	1	158687224	158687224	+	Missense_Mutation	SNP	G	G	A	rs857703	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158687224G>A	ENST00000368146.1	-	1	729	c.730C>T	c.(730-732)Ccc>Tcc	p.P244S	OR6K3_ENST00000368145.1_Missense_Mutation_p.P228S			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	244			P -> S (in dbSNP:rs857703). {ECO:0000269|PubMed:14983052}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P244S(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					TCAGAAGAGGGAATCCTCAAT	0.438													G|||	1404	0.280351	0.09	0.389	5008	,	,		23447	0.4474		0.3946	False		,,,				2504	0.1708				p.P228S		Atlas-SNP	.											OR6K3,NS,carcinoma,0,1	OR6K3	101	1	1	Substitution - Missense(1)	stomach(1)	c.C682T						PASS	.	G	SER/PRO	589,3817	259.5+/-263.1	47,495,1661	107.0	96.0	100.0		682	0.8	0.0	1	dbSNP_86	100	3247,5353	487.5+/-372.1	610,2027,1663	yes	missense	OR6K3	NM_001005327.2	74	657,2522,3324	AA,AG,GG		37.7558,13.3681,29.4941	benign	228/316	158687224	3836,9170	2203	4300	6503	SO:0001583	missense	391114	exon1			AAGAGGGAATCCT	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.730C>T	1.37:g.158687224G>A	ENSP00000357128:p.Pro244Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_001005327	Q5VUV0|Q6IFR5	Missense_Mutation	SNP	ENST00000368146.1	37		732	0.33516483516483514	56	0.11382113821138211	140	0.3867403314917127	238	0.4160839160839161	298	0.39313984168865435	G	13.46	2.243764	0.39697	0.133681	0.377558	ENSG00000203757	ENST00000368145;ENST00000368146	T;T	0.36878	1.23;1.23	3.77	0.813	0.18749	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.12987	0.0315	L	0.45137	1.4	0.80722	P	0.0	B	0.23128	0.08	B	0.24006	0.05	T	0.10776	-1.0615	8	0.48119	T	0.1	.	7.9959	0.30267	0.2855:0.0:0.7145:0.0	rs857703;rs52791601;rs56909898;rs857703	244	Q8NGY3	OR6K3_HUMAN	S	228;244	ENSP00000357127:P228S;ENSP00000357128:P244S	ENSP00000357127:P228S	P	-	1	0	OR6K3	156953848	0.000000	0.05858	0.001000	0.08648	0.627000	0.37826	-0.113000	0.10774	0.055000	0.16094	0.467000	0.42956	CCC	G|0.696;A|0.304	0.304	strong		0.438	OR6K3-201	KNOWN	basic	protein_coding	protein_coding			
CBLB	868	hgsc.bcm.edu	37	3	105439026	105439026	+	Silent	SNP	G	G	A	rs2305035	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:105439026G>A	ENST00000264122.4	-	10	1593	c.1272C>T	c.(1270-1272)gaC>gaT	p.D424D	CBLB_ENST00000403724.1_Silent_p.D424D|CBLB_ENST00000405772.1_Silent_p.D424D|CBLB_ENST00000545639.1_3'UTR|CBLB_ENST00000394027.3_Silent_p.D446D	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	424					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|negative regulation of T cell receptor signaling pathway (GO:0050860)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of T cell anergy (GO:0002669)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(2)|urinary_tract(2)	49						GATCAAAGGGGTCCACGATTA	0.478			Mis S		AML								G|||	1052	0.210064	0.1929	0.2983	5008	,	,		18868	0.2183		0.2376	False		,,,				2504	0.1339				p.D424D	GBM(93;588 1337 9788 29341 43499)	Atlas-SNP	.		Rec	yes		3	3q13.11	868	Cas-Br-M (murine) ecotropic retroviral transforming sequence b		L	.	CBLB	118	.	0			c.C1272T						PASS	.	G		812,3594	324.5+/-298.6	75,662,1466	100.0	87.0	91.0		1272	0.4	1.0	3	dbSNP_100	91	1845,6755	329.3+/-318.7	205,1435,2660	no	coding-synonymous	CBLB	NM_170662.3		280,2097,4126	AA,AG,GG		21.4535,18.4294,20.429		424/983	105439026	2657,10349	2203	4300	6503	SO:0001819	synonymous_variant	868	exon10			AAAGGGGTCCACG	U26710	CCDS2948.1	3q	2013-07-09	2013-07-09		ENSG00000114423	ENSG00000114423		"""RING-type (C3HC4) zinc fingers"""	1542	protein-coding gene	gene with protein product		604491	"""Cas-Br-M (murine) ectropic retroviral transforming sequence b"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence b"""			7784085	Standard	XM_005247853		Approved	RNF56, Cbl-b	uc003dwc.3	Q13191	OTTHUMG00000150654	ENST00000264122.4:c.1272C>T	3.37:g.105439026G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	132	59	0.44697	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Silent	SNP	ENST00000264122.4	37	CCDS2948.1																																																																																			G|0.787;A|0.213	0.213	strong		0.478	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971162	45971162	+	Silent	SNP	C	C	T	rs199922020	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45971162C>T	ENST00000391621.1	-	1	226	c.180G>A	c.(178-180)gcG>gcA	p.A60A	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	60	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GCTCACAGGCCGCCTGGCAGC	0.706																																					p.A60A		Atlas-SNP	.											KRTAP10-2,colon,carcinoma,0,1	KRTAP10-2	21	1	0			c.G180A						scavenged	.																																			SO:0001819	synonymous_variant	386679	exon1			ACAGGCCGCCTGG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.180G>A	21.37:g.45971162C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	62	10	0.16129	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			.	.	weak		0.706	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
WDR62	284403	hgsc.bcm.edu	37	19	36594369	36594369	+	Silent	SNP	C	C	T	rs45470992	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36594369C>T	ENST00000270301.7	+	30	3624	c.3624C>T	c.(3622-3624)tcC>tcT	p.S1208S	WDR62_ENST00000401500.2_Silent_p.S1213S			O43379	WDR62_HUMAN	WD repeat domain 62	1208					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ATGCCCCCTCCACCTGTTCCT	0.647													C|||	247	0.0493211	0.0083	0.0331	5008	,	,		19456	0.1062		0.0358	False		,,,				2504	0.0716				p.S1213S		Atlas-SNP	.											.	WDR62	102	.	0			c.C3639T						PASS	.	C	,	71,4335	64.1+/-101.4	0,71,2132	96.0	87.0	90.0		3639,3624	-2.0	0.0	19	dbSNP_127	90	336,8264	115.0+/-174.9	3,330,3967	no	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	3,401,6099	TT,TC,CC		3.907,1.6114,3.1293	,	1213/1524,1208/1519	36594369	407,12599	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon30			CCCCTCCACCTGT	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.3624C>T	19.37:g.36594369C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			C|0.963;T|0.037	0.037	strong		0.647	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
VWF	7450	hgsc.bcm.edu	37	12	6105387	6105387	+	Splice_Site	SNP	G	G	A	rs216902	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6105387G>A	ENST00000261405.5	-	35	6098	c.5844C>T	c.(5842-5844)tgC>tgT	p.C1948C		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	1948					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CTGTGCACACGCCTGGACAGA	0.507													G|||	2284	0.45607	0.2784	0.4179	5008	,	,		20719	0.7252		0.3648	False		,,,				2504	0.5399				p.C1948C		Atlas-SNP	.											.	VWF	338	.	0			c.C5844T						PASS	.	G		1365,3041	448.5+/-348.7	201,963,1039	38.0	34.0	35.0		5844	0.5	1.0	12	dbSNP_79	35	3266,5334	480.2+/-370.3	615,2036,1649	yes	coding-synonymous-near-splice	VWF	NM_000552.3		816,2999,2688	AA,AG,GG		37.9767,30.9805,35.6066		1948/2814	6105387	4631,8375	2203	4300	6503	SO:0001630	splice_region_variant	7450	exon35			GCACACGCCTGGA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.5843-1C>T	12.37:g.6105387G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			G|0.580;A|0.420	0.420	strong		0.507	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	Silent
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 GAIIx	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	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	103	56	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	
SENP1	29843	hgsc.bcm.edu	37	12	48477422	48477422	+	Silent	SNP	A	A	G	rs886588	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48477422A>G	ENST00000004980.5	-	6	982	c.504T>C	c.(502-504)ctT>ctC	p.L168L	SENP1_ENST00000549595.1_Silent_p.L168L|SENP1_ENST00000448372.1_Silent_p.L168L|SENP1_ENST00000339976.6_3'UTR|RNU6-1203P_ENST00000410703.1_RNA|SENP1_ENST00000551330.1_Silent_p.L168L|SENP1_ENST00000547886.1_5'UTR|SENP1_ENST00000549518.1_Silent_p.L168L			Q9P0U3	SENP1_HUMAN	SUMO1/sentrin specific peptidase 1	168	Ser-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic signaling pathway (GO:0097190)|cellular protein metabolic process (GO:0044267)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|proteolysis (GO:0006508)|regulation of definitive erythrocyte differentiation (GO:0010724)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|SUMO-specific protease activity (GO:0016929)	p.L168L(1)		large_intestine(3)|lung(1)|pancreas(2)|stomach(1)	7		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)				TGGGGCTCAAAAGACTTCGAC	0.408													A|||	803	0.160343	0.053	0.1744	5008	,	,		18083	0.2371		0.2177	False		,,,				2504	0.1575				p.L168L		Atlas-SNP	.											SENP1,NS,carcinoma,0,1	SENP1	44	1	1	Substitution - coding silent(1)	stomach(1)	c.T504C						PASS	.	A		253,3463		11,231,1616	120.0	111.0	114.0		504	1.8	1.0	12	dbSNP_86	114	1803,6381		192,1419,2481	no	coding-synonymous	SENP1	NM_014554.2		203,1650,4097	GG,GA,AA		22.0308,6.8084,17.2773		168/644	48477422	2056,9844	1858	4092	5950	SO:0001819	synonymous_variant	29843	exon6			GCTCAAAAGACTT	AF149770	CCDS44868.1, CCDS44868.2	12q13.1	2008-02-05	2005-08-17			ENSG00000079387			17927	protein-coding gene	gene with protein product		612157	"""SUMO1/sentrin specific protease 1"""			10652325, 14563852	Standard	NM_001267595		Approved		uc009zkx.4	Q9P0U3	OTTHUMG00000169896	ENST00000004980.5:c.504T>C	12.37:g.48477422A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_001267594	A8K7P5|Q86XC8	Silent	SNP	ENST00000004980.5	37	CCDS44868.2																																																																																			A|0.817;G|0.183	0.183	strong		0.408	SENP1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406471.1	NM_014554	
ABCA7	10347	hgsc.bcm.edu	37	19	1049269	1049269	+	Silent	SNP	G	G	A	rs4147914	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1049269G>A	ENST00000263094.6	+	18	2616	c.2385G>A	c.(2383-2385)ctG>ctA	p.L795L	ABCA7_ENST00000435683.2_Silent_p.L657L|ABCA7_ENST00000433129.1_Silent_p.L795L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	795					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)		CTGCAGTGCTGGTAGAAGAGG	0.677													G|||	1205	0.240615	0.1762	0.1182	5008	,	,		10336	0.3938		0.166	False		,,,				2504	0.3333				p.L795L		Atlas-SNP	.											ABCA7,NS,carcinoma,0,1	ABCA7	174	1	0			c.G2385A						PASS	.	G		748,3656	284.9+/-277.9	59,630,1513	52.0	61.0	58.0		2385	2.4	0.7	19	dbSNP_110	58	1238,7350	235.3+/-267.9	94,1050,3150	no	coding-synonymous	ABCA7	NM_019112.3		153,1680,4663	AA,AG,GG		14.4155,16.9846,15.2863		795/2147	1049269	1986,11006	2202	4294	6496	SO:0001819	synonymous_variant	10347	exon18			AGTGCTGGTAGAA	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.2385G>A	19.37:g.1049269G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	167	74	0.443114	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			G|0.831;A|0.169	0.169	strong		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
MBP	4155	hgsc.bcm.edu	37	18	74728823	74728823	+	Missense_Mutation	SNP	C	C	T	rs61742988	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:74728823C>T	ENST00000397869.3	-	1	188	c.142G>A	c.(142-144)Ggt>Agt	p.G48S	MBP_ENST00000487778.1_5'Flank|MBP_ENST00000527041.1_Missense_Mutation_p.G48S|MBP_ENST00000359645.3_Missense_Mutation_p.G48S|MBP_ENST00000354542.4_Missense_Mutation_p.G48S|MBP_ENST00000397860.3_Missense_Mutation_p.G181S|MBP_ENST00000580402.1_Missense_Mutation_p.G181S|MBP_ENST00000578193.1_Missense_Mutation_p.G48S|MBP_ENST00000382582.3_Missense_Mutation_p.G48S|MBP_ENST00000355994.2_Missense_Mutation_p.G181S|MBP_ENST00000397866.4_Missense_Mutation_p.G48S|MBP_ENST00000528160.1_Intron|MBP_ENST00000397865.5_Missense_Mutation_p.G48S|MBP_ENST00000397875.3_Missense_Mutation_p.G48S|MBP_ENST00000526111.1_Missense_Mutation_p.G26S|MBP_ENST00000579129.1_Missense_Mutation_p.G181S|MBP_ENST00000397863.1_Missense_Mutation_p.G181S			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	CCCCTGTCACCGCCAAAGAAG	0.557													C|||	134	0.0267572	0.0182	0.0058	5008	,	,		18628	0.0188		0.0229	False		,,,				2504	0.0654				p.G181S	NSCLC(17;72 1131 19392)	Atlas-SNP	.											.	MBP	45	.	0			c.G541A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	72,4334	62.9+/-100.1	0,72,2131	59.0	57.0	58.0		142,142,142,541,541,142	1.4	0.0	18	dbSNP_129	58	222,8378	92.8+/-154.8	1,220,4079	yes	missense,missense,missense,missense,missense,missense	MBP	NM_001025081.1,NM_001025090.1,NM_001025092.1,NM_001025100.1,NM_001025101.1,NM_002385.2	56,56,56,56,56,56	1,292,6210	TT,TC,CC		2.5814,1.6341,2.2605	benign,benign,benign,benign,benign,benign	48/198,48/172,48/161,181/198,181/305,48/187	74728823	294,12712	2203	4300	6503	SO:0001583	missense	4155	exon4			TGTCACCGCCAAA		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.142G>A	18.37:g.74728823C>T	ENSP00000380967:p.Gly48Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_001025100	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Missense_Mutation	SNP	ENST00000397869.3	37		38	0.0173992673992674	15	0.03048780487804878	1	0.0027624309392265192	5	0.008741258741258742	17	0.022427440633245383	C	15.47	2.842476	0.51057	0.016341	0.025814	ENSG00000197971	ENST00000382582;ENST00000355994;ENST00000397875;ENST00000397866;ENST00000397865;ENST00000527041;ENST00000359645;ENST00000397869;ENST00000354542;ENST00000526111;ENST00000397868;ENST00000498683;ENST00000397863;ENST00000397860	.	.	.	5.22	1.38	0.22167	.	0.259390	0.37669	N	0.001984	T	0.30448	0.0765	M	0.67397	2.05	0.37006	D	0.895489	D;P;B;B;B;B	0.62365	0.991;0.491;0.105;0.011;0.037;0.037	P;B;B;B;B;B	0.52189	0.692;0.126;0.016;0.009;0.03;0.036	T	0.48281	-0.9049	9	0.46703	T	0.11	-6.3446	6.7392	0.23426	0.1249:0.6711:0.0:0.204	rs61742988	48;181;181;48;48;48	B7Z3Y6;P02686;P02686-2;P02686-6;P02686-4;P02686-3	.;MBP_HUMAN;.;.;.;.	S	48;181;48;48;48;48;48;48;48;26;48;48;181;181	.	ENSP00000346545:G48S	G	-	1	0	MBP	72857811	1.000000	0.71417	0.047000	0.18901	0.953000	0.61014	2.646000	0.46630	-0.032000	0.13758	-0.150000	0.13652	GGT	C|0.979;T|0.021	0.021	strong		0.557	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081	
ABCA13	154664	hgsc.bcm.edu	37	7	48317708	48317708	+	Missense_Mutation	SNP	A	A	C	rs78334925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48317708A>C	ENST00000435803.1	+	18	6941	c.6917A>C	c.(6916-6918)aAa>aCa	p.K2306T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2306					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						CCAAAAGATAAAATTCTAGAA	0.234													A|||	487	0.0972444	0.1452	0.0548	5008	,	,		10236	0.1508		0.0487	False		,,,				2504	0.0573				p.K2306T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A6917C						PASS	.	A	THR/LYS	352,3094		19,314,1390	11.0	10.0	11.0		6917	3.7	0.5	7	dbSNP_131	11	426,7404		15,396,3504	yes	missense	ABCA13	NM_152701.3	78	34,710,4894	CC,CA,AA		5.4406,10.2147,6.8996	probably-damaging	2306/5059	48317708	778,10498	1723	3915	5638	SO:0001583	missense	154664	exon18			AAGATAAAATTCT	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.6917A>C	7.37:g.48317708A>C	ENSP00000411096:p.Lys2306Thr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	34	29	0.852941	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	242	0.1108058608058608	81	0.16463414634146342	25	0.06906077348066299	97	0.16958041958041958	39	0.051451187335092345	A	12.75	2.032480	0.35893	0.102147	0.054406	ENSG00000179869	ENST00000435803	T	0.60040	0.22	4.88	3.68	0.42216	.	0.000000	0.52532	D	0.000070	T	0.00210	0.0006	M	0.61703	1.905	0.09310	P	0.9999999402452	B	0.27997	0.197	B	0.28638	0.092	T	0.11446	-1.0587	9	0.87932	D	0	.	8.7131	0.34395	0.8074:0.1926:0.0:0.0	.	2306	Q86UQ4	ABCAD_HUMAN	T	2306	ENSP00000411096:K2306T	ENSP00000411096:K2306T	K	+	2	0	ABCA13	48288254	0.970000	0.33590	0.509000	0.27700	0.979000	0.70002	1.860000	0.39428	0.781000	0.33589	0.528000	0.53228	AAA	A|0.900;C|0.100	0.100	strong		0.234	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
MED11	400569	hgsc.bcm.edu	37	17	4638484	4638484	+	IGR	SNP	T	T	C	rs1876444	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4638484T>C	ENST00000293777.5	+	0	833				CXCL16_ENST00000293778.6_Silent_p.P226P|CXCL16_ENST00000576153.1_5'UTR|CXCL16_ENST00000574412.1_Silent_p.P226P|RP11-314A20.5_ENST00000570493.2_RNA	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.P226P(1)		lung(2)|ovary(2)	4						GGCACAGGACTGGCACTGTGG	0.612													C|||	2658	0.530751	0.3555	0.5764	5008	,	,		19019	0.5933		0.5765	False		,,,				2504	0.6237				p.P226P		Atlas-SNP	.											CXCL16_ENST00000293778,NS,carcinoma,0,1	CXCL16	30	1	1	Substitution - coding silent(1)	stomach(1)	c.A678G						PASS	.	C	,	1717,2689	650.6+/-399.1	336,1045,822	64.0	55.0	58.0		678,678	-11.2	0.0	17	dbSNP_92	58	4866,3734	532.8+/-382.3	1366,2134,800	no	coding-synonymous,coding-synonymous	CXCL16	NM_001100812.1,NM_022059.2	,	1702,3179,1622	CC,CT,TT		43.4186,38.9696,49.3849	,	226/274,226/274	4638484	6583,6423	2203	4300	6503	SO:0001628	intergenic_variant	58191	exon4			CAGGACTGGCACT	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086			17.37:g.4638484T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	89	49	0.550562	NM_022059	Q6NS89	Silent	SNP	ENST00000293777.5	37	CCDS32533.1																																																																																			T|0.485;C|0.515	0.515	strong		0.612	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
TSHZ2	128553	hgsc.bcm.edu	37	20	51870336	51870336	+	Missense_Mutation	SNP	G	G	C	rs739869	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:51870336G>C	ENST00000371497.5	+	2	1226	c.339G>C	c.(337-339)agG>agC	p.R113S	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R110S|TSHZ2_ENST00000603338.2_Missense_Mutation_p.R110S	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	113			R -> S (in dbSNP:rs739869). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		multicellular organismal development (GO:0007275)|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(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CTCACGTCAGGCTTCCAAACG	0.532													G|||	264	0.0527157	0.0514	0.0591	5008	,	,		22214	0.0		0.1262	False		,,,				2504	0.0286				p.R113S		Atlas-SNP	.											.	TSHZ2	209	.	0			c.G339C						PASS	.	G	SER/ARG,SER/ARG	258,4148	148.0+/-182.4	5,248,1950	83.0	72.0	75.0		330,339	1.1	0.4	20	dbSNP_86	75	1023,7577	219.9+/-257.8	63,897,3340	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	110,110	68,1145,5290	CC,CG,GG		11.8953,5.8557,9.8493	benign,benign	110/1032,113/1035	51870336	1281,11725	2203	4300	6503	SO:0001583	missense	128553	exon2			CGTCAGGCTTCCA	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.339G>C	20.37:g.51870336G>C	ENSP00000360552:p.Arg113Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	135	0.061813186813186816	20	0.04065040650406504	26	0.0718232044198895	0	0.0	89	0.11741424802110818	G	0.268	-0.994872	0.02145	0.058557	0.118953	ENSG00000182463	ENST00000371497;ENST00000329613	T;T	0.12774	2.65;2.65	5.7	1.09	0.20402	.	0.141334	0.64402	D	0.000008	T	0.00109	0.0003	N	0.14661	0.345	0.53005	P	3.6999999999953737E-5	B	0.12630	0.006	B	0.14023	0.01	T	0.38564	-0.9655	9	0.23302	T	0.38	-30.2724	7.7223	0.28740	0.5865:0.0:0.4135:0.0	rs739869;rs52792789;rs739869	113	Q9NRE2	TSH2_HUMAN	S	113;110	ENSP00000360552:R113S;ENSP00000333114:R110S	ENSP00000333114:R110S	R	+	3	2	TSHZ2	51303743	0.899000	0.30636	0.370000	0.25965	0.020000	0.10135	0.479000	0.22228	0.285000	0.22329	0.643000	0.83706	AGG	G|0.921;C|0.079	0.079	strong		0.532	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
TBX1	6899	hgsc.bcm.edu	37	22	19766782	19766782	+	Missense_Mutation	SNP	C	C	T	rs4819522	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:19766782C>T	ENST00000329705.7	+	9	1178	c.1049C>T	c.(1048-1050)aCg>aTg	p.T350M	TBX1_ENST00000359500.3_Intron	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	350			T -> M (in dbSNP:rs4819522).		angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				AAAGCTGAGACGTCTAGGAAC	0.547													C|||	1048	0.209265	0.1551	0.255	5008	,	,		19033	0.119		0.169	False		,,,				2504	0.3845				p.T350M		Atlas-SNP	.											TBX1_ENST00000329705,colon,carcinoma,0,1	TBX1	62	1	0			c.C1049T						PASS	.	C	,MET/THR	666,3740	284.0+/-277.4	61,544,1598	93.0	78.0	83.0		,1049	-3.4	0.0	22	dbSNP_111	83	1577,7023	295.1+/-302.2	155,1267,2878	yes	intron,missense	TBX1	NM_005992.1,NM_080646.1	,81	216,1811,4476	TT,TC,CC		18.3372,15.1158,17.2459	,	,350/399	19766782	2243,10763	2203	4300	6503	SO:0001583	missense	6899	exon9			CTGAGACGTCTAG	AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"""T-boxes"""	11592	protein-coding gene	gene with protein product		602054	"""velocardiofacial syndrome"""	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.1049C>T	22.37:g.19766782C>T	ENSP00000331176:p.Thr350Met	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_080646	C6G493|C6G494|O43436|Q96RJ2	Missense_Mutation	SNP	ENST00000329705.7	37	CCDS13766.1	368	0.1684981684981685	90	0.18292682926829268	83	0.2292817679558011	68	0.11888111888111888	127	0.16754617414248021	C	12.48	1.950373	0.34377	0.151158	0.183372	ENSG00000184058	ENST00000329705	D	0.86956	-2.19	1.69	-3.37	0.04898	.	.	.	.	.	T	0.00109	0.0003	N	0.19112	0.55	0.80722	P	0.0	D	0.69078	0.997	P	0.53861	0.736	T	0.17410	-1.0370	8	0.44086	T	0.13	.	3.5111	0.07708	0.0:0.2533:0.4805:0.2661	rs4819522;rs59530459;rs4819522	350	O43435	TBX1_HUMAN	M	350	ENSP00000331176:T350M	ENSP00000331176:T350M	T	+	2	0	TBX1	18146782	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.716000	0.04991	-0.727000	0.04888	0.555000	0.69702	ACG	C|0.829;T|0.171	0.171	strong		0.547	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647	
MYO3A	53904	hgsc.bcm.edu	37	10	26463130	26463130	+	Missense_Mutation	SNP	C	C	A	rs1999240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:26463130C>A	ENST00000265944.5	+	30	4103	c.3937C>A	c.(3937-3939)Cgt>Agt	p.R1313S	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1313			R -> S (in dbSNP:rs1999240). {ECO:0000269|PubMed:10936054, ECO:0000269|PubMed:12032315, ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AGTTACCCAGCGTGCACCGAT	0.458													A|||	3010	0.601038	0.5545	0.634	5008	,	,		21700	0.6329		0.6004	False		,,,				2504	0.6084				p.R1313S		Atlas-SNP	.											MYO3A,colon,carcinoma,-1,1	MYO3A	371	1	0			c.C3937A						PASS	.	A	SER/ARG	2403,2003	559.9+/-380.3	658,1087,458	115.0	122.0	120.0		3937	4.1	0.6	10	dbSNP_92	120	4916,3684	527.3+/-381.1	1417,2082,801	yes	missense	MYO3A	NM_017433.4	110	2075,3169,1259	AA,AC,CC		42.8372,45.4607,43.726	benign	1313/1617	26463130	7319,5687	2203	4300	6503	SO:0001583	missense	53904	exon30			ACCCAGCGTGCAC	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3937C>A	10.37:g.26463130C>A	ENSP00000265944:p.Arg1313Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	1348	0.6172161172161172	286	0.5813008130081301	216	0.5966850828729282	385	0.6730769230769231	461	0.6081794195250659	A	0.007	-1.940455	0.00479	0.545393	0.571628	ENSG00000095777	ENST00000265944	T	0.78246	-1.16	5.22	4.07	0.47477	.	0.302191	0.40302	N	0.001124	T	0.00012	0.0000	N	0.08118	0	0.21553	P	0.999643656	B	0.02656	0.0	B	0.01281	0.0	T	0.46247	-0.9205	9	0.08837	T	0.75	.	8.6585	0.34077	0.4916:0.393:0.0:0.1154	rs1999240;rs3740230;rs17667000;rs52822170;rs57559611;rs1999240	1313	Q8NEV4	MYO3A_HUMAN	S	1313	ENSP00000265944:R1313S	ENSP00000265944:R1313S	R	+	1	0	MYO3A	26503136	0.993000	0.37304	0.583000	0.28640	0.147000	0.21601	3.235000	0.51328	0.300000	0.22699	-0.362000	0.07510	CGT	C|0.401;A|0.599	0.599	strong		0.458	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
CDH22	64405	hgsc.bcm.edu	37	20	44806727	44806727	+	Silent	SNP	G	G	A	rs35585191	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44806727G>A	ENST00000372262.3	-	10	2173	c.1773C>T	c.(1771-1773)agC>agT	p.S591S	CDH22_ENST00000537909.1_Silent_p.S591S	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	591	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(3)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	44		Myeloproliferative disorder(115;0.0122)				GCGTGCCTGTGCTGCTCAGTG	0.652													G|||	285	0.0569089	0.034	0.0764	5008	,	,		16965	0.0129		0.1024	False		,,,				2504	0.0726				p.S591S		Atlas-SNP	.											.	CDH22	112	.	0			c.C1773T						PASS	.	G		238,4168	138.4+/-174.2	6,226,1971	102.0	72.0	82.0		1773	1.3	1.0	20	dbSNP_126	82	1070,7530	224.7+/-261.0	72,926,3302	no	coding-synonymous	CDH22	NM_021248.1		78,1152,5273	AA,AG,GG		12.4419,5.4017,10.0569		591/829	44806727	1308,11698	2203	4300	6503	SO:0001819	synonymous_variant	64405	exon11			GCCTGTGCTGCTC	AF035300	CCDS13395.1	20q13.1	2010-01-26	2009-11-20		ENSG00000149654	ENSG00000149654		"""Cadherins / Major cadherins"""	13251	protein-coding gene	gene with protein product		609920	"""cadherin-like 22"""	C20orf25		8626716	Standard	NM_021248		Approved	dJ998H6.1	uc010ghk.2	Q9UJ99	OTTHUMG00000033073	ENST00000372262.3:c.1773C>T	20.37:g.44806727G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	124	53	0.427419	NM_021248	B9EGK7|O43205	Silent	SNP	ENST00000372262.3	37	CCDS13395.1																																																																																			G|0.914;A|0.086	0.086	strong		0.652	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248	
CACNA1F	778	hgsc.bcm.edu	37	X	49071964	49071964	+	Silent	SNP	A	A	G	rs2075866	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49071964A>G	ENST00000376265.2	-	28	3370	c.3309T>C	c.(3307-3309)caT>caC	p.H1103H	CACNA1F_ENST00000323022.5_Silent_p.H1092H|CACNA1F_ENST00000376251.1_Silent_p.H1038H	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1103	Dihydropyridine binding. {ECO:0000250}.				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)	AGATGGGGCCATGGTCCTCTG	0.522													g|||	2084	0.552053	0.6278	0.4481	3775	,	,		9881	0.5179		0.2097	False		,,,				2504	0.2147				p.H1103H		Atlas-SNP	.											.	CACNA1F	218	.	0			c.T3309C						PASS	.			2842,993		912,603,415,117,156	99.0	80.0	86.0		3309	-0.1	0.0	X	dbSNP_96	86	1971,4757		217,988,549,1223,1323	no	coding-synonymous	CACNA1F	NM_005183.2		1129,1591,964,1340,1479	GG,GA,G,AA,A		29.2955,25.8931,45.5647		1103/1978	49071964	4813,5750	2203	4300	6503	SO:0001819	synonymous_variant	778	exon28			GGGGCCATGGTCC	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.3309T>C	X.37:g.49071964A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	96	21	0.21875	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	37	CCDS35253.1																																																																																			0|0.014;T|0.004	.	strong		0.522	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
TPST2	8459	hgsc.bcm.edu	37	22	26936897	26936897	+	Silent	SNP	G	G	A	rs12169509	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:26936897G>A	ENST00000338754.4	-	3	970	c.700C>T	c.(700-702)Ctg>Ttg	p.L234L	TPST2_ENST00000403880.1_Silent_p.L234L|TPST2_ENST00000398110.2_Silent_p.L234L	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	234					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						TACACAGGCAGGCACTTCTCC	0.607													G|||	515	0.102835	0.1059	0.1081	5008	,	,		20781	0.003		0.2386	False		,,,				2504	0.0583				p.L234L		Atlas-SNP	.											.	TPST2	23	.	0			c.C700T						PASS	.	G	,	477,3929	226.2+/-241.8	22,433,1748	92.0	76.0	81.0		700,700	2.5	1.0	22	dbSNP_120	81	1951,6649	344.1+/-325.2	213,1525,2562	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	235,1958,4310	AA,AG,GG		22.686,10.8261,18.6683	,	234/378,234/378	26936897	2428,10578	2203	4300	6503	SO:0001819	synonymous_variant	8459	exon3			CAGGCAGGCACTT	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12021	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog B (Drosophila)"""	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.700C>T	22.37:g.26936897G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			G|0.823;A|0.177	0.177	strong		0.607	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
TLR1	7096	hgsc.bcm.edu	37	4	38799710	38799710	+	Missense_Mutation	SNP	T	T	C	rs4833095	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38799710T>C	ENST00000502213.2	-	3	972	c.743A>G	c.(742-744)aAt>aGt	p.N248S	TLR1_ENST00000308979.2_Missense_Mutation_p.N248S			Q15399	TLR1_HUMAN	toll-like receptor 1	248			N -> S (may confer susceptibility to leprosy; dbSNP:rs4833095). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21618349, ECO:0000269|PubMed:9435236}.		cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TAAGGTAAGATTTGATAACTT	0.333													C|||	2878	0.574681	0.8797	0.4726	5008	,	,		21271	0.5992		0.2803	False		,,,				2504	0.5123				p.N248S	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.A743G						PASS	.	C	SER/ASN	3424,982	331.5+/-302.0	1332,760,111	60.0	66.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743	-3.2	0.0	4	dbSNP_111	64	2141,6457	702.3+/-405.3	278,1585,2436	yes	missense	TLR1	NM_003263.3	46	1610,2345,2547	CC,CT,TT		24.9011,22.2878,42.7945	benign	248/787	38799710	5565,7439	2203	4299	6502	SO:0001583	missense	7096	exon4			GTAAGATTTGATA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.743A>G	4.37:g.38799710T>C	ENSP00000421259:p.Asn248Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Missense_Mutation	SNP	ENST00000502213.2	37	CCDS33973.1	1156	0.5293040293040293	436	0.8861788617886179	160	0.4419889502762431	377	0.6590909090909091	183	0.24142480211081793	C	1.852	-0.464903	0.04476	0.777122	0.249011	ENSG00000174125	ENST00000308979;ENST00000502213	T;T	0.29917	1.55;1.55	4.69	-3.18	0.05186	.	0.539821	0.18243	N	0.147178	T	0.00012	0.0000	L	0.31207	0.915	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.20739	-1.0266	9	0.30078	T	0.28	.	11.4828	0.50335	0.0:0.3819:0.0:0.6181	rs4833095;rs58946512;rs4833095	248	Q15399	TLR1_HUMAN	S	248	ENSP00000354932:N248S;ENSP00000421259:N248S	ENSP00000354932:N248S	N	-	2	0	TLR1	38476105	0.001000	0.12720	0.013000	0.15412	0.001000	0.01503	-0.228000	0.09114	-1.061000	0.03185	-1.073000	0.02249	AAT	T|0.512;C|0.488	0.488	strong		0.333	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
ATL1	51062	hgsc.bcm.edu	37	14	51054598	51054598	+	Silent	SNP	A	A	G	rs35014209	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:51054598A>G	ENST00000358385.6	+	2	325	c.84A>G	c.(82-84)ccA>ccG	p.P28P	ATL1_ENST00000354525.4_Silent_p.P28P|ATL1_ENST00000441560.2_Silent_p.P28P|ATL1_ENST00000556478.2_3'UTR|ATL1_ENST00000357032.3_Silent_p.P28P	NM_015915.4	NP_056999.2	Q8WXF7	ATLA1_HUMAN	atlastin GTPase 1	28					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(3)	18						AGGAGGAGCCAGTGAAAAAGG	0.453													A|||	822	0.164137	0.3623	0.1225	5008	,	,		20809	0.0655		0.1282	False		,,,				2504	0.0644				p.P28P		Atlas-SNP	.											.	ATL1	46	.	0			c.A84G						PASS	.	A	,,	1384,3022	456.1+/-351.2	209,966,1028	109.0	105.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	84,84,84	-1.2	1.0	14	dbSNP_126	107	1236,7364	247.4+/-275.4	96,1044,3160	no	coding-synonymous,coding-synonymous,coding-synonymous	ATL1	NM_001127713.1,NM_015915.4,NM_181598.3	,,	305,2010,4188	GG,GA,AA		14.3721,31.4117,20.1445	,,	28/554,28/559,28/554	51054598	2620,10386	2203	4300	6503	SO:0001819	synonymous_variant	51062	exon2			GGAGCCAGTGAAA	AF131801	CCDS9700.1, CCDS32077.1	14q21.3	2014-09-17	2008-09-17	2008-09-17	ENSG00000198513	ENSG00000198513			11231	protein-coding gene	gene with protein product	"""atlastin"""	606439	"""spastic paraplegia 3A (autosomal dominant)"""	SPG3, SPG3A		8252041, 7825576	Standard	NM_015915		Approved	FSP1, AD-FSP	uc001wyd.4	Q8WXF7	OTTHUMG00000140297	ENST00000358385.6:c.84A>G	14.37:g.51054598A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_015915	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000358385.6	37	CCDS9700.1																																																																																			A|0.807;G|0.193	0.193	strong		0.453	ATL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276884.2		
TACC1	6867	hgsc.bcm.edu	37	8	38677932	38677932	+	Silent	SNP	A	A	G	rs2013586	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:38677932A>G	ENST00000317827.4	+	3	1549	c.1170A>G	c.(1168-1170)gaA>gaG	p.E390E	TACC1_ENST00000520615.1_Silent_p.E195E|TACC1_ENST00000379931.3_Silent_p.E390E|TACC1_ENST00000330691.6_Intron|TACC1_ENST00000520611.1_5'Flank|TACC1_ENST00000519416.1_Silent_p.E195E|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000443286.2_Silent_p.E406E|TACC1_ENST00000520973.1_Silent_p.E195E|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000520340.1_Silent_p.E354E|TACC1_ENST00000518415.1_Silent_p.E345E	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	390	Interaction with YEATS4.|SPAZ 2.				cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.E390E(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			GTCAGTGGGAAAGCCCCAGCT	0.547													A|||	1257	0.250998	0.112	0.2594	5008	,	,		17274	0.2688		0.3887	False		,,,				2504	0.273				p.E390E		Atlas-SNP	.											TACC1_ENST00000317827,NS,carcinoma,0,1	TACC1	98	1	1	Substitution - coding silent(1)	stomach(1)	c.A1170G						PASS	.	A	,,	690,3716	288.9+/-280.1	39,612,1552	112.0	114.0	113.0		,585,1170	-7.8	0.0	8	dbSNP_92	113	3562,5038	517.0+/-379.0	754,2054,1492	no	intron,coding-synonymous,coding-synonymous	TACC1	NM_001122824.1,NM_001146216.2,NM_006283.2	,,	793,2666,3044	GG,GA,AA		41.4186,15.6605,32.6926	,,	,195/611,390/806	38677932	4252,8754	2203	4300	6503	SO:0001819	synonymous_variant	6867	exon3			GTGGGAAAGCCCC	AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526			11522	protein-coding gene	gene with protein product		605301					Standard	NM_006283		Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.1170A>G	8.37:g.38677932A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	93	51	0.548387	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Silent	SNP	ENST00000317827.4	37	CCDS6109.1	608	0.2783882783882784	59	0.11991869918699187	94	0.2596685082872928	154	0.2692307692307692	301	0.3970976253298153	A	5.770	0.326458	0.10900	0.156605	0.414186	ENSG00000147526	ENST00000521866;ENST00000518809	.	.	.	5.4	-7.82	0.01205	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.47341	P	6.059999999999954E-4	.	.	.	.	.	.	T	0.34030	-0.9845	3	.	.	.	0.0051	5.4787	0.16710	0.1022:0.4703:0.1079:0.3196	rs2013586;rs3739249;rs17514141;rs17854120;rs58803062;rs2013586	.	.	.	R	165;28	.	.	K	+	2	0	TACC1	38797089	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.316000	0.02710	-1.870000	0.01139	-0.890000	0.02929	AAA	A|0.696;G|0.304	0.304	strong		0.547	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283	
NEU4	129807	hgsc.bcm.edu	37	2	242758326	242758326	+	Silent	SNP	G	G	A	rs2293761	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242758326G>A	ENST00000391969.2	+	5	2118	c.1407G>A	c.(1405-1407)aaG>aaA	p.K469K	NEU4_ENST00000405370.1_Silent_p.K469K|NEU4_ENST00000404257.1_Silent_p.K481K|NEU4_ENST00000325935.6_Silent_p.K482K|NEU4_ENST00000407683.1_Silent_p.K469K	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	469					ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		CCAGCCCCAAGCCGCCCAACC	0.657													G|||	2224	0.444089	0.4864	0.3458	5008	,	,		12711	0.4216		0.3847	False		,,,				2504	0.5409				p.K482K		Atlas-SNP	.											NEU4,rectum,carcinoma,0,1	NEU4	39	1	0			c.G1446A						scavenged	.		,,,,	1448,1946		319,810,568	12.0	14.0	13.0		1446,1407,1407,1407,1443	3.7	0.0	2	dbSNP_100	13	2170,4686		383,1404,1641	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	,,,,	702,2214,2209	AA,AG,GG		31.6511,42.6635,35.2976	,,,,	482/498,469/485,469/485,469/485,481/497	242758326	3618,6632	1697	3428	5125	SO:0001819	synonymous_variant	129807	exon4			CCCCAAGCCGCCC	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.1407G>A	2.37:g.242758326G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	31	8	0.258065	NM_001167599	A8K056|J3KNJ5|Q96D64	Silent	SNP	ENST00000391969.2	37	CCDS54442.1																																																																																			G|0.618;A|0.382	0.382	strong		0.657	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
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 GAIIx	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	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	270	153	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	
CAPN12	147968	hgsc.bcm.edu	37	19	39228244	39228244	+	Missense_Mutation	SNP	T	T	C	rs73038948	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39228244T>C	ENST00000328867.4	-	9	1308	c.1000A>G	c.(1000-1002)Acc>Gcc	p.T334A	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Missense_Mutation_p.T185A	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	334	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			ATCTGCACGGTGTCGAAATGG	0.692													T|||	578	0.115415	0.0688	0.1556	5008	,	,		11196	0.0089		0.2266	False		,,,				2504	0.1452				p.T334A		Atlas-SNP	.											CAPN12,NS,carcinoma,0,1	CAPN12	43	1	0			c.A1000G						PASS	.	T	ALA/THR	377,4021		20,337,1842	27.0	29.0	29.0		1000	3.9	0.9	19	dbSNP_131	29	1569,7013		147,1275,2869	yes	missense	CAPN12	NM_144691.3	58	167,1612,4711	CC,CT,TT		18.2825,8.5721,14.9923	possibly-damaging	334/720	39228244	1946,11034	2199	4291	6490	SO:0001583	missense	147968	exon9			GCACGGTGTCGAA	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1000A>G	19.37:g.39228244T>C	ENSP00000331636:p.Thr334Ala	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_144691		Missense_Mutation	SNP	ENST00000328867.4	37	CCDS12519.1	267	0.12225274725274725	37	0.07520325203252033	63	0.17403314917127072	1	0.0017482517482517483	166	0.21899736147757257	T	21.2	4.120996	0.77436	0.085721	0.182825	ENSG00000182472	ENST00000328867	D	0.87103	-2.21	3.9	3.9	0.45041	Peptidase C2, calpain, catalytic domain (3);	0.385817	0.26286	N	0.025250	T	0.00271	0.0008	L	0.43646	1.37	0.32387	P	0.553802	P	0.52463	0.953	P	0.54759	0.76	T	0.02837	-1.1104	9	0.62326	D	0.03	.	10.9882	0.47534	0.0:0.0:0.0:1.0	.	334	Q6ZSI9	CAN12_HUMAN	A	334	ENSP00000331636:T334A	ENSP00000331636:T334A	T	-	1	0	CAPN12	43920084	0.121000	0.22262	0.873000	0.34254	0.862000	0.49288	0.567000	0.23608	1.766000	0.52107	0.454000	0.30748	ACC	T|0.867;C|0.133	0.133	strong		0.692	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
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 GAIIx	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	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	36	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	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20905250	20905250	+	Silent	SNP	C	C	T	rs6487138	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:20905250C>T	ENST00000266509.2	+	15	2295	c.1927C>T	c.(1927-1929)Ctg>Ttg	p.L643L	SLCO1C1_ENST00000545604.1_Missense_Mutation_p.S677F|SLCO1C1_ENST00000540354.1_Silent_p.L594L|SLCO1C1_ENST00000545102.1_Missense_Mutation_p.S559F|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.S677F	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	643					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	ACATATATATCTGGGACTAAC	0.299													C|||	2351	0.469449	0.2012	0.5677	5008	,	,		17354	0.5923		0.495	False		,,,				2504	0.6094				p.S677F		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C2030T						PASS	.	C	PHE/SER,,PHE/SER,	1092,3312	370.3+/-319.5	138,816,1248	41.0	41.0	41.0		1676,1780,2030,1927	5.4	1.0	12	dbSNP_116	41	4649,3947	591.6+/-392.9	1248,2153,897	yes	missense,coding-synonymous,missense,coding-synonymous	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	155,,155,	1386,2969,2145	TT,TC,CC		45.9167,24.7956,44.1615	,,,	559/613,594/664,677/731,643/713	20905250	5741,7259	2202	4298	6500	SO:0001819	synonymous_variant	53919	exon16			ATATATCTGGGAC	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1927C>T	12.37:g.20905250C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	126	51	0.404762	NM_001145946	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	1046	0.47893772893772896	110	0.22357723577235772	192	0.5303867403314917	358	0.6258741258741258	386	0.5092348284960422	C	16.43	3.120305	0.56613	0.247956	0.540833	ENSG00000139155	ENST00000545604;ENST00000381552;ENST00000545102	T;T;T	0.39997	1.05;1.05;1.11	5.37	5.37	0.77165	.	2.483440	0.01020	N	0.003979	T	0.00012	0.0000	.	.	.	0.31879	P	0.618765	P;P	0.51537	0.946;0.91	P;P	0.55999	0.789;0.498	T	0.46275	-0.9203	8	0.59425	D	0.04	.	16.1483	0.81586	0.0:1.0:0.0:0.0	rs6487138	559;677	F5GZD6;Q5JPA4	.;.	F	677;677;559	ENSP00000444149:S677F;ENSP00000370964:S677F;ENSP00000444527:S559F	ENSP00000370964:S677F	S	+	2	0	SLCO1C1	20796517	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.654000	0.46699	2.797000	0.96272	0.655000	0.94253	TCT	C|0.547;T|0.453	0.453	strong		0.299	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
XRRA1	143570	hgsc.bcm.edu	37	11	74559481	74559481	+	Silent	SNP	C	C	T	rs4944961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:74559481C>T	ENST00000340360.6	-	15	1714	c.1383G>A	c.(1381-1383)ccG>ccA	p.P461P	XRRA1_ENST00000527087.1_Silent_p.P374P|RN7SL239P_ENST00000490061.2_RNA|XRRA1_ENST00000321448.8_Silent_p.P186P	NM_182969.2	NP_892014.1			X-ray radiation resistance associated 1											breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(3)	20						GAGGCTGCTTCGGCACCTTTG	0.532													C|||	1400	0.279553	0.0946	0.4957	5008	,	,		19444	0.5089		0.3181	False		,,,				2504	0.1002				p.P461P		Atlas-SNP	.											.	XRRA1	46	.	0			c.G1383A						PASS	.	C		538,3472		48,442,1515	44.0	46.0	45.0		1383	-4.9	1.0	11	dbSNP_111	45	2506,5822		377,1752,2035	no	coding-synonymous	XRRA1	NM_182969.1		425,2194,3550	TT,TC,CC		30.0913,13.4165,24.6717		461/793	74559481	3044,9294	2005	4164	6169	SO:0001819	synonymous_variant	143570	exon15			CTGCTTCGGCACC	AK074152	CCDS44680.1, CCDS58159.1, CCDS58160.1	11q13.4	2010-03-19			ENSG00000166435	ENSG00000166435			18868	protein-coding gene	gene with protein product		609788				12908878, 17295261	Standard	NM_182969		Approved	FLJ00225	uc009yub.3	Q6P2D8		ENST00000340360.6:c.1383G>A	11.37:g.74559481C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_182969		Silent	SNP	ENST00000340360.6	37	CCDS44680.1																																																																																			C|0.687;T|0.313	0.313	strong		0.532	XRRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384715.1	NM_182969	
KCNH5	27133	hgsc.bcm.edu	37	14	63174960	63174960	+	Missense_Mutation	SNP	C	C	T	rs4902176	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:63174960C>T	ENST00000322893.7	-	11	2501	c.2233G>A	c.(2233-2235)Gcc>Acc	p.A745T	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	745			A -> T (in dbSNP:rs4902176). {ECO:0000269|PubMed:11943152, ECO:0000269|PubMed:12135768, ECO:0000269|PubMed:15489334}.		potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		GTGATGGAGGCTCCATTCTGT	0.527													c|||	1108	0.221246	0.1936	0.2997	5008	,	,		18594	0.1478		0.3479	False		,,,				2504	0.1483				p.A745T		Atlas-SNP	.											.	KCNH5	320	.	0			c.G2233A						PASS	.	C	THR/ALA,	906,3500	350.0+/-310.6	98,710,1395	107.0	95.0	99.0		2233,	5.5	1.0	14	dbSNP_111	99	2985,5615	462.4+/-365.7	517,1951,1832	yes	missense,utr-3	KCNH5	NM_139318.3,NM_172375.1	58,	615,2661,3227	TT,TC,CC		34.7093,20.5629,29.917	benign,	745/989,	63174960	3891,9115	2203	4300	6503	SO:0001583	missense	27133	exon11			TGGAGGCTCCATT	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.2233G>A	14.37:g.63174960C>T	ENSP00000321427:p.Ala745Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	69	0.547619	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	552	0.25274725274725274	97	0.19715447154471544	120	0.3314917127071823	87	0.1520979020979021	248	0.32717678100263853	C	2.888	-0.230279	0.05983	0.205629	0.347093	ENSG00000140015	ENST00000322893	D	0.98901	-5.22	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	1.0	B	0.16396	0.017	B	0.08055	0.003	T	0.47824	-0.9087	9	0.13470	T	0.59	.	19.4558	0.94889	0.0:1.0:0.0:0.0	rs4902176;rs17256625;rs52818800;rs58489583;rs4902176	745	Q8NCM2	KCNH5_HUMAN	T	745	ENSP00000321427:A745T	ENSP00000321427:A745T	A	-	1	0	KCNH5	62244713	0.997000	0.39634	0.997000	0.53966	0.521000	0.34408	3.750000	0.55157	2.611000	0.88343	0.655000	0.94253	GCC	C|0.730;T|0.270	0.270	strong		0.527	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
P2RX6	9127	hgsc.bcm.edu	37	22	21377301	21377301	+	Silent	SNP	C	C	A	rs1548411	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:21377301C>A	ENST00000413302.2	+	5	682	c.534C>A	c.(532-534)ccC>ccA	p.P178P	P2RX6_ENST00000402329.3_3'UTR|P2RX6_ENST00000336296.2_Silent_p.P168P|P2RX6_ENST00000401443.1_Silent_p.P152P|P2RX6_ENST00000443995.3_Silent_p.P125P			O15547	P2RX6_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 6	178					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|channel activity (GO:0015267)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)										GTTGGTGCCCCGTGGAGAGTG	0.577													A|||	3157	0.630391	0.7587	0.67	5008	,	,		18740	0.6349		0.5358	False		,,,				2504	0.5215				p.P178P		Atlas-SNP	.											.	.	.	.	0			c.C534A						PASS	.	A	,	3215,1191	418.3+/-338.2	1193,829,181	163.0	162.0	162.0		456,534	-10.6	0.3	22	dbSNP_88	162	4505,4095	561.9+/-387.9	1201,2103,996	no	coding-synonymous,coding-synonymous	P2RX6	NM_001159554.1,NM_005446.3	,	2394,2932,1177	AA,AC,CC		47.6163,27.0313,40.6428	,	152/416,178/442	21377301	7720,5286	2203	4300	6503	SO:0001819	synonymous_variant	9127	exon5			GTGCCCCGTGGAG		CCDS13788.2, CCDS54504.1	22q11.21	2012-01-17	2008-03-28	2008-03-28	ENSG00000099957	ENSG00000099957		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8538	protein-coding gene	gene with protein product		608077	"""purinergic receptor P2X-like 1, orphan receptor"""	P2RXL1		9242461, 10591208, 8786426	Standard	NM_005446		Approved	P2XM, MGC129625, P2X6	uc010gsu.1	O15547	OTTHUMG00000150689	ENST00000413302.2:c.534C>A	22.37:g.21377301C>A		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_005446	F6V3D7|Q32MB6|Q58F04|Q6IC33|Q9UL50	Silent	SNP	ENST00000413302.2	37	CCDS13788.2																																																																																			C|0.383;A|0.617	0.617	strong		0.577	P2RX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319625.2	NM_005446	
ZBTB7C	201501	hgsc.bcm.edu	37	18	45566276	45566276	+	Silent	SNP	G	G	A	rs45501996	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:45566276G>A	ENST00000588982.1	-	3	1704	c.1203C>T	c.(1201-1203)ttC>ttT	p.F401F	ZBTB7C_ENST00000590800.1_Silent_p.F401F|ZBTB7C_ENST00000586438.1_Silent_p.F401F|ZBTB7C_ENST00000535628.2_Silent_p.F401F|ZBTB7C_ENST00000332053.2_Silent_p.F401F			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	401							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						CGCACCTGGTGAAGCGGACCT	0.662													G|||	984	0.196486	0.2632	0.1988	5008	,	,		18158	0.2252		0.174	False		,,,				2504	0.0982				p.F401F		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.C1203T						PASS	.	G		1130,3276	394.7+/-329.4	161,808,1234	63.0	64.0	63.0		1203	1.5	1.0	18	dbSNP_130	63	1430,7170	271.9+/-289.8	114,1202,2984	yes	coding-synonymous	ZBTB7C	NM_001039360.2		275,2010,4218	AA,AG,GG		16.6279,25.6468,19.6832		401/620	45566276	2560,10446	2203	4300	6503	SO:0001819	synonymous_variant	201501	exon2			CCTGGTGAAGCGG	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31700	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 36"""	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.1203C>T	18.37:g.45566276G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	16	8	0.5	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																			G|0.804;A|0.196	0.196	strong		0.662	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2396611	2396611	+	Missense_Mutation	SNP	C	C	T	rs17685098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:2396611C>T	ENST00000332578.3	+	2	217	c.217C>T	c.(217-219)Cgg>Tgg	p.R73W	TMPRSS9_ENST00000592650.1_3'UTR	NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	73			R -> W (in dbSNP:rs17685098).		plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		CAGCAGTTTGCGGCGGGAGAC	0.677													C|||	1950	0.389377	0.4206	0.4524	5008	,	,		15343	0.504		0.2286	False		,,,				2504	0.3497				p.R73W		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C217T						PASS	.	C	TRP/ARG	1711,2693	486.2+/-360.5	314,1083,805	30.0	25.0	27.0		217	2.9	0.3	19	dbSNP_123	27	2118,6482	340.1+/-323.5	271,1576,2453	yes	missense	TMPRSS9	NM_182973.1	101	585,2659,3258	TT,TC,CC		24.6279,38.851,29.4448	possibly-damaging	73/1060	2396611	3829,9175	2202	4300	6502	SO:0001583	missense	360200	exon2			AGTTTGCGGCGGG	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.217C>T	19.37:g.2396611C>T	ENSP00000330264:p.Arg73Trp	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	834	0.38186813186813184	204	0.4146341463414634	146	0.40331491712707185	304	0.5314685314685315	180	0.23746701846965698	C	14.50	2.553839	0.45487	0.38851	0.246279	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.88277	-2.36	3.98	2.94	0.34122	.	0.554254	0.16316	N	0.219795	T	0.00012	0.0000	N	0.22421	0.69	0.40885	P	0.015978000000000048	P;D	0.69078	0.926;0.997	B;P	0.57283	0.153;0.817	T	0.33650	-0.9860	9	0.72032	D	0.01	.	10.2282	0.43238	0.0:0.8987:0.0:0.1013	rs17685098;rs52790524;rs61077488;rs17685098	73;73	Q7Z410;E7EMP4	TMPS9_HUMAN;.	W	73	ENSP00000330264:R73W	ENSP00000330264:R73W	R	+	1	2	TMPRSS9	2347611	0.578000	0.26717	0.274000	0.24659	0.016000	0.09150	1.370000	0.34238	0.795000	0.33922	0.555000	0.69702	CGG	C|0.673;T|0.327	0.327	strong		0.677	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
FRMD4B	23150	hgsc.bcm.edu	37	3	69299233	69299233	+	Missense_Mutation	SNP	C	C	G	rs4361282	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:69299233C>G	ENST00000398540.3	-	6	602	c.519G>C	c.(517-519)gaG>gaC	p.E173D	FRMD4B_ENST00000542259.1_Missense_Mutation_p.E119D	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	173	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TGGTTTCGCTCTCTACTTCGA	0.433													G|||	1237	0.247005	0.3457	0.2133	5008	,	,		18600	0.2649		0.2237	False		,,,				2504	0.1431				p.E173D		Atlas-SNP	.											.	FRMD4B	90	.	0			c.G519C						PASS	.	G	ASP/GLU	1174,2712		165,844,934	279.0	271.0	273.0		519	4.3	1.0	3	dbSNP_111	273	1816,6458		195,1426,2516	yes	missense	FRMD4B	NM_015123.1	45	360,2270,3450	GG,GC,CC		21.9483,30.211,24.5888	benign	173/1035	69299233	2990,9170	1943	4137	6080	SO:0001583	missense	23150	exon6			TTCGCTCTCTACT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.519G>C	3.37:g.69299233C>G	ENSP00000381549:p.Glu173Asp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	577	0.2641941391941392	176	0.35772357723577236	73	0.20165745856353592	143	0.25	185	0.24406332453825857	G	1.525	-0.545949	0.04024	0.30211	0.219483	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000493880;ENST00000473029;ENST00000460709	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.33	4.33	0.51752	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.106811	0.64402	N	0.000007	T	0.00012	0.0000	N	0.11560	0.145	0.51233	P	8.60000000000305E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10474	-1.0628	9	0.02654	T	1	-15.1785	7.5424	0.27746	0.0:0.1412:0.5798:0.279	rs4361282;rs52807668;rs4361282	17;173	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	D	173;119;64;119;119	ENSP00000381549:E173D;ENSP00000437658:E119D;ENSP00000418962:E64D;ENSP00000418373:E119D;ENSP00000418023:E119D	ENSP00000381549:E173D	E	-	3	2	FRMD4B	69381923	1.000000	0.71417	0.999000	0.59377	0.706000	0.40770	1.131000	0.31406	1.400000	0.46741	-0.187000	0.12897	GAG	C|0.742;G|0.258	0.258	strong		0.433	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
POLQ	10721	hgsc.bcm.edu	37	3	121206402	121206402	+	Silent	SNP	C	C	T	rs369852464		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:121206402C>T	ENST00000264233.5	-	16	5504	c.5376G>A	c.(5374-5376)ggG>ggA	p.G1792G		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1792					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)		TGTCTTTGAACCCATTTCTAC	0.373								DNA polymerases (catalytic subunits)																													p.G1792G	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											POLQ,NS,carcinoma,-1,1	POLQ	273	1	0			c.G5376A						scavenged	.						110.0	107.0	108.0					3																	121206402		2203	4300	6503	SO:0001819	synonymous_variant	10721	exon16			TTTGAACCCATTT	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.5376G>A	3.37:g.121206402C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	193	2	0.0103627	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																			.	.	alt		0.373	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
BCAR1	9564	hgsc.bcm.edu	37	16	75269477	75269477	+	Silent	SNP	A	A	C	rs61729595	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:75269477A>C	ENST00000162330.5	-	5	1446	c.1320T>G	c.(1318-1320)tcT>tcG	p.S440S	BCAR1_ENST00000546196.1_Silent_p.S411S|BCAR1_ENST00000418647.3_Silent_p.S486S|BCAR1_ENST00000542031.2_Silent_p.S438S|BCAR1_ENST00000420641.3_Silent_p.S458S|BCAR1_ENST00000535626.2_Silent_p.S292S|BCAR1_ENST00000393422.2_Silent_p.S458S|BCAR1_ENST00000393420.6_Silent_p.S458S|BCAR1_ENST00000538440.2_Silent_p.S440S|BCAR1_ENST00000566982.1_5'UTR	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	440	Ser-rich.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.S458S(1)|p.S440S(1)		breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		AGGAGGACGCAGACTGGCTGC	0.701													A|||	169	0.033746	0.003	0.0375	5008	,	,		15021	0.001		0.0855	False		,,,				2504	0.0532				p.S486S		Atlas-SNP	.											BCAR1_ENST00000393420,NS,carcinoma,0,2	BCAR1	184	2	2	Substitution - coding silent(2)	prostate(2)	c.T1458G						PASS	.	A	,,,,,,,,	69,4303		0,69,2117	10.0	15.0	13.0		1458,1374,1374,1374,1320,1314,876,690,1320	-7.5	0.0	16	dbSNP_129	13	590,7978		14,562,3708	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCAR1	NM_001170714.1,NM_001170715.1,NM_001170716.1,NM_001170717.1,NM_001170718.1,NM_001170719.1,NM_001170720.1,NM_001170721.1,NM_014567.3	,,,,,,,,	14,631,5825	CC,CA,AA		6.8861,1.5782,5.0927	,,,,,,,,	486/917,458/889,458/889,458/889,440/871,438/869,292/723,230/661,440/871	75269477	659,12281	2186	4284	6470	SO:0001819	synonymous_variant	9564	exon6			GGACGCAGACTGG	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1320T>G	16.37:g.75269477A>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Silent	SNP	ENST00000162330.5	37	CCDS10915.1																																																																																			A|0.962;C|0.038	0.038	strong		0.701	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
PTPN5	84867	hgsc.bcm.edu	37	11	18764026	18764026	+	Missense_Mutation	SNP	G	G	C	rs4757707	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18764026G>C	ENST00000358540.2	-	7	938	c.508C>G	c.(508-510)Cca>Gca	p.P170A	PTPN5_ENST00000477854.1_5'UTR|PTPN5_ENST00000396170.1_Missense_Mutation_p.P138A|PTPN5_ENST00000496201.2_5'UTR|PTPN5_ENST00000396168.1_Missense_Mutation_p.P146A|RP11-1081L13.4_ENST00000527285.1_RNA|PTPN5_ENST00000396171.4_Missense_Mutation_p.P170A|PTPN5_ENST00000396167.2_Missense_Mutation_p.P138A	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	170			P -> A (in dbSNP:rs4757707). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)	p.P170A(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GGTGGCTCTGGGGGTGTCCTC	0.632													G|||	1489	0.297324	0.0242	0.4899	5008	,	,		16566	0.3194		0.3857	False		,,,				2504	0.4162				p.P170A		Atlas-SNP	.											PTPN5_ENST00000358540,caecum,carcinoma,0,3	PTPN5	163	3	1	Substitution - Missense(1)	skin(1)	c.C508G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO	419,3979	203.5+/-225.9	22,375,1802	41.0	45.0	43.0		412,508,508	1.4	0.8	11	dbSNP_111	43	3372,5214	497.7+/-374.6	674,2024,1595	yes	missense,missense,missense	PTPN5	NM_001039970.1,NM_006906.1,NM_032781.3	27,27,27	696,2399,3397	CC,CG,GG		39.2732,9.5271,29.1975	benign,benign,benign	138/534,170/566,170/566	18764026	3791,9193	2199	4293	6492	SO:0001583	missense	84867	exon7			GCTCTGGGGGTGT	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.508C>G	11.37:g.18764026G>C	ENSP00000351342:p.Pro170Ala	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Missense_Mutation	SNP	ENST00000358540.2	37	CCDS7845.1	679	0.3108974358974359	20	0.04065040650406504	191	0.5276243093922652	173	0.30244755244755245	295	0.3891820580474934	G	11.26	1.587311	0.28268	0.095271	0.392732	ENSG00000110786	ENST00000358540;ENST00000396170;ENST00000396171;ENST00000396167;ENST00000396168	T;T;T;T;T	0.03831	3.79;3.92;3.79;3.92;3.81	4.41	1.4	0.22301	.	0.320871	0.27039	N	0.021226	T	0.00012	0.0000	N	0.24115	0.695	0.40928	P	0.015637000000000012	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31668	-0.9935	9	0.13108	T	0.6	.	9.4819	0.38906	0.0:0.3185:0.5364:0.1451	rs4757707;rs4757707	170;138	P54829;B3KXG7	PTN5_HUMAN;.	A	170;138;170;138;146	ENSP00000351342:P170A;ENSP00000379473:P138A;ENSP00000379474:P170A;ENSP00000379470:P138A;ENSP00000379471:P146A	ENSP00000351342:P170A	P	-	1	0	PTPN5	18720602	0.979000	0.34478	0.803000	0.32268	0.930000	0.56654	1.786000	0.38694	0.111000	0.17947	0.561000	0.74099	CCA	G|0.702;C|0.298	0.298	strong		0.632	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482989	54482989	+	Silent	SNP	C	C	T	rs6740641	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54482989C>T	ENST00000317802.7	-	1	420	c.300G>A	c.(298-300)gcG>gcA	p.A100A	ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000303536.4_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	100					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.A100A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						AGGCAGAGGCCGCTTCTAGGC	0.607													T|||	694	0.138578	0.1263	0.0994	5008	,	,		16663	0.1835		0.1093	False		,,,				2504	0.1667				p.A100A		Atlas-SNP	.											TSPYL6,NS,carcinoma,0,1	TSPYL6	54	1	1	Substitution - coding silent(1)	stomach(1)	c.G300A						PASS	.	T	,	602,3542		69,464,1539	35.0	40.0	38.0		300,	-0.2	0.0	2	dbSNP_116	38	1221,7165		86,1049,3058	no	coding-synonymous,intron	ACYP2,TSPYL6	NM_001003937.2,NM_138448.3	,	155,1513,4597	TT,TC,CC		14.56,14.527,14.5491	,	100/411,	54482989	1823,10707	2072	4193	6265	SO:0001819	synonymous_variant	388951	exon1			AGAGGCCGCTTCT	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.300G>A	2.37:g.54482989C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_001003937	Q6NUJ3	Silent	SNP	ENST00000317802.7	37	CCDS42682.1																																																																																			C|0.869;G|0.001;T|0.130	0.130	strong		0.607	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
CX3CR1	1524	hgsc.bcm.edu	37	3	39307256	39307256	+	Missense_Mutation	SNP	C	C	T	rs3732379	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:39307256C>T	ENST00000541347.1	-	2	984	c.745G>A	c.(745-747)Gtt>Att	p.V249I	CX3CR1_ENST00000542107.1_Missense_Mutation_p.V249I|CX3CR1_ENST00000399220.2_Missense_Mutation_p.V249I|CX3CR1_ENST00000358309.3_Missense_Mutation_p.V281I	NM_001171171.1	NP_001164642.1	P49238	CX3C1_HUMAN	chemokine (C-X3-C motif) receptor 1	249			V -> I (common polymorphism in Caucasian population; associated with a markedly reduced risk of acute coronary artery disease; associated with higher risk of developing ARMD12; chemotaxis of monocytes of individuals with homozygous Ile-249 and Met-280 genotypes is impaired in the presence of bound CX3CR1 protein; dbSNP:rs3732379). {ECO:0000269|PubMed:10731151, ECO:0000269|PubMed:11264153, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15208270, ECO:0000269|Ref.6}.		cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cerebral cortex cell migration (GO:0021795)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|macrophage chemotaxis (GO:0048246)|microglial cell activation involved in immune response (GO:0002282)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|response to wounding (GO:0009611)|viral process (GO:0016032)	integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|neuronal cell body membrane (GO:0032809)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-X3-C chemokine receptor activity (GO:0016495)|chemokine receptor activity (GO:0004950)			endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0557)|Kidney(284;0.0699)		AAAATCATAACGTTGTAGGGT	0.483													C|||	723	0.144369	0.0893	0.2378	5008	,	,		22318	0.0278		0.2853	False		,,,				2504	0.1278				p.V281I		Atlas-SNP	.											.	CX3CR1	91	.	0			c.G841A	GRCh37	CM000504	CX3CR1	M	rs3732379	PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	515,3329		36,443,1443	112.0	115.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	745,745,841,745	-2.3	0.0	3	dbSNP_107	114	2281,5975		311,1659,2158	yes	missense,missense,missense,missense	CX3CR1	NM_001171171.1,NM_001171172.1,NM_001171174.1,NM_001337.3	29,29,29,29	347,2102,3601	TT,TC,CC		27.6284,13.3975,23.1074	benign,benign,benign,benign	249/356,249/356,281/388,249/356	39307256	2796,9304	1922	4128	6050	SO:0001583	missense	1524	exon2			TCATAACGTTGTA	BC028078	CCDS43069.1, CCDS54571.1	3p21.3	2012-08-08	2002-08-22		ENSG00000168329	ENSG00000168329		"""GPCR / Class A : Chemokine receptors : C-X-3-C motif"""	2558	protein-coding gene	gene with protein product		601470	"""chemokine (C-X3-C) receptor 1"""	GPR13, CMKBRL1		9726990, 7646814	Standard	NM_001171171		Approved	CMKDR1, V28, CCRL1	uc021wwc.1	P49238	OTTHUMG00000156249	ENST00000541347.1:c.745G>A	3.37:g.39307256C>T	ENSP00000439140:p.Val249Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	131	60	0.458015	NM_001171174	A0N0N6|B2R5Z4|J3KP17	Missense_Mutation	SNP	ENST00000541347.1	37	CCDS43069.1	380	0.17399267399267399	55	0.11178861788617886	93	0.2569060773480663	20	0.03496503496503497	212	0.2796833773087071	C	0.008	-1.863526	0.00552	0.133975	0.276284	ENSG00000168329	ENST00000399220;ENST00000538756;ENST00000358309;ENST00000541347;ENST00000542107	T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4	5.77	-2.32	0.06745	GPCR, rhodopsin-like superfamily (1);	0.526611	0.21488	N	0.073733	T	0.00012	0.0000	N	0.10733	0.035	0.80722	P	0.0	B	0.19073	0.033	B	0.17433	0.018	T	0.11299	-1.0593	9	0.02654	T	1	.	12.3125	0.54935	0.0:0.3682:0.0:0.6318	rs3732379;rs17792918;rs52808794;rs59717546;rs3732379	249	P49238	CX3C1_HUMAN	I	249;257;281;249;249	ENSP00000382166:V249I;ENSP00000351059:V281I;ENSP00000439140:V249I;ENSP00000444928:V249I	ENSP00000351059:V281I	V	-	1	0	CX3CR1	39282260	0.000000	0.05858	0.000000	0.03702	0.225000	0.24961	-1.393000	0.02521	-0.555000	0.06142	-0.794000	0.03295	GTT	C|0.832;T|0.168	0.168	strong		0.483	CX3CR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343613.1	NM_001337	
SPRR3	6707	hgsc.bcm.edu	37	1	152975739	152975739	+	Silent	SNP	T	T	A	rs17851565	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152975739T>A	ENST00000295367.4	+	2	285	c.243T>A	c.(241-243)ggT>ggA	p.G81G	SPRR3_ENST00000542696.1_Silent_p.G81G|SPRR3_ENST00000331860.3_Silent_p.G81G	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	81	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)	p.G81G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGAGCCAGGTTGTACCAAGG	0.592																																					p.G81G		Atlas-SNP	.											SPRR3,colon,carcinoma,0,4	SPRR3	45	4	1	Substitution - coding silent(1)	prostate(1)	c.T243A						PASS	.						61.0	52.0	55.0					1																	152975739		2203	4299	6502	SO:0001819	synonymous_variant	6707	exon2			GCCAGGTTGTACC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.243T>A	1.37:g.152975739T>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	56	4	0.0714286	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			A|0.010;C|0.001;T|0.988	0.010	strong		0.592	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
CRHR1	1394	hgsc.bcm.edu	37	17	43907896	43907896	+	Silent	SNP	T	T	C	rs16940665	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:43907896T>C	ENST00000398285.3	+	8	756	c.756T>C	c.(754-756)acT>acC	p.T252T	CRHR1_ENST00000293493.7_Silent_p.T48T|CRHR1_ENST00000314537.5_Silent_p.T223T|CRHR1_ENST00000339069.5_Silent_p.T122T|CRHR1_ENST00000352855.5_Silent_p.T183T|CRHR1_ENST00000577353.1_Silent_p.T223T	NM_001145146.1	NP_001138618.1	P34998	CRFR1_HUMAN	corticotropin releasing hormone receptor 1	252					activation of adenylate cyclase activity (GO:0007190)|adrenal gland development (GO:0030325)|behavioral response to cocaine (GO:0048148)|behavioral response to ethanol (GO:0048149)|behavioral response to pain (GO:0048266)|cellular response to corticotropin-releasing hormone stimulus (GO:0071376)|corticotropin secretion (GO:0051458)|epithelial cell differentiation (GO:0030855)|fear response (GO:0042596)|female pregnancy (GO:0007565)|general adaptation syndrome, behavioral process (GO:0051867)|hypothalamus development (GO:0021854)|immune response (GO:0006955)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neuron death (GO:1901215)|negative regulation of voltage-gated calcium channel activity (GO:1901386)|neuropeptide signaling pathway (GO:0007218)|parturition (GO:0007567)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mast cell degranulation (GO:0043306)|regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010578)|regulation of corticosterone secretion (GO:2000852)|response to hypoxia (GO:0001666)|response to immobilization stress (GO:0035902)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|vesicle (GO:0031982)	corticotrophin-releasing factor receptor activity (GO:0015056)|corticotropin-releasing hormone binding (GO:0051424)|corticotropin-releasing hormone receptor activity (GO:0043404)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(15)|pancreas(1)|skin(1)	24	Colorectal(2;0.0416)			BRCA - Breast invasive adenocarcinoma(366;0.161)		CCTACTCCACTGACCGGCTGC	0.622													C|||	431	0.0860623	0.0151	0.1571	5008	,	,		20880	0.001		0.2396	False		,,,				2504	0.0613				p.T252T	Ovarian(110;57 1568 10207 38216 49865)	Atlas-SNP	.											.	CRHR1	48	.	0			c.T756C						PASS	.	C	,,,	200,4202	777.7+/-414.2	5,190,2006	91.0	94.0	93.0		756,549,669,669	-4.0	0.9	17	dbSNP_123	93	1925,6675	717.6+/-406.2	221,1483,2596	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CRHR1	NM_001145146.1,NM_001145147.1,NM_001145148.1,NM_004382.4	,,,	226,1673,4602	CC,CT,TT		22.3837,4.5434,16.3436	,,,	252/445,183/376,223/402,223/416	43907896	2125,10877	2201	4300	6501	SO:0001819	synonymous_variant	1394	exon8			CTCCACTGACCGG	L23332	CCDS42350.1, CCDS45712.1, CCDS45713.1, CCDS45714.1	17q12-q22	2012-08-14			ENSG00000120088	ENSG00000120088		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2357	protein-coding gene	gene with protein product	"""corticotropin-releasing factor receptor"""	122561		CRHR		7590738	Standard	NM_004382		Approved	CRF-R, CRF1	uc010dap.3	P34998		ENST00000398285.3:c.756T>C	17.37:g.43907896T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001145146	B4DIE9|Q13008|Q4QRJ1|Q9UK64	Silent	SNP	ENST00000398285.3	37	CCDS45712.1																																																																																			T|0.862;C|0.138	0.138	strong		0.622	CRHR1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000441241.3		
TTC12	54970	hgsc.bcm.edu	37	11	113222885	113222885	+	Missense_Mutation	SNP	A	A	T	rs35852218	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:113222885A>T	ENST00000529221.1	+	16	1507	c.1402A>T	c.(1402-1404)Atg>Ttg	p.M468L	TTC12_ENST00000483239.2_Missense_Mutation_p.M474L|TTC12_ENST00000393020.1_Missense_Mutation_p.M468L|TTC12_ENST00000478125.1_3'UTR|TTC12_ENST00000314756.3_Missense_Mutation_p.M468L	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	468			M -> L (in dbSNP:rs35852218).							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)		CCGAAGACACATGGCGGCCTG	0.507													A|||	17	0.00339457	0.0	0.0043	5008	,	,		15500	0.0		0.0099	False		,,,				2504	0.0041				p.M468L		Atlas-SNP	.											.	TTC12	66	.	0			c.A1402T						PASS	.	A	LEU/MET	20,4382	28.1+/-56.4	0,20,2181	133.0	129.0	130.0		1402	1.2	0.3	11	dbSNP_126	130	153,8439	73.8+/-136.5	3,147,4146	yes	missense	TTC12	NM_017868.3	15	3,167,6327	TT,TA,AA		1.7807,0.4543,1.3314	benign	468/706	113222885	173,12821	2201	4296	6497	SO:0001583	missense	54970	exon16			AGACACATGGCGG	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.1402A>T	11.37:g.113222885A>T	ENSP00000433757:p.Met468Leu	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	202	167	0.826733	NM_017868	Q8N5H9|Q9NWY3	Missense_Mutation	SNP	ENST00000529221.1	37	CCDS8360.2	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	A	2.448	-0.326970	0.05350	0.004543	0.017807	ENSG00000149292	ENST00000529221;ENST00000314756;ENST00000393020;ENST00000483239	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	5.29	1.24	0.21308	Armadillo-like helical (1);Armadillo-type fold (1);	0.259498	0.31031	N	0.008393	T	0.11623	0.0283	L	0.33753	1.03	0.29965	N	0.819077	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.21109	-1.0255	10	0.10377	T	0.69	-18.4954	11.1448	0.48424	0.5428:0.4572:0.0:0.0	rs35852218;rs61903988	468;468	A8K8G6;Q9H892	.;TTC12_HUMAN	L	468;468;468;474	ENSP00000433757:M468L;ENSP00000315160:M468L;ENSP00000376743:M468L;ENSP00000419652:M474L	ENSP00000315160:M468L	M	+	1	0	TTC12	112728095	1.000000	0.71417	0.349000	0.25694	0.017000	0.09413	0.621000	0.24418	0.365000	0.24400	0.533000	0.62120	ATG	A|0.989;T|0.011	0.011	strong		0.507	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868	
USP40	55230	hgsc.bcm.edu	37	2	234394487	234394487	+	Missense_Mutation	SNP	G	G	A	rs1048603	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:234394487G>A	ENST00000427112.2	-	28	3366	c.3331C>T	c.(3331-3333)Cgt>Tgt	p.R1111C	USP40_ENST00000496298.1_5'UTR|USP40_ENST00000251722.6_Missense_Mutation_p.R1111C|USP40_ENST00000450966.1_Missense_Mutation_p.R1123C			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1111			R -> C (in dbSNP:rs1048603).		ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		ACGGGAAGACGATAGAAATCG	0.562													A|||	2004	0.40016	0.7489	0.2709	5008	,	,		17737	0.1944		0.3618	False		,,,				2504	0.272				p.R1123C		Atlas-SNP	.											.	USP40	174	.	0			c.C3367T						PASS	.	A	CYS/ARG	2480,1328		819,842,243	21.0	24.0	23.0		3367	-2.4	0.0	2	dbSNP_86	23	2595,5643		414,1767,1938	yes	missense	USP40	NM_018218.2	180	1233,2609,2181	AA,AG,GG		31.5004,34.8739,42.1302	benign	1123/1248	234394487	5075,6971	1904	4119	6023	SO:0001583	missense	55230	exon28			GAAGACGATAGAA	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3331C>T	2.37:g.234394487G>A	ENSP00000387898:p.Arg1111Cys	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	805	0.3685897435897436	351	0.7134146341463414	96	0.26519337016574585	96	0.16783216783216784	262	0.34564643799472294	A	7.624	0.677480	0.14841	0.651261	0.315004	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.04603	3.59;3.59;3.59	5.75	-2.41	0.06562	.	1.068780	0.07073	N	0.835760	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.22800	-1.0206	9	0.45353	T	0.12	.	12.5667	0.56314	0.429:0.5121:0.0588:0.0	rs1048603;rs3188607;rs17668936;rs52816184;rs58082988;rs1048603	1123	Q9NVE5-3	.	C	1123;1111;1111	ENSP00000415434:R1123C;ENSP00000251722:R1111C;ENSP00000387898:R1111C	ENSP00000251722:R1111C	R	-	1	0	USP40	234059226	0.316000	0.24580	0.000000	0.03702	0.138000	0.21146	0.262000	0.18460	-0.485000	0.06754	-1.189000	0.01698	CGT	G|0.604;T|0.006	.	strong		0.562	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
DHX33	56919	hgsc.bcm.edu	37	17	5347576	5347576	+	Silent	SNP	G	G	A	rs2074438	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5347576G>A	ENST00000225296.3	-	12	2273	c.2073C>T	c.(2071-2073)taC>taT	p.Y691Y	DHX33_ENST00000433302.3_Silent_p.Y467Y	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	691					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						GGGCAGCCTCGTACAGCCACT	0.582													G|||	1412	0.281949	0.0356	0.3026	5008	,	,		18065	0.6419		0.1471	False		,,,				2504	0.3681				p.Y691Y		Atlas-SNP	.											.	DHX33	41	.	0			c.C2073T						PASS	.	G	,	249,4157	142.3+/-177.5	8,233,1962	66.0	54.0	58.0		1554,2073	1.3	1.0	17	dbSNP_96	58	1008,7592	217.1+/-255.9	52,904,3344	no	coding-synonymous,coding-synonymous	DHX33	NM_001199699.1,NM_020162.3	,	60,1137,5306	AA,AG,GG		11.7209,5.6514,9.6648	,	518/535,691/708	5347576	1257,11749	2203	4300	6503	SO:0001819	synonymous_variant	56919	exon12			AGCCTCGTACAGC	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.2073C>T	17.37:g.5347576G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	46	0.567901	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Silent	SNP	ENST00000225296.3	37	CCDS11072.1																																																																																			G|0.837;A|0.163	0.163	strong		0.582	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
NEBL	10529	hgsc.bcm.edu	37	10	21139389	21139389	+	Missense_Mutation	SNP	T	T	C	rs4025981	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:21139389T>C	ENST00000377122.4	-	11	1447	c.1051A>G	c.(1051-1053)Atg>Gtg	p.M351V	NEBL_ENST00000377159.4_Intron|NEBL_ENST00000417816.2_Intron	NM_006393.2	NP_006384.1	O76041	NEBL_HUMAN	nebulette	351			M -> V (in dbSNP:rs4025981). {ECO:0000269|PubMed:11140941}.		cardiac muscle thin filament assembly (GO:0071691)	extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|filamin binding (GO:0031005)|structural constituent of muscle (GO:0008307)|tropomyosin binding (GO:0005523)	p.M351V(1)		NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(8)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AATTCAAGCATTGGCTTTCCC	0.318													T|||	194	0.038738	0.0053	0.0461	5008	,	,		19089	0.0268		0.0835	False		,,,				2504	0.045				p.M351V		Atlas-SNP	.											NEBL,NS,carcinoma,0,1	NEBL	199	1	1	Substitution - Missense(1)	stomach(1)	c.A1051G						PASS	.	T	,VAL/MET,	78,4328	68.7+/-106.4	0,78,2125	179.0	170.0	173.0		,1051,	4.1	0.8	10	dbSNP_108	173	717,7883	175.3+/-225.4	28,661,3611	yes	intron,missense,intron	NEBL	NM_001173484.1,NM_006393.2,NM_213569.2	,21,	28,739,5736	CC,CT,TT		8.3372,1.7703,6.1126	,benign,	,351/1015,	21139389	795,12211	2203	4300	6503	SO:0001583	missense	10529	exon11			CAAGCATTGGCTT	Y16241	CCDS7133.1, CCDS7134.1	10p12	2014-09-17			ENSG00000078114	ENSG00000078114			16932	protein-coding gene	gene with protein product		605491				9733644, 10470015	Standard	NM_213569		Approved		uc001iqi.3	O76041	OTTHUMG00000017788	ENST00000377122.4:c.1051A>G	10.37:g.21139389T>C	ENSP00000366326:p.Met351Val	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_006393	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000377122.4	37	CCDS7134.1	102	0.046703296703296704	8	0.016260162601626018	20	0.055248618784530384	15	0.026223776223776224	59	0.07783641160949868	T	10.23	1.293962	0.23564	0.017703	0.083372	ENSG00000078114	ENST00000377122	T	0.04406	3.63	5.27	4.11	0.48088	.	0.150621	0.64402	D	0.000008	T	0.00384	0.0012	M	0.62209	1.925	0.80722	D	1	B	0.16396	0.017	B	0.17722	0.019	T	0.33214	-0.9877	10	0.52906	T	0.07	.	9.0093	0.36131	0.2954:0.0:0.0:0.7046	rs4025981;rs4025981	351	O76041	NEBL_HUMAN	V	351	ENSP00000366326:M351V	ENSP00000366326:M351V	M	-	1	0	NEBL	21179395	0.984000	0.35163	0.762000	0.31397	0.935000	0.57460	1.954000	0.40362	0.924000	0.37069	0.533000	0.62120	ATG	T|0.942;C|0.058	0.058	strong		0.318	NEBL-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047113.1	NM_006393	
CAT	847	hgsc.bcm.edu	37	11	34482908	34482908	+	Silent	SNP	C	C	T	rs769217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:34482908C>T	ENST00000241052.4	+	9	1256	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	389					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	ACCAGCGTGACGGCCCGATGT	0.607													C|||	1316	0.26278	0.1422	0.2896	5008	,	,		18460	0.5		0.2147	False		,,,				2504	0.2117				p.D389D		Atlas-SNP	.											.	CAT	42	.	0			c.C1167T	GRCh37	CM025323	CAT	M	rs769217	PASS	.	C		739,3665	305.8+/-289.2	57,625,1520	113.0	106.0	108.0		1167	-2.6	1.0	11	dbSNP_92	108	2007,6589	351.1+/-328.1	209,1589,2500	no	coding-synonymous	CAT	NM_001752.3		266,2214,4020	TT,TC,CC		23.3481,16.7802,21.1231		389/528	34482908	2746,10254	2202	4298	6500	SO:0001819	synonymous_variant	847	exon9			GCGTGACGGCCCG	AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.1167C>T	11.37:g.34482908C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001752	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Silent	SNP	ENST00000241052.4	37	CCDS7891.1																																																																																			C|0.745;T|0.255	0.255	strong		0.607	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752	
DDX11	1663	hgsc.bcm.edu	37	12	31256615	31256615	+	Missense_Mutation	SNP	C	C	A	rs3893680		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:31256615C>A	ENST00000407793.2	+	26	2887	c.2636C>A	c.(2635-2637)cCg>cAg	p.P879Q	DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000545668.1_Missense_Mutation_p.P879Q|DDX11_ENST00000350437.4_Missense_Mutation_p.R831S|DDX11_ENST00000542838.1_Missense_Mutation_p.R881S|DDX11_ENST00000228264.6_Missense_Mutation_p.R855S	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	879					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GATCCGAGCCCGTGTGGAGGT	0.607										Multiple Myeloma(12;0.14)																											p.R881S		Atlas-SNP	.											DDX11,lower_third,carcinoma,-2,1	DDX11	188	1	0			c.C2641A						scavenged	.						71.0	79.0	77.0					12																	31256615		2203	4300	6503	SO:0001583	missense	1663	exon26			CGAGCCCGTGTGG	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.2636C>A	12.37:g.31256615C>A	ENSP00000384703:p.Pro879Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	108	6	0.0555556	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.916|1.916	-0.449442|-0.449442	0.04572|0.04572	.|.	.|.	ENSG00000013573|ENSG00000013573	ENST00000407793;ENST00000545668|ENST00000542838;ENST00000228264;ENST00000350437	T;T|T;T;T	0.71341|0.80123	-0.56;-0.56|-1.34;-1.25;-1.06	3.14|3.14	2.24|2.24	0.28232|0.28232	.|.	.|1.099370	.|0.07030	.|N	.|0.828301	T|T	0.63070|0.63070	0.2480|0.2480	N|N	0.20986|0.20986	0.625|0.625	0.80722|0.80722	D|D	1|1	B|B;B;B	0.26845|0.21452	0.161|0.056;0.056;0.056	B|B;B;B	0.19391|0.24394	0.025|0.053;0.049;0.053	T|T	0.55927|0.55927	-0.8063|-0.8063	9|10	0.87932|0.02654	D|T	0|1	.|.	3.6922|3.6922	0.08350|0.08350	0.2415:0.6231:0.0:0.1355|0.2415:0.6231:0.0:0.1355	rs3893680|rs3893680	879|855;831;881	Q96FC9|Q96FC9-3;Q96FC9-4;Q96FC9-2	DDX11_HUMAN|.;.;.	Q|S	879|881;855;831	ENSP00000384703:P879Q;ENSP00000440402:P879Q|ENSP00000443426:R881S;ENSP00000228264:R855S;ENSP00000309965:R831S	ENSP00000384703:P879Q|ENSP00000228264:R855S	P|R	+|+	2|1	0|0	DDX11|DDX11	31147882|31147882	0.998000|0.998000	0.40836|0.40836	0.986000|0.986000	0.45419|0.45419	0.053000|0.053000	0.15095|0.15095	1.393000|1.393000	0.34497|0.34497	0.518000|0.518000	0.28383|0.28383	0.430000|0.430000	0.28490|0.28490	CCG|CGT	.	.	weak		0.607	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
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 GAIIx	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		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	42	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	
SYNC	81493	hgsc.bcm.edu	37	1	33161264	33161264	+	Silent	SNP	C	C	T	rs74519835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:33161264C>T	ENST00000409190.3	-	2	893	c.435G>A	c.(433-435)agG>agA	p.R145R	SYNC_ENST00000373484.3_Silent_p.R145R	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	145	Head.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						ATTTCTCCGCCCTTGTGACTG	0.582													C|||	322	0.0642971	0.003	0.1772	5008	,	,		10303	0.1062		0.0298	False		,,,				2504	0.0593				p.R145R		Atlas-SNP	.											.	SYNC	36	.	0			c.G435A						PASS	.	C	,	19,1365		0,19,673	92.0	80.0	84.0		435,435	-2.5	0.0	1	dbSNP_132	84	125,3057		2,121,1468	no	coding-synonymous,coding-synonymous	SYNC	NM_001161708.1,NM_030786.2	,	2,140,2141	TT,TC,CC		3.9283,1.3728,3.1537	,	145/477,145/483	33161264	144,4422	692	1591	2283	SO:0001819	synonymous_variant	81493	exon2			CTCCGCCCTTGTG	AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"""Intermediate filaments type III"""	28897	protein-coding gene	gene with protein product		611750	"""syncoilin, intermediate filament 1"""	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.435G>A	1.37:g.33161264C>T		Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	303	134	0.442244	NM_001161708	B4DNK8|B4DY58|C9IY41	Silent	SNP	ENST00000409190.3	37	CCDS367.2																																																																																			C|0.942;T|0.058	0.058	strong		0.582	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786	
SLC6A3	6531	hgsc.bcm.edu	37	5	1443199	1443199	+	Silent	SNP	G	G	A	rs6350	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:1443199G>A	ENST00000270349.9	-	2	241	c.114C>T	c.(112-114)aaC>aaT	p.N38N	SLC6A3_ENST00000453492.2_Silent_p.N38N	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	38					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GCTGCACTCCGTTCTGCTCCT	0.632													G|||	228	0.0455272	0.0401	0.0504	5008	,	,		18656	0.0109		0.0815	False		,,,				2504	0.0481				p.N38N		Atlas-SNP	.											.	SLC6A3	102	.	0			c.C114T						PASS	.	G		229,4177	135.7+/-171.8	5,219,1979	81.0	79.0	80.0		114	-8.4	0.5	5	dbSNP_52	80	569,8031	153.4+/-207.8	17,535,3748	no	coding-synonymous	SLC6A3	NM_001044.4		22,754,5727	AA,AG,GG		6.6163,5.1975,6.1356		38/621	1443199	798,12208	2203	4300	6503	SO:0001819	synonymous_variant	6531	exon2			CACTCCGTTCTGC		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"""Solute carriers"""	11049	protein-coding gene	gene with protein product	"""dopamine transporter"""	126455	"""solute carrier family 6 (neurotransmitter transporter, dopamine), member 3"", ""dopamine transporter 1"""	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.114C>T	5.37:g.1443199G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	99	57	0.575758	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	37	CCDS3863.1																																																																																			G|0.943;A|0.057	0.057	strong		0.632	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044	
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 GAIIx	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	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	113	57	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	
CDON	50937	hgsc.bcm.edu	37	11	125848261	125848261	+	Silent	SNP	C	C	T	rs3740904	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:125848261C>T	ENST00000392693.3	-	18	3421	c.3294G>A	c.(3292-3294)acG>acA	p.T1098T	CDON_ENST00000531738.1_Silent_p.T475T|CDON_ENST00000263577.7_Silent_p.T1098T	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1098					anterior/posterior pattern specification (GO:0009952)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cerebral cortex development (GO:0021987)|embryonic body morphogenesis (GO:0010172)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|lens development in camera-type eye (GO:0002088)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein heterodimerization activity (GO:0043497)|skeletal muscle satellite cell differentiation (GO:0014816)|smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.T1098T(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(9)|ovary(3)|prostate(2)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	61	all_hematologic(175;0.177)	Breast(109;0.00157)|Lung NSC(97;0.0127)|all_lung(97;0.0133)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.51e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0604)		GAGGCACGGCCGTGTACATTC	0.438													C|||	2001	0.399561	0.382	0.4337	5008	,	,		19124	0.4127		0.3797	False		,,,				2504	0.4059				p.T1098T		Atlas-SNP	.											CDON,NS,carcinoma,0,1	CDON	137	1	1	Substitution - coding silent(1)	stomach(1)	c.G3294A						scavenged	.	C		1534,2868	476.6+/-357.7	256,1022,923	82.0	63.0	70.0		3294	-3.9	0.7	11	dbSNP_107	70	3100,5498	465.6+/-366.6	571,1958,1770	yes	coding-synonymous	CDON	NM_016952.4		827,2980,2693	TT,TC,CC		36.0549,34.8478,35.6462		1098/1265	125848261	4634,8366	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon18			CACGGCCGTGTAC	AF004841	CCDS8468.1, CCDS58192.1	11q24.2	2013-02-11	2012-12-07		ENSG00000064309	ENSG00000064309		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17104	protein-coding gene	gene with protein product	"""cell adhesion molecule-related/down-regulated by oncogenes"""	608707	"""Cdon homolog (mouse)"""			9214393	Standard	NM_016952		Approved	ORCAM, CDO, CDON1	uc009zbw.3	Q4KMG0	OTTHUMG00000165862	ENST00000392693.3:c.3294G>A	11.37:g.125848261C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	4	0.0625	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			C|0.626;T|0.374	0.374	strong		0.438	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
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 GAIIx	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		Somatic	71	0	0	698	WXS	Illumina HiSeq	Phase_I	83	5	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	
OR2T8	343172	hgsc.bcm.edu	37	1	248084471	248084471	+	Missense_Mutation	SNP	A	A	G	rs149623571	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248084471A>G	ENST00000319968.4	+	1	152	c.152A>G	c.(151-153)cAc>cGc	p.H51R		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CACTGGGACCACCGGCTCCAC	0.532													G|||	776	0.154952	0.2821	0.2392	5008	,	,		14590	0.004		0.1581	False		,,,				2504	0.0757				p.H51R		Atlas-SNP	.											OR2T8,rectum,carcinoma,+1,2	OR2T8	67	2	0			c.A152G						scavenged	.						60.0	59.0	60.0					1																	248084471		2201	4297	6498	SO:0001583	missense	343172	exon1			GGGACCACCGGCT		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.152A>G	1.37:g.248084471A>G	ENSP00000326225:p.His51Arg	Somatic	369	2	0.00542005		WXS	Illumina HiSeq	Phase_I	418	51	0.12201	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	320	0.14652014652014653	112	0.22764227642276422	88	0.2430939226519337	4	0.006993006993006993	116	0.15303430079155672	N	4.374	0.068886	0.08436	.	.	ENSG00000177462	ENST00000319968	T	0.00424	7.45	3.65	-7.3	0.01446	GPCR, rhodopsin-like superfamily (1);	3.036110	0.01499	N	0.017405	T	0.00012	0.0000	N	0.05031	-0.125	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	9	0.34782	T	0.22	.	3.6878	0.08335	0.5299:0.2034:0.1819:0.0848	.	51	A6NH00	OR2T8_HUMAN	R	51	ENSP00000326225:H51R	ENSP00000326225:H51R	H	+	2	0	OR2T8	246151094	0.363000	0.24989	0.000000	0.03702	0.006000	0.05464	0.922000	0.28734	-2.024000	0.00936	-1.176000	0.01726	CAC	A|0.875;G|0.125	0.125	strong		0.532	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
ZGLP1	100125288	hgsc.bcm.edu	37	19	10419130	10419130	+	Silent	SNP	C	C	T	rs281417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10419130C>T	ENST00000403903.3	-	1	1426	c.228G>A	c.(226-228)ccG>ccA	p.P76P	FDX1L_ENST00000541276.1_Intron|ZGLP1_ENST00000403352.1_5'UTR|CTD-2369P2.10_ENST00000452032.2_Intron|FDX1L_ENST00000492239.1_5'Flank	NM_001103167.1	NP_001096637.1	P0C6A0	ZGLP1_HUMAN	zinc finger, GATA-like protein 1	76					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P76P(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|ovary(1)	6						GCCCCAGGACCGGGGTGTCCT	0.657													C|||	1274	0.254393	0.3328	0.2061	5008	,	,		14662	0.1121		0.2922	False		,,,				2504	0.2904				p.P76P		Atlas-SNP	.											ZGLP1_ENST00000403903,NS,lymphoid_neoplasm,0,2	ZGLP1	18	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.G228A						PASS	.	C		1084,2734		132,820,957	21.0	24.0	23.0		228	-2.4	0.0	19	dbSNP_79	23	2622,5616		417,1788,1914	no	coding-synonymous	ZGLP1	NM_001103167.1		549,2608,2871	TT,TC,CC		31.8281,28.3918,30.7399		76/272	10419130	3706,8350	1909	4119	6028	SO:0001819	synonymous_variant	100125288	exon1			CAGGACCGGGGTG	AK096830	CCDS45959.1	19p13.2	2013-01-25			ENSG00000220201	ENSG00000220201		"""GATA zinc finger domain containing"""	37245	protein-coding gene	gene with protein product	"""GATA like protein 1"", ""GATA zinc finger domain containing 3"""	611639				16982049	Standard	NM_001103167		Approved	GLP1, GLP-1, GATAD3	uc002mnw.4	P0C6A0	OTTHUMG00000152114	ENST00000403903.3:c.228G>A	19.37:g.10419130C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_001103167		Silent	SNP	ENST00000403903.3	37	CCDS45959.1																																																																																			C|0.758;T|0.242	0.242	strong		0.657	ZGLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325278.1	NM_001103167	
DNMBP	23268	hgsc.bcm.edu	37	10	101639796	101639796	+	Silent	SNP	G	G	A	rs2255901	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101639796G>A	ENST00000324109.4	-	16	4411	c.4320C>T	c.(4318-4320)tcC>tcT	p.S1440S	DNMBP_ENST00000540316.1_Silent_p.S376S|DNMBP_ENST00000342239.3_Silent_p.S1464S|DNMBP_ENST00000543621.1_Silent_p.S686S	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	1440	Ser-rich.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		GCTGGGAGGTGGAGTCTGGGT	0.532													A|||	2326	0.464457	0.5386	0.4798	5008	,	,		21013	0.2679		0.5388	False		,,,				2504	0.4796				p.S1440S		Atlas-SNP	.											DNMBP,NS,adenoma,0,1	DNMBP	173	1	0			c.C4320T						PASS	.			2356,2050	568.5+/-382.4	629,1098,476	154.0	150.0	151.0		4320	-1.7	0.0	10	dbSNP_100	151	4503,4097	562.1+/-387.9	1190,2123,987	no	coding-synonymous	DNMBP	NM_015221.2		1819,3221,1463	AA,AG,GG		47.6395,46.5275,47.2628		1440/1578	101639796	6859,6147	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon16			GGAGGTGGAGTCT	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.4320C>T	10.37:g.101639796G>A		Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	223	223	1	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			G|0.502;A|0.498	0.498	strong		0.532	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
HSPG2	3339	hgsc.bcm.edu	37	1	22154387	22154387	+	Silent	SNP	G	G	A	rs11552570	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22154387G>A	ENST00000374695.3	-	91	12637	c.12558C>T	c.(12556-12558)tcC>tcT	p.S4186S	HSPG2_ENST00000486901.1_5'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	4186					angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GATGCCAGTCGGACTCTGCTA	0.597													G|||	146	0.0291534	0.0015	0.0231	5008	,	,		18717	0.0		0.0398	False		,,,				2504	0.09				p.S4186S		Atlas-SNP	.											.	HSPG2	311	.	0			c.C12558T						PASS	.	G		38,4364		0,38,2163	50.0	46.0	47.0		12558	-3.4	0.7	1	dbSNP_120	47	417,8179		14,389,3895	no	coding-synonymous	HSPG2	NM_005529.5		14,427,6058	AA,AG,GG		4.8511,0.8632,3.5005		4186/4392	22154387	455,12543	2201	4298	6499	SO:0001819	synonymous_variant	3339	exon91			CCAGTCGGACTCT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.12558C>T	1.37:g.22154387G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			G|0.971;C|0.000;A|0.029	0.029	strong		0.597	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
OSCAR	126014	hgsc.bcm.edu	37	19	54599222	54599222	+	Silent	SNP	G	G	T	rs61742144	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54599222G>T	ENST00000284648.6	-	5	767	c.570C>A	c.(568-570)ccC>ccA	p.P190P	OSCAR_ENST00000391761.1_Silent_p.P179P|OSCAR_ENST00000358375.4_Silent_p.P190P|OSCAR_ENST00000351806.4_Silent_p.P179P|OSCAR_ENST00000356532.3_Silent_p.P194P|OSCAR_ENST00000359649.4_Silent_p.P194P|OSCAR_ENST00000391760.1_Silent_p.R133R			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor	190	Ig-like 2.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					TGTAGGTGCCGGGGGCGCGGG	0.711													g|||	640	0.127796	0.1831	0.1182	5008	,	,		11804	0.0526		0.1113	False		,,,				2504	0.1544				p.P194P		Atlas-SNP	.											OSCAR_ENST00000356532,NS,carcinoma,0,2	OSCAR	22	2	0			c.C582A						PASS	.	T	,,,	640,3676		47,546,1565	7.0	8.0	8.0		582,537,570,582	-8.1	0.0	19	dbSNP_129	8	968,7474		66,836,3319	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSCAR	NM_130771.3,NM_133168.3,NM_133169.3,NM_206818.1	,,,	113,1382,4884	TT,TG,GG		11.4665,14.8285,12.6039	,,,	194/268,179/253,190/264,194/287	54599222	1608,11150	2158	4221	6379	SO:0001819	synonymous_variant	126014	exon5			GGTGCCGGGGGCG	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.570C>A	19.37:g.54599222G>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_130771	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Silent	SNP	ENST00000284648.6	37																																																																																				G|0.886;T|0.114	0.114	strong		0.711	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169	
CSMD1	64478	hgsc.bcm.edu	37	8	2800096	2800096	+	Missense_Mutation	SNP	C	C	T	rs11984691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:2800096C>T	ENST00000520002.1	-	70	10991	c.10436G>A	c.(10435-10437)aGt>aAt	p.S3479N	CSMD1_ENST00000400186.3_Missense_Mutation_p.S3302N|CSMD1_ENST00000542608.1_Missense_Mutation_p.S3301N|CSMD1_ENST00000602557.1_Missense_Mutation_p.S3479N|CSMD1_ENST00000537824.1_Missense_Mutation_p.S3478N|CSMD1_ENST00000602723.1_Missense_Mutation_p.S3302N			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3479			S -> N (in dbSNP:rs11984691).			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)		GTGGTAATGACTGGAAGAGTC	0.378													c|||	303	0.0605032	0.177	0.0346	5008	,	,		16155	0.0069		0.0119	False		,,,				2504	0.0266				p.S3478N		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G10433A						PASS	.	T	ASN/SER	559,3139		50,459,1340	47.0	50.0	49.0		10433	0.6	0.0	8	dbSNP_120	49	146,8032		3,140,3946	yes	missense	CSMD1	NM_033225.5	46	53,599,5286	TT,TC,CC		1.7853,15.1163,5.9363	benign	3478/3565	2800096	705,11171	1849	4089	5938	SO:0001583	missense	64478	exon69			TAATGACTGGAAG			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.10436G>A	8.37:g.2800096C>T	ENSP00000430733:p.Ser3479Asn	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		133	0.060897435897435896	106	0.21544715447154472	17	0.04696132596685083	4	0.006993006993006993	6	0.0079155672823219	c	0.274	-0.990665	0.02162	0.151163	0.017853	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.22539	1.95;2.03;2.05;1.95	5.67	0.558	0.17266	.	0.121454	0.53938	N	0.000060	T	0.00012	0.0000	N	0.01505	-0.83	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.45411	-0.9263	9	0.02654	T	1	.	11.0611	0.47948	0.0:0.2633:0.0:0.7367	rs11984691;rs52793013;rs59724479;rs11984691	3479;3479;3301	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	N	3302;3479;3340;3478;3301	ENSP00000383047:S3302N;ENSP00000430733:S3479N;ENSP00000441462:S3478N;ENSP00000446243:S3301N	ENSP00000320445:S3340N	S	-	2	0	CSMD1	2787503	0.957000	0.32711	0.000000	0.03702	0.003000	0.03518	1.593000	0.36686	-0.388000	0.07797	-2.082000	0.00379	AGT	C|0.939;T|0.061	0.061	strong		0.378	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
PNMAL2	57469	hgsc.bcm.edu	37	19	46998236	46998236	+	Missense_Mutation	SNP	C	C	T	rs4803967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46998236C>T	ENST00000377655.2	-	1	486	c.487G>A	c.(487-489)Ggt>Agt	p.G163S	PNMAL2_ENST00000594749.1_Intron|PNMAL2_ENST00000599531.1_Missense_Mutation_p.G163S|AC011484.1_ENST00000377652.3_Missense_Mutation_p.P116L			Q9ULN7	PNML2_HUMAN	paraneoplastic Ma antigen family-like 2	163	Arg-rich.									central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(4)	8		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000322)|all cancers(93;0.00233)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		TTTCTGCGACCCCGACGGCCC	0.657													C|||	413	0.0824681	0.0976	0.1311	5008	,	,		15032	0.0069		0.1551	False		,,,				2504	0.0307				p.G163S		Atlas-SNP	.											.	PNMAL2	44	.	0			c.G487A						PASS	.	C	,SER/GLY	548,3858	245.6+/-254.5	27,494,1682	64.0	61.0	62.0		,487	2.9	0.0	19	dbSNP_111	62	1361,7239	264.3+/-285.5	123,1115,3062	yes	intron,missense	PNMAL2,LOC100506012	NM_001205281.1,NM_020709.1	,56	150,1609,4744	TT,TC,CC		15.8256,12.4376,14.6778	,probably-damaging	,163/636	46998236	1909,11097	2203	4300	6503	SO:0001583	missense	57469	exon1			TGCGACCCCGACG	AB033009	CCDS59400.1	19q13.32	2014-02-12	2012-02-09		ENSG00000204851	ENSG00000204851		"""Paraneoplastic Ma antigens"""	29206	protein-coding gene	gene with protein product			"""PNMA-like 2"""			10574461	Standard	NM_020709		Approved	KIAA1183	uc002pes.2	Q9ULN7		ENST00000377655.2:c.487G>A	19.37:g.46998236C>T	ENSP00000366883:p.Gly163Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_020709	C9JGD5|M0R374|Q08E79|Q0D2F9|Q6ZVD1	Missense_Mutation	SNP	ENST00000377655.2	37		231|231	0.10576923076923077|0.10576923076923077	51|51	0.10365853658536585|0.10365853658536585	58|58	0.16022099447513813|0.16022099447513813	3|3	0.005244755244755245|0.005244755244755245	119|119	0.15699208443271767|0.15699208443271767	C|C	18.53|18.53	3.644613|3.644613	0.67358|0.67358	0.124376|0.124376	0.158256|0.158256	ENSG00000204851|ENSG00000204850	ENST00000377655|ENST00000377652	T|.	0.35048|.	1.33|.	2.93|2.93	2.93|2.93	0.34026|0.34026	.|.	.|.	.|.	.|.	.|.	T|T	0.00241|0.00241	0.0007|0.0007	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	D|D	0.67145|0.61080	0.996|0.989	D|P	0.64237|0.62014	0.923|0.897	T|T	0.09228|0.09228	-1.0684|-1.0684	8|7	0.20519|0.87932	T|D	0.43|0	-6.8798|-6.8798	9.5575|9.5575	0.39348|0.39348	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs4803967;rs4803967|rs4803967;rs4803967	163|116	Q9ULN7|Q6ZVU4	PNML2_HUMAN|.	S|L	163|116	ENSP00000366883:G163S|.	ENSP00000366883:G163S|ENSP00000366880:P116L	G|P	-|+	1|2	0|0	PNMAL2|AC011484.1	51690076|51690076	0.022000|0.022000	0.18835|0.18835	0.014000|0.014000	0.15608|0.15608	0.692000|0.692000	0.40212|0.40212	1.437000|1.437000	0.34991|0.34991	1.922000|1.922000	0.55676|0.55676	0.491000|0.491000	0.48974|0.48974	GGT|CCC	C|0.876;T|0.124	0.124	strong		0.657	PNMAL2-201	KNOWN	basic	protein_coding	protein_coding		NM_020709	
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 GAIIx	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	RP11-767N6.7_ENST00000430643.1_RNA|TMEM69_ENST00000496366.1_3'UTR	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		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	38	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	
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 GAIIx	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	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	113	6	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	
DENND1C	79958	hgsc.bcm.edu	37	19	6468331	6468331	+	Missense_Mutation	SNP	T	T	C	rs62107586	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:6468331T>C	ENST00000381480.2	-	22	1817	c.1705A>G	c.(1705-1707)Atg>Gtg	p.M569V	DENND1C_ENST00000543576.1_Missense_Mutation_p.M525V	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	569					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						TTGGCTCCCATGCTAAGACTG	0.582													C|||	1147	0.229034	0.3245	0.245	5008	,	,		17696	0.003		0.3877	False		,,,				2504	0.1585				p.M569V		Atlas-SNP	.											.	DENND1C	93	.	0			c.A1705G						PASS	.	C	VAL/MET	1327,2747		224,879,934	50.0	52.0	51.0		1705	-5.2	0.0	19	dbSNP_129	51	3596,4782		756,2084,1349	yes	missense	DENND1C	NM_024898.2	21	980,2963,2283	CC,CT,TT		42.9219,32.5724,39.5358	benign	569/802	6468331	4923,7529	2037	4189	6226	SO:0001583	missense	79958	exon22			CTCCCATGCTAAG	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1705A>G	19.37:g.6468331T>C	ENSP00000370889:p.Met569Val	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	560	0.2564102564102564	176	0.35772357723577236	99	0.27348066298342544	2	0.0034965034965034965	283	0.3733509234828496	C	0.015	-1.565636	0.00903	0.325724	0.429219	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.08546	3.25;3.08	4.75	-5.17	0.02849	.	1.339980	0.05292	N	0.521292	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46555	-0.9183	9	0.02654	T	1	0.2663	6.0997	0.20041	0.0:0.22:0.2458:0.5342	rs62107586	569	Q8IV53	DEN1C_HUMAN	V	569;525	ENSP00000370889:M569V;ENSP00000437805:M525V	ENSP00000370889:M569V	M	-	1	0	DENND1C	6419331	0.000000	0.05858	0.000000	0.03702	0.392000	0.30506	-1.413000	0.02473	-0.799000	0.04439	-0.684000	0.03749	ATG	A|0.000;C|0.295;G|0.000;T|0.705	0.295	strong		0.582	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
CLOCK	9575	hgsc.bcm.edu	37	4	56325365	56325365	+	Missense_Mutation	SNP	G	G	C	rs34897046	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:56325365G>C	ENST00000309964.4	-	9	873	c.623C>G	c.(622-624)tCt>tGt	p.S208C	CLOCK_ENST00000513440.1_Missense_Mutation_p.S208C|CLOCK_ENST00000381322.1_Missense_Mutation_p.S208C	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	208			S -> C (in dbSNP:rs34897046).		cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|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 (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			TTCATAGGTAGATGGCTCCTT	0.303													G|||	97	0.019369	0.0038	0.0245	5008	,	,		18720	0.001		0.0447	False		,,,				2504	0.0297				p.S208C		Atlas-SNP	.											.	CLOCK	81	.	0			c.C623G						PASS	.	G	CYS/SER	49,4355	49.6+/-84.7	0,49,2153	53.0	53.0	53.0		623	5.9	1.0	4	dbSNP_126	53	445,8147	133.8+/-191.2	14,417,3865	yes	missense	CLOCK	NM_004898.2	112	14,466,6018	CC,CG,GG		5.1792,1.1126,3.8012	benign	208/847	56325365	494,12502	2202	4296	6498	SO:0001583	missense	9575	exon10			TAGGTAGATGGCT	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	2082	protein-coding gene	gene with protein product		601851	"""clock (mouse) homolog"", ""clock homolog (mouse)"""			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.623C>G	4.37:g.56325365G>C	ENSP00000308741:p.Ser208Cys	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	133	65	0.488722	NM_004898	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	54	0.024725274725274724	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	40	0.052770448548812667	G	21.2	4.116404	0.77323	0.011126	0.051792	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	T;T;T	0.04454	3.62;3.62;3.62	5.87	5.87	0.94306	.	0.259104	0.46442	D	0.000289	T	0.01124	0.0037	L	0.32530	0.975	0.48571	D	0.999677	P	0.40250	0.709	B	0.42087	0.375	T	0.21586	-1.0241	10	0.72032	D	0.01	.	20.2147	0.98293	0.0:0.0:1.0:0.0	rs34897046	208	O15516	CLOCK_HUMAN	C	208	ENSP00000308741:S208C;ENSP00000370723:S208C;ENSP00000426983:S208C	ENSP00000308741:S208C	S	-	2	0	CLOCK	56020122	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.388000	0.97237	2.785000	0.95823	0.591000	0.81541	TCT	G|0.964;C|0.036	0.036	strong		0.303	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898	
ZNF653	115950	hgsc.bcm.edu	37	19	11598483	11598483	+	Silent	SNP	T	T	C	rs311805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:11598483T>C	ENST00000293771.5	-	4	931	c.795A>G	c.(793-795)ccA>ccG	p.P265P	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						CATTGCCTGCTGGGTTGGAGC	0.662													C|||	1540	0.307508	0.7632	0.2089	5008	,	,		14453	0.1181		0.1153	False		,,,				2504	0.1544				p.P265P	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											ZNF653,NS,carcinoma,0,2	ZNF653	48	2	0			c.A795G						PASS	.	C		2938,1468	448.3+/-348.6	988,962,253	43.0	46.0	45.0		795	-9.0	0.0	19	dbSNP_79	45	847,7751	757.7+/-407.5	45,757,3497	no	coding-synonymous	ZNF653	NM_138783.3		1033,1719,3750	CC,CT,TT		9.8511,33.3182,29.1064		265/616	11598483	3785,9219	2203	4299	6502	SO:0001819	synonymous_variant	115950	exon4			GCCTGCTGGGTTG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.795A>G	19.37:g.11598483T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	165	79	0.478788	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			T|0.731;C|0.269	0.269	strong		0.662	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
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 GAIIx	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		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	102	58	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	
SLCO6A1	133482	hgsc.bcm.edu	37	5	101724448	101724448	+	Missense_Mutation	SNP	G	G	C	rs10055840	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:101724448G>C	ENST00000506729.1	-	12	2132	c.1961C>G	c.(1960-1962)aCa>aGa	p.T654R	SLCO6A1_ENST00000389019.3_Missense_Mutation_p.T592R|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.T401R|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.T401R|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.T654R			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	654			T -> R (in dbSNP:rs10055840). {ECO:0000269|PubMed:14702039}.			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)		ACAACGTCCTGTGTGTCCACA	0.303													G|||	1022	0.204073	0.171	0.1686	5008	,	,		14921	0.1706		0.3022	False		,,,				2504	0.2076				p.T654R		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.C1961G						PASS	.	G	ARG/THR	761,3641	307.2+/-289.9	71,619,1511	72.0	72.0	72.0		1961	-10.1	0.0	5	dbSNP_119	72	2284,6308	382.7+/-340.5	306,1672,2318	yes	missense	SLCO6A1	NM_173488.3	71	377,2291,3829	CC,CG,GG		26.5829,17.2876,23.4339	benign	654/720	101724448	3045,9949	2201	4296	6497	SO:0001583	missense	133482	exon12			CGTCCTGTGTGTC	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.1961C>G	5.37:g.101724448G>C	ENSP00000421339:p.Thr654Arg	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	180	91	0.505556	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	487	0.222985347985348	94	0.1910569105691057	71	0.19613259668508287	96	0.16783216783216784	226	0.29815303430079154	G	0.068	-1.208966	0.01568	0.172876	0.265829	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27	5.06	-10.1	0.00402	Major facilitator superfamily domain, general substrate transporter (1);	2.166740	0.01881	N	0.037874	T	0.00012	0.0000	N	0.10972	0.075	0.80722	P	0.0	B;B;B	0.18310	0.001;0.027;0.001	B;B;B	0.28385	0.003;0.089;0.008	T	0.04930	-1.0917	9	0.14656	T	0.56	.	2.5457	0.04736	0.1226:0.3074:0.3555:0.2146	rs10055840;rs17273123;rs10055840	592;401;654	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	R	654;654;592;401;401	ENSP00000421339:T654R;ENSP00000369135:T654R;ENSP00000373671:T592R;ENSP00000421990:T401R;ENSP00000369138:T401R	ENSP00000369135:T654R	T	-	2	0	SLCO6A1	101752347	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.032000	0.00309	-5.239000	0.00018	-0.145000	0.13849	ACA	G|0.778;C|0.222	0.222	strong		0.303	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
CACNA1A	773	hgsc.bcm.edu	37	19	13482554	13482554	+	Silent	SNP	C	C	T	rs41276894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:13482554C>T	ENST00000360228.5	-	4	578	c.579G>A	c.(577-579)acG>acA	p.T193T	CACNA1A_ENST00000573710.2_Silent_p.T193T	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	193					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CTGCCCTCAGCGTCCGTAGGT	0.592													C|||	20	0.00399361	0.0023	0.0029	5008	,	,		17505	0.0		0.0129	False		,,,				2504	0.002				p.T193T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G579A						PASS	.	C	,,,,	18,3972		0,18,1977	19.0	23.0	21.0		579,579,579,579,579	-5.9	0.9	19	dbSNP_127	21	151,8163		0,151,4006	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	0,169,5983	TT,TC,CC		1.8162,0.4511,1.3735	,,,,	193/2267,193/2262,193/2507,193/2264,193/2513	13482554	169,12135	1995	4157	6152	SO:0001819	synonymous_variant	773	exon4			CCTCAGCGTCCGT	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.579G>A	19.37:g.13482554C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.994;T|0.006	0.006	strong		0.592	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
SYDE2	84144	hgsc.bcm.edu	37	1	85656421	85656421	+	Missense_Mutation	SNP	C	C	T	rs192842795	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:85656421C>T	ENST00000341460.5	-	2	809	c.760G>A	c.(760-762)Gcc>Acc	p.A254T		NM_032184.1	NP_115560.1	Q5VT97	SYDE2_HUMAN	synapse defective 1, Rho GTPase, homolog 2 (C. elegans)	254					activation of Rho GTPase activity (GO:0032862)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	20				all cancers(265;0.0126)|Epithelial(280;0.0336)		GACCCATAGGCATTTTCAAAT	0.338													C|||	3	0.000599042	0.0	0.0	5008	,	,		16650	0.0		0.003	False		,,,				2504	0.0				p.A254T		Atlas-SNP	.											.	SYDE2	135	.	0			c.G760A						PASS	.	C	THR/ALA	5,3615		0,5,1805	136.0	133.0	134.0		760	3.3	0.9	1		134	58,8078		0,58,4010	yes	missense	SYDE2	NM_032184.1	58	0,63,5815	TT,TC,CC		0.7129,0.1381,0.5359	benign	254/1195	85656421	63,11693	1810	4068	5878	SO:0001583	missense	84144	exon2			CATAGGCATTTTC	AL834286	CCDS44169.1	1p22.3	2008-02-05		2005-08-09	ENSG00000097096	ENSG00000097096			25841	protein-coding gene	gene with protein product							Standard	NM_032184		Approved	FLJ13815	uc009wcm.3	Q5VT97	OTTHUMG00000009956	ENST00000341460.5:c.760G>A	1.37:g.85656421C>T	ENSP00000340594:p.Ala254Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_032184	Q5VT96|Q8NDB8|Q9H8A6	Missense_Mutation	SNP	ENST00000341460.5	37	CCDS44169.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.31	3.086965	0.55861	0.001381	0.007129	ENSG00000097096	ENST00000341460	T	0.07688	3.17	6.17	3.29	0.37713	.	0.270733	0.35772	N	0.002999	T	0.01905	0.0060	N	0.22421	0.69	0.26817	N	0.96887	B;B	0.29301	0.094;0.241	B;B	0.25140	0.026;0.058	T	0.40515	-0.9559	10	0.72032	D	0.01	.	8.869	0.35305	0.1238:0.7491:0.0:0.1271	.	254;254	Q5VT97;Q5VT97-2	SYDE2_HUMAN;.	T	254	ENSP00000340594:A254T	ENSP00000340594:A254T	A	-	1	0	SYDE2	85429009	1.000000	0.71417	0.879000	0.34478	0.955000	0.61496	2.368000	0.44222	0.471000	0.27319	0.655000	0.94253	GCC	C|0.998;T|0.002	0.002	strong		0.338	SYDE2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127989.2		
OR2T4	127074	hgsc.bcm.edu	37	1	248525071	248525071	+	Silent	SNP	T	T	C	rs28499298	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248525071T>C	ENST00000366475.1	+	1	189	c.189T>C	c.(187-189)atT>atC	p.I63I		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	63						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	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)			GTGTGGTCATTTTTGTGGTTT	0.483													t|||	1734	0.346246	0.3926	0.2896	5008	,	,		21339	0.4385		0.1948	False		,,,				2504	0.3845				p.I63I		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	1	0			c.T189C						scavenged	.						196.0	194.0	195.0					1																	248525071		2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			GGTCATTTTTGTG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.189T>C	1.37:g.248525071T>C		Somatic	527	0	0		WXS	Illumina HiSeq	Phase_I	521	29	0.0556622	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			T|0.769;C|0.231	0.231	strong		0.483	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
CHRNG	1146	hgsc.bcm.edu	37	2	233410294	233410294	+	Silent	SNP	C	C	T	rs2099489	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233410294C>T	ENST00000389494.3	+	12	1443	c.1422C>T	c.(1420-1422)cgC>cgT	p.R474R	CHRNG_ENST00000389492.3_Silent_p.R422R	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	474					muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)			breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		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;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	TGCTGGACCGCGTCTGCTTCC	0.647													C|||	761	0.151957	0.1051	0.134	5008	,	,		17988	0.1181		0.1928	False		,,,				2504	0.2209				p.R474R		Atlas-SNP	.											.	CHRNG	54	.	0			c.C1422T						PASS	.	C		551,3855	247.8+/-255.9	43,465,1695	111.0	81.0	91.0		1422	-9.1	0.8	2	dbSNP_96	91	1744,6856	318.2+/-313.6	182,1380,2738	no	coding-synonymous	CHRNG	NM_005199.4		225,1845,4433	TT,TC,CC		20.2791,12.5057,17.6457		474/518	233410294	2295,10711	2203	4300	6503	SO:0001819	synonymous_variant	1146	exon12			GGACCGCGTCTGC	X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1967	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, gamma (muscle)"""	100730	"""cholinergic receptor, nicotinic, gamma"""	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.1422C>T	2.37:g.233410294C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_005199	B3KWM8|Q14DU4|Q53RG2	Silent	SNP	ENST00000389494.3	37	CCDS33400.1																																																																																			C|0.836;T|0.164	0.164	strong		0.647	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199	
CCDC65	85478	hgsc.bcm.edu	37	12	49314862	49314862	+	Silent	SNP	C	C	A	rs10875894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49314862C>A	ENST00000320516.4	+	7	1364	c.1176C>A	c.(1174-1176)acC>acA	p.T392T	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Silent_p.T392T	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	392										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						AGGAGCTCACCAAGGTAAAGC	0.498													C|||	1544	0.308307	0.1014	0.4942	5008	,	,		18415	0.4454		0.4095	False		,,,				2504	0.2106				p.T392T		Atlas-SNP	.											CCDC65,NS,carcinoma,+1,2	CCDC65	41	2	0			c.C1176A						PASS	.	C		690,3716	279.6+/-274.9	70,550,1583	45.0	48.0	47.0		1176	-5.2	0.0	12	dbSNP_120	47	3281,5319	484.2+/-371.3	618,2045,1637	no	coding-synonymous	CCDC65	NM_033124.4		688,2595,3220	AA,AC,CC		38.1512,15.6605,30.5321		392/485	49314862	3971,9035	2203	4300	6503	SO:0001819	synonymous_variant	85478	exon7			GCTCACCAAGGTA		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.1176C>A	12.37:g.49314862C>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Silent	SNP	ENST00000320516.4	37	CCDS8772.1																																																																																			C|0.681;A|0.319	0.319	strong		0.498	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
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 GAIIx	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		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	125	62	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	
MUC5B	727897	hgsc.bcm.edu	37	11	1268481	1268481	+	Silent	SNP	G	G	A	rs186744090	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1268481G>A	ENST00000529681.1	+	31	10429	c.10371G>A	c.(10369-10371)cgG>cgA	p.R3457R	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.R3460R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3457	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	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)		CACACGGGCGGTCCCTGCCCC	0.677																																					p.R3457R		Atlas-SNP	.											MUC5B,NS,haematopoietic_neoplasm,0,4	MUC5B	473	4	0			c.G10371A						scavenged	.						99.0	137.0	124.0					11																	1268481		2117	4240	6357	SO:0001819	synonymous_variant	727897	exon31			CGGGCGGTCCCTG	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.10371G>A	11.37:g.1268481G>A		Somatic	402	0	0		WXS	Illumina HiSeq	Phase_I	390	109	0.279487	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.973;A|0.027	0.027	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
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 GAIIx	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_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_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		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	92	24	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 GAIIx	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_ENST00000312917.5_Silent_p.I185I|PNPLA1_ENST00000388715.3_Silent_p.I176I	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		Somatic	108	0	0	861	WXS	Illumina HiSeq	Phase_I	87	61	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	
GPRC6A	222545	hgsc.bcm.edu	37	6	117130544	117130544	+	Missense_Mutation	SNP	A	A	C	rs28360548	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:117130544A>C	ENST00000310357.3	-	2	452	c.431T>G	c.(430-432)aTa>aGa	p.I144R	GPRC6A_ENST00000368549.3_Missense_Mutation_p.I144R|GPRC6A_ENST00000530250.1_Missense_Mutation_p.I144R	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	144			I -> R (in dbSNP:rs28360548).		calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CCCAGAACCTATGACAGCCTT	0.433													A|||	939	0.1875	0.1657	0.17	5008	,	,		19939	0.0218		0.33	False		,,,				2504	0.2536				p.I144R		Atlas-SNP	.											.	GPRC6A	152	.	0			c.T431G						PASS	.	A	ARG/ILE	822,3584	325.9+/-299.3	86,650,1467	93.0	89.0	90.0		431	4.9	1.0	6	dbSNP_125	90	2897,5703	454.1+/-363.4	486,1925,1889	yes	missense	GPRC6A	NM_148963.2	97	572,2575,3356	CC,CA,AA		33.686,18.6564,28.5945	probably-damaging	144/927	117130544	3719,9287	2203	4300	6503	SO:0001583	missense	222545	exon2			GAACCTATGACAG	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.431T>G	6.37:g.117130544A>C	ENSP00000309493:p.Ile144Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	CCDS5112.1	402	0.18406593406593408	78	0.15853658536585366	66	0.18232044198895028	13	0.022727272727272728	245	0.3232189973614776	A	18.19	3.568339	0.65651	0.186564	0.33686	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.87179	-2.22;-2.22;-2.22	4.86	4.86	0.63082	Extracellular ligand-binding receptor (1);	0.063736	0.56097	D	0.000023	D	0.91828	0.7414	M	0.88775	2.98	0.27601	P	0.9489647999999999	D;D;D	0.69078	0.997;0.996;0.996	D;D;D	0.69479	0.949;0.931;0.964	D	0.93396	0.6756	9	0.87932	D	0	.	9.4609	0.38785	0.9097:0.0:0.0903:0.0	rs28360548	144;144;144	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	R	144	ENSP00000309493:I144R;ENSP00000357537:I144R;ENSP00000433465:I144R	ENSP00000309493:I144R	I	-	2	0	GPRC6A	117237237	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.904000	0.56325	2.047000	0.60756	0.477000	0.44152	ATA	A|0.747;C|0.253	0.253	strong		0.433	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
GABRD	2563	hgsc.bcm.edu	37	1	1961466	1961466	+	Silent	SNP	C	C	T	rs28398772	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1961466C>T	ENST00000378585.4	+	9	1187	c.1104C>T	c.(1102-1104)gcC>gcT	p.A368A		NM_000815.4	NP_000806.2	O14764	GBRD_HUMAN	gamma-aminobutyric acid (GABA) A receptor, delta	368					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			central_nervous_system(2)|endometrium(3)|kidney(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;2.7e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.19e-38)|OV - Ovarian serous cystadenocarcinoma(86;3.17e-24)|GBM - Glioblastoma multiforme(42;9.56e-08)|Colorectal(212;4.12e-05)|COAD - Colon adenocarcinoma(227;0.000194)|Kidney(185;0.00231)|BRCA - Breast invasive adenocarcinoma(365;0.00441)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCTCTGCTGCCGGCGTCACGC	0.687													C|||	196	0.0391374	0.0008	0.0187	5008	,	,		15262	0.119		0.0249	False		,,,				2504	0.0378				p.A368A		Atlas-SNP	.											.	GABRD	49	.	0			c.C1104T						PASS	.	C		27,4369	30.8+/-60.4	0,27,2171	41.0	41.0	41.0		1104	-7.6	0.3	1	dbSNP_125	41	237,8339	92.8+/-154.8	2,233,4053	no	coding-synonymous	GABRD	NM_000815.4		2,260,6224	TT,TC,CC		2.7635,0.6142,2.0352		368/453	1961466	264,12708	2198	4288	6486	SO:0001819	synonymous_variant	2563	exon9			TGCTGCCGGCGTC	BC033801	CCDS36.1	1p36.3	2012-06-22			ENSG00000187730	ENSG00000187730		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4084	protein-coding gene	gene with protein product	"""GABA(A) receptor, delta"""	137163				2176788, 10965146	Standard	NM_000815		Approved		uc001aip.2	O14764	OTTHUMG00000041064	ENST00000378585.4:c.1104C>T	1.37:g.1961466C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	137	75	0.547445	NM_000815	Q8N4N9	Silent	SNP	ENST00000378585.4	37	CCDS36.1																																																																																			C|0.971;T|0.029	0.029	strong		0.687	GABRD-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098493.1	NM_000815	
ATPIF1	93974	hgsc.bcm.edu	37	1	28564279	28564279	+	Intron	SNP	A	A	G	rs9508	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:28564279A>G	ENST00000335514.5	+	3	230				RP5-1092A3.4_ENST00000604716.1_RNA|ATPIF1_ENST00000497986.1_Missense_Mutation_p.R63G|ATPIF1_ENST00000465645.1_3'UTR|ATPIF1_ENST00000468425.2_Intron	NM_016311.4	NP_057395.1	Q9UII2	ATIF1_HUMAN	ATPase inhibitory factor 1						angiogenesis (GO:0001525)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of nucleotide metabolic process (GO:0045980)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|reactive oxygen species metabolic process (GO:0072593)	cell surface (GO:0009986)|mitochondrion (GO:0005739)	angiostatin binding (GO:0043532)|ATPase binding (GO:0051117)|ATPase inhibitor activity (GO:0042030)|calmodulin binding (GO:0005516)|enzyme inhibitor activity (GO:0004857)|protein homodimerization activity (GO:0042803)			lung(4)	4		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;4.76e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;2.36e-22)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|BRCA - Breast invasive adenocarcinoma(304;0.00574)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		TAGACATTACAGGTTATGCTT	0.433													a|||	1655	0.330471	0.6596	0.2478	5008	,	,		20867	0.0992		0.2932	False		,,,				2504	0.2209				p.R63G		Atlas-SNP	.											.	ATPIF1	7	.	0			c.A187G						PASS	.	G	,GLY/ARG,	2657,1749	644.5+/-398.0	806,1045,352	116.0	111.0	113.0		,187,	-6.6	0.0	1	dbSNP_52	113	2581,6019	419.1+/-353.0	378,1825,2097	yes	intron,missense,utr-3	ATPIF1	NM_016311.4,NM_178190.2,NM_178191.2	,125,	1184,2870,2449	GG,GA,AA		30.0116,39.6959,40.2737	,,	,63/72,	28564279	5238,7768	2203	4300	6503	SO:0001627	intron_variant	93974	exon3			CATTACAGGTTAT	AL050386	CCDS319.1, CCDS320.1, CCDS44096.1	1p35.3	2011-07-04			ENSG00000130770	ENSG00000130770		"""Mitochondrial respiratory chain complex / Complex V"""	871	protein-coding gene	gene with protein product	"""ATPase inhibitor protein"", ""ATP synthase inhibitor protein"""	614981				10664857, 19559621	Standard	NM_016311		Approved	ATPI, IP, ATPIP, MGC1167, MGC8898	uc001bpq.3	Q9UII2	OTTHUMG00000003533	ENST00000335514.5:c.180-69A>G	1.37:g.28564279A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_178190	Q5JXL8|Q6IAQ7|Q9BSL9	Missense_Mutation	SNP	ENST00000335514.5	37	CCDS319.1	746	0.3415750915750916	335	0.6808943089430894	110	0.30386740331491713	69	0.12062937062937062	232	0.30606860158311344	a	1.761	-0.486726	0.04352	0.603041	0.300116	ENSG00000130770	ENST00000497986	.	.	.	4.04	-6.62	0.01813	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.33292	-0.9874	6	0.06236	T	0.91	.	8.5822	0.33634	0.3894:0.1183:0.4923:0.0	rs9508;rs1466786;rs3170652;rs17163023;rs56454924;rs57778066;rs9508	63	Q9UII2-2	.	G	63	.	ENSP00000435579:R63G	R	+	1	2	ATPIF1	28436866	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-1.794000	0.01753	-1.963000	0.01013	-2.668000	0.00145	AGG	A|0.626;G|0.374	0.374	strong		0.433	ATPIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009841.1	NM_016311	
ZHX2	22882	hgsc.bcm.edu	37	8	123964431	123964431	+	Silent	SNP	G	G	A	rs3204141	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:123964431G>A	ENST00000314393.4	+	3	1516	c.681G>A	c.(679-681)tcG>tcA	p.S227S		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	227	Required for homodimerization.				mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S227S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			AGATCCTCTCGAGACTCGGCG	0.597													G|||	1162	0.232029	0.0174	0.3256	5008	,	,		17175	0.1319		0.3549	False		,,,				2504	0.4325				p.S227S	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											ZHX2,NS,carcinoma,0,1	ZHX2	106	1	1	Substitution - coding silent(1)	stomach(1)	c.G681A						PASS	.	G		323,4083	170.5+/-200.9	11,301,1891	112.0	120.0	117.0		681	-6.4	0.5	8	dbSNP_105	117	2984,5616	462.5+/-365.7	510,1964,1826	no	coding-synonymous	ZHX2	NM_014943.3		521,2265,3717	AA,AG,GG		34.6977,7.3309,25.4267		227/838	123964431	3307,9699	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CCTCTCGAGACTC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.681G>A	8.37:g.123964431G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	109	54	0.495413	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			G|0.767;A|0.233	0.233	strong		0.597	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
OTC	5009	hgsc.bcm.edu	37	X	38268220	38268220	+	Missense_Mutation	SNP	A	A	G	rs1800328	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:38268220A>G	ENST00000039007.4	+	8	961	c.809A>G	c.(808-810)cAa>cGa	p.Q270R	TM4SF2_ENST00000465127.1_Intron	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	270			Q -> R (in about 5% of population; dbSNP:rs1800328). {ECO:0000269|PubMed:10070627, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:6372096}.		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)	p.Q270R(1)		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)	AGCATGGGACAAGAAGAGGAG	0.428													A|||	63	0.0166887	0.0	0.0173	3775	,	,		13014	0.001		0.0408	False		,,,				2504	0.0092				p.Q270R		Atlas-SNP	.											.	OTC	60	.	1	Substitution - Missense(1)	breast(1)	c.A809G	GRCh37	CM062960	OTC	M	rs1800328	PASS	.	A	ARG/GLN	22,3811		0,18,4,1613,567	90.0	81.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	809	5.6	1.0	X	dbSNP_89	84	329,6399		6,228,89,2194,1783	yes	missense	OTC	NM_000531.5	43	6,246,93,3807,2350	GG,GA,G,AA,A		4.89,0.574,3.3235	possibly-damaging	270/355	38268220	351,10210	2202	4300	6502	SO:0001583	missense	5009	exon8			TGGGACAAGAAGA	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.809A>G	X.37:g.38268220A>G	ENSP00000039007:p.Gln270Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	129	83	0.643411	NM_000531	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	34	0.020494273658830622	0	0.0	5	0.013888888888888888	1	0.0017482517482517483	19	0.025606469002695417	A	25.9	4.686268	0.88639	0.00574	0.0489	ENSG00000036473	ENST00000039007	D	0.98996	-5.31	5.58	5.58	0.84498	Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain (1);	0.150159	0.64402	D	0.000009	D	0.95884	0.8660	M	0.89968	3.075	0.19775	P	0.9999511488	D	0.56746	0.977	P	0.57720	0.826	D	0.86246	0.1646	9	0.62326	D	0.03	-15.2042	14.9212	0.70838	1.0:0.0:0.0:0.0	rs1800328;rs17359331	270	P00480	OTC_HUMAN	R	270	ENSP00000039007:Q270R	ENSP00000039007:Q270R	Q	+	2	0	OTC	38153164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.854000	0.92228	1.973000	0.57446	0.486000	0.48141	CAA	A|0.970;G|0.030	0.030	strong		0.428	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2		
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526044	150526044	+	Missense_Mutation	SNP	G	G	C	rs41317515	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:150526044G>C	ENST00000369038.2	+	4	778	c.577G>C	c.(577-579)Gct>Cct	p.A193P	ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.A193P|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.A193P|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.A193P			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	193			A -> P (in dbSNP:rs41317515). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			AGGGGAAGAGGCTATTCCGTC	0.607													C|||	2646	0.528355	0.6074	0.4337	5008	,	,		15288	0.5675		0.5338	False		,,,				2504	0.4427				p.A193P		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.G577C						PASS	.	C	PRO/ALA,PRO/ALA	2600,1806	530.3+/-372.9	787,1026,390	118.0	115.0	116.0		577,577	-4.6	0.0	1	dbSNP_127	116	4515,4085	561.1+/-387.7	1178,2159,963	yes	missense,missense	ADAMTSL4	NM_019032.4,NM_025008.3	27,27	1965,3185,1353	CC,CG,GG		47.5,40.9896,45.2945	benign,benign	193/1075,193/878	150526044	7115,5891	2203	4300	6503	SO:0001583	missense	54507	exon6			GAAGAGGCTATTC	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.577G>C	1.37:g.150526044G>C	ENSP00000358034:p.Ala193Pro	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	1217	0.5572344322344323	295	0.5995934959349594	177	0.4889502762430939	319	0.5576923076923077	426	0.5620052770448549	C	0.516	-0.864147	0.02590	0.590104	0.525	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000369039;ENST00000369038	T;T;T;T	0.63255	0.05;-0.03;0.23;-0.03	3.65	-4.57	0.03421	.	.	.	.	.	T	0.12603	0.0306	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.11641	-1.0579	8	0.28530	T	0.3	.	3.1698	0.06549	0.1886:0.2054:0.4843:0.1217	rs41317515;rs59910312;rs61819441	193;193;193	F8WAD0;Q6UY14;Q6UY14-2	.;ATL4_HUMAN;.	P	193	ENSP00000358037:A193P;ENSP00000271643:A193P;ENSP00000358035:A193P;ENSP00000358034:A193P	ENSP00000271643:A193P	A	+	1	0	ADAMTSL4	148792668	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	-1.494000	0.02296	-1.085000	0.03088	-1.087000	0.02190	GCT	G|0.456;C|0.544	0.544	strong		0.607	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
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 GAIIx	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	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	86	26	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		
PTK2B	2185	hgsc.bcm.edu	37	8	27277537	27277537	+	Silent	SNP	G	G	A	rs1030526	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27277537G>A	ENST00000397501.1	+	8	1138	c.330G>A	c.(328-330)acG>acA	p.T110T	PTK2B_ENST00000544172.1_Silent_p.T110T|PTK2B_ENST00000517339.1_Silent_p.T110T|PTK2B_ENST00000338238.4_Silent_p.T110T|PTK2B_ENST00000420218.2_Silent_p.T110T|PTK2B_ENST00000346049.5_Silent_p.T110T	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	110	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				activation of Janus kinase activity (GO:0042976)|activation of Rac GTPase activity (GO:0032863)|apoptotic process (GO:0006915)|blood vessel endothelial cell migration (GO:0043534)|bone resorption (GO:0045453)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|cellular response to retinoic acid (GO:0071300)|chemokine-mediated signaling pathway (GO:0070098)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|glial cell proliferation (GO:0014009)|integrin-mediated signaling pathway (GO:0007229)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term synaptic potentiation (GO:0060291)|MAPK cascade (GO:0000165)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of potassium ion transport (GO:0043267)|neuron projection development (GO:0031175)|oocyte maturation (GO:0001556)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of cell growth (GO:0030307)|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 cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of establishment of cell polarity (GO:2000114)|regulation of inositol trisphosphate biosynthetic process (GO:0032960)|regulation of macrophage chemotaxis (GO:0010758)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000058)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to calcium ion (GO:0051592)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|signal complex assembly (GO:0007172)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|stress fiber assembly (GO:0043149)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	apical dendrite (GO:0097440)|axon (GO:0030424)|cell body (GO:0044297)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane raft (GO:0045121)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(17)|ovary(4)|skin(12)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Ovarian(32;2.72e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|Epithelial(17;6.61e-10)|BRCA - Breast invasive adenocarcinoma(99;0.226)|Colorectal(74;0.229)	Leflunomide(DB01097)	CACAGATGACGGTGGGTGAGG	0.582													G|||	1936	0.386581	0.4228	0.2738	5008	,	,		19922	0.2718		0.4076	False		,,,				2504	0.5143				p.T110T		Atlas-SNP	.											.	PTK2B	304	.	0			c.G330A						PASS	.	G	,,,	1867,2539	540.1+/-375.4	400,1067,736	100.0	84.0	90.0		330,330,330,330	-10.3	0.2	8	dbSNP_86	90	3484,5116	508.9+/-377.2	727,2030,1543	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	1127,3097,2279	AA,AG,GG		40.5116,42.374,41.1425	,,,	110/1010,110/1010,110/968,110/1010	27277537	5351,7655	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon8			GATGACGGTGGGT	U33284	CCDS6057.1, CCDS6058.1	8p21.1	2013-02-18	2013-02-18		ENSG00000120899	ENSG00000120899			9612	protein-coding gene	gene with protein product		601212	"""protein tyrosine kinase 2 beta"", ""PTK2B protein tyrosine kinase 2 beta"""	FAK2		7544443, 7499242	Standard	NM_173174		Approved	CAKB, PYK2, RAFTK, PTK, CADTK	uc003xfp.2	Q14289	OTTHUMG00000102082	ENST00000397501.1:c.330G>A	8.37:g.27277537G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			G|0.621;A|0.379	0.379	strong		0.582	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
OR2D3	120775	hgsc.bcm.edu	37	11	6942628	6942628	+	Silent	SNP	A	A	C	rs11605995	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6942628A>C	ENST00000317834.3	+	1	424	c.396A>C	c.(394-396)gcA>gcC	p.A132A		NM_001004684.1	NP_001004684.1	Q8NGH3	OR2D3_HUMAN	olfactory receptor, family 2, subfamily D, member 3	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(2)|large_intestine(7)|lung(12)|prostate(3)|skin(1)|stomach(1)	27		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		CGCTGCTGGCAGTGATGTCCT	0.483													C|||	2040	0.407348	0.6241	0.3329	5008	,	,		19923	0.4464		0.1948	False		,,,				2504	0.3456				p.A132A		Atlas-SNP	.											.	OR2D3	51	.	0			c.A396C						PASS	.	C		2479,1923	547.5+/-377.3	692,1095,414	165.0	155.0	158.0		396	-10.1	0.0	11	dbSNP_120	158	1701,6891	738.4+/-407.1	172,1357,2767	no	coding-synonymous	OR2D3	NM_001004684.1		864,2452,3181	CC,CA,AA		19.7975,43.6847,32.1687		132/331	6942628	4180,8814	2201	4296	6497	SO:0001819	synonymous_variant	120775	exon1			GCTGGCAGTGATG	BK004294	CCDS31417.1	11p15.4	2012-08-09			ENSG00000178358	ENSG00000178358		"""GPCR / Class A : Olfactory receptors"""	15146	protein-coding gene	gene with protein product							Standard	NM_001004684		Approved		uc010rav.2	Q8NGH3	OTTHUMG00000165742	ENST00000317834.3:c.396A>C	11.37:g.6942628A>C		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	191	85	0.445026	NM_001004684	B2RP06|Q6IFG8|Q96R51	Silent	SNP	ENST00000317834.3	37	CCDS31417.1																																																																																			A|0.655;C|0.345	0.345	strong		0.483	OR2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385987.1	NM_001004684	
ABLIM3	22885	hgsc.bcm.edu	37	5	148626067	148626067	+	Silent	SNP	G	G	A	rs61999264	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148626067G>A	ENST00000506113.1	+	16	1991	c.1509G>A	c.(1507-1509)tcG>tcA	p.S503S	RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000517451.1_5'UTR|ABLIM3_ENST00000508983.1_Silent_p.S470S|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000309868.7_Silent_p.S503S|ABLIM3_ENST00000504238.1_Silent_p.S392S|ABLIM3_ENST00000326685.7_Silent_p.S408S|RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000356541.3_Silent_p.S392S			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	503					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)			GAAGGTTCTCGTCTGGAGGAG	0.488													G|||	40	0.00798722	0.0015	0.0144	5008	,	,		17053	0.005		0.0149	False		,,,				2504	0.0082				p.S503S		Atlas-SNP	.											.	ABLIM3	91	.	0			c.G1509A						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	96.0	85.0	89.0		1509	-3.3	1.0	5	dbSNP_129	89	157,8443	74.5+/-137.1	3,151,4146	no	coding-synonymous	ABLIM3	NM_014945.2		3,160,6340	AA,AG,GG		1.8256,0.2043,1.2763		503/684	148626067	166,12840	2203	4300	6503	SO:0001819	synonymous_variant	22885	exon17			GTTCTCGTCTGGA	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.1509G>A	5.37:g.148626067G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Silent	SNP	ENST00000506113.1	37	CCDS4294.1																																																																																			G|0.989;A|0.011	0.011	strong		0.488	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
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 GAIIx	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	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	69	18	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 GAIIx	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_ENST00000311129.5_Missense_Mutation_p.A13T|PPP2R1B_ENST00000427203.2_5'UTR|PPP2R1B_ENST00000393055.2_Missense_Mutation_p.A13T|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.A13T|RP11-108O10.2_ENST00000529841.1_lincRNA|PPP2R1B_ENST00000341980.6_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	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	35	17	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	
SPRR4	163778	hgsc.bcm.edu	37	1	152944594	152944594	+	Silent	SNP	C	C	T	rs3170863	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152944594C>T	ENST00000328051.2	+	2	277	c.228C>T	c.(226-228)agC>agT	p.S76S		NM_173080.1	NP_775103.1	Q96PI1	SPRR4_HUMAN	small proline-rich protein 4	76	Gln-rich.				keratinization (GO:0031424)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)				lung(1)|prostate(1)	2	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTCCAAGAGCAAACAGAAGT	0.527													T|||	3131	0.6252	0.8306	0.4986	5008	,	,		21757	0.6319		0.5656	False		,,,				2504	0.4918				p.S76S		Atlas-SNP	.											.	SPRR4	8	.	0			c.C228T						PASS	.	T		3425,981	368.1+/-318.5	1336,753,114	125.0	100.0	108.0		228	2.5	0.9	1	dbSNP_105	108	4912,3688	528.4+/-381.4	1434,2044,822	no	coding-synonymous	SPRR4	NM_173080.1		2770,2797,936	TT,TC,CC		42.8837,22.2651,35.8988		76/80	152944594	8337,4669	2203	4300	6503	SO:0001819	synonymous_variant	163778	exon2			CAAGAGCAAACAG	AF335109	CCDS1031.1	1q21.3	2008-02-05	2006-11-29		ENSG00000184148	ENSG00000184148			23173	protein-coding gene	gene with protein product						11719550, 11279051	Standard	NM_173080		Approved		uc001fav.1	Q96PI1	OTTHUMG00000012450	ENST00000328051.2:c.228C>T	1.37:g.152944594C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_173080	Q2M1Y7|Q5T522	Silent	SNP	ENST00000328051.2	37	CCDS1031.1																																																																																			C|0.355;T|0.645	0.645	strong		0.527	SPRR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034663.1	NM_173080	
PCDHGA3	56112	hgsc.bcm.edu	37	5	140723835	140723835	+	Missense_Mutation	SNP	C	C	T	rs11575947	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140723835C>T	ENST00000253812.6	+	1	235	c.235C>T	c.(235-237)Ccg>Tcg	p.P79S	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	79	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> S (in dbSNP:rs11575947).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTCTGAATCCGCAAAGCGG	0.597											OREG0016855	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	215	0.0429313	0.0068	0.0793	5008	,	,		15088	0.0		0.1272	False		,,,				2504	0.0235				p.P79S		Atlas-SNP	.											PCDHGA3_ENST00000253812,NS,carcinoma,-2,3	PCDHGA3	246	3	0			c.C235T						PASS	.	C	,,SER/PRO,SER/PRO	106,4236		0,106,2065	57.0	67.0	64.0		,,235,235	1.5	0.1	5	dbSNP_120	64	1087,7497		61,965,3266	no	intron,intron,missense,missense	PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_032011.1	,,74,74	61,1071,5331	TT,TC,CC		12.6631,2.4413,9.2295	,,,	,,79/933,79/830	140723835	1193,11733	2171	4292	6463	SO:0001583	missense	56112	exon1			CTGAATCCGCAAA	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.235C>T	5.37:g.140723835C>T	ENSP00000253812:p.Pro79Ser	Somatic	66	0	0	1658	WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	118	0.05402930402930403	4	0.008130081300813009	27	0.07458563535911603	0	0.0	87	0.11477572559366754	.	0.040	-1.289463	0.01387	0.024413	0.126631	ENSG00000254245	ENST00000253812	T	0.38077	1.16	5.65	1.48	0.22813	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	1.414840	0.06193	U	0.681803	T	0.00300	0.0009	L	0.59912	1.85	0.80722	P	0.0	B;B	0.14012	0.009;0.001	B;B	0.19666	0.013;0.026	T	0.19811	-1.0294	9	0.16420	T	0.52	.	1.9256	0.03316	0.2429:0.2403:0.3708:0.1459	rs11575947;rs11575947	79;79	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	S	79	ENSP00000253812:P79S	ENSP00000253812:P79S	P	+	1	0	PCDHGA3	140704019	0.000000	0.05858	0.053000	0.19242	0.032000	0.12392	-1.107000	0.03316	0.773000	0.33404	0.655000	0.94253	CCG	C|0.935;T|0.065	0.065	strong		0.597	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
KIF13A	63971	hgsc.bcm.edu	37	6	17764755	17764755	+	Silent	SNP	T	T	C	rs2296197	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:17764755T>C	ENST00000259711.6	-	39	5109	c.5004A>G	c.(5002-5004)ccA>ccG	p.P1668P	KIF13A_ENST00000378843.2_Silent_p.P1620P|KIF13A_ENST00000378816.5_Silent_p.P1633P|KIF13A_ENST00000378826.2_Silent_p.P1633P|KIF13A_ENST00000378814.5_Silent_p.P1620P	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1668					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			TTTCCTTGAGTGGCACCACAA	0.478													T|||	871	0.173922	0.0635	0.3069	5008	,	,		19756	0.1944		0.2386	False		,,,				2504	0.1411				p.P1668P		Atlas-SNP	.											.	KIF13A	276	.	0			c.A5004G						PASS	.	T	,,,	378,3630		20,338,1646	112.0	108.0	109.0		4899,4860,4860,5004	-2.7	1.0	6	dbSNP_100	109	1835,6527		207,1421,2553	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	227,1759,4199	CC,CT,TT		21.9445,9.4311,17.8901	,,,	1633/1771,1620/1758,1620/1750,1668/1806	17764755	2213,10157	2004	4181	6185	SO:0001819	synonymous_variant	63971	exon39			CTTGAGTGGCACC	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.5004A>G	6.37:g.17764755T>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	116	96	0.827586	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			A|0.000;C|0.183;T|0.817	0.183	strong		0.478	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
CCDC102A	92922	hgsc.bcm.edu	37	16	57555076	57555076	+	Silent	SNP	C	C	T	rs28446687	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57555076C>T	ENST00000258214.2	-	4	1071	c.825G>A	c.(823-825)gcG>gcA	p.A275A		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	275										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						TCCTGCTCAACGCCAGTTTAT	0.582													c|||	926	0.184904	0.3162	0.134	5008	,	,		17816	0.0298		0.2366	False		,,,				2504	0.1503				p.A275A		Atlas-SNP	.											.	CCDC102A	22	.	0			c.G825A						PASS	.	T		1326,3070	446.5+/-348.0	206,914,1078	137.0	114.0	122.0		825	-6.7	0.9	16	dbSNP_125	122	1908,6692	337.3+/-322.2	210,1488,2602	no	coding-synonymous	CCDC102A	NM_033212.3		416,2402,3680	TT,TC,CC		22.186,30.1638,24.8846		275/551	57555076	3234,9762	2198	4300	6498	SO:0001819	synonymous_variant	92922	exon4			GCTCAACGCCAGT	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.825G>A	16.37:g.57555076C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_033212	Q9BT74	Silent	SNP	ENST00000258214.2	37	CCDS10784.1																																																																																			C|0.768;T|0.232	0.232	strong		0.582	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212	
ST6GALNAC2	10610	hgsc.bcm.edu	37	17	74570559	74570559	+	Silent	SNP	C	C	T	rs17513606	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74570559C>T	ENST00000225276.5	-	3	568	c.249G>A	c.(247-249)ctG>ctA	p.L83L	ST6GALNAC2_ENST00000586520.1_5'UTR	NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	83					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						AGAGATTGAACAGGCCACGGA	0.652													c|||	60	0.0119808	0.0023	0.0159	5008	,	,		12712	0.0		0.0408	False		,,,				2504	0.0051				p.L83L		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.G249A						PASS	.			30,4376	34.3+/-65.2	0,30,2173	40.0	40.0	40.0		249	-1.9	0.3	17	dbSNP_123	40	351,8249	117.6+/-177.1	9,333,3958	no	coding-synonymous	ST6GALNAC2	NM_006456.2		9,363,6131	TT,TC,CC		4.0814,0.6809,2.9294		83/375	74570559	381,12625	2203	4300	6503	SO:0001819	synonymous_variant	10610	exon3			ATTGAACAGGCCA	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"""Sialyltransferases"""	10867	protein-coding gene	gene with protein product		610137	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"", ""sialyltransferase-like 1"""	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.249G>A	17.37:g.74570559C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	146	79	0.541096	NM_006456	Q12971	Silent	SNP	ENST00000225276.5	37	CCDS11747.1																																																																																			C|0.975;T|0.025	0.025	strong		0.652	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456	
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 GAIIx	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_ENST00000524510.1_5'UTR|PVRL1_ENST00000340882.2_Missense_Mutation_p.R199Q|PVRL1_ENST00000341398.2_Missense_Mutation_p.R199Q	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	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	208	34	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		
UGGT1	56886	hgsc.bcm.edu	37	2	128939799	128939799	+	Silent	SNP	C	C	T	rs17178720	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:128939799C>T	ENST00000259253.6	+	37	4226	c.4179C>T	c.(4177-4179)gaC>gaT	p.D1393D	UGGT1_ENST00000375990.3_Silent_p.D1369D	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1393	Glucosyltransferase. {ECO:0000250}.				'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GAGAAATGGACGGCTACAGGT	0.458													C|||	356	0.0710863	0.0061	0.1427	5008	,	,		18454	0.0		0.1869	False		,,,				2504	0.0624				p.D1393D		Atlas-SNP	.											.	UGGT1	126	.	0			c.C4179T						PASS	.	C		149,4257	104.7+/-143.2	0,149,2054	112.0	114.0	114.0		4179	-3.3	1.0	2	dbSNP_123	114	1622,6978	300.8+/-305.1	146,1330,2824	no	coding-synonymous	UGGT1	NM_020120.3		146,1479,4878	TT,TC,CC		18.8605,3.3818,13.6168		1393/1556	128939799	1771,11235	2203	4300	6503	SO:0001819	synonymous_variant	56886	exon37			AATGGACGGCTAC	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.4179C>T	2.37:g.128939799C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	88	66	0.75	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			C|0.882;T|0.118	0.118	strong		0.458	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
CAV2	858	hgsc.bcm.edu	37	7	116146074	116146074	+	Missense_Mutation	SNP	C	C	G	rs8940	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:116146074C>G	ENST00000222693.4	+	3	780	c.388C>G	c.(388-390)Cag>Gag	p.Q130E	CAV2_ENST00000343213.2_Missense_Mutation_p.A67G|CAV2_ENST00000462876.1_3'UTR	NM_001206747.1|NM_001206748.1|NM_001233.4	NP_001193676.1|NP_001193677.1|NP_001224.1	P51636	CAV2_HUMAN	caveolin 2	130			Q -> E (in dbSNP:rs8940).		caveola assembly (GO:0070836)|endoplasmic reticulum organization (GO:0007029)|mitochondrion organization (GO:0007005)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of endothelial cell proliferation (GO:0001938)|protein oligomerization (GO:0051259)|regulation of mitosis (GO:0007088)|skeletal muscle fiber development (GO:0048741)|synaptic transmission (GO:0007268)|vesicle docking (GO:0048278)|vesicle fusion (GO:0006906)|vesicle organization (GO:0016050)	acrosomal membrane (GO:0002080)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transport vesicle (GO:0030133)	D1 dopamine receptor binding (GO:0031748)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(1)|skin(1)	3	all_epithelial(6;1.53e-06)|Lung NSC(10;0.00592)|all_lung(10;0.00642)		STAD - Stomach adenocarcinoma(10;0.00878)			GCCTTCAGTGCAGACAATATG	0.448													C|||	706	0.140974	0.1921	0.1499	5008	,	,		19664	0.0089		0.164	False		,,,				2504	0.1779				p.Q130E		Atlas-SNP	.											.	CAV2	10	.	0			c.C388G						PASS	.	C	GLU/GLN,GLU/GLN,GLU/GLN,GLY/ALA	845,3561	334.1+/-303.3	74,697,1432	163.0	142.0	149.0		349,139,388,200	5.9	1.0	7	dbSNP_52	149	1670,6930	307.8+/-308.6	186,1298,2816	yes	missense,missense,missense,missense	CAV2	NM_001206747.1,NM_001206748.1,NM_001233.4,NM_198212.2	29,29,29,60	260,1995,4248	GG,GC,CC		19.4186,19.1784,19.3372	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	117/150,47/80,130/163,67/113	116146074	2515,10491	2203	4300	6503	SO:0001583	missense	858	exon3			TCAGTGCAGACAA	AF035752	CCDS5765.1, CCDS5766.1	7q31	2006-02-09			ENSG00000105971	ENSG00000105971			1528	protein-coding gene	gene with protein product		601048				8552590, 10087206	Standard	NM_001233		Approved	CAV	uc003vid.3	P51636	OTTHUMG00000023414	ENST00000222693.4:c.388C>G	7.37:g.116146074C>G	ENSP00000222693:p.Gln130Glu	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	154	88	0.571429	NM_001233	A4D0U2|Q9UGM7	Missense_Mutation	SNP	ENST00000222693.4	37	CCDS5766.1	264|264	0.12087912087912088|0.12087912087912088	90|90	0.18292682926829268|0.18292682926829268	55|55	0.15193370165745856|0.15193370165745856	4|4	0.006993006993006993|0.006993006993006993	115|115	0.1517150395778364|0.1517150395778364	C|C	25.5|25.5	4.645540|4.645540	0.87859|0.87859	0.191784|0.191784	0.194186|0.194186	ENSG00000105971|ENSG00000105971	ENST00000343213|ENST00000222693	.|D	.|0.92545	.|-3.06	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|0.163752	.|0.56097	.|D	.|0.000024	T|T	0.01320|0.01320	0.0043|0.0043	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	D|B	0.69078|0.34241	0.997|0.444	P|B	0.61940|0.41135	0.896|0.348	T|T	0.35201|0.35201	-0.9798|-0.9798	6|8	0.87932|0.33141	D|T	0|0.24	-8.8607|-8.8607	20.5827|20.5827	0.99408|0.99408	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs8940;rs1055892;rs3173921;rs11539795;rs17515863;rs52790866;rs8940|rs8940;rs1055892;rs3173921;rs11539795;rs17515863;rs52790866;rs8940	67|130	P51636-3|P51636	.|CAV2_HUMAN	G|E	67|130	.|ENSP00000222693:Q130E	ENSP00000345679:A67G|ENSP00000222693:Q130E	A|Q	+|+	2|1	0|0	CAV2|CAV2	115933310|115933310	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.355000|4.355000	0.59424|0.59424	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCA|CAG	C|0.830;G|0.170	0.170	strong		0.448	CAV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059735.4	NM_001233	
ANKRD53	79998	hgsc.bcm.edu	37	2	71211989	71211989	+	Silent	SNP	A	A	G	rs3796099	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71211989A>G	ENST00000360589.3	+	6	1186	c.1152A>G	c.(1150-1152)acA>acG	p.T384T	ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000272421.6_3'UTR|AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000457410.1_Silent_p.T350T	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	384										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						AGCGGCCCACAATGTGGAATG	0.637											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3372	0.673323	0.8464	0.6398	5008	,	,		15211	0.4782		0.6312	False		,,,				2504	0.7076				p.T384T		Atlas-SNP	.											.	ANKRD53	55	.	0			c.A1152G						PASS	.	G	,	1149,235		475,199,18	32.0	36.0	35.0		1152,	-2.6	0.0	2	dbSNP_107	35	1960,1222		588,784,219	no	coding-synonymous,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	,	1063,983,237	GG,GA,AA		38.4035,16.9798,31.9098	,	384/531,	71211989	3109,1457	692	1591	2283	SO:0001819	synonymous_variant	79998	exon6			GCCCACAATGTGG	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1152A>G	2.37:g.71211989A>G		Somatic	121	0	0	1128	WXS	Illumina HiSeq	Phase_I	69	16	0.231884	NM_001115116	Q8IYP8	Silent	SNP	ENST00000360589.3	37	CCDS46321.1																																																																																			A|0.366;C|0.000;G|0.634	0.634	strong		0.637	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
ZNF3	7551	hgsc.bcm.edu	37	7	99669802	99669802	+	Missense_Mutation	SNP	A	A	G	rs11550034	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99669802A>G	ENST00000424697.1	-	6	611	c.305T>C	c.(304-306)aTt>aCt	p.I102T	ZNF3_ENST00000413658.2_Intron|ZNF3_ENST00000299667.4_Missense_Mutation_p.I102T|ZNF3_ENST00000303915.6_Missense_Mutation_p.I102T	NM_001278284.1|NM_001278287.1|NM_001278290.1|NM_001278291.1|NM_001278292.1|NM_032924.3	NP_001265213.1|NP_001265216.1|NP_001265219.1|NP_001265220.1|NP_001265221.1|NP_116313.3	P17036	ZNF3_HUMAN	zinc finger protein 3	102	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		I -> T (in dbSNP:rs11550034).		cell differentiation (GO:0030154)|leukocyte activation (GO:0045321)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	25	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)	Ovarian(593;2.06e-05)|Myeloproliferative disorder(862;0.0122)|Breast(660;0.029)	STAD - Stomach adenocarcinoma(171;0.129)			GTCTTCAGAAATTTCTTGATC	0.393													A|||	529	0.105631	0.0371	0.147	5008	,	,		21325	0.1399		0.1223	False		,,,				2504	0.1166				p.I102T		Atlas-SNP	.											.	ZNF3	54	.	0			c.T305C						PASS	.	A	,THR/ILE	188,3516		6,176,1670	100.0	90.0	93.0		,305	5.0	1.0	7	dbSNP_120	93	1097,7093		80,937,3078	yes	intron,missense	ZNF3	NM_017715.2,NM_032924.3	,89	86,1113,4748	GG,GA,AA		13.3944,5.0756,10.8038	,benign	,102/447	99669802	1285,10609	1852	4095	5947	SO:0001583	missense	7551	exon6			TCAGAAATTTCTT	AF027136	CCDS43618.1, CCDS43619.1	7q22.1	2013-01-08	2006-05-05					"""Zinc fingers, C2H2-type"", ""-"""	13089	protein-coding gene	gene with protein product		194510	"""zinc finger protein 3 (A8-51)"""				Standard	NM_032924		Approved	A8-51, KOX25, PP838, FLJ20216, HF.12, Zfp113	uc003usr.4	P17036		ENST00000424697.1:c.305T>C	7.37:g.99669802A>G	ENSP00000415358:p.Ile102Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_032924	D6W5U0|P13683|Q9HBR4|Q9NNX8|Q9NXJ1|Q9UC15|Q9UC16	Missense_Mutation	SNP	ENST00000424697.1	37	CCDS43619.1	240	0.10989010989010989	13	0.026422764227642278	55	0.15193370165745856	77	0.1346153846153846	95	0.12532981530343007	A	8.294	0.818412	0.16607	0.050756	0.133944	ENSG00000166526	ENST00000424697;ENST00000303915;ENST00000299667;ENST00000412947;ENST00000449785;ENST00000428683;ENST00000441298;ENST00000415068	T;T;T;T;T;T;T;T	0.07908	3.15;3.15;3.15;4.9;5.04;5.04;4.86;4.76	5.01	5.01	0.66863	Krueppel-associated box (3);	0.250008	0.28612	N	0.014733	T	0.00039	0.0001	L	0.38175	1.15	0.33188	P	0.449523	P;P	0.44627	0.839;0.455	B;B	0.41236	0.351;0.149	T	0.42682	-0.9437	9	0.18710	T	0.47	-13.4665	7.34	0.26632	0.9043:0.0:0.0957:0.0	rs11550034;rs11982602;rs17852252;rs60937757;rs11550034	85;102	B3KRP4;P17036	.;ZNF3_HUMAN	T	102;102;102;66;102;102;66;102	ENSP00000415358:I102T;ENSP00000306372:I102T;ENSP00000299667:I102T;ENSP00000416088:I66T;ENSP00000405970:I102T;ENSP00000388042:I102T;ENSP00000394113:I66T;ENSP00000416686:I102T	ENSP00000299667:I102T	I	-	2	0	ZNF3	99507738	0.000000	0.05858	0.960000	0.40013	0.824000	0.46624	0.352000	0.20113	2.114000	0.64651	0.402000	0.26972	ATT	A|0.890;G|0.110	0.110	strong		0.393	ZNF3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336247.3	NM_017715	
CPB1	1360	hgsc.bcm.edu	37	3	148562310	148562310	+	Missense_Mutation	SNP	G	G	A	rs1059502	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:148562310G>A	ENST00000491148.1	+	8	956	c.622G>A	c.(622-624)Gac>Aac	p.D208N	CPB1_ENST00000282957.4_Missense_Mutation_p.D208N			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	208			D -> N (in dbSNP:rs1059502). {ECO:0000269|PubMed:9524066}.			extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			AGAGCTTCTCGACAAGTTAGA	0.413													G|||	1353	0.270168	0.3495	0.1412	5008	,	,		16749	0.2956		0.2048	False		,,,				2504	0.2955				p.D208N		Atlas-SNP	.											.	CPB1	74	.	0			c.G622A						PASS	.	G	ASN/ASP	1358,3048	452.4+/-350.0	197,964,1042	111.0	91.0	98.0		622	-2.8	0.0	3	dbSNP_86	98	1769,6831	320.3+/-314.5	169,1431,2700	yes	missense	CPB1	NM_001871.2	23	366,2395,3742	AA,AG,GG		20.5698,30.8216,24.0427	benign	208/418	148562310	3127,9879	2203	4300	6503	SO:0001583	missense	1360	exon7			CTTCTCGACAAGT	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"""pancreatic carboxypeptidase B"", ""tissue carboxypeptidase B"", ""protaminase"""	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.622G>A	3.37:g.148562310G>A	ENSP00000417222:p.Asp208Asn	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_001871	O60834|Q53XJ0|Q96BQ8	Missense_Mutation	SNP	ENST00000491148.1	37	CCDS33874.1	518	0.23717948717948717	166	0.33739837398373984	52	0.143646408839779	139	0.243006993006993	161	0.21240105540897097	G	0.010	-1.761315	0.00657	0.308216	0.205698	ENSG00000153002	ENST00000491148;ENST00000282957;ENST00000468341	T;T;T	0.32515	1.45;1.45;1.45	5.78	-2.76	0.05896	Peptidase M14, carboxypeptidase A (2);	0.697197	0.15191	N	0.275529	T	0.00012	0.0000	N	0.25094	0.71	0.58432	P	1.999999999946489E-6	B	0.12013	0.005	B	0.14023	0.01	T	0.42616	-0.9441	9	0.07482	T	0.82	.	10.2126	0.43150	0.3714:0.0838:0.5448:0.0	rs1059502;rs3200197;rs56471857;rs60324209;rs1059502	208	P15086	CBPB1_HUMAN	N	208;208;174	ENSP00000417222:D208N;ENSP00000282957:D208N;ENSP00000419427:D174N	ENSP00000282957:D208N	D	+	1	0	CPB1	150045000	0.000000	0.05858	0.000000	0.03702	0.114000	0.19823	-0.672000	0.05244	-0.671000	0.05274	-2.480000	0.00198	GAC	G|0.743;A|0.257	0.257	strong		0.413	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871	
MTOR	2475	hgsc.bcm.edu	37	1	11181327	11181327	+	Silent	SNP	C	C	T	rs11121691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11181327C>T	ENST00000361445.4	-	49	6985	c.6909G>A	c.(6907-6909)ctG>ctA	p.L2303L	MTOR_ENST00000376838.1_Silent_p.L508L	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2303	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	TTTTCAGCCACAGCAGCTTGG	0.587													C|||	1105	0.220647	0.4365	0.1542	5008	,	,		17412	0.0565		0.2356	False		,,,				2504	0.1299				p.L2303L		Atlas-SNP	.											.	MTOR	327	.	0			c.G6909A						PASS	.	C		1875,2531	541.3+/-375.7	383,1109,711	80.0	68.0	72.0		6909	3.9	1.0	1	dbSNP_120	72	2054,6546	356.9+/-330.5	249,1556,2495	no	coding-synonymous	MTOR	NM_004958.3		632,2665,3206	TT,TC,CC		23.8837,42.5556,30.2091		2303/2550	11181327	3929,9077	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon49			CAGCCACAGCAGC	L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.6909G>A	1.37:g.11181327C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			C|0.721;T|0.279	0.279	strong		0.587	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
TTN	7273	hgsc.bcm.edu	37	2	179444939	179444939	+	Missense_Mutation	SNP	C	C	T	rs2303838	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179444939C>T	ENST00000591111.1	-	268	62376	c.62152G>A	c.(62152-62154)Gtc>Atc	p.V20718I	TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.V22359I|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V13486I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V13419I|TTN_ENST00000460472.2_Missense_Mutation_p.V13294I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V19791I|RP11-171I2.5_ENST00000604215.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20718	Fibronectin type-III 50. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I. {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:7569978}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTCACATTGACAGGTGGCCCA	0.348													C|||	1759	0.351238	0.3434	0.2147	5008	,	,		20260	0.631		0.1849	False		,,,				2504	0.3415				p.V22359I		Atlas-SNP	.											.	TTN	18412	.	0			c.G67075A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1207,2467		202,803,832	62.0	60.0	61.0		40456,40255,59371,39880	2.6	0.9	2	dbSNP_100	61	1445,6723		128,1189,2767	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	330,1992,3599	TT,TC,CC		17.691,32.8525,22.3949	benign,benign,benign,benign	13486/27119,13419/27052,19791/33424,13294/26927	179444939	2652,9190	1837	4084	5921	SO:0001583	missense	7273	exon318			CATTGACAGGTGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.62152G>A	2.37:g.179444939C>T	ENSP00000465570:p.Val20718Ile	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	77	49	0.636364	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		710	0.3250915750915751	157	0.31910569105691056	73	0.20165745856353592	344	0.6013986013986014	136	0.17941952506596306	C	9.291	1.050609	0.19827	0.328525	0.17691	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.41	2.61	0.31194	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.54965	1.715	0.27033	P	0.9641858	B;B;B;B	0.10296	0.003;0.003;0.003;0.003	B;B;B;B	0.14578	0.011;0.011;0.011;0.011	T	0.39396	-0.9616	8	0.87932	D	0	.	6.7606	0.23538	0.0:0.6119:0.1229:0.2652	rs2303838;rs52803332;rs59721271;rs2303838	13294;13419;13486;20718	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	19791;13294;13486;13419;13292	ENSP00000343764:V19791I;ENSP00000434586:V13294I;ENSP00000340554:V13486I;ENSP00000352154:V13419I	ENSP00000340554:V13486I	V	-	1	0	TTN	179153185	0.001000	0.12720	0.932000	0.37286	0.972000	0.66771	-0.020000	0.12525	0.261000	0.21753	-0.253000	0.11424	GTC	C|0.677;T|0.323	0.323	strong		0.348	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DENND4A	10260	hgsc.bcm.edu	37	15	65994733	65994733	+	Silent	SNP	C	C	T	rs17810074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:65994733C>T	ENST00000431932.2	-	17	2548	c.2340G>A	c.(2338-2340)gtG>gtA	p.V780V	DENND4A_ENST00000443035.3_Silent_p.V780V	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	780					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GACAGACTTTCACATAAGCTG	0.408													C|||	1234	0.246406	0.0711	0.3977	5008	,	,		18286	0.1935		0.326	False		,,,				2504	0.3487				p.V780V		Atlas-SNP	.											.	DENND4A	217	.	0			c.G2340A						PASS	.	C	,	357,3345		18,321,1512	62.0	54.0	56.0		2340,2340	4.8	1.0	15	dbSNP_123	56	2417,5779		363,1691,2044	no	coding-synonymous,coding-synonymous	DENND4A	NM_001144823.1,NM_005848.3	,	381,2012,3556	TT,TC,CC		29.49,9.6434,23.3148	,	780/1907,780/1864	65994733	2774,9124	1851	4098	5949	SO:0001819	synonymous_variant	10260	exon17			GACTTTCACATAA	AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.2340G>A	15.37:g.65994733C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	170	86	0.505882	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																			C|0.761;T|0.239	0.239	strong		0.408	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
GPR162	27239	hgsc.bcm.edu	37	12	6933787	6933787	+	Silent	SNP	A	A	G	rs1051409	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6933787A>G	ENST00000311268.3	+	2	1510	c.723A>G	c.(721-723)gtA>gtG	p.V241V	GPR162_ENST00000382315.3_Intron|GPR162_ENST00000428545.2_Intron	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						CTTTTGAGGTACCAGCCATTG	0.692													G|||	2451	0.489417	0.5734	0.5144	5008	,	,		-128	0.5675		0.4563	False		,,,				2504	0.3119				p.V241V		Atlas-SNP	.											.	GPR162	55	.	0			c.A723G						PASS	.	G	,	2427,1979	556.5+/-379.5	679,1069,455	49.0	51.0	50.0		,723	2.5	1.0	12	dbSNP_86	50	3933,4667	602.4+/-394.5	912,2109,1279	no	intron,coding-synonymous	GPR162	NM_014449.1,NM_019858.1	,	1591,3178,1734	GG,GA,AA		45.7326,44.916,48.9005	,	,241/589	6933787	6360,6646	2203	4300	6503	SO:0001819	synonymous_variant	27239	exon2			TGAGGTACCAGCC	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"""GPCR / Class A : Orphans"""	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.723A>G	12.37:g.6933787A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_019858	Q16664|Q59EH5|Q66K56	Silent	SNP	ENST00000311268.3	37	CCDS8563.1																																																																																			A|0.507;G|0.493	0.493	strong		0.692	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
ALPPL2	251	hgsc.bcm.edu	37	2	233273011	233273011	+	Missense_Mutation	SNP	C	C	G	rs75920311		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:233273011C>G	ENST00000295453.3	+	6	735	c.683C>G	c.(682-684)cCc>cGc	p.P228R		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	228					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		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;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	TACATGTTTCCCATGGGGACC	0.612																																					p.P228R		Atlas-SNP	.											.	ALPPL2	36	.	0			c.C683G						PASS	.						89.0	98.0	95.0					2																	233273011		2199	4295	6494	SO:0001583	missense	251	exon6			TGTTTCCCATGGG	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.683C>G	2.37:g.233273011C>G	ENSP00000295453:p.Pro228Arg	Somatic	333	0	0		WXS	Illumina HiSeq	Phase_I	190	59	0.310526	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	37	CCDS2491.1	194	0.08882783882783883	45	0.09146341463414634	18	0.049723756906077346	80	0.13986013986013987	51	0.06728232189973615	c	13.23	2.176361	0.38413	.	.	ENSG00000163286	ENST00000295453	D	0.96774	-4.12	3.24	1.12	0.20585	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.053184	0.85682	N	0.000000	T	0.31295	0.0792	H	0.96080	3.765	0.41109	D	0.985721	B	0.25390	0.125	B	0.40677	0.337	T	0.72966	-0.4131	10	0.52906	T	0.07	.	7.2384	0.26082	0.0:0.7275:0.1716:0.1009	.	228	P10696	PPBN_HUMAN	R	228	ENSP00000295453:P228R	ENSP00000295453:P228R	P	+	2	0	ALPPL2	232981255	0.860000	0.29831	0.587000	0.28692	0.582000	0.36321	3.559000	0.53756	0.452000	0.26830	0.205000	0.17691	CCC	C|0.910;G|0.090	0.090	strong		0.612	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313	
KDM2B	84678	hgsc.bcm.edu	37	12	121878659	121878659	+	Silent	SNP	C	C	T	rs1064951	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121878659C>T	ENST00000377071.4	-	21	3642	c.3570G>A	c.(3568-3570)caG>caA	p.Q1190Q	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Silent_p.Q1121Q|KDM2B_ENST00000542973.1_Silent_p.Q558Q	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1190					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						GATCCCGCATCTGGGCATCCT	0.632													C|||	1675	0.334465	0.1573	0.4006	5008	,	,		16903	0.4514		0.4046	False		,,,				2504	0.3344				p.Q1190Q		Atlas-SNP	.											.	KDM2B	218	.	0			c.G3570A						PASS	.	C	,	783,3405		80,623,1391	37.0	44.0	42.0		3363,3570	4.1	1.0	12	dbSNP_86	42	3208,5234		606,1996,1619	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	686,2619,3010	TT,TC,CC		38.0005,18.6963,31.5994	,	1121/1266,1190/1337	121878659	3991,8639	2094	4221	6315	SO:0001819	synonymous_variant	84678	exon21			CCGCATCTGGGCA	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3570G>A	12.37:g.121878659C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			C|0.667;T|0.333	0.333	strong		0.632	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
CORO1B	57175	hgsc.bcm.edu	37	11	67209515	67209515	+	Silent	SNP	C	C	T	rs111451405	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67209515C>T	ENST00000341356.5	-	3	356	c.246G>A	c.(244-246)acG>acA	p.T82T	CORO1B_ENST00000539724.1_5'Flank|CORO1B_ENST00000453768.2_Silent_p.T82T|CORO1B_ENST00000545016.1_Silent_p.T82T|CORO1B_ENST00000393893.1_Silent_p.T82T	NM_020441.2	NP_065174.1	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B	82					actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|endothelial cell chemotaxis (GO:0035767)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|positive regulation of lamellipodium morphogenesis (GO:2000394)|protein localization to cell leading edge (GO:1902463)|ruffle organization (GO:0031529)|wound healing (GO:0042060)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|identical protein binding (GO:0042802)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			GGACAGGTCCCGTGTGCCCAC	0.642													c|||	222	0.0443291	0.0015	0.2622	5008	,	,		16432	0.0347		0.003	False		,,,				2504	0.0				p.T82T		Atlas-SNP	.											CORO1B,NS,carcinoma,-1,1	CORO1B	30	1	0			c.G246A						PASS	.	T	,	14,4386	19.1+/-41.9	0,14,2186	68.0	53.0	58.0		246,246	-8.7	0.0	11	dbSNP_132	58	28,8562	16.6+/-54.9	1,26,4268	no	coding-synonymous,coding-synonymous	CORO1B	NM_001018070.2,NM_020441.2	,	1,40,6454	TT,TC,CC		0.326,0.3182,0.3233	,	82/490,82/490	67209515	42,12948	2200	4295	6495	SO:0001819	synonymous_variant	57175	exon3			AGGTCCCGTGTGC	AK000860	CCDS8164.1	11q13.1	2013-01-10	2001-11-28		ENSG00000172725	ENSG00000172725		"""Coronins"", ""WD repeat domain containing"""	2253	protein-coding gene	gene with protein product		609849	"""coronin, actin-binding protein, 1B"""			9778037	Standard	NM_001018070		Approved	coronin-2	uc001olk.1	Q9BR76	OTTHUMG00000167775	ENST00000341356.5:c.246G>A	11.37:g.67209515C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	42	4	0.0952381	NM_020441	B2RD45	Silent	SNP	ENST00000341356.5	37	CCDS8164.1																																																																																			C|0.986;T|0.014	0.014	strong		0.642	CORO1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396220.1	NM_020441	
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 GAIIx	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		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	43	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	
PLCB1	23236	hgsc.bcm.edu	37	20	8770822	8770822	+	Splice_Site	SNP	C	C	T	rs2294597	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:8770822C>T	ENST00000338037.6	+	31	3364	c.3337C>T	c.(3337-3339)Cta>Tta	p.L1113L	PLCB1_ENST00000378641.3_Splice_Site_p.L1113L|PLCB1_ENST00000378637.2_Splice_Site_p.L1113L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	1113					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TTTCTTATAGCTAGAAGAAGC	0.368													C|||	1145	0.228634	0.1263	0.2219	5008	,	,		19106	0.1329		0.3022	False		,,,				2504	0.3947				p.G1113X		Atlas-SNP	.											.	PLCB1	394	.	0			c.G3337T						PASS	.	C	,	622,3784	259.2+/-262.9	54,514,1635	47.0	47.0	47.0		3337,3337	3.3	1.0	20	dbSNP_100	47	2673,5927	408.4+/-349.5	451,1771,2078	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PLCB1	NM_015192.2,NM_182734.1	,	505,2285,3713	TT,TC,CC		31.0814,14.1171,25.3345	,	1113/1217,1113/1174	8770822	3295,9711	2203	4300	6503	SO:0001630	splice_region_variant	23236	exon31			TTATAGCTAGAAG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.3337-1C>T	20.37:g.8770822C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_182734	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Nonsense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			C|0.774;T|0.226	0.226	strong		0.368	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Silent
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 GAIIx	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_ENST00000444204.2_Missense_Mutation_p.Y111H|ADIPOQ_ENST00000320741.2_Missense_Mutation_p.Y111H|ADIPOQ-AS1_ENST00000422718.1_RNA			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	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	173	69	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 GAIIx	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	Somatic	307	1	0.00325733		WXS	Illumina HiSeq	Phase_I	297	144	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	
SP140L	93349	hgsc.bcm.edu	37	2	231222655	231222655	+	Silent	SNP	G	G	T	rs10498250	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:231222655G>T	ENST00000415673.2	+	3	329	c.243G>T	c.(241-243)cgG>cgT	p.R81R	SP140L_ENST00000243810.6_Silent_p.R81R|SP140L_ENST00000444636.1_Silent_p.R81R|SP140L_ENST00000458341.1_5'UTR|SP140_ENST00000486687.2_3'UTR|SP140L_ENST00000396563.4_Silent_p.R81R	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	81	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						TCCGCGATCGGGAACTCATCA	0.358													T|||	579	0.115615	0.1293	0.1311	5008	,	,		21124	0.1042		0.1252	False		,,,				2504	0.0879				p.R81R		Atlas-SNP	.											SP140L_ENST00000415673,NS,carcinoma,+2,2	SP140L	68	2	0			c.G243T						PASS	.	T		529,3791		39,451,1670	136.0	146.0	143.0		243	-0.9	0.0	2	dbSNP_119	143	1033,7547		67,899,3324	no	coding-synonymous	SP140L	NM_138402.4		106,1350,4994	TT,TG,GG		12.0396,12.2454,12.1085		81/581	231222655	1562,11338	2160	4290	6450	SO:0001819	synonymous_variant	93349	exon3			CGATCGGGAACTC	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.243G>T	2.37:g.231222655G>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Silent	SNP	ENST00000415673.2	37	CCDS46538.1																																																																																			G|0.883;T|0.117	0.117	strong		0.358	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
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 GAIIx	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	Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	241	161	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	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907449	12907449	+	Missense_Mutation	SNP	C	C	G	rs78163065	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907449C>G	ENST00000317869.6	-	2	919	c.694G>C	c.(694-696)Gat>Cat	p.D232H		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	232						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						TGAGTCTCATCTTTCTTCATG	0.468																																					p.D232H		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	0			c.G694C						PASS	.	C	HIS/ASP	100,4306		1,98,2104	119.0	119.0	119.0		694	0.8	0.2	1	dbSNP_131	119	379,8217		6,367,3925	no	missense	HNRNPCL1	NM_001013631.1	81	7,465,6029	GG,GC,CC		4.409,2.2696,3.684	probably-damaging	232/294	12907449	479,12523	2203	4298	6501	SO:0001583	missense	343069	exon2			TCTCATCTTTCTT	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.694G>C	1.37:g.12907449C>G	ENSP00000365370:p.Asp232His	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	249	68	0.273092	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	134	0.06135531135531135	3	0.006097560975609756	8	0.022099447513812154	99	0.17307692307692307	24	0.0316622691292876	.	1.300	-0.605036	0.03717	0.022696	0.04409	ENSG00000179172	ENST00000317869	T	0.11385	2.78	0.792	0.792	0.18625	.	0.237816	0.31268	U	0.007943	T	0.00039	0.0001	L	0.39397	1.21	0.44055	D	0.996795	B	0.10296	0.003	B	0.11329	0.006	T	0.51260	-0.8728	10	0.66056	D	0.02	.	7.4751	0.27371	0.0:0.9999:0.0:1.0E-4	.	232	O60812	HNRCL_HUMAN	H	232	ENSP00000365370:D232H	ENSP00000365370:D232H	D	-	1	0	HNRNPCL1	12830036	1.000000	0.71417	0.158000	0.22627	0.005000	0.04900	3.152000	0.50677	0.735000	0.32537	0.416000	0.27883	GAT	C|0.961;G|0.039	0.039	strong		0.468	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
CCDC114	93233	hgsc.bcm.edu	37	19	48800914	48800914	+	Missense_Mutation	SNP	G	G	A	rs35461177	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48800914G>A	ENST00000315396.7	-	13	2085	c.1403C>T	c.(1402-1404)cCg>cTg	p.P468L		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	468			P -> L (in dbSNP:rs35461177).		outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)		p.P261L(1)		cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		CTCAAAACCCGGGGGGTCTTC	0.627													G|||	839	0.167532	0.1036	0.2277	5008	,	,		15478	0.1329		0.2803	False		,,,				2504	0.1309				p.P468L		Atlas-SNP	.											CCDC114,NS,carcinoma,0,1	CCDC114	100	1	1	Substitution - Missense(1)	stomach(1)	c.C1403T						PASS	.	G	LEU/PRO	567,3839		48,471,1684	20.0	22.0	21.0		1403	1.8	0.7	19	dbSNP_126	21	2455,6145		376,1703,2221	yes	missense	CCDC114	NM_144577.3	98	424,2174,3905	AA,AG,GG		28.5465,12.8688,23.2354	possibly-damaging	468/671	48800914	3022,9984	2203	4300	6503	SO:0001583	missense	93233	exon13			AAACCCGGGGGGT	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.1403C>T	19.37:g.48800914G>A	ENSP00000318429:p.Pro468Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	37	CCDS12714.2	428	0.19597069597069597	48	0.0975609756097561	101	0.27900552486187846	81	0.14160839160839161	198	0.2612137203166227	G	15.40	2.822657	0.50739	0.128688	0.285465	ENSG00000105479	ENST00000315396	T	0.21932	1.98	3.98	1.84	0.25277	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.34643	P	0.27919099999999997	P;B	0.37708	0.606;0.163	B;B	0.27170	0.077;0.019	T	0.45249	-0.9274	8	0.66056	D	0.02	-3.1936	5.4686	0.16658	0.2523:0.0:0.7477:0.0	rs35461177	468;468	Q96M63;Q96M63-5	CC114_HUMAN;.	L	468	ENSP00000318429:P468L	ENSP00000318429:P468L	P	-	2	0	CCDC114	53492726	0.967000	0.33354	0.700000	0.30305	0.760000	0.43138	1.490000	0.35573	0.965000	0.38133	-0.136000	0.14681	CCG	G|0.793;A|0.207	0.207	strong		0.627	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329892	55329892	+	Missense_Mutation	SNP	A	A	G	rs149123986	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55329892A>G	ENST00000391728.4	+	3	226	c.193A>G	c.(193-195)Aga>Gga	p.R65G	KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.R65G|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.R65G|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.R65G|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.R65G	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	65	Ig-like C2-type 1.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CAAAGAAGACAGAATCCACAT	0.507													a|||	512	0.102236	0.0893	0.1398	5008	,	,		13666	0.001		0.2435	False		,,,				2504	0.0521				p.R65G		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.A193G						PASS	.	A	GLY/ARG	602,3742		197,208,1767	65.0	92.0	83.0		193	-2.5	0.0	19	dbSNP_134	83	1898,6330		595,708,2811	yes	missense	KIR3DL1	NM_013289.2	125	792,916,4578	GG,GA,AA		23.0676,13.8582,19.8855		65/445	55329892	2500,10072	2172	4114	6286	SO:0001583	missense	3811	exon3			GAAGACAGAATCC	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.193A>G	19.37:g.55329892A>G	ENSP00000375608:p.Arg65Gly	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	26	24	0.923077	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	306	0.1401098901098901	46	0.09349593495934959	52	0.143646408839779	2	0.0034965034965034965	206	0.2717678100263852	A	0.005	-2.154994	0.00325	0.138582	0.230676	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.00730	5.77;5.77;5.77;5.77;5.77	1.25	-2.51	0.06365	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	179.731000	0.00166	U	0.000000	T	0.00012	0.0000	N	0.03983	-0.305	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.42882	-0.9425	9	0.23302	T	0.38	.	4.707	0.12855	0.5341:0.0:0.4659:0.0	.	65;65;65	Q15702;F6QF33;P43629	.;.;KI3L1_HUMAN	G	65;65;65;43;65;65	ENSP00000384528:R65G;ENSP00000443350:R65G;ENSP00000442355:R65G;ENSP00000375608:R65G;ENSP00000326868:R65G	ENSP00000326868:R65G	R	+	1	2	KIR3DL1	60021704	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.579000	0.05834	-0.706000	0.05028	-1.194000	0.01681	AGA	A|0.860;G|0.140	0.140	strong		0.507	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
CHI3L2	1117	hgsc.bcm.edu	37	1	111778325	111778325	+	Missense_Mutation	SNP	C	C	T	rs11556868	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:111778325C>T	ENST00000445067.2	+	8	1316	c.545C>T	c.(544-546)gCg>gTg	p.A182V	CHI3L2_ENST00000369744.2_Missense_Mutation_p.A172V|CHI3L2_ENST00000466741.1_Missense_Mutation_p.A103V|CHI3L2_ENST00000524472.1_Missense_Mutation_p.A103V|CHI3L2_ENST00000369748.4_Missense_Mutation_p.A182V			Q15782	CH3L2_HUMAN	chitinase 3-like 2	182			A -> V (in dbSNP:rs11556868). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		CTCTTGACTGCGGGCGTATCT	0.453													C|||	364	0.0726837	0.0303	0.0634	5008	,	,		22784	0.0089		0.1223	False		,,,				2504	0.1513				p.A182V		Atlas-SNP	.											.	CHI3L2	38	.	0			c.C545T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	183,4223	117.5+/-155.4	2,179,2022	102.0	96.0	98.0		515,308,545	3.4	1.0	1	dbSNP_120	98	1089,7511	228.3+/-263.4	56,977,3267	yes	missense,missense,missense	CHI3L2	NM_001025197.1,NM_001025199.1,NM_004000.2	64,64,64	58,1156,5289	TT,TC,CC		12.6628,4.1534,9.7801	probably-damaging,probably-damaging,probably-damaging	172/381,103/312,182/391	111778325	1272,11734	2203	4300	6503	SO:0001583	missense	1117	exon6			TGACTGCGGGCGT	U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.545C>T	1.37:g.111778325C>T	ENSP00000437082:p.Ala182Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	146	86	0.589041	NM_004000	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Missense_Mutation	SNP	ENST00000445067.2	37	CCDS30802.1	128	0.05860805860805861	12	0.024390243902439025	21	0.058011049723756904	0	0.0	95	0.12532981530343007	C	19.16	3.774289	0.69992	0.041534	0.126628	ENSG00000064886	ENST00000445067;ENST00000528451;ENST00000486561;ENST00000369744;ENST00000369748;ENST00000474304;ENST00000466741;ENST00000477185;ENST00000467038;ENST00000497587;ENST00000524472;ENST00000497220	T;T;T;T;T;T;T;T;T;T;T	0.06608	3.28;3.28;3.28;3.28;3.28;3.28;3.28;3.28;3.28;3.28;3.28	3.39	3.39	0.38822	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.41938	D	0.000786	T	0.10680	0.0261	L	0.60455	1.87	0.21782	P	0.999544656	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.63877	0.919;0.919;0.919	T	0.01440	-1.1354	9	0.66056	D	0.02	-7.4821	12.661	0.56813	0.0:1.0:0.0:0.0	rs11556868;rs17845289;rs17858122;rs59153550;rs11556868	103;172;182	B4DPR7;A6NNY3;Q15782	.;.;CH3L2_HUMAN	V	182;182;182;172;182;163;103;103;84;103;103;36	ENSP00000437082:A182V;ENSP00000436077:A182V;ENSP00000431968:A182V;ENSP00000358759:A172V;ENSP00000358763:A182V;ENSP00000437086:A103V;ENSP00000436272:A103V;ENSP00000431978:A84V;ENSP00000436006:A103V;ENSP00000432049:A103V;ENSP00000435250:A36V	ENSP00000358759:A172V	A	+	2	0	CHI3L2	111579848	0.999000	0.42202	0.993000	0.49108	0.497000	0.33675	1.881000	0.39638	1.857000	0.53885	0.561000	0.74099	GCG	C|0.915;T|0.085	0.085	strong		0.453	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000	
RP1	6101	hgsc.bcm.edu	37	8	55541617	55541617	+	Silent	SNP	A	A	G	rs441800	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:55541617A>G	ENST00000220676.1	+	4	5323	c.5175A>G	c.(5173-5175)caA>caG	p.Q1725Q		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1725					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)			GTACAAAACAAAATGATGATA	0.403													A|||	1206	0.240815	0.056	0.2709	5008	,	,		22859	0.4415		0.2604	False		,,,				2504	0.2423				p.Q1725Q	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A5175G						PASS	.	A		404,4002	199.1+/-222.7	20,364,1819	127.0	123.0	125.0		5175	0.9	0.0	8	dbSNP_80	125	2200,6400	373.5+/-337.0	274,1652,2374	no	coding-synonymous	RP1	NM_006269.1		294,2016,4193	GG,GA,AA		25.5814,9.1693,20.0215		1725/2157	55541617	2604,10402	2203	4300	6503	SO:0001819	synonymous_variant	6101	exon4			AAAACAAAATGAT	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.5175A>G	8.37:g.55541617A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_006269		Silent	SNP	ENST00000220676.1	37	CCDS6160.1																																																																																			A|0.776;G|0.224	0.224	strong		0.403	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
MICALL2	79778	hgsc.bcm.edu	37	7	1486451	1486451	+	Missense_Mutation	SNP	G	G	A	rs75056037	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:1486451G>A	ENST00000297508.7	-	5	714	c.539C>T	c.(538-540)gCg>gTg	p.A180V	MICALL2_ENST00000405088.4_Intron	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	180	Forms an intramolecular interaction with the C-terminal coiled coil domain keeping the protein in a closed conformation. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CAAGCTGCCCGCCAATGCCTG	0.677													G|||	512	0.102236	0.1354	0.2435	5008	,	,		11409	0.0288		0.0805	False		,,,				2504	0.0552				p.A180V		Atlas-SNP	.											MICALL2,NS,carcinoma,0,2	MICALL2	63	2	0			c.C539T						PASS	.		VAL/ALA	563,3787		36,491,1648	26.0	23.0	24.0		539	-1.4	0.0	7	dbSNP_131	24	666,7874		22,622,3626	yes	missense	MICALL2	NM_182924.3	64	58,1113,5274	AA,AG,GG		7.7986,12.9425,9.5345	benign	180/905	1486451	1229,11661	2175	4270	6445	SO:0001583	missense	79778	exon5			CTGCCCGCCAATG	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.539C>T	7.37:g.1486451G>A	ENSP00000297508:p.Ala180Val	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	252	0.11538461538461539	84	0.17073170731707318	82	0.2265193370165746	26	0.045454545454545456	60	0.079155672823219	g	7.658	0.684264	0.14907	0.129425	0.077986	ENSG00000164877	ENST00000297508	T	0.71817	-0.6	4.01	-1.36	0.09085	.	1.202540	0.06530	N	0.741370	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.02070	-1.1219	9	0.27785	T	0.31	.	5.868	0.18786	0.435:0.1391:0.4259:0.0	.	180	Q8IY33	MILK2_HUMAN	V	180	ENSP00000297508:A180V	ENSP00000297508:A180V	A	-	2	0	MICALL2	1452977	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.106000	0.10890	-0.873000	0.04032	-1.509000	0.00949	GCG	G|0.901;A|0.099	0.099	strong		0.677	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
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 GAIIx	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_ENST00000535192.1_Missense_Mutation_p.S745C|PTK2_ENST00000395218.2_Missense_Mutation_p.S791C|PTK2_ENST00000517887.1_Missense_Mutation_p.S835C|PTK2_ENST00000538769.1_Missense_Mutation_p.S459C|PTK2_ENST00000430260.2_Missense_Mutation_p.S101C|PTK2_ENST00000519465.1_Missense_Mutation_p.S419C|PTK2_ENST00000340930.3_Missense_Mutation_p.S791C|PTK2_ENST00000521059.1_Missense_Mutation_p.S791C|PTK2_ENST00000519419.1_Missense_Mutation_p.S835C	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	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	140	67	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	
PDZD7	79955	hgsc.bcm.edu	37	10	102782113	102782113	+	Missense_Mutation	SNP	A	A	T	rs118098246	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:102782113A>T	ENST00000370215.3	-	5	797	c.572T>A	c.(571-573)gTg>gAg	p.V191E		NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	191						cilium (GO:0005929)|extracellular space (GO:0005615)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		GCACTTCTCCACTACCAGGCG	0.617													A|||	6	0.00119808	0.0	0.0014	5008	,	,		17580	0.0		0.005	False		,,,				2504	0.0				p.V191E		Atlas-SNP	.											.	PDZD7	101	.	0			c.T572A						PASS	.	A	GLU/VAL,GLU/VAL	8,4398	14.3+/-33.2	0,8,2195	111.0	99.0	103.0		572,572	5.3	1.0	10	dbSNP_132	103	78,8522	46.3+/-105.2	0,78,4222	yes	missense,missense	PDZD7	NM_001195263.1,NM_024895.4	121,121	0,86,6417	TT,TA,AA		0.907,0.1816,0.6612	possibly-damaging,possibly-damaging	191/1034,191/518	102782113	86,12920	2203	4300	6503	SO:0001583	missense	79955	exon5			TTCTCCACTACCA	AK026862	CCDS31269.1, CCDS73182.1	10q24.32	2006-01-24		2006-01-24	ENSG00000186862	ENSG00000186862			26257	protein-coding gene	gene with protein product		612971		PDZK7		12477932	Standard	NM_024895		Approved	FLJ23209, bA108L7.8	uc021pxc.1	Q9H5P4	OTTHUMG00000018916	ENST00000370215.3:c.572T>A	10.37:g.102782113A>T	ENSP00000359234:p.Val191Glu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_001195263	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	37	CCDS31269.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	A	22.3	4.275685	0.80580	0.001816	0.00907	ENSG00000186862	ENST00000393462;ENST00000370215	T	0.12672	2.66	5.29	5.29	0.74685	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.20618	0.0496	L	0.55481	1.735	0.80722	D	1	P;D	0.89917	0.95;1.0	P;D	0.91635	0.742;0.999	T	0.06463	-1.0825	10	0.02654	T	1	.	15.2184	0.73288	1.0:0.0:0.0:0.0	.	191;191	Q9H5P4;Q9H5P4-2	PDZD7_HUMAN;.	E	191	ENSP00000359234:V191E	ENSP00000359234:V191E	V	-	2	0	PDZD7	102772103	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	6.096000	0.71446	2.006000	0.58801	0.379000	0.24179	GTG	A|0.996;T|0.004	0.004	strong		0.617	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895	
HNF1A	6927	hgsc.bcm.edu	37	12	121416650	121416650	+	Missense_Mutation	SNP	A	A	C	rs1169288	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121416650A>C	ENST00000257555.6	+	1	305	c.79A>C	c.(79-81)Atc>Ctc	p.I27L	HNF1A-AS1_ENST00000537361.1_RNA|HNF1A_ENST00000402929.1_Missense_Mutation_p.I27L|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000544413.1_Missense_Mutation_p.I27L|HNF1A_ENST00000541395.1_Missense_Mutation_p.I27L|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000400024.2_Missense_Mutation_p.I27L|HNF1A_ENST00000538626.1_Intron			P20823	HNF1A_HUMAN	HNF1 homeobox A	27	Dimerization.		I -> L (in dbSNP:rs1169288). {ECO:0000269|PubMed:15489334, 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)	p.I27_L30delIQAL(1)|p.A25_Q28del(1)|p.?(1)		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)					AGAGGCACTGATCCAGGCACT	0.677									Hepatic Adenoma, Familial Clustering of				A|||	1495	0.298522	0.0832	0.33	5008	,	,		12439	0.3889		0.339	False		,,,				2504	0.4325				p.I27L		Atlas-SNP	.											HNF1A,NS,carcinoma,0,1	HNF1A	302	1	3	Deletion - In frame(2)|Unknown(1)	liver(2)|endometrium(1)	c.A79C	GRCh37	CM001349	HNF1A	M	rs1169288	PASS	.	A	LEU/ILE	532,3874		43,446,1714	25.0	28.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	79	4.4	1.0	12	dbSNP_87	27	2881,5715		500,1881,1917	yes	missense	HNF1A	NM_000545.5	5	543,2327,3631	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	33.5156,12.0744,26.2498	benign	27/632	121416650	3413,9589	2203	4298	6501	SO:0001583	missense	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	GCACTGATCCAGG	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.79A>C	12.37:g.121416650A>C	ENSP00000257555:p.Ile27Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	654	0.29945054945054944	35	0.07113821138211382	123	0.3397790055248619	243	0.42482517482517484	253	0.3337730870712401	A	14.27	2.485259	0.44147	0.120744	0.335156	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D	0.98550	-4.99;-4.99;-4.99	4.45	4.45	0.53987	Hepatocyte nuclear factor 1, dimerisation domain (1);Hepatocyte nuclear factor 1, N-terminal (1);	0.102545	0.43260	D	0.000599	T	0.00012	0.0000	L	0.46157	1.445	0.09310	P	0.9999999999999999	B;B;B;B	0.18013	0.02;0.025;0.015;0.006	B;B;B;B	0.23574	0.013;0.022;0.047;0.012	T	0.00149	-1.1988	9	0.26408	T	0.33	-28.5113	12.8999	0.58119	1.0:0.0:0.0:0.0	rs1169288;rs3751160;rs16950605;rs17847506;rs1169288	27;27;27;27	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	L	27	ENSP00000257555:I27L;ENSP00000443112:I27L;ENSP00000438804:I27L	ENSP00000257555:I27L	I	+	1	0	HNF1A	119901033	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.135000	0.50546	1.637000	0.50538	0.482000	0.46254	ATC	T|0.002;G|0.007	.	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
RTP4	64108	hgsc.bcm.edu	37	3	187088612	187088612	+	Silent	SNP	C	C	T	rs33927333	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:187088612C>T	ENST00000259030.2	+	2	302	c.192C>T	c.(190-192)tcC>tcT	p.S64S		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	64					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|protein targeting to membrane (GO:0006612)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	all_cancers(143;4.66e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;5.56e-18)	GBM - Glioblastoma multiforme(93;0.0269)		GTTGGGCTTCCGCCCAAGTGC	0.552													C|||	396	0.0790735	0.0113	0.1066	5008	,	,		19676	0.0159		0.168	False		,,,				2504	0.1247				p.S64S		Atlas-SNP	.											.	RTP4	20	.	0			c.C192T						PASS	.	C		151,4255	105.2+/-143.6	0,151,2052	51.0	47.0	48.0		192	-7.8	0.2	3	dbSNP_126	48	1419,7181	273.5+/-290.7	111,1197,2992	yes	coding-synonymous	RTP4	NM_022147.2		111,1348,5044	TT,TC,CC		16.5,3.4271,12.0714		64/247	187088612	1570,11436	2203	4300	6503	SO:0001819	synonymous_variant	64108	exon2			GGCTTCCGCCCAA	BC013161	CCDS33910.1	3q27.3	2014-02-20	2006-11-21		ENSG00000136514	ENSG00000136514		"""Receptor transporter proteins"""	23992	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 4"""	609350	"""receptor transporter protein 4"""			16271481, 15550249, 16720576	Standard	NM_022147		Approved	IFRG28, Z3CXXC4	uc003frm.3	Q96DX8	OTTHUMG00000156459	ENST00000259030.2:c.192C>T	3.37:g.187088612C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	190	94	0.494737	NM_022147	Q9H4F3	Silent	SNP	ENST00000259030.2	37	CCDS33910.1																																																																																			C|0.885;T|0.115	0.115	strong		0.552	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
EMC10	284361	hgsc.bcm.edu	37	19	50983930	50983930	+	Silent	SNP	C	C	T	rs10409679	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50983930C>T	ENST00000334976.6	+	5	541	c.495C>T	c.(493-495)ccC>ccT	p.P165P	CTD-2545M3.2_ENST00000598194.1_RNA|EMC10_ENST00000598585.1_Silent_p.P165P|EMC10_ENST00000376918.3_Silent_p.P165P	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	165						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											TGACGCACCCCGGGGGCTGCC	0.697													C|||	2712	0.541534	0.3389	0.6297	5008	,	,		13105	0.5556		0.5875	False		,,,				2504	0.6912				p.P165P		Atlas-SNP	.											C19orf63_ENST00000376918,rectum,carcinoma,0,2	.	.	2	0			c.C495T						PASS	.	C	,	1652,2732		318,1016,858	24.0	25.0	25.0		495,495	-8.5	0.1	19	dbSNP_119	25	5033,3555		1498,2037,759	no	coding-synonymous,coding-synonymous	C19orf63	NM_175063.4,NM_206538.2	,	1816,3053,1617	TT,TC,CC		41.395,37.6825,48.4659	,	165/255,165/263	50983930	6685,6287	2192	4294	6486	SO:0001819	synonymous_variant	284361	exon5			GCACCCCGGGGGC	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"""hematopoietic signal peptide-containing secreted 1"", ""hematopoietic signal peptide-containing membrane domain-containing 1"""	614545	"""chromosome 19 open reading frame 63"""	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.495C>T	19.37:g.50983930C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Silent	SNP	ENST00000334976.6	37	CCDS12796.1																																																																																			C|0.493;T|0.507	0.507	strong		0.697	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063	
WRN	7486	hgsc.bcm.edu	37	8	30973957	30973957	+	Silent	SNP	G	G	T	rs1800392	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:30973957G>T	ENST00000298139.5	+	20	2610	c.2361G>T	c.(2359-2361)ctG>ctT	p.L787L		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	787	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TTAGGAAACTGAATCTATCCT	0.383			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				G|||	2360	0.471246	0.4175	0.5764	5008	,	,		18469	0.624		0.4493	False		,,,				2504	0.3344				p.L787L	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.G2361T						PASS	.	G		1810,2596	531.1+/-373.1	364,1082,757	126.0	116.0	119.0		2361	3.8	0.6	8	dbSNP_89	119	4019,4581	556.1+/-386.8	928,2163,1209	yes	coding-synonymous	WRN	NM_000553.4		1292,3245,1966	TT,TG,GG		46.7326,41.0803,44.8178		787/1433	30973957	5829,7177	2203	4300	6503	SO:0001819	synonymous_variant	7486	exon20	Familial Cancer Database	WS, Adult Progeria	GAAACTGAATCTA		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.2361G>T	8.37:g.30973957G>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	37	CCDS6082.1																																																																																			G|0.509;T|0.491	0.491	strong		0.383	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
TMC4	147798	hgsc.bcm.edu	37	19	54665970	54665970	+	Silent	SNP	C	C	T	rs36655	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54665970C>T	ENST00000376591.4	-	11	1703	c.1572G>A	c.(1570-1572)caG>caA	p.Q524Q	TMC4_ENST00000416963.1_Silent_p.Q106Q|TMC4_ENST00000301187.4_Silent_p.Q518Q|LENG1_ENST00000222224.3_5'Flank|TMC4_ENST00000476013.2_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	524					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCTGGAACTCCTGGGTCCCCG	0.687													C|||	1237	0.247005	0.1808	0.2464	5008	,	,		9717	0.1558		0.328	False		,,,				2504	0.3476				p.Q524Q		Atlas-SNP	.											.	TMC4	89	.	0			c.G1572A						PASS	.	C	,	898,3500		88,722,1389	28.0	30.0	29.0		1572,1554	4.7	1.0	19	dbSNP_76	29	2769,5831		434,1901,1965	no	coding-synonymous,coding-synonymous	TMC4	NM_001145303.1,NM_144686.2	,	522,2623,3354	TT,TC,CC		32.1977,20.4184,28.212	,	524/713,518/707	54665970	3667,9331	2199	4300	6499	SO:0001819	synonymous_variant	147798	exon11			GAACTCCTGGGTC	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.1572G>A	19.37:g.54665970C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Silent	SNP	ENST00000376591.4	37	CCDS46174.1																																																																																			C|0.743;T|0.257	0.257	strong		0.687	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
OGDHL	55753	hgsc.bcm.edu	37	10	50960209	50960209	+	Silent	SNP	G	G	A	rs1258184	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50960209G>A	ENST00000374103.4	-	5	649	c.564C>T	c.(562-564)ctC>ctT	p.L188L	OGDHL_ENST00000432695.1_5'UTR|OGDHL_ENST00000419399.1_Silent_p.L131L	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	188					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)			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						CCCGCAGAGAGAGGGTGTTTT	0.592													G|||	2325	0.464257	0.1407	0.4798	5008	,	,		18974	0.9107		0.4642	False		,,,				2504	0.4305				p.L188L		Atlas-SNP	.											.	OGDHL	149	.	0			c.C564T						PASS	.	G	,,	875,3531	338.4+/-305.3	95,685,1423	55.0	55.0	55.0		393,,564	-9.7	0.7	10	dbSNP_87	55	4170,4430	565.4+/-388.5	1014,2142,1144	no	coding-synonymous,utr-5,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	1109,2827,2567	AA,AG,GG		48.4884,19.8593,38.7898	,,	131/954,,188/1011	50960209	5045,7961	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon5			CAGAGAGAGGGTG	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.564C>T	10.37:g.50960209G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			G|0.567;A|0.433	0.433	strong		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
SLC24A2	25769	hgsc.bcm.edu	37	9	19786217	19786217	+	Silent	SNP	G	G	A	rs1536517	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:19786217G>A	ENST00000341998.2	-	1	709	c.648C>T	c.(646-648)atC>atT	p.I216I	SLC24A2_ENST00000286344.3_Silent_p.I216I	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	216					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)	p.I216I(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		TAACAAAGAGGATGTTGAATA	0.438													G|||	757	0.151158	0.1868	0.0764	5008	,	,		22564	0.4077		0.0119	False		,,,				2504	0.0348				p.I216I		Atlas-SNP	.											SLC24A2,NS,carcinoma,0,1	SLC24A2	93	1	1	Substitution - coding silent(1)	stomach(1)	c.C648T						scavenged	.	G	,	708,3698	295.3+/-283.6	60,588,1555	106.0	99.0	102.0		648,648	4.1	1.0	9	dbSNP_88	102	96,8504	52.7+/-113.3	1,94,4205	no	coding-synonymous,coding-synonymous	SLC24A2	NM_001193288.2,NM_020344.3	,	61,682,5760	AA,AG,GG		1.1163,16.069,6.1818	,	216/645,216/662	19786217	804,12202	2203	4300	6503	SO:0001819	synonymous_variant	25769	exon1			AAAGAGGATGTTG	AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"""Solute carriers"""	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.648C>T	9.37:g.19786217G>A		Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	59	20	0.338983	NM_001193288	B7ZLL8|Q9NTN5|Q9NZQ4	Silent	SNP	ENST00000341998.2	37	CCDS6493.1																																																																																			G|0.882;A|0.118	0.118	strong		0.438	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344	
CNDP2	55748	hgsc.bcm.edu	37	18	72168608	72168608	+	Silent	SNP	G	G	A	rs2303463	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72168608G>A	ENST00000324262.4	+	3	421	c.105G>A	c.(103-105)ccG>ccA	p.P35P	CNDP2_ENST00000579847.1_Silent_p.P35P|CNDP2_ENST00000324301.8_Silent_p.P35P	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	35					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.P35P(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		CTGCGTGGCCGGAGAAGAGAG	0.507													G|||	1233	0.246206	0.2231	0.3127	5008	,	,		19326	0.2956		0.164	False		,,,				2504	0.2638				p.P35P		Atlas-SNP	.											CNDP2,caecum,carcinoma,0,2	CNDP2	55	2	1	Substitution - coding silent(1)	stomach(1)	c.G105A						PASS	.	G	,	937,3469	358.4+/-314.3	119,699,1385	173.0	152.0	159.0		105,105	-11.6	0.3	18	dbSNP_100	159	1623,6977	301.7+/-305.6	134,1355,2811	no	coding-synonymous,coding-synonymous	CNDP2	NM_001168499.1,NM_018235.2	,	253,2054,4196	AA,AG,GG		18.8721,21.2665,19.6832	,	35/392,35/476	72168608	2560,10446	2203	4300	6503	SO:0001819	synonymous_variant	55748	exon2			GTGGCCGGAGAAG	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.105G>A	18.37:g.72168608G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_001168499	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Silent	SNP	ENST00000324262.4	37	CCDS12006.1																																																																																			G|0.791;A|0.209	0.209	strong		0.507	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107533175	107533175	+	Missense_Mutation	SNP	C	C	G	rs3739741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107533175C>G	ENST00000374762.3	+	4	547	c.476C>G	c.(475-477)gCt>gGt	p.A159G	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	159			A -> G (in dbSNP:rs3739741). {ECO:0000269|PubMed:14702039}.					p.A159G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						GGTGGGCCAGCTCTGTGGGGT	0.383													C|||	882	0.176118	0.0257	0.1427	5008	,	,		17296	0.2847		0.1769	False		,,,				2504	0.2904				p.A159G		Atlas-SNP	.											NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	1	Substitution - Missense(1)	stomach(1)	c.C476G						PASS	.	C	GLY/ALA	199,4207	126.1+/-163.2	6,187,2010	136.0	129.0	131.0		476	2.4	1.0	9	dbSNP_107	131	1631,6969	302.9+/-306.2	172,1287,2841	yes	missense	NIPSNAP3B	NM_018376.2	60	178,1474,4851	GG,GC,CC		18.9651,4.5166,14.0704	benign	159/248	107533175	1830,11176	2203	4300	6503	SO:0001583	missense	55335	exon4			GGCCAGCTCTGTG	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.476C>G	9.37:g.107533175C>G	ENSP00000363894:p.Ala159Gly	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	65	0.477941	NM_018376	Q5VX30|Q9NUM2	Missense_Mutation	SNP	ENST00000374762.3	37	CCDS6761.1	356	0.163003663003663	15	0.03048780487804878	59	0.16298342541436464	146	0.25524475524475526	136	0.17941952506596306	C	19.13	3.767716	0.69878	0.045166	0.189651	ENSG00000165028	ENST00000374762	T	0.70986	-0.53	4.3	2.44	0.29823	Dimeric alpha-beta barrel (1);	0.177687	0.47852	D	0.000203	T	0.00039	0.0001	M	0.67625	2.065	0.24750	P	0.99298667	D	0.76494	0.999	D	0.74023	0.982	T	0.07271	-1.0781	9	0.22706	T	0.39	-9.1353	10.6947	0.45892	0.0:0.8331:0.0:0.1669	rs3739741;rs3739741	159	Q9BS92	NPS3B_HUMAN	G	159	ENSP00000363894:A159G	ENSP00000363894:A159G	A	+	2	0	NIPSNAP3B	106572996	0.974000	0.33945	1.000000	0.80357	0.980000	0.70556	1.528000	0.35985	1.148000	0.42385	0.655000	0.94253	GCT	C|0.851;G|0.149	0.149	strong		0.383	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376	
LTF	4057	hgsc.bcm.edu	37	3	46484964	46484964	+	Silent	SNP	G	G	A	rs1042073	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46484964G>A	ENST00000231751.4	-	13	1918	c.1623C>T	c.(1621-1623)aaC>aaT	p.N541N	LTF_ENST00000426532.2_Silent_p.N497N|LTF_ENST00000493056.1_5'Flank|LTF_ENST00000417439.1_Silent_p.N539N	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	541	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		AGTATCTCTCGTTGCTGTTGG	0.542													A|||	2248	0.448882	0.4115	0.2997	5008	,	,		21020	0.6409		0.337	False		,,,				2504	0.5225				p.N541N		Atlas-SNP	.											.	LTF	98	.	0			c.C1623T						PASS	.	A	,	1763,2643	645.2+/-398.2	345,1073,785	239.0	222.0	227.0		1491,1623	-10.6	0.0	3	dbSNP_86	227	2588,6004	689.5+/-404.4	384,1820,2092	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	729,2893,2877	AA,AG,GG		30.121,40.0136,33.4744	,	497/667,541/711	46484964	4351,8647	2203	4296	6499	SO:0001819	synonymous_variant	4057	exon13			TCTCTCGTTGCTG		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1623C>T	3.37:g.46484964G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			G|0.597;A|0.403	0.403	strong		0.542	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
LRWD1	222229	hgsc.bcm.edu	37	7	102112980	102112980	+	Silent	SNP	G	G	A	rs3800987	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:102112980G>A	ENST00000292616.5	+	13	1766	c.1614G>A	c.(1612-1614)acG>acA	p.T538T	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	538					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						GCCAGTCCACGGTGGCAGTGG	0.716													G|||	2312	0.461661	0.3139	0.5519	5008	,	,		15340	0.372		0.662	False		,,,				2504	0.4836				p.T538T		Atlas-SNP	.											LRWD1,NS,carcinoma,0,1	LRWD1	41	1	0			c.G1614A						scavenged	.	G		1560,2790		317,926,932	11.0	9.0	10.0		1614	-10.2	0.0	7	dbSNP_107	10	5482,3026		1822,1838,594	no	coding-synonymous	LRWD1	NM_152892.1		2139,2764,1526	AA,AG,GG		35.5665,35.8621,45.2325		538/648	102112980	7042,5816	2175	4254	6429	SO:0001819	synonymous_variant	222229	exon13			GTCCACGGTGGCA	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"""WD repeat domain containing"""	21769	protein-coding gene	gene with protein product	"""origin recognition complex associated"", ""centromere protein 33"""	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.1614G>A	7.37:g.102112980G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	10	7	0.7	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1	1113	0.5096153846153846	173	0.3516260162601626	215	0.5939226519337016	227	0.3968531468531469	498	0.6569920844327177	G	0.094	-1.162080	0.01673	0.358621	0.644335	ENSG00000161036	ENST00000488689;ENST00000468175	.	.	.	5.1	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.51767	P	6.799999999995698E-5	.	.	.	.	.	.	T	0.16719	-1.0393	3	.	.	.	-0.1259	4.6709	0.12689	0.5376:0.2198:0.0955:0.1471	rs3800987;rs10316934;rs13244777;rs17845221;rs17858035;rs17858491	.	.	.	Q	149;124	.	.	R	+	2	0	LRWD1	101899985	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-7.784000	0.00030	-3.315000	0.00189	-1.058000	0.02302	CGG	G|0.476;A|0.524	0.524	strong		0.716	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
CHRNB3	1142	hgsc.bcm.edu	37	8	42587659	42587659	+	Silent	SNP	G	G	C	rs4953	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:42587659G>C	ENST00000289957.2	+	5	1337	c.1209G>C	c.(1207-1209)tcG>tcC	p.S403S		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	403					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	GATACATTTCGAGACATGTGA	0.368													A|||	184	0.0367412	0.0575	0.0216	5008	,	,		19624	0.002		0.0358	False		,,,				2504	0.0562				p.S403S		Atlas-SNP	.											CHRNB3,NS,carcinoma,0,1	CHRNB3	74	1	0			c.G1209C						PASS	.	A		214,4192		5,204,1994	30.0	32.0	32.0		1209	-11.7	0.0	8	dbSNP_52	32	333,8259		8,317,3971	no	coding-synonymous	CHRNB3	NM_000749.3		13,521,5965	CC,CG,GG		3.8757,4.857,4.2083		403/459	42587659	547,12451	2203	4296	6499	SO:0001819	synonymous_variant	1142	exon5			CATTTCGAGACAT	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1963	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 3 (neuronal)"""	118508	"""cholinergic receptor, nicotinic, beta polypeptide 3"""			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.1209G>C	8.37:g.42587659G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_000749	Q15827	Silent	SNP	ENST00000289957.2	37	CCDS6134.1																																																																																			G|0.959;C|0.041	0.041	strong		0.368	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1		
LOXHD1	125336	hgsc.bcm.edu	37	18	44104437	44104437	+	Missense_Mutation	SNP	T	T	C	rs12606417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44104437T>C	ENST00000398722.4	-	24	4033	c.4034A>G	c.(4033-4035)gAg>gGg	p.E1345G	LOXHD1_ENST00000441551.2_Missense_Mutation_p.E1417G|LOXHD1_ENST00000582408.1_Missense_Mutation_p.E512G|LOXHD1_ENST00000300591.6_Missense_Mutation_p.E512G|LOXHD1_ENST00000579038.1_Missense_Mutation_p.E416G|LOXHD1_ENST00000536736.1_Missense_Mutation_p.E1623G|LOXHD1_ENST00000441893.2_Missense_Mutation_p.E556G			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1345			E -> G (in dbSNP:rs12606417).		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						ACTTGGGCCCTCTTGAACGTA	0.562													T|||	313	0.0625	0.0136	0.085	5008	,	,		19088	0.0784		0.1064	False		,,,				2504	0.0511				p.E1623G		Atlas-SNP	.											.	LOXHD1	367	.	0			c.A4868G						PASS	.	T	GLY/GLU,GLY/GLU	36,1348		0,36,656	61.0	56.0	58.0		1535,4868	5.1	1.0	18	dbSNP_120	58	366,2816		21,324,1246	yes	missense,missense	LOXHD1	NM_001145472.2,NM_144612.6	98,98	21,360,1902	CC,CT,TT		11.5022,2.6012,8.8042	probably-damaging,probably-damaging	512/1115,1623/2212	44104437	402,4164	692	1591	2283	SO:0001583	missense	125336	exon31			GGGCCCTCTTGAA	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.4034A>G	18.37:g.44104437T>C	ENSP00000381707:p.Glu1345Gly	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		153	0.07005494505494506	1	0.0020325203252032522	35	0.09668508287292818	45	0.07867132867132867	72	0.09498680738786279	T	10.72	1.428610	0.25726	0.026012	0.115022	ENSG00000167210	ENST00000300591;ENST00000398722;ENST00000536736;ENST00000441893;ENST00000335730	T;T;T;T	0.30448	1.74;3.22;3.18;1.53	5.06	5.06	0.68205	Lipase/lipooxygenase, PLAT/LH2 (1);	0.139247	0.49305	D	0.000147	T	0.00412	0.0013	L	0.27053	0.805	0.26487	P	0.9750093	D;B;B;P	0.56035	0.974;0.081;0.135;0.919	P;B;B;B	0.51415	0.669;0.068;0.121;0.395	T	0.07385	-1.0775	9	0.27082	T	0.32	.	12.6362	0.56685	0.0:0.0:0.0:1.0	rs12606417;rs12606417	1623;556;1345;1345	F5GZB4;F8WA52;Q8IVV2-2;Q8IVV2	.;.;.;LOXH1_HUMAN	G	512;1345;1623;556;1345	ENSP00000300591:E512G;ENSP00000381707:E1345G;ENSP00000444586:E1623G;ENSP00000409062:E556G	ENSP00000300591:E512G	E	-	2	0	LOXHD1	42358435	1.000000	0.71417	1.000000	0.80357	0.387000	0.30353	4.364000	0.59479	2.028000	0.59812	0.379000	0.24179	GAG	T|0.934;C|0.066	0.066	strong		0.562	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
HK1	3098	hgsc.bcm.edu	37	10	71103597	71103597	+	Silent	SNP	C	C	G	rs1133189	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:71103597C>G	ENST00000359426.6	+	2	182	c.78C>G	c.(76-78)ctC>ctG	p.L26L	HK1_ENST00000360289.2_Silent_p.L14L|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000448642.2_Silent_p.L61L|HK1_ENST00000298649.3_Silent_p.L25L|HK1_ENST00000404387.2_Silent_p.L30L	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	26	Hexokinase type-1 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						ACAAGTATCTCTATGCCATGC	0.537													C|||	1419	0.283347	0.3873	0.2334	5008	,	,		20035	0.122		0.3728	False		,,,				2504	0.2526				p.L30L		Atlas-SNP	.											.	HK1	170	.	0			c.C90G						PASS	.	C	,,,,	1734,2672	517.8+/-369.5	352,1030,821	167.0	159.0	162.0		78,75,90,90,42	0.6	1.0	10	dbSNP_86	162	3159,5441	480.7+/-370.5	570,2019,1711	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HK1	NM_000188.2,NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2	,,,,	922,3049,2532	GG,GC,CC		36.7326,39.3554,37.6211	,,,,	26/918,25/917,30/922,30/922,14/906	71103597	4893,8113	2203	4300	6503	SO:0001819	synonymous_variant	3098	exon5			GTATCTCTATGCC	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.78C>G	10.37:g.71103597C>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	37	CCDS7292.1																																																																																			C|0.651;G|0.349	0.349	strong		0.537	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
RBM19	9904	hgsc.bcm.edu	37	12	114377877	114377877	+	Missense_Mutation	SNP	T	T	C	rs2290789	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:114377877T>C	ENST00000545145.2	-	15	1904	c.1826A>G	c.(1825-1827)cAt>cGt	p.H609R	RBM19_ENST00000392561.3_Missense_Mutation_p.H609R|RBM19_ENST00000261741.5_Missense_Mutation_p.H609R|RP11-780K2.1_ENST00000550206.1_RNA	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	609	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.		H -> R (in dbSNP:rs2290789). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GCTGCCAAAATGGCCGAAGGT	0.642													C|||	996	0.198882	0.3464	0.0764	5008	,	,		17496	0.1885		0.1133	False		,,,				2504	0.1851				p.H609R		Atlas-SNP	.											.	RBM19	117	.	0			c.A1826G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS	1442,2964	676.6+/-403.3	255,932,1016	63.0	69.0	67.0		1826,1826,1826	0.2	0.0	12	dbSNP_100	67	886,7714	776.2+/-407.7	38,810,3452	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	29,29,29	293,1742,4468	CC,CT,TT		10.3023,32.7281,17.8994	benign,benign,benign	609/961,609/961,609/961	114377877	2328,10678	2203	4300	6503	SO:0001583	missense	9904	exon15			CCAAAATGGCCGA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1826A>G	12.37:g.114377877T>C	ENSP00000442053:p.His609Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	61	19	0.311475	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	362	0.16575091575091574	147	0.29878048780487804	27	0.07458563535911603	102	0.17832167832167833	86	0.11345646437994723	C	0	-2.782507	0.00079	0.327281	0.103023	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05319	3.46;3.46;3.46	4.29	0.25	0.15535	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.381500	0.26387	N	0.024675	T	0.00012	0.0000	N	0.00280	-1.71	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40961	-0.9535	9	0.05833	T	0.94	-0.08	6.9575	0.24580	0.0:0.4211:0.1156:0.4633	rs2290789;rs17856105;rs17856174;rs2290789	609	Q9Y4C8	RBM19_HUMAN	R	609	ENSP00000442053:H609R;ENSP00000376344:H609R;ENSP00000261741:H609R	ENSP00000261741:H609R	H	-	2	0	RBM19	112862260	0.437000	0.25593	0.025000	0.17156	0.040000	0.13550	0.866000	0.27954	-0.236000	0.09753	-1.007000	0.02485	CAT	T|0.830;C|0.170	0.170	strong		0.642	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
PGLYRP4	57115	hgsc.bcm.edu	37	1	153317723	153317723	+	Missense_Mutation	SNP	T	T	C	rs3006453	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153317723T>C	ENST00000359650.5	-	4	339	c.275A>G	c.(274-276)cAg>cGg	p.Q92R	PGLYRP4_ENST00000368739.3_Missense_Mutation_p.Q88R|PGLYRP4_ENST00000490266.1_5'UTR	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	92			Q -> R (in dbSNP:rs3006453).		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	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)			GCAGACTGTCTGGTCGTGACA	0.562													T|||	105	0.0209665	0.003	0.0346	5008	,	,		19662	0.0		0.0577	False		,,,				2504	0.0194				p.Q92R		Atlas-SNP	.											.	PGLYRP4	45	.	0			c.A275G						PASS	.	T	ARG/GLN	48,4358	48.9+/-83.8	0,48,2155	115.0	101.0	105.0		275	0.8	0.0	1	dbSNP_101	105	504,8096	143.3+/-199.3	16,472,3812	yes	missense	PGLYRP4	NM_020393.2	43	16,520,5967	CC,CT,TT		5.8605,1.0894,4.2442	possibly-damaging	92/374	153317723	552,12454	2203	4300	6503	SO:0001583	missense	57115	exon4			ACTGTCTGGTCGT	AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I beta precursor"""	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.275A>G	1.37:g.153317723T>C	ENSP00000352672:p.Gln92Arg	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_020393	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Missense_Mutation	SNP	ENST00000359650.5	37	CCDS30871.1	53	0.024267399267399268	1	0.0020325203252032522	15	0.04143646408839779	0	0.0	37	0.048812664907651716	T	2.829	-0.243014	0.05906	0.010894	0.058605	ENSG00000163218	ENST00000368739;ENST00000359650	T;T	0.23552	1.9;1.9	3.2	0.772	0.18510	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	.	.	.	.	T	0.12817	0.0311	L	0.43701	1.375	0.09310	N	1	P;P	0.51449	0.945;0.923	P;P	0.54544	0.641;0.755	T	0.11743	-1.0575	9	0.21540	T	0.41	-23.4138	5.1149	0.14829	0.0:0.2693:0.0:0.7307	rs3006453;rs52793149;rs3006453	88;92	Q96LB8-2;Q96LB8	.;PGRP4_HUMAN	R	88;92	ENSP00000357728:Q88R;ENSP00000352672:Q92R	ENSP00000352672:Q92R	Q	-	2	0	PGLYRP4	151584347	0.003000	0.15002	0.001000	0.08648	0.036000	0.12997	0.142000	0.16096	0.039000	0.15632	-0.856000	0.03024	CAG	T|0.964;C|0.036	0.036	strong		0.562	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1	NM_020393	
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 GAIIx	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		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				.	.	weak		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
COL5A1	1289	hgsc.bcm.edu	37	9	137711997	137711997	+	Silent	SNP	G	G	C	rs2228560	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:137711997G>C	ENST00000371817.3	+	58	4896	c.4482G>C	c.(4480-4482)ccG>ccC	p.P1494P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1494	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TCGGTCCTCCGGGTGAACAGG	0.627													G|||	2044	0.408147	0.5416	0.3256	5008	,	,		21008	0.375		0.3439	False		,,,				2504	0.3865				p.P1494P		Atlas-SNP	.											.	COL5A1	323	.	0			c.G4482C						PASS	.	G		2257,2149		590,1077,536	101.0	95.0	97.0		4482	-9.4	0.0	9	dbSNP_107	97	3273,5327		731,1811,1758	no	coding-synonymous	COL5A1	NM_000093.3		1321,2888,2294	CC,CG,GG		38.0581,48.7744,42.5188		1494/1839	137711997	5530,7476	2203	4300	6503	SO:0001819	synonymous_variant	1289	exon58			TCCTCCGGGTGAA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.4482G>C	9.37:g.137711997G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			A|0.009;C|0.408;G|0.583	0.408	strong		0.627	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
ADD1	118	hgsc.bcm.edu	37	4	2916762	2916762	+	Missense_Mutation	SNP	C	C	G	rs4963	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:2916762C>G	ENST00000398129.1	+	12	1777	c.1757C>G	c.(1756-1758)tCt>tGt	p.S586C	ADD1_ENST00000398123.2_Missense_Mutation_p.S617C|ADD1_ENST00000503455.2_Missense_Mutation_p.S617C|ADD1_ENST00000398125.1_Missense_Mutation_p.S617C|ADD1_ENST00000355842.3_Missense_Mutation_p.S617C|ADD1_ENST00000446856.1_Missense_Mutation_p.S586C|ADD1_ENST00000513328.2_Missense_Mutation_p.S586C|ADD1_ENST00000264758.7_Missense_Mutation_p.S617C			P35611	ADDA_HUMAN	adducin 1 (alpha)	586			S -> C (in dbSNP:rs4963). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:1840603}.		actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		CAGAAGGGCTCTGAAGGTGAG	0.597													C|||	1191	0.237819	0.1702	0.1772	5008	,	,		18849	0.4524		0.1909	False		,,,				2504	0.1994				p.S617C	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.C1850G						PASS	.	C	CYS/SER,CYS/SER,CYS/SER,CYS/SER	777,3629	310.2+/-291.5	61,655,1487	98.0	96.0	96.0		1757,1850,1757,1850	4.6	0.5	4	dbSNP_52	96	1582,7018	291.6+/-300.4	143,1296,2861	yes	missense,missense,missense,missense	ADD1	NM_001119.4,NM_014189.3,NM_014190.3,NM_176801.2	112,112,112,112	204,1951,4348	GG,GC,CC		18.3953,17.635,18.1378	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	586/738,617/769,586/632,617/663	2916762	2359,10647	2203	4300	6503	SO:0001583	missense	118	exon13			AGGGCTCTGAAGG	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.1757C>G	4.37:g.2916762C>G	ENSP00000381197:p.Ser586Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	53	16	0.301887	NM_176801	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Missense_Mutation	SNP	ENST00000398129.1	37	CCDS43205.1	592|592	0.27106227106227104|0.27106227106227104	82|82	0.16666666666666666|0.16666666666666666	68|68	0.1878453038674033|0.1878453038674033	288|288	0.5034965034965035|0.5034965034965035	154|154	0.20316622691292877|0.20316622691292877	C|C	11.65|11.65	1.700709|1.700709	0.30142|0.30142	0.17635|0.17635	0.183953|0.183953	ENSG00000087274|ENSG00000087274	ENST00000514940;ENST00000541843|ENST00000264758;ENST00000446856;ENST00000398125;ENST00000513328;ENST00000503455;ENST00000355842;ENST00000398123;ENST00000398129	.|T;T;T;T;T;T;T;T	.|0.19250	.|2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16	5.44|5.44	4.6|4.6	0.57074|0.57074	.|.	.|0.718287	.|0.13902	.|N	.|0.354858	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	P|P	0.0|0.0	.|B;B;P;B;B	.|0.50943	.|0.375;0.438;0.94;0.415;0.396	.|B;B;P;B;B	.|0.52267	.|0.345;0.401;0.694;0.163;0.195	T|T	0.50021|0.50021	-0.8876|-0.8876	4|9	.|0.42905	.|T	.|0.14	-1.6519|-1.6519	16.4208|16.4208	0.83758|0.83758	0.0:0.8683:0.1317:0.0|0.0:0.8683:0.1317:0.0	rs4963;rs52811169;rs58002748;rs4963|rs4963;rs52811169;rs58002748;rs4963	.|617;586;617;586;617	.|Q86XM2;P35611;P35611-3;P35611-2;A2A3N8	.|.;ADDA_HUMAN;.;.;.	V|C	323;32|617;586;617;586;617;617;617;586	.|ENSP00000264758:S617C;ENSP00000399828:S586C;ENSP00000381193:S617C;ENSP00000421907:S586C;ENSP00000423024:S617C;ENSP00000348100:S617C;ENSP00000381191:S617C;ENSP00000381197:S586C	.|ENSP00000264758:S617C	L|S	+|+	1|2	2|0	ADD1|ADD1	2886560|2886560	0.007000|0.007000	0.16637|0.16637	0.533000|0.533000	0.28001|0.28001	0.724000|0.724000	0.41520|0.41520	1.284000|1.284000	0.33249|0.33249	1.306000|1.306000	0.44926|0.44926	-0.217000|-0.217000	0.12591|0.12591	CTG|TCT	C|0.773;G|0.227;N|0.000	0.227	strong		0.597	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189	
MARK1	4139	hgsc.bcm.edu	37	1	220804451	220804451	+	Silent	SNP	G	G	A	rs35322308	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:220804451G>A	ENST00000366917.4	+	10	1250	c.984G>A	c.(982-984)ccG>ccA	p.P328P	MARK1_ENST00000366918.4_Silent_p.P306P|MARK1_ENST00000402574.1_Silent_p.P193P					MAP/microtubule affinity-regulating kinase 1									p.P328P(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(12)|lung(22)|ovary(4)|pancreas(1)|skin(3)|stomach(3)|urinary_tract(1)	63				GBM - Glioblastoma multiforme(131;0.0407)		AGCCTGATCCGGATTTCAATG	0.368													g|||	78	0.0155751	0.0	0.0173	5008	,	,		19137	0.001		0.0099	False		,,,				2504	0.0562				p.P328P		Atlas-SNP	.											MARK1,NS,carcinoma,0,1	MARK1	161	1	1	Substitution - coding silent(1)	stomach(1)	c.G984A						PASS	.	G		26,4380	31.7+/-61.6	0,26,2177	102.0	99.0	100.0		984	-0.7	1.0	1	dbSNP_126	100	180,8420	81.5+/-144.1	3,174,4123	no	coding-synonymous	MARK1	NM_018650.3		3,200,6300	AA,AG,GG		2.093,0.5901,1.5839		328/796	220804451	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	4139	exon10			TGATCCGGATTTC	AF154845	CCDS31029.2, CCDS65789.1, CCDS73033.1, CCDS73034.1	1q41	2013-06-27			ENSG00000116141	ENSG00000116141			6896	protein-coding gene	gene with protein product		606511				9108484	Standard	NM_018650		Approved	MARK, PAR-1C	uc001hmn.4	Q9P0L2	OTTHUMG00000037351	ENST00000366917.4:c.984G>A	1.37:g.220804451G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	35	0.406977	NM_018650		Silent	SNP	ENST00000366917.4	37	CCDS31029.2																																																																																			G|0.985;A|0.015	0.015	strong		0.368	MARK1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090899.1		
ATXN1	6310	hgsc.bcm.edu	37	6	16327912	16327912	+	Missense_Mutation	SNP	C	C	A	rs369629396|rs368218879		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:16327912C>A	ENST00000244769.4	-	8	1566	c.630G>T	c.(628-630)caG>caT	p.Q210H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q210H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	210	Poly-Gln.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.H209_H211delHQH(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgatgctgatgctgct	0.667																																					p.Q210H		Atlas-SNP	.											ATXN1,colon,carcinoma,0,2	ATXN1	117	2	1	Deletion - In frame(1)	prostate(1)	c.G630T						scavenged	.						5.0	8.0	7.0					6																	16327912		1576	3508	5084	SO:0001583	missense	6310	exon7			CTGATGCTGATGC	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.630G>T	6.37:g.16327912C>A	ENSP00000244769:p.Gln210His	Somatic	34	1	0.0294118		WXS	Illumina HiSeq	Phase_I	44	6	0.136364	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	4.990	0.183769	0.09495	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.50001	0.76;0.76	.	.	.	.	.	.	.	.	T	0.07413	0.0187	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.37709	-0.9694	5	0.15952	T	0.53	.	.	.	.	.	210	P54253	ATX1_HUMAN	H	210	ENSP00000244769:Q210H;ENSP00000416360:Q210H	ENSP00000244769:Q210H	Q	-	3	2	ATXN1	16435891	0.501000	0.26099	0.020000	0.16555	0.059000	0.15707	0.066000	0.14489	0.000000	0.14550	0.000000	0.15137	CAG	.	.	weak		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
FAT4	79633	hgsc.bcm.edu	37	4	126411594	126411594	+	Silent	SNP	G	G	A	rs62312781	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:126411594G>A	ENST00000394329.3	+	17	13630	c.13617G>A	c.(13615-13617)gaG>gaA	p.E4539E	FAT4_ENST00000335110.5_Silent_p.E2780E	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4539					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						ATCCCAAAGAGGAGAAGAAAC	0.522													G|||	786	0.156949	0.236	0.2349	5008	,	,		19314	0.0		0.1819	False		,,,				2504	0.1309				p.E4539E		Atlas-SNP	.											.	FAT4	1752	.	0			c.G13617A						PASS	.	G		916,3490	348.2+/-309.8	108,700,1395	69.0	72.0	71.0		13617	1.8	0.9	4	dbSNP_129	71	1587,7013	293.9+/-301.6	145,1297,2858	no	coding-synonymous	FAT4	NM_024582.4		253,1997,4253	AA,AG,GG		18.4535,20.7898,19.245		4539/4982	126411594	2503,10503	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon17			CAAAGAGGAGAAG	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.13617G>A	4.37:g.126411594G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			G|0.825;A|0.175	0.175	strong		0.522	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
ZBTB8OS	339487	hgsc.bcm.edu	37	1	33099637	33099637	+	Silent	SNP	A	A	G	rs704878	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:33099637A>G	ENST00000468695.1	-	3	213	c.195T>C	c.(193-195)ttT>ttC	p.F65F	ZBTB8OS_ENST00000492007.1_Intron|ZBTB8OS_ENST00000341885.5_Intron|ZBTB8OS_ENST00000373501.2_Silent_p.F53F	NM_178547.2	NP_848642.1	Q8IWT0	ARCH_HUMAN	zinc finger and BTB domain containing 8 opposite strand	53					tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	extracellular vesicular exosome (GO:0070062)|tRNA-splicing ligase complex (GO:0072669)	metal ion binding (GO:0046872)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CACATTGCTCAAATGCTTCCT	0.413													G|||	1070	0.213658	0.4947	0.2464	5008	,	,		16261	0.1319		0.0368	False		,,,				2504	0.0767				p.F65F		Atlas-SNP	.											.	ZBTB8OS	9	.	0			c.T195C						PASS	.	G		1870,2536	631.5+/-395.7	423,1024,756	118.0	105.0	110.0		195	3.1	1.0	1	dbSNP_86	110	341,8259	804.3+/-407.3	7,327,3966	no	coding-synonymous	ZBTB8OS	NM_178547.2		430,1351,4722	GG,GA,AA		3.9651,42.4421,16.9998		65/180	33099637	2211,10795	2203	4300	6503	SO:0001819	synonymous_variant	339487	exon3			TTGCTCAAATGCT	AY151084	CCDS365.1	1p35.1	2010-09-30			ENSG00000176261	ENSG00000176261			24094	protein-coding gene	gene with protein product	"""archease"""	615891				12477932	Standard	NM_178547		Approved	ARCH	uc001bvp.3	Q8IWT0	OTTHUMG00000007856	ENST00000468695.1:c.195T>C	1.37:g.33099637A>G		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	171	74	0.432749	NM_178547	Q5TGK5|Q6PDA1|Q8IWS9|Q8NEV6|Q8NEV7	Silent	SNP	ENST00000468695.1	37	CCDS365.1	395	0.18086080586080586	219	0.4451219512195122	79	0.21823204419889503	73	0.12762237762237763	24	0.0316622691292876	G	10.31	1.314977	0.23908	0.424421	0.039651	ENSG00000176261	ENST00000436661	.	.	.	5.35	3.06	0.35304	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-17.8943	10.6057	0.45392	0.8512:0.0:0.1488:0.0	rs704878	.	.	.	R	64	.	.	X	-	1	0	ZBTB8OS	32872224	1.000000	0.71417	0.994000	0.49952	0.976000	0.68499	1.578000	0.36525	0.115000	0.18071	-1.163000	0.01768	TGA	A|0.831;G|0.169	0.169	strong		0.413	ZBTB8OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021669.3	NM_178547	
UBR3	130507	hgsc.bcm.edu	37	2	170762566	170762566	+	Silent	SNP	A	A	T	rs10194785	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:170762566A>T	ENST00000272793.5	+	10	1721	c.1671A>T	c.(1669-1671)ctA>ctT	p.L557L	UBR3_ENST00000418381.1_Silent_p.L557L			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	557					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						AGCGAGAACTAAACGAGCATG	0.408													A|||	1388	0.277157	0.2663	0.1945	5008	,	,		16538	0.376		0.1581	False		,,,				2504	0.3712				p.L557L		Atlas-SNP	.											.	UBR3	182	.	0			c.A1671T						PASS	.	A		383,1001		58,267,367	119.0	103.0	108.0		1671	1.6	1.0	2	dbSNP_119	108	545,2637		49,447,1095	no	coding-synonymous	UBR3	NM_172070.3		107,714,1462	TT,TA,AA		17.1276,27.6734,20.3241		557/1889	170762566	928,3638	692	1591	2283	SO:0001819	synonymous_variant	130507	exon10			AGAACTAAACGAG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.1671A>T	2.37:g.170762566A>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				A|0.748;T|0.252	0.252	strong		0.408	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
FMO1	2326	hgsc.bcm.edu	37	1	171252287	171252287	+	Silent	SNP	A	A	G	rs1126692	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171252287A>G	ENST00000354841.4	+	7	1319	c.1188A>G	c.(1186-1188)gtA>gtG	p.V396V	FMO1_ENST00000367750.3_Silent_p.V396V|FMO1_ENST00000469112.1_3'UTR|FMO1_ENST00000402921.2_Silent_p.V333V	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	396					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CTACAGGTGTAAATAAGTTAC	0.353													A|||	1255	0.250599	0.593	0.121	5008	,	,		15383	0.0367		0.1412	False		,,,				2504	0.2127				p.V396V		Atlas-SNP	.											FMO1,left_upper_lobe,carcinoma,+2,1	FMO1	79	1	0			c.A1188G						PASS	.	A		2260,2146	595.1+/-388.4	580,1100,523	119.0	121.0	120.0		1188	-10.3	0.0	1	dbSNP_86	120	1166,7434	237.5+/-269.3	78,1010,3212	no	coding-synonymous	FMO1	NM_002021.1		658,2110,3735	GG,GA,AA		13.5581,48.7063,26.3417		396/533	171252287	3426,9580	2203	4300	6503	SO:0001819	synonymous_variant	2326	exon8			AGGTGTAAATAAG	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.1188A>G	1.37:g.171252287A>G		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	256	125	0.488281	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Silent	SNP	ENST00000354841.4	37	CCDS1294.1																																																																																			A|0.769;C|0.000;G|0.231	0.231	strong		0.353	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021	
ACP1	52	hgsc.bcm.edu	37	2	277003	277003	+	Missense_Mutation	SNP	A	A	G	rs79716074	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:277003A>G	ENST00000272065.5	+	5	410	c.317A>G	c.(316-318)cAa>cGa	p.Q106R	ACP1_ENST00000272067.6_Missense_Mutation_p.Q106R|ACP1_ENST00000484464.1_3'UTR	NM_004300.3	NP_004291.1	P24666	PPAC_HUMAN	acid phosphatase 1, soluble	106			Q -> R (in allele ACP1*A; dbSNP:rs7576247). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	12	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.00175)|Lung NSC(108;0.216)|all_epithelial(98;0.236)		all cancers(51;0.000391)|Epithelial(75;0.00281)|OV - Ovarian serous cystadenocarcinoma(76;0.00542)|GBM - Glioblastoma multiforme(21;0.127)	Adenine(DB00173)	AAAAGTAATCAAGTTAAAACC	0.323													A|||	1323	0.264177	0.2065	0.2363	5008	,	,		18004	0.246		0.335	False		,,,				2504	0.3078				p.Q106R		Atlas-SNP	.											ACP1_ENST00000272067,NS,carcinoma,+1,4	ACP1	42	4	0			c.A317G						PASS	.	A	ARG/GLN,ARG/GLN	983,3417	336.0+/-304.2	107,769,1324	52.0	55.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	317,317	3.1	1.0	2	dbSNP_131	54	2959,5631	442.4+/-360.1	483,1993,1819	yes	missense,missense	ACP1	NM_004300.3,NM_007099.3	43,43	590,2762,3143	GG,GA,AA		34.447,22.3409,30.3464	benign,benign	106/159,106/159	277003	3942,9048	2200	4295	6495	SO:0001583	missense	52	exon5			GTAATCAAGTTAA	M87546	CCDS1639.1, CCDS1640.1, CCDS46217.1	2p25	2011-06-09			ENSG00000143727	ENSG00000143727	3.1.3.2	"""Protein tyrosine phosphatases / Class II Cys-based PTPs"""	122	protein-coding gene	gene with protein product		171500					Standard	NM_001040649		Approved		uc002qwf.3	P24666	OTTHUMG00000086933	ENST00000272065.5:c.317A>G	2.37:g.277003A>G	ENSP00000272065:p.Gln106Arg	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_007099	A8K1L9|B5MCC7|P24667|Q16035|Q16036|Q16725|Q3KQX8|Q53RU0	Missense_Mutation	SNP	ENST00000272065.5	37	CCDS1639.1	551	0.2522893772893773	87	0.17682926829268292	87	0.24033149171270718	126	0.2202797202797203	251	0.3311345646437995	A	11.29	1.595656	0.28445	0.223409	0.34447	ENSG00000143727	ENST00000272067;ENST00000272065	T;T	0.16457	2.34;2.34	5.48	3.09	0.35607	Phosphotyrosine protein phosphatase I superfamily (3);	0.404011	0.29624	N	0.011622	T	0.00012	0.0000	N	0.05414	-0.055	0.09310	P	0.9999999842883	B;B	0.10296	0.0;0.003	B;B	0.14578	0.003;0.011	T	0.49679	-0.8914	9	0.23302	T	0.38	-2.9532	6.7926	0.23707	0.7665:0.1527:0.0807:0.0	rs7576247;rs17357270;rs59972259	106;106	P24666-2;P24666	.;PPAC_HUMAN	R	106	ENSP00000272067:Q106R;ENSP00000272065:Q106R	ENSP00000272065:Q106R	Q	+	2	0	ACP1	267003	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.840000	0.48215	0.370000	0.24538	0.533000	0.62120	CAA	A|0.725;G|0.275	0.275	strong		0.323	ACP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195862.3		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557510	32557510	+	Silent	SNP	G	G	A	rs201125976	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32557510G>A	ENST00000360004.5	-	1	115	c.10C>T	c.(10-12)Ctg>Ttg	p.L4L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	4					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GGGAGCTTCAGACACACCATG	0.572										Multiple Myeloma(14;0.17)			G|||	113	0.0225639	0.0386	0.0245	5008	,	,		24903	0.0099		0.0288	False		,,,				2504	0.0061				p.L4L		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C10T						PASS	.						75.0	89.0	84.0					6																	32557510		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon1			GCTTCAGACACAC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.10C>T	6.37:g.32557510G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	220	36	0.163636	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.981;A|0.019	0.019	strong		0.572	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
GM2A	2760	hgsc.bcm.edu	37	5	150639439	150639439	+	Missense_Mutation	SNP	A	A	G	rs153478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150639439A>G	ENST00000357164.3	+	2	530	c.205A>G	c.(205-207)Atg>Gtg	p.M69V		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	69			M -> V (in dbSNP:rs153478). {ECO:0000269|PubMed:10364519, ECO:0000269|PubMed:1427911, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1915857, ECO:0000269|PubMed:2059210, ECO:0000269|PubMed:2753159}.		ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTCAGTGTCATGGGCAGCAC	0.607													G|||	4308	0.860224	0.8654	0.8112	5008	,	,		18251	1.0		0.675	False		,,,				2504	0.9346				p.M69V		Atlas-SNP	.											.	GM2A	24	.	0			c.A205G						PASS	.	G	VAL/MET,VAL/MET	3750,656	281.4+/-275.9	1593,564,46	56.0	48.0	51.0		205,205	-2.4	0.0	5	dbSNP_79	51	5652,2948	459.7+/-365.0	1859,1934,507	yes	missense,missense	GM2A	NM_000405.4,NM_001167607.1	21,21	3452,2498,553	GG,GA,AA		34.2791,14.8888,27.7103	benign,benign	69/194,69/187	150639439	9402,3604	2203	4300	6503	SO:0001583	missense	2760	exon2			AGTGTCATGGGCA		CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"""cerebroside sulfate activator protein"", ""sphingolipid activator protein 3"""	613109	"""GM2 ganglioside activator protein"""			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.205A>G	5.37:g.150639439A>G	ENSP00000349687:p.Met69Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001167607	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Missense_Mutation	SNP	ENST00000357164.3	37	CCDS4313.1	1780|1780	0.815018315018315|0.815018315018315	414|414	0.8414634146341463|0.8414634146341463	285|285	0.787292817679558|0.787292817679558	572|572	1.0|1.0	509|509	0.6715039577836411|0.6715039577836411	G|G	6.468|6.468	0.454547|0.454547	0.12283|0.12283	0.851112|0.851112	0.657209|0.657209	ENSG00000196743|ENSG00000196743	ENST00000523004|ENST00000523466;ENST00000357164	.|T;T	.|0.69175	.|-0.38;-0.38	5.36|5.36	-2.41|-2.41	0.06562|0.06562	.|MD-2-related lipid-recognition (1);	.|0.847959	.|0.10887	.|N	.|0.623184	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00841|0.00841	-1.15|-1.15	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.31364|0.31364	-0.9946|-0.9946	4|9	.|0.27785	.|T	.|0.31	-19.5979|-19.5979	1.2149|1.2149	0.01912|0.01912	0.4098:0.1012:0.2007:0.2883|0.4098:0.1012:0.2007:0.2883	rs153478;rs976513;rs1048720;rs3188752;rs17716116;rs17856299;rs52826411;rs57274776;rs153478|rs153478;rs976513;rs1048720;rs3188752;rs17716116;rs17856299;rs52826411;rs57274776;rs153478	.|69	.|P17900	.|SAP3_HUMAN	R|V	27|84;69	.|ENSP00000429100:M84V;ENSP00000349687:M69V	.|ENSP00000349687:M69V	H|M	+|+	2|1	0|0	GM2A|GM2A	150619632|150619632	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.529000|0.529000	0.23019|0.23019	-0.846000|-0.846000	0.04174|0.04174	-1.656000|-1.656000	0.00753|0.00753	CAT|ATG	A|0.237;G|0.763	0.763	strong		0.607	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405	
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 GAIIx	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	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	57	5	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 GAIIx	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	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	30	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	
MUC16	94025	hgsc.bcm.edu	37	19	9083427	9083427	+	Silent	SNP	A	A	G	rs1609453	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9083427A>G	ENST00000397910.4	-	1	8591	c.8388T>C	c.(8386-8388)gcT>gcC	p.A2796A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2796	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCCAGAGCTAGCCATACCCT	0.502													G|||	1065	0.21266	0.1536	0.2752	5008	,	,		21615	0.3036		0.173	False		,,,				2504	0.1953				p.A2796A		Atlas-SNP	.											.	MUC16	4315	.	0			c.T8388C						PASS	.	G		565,3315		41,483,1416	64.0	64.0	64.0		8388	0.2	0.0	19	dbSNP_88	64	1489,6807		127,1235,2786	no	coding-synonymous	MUC16	NM_024690.2		168,1718,4202	GG,GA,AA		17.9484,14.5619,16.8693		2796/14508	9083427	2054,10122	1940	4148	6088	SO:0001819	synonymous_variant	94025	exon1			AGAGCTAGCCATA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8388T>C	19.37:g.9083427A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	99	40	0.40404	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			A|0.789;G|0.211	0.211	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MKL1	57591	hgsc.bcm.edu	37	22	40814500	40814500	+	Missense_Mutation	SNP	T	T	C	rs878756	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:40814500T>C	ENST00000355630.3	-	12	2532	c.1942A>G	c.(1942-1944)Agc>Ggc	p.S648G	MKL1_ENST00000396617.3_Missense_Mutation_p.S648G|MKL1_ENST00000402042.1_Missense_Mutation_p.S598G|MKL1_ENST00000407029.1_Missense_Mutation_p.S648G	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	648	Pro-rich.		S -> G (in dbSNP:rs878756). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:17974005}.		negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.S648G(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						TTGATGAGGCTGGGGCCCTGA	0.677			T	RBM15	acute megakaryocytic leukemia								C|||	2420	0.483227	0.9448	0.2839	5008	,	,		11023	0.1111		0.3797	False		,,,				2504	0.4908				p.S648G		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	MKL1,NS,carcinoma,0,1	MKL1	69	1	1	Substitution - Missense(1)	stomach(1)	c.A1942G						PASS	.	C	GLY/SER	3792,614	258.0+/-262.2	1646,500,57	55.0	58.0	57.0		1942	-8.5	0.0	22	dbSNP_86	57	3414,5186	622.5+/-397.3	705,2004,1591	yes	missense	MKL1	NM_020831.3	56	2351,2504,1648	CC,CT,TT		39.6977,13.9355,44.5948	benign	648/932	40814500	7206,5800	2203	4300	6503	SO:0001583	missense	57591	exon12			TGAGGCTGGGGCC	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1942A>G	22.37:g.40814500T>C	ENSP00000347847:p.Ser648Gly	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	154	153	0.993506	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	917	0.4198717948717949	459	0.9329268292682927	109	0.3011049723756906	66	0.11538461538461539	283	0.3733509234828496	C	0.261	-0.999638	0.02128	0.860645	0.396977	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	4.45	-8.52	0.00920	.	1.024570	0.07702	N	0.940646	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.29941	-0.9995	9	0.14252	T	0.57	-1.3436	18.4959	0.90865	0.0:0.5986:0.0:0.4014	rs878756;rs17424984;rs58451515;rs878756	598;648;648	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	G	648;648;598;648	ENSP00000347847:S648G;ENSP00000379861:S648G;ENSP00000385584:S598G;ENSP00000385835:S648G	ENSP00000347847:S648G	S	-	1	0	MKL1	39144446	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-2.523000	0.00949	-2.402000	0.00577	-2.030000	0.00424	AGC	T|0.474;C|0.526	0.526	strong		0.677	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
KRTAP10-11	386678	hgsc.bcm.edu	37	21	46067180	46067180	+	Missense_Mutation	SNP	C	C	T	rs462007	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46067180C>T	ENST00000334670.8	+	1	850	c.805C>T	c.(805-807)Cgc>Tgc	p.R269C	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	269	25 X 5 AA repeats of C-C-X(3).			R -> C (in Ref. 1; BAD01546 and 3; AAI31612). {ECO:0000305}.		keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CAGCTGCTGCCGCCCGGCCTC	0.682													T|||	4087	0.816094	0.9887	0.7954	5008	,	,		19081	0.6796		0.8062	False		,,,				2504	0.7485				p.R269C		Atlas-SNP	.											.	KRTAP10-11	36	.	0			c.C805T						PASS	.	T	,CYS/ARG	4211,193	107.3+/-145.7	2012,187,3	42.0	54.0	50.0		,805	3.0	0.3	21	dbSNP_80	50	6723,1865	319.0+/-313.9	2635,1453,206	no	intron,missense	TSPEAR,KRTAP10-11	NM_144991.2,NM_198692.2	,180	4647,1640,209	TT,TC,CC		21.7163,4.3824,15.8405	,probably-damaging	,269/299	46067180	10934,2058	2202	4294	6496	SO:0001583	missense	386678	exon1			TGCTGCCGCCCGG	AB076359	CCDS42962.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000243489	ENSG00000243489		"""Keratin associated proteins"""	20528	protein-coding gene	gene with protein product			"""keratin associated protein 10-11"""	KRTAP18-11			Standard	NM_198692		Approved	KRTAP18.11, KAP18.11, KAP10.11	uc002zfr.4	P60412	OTTHUMG00000057626	ENST00000334670.8:c.805C>T	21.37:g.46067180C>T	ENSP00000334197:p.Arg269Cys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	97	38	0.391753	NM_198692	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	1775	0.8127289377289377	480	0.975609756097561	298	0.8232044198895028	383	0.6695804195804196	614	0.8100263852242744	t	8.562	0.877898	0.17395	0.956176	0.782837	ENSG00000243489	ENST00000334670	T	0.00686	5.85	3.93	3.04	0.35103	.	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	0.37916	P	0.06845500000000004	D	0.89917	1.0	P	0.61874	0.895	T	0.43410	-0.9393	8	0.54805	T	0.06	.	6.258	0.20884	0.1641:0.725:0.0:0.1109	rs462007;rs58847266	269	P60412	KR10B_HUMAN	C	269	ENSP00000334197:R269C	ENSP00000334197:R269C	R	+	1	0	KRTAP10-11	44891608	0.000000	0.05858	0.334000	0.25495	0.053000	0.15095	-1.248000	0.02890	0.187000	0.20147	-1.295000	0.01343	CGC	C|0.202;T|0.798	0.798	strong		0.682	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692	
OTOA	146183	hgsc.bcm.edu	37	16	21742174	21742174	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:21742174A>G	ENST00000286149.4	+	20	2267	c.2266A>G	c.(2266-2268)Aca>Gca	p.T756A	OTOA_ENST00000388957.3_Missense_Mutation_p.T418A|OTOA_ENST00000388958.3_Missense_Mutation_p.T742A|OTOA_ENST00000388956.4_Missense_Mutation_p.T663A			Q7RTW8	OTOAN_HUMAN	otoancorin	756					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)	46				GBM - Glioblastoma multiforme(48;0.0414)		TCAGCACTGGACAGCCGAGAC	0.443																																					p.T742A		Atlas-SNP	.											OTOA,NS,carcinoma,-1,1	OTOA	144	1	0			c.A2224G						scavenged	.						98.0	79.0	85.0					16																	21742174		2195	4271	6466	SO:0001583	missense	146183	exon20			CACTGGACAGCCG	AK057335	CCDS10600.2, CCDS32403.1, CCDS53994.1	16p12.2	2009-08-18	2002-07-05		ENSG00000155719	ENSG00000155719			16378	protein-coding gene	gene with protein product	"""cancer/testis antigen 108"""	607038	"""deafness, autosomal recessive 22"""	DFNB22		11972037, 19088187	Standard	NM_170664		Approved	CT108	uc002djh.3	Q7RTW8	OTTHUMG00000090721	ENST00000286149.4:c.2266A>G	16.37:g.21742174A>G	ENSP00000286149:p.Thr756Ala	Somatic	737	5	0.00678426		WXS	Illumina HiSeq	Phase_I	794	11	0.0138539	NM_144672	A1L3A8|A2VDI0|B3KWU3|E9PF51|Q8NA86|Q96M76	Missense_Mutation	SNP	ENST00000286149.4	37		.	.	.	.	.	.	.	.	.	.	A	15.35	2.808974	0.50421	.	.	ENSG00000155719	ENST00000388958;ENST00000286149;ENST00000388956;ENST00000388957;ENST00000338456	T;T;T;T	0.69685	-0.42;-0.41;-0.42;-0.4	4.11	4.11	0.48088	.	0.067720	0.64402	D	0.000014	T	0.76499	0.3996	M	0.68952	2.095	0.40699	D	0.982465	D;D;D;D	0.71674	0.998;0.998;0.992;0.998	D;D;P;D	0.69479	0.964;0.964;0.798;0.964	T	0.78209	-0.2293	10	0.54805	T	0.06	-10.4772	9.663	0.39967	1.0:0.0:0.0:0.0	.	756;663;418;742	Q7RTW8;B3KWU3;Q7RTW8-2;E9PF51	OTOAN_HUMAN;.;.;.	A	742;756;663;418;151	ENSP00000373610:T742A;ENSP00000286149:T756A;ENSP00000373608:T663A;ENSP00000373609:T418A	ENSP00000286149:T756A	T	+	1	0	OTOA	21649675	1.000000	0.71417	0.995000	0.50966	0.634000	0.38068	3.242000	0.51384	1.834000	0.53371	0.496000	0.49642	ACA	.	.	none		0.443	OTOA-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000430021.1		
EFCAB7	84455	hgsc.bcm.edu	37	1	63999826	63999826	+	Missense_Mutation	SNP	C	C	T	rs6693255	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:63999826C>T	ENST00000371088.4	+	6	989	c.743C>T	c.(742-744)aCa>aTa	p.T248I	RNU7-123P_ENST00000515911.1_RNA	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	248			T -> I (in dbSNP:rs6693255). {ECO:0000269|PubMed:15489334}.				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						GTTTCCTTCACAGTTACCATG	0.353													C|||	726	0.144968	0.0855	0.1614	5008	,	,		15556	0.1855		0.1441	False		,,,				2504	0.1728				p.T248I		Atlas-SNP	.											EFCAB7,NS,carcinoma,+1,1	EFCAB7	45	1	0			c.C743T						PASS	.	C	ILE/THR	393,4013	195.0+/-219.7	13,367,1823	100.0	98.0	98.0		743	1.5	1.0	1	dbSNP_116	98	1325,7275	260.5+/-283.3	92,1141,3067	yes	missense	EFCAB7	NM_032437.2	89	105,1508,4890	TT,TC,CC		15.407,8.9197,13.2093	benign	248/630	63999826	1718,11288	2203	4300	6503	SO:0001583	missense	84455	exon6			CCTTCACAGTTAC	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.743C>T	1.37:g.63999826C>T	ENSP00000360129:p.Thr248Ile	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	125	76	0.608	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	325	0.1488095238095238	51	0.10365853658536585	61	0.1685082872928177	105	0.18356643356643357	108	0.1424802110817942	C	3.616	-0.078505	0.07184	0.089197	0.15407	ENSG00000203965	ENST00000371088	T	0.58652	0.32	5.65	1.49	0.22878	.	0.529823	0.23072	N	0.052243	T	0.25269	0.0614	L	0.47716	1.5	0.21719	P	0.999579407	B	0.30763	0.294	B	0.26517	0.07	T	0.06356	-1.0831	9	0.72032	D	0.01	-5.8298	4.209	0.10502	0.1277:0.5984:0.1245:0.1495	rs6693255;rs17856494;rs52831553;rs56659953;rs6693255	248	A8K855	EFCB7_HUMAN	I	248	ENSP00000360129:T248I	ENSP00000360129:T248I	T	+	2	0	EFCAB7	63772414	0.160000	0.22878	0.976000	0.42696	0.393000	0.30537	0.578000	0.23773	0.744000	0.32741	-0.136000	0.14681	ACA	C|0.857;T|0.143	0.143	strong		0.353	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
BEND7	222389	hgsc.bcm.edu	37	10	13494594	13494594	+	Silent	SNP	T	T	C	rs2277222	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:13494594T>C	ENST00000396900.2	-	7	1127	c.1128A>G	c.(1126-1128)gtA>gtG	p.V376V	BEND7_ENST00000486542.1_5'UTR|BEND7_ENST00000378605.3_Silent_p.V337V|BEND7_ENST00000396898.2_Silent_p.V389V|BEND7_ENST00000341083.3_Silent_p.V324V			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	376	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.					extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						GTAGAATCTGTACCCAATCTC	0.363													T|||	1785	0.35643	0.1218	0.3458	5008	,	,		18852	0.6696		0.3429	False		,,,				2504	0.3722				p.V337V		Atlas-SNP	.											.	BEND7	85	.	0			c.A1011G						PASS	.	T	,	697,3709	291.8+/-281.7	60,577,1566	142.0	143.0	143.0		1011,972	-5.5	0.9	10	dbSNP_100	143	2829,5771	446.0+/-361.1	458,1913,1929	no	coding-synonymous,coding-synonymous	BEND7	NM_001100912.1,NM_152751.2	,	518,2490,3495	CC,CT,TT		32.8953,15.8193,27.1106	,	337/375,324/469	13494594	3526,9480	2203	4300	6503	SO:0001819	synonymous_variant	222389	exon6			AATCTGTACCCAA	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.1128A>G	10.37:g.13494594T>C		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	232	231	0.99569	NM_001100912	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				T|0.677;C|0.323	0.323	strong		0.363	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
FSHB	2488	hgsc.bcm.edu	37	11	30255185	30255185	+	Silent	SNP	C	C	T	rs6169	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:30255185C>T	ENST00000417547.1	+	3	267	c.228C>T	c.(226-228)taC>taT	p.Y76Y	FSHB_ENST00000533718.1_Silent_p.Y76Y|FSHB_ENST00000254122.3_Silent_p.Y76Y	NM_001018080.1	NP_001018090.1	P01225	FSHB_HUMAN	follicle stimulating hormone, beta polypeptide	76					cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|female pregnancy (GO:0007565)|follicle-stimulating hormone signaling pathway (GO:0042699)|peptide hormone processing (GO:0016486)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone biosynthetic process (GO:0006701)|regulation of osteoclast differentiation (GO:0045670)|Sertoli cell proliferation (GO:0060011)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	12						AACTGGTATACGAAACAGTGA	0.498													T|||	3079	0.614816	0.7572	0.5317	5008	,	,		18146	0.6696		0.4503	False		,,,				2504	0.5941				p.Y76Y		Atlas-SNP	.											.	FSHB	28	.	0			c.C228T						PASS	.	T	,	3124,1280	437.6+/-345.0	1100,924,178	107.0	94.0	99.0		228,228	-8.5	0.5	11	dbSNP_52	99	3747,4851	617.0+/-396.6	825,2097,1377	no	coding-synonymous,coding-synonymous	FSHB	NM_000510.2,NM_001018080.1	,	1925,3021,1555	TT,TC,CC		43.5799,29.0645,47.1543	,	76/130,76/130	30255185	6871,6131	2202	4299	6501	SO:0001819	synonymous_variant	2488	exon3			GGTATACGAAACA		CCDS7868.1	11p13	2013-02-26				ENSG00000131808		"""Endogenous ligands"""	3964	protein-coding gene	gene with protein product	"""follitropin, beta chain"", ""follicle-stimulating hormone beta subunit"""	136530				2885163, 3151250	Standard	NM_000510		Approved		uc001msm.3	P01225		ENST00000417547.1:c.228C>T	11.37:g.30255185C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_000510	A2TF08|A5JVV3|Q14D61	Silent	SNP	ENST00000417547.1	37	CCDS7868.1																																																																																			C|0.436;T|0.564	0.564	strong		0.498	FSHB-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389757.1	NM_000510	
ZNF69	7620	hgsc.bcm.edu	37	19	11998777	11998777	+	Silent	SNP	C	C	T	rs3810314	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:11998777C>T	ENST00000429654.2	+	1	179	c.39C>T	c.(37-39)ccC>ccT	p.P13P	ZNF69_ENST00000340180.5_Silent_p.P13P			Q9UC07	ZNF69_HUMAN	zinc finger protein 69	13					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)|large_intestine(1)|skin(2)	4				Lung(535;0.011)		GAGAGGACCCCGGGACATCTG	0.637													c|||	579	0.115615	0.3389	0.0432	5008	,	,		16314	0.0228		0.0239	False		,,,				2504	0.0552				p.P13P		Atlas-SNP	.											.	ZNF69	27	.	0			c.C39T						PASS	.	C		1247,3159	428.7+/-342.0	173,901,1129	77.0	66.0	70.0		39	-1.1	0.0	19	dbSNP_107	70	164,8436	76.9+/-139.5	1,162,4137	no	coding-synonymous	ZNF69	NM_021915.2		174,1063,5266	TT,TC,CC		1.907,28.3023,10.8488		13/150	11998777	1411,11595	2203	4300	6503	SO:0001819	synonymous_variant	7620	exon1			GGACCCCGGGACA	X60076	CCDS32914.1	19p13.2	2013-01-08	2006-05-12		ENSG00000198429	ENSG00000198429		"""Zinc fingers, C2H2-type"", ""-"""	13138	protein-coding gene	gene with protein product		194543	"""zinc finger protein 69 (Cos5)"""			1639391	Standard	NM_021915		Approved	Cos5	uc002mst.4	Q9UC07	OTTHUMG00000156526	ENST00000429654.2:c.39C>T	19.37:g.11998777C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_021915	Q86VA7	Silent	SNP	ENST00000429654.2	37																																																																																				C|0.897;T|0.103	0.103	strong		0.637	ZNF69-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000344082.1	NM_021915	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37455583	37455583	+	Silent	SNP	G	G	A	rs41276132		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:37455583G>A	ENST00000374660.1	+	19	2046	c.1947G>A	c.(1945-1947)gcG>gcA	p.A649A	ANKRD30A_ENST00000361713.1_Silent_p.A649A|ANKRD30A_ENST00000602533.1_Intron			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	586					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CCAAGGCTGCGCATCAAAAAG	0.299																																					p.A649A		Atlas-SNP	.											ANKRD30A,NS,haematopoietic_neoplasm,+1,1	ANKRD30A	448	1	0			c.G1947A						scavenged	.						3.0	3.0	3.0					10																	37455583		1398	3151	4549	SO:0001819	synonymous_variant	91074	exon19			GGCTGCGCATCAA	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000374660.1:c.1947G>A	10.37:g.37455583G>A		Somatic	470	6	0.012766		WXS	Illumina HiSeq	Phase_I	301	7	0.0232558	NM_052997	Q5W025	Silent	SNP	ENST00000374660.1	37																																																																																				A|1.000;|0.000	1.000	weak		0.299	ANKRD30A-002	PUTATIVE	NMD_exception|basic	protein_coding	protein_coding	OTTHUMT00000047589.2	NM_052997	
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 GAIIx	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	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	113	28	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	
AFAP1	60312	hgsc.bcm.edu	37	4	7802292	7802292	+	Silent	SNP	G	G	A	rs11728778	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:7802292G>A	ENST00000360265.4	-	9	1377	c.1143C>T	c.(1141-1143)acC>acT	p.T381T	AFAP1_ENST00000358461.2_Silent_p.T381T|AFAP1_ENST00000420658.1_Silent_p.T381T|AFAP1_ENST00000513842.1_5'Flank|AFAP1_ENST00000382543.3_Silent_p.T381T			Q8N556	AFAP1_HUMAN	actin filament associated protein 1	381	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|skin(4)|stomach(2)	32						TCTTCAGGTCGGTCCTGTCCT	0.562													G|||	559	0.111621	0.0106	0.1484	5008	,	,		19505	0.0615		0.3042	False		,,,				2504	0.0757				p.T381T		Atlas-SNP	.											.	AFAP1	93	.	0			c.C1143T						PASS	.	G	,	246,4160	144.2+/-179.2	7,232,1964	134.0	122.0	126.0		1143,1143	-8.9	0.1	4	dbSNP_120	126	2607,5993	423.4+/-354.3	421,1765,2114	no	coding-synonymous,coding-synonymous	AFAP1	NM_001134647.1,NM_198595.2	,	428,1997,4078	AA,AG,GG		30.314,5.5833,21.936	,	381/815,381/731	7802292	2853,10153	2203	4300	6503	SO:0001819	synonymous_variant	60312	exon10			CAGGTCGGTCCTG	AB209676	CCDS3397.1, CCDS47010.1	4p16	2014-02-12	2007-02-07		ENSG00000196526	ENSG00000196526		"""Pleckstrin homology (PH) domain containing"""	24017	protein-coding gene	gene with protein product		608252				14755689, 11641786, 11607843	Standard	NM_198595		Approved	AFAP-110, AFAP	uc011bwk.1	Q8N556	OTTHUMG00000125515	ENST00000360265.4:c.1143C>T	4.37:g.7802292G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_001134647	A8K442|B4DMU2|E9PDT7|Q59EY5|Q9HBY1	Silent	SNP	ENST00000360265.4	37	CCDS3397.1																																																																																			G|0.812;A|0.188	0.188	strong		0.562	AFAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246842.2	NM_021638	
OR13C9	286362	hgsc.bcm.edu	37	9	107380414	107380414	+	Missense_Mutation	SNP	C	C	A	rs2900373	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107380414C>A	ENST00000259362.1	-	1	71	c.72G>T	c.(70-72)gaG>gaT	p.E24D		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	24			E -> D (in dbSNP:rs2900373).			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)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AAAAGAGTAACTCAAGCCTTG	0.403													C|||	2138	0.426917	0.6142	0.2262	5008	,	,		18141	0.5754		0.1779	False		,,,				2504	0.4192				p.E24D		Atlas-SNP	.											.	OR13C9	42	.	0			c.G72T						PASS	.	C	ASP/GLU	2419,1987	617.9+/-393.1	668,1083,452	127.0	125.0	125.0		72	3.9	1.0	9	dbSNP_101	125	1664,6936	306.9+/-308.1	183,1298,2819	no	missense	OR13C9	NM_001001956.1	45	851,2381,3271	AA,AC,CC		19.3488,45.0976,31.3932	possibly-damaging	24/319	107380414	4083,8923	2203	4300	6503	SO:0001583	missense	286362	exon1			GAGTAACTCAAGC		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.72G>T	9.37:g.107380414C>A	ENSP00000259362:p.Glu24Asp	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	212	95	0.448113	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	826	0.3782051282051282	284	0.5772357723577236	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	C	11.21	1.571963	0.28092	0.549024	0.193488	ENSG00000136839	ENST00000259362	T	0.01092	5.35	4.79	3.89	0.44902	.	0.134094	0.33753	N	0.004592	T	0.00012	0.0000	M	0.69358	2.11	0.58432	P	1.0000000000287557E-6	B	0.28971	0.229	B	0.25614	0.062	T	0.10941	-1.0608	9	0.87932	D	0	.	10.9252	0.47187	0.0:0.9082:0.0:0.0918	rs2900373;rs56843910;rs2900373	24	Q8NGT0	O13C9_HUMAN	D	24	ENSP00000259362:E24D	ENSP00000259362:E24D	E	-	3	2	OR13C9	106420235	0.557000	0.26546	0.982000	0.44146	0.622000	0.37654	1.318000	0.33643	1.236000	0.43740	0.573000	0.79308	GAG	A|0.365;C|0.635	0.365	strong		0.403	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
GFM1	85476	hgsc.bcm.edu	37	3	158362441	158362441	+	Silent	SNP	T	T	C	rs1864507	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:158362441T>C	ENST00000486715.1	+	1	375	c.18T>C	c.(16-18)gcT>gcC	p.A6A	GFM1_ENST00000478576.1_Silent_p.A6A|GFM1_ENST00000264263.5_Silent_p.A6A	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			TCCTGGGAGCTGCAGCCGTCG	0.662											OREG0015898	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2920	0.583067	0.7708	0.5303	5008	,	,		13649	0.3849		0.5437	False		,,,				2504	0.6115				p.A6A		Atlas-SNP	.											.	GFM1	83	.	0			c.T18C						PASS	.	C		3113,1231		1158,797,217	6.0	8.0	8.0		18	-2.5	0.0	3	dbSNP_92	8	4577,3917		1317,1943,987	no	coding-synonymous	GFM1	NM_024996.5		2475,2740,1204	CC,CT,TT		46.1149,28.3379,40.0997		6/752	158362441	7690,5148	2172	4247	6419	SO:0001819	synonymous_variant	85476	exon1			GGGAGCTGCAGCC	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"""G translation elongation factor, mitochondrial"""			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.18T>C	3.37:g.158362441T>C		Somatic	132	0	0	1793	WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_024996		Silent	SNP	ENST00000486715.1	37	CCDS33885.1																																																																																			T|0.450;C|0.550	0.550	strong		0.662	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996	
SLC22A12	116085	hgsc.bcm.edu	37	11	64359274	64359274	+	Silent	SNP	C	C	T	rs3825017	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64359274C>T	ENST00000377574.1	+	1	993	c.246C>T	c.(244-246)aaC>aaT	p.N82N	SLC22A12_ENST00000473690.1_5'UTR|SLC22A12_ENST00000377567.2_Silent_p.N82N|SLC22A12_ENST00000377572.1_Silent_p.N82N|SLC22A12_ENST00000336464.7_Silent_p.N82N	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	82					cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	CGGGCCCCAACCAGAGGCCCC	0.687													C|||	354	0.0706869	0.0038	0.0634	5008	,	,		12568	0.2956		0.004	False		,,,				2504	0.0031				p.N82N		Atlas-SNP	.											.	SLC22A12	68	.	0			c.C246T						PASS	.	C	,	23,4379	28.1+/-56.4	0,23,2178	28.0	31.0	30.0		246,	3.5	0.0	11	dbSNP_107	30	20,8574	11.9+/-42.8	0,20,4277	no	coding-synonymous,utr-5	SLC22A12	NM_144585.2,NM_153378.1	,	0,43,6455	TT,TC,CC		0.2327,0.5225,0.3309	,	82/554,	64359274	43,12953	2201	4297	6498	SO:0001819	synonymous_variant	116085	exon1			CCCCAACCAGAGG	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"""Solute carriers"""	17989	protein-coding gene	gene with protein product		607096	"""solute carrier family 22 (organic anion/cation transporter), member 12"""			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.246C>T	11.37:g.64359274C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	35	17	0.485714	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Silent	SNP	ENST00000377574.1	37	CCDS8075.1																																																																																			C|0.976;T|0.024	0.024	strong		0.687	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585	
AASDH	132949	hgsc.bcm.edu	37	4	57211352	57211352	+	Missense_Mutation	SNP	T	T	C	rs12498340	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57211352T>C	ENST00000205214.6	-	12	2773	c.2593A>G	c.(2593-2595)Acc>Gcc	p.T865A	AASDH_ENST00000434343.2_Missense_Mutation_p.T380A|AASDH_ENST00000602986.1_Intron|AASDH_ENST00000451613.1_Intron|AASDH_ENST00000513376.1_Missense_Mutation_p.T765A	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	865			T -> A (in dbSNP:rs12498340).		fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				AGTCCTGTGGTTGGATCCATG	0.393													T|||	1101	0.219848	0.1974	0.3775	5008	,	,		18367	0.2173		0.1302	False		,,,				2504	0.2331				p.T865A		Atlas-SNP	.											.	AASDH	101	.	0			c.A2593G						PASS	.	T	ALA/THR	842,3564	332.5+/-302.5	80,682,1441	201.0	186.0	191.0		2593	3.4	1.0	4	dbSNP_120	191	1096,7504	228.3+/-263.4	70,956,3274	yes	missense	AASDH	NM_181806.2	58	150,1638,4715	CC,CT,TT		12.7442,19.1103,14.9008	benign	865/1099	57211352	1938,11068	2203	4300	6503	SO:0001583	missense	132949	exon12			CTGTGGTTGGATC	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.2593A>G	4.37:g.57211352T>C	ENSP00000205214:p.Thr865Ala	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Missense_Mutation	SNP	ENST00000205214.6	37	CCDS3504.1	424	0.19413919413919414	89	0.18089430894308944	117	0.32320441988950277	119	0.20804195804195805	99	0.13060686015831136	T	13.89	2.371977	0.42003	0.191103	0.127442	ENSG00000157426	ENST00000205214;ENST00000513376;ENST00000434343	T;T;T	0.60299	1.01;0.2;1.01	6.03	3.43	0.39272	Quinonprotein alcohol dehydrogenase-like (2);	0.846265	0.11368	N	0.571223	T	0.00012	0.0000	N	0.17631	0.505	0.20975	P	0.999810126	B	0.28178	0.202	B	0.33846	0.171	T	0.30001	-0.9993	9	0.40728	T	0.16	-1.2383	5.8582	0.18732	0.4903:0.0:0.1117:0.398	rs12498340;rs52797375;rs57654214;rs12498340	865	Q4L235	ACSF4_HUMAN	A	865;765;380	ENSP00000205214:T865A;ENSP00000423760:T765A;ENSP00000392158:T380A	ENSP00000205214:T865A	T	-	1	0	AASDH	56906109	0.029000	0.19370	0.987000	0.45799	0.967000	0.64934	0.122000	0.15687	1.052000	0.40392	0.533000	0.62120	ACC	T|0.830;C|0.170	0.170	strong		0.393	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
CD83	9308	hgsc.bcm.edu	37	6	14131854	14131854	+	Missense_Mutation	SNP	A	A	G	rs35118414	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:14131854A>G	ENST00000379153.3	+	3	428	c.257A>G	c.(256-258)aAt>aGt	p.N86S		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	86	Ig-like V-type.				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)				GACGCCCCCAATGAAAGGCCC	0.547													A|||	194	0.038738	0.0643	0.0375	5008	,	,		20463	0.0198		0.0288	False		,,,				2504	0.0348				p.N86S		Atlas-SNP	.											.	CD83	23	.	0			c.A257G						PASS	.	A	SER/ASN,SER/ASN	258,4148	149.2+/-183.4	6,246,1951	130.0	121.0	124.0		257,257	-1.2	0.0	6	dbSNP_126	124	333,8267	116.1+/-175.8	5,323,3972	yes	missense,missense	CD83	NM_001040280.1,NM_004233.3	46,46	11,569,5923	GG,GA,AA		3.8721,5.8557,4.5441	benign,benign	86/205,86/206	14131854	591,12415	2203	4300	6503	SO:0001583	missense	9308	exon3			CCCCCAATGAAAG	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.257A>G	6.37:g.14131854A>G	ENSP00000368450:p.Asn86Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	113	20	0.176991	NM_004233	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	37	CCDS4532.1	88	0.040293040293040296	33	0.06707317073170732	15	0.04143646408839779	16	0.027972027972027972	24	0.0316622691292876	A	1.969	-0.437052	0.04636	0.058557	0.038721	ENSG00000112149	ENST00000379153	T	0.60920	0.15	5.39	-1.24	0.09435	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.293720	0.01187	N	0.007226	T	0.05090	0.0136	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.13308	-1.0514	10	0.08179	T	0.78	-14.691	2.083	0.03639	0.3074:0.122:0.4459:0.1246	rs35118414;rs61761633	86	Q01151	CD83_HUMAN	S	86	ENSP00000368450:N86S	ENSP00000368450:N86S	N	+	2	0	CD83	14239833	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.293000	0.08320	-0.146000	0.11274	-0.146000	0.13790	AAT	A|0.956;G|0.044	0.044	strong		0.547	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29910663	29910663	+	Missense_Mutation	SNP	G	G	A	rs707910	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29910663G>A	ENST00000396634.1	+	4	544	c.203G>A	c.(202-204)aGg>aAg	p.R68K	HLA-A_ENST00000376806.5_Missense_Mutation_p.R68K|HLA-A_ENST00000376802.2_Missense_Mutation_p.R68K|HLA-A_ENST00000376809.5_Missense_Mutation_p.R68K			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	68	Alpha-1.				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 peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCGAGCCAGAGGATGGAGCCG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	454	0.090655	0.0847	0.0476	5008	,	,		14754	0.0188		0.1262	False		,,,				2504	0.1667				p.R68K		Atlas-SNP	.											.	HLA-A	89	.	0			c.G203A						PASS	.	G	LYS/ARG	347,4057		17,313,1872	48.0	46.0	47.0		203	2.8	0.4	6	dbSNP_86	47	1395,7203		130,1135,3034	no	missense	HLA-A	NM_002116.7	26	147,1448,4906	AA,AG,GG		16.2247,7.8792,13.3979	benign	68/366	29910663	1742,11260	2202	4299	6501	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCCAGAGGATGGA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.203G>A	6.37:g.29910663G>A	ENSP00000379873:p.Arg68Lys	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	140	119	0.85	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	168	0.07692307692307693	39	0.07926829268292683	17	0.04696132596685083	10	0.017482517482517484	102	0.1345646437994723	.	13.11	2.139534	0.37728	0.078792	0.162247	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00816	5.66;5.66;5.66;5.66	3.72	2.85	0.33270	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.236115	0.21148	U	0.079368	T	0.02047	0.0064	M	0.80508	2.5	0.58432	P	5.000000000032756E-6	P;B;B;B;B	0.51147	0.942;0.0;0.0;0.0;0.0	D;B;B;B;B	0.74348	0.983;0.001;0.002;0.001;0.004	T	0.23547	-1.0185	9	0.87932	D	0	.	7.302	0.26426	0.1248:0.0:0.8752:0.0	rs707910;rs2230979;rs3200124;rs9260131;rs16896268;rs41541315	68;68;68;68;68	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	K	68	ENSP00000379873:R68K;ENSP00000366002:R68K;ENSP00000366005:R68K;ENSP00000365998:R68K	ENSP00000348012:R68K	R	+	2	0	HLA-A	30018642	0.002000	0.14202	0.442000	0.26870	0.608000	0.37181	0.867000	0.27968	0.936000	0.37367	0.478000	0.44815	AGG	A|0.112;G|0.888	0.112	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CCDC170	80129	hgsc.bcm.edu	37	6	151894340	151894340	+	Missense_Mutation	SNP	C	C	T	rs12205837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:151894340C>T	ENST00000239374.7	+	6	905	c.806C>T	c.(805-807)gCt>gTt	p.A269V	CCDC170_ENST00000367290.5_Missense_Mutation_p.A269V	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	269			A -> V (in dbSNP:rs12205837).														GCAAAAGAAGCTCTTGAAAGG	0.458													C|||	384	0.0766773	0.0787	0.0865	5008	,	,		19899	0.0704		0.0795	False		,,,				2504	0.0706				p.A269V		Atlas-SNP	.											.	.	.	.	0			c.C806T						PASS	.	C	VAL/ALA	272,3478		9,254,1612	57.0	56.0	56.0		806	2.3	0.8	6	dbSNP_120	56	888,7352		40,808,3272	yes	missense	C6orf97	NM_025059.3	64	49,1062,4884	TT,TC,CC		10.7767,7.2533,9.6747	benign	269/716	151894340	1160,10830	1875	4120	5995	SO:0001583	missense	80129	exon6			AAGAAGCTCTTGA	AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.806C>T	6.37:g.151894340C>T	ENSP00000239374:p.Ala269Val	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	182	0.08333333333333333	60	0.12195121951219512	32	0.08839779005524862	30	0.05244755244755245	60	0.079155672823219	C	13.23	2.174854	0.38413	0.072533	0.107767	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.08634	3.1;3.07	5.35	2.34	0.29019	.	0.441618	0.24532	N	0.037710	T	0.02571	0.0078	L	0.41027	1.25	0.40540	P	0.018985999999999947	B	0.15930	0.015	B	0.16289	0.015	T	0.33240	-0.9876	9	0.33940	T	0.23	-9.5343	9.0511	0.36376	0.1324:0.419:0.4486:0.0	rs12205837;rs52799427;rs12205837	269	Q8IYT3	CF097_HUMAN	V	269	ENSP00000239374:A269V;ENSP00000356259:A269V	ENSP00000239374:A269V	A	+	2	0	C6orf97	151936033	0.730000	0.28100	0.825000	0.32803	0.813000	0.45954	0.908000	0.28545	1.317000	0.45149	0.643000	0.83706	GCT	C|0.911;T|0.089	0.089	strong		0.458	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
HSPG2	3339	hgsc.bcm.edu	37	1	22158157	22158157	+	Silent	SNP	A	A	G	rs2229488	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22158157A>G	ENST00000374695.3	-	82	11419	c.11340T>C	c.(11338-11340)aaT>aaC	p.N3780N	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3780	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGGAGGTCCCATTGACCGGGG	0.647													g|||	417	0.0832668	0.1687	0.0519	5008	,	,		18250	0.0		0.0666	False		,,,				2504	0.093				p.N3780N		Atlas-SNP	.											.	HSPG2	311	.	0			c.T11340C						PASS	.			760,3646	733.1+/-410.4	67,626,1510	43.0	53.0	50.0		11340	-5.6	0.5	1	dbSNP_98	50	664,7932	771.5+/-407.7	28,608,3662	no	coding-synonymous	HSPG2	NM_005529.5		95,1234,5172	GG,GA,AA		7.7245,17.2492,10.9522		3780/4392	22158157	1424,11578	2203	4298	6501	SO:0001819	synonymous_variant	3339	exon82			GGTCCCATTGACC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.11340T>C	1.37:g.22158157A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	174	78	0.448276	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			A|0.904;G|0.096	0.096	strong		0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
PCDHGB2	56103	hgsc.bcm.edu	37	5	140739874	140739874	+	Missense_Mutation	SNP	G	G	A	rs13171859	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140739874G>A	ENST00000522605.1	+	1	172	c.172G>A	c.(172-174)Gtc>Atc	p.V58I	PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	58	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> I (in dbSNP:rs13171859).		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(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGCTCAGCGTCCGGGACTT	0.557													.|||	222	0.0443291	0.0068	0.0821	5008	,	,		16135	0.0		0.1322	False		,,,				2504	0.0235				p.V58I		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.G172A						PASS	.	G	,,,,,ILE/VAL,ILE/VAL	88,3596		0,88,1754	52.0	55.0	54.0		,,,,,172,172	2.3	0.0	5	dbSNP_121	54	1063,7109		57,949,3080	yes	intron,intron,intron,intron,intron,missense,missense	PCDHGB2,PCDHGB1,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018922.2,NM_018923.2,NM_032096.1	,,,,,29,29	57,1037,4834	AA,AG,GG		13.0078,2.3887,9.7082	,,,,,,	,,,,,58/932,58/812	140739874	1151,10705	1842	4086	5928	SO:0001583	missense	56103	exon1			CTCAGCGTCCGGG	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"""Cadherins / Protocadherins : Clustered"""	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.172G>A	5.37:g.140739874G>A	ENSP00000429018:p.Val58Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	124	0.056776556776556776	4	0.008130081300813009	29	0.08011049723756906	0	0.0	91	0.12005277044854881	.	3.743	-0.053164	0.07362	0.023887	0.130078	ENSG00000253910	ENST00000522605	T	0.29142	1.58	5.11	2.26	0.28386	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.00210	0.0006	L	0.36672	1.1	0.80722	P	0.0	B;P	0.35959	0.173;0.53	B;B	0.34180	0.032;0.177	T	0.11966	-1.0566	8	0.33141	T	0.24	.	5.7356	0.18065	0.23:0.1438:0.6262:0.0	rs13171859;rs13171859	58;58	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	I	58	ENSP00000429018:V58I	ENSP00000429018:V58I	V	+	1	0	PCDHGB2	140720058	0.000000	0.05858	0.001000	0.08648	0.026000	0.11368	-0.183000	0.09712	0.625000	0.30304	0.563000	0.77884	GTC	G|0.930;A|0.070	0.070	strong		0.557	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923	
OSBPL7	114881	hgsc.bcm.edu	37	17	45885756	45885756	+	Silent	SNP	C	C	T	rs9911983	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:45885756C>T	ENST00000007414.3	-	23	2621	c.2430G>A	c.(2428-2430)acG>acA	p.T810T	OSBPL7_ENST00000392507.3_Silent_p.T810T	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	810					cellular response to cholesterol (GO:0071397)|lipid transport (GO:0006869)|positive regulation of proteasomal protein catabolic process (GO:1901800)	autophagic vacuole (GO:0005776)|cytosol (GO:0005829)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			autonomic_ganglia(1)|endometrium(6)|kidney(2)|large_intestine(5)|liver(2)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32						CGCTGCTATCCGTCTGCCGCC	0.627													T|||	2374	0.474042	0.7005	0.4352	5008	,	,		19535	0.1528		0.5298	False		,,,				2504	0.4693				p.T810T		Atlas-SNP	.											OSBPL7,colon,carcinoma,-1,1	OSBPL7	65	1	0			c.G2430A						PASS	.	T		3093,1313	444.5+/-347.4	1094,905,204	61.0	56.0	58.0		2430	-8.4	0.8	17	dbSNP_119	58	4785,3815	538.2+/-383.4	1362,2061,877	no	coding-synonymous	OSBPL7	NM_145798.2		2456,2966,1081	TT,TC,CC		44.3605,29.8003,39.428		810/843	45885756	7878,5128	2203	4300	6503	SO:0001819	synonymous_variant	114881	exon23			GCTATCCGTCTGC	AF392446	CCDS11515.1	17q21	2013-01-10				ENSG00000006025		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16387	protein-coding gene	gene with protein product		606735				14593528, 11735225	Standard	NM_145798		Approved	ORP7, MGC71150	uc002ilx.1	Q9BZF2		ENST00000007414.3:c.2430G>A	17.37:g.45885756C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	51	0.451327	NM_145798	D3DTT6|Q6PIV6	Silent	SNP	ENST00000007414.3	37	CCDS11515.1																																																																																			C|0.449;T|0.551	0.551	strong		0.627	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731	
CCDC50	152137	hgsc.bcm.edu	37	3	191093053	191093053	+	Intron	SNP	T	T	C	rs2028572	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:191093053T>C	ENST00000392455.3	+	6	1046				CCDC50_ENST00000392456.3_Silent_p.H217H	NM_174908.3	NP_777568.1	Q8IVM0	CCD50_HUMAN	coiled-coil domain containing 50							cytoplasm (GO:0005737)	ubiquitin protein ligase binding (GO:0031625)			endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|stomach(1)	23	all_cancers(143;8.88e-09)|Ovarian(172;0.103)|Breast(254;0.221)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000136)		ACAATCCCCATATTAACAATG	0.502													T|||	2514	0.501997	0.7239	0.4697	5008	,	,		21524	0.4702		0.4105	False		,,,				2504	0.3517				p.H217H		Atlas-SNP	.											.	CCDC50	39	.	0			c.T651C						PASS	.	T	,	2955,1451	680.4+/-403.8	985,985,233	83.0	75.0	78.0		,651	-7.5	0.0	3	dbSNP_94	78	3404,5196	501.4+/-375.5	674,2056,1570	no	intron,coding-synonymous	CCDC50	NM_174908.3,NM_178335.2	,	1659,3041,1803	CC,CT,TT		39.5814,32.9324,48.8928	,	,217/483	191093053	6359,6647	2203	4300	6503	SO:0001627	intron_variant	152137	exon6			TCCCCATATTAAC	AJ416916	CCDS33912.1, CCDS33913.1	3q28	2010-12-24		2005-12-23	ENSG00000152492	ENSG00000152492			18111	protein-coding gene	gene with protein product		611051	"""deafness, autosomal dominant 44"""	C3orf6, DFNA44		16803894, 17503326	Standard	NM_178335		Approved	Ymer	uc003fsv.3	Q8IVM0	OTTHUMG00000156177	ENST00000392455.3:c.449-4895T>C	3.37:g.191093053T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	163	85	0.521472	NM_178335	Q86VH7	Silent	SNP	ENST00000392455.3	37	CCDS33913.1																																																																																			T|0.501;C|0.499	0.499	strong		0.502	CCDC50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343315.1	NM_174908	
PIEZO1	9780	hgsc.bcm.edu	37	16	88779739	88779739	+	IGR	SNP	A	A	G	rs11549837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88779739A>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Missense_Mutation_p.M253V|CTU2_ENST00000567949.1_Missense_Mutation_p.M324V|CTU2_ENST00000378384.3_Missense_Mutation_p.M166V|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000312060.5_Missense_Mutation_p.M253V	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						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						GATCCTCCACATGGCCCGAGC	0.652													A|||	2267	0.452676	0.4372	0.4308	5008	,	,		12324	0.6637		0.3439	False		,,,				2504	0.3834				p.M253V		Atlas-SNP	.											.	CTU2	66	.	0			c.A757G						PASS	.	A	VAL/MET,VAL/MET	1823,2551	528.6+/-372.4	375,1073,739	55.0	56.0	55.0		757,757	1.5	1.0	16	dbSNP_120	55	2924,5664	454.5+/-363.5	500,1924,1870	yes	missense,missense	CTU2	NM_001012759.1,NM_001012762.1	21,21	875,2997,2609	GG,GA,AA		34.0475,41.6781,36.6224	benign,benign	253/516,253/486	88779739	4747,8215	2187	4294	6481	SO:0001628	intergenic_variant	348180	exon8			CTCCACATGGCCC	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		16.37:g.88779739A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	988	0.4523809523809524	189	0.38414634146341464	145	0.4005524861878453	375	0.6555944055944056	279	0.36807387862796836	A	0.119	-1.128461	0.01756	0.416781	0.340475	ENSG00000174177	ENST00000378384;ENST00000312060;ENST00000453996	T;T;T	0.14766	2.48;2.48;2.48	5.04	1.54	0.23209	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.534670	0.19256	N	0.118787	T	0.00012	0.0000	N	0.00101	-2.135	0.46927	P	7.420000000000204E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.27157	-1.0082	9	0.09843	T	0.71	.	4.674	0.12703	0.2557:0.0:0.5924:0.1518	rs11549837;rs59473378	166;253;253	Q2VPK5-3;Q2VPK5-5;Q2VPK5	.;.;CTU2_HUMAN	V	166;253;253	ENSP00000367635:M166V;ENSP00000308617:M253V;ENSP00000388320:M253V	ENSP00000308617:M253V	M	+	1	0	CTU2	87307240	0.000000	0.05858	0.986000	0.45419	0.760000	0.43138	0.845000	0.27668	0.492000	0.27815	-0.177000	0.13119	ATG	A|0.607;G|0.393	0.393	strong		0.652	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
UBTF	7343	hgsc.bcm.edu	37	17	42287519	42287519	+	Silent	SNP	C	C	T	rs2071167	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:42287519C>T	ENST00000302904.4	-	15	2091	c.1599G>A	c.(1597-1599)aaG>aaA	p.K533K	UBTF_ENST00000526094.1_Silent_p.K496K|UBTF_ENST00000529383.1_Silent_p.K533K|UBTF_ENST00000343638.5_Silent_p.K496K|UBTF_ENST00000527034.1_Silent_p.K496K|UBTF_ENST00000533177.1_Silent_p.K496K|UBTF_ENST00000393606.3_Silent_p.K496K|UBTF_ENST00000436088.1_Silent_p.K533K|CTB-175E5.7_ENST00000586560.1_RNA			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	533					chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|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)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CTTCGGCTGCCTTCTTAATCC	0.512											OREG0024456	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2261	0.451478	0.6157	0.3646	5008	,	,		21021	0.6915		0.2416	False		,,,				2504	0.2597				p.K533K		Atlas-SNP	.											.	UBTF	65	.	0			c.G1599A						PASS	.	C	,,	2335,2071	605.8+/-390.6	617,1101,485	187.0	195.0	192.0		1488,1488,1599	3.3	1.0	17	dbSNP_96	192	2174,6426	372.0+/-336.5	280,1614,2406	no	coding-synonymous,coding-synonymous,coding-synonymous	UBTF	NM_001076683.1,NM_001076684.2,NM_014233.3	,,	897,2715,2891	TT,TC,CC		25.2791,47.0041,34.6686	,,	496/728,496/728,533/765	42287519	4509,8497	2203	4300	6503	SO:0001819	synonymous_variant	7343	exon15			GGCTGCCTTCTTA	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.1599G>A	17.37:g.42287519C>T		Somatic	204	0	0	907	WXS	Illumina HiSeq	Phase_I	249	111	0.445783	NM_014233	A8K6R8	Silent	SNP	ENST00000302904.4	37	CCDS11480.1																																																																																			C|0.599;T|0.401	0.401	strong		0.512	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
NID2	22795	hgsc.bcm.edu	37	14	52509501	52509501	+	Splice_Site	SNP	T	T	C	rs3818186	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:52509501T>C	ENST00000216286.5	-	6	1577	c.1578A>G	c.(1576-1578)gaA>gaG	p.E526E	NID2_ENST00000541773.1_Splice_Site_p.E473E	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	526					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GTCAATTACCTTCAGGCAGAC	0.517													t|||	1936	0.386581	0.3933	0.4222	5008	,	,		19771	0.5466		0.2505	False		,,,				2504	0.3272				p.E526E		Atlas-SNP	.											.	NID2	201	.	0			c.A1578G						PASS	.	T		1573,2833	489.6+/-361.5	277,1019,907	117.0	104.0	109.0		1578	5.8	1.0	14	dbSNP_107	109	2127,6473	363.9+/-333.3	250,1627,2423	yes	coding-synonymous-near-splice	NID2	NM_007361.3		527,2646,3330	CC,CT,TT		24.7326,35.7013,28.4484		526/1376	52509501	3700,9306	2203	4300	6503	SO:0001630	splice_region_variant	22795	exon6			ATTACCTTCAGGC	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1579+1A>G	14.37:g.52509501T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	51	0.548387	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1																																																																																			T|0.667;C|0.333	0.333	strong		0.517	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		Silent
NRG3	10718	hgsc.bcm.edu	37	10	84744926	84744926	+	Missense_Mutation	SNP	C	C	A	rs17101193	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:84744926C>A	ENST00000404547.1	+	10	1728	c.1728C>A	c.(1726-1728)aaC>aaA	p.N576K	NRG3_ENST00000545131.1_Missense_Mutation_p.N202K|NRG3_ENST00000556918.1_Missense_Mutation_p.N382K|NRG3_ENST00000537893.1_Missense_Mutation_p.N202K|NRG3_ENST00000372141.2_Missense_Mutation_p.N552K|NRG3_ENST00000404576.2_Missense_Mutation_p.N356K|NRG3_ENST00000372142.2_Missense_Mutation_p.N355K			P56975	NRG3_HUMAN	neuregulin 3	576					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		GAGAGACAAACCCCTATTTTA	0.423													C|||	477	0.0952476	0.1732	0.1571	5008	,	,		18705	0.0109		0.0567	False		,,,				2504	0.0726				p.N552K		Atlas-SNP	.											.	NRG3	301	.	0			c.C1656A						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN	682,3724	279.3+/-274.7	56,570,1577	145.0	163.0	157.0		1656,1653,1065	2.7	1.0	10	dbSNP_123	157	499,8101	142.0+/-198.3	15,469,3816	yes	missense,missense,missense	NRG3	NM_001010848.3,NM_001165972.1,NM_001165973.1	94,94,94	71,1039,5393	AA,AC,CC		5.8023,15.4789,9.0804	benign,benign,benign	552/697,551/696,355/500	84744926	1181,11825	2203	4300	6503	SO:0001583	missense	10718	exon9			GACAAACCCCTAT	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.1728C>A	10.37:g.84744926C>A	ENSP00000384796:p.Asn576Lys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_001010848	A4D7U1|Q0PEH2|Q5VYH3	Missense_Mutation	SNP	ENST00000404547.1	37	CCDS31233.1	189	0.08653846153846154	92	0.18699186991869918	51	0.1408839779005525	9	0.015734265734265736	37	0.048812664907651716	C	7.793	0.712044	0.15306	0.154789	0.058023	ENSG00000185737	ENST00000372141;ENST00000404547;ENST00000537287;ENST00000372142;ENST00000404576;ENST00000556918;ENST00000545131;ENST00000537893	T;T;T;T;T;T;T	0.53857	1.6;1.57;1.57;0.6;0.6;0.6;0.6	5.95	2.74	0.32292	.	0.280347	0.33875	N	0.004474	T	0.00039	0.0001	N	0.14661	0.345	0.39742	P	0.028237999999999985	B;B;B;B	0.06786	0.0;0.0;0.001;0.001	B;B;B;B	0.09377	0.002;0.001;0.004;0.003	T	0.06180	-1.0841	9	0.39692	T	0.17	-37.4496	4.4692	0.11704	0.2732:0.533:0.0:0.1938	rs17101193;rs52798772;rs17101193	551;576;355;552	B9EGV5;P56975;P56975-3;P56975-4	.;NRG3_HUMAN;.;.	K	552;576;551;355;356;382;202;202	ENSP00000361214:N552K;ENSP00000384796:N576K;ENSP00000361215:N355K;ENSP00000385804:N356K;ENSP00000451376:N382K;ENSP00000441201:N202K;ENSP00000440377:N202K	ENSP00000361214:N552K	N	+	3	2	NRG3	84734906	0.867000	0.29959	1.000000	0.80357	0.983000	0.72400	-0.264000	0.08658	0.788000	0.33755	0.650000	0.86243	AAC	C|0.910;A|0.090	0.090	strong		0.423	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
ATF7	11016	hgsc.bcm.edu	37	12	53946410	53946410	+	Silent	SNP	G	G	A	rs33921258	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53946410G>A	ENST00000548446.2	-	3	172	c.60C>T	c.(58-60)aaC>aaT	p.N20N	ATF7_ENST00000456903.4_Silent_p.N20N|ATF7_ENST00000328463.7_Silent_p.N20N|ATF7_ENST00000420353.2_Silent_p.N20N|RP11-793H13.10_ENST00000591834.1_Silent_p.N20N|ATF7_ENST00000415113.1_Silent_p.N20N|ATF7_ENST00000591397.1_Silent_p.N20N|ATF7_ENST00000548118.2_Silent_p.N20N			P17544	ATF7_HUMAN	activating transcription factor 7	20	Transactivation domain.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9					Pseudoephedrine(DB00852)	GGTGGTCCTCGTTTGTAAATC	0.418													G|||	213	0.0425319	0.0023	0.0634	5008	,	,		19842	0.0228		0.1153	False		,,,				2504	0.0276				p.N20N		Atlas-SNP	.											.	ATF7	51	.	0			c.C60T						PASS	.	G	,,,,	78,3680		0,78,1801	109.0	103.0	105.0		60,60,60,60,60	0.4	1.0	12	dbSNP_126	105	878,7348		53,772,3288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATF7	NM_001130059.1,NM_001130060.1,NM_001206682.1,NM_001206683.1,NM_006856.2	,,,,	53,850,5089	AA,AG,GG		10.6735,2.0756,7.9773	,,,,	20/495,20/463,20/118,20/118,20/484	53946410	956,11028	1879	4113	5992	SO:0001819	synonymous_variant	11016	exon3			GTCCTCGTTTGTA	X52943	CCDS44906.1, CCDS58238.1	12q13	2013-01-10				ENSG00000170653		"""basic leucine zipper proteins"""	792	protein-coding gene	gene with protein product		606371				1694576, 11278933	Standard	NM_006856		Approved	ATFA	uc001sdz.3	P17544	OTTHUMG00000169776	ENST00000548446.2:c.60C>T	12.37:g.53946410G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	116	65	0.560345	NM_001130060	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Silent	SNP	ENST00000548446.2	37																																																																																				G|0.934;A|0.066	0.066	strong		0.418	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059	
PDIA2	64714	hgsc.bcm.edu	37	16	334899	334899	+	Missense_Mutation	SNP	G	G	A	rs141542731	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:334899G>A	ENST00000219406.6	+	4	580	c.562G>A	c.(562-564)Gcc>Acc	p.A188T	PDIA2_ENST00000462950.1_3'UTR|PDIA2_ENST00000404312.1_Missense_Mutation_p.A185T	NM_006849.2	NP_006840.2	Q13087	PDIA2_HUMAN	protein disulfide isomerase family A, member 2	188					cell redox homeostasis (GO:0045454)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein retention in ER lumen (GO:0006621)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)	protein disulfide isomerase activity (GO:0003756)|steroid binding (GO:0005496)			breast(1)|central_nervous_system(4)|kidney(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	17		all_cancers(16;6.71e-07)|all_epithelial(16;1.59e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00769)|all_lung(18;0.0186)				CGAGGACGTGGCCACCTTCTT	0.672													g|||	8	0.00159744	0.0	0.0014	5008	,	,		16585	0.0		0.006	False		,,,				2504	0.001				p.A188T		Atlas-SNP	.											PDIA2,NS,lymphoid_neoplasm,0,1	PDIA2	51	1	0			c.G562A						PASS	.	G	THR/ALA	7,4111		0,7,2052	43.0	50.0	48.0		562	3.8	0.8	16	dbSNP_134	48	98,8272		0,98,4087	yes	missense	PDIA2	NM_006849.2	58	0,105,6139	AA,AG,GG		1.1708,0.17,0.8408	possibly-damaging	188/526	334899	105,12383	2059	4185	6244	SO:0001583	missense	64714	exon4			GACGTGGCCACCT	U19948	CCDS42089.1	16p13.3	2009-11-20	2005-06-29	2005-03-03	ENSG00000185615	ENSG00000185615	5.3.4.1	"""Protein disulfide isomerases"""	14180	protein-coding gene	gene with protein product		608012	"""protein disulfide isomerase, pancreatic"", ""protein disulfide isomerase-associated 2"""	PDIP		8561901	Standard	NM_006849		Approved	PDA2, PDI, PDIR	uc002cgo.1	Q13087	OTTHUMG00000064891	ENST00000219406.6:c.562G>A	16.37:g.334899G>A	ENSP00000219406:p.Ala188Thr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_006849	A6ZJ64|B4DI27|Q2WGM4|Q4TT67|Q6B010|Q96KJ6|Q9BW95	Missense_Mutation	SNP	ENST00000219406.6	37	CCDS42089.1	9	0.004120879120879121	0	0.0	4	0.011049723756906077	0	0.0	5	0.006596306068601583	g	9.501	1.103229	0.20632	0.0017	0.011708	ENSG00000185615	ENST00000219406;ENST00000455994;ENST00000404312	T;T	0.28895	1.59;1.59	3.75	3.75	0.43078	Thioredoxin-like fold (2);	0.322570	0.28736	N	0.014301	T	0.22126	0.0533	L	0.55481	1.735	0.09310	N	1	B	0.23249	0.082	B	0.33568	0.166	T	0.23226	-1.0194	10	0.66056	D	0.02	.	5.2577	0.15555	0.1147:0.2124:0.6729:0.0	.	188	Q13087	PDIA2_HUMAN	T	188;157;185	ENSP00000219406:A188T;ENSP00000384410:A185T	ENSP00000219406:A188T	A	+	1	0	PDIA2	274900	0.384000	0.25164	0.792000	0.32020	0.564000	0.35744	2.460000	0.45031	1.925000	0.55765	0.457000	0.33378	GCC	G|0.994;A|0.006	0.006	strong		0.672	PDIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139315.3	NM_006849	
MYO9B	4650	hgsc.bcm.edu	37	19	17318018	17318018	+	Silent	SNP	G	G	A	rs17535005	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17318018G>A	ENST00000594824.1	+	35	5736	c.5589G>A	c.(5587-5589)ccG>ccA	p.P1863P	MYO9B_ENST00000397274.2_Silent_p.P1863P|MYO9B_ENST00000595618.1_Silent_p.P1863P|CTD-3032J10.3_ENST00000601929.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	1863	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.|Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						ACTCGGACCCGCTGACCAGCA	0.662													G|||	155	0.0309505	0.0303	0.0447	5008	,	,		13996	0.001		0.0746	False		,,,				2504	0.0082				p.P1863P		Atlas-SNP	.											.	MYO9B	264	.	0			c.G5589A						PASS	.	G	,	217,4167		3,211,1978	29.0	32.0	31.0		5589,5589	-8.3	0.9	19	dbSNP_123	31	647,7931		19,609,3661	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	22,820,5639	AA,AG,GG		7.5426,4.9498,6.6656	,	1863/2023,1863/2158	17318018	864,12098	2192	4289	6481	SO:0001819	synonymous_variant	4650	exon35			GGACCCGCTGACC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.5589G>A	19.37:g.17318018G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	176	82	0.465909	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				G|0.955;A|0.045	0.045	strong		0.662	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
CR1	1378	hgsc.bcm.edu	37	1	207753621	207753621	+	Missense_Mutation	SNP	A	A	G	rs2274567	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207753621A>G	ENST00000367049.4	+	30	4973	c.4973A>G	c.(4972-4974)cAt>cGt	p.H1658R	CR1_ENST00000367052.1_Missense_Mutation_p.H1208R|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367051.1_Missense_Mutation_p.H1208R|CR1_ENST00000367053.1_Missense_Mutation_p.H1208R|CR1_ENST00000400960.2_Missense_Mutation_p.H1208R|RP11-78B10.2_ENST00000596003.1_RNA	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1208	Sushi 26. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CATGGTGAGCATACCCCAAGC	0.522													A|||	1474	0.294329	0.2186	0.2709	5008	,	,		18110	0.3274		0.1819	False		,,,				2504	0.4949				p.H1658R		Atlas-SNP	.											.	CR1	354	.	0			c.A4973G						PASS	.	A	ARG/HIS,ARG/HIS	875,3049		94,687,1181	126.0	127.0	126.0		3623,4973	0.2	0.0	1	dbSNP_100	126	1524,6788		129,1266,2761	no	missense,missense	CR1	NM_000573.3,NM_000651.4	29,29	223,1953,3942	GG,GA,AA		18.3349,22.2987,19.6061	probably-damaging,probably-damaging	1208/2040,1658/2490	207753621	2399,9837	1962	4156	6118	SO:0001583	missense	1378	exon30			GTGAGCATACCCC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.4973A>G	1.37:g.207753621A>G	ENSP00000356016:p.His1658Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	141	140	0.992908	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	487	0.222985347985348	114	0.23170731707317074	108	0.2983425414364641	134	0.23426573426573427	131	0.17282321899736147	A	0.454	-0.892160	0.02491	0.222987	0.183349	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	4.34	0.182	0.15077	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B;B;D	0.65815	0.147;0.08;0.995	B;B;D	0.74674	0.168;0.049;0.984	T	0.09907	-1.0653	8	0.25106	T	0.35	.	1.2006	0.01884	0.5248:0.1803:0.1191:0.1757	rs2274567;rs3860293;rs17047280;rs52826014;rs60859711;rs2274567	1208;1208;1658	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	R	1208;1208;1208;1208;758;1658	ENSP00000356019:H1208R;ENSP00000356018:H1208R;ENSP00000356020:H1208R;ENSP00000383744:H1208R;ENSP00000436139:H758R;ENSP00000356016:H1658R	ENSP00000356016:H1658R	H	+	2	0	CR1	205820244	0.000000	0.05858	0.001000	0.08648	0.091000	0.18340	0.814000	0.27239	0.164000	0.19529	0.529000	0.55759	CAT	A|0.785;G|0.214	0.214	strong		0.522	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
HTT	3064	hgsc.bcm.edu	37	4	3227419	3227419	+	Silent	SNP	A	A	G	rs362273	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:3227419A>G	ENST00000355072.5	+	57	7942	c.7797A>G	c.(7795-7797)ctA>ctG	p.L2599L		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2599					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		AGCTGCTGCTACAGATCAACC	0.647													G|||	1234	0.246406	0.1218	0.304	5008	,	,		14498	0.3393		0.3191	False		,,,				2504	0.2035				p.L2599L		Atlas-SNP	.											HTT,caecum,carcinoma,0,1	HTT	221	1	0			c.A7797G						scavenged	.	G		636,3396		56,524,1436	28.0	32.0	31.0		7797	3.1	1.0	4	dbSNP_79	31	2492,5908		355,1782,2063	no	coding-synonymous	HTT	NM_002111.6		411,2306,3499	GG,GA,AA		29.6667,15.7738,25.1609		2599/3143	3227419	3128,9304	2016	4200	6216	SO:0001819	synonymous_variant	3064	exon57			GCTGCTACAGATC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.7797A>G	4.37:g.3227419A>G		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	113	40	0.353982	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			A|0.737;G|0.263	0.263	strong		0.647	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
BIRC7	79444	hgsc.bcm.edu	37	20	61869826	61869826	+	Silent	SNP	C	C	T	rs2273487	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61869826C>T	ENST00000217169.3	+	3	742	c.528C>T	c.(526-528)tcC>tcT	p.S176S	BIRC7_ENST00000395306.1_Silent_p.S89S|NKAIN4_ENST00000466885.1_5'Flank|MIR3196_ENST00000579556.1_RNA|BIRC7_ENST00000342412.6_Silent_p.S176S	NM_139317.1	NP_647478.1	Q96CA5	BIRC7_HUMAN	baculoviral IAP repeat containing 7	176					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of natural killer cell apoptotic process (GO:0070247)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(9)|ovary(1)	12	all_cancers(38;2.72e-09)					TGCTGGGCTCCTGGGTGAGCG	0.622													C|||	2228	0.444888	0.3638	0.4798	5008	,	,		17002	0.4931		0.4404	False		,,,				2504	0.4847				p.S176S		Atlas-SNP	.											.	BIRC7	25	.	0			c.C528T						PASS	.	C	,	1666,2738	501.2+/-364.9	313,1040,849	57.0	61.0	59.0		528,528	3.6	1.0	20	dbSNP_100	59	3982,4618	549.6+/-385.6	952,2078,1270	no	coding-synonymous,coding-synonymous	BIRC7	NM_022161.2,NM_139317.1	,	1265,3118,2119	TT,TC,CC		46.3023,37.8292,43.4328	,	176/281,176/299	61869826	5648,7356	2202	4300	6502	SO:0001819	synonymous_variant	79444	exon3			GGGCTCCTGGGTG	AF301009	CCDS13512.1, CCDS13513.1	20q13.3	2011-01-25	2011-01-25		ENSG00000101197	ENSG00000101197		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	13702	protein-coding gene	gene with protein product	"""melanoma inhibitor of apoptosis protein"", ""kidney inhibitor of apoptosis protein"", ""livin inhibitor-of-apoptosis"", ""livin"""	605737	"""baculoviral IAP repeat-containing 7"""			11024045, 11162435	Standard	NM_139317		Approved	mliap, ML-IAP, KIAP, RNF50	uc002yej.3	Q96CA5	OTTHUMG00000032957	ENST00000217169.3:c.528C>T	20.37:g.61869826C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_139317	Q9BQV0|Q9H2A8|Q9HAP7	Silent	SNP	ENST00000217169.3	37	CCDS13513.1																																																																																			C|0.554;T|0.446	0.446	strong		0.622	BIRC7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080114.2	NM_139317	
DENND4C	55667	hgsc.bcm.edu	37	9	19346710	19346710	+	Missense_Mutation	SNP	A	A	G	rs17818730	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:19346710A>G	ENST00000380432.2	+	18	3121	c.3088A>G	c.(3088-3090)Act>Gct	p.T1030A	DENND4C_ENST00000602925.1_Missense_Mutation_p.T1266A|DENND4C_ENST00000434457.2_Missense_Mutation_p.T1315A			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1030			T -> A (in dbSNP:rs17818730).		cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GTCTGGCATGACTACTGCATT	0.413													A|||	239	0.0477236	0.0053	0.1787	5008	,	,		19791	0.003		0.0835	False		,,,				2504	0.0215				p.T1266A		Atlas-SNP	.											.	DENND4C	120	.	0			c.A3796G						PASS	.	A	ALA/THR	79,4327	69.2+/-107.0	3,73,2127	95.0	94.0	94.0		3088	-2.1	0.0	9	dbSNP_123	94	697,7903	172.0+/-222.8	32,633,3635	yes	missense	DENND4C	NM_017925.4	58	35,706,5762	GG,GA,AA		8.1047,1.793,5.9665	benign	1030/1674	19346710	776,12230	2203	4300	6503	SO:0001583	missense	55667	exon22			GGCATGACTACTG	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.3088A>G	9.37:g.19346710A>G	ENSP00000369797:p.Thr1030Ala	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		137	0.06272893772893773	6	0.012195121951219513	56	0.15469613259668508	3	0.005244755244755245	72	0.09498680738786279	A	1.138	-0.650347	0.03506	0.01793	0.081047	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024	T;T;T	0.21191	2.02;2.02;3.72	5.72	-2.13	0.07144	.	1.133050	0.06790	N	0.786893	T	0.00039	0.0001	N	0.08118	0	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	0.001;0.001;0.001;0.0	T	0.39742	-0.9599	9	0.19590	T	0.45	-0.0033	1.6169	0.02705	0.3438:0.2745:0.0779:0.3038	rs17818730;rs52803664;rs17818730	360;1030;212;1030	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	A	1030;503;212;360;503;212;27	ENSP00000305795:T503A;ENSP00000443804:T360A;ENSP00000369797:T503A	ENSP00000305795:T503A	T	+	1	0	DENND4C	19336710	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.082000	0.03400	-0.181000	0.10619	0.528000	0.53228	ACT	A|0.940;G|0.060	0.060	strong		0.413	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
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 GAIIx	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	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	68	5	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 GAIIx	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	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	160	18	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	
GCSAM	257144	hgsc.bcm.edu	37	3	111842539	111842539	+	Silent	SNP	C	C	T	rs34879456	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111842539C>T	ENST00000308910.4	-	6	484	c.300G>A	c.(298-300)ggG>ggA	p.G100G	C3orf52_ENST00000467942.2_Intron|GCSAM_ENST00000484193.1_Silent_p.G102G	NM_001190259.1|NM_001190260.1|NM_152785.4	NP_001177188.1|NP_001177189.1|NP_689998.1	Q8N6F7	GCSAM_HUMAN	germinal center-associated, signaling and motility	100					negative regulation of lymphocyte migration (GO:2000402)|regulation of B cell receptor signaling pathway (GO:0050855)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|myosin II binding (GO:0045159)|protein kinase binding (GO:0019901)										CAGCAGAGTTCCCTGATGGCC	0.478													C|||	118	0.0235623	0.0023	0.0159	5008	,	,		22452	0.001		0.0358	False		,,,				2504	0.0685				p.G102G		Atlas-SNP	.											.	.	.	.	0			c.G306A						PASS	.	C	,,	27,4379	33.5+/-64.1	0,27,2176	131.0	115.0	120.0		306,255,300	-1.0	0.0	3	dbSNP_126	120	259,8341	100.8+/-162.1	3,253,4044	no	coding-synonymous,coding-synonymous,coding-synonymous	GCET2	NM_001190259.1,NM_001190260.1,NM_152785.4	,,	3,280,6220	TT,TC,CC		3.0116,0.6128,2.199	,,	102/181,85/164,100/179	111842539	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	257144	exon6			AGAGTTCCCTGAT	BC030506	CCDS2964.1, CCDS54621.1, CCDS54622.1	3q13.13	2012-09-03	2012-08-23	2012-08-23	ENSG00000174500	ENSG00000174500			20253	protein-coding gene	gene with protein product	"""human germinal center-associated lymphoma"""	607792	"""germinal center expressed transcript 2"""	GCET2			Standard	NM_152785		Approved	MGC40441, HGAL	uc021xcl.1	Q8N6F7	OTTHUMG00000159231	ENST00000308910.4:c.300G>A	3.37:g.111842539C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	169	78	0.461538	NM_001190259	C9JD17|C9JUG6	Silent	SNP	ENST00000308910.4	37	CCDS2964.1																																																																																			C|0.979;T|0.021	0.021	strong		0.478	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785	
NACC2	138151	hgsc.bcm.edu	37	9	138905136	138905136	+	Silent	SNP	C	C	T	rs2280486	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:138905136C>T	ENST00000371753.1	-	4	1222	c.1164G>A	c.(1162-1164)acG>acA	p.T388T	NACC2_ENST00000277554.2_Silent_p.T388T|NACC2_ENST00000467669.1_5'Flank			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	388	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.				cellular protein complex localization (GO:0034629)|histone deacetylation (GO:0016575)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter (GO:1900477)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|posttranscriptional regulation of gene expression (GO:0010608)|protein homooligomerization (GO:0051260)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)			endometrium(2)|kidney(1)|lung(1)|urinary_tract(1)	5						TGTTGGCCAGCGTGTTCCTGG	0.672													C|||	2325	0.464257	0.5469	0.4741	5008	,	,		11939	0.4494		0.4284	False		,,,				2504	0.3978				p.T388T		Atlas-SNP	.											.	NACC2	16	.	0			c.G1164A						PASS	.	C		2254,2150	576.4+/-384.2	586,1082,534	43.0	47.0	46.0		1164	-9.9	0.6	9	dbSNP_100	46	3615,4977	512.0+/-377.8	765,2085,1446	no	coding-synonymous	NACC2	NM_144653.4		1351,3167,1980	TT,TC,CC		42.074,48.8193,45.16		388/588	138905136	5869,7127	2202	4296	6498	SO:0001819	synonymous_variant	138151	exon5			GGCCAGCGTGTTC	BC015649	CCDS6993.1	9q34.3	2013-01-09	2008-10-03	2008-10-03	ENSG00000148411	ENSG00000148411		"""BEN domain containing"", ""BTB/POZ domain containing"""	23846	protein-coding gene	gene with protein product	"""BEN domain containing 9"""	615786	"""BTB (POZ) domain containing 14A"""	BTBD14A		12477932	Standard	NM_144653		Approved	MGC23427, BEND9, BTBD31	uc004cgv.4	Q96BF6	OTTHUMG00000020921	ENST00000371753.1:c.1164G>A	9.37:g.138905136C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_144653		Silent	SNP	ENST00000371753.1	37	CCDS6993.1																																																																																			C|0.543;T|0.457	0.457	strong		0.672	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653	
CTAGE1	64693	hgsc.bcm.edu	37	18	19996011	19996011	+	5'Flank	SNP	G	G	A	rs7227477	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:19996011G>A	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Silent_p.L588L			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					TTTGTGGAGGGAGAGCTGAAT	0.473													A|||	2475	0.494209	0.4667	0.5576	5008	,	,		18710	0.5655		0.5159	False		,,,				2504	0.3906				p.L588L		Atlas-SNP	.											.	CTAGE1	146	.	0			c.C1764T						PASS	.	A		1971,2407		478,1015,696	58.0	61.0	60.0		1764	-0.0	0.0	18	dbSNP_116	60	3953,4629		961,2031,1299	no	coding-synonymous	CTAGE1	NM_172241.2		1439,3046,1995	AA,AG,GG		46.0615,45.0206,45.7099		588/746	19996011	5924,7036	2189	4291	6480	SO:0001631	upstream_gene_variant	64693	exon1			TGGAGGGAGAGCT	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 1"", ""cutaneous T-cell lymphoma-associated antigen 2"", ""cancer/testis antigen family 21, member 1"", ""cancer/testis antigen family 21, member 2"""	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19996011G>A	Exception_encountered	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	140	67	0.478571	NM_172241	B0YIZ3	Silent	SNP	ENST00000525417.1	37																																																																																				G|0.539;A|0.461	0.461	strong		0.473	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241	
DDX11	1663	hgsc.bcm.edu	37	12	31237922	31237922	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:31237922G>C	ENST00000407793.2	+	5	751	c.500G>C	c.(499-501)aGa>aCa	p.R167T	DDX11_ENST00000251758.5_Missense_Mutation_p.R167T|DDX11_ENST00000545668.1_Missense_Mutation_p.R167T|DDX11_ENST00000350437.4_Missense_Mutation_p.R167T|DDX11_ENST00000542838.1_Missense_Mutation_p.R167T|DDX11_ENST00000228264.6_Missense_Mutation_p.R141T	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	167	Glu-rich.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.R167T(11)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					GAAGAAGAAAGAGAGAATCTC	0.612										Multiple Myeloma(12;0.14)																											p.R167T		Atlas-SNP	.											DDX11_ENST00000407793,right_upper_lobe,carcinoma,0,16	DDX11	188	16	11	Substitution - Missense(11)	lung(6)|kidney(2)|large_intestine(1)|prostate(1)|central_nervous_system(1)	c.G500C						scavenged	.						18.0	20.0	19.0					12																	31237922		2203	4299	6502	SO:0001583	missense	1663	exon5			AAGAAAGAGAGAA	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.500G>C	12.37:g.31237922G>C	ENSP00000384703:p.Arg167Thr	Somatic	168	5	0.0297619		WXS	Illumina HiSeq	Phase_I	190	11	0.0578947	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.810541	0.00600	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000251758;ENST00000228264;ENST00000438391;ENST00000415475;ENST00000545668;ENST00000350437	T;T;T;T;T;T;T;T	0.59224	4.17;4.17;4.17;4.17;0.28;4.17;4.17;4.17	3.87	0.233	0.15386	Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.241085	0.41938	N	0.000785	T	0.18635	0.0447	N	0.00841	-1.15	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.25779	-1.0122	10	0.12430	T	0.62	.	5.1988	0.15252	0.0:0.4995:0.1963:0.3042	.	167;167;167;167	B4DZY1;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	T	167;167;167;141;138;141;167;167	ENSP00000443426:R167T;ENSP00000384703:R167T;ENSP00000251758:R167T;ENSP00000228264:R141T;ENSP00000407646:R138T;ENSP00000406457:R141T;ENSP00000440402:R167T;ENSP00000309965:R167T	ENSP00000228264:R141T	R	+	2	0	DDX11	31129189	0.211000	0.23529	0.000000	0.03702	0.000000	0.00434	0.680000	0.25306	-0.264000	0.09365	-1.993000	0.00448	AGA	.	.	none		0.612	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
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 GAIIx	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_ENST00000412216.1_Intron|ZNF577_ENST00000451628.2_Silent_p.T404T|ZNF577_ENST00000420592.1_Silent_p.T404T|ZNF577_ENST00000485702.1_Intron	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		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	18	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	
NSF	4905	hgsc.bcm.edu	37	17	44828931	44828931	+	Silent	SNP	G	G	A	rs199533	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44828931G>A	ENST00000398238.4	+	19	2213	c.2106G>A	c.(2104-2106)aaG>aaA	p.K702K	NSF_ENST00000575068.1_Silent_p.K697K|NSF_ENST00000225282.8_Silent_p.K608K	NM_006178.3	NP_006169.2	P46459	NSF_HUMAN	N-ethylmaleimide-sensitive factor	702					exocytosis (GO:0006887)|plasma membrane fusion (GO:0045026)|positive regulation of receptor recycling (GO:0001921)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|syntaxin-1 binding (GO:0017075)			kidney(2)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	14		Melanoma(429;0.203)	BRCA - Breast invasive adenocarcinoma(9;0.0257)	BRCA - Breast invasive adenocarcinoma(366;0.241)		AAGGGAAGAAGGTCTGGATAG	0.408													G|||	396	0.0790735	0.0106	0.1513	5008	,	,		17691	0.001		0.2227	False		,,,				2504	0.0532				p.K702K	Ovarian(25;472 742 1472 36813 50223)	Atlas-SNP	.											.	NSF	27	.	0			c.G2106A						PASS	.	G		146,3720		4,138,1791	115.0	107.0	110.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2106	0.6	1.0	17	dbSNP_79	110	1742,6542		181,1380,2581	yes	coding-synonymous	NSF	NM_006178.3		185,1518,4372	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	21.0285,3.7765,15.5391		702/745	44828931	1888,10262	1933	4142	6075	SO:0001819	synonymous_variant	4905	exon19			GAAGAAGGTCTGG		CCDS42354.1	17q21	2010-04-21			ENSG00000073969	ENSG00000073969		"""ATPases / AAA-type"""	8016	protein-coding gene	gene with protein product	"""N-ethylmaleimide-sensitive factor-like protein"""	601633				1315316, 8875895	Standard	NM_006178		Approved	SKD2	uc002iku.3	P46459	OTTHUMG00000134315	ENST00000398238.4:c.2106G>A	17.37:g.44828931G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_006178	A8K2D9|B4DFA2|Q8N6D7|Q9UKZ2	Silent	SNP	ENST00000398238.4	37	CCDS42354.1																																																																																			G|0.874;A|0.126	0.126	strong		0.408	NSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259348.2	NM_006178	
KCNA1	3736	hgsc.bcm.edu	37	12	5021348	5021348	+	Silent	SNP	G	G	C	rs2227910	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:5021348G>C	ENST00000382545.3	+	2	1911	c.804G>C	c.(802-804)acG>acC	p.T268T	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	268					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)			NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	ATTTCATCACGCTGGGCACCG	0.527													C|||	2671	0.533347	0.4796	0.5764	5008	,	,		20613	0.6627		0.5159	False		,,,				2504	0.4601				p.T268T		Atlas-SNP	.											.	KCNA1	112	.	0			c.G804C						PASS	.	C		2052,2354	607.7+/-391.0	460,1132,611	73.0	74.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	804	-3.2	0.8	12	dbSNP_98	74	4496,4104	561.3+/-387.7	1175,2146,979	no	coding-synonymous	KCNA1	NM_000217.2		1635,3278,1590	CC,CG,GG		47.7209,46.5729,49.654		268/496	5021348	6548,6458	2203	4300	6503	SO:0001819	synonymous_variant	3736	exon2			CATCACGCTGGGC	L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.804G>C	12.37:g.5021348G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_000217	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	37	CCDS8535.1																																																																																			G|0.461;C|0.539	0.539	strong		0.527	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
BTN3A3	10384	hgsc.bcm.edu	37	6	26446209	26446209	+	Silent	SNP	C	C	T	rs3846848	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26446209C>T	ENST00000244519.2	+	5	954	c.711C>T	c.(709-711)atC>atT	p.I237I	BTN3A3_ENST00000339789.4_Silent_p.I195I|BTN3A3_ENST00000361232.3_Silent_p.I195I	NM_006994.4	NP_008925.1	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3	237					T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30						GCATATCCATCGCAGGTCAGT	0.542													C|||	725	0.144768	0.1634	0.1772	5008	,	,		21137	0.0308		0.165	False		,,,				2504	0.1933				p.I237I		Atlas-SNP	.											.	BTN3A3	56	.	0			c.C711T						PASS	.	C	,,	787,3619	318.2+/-295.5	65,657,1481	118.0	111.0	113.0		,711,585	-6.2	0.0	6	dbSNP_108	113	1450,7150	279.0+/-293.7	125,1200,2975	no	intron,coding-synonymous,coding-synonymous	BTN3A3	NM_001242803.1,NM_006994.4,NM_197974.2	,,	190,1857,4456	TT,TC,CC		16.8605,17.862,17.1998	,,	,237/585,195/536	26446209	2237,10769	2203	4300	6503	SO:0001819	synonymous_variant	10384	exon5			ATCCATCGCAGGT	U90548	CCDS4611.1, CCDS4612.1, CCDS4612.2	6p22.1	2014-01-14			ENSG00000111801	ENSG00000111801		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1140	protein-coding gene	gene with protein product		613595				10354554, 9149941	Standard	NM_006994		Approved	BTF3, BTN3.3	uc003nhz.3	O00478	OTTHUMG00000014451	ENST00000244519.2:c.711C>T	6.37:g.26446209C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	122	26	0.213115	NM_006994	B4DWI7|E9PCP5	Silent	SNP	ENST00000244519.2	37	CCDS4611.1																																																																																			C|0.838;T|0.162	0.162	strong		0.542	BTN3A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040116.2	NM_006994	
HDGF	3068	hgsc.bcm.edu	37	1	156713558	156713558	+	Missense_Mutation	SNP	G	G	A	rs4399146	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156713558G>A	ENST00000357325.5	-	5	916	c.602C>T	c.(601-603)cCc>cTc	p.P201L	HDGF_ENST00000537739.1_Missense_Mutation_p.P201L|HDGF_ENST00000368209.5_Missense_Mutation_p.P194L|HDGF_ENST00000368206.5_Missense_Mutation_p.P217L|MRPL24_ENST00000361531.2_5'Flank|MRPL24_ENST00000368211.4_5'Flank|HDGF_ENST00000416666.2_Missense_Mutation_p.P169L|HDGF_ENST00000465180.1_5'UTR	NM_004494.2	NP_004485.1	P51858	HDGF_HUMAN	hepatoma-derived growth factor	201	Glu-rich.		P -> L (in dbSNP:rs4399146). {ECO:0000269|PubMed:14702039}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription corepressor binding (GO:0001222)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)	Breast(1374;0.198)		Colorectal(1306;0.018)		GGGCTCAGAGGGGGTGCTATT	0.602													G|||	962	0.192093	0.0666	0.2219	5008	,	,		17389	0.125		0.334	False		,,,				2504	0.2638				p.P217L		Atlas-SNP	.											.	HDGF	60	.	0			c.C650T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	499,3907	224.6+/-240.7	31,437,1735	36.0	38.0	37.0		650,581,602	1.7	1.0	1	dbSNP_111	37	2966,5634	436.8+/-358.4	533,1900,1867	yes	missense,missense,missense	HDGF	NM_001126050.1,NM_001126051.1,NM_004494.2	98,98,98	564,2337,3602	AA,AG,GG		34.4884,11.3255,26.6416	benign,benign,benign	217/257,194/234,201/241	156713558	3465,9541	2203	4300	6503	SO:0001583	missense	3068	exon5			TCAGAGGGGGTGC	D16431	CCDS1156.1, CCDS44247.1, CCDS44248.1	1q23.1	2013-10-14	2010-03-19		ENSG00000143321	ENSG00000143321			4856	protein-coding gene	gene with protein product	"""high-mobility group protein 1-like"""	600339	"""hepatoma-derived growth factor (high-mobility group protein 1-like)"""			8833162	Standard	NM_004494		Approved	HMG1L2	uc001fpy.4	P51858	OTTHUMG00000041295	ENST00000357325.5:c.602C>T	1.37:g.156713558G>A	ENSP00000349878:p.Pro201Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	NM_001126050	B3KU21|D3DVC9|Q5SZ07|Q5SZ08|Q5SZ09	Missense_Mutation	SNP	ENST00000357325.5	37	CCDS1156.1	449	0.20558608058608058	26	0.052845528455284556	99	0.27348066298342544	73	0.12762237762237763	251	0.3311345646437995	G	10.57	1.385885	0.25031	0.113255	0.344884	ENSG00000143321	ENST00000357325;ENST00000368209;ENST00000537739;ENST00000416666;ENST00000368206;ENST00000406805	T;T;T;T;T	0.39406	1.67;1.15;1.67;1.22;1.08	4.67	1.7	0.24286	.	0.957193	0.08579	U	0.924918	T	0.17534	0.0421	L	0.50333	1.59	0.31954	P	0.609266	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.16512	-1.0400	9	0.52906	T	0.07	-1.8131	6.7766	0.23622	0.0948:0.343:0.5621:0.0	rs4399146;rs4399146	176;217;194;201	B7Z958;Q5SZ07;Q5SZ08;P51858	.;.;.;HDGF_HUMAN	L	201;194;201;169;217;224	ENSP00000349878:P201L;ENSP00000357192:P194L;ENSP00000443120:P201L;ENSP00000416752:P169L;ENSP00000357189:P217L	ENSP00000349878:P201L	P	-	2	0	HDGF	154980182	0.750000	0.28316	0.985000	0.45067	0.759000	0.43091	0.827000	0.27421	0.192000	0.20272	-0.366000	0.07423	CCC	G|0.790;A|0.210	0.210	strong		0.602	HDGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098946.1	NM_004494	
TARSL2	123283	hgsc.bcm.edu	37	15	102264476	102264476	+	Missense_Mutation	SNP	C	C	A	rs1143136	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:102264476C>A	ENST00000335968.3	-	1	331	c.115G>T	c.(115-117)Gcg>Tcg	p.A39S		NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	39					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CTGTAGGGCGCGTTCAGCTGC	0.746													C|||	963	0.192292	0.2897	0.2853	5008	,	,		9080	0.0099		0.2237	False		,,,				2504	0.1503				p.A39S		Atlas-SNP	.											.	TARSL2	63	.	0			c.G115T						PASS	.	C	SER/ALA	763,2699		89,585,1057	6.0	6.0	6.0		115	2.3	0.2	15	dbSNP_86	6	1417,5697		175,1067,2315	yes	missense	TARSL2	NM_152334.2	99	264,1652,3372	AA,AC,CC		19.9185,22.0393,20.6127	benign	39/803	102264476	2180,8396	1731	3557	5288	SO:0001583	missense	123283	exon1			AGGGCGCGTTCAG	AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.115G>T	15.37:g.102264476C>A	ENSP00000338093:p.Ala39Ser	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	31	24	0.774194	NM_152334	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	37	CCDS10394.1	442	0.20238095238095238	155	0.3150406504065041	103	0.2845303867403315	6	0.01048951048951049	178	0.23482849604221637	.	10.09	1.254065	0.22965	0.220393	0.199185	ENSG00000185418	ENST00000335968;ENST00000333018;ENST00000539112	.	.	.	3.28	2.33	0.28932	.	1.372480	0.04874	N	0.446500	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.27732	0.187	B	0.21151	0.033	T	0.18745	-1.0327	8	0.45353	T	0.12	-0.7096	7.7599	0.28946	0.2501:0.7499:0.0:0.0	rs1143136;rs58456433	39	A2RTX5	SYTC2_HUMAN	S	39	.	ENSP00000329291:A39S	A	-	1	0	TARSL2	100081999	0.256000	0.24012	0.208000	0.23602	0.288000	0.27193	0.678000	0.25277	0.708000	0.31955	0.298000	0.19748	GCG	C|0.794;A|0.206	0.206	strong		0.746	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334	
MUC5B	727897	hgsc.bcm.edu	37	11	1266561	1266561	+	Silent	SNP	G	G	A	rs200970694	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1266561G>A	ENST00000529681.1	+	31	8509	c.8451G>A	c.(8449-8451)agG>agA	p.R2817R	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.R2820R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2817	7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	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)		CTAGCAGCAGGACCACCGAGT	0.682																																					p.R2817R		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.G8451A						scavenged	.						27.0	43.0	38.0					11																	1266561		1927	4011	5938	SO:0001819	synonymous_variant	727897	exon31			CAGCAGGACCACC	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.8451G>A	11.37:g.1266561G>A		Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	300	19	0.0633333	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.989;A|0.011	0.011	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
GPR56	9289	hgsc.bcm.edu	37	16	57689805	57689805	+	Missense_Mutation	SNP	A	A	C	rs1801255	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57689805A>C	ENST00000388812.4	+	7	1358	c.918A>C	c.(916-918)caA>caC	p.Q306H	GPR56_ENST00000568908.1_Missense_Mutation_p.Q306H|GPR56_ENST00000567835.1_Missense_Mutation_p.Q306H|GPR56_ENST00000562558.1_Missense_Mutation_p.Q306H|GPR56_ENST00000568909.1_Missense_Mutation_p.Q306H|GPR56_ENST00000456916.1_Missense_Mutation_p.Q306H|GPR56_ENST00000379694.4_Missense_Mutation_p.Q136H|GPR56_ENST00000544297.1_Missense_Mutation_p.Q131H|GPR56_ENST00000538815.1_Missense_Mutation_p.Q306H|GPR56_ENST00000388813.5_Missense_Mutation_p.Q306H|GPR56_ENST00000540164.2_Missense_Mutation_p.Q306H|GPR56_ENST00000562631.1_Missense_Mutation_p.Q306H|GPR56_ENST00000379696.3_Missense_Mutation_p.Q306H			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	306			Q -> H (in dbSNP:rs1801255). {ECO:0000269|PubMed:10049584, ECO:0000269|PubMed:10100861, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.7}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						ATTCCAGCCAAGTCCTGGGTG	0.552													A|||	566	0.113019	0.0734	0.1484	5008	,	,		18820	0.006		0.2843	False		,,,				2504	0.0757				p.Q311H		Atlas-SNP	.											.	GPR56	44	.	0			c.A933C						PASS	.	A	HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN,HIS/GLN	430,3966	209.5+/-230.2	32,366,1800	119.0	117.0	118.0		918,918,918,933,918,918,918,918	-0.6	1.0	16	dbSNP_89	118	2284,6316	385.1+/-341.3	340,1604,2356	yes	missense,missense,missense,missense,missense,missense,missense,missense	GPR56	NM_001145770.1,NM_001145771.1,NM_001145772.1,NM_001145773.1,NM_001145774.1,NM_005682.5,NM_201524.2,NM_201525.2	24,24,24,24,24,24,24,24	372,1970,4156	CC,CA,AA		26.5581,9.7816,20.8833	benign,benign,benign,benign,benign,benign,benign,benign	306/688,306/694,306/688,311/693,306/688,306/694,306/688,306/688	57689805	2714,10282	2198	4300	6498	SO:0001583	missense	9289	exon7			CAGCCAAGTCCTG	AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"""-"", ""GPCR / Class B : Orphans"""	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.918A>C	16.37:g.57689805A>C	ENSP00000373464:p.Gln306His	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	80	46	0.575	NM_001145773	A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Missense_Mutation	SNP	ENST00000388812.4	37	CCDS32460.1	309	0.14148351648351648	40	0.08130081300813008	57	0.1574585635359116	5	0.008741258741258742	207	0.27308707124010556	A	10.03	1.237897	0.22711	0.097816	0.265581	ENSG00000205336	ENST00000388813;ENST00000388812;ENST00000538815;ENST00000456916;ENST00000540164;ENST00000544297;ENST00000379694;ENST00000379696	T;T;T;T;T;T;T;T	0.44881	0.92;0.91;0.92;0.91;0.92;1.76;1.17;0.91	5.59	-0.618	0.11576	.	0.199890	0.35646	N	0.003069	T	0.00012	0.0000	L	0.42245	1.32	0.38031	P	0.06483099999999997	B;B;B;B	0.33964	0.028;0.012;0.016;0.434	B;B;B;B	0.28232	0.027;0.012;0.007;0.087	T	0.28490	-1.0042	9	0.35671	T	0.21	.	6.5868	0.22624	0.4196:0.1564:0.424:0.0	rs1801255;rs17326320;rs17855398;rs52830657;rs60204048;rs1801255	131;306;306;136	F5H144;Q9Y653-2;Q9Y653;E7ENB2	.;.;GPR56_HUMAN;.	H	306;306;306;306;306;131;136;306	ENSP00000373465:Q306H;ENSP00000373464:Q306H;ENSP00000444415:Q306H;ENSP00000398034:Q306H;ENSP00000444911:Q306H;ENSP00000438006:Q131H;ENSP00000369016:Q136H;ENSP00000369018:Q306H	ENSP00000369016:Q136H	Q	+	3	2	GPR56	56247306	0.808000	0.29022	0.993000	0.49108	0.811000	0.45836	-0.205000	0.09411	-0.161000	0.10983	-0.290000	0.09829	CAA	A|0.834;C|0.166	0.166	strong		0.552	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3		
LOXHD1	125336	hgsc.bcm.edu	37	18	44063598	44063598	+	Missense_Mutation	SNP	G	G	A	rs1377016	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44063598G>A	ENST00000398722.4	-	33	5458	c.5459C>T	c.(5458-5460)gCc>gTc	p.A1820V	LOXHD1_ENST00000441551.2_Missense_Mutation_p.A1892V|LOXHD1_ENST00000582408.1_Missense_Mutation_p.A925V|LOXHD1_ENST00000398686.4_Missense_Mutation_p.A337V|LOXHD1_ENST00000398705.2_Missense_Mutation_p.A337V|LOXHD1_ENST00000300591.6_Missense_Mutation_p.A987V|LOXHD1_ENST00000579038.1_Missense_Mutation_p.A891V|LOXHD1_ENST00000536736.1_Missense_Mutation_p.A2036V|LOXHD1_ENST00000441893.2_Missense_Mutation_p.A969V			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1820	PLAT 13. {ECO:0000255|PROSITE- ProRule:PRU00152}.			A -> V (in Ref. 4; AAH47720). {ECO:0000305}.	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						GACATGCCAGGCAAGTTCTCT	0.552													A|||	1898	0.378994	0.2005	0.3905	5008	,	,		22330	0.7292		0.3121	False		,,,				2504	0.32				p.A2036V		Atlas-SNP	.											.	LOXHD1	367	.	0			c.C6107T						PASS	.						143.0	116.0	124.0					18																	44063598		692	1591	2283	SO:0001583	missense	125336	exon39			TGCCAGGCAAGTT	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.5459C>T	18.37:g.44063598G>A	ENSP00000381707:p.Ala1820Val	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	131	130	0.992366	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		894	0.40934065934065933	82	0.16666666666666666	146	0.40331491712707185	434	0.7587412587412588	232	0.30606860158311344	A	9.892	1.204488	0.22205	.	.	ENSG00000167210	ENST00000300591;ENST00000398722;ENST00000398705;ENST00000536736;ENST00000441893;ENST00000398686	T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.78	3.21	0.36854	Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.40701	-0.9549	8	0.16896	T	0.51	.	4.2209	0.10558	0.5165:0.0:0.249:0.2345	rs1377016;rs17846413;rs17859457;rs57156492;rs1377016	2036;969;1820	F5GZB4;F8WA52;Q8IVV2	.;.;LOXH1_HUMAN	V	987;1820;337;2036;969;337	ENSP00000300591:A987V;ENSP00000381707:A1820V;ENSP00000381692:A337V;ENSP00000444586:A2036V;ENSP00000409062:A969V;ENSP00000381676:A337V	ENSP00000300591:A987V	A	-	2	0	LOXHD1	42317596	0.993000	0.37304	0.978000	0.43139	0.744000	0.42396	0.675000	0.25232	0.066000	0.16515	-0.360000	0.07572	GCC	G|0.598;A|0.402	0.402	strong		0.552	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
CEACAM5	1048	hgsc.bcm.edu	37	19	42213872	42213872	+	Missense_Mutation	SNP	T	T	C	rs35091611	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:42213872T>C	ENST00000221992.6	+	2	452	c.338T>C	c.(337-339)aTc>aCc	p.I113T	CEA_ENST00000598976.1_Missense_Mutation_p.I113T|CEACAM5_ENST00000405816.1_Missense_Mutation_p.I113T|CEACAM7_ENST00000599715.1_5'Flank|CEACAM5_ENST00000398599.4_Missense_Mutation_p.I113T	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	113	Ig-like 1.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CAGAACATCATCCAGAATGAC	0.473													t|||	649	0.129593	0.2799	0.0865	5008	,	,		19881	0.0		0.1958	False		,,,				2504	0.0225				p.I113T		Atlas-SNP	.											.	CEACAM5	84	.	0			c.T338C						PASS	.	T	THR/ILE	1021,3385		181,659,1363	229.0	232.0	231.0		338	-6.2	0.0	19	dbSNP_126	231	1178,7422		115,948,3237	no	missense	CEACAM5	NM_004363.2	89	296,1607,4600	CC,CT,TT		13.6977,23.1729,16.9076	benign	113/703	42213872	2199,10807	2203	4300	6503	SO:0001583	missense	1048	exon2			ACATCATCCAGAA	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.338T>C	19.37:g.42213872T>C	ENSP00000221992:p.Ile113Thr	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	168	90	0.535714	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	262	0.11996336996336997	96	0.1951219512195122	34	0.09392265193370165	0	0.0	132	0.1741424802110818	-	0.006	-2.111474	0.00353	0.231729	0.136977	ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181	T;T	0.62232	0.04;0.04	3.09	-6.19	0.02078	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00000	-3.95	0.80722	P	0.0	B;B;B	0.17852	0.024;0.0;0.0	B;B;B	0.15484	0.013;0.0;0.0	T	0.35425	-0.9789	8	0.02654	T	1	.	2.1955	0.03910	0.1443:0.2142:0.4287:0.2128	rs35091611	113;113;113	Q8N4D0;P06731;Q53G30	.;CEAM5_HUMAN;.	T	113	ENSP00000221992:I113T;ENSP00000385072:I113T	ENSP00000221992:I113T	I	+	2	0	CEACAM5	46905712	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.653000	0.05360	-1.023000	0.03342	-1.889000	0.00537	ATC	T|0.832;C|0.168	0.168	strong		0.473	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
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 GAIIx	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|BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000540415.1_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	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	93	46	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		
XDH	7498	hgsc.bcm.edu	37	2	31593265	31593265	+	Missense_Mutation	SNP	T	T	C	rs17323225	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:31593265T>C	ENST00000379416.3	-	18	1984	c.1936A>G	c.(1936-1938)Ata>Gta	p.I646V		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	646			I -> V (in dbSNP:rs17323225). {ECO:0000269|Ref.6}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	ATTCCAGTTATGTTACTCCCA	0.353													T|||	97	0.019369	0.0053	0.0159	5008	,	,		20409	0.004		0.0467	False		,,,				2504	0.0286				p.I646V	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.A1936G						PASS	.	T	VAL/ILE	30,4376	36.8+/-68.6	0,30,2173	105.0	99.0	101.0		1936	-9.7	0.0	2	dbSNP_123	101	292,8308	107.0+/-167.8	4,284,4012	yes	missense	XDH	NM_000379.3	29	4,314,6185	CC,CT,TT		3.3953,0.6809,2.4758	benign	646/1334	31593265	322,12684	2203	4300	6503	SO:0001583	missense	7498	exon18			CAGTTATGTTACT	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.1936A>G	2.37:g.31593265T>C	ENSP00000368727:p.Ile646Val	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_000379	Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	37	CCDS1775.1	38	0.0173992673992674	6	0.012195121951219513	6	0.016574585635359115	0	0.0	26	0.03430079155672823	T	2.440	-0.328875	0.05314	0.006809	0.033953	ENSG00000158125	ENST00000379416	T	0.16457	2.34	6.17	-9.66	0.00534	Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead (3);	1.433710	0.03555	N	0.226175	T	0.02688	0.0081	N	0.20401	0.57	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.16041	-1.0416	10	0.15066	T	0.55	.	10.4692	0.44626	0.0:0.4161:0.1475:0.4365	rs17323225;rs52823262;rs60097147;rs17323225	646	P47989	XDH_HUMAN	V	646	ENSP00000368727:I646V	ENSP00000368727:I646V	I	-	1	0	XDH	31446769	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-2.756000	0.00789	-2.073000	0.00878	-1.231000	0.01572	ATA	T|0.978;C|0.022	0.022	strong		0.353	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
IGF2BP3	10643	hgsc.bcm.edu	37	7	23353246	23353246	+	Missense_Mutation	SNP	A	A	C	rs199812608		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:23353246A>C	ENST00000258729.3	-	13	1778	c.1422T>G	c.(1420-1422)atT>atG	p.I474M		NM_006547.2	NP_006538.2	O00425	IF2B3_HUMAN	insulin-like growth factor 2 mRNA binding protein 3	474					anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation regulator activity (GO:0045182)	p.I474M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|ovary(2)|prostate(2)|skin(4)|stomach(1)	34						TTTCTTCTTTAATTTTTCCAT	0.383																																					p.I474M		Atlas-SNP	.											IGF2BP3,NS,carcinoma,0,1	IGF2BP3	71	1	1	Substitution - Missense(1)	endometrium(1)	c.T1422G						scavenged	.						87.0	84.0	85.0					7																	23353246		2203	4300	6503	SO:0001583	missense	10643	exon13			TTCTTTAATTTTT	AF117108	CCDS5382.1	7p15.3	2014-02-19			ENSG00000136231	ENSG00000136231		"""RNA binding motif (RRM) containing"""	28868	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 3"", ""cancer/testis antigen 98"""	608259				9891060, 9178771	Standard	NM_006547		Approved	IMP-3, CT98, IMP3	uc003swg.3	O00425	OTTHUMG00000128445	ENST00000258729.3:c.1422T>G	7.37:g.23353246A>C	ENSP00000258729:p.Ile474Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	61	2	0.0327869	NM_006547	A0A4Z5|Q63HM0|Q6MZZ2|Q86VB1	Missense_Mutation	SNP	ENST00000258729.3	37	CCDS5382.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.582136	0.28180	.	.	ENSG00000136231	ENST00000258729	T	0.65916	-0.18	5.55	1.78	0.24846	K Homology (1);	0.172230	0.51477	D	0.000097	T	0.28764	0.0713	N	0.04880	-0.145	0.35528	D	0.802005	P	0.37158	0.585	B	0.32090	0.14	T	0.14392	-1.0474	10	0.22109	T	0.4	-2.3591	2.611	0.04891	0.6156:0.126:0.1369:0.1214	.	474	O00425	IF2B3_HUMAN	M	474	ENSP00000258729:I474M	ENSP00000258729:I474M	I	-	3	3	IGF2BP3	23319771	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.434000	0.34958	0.449000	0.26747	0.533000	0.62120	ATT	.	.	weak		0.383	IGF2BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250243.2	NM_006547	
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 GAIIx	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	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	42	11	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		
RBMXL1	494115	hgsc.bcm.edu	37	1	89449383	89449383	+	Missense_Mutation	SNP	G	G	A	rs147771633	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:89449383G>A	ENST00000321792.5	-	2	554	c.127C>T	c.(127-129)Cgt>Tgt	p.R43C	RBMXL1_ENST00000399794.2_Missense_Mutation_p.R43C|CCBL2_ENST00000260508.4_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	43	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										TTGGTTTCACGGTCTTTTATC	0.413											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R43C		Atlas-SNP	.											CCBL2,NS,carcinoma,0,1	.	.	1	0			c.C127T						scavenged	.	G	,,CYS/ARG,CYS/ARG	2,4404	2.1+/-5.4	0,2,2201	208.0	196.0	200.0		,,127,127	-0.9	1.0	1	dbSNP_134	200	13,8587	6.4+/-24.3	0,13,4287	no	intron,intron,missense,missense	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	,,180,180	0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153	,,probably-damaging,probably-damaging	,,43/391,43/391	89449383	15,12991	2203	4300	6503	SO:0001583	missense	494115	exon3			TTTCACGGTCTTT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.127C>T	1.37:g.89449383G>A	ENSP00000318415:p.Arg43Cys	Somatic	257	2	0.0077821	1267	WXS	Illumina HiSeq	Phase_I	244	66	0.270492	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008797	0.75046	4.54E-4	0.001512	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.85702	-2.02;-2.02	1.59	-0.931	0.10438	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	U	0.000000	D	0.84938	0.5583	M	0.80616	2.505	0.49687	D	0.999813	D	0.71674	0.998	D	0.65987	0.94	T	0.81988	-0.0680	10	0.87932	D	0	-3.8545	4.2107	0.10510	0.4537:0.0:0.5463:0.0	.	43	Q96E39	RBMXL_HUMAN	C	43	ENSP00000318415:R43C;ENSP00000446099:R43C	ENSP00000318415:R43C	R	-	1	0	RBMXL1	89221971	1.000000	0.71417	0.976000	0.42696	0.893000	0.52053	3.231000	0.51294	-0.417000	0.07461	0.306000	0.20318	CGT	G|0.500;A|0.500	0.500	weak		0.413	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
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 GAIIx	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_ENST00000489468.1_3'UTR|IAH1_ENST00000470914.1_Intron|IAH1_ENST00000482918.1_5'UTR|IAH1_ENST00000545602.1_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	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	179	178	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	
PDE6A	5145	hgsc.bcm.edu	37	5	149323906	149323906	+	Silent	SNP	T	T	G	rs2277925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149323906T>G	ENST00000255266.5	-	1	450	c.331A>C	c.(331-333)Agg>Cgg	p.R111R		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	111	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)	p.R111R(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	TTGAAAAGCCTGGTGGCCAGC	0.562													G|||	1415	0.282548	0.3994	0.2363	5008	,	,		18477	0.246		0.167	False		,,,				2504	0.3139				p.R111R		Atlas-SNP	.											PDE6A,NS,carcinoma,0,1	PDE6A	98	1	1	Substitution - coding silent(1)	stomach(1)	c.A331C						PASS	.	G		1463,2943	680.2+/-403.8	237,989,977	82.0	82.0	82.0		331	2.2	0.9	5	dbSNP_100	82	1234,7366	761.9+/-407.6	102,1030,3168	no	coding-synonymous	PDE6A	NM_000440.2		339,2019,4145	GG,GT,TT		14.3488,33.2047,20.7366		111/861	149323906	2697,10309	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			AAAGCCTGGTGGC		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.331A>C	5.37:g.149323906T>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			T|0.786;G|0.214	0.214	strong		0.562	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
WWC2	80014	hgsc.bcm.edu	37	4	184190233	184190233	+	Missense_Mutation	SNP	G	G	T	rs11941467	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:184190233G>T	ENST00000403733.3	+	15	2516	c.2317G>T	c.(2317-2319)Gcc>Tcc	p.A773S	WWC2_ENST00000448232.2_Missense_Mutation_p.A773S|WWC2_ENST00000504005.1_Missense_Mutation_p.A455S|WWC2_ENST00000506225.1_3'UTR|WWC2_ENST00000378925.3_Missense_Mutation_p.A675S|WWC2_ENST00000513834.1_Missense_Mutation_p.A724S	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	773	C2.		A -> S (in dbSNP:rs11941467). {ECO:0000269|PubMed:15489334}.		negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		GTTCAGAGTCGCCATTTCCCA	0.453													G|||	500	0.0998403	0.0166	0.072	5008	,	,		18521	0.0933		0.1143	False		,,,				2504	0.2239				p.A773S		Atlas-SNP	.											.	WWC2	78	.	0			c.G2317T						PASS	.	G	SER/ALA	164,4242	109.9+/-148.2	4,156,2043	148.0	146.0	146.0		2317	3.5	1.0	4	dbSNP_120	146	947,7653	208.3+/-249.8	60,827,3413	yes	missense	WWC2	NM_024949.5	99	64,983,5456	TT,TG,GG		11.0116,3.7222,8.5422	benign	773/1193	184190233	1111,11895	2203	4300	6503	SO:0001583	missense	80014	exon15			AGAGTCGCCATTT	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2317G>T	4.37:g.184190233G>T	ENSP00000384222:p.Ala773Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	158	0.07234432234432235	3	0.006097560975609756	29	0.08011049723756906	46	0.08041958041958042	80	0.10554089709762533	G	6.837	0.523552	0.13066	0.037222	0.110116	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.35	3.5	0.40072	C2 calcium/lipid-binding domain, CaLB (1);	0.255724	0.33496	N	0.004843	T	0.00178	0.0005	N	0.12471	0.22	0.31698	N	0.641027	B;B;B	0.24186	0.044;0.01;0.099	B;B;B	0.22601	0.03;0.024;0.04	T	0.12915	-1.0529	10	0.14252	T	0.57	-6.6582	13.7162	0.62697	0.0:0.0:0.505:0.495	rs11941467;rs52814359;rs59395067;rs11941467	773;773;724	Q6AWC2-6;Q6AWC2;Q6AWC2-4	.;WWC2_HUMAN;.	S	773;675;724;773;455	ENSP00000384222:A773S;ENSP00000368205:A675S;ENSP00000425054:A724S;ENSP00000398577:A773S;ENSP00000427569:A455S	ENSP00000368205:A675S	A	+	1	0	WWC2	184427227	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.546000	0.36179	1.430000	0.47334	0.555000	0.69702	GCC	G|0.917;T|0.083	0.083	strong		0.453	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
C17orf67	339210	hgsc.bcm.edu	37	17	54872439	54872439	+	Missense_Mutation	SNP	T	T	C	rs72837329	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:54872439T>C	ENST00000575658.1	-	7	1537	c.331A>G	c.(331-333)Att>Gtt	p.I111V	C17orf67_ENST00000397861.2_Missense_Mutation_p.I87V|C17orf67_ENST00000397862.2_Missense_Mutation_p.I111V	NM_001085430.2	NP_001078899.2	Q0P5P2	CQ067_HUMAN	chromosome 17 open reading frame 67	111						extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	7	Breast(9;2.49e-06)					ACAGGATGAATCCTGTTCCTG	0.597													C|||	632	0.126198	0.1528	0.1124	5008	,	,		21029	0.0179		0.1769	False		,,,				2504	0.1595				p.I87V		Atlas-SNP	.											.	C17orf67	13	.	0			c.A259G						PASS	.	C	VAL/ILE	576,3562		38,500,1531	88.0	101.0	97.0		331	3.7	0.0	17	dbSNP_130	97	1202,7240		83,1036,3102	yes	missense	C17orf67	NM_001085430.1	29	121,1536,4633	CC,CT,TT		14.2383,13.9198,14.1335	benign	111/115	54872439	1778,10802	2069	4221	6290	SO:0001583	missense	339210	exon7			GATGAATCCTGTT	BC041467	CCDS42364.1, CCDS42364.2	17q23.2	2012-10-11			ENSG00000214226	ENSG00000214226			27900	protein-coding gene	gene with protein product						12477932	Standard	NM_001085430		Approved		uc002iuq.4	Q0P5P2	OTTHUMG00000132083	ENST00000575658.1:c.331A>G	17.37:g.54872439T>C	ENSP00000461483:p.Ile111Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001085430		Missense_Mutation	SNP	ENST00000575658.1	37		284	0.13003663003663005	84	0.17073170731707318	49	0.13535911602209943	14	0.024475524475524476	137	0.18073878627968337	C	2.267	-0.367989	0.05069	0.139198	0.142383	ENSG00000214226	ENST00000397861;ENST00000397862	.	.	.	4.69	3.7	0.42460	.	0.140081	0.28515	N	0.015080	T	0.00039	0.0001	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18777	-1.0326	8	0.02654	T	1	-19.4414	10.6281	0.45519	0.0:0.8372:0.0:0.1628	.	111	Q0P5P2	CQ067_HUMAN	V	111	.	ENSP00000380959:I111V	I	-	1	0	C17orf67	52227438	0.945000	0.32115	0.010000	0.14722	0.022000	0.10575	2.010000	0.40913	0.515000	0.28320	-0.213000	0.12676	ATT	T|0.870;C|0.130	0.130	strong		0.597	C17orf67-202	KNOWN	basic	protein_coding	protein_coding		NM_001085430	
TTN	7273	hgsc.bcm.edu	37	2	179650408	179650408	+	Missense_Mutation	SNP	G	G	A	rs35813871	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:179650408G>A	ENST00000591111.1	-	15	2656	c.2432C>T	c.(2431-2433)aCa>aTa	p.T811I	TTN_ENST00000360870.5_Missense_Mutation_p.T811I|TTN_ENST00000589042.1_Missense_Mutation_p.T811I|TTN_ENST00000342175.6_Missense_Mutation_p.T765I|TTN_ENST00000359218.5_Missense_Mutation_p.T765I|TTN_ENST00000460472.2_Missense_Mutation_p.T765I|TTN_ENST00000342992.6_Missense_Mutation_p.T811I			Q8WZ42	TITIN_HUMAN	titin	33642			T -> I (in dbSNP:rs35813871). {ECO:0000269|PubMed:17344846}.		adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGGGCTAGCTGTGCGGGGGCG	0.388													G|||	503	0.100439	0.0862	0.1499	5008	,	,		21394	0.001		0.2157	False		,,,				2504	0.0685				p.T811I		Atlas-SNP	.											.	TTN	18412	.	0			c.C2432T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR,ILE/THR	450,3956	216.4+/-235.1	25,400,1778	183.0	178.0	179.0		2294,2432,2432,2294,2294	5.5	1.0	2	dbSNP_126	179	2017,6583	352.4+/-328.6	240,1537,2523	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	89,89,89,89,89	265,1937,4301	AA,AG,GG		23.4535,10.2133,18.9682	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	765/26927,811/33424,811/5605,765/27052,765/27119	179650408	2467,10539	2203	4300	6503	SO:0001583	missense	7273	exon15			CTAGCTGTGCGGG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.2432C>T	2.37:g.179650408G>A	ENSP00000465570:p.Thr811Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	97	43	0.443299	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		289	0.13232600732600733	60	0.12195121951219512	62	0.1712707182320442	0	0.0	167	0.22031662269129287	G	14.19	2.460217	0.43736	0.102133	0.234535	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.64085	-0.08;0.16;0.17;0.16;0.25	5.51	5.51	0.81932	Ribonuclease H-like (1);	.	.	.	.	T	0.00073	0.0002	L	0.29908	0.895	0.37180	P	0.09653599999999996	D;D;D;D;D	0.76494	0.995;0.995;0.995;0.997;0.999	P;P;P;P;D	0.67382	0.593;0.593;0.593;0.794;0.951	T	0.02424	-1.1161	8	0.87932	D	0	.	19.7837	0.96428	0.0:0.0:1.0:0.0	rs35813871;rs62176570	765;765;765;811;811	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	I	811;765;765;765;765;811	ENSP00000343764:T811I;ENSP00000434586:T765I;ENSP00000340554:T765I;ENSP00000352154:T765I;ENSP00000354117:T811I	ENSP00000340554:T765I	T	-	2	0	TTN	179358653	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.619000	0.67729	2.738000	0.93877	0.655000	0.94253	ACA	G|0.827;A|0.173	0.173	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CCDC88B	283234	hgsc.bcm.edu	37	11	64110683	64110683	+	Silent	SNP	G	G	C	rs479552	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64110683G>C	ENST00000356786.5	+	11	1139	c.1095G>C	c.(1093-1095)gcG>gcC	p.A365A	CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_5'Flank	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	365						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGCTGGAGGCGTCCAAGGCGC	0.706													C|||	1761	0.351637	0.3366	0.3991	5008	,	,		10651	0.248		0.3718	False		,,,				2504	0.4243				p.A365A		Atlas-SNP	.											CCDC88B,NS,carcinoma,0,1	CCDC88B	89	1	0			c.G1095C						PASS	.	C		1282,2854		246,790,1032	10.0	9.0	9.0		1095	1.9	1.0	11	dbSNP_83	9	2672,5414		532,1608,1903	no	coding-synonymous	CCDC88B	NM_032251.5		778,2398,2935	CC,CG,GG		33.0448,30.9961,32.3515		365/1477	64110683	3954,8268	2068	4043	6111	SO:0001819	synonymous_variant	283234	exon11			GGAGGCGTCCAAG	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.1095G>C	11.37:g.64110683G>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	18	10	0.555556	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.651;C|0.349	0.349	strong		0.706	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634303	32634303	+	Silent	SNP	G	G	A	rs1049061|rs67851506	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32634303G>A	ENST00000399082.3	-	1	126	c.82C>T	c.(82-84)Cta>Tta	p.L28L	HLA-DQB1_ENST00000399079.3_Silent_p.L28L|HLA-DQB1_ENST00000374943.4_Silent_p.L28L|HLA-DQB1_ENST00000399084.1_Silent_p.L28L|HLA-DQB1_ENST00000434651.2_Silent_p.L28L			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	28			P -> L (in allele DQB1*06:02 and allele DQB1*06:12; dbSNP:rs1049062).|P -> S (in allele DQB1*05:01 and allele DQB1*05:02). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TCAGCCAGTAGGGAGCTCAGC	0.592									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				G|||	1068	0.213259	0.2269	0.1513	5008	,	,		8486	0.246		0.1968	False		,,,				2504	0.2219				p.L28L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C82T						PASS	.						47.0	45.0	45.0					6																	32634303		1943	4108	6051	SO:0001819	synonymous_variant	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CCAGTAGGGAGCT		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.82C>T	6.37:g.32634303G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	13	8	0.615385	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				G|0.848;A|0.152	0.152	strong		0.592	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
CEP112	201134	hgsc.bcm.edu	37	17	63822357	63822357	+	Intron	SNP	T	T	C	rs62065084	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:63822357T>C	ENST00000392769.2	-	21	2613				CEP112_ENST00000317442.8_Missense_Mutation_p.I21V|CEP112_ENST00000580482.1_Intron|CEP112_ENST00000535342.2_Intron|CEP112_ENST00000537949.1_Intron|CEP112_ENST00000541355.1_Intron	NM_145036.3	NP_659473.2	Q8N8E3	CE112_HUMAN	centrosomal protein 112kDa						receptor localization to synapse (GO:0097120)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(11)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	28						CTCATCTCTATCAGTCTCAGG	0.463													T|||	1074	0.214457	0.2368	0.2262	5008	,	,		21080	0.125		0.2207	False		,,,				2504	0.2618				p.I21V		Atlas-SNP	.											.	CEP112	192	.	0			c.A61G						PASS	.	T	VAL/ILE,,	1069,3337	390.7+/-327.8	141,787,1275	259.0	258.0	258.0		61,,	-0.8	0.0	17	dbSNP_129	258	2066,6534	359.0+/-331.4	238,1590,2472	yes	missense,intron,intron	CEP112	NM_001037325.2,NM_001199165.1,NM_145036.3	29,,	379,2377,3747	CC,CT,TT		24.0233,24.2624,24.1043	,,	21/212,,	63822357	3135,9871	2203	4300	6503	SO:0001627	intron_variant	201134	exon1			TCTCTATCAGTCT	AF458591	CCDS32710.1, CCDS32711.1	17q24.2	2014-02-20	2011-05-06	2011-05-06	ENSG00000154240	ENSG00000154240			28514	protein-coding gene	gene with protein product			"""coiled-coil domain containing 46"""	CCDC46		21399614	Standard	NM_145036		Approved	MGC33887	uc002jfl.3	Q8N8E3		ENST00000392769.2:c.2394+25564A>G	17.37:g.63822357T>C		Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	248	246	0.991935	NM_001037325	Q6PIB5|Q8NCR4|Q8NFR4	Missense_Mutation	SNP	ENST00000392769.2	37	CCDS32710.1	440	0.20146520146520147	115	0.23373983739837398	86	0.23756906077348067	77	0.1346153846153846	162	0.21372031662269128	T	8.616	0.890231	0.17613	0.242624	0.240233	ENSG00000154240	ENST00000317442	.	.	.	3.01	-0.831	0.10789	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.32981	-0.9886	6	0.24483	T	0.36	.	4.3253	0.11038	0.0:0.1211:0.4057:0.4732	rs62065084	21	Q8N8E3-2	.	V	21	.	ENSP00000320592:I21V	I	-	1	0	CEP112	61252819	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.252000	0.08806	-0.210000	0.10140	0.454000	0.30748	ATA	T|0.765;C|0.235	0.235	strong		0.463	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	
ATP8B3	148229	hgsc.bcm.edu	37	19	1789556	1789556	+	Silent	SNP	C	C	T	rs12978609	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1789556C>T	ENST00000310127.6	-	23	2887	c.2649G>A	c.(2647-2649)caG>caA	p.Q883Q	ATP8B3_ENST00000525591.1_Silent_p.Q846Q|ATP8B3_ENST00000539485.1_Silent_p.Q893Q	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	883					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		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)		CTCTGGAGTCCTGGGCTGGCG	0.706													.|||	1551	0.309704	0.2988	0.2882	5008	,	,		7109	0.4395		0.2515	False		,,,				2504	0.2658				p.Q883Q		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G2649A						PASS	.	C	,	1059,2769		176,707,1031	7.0	9.0	9.0		2538,2649	-4.6	0.0	19	dbSNP_121	9	1989,6143		269,1451,2346	no	coding-synonymous,coding-synonymous	ATP8B3	NM_001178002.1,NM_138813.2	,	445,2158,3377	TT,TC,CC		24.4589,27.6646,25.4849	,	846/1264,883/1301	1789556	3048,8912	1914	4066	5980	SO:0001819	synonymous_variant	148229	exon23			GGAGTCCTGGGCT	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.2649G>A	19.37:g.1789556C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	11	4	0.363636	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Silent	SNP	ENST00000310127.6	37	CCDS45901.1																																																																																			C|0.670;T|0.330	0.330	strong		0.706	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
MTMR9	66036	hgsc.bcm.edu	37	8	11162496	11162496	+	Silent	SNP	A	A	C	rs2164272	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11162496A>C	ENST00000221086.3	+	4	1037	c.564A>C	c.(562-564)ctA>ctC	p.L188L	MTMR9_ENST00000526292.1_Silent_p.L103L	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	188	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		TCCCAGTACTAAGCTATTACC	0.463													A|||	2004	0.40016	0.1536	0.353	5008	,	,		21032	0.7063		0.3917	False		,,,				2504	0.4601				p.L188L		Atlas-SNP	.											.	MTMR9	58	.	0			c.A564C						PASS	.	A		881,3525	342.8+/-307.3	94,693,1416	123.0	104.0	110.0		564	-5.6	0.9	8	dbSNP_96	110	3482,5118	510.7+/-377.6	707,2068,1525	no	coding-synonymous	MTMR9	NM_015458.3		801,2761,2941	CC,CA,AA		40.4884,19.9955,33.5461		188/550	11162496	4363,8643	2203	4300	6503	SO:0001819	synonymous_variant	66036	exon4			AGTACTAAGCTAT	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	14596	protein-coding gene	gene with protein product		606260	"""myotubularin related protein 8"""	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.564A>C	8.37:g.11162496A>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	98	44	0.44898	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Silent	SNP	ENST00000221086.3	37	CCDS5979.1																																																																																			A|0.640;C|0.360	0.360	strong		0.463	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458	
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 GAIIx	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		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	60	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	
TEX15	56154	hgsc.bcm.edu	37	8	30702602	30702602	+	Missense_Mutation	SNP	T	T	C	rs323345	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:30702602T>C	ENST00000256246.2	-	1	4006	c.3932A>G	c.(3931-3933)aAc>aGc	p.N1311S		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1311			N -> S (in dbSNP:rs323345). {ECO:0000269|PubMed:11279525}.		fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		TGTAATAATGTTTTGTTTGGG	0.358													C|||	1642	0.327875	0.8487	0.1599	5008	,	,		20157	0.0704		0.1272	False		,,,				2504	0.2147				p.N1311S		Atlas-SNP	.											.	TEX15	350	.	0			c.A3932G						PASS	.	C	SER/ASN	3195,1211	399.9+/-331.4	1171,853,179	107.0	115.0	113.0		3932	-7.4	0.0	8	dbSNP_79	113	1012,7584	765.7+/-407.6	66,880,3352	yes	missense	TEX15	NM_031271.3	46	1237,1733,3531	CC,CT,TT		11.7729,27.4852,32.3566	benign	1311/2790	30702602	4207,8795	2203	4298	6501	SO:0001583	missense	56154	exon1			ATAATGTTTTGTT	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.3932A>G	8.37:g.30702602T>C	ENSP00000256246:p.Asn1311Ser	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	605	0.27701465201465203	411	0.8353658536585366	62	0.1712707182320442	39	0.06818181818181818	93	0.12269129287598944	C	3.112	-0.182359	0.06340	0.725148	0.117729	ENSG00000133863	ENST00000256246	T	0.21031	2.03	6.07	-7.43	0.01383	.	0.922343	0.09316	N	0.818928	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.28554	-1.0040	9	0.87932	D	0	.	5.6396	0.17557	0.0937:0.1285:0.1853:0.5925	rs323345;rs52829503;rs60104740;rs323345	1311	Q9BXT5	TEX15_HUMAN	S	1311	ENSP00000256246:N1311S	ENSP00000256246:N1311S	N	-	2	0	TEX15	30822144	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.083000	0.03397	-2.295000	0.00662	-0.735000	0.03563	AAC	T|0.707;C|0.293	0.293	strong		0.358	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
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 GAIIx	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_ENST00000359388.4_Missense_Mutation_p.S97T|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000413338.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.S114T|DYNC1I1_ENST00000447467.2_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	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	63	7	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	
GIMAP7	168537	hgsc.bcm.edu	37	7	150217248	150217248	+	Silent	SNP	A	A	G	rs3735081	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150217248A>G	ENST00000313543.4	+	2	343	c.186A>G	c.(184-186)gtA>gtG	p.V62V		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	62	AIG1-type G.				GTP catabolic process (GO:0006184)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)			breast(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTCTTGTTGTAGACACTCCAG	0.522													G|||	3914	0.78155	0.9713	0.7277	5008	,	,		18549	0.7421		0.6302	False		,,,				2504	0.7597				p.V62V		Atlas-SNP	.											GIMAP7,NS,carcinoma,+2,1	GIMAP7	47	1	0			c.A186G						PASS	.	G		4031,375	191.2+/-216.9	1849,333,21	53.0	51.0	52.0		186	-7.2	0.2	7	dbSNP_107	52	5377,3223	486.1+/-371.8	1691,1995,614	no	coding-synonymous	GIMAP7	NM_153236.3		3540,2328,635	GG,GA,AA		37.4767,8.5111,27.6642		62/301	150217248	9408,3598	2203	4300	6503	SO:0001819	synonymous_variant	168537	exon2			TGTTGTAGACACT	BC027613	CCDS5903.1	7q36.1	2014-04-04			ENSG00000179144	ENSG00000179144		"""GTPases, IMAP"""	22404	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 7"""					15474311	Standard	NM_153236		Approved	MGC27027, IAN7	uc003whk.3	Q8NHV1	OTTHUMG00000157626	ENST00000313543.4:c.186A>G	7.37:g.150217248A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_153236		Silent	SNP	ENST00000313543.4	37	CCDS5903.1																																																																																			A|0.252;G|0.748	0.748	strong		0.522	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835218	27835218	+	Silent	SNP	G	G	A	rs17763089	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27835218G>A	ENST00000331442.3	-	1	141	c.90C>T	c.(88-90)ggC>ggT	p.G30G		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	30					chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						CAGCGCCGGCGCCGGCAGCCT	0.617													G|||	103	0.0205671	0.0023	0.0389	5008	,	,		13957	0.0		0.0726	False		,,,				2504	0.0				p.G30G		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C90T						PASS	.	G		90,4302		2,86,2108	31.0	38.0	36.0		90	-5.1	0.0	6	dbSNP_123	36	768,7824		35,698,3563	no	coding-synonymous	HIST1H1B	NM_005322.2		37,784,5671	AA,AG,GG		8.9385,2.0492,6.6081		30/227	27835218	858,12126	2196	4296	6492	SO:0001819	synonymous_variant	3009	exon1			GCCGGCGCCGGCA	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.90C>T	6.37:g.27835218G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	111	88	0.792793	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			G|0.945;A|0.055	0.055	strong		0.617	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
SLC18A1	6570	hgsc.bcm.edu	37	8	20036827	20036827	+	Missense_Mutation	SNP	C	C	G	rs2270637	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:20036827C>G	ENST00000276373.5	-	3	559	c.293G>C	c.(292-294)aGt>aCt	p.S98T	SLC18A1_ENST00000519026.1_Missense_Mutation_p.S98T|SLC18A1_ENST00000381608.4_Missense_Mutation_p.S98T|SLC18A1_ENST00000265808.7_Missense_Mutation_p.S98T|SLC18A1_ENST00000440926.1_Missense_Mutation_p.S98T|SLC18A1_ENST00000437980.1_Missense_Mutation_p.S98T	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	98			S -> T (in dbSNP:rs2270637).		monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29				Colorectal(74;0.0747)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	TGCTATTCCACTAGGTACGCT	0.517													C|||	953	0.190296	0.233	0.1499	5008	,	,		18977	0.1448		0.1889	False		,,,				2504	0.2096				p.S98T		Atlas-SNP	.											SLC18A1,colon,carcinoma,0,1	SLC18A1	68	1	0			c.G293C						PASS	.	C	THR/SER,THR/SER,THR/SER,THR/SER	978,3428	366.4+/-317.8	111,756,1336	169.0	112.0	131.0		293,293,293,293	-5.8	0.0	8	dbSNP_100	131	1640,6960	303.7+/-306.6	153,1334,2813	yes	missense,missense,missense,missense	SLC18A1	NM_001135691.2,NM_001142324.1,NM_001142325.1,NM_003053.3	58,58,58,58	264,2090,4149	GG,GC,CC		19.0698,22.197,20.1292	benign,benign,benign,benign	98/526,98/494,98/473,98/526	20036827	2618,10388	2203	4300	6503	SO:0001583	missense	6570	exon4			ATTCCACTAGGTA		CCDS6013.1, CCDS47814.1, CCDS47815.1	8p21.3	2013-07-18	2013-07-18		ENSG00000036565	ENSG00000036565		"""Solute carriers"""	10934	protein-coding gene	gene with protein product		193002		VMAT1, VAT1			Standard	NM_003053		Approved	CGAT	uc003wzm.3	P54219	OTTHUMG00000097017	ENST00000276373.5:c.293G>C	8.37:g.20036827C>G	ENSP00000276373:p.Ser98Thr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_001142324	E9PDJ5|Q9BRE4	Missense_Mutation	SNP	ENST00000276373.5	37	CCDS6013.1	413	0.1891025641025641	113	0.22967479674796748	49	0.13535911602209943	103	0.18006993006993008	148	0.19525065963060687	C	4.515	0.095568	0.08681	0.22197	0.190698	ENSG00000036565	ENST00000265808;ENST00000276373;ENST00000440926;ENST00000437980;ENST00000519026;ENST00000381608;ENST00000522513	T;T;T;T;T;T;T	0.04454	3.9;3.91;3.91;3.9;3.9;3.9;3.62	5.95	-5.81	0.02340	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.659160	0.02116	N	0.055177	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.21225	0.0;0.053;0.033	B;B;B	0.27170	0.01;0.056;0.077	T	0.46624	-0.9178	9	0.17832	T	0.49	14.038	3.2589	0.06842	0.1298:0.2963:0.0947:0.4792	rs2270637;rs17215794;rs17840572;rs2270637	98;98;98	E9PB33;E9PDJ5;P54219	.;.;VMAT1_HUMAN	T	98	ENSP00000265808:S98T;ENSP00000276373:S98T;ENSP00000387549:S98T;ENSP00000413361:S98T;ENSP00000429664:S98T;ENSP00000371021:S98T;ENSP00000428999:S98T	ENSP00000265808:S98T	S	-	2	0	SLC18A1	20081107	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.746000	0.04829	-0.799000	0.04439	-0.880000	0.02959	AGT	C|0.796;G|0.204	0.204	strong		0.517	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1		
PHLDB3	653583	hgsc.bcm.edu	37	19	43983740	43983740	+	Silent	SNP	T	T	C	rs1133929	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43983740T>C	ENST00000292140.5	-	14	1851	c.1491A>G	c.(1489-1491)ccA>ccG	p.P497P		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	497							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GTGGGGTGGGTGGGGCCTGGG	0.637													C|||	3817	0.762181	0.9115	0.683	5008	,	,		5666	0.7659		0.6551	False		,,,				2504	0.7229				p.P497P		Atlas-SNP	.											.	PHLDB3	30	.	0			c.A1491G						PASS	.	C		1594,120		739,116,2	1.0	1.0	1.0		1491	-3.2	0.5	19	dbSNP_86	1	3156,674		1263,630,22	no	coding-synonymous	PHLDB3	NM_198850.3		2002,746,24	CC,CT,TT		17.5979,7.0012,14.3218		497/641	43983740	4750,794	857	1915	2772	SO:0001819	synonymous_variant	653583	exon14			GGTGGGTGGGGCC		CCDS12621.2	19q13.31	2013-01-10			ENSG00000176531	ENSG00000176531		"""Pleckstrin homology (PH) domain containing"""	30499	protein-coding gene	gene with protein product							Standard	NM_198850		Approved	FLJ40193	uc002own.4	Q6NSJ2	OTTHUMG00000150693	ENST00000292140.5:c.1491A>G	19.37:g.43983740T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_198850	Q8N7Z4	Silent	SNP	ENST00000292140.5	37	CCDS12621.2																																																																																			T|0.268;C|0.732	0.732	strong		0.637	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
LRRK2	120892	hgsc.bcm.edu	37	12	40713901	40713901	+	Missense_Mutation	SNP	T	T	A	rs11564148	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:40713901T>A	ENST00000298910.7	+	34	4997	c.4939T>A	c.(4939-4941)Tca>Aca	p.S1647T		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1647			S -> T (in dbSNP:rs11564148). {ECO:0000269|PubMed:16172858, ECO:0000269|PubMed:22415848}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				GAACTACATGTCACAGTATTT	0.343											OREG0003827	type=REGULATORY REGION|Gene=LOC486608|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	T|||	1432	0.285942	0.174	0.2349	5008	,	,		15026	0.3373		0.3171	False		,,,				2504	0.3885				p.S1647T		Atlas-SNP	.											.	LRRK2	763	.	0			c.T4939A						PASS	.	T	THR/SER	787,3611	282.8+/-276.7	65,657,1477	48.0	56.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4939	0.4	0.9	12	dbSNP_120	54	2561,6031	400.1+/-346.7	365,1831,2100	yes	missense	LRRK2	NM_198578.3	58	430,2488,3577	AA,AT,TT		29.8068,17.8945,25.7737	benign	1647/2528	40713901	3348,9642	2199	4296	6495	SO:0001583	missense	120892	exon34			TACATGTCACAGT	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.4939T>A	12.37:g.40713901T>A	ENSP00000298910:p.Ser1647Thr	Somatic	71	0	0	895	WXS	Illumina HiSeq	Phase_I	93	34	0.365591	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	601	0.2751831501831502	84	0.17073170731707318	84	0.23204419889502761	186	0.32517482517482516	247	0.3258575197889182	T	8.769	0.925573	0.18056	0.178945	0.298068	ENSG00000188906	ENST00000298910	T	0.71934	-0.61	5.7	0.447	0.16608	.	0.627416	0.16568	N	0.208778	T	0.00012	0.0000	N	0.20685	0.6	0.28700	P	0.904148	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	9	0.12430	T	0.62	.	2.5413	0.04726	0.1726:0.0729:0.2196:0.5348	rs11564148;rs17443986;rs17461817;rs17583879;rs52790032;rs11564148	1647	Q5S007	LRRK2_HUMAN	T	1647	ENSP00000298910:S1647T	ENSP00000298910:S1647T	S	+	1	0	LRRK2	39000168	0.989000	0.36119	0.936000	0.37596	0.987000	0.75469	0.833000	0.27504	-0.154000	0.11118	0.482000	0.46254	TCA	A|0.266;N|0.000	0.266	strong		0.343	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
SETX	23064	hgsc.bcm.edu	37	9	135173685	135173685	+	Missense_Mutation	SNP	T	T	C	rs2296871	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135173685T>C	ENST00000224140.5	-	13	5745	c.5563A>G	c.(5563-5565)Act>Gct	p.T1855A	SETX_ENST00000372169.2_Missense_Mutation_p.T1855A|SETX_ENST00000393220.1_Missense_Mutation_p.T1855A	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	1855			T -> A (in dbSNP:rs2296871). {ECO:0000269|PubMed:15489334}.|T -> P (in dbSNP:rs2296871).		cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		TAACACTCAGTTTTCCCATTA	0.368													C|||	2219	0.443091	0.6929	0.2262	5008	,	,		21142	0.6379		0.1382	False		,,,				2504	0.3722				p.T1855A		Atlas-SNP	.											.	SETX	234	.	0			c.A5563G						PASS	.	C	ALA/THR	2656,1750	515.0+/-368.8	823,1010,370	75.0	72.0	73.0		5563	-8.4	0.0	9	dbSNP_100	73	1334,7266	754.4+/-407.5	97,1140,3063	yes	missense	SETX	NM_015046.5	58	920,2150,3433	CC,CT,TT		15.5116,39.7186,30.6781	benign	1855/2678	135173685	3990,9016	2203	4300	6503	SO:0001583	missense	23064	exon13			ACTCAGTTTTCCC	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.5563A>G	9.37:g.135173685T>C	ENSP00000224140:p.Thr1855Ala	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	905	0.4143772893772894	333	0.676829268292683	83	0.2292817679558011	384	0.6713286713286714	105	0.13852242744063326	C	0.839	-0.742489	0.03088	0.602814	0.155116	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.90069	-2.06;-2.61;-2.15;-1.77	5.88	-8.41	0.00961	.	1.218760	0.05711	N	0.595916	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24048	-1.0171	9	0.02654	T	1	.	9.7534	0.40490	0.1415:0.6259:0.0601:0.1724	rs2296871;rs58627825;rs2296871	1855;1855;1855	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	A	1855;97;1855;1855	ENSP00000224140:T1855A;ENSP00000409143:T97A;ENSP00000361242:T1855A;ENSP00000376913:T1855A	ENSP00000224140:T1855A	T	-	1	0	SETX	134163506	0.000000	0.05858	0.001000	0.08648	0.174000	0.22865	-0.963000	0.03837	-1.814000	0.01224	-2.561000	0.00173	ACT	C|0.380;N|0.000;T|0.620	0.380	strong		0.368	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
SNX21	90203	hgsc.bcm.edu	37	20	44469290	44469290	+	Missense_Mutation	SNP	G	G	A	rs4638862	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44469290G>A	ENST00000491381.1	+	4	528	c.460G>A	c.(460-462)Gcc>Acc	p.A154T	SNX21_ENST00000462307.1_Silent_p.S157S|SNX21_ENST00000372542.1_Missense_Mutation_p.A145T|SNX21_ENST00000372541.1_Silent_p.S148S|SNX21_ENST00000342644.5_Missense_Mutation_p.A154T|SNX21_ENST00000344780.4_3'UTR			Q969T3	SNX21_HUMAN	sorting nexin family member 21	154	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		A -> T (in dbSNP:rs4638862). {ECO:0000269|PubMed:15489334}.		protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	7		Myeloproliferative disorder(115;0.0122)				CTACACCCTCGCCGTGATCGG	0.642													G|||	1754	0.35024	0.0658	0.5202	5008	,	,		14028	0.4276		0.5298	False		,,,				2504	0.3497				p.A154T		Atlas-SNP	.											.	SNX21	23	.	0			c.G460A						PASS	.	G	,,THR/ALA,THR/ALA	692,3714	286.0+/-278.5	64,564,1575	84.0	87.0	86.0		453,471,460,460	2.4	1.0	20	dbSNP_111	86	4586,4014	591.5+/-392.8	1222,2142,936	yes	coding-synonymous,coding-synonymous,missense,missense	SNX21	NM_001042632.1,NM_001042633.1,NM_033421.2,NM_152897.1	,,58,58	1286,2706,2511	AA,AG,GG		46.6744,15.7059,40.5813	,,probably-damaging,probably-damaging	151/153,157/159,154/374,154/200	44469290	5278,7728	2203	4300	6503	SO:0001583	missense	90203	exon4			ACCCTCGCCGTGA	AK095851	CCDS13376.1, CCDS13377.1, CCDS42883.1	20q13.12	2013-01-10	2006-07-24	2006-07-24	ENSG00000124104	ENSG00000124104		"""Sorting nexins"", ""Tetratricopeptide (TTC) repeat domain containing"""	16154	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 161"""	C20orf161		12461558, 12459172	Standard	NM_152897		Approved	dJ337O18.4, SNX-L	uc002xpv.1	Q969T3	OTTHUMG00000032624	ENST00000491381.1:c.460G>A	20.37:g.44469290G>A	ENSP00000418593:p.Ala154Thr	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	71	18	0.253521	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Missense_Mutation	SNP	ENST00000491381.1	37	CCDS13377.1	873	0.39972527472527475	34	0.06910569105691057	172	0.47513812154696133	252	0.4405594405594406	415	0.5474934036939314	G	8.862	0.947087	0.18356	0.157059	0.533256	ENSG00000124104	ENST00000491381;ENST00000342644;ENST00000372542	T;T;T	0.27720	1.65;1.65;1.65	4.34	2.39	0.29439	Phox homologous domain (4);	0.416437	0.25869	N	0.027770	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999974067	B;B;B	0.20988	0.004;0.007;0.05	B;B;B	0.15484	0.005;0.005;0.013	T	0.45644	-0.9247	8	0.22706	T	0.39	-4.6567	3.9307	0.09283	0.1956:0.0:0.5137:0.2907	rs4638862;rs17851752;rs52829951;rs58614376;rs4638862	145;154;154	Q5JZH3;Q969T3;Q5JZH5	.;SNX21_HUMAN;.	T	154;154;145	ENSP00000418593:A154T;ENSP00000344586:A154T;ENSP00000361620:A145T	ENSP00000344586:A154T	A	+	1	0	SNX21	43902697	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	1.246000	0.32803	0.473000	0.27368	0.462000	0.41574	GCC	G|0.611;A|0.389	0.389	strong		0.642	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421	
MUC16	94025	hgsc.bcm.edu	37	19	9084183	9084183	+	Silent	SNP	G	G	A	rs1609460	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9084183G>A	ENST00000397910.4	-	1	7835	c.7632C>T	c.(7630-7632)ccC>ccT	p.P2544P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2544	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTGAGAGATGGGGAGTGAAGG	0.507													G|||	2085	0.416334	0.3411	0.5677	5008	,	,		20799	0.3264		0.4831	False		,,,				2504	0.4346				p.P2544P		Atlas-SNP	.											.	MUC16	4315	.	0			c.C7632T						PASS	.	G		1404,2822		255,894,964	101.0	104.0	103.0		7632	-0.4	0.2	19	dbSNP_88	103	4302,4176		1117,2068,1054	no	coding-synonymous	MUC16	NM_024690.2		1372,2962,2018	AA,AG,GG		49.2569,33.2229,44.915		2544/14508	9084183	5706,6998	2113	4239	6352	SO:0001819	synonymous_variant	94025	exon1			GAGATGGGGAGTG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.7632C>T	19.37:g.9084183G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	197	194	0.984772	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.573;A|0.427	0.427	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
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 GAIIx	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	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	37	15	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	
SLC1A5	6510	hgsc.bcm.edu	37	19	47278938	47278938	+	Silent	SNP	G	G	A	rs1060043	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47278938G>A	ENST00000542575.2	-	8	2083	c.1455C>T	c.(1453-1455)taC>taT	p.Y485Y	SLC1A5_ENST00000412532.2_Silent_p.Y257Y|SLC1A5_ENST00000594991.1_Silent_p.Y309Y|SLC1A5_ENST00000434726.2_Silent_p.Y283Y|FKRP_ENST00000600646.1_Intron	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	485					amino acid transport (GO:0006865)|extracellular amino acid transport (GO:0006860)|glutamine transport (GO:0006868)|ion transport (GO:0006811)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-glutamine transmembrane transporter activity (GO:0015186)|L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)|receptor activity (GO:0004872)|sodium:dicarboxylate symporter activity (GO:0017153)|virus receptor activity (GO:0001618)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(2)|stomach(1)	13		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	TACGGTCCACGTAATTTTGGA	0.557													-|||	295	0.0589058	0.0212	0.0677	5008	,	,		15671	0.0218		0.1093	False		,,,				2504	0.09				p.Y485Y		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C1455T						PASS	.		,,	135,4271		1,133,2069	102.0	90.0	94.0		771,849,1455	-6.2	0.1	19	dbSNP_86	94	898,7702		44,810,3446	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC1A5	NM_001145144.1,NM_001145145.1,NM_005628.2	,,	45,943,5515	AA,AG,GG		10.4419,3.064,7.9425	,,	257/314,283/340,485/542	47278938	1033,11973	2203	4300	6503	SO:0001819	synonymous_variant	6510	exon8			GTCCACGTAATTT	U53347	CCDS12692.1, CCDS46125.1, CCDS46126.1	19q13.32	2013-07-15			ENSG00000105281	ENSG00000105281		"""Solute carriers"""	10943	protein-coding gene	gene with protein product		109190		RDRC, M7V1		8702519, 10051606	Standard	NM_005628		Approved	AAAT, ASCT2	uc002pfs.3	Q15758	OTTHUMG00000183434	ENST00000542575.2:c.1455C>T	19.37:g.47278938G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	143	66	0.461538	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Silent	SNP	ENST00000542575.2	37	CCDS12692.1																																																																																			G|0.933;A|0.067	0.067	strong		0.557	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
ELSPBP1	64100	hgsc.bcm.edu	37	19	48525466	48525466	+	Missense_Mutation	SNP	C	C	T	rs35700000	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48525466C>T	ENST00000339841.2	+	6	732	c.554C>T	c.(553-555)cCg>cTg	p.P185L	ELSPBP1_ENST00000597519.1_Missense_Mutation_p.P37L	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	185	Fibronectin type-II 4. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		TGTCACTTTCCGTTCAACTAT	0.443													c|||	69	0.013778	0.0023	0.0072	5008	,	,		20502	0.0		0.0288	False		,,,				2504	0.0327				p.P185L		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.C554T						PASS	.	C	LEU/PRO	19,4387	27.2+/-55.0	0,19,2184	192.0	171.0	178.0		554	3.7	0.9	19	dbSNP_126	178	252,8348	99.5+/-161.0	5,242,4053	yes	missense	ELSPBP1	NM_022142.4	98	5,261,6237	TT,TC,CC		2.9302,0.4312,2.0837	probably-damaging	185/224	48525466	271,12735	2203	4300	6503	SO:0001583	missense	64100	exon6			ACTTTCCGTTCAA	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.554C>T	19.37:g.48525466C>T	ENSP00000340660:p.Pro185Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	35	0.016025641025641024	4	0.008130081300813009	7	0.019337016574585635	0	0.0	24	0.0316622691292876	C	15.92	2.973836	0.53720	0.004312	0.029302	ENSG00000169393	ENST00000339841	D	0.93488	-3.23	3.66	3.66	0.41972	Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);	0.000000	0.48286	D	0.000187	D	0.92593	0.7647	H	0.94658	3.565	0.39211	D	0.963313	D	0.89917	1.0	D	0.87578	0.998	D	0.91856	0.5495	10	0.87932	D	0	.	7.6915	0.28571	0.0:0.8769:0.0:0.1231	rs35700000	185	Q96BH3	ESPB1_HUMAN	L	185	ENSP00000340660:P185L	ENSP00000340660:P185L	P	+	2	0	ELSPBP1	53217278	0.967000	0.33354	0.940000	0.37924	0.712000	0.41017	2.829000	0.48128	1.968000	0.57251	0.609000	0.83330	CCG	C|0.980;T|0.020	0.020	strong		0.443	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
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 GAIIx	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	RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.P55S|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.P55S|SLCO6A1_ENST00000514551.1_5'Flank|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.P55S|SLCO6A1_ENST00000379807.3_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	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	122	5	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	
DMP1	1758	hgsc.bcm.edu	37	4	88584148	88584148	+	Silent	SNP	C	C	T	rs2615498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:88584148C>T	ENST00000339673.6	+	6	1317	c.1218C>T	c.(1216-1218)agC>agT	p.S406S	RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA|DMP1_ENST00000282479.7_Silent_p.S390S|RP11-742B18.1_ENST00000506480.1_RNA	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	406					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		AAGCAGACAGCGAATCCAGTG	0.557													C|||	880	0.175719	0.0431	0.1527	5008	,	,		20684	0.2401		0.1968	False		,,,				2504	0.2832				p.S406S		Atlas-SNP	.											.	DMP1	72	.	0			c.C1218T						PASS	.	C	,	322,4084	170.1+/-200.6	11,300,1892	91.0	95.0	94.0		1170,1218	-2.9	0.0	4	dbSNP_100	94	1646,6954	304.6+/-307.0	141,1364,2795	no	coding-synonymous,coding-synonymous	DMP1	NM_001079911.2,NM_004407.3	,	152,1664,4687	TT,TC,CC		19.1395,7.3082,15.1315	,	390/498,406/514	88584148	1968,11038	2203	4300	6503	SO:0001819	synonymous_variant	1758	exon6			AGACAGCGAATCC	U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"""dentin matrix acidic phosphoprotein"""			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.1218C>T	4.37:g.88584148C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_004407	A1L4L3|O43265	Silent	SNP	ENST00000339673.6	37	CCDS3623.1																																																																																			C|0.850;T|0.150	0.150	strong		0.557	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1		
RXRG	6258	hgsc.bcm.edu	37	1	165398115	165398115	+	Silent	SNP	T	T	C	rs113471	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:165398115T>C	ENST00000359842.5	-	2	440	c.138A>G	c.(136-138)acA>acG	p.T46T		NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	46	Modulating. {ECO:0000250}.				gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	CTGGGGTATCTGTGTAGCTGG	0.602													C|||	1252	0.25	0.416	0.2896	5008	,	,		17907	0.246		0.1531	False		,,,				2504	0.1012				p.T46T		Atlas-SNP	.											RXRG,NS,carcinoma,-2,1	RXRG	91	1	0			c.A138G						PASS	.	C		1531,2875	672.4+/-402.6	254,1023,926	64.0	59.0	61.0		138	-6.1	0.7	1	dbSNP_79	61	1321,7279	757.8+/-407.5	113,1095,3092	no	coding-synonymous	RXRG	NM_006917.4		367,2118,4018	CC,CT,TT		15.3605,34.7481,21.9283		46/464	165398115	2852,10154	2203	4300	6503	SO:0001819	synonymous_variant	6258	exon2			GGTATCTGTGTAG	U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"""Nuclear hormone receptors"""	10479	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 3"""	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.138A>G	1.37:g.165398115T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_006917	A6NIP1|Q6IBU7	Silent	SNP	ENST00000359842.5	37	CCDS1248.1																																																																																			T|0.776;G|0.003	.	strong		0.602	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917	
TEKT1	83659	hgsc.bcm.edu	37	17	6716242	6716242	+	Missense_Mutation	SNP	G	G	A	rs3744395	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6716242G>A	ENST00000338694.2	-	6	889	c.760C>T	c.(760-762)Cgc>Tgc	p.R254C	TEKT1_ENST00000535086.1_Missense_Mutation_p.R108C	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	254			R -> C (in dbSNP:rs3744395).			cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)	20		Myeloproliferative disorder(207;0.0255)				CACTGCTTGCGCAGATCATTG	0.547													G|||	1234	0.246406	0.1006	0.2853	5008	,	,		19693	0.4365		0.2087	False		,,,				2504	0.2587				p.R254C		Atlas-SNP	.											.	TEKT1	49	.	0			c.C760T						PASS	.	G	CYS/ARG	541,3865	246.2+/-254.9	40,461,1702	205.0	170.0	182.0		760	0.2	0.5	17	dbSNP_107	182	1780,6820	321.3+/-315.0	178,1424,2698	yes	missense	TEKT1	NM_053285.1	180	218,1885,4400	AA,AG,GG		20.6977,12.2787,17.8456	benign	254/419	6716242	2321,10685	2203	4300	6503	SO:0001583	missense	83659	exon6			GCTTGCGCAGATC		CCDS11083.1	17p13.2	2011-05-23			ENSG00000167858	ENSG00000167858			15534	protein-coding gene	gene with protein product		609002				11606253	Standard	NM_053285		Approved		uc002gdt.3	Q969V4	OTTHUMG00000102063	ENST00000338694.2:c.760C>T	17.37:g.6716242G>A	ENSP00000341346:p.Arg254Cys	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	123	57	0.463415	NM_053285	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	37	CCDS11083.1	543	0.24862637362637363	38	0.07723577235772358	85	0.23480662983425415	267	0.46678321678321677	153	0.20184696569920843	G	10.51	1.371713	0.24857	0.122787	0.206977	ENSG00000167858	ENST00000338694;ENST00000535086	T;T	0.03004	4.08;4.08	4.79	0.207	0.15214	.	0.388910	0.29152	N	0.012988	T	0.00012	0.0000	L	0.42632	1.34	0.23043	P	0.99838246	B	0.19583	0.037	B	0.21546	0.035	T	0.43523	-0.9386	9	0.45353	T	0.12	.	4.4768	0.11748	0.1689:0.0:0.3788:0.4522	rs3744395;rs52821534;rs57626019;rs3744395	254	Q969V4	TEKT1_HUMAN	C	254;108	ENSP00000341346:R254C;ENSP00000444142:R108C	ENSP00000341346:R254C	R	-	1	0	TEKT1	6656966	0.970000	0.33590	0.489000	0.27452	0.533000	0.34776	1.082000	0.30803	-0.088000	0.12506	0.591000	0.81541	CGC	G|0.790;A|0.210	0.210	strong		0.547	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	
CD200	4345	hgsc.bcm.edu	37	3	112063850	112063850	+	De_novo_Start_OutOfFrame	SNP	C	C	A	rs2272022	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112063850C>A	ENST00000383681.3	+	0	89				CD200_ENST00000473539.1_Missense_Mutation_p.P71T|CD200_ENST00000315711.8_Missense_Mutation_p.P46T			P41217	OX2G_HUMAN	CD200 molecule						regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				GCTGTACACACCTGCTTCCTT	0.413													C|||	1014	0.202476	0.1188	0.2709	5008	,	,		19654	0.1359		0.3907	False		,,,				2504	0.1421				p.P71T		Atlas-SNP	.											.	CD200	33	.	0			c.C211A						PASS	.	C	THR/PRO,THR/PRO	626,3780	268.3+/-268.4	44,538,1621	66.0	62.0	64.0		211,136	4.2	1.0	3	dbSNP_100	64	3141,5459	473.7+/-368.7	553,2035,1712	yes	missense,missense	CD200	NM_001004196.2,NM_005944.5	38,38	597,2573,3333	AA,AC,CC		36.5233,14.2079,28.9636	benign,benign	71/295,46/270	112063850	3767,9239	2203	4300	6503			4345	exon4			TACACACCTGCTT		CCDS2965.1, CCDS33818.1	3q13.2	2013-09-20	2006-03-28	2004-09-01	ENSG00000091972	ENSG00000091972		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7203	protein-coding gene	gene with protein product		155970	"""antigen identified by monoclonal antibody MRC OX-2"", ""CD200 antigen"""	MOX1, MOX2			Standard	XM_005247482		Approved	MRC, OX-2	uc003dyw.3	P41217	OTTHUMG00000159248	ENST00000383681.3:c.-87C>A	3.37:g.112063850C>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_001004196	B3KQI1|B4DLW9|D3DN65|Q6J2Q6|Q6PIQ4|Q8TB85|Q9H3J3	Missense_Mutation	SNP	ENST00000383681.3	37		517	0.2367216117216117	60	0.12195121951219512	94	0.2596685082872928	65	0.11363636363636363	298	0.39313984168865435	C	4.367	0.067615	0.08436	0.142079	0.365233	ENSG00000091972	ENST00000315711;ENST00000473539	T;T	0.24908	1.83;1.83	6.02	4.19	0.49359	.	0.219660	0.32736	N	0.005710	T	0.00012	0.0000	N	0.16478	0.41	0.09310	P	0.9999999999999996	P;B	0.35628	0.513;0.015	B;B	0.32533	0.147;0.023	T	0.42799	-0.9430	9	0.09338	T	0.73	-4.9917	7.3101	0.26469	0.1736:0.7413:0.0:0.085	rs2272022;rs52832861;rs57361377;rs2272022	46;71	P41217-2;P41217-3	.;.	T	46;71	ENSP00000312766:P46T;ENSP00000420298:P71T	ENSP00000312766:P46T	P	+	1	0	CD200	113546540	0.599000	0.26891	0.994000	0.49952	0.260000	0.26232	0.953000	0.29162	0.831000	0.34780	0.655000	0.94253	CCT	C|0.748;A|0.252	0.252	strong		0.413	CD200-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000354080.1		
LOXHD1	125336	hgsc.bcm.edu	37	18	44149474	44149474	+	Silent	SNP	G	G	A	rs2086005	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44149474G>A	ENST00000398722.4	-	9	1340	c.1341C>T	c.(1339-1341)aaC>aaT	p.N447N	LOXHD1_ENST00000441551.2_Silent_p.N725N|LOXHD1_ENST00000536736.1_Silent_p.N725N			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	447	PLAT 4. {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						CTTTGAGGTTGTTGTCAGAGA	0.488													G|||	309	0.0617013	0.0045	0.1052	5008	,	,		21822	0.0496		0.1372	False		,,,				2504	0.0429				p.N725N		Atlas-SNP	.											.	LOXHD1	367	.	0			c.C2175T						PASS	.	G		33,1351		1,31,660	133.0	116.0	121.0		2175	0.2	1.0	18	dbSNP_96	121	506,2676		41,424,1126	no	coding-synonymous	LOXHD1	NM_144612.6		42,455,1786	AA,AG,GG		15.9019,2.3844,11.8046		725/2212	44149474	539,4027	692	1591	2283	SO:0001819	synonymous_variant	125336	exon16			GAGGTTGTTGTCA	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.1341C>T	18.37:g.44149474G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000398722.4	37		173	0.07921245421245421	3	0.006097560975609756	44	0.12154696132596685	29	0.050699300699300696	97	0.1279683377308707	G	9.503	1.103818	0.20632	0.023844	0.159019	ENSG00000167210	ENST00000441551	.	.	.	5.66	0.187	0.15109	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6151	0.51086	0.4543:0.0:0.5456:0.0	rs2086005;rs2086005	.	.	.	X	706	.	.	Q	-	1	0	LOXHD1	42403472	0.995000	0.38212	0.997000	0.53966	0.988000	0.76386	0.430000	0.21428	0.082000	0.17018	0.655000	0.94253	CAA	G|0.917;A|0.083	0.083	strong		0.488	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
ZFP36L2	678	hgsc.bcm.edu	37	2	43452334	43452334	+	Silent	SNP	G	G	A	rs397823004|rs8098	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:43452334G>A	ENST00000282388.3	-	2	902	c.609C>T	c.(607-609)atC>atT	p.I203I	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	203	RNA-binding.				cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				GGCAGAAGCCGATGGTATGAA	0.672													G|||	576	0.115016	0.2141	0.0519	5008	,	,		13494	0.003		0.0676	False		,,,				2504	0.1902				p.I203I		Atlas-SNP	.											.	ZFP36L2	56	.	0			c.C609T						PASS	.	G		842,3564	312.2+/-292.5	92,658,1453	31.0	29.0	30.0		609	0.6	1.0	2	dbSNP_52	30	618,7982	156.7+/-210.5	24,570,3706	no	coding-synonymous	ZFP36L2	NM_006887.4		116,1228,5159	AA,AG,GG		7.186,19.1103,11.2256		203/495	43452334	1460,11546	2203	4300	6503	SO:0001819	synonymous_variant	678	exon2			GAAGCCGATGGTA	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"""RING-type (C3HC4) zinc fingers"""	1108	protein-coding gene	gene with protein product		612053	"""zinc finger protein 36, C3H type-like 1"", ""zinc finger protein 36, C3H type-like 2"""	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.609C>T	2.37:g.43452334G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_006887	Q53TB4|Q9BSJ3	Silent	SNP	ENST00000282388.3	37	CCDS1811.1																																																																																			G|0.886;A|0.114	0.114	strong		0.672	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887	
SPNS3	201305	hgsc.bcm.edu	37	17	4352636	4352636	+	Missense_Mutation	SNP	G	G	A	rs34457931	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4352636G>A	ENST00000355530.2	+	7	1157	c.877G>A	c.(877-879)Ggg>Agg	p.G293R	SPNS3_ENST00000576069.1_Intron|SPNS3_ENST00000333476.2_Missense_Mutation_p.G166R	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	293			G -> R (in dbSNP:rs34457931). {ECO:0000269|PubMed:14702039}.		lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						CGTGGTTCACGGGCTGCAGCC	0.682													g|||	481	0.0960463	0.0159	0.1138	5008	,	,		15672	0.0694		0.1372	False		,,,				2504	0.1769				p.G293R		Atlas-SNP	.											.	SPNS3	52	.	0			c.G877A						PASS	.		ARG/GLY	149,4257	103.4+/-141.9	3,143,2057	51.0	45.0	47.0		877	2.9	0.4	17	dbSNP_126	47	1055,7545	221.9+/-259.1	71,913,3316	yes	missense	SPNS3	NM_182538.4	125	74,1056,5373	AA,AG,GG		12.2674,3.3818,9.2573	benign	293/513	4352636	1204,11802	2203	4300	6503	SO:0001583	missense	201305	exon7			GTTCACGGGCTGC		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.877G>A	17.37:g.4352636G>A	ENSP00000347721:p.Gly293Arg	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	42	12	0.285714	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	37	CCDS11045.1	195	0.08928571428571429	4	0.008130081300813009	49	0.13535911602209943	40	0.06993006993006994	102	0.1345646437994723	g	14.56	2.572599	0.45798	0.033818	0.122674	ENSG00000182557	ENST00000355530;ENST00000333476	T;T	0.71579	-0.58;-0.58	5.05	2.94	0.34122	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.01156	0.0038	M	0.70903	2.155	0.30053	P	0.811621	D;P	0.60160	0.987;0.801	P;B	0.50049	0.629;0.362	T	0.38415	-0.9662	9	0.33940	T	0.23	-16.8041	5.8944	0.18931	0.1814:0.16:0.6585:0.0	rs34457931	166;293	Q6ZMD2-2;Q6ZMD2	.;SPNS3_HUMAN	R	293;166	ENSP00000347721:G293R;ENSP00000333207:G166R	ENSP00000333207:G166R	G	+	1	0	SPNS3	4299385	1.000000	0.71417	0.415000	0.26534	0.465000	0.32709	3.821000	0.55700	1.253000	0.44018	0.651000	0.88453	GGG	G|0.906;A|0.094	0.094	strong		0.682	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
DNAI2	64446	hgsc.bcm.edu	37	17	72301432	72301432	+	Silent	SNP	A	A	G	rs8073660	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72301432A>G	ENST00000311014.6	+	9	1129	c.1062A>G	c.(1060-1062)gaA>gaG	p.E354E	AC103809.1_ENST00000516976.1_RNA|DNAI2_ENST00000446837.2_Silent_p.E354E|DNAI2_ENST00000579490.1_Silent_p.E411E|RP11-647F2.2_ENST00000585167.1_RNA|DNAI2_ENST00000582036.1_Silent_p.E354E|DNAI2_ENST00000307504.5_Silent_p.E211E			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	354					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						CGTCAGCTGAAAAGATTGTGT	0.592									Kartagener syndrome				G|||	1997	0.398762	0.2965	0.3732	5008	,	,		18768	0.254		0.6103	False		,,,				2504	0.4867				p.E354E		Atlas-SNP	.											.	DNAI2	102	.	0			c.A1062G						PASS	.	G	,	1607,2799	664.0+/-401.3	316,975,912	107.0	87.0	94.0		1062,1062	5.0	1.0	17	dbSNP_116	94	5345,3255	489.4+/-372.6	1675,1995,630	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	1991,2970,1542	GG,GA,AA		37.8488,36.473,46.5477	,	354/594,354/606	72301432	6952,6054	2203	4300	6503	SO:0001819	synonymous_variant	64446	exon9	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGCTGAAAAGATT	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"""Axonemal dyneins"", ""WD repeat domain containing"""	18744	protein-coding gene	gene with protein product	"""dynein intermediate chain 2"""	605483	"""dynein, axonemal, intermediate polypeptide 2"""			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.1062A>G	17.37:g.72301432A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			A|0.535;G|0.465	0.465	strong		0.592	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
AQP1	358	hgsc.bcm.edu	37	7	30961790	30961790	+	Missense_Mutation	SNP	G	G	A	rs28362731	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:30961790G>A	ENST00000311813.4	+	2	549	c.494G>A	c.(493-495)gGt>gAt	p.G165D	AQP1_ENST00000482461.1_3'UTR|AQP1_ENST00000409611.1_Missense_Mutation_p.G114D|AQP1_ENST00000434909.2_Missense_Mutation_p.G225D|AQP1_ENST00000441328.2_Missense_Mutation_p.G82D|AQP1_ENST00000409899.1_Missense_Mutation_p.G50D|AQP1_ENST00000509504.1_Missense_Mutation_p.G342D	NM_198098.2	NP_932766.1	P29972	AQP1_HUMAN	aquaporin 1 (Colton blood group)	165			G -> D (in dbSNP:rs28362731). {ECO:0000269|Ref.6}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|bicarbonate transport (GO:0015701)|camera-type eye morphogenesis (GO:0048593)|carbon dioxide transmembrane transport (GO:0035378)|carbon dioxide transport (GO:0015670)|cation transmembrane transport (GO:0098655)|cell volume homeostasis (GO:0006884)|cellular homeostasis (GO:0019725)|cellular hyperosmotic response (GO:0071474)|cellular response to cAMP (GO:0071320)|cellular response to copper ion (GO:0071280)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to inorganic substance (GO:0071241)|cellular response to mechanical stimulus (GO:0071260)|cellular response to mercury ion (GO:0071288)|cellular response to nitric oxide (GO:0071732)|cellular response to retinoic acid (GO:0071300)|cellular response to salt stress (GO:0071472)|cellular response to stress (GO:0033554)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|cGMP biosynthetic process (GO:0006182)|corticotropin secretion (GO:0051458)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|glomerular filtration (GO:0003094)|glycerol transport (GO:0015793)|hyperosmotic salinity response (GO:0042538)|lateral ventricle development (GO:0021670)|lipid digestion (GO:0044241)|maintenance of symbiont-containing vacuole by host (GO:0085018)|metanephric descending thin limb development (GO:0072220)|metanephric glomerulus vasculature development (GO:0072239)|metanephric proximal convoluted tubule segment 2 development (GO:0072232)|metanephric proximal straight tubule development (GO:0072230)|multicellular organismal water homeostasis (GO:0050891)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|nitric oxide transport (GO:0030185)|odontogenesis (GO:0042476)|pancreatic juice secretion (GO:0030157)|positive regulation of angiogenesis (GO:0045766)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of saliva secretion (GO:0046878)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|renal water absorption (GO:0070295)|renal water transport (GO:0003097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|secretory granule organization (GO:0033363)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)|transepithelial water transport (GO:0035377)|transmembrane transport (GO:0055085)|water transport (GO:0006833)|wound healing (GO:0042060)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon terminus (GO:0043679)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|symbiont-containing vacuole (GO:0020003)	ammonium transmembrane transporter activity (GO:0008519)|carbon dioxide transmembrane transporter activity (GO:0035379)|glycerol transmembrane transporter activity (GO:0015168)|intracellular cGMP activated cation channel activity (GO:0005223)|nitric oxide transmembrane transporter activity (GO:0030184)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)|transmembrane transporter activity (GO:0022857)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			kidney(1)|large_intestine(2)|lung(9)	12		Melanoma(862;0.16)			Acetazolamide(DB00819)	CGTGACCTTGGTGGCTCAGCC	0.672													G|||	108	0.0215655	0.0015	0.0389	5008	,	,		14449	0.0		0.0437	False		,,,				2504	0.0358				p.G165D		Atlas-SNP	.											.	AQP1	38	.	0			c.G494A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	42,4364	44.6+/-78.6	1,40,2162	64.0	57.0	60.0		245,341,149,494	4.5	0.7	7	dbSNP_125	60	362,8238	120.6+/-179.8	7,348,3945	yes	missense,missense,missense,missense	AQP1	NM_001185060.1,NM_001185061.1,NM_001185062.1,NM_198098.2	94,94,94,94	8,388,6107	AA,AG,GG		4.2093,0.9532,3.1063	,,,	82/187,114/219,50/155,165/270	30961790	404,12602	2203	4300	6503	SO:0001583	missense	358	exon2			ACCTTGGTGGCTC	M77829	CCDS5431.1, CCDS55096.1, CCDS55097.1, CCDS55098.1	7p14	2014-07-19	2014-01-02		ENSG00000240583	ENSG00000240583		"""Ion channels / Aquaporins"", ""Blood group antigens"""	633	protein-coding gene	gene with protein product		107776	"""Colton blood group"", ""aquaporin 1 (channel-forming integral protein, 28kDa)"", ""aquaporin 1 (channel-forming integral protein, 28kDa, CO blood group)"", ""aquaporin 1"""	CO		1722319, 3166547	Standard	NM_198098		Approved	CHIP28		P29972	OTTHUMG00000023944	ENST00000311813.4:c.494G>A	7.37:g.30961790G>A	ENSP00000311165:p.Gly165Asp	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	42	29	0.690476	NM_198098	B5BU39|E7EM69|E9PC21|F5GY19|Q8TBI5|Q8TDC1	Missense_Mutation	SNP	ENST00000311813.4	37	CCDS5431.1	39	0.017857142857142856	0	0.0	13	0.03591160220994475	0	0.0	26	0.03430079155672823	G	10.56	1.385791	0.25031	0.009532	0.042093	ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000240583;ENSG00000250424	ENST00000434909;ENST00000265298;ENST00000311813;ENST00000413400;ENST00000441328;ENST00000409899;ENST00000409611;ENST00000509504	D;D;D;D;D;D	0.84660	-1.88;-1.88;-1.88;-1.88;-1.88;-1.88	5.45	4.52	0.55395	Aquaporin-like (2);	0.449907	0.24970	N	0.034158	T	0.56352	0.1979	L	0.35341	1.055	0.09310	N	1	P;P;P;P	0.51057	0.926;0.941;0.627;0.511	P;P;P;B	0.51742	0.678;0.603;0.453;0.155	T	0.63233	-0.6683	10	0.12103	T	0.63	2.6832	13.4995	0.61445	0.0:0.2415:0.7585:0.0	rs28362731;rs28362731	225;114;50;165	B4E220;E7EM69;E9PC21;P29972	.;.;.;AQP1_HUMAN	D	225;70;165;150;82;50;114;342	ENSP00000395059:G225D;ENSP00000311165:G165D;ENSP00000405698:G82D;ENSP00000386712:G50D;ENSP00000387178:G114D;ENSP00000421315:G342D	ENSP00000265298:G70D	G	+	2	0	RP5-877J2.1;AQP1	30928315	0.000000	0.05858	0.659000	0.29680	0.609000	0.37215	0.719000	0.25881	2.569000	0.86673	0.561000	0.74099	GGT	G|0.972;A|0.028	0.028	strong		0.672	AQP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215002.3	NM_000385	
NPHS1	4868	hgsc.bcm.edu	37	19	36342212	36342212	+	Missense_Mutation	SNP	C	C	T	rs3814995	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36342212C>T	ENST00000378910.5	-	3	348	c.349G>A	c.(349-351)Gag>Aag	p.E117K	NPHS1_ENST00000353632.6_Missense_Mutation_p.E117K|NPHS1_ENST00000591817.1_5'Flank	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	117	Ig-like C2-type 1.		E -> K (in dbSNP:rs3814995). {ECO:0000269|PubMed:11317351, ECO:0000269|PubMed:19309778, ECO:0000269|PubMed:22009864, ECO:0000269|PubMed:9915943}.		cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GGCCCCATCTCAGAGCGGCCG	0.637													C|||	1462	0.291933	0.056	0.3444	5008	,	,		17564	0.5982		0.3111	False		,,,				2504	0.2382				p.E117K		Atlas-SNP	.											.	NPHS1	165	.	0			c.G349A						PASS	.	C	LYS/GLU	405,4001	196.7+/-221.0	16,373,1814	33.0	34.0	34.0		349	5.9	0.7	19	dbSNP_107	34	2628,5972	418.3+/-352.7	402,1824,2074	yes	missense	NPHS1	NM_004646.3	56	418,2197,3888	TT,TC,CC		30.5581,9.192,23.32	possibly-damaging	117/1242	36342212	3033,9973	2203	4300	6503	SO:0001583	missense	4868	exon3			CCATCTCAGAGCG		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.349G>A	19.37:g.36342212C>T	ENSP00000368190:p.Glu117Lys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	738	0.33791208791208793	36	0.07317073170731707	101	0.27900552486187846	359	0.6276223776223776	242	0.31926121372031663	C	18.75	3.690627	0.68271	0.09192	0.305581	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.65916	-0.18;-0.18	5.92	5.92	0.95590	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);	0.059087	0.64402	D	0.000003	T	0.00012	0.0000	L	0.39514	1.22	0.09310	P	0.99999864835	D	0.76494	0.999	D	0.71414	0.973	T	0.28459	-1.0043	9	0.06236	T	0.91	-23.6864	17.8963	0.88890	0.0:1.0:0.0:0.0	rs3814995;rs3814995	117	O60500	NPHN_HUMAN	K	117	ENSP00000368190:E117K;ENSP00000343634:E117K	ENSP00000343634:E117K	E	-	1	0	NPHS1	41034052	0.978000	0.34361	0.706000	0.30403	0.004000	0.04260	2.555000	0.45854	2.828000	0.97474	0.650000	0.86243	GAG	C|0.735;T|0.265	0.265	strong		0.637	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
CCDC114	93233	hgsc.bcm.edu	37	19	48807367	48807367	+	Silent	SNP	C	C	A	rs28582401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48807367C>A	ENST00000315396.7	-	7	1267	c.585G>T	c.(583-585)ctG>ctT	p.L195L		NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	195					outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		CGCGCTCCCGCAGCAAGCCCA	0.682													C|||	771	0.153954	0.1422	0.0965	5008	,	,		15049	0.124		0.1988	False		,,,				2504	0.1953				p.L195L		Atlas-SNP	.											.	CCDC114	100	.	0			c.G585T						PASS	.	C		744,3662	296.7+/-284.4	66,612,1525	43.0	43.0	43.0		585	-0.5	1.0	19	dbSNP_125	43	1589,7011	285.2+/-297.1	159,1271,2870	no	coding-synonymous	CCDC114	NM_144577.3		225,1883,4395	AA,AC,CC		18.4767,16.8861,17.9379		195/671	48807367	2333,10673	2203	4300	6503	SO:0001819	synonymous_variant	93233	exon7			CTCCCGCAGCAAG	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.585G>T	19.37:g.48807367C>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	40	17	0.425	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Silent	SNP	ENST00000315396.7	37	CCDS12714.2																																																																																			C|0.817;A|0.183	0.183	strong		0.682	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
DRC7	84229	hgsc.bcm.edu	37	16	57741404	57741404	+	Silent	SNP	C	C	T	rs114955852	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57741404C>T	ENST00000360716.3	+	8	1112	c.891C>T	c.(889-891)caC>caT	p.H297H	CCDC135_ENST00000394337.4_Silent_p.H297H|CCDC135_ENST00000336825.8_Silent_p.H232H			Q8IY82	CC135_HUMAN		297					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				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						ATGCCCTGCACGGCCTGCGGG	0.597													t|||	38	0.00758786	0.0008	0.0043	5008	,	,		20638	0.0228		0.007	False		,,,				2504	0.0041				p.H297H		Atlas-SNP	.											.	CCDC135	97	.	0			c.C891T						PASS	.	T		2,4394		0,2,2196	51.0	53.0	52.0		891	-8.1	0.7	16	dbSNP_132	52	42,8556		0,42,4257	no	coding-synonymous	CCDC135	NM_032269.5		0,44,6453	TT,TC,CC		0.4885,0.0455,0.3386		297/875	57741404	44,12950	2198	4299	6497	SO:0001819	synonymous_variant	84229	exon7			CCTGCACGGCCTG																												ENST00000360716.3:c.891C>T	16.37:g.57741404C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_032269	A8K943|Q8NAA0|Q9H080	Silent	SNP	ENST00000360716.3	37	CCDS10787.1																																																																																			C|0.996;T|0.004	0.004	strong		0.597	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107531152	107531152	+	Missense_Mutation	SNP	G	G	C	rs10761084	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:107531152G>C	ENST00000374762.3	+	3	351	c.280G>C	c.(280-282)Gct>Cct	p.A94P	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	94			A -> P (in dbSNP:rs10761084). {ECO:0000269|PubMed:14702039}.					p.A94P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						AGATAATTTTGCTCATCGAGC	0.358													.|||	890	0.177716	0.0257	0.1455	5008	,	,		15655	0.2857		0.1769	False		,,,				2504	0.2955				p.A94P		Atlas-SNP	.											NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	1	Substitution - Missense(1)	stomach(1)	c.G280C						PASS	.	G	PRO/ALA	199,4207	124.5+/-161.8	6,187,2010	62.0	59.0	60.0		280	3.8	1.0	9	dbSNP_120	60	1633,6967	301.6+/-305.5	171,1291,2838	yes	missense	NIPSNAP3B	NM_018376.2	27	177,1478,4848	CC,CG,GG		18.9884,4.5166,14.0858	possibly-damaging	94/248	107531152	1832,11174	2203	4300	6503	SO:0001583	missense	55335	exon3			AATTTTGCTCATC	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.280G>C	9.37:g.107531152G>C	ENSP00000363894:p.Ala94Pro	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_018376	Q5VX30|Q9NUM2	Missense_Mutation	SNP	ENST00000374762.3	37	CCDS6761.1	357	0.16346153846153846	15	0.03048780487804878	60	0.16574585635359115	146	0.25524475524475526	136	0.17941952506596306	G	17.64	3.439372	0.63067	0.045166	0.189884	ENSG00000165028	ENST00000374762	T	0.50813	0.73	3.77	3.77	0.43336	Dimeric alpha-beta barrel (1);	0.060953	0.64402	U	0.000004	T	0.00039	0.0001	M	0.81239	2.535	0.20821	P	0.999845625	D	0.63880	0.993	D	0.70487	0.969	T	0.04281	-1.0963	9	0.30854	T	0.27	-6.9526	12.9916	0.58622	0.0:0.0:1.0:0.0	rs10761084;rs56447258;rs10761084	94	Q9BS92	NPS3B_HUMAN	P	94	ENSP00000363894:A94P	ENSP00000363894:A94P	A	+	1	0	NIPSNAP3B	106570973	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.087000	0.50167	2.088000	0.63022	0.650000	0.86243	GCT	G|0.846;C|0.154	0.154	strong		0.358	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376	
AHNAK2	113146	hgsc.bcm.edu	37	14	105423809	105423809	+	Missense_Mutation	SNP	G	G	A	rs76650680	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105423809G>A	ENST00000333244.5	-	3	270	c.151C>T	c.(151-153)Cgg>Tgg	p.R51W		NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	51						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCCTGCGGCCGTGGTCGAATG	0.617													G|||	75	0.014976	0.0023	0.0303	5008	,	,		19958	0.0		0.0348	False		,,,				2504	0.0164				p.R51W		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C151T						PASS	.	G	TRP/ARG	41,3879		0,41,1919	26.0	30.0	29.0		151	1.2	0.4	14	dbSNP_132	29	400,7862		6,388,3737	yes	missense	AHNAK2	NM_138420.2	101	6,429,5656	AA,AG,GG		4.8414,1.0459,3.6201	possibly-damaging	51/5796	105423809	441,11741	1960	4131	6091	SO:0001583	missense	113146	exon3			GCGGCCGTGGTCG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.151C>T	14.37:g.105423809G>A	ENSP00000353114:p.Arg51Trp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	35	0.016025641025641024	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	22	0.029023746701846966	G	11.24	1.581270	0.28180	0.010459	0.048414	ENSG00000185567	ENST00000333244	T	0.04809	3.55	3.21	1.22	0.21188	.	.	.	.	.	T	0.02230	0.0069	L	0.57536	1.79	0.19945	N	0.99994	D	0.89917	1.0	D	0.87578	0.998	T	0.05649	-1.0872	9	0.87932	D	0	.	9.7841	0.40666	0.0:0.0:0.3403:0.6597	.	51	Q8IVF2	AHNK2_HUMAN	W	51	ENSP00000353114:R51W	ENSP00000353114:R51W	R	-	1	2	AHNAK2	104494854	0.669000	0.27502	0.354000	0.25760	0.115000	0.19883	0.931000	0.28871	0.319000	0.23209	0.655000	0.94253	CGG	A|0.017;C|0.000;G|0.982	0.017	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SLC8A2	6543	hgsc.bcm.edu	37	19	47969394	47969394	+	Silent	SNP	G	G	A	rs12459087	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47969394G>A	ENST00000236877.6	-	2	662	c.267C>T	c.(265-267)atC>atT	p.I89I	SLC8A2_ENST00000539381.1_Intron|SLC8A2_ENST00000542837.1_Intron	NM_015063.2	NP_055878.1	Q9UPR5	NAC2_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 2	89					blood coagulation (GO:0007596)|cell communication (GO:0007154)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(5)|stomach(1)	31		all_cancers(25;3.05e-07)|all_lung(116;4.19e-06)|Lung NSC(112;7.16e-06)|all_epithelial(76;7.65e-06)|all_neural(266;0.0652)|Ovarian(192;0.086)|Breast(70;0.173)		OV - Ovarian serous cystadenocarcinoma(262;0.000501)|all cancers(93;0.00058)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0457)		AACGGTCGGCGATGATGGACA	0.602													G|||	311	0.0621006	0.0015	0.0634	5008	,	,		16756	0.0655		0.1054	False		,,,				2504	0.0951				p.I89I		Atlas-SNP	.											.	SLC8A2	77	.	0			c.C267T						PASS	.	G		92,4314	75.7+/-113.9	0,92,2111	118.0	82.0	94.0		267	0.8	1.0	19	dbSNP_120	94	940,7660	207.0+/-248.9	59,822,3419	no	coding-synonymous	SLC8A2	NM_015063.2		59,914,5530	AA,AG,GG		10.9302,2.0881,7.9348		89/922	47969394	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	6543	exon2			GTCGGCGATGATG	AB029010	CCDS33065.1	19q13.32	2013-07-15	2008-09-02		ENSG00000118160	ENSG00000118160		"""Solute carriers"""	11069	protein-coding gene	gene with protein product		601901				8021246	Standard	NM_015063		Approved	NCX2, KIAA1087	uc002pgx.3	Q9UPR5	OTTHUMG00000183529	ENST00000236877.6:c.267C>T	19.37:g.47969394G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	170	92	0.541176	NM_015063	B4DYQ9	Silent	SNP	ENST00000236877.6	37	CCDS33065.1																																																																																			G|0.927;A|0.073	0.073	strong		0.602	SLC8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466997.1		
ARHGEF25	115557	hgsc.bcm.edu	37	12	58010163	58010163	+	Missense_Mutation	SNP	A	A	G	rs57224884|rs1564374	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:58010163A>G	ENST00000286494.4	+	14	1977	c.1517A>G	c.(1516-1518)cAg>cGg	p.Q506R	AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000593846.1_RNA|ARHGEF25_ENST00000333972.7_Missense_Mutation_p.Q545R|AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000610219.1_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	506			Q -> R (in dbSNP:rs1564374). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						GGAAGAATTCAGCTTGGAGAT	0.617													G|||	3156	0.630192	0.5197	0.6657	5008	,	,		16921	0.7222		0.5527	False		,,,				2504	0.7393				p.Q545R		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.A1634G						PASS	.	G	ARG/GLN,ARG/GLN	2353,2053		632,1089,482	74.0	73.0	73.0		1634,1517	3.7	0.4	12	dbSNP_88	73	4851,3749		1381,2089,830	yes	missense,missense	ARHGEF25	NM_001111270.1,NM_182947.2	43,43	2013,3178,1312	GG,GA,AA		43.593,46.5956,44.6102	benign,benign	545/620,506/581	58010163	7204,5802	2203	4300	6503	SO:0001583	missense	115557	exon15			GAATTCAGCTTGG		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"""Rho guanine nucleotide exchange factors"""	30275	protein-coding gene	gene with protein product	"""RAC/CDC42 exchange factor"""	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1517A>G	12.37:g.58010163A>G	ENSP00000286494:p.Gln506Arg	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	37	CCDS8947.1	1398	0.6401098901098901	284	0.5772357723577236	222	0.6132596685082873	453	0.791958041958042	439	0.579155672823219	N	0.006	-2.114913	0.00349	0.534044	0.56407	ENSG00000240771	ENST00000333972;ENST00000286494	T;T	0.37411	1.23;1.2	4.56	3.66	0.41972	.	0.252152	0.21027	N	0.081419	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39961	-0.9588	9	0.02654	T	1	.	7.6461	0.28321	0.1977:0.0:0.8023:0.0	rs1564374;rs17856409;rs17857334;rs56537767;rs1564374	545;506	F8W7Z4;Q86VW2	.;ARHGP_HUMAN	R	545;506	ENSP00000335560:Q545R;ENSP00000286494:Q506R	ENSP00000286494:Q506R	Q	+	2	0	ARHGEF25	56296430	0.247000	0.23920	0.431000	0.26735	0.122000	0.20287	0.321000	0.19558	0.659000	0.30945	-0.128000	0.14901	CAG	A|0.402;G|0.598;T|0.000	0.598	strong		0.617	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483	
CCDC18	343099	hgsc.bcm.edu	37	1	93720070	93720070	+	Missense_Mutation	SNP	C	C	G	rs12030843	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:93720070C>G	ENST00000343253.7	+	24	3740	c.3238C>G	c.(3238-3240)Ctt>Gtt	p.L1080V	CCDC18_ENST00000557479.1_Missense_Mutation_p.L1199V|CCDC18_ENST00000401026.3_Missense_Mutation_p.L1081V|CCDC18_ENST00000338949.4_3'UTR|CCDC18_ENST00000334652.5_3'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	1080										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		TAAAGAACAGCTTCGAGAAAA	0.279													C|||	1163	0.232228	0.1974	0.2392	5008	,	,		19962	0.3175		0.1511	False		,,,				2504	0.2699				p.L1081V		Atlas-SNP	.											.	CCDC18	93	.	0			c.C3241G						PASS	.	C	VAL/LEU	670,2966		61,548,1209	73.0	72.0	73.0		3241	4.2	1.0	1	dbSNP_120	73	1335,6811		128,1079,2866	yes	missense	CCDC18	NM_206886.3	32	189,1627,4075	GG,GC,CC		16.3884,18.4268,17.0175	probably-damaging	1081/1300	93720070	2005,9777	1818	4073	5891	SO:0001583	missense	343099	exon24			GAACAGCTTCGAG			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.3238C>G	1.37:g.93720070C>G	ENSP00000343377:p.Leu1080Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		467|467	0.21382783882783882|0.21382783882783882	91|91	0.18495934959349594|0.18495934959349594	84|84	0.23204419889502761|0.23204419889502761	172|172	0.3006993006993007|0.3006993006993007	120|120	0.158311345646438|0.158311345646438	C|C	15.69|15.69	2.909205|2.909205	0.52439|0.52439	0.184268|0.184268	0.163884|0.163884	ENSG00000122483|ENSG00000122483	ENST00000343253;ENST00000401026;ENST00000557479|ENST00000370276	T;T|.	0.78595|.	-1.19;-1.19|.	5.15|5.15	4.22|4.22	0.49857|0.49857	.|.	0.070956|.	0.56097|.	D|.	0.000040|.	T|T	0.48370|0.48370	0.1496|0.1496	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	P|P	0.9999999999999999|0.9999999999999999	P|.	0.35107|.	0.484|.	B|.	0.37267|.	0.245|.	T|T	0.49916|0.49916	-0.8888|-0.8888	9|4	0.39692|.	T|.	0.17|.	.|.	13.6901|13.6901	0.62539|0.62539	0.2993:0.7007:0.0:0.0|0.2993:0.7007:0.0:0.0	rs12030843;rs52792110;rs12030843|rs12030843;rs52792110;rs12030843	1199|.	G3V388|.	.|.	V|R	1080;1081;1199|1133	ENSP00000383808:L1081V;ENSP00000451099:L1199V|.	ENSP00000343377:L1080V|.	L|S	+|+	1|3	0|2	CCDC18|CCDC18	93492658|93492658	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	1.164000|1.164000	0.31810|0.31810	1.239000|1.239000	0.43787|0.43787	-0.410000|-0.410000	0.06199|0.06199	CTT|AGC	C|0.809;G|0.191	0.191	strong		0.279	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
MICB	4277	hgsc.bcm.edu	37	6	31473957	31473957	+	Missense_Mutation	SNP	C	C	G	rs3134900	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31473957C>G	ENST00000252229.6	+	3	442	c.363C>G	c.(361-363)atC>atG	p.I121M	MICB_ENST00000538442.1_Missense_Mutation_p.I89M|MICB_ENST00000399150.3_Intron	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						TCTGTGAGATCCATGAAGACA	0.562													c|||	385	0.076877	0.1188	0.0447	5008	,	,		17796	0.0685		0.0895	False		,,,				2504	0.0389				p.I121M		Atlas-SNP	.											MICB,NS,neuroblastoma,0,2	MICB	26	2	0			c.C363G						PASS	.	-	MET/ILE	479,3385		32,415,1485	28.0	30.0	30.0		363	1.4	0.0	6	dbSNP_103	30	975,7281		62,851,3215	no	missense	MICB	NM_005931.3	10	94,1266,4700	GG,GC,CC		11.8096,12.3965,11.9967	probably-damaging	121/384	31473957	1454,10666	1932	4128	6060	SO:0001583	missense	4277	exon3			TGAGATCCATGAA		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"""Immunoglobulin superfamily / C1-set domain containing"""	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.363C>G	6.37:g.31473957C>G	ENSP00000252229:p.Ile121Met	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	116	94	0.810345	NM_005931		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	162	0.07417582417582418	53	0.10772357723577236	14	0.03867403314917127	26	0.045454545454545456	69	0.09102902374670185	N	8.773	0.926504	0.18056	0.123965	0.118096	ENSG00000204516	ENST00000538442;ENST00000252229	T;T	0.00856	5.61;5.61	2.33	1.44	0.22558	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.455993	0.16197	U	0.225128	T	0.01421	0.0046	M	0.69823	2.125	0.80722	P	0.0	D;D	0.76494	0.991;0.999	D;D	0.87578	0.994;0.998	T	0.48917	-0.8992	9	0.59425	D	0.04	.	3.8543	0.08968	0.0:0.5964:0.2512:0.1524	rs3134900	89;121	F5H7Q8;Q29980	.;MICB_HUMAN	M	89;121	ENSP00000442345:I89M;ENSP00000252229:I121M	ENSP00000252229:I121M	I	+	3	3	MICB	31581936	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.976000	0.03786	0.543000	0.28864	-0.755000	0.03482	ATC	C|0.918;G|0.082	0.082	strong		0.562	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931	
PLEC	5339	hgsc.bcm.edu	37	8	145001031	145001031	+	Missense_Mutation	SNP	T	T	C	rs55895668	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145001031T>C	ENST00000322810.4	-	30	4545	c.4376A>G	c.(4375-4377)cAc>cGc	p.H1459R	PLEC_ENST00000354589.3_Missense_Mutation_p.H1322R|PLEC_ENST00000357649.2_Missense_Mutation_p.H1326R|PLEC_ENST00000436759.2_Missense_Mutation_p.H1349R|PLEC_ENST00000354958.2_Missense_Mutation_p.H1300R|PLEC_ENST00000527096.1_Missense_Mutation_p.H1345R|PLEC_ENST00000345136.3_Missense_Mutation_p.H1322R|PLEC_ENST00000356346.3_Missense_Mutation_p.H1308R|PLEC_ENST00000398774.2_Missense_Mutation_p.H1290R	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1459	Globular 1.		H -> R (in dbSNP:rs55895668).		apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.H1349R(1)|p.H1459R(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CTCGCTGTAGTGCGTACGCAG	0.622													C|||	2337	0.466653	0.8782	0.3674	5008	,	,		15191	0.1429		0.4344	False		,,,				2504	0.3476				p.H1459R		Atlas-SNP	.											PLEC_ENST00000436759,NS,carcinoma,0,2	PLEC	1144	2	2	Substitution - Missense(2)	stomach(2)	c.A4376G						scavenged	.	C	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	3556,766		1479,598,84	106.0	116.0	112.0		3965,3977,3965,3869,4376,3899,3923,4046	3.9	0.9	8	dbSNP_129	112	3666,4872		820,2026,1423	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_201384.1,NM_201383.1,NM_201382.2,NM_201381.1,NM_201380.2,NM_201379.1,NM_201378.2,NM_000445.3	29,29,29,29,29,29,29,29	2299,2624,1507	CC,CT,TT		42.9375,17.7233,43.8414	benign,benign,benign,benign,benign,benign,benign,benign	1322/4548,1326/4552,1322/4548,1290/4516,1459/4685,1300/4526,1308/4534,1349/4575	145001031	7222,5638	2161	4269	6430	SO:0001583	missense	5339	exon30			CTGTAGTGCGTAC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.4376A>G	8.37:g.145001031T>C	ENSP00000323856:p.His1459Arg	Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	974|974	0.445970695970696|0.445970695970696	421|421	0.8556910569105691|0.8556910569105691	137|137	0.3784530386740331|0.3784530386740331	94|94	0.16433566433566432|0.16433566433566432	322|322	0.42480211081794195|0.42480211081794195	C|C	8.506|8.506	0.865407|0.865407	0.17250|0.17250	0.822767|0.822767	0.429375|0.429375	ENSG00000178209|ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096|ENST00000527303	T;T;T;T;T;T;T;T;T|.	0.26810|.	1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71;1.71|.	4.79|4.79	3.9|3.9	0.45041|0.45041	.|.	0.084010|.	0.44688|.	N|.	0.000425|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00170|0.00170	-1.935|-1.935	0.47819|0.47819	P|P	4.709999999999992E-4|4.709999999999992E-4	B;B;B;B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0|.	T|T	0.29882|0.29882	-0.9997|-0.9997	9|4	0.02654|.	T|.	1|.	.|.	7.4776|7.4776	0.27385|0.27385	0.0:0.697:0.0:0.303|0.0:0.697:0.0:0.303	rs55895668;rs61296353;rs62522551|rs55895668;rs61296353;rs62522551	1349;1308;1300;1459;1290;1322;1326;1322|.	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4|.	.;.;.;PLEC_HUMAN;.;.;.;.|.	R|A	1322;1326;1322;1290;1459;1300;1308;1349;1345|19	ENSP00000344848:H1322R;ENSP00000350277:H1326R;ENSP00000346602:H1322R;ENSP00000381756:H1290R;ENSP00000323856:H1459R;ENSP00000347044:H1300R;ENSP00000348702:H1308R;ENSP00000388180:H1349R;ENSP00000434583:H1345R|.	ENSP00000323856:H1459R|.	H|T	-|-	2|1	0|0	PLEC|PLEC	145073019|145073019	0.981000|0.981000	0.34729|0.34729	0.870000|0.870000	0.34147|0.34147	0.410000|0.410000	0.31052|0.31052	1.623000|1.623000	0.37008|0.37008	1.009000|1.009000	0.39289|0.39289	-0.380000|-0.380000	0.06706|0.06706	CAC|ACT	T|0.550;C|0.450	0.450	strong		0.622	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
FAHD1	81889	hgsc.bcm.edu	37	16	1877698	1877698	+	Silent	SNP	C	C	G	rs3743852	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1877698C>G	ENST00000427358.2	+	1	474	c.468C>G	c.(466-468)ctC>ctG	p.L156L	HAGH_ENST00000566709.1_5'Flank|FAHD1_ENST00000382668.4_Silent_p.L156L|HAGH_ENST00000455446.2_5'Flank|FAHD1_ENST00000382666.4_Silent_p.L156L|HAGH_ENST00000397353.2_5'Flank|HAGH_ENST00000397356.3_5'Flank	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	156						cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)			NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						ACGGCGAACTCAGACAGGAGG	0.507													C|||	588	0.117412	0.1006	0.0908	5008	,	,		20959	0.1042		0.1342	False		,,,				2504	0.1554				p.L156L		Atlas-SNP	.											FAHD1,colon,carcinoma,0,1	FAHD1	18	1	0			c.C468G						PASS	.	C	,,	446,3952	212.8+/-232.6	18,410,1771	62.0	49.0	53.0		468,468,468	1.2	1.0	16	dbSNP_107	53	1172,7428	239.3+/-270.5	91,990,3219	no	coding-synonymous,coding-synonymous,coding-synonymous	FAHD1	NM_001018104.2,NM_001142398.1,NM_031208.3	,,	109,1400,4990	GG,GC,CC		13.6279,10.141,12.4481	,,	156/249,156/227,156/225	1877698	1618,11380	2199	4300	6499	SO:0001819	synonymous_variant	81889	exon1			CGAACTCAGACAG	BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 36"""	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.468C>G	16.37:g.1877698C>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_031208	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Silent	SNP	ENST00000427358.2	37	CCDS10448.1																																																																																			C|0.878;G|0.122	0.122	strong		0.507	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104	
GUCA1B	2979	hgsc.bcm.edu	37	6	42162388	42162388	+	Silent	SNP	A	A	G	rs3749921	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42162388A>G	ENST00000230361.3	-	1	266	c.171T>C	c.(169-171)taT>taC	p.Y57Y		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	57	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				body fluid secretion (GO:0007589)|cell-cell signaling (GO:0007267)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			large_intestine(3)|lung(3)|skin(2)	8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)			TGCCCTCTACATACTGGGAGG	0.552													A|||	2929	0.584864	0.2035	0.6354	5008	,	,		19260	0.8204		0.6372	False		,,,				2504	0.7679				p.Y57Y		Atlas-SNP	.											.	GUCA1B	19	.	0			c.T171C						PASS	.	A		1380,3026	455.9+/-351.1	216,948,1039	116.0	96.0	103.0		171	-7.9	0.1	6	dbSNP_107	103	5303,3297	646.2+/-400.2	1613,2077,610	no	coding-synonymous	GUCA1B	NM_002098.5		1829,3025,1649	GG,GA,AA		38.3372,31.3209,48.616		57/201	42162388	6683,6323	2203	4300	6503	SO:0001819	synonymous_variant	2979	exon1			CTCTACATACTGG	AF173227	CCDS4865.1	6p21.1	2013-02-14			ENSG00000112599	ENSG00000112599		"""EF-hand domain containing"""	4679	protein-coding gene	gene with protein product		602275				9119368	Standard	NM_002098		Approved	GCAP2, RP48	uc003orz.3	Q9UMX6	OTTHUMG00000014697	ENST00000230361.3:c.171T>C	6.37:g.42162388A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_002098	Q9NU15	Silent	SNP	ENST00000230361.3	37	CCDS4865.1																																																																																			A|0.459;G|0.541	0.541	strong		0.552	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098	
DPCD	25911	hgsc.bcm.edu	37	10	103368654	103368654	+	Missense_Mutation	SNP	T	T	C	rs7006	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:103368654T>C	ENST00000370151.4	+	5	516	c.467T>C	c.(466-468)tTg>tCg	p.L156S	DPCD_ENST00000370148.2_Missense_Mutation_p.C170R|DPCD_ENST00000370147.1_Missense_Mutation_p.C170R|FBXW4_ENST00000470093.1_5'Flank	NM_015448.1	NP_056263.1	Q9BVM2	DPCD_HUMAN	deleted in primary ciliary dyskinesia homolog (mouse)	156			L -> S (in dbSNP:rs7006). {ECO:0000269|PubMed:14630615, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		determination of left/right symmetry (GO:0007368)|epithelial cilium movement (GO:0003351)|lateral ventricle development (GO:0021670)|left/right pattern formation (GO:0060972)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)	nucleus (GO:0005634)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)	5						GATGACGCCTTGCTGAGCTTT	0.537													T|||	1138	0.227236	0.2882	0.2233	5008	,	,		21971	0.1637		0.3111	False		,,,				2504	0.1268				p.L156S		Atlas-SNP	.											.	DPCD	15	.	0			c.T467C						PASS	.	T	SER/LEU	1354,3052	450.8+/-349.5	195,964,1044	211.0	189.0	196.0		467	-0.6	0.1	10	dbSNP_52	196	2639,5961	426.7+/-355.4	422,1795,2083	yes	missense	DPCD	NM_015448.1	145	617,2759,3127	CC,CT,TT		30.686,30.7308,30.7012	benign	156/204	103368654	3993,9013	2203	4300	6503	SO:0001583	missense	25911	exon5			ACGCCTTGCTGAG		CCDS7514.1	10q24.32	2012-05-03			ENSG00000166171	ENSG00000166171			24542	protein-coding gene	gene with protein product						14630615	Standard	NM_015448		Approved	DKFZP566F084, RP11-529I10.4	uc001ktn.3	Q9BVM2	OTTHUMG00000018934	ENST00000370151.4:c.467T>C	10.37:g.103368654T>C	ENSP00000359170:p.Leu156Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_015448	A8K289|Q6QNL3|Q8N5R1|Q9UFY6	Missense_Mutation	SNP	ENST00000370151.4	37	CCDS7514.1	551|551	0.2522893772893773|0.2522893772893773	157|157	0.31910569105691056|0.31910569105691056	84|84	0.23204419889502761|0.23204419889502761	79|79	0.1381118881118881|0.1381118881118881	231|231	0.30474934036939316|0.30474934036939316	T|T	16.00|16.00	2.997571|2.997571	0.54147|0.54147	0.307308|0.307308	0.30686|0.30686	ENSG00000166171|ENSG00000166171	ENST00000370147;ENST00000370148|ENST00000370151	T;T|T	0.47869|0.28069	0.83;0.83|1.63	5.93|5.93	-0.552|-0.552	0.11818|0.11818	.|.	.|0.444204	.|0.25241	.|N	.|0.032083	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.12182|0.12182	0.205|0.205	0.22693|0.22693	P|P	0.99884019|0.99884019	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.44406|0.44406	-0.9330|-0.9330	6|9	0.87932|0.07990	D|T	0|0.79	-14.2862|-14.2862	10.3322|10.3322	0.43829|0.43829	0.0:0.5911:0.0:0.4089|0.0:0.5911:0.0:0.4089	rs7006;rs1047015;rs3187013;rs52814802;rs56505439;rs60202911;rs7006|rs7006;rs1047015;rs3187013;rs52814802;rs56505439;rs60202911;rs7006	.|156	.|Q9BVM2	.|DPCD_HUMAN	R|S	170|156	ENSP00000359166:C170R;ENSP00000359167:C170R|ENSP00000359170:L156S	ENSP00000359166:C170R|ENSP00000359170:L156S	C|L	+|+	1|2	0|0	DPCD|DPCD	103358644|103358644	0.055000|0.055000	0.20627|0.20627	0.079000|0.079000	0.20413|0.20413	0.768000|0.768000	0.43524|0.43524	0.568000|0.568000	0.23623|0.23623	-0.384000|-0.384000	0.07845|0.07845	-0.366000|-0.366000	0.07423|0.07423	TGC|TTG	T|0.720;C|0.280	0.280	strong		0.537	DPCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049958.2		
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 GAIIx	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	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	234	125	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	
MPP3	4356	hgsc.bcm.edu	37	17	41901366	41901366	+	Missense_Mutation	SNP	G	G	T	rs189143886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:41901366G>T	ENST00000398389.4	-	10	782	c.617C>A	c.(616-618)tCc>tAc	p.S206Y	MPP3_ENST00000398393.1_Missense_Mutation_p.S231Y	NM_001932.4	NP_001923.2	Q13368	MPP3_HUMAN	membrane protein, palmitoylated 3 (MAGUK p55 subfamily member 3)	206	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)	guanylate kinase activity (GO:0004385)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Breast(137;0.00394)		BRCA - Breast invasive adenocarcinoma(366;0.119)		GGATCCCTGGGACTGGGCCTG	0.532													G|||	3	0.000599042	0.0	0.0014	5008	,	,		16890	0.0		0.002	False		,,,				2504	0.0				p.S206Y		Atlas-SNP	.											.	MPP3	42	.	0			c.C617A						PASS	.	G	TYR/SER	7,3835		0,7,1914	120.0	123.0	122.0		617	4.7	1.0	17		122	61,8201		0,61,4070	yes	missense	MPP3	NM_001932.4	144	0,68,5984	TT,TG,GG		0.7383,0.1822,0.5618	probably-damaging	206/586	41901366	68,12036	1921	4131	6052	SO:0001583	missense	4356	exon10			CCCTGGGACTGGG		CCDS42344.1	17q12-q21	2008-07-18			ENSG00000161647	ENSG00000161647			7221	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 3"", ""discs, large (Drosophila) homolog 3"", ""membrane protein palmitoylated 3"""	601114		DLG3		8824795	Standard	NR_003562		Approved		uc002iei.4	Q13368	OTTHUMG00000133838	ENST00000398389.4:c.617C>A	17.37:g.41901366G>T	ENSP00000381425:p.Ser206Tyr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	139	56	0.402878	NM_001932	B2R7N0|D3DX47|Q4GX05|Q6PGR3|Q86SV1	Missense_Mutation	SNP	ENST00000398389.4	37	CCDS42344.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	24.5	4.537709	0.85917	0.001822	0.007383	ENSG00000161647	ENST00000398393;ENST00000398389;ENST00000356492	T;T	0.30981	1.51;1.51	4.71	4.71	0.59529	Src homology-3 domain (1);PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.55065	0.1897	M	0.88842	2.985	0.80722	D	1	D;D;D	0.89917	0.995;0.999;1.0	D;D;D	0.76575	0.929;0.988;0.988	T	0.69881	-0.5025	10	0.87932	D	0	.	17.8567	0.88765	0.0:0.0:1.0:0.0	.	231;206;231	B4DS20;Q13368;D3DX46	.;MPP3_HUMAN;.	Y	231;206;231	ENSP00000381430:S231Y;ENSP00000381425:S206Y	ENSP00000348885:S231Y	S	-	2	0	MPP3	39256892	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.565000	0.98154	2.432000	0.82394	0.467000	0.42956	TCC	G|0.996;T|0.004	0.004	strong		0.532	MPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258371.1	NM_001932	
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 GAIIx	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		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	38	22	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	
GPATCH1	55094	hgsc.bcm.edu	37	19	33608733	33608733	+	Silent	SNP	C	C	A	rs2287681	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:33608733C>A	ENST00000170564.2	+	16	2513	c.2199C>A	c.(2197-2199)acC>acA	p.T733T		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	733					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					CAATACAGACCGTCAACAAAG	0.463													A|||	1810	0.361422	0.2746	0.4899	5008	,	,		18763	0.4831		0.2396	False		,,,				2504	0.3875				p.T733T	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C2199A						PASS	.	A		1141,3265	716.3+/-408.6	148,845,1210	81.0	80.0	80.0		2199	-4.8	0.0	19	dbSNP_100	80	2117,6483	716.2+/-406.1	258,1601,2441	yes	coding-synonymous	GPATCH1	NM_018025.2		406,2446,3651	AA,AC,CC		24.6163,25.8965,25.05		733/932	33608733	3258,9748	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon16			ACAGACCGTCAAC	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.2199C>A	19.37:g.33608733C>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	36	0.631579	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.699;A|0.301	0.301	strong		0.463	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
MAGEC2	51438	hgsc.bcm.edu	37	X	141290865	141290865	+	Silent	SNP	C	C	T	rs3765272	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:141290865C>T	ENST00000247452.3	-	3	1256	c.909G>A	c.(907-909)ccG>ccA	p.P303P		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	303	Interaction with TRIM28.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				cellular protein catabolic process (GO:0044257)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin protein ligase binding (GO:0031625)			NS(2)|breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(3)	47	Acute lymphoblastic leukemia(192;6.56e-05)					AATGGGCTCTCGGACCCCACA	0.478										HNSCC(46;0.14)			.|||	2693	0.713377	0.4365	0.5865	3775	,	,		14813	0.6657		0.5477	False		,,,				2504	0.498				p.P303P		Atlas-SNP	.											.	MAGEC2	102	.	0			c.G909A						PASS	.	C		2297,1538		584,785,344,263,227	87.0	86.0	86.0		909	-2.0	0.6	X	dbSNP_107	86	4710,2018		1207,1008,1288,213,584	no	coding-synonymous	MAGEC2	NM_016249.3		1791,1793,1632,476,811	TT,TC,T,CC,C		29.9941,40.1043,33.6647		303/374	141290865	7007,3556	2203	4300	6503	SO:0001819	synonymous_variant	51438	exon3			GGCTCTCGGACCC	AF116195	CCDS14678.1	Xq27	2009-03-25	2004-06-08	2004-06-09	ENSG00000046774	ENSG00000046774			13574	protein-coding gene	gene with protein product	"""cancer/testis antigen 10"""	300468	"""melanoma antigen, family E, 1, cancer/testis specific"""	MAGEE1		10699956	Standard	NM_016249		Approved	CT10, MAGE-C2	uc004fbu.2	Q9UBF1	OTTHUMG00000022574	ENST00000247452.3:c.909G>A	X.37:g.141290865C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Silent	SNP	ENST00000247452.3	37	CCDS14678.1																																																																																			C|0.316;T|0.684	0.684	strong		0.478	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249	
OR2T4	127074	hgsc.bcm.edu	37	1	248525138	248525138	+	Missense_Mutation	SNP	C	C	T	rs75096121	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248525138C>T	ENST00000366475.1	+	1	256	c.256C>T	c.(256-258)Cac>Tac	p.H86Y		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	86						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	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)			CTGTGACGCCCACCTCCACAC	0.478													c|||	1540	0.307508	0.3343	0.2392	5008	,	,		24623	0.3819		0.2207	False		,,,				2504	0.3323				p.H86Y		Atlas-SNP	.											.	OR2T4	126	.	0			c.C256T						PASS	.						473.0	323.0	374.0					1																	248525138		2203	4300	6503	SO:0001583	missense	127074	exon1			GACGCCCACCTCC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.256C>T	1.37:g.248525138C>T	ENSP00000355431:p.His86Tyr	Somatic	448	0	0		WXS	Illumina HiSeq	Phase_I	540	101	0.187037	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	C	4.270	0.049213	0.08243	.	.	ENSG00000196944	ENST00000366475	T	0.00792	5.69	3.48	1.54	0.23209	GPCR, rhodopsin-like superfamily (1);	0.289324	0.24618	N	0.036991	T	0.01156	0.0038	M	0.71920	2.185	0.09310	N	1	B	0.10296	0.003	B	0.18561	0.022	T	0.44757	-0.9307	10	0.87932	D	0	.	4.5422	0.12064	0.1712:0.6319:0.0:0.1968	.	86	Q8NH00	OR2T4_HUMAN	Y	86	ENSP00000355431:H86Y	ENSP00000355431:H86Y	H	+	1	0	OR2T4	246591761	0.000000	0.05858	0.033000	0.17914	0.153000	0.21895	-0.656000	0.05342	0.026000	0.15269	0.485000	0.47835	CAC	C|0.500;T|0.500	0.500	weak		0.478	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
DSCAML1	57453	hgsc.bcm.edu	37	11	117303858	117303858	+	Silent	SNP	T	T	C	rs11216382	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:117303858T>C	ENST00000321322.6	-	29	5203	c.5202A>G	c.(5200-5202)caA>caG	p.Q1734Q	DSCAML1_ENST00000527706.1_Silent_p.Q1464Q	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1674					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		ACTCACCCAGTTGCTTGATGC	0.587													C|||	706	0.140974	0.2557	0.1758	5008	,	,		18607	0.0565		0.1551	False		,,,				2504	0.0337				p.Q1734Q		Atlas-SNP	.											DSCAML1,NS,carcinoma,-2,1	DSCAML1	286	1	0			c.A5202G						PASS	.	C		1077,3325	719.8+/-409.0	131,815,1255	111.0	94.0	100.0		5202	2.6	1.0	11	dbSNP_120	100	1439,7153	749.8+/-407.4	118,1203,2975	yes	coding-synonymous	DSCAML1	NM_020693.2		249,2018,4230	CC,CT,TT		16.7481,24.4662,19.3628		1734/2114	117303858	2516,10478	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon29			ACCCAGTTGCTTG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.5202A>G	11.37:g.117303858T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	113	15	0.132743	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			T|0.826;C|0.174	0.174	strong		0.587	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
MLPH	79083	hgsc.bcm.edu	37	2	238449108	238449108	+	Missense_Mutation	SNP	G	G	T	rs61737681|rs386656756	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238449108G>T	ENST00000264605.3	+	10	1516	c.1222G>T	c.(1222-1224)Gcc>Tcc	p.A408S	MLPH_ENST00000338530.4_Missense_Mutation_p.A380S|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Missense_Mutation_p.A408S|MLPH_ENST00000409373.1_Missense_Mutation_p.A340S|MLPH_ENST00000410032.1_Missense_Mutation_p.A265S	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	408					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		GGAGGAGGAAGCCAAGGACGA	0.627													G|||	455	0.0908546	0.1641	0.0403	5008	,	,		20228	0.0645		0.0278	False		,,,				2504	0.1196				p.A408S		Atlas-SNP	.											.	MLPH	41	.	0			c.G1222T						PASS	.						78.0	75.0	76.0					2																	238449108		2203	4299	6502	SO:0001583	missense	79083	exon10			GAGGAAGCCAAGG	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1222G>T	2.37:g.238449108G>T	ENSP00000264605:p.Ala408Ser	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_024101	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	115|115|115	0.052655677655677656|0.052655677655677656|0.052655677655677656	50|50|50	0.1016260162601626|0.1016260162601626|0.1016260162601626	15|15|15	0.04143646408839779|0.04143646408839779|0.04143646408839779	32|32|32	0.055944055944055944|0.055944055944055944|0.055944055944055944	18|18|18	0.023746701846965697|0.023746701846965697|0.023746701846965697	G|G|G	0.005|0.005|0.005	-2.195400|-2.195400|-2.195400	0.00299|0.00299|0.00299	.|.|.	.|.|.	ENSG00000115648|ENSG00000115648|ENSG00000115648	ENST00000410032;ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373;ENST00000437893|ENST00000436965|ENST00000415753	T;T;T;T;T;T|.|.	0.25912|.|.	2.0;2.13;2.0;1.95;1.77;1.89|.|.	2.76|2.76|2.76	0.753|0.753|0.753	0.18404|0.18404|0.18404	.|.|.	1.576280|.|.	0.03676|.|.	N|.|.	0.244858|.|.	T|T|T	0.00384|0.00384|0.00384	0.0012|0.0012|0.0012	N|N|N	0.05078|0.05078|0.05078	-0.115|-0.115|-0.115	0.80722|0.80722|0.80722	P|P|P	0.0|0.0|0.0	B;B;B;B;B;B;B;B|.|.	0.25169|.|.	0.004;0.017;0.005;0.003;0.01;0.012;0.004;0.119|.|.	B;B;B;B;B;B;B;B|.|.	0.23419|.|.	0.002;0.004;0.003;0.004;0.007;0.005;0.002;0.046|.|.	T|T|T	0.28427|0.28427|0.28427	-1.0044|-1.0044|-1.0044	9|4|4	0.07325|.|.	T|.|.	0.83|.|.	-7.0745|-7.0745|-7.0745	5.2636|5.2636|5.2636	0.15588|0.15588|0.15588	0.4717:0.0:0.5283:0.0|0.4717:0.0:0.5283:0.0|0.4717:0.0:0.5283:0.0	rs61737681|rs61737681|rs61737681	69;408;264;380;340;380;408;265|.|.	Q53QV8;B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36;G5E9G5|.|.	.;.;.;.;.;.;MELPH_HUMAN;.|.|.	S|N|I	265;408;408;380;340;168|128|95	ENSP00000386338:A265S;ENSP00000264605:A408S;ENSP00000414849:A408S;ENSP00000341845:A380S;ENSP00000386780:A340S;ENSP00000412438:A168S|.|.	ENSP00000264605:A408S|.|.	A|K|S	+|+|+	1|3|2	0|2|0	MLPH|MLPH|MLPH	238113847|238113847|238113847	0.002000|0.002000|0.002000	0.14202|0.14202|0.14202	0.011000|0.011000|0.011000	0.14972|0.14972|0.14972	0.023000|0.023000|0.023000	0.10783|0.10783|0.10783	-0.502000|-0.502000|-0.502000	0.06390|0.06390|0.06390	-0.080000|-0.080000|-0.080000	0.12685|0.12685|0.12685	-0.143000|-0.143000|-0.143000	0.13931|0.13931|0.13931	GCC|AAG|AGC	C|0.000;G|0.952;T|0.047	0.047	strong		0.627	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
DNMBP	23268	hgsc.bcm.edu	37	10	101716112	101716112	+	Missense_Mutation	SNP	G	G	C	rs35924554	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101716112G>C	ENST00000324109.4	-	4	1210	c.1119C>G	c.(1117-1119)aaC>aaG	p.N373K	DNMBP_ENST00000342239.3_Missense_Mutation_p.N373K|DNMBP-AS1_ENST00000434409.1_RNA	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	373			N -> K (in dbSNP:rs35924554).		intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		CCTGATAAGAGTTTCTGTCTG	0.557													G|||	248	0.0495208	0.0893	0.062	5008	,	,		18015	0.0288		0.0398	False		,,,				2504	0.0184				p.N373K		Atlas-SNP	.											.	DNMBP	173	.	0			c.C1119G						PASS	.		LYS/ASN	338,4068	176.6+/-205.7	9,320,1874	93.0	94.0	93.0		1119	-1.3	0.0	10	dbSNP_126	93	344,8256	117.4+/-177.0	5,334,3961	yes	missense	DNMBP	NM_015221.2	94	14,654,5835	CC,CG,GG		4.0,7.6714,5.2437	benign	373/1578	101716112	682,12324	2203	4300	6503	SO:0001583	missense	23268	exon4			ATAAGAGTTTCTG	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.1119C>G	10.37:g.101716112G>C	ENSP00000315659:p.Asn373Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	37	CCDS7485.1	116	0.05311355311355311	49	0.09959349593495935	21	0.058011049723756904	20	0.03496503496503497	26	0.03430079155672823	G	3.528	-0.096237	0.07010	0.076714	0.04	ENSG00000107554	ENST00000342239;ENST00000324109	T;T	0.11169	2.85;2.8	5.53	-1.33	0.09172	.	1.860880	0.02542	N	0.094741	T	0.00178	0.0005	N	0.19112	0.55	0.80722	P	0.0	B	0.20887	0.049	B	0.16722	0.016	T	0.27806	-1.0063	9	0.06494	T	0.89	2.8121	5.6267	0.17487	0.3019:0.2417:0.4563:0.0	rs35924554;rs61751506	373	Q6XZF7	DNMBP_HUMAN	K	373	ENSP00000344914:N373K;ENSP00000315659:N373K	ENSP00000315659:N373K	N	-	3	2	DNMBP	101706102	0.005000	0.15991	0.000000	0.03702	0.106000	0.19336	0.245000	0.18142	0.069000	0.16605	0.561000	0.74099	AAC	G|0.947;C|0.053	0.053	strong		0.557	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
FAM47A	158724	hgsc.bcm.edu	37	X	34149267	34149267	+	Missense_Mutation	SNP	C	C	A	rs1811716	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:34149267C>A	ENST00000346193.3	-	1	1180	c.1129G>T	c.(1129-1131)Gcg>Tcg	p.A377S		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	377			A -> S (in dbSNP:rs1811716).							NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						GAAGGCTCCGCGTGGAGACTG	0.642													a|||	941	0.249272	0.2716	0.1542	3775	,	,		10190	0.2183		0.1233	False		,,,				2504	0.1339				p.A377S		Atlas-SNP	.											.	FAM47A	249	.	0			c.G1129T						PASS	.	C	SER/ALA	1476,2351		244,753,235,631,336	36.0	37.0	37.0		1129	-0.4	0.0	X	dbSNP_92	37	1107,5620		74,638,321,1716,1550	no	missense	FAM47A	NM_203408.3	99	318,1391,556,2347,1886	AA,AC,A,CC,C		16.4561,38.5681,24.4741	benign	377/792	34149267	2583,7971	2199	4299	6498	SO:0001583	missense	158724	exon1			GCTCCGCGTGGAG	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1129G>T	X.37:g.34149267C>A	ENSP00000345029:p.Ala377Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	101	62	0.613861	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	394	0.23749246534056662	96	0.23529411764705882	29	0.08734939759036145	81	0.16396761133603238	67	0.09463276836158192	c	0.019	-1.448633	0.01080	0.385681	0.164561	ENSG00000185448	ENST00000346193	T	0.13657	2.57	0.226	-0.452	0.12205	.	.	.	.	.	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.46275	-0.9203	7	0.32370	T	0.25	.	.	.	.	rs1811716;rs61464828	377	Q5JRC9	FA47A_HUMAN	S	377	ENSP00000345029:A377S	ENSP00000345029:A377S	A	-	1	0	FAM47A	34059188	0.052000	0.20516	0.000000	0.03702	0.000000	0.00434	-2.597000	0.00894	-3.949000	0.00088	-3.925000	0.00016	GCG	C|0.751;A|0.249	0.249	strong		0.642	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408	
IRF2BP1	26145	hgsc.bcm.edu	37	19	46387344	46387344	+	Silent	SNP	G	G	A	rs11550348	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46387344G>A	ENST00000302165.3	-	1	2032	c.1689C>T	c.(1687-1689)ttC>ttT	p.F563F		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	563					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)			cervix(1)|kidney(1)|lung(2)	4		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0402)|Epithelial(262;0.231)		CGCCCTGCATGAAGGCCCAGG	0.652											OREG0025563	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	684	0.136581	0.3185	0.1023	5008	,	,		14190	0.001		0.1034	False		,,,				2504	0.089				p.F563F		Atlas-SNP	.											.	IRF2BP1	23	.	0			c.C1689T						PASS	.	G		1262,3144	427.0+/-341.4	202,858,1143	57.0	52.0	54.0		1689	1.2	1.0	19	dbSNP_120	54	1115,7485	229.1+/-263.9	85,945,3270	no	coding-synonymous	IRF2BP1	NM_015649.1		287,1803,4413	AA,AG,GG		12.9651,28.6428,18.2762		563/585	46387344	2377,10629	2203	4300	6503	SO:0001819	synonymous_variant	26145	exon1			CTGCATGAAGGCC	AY278022	CCDS12678.1	19q13.32	2008-02-05							21728	protein-coding gene	gene with protein product		615331				12799427	Standard	NM_015649		Approved	DKFZP434M154, IRF-2BP1	uc002pds.1	Q8IU81		ENST00000302165.3:c.1689C>T	19.37:g.46387344G>A		Somatic	70	0	0	938	WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Silent	SNP	ENST00000302165.3	37	CCDS12678.1																																																																																			G|0.836;A|0.164	0.164	strong		0.652	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649	
MAGEB10	139422	hgsc.bcm.edu	37	X	27839572	27839572	+	Missense_Mutation	SNP	T	T	C	rs1368769	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:27839572T>C	ENST00000356790.2	+	3	394	c.149T>C	c.(148-150)tTc>tCc	p.F50S		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	50			F -> S (in dbSNP:rs1368769). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						AAGGATGTTTTCCAGAGTTCA	0.517													C|||	1304	0.34543	0.3775	0.2248	3775	,	,		13537	0.0645		0.3827	False		,,,				2504	0.2035				p.F50S		Atlas-SNP	.											.	MAGEB10	107	.	0			c.T149C						PASS	.	C	SER/PHE	1913,1920		398,834,283,399,288	57.0	49.0	52.0		149	1.5	0.0	X	dbSNP_88	52	3580,3148		693,1196,998,539,874	yes	missense	MAGEB10	NM_182506.3	155	1091,2030,1281,938,1162	CC,CT,C,TT,T		46.7895,49.9087,47.9879	benign	50/348	27839572	5493,5068	2202	4300	6502	SO:0001583	missense	139422	exon3			ATGTTTTCCAGAG		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.149T>C	X.37:g.27839572T>C	ENSP00000368304:p.Phe50Ser	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	43	0.955556	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Missense_Mutation	SNP	ENST00000356790.2	37	CCDS35221.1	604	0.3640747438215793	137	0.3549222797927461	64	0.2119205298013245	25	0.04562043795620438	199	0.33728813559322035	C	0.077	-1.191488	0.01607	0.499087	0.532105	ENSG00000177689	ENST00000356790	T	0.04156	3.69	2.37	1.45	0.22620	Melanoma associated antigen, MAGE, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38585	-0.9654	8	0.02654	T	1	.	3.2031	0.06656	0.0:0.524:0.2915:0.1845	rs1368769;rs59237909;rs1368769	50	Q96LZ2	MAGBA_HUMAN	S	50	ENSP00000368304:F50S	ENSP00000368304:F50S	F	+	2	0	MAGEB10	27749493	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.595000	0.05727	0.002000	0.14630	-0.416000	0.06073	TTC	0|0.029;C|0.421	0.421	strong		0.517	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506	
LAX1	54900	hgsc.bcm.edu	37	1	203743798	203743798	+	Missense_Mutation	SNP	C	C	T	rs41264261	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203743798C>T	ENST00000442561.2	+	5	1576	c.1186C>T	c.(1186-1188)Cct>Tct	p.P396S	LAX1_ENST00000367217.5_Missense_Mutation_p.P380S|LAX1_ENST00000367215.1_3'UTR	NM_017773.3	NP_060243.2	Q8IWV1	LAX1_HUMAN	lymphocyte transmembrane adaptor 1	396					antigen receptor-mediated signaling pathway (GO:0050851)|B cell activation (GO:0042113)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|inactivation of MAPK activity (GO:0000188)|intracellular signal transduction (GO:0035556)|negative regulation of T cell activation (GO:0050868)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)			central_nervous_system(2)|endometrium(3)|large_intestine(2)|lung(13)|prostate(1)|stomach(1)|urinary_tract(2)	24	all_cancers(21;0.0915)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TCAGCTCCTTCCTGATGAATG	0.502													C|||	41	0.0081869	0.0015	0.0086	5008	,	,		19392	0.001		0.0288	False		,,,				2504	0.0031				p.P396S		Atlas-SNP	.											.	LAX1	48	.	0			c.C1186T						PASS	.	C	SER/PRO,SER/PRO	24,4382	29.9+/-59.1	0,24,2179	37.0	38.0	38.0		1138,1186	3.4	0.2	1	dbSNP_127	38	284,8316	100.1+/-161.6	4,276,4020	yes	missense,missense	LAX1	NM_001136190.1,NM_017773.3	74,74	4,300,6199	TT,TC,CC		3.3023,0.5447,2.3681	probably-damaging,probably-damaging	380/383,396/399	203743798	308,12698	2203	4300	6503	SO:0001583	missense	54900	exon5			CTCCTTCCTGATG	AK000347	CCDS1441.2, CCDS44297.1	1q32.1	2008-02-05			ENSG00000122188	ENSG00000122188			26005	protein-coding gene	gene with protein product	"""LAT-like membrane associated protein"", ""linker for activation of x cells"""					12359715	Standard	NM_017773		Approved	LAX, FLJ20340	uc001haa.3	Q8IWV1	OTTHUMG00000035908	ENST00000442561.2:c.1186C>T	1.37:g.203743798C>T	ENSP00000406970:p.Pro396Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_017773	B7Z744|J3KP69|Q6NSZ6|Q9NXB4	Missense_Mutation	SNP	ENST00000442561.2	37	CCDS1441.2	27	0.012362637362637362	2	0.0040650406504065045	5	0.013812154696132596	1	0.0017482517482517483	19	0.025065963060686015	C	13.62	2.291450	0.40494	0.005447	0.033023	ENSG00000122188	ENST00000442561;ENST00000367217	.	.	.	5.4	3.4	0.38934	.	0.357044	0.20714	N	0.087035	T	0.06371	0.0164	N	0.14661	0.345	0.09310	N	0.999999	P;P	0.50943	0.94;0.94	P;P	0.47015	0.534;0.534	T	0.04153	-1.0973	9	0.19147	T	0.46	-2.1379	6.6324	0.22863	0.1774:0.7243:0.0:0.0983	rs41264261	380;396	B7Z744;Q8IWV1	.;LAX1_HUMAN	S	396;380	.	ENSP00000356186:P380S	P	+	1	0	LAX1	202010421	0.994000	0.37717	0.186000	0.23195	0.660000	0.38997	1.048000	0.30379	1.397000	0.46682	0.655000	0.94253	CCT	C|0.979;T|0.021	0.021	strong		0.502	LAX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087468.3	NM_017773	
IKBKE	9641	hgsc.bcm.edu	37	1	206651107	206651107	+	Silent	SNP	G	G	A	rs2297545	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:206651107G>A	ENST00000367120.3	+	8	1090	c.717G>A	c.(715-717)acG>acA	p.T239T	IKBKE_ENST00000537984.1_Silent_p.T154T	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GGATCACCACGGAGAAGCCGG	0.652													G|||	1580	0.315495	0.1558	0.402	5008	,	,		15713	0.6131		0.2286	False		,,,				2504	0.2526				p.T239T		Atlas-SNP	.											IKBKE,NS,carcinoma,0,1	IKBKE	77	1	0			c.G717A						PASS	.	G	,,	716,3650		56,604,1523	13.0	14.0	13.0		462,717,717	-9.1	0.1	1	dbSNP_100	13	1791,6755		176,1439,2658	no	coding-synonymous,coding-synonymous,coding-synonymous	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	,,	232,2043,4181	AA,AG,GG		20.9572,16.3995,19.416	,,	154/632,239/658,239/717	206651107	2507,10405	2183	4273	6456	SO:0001819	synonymous_variant	9641	exon8			CACCACGGAGAAG	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.717G>A	1.37:g.206651107G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	37	CCDS30996.1																																																																																			G|0.745;A|0.255	0.255	strong		0.652	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
KIAA0753	9851	hgsc.bcm.edu	37	17	6524298	6524298	+	Missense_Mutation	SNP	T	T	A	rs9889363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6524298T>A	ENST00000361413.3	-	7	1483	c.1125A>T	c.(1123-1125)gaA>gaT	p.E375D	KIAA0753_ENST00000572370.1_Missense_Mutation_p.E76D|KIAA0753_ENST00000589033.1_5'Flank|KIAA0753_ENST00000542606.1_Missense_Mutation_p.E76D	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	375			E -> D (in dbSNP:rs9889363).|E -> G (in dbSNP:rs17794522).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		ACAGTTTCTTTTCCAGGAGAG	0.373													T|||	1542	0.307907	0.1581	0.4006	5008	,	,		15891	0.3562		0.3489	False		,,,				2504	0.3528				p.E375D		Atlas-SNP	.											.	KIAA0753	63	.	0			c.A1125T						PASS	.	T	ASP/GLU	734,2898		74,586,1156	62.0	60.0	60.0		1125	3.8	1.0	17	dbSNP_119	60	3078,5082		548,1982,1550	yes	missense	KIAA0753	NM_014804.2	45	622,2568,2706	AA,AT,TT		37.7206,20.2093,32.327	probably-damaging	375/968	6524298	3812,7980	1816	4080	5896	SO:0001583	missense	9851	exon7			TTTCTTTTCCAGG		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.1125A>T	17.37:g.6524298T>A	ENSP00000355250:p.Glu375Asp	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	669	0.30631868131868134	83	0.16869918699186992	154	0.425414364640884	178	0.3111888111888112	254	0.33509234828496043	T	24.0	4.484199	0.84854	0.202093	0.377206	ENSG00000198920	ENST00000361413;ENST00000542606	D;D	0.86956	-2.19;-2.19	4.92	3.84	0.44239	.	0.429523	0.27901	N	0.017391	T	0.00012	0.0000	M	0.76574	2.34	0.09310	P	0.9999999999992082	D	0.76494	0.999	D	0.80764	0.994	T	0.01074	-1.1460	9	0.62326	D	0.03	-12.5411	7.6264	0.28214	0.0:0.099:0.0:0.901	rs9889363;rs17804307;rs9889363	375	Q2KHM9	K0753_HUMAN	D	375;76	ENSP00000355250:E375D;ENSP00000444634:E76D	ENSP00000355250:E375D	E	-	3	2	KIAA0753	6465022	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.810000	0.27183	0.991000	0.38814	0.377000	0.23210	GAA	T|0.697;A|0.303	0.303	strong		0.373	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573439	140573439	+	Silent	SNP	G	G	C	rs610836	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140573439G>C	ENST00000239446.4	+	1	1498	c.1314G>C	c.(1312-1314)acG>acC	p.T438T		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	438	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAACATAACGGTCCTGGTCT	0.587													C|||	2442	0.48762	0.5076	0.5461	5008	,	,		14303	0.5685		0.4076	False		,,,				2504	0.4182				p.T438T		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G1314C						PASS	.						82.0	79.0	80.0					5																	140573439		2203	4298	6501	SO:0001819	synonymous_variant	56126	exon1			CATAACGGTCCTG	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1314G>C	5.37:g.140573439G>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			G|0.551;C|0.449	0.449	strong		0.587	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
SPATA31A6	389730	hgsc.bcm.edu	37	9	43625382	43625382	+	Missense_Mutation	SNP	G	G	A	rs143826416	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:43625382G>A	ENST00000332857.6	-	4	3333	c.3305C>T	c.(3304-3306)cCt>cTt	p.P1102L	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	1102					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTTGTGAATAGGGGGAAACAT	0.483													G|||	2248	0.448882	0.3132	0.4625	5008	,	,		13804	0.6458		0.5	False		,,,				2504	0.3671				p.P1102L		Atlas-SNP	.											FAM75A6,NS,carcinoma,0,3	.	.	3	0			c.C3305T						scavenged	.						1.0	2.0	2.0					9																	43625382		372	1032	1404	SO:0001583	missense	389730	exon4			TGAATAGGGGGAA		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A6"""	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.3305C>T	9.37:g.43625382G>A	ENSP00000329825:p.Pro1102Leu	Somatic	191	2	0.0104712		WXS	Illumina HiSeq	Phase_I	81	75	0.925926	NM_001145196		Missense_Mutation	SNP	ENST00000332857.6	37	CCDS47973.1	.	.	.	.	.	.	.	.	.	.	G	11.85	1.762340	0.31228	.	.	ENSG00000185775	ENST00000332857	T	0.04970	3.52	2.44	0.396	0.16309	.	1.512980	0.04100	N	0.312673	T	0.12860	0.0312	M	0.71206	2.165	0.80722	P	0.0	B	0.33044	0.395	B	0.42495	0.389	T	0.36648	-0.9739	9	0.56958	D	0.05	.	2.8448	0.05540	0.1624:0.0:0.5643:0.2733	.	1102	Q5VVP1	F75A6_HUMAN	L	1102	ENSP00000329825:P1102L	ENSP00000329825:P1102L	P	-	2	0	FAM75A6	43565378	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.063000	0.14410	0.111000	0.17947	0.383000	0.25322	CCT	A|1.000;|0.000	1.000	weak		0.483	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196	
DRG2	1819	hgsc.bcm.edu	37	17	17997209	17997209	+	Silent	SNP	G	G	A	rs2230316	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:17997209G>A	ENST00000225729.3	+	2	285	c.147G>A	c.(145-147)tcG>tcA	p.S49S	DRG2_ENST00000395726.4_Silent_p.S49S|DRG2_ENST00000583355.1_Silent_p.S49S	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	49					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					AATCGGCCTCGTCCAAAGGAG	0.552													G|||	1251	0.2498	0.1467	0.3804	5008	,	,		18796	0.0645		0.5358	False		,,,				2504	0.1933				p.S49S		Atlas-SNP	.											.	DRG2	27	.	0			c.G147A						PASS	.	G		906,3500	350.3+/-310.7	94,718,1391	148.0	125.0	133.0		147	-11.1	0.3	17	dbSNP_98	133	5053,3547	630.8+/-398.4	1484,2085,731	no	coding-synonymous	DRG2	NM_001388.3		1578,2803,2122	AA,AG,GG		41.2442,20.5629,45.8173		49/365	17997209	5959,7047	2203	4300	6503	SO:0001819	synonymous_variant	1819	exon2			GGCCTCGTCCAAA	X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591			3030	protein-coding gene	gene with protein product		602986	"""developmentally regulated GTP-binding protein 2"""			9605870, 7929244	Standard	NM_001388		Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000225729.3:c.147G>A	17.37:g.17997209G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	204	100	0.490196	NM_001388	B2R8G5|Q53Y50|Q9BWB2	Silent	SNP	ENST00000225729.3	37	CCDS11191.1																																																																																			G|0.609;A|0.391	0.391	strong		0.552	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	NM_001388	
STPG2	285555	hgsc.bcm.edu	37	4	99049593	99049593	+	Missense_Mutation	SNP	A	A	G	rs17558193	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:99049593A>G	ENST00000295268.3	-	3	462	c.373T>C	c.(373-375)Tac>Cac	p.Y125H		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	125			Y -> H (in dbSNP:rs17558193).														TGAGGTTTGTAGTATGCTGGA	0.318													A|||	1879	0.3752	0.4425	0.2882	5008	,	,		16898	0.2748		0.4026	False		,,,				2504	0.4213				p.Y125H		Atlas-SNP	.											.	.	.	.	0			c.T373C						PASS	.	A	HIS/TYR	1973,2433	553.7+/-378.8	454,1065,684	65.0	62.0	63.0		373	5.2	0.7	4	dbSNP_123	63	3409,5189	501.0+/-375.3	694,2021,1584	yes	missense	C4orf37	NM_174952.2	83	1148,3086,2268	GG,GA,AA		39.6488,44.7798,41.3873	probably-damaging	125/460	99049593	5382,7622	2203	4299	6502	SO:0001583	missense	285555	exon3			GTTTGTAGTATGC	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.373T>C	4.37:g.99049593A>G	ENSP00000295268:p.Tyr125His	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	177	77	0.435028	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	759	0.3475274725274725	192	0.3902439024390244	106	0.292817679558011	161	0.28146853146853146	300	0.39577836411609496	A	17.14	3.312649	0.60414	0.447798	0.396488	ENSG00000163116	ENST00000295268	T	0.28666	1.6	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.66939	2.045	0.28965	P	0.8896	D	0.89917	1.0	D	0.91635	0.999	T	0.47824	-0.9087	9	0.87932	D	0	-19.6536	12.8257	0.57718	1.0:0.0:0.0:0.0	rs17558193;rs52818476;rs17558193	125	Q8N412	CD037_HUMAN	H	125	ENSP00000295268:Y125H	ENSP00000295268:Y125H	Y	-	1	0	C4orf37	99268616	1.000000	0.71417	0.696000	0.30242	0.819000	0.46315	4.980000	0.63812	2.064000	0.61679	0.533000	0.62120	TAC	A|0.611;G|0.389	0.389	strong		0.318	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
RNF213	57674	hgsc.bcm.edu	37	17	78337058	78337058	+	Missense_Mutation	SNP	G	G	C	rs35332090	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78337058G>C	ENST00000582970.1	+	40	11655	c.11512G>C	c.(11512-11514)Gtt>Ctt	p.V3838L	CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.V1911L|RNF213_ENST00000508628.2_Missense_Mutation_p.V3887L|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3838					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTACCCTCAGGTTCTCCACAG	0.572													G|||	732	0.146166	0.292	0.1066	5008	,	,		16736	0.0417		0.1044	False		,,,				2504	0.1278				p.V3838L		Atlas-SNP	.											.	RNF213	766	.	0			c.G11512C						PASS	.	G	LEU/VAL	1082,3324	392.4+/-328.5	138,806,1259	102.0	93.0	96.0		11659	-3.9	0.0	17	dbSNP_126	96	930,7670	205.6+/-248.0	60,810,3430	yes	missense	RNF213	NM_020914.4	32	198,1616,4689	CC,CG,GG		10.814,24.5574,15.4698	benign	3887/5257	78337058	2012,10994	2203	4300	6503	SO:0001583	missense	57674	exon40			CCTCAGGTTCTCC	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11512G>C	17.37:g.78337058G>C	ENSP00000464087:p.Val3838Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	284	0.13003663003663005	151	0.30691056910569103	37	0.10220994475138122	25	0.043706293706293704	71	0.09366754617414248	G	10.83	1.460066	0.26248	0.245574	0.10814	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.23950	1.88	5.59	-3.89	0.04193	.	0.477816	0.23492	N	0.047598	T	0.00012	0.0000	M	0.61703	1.905	0.80722	P	0.0	B;B	0.31318	0.319;0.002	B;B	0.34301	0.179;0.002	T	0.24584	-1.0156	9	0.36615	T	0.2	.	11.9394	0.52892	0.4701:0.0:0.5299:0.0	rs35332090;rs61729893	3887;1911	C9JCP4;Q63HN8	.;RN213_HUMAN	L	3838;3887;1911	ENSP00000338218:V1911L	ENSP00000338218:V1911L	V	+	1	0	RNF213	75951653	0.949000	0.32298	0.000000	0.03702	0.001000	0.01503	1.111000	0.31159	-1.071000	0.03145	-1.202000	0.01658	GTT	G|0.852;C|0.148	0.148	strong		0.572	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
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 GAIIx	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_ENST00000380368.2_Missense_Mutation_p.V151I|BPHL_ENST00000434640.1_Missense_Mutation_p.V151I|BPHL_ENST00000380375.3_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	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	71	25	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		
CYP11B2	1585	hgsc.bcm.edu	37	8	143996553	143996553	+	Silent	SNP	G	G	A	rs4546	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:143996553G>A	ENST00000323110.2	-	3	506	c.504C>T	c.(502-504)ttC>ttT	p.F168F		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	168					aldosterone biosynthetic process (GO:0032342)|C21-steroid hormone biosynthetic process (GO:0006700)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|mineralocorticoid biosynthetic process (GO:0006705)|potassium ion homeostasis (GO:0055075)|regulation of blood volume by renal aldosterone (GO:0002017)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	corticosterone 18-monooxygenase activity (GO:0047783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(22)|ovary(3)|upper_aerodigestive_tract(3)	39	all_cancers(97;5.56e-11)|all_epithelial(106;2.49e-08)|Lung NSC(106;0.000228)|all_lung(105;0.000633)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)				Eplerenone(DB00700)|Etomidate(DB00292)|Hydrocortisone(DB00741)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Spironolactone(DB00421)	GGGCCTGGGAGAAGTCCCTGG	0.622									Familial Hyperaldosteronism type I				.|||	1730	0.345447	0.1838	0.4697	5008	,	,		19590	0.2867		0.4841	False		,,,				2504	0.3937				p.F168F		Atlas-SNP	.											CYP11B2,rectum,carcinoma,0,1	CYP11B2	107	1	0			c.C504T						PASS	.	G		1021,3385		122,777,1304	43.0	39.0	41.0		504	1.6	0.0	8	dbSNP_52	41	3861,4735		876,2109,1313	no	coding-synonymous	CYP11B2	NM_000498.3		998,2886,2617	AA,AG,GG		44.9162,23.1729,37.5481		168/504	143996553	4882,8120	2203	4298	6501	SO:0001819	synonymous_variant	1585	exon3	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CTGGGAGAAGTCC	X54741	CCDS6393.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000179142	ENSG00000179142	1.14.15.4	"""Cytochrome P450s"""	2592	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	124080	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 2"""	CYP11B		1303253	Standard	NM_000498		Approved	CYP11BL, CPN2, P-450C18, P450aldo, ALDOS	uc003yxk.1	P19099	OTTHUMG00000160254	ENST00000323110.2:c.504C>T	8.37:g.143996553G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	129	54	0.418605	NM_000498	B0ZBE4|Q16726	Silent	SNP	ENST00000323110.2	37	CCDS6393.1																																																																																			G|0.655;A|0.345	0.345	strong		0.622	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
YWHAG	7532	hgsc.bcm.edu	37	7	75959188	75959188	+	Silent	SNP	G	G	A	rs2072435	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:75959188G>A	ENST00000307630.3	-	2	672	c.450C>T	c.(448-450)tcC>tcT	p.S150S		NM_012479.3	NP_036611.2	P61981	1433G_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma	150					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein targeting (GO:0006605)|regulation of neuron differentiation (GO:0045664)|regulation of signal transduction (GO:0009966)|regulation of synaptic plasticity (GO:0048167)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	insulin-like growth factor receptor binding (GO:0005159)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)|protein kinase C inhibitor activity (GO:0008426)			endometrium(2)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)	8						AGGCCTTCTCGGAGGACTCCA	0.562													G|||	1565	0.3125	0.329	0.2896	5008	,	,		17236	0.4454		0.2982	False		,,,				2504	0.184				p.S150S		Atlas-SNP	.											.	YWHAG	24	.	0			c.C450T						PASS	.	G		1334,3072	448.1+/-348.6	198,938,1067	148.0	151.0	150.0		450	-10.8	0.1	7	dbSNP_96	150	2450,6150	405.0+/-348.4	351,1748,2201	no	coding-synonymous	YWHAG	NM_012479.3		549,2686,3268	AA,AG,GG		28.4884,30.2769,29.0943		150/248	75959188	3784,9222	2203	4300	6503	SO:0001819	synonymous_variant	7532	exon2			CTTCTCGGAGGAC	AF142498	CCDS5584.1	7q11.23	2014-06-13	2013-12-03		ENSG00000170027	ENSG00000170027			12852	protein-coding gene	gene with protein product	"""14-3-3 gamma"", ""protein phosphatase 1, regulatory subunit 170"""	605356	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide"""			10486217, 10433554	Standard	NM_012479		Approved	PPP1R170	uc011kgj.1	P61981	OTTHUMG00000022862	ENST00000307630.3:c.450C>T	7.37:g.75959188G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_012479	O70457|P35214|Q6FH52|Q9UDP2|Q9UN99	Silent	SNP	ENST00000307630.3	37	CCDS5584.1																																																																																			G|0.697;A|0.303	0.303	strong		0.562	YWHAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253002.1	NM_012479	
ZFHX3	463	hgsc.bcm.edu	37	16	72830539	72830539	+	Missense_Mutation	SNP	C	C	G	rs62051555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:72830539C>G	ENST00000268489.5	-	9	6714	c.6042G>C	c.(6040-6042)caG>caC	p.Q2014H	ZFHX3_ENST00000397992.5_Missense_Mutation_p.Q1100H	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	2014					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ACCTCTCGAGCTGTTTGAAAG	0.498													C|||	72	0.014377	0.0015	0.036	5008	,	,		12747	0.0		0.0427	False		,,,				2504	0.002				p.Q2014H		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G6042C						PASS	.	C	HIS/GLN,HIS/GLN	36,4360	40.0+/-72.8	0,36,2162	96.0	99.0	98.0		3300,6042	4.8	1.0	16	dbSNP_129	98	338,8262	113.7+/-173.7	11,316,3973	yes	missense,missense	ZFHX3	NM_001164766.1,NM_006885.3	24,24	11,352,6135	GG,GC,CC		3.9302,0.8189,2.8778	probably-damaging,probably-damaging	1100/2790,2014/3704	72830539	374,12622	2198	4300	6498	SO:0001583	missense	463	exon9			CTCGAGCTGTTTG	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.6042G>C	16.37:g.72830539C>G	ENSP00000268489:p.Gln2014His	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	124	56	0.451613	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	49	0.022435897435897436	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	32	0.04221635883905013	C	8.314	0.822681	0.16678	0.008189	0.039302	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.73575	-0.76;-0.74	5.75	4.79	0.61399	.	0.000000	0.47852	D	0.000219	T	0.29389	0.0732	N	0.19112	0.55	0.38167	D	0.939201	P	0.51653	0.947	P	0.44561	0.453	T	0.57487	-0.7803	10	0.48119	T	0.1	.	11.3527	0.49598	0.0:0.8606:0.0:0.1394	rs62051555	2014	Q15911	ZFHX3_HUMAN	H	2014;1100	ENSP00000268489:Q2014H;ENSP00000438926:Q1100H	ENSP00000268489:Q2014H	Q	-	3	2	ZFHX3	71388040	1.000000	0.71417	1.000000	0.80357	0.555000	0.35460	2.250000	0.43178	2.696000	0.92011	0.655000	0.94253	CAG	C|0.973;G|0.027	0.027	strong		0.498	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
EMR1	2015	hgsc.bcm.edu	37	19	6897464	6897464	+	Missense_Mutation	SNP	C	C	G	rs330880	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:6897464C>G	ENST00000312053.4	+	5	457	c.420C>G	c.(418-420)agC>agG	p.S140R	AC020895.1_ENST00000580648.1_RNA|EMR1_ENST00000450315.3_Splice_Site|EMR1_ENST00000381407.5_Intron|EMR1_ENST00000381404.4_Missense_Mutation_p.S88R|EMR1_ENST00000601198.1_3'UTR|EMR1_ENST00000250572.8_Missense_Mutation_p.S140R	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	140	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		S -> R (in dbSNP:rs330880). {ECO:0000269|PubMed:7601460}.		cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					TCACCAGCAGCGTCTGCCCTG	0.488													g|||	2513	0.501797	0.8328	0.4496	5008	,	,		18558	0.4831		0.2734	False		,,,				2504	0.3456				p.S140R		Atlas-SNP	.											.	EMR1	153	.	0			c.C420G						PASS	.	G	ARG/SER	3211,1195	416.3+/-337.5	1181,849,173	96.0	79.0	85.0		420	-3.2	0.0	19	dbSNP_79	85	2630,5970	687.8+/-404.2	410,1810,2080	yes	missense	EMR1	NM_001974.3	110	1591,2659,2253	GG,GC,CC		30.5814,27.1221,44.91	benign	140/887	6897464	5841,7165	2203	4300	6503	SO:0001583	missense	2015	exon5			CAGCAGCGTCTGC	X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.420C>G	19.37:g.6897464C>G	ENSP00000311545:p.Ser140Arg	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	154	89	0.577922	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	1030|1030	0.4716117216117216|0.4716117216117216	395|395	0.8028455284552846|0.8028455284552846	147|147	0.40607734806629836|0.40607734806629836	290|290	0.506993006993007|0.506993006993007	198|198	0.2612137203166227|0.2612137203166227	G|G	2.796|2.796	-0.250332|-0.250332	0.05867|0.05867	0.728779|0.728779	0.305814|0.305814	ENSG00000174837|ENSG00000174837	ENST00000450315|ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572	.|D;D;D	.|0.91996	.|-2.95;-2.95;-2.95	4.12|4.12	-3.22|-3.22	0.05125|0.05125	.|EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|.	.|.	.|.	.|.	.|T	.|0.00012	.|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.52501|0.52501	P|P	4.599999999999049E-5|4.599999999999049E-5	.|B;B;B	.|0.06786	.|0.0;0.0;0.001	.|B;B;B	.|0.12156	.|0.001;0.005;0.007	.|T	.|0.38067	.|-0.9678	.|8	.|0.15499	.|T	.|0.54	.|.	5.443|5.443	0.16519|0.16519	0.3573:0.4541:0.1886:0.0|0.3573:0.4541:0.1886:0.0	rs330880;rs2228537;rs52813683;rs60071314;rs330880|rs330880;rs2228537;rs52813683;rs60071314;rs330880	.|140;88;140	.|Q14246-2;E9PD45;Q14246	.|.;.;EMR1_HUMAN	.|R	-1|140;140;88;140	.|ENSP00000311545:S140R;ENSP00000370811:S88R;ENSP00000250572:S140R	.|ENSP00000250572:S140R	.|S	+|+	.|3	.|2	EMR1|EMR1	6848464|6848464	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.976000|-1.976000	0.01497|0.01497	-0.762000|-0.762000	0.04664|0.04664	-0.215000|-0.215000	0.12644|0.12644	.|AGC	C|0.551;G|0.449	0.449	strong		0.488	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
GJD4	219770	hgsc.bcm.edu	37	10	35896957	35896957	+	Silent	SNP	G	G	A	rs595652	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:35896957G>A	ENST00000321660.1	+	2	674	c.516G>A	c.(514-516)aaG>aaA	p.K172K	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	172					cell communication (GO:0007154)|regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014717)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						CCCCGAAGAAGTTCCCTTGCA	0.637													G|||	1062	0.212061	0.0151	0.2651	5008	,	,		12095	0.3234		0.2376	False		,,,				2504	0.2996				p.K172K		Atlas-SNP	.											.	GJD4	38	.	0			c.G516A						PASS	.	G		216,4190	126.1+/-163.2	6,204,1993	26.0	24.0	25.0		516	-11.2	0.0	10	dbSNP_83	25	1933,6667	306.2+/-307.8	211,1511,2578	no	coding-synonymous	GJD4	NM_153368.2		217,1715,4571	AA,AG,GG		22.4767,4.9024,16.5231		172/371	35896957	2149,10857	2203	4300	6503	SO:0001819	synonymous_variant	219770	exon2			GAAGAAGTTCCCT	AJ414564	CCDS7191.1	10p11.22	2007-11-27			ENSG00000177291	ENSG00000177291		"""Ion channels / Gap junction proteins (connexins)"""	23296	protein-coding gene	gene with protein product	"""connexin 40.1"""	611922				12477932	Standard	NM_153368		Approved	CX40.1, FLJ90023	uc001iyy.1	Q96KN9	OTTHUMG00000017957	ENST00000321660.1:c.516G>A	10.37:g.35896957G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_153368	Q8N2R7	Silent	SNP	ENST00000321660.1	37	CCDS7191.1																																																																																			G|0.825;A|0.175	0.175	strong		0.637	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047576.1	NM_153368	
BTBD10	84280	hgsc.bcm.edu	37	11	13441250	13441250	+	Missense_Mutation	SNP	C	C	T	rs199534943		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:13441250C>T	ENST00000278174.5	-	4	586	c.341G>A	c.(340-342)cGt>cAt	p.R114H	BTBD10_ENST00000530907.1_Missense_Mutation_p.R122H|BTBD10_ENST00000532261.1_5'UTR|BTBD10_ENST00000528120.1_Missense_Mutation_p.R66H	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10	114	Ser-rich.					nucleus (GO:0005634)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|prostate(1)	20				Epithelial(150;0.0214)		TTTTTGAGGACGCGGACTGCT	0.418																																					p.R114H		Atlas-SNP	.											BTBD10,NS,carcinoma,0,1	BTBD10	43	1	0			c.G341A						scavenged	.						169.0	163.0	165.0					11																	13441250		2200	4294	6494	SO:0001583	missense	84280	exon4			TGAGGACGCGGAC	AY221959	CCDS7811.1, CCDS73261.1	11p15.2	2013-01-24			ENSG00000148925	ENSG00000148925		"""BTB/POZ domain containing"""	21445	protein-coding gene	gene with protein product		615933				15556295	Standard	XM_005253164		Approved	GMRP1, GMRP-1, MGC13007	uc001mkz.3	Q9BSF8	OTTHUMG00000165787	ENST00000278174.5:c.341G>A	11.37:g.13441250C>T	ENSP00000278174:p.Arg114His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	136	2	0.0147059	NM_032320	B7Z228|Q86WG1	Missense_Mutation	SNP	ENST00000278174.5	37	CCDS7811.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.035255	0.93630	.	.	ENSG00000148925	ENST00000278174;ENST00000530907;ENST00000528120	T;T;T	0.33865	1.39;1.39;1.42	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.49098	0.1537	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.994;0.994;0.994;0.994	T	0.35699	-0.9778	10	0.30854	T	0.27	-50.5214	18.7093	0.91651	0.0:1.0:0.0:0.0	.	83;122;114;114	B7Z2J1;B7Z228;D3DQW7;Q9BSF8	.;.;.;BTBDA_HUMAN	H	114;122;66	ENSP00000278174:R114H;ENSP00000431186:R122H;ENSP00000435257:R66H	ENSP00000278174:R114H	R	-	2	0	BTBD10	13397826	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.274000	0.78538	2.519000	0.84933	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	weak		0.418	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
PCK1	5105	hgsc.bcm.edu	37	20	56137834	56137834	+	Silent	SNP	A	A	G	rs1062601	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:56137834A>G	ENST00000319441.4	+	4	653	c.489A>G	c.(487-489)tcA>tcG	p.S163S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Silent_p.S31S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	163					carbohydrate metabolic process (GO:0005975)|drug metabolic process (GO:0017144)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycerol biosynthetic process from pyruvate (GO:0046327)|internal protein amino acid acetylation (GO:0006475)|oxaloacetate metabolic process (GO:0006107)|response to activity (GO:0014823)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxylic acid binding (GO:0031406)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoenolpyruvate carboxykinase (GTP) activity (GO:0004613)			endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(19)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	34	Lung NSC(12;0.000764)|all_lung(29;0.00264)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;9.88e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.13e-07)			TGACGGATTCACCCTACGTGG	0.607													A|||	1573	0.314097	0.323	0.3372	5008	,	,		16924	0.0308		0.5229	False		,,,				2504	0.363				p.S163S		Atlas-SNP	.											.	PCK1	95	.	0			c.A489G						PASS	.	A		1505,2901	481.2+/-359.0	228,1049,926	73.0	61.0	65.0		489	-8.8	0.4	20	dbSNP_86	65	4342,4258	580.1+/-391.0	1083,2176,1041	no	coding-synonymous	PCK1	NM_002591.3		1311,3225,1967	GG,GA,AA		49.5116,34.158,44.9562		163/623	56137834	5847,7159	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon4			GGATTCACCCTAC		CCDS13460.1	20q13.31	2007-11-06			ENSG00000124253	ENSG00000124253	4.1.1.32		8724	protein-coding gene	gene with protein product		614168				1492743	Standard	NM_002591		Approved	PEPCK-C	uc002xyn.4	P35558	OTTHUMG00000032825	ENST00000319441.4:c.489A>G	20.37:g.56137834A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			A|0.609;G|0.391	0.391	strong		0.607	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
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 GAIIx	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_ENST00000544477.1_Missense_Mutation_p.R182C|RABEP2_ENST00000357573.6_Missense_Mutation_p.R253C	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	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	112	57	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	
FASTKD5	60493	hgsc.bcm.edu	37	20	3128578	3128578	+	Missense_Mutation	SNP	A	A	C	rs41304800	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3128578A>C	ENST00000380266.3	-	2	1460	c.1139T>G	c.(1138-1140)aTa>aGa	p.I380R	UBOX5_ENST00000348031.2_Intron|UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000217173.2_Intron	NM_021826.4	NP_068598.1	Q7L8L6	FAKD5_HUMAN	FAST kinase domains 5	380					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(2)|endometrium(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(2)	19						CTGAGGAGCTATCTCTCCAAT	0.443													A|||	214	0.0427316	0.0219	0.0663	5008	,	,		20819	0.0		0.1064	False		,,,				2504	0.0327				p.I380R		Atlas-SNP	.											FASTKD5,right_upper_lobe,carcinoma,-1,1	FASTKD5	63	1	0			c.T1139G						PASS	.	A	,ARG/ILE,	180,4226	116.3+/-154.2	1,178,2024	96.0	90.0	92.0		,1139,	5.5	1.0	20	dbSNP_127	92	937,7663	207.2+/-249.0	44,849,3407	yes	intron,missense,intron	UBOX5,FASTKD5	NM_014948.2,NM_021826.4,NM_199415.1	,97,	45,1027,5431	CC,CA,AA		10.8953,4.0853,8.5883	,benign,	,380/765,	3128578	1117,11889	2203	4300	6503	SO:0001583	missense	60493	exon2			GGAGCTATCTCTC	BC007413	CCDS13048.1	20p13	2006-07-07			ENSG00000215251	ENSG00000215251			25790	protein-coding gene	gene with protein product		614272				11347906	Standard	NM_021826		Approved	FLJ13149	uc002whz.4	Q7L8L6	OTTHUMG00000031727	ENST00000380266.3:c.1139T>G	20.37:g.3128578A>C	ENSP00000369618:p.Ile380Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	120	48	0.4	NM_021826	Q96JN3|Q9H5D1|Q9H8Y3	Missense_Mutation	SNP	ENST00000380266.3	37	CCDS13048.1	112	0.05128205128205128	12	0.024390243902439025	24	0.06629834254143646	0	0.0	76	0.10026385224274406	A	11.73	1.724478	0.30593	0.040853	0.108953	ENSG00000215251	ENST00000380266	T	0.16196	2.36	5.48	5.48	0.80851	.	0.464976	0.21773	N	0.069334	T	0.00356	0.0011	L	0.29908	0.895	0.20196	P	0.9999234467	P	0.49961	0.93	P	0.48030	0.564	T	0.26815	-1.0092	9	0.21540	T	0.41	.	15.5604	0.76240	1.0:0.0:0.0:0.0	rs41304800	380	Q7L8L6	FAKD5_HUMAN	R	380	ENSP00000369618:I380R	ENSP00000369618:I380R	I	-	2	0	FASTKD5	3076578	0.975000	0.34042	0.995000	0.50966	0.559000	0.35586	5.124000	0.64709	2.088000	0.63022	0.260000	0.18958	ATA	A|0.921;C|0.079	0.079	strong		0.443	FASTKD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077701.2	NM_021826	
ZNF768	79724	hgsc.bcm.edu	37	16	30536918	30536918	+	Missense_Mutation	SNP	C	C	G	rs10871453	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:30536918C>G	ENST00000380412.5	-	2	718	c.543G>C	c.(541-543)gaG>gaC	p.E181D	ZNF768_ENST00000562803.1_Missense_Mutation_p.E150D	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	181			E -> D (in dbSNP:rs10871453). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						GACTCTTTTCCTCGGGGTTCA	0.527													C|||	1342	0.267971	0.4856	0.2695	5008	,	,		16355	0.005		0.3827	False		,,,				2504	0.1258				p.E181D		Atlas-SNP	.											.	ZNF768	28	.	0			c.G543C						PASS	.	C	ASP/GLU	2024,2370	564.0+/-381.3	463,1098,636	108.0	115.0	112.0		543	0.6	0.9	16	dbSNP_120	112	3348,5252	497.9+/-374.6	642,2064,1594	yes	missense	ZNF768	NM_024671.3	45	1105,3162,2230	GG,GC,CC		38.9302,46.0628,41.3422	possibly-damaging	181/541	30536918	5372,7622	2197	4300	6497	SO:0001583	missense	79724	exon2			CTTTTCCTCGGGG	BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"""Zinc fingers, C2H2-type"""	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.543G>C	16.37:g.30536918C>G	ENSP00000369777:p.Glu181Asp	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_024671	Q569L7|Q96CX4	Missense_Mutation	SNP	ENST00000380412.5	37	CCDS10681.2	629	0.288003663003663	240	0.4878048780487805	111	0.30662983425414364	1	0.0017482517482517483	277	0.3654353562005277	C	15.47	2.842609	0.51057	0.460628	0.389302	ENSG00000169957	ENST00000380412;ENST00000538507	T	0.07216	3.21	5.06	0.635	0.17723	.	0.000000	0.45867	D	0.000332	T	0.00012	0.0000	N	0.08118	0	0.36384	P	0.13787899999999997	D	0.53885	0.963	P	0.47299	0.543	T	0.36407	-0.9749	9	0.25751	T	0.34	-12.5986	3.7619	0.08607	0.1637:0.4368:0.0:0.3994	rs10871453;rs17845396;rs17858253;rs60711858;rs10871453	181	Q9H5H4	ZN768_HUMAN	D	181;150	ENSP00000369777:E181D	ENSP00000369777:E181D	E	-	3	2	ZNF768	30444419	0.998000	0.40836	0.914000	0.36105	0.628000	0.37860	0.396000	0.20867	-0.007000	0.14345	0.561000	0.74099	GAG	C|0.640;G|0.360	0.360	strong		0.527	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671	
ACAN	176	hgsc.bcm.edu	37	15	89417238	89417238	+	Missense_Mutation	SNP	A	A	G	rs1126823	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89417238A>G	ENST00000561243.1	+	16	7499	c.7499A>G	c.(7498-7500)cAg>cGg	p.Q2500R	ACAN_ENST00000559004.1_Missense_Mutation_p.Q2462R|ACAN_ENST00000439576.2_Missense_Mutation_p.Q2500R|ACAN_ENST00000352105.7_Intron			P16112	PGCA_HUMAN	aggrecan	2385					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)			GAGGAGCCTCAGATCACCTGC	0.642													G|||	2037	0.406749	0.7557	0.2939	5008	,	,		17716	0.2639		0.2366	False		,,,				2504	0.3374				p.Q2500R		Atlas-SNP	.											.	ACAN	220	.	0			c.A7499G						PASS	.	G	,ARG/GLN	2941,1391		1018,905,243	37.0	46.0	43.0		,7499	2.9	1.0	15	dbSNP_86	43	2138,6378		265,1608,2385	yes	intron,missense	ACAN	NM_001135.3,NM_013227.3	,43	1283,2513,2628	GG,GA,AA		25.1057,32.1099,39.5314	,benign	,2500/2531	89417238	5079,7769	2166	4258	6424	SO:0001583	missense	176	exon17			AGCCTCAGATCAC	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.7499A>G	15.37:g.89417238A>G	ENSP00000453342:p.Gln2500Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_013227	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	778	0.35622710622710624	355	0.7215447154471545	116	0.32044198895027626	142	0.24825174825174826	165	0.21767810026385223	G	3.690	-0.063804	0.07273	0.678901	0.251057	ENSG00000157766	ENST00000439576;ENST00000268134	T	0.65178	-0.14	5.17	2.92	0.33932	.	0.000000	0.29752	N	0.011285	T	0.00012	0.0000	.	.	.	0.49582	P	1.9299999999999873E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.43621	-0.9380	8	0.02654	T	1	-7.0478	11.1267	0.48322	0.2384:0.0:0.7616:0.0	rs1126823;rs2280467;rs3182090;rs17415701;rs52823483;rs56687304;rs1126823	2500	E7EX88	.	R	2500;2386	ENSP00000387356:Q2500R	ENSP00000268134:Q2386R	Q	+	2	0	ACAN	87218242	1.000000	0.71417	0.993000	0.49108	0.969000	0.65631	1.990000	0.40717	0.591000	0.29711	-0.119000	0.15052	CAG	A|0.613;G|0.387	0.387	strong		0.642	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19756040	19756040	+	Missense_Mutation	SNP	C	C	G	rs2824790	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:19756040C>G	ENST00000284885.3	-	4	433	c.400G>C	c.(400-402)Gaa>Caa	p.E134Q		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	134	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.		E -> Q (in dbSNP:rs2824790). {ECO:0000269|PubMed:11719902, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7718557}.			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						TTTACATTTTCATCTGACACC	0.388													C|||	1130	0.225639	0.2489	0.2925	5008	,	,		17799	0.0883		0.3101	False		,,,				2504	0.2014				p.E134Q		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.G400C						PASS	.	C	GLN/GLU	1065,3341	385.4+/-325.7	139,787,1277	118.0	104.0	109.0		400	2.0	1.0	21	dbSNP_100	109	2462,6138	404.3+/-348.1	344,1774,2182	yes	missense	TMPRSS15	NM_002772.2	29	483,2561,3459	GG,GC,CC		28.6279,24.1716,27.1183	possibly-damaging	134/1020	19756040	3527,9479	2203	4300	6503	SO:0001583	missense	5651	exon4			CATTTTCATCTGA		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.400G>C	21.37:g.19756040C>G	ENSP00000284885:p.Glu134Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	148	92	0.621622	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	521	0.23855311355311357	125	0.2540650406504065	112	0.30939226519337015	51	0.08916083916083917	233	0.3073878627968338	C	14.17	2.456114	0.43634	0.241716	0.286279	ENSG00000154646	ENST00000284885;ENST00000422787	T;T	0.38887	1.11;1.11	5.81	1.98	0.26296	SEA (3);	0.470448	0.23941	N	0.043054	T	0.00012	0.0000	L	0.40543	1.245	0.45390	P	0.0016239999999999588	P	0.48162	0.906	P	0.48114	0.567	T	0.30563	-0.9974	8	.	.	.	.	8.0508	0.30577	0.0:0.6731:0.0:0.3269	rs2824790;rs17771985;rs52832529;rs2824790	134	P98073	ENTK_HUMAN	Q	134;89	ENSP00000284885:E134Q;ENSP00000398253:E89Q	.	E	-	1	0	TMPRSS15	18677911	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	0.872000	0.28037	0.092000	0.17331	0.655000	0.94253	GAA	C|0.739;G|0.261	0.261	strong		0.388	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
CRB2	286204	hgsc.bcm.edu	37	9	126133497	126133497	+	Silent	SNP	C	C	T	rs13290763	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:126133497C>T	ENST00000373631.3	+	8	2077	c.2076C>T	c.(2074-2076)tcC>tcT	p.S692S	CRB2_ENST00000373629.2_Silent_p.S360S|CRB2_ENST00000359999.3_Silent_p.S692S	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	692	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						CCAATGACTCCGCAGCTGGCC	0.617													C|||	981	0.195887	0.053	0.1729	5008	,	,		20100	0.254		0.2734	False		,,,				2504	0.2658				p.S692S		Atlas-SNP	.											.	CRB2	86	.	0			c.C2076T						PASS	.	C		373,4033		16,341,1846	129.0	138.0	135.0		2076	-9.1	0.0	9	dbSNP_121	135	2696,5904		427,1842,2031	no	coding-synonymous	CRB2	NM_173689.5		443,2183,3877	TT,TC,CC		31.3488,8.4657,23.5968		692/1286	126133497	3069,9937	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon8			TGACTCCGCAGCT	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.2076C>T	9.37:g.126133497C>T		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	137	134	0.978102	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			C|0.763;T|0.237	0.237	strong		0.617	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
ABLIM1	3983	hgsc.bcm.edu	37	10	116335246	116335246	+	Silent	SNP	G	G	A	rs985273	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:116335246G>A	ENST00000277895.5	-	3	589	c.492C>T	c.(490-492)ttC>ttT	p.F164F	ABLIM1_ENST00000533213.2_Silent_p.F104F|ABLIM1_ENST00000369252.4_Silent_p.F104F	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	164	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)	p.F104F(1)		breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		CGCCCTCCACGAACTCCCCAC	0.537													G|||	1525	0.304513	0.475	0.3602	5008	,	,		19474	0.2321		0.2078	False		,,,				2504	0.2086				p.F164F		Atlas-SNP	.											ABLIM1,NS,carcinoma,0,1	ABLIM1	131	1	1	Substitution - coding silent(1)	stomach(1)	c.C492T						scavenged	.	G	,,	1935,2471	549.1+/-377.7	436,1063,704	141.0	113.0	122.0		312,312,492	-3.2	1.0	10	dbSNP_86	122	1537,7063	289.4+/-299.3	147,1243,2910	no	coding-synonymous,coding-synonymous,coding-synonymous	ABLIM1	NM_001003407.1,NM_001003408.1,NM_002313.5	,,	583,2306,3614	AA,AG,GG		17.8721,43.9174,26.6954	,,	104/719,104/747,164/779	116335246	3472,9534	2203	4300	6503	SO:0001819	synonymous_variant	3983	exon3			CTCCACGAACTCC	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.492C>T	10.37:g.116335246G>A		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Silent	SNP	ENST00000277895.5	37	CCDS7590.1																																																																																			G|0.719;A|0.281	0.281	strong		0.537	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3		
SNX5	27131	hgsc.bcm.edu	37	20	17950545	17950545	+	5'Flank	SNP	A	A	T	rs11551768	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:17950545A>T	ENST00000377768.3	-	0	0				MGME1_ENST00000377710.5_Missense_Mutation_p.S15C|SNX5_ENST00000481323.1_5'Flank|SNX5_ENST00000377759.4_5'Flank|SNX5_ENST00000606557.1_5'Flank|MGME1_ENST00000377709.1_Missense_Mutation_p.S15C|SNX5_ENST00000486039.1_5'Flank|MGME1_ENST00000377704.4_Missense_Mutation_p.S15C|SNX5_ENST00000606602.1_5'Flank	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5						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						GCAGCTCAGGAGTTCAAAGTT	0.408													A|||	427	0.0852636	0.0582	0.1066	5008	,	,		18875	0.0288		0.1362	False		,,,				2504	0.1125				p.S15C		Atlas-SNP	.											.	.	.	.	0			c.A43T						PASS	.	A	CYS/SER	313,4093	164.0+/-195.7	13,287,1903	59.0	60.0	60.0		43	-0.9	0.0	20	dbSNP_120	60	1129,7471	228.0+/-263.2	64,1001,3235	yes	missense	C20orf72	NM_052865.2	112	77,1288,5138	TT,TA,AA		13.1279,7.1039,11.0872	possibly-damaging	15/345	17950545	1442,11564	2203	4300	6503	SO:0001631	upstream_gene_variant	92667	exon2			CTCAGGAGTTCAA	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		20.37:g.17950545A>T	Exception_encountered	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	74	72	0.972973	NM_052865	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	173	0.07921245421245421	25	0.0508130081300813	43	0.11878453038674033	17	0.02972027972027972	88	0.11609498680738786	A	11.12	1.544737	0.27563	0.071039	0.131279	ENSG00000125871	ENST00000377710;ENST00000377709;ENST00000377704	T;T;T	0.51325	0.79;0.74;0.71	5.67	-0.887	0.10587	.	1.937770	0.01666	N	0.025351	T	0.00608	0.0020	L	0.44542	1.39	0.09310	N	1	D	0.59357	0.985	P	0.46796	0.527	T	0.21075	-1.0256	10	0.62326	D	0.03	2.34	9.91	0.41399	0.2479:0.5412:0.0:0.2109	rs11551768;rs28970272	15	Q9BQP7	CT072_HUMAN	C	15	ENSP00000366939:S15C;ENSP00000366938:S15C;ENSP00000366933:S15C	ENSP00000366933:S15C	S	+	1	0	C20orf72	17898545	0.000000	0.05858	0.000000	0.03702	0.126000	0.20510	0.776000	0.26704	-0.475000	0.06852	-0.488000	0.04728	AGT	A|0.900;T|0.100	0.100	strong		0.408	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
KRT6B	3854	hgsc.bcm.edu	37	12	52844246	52844246	+	Silent	SNP	A	A	G	rs28542657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52844246A>G	ENST00000252252.3	-	2	746	c.699T>C	c.(697-699)ggT>ggC	p.G233G		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	233	Coil 1B.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)	p.G233G(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		AGTCCAGACGACCCCGTTCCC	0.557													G|||	394	0.0786741	0.0061	0.0821	5008	,	,		23280	0.1875		0.0875	False		,,,				2504	0.0532				p.G233G		Atlas-SNP	.											KRT6B,NS,carcinoma,0,1	KRT6B	90	1	1	Substitution - coding silent(1)	ovary(1)	c.T699C						scavenged	.						210.0	184.0	193.0					12																	52844246		2203	4300	6503	SO:0001819	synonymous_variant	3854	exon2			CAGACGACCCCGT	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.699T>C	12.37:g.52844246A>G		Somatic	207	4	0.0193237		WXS	Illumina HiSeq	Phase_I	224	51	0.227679	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			.	.	weak		0.557	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
ZNF285	26974	hgsc.bcm.edu	37	19	44891043	44891043	+	Missense_Mutation	SNP	G	G	T	rs77661661		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:44891043G>T	ENST00000330997.4	-	4	1428	c.1364C>A	c.(1363-1365)cCa>cAa	p.P455Q	ZNF285_ENST00000544719.2_Missense_Mutation_p.P455Q|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Missense_Mutation_p.P462Q	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	455					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P455Q(1)		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						GCATTTGTATGGTTTCTCCCC	0.448																																					p.P455Q		Atlas-SNP	.											ZNF285,trunk,malignant_melanoma,0,1	ZNF285	86	1	1	Substitution - Missense(1)	skin(1)	c.C1364A						scavenged	.																																			SO:0001583	missense	26974	exon4			TTGTATGGTTTCT	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.1364C>A	19.37:g.44891043G>T	ENSP00000333595:p.Pro455Gln	Somatic	82	2	0.0243902		WXS	Illumina HiSeq	Phase_I	92	8	0.0869565	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.224441	0.58668	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.17213	2.29	3.36	3.36	0.38483	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41834	0.1176	M	0.75447	2.3	0.30665	N	0.754012	D;B	0.89917	1.0;0.012	D;B	0.83275	0.996;0.04	T	0.45323	-0.9269	9	0.62326	D	0.03	.	13.918	0.63914	0.0:0.0:1.0:0.0	.	479;455	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	Q	478;455	ENSP00000333595:P455Q	ENSP00000333595:P455Q	P	-	2	0	ZNF285	49582883	1.000000	0.71417	0.862000	0.33874	0.982000	0.71751	5.120000	0.64685	1.598000	0.50083	0.298000	0.19748	CCA	.	.	weak		0.448	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
ZC3H4	23211	hgsc.bcm.edu	37	19	47588325	47588325	+	Silent	SNP	G	G	A	rs2287842	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47588325G>A	ENST00000253048.5	-	8	1132	c.1095C>T	c.(1093-1095)gaC>gaT	p.D365D	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	365	Gly-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		CCATGTCCTCGTCATAGAAGT	0.542													g|||	1043	0.208267	0.0492	0.2882	5008	,	,		18863	0.2579		0.2972	False		,,,				2504	0.2239				p.D365D		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C1095T						PASS	.	G		391,3875		18,355,1760	285.0	300.0	295.0		1095	-5.3	0.4	19	dbSNP_100	295	2413,6041		335,1743,2149	no	coding-synonymous	ZC3H4	NM_015168.1		353,2098,3909	AA,AG,GG		28.5427,9.1655,22.044		365/1304	47588325	2804,9916	2133	4227	6360	SO:0001819	synonymous_variant	23211	exon8			GTCCTCGTCATAG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1095C>T	19.37:g.47588325G>A		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	192	191	0.994792	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			G|0.775;A|0.225	0.225	strong		0.542	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
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 GAIIx	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		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	28	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	
PRR22	163154	hgsc.bcm.edu	37	19	5783712	5783712	+	Silent	SNP	C	C	T	rs2446211	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5783712C>T	ENST00000419421.2	-	3	650	c.546G>A	c.(544-546)ccG>ccA	p.P182P		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	182	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GGGGTGGCAGCGGGGCCGGGC	0.716													c|||	1687	0.336861	0.4228	0.1931	5008	,	,		8488	0.5456		0.165	False		,,,				2504	0.2843				p.P182P		Atlas-SNP	.											PRR22_ENST00000419421,NS,carcinoma,0,2	PRR22	25	2	0			c.G546A						PASS	.	T		1038,2702		151,736,983	3.0	5.0	4.0		546	-5.2	0.0	19	dbSNP_100	4	1020,6676		80,860,2908	no	coding-synonymous	PRR22	NM_001134316.1		231,1596,3891	TT,TC,CC		13.2536,27.754,17.9958		182/423	5783712	2058,9378	1870	3848	5718	SO:0001819	synonymous_variant	163154	exon3			TGGCAGCGGGGCC	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.546G>A	19.37:g.5783712C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	28	17	0.607143	NM_001134316	E9PB31	Silent	SNP	ENST00000419421.2	37	CCDS45933.1																																																																																			C|0.689;T|0.311	0.311	strong		0.716	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
MUC16	94025	hgsc.bcm.edu	37	19	9058624	9058624	+	Missense_Mutation	SNP	G	G	A	rs11878666	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9058624G>A	ENST00000397910.4	-	3	29025	c.28822C>T	c.(28822-28824)Ccc>Tcc	p.P9608S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9610	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCACCAGAGGGCATCTTGTAA	0.527													G|||	964	0.192492	0.0908	0.2824	5008	,	,		21210	0.3313		0.167	False		,,,				2504	0.1493				p.P9608S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C28822T						PASS	.	G	SER/PRO	409,3633		18,373,1630	106.0	98.0	100.0		28822	-5.0	0.0	19	dbSNP_120	100	1518,6844		136,1246,2799	yes	missense	MUC16	NM_024690.2	74	154,1619,4429	AA,AG,GG		18.1536,10.1188,15.5353	benign	9608/14508	9058624	1927,10477	2021	4181	6202	SO:0001583	missense	94025	exon3			CAGAGGGCATCTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28822C>T	19.37:g.9058624G>A	ENSP00000381008:p.Pro9608Ser	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	155	85	0.548387	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	481	0.22023809523809523	54	0.10975609756097561	93	0.2569060773480663	208	0.36363636363636365	126	0.1662269129287599	g	8.218	0.801892	0.16397	0.101188	0.181536	ENSG00000181143	ENST00000397910	T	0.01505	4.82	2.5	-5.0	0.03001	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	B	0.19817	0.039	B	0.18263	0.021	T	0.46596	-0.9180	7	0.87932	D	0	.	2.0697	0.03610	0.5346:0.1429:0.1786:0.144	rs11878666;rs52808802;rs11878666	9608	B5ME49	.	S	9608	ENSP00000381008:P9608S	ENSP00000381008:P9608S	P	-	1	0	MUC16	8919624	0.000000	0.05858	0.000000	0.03702	0.542000	0.35054	-0.925000	0.03992	-1.950000	0.01030	0.305000	0.20034	CCC	G|0.785;A|0.215	0.215	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
STPG2	285555	hgsc.bcm.edu	37	4	99027184	99027184	+	Missense_Mutation	SNP	T	T	C	rs2903150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:99027184T>C	ENST00000295268.3	-	5	621	c.532A>G	c.(532-534)Atc>Gtc	p.I178V		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	178			I -> V (in dbSNP:rs2903150).														TCTCTCTTGATGTTAACATTT	0.254													t|||	1879	0.3752	0.4425	0.2882	5008	,	,		15525	0.2748		0.4026	False		,,,				2504	0.4213				p.I178V		Atlas-SNP	.											.	.	.	.	0			c.A532G						PASS	.	C	VAL/ILE	1967,2429	529.8+/-372.8	454,1059,685	81.0	83.0	82.0		532	2.6	1.0	4	dbSNP_101	82	3400,5194	487.8+/-372.2	692,2016,1589	yes	missense	C4orf37	NM_174952.2	29	1146,3075,2274	CC,CT,TT		39.5625,44.7452,41.3164	benign	178/460	99027184	5367,7623	2198	4297	6495	SO:0001583	missense	285555	exon5			TCTTGATGTTAAC	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.532A>G	4.37:g.99027184T>C	ENSP00000295268:p.Ile178Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	31	0.382716	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	760	0.34798534798534797	193	0.39227642276422764	106	0.292817679558011	161	0.28146853146853146	300	0.39577836411609496	t	0.674	-0.800947	0.02841	0.447452	0.395625	ENSG00000163116	ENST00000295268	T	0.11385	2.78	5.04	2.61	0.31194	.	0.361157	0.28712	N	0.014387	T	0.00012	0.0000	L	0.52011	1.625	0.58432	P	8.000000000008E-6	B	0.22746	0.074	B	0.31614	0.133	T	0.46233	-0.9206	9	0.22109	T	0.4	-32.5742	6.054	0.19800	0.1206:0.1463:0.0:0.7331	rs2903150;rs52793168;rs61326598;rs2903150	178	Q8N412	CD037_HUMAN	V	178	ENSP00000295268:I178V	ENSP00000295268:I178V	I	-	1	0	C4orf37	99246207	1.000000	0.71417	0.997000	0.53966	0.048000	0.14542	0.706000	0.25690	0.089000	0.17243	-1.245000	0.01525	ATC	T|0.617;C|0.383	0.383	strong		0.254	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952	
TCF7	6932	hgsc.bcm.edu	37	5	133481467	133481467	+	Missense_Mutation	SNP	G	G	A	rs30489	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:133481467G>A	ENST00000321584.4	+	10	1307	c.1111G>A	c.(1111-1113)Gga>Aga	p.G371R	TCF7_ENST00000395023.1_Intron|TCF7_ENST00000520958.1_Intron|TCF7_ENST00000342854.5_Intron|TCF7_ENST00000395029.1_Intron|TCF7_ENST00000518915.1_Missense_Mutation_p.G256R|TCF7_ENST00000378560.4_Intron|TCF7_ENST00000432532.2_Intron|TCF7_ENST00000321603.6_Intron			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	371					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GGATGGTAATGGACAAGAGTC	0.517											OREG0016787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	768	0.153355	0.0015	0.2161	5008	,	,		23862	0.4167		0.0865	False		,,,				2504	0.1115				p.G256R		Atlas-SNP	.											.	TCF7	81	.	0			c.G766A						PASS	.	G	ARG/GLY,,,,	97,3823		1,95,1864	96.0	99.0	98.0		766,,,,	-2.6	0.0	5	dbSNP_76	98	692,7614		27,638,3488	yes	missense,intron,intron,intron,intron	TCF7	NM_001134851.2,NM_003202.3,NM_201632.3,NM_201634.3,NM_213648.3	125,,,,	28,733,5352	AA,AG,GG		8.3313,2.4745,6.4535	,,,,	256/270,,,,	133481467	789,11437	1960	4153	6113	SO:0001583	missense	6932	exon9			GGTAATGGACAAG	Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.1111G>A	5.37:g.133481467G>A	ENSP00000326540:p.Gly371Arg	Somatic	67	0	0	1603	WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_001134851	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	37		365	0.1671245421245421	2	0.0040650406504065045	64	0.17679558011049723	234	0.4090909090909091	65	0.08575197889182058	G	14.05	2.420989	0.42918	0.024745	0.083313	ENSG00000081059	ENST00000321584;ENST00000518915	D;D	0.99143	-5.48;-5.47	3.77	-2.61	0.06171	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	7	0.87932	D	0	.	4.5923	0.12313	0.3564:0.1878:0.4558:0.0	rs30489;rs52826316;rs59858442;rs30489	371	P36402	TCF7_HUMAN	R	371;256	ENSP00000326540:G371R;ENSP00000430179:G256R	ENSP00000326540:G371R	G	+	1	0	TCF7	133509366	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.239000	0.08965	-0.429000	0.07329	0.655000	0.94253	GGA	G|0.827;N|0.000	.	strong		0.517	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634	
OR2A25	392138	hgsc.bcm.edu	37	7	143771408	143771408	+	Silent	SNP	G	G	C	rs59319753	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143771408G>C	ENST00000408898.2	+	1	134	c.96G>C	c.(94-96)ctG>ctC	p.L32L		NM_001004488.1	NP_001004488.1	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A, member 25	32						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(16)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	24	Melanoma(164;0.0783)					TCTTCTCCCTGTTCTACATCT	0.527													.|||	1689	0.33726	0.2186	0.4467	5008	,	,		19151	0.628		0.2107	False		,,,				2504	0.2505				p.L32L		Atlas-SNP	.											.	OR2A25	66	.	0			c.G96C						PASS	.	G		899,3507	336.5+/-304.4	82,735,1386	80.0	84.0	83.0		96	0.6	1.0	7	dbSNP_129	83	1794,6806	320.0+/-314.4	190,1414,2696	no	coding-synonymous	OR2A25	NM_001004488.1		272,2149,4082	CC,CG,GG		20.8605,20.404,20.7058		32/311	143771408	2693,10313	2203	4300	6503	SO:0001819	synonymous_variant	392138	exon1			CTCCCTGTTCTAC		CCDS43669.1	7q35	2012-08-09		2004-03-10	ENSG00000221933	ENSG00000221933		"""GPCR / Class A : Olfactory receptors"""	19562	protein-coding gene	gene with protein product				OR2A25P, OR2A27			Standard	NM_001004488		Approved		uc011ktx.2	A4D2G3	OTTHUMG00000158013	ENST00000408898.2:c.96G>C	7.37:g.143771408G>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_001004488	B2RNC9	Silent	SNP	ENST00000408898.2	37	CCDS43669.1																																																																																			G|0.684;C|0.316	0.316	strong		0.527	OR2A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350000.1		
CD82	3732	hgsc.bcm.edu	37	11	44636833	44636833	+	Silent	SNP	G	G	A	rs2303865	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:44636833G>A	ENST00000227155.4	+	7	596	c.348G>A	c.(346-348)gaG>gaA	p.E116E	CD82_ENST00000342935.3_Silent_p.E91E|CD82_ENST00000530931.1_3'UTR	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	116						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						TGAAGCAGGAGATGGGCGGCA	0.602													G|||	1231	0.245807	0.0129	0.3141	5008	,	,		19730	0.4653		0.1322	False		,,,				2504	0.4029				p.E116E		Atlas-SNP	.											.	CD82	27	.	0			c.G348A						PASS	.	G	,	156,4250	104.7+/-143.2	2,152,2049	71.0	58.0	62.0		273,348	1.7	1.0	11	dbSNP_100	62	1158,7440	237.4+/-269.2	68,1022,3209	no	coding-synonymous,coding-synonymous	CD82	NM_001024844.1,NM_002231.3	,	70,1174,5258	AA,AG,GG		13.4682,3.5406,10.1046	,	91/243,116/268	44636833	1314,11690	2203	4299	6502	SO:0001819	synonymous_variant	3732	exon7			GCAGGAGATGGGC	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"""CD molecules"", ""Tetraspanins"""	6210	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 6"", ""R2 leukocyte antigen"""	600623	"""kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))"", ""CD82 antigen"""	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.348G>A	11.37:g.44636833G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	166	74	0.445783	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Silent	SNP	ENST00000227155.4	37	CCDS7909.1																																																																																			G|0.866;A|0.134	0.134	strong		0.602	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1		
CNOT1	23019	hgsc.bcm.edu	37	16	58579274	58579274	+	Silent	SNP	C	C	T	rs246258	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:58579274C>T	ENST00000317147.5	-	30	4460	c.4128G>A	c.(4126-4128)ctG>ctA	p.L1376L	CNOT1_ENST00000441024.2_Silent_p.L1376L|CNOT1_ENST00000245138.4_Silent_p.L227L|CNOT1_ENST00000569240.1_Silent_p.L1371L	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1376	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CTGTTGGATTCAGAGTAATGT	0.478													T|||	1424	0.284345	0.1339	0.4135	5008	,	,		19153	0.3839		0.2416	False		,,,				2504	0.3374				p.L1376L		Atlas-SNP	.											.	CNOT1	359	.	0			c.G4128A						PASS	.	T	,	668,3728	762.9+/-413.2	58,552,1588	246.0	201.0	216.0		4128,4128	1.9	1.0	16	dbSNP_79	216	2214,6386	710.5+/-405.8	289,1636,2375	no	coding-synonymous,coding-synonymous	CNOT1	NM_016284.3,NM_206999.1	,	347,2188,3963	TT,TC,CC		25.7442,15.1956,22.1761	,	1376/2377,1376/1552	58579274	2882,10114	2198	4300	6498	SO:0001819	synonymous_variant	23019	exon30			TGGATTCAGAGTA	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4128G>A	16.37:g.58579274C>T		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	201	101	0.502488	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																			C|0.754;T|0.246	0.246	strong		0.478	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
VWA5B2	90113	hgsc.bcm.edu	37	3	183953972	183953972	+	Silent	SNP	G	G	A	rs1709657	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183953972G>A	ENST00000426955.2	+	8	1234	c.1134G>A	c.(1132-1134)ccG>ccA	p.P378P	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_Silent_p.P159P	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	389	VWFA.									breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						AGTCCCTCCCGCCCCAGACGC	0.627													G|||	998	0.199281	0.1369	0.1888	5008	,	,		17637	0.2351		0.2256	False		,,,				2504	0.227				p.P378P		Atlas-SNP	.											.	VWA5B2	47	.	0			c.G1134A						PASS	.	G		207,1177		17,173,502	78.0	72.0	74.0		1134	-7.7	0.0	3	dbSNP_89	74	660,2522		69,522,1000	yes	coding-synonymous	VWA5B2	NM_138345.1		86,695,1502	AA,AG,GG		20.7417,14.9566,18.9882		378/1243	183953972	867,3699	692	1591	2283	SO:0001819	synonymous_variant	90113	exon8			CCTCCCGCCCCAG		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.1134G>A	3.37:g.183953972G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	170	62	0.364706	NM_138345	B9EGN7	Silent	SNP	ENST00000426955.2	37	CCDS54686.1																																																																																			G|0.823;A|0.177	0.177	strong		0.627	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
HSPA9	3313	hgsc.bcm.edu	37	5	137902339	137902339	+	Silent	SNP	T	T	C	rs1042665	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:137902339T>C	ENST00000297185.3	-	9	1073	c.948A>G	c.(946-948)aaA>aaG	p.K316K	HSPA9_ENST00000501917.2_5'UTR	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	316					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGAGTTCACATTTAGCCTTTT	0.408													T|||	2103	0.419928	0.3464	0.2464	5008	,	,		18698	0.7629		0.2485	False		,,,				2504	0.4652				p.K316K		Atlas-SNP	.											.	HSPA9	49	.	0			c.A948G						PASS	.	T		1401,3005	460.3+/-352.6	225,951,1027	156.0	143.0	147.0		948	-1.3	0.8	5	dbSNP_86	147	1896,6704	337.2+/-322.2	191,1514,2595	no	coding-synonymous	HSPA9	NM_004134.6		416,2465,3622	CC,CT,TT		22.0465,31.7975,25.3498		316/680	137902339	3297,9709	2203	4300	6503	SO:0001819	synonymous_variant	3313	exon9			TTCACATTTAGCC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"""Heat shock proteins / HSP70"""	5244	protein-coding gene	gene with protein product		600548	"""heat shock 70kDa protein 9B (mortalin-2)"""	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.948A>G	5.37:g.137902339T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	61	22	0.360656	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Silent	SNP	ENST00000297185.3	37	CCDS4208.1																																																																																			T|0.686;C|0.314	0.314	strong		0.408	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
OR10X1	128367	hgsc.bcm.edu	37	1	158549421	158549421	+	Missense_Mutation	SNP	G	G	A	rs77690058	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158549421G>A	ENST00000368150.1	-	1	268	c.269C>T	c.(268-270)aCg>aTg	p.T90M		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	90						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					GATGGTCAGCGTATAGCAGGT	0.493													G|||	190	0.0379393	0.0068	0.0562	5008	,	,		21015	0.0		0.0984	False		,,,				2504	0.044				p.T90M		Atlas-SNP	.											OR10X1,face,carcinoma,-1,1	OR10X1	96	1	0			c.C269T						PASS	.	G	MET/THR	95,4311	78.3+/-116.7	1,93,2109	108.0	101.0	103.0		269	5.1	1.0	1	dbSNP_131	103	852,7748	194.2+/-239.7	35,782,3483	yes	missense	OR10X1	NM_001004477.1	81	36,875,5592	AA,AG,GG		9.907,2.1562,7.2813	probably-damaging	90/327	158549421	947,12059	2203	4300	6503	SO:0001583	missense	128367	exon1			GTCAGCGTATAGC	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.269C>T	1.37:g.158549421G>A	ENSP00000357132:p.Thr90Met	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	125	47	0.376	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	104	0.047619047619047616	5	0.01016260162601626	22	0.06077348066298342	0	0.0	77	0.10158311345646438	G	14.28	2.488577	0.44249	0.021562	0.09907	ENSG00000186400	ENST00000368150	T	0.00581	6.42	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000120	T	0.02267	0.0070	M	0.90650	3.135	0.32554	N	0.532028	D	0.89917	1.0	D	0.87578	0.998	T	0.06075	-1.0847	10	0.72032	D	0.01	.	17.5191	0.87782	0.0:0.0:1.0:0.0	.	90	Q8NGY0	O10X1_HUMAN	M	90	ENSP00000357132:T90M	ENSP00000357132:T90M	T	-	2	0	OR10X1	156816045	0.002000	0.14202	0.953000	0.39169	0.229000	0.25112	1.249000	0.32839	2.648000	0.89879	0.650000	0.86243	ACG	G|0.926;A|0.074	0.074	strong		0.493	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
SLC35G2	80723	hgsc.bcm.edu	37	3	136574521	136574521	+	Silent	SNP	C	C	T	rs1052620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:136574521C>T	ENST00000446465.2	+	2	1847	c.1219C>T	c.(1219-1221)Cta>Tta	p.L407L	RP11-85F14.5_ENST00000470236.1_RNA|RP11-85F14.5_ENST00000474250.1_RNA|RP11-85F14.5_ENST00000461864.1_RNA|SLC35G2_ENST00000393079.3_Silent_p.L407L	NM_025246.2	NP_079522.2			solute carrier family 35, member G2																		CCAGGAAATACTAGACTCTCC	0.323													C|||	439	0.0876597	0.0098	0.0908	5008	,	,		16135	0.001		0.1889	False		,,,				2504	0.1759				p.L407L		Atlas-SNP	.											.	.	.	.	0			c.C1219T						PASS	.	C	,,	184,4222	116.7+/-154.6	6,172,2025	66.0	63.0	64.0		1219,1219,1219	3.0	1.0	3	dbSNP_86	64	2014,6586	339.1+/-323.0	232,1550,2518	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM22	NM_001097599.1,NM_001097600.1,NM_025246.2	,,	238,1722,4543	TT,TC,CC		23.4186,4.1761,16.8999	,,	407/413,407/413,407/413	136574521	2198,10808	2203	4300	6503	SO:0001819	synonymous_variant	80723	exon2			GAAATACTAGACT	BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"""Solute carriers"""	28480	protein-coding gene	gene with protein product			"""transmembrane protein 22"""	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.1219C>T	3.37:g.136574521C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	92	38	0.413043	NM_025246		Silent	SNP	ENST00000446465.2	37	CCDS3091.1																																																																																			C|0.857;T|0.143	0.143	strong		0.323	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246	
KLK3	354	hgsc.bcm.edu	37	19	51361472	51361472	+	Missense_Mutation	SNP	C	C	A	rs2003783	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51361472C>A	ENST00000326003.2	+	3	435	c.394C>A	c.(394-396)Ctc>Atc	p.L132I	KLK3_ENST00000595952.1_Missense_Mutation_p.L89I|KLK3_ENST00000593997.1_Missense_Mutation_p.L132I|KLK3_ENST00000360617.3_Missense_Mutation_p.L132I|KLK3_ENST00000597483.1_Missense_Mutation_p.L89I	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	132	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		L -> I (in dbSNP:rs2003783). {ECO:0000269|PubMed:23842001}.		cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		GCCTGCCGAGCTCACGGATGC	0.617													A|||	446	0.0890575	0.1483	0.0879	5008	,	,		19555	0.0694		0.0954	False		,,,				2504	0.0235				p.L132I	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.C394A						PASS	.	A	ILE/LEU,ILE/LEU,ILE/LEU	634,3772	766.9+/-413.5	51,532,1620	74.0	63.0	67.0		394,265,394	-3.7	0.0	19	dbSNP_92	67	743,7857	785.8+/-407.6	28,687,3585	yes	missense,missense,missense	KLK3	NM_001030047.1,NM_001030048.1,NM_001648.2	5,5,5	79,1219,5205	AA,AC,CC		8.6395,14.3895,10.5874	,,	132/239,89/219,132/262	51361472	1377,11629	2203	4300	6503	SO:0001583	missense	354	exon3			GCCGAGCTCACGG	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.394C>A	19.37:g.51361472C>A	ENSP00000314151:p.Leu132Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_001030047	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Missense_Mutation	SNP	ENST00000326003.2	37	CCDS12807.1	214	0.09798534798534798	67	0.13617886178861788	39	0.10773480662983426	48	0.08391608391608392	60	0.079155672823219	A	0.007	-2.005041	0.00426	0.143895	0.086395	ENSG00000142515	ENST00000326003;ENST00000422986;ENST00000360617	T;T	0.08008	3.14;3.14	2.31	-3.68	0.04463	.	0.404855	0.18025	N	0.154101	T	0.00039	0.0001	L	0.31157	0.91	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.46693	-0.9173	9	0.02654	T	1	.	9.9961	0.41900	0.1921:0.7008:0.1071:0.0	rs2003783;rs2271091;rs16987763;rs52794924;rs2003783	132;89	G3XAE3;G3V0H4	.;.	I	132;89;132	ENSP00000314151:L132I;ENSP00000353829:L132I	ENSP00000314151:L132I	L	+	1	0	KLK3	56053284	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.882000	0.04174	-1.811000	0.01229	-1.453000	0.01033	CTC	C|0.896;A|0.104	0.104	strong		0.617	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
EPHX2	2053	hgsc.bcm.edu	37	8	27396208	27396208	+	Splice_Site	SNP	G	G	A	rs4149253	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27396208G>A	ENST00000521400.1	+	14	1705	c.1275G>A	c.(1273-1275)gcG>gcA	p.A425A	EPHX2_ENST00000518379.1_Splice_Site_p.A393A|EPHX2_ENST00000380476.3_Splice_Site_p.A372A|EPHX2_ENST00000521780.1_Splice_Site_p.A359A|EPHX2_ENST00000517536.1_Splice_Site_p.A242A	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	425	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		TCTGTGAAGCGGGTAAGAGAC	0.433													G|||	569	0.113618	0.115	0.0648	5008	,	,		21023	0.1746		0.0596	False		,,,				2504	0.1391				p.A425A		Atlas-SNP	.											.	EPHX2	57	.	0			c.G1275A						PASS	.	G		446,3960	213.1+/-232.8	19,408,1776	126.0	120.0	122.0		1275	2.8	0.8	8	dbSNP_110	122	507,8093	144.0+/-200.0	15,477,3808	yes	coding-synonymous-near-splice	EPHX2	NM_001979.4		34,885,5584	AA,AG,GG		5.8953,10.1226,7.3274		425/556	27396208	953,12053	2203	4300	6503	SO:0001630	splice_region_variant	2053	exon14			TGAAGCGGGTAAG	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1276+1G>A	8.37:g.27396208G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1																																																																																			G|0.907;A|0.093	0.093	strong		0.433	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		Silent
PRDM9	56979	hgsc.bcm.edu	37	5	23527323	23527323	+	Missense_Mutation	SNP	C	C	G	rs200539936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:23527323C>G	ENST00000296682.3	+	11	2308	c.2126C>G	c.(2125-2127)aCt>aGt	p.T709S		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	709					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						GTCCTCCTCACTCACCAGAGG	0.587										HNSCC(3;0.000094)			c|||	492	0.0982428	0.2398	0.0893	5008	,	,		21450	0.0387		0.0298	False		,,,				2504	0.045				p.T709S		Atlas-SNP	.											PRDM9,NS,carcinoma,0,1	PRDM9	344	1	0			c.C2126G						scavenged	.						16.0	15.0	15.0					5																	23527323		1825	3640	5465	SO:0001583	missense	56979	exon11			TCCTCACTCACCA	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.2126C>G	5.37:g.23527323C>G	ENSP00000296682:p.Thr709Ser	Somatic	63	5	0.0793651		WXS	Illumina HiSeq	Phase_I	75	18	0.24	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	c	0.001	-4.409211	0.00000	.	.	ENSG00000164256	ENST00000296682	T	0.17370	2.28	2.57	-5.13	0.02884	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	3.203060	0.01089	N	0.005146	T	0.07999	0.0200	N	0.12920	0.275	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32771	-0.9894	10	0.10111	T	0.7	.	1.0864	0.01654	0.2843:0.3342:0.1048:0.2768	.	709	Q9NQV7	PRDM9_HUMAN	S	709	ENSP00000296682:T709S	ENSP00000296682:T709S	T	+	2	0	PRDM9	23563080	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-20.000000	0.00000	-6.649000	0.00003	-6.748000	0.00000	ACT	C|0.934;G|0.066	0.066	strong		0.587	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
CD6	923	hgsc.bcm.edu	37	11	60777073	60777073	+	Missense_Mutation	SNP	G	G	A	rs12360861	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:60777073G>A	ENST00000313421.7	+	5	997	c.811G>A	c.(811-813)Gct>Act	p.A271T	CD6_ENST00000352009.5_Missense_Mutation_p.A271T|CD6_ENST00000452451.2_Missense_Mutation_p.A271T|CD6_ENST00000346437.4_Missense_Mutation_p.A271T|CD6_ENST00000344028.5_Missense_Mutation_p.A271T|CD6_ENST00000545105.1_Intron	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	271	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.		A -> T (in dbSNP:rs12360861).		cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GACAGGGGGCGCTGACCGCTG	0.637													G|||	384	0.0766773	0.0401	0.121	5008	,	,		19148	0.001		0.1938	False		,,,				2504	0.0521				p.A271T	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											CD6_ENST00000313421,rectum,carcinoma,0,2	CD6	122	2	0			c.G811A						PASS	.	G	THR/ALA	267,4139	145.0+/-179.8	8,251,1944	40.0	38.0	38.0		811	-9.8	0.0	11	dbSNP_120	38	1562,7036	285.1+/-297.0	144,1274,2881	yes	missense	CD6	NM_006725.3	58	152,1525,4825	AA,AG,GG		18.167,6.0599,14.0649	benign	271/669	60777073	1829,11175	2203	4299	6502	SO:0001583	missense	923	exon5			GGGGGCGCTGACC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.811G>A	11.37:g.60777073G>A	ENSP00000323280:p.Ala271Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	221	0.10119047619047619	19	0.03861788617886179	51	0.1408839779005525	1	0.0017482517482517483	150	0.19788918205804748	G	1.521	-0.546883	0.04024	0.060599	0.18167	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000452451;ENST00000352009	T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34	4.9	-9.81	0.00487	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.748670	0.02962	N	0.143237	T	0.00012	0.0000	N	0.11284	0.12	0.80722	P	0.0	B;B;B;B	0.22414	0.055;0.069;0.041;0.054	B;B;B;B	0.15484	0.01;0.01;0.011;0.013	T	0.04495	-1.0947	9	0.12766	T	0.61	.	5.9428	0.19201	0.6054:0.0724:0.1293:0.1929	rs12360861	271;271;271;271	P30203-5;P30203-4;P30203;Q8N4Q7	.;.;CD6_HUMAN;.	T	271	ENSP00000344108:A271T;ENSP00000345566:A271T;ENSP00000323280:A271T;ENSP00000390676:A271T;ENSP00000340628:A271T	ENSP00000323280:A271T	A	+	1	0	CD6	60533649	0.000000	0.05858	0.000000	0.03702	0.346000	0.29079	-7.571000	0.00034	-2.169000	0.00777	-0.266000	0.10368	GCT	G|0.878;A|0.122	0.122	strong		0.637	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
C2orf73	129852	hgsc.bcm.edu	37	2	54587659	54587659	+	Missense_Mutation	SNP	G	G	C	rs13184	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54587659G>C	ENST00000398634.2	+	5	866	c.824G>C	c.(823-825)aGg>aCg	p.R275T	C2orf73_ENST00000491538.1_Intron|C2orf73_ENST00000405749.1_Intron	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	275			R -> T (in dbSNP:rs13184). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.							breast(2)	2						CTTTTCACTAGGCACAAGCCT	0.423													G|||	892	0.178115	0.2231	0.1671	5008	,	,		17785	0.126		0.2127	False		,,,				2504	0.1431				p.R275T		Atlas-SNP	.											.	C2orf73	17	.	0			c.G824C						PASS	.	G	THR/ARG	835,2879		108,619,1130	24.0	24.0	24.0		824	-0.2	0.0	2	dbSNP_52	24	1682,6474		187,1308,2583	yes	missense	C2orf73	NM_001100396.1	71	295,1927,3713	CC,CG,GG		20.6229,22.4825,21.2047	benign	275/288	54587659	2517,9353	1857	4078	5935	SO:0001583	missense	129852	exon5			TCACTAGGCACAA	BC031669, AK097617	CCDS46285.1	2p16.2	2008-07-07			ENSG00000177994	ENSG00000177994			26861	protein-coding gene	gene with protein product						14702039	Standard	NM_001100396		Approved	FLJ40298	uc002rxt.1	Q8N5S3	OTTHUMG00000151826	ENST00000398634.2:c.824G>C	2.37:g.54587659G>C	ENSP00000381631:p.Arg275Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_001100396	A0AV79|A0AV81|Q8N7V4	Missense_Mutation	SNP	ENST00000398634.2	37	CCDS46285.1	432	0.1978021978021978	124	0.25203252032520324	55	0.15193370165745856	80	0.13986013986013987	173	0.22823218997361477	G	11.16	1.558244	0.27827	0.224825	0.206229	ENSG00000177994	ENST00000398634	T	0.26810	1.71	5.05	-0.156	0.13391	.	0.130068	0.35772	N	0.002997	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P;P	0.41848	0.763;0.589	B;B	0.41619	0.361;0.288	T	0.39820	-0.9595	8	.	.	.	-26.6081	5.6486	0.17604	0.2039:0.0:0.5586:0.2375	rs13184;rs3204720;rs17045840;rs52811026;rs13184	217;275	B7ZM12;Q8N5S3	.;CB073_HUMAN	T	275	ENSP00000381631:R275T	.	R	+	2	0	C2orf73	54441163	0.695000	0.27747	0.034000	0.17996	0.003000	0.03518	1.265000	0.33027	-0.017000	0.14103	-0.259000	0.10710	AGG	G|0.813;C|0.186	0.186	strong		0.423	C2orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324075.2	NM_001100396	
ALMS1	7840	hgsc.bcm.edu	37	2	73679280	73679280	+	Missense_Mutation	SNP	A	A	G	rs6546838	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73679280A>G	ENST00000264448.6	+	8	5734	c.5623A>G	c.(5623-5625)Ata>Gta	p.I1875V	ALMS1_ENST00000409009.1_Missense_Mutation_p.I1833V|ALMS1_ENST00000377715.1_Missense_Mutation_p.I1875V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1875	34 X 47 AA approximate tandem repeat.		I -> V (in dbSNP:rs6546838).		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						TTTGAAAGCAATAGGGGTTCC	0.443													G|||	1797	0.358826	0.8585	0.3919	5008	,	,		18751	0.0089		0.2276	False		,,,				2504	0.1554				p.I1875V		Atlas-SNP	.											.	ALMS1	384	.	0			c.A5623G						PASS	.	G	VAL/ILE	2708,1020		995,718,151	62.0	61.0	62.0		5623	-3.3	0.0	2	dbSNP_116	62	1951,6229		221,1509,2360	yes	missense	ALMS1	NM_015120.4	29	1216,2227,2511	GG,GA,AA		23.8509,27.3605,39.125	benign	1875/4168	73679280	4659,7249	1864	4090	5954	SO:0001583	missense	7840	exon8			AAAGCAATAGGGG	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.5623A>G	2.37:g.73679280A>G	ENSP00000264448:p.Ile1875Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	45	34	0.755556	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	731	0.3347069597069597	419	0.8516260162601627	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	G	0.013	-1.607239	0.00842	0.726395	0.238509	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.12879	3.53;3.53;2.64	4.38	-3.33	0.04958	.	2.320940	0.02370	N	0.077734	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.001	T	0.33137	-0.9880	9	0.02654	T	1	.	5.2394	0.15464	0.2773:0.0:0.2757:0.447	rs6546838;rs17434110;rs52790418;rs60669356;rs6546838	1875;1833;1875	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	V	1833;1875;1875	ENSP00000386627:I1833V;ENSP00000264448:I1875V;ENSP00000366944:I1875V	ENSP00000264448:I1875V	I	+	1	0	ALMS1	73532788	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.185000	0.09684	-0.997000	0.03450	-1.234000	0.01563	ATA	A|0.663;G|0.337	0.337	strong		0.443	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
LPP	4026	hgsc.bcm.edu	37	3	188590446	188590446	+	Silent	SNP	A	A	G	rs1136644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:188590446A>G	ENST00000312675.4	+	10	1851	c.1605A>G	c.(1603-1605)cgA>cgG	p.R535R	LPP_ENST00000543006.1_Silent_p.R535R	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	535	LIM zinc-binding 3. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TTGCCCCGCGATGTTCTGTGT	0.522			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								A|||	2005	0.400359	0.2602	0.3919	5008	,	,		21140	0.4345		0.5298	False		,,,				2504	0.4274				p.R535R		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	LPP_ENST00000312675,NS,carcinoma,+1,1	LPP	72	1	0			c.A1605G						PASS	.	A	,,	1244,3162	429.5+/-342.2	184,876,1143	139.0	128.0	132.0		1605,1164,1605	0.0	1.0	3	dbSNP_86	132	4360,4240	582.0+/-391.3	1118,2124,1058	no	coding-synonymous,coding-synonymous,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	1302,3000,2201	GG,GA,AA		49.3023,28.2342,43.0878	,,	535/613,388/466,535/613	188590446	5604,7402	2203	4300	6503	SO:0001819	synonymous_variant	4026	exon10			CCCGCGATGTTCT	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1605A>G	3.37:g.188590446A>G		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	191	83	0.434555	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																			A|0.579;G|0.421	0.421	strong		0.522	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318770	21318770	+	Missense_Mutation	SNP	G	G	A	rs3752033	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:21318770G>A	ENST00000583088.1	+	3	1011	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	KCNJ12_ENST00000331718.5_Missense_Mutation_p.R39Q	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	39					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	GTGCACACGCGGCGCAGGTGC	0.617										Prostate(3;0.18)			.|||	1734	0.346246	0.1505	0.366	5008	,	,		36674	0.4812		0.3559	False		,,,				2504	0.4479				p.R39Q		Atlas-SNP	.											.	.	.	.	0			c.G116A						PASS	.	G	GLN/ARG	526,3880		0,526,1677	114.0	87.0	96.0		116	5.3	1.0	17	dbSNP_107	96	2294,6306		0,2294,2006	yes	missense	KCNJ12	NM_021012.4	43	0,2820,3683	AA,AG,GG		26.6744,11.9383,21.6823	possibly-damaging	39/434	21318770	2820,10186	2203	4300	6503	SO:0001583	missense	100134444	exon3			ACACGCGGCGCAG	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.116G>A	17.37:g.21318770G>A	ENSP00000463778:p.Arg39Gln	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	115	39	0.33913	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	714	0.3269230769230769	78	0.15853658536585366	121	0.3342541436464088	267	0.46678321678321677	248	0.32717678100263853	G	22.8	4.332021	0.81801	0.119383	0.266744	ENSG00000184185	ENST00000331718	T	0.61980	0.06	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.193728	0.40385	U	0.001108	T	0.00012	0.0000	L	0.52759	1.655	0.58432	D	0.999999	P	0.37276	0.589	B	0.36766	0.232	T	0.43909	-0.9362	10	0.42905	T	0.14	.	19.026	0.92932	0.0:0.0:1.0:0.0	rs3752033;rs3752033	39	Q14500	IRK12_HUMAN	Q	39	ENSP00000328150:R39Q	ENSP00000328150:R39Q	R	+	2	0	KCNJ12	21259363	1.000000	0.71417	0.985000	0.45067	0.979000	0.70002	9.690000	0.98676	2.506000	0.84524	0.591000	0.81541	CGG	G|0.743;A|0.257	0.257	strong		0.617	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
TMEM79	84283	hgsc.bcm.edu	37	1	156255456	156255456	+	Missense_Mutation	SNP	G	G	A	rs6684514	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156255456G>A	ENST00000405535.2	+	2	610	c.439G>A	c.(439-441)Gtg>Atg	p.V147M	TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000295694.5_Missense_Mutation_p.V147M|TMEM79_ENST00000357501.2_Intron|SMG5_ENST00000361813.5_5'Flank|SMG5_ENST00000368267.5_5'Flank	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	147			V -> M (polymorphism that may be associated with atopic dermatitis; dbSNP:rs6684514). {ECO:0000269|PubMed:24084074}.		cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					AGACCTTATCGTGCGCTGTGA	0.647													G|||	1016	0.202875	0.0794	0.2781	5008	,	,		14706	0.2272		0.2694	False		,,,				2504	0.2229				p.V147M		Atlas-SNP	.											.	TMEM79	43	.	0			c.G439A						PASS	.	G	MET/VAL	522,3884	239.6+/-250.7	29,464,1710	61.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/pubmed?term	439	0.2	0.0	1	dbSNP_116	61	2522,6078	410.9+/-350.3	385,1752,2163	yes	missense	TMEM79	NM_032323.2	21	414,2216,3873	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	29.3256,11.8475,23.4046	benign	147/395	156255456	3044,9962	2203	4300	6503	SO:0001583	missense	84283	exon2			CTTATCGTGCGCT	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"""mattrin"""	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.439G>A	1.37:g.156255456G>A	ENSP00000384748:p.Val147Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	64	38	0.59375	NM_032323	B2RE22|D3DVB8	Missense_Mutation	SNP	ENST00000405535.2	37	CCDS1138.1	462	0.21153846153846154	40	0.08130081300813008	82	0.2265193370165746	135	0.23601398601398602	205	0.2704485488126649	G	5.517	0.280376	0.10458	0.118475	0.293256	ENSG00000163472	ENST00000295694;ENST00000405535	T;T	0.50813	0.73;0.73	5.45	0.157	0.14915	.	0.870941	0.10161	N	0.708272	T	0.13543	0.0328	L	0.34521	1.04	0.80722	P	0.0	B	0.25719	0.132	B	0.24974	0.057	T	0.17623	-1.0363	9	0.44086	T	0.13	-0.5773	3.24	0.06777	0.2261:0.1186:0.5339:0.1215	rs6684514;rs59950097;rs6684514	147	Q9BSE2	TMM79_HUMAN	M	147	ENSP00000295694:V147M;ENSP00000384748:V147M	ENSP00000295694:V147M	V	+	1	0	TMEM79	154522080	0.001000	0.12720	0.000000	0.03702	0.167000	0.22549	0.585000	0.23879	-0.510000	0.06523	-1.134000	0.01955	GTG	G|0.784;A|0.216	0.216	strong		0.647	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323	
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 GAIIx	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	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	48	14	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	
PTK7	5754	hgsc.bcm.edu	37	6	43109751	43109751	+	Silent	SNP	G	G	A	rs6905948	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:43109751G>A	ENST00000230419.4	+	12	2072	c.1851G>A	c.(1849-1851)ggG>ggA	p.G617G	PTK7_ENST00000481273.1_Silent_p.G625G|PTK7_ENST00000349241.2_Silent_p.G487G|PTK7_ENST00000352931.2_Silent_p.G617G|PTK7_ENST00000345201.2_Silent_p.G577G	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	617	Ig-like C2-type 7.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGGCCCAGGGGGACCCCAAGC	0.597													G|||	1693	0.338059	0.4781	0.4179	5008	,	,		17142	0.0972		0.3887	False		,,,				2504	0.2883				p.G625G		Atlas-SNP	.											PTK7,NS,carcinoma,+2,1	PTK7	101	1	0			c.G1875A						PASS	.	G	,,,	1975,2431	547.8+/-377.4	451,1073,679	54.0	58.0	57.0		1851,1731,1461,1851	-8.6	1.0	6	dbSNP_116	57	3262,5338	481.8+/-370.7	596,2070,1634	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK7	NM_002821.3,NM_152880.2,NM_152881.2,NM_152882.2	,,,	1047,3143,2313	AA,AG,GG		37.9302,44.8252,40.266	,,,	617/1071,577/1031,487/941,617/1015	43109751	5237,7769	2203	4300	6503	SO:0001819	synonymous_variant	5754	exon12			CCAGGGGGACCCC	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9618	protein-coding gene	gene with protein product		601890	"""PTK7 protein tyrosine kinase 7"""			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.1851G>A	6.37:g.43109751G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001270398	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	37	CCDS4884.1																																																																																			G|0.619;A|0.381	0.381	strong		0.597	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2		
CDHR3	222256	hgsc.bcm.edu	37	7	105658451	105658451	+	Missense_Mutation	SNP	G	G	A	rs6967330	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:105658451G>A	ENST00000317716.9	+	12	1666	c.1586G>A	c.(1585-1587)tGt>tAt	p.C529Y	CDHR3_ENST00000478080.1_Missense_Mutation_p.C441Y|CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000542731.1_Missense_Mutation_p.C529Y|CDHR3_ENST00000343407.5_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	529	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		C -> Y (in dbSNP:rs6967330).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AAAGTGGACTGTGAAACAACC	0.488													A|||	925	0.184704	0.2648	0.1427	5008	,	,		18561	0.0704		0.2078	False		,,,				2504	0.2004				p.C529Y		Atlas-SNP	.											.	CDHR3	153	.	0			c.G1586A						PASS	.	A	TYR/CYS	967,2915		121,725,1095	68.0	67.0	67.0		1586	4.4	0.9	7	dbSNP_116	67	1405,6889		136,1133,2878	yes	missense	CDHR3	NM_152750.4	194	257,1858,3973	AA,AG,GG		16.94,24.9098,19.4809	benign	529/886	105658451	2372,9804	1941	4147	6088	SO:0001583	missense	222256	exon12			TGGACTGTGAAAC	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1586G>A	7.37:g.105658451G>A	ENSP00000325954:p.Cys529Tyr	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	38	22	0.578947	NM_152750	Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	380	0.17399267399267399	127	0.258130081300813	61	0.1685082872928177	39	0.06818181818181818	153	0.20184696569920843	A	0.008	-1.879772	0.00537	0.249098	0.1694	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080	T;T;T	0.47177	0.85;0.85;0.85	5.66	4.39	0.52855	Cadherin (5);Cadherin-like (1);	0.441716	0.23328	N	0.049375	T	0.00012	0.0000	N	0.00033	-2.575	0.09310	P	0.9999999756686	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29427	-1.0012	9	0.02654	T	1	-2.7833	7.8022	0.29180	0.795:0.0:0.073:0.132	rs6967330;rs58478557;rs6967330	516;529	B3KYA0;Q6ZTQ4	.;CDHR3_HUMAN	Y	529;529;441	ENSP00000439766:C529Y;ENSP00000325954:C529Y;ENSP00000417771:C441Y	ENSP00000325954:C529Y	C	+	2	0	CDHR3	105445687	1.000000	0.71417	0.931000	0.37212	0.057000	0.15508	3.349000	0.52217	0.986000	0.38683	-0.254000	0.11334	TGT	G|0.826;A|0.174	0.174	strong		0.488	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
PRKCD	5580	hgsc.bcm.edu	37	3	53220215	53220215	+	Silent	SNP	G	G	A	rs2230494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:53220215G>A	ENST00000394729.2	+	12	1447	c.1119G>A	c.(1117-1119)gaG>gaA	p.E373E	PRKCD_ENST00000330452.3_Silent_p.E373E	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	GCAGAGGAGAGTACTTTGCCA	0.602													G|||	1413	0.282149	0.3411	0.2925	5008	,	,		20269	0.2202		0.2863	False		,,,				2504	0.2546				p.E373E		Atlas-SNP	.											PRKCD_ENST00000394729,NS,adenoma,0,2	PRKCD	124	2	0			c.G1119A						PASS	.	G	,	1417,2989	464.7+/-354.0	231,955,1017	97.0	87.0	90.0		1119,1119	2.3	0.5	3	dbSNP_98	90	2442,6158	402.0+/-347.3	338,1766,2196	no	coding-synonymous,coding-synonymous	PRKCD	NM_006254.3,NM_212539.1	,	569,2721,3213	AA,AG,GG		28.3953,32.1607,29.6709	,	373/677,373/677	53220215	3859,9147	2203	4300	6503	SO:0001819	synonymous_variant	5580	exon12			AGGAGAGTACTTT		CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.1119G>A	3.37:g.53220215G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	65	41	0.630769	NM_212539	B0KZ81|B2R834|Q15144|Q86XJ6	Silent	SNP	ENST00000394729.2	37	CCDS2870.1																																																																																			A|0.289;C|0.000;G|0.710;N|0.000	0.289	strong		0.602	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1		
CASQ2	845	hgsc.bcm.edu	37	1	116310967	116310967	+	Missense_Mutation	SNP	T	T	C	rs4074536	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:116310967T>C	ENST00000261448.5	-	1	435	c.196A>G	c.(196-198)Acg>Gcg	p.T66A	CASQ2_ENST00000456138.2_Missense_Mutation_p.T66A	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	66			T -> A (no effect on calcium-binding and calcium-dependent dimerization; dbSNP:rs4074536). {ECO:0000269|PubMed:14571276, ECO:0000269|PubMed:17881003}.		cardiac muscle contraction (GO:0060048)|cellular response to caffeine (GO:0071313)|detection of calcium ion (GO:0005513)|ion transmembrane transport (GO:0034220)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|protein polymerization (GO:0051258)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of heart rate (GO:0002027)|regulation of membrane repolarization (GO:0060306)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|sequestering of calcium ion (GO:0051208)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|junctional sarcoplasmic reticulum membrane (GO:0014701)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	18	Lung SC(450;0.211)	all_cancers(81;1.25e-06)|all_epithelial(167;1.02e-06)|all_lung(203;8.03e-06)|Lung NSC(69;5.01e-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)		TGTTTTTGCGTGACCTTATCT	0.473													C|||	2009	0.401158	0.4856	0.3674	5008	,	,		19899	0.5159		0.2922	False		,,,				2504	0.3047				p.T66A		Atlas-SNP	.											CASQ2,colon,carcinoma,0,1	CASQ2	54	1	0			c.A196G						PASS	.	C	ALA/THR	1928,2478	622.1+/-393.9	416,1096,691	175.0	166.0	169.0	http://www.ncbi.nlm.nih.gov/pubmed?term	196	3.4	0.0	1	dbSNP_108	169	2486,6114	695.2+/-404.8	347,1792,2161	yes	missense	CASQ2	NM_001232.3	58	763,2888,2852	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	28.907,43.7585,33.9382	benign	66/400	116310967	4414,8592	2203	4300	6503	SO:0001583	missense	845	exon1			TTTGCGTGACCTT	BC022288	CCDS884.1	1p13.1	2014-09-17			ENSG00000118729	ENSG00000118729		"""Protein disulfide isomerases"""	1513	protein-coding gene	gene with protein product		114251				8406504	Standard	NM_001232		Approved	PDIB2	uc001efx.4	O14958	OTTHUMG00000011970	ENST00000261448.5:c.196A>G	1.37:g.116310967T>C	ENSP00000261448:p.Thr66Ala	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_001232	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Missense_Mutation	SNP	ENST00000261448.5	37	CCDS884.1	902	0.413003663003663	253	0.5142276422764228	133	0.3674033149171271	285	0.4982517482517482	231	0.30474934036939316	C	0.005	-2.171649	0.00315	0.437585	0.28907	ENSG00000118729	ENST00000261448;ENST00000456138;ENST00000446755	T;T	0.37752	1.18;1.18	5.49	3.44	0.39384	Thioredoxin-like fold (2);	0.442334	0.26300	N	0.025162	T	0.02047	0.0064	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43410	-0.9393	9	0.05959	T	0.93	-3.1292	8.6205	0.33857	0.3705:0.5482:0.0:0.0813	rs4074536;rs52800545;rs59883665;rs4074536	66;66	B4DIB0;O14958	.;CASQ2_HUMAN	A	66	ENSP00000261448:T66A;ENSP00000403858:T66A	ENSP00000261448:T66A	T	-	1	0	CASQ2	116112490	0.257000	0.24022	0.001000	0.08648	0.019000	0.09904	1.594000	0.36697	0.685000	0.31468	-0.186000	0.12905	ACG	T|0.631;C|0.369	0.369	strong		0.473	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232	
SLC6A12	6539	hgsc.bcm.edu	37	12	319125	319125	+	Missense_Mutation	SNP	A	A	G	rs557881	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:319125A>G	ENST00000428720.1	-	3	771	c.28T>C	c.(28-30)Tgt>Cgt	p.C10R	SLC6A12_ENST00000536824.1_Missense_Mutation_p.C10R|SLC6A12_ENST00000397296.2_Missense_Mutation_p.C10R|SLC6A12_ENST00000424061.2_Missense_Mutation_p.C10R|SLC6A12_ENST00000359674.4_Missense_Mutation_p.C10R	NM_001122848.2	NP_001116320.1	P48065	S6A12_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 12	10			C -> R (in dbSNP:rs557881). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7589472}.	C -> Y (in Ref. 2; AAA66574). {ECO:0000305}.	amino acid transport (GO:0006865)|cellular hyperosmotic response (GO:0071474)|cellular water homeostasis (GO:0009992)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|response to organic substance (GO:0010033)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	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:sodium symporter activity (GO:0005328)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0172)|all_epithelial(11;0.0283)|all_lung(10;0.0392)|Lung NSC(10;0.0567)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00227)			GGAGGCCCACACTCTTGCACT	0.622													G|||	2629	0.52496	0.7126	0.4308	5008	,	,		17088	0.3145		0.5229	False		,,,				2504	0.5573				p.C10R		Atlas-SNP	.											.	SLC6A12	60	.	0			c.T28C						PASS	.	G	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	3094,1312	443.1+/-346.9	1082,930,191	79.0	69.0	73.0		28,28,28,28	2.8	0.0	12	dbSNP_83	73	4550,4050	558.0+/-387.2	1194,2162,944	yes	missense,missense,missense,missense	SLC6A12	NM_001122847.2,NM_001122848.2,NM_001206931.1,NM_003044.4	180,180,180,180	2276,3092,1135	GG,GA,AA		47.093,29.7776,41.2271	benign,benign,benign,benign	10/615,10/615,10/615,10/615	319125	7644,5362	2203	4300	6503	SO:0001583	missense	6539	exon3			GCCCACACTCTTG	L42300	CCDS8501.1	12p13	2013-07-19	2013-07-19		ENSG00000111181	ENSG00000111181		"""Solute carriers"""	11045	protein-coding gene	gene with protein product	"""betaine/GABA transporter-1"""	603080	"""solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12"""			7589472	Standard	NM_003044		Approved	BGT-1	uc009zdh.2	P48065	OTTHUMG00000090309	ENST00000428720.1:c.28T>C	12.37:g.319125A>G	ENSP00000388184:p.Cys10Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_001122848	A0AV52|B2R992|D3DUN8	Missense_Mutation	SNP	ENST00000428720.1	37	CCDS8501.1	1087	0.4977106227106227	359	0.7296747967479674	156	0.430939226519337	182	0.3181818181818182	390	0.5145118733509235	G	4.749	0.139228	0.09083	0.702224	0.52907	ENSG00000111181	ENST00000359674;ENST00000397296;ENST00000428720;ENST00000424061;ENST00000536824;ENST00000537793;ENST00000535347	T;T;T;T;T;T;T	0.72051	-0.62;-0.62;-0.62;-0.62;-0.62;-0.35;0.79	5.63	2.81	0.32909	.	0.597438	0.15804	N	0.243826	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40813	-0.9543	9	0.21540	T	0.41	.	3.4038	0.07333	0.1178:0.4645:0.2717:0.146	rs557881;rs60807272;rs557881	10	P48065	S6A12_HUMAN	R	10	ENSP00000352702:C10R;ENSP00000380464:C10R;ENSP00000388184:C10R;ENSP00000399136:C10R;ENSP00000444268:C10R;ENSP00000439351:C10R;ENSP00000446082:C10R	ENSP00000352702:C10R	C	-	1	0	SLC6A12	189386	0.079000	0.21365	0.003000	0.11579	0.001000	0.01503	1.456000	0.35201	0.339000	0.23719	-0.213000	0.12676	TGT	A|0.466;G|0.534	0.534	strong		0.622	SLC6A12-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206671.2	NM_003044	
TTF1	7270	hgsc.bcm.edu	37	9	135277341	135277341	+	Missense_Mutation	SNP	C	C	A	rs8999	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135277341C>A	ENST00000334270.2	-	2	907	c.868G>T	c.(868-870)Gca>Tca	p.A290S		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	290			A -> S (in dbSNP:rs8999).		chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		ATGGCCAATGCCTCAAATTCC	0.473													C|||	760	0.151757	0.1316	0.1066	5008	,	,		18978	0.252		0.0825	False		,,,				2504	0.1789				p.A290S		Atlas-SNP	.											.	TTF1	82	.	0			c.G868T						PASS	.	C	,SER/ALA	557,3849	248.1+/-256.1	33,491,1679	151.0	147.0	148.0		,868	-0.6	0.0	9	dbSNP_52	148	592,8008	157.3+/-211.0	24,544,3732	yes	intron,missense	TTF1	NM_001205296.1,NM_007344.3	,99	57,1035,5411	AA,AC,CC		6.8837,12.6419,8.8344	,possibly-damaging	,290/906	135277341	1149,11857	2203	4300	6503	SO:0001583	missense	7270	exon2			CCAATGCCTCAAA	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.868G>T	9.37:g.135277341C>A	ENSP00000333920:p.Ala290Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	28	0.451613	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	324	0.14835164835164835	77	0.1565040650406504	36	0.09944751381215469	152	0.26573426573426573	59	0.07783641160949868	C	4.220	0.039741	0.08148	0.126419	0.068837	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.09255	3.0	2.52	-0.643	0.11482	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.24576	0.106	B	0.10450	0.005	T	0.42816	-0.9429	8	0.02654	T	1	.	2.3524	0.04287	0.3905:0.4102:0.0:0.1993	rs8999;rs3188185;rs3739913;rs52817153;rs61483795;rs8999	290	Q15361	TTF1_HUMAN	S	290	ENSP00000333920:A290S	ENSP00000245588:A290S	A	-	1	0	TTF1	134267162	0.000000	0.05858	0.010000	0.14722	0.017000	0.09413	0.141000	0.16076	0.153000	0.19213	0.467000	0.42956	GCA	C|0.878;A|0.122	0.122	strong		0.473	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344	
ZNF117	51351	hgsc.bcm.edu	37	7	64439613	64439613	+	Missense_Mutation	SNP	T	T	G	rs3807068	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:64439613T>G	ENST00000282869.6	-	4	1620	c.336A>C	c.(334-336)aaA>aaC	p.K112N		NM_015852.3	NP_056936.2	Q03924	ZN117_HUMAN	zinc finger protein 117	112			K -> N (in dbSNP:rs3807068).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(1)|skin(1)	22		Lung NSC(55;0.0295)|all_lung(88;0.0691)				TGCGACATTCTTTACATTTAA	0.279													T|||	1939	0.387181	0.3964	0.2637	5008	,	,		19187	0.4058		0.4016	False		,,,				2504	0.4284				p.K112N		Atlas-SNP	.											ZNF117,NS,carcinoma,0,1	ZNF117	56	1	0			c.A336C						PASS	.	T	ASN/LYS	1557,2601		297,963,819	61.0	59.0	60.0		336	-2.3	0.0	7	dbSNP_107	60	3190,5280		596,1998,1641	no	missense	ZNF117	NM_015852.3	94	893,2961,2460	GG,GT,TT		37.6623,37.4459,37.5911	benign	112/484	64439613	4747,7881	2079	4235	6314	SO:0001583	missense	51351	exon4			ACATTCTTTACAT	M27879	CCDS43593.1	7q11.2	2013-01-08	2006-06-12		ENSG00000152926	ENSG00000152926		"""Zinc fingers, C2H2-type"""	12897	protein-coding gene	gene with protein product		194624	"""zinc finger protein 117 (HPF9)"""			1427907	Standard	NM_015852		Approved	HPF9, H-plk	uc003ttr.2	Q03924	OTTHUMG00000156631	ENST00000282869.6:c.336A>C	7.37:g.64439613T>G	ENSP00000282869:p.Lys112Asn	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_015852	Q02313|Q7Z7Q7	Missense_Mutation	SNP	ENST00000282869.6	37	CCDS43593.1	855	0.3914835164835165	196	0.3983739837398374	116	0.32044198895027626	223	0.38986013986013984	320	0.42216358839050133	.	8.568	0.879357	0.17467	0.374459	0.376623	ENSG00000152926	ENST00000398695;ENST00000282869	T	0.01209	5.17	1.49	-2.31	0.06765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.37750	1.13	0.80722	P	0.0	D	0.67145	0.996	D	0.72982	0.979	T	0.47837	-0.9086	8	0.25106	T	0.35	.	4.72	0.12913	0.4399:0.0:0.0:0.5601	rs3807068;rs3807068	112	Q03924	ZN117_HUMAN	N	112	ENSP00000282869:K112N	ENSP00000282869:K112N	K	-	3	2	ZNF117	64077048	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-6.380000	0.00068	-0.188000	0.10499	0.260000	0.18958	AAA	T|0.611;G|0.389	0.389	strong		0.279	ZNF117-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344863.3	NM_024498	
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 GAIIx	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_ENST00000483569.1_3'UTR|EEFSEC_ENST00000483457.1_Missense_Mutation_p.P298S	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	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	95	52	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	
C2CD3	26005	hgsc.bcm.edu	37	11	73806443	73806443	+	Missense_Mutation	SNP	C	C	T	rs11235995	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:73806443C>T	ENST00000334126.7	-	17	3216	c.2990G>A	c.(2989-2991)cGa>cAa	p.R997Q	C2CD3_ENST00000313663.7_Missense_Mutation_p.R997Q			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	997			R -> Q (in dbSNP:rs11235995). {ECO:0000269|PubMed:15489334}.		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TCCATTTCCTCGGTCCTCTGC	0.413													C|||	1141	0.227835	0.3041	0.0994	5008	,	,		17838	0.2758		0.175	False		,,,				2504	0.2209				p.R997Q		Atlas-SNP	.											.	C2CD3	288	.	0			c.G2990A						PASS	.	C	GLN/ARG	1310,3090	441.8+/-346.5	188,934,1078	125.0	117.0	119.0		2990	4.6	1.0	11	dbSNP_120	119	1538,7048	289.6+/-299.4	145,1248,2900	yes	missense	C2CD3	NM_015531.4	43	333,2182,3978	TT,TC,CC		17.9129,29.7727,21.9313	benign	997/1964	73806443	2848,10138	2200	4293	6493	SO:0001583	missense	26005	exon17			TTTCCTCGGTCCT	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.2990G>A	11.37:g.73806443C>T	ENSP00000334379:p.Arg997Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	57	10	0.175439	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		473	0.21657509157509158	128	0.2601626016260163	38	0.10497237569060773	165	0.28846153846153844	142	0.18733509234828497	C	1.450	-0.565219	0.03939	0.297727	0.179129	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681	T;T	0.38240	1.15;1.15	5.71	4.59	0.56863	.	0.240936	0.42821	N	0.000649	T	0.00012	0.0000	N	0.00538	-1.39	0.36710	P	0.11942799999999998	B	0.12013	0.005	B	0.04013	0.001	T	0.35943	-0.9768	9	0.02654	T	1	-0.3246	10.735	0.46120	0.0:0.0766:0.0:0.9234	rs11235995;rs52827469;rs11235995	997	Q4AC94-1	.	Q	997	ENSP00000334379:R997Q;ENSP00000323339:R997Q	ENSP00000323339:R997Q	R	-	2	0	C2CD3	73484091	1.000000	0.71417	0.959000	0.39883	0.245000	0.25701	2.128000	0.42045	1.000000	0.39049	-0.312000	0.09012	CGA	C|0.780;N|0.000	.	strong		0.413	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
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 GAIIx	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_ENST00000356435.5_Missense_Mutation_p.E1510D|PTPRD_ENST00000397611.3_Missense_Mutation_p.E1100D|PTPRD_ENST00000358503.5_Missense_Mutation_p.E1488D|PTPRD_ENST00000537002.1_Missense_Mutation_p.E1100D|PTPRD_ENST00000360074.4_Missense_Mutation_p.E1497D|PTPRD_ENST00000486161.1_Missense_Mutation_p.E1103D|PTPRD_ENST00000397617.3_Missense_Mutation_p.E1103D|PTPRD_ENST00000397606.3_Missense_Mutation_p.E1103D|PTPRD_ENST00000540109.1_Missense_Mutation_p.E1510D|PTPRD_ENST00000355233.5_Missense_Mutation_p.E1104D	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	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	56	5	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 GAIIx	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	43	19	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	
DNMT1	1786	hgsc.bcm.edu	37	19	10273372	10273372	+	Missense_Mutation	SNP	T	T	C	rs2228612	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10273372T>C	ENST00000340748.4	-	12	1166	c.931A>G	c.(931-933)Att>Gtt	p.I311V	DNMT1_ENST00000540357.1_Missense_Mutation_p.I311V|DNMT1_ENST00000359526.4_Missense_Mutation_p.I327V			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	311	Homodimerization.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.		I -> V (in dbSNP:rs2228612).		cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	TCATCAGAAATCTGTGGATTT	0.398													T|||	993	0.198283	0.1483	0.1844	5008	,	,		15619	0.3681		0.0676	False		,,,				2504	0.2352				p.I327V		Atlas-SNP	.											.	DNMT1	148	.	0			c.A979G						PASS	.	T	VAL/ILE,VAL/ILE	562,3844	250.9+/-257.8	35,492,1676	132.0	131.0	131.0		979,931	-4.7	0.0	19	dbSNP_98	131	560,8040	151.9+/-206.6	16,528,3756	yes	missense,missense	DNMT1	NM_001130823.1,NM_001379.2	29,29	51,1020,5432	CC,CT,TT		6.5116,12.7553,8.6268	benign,benign	327/1633,311/1617	10273372	1122,11884	2203	4300	6503	SO:0001583	missense	1786	exon13			CAGAAATCTGTGG	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.931A>G	19.37:g.10273372T>C	ENSP00000345739:p.Ile311Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	37	CCDS12228.1	403	0.18452380952380953	70	0.14227642276422764	63	0.17403314917127072	221	0.38636363636363635	49	0.06464379947229551	t	3.128	-0.178965	0.06380	0.127553	0.065116	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.79653	-1.29;-1.29;-1.29	4.22	-4.65	0.03339	.	2.380820	0.01537	N	0.019056	T	0.00012	0.0000	N	0.02960	-0.455	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04885	-1.0920	9	0.27785	T	0.31	.	8.6302	0.33915	0.0:0.6151:0.1379:0.247	rs2228612;rs8111085;rs61728392;rs8111085	311;327;311	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	V	327;311;311;179	ENSP00000352516:I327V;ENSP00000440457:I311V;ENSP00000345739:I311V	ENSP00000345739:I311V	I	-	1	0	DNMT1	10134372	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.720000	0.04969	-1.016000	0.03371	-0.474000	0.04947	ATT	T|0.712;G|0.042;C|0.092;A|0.154	0.092	strong		0.398	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
DEGS2	123099	hgsc.bcm.edu	37	14	100625902	100625902	+	Missense_Mutation	SNP	C	C	T	rs7157599	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:100625902C>T	ENST00000553834.1	-	1	30	c.23G>A	c.(22-24)aGc>aAc	p.S8N	DEGS2_ENST00000305631.5_Missense_Mutation_p.S8N					delta(4)-desaturase, sphingolipid 2											breast(1)|lung(6)|skin(1)	8		Melanoma(154;0.212)				CTCGAAGTCGCTGCGGCTCGC	0.766													c|||	3842	0.767173	0.8661	0.768	5008	,	,		8798	0.7282		0.6948	False		,,,				2504	0.7474				p.S8N		Atlas-SNP	.											.	DEGS2	25	.	0			c.G23A						PASS	.	T	ASN/SER	2896,464		1254,388,38	8.0	7.0	8.0	http://www.ncbi.nlm.nih.gov/pubmed?term	23	0.5	1.0	14	dbSNP_116	8	4583,1505		1740,1103,201	yes	missense	DEGS2	NM_206918.2	46	2994,1491,239	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	24.7208,13.8095,20.8404	benign	8/324	100625902	7479,1969	1680	3044	4724	SO:0001583	missense	123099	exon1			AAGTCGCTGCGGC		CCDS9956.1	14q32.2	2013-09-02	2011-12-09	2004-12-14	ENSG00000168350	ENSG00000168350		"""Fatty acid desaturases"""	20113	protein-coding gene	gene with protein product	"""sphingolipid delta(4)-desaturase 2"", ""dihydroceramide desaturase 2"""	610862	"""chromosome 14 open reading frame 66"", ""degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)"""	C14orf66			Standard	NM_206918		Approved	DES2, FADS8	uc001ygx.2	Q6QHC5	OTTHUMG00000171537	ENST00000553834.1:c.23G>A	14.37:g.100625902C>T	ENSP00000450637:p.Ser8Asn	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	9	6	0.666667	NM_206918		Missense_Mutation	SNP	ENST00000553834.1	37		1662	0.760989010989011	431	0.8760162601626016	274	0.7569060773480663	424	0.7412587412587412	533	0.7031662269129287	.	9.769	1.172237	0.21704	0.861905	0.752792	ENSG00000168350	ENST00000305631;ENST00000553834	T;T	0.40476	1.03;1.03	4.72	0.456	0.16655	Sphingolipid delta4-desaturase, N-terminal (1);	0.817312	0.11149	N	0.594331	T	0.00012	0.0000	N	0.13003	0.285	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.21827	-1.0234	9	0.17369	T	0.5	-1.5775	5.1779	0.15145	0.1384:0.5173:0.2681:0.0762	rs7157599;rs60508435;rs7157599	8	Q6QHC5	DEGS2_HUMAN	N	8	ENSP00000307126:S8N;ENSP00000450637:S8N	ENSP00000307126:S8N	S	-	2	0	DEGS2	99695655	0.085000	0.21516	0.990000	0.47175	0.532000	0.34746	-0.317000	0.08060	-0.209000	0.10156	-0.336000	0.08194	AGC	C|0.235;T|0.765	0.765	strong		0.766	DEGS2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414004.1	NM_206918	
FBXO43	286151	hgsc.bcm.edu	37	8	101153024	101153024	+	Silent	SNP	G	G	A	rs1460934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:101153024G>A	ENST00000428847.2	-	2	1774	c.1458C>T	c.(1456-1458)atC>atT	p.I486I		NM_001029860.3	NP_001025031.2	Q4G163	FBX43_HUMAN	F-box protein 43	486					meiotic nuclear division (GO:0007126)|negative regulation of meiosis (GO:0045835)|negative regulation of protein catabolic process (GO:0042177)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(5)|lung(14)|prostate(1)|skin(5)|urinary_tract(1)	31	all_cancers(14;0.000139)|all_epithelial(15;2.84e-07)|Lung NSC(17;0.000274)|all_lung(17;0.000798)		Epithelial(11;1.17e-09)|all cancers(13;1.34e-07)|OV - Ovarian serous cystadenocarcinoma(57;3.82e-05)|STAD - Stomach adenocarcinoma(118;0.0957)			TTTTCTTGCCGATCAGTCCTG	0.378													A|||	3296	0.658147	0.7337	0.6888	5008	,	,		18106	0.7292		0.5557	False		,,,				2504	0.5665				p.I486I		Atlas-SNP	.											.	FBXO43	155	.	0			c.C1458T						PASS	.	A		2555,1101		891,773,164	198.0	183.0	188.0		1458	2.5	1.0	8	dbSNP_88	188	4461,3721		1212,2037,842	yes	coding-synonymous	FBXO43	NM_001029860.3		2103,2810,1006	AA,AG,GG		45.4779,30.1149,40.7332		486/709	101153024	7016,4822	1828	4091	5919	SO:0001819	synonymous_variant	286151	exon2			CTTGCCGATCAGT	BC028709	CCDS47904.1	8q22.3	2004-08-24			ENSG00000156509	ENSG00000156509		"""F-boxes /  ""other"""""	28521	protein-coding gene	gene with protein product		609110					Standard	NR_036491		Approved	Fbx43	uc003yjd.3	Q4G163	OTTHUMG00000164803	ENST00000428847.2:c.1458C>T	8.37:g.101153024G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	107	45	0.420561	NM_001029860		Silent	SNP	ENST00000428847.2	37	CCDS47904.1																																																																																			G|0.370;A|0.630	0.630	strong		0.378	FBXO43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380380.1	XM_209918	
FAM46C	54855	hgsc.bcm.edu	37	1	118165577	118165577	+	Silent	SNP	C	C	G	rs865443	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:118165577C>G	ENST00000369448.3	+	2	334	c.87C>G	c.(85-87)ctC>ctG	p.L29L		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	29										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		ATGAGGTCCTCACTGAAGTTG	0.557			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			G|||	635	0.126797	0.2617	0.085	5008	,	,		21909	0.122		0.0626	False		,,,				2504	0.045				p.L29L		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C87G						PASS	.	G		948,3458	735.6+/-410.7	109,730,1364	102.0	87.0	92.0		87	4.1	1.0	1	dbSNP_86	92	501,8099	796.8+/-407.5	12,477,3811	no	coding-synonymous	FAM46C	NM_017709.3		121,1207,5175	GG,GC,CC		5.8256,21.5161,11.141		29/392	118165577	1449,11557	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			GGTCCTCACTGAA	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.87C>G	1.37:g.118165577C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	141	63	0.446809	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.882;G|0.118	0.118	strong		0.557	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629155	32629155	+	Silent	SNP	C	C	A	rs1130431	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32629155C>A	ENST00000399084.1	-	5	919	c.741G>T	c.(739-741)ctG>ctT	p.L247L	HLA-DQB1_ENST00000399079.3_Intron|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000374943.4_Silent_p.L247L|HLA-DQB1-AS1_ENST00000419852.1_RNA|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Silent_p.L247L			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	247					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TGATAAGGCCCAGCCCAAGGA	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1368	0.273163	0.2821	0.196	5008	,	,		12357	0.3254		0.2485	False		,,,				2504	0.2873				p.L247L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G741T						PASS	.	C		1110,2826		383,344,1241	34.0	30.0	31.0		741	-1.8	0.1	6	dbSNP_130	31	1989,5829		704,581,2624	no	coding-synonymous	HLA-DQB1	NM_002123.4		1087,925,3865	AA,AC,CC		25.4413,28.2012,26.3655		247/262	32629155	3099,8655	1968	3909	5877	SO:0001819	synonymous_variant	3119	exon4	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AAGGCCCAGCCCA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.741G>T	6.37:g.32629155C>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	45	23	0.511111	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			C|0.805;A|0.195	0.195	strong		0.562	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
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 GAIIx	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	PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.P453A|PCDHA6_ENST00000529310.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_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	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	6	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 GAIIx	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		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	107	52	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	
PTPRB	5787	hgsc.bcm.edu	37	12	70988287	70988287	+	Silent	SNP	A	A	G	rs34615667	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:70988287A>G	ENST00000261266.5	-	4	851	c.822T>C	c.(820-822)gcT>gcC	p.A274A	PTPRB_ENST00000550358.1_Silent_p.A492A|PTPRB_ENST00000538708.1_Silent_p.A274A|PTPRB_ENST00000551525.1_Silent_p.A491A|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550857.1_Silent_p.A274A|PTPRB_ENST00000334414.6_Silent_p.A492A|PTPRB_ENST00000451516.2_Silent_p.A274A	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	274	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			GCAGCCCTGCAGCCTCAGTCA	0.468													G|||	372	0.0742812	0.0756	0.098	5008	,	,		18469	0.001		0.1392	False		,,,				2504	0.0644				p.A492A		Atlas-SNP	.											.	PTPRB	676	.	0			c.T1476C						PASS	.	G	,,,	327,3581		7,313,1634	117.0	116.0	116.0		1476,822,822,822	-11.2	0.0	12	dbSNP_126	116	1186,7106		98,990,3058	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	,,,	105,1303,4692	GG,GA,AA		14.3029,8.3675,12.4016	,,,	492/2216,274/1908,274/1908,274/1998	70988287	1513,10687	1954	4146	6100	SO:0001819	synonymous_variant	5787	exon6			CCCTGCAGCCTCA	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.822T>C	12.37:g.70988287A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1																																																																																			A|0.905;G|0.095	0.095	strong		0.468	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
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 GAIIx	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		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	91	25	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	
FAM83B	222584	hgsc.bcm.edu	37	6	54804798	54804798	+	Silent	SNP	T	T	C	rs9370340	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:54804798T>C	ENST00000306858.7	+	5	1145	c.1029T>C	c.(1027-1029)taT>taC	p.Y343Y		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	343										autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GAGGGATATATACTTTAAATG	0.343													t|||	154	0.0307508	0.0295	0.0274	5008	,	,		20220	0.0635		0.0229	False		,,,				2504	0.0092				p.Y343Y		Atlas-SNP	.											FAM83B,colon,carcinoma,+1,1	FAM83B	186	1	0			c.T1029C						PASS	.	C		132,4274	92.0+/-130.7	0,132,2071	55.0	57.0	56.0		1029	1.7	0.2	6	dbSNP_119	56	188,8410	82.6+/-145.2	3,182,4114	no	coding-synonymous	FAM83B	NM_001010872.1		3,314,6185	CC,CT,TT		2.1866,2.9959,2.4608		343/1012	54804798	320,12684	2203	4299	6502	SO:0001819	synonymous_variant	222584	exon5			GATATATACTTTA	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.1029T>C	6.37:g.54804798T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_001010872	Q2M1P3|Q96DQ2	Silent	SNP	ENST00000306858.7	37	CCDS34479.1																																																																																			T|0.971;C|0.029	0.029	strong		0.343	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
PRDM1	639	hgsc.bcm.edu	37	6	106555025	106555025	+	Silent	SNP	G	G	A	rs1010273	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:106555025G>A	ENST00000369096.4	+	7	2376	c.2142G>A	c.(2140-2142)ccG>ccA	p.P714P	PRDM1_ENST00000369089.3_Silent_p.P580P|PRDM1_ENST00000369091.2_Silent_p.P678P	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	714					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CTGCGGCCCCGGCGCCTGGGC	0.577			"""D, N, Mis, F, S"""		DLBCL								G|||	457	0.091254	0.0197	0.0951	5008	,	,		19218	0.1865		0.1153	False		,,,				2504	0.0624				p.P714P		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	0			c.G2142A						PASS	.	G	,	126,4280	91.1+/-129.8	3,120,2080	156.0	176.0	169.0		2142,1740	-11.9	0.0	6	dbSNP_86	169	857,7743	196.3+/-241.3	45,767,3488	no	coding-synonymous,coding-synonymous	PRDM1	NM_001198.3,NM_182907.1	,	48,887,5568	AA,AG,GG		9.9651,2.8597,7.5581	,	714/826,580/692	106555025	983,12023	2203	4300	6503	SO:0001819	synonymous_variant	639	exon7			GGCCCCGGCGCCT		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.2142G>A	6.37:g.106555025G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_001198	B2REA6|E1P5E0|Q86WM7	Silent	SNP	ENST00000369096.4	37	CCDS5054.2																																																																																			G|0.910;A|0.090	0.090	strong		0.577	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
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 GAIIx	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		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	114	28	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
ANO4	121601	hgsc.bcm.edu	37	12	101336201	101336201	+	Missense_Mutation	SNP	G	G	C	rs34162417	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:101336201G>C	ENST00000392977.3	+	5	554	c.344G>C	c.(343-345)gGa>gCa	p.G115A	ANO4_ENST00000538618.1_Missense_Mutation_p.G281A|ANO4_ENST00000299222.9_5'UTR|ANO4_ENST00000392979.3_Missense_Mutation_p.G80A			Q32M45	ANO4_HUMAN	anoctamin 4	115			G -> A (in dbSNP:rs34162417).		chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.G80A(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(4)|prostate(5)|skin(7)|stomach(2)|urinary_tract(1)	78						TTTCGAGATGGAAAGTGTCGA	0.383										HNSCC(74;0.22)			G|||	251	0.0501198	0.0446	0.0259	5008	,	,		17182	0.1111		0.0408	False		,,,				2504	0.0215				p.G80A		Atlas-SNP	.											ANO4,NS,carcinoma,0,1	ANO4	183	1	1	Substitution - Missense(1)	stomach(1)	c.G239C						PASS	.	G	ALA/GLY	190,4216	122.9+/-160.3	3,184,2016	137.0	139.0	138.0		239	5.6	1.0	12	dbSNP_126	138	413,8187	129.8+/-187.9	8,397,3895	yes	missense	ANO4	NM_178826.3	60	11,581,5911	CC,CG,GG		4.8023,4.3123,4.6363	probably-damaging	80/921	101336201	603,12403	2203	4300	6503	SO:0001583	missense	121601	exon4			GAGATGGAAAGTG	AK091540	CCDS31884.1, CCDS66445.1	12q23.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000151572	ENSG00000151572		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	23837	protein-coding gene	gene with protein product		610111	"""transmembrane protein 16D"""	TMEM16D		12739008, 15067359, 24692353	Standard	NM_178826		Approved	FLJ34221, FLJ34272, FLJ35277	uc001thw.2	Q32M45		ENST00000392977.3:c.344G>C	12.37:g.101336201G>C	ENSP00000376703:p.Gly115Ala	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Missense_Mutation	SNP	ENST00000392977.3	37		107	0.04899267399267399	27	0.054878048780487805	14	0.03867403314917127	41	0.07167832167832168	25	0.032981530343007916	G	24.4	4.525089	0.85600	0.043123	0.048023	ENSG00000151572	ENST00000538618;ENST00000392979;ENST00000392977	T;T;T	0.46063	0.88;0.88;0.88	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000001	T	0.17365	0.0417	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.987;0.999	T	0.57888	-0.7733	10	0.87932	D	0	.	19.6214	0.95658	0.0:0.0:1.0:0.0	rs34162417	115;80	Q32M45;Q32M45-2	ANO4_HUMAN;.	A	281;80;115	ENSP00000443751:G281A;ENSP00000376705:G80A;ENSP00000376703:G115A	ENSP00000376703:G115A	G	+	2	0	ANO4	99860332	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	8.752000	0.91632	2.644000	0.89710	0.655000	0.94253	GGA	G|0.953;C|0.047	0.047	strong		0.383	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826	
CDH23	64072	hgsc.bcm.edu	37	10	73270906	73270906	+	Silent	SNP	T	T	C	rs3802720	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73270906T>C	ENST00000224721.6	+	5	371	c.366T>C	c.(364-366)gtT>gtC	p.V122V	CDH23-AS1_ENST00000428918.1_RNA|CDH23_ENST00000461841.3_Silent_p.V167V|CDH23_ENST00000299366.7_Silent_p.V167V|CDH23_ENST00000398842.3_Silent_p.V122V|CDH23_ENST00000398809.4_Silent_p.V122V	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	122	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ACATCCAGGTTGGGGATGTGA	0.572													C|||	3679	0.734625	0.9856	0.5	5008	,	,		19305	0.7758		0.6889	False		,,,				2504	0.5665				p.V122V		Atlas-SNP	.											.	CDH23	365	.	0			c.T366C						PASS	.	C	,,,,	3771,271		1762,247,12	106.0	116.0	113.0		366,366,366,366,366	-11.2	0.1	10	dbSNP_107	113	5521,2833		1835,1851,491	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_001171932.1,NM_022124.5,NM_052836.3	,,,,	3597,2098,503	CC,CT,TT		33.9119,6.7046,25.0403	,,,,	122/1382,122/1062,122/407,122/3355,122/531	73270906	9292,3104	2021	4177	6198	SO:0001819	synonymous_variant	64072	exon6			CCAGGTTGGGGAT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.366T>C	10.37:g.73270906T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				T|0.244;C|0.756	0.756	strong		0.572	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
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 GAIIx	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	LA16c-349E10.1_ENST00000573609.1_RNA|WDR90_ENST00000549091.1_Silent_p.R532R			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		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	26	14	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	
SARDH	1757	hgsc.bcm.edu	37	9	136555629	136555629	+	Missense_Mutation	SNP	T	T	C	rs886016	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136555629T>C	ENST00000371872.4	-	16	2199	c.1942A>G	c.(1942-1944)Atg>Gtg	p.M648V	SARDH_ENST00000422262.2_Missense_Mutation_p.M480V|SARDH_ENST00000439388.1_Missense_Mutation_p.M648V|SARDH_ENST00000371868.1_Missense_Mutation_p.M76V	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	648			M -> V (in dbSNP:rs886016). {ECO:0000269|PubMed:10686491}.		glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		GCCCCGCCCATGGCCAGGTAG	0.647													C|||	2777	0.554513	0.8404	0.4914	5008	,	,		17364	0.4444		0.4394	False		,,,				2504	0.4448				p.M648V		Atlas-SNP	.											.	SARDH	112	.	0			c.A1942G						PASS	.	C	VAL/MET,VAL/MET	3347,1059	381.8+/-324.2	1276,795,132	69.0	71.0	70.0		1942,1942	5.0	0.9	9	dbSNP_86	70	3384,5216	637.7+/-399.2	672,2040,1588	yes	missense,missense	SARDH	NM_001134707.1,NM_007101.3	21,21	1948,2835,1720	CC,CT,TT		39.3488,24.0354,48.247	benign,benign	648/919,648/919	136555629	6731,6275	2203	4300	6503	SO:0001583	missense	1757	exon16			CGCCCATGGCCAG		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1942A>G	9.37:g.136555629T>C	ENSP00000360938:p.Met648Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	1168	0.5347985347985348	404	0.8211382113821138	175	0.48342541436464087	250	0.4370629370629371	339	0.4472295514511873	C	0.874	-0.731017	0.03135	0.759646	0.393488	ENSG00000123453	ENST00000371872;ENST00000371868;ENST00000439388;ENST00000422262	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.02	5.02	0.67125	Glycine cleavage T-protein, N-terminal (1);	0.134381	0.52532	N	0.000076	T	0.00012	0.0000	N	0.00068	-2.285	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41466	-0.9507	9	0.11485	T	0.65	-18.2222	8.5544	0.33471	0.0:0.7583:0.0:0.2417	rs886016;rs17662860;rs57614772;rs886016	648;76	Q9UL12;Q5SYV2	SARDH_HUMAN;.	V	648;76;648;480	ENSP00000360938:M648V;ENSP00000360934:M76V;ENSP00000403084:M648V;ENSP00000415537:M480V	ENSP00000360934:M76V	M	-	1	0	SARDH	135545450	0.995000	0.38212	0.883000	0.34634	0.885000	0.51271	2.882000	0.48546	1.114000	0.41781	-0.338000	0.08134	ATG	T|0.470;C|0.530	0.530	strong		0.647	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
MYO18A	399687	hgsc.bcm.edu	37	17	27422053	27422053	+	Silent	SNP	C	C	T	rs2320786	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27422053C>T	ENST00000527372.1	-	29	4590	c.4410G>A	c.(4408-4410)gcG>gcA	p.A1470A	MYO18A_ENST00000531253.1_Silent_p.A1470A|MYO18A_ENST00000533112.1_Silent_p.A1470A|MYO18A_ENST00000354329.4_Silent_p.A1470A	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1470					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CCTCCTCATGCGCCTGCGAGA	0.627													C|||	2545	0.508187	0.534	0.3718	5008	,	,		19849	0.8571		0.336	False		,,,				2504	0.3875				p.A1470A	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G4410A						PASS	.	C	,	2080,2110		554,972,569	15.0	16.0	16.0		4410,4410	-11.6	0.0	17	dbSNP_100	16	2818,5630		494,1830,1900	no	coding-synonymous,coding-synonymous	MYO18A	NM_078471.3,NM_203318.1	,	1048,2802,2469	TT,TC,CC		33.357,49.642,38.7561	,	1470/2055,1470/2040	27422053	4898,7740	2095	4224	6319	SO:0001819	synonymous_variant	399687	exon29			CTCATGCGCCTGC	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.4410G>A	17.37:g.27422053C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	37	CCDS45642.1																																																																																			C|0.497;T|0.503	0.503	strong		0.627	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
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 GAIIx	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|ACTG1_ENST00000573283.1_Missense_Mutation_p.L65M|ACTG1_ENST00000575087.1_Missense_Mutation_p.L65M|AC139149.1_ENST00000584254.1_RNA|RP13-766D20.2_ENST00000430912.1_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	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	37	10	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	
FSIP1	161835	hgsc.bcm.edu	37	15	39910052	39910052	+	Missense_Mutation	SNP	C	C	G	rs16969386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:39910052C>G	ENST00000350221.3	-	11	1792	c.1583G>C	c.(1582-1584)gGc>gCc	p.G528A		NM_152597.4	NP_689810.3	Q8NA03	FSIP1_HUMAN	fibrous sheath interacting protein 1	528			G -> A (in dbSNP:rs16969386).					p.G528A(1)		NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|skin(4)|stomach(2)|urinary_tract(1)	23		all_cancers(109;2.66e-19)|all_epithelial(112;2.66e-16)|Lung NSC(122;1.5e-11)|all_lung(180;4.03e-10)|Melanoma(134;0.0575)|Ovarian(310;0.0827)|Colorectal(260;0.119)		GBM - Glioblastoma multiforme(113;8.22e-06)|BRCA - Breast invasive adenocarcinoma(123;0.142)		TCTCCCAATGCCAAGAGTCTT	0.408													C|||	788	0.157348	0.0333	0.1196	5008	,	,		21212	0.2907		0.1471	False		,,,				2504	0.2249				p.G528A		Atlas-SNP	.											FSIP1,NS,carcinoma,0,1	FSIP1	53	1	1	Substitution - Missense(1)	stomach(1)	c.G1583C						scavenged	.	C	ALA/GLY	233,4167	136.5+/-172.5	4,225,1971	109.0	102.0	104.0		1583	4.8	1.0	15	dbSNP_123	104	1124,7470	231.9+/-265.7	65,994,3238	yes	missense	FSIP1	NM_152597.4	60	69,1219,5209	GG,GC,CC		13.0789,5.2955,10.4433	probably-damaging	528/582	39910052	1357,11637	2200	4297	6497	SO:0001583	missense	161835	exon11			CCAATGCCAAGAG	BC045191	CCDS10050.1	15q14	2012-11-19			ENSG00000150667	ENSG00000150667			21674	protein-coding gene	gene with protein product		615795				14702039	Standard	NM_152597		Approved	FLJ35989	uc001zki.3	Q8NA03	OTTHUMG00000172456	ENST00000350221.3:c.1583G>C	15.37:g.39910052C>G	ENSP00000280236:p.Gly528Ala	Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	120	45	0.375	NM_152597	Q6X2C8|Q86Y89	Missense_Mutation	SNP	ENST00000350221.3	37	CCDS10050.1	349	0.15979853479853479	16	0.032520325203252036	48	0.13259668508287292	178	0.3111888111888112	107	0.14116094986807387	C	17.76	3.467593	0.63625	0.052955	0.130789	ENSG00000150667	ENST00000350221	T	0.14144	2.53	4.84	4.84	0.62591	.	0.168900	0.38005	N	0.001843	T	0.00012	0.0000	L	0.29908	0.895	0.35187	P	0.22696400000000005	D	0.76494	0.999	D	0.69654	0.965	T	0.46373	-0.9196	8	.	.	.	-7.1189	10.4881	0.44735	0.0:0.9018:0.0:0.0982	rs16969386;rs57363512;rs16969386	528	Q8NA03	FSIP1_HUMAN	A	528	ENSP00000280236:G528A	.	G	-	2	0	FSIP1	37697344	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.819000	0.48049	2.669000	0.90835	0.591000	0.81541	GGC	C|0.858;G|0.142	0.142	strong		0.408	FSIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252118.2	NM_152597	
SORT1	6272	hgsc.bcm.edu	37	1	109897100	109897100	+	Silent	SNP	T	T	C	rs72646560	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109897100T>C	ENST00000256637.6	-	5	655	c.597A>G	c.(595-597)agA>agG	p.R199R	SORT1_ENST00000482236.1_5'Flank|SORT1_ENST00000538502.1_Silent_p.R63R	NM_002959.5	NP_002950.3	Q99523	SORT_HUMAN	sortilin 1	199					endocytosis (GO:0006897)|endosome to lysosome transport (GO:0008333)|endosome transport via multivesicular body sorting pathway (GO:0032509)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose import (GO:0046323)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|negative regulation of lipoprotein lipase activity (GO:0051005)|nerve growth factor signaling pathway (GO:0038180)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|plasma membrane to endosome transport (GO:0048227)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|vesicle organization (GO:0016050)	cell surface (GO:0009986)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	enzyme binding (GO:0019899)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotensin receptor activity, non-G-protein coupled (GO:0030379)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(5)|ovary(2)|prostate(1)|skin(1)	26		all_epithelial(167;4.69e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0529)|Colorectal(144;0.142)|Epithelial(280;0.145)|Kidney(133;0.169)|all cancers(265;0.184)		AATCTGATGATCTAAAGATTC	0.408													.|||	172	0.034345	0.0325	0.0144	5008	,	,		19639	0.002		0.0537	False		,,,				2504	0.0644				p.R199R		Atlas-SNP	.											.	SORT1	48	.	0			c.A597G						PASS	.	T	,	207,4199	127.4+/-164.3	4,199,2000	154.0	145.0	148.0		189,597	-2.3	1.0	1	dbSNP_130	148	475,8125	139.5+/-196.2	11,453,3836	no	coding-synonymous,coding-synonymous	SORT1	NM_001205228.1,NM_002959.5	,	15,652,5836	CC,CT,TT		5.5233,4.6981,5.2437	,	63/695,199/832	109897100	682,12324	2203	4300	6503	SO:0001819	synonymous_variant	6272	exon5			TGATGATCTAAAG	BC023542	CCDS798.1, CCDS55618.1	1p13.3	2008-05-14			ENSG00000134243	ENSG00000134243			11186	protein-coding gene	gene with protein product		602458					Standard	NM_002959		Approved	Gp95, NT3	uc001dxm.2	Q99523	OTTHUMG00000011999	ENST00000256637.6:c.597A>G	1.37:g.109897100T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	87	44	0.505747	NM_002959	B4DWI3|C0JYZ0|Q8IZ49	Silent	SNP	ENST00000256637.6	37	CCDS798.1																																																																																			T|0.955;C|0.045	0.045	strong		0.408	SORT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033179.1	NM_002959	
PRKCDBP	112464	hgsc.bcm.edu	37	11	6340706	6340706	+	Missense_Mutation	SNP	A	A	G	rs1051992	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6340706A>G	ENST00000303927.3	-	2	643	c.473T>C	c.(472-474)cTg>cCg	p.L158P	PRKCDBP_ENST00000530979.1_Missense_Mutation_p.L190P	NM_145040.2	NP_659477.2	Q969G5	PRDBP_HUMAN	protein kinase C, delta binding protein	158			L -> P (in dbSNP:rs1051992).		cortical actin cytoskeleton organization (GO:0030866)|negative regulation of fermentation (GO:1901003)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	caveola (GO:0005901)|protein complex (GO:0043234)				large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TTCGGCCTCCAGCTGCTCTGG	0.677													A|||	2644	0.527955	0.3873	0.4726	5008	,	,		13961	0.623		0.5805	False		,,,				2504	0.6053				p.L158P		Atlas-SNP	.											PRKCDBP,caecum,carcinoma,0,2	PRKCDBP	19	2	0			c.T473C						PASS	.	A	PRO/LEU	1736,2652		347,1042,805	14.0	17.0	16.0		473	-3.6	0.0	11	dbSNP_86	16	4636,3944		1273,2090,927	yes	missense	PRKCDBP	NM_145040.2	98	1620,3132,1732	GG,GA,AA		45.9674,39.5624,49.1363	benign	158/262	6340706	6372,6596	2194	4290	6484	SO:0001583	missense	112464	exon2			GCCTCCAGCTGCT	AF339881	CCDS7762.1	11p15.4	2011-04-20			ENSG00000170955	ENSG00000170955			9400	protein-coding gene	gene with protein product	"""sdr-related gene product that binds to c-kinase"""					9054438	Standard	NM_145040		Approved	SRBC, HSRBC, MGC20400, cavin-3, CAVIN3	uc001mcu.1	Q969G5	OTTHUMG00000133378	ENST00000303927.3:c.473T>C	11.37:g.6340706A>G	ENSP00000307292:p.Leu158Pro	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_145040		Missense_Mutation	SNP	ENST00000303927.3	37	CCDS7762.1	1163	0.5325091575091575	196	0.3983739837398374	168	0.46408839779005523	355	0.6206293706293706	444	0.5857519788918206	A	6.291	0.421878	0.11928	0.395624	0.540326	ENSG00000170955	ENST00000303927;ENST00000530979	T;T	0.60171	0.21;0.21	5.08	-3.56	0.04626	.	0.744664	0.13090	N	0.414621	T	0.00012	0.0000	N	0.01576	-0.805	0.48341	P	3.689999999999527E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.44421	-0.9329	9	0.34782	T	0.22	0.097	3.9686	0.09443	0.3954:0.0:0.3447:0.2599	rs1051992;rs3802982;rs17240728;rs58428819;rs1051992	158	Q969G5	PRDBP_HUMAN	P	158;190	ENSP00000307292:L158P;ENSP00000432047:L190P	ENSP00000307292:L158P	L	-	2	0	PRKCDBP	6297282	0.000000	0.05858	0.004000	0.12327	0.432000	0.31715	-1.174000	0.03105	-0.455000	0.07054	-1.559000	0.00887	CTG	A|0.509;G|0.491	0.491	strong		0.677	PRKCDBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257228.2	NM_145040	
MUC4	4585	hgsc.bcm.edu	37	3	195510156	195510156	+	Silent	SNP	G	G	A	rs201141296	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195510156G>A	ENST00000463781.3	-	2	8754	c.8295C>T	c.(8293-8295)caC>caT	p.H2765H	MUC4_ENST00000475231.1_Silent_p.H2765H|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_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)	p.H2765H(1)		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)		GAGGGGTGGCGTGACCTGTGG	0.572													.|||	185	0.0369409	0.0129	0.0447	5008	,	,		4806	0.0298		0.0437	False		,,,				2504	0.0644				p.H2765H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	1	Substitution - coding silent(1)	prostate(1)	c.C8295T						scavenged	.						28.0	17.0	21.0					3																	195510156		686	1527	2213	SO:0001819	synonymous_variant	4585	exon2			GGTGGCGTGACCT	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.8295C>T	3.37:g.195510156G>A		Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	66	16	0.242424	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|0.996;A|0.004	0.004	strong		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC25A10	1468	hgsc.bcm.edu	37	17	79682558	79682558	+	Silent	SNP	T	T	C	rs2072700	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79682558T>C	ENST00000350690.5	+	3	350	c.264T>C	c.(262-264)cgT>cgC	p.R88R	SLC25A10_ENST00000331531.5_Silent_p.R88R|SLC25A10_ENST00000545862.1_Silent_p.R45R|SLC25A10_ENST00000541223.1_Silent_p.R243R|SLC25A10_ENST00000571730.1_Silent_p.R243R	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	88					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	TGCGGGACCGTGTGGCCAAGG	0.701													C|||	2135	0.426318	0.4985	0.4582	5008	,	,		14533	0.3859		0.4384	False		,,,				2504	0.3354				p.R88R		Atlas-SNP	.											SLC25A10,NS,carcinoma,0,1	SLC25A10	24	1	0			c.T264C						scavenged	.	C		2153,2253	590.6+/-387.4	533,1087,583	131.0	136.0	134.0		264	-7.8	0.0	17	dbSNP_96	134	3457,5143	631.6+/-398.5	717,2023,1560	no	coding-synonymous	SLC25A10	NM_012140.3		1250,3110,2143	CC,CT,TT		40.1977,48.8652,43.1339		88/288	79682558	5610,7396	2203	4300	6503	SO:0001819	synonymous_variant	1468	exon3			GGACCGTGTGGCC		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"""Solute carriers"""	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.264T>C	17.37:g.79682558T>C		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Silent	SNP	ENST00000350690.5	37	CCDS11786.1																																																																																			T|0.579;C|0.421	0.421	strong		0.701	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1		
USP53	54532	hgsc.bcm.edu	37	4	120214030	120214030	+	Missense_Mutation	SNP	T	T	G	rs3749591	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:120214030T>G	ENST00000274030.6	+	19	4065	c.2886T>G	c.(2884-2886)agT>agG	p.S962R	USP53_ENST00000450251.1_Missense_Mutation_p.S962R	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53									p.S961R(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						CGAAGCACAGTTTAAGTACAG	0.388													T|||	1226	0.244808	0.1195	0.2824	5008	,	,		21325	0.3859		0.3032	False		,,,				2504	0.182				p.S962R		Atlas-SNP	.											USP53,NS,carcinoma,0,1	USP53	69	1	1	Substitution - Missense(1)	stomach(1)	c.T2886G						PASS	.	T	ARG/SER	527,3265		37,453,1406	81.0	73.0	76.0		2886	-1.7	0.0	4	dbSNP_107	76	2598,5662		400,1798,1932	yes	missense	USP53	NM_019050.2	110	437,2251,3338	GG,GT,TT		31.4528,13.8977,25.9293	benign	962/1074	120214030	3125,8927	1896	4130	6026	SO:0001583	missense	54532	exon18			GCACAGTTTAAGT	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"""Ubiquitin-specific peptidases"""	29255	protein-coding gene	gene with protein product			"""ubiquitin specific protease 53"""			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.2886T>G	4.37:g.120214030T>G	ENSP00000274030:p.Ser962Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	37	CCDS43265.1	601	0.2751831501831502	52	0.10569105691056911	87	0.24033149171270718	231	0.40384615384615385	231	0.30474934036939316	T	12.58	1.979529	0.34942	0.138977	0.314528	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.47869	0.83;0.83	5.02	-1.66	0.08265	.	0.901431	0.09698	N	0.767375	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P	0.35433	0.501	B	0.27500	0.08	T	0.34850	-0.9812	9	0.54805	T	0.06	-6.1731	6.3273	0.21251	0.1345:0.43:0.0:0.4356	rs3749591;rs17595370;rs52832840;rs59311247;rs3749591	962	Q70EK8	UBP53_HUMAN	R	962	ENSP00000274030:S962R;ENSP00000409906:S962R	ENSP00000274030:S962R	S	+	3	2	USP53	120433478	0.000000	0.05858	0.000000	0.03702	0.977000	0.68977	-0.174000	0.09839	-0.151000	0.11176	-0.361000	0.07541	AGT	T|0.725;G|0.275	0.275	strong		0.388	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
IGSF10	285313	hgsc.bcm.edu	37	3	151154666	151154666	+	Silent	SNP	T	T	C	rs2172250	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:151154666T>C	ENST00000282466.3	-	6	7682	c.7683A>G	c.(7681-7683)acA>acG	p.T2561T	MED12L_ENST00000474524.1_3'UTR|IGSF10_ENST00000495443.1_5'UTR	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	2561	Ig-like C2-type 12.				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)			GCATCTCCCATGTGATTTCTG	0.517													C|||	4264	0.851438	0.8563	0.8285	5008	,	,		19464	0.8988		0.8539	False		,,,				2504	0.8098				p.T2561T		Atlas-SNP	.											.	IGSF10	279	.	0			c.A7683G						PASS	.	C	,,	3721,685	290.1+/-280.8	1573,575,55	74.0	68.0	70.0		1764,1620,7683	-9.2	0.5	3	dbSNP_96	70	7288,1312	257.3+/-281.4	3094,1100,106	yes	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	4667,1675,161	CC,CT,TT		15.2558,15.547,15.3545	,,	588/651,540/603,2561/2624	151154666	11009,1997	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			CTCCCATGTGATT	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.7683A>G	3.37:g.151154666T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	49	0.408333	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			T|0.152;C|0.848	0.848	strong		0.517	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
ZNF79	7633	hgsc.bcm.edu	37	9	130191186	130191186	+	Missense_Mutation	SNP	C	C	T	rs13292096	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:130191186C>T	ENST00000342483.5	+	2	498	c.92C>T	c.(91-93)aCa>aTa	p.T31I	ZNF79_ENST00000543471.1_Missense_Mutation_p.T7I	NM_007135.2	NP_009066.2	Q15937	ZNF79_HUMAN	zinc finger protein 79	31			T -> I (in dbSNP:rs13292096). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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(2)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|stomach(2)	28						GGTCTCCTCACAGCTGGGCCC	0.473													C|||	2792	0.557508	0.6074	0.6499	5008	,	,		18182	0.4107		0.6342	False		,,,				2504	0.4969				p.T31I		Atlas-SNP	.											ZNF79,NS,carcinoma,+1,2	ZNF79	47	2	0			c.C92T						PASS	.	C	ILE/THR	2822,1584	664.1+/-401.3	892,1038,273	47.0	49.0	48.0		92	2.0	0.0	9	dbSNP_121	48	5061,3539	628.7+/-398.1	1499,2063,738	yes	missense	ZNF79	NM_007135.2	89	2391,3101,1011	TT,TC,CC		41.1512,35.951,39.3895	possibly-damaging	31/499	130191186	7883,5123	2203	4300	6503	SO:0001583	missense	7633	exon2			TCCTCACAGCTGG	X65232	CCDS6871.1, CCDS69664.1, CCDS75904.1	9q34	2013-01-08	2006-05-12		ENSG00000196152	ENSG00000196152		"""Zinc fingers, C2H2-type"""	13153	protein-coding gene	gene with protein product		194552	"""zinc finger protein 79 (pT7)"""			8478004	Standard	NM_007135		Approved	pT7	uc004bqw.4	Q15937	OTTHUMG00000020703	ENST00000342483.5:c.92C>T	9.37:g.130191186C>T	ENSP00000362446:p.Thr31Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_007135	Q5VVW1|Q96NV1	Missense_Mutation	SNP	ENST00000342483.5	37	CCDS6871.1	1248	0.5714285714285714	302	0.6138211382113821	222	0.6132596685082873	237	0.4143356643356643	487	0.6424802110817942	C	18.88	3.716732	0.68844	0.64049	0.588488	ENSG00000196152	ENST00000342483;ENST00000543471	T;T	0.07114	3.22;3.22	3.91	1.95	0.26073	Krueppel-associated box (1);	.	.	.	.	T	0.00012	0.0000	L	0.53671	1.685	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.20438	-1.0275	8	0.39692	T	0.17	.	4.3916	0.11343	0.2228:0.658:0.0:0.1192	rs13292096;rs17855744;rs60610092;rs13292096	31	Q15937	ZNF79_HUMAN	I	31;7	ENSP00000362446:T31I;ENSP00000438418:T7I	ENSP00000362446:T31I	T	+	2	0	ZNF79	129231007	0.002000	0.14202	0.009000	0.14445	0.986000	0.74619	0.588000	0.23924	0.381000	0.24851	0.655000	0.94253	ACA	C|0.414;T|0.586	0.586	strong		0.473	ZNF79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054188.1	NM_007135	
CCHCR1	54535	hgsc.bcm.edu	37	6	31110391	31110391	+	Missense_Mutation	SNP	G	G	C	rs1576	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31110391G>C	ENST00000376266.5	-	18	2449	c.2327C>G	c.(2326-2328)tCc>tGc	p.S776C	CCHCR1_ENST00000396263.2_Missense_Mutation_p.S723C|CCHCR1_ENST00000396268.3_Missense_Mutation_p.S865C|CCHCR1_ENST00000451521.2_Missense_Mutation_p.S829C	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	776			S -> C (in allele HCR*WWCC; associated with psoriasis; dbSNP:rs1576). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:10888604, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CTGGGGATTGGAGCTGGAGCA	0.567													G|||	1117	0.223043	0.2315	0.2767	5008	,	,		20640	0.0724		0.3141	False		,,,				2504	0.2352				p.S865C		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C2594G						PASS	.	G	CYS/SER,CYS/SER,CYS/SER	1094,3312	396.3+/-330.0	134,826,1243	92.0	79.0	84.0		2486,2594,2327	-5.4	0.0	6	dbSNP_36	84	2776,5824	439.7+/-359.3	464,1848,1988	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	112,112,112	598,2674,3231	CC,CG,GG		32.2791,24.8298,29.7555	benign,benign,benign	829/836,865/872,776/783	31110391	3870,9136	2203	4300	6503	SO:0001583	missense	54535	exon18			GGATTGGAGCTGG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.2327C>G	6.37:g.31110391G>C	ENSP00000365442:p.Ser776Cys	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	25	21	0.84	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	525	0.2403846153846154	121	0.2459349593495935	105	0.2900552486187845	49	0.08566433566433566	250	0.32981530343007914	G	8.219	0.802047	0.16397	0.248298	0.322791	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.03717	3.83;3.83;3.83;3.83	4.04	-5.36	0.02689	.	4.983430	0.00644	N	0.000536	T	0.01287	0.0042	L	0.51422	1.61	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	0.001;0.001;0.001;0.0	T	0.46707	-0.9172	9	0.38643	T	0.18	.	7.4966	0.27492	0.2789:0.5368:0.1843:0.0	rs1576;rs130081;rs3173366;rs17456616;rs1576	762;776;829;865	B4DIA2;Q8TD31;E9PE84;Q8TD31-2	.;CCHCR_HUMAN;.;.	C	865;776;723;762;829	ENSP00000379566:S865C;ENSP00000365442:S776C;ENSP00000379561:S723C;ENSP00000401039:S829C	ENSP00000365442:S776C	S	-	2	0	CCHCR1	31218370	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.312000	0.08113	-0.977000	0.03537	-0.326000	0.08463	TCC	G|0.722;C|0.278	0.278	strong		0.567	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
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 GAIIx	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_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Missense_Mutation_p.P84L|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	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	109	55	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	
PPP1R36	145376	hgsc.bcm.edu	37	14	65031534	65031534	+	Missense_Mutation	SNP	C	C	T	rs6573560	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:65031534C>T	ENST00000298705.1	+	4	344	c.248C>T	c.(247-249)aCt>aTt	p.T83I	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	83			T -> I (in dbSNP:rs6573560). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TTTGCAGAAACTGATGGTCCA	0.418													T|||	3094	0.617812	0.7209	0.6095	5008	,	,		20958	0.6597		0.493	False		,,,				2504	0.5695				p.T83I		Atlas-SNP	.											.	.	.	.	0			c.C248T						PASS	.	T	ILE/THR	3041,1365	452.2+/-349.9	1043,955,205	226.0	227.0	227.0		248	-4.0	0.0	14	dbSNP_116	227	4394,4206	571.7+/-389.6	1102,2190,1008	yes	missense	C14orf50	NM_172365.1	89	2145,3145,1213	TT,TC,CC		48.907,30.9805,42.8341	benign	83/423	65031534	7435,5571	2203	4300	6503	SO:0001583	missense	145376	exon4			CAGAAACTGATGG		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20097	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 50"""	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.248C>T	14.37:g.65031534C>T	ENSP00000298705:p.Thr83Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	1335	0.6112637362637363	356	0.7235772357723578	217	0.5994475138121547	380	0.6643356643356644	382	0.503957783641161	T	0.016	-1.511987	0.00984	0.690195	0.51093	ENSG00000165807	ENST00000298705	T	0.35973	1.28	5.9	-4.04	0.04010	.	0.942352	0.08875	N	0.880906	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40515	-0.9559	9	0.12103	T	0.63	-0.0323	1.7676	0.03005	0.1165:0.2952:0.2159:0.3725	rs6573560;rs17824809;rs60418610;rs6573560	83	Q96LQ0	PPR36_HUMAN	I	83	ENSP00000298705:T83I	ENSP00000298705:T83I	T	+	2	0	C14orf50	64101287	0.006000	0.16342	0.043000	0.18650	0.199000	0.23934	-1.585000	0.02112	-0.715000	0.04968	-0.360000	0.07572	ACT	C|0.407;N|0.000	.	strong		0.418	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
ATF6	22926	hgsc.bcm.edu	37	1	161751741	161751741	+	Missense_Mutation	SNP	A	A	G	rs1058405	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:161751741A>G	ENST00000367942.3	+	3	266	c.199A>G	c.(199-201)Atg>Gtg	p.M67V		NM_007348.3	NP_031374.2	P18850	ATF6A_HUMAN	activating transcription factor 6	67	Transcription activation.		M -> L (in dbSNP:rs1058405). {ECO:0000269|PubMed:9271374}.|M -> V (in dbSNP:rs1058405). {ECO:0000269|PubMed:15489334}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response (GO:0006990)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to stress (GO:0006950)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(14)|ovary(3)|skin(1)|stomach(1)	34	all_hematologic(112;0.156)		BRCA - Breast invasive adenocarcinoma(70;0.00953)		Pseudoephedrine(DB00852)	TTTGGATTTGATGCCTTGGGA	0.284													A|||	836	0.166933	0.0113	0.17	5008	,	,		18662	0.2629		0.2724	False		,,,				2504	0.1677				p.M67V		Atlas-SNP	.											.	ATF6	84	.	0			c.A199G	GRCh37	CM077506	ATF6	M	rs1058405	PASS	.	A	VAL/MET	250,4156	145.0+/-179.8	6,238,1959	94.0	91.0	92.0		199	3.8	1.0	1	dbSNP_86	92	2505,6095	409.7+/-349.9	336,1833,2131	yes	missense	ATF6	NM_007348.3	21	342,2071,4090	GG,GA,AA		29.1279,5.6741,21.1825	possibly-damaging	67/671	161751741	2755,10251	2203	4300	6503	SO:0001583	missense	22926	exon3			GATTTGATGCCTT	AB015856	CCDS1235.1	1q22-q23	2013-01-10			ENSG00000118217	ENSG00000118217		"""basic leucine zipper proteins"""	791	protein-coding gene	gene with protein product	"""activating transcription factor 6 alpha"""	605537				9837962, 9271374, 11256944	Standard	NM_007348		Approved	ATF6A	uc001gbs.3	P18850	OTTHUMG00000023961	ENST00000367942.3:c.199A>G	1.37:g.161751741A>G	ENSP00000356919:p.Met67Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_007348	O15139|Q5VW62|Q6IPB5|Q9UEC9	Missense_Mutation	SNP	ENST00000367942.3	37	CCDS1235.1	462	0.21153846153846154	11	0.022357723577235773	74	0.20441988950276244	169	0.29545454545454547	208	0.27440633245382584	A	9.163	1.019228	0.19355	0.056741	0.291279	ENSG00000118217	ENST00000367942	T	0.13901	2.55	5.04	3.83	0.44106	.	0.093620	0.85682	D	0.000000	T	0.05456	0.0144	L	0.53249	1.67	0.38764	P	0.04560299999999995	B	0.20887	0.049	B	0.22386	0.039	T	0.15752	-1.0426	9	0.27785	T	0.31	-7.2503	8.4476	0.32852	0.8028:0.1972:0.0:0.0	rs1058405;rs17407301;rs17845445;rs17858317;rs52823149;rs61419510;rs1058405	67	P18850	ATF6A_HUMAN	V	67	ENSP00000356919:M67V	ENSP00000356919:M67V	M	+	1	0	ATF6	160018365	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.129000	0.42055	2.023000	0.59567	0.454000	0.30748	ATG	A|0.793;G|0.207	0.207	strong		0.284	ATF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060304.2	NM_007348	
FCHO1	23149	hgsc.bcm.edu	37	19	17885270	17885270	+	Silent	SNP	A	A	G	rs2287859	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17885270A>G	ENST00000596536.1	+	13	1186	c.903A>G	c.(901-903)ccA>ccG	p.P301P	FCHO1_ENST00000600676.1_Silent_p.P301P|FCHO1_ENST00000594202.1_Silent_p.P301P|FCHO1_ENST00000597512.1_Silent_p.P308P|FCHO1_ENST00000539407.1_Silent_p.P301P|FCHO1_ENST00000596951.1_Silent_p.P301P|FCHO1_ENST00000389133.4_Silent_p.P301P|FCHO1_ENST00000252771.7_Silent_p.P301P|FCHO1_ENST00000595033.1_Silent_p.P251P	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	301	Mediates interaction with the adaptor protein complex AP-2.				clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	AP-2 adaptor complex binding (GO:0035612)			NS(2)|breast(1)|large_intestine(6)|liver(1)|lung(12)	22						AGCGGGAGCCAGAGCCACCTG	0.647													G|||	2978	0.594649	0.5772	0.5937	5008	,	,		16879	0.8254		0.4056	False		,,,				2504	0.5757				p.P301P		Atlas-SNP	.											.	FCHO1	69	.	0			c.A903G						PASS	.	G	,,,	2455,1951	537.5+/-374.7	687,1081,435	34.0	39.0	37.0		903,903,753,903	-6.4	0.1	19	dbSNP_100	37	3523,5075	621.9+/-397.2	750,2023,1526	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCHO1	NM_001161357.1,NM_001161358.1,NM_001161359.1,NM_015122.2	,,,	1437,3104,1961	GG,GA,AA		40.9746,44.2805,45.9705	,,,	301/892,301/890,251/840,301/890	17885270	5978,7026	2203	4299	6502	SO:0001819	synonymous_variant	23149	exon12			GGAGCCAGAGCCA	AB006628	CCDS32955.1, CCDS59365.1, CCDS59366.1	19p13.12	2008-02-05				ENSG00000130475			29002	protein-coding gene	gene with protein product		613437				12477932	Standard	NM_001161357		Approved	KIAA0290	uc002nhg.3	O14526		ENST00000596536.1:c.903A>G	19.37:g.17885270A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Silent	SNP	ENST00000596536.1	37	CCDS32955.1																																																																																			A|0.495;G|0.505	0.505	strong		0.647	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122	
DOCK10	55619	hgsc.bcm.edu	37	2	225684166	225684166	+	Silent	SNP	A	A	G	rs7572725	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:225684166A>G	ENST00000258390.7	-	29	3331	c.3264T>C	c.(3262-3264)ctT>ctC	p.L1088L	DOCK10_ENST00000409592.3_Silent_p.L1082L	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1088					regulation of cell migration (GO:0030334)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(10)|large_intestine(16)|lung(40)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	87		Renal(207;0.0113)|all_lung(227;0.0486)|Lung NSC(271;0.0653)|all_hematologic(139;0.14)		Epithelial(121;2.37e-10)|all cancers(144;2.26e-07)|Lung(261;0.0143)|LUSC - Lung squamous cell carcinoma(224;0.0178)		TTCTTACCTTAAGGTCACCGG	0.373													G|||	1250	0.249601	0.6641	0.1196	5008	,	,		18217	0.0228		0.1511	False		,,,				2504	0.1166				p.L1088L		Atlas-SNP	.											.	DOCK10	308	.	0			c.T3264C						PASS	.	G		2120,1644		587,946,349	109.0	106.0	107.0		3264	2.0	0.9	2	dbSNP_116	107	1089,7123		77,935,3094	no	coding-synonymous	DOCK10	NM_014689.2		664,1881,3443	GG,GA,AA		13.2611,43.6769,26.7953		1088/2187	225684166	3209,8767	1882	4106	5988	SO:0001819	synonymous_variant	55619	exon29			TACCTTAAGGTCA	AB014594	CCDS46528.1, CCDS74661.1	2q36.3	2013-01-10			ENSG00000135905	ENSG00000135905		"""Pleckstrin homology (PH) domain containing"""	23479	protein-coding gene	gene with protein product	"""zizimin3"""	611518				12432077	Standard	NM_014689		Approved	ZIZ3, KIAA0694	uc010fwz.1	Q96BY6	OTTHUMG00000153428	ENST00000258390.7:c.3264T>C	2.37:g.225684166A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																			A|0.757;G|0.243	0.243	strong		0.373	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1		
LMAN1	3998	hgsc.bcm.edu	37	18	57000469	57000469	+	Missense_Mutation	SNP	T	T	A	rs2298711	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:57000469T>A	ENST00000251047.5	-	11	1945	c.1228A>T	c.(1228-1230)Atg>Ttg	p.M410L		NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	410			M -> L (in dbSNP:rs2298711). {ECO:0000269|PubMed:10090935, ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	GTTTCACTCATGGAATTTCTG	0.393													T|||	426	0.0850639	0.0113	0.1599	5008	,	,		14694	0.0893		0.1421	False		,,,				2504	0.0685				p.M410L		Atlas-SNP	.											.	LMAN1	57	.	0			c.A1228T						PASS	.	T	LEU/MET	152,4254	104.3+/-142.8	5,142,2056	53.0	49.0	51.0		1228	-1.1	1.0	18	dbSNP_100	51	1165,7435	237.1+/-269.0	85,995,3220	yes	missense	LMAN1	NM_005570.3	15	90,1137,5276	AA,AT,TT		13.5465,3.4498,10.1261	benign	410/511	57000469	1317,11689	2203	4300	6503	SO:0001583	missense	3998	exon11			CACTCATGGAATT	X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"""endoplasmic reticulum-golgi intermediate compartment protein 53"""	601567	"""coagulation factor V-factor VIII combined deficiency"""	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.1228A>T	18.37:g.57000469T>A	ENSP00000251047:p.Met410Leu	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_005570	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Missense_Mutation	SNP	ENST00000251047.5	37	CCDS11974.1	237	0.10851648351648352	14	0.028455284552845527	61	0.1685082872928177	58	0.10139860139860139	104	0.13720316622691292	T	9.554	1.116648	0.20795	0.034498	0.135465	ENSG00000074695	ENST00000251047	T	0.52754	0.65	5.87	-1.14	0.09741	.	0.231510	0.52532	N	0.000066	T	0.00073	0.0002	L	0.41236	1.265	0.35285	P	0.21830000000000005	B	0.02656	0.0	B	0.01281	0.0	T	0.11421	-1.0588	9	0.20046	T	0.44	-12.6956	4.3905	0.11337	0.2219:0.1898:0.0:0.5882	rs2298711;rs17696617;rs17853038;rs52809248;rs2298711	410	P49257	LMAN1_HUMAN	L	410	ENSP00000251047:M410L	ENSP00000251047:M410L	M	-	1	0	LMAN1	55151449	1.000000	0.71417	0.984000	0.44739	0.049000	0.14656	1.670000	0.37502	-0.405000	0.07599	-0.250000	0.11733	ATG	T|0.893;A|0.107	0.107	strong		0.393	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570	
CCND3	896	hgsc.bcm.edu	37	6	41903782	41903782	+	Missense_Mutation	SNP	A	A	C	rs386700585|rs1051130	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41903782A>C	ENST00000372991.4	-	5	973	c.775T>G	c.(775-777)Tct>Gct	p.S259A	CCND3_ENST00000372988.4_Missense_Mutation_p.S178A|CCND3_ENST00000372987.4_Missense_Mutation_p.S209A|CCND3_ENST00000510503.1_Missense_Mutation_p.L132R|CCND3_ENST00000511642.1_Missense_Mutation_p.S178A|CCND3_ENST00000415497.2_Missense_Mutation_p.S63A|CCND3_ENST00000414200.2_Missense_Mutation_p.S187A|CCND3_ENST00000511686.1_5'UTR	NM_001760.3	NP_001751.1	P30281	CCND3_HUMAN	cyclin D3	259			S -> A (in dbSNP:rs1051130). {ECO:0000269|PubMed:1386336, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3, ECO:0000269|Ref.4, ECO:0000269|Ref.6, ECO:0000269|Ref.8}.		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)			CTGGTCTGAGAGGCTTCCCTG	0.632			T	IGH@	MM								C|||	2967	0.592452	0.8487	0.5058	5008	,	,		14955	0.504		0.5467	False		,,,				2504	0.4458				p.S259A		Atlas-SNP	.		Dom	yes		6	6p21	896	cyclin D3		L	CCND3,NS,carcinoma,0,2	CCND3	40	2	0			c.T775G						PASS	.	C	ALA/SER,ALA/SER,ALA/SER,ALA/SER	3420,986		1391,638,174	43.0	48.0	47.0		532,559,187,775	0.2	0.0	6	dbSNP_86	47	4700,3900		1294,2112,894	no	missense,missense,missense,missense	CCND3	NM_001136017.2,NM_001136125.1,NM_001136126.1,NM_001760.3	99,99,99,99	2685,2750,1068	CC,CA,AA		45.3488,22.3786,37.5673	benign,benign,benign,benign	178/212,187/221,63/97,259/293	41903782	8120,4886	2203	4300	6503	SO:0001583	missense	896	exon5			TCTGAGAGGCTTC		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.775T>G	6.37:g.41903782A>C	ENSP00000362082:p.Ser259Ala	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	51	0.796875	NM_001760	B2RD63|B3KQ22|E9PAS4|E9PB36|Q5T8J0|Q6FG62|Q96F49	Missense_Mutation	SNP	ENST00000372991.4	37	CCDS4863.1	1276|1276	0.5842490842490843|0.5842490842490843	409|409	0.8313008130081301|0.8313008130081301	164|164	0.4530386740331492|0.4530386740331492	291|291	0.5087412587412588|0.5087412587412588	412|412	0.5435356200527705|0.5435356200527705	N|N	0.008|0.008	-1.896571|-1.896571	0.00522|0.00522	0.776214|0.776214	0.546512|0.546512	ENSG00000112576|ENSG00000112576	ENST00000510503|ENST00000372991;ENST00000511642;ENST00000372987;ENST00000372988;ENST00000415497;ENST00000414200	T|T;T;T;T;T;T	0.36699|0.22945	1.24|1.93;1.93;1.93;1.93;1.93;1.93	5.47|5.47	0.192|0.192	0.15134|0.15134	.|Cyclin, C-terminal (1);	.|0.519042	.|0.17605	.|N	.|0.168274	T|T	0.03390|0.03390	0.0098|0.0098	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.04013	.|0.001;0.001;0.001	T|T	0.44544|0.44544	-0.9321|-0.9321	6|9	0.59425|0.05959	D|T	0.04|0.93	.|.	8.2262|8.2262	0.31570|0.31570	0.63:0.2332:0.0:0.1368|0.63:0.2332:0.0:0.1368	rs1051130;rs2230640;rs3191514;rs57940297;rs1051130|rs1051130;rs2230640;rs3191514;rs57940297;rs1051130	.|187;259;209	.|E9PAS4;P30281;Q5T8J1	.|.;CCND3_HUMAN;.	R|A	132|259;178;209;178;63;187	ENSP00000425986:L132R|ENSP00000362082:S259A;ENSP00000426212:S178A;ENSP00000362078:S209A;ENSP00000362079:S178A;ENSP00000401595:S63A;ENSP00000397545:S187A	ENSP00000425986:L132R|ENSP00000362078:S209A	L|S	-|-	2|1	0|0	CCND3|CCND3	42011760|42011760	0.102000|0.102000	0.21896|0.21896	0.012000|0.012000	0.15200|0.15200	0.242000|0.242000	0.25591|0.25591	0.467000|0.467000	0.22035|0.22035	-0.245000|-0.245000	0.09625|0.09625	-0.352000|-0.352000	0.07741|0.07741	CTC|TCT	T|0.000;G|0.000;C|0.610;A|0.389	0.610	strong		0.632	CCND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040540.2	NM_001760	
PKHD1	5314	hgsc.bcm.edu	37	6	51613177	51613177	+	Silent	SNP	C	C	T	rs765525	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:51613177C>T	ENST00000371117.3	-	58	9512	c.9237G>A	c.(9235-9237)gcG>gcA	p.A3079A	PKHD1_ENST00000340994.4_Silent_p.A3079A	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3079					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CTTTGATTCCCGCCACCCAAA	0.517													T|||	1933	0.385982	0.0318	0.4769	5008	,	,		21619	0.6548		0.3926	False		,,,				2504	0.5164				p.A3079A		Atlas-SNP	.											.	PKHD1	927	.	0			c.G9237A						PASS	.	T	,	452,3954	784.9+/-414.7	16,420,1767	190.0	166.0	174.0		9237,9237	3.3	1.0	6	dbSNP_86	174	3112,5488	658.0+/-401.5	567,1978,1755	yes	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	583,2398,3522	TT,TC,CC		36.186,10.2587,27.4027	,	3079/4075,3079/3397	51613177	3564,9442	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon58			GATTCCCGCCACC	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.9237G>A	6.37:g.51613177C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	65	40	0.615385	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			T|0.317;G|0.011	0.317	strong		0.517	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118364967	118364967	+	Missense_Mutation	SNP	G	G	C	rs2305204	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:118364967G>C	ENST00000528052.1	+	12	1313	c.1242G>C	c.(1240-1242)gaG>gaC	p.E414D	PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.E414D|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.E414D			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	414	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.		E -> D (in dbSNP:rs2305204). {ECO:0000269|PubMed:15489334}.		lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		GAACAATTGAGAAAGTCAAGT	0.423													-|||	628	0.125399	0.0091	0.0576	5008	,	,		18441	0.4107		0.0567	False		,,,				2504	0.1074				p.E414D		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.G1242C						PASS	.		ASP/GLU	83,4323		1,81,2121	138.0	137.0	138.0		1242	4.6	1.0	10	dbSNP_100	138	590,8010		20,550,3730	yes	missense	PNLIPRP1	NM_006229.2	45	21,631,5851	CC,CG,GG		6.8605,1.8838,5.1745	benign	414/468	118364967	673,12333	2203	4300	6503	SO:0001583	missense	5407	exon12			AATTGAGAAAGTC	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.1242G>C	10.37:g.118364967G>C	ENSP00000433933:p.Glu414Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	37	CCDS7595.1	306	0.1401098901098901	9	0.018292682926829267	18	0.049723756906077346	241	0.42132867132867136	38	0.05013192612137203	-	11.16	1.556195	0.27827	0.018838	0.068605	ENSG00000187021	ENST00000358834;ENST00000528052;ENST00000534537	T;T;T	0.64803	-0.12;-0.12;-0.12	5.53	4.63	0.57726	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.406518	0.25288	N	0.031749	T	0.00012	0.0000	L	0.41632	1.29	0.09310	P	0.999999999708388	B	0.02656	0.0	B	0.04013	0.001	T	0.39583	-0.9607	9	0.15499	T	0.54	-15.4607	7.0954	0.25307	0.0818:0.0:0.649:0.2692	rs2305204;rs17848308;rs17855511;rs52801749;rs2305204	414	P54315	LIPR1_HUMAN	D	414	ENSP00000351695:E414D;ENSP00000433933:E414D;ENSP00000434159:E414D	ENSP00000351695:E414D	E	+	3	2	PNLIPRP1	118354957	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	0.781000	0.26774	1.331000	0.45412	0.550000	0.68814	GAG	G|0.919;C|0.081	0.081	strong		0.423	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047710	46047710	+	Silent	SNP	T	T	C	rs8131142	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46047710T>C	ENST00000397911.3	+	1	671	c.622T>C	c.(622-624)Ttg>Ctg	p.L208L	KRTAP10-9_ENST00000484861.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	208	25 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GGCTTCCTCTTTGTGCTGCCA	0.632													C|||	3246	0.648163	0.5711	0.6787	5008	,	,		20040	0.6637		0.7107	False		,,,				2504	0.6503				p.L208L		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.T622C						PASS	.	C	,	2517,1889	542.5+/-376.0	725,1067,411	192.0	214.0	206.0		,622	-1.4	0.0	21	dbSNP_116	206	5789,2811	442.8+/-360.2	1943,1903,454	no	intron,coding-synonymous	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,	2668,2970,865	CC,CT,TT		32.686,42.8734,36.1372	,	,208/293	46047710	8306,4700	2203	4300	6503	SO:0001819	synonymous_variant	386676	exon1			TCCTCTTTGTGCT	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.622T>C	21.37:g.46047710T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	101	39	0.386139	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Silent	SNP	ENST00000397911.3	37	CCDS42961.1																																																																																			T|0.339;C|0.661	0.661	strong		0.632	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
C5orf52	100190949	hgsc.bcm.edu	37	5	157102185	157102185	+	Missense_Mutation	SNP	A	A	G	rs6884959	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:157102185A>G	ENST00000409999.3	+	2	360	c.298A>G	c.(298-300)Aca>Gca	p.T100A		NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	100										endometrium(2)|lung(1)	3						TAACCGCATCACACAACGAAT	0.428													.|||	2594	0.517971	0.9085	0.3775	5008	,	,		19463	0.2887		0.3907	False		,,,				2504	0.4571				p.T100A		Atlas-SNP	.											.	C5orf52	17	.	0			c.A298G						PASS	.	G	ALA/THR	1167,217		490,187,15	104.0	98.0	99.0		298	2.2	1.0	5	dbSNP_116	99	1236,1946		246,744,601	yes	missense	C5orf52	NM_001145132.1	58	736,931,616	GG,GA,AA		38.8435,15.6792,47.3719	benign	100/160	157102185	2403,2163	692	1591	2283	SO:0001583	missense	100190949	exon2			CGCATCACACAAC	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.298A>G	5.37:g.157102185A>G	ENSP00000387027:p.Thr100Ala	Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001145132		Missense_Mutation	SNP	ENST00000409999.3	37	CCDS47329.1	1047	0.4793956043956044	442	0.8983739837398373	131	0.36187845303867405	177	0.3094405594405594	297	0.391820580474934	G	0.058	-1.231532	0.01505	0.843208	0.388435	ENSG00000187658	ENST00000409999	T	0.26373	1.74	2.22	2.22	0.28083	.	.	.	.	.	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.31475	-0.9942	8	0.02654	T	1	-15.7143	5.0875	0.14691	0.188:0.0:0.812:0.0	rs6884959;rs17451564;rs52828955;rs58650472;rs6884959	100	A6NGY3	CE052_HUMAN	A	100	ENSP00000387027:T100A	ENSP00000387027:T100A	T	+	1	0	C5orf52	157034763	0.854000	0.29725	0.974000	0.42286	0.771000	0.43674	0.383000	0.20651	0.269000	0.21961	-0.642000	0.03964	ACA	A|0.478;G|0.522	0.522	strong		0.428	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
MUC2	4583	hgsc.bcm.edu	37	11	1093769	1093769	+	Missense_Mutation	SNP	G	G	A	rs41361144	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1093769G>A	ENST00000441003.2	+	30	5615	c.5588G>A	c.(5587-5589)cGg>cAg	p.R1863Q	MUC2_ENST00000333592.6_Missense_Mutation_p.R151Q|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4225					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)		p.R1863L(1)		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)	CAGACCTCTCGGTCCACCTCT	0.617													G|||	325	0.0648962	0.0681	0.0418	5008	,	,		18686	0.0585		0.0825	False		,,,				2504	0.0654				p.R1859Q		Atlas-SNP	.											.	MUC2	614	.	1	Substitution - Missense(1)	lung(1)	c.G5576A						PASS	.	G	GLN/ARG	241,4075		7,227,1924	246.0	294.0	278.0		5573	-3.4	0.0	11	dbSNP_127	278	662,7836		18,626,3605	yes	missense	MUC2	NM_002457.2	43	25,853,5529	AA,AG,GG		7.7901,5.5839,7.047	benign	1858/2813	1093769	903,11911	2158	4249	6407	SO:0001583	missense	4583	exon31			CCTCTCGGTCCAC	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.5588G>A	11.37:g.1093769G>A	ENSP00000415183:p.Arg1863Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		128	0.05860805860805861	23	0.046747967479674794	16	0.04419889502762431	29	0.050699300699300696	60	0.079155672823219	G	0.371	-0.934206	0.02340	0.055839	0.077901	ENSG00000198788	ENST00000441003;ENST00000333592	T;T	0.12255	2.7;3.1	1.7	-3.39	0.04868	.	.	.	.	.	T	0.00328	0.0010	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43376	-0.9395	8	0.13108	T	0.6	.	4.124	0.10118	0.4559:0.3763:0.1678:0.0	rs41361144	1863	E7EUV1	.	Q	1863;151	ENSP00000415183:R1863Q;ENSP00000331373:R151Q	ENSP00000331373:R151Q	R	+	2	0	MUC2	1083769	0.000000	0.05858	0.001000	0.08648	0.040000	0.13550	-4.255000	0.00265	-1.321000	0.02281	-0.727000	0.03589	CGG	G|0.937;A|0.063	0.063	strong		0.617	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZNF202	7753	hgsc.bcm.edu	37	11	123598941	123598941	+	Silent	SNP	T	T	C	rs2282644	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:123598941T>C	ENST00000529691.1	-	5	951	c.732A>G	c.(730-732)gtA>gtG	p.V244V	ZNF202_ENST00000336139.4_Silent_p.V244V|ZNF202_ENST00000530393.1_Silent_p.V244V			O95125	ZN202_HUMAN	zinc finger protein 202	244	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				lipid metabolic process (GO:0006629)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)			endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.03)		GGGAAAAGCATACGGCCACAT	0.458													T|||	1148	0.229233	0.0159	0.2968	5008	,	,		20310	0.3552		0.2694	False		,,,				2504	0.2986				p.V244V		Atlas-SNP	.											.	ZNF202	72	.	0			c.A732G						PASS	.	T		264,4140	149.2+/-183.4	13,238,1951	124.0	115.0	118.0		732	-8.9	0.1	11	dbSNP_100	118	2411,6187	402.3+/-347.4	342,1727,2230	no	coding-synonymous	ZNF202	NM_003455.2		355,1965,4181	CC,CT,TT		28.0414,5.9946,20.5738		244/649	123598941	2675,10327	2202	4299	6501	SO:0001819	synonymous_variant	7753	exon7			AAAGCATACGGCC	AF027219	CCDS8443.1	11q23.3	2013-01-09				ENSG00000166261		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12994	protein-coding gene	gene with protein product		603430				9790754	Standard	XM_005271659		Approved	ZKSCAN10, ZSCAN42	uc001pzd.1	O95125		ENST00000529691.1:c.732A>G	11.37:g.123598941T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	133	110	0.827068	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Silent	SNP	ENST00000529691.1	37	CCDS8443.1																																																																																			T|0.784;C|0.216	0.216	strong		0.458	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455	
RXFP2	122042	hgsc.bcm.edu	37	13	32360583	32360583	+	Silent	SNP	A	A	G	rs9549106	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:32360583A>G	ENST00000298386.2	+	12	1064	c.993A>G	c.(991-993)ctA>ctG	p.L331L	RXFP2_ENST00000380314.1_Silent_p.L307L	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	331					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)		TGAAGCTTCTACAAAAGCTGT	0.348													A|||	678	0.135383	0.0855	0.1657	5008	,	,		18830	0.1905		0.1551	False		,,,				2504	0.1043				p.L331L		Atlas-SNP	.											.	RXFP2	95	.	0			c.A993G						PASS	.	A	,	556,3850	246.2+/-254.9	28,500,1675	89.0	83.0	85.0		921,993	-3.4	1.0	13	dbSNP_119	85	1227,7373	246.7+/-275.0	89,1049,3162	no	coding-synonymous,coding-synonymous	RXFP2	NM_001166058.1,NM_130806.3	,	117,1549,4837	GG,GA,AA		14.2674,12.6192,13.7091	,	307/731,331/755	32360583	1783,11223	2203	4300	6503	SO:0001819	synonymous_variant	122042	exon12			GCTTCTACAAAAG	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.993A>G	13.37:g.32360583A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_130806	B1ALE9|Q3KU23	Silent	SNP	ENST00000298386.2	37	CCDS9342.1																																																																																			A|0.860;G|0.140	0.140	strong		0.348	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806	
HAPLN3	145864	hgsc.bcm.edu	37	15	89421327	89421327	+	Silent	SNP	A	A	G	rs2280463	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89421327A>G	ENST00000359595.3	-	5	1171	c.957T>C	c.(955-957)ggT>ggC	p.G319G	HAPLN3_ENST00000562889.1_Silent_p.G381G	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	319	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	AGCGGACGCTACCATCTGCCA	0.647													G|||	2193	0.437899	0.8139	0.3228	5008	,	,		14462	0.256		0.2932	False		,,,				2504	0.3476				p.G319G		Atlas-SNP	.											.	HAPLN3	43	.	0			c.T957C						PASS	.	G		3289,1111	398.5+/-330.9	1243,803,154	94.0	93.0	93.0		957	2.5	1.0	15	dbSNP_100	93	2665,5933	684.5+/-404.0	393,1879,2027	no	coding-synonymous	HAPLN3	NM_178232.2		1636,2682,2181	GG,GA,AA		30.9956,25.25,45.807		319/361	89421327	5954,7044	2200	4299	6499	SO:0001819	synonymous_variant	145864	exon5			GACGCTACCATCT	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.957T>C	15.37:g.89421327A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_178232	A8K7P0	Silent	SNP	ENST00000359595.3	37	CCDS10346.1																																																																																			A|0.561;G|0.439	0.439	strong		0.647	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
POLR2J3	548644	hgsc.bcm.edu	37	7	102212939	102212939	+	Missense_Mutation	SNP	G	G	C	rs139049967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:102212939G>C	ENST00000511313.1	-	1	91	c.30C>G	c.(28-30)ttC>ttG	p.F10L	POLR2J3_ENST00000504157.1_5'UTR|RP11-514P8.7_ENST00000514917.2_Intron|POLR2J3_ENST00000513438.1_Missense_Mutation_p.F10L			Q9H1A7	RPB1C_HUMAN	polymerase (RNA) II (DNA directed) polypeptide J3	10					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)										CGAAGAGCAAGAACGACTCGA	0.662																																					p.F10L		Atlas-SNP	.											.	POLR2J3	2	.	0			c.C30G						PASS	.	G	LEU/PHE	124,4270		0,124,2073	52.0	53.0	53.0		30	1.0	0.7	7	dbSNP_134	53	451,8069		0,451,3809	no	missense	POLR2J3	NM_001097615.2	22	0,575,5882	CC,CG,GG		5.2934,2.822,4.4525	possibly-damaging	10/116	102212939	575,12339	2197	4260	6457	SO:0001583	missense	548644	exon1			GAGCAAGAACGAC		CCDS47673.1	7q22.1	2013-01-21			ENSG00000168255	ENSG00000168255		"""RNA polymerase subunits"""	33853	protein-coding gene	gene with protein product						15586814	Standard	NM_001097615		Approved		uc010lid.1	Q9H1A7	OTTHUMG00000150384	ENST00000511313.1:c.30C>G	7.37:g.102212939G>C	ENSP00000422109:p.Phe10Leu	Somatic	1201	1	0.000832639		WXS	Illumina HiSeq	Phase_I	1070	129	0.120561	NM_001097615	A6NKA1	Missense_Mutation	SNP	ENST00000511313.1	37		.	.	.	.	.	.	.	.	.	.	g	16.96	3.264917	0.59431	0.02822	0.052934	ENSG00000168255	ENST00000513506;ENST00000511313;ENST00000513438	D;D;D	0.91945	-2.94;-2.94;-2.94	0.976	0.976	0.19727	DNA-directed RNA polymerase, RBP11-like (1);	0.000000	0.85682	D	0.000000	T	0.69984	0.3172	M	0.79343	2.45	0.80722	D	1	D	0.71674	0.998	P	0.50659	0.647	T	0.78563	-0.2156	10	0.48119	T	0.1	.	3.3598	0.07182	0.3078:0.0:0.6922:0.0	.	10	Q9GZM3	RPB1B_HUMAN	L	10	ENSP00000421085:F10L;ENSP00000422109:F10L;ENSP00000421950:F10L	ENSP00000368645:F10L	F	-	3	2	POLR2J3	102000044	1.000000	0.71417	0.708000	0.30435	0.103000	0.19146	0.264000	0.18497	0.453000	0.26858	0.184000	0.17185	TTC	G|0.980;C|0.020	0.020	strong		0.662	POLR2J3-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000358591.1	NM_001097615	
PLCB2	5330	hgsc.bcm.edu	37	15	40590134	40590134	+	Silent	SNP	G	G	A	rs2229690	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:40590134G>A	ENST00000260402.3	-	12	1431	c.1182C>T	c.(1180-1182)agC>agT	p.S394S	PLCB2_ENST00000456256.2_Silent_p.S394S|PLCB2_ENST00000557821.1_Silent_p.S394S|PLCB2-AS1_ENST00000559520.1_RNA	NM_001284297.1|NM_004573.2	NP_001271226.1|NP_004564.2	Q00722	PLCB2_HUMAN	phospholipase C, beta 2	394	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				activation of phospholipase C activity (GO:0007202)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|sensory perception of bitter taste (GO:0050913)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.S394R(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(3)	39		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.38e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0508)		TCTTAAAGGCGCTTTCTGCAA	0.542													A|||	3458	0.690495	0.8298	0.6744	5008	,	,		20222	0.7887		0.4742	False		,,,				2504	0.635				p.S394S		Atlas-SNP	.											PLCB2_ENST00000260402,NS,carcinoma,0,2	PLCB2	177	2	1	Substitution - Missense(1)	pancreas(1)	c.C1182T						PASS	.	A		3353,941		1314,725,108	91.0	111.0	105.0		1182	-0.4	1.0	15	dbSNP_98	105	4142,4372		1011,2120,1126	no	coding-synonymous	PLCB2	NM_004573.2		2325,2845,1234	AA,AG,GG		48.6493,21.9143,41.4819		394/1186	40590134	7495,5313	2147	4257	6404	SO:0001819	synonymous_variant	5330	exon12			AAAGGCGCTTTCT		CCDS42020.1, CCDS61591.1, CCDS61592.1, CCDS73704.1	15q15.1	2012-01-23			ENSG00000137841	ENSG00000137841	3.1.4.11		9055	protein-coding gene	gene with protein product		604114				1644792, 9925923	Standard	XM_005254448		Approved	FLJ38135	uc001zld.3	Q00722	OTTHUMG00000172412	ENST00000260402.3:c.1182C>T	15.37:g.40590134G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_004573	A8K6J2|B9EGH5	Silent	SNP	ENST00000260402.3	37	CCDS42020.1																																																																																			G|0.349;A|0.651	0.651	strong		0.542	PLCB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418430.1		
NUP88	4927	hgsc.bcm.edu	37	17	5290033	5290033	+	Silent	SNP	T	T	C	rs1071705	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5290033T>C	ENST00000573584.1	-	16	2666	c.2157A>G	c.(2155-2157)aaA>aaG	p.K719K	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	719					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CTTACTCCTCTTTCAGGATGG	0.398													C|||	2768	0.552716	0.3994	0.4236	5008	,	,		20862	0.8244		0.4404	False		,,,				2504	0.6871				p.K719K		Atlas-SNP	.											.	NUP88	47	.	0			c.A2157G						PASS	.	C		1852,2554	633.4+/-396.0	411,1030,762	184.0	170.0	175.0		2157	3.5	1.0	17	dbSNP_86	175	3390,5210	639.9+/-399.5	666,2058,1576	no	coding-synonymous	NUP88	NM_002532.4		1077,3088,2338	CC,CT,TT		39.4186,42.0336,40.3045		719/742	5290033	5242,7764	2203	4300	6503	SO:0001819	synonymous_variant	4927	exon16			CTCCTCTTTCAGG	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.2157A>G	17.37:g.5290033T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	141	66	0.468085	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			T|0.566;C|0.434	0.434	strong		0.398	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
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 GAIIx	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	NEFM_ENST00000518131.1_Missense_Mutation_p.H426Q|NEFM_ENST00000521540.1_3'UTR|NEFM_ENST00000437366.2_Missense_Mutation_p.H426Q|NEFM_ENST00000433454.2_Missense_Mutation_p.H50Q|GS1-72M22.1_ENST00000607058.1_RNA			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	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	140	79	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	
JPH2	57158	hgsc.bcm.edu	37	20	42747247	42747247	+	Missense_Mutation	SNP	C	C	T	rs3810510	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:42747247C>T	ENST00000372980.3	-	3	2058	c.1186G>A	c.(1186-1188)Gcc>Acc	p.A396T		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	396	Ala-rich.		A -> T (in dbSNP:rs3810510).		calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			TCAGCTTTGGCCTTGGCGTGG	0.592													C|||	1354	0.270367	0.3933	0.1009	5008	,	,		19145	0.3571		0.1163	False		,,,				2504	0.2935				p.A396T		Atlas-SNP	.											JPH2,caecum,carcinoma,0,1	JPH2	86	1	0			c.G1186A						PASS	.	C	THR/ALA	1455,2951	470.0+/-355.6	249,957,997	90.0	91.0	90.0		1186	3.8	1.0	20	dbSNP_107	90	1109,7491	231.1+/-265.2	78,953,3269	yes	missense	JPH2	NM_020433.4	58	327,1910,4266	TT,TC,CC		12.8953,33.0232,19.714	probably-damaging	396/697	42747247	2564,10442	2203	4300	6503	SO:0001583	missense	57158	exon3			CTTTGGCCTTGGC	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.1186G>A	20.37:g.42747247C>T	ENSP00000362071:p.Ala396Thr	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	21	16	0.761905	NM_020433	E1P5X1|O95913|Q5JY74|Q9UJN4	Missense_Mutation	SNP	ENST00000372980.3	37	CCDS13325.1	527	0.2413003663003663	185	0.37601626016260165	39	0.10773480662983426	217	0.3793706293706294	86	0.11345646437994723	C	21.7	4.194721	0.78902	0.330232	0.128953	ENSG00000149596	ENST00000372980	T	0.61980	0.06	4.78	3.84	0.44239	.	0.516515	0.20203	N	0.097052	T	0.00012	0.0000	L	0.48877	1.53	0.09310	P	1.0	D	0.54601	0.967	P	0.49276	0.605	T	0.29640	-1.0005	9	0.37606	T	0.19	.	11.654	0.51306	0.0:0.9117:0.0:0.0883	rs3810510;rs60986665;rs3810510	396	Q9BR39	JPH2_HUMAN	T	396	ENSP00000362071:A396T	ENSP00000362071:A396T	A	-	1	0	JPH2	42180661	1.000000	0.71417	0.998000	0.56505	0.896000	0.52359	4.050000	0.57404	1.005000	0.39183	0.561000	0.74099	GCC	C|0.772;T|0.228	0.228	strong		0.592	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1		
SALL3	27164	hgsc.bcm.edu	37	18	76753491	76753491	+	Silent	SNP	C	C	T	rs7233194	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:76753491C>T	ENST00000537592.2	+	2	1500	c.1500C>T	c.(1498-1500)ggC>ggT	p.G500G	SALL3_ENST00000536229.3_Silent_p.G367G|SALL3_ENST00000575389.2_Silent_p.G500G	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	500					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|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(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		TCCCCTACGGCATGTCGCTGC	0.667													C|||	75	0.014976	0.0023	0.0288	5008	,	,		13976	0.0		0.0457	False		,,,				2504	0.0061				p.G500G		Atlas-SNP	.											.	SALL3	162	.	0			c.C1500T						PASS	.	C		32,4374	36.8+/-68.6	1,30,2172	38.0	33.0	35.0		1500	-1.8	1.0	18	dbSNP_116	35	357,8243	117.0+/-176.6	11,335,3954	no	coding-synonymous	SALL3	NM_171999.2		12,365,6126	TT,TC,CC		4.1512,0.7263,2.9909		500/1301	76753491	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	27164	exon2			CTACGGCATGTCG	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1500C>T	18.37:g.76753491C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	37	CCDS12013.1																																																																																			C|0.974;T|0.026	0.026	strong		0.667	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
GCSAM	257144	hgsc.bcm.edu	37	3	111842431	111842431	+	Silent	SNP	T	T	C	rs16859261	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111842431T>C	ENST00000308910.4	-	6	592	c.408A>G	c.(406-408)acA>acG	p.T136T	C3orf52_ENST00000467942.2_Intron|GCSAM_ENST00000484193.1_Silent_p.T138T	NM_001190259.1|NM_001190260.1|NM_152785.4	NP_001177188.1|NP_001177189.1|NP_689998.1	Q8N6F7	GCSAM_HUMAN	germinal center-associated, signaling and motility	136					negative regulation of lymphocyte migration (GO:2000402)|regulation of B cell receptor signaling pathway (GO:0050855)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|myosin II binding (GO:0045159)|protein kinase binding (GO:0019901)										GCCTGGGGTCTGTAGAAGGCA	0.493													-|||	233	0.0465256	0.0023	0.036	5008	,	,		21153	0.0605		0.0358	False		,,,				2504	0.1104				p.T138T		Atlas-SNP	.											.	.	.	.	0			c.A414G						PASS	.	-	,,	29,4377		0,29,2174	136.0	139.0	138.0		414,363,408		0.0	3	dbSNP_123	138	267,8333		3,261,4036	no	coding-synonymous,coding-synonymous,coding-synonymous	GCET2	NM_001190259.1,NM_001190260.1,NM_152785.4	,,	3,290,6210	CC,CT,TT		3.1047,0.6582,2.2759	,,	138/181,121/164,136/179	111842431	296,12710	2203	4300	6503	SO:0001819	synonymous_variant	257144	exon6			GGGGTCTGTAGAA	BC030506	CCDS2964.1, CCDS54621.1, CCDS54622.1	3q13.13	2012-09-03	2012-08-23	2012-08-23	ENSG00000174500	ENSG00000174500			20253	protein-coding gene	gene with protein product	"""human germinal center-associated lymphoma"""	607792	"""germinal center expressed transcript 2"""	GCET2			Standard	NM_152785		Approved	MGC40441, HGAL	uc021xcl.1	Q8N6F7	OTTHUMG00000159231	ENST00000308910.4:c.408A>G	3.37:g.111842431T>C		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	220	103	0.468182	NM_001190259	C9JD17|C9JUG6	Silent	SNP	ENST00000308910.4	37	CCDS2964.1																																																																																			T|0.970;C|0.030	0.030	strong		0.493	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785	
ADCK1	57143	hgsc.bcm.edu	37	14	78390880	78390880	+	Silent	SNP	T	T	C	rs2302944	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:78390880T>C	ENST00000238561.5	+	8	1038	c.939T>C	c.(937-939)aaT>aaC	p.N313N	ADCK1_ENST00000341211.5_Silent_p.N245N|ADCK1_ENST00000556560.1_3'UTR	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	320	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		ACCCCGGCAATGTACTGGTGC	0.572													T|||	1175	0.234625	0.1626	0.196	5008	,	,		18266	0.2798		0.2127	False		,,,				2504	0.3354				p.N313N		Atlas-SNP	.											.	ADCK1	81	.	0			c.T939C						PASS	.	T	,	775,3631	314.9+/-293.9	66,643,1494	97.0	90.0	92.0		735,939	-8.7	0.6	14	dbSNP_100	92	1829,6771	328.0+/-318.1	187,1455,2658	no	coding-synonymous,coding-synonymous	ADCK1	NM_001142545.1,NM_020421.3	,	253,2098,4152	CC,CT,TT		21.2674,17.5897,20.0215	,	245/456,313/524	78390880	2604,10402	2203	4300	6503	SO:0001819	synonymous_variant	57143	exon8			CGGCAATGTACTG	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.939T>C	14.37:g.78390880T>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	45	15	0.333333	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Silent	SNP	ENST00000238561.5	37	CCDS9869.1																																																																																			T|0.791;C|0.209	0.209	strong		0.572	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
PGM2	55276	hgsc.bcm.edu	37	4	37836302	37836302	+	Silent	SNP	T	T	C	rs3752683	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:37836302T>C	ENST00000381967.4	+	3	412	c.312T>C	c.(310-312)agT>agC	p.S104S	PGM2_ENST00000537241.1_Intron|PGM2_ENST00000544359.1_5'UTR	NM_018290.3	NP_060760.2	Q96G03	PGM2_HUMAN	phosphoglucomutase 2	104					carbohydrate metabolic process (GO:0005975)|deoxyribose phosphate catabolic process (GO:0046386)|galactose catabolic process (GO:0019388)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)|phosphopentomutase activity (GO:0008973)			breast(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	19						TCGTGATCAGTTTTGACGCCC	0.338													C|||	1722	0.34385	0.6755	0.2781	5008	,	,		14222	0.2748		0.2167	False		,,,				2504	0.1442				p.S104S		Atlas-SNP	.											.	PGM2	45	.	0			c.T312C						PASS	.	C		2711,1695	651.8+/-399.3	835,1041,327	91.0	102.0	99.0		312	2.3	1.0	4	dbSNP_107	99	1856,6744	331.4+/-319.6	196,1464,2640	no	coding-synonymous	PGM2	NM_018290.3		1031,2505,2967	CC,CT,TT		21.5814,38.4703,35.1146		104/613	37836302	4567,8439	2203	4300	6503	SO:0001819	synonymous_variant	55276	exon3			GATCAGTTTTGAC	BC010087	CCDS3443.1	4p14	2012-10-02			ENSG00000169299	ENSG00000169299	5.4.2.2		8906	protein-coding gene	gene with protein product	"""phosphopentomutase"""	172000				9549096	Standard	NM_018290		Approved	FLJ10983	uc011byb.1	Q96G03	OTTHUMG00000097813	ENST00000381967.4:c.312T>C	4.37:g.37836302T>C		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	235	117	0.497872	NM_018290	B4E0G8|Q53FP5|Q5QTR0|Q9H0P9|Q9NV22	Silent	SNP	ENST00000381967.4	37	CCDS3443.1																																																																																			T|0.651;C|0.349	0.349	strong		0.338	PGM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215079.2	NM_018290	
CRY1	1407	hgsc.bcm.edu	37	12	107395106	107395106	+	Silent	SNP	A	A	G	rs8192440	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:107395106A>G	ENST00000008527.5	-	5	1503	c.636T>C	c.(634-636)ggT>ggC	p.G212G		NM_004075.4	NP_004066.1	Q16526	CRY1_HUMAN	cryptochrome circadian clock 1	212					blue light signaling pathway (GO:0009785)|circadian regulation of gene expression (GO:0032922)|DNA damage induced protein phosphorylation (GO:0006975)|DNA repair (GO:0006281)|entrainment of circadian clock by photoperiod (GO:0043153)|gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|lipid storage (GO:0019915)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of glucocorticoid secretion (GO:2000850)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein-chromophore linkage (GO:0018298)|regulation of circadian rhythm (GO:0042752)|regulation of DNA damage checkpoint (GO:2000001)|response to glucagon (GO:0033762)|response to insulin (GO:0032868)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	blue light photoreceptor activity (GO:0009882)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|DNA photolyase activity (GO:0003913)|double-stranded DNA binding (GO:0003690)|nuclear hormone receptor binding (GO:0035257)|nucleotide binding (GO:0000166)|phosphatase binding (GO:0019902)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin binding (GO:0043130)			NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|skin(1)	29						CAGTTTCTCCACCTGGCCACA	0.348													G|||	3955	0.789736	0.857	0.7579	5008	,	,		17073	0.9554		0.6282	False		,,,				2504	0.7168				p.G212G		Atlas-SNP	.											CRY1,NS,carcinoma,-2,1	CRY1	74	1	0			c.T636C						PASS	.	G		3618,788	316.3+/-294.6	1494,630,79	100.0	103.0	102.0		636	-11.4	0.7	12	dbSNP_117	102	5367,3233	486.6+/-371.9	1642,2083,575	no	coding-synonymous	CRY1	NM_004075.3		3136,2713,654	GG,GA,AA		37.593,17.8847,30.9165		212/587	107395106	8985,4021	2203	4300	6503	SO:0001819	synonymous_variant	1407	exon5			TTCTCCACCTGGC	BC030519	CCDS9112.1	12q23-q24.1	2014-01-17	2014-01-17		ENSG00000008405	ENSG00000008405			2384	protein-coding gene	gene with protein product		601933	"""cryptochrome 1 (photolyase-like)"""	PHLL1		8921389	Standard	NM_004075		Approved		uc001tmi.4	Q16526	OTTHUMG00000170005	ENST00000008527.5:c.636T>C	12.37:g.107395106A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	175	174	0.994286	NM_004075		Silent	SNP	ENST00000008527.5	37	CCDS9112.1																																																																																			A|0.264;G|0.736	0.736	strong		0.348	CRY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406827.1	NM_004075	
FAT1	2195	hgsc.bcm.edu	37	4	187629538	187629538	+	Missense_Mutation	SNP	C	C	T	rs3733413	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187629538C>T	ENST00000441802.2	-	2	1653	c.1444G>A	c.(1444-1446)Gtc>Atc	p.V482I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	482	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.			V -> I (in Ref. 1; CAA60685). {ECO:0000305}.	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						AGGCTCATGACAGTAGTACCA	0.468										HNSCC(5;0.00058)			C|||	1697	0.338858	0.1581	0.4798	5008	,	,		21218	0.1399		0.5765	False		,,,				2504	0.4438				p.V482I	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G1444A						PASS	.	C	ILE/VAL	907,3177		110,687,1245	153.0	147.0	149.0		1444	2.8	0.3	4	dbSNP_107	149	4828,3536		1392,2044,746	yes	missense	FAT1	NM_005245.3	29	1502,2731,1991	TT,TC,CC		42.2764,22.2086,46.0717	probably-damaging	482/4589	187629538	5735,6713	2042	4182	6224	SO:0001583	missense	2195	exon2			TCATGACAGTAGT	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.1444G>A	4.37:g.187629538C>T	ENSP00000406229:p.Val482Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	793	0.3630952380952381	93	0.18902439024390244	193	0.5331491712707183	75	0.13111888111888112	432	0.5699208443271768	C	12.18	1.860644	0.32884	0.222086	0.577236	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	T;T	0.60797	0.44;0.16	5.45	2.77	0.32553	Cadherin (4);Cadherin-like (1);	0.114202	0.64402	N	0.000016	T	0.00012	0.0000	L	0.58583	1.82	0.09310	P	0.999999538415	B	0.21688	0.059	B	0.28465	0.09	T	0.46748	-0.9169	9	0.27082	T	0.32	.	11.1193	0.48279	0.0:0.7968:0.0:0.2032	rs3733413;rs59353175;rs3733413	482	Q14517	FAT1_HUMAN	I	482	ENSP00000406229:V482I;ENSP00000423736:V482I	ENSP00000260147:V482I	V	-	1	0	FAT1	187866532	0.998000	0.40836	0.329000	0.25429	0.320000	0.28249	3.947000	0.56652	0.872000	0.35775	-0.258000	0.10820	GTC	C|0.650;T|0.350	0.350	strong		0.468	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
KIAA1244	57221	hgsc.bcm.edu	37	6	138642258	138642258	+	Silent	SNP	C	C	T	rs17510658	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:138642258C>T	ENST00000251691.4	+	29	4828	c.4662C>T	c.(4660-4662)taC>taT	p.Y1554Y		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		ATATCAGGTACGAGAGCATGA	0.478													C|||	191	0.038139	0.0605	0.0317	5008	,	,		18349	0.0099		0.0328	False		,,,				2504	0.047				p.Y1554Y		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C4662T						PASS	.	C		267,4137		11,245,1946	82.0	65.0	71.0		4662	-8.8	0.7	6	dbSNP_123	71	384,8204		5,374,3915	no	coding-synonymous	KIAA1244	NM_020340.4		16,619,5861	TT,TC,CC		4.4714,6.0627,5.0108		1554/2178	138642258	651,12341	2202	4294	6496	SO:0001819	synonymous_variant	57221	exon29			CAGGTACGAGAGC	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.4662C>T	6.37:g.138642258C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	57	19	0.333333	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																			C|0.957;T|0.043	0.043	strong		0.478	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
SLC5A4	6527	hgsc.bcm.edu	37	22	32625210	32625210	+	Silent	SNP	C	C	T	rs5998322	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:32625210C>T	ENST00000266086.4	-	11	1262	c.1251G>A	c.(1249-1251)gcG>gcA	p.A417A	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	417					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CTTTCTCCGACGCTTGCTTCC	0.542													C|||	373	0.0744808	0.1172	0.1023	5008	,	,		18824	0.0159		0.0537	False		,,,				2504	0.0787				p.A417A		Atlas-SNP	.											SLC5A4,NS,lymphoid_neoplasm,-1,1	SLC5A4	82	1	0			c.G1251A						PASS	.	C		492,3914	230.1+/-244.4	31,430,1742	173.0	165.0	168.0		1251	0.8	0.9	22	dbSNP_114	168	503,8097	143.7+/-199.7	13,477,3810	no	coding-synonymous	SLC5A4	NM_014227.2		44,907,5552	TT,TC,CC		5.8488,11.1666,7.6503		417/660	32625210	995,12011	2203	4300	6503	SO:0001819	synonymous_variant	6527	exon11			CTCCGACGCTTGC	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"""Solute carriers"""	11039	protein-coding gene	gene with protein product			"""solute carrier family 5 (low affinity glucose cotransporter), member 4"""			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.1251G>A	22.37:g.32625210C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_014227	O15279	Silent	SNP	ENST00000266086.4	37	CCDS13903.1																																																																																			C|0.931;T|0.069	0.069	strong		0.542	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	
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 GAIIx	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_ENST00000469391.1_Missense_Mutation_p.S977N|DOCK8_ENST00000432829.2_Missense_Mutation_p.S1009N|DOCK8_ENST00000382329.1_Missense_Mutation_p.S544N|DOCK8_ENST00000382331.1_Missense_Mutation_p.S379N			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	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	96	40	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	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38652993	38652993	+	Silent	SNP	C	C	T	rs332864	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:38652993C>T	ENST00000222345.6	+	14	4271	c.3762C>T	c.(3760-3762)tcC>tcT	p.S1254S		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1254					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GCAAAGATTCCCCCAACAGGC	0.632													C|||	1454	0.290335	0.0915	0.2968	5008	,	,		19272	0.2381		0.4682	False		,,,				2504	0.4254				p.S1254S		Atlas-SNP	.											SIPA1L3,NS,adenoma,0,1	SIPA1L3	150	1	0			c.C3762T						PASS	.	C		611,3795	265.9+/-266.9	50,511,1642	96.0	75.0	82.0		3762	2.3	1.0	19	dbSNP_79	82	3808,4792	537.5+/-383.2	806,2196,1298	no	coding-synonymous	SIPA1L3	NM_015073.1		856,2707,2940	TT,TC,CC		44.2791,13.8675,33.9766		1254/1782	38652993	4419,8587	2203	4300	6503	SO:0001819	synonymous_variant	23094	exon14			AGATTCCCCCAAC	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.3762C>T	19.37:g.38652993C>T		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_015073	Q2TV87	Silent	SNP	ENST00000222345.6	37	CCDS33007.1																																																																																			C|0.679;T|0.321	0.321	strong		0.632	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
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 GAIIx	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	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	111	57	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		
ZNF608	57507	hgsc.bcm.edu	37	5	123976967	123976967	+	Silent	SNP	C	C	T	rs7703447	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:123976967C>T	ENST00000306315.5	-	7	4863	c.4428G>A	c.(4426-4428)ccG>ccA	p.P1476P	ZNF608_ENST00000504926.1_Silent_p.P1049P|ZNF608_ENST00000513985.1_5'UTR	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	1476							metal ion binding (GO:0046872)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		CATATTGACCCGGGATTAGCG	0.517																																					p.P1476P		Atlas-SNP	.											ZNF608,NS,carcinoma,-1,1	ZNF608	117	1	0			c.G4428A						PASS	.	C		939,3467	357.4+/-313.9	109,721,1373	199.0	197.0	198.0		4428	-10.8	0.6	5	dbSNP_116	198	597,8003	157.9+/-211.5	14,569,3717	no	coding-synonymous	ZNF608	NM_020747.2		123,1290,5090	TT,TC,CC		6.9419,21.3118,11.8099		1476/1513	123976967	1536,11470	2203	4300	6503	SO:0001819	synonymous_variant	57507	exon7			TTGACCCGGGATT	AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"""Zinc fingers, C2H2-type"""	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.4428G>A	5.37:g.123976967C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	37	CCDS34219.1																																																																																			C|0.880;T|0.120	0.120	strong		0.517	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432	
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 GAIIx	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_ENST00000379245.4_Silent_p.V104V|FEZ2_ENST00000305852.7_5'UTR	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		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	197	92	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		
SGOL1	151648	hgsc.bcm.edu	37	3	20216519	20216519	+	Silent	SNP	T	T	A	rs61729306	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:20216519T>A	ENST00000263753.4	-	6	643	c.504A>T	c.(502-504)acA>acT	p.T168T	SGOL1_ENST00000452020.1_Intron|SGOL1_ENST00000442720.1_Intron|SGOL1_ENST00000383774.1_Silent_p.T168T|SGOL1_ENST00000421451.1_Silent_p.T168T|SGOL1_ENST00000412997.1_Silent_p.T168T|SGOL1_ENST00000437051.1_Silent_p.T168T|SGOL1-AS1_ENST00000441442.1_RNA|SGOL1_ENST00000419233.2_Silent_p.T168T|SGOL1_ENST00000425061.1_Silent_p.T168T|SGOL1_ENST00000306698.2_Intron|SGOL1-AS1_ENST00000448208.1_RNA|SGOL1_ENST00000412868.1_Silent_p.T168T|SGOL1_ENST00000429446.3_Intron|SGOL1_ENST00000443724.1_Silent_p.T168T|SGOL1_ENST00000417364.1_Silent_p.T168T	NM_001012410.3|NM_001199252.1	NP_001012410.1|NP_001186181.1	Q5FBB7	SGOL1_HUMAN	shugoshin-like 1 (S. pombe)	168	Necessary for interaction with PPP2CA and PPP2R1A.				attachment of spindle microtubules to kinetochore (GO:0008608)|centriole-centriole cohesion (GO:0010457)|chromosome segregation (GO:0007059)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|chromosome, centromeric region (GO:0000775)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase binding (GO:0019900)			kidney(1)|large_intestine(4)|lung(6)|skin(1)|urinary_tract(2)	14						CAACTCCCAGTGTGTCTTGAG	0.313													T|||	1331	0.265775	0.1687	0.2882	5008	,	,		19471	0.4167		0.165	False		,,,				2504	0.3292				p.T168T		Atlas-SNP	.											.	SGOL1	55	.	0			c.A504T						PASS	.	T	,,,,,,,,,,,,	748,3658	284.9+/-277.9	64,620,1519	46.0	47.0	47.0		504,504,504,504,,504,504,504,504,,,504,	-0.6	0.0	3	dbSNP_129	47	1385,7213	263.2+/-284.9	125,1135,3039	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	SGOL1	NM_001012409.2,NM_001012410.3,NM_001012411.2,NM_001012412.3,NM_001012413.2,NM_001199251.1,NM_001199252.1,NM_001199253.1,NM_001199254.1,NM_001199255.1,NM_001199256.1,NM_001199257.1,NM_138484.3	,,,,,,,,,,,,	189,1755,4558	AA,AT,TT		16.1084,16.9768,16.4026	,,,,,,,,,,,,	168/528,168/562,168/276,168/310,,168/528,168/562,168/276,168/310,,,168/216,	20216519	2133,10871	2203	4299	6502	SO:0001819	synonymous_variant	151648	exon6			TCCCAGTGTGTCT	BC001339	CCDS2635.1, CCDS33716.1, CCDS46771.1, CCDS46772.1, CCDS46773.1, CCDS46774.1, CCDS56243.1	3p24.3	2005-07-27			ENSG00000129810	ENSG00000129810			25088	protein-coding gene	gene with protein product		609168				12747765	Standard	NM_001199251		Approved	NY-BR-85	uc003cbu.3	Q5FBB7	OTTHUMG00000130479	ENST00000263753.4:c.504A>T	3.37:g.20216519T>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	151	77	0.509934	NM_001199253	Q588H5|Q5FBB4|Q5FBB5|Q5FBB6|Q5FBB8|Q8N579|Q8WVL0|Q9BVA8|Q9H275	Silent	SNP	ENST00000263753.4	37	CCDS33716.1																																																																																			T|0.811;A|0.189	0.189	strong		0.313	SGOL1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340498.1	NM_138484	
FYB	2533	hgsc.bcm.edu	37	5	39110463	39110463	+	Silent	SNP	C	C	T	rs35970892	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:39110463C>T	ENST00000351578.6	-	16	2482	c.2292G>A	c.(2290-2292)gcG>gcA	p.A764A	FYB_ENST00000512982.1_Silent_p.A810A|FYB_ENST00000505428.1_Silent_p.A810A|FYB_ENST00000540520.1_Silent_p.A820A|FYB_ENST00000515010.1_Silent_p.A764A	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	764					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			CTTACTTGTCCGCTAGGTAAC	0.294													C|||	53	0.0105831	0.0008	0.0159	5008	,	,		15541	0.0		0.0368	False		,,,				2504	0.0041				p.A820A		Atlas-SNP	.											FYB_ENST00000540520,NS,carcinoma,-1,3	FYB	354	3	0			c.G2460A						PASS	.	C	,	23,3587		0,23,1782	52.0	49.0	50.0		2430,2292	-9.6	0.0	5	dbSNP_126	50	262,7882		1,260,3811	no	coding-synonymous,coding-synonymous	FYB	NM_001465.4,NM_199335.3	,	1,283,5593	TT,TC,CC		3.2171,0.6371,2.4247	,	810/830,764/784	39110463	285,11469	1805	4072	5877	SO:0001819	synonymous_variant	2533	exon17			CTTGTCCGCTAGG	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.2292G>A	5.37:g.39110463C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	169	76	0.449704	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	37	CCDS47200.1																																																																																			C|0.985;T|0.015	0.015	strong		0.294	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
CPA4	51200	hgsc.bcm.edu	37	7	129938598	129938598	+	Missense_Mutation	SNP	G	G	T	rs34587586	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:129938598G>T	ENST00000222482.4	+	2	109	c.81G>T	c.(79-81)ttG>ttT	p.L27F	CPA4_ENST00000445470.2_Missense_Mutation_p.L27F|CPA4_ENST00000493259.1_Intron	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	27			L -> F (in dbSNP:rs34587586).		histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					ACCAAGTTTTGAGGATTAATG	0.428													T|||	1783	0.35603	0.3253	0.3458	5008	,	,		20606	0.3581		0.3877	False		,,,				2504	0.3701				p.L27F		Atlas-SNP	.											.	CPA4	47	.	0			c.G81T						PASS	.	T	PHE/LEU,PHE/LEU	1486,2920	676.9+/-403.3	252,982,969	126.0	125.0	125.0		81,81	4.5	1.0	7	dbSNP_126	125	3453,5147	636.4+/-399.1	715,2023,1562	yes	missense,missense	CPA4	NM_001163446.1,NM_016352.3	22,22	967,3005,2531	TT,TG,GG		40.1512,33.7267,37.9748	benign,benign	27/389,27/422	129938598	4939,8067	2203	4300	6503	SO:0001583	missense	51200	exon2			AGTTTTGAGGATT	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.81G>T	7.37:g.129938598G>T	ENSP00000222482:p.Leu27Phe	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	178	81	0.455056	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	37	CCDS5818.1	793	0.3630952380952381	159	0.3231707317073171	141	0.38950276243093923	213	0.3723776223776224	280	0.36939313984168864	T	7.318	0.616383	0.14129	0.337267	0.401512	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000492072;ENST00000473956	T;T;T;T	0.14893	2.47;2.47;2.47;2.47	5.61	4.47	0.54385	Proteinase inhibitor, propeptide (1);Proteinase inhibitor, carboxypeptidase propeptide (2);	0.227453	0.39146	N	0.001446	T	0.00012	0.0000	N	0.20483	0.58	0.42641	P	0.006581999999999977	B;B	0.13594	0.008;0.002	B;B	0.36186	0.219;0.023	T	0.48906	-0.8993	9	0.12103	T	0.63	.	5.3961	0.16271	0.0:0.0931:0.1772:0.7297	rs34587586	27;27	B7Z576;Q9UI42	.;CBPA4_HUMAN	F	27	ENSP00000412947:L27F;ENSP00000222482:L27F;ENSP00000417255:L27F;ENSP00000418392:L27F	ENSP00000222482:L27F	L	+	3	2	CPA4	129725834	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	0.604000	0.24164	0.512000	0.28257	-0.525000	0.04345	TTG	G|0.630;T|0.370	0.370	strong		0.428	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
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 GAIIx	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		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	81	34	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		
TRMT11	60487	hgsc.bcm.edu	37	6	126332554	126332554	+	Missense_Mutation	SNP	A	A	G	rs116913944	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:126332554A>G	ENST00000334379.5	+	9	1037	c.916A>G	c.(916-918)Att>Gtt	p.I306V	TRMT11_ENST00000368332.3_Missense_Mutation_p.I306V	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	306					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		TGATGCAATCATTACTGATCG	0.328													A|||	65	0.0129792	0.0	0.0288	5008	,	,		19403	0.0		0.0388	False		,,,				2504	0.0061				p.I306V		Atlas-SNP	.											.	TRMT11	43	.	0			c.A916G						PASS	.	A	VAL/ILE	46,4360	48.2+/-83.0	0,46,2157	79.0	66.0	70.0		916	4.3	1.0	6	dbSNP_132	70	448,8152	133.9+/-191.4	13,422,3865	yes	missense	TRMT11	NM_001031712.2	29	13,468,6022	GG,GA,AA		5.2093,1.044,3.7982	benign	306/464	126332554	494,12512	2203	4300	6503	SO:0001583	missense	60487	exon9			GCAATCATTACTG	AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651			21080	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 75"""	C6orf75			Standard	XM_006715546		Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000334379.5:c.916A>G	6.37:g.126332554A>G	ENSP00000333934:p.Ile306Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_001031712	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Missense_Mutation	SNP	ENST00000334379.5	37	CCDS35496.1	41|41	0.018772893772893772|0.018772893772893772	0|0	0.0|0.0	16|16	0.04419889502762431|0.04419889502762431	0|0	0.0|0.0	25|25	0.032981530343007916|0.032981530343007916	A|A	15.45|15.45	2.836034|2.836034	0.50951|0.50951	0.01044|0.01044	0.052093|0.052093	ENSG00000066651|ENSG00000066651	ENST00000453993|ENST00000334379;ENST00000368332	.|T;T	.|0.26223	.|1.75;1.75	5.49|5.49	4.26|4.26	0.50523|0.50523	.|Putative RNA methylase (1);DNA methylase, N-6 adenine-specific, conserved site (1);	.|0.045296	.|0.85682	.|D	.|0.000000	T|T	0.05181|0.05181	0.0138|0.0138	N|N	0.16567|0.16567	0.415|0.415	0.80722|0.80722	D|D	1|1	.|P;B	.|0.36010	.|0.532;0.29	.|B;B	.|0.35073	.|0.195;0.113	T|T	0.06734|0.06734	-1.0810|-1.0810	5|10	.|0.02654	.|T	.|1	-9.8216|-9.8216	12.187|12.187	0.54245|0.54245	0.8575:0.1425:0.0:0.0|0.8575:0.1425:0.0:0.0	.|.	.|306;306	.|Q7Z4G4-2;Q7Z4G4	.|.;TRM11_HUMAN	R|V	104|306	.|ENSP00000333934:I306V;ENSP00000357316:I306V	.|ENSP00000333934:I306V	H|I	+|+	2|1	0|0	TRMT11|TRMT11	126374247|126374247	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	3.376000|3.376000	0.52417|0.52417	2.089000|2.089000	0.63090|0.63090	0.533000|0.533000	0.62120|0.62120	CAT|ATT	A|0.966;G|0.034	0.034	strong		0.328	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820	
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 GAIIx	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	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	210	92	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	
UNC79	57578	hgsc.bcm.edu	37	14	93943998	93943998	+	Silent	SNP	G	G	A	rs61992606	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:93943998G>A	ENST00000393151.2	+	4	543	c.543G>A	c.(541-543)acG>acA	p.T181T	UNC79_ENST00000555664.1_Silent_p.T181T|UNC79_ENST00000256339.4_Silent_p.T4T|UNC79_ENST00000553484.1_Silent_p.T181T			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	181					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TGATATCAACGTTGGCTACCT	0.358													G|||	1867	0.372804	0.267	0.2421	5008	,	,		18127	0.6964		0.2883	False		,,,				2504	0.362				p.T4T		Atlas-SNP	.											.	UNC79	366	.	0			c.G12A						PASS	.	G		1214,3192	421.7+/-339.5	161,892,1150	270.0	225.0	240.0		12	-0.3	1.0	14	dbSNP_129	240	2640,5960	426.2+/-355.2	419,1802,2079	no	coding-synonymous	UNC79	NM_020818.3		580,2694,3229	AA,AG,GG		30.6977,27.5533,29.6325		4/2459	93943998	3854,9152	2203	4300	6503	SO:0001819	synonymous_variant	57578	exon4			ATCAACGTTGGCT	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.543G>A	14.37:g.93943998G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	NM_020818	B5MDL6|Q6ZUT7	Silent	SNP	ENST00000393151.2	37																																																																																				G|0.684;A|0.316	0.316	strong		0.358	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
NOC3L	64318	hgsc.bcm.edu	37	10	96104665	96104665	+	Missense_Mutation	SNP	T	T	G	rs3758526	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96104665T>G	ENST00000371361.3	-	12	1515	c.1415A>C	c.(1414-1416)gAg>gCg	p.E472A	NOC3L_ENST00000543788.1_Missense_Mutation_p.E210A|NOC3L_ENST00000371350.1_Missense_Mutation_p.E472A|NOC3L_ENST00000463649.1_5'Flank	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	472			E -> A (in dbSNP:rs3758526). {ECO:0000269|PubMed:14702039}.		fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				AAGCTCTCGCTCTAGTTTCTC	0.363													T|||	1036	0.206869	0.1657	0.0908	5008	,	,		18959	0.2937		0.1213	False		,,,				2504	0.3436				p.E472A		Atlas-SNP	.											.	NOC3L	67	.	0			c.A1415C						PASS	.	T	ALA/GLU	727,3677	298.4+/-285.3	62,603,1537	115.0	108.0	111.0		1415	4.9	1.0	10	dbSNP_107	111	1050,7548	221.2+/-258.7	65,920,3314	yes	missense	NOC3L	NM_022451.9	107	127,1523,4851	GG,GT,TT		12.2121,16.5077,13.6671	probably-damaging	472/801	96104665	1777,11225	2202	4299	6501	SO:0001583	missense	64318	exon12			TCTCGCTCTAGTT	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"""chromosome 10 open reading frame 117"""	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.1415A>C	10.37:g.96104665T>G	ENSP00000360412:p.Glu472Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	62	40	0.645161	NM_022451	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	400	0.18315018315018314	90	0.18292682926829268	38	0.10497237569060773	181	0.31643356643356646	91	0.12005277044854881	T	17.97	3.517429	0.64634	0.165077	0.122121	ENSG00000173145	ENST00000543788;ENST00000371361;ENST00000371350	T;T;T	0.17370	2.28;2.38;2.38	6.07	4.92	0.64577	.	0.140487	0.64402	D	0.000006	T	0.00012	0.0000	L	0.52823	1.66	0.24525	P	0.99414929	D	0.53745	0.962	P	0.50314	0.637	T	0.46830	-0.9163	9	0.34782	T	0.22	-19.9256	13.4707	0.61281	0.0:0.0:0.1307:0.8693	rs3758526;rs52826368;rs3758526	472	Q8WTT2	NOC3L_HUMAN	A	210;472;472	ENSP00000437838:E210A;ENSP00000360412:E472A;ENSP00000360401:E472A	ENSP00000360401:E472A	E	-	2	0	NOC3L	96094655	1.000000	0.71417	0.980000	0.43619	0.981000	0.71138	7.007000	0.76335	1.095000	0.41419	0.528000	0.53228	GAG	T|0.852;G|0.148	0.148	strong		0.363	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	
AP2M1	1173	hgsc.bcm.edu	37	3	183899832	183899832	+	Silent	SNP	C	C	T	rs8478	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183899832C>T	ENST00000292807.5	+	9	1108	c.960C>T	c.(958-960)atC>atT	p.I320I	AP2M1_ENST00000439647.1_Silent_p.I318I|AP2M1_ENST00000411763.2_Silent_p.I345I|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Silent_p.I318I|AP2M1_ENST00000461733.1_3'UTR	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	320	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTCAGAAGATCGAGGTGAGGA	0.542													T|||	719	0.14357	0.2421	0.1066	5008	,	,		23976	0.004		0.164	False		,,,				2504	0.1595				p.I318I		Atlas-SNP	.											.	AP2M1	35	.	0			c.C954T						PASS	.	T	,	826,3196		85,656,1270	45.0	47.0	46.0		954,960	3.8	1.0	3	dbSNP_52	46	1442,6912		119,1204,2854	yes	coding-synonymous,coding-synonymous	AP2M1	NM_001025205.1,NM_004068.3	,	204,1860,4124	TT,TC,CC		17.2612,20.537,18.3258	,	318/434,320/436	183899832	2268,10108	2011	4177	6188	SO:0001819	synonymous_variant	1173	exon8			GAAGATCGAGGTG	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, medium 1"", ""plasma membrane adaptor AP-2 50kDA protein"", ""clathrin coat adaptor protein AP50"", ""clathrin adaptor complex AP2, mu subunit"", ""HA2 50 kDA subunit"", ""clathrin assembly protein complex 2 medium chain"", ""AP-2 mu 2 chain"""	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.960C>T	3.37:g.183899832C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Silent	SNP	ENST00000292807.5	37	CCDS43177.1																																																																																			C|0.853;T|0.147	0.147	strong		0.542	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068	
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 GAIIx	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	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	246	31	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	
FAT2	2196	hgsc.bcm.edu	37	5	150924769	150924769	+	Silent	SNP	G	G	A	rs998076	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:150924769G>A	ENST00000261800.5	-	9	5931	c.5919C>T	c.(5917-5919)taC>taT	p.Y1973Y		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1973	Cadherin 17. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAGCTGCCCAGTAGACATCCT	0.468													A|||	580	0.115815	0.1717	0.0836	5008	,	,		21717	0.1329		0.0924	False		,,,				2504	0.0695				p.Y1973Y		Atlas-SNP	.											.	FAT2	465	.	0			c.C5919T						PASS	.	A		681,3725	746.9+/-411.8	57,567,1579	56.0	59.0	58.0		5919	0.8	0.0	5	dbSNP_86	58	613,7987	788.8+/-407.6	20,573,3707	no	coding-synonymous	FAT2	NM_001447.2		77,1140,5286	AA,AG,GG		7.1279,15.4562,9.9493		1973/4350	150924769	1294,11712	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon9			TGCCCAGTAGACA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.5919C>T	5.37:g.150924769G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.887;A|0.113	0.113	strong		0.468	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
KANSL1	284058	hgsc.bcm.edu	37	17	44110541	44110541	+	Silent	SNP	G	G	A	rs35833914	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44110541G>A	ENST00000262419.6	-	13	3212	c.2742C>T	c.(2740-2742)gaC>gaT	p.D914D	KANSL1_ENST00000575318.1_Silent_p.D850D|KANSL1_ENST00000432791.1_Silent_p.D914D|RP11-669E14.6_ENST00000570454.1_RNA|KANSL1_ENST00000393476.3_Silent_p.D208D|KANSL1_ENST00000574590.1_Silent_p.D914D|KANSL1_ENST00000572904.1_Silent_p.D914D	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	914	Sufficient for interaction with KAT8.				chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CGAAGGCTGCGTCGGATAGGT	0.592													G|||	432	0.086262	0.0151	0.1571	5008	,	,		19747	0.001		0.2406	False		,,,				2504	0.0613				p.D914D		Atlas-SNP	.											.	.	.	.	0			c.C2742T						PASS	.	G	,,	202,4204		5,192,2006	63.0	62.0	62.0		2739,2742,2742	-3.2	0.8	17	dbSNP_126	62	1914,6686		214,1486,2600	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	,,	219,1678,4606	AA,AG,GG		22.2558,4.5847,16.2694	,,	913/1105,914/1106,914/1106	44110541	2116,10890	2203	4300	6503	SO:0001819	synonymous_variant	284058	exon13			GGCTGCGTCGGAT	BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2742C>T	17.37:g.44110541G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Silent	SNP	ENST00000262419.6	37	CCDS11503.1																																																																																			A|0.144;C|0.000;G|0.856;T|0.000	0.144	strong		0.592	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
OR4D6	219983	hgsc.bcm.edu	37	11	59224608	59224608	+	Missense_Mutation	SNP	A	A	G	rs1453544	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:59224608A>G	ENST00000300127.2	+	1	198	c.175A>G	c.(175-177)Atg>Gtg	p.M59V		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	59			M -> V (in dbSNP:rs1453544).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	34						ACACACTCCTATGTACTTTCT	0.448													A|||	627	0.1252	0.0197	0.1326	5008	,	,		20337	0.1141		0.2525	False		,,,				2504	0.1431				p.M59V		Atlas-SNP	.											OR4D6,NS,adenoma,0,1	OR4D6	65	1	0			c.A175G						PASS	.	A	VAL/MET	244,4158	143.8+/-178.8	10,224,1967	145.0	122.0	130.0		175	4.9	0.9	11	dbSNP_88	130	2264,6326	383.5+/-340.8	283,1698,2314	yes	missense	OR4D6	NM_001004708.1	21	293,1922,4281	GG,GA,AA		26.3562,5.5429,19.3042	probably-damaging	59/315	59224608	2508,10484	2201	4295	6496	SO:0001583	missense	219983	exon1			ACTCCTATGTACT	AB065803	CCDS31562.1	11q12.1	2012-08-09			ENSG00000166884	ENSG00000166884		"""GPCR / Class A : Olfactory receptors"""	15175	protein-coding gene	gene with protein product							Standard	NM_001004708		Approved		uc010rku.2	Q8NGJ1	OTTHUMG00000167340	ENST00000300127.2:c.175A>G	11.37:g.59224608A>G	ENSP00000300127:p.Met59Val	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	238	105	0.441176	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	349	0.15979853479853479	18	0.036585365853658534	59	0.16298342541436464	71	0.12412587412587413	201	0.26517150395778366	A	13.29	2.192610	0.38707	0.055429	0.263562	ENSG00000166884	ENST00000300127	T	0.09350	2.99	6.01	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	M	0.91406	3.205	0.32048	P	0.5973200000000001	P	0.50819	0.939	P	0.54759	0.76	T	0.10989	-1.0606	9	0.87932	D	0	-29.9948	11.1494	0.48449	0.9274:0.0:0.0726:0.0	rs1453544;rs52794667;rs57726108;rs1453544	59	Q8NGJ1	OR4D6_HUMAN	V	59	ENSP00000300127:M59V	ENSP00000300127:M59V	M	+	1	0	OR4D6	58981184	1.000000	0.71417	0.862000	0.33874	0.497000	0.33675	7.516000	0.81772	1.088000	0.41272	0.533000	0.62120	ATG	A|0.815;G|0.185	0.185	strong		0.448	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708	
EPG5	57724	hgsc.bcm.edu	37	18	43490602	43490602	+	Silent	SNP	G	G	A	rs3744996	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:43490602G>A	ENST00000282041.5	-	23	4123	c.4089C>T	c.(4087-4089)caC>caT	p.H1363H	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1363					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						TTGCAGCATGGTGGAAGTCAG	0.507											OREG0024952	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1334	0.266374	0.2632	0.3055	5008	,	,		20007	0.3095		0.166	False		,,,				2504	0.3016				p.H1363H		Atlas-SNP	.											.	EPG5	199	.	0			c.C4089T						PASS	.	G		947,2861		112,723,1069	86.0	86.0	86.0		4089	3.2	1.0	18	dbSNP_107	86	1170,7092		82,1006,3043	no	coding-synonymous	EPG5	NM_020964.2		194,1729,4112	AA,AG,GG		14.1612,24.8687,17.5394		1363/2580	43490602	2117,9953	1904	4131	6035	SO:0001819	synonymous_variant	57724	exon23			AGCATGGTGGAAG	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.4089C>T	18.37:g.43490602G>A		Somatic	62	0	0	916	WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	37	CCDS11926.2																																																																																			G|0.786;A|0.214	0.214	strong		0.507	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
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 GAIIx	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	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	62	4	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	
OR2T4	127074	hgsc.bcm.edu	37	1	248525290	248525290	+	Silent	SNP	C	C	T	rs202028348|rs141576206|rs386642002|rs374193555|rs57728407	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248525290C>T	ENST00000366475.1	+	1	408	c.408C>T	c.(406-408)taC>taT	p.Y136Y		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y136*(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	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)			TGTTCTTCTACGTGACACTAG	0.522													t|||	1549	0.309305	0.2678	0.2752	5008	,	,		19688	0.4405		0.1899	False		,,,				2504	0.3773				p.Y136Y		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	1	1	Substitution - Nonsense(1)	lung(1)	c.C408T						scavenged	.																																			SO:0001819	synonymous_variant	127074	exon1			CTTCTACGTGACA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.408C>T	1.37:g.248525290C>T		Somatic	657	1	0.00152207		WXS	Illumina HiSeq	Phase_I	655	19	0.0290076	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			C|0.840;T|0.160	0.160	strong		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
PLP1	5354	hgsc.bcm.edu	37	X	103042882	103042882	+	Silent	SNP	T	T	C	rs1126707	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:103042882T>C	ENST00000303958.2	+	4	755	c.609T>C	c.(607-609)gaT>gaC	p.D203D	PLP1_ENST00000418604.1_Silent_p.D203D|PLP1_ENST00000466486.1_3'UTR|PLP1_ENST00000361621.2_Silent_p.D168D	NM_000533.3	NP_000524.3	P60201	MYPR_HUMAN	proteolipid protein 1	203			D -> E (in HLD1). {ECO:0000269|PubMed:10417279, ECO:0000269|PubMed:11093273}.|D -> G (in HLD1). {ECO:0000269|PubMed:10417279}.|D -> H (in HLD1). {ECO:0000269|PubMed:1376966}.|D -> N (in HLD1). {ECO:0000269|PubMed:10417279}.|D -> V (in HLD1). {ECO:0000269|PubMed:9747038}.		astrocyte development (GO:0014002)|axon development (GO:0061564)|axon ensheathment (GO:0008366)|cell death (GO:0008219)|cell maturation (GO:0048469)|central nervous system myelination (GO:0022010)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|long-chain fatty acid biosynthetic process (GO:0042759)|positive regulation of gene expression (GO:0010628)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)|plasma membrane (GO:0005886)	structural constituent of myelin sheath (GO:0019911)|structural molecule activity (GO:0005198)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	17						TCTGTGCTGATGCCAGAATGT	0.488													T|||	780	0.206623	0.0628	0.2738	3775	,	,		15438	0.1736		0.2107	False		,,,				2504	0.1227				p.D203D		Atlas-SNP	.											.	PLP1	37	.	0			c.T609C	GRCh37	CM002830	PLP1	M	rs1126707	PASS	.	T	,,	489,3346		41,348,59,1243,512	159.0	116.0	130.0		609,609,504	4.4	1.0	X	dbSNP_86	130	2100,4628		212,1073,603,1143,1269	no	coding-synonymous,coding-synonymous,coding-synonymous	PLP1	NM_000533.3,NM_001128834.1,NM_199478.1	,,	253,1421,662,2386,1781	CC,CT,C,TT,T		31.2128,12.751,24.5101	,,	203/278,203/278,168/243	103042882	2589,7974	2203	4300	6503	SO:0001819	synonymous_variant	5354	exon5			TGCTGATGCCAGA	M27110	CCDS14513.1, CCDS14514.1	Xq22	2013-05-14	2008-07-28		ENSG00000123560	ENSG00000123560			9086	protein-coding gene	gene with protein product	"""Pelizaeus-Merzbacher disease"""	300401	"""spastic paraplegia 2, uncomplicated"""	SPG2, PLP			Standard	NM_001128834		Approved	GPM6C	uc004elk.3	P60201	OTTHUMG00000022111	ENST00000303958.2:c.609T>C	X.37:g.103042882T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_001128834	P04400|P06905|Q502Y1|Q6FHZ6	Silent	SNP	ENST00000303958.2	37	CCDS14513.1																																																																																			T|0.774;C|0.226	0.226	strong		0.488	PLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057743.2		
CDC20B	166979	hgsc.bcm.edu	37	5	54420799	54420799	+	Silent	SNP	A	A	C	rs382402	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:54420799A>C	ENST00000381375.2	-	9	1192	c.1047T>G	c.(1045-1047)gtT>gtG	p.V349V	CDC20B_ENST00000322374.6_Silent_p.V349V|CDC20B_ENST00000334206.5_3'UTR|CDC20B_ENST00000296733.1_Silent_p.V349V			Q86Y33	CD20B_HUMAN	cell division cycle 20B	349								p.V349V(1)		kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			GAAGTGTTCCAACATGATGCT	0.507													A|||	858	0.171326	0.0424	0.147	5008	,	,		17943	0.1915		0.2147	False		,,,				2504	0.2975				p.V349V		Atlas-SNP	.											CDC20B,NS,carcinoma,0,1	CDC20B	61	1	1	Substitution - coding silent(1)	stomach(1)	c.T1047G						PASS	.	A	,,	288,4118	160.7+/-193.0	15,258,1930	140.0	120.0	127.0		1047,1047,1047	-9.3	0.0	5	dbSNP_80	127	1641,6959	302.4+/-305.9	160,1321,2819	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC20B	NM_001145734.2,NM_001170402.1,NM_152623.2	,,	175,1579,4749	CC,CA,AA		19.0814,6.5365,14.8316	,,	349/478,349/520,349/516	54420799	1929,11077	2203	4300	6503	SO:0001819	synonymous_variant	166979	exon9			TGTTCCAACATGA	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.1047T>G	5.37:g.54420799A>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	51	16	0.313726	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Silent	SNP	ENST00000381375.2	37	CCDS54852.1																																																																																			A|0.851;C|0.149	0.149	strong		0.507	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
CD200R1L	344807	hgsc.bcm.edu	37	3	112546473	112546473	+	Silent	SNP	G	G	A	rs1997281	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112546473G>A	ENST00000398214.1	-	3	396	c.171C>T	c.(169-171)atC>atT	p.I57I	CD200R1L_ENST00000488794.1_Silent_p.I36I|CD200R1L_ENST00000448932.1_Silent_p.I36I	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	57	Ig-like V-type.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						TTCTTAATGCGATAGGAGGGC	0.388													G|||	1467	0.292931	0.093	0.3703	5008	,	,		19509	0.376		0.4026	False		,,,				2504	0.3098				p.I57I		Atlas-SNP	.											CD200R1L,colon,carcinoma,-2,1	CD200R1L	47	1	0			c.C171T						scavenged	.	G	,	624,3782	267.1+/-267.6	36,552,1615	125.0	117.0	120.0		171,108	-2.2	0.0	3	dbSNP_92	120	3433,5167	503.2+/-375.9	695,2043,1562	no	coding-synonymous,coding-synonymous	CD200R1L	NM_001008784.2,NM_001199215.1	,	731,2595,3177	AA,AG,GG		39.9186,14.1625,31.1933	,	57/272,36/251	112546473	4057,8949	2203	4300	6503	SO:0001819	synonymous_variant	344807	exon3			TAATGCGATAGGA	AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"""Immunoglobulin superfamily / C2-set domain containing"""	24665	protein-coding gene	gene with protein product	"""CD200 receptor 2"""						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.171C>T	3.37:g.112546473G>A		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_001008784	Q6WHB7	Silent	SNP	ENST00000398214.1	37	CCDS43131.1																																																																																			.	.	weak		0.388	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784	
CSMD2	114784	hgsc.bcm.edu	37	1	34238283	34238283	+	Missense_Mutation	SNP	T	T	C	rs474474	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:34238283T>C	ENST00000338325.1	-	7	969	c.557A>G	c.(556-558)cAc>cGc	p.H186R	CSMD2_ENST00000373381.4_Missense_Mutation_p.H578R			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	538	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCACCGTGGTGAAACCGGGA	0.537													C|||	1901	0.379593	0.5333	0.317	5008	,	,		19833	0.2659		0.2406	False		,,,				2504	0.4765				p.H538R		Atlas-SNP	.											.	CSMD2	946	.	0			c.A1613G						PASS	.	C	ARG/HIS	2143,2263	596.7+/-388.7	525,1093,585	111.0	105.0	107.0		1613	-1.3	0.9	1	dbSNP_83	107	2291,6309	706.5+/-405.5	301,1689,2310	yes	missense	CSMD2	NM_052896.3	29	826,2782,2895	CC,CT,TT		26.6395,48.6382,34.092	benign	538/3488	34238283	4434,8572	2203	4300	6503	SO:0001583	missense	114784	exon13			CCGTGGTGAAACC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000338325.1:c.557A>G	1.37:g.34238283T>C	ENSP00000340311:p.His186Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000338325.1	37		682	0.31227106227106227	238	0.483739837398374	96	0.26519337016574585	168	0.2937062937062937	180	0.23746701846965698	C	9.737	1.163742	0.21538	0.486382	0.266395	ENSG00000121904	ENST00000373381;ENST00000338325	T;T	0.62941	-0.01;-0.01	6.06	-1.29	0.09288	Complement control module (2);Sushi/SCR/CCP (3);	0.180087	0.50627	N	0.000119	T	0.00012	0.0000	N	0.01284	-0.91	0.09310	P	0.999999999946275	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41197	-0.9522	9	0.10636	T	0.68	.	6.7188	0.23318	0.1097:0.4467:0.0:0.4436	rs474474;rs56977083;rs474474	538;578	Q7Z408;E7EUA6	CSMD2_HUMAN;.	R	578;186	ENSP00000362479:H578R;ENSP00000340311:H186R	ENSP00000241312:H538R	H	-	2	0	CSMD2	34010870	0.032000	0.19561	0.934000	0.37439	0.987000	0.75469	-0.069000	0.11542	-0.514000	0.06488	-0.733000	0.03571	CAC	T|0.662;C|0.338	0.338	strong		0.537	CSMD2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000036404.2	NM_052896	
CIITA	4261	hgsc.bcm.edu	37	16	11001914	11001914	+	Silent	SNP	G	G	A	rs2229321	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11001914G>A	ENST00000324288.8	+	11	2698	c.2565G>A	c.(2563-2565)gcG>gcA	p.A855A	CIITA_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	855					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						TGGAGGCGGCGGGCCAAGACT	0.652			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								G|||	199	0.0397364	0.0348	0.0375	5008	,	,		15561	0.0		0.0944	False		,,,				2504	0.0327				p.A855A		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.G2565A						PASS	.	G		168,4222		2,164,2029	15.0	17.0	16.0		2565	-9.7	0.0	16	dbSNP_98	16	752,7832		39,674,3579	no	coding-synonymous	CIITA	NM_000246.3		41,838,5608	AA,AG,GG		8.7605,3.8269,7.0911		855/1131	11001914	920,12054	2195	4292	6487	SO:0001819	synonymous_variant	4261	exon11			GGCGGCGGGCCAA	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.2565G>A	16.37:g.11001914G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			G|0.932;A|0.068	0.068	strong		0.652	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
MAPT	4137	hgsc.bcm.edu	37	17	44073973	44073973	+	Silent	SNP	T	T	C	rs17652121	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44073973T>C	ENST00000571987.1	+	9	1716	c.1716T>C	c.(1714-1716)aaT>aaC	p.N572N	MAPT_ENST00000334239.8_Silent_p.N197N|MAPT_ENST00000535772.1_Silent_p.N255N|MAPT_ENST00000347967.5_Silent_p.N161N|MAPT_ENST00000351559.5_Silent_p.N255N|MAPT_ENST00000344290.5_Silent_p.N590N|MAPT_ENST00000420682.2_Silent_p.N226N|MAPT_ENST00000340799.5_Silent_p.N226N|MAPT_ENST00000446361.3_Silent_p.N197N|MAPT_ENST00000262410.5_Silent_p.N572N|MAPT_ENST00000570299.1_3'UTR|STH_ENST00000537309.1_5'Flank|MAPT_ENST00000576518.1_Silent_p.N186N|MAPT_ENST00000431008.3_Silent_p.N255N|MAPT_ENST00000415613.2_Silent_p.N590N|MAPT_ENST00000574436.1_Silent_p.N255N			P10636	TAU_HUMAN	microtubule-associated protein tau	572					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	ACCTGAAGAATGTCAAGTCCA	0.652													C|||	439	0.0876597	0.0204	0.1571	5008	,	,		13729	0.001		0.2406	False		,,,				2504	0.0613				p.N590N		Atlas-SNP	.											.	MAPT	135	.	0			c.T1770C						PASS	.	C	,,,,,,,	226,4180	793.7+/-415.2	6,214,1983	43.0	37.0	39.0		1770,678,678,765,765,591,1716,591	1.8	1.0	17	dbSNP_123	39	1925,6675	718.0+/-406.2	220,1485,2595	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPT	NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,	226,1699,4578	CC,CT,TT		22.3837,5.1294,16.5385	,,,,,,,	590/777,226/413,226/382,255/411,255/442,197/384,572/759,197/353	44073973	2151,10855	2203	4300	6503	SO:0001819	synonymous_variant	4137	exon11			GAAGAATGTCAAG	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1716T>C	17.37:g.44073973T>C		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Silent	SNP	ENST00000571987.1	37	CCDS11501.1																																																																																			T|0.860;C|0.140	0.140	strong		0.652	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
CCBL2	56267	hgsc.bcm.edu	37	1	89426902	89426902	+	Silent	SNP	G	G	A	rs3738055	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:89426902G>A	ENST00000260508.4	-	8	1072	c.735C>T	c.(733-735)agC>agT	p.S245S	CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000370491.3_Silent_p.S211S|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	245					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)	p.S211S(1)		endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		AAACCTCATCGCTGATGCAGA	0.373													G|||	1850	0.369409	0.2307	0.5043	5008	,	,		20966	0.4633		0.4771	False		,,,				2504	0.2536				p.S245S		Atlas-SNP	.											CCBL2_ENST00000370491,NS,carcinoma,0,1	CCBL2	138	1	1	Substitution - coding silent(1)	stomach(1)	c.C735T						PASS	.	G	,	1257,3149	432.4+/-343.3	188,881,1134	158.0	153.0	154.0		735,633	1.2	1.0	1	dbSNP_107	154	4220,4380	571.1+/-389.5	1042,2136,1122	no	coding-synonymous,coding-synonymous	CCBL2	NM_001008661.2,NM_001008662.2	,	1230,3017,2256	AA,AG,GG		49.0698,28.5293,42.1113	,	245/455,211/421	89426902	5477,7529	2203	4300	6503	SO:0001819	synonymous_variant	56267	exon8			CTCATCGCTGATG	AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.735C>T	1.37:g.89426902G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Silent	SNP	ENST00000260508.4	37	CCDS30766.1																																																																																			G|0.584;A|0.416	0.416	strong		0.373	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661	
LYST	1130	hgsc.bcm.edu	37	1	235955150	235955150	+	Silent	SNP	G	G	A	rs11583387	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:235955150G>A	ENST00000389794.3	-	12	4566	c.4392C>T	c.(4390-4392)aaC>aaT	p.N1464N	LYST_ENST00000389793.2_Silent_p.N1464N|LYST_ENST00000536965.1_Intron			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1464					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)			GTGGCCAGCAGTTTTGCCCCA	0.478													G|||	322	0.0642971	0.053	0.0879	5008	,	,		17612	0.0407		0.1272	False		,,,				2504	0.0225				p.N1464N		Atlas-SNP	.											.	LYST	370	.	0			c.C4392T						PASS	.	G		310,4096	164.7+/-196.3	5,300,1898	113.0	115.0	114.0		4392	2.7	1.0	1	dbSNP_120	114	961,7639	211.0+/-251.7	49,863,3388	no	coding-synonymous	LYST	NM_000081.2		54,1163,5286	AA,AG,GG		11.1744,7.0359,9.7724		1464/3802	235955150	1271,11735	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon12			CCAGCAGTTTTGC	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.4392C>T	1.37:g.235955150G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			G|0.905;A|0.095	0.095	strong		0.478	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
CD207	50489	hgsc.bcm.edu	37	2	71061108	71061108	+	Silent	SNP	G	G	A	rs17662453	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71061108G>A	ENST00000410009.3	-	3	279	c.234C>T	c.(232-234)gtC>gtT	p.V78V		NM_015717.3	NP_056532	Q9UJ71	CLC4K_HUMAN	CD207 molecule, langerin	78					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)|defense response to virus (GO:0051607)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|mannose binding (GO:0005537)			endometrium(1)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|stomach(1)	20						TCAGCAACTGGACATTGGTCT	0.517													G|||	712	0.142173	0.1059	0.219	5008	,	,		19065	0.0972		0.1839	False		,,,				2504	0.1401				p.V78V		Atlas-SNP	.											.	CD207	47	.	0			c.C234T						PASS	.	T		473,3465		30,413,1526	46.0	41.0	42.0		234	-2.0	0.0	2	dbSNP_123	42	1789,6511		190,1409,2551	no	coding-synonymous	CD207	NM_015717.3		220,1822,4077	AA,AG,GG		21.5542,12.0112,18.4834		78/329	71061108	2262,9976	1969	4150	6119	SO:0001819	synonymous_variant	50489	exon3			CAACTGGACATTG	AJ242859	CCDS74520.1	2p13	2011-08-30	2006-03-28		ENSG00000116031	ENSG00000116031		"""C-type lectin domain containing"", ""CD molecules"""	17935	protein-coding gene	gene with protein product		604862	"""CD207 antigen, langerin"""			10661407, 9847074	Standard	NM_015717		Approved	Langerin, CLEC4K	uc002shg.3	Q9UJ71	OTTHUMG00000153176	ENST00000410009.3:c.234C>T	2.37:g.71061108G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	62	21	0.33871	NM_015717		Silent	SNP	ENST00000410009.3	37																																																																																				G|0.858;A|0.142	0.142	strong		0.517	CD207-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000329959.4	NM_015717	
PLCB3	5331	hgsc.bcm.edu	37	11	64023270	64023270	+	Silent	SNP	C	C	T	rs12419663	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64023270C>T	ENST00000540288.1	+	8	778	c.675C>T	c.(673-675)gaC>gaT	p.D225D	PLCB3_ENST00000325234.5_Silent_p.D158D|PLCB3_ENST00000279230.6_Silent_p.D225D	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	225					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						TGCGGCCGGACATTGACAAGA	0.562													C|||	40	0.00798722	0.0008	0.0115	5008	,	,		16159	0.0		0.0268	False		,,,				2504	0.0041				p.D225D		Atlas-SNP	.											.	PLCB3	103	.	0			c.C675T						PASS	.	C	,	34,4368	40.0+/-72.8	0,34,2167	102.0	104.0	103.0		675,474	3.1	1.0	11	dbSNP_120	103	204,8390	88.1+/-150.5	5,194,4098	no	coding-synonymous,coding-synonymous	PLCB3	NM_000932.2,NM_001184883.1	,	5,228,6265	TT,TC,CC		2.3737,0.7724,1.8313	,	225/1235,158/1168	64023270	238,12758	2201	4297	6498	SO:0001819	synonymous_variant	5331	exon8			GCCGGACATTGAC	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.675C>T	11.37:g.64023270C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																			C|0.982;T|0.018	0.018	strong		0.562	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
SERPINB2	5055	hgsc.bcm.edu	37	18	61570503	61570503	+	Missense_Mutation	SNP	C	C	G	rs6103	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61570503C>G	ENST00000299502.4	+	8	1292	c.1212C>G	c.(1210-1212)aaC>aaG	p.N404K	SERPINB2_ENST00000457692.1_Missense_Mutation_p.N404K	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	404			N -> K (in dbSNP:rs6103). {ECO:0000269|PubMed:10391209}.		blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	AGATAACCAACTGCATTTTAT	0.418													G|||	1750	0.349441	0.3676	0.3559	5008	,	,		18933	0.499		0.2296	False		,,,				2504	0.2894				p.N404K		Atlas-SNP	.											.	SERPINB2	63	.	0			c.C1212G						PASS	.	G	LYS/ASN,LYS/ASN	1624,2782	661.3+/-400.9	293,1038,872	68.0	77.0	74.0		1212,1212	-2.4	0.0	18	dbSNP_52	74	1877,6723	728.4+/-406.7	205,1467,2628	yes	missense,missense	SERPINB2	NM_001143818.1,NM_002575.2	94,94	498,2505,3500	GG,GC,CC		21.8256,36.8588,26.9183	benign,benign	404/416,404/416	61570503	3501,9505	2203	4300	6503	SO:0001583	missense	5055	exon8			AACCAACTGCATT	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.1212C>G	18.37:g.61570503C>G	ENSP00000299502:p.Asn404Lys	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	116	38	0.327586	NM_002575	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	37	CCDS11989.1	720	0.32967032967032966	172	0.34959349593495936	118	0.3259668508287293	261	0.4562937062937063	169	0.22295514511873352	G	0.009	-1.839191	0.00573	0.368588	0.218256	ENSG00000197632	ENST00000299502;ENST00000457692	T;T	0.11604	2.76;2.76	5.51	-2.38	0.06622	Serpin domain (3);	0.662303	0.16418	N	0.215262	T	0.00012	0.0000	N	0.05050	-0.12	0.49798	P	1.7699999999998273E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.39663	-0.9603	9	0.08837	T	0.75	.	4.321	0.11016	0.1426:0.4748:0.1427:0.2399	rs6103;rs3177799;rs60309021;rs6103	404	P05120	PAI2_HUMAN	K	404	ENSP00000299502:N404K;ENSP00000401645:N404K	ENSP00000299502:N404K	N	+	3	2	SERPINB2	59721483	0.000000	0.05858	0.001000	0.08648	0.049000	0.14656	-1.506000	0.02271	-0.415000	0.07484	-0.365000	0.07479	AAC	C|0.647;G|0.353	0.353	strong		0.418	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
NRD1	4898	hgsc.bcm.edu	37	1	52266242	52266242	+	Silent	SNP	G	G	A	rs8375	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:52266242G>A	ENST00000354831.7	-	23	2820	c.2631C>T	c.(2629-2631)ccC>ccT	p.P877P	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_Silent_p.P677P|RP4-657D16.3_ENST00000588291.1_RNA|RP4-657D16.3_ENST00000591675.1_RNA|RP4-657D16.3_ENST00000586761.1_RNA|RP4-657D16.6_ENST00000607338.1_RNA|NRD1_ENST00000539524.1_Silent_p.P745P|NRD1_ENST00000352171.7_Silent_p.P809P	NM_002525.2	NP_002516.2	O43847	NRDC_HUMAN	nardilysin (N-arginine dibasic convertase)	808					cell migration (GO:0016477)|cell proliferation (GO:0008283)|neuromuscular junction development (GO:0007528)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)	cell surface (GO:0009986)|cytosol (GO:0005829)	epidermal growth factor binding (GO:0048408)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)	27						CCAAAGTCTCGGGCTTGATGA	0.423													G|||	2449	0.489018	0.2224	0.5937	5008	,	,		20173	0.8234		0.5298	False		,,,				2504	0.3885				p.P877P		Atlas-SNP	.											.	NRD1	89	.	0			c.C2631T						PASS	.	G	,,	1228,3178	426.2+/-341.1	165,898,1140	181.0	171.0	174.0		2427,2235,2631	-4.1	1.0	1	dbSNP_52	174	4321,4279	579.3+/-390.9	1083,2155,1062	no	coding-synonymous,coding-synonymous,coding-synonymous	NRD1	NM_001101662.1,NM_001242361.1,NM_002525.2	,,	1248,3053,2202	AA,AG,GG		49.7558,27.8711,42.6649	,,	809/1152,745/1088,877/1220	52266242	5549,7457	2203	4300	6503	SO:0001819	synonymous_variant	4898	exon23			AGTCTCGGGCTTG	X93207	CCDS559.1, CCDS41335.1, CCDS55599.1	1p32.2-p32.1	2008-07-18			ENSG00000078618	ENSG00000078618			7995	protein-coding gene	gene with protein product		602651				9581555, 9479496	Standard	NM_002525		Approved	hNRD1, hNRD2	uc001ctc.4	O43847	OTTHUMG00000008278	ENST00000354831.7:c.2631C>T	1.37:g.52266242G>A		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	228	104	0.45614	NM_002525	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	37	CCDS559.1	1176	0.5384615384615384	114	0.23170731707317074	202	0.5580110497237569	466	0.8146853146853147	394	0.5197889182058048	G	6.926	0.540470	0.13250	0.278711	0.502442	ENSG00000078618	ENST00000440943	.	.	.	4.91	-4.12	0.03916	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999272099	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.6477	1.9029	0.03271	0.3099:0.0964:0.3421:0.2516	rs8375;rs1126997;rs2273199;rs3182412;rs10888734;rs11558620;rs17295088;rs17349599;rs17371636;rs17845186;rs17857996;rs56482093;rs60687281;rs10888734	.	.	.	X	224	.	.	R	-	1	2	NRD1	52038830	0.000000	0.05858	0.990000	0.47175	0.950000	0.60333	-3.991000	0.00318	-0.487000	0.06735	-2.102000	0.00361	CGA	T|0.088;G|0.434;C|0.096;A|0.382	0.382	strong		0.423	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525	
TRPV5	56302	hgsc.bcm.edu	37	7	142626549	142626549	+	Missense_Mutation	SNP	C	C	T	rs4236480	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:142626549C>T	ENST00000265310.1	-	4	809	c.461G>A	c.(460-462)cGt>cAt	p.R154H	TRPV5_ENST00000442623.1_Missense_Mutation_p.R154H	NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	154			R -> H (in dbSNP:rs4236480). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					GCGGGGACTACGGCGGAAGGC	0.622													C|||	1667	0.332867	0.6301	0.2464	5008	,	,		20913	0.0873		0.3042	False		,,,				2504	0.2751				p.R154H		Atlas-SNP	.											.	TRPV5	164	.	0			c.G461A						PASS	.	C	HIS/ARG	2562,1844	625.0+/-394.4	748,1066,389	82.0	70.0	74.0		461	-8.8	0.0	7	dbSNP_111	74	2293,6307	382.2+/-340.3	308,1677,2315	no	missense	TRPV5	NM_019841.4	29	1056,2743,2704	TT,TC,CC		26.6628,41.852,37.3289	possibly-damaging	154/730	142626549	4855,8151	2203	4300	6503	SO:0001583	missense	56302	exon4			GGACTACGGCGGA	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	3145	protein-coding gene	gene with protein product		606679	"""epithelial calcium channel 1"""	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.461G>A	7.37:g.142626549C>T	ENSP00000265310:p.Arg154His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Missense_Mutation	SNP	ENST00000265310.1	37	CCDS5875.1	664	0.304029304029304	281	0.5711382113821138	102	0.281767955801105	49	0.08566433566433566	232	0.30606860158311344	C	6.784	0.513699	0.12944	0.58148	0.266628	ENSG00000127412	ENST00000265310;ENST00000439304;ENST00000442623	T;T;T	0.52983	0.64;0.64;0.64	4.85	-8.82	0.00810	Ankyrin repeat-containing domain (4);	0.444160	0.24544	N	0.037614	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.14805	0.002;0.011	B;B	0.14578	0.009;0.011	T	0.40175	-0.9577	9	0.56958	D	0.05	-3.0204	5.8024	0.18422	0.3521:0.2358:0.0:0.4121	rs4236480;rs10376607;rs17853324;rs52832074;rs59004456;rs4236480	154;154	E9PBZ6;Q9NQA5	.;TRPV5_HUMAN	H	154;148;154	ENSP00000265310:R154H;ENSP00000406361:R148H;ENSP00000406572:R154H	ENSP00000265310:R154H	R	-	2	0	TRPV5	142336671	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.593000	0.05740	-2.131000	0.00815	-1.084000	0.02203	CGT	C|0.656;T|0.344	0.344	strong		0.622	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841	
FOLH1	2346	hgsc.bcm.edu	37	11	49204779	49204779	+	Missense_Mutation	SNP	C	C	T	rs116795343	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:49204779C>T	ENST00000256999.2	-	7	1102	c.842G>A	c.(841-843)cGt>cAt	p.R281H	FOLH1_ENST00000343844.4_De_novo_Start_OutOfFrame|FOLH1_ENST00000533034.1_Missense_Mutation_p.R266H|FOLH1_ENST00000356696.3_Missense_Mutation_p.R281H|FOLH1_ENST00000340334.7_Missense_Mutation_p.R266H	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	281	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)	p.R281L(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGCAATTCCACGCCTATAAGC	0.348																																					p.R281H		Atlas-SNP	.											FOLH1,NS,carcinoma,-1,2	FOLH1	141	2	1	Substitution - Missense(1)	lung(1)	c.G842A						scavenged	.						72.0	73.0	73.0					11																	49204779		2201	4298	6499	SO:0001583	missense	2346	exon7			ATTCCACGCCTAT	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.842G>A	11.37:g.49204779C>T	ENSP00000256999:p.Arg281His	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	123	16	0.130081	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	2.929	-0.221410	0.06061	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	2.76	-1.12	0.09808	.	0.978445	0.08346	N	0.960084	T	0.21427	0.0516	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.06405	0.001;0.0;0.002;0.0	T	0.23655	-1.0182	10	0.14656	T	0.56	.	6.6038	0.22714	0.0:0.3193:0.0:0.6807	.	266;266;281;281	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	H	281;281;266;266;281	ENSP00000256999:R281H;ENSP00000349129:R281H;ENSP00000344131:R266H;ENSP00000431463:R266H	ENSP00000256999:R281H	R	-	2	0	FOLH1	49161355	0.002000	0.14202	0.792000	0.32020	0.272000	0.26649	-0.922000	0.04004	-0.085000	0.12573	0.194000	0.17425	CGT	C|0.974;T|0.026	0.026	strong		0.348	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
MYOM3	127294	hgsc.bcm.edu	37	1	24418768	24418768	+	Silent	SNP	T	T	C	rs7556176	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:24418768T>C	ENST00000374434.3	-	11	1290	c.1128A>G	c.(1126-1128)ccA>ccG	p.P376P	MYOM3_ENST00000330966.7_Silent_p.P377P|MYOM3_ENST00000329601.7_Silent_p.P376P|MYOM3_ENST00000475306.1_5'UTR	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	376	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		GGACGTTCAGTGGGGAGCCTG	0.642													C|||	1884	0.376198	0.472	0.3199	5008	,	,		14860	0.3522		0.4662	False		,,,				2504	0.2188				p.P376P		Atlas-SNP	.											.	MYOM3	131	.	0			c.A1128G						PASS	.	C		1692,2080		382,928,576	44.0	50.0	48.0		1128	-10.7	0.0	1	dbSNP_116	48	3646,4546		827,1992,1277	no	coding-synonymous	MYOM3	NM_152372.3		1209,2920,1853	CC,CT,TT		44.5068,44.8568,44.6172		376/1438	24418768	5338,6626	1886	4096	5982	SO:0001819	synonymous_variant	127294	exon11			GTTCAGTGGGGAG	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.1128A>G	1.37:g.24418768T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Silent	SNP	ENST00000374434.3	37	CCDS41281.1																																																																																			T|0.586;C|0.414	0.414	strong		0.642	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
ITGAE	3682	hgsc.bcm.edu	37	17	3649214	3649214	+	Silent	SNP	G	G	A	rs1183610	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:3649214G>A	ENST00000263087.4	-	18	2261	c.2163C>T	c.(2161-2163)cgC>cgT	p.R721R		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	721					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		GAAGTGCCTCGCGGAGGCCTG	0.612													G|||	3581	0.715056	0.9244	0.8271	5008	,	,		15418	0.4524		0.831	False		,,,				2504	0.5041				p.R721R	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.C2163T						PASS	.	G		4008,398	790.3+/-415.0	1822,364,17	104.0	89.0	94.0		2163	-0.5	0.0	17	dbSNP_87	94	6788,1812	732.0+/-406.8	2687,1414,199	no	coding-synonymous	ITGAE	NM_002208.4		4509,1778,216	AA,AG,GG		21.0698,9.0331,16.9922		721/1180	3649214	10796,2210	2203	4300	6503	SO:0001819	synonymous_variant	3682	exon18			TGCCTCGCGGAGG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.2163C>T	17.37:g.3649214G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_002208	Q17RS6|Q9NZU9	Silent	SNP	ENST00000263087.4	37	CCDS32531.1																																																																																			G|0.215;A|0.785	0.785	strong		0.612	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
TNXB	7148	hgsc.bcm.edu	37	6	32029205	32029205	+	Silent	SNP	G	G	A	rs1150757	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32029205G>A	ENST00000375244.3	-	21	7662	c.7461C>T	c.(7459-7461)cgC>cgT	p.R2487R	TNXB_ENST00000375247.2_Silent_p.R2487R			P22105	TENX_HUMAN	tenascin XB	2547	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCGGGCCCACGCGCCGCCCCT	0.647													G|||	95	0.0189696	0.0023	0.0231	5008	,	,		18289	0.0		0.0755	False		,,,				2504	0.0				p.R2487R		Atlas-SNP	.											.	TNXB	553	.	0			c.C7461T						PASS	.	G		50,2618		3,44,1287	105.0	124.0	117.0		7461	-2.1	0.8	6	dbSNP_87	117	530,4624		29,472,2076	no	coding-synonymous	TNXB	NM_019105.6		32,516,3363	AA,AG,GG		10.2833,1.8741,7.415		2487/4243	32029205	580,7242	1334	2577	3911	SO:0001819	synonymous_variant	7148	exon21			GCCCACGCGCCGC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7461C>T	6.37:g.32029205G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	84	67	0.797619	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.959;A|0.041	0.041	strong		0.647	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
GPBP1L1	60313	hgsc.bcm.edu	37	1	46094027	46094027	+	Silent	SNP	A	A	G	rs1250	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46094027A>G	ENST00000290795.3	-	12	2547	c.1326T>C	c.(1324-1326)agT>agC	p.S442S	GPBP1L1_ENST00000355105.3_Silent_p.S442S|GPBP1L1_ENST00000479235.1_5'UTR			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	442					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S442S(1)	GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					GGGAGAACAGACTGGAACTGC	0.448													G|||	1615	0.322484	0.2648	0.3458	5008	,	,		17803	0.3472		0.2823	False		,,,				2504	0.3998				p.S442S		Atlas-SNP	.											GPBP1L1,NS,carcinoma,0,1	GPBP1L1	43	1	1	Substitution - coding silent(1)	stomach(1)	c.T1326C						PASS	.	G		1118,3288	718.0+/-408.8	148,822,1233	123.0	118.0	120.0		1326	6.0	1.0	1	dbSNP_36	120	2535,6065	692.7+/-404.6	387,1761,2152	no	coding-synonymous	GPBP1L1	NM_021639.4		535,2583,3385	GG,GA,AA		29.4767,25.3745,28.087		442/475	46094027	3653,9353	2203	4300	6503	SO:0001819	synonymous_variant	60313	exon13			GAACAGACTGGAA		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.1326T>C	1.37:g.46094027A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	37	CCDS528.1																																																																																			A|0.704;G|0.296	0.296	strong		0.448	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
NLRC5	84166	hgsc.bcm.edu	37	16	57075406	57075406	+	Silent	SNP	T	T	C	rs56171037	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57075406T>C	ENST00000262510.6	+	18	3174	c.2949T>C	c.(2947-2949)caT>caC	p.H983H	NLRC5_ENST00000539144.1_Silent_p.H983H|NLRC5_ENST00000308149.7_Silent_p.H983H|NLRC5_ENST00000436936.1_Silent_p.H983H	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	983					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GGCTGACACATTGTGGCCTCC	0.592													T|||	270	0.0539137	0.0696	0.0375	5008	,	,		18131	0.001		0.0964	False		,,,				2504	0.0552				p.H983H		Atlas-SNP	.											.	NLRC5	186	.	0			c.T2949C						PASS	.	T		338,4058	175.9+/-205.1	17,304,1877	68.0	63.0	65.0		2949	0.6	0.7	16	dbSNP_129	65	649,7951	165.1+/-217.3	29,591,3680	no	coding-synonymous	NLRC5	NM_032206.3		46,895,5557	CC,CT,TT		7.5465,7.6888,7.5946		983/1867	57075406	987,12009	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon17			GACACATTGTGGC	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2949T>C	16.37:g.57075406T>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1																																																																																			T|0.932;C|0.068	0.068	strong		0.592	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
ASS1	445	hgsc.bcm.edu	37	9	133364757	133364757	+	Silent	SNP	T	T	C	rs1057484	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:133364757T>C	ENST00000372394.1	+	13	1357	c.876T>C	c.(874-876)caT>caC	p.H292H	ASS1_ENST00000493984.2_3'UTR|ASS1_ENST00000372393.3_Silent_p.H292H|ASS1_ENST00000352480.5_Silent_p.H292H			P00966	ASSY_HUMAN	argininosuccinate synthase 1	292					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	TCCTTTACCATGCTCATTTAG	0.498													T|||	384	0.0766773	0.1188	0.0504	5008	,	,		15776	0.001		0.1262	False		,,,				2504	0.0654				p.H292H		Atlas-SNP	.											.	ASS1	37	.	0			c.T876C						PASS	.	T	,	491,3915	228.8+/-243.5	26,439,1738	113.0	122.0	119.0		876,876	2.6	1.0	9	dbSNP_86	119	847,7753	193.9+/-239.5	43,761,3496	no	coding-synonymous,coding-synonymous	ASS1	NM_000050.4,NM_054012.3	,	69,1200,5234	CC,CT,TT		9.8488,11.1439,10.2876	,	292/413,292/413	133364757	1338,11668	2203	4300	6503	SO:0001819	synonymous_variant	445	exon12			TTACCATGCTCAT	X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"""argininosuccinate synthetase"""	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.876T>C	9.37:g.133364757T>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	41	24	0.585366	NM_054012	Q6LDL2|Q86UZ0|Q96GT4	Silent	SNP	ENST00000372394.1	37	CCDS6933.1																																																																																			T|0.900;C|0.100	0.100	strong		0.498	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050	
BAALC	79870	hgsc.bcm.edu	37	8	104153137	104153137	+	Silent	SNP	C	C	T	rs3736043	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:104153137C>T	ENST00000297574.6	+	1	151	c.12C>T	c.(10-12)ggC>ggT	p.G4G	BAALC_ENST00000438105.2_Silent_p.G4G|C8orf56_ENST00000436771.1_Intron|C8orf56_ENST00000521246.1_Intron|BAALC_ENST00000306391.6_Silent_p.G4G|BAALC_ENST00000330955.5_Silent_p.G4G|BAALC_ENST00000309982.5_Silent_p.G4G			Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic	4	Interaction with CAMK2A. {ECO:0000250}.					cytoplasm (GO:0005737)|membrane (GO:0016020)				kidney(1)|large_intestine(3)|lung(3)	7			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			TGGGCTGCGGCGGGAGCCGGG	0.751													C|||	159	0.0317492	0.0053	0.0403	5008	,	,		4112	0.0238		0.0765	False		,,,				2504	0.0235				p.G4G		Atlas-SNP	.											.	BAALC	15	.	0			c.C12T						PASS	.	C	,	106,3646		3,100,1773	4.0	6.0	6.0		12,12	-2.1	1.0	8	dbSNP_107	6	794,6762		49,696,3033	no	coding-synonymous,coding-synonymous	BAALC	NM_001024372.1,NM_024812.2	,	52,796,4806	TT,TC,CC		10.5082,2.8252,7.959	,	4/55,4/146	104153137	900,10408	1876	3778	5654	SO:0001819	synonymous_variant	79870	exon1			CTGCGGCGGGAGC	AF363578	CCDS6297.1, CCDS47906.1	8q22.3	2008-07-29			ENSG00000164929	ENSG00000164929			14333	protein-coding gene	gene with protein product		606602				11707601	Standard	NM_024812		Approved		uc003yld.3	Q8WXS3	OTTHUMG00000164782	ENST00000297574.6:c.12C>T	8.37:g.104153137C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	22	13	0.590909	NM_001024372	Q8WTP6|Q8WXS0|Q8WXS1|Q8WXS2|Q9HA93	Silent	SNP	ENST00000297574.6	37																																																																																				C|0.958;T|0.042	0.042	strong		0.751	BAALC-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000380257.1		
ZNF407	55628	hgsc.bcm.edu	37	18	72344553	72344553	+	Silent	SNP	G	G	A	rs7227391	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72344553G>A	ENST00000299687.5	+	1	1578	c.1578G>A	c.(1576-1578)acG>acA	p.T526T	ZNF407_ENST00000577538.1_Silent_p.T526T|ZNF407_ENST00000309902.6_Silent_p.T526T|ZNF407_ENST00000582337.1_Silent_p.T526T	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	526					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GCTCTCAGACGTTGTGTGCTT	0.542													G|||	341	0.0680911	0.112	0.0663	5008	,	,		19719	0.003		0.1064	False		,,,				2504	0.0378				p.T526T		Atlas-SNP	.											.	ZNF407	231	.	0			c.G1578A						PASS	.	G	,,	401,3607		17,367,1620	138.0	147.0	144.0		1578,1578,1578	3.0	0.0	18	dbSNP_116	144	1159,7179		87,985,3097	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	104,1352,4717	AA,AG,GG		13.9002,10.005,12.6357	,,	526/1816,526/1661,526/2249	72344553	1560,10786	2004	4169	6173	SO:0001819	synonymous_variant	55628	exon1			TCAGACGTTGTGT	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1578G>A	18.37:g.72344553G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			G|0.907;A|0.093	0.093	strong		0.542	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
KCNV2	169522	hgsc.bcm.edu	37	9	2718654	2718654	+	Silent	SNP	G	G	A	rs7859993	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:2718654G>A	ENST00000382082.3	+	1	1153	c.915G>A	c.(913-915)gtG>gtA	p.V305V		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	305					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		TGGAGCACGTGGAGATGCTGT	0.692													G|||	133	0.0265575	0.0386	0.0317	5008	,	,		17166	0.0		0.0467	False		,,,				2504	0.0133				p.V305V		Atlas-SNP	.											.	KCNV2	72	.	0			c.G915A						PASS	.	G		180,4222	107.3+/-145.7	6,168,2027	38.0	43.0	41.0		915	4.2	1.0	9	dbSNP_116	41	429,8169	126.3+/-184.8	10,409,3880	no	coding-synonymous	KCNV2	NM_133497.3		16,577,5907	AA,AG,GG		4.9895,4.0891,4.6846		305/546	2718654	609,12391	2201	4299	6500	SO:0001819	synonymous_variant	169522	exon1			GCACGTGGAGATG	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.915G>A	9.37:g.2718654G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_133497	Q5T6X0	Silent	SNP	ENST00000382082.3	37	CCDS6447.1	72	0.03296703296703297	19	0.03861788617886179	15	0.04143646408839779	0	0.0	38	0.05013192612137203	G	8.471	0.857550	0.17106	0.040891	0.049895	ENSG00000168263	ENST00000423608	.	.	.	5.11	4.18	0.49190	.	.	.	.	.	T	0.26955	0.0660	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55036	-0.8203	5	0.62326	D	0.03	.	11.4245	0.50003	0.0:0.1258:0.7279:0.1463	rs7859993;rs17656699;rs7859993	.	.	.	R	256	.	ENSP00000409635:G256R	G	+	1	0	KCNV2	2708654	0.997000	0.39634	1.000000	0.80357	0.991000	0.79684	0.314000	0.19432	2.362000	0.80069	0.563000	0.77884	GGA	G|0.957;A|0.043	0.043	strong		0.692	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
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 GAIIx	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		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	52	26	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		
FAM114A1	92689	hgsc.bcm.edu	37	4	38930921	38930921	+	Silent	SNP	A	A	G	rs3188469	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38930921A>G	ENST00000358869.2	+	10	1304	c.1128A>G	c.(1126-1128)ttA>ttG	p.L376L	FAM114A1_ENST00000515037.1_Silent_p.L169L	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	376						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						TCTTTGAATTACATGTGGCGG	0.398													A|||	278	0.0555112	0.0318	0.0677	5008	,	,		19393	0.001		0.1412	False		,,,				2504	0.047				p.L376L		Atlas-SNP	.											.	FAM114A1	42	.	0			c.A1128G						PASS	.	A		256,4150	147.6+/-182.1	5,246,1952	84.0	85.0	84.0		1128	-1.7	1.0	4	dbSNP_105	84	1398,7202	271.7+/-289.7	114,1170,3016	yes	coding-synonymous	FAM114A1	NM_138389.2		119,1416,4968	GG,GA,AA		16.2558,5.8103,12.7172		376/564	38930921	1654,11352	2203	4300	6503	SO:0001819	synonymous_variant	92689	exon10			TGAATTACATGTG		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1128A>G	4.37:g.38930921A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	50	33	0.66	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Silent	SNP	ENST00000358869.2	37	CCDS3447.1																																																																																			A|0.887;G|0.113	0.113	strong		0.398	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
STRA8	346673	hgsc.bcm.edu	37	7	134925411	134925411	+	Silent	SNP	G	G	A	rs7805859	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:134925411G>A	ENST00000275764.3	+	2	201	c.201G>A	c.(199-201)gcG>gcA	p.A67A		NM_182489.1	NP_872295.1			stimulated by retinoic acid 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(1)	16						CCCTGGCAGCGCTCTTCAACA	0.617													G|||	1957	0.390775	0.3487	0.4063	5008	,	,		15246	0.2133		0.4553	False		,,,				2504	0.5532				p.A67A		Atlas-SNP	.											.	STRA8	39	.	0			c.G201A						PASS	.	G		1629,2777	497.1+/-363.7	302,1025,876	58.0	60.0	59.0		201	-2.2	0.2	7	dbSNP_116	59	3858,4742	537.5+/-383.2	890,2078,1332	no	coding-synonymous	STRA8	NM_182489.1		1192,3103,2208	AA,AG,GG		44.8605,36.9723,42.1882		67/331	134925411	5487,7519	2203	4300	6503	SO:0001819	synonymous_variant	346673	exon2			GGCAGCGCTCTTC	AF513502	CCDS5839.1	7q33	2012-12-07	2012-12-07		ENSG00000146857	ENSG00000146857			30653	protein-coding gene	gene with protein product		609987	"""stimulated by retinoic acid gene 8 homolog (mouse)"", ""stimulated by retinoic acid 8 homolog (mouse)"""			12489526	Standard	NM_182489		Approved		uc011kpx.2	Q7Z7C7	OTTHUMG00000155415	ENST00000275764.3:c.201G>A	7.37:g.134925411G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	154	150	0.974026	NM_182489		Silent	SNP	ENST00000275764.3	37	CCDS5839.1																																																																																			G|0.591;A|0.409	0.409	strong		0.617	STRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340028.1	NM_182489	
WRN	7486	hgsc.bcm.edu	37	8	31024654	31024654	+	Missense_Mutation	SNP	T	T	C	rs1346044	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:31024654T>C	ENST00000298139.5	+	34	4348	c.4099T>C	c.(4099-4101)Tgt>Cgt	p.C1367R	RP11-363L24.3_ENST00000521252.1_RNA	NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1367			C -> R (polymorphism associated with a higher risk of myocardial infarction; dbSNP:rs1346044). {ECO:0000269|PubMed:10069711, ECO:0000269|PubMed:11161804, ECO:0000269|PubMed:9021029, ECO:0000269|Ref.4}.		aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TCAACCTTCATGTGATGTCAA	0.403			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				T|||	965	0.192692	0.1475	0.1729	5008	,	,		17332	0.1042		0.2664	False		,,,				2504	0.2832				p.C1367R	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.T4099C	GRCh37	CM971591	WRN	M	rs1346044	PASS	.	T	ARG/CYS	757,3649	308.8+/-290.8	69,619,1515	120.0	105.0	110.0		4099	2.5	0.1	8	dbSNP_88	110	2200,6400	374.4+/-337.4	301,1598,2401	yes	missense	WRN	NM_000553.4	180	370,2217,3916	CC,CT,TT		25.5814,17.1811,22.7357	possibly-damaging	1367/1433	31024654	2957,10049	2203	4300	6503	SO:0001583	missense	7486	exon34	Familial Cancer Database	WS, Adult Progeria	CCTTCATGTGATG		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.4099T>C	8.37:g.31024654T>C	ENSP00000298139:p.Cys1367Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	400	0.18315018315018314	81	0.16463414634146342	64	0.17679558011049723	56	0.0979020979020979	199	0.262532981530343	T	8.055	0.766747	0.15983	0.171811	0.255814	ENSG00000165392	ENST00000298139	T	0.44083	0.93	4.86	2.45	0.29901	.	0.692798	0.13759	N	0.364736	T	0.00012	0.0000	M	0.70595	2.14	0.27730	P	0.9448488	P	0.41265	0.744	B	0.39068	0.289	T	0.09487	-1.0672	9	0.48119	T	0.1	-0.0497	5.6058	0.17379	0.0:0.1646:0.1451:0.6903	rs1346044;rs2230015;rs17652782;rs17847579;rs52814593;rs58743977;rs1346044	1367	Q14191	WRN_HUMAN	R	1367	ENSP00000298139:C1367R	ENSP00000298139:C1367R	C	+	1	0	WRN	31144196	0.589000	0.26807	0.090000	0.20809	0.295000	0.27426	0.579000	0.23788	0.406000	0.25560	0.533000	0.62120	TGT	T|0.798;C|0.202	0.202	strong		0.403	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
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 GAIIx	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	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	106	8	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	
INPP4A	3631	hgsc.bcm.edu	37	2	99193496	99193496	+	Silent	SNP	C	C	T	rs2230388	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:99193496C>T	ENST00000523221.1	+	23	2691	c.2691C>T	c.(2689-2691)agC>agT	p.S897S	INPP4A_ENST00000074304.5_Silent_p.S897S|INPP4A_ENST00000545415.1_Silent_p.S858S|INPP4A_ENST00000409851.3_Silent_p.S892S|INPP4A_ENST00000409540.3_Silent_p.S858S|INPP4A_ENST00000409463.1_Silent_p.S226S|INPP4A_ENST00000409016.4_Silent_p.S858S			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	897					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						GCTGCAAGAGCGCTAAGGACC	0.612													C|||	1284	0.25639	0.1589	0.2968	5008	,	,		17232	0.2937		0.2714	False		,,,				2504	0.3057				p.S897S		Atlas-SNP	.											.	INPP4A	205	.	0			c.C2691T						PASS	.	C	,,,	704,3520		63,578,1471	62.0	66.0	65.0		2691,2676,2574,2574	-3.1	1.0	2	dbSNP_98	65	2195,6257		291,1613,2322	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	354,2191,3793	TT,TC,CC		25.9702,16.6667,22.87	,,,	897/978,892/973,858/955,858/939	99193496	2899,9777	2112	4226	6338	SO:0001819	synonymous_variant	3631	exon25			CAAGAGCGCTAAG	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.2691C>T	2.37:g.99193496C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	197	87	0.441624	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			C|0.753;T|0.247	0.247	strong		0.612	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
SERPINB2	5055	hgsc.bcm.edu	37	18	61570529	61570529	+	Missense_Mutation	SNP	C	C	G	rs6104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61570529C>G	ENST00000299502.4	+	8	1318	c.1238C>G	c.(1237-1239)tCc>tGc	p.S413C	SERPINB2_ENST00000457692.1_Missense_Mutation_p.S413C	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	413			S -> C (in dbSNP:rs6104). {ECO:0000269|PubMed:10391209}.		blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	GGCAGATTTTCCTCACCCTAA	0.378													C|||	1748	0.349042	0.3669	0.3559	5008	,	,		18748	0.499		0.2296	False		,,,				2504	0.2883				p.S413C		Atlas-SNP	.											.	SERPINB2	63	.	0			c.C1238G						PASS	.	C	CYS/SER,CYS/SER	1624,2782	487.6+/-361.0	295,1034,874	56.0	64.0	61.0		1238,1238	1.3	0.2	18	dbSNP_52	61	1869,6731	326.6+/-317.4	205,1459,2636	yes	missense,missense	SERPINB2	NM_001143818.1,NM_002575.2	112,112	500,2493,3510	GG,GC,CC		21.7326,36.8588,26.8568	benign,benign	413/416,413/416	61570529	3493,9513	2203	4300	6503	SO:0001583	missense	5055	exon8			GATTTTCCTCACC	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.1238C>G	18.37:g.61570529C>G	ENSP00000299502:p.Ser413Cys	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	71	21	0.295775	NM_002575	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	37	CCDS11989.1	720	0.32967032967032966	172	0.34959349593495936	118	0.3259668508287293	261	0.4562937062937063	169	0.22295514511873352	C	2.187	-0.386200	0.04966	0.368588	0.217326	ENSG00000197632	ENST00000299502;ENST00000457692	D;D	0.84589	-1.87;-1.87	5.51	1.29	0.21616	Serpin domain (3);	0.417620	0.31323	N	0.007849	T	0.00012	0.0000	N	0.17312	0.475	0.09310	P	0.99999999603291	B	0.10296	0.003	B	0.10450	0.005	T	0.28650	-1.0037	9	0.02654	T	1	.	1.5526	0.02578	0.1203:0.4057:0.208:0.2659	rs6104;rs57367129;rs6104	413	P05120	PAI2_HUMAN	C	413	ENSP00000299502:S413C;ENSP00000401645:S413C	ENSP00000299502:S413C	S	+	2	0	SERPINB2	59721509	0.029000	0.19370	0.250000	0.24296	0.051000	0.14879	0.425000	0.21346	0.381000	0.24851	0.460000	0.39030	TCC	C|0.705;G|0.295	0.295	strong		0.378	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
LANCL2	55915	hgsc.bcm.edu	37	7	55459563	55459563	+	Silent	SNP	A	A	G	rs2049497	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:55459563A>G	ENST00000254770.2	+	2	860	c.282A>G	c.(280-282)acA>acG	p.T94T		NM_018697.3	NP_061167.1	Q9NS86	LANC2_HUMAN	LanC lantibiotic synthetase component C-like 2 (bacterial)	94					negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of abscisic acid-activated signaling pathway (GO:0009789)	cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|GTP binding (GO:0005525)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(11)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	25	Breast(14;0.0379)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00128)|Epithelial(13;0.0706)			GGCTGAAGACAGCTGATCCCC	0.403													A|||	2040	0.407348	0.3109	0.5634	5008	,	,		18162	0.5694		0.337	False		,,,				2504	0.3323				p.T94T		Atlas-SNP	.											.	LANCL2	54	.	0			c.A282G						PASS	.	A		1484,2922	475.0+/-357.2	275,934,994	100.0	102.0	102.0		282	1.9	1.0	7	dbSNP_94	102	2989,5611	461.9+/-365.5	501,1987,1812	no	coding-synonymous	LANCL2	NM_018697.3		776,2921,2806	GG,GA,AA		34.7558,33.6813,34.3918		94/451	55459563	4473,8533	2203	4300	6503	SO:0001819	synonymous_variant	55915	exon2			GAAGACAGCTGAT	AJ278245	CCDS5517.1	7q31.1-q31.33	2008-07-18	2001-12-04		ENSG00000132434	ENSG00000132434			6509	protein-coding gene	gene with protein product	"""testis-specific adriamycin sensitivity protein"", ""G protein-coupled receptor 69B"""	612919	"""LanC (bacterial lantibiotic synthetase component C)-like 2"""	GPR69B		11762191	Standard	NM_018697		Approved	TASP	uc003tqp.3	Q9NS86	OTTHUMG00000023779	ENST00000254770.2:c.282A>G	7.37:g.55459563A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_018697	B2R8D4|Q6NSL4|Q8TCQ3|Q9BSR1	Silent	SNP	ENST00000254770.2	37	CCDS5517.1																																																																																			A|0.628;G|0.372	0.372	strong		0.403	LANCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251459.1	NM_018697	
SLC25A29	123096	hgsc.bcm.edu	37	14	100759277	100759277	+	Silent	SNP	C	C	T	rs3742379	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:100759277C>T	ENST00000359232.3	-	4	555	c.255G>A	c.(253-255)cgG>cgA	p.R85R	SLC25A29_ENST00000554912.1_Silent_p.R19R|RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000556505.1_Silent_p.R19R|SLC25A29_ENST00000539621.1_Silent_p.R19R|AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000392908.3_Missense_Mutation_p.G71S|SLC25A29_ENST00000555927.1_Silent_p.R19R	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	85						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	acyl carnitine transmembrane transporter activity (GO:0015227)			NS(1)|endometrium(1)|ovary(1)	3		Melanoma(154;0.152)			L-Carnitine(DB00583)	GGCCCAGGGCCCGGAGGGTGT	0.701													C|||	1400	0.279553	0.1876	0.2565	5008	,	,		14810	0.5317		0.3121	False		,,,				2504	0.1268				p.R85R		Atlas-SNP	.											SLC25A29,NS,carcinoma,0,1	SLC25A29	14	1	0			c.G255A						PASS	.	C		816,3446		90,636,1405	10.0	13.0	12.0		255	2.0	1.0	14	dbSNP_107	12	2498,5870		389,1720,2075	no	coding-synonymous	SLC25A29	NM_001039355.1		479,2356,3480	TT,TC,CC		29.8518,19.1459,26.2391		85/304	100759277	3314,9316	2131	4184	6315	SO:0001819	synonymous_variant	123096	exon4			CAGGGCCCGGAGG	AK095532	CCDS32156.1	14q32.2	2013-05-22	2012-03-29	2004-01-21	ENSG00000197119	ENSG00000197119		"""Solute carriers"""	20116	protein-coding gene	gene with protein product		615064	"""chromosome 14 open reading frame 69"", ""solute carrier family 25, member 29"""	C14orf69			Standard	XM_005267343		Approved	FLJ38975	uc010twx.2	Q8N8R3	OTTHUMG00000171569	ENST00000359232.3:c.255G>A	14.37:g.100759277C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_001039355	A3KMR5|Q541V0	Silent	SNP	ENST00000359232.3	37	CCDS32156.1	697	0.3191391941391941	77	0.1565040650406504	90	0.24861878453038674	307	0.5367132867132867	223	0.2941952506596306	C	6.911	0.537720	0.13188	0.191459	0.298518	ENSG00000197119	ENST00000392908;ENST00000554060	.	.	.	4.99	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45775	-0.9238	4	0.87932	D	0	-41.4631	3.2678	0.06871	0.3516:0.3279:0.2417:0.0788	rs3742379	.	.	.	S	71	.	ENSP00000376640:G71S	G	-	1	0	SLC25A29	99829030	0.824000	0.29247	0.983000	0.44433	0.355000	0.29361	0.082000	0.14847	0.111000	0.17947	-0.302000	0.09304	GGC	C|0.688;G|0.000;T|0.312	0.312	strong		0.701	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3		
MED13L	23389	hgsc.bcm.edu	37	12	116408538	116408538	+	Silent	SNP	A	A	G	rs2304460	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:116408538A>G	ENST00000281928.3	-	27	6134	c.5928T>C	c.(5926-5928)acT>acC	p.T1976T		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1976						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.T1976T(1)		NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TGTTCAGTGCAGTACTTCGGC	0.428													A|||	765	0.152756	0.0696	0.1311	5008	,	,		20349	0.1696		0.1899	False		,,,				2504	0.2249				p.T1976T		Atlas-SNP	.											MED13L,NS,carcinoma,0,1	MED13L	193	1	1	Substitution - coding silent(1)	stomach(1)	c.T5928C						PASS	.	A		412,3994	203.1+/-225.7	13,386,1804	142.0	116.0	125.0		5928	3.2	1.0	12	dbSNP_100	125	1552,7048	292.0+/-300.6	122,1308,2870	no	coding-synonymous	MED13L	NM_015335.4		135,1694,4674	GG,GA,AA		18.0465,9.3509,15.1007		1976/2211	116408538	1964,11042	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon27			CAGTGCAGTACTT	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.5928T>C	12.37:g.116408538A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1	332	0.152014652014652	61	0.12398373983739837	50	0.13812154696132597	91	0.1590909090909091	130	0.17150395778364116	A	9.767	1.171638	0.21704	0.093509	0.180465	ENSG00000123066	ENST00000552447	.	.	.	5.55	3.21	0.36854	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16247	-1.0409	3	.	.	.	-16.2838	1.7372	0.02944	0.5402:0.1283:0.208:0.1235	rs2304460;rs17426149;rs58700742;rs2304460	.	.	.	R	181	.	.	C	-	1	0	MED13L	114892921	0.994000	0.37717	1.000000	0.80357	0.998000	0.95712	0.413000	0.21148	0.534000	0.28695	0.533000	0.62120	TGC	A|0.842;G|0.158	0.158	strong		0.428	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
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 GAIIx	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_ENST00000444449.2_Silent_p.L114L|AP1M1_ENST00000590756.1_Silent_p.L42L|AP1M1_ENST00000541844.1_Silent_p.L42L|AP1M1_ENST00000429941.2_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		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	112	58	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	
NUP210	23225	hgsc.bcm.edu	37	3	13407556	13407556	+	Missense_Mutation	SNP	T	T	C	rs3732671	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:13407556T>C	ENST00000254508.5	-	14	1904	c.1822A>G	c.(1822-1824)Atc>Gtc	p.I608V		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	608			I -> V (in dbSNP:rs3732671).		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					TTTACCCGGATGCCGCTGCAG	0.547													C|||	2898	0.578674	0.9024	0.4467	5008	,	,		18999	0.4107		0.5447	False		,,,				2504	0.4427				p.I608V		Atlas-SNP	.											.	NUP210	182	.	0			c.A1822G						PASS	.	C	VAL/ILE	3685,721	296.1+/-284.1	1539,607,57	72.0	69.0	70.0		1822	3.2	0.0	3	dbSNP_107	70	4849,3751	532.8+/-382.3	1366,2117,817	yes	missense	NUP210	NM_024923.2	29	2905,2724,874	CC,CT,TT		43.6163,16.364,34.3841	benign	608/1888	13407556	8534,4472	2203	4300	6503	SO:0001583	missense	23225	exon14			CCCGGATGCCGCT	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.1822A>G	3.37:g.13407556T>C	ENSP00000254508:p.Ile608Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	21	0.313433	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	1252	0.5732600732600732	433	0.8800813008130082	174	0.48066298342541436	246	0.43006993006993005	399	0.5263852242744064	C	0.006	-2.035635	0.00406	0.83636	0.563837	ENSG00000132182	ENST00000254508	T	0.04758	3.56	5.04	3.17	0.36434	.	0.066180	0.64402	N	0.000012	T	0.00012	0.0000	N	0.01277	-0.915	0.53688	P	2.8000000000028002E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.27123	-1.0083	9	0.02654	T	1	.	7.9524	0.30023	0.0:0.6659:0.0:0.3341	rs3732671;rs17780201;rs57881220;rs3732671	608;608	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	V	608	ENSP00000254508:I608V	ENSP00000254508:I608V	I	-	1	0	NUP210	13382556	0.985000	0.35326	0.004000	0.12327	0.002000	0.02628	2.684000	0.46951	0.134000	0.18681	-0.726000	0.03593	ATC	T|0.368;C|0.631	0.631	strong		0.547	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
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 GAIIx	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		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	119	62	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	
RERGL	79785	hgsc.bcm.edu	37	12	18234256	18234256	+	Missense_Mutation	SNP	T	T	C	rs941048	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:18234256T>C	ENST00000229002.2	-	6	693	c.487A>G	c.(487-489)Atg>Gtg	p.M163V	RERGL_ENST00000538724.1_Missense_Mutation_p.M162V|RERGL_ENST00000541632.1_5'Flank	NM_024730.2	NP_079006.1	Q9H628	RERGL_HUMAN	RERG/RAS-like	163	Small GTPase-like.		M -> V (in dbSNP:rs941048).		GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(5)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	17						ATAAACATCATTTCCACCTCC	0.438													T|||	415	0.0828674	0.1021	0.0793	5008	,	,		15404	0.002		0.1322	False		,,,				2504	0.092				p.M163V		Atlas-SNP	.											.	RERGL	66	.	0			c.A487G						PASS	.	T	VAL/MET	521,3885	239.6+/-250.7	30,461,1712	119.0	110.0	113.0		487	-0.2	1.0	12	dbSNP_86	113	1038,7562	222.0+/-259.2	60,918,3322	yes	missense	RERGL	NM_024730.2	21	90,1379,5034	CC,CT,TT		12.0698,11.8248,11.9868	benign	163/206	18234256	1559,11447	2203	4300	6503	SO:0001583	missense	79785	exon6			ACATCATTTCCAC	AK026308	CCDS8679.1, CCDS66332.1	12p12.3	2014-08-12			ENSG00000111404	ENSG00000111404			26213	protein-coding gene	gene with protein product						24127187	Standard	NM_001286201		Approved	FLJ22655	uc001rdq.3	Q9H628	OTTHUMG00000168820	ENST00000229002.2:c.487A>G	12.37:g.18234256T>C	ENSP00000229002:p.Met163Val	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	88	52	0.590909	NM_024730		Missense_Mutation	SNP	ENST00000229002.2	37	CCDS8679.1	165	0.07554945054945054	48	0.0975609756097561	35	0.09668508287292818	0	0.0	82	0.10817941952506596	T	10.84	1.463589	0.26248	0.118248	0.120698	ENSG00000111404	ENST00000229002;ENST00000538724	T;T	0.79352	-1.26;-1.26	5.16	-0.171	0.13331	.	0.620010	0.17458	N	0.173549	T	0.00754	0.0025	N	0.02916	-0.46	0.09310	P	0.999999623498	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.06625	-1.0816	9	0.48119	T	0.1	.	0.3938	0.00415	0.2:0.2895:0.206:0.3046	rs941048;rs17340563;rs52793354;rs60101325;rs941048	162;163	F5H686;Q9H628	.;RERGL_HUMAN	V	163;162	ENSP00000229002:M163V;ENSP00000437814:M162V	ENSP00000229002:M163V	M	-	1	0	RERGL	18125523	0.109000	0.22037	0.992000	0.48379	0.923000	0.55619	0.052000	0.14163	0.353000	0.24079	0.451000	0.29950	ATG	T|0.897;C|0.103	0.103	strong		0.438	RERGL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401198.1	NM_024730	
MARCH1	55016	hgsc.bcm.edu	37	4	165118253	165118253	+	Intron	SNP	T	T	C	rs2288676	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:165118253T>C	ENST00000503008.1	-	2	864				MARCH1_ENST00000514618.1_Intron|MARCH1_ENST00000508725.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				ttcatcctcctcgtcccctcc	0.512													T|||	600	0.119808	0.0053	0.2147	5008	,	,		17052	0.1696		0.0746	False		,,,				2504	0.2025				p.E204G		Atlas-SNP	.											ANP32C,NS,carcinoma,-1,1	ANP32C	59	1	0			c.A611G						scavenged	.	T	,GLY/GLU	56,4350	53.6+/-89.4	1,54,2148	221.0	172.0	189.0		,611	0.2	0.1	4	dbSNP_100	189	556,8044	149.4+/-204.5	21,514,3765	no	intron,missense	ANP32C,MARCH1	NM_001166373.1,NM_012403.1	,98	22,568,5913	CC,CT,TT		6.4651,1.271,4.7055	,benign	,204/235	165118253	612,12394	2203	4300	6503	SO:0001627	intron_variant	23520	exon1			TCCTCCTCGTCCC	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26077	protein-coding gene	gene with protein product		613331	"""membrane-associated ring finger (C3HC4) 1"""			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-85439A>G	4.37:g.165118253T>C		Somatic	165	8	0.0484848		WXS	Illumina HiSeq	Phase_I	159	77	0.484277	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			T|0.938;C|0.062	0.062	strong		0.512	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
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 GAIIx	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_ENST00000406599.1_Intron|ESR1_ENST00000440973.1_Silent_p.A239A|ESR1_ENST00000338799.5_Silent_p.A239A|ESR1_ENST00000456483.2_Silent_p.A239A|ESR1_ENST00000427531.2_Silent_p.A66A|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		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	50	4	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		
CCDC171	203238	hgsc.bcm.edu	37	9	15591372	15591372	+	Missense_Mutation	SNP	T	T	A	rs4741510	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:15591372T>A	ENST00000380701.3	+	5	689	c.361T>A	c.(361-363)Tca>Aca	p.S121T	CCDC171_ENST00000297641.3_Missense_Mutation_p.S121T|CCDC171_ENST00000535968.1_Missense_Mutation_p.S121T	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	121	Glu-rich.		S -> T (in dbSNP:rs4741510).					p.S121T(1)									AGCACAGAATTCAGAACTTCA	0.348													T|||	1773	0.354034	0.0204	0.4366	5008	,	,		17357	0.5923		0.4503	False		,,,				2504	0.4018				p.S121T		Atlas-SNP	.											C9orf93,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T361A						PASS	.	T	THR/SER	365,4041	176.9+/-206.0	18,329,1856	48.0	47.0	47.0		361	2.0	1.0	9	dbSNP_111	47	3513,5083	501.2+/-375.4	699,2115,1484	yes	missense	C9orf93	NM_173550.2	58	717,2444,3340	AA,AT,TT		40.8678,8.2842,29.8262	benign	121/1327	15591372	3878,9124	2203	4298	6501	SO:0001583	missense	203238	exon5			CAGAATTCAGAAC	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.361T>A	9.37:g.15591372T>A	ENSP00000370077:p.Ser121Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	852	0.3901098901098901	16	0.032520325203252036	159	0.43922651933701656	341	0.5961538461538461	336	0.44327176781002636	T	11.37	1.617292	0.28801	0.082842	0.408678	ENSG00000164989	ENST00000535968;ENST00000297641;ENST00000380701	T;T;T	0.47177	0.85;0.85;0.85	5.72	1.95	0.26073	.	1.326280	0.04833	N	0.439153	T	0.00012	0.0000	L	0.27053	0.805	0.52501	P	4.199999999998649E-5	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.06405	0.001;0.001;0.001;0.002	T	0.46020	-0.9221	9	0.26408	T	0.33	0.1965	1.8219	0.03112	0.1871:0.0817:0.2548:0.4764	rs4741510;rs52829905;rs4741510	121;121;121;121	B7ZM22;Q6TFL3-3;Q6TFL3;Q7Z3F8	.;.;CI093_HUMAN;.	T	121	ENSP00000438838:S121T;ENSP00000297641:S121T;ENSP00000370077:S121T	ENSP00000297641:S121T	S	+	1	0	C9orf93	15581372	0.985000	0.35326	0.998000	0.56505	0.692000	0.40212	0.079000	0.14782	0.068000	0.16574	0.524000	0.50904	TCA	T|0.666;A|0.334	0.334	strong		0.348	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
KDM6B	23135	hgsc.bcm.edu	37	17	7754993	7754993	+	Silent	SNP	G	G	A	rs12939056	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7754993G>A	ENST00000448097.2	+	17	4375	c.4044G>A	c.(4042-4044)ctG>ctA	p.L1348L	KDM6B_ENST00000254846.5_Silent_p.L1348L			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	1348	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						AGGAGCTGCTGAAGCTGCCCG	0.647											OREG0024145	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	937	0.187101	0.0129	0.2709	5008	,	,		16032	0.002		0.5785	False		,,,				2504	0.1513				p.L1348L		Atlas-SNP	.											.	KDM6B	95	.	0			c.G4044A						PASS	.	G		485,3899		44,397,1751	17.0	18.0	17.0		4044	2.0	1.0	17	dbSNP_121	17	4839,3737		1398,2043,847	no	coding-synonymous	KDM6B	NM_001080424.1		1442,2440,2598	AA,AG,GG		43.5751,11.063,41.0802		1348/1683	7754993	5324,7636	2192	4288	6480	SO:0001819	synonymous_variant	23135	exon17			GCTGCTGAAGCTG	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.4044G>A	17.37:g.7754993G>A		Somatic	38	0	0	644	WXS	Illumina HiSeq	Phase_I	34	12	0.352941	NM_001080424	C9IZ40|Q96G33	Silent	SNP	ENST00000448097.2	37																																																																																				A|0.324;C|0.000;G|0.675	0.324	strong		0.647	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
SIGLEC8	27181	hgsc.bcm.edu	37	19	51960940	51960940	+	Missense_Mutation	SNP	A	A	G	rs10409962	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51960940A>G	ENST00000321424.3	-	2	574	c.508T>C	c.(508-510)Tcc>Ccc	p.S170P	SIGLEC8_ENST00000597352.1_5'UTR|SIGLEC8_ENST00000340550.5_Intron|SIGLEC8_ENST00000430817.1_Intron	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	170	Ig-like C2-type 1.		S -> P (in dbSNP:rs10409962). {ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.S170P(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		AGGTTCCTGGAGTGGCCAGAC	0.617													G|||	1148	0.229233	0.5855	0.1527	5008	,	,		17793	0.1022		0.0795	False		,,,				2504	0.0869				p.S170P		Atlas-SNP	.											SIGLEC8,colon,carcinoma,+1,2	SIGLEC8	130	2	1	Substitution - Missense(1)	stomach(1)	c.T508C						PASS	.	G	PRO/SER	2183,2223		536,1111,556	78.0	86.0	83.0		508	0.3	0.0	19	dbSNP_119	83	614,7986		24,566,3710	yes	missense	SIGLEC8	NM_014442.2	74	560,1677,4266	GG,GA,AA		7.1395,49.5461,21.5055	benign	170/500	51960940	2797,10209	2203	4300	6503	SO:0001583	missense	27181	exon2			TCCTGGAGTGGCC	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.508T>C	19.37:g.51960940A>G	ENSP00000321077:p.Ser170Pro	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_014442	Q7Z728	Missense_Mutation	SNP	ENST00000321424.3	37	CCDS33086.1	452	0.20695970695970695	274	0.556910569105691	57	0.1574585635359116	54	0.0944055944055944	67	0.08839050131926121	.	0.010	-1.781355	0.00634	0.495461	0.071395	ENSG00000105366	ENST00000321424	T	0.26810	1.71	2.69	0.336	0.15958	Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.596060	0.14002	N	0.348073	T	0.00012	0.0000	N	0.00298	-1.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	9	0.02654	T	1	.	2.171	0.03849	0.3096:0.0:0.4397:0.2507	rs10409962;rs17846502;rs17859571;rs10409962	170	Q9NYZ4	SIGL8_HUMAN	P	170	ENSP00000321077:S170P	ENSP00000321077:S170P	S	-	1	0	SIGLEC8	56652752	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.512000	0.06313	0.008000	0.14787	-0.304000	0.09214	TCC	A|0.783;G|0.217	0.217	strong		0.617	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442	
LILRA6	79168	hgsc.bcm.edu	37	19	54745907	54745907	+	Missense_Mutation	SNP	A	A	G	rs62133127	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54745907A>G	ENST00000396365.2	-	3	389	c.350T>C	c.(349-351)aTg>aCg	p.M117T	LILRB3_ENST00000407860.2_Missense_Mutation_p.M117T|LILRA6_ENST00000440558.2_Missense_Mutation_p.M117T|LILRA6_ENST00000391735.3_Missense_Mutation_p.M117T|LILRA6_ENST00000270464.5_Missense_Mutation_p.M117T|LILRA6_ENST00000245621.5_Missense_Mutation_p.M117T|LILRA6_ENST00000419410.2_Missense_Mutation_p.M117T	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	117					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTCACCTGTCATCACCAGCTC	0.647																																					p.M117T		Atlas-SNP	.											LILRA6,NS,neuroblastoma,0,2	LILRA6	75	2	0			c.T350C						PASS	.						184.0	183.0	183.0					19																	54745907		2203	4300	6503	SO:0001583	missense	79168	exon3			CCTGTCATCACCA	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.350T>C	19.37:g.54745907A>G	ENSP00000379651:p.Met117Thr	Somatic	380	1	0.00263158		WXS	Illumina HiSeq	Phase_I	369	105	0.284553	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	209	0.09569597069597069	6	0.012195121951219513	50	0.13812154696132597	30	0.05244755244755245	123	0.16226912928759896	A	5.562	0.288572	0.10513	.	.	ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T;T	0.09163	3.01;3.01;3.01;3.01;3.01;3.01;3.01	3.4	3.4	0.38934	Immunoglobulin-like fold (1);	0.267597	0.26355	N	0.024855	T	0.00073	0.0002	M	0.69358	2.11	0.09310	N	0.999999	B;B;B;B;D;B;B;B;B;B	0.53151	0.015;0.128;0.019;0.001;0.958;0.02;0.029;0.051;0.041;0.041	B;B;B;B;P;B;B;B;B;B	0.53062	0.112;0.136;0.06;0.015;0.717;0.043;0.01;0.033;0.164;0.019	T	0.03077	-1.1075	10	0.87932	D	0	.	8.4256	0.32727	1.0:0.0:0.0:0.0	rs62133127	117;117;117;117;117;117;117;117;117;117	C9JFH3;Q6PI73-2;B5MCX0;B5ME96;Q6PI73;F8WCY4;F8WD89;D3YTC4;F8W6G6;O75022-2	.;.;.;.;LIRA6_HUMAN;.;.;.;.;.	T	117	ENSP00000384274:M117T;ENSP00000390120:M117T;ENSP00000270464:M117T;ENSP00000411227:M117T;ENSP00000375615:M117T;ENSP00000379651:M117T;ENSP00000245621:M117T	ENSP00000245621:M117T	M	-	2	0	LILRB3;LILRA6	59437719	0.209000	0.23505	0.996000	0.52242	0.049000	0.14656	1.457000	0.35212	1.574000	0.49760	0.155000	0.16302	ATG	A|0.250;G|0.750	0.750	weak		0.647	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
SNAI1	6615	hgsc.bcm.edu	37	20	48600557	48600557	+	Silent	SNP	T	T	C	rs4647959	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:48600557T>C	ENST00000244050.2	+	2	340	c.279T>C	c.(277-279)gaT>gaC	p.D93D		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	93	Ser-rich.				cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|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)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			CCCTGTCAGATGAGGACAGTG	0.642													C|||	1466	0.292732	0.7171	0.232	5008	,	,		15499	0.0913		0.1262	False		,,,				2504	0.1411				p.D93D		Atlas-SNP	.											.	SNAI1	28	.	0			c.T279C						PASS	.	C		2735,1671	501.0+/-364.9	874,987,342	47.0	57.0	53.0		279	-7.4	0.6	20	dbSNP_111	53	1059,7541	760.8+/-407.6	65,929,3306	no	coding-synonymous	SNAI1	NM_005985.3		939,1916,3648	CC,CT,TT		12.314,37.9256,29.1712		93/265	48600557	3794,9212	2203	4300	6503	SO:0001819	synonymous_variant	6615	exon2			GTCAGATGAGGAC	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	11128	protein-coding gene	gene with protein product		604238	"""snail 1 (drosophila homolog), zinc finger protein"", ""snail homolog 1 (Drosophila)"""			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.279T>C	20.37:g.48600557T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Silent	SNP	ENST00000244050.2	37	CCDS13423.1																																																																																			T|0.712;C|0.288	0.288	strong		0.642	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1		
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 GAIIx	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	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	58	30	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	
C10orf54	64115	hgsc.bcm.edu	37	10	73521371	73521371	+	Silent	SNP	C	C	T	rs3747867	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:73521371C>T	ENST00000394957.3	-	2	553	c.495G>A	c.(493-495)gaG>gaA	p.E165E	C10orf54_ENST00000481568.2_5'UTR|CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	165					BMP signaling pathway (GO:0030509)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of T cell cytokine production (GO:0002725)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of stem cell differentiation (GO:2000738)|stem cell differentiation (GO:0048863)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	9						GCACCTGCAGCTCCATGGCAC	0.622													C|||	934	0.186502	0.1551	0.1729	5008	,	,		23685	0.1935		0.2744	False		,,,				2504	0.1411				p.E165E		Atlas-SNP	.											.	C10orf54	29	.	0			c.G495A						PASS	.	C	,	800,3606	303.8+/-288.1	67,666,1470	37.0	29.0	32.0		,495	3.8	1.0	10	dbSNP_107	32	2175,6425	356.1+/-330.2	267,1641,2392	no	intron,coding-synonymous	CDH23,C10orf54	NM_022124.5,NM_022153.1	,	334,2307,3862	TT,TC,CC		25.2907,18.1571,22.8741	,	,165/312	73521371	2975,10031	2203	4300	6503	SO:0001819	synonymous_variant	64115	exon2			CTGCAGCTCCATG	AF193048	CCDS31218.1	10q22.1	2013-11-28			ENSG00000107738	ENSG00000107738		"""Immunoglobulin superfamily / V-set domain containing"""	30085	protein-coding gene	gene with protein product	"""stress induced secreted protein 1"""	615608				12975309	Standard	NM_022153		Approved	SISP1, GI24, B7-H5, B7H5	uc001jsd.3	Q9H7M9	OTTHUMG00000018426	ENST00000394957.3:c.495G>A	10.37:g.73521371C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Silent	SNP	ENST00000394957.3	37	CCDS31218.1																																																																																			C|0.779;T|0.221	0.221	strong		0.622	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153	
FNDC3B	64778	hgsc.bcm.edu	37	3	171969077	171969077	+	Missense_Mutation	SNP	C	C	G	rs7652177	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:171969077C>G	ENST00000336824.4	+	6	635	c.536C>G	c.(535-537)aCc>aGc	p.T179S	FNDC3B_ENST00000415807.2_Missense_Mutation_p.T179S|FNDC3B_ENST00000416957.1_Missense_Mutation_p.T179S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	179			T -> S (in dbSNP:rs7652177). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15564382, ECO:0000269|Ref.5}.		cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.T179S(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GGAATGTCAACCTACATCACC	0.388													G|||	3229	0.644768	0.9228	0.5634	5008	,	,		16403	0.5536		0.5169	False		,,,				2504	0.5521				p.T179S		Atlas-SNP	.											FNDC3B,NS,carcinoma,0,1	FNDC3B	118	1	1	Substitution - Missense(1)	stomach(1)	c.C536G						PASS	.	G	SER/THR,SER/THR	3758,648	277.2+/-273.6	1605,548,50	49.0	53.0	51.0		536,536	6.0	1.0	3	dbSNP_116	51	4236,4364	581.3+/-391.2	1028,2180,1092	yes	missense,missense	FNDC3B	NM_001135095.1,NM_022763.3	58,58	2633,2728,1142	GG,GC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	49.2558,14.7072,38.5361	benign,benign	179/1205,179/1205	171969077	7994,5012	2203	4300	6503	SO:0001583	missense	64778	exon6			TGTCAACCTACAT	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.536C>G	3.37:g.171969077C>G	ENSP00000338523:p.Thr179Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	26	0.333333	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	1336	0.6117216117216118	449	0.9126016260162602	209	0.5773480662983426	289	0.5052447552447552	389	0.5131926121372031	G	9.197	1.027387	0.19512	0.852928	0.492558	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957;ENST00000443501	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.98	5.98	0.97165	.	0.114990	0.85682	N	0.000000	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34079	-0.9843	9	0.07325	T	0.83	-17.7311	17.4819	0.87674	0.0:0.1242:0.8758:0.0	rs7652177;rs17281567;rs52833274;rs60495250;rs7652177	179;179	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	S	179;179;179;152	ENSP00000411242:T179S;ENSP00000338523:T179S;ENSP00000389094:T179S;ENSP00000389064:T152S	ENSP00000338523:T179S	T	+	2	0	FNDC3B	173451771	1.000000	0.71417	0.996000	0.52242	0.891000	0.51852	4.977000	0.63792	1.554000	0.49487	-0.187000	0.12897	ACC	C|0.384;G|0.616	0.616	strong		0.388	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
FAM114A1	92689	hgsc.bcm.edu	37	4	38945169	38945169	+	Silent	SNP	A	A	G	rs1060582	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:38945169A>G	ENST00000358869.2	+	15	1859	c.1683A>G	c.(1681-1683)gcA>gcG	p.A561A	FAM114A1_ENST00000515037.1_Silent_p.A354A	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	561						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						GTTTGAAAGCACAGCCGTGAC	0.527													A|||	535	0.106829	0.053	0.1787	5008	,	,		17632	0.0903		0.1233	False		,,,				2504	0.1288				p.A561A		Atlas-SNP	.											.	FAM114A1	42	.	0			c.A1683G						PASS	.	A		330,4076	175.9+/-205.1	13,304,1886	104.0	85.0	91.0		1683	-1.9	0.4	4	dbSNP_86	91	1287,7313	255.5+/-280.4	88,1111,3101	no	coding-synonymous	FAM114A1	NM_138389.2		101,1415,4987	GG,GA,AA		14.9651,7.4898,12.4327		561/564	38945169	1617,11389	2203	4300	6503	SO:0001819	synonymous_variant	92689	exon15			GAAAGCACAGCCG		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1683A>G	4.37:g.38945169A>G		Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Silent	SNP	ENST00000358869.2	37	CCDS3447.1																																																																																			A|0.883;G|0.117	0.117	strong		0.527	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
SPRY2	10253	hgsc.bcm.edu	37	13	80911525	80911525	+	Missense_Mutation	SNP	G	G	A	rs504122	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:80911525G>A	ENST00000377102.1	-	2	1293	c.316C>T	c.(316-318)Cct>Tct	p.P106S	SPRY2_ENST00000377104.3_Missense_Mutation_p.P106S|SPRY2_ENST00000540649.1_Missense_Mutation_p.P106S			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	106			P -> S (in dbSNP:rs504122).		bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment of mitotic spindle orientation (GO:0000132)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inner ear morphogenesis (GO:0042472)|lung growth (GO:0060437)|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 ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of Ras GTPase activity (GO:0034261)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|sensory perception of sound (GO:0007605)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase inhibitor activity (GO:0030291)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	12	Medulloblastoma(90;0.18)	Acute lymphoblastic leukemia(28;0.218)|Breast(118;0.244)		GBM - Glioblastoma multiforme(99;0.0318)		CTGGACAGAGGGGCTCGTGCA	0.597													G|||	1436	0.286741	0.0182	0.4539	5008	,	,		20149	0.4345		0.3529	False		,,,				2504	0.3108				p.P106S		Atlas-SNP	.											.	SPRY2	28	.	0			c.C316T						PASS	.	G	SER/PRO	354,4052	180.8+/-209.0	13,328,1862	92.0	87.0	89.0		316	0.6	0.1	13	dbSNP_83	89	3087,5513	469.1+/-367.5	550,1987,1763	yes	missense	SPRY2	NM_005842.2	74	563,2315,3625	AA,AG,GG		35.8953,8.0345,26.457	benign	106/316	80911525	3441,9565	2203	4300	6503	SO:0001583	missense	10253	exon2			ACAGAGGGGCTCG	AF039843	CCDS9463.1	13q31.1	2008-05-14	2001-11-28		ENSG00000136158	ENSG00000136158			11270	protein-coding gene	gene with protein product		602466	"""sprouty (Drosophila) homolog 2"""			9458049	Standard	NM_005842		Approved	hSPRY2	uc001vlj.3	O43597	OTTHUMG00000017140	ENST00000377102.1:c.316C>T	13.37:g.80911525G>A	ENSP00000366306:p.Pro106Ser	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	95	27	0.284211	NM_005842	B2R9J9|Q5T6Z7	Missense_Mutation	SNP	ENST00000377102.1	37	CCDS9463.1	674	0.3086080586080586	14	0.028455284552845527	148	0.4088397790055249	245	0.42832167832167833	267	0.35224274406332456	G	9.125	1.009882	0.19277	0.080345	0.358953	ENSG00000136158	ENST00000377104;ENST00000377102;ENST00000541655;ENST00000540649	T;T;T	0.57107	0.42;0.42;0.42	5.48	0.638	0.17742	.	0.226724	0.45867	N	0.000333	T	0.00012	0.0000	M	0.66939	2.045	0.44175	P	0.0030120000000000147	B	0.02656	0.0	B	0.04013	0.001	T	0.36720	-0.9736	9	0.36615	T	0.2	.	4.6416	0.12552	0.1252:0.2223:0.5371:0.1154	rs504122;rs3825414;rs17845004;rs17857765;rs57585481;rs504122	106	O43597	SPY2_HUMAN	S	106	ENSP00000366308:P106S;ENSP00000366306:P106S;ENSP00000439027:P106S	ENSP00000366306:P106S	P	-	1	0	SPRY2	79809526	0.534000	0.26362	0.051000	0.19133	0.952000	0.60782	0.958000	0.29227	-0.211000	0.10124	0.655000	0.94253	CCT	G|0.726;N|0.000	.	strong		0.597	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1		
ZNF417	147687	hgsc.bcm.edu	37	19	58420167	58420167	+	Silent	SNP	T	T	C	rs17852300	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58420167T>C	ENST00000312026.5	-	3	1643	c.1479A>G	c.(1477-1479)gaA>gaG	p.E493E	ZNF417_ENST00000595559.1_Silent_p.E492E|CTD-2583A14.9_ENST00000602124.1_Intron|ZNF417_ENST00000536263.1_Silent_p.E294E	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	493					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E493E(1)		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)		ATTCATTGCATTCATACGGCC	0.408													T|||	1233	0.246206	0.1543	0.219	5008	,	,		21542	0.2847		0.2972	False		,,,				2504	0.2975				p.E493E		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - coding silent(1)	stomach(1)	c.A1479G						scavenged	.	T		525,3881		63,399,1741	112.0	93.0	100.0		1479	-4.8	0.0	19	dbSNP_123	100	2020,6578		348,1324,2627	no	coding-synonymous	ZNF417	NM_152475.2		411,1723,4368	CC,CT,TT		23.4938,11.9156,19.5709		493/576	58420167	2545,10459	2203	4299	6502	SO:0001819	synonymous_variant	147687	exon3			ATTGCATTCATAC	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.1479A>G	19.37:g.58420167T>C		Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	138	47	0.34058	NM_152475	B4DEU1	Silent	SNP	ENST00000312026.5	37	CCDS12965.1																																																																																			T|0.773;C|0.227	0.227	strong		0.408	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
ZRANB2	9406	hgsc.bcm.edu	37	1	71538191	71538191	+	Silent	SNP	A	A	G	rs11556475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:71538191A>G	ENST00000370920.3	-	5	643	c.342T>C	c.(340-342)taT>taC	p.Y114Y	ZRANB2_ENST00000254821.6_Silent_p.Y114Y	NM_203350.2	NP_976225.1	O95218	ZRAB2_HUMAN	zinc finger, RAN-binding domain containing 2	114					mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(4)|ovary(2)|stomach(1)	15						CTCTTTCTATATATTCAACAT	0.284													A|||	355	0.0708866	0.1589	0.0692	5008	,	,		15666	0.0		0.0855	False		,,,				2504	0.0112				p.Y114Y		Atlas-SNP	.											.	ZRANB2	75	.	0			c.T342C						PASS	.	A	,	691,3711	287.5+/-279.3	42,607,1552	65.0	69.0	68.0		342,342	0.3	1.0	1	dbSNP_120	68	725,7857	176.2+/-226.1	36,653,3602	no	coding-synonymous,coding-synonymous	ZRANB2	NM_005455.4,NM_203350.2	,	78,1260,5154	GG,GA,AA		8.4479,15.6974,10.9057	,	114/321,114/331	71538191	1416,11568	2201	4291	6492	SO:0001819	synonymous_variant	9406	exon5			TTCTATATATTCA	AF065391	CCDS659.1, CCDS660.1	1p31	2008-02-05	2006-06-28	2006-06-28	ENSG00000132485	ENSG00000132485		"""Zinc fingers, RAN-binding domain containing"""	13058	protein-coding gene	gene with protein product		604347	"""zinc finger protein 265"""	ZNF265		9931435	Standard	NM_005455		Approved	ZIS, ZIS1, ZIS2	uc001dft.3	O95218	OTTHUMG00000009660	ENST00000370920.3:c.342T>C	1.37:g.71538191A>G		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	268	129	0.481343	NM_203350	D3DQ75|Q53GS3|Q59F92|Q5VV33|Q5VV34|Q8IXN6|Q9UP63	Silent	SNP	ENST00000370920.3	37	CCDS659.1																																																																																			A|0.898;G|0.102	0.102	strong		0.284	ZRANB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026636.1	NM_203350	
C3	718	hgsc.bcm.edu	37	19	6709848	6709848	+	Silent	SNP	C	C	T	rs2230204	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:6709848C>T	ENST00000245907.6	-	14	1784	c.1692G>A	c.(1690-1692)gtG>gtA	p.V564V		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	564					complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CGCTTTTTACCACCAGCTGTG	0.617													C|||	2180	0.435304	0.5477	0.3718	5008	,	,		11813	0.4613		0.2823	False		,,,				2504	0.4591				p.V564V		Atlas-SNP	.											.	C3	192	.	0			c.G1692A						PASS	.			2346,2060	601.5+/-389.7	625,1096,482	42.0	43.0	43.0		1692	3.0	1.0	19	dbSNP_98	43	2342,6258	387.0+/-342.0	303,1736,2261	no	coding-synonymous	C3	NM_000064.2		928,2832,2743	TT,TC,CC		27.2326,46.7544,36.0449		564/1664	6709848	4688,8318	2203	4300	6503	SO:0001819	synonymous_variant	718	exon14			TTTTACCACCAGC	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1692G>A	19.37:g.6709848C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																			C|0.634;N|0.001	.	strong		0.617	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
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 GAIIx	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	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	140	72	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	
SLC9C1	285335	hgsc.bcm.edu	37	3	111887788	111887788	+	Missense_Mutation	SNP	A	A	G	rs73853324	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111887788A>G	ENST00000305815.5	-	25	3425	c.3173T>C	c.(3172-3174)gTa>gCa	p.V1058A	SLC9C1_ENST00000487372.1_Missense_Mutation_p.V1010A	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	1058					cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										ACAATCTTCTACAGCTCCATG	0.308													A|||	266	0.053115	0.0666	0.0418	5008	,	,		20809	0.002		0.0547	False		,,,				2504	0.0941				p.V1058A		Atlas-SNP	.											.	.	.	.	0			c.T3173C						PASS	.	A	ALA/VAL	256,4148	146.5+/-181.1	12,232,1958	124.0	130.0	128.0		3173	2.4	1.0	3	dbSNP_130	128	457,8141	135.7+/-192.9	11,435,3853	yes	missense	SLC9A10	NM_183061.1	64	23,667,5811	GG,GA,AA		5.3152,5.8129,5.4838	benign	1058/1178	111887788	713,12289	2202	4299	6501	SO:0001583	missense	285335	exon25			TCTTCTACAGCTC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.3173T>C	3.37:g.111887788A>G	ENSP00000306627:p.Val1058Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	95	0.043498168498168496	32	0.06504065040650407	22	0.06077348066298342	0	0.0	41	0.05408970976253298	A	12.92	2.082593	0.36758	0.058129	0.053152	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.79653	-1.29;-1.29	6.06	2.42	0.29668	.	0.333153	0.25807	N	0.028179	T	0.18299	0.0439	L	0.38175	1.15	0.23320	N	0.997917	B;B	0.22541	0.071;0.006	B;B	0.33750	0.169;0.005	T	0.40553	-0.9557	10	0.36615	T	0.2	-0.1852	7.4468	0.27215	0.7407:0.0:0.2593:0.0	.	1010;1058	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	A	1058;1010	ENSP00000306627:V1058A;ENSP00000420688:V1010A	ENSP00000306627:V1058A	V	-	2	0	SLC9A10	113370478	0.992000	0.36948	0.997000	0.53966	0.865000	0.49528	1.593000	0.36686	0.556000	0.29098	0.528000	0.53228	GTA	A|0.946;G|0.054	0.054	strong		0.308	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
UGT2B7	7364	hgsc.bcm.edu	37	4	69962610	69962610	+	Silent	SNP	A	A	G	rs28365063	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:69962610A>G	ENST00000508661.1	+	1	399	c.372A>G	c.(370-372)agA>agG	p.R124R	UGT2B7_ENST00000305231.7_Silent_p.R124R|UGT2B7_ENST00000509763.1_Intron			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	124					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	ACATAACTAGAAAGTTCTGTA	0.313													A|||	669	0.133586	0.0749	0.0908	5008	,	,		20982	0.1706		0.1909	False		,,,				2504	0.1462				p.R124R		Atlas-SNP	.											.	UGT2B7	79	.	0			c.A372G						PASS	.	A		329,4045	151.0+/-185.0	13,303,1871	52.0	53.0	52.0		372	-0.4	0.0	4	dbSNP_126	52	1508,7086	272.6+/-290.2	137,1234,2926	no	coding-synonymous	UGT2B7	NM_001074.2		150,1537,4797	GG,GA,AA		17.5471,7.5217,14.1656		124/530	69962610	1837,11131	2187	4297	6484	SO:0001819	synonymous_variant	7364	exon1			AACTAGAAAGTTC	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.372A>G	4.37:g.69962610A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	130	68	0.523077	NM_001074	B2R810|Q6GTW0	Silent	SNP	ENST00000508661.1	37																																																																																				A|0.850;G|0.150	0.150	strong		0.313	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
CEP120	153241	hgsc.bcm.edu	37	5	122685727	122685727	+	Missense_Mutation	SNP	C	C	G	rs1047437	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:122685727C>G	ENST00000306467.5	-	19	2941	c.2637G>C	c.(2635-2637)caG>caC	p.Q879H	CEP120_ENST00000328236.5_Missense_Mutation_p.Q879H|CEP120_ENST00000306481.6_Missense_Mutation_p.Q853H			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	879			Q -> H (in dbSNP:rs1047437).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						GTAGTCTCATCTGTTCCAATT	0.363													C|||	928	0.185304	0.118	0.2147	5008	,	,		17011	0.244		0.1581	False		,,,				2504	0.2229				p.Q879H		Atlas-SNP	.											.	CEP120	72	.	0			c.G2637C						PASS	.	C	HIS/GLN,HIS/GLN	591,3815	259.8+/-263.3	35,521,1647	130.0	125.0	126.0		2559,2637	2.6	1.0	5	dbSNP_86	126	1425,7173	273.5+/-290.7	118,1189,2992	yes	missense,missense	CEP120	NM_001166226.1,NM_153223.3	24,24	153,1710,4639	GG,GC,CC		16.5736,13.4135,15.5029	benign,benign	853/961,879/987	122685727	2016,10988	2203	4299	6502	SO:0001583	missense	153241	exon20			TCTCATCTGTTCC	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.2637G>C	5.37:g.122685727C>G	ENSP00000303058:p.Gln879His	Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	311	155	0.498392	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	37	CCDS4134.2	406	0.1858974358974359	68	0.13821138211382114	71	0.19613259668508287	141	0.2465034965034965	126	0.1662269129287599	C	10.36	1.329111	0.24167	0.134135	0.165736	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481	T;T;T	0.22134	1.97;1.97;1.97	5.6	2.59	0.31030	.	0.269957	0.29806	U	0.011148	T	0.00012	0.0000	N	0.00801	-1.175	0.09310	P	0.9999999999997833	B	0.02656	0.0	B	0.04013	0.001	T	0.43065	-0.9414	9	0.23891	T	0.37	-5.1679	4.5832	0.12269	0.1132:0.4271:0.37:0.0896	rs1047437;rs3187444;rs52793214;rs1047437	879	Q8N960	CE120_HUMAN	H	879;879;853	ENSP00000303058:Q879H;ENSP00000327504:Q879H;ENSP00000307419:Q853H	ENSP00000303058:Q879H	Q	-	3	2	CEP120	122713626	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.127000	0.42035	1.371000	0.46172	0.563000	0.77884	CAG	C|0.836;G|0.164	0.164	strong		0.363	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
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 GAIIx	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_ENST00000369134.4_Missense_Mutation_p.V123I|GRIK2_ENST00000318991.6_Missense_Mutation_p.V172I|GRIK2_ENST00000369138.1_Missense_Mutation_p.V172I|GRIK2_ENST00000369137.3_Missense_Mutation_p.V172I|GRIK2_ENST00000413795.1_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	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	60	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		
STK31	56164	hgsc.bcm.edu	37	7	23794029	23794029	+	Missense_Mutation	SNP	G	G	A	rs4722266	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:23794029G>A	ENST00000355870.3	+	10	1348	c.1229G>A	c.(1228-1230)gGa>gAa	p.G410E	STK31_ENST00000428484.1_Missense_Mutation_p.G387E|STK31_ENST00000433467.2_Missense_Mutation_p.G410E|STK31_ENST00000354639.3_Missense_Mutation_p.G387E|STK31_ENST00000405627.3_3'UTR	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	410			G -> E (in dbSNP:rs4722266). {ECO:0000269|PubMed:17344846}.			acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TCTTTGAATGGATTAGAGATA	0.388													G|||	1096	0.21885	0.1982	0.3112	5008	,	,		16388	0.2073		0.1342	False		,,,				2504	0.2802				p.G410E		Atlas-SNP	.											STK31,NS,carcinoma,+1,1	STK31	175	1	0			c.G1229A						PASS	.	G	GLU/GLY,GLU/GLY,GLU/GLY	879,3527	342.5+/-307.2	95,689,1419	169.0	170.0	170.0		1160,1229,1160	3.4	1.0	7	dbSNP_111	170	1218,7382	245.1+/-274.1	84,1050,3166	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	98,98,98	179,1739,4585	AA,AG,GG		14.1628,19.9501,16.1233	benign,benign,benign	387/997,410/1020,387/997	23794029	2097,10909	2203	4300	6503	SO:0001583	missense	56164	exon10			TGAATGGATTAGA	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1229G>A	7.37:g.23794029G>A	ENSP00000348132:p.Gly410Glu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	137	86	0.627737	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	432	0.1978021978021978	106	0.21544715447154472	103	0.2845303867403315	125	0.21853146853146854	98	0.12928759894459102	G	1.635	-0.518037	0.04171	0.199501	0.141628	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.12255	2.7;2.7;2.7;2.7	5.76	3.36	0.38483	.	0.639291	0.16334	N	0.218991	T	0.00012	0.0000	N	0.00677	-1.265	0.45108	P	0.0018799999999999928	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45381	-0.9265	9	0.02654	T	1	-3.9124	6.2179	0.20665	0.754:0.1611:0.0849:0.0	rs4722266;rs17148339;rs52807853;rs58668439;rs4722266	410;410	B4DZ06;Q9BXU1	.;STK31_HUMAN	E	410;410;387;387	ENSP00000348132:G410E;ENSP00000411852:G410E;ENSP00000346660:G387E;ENSP00000406146:G387E	ENSP00000346660:G387E	G	+	2	0	STK31	23760554	0.993000	0.37304	1.000000	0.80357	0.776000	0.43924	2.818000	0.48041	0.435000	0.26365	-0.482000	0.04802	GGA	G|0.817;A|0.183	0.183	strong		0.388	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
PASD1	139135	hgsc.bcm.edu	37	X	150840916	150840916	+	Silent	SNP	C	C	T	rs41299110	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:150840916C>T	ENST00000370357.4	+	14	1944	c.1699C>T	c.(1699-1701)Ctg>Ttg	p.L567L		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	567						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					gaagcagcagctgcaagagca	0.547													T|||	732	0.193907	0.1074	0.2378	3775	,	,		13298	0.0536		0.1928	False		,,,				2504	0.181				p.L567L		Atlas-SNP	.											.	PASD1	286	.	0			c.C1699T						PASS	.	T		526,3309		34,381,77,1217,494	104.0	79.0	87.0		1699	-1.9	0.0	X	dbSNP_127	87	1626,5102		151,883,441,1394,1431	no	coding-synonymous	PASD1	NM_173493.2		185,1264,518,2611,1925	TT,TC,T,CC,C		24.1677,13.7158,20.373		567/774	150840916	2152,8411	2203	4300	6503	SO:0001819	synonymous_variant	139135	exon14			CAGCAGCTGCAAG	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1699C>T	X.37:g.150840916C>T		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	181	173	0.955801	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Silent	SNP	ENST00000370357.4	37	CCDS35431.1																																																																																			C|0.803;T|0.197	0.197	strong		0.547	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
HSPA8	3312	hgsc.bcm.edu	37	11	122929407	122929407	+	Silent	SNP	T	T	G	rs1064585	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:122929407T>G	ENST00000532636.1	-	7	1574	c.1455A>C	c.(1453-1455)atA>atC	p.I485I	HSPA8_ENST00000453788.2_Intron|HSPA8_ENST00000227378.3_Silent_p.I485I|HSPA8_ENST00000534319.1_Silent_p.I249I|SNORD14D_ENST00000384390.1_RNA|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000526110.1_Silent_p.I466I|HSPA8_ENST00000534624.1_Silent_p.I485I|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000533540.1_Silent_p.I339I|HSPA8_ENST00000526862.1_5'Flank			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	485					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AGACATTGAGTATACCATTGG	0.458													G|||	1216	0.242812	0.4289	0.1758	5008	,	,		23611	0.0813		0.159	False		,,,				2504	0.2914				p.I485I	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.A1455C						PASS	.	G	,	1736,2668	647.4+/-398.5	339,1058,805	147.0	139.0	142.0		1455,	-4.3	0.2	11	dbSNP_86	142	1469,7129	750.0+/-407.4	136,1197,2966	no	coding-synonymous,intron	HSPA8	NM_006597.4,NM_153201.2	,	475,2255,3771	GG,GT,TT		17.0854,39.4187,24.6501	,	485/647,	122929407	3205,9797	2202	4299	6501	SO:0001819	synonymous_variant	3312	exon7			ATTGAGTATACCA	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1455A>C	11.37:g.122929407T>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_006597	Q9H3R6	Silent	SNP	ENST00000532636.1	37	CCDS8440.1																																																																																			T|0.770;G|0.230	0.230	strong		0.458	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
DNAI2	64446	hgsc.bcm.edu	37	17	72295966	72295966	+	Silent	SNP	C	C	T	rs34159194	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72295966C>T	ENST00000311014.6	+	7	901	c.834C>T	c.(832-834)acC>acT	p.T278T	DNAI2_ENST00000446837.2_Silent_p.T278T|DNAI2_ENST00000579490.1_Silent_p.T335T|DNAI2_ENST00000582036.1_Silent_p.T278T|DNAI2_ENST00000307504.5_Silent_p.T135T			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	278					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						AGACGGGCACCGAGTGCTTCT	0.612									Kartagener syndrome				C|||	370	0.0738818	0.0129	0.0865	5008	,	,		16936	0.003		0.171	False		,,,				2504	0.1207				p.T278T		Atlas-SNP	.											.	DNAI2	102	.	0			c.C834T						PASS	.	C	,	205,4201	126.1+/-163.2	5,195,2003	64.0	47.0	53.0		834,834	-10.3	0.8	17	dbSNP_126	53	1612,6988	298.9+/-304.1	152,1308,2840	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	157,1503,4843	TT,TC,CC		18.7442,4.6527,13.9705	,	278/594,278/606	72295966	1817,11189	2203	4300	6503	SO:0001819	synonymous_variant	64446	exon7	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGGCACCGAGTGC	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"""Axonemal dyneins"", ""WD repeat domain containing"""	18744	protein-coding gene	gene with protein product	"""dynein intermediate chain 2"""	605483	"""dynein, axonemal, intermediate polypeptide 2"""			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.834C>T	17.37:g.72295966C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			C|0.883;T|0.117	0.117	strong		0.612	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
PALD1	27143	hgsc.bcm.edu	37	10	72289701	72289701	+	Silent	SNP	G	G	A	rs2275059	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72289701G>A	ENST00000263563.6	+	4	613	c.345G>A	c.(343-345)gtG>gtA	p.V115V		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	115						cytosol (GO:0005829)											TGGGCACCGTGGGAAGCTGTG	0.647													G|||	1092	0.218051	0.0166	0.2046	5008	,	,		16247	0.503		0.1491	False		,,,				2504	0.2771				p.V115V		Atlas-SNP	.											.	.	.	.	0			c.G345A						PASS	.	G		185,4221	116.3+/-154.2	1,183,2019	43.0	42.0	42.0		345	3.4	0.1	10	dbSNP_100	42	1223,7377	245.0+/-274.0	87,1049,3164	no	coding-synonymous	KIAA1274	NM_014431.2		88,1232,5183	AA,AG,GG		14.2209,4.1988,10.8258		115/857	72289701	1408,11598	2203	4300	6503	SO:0001819	synonymous_variant	27143	exon4			CACCGTGGGAAGC	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.345G>A	10.37:g.72289701G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Silent	SNP	ENST00000263563.6	37	CCDS31215.1																																																																																			G|0.845;A|0.155	0.155	strong		0.647	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
TMCC2	9911	hgsc.bcm.edu	37	1	205240251	205240251	+	Silent	SNP	C	C	T	rs1668867	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:205240251C>T	ENST00000358024.3	+	4	2075	c.1686C>T	c.(1684-1686)taC>taT	p.Y562Y	TMCC2_ENST00000329800.7_Silent_p.Y322Y|TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000330675.7_Silent_p.Y337Y|TMCC2_ENST00000545499.1_Silent_p.Y484Y	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	562						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(3)|pancreas(1)|skin(1)|urinary_tract(1)	20	Breast(84;0.0871)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CCGCCAGGTACGAGCGGCTGG	0.552													T|||	811	0.161941	0.1483	0.1931	5008	,	,		20194	0.0516		0.3549	False		,,,				2504	0.0736				p.Y562Y		Atlas-SNP	.											.	TMCC2	89	.	0			c.C1686T						PASS	.	T	,	817,3589	746.3+/-411.7	78,661,1464	52.0	50.0	51.0		1452,1686	-3.7	0.8	1	dbSNP_89	51	3054,5546	659.5+/-401.7	545,1964,1791	no	coding-synonymous,coding-synonymous	TMCC2	NM_001242925.1,NM_014858.3	,	623,2625,3255	TT,TC,CC		35.5116,18.5429,29.7632	,	484/632,562/710	205240251	3871,9135	2203	4300	6503	SO:0001819	synonymous_variant	9911	exon4			CAGGTACGAGCGG	AB001596	CCDS30984.1, CCDS55676.1, CCDS73010.1	1q32.1	2008-02-05	2005-07-13		ENSG00000133069	ENSG00000133069		"""Transmembrane and coiled-coil domain containing"""	24239	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 2"""			9455484	Standard	NM_014858		Approved	HUCEP11, FLJ38497	uc021pia.1	O75069	OTTHUMG00000037195	ENST00000358024.3:c.1686C>T	1.37:g.205240251C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Silent	SNP	ENST00000358024.3	37	CCDS30984.1																																																																																			C|0.762;T|0.238	0.238	strong		0.552	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858	
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 GAIIx	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	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	109	7	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	
OBSCN	84033	hgsc.bcm.edu	37	1	228482028	228482028	+	Silent	SNP	G	G	C	rs4653547	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:228482028G>C	ENST00000422127.1	+	42	11351	c.11307G>C	c.(11305-11307)ctG>ctC	p.L3769L	OBSCN_ENST00000284548.11_Silent_p.L3769L|OBSCN_ENST00000359599.6_Silent_p.L2616L|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000366709.4_Silent_p.L888L|OBSCN_ENST00000366707.4_Silent_p.L888L|OBSCN_ENST00000570156.2_Silent_p.L4198L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3769	Ig-like 38.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGTGTGAGCTGCAGATCCGTG	0.632													G|||	1064	0.21246	0.3139	0.2795	5008	,	,		20554	0.1835		0.164	False		,,,				2504	0.1074				p.L4198L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G12594C						PASS	.	G	,	1291,3025		202,887,1069	143.0	149.0	147.0		11307,11307	4.1	1.0	1	dbSNP_111	147	1502,7004		146,1210,2897	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	348,2097,3966	CC,CG,GG		17.6581,29.912,21.7829	,	3769/7969,3769/6621	228482028	2793,10029	2158	4253	6411	SO:0001819	synonymous_variant	84033	exon47			TGAGCTGCAGATC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11307G>C	1.37:g.228482028G>C		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	157	76	0.484076	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.788;C|0.212	0.212	strong		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SUSD2	56241	hgsc.bcm.edu	37	22	24582041	24582041	+	Missense_Mutation	SNP	A	A	G	rs8141797	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:24582041A>G	ENST00000358321.3	+	9	1658	c.1397A>G	c.(1396-1398)aAt>aGt	p.N466S		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	466	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.		N -> S (in dbSNP:rs8141797).		immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	26						TTCACATTCAATGGGCGCGGA	0.667													A|||	577	0.115216	0.1717	0.1167	5008	,	,		20075	0.0764		0.0616	False		,,,				2504	0.1329				p.N466S		Atlas-SNP	.											.	SUSD2	68	.	0			c.A1397G						PASS	.	A	SER/ASN	744,3662	291.8+/-281.7	56,632,1515	32.0	33.0	33.0		1397	4.0	0.8	22	dbSNP_116	33	545,8055	147.7+/-203.1	16,513,3771	yes	missense	SUSD2	NM_019601.3	46	72,1145,5286	GG,GA,AA		6.3372,16.8861,9.9108	benign	466/823	24582041	1289,11717	2203	4300	6503	SO:0001583	missense	56241	exon9			CATTCAATGGGCG	AK026431	CCDS13824.1	22q11-q12	2005-08-16			ENSG00000099994	ENSG00000099994			30667	protein-coding gene	gene with protein product		615825				12477932	Standard	NM_019601		Approved	BK65A6.2, FLJ22778	uc002zzn.1	Q9UGT4	OTTHUMG00000150792	ENST00000358321.3:c.1397A>G	22.37:g.24582041A>G	ENSP00000351075:p.Asn466Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	129	64	0.496124	NM_019601	Q9H5Y6	Missense_Mutation	SNP	ENST00000358321.3	37	CCDS13824.1	219	0.10027472527472528	88	0.17886178861788618	30	0.08287292817679558	61	0.10664335664335664	40	0.052770448548812667	A	16.71	3.198632	0.58126	0.168861	0.063372	ENSG00000099994	ENST00000358321	T	0.59638	0.25	5.05	4.01	0.46588	von Willebrand factor, type D domain (3);	0.199114	0.50627	N	0.000114	T	0.00144	0.0004	L	0.60904	1.88	0.32903	P	0.48656900000000003	P	0.36753	0.568	B	0.39068	0.289	T	0.07849	-1.0751	9	0.44086	T	0.13	-18.0237	8.501	0.33159	0.9047:0.0:0.0953:0.0	rs8141797;rs56709043;rs8141797	466	Q9UGT4	SUSD2_HUMAN	S	466	ENSP00000351075:N466S	ENSP00000351075:N466S	N	+	2	0	SUSD2	22912041	1.000000	0.71417	0.818000	0.32626	0.537000	0.34900	4.724000	0.61972	0.913000	0.36797	0.454000	0.30748	AAT	A|0.901;G|0.099	0.099	strong		0.667	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601	
BEND2	139105	hgsc.bcm.edu	37	X	18230715	18230715	+	Missense_Mutation	SNP	A	A	C	rs17274127	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:18230715A>C	ENST00000380033.4	-	4	594	c.462T>G	c.(460-462)ttT>ttG	p.F154L	BEND2_ENST00000380030.3_Missense_Mutation_p.F154L	NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	154			F -> L (in dbSNP:rs17274127).							NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						CTCTTTTTGGAAAATCCACTT	0.348													C|||	770	0.203974	0.1528	0.0807	3775	,	,		12412	0.2599		0.1441	False		,,,				2504	0.1074				p.F154L		Atlas-SNP	.											.	BEND2	108	.	0			c.T462G						PASS	.	C	LEU/PHE,LEU/PHE	736,3099		48,526,114,1058,457	168.0	155.0	159.0		462,462	-0.4	0.0	X	dbSNP_123	159	1295,5433		95,747,358,1586,1514	yes	missense,missense	BEND2	NM_001184767.1,NM_153346.4	22,22	143,1273,472,2644,1971	CC,CA,C,AA,A		19.2479,19.1917,19.2275	benign,benign	154/646,154/800	18230715	2031,8532	2203	4300	6503	SO:0001583	missense	139105	exon4			TTTTGGAAAATCC	AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"""BEN domain containing"""	28509	protein-coding gene	gene with protein product			"""chromosome X open reading frame 20"""	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.462T>G	X.37:g.18230715A>C	ENSP00000369372:p.Phe154Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	77	52	0.675325	NM_001184767	E9PFY2|Q4V9S2|Q5JXE5	Missense_Mutation	SNP	ENST00000380033.4	37	CCDS14184.1	382	0.23025919228450875	63	0.13695652173913042	26	0.07514450867052024	107	0.2296137339055794	72	0.10526315789473684	C	0.006	-2.111741	0.00353	0.191917	0.192479	ENSG00000177324	ENST00000380033;ENST00000380030	T;T	0.26223	1.82;1.75	1.22	-0.388	0.12459	.	1.468090	0.05061	N	0.479850	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21690	-1.0238	9	0.02654	T	1	.	1.6358	0.02742	0.2993:0.3281:0.0:0.3726	rs17274127;rs17274127	154;154	E9PFY2;Q8NDZ0	.;BEND2_HUMAN	L	154	ENSP00000369372:F154L;ENSP00000369369:F154L	ENSP00000369369:F154L	F	-	3	2	BEND2	18140636	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.955000	0.03869	-0.791000	0.04486	-0.418000	0.06021	TTT	A|0.766;0|0.015	.	strong		0.348	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346	
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 GAIIx	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_ENST00000392685.2_Silent_p.P120P|KCNMB3_ENST00000349697.2_Silent_p.P122P|KCNMB3_ENST00000485523.1_Silent_p.P102P|KCNMB3_ENST00000497599.1_Silent_p.P122P|KCNMB3_ENST00000486944.1_5'Flank	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		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	197	97	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		
ARMC3	219681	hgsc.bcm.edu	37	10	23297252	23297252	+	Missense_Mutation	SNP	G	G	A	rs10828395	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:23297252G>A	ENST00000298032.5	+	15	1961	c.1877G>A	c.(1876-1878)cGa>cAa	p.R626Q	ARMC3_ENST00000409049.3_Missense_Mutation_p.R626Q|ARMC3_ENST00000376528.4_Missense_Mutation_p.R363Q|ARMC3_ENST00000409983.3_Missense_Mutation_p.R626Q	NM_173081.3	NP_775104.2	Q5W041	ARMC3_HUMAN	armadillo repeat containing 3	626			R -> Q (in dbSNP:rs10828395). {ECO:0000269|PubMed:15489334}.			extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(24)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						GGTTATGGACGAAGTATTTCT	0.279													g|||	944	0.188498	0.2821	0.0951	5008	,	,		16534	0.12		0.1859	False		,,,				2504	0.2014				p.R626Q		Atlas-SNP	.											.	ARMC3	102	.	0			c.G1877A						PASS	.	G	GLN/ARG	1197,3185		171,855,1165	36.0	32.0	34.0		1877	5.6	1.0	10	dbSNP_120	34	1544,6994		144,1256,2869	yes	missense	ARMC3	NM_173081.3	43	315,2111,4034	AA,AG,GG		18.0839,27.3163,21.2152	benign	626/873	23297252	2741,10179	2191	4269	6460	SO:0001583	missense	219681	exon15			ATGGACGAAGTAT	AK057389	CCDS7142.1, CCDS60499.1, CCDS60500.1, CCDS73073.1	10p12.31	2013-02-14			ENSG00000165309	ENSG00000165309		"""Armadillo repeat containing"""	30964	protein-coding gene	gene with protein product	"""cancer/testis antigen 81"""	611226					Standard	XM_005252380		Approved	FLJ32827, CT81	uc001irm.4	Q5W041	OTTHUMG00000017811	ENST00000298032.5:c.1877G>A	10.37:g.23297252G>A	ENSP00000298032:p.Arg626Gln	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_173081	A0PG76|A6NH64|B4DZL3|B7ZBN6|B7ZBN7|Q8IXS5|Q8N7B0|Q96M49	Missense_Mutation	SNP	ENST00000298032.5	37	CCDS7142.1	359	0.16437728937728938	120	0.24390243902439024	37	0.10220994475138122	64	0.11188811188811189	138	0.1820580474934037	g	13.55	2.271992	0.40194	0.273163	0.180839	ENSG00000165309	ENST00000298032;ENST00000409983;ENST00000409049;ENST00000376528	T;T;T;T	0.37752	1.19;1.18;1.2;2.42	5.56	5.56	0.83823	.	1.341930	0.04522	N	0.384715	T	0.00012	0.0000	N	0.20986	0.625	0.35374	P	0.210704	B;B	0.30605	0.236;0.287	B;B	0.21708	0.036;0.024	T	0.10064	-1.0646	9	0.11182	T	0.66	-12.0527	15.0276	0.71682	0.0:0.0:1.0:0.0	rs10828395;rs17538475;rs17853918;rs52807337;rs59139275;rs10828395	626;626	Q5W041-4;Q5W041	.;ARMC3_HUMAN	Q	626;626;626;363	ENSP00000298032:R626Q;ENSP00000386943:R626Q;ENSP00000387288:R626Q;ENSP00000365711:R363Q	ENSP00000298032:R626Q	R	+	2	0	ARMC3	23337258	0.997000	0.39634	0.999000	0.59377	0.877000	0.50540	2.748000	0.47483	2.603000	0.88011	0.563000	0.77884	CGA	G|0.805;A|0.194	0.194	strong		0.279	ARMC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047197.2	NM_173081	
LMOD1	25802	hgsc.bcm.edu	37	1	201869257	201869257	+	Missense_Mutation	SNP	G	G	A	rs2820312	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:201869257G>A	ENST00000367288.4	-	2	1130	c.884C>T	c.(883-885)aCg>aTg	p.T295M	RP11-307B6.3_ENST00000414927.1_RNA|RP11-307B6.3_ENST00000458139.1_RNA	NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	295			T -> M (in dbSNP:rs2820312).		muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GCCACTGGGCGTCTGTTTCTC	0.507													g|||	1091	0.217851	0.205	0.2219	5008	,	,		20434	0.1012		0.3032	False		,,,				2504	0.2648				p.T295M		Atlas-SNP	.											.	LMOD1	59	.	0			c.C884T						PASS	.	A	MET/THR	830,3194		66,698,1248	72.0	74.0	73.0		884	0.6	0.0	1	dbSNP_100	73	2618,5716		402,1814,1951	yes	missense	LMOD1	NM_012134.2	81	468,2512,3199	AA,AG,GG		31.4135,20.6262,27.901	possibly-damaging	295/601	201869257	3448,8910	2012	4167	6179	SO:0001583	missense	25802	exon2			CTGGGCGTCTGTT	X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.884C>T	1.37:g.201869257G>A	ENSP00000356257:p.Thr295Met	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	238	127	0.533613	NM_012134	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	37	CCDS53457.1	527	0.2413003663003663	132	0.2682926829268293	89	0.24585635359116023	64	0.11188811188811189	242	0.31926121372031663	g	10.27	1.305016	0.23736	0.206262	0.314135	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	D	0.92397	-3.03	5.32	0.581	0.17407	.	1.726880	0.03514	N	0.219988	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;P	0.51653	0.004;0.947	B;B	0.31547	0.002;0.132	T	0.14896	-1.0456	9	0.30078	T	0.28	-2.9137	8.7241	0.34458	0.1205:0.2326:0.6469:0.0	rs2820312;rs3820435;rs52806101;rs58496028;rs2820312	244;295	B4E3S9;P29536	.;LMOD1_HUMAN	M	295;295;244	ENSP00000356257:T295M	ENSP00000356257:T295M	T	-	2	0	LMOD1	200135880	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.111000	0.15458	-0.089000	0.12484	-2.465000	0.00204	ACG	G|0.763;A|0.237	0.237	strong		0.507	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2		
KIAA1804	84451	hgsc.bcm.edu	37	1	233514934	233514934	+	Missense_Mutation	SNP	G	G	A	rs3795375	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:233514934G>A	ENST00000366624.3	+	9	2443	c.2182G>A	c.(2182-2184)Gtc>Atc	p.V728I	MLK4_ENST00000366622.1_Missense_Mutation_p.V174I	NM_032435.2	NP_115811.2												p.V728I(1)									TGGGTGCACCGTCCTTCTGGC	0.522													G|||	1308	0.261182	0.1853	0.3415	5008	,	,		18088	0.3433		0.172	False		,,,				2504	0.3139				p.V728I		Atlas-SNP	.											KIAA1804,NS,carcinoma,0,1	KIAA1804	129	1	1	Substitution - Missense(1)	stomach(1)	c.G2182A						PASS	.	G	ILE/VAL	793,3613	320.4+/-296.6	64,665,1474	73.0	79.0	77.0		2182	-3.1	0.0	1	dbSNP_107	77	1573,7027	293.9+/-301.6	147,1279,2874	yes	missense	KIAA1804	NM_032435.2	29	211,1944,4348	AA,AG,GG		18.2907,17.9982,18.1916	benign	728/1037	233514934	2366,10640	2203	4300	6503	SO:0001583	missense	0	exon9			TGCACCGTCCTTC																												ENST00000366624.3:c.2182G>A	1.37:g.233514934G>A	ENSP00000355583:p.Val728Ile	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	520	0.23809523809523808	99	0.20121951219512196	98	0.27071823204419887	194	0.33916083916083917	129	0.17018469656992086	G	9.218	1.032541	0.19590	0.179982	0.182907	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.29397	1.57;1.57	4.94	-3.12	0.05282	.	1.154050	0.06191	N	0.681408	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	P;P	0.47841	0.901;0.454	B;B	0.37601	0.254;0.109	T	0.27606	-1.0069	9	0.41790	T	0.15	.	11.0154	0.47685	0.4776:0.0:0.5224:0.0	rs3795375;rs61549279;rs3795375	175;728	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	I	728;174	ENSP00000355583:V728I;ENSP00000355581:V174I	ENSP00000355581:V174I	V	+	1	0	RP5-862P8.2	231581557	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	0.129000	0.15830	-0.887000	0.03961	-0.145000	0.13849	GTC	G|0.789;A|0.211	0.211	strong		0.522	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
WWC1	23286	hgsc.bcm.edu	37	5	167868779	167868779	+	Silent	SNP	A	A	G	rs3733981	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:167868779A>G	ENST00000265293.4	+	16	2875	c.2373A>G	c.(2371-2373)aaA>aaG	p.K791K	WWC1_ENST00000521089.1_Silent_p.K791K|WWC1_ENST00000522140.1_3'UTR	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	791					cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		ACTTGAAGAAACAGAGCAGGG	0.632													A|||	2743	0.547724	0.7595	0.4006	5008	,	,		15530	0.6151		0.335	False		,,,				2504	0.5153				p.K791K		Atlas-SNP	.											.	WWC1	98	.	0			c.A2373G						PASS	.	A	,,	3061,1345	689.4+/-405.1	1081,899,223	40.0	40.0	40.0		2373,2373,2373	-3.5	1.0	5	dbSNP_107	40	2963,5637	458.1+/-364.5	518,1927,1855	no	coding-synonymous,coding-synonymous,coding-synonymous	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	,,	1599,2826,2078	GG,GA,AA		34.4535,30.5266,46.3171	,,	791/1120,791/1119,791/1114	167868779	6024,6982	2203	4300	6503	SO:0001819	synonymous_variant	23286	exon16			GAAGAAACAGAGC	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"""WW, C2 and coiled-coil domain containing"""	29435	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 168"""	610533	"""WW, C2 and coiled-coil domain containing 1"""			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.2373A>G	5.37:g.167868779A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	119	68	0.571429	NM_015238	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Silent	SNP	ENST00000265293.4	37	CCDS4366.1	1120	0.5128205128205128	385	0.782520325203252	161	0.4447513812154696	347	0.6066433566433567	227	0.2994722955145119	A	10.85	1.466417	0.26335	0.694734	0.344535	ENSG00000113645	ENST00000393895;ENST00000524228	.	.	.	5.31	-3.53	0.04667	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999148424	.	.	.	.	.	.	T	0.27872	-1.0061	3	.	.	.	.	11.9069	0.52717	0.4652:0.0:0.5348:0.0	rs3733981;rs56965563;rs3733981	.	.	.	A	753;568	.	.	T	+	1	0	WWC1	167801357	0.920000	0.31207	0.970000	0.41538	0.985000	0.73830	0.139000	0.16036	-0.512000	0.06505	0.374000	0.22700	ACA	A|0.525;G|0.475	0.475	strong		0.632	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
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 GAIIx	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	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	110	45	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	
SHD	56961	hgsc.bcm.edu	37	19	4288332	4288332	+	Missense_Mutation	SNP	A	A	G	rs888930	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4288332A>G	ENST00000543264.2	+	5	2272	c.809A>G	c.(808-810)aAc>aGc	p.N270S	SHD_ENST00000599689.1_Intron	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	270	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		N -> S (in dbSNP:rs888930). {ECO:0000269|PubMed:14702039}.					p.N270S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		AGTGAGACCAACCCCCAGGAC	0.582													G|||	2424	0.484026	0.6203	0.5591	5008	,	,		18076	0.3393		0.3787	False		,,,				2504	0.5041				p.N270S		Atlas-SNP	.											SHD,NS,carcinoma,0,3	SHD	33	3	1	Substitution - Missense(1)	stomach(1)	c.A809G						PASS	.	G	SER/ASN	2534,1872	537.6+/-374.8	745,1044,414	78.0	66.0	70.0		809	4.0	1.0	19	dbSNP_86	70	3154,5446	653.7+/-401.1	567,2020,1713	yes	missense	SHD	NM_020209.3	46	1312,3064,2127	GG,GA,AA		36.6744,42.4875,43.7337	benign	270/341	4288332	5688,7318	2203	4300	6503	SO:0001583	missense	56961	exon5			AGACCAACCCCCA	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"""SH2 domain containing"""	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.809A>G	19.37:g.4288332A>G	ENSP00000446058:p.Asn270Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	36	25	0.694444	NM_020209	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	37	CCDS12125.1	1011	0.46291208791208793	331	0.6727642276422764	197	0.5441988950276243	198	0.34615384615384615	285	0.3759894459102902	G	7.008	0.556285	0.13436	0.575125	0.366744	ENSG00000105251	ENST00000543264;ENST00000221852	D	0.88046	-2.33	5.02	3.99	0.46301	SH2 motif (4);	0.262943	0.40554	N	0.001075	T	0.00012	0.0000	N	0.02181	-0.65	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.41752	-0.9491	9	0.02654	T	1	-4.3447	9.4055	0.38460	0.1725:0.0:0.8275:0.0	rs888930;rs1043817;rs3170373;rs52826654;rs59490546;rs888930	270	Q96IW2	SHD_HUMAN	S	270;185	ENSP00000446058:N270S	ENSP00000221852:N185S	N	+	2	0	SHD	4239332	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	5.276000	0.65580	0.738000	0.32606	-0.222000	0.12452	AAC	A|0.552;G|0.446	0.446	strong		0.582	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209	
UTS2B	257313	hgsc.bcm.edu	37	3	190999917	190999917	+	Missense_Mutation	SNP	C	C	A	rs6788319	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:190999917C>A	ENST00000340524.5	-	5	848	c.62G>T	c.(61-63)aGt>aTt	p.S21I	UTS2B_ENST00000427544.2_Missense_Mutation_p.S21I	NM_198152.3	NP_937795.2	Q765I0	UTS2B_HUMAN	urotensin 2B	21			S -> I (in dbSNP:rs6788319). {ECO:0000269|PubMed:14550283, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.		regulation of blood pressure (GO:0008217)|regulation of vasodilation (GO:0042312)	extracellular region (GO:0005576)		p.S21I(1)									TTGTAAAAAACTCAACACGGA	0.363													t|||	2361	0.471446	0.1997	0.585	5008	,	,		18107	0.5546		0.6133	False		,,,				2504	0.5266				p.S21I		Atlas-SNP	.											UTS2D,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.G62T						PASS	.	T	ILE/SER	1203,3203		162,879,1162	96.0	87.0	90.0		62	1.2	0.0	3	dbSNP_116	90	5205,3395		1562,2081,657	yes	missense	UTS2D	NM_198152.3	142	1724,2960,1819	AA,AC,CC		39.4767,27.3037,49.2696	benign	21/120	190999917	6408,6598	2203	4300	6503	SO:0001583	missense	257313	exon5			AAAAAACTCAACA	AB116021	CCDS3300.1	3q28	2013-02-28	2013-02-28	2013-02-28	ENSG00000188958	ENSG00000188958		"""Endogenous ligands"""	30894	protein-coding gene	gene with protein product	"""prepro-URP"""		"""urotensin 2 domain containing"""	UTS2D		14550283	Standard	NM_198152		Approved	URP, U2B	uc003fsu.3	Q765I0	OTTHUMG00000156192	ENST00000340524.5:c.62G>T	3.37:g.190999917C>A	ENSP00000340526:p.Ser21Ile	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	172	69	0.401163	NM_198152	B3KQY8|D3DNW1|Q2M1Z2	Missense_Mutation	SNP	ENST00000340524.5	37	CCDS3300.1	1142	0.5228937728937729	118	0.23983739837398374	223	0.6160220994475138	332	0.5804195804195804	469	0.6187335092348285	t	0.924	-0.714836	0.03206	0.273037	0.605233	ENSG00000188958	ENST00000340524;ENST00000427544;ENST00000432514	T;T;T	0.42513	0.97;0.97;1.01	4.91	1.17	0.20885	.	0.631378	0.14833	N	0.295722	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40478	-0.9561	9	0.06625	T	0.88	-1.6116	1.3964	0.02261	0.4546:0.1579:0.0846:0.3029	rs6788319;rs52792650;rs59424657;rs6788319	21	Q765I0	UTS2B_HUMAN	I	21	ENSP00000340526:S21I;ENSP00000398761:S21I;ENSP00000401028:S21I	ENSP00000340526:S21I	S	-	2	0	UTS2D	192482611	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.909000	0.28558	-0.102000	0.12197	-1.002000	0.02502	AGT	C|0.495;A|0.505	0.505	strong		0.363	UTS2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343353.1	NM_198152	
OR4L1	122742	hgsc.bcm.edu	37	14	20528528	20528528	+	Missense_Mutation	SNP	G	G	A	rs2775254	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20528528G>A	ENST00000315683.1	+	1	325	c.325G>A	c.(325-327)Ggt>Agt	p.G109S		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	109			G -> S (in dbSNP:rs2775254).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		CTTCTTTGGGGGTGCTGAGAT	0.473													G|||	2134	0.426118	0.3623	0.3934	5008	,	,		18993	0.5347		0.3221	False		,,,				2504	0.5307				p.G109S		Atlas-SNP	.											.	OR4L1	98	.	0			c.G325A						PASS	.	G	SER/GLY	1578,2828		284,1010,909	142.0	126.0	132.0		325	4.0	1.0	14	dbSNP_100	132	2761,5839		481,1799,2020	yes	missense	OR4L1	NM_001004717.1	56	765,2809,2929	AA,AG,GG		32.1047,35.8148,33.3615	probably-damaging	109/313	20528528	4339,8667	2203	4300	6503	SO:0001583	missense	122742	exon1			TTTGGGGGTGCTG		CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.325G>A	14.37:g.20528528G>A	ENSP00000319217:p.Gly109Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_001004717	Q6IEZ5	Missense_Mutation	SNP	ENST00000315683.1	37	CCDS32029.1	889	0.40705128205128205	184	0.37398373983739835	140	0.3867403314917127	303	0.5297202797202797	262	0.34564643799472294	.	15.15	2.747603	0.49257	0.358148	0.321047	ENSG00000176246	ENST00000315683	T	0.09445	2.98	3.99	3.99	0.46301	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000024	T	0.00012	0.0000	L	0.53780	1.695	0.58432	P	5.000000000032756E-6	D	0.56521	0.976	P	0.49361	0.608	T	0.47861	-0.9084	9	0.72032	D	0.01	.	13.9601	0.64172	0.0:0.0:1.0:0.0	rs2775254;rs2994400;rs52809408;rs57715101;rs2775254	109	Q8NH43	OR4L1_HUMAN	S	109	ENSP00000319217:G109S	ENSP00000319217:G109S	G	+	1	0	OR4L1	19598368	0.000000	0.05858	0.998000	0.56505	0.477000	0.33069	-0.577000	0.05847	2.213000	0.71641	0.650000	0.86243	GGT	G|0.625;A|0.375	0.375	strong		0.473	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404381.1		
ELP2	55250	hgsc.bcm.edu	37	18	33739735	33739735	+	Silent	SNP	G	G	C	rs139343265	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:33739735G>C	ENST00000358232.6	+	15	1635	c.1572G>C	c.(1570-1572)ctG>ctC	p.L524L	ELP2_ENST00000542050.1_3'UTR|ELP2_ENST00000351393.6_Silent_p.L498L|ELP2_ENST00000423854.2_Silent_p.L454L|ELP2_ENST00000350494.6_Silent_p.L519L|ELP2_ENST00000442325.2_Silent_p.L589L|ELP2_ENST00000542824.1_Silent_p.L454L	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	524					chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|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)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						AAGAGGAGCTGTTAACTAGTA	0.378													G|||	6	0.00119808	0.0	0.0014	5008	,	,		20035	0.0		0.004	False		,,,				2504	0.001				p.L589L		Atlas-SNP	.											.	ELP2	70	.	0			c.G1767C						PASS	.	G	,,,,,	7,4399	11.4+/-27.6	0,7,2196	143.0	142.0	142.0		1767,1557,1494,1362,1362,1572	-2.1	1.0	18	dbSNP_134	142	65,8535	39.3+/-95.6	0,65,4235	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ELP2	NM_001242875.1,NM_001242876.1,NM_001242877.1,NM_001242878.1,NM_001242879.1,NM_018255.2	,,,,,	0,72,6431	CC,CG,GG		0.7558,0.1589,0.5536	,,,,,	589/892,519/822,498/801,454/757,454/757,524/827	33739735	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	55250	exon16			GGAGCTGTTAACT	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"""Elongator acetyltransferase complex subunits"", ""WD repeat domain containing"""	18248	protein-coding gene	gene with protein product			"""signal transducer and activator of transcription 3 interacting protein 1"", ""elongation protein 2 homolog (S. cerevisiae)"""	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.1572G>C	18.37:g.33739735G>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_001242875	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Silent	SNP	ENST00000358232.6	37	CCDS11918.1																																																																																			G|0.996;C|0.004	0.004	strong		0.378	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255	
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 GAIIx	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		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	162	70	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	
ZZEF1	23140	hgsc.bcm.edu	37	17	4016096	4016096	+	Silent	SNP	T	T	C	rs74887186	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4016096T>C	ENST00000381638.2	-	5	997	c.873A>G	c.(871-873)aaA>aaG	p.K291K	ZZEF1_ENST00000574474.1_5'UTR|snoU13_ENST00000459263.1_RNA	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	291	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.						calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						CTGGCTTCATTTTTAAACTGG	0.443													T|||	85	0.0169728	0.0	0.0418	5008	,	,		19670	0.0		0.0487	False		,,,				2504	0.0072				p.K291K		Atlas-SNP	.											.	ZZEF1	195	.	0			c.A873G						PASS	.	T		19,4387	22.3+/-47.3	0,19,2184	39.0	34.0	36.0		873	-0.9	1.0	17	dbSNP_132	36	282,8318	96.8+/-158.5	3,276,4021	no	coding-synonymous	ZZEF1	NM_015113.3		3,295,6205	CC,CT,TT		3.2791,0.4312,2.3143		291/2962	4016096	301,12705	2203	4300	6503	SO:0001819	synonymous_variant	23140	exon5			CTTCATTTTTAAA	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.873A>G	17.37:g.4016096T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Silent	SNP	ENST00000381638.2	37	CCDS11043.1																																																																																			T|0.978;C|0.022	0.022	strong		0.443	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
PLXDC1	57125	hgsc.bcm.edu	37	17	37262117	37262117	+	Silent	SNP	C	C	T	rs17705646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:37262117C>T	ENST00000315392.4	-	7	1012	c.801G>A	c.(799-801)ccG>ccA	p.P267P	PLXDC1_ENST00000493200.1_5'UTR|PLXDC1_ENST00000444911.2_Silent_p.P227P|PLXDC1_ENST00000539608.1_Silent_p.P194P|PLXDC1_ENST00000394316.2_Silent_p.P267P	NM_020405.4	NP_065138.2	Q8IUK5	PLDX1_HUMAN	plexin domain containing 1	267					angiogenesis (GO:0001525)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)	receptor activity (GO:0004872)			kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						CTGGCACATCCGGGGATGGAT	0.602													C|||	94	0.01877	0.0015	0.0202	5008	,	,		14552	0.001		0.0427	False		,,,				2504	0.0348				p.P267P		Atlas-SNP	.											.	PLXDC1	45	.	0			c.G801A						PASS	.	C		31,4375	36.0+/-67.5	1,29,2173	131.0	130.0	131.0		801	-10.0	0.0	17	dbSNP_123	131	362,8238	121.3+/-180.4	5,352,3943	no	coding-synonymous	PLXDC1	NM_020405.4		6,381,6116	TT,TC,CC		4.2093,0.7036,3.0217		267/501	37262117	393,12613	2203	4300	6503	SO:0001819	synonymous_variant	57125	exon7			CACATCCGGGGAT	AF279144	CCDS11333.1	17q21.1	2006-04-12			ENSG00000161381	ENSG00000161381			20945	protein-coding gene	gene with protein product	"""tumor endothelial marker 7 precursor"""	606826				10947988, 11559528	Standard	NM_020405		Approved	TEM3, TEM7	uc002hrg.2	Q8IUK5	OTTHUMG00000133183	ENST00000315392.4:c.801G>A	17.37:g.37262117C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	64	37	0.578125	NM_020405	B2R7I8|Q5QCZ7|Q5QCZ8|Q5QCZ9|Q9HCT9	Silent	SNP	ENST00000315392.4	37	CCDS11333.1	39	0.017857142857142856	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	29	0.03825857519788918	C	5.914	0.352797	0.11182	0.007036	0.042093	ENSG00000161381	ENST00000444435	.	.	.	4.99	-9.98	0.00438	.	.	.	.	.	T	0.03477	0.0100	.	.	.	0.21697	N	0.99959	.	.	.	.	.	.	T	0.04481	-1.0948	4	.	.	.	-7.1747	3.4137	0.07368	0.244:0.0818:0.1373:0.537	rs17705646;rs17705646	.	.	.	Q	51	.	.	R	-	2	0	PLXDC1	34515643	0.000000	0.05858	0.000000	0.03702	0.791000	0.44710	-4.237000	0.00268	-3.639000	0.00128	-1.036000	0.02392	CGG	C|0.974;T|0.026	0.026	strong		0.602	PLXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256892.2	NM_020405	
SDK2	54549	hgsc.bcm.edu	37	17	71426656	71426656	+	Missense_Mutation	SNP	G	G	T	rs1105353	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:71426656G>T	ENST00000392650.3	-	12	1577	c.1577C>A	c.(1576-1578)aCc>aAc	p.T526N	SDK2_ENST00000388726.3_Missense_Mutation_p.T526N	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	526	Ig-like C2-type 6.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						GTACCTGATGGTTACTCGGGG	0.607													G|||	678	0.135383	0.0431	0.1974	5008	,	,		15499	0.0704		0.2922	False		,,,				2504	0.1217				p.T526N		Atlas-SNP	.											.	SDK2	219	.	0			c.C1577A						PASS	.	G	ASN/THR	367,4039	175.9+/-205.1	13,341,1849	44.0	33.0	37.0		1577	3.9	0.8	17	dbSNP_86	37	2312,6288	358.6+/-331.2	318,1676,2306	yes	missense	SDK2	NM_001144952.1	65	331,2017,4155	TT,TG,GG		26.8837,8.3296,20.5982	benign	526/2173	71426656	2679,10327	2203	4300	6503	SO:0001583	missense	54549	exon12			CTGATGGTTACTC	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.1577C>A	17.37:g.71426656G>T	ENSP00000376421:p.Thr526Asn	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	375|375	0.1717032967032967|0.1717032967032967	27|27	0.054878048780487805|0.054878048780487805	74|74	0.20441988950276244|0.20441988950276244	45|45	0.07867132867132867|0.07867132867132867	229|229	0.3021108179419525|0.3021108179419525	G|G	1.954|1.954	-0.440461|-0.440461	0.04636|0.04636	0.083296|0.083296	0.268837|0.268837	ENSG00000069188|ENSG00000069188	ENST00000416616|ENST00000409227;ENST00000392650;ENST00000388726;ENST00000316893	.|T;T	.|0.67698	.|-0.28;-0.28	3.89|3.89	3.89|3.89	0.44902|0.44902	.|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.511109	.|0.19375	.|N	.|0.115809	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.58510|0.58510	1.815|1.815	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	.|B;B	.|0.12630	.|0.002;0.006	.|B;B	.|0.13407	.|0.009;0.009	T|T	0.11542|0.11542	-1.0583|-1.0583	4|9	.|0.17369	.|T	.|0.5	.|.	6.8444|6.8444	0.23980|0.23980	0.0977:0.0:0.7258:0.1765|0.0977:0.0:0.7258:0.1765	rs1105353;rs17184965;rs1105353|rs1105353;rs17184965;rs1105353	.|526;526	.|Q58EX2-2;Q58EX2	.|.;SDK2_HUMAN	K|N	430|150;526;526;526	.|ENSP00000376421:T526N;ENSP00000373378:T526N	.|ENSP00000324967:T526N	N|T	-|-	3|2	2|0	SDK2|SDK2	68938251|68938251	0.177000|0.177000	0.23109|0.23109	0.815000|0.815000	0.32552|0.32552	0.028000|0.028000	0.11728|0.11728	2.817000|2.817000	0.48034|0.48034	1.887000|1.887000	0.54652|0.54652	0.462000|0.462000	0.41574|0.41574	AAC|ACC	G|0.817;N|0.000	.	strong		0.607	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
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 GAIIx	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|ACTG1_ENST00000573283.1_Missense_Mutation_p.R62C|ACTG1_ENST00000575087.1_Missense_Mutation_p.R62C|AC139149.1_ENST00000584254.1_RNA|RP13-766D20.2_ENST00000430912.1_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	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	37	9	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127541743A>G	ENST00000284690.3	-	5	1583				DHX32_ENST00000368721.1_Intron|BCCIP_ENST00000368759.5_Silent_p.L300L|DHX32_ENST00000284688.6_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		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	61	28	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	
SPTA1	6708	hgsc.bcm.edu	37	1	158597507	158597507	+	Missense_Mutation	SNP	G	G	C	rs3737515	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158597507G>C	ENST00000368147.4	-	40	5752	c.5572C>G	c.(5572-5574)Cta>Gta	p.L1858V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1858			L -> V (in dbSNP:rs3737515). {ECO:0000269|PubMed:8486776}.		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGCTTCATTAGCAAGCTCTGC	0.403													G|||	1141	0.227835	0.1906	0.2133	5008	,	,		19212	0.2054		0.2863	False		,,,				2504	0.2515				p.L1858V		Atlas-SNP	.											.	SPTA1	720	.	0			c.C5572G						PASS	.	G	VAL/LEU	710,2988		63,584,1202	143.0	127.0	132.0		5572	2.7	0.7	1	dbSNP_107	132	2255,5929		309,1637,2146	yes	missense	SPTA1	NM_003126.2	32	372,2221,3348	CC,CG,GG		27.5538,19.1996,24.9537	benign	1858/2420	158597507	2965,8917	1849	4092	5941	SO:0001583	missense	6708	exon40			TCATTAGCAAGCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5572C>G	1.37:g.158597507G>C	ENSP00000357129:p.Leu1858Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	538	0.24633699633699635	104	0.21138211382113822	83	0.2292817679558011	124	0.21678321678321677	227	0.2994722955145119	G	13.00	2.107732	0.37242	0.191996	0.275538	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48201	0.82;0.82	5.55	2.68	0.31781	.	0.398187	0.14832	N	0.295829	T	0.37320	0.0999	M	0.75447	2.3	0.26869	P	0.9677948	P	0.37594	0.601	B	0.42692	0.395	T	0.28427	-1.0044	9	0.56958	D	0.05	.	10.2495	0.43360	0.2184:0.0:0.7816:0.0	rs3737515;rs52827684;rs56522116;rs59553946;rs3737515	1858	P02549	SPTA1_HUMAN	V	1858	ENSP00000357130:L1858V;ENSP00000357129:L1858V	ENSP00000357129:L1858V	L	-	1	2	SPTA1	156864131	1.000000	0.71417	0.678000	0.29963	0.560000	0.35617	2.457000	0.45005	0.451000	0.26802	-0.136000	0.14681	CTA	G|0.758;C|0.242	0.242	strong		0.403	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
CCHCR1	54535	hgsc.bcm.edu	37	6	31112737	31112737	+	Missense_Mutation	SNP	C	C	A	rs130079	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31112737C>A	ENST00000376266.5	-	14	1845	c.1723G>T	c.(1723-1725)Ggc>Tgc	p.G575C	CCHCR1_ENST00000396263.2_Missense_Mutation_p.G522C|CCHCR1_ENST00000396268.3_Missense_Mutation_p.G664C|CCHCR1_ENST00000451521.2_Missense_Mutation_p.G628C	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	575			G -> C (in allele HCR*WWCC; associated with psoriasis; dbSNP:rs130079). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:10888604, ECO:0000269|PubMed:11348465, ECO:0000269|PubMed:11875053, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						TCCTGCTGGCCCTGGCGTGCT	0.652													C|||	710	0.141773	0.1649	0.1383	5008	,	,		17573	0.0377		0.2018	False		,,,				2504	0.1585				p.G664C		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1990T						PASS	.	C	CYS/GLY,CYS/GLY,CYS/GLY	835,3571	330.4+/-301.5	89,657,1457	59.0	58.0	59.0		1882,1990,1723	1.5	1.0	6	dbSNP_78	59	2031,6569	351.3+/-328.2	247,1537,2516	yes	missense,missense,missense	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	159,159,159	336,2194,3973	AA,AC,CC		23.6163,18.9514,22.036	benign,benign,benign	628/836,664/872,575/783	31112737	2866,10140	2203	4300	6503	SO:0001583	missense	54535	exon14			GCTGGCCCTGGCG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1723G>T	6.37:g.31112737C>A	ENSP00000365442:p.Gly575Cys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	26	0.742857	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	37	CCDS4695.1	329	0.15064102564102563	90	0.18292682926829268	51	0.1408839779005525	26	0.045454545454545456	162	0.21372031662269128	C	12.17	1.857747	0.32791	0.189514	0.236163	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000396263;ENST00000440185;ENST00000451521	T;T;T;T	0.10477	2.87;2.87;2.87;2.87	4.79	1.49	0.22878	.	0.872767	0.09696	N	0.767660	T	0.05502	0.0145	M	0.65975	2.015	0.36574	P	0.12684600000000001	B;B;B;B;B	0.25206	0.077;0.01;0.029;0.12;0.099	B;B;B;B;B	0.29663	0.064;0.015;0.041;0.105;0.064	T	0.24297	-1.0164	9	0.51188	T	0.08	-4.183	7.474	0.27365	0.0:0.6716:0.0:0.3284	rs130079;rs1265077;rs16898850;rs17840016;rs52811991;rs57918849;rs130079	575;575;575;628;664	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	C	664;575;522;575;628	ENSP00000379566:G664C;ENSP00000365442:G575C;ENSP00000379561:G522C;ENSP00000401039:G628C	ENSP00000365442:G575C	G	-	1	0	CCHCR1	31220716	1.000000	0.71417	0.998000	0.56505	0.804000	0.45430	1.297000	0.33400	0.446000	0.26666	0.448000	0.29417	GGC	C|0.801;A|0.199	0.199	strong		0.652	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
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 GAIIx	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	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	126	39	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	
MEIOB	254528	hgsc.bcm.edu	37	16	1912021	1912021	+	Missense_Mutation	SNP	T	T	G	rs1657125	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1912021T>G	ENST00000397344.3	-	4	418	c.224A>C	c.(223-225)aAg>aCg	p.K75T	MEIOB_ENST00000470044.1_5'UTR|MEIOB_ENST00000452149.2_Missense_Mutation_p.K75T|MEIOB_ENST00000412554.2_Missense_Mutation_p.K75T|MEIOB_ENST00000325962.3_Missense_Mutation_p.K75T	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	75			K -> T (in dbSNP:rs1657125).		double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										AGAAAGAGACTTGATGTAATC	0.393													T|||	837	0.167133	0.1657	0.0994	5008	,	,		18060	0.2421		0.1312	False		,,,				2504	0.1769				p.K75T		Atlas-SNP	.											C16orf73_ENST00000412554,caecum,carcinoma,0,1	.	.	1	0			c.A224C						scavenged	.	T	THR/LYS,THR/LYS	244,1140		25,194,473	169.0	150.0	155.0		224,224	1.4	0.9	16	dbSNP_89	155	405,2777		30,345,1216	yes	missense,missense	C16orf73	NM_001163560.2,NM_152764.2	78,78	55,539,1689	GG,GT,TT		12.7278,17.6301,14.2138	benign,benign	75/472,75/443	1912021	649,3917	692	1591	2283	SO:0001583	missense	254528	exon4			AGAGACTTGATGT	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.224A>C	16.37:g.1912021T>G	ENSP00000380504:p.Lys75Thr	Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_001163560	B1AK39|C9J0S1|Q96RY0	Missense_Mutation	SNP	ENST00000397344.3	37	CCDS10449.2	385	0.1762820512820513	95	0.19308943089430894	44	0.12154696132596685	151	0.263986013986014	95	0.12532981530343007	T	10.83	1.461584	0.26248	0.176301	0.127278	ENSG00000162039	ENST00000412554;ENST00000452149;ENST00000325962;ENST00000397344	T;T;T;T	0.16457	2.34;2.34;2.34;2.34	4.89	1.37	0.22104	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.298244	0.36409	N	0.002605	T	0.00012	0.0000	L	0.47716	1.5	0.48975	P	2.609999999999557E-4	B;B	0.18310	0.027;0.008	B;B	0.15052	0.012;0.012	T	0.43523	-0.9386	9	0.24483	T	0.36	.	8.4745	0.33005	0.0:0.5342:0.0:0.4658	rs1657125;rs52823192;rs60983146;rs1657125	75;75	C9J0S1;Q8N635	.;CP073_HUMAN	T	75	ENSP00000390778:K75T;ENSP00000391033:K75T;ENSP00000314484:K75T;ENSP00000380504:K75T	ENSP00000314484:K75T	K	-	2	0	C16orf73	1852022	0.934000	0.31675	0.913000	0.36048	0.982000	0.71751	0.450000	0.21762	0.091000	0.17302	0.528000	0.53228	AAG	T|0.820;G|0.180	0.180	strong		0.393	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
MOV10	4343	hgsc.bcm.edu	37	1	113243048	113243048	+	Silent	SNP	C	C	T	rs6679	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:113243048C>T	ENST00000413052.2	+	21	3321	c.2931C>T	c.(2929-2931)agC>agT	p.S977S	MOV10_ENST00000369645.1_Silent_p.S977S|RP11-426L16.10_ENST00000471038.2_5'Flank|MOV10_ENST00000357443.2_Silent_p.S977S|MOV10_ENST00000369644.1_Silent_p.S921S|MOV10_ENST00000468624.1_3'UTR	NM_001130079.1|NM_020963.3	NP_001123551.1|NP_066014.1	Q9HCE1	MOV10_HUMAN	Mov10 RISC complex RNA helicase	977					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mRNA cleavage involved in gene silencing by miRNA (GO:0035279)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(3)	38	Lung SC(450;0.246)	all_cancers(81;3.31e-11)|all_epithelial(167;5.69e-10)|all_lung(203;3.73e-05)|Breast(1374;0.000525)|Lung NSC(69;0.000954)|Ovarian(761;0.0367)|Lung SC(238;0.114)		OV - Ovarian serous cystadenocarcinoma(397;3.99e-67)|all cancers(265;1e-62)|Epithelial(280;4.78e-61)|Lung(183;0.0234)|Colorectal(144;0.0686)|READ - Rectum adenocarcinoma(129;0.0929)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)|BRCA - Breast invasive adenocarcinoma(282;0.24)		GGCCCCACAGCCATGACTACC	0.607													T|||	1422	0.283946	0.1702	0.2911	5008	,	,		18569	0.5407		0.2346	False		,,,				2504	0.2188				p.S977S		Atlas-SNP	.											.	MOV10	74	.	0			c.C2931T						PASS	.	T	,	822,3584	749.2+/-412.0	90,642,1471	85.0	88.0	87.0		2931,2931	-0.8	0.0	1	dbSNP_52	87	1769,6831	734.4+/-406.9	182,1405,2713	no	coding-synonymous,coding-synonymous	MOV10	NM_001130079.1,NM_020963.3	,	272,2047,4184	TT,TC,CC		20.5698,18.6564,19.9216	,	977/1004,977/1004	113243048	2591,10415	2203	4300	6503	SO:0001819	synonymous_variant	4343	exon21			CCACAGCCATGAC	AL833353	CCDS853.1, CCDS65615.1	1p13.2	2014-07-02	2014-07-02		ENSG00000155363	ENSG00000155363			7200	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 113"""	610742	"""Mov10 (Moloney leukemia virus 10, mouse) homolog"", ""Mov10, Moloney leukemia virus 10, homolog (mouse)"""			12226669	Standard	NM_001286072		Approved	gb110, MGC2948, fSAP113	uc001eck.3	Q9HCE1	OTTHUMG00000011906	ENST00000413052.2:c.2931C>T	1.37:g.113243048C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	153	80	0.522876	NM_020963	Q5JR03|Q8TEF0|Q9BSY3|Q9BUJ9	Silent	SNP	ENST00000413052.2	37	CCDS853.1																																																																																			C|0.753;T|0.247	0.247	strong		0.607	MOV10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032906.1	NM_020963	
HDAC10	83933	hgsc.bcm.edu	37	22	50684256	50684256	+	Splice_Site	SNP	T	T	C	rs75596977|rs11553696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50684256T>C	ENST00000216271.5	-	19	2186	c.1834A>G	c.(1834-1836)Aac>Gac	p.N612D	TUBGCP6_ENST00000248846.5_5'Flank|MAPK12_ENST00000497036.1_Intron|HDAC10_ENST00000448072.1_Splice_Site_p.N562D|TUBGCP6_ENST00000439308.2_5'Flank|HDAC10_ENST00000349505.4_Splice_Site_p.N592D|HDAC10_ENST00000498366.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	612					chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGTGTGGAGTTCTGGACCAGG	0.657													C|||	267	0.0533147	0.0424	0.0259	5008	,	,		17808	0.129		0.0099	False		,,,				2504	0.0542				p.N612D		Atlas-SNP	.											.	HDAC10	29	.	0			c.A1834G						PASS	.	C	ASP/ASN,ASP/ASN	129,4245		3,123,2061	30.0	24.0	26.0		1774,1834	5.0	1.0	22	dbSNP_131	26	81,8463		0,81,4191	yes	missense-near-splice,missense-near-splice	HDAC10	NM_001159286.1,NM_032019.5	23,23	3,204,6252	CC,CT,TT		0.948,2.9492,1.6256	benign,benign	592/650,612/670	50684256	210,12708	2187	4272	6459	SO:0001630	splice_region_variant	83933	exon19			TGGAGTTCTGGAC	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.1834-1A>G	22.37:g.50684256T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Missense_Mutation	SNP	ENST00000216271.5	37	CCDS14088.1	112	0.05128205128205128	16	0.032520325203252036	9	0.024861878453038673	78	0.13636363636363635	9	0.011873350923482849	C	5.699	0.313573	0.10789	0.029492	0.00948	ENSG00000100429	ENST00000216271;ENST00000448072;ENST00000349505	T;T;T	0.27557	1.66;1.66;1.66	5.03	5.03	0.67393	Histone deacetylase domain (1);	1.044170	0.07581	N	0.920373	T	0.00144	0.0004	N	0.08118	0	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.20874	-1.0262	10	0.51188	T	0.08	-1.502	7.2233	0.26002	0.0:0.7396:0.1703:0.0901	rs11553696	592;562;612	Q969S8-2;C9J8B8;Q969S8	.;.;HDA10_HUMAN	D	612;562;592	ENSP00000216271:N612D;ENSP00000397542:N562D;ENSP00000343540:N592D	ENSP00000216271:N612D	N	-	1	0	HDAC10	49026383	0.895000	0.30542	0.955000	0.39395	0.106000	0.19336	1.085000	0.30840	1.369000	0.46134	-0.355000	0.07637	AAC	T|0.966;C|0.034	0.034	strong		0.657	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	Missense_Mutation
PDS5B	23047	hgsc.bcm.edu	37	13	33232435	33232435	+	Silent	SNP	A	A	G	rs2301393	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:33232435A>G	ENST00000315596.10	+	4	558	c.372A>G	c.(370-372)caA>caG	p.Q124Q		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	124					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		AGAGCCCACAATTCAATAGGT	0.269													A|||	1359	0.271366	0.2337	0.3559	5008	,	,		14898	0.1389		0.4702	False		,,,				2504	0.1943				p.Q124Q		Atlas-SNP	.											.	PDS5B	141	.	0			c.A372G						PASS	.	A		973,2617		134,705,956	54.0	51.0	52.0		372	-1.5	1.0	13	dbSNP_100	52	3475,4649		756,1963,1343	no	coding-synonymous	PDS5B	NM_015032.3		890,2668,2299	GG,GA,AA		42.7745,27.1031,37.9717		124/1448	33232435	4448,7266	1795	4062	5857	SO:0001819	synonymous_variant	23047	exon4			CCCACAATTCAAT	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.372A>G	13.37:g.33232435A>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Silent	SNP	ENST00000315596.10	37	CCDS41878.1																																																																																			A|0.686;G|0.314	0.314	strong		0.269	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
SEMA5B	54437	hgsc.bcm.edu	37	3	122646734	122646734	+	Silent	SNP	C	C	T	rs2276775	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:122646734C>T	ENST00000357599.3	-	8	1139	c.753G>A	c.(751-753)acG>acA	p.T251T	SEMA5B_ENST00000451055.2_Silent_p.T305T|AC078794.1_ENST00000408284.1_RNA|SEMA5B_ENST00000195173.4_Silent_p.T251T	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	251	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		AGTCGATGACCGTGGCTGCAT	0.587													C|||	421	0.0840655	0.0726	0.1167	5008	,	,		18724	0.0575		0.0954	False		,,,				2504	0.092				p.T305T		Atlas-SNP	.											.	SEMA5B	303	.	0			c.G915A						PASS	.	C		324,4082	174.1+/-203.8	9,306,1888	87.0	82.0	84.0		753	-11.1	0.0	3	dbSNP_100	84	948,7652	209.0+/-250.3	54,840,3406	no	coding-synonymous	SEMA5B	NM_001031702.2		63,1146,5294	TT,TC,CC		11.0233,7.3536,9.7801		251/1152	122646734	1272,11734	2203	4300	6503	SO:0001819	synonymous_variant	54437	exon8			GATGACCGTGGCT	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.753G>A	3.37:g.122646734C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1																																																																																			C|0.906;T|0.094	0.094	strong		0.587	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
MTCH2	23788	hgsc.bcm.edu	37	11	47640429	47640429	+	Missense_Mutation	SNP	G	G	C	rs1064608	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:47640429G>C	ENST00000302503.3	-	13	1025	c.868C>G	c.(868-870)Ccc>Gcc	p.P290A	MTCH2_ENST00000542981.1_Missense_Mutation_p.P142A|MTCH2_ENST00000534074.1_5'UTR	NM_014342.3	NP_055157.1	Q9Y6C9	MTCH2_HUMAN	mitochondrial carrier 2	290			P -> A (in dbSNP:rs1064608).		protein localization to mitochondrion (GO:0070585)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)		p.P290A(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11						TTCCCAAAGGGGACCTTCCGG	0.408													G|||	1289	0.257388	0.0454	0.4035	5008	,	,		19522	0.2768		0.3539	False		,,,				2504	0.3211				p.P290A		Atlas-SNP	.											MTCH2,NS,carcinoma,0,1	MTCH2	25	1	1	Substitution - Missense(1)	stomach(1)	c.C868G						PASS	.	G	ALA/PRO	427,3975	207.2+/-228.6	28,371,1802	97.0	104.0	101.0		868	5.1	1.0	11	dbSNP_86	101	3023,5573	466.3+/-366.7	527,1969,1802	yes	missense	MTCH2	NM_014342.3	27	555,2340,3604	CC,CG,GG		35.1675,9.7001,26.5425	probably-damaging	290/304	47640429	3450,9548	2201	4298	6499	SO:0001583	missense	23788	exon13			CAAAGGGGACCTT	AF085361	CCDS7943.1	11p11.2	2013-05-22	2011-05-19		ENSG00000109919	ENSG00000109919		"""Solute carriers"""	17587	protein-coding gene	gene with protein product	"""solute carrier family 25, member 50"""	613221	"""mitochondrial carrier homolog 2 (C. elegans)"""				Standard	NM_014342		Approved	SLC25A50	uc010rho.2	Q9Y6C9	OTTHUMG00000166926	ENST00000302503.3:c.868C>G	11.37:g.47640429G>C	ENSP00000303222:p.Pro290Ala	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_014342	B2R7L8	Missense_Mutation	SNP	ENST00000302503.3	37	CCDS7943.1	618	0.28296703296703296	28	0.056910569105691054	131	0.36187845303867405	189	0.3304195804195804	270	0.3562005277044855	G	21.2	4.119413	0.77323	0.097001	0.351675	ENSG00000109919	ENST00000302503;ENST00000542981	D;T	0.81908	-1.55;-0.55	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.64567	1.98	0.21604	P	0.999620262	D	0.57571	0.98	P	0.60949	0.881	T	0.00003	-1.2590	9	0.66056	D	0.02	.	15.5263	0.75910	0.0:0.0:1.0:0.0	rs1064608;rs1064608	290	Q9Y6C9	MTCH2_HUMAN	A	290;142	ENSP00000303222:P290A;ENSP00000439013:P142A	ENSP00000303222:P290A	P	-	1	0	MTCH2	47597005	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.708000	0.74660	2.387000	0.81309	0.555000	0.69702	CCC	G|0.727;C|0.273	0.273	strong		0.408	MTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391921.2	NM_014342	
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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.M158L|SGK1_ENST00000367857.5_Missense_Mutation_p.M134L|SGK1_ENST00000475719.2_Intron|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367858.5_Missense_Mutation_p.M239L|SGK1_ENST00000528577.1_Missense_Mutation_p.M172L	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	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	20	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		
FMN2	56776	hgsc.bcm.edu	37	1	240370985	240370985	+	Missense_Mutation	SNP	C	C	T	rs111896385	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:240370985C>T	ENST00000319653.9	+	5	3103	c.2873C>T	c.(2872-2874)cCt>cTt	p.P958L		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	958	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CCTCCGCCCCCTCTTCCCGGG	0.692																																					p.P958L		Atlas-SNP	.											.	FMN2	451	.	0			c.C2873T						PASS	.						20.0	23.0	22.0					1																	240370985		2203	4296	6499	SO:0001583	missense	56776	exon5			CGCCCCCTCTTCC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2873C>T	1.37:g.240370985C>T	ENSP00000318884:p.Pro958Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	398	0.18223443223443223	65	0.13211382113821138	59	0.16298342541436464	125	0.21853146853146854	149	0.19656992084432717	C	10.82	1.457343	0.26161	.	.	ENSG00000155816	ENST00000319653	T	0.65549	-0.16	3.8	2.88	0.33553	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.00144	0.0004	M	0.89904	3.07	0.09310	P	1.0	D	0.60575	0.988	P	0.59056	0.851	T	0.09997	-1.0649	7	.	.	.	.	8.7103	0.34380	0.0:0.8893:0.0:0.1107	.	958	Q9NZ56	FMN2_HUMAN	L	958	ENSP00000318884:P958L	.	P	+	2	0	FMN2	238437608	0.002000	0.14202	0.036000	0.18154	0.002000	0.02628	1.177000	0.31969	0.978000	0.38470	-0.385000	0.06624	CCT	C|0.803;T|0.197	0.197	strong		0.692	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
HSPA8	3312	hgsc.bcm.edu	37	11	122928622	122928622	+	Silent	SNP	A	A	G	rs4802	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:122928622A>G	ENST00000532636.1	-	9	1880	c.1761T>C	c.(1759-1761)gcT>gcC	p.A587A	HSPA8_ENST00000453788.2_Intron|HSPA8_ENST00000227378.3_Silent_p.A587A|HSPA8_ENST00000534319.1_Silent_p.A351A|SNORD14D_ENST00000384390.1_RNA|SNORD14E_ENST00000364009.1_RNA|HSPA8_ENST00000526110.1_Silent_p.A568A|HSPA8_ENST00000534624.1_Silent_p.A587A|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000533540.1_Silent_p.A441A|HSPA8_ENST00000526862.1_5'Flank			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	587					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CTTCCTTCTCAGCAGTCTGAG	0.433													G|||	2165	0.432308	0.5703	0.3631	5008	,	,		20850	0.5506		0.2227	False		,,,				2504	0.3885				p.A587A	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.T1761C						PASS	.	G	,	2261,2143	572.6+/-383.4	576,1109,517	103.0	112.0	109.0		1761,	-6.5	0.9	11	dbSNP_52	109	2054,6544	717.9+/-406.2	255,1544,2500	no	coding-synonymous,intron	HSPA8	NM_006597.4,NM_153201.2	,	831,2653,3017	GG,GA,AA		23.8893,48.6603,33.1872	,	587/647,	122928622	4315,8687	2202	4299	6501	SO:0001819	synonymous_variant	3312	exon9			CTTCTCAGCAGTC	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.1761T>C	11.37:g.122928622A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_006597	Q9H3R6	Silent	SNP	ENST00000532636.1	37	CCDS8440.1																																																																																			A|0.653;G|0.347	0.347	strong		0.433	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
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 GAIIx	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	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	79	31	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 GAIIx	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_ENST00000557275.1_Missense_Mutation_p.L928F|SYNE3_ENST00000554873.1_Missense_Mutation_p.L690F	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	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	81	7	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	
ZNF423	23090	hgsc.bcm.edu	37	16	49671177	49671177	+	Missense_Mutation	SNP	T	T	C	rs34214571	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:49671177T>C	ENST00000561648.1	-	4	1939	c.1886A>G	c.(1885-1887)aAt>aGt	p.N629S	ZNF423_ENST00000562871.1_Missense_Mutation_p.N569S|ZNF423_ENST00000562520.1_Missense_Mutation_p.N569S|ZNF423_ENST00000535559.1_Missense_Mutation_p.N512S|ZNF423_ENST00000567169.1_Missense_Mutation_p.N512S|ZNF423_ENST00000262383.2_Missense_Mutation_p.N629S|ZNF423_ENST00000563137.2_Missense_Mutation_p.N569S	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	629			N -> S (in dbSNP:rs34214571).		cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				ATACTCCCCATTGGAGATGGA	0.577													T|||	111	0.0221645	0.0129	0.0144	5008	,	,		21834	0.0149		0.0398	False		,,,				2504	0.0297				p.N629S		Atlas-SNP	.											.	ZNF423	463	.	0			c.A1886G						PASS	.	T	SER/ASN	82,4314	70.3+/-108.2	0,82,2116	76.0	71.0	73.0		1886	4.8	1.0	16	dbSNP_126	73	275,8325	104.8+/-165.8	4,267,4029	yes	missense	ZNF423	NM_015069.2	46	4,349,6145	CC,CT,TT		3.1977,1.8653,2.747	benign	629/1285	49671177	357,12639	2198	4300	6498	SO:0001583	missense	23090	exon4			TCCCCATTGGAGA	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.1886A>G	16.37:g.49671177T>C	ENSP00000455426:p.Asn629Ser	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	48	0.02197802197802198	7	0.014227642276422764	5	0.013812154696132596	5	0.008741258741258742	31	0.040897097625329816	T	5.315	0.243536	0.10077	0.018653	0.031977	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.08720	3.06;3.11	4.78	4.78	0.61160	.	0.044527	0.85682	D	0.000000	T	0.01287	0.0042	N	0.19112	0.55	0.45403	D	0.998388	B	0.09022	0.002	B	0.09377	0.004	T	0.43458	-0.9390	9	.	.	.	.	14.3363	0.66592	0.0:0.0:0.0:1.0	rs34214571	629	Q2M1K9	ZN423_HUMAN	S	629;512	ENSP00000262383:N629S;ENSP00000442321:N512S	.	N	-	2	0	ZNF423	48228678	1.000000	0.71417	0.987000	0.45799	0.959000	0.62525	5.940000	0.70187	1.793000	0.52555	0.459000	0.35465	AAT	T|0.972;C|0.028	0.028	strong		0.577	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
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 GAIIx	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	Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	224	104	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	
MUC16	94025	hgsc.bcm.edu	37	19	9077581	9077581	+	Missense_Mutation	SNP	G	G	T	rs73011014	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9077581G>T	ENST00000397910.4	-	3	10068	c.9865C>A	c.(9865-9867)Cca>Aca	p.P3289T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3290	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GCCTCAGGTGGGGATGGGGAG	0.542													G|||	938	0.1873	0.0946	0.2536	5008	,	,		20999	0.3254		0.1322	False		,,,				2504	0.18				p.P3289T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C9865A						PASS	.	G	THR/PRO	392,3698		18,356,1671	101.0	103.0	102.0		9865	-0.8	0.0	19	dbSNP_130	102	1158,7206		72,1014,3096	yes	missense	MUC16	NM_024690.2	38	90,1370,4767	TT,TG,GG		13.8451,9.5844,12.4458	probably-damaging	3289/14508	9077581	1550,10904	2045	4182	6227	SO:0001583	missense	94025	exon3			CAGGTGGGGATGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.9865C>A	19.37:g.9077581G>T	ENSP00000381008:p.Pro3289Thr	Somatic	370	0	0		WXS	Illumina HiSeq	Phase_I	366	209	0.571038	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	439	0.20100732600732601	56	0.11382113821138211	80	0.22099447513812154	205	0.3583916083916084	98	0.12928759894459102	g	8.427	0.847619	0.17034	0.095844	0.138451	ENSG00000181143	ENST00000397910	T	0.03181	4.02	1.67	-0.84	0.10755	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.65815	0.995	P	0.55577	0.779	T	0.53056	-0.8492	8	0.87932	D	0	.	4.138	0.10179	0.4727:0.0:0.5273:0.0	.	3289	B5ME49	.	T	3289	ENSP00000381008:P3289T	ENSP00000381008:P3289T	P	-	1	0	MUC16	8938581	0.001000	0.12720	0.000000	0.03702	0.851000	0.48451	-0.230000	0.09083	-0.166000	0.10890	0.313000	0.20887	CCA	G|0.809;T|0.191	0.191	strong		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GNRH1	2796	hgsc.bcm.edu	37	8	25280800	25280800	+	Missense_Mutation	SNP	C	C	G	rs6185	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:25280800C>G	ENST00000276414.4	-	1	1370	c.47G>C	c.(46-48)tGg>tCg	p.W16S	RP11-395I14.2_ENST00000523840.1_lincRNA|GNRH1_ENST00000421054.2_Missense_Mutation_p.W16S	NM_000825.3	NP_000816.4	P01148	GON1_HUMAN	gonadotropin-releasing hormone 1 (luteinizing-releasing hormone)	16			W -> S (in dbSNP:rs6185). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:6090951}.		cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|ovulation cycle (GO:0042698)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|response to corticosteroid (GO:0031960)|response to ethanol (GO:0045471)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	gonadotropin hormone-releasing hormone activity (GO:0005183)|hormone activity (GO:0005179)			large_intestine(1)	1		all_cancers(63;0.0423)|Ovarian(32;0.000626)|all_epithelial(46;0.0186)|Hepatocellular(4;0.114)|Breast(100;0.14)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0201)|Epithelial(17;1.25e-12)|Colorectal(74;0.0113)|COAD - Colon adenocarcinoma(73;0.0385)		TTCCACGCACCAAGTCAGTAG	0.448													C|||	1123	0.224241	0.0552	0.1931	5008	,	,		17847	0.5476		0.2425	False		,,,				2504	0.1227				p.W20S		Atlas-SNP	.											.	GNRH1	8	.	0			c.G59C						PASS	.	C	SER/TRP,SER/TRP	348,3418		14,320,1549	79.0	78.0	78.0		47,47	2.9	0.0	8	dbSNP_52	78	2064,6144		272,1520,2312	yes	missense,missense	GNRH1	NM_000825.3,NM_001083111.1	177,177	286,1840,3861	GG,GC,CC		25.1462,9.2406,20.1436	benign,benign	16/93,16/93	25280800	2412,9562	1883	4104	5987	SO:0001583	missense	2796	exon1			ACGCACCAAGTCA	X01059	CCDS43725.1	8p21-p11.2	2013-02-26	2004-10-13		ENSG00000147437	ENSG00000147437		"""Endogenous ligands"""	4419	protein-coding gene	gene with protein product		152760	"""gonadotropin-releasing hormone 1 (leutinizing-releasing hormone)"""	GRH, GNRH, LHRH		6090951	Standard	NM_000825		Approved		uc003xem.4	P01148	OTTHUMG00000163852	ENST00000276414.4:c.47G>C	8.37:g.25280800C>G	ENSP00000276414:p.Trp16Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_000825	A0AVP0	Missense_Mutation	SNP	ENST00000276414.4	37	CCDS43725.1	593	0.2715201465201465	20	0.04065040650406504	80	0.22099447513812154	307	0.5367132867132867	186	0.24538258575197888	C	6.004	0.369183	0.11352	0.092406	0.251462	ENSG00000147437	ENST00000421054;ENST00000276414	T;T	0.40476	1.03;1.03	5.29	2.9	0.33743	.	1.973800	0.02558	N	0.096387	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.46261	-0.9204	8	0.51188	T	0.08	-0.0022	4.5292	0.11997	0.6642:0.1675:0.1683:0.0	rs6185;rs3191535;rs6185	16	P01148	GON1_HUMAN	S	16	ENSP00000391280:W16S;ENSP00000276414:W16S	ENSP00000276414:W16S	W	-	2	0	GNRH1	25336717	0.022000	0.18835	0.000000	0.03702	0.000000	0.00434	3.083000	0.50136	0.457000	0.26962	-1.092000	0.02172	TGG	C|0.738;G|0.262	0.262	strong		0.448	GNRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375982.1	NM_001083111	
QRICH2	84074	hgsc.bcm.edu	37	17	74287204	74287204	+	Missense_Mutation	SNP	C	C	G	rs2279052	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74287204C>G	ENST00000262765.5	-	4	3285	c.3106G>C	c.(3106-3108)Gag>Cag	p.E1036Q		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	1036			E -> Q (in dbSNP:rs2279052). {ECO:0000269|PubMed:14702039}.							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						CTACTGAGCTCTCCCATCAGA	0.532													C|||	2082	0.415735	0.5113	0.2939	5008	,	,		19627	0.5734		0.2753	False		,,,				2504	0.3548				p.E1036Q		Atlas-SNP	.											.	QRICH2	143	.	0			c.G3106C						PASS	.	C	GLN/GLU	2167,2239	585.7+/-386.3	531,1105,567	115.0	112.0	113.0		3106	5.5	0.3	17	dbSNP_100	113	2475,6125	406.0+/-348.7	346,1783,2171	yes	missense	QRICH2	NM_032134.1	29	877,2888,2738	GG,GC,CC		28.7791,49.1829,35.6912	probably-damaging	1036/1664	74287204	4642,8364	2203	4300	6503	SO:0001583	missense	84074	exon4			TGAGCTCTCCCAT	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.3106G>C	17.37:g.74287204C>G	ENSP00000262765:p.Glu1036Gln	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	895	0.4097985347985348	265	0.5386178861788617	101	0.27900552486187846	333	0.5821678321678322	196	0.25857519788918204	C	11.06	1.528788	0.27387	0.491829	0.287791	ENSG00000129646	ENST00000262765;ENST00000447564;ENST00000301613	T;T	0.53857	2.7;0.6	5.54	5.54	0.83059	.	.	.	.	.	T	0.00012	0.0000	N	0.20986	0.625	0.37391	P	0.08755999999999997	D;P	0.55605	0.972;0.938	D;P	0.65140	0.932;0.636	T	0.49322	-0.8952	8	0.45353	T	0.12	-19.3391	14.9968	0.71439	0.0:1.0:0.0:0.0	rs2279052;rs52800512;rs2279052	1036;1036	B5MD94;Q9H0J4	.;QRIC2_HUMAN	Q	1036;44;1036	ENSP00000262765:E1036Q;ENSP00000394461:E44Q	ENSP00000262765:E1036Q	E	-	1	0	QRICH2	71798799	0.976000	0.34144	0.280000	0.24747	0.101000	0.19017	3.799000	0.55529	2.610000	0.88304	0.555000	0.69702	GAG	C|0.613;G|0.387	0.387	strong		0.532	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
C14orf105	55195	hgsc.bcm.edu	37	14	57947421	57947421	+	Nonsense_Mutation	SNP	G	G	A	rs34960436	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:57947421G>A	ENST00000216445.3	-	5	683	c.547C>T	c.(547-549)Caa>Taa	p.Q183*	C14orf105_ENST00000422976.2_Nonsense_Mutation_p.Q182*|C14orf105_ENST00000534126.1_Nonsense_Mutation_p.Q182*	NM_001283057.1|NM_018168.2	NP_001269986.1|NP_060638.2	Q9NVL8	CN105_HUMAN	chromosome 14 open reading frame 105	183										breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)	11						CTTGGACTTTGCTTATTAATT	0.398													G|||	69	0.013778	0.0015	0.0187	5008	,	,		19260	0.0		0.0278	False		,,,				2504	0.0266				p.Q183X		Atlas-SNP	.											.	C14orf105	26	.	0			c.C547T						PASS	.	G	stop/GLN	30,4376	36.8+/-68.6	0,30,2173	240.0	231.0	234.0		547	4.9	0.8	14	dbSNP_126	234	303,8297	109.8+/-170.3	6,291,4003	yes	stop-gained	C14orf105	NM_018168.2		6,321,6176	AA,AG,GG		3.5233,0.6809,2.5604		183/297	57947421	333,12673	2203	4300	6503	SO:0001587	stop_gained	55195	exon5			GACTTTGCTTATT	AK001512	CCDS9730.1, CCDS61458.1, CCDS61459.1	14q22.2	2012-09-25			ENSG00000100557	ENSG00000100557			20189	protein-coding gene	gene with protein product							Standard	XM_005267806		Approved	FLJ10650	uc001xcy.2	Q9NVL8	OTTHUMG00000140317	ENST00000216445.3:c.547C>T	14.37:g.57947421G>A	ENSP00000216445:p.Gln183*	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_018168	Q53G04	Nonsense_Mutation	SNP	ENST00000216445.3	37	CCDS9730.1	36	0.016483516483516484	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	23	0.030343007915567283	G	11.47	1.649670	0.29336	0.006809	0.035233	ENSG00000100557	ENST00000216445;ENST00000422976;ENST00000534126	.	.	.	5.83	4.94	0.65067	.	0.106098	0.41712	D	0.000833	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-9.2538	12.9909	0.58618	0.0:0.1621:0.8379:0.0	rs34960436	.	.	.	X	183;182;182	.	ENSP00000216445:Q183X	Q	-	1	0	C14orf105	57017174	0.995000	0.38212	0.822000	0.32727	0.102000	0.19082	2.422000	0.44696	1.450000	0.47717	0.650000	0.86243	CAA	G|0.976;A|0.024	0.024	strong		0.398	C14orf105-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276921.2	NM_018168	
ADCY9	115	hgsc.bcm.edu	37	16	4164337	4164337	+	Silent	SNP	C	C	T	rs887248	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4164337C>T	ENST00000294016.3	-	2	1645	c.1107G>A	c.(1105-1107)agG>agA	p.R369R		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	369					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ACTTTTTCTTCCTGTTCTTGG	0.463													C|||	97	0.019369	0.0023	0.0274	5008	,	,		21885	0.0		0.0616	False		,,,				2504	0.0133				p.R369R		Atlas-SNP	.											.	ADCY9	151	.	0			c.G1107A						PASS	.	C		55,4339	55.5+/-91.7	0,55,2142	146.0	141.0	143.0		1107	4.6	1.0	16	dbSNP_86	143	554,8046	151.9+/-206.6	14,526,3760	no	coding-synonymous	ADCY9	NM_001116.3		14,581,5902	TT,TC,CC		6.4419,1.2517,4.6868		369/1354	4164337	609,12385	2197	4300	6497	SO:0001819	synonymous_variant	115	exon2			TTTCTTCCTGTTC	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.1107G>A	16.37:g.4164337C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																			C|0.956;T|0.044	0.044	strong		0.463	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
EMILIN3	90187	hgsc.bcm.edu	37	20	39990700	39990700	+	Silent	SNP	T	T	C	rs41278104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:39990700T>C	ENST00000332312.3	-	4	1701	c.1509A>G	c.(1507-1509)gtA>gtG	p.V503V		NM_052846.1	NP_443078.1	Q9NT22	EMIL3_HUMAN	elastin microfibril interfacer 3	503						cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)				biliary_tract(1)|endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(3)|urinary_tract(2)	30		Myeloproliferative disorder(115;0.00425)				GCTCTGTCTGTACAAGGGGCC	0.632													C|||	764	0.152556	0.3132	0.147	5008	,	,		17537	0.003		0.1799	False		,,,				2504	0.0654				p.V503V		Atlas-SNP	.											.	EMILIN3	63	.	0			c.A1509G						PASS	.	C		1392,3014	683.9+/-404.3	220,952,1031	70.0	65.0	66.0		1509	4.2	0.9	20	dbSNP_127	66	1492,7108	746.0+/-407.3	141,1210,2949	no	coding-synonymous	EMILIN3	NM_052846.1		361,2162,3980	CC,CT,TT		17.3488,31.5933,22.1744		503/767	39990700	2884,10122	2203	4300	6503	SO:0001819	synonymous_variant	90187	exon4			TGTCTGTACAAGG	AL031667	CCDS13316.1	20q12	2005-11-06	2004-03-02	2004-03-02	ENSG00000183798	ENSG00000183798		"""EMI domain containing"""	16123	protein-coding gene	gene with protein product	"""chromosome 20 open reading frame 130"""	608929	"""elastin microfibril interfacer 5"""	C20orf130, EMILIN5		12221002	Standard	NM_052846		Approved	dJ620E11.4	uc002xjy.1	Q9NT22	OTTHUMG00000046304	ENST00000332312.3:c.1509A>G	20.37:g.39990700T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_052846	Q495S5|Q495S6|Q495S7|Q76KT4	Silent	SNP	ENST00000332312.3	37	CCDS13316.1																																																																																			T|0.802;C|0.198	0.198	strong		0.632	EMILIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106876.2	XM_029741	
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 GAIIx	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	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	145	76	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		
KRT16	3868	hgsc.bcm.edu	37	17	39767744	39767744	+	Silent	SNP	A	A	G	rs4796681	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39767744A>G	ENST00000301653.4	-	3	688	c.624T>C	c.(622-624)caT>caC	p.H208H		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	208	Coil 1B.|Rod.			HELA -> ARTG (in Ref. 1; AAA59460). {ECO:0000305}.	aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				GGGCCAGTTCATGCTCATACC	0.652													g|||	3877	0.774161	0.7239	0.7608	5008	,	,		19211	1.0		0.6123	False		,,,				2504	0.7853				p.H208H		Atlas-SNP	.											.	KRT16	45	.	0			c.T624C						PASS	.	G		3132,1274	431.0+/-342.8	1112,908,183	44.0	45.0	44.0		624	-3.8	0.9	17	dbSNP_111	44	5040,3560	506.6+/-376.6	1474,2092,734	no	coding-synonymous	KRT16	NM_005557.3		2586,3000,917	GG,GA,AA		41.3953,28.9151,37.1675		208/474	39767744	8172,4834	2203	4300	6503	SO:0001819	synonymous_variant	3868	exon3			CAGTTCATGCTCA	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6423	protein-coding gene	gene with protein product	"""focal non-epidermolytic palmoplantar keratoderma"""	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.624T>C	17.37:g.39767744A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Silent	SNP	ENST00000301653.4	37	CCDS11401.1																																																																																			A|0.328;G|0.672	0.672	strong		0.652	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
MYADML2	255275	hgsc.bcm.edu	37	17	79898933	79898933	+	Missense_Mutation	SNP	G	G	A	rs62077244	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79898933G>A	ENST00000409745.2	-	3	1039	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	AC137723.5_ENST00000415556.1_RNA|MYADML2_ENST00000330655.3_Missense_Mutation_p.R229W	NM_001145113.2	NP_001138585.2	A6NDP7	MADL2_HUMAN	myeloid-associated differentiation marker-like 2	229	MARVEL 2. {ECO:0000255|PROSITE- ProRule:PRU00581}.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(1)	1						ACCACCAGCCGGTCAAAGGGG	0.642													G|||	112	0.0223642	0.0	0.013	5008	,	,		17755	0.001		0.0447	False		,,,				2504	0.0583				p.R229W		Atlas-SNP	.											.	MYADML2	11	.	0			c.C685T						PASS	.	G	TRP/ARG	9,1375		0,9,683	20.0	30.0	27.0		685	4.7	1.0	17	dbSNP_129	27	146,3034		2,142,1446	yes	missense	MYADML2	NM_001145113.2	101	2,151,2129	AA,AG,GG		4.5912,0.6503,3.3961	probably-damaging	229/308	79898933	155,4409	692	1590	2282	SO:0001583	missense	255275	exon3			CCAGCCGGTCAAA	AC137723, BC029306	CCDS45815.1	17q25.3	2008-10-15			ENSG00000185105	ENSG00000185105			34548	protein-coding gene	gene with protein product							Standard	NM_001145113		Approved	LOC255275	uc010wvf.1	A6NDP7	OTTHUMG00000154388	ENST00000409745.2:c.685C>T	17.37:g.79898933G>A	ENSP00000386702:p.Arg229Trp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	77	43	0.558442	NM_001145113		Missense_Mutation	SNP	ENST00000409745.2	37	CCDS45815.1	41	0.018772893772893772	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	34	0.044854881266490766	G	18.24	3.581336	0.65992	0.006503	0.045912	ENSG00000185105	ENST00000409745;ENST00000330655	T;T	0.24908	1.83;1.83	4.67	4.67	0.58626	Marvel (1);MARVEL-like domain (1);	.	.	.	.	T	0.12178	0.0296	M	0.75264	2.295	0.42835	D	0.994037	D	0.71674	0.998	P	0.59643	0.861	T	0.06215	-1.0839	9	0.35671	T	0.21	0.0843	17.7395	0.88404	0.0:0.0:1.0:0.0	rs62077244	229	A6NDP7	MADL2_HUMAN	W	229	ENSP00000386702:R229W;ENSP00000327718:R229W	ENSP00000327718:R229W	R	-	1	2	MYADML2	77492224	1.000000	0.71417	0.988000	0.46212	0.774000	0.43823	5.164000	0.64954	2.431000	0.82371	0.462000	0.41574	CGG	G|0.981;A|0.019	0.019	strong		0.642	MYADML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335008.2	XR_041347	
KIAA1328	57536	hgsc.bcm.edu	37	18	34647323	34647323	+	Silent	SNP	T	T	A	rs3747896	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:34647323T>A	ENST00000280020.5	+	7	1069	c.1047T>A	c.(1045-1047)ggT>ggA	p.G349G	KIAA1328_ENST00000591619.1_Silent_p.G345G|KIAA1328_ENST00000435985.2_Silent_p.G65G|KIAA1328_ENST00000543923.1_Silent_p.G241G|KIAA1328_ENST00000586135.1_Silent_p.G65G|KIAA1328_ENST00000586501.1_Silent_p.G65G	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	349										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		TGCATGGTGGTGGGGCACTGC	0.448													A|||	1299	0.259385	0.6445	0.1311	5008	,	,		19160	0.1101		0.1292	False		,,,				2504	0.1176				p.G349G		Atlas-SNP	.											.	KIAA1328	39	.	0			c.T1047A						PASS	.	A		2353,1669		730,893,388	72.0	69.0	70.0		1047	-0.9	0.0	18	dbSNP_107	70	1345,7043		269,807,3118	no	coding-synonymous	KIAA1328	NM_020776.1		999,1700,3506	AA,AT,TT		16.0348,41.4968,29.7985		349/578	34647323	3698,8712	2011	4194	6205	SO:0001819	synonymous_variant	57536	exon7			TGGTGGTGGGGCA	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.1047T>A	18.37:g.34647323T>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_020776	Q05DL0|Q49AG6|Q9P2L8	Silent	SNP	ENST00000280020.5	37	CCDS45855.1																																																																																			A|0.237;G|0.031;T|0.732	0.237	strong		0.448	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776	
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 GAIIx	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_ENST00000435849.3_Missense_Mutation_p.R176H|ZFYVE20_ENST00000449964.2_5'UTR|ZFYVE20_ENST00000476527.2_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	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	123	58	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	
NCR2	9436	hgsc.bcm.edu	37	6	41309552	41309552	+	Missense_Mutation	SNP	T	T	C	rs2236369	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41309552T>C	ENST00000373089.5	+	3	503	c.415T>C	c.(415-417)Tcc>Ccc	p.S139P	NCR2_ENST00000373083.4_Missense_Mutation_p.S139P|NCR2_ENST00000373086.3_Missense_Mutation_p.S139P	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	139			S -> P (in dbSNP:rs2236369). {ECO:0000269|PubMed:10049942, ECO:0000269|Ref.2}.		cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					CACACAGACCTCCTGGACTCC	0.622													T|||	2452	0.489617	0.1846	0.6787	5008	,	,		17573	0.5764		0.5885	False		,,,				2504	0.5767				p.S139P		Atlas-SNP	.											NCR2,colon,carcinoma,0,1	NCR2	44	1	0			c.T415C						scavenged	.	T	PRO/SER,PRO/SER,PRO/SER	1075,3331	387.0+/-326.3	130,815,1258	80.0	76.0	77.0		415,415,415	-1.5	0.2	6	dbSNP_98	77	5106,3494	631.1+/-398.4	1562,1982,756	yes	missense,missense,missense	NCR2	NM_001199509.1,NM_001199510.1,NM_004828.3	74,74,74	1692,2797,2014	CC,CT,TT		40.6279,24.3985,47.5242	benign,benign,benign	139/271,139/259,139/277	41309552	6181,6825	2203	4300	6503	SO:0001583	missense	9436	exon3			CAGACCTCCTGGA	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	6732	protein-coding gene	gene with protein product		604531	"""lymphocyte antigen 95 (activating NK-receptor; NK-p44)"""	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.415T>C	6.37:g.41309552T>C	ENSP00000362181:p.Ser139Pro	Somatic	49	2	0.0408163		WXS	Illumina HiSeq	Phase_I	55	50	0.909091	NM_004828	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Missense_Mutation	SNP	ENST00000373089.5	37	CCDS4855.1	1108	0.5073260073260073	118	0.23983739837398374	240	0.6629834254143646	308	0.5384615384615384	442	0.58311345646438	T	6.341	0.431064	0.12045	0.243985	0.593721	ENSG00000096264	ENST00000373083;ENST00000373089;ENST00000373086	T;T;T	0.14766	2.53;2.7;2.48	1.69	-1.52	0.08637	.	.	.	.	.	T	0.01592	0.0051	N	0.14661	0.345	0.80722	P	0.0	B;B;P	0.35363	0.396;0.34;0.497	B;B;B	0.34242	0.178;0.093;0.062	T	0.43621	-0.9380	8	0.20046	T	0.44	.	2.3519	0.04286	0.443:0.2713:0.0:0.2858	rs2236369;rs61406687;rs2236369	139;139;139	O95944-3;O95944-2;O95944	.;.;NCTR2_HUMAN	P	139	ENSP00000362175:S139P;ENSP00000362181:S139P;ENSP00000362178:S139P	ENSP00000362175:S139P	S	+	1	0	NCR2	41417530	0.005000	0.15991	0.214000	0.23707	0.212000	0.24457	-0.192000	0.09587	-0.289000	0.09038	-0.878000	0.02970	TCC	A|0.004;C|0.466	0.466	strong		0.622	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3		
PKD1	5310	hgsc.bcm.edu	37	16	2167594	2167594	+	Silent	SNP	C	C	T	rs141553109	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:2167594C>T	ENST00000262304.4	-	6	1489	c.1281G>A	c.(1279-1281)gcG>gcA	p.A427A	PKD1_ENST00000423118.1_Silent_p.A427A|RP11-304L19.2_ENST00000562027.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	427	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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						GCAGCCAGGCCGCCTTCTCCA	0.706													c|||	2	0.000399361	0.0	0.0	5008	,	,		17548	0.0		0.002	False		,,,				2504	0.0				p.A427A		Atlas-SNP	.											.	PKD1	184	.	0			c.G1281A						PASS	.	C	,	1,4309		0,1,2154	11.0	13.0	12.0		1281,1281	-10.1	0.2	16	dbSNP_134	12	10,8484		0,10,4237	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	0,11,6391	TT,TC,CC		0.1177,0.0232,0.0859	,	427/4303,427/4304	2167594	11,12793	2155	4247	6402	SO:0001819	synonymous_variant	5310	exon6			CCAGGCCGCCTTC	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.1281G>A	16.37:g.2167594C>T		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	189	99	0.52381	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			C|0.999;T|0.001	0.001	strong		0.706	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
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 GAIIx	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		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	14	5	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
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549563	32549563	+	Silent	SNP	G	G	A	rs77689370	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32549563G>A	ENST00000360004.5	-	3	528	c.423C>T	c.(421-423)caC>caT	p.H141H		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	141	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CCAGGAGGTTGTGGTGCTGCA	0.517										Multiple Myeloma(14;0.17)																											p.H141H		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C423T						PASS	.						92.0	112.0	105.0					6																	32549563		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon3			GAGGTTGTGGTGC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.423C>T	6.37:g.32549563G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	132	72	0.545455	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			A|0.051;C|0.002;G|0.947	0.051	strong		0.517	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ASB1	51665	hgsc.bcm.edu	37	2	239353001	239353001	+	Silent	SNP	C	C	T	rs2290075	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:239353001C>T	ENST00000264607.4	+	4	760	c.513C>T	c.(511-513)gaC>gaT	p.D171D	ASB1_ENST00000409297.1_Silent_p.D70D	NM_001040445.1	NP_001035535.1	Q9Y576	ASB1_HUMAN	ankyrin repeat and SOCS box containing 1	171					intracellular signal transduction (GO:0035556)|male genitalia development (GO:0030539)|negative regulation of cytokine biosynthetic process (GO:0042036)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				breast(1)|kidney(1)|large_intestine(3)|lung(2)|skin(1)	8		all_epithelial(40;2.65e-14)|Breast(86;7.61e-05)|Renal(207;0.00183)|all_lung(227;0.0283)|Ovarian(221;0.0365)|Lung NSC(271;0.0941)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)		CTGATGTTGACGTCAACCACC	0.582													C|||	425	0.0848642	0.1505	0.0173	5008	,	,		18357	0.0794		0.0417	False		,,,				2504	0.0941				p.D171D		Atlas-SNP	.											.	ASB1	25	.	0			c.C513T						PASS	.	C		599,3807	246.2+/-254.9	33,533,1637	61.0	49.0	53.0		513	-5.1	0.7	2	dbSNP_100	53	214,8386	84.5+/-147.0	1,212,4087	no	coding-synonymous	ASB1	NM_001040445.1		34,745,5724	TT,TC,CC		2.4884,13.5951,6.251		171/336	239353001	813,12193	2203	4300	6503	SO:0001819	synonymous_variant	51665	exon4			TGTTGACGTCAAC	AF156777	CCDS33416.1	2q37	2013-01-10	2011-01-25		ENSG00000065802	ENSG00000065802		"""Ankyrin repeat domain containing"""	16011	protein-coding gene	gene with protein product		605758	"""ankyrin repeat and SOCS box-containing 1"""				Standard	XR_241235		Approved	ASB-1	uc002vyg.3	Q9Y576	OTTHUMG00000152866	ENST00000264607.4:c.513C>T	2.37:g.239353001C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001040445	A6NL50|Q4ZG29|Q9ULS4	Silent	SNP	ENST00000264607.4	37	CCDS33416.1																																																																																			C|0.937;T|0.063	0.063	strong		0.582	ASB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328294.1	NM_001040445	
LILRB3	11025	hgsc.bcm.edu	37	19	54725980	54725980	+	Silent	SNP	G	G	A	rs150024950	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54725980G>A	ENST00000391750.1	-	5	514	c.378C>T	c.(376-378)ctC>ctT	p.L126L	LILRB3_ENST00000407860.2_Silent_p.L126L|LILRA6_ENST00000440558.2_Intron|LILRA6_ENST00000391735.3_Intron|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000245620.9_Silent_p.L126L|LILRA6_ENST00000270464.5_Intron|LILRB3_ENST00000346401.6_Silent_p.L126L|LILRB3_ENST00000424807.1_Silent_p.L126L|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000419410.2_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	126	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.L126L(1)		endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCAGGGCTGAGAGGGTGGGTT	0.582													.|||	570	0.113818	0.0507	0.1037	5008	,	,		13484	0.0486		0.1471	False		,,,				2504	0.2393				p.L126L		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	1	Substitution - coding silent(1)	kidney(1)	c.C378T						scavenged	.						55.0	36.0	42.0					19																	54725980		2117	3871	5988	SO:0001819	synonymous_variant	11025	exon4			GGCTGAGAGGGTG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.378C>T	19.37:g.54725980G>A		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	95	7	0.0736842	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Silent	SNP	ENST00000391750.1	37	CCDS33105.1																																																																																			G|0.947;A|0.053	0.053	strong		0.582	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086718	46086718	+	Missense_Mutation	SNP	G	G	C	rs7275281|rs368303093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46086718G>C	ENST00000360770.3	-	1	126	c.86C>G	c.(85-87)tCc>tGc	p.S29C	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	29	23 X 5 AA approximate repeats.		S -> C (in dbSNP:rs7275281).|S -> P (in dbSNP:rs7276859).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						TGCCTGGCAGGAGCTGGGCAC	0.677													G|||	3070	0.613019	0.7262	0.5807	5008	,	,		16465	0.5675		0.5547	False		,,,				2504	0.59				p.S29C		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.C86G						PASS	.	G	CYS/SER,	1259,3073		510,239,1417	35.0	42.0	39.0		86,	-2.7	0.0	21	dbSNP_116	39	1526,6972		615,296,3338	no	missense,intron	TSPEAR,KRTAP12-2	NM_181684.2,NM_144991.2	112,	1125,535,4755	CC,CG,GG		17.9572,29.0628,21.7069	probably-damaging,	29/147,	46086718	2785,10045	2166	4249	6415	SO:0001583	missense	353323	exon1			TGGCAGGAGCTGG	AJ566389	CCDS42965.1	21q22.3	2006-03-13			ENSG00000221864	ENSG00000221864		"""Keratin associated proteins"""	20530	protein-coding gene	gene with protein product							Standard	NM_181684		Approved	KRTAP12.2, KAP12.2	uc002zfu.3	P59991	OTTHUMG00000057636	ENST00000360770.3:c.86C>G	21.37:g.46086718G>C	ENSP00000354001:p.Ser29Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	21	0.291667	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	1165	0.5334249084249084	318	0.6463414634146342	199	0.5497237569060773	279	0.48776223776223776	369	0.4868073878627968	g	6.477	0.456248	0.12283	0.290628	0.179572	ENSG00000221864	ENST00000360770	T	0.03035	4.07	3.4	-2.73	0.05950	.	.	.	.	.	T	0.00012	0.0000	N	0.01761	-0.735	0.80722	P	0.0	D	0.58620	0.983	P	0.51297	0.665	T	0.36237	-0.9756	8	0.19147	T	0.46	.	3.0179	0.06066	0.0978:0.415:0.2069:0.2803	rs7275281	29	P59991	KR122_HUMAN	C	29	ENSP00000354001:S29C	ENSP00000354001:S29C	S	-	2	0	KRTAP12-2	44911146	0.004000	0.15560	0.000000	0.03702	0.019000	0.09904	-0.386000	0.07370	-1.078000	0.03117	0.462000	0.41574	TCC	.	.	alt		0.677	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
ANKRD50	57182	hgsc.bcm.edu	37	4	125592188	125592188	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:125592188G>T	ENST00000504087.1	-	4	3281	c.2244C>A	c.(2242-2244)ggC>ggA	p.G748G	ANKRD50_ENST00000515641.1_Silent_p.G569G	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	748										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						GTGGAGTCATGCCATCTTTAT	0.463																																					p.G748G		Atlas-SNP	.											ANKRD50,NS,carcinoma,-1,1	ANKRD50	136	1	0			c.C2244A						scavenged	.						133.0	116.0	122.0					4																	125592188		2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			AGTCATGCCATCT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.2244C>A	4.37:g.125592188G>T		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	115	2	0.0173913	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			.	.	none		0.463	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
SREK1	140890	hgsc.bcm.edu	37	5	65455141	65455141	+	Silent	SNP	G	G	A	rs72770236	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:65455141G>A	ENST00000380918.3	+	4	702	c.42G>A	c.(40-42)ccG>ccA	p.P14P	SREK1_ENST00000284041.3_3'UTR|SREK1_ENST00000334121.6_Silent_p.P130P	NM_139168.3	NP_631907.1	Q8WXA9	SREK1_HUMAN	splicing regulatory glutamine/lysine-rich protein 1	14					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(3)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)	9						TTCCAATACCGACCCCAAATC	0.443													G|||	20	0.00399361	0.0	0.0043	5008	,	,		14096	0.0		0.0129	False		,,,				2504	0.0041				p.P130P	GBM(10;31 347 27684 38976 41583)	Atlas-SNP	.											SREK1_ENST00000334121,NS,carcinoma,0,4	SREK1	58	4	0			c.G390A						PASS	.	G	,	19,4387	26.2+/-53.5	0,19,2184	89.0	83.0	85.0		390,42	-10.1	0.8	5	dbSNP_130	85	122,8478	64.2+/-126.4	0,122,4178	no	coding-synonymous,coding-synonymous	SREK1	NM_001077199.1,NM_139168.2	,	0,141,6362	AA,AG,GG		1.4186,0.4312,1.0841	,	130/625,14/509	65455141	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	140890	exon3			AATACCGACCCCA	AF459094	CCDS3991.1, CCDS43323.1, CCDS75253.1	5q11.2-q12.1	2013-02-12	2010-09-08	2010-09-08	ENSG00000153914	ENSG00000153914		"""RNA binding motif (RRM) containing"""	17882	protein-coding gene	gene with protein product	"""serine-arginine-rich splicing regulatory protein 508"""	609268	"""splicing factor, arginine/serine-rich 12"""	SFRS12		12043562	Standard	NM_001077199		Approved	DKFZp564B176, SRrp86, SRrp508	uc003jun.4	Q8WXA9	OTTHUMG00000097809	ENST00000380918.3:c.42G>A	5.37:g.65455141G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_001077199	A4FTW3|Q2M1J0|Q86X37	Silent	SNP	ENST00000380918.3	37	CCDS3991.1																																																																																			G|0.990;A|0.010	0.010	strong		0.443	SREK1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381118.1	NM_001077199	
CIITA	4261	hgsc.bcm.edu	37	16	11001694	11001694	+	Missense_Mutation	SNP	T	T	C	rs13336804	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11001694T>C	ENST00000324288.8	+	11	2478	c.2345T>C	c.(2344-2346)gTg>gCg	p.V782A	CIITA_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	782			V -> A (in dbSNP:rs13336804).		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						GCTGCCTCGGTGGACAGGAAG	0.697			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								C|||	200	0.0399361	0.0356	0.0389	5008	,	,		12514	0.0		0.0944	False		,,,				2504	0.0317				p.V782A		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	CIITA	92	.	0			c.T2345C						PASS	.	C	ALA/VAL	159,4213		2,155,2029	24.0	31.0	29.0		2345	-6.0	0.0	16	dbSNP_121	29	717,7867		29,659,3604	yes	missense	CIITA	NM_000246.3	64	31,814,5633	CC,CT,TT		8.3527,3.6368,6.7613	benign	782/1131	11001694	876,12080	2186	4292	6478	SO:0001583	missense	4261	exon11			CCTCGGTGGACAG	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.2345T>C	16.37:g.11001694T>C	ENSP00000316328:p.Val782Ala	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	111	0.050824175824175824	26	0.052845528455284556	14	0.03867403314917127	0	0.0	71	0.09366754617414248	C	0.351	-0.944799	0.02304	0.036368	0.083527	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.74526	-0.85	5.15	-6.02	0.02192	.	0.859684	0.10008	N	0.727522	T	0.01222	0.0040	N	0.00419	-1.52	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.0;0.002;0.001	T	0.24154	-1.0168	9	0.07325	T	0.83	.	9.9208	0.41464	0.0:0.3104:0.0968:0.5928	rs13336804	782;782;734;782	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	A	782;734	ENSP00000316328:V782A	ENSP00000316328:V782A	V	+	2	0	CIITA	10909195	0.993000	0.37304	0.000000	0.03702	0.000000	0.00434	0.406000	0.21032	-1.438000	0.01965	-0.726000	0.03593	GTG	T|0.935;C|0.065	0.065	strong		0.697	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
SULT1C2	6819	hgsc.bcm.edu	37	2	108922036	108922036	+	Missense_Mutation	SNP	T	T	G	rs17036104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:108922036T>G	ENST00000437390.2	+	7	982	c.805T>G	c.(805-807)Tcc>Gcc	p.S269A	SULT1C2_ENST00000251481.6_Missense_Mutation_p.S255A|SULT1C2_ENST00000326853.5_Missense_Mutation_p.S266A|SULT1C2_ENST00000409880.1_Missense_Mutation_p.S218A			O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 2	261					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						GTCAATTTCCTCCTTCATGAG	0.373													T|||	276	0.0551118	0.0265	0.0317	5008	,	,		19945	0.1151		0.0586	False		,,,				2504	0.045				p.S266A		Atlas-SNP	.											.	SULT1C2	82	.	0			c.T796G						PASS	.	T	ALA/SER,ALA/SER	131,4275	93.4+/-132.2	1,129,2073	73.0	72.0	73.0		763,796	0.6	1.0	2	dbSNP_126	73	475,8125	139.8+/-196.4	17,441,3842	yes	missense,missense	SULT1C2	NM_001056.3,NM_176825.2	99,99	18,570,5915	GG,GT,TT		5.5233,2.9732,4.6594	benign,benign	255/297,266/308	108922036	606,12400	2203	4300	6503	SO:0001583	missense	6819	exon8			ATTTCCTCCTTCA	U66036, AF186255	CCDS2075.1, CCDS2076.1	2q12.3	2010-09-30	2007-03-16	2007-03-16	ENSG00000198203	ENSG00000198203		"""Sulfotransferases, cytosolic"""	11456	protein-coding gene	gene with protein product		602385	"""sulfotransferase family, cytosolic, 1C, member 1"""	SULT1C1		9169148, 10783263	Standard	NM_001056		Approved	ST1C1	uc002tdx.3	O00338	OTTHUMG00000153215	ENST00000437390.2:c.805T>G	2.37:g.108922036T>G	ENSP00000399651:p.Ser269Ala	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_176825	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000437390.2	37		120	0.054945054945054944	17	0.034552845528455285	12	0.03314917127071823	49	0.08566433566433566	42	0.055408970976253295	T	13.01	2.110832	0.37242	0.029732	0.055233	ENSG00000198203	ENST00000251481;ENST00000326853;ENST00000409880;ENST00000437390	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	4.66	0.617	0.17619	Sulfotransferase domain (1);	0.187541	0.36444	N	0.002582	T	0.05044	0.0135	N	0.04320	-0.23	0.23030	N	0.998404	B;B;B;B	0.09022	0.001;0.002;0.001;0.001	B;B;B;B	0.09377	0.002;0.002;0.004;0.002	T	0.11397	-1.0589	10	0.36615	T	0.2	.	8.7383	0.34541	0.0:0.6791:0.0:0.3209	rs17036104;rs52799520;rs57242700;rs17036104	269;170;255;266	B4DLP0;B4DPE8;O00338;O00338-2	.;.;ST1C2_HUMAN;.	A	255;266;218;269	ENSP00000251481:S255A;ENSP00000319622:S266A;ENSP00000387054:S218A;ENSP00000399651:S269A	ENSP00000251481:S255A	S	+	1	0	SULT1C2	108288468	0.030000	0.19436	0.995000	0.50966	0.955000	0.61496	0.747000	0.26290	0.023000	0.15187	-0.177000	0.13119	TCC	T|0.948;G|0.052	0.052	strong		0.373	SULT1C2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000329969.2	NM_176825	
NDST4	64579	hgsc.bcm.edu	37	4	115749005	115749005	+	Silent	SNP	C	C	T	rs6843860	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:115749005C>T	ENST00000264363.2	-	14	3264	c.2586G>A	c.(2584-2586)tcG>tcA	p.S862S		NM_022569.1	NP_072091.1	Q9H3R1	NDST4_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4	862	Heparan sulfate N-sulfotransferase 4.				heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(43)|ovary(1)|prostate(7)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	81		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000562)		GTCTCAGCCACGATGGCAGAG	0.403													T|||	1543	0.308107	0.553	0.2493	5008	,	,		17302	0.1567		0.169	False		,,,				2504	0.318				p.S862S		Atlas-SNP	.											.	NDST4	193	.	0			c.G2586A						PASS	.	T		2205,2201	587.5+/-386.7	557,1091,555	110.0	107.0	108.0		2586	-7.0	0.2	4	dbSNP_116	108	1270,7328	759.3+/-407.5	101,1068,3130	no	coding-synonymous	NDST4	NM_022569.1		658,2159,3685	TT,TC,CC		14.7709,49.9546,26.7225		862/873	115749005	3475,9529	2203	4299	6502	SO:0001819	synonymous_variant	64579	exon14			CAGCCACGATGGC	AB036429	CCDS3706.1	4q26	2008-02-05			ENSG00000138653	ENSG00000138653		"""Sulfotransferases, membrane-bound"""	20779	protein-coding gene	gene with protein product		615039				11087757	Standard	NM_022569		Approved		uc003ibu.3	Q9H3R1	OTTHUMG00000132916	ENST00000264363.2:c.2586G>A	4.37:g.115749005C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_022569	Q2KHM8	Silent	SNP	ENST00000264363.2	37	CCDS3706.1																																																																																			C|0.735;T|0.265	0.265	strong		0.403	NDST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256427.1	NM_022569	
C6orf118	168090	hgsc.bcm.edu	37	6	165712942	165712942	+	Missense_Mutation	SNP	G	G	C	rs61733397	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:165712942G>C	ENST00000230301.8	-	4	946	c.926C>G	c.(925-927)gCa>gGa	p.A309G	C6orf118_ENST00000543069.1_Missense_Mutation_p.A205G	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	309										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)		CTCGTACTGTGCTGCAGGCTG	0.468													G|||	51	0.0101837	0.0023	0.0086	5008	,	,		15702	0.001		0.0249	False		,,,				2504	0.0164				p.A309G		Atlas-SNP	.											.	C6orf118	116	.	0			c.C926G						PASS	.	G	GLY/ALA	45,4361	49.6+/-84.7	0,45,2158	108.0	94.0	99.0		926	-0.9	0.0	6	dbSNP_129	99	318,8282	112.1+/-172.3	4,310,3986	yes	missense	C6orf118	NM_144980.3	60	4,355,6144	CC,CG,GG		3.6977,1.0213,2.791	possibly-damaging	309/470	165712942	363,12643	2203	4300	6503	SO:0001583	missense	168090	exon4			TACTGTGCTGCAG		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.926C>G	6.37:g.165712942G>C	ENSP00000230301:p.Ala309Gly	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	20	0.009157509157509158	2	0.0040650406504065045	2	0.0055248618784530384	1	0.0017482517482517483	15	0.01978891820580475	G	7.784	0.710067	0.15239	0.010213	0.036977	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.15718	2.4;2.4	5.21	-0.902	0.10537	.	1.456460	0.03902	N	0.280408	T	0.04588	0.0125	L	0.38175	1.15	0.09310	N	1	B	0.26547	0.152	B	0.28011	0.085	T	0.40572	-0.9556	10	0.29301	T	0.29	-2.0621	6.4703	0.22005	0.1142:0.0:0.334:0.5517	rs61733397	309	Q5T5N4	CF118_HUMAN	G	309;205	ENSP00000230301:A309G;ENSP00000439288:A205G	ENSP00000230301:A309G	A	-	2	0	C6orf118	165632932	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.183000	0.09712	-0.096000	0.12329	-0.314000	0.08810	GCA	G|0.968;C|0.032	0.032	strong		0.468	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980	
PLEK2	26499	hgsc.bcm.edu	37	14	67878765	67878765	+	Silent	SNP	G	G	A	rs115017102	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:67878765G>A	ENST00000216446.4	-	1	152	c.12C>T	c.(10-12)ggC>ggT	p.G4G	PLEK2_ENST00000557388.1_5'UTR	NM_016445.1	NP_057529.1	Q9NYT0	PLEK2_HUMAN	pleckstrin 2	4	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	15				all cancers(60;0.000728)|OV - Ovarian serous cystadenocarcinoma(108;0.00593)|BRCA - Breast invasive adenocarcinoma(234;0.00953)		CCTTGAGCACGCCGTCCTCCA	0.761													G|||	95	0.0189696	0.0287	0.0144	5008	,	,		12537	0.0		0.0278	False		,,,				2504	0.0194				p.G4G		Atlas-SNP	.											.	PLEK2	23	.	0			c.C12T						PASS	.	G		120,4238		0,120,2059	23.0	16.0	18.0		12	0.6	1.0	14	dbSNP_132	18	271,8281		5,261,4010	no	coding-synonymous	PLEK2	NM_016445.1		5,381,6069	AA,AG,GG		3.1688,2.7536,3.0287		4/354	67878765	391,12519	2179	4276	6455	SO:0001819	synonymous_variant	26499	exon1			GAGCACGCCGTCC	AF228603	CCDS9782.1	14q23.3	2014-08-12			ENSG00000100558	ENSG00000100558		"""Pleckstrin homology (PH) domain containing"""	19238	protein-coding gene	gene with protein product		608007				11911883, 17658464	Standard	NM_016445		Approved		uc001xjh.1	Q9NYT0	OTTHUMG00000171247	ENST00000216446.4:c.12C>T	14.37:g.67878765G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	24	7	0.291667	NM_016445	Q96JT0	Silent	SNP	ENST00000216446.4	37	CCDS9782.1																																																																																			G|0.976;A|0.024	0.024	strong		0.761	PLEK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412547.2		
CYP1B1	1545	hgsc.bcm.edu	37	2	38298150	38298150	+	Silent	SNP	A	A	G	rs1056837	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:38298150A>G	ENST00000260630.3	-	3	1748	c.1347T>C	c.(1345-1347)gaT>gaC	p.D449D	CYP1B1_ENST00000494864.1_5'UTR|CYP1B1_ENST00000407341.1_Silent_p.D449D	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	449			D -> E (in dbSNP:rs1056837).		angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|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)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	TGATGAGGCCATCCTTGTCCA	0.478													G|||	3106	0.620208	0.2012	0.7277	5008	,	,		20544	0.9087		0.6024	False		,,,				2504	0.8313				p.D449D		Atlas-SNP	.											.	CYP1B1	39	.	0			c.T1347C						PASS	.	G		1119,3287	718.6+/-408.9	159,801,1243	84.0	77.0	79.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1347	-7.2	0.2	2	dbSNP_86	79	4782,3818	538.6+/-383.4	1344,2094,862	no	coding-synonymous	CYP1B1	NM_000104.3		1503,2895,2105	GG,GA,AA		44.3953,25.3972,45.3714		449/544	38298150	5901,7105	2203	4300	6503	SO:0001819	synonymous_variant	1545	exon3			GAGGCCATCCTTG	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.1347T>C	2.37:g.38298150A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_000104	Q5TZW8|Q93089|Q9H316	Silent	SNP	ENST00000260630.3	37	CCDS1793.1																																																																																			G|0.522;A|0.478	0.522	strong		0.478	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
ZBBX	79740	hgsc.bcm.edu	37	3	167023624	167023624	+	Missense_Mutation	SNP	A	A	G	rs35190925	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:167023624A>G	ENST00000392766.2	-	17	1872	c.1532T>C	c.(1531-1533)aTa>aCa	p.I511T	ZBBX_ENST00000455345.2_Missense_Mutation_p.I511T|ZBBX_ENST00000392767.2_Missense_Mutation_p.I511T|ZBBX_ENST00000307529.5_Missense_Mutation_p.I511T|ZBBX_ENST00000392764.1_Missense_Mutation_p.I482T	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	511			I -> T (in dbSNP:rs35190925).			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						TTCTAAACCTATATTTTTCTC	0.353													A|||	238	0.047524	0.0091	0.0677	5008	,	,		13576	0.001		0.1113	False		,,,				2504	0.0675				p.I511T		Atlas-SNP	.											.	ZBBX	299	.	0			c.T1532C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE	101,3489		3,95,1697	58.0	51.0	53.0		1532,1445,1532	1.6	0.0	3	dbSNP_126	53	1000,7136		59,882,3127	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	89,89,89	62,977,4824	GG,GA,AA		12.2911,2.8134,9.3894	probably-damaging,probably-damaging,probably-damaging	511/840,482/772,511/801	167023624	1101,10625	1795	4068	5863	SO:0001583	missense	79740	exon17			AAACCTATATTTT	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.1532T>C	3.37:g.167023624A>G	ENSP00000376519:p.Ile511Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	137	60	0.437956	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	118	0.05402930402930403	6	0.012195121951219513	30	0.08287292817679558	0	0.0	82	0.10817941952506596	A	12.60	1.986851	0.35036	0.028134	0.122911	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.10382	3.05;3.05;3.04;3.04;2.88	5.54	1.61	0.23674	.	0.421904	0.26355	N	0.024850	T	0.00144	0.0004	L	0.55481	1.735	0.80722	P	0.0	B;B	0.24721	0.077;0.11	B;B	0.21917	0.037;0.024	T	0.12604	-1.0541	9	0.62326	D	0.03	-2.0201	4.4261	0.11503	0.6568:0.1678:0.1753:0.0	rs35190925	511;511	A8MT70-2;A8MT70	.;ZBBX_HUMAN	T	511;511;511;511;482	ENSP00000376519:I511T;ENSP00000376520:I511T;ENSP00000390232:I511T;ENSP00000305065:I511T;ENSP00000376517:I482T	ENSP00000305065:I511T	I	-	2	0	ZBBX	168506318	0.003000	0.15002	0.005000	0.12908	0.034000	0.12701	0.240000	0.18042	0.477000	0.27464	0.528000	0.53228	ATA	A|0.918;G|0.082	0.082	strong		0.353	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
PCDHB7	56129	hgsc.bcm.edu	37	5	140552975	140552975	+	Missense_Mutation	SNP	G	G	A	rs17096946	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140552975G>A	ENST00000231137.3	+	1	733	c.559G>A	c.(559-561)Gag>Aag	p.E187K		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	187	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> K (in dbSNP:rs17096946).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGATAGCGGGGAGGGGAATAT	0.493																																					p.E187K		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G559A						PASS	.	G	LYS/GLU	779,3627	312.5+/-292.6	78,623,1502	64.0	61.0	62.0		559	3.7	0.4	5	dbSNP_123	62	119,8481	62.1+/-124.0	0,119,4181	yes	missense	PCDHB7	NM_018940.2	56	78,742,5683	AA,AG,GG		1.3837,17.6804,6.9045	benign	187/794	140552975	898,12108	2203	4300	6503	SO:0001583	missense	56129	exon1			AGCGGGGAGGGGA	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.559G>A	5.37:g.140552975G>A	ENSP00000231137:p.Glu187Lys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	127	0.05815018315018315	102	0.2073170731707317	17	0.04696132596685083	0	0.0	8	0.010554089709762533	G	8.336	0.827664	0.16749	0.176804	0.013837	ENSG00000113212	ENST00000231137	T	0.19938	2.11	4.61	3.72	0.42706	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.37630	1.12	0.35616	P	0.19096400000000002	B	0.17038	0.02	B	0.21360	0.034	T	0.14839	-1.0458	8	0.56958	D	0.05	.	9.3572	0.38173	0.0828:0.1475:0.7697:0.0	rs17096946;rs52797263;rs17096946	187	Q9Y5E2	PCDB7_HUMAN	K	187	ENSP00000231137:E187K	ENSP00000231137:E187K	E	+	1	0	PCDHB7	140533159	0.022000	0.18835	0.357000	0.25798	0.160000	0.22226	1.427000	0.34881	1.003000	0.39130	0.655000	0.94253	GAG	G|0.932;A|0.068	0.068	strong		0.493	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907848	12907848	+	Missense_Mutation	SNP	G	G	C	rs140567799		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907848G>C	ENST00000317869.6	-	2	520	c.295C>G	c.(295-297)Cga>Gga	p.R99G		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	99						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						GCTGCTGATCGTTTCACACCT	0.488																																					p.R99G		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,0,1	HNRNPCL1	68	1	0			c.C295G						scavenged	.						133.0	126.0	129.0					1																	12907848		2203	4300	6503	SO:0001583	missense	343069	exon2			CTGATCGTTTCAC	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.295C>G	1.37:g.12907848G>C	ENSP00000365370:p.Arg99Gly	Somatic	234	1	0.0042735		WXS	Illumina HiSeq	Phase_I	236	29	0.122881	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	8.058	0.767427	0.15983	.	.	ENSG00000179172	ENST00000317869	T	0.14640	2.49	1.09	-1.25	0.09405	.	0.087727	0.46145	U	0.000308	T	0.15565	0.0375	M	0.79475	2.455	0.43110	D	0.994815	P	0.38110	0.618	B	0.39805	0.31	T	0.02596	-1.1136	10	0.56958	D	0.05	.	5.4144	0.16365	0.3852:0.0:0.6148:0.0	.	99	O60812	HNRCL_HUMAN	G	99	ENSP00000365370:R99G	ENSP00000365370:R99G	R	-	1	2	HNRNPCL1	12830435	0.958000	0.32768	0.045000	0.18777	0.022000	0.10575	0.621000	0.24418	-0.426000	0.07360	-0.482000	0.04802	CGA	.	.	weak		0.488	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
LOXL4	84171	hgsc.bcm.edu	37	10	100013438	100013438	+	Silent	SNP	C	C	T	rs17524355	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:100013438C>T	ENST00000260702.3	-	11	1857	c.1707G>A	c.(1705-1707)gcG>gcA	p.A569A	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	569	Lysyl-oxidase like.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		CCATGTGATCCGCAGACTTGG	0.592													C|||	659	0.131589	0.1528	0.1484	5008	,	,		18566	0.0288		0.2207	False		,,,				2504	0.1053				p.A569A		Atlas-SNP	.											LOXL4,caecum,carcinoma,-1,2	LOXL4	60	2	0			c.G1707A						PASS	.	C		767,3639	311.1+/-291.9	75,617,1511	110.0	99.0	102.0		1707	-8.3	0.6	10	dbSNP_123	102	1841,6759	330.9+/-319.4	193,1455,2652	no	coding-synonymous	LOXL4	NM_032211.6		268,2072,4163	TT,TC,CC		21.407,17.4081,20.0523		569/757	100013438	2608,10398	2203	4300	6503	SO:0001819	synonymous_variant	84171	exon11			GTGATCCGCAGAC	AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.1707G>A	10.37:g.100013438C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Silent	SNP	ENST00000260702.3	37	CCDS7473.1																																																																																			C|0.826;T|0.174	0.174	strong		0.592	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
DMD	1756	hgsc.bcm.edu	37	X	31697636	31697636	+	Silent	SNP	A	A	G	rs1801188	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:31697636A>G	ENST00000357033.4	-	53	7934	c.7728T>C	c.(7726-7728)aaT>aaC	p.N2576N	DMD_ENST00000378707.3_Silent_p.N116N|DMD_ENST00000359836.1_Silent_p.N116N|DMD_ENST00000378677.2_Silent_p.N2572N|DMD_ENST00000541735.1_Silent_p.N116N|DMD_ENST00000474231.1_Silent_p.N116N|DMD_ENST00000343523.2_Silent_p.N116N	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2576					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTAACATTTCATTCAACTGTT	0.413													A|||	684	0.181192	0.0711	0.1182	3775	,	,		11946	0.2887		0.1193	False		,,,				2504	0.0992				p.N2576N		Atlas-SNP	.											.	DMD	2127	.	0			c.T7728C						PASS	.	A	,,,,,,,,,,,	409,3424		15,323,56,1293,515	177.0	144.0	155.0		7704,7728,7359,7716,7359,3705,3696,348,348,348,348,348	3.5	1.0	X	dbSNP_89	155	1364,5364		109,765,381,1554,1491	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3,NM_004011.3,NM_004012.3,NM_004013.2,NM_004020.3,NM_004021.2,NM_004022.2,NM_004023.2	,,,,,,,,,,,	124,1088,437,2847,2006	GG,GA,G,AA,A		20.2735,10.6705,16.7882	,,,,,,,,,,,	2568/3678,2576/3686,2453/3563,2572/3682,2453/3563,1235/2345,1232/2342,116/1226,116/1116,116/1244,116/1231,116/1134	31697636	1773,8788	2202	4300	6502	SO:0001819	synonymous_variant	1756	exon53			CATTTCATTCAAC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.7728T>C	X.37:g.31697636A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1	332	0.2001205545509343	21	0.04375	25	0.0748502994011976	118	0.2610619469026549	67	0.0938375350140056	A	9.387	1.074424	0.20227	0.106705	0.202735	ENSG00000198947	ENST00000465285	.	.	.	5.89	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999795826	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.9442	0.09341	0.5906:0.0:0.1497:0.2597	rs1801188;rs17338646;rs1801188	.	.	.	R	305	.	.	X	-	1	0	DMD	31607557	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.065000	0.30592	0.833000	0.34828	0.441000	0.28932	TGA	0|0.002;G|0.185	0.185	strong		0.413	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
ZNF211	10520	hgsc.bcm.edu	37	19	58152817	58152817	+	Silent	SNP	G	G	C	rs11880050	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58152817G>C	ENST00000347302.3	+	3	1142	c.963G>C	c.(961-963)tcG>tcC	p.S321S	ZNF211_ENST00000299871.5_Silent_p.S386S|ZNF211_ENST00000254182.7_Silent_p.S312S|ZNF211_ENST00000420680.1_Silent_p.S325S|ZNF211_ENST00000240731.4_Silent_p.S334S|ZNF211_ENST00000544273.1_Silent_p.S333S|ZNF211_ENST00000541801.1_Silent_p.S312S|ZNF211_ENST00000391703.3_Silent_p.S260S	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	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)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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;0.026)		GTGGGAAATCGTTTAGTCAGA	0.413													C|||	1072	0.214058	0.2352	0.1297	5008	,	,		21915	0.3214		0.159	False		,,,				2504	0.1912				p.S386S		Atlas-SNP	.											.	ZNF211	78	.	0			c.G1158C						PASS	.	C	,	980,3426	731.2+/-410.2	117,746,1340	72.0	73.0	73.0		1002,963	-4.2	0.0	19	dbSNP_120	73	1344,7256	755.7+/-407.5	97,1150,3053	no	coding-synonymous,coding-synonymous	ZNF211	NM_006385.3,NM_198855.2	,	214,1896,4393	CC,CG,GG		15.6279,22.2424,17.8687	,	334/578,321/565	58152817	2324,10682	2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			GAAATCGTTTAGT	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.963G>C	19.37:g.58152817G>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	37	CCDS12957.1	485	0.22206959706959706	135	0.27439024390243905	52	0.143646408839779	180	0.3146853146853147	118	0.15567282321899736	C	5.103	0.204570	0.09704	0.222424	0.156279	ENSG00000121417	ENST00000407202	.	.	.	3.21	-4.21	0.03812	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19575	P	0.9999641552	.	.	.	.	.	.	T	0.41305	-0.9516	3	.	.	.	.	1.3807	0.02230	0.2524:0.1475:0.1254:0.4747	rs11880050;rs11880050	.	.	.	L	325	.	.	V	+	1	0	ZNF211	62844629	0.000000	0.05858	0.012000	0.15200	0.866000	0.49608	-4.980000	0.00163	-0.850000	0.04152	-0.977000	0.02584	GTT	G|0.804;C|0.196	0.196	strong		0.413	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
PIM3	415116	hgsc.bcm.edu	37	22	50354819	50354819	+	Silent	SNP	C	C	A	rs11541025	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50354819C>A	ENST00000360612.4	+	2	567	c.132C>A	c.(130-132)gcC>gcA	p.A44A		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	44	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		AGGTGGGCGCCGTGCTGGGTA	0.766													c|||	1862	0.371805	0.3676	0.2867	5008	,	,		6787	0.3383		0.2922	False		,,,				2504	0.5542				p.A44A		Atlas-SNP	.											.	PIM3	15	.	0			c.C132A						PASS	.	G		1402,2728		306,790,969	6.0	6.0	6.0		132	-4.2	0.3	22	dbSNP_120	6	2589,5681		503,1583,2049	no	coding-synonymous	PIM3	NM_001001852.3		809,2373,3018	AA,AC,CC		31.3059,33.9467,32.1855		44/327	50354819	3991,8409	2065	4135	6200	SO:0001819	synonymous_variant	415116	exon2			GGGCGCCGTGCTG	BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"""pim-3 oncogene"""			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.132C>A	22.37:g.50354819C>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_001001852	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Silent	SNP	ENST00000360612.4	37	CCDS33678.1																																																																																			C|0.669;A|0.331	0.331	strong		0.766	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852	
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 GAIIx	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	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	134	52	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	
GCNT2	2651	hgsc.bcm.edu	37	6	10556872	10556872	+	Intron	SNP	C	C	T	rs2230906	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:10556872C>T	ENST00000379597.3	+	1	1481				GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000316170.3_Silent_p.C72C			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		AGTCTTCTTGCAAGGAATACT	0.413													C|||	270	0.0539137	0.0318	0.0533	5008	,	,		20722	0.0089		0.1322	False		,,,				2504	0.0501				p.C72C		Atlas-SNP	.											.	GCNT2	123	.	0			c.C216T						PASS	.	C	,	222,4184	134.5+/-170.7	11,200,1992	131.0	124.0	126.0		216,	4.2	0.5	6	dbSNP_98	126	1130,7470	233.6+/-266.8	90,950,3260	no	coding-synonymous,intron	GCNT2	NM_001491.2,NM_145649.4	,	101,1150,5252	TT,TC,CC		13.1395,5.0386,10.3952	,	72/401,	10556872	1352,11654	2203	4300	6503	SO:0001627	intron_variant	2651	exon1			TTCTTGCAAGGAA	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.925+26803C>T	6.37:g.10556872C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	115	23	0.2	NM_001491		Silent	SNP	ENST00000379597.3	37	CCDS34338.1																																																																																			C|0.905;T|0.095	0.095	strong		0.413	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
NEK1	4750	hgsc.bcm.edu	37	4	170482883	170482883	+	Silent	SNP	A	A	G	rs56064008	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:170482883A>G	ENST00000439128.2	-	14	1786	c.1146T>C	c.(1144-1146)atT>atC	p.I382I	NEK1_ENST00000507142.1_Silent_p.I382I|NEK1_ENST00000511633.1_Silent_p.I382I|NEK1_ENST00000512193.1_Silent_p.I382I|NEK1_ENST00000510533.1_Silent_p.I382I	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	382					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TCATTAAACTAATAATCTGTA	0.299													A|||	140	0.0279553	0.0045	0.0447	5008	,	,		15015	0.0		0.0895	False		,,,				2504	0.0133				p.I382I		Atlas-SNP	.											.	NEK1	203	.	0			c.T1146C						PASS	.	A	,,,,	53,3491		1,51,1720	24.0	24.0	24.0		1146,1146,1146,1146,1146	0.7	1.0	4	dbSNP_129	24	685,7403		26,633,3385	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	,,,,	27,684,5105	GG,GA,AA		8.4693,1.4955,6.3446	,,,,	382/1287,382/1243,382/1190,382/1215,382/1259	170482883	738,10894	1772	4044	5816	SO:0001819	synonymous_variant	4750	exon15			TAAACTAATAATC	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.1146T>C	4.37:g.170482883A>G		Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	294	135	0.459184	NM_001199399	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	ENST00000439128.2	37	CCDS47162.1																																																																																			A|0.953;G|0.047	0.047	strong		0.299	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
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 GAIIx	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	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	25	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	
OR1S1	219959	hgsc.bcm.edu	37	11	57982584	57982584	+	Missense_Mutation	SNP	T	T	C	rs1966835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57982584T>C	ENST00000309433.6	+	1	368	c.368T>C	c.(367-369)aTt>aCt	p.I123T		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	123			I -> T (in dbSNP:rs1966835).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				TTTGTCGTCATTGACAATTTG	0.448													T|||	2620	0.523163	0.2844	0.5418	5008	,	,		22315	0.8036		0.4225	False		,,,				2504	0.6472				p.I123T		Atlas-SNP	.											.	OR1S1	139	.	0			c.T368C						PASS	.	T	THR/ILE	1323,3079	445.3+/-347.6	197,929,1075	183.0	172.0	176.0		368	-2.6	0.4	11	dbSNP_92	176	3643,4949	524.4+/-380.5	785,2073,1438	no	missense	OR1S1	NM_001004458.1	89	982,3002,2513	CC,CT,TT		42.3999,30.0545,38.2176	benign	123/326	57982584	4966,8028	2201	4296	6497	SO:0001583	missense	219959	exon1			TCGTCATTGACAA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.368T>C	11.37:g.57982584T>C	ENSP00000311688:p.Ile123Thr	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	211	211	1	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	1080	0.4945054945054945	147	0.29878048780487804	187	0.5165745856353591	432	0.7552447552447552	314	0.41424802110817943	T	0.360	-0.939776	0.02322	0.300545	0.423999	ENSG00000172774	ENST00000309433	T	0.01685	4.69	3.27	-2.56	0.06268	GPCR, rhodopsin-like superfamily (1);	0.522752	0.16164	N	0.226633	T	0.00012	0.0000	N	0.01515	-0.825	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.16394	-1.0404	9	0.62326	D	0.03	.	1.4226	0.02315	0.1409:0.3037:0.1431:0.4123	rs1966835;rs52810501;rs1966835	123	Q8NH92	OR1S1_HUMAN	T	123	ENSP00000311688:I123T	ENSP00000311688:I123T	I	+	2	0	OR1S1	57739160	0.000000	0.05858	0.354000	0.25760	0.142000	0.21351	-1.070000	0.03440	-0.406000	0.07588	-1.267000	0.01435	ATT	T|0.569;C|0.431	0.431	strong		0.448	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
ZNF180	7733	hgsc.bcm.edu	37	19	45001346	45001346	+	Missense_Mutation	SNP	G	G	A	rs2571108	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:45001346G>A	ENST00000221327.4	-	2	403	c.122C>T	c.(121-123)gCc>gTc	p.A41V	ZNF180_ENST00000586637.1_Missense_Mutation_p.P10S|ZNF180_ENST00000391956.4_Missense_Mutation_p.A41V|ZNF180_ENST00000592529.1_Missense_Mutation_p.A14V|ZNF180_ENST00000587047.1_Missense_Mutation_p.P43S|ZNF180_ENST00000585514.1_5'UTR	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	41			A -> V (in dbSNP:rs2571108). {ECO:0000269|PubMed:12743021}.		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)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CTGTGCACAGGCCTTCGGGGG	0.622													G|||	1307	0.260982	0.1498	0.1844	5008	,	,		15070	0.3562		0.3857	False		,,,				2504	0.2393				p.A41V	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											ZNF180,colon,carcinoma,0,1	ZNF180	103	1	0			c.C122T						PASS	.	G	VAL/ALA	884,3522	336.5+/-304.4	97,690,1416	39.0	38.0	38.0		122	0.4	0.0	19	dbSNP_100	38	3057,5543	465.4+/-366.5	553,1951,1796	yes	missense	ZNF180	NM_013256.3	64	650,2641,3212	AA,AG,GG		35.5465,20.0635,30.3014	benign	41/693	45001346	3941,9065	2203	4300	6503	SO:0001583	missense	7733	exon2			GCACAGGCCTTCG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.122C>T	19.37:g.45001346G>A	ENSP00000221327:p.Ala41Val	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	663	0.30357142857142855	67	0.13617886178861788	71	0.19613259668508287	222	0.3881118881118881	303	0.3997361477572559	G	9.934	1.215647	0.22373	0.200635	0.355465	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.08720	3.21;3.06	3.85	0.423	0.16463	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.10450	0.005;0.002;0.002	T	0.46233	-0.9206	8	0.02654	T	1	0.0079	4.3819	0.11299	0.2115:0.1858:0.6027:0.0	rs2571108;rs2571108	41;40;41	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	V	41	ENSP00000221327:A41V;ENSP00000375818:A41V	ENSP00000221327:A41V	A	-	2	0	ZNF180	49693186	0.053000	0.20554	0.005000	0.12908	0.043000	0.13939	0.391000	0.20784	0.219000	0.20840	-0.165000	0.13383	GCC	G|0.703;A|0.297	0.297	strong		0.622	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
ZNF470	388566	hgsc.bcm.edu	37	19	57088850	57088850	+	Silent	SNP	T	T	C	rs3752180	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57088850T>C	ENST00000330619.8	+	6	1739	c.1053T>C	c.(1051-1053)gaT>gaC	p.D351D	ZNF470_ENST00000391709.3_Silent_p.D351D|ZNF470_ENST00000601902.1_Intron	NM_001001668.3	NP_001001668.3	Q6ECI4	ZN470_HUMAN	zinc finger protein 470	351					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(7)|large_intestine(12)|lung(11)|ovary(1)|pancreas(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	41		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0294)		CTTTTAGTGATTGCTCATCCC	0.438													T|||	1455	0.290535	0.1362	0.3401	5008	,	,		21092	0.379		0.3867	False		,,,				2504	0.274				p.D351D		Atlas-SNP	.											.	ZNF470	103	.	0			c.T1053C						PASS	.	T		801,3605	320.4+/-296.6	64,673,1466	86.0	82.0	84.0		1053	-2.2	0.7	19	dbSNP_107	84	3198,5402	482.3+/-370.9	598,2002,1700	no	coding-synonymous	ZNF470	NM_001001668.3		662,2675,3166	CC,CT,TT		37.186,18.1798,30.7473		351/718	57088850	3999,9007	2203	4300	6503	SO:0001819	synonymous_variant	388566	exon6			TAGTGATTGCTCA	AK129686	CCDS33122.1	19q13.43	2013-01-08				ENSG00000197016		"""Zinc fingers, C2H2-type"", ""-"""	22220	protein-coding gene	gene with protein product						15302581	Standard	NM_001001668		Approved	CZF-1, FLJ26175	uc002qnl.4	Q6ECI4		ENST00000330619.8:c.1053T>C	19.37:g.57088850T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_001001668	A8MTW0|B9EGU1|Q6ZPA1|Q9Y2N9	Silent	SNP	ENST00000330619.8	37	CCDS33122.1																																																																																			T|0.693;C|0.307	0.307	strong		0.438	ZNF470-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459707.2	NM_001001668	
EPX	8288	hgsc.bcm.edu	37	17	56271094	56271094	+	Missense_Mutation	SNP	G	G	C	rs34702287|rs11652709	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:56271094G>C	ENST00000225371.5	+	4	476	c.366G>C	c.(364-366)caG>caC	p.Q122H		NM_000502.4	NP_000493.1	P11678	PERE_HUMAN	eosinophil peroxidase	122			Q -> H (in dbSNP:rs11652709). {ECO:0000269|Ref.2}.		defense response to nematode (GO:0002215)|eosinophil migration (GO:0072677)|hydrogen peroxide catabolic process (GO:0042744)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-5 production (GO:0032714)|positive regulation of interleukin-4 production (GO:0032753)	extracellular vesicular exosome (GO:0070062)	heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(2)|endometrium(9)|kidney(1)|large_intestine(9)|liver(2)|lung(20)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	48					Melatonin(DB01065)	CAGAACCACAGCTGCGGCTGC	0.617													G|||	1070	0.213658	0.2073	0.1873	5008	,	,		17734	0.0923		0.3091	False		,,,				2504	0.2679				p.Q122H		Atlas-SNP	.											.	EPX	95	.	0			c.G366C	GRCh37	CM067664	EPX	M	rs11652709	PASS	.	G	HIS/GLN	1070,3336	380.2+/-323.6	129,812,1262	41.0	35.0	37.0		366	3.6	1.0	17	dbSNP_120	37	2731,5869	425.3+/-354.9	445,1841,2014	yes	missense	EPX	NM_000502.4	24	574,2653,3276	CC,CG,GG		31.7558,24.2851,29.225	probably-damaging	122/716	56271094	3801,9205	2203	4300	6503	SO:0001583	missense	8288	exon4			ACCACAGCTGCGG	M26515	CCDS11602.1	17q23.1	2006-09-25				ENSG00000121053	1.11.1.7		3423	protein-coding gene	gene with protein product		131399				2550461, 2541222	Standard	NM_000502		Approved	EPO, EPP, EPX-PEN	uc002ivq.3	P11678		ENST00000225371.5:c.366G>C	17.37:g.56271094G>C	ENSP00000225371:p.Gln122His	Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	193	93	0.481865	NM_000502	Q4TVP3	Missense_Mutation	SNP	ENST00000225371.5	37	CCDS11602.1	459	0.21016483516483517	106	0.21544715447154472	67	0.1850828729281768	43	0.07517482517482517	243	0.32058047493403696	G	11.40	1.628503	0.28978	0.242851	0.317558	ENSG00000121053	ENST00000225371	T	0.71222	-0.55	4.6	3.62	0.41486	.	0.113680	0.64402	D	0.000012	T	0.00012	0.0000	M	0.81802	2.56	0.31379	P	0.6792549999999999	D	0.89917	1.0	D	0.91635	0.999	T	0.39057	-0.9632	9	0.15952	T	0.53	-13.706	7.6582	0.28388	0.1973:0.0:0.8027:0.0	rs11652709;rs17762614;rs11652709	122	P11678	PERE_HUMAN	H	122	ENSP00000225371:Q122H	ENSP00000225371:Q122H	Q	+	3	2	EPX	53626093	0.996000	0.38824	0.993000	0.49108	0.142000	0.21351	2.524000	0.45589	1.058000	0.40530	0.442000	0.29010	CAG	G|0.745;C|0.254	0.254	strong		0.617	EPX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443367.1	NM_000502	
CEP192	55125	hgsc.bcm.edu	37	18	13116432	13116432	+	Missense_Mutation	SNP	G	G	T	rs1786263	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:13116432G>T	ENST00000325971.8	+	41	7151	c.5558G>T	c.(5557-5559)cGg>cTg	p.R1853L	CEP192_ENST00000506447.1_Missense_Mutation_p.R2449L|CEP192_ENST00000430049.2_Missense_Mutation_p.R1974L|CEP192_ENST00000540847.2_3'UTR			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1853			R -> L (in dbSNP:rs1786263). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12693554, ECO:0000269|PubMed:14702039}.		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TACAGGTTCCGGCCGACTAGT	0.428													T|||	3884	0.775559	0.9788	0.6441	5008	,	,		15909	0.8075		0.6113	False		,,,				2504	0.7301				p.R2449L		Atlas-SNP	.											.	CEP192	340	.	0			c.G7346T						PASS	.	T	LEU/ARG	4056,350	180.1+/-208.5	1868,320,15	96.0	90.0	92.0		7346	4.8	1.0	18	dbSNP_89	92	5297,3303	493.6+/-373.6	1642,2013,645	yes	missense	CEP192	NM_032142.3	102	3510,2333,660	TT,TG,GG		38.407,7.9437,28.087	benign	2449/2538	13116432	9353,3653	2203	4300	6503	SO:0001583	missense	55125	exon43			GGTTCCGGCCGAC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.5558G>T	18.37:g.13116432G>T	ENSP00000317156:p.Arg1853Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		1642	0.7518315018315018	476	0.967479674796748	237	0.6546961325966851	462	0.8076923076923077	467	0.6160949868073878	T	2.675	-0.276722	0.05679	0.920563	0.61593	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049;ENST00000540847	T;T;T	0.04862	3.54;3.54;3.54	4.76	4.76	0.60689	.	0.077542	0.53938	N	0.000042	T	0.00012	0.0000	N	0.00128	-2.045	0.53688	P	2.8000000000028002E-5	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.29822	-0.9999	9	0.02654	T	1	-2.2435	4.8966	0.13753	0.0:0.159:0.1629:0.6781	rs1786263;rs17661484;rs52836864;rs61351048;rs1786263	1974;2449;453;1052	C9JT09;E9PF99;F5GZ47;Q9HCK3	.;.;.;.	L	2449;1853;1853;1974;453	ENSP00000427550:R2449L;ENSP00000317156:R1853L;ENSP00000389190:R1974L	ENSP00000317156:R1853L	R	+	2	0	CEP192	13106432	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	0.755000	0.26405	0.785000	0.33685	-0.520000	0.04383	CGG	G|0.251;T|0.749	0.749	strong		0.428	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
OR9Q2	219957	hgsc.bcm.edu	37	11	57958775	57958775	+	Silent	SNP	C	C	T	rs7120468	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57958775C>T	ENST00000311591.3	+	1	870	c.813C>T	c.(811-813)gaC>gaT	p.D271D		NM_001005283.2	NP_001005283.1	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q, member 2	271						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D271D(1)		breast(2)|central_nervous_system(2)|endometrium(1)|large_intestine(3)|lung(24)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41		Breast(21;0.0589)				CCGAGGGAGACCGAGTGGTGT	0.557													C|||	2123	0.423922	0.2209	0.3847	5008	,	,		19568	0.752		0.3082	False		,,,				2504	0.5072				p.D271D		Atlas-SNP	.											OR9Q2,NS,carcinoma,0,1	OR9Q2	78	1	1	Substitution - coding silent(1)	stomach(1)	c.C813T						PASS	.	C		1068,3334	390.0+/-327.5	126,816,1259	102.0	94.0	97.0		813	3.1	0.4	11	dbSNP_116	97	2749,5843	437.8+/-358.7	458,1833,2005	no	coding-synonymous	OR9Q2	NM_001005283.2		584,2649,3264	TT,TC,CC		31.9949,24.2617,29.3751		271/315	57958775	3817,9177	2201	4296	6497	SO:0001819	synonymous_variant	219957	exon1			GGGAGACCGAGTG	AB065859	CCDS31544.1	11q12.1	2012-08-09		2004-03-10	ENSG00000186513	ENSG00000186513		"""GPCR / Class A : Olfactory receptors"""	15328	protein-coding gene	gene with protein product				OR9Q2P			Standard	NM_001005283		Approved		uc010rka.2	Q8NGE9	OTTHUMG00000167414	ENST00000311591.3:c.813C>T	11.37:g.57958775C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_001005283		Silent	SNP	ENST00000311591.3	37	CCDS31544.1																																																																																			C|0.651;T|0.349	0.349	strong		0.557	OR9Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394540.1	NM_001005283	
SLC9C1	285335	hgsc.bcm.edu	37	3	111985107	111985107	+	Missense_Mutation	SNP	T	T	C	rs9872691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111985107T>C	ENST00000305815.5	-	8	1108	c.856A>G	c.(856-858)Att>Gtt	p.I286V	SLC9C1_ENST00000487372.1_Missense_Mutation_p.I286V	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	286			I -> V (in dbSNP:rs9872691). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										GTTTCTTCAATTGCTGCTTTA	0.289													T|||	1648	0.329073	0.3449	0.4035	5008	,	,		15497	0.3393		0.2376	False		,,,				2504	0.3384				p.I286V		Atlas-SNP	.											.	.	.	.	0			c.A856G						PASS	.	T	VAL/ILE	1483,2923	464.7+/-354.0	256,971,976	67.0	75.0	72.0		856	3.2	1.0	3	dbSNP_119	72	2324,6268	385.5+/-341.5	322,1680,2294	yes	missense	SLC9A10	NM_183061.1	29	578,2651,3270	CC,CT,TT		27.0484,33.6586,29.2891	benign	286/1178	111985107	3807,9191	2203	4296	6499	SO:0001583	missense	285335	exon8			CTTCAATTGCTGC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.856A>G	3.37:g.111985107T>C	ENSP00000306627:p.Ile286Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	192	99	0.515625	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	679	0.3108974358974359	171	0.3475609756097561	138	0.3812154696132597	185	0.32342657342657344	185	0.24406332453825857	T	0.009	-1.855283	0.00558	0.336586	0.270484	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.03386	3.95;3.95	5.04	3.23	0.37069	Cation/H+ exchanger (1);	0.574613	0.15538	N	0.257133	T	0.00012	0.0000	N	0.01297	-0.9	0.53005	P	3.500000000000725E-5	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.002	T	0.37526	-0.9702	9	0.09843	T	0.71	-2.2326	7.8574	0.29491	0.0:0.8079:0.0:0.1921	rs9872691;rs52814342;rs56679245;rs9872691	286;286	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	V	286	ENSP00000306627:I286V;ENSP00000420688:I286V	ENSP00000306627:I286V	I	-	1	0	SLC9A10	113467797	0.992000	0.36948	0.997000	0.53966	0.235000	0.25334	0.291000	0.18994	0.647000	0.30713	-0.186000	0.12905	ATT	T|0.705;C|0.295	0.295	strong		0.289	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
PLXNC1	10154	hgsc.bcm.edu	37	12	94673277	94673277	+	Silent	SNP	G	G	A	rs2230760	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:94673277G>A	ENST00000258526.4	+	22	3876	c.3627G>A	c.(3625-3627)ccG>ccA	p.P1209P	PLXNC1_ENST00000545312.1_5'UTR|RP11-1105G2.3_ENST00000551941.1_Intron|PLXNC1_ENST00000547057.1_Silent_p.P256P|RP11-1105G2.4_ENST00000550111.1_RNA|RP11-1105G2.3_ENST00000547927.1_5'Flank	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	1209					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|receptor binding (GO:0005102)	p.P1209P(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(12)|lung(30)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						AAAAAATCCCGGAAAACGAGA	0.388													G|||	530	0.105831	0.062	0.1441	5008	,	,		15979	0.1696		0.1282	False		,,,				2504	0.0491				p.P1209P		Atlas-SNP	.											PLXNC1,NS,carcinoma,0,1	PLXNC1	135	1	1	Substitution - coding silent(1)	stomach(1)	c.G3627A						PASS	.	G		268,4138	153.7+/-187.2	6,256,1941	92.0	88.0	89.0		3627	-4.1	1.0	12	dbSNP_116	89	1036,7564	219.2+/-257.4	64,908,3328	no	coding-synonymous	PLXNC1	NM_005761.2		70,1164,5269	AA,AG,GG		12.0465,6.0826,10.0261		1209/1569	94673277	1304,11702	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon22			AATCCCGGAAAAC	AF030339	CCDS9049.1	12q23	2009-04-17				ENSG00000136040		"""CD molecules"", ""Plexins"""	9106	protein-coding gene	gene with protein product		604259					Standard	NR_037687		Approved	VESPR, CD232	uc001tdc.3	O60486	OTTHUMG00000170235	ENST00000258526.4:c.3627G>A	12.37:g.94673277G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			G|0.888;A|0.112	0.112	strong		0.388	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2		
CEP131	22994	hgsc.bcm.edu	37	17	79170576	79170576	+	Silent	SNP	C	C	T	rs1542961	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79170576C>T	ENST00000269392.4	-	15	2080	c.1833G>A	c.(1831-1833)gcG>gcA	p.A611A	AZI1_ENST00000450824.2_Silent_p.A608A|AZI1_ENST00000374782.3_Silent_p.A608A|AZI1_ENST00000575907.1_Silent_p.A611A|RP11-455O6.2_ENST00000571085.1_RNA	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		611					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GCCGGCTCAGCGCCTTCTCTG	0.701													C|||	1108	0.221246	0.2927	0.2622	5008	,	,		12663	0.0149		0.4036	False		,,,				2504	0.1207				p.A608A		Atlas-SNP	.											AZI1_ENST00000450824,NS,carcinoma,0,2	AZI1	145	2	0			c.G1824A						PASS	.	C	,	1300,3068		187,926,1071	23.0	22.0	22.0		1824,1824	0.6	0.1	17	dbSNP_88	22	3373,5197		688,1997,1600	no	coding-synonymous,coding-synonymous	AZI1	NM_001009811.2,NM_014984.2	,	875,2923,2671	TT,TC,CC		39.3582,29.7619,36.1184	,	608/1045,608/1081	79170576	4673,8265	2184	4285	6469	SO:0001819	synonymous_variant	22994	exon15			GCTCAGCGCCTTC																												ENST00000269392.4:c.1833G>A	17.37:g.79170576C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_014984	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																				C|0.699;T|0.301	0.301	strong		0.701	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
TMC4	147798	hgsc.bcm.edu	37	19	54676763	54676763	+	Missense_Mutation	SNP	C	C	T	rs641738	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54676763C>T	ENST00000376591.4	-	1	181	c.50G>A	c.(49-51)gGg>gAg	p.G17E	TMC4_ENST00000301187.4_Missense_Mutation_p.G17E|TMC4_ENST00000476013.2_5'Flank	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	17			G -> E (in dbSNP:rs641738). {ECO:0000269|PubMed:12812529}.		ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(7)|large_intestine(4)|lung(6)|pancreas(1)|skin(1)|urinary_tract(1)	22	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GGCCAGCCACCCCCTAGAGGA	0.632													C|||	1872	0.373802	0.32	0.3429	5008	,	,		15567	0.2173		0.4404	False		,,,				2504	0.5613				p.G17E		Atlas-SNP	.											.	TMC4	89	.	0			c.G50A						PASS	.	C	GLU/GLY,GLU/GLY	1567,2839	480.3+/-358.8	280,1007,916	91.0	105.0	100.0		50,50	0.2	0.0	19	dbSNP_83	100	3725,4875	524.7+/-380.6	785,2155,1360	yes	missense,missense	TMC4	NM_001145303.1,NM_144686.2	98,98	1065,3162,2276	TT,TC,CC		43.314,35.5651,40.6889	benign,benign	17/713,17/707	54676763	5292,7714	2203	4300	6503	SO:0001583	missense	147798	exon1			AGCCACCCCCTAG	AY236492	CCDS12882.1, CCDS46174.1	19q13.42	2008-02-05			ENSG00000167608	ENSG00000167608			22998	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005277069		Approved		uc010erf.3	Q7Z404	OTTHUMG00000066485	ENST00000376591.4:c.50G>A	19.37:g.54676763C>T	ENSP00000365776:p.Gly17Glu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	37	CCDS46174.1	737	0.3374542124542125	159	0.3231707317073171	128	0.35359116022099446	112	0.1958041958041958	338	0.44591029023746703	C	11.35	1.613979	0.28712	0.355651	0.43314	ENSG00000167608	ENST00000301187;ENST00000376591	T;T	0.72615	-0.62;-0.67	3.92	0.213	0.15244	.	6.366860	0.00725	N	0.000915	T	0.00012	0.0000	L	0.45581	1.43	0.58432	P	9.000000000036756E-6	B;B	0.06786	0.001;0.001	B;B	0.08055	0.001;0.003	T	0.29088	-1.0023	9	0.05351	T	0.99	-3.0961	4.0735	0.09892	0.0:0.5573:0.1929:0.2497	rs641738;rs61242378;rs641738	17;17	Q7Z404;Q7Z404-1	TMC4_HUMAN;.	E	17	ENSP00000301187:G17E;ENSP00000365776:G17E	ENSP00000301187:G17E	G	-	2	0	TMC4	59368575	0.000000	0.05858	0.000000	0.03702	0.284000	0.27059	-1.506000	0.02271	0.015000	0.14971	0.462000	0.41574	GGG	C|0.615;T|0.385	0.385	strong		0.632	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
SERPINH1	871	hgsc.bcm.edu	37	11	75279846	75279846	+	Silent	SNP	C	C	T	rs649257	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:75279846C>T	ENST00000524558.1	+	3	2128	c.693C>T	c.(691-693)acC>acT	p.T231T	SERPINH1_ENST00000525876.1_Silent_p.T14T|SERPINH1_ENST00000533603.1_Silent_p.T231T|SERPINH1_ENST00000530284.1_Silent_p.T231T|SERPINH1_ENST00000358171.3_Silent_p.T231T			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	231					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T231T(1)		endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					GGTCCTATACCGTGGGTGTCA	0.567													C|||	1888	0.376997	0.4766	0.379	5008	,	,		19111	0.2103		0.2972	False		,,,				2504	0.4949				p.T231T		Atlas-SNP	.											SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	1	Substitution - coding silent(1)	stomach(1)	c.C693T						PASS	.	C	,	1954,2446	553.2+/-378.7	444,1066,690	149.0	113.0	125.0		693,693	-11.4	0.2	11	dbSNP_83	125	2616,5970	422.8+/-354.1	383,1850,2060	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	827,2916,2750	TT,TC,CC		30.4682,44.4091,35.1917	,	231/419,231/419	75279846	4570,8416	2200	4293	6493	SO:0001819	synonymous_variant	871	exon3			CTATACCGTGGGT	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.693C>T	11.37:g.75279846C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	22	0.23913	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			C|0.660;T|0.340	0.340	strong		0.567	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
HSPG2	3339	hgsc.bcm.edu	37	1	22167605	22167605	+	Missense_Mutation	SNP	C	C	T	rs2228349	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22167605C>T	ENST00000374695.3	-	71	9581	c.9502G>A	c.(9502-9504)Gcg>Acg	p.A3168T		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3168	Ig-like C2-type 17.		A -> T (in dbSNP:rs2228349). {ECO:0000269|PubMed:1730768}.		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGCAGCACCGCGTGGCTGTCC	0.652													C|||	419	0.0836661	0.1589	0.0504	5008	,	,		17437	0.0		0.0676	False		,,,				2504	0.1084				p.A3168T		Atlas-SNP	.											.	HSPG2	311	.	0			c.G9502A						PASS	.	C	THR/ALA	693,3705		52,589,1558	16.0	18.0	17.0		9502	-0.4	0.0	1	dbSNP_98	17	648,7940		26,596,3672	yes	missense	HSPG2	NM_005529.5	58	78,1185,5230	TT,TC,CC		7.5454,15.7572,10.3265	benign	3168/4392	22167605	1341,11645	2199	4294	6493	SO:0001583	missense	3339	exon71			GCACCGCGTGGCT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.9502G>A	1.37:g.22167605C>T	ENSP00000363827:p.Ala3168Thr	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	157	0.07188644688644688	85	0.17276422764227642	23	0.06353591160220995	0	0.0	49	0.06464379947229551	C	5.966	0.362139	0.11296	0.157572	0.075454	ENSG00000142798	ENST00000374695	T	0.67171	-0.25	4.74	-0.426	0.12314	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.681821	0.11989	N	0.509993	T	0.00210	0.0006	L	0.33668	1.02	0.80722	P	0.0	B;B	0.12630	0.006;0.006	B;B	0.19946	0.027;0.007	T	0.09862	-1.0655	9	0.22706	T	0.39	.	10.3134	0.43723	0.0:0.7534:0.0:0.2466	rs2228349;rs6701253	1108;3168	Q59EG0;P98160	.;PGBM_HUMAN	T	3168	ENSP00000363827:A3168T	ENSP00000363827:A3168T	A	-	1	0	HSPG2	22040192	0.823000	0.29233	0.022000	0.16811	0.010000	0.07245	0.911000	0.28584	0.024000	0.15214	-0.367000	0.07326	GCG	C|0.909;T|0.091	0.091	strong		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
USH2A	7399	hgsc.bcm.edu	37	1	216496947	216496947	+	Silent	SNP	G	G	A	rs1805050	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:216496947G>A	ENST00000307340.3	-	8	1805	c.1419C>T	c.(1417-1419)acC>acT	p.T473T	USH2A_ENST00000366943.2_Silent_p.T473T|USH2A_ENST00000366942.3_Silent_p.T473T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	473	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GAAGAGATGGGGTATTATAGA	0.393										HNSCC(13;0.011)			G|||	1317	0.262979	0.3911	0.2824	5008	,	,		13391	0.129		0.2386	False		,,,				2504	0.2393				p.T473T		Atlas-SNP	.											.	USH2A	1168	.	0			c.C1419T						PASS	.	G	,	1694,2712	512.1+/-368.0	340,1014,849	147.0	149.0	148.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1419,1419	0.5	1.0	1	dbSNP_89	148	2149,6451	369.5+/-335.5	280,1589,2431	no	coding-synonymous,coding-synonymous	USH2A	NM_007123.5,NM_206933.2	,	620,2603,3280	AA,AG,GG		24.9884,38.4476,29.5479	,	473/1547,473/5203	216496947	3843,9163	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon8			AGATGGGGTATTA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.1419C>T	1.37:g.216496947G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_007123	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			G|0.716;A|0.284	0.284	strong		0.393	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
TAF1C	9013	hgsc.bcm.edu	37	16	84218565	84218565	+	Silent	SNP	T	T	C	rs2230126	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84218565T>C	ENST00000567759.1	-	2	212	c.30A>G	c.(28-30)gcA>gcG	p.A10A	TAF1C_ENST00000378541.4_Silent_p.A10A|TAF1C_ENST00000341690.6_Intron|TAF1C_ENST00000541676.1_Intron|TAF1C_ENST00000565544.1_5'Flank|TAF1C_ENST00000570117.1_Intron|TAF1C_ENST00000566732.1_Silent_p.A10A	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	10					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						TCAGAAACAATGCAGGGCGGA	0.617													C|||	990	0.197684	0.2421	0.0749	5008	,	,		19474	0.2639		0.1521	False		,,,				2504	0.2035				p.A10A		Atlas-SNP	.											.	TAF1C	60	.	0			c.A30G						PASS	.	C	,	973,3427	721.9+/-409.2	111,751,1338	41.0	35.0	37.0		30,	-8.0	0.0	16	dbSNP_98	37	1252,7346	754.5+/-407.5	82,1088,3129	no	coding-synonymous,intron	TAF1C	NM_005679.3,NM_139353.2	,	193,1839,4467	CC,CT,TT		14.5615,22.1136,17.118	,	10/870,	84218565	2225,10773	2200	4299	6499	SO:0001819	synonymous_variant	9013	exon2			AAACAATGCAGGG	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.30A>G	16.37:g.84218565T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_001243156	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			T|0.829;C|0.171	0.171	strong		0.617	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
PAK2	5062	hgsc.bcm.edu	37	3	196544948	196544948	+	Silent	SNP	T	T	C	rs56172538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:196544948T>C	ENST00000327134.3	+	12	1396	c.1074T>C	c.(1072-1074)ttT>ttC	p.F358F		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	358	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		CATTGGAGTTTTTACATGCTA	0.398													T|||	494	0.0986422	0.2844	0.0519	5008	,	,		15485	0.0		0.0378	False		,,,				2504	0.045				p.F358F		Atlas-SNP	.											.	PAK2	113	.	0			c.T1074C						PASS	.	T		1136,3270	405.5+/-333.5	142,852,1209	116.0	103.0	107.0		1074	5.8	1.0	3	dbSNP_129	107	382,8218	123.8+/-182.6	12,358,3930	no	coding-synonymous	PAK2	NM_002577.4		154,1210,5139	CC,CT,TT		4.4419,25.783,11.6715		358/525	196544948	1518,11488	2203	4300	6503	SO:0001819	synonymous_variant	5062	exon12			GGAGTTTTTACAT	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.1074T>C	3.37:g.196544948T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1	160	0.07326007326007326	116	0.23577235772357724	17	0.04696132596685083	0	0.0	27	0.03562005277044855	T	10.14	1.268826	0.23136	0.25783	0.044419	ENSG00000180370	ENST00000426668	T	0.68025	-0.3	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.39981	-0.9587	6	0.66056	D	0.02	.	6.417	0.21721	0.0:0.1886:0.0:0.8114	rs56172538;rs61735863	.	.	.	S	101	ENSP00000402927:F101S	ENSP00000402927:F101S	F	+	2	0	PAK2	198029345	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.134000	0.31442	2.326000	0.78906	0.533000	0.62120	TTT	T|0.896;C|0.104	0.104	strong		0.398	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
PEG3	5178	hgsc.bcm.edu	37	19	57335022	57335022	+	Silent	SNP	G	G	A	rs1860565	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57335022G>A	ENST00000326441.9	-	5	783	c.420C>T	c.(418-420)agC>agT	p.S140S	ZIM2_ENST00000593711.1_Silent_p.S14S|PEG3_ENST00000598410.1_Silent_p.S14S|ZIM2_ENST00000221722.5_Silent_p.S14S|ZIM2_ENST00000599935.1_Silent_p.S14S|ZIM2_ENST00000601070.1_Silent_p.S14S|PEG3_ENST00000594706.1_5'Flank|ZIM2_ENST00000391708.3_Silent_p.S14S|ZIM2_ENST00000593931.1_Silent_p.S14S|PEG3_ENST00000423103.2_Silent_p.S140S|PEG3_ENST00000593695.1_Silent_p.S14S	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	140					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)		TGTCGTCGTCGCTGGTCACGT	0.557													G|||	1020	0.203674	0.0424	0.3285	5008	,	,		18634	0.1677		0.2773	False		,,,				2504	0.2945				p.S140S		Atlas-SNP	.											.	PEG3	414	.	0			c.C420T						PASS	.	G	,,,,,,,	340,4066	177.3+/-206.3	16,308,1879	287.0	210.0	236.0		420,42,420,42,42,42,420,42	-7.9	0.0	19	dbSNP_92	236	2462,6138	405.2+/-348.4	366,1730,2204	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PEG3,ZIM2	NM_001146184.1,NM_001146185.1,NM_001146186.1,NM_001146187.1,NM_001146326.1,NM_001146327.1,NM_006210.2,NM_015363.4	,,,,,,,	382,2038,4083	AA,AG,GG		28.6279,7.7167,21.5439	,,,,,,,	140/1589,14/1463,140/1589,14/1465,14/528,14/528,140/1589,14/528	57335022	2802,10204	2203	4300	6503	SO:0001819	synonymous_variant	5178	exon4			GTCGTCGCTGGTC	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.420C>T	19.37:g.57335022G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	37	CCDS12948.1																																																																																			G|0.798;A|0.202	0.202	strong		0.557	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
TMEM71	137835	hgsc.bcm.edu	37	8	133759318	133759318	+	Silent	SNP	A	A	G	rs74775484	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:133759318A>G	ENST00000377901.4	-	5	499	c.357T>C	c.(355-357)tcT>tcC	p.S119S	TMEM71_ENST00000517538.1_5'UTR|TMEM71_ENST00000356838.3_Intron|TMEM71_ENST00000523829.1_Silent_p.S119S	NM_001145153.1	NP_001138625.1	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	119						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			GGTTGAAGAGAGAAGAAAAGG	0.393													A|||	210	0.0419329	0.0076	0.0937	5008	,	,		20297	0.0		0.0974	False		,,,				2504	0.0378				p.S119S		Atlas-SNP	.											TMEM71_ENST00000377901,right_upper_lobe,carcinoma,0,1	TMEM71	55	1	0			c.T357C						PASS	.	A	,	82,4324	70.3+/-108.2	1,80,2122	78.0	71.0	74.0		357,	-1.5	1.0	8	dbSNP_132	74	1029,7571	214.1+/-253.8	61,907,3332	no	coding-synonymous,intron	TMEM71	NM_001145153.1,NM_144649.2	,	62,987,5454	GG,GA,AA		11.9651,1.8611,8.5422	,	119/233,	133759318	1111,11895	2203	4300	6503	SO:0001819	synonymous_variant	137835	exon5			GAAGAGAGAAGAA	AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000377901.4:c.357T>C	8.37:g.133759318A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_001145153	Q3KRC2|Q8WVZ4|Q96LX9	Silent	SNP	ENST00000377901.4	37	CCDS47921.1																																																																																			A|0.937;G|0.063	0.063	strong		0.393	TMEM71-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000379592.1	NM_144649	
RNF213	57674	hgsc.bcm.edu	37	17	78327358	78327358	+	Silent	SNP	G	G	A	rs7216493	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78327358G>A	ENST00000582970.1	+	34	10613	c.10470G>A	c.(10468-10470)gaG>gaA	p.E3490E	CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Silent_p.E1563E|RNF213_ENST00000508628.2_Silent_p.E3539E|CTD-2047H16.4_ENST00000572151.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3490					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E1563E(1)|p.E3539E(1)		NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGGCGATGGAGACGGAGGCCA	0.582													A|||	3150	0.628994	0.6967	0.5086	5008	,	,		17572	0.5486		0.7346	False		,,,				2504	0.5971				p.E3490E		Atlas-SNP	.											RNF213_ENST00000411702,NS,carcinoma,0,2	RNF213	766	2	2	Substitution - coding silent(2)	stomach(2)	c.G10470A						PASS	.	A		3077,1329	445.3+/-347.6	1089,899,215	86.0	73.0	77.0		10617	-5.8	0.0	17	dbSNP_116	77	6149,2451	402.5+/-347.5	2202,1745,353	no	coding-synonymous	RNF213	NM_020914.4		3291,2644,568	AA,AG,GG		28.5,30.1634,29.0635		3539/5257	78327358	9226,3780	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon34			GATGGAGACGGAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.10470G>A	17.37:g.78327358G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			G|0.313;A|0.687	0.687	strong		0.582	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242198	81242198	+	RNA	SNP	G	G	A	rs7499011	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:81242198G>A	ENST00000525539.1	-	0	657				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGTAGCTCCTGGCACTGGCCT	0.552													G|||	810	0.161741	0.0923	0.2349	5008	,	,		20582	0.003		0.3837	False		,,,				2504	0.1391				p.Q220X		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C658T						PASS	.	G	stop/GLN,stop/GLN	597,3607		50,497,1555	66.0	63.0	64.0		658,658	4.3	1.0	16	dbSNP_116	64	3074,5372		536,2002,1685	yes	stop-gained,stop-gained	PKD1L2	NM_001076780.1,NM_052892.3	,	586,2499,3240	AA,AG,GG		36.3959,14.2008,29.0198	,	220/992,220/2460	81242198	3671,8979	2102	4223	6325			114780	exon4			GCTCCTGGCACTG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242198G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	34	11	0.323529	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Nonsense_Mutation	SNP	ENST00000525539.1	37		427	0.1955128205128205	39	0.07926829268292683	109	0.3011049723756906	1	0.0017482517482517483	278	0.36675461741424803	G	30	5.056326	0.93793	0.142008	0.363959	ENSG00000166473	ENST00000337114	.	.	.	4.31	4.31	0.51392	.	0.067881	0.64402	D	0.000017	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-12.5705	16.402	0.83643	0.0:0.0:1.0:0.0	rs7499011	.	.	.	X	220	.	ENSP00000337397:Q220X	Q	-	1	0	PKD1L2	79799699	1.000000	0.71417	1.000000	0.80357	0.521000	0.34408	7.373000	0.79623	1.957000	0.56846	0.313000	0.20887	CAG	G|0.742;A|0.258	0.258	strong		0.552	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
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 GAIIx	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	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	169	72	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	
NRBP2	340371	hgsc.bcm.edu	37	8	144917880	144917880	+	Silent	SNP	G	G	A	rs72693365	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144917880G>A	ENST00000442628.2	-	18	1597	c.1458C>T	c.(1456-1458)gcC>gcT	p.A486A	NRBP2_ENST00000327830.5_Silent_p.A243A|RP11-299M14.2_ENST00000534006.1_RNA	NM_178564.3	NP_848659.2			nuclear receptor binding protein 2											central_nervous_system(2)|kidney(1)|large_intestine(2)	5	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-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;1.23e-39)|all cancers(56;6.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			CCAGGAAGGCGGCCAGCTTCA	0.751													G|||	213	0.0425319	0.0106	0.0504	5008	,	,		11476	0.0109		0.0944	False		,,,				2504	0.0593				p.A486A		Atlas-SNP	.											.	NRBP2	20	.	0			c.C1458T						PASS	.	G		103,4299	79.9+/-118.3	3,97,2101	35.0	34.0	34.0		1458	-5.0	0.2	8	dbSNP_130	34	791,7807	180.8+/-229.6	44,703,3552	no	coding-synonymous	NRBP2	NM_178564.3		47,800,5653	AA,AG,GG		9.1998,2.3398,6.8769		486/502	144917880	894,12106	2201	4299	6500	SO:0001819	synonymous_variant	340371	exon18			GAAGGCGGCCAGC	BC037396	CCDS34959.1, CCDS34959.2	8q24.3	2005-01-24							19339	protein-coding gene	gene with protein product		615563				14702039	Standard	NM_178564		Approved	DKFZp434P086	uc011lkt.2	Q9NSY0		ENST00000442628.2:c.1458C>T	8.37:g.144917880G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_178564		Silent	SNP	ENST00000442628.2	37	CCDS34959.2	105	0.04807692307692308	4	0.008130081300813009	25	0.06906077348066299	6	0.01048951048951049	70	0.09234828496042216	G	11.59	1.684044	0.29872	0.023398	0.091998	ENSG00000185189	ENST00000530123	.	.	.	3.8	-5.0	0.03001	.	.	.	.	.	T	0.00608	0.0020	.	.	.	0.23243	P	0.99805051	.	.	.	.	.	.	T	0.19679	-1.0298	3	.	.	.	-27.4645	2.2889	0.04134	0.4716:0.1213:0.2783:0.1288	.	.	.	.	L	78	.	.	P	-	2	0	NRBP2	144989868	0.000000	0.05858	0.212000	0.23672	0.794000	0.44872	-2.313000	0.01126	-1.097000	0.03042	-0.291000	0.09656	CCG	G|0.942;A|0.058	0.058	strong		0.751	NRBP2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382247.1	NM_178564	
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 GAIIx	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_ENST00000354233.3_Silent_p.T634T|HCFC1_ENST00000369984.4_Silent_p.T703T|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		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	98	22	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	
FBF1	85302	hgsc.bcm.edu	37	17	73926121	73926121	+	Missense_Mutation	SNP	C	C	A	rs1135889	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73926121C>A	ENST00000586717.1	-	6	467	c.194G>T	c.(193-195)gGt>gTt	p.G65V	FBF1_ENST00000389570.4_Missense_Mutation_p.G65V|FBF1_ENST00000319129.5_Missense_Mutation_p.G65V			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	65			G -> V (in dbSNP:rs1135889). {ECO:0000269|PubMed:18838552}.		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)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						CTCTGAGATACCTGAAACCTA	0.537													C|||	887	0.177117	0.1755	0.1585	5008	,	,		14754	0.1597		0.2386	False		,,,				2504	0.1472				p.G65V		Atlas-SNP	.											FBF1_ENST00000319129,NS,carcinoma,0,1	FBF1	48	1	0			c.G194T						PASS	.	C	VAL/GLY	672,3230		69,534,1348	27.0	26.0	26.0		194	2.8	0.0	17	dbSNP_86	26	1782,6454		205,1372,2541	yes	missense	FBF1	NM_001080542.1	109	274,1906,3889	AA,AC,CC		21.6367,17.2219,20.2175	benign	65/1134	73926121	2454,9684	1951	4118	6069	SO:0001583	missense	85302	exon6			GAGATACCTGAAA	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.194G>T	17.37:g.73926121C>A	ENSP00000465132:p.Gly65Val	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		418	0.19139194139194138	75	0.1524390243902439	68	0.1878453038674033	102	0.17832167832167833	173	0.22823218997361477	C	8.830	0.939757	0.18281	0.172219	0.216367	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.17370	2.28;2.28	4.97	2.76	0.32466	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P;P;P	0.49090	0.919;0.646;0.589	B;B;B	0.41894	0.277;0.369;0.277	T	0.41052	-0.9530	8	0.52906	T	0.07	-3.5376	7.7876	0.29101	0.0:0.2708:0.0:0.7292	rs1135889;rs3198846;rs3803732;rs17420316;rs17497868;rs17856696;rs52809303;rs60937677;rs1135889	79;65;65	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	V	65;65;65;78	ENSP00000374221:G65V;ENSP00000324292:G65V	ENSP00000324292:G65V	G	-	2	0	FBF1	71437716	0.551000	0.26497	0.041000	0.18516	0.458000	0.32498	2.204000	0.42761	0.264000	0.21851	-0.302000	0.09304	GGT	C|0.810;A|0.190	0.190	strong		0.537	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
OR2A2	442361	hgsc.bcm.edu	37	7	143806688	143806688	+	Missense_Mutation	SNP	C	C	A	rs10230228	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143806688C>A	ENST00000408979.2	+	1	82	c.13C>A	c.(13-15)Cag>Aag	p.Q5K		NM_001005480.2	NP_001005480.2	Q6IF42	OR2A2_HUMAN	olfactory receptor, family 2, subfamily A, member 2	5			Q -> K (in dbSNP:rs10230228).			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(1)|large_intestine(2)|lung(13)|prostate(1)|skin(4)	22	Melanoma(164;0.0783)					GGAAGGCAACCAGACATGGAT	0.498													.|||	780	0.155751	0.3888	0.1297	5008	,	,		18028	0.0		0.166	False		,,,				2504	0.0092				p.Q5K		Atlas-SNP	.											OR2A2,rectum,carcinoma,-2,1	OR2A2	48	1	0			c.C13A						scavenged	.	C	LYS/GLN	1435,2573		247,941,816	106.0	103.0	104.0		13	2.7	1.0	7	dbSNP_119	104	1680,6692		156,1368,2662	yes	missense	OR2A2	NM_001005480.2	53	403,2309,3478	AA,AC,CC		20.0669,35.8034,25.1616	benign	5/319	143806688	3115,9265	2004	4186	6190	SO:0001583	missense	442361	exon1			GGCAACCAGACAT		CCDS43671.1	7q35	2013-09-20		2004-03-10	ENSG00000221989	ENSG00000221989		"""GPCR / Class A : Olfactory receptors"""	8230	protein-coding gene	gene with protein product				OR2A2P, OR2A17P			Standard	NM_001005480		Approved	OST008	uc011ktz.2	Q6IF42	OTTHUMG00000158001	ENST00000408979.2:c.13C>A	7.37:g.143806688C>A	ENSP00000386209:p.Gln5Lys	Somatic	152	1	0.00657895		WXS	Illumina HiSeq	Phase_I	172	76	0.44186	NM_001005480	B2RN85|Q8NGT6	Missense_Mutation	SNP	ENST00000408979.2	37	CCDS43671.1	364	0.16666666666666666	193	0.39227642276422764	51	0.1408839779005525	0	0.0	120	0.158311345646438	C	11.74	1.729249	0.30684	0.358034	0.200669	ENSG00000221989	ENST00000408979	T	0.00625	6.14	3.61	2.68	0.31781	.	.	.	.	.	T	0.00012	0.0000	L	0.54908	1.71	0.80722	P	0.0	B	0.15719	0.014	B	0.17433	0.018	T	0.29941	-0.9995	8	0.45353	T	0.12	.	8.8126	0.34976	0.0:0.7679:0.2321:0.0	rs10230228	5	Q6IF42	OR2A2_HUMAN	K	5	ENSP00000386209:Q5K	ENSP00000386209:Q5K	Q	+	1	0	OR2A2	143437621	0.002000	0.14202	0.996000	0.52242	0.990000	0.78478	-0.074000	0.11450	0.802000	0.34089	0.609000	0.83330	CAG	C|0.826;A|0.174	0.174	strong		0.498	OR2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349978.1		
MARC2	54996	hgsc.bcm.edu	37	1	220928313	220928313	+	Silent	SNP	T	T	C	rs12044903	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:220928313T>C	ENST00000366913.3	+	2	495	c.297T>C	c.(295-297)gaT>gaC	p.D99D	MARC2_ENST00000359316.2_Silent_p.D99D	NM_017898.3	NP_060368.2	Q969Z3	MARC2_HUMAN	mitochondrial amidoxime reducing component 2	99					detoxification of nitrogen compound (GO:0051410)|nitrate metabolic process (GO:0042126)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|nitrate reductase activity (GO:0008940)|pyridoxal phosphate binding (GO:0030170)										TTAAGGAAGATGGACACATGG	0.512													T|||	111	0.0221645	0.003	0.0014	5008	,	,		19008	0.0585		0.0099	False		,,,				2504	0.0378				p.D99D		Atlas-SNP	.											.	.	.	.	0			c.T297C						PASS	.	T		15,4391	22.3+/-47.3	0,15,2188	177.0	176.0	176.0		297	1.9	0.9	1	dbSNP_120	176	47,8553	30.1+/-81.4	0,47,4253	no	coding-synonymous	MOSC2	NM_017898.3		0,62,6441	CC,CT,TT		0.5465,0.3404,0.4767		99/336	220928313	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	54996	exon2			GGAAGATGGACAC		CCDS1525.1	1q41	2011-11-02	2011-11-02	2011-11-02	ENSG00000117791	ENSG00000117791			26064	protein-coding gene	gene with protein product		614127	"""MOCO sulphurase C-terminal domain containing 2"""	MOSC2		11886751	Standard	NM_017898		Approved	FLJ20605	uc001hmq.3	Q969Z3	OTTHUMG00000037354	ENST00000366913.3:c.297T>C	1.37:g.220928313T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	102	42	0.411765	NM_017898	B2D0R5|D3DTB3|Q0JSK7|Q5VT67|Q5VXC7|Q7L317|Q9H066|Q9NWU0	Silent	SNP	ENST00000366913.3	37	CCDS1525.1																																																																																			T|0.984;C|0.016	0.016	strong		0.512	MARC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090911.1	NM_017898	
COL3A1	1281	hgsc.bcm.edu	37	2	189864080	189864080	+	Missense_Mutation	SNP	G	G	A	rs1800255	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:189864080G>A	ENST00000304636.3	+	30	2262	c.2092G>A	c.(2092-2094)Gct>Act	p.A698T	COL3A1_ENST00000317840.5_Missense_Mutation_p.A698T	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	698	Triple-helical region.		A -> T (in dbSNP:rs1800255). {ECO:0000269|PubMed:18272325, ECO:0000269|PubMed:2235526}.		aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	TAGAGGTGGAGCTGGTCCCCC	0.463													G|||	1094	0.21845	0.1051	0.2522	5008	,	,		15459	0.2331		0.2624	False		,,,				2504	0.2873				p.A698T		Atlas-SNP	.											.	COL3A1	292	.	0			c.G2092A	GRCh37	CM086593	COL3A1	M	rs1800255	PASS	.	G	THR/ALA	592,3814		40,512,1651	36.0	38.0	37.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2092	0.9	1.0	2	dbSNP_89	37	2190,6410		297,1596,2407	yes	missense	COL3A1	NM_000090.3	58	337,2108,4058	AA,AG,GG		25.4651,13.4362,21.3901	benign	698/1467	189864080	2782,10224	2203	4300	6503	SO:0001583	missense	1281	exon30			GGTGGAGCTGGTC	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2092G>A	2.37:g.189864080G>A	ENSP00000304408:p.Ala698Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	456	0.2087912087912088	39	0.07926829268292683	85	0.23480662983425415	139	0.243006993006993	193	0.2546174142480211	G	14.88	2.666284	0.47677	0.134362	0.254651	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.93488	-3.23;-3.22	4.96	0.873	0.19118	.	0.169588	0.27912	N	0.017354	T	0.00073	0.0002	N	0.16266	0.395	0.34524	P	0.291559	B	0.02656	0.0	B	0.01281	0.0	T	0.11767	-1.0574	9	0.28530	T	0.3	.	1.7367	0.02943	0.2601:0.2137:0.4107:0.1155	rs1800255;rs3817316;rs17831227;rs52832986;rs1800255	698	P02461	CO3A1_HUMAN	T	698	ENSP00000304408:A698T;ENSP00000315243:A698T	ENSP00000304408:A698T	A	+	1	0	COL3A1	189572325	0.046000	0.20272	0.979000	0.43373	0.998000	0.95712	0.487000	0.22356	0.246000	0.21394	0.650000	0.86243	GCT	G|0.808;A|0.192	0.192	strong		0.463	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
OR10A2	341276	hgsc.bcm.edu	37	11	6891528	6891528	+	Silent	SNP	C	C	G	rs7117739	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6891528C>G	ENST00000307322.4	+	1	605	c.543C>G	c.(541-543)ctC>ctG	p.L181L		NM_001004460.1	NP_001004460.1	Q9H208	O10A2_HUMAN	olfactory receptor, family 10, subfamily A, member 2	181						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)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(12)|urinary_tract(1)	24		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.89e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		ACACAGCACTCTTTGAGATCT	0.512													-|||	1643	0.328075	0.2073	0.379	5008	,	,		21095	0.3135		0.3678	False		,,,				2504	0.4294				p.L181L		Atlas-SNP	.											.	OR10A2	55	.	0			c.C543G						PASS	.	G		898,3504		92,714,1395	221.0	171.0	188.0		543	0.9	0.4	11	dbSNP_116	188	3344,5248		664,2016,1616	yes	coding-synonymous	OR10A2	NM_001004460.1		756,2730,3011	GG,GC,CC		38.9199,20.3998,32.6458		181/304	6891528	4242,8752	2201	4296	6497	SO:0001819	synonymous_variant	341276	exon1			AGCACTCTTTGAG	BK004293	CCDS31415.1	11p15.4	2012-08-09		2004-03-10	ENSG00000170790	ENSG00000170790		"""GPCR / Class A : Olfactory receptors"""	8161	protein-coding gene	gene with protein product				OR10A2P			Standard	NM_001004460		Approved	OST363	uc001meu.1	Q9H208	OTTHUMG00000165739	ENST00000307322.4:c.543C>G	11.37:g.6891528C>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	161	66	0.409938	NM_001004460	B2RNL9|Q6IFG9	Silent	SNP	ENST00000307322.4	37	CCDS31415.1																																																																																			C|0.680;G|0.320	0.320	strong		0.512	OR10A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385984.1	NM_001004460	
HSPA4L	22824	hgsc.bcm.edu	37	4	128741710	128741710	+	Missense_Mutation	SNP	T	T	C	rs35518193	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:128741710T>C	ENST00000296464.4	+	14	2213	c.1802T>C	c.(1801-1803)aTt>aCt	p.I601T	HSPA4L_ENST00000505726.1_Missense_Mutation_p.I575T|HSPA4L_ENST00000439123.2_Missense_Mutation_p.I632T|HSPA4L_ENST00000508776.1_Missense_Mutation_p.I601T	NM_014278.2	NP_055093.2	O95757	HS74L_HUMAN	heat shock 70kDa protein 4-like	601			I -> T (in dbSNP:rs35518193).		protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)			central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						AACAGCTACATTGAAAATGAG	0.343													T|||	100	0.0199681	0.003	0.0447	5008	,	,		16572	0.001		0.0537	False		,,,				2504	0.0102				p.I601T		Atlas-SNP	.											HSPA4L,NS,carcinoma,-1,2	HSPA4L	82	2	0			c.T1802C						PASS	.	T	THR/ILE	53,4353	52.3+/-87.9	0,53,2150	92.0	85.0	87.0		1802	4.7	1.0	4	dbSNP_126	87	451,8149	134.9+/-192.2	14,423,3863	yes	missense	HSPA4L	NM_014278.2	89	14,476,6013	CC,CT,TT		5.2442,1.2029,3.8751	benign	601/840	128741710	504,12502	2203	4300	6503	SO:0001583	missense	22824	exon14			GCTACATTGAAAA	AB023421	CCDS3734.1	4q28	2011-09-07			ENSG00000164070	ENSG00000164070		"""Heat shock proteins / HSP70"""	17041	protein-coding gene	gene with protein product						10524232	Standard	NM_014278		Approved	APG-1, Osp94, HSPH3	uc003ifm.3	O95757	OTTHUMG00000133302	ENST00000296464.4:c.1802T>C	4.37:g.128741710T>C	ENSP00000296464:p.Ile601Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_014278	A2ICT2|Q4W5M5|Q8IWA2	Missense_Mutation	SNP	ENST00000296464.4	37	CCDS3734.1	58	0.026556776556776556	2	0.0040650406504065045	18	0.049723756906077346	1	0.0017482517482517483	37	0.048812664907651716	T	13.09	2.133545	0.37630	0.012029	0.052442	ENSG00000164070	ENST00000508776;ENST00000439123;ENST00000296464;ENST00000505726	T;T;T;T	0.01076	5.37;5.37;5.37;5.37	4.72	4.72	0.59763	.	0.064564	0.64402	D	0.000008	T	0.00241	0.0007	N	0.20574	0.59	0.47737	D	0.9995	B;P;P	0.43826	0.117;0.818;0.818	B;B;B	0.42163	0.223;0.378;0.378	T	0.82174	-0.0588	10	0.19147	T	0.46	.	14.3819	0.66916	0.0:0.0:0.0:1.0	rs35518193;rs61752611;rs35518193	575;601;601	E9PDE8;A2ICT2;O95757	.;.;HS74L_HUMAN	T	601;632;601;575	ENSP00000422482:I601T;ENSP00000393926:I632T;ENSP00000296464:I601T;ENSP00000425645:I575T	ENSP00000296464:I601T	I	+	2	0	HSPA4L	128961160	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.923000	0.75817	1.984000	0.57885	0.528000	0.53228	ATT	T|0.967;C|0.033	0.033	strong		0.343	HSPA4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257096.3	NM_014278	
RPS6KB2	6199	hgsc.bcm.edu	37	11	67200819	67200819	+	Silent	SNP	C	C	T	rs4930427	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:67200819C>T	ENST00000312629.5	+	10	852	c.807C>T	c.(805-807)ttC>ttT	p.F269F	AP003419.16_ENST00000535922.1_RNA	NM_003952.2	NP_003943.2	Q9UBS0	KS6B2_HUMAN	ribosomal protein S6 kinase, 70kDa, polypeptide 2	269	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of translational initiation (GO:0045948)|protein kinase B signaling (GO:0043491)|signal transduction (GO:0007165)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|peptide binding (GO:0042277)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)	p.F269F(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|prostate(3)|salivary_gland(1)|stomach(2)	25			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			AGCCGCCCTTCACCGCAGAGA	0.637													C|||	1783	0.35603	0.3283	0.5389	5008	,	,		17222	0.3264		0.4225	False		,,,				2504	0.226				p.F269F		Atlas-SNP	.											RPS6KB2_ENST00000312629,NS,carcinoma,0,1	RPS6KB2	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C807T						PASS	.	C		1221,2719		198,825,947	89.0	100.0	97.0		807	0.6	1.0	11	dbSNP_111	97	3473,4791		759,1955,1418	no	coding-synonymous	RPS6KB2	NM_003952.2		957,2780,2365	TT,TC,CC		42.0257,30.9898,38.4628		269/483	67200819	4694,7510	1970	4132	6102	SO:0001819	synonymous_variant	6199	exon10			GCCCTTCACCGCA	AB019245	CCDS41677.1	11q13.1	2011-04-05	2002-08-29		ENSG00000175634	ENSG00000175634			10437	protein-coding gene	gene with protein product		608939	"""ribosomal protein S6 kinase, 70kD, polypeptide 2"""			9878560, 9804755	Standard	XM_005274164		Approved	p70S6Kb, P70-BETA, STK14B, KLS	uc001old.3	Q9UBS0	OTTHUMG00000167673	ENST00000312629.5:c.807C>T	11.37:g.67200819C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	35	33	0.942857	NM_003952	B2RMZ9|B4DML8|O94809|Q9UEC1	Silent	SNP	ENST00000312629.5	37	CCDS41677.1																																																																																			A|0.000;C|0.599;T|0.400	0.400	strong		0.637	RPS6KB2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395508.1	NM_003952	
GZMB	3002	hgsc.bcm.edu	37	14	25102160	25102160	+	Missense_Mutation	SNP	C	C	T	rs8192917	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:25102160C>T	ENST00000216341.4	-	2	270	c.164G>A	c.(163-165)cGa>cAa	p.R55Q	GZMB_ENST00000382542.1_Missense_Mutation_p.R89Q|RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000415355.3_Missense_Mutation_p.R43Q|GZMB_ENST00000382540.1_Missense_Mutation_p.R55Q|GZMB_ENST00000526004.1_Missense_Mutation_p.R55Q|RP11-104E19.1_ENST00000555300.1_RNA			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	55	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> Q (in dbSNP:rs8192917). {ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2332171, ECO:0000269|PubMed:2365998, ECO:0000269|PubMed:2788607, ECO:0000269|PubMed:2953813, ECO:0000269|PubMed:3261871}.		apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		GAAGTCGTCTCGTATCAGGAA	0.567													C|||	3409	0.680711	0.5605	0.781	5008	,	,		18657	0.7133		0.7525	False		,,,				2504	0.6646				p.R55Q		Atlas-SNP	.											.	GZMB	73	.	0			c.G164A	GRCh37	CM033775	GZMB	M	rs8192917	PASS	.	C	GLN/ARG	2622,1784	643.2+/-397.8	773,1076,354	93.0	86.0	89.0	http://www.ncbi.nlm.nih.gov/pubmed?term	164	-1.1	0.0	14	dbSNP_117	89	6567,2033	721.1+/-406.3	2509,1549,242	yes	missense	GZMB	NM_004131.4	43	3282,2625,596	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	23.6395,40.4902,29.348	benign	55/248	25102160	9189,3817	2203	4300	6503	SO:0001583	missense	3002	exon2			TCGTCTCGTATCA	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.164G>A	14.37:g.25102160C>T	ENSP00000216341:p.Arg55Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_004131	Q8N1D2|Q9UCC1	Missense_Mutation	SNP	ENST00000216341.4	37	CCDS9633.1	1561	0.7147435897435898	283	0.5752032520325203	278	0.7679558011049724	434	0.7587412587412588	566	0.7467018469656992	C	15.26	2.780393	0.49891	0.595098	0.763605	ENSG00000100453	ENST00000415355;ENST00000216341;ENST00000382542;ENST00000382540;ENST00000526004	T;D;D;T;T	0.92858	0.29;-3.12;-3.12;1.57;-1.49	5.04	-1.15	0.09709	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.691781	0.11207	N	0.588120	T	0.00012	0.0000	N	0.05574	-0.02	0.80722	P	0.0	B	0.31879	0.344	B	0.19946	0.027	T	0.43621	-0.9380	9	0.27082	T	0.32	.	8.5337	0.33351	0.0:0.421:0.0:0.579	rs8192917;rs17852739;rs52814528;rs58138662;rs8192917	55	P10144	GRAB_HUMAN	Q	43;55;89;55;55	ENSP00000387385:R43Q;ENSP00000216341:R55Q;ENSP00000371982:R89Q;ENSP00000371980:R55Q;ENSP00000434213:R55Q	ENSP00000216341:R55Q	R	-	2	0	GZMB	24172000	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-1.293000	0.02770	-0.100000	0.12241	-0.150000	0.13652	CGA	C|0.297;T|0.703	0.703	strong		0.567	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
PCDHB15	56121	hgsc.bcm.edu	37	5	140625629	140625629	+	Silent	SNP	C	C	T	rs150283740	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140625629C>T	ENST00000231173.3	+	1	483	c.483C>T	c.(481-483)gaC>gaT	p.D161D		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	161	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(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGGACTTGGACGTGGGCAGCA	0.463													C|||	14	0.00279553	0.0	0.013	5008	,	,		19285	0.0		0.005	False		,,,				2504	0.0				p.D161D		Atlas-SNP	.											PCDHB15,NS,carcinoma,+2,1	PCDHB15	138	1	0			c.C483T						PASS	.	C		10,4396	817.8+/-416.3	0,10,2193	52.0	55.0	54.0		483	0.4	1.0	5	dbSNP_134	54	69,8531	809.7+/-407.1	0,69,4231	no	coding-synonymous	PCDHB15	NM_018935.2		0,79,6424	TT,TC,CC		0.8023,0.227,0.6074		161/788	140625629	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	56121	exon1			CTTGGACGTGGGC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.483C>T	5.37:g.140625629C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			C|0.994;T|0.006	0.006	strong		0.463	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
MATN1	4146	hgsc.bcm.edu	37	1	31188089	31188089	+	Silent	SNP	C	C	T	rs1065755	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:31188089C>T	ENST00000373765.4	-	6	1310	c.1275G>A	c.(1273-1275)gaG>gaA	p.E425E	MATN1_ENST00000477320.1_5'Flank	NM_002379.3	NP_002370.1	P21941	MATN1_HUMAN	matrilin 1, cartilage matrix protein	425	VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|growth plate cartilage chondrocyte morphogenesis (GO:0003429)|protein complex assembly (GO:0006461)|regulation of bone mineralization (GO:0030500)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.00792)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)|Ovarian(437;0.0563)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		Colorectal(126;1.29e-05)|COAD - Colon adenocarcinoma(152;0.000726)|STAD - Stomach adenocarcinoma(196;0.0183)|READ - Rectum adenocarcinoma(331;0.0649)		CTGCCACAGGCTCTGAGGCTA	0.532													C|||	1440	0.28754	0.2564	0.4121	5008	,	,		22606	0.1835		0.3638	False		,,,				2504	0.2699				p.E425E		Atlas-SNP	.											.	MATN1	28	.	0			c.G1275A						PASS	.	C		1282,3124	436.4+/-344.6	173,936,1094	224.0	184.0	198.0		1275	-0.2	0.9	1	dbSNP_86	198	2922,5678	455.2+/-363.7	504,1914,1882	no	coding-synonymous	MATN1	NM_002379.3		677,2850,2976	TT,TC,CC		33.9767,29.0967,32.3235		425/497	31188089	4204,8802	2203	4300	6503	SO:0001819	synonymous_variant	4146	exon6			CACAGGCTCTGAG	M55675	CCDS336.1	1p35	2008-02-05			ENSG00000162510	ENSG00000162510			6907	protein-coding gene	gene with protein product		115437		CRTM, CMP		2246248, 9083061	Standard	NM_002379		Approved		uc001brz.3	P21941	OTTHUMG00000003705	ENST00000373765.4:c.1275G>A	1.37:g.31188089C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	196	104	0.530612	NM_002379	B2R7E3|Q5TBB9	Silent	SNP	ENST00000373765.4	37	CCDS336.1																																																																																			C|0.696;T|0.304	0.304	strong		0.532	MATN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010458.1	NM_002379	
FLRT2	23768	hgsc.bcm.edu	37	14	86089315	86089315	+	Missense_Mutation	SNP	G	G	A	rs17646457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:86089315G>A	ENST00000330753.4	+	2	2224	c.1457G>A	c.(1456-1458)cGa>cAa	p.R486Q	FLRT2_ENST00000554746.1_Missense_Mutation_p.R486Q	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	486	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> Q (in dbSNP:rs17646457). {ECO:0000269|PubMed:15489334}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.R486Q(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TTAGAGCCCCGATCCACCTAT	0.522													G|||	594	0.11861	0.0189	0.2118	5008	,	,		17172	0.0605		0.1481	False		,,,				2504	0.2168				p.R486Q		Atlas-SNP	.											FLRT2,NS,carcinoma,0,1	FLRT2	168	1	1	Substitution - Missense(1)	stomach(1)	c.G1457A						PASS	.	G	GLN/ARG	151,4255	103.0+/-141.5	1,149,2053	149.0	130.0	136.0		1457	2.9	1.0	14	dbSNP_123	136	1287,7313	255.8+/-280.5	107,1073,3120	yes	missense	FLRT2	NM_013231.4	43	108,1222,5173	AA,AG,GG		14.9651,3.4271,11.0564	benign	486/661	86089315	1438,11568	2203	4300	6503	SO:0001583	missense	23768	exon2			AGCCCCGATCCAC	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1457G>A	14.37:g.86089315G>A	ENSP00000332879:p.Arg486Gln	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	221	96	0.434389	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	224	0.10256410256410256	13	0.026422764227642278	65	0.17955801104972377	36	0.06293706293706294	110	0.14511873350923482	G	9.487	1.099582	0.20552	0.034271	0.149651	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.56776	0.44;0.44	5.87	2.87	0.33458	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.339988	0.32120	N	0.006545	T	0.00073	0.0002	N	0.19112	0.55	0.28600	P	0.9092117	B	0.11235	0.004	B	0.09377	0.004	T	0.09079	-1.0691	9	0.21540	T	0.41	-5.0916	5.9999	0.19515	0.4962:0.0:0.5038:0.0	rs17646457;rs52800076;rs17646457	486	O43155	FLRT2_HUMAN	Q	486;486;139	ENSP00000332879:R486Q;ENSP00000451050:R486Q	ENSP00000332879:R486Q	R	+	2	0	FLRT2	85159068	1.000000	0.71417	0.989000	0.46669	0.367000	0.29736	3.060000	0.49955	0.865000	0.35603	0.655000	0.94253	CGA	G|0.899;A|0.101	0.101	strong		0.522	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
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 GAIIx	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		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	45	18	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		
DRAXIN	374946	hgsc.bcm.edu	37	1	11771988	11771988	+	Silent	SNP	A	A	G	rs17037327	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11771988A>G	ENST00000294485.5	+	4	858	c.723A>G	c.(721-723)ttA>ttG	p.L241L		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		ATGAAGACTTAAAACCTGATG	0.582													A|||	484	0.0966454	0.0938	0.0821	5008	,	,		20678	0.0655		0.1262	False		,,,				2504	0.1125				p.L241L		Atlas-SNP	.											.	.	.	.	0			c.A723G						PASS	.	A		423,3983	204.1+/-226.4	19,385,1799	90.0	61.0	71.0		723	-1.9	0.8	1	dbSNP_123	71	1134,7466	232.1+/-265.8	55,1024,3221	no	coding-synonymous	C1orf187	NM_198545.3		74,1409,5020	GG,GA,AA		13.186,9.6005,11.9714		241/350	11771988	1557,11449	2203	4300	6503	SO:0001819	synonymous_variant	374946	exon4			AGACTTAAAACCT	AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"""dorsal repulsive axon guidance protein"", ""neural tissue-specific cysteine-rich protein"""	612682	"""chromosome 1 open reading frame 187"""	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.723A>G	1.37:g.11771988A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	50	30	0.6	NM_198545		Silent	SNP	ENST00000294485.5	37	CCDS135.1																																																																																			A|0.885;G|0.115	0.115	strong		0.582	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545	
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 GAIIx	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_ENST00000394396.1_Missense_Mutation_p.R62H|TMEM155_ENST00000394394.1_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	Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	243	125	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	
BEGAIN	57596	hgsc.bcm.edu	37	14	101005215	101005215	+	Silent	SNP	T	T	C	rs12893951	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:101005215T>C	ENST00000355173.2	-	7	944	c.873A>G	c.(871-873)gcA>gcG	p.A291A	CTD-2062F14.3_ENST00000553301.1_lincRNA|BEGAIN_ENST00000556751.1_Silent_p.A227A|BEGAIN_ENST00000443071.2_Silent_p.A291A	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	291						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				GCAGTGAGCCTGCGTAGCTGG	0.706													C|||	3260	0.650958	0.969	0.6254	5008	,	,		13674	0.7093		0.4274	False		,,,				2504	0.409				p.A291A	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.A873G						PASS	.	C	,	3873,527		1715,443,42	23.0	26.0	25.0		873,873	1.5	0.9	14	dbSNP_121	25	3508,5090		752,2004,1543	no	coding-synonymous,coding-synonymous	BEGAIN	NM_001159531.1,NM_020836.3	,	2467,2447,1585	CC,CT,TT		40.8002,11.9773,43.2143	,	291/594,291/594	101005215	7381,5617	2200	4299	6499	SO:0001819	synonymous_variant	57596	exon7			TGAGCCTGCGTAG	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"""brain-enriched guanylate kinase-associated homolog (rat)"""			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.873A>G	14.37:g.101005215T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_020836	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	37	CCDS9962.1																																																																																			T|0.388;C|0.612	0.612	strong		0.706	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836	
TMTC1	83857	hgsc.bcm.edu	37	12	29736480	29736480	+	Silent	SNP	A	A	G	rs2113879	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:29736480A>G	ENST00000539277.1	-	8	1336	c.1278T>C	c.(1276-1278)caT>caC	p.H426H	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000256062.5_Silent_p.H318H|TMTC1_ENST00000381224.2_Silent_p.H380H|TMTC1_ENST00000552618.1_Silent_p.H488H|TMTC1_ENST00000551659.1_Silent_p.H488H	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	426						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					TGCTCAGTCCATGCACAAAAA	0.502													A|||	1854	0.370208	0.5182	0.3112	5008	,	,		16546	0.4623		0.2376	False		,,,				2504	0.2536				p.H426H		Atlas-SNP	.											.	TMTC1	147	.	0			c.T1278C						PASS	.	A	,	2008,2398	560.3+/-380.4	454,1100,649	64.0	62.0	63.0		1278,954	-1.8	1.0	12	dbSNP_96	63	2060,6540	357.0+/-330.6	245,1570,2485	no	coding-synonymous,coding-synonymous	TMTC1	NM_001193451.1,NM_175861.3	,	699,2670,3134	GG,GA,AA		23.9535,45.5742,31.2779	,	426/883,318/775	29736480	4068,8938	2203	4300	6503	SO:0001819	synonymous_variant	83857	exon8			CAGTCCATGCACA		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.1278T>C	12.37:g.29736480A>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Silent	SNP	ENST00000539277.1	37	CCDS53772.1																																																																																			A|0.662;G|0.338	0.338	strong		0.502	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	
ENGASE	64772	hgsc.bcm.edu	37	17	77075670	77075670	+	Silent	SNP	C	C	T	rs140106265|rs3744184	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77075670C>T	ENST00000579016.1	+	4	516	c.516C>T	c.(514-516)ccC>ccT	p.P172P	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	172						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						TCACCATTCCCCCAGTGGGCT	0.587													C|||	2055	0.410343	0.6135	0.402	5008	,	,		19932	0.377		0.173	False		,,,				2504	0.4202				p.P172P		Atlas-SNP	.											ENGASE,upper_leg,malignant_melanoma,+1,1	ENGASE	55	1	0			c.C516T						PASS	.						99.0	125.0	116.0					17																	77075670		2113	4220	6333	SO:0001819	synonymous_variant	64772	exon4			CATTCCCCCAGTG	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.516C>T	17.37:g.77075670C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	47	15	0.319149	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			C|0.738;T|0.262	0.262	strong		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340906	55340906	+	Missense_Mutation	SNP	G	G	A	rs45542639	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55340906G>A	ENST00000391728.4	+	7	1124	c.1091G>A	c.(1090-1092)tGc>tAc	p.C364Y	KIR3DL1_ENST00000358178.4_Missense_Mutation_p.C269Y|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.C347Y|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.C364Y|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.C347Y	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	364					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		catctcTGGTGCTCCAACAAA	0.537													g|||	525	0.104832	0.093	0.1427	5008	,	,		14730	0.001		0.2475	False		,,,				2504	0.0542				p.C364Y		Atlas-SNP	.											KIR3DL1_ENST00000391728,NS,carcinoma,+1,1	KIR3DL1	174	1	0			c.G1091A						PASS	.	G	TYR/CYS	488,3852		82,324,1764	178.0	138.0	152.0		1091	-0.4	0.0	19	dbSNP_127	152	1718,6576		424,870,2853	no	missense	KIR3DL1	NM_013289.2	194	506,1194,4617	AA,AG,GG		20.7138,11.2442,17.4608		364/445	55340906	2206,10428	2170	4147	6317	SO:0001583	missense	3811	exon7			TCTGGTGCTCCAA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1091G>A	19.37:g.55340906G>A	ENSP00000375608:p.Cys364Tyr	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	265	0.12133699633699634	35	0.07113821138211382	46	0.1270718232044199	2	0.0034965034965034965	182	0.24010554089709762	-	7.282	0.609265	0.14066	0.112442	0.207138	ENSG00000167633	ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T	0.00483	7.09;7.16;7.09;7.16;7.09	0.743	-0.445	0.12242	.	4.446860	0.01420	U	0.014336	T	0.00012	0.0000	M	0.93062	3.375	0.80722	P	0.0	D;D;D	0.76494	0.963;0.999;0.992	P;D;D	0.74674	0.776;0.984;0.954	T	0.46857	-0.9161	9	0.62326	D	0.03	.	3.1214	0.06392	0.3487:0.0:0.6513:0.0	rs45542639	347;269;364	Q15702;Q14946;P43629	.;.;KI3L1_HUMAN	Y	364;347;342;364;347;269	ENSP00000443350:C364Y;ENSP00000442355:C347Y;ENSP00000375608:C364Y;ENSP00000326868:C347Y;ENSP00000350901:C269Y	ENSP00000326868:C347Y	C	+	2	0	KIR3DL1	60032718	0.022000	0.18835	0.001000	0.08648	0.031000	0.12232	-0.184000	0.09698	-0.103000	0.12175	0.184000	0.17185	TGC	G|0.875;A|0.125	0.125	strong		0.537	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
OR2G6	391211	hgsc.bcm.edu	37	1	248685719	248685719	+	Missense_Mutation	SNP	A	A	T	rs9330305	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248685719A>T	ENST00000343414.4	+	1	804	c.772A>T	c.(772-774)Atg>Ttg	p.M258L		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	258			M -> L (in dbSNP:rs9330305).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M258L(1)		NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	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)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATCATATTCATGTACCTTCA	0.443													.|||	797	0.159145	0.2973	0.1167	5008	,	,		19802	0.0913		0.1173	False		,,,				2504	0.1155				p.M258L		Atlas-SNP	.											OR2G6,NS,carcinoma,0,1	OR2G6	124	1	1	Substitution - Missense(1)	stomach(1)	c.A772T						PASS	.	A	LEU/MET	1172,3234		147,878,1178	116.0	117.0	117.0		772	3.8	1.0	1	dbSNP_119	117	1049,7551		72,905,3323	yes	missense	OR2G6	NM_001013355.1	15	219,1783,4501	TT,TA,AA		12.1977,26.6001,17.0767	benign	258/317	248685719	2221,10785	2203	4300	6503	SO:0001583	missense	391211	exon1			ATATTCATGTACC		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"""GPCR / Class A : Olfactory receptors"""	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.772A>T	1.37:g.248685719A>T	ENSP00000341291:p.Met258Leu	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_001013355	B2RP33	Missense_Mutation	SNP	ENST00000343414.4	37	CCDS31119.1	336	0.15384615384615385	135	0.27439024390243905	48	0.13259668508287292	55	0.09615384615384616	98	0.12928759894459102	N	15.96	2.987563	0.53934	0.266001	0.121977	ENSG00000188558	ENST00000343414	T	0.00115	8.71	3.83	3.83	0.44106	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	U	0.000051	T	0.00012	0.0000	M	0.63169	1.94	0.51767	P	6.499999999998174E-5	P	0.50369	0.934	P	0.50934	0.654	T	0.60480	-0.7255	9	0.66056	D	0.02	.	11.7146	0.51645	1.0:0.0:0.0:0.0	rs9330305;rs52814416;rs9330305	258	Q5TZ20	OR2G6_HUMAN	L	258	ENSP00000341291:M258L	ENSP00000341291:M258L	M	+	1	0	OR2G6	246752342	0.000000	0.05858	0.966000	0.40874	0.615000	0.37417	0.266000	0.18534	1.598000	0.50083	0.329000	0.21502	ATG	A|0.832;T|0.168	0.168	strong		0.443	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842	
WDR25	79446	hgsc.bcm.edu	37	14	100847437	100847437	+	Missense_Mutation	SNP	A	A	G	rs2273801	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:100847437A>G	ENST00000335290.6	+	2	402	c.176A>G	c.(175-177)aAa>aGa	p.K59R	WDR25_ENST00000554998.1_Missense_Mutation_p.K59R|WDR25_ENST00000542471.2_5'Flank|WDR25_ENST00000554175.1_Missense_Mutation_p.K59R|WDR25_ENST00000402312.3_Missense_Mutation_p.K59R	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	59			K -> R (in dbSNP:rs2273801).							central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				GATGTGCCCAAAGCAGGGGCA	0.567													A|||	255	0.0509185	0.1021	0.0259	5008	,	,		18190	0.0506		0.0328	False		,,,				2504	0.0184				p.K59R		Atlas-SNP	.											.	WDR25	37	.	0			c.A176G						PASS	.	A	ARG/LYS,ARG/LYS	351,4055	180.1+/-208.5	20,311,1872	49.0	47.0	48.0		176,176	-0.7	0.0	14	dbSNP_100	48	291,8309	107.6+/-168.3	3,285,4012	yes	missense,missense	WDR25	NM_001161476.1,NM_024515.4	26,26	23,596,5884	GG,GA,AA		3.3837,7.9664,4.9362	benign,benign	59/545,59/545	100847437	642,12364	2203	4300	6503	SO:0001583	missense	79446	exon2			TGCCCAAAGCAGG	BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"""WD repeat domain containing"""	21064	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 67"""	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.176A>G	14.37:g.100847437A>G	ENSP00000334148:p.Lys59Arg	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	37	CCDS32157.1	126	0.057692307692307696	63	0.12804878048780488	10	0.027624309392265192	27	0.0472027972027972	26	0.03430079155672823	A	12.29	1.894871	0.33442	0.079664	0.033837	ENSG00000176473	ENST00000554998;ENST00000402312;ENST00000335290;ENST00000554175	T;T;T;T	0.59502	0.26;0.26;0.26;2.23	5.07	-0.698	0.11280	.	1.962480	0.02125	N	0.055933	T	0.00496	0.0016	L	0.34521	1.04	0.09310	N	1	B	0.26400	0.148	B	0.17433	0.018	T	0.01424	-1.1358	10	0.16420	T	0.52	1.1005	6.4628	0.21966	0.4143:0.4931:0.0925:0.0	rs2273801;rs2273801	59	Q64LD2	WDR25_HUMAN	R	59	ENSP00000450661:K59R;ENSP00000385540:K59R;ENSP00000334148:K59R;ENSP00000450727:K59R	ENSP00000334148:K59R	K	+	2	0	WDR25	99917190	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-0.205000	0.09411	-0.047000	0.13423	0.418000	0.28097	AAA	A|0.948;G|0.052	0.052	strong		0.567	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515	
CEP170B	283638	hgsc.bcm.edu	37	14	105350178	105350178	+	Silent	SNP	C	C	T	rs45449696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105350178C>T	ENST00000414716.3	+	9	1290	c.1062C>T	c.(1060-1062)caC>caT	p.H354H	CEP170B_ENST00000418279.1_Silent_p.H284H|CEP170B_ENST00000453495.1_Silent_p.H355H|CEP170B_ENST00000556508.1_Silent_p.H284H	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	354						cytoplasm (GO:0005737)|microtubule (GO:0005874)											GCCACAAGCACGAGGACGGCA	0.667													C|||	1100	0.219649	0.1853	0.3242	5008	,	,		14088	0.003		0.3618	False		,,,				2504	0.2689				p.H354H		Atlas-SNP	.											.	.	.	.	0			c.C1062T						PASS	.	C	,	739,3217		74,591,1313	6.0	7.0	7.0		1062,852	-5.3	0.8	14	dbSNP_127	7	2964,5248		574,1816,1716	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	648,2407,3029	TT,TC,CC		36.0935,18.6805,30.4323	,	354/1555,284/1520	105350178	3703,8465	1978	4106	6084	SO:0001819	synonymous_variant	283638	exon9			CAAGCACGAGGAC	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.1062C>T	14.37:g.105350178C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																			C|0.760;T|0.240	0.240	strong		0.667	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
COL6A1	1291	hgsc.bcm.edu	37	21	47423636	47423636	+	Silent	SNP	C	C	T	rs1053320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:47423636C>T	ENST00000361866.3	+	35	2910	c.2796C>T	c.(2794-2796)tcC>tcT	p.S932S	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	932	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		AGGCCTCGTCCGGCGCTGCCA	0.657													C|||	1323	0.264177	0.4251	0.2752	5008	,	,		17479	0.1329		0.2555	False		,,,				2504	0.183				p.S932S		Atlas-SNP	.											COL6A1,NS,carcinoma,0,1	COL6A1	101	1	0			c.C2796T						PASS	.	C		1773,2631		363,1047,792	28.0	24.0	25.0		2796	-9.5	0.0	21	dbSNP_86	25	2479,6115		383,1713,2201	no	coding-synonymous	COL6A1	NM_001848.2		746,2760,2993	TT,TC,CC		28.8457,40.2589,32.7127		932/1029	47423636	4252,8746	2202	4297	6499	SO:0001819	synonymous_variant	1291	exon35			CTCGTCCGGCGCT	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2796C>T	21.37:g.47423636C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	180	119	0.661111	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Silent	SNP	ENST00000361866.3	37	CCDS13727.1																																																																																			C|0.700;T|0.300	0.300	strong		0.657	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
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 GAIIx	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_ENST00000412216.1_Intron|ZNF577_ENST00000451628.2_Silent_p.R387R|ZNF577_ENST00000420592.1_Silent_p.R387R|ZNF577_ENST00000485702.1_Intron	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		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	76	17	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	
FANCI	55215	hgsc.bcm.edu	37	15	89858602	89858602	+	Silent	SNP	T	T	C	rs1138465	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89858602T>C	ENST00000310775.7	+	37	3992	c.3906T>C	c.(3904-3906)ggT>ggC	p.G1302G	FANCI_ENST00000566615.1_3'UTR|FANCI_ENST00000300027.8_Silent_p.G1242G	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	1302					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					GAGAGGATGGTGAAGATGAAA	0.493								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	2065	0.41234	0.4667	0.3934	5008	,	,		20191	0.4256		0.3996	False		,,,				2504	0.3517				p.G1302G		Atlas-SNP	.											.	FANCI	129	.	0			c.T3906C						PASS	.	C	,	1920,2480	625.3+/-394.5	403,1114,683	118.0	94.0	102.0		3906,3726	-2.9	0.0	15	dbSNP_86	102	3404,5194	639.8+/-399.5	676,2052,1571	no	coding-synonymous,coding-synonymous	FANCI	NM_001113378.1,NM_018193.2	,	1079,3166,2254	CC,CT,TT		39.5906,43.6364,40.9601	,	1302/1329,1242/1269	89858602	5324,7674	2200	4299	6499	SO:0001819	synonymous_variant	55215	exon37	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGATGGTGAAGAT	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.3906T>C	15.37:g.89858602T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	82	30	0.365854	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Silent	SNP	ENST00000310775.7	37	CCDS45346.1																																																																																			T|0.586;C|0.414	0.414	strong		0.493	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
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 GAIIx	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_ENST00000356476.2_5'Flank|HIST1H2BF_ENST00000359985.1_5'Flank|HIST1H3D_ENST00000377831.5_5'UTR	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		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	164	31	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	
ALMS1	7840	hgsc.bcm.edu	37	2	73717567	73717567	+	Missense_Mutation	SNP	G	G	T	rs2056486	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73717567G>T	ENST00000264448.6	+	10	8589	c.8478G>T	c.(8476-8478)agG>agT	p.R2826S	ALMS1_ENST00000409009.1_Missense_Mutation_p.R2784S|AC096546.1_ENST00000408160.1_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2826					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						CCAGTACCAGGGCAAATTGTA	0.393													T|||	1794	0.358227	0.8578	0.3905	5008	,	,		19374	0.0089		0.2266	False		,,,				2504	0.1554				p.R2826S		Atlas-SNP	.											.	ALMS1	384	.	0			c.G8478T						PASS	.	T	SER/ARG	2699,1011		994,711,150	60.0	57.0	58.0		8478	0.3	0.0	2	dbSNP_94	58	1935,6237		218,1499,2369	yes	missense	ALMS1	NM_015120.4	110	1212,2210,2519	TT,TG,GG		23.6784,27.2507,39.0002	benign	2826/4168	73717567	4634,7248	1855	4086	5941	SO:0001583	missense	7840	exon10			TACCAGGGCAAAT	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.8478G>T	2.37:g.73717567G>T	ENSP00000264448:p.Arg2826Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	44	29	0.659091	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	730	0.3342490842490842	418	0.8495934959349594	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	T	0.011	-1.709383	0.00712	0.727493	0.236784	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.04654	3.58;3.58	4.33	0.258	0.15578	.	0.517985	0.18103	N	0.151608	T	0.00012	0.0000	N	0.00729	-1.24	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.16070	-1.0415	9	0.02654	T	1	.	6.6891	0.23161	0.1571:0.0:0.4864:0.3565	rs2056486;rs17349629;rs17848863;rs52800268;rs60591669;rs2056486	2826;2784;2826	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	S	2784;2826	ENSP00000386627:R2784S;ENSP00000264448:R2826S	ENSP00000264448:R2826S	R	+	3	2	ALMS1	73571075	0.000000	0.05858	0.000000	0.03702	0.746000	0.42486	-0.037000	0.12164	-0.189000	0.10482	-0.264000	0.10439	AGG	G|0.663;T|0.337	0.337	strong		0.393	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SPTBN5	51332	hgsc.bcm.edu	37	15	42150888	42150888	+	Missense_Mutation	SNP	G	G	A	rs890503	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:42150888G>A	ENST00000320955.6	-	49	8365	c.8138C>T	c.(8137-8139)aCa>aTa	p.T2713I		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	2713					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)	p.T2713I(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CAGCATGGCTGTGTCCAGCAA	0.632													G|||	1133	0.226238	0.295	0.2061	5008	,	,		20335	0.0357		0.325	False		,,,				2504	0.2423				p.T2678I		Atlas-SNP	.											SPTBN5,NS,carcinoma,0,3	SPTBN5	171	3	2	Substitution - Missense(2)	ovary(1)|prostate(1)	c.C8033T						scavenged	.	G	ILE/THR	1330,2976		208,914,1031	26.0	29.0	28.0		8033	4.0	0.1	15	dbSNP_86	28	2670,5846		414,1842,2002	yes	missense	SPTBN5	NM_016642.2	89	622,2756,3033	AA,AG,GG		31.3527,30.8871,31.1964	benign	2678/3640	42150888	4000,8822	2153	4258	6411	SO:0001583	missense	51332	exon49			ATGGCTGTGTCCA	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.8138C>T	15.37:g.42150888G>A	ENSP00000317790:p.Thr2713Ile	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		461	0.21108058608058608	135	0.27439024390243905	76	0.20994475138121546	14	0.024475524475524476	236	0.3113456464379947	.	10.42	1.345440	0.24426	0.308871	0.313527	ENSG00000137877	ENST00000320955	T	0.45668	0.89	4.94	4.03	0.46877	.	0.085238	0.47852	D	0.000214	T	0.00012	0.0000	N	0.12182	0.205	0.41138	P	0.01406099999999999	P	0.35821	0.523	B	0.35859	0.212	T	0.39860	-0.9593	9	0.14656	T	0.56	.	10.4904	0.44748	0.1566:0.0:0.8434:0.0	rs890503;rs890503	2713	Q9NRC6	SPTN5_HUMAN	I	2713	ENSP00000317790:T2713I	ENSP00000317790:T2713I	T	-	2	0	SPTBN5	39938180	1.000000	0.71417	0.094000	0.20943	0.007000	0.05969	5.383000	0.66219	1.067000	0.40740	0.467000	0.42956	ACA	G|0.757;T|0.009	.	strong		0.632	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
POTEC	388468	hgsc.bcm.edu	37	18	14542949	14542949	+	Missense_Mutation	SNP	T	T	C	rs9807555		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:14542949T>C	ENST00000358970.5	-	1	196	c.197A>G	c.(196-198)cAc>cGc	p.H66R	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	66			H -> R (in dbSNP:rs9807555).							NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GAAGCAGTGGTGGCAACACTT	0.582																																					p.H66R		Atlas-SNP	.											POTEC,right_upper_lobe,carcinoma,+1,1	POTEC	129	1	0			c.A197G						scavenged	.						74.0	82.0	80.0					18																	14542949		692	1591	2283	SO:0001583	missense	388468	exon1			CAGTGGTGGCAAC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.197A>G	18.37:g.14542949T>C	ENSP00000351856:p.His66Arg	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	254	42	0.165354	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-3.031815	0.00041	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.25085	1.82	0.429	-0.857	0.10693	.	.	.	.	.	T	0.10852	0.0265	N	0.12182	0.205	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28808	-1.0032	8	0.27785	T	0.31	.	.	.	.	rs9807555;rs56998137	66	B2RU33	POTEC_HUMAN	R	66	ENSP00000351856:H66R	ENSP00000351856:H66R	H	-	2	0	POTEC	14532949	0.000000	0.05858	0.002000	0.10522	0.036000	0.12997	-3.614000	0.00414	-1.006000	0.03412	-1.522000	0.00932	CAC	T|1.000;|0.000	.	weak		0.582	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
SAMD9	54809	hgsc.bcm.edu	37	7	92734051	92734051	+	Missense_Mutation	SNP	C	C	T	rs117649834	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92734051C>T	ENST00000379958.2	-	3	1629	c.1360G>A	c.(1360-1362)Gct>Act	p.A454T		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	454						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TCTTTGTAAGCTTTGACCACT	0.378													C|||	306	0.0611022	0.0023	0.0303	5008	,	,		18949	0.0367		0.0497	False		,,,				2504	0.1994				p.A454T		Atlas-SNP	.											.	SAMD9	239	.	0			c.G1360A						PASS	.	C	THR/ALA,THR/ALA	39,4367	43.1+/-76.7	0,39,2164	54.0	50.0	52.0		1360,1360	1.6	0.2	7	dbSNP_132	52	369,8231	118.5+/-177.9	8,353,3939	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	58,58	8,392,6103	TT,TC,CC		4.2907,0.8852,3.137	possibly-damaging,possibly-damaging	454/1590,454/1590	92734051	408,12598	2203	4300	6503	SO:0001583	missense	54809	exon2			TGTAAGCTTTGAC	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.1360G>A	7.37:g.92734051C>T	ENSP00000369292:p.Ala454Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	69	0.03159340659340659	0	0.0	15	0.04143646408839779	17	0.02972027972027972	37	0.048812664907651716	C	0.013	-1.636630	0.00806	0.008852	0.042907	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.18657	2.2;2.2	4.38	1.58	0.23477	.	0.573661	0.15927	N	0.237860	T	0.02304	0.0071	L	0.55481	1.735	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.22765	-1.0207	10	0.26408	T	0.33	0.5043	3.5886	0.07979	0.1689:0.4589:0.0:0.3722	.	454	Q5K651	SAMD9_HUMAN	T	454	ENSP00000369292:A454T;ENSP00000414529:A454T	ENSP00000369292:A454T	A	-	1	0	SAMD9	92571987	0.004000	0.15560	0.166000	0.22797	0.100000	0.18952	0.791000	0.26915	0.227000	0.20999	-0.199000	0.12753	GCT	C|0.965;T|0.035	0.035	strong		0.378	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
WDPCP	51057	hgsc.bcm.edu	37	2	63660902	63660902	+	Missense_Mutation	SNP	C	C	T	rs17617459	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:63660902C>T	ENST00000272321.7	-	9	1329	c.802G>A	c.(802-804)Ggt>Agt	p.G268S	WDPCP_ENST00000409562.3_Missense_Mutation_p.G268S|WDPCP_ENST00000409120.1_Missense_Mutation_p.G76S|WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000398544.3_Missense_Mutation_p.G109S|WDPCP_ENST00000409199.1_Missense_Mutation_p.G76S	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	268			G -> S (in dbSNP:rs17617459).		auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						TGAGCATAACCCAGGAGGAGT	0.373													C|||	86	0.0171725	0.0045	0.0231	5008	,	,		15439	0.0		0.0557	False		,,,				2504	0.0082				p.G268S		Atlas-SNP	.											.	WDPCP	79	.	0			c.G802A						PASS	.	C	SER/GLY	41,3665		1,39,1813	60.0	57.0	58.0		802	4.6	1.0	2	dbSNP_123	58	490,7702		13,464,3619	yes	missense	WDPCP	NM_015910.5	56	14,503,5432	TT,TC,CC		5.9814,1.1063,4.4629	benign	268/747	63660902	531,11367	1853	4096	5949	SO:0001583	missense	51057	exon9			CATAACCCAGGAG		CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"""chromosome 2 open reading frame 86"""	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.802G>A	2.37:g.63660902C>T	ENSP00000272321:p.Gly268Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	17	0.269841	NM_015910	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	50	0.022893772893772892	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	44	0.05804749340369393	C	9.131	1.011327	0.19277	0.011063	0.059814	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544;ENST00000409562	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	5.43	4.56	0.56223	.	0.194738	0.45126	N	0.000394	T	0.02571	0.0078	N	0.14661	0.345	0.29805	N	0.832089	B;B;B;B	0.17465	0.022;0.002;0.01;0.003	B;B;B;B	0.17433	0.018;0.012;0.012;0.005	T	0.05767	-1.0865	10	0.20519	T	0.43	-6.9153	9.621	0.39721	0.0:0.8411:0.0:0.1589	rs17617459;rs52811496;rs17617459	76;268;268;109	E9PFG9;O95876-2;O95876;O95876-3	.;.;FRITZ_HUMAN;.	S	268;76;76;109;268	ENSP00000272321:G268S;ENSP00000386592:G76S;ENSP00000386769:G76S;ENSP00000381552:G109S;ENSP00000387222:G268S	ENSP00000272321:G268S	G	-	1	0	WDPCP	63514406	0.992000	0.36948	0.996000	0.52242	0.992000	0.81027	0.541000	0.23207	1.297000	0.44761	0.563000	0.77884	GGT	C|0.970;T|0.030	0.030	strong		0.373	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910	
ASB10	136371	hgsc.bcm.edu	37	7	150873754	150873754	+	Missense_Mutation	SNP	G	G	A	rs62489646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150873754G>A	ENST00000420175.2	-	4	1138	c.1114C>T	c.(1114-1116)Cgc>Tgc	p.R372C	ASB10_ENST00000422024.1_Missense_Mutation_p.R417C|ASB10_ENST00000377867.3_Missense_Mutation_p.R357C|GBX1_ENST00000475831.1_5'Flank|ASB10_ENST00000275838.1_Intron|ASB10_ENST00000434669.1_Intron			Q8WXI3	ASB10_HUMAN	ankyrin repeat and SOCS box containing 10	372			R -> C. {ECO:0000269|PubMed:22156576}.		intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(2)|lung(7)|skin(2)	12			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTGCTCCAGCGCTCCAGCACC	0.577													G|||	384	0.0766773	0.1135	0.0735	5008	,	,		18140	0.0833		0.0706	False		,,,				2504	0.0286				p.R372C		Atlas-SNP	.											.	ASB10	99	.	0			c.C1114T						PASS	.						45.0	50.0	49.0					7																	150873754		692	1591	2283	SO:0001583	missense	136371	exon4			TCCAGCGCTCCAG	AK055536	CCDS5921.2, CCDS47749.1, CCDS47750.1, CCDS47749.2, CCDS47750.2	7q35	2014-02-04	2011-01-25		ENSG00000146926	ENSG00000146926		"""Ankyrin repeat domain containing"""	17185	protein-coding gene	gene with protein product		615054	"""ankyrin repeat and SOCS box-containing 10"", ""glaucoma 1, open angle, F (adult-onset)"""	GLC1F		22156576	Standard	NM_080871		Approved		uc003wjm.1	Q8WXI3	OTTHUMG00000157013	ENST00000420175.2:c.1114C>T	7.37:g.150873754G>A	ENSP00000391137:p.Arg372Cys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_001142459	A0AVH0|Q6ZUL6	Missense_Mutation	SNP	ENST00000420175.2	37	CCDS47750.2	199	0.09111721611721611	64	0.13008130081300814	29	0.08011049723756906	49	0.08566433566433566	57	0.07519788918205805	G	14.96	2.690641	0.48097	.	.	ENSG00000146926	ENST00000377867;ENST00000422024;ENST00000420175	T;T;T	0.68624	-0.3;-0.33;-0.34	4.52	4.52	0.55395	.	0.261633	0.40385	N	0.001107	T	0.01870	0.0059	L	0.54323	1.7	0.09310	P	0.9999999999948537	P;D	0.89917	0.492;1.0	B;D	0.64410	0.125;0.925	T	0.52087	-0.8622	9	0.44086	T	0.13	-12.9845	6.9355	0.24464	0.2017:0.0:0.7983:0.0	rs62489646	357;372	Q8WXI3-3;Q8WXI3	.;ASB10_HUMAN	C	357;417;372	ENSP00000367098:R357C;ENSP00000401369:R417C;ENSP00000391137:R372C	ENSP00000367098:R357C	R	-	1	0	ASB10	150504687	1.000000	0.71417	0.998000	0.56505	0.629000	0.37895	4.038000	0.57318	2.227000	0.72691	0.561000	0.74099	CGC	G|0.909;A|0.091	0.091	strong		0.577	ASB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347096.3	NM_080871	
HSPG2	3339	hgsc.bcm.edu	37	1	22154845	22154845	+	Silent	SNP	A	A	G	rs2228347	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22154845A>G	ENST00000374695.3	-	89	12391	c.12312T>C	c.(12310-12312)gaT>gaC	p.D4104D	HSPG2_ENST00000486901.1_5'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	4104	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	ATGGGGAGCTATCATAGCATT	0.587													G|||	1288	0.257188	0.1172	0.2161	5008	,	,		18078	0.1577		0.3241	False		,,,				2504	0.5092				p.D4104D		Atlas-SNP	.											.	HSPG2	311	.	0			c.T12312C						PASS	.	G		648,3758	764.0+/-413.3	57,534,1612	99.0	85.0	90.0		12312	3.5	1.0	1	dbSNP_98	90	2634,5966	686.8+/-404.2	403,1828,2069	no	coding-synonymous	HSPG2	NM_005529.5		460,2362,3681	GG,GA,AA		30.6279,14.7072,25.2345		4104/4392	22154845	3282,9724	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon89			GGAGCTATCATAG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.12312T>C	1.37:g.22154845A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			T|0.000;G|0.250;A|0.750	0.250	strong		0.587	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
MYH4	4622	hgsc.bcm.edu	37	17	10348354	10348354	+	Missense_Mutation	SNP	T	T	C	rs2277649	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:10348354T>C	ENST00000255381.2	-	37	5515	c.5405A>G	c.(5404-5406)gAt>gGt	p.D1802G	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1802			D -> G (in dbSNP:rs2277649). {ECO:0000269|PubMed:10388558}.		actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CTCAGCCTCATCCAGACGGAG	0.567													T|||	2278	0.454872	0.233	0.4755	5008	,	,		18937	0.8214		0.3181	False		,,,				2504	0.5031				p.D1802G		Atlas-SNP	.											.	MYH4	349	.	0			c.A5405G						PASS	.	T	GLY/ASP	1137,3269	405.8+/-333.6	141,855,1207	143.0	140.0	141.0		5405	5.5	0.9	17	dbSNP_100	141	3050,5550	469.9+/-367.7	536,1978,1786	no	missense	MYH4	NM_017533.2	94	677,2833,2993	CC,CT,TT		35.4651,25.8057,32.1928	possibly-damaging	1802/1940	10348354	4187,8819	2203	4300	6503	SO:0001583	missense	4622	exon37			GCCTCATCCAGAC		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.5405A>G	17.37:g.10348354T>C	ENSP00000255381:p.Asp1802Gly	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	157	69	0.43949	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	979	0.4482600732600733	106	0.21544715447154472	162	0.44751381215469616	473	0.8269230769230769	238	0.31398416886543534	T	19.34	3.809062	0.70797	0.258057	0.354651	ENSG00000141048	ENST00000255381	T	0.78481	-1.18	5.5	5.5	0.81552	Myosin tail (1);	0.000000	0.38605	U	0.001638	T	0.00012	0.0000	H	0.95079	3.62	0.09310	P	0.999999246958	D	0.63880	0.993	D	0.70487	0.969	T	0.47761	-0.9092	9	0.87932	D	0	.	15.8867	0.79255	0.0:0.0:0.0:1.0	rs2277649;rs61532457;rs2277649	1802	Q9Y623	MYH4_HUMAN	G	1802	ENSP00000255381:D1802G	ENSP00000255381:D1802G	D	-	2	0	MYH4	10289079	1.000000	0.71417	0.938000	0.37757	0.170000	0.22686	6.257000	0.72480	2.214000	0.71695	0.482000	0.46254	GAT	T|0.644;C|0.356	0.356	strong		0.567	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
TAAR1	134864	hgsc.bcm.edu	37	6	132966279	132966279	+	Silent	SNP	T	T	C	rs8192620	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:132966279T>C	ENST00000275216.1	-	1	863	c.864A>G	c.(862-864)gtA>gtG	p.V288V		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	288					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	ACCAAATCAATACATCATTCA	0.363													T|||	1053	0.210264	0.1029	0.1729	5008	,	,		18060	0.3185		0.2376	False		,,,				2504	0.2423				p.V288V		Atlas-SNP	.											.	TAAR1	41	.	0			c.A864G						PASS	.	T		539,3867	241.5+/-251.9	31,477,1695	79.0	74.0	76.0		864	-1.5	0.0	6	dbSNP_117	76	1969,6627	341.9+/-324.3	216,1537,2545	no	coding-synonymous	TAAR1	NM_138327.1		247,2014,4240	CC,CT,TT		22.906,12.2333,19.2893		288/340	132966279	2508,10494	2203	4298	6501	SO:0001819	synonymous_variant	134864	exon1			AATCAATACATCA	AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"""GPCR / Class A : Trace amine associated receptors"""	17734	protein-coding gene	gene with protein product		609333	"""trace amine receptor 1"""	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.864A>G	6.37:g.132966279T>C		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	164	88	0.536585	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Silent	SNP	ENST00000275216.1	37	CCDS5158.1																																																																																			T|0.792;C|0.208	0.208	strong		0.363	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327	
UNC13D	201294	hgsc.bcm.edu	37	17	73824121	73824121	+	Silent	SNP	T	T	C	rs7210574	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73824121T>C	ENST00000207549.4	-	32	3577	c.3198A>G	c.(3196-3198)gaA>gaG	p.E1066E	UNC13D_ENST00000412096.2_Silent_p.E1066E	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	1066					defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGACCTGGGCTTCTCGGTCAC	0.687									Familial Hemophagocytic Lymphohistiocytosis				C|||	2635	0.526158	0.9614	0.3372	5008	,	,		16424	0.4365		0.34	False		,,,				2504	0.3558				p.E1066E		Atlas-SNP	.											.	UNC13D	68	.	0			c.A3198G						PASS	.	C		3743,623		1625,493,65	13.0	15.0	14.0		3198	3.0	1.0	17	dbSNP_116	14	2977,5593		561,1855,1869	no	coding-synonymous	UNC13D	NM_199242.2		2186,2348,1934	CC,CT,TT		34.7375,14.2694,48.0519		1066/1091	73824121	6720,6216	2183	4285	6468	SO:0001819	synonymous_variant	201294	exon32	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CTGGGCTTCTCGG	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.3198A>G	17.37:g.73824121T>C		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			T|0.444;C|0.556	0.556	strong		0.687	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
ANKRD61	100310846	hgsc.bcm.edu	37	7	6071115	6071115	+	Missense_Mutation	SNP	A	A	G	rs12334093	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6071115A>G	ENST00000409061.1	+	1	109	c.109A>G	c.(109-111)Atg>Gtg	p.M37V	EIF2AK1_ENST00000199389.6_Intron|EIF2AK1_ENST00000536084.1_Intron	NM_001271700.1	NP_001258629.1	A6NGH8	ANR61_HUMAN	ankyrin repeat domain 61	37																	TGAAGCCATCATGAGAGAAGA	0.507													A|||	574	0.114617	0.2413	0.1138	5008	,	,		18893	0.0268		0.0984	False		,,,				2504	0.0511				p.M37V		Atlas-SNP	.											.	.	.	.	0			c.A109G						PASS	.																																			SO:0001583	missense	100310846	exon1			GCCATCATGAGAG		CCDS64590.1	7p22	2013-01-10			ENSG00000157999	ENSG00000157999		"""Ankyrin repeat domain containing"""	22467	protein-coding gene	gene with protein product							Standard	NM_001271700		Approved		uc031swn.1	A6NGH8	OTTHUMG00000154561	ENST00000409061.1:c.109A>G	7.37:g.6071115A>G	ENSP00000386502:p.Met37Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	150	48	0.32	NM_001271700		Missense_Mutation	SNP	ENST00000409061.1	37		223	0.1021062271062271	107	0.21747967479674796	37	0.10220994475138122	10	0.017482517482517484	69	0.09102902374670185	A	5.583	0.292429	0.10567	.	.	ENSG00000157999	ENST00000409061	T	0.53423	0.62	5.69	0.268	0.15626	.	0.298325	0.29119	N	0.013091	T	0.00039	0.0001	.	.	.	0.29275	P	0.870392	.	.	.	.	.	.	T	0.18524	-1.0334	6	0.22109	T	0.4	-13.9545	6.9436	0.24506	0.4099:0.4344:0.0:0.1558	rs12334093;rs52791415;rs58280047;rs12334093	.	.	.	V	37	ENSP00000386502:M37V	ENSP00000386502:M37V	M	+	1	0	ANKRD61	6037641	0.884000	0.30299	0.150000	0.22450	0.058000	0.15608	0.142000	0.16096	-0.174000	0.10743	0.533000	0.62120	ATG	A|0.885;G|0.115	0.115	strong		0.507	ANKRD61-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000335991.1		
EHBP1	23301	hgsc.bcm.edu	37	2	63176139	63176139	+	Missense_Mutation	SNP	A	A	C	rs17432615	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:63176139A>C	ENST00000263991.5	+	14	2745	c.2263A>C	c.(2263-2265)Aaa>Caa	p.K755Q	EHBP1_ENST00000405289.1_Missense_Mutation_p.K720Q|EHBP1_ENST00000431489.1_Missense_Mutation_p.K720Q|EHBP1_ENST00000354487.3_Missense_Mutation_p.K720Q|EHBP1_ENST00000405015.3_Missense_Mutation_p.K720Q	NM_015252.3	NP_056067.2	Q8NDI1	EHBP1_HUMAN	EH domain binding protein 1	755			K -> Q (in dbSNP:rs17432615).			cytoplasm (GO:0005737)|membrane (GO:0016020)				biliary_tract(1)|breast(3)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(22)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	47	Lung NSC(7;0.0951)|all_lung(7;0.169)		LUSC - Lung squamous cell carcinoma(7;7.74e-05)|Epithelial(17;0.189)			TCCTATCAAAAAAACAAGTTT	0.373													A|||	307	0.0613019	0.0219	0.0764	5008	,	,		18003	0.0347		0.1083	False		,,,				2504	0.0828				p.K755Q		Atlas-SNP	.											.	EHBP1	127	.	0			c.A2263C						PASS	.	A	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS	174,4230	108.2+/-146.6	6,162,2034	41.0	45.0	44.0		2158,2158,2158,2263	6.0	1.0	2	dbSNP_123	44	1145,7453	225.7+/-261.6	79,987,3233	yes	missense,missense,missense,missense	EHBP1	NM_001142614.1,NM_001142615.2,NM_001142616.1,NM_015252.3	53,53,53,53	85,1149,5267	CC,CA,AA		13.3171,3.951,10.1446	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	720/1197,720/1161,720/1161,755/1232	63176139	1319,11683	2202	4299	6501	SO:0001583	missense	23301	exon14			ATCAAAAAAACAA	AL833968	CCDS1872.1, CCDS46299.1, CCDS46300.1	2p15	2008-02-05			ENSG00000115504	ENSG00000115504			29144	protein-coding gene	gene with protein product		609922				10048485	Standard	NM_015252		Approved	KIAA0903, NACSIN	uc002sby.3	Q8NDI1	OTTHUMG00000129453	ENST00000263991.5:c.2263A>C	2.37:g.63176139A>C	ENSP00000263991:p.Lys755Gln	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	173	172	0.99422	NM_015252	O94977|Q53TG7|Q53TV6|Q580X2|Q6NX72|Q6PIT3|Q6QNV2|Q9NWI9	Missense_Mutation	SNP	ENST00000263991.5	37	CCDS1872.1	144|144	0.06593406593406594|0.06593406593406594	10|10	0.02032520325203252|0.02032520325203252	25|25	0.06906077348066299|0.06906077348066299	20|20	0.03496503496503497|0.03496503496503497	89|89	0.11741424802110818|0.11741424802110818	A|A	17.80|17.80	3.478474|3.478474	0.63849|0.63849	0.03951|0.03951	0.133171|0.133171	ENSG00000115504|ENSG00000115504	ENST00000454124|ENST00000405015;ENST00000431489;ENST00000263991;ENST00000354487;ENST00000405289	T|T;T;T;T;T	0.46451|0.75050	0.87|-0.9;-0.9;-0.88;-0.88;-0.88	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	0.172511|0.172511	0.50627|0.50627	D|D	0.000112|0.000112	T|T	0.03651|0.03651	0.0104|0.0104	L|L	0.59436|0.59436	1.845|1.845	0.31326|0.31326	P|P	0.685439|0.685439	.|D;P;D	.|0.56746	.|0.977;0.763;0.977	.|P;B;P	.|0.59221	.|0.854;0.372;0.827	T|T	0.33497|0.33497	-0.9866|-0.9866	7|9	0.62326|0.22706	D|T	0.03|0.39	.|.	16.5582|16.5582	0.84512|0.84512	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs17432615;rs52811992;rs17432615|rs17432615;rs52811992;rs17432615	.|720;720;755	.|Q8NDI1-2;Q8NDI1-3;Q8NDI1	.|.;.;EHBP1_HUMAN	N|Q	24|720;720;755;720;720	ENSP00000396186:K24N|ENSP00000384143:K720Q;ENSP00000403783:K720Q;ENSP00000263991:K755Q;ENSP00000346482:K720Q;ENSP00000385524:K720Q	ENSP00000396186:K24N|ENSP00000263991:K755Q	K|K	+|+	3|1	2|0	EHBP1|EHBP1	63029643|63029643	1.000000|1.000000	0.71417|0.71417	0.967000|0.967000	0.41034|0.41034	0.397000|0.397000	0.30659|0.30659	6.179000|6.179000	0.71974|0.71974	2.308000|2.308000	0.77769|0.77769	0.533000|0.533000	0.62120|0.62120	AAA|AAA	A|0.917;C|0.083	0.083	strong		0.373	EHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251616.1	NM_015252	
LZTS1	11178	hgsc.bcm.edu	37	8	20110641	20110641	+	Silent	SNP	C	C	T	rs2645386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:20110641C>T	ENST00000381569.1	-	3	1158	c.801G>A	c.(799-801)gaG>gaA	p.E267E	LZTS1_ENST00000265801.6_Silent_p.E267E|LZTS1_ENST00000522290.1_Silent_p.E267E			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	267					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		ACAGCTTCTGCTCCAGCTCCT	0.657													C|||	1796	0.358626	0.3843	0.2205	5008	,	,		17260	0.4623		0.3231	False		,,,				2504	0.3517				p.E267E		Atlas-SNP	.											.	LZTS1	72	.	0			c.G801A						PASS	.	C		1774,2626		384,1006,810	49.0	45.0	46.0		801	5.6	1.0	8	dbSNP_100	46	2966,5612		546,1874,1869	no	coding-synonymous	LZTS1	NM_021020.2		930,2880,2679	TT,TC,CC		34.5768,40.3182,36.5233		267/597	20110641	4740,8238	2200	4289	6489	SO:0001819	synonymous_variant	11178	exon2			CTTCTGCTCCAGC	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"""F37/Esophageal cancer-related gene-coding leucine-zipper motif"""			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.801G>A	8.37:g.20110641C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	37	CCDS6015.1																																																																																			C|0.631;T|0.369	0.369	strong		0.657	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020	
MRPL38	64978	hgsc.bcm.edu	37	17	73900688	73900688	+	Silent	SNP	T	T	C	rs3744015	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73900688T>C	ENST00000309352.3	-	2	717	c.180A>G	c.(178-180)cgA>cgG	p.R60R	MRPL38_ENST00000409963.3_5'UTR|MRPL38_ENST00000585475.1_5'UTR	NM_032478.3	NP_115867.2	Q96DV4	RM38_HUMAN	mitochondrial ribosomal protein L38	60						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)			CCTGCTCTGCTCGGCGCCGGT	0.682													C|||	2236	0.446486	0.8411	0.3156	5008	,	,		8697	0.2123		0.3509	False		,,,				2504	0.3456				p.R60R		Atlas-SNP	.											.	MRPL38	26	.	0			c.A180G						PASS	.	C		3264,1106		1242,780,163	10.0	12.0	11.0		180	-2.7	0.6	17	dbSNP_107	11	2855,5713		524,1807,1953	yes	coding-synonymous	MRPL38	NM_032478.3		1766,2587,2116	CC,CT,TT		33.3217,25.3089,47.2948		60/381	73900688	6119,6819	2185	4284	6469	SO:0001819	synonymous_variant	64978	exon2			CTCTGCTCGGCGC	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.180A>G	17.37:g.73900688T>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_032478	B3KN96|Q96Q66|Q9P0B9	Silent	SNP	ENST00000309352.3	37	CCDS11733.2																																																																																			T|0.523;C|0.477	0.477	strong		0.682	MRPL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328829.1	NM_032478	
CDH2	1000	hgsc.bcm.edu	37	18	25543387	25543387	+	Silent	SNP	G	G	A	rs1041985	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:25543387G>A	ENST00000269141.3	-	15	2871	c.2448C>T	c.(2446-2448)gcC>gcT	p.A816A	CDH2_ENST00000399380.3_Silent_p.A785A|AC015933.2_ENST00000423367.1_RNA	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	816					adherens junction organization (GO:0034332)|blood vessel morphogenesis (GO:0048514)|calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell-cell adhesion mediated by cadherin (GO:0044331)|cell-cell junction organization (GO:0045216)|glial cell differentiation (GO:0010001)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neuronal stem cell maintenance (GO:0097150)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of muscle cell differentiation (GO:0051149)|striated muscle cell differentiation (GO:0051146)	apical plasma membrane (GO:0016324)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|synapse (GO:0045202)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)	p.A816A(1)		NS(1)|breast(5)|cervix(2)|endometrium(7)|kidney(3)|large_intestine(22)|lung(32)|ovary(4)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACTGGGGCTCGGCGTGGATGG	0.537													G|||	1640	0.327476	0.1498	0.464	5008	,	,		15977	0.4216		0.3419	False		,,,				2504	0.3589				p.A816A		Atlas-SNP	.											CDH2,colon,carcinoma,-2,2	CDH2	194	2	1	Substitution - coding silent(1)	stomach(1)	c.C2448T						PASS	.	G		785,3621	316.9+/-294.8	80,625,1498	90.0	71.0	78.0		2448	-11.7	0.1	18	dbSNP_86	78	2690,5910	432.0+/-357.0	405,1880,2015	no	coding-synonymous	CDH2	NM_001792.3		485,2505,3513	AA,AG,GG		31.2791,17.8166,26.7184		816/907	25543387	3475,9531	2203	4300	6503	SO:0001819	synonymous_variant	1000	exon15			GGGCTCGGCGTGG	S42303	CCDS11891.1	18q12.1	2010-01-26			ENSG00000170558	ENSG00000170558		"""CD molecules"", ""Cadherins / Major cadherins"""	1759	protein-coding gene	gene with protein product	"""N-cadherin"""	114020		NCAD		2384753, 7731968, 2216790	Standard	NM_001792		Approved	CDHN, CD325	uc002kwg.2	P19022	OTTHUMG00000059940	ENST00000269141.3:c.2448C>T	18.37:g.25543387G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Silent	SNP	ENST00000269141.3	37	CCDS11891.1																																																																																			G|0.706;A|0.294	0.294	strong		0.537	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792	
HDAC10	83933	hgsc.bcm.edu	37	22	50687595	50687595	+	Silent	SNP	A	A	G	rs75455741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50687595A>G	ENST00000216271.5	-	8	1045	c.693T>C	c.(691-693)gtT>gtC	p.V231V	MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000448072.1_Silent_p.V231V|HDAC10_ENST00000349505.4_Silent_p.V231V|HDAC10_ENST00000498366.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	231	Histone deacetylase.				chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TTCCCATCCCAACCTGGCAGG	0.677													G|||	281	0.0561102	0.0635	0.0389	5008	,	,		9162	0.0873		0.0298	False		,,,				2504	0.0532				p.V231V		Atlas-SNP	.											.	HDAC10	29	.	0			c.T693C						PASS	.	G	,	234,4154		4,226,1964	46.0	31.0	36.0		693,693	-9.1	0.2	22	dbSNP_131	36	194,8394		1,192,4101	no	coding-synonymous,coding-synonymous	HDAC10	NM_001159286.1,NM_032019.5	,	5,418,6065	GG,GA,AA		2.259,5.3327,3.2984	,	231/650,231/670	50687595	428,12548	2194	4294	6488	SO:0001819	synonymous_variant	83933	exon8			CATCCCAACCTGG	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.693T>C	22.37:g.50687595A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Silent	SNP	ENST00000216271.5	37	CCDS14088.1																																																																																			A|0.958;G|0.042	0.042	strong		0.677	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	
ABCA13	154664	hgsc.bcm.edu	37	7	48528923	48528923	+	Missense_Mutation	SNP	G	G	C	rs73694648	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48528923G>C	ENST00000435803.1	+	48	13297	c.13273G>C	c.(13273-13275)Gtg>Ctg	p.V4425L	ABCA13_ENST00000544596.1_Missense_Mutation_p.V155L	NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4425					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						ACCCCCTACTGTGGACTGGAG	0.348													G|||	288	0.057508	0.1203	0.0375	5008	,	,		17998	0.0		0.0537	False		,,,				2504	0.0501				p.V4425L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G13273C						PASS	.	G	LEU/VAL	378,3346		16,346,1500	82.0	75.0	77.0		13273	3.6	0.0	7	dbSNP_130	77	462,7722		10,442,3640	yes	missense	ABCA13	NM_152701.3	32	26,788,5140	CC,CG,GG		5.6452,10.1504,7.0541	benign	4425/5059	48528923	840,11068	1862	4092	5954	SO:0001583	missense	154664	exon48			CCTACTGTGGACT	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.13273G>C	7.37:g.48528923G>C	ENSP00000411096:p.Val4425Leu	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	132	35	0.265152	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	108	0.04945054945054945	53	0.10772357723577236	14	0.03867403314917127	0	0.0	41	0.05408970976253298	G	9.218	1.032684	0.19590	0.101504	0.056452	ENSG00000179869	ENST00000435803;ENST00000411975;ENST00000544596	D;D;D	0.86694	-1.98;-2.16;-2.12	5.44	3.64	0.41730	.	0.681049	0.12642	N	0.451250	T	0.09423	0.0232	L	0.56769	1.78	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.002;0.002;0.004	T	0.31110	-0.9955	10	0.21014	T	0.42	.	8.4463	0.32843	0.0825:0.1547:0.7628:0.0	.	155;2127;4425	F5H7B7;Q86UQ4-3;Q86UQ4	.;.;ABCAD_HUMAN	L	4425;198;155	ENSP00000411096:V4425L;ENSP00000391042:V198L;ENSP00000442634:V155L	ENSP00000391042:V198L	V	+	1	0	ABCA13	48499469	0.006000	0.16342	0.002000	0.10522	0.901000	0.52897	1.411000	0.34702	0.670000	0.31165	-0.150000	0.13652	GTG	G|0.951;C|0.049	0.049	strong		0.348	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
CCDC183	84960	hgsc.bcm.edu	37	9	139693596	139693596	+	Missense_Mutation	SNP	T	T	C	rs945386	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139693596T>C	ENST00000338005.6	+	2	148	c.113T>C	c.(112-114)aTg>aCg	p.M38T	RP11-216L13.18_ENST00000471502.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.M94T|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		38			M -> T (in dbSNP:rs945386).							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		AAAGAGAATATGGACCAGAAC	0.637													C|||	1369	0.273363	0.3374	0.2968	5008	,	,		18525	0.2421		0.2147	False		,,,				2504	0.2628				p.M38T		Atlas-SNP	.											.	KIAA1984	39	.	0			c.T113C						PASS	.	C	THR/MET	1221,2859		191,839,1010	53.0	62.0	59.0		113	1.0	0.0	9	dbSNP_86	59	1821,6553		208,1405,2574	yes	missense	KIAA1984	NM_001039374.4	81	399,2244,3584	CC,CT,TT		21.7459,29.9265,24.4259	benign	38/535	139693596	3042,9412	2040	4187	6227	SO:0001583	missense	84960	exon2			AGAATATGGACCA																												ENST00000338005.6:c.113T>C	9.37:g.139693596T>C	ENSP00000338013:p.Met38Thr	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	88	53	0.602273	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	539	0.2467948717948718	160	0.3252032520325203	98	0.27071823204419887	124	0.21678321678321677	157	0.20712401055408972	C	1.102	-0.660878	0.03454	0.299265	0.217459	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.10960	2.82	3.91	1.02	0.19986	.	0.979372	0.08252	N	0.974461	T	0.00012	0.0000	N	0.02142	-0.665	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49312	-0.8953	9	0.20519	T	0.43	-3.8689	7.3765	0.26831	0.0:0.6152:0.0:0.3848	rs945386;rs945386	38	Q5T5S1	K1984_HUMAN	T	38	ENSP00000338013:M38T	ENSP00000338013:M38T	M	+	2	0	KIAA1984	138813417	0.207000	0.23482	0.025000	0.17156	0.000000	0.00434	0.284000	0.18864	-0.124000	0.11724	-0.994000	0.02522	ATG	T|0.759;C|0.241	0.241	strong		0.637	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
PLD1	5337	hgsc.bcm.edu	37	3	171404478	171404478	+	Missense_Mutation	SNP	C	C	A	rs2290480	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:171404478C>A	ENST00000351298.4	-	16	1990	c.1864G>T	c.(1864-1866)Gct>Tct	p.A622S	PLD1_ENST00000356327.5_Intron|PLD1_ENST00000342215.6_Intron|PLD1_ENST00000340989.4_Missense_Mutation_p.A622S	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	622	Catalytic.		A -> S (in dbSNP:rs2290480).		chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	TACTTACCAGCATGAGGTCTA	0.438													C|||	829	0.165535	0.1384	0.1052	5008	,	,		17750	0.13		0.1988	False		,,,				2504	0.2474				p.A622S	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											PLD1,NS,carcinoma,0,2	PLD1	134	2	0			c.G1864T						PASS	.	C	,SER/ALA	564,3842	252.4+/-258.8	34,496,1673	132.0	136.0	135.0		,1864	-8.8	0.0	3	dbSNP_100	135	1762,6838	319.1+/-314.0	195,1372,2733	yes	intron,missense	PLD1	NM_001130081.2,NM_002662.4	,99	229,1868,4406	AA,AC,CC		20.4884,12.8007,17.8841	,benign	,622/1075	171404478	2326,10680	2203	4300	6503	SO:0001583	missense	5337	exon16			TACCAGCATGAGG	U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.1864G>T	3.37:g.171404478C>A	ENSP00000342793:p.Ala622Ser	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	37	CCDS3216.1	326	0.14926739926739926	65	0.13211382113821138	42	0.11602209944751381	67	0.11713286713286714	152	0.20052770448548812	C	6.267	0.417295	0.11870	0.128007	0.204884	ENSG00000075651	ENST00000351298;ENST00000340989	T;T	0.06528	3.43;3.29	5.46	-8.81	0.00813	.	3.181240	0.00582	N	0.000327	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.38950	-0.9637	9	0.07482	T	0.82	.	9.5572	0.39346	0.095:0.3045:0.0:0.6005	rs2290480;rs2290480	622	Q13393	PLD1_HUMAN	S	622	ENSP00000342793:A622S;ENSP00000340326:A622S	ENSP00000340326:A622S	A	-	1	0	PLD1	172887172	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-3.644000	0.00405	-2.053000	0.00901	0.557000	0.71058	GCT	C|0.841;A|0.159	0.159	strong		0.438	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
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 GAIIx	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	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	71	35	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		
KDF1	126695	hgsc.bcm.edu	37	1	27278521	27278521	+	Silent	SNP	G	G	A	rs3010110	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:27278521G>A	ENST00000320567.5	-	2	439	c.351C>T	c.(349-351)gaC>gaT	p.D117D		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		117					developmental growth (GO:0048589)|establishment of skin barrier (GO:0061436)|keratinocyte development (GO:0003334)|limb epidermis development (GO:0060887)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of stem cell proliferation (GO:2000647)|positive regulation of epidermal cell differentiation (GO:0045606)|regulation of epidermal cell division (GO:0010482)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)				NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	17		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;3.37e-51)|OV - Ovarian serous cystadenocarcinoma(117;2.22e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)		CCTCAGTGGAGTCCTCAGTAG	0.687													G|||	639	0.127596	0.0144	0.121	5008	,	,		15443	0.0288		0.2604	False		,,,				2504	0.2505				p.D117D		Atlas-SNP	.											.	C1orf172	38	.	0			c.C351T						PASS	.	G		223,4181		4,215,1983	17.0	19.0	18.0		351	4.9	1.0	1	dbSNP_101	18	2254,6346		286,1682,2332	no	coding-synonymous	C1orf172	NM_152365.2		290,1897,4315	AA,AG,GG		26.2093,5.0636,19.048		117/399	27278521	2477,10527	2202	4300	6502	SO:0001819	synonymous_variant	126695	exon2			AGTGGAGTCCTCA																												ENST00000320567.5:c.351C>T	1.37:g.27278521G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	149	84	0.563758	NM_152365	Q5QP32|Q8N0S7	Silent	SNP	ENST00000320567.5	37	CCDS293.1	279	0.12774725274725274	11	0.022357723577235773	49	0.13535911602209943	18	0.03146853146853147	201	0.26517150395778366	G	0.294	-0.978044	0.02197	0.050636	0.262093	ENSG00000175707	ENST00000374109	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.00015	-1.2392	4	0.46703	T	0.11	.	18.3122	0.90204	0.0:0.0:1.0:0.0	rs3010110;rs17356895;rs60594052;rs3010110	.	.	.	I	78	.	ENSP00000363223:T78I	T	-	2	0	C1orf172	27151108	1.000000	0.71417	1.000000	0.80357	0.124000	0.20399	3.711000	0.54868	2.547000	0.85894	0.557000	0.71058	ACT	G|0.848;A|0.152	0.152	strong		0.687	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1		
SLC44A1	23446	hgsc.bcm.edu	37	9	108147763	108147763	+	Missense_Mutation	SNP	T	T	G	rs3199966	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:108147763T>G	ENST00000374720.3	+	15	2177	c.1930T>G	c.(1930-1932)Tcc>Gcc	p.S644A	SLC44A1_ENST00000374723.1_Missense_Mutation_p.S644A|SLC44A1_ENST00000374724.1_Missense_Mutation_p.S644A|SLC44A1_ENST00000343170.7_Missense_Mutation_p.S436A	NM_080546.3	NP_536856.2	Q8WWI5	CTL1_HUMAN	solute carrier family 44 (choline transporter), member 1	644			S -> A (in dbSNP:rs3199966). {ECO:0000269|PubMed:11698453}.		choline transport (GO:0015871)|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)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)			breast(4)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(16)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	38					Choline(DB00122)	CGTCGCTGATTCCAGAGAGCT	0.473													G|||	961	0.191893	0.4917	0.1499	5008	,	,		18749	0.001		0.0805	False		,,,				2504	0.1278				p.S644A		Atlas-SNP	.											.	SLC44A1	61	.	0			c.T1930G						PASS	.	G	ALA/SER	1801,2595		368,1065,765	54.0	51.0	52.0		1930	4.7	1.0	9	dbSNP_105	52	719,7873		22,675,3599	yes	missense	SLC44A1	NM_080546.3	99	390,1740,4364	GG,GT,TT		8.3682,40.9691,19.4025	benign	644/658	108147763	2520,10468	2198	4296	6494	SO:0001583	missense	23446	exon15			GCTGATTCCAGAG	AJ420812	CCDS6763.1, CCDS75868.1	9q31.2	2014-01-28	2013-07-17	2005-09-06	ENSG00000070214	ENSG00000070214		"""CD molecules"", ""Solute carriers"""	18798	protein-coding gene	gene with protein product		606105	"""CDW92 antigen"""	CDW92		11698453, 10677542	Standard	NM_080546		Approved	CDw92, CTL1, CHTL1, CD92	uc004bcn.3	Q8WWI5	OTTHUMG00000020421	ENST00000374720.3:c.1930T>G	9.37:g.108147763T>G	ENSP00000363852:p.Ser644Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_080546	A6NLZ9|Q5VUB3|Q8WVB0|Q96KU3|Q9NY69	Missense_Mutation	SNP	ENST00000374720.3	37	CCDS6763.1	346	0.15842490842490842	246	0.5	45	0.12430939226519337	1	0.0017482517482517483	54	0.0712401055408971	G	6.374	0.437099	0.12104	0.409691	0.083682	ENSG00000070214	ENST00000374723;ENST00000374720;ENST00000374724;ENST00000343170	T;T;T;T	0.16324	3.18;3.18;3.2;2.35	5.71	4.74	0.60224	.	0.368046	0.31519	N	0.007510	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.45469	-0.9259	9	0.05351	T	0.99	-9.7919	16.5282	0.84344	0.0:0.0:0.7505:0.2495	rs3199966;rs7030899;rs59332972;rs3199966	644;644;644	Q8WWI5-3;Q8WWI5-2;Q8WWI5	.;.;CTL1_HUMAN	A	644;644;644;436	ENSP00000363855:S644A;ENSP00000363852:S644A;ENSP00000363856:S644A;ENSP00000341856:S436A	ENSP00000341856:S436A	S	+	1	0	SLC44A1	107187584	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.878000	0.56130	1.436000	0.47453	-0.121000	0.15023	TCC	T|0.803;G|0.197	0.197	strong		0.473	SLC44A1-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053500.1	NM_080546	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100846936	100846936	+	Silent	SNP	A	A	G	rs654593	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:100846936A>G	ENST00000298815.8	+	20	2007	c.2004A>G	c.(2002-2004)ccA>ccG	p.P668P	ARHGAP42_ENST00000524892.2_Silent_p.P634P	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	668	Ser-rich.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGCAACCCCATCATCTTCCA	0.473													G|||	2874	0.573882	0.2511	0.6081	5008	,	,		20996	0.997		0.4344	False		,,,				2504	0.6933				p.P668P		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A2004G						PASS	.	G		471,913		83,305,304	54.0	43.0	46.0		2004	-7.1	0.1	11	dbSNP_83	46	1401,1781		313,775,503	no	coding-synonymous	ARHGAP42	NM_152432.2		396,1080,807	GG,GA,AA		44.0289,34.0318,40.9987		668/875	100846936	1872,2694	692	1591	2283	SO:0001819	synonymous_variant	143872	exon20			AACCCCATCATCT			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2004A>G	11.37:g.100846936A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.462;G|0.538	0.538	strong		0.473	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
CYP2C19	1557	hgsc.bcm.edu	37	10	96602622	96602622	+	Silent	SNP	C	C	T	rs3758580	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:96602622C>T	ENST00000371321.3	+	7	1072	c.990C>T	c.(988-990)gtC>gtT	p.V330V	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	330					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|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)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)	p.V330V(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	TTGAACGTGTCGTTGGCAGAA	0.507													c|||	1108	0.221246	0.1702	0.1037	5008	,	,		19622	0.3125		0.1451	False		,,,				2504	0.3579				p.V330V		Atlas-SNP	.											CYP2C19,colon,carcinoma,0,1	CYP2C19	88	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C990T						PASS	.	G		731,3675		61,609,1533	164.0	145.0	152.0		990	-1.4	0.0	10	dbSNP_107	152	1274,7326		95,1084,3121	no	coding-synonymous	CYP2C19	NM_000769.1		156,1693,4654	TT,TC,CC		14.814,16.591,15.416		330/491	96602622	2005,11001	2203	4300	6503	SO:0001819	synonymous_variant	1557	exon7			ACGTGTCGTTGGC	M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"""Cytochrome P450s"""	2621	protein-coding gene	gene with protein product		124020	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"""	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.990C>T	10.37:g.96602622C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_000769	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Silent	SNP	ENST00000371321.3	37	CCDS7436.1																																																																																			C|0.826;T|0.174	0.174	strong		0.507	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769	
CCNL1	57018	hgsc.bcm.edu	37	3	156877707	156877707	+	Silent	SNP	A	A	T	rs9814142	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:156877707A>T	ENST00000295926.3	-	1	295	c.177T>A	c.(175-177)atT>atA	p.I59I	CCNL1_ENST00000461804.1_Silent_p.I59I|CCNL1_ENST00000295925.4_Silent_p.I59I	NM_020307.2	NP_064703.1	Q9UK58	CCNL1_HUMAN	cyclin L1	59					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	nuclear speck (GO:0016607)|nucleus (GO:0005634)				NS(1)|breast(1)|cervix(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0295)|Lung(72;0.0308)			TCTCCTCCGGAATCAGAGAGT	0.632													A|||	329	0.0656949	0.034	0.0879	5008	,	,		14739	0.0903		0.0477	False		,,,				2504	0.0859				p.I59I		Atlas-SNP	.											CCNL1,NS,carcinoma,0,1	CCNL1	53	1	0			c.T177A						PASS	.	A		157,4249		2,153,2048	33.0	29.0	31.0		177	-9.6	0.0	3	dbSNP_119	31	365,8235		10,345,3945	no	coding-synonymous	CCNL1	NM_020307.2		12,498,5993	TT,TA,AA		4.2442,3.5633,4.0135		59/527	156877707	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	57018	exon1			CTCCGGAATCAGA	AF180920	CCDS3178.1	3q25.31	2008-02-05			ENSG00000163660	ENSG00000163660			20569	protein-coding gene	gene with protein product		613384				11980906	Standard	NM_020307		Approved	ania-6a	uc003fbf.3	Q9UK58	OTTHUMG00000158713	ENST00000295926.3:c.177T>A	3.37:g.156877707A>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_020307	B3KMY3|Q6NVY9|Q6UWS7|Q8NI48|Q96QT0|Q9NZF3	Silent	SNP	ENST00000295926.3	37	CCDS3178.1																																																																																			A|0.954;T|0.046	0.046	strong		0.632	CCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351859.1	NM_020307	
MUC2	4583	hgsc.bcm.edu	37	11	1080576	1080576	+	Silent	SNP	G	G	A	rs41349846	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1080576G>A	ENST00000441003.2	+	9	1245	c.1218G>A	c.(1216-1218)acG>acA	p.T406T	MUC2_ENST00000359061.5_Silent_p.T406T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	406	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	ATGGGAAGACGTACACCTTCC	0.652													G|||	1334	0.266374	0.2648	0.2767	5008	,	,		16211	0.3393		0.0984	False		,,,				2504	0.3589				p.T406T		Atlas-SNP	.											.	MUC2	614	.	0			c.G1218A						PASS	.	G		996,3082		136,724,1179	28.0	32.0	30.0		1218	-1.7	0.0	11	dbSNP_127	30	733,7643		38,657,3493	no	coding-synonymous	MUC2	NM_002457.2		174,1381,4672	AA,AG,GG		8.7512,24.4237,13.8831		406/2813	1080576	1729,10725	2039	4188	6227	SO:0001819	synonymous_variant	4583	exon9			GAAGACGTACACC	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.1218G>A	11.37:g.1080576G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	195	95	0.487179	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				G|0.804;A|0.196	0.196	strong		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ZNF462	58499	hgsc.bcm.edu	37	9	109691676	109691676	+	Missense_Mutation	SNP	A	A	G	rs3814538	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:109691676A>G	ENST00000277225.5	+	3	5772	c.5483A>G	c.(5482-5484)aAc>aGc	p.N1828S	ZNF462_ENST00000457913.1_Missense_Mutation_p.N1828S|ZNF462_ENST00000441147.2_Missense_Mutation_p.N673S			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1828			N -> S (in dbSNP:rs3814538).		chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						GAGAGAGGCAACTTTGAGAAA	0.542													G|||	2802	0.559505	0.8623	0.4625	5008	,	,		19918	0.4782		0.3917	False		,,,				2504	0.4755				p.N1828S		Atlas-SNP	.											.	ZNF462	322	.	0			c.A5483G						PASS	.	G	SER/ASN	3402,1004	361.6+/-315.8	1329,744,130	83.0	73.0	77.0		5483	3.9	1.0	9	dbSNP_107	77	3126,5474	647.7+/-400.4	542,2042,1716	yes	missense	ZNF462	NM_021224.4	46	1871,2786,1846	GG,GA,AA		36.3488,22.7871,49.8078	benign	1828/2507	109691676	6528,6478	2203	4300	6503	SO:0001583	missense	58499	exon3			GAGGCAACTTTGA	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5483A>G	9.37:g.109691676A>G	ENSP00000277225:p.Asn1828Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	1134	0.5192307692307693	411	0.8353658536585366	170	0.4696132596685083	258	0.45104895104895104	295	0.3891820580474934	G	0.006	-2.046486	0.00398	0.772129	0.363488	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.04654	3.58;4.03;4.14;4.16	5.92	3.86	0.44501	.	0.653773	0.17254	N	0.181055	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19353	-1.0308	9	0.07030	T	0.85	.	5.0988	0.14749	0.4595:0.0:0.5405:0.0	rs3814538;rs17788089;rs17846198;rs17859213;rs52813323;rs57069281;rs3814538	1828;1828	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	S	1828;1828;711;673	ENSP00000277225:N1828S;ENSP00000414570:N1828S;ENSP00000363818:N711S;ENSP00000397306:N673S	ENSP00000277225:N1828S	N	+	2	0	ZNF462	108731497	0.013000	0.17824	0.991000	0.47740	0.824000	0.46624	1.305000	0.33493	0.858000	0.35431	-0.215000	0.12644	AAC	G|0.519;N|0.001	0.519	strong		0.542	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951581	130951581	+	Silent	SNP	A	A	G	rs1052312	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:130951581A>G	ENST00000312988.7	-	4	934	c.834T>C	c.(832-834)gcT>gcC	p.A278A		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	278					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					AGGCCTTCTCAGCTGAGATGA	0.597													.|||	2348	0.46885	0.587	0.5014	5008	,	,		21460	0.4365		0.3628	False		,,,				2504	0.4284				p.A278A		Atlas-SNP	.											.	TUBA3E	73	.	0			c.T834C						PASS	.						113.0	101.0	105.0					2																	130951581		2203	4300	6503	SO:0001819	synonymous_variant	112714	exon4			CTTCTCAGCTGAG	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.834T>C	2.37:g.130951581A>G		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	108	21	0.194444	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			A|0.790;G|0.210	0.210	strong		0.597	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
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 GAIIx	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	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	254	113	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		
NBEA	26960	hgsc.bcm.edu	37	13	35692378	35692378	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:35692378A>C	ENST00000400445.3	+	15	2630	c.2096A>C	c.(2095-2097)aAg>aCg	p.K699T	NBEA_ENST00000540320.1_Missense_Mutation_p.K699T|NBEA_ENST00000379939.2_Missense_Mutation_p.K699T|NBEA_ENST00000310336.4_Missense_Mutation_p.K699T	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	699					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		CGAGGGGTCAAGGAAGATGAA	0.249																																					p.K699T		Atlas-SNP	.											NBEA,NS,carcinoma,-1,1	NBEA	340	1	0			c.A2096C						scavenged	.						48.0	42.0	43.0					13																	35692378		1780	4037	5817	SO:0001583	missense	26960	exon15			GGGTCAAGGAAGA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2096A>C	13.37:g.35692378A>C	ENSP00000383295:p.Lys699Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	76	3	0.0394737	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.964126	0.53507	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.59595	0.2205	L	0.50333	1.59	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.55283	-0.8165	10	0.23302	T	0.38	.	13.4084	0.60926	1.0:0.0:0.0:0.0	.	699	Q5T321	.	T	699	ENSP00000440951:K699T;ENSP00000383295:K699T;ENSP00000369271:K699T;ENSP00000308534:K699T	ENSP00000308534:K699T	K	+	2	0	NBEA	34590378	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.932000	0.75869	1.570000	0.49709	0.377000	0.23210	AAG	.	.	none		0.249	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
PRPF4	9128	hgsc.bcm.edu	37	9	116044998	116044998	+	Silent	SNP	A	A	G	rs11552582	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:116044998A>G	ENST00000374198.4	+	4	570	c.468A>G	c.(466-468)aaA>aaG	p.K156K	PRPF4_ENST00000374199.4_Silent_p.K155K|PRPF4_ENST00000488937.1_3'UTR	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	156					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						AGAAGTCTAAAAAGTCCAAAG	0.343													G|||	2074	0.414137	0.4599	0.2104	5008	,	,		18745	0.4306		0.3231	False		,,,				2504	0.5736				p.K156K		Atlas-SNP	.											.	PRPF4	56	.	0			c.A468G						PASS	.	G		1978,2428	616.8+/-392.8	458,1062,683	83.0	81.0	82.0		468	2.6	1.0	9	dbSNP_120	82	2958,5642	664.5+/-402.2	520,1918,1862	no	coding-synonymous	PRPF4	NM_004697.3		978,2980,2545	GG,GA,AA		34.3953,44.8933,37.9517		156/523	116044998	4936,8070	2203	4300	6503	SO:0001819	synonymous_variant	9128	exon4			GTCTAAAAAGTCC	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.468A>G	9.37:g.116044998A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	37	CCDS6791.1																																																																																			A|0.602;G|0.398	0.398	strong		0.343	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
MUC2	4583	hgsc.bcm.edu	37	11	1088835	1088835	+	Missense_Mutation	SNP	C	C	T	rs41389046	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1088835C>T	ENST00000441003.2	+	26	3647	c.3620C>T	c.(3619-3621)aCc>aTc	p.T1207I	MUC2_ENST00000359061.5_Missense_Mutation_p.T1207I	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1207					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)	ACCGAGGAGACCTGCAAGTCC	0.572													T|||	326	0.0650958	0.053	0.0591	5008	,	,		23089	0.0556		0.0974	False		,,,				2504	0.0624				p.T1207I		Atlas-SNP	.											MUC2_ENST00000441003,colon,carcinoma,0,2	MUC2	614	2	0			c.C3620T						PASS	.	T	ILE/THR	227,3961		5,217,1872	51.0	53.0	52.0		3620	-7.2	0.0	11	dbSNP_127	52	782,7632		36,710,3461	yes	missense	MUC2	NM_002457.2	89	41,927,5333	TT,TC,CC		9.294,5.4202,8.0067	benign	1207/2813	1088835	1009,11593	2094	4207	6301	SO:0001583	missense	4583	exon26			AGGAGACCTGCAA	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.3620C>T	11.37:g.1088835C>T	ENSP00000415183:p.Thr1207Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		136	0.06227106227106227	21	0.042682926829268296	18	0.049723756906077346	28	0.04895104895104895	69	0.09102902374670185	T	4.811	0.150695	0.09185	0.054202	0.09294	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13196	2.67;2.61	3.61	-7.21	0.01490	.	8.859210	0.01114	N	0.005658	T	0.00178	0.0005	N	0.00742	-1.23	0.58432	P	2.9999999999752447E-6	B	0.14805	0.011	B	0.15870	0.014	T	0.38735	-0.9647	9	0.39692	T	0.17	.	8.0296	0.30457	0.5745:0.2881:0.0:0.1374	rs41389046;rs61732138	1207	E7EUV1	.	I	1207	ENSP00000415183:T1207I;ENSP00000351956:T1207I	ENSP00000351956:T1207I	T	+	2	0	MUC2	1078835	0.002000	0.14202	0.000000	0.03702	0.068000	0.16541	-0.083000	0.11286	-3.281000	0.00197	-0.847000	0.03039	ACC	C|0.932;T|0.068	0.068	strong		0.572	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ASCC2	84164	hgsc.bcm.edu	37	22	30189642	30189642	+	Missense_Mutation	SNP	C	C	T	rs61736786	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30189642C>T	ENST00000397771.2	-	17	1889	c.1712G>A	c.(1711-1713)cGg>cAg	p.R571Q	ASCC2_ENST00000542393.1_Missense_Mutation_p.R495Q|ASCC2_ENST00000307790.3_Missense_Mutation_p.R571Q			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	571					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					endometrium(3)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(5;0.000103)|Epithelial(10;0.0169)|all cancers(5;0.0259)			CAGCAAACTCCGCGTGTTTTC	0.597													C|||	156	0.0311502	0.0	0.062	5008	,	,		20424	0.0675		0.0249	False		,,,				2504	0.0204				p.R571Q		Atlas-SNP	.											.	ASCC2	53	.	0			c.G1712A						PASS	.	C	GLN/ARG,GLN/ARG	19,4385		0,19,2183	39.0	25.0	30.0		1484,1712	5.3	1.0	22	dbSNP_129	30	236,8362		3,230,4066	yes	missense,missense	ASCC2	NM_001242906.1,NM_032204.4	43,43	3,249,6249	TT,TC,CC		2.7448,0.4314,1.9612	possibly-damaging,possibly-damaging	495/682,571/758	30189642	255,12747	2202	4299	6501	SO:0001583	missense	84164	exon16			AAACTCCGCGTGT	AY013289	CCDS13869.1, CCDS56226.1	22q12.1	2004-07-27			ENSG00000100325	ENSG00000100325			24103	protein-coding gene	gene with protein product	"""ASC 1 complex subunit P100"""	614216				12077347, 9847074	Standard	NM_032204		Approved	ASC1p100, FLJ21588, DKFZp586O0223	uc003agr.3	Q9H1I8	OTTHUMG00000067658	ENST00000397771.2:c.1712G>A	22.37:g.30189642C>T	ENSP00000380877:p.Arg571Gln	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_032204	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	ENST00000397771.2	37	CCDS13869.1	86	0.039377289377289376	0	0.0	18	0.049723756906077346	48	0.08391608391608392	20	0.026385224274406333	C	12.76	2.034215	0.35893	0.004314	0.027448	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000542393;ENST00000411532	T;T;T;T	0.32753	3.05;3.05;3.05;1.44	5.26	5.26	0.73747	.	0.131042	0.52532	D	0.000071	T	0.01092	0.0036	L	0.45228	1.405	0.46927	D	0.999252	B;B	0.31485	0.325;0.181	B;B	0.22601	0.04;0.018	T	0.03473	-1.1033	10	0.15066	T	0.55	-23.8892	11.4524	0.50160	0.0:0.9188:0.0:0.0812	.	495;571	F5H6J9;Q9H1I8	.;ASCC2_HUMAN	Q	571;571;495;62	ENSP00000305502:R571Q;ENSP00000380877:R571Q;ENSP00000437570:R495Q;ENSP00000414545:R62Q	ENSP00000305502:R571Q	R	-	2	0	ASCC2	28519642	0.011000	0.17503	0.995000	0.50966	0.148000	0.21650	1.492000	0.35594	2.735000	0.93741	0.561000	0.74099	CGG	C|0.974;T|0.026	0.026	strong		0.597	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204	
OR5P2	120065	hgsc.bcm.edu	37	11	7817665	7817665	+	Silent	SNP	T	T	C	rs72484720	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7817665T>C	ENST00000329434.2	-	1	855	c.825A>G	c.(823-825)acA>acG	p.T275T	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	275						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GAATCACCACTGTGTACAACA	0.448													C|||	1185	0.236621	0.3472	0.2911	5008	,	,		18498	0.128		0.2763	False		,,,				2504	0.1196				p.T275T		Atlas-SNP	.											.	OR5P2	68	.	0			c.A825G						PASS	.	C		1371,2845		401,569,1138	114.0	122.0	120.0		825	2.4	1.0	11	dbSNP_130	120	2425,6159		393,1639,2260	no	coding-synonymous	OR5P2	NM_153444.1		794,2208,3398	CC,CT,TT		28.2502,32.519,29.6562		275/323	7817665	3796,9004	2108	4292	6400	SO:0001819	synonymous_variant	120065	exon1			CACCACTGTGTAC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.825A>G	11.37:g.7817665T>C		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_153444	Q3MIS8	Silent	SNP	ENST00000329434.2	37	CCDS7782.1																																																																																			T|0.738;C|0.262	0.262	strong		0.448	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
RBMS1	5937	hgsc.bcm.edu	37	2	161174693	161174693	+	Silent	SNP	C	C	T	rs1430	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:161174693C>T	ENST00000348849.3	-	3	727	c.297G>A	c.(295-297)acG>acA	p.T99T	RBMS1_ENST00000392753.3_Silent_p.T99T|RBMS1_ENST00000409075.1_Silent_p.T66T|RBMS1_ENST00000409289.2_Silent_p.T66T|RBMS1_ENST00000409972.1_Silent_p.T66T|RBMS1_ENST00000474820.1_5'UTR	NM_002897.4|NM_016836.3	NP_002888.1|NP_058520.1	P29558	RBMS1_HUMAN	RNA binding motif, single stranded interacting protein 1	99	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				DNA replication (GO:0006260)|RNA processing (GO:0006396)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)		PLA2R1/RBMS1(2)								TGCATTTGTTCGTTGTCTTAT	0.284													c|||	1308	0.261182	0.1195	0.2104	5008	,	,		14319	0.5308		0.3032	False		,,,				2504	0.1677				p.T99T		Atlas-SNP	.											RBMS1_ENST00000348849,caecum,carcinoma,0,1	RBMS1	34	1	0			c.G297A						scavenged	.	T	,	663,3743	277.2+/-273.6	48,567,1588	118.0	112.0	114.0		297,297	-12.1	0.1	2	dbSNP_36	114	2494,6104	408.8+/-349.6	380,1734,2185	no	coding-synonymous,coding-synonymous	RBMS1	NM_002897.4,NM_016836.3	,	428,2301,3773	TT,TC,CC		29.0067,15.0477,24.2771	,	99/404,99/407	161174693	3157,9847	2203	4299	6502	SO:0001819	synonymous_variant	5937	exon3			TTTGTTCGTTGTC	D28482	CCDS2213.1	2q24.2	2013-02-12			ENSG00000153250	ENSG00000153250		"""RNA binding motif (RRM) containing"""	9907	protein-coding gene	gene with protein product	"""suppressor of cdc 2 (cdc13) with RNA binding motif 2"", ""c-myc gene single strand binding protein 2"""	602310	"""chromosome 2 open reading frame 12"""	C2orf12		8041632, 8134115, 7838710	Standard	NM_016836		Approved	SCR2, MSSP-1, MSSP-2, MSSP-3, YC1, HCC-4, DKFZp564H0764	uc002ubo.3	P29558	OTTHUMG00000132031	ENST00000348849.3:c.297G>A	2.37:g.161174693C>T		Somatic	66	3	0.0454545		WXS	Illumina HiSeq	Phase_I	30	21	0.7	NM_016836	Q14869|Q15433|Q53P46|Q53QX8|Q53RG6|Q8WV20	Silent	SNP	ENST00000348849.3	37	CCDS2213.1																																																																																			C|0.733;T|0.267	0.267	strong		0.284	RBMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255043.4	NM_016836	
ACADSB	36	hgsc.bcm.edu	37	10	124806770	124806770	+	Missense_Mutation	SNP	A	A	G	rs1131430	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124806770A>G	ENST00000358776.4	+	8	960	c.946A>G	c.(946-948)Att>Gtt	p.I316V	ACADSB_ENST00000368869.4_Missense_Mutation_p.I214V	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	316			I -> V (in dbSNP:rs1131430). {ECO:0000269|PubMed:17974005}.		branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	TATTCCATATATTAAAGAAAG	0.313													A|||	195	0.0389377	0.0386	0.062	5008	,	,		19842	0.001		0.0815	False		,,,				2504	0.0184				p.I316V		Atlas-SNP	.											.	ACADSB	45	.	0			c.A946G						PASS	.	A	VAL/ILE	192,4214	119.2+/-156.9	1,190,2012	85.0	93.0	90.0		946	1.4	1.0	10	dbSNP_86	90	725,7875	176.3+/-226.2	32,661,3607	yes	missense	ACADSB	NM_001609.3	29	33,851,5619	GG,GA,AA		8.4302,4.3577,7.0506	benign	316/433	124806770	917,12089	2203	4300	6503	SO:0001583	missense	36	exon8			CCATATATTAAAG	U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"""acyl-Coenzyme A dehydrogenase, short/branched chain"""			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.946A>G	10.37:g.124806770A>G	ENSP00000357873:p.Ile316Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	47	26	0.553191	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Missense_Mutation	SNP	ENST00000358776.4	37	CCDS7634.1	109	0.04990842490842491	19	0.03861788617886179	27	0.07458563535911603	0	0.0	63	0.08311345646437995	A	1.662	-0.511306	0.04231	0.043577	0.084302	ENSG00000196177	ENST00000368869;ENST00000358776	D;D	0.95377	-3.69;-3.69	5.5	1.38	0.22167	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.356115	0.30695	N	0.009077	T	0.22742	0.0549	N	0.01048	-1.04	0.26763	N	0.969962	B	0.18166	0.026	B	0.26202	0.067	T	0.63368	-0.6653	10	0.02654	T	1	.	8.6286	0.33906	0.6732:0.2534:0.0734:0.0	rs1131430;rs2229256;rs3191331;rs17417130;rs41291344;rs61401267	316	P45954	ACDSB_HUMAN	V	214;316	ENSP00000357862:I214V;ENSP00000357873:I316V	ENSP00000357873:I316V	I	+	1	0	ACADSB	124796760	1.000000	0.71417	0.974000	0.42286	0.709000	0.40893	2.114000	0.41911	0.340000	0.23745	0.528000	0.53228	ATT	A|0.935;G|0.065	0.065	strong		0.313	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609	
ZP1	22917	hgsc.bcm.edu	37	11	60638461	60638461	+	Silent	SNP	C	C	T	rs10897122	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:60638461C>T	ENST00000278853.5	+	5	858	c.858C>T	c.(856-858)ttC>ttT	p.F286F		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	286	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						ATGGCTACTTCGTCCTCGTAG	0.577													C|||	1551	0.309704	0.034	0.3098	5008	,	,		20608	0.626		0.2207	False		,,,				2504	0.4479				p.F286F		Atlas-SNP	.											.	ZP1	69	.	0			c.C858T						PASS	.	C		298,4108	162.5+/-194.5	11,276,1916	249.0	216.0	227.0		858	-1.5	0.0	11	dbSNP_120	227	1961,6637	345.4+/-325.7	228,1505,2566	no	coding-synonymous	ZP1	NM_207341.2		239,1781,4482	TT,TC,CC		22.8076,6.7635,17.3716		286/639	60638461	2259,10745	2203	4299	6502	SO:0001819	synonymous_variant	22917	exon5			CTACTTCGTCCTC	BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"""Zona pellucida glycoproteins"""	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.858C>T	11.37:g.60638461C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	94	50	0.531915	NM_207341		Silent	SNP	ENST00000278853.5	37	CCDS31572.1																																																																																			C|0.776;N|0.000	.	strong		0.577	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341	
COL20A1	57642	hgsc.bcm.edu	37	20	61943089	61943089	+	Missense_Mutation	SNP	G	G	A	rs6089877	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61943089G>A	ENST00000358894.6	+	13	1752	c.1652G>A	c.(1651-1653)cGt>cAt	p.R551H	COL20A1_ENST00000422202.1_Missense_Mutation_p.R558H|COL20A1_ENST00000326996.6_Missense_Mutation_p.R551H|COL20A1_ENST00000435874.1_Missense_Mutation_p.R558H	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	551	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					CGGGGCATCCGTGCCAGGACC	0.697													g|||	129	0.0257588	0.0484	0.0144	5008	,	,		13121	0.005		0.0139	False		,,,				2504	0.0368				p.R551H		Atlas-SNP	.											.	COL20A1	137	.	0			c.G1652A						PASS	.	A	HIS/ARG	169,3847		3,163,1842	12.0	18.0	16.0		1652	-6.7	0.0	20	dbSNP_114	16	127,8183		2,123,4030	no	missense	COL20A1	NM_020882.2	29	5,286,5872	AA,AG,GG		1.5283,4.2082,2.4014	benign	551/1285	61943089	296,12030	2008	4155	6163	SO:0001583	missense	57642	exon13			GCATCCGTGCCAG	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.1652G>A	20.37:g.61943089G>A	ENSP00000351767:p.Arg551His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	35	0.016025641025641024	18	0.036585365853658534	6	0.016574585635359115	0	0.0	11	0.014511873350923483	g	2.798	-0.249837	0.05867	0.042082	0.015283	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	D;D;D;D	0.87179	-2.21;-2.22;-2.19;-2.19	3.34	-6.67	0.01783	Fibronectin, type III (2);Immunoglobulin-like fold (1);	1.180410	0.06015	N	0.650168	T	0.51805	0.1696	L	0.46819	1.47	0.09310	N	1	B;B	0.17268	0.021;0.005	B;B	0.06405	0.002;0.001	T	0.57562	-0.7790	10	0.37606	T	0.19	.	7.7155	0.28702	0.7207:0.0:0.1659:0.1135	rs6089877;rs6089877	558;551	Q9P218-2;Q9P218	.;COKA1_HUMAN	H	551;551;558;558	ENSP00000351767:R551H;ENSP00000323077:R551H;ENSP00000408690:R558H;ENSP00000414753:R558H	ENSP00000323077:R551H	R	+	2	0	COL20A1	61413534	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-2.376000	0.01070	-1.744000	0.01338	-1.740000	0.00687	CGT	G|0.985;A|0.015	0.015	strong		0.697	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
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 GAIIx	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_ENST00000354209.3_Missense_Mutation_p.S5N|PRKAA1_ENST00000296800.4_5'Flank	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	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	117	22	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	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289714	98289714	+	Missense_Mutation	SNP	G	G	C	rs2635164	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:98289714G>C	ENST00000322128.3	-	1	462	c.359C>G	c.(358-360)aCt>aGt	p.T120S		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	120			T -> S (in dbSNP:rs2635164).		cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					CACGAAGACAGTGTCTGCGGC	0.721													G|||	1178	0.235224	0.5129	0.1787	5008	,	,		12121	0.0933		0.1372	False		,,,				2504	0.1472				p.T120S		Atlas-SNP	.											.	TSPYL5	48	.	0			c.C359G						PASS	.	G	SER/THR	1792,2522		386,1020,751	10.0	12.0	11.0		359	3.3	0.6	8	dbSNP_100	11	1062,7310		85,892,3209	yes	missense	TSPYL5	NM_033512.2	58	471,1912,3960	CC,CG,GG		12.6851,41.5392,22.4972	possibly-damaging	120/418	98289714	2854,9832	2157	4186	6343	SO:0001583	missense	85453	exon1			AAGACAGTGTCTG	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.359C>G	8.37:g.98289714G>C	ENSP00000322802:p.Thr120Ser	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	445	0.20375457875457875	228	0.4634146341463415	66	0.18232044198895028	45	0.07867132867132867	106	0.13984168865435356	G	5.440	0.266334	0.10294	0.415392	0.126851	ENSG00000180543	ENST00000322128	T	0.12774	2.65	4.16	3.27	0.37495	.	0.252185	0.20796	N	0.085534	T	0.00012	0.0000	N	0.00926	-1.1	0.45194	P	0.001794999999999991	P	0.37061	0.58	B	0.35114	0.196	T	0.30650	-0.9971	9	0.02654	T	1	-2.746	8.3789	0.32459	0.1076:0.0:0.8924:0.0	rs2635164	120	Q86VY4	TSYL5_HUMAN	S	120	ENSP00000322802:T120S	ENSP00000322802:T120S	T	-	2	0	TSPYL5	98358890	0.973000	0.33851	0.646000	0.29493	0.871000	0.50021	1.939000	0.40213	1.298000	0.44778	0.650000	0.86243	ACT	G|0.810;C|0.190	0.190	strong		0.721	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
CXCR5	643	hgsc.bcm.edu	37	11	118765231	118765231	+	Silent	SNP	C	C	T	rs12795395	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:118765231C>T	ENST00000292174.4	+	2	1154	c.978C>T	c.(976-978)ggC>ggT	p.G326G	BCL9L_ENST00000334801.3_3'UTR	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	326					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		CTTTCGCCGGCGTGAAGTTCC	0.642													C|||	49	0.00978435	0.0023	0.0043	5008	,	,		21758	0.0		0.0268	False		,,,				2504	0.0164				p.G326G		Atlas-SNP	.											.	CXCR5	34	.	0			c.C978T						PASS	.	C	,	22,4378	29.0+/-57.7	1,20,2179	94.0	81.0	86.0		978,843	-0.4	1.0	11	dbSNP_121	86	257,8333	99.7+/-161.2	5,247,4043	no	coding-synonymous,coding-synonymous	CXCR5	NM_001716.4,NM_032966.2	,	6,267,6222	TT,TC,CC		2.9919,0.5,2.1478	,	326/373,281/328	118765231	279,12711	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CGCCGGCGTGAAG	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	1060	protein-coding gene	gene with protein product		601613	"""Burkitt lymphoma receptor 1, GTP-binding protein"", ""Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"""	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.978C>T	11.37:g.118765231C>T		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	58	12	0.206897	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			C|0.980;T|0.020	0.020	strong		0.642	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
ZNF205	7755	hgsc.bcm.edu	37	16	3165425	3165425	+	Missense_Mutation	SNP	A	A	G	rs909410	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3165425A>G	ENST00000382192.3	+	3	332	c.127A>G	c.(127-129)Act>Gct	p.T43A	ZNF205-AS1_ENST00000576943.1_RNA|ZNF205-AS1_ENST00000572691.1_RNA|RP11-473M20.14_ENST00000575139.1_RNA|ZNF205_ENST00000219091.4_Missense_Mutation_p.T43A|RP11-473M20.14_ENST00000576490.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	43			T -> A (in dbSNP:rs909410). {ECO:0000269|PubMed:15489334}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						TTCAGGGGACACTCAGGAGTC	0.597													G|||	1961	0.391573	0.4909	0.3761	5008	,	,		19739	0.1776		0.4016	False		,,,				2504	0.4785				p.T43A		Atlas-SNP	.											.	ZNF205	42	.	0			c.A127G						PASS	.	G	ALA/THR,ALA/THR	2149,2245	594.7+/-388.3	533,1083,581	76.0	76.0	76.0		127,127	-9.4	0.0	16	dbSNP_86	76	3525,5075	630.9+/-398.4	725,2075,1500	yes	missense,missense	ZNF205	NM_001042428.1,NM_003456.2	58,58	1258,3158,2081	GG,GA,AA		40.9884,48.9076,43.6663	benign,benign	43/555,43/555	3165425	5674,7320	2197	4300	6497	SO:0001583	missense	7755	exon3			GGGGACACTCAGG	AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"""Zinc fingers, C2H2-type"", ""-"""	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.127A>G	16.37:g.3165425A>G	ENSP00000371627:p.Thr43Ala	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_003456	A8MZK0|D3DUB4|Q9BU95	Missense_Mutation	SNP	ENST00000382192.3	37	CCDS10494.2	764	0.3498168498168498	232	0.4715447154471545	135	0.3729281767955801	98	0.17132867132867133	299	0.3944591029023747	G	2.133	-0.398560	0.04865	0.489076	0.409884	ENSG00000122386	ENST00000382192;ENST00000219091;ENST00000444510;ENST00000414351	T;T;T;T	0.41065	3.24;3.24;1.01;3.33	4.7	-9.4	0.00616	.	1.652040	0.03697	N	0.248039	T	0.00012	0.0000	N	0.04043	-0.29	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.19549	-1.0302	9	0.07175	T	0.84	0.2918	12.8468	0.57833	0.7248:0.0:0.1928:0.0824	rs909410;rs17606856;rs17856076;rs59295872;rs909410	43	O95201	ZN205_HUMAN	A	43	ENSP00000371627:T43A;ENSP00000219091:T43A;ENSP00000394360:T43A;ENSP00000403306:T43A	ENSP00000219091:T43A	T	+	1	0	ZNF205	3105426	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.231000	0.01206	-3.741000	0.00113	-3.098000	0.00064	ACT	A|0.601;G|0.399	0.399	strong		0.597	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
ZNF485	220992	hgsc.bcm.edu	37	10	44104101	44104101	+	Missense_Mutation	SNP	C	C	T	rs45545532	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:44104101C>T	ENST00000361807.3	+	3	258	c.64C>T	c.(64-66)Cgg>Tgg	p.R22W	ZNF485_ENST00000374437.2_Intron|ZNF485_ENST00000374435.3_Missense_Mutation_p.R22W	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	22	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	16						GGCCTTTACCCGGATTGAGTG	0.562													C|||	312	0.0623003	0.056	0.0865	5008	,	,		17332	0.0119		0.1163	False		,,,				2504	0.0501				p.R22W		Atlas-SNP	.											.	ZNF485	102	.	0			c.C64T						PASS	.	C	TRP/ARG	98,1286		5,88,599	171.0	161.0	164.0		64	2.0	0.0	10	dbSNP_127	164	431,2751		33,365,1193	yes	missense	ZNF485	NM_145312.3	101	38,453,1792	TT,TC,CC		13.5449,7.0809,11.5856	possibly-damaging	22/442	44104101	529,4037	692	1591	2283	SO:0001583	missense	220992	exon3			TTTACCCGGATTG	AK074679	CCDS7205.2	10q11.21	2013-01-08			ENSG00000198298	ENSG00000198298		"""Zinc fingers, C2H2-type"", ""-"""	23440	protein-coding gene	gene with protein product							Standard	NM_145312		Approved		uc010qfc.2	Q8NCK3	OTTHUMG00000018040	ENST00000361807.3:c.64C>T	10.37:g.44104101C>T	ENSP00000354694:p.Arg22Trp	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	220	111	0.504545	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	37	CCDS7205.2	165	0.07554945054945054	26	0.052845528455284556	40	0.11049723756906077	8	0.013986013986013986	91	0.12005277044854881	C	13.31	2.199318	0.38806	0.070809	0.135449	ENSG00000198298	ENST00000361807;ENST00000430885;ENST00000374435	T;T;T	0.01887	4.58;4.58;4.58	2.96	2.04	0.26737	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	N	0.04148	-0.265	0.51482	P	7.199999999996098E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.45440	-0.9261	8	0.45353	T	0.12	.	4.2694	0.10778	0.0:0.6208:0.2395:0.1397	rs45545532;rs61729737	22	Q8NCK3	ZN485_HUMAN	W	22	ENSP00000354694:R22W;ENSP00000393570:R22W;ENSP00000363558:R22W	ENSP00000354694:R22W	R	+	1	2	ZNF485	43424107	0.000000	0.05858	0.015000	0.15790	0.921000	0.55340	-0.817000	0.04472	0.567000	0.29293	0.462000	0.41574	CGG	C|0.915;T|0.085	0.085	strong		0.562	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312	
OR8B2	26595	hgsc.bcm.edu	37	11	124252417	124252417	+	Missense_Mutation	SNP	C	C	G	rs139038842	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124252417C>G	ENST00000375013.2	-	1	841	c.823G>C	c.(823-825)Gtt>Ctt	p.V275L		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	275						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)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		GTGTAGAAAACAGAAGAAACT	0.403													c|||	9	0.00179712	0.0	0.0029	5008	,	,		18536	0.0		0.007	False		,,,				2504	0.0				p.V275L		Atlas-SNP	.											.	OR8B2	42	.	0			c.G823C						PASS	.	C	LEU/VAL	2,4400	4.2+/-10.8	0,2,2199	64.0	68.0	67.0		823	2.9	0.1	11	dbSNP_134	67	40,8558	26.8+/-75.7	0,40,4259	no	missense	OR8B2	NM_001005468.1	32	0,42,6458	GG,GC,CC		0.4652,0.0454,0.3231	possibly-damaging	275/314	124252417	42,12958	2201	4299	6500	SO:0001583	missense	26595	exon1			AGAAAACAGAAGA	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.823G>C	11.37:g.124252417C>G	ENSP00000364152:p.Val275Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	242	42	0.173554	NM_001005468	Q8NGH2	Missense_Mutation	SNP	ENST00000375013.2	37	CCDS31708.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	c	10.41	1.342031	0.24339	4.54E-4	0.004652	ENSG00000204293	ENST00000375013	T	0.00245	8.45	3.81	2.89	0.33648	GPCR, rhodopsin-like superfamily (1);	0.268809	0.26700	N	0.022943	T	0.00109	0.0003	L	0.43598	1.365	0.09310	N	1	B	0.29531	0.247	B	0.34590	0.186	T	0.23119	-1.0197	10	0.48119	T	0.1	.	6.3075	0.21147	0.0:0.5938:0.3002:0.106	.	275	Q96RD0	OR8B2_HUMAN	L	275	ENSP00000364152:V275L	ENSP00000364152:V275L	V	-	1	0	OR8B2	123757627	0.000000	0.05858	0.066000	0.19879	0.504000	0.33889	-0.610000	0.05629	0.943000	0.37553	-0.424000	0.05967	GTT	C|0.997;G|0.003	0.003	strong		0.403	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
CPO	130749	hgsc.bcm.edu	37	2	207824384	207824384	+	Missense_Mutation	SNP	T	T	G	rs11903403	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:207824384T>G	ENST00000272852.3	+	5	448	c.402T>G	c.(400-402)agT>agG	p.S134R		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	134			S -> R (in dbSNP:rs11903403). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		ACAACTCAAGTATACGCAAGC	0.343													G|||	2174	0.434105	0.5454	0.2752	5008	,	,		18780	0.4058		0.4592	False		,,,				2504	0.3998				p.S134R		Atlas-SNP	.											CPO,NS,carcinoma,+2,1	CPO	42	1	0			c.T402G						PASS	.	G	ARG/SER	2306,2100	574.0+/-383.7	627,1052,524	126.0	124.0	124.0		402	1.1	0.6	2	dbSNP_120	124	4115,4485	592.0+/-392.9	991,2133,1176	yes	missense	CPO	NM_173077.2	110	1618,3185,1700	GG,GT,TT		47.8488,47.6623,49.3695	benign	134/375	207824384	6421,6585	2203	4300	6503	SO:0001583	missense	130749	exon5			CTCAAGTATACGC		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.402T>G	2.37:g.207824384T>G	ENSP00000272852:p.Ser134Arg	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	178	84	0.47191	NM_173077	Q2M277|Q7RTW7	Missense_Mutation	SNP	ENST00000272852.3	37	CCDS2372.1	930	0.4258241758241758	253	0.5142276422764228	111	0.30662983425414364	224	0.3916083916083916	342	0.45118733509234826	G	0.758	-0.770360	0.02974	0.523377	0.478488	ENSG00000144410	ENST00000272852	T	0.09911	2.93	5.03	1.12	0.20585	Peptidase M14, carboxypeptidase A (2);	0.141579	0.64402	N	0.000005	T	0.00012	0.0000	N	0.03917	-0.325	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39057	-0.9632	9	0.13108	T	0.6	.	2.624	0.04924	0.2234:0.1256:0.522:0.129	rs11903403;rs17597000;rs52828262;rs57874803;rs11903403	134	Q8IVL8	CBPO_HUMAN	R	134	ENSP00000272852:S134R	ENSP00000272852:S134R	S	+	3	2	CPO	207532629	0.979000	0.34478	0.611000	0.29010	0.146000	0.21551	0.471000	0.22100	0.051000	0.15978	-0.217000	0.12591	AGT	T|0.526;G|0.474	0.474	strong		0.343	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
KRT6C	286887	hgsc.bcm.edu	37	12	52863038	52863038	+	Silent	SNP	G	G	A	rs410562	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52863038G>A	ENST00000252250.6	-	9	1550	c.1503C>T	c.(1501-1503)agC>agT	p.S501S		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	501	Tail.				intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|prostate(2)|skin(2)	23				BRCA - Breast invasive adenocarcinoma(357;0.0828)		TGCCGACACCGCTGGCACCGC	0.612													G|||	1253	0.2502	0.0242	0.2651	5008	,	,		19993	0.4812		0.3628	False		,,,				2504	0.1912				p.S501S		Atlas-SNP	.											.	KRT6C	55	.	0			c.C1503T						PASS	.	G		314,4092	166.2+/-197.5	15,284,1904	42.0	40.0	41.0		1503	-6.3	0.0	12	dbSNP_80	41	3150,5450	457.5+/-364.3	579,1992,1729	no	coding-synonymous	KRT6C	NM_173086.4		594,2276,3633	AA,AG,GG		36.6279,7.1266,26.6339		501/565	52863038	3464,9542	2203	4300	6503	SO:0001819	synonymous_variant	286887	exon9			GACACCGCTGGCA	L42611	CCDS8829.1	12q13.13	2013-01-16	2006-07-17	2006-07-17	ENSG00000170465	ENSG00000170465		"""-"", ""Intermediate filaments type II, keratins (basic)"""	20406	protein-coding gene	gene with protein product		612315	"""keratin 6E"""	KRT6E		7543104, 16831889	Standard	NM_173086		Approved		uc001sal.4	P48668	OTTHUMG00000169596	ENST00000252250.6:c.1503C>T	12.37:g.52863038G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	25	0.3125	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			G|0.731;A|0.269	0.269	strong		0.612	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
GIMAP4	55303	hgsc.bcm.edu	37	7	150269542	150269542	+	Missense_Mutation	SNP	G	G	T	rs2293172	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:150269542G>T	ENST00000255945.2	+	3	559	c.384G>T	c.(382-384)gaG>gaT	p.E128D	GIMAP4_ENST00000494750.1_3'UTR|GIMAP4_ENST00000461940.1_Missense_Mutation_p.E142D	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	128	AIG1-type G.		E -> D (in dbSNP:rs2293172).			cytosol (GO:0005829)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTTACACTGAGGAAGAGCACA	0.488													G|||	685	0.136781	0.0734	0.1412	5008	,	,		20430	0.2173		0.1561	False		,,,				2504	0.1166				p.E128D		Atlas-SNP	.											.	GIMAP4	61	.	0			c.G384T						PASS	.	G	ASP/GLU	348,4058	179.4+/-207.9	14,320,1869	81.0	78.0	79.0		384	2.9	0.8	7	dbSNP_100	79	1353,7247	265.7+/-286.3	109,1135,3056	yes	missense	GIMAP4	NM_018326.2	45	123,1455,4925	TT,TG,GG		15.7326,7.8983,13.0786	benign	128/330	150269542	1701,11305	2203	4300	6503	SO:0001583	missense	55303	exon3			CACTGAGGAAGAG	AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"""GTPases, IMAP"""	21872	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 1"""	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.384G>T	7.37:g.150269542G>T	ENSP00000255945:p.Glu128Asp	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	121	61	0.504132	NM_018326		Missense_Mutation	SNP	ENST00000255945.2	37	CCDS5904.1	338	0.15476190476190477	30	0.06097560975609756	60	0.16574585635359115	120	0.2097902097902098	128	0.16886543535620052	G	4.023	0.001695	0.07819	0.078983	0.157326	ENSG00000133574	ENST00000255945;ENST00000461940;ENST00000479232	T;T;T	0.62498	0.02;0.02;0.02	4.72	2.86	0.33363	AIG1 (1);	2.302990	0.01535	N	0.018966	T	0.00039	0.0001	N	0.21097	0.63	0.58432	P	1.0000000000287557E-6	B;B	0.19817	0.039;0.008	B;B	0.17979	0.014;0.02	T	0.03025	-1.1081	9	0.29301	T	0.29	.	7.4594	0.27285	0.203:0.0:0.797:0.0	rs2293172;rs11539192;rs52811237;rs57984509;rs2293172	142;128	G5E9W9;Q9NUV9	.;GIMA4_HUMAN	D	128;142;142	ENSP00000255945:E128D;ENSP00000419545:E142D;ENSP00000418615:E142D	ENSP00000255945:E128D	E	+	3	2	GIMAP4	149900475	0.000000	0.05858	0.821000	0.32701	0.011000	0.07611	-0.964000	0.03833	1.226000	0.43582	0.655000	0.94253	GAG	G|0.866;T|0.134	0.134	strong		0.488	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326	
DNAJA1	3301	hgsc.bcm.edu	37	9	33026572	33026572	+	Silent	SNP	T	T	C	rs20583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33026572T>C	ENST00000330899.4	+	2	273	c.90T>C	c.(88-90)gcT>gcC	p.A30A	APTX_ENST00000473270.1_5'Flank|DNAJA1_ENST00000495015.1_Intron|DNAJA1_ENST00000544625.1_5'UTR	NM_001539.2	NP_001530.1	P31689	DNJA1_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 1	30	J.				androgen receptor signaling pathway (GO:0030521)|DNA damage response, detection of DNA damage (GO:0042769)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of apoptotic process (GO:0043065)|protein folding (GO:0006457)|protein localization to mitochondrion (GO:0070585)|regulation of protein transport (GO:0051223)|response to heat (GO:0009408)|response to unfolded protein (GO:0006986)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasmic side of endoplasmic reticulum membrane (GO:0098554)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|G-protein coupled receptor binding (GO:0001664)|Hsp70 protein binding (GO:0030544)|low-density lipoprotein particle receptor binding (GO:0050750)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			large_intestine(2)|ovary(1)|skin(3)	6			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.102)		GGAAACTGGCTTTGAAGTACC	0.388													C|||	2994	0.597843	0.857	0.4784	5008	,	,		18511	0.5744		0.5119	False		,,,				2504	0.4448				p.A30A		Atlas-SNP	.											.	DNAJA1	26	.	0			c.T90C						PASS	.	C		3496,910	351.1+/-311.1	1396,704,103	81.0	80.0	80.0		90	3.0	1.0	9	dbSNP_67	80	4443,4157	564.5+/-388.3	1159,2125,1016	no	coding-synonymous	DNAJA1	NM_001539.2		2555,2829,1119	CC,CT,TT		48.3372,20.6537,38.9589		30/398	33026572	7939,5067	2203	4300	6503	SO:0001819	synonymous_variant	3301	exon2			ACTGGCTTTGAAG	L08069	CCDS6533.1	9p13.3	2011-09-02			ENSG00000086061	ENSG00000086061		"""Heat shock proteins / DNAJ (HSP40)"""	5229	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 7"""	602837		HSJ2		8334160, 11147971	Standard	NM_001539		Approved	HSPF4, hdj-2, dj-2, NEDD7	uc003zsd.1	P31689	OTTHUMG00000019760	ENST00000330899.4:c.90T>C	9.37:g.33026572T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_001539	Q5T7Q0|Q86TL9	Silent	SNP	ENST00000330899.4	37	CCDS6533.1																																																																																			A|0.004;C|0.607	0.607	strong		0.388	DNAJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052031.1		
CSPG4	1464	hgsc.bcm.edu	37	15	75982072	75982072	+	Missense_Mutation	SNP	G	G	A	rs77681934	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:75982072G>A	ENST00000308508.5	-	3	1426	c.1334C>T	c.(1333-1335)gCc>gTc	p.A445V		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	445	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.A445V(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CTCAAGCCAGGCTGTGCCCCC	0.642																																					p.A445V		Atlas-SNP	.											CSPG4,NS,carcinoma,0,1	CSPG4	175	1	1	Substitution - Missense(1)	liver(1)	c.C1334T						PASS	.						49.0	47.0	48.0					15																	75982072		2197	4293	6490	SO:0001583	missense	1464	exon3			AGCCAGGCTGTGC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1334C>T	15.37:g.75982072G>A	ENSP00000312506:p.Ala445Val	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	149	16	0.107383	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	18.33	3.601347	0.66445	.	.	ENSG00000173546	ENST00000308508	T	0.26223	1.75	5.26	5.26	0.73747	.	0.180168	0.38381	N	0.001715	T	0.21761	0.0524	L	0.57536	1.79	0.54753	D	0.999986	P	0.48503	0.911	B	0.36766	0.232	T	0.03503	-1.1030	10	0.23302	T	0.38	.	11.3564	0.49617	0.0831:0.0:0.9168:0.0	.	445	Q6UVK1	CSPG4_HUMAN	V	445	ENSP00000312506:A445V	ENSP00000312506:A445V	A	-	2	0	CSPG4	73769127	1.000000	0.71417	0.995000	0.50966	0.920000	0.55202	4.849000	0.62882	2.463000	0.83235	0.555000	0.69702	GCC	G|0.918;A|0.082	0.082	strong		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
SPTA1	6708	hgsc.bcm.edu	37	1	158606449	158606449	+	Silent	SNP	G	G	T	rs3738791	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:158606449G>T	ENST00000368147.4	-	37	5472	c.5292C>A	c.(5290-5292)gcC>gcA	p.A1764A		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1764					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAGGCTCATGGGCCACCAGCT	0.473													T|||	1605	0.320487	0.4743	0.2522	5008	,	,		18998	0.2054		0.3101	False		,,,				2504	0.2904				p.A1764A		Atlas-SNP	.											.	SPTA1	720	.	0			c.C5292A						PASS	.	T		1660,2086		356,948,569	100.0	99.0	99.0		5292	-4.1	1.0	1	dbSNP_107	99	2380,5832		343,1694,2069	no	coding-synonymous	SPTA1	NM_003126.2		699,2642,2638	TT,TG,GG		28.982,44.3139,33.7849		1764/2420	158606449	4040,7918	1873	4106	5979	SO:0001819	synonymous_variant	6708	exon37			CTCATGGGCCACC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5292C>A	1.37:g.158606449G>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	112	61	0.544643	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.676;T|0.324	0.324	strong		0.473	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
IL17RA	23765	hgsc.bcm.edu	37	22	17589567	17589567	+	Silent	SNP	C	C	T	rs879575	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:17589567C>T	ENST00000319363.6	+	13	1591	c.1458C>T	c.(1456-1458)atC>atT	p.I486I		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	486	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		TGAACATGATCCTCCCGGACT	0.672													C|||	821	0.163938	0.1831	0.1268	5008	,	,		15139	0.0685		0.2555	False		,,,				2504	0.1687				p.I486I		Atlas-SNP	.											.	IL17RA	62	.	0			c.C1458T						PASS	.	C		754,3652	296.7+/-284.4	71,612,1520	31.0	34.0	33.0		1458	2.4	1.0	22	dbSNP_86	33	2067,6533	352.2+/-328.6	256,1555,2489	no	coding-synonymous	IL17RA	NM_014339.5		327,2167,4009	TT,TC,CC		24.0349,17.113,21.69		486/867	17589567	2821,10185	2203	4300	6503	SO:0001819	synonymous_variant	23765	exon13			CATGATCCTCCCG	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"""Interleukins and interleukin receptors"", ""CD molecules"""	5985	protein-coding gene	gene with protein product		605461	"""interleukin 17 receptor"""	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1458C>T	22.37:g.17589567C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	18	18	1	NM_014339	O43844|Q20WK1	Silent	SNP	ENST00000319363.6	37	CCDS13739.1																																																																																			C|0.809;T|0.191	0.191	strong		0.672	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339	
SP140L	93349	hgsc.bcm.edu	37	2	231248261	231248261	+	Missense_Mutation	SNP	C	C	T	rs28497362	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:231248261C>T	ENST00000415673.2	+	8	760	c.674C>T	c.(673-675)aCg>aTg	p.T225M	SP140L_ENST00000243810.6_Missense_Mutation_p.T225M|SP140L_ENST00000444636.1_Missense_Mutation_p.T225M|SP140L_ENST00000396563.4_Missense_Mutation_p.T225M	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	225			T -> M (in dbSNP:rs28497362).			nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						AGAATGGGAACGAGAACGCAG	0.368													C|||	1153	0.230232	0.1868	0.1599	5008	,	,		20124	0.1448		0.1551	False		,,,				2504	0.5041				p.T225M		Atlas-SNP	.											.	SP140L	68	.	0			c.C674T						PASS	.	C	MET/THR	609,3149		50,509,1320	99.0	106.0	104.0		674	-3.2	0.0	2	dbSNP_125	104	1213,7005		88,1037,2984	yes	missense	SP140L	NM_138402.4	81	138,1546,4304	TT,TC,CC		14.7603,16.2054,15.2138	benign	225/581	231248261	1822,10154	1879	4109	5988	SO:0001583	missense	93349	exon8			TGGGAACGAGAAC	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.674C>T	2.37:g.231248261C>T	ENSP00000397911:p.Thr225Met	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	185	81	0.437838	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	348	0.15934065934065933	87	0.17682926829268292	54	0.14917127071823205	94	0.16433566433566432	113	0.14907651715039577	C	1.288	-0.608551	0.03717	0.162054	0.147603	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	D;T;D;D	0.83163	-1.56;-1.21;-1.56;-1.69	2.4	-3.15	0.05233	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.25772	0.134;0.112	B;B	0.21546	0.035;0.013	T	0.03463	-1.1034	8	0.44086	T	0.13	.	1.0792	0.01639	0.2154:0.3363:0.2813:0.1669	rs28497362;rs28497362	225;225	Q9H930-2;Q9H930-4	.;.	M	225	ENSP00000395195:T225M;ENSP00000397911:T225M;ENSP00000243810:T225M;ENSP00000379811:T225M	ENSP00000243810:T225M	T	+	2	0	SP140L	230956505	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.927000	0.01561	-0.989000	0.03485	-0.893000	0.02921	ACG	C|0.819;T|0.181	0.181	strong		0.368	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
ATXN1L	342371	hgsc.bcm.edu	37	16	71885423	71885423	+	Missense_Mutation	SNP	A	A	G	rs61747555	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:71885423A>G	ENST00000427980.2	+	3	2073	c.1780A>G	c.(1780-1782)Agc>Ggc	p.S594G	ATXN1L_ENST00000569119.1_Intron	NM_001137675.3	NP_001131147.1	P0C7T5	ATX1L_HUMAN	ataxin 1-like	594					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)	4						TTCTCAGGCCAGCTGTGCTCC	0.567													A|||	848	0.169329	0.0189	0.2219	5008	,	,		18533	0.2927		0.1889	False		,,,				2504	0.1881				p.S594G		Atlas-SNP	.											.	ATXN1L	18	.	0			c.A1780G						PASS	.	A	GLY/SER	46,1338		2,42,648	34.0	39.0	37.0		1780	3.0	1.0	16	dbSNP_129	37	650,2532		57,536,998	yes	missense	ATXN1L	NM_001137675.2	56	59,578,1646	GG,GA,AA		20.4274,3.3237,15.2431	benign	594/690	71885423	696,3870	692	1591	2283	SO:0001583	missense	342371	exon3			CAGGCCAGCTGTG		CCDS45523.1	16q22.2	2014-09-04			ENSG00000224470	ENSG00000224470			33279	protein-coding gene	gene with protein product	"""brother of ataxin 1"""	614301				16121196, 17322884, 21475249	Standard	NM_001137675		Approved	BOAT1	uc002fbd.3	P0C7T5	OTTHUMG00000176872	ENST00000427980.2:c.1780A>G	16.37:g.71885423A>G	ENSP00000415822:p.Ser594Gly	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_001137675		Missense_Mutation	SNP	ENST00000427980.2	37	CCDS45523.1	377	0.17261904761904762	12	0.024390243902439025	68	0.1878453038674033	158	0.2762237762237762	139	0.18337730870712401	A	8.360	0.832987	0.16820	0.033237	0.204274	ENSG00000224470	ENST00000427980	T	0.32988	1.43	5.61	3.01	0.34805	.	.	.	.	.	T	0.00012	0.0000	N	0.04959	-0.14	0.30424	P	0.777807	B	0.02656	0.0	B	0.04013	0.001	T	0.41016	-0.9532	8	0.22109	T	0.4	-0.0444	9.8813	0.41236	0.8169:0.0:0.1831:0.0	rs61747555	594	P0C7T5	ATX1L_HUMAN	G	594	ENSP00000415822:S594G	ENSP00000415822:S594G	S	+	1	0	ATXN1L	70442924	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.465000	0.53064	1.040000	0.40099	0.454000	0.30748	AGC	A|0.828;G|0.172	0.172	strong		0.567	ATXN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434171.1	NM_001137675.2	
CCHCR1	54535	hgsc.bcm.edu	37	6	31116210	31116210	+	Silent	SNP	G	G	A	rs130071	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31116210G>A	ENST00000376266.5	-	10	1407	c.1285C>T	c.(1285-1287)Ctg>Ttg	p.L429L	CCHCR1_ENST00000480060.1_5'Flank|CCHCR1_ENST00000396263.2_Silent_p.L429L|CCHCR1_ENST00000396268.3_Silent_p.L518L|CCHCR1_ENST00000451521.2_Silent_p.L482L	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	429					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						ACAAGCCTCAGCTGCTCCTCG	0.622													G|||	979	0.195487	0.1815	0.2608	5008	,	,		17553	0.0575		0.2793	False		,,,				2504	0.2239				p.L518L		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C1552T						PASS	.		,,	649,2367		69,511,928	114.0	112.0	113.0		1444,1552,1285	3.3	1.0	6	dbSNP_78	113	1572,3844		242,1088,1378	yes	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	311,1599,2306	AA,AG,GG		29.0251,21.5186,26.3401	,,	482/836,518/872,429/783	31116210	2221,6211	1508	2708	4216	SO:0001819	synonymous_variant	54535	exon10			GCCTCAGCTGCTC	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1285C>T	6.37:g.31116210G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	144	115	0.798611	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			G|0.746;A|0.254	0.254	strong		0.622	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
VPS13C	54832	hgsc.bcm.edu	37	15	62223303	62223303	+	Missense_Mutation	SNP	C	C	G	rs78071599	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62223303C>G	ENST00000261517.5	-	50	6097	c.6024G>C	c.(6022-6024)gaG>gaC	p.E2008D	VPS13C_ENST00000395896.4_Missense_Mutation_p.E2008D|VPS13C_ENST00000395898.3_Missense_Mutation_p.E1965D|VPS13C_ENST00000249837.3_Missense_Mutation_p.E1965D	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						ATGTTGCTCTCTCAATTCCTT	0.443													C|||	35	0.00698882	0.0	0.0101	5008	,	,		17268	0.002		0.0199	False		,,,				2504	0.0061				p.E2008D		Atlas-SNP	.											.	VPS13C	506	.	0			c.G6024C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	26,4380	32.6+/-62.9	0,26,2177	141.0	120.0	127.0		6024,5895,5895,6024	3.5	1.0	15	dbSNP_132	127	174,8426	79.8+/-142.4	3,168,4129	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	45,45,45,45	3,194,6306	GG,GC,CC		2.0233,0.5901,1.5378	benign,benign,benign,benign	2008/3629,1965/3711,1965/3586,2008/3754	62223303	200,12806	2203	4300	6503	SO:0001583	missense	54832	exon50			TGCTCTCTCAATT	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.6024G>C	15.37:g.62223303C>G	ENSP00000261517:p.Glu2008Asp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	C	15.37	2.812416	0.50527	0.005901	0.020233	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.46451	0.87;0.87;1.04	5.41	3.49	0.39957	.	0.454224	0.24937	N	0.034409	T	0.21186	0.0510	L	0.57536	1.79	0.32706	N	0.512236	B;B;P;B	0.36048	0.321;0.321;0.534;0.215	B;B;B;B	0.38842	0.205;0.205;0.283;0.101	T	0.34254	-0.9836	10	0.18276	T	0.48	.	7.8042	0.29191	0.1368:0.7269:0.0:0.1363	.	1965;2008;1965;2008	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	D	1965;2008;2008;2008	ENSP00000249837:E1965D;ENSP00000261517:E2008D;ENSP00000379233:E2008D	ENSP00000249837:E1965D	E	-	3	2	VPS13C	60010595	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.312000	0.43726	1.395000	0.46643	0.650000	0.86243	GAG	C|0.986;G|0.014	0.014	strong		0.443	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
ELF1	1997	hgsc.bcm.edu	37	13	41515118	41515118	+	Missense_Mutation	SNP	C	C	T	rs34905611	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:41515118C>T	ENST00000239882.3	-	8	1509	c.1195G>A	c.(1195-1197)Gaa>Aaa	p.E399K	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Missense_Mutation_p.E375K	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	399					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		CTAGCTGCTTCTCCCTCTGGG	0.458													C|||	25	0.00499201	0.0008	0.0043	5008	,	,		18473	0.0		0.0169	False		,,,				2504	0.0041				p.E399K		Atlas-SNP	.											.	ELF1	65	.	0			c.G1195A						PASS	.	C	LYS/GLU,LYS/GLU	17,4389	24.3+/-50.5	0,17,2186	114.0	109.0	111.0		1123,1195	4.1	1.0	13	dbSNP_126	111	161,8439	75.7+/-138.4	1,159,4140	yes	missense,missense	ELF1	NM_001145353.1,NM_172373.3	56,56	1,176,6326	TT,TC,CC		1.8721,0.3858,1.3686	possibly-damaging,possibly-damaging	375/596,399/620	41515118	178,12828	2203	4300	6503	SO:0001583	missense	1997	exon8			CTGCTTCTCCCTC	M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.1195G>A	13.37:g.41515118C>T	ENSP00000239882:p.Glu399Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	131	82	0.625954	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	16	0.007326007326007326	0	0.0	1	0.0027624309392265192	0	0.0	15	0.01978891820580475	C	15.58	2.875433	0.51695	0.003858	0.018721	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.19806	2.12;2.12	5.04	4.14	0.48551	.	0.401258	0.24412	N	0.038759	T	0.08088	0.0202	L	0.27053	0.805	0.29239	N	0.87277	B;B	0.18013	0.025;0.025	B;B	0.21708	0.033;0.036	T	0.04360	-1.0957	10	0.38643	T	0.18	.	14.0167	0.64527	0.0:0.7536:0.2464:0.0	rs34905611	375;399	E9PDQ9;P32519	.;ELF1_HUMAN	K	375;141;399	ENSP00000405580:E375K;ENSP00000239882:E399K	ENSP00000239882:E399K	E	-	1	0	ELF1	40413118	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.651000	0.37302	2.505000	0.84491	0.655000	0.94253	GAA	C|0.989;T|0.011	0.011	strong		0.458	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
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 GAIIx	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		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	60	24	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	
LTA	4049	hgsc.bcm.edu	37	6	31540784	31540784	+	Missense_Mutation	SNP	C	C	A	rs1041981	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31540784C>A	ENST00000454783.1	+	3	437	c.179C>A	c.(178-180)aCc>aAc	p.T60N	TNF_ENST00000449264.2_5'Flank|LTA_ENST00000418386.2_Missense_Mutation_p.T60N	NM_001159740.2	NP_001153212.1	P01374	TNFB_HUMAN	lymphotoxin alpha	60			T -> N (in allele TNFB*2; dbSNP:rs1041981). {ECO:0000269|PubMed:1451807, ECO:0000269|PubMed:1670638, ECO:0000269|Ref.10, ECO:0000269|Ref.11}.		apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|humoral immune response (GO:0006959)|lymph node development (GO:0048535)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of interferon-gamma production (GO:0032729)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|membrane (GO:0016020)	receptor binding (GO:0005102)			endometrium(2)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9					Etanercept(DB00005)	GCCCACAGCACCCTCAAACCT	0.592													C|||	1951	0.389577	0.5136	0.3386	5008	,	,		15261	0.4692		0.3062	False		,,,				2504	0.2618				p.T60N		Atlas-SNP	.											.	LTA	18	.	0			c.C179A	GRCh37	CM024124	LTA	M	rs1041981	PASS	.	C	ASN/THR,ASN/THR	1543,1479		371,801,339	136.0	90.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	179,179	3.2	0.8	6	dbSNP_86	107	1793,3625		294,1205,1210	yes	missense,missense	LTA	NM_000595.2,NM_001159740.1	65,65	665,2006,1549	AA,AC,CC		33.0934,48.9411,39.5261	possibly-damaging,possibly-damaging	60/206,60/206	31540784	3336,5104	1511	2709	4220	SO:0001583	missense	4049	exon3			ACAGCACCCTCAA	X01393	CCDS4701.1	6p21.3	2013-05-22	2013-05-22		ENSG00000226979	ENSG00000226979		"""Tumor necrosis factor (ligand) superfamily"""	6709	protein-coding gene	gene with protein product	"""TNF superfamily member 1"""	153440	"""lymphotoxin alpha (TNF superfamily, member 1)"""	TNFB		2995927, 3001529	Standard	NM_001159740		Approved	TNFSF1, LT	uc011dnu.2	P01374	OTTHUMG00000031135	ENST00000454783.1:c.179C>A	6.37:g.31540784C>A	ENSP00000403495:p.Thr60Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	72	60	0.833333	NM_001159740	Q8N4C3|Q9UKS8	Missense_Mutation	SNP	ENST00000454783.1	37	CCDS4701.1	871	0.39880952380952384	261	0.5304878048780488	114	0.3149171270718232	255	0.4458041958041958	241	0.3179419525065963	C	9.721	1.159641	0.21454	0.510589	0.330934	ENSG00000226979	ENST00000454783;ENST00000418386;ENST00000436827	T;T	0.15487	2.42;2.42	5.01	3.15	0.36227	.	0.411685	0.25552	N	0.029886	T	0.05868	0.0153	L	0.59436	1.845	0.36409	P	0.13637600000000005	B;B	0.16802	0.019;0.005	B;B	0.18561	0.022;0.005	T	0.18871	-1.0323	9	0.33141	T	0.24	-27.9588	5.2294	0.15414	0.2031:0.6916:0.0:0.1053	rs1041981;rs1800509;rs2229093;rs3181466;rs17846104;rs17859107;rs57361933;rs1041981	60;60	E7ET53;P01374	.;TNFB_HUMAN	N	60	ENSP00000403495:T60N;ENSP00000413450:T60N	ENSP00000413450:T60N	T	+	2	0	LTA	31648763	0.552000	0.26505	0.829000	0.32907	0.958000	0.62258	0.849000	0.27723	0.641000	0.30601	0.655000	0.94253	ACC	C|0.603;A|0.397	0.397	strong		0.592	LTA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259097.1		
DHDH	27294	hgsc.bcm.edu	37	19	49438363	49438363	+	Missense_Mutation	SNP	G	G	A	rs2270941	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49438363G>A	ENST00000221403.2	+	2	237	c.197G>A	c.(196-198)aGc>aAc	p.S66N	DHDH_ENST00000523250.1_Missense_Mutation_p.S66N|DHDH_ENST00000522614.1_Missense_Mutation_p.S66N	NM_014475.3	NP_055290.1	Q9UQ10	DHDH_HUMAN	dihydrodiol dehydrogenase (dimeric)	66			S -> N (in dbSNP:rs2270941).		carbohydrate metabolic process (GO:0005975)|D-xylose catabolic process (GO:0042843)		D-xylose 1-dehydrogenase (NADP+) activity (GO:0047837)|electron carrier activity (GO:0009055)|NAD(P)+ transhydrogenase activity (GO:0008746)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			central_nervous_system(1)|large_intestine(3)|lung(3)|ovary(1)|soft_tissue(1)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000158)|all cancers(93;0.000258)|Epithelial(262;0.0173)|GBM - Glioblastoma multiforme(486;0.0179)		AAGGACCCGAGCGTGGGTGAG	0.692													A|||	2561	0.511382	0.7958	0.4308	5008	,	,		14256	0.5456		0.2535	False		,,,				2504	0.4141				p.S66N		Atlas-SNP	.											DHDH,NS,carcinoma,0,1	DHDH	35	1	0			c.G197A						PASS	.	A	ASN/SER	3081,1311		1099,883,214	22.0	17.0	19.0		197	4.7	0.3	19	dbSNP_100	19	1842,6740		209,1424,2658	yes	missense	DHDH	NM_014475.3	46	1308,2307,2872	AA,AG,GG		21.4635,29.8497,37.9451	benign	66/335	49438363	4923,8051	2196	4291	6487	SO:0001583	missense	27294	exon2			ACCCGAGCGTGGG	AB021933	CCDS12741.1	19q13.3	2008-02-05			ENSG00000104808	ENSG00000104808	1.3.1.20		17887	protein-coding gene	gene with protein product		606377				10477285	Standard	NM_014475		Approved	HUM2DD	uc002ple.1	Q9UQ10	OTTHUMG00000165029	ENST00000221403.2:c.197G>A	19.37:g.49438363G>A	ENSP00000221403:p.Ser66Asn	Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_014475		Missense_Mutation	SNP	ENST00000221403.2	37	CCDS12741.1	1018	0.4661172161172161	367	0.7459349593495935	141	0.38950276243093923	305	0.5332167832167832	205	0.2704485488126649	A	8.755	0.922187	0.17982	0.701503	0.214635	ENSG00000104808	ENST00000221403;ENST00000523250;ENST00000522614	T;T;T	0.21361	2.01;2.01;2.01	4.74	4.74	0.60224	Oxidoreductase, N-terminal (1);NAD(P)-binding domain (1);	0.254938	0.43919	N	0.000502	T	0.00012	0.0000	N	0.00966	-1.09	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38045	-0.9679	9	0.02654	T	1	-20.6016	8.936	0.35700	0.9105:0.0:0.0895:0.0	rs2270941;rs17239182;rs52799839;rs58054167;rs2270941	66	Q9UQ10	DHDH_HUMAN	N	66	ENSP00000221403:S66N;ENSP00000428935:S66N;ENSP00000428672:S66N	ENSP00000221403:S66N	S	+	2	0	DHDH	54130175	0.322000	0.24634	0.282000	0.24776	0.680000	0.39746	4.951000	0.63610	0.951000	0.37770	-0.556000	0.04195	AGC	G|0.533;A|0.467	0.467	strong		0.692	DHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381477.1	NM_014475	
MYBPC2	4606	hgsc.bcm.edu	37	19	50965272	50965272	+	Silent	SNP	T	T	C	rs25668	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50965272T>C	ENST00000357701.5	+	26	3258	c.3207T>C	c.(3205-3207)tgT>tgC	p.C1069C		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	1069	Ig-like C2-type 7.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CCCTCAACTGTGCTGTCAGAG	0.582													C|||	3977	0.794129	0.9667	0.7824	5008	,	,		14210	0.7054		0.6789	False		,,,				2504	0.7791				p.C1069C		Atlas-SNP	.											.	MYBPC2	103	.	0			c.T3207C						PASS	.	C		3750,350		1719,312,19	33.0	34.0	34.0		3207	-7.6	0.1	19	dbSNP_72	34	5618,2748		1899,1820,464	no	coding-synonymous	MYBPC2	NM_004533.3		3618,2132,483	CC,CT,TT		32.8472,8.5366,24.8516		1069/1142	50965272	9368,3098	2050	4183	6233	SO:0001819	synonymous_variant	4606	exon26			CAACTGTGCTGTC		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.3207T>C	19.37:g.50965272T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_004533	A1L4G9	Silent	SNP	ENST00000357701.5	37	CCDS46152.1																																																																																			T|0.231;C|0.769	0.769	strong		0.582	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
SCARF2	91179	hgsc.bcm.edu	37	22	20784050	20784050	+	Missense_Mutation	SNP	T	T	A	rs2241230	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:20784050T>A	ENST00000266214.5	-	7	1377	c.1273A>T	c.(1273-1275)Acg>Tcg	p.T425S	SCARF2_ENST00000405555.3_Missense_Mutation_p.T425S	NM_153334.4	NP_699165.2	Q96GP6	SREC2_HUMAN	scavenger receptor class F, member 2	425			T -> S (in dbSNP:rs2241230).		cell adhesion (GO:0007155)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(2)	10	Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GGGTCGCACGTGTCCTCGTGG	0.652													A|||	1104	0.220447	0.1641	0.255	5008	,	,		11596	0.4782		0.0517	False		,,,				2504	0.18				p.T425S		Atlas-SNP	.											.	SCARF2	23	.	0			c.A1273T						PASS	.	A	SER/THR,SER/THR	572,3834	771.0+/-413.8	46,480,1677	67.0	65.0	66.0		1273,1273	4.1	1.0	22	dbSNP_98	66	582,8018	792.3+/-407.5	17,548,3735	yes	missense,missense	SCARF2	NM_153334.4,NM_182895.2	58,58	63,1028,5412	AA,AT,TT		6.7674,12.9823,8.8728	benign,benign	425/871,425/866	20784050	1154,11852	2203	4300	6503	SO:0001583	missense	91179	exon7			CGCACGTGTCCTC	AF522196	CCDS13779.1, CCDS46666.1	22q11.21	2011-10-10			ENSG00000244486	ENSG00000244486			19869	protein-coding gene	gene with protein product		613619				12154095	Standard	XM_006724364		Approved	SREC-II, SREC2, HUMZD58C02	uc002zsk.2	Q96GP6	OTTHUMG00000150779	ENST00000266214.5:c.1273A>T	22.37:g.20784050T>A	ENSP00000266214:p.Thr425Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	124	58	0.467742	NM_182895	E5RFB8|Q58A83|Q8IXF3|Q9BW74	Missense_Mutation	SNP	ENST00000266214.5	37	CCDS13779.1	499	0.22847985347985347	82	0.16666666666666666	83	0.2292817679558011	289	0.5052447552447552	45	0.059366754617414245	A	8.869	0.948705	0.18356	0.129823	0.067674	ENSG00000244486	ENST00000405555;ENST00000341328;ENST00000266214	T;T	0.56103	0.48;0.48	4.11	4.11	0.48088	.	0.403701	0.21295	N	0.076919	T	0.00012	0.0000	N	0.01048	-1.04	0.20873	P	0.999833467	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46952	-0.9154	9	0.15066	T	0.55	-13.3723	7.0384	0.25006	0.6342:0.0:0.0:0.3658	rs2241230;rs59375832;rs2241230	425;425	E5RFB8;Q96GP6	.;SREC2_HUMAN	S	425	ENSP00000385589:T425S;ENSP00000266214:T425S	ENSP00000266214:T425S	T	-	1	0	SCARF2	19114050	0.045000	0.20229	0.987000	0.45799	0.647000	0.38526	0.782000	0.26788	0.546000	0.28920	-0.522000	0.04353	ACG	T|0.861;A|0.139	0.139	strong		0.652	SCARF2-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320047.1		
GPRC5D	55507	hgsc.bcm.edu	37	12	13102605	13102605	+	Silent	SNP	G	G	A	rs4630382	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:13102605G>A	ENST00000228887.1	-	1	713	c.714C>T	c.(712-714)gaC>gaT	p.D238D	GPRC5D_ENST00000396333.3_Silent_p.D238D|RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000540198.1_RNA|RP11-392P7.6_ENST00000538231.1_RNA|RP11-392P7.6_ENST00000542078.1_RNA|RP11-392P7.6_ENST00000394742.3_RNA|RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			kidney(2)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		CGACCGGGTCGTCCCACTGGG	0.552													g|||	1035	0.206669	0.0204	0.2046	5008	,	,		20154	0.1865		0.3817	False		,,,				2504	0.3006				p.D238D		Atlas-SNP	.											.	GPRC5D	23	.	0			c.C714T						PASS	.	A		350,4056	180.8+/-209.0	12,326,1865	97.0	99.0	98.0		714	-3.6	0.9	12	dbSNP_111	98	3395,5205	502.3+/-375.6	674,2047,1579	no	coding-synonymous	GPRC5D	NM_018654.1		686,2373,3444	AA,AG,GG		39.4767,7.9437,28.7944		238/346	13102605	3745,9261	2203	4300	6503	SO:0001819	synonymous_variant	55507	exon1			CGGGTCGTCCCAC	AF209923	CCDS8658.1	12p13.3	2014-01-30	2014-01-30		ENSG00000111291	ENSG00000111291		"""GPCR / Class C : Orphans"""	13310	protein-coding gene	gene with protein product		607437	"""G protein-coupled receptor, family C, group 5, member D"""				Standard	XM_005253421		Approved		uc010shp.2	Q9NZD1	OTTHUMG00000168711	ENST00000228887.1:c.714C>T	12.37:g.13102605G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_018654	Q3KNV3|Q7Z5J9|Q8TDS6	Silent	SNP	ENST00000228887.1	37	CCDS8658.1																																																																																			G|0.739;A|0.261	0.261	strong		0.552	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1		
CEP83	51134	hgsc.bcm.edu	37	12	94769769	94769769	+	Missense_Mutation	SNP	G	G	A	rs74340001	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:94769769G>A	ENST00000397809.5	-	8	1375	c.826C>T	c.(826-828)Cgg>Tgg	p.R276W	CCDC41_ENST00000547575.1_Missense_Mutation_p.R276W|CCDC41_ENST00000397807.2_Missense_Mutation_p.R243W|CCDC41_ENST00000549352.1_5'UTR|CCDC41_ENST00000339839.5_Missense_Mutation_p.R276W	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		268					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						CGTTCTGCCCGTAAATTAGCT	0.269													G|||	117	0.0233626	0.0045	0.0331	5008	,	,		14813	0.0		0.0666	False		,,,				2504	0.0215				p.R276W		Atlas-SNP	.											.	CCDC41	59	.	0			c.C826T						PASS	.	G	TRP/ARG,TRP/ARG	49,3553		0,49,1752	67.0	62.0	63.0		826,826	5.4	1.0	12	dbSNP_131	63	569,7567		20,529,3519	yes	missense,missense	CCDC41	NM_001042399.1,NM_016122.2	101,101	20,578,5271	AA,AG,GG		6.9936,1.3604,5.265	possibly-damaging,possibly-damaging	276/702,276/702	94769769	618,11120	1801	4068	5869	SO:0001583	missense	51134	exon8			CTGCCCGTAAATT																												ENST00000397809.5:c.826C>T	12.37:g.94769769G>A	ENSP00000380911:p.Arg276Trp	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_016122	A4FVB1|Q08AP1	Missense_Mutation	SNP	ENST00000397809.5	37	CCDS41820.1	63	0.028846153846153848	3	0.006097560975609756	11	0.03038674033149171	0	0.0	49	0.06464379947229551	G	17.52	3.410935	0.62399	0.013604	0.069936	ENSG00000173588	ENST00000339839;ENST00000397809;ENST00000397807;ENST00000547575	T;T;T;T	0.22539	1.95;1.95;1.95;1.95	5.37	5.37	0.77165	.	.	.	.	.	T	0.01287	0.0042	N	0.08118	0	0.31637	N	0.648337	D;D;P	0.54964	0.969;0.969;0.924	B;P;B	0.46975	0.409;0.533;0.409	T	0.01337	-1.1381	9	0.87932	D	0	-0.0579	19.1187	0.93353	0.0:0.0:1.0:0.0	.	276;243;268	F8VYN8;Q9Y592-2;Q9Y592	.;.;CCD41_HUMAN	W	276;276;243;276	ENSP00000344655:R276W;ENSP00000380911:R276W;ENSP00000380909:R243W;ENSP00000448913:R276W	ENSP00000344655:R276W	R	-	1	2	CCDC41	93293900	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	7.998000	0.88491	2.530000	0.85305	0.557000	0.71058	CGG	G|0.962;A|0.038	0.038	strong		0.269	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3		
CDHR4	389118	hgsc.bcm.edu	37	3	49836707	49836707	+	Silent	SNP	G	G	A	rs7629936	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49836707G>A	ENST00000412678.2	-	2	221	c.213C>T	c.(211-213)gcC>gcT	p.A71A	CDHR4_ENST00000343366.4_Silent_p.A71A|CDHR4_ENST00000487256.1_Silent_p.A71A	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	71					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(3)	11						CTTGCCACCTGGCCAAGCTGG	0.567													G|||	1168	0.233227	0.2632	0.1844	5008	,	,		19701	0.1488		0.2386	False		,,,				2504	0.3088				p.A71A		Atlas-SNP	.											CDHR4,caecum,carcinoma,0,1	CDHR4	37	1	0			c.C213T						PASS	.	G		938,3054		111,716,1169	74.0	78.0	76.0		213	-3.8	0.0	3	dbSNP_116	76	1927,6429		212,1503,2463	no	coding-synonymous	CDHR4	NM_001007540.2		323,2219,3632	AA,AG,GG		23.0613,23.497,23.2021		71/789	49836707	2865,9483	1996	4178	6174	SO:0001819	synonymous_variant	389118	exon2			CCACCTGGCCAAG		CCDS46829.1	3p21.31	2011-07-01	2010-01-25	2010-01-25	ENSG00000187492	ENSG00000187492		"""Cadherins / Cadherin-related"""	34527	protein-coding gene	gene with protein product			"""cadherin-like 29"""	CDH29			Standard	NM_001007540		Approved	VLLR9392	uc010hkz.3	A6H8M9	OTTHUMG00000158198	ENST00000412678.2:c.213C>T	3.37:g.49836707G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	169	86	0.508876	NM_001007540	Q6UXT0	Silent	SNP	ENST00000412678.2	37	CCDS46829.1																																																																																			G|0.775;A|0.225	0.225	strong		0.567	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540	
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 GAIIx	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_ENST00000474395.1_5'UTR|LY6G5C_ENST00000375858.3_Splice_Site_p.G38G|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		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	69	18	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
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329854	55329854	+	Missense_Mutation	SNP	G	G	A	rs144994606	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55329854G>A	ENST00000391728.4	+	3	188	c.155G>A	c.(154-156)cGt>cAt	p.R52H	KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.R52H|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.R52H|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.R52H|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.R52H	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	52	Ig-like C2-type 1.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TGTCACTATCGTCATAGGTTT	0.517													g|||	617	0.123203	0.0915	0.1657	5008	,	,		13130	0.001		0.2247	False		,,,				2504	0.1575				p.R52H		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.G155A						PASS	.	G	HIS/ARG	523,3827		81,361,1733	98.0	101.0	100.0		155	-2.3	0.0	19	dbSNP_134	100	2261,5995		614,1033,2481	no	missense	KIR3DL1	NM_013289.2	29	695,1394,4214	AA,AG,GG		27.3861,12.023,22.0847		52/445	55329854	2784,9822	2175	4128	6303	SO:0001583	missense	3811	exon3			ACTATCGTCATAG	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.155G>A	19.37:g.55329854G>A	ENSP00000375608:p.Arg52His	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	318	0.14560439560439561	40	0.08130081300813008	68	0.1878453038674033	0	0.0	210	0.2770448548812665	G	1.011	-0.687880	0.03328	0.12023	0.273861	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71	1.15	-2.29	0.06805	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.26042	0.785	0.80722	P	0.0	B;B	0.11235	0.002;0.004	B;B	0.10450	0.003;0.005	T	0.45338	-0.9268	8	0.42905	T	0.14	.	5.2208	0.15368	0.4452:0.0:0.5548:0.0	.	52;52	F6QF33;P43629	.;KI3L1_HUMAN	H	52;52;52;30;52;52	ENSP00000384528:R52H;ENSP00000443350:R52H;ENSP00000442355:R52H;ENSP00000375608:R52H;ENSP00000326868:R52H	ENSP00000326868:R52H	R	+	2	0	KIR3DL1	60021666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.812000	0.04496	-0.923000	0.03785	-1.109000	0.02080	CGT	G|0.854;A|0.146	0.146	strong		0.517	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
HLA-DOA	3111	hgsc.bcm.edu	37	6	32974934	32974934	+	Silent	SNP	G	G	A	rs378352	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32974934G>A	ENST00000229829.5	-	4	747	c.672C>T	c.(670-672)ggC>ggT	p.G224G	HLA-DOA_ENST00000495532.1_5'Flank|HLA-DOA_ENST00000450833.2_Intron	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	224					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						CGATGGCCAGGCCCAGGGCAC	0.597													G|||	834	0.166534	0.0151	0.1095	5008	,	,		17888	0.3492		0.2247	False		,,,				2504	0.1636				p.G224G		Atlas-SNP	.											.	HLA-DOA	22	.	0			c.C672T						PASS	.	G		223,4183		6,211,1986	68.0	71.0	70.0		672	2.8	1.0	6	dbSNP_80	70	1841,6757		195,1451,2653	no	coding-synonymous	HLA-DOA	NM_002119.3		201,1662,4639	AA,AG,GG		21.412,5.0613,15.872		224/251	32974934	2064,10940	2203	4299	6502	SO:0001819	synonymous_variant	3111	exon4			GGCCAGGCCCAGG	M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.672C>T	6.37:g.32974934G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	184	139	0.755435	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1																																																																																			G|0.833;A|0.167	0.167	strong		0.597	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119	
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 GAIIx	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		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	119	63	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 GAIIx	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	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	70	28	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	
PKD1L1	168507	hgsc.bcm.edu	37	7	47851623	47851623	+	Missense_Mutation	SNP	C	C	T	rs73692834	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:47851623C>T	ENST00000289672.2	-	50	7423	c.7373G>A	c.(7372-7374)cGa>cAa	p.R2458Q	C7orf69_ENST00000258776.4_Intron|PKD1L1_ENST00000462350.1_5'Flank|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2458					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GGCCCTGAGTCGGGACAGGGC	0.587													C|||	767	0.153155	0.0431	0.1974	5008	,	,		20821	0.2153		0.17	False		,,,				2504	0.1892				p.R2458Q		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G7373A						PASS	.	C	,GLN/ARG	301,4103		7,287,1908	55.0	45.0	48.0		,7373	-1.1	0.0	7	dbSNP_130	48	1291,7301		87,1117,3092	yes	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,43	94,1404,5000	TT,TC,CC		15.0256,6.8347,12.2499	,possibly-damaging	,2458/2850	47851623	1592,11404	2202	4296	6498	SO:0001583	missense	168507	exon50			CTGAGTCGGGACA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7373G>A	7.37:g.47851623C>T	ENSP00000289672:p.Arg2458Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	49	0.816667	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	339	0.15521978021978022	20	0.04065040650406504	80	0.22099447513812154	111	0.19405594405594406	128	0.16886543535620052	C	8.932	0.963576	0.18583	0.068347	0.150256	ENSG00000158683	ENST00000289672	T	0.69561	-0.41	5.49	-1.15	0.09709	Polycystin cation channel, PKD1/PKD2 (1);	2.463310	0.01843	N	0.035450	T	0.00039	0.0001	N	0.25890	0.77	0.80722	P	0.0	D	0.55605	0.972	B	0.43623	0.425	T	0.02064	-1.1220	9	0.28530	T	0.3	1.3162	6.6941	0.23189	0.0:0.29:0.1582:0.5519	.	2458	Q8TDX9	PK1L1_HUMAN	Q	2458	ENSP00000289672:R2458Q	ENSP00000289672:R2458Q	R	-	2	0	PKD1L1	47818148	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.321000	0.08018	-0.120000	0.11809	0.453000	0.30009	CGA	C|0.871;T|0.129	0.129	strong		0.587	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
PARVB	29780	hgsc.bcm.edu	37	22	44489868	44489868	+	Missense_Mutation	SNP	T	T	C	rs1983609	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44489868T>C	ENST00000338758.7	+	2	236	c.173T>C	c.(172-174)gTg>gCg	p.V58A	PARVB_ENST00000477795.1_3'UTR|PARVB_ENST00000404989.1_Missense_Mutation_p.V21A|PARVB_ENST00000406477.3_Missense_Mutation_p.V91A	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	58			V -> A (in dbSNP:rs1983609). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18691976, ECO:0000269|Ref.1}.		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)				CCCGCCCTGGTGGATGTTCAC	0.547													C|||	4368	0.872204	0.9773	0.8818	5008	,	,		17134	0.9593		0.7386	False		,,,				2504	0.771				p.V91A		Atlas-SNP	.											.	PARVB	44	.	0			c.T272C						PASS	.	C	ALA/VAL,ALA/VAL	4179,227	136.5+/-172.5	1983,213,7	93.0	94.0	94.0		272,173	-4.1	0.0	22	dbSNP_92	94	6540,2060	358.0+/-331.0	2486,1568,246	yes	missense,missense	PARVB	NM_001003828.2,NM_013327.4	64,64	4469,1781,253	CC,CT,TT		23.9535,5.1521,17.5842	benign,benign	91/398,58/365	44489868	10719,2287	2203	4300	6503	SO:0001583	missense	29780	exon3			CCCTGGTGGATGT	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.173T>C	22.37:g.44489868T>C	ENSP00000342492:p.Val58Ala	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	1900	0.86996336996337	477	0.9695121951219512	314	0.8674033149171271	553	0.9667832167832168	556	0.7335092348284961	C	0.075	-1.193909	0.01594	0.948479	0.760465	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000402876;ENST00000444029;ENST00000404989	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	4.91	-4.14	0.03892	Calponin homology domain (1);	0.810877	0.11826	N	0.525663	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B;B;B;B	0.10296	0.0;0.0;0.0;0.003	B;B;B;B	0.10450	0.0;0.001;0.001;0.005	T	0.17653	-1.0362	9	0.10111	T	0.7	-9.3018	8.9807	0.35964	0.0:0.4397:0.1084:0.4519	rs1983609;rs5764516;rs17857311;rs52834884;rs61460848;rs1983609	58;21;58;91	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	A	91;58;58;56;21	ENSP00000384515:V91A;ENSP00000342492:V58A;ENSP00000385331:V58A;ENSP00000393758:V56A;ENSP00000384353:V21A	ENSP00000342492:V58A	V	+	2	0	PARVB	42821201	0.004000	0.15560	0.001000	0.08648	0.001000	0.01503	0.009000	0.13219	-1.601000	0.01601	-1.073000	0.02249	GTG	T|0.150;C|0.850	0.850	strong		0.547	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
SLC22A15	55356	hgsc.bcm.edu	37	1	116609185	116609185	+	Silent	SNP	G	G	A	rs3748742	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:116609185G>A	ENST00000369503.4	+	11	1540	c.1410G>A	c.(1408-1410)acG>acA	p.T470T		NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	470					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)		TCGGAGCCACGGGTCTGACCT	0.488													C|||	587	0.117212	0.1876	0.0648	5008	,	,		17717	0.1181		0.0835	False		,,,				2504	0.093				p.T470T		Atlas-SNP	.											.	SLC22A15	65	.	0			c.G1410A						PASS	.	C		529,3213		39,451,1381	58.0	52.0	54.0		1410	-11.4	0.0	1	dbSNP_107	54	628,7594		21,586,3504	no	coding-synonymous	SLC22A15	NM_018420.2		60,1037,4885	AA,AG,GG		7.638,14.1368,9.6707		470/548	116609185	1157,10807	1871	4111	5982	SO:0001819	synonymous_variant	55356	exon11			AGCCACGGGTCTG	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.1410G>A	1.37:g.116609185G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Silent	SNP	ENST00000369503.4	37	CCDS44198.1																																																																																			G|0.891;A|0.109	0.109	strong		0.488	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420	
GRM1	2911	hgsc.bcm.edu	37	6	146755140	146755140	+	Silent	SNP	G	G	A	rs2942	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:146755140G>A	ENST00000282753.1	+	8	3028	c.2793G>A	c.(2791-2793)aaG>aaA	p.K931K	GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000361719.2_Silent_p.K931K|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000492807.2_3'UTR			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	931					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CCGTCATCAAGCCCCTCACTA	0.557													G|||	2677	0.534545	0.4902	0.4568	5008	,	,		16697	0.5466		0.5457	False		,,,				2504	0.6258				p.K931K		Atlas-SNP	.											.	GRM1	419	.	0			c.G2793A						PASS	.	G	,	2163,2243	583.1+/-385.7	522,1119,562	93.0	98.0	96.0		2793,	1.5	1.0	6	dbSNP_36	96	4583,4017	597.8+/-393.8	1239,2105,956	no	coding-synonymous,utr-3	GRM1	NM_000838.3,NM_001114329.1	,	1761,3224,1518	AA,AG,GG		46.7093,49.0921,48.1316	,	931/1195,	146755140	6746,6260	2203	4300	6503	SO:0001819	synonymous_variant	2911	exon9			CATCAAGCCCCTC	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2793G>A	6.37:g.146755140G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	45	17	0.377778	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Silent	SNP	ENST00000282753.1	37	CCDS5209.1																																																																																			G|0.481;A|0.519	0.519	strong		0.557	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
DSC3	1825	hgsc.bcm.edu	37	18	28574150	28574150	+	Silent	SNP	T	T	C	rs114143100	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:28574150T>C	ENST00000360428.4	-	16	2762	c.2682A>G	c.(2680-2682)acA>acG	p.T894T	DSC3_ENST00000434452.1_3'UTR	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	894					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|protein stabilization (GO:0050821)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(29)|ovary(2)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56			OV - Ovarian serous cystadenocarcinoma(10;0.125)			ATTATCTCTTTGTGCATGCTT	0.358													T|||	22	0.00439297	0.0	0.0072	5008	,	,		15758	0.0		0.0169	False		,,,				2504	0.0				p.T894T		Atlas-SNP	.											.	DSC3	225	.	0			c.A2682G						PASS	.	T	,	19,4387	26.2+/-53.5	0,19,2184	71.0	73.0	72.0		2682,	-3.2	1.0	18	dbSNP_132	72	136,8464	68.0+/-130.5	2,132,4166	no	coding-synonymous,utr-3	DSC3	NM_001941.3,NM_024423.2	,	2,151,6350	CC,CT,TT		1.5814,0.4312,1.1918	,	894/897,	28574150	155,12851	2203	4300	6503	SO:0001819	synonymous_variant	1825	exon16			TCTCTTTGTGCAT	X83929	CCDS32810.1	18q12.1	2014-07-30			ENSG00000134762	ENSG00000134762		"""Cadherins / Major cadherins"""	3037	protein-coding gene	gene with protein product		600271		DSC4		7774948, 8486729	Standard	NM_001941		Approved	CDHF3, DSC, DSC1, DSC2	uc002kwj.4	Q14574	OTTHUMG00000179622	ENST00000360428.4:c.2682A>G	18.37:g.28574150T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	182	83	0.456044	NM_001941	A6NN35|Q14200|Q9HAZ9	Silent	SNP	ENST00000360428.4	37	CCDS32810.1																																																																																			T|0.989;C|0.011	0.011	strong		0.358	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423	
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 GAIIx	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		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	18	11	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	
CSPG4	1464	hgsc.bcm.edu	37	15	75982239	75982239	+	Silent	SNP	G	G	A	rs148229217	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:75982239G>A	ENST00000308508.5	-	3	1259	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	389	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CATAGGCATCGTCCTCATACT	0.627													G|||	467	0.0932508	0.0688	0.0908	5008	,	,		21001	0.001		0.1342	False		,,,				2504	0.181				p.D389D		Atlas-SNP	.											CSPG4,NS,carcinoma,0,2	CSPG4	175	2	0			c.C1167T						PASS	.	G		270,4096		6,258,1919	16.0	18.0	17.0		1167	-8.7	0.3	15	dbSNP_134	17	1141,7421		60,1021,3200	no	coding-synonymous	CSPG4	NM_001897.4		66,1279,5119	AA,AG,GG		13.3263,6.1842,10.9143		389/2323	75982239	1411,11517	2183	4281	6464	SO:0001819	synonymous_variant	1464	exon3			GGCATCGTCCTCA	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1167C>T	15.37:g.75982239G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			G|0.899;A|0.101	0.101	strong		0.627	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
MDN1	23195	hgsc.bcm.edu	37	6	90390443	90390443	+	Missense_Mutation	SNP	C	C	A	rs9353689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:90390443C>A	ENST00000369393.3	-	74	12245	c.12130G>T	c.(12130-12132)Gct>Tct	p.A4044S	MDN1_ENST00000428876.1_Missense_Mutation_p.A4044S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4044			A -> S (in dbSNP:rs9353689).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GAAGGAGCAGCGCCCTGACAC	0.542													C|||	3064	0.611821	0.612	0.7046	5008	,	,		20137	0.9077		0.4712	False		,,,				2504	0.3855				p.A4044S		Atlas-SNP	.											.	MDN1	478	.	0			c.G12130T						PASS	.	C	SER/ALA	2702,1704	651.9+/-399.3	845,1012,346	63.0	58.0	60.0		12130	-0.3	0.0	6	dbSNP_119	60	4126,4474	564.3+/-388.3	1021,2084,1195	yes	missense	MDN1	NM_014611.1	99	1866,3096,1541	AA,AC,CC		47.9767,38.6745,47.5012	benign	4044/5597	90390443	6828,6178	2203	4300	6503	SO:0001583	missense	23195	exon74			GAGCAGCGCCCTG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.12130G>T	6.37:g.90390443C>A	ENSP00000358400:p.Ala4044Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	1449	0.6634615384615384	312	0.6341463414634146	245	0.6767955801104972	524	0.916083916083916	368	0.48548812664907653	C	7.498	0.652024	0.14580	0.613255	0.479767	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03035	4.07;4.07	3.7	-0.328	0.12690	.	1.203530	0.05725	N	0.598418	T	0.00998	0.0033	L	0.43152	1.355	0.80722	P	0.0	B	0.26258	0.145	B	0.23716	0.048	T	0.46748	-0.9169	9	0.07644	T	0.81	.	8.681	0.34209	0.0:0.6252:0.0:0.3748	rs9353689;rs52797926;rs60292364;rs9353689	4044	Q9NU22	MDN1_HUMAN	S	4044	ENSP00000358400:A4044S;ENSP00000413970:A4044S	ENSP00000358400:A4044S	A	-	1	0	MDN1	90447164	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.218000	0.09240	-0.083000	0.12618	-0.254000	0.11334	GCT	C|0.413;A|0.587	0.587	strong		0.542	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ZC3H3	23144	hgsc.bcm.edu	37	8	144620183	144620183	+	Missense_Mutation	SNP	T	T	C	rs4874147	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144620183T>C	ENST00000262577.5	-	2	1385	c.1354A>G	c.(1354-1356)Agc>Ggc	p.S452G		NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	452			S -> G (in dbSNP:rs4874147). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8590280}.		mRNA polyadenylation (GO:0006378)|poly(A)+ mRNA export from nucleus (GO:0016973)|regulation of mRNA export from nucleus (GO:0010793)	nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(97;8.64e-11)|all_epithelial(106;6.43e-09)|Lung NSC(106;0.000202)|all_lung(105;0.000548)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.107)			CTTGTGCTGCTGCGTCTCCGG	0.607													C|||	3886	0.775958	0.6899	0.7594	5008	,	,		18184	0.9256		0.7366	False		,,,				2504	0.7904				p.S452G		Atlas-SNP	.											.	ZC3H3	75	.	0			c.A1354G	GRCh37	CM066263	ZC3H3	M	rs4874147	PASS	.	C	GLY/SER	3041,1365	447.9+/-348.5	1061,919,223	48.0	52.0	51.0		1354	4.3	0.3	8	dbSNP_111	51	6273,2327	387.1+/-342.1	2303,1667,330	yes	missense	ZC3H3	NM_015117.2	56	3364,2586,553	CC,CT,TT		27.0581,30.9805,28.3869	benign	452/949	144620183	9314,3692	2203	4300	6503	SO:0001583	missense	23144	exon2			TGCTGCTGCGTCT	D63484	CCDS6402.1	8q24.3	2012-07-05	2005-06-02	2005-06-02	ENSG00000014164	ENSG00000014164		"""Zinc fingers, CCCH-type domain containing"""	28972	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 3"""	ZC3HDC3		8590280	Standard	NM_015117		Approved	KIAA0150	uc003yyd.2	Q8IXZ2	OTTHUMG00000165127	ENST00000262577.5:c.1354A>G	8.37:g.144620183T>C	ENSP00000262577:p.Ser452Gly	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	1725	0.7898351648351648	339	0.6890243902439024	272	0.7513812154696132	539	0.9423076923076923	575	0.758575197889182	C	0.005	-2.158348	0.00321	0.690195	0.729419	ENSG00000014164	ENST00000262577	T	0.02656	4.21	5.21	4.33	0.51752	.	0.136162	0.47852	N	0.000209	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24297	-1.0164	9	0.02654	T	1	-8.7578	8.9182	0.35594	0.0:0.7736:0.0:0.2264	rs4874147;rs11548252;rs17728486;rs17857166;rs59863095;rs4874147	452	Q8IXZ2	ZC3H3_HUMAN	G	452	ENSP00000262577:S452G	ENSP00000262577:S452G	S	-	1	0	ZC3H3	144691326	0.008000	0.16893	0.261000	0.24466	0.026000	0.11368	0.821000	0.27338	0.608000	0.30000	-0.215000	0.12644	AGC	T|0.251;C|0.749	0.749	strong		0.607	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73090261	73090261	+	Silent	SNP	T	T	C	rs7716253	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:73090261T>C	ENST00000426542.2	+	7	965	c.945T>C	c.(943-945)gcT>gcC	p.A315A	ARHGEF28_ENST00000287898.5_Silent_p.A315A|ARHGEF28_ENST00000545377.1_Silent_p.A315A|ARHGEF28_ENST00000437974.1_Silent_p.A315A|ARHGEF28_ENST00000296794.6_Silent_p.A315A|ARHGEF28_ENST00000513042.2_Silent_p.A315A			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	315					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										GATCAGCAGCTGAAAAGGAAG	0.343													C|||	3072	0.613419	0.8215	0.5346	5008	,	,		16966	0.5327		0.508	False		,,,				2504	0.5798				p.A315A		Atlas-SNP	.											.	.	.	.	0			c.T945C						PASS	.	C	,	2932,776		1161,610,83	66.0	72.0	70.0		945,945	-11.4	0.0	5	dbSNP_116	70	4269,3947		1142,1985,981	no	coding-synonymous,coding-synonymous	RGNEF	NM_001080479.2,NM_001177693.1	,	2303,2595,1064	CC,CT,TT		48.0404,20.9277,39.6092	,	315/1732,315/1706	73090261	7201,4723	1854	4108	5962	SO:0001819	synonymous_variant	64283	exon8			AGCAGCTGAAAAG		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.945T>C	5.37:g.73090261T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	52	0.597701	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			T|0.404;C|0.596	0.596	strong		0.343	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
DYNC1H1	1778	hgsc.bcm.edu	37	14	102446161	102446161	+	Silent	SNP	G	G	A	rs3818188	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:102446161G>A	ENST00000360184.4	+	4	788	c.624G>A	c.(622-624)ccG>ccA	p.P208P		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	208	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TCAGCCTGCCGATTCATCCAA	0.408													G|||	1044	0.208466	0.0242	0.3357	5008	,	,		19557	0.4405		0.1958	False		,,,				2504	0.1411				p.P208P		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G624A						PASS	.	G		218,4188	132.1+/-168.6	6,206,1991	129.0	136.0	134.0		624	-9.8	0.0	14	dbSNP_107	134	1642,6958	304.2+/-306.8	177,1288,2835	no	coding-synonymous	DYNC1H1	NM_001376.4		183,1494,4826	AA,AG,GG		19.093,4.9478,14.3011		208/4647	102446161	1860,11146	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon4			CCTGCCGATTCAT	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.624G>A	14.37:g.102446161G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	135	50	0.37037	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			G|0.812;A|0.188	0.188	strong		0.408	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
LIPI	149998	hgsc.bcm.edu	37	21	15558346	15558346	+	Silent	SNP	G	G	A	rs397517	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:15558346G>A	ENST00000536861.1	-	3	476	c.477C>T	c.(475-477)agC>agT	p.S159S	LIPI_ENST00000344577.2_Silent_p.S180S			Q6XZB0	LIPI_HUMAN	lipase, member I	159					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		GAGCCCCTAAGCTCACACCTA	0.308													G|||	893	0.178315	0.0484	0.1138	5008	,	,		15447	0.2669		0.2177	False		,,,				2504	0.2679				p.S180S		Atlas-SNP	.											.	LIPI	95	.	0			c.C540T	GRCh37	CM035698	LIPI	M	rs397517	PASS	.	G		330,4076	173.0+/-202.9	16,298,1889	111.0	110.0	111.0		540	2.1	1.0	21	dbSNP_80	111	1927,6673	339.2+/-323.1	205,1517,2578	no	coding-synonymous	LIPI	NM_198996.2		221,1815,4467	AA,AG,GG		22.407,7.4898,17.3535		180/482	15558346	2257,10749	2203	4300	6503	SO:0001819	synonymous_variant	149998	exon3			CCCTAAGCTCACA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.477C>T	21.37:g.15558346G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Silent	SNP	ENST00000536861.1	37		379	0.17353479853479853	21	0.042682926829268296	39	0.10773480662983426	145	0.2534965034965035	174	0.22955145118733508	G	8.789	0.930140	0.18131	0.074898	0.22407	ENSG00000188992	ENST00000400211	.	.	.	5.37	2.07	0.26955	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999977598	.	.	.	.	.	.	T	0.19128	-1.0315	3	.	.	.	.	6.2333	0.20747	0.2278:0.0:0.6235:0.1487	rs397517	.	.	.	F	39	.	.	L	-	1	0	LIPI	14480217	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	0.986000	0.29590	0.762000	0.33152	0.650000	0.86243	CTT	G|0.827;A|0.173	0.173	strong		0.308	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
LCA5L	150082	hgsc.bcm.edu	37	21	40778182	40778182	+	Missense_Mutation	SNP	C	C	T	rs11558767	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:40778182C>T	ENST00000358268.2	-	10	2167	c.1639G>A	c.(1639-1641)Ggc>Agc	p.G547S	WRB_ENST00000541890.1_Intron|LCA5L_ENST00000495240.1_5'UTR|LCA5L_ENST00000288350.3_Missense_Mutation_p.G547S|LCA5L_ENST00000380671.2_Missense_Mutation_p.G547S			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	547			G -> S (in dbSNP:rs11558767). {ECO:0000269|PubMed:15489334}.							breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				CTCATGTTGCCGGCATTGGCT	0.498													C|||	243	0.0485224	0.0174	0.0548	5008	,	,		19065	0.002		0.0924	False		,,,				2504	0.089				p.G547S		Atlas-SNP	.											LCA5L,NS,carcinoma,+2,2	LCA5L	57	2	0			c.G1639A						scavenged	.	C	SER/GLY	148,4258	103.0+/-141.5	1,146,2056	97.0	94.0	95.0		1639	2.0	0.0	21	dbSNP_120	95	933,7667	206.1+/-248.3	48,837,3415	yes	missense	LCA5L	NM_152505.3	56	49,983,5471	TT,TC,CC		10.8488,3.3591,8.3115	benign	547/671	40778182	1081,11925	2203	4300	6503	SO:0001583	missense	150082	exon10			TGTTGCCGGCATT	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 13"""	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.1639G>A	21.37:g.40778182C>T	ENSP00000351008:p.Gly547Ser	Somatic	167	2	0.011976		WXS	Illumina HiSeq	Phase_I	206	69	0.334951	NM_152505	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	101	0.04624542124542125	7	0.014227642276422764	20	0.055248618784530384	1	0.0017482517482517483	73	0.09630606860158311	C	7.449	0.642255	0.14451	0.033591	0.108488	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268	T;T;T	0.56941	0.43;0.43;0.43	4.82	1.99	0.26369	.	0.706882	0.13177	N	0.407836	T	0.00936	0.0031	L	0.59436	1.845	0.09310	N	1	B	0.30021	0.265	B	0.20577	0.03	T	0.01136	-1.1440	10	0.33940	T	0.23	-0.8746	7.2789	0.26300	0.0:0.6447:0.0:0.3553	rs11558767;rs57390824;rs11558767	547	O95447	LCA5L_HUMAN	S	547	ENSP00000288350:G547S;ENSP00000370046:G547S;ENSP00000351008:G547S	ENSP00000288350:G547S	G	-	1	0	LCA5L	39700052	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-0.400000	0.07241	0.565000	0.29255	0.655000	0.94253	GGC	C|0.932;T|0.068	0.068	strong		0.498	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505	
CHRNB3	1142	hgsc.bcm.edu	37	8	42587065	42587065	+	Silent	SNP	C	C	T	rs4952	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:42587065C>T	ENST00000289957.2	+	5	743	c.615C>T	c.(613-615)aaC>aaT	p.N205N		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	205					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	AAATACTGAACGCAAAGGGGA	0.458													C|||	115	0.0229633	0.0061	0.0202	5008	,	,		22412	0.002		0.0358	False		,,,				2504	0.0562				p.N205N		Atlas-SNP	.											.	CHRNB3	74	.	0			c.C615T						PASS	.	C		57,4349	56.2+/-92.4	2,53,2148	104.0	105.0	105.0		615	-5.7	0.0	8	dbSNP_52	105	353,8247	118.3+/-177.8	7,339,3954	no	coding-synonymous	CHRNB3	NM_000749.3		9,392,6102	TT,TC,CC		4.1047,1.2937,3.1524		205/459	42587065	410,12596	2203	4300	6503	SO:0001819	synonymous_variant	1142	exon5			ACTGAACGCAAAG	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1963	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 3 (neuronal)"""	118508	"""cholinergic receptor, nicotinic, beta polypeptide 3"""			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.615C>T	8.37:g.42587065C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_000749	Q15827	Silent	SNP	ENST00000289957.2	37	CCDS6134.1																																																																																			C|0.968;T|0.032	0.032	strong		0.458	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1		
NRP1	8829	hgsc.bcm.edu	37	10	33469181	33469181	+	Silent	SNP	A	A	G	rs1048804	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:33469181A>G	ENST00000265371.4	-	18	3120	c.2595T>C	c.(2593-2595)agT>agC	p.S865S	NRP1_ENST00000395995.1_Silent_p.S848S|NRP1_ENST00000374875.1_Silent_p.S677S|NRP1_ENST00000374867.2_Silent_p.S865S			O14786	NRP1_HUMAN	neuropilin 1	865					angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.S865S(1)		NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	CCCCCAGGGCACTCATGGCTA	0.532													G|||	2125	0.424321	0.5666	0.2061	5008	,	,		18341	0.622		0.2455	False		,,,				2504	0.3671				p.S865S	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											NRP1,NS,carcinoma,0,1	NRP1	126	1	1	Substitution - coding silent(1)	stomach(1)	c.T2595C						scavenged	.	G		2210,2196	585.1+/-386.2	574,1062,567	187.0	177.0	181.0		2595	-4.9	0.8	10	dbSNP_86	181	2024,6576	721.1+/-406.3	223,1578,2499	no	coding-synonymous	NRP1	NM_003873.5		797,2640,3066	GG,GA,AA		23.5349,49.8411,32.5542		865/924	33469181	4234,8772	2203	4300	6503	SO:0001819	synonymous_variant	8829	exon17			CAGGGCACTCATG	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.2595T>C	10.37:g.33469181A>G		Somatic	217	3	0.0138249		WXS	Illumina HiSeq	Phase_I	244	123	0.504098	NM_003873	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	37	CCDS7177.1																																																																																			A|0.634;G|0.366	0.366	strong		0.532	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
TH	7054	hgsc.bcm.edu	37	11	2190951	2190951	+	Missense_Mutation	SNP	C	C	T	rs6356	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:2190951C>T	ENST00000381178.1	-	3	352	c.334G>A	c.(334-336)Gtg>Atg	p.V112M	TH_ENST00000381175.1_Missense_Mutation_p.V108M|TH_ENST00000333684.5_Missense_Mutation_p.V85M|TH_ENST00000352909.3_Missense_Mutation_p.V81M	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	112			V -> M (common polymorphism; dbSNP:rs6356). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21940685, ECO:0000269|PubMed:7789962, ECO:0000269|PubMed:9613851}.		anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	AGGTTTAGCACGGCCTTCCCC	0.697													C|||	2156	0.430511	0.1014	0.3919	5008	,	,		15378	0.7877		0.4026	False		,,,				2504	0.5634				p.V112M		Atlas-SNP	.											.	TH	43	.	0			c.G334A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	623,3779	265.6+/-266.7	36,551,1614	58.0	60.0	60.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	241,334,322	-1.8	0.0	11	dbSNP_52	60	3121,5477	472.4+/-368.3	569,1983,1747	yes	missense,missense,missense	TH	NM_000360.3,NM_199292.2,NM_199293.2	21,21,21	605,2534,3361	TT,TC,CC		36.2991,14.1527,28.8	benign,benign,benign	81/498,112/529,108/525	2190951	3744,9256	2201	4299	6500	SO:0001583	missense	7054	exon3			TTAGCACGGCCTT	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.334G>A	11.37:g.2190951C>T	ENSP00000370571:p.Val112Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	117	54	0.461538	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Missense_Mutation	SNP	ENST00000381178.1	37	CCDS7731.1	913	0.41804029304029305	52	0.10569105691056911	127	0.35082872928176795	443	0.7744755244755245	291	0.3839050131926121	C	13.68	2.310931	0.40895	0.141527	0.362991	ENSG00000180176	ENST00000381178;ENST00000381175;ENST00000352909;ENST00000333684	D;D;D;D	0.98419	-4.92;-4.92;-4.92;-4.92	3.59	-1.8	0.07907	.	0.577810	0.17552	N	0.170143	T	0.00012	0.0000	L	0.31664	0.95	0.80722	P	0.0	B;B;B;B;B	0.24576	0.037;0.037;0.044;0.016;0.106	B;B;B;B;B	0.21151	0.006;0.006;0.02;0.005;0.033	T	0.41662	-0.9496	9	0.33141	T	0.24	.	4.7289	0.12955	0.0:0.2915:0.2918:0.4167	rs6356;rs57599796;rs6356	85;81;81;112;108	Q0PWM2;Q0PWM3;P07101-3;P07101;P07101-2	.;.;.;TY3H_HUMAN;.	M	112;108;81;85	ENSP00000370571:V112M;ENSP00000370567:V108M;ENSP00000325951:V81M;ENSP00000328814:V85M	ENSP00000328814:V85M	V	-	1	0	TH	2147527	0.000000	0.05858	0.000000	0.03702	0.948000	0.59901	-0.327000	0.07955	-0.189000	0.10482	0.491000	0.48974	GTG	C|0.652;T|0.348	0.348	strong		0.697	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
PAMR1	25891	hgsc.bcm.edu	37	11	35492351	35492351	+	Silent	SNP	G	G	A	rs16927500	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:35492351G>A	ENST00000378880.2	-	5	955	c.510C>T	c.(508-510)agC>agT	p.S170S	PAMR1_ENST00000378878.3_Intron|PAMR1_ENST00000534803.1_5'UTR|PAMR1_ENST00000532848.1_Silent_p.S130S|PAMR1_ENST00000278360.3_Silent_p.S170S	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	170	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						CAAACTCCAGGCTCAACATGA	0.557													A|||	464	0.0926518	0.2595	0.0591	5008	,	,		22839	0.0377		0.0249	False		,,,				2504	0.0174				p.S170S		Atlas-SNP	.											.	PAMR1	85	.	0			c.C510T						PASS	.	A	,	1006,3398	729.6+/-410.1	95,816,1291	111.0	80.0	90.0		510,510	1.5	1.0	11	dbSNP_123	90	183,8413	810.9+/-407.1	3,177,4118	no	coding-synonymous,coding-synonymous	PAMR1	NM_001001991.1,NM_015430.2	,	98,993,5409	AA,AG,GG		2.1289,22.8429,9.1462	,	170/721,170/738	35492351	1189,11811	2202	4298	6500	SO:0001819	synonymous_variant	25891	exon5			CTCCAGGCTCAAC		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.510C>T	11.37:g.35492351G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_001001991	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Silent	SNP	ENST00000378880.2	37	CCDS31460.1																																																																																			G|0.906;A|0.094	0.094	strong		0.557	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	
TRIM65	201292	hgsc.bcm.edu	37	17	73888423	73888423	+	Silent	SNP	A	A	G	rs7222755	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73888423A>G	ENST00000269383.3	-	3	734	c.669T>C	c.(667-669)caT>caC	p.H223H		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	223						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CAGCCTCCAAATGGACCCGCA	0.647													G|||	2044	0.408147	0.7859	0.2709	5008	,	,		16113	0.2212		0.2972	False		,,,				2504	0.3016				p.H223H		Atlas-SNP	.											.	TRIM65	23	.	0			c.T669C						PASS	.	G		3126,1276		1135,856,210	23.0	27.0	26.0		669	3.2	0.9	17	dbSNP_116	26	2536,6062		386,1764,2149	no	coding-synonymous	TRIM65	NM_173547.2		1521,2620,2359	GG,GA,AA		29.4952,28.9868,43.5538		223/518	73888423	5662,7338	2201	4299	6500	SO:0001819	synonymous_variant	201292	exon3			CTCCAAATGGACC	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.669T>C	17.37:g.73888423A>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_001256124	Q4G0F0|Q6DKJ6|Q9BRP6	Silent	SNP	ENST00000269383.3	37	CCDS11732.1	843|843	0.385989010989011|0.385989010989011	374|374	0.7601626016260162|0.7601626016260162	109|109	0.3011049723756906|0.3011049723756906	147|147	0.256993006993007|0.256993006993007	213|213	0.28100263852242746|0.28100263852242746	G|G	0.396|0.396	-0.920654|-0.920654	0.02396|0.02396	0.710132|0.710132	0.294952|0.294952	ENSG00000141569|ENSG00000141569	ENST00000540128|ENST00000543309	.|.	.|.	.|.	4.23|4.23	3.23|3.23	0.37069|0.37069	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.99999999509411|0.99999999509411	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24728|0.24728	-1.0152|-1.0152	3|3	.|.	.|.	.|.	.|.	7.3708|7.3708	0.26800|0.26800	0.0908:0.3209:0.5883:0.0|0.0908:0.3209:0.5883:0.0	rs7222755;rs60028486|rs7222755;rs60028486	.|.	.|.	.|.	L|T	215|97	.|.	.|.	F|I	-|-	1|2	0|0	TRIM65|TRIM65	71400018|71400018	0.927000|0.927000	0.31430|0.31430	0.939000|0.939000	0.37840|0.37840	0.013000|0.013000	0.08279|0.08279	0.449000|0.449000	0.21744|0.21744	0.429000|0.429000	0.26202|0.26202	-0.355000|-0.355000	0.07637|0.07637	TTT|ATT	A|0.591;G|0.409	0.409	strong		0.647	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
ZBTB7C	201501	hgsc.bcm.edu	37	18	45555829	45555829	+	Silent	SNP	T	T	C	rs7231151	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:45555829T>C	ENST00000588982.1	-	4	2163	c.1662A>G	c.(1660-1662)acA>acG	p.T554T	ZBTB7C_ENST00000590800.1_Silent_p.T554T|ZBTB7C_ENST00000586438.1_Silent_p.T554T|ZBTB7C_ENST00000535628.2_Silent_p.T554T|ZBTB7C_ENST00000332053.2_Silent_p.T554T			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	554							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						GCTTCATCTGTGTCTCCTCGA	0.721													C|||	2061	0.411542	0.562	0.366	5008	,	,		9999	0.4673		0.2594	False		,,,				2504	0.3395				p.T554T		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.A1662G						PASS	.	C		2040,2344		497,1046,649	12.0	12.0	12.0		1662	0.5	1.0	18	dbSNP_116	12	2358,6186		325,1708,2239	no	coding-synonymous	ZBTB7C	NM_001039360.2		822,2754,2888	CC,CT,TT		27.5983,46.5328,34.0192		554/620	45555829	4398,8530	2192	4272	6464	SO:0001819	synonymous_variant	201501	exon3			CATCTGTGTCTCC	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31700	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 36"""	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.1662A>G	18.37:g.45555829T>C		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	25	8	0.32	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																			T|0.652;C|0.348	0.348	strong		0.721	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
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 GAIIx	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_ENST00000528778.1_5'UTR|DUSP8_ENST00000331588.4_Missense_Mutation_p.T162S	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	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	121	34	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	
KCNQ4	9132	hgsc.bcm.edu	37	1	41285553	41285553	+	Silent	SNP	T	T	C	rs55737429	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:41285553T>C	ENST00000347132.5	+	6	923	c.841T>C	c.(841-843)Ttg>Ctg	p.L281L	KCNQ4_ENST00000506017.1_3'UTR|KCNQ4_ENST00000509682.2_Silent_p.L281L	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	281			L -> S (in DFNA2A). {ECO:0000269|PubMed:10571947}.		inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	CCAGATTACATTGACAACCAT	0.577													T|||	191	0.038139	0.0038	0.0605	5008	,	,		19432	0.0635		0.0567	False		,,,				2504	0.0235				p.L281L		Atlas-SNP	.											.	KCNQ4	58	.	0			c.T841C						PASS	.	T	,	73,4333	65.3+/-102.7	0,73,2130	155.0	155.0	155.0		841,841	2.8	0.8	1	dbSNP_129	155	430,8170	131.8+/-189.6	8,414,3878	no	coding-synonymous,coding-synonymous	KCNQ4	NM_004700.3,NM_172163.2	,	8,487,6008	CC,CT,TT		5.0,1.6568,3.8674	,	281/696,281/642	41285553	503,12503	2203	4300	6503	SO:0001819	synonymous_variant	9132	exon6			ATTACATTGACAA	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.841T>C	1.37:g.41285553T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	154	86	0.558442	NM_004700	O96025	Silent	SNP	ENST00000347132.5	37	CCDS456.1	99	0.04532967032967033	2	0.0040650406504065045	27	0.07458563535911603	33	0.057692307692307696	37	0.048812664907651716	T	9.488	1.099931	0.20552	0.016568	0.05	ENSG00000117013	ENST00000443478	.	.	.	5.71	2.82	0.32997	.	.	.	.	.	T	0.09113	0.0225	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02546	-1.1143	4	.	.	.	-15.4036	7.7218	0.28736	0.0:0.6685:0.0:0.3315	rs55737429;rs61739881	.	.	.	T	176	.	.	I	+	2	0	KCNQ4	41058140	0.957000	0.32711	0.837000	0.33122	0.782000	0.44232	2.201000	0.42734	0.342000	0.23796	-0.899000	0.02877	ATT	T|0.959;C|0.041	0.041	strong		0.577	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
COL11A2	1302	hgsc.bcm.edu	37	6	33144243	33144243	+	Silent	SNP	T	T	A	rs1799908	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33144243T>A	ENST00000374708.4	-	25	2136	c.1878A>T	c.(1876-1878)ggA>ggT	p.G626G	COL11A2_ENST00000341947.2_Silent_p.G712G|COL11A2_ENST00000374714.1_Silent_p.G686G|COL11A2_ENST00000374712.1_Silent_p.G631G|COL11A2_ENST00000374713.1_Silent_p.G665G|COL11A2_ENST00000357486.1_Silent_p.G691G|COL11A2_ENST00000477772.1_Intron|COL11A2_ENST00000361917.1_Silent_p.G605G|COL11A2_ENST00000395197.1_Silent_p.G652G	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	712	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						ATCCTAGAGGTCCCTGAGGTC	0.562													A|||	2740	0.547125	0.5242	0.5144	5008	,	,		17786	0.7192		0.4414	False		,,,				2504	0.5327				p.G712G	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											COL11A2,NS,carcinoma,0,2	COL11A2	124	2	0			c.A2136T						PASS	.	A	,,	1490,1532		365,760,386	36.0	39.0	38.0		1815,2136,1878	1.1	1.0	6	dbSNP_89	38	2209,3207		447,1315,946	yes	coding-synonymous,coding-synonymous,coding-synonymous	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	,,	812,2075,1332	AA,AT,TT		40.7866,49.3051,43.8374	,,	605/1630,712/1737,626/1651	33144243	3699,4739	1511	2708	4219	SO:0001819	synonymous_variant	1302	exon27			TAGAGGTCCCTGA	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.1878A>T	6.37:g.33144243T>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	78	14	0.179487	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	37	CCDS43452.1																																																																																			T|0.527;A|0.473	0.473	strong		0.562	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
VPS13C	54832	hgsc.bcm.edu	37	15	62202482	62202482	+	Missense_Mutation	SNP	C	C	T	rs10851704	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:62202482C>T	ENST00000261517.5	-	64	8811	c.8738G>A	c.(8737-8739)aGt>aAt	p.S2913N	VPS13C_ENST00000395896.4_Missense_Mutation_p.S2913N|VPS13C_ENST00000395898.3_Missense_Mutation_p.S2870N|VPS13C_ENST00000249837.3_Missense_Mutation_p.S2870N	NM_020821.2	NP_065872.1			vacuolar protein sorting 13 homolog C (S. cerevisiae)											NS(3)|breast(4)|endometrium(4)|kidney(9)|large_intestine(26)|lung(46)|ovary(5)|prostate(6)|skin(6)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	117						GCCTGACAAACTTTCTGGCCA	0.338													T|||	2586	0.516374	0.4841	0.6671	5008	,	,		9613	0.4732		0.5517	False		,,,				2504	0.4611				p.S2913N		Atlas-SNP	.											.	VPS13C	506	.	0			c.G8738A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER,ASN/SER	2198,2208	586.2+/-386.4	563,1072,568	50.0	52.0	51.0		8738,8609,8609,8738	3.5	1.0	15	dbSNP_120	51	4603,3997	552.6+/-386.1	1235,2133,932	yes	missense,missense,missense,missense	VPS13C	NM_001018088.2,NM_017684.4,NM_018080.3,NM_020821.2	46,46,46,46	1798,3205,1500	TT,TC,CC		46.4767,49.8865,47.7087	benign,benign,benign,benign	2913/3629,2870/3711,2870/3586,2913/3754	62202482	6801,6205	2203	4300	6503	SO:0001583	missense	54832	exon64			GACAAACTTTCTG	AJ608770	CCDS10180.1, CCDS32257.1, CCDS45272.1, CCDS58367.1	15q21.3	2009-07-09	2006-04-04		ENSG00000129003	ENSG00000129003			23594	protein-coding gene	gene with protein product		608879	"""vacuolar protein sorting 13C (yeast)"""				Standard	NM_018080		Approved	FLJ20136, FLJ10381, KIAA1421	uc002agz.3	Q709C8	OTTHUMG00000132801	ENST00000261517.5:c.8738G>A	15.37:g.62202482C>T	ENSP00000261517:p.Ser2913Asn	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	1177	0.5389194139194139	242	0.491869918699187	231	0.638121546961326	281	0.49125874125874125	423	0.558047493403694	T	4.368	0.067920	0.08436	0.498865	0.535233	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.27720	1.65;1.65;1.65	5.85	3.54	0.40534	Vacuolar protein sorting-associated protein (1);	0.145640	0.64402	N	0.000014	T	0.00012	0.0000	N	0.01656	-0.775	0.54753	P	1.3000000000040757E-5	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.47182	-0.9137	9	0.02654	T	1	.	9.5913	0.39548	0.0:0.2007:0.0:0.7993	rs10851704;rs52801554;rs59009682;rs10851704	2913;2870;2913;2870;2913	F5GZG8;Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;.;VP13C_HUMAN	N	2870;2913;2913;2913	ENSP00000249837:S2870N;ENSP00000261517:S2913N;ENSP00000379233:S2913N	ENSP00000249837:S2870N	S	-	2	0	VPS13C	59989774	1.000000	0.71417	0.971000	0.41717	0.983000	0.72400	0.853000	0.27777	0.133000	0.18654	-0.254000	0.11334	AGT	C|0.476;T|0.524	0.524	strong		0.338	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684	
ZNF407	55628	hgsc.bcm.edu	37	18	72344238	72344238	+	Silent	SNP	C	C	T	rs17817969	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:72344238C>T	ENST00000299687.5	+	1	1263	c.1263C>T	c.(1261-1263)ctC>ctT	p.L421L	ZNF407_ENST00000577538.1_Silent_p.L421L|ZNF407_ENST00000309902.6_Silent_p.L421L|ZNF407_ENST00000582337.1_Silent_p.L421L	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	421					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		GAAATATTCTCGTGTTGGGTA	0.438													C|||	340	0.0678914	0.112	0.0663	5008	,	,		21706	0.002		0.1064	False		,,,				2504	0.0378				p.L421L		Atlas-SNP	.											.	ZNF407	231	.	0			c.C1263T						PASS	.	C	,,	387,3373		18,351,1511	63.0	65.0	64.0		1263,1263,1263	-7.7	0.0	18	dbSNP_123	64	1145,7097		88,969,3064	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	106,1320,4575	TT,TC,CC		13.8923,10.2926,12.7645	,,	421/1816,421/1661,421/2249	72344238	1532,10470	1880	4121	6001	SO:0001819	synonymous_variant	55628	exon1			TATTCTCGTGTTG	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1263C>T	18.37:g.72344238C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			C|0.907;T|0.093	0.093	strong		0.438	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
DDX20	11218	hgsc.bcm.edu	37	1	112308953	112308953	+	Missense_Mutation	SNP	T	T	C	rs197412	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:112308953T>C	ENST00000369702.4	+	11	2527	c.1907T>C	c.(1906-1908)aTt>aCt	p.I636T	DDX20_ENST00000475700.1_Missense_Mutation_p.I244T	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	636			I -> T (in dbSNP:rs197412). {ECO:0000269|PubMed:15489334}.		ATP catabolic process (GO:0006200)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oogenesis (GO:0048477)|positive regulation of apoptotic process (GO:0043065)|regulation of steroid biosynthetic process (GO:0050810)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|spliceosomal snRNP assembly (GO:0000387)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)|transcriptional repressor complex (GO:0017053)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)			endometrium(3)|kidney(7)|large_intestine(6)|lung(3)|pancreas(1)|prostate(1)	21		all_cancers(81;1.06e-05)|all_epithelial(167;7.36e-06)|all_lung(203;2.44e-05)|Lung NSC(69;4.15e-05)		Lung(183;0.0234)|Colorectal(144;0.0282)|all cancers(265;0.0614)|Epithelial(280;0.0999)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AATAAAGTTATTGAACAGAGA	0.453													C|||	2376	0.474441	0.7247	0.5072	5008	,	,		19469	0.3403		0.4185	False		,,,				2504	0.3088				p.I636T		Atlas-SNP	.											DDX20,NS,carcinoma,+1,1	DDX20	50	1	0			c.T1907C						PASS	.	C	THR/ILE	2950,1456	465.7+/-354.3	991,968,244	49.0	49.0	49.0		1907	3.9	0.3	1	dbSNP_79	49	3345,5255	640.4+/-399.6	669,2007,1624	yes	missense	DDX20	NM_007204.4	89	1660,2975,1868	CC,CT,TT		38.8953,33.0458,48.4007	benign	636/825	112308953	6295,6711	2203	4300	6503	SO:0001583	missense	11218	exon11			AAGTTATTGAACA	AF106019	CCDS842.1	1p21.1-p13.2	2008-02-05	2003-06-13		ENSG00000064703	ENSG00000064703		"""DEAD-boxes"""	2743	protein-coding gene	gene with protein product		606168	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 20, 103kD"""			10383418	Standard	NM_007204		Approved	DP103, GEMIN3	uc001ebs.3	Q9UHI6	OTTHUMG00000011956	ENST00000369702.4:c.1907T>C	1.37:g.112308953T>C	ENSP00000358716:p.Ile636Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Missense_Mutation	SNP	ENST00000369702.4	37	CCDS842.1	1038	0.47527472527472525	360	0.7317073170731707	162	0.44751381215469616	198	0.34615384615384615	318	0.41952506596306066	C	0.006	-2.070387	0.00379	0.669542	0.388953	ENSG00000064703	ENST00000369702;ENST00000475700	T;T	0.32023	1.47;1.98	5.72	3.86	0.44501	.	2.200060	0.01328	N	0.011173	T	0.02929	0.0087	N	0.00926	-1.1	0.44899	P	0.0020820000000000283	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33828	-0.9853	8	.	.	.	0.4742	5.1813	0.15161	0.1427:0.6287:0.0:0.2286	rs197412;rs482352;rs17569500;rs17845940;rs17856358;rs17857030;rs17858920;rs52814398;rs60229681;rs197412	244;636	E9PJ60;Q9UHI6	.;DDX20_HUMAN	T	636;244	ENSP00000358716:I636T;ENSP00000435660:I244T	.	I	+	2	0	DDX20	112110476	0.906000	0.30813	0.331000	0.25455	0.101000	0.19017	2.183000	0.42565	0.463000	0.27118	-0.766000	0.03442	ATT	C|0.483;N|0.000	0.483	strong		0.453	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204	
NLRC5	84166	hgsc.bcm.edu	37	16	57111232	57111232	+	Silent	SNP	C	C	T	rs11864231	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57111232C>T	ENST00000262510.6	+	41	5085	c.4860C>T	c.(4858-4860)gaC>gaT	p.D1620D	NLRC5_ENST00000539144.1_Silent_p.D1591D|NLRC5_ENST00000308149.7_Silent_p.D1591D|NLRC5_ENST00000436936.1_3'UTR	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1620					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AGATTGGAGACGCTGGTGTCC	0.567													C|||	864	0.172524	0.1036	0.1816	5008	,	,		19784	0.1468		0.2326	False		,,,				2504	0.2239				p.D1620D		Atlas-SNP	.											.	NLRC5	186	.	0			c.C4860T						PASS	.	C		590,3806	260.4+/-263.7	40,510,1648	82.0	70.0	74.0		4860	-2.4	0.0	16	dbSNP_120	74	1835,6765	327.9+/-318.0	202,1431,2667	no	coding-synonymous	NLRC5	NM_032206.3		242,1941,4315	TT,TC,CC		21.3372,13.4213,18.6596		1620/1867	57111232	2425,10571	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon40			TGGAGACGCTGGT	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.4860C>T	16.37:g.57111232C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1																																																																																			C|0.819;T|0.181	0.181	strong		0.567	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
CD276	80381	hgsc.bcm.edu	37	15	74000729	74000729	+	Silent	SNP	G	G	C	rs2291012	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:74000729G>C	ENST00000318443.5	+	7	1721	c.1419G>C	c.(1417-1419)ctG>ctC	p.L473L	CD276_ENST00000537340.2_Silent_p.L327L|CD276_ENST00000318424.5_Silent_p.L255L|CD276_ENST00000561213.1_Silent_p.L473L|CD276_ENST00000564751.1_Silent_p.L255L	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	473				L -> P (in Ref. 4; BAC11243). {ECO:0000305}.	cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						CCGTGGGGCTGTCTGTCTGTC	0.567													G|||	999	0.199481	0.4274	0.1009	5008	,	,		22078	0.1349		0.0944	False		,,,				2504	0.136				p.L473L		Atlas-SNP	.											.	CD276	29	.	0			c.G1419C						PASS	.	G	,	1700,2696	513.2+/-368.3	351,998,849	138.0	116.0	124.0		1419,765	-4.3	0.4	15	dbSNP_100	124	828,7766	191.5+/-237.7	32,764,3501	yes	coding-synonymous,coding-synonymous	CD276	NM_001024736.1,NM_025240.2	,	383,1762,4350	CC,CG,GG		9.6346,38.6715,19.4611	,	473/535,255/317	74000729	2528,10462	2198	4297	6495	SO:0001819	synonymous_variant	80381	exon7			GGGGCTGTCTGTC	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.1419G>C	15.37:g.74000729G>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Silent	SNP	ENST00000318443.5	37	CCDS32288.1	391	0.17902930402930403	205	0.4166666666666667	41	0.1132596685082873	73	0.12762237762237763	72	0.09498680738786279	G	0.065	-1.215225	0.01542	0.386715	0.096346	ENSG00000103855	ENST00000543481	.	.	.	5.13	-4.27	0.03744	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999749	.	.	.	.	.	.	T	0.30208	-0.9986	3	.	.	.	-20.3435	15.0849	0.72145	0.0:0.2663:0.6051:0.1285	rs2291012;rs60714145;rs2291012	.	.	.	L	118	.	.	V	+	1	0	CD276	71787782	0.996000	0.38824	0.357000	0.25798	0.006000	0.05464	0.239000	0.18023	-0.707000	0.05022	-2.000000	0.00444	GTC	G|0.817;C|0.183	0.183	strong		0.567	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
PCDHB6	56130	hgsc.bcm.edu	37	5	140530852	140530852	+	Silent	SNP	G	G	C	rs246708	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140530852G>C	ENST00000231136.1	+	1	1014	c.1014G>C	c.(1012-1014)gtG>gtC	p.V338V	PCDHB6_ENST00000543635.1_Silent_p.V202V	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	338	Cadherin 3. {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)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCTGGACGTGAATGACAATG	0.468													G|||	1122	0.224042	0.4909	0.2406	5008	,	,		18488	0.0407		0.169	False		,,,				2504	0.0971				p.V338V		Atlas-SNP	.											PCDHB6,NS,carcinoma,+2,1	PCDHB6	161	1	0			c.G1014C						PASS	.	G		1871,2535	542.4+/-376.0	393,1085,725	102.0	98.0	99.0		1014	0.0	0.9	5	dbSNP_79	99	1580,7020	295.5+/-302.4	152,1276,2872	no	coding-synonymous	PCDHB6	NM_018939.2		545,2361,3597	CC,CG,GG		18.3721,42.4648,26.5339		338/795	140530852	3451,9555	2203	4300	6503	SO:0001819	synonymous_variant	56130	exon1			GGACGTGAATGAC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1014G>C	5.37:g.140530852G>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	142	81	0.570423	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																			G|0.747;C|0.253	0.253	strong		0.468	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
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 GAIIx	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_ENST00000455089.1_Silent_p.T584T|EGFR_ENST00000442591.1_Silent_p.T629T|EGFR_ENST00000454757.2_Silent_p.T576T	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		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	40	14	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	
ALLC	55821	hgsc.bcm.edu	37	2	3729254	3729254	+	Missense_Mutation	SNP	C	C	T	rs13426642	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:3729254C>T	ENST00000252505.3	+	6	491	c.329C>T	c.(328-330)aCc>aTc	p.T110I		NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	129					allantoin catabolic process (GO:0000256)		allantoicase activity (GO:0004037)			breast(4)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	30	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.088)	all_cancers(51;0.24)		OV - Ovarian serous cystadenocarcinoma(76;0.088)|all cancers(51;0.151)|Epithelial(75;0.206)		GAAAGAGGAACCAGGACAGGA	0.443										HNSCC(21;0.051)			T|||	958	0.191294	0.3487	0.1326	5008	,	,		18597	0.13		0.174	False		,,,				2504	0.1012				p.T110I		Atlas-SNP	.											.	ALLC	61	.	0			c.C329T						PASS	.	T	ILE/THR	1109,2681		150,809,936	53.0	56.0	55.0		329	-1.7	0.0	2	dbSNP_121	55	1577,6649		159,1259,2695	yes	missense	ALLC	NM_018436.3	89	309,2068,3631	TT,TC,CC		19.1709,29.2612,22.3535	benign	110/392	3729254	2686,9330	1895	4113	6008	SO:0001583	missense	55821	exon6			GAGGAACCAGGAC	AF215924	CCDS46223.1	2p25.3	2008-02-05			ENSG00000151360	ENSG00000151360			17377	protein-coding gene	gene with protein product		612396				11054555	Standard	NM_018436		Approved	ALC	uc010ewt.3	Q8N6M5	OTTHUMG00000151485	ENST00000252505.3:c.329C>T	2.37:g.3729254C>T	ENSP00000252505:p.Thr110Ile	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	90	88	0.977778	NM_018436	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	428	0.19597069597069597	175	0.3556910569105691	53	0.1464088397790055	69	0.12062937062937062	131	0.17282321899736147	T	2.425	-0.332270	0.05314	0.292612	0.191709	ENSG00000151360	ENST00000252505	.	.	.	4.98	-1.69	0.08186	Allantoicase domain (1);Galactose-binding domain-like (1);	1.431930	0.04091	N	0.311285	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.40403	-0.9565	8	0.36615	T	0.2	-6.0446	1.6428	0.02756	0.148:0.3466:0.153:0.3524	rs13426642;rs17856846;rs59065366;rs13426642	129	Q8N6M5	ALLC_HUMAN	I	110	.	ENSP00000252505:T110I	T	+	2	0	ALLC	3707129	0.000000	0.05858	0.005000	0.12908	0.006000	0.05464	-0.729000	0.04920	-0.411000	0.07530	-0.269000	0.10298	ACC	C|0.801;T|0.199	0.199	strong		0.443	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1		
CDKL5	6792	hgsc.bcm.edu	37	X	18638082	18638082	+	Missense_Mutation	SNP	A	A	C	rs35478150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:18638082A>C	ENST00000379989.3	+	17	2657	c.2372A>C	c.(2371-2373)cAa>cCa	p.Q791P	CDKL5_ENST00000379996.3_Missense_Mutation_p.Q791P	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	791			Q -> P (in dbSNP:rs35478150). {ECO:0000269|PubMed:12736870, ECO:0000269|PubMed:15499549, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:19241098}.		neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					AAGAAATCTCAAACAGTAAGT	0.308													A|||	63	0.0166887	0.0	0.0187	3775	,	,		13500	0.0		0.0437	False		,,,				2504	0.0061				p.Q791P		Atlas-SNP	.											.	CDKL5	124	.	0			c.A2372C						PASS	.	A	PRO/GLN,PRO/GLN	22,3798		0,20,2,1607,564	24.0	24.0	24.0		2372,2372	5.5	1.0	X	dbSNP_126	24	326,6374		6,230,84,2185,1774	yes	missense,missense	CDKL5	NM_001037343.1,NM_003159.2	76,76	6,250,86,3792,2338	CC,CA,C,AA,A		4.8657,0.5759,3.308	probably-damaging,probably-damaging	791/1031,791/1031	18638082	348,10172	2193	4279	6472	SO:0001583	missense	6792	exon16			AATCTCAAACAGT	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"""Cyclin-dependent kinases"""	11411	protein-coding gene	gene with protein product		300203	"""serine/threonine kinase 9"""	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2372A>C	X.37:g.18638082A>C	ENSP00000369325:p.Gln791Pro	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	47	25	0.531915	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Missense_Mutation	SNP	ENST00000379989.3	37	CCDS14186.1	33	0.019891500904159132	0	0.0	4	0.011111111111111112	0	0.0	16	0.021798365122615803	A	19.27	3.795056	0.70452	0.005759	0.048657	ENSG00000008086	ENST00000379996;ENST00000379989	T;T	0.78816	-1.21;-1.21	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.48537	0.1505	L	0.34521	1.04	0.26319	P	0.9777068	D	0.71674	0.998	D	0.75484	0.986	T	0.77256	-0.2655	9	0.87932	D	0	-22.4062	13.8874	0.63717	1.0:0.0:0.0:0.0	rs35478150	791	O76039	CDKL5_HUMAN	P	791	ENSP00000369332:Q791P;ENSP00000369325:Q791P	ENSP00000369325:Q791P	Q	+	2	0	CDKL5	18548003	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.334000	0.79224	1.944000	0.56390	0.417000	0.27973	CAA	A|0.976;C|0.024	0.024	strong		0.308	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	
SIRPD	128646	hgsc.bcm.edu	37	20	1538266	1538266	+	Silent	SNP	G	G	A	rs11697395	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:1538266G>A	ENST00000381623.3	-	1	1223	c.34C>T	c.(34-36)Ctg>Ttg	p.L12L	SIRPD_ENST00000381621.1_Silent_p.L12L|RP4-576H24.4_ENST00000564763.1_Intron			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	12						extracellular region (GO:0005576)				breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						AAGGAAGGCAGAGGTGGGTGG	0.577													G|||	476	0.0950479	0.0575	0.1023	5008	,	,		18036	0.003		0.2167	False		,,,				2504	0.1104				p.L12L		Atlas-SNP	.											.	SIRPD	34	.	0			c.C34T						PASS	.	G		395,4011		15,365,1823	241.0	182.0	202.0		34	1.4	0.0	20	dbSNP_120	202	1756,6844		189,1378,2733	no	coding-synonymous	SIRPD	NM_178460.2		204,1743,4556	AA,AG,GG		20.4186,8.965,16.5385		12/198	1538266	2151,10855	2203	4300	6503	SO:0001819	synonymous_variant	128646	exon1			AAGGCAGAGGTGG	AL049634	CCDS13018.1	20p13	2013-01-11	2006-02-03	2006-02-03	ENSG00000125900	ENSG00000125900		"""Signal-regulatory proteins"", ""Immunoglobulin superfamily / V-set domain containing"""	16248	protein-coding gene	gene with protein product			"""protein tyrosine phosphatase, non-receptor type substrate 1-like 2"""	PTPNS1L2		16339511	Standard	NM_178460		Approved	dJ576H24.4	uc002wfi.3	Q9H106	OTTHUMG00000031674	ENST00000381623.3:c.34C>T	20.37:g.1538266G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	68	32	0.470588	NM_178460	B3KS88|Q5TFQ6	Silent	SNP	ENST00000381623.3	37	CCDS13018.1																																																																																			G|0.853;A|0.147	0.147	strong		0.577	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460	
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 GAIIx	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_ENST00000394139.1_Silent_p.H233H|CYP26A1_ENST00000371531.1_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		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	94	4	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		
POLE	5426	hgsc.bcm.edu	37	12	133219831	133219831	+	Silent	SNP	T	T	C	rs5744944	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:133219831T>C	ENST00000320574.5	-	35	4573	c.4530A>G	c.(4528-4530)gcA>gcG	p.A1510A	POLE_ENST00000535270.1_Silent_p.A1483A|POLE_ENST00000434528.3_5'Flank	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1510					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|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)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	CAAAGACGGATGCCCTGCGCT	0.602								DNA polymerases (catalytic subunits)					C|||	3031	0.605232	0.761	0.5317	5008	,	,		20994	0.6736		0.4304	False		,,,				2504	0.5562				p.A1510A		Atlas-SNP	.											.	POLE	416	.	0			c.A4530G						PASS	.	C		3091,1315	441.2+/-346.3	1076,939,188	101.0	91.0	94.0		4530	-11.9	0.1	12	dbSNP_114	94	3703,4897	619.4+/-396.9	797,2109,1394	no	coding-synonymous	POLE	NM_006231.2		1873,3048,1582	CC,CT,TT		43.0581,29.8457,47.7626		1510/2287	133219831	6794,6212	2203	4300	6503	SO:0001819	synonymous_variant	5426	exon35			GACGGATGCCCTG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.4530A>G	12.37:g.133219831T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			T|0.448;C|0.552	0.552	strong		0.602	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
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 GAIIx	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_ENST00000392400.1_Silent_p.P731P|TNK2_ENST00000428187.1_Silent_p.P763P|TNK2_ENST00000381916.2_Silent_p.P809P	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		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	21	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	
ITGB4	3691	hgsc.bcm.edu	37	17	73750859	73750859	+	Silent	SNP	C	C	G	rs8669	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73750859C>G	ENST00000200181.3	+	34	4708	c.4521C>G	c.(4519-4521)ccC>ccG	p.P1507P	ITGB4_ENST00000579662.1_Silent_p.P1437P|ITGB4_ENST00000449880.2_Silent_p.P1437P|ITGB4_ENST00000339591.3_Silent_p.P1437P|GALK1_ENST00000225614.2_Intron|ITGB4_ENST00000450894.3_Silent_p.P1437P	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1507					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCACACTGCCCAGGGACTACT	0.622													C|||	1889	0.377196	0.0756	0.4539	5008	,	,		19393	0.5149		0.4732	False		,,,				2504	0.4898				p.P1507P		Atlas-SNP	.											.	ITGB4	165	.	0			c.C4521G						PASS	.	C	,,	653,3753	279.9+/-275.1	55,543,1605	316.0	189.0	232.0		4521,4311,4311	4.4	1.0	17	dbSNP_52	232	4101,4499	561.4+/-387.8	957,2187,1156	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,,	1012,2730,2761	GG,GC,CC		47.686,14.8207,36.5524	,,	1507/1823,1437/1806,1437/1753	73750859	4754,8252	2203	4300	6503	SO:0001819	synonymous_variant	3691	exon34			ACTGCCCAGGGAC		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.4521C>G	17.37:g.73750859C>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_000213	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																			C|0.640;G|0.360	0.360	strong		0.622	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
AQP10	89872	hgsc.bcm.edu	37	1	154293675	154293675	+	Missense_Mutation	SNP	G	G	A	rs6668968	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:154293675G>A	ENST00000324978.3	+	1	84	c.44G>A	c.(43-45)cGg>cAg	p.R15Q	AQP10_ENST00000355197.4_3'UTR|AQP10_ENST00000484864.1_Missense_Mutation_p.R15Q	NM_080429.2	NP_536354.2	Q96PS8	AQP10_HUMAN	aquaporin 10	15			R -> Q (in dbSNP:rs6668968).		response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(14)|stomach(2)|upper_aerodigestive_tract(1)	23	all_lung(78;2.62e-30)|Lung NSC(65;3.94e-28)|Hepatocellular(266;0.0877)		LUSC - Lung squamous cell carcinoma(543;0.185)			GGCCACCTCCGGATACGCAGC	0.567													G|||	1368	0.273163	0.2685	0.2349	5008	,	,		19235	0.2093		0.3181	False		,,,				2504	0.3262				p.R15Q		Atlas-SNP	.											.	AQP10	44	.	0			c.G44A						PASS	.	G	GLN/ARG	1164,3242	413.3+/-336.4	159,846,1198	58.0	55.0	56.0		44	-1.3	0.1	1	dbSNP_116	56	2539,6061	414.0+/-351.3	393,1753,2154	no	missense	AQP10	NM_080429.2	43	552,2599,3352	AA,AG,GG		29.5233,26.4185,28.4715	benign	15/302	154293675	3703,9303	2203	4300	6503	SO:0001583	missense	89872	exon1			ACCTCCGGATACG	AF159174	CCDS1065.1	1q21.3	2008-02-05			ENSG00000143595	ENSG00000143595		"""Ion channels / Aquaporins"""	16029	protein-coding gene	gene with protein product		606578				11573934	Standard	NM_080429		Approved		uc001feu.3	Q96PS8	OTTHUMG00000035980	ENST00000324978.3:c.44G>A	1.37:g.154293675G>A	ENSP00000318355:p.Arg15Gln	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	NM_080429	Q5VYD3|Q5VYD4|Q8NG70	Missense_Mutation	SNP	ENST00000324978.3	37	CCDS1065.1	562	0.2573260073260073	136	0.2764227642276423	85	0.23480662983425415	109	0.19055944055944055	232	0.30606860158311344	G	12.26	1.885123	0.33255	0.264185	0.295233	ENSG00000143595	ENST00000324978;ENST00000484864	D;D	0.84944	-1.8;-1.92	5.09	-1.33	0.09172	.	0.246884	0.32687	N	0.005773	T	0.55449	0.1921	L	0.39397	1.21	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.004	T	0.37572	-0.9700	9	0.08381	T	0.77	.	10.0901	0.42443	0.4269:0.0:0.5731:0.0	rs6668968;rs52819618;rs6668968	15;15	Q96PS8-2;Q96PS8	.;AQP10_HUMAN	Q	15	ENSP00000318355:R15Q;ENSP00000420341:R15Q	ENSP00000318355:R15Q	R	+	2	0	AQP10	152560299	0.038000	0.19896	0.113000	0.21522	0.918000	0.54935	-0.528000	0.06193	-0.423000	0.07394	0.505000	0.49811	CGG	G|0.718;A|0.282	0.282	strong		0.567	AQP10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087661.1	NM_080429	
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 GAIIx	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		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	84	36	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 GAIIx	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_ENST00000550102.1_Silent_p.A66A|CHMP1A_ENST00000253475.5_Missense_Mutation_p.V60I|CHMP1A_ENST00000547614.1_5'UTR|CHMP1A_ENST00000535997.2_Silent_p.A2A	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		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	80	44	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	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72513682	72513682	+	Silent	SNP	C	C	T	rs2587475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72513682C>T	ENST00000373207.1	+	19	2856	c.2856C>T	c.(2854-2856)tgC>tgT	p.C952C	ADAMTS14_ENST00000373208.1_Silent_p.C955C	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	952	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CCAAAGCCTGCGCCGGGGACC	0.692													C|||	2630	0.52516	0.5182	0.6614	5008	,	,		14920	0.4395		0.5447	False		,,,				2504	0.5061				p.C955C		Atlas-SNP	.											.	ADAMTS14	148	.	0			c.C2865T						PASS	.	C	,	2225,2161		586,1053,554	15.0	13.0	14.0		2856,2865	0.7	0.1	10	dbSNP_100	14	4851,3719		1397,2057,831	no	coding-synonymous,coding-synonymous	ADAMTS14	NM_080722.3,NM_139155.2	,	1983,3110,1385	TT,TC,CC		43.3956,49.2704,45.3844	,	952/1224,955/1227	72513682	7076,5880	2193	4285	6478	SO:0001819	synonymous_variant	140766	exon19			AGCCTGCGCCGGG	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.2856C>T	10.37:g.72513682C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	33	10	0.30303	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			C|0.469;T|0.531	0.531	strong		0.692	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
KCNQ2	3785	hgsc.bcm.edu	37	20	62038277	62038277	+	Missense_Mutation	SNP	T	T	G	rs1801475	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62038277T>G	ENST00000359125.2	-	17	2513	c.2339A>C	c.(2338-2340)aAc>aCc	p.N780T	KCNQ2_ENST00000344462.4_Missense_Mutation_p.N749T|KCNQ2_ENST00000354587.3_Missense_Mutation_p.N788T|KCNQ2_ENST00000357249.2_Missense_Mutation_p.N762T|KCNQ2_ENST00000370224.1_Missense_Mutation_p.N788T|KCNQ2_ENST00000359689.1_Missense_Mutation_p.N780T|KCNQ2_ENST00000360480.3_Missense_Mutation_p.N752T	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	780			N -> T (in dbSNP:rs1801475). {ECO:0000269|PubMed:10323247}.		axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GTCCCGCAGGTTCCCCTCGGG	0.692													G|||	2957	0.590455	0.4629	0.5519	5008	,	,		11476	0.6687		0.6382	False		,,,				2504	0.6605				p.N780T		Atlas-SNP	.											.	KCNQ2	201	.	0			c.A2339C						PASS	.	G	THR/ASN,THR/ASN,THR/ASN,THR/ASN	2225,2139		578,1069,535	30.0	22.0	25.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2255,2285,2339,2246	0.1	0.0	20	dbSNP_89	25	5527,3057		1808,1911,573	yes	missense,missense,missense,missense	KCNQ2	NM_004518.4,NM_172106.1,NM_172107.2,NM_172108.3	65,65,65,65	2386,2980,1108	GG,GT,TT		35.6128,49.0147,40.1297	benign,benign,benign,benign	752/845,762/855,780/873,749/842	62038277	7752,5196	2182	4292	6474	SO:0001583	missense	3785	exon17			CGCAGGTTCCCCT	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.2339A>C	20.37:g.62038277T>G	ENSP00000352035:p.Asn780Thr	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	37	CCDS13520.1	1284	0.5879120879120879	225	0.4573170731707317	208	0.574585635359116	362	0.6328671328671329	489	0.6451187335092349	G	2.801	-0.249080	0.05867	0.509853	0.643872	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224	T;T;T;T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96;0.96	4.95	0.0918	0.14469	.	0.369213	0.27008	N	0.021394	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40572	-0.9556	9	0.23302	T	0.38	-26.1325	7.214	0.25949	0.0685:0.4363:0.3833:0.1119	rs1801475;rs60103677	752;762;749;780	O43526-3;O43526-2;O43526-4;O43526	.;.;.;KCNQ2_HUMAN	T	762;780;750;788;780;749;752;776;788	ENSP00000349789:N762T;ENSP00000352035:N780T;ENSP00000359246:N750T;ENSP00000346601:N788T;ENSP00000352718:N780T;ENSP00000399612:N749T;ENSP00000353668:N752T;ENSP00000339611:N776T;ENSP00000359244:N788T	ENSP00000339611:N776T	N	-	2	0	KCNQ2	61508721	0.958000	0.32768	0.004000	0.12327	0.026000	0.11368	1.872000	0.39549	-0.549000	0.06191	-0.323000	0.08544	AAC	T|0.412;G|0.578	0.578	strong		0.692	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
TNMD	64102	hgsc.bcm.edu	37	X	99849017	99849017	+	Silent	SNP	G	G	A	rs2073162	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:99849017G>A	ENST00000373031.4	+	3	523	c.306G>A	c.(304-306)gtG>gtA	p.V102V	TNMD_ENST00000485971.1_3'UTR	NM_022144.2	NP_071427.2	Q9H2S6	TNMD_HUMAN	tenomodulin	102	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				cellular response to BMP stimulus (GO:0071773)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|tendon cell differentiation (GO:0035990)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(7)|skin(1)	16						CATTGGAAGTGCACGACTTTA	0.368													A|||	1788	0.473642	0.329	0.3631	3775	,	,		14013	0.5139		0.3052	False		,,,				2504	0.2822				p.V102V		Atlas-SNP	.											.	TNMD	40	.	0			c.G306A						PASS	.	A		1640,2195		290,802,258,540,313	106.0	98.0	101.0		306	-1.5	1.0	X	dbSNP_96	101	2455,4273		343,1089,680,996,1192	no	coding-synonymous	TNMD	NM_022144.2		633,1891,938,1536,1505	AA,AG,A,GG,G		36.4893,42.764,38.7674		102/318	99849017	4095,6468	2203	4300	6503	SO:0001819	synonymous_variant	64102	exon3			GGAAGTGCACGAC	AF191770	CCDS14469.1	Xq21.33-q23	2012-10-10			ENSG00000000005	ENSG00000000005		"""BRICHOS domain containing"""	17757	protein-coding gene	gene with protein product	"""BRICHOS domain containing 4"""	300459					Standard	NM_022144		Approved	myodulin, ChM1L, tendin, TEM, BRICD4	uc004efy.4	Q9H2S6	OTTHUMG00000022001	ENST00000373031.4:c.306G>A	X.37:g.99849017G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	207	135	0.652174	NM_022144	Q9HBX0|Q9UJG0	Silent	SNP	ENST00000373031.4	37	CCDS14469.1																																																																																			0|0.015;A|0.433	0.433	strong		0.368	TNMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057481.1	NM_022144	
SETX	23064	hgsc.bcm.edu	37	9	135139901	135139901	+	Missense_Mutation	SNP	T	T	C	rs1056899	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135139901T>C	ENST00000224140.5	-	26	7941	c.7759A>G	c.(7759-7761)Ata>Gta	p.I2587V	SETX_ENST00000372169.2_Missense_Mutation_p.I2616V|SETX_ENST00000477049.1_5'UTR|SETX_ENST00000393220.1_Missense_Mutation_p.I2554V	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2587			I -> V (in dbSNP:rs1056899). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GGCTGCTGTATATGGCTCAGG	0.632													C|||	2698	0.538738	0.8094	0.3487	5008	,	,		15929	0.6835		0.2694	False		,,,				2504	0.4356				p.I2587V		Atlas-SNP	.											.	SETX	234	.	0			c.A7759G						PASS	.	C	VAL/ILE	3227,1179	410.0+/-335.2	1199,829,175	65.0	76.0	72.0		7759	-3.8	0.0	9	dbSNP_86	72	2550,6050	690.4+/-404.4	374,1802,2124	yes	missense	SETX	NM_015046.5	29	1573,2631,2299	CC,CT,TT		29.6512,26.759,44.418	benign	2587/2678	135139901	5777,7229	2203	4300	6503	SO:0001583	missense	23064	exon26			GCTGTATATGGCT	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.7759A>G	9.37:g.135139901T>C	ENSP00000224140:p.Ile2587Val	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	1114	0.51007326007326	380	0.7723577235772358	137	0.3784530386740331	395	0.6905594405594405	202	0.26649076517150394	C	0.692	-0.794242	0.02862	0.73241	0.296512	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.89681	-1.95;-2.55;-2.03;-1.66	5.0	-3.8	0.04307	.	1.973910	0.02590	N	0.099880	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48581	-0.9023	9	0.02654	T	1	.	0.0833	0.00033	0.3191:0.1632:0.2101:0.3076	rs1056899;rs3197515;rs3739926;rs59785171;rs1056899	2554;2587;2616	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	2587;858;2616;2554	ENSP00000224140:I2587V;ENSP00000409143:I858V;ENSP00000361242:I2616V;ENSP00000376913:I2554V	ENSP00000224140:I2587V	I	-	1	0	SETX	134129722	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.111000	0.03303	-0.616000	0.05671	-1.383000	0.01170	ATA	T|0.505;C|0.495	0.495	strong		0.632	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
HIST1H2AI	8329	hgsc.bcm.edu	37	6	27776002	27776002	+	Silent	SNP	C	C	T	rs493283	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27776002C>T	ENST00000358739.3	+	1	104	c.15C>T	c.(13-15)ggC>ggT	p.G5G	HIST1H3H_ENST00000369163.2_5'Flank|HIST1H2BL_ENST00000377401.2_5'Flank	NM_003509.2	NP_003500.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ai	5						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			lung(3)	3						CTGGGCGTGGCAAGCAGGGAG	0.547																																					p.G5G		Atlas-SNP	.											.	HIST1H2AI	9	.	0			c.C15T						PASS	.						66.0	77.0	73.0					6																	27776002		2203	4300	6503	SO:0001819	synonymous_variant	8329	exon1			GCGTGGCAAGCAG	Z83742	CCDS4626.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196747	ENSG00000196747		"""Histones / Replication-dependent"""	4725	protein-coding gene	gene with protein product		602787	"""H2A histone family, member C"", ""histone 1, H2ai"""	H2AFC		9439656, 12408966	Standard	NM_003509		Approved	H2A/c		P0C0S8	OTTHUMG00000014484	ENST00000358739.3:c.15C>T	6.37:g.27776002C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	214	42	0.196262	NM_003509	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000358739.3	37	CCDS4626.1																																																																																			C|0.988;T|0.012	0.012	strong		0.547	HIST1H2AI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040152.1	NM_003509	
TENC1	23371	hgsc.bcm.edu	37	12	53442956	53442956	+	5'Flank	SNP	G	G	C	rs12369033	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:53442956G>C	ENST00000314250.6	+	0	0				TENC1_ENST00000549700.1_5'Flank|RP11-983P16.4_ENST00000552905.1_RNA|RP11-983P16.4_ENST00000546793.1_RNA|TENC1_ENST00000314276.3_Missense_Mutation_p.R10T|TENC1_ENST00000451358.1_5'Flank|TENC1_ENST00000552570.1_5'Flank|RP11-983P16.4_ENST00000546566.1_RNA|TENC1_ENST00000379902.3_Intron|RP11-983P16.4_ENST00000550601.1_RNA|TENC1_ENST00000546602.1_5'Flank	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)						cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						TGTGTTGGGAGGGGGGACCTC	0.637													G|||	1870	0.373403	0.1868	0.4452	5008	,	,		16325	0.1329		0.7237	False		,,,				2504	0.4622				p.R10T		Atlas-SNP	.											.	TENC1	148	.	0			c.G29C						PASS	.	G	THR/ARG,	1120,3286	397.6+/-330.5	158,804,1241	53.0	58.0	56.0		29,	2.8	1.0	12	dbSNP_120	56	6017,2583	687.5+/-404.2	2078,1861,361	yes	missense,intron	TENC1	NM_015319.2,NM_198316.1	71,	2236,2665,1602	CC,CG,GG		30.0349,25.4199,45.1253	,	10/1420,	53442956	7137,5869	2203	4300	6503	SO:0001631	upstream_gene_variant	23371	exon1			TTGGGAGGGGGGA	AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730		12.37:g.53442956G>C	Exception_encountered	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Missense_Mutation	SNP	ENST00000314250.6	37	CCDS8843.1	902	0.413003663003663	104	0.21138211382113822	178	0.49171270718232046	81	0.14160839160839161	539	0.7110817941952506	G	9.637	1.137981	0.21123	0.254199	0.699651	ENSG00000111077	ENST00000314276	D	0.94330	-3.4	3.64	2.75	0.32379	.	1.467820	0.05017	N	0.471991	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996672	B	0.25609	0.13	B	0.24269	0.052	T	0.43163	-0.9408	8	0.48119	T	0.1	.	6.9137	0.24347	0.125:0.0:0.875:0.0	rs12369033	10	Q63HR2-4	.	T	10	ENSP00000319756:R10T	ENSP00000319756:R10T	R	+	2	0	TENC1	51729223	0.999000	0.42202	0.996000	0.52242	0.056000	0.15407	1.397000	0.34543	1.118000	0.41863	0.561000	0.74099	AGG	G|0.494;C|0.506	0.506	strong		0.637	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754	
GJA9	81025	hgsc.bcm.edu	37	1	39340862	39340862	+	Silent	SNP	A	A	G	rs874243	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:39340862A>G	ENST00000360786.3	-	1	1161	c.909T>C	c.(907-909)tcT>tcC	p.S303S	RP5-864K19.4_ENST00000456813.1_RNA|MYCBP_ENST00000489803.1_5'UTR|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000454994.2_Silent_p.S303S|MYCBP_ENST00000397572.2_5'Flank|GJA9_ENST00000357771.3_Silent_p.S303S|RP5-864K19.4_ENST00000433671.2_RNA			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	303					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			GGAATACAGAAGATGAATTTA	0.383													A|||	519	0.103634	0.0061	0.1167	5008	,	,		19276	0.1319		0.2177	False		,,,				2504	0.0798				p.S303S		Atlas-SNP	.											.	GJA9	55	.	0			c.T909C						PASS	.	A		189,4217	119.6+/-157.3	8,173,2022	97.0	95.0	96.0		909	3.8	0.1	1	dbSNP_86	96	1824,6776	326.6+/-317.4	199,1426,2675	no	coding-synonymous	GJA9	NM_030772.4		207,1599,4697	GG,GA,AA		21.2093,4.2896,15.4775		303/516	39340862	2013,10993	2203	4300	6503	SO:0001819	synonymous_variant	81025	exon2			TACAGAAGATGAA	AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"""Ion channels / Gap junction proteins (connexins)"""	19155	protein-coding gene	gene with protein product	"""connexin 59"""	611923	"""gap junction protein, alpha 10, 59kDa"""	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.909T>C	1.37:g.39340862A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	231	114	0.493506	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000360786.3	37	CCDS432.1																																																																																			G|0.140;N|0.000	0.140	strong		0.383	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
CDC27	996	hgsc.bcm.edu	37	17	45214643	45214643	+	Silent	SNP	A	A	T	rs138020641		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:45214643A>T	ENST00000066544.3	-	14	1881	c.1788T>A	c.(1786-1788)gtT>gtA	p.V596V	CDC27_ENST00000531206.1_Silent_p.V602V|CDC27_ENST00000527547.1_Silent_p.V595V|CDC27_ENST00000446365.2_Silent_p.V535V	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	596					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AATTTGGATCAACTTGGATAG	0.398																																					p.V602V		Atlas-SNP	.											.	CDC27	337	.	0			c.T1806A						PASS	.						54.0	56.0	56.0					17																	45214643		2203	4299	6502	SO:0001819	synonymous_variant	996	exon14			TGGATCAACTTGG	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1788T>A	17.37:g.45214643A>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	18	6	0.333333	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			.	.	weak		0.398	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
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 GAIIx	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		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	61	26	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 GAIIx	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	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	132	42	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 GAIIx	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	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	159	88	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 GAIIx	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	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	191	37	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		
KRTAP19-8	728299	hgsc.bcm.edu	37	21	32410600	32410600	+	Missense_Mutation	SNP	C	C	T	rs200348786		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:32410600C>T	ENST00000382822.2	-	1	195	c.163G>A	c.(163-165)Gga>Aga	p.G55R		NM_001099219.1	NP_001092689.1	Q3LI54	KR198_HUMAN	keratin associated protein 19-8	55						intermediate filament (GO:0005882)				endometrium(2)|upper_aerodigestive_tract(1)	3						CCATATCCTCCGTAGTATAAT	0.483																																					p.G55R		Atlas-SNP	.											KRTAP19-8,caecum,carcinoma,0,1	KRTAP19-8	9	1	0			c.G163A						scavenged	.	C	ARG/GLY	1,4397	2.1+/-5.4	0,1,2198	90.0	109.0	103.0		163	3.4	0.0	21		103	2,8594	2.2+/-6.3	0,2,4296	yes	missense	KRTAP19-8	NM_001099219.1	125	0,3,6494	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	55/64	32410600	3,12991	2199	4298	6497	SO:0001583	missense	728299	exon1			ATCCTCCGTAGTA	AB096964	CCDS42917.1	21q22.11	2007-11-23			ENSG00000206102	ENSG00000206102		"""Keratin associated proteins"""	33898	protein-coding gene	gene with protein product							Standard	NM_001099219		Approved		uc010glt.3	Q3LI54	OTTHUMG00000057787	ENST00000382822.2:c.163G>A	21.37:g.32410600C>T	ENSP00000372272:p.Gly55Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	106	2	0.0188679	NM_001099219		Missense_Mutation	SNP	ENST00000382822.2	37	CCDS42917.1	.	.	.	.	.	.	.	.	.	.	C	8.147	0.786430	0.16189	2.27E-4	2.33E-4	ENSG00000206102	ENST00000382822	T	0.11277	2.79	4.31	3.41	0.39046	.	0.480462	0.14821	N	0.296474	T	0.19725	0.0474	.	.	.	0.09310	N	1	D	0.57899	0.981	P	0.54460	0.753	T	0.04885	-1.0920	9	0.87932	D	0	.	8.1256	0.30997	0.0:0.8883:0.0:0.1117	.	55	Q3LI54	KR198_HUMAN	R	55	ENSP00000372272:G55R	ENSP00000372272:G55R	G	-	1	0	KRTAP19-8	31332471	0.005000	0.15991	0.028000	0.17463	0.010000	0.07245	0.208000	0.17415	1.152000	0.42452	0.505000	0.49811	GGA	.	.	weak		0.483	KRTAP19-8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000128239.3	NM_001099219	
KRT32	3882	hgsc.bcm.edu	37	17	39616453	39616453	+	Missense_Mutation	SNP	G	G	A	rs146527191		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39616453G>A	ENST00000225899.3	-	7	1359	c.1256C>T	c.(1255-1257)aCc>aTc	p.T419I		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	419	Tail.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				GGGCACACAGGTGGTGCAGGA	0.607													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20217	0.0		0.0	False		,,,				2504	0.0				p.T419I		Atlas-SNP	.											.	KRT32	57	.	0			c.C1256T						PASS	.	G	ILE/THR	1,4391	2.1+/-5.4	0,1,2195	83.0	57.0	66.0		1256	2.9	0.0	17	dbSNP_134	66	16,8576	11.2+/-40.8	0,16,4280	yes	missense	KRT32	NM_002278.3	89	0,17,6475	AA,AG,GG		0.1862,0.0228,0.1309	benign	419/449	39616453	17,12967	2196	4296	6492	SO:0001583	missense	3882	exon7			ACACAGGTGGTGC	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.1256C>T	17.37:g.39616453G>A	ENSP00000225899:p.Thr419Ile	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	149	71	0.47651	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.247761	0.22880	2.28E-4	0.001862	ENSG00000108759	ENST00000225899	D	0.88509	-2.39	3.89	2.89	0.33648	.	1.128110	0.07024	N	0.827346	T	0.78541	0.4299	N	0.08118	0	0.09310	N	1	B	0.23854	0.092	B	0.18561	0.022	T	0.67393	-0.5682	10	0.52906	T	0.07	.	8.7883	0.34835	0.0:0.0:0.7743:0.2257	.	419	Q14532	K1H2_HUMAN	I	419	ENSP00000225899:T419I	ENSP00000225899:T419I	T	-	2	0	KRT32	36869979	0.006000	0.16342	0.004000	0.12327	0.003000	0.03518	1.115000	0.31209	0.940000	0.37473	0.511000	0.50034	ACC	G|0.999;A|0.001	0.001	strong		0.607	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
IQSEC1	9922	hgsc.bcm.edu	37	3	12962074	12962074	+	Missense_Mutation	SNP	G	G	A	rs35319679	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:12962074G>A	ENST00000273221.4	-	6	2134	c.1918C>T	c.(1918-1920)Cct>Tct	p.P640S		NM_014869.5	NP_055684.3	Q6DN90	IQEC1_HUMAN	IQ motif and Sec7 domain 1	640	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.		P -> S (in dbSNP:rs35319679).		actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			breast(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACCACCCCAGGGTTGCAGATG	0.632													G|||	400	0.0798722	0.0091	0.0865	5008	,	,		18375	0.1627		0.1362	False		,,,				2504	0.0276				p.P640S		Atlas-SNP	.											.	IQSEC1	88	.	0			c.C1918T						PASS	.	G	SER/PRO,SER/PRO	164,4242	108.2+/-146.6	2,160,2041	110.0	99.0	103.0		1876,1918	4.6	1.0	3	dbSNP_126	103	1164,7436	238.9+/-270.2	74,1016,3210	yes	missense,missense	IQSEC1	NM_001134382.1,NM_014869.4	74,74	76,1176,5251	AA,AG,GG		13.5349,3.7222,10.2107	benign,benign	626/1115,640/964	12962074	1328,11678	2203	4300	6503	SO:0001583	missense	9922	exon6			CCCCAGGGTTGCA	BC010267	CCDS33703.1, CCDS74902.1	3p25.2	2011-09-23			ENSG00000144711	ENSG00000144711			29112	protein-coding gene	gene with protein product	"""brefeldin A-resistant ARF-GEF2"""	610166				9872452, 8619474	Standard	NM_001134382		Approved	KIAA0763, GEP100, BRAG2, ARF-GEP100	uc011auw.2	Q6DN90	OTTHUMG00000155398	ENST00000273221.4:c.1918C>T	3.37:g.12962074G>A	ENSP00000273221:p.Pro640Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	109	50	0.458716	NM_014869	O94863|Q96D85	Missense_Mutation	SNP	ENST00000273221.4	37	CCDS33703.1	245|245	0.11217948717948718|0.11217948717948718	2|2	0.0040650406504065045|0.0040650406504065045	37|37	0.10220994475138122|0.10220994475138122	113|113	0.19755244755244755|0.19755244755244755	93|93	0.12269129287598944|0.12269129287598944	G|G	25.9|25.9	4.682337|4.682337	0.88542|0.88542	0.037222|0.037222	0.135349|0.135349	ENSG00000144711|ENSG00000144711	ENST00000450726|ENST00000273221;ENST00000435445;ENST00000429247	.|T;T	.|0.58060	.|0.36;0.36	4.59|4.59	4.59|4.59	0.56863|0.56863	.|SEC7-like, alpha orthogonal bundle (1);SEC7-like (4);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.00210|0.00210	0.0006|0.0006	.|.	.|.	.|.	0.09310|0.09310	P|P	0.99999999979479|0.99999999979479	.|P;D;B	.|0.63880	.|0.614;0.993;0.107	.|P;D;B	.|0.67382	.|0.525;0.951;0.297	T|T	0.00885|0.00885	-1.1527|-1.1527	4|8	.|0.62326	.|D	.|0.03	.|.	17.3729|17.3729	0.87383|0.87383	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs35319679|rs35319679	.|626;626;640	.|E9PG60;C9JMG9;Q6DN90	.|.;.;IQEC1_HUMAN	L|S	640|640;626;626	.|ENSP00000273221:P640S;ENSP00000402299:P626S	.|ENSP00000273221:P640S	P|P	-|-	2|1	0|0	IQSEC1|IQSEC1	12937074|12937074	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.837000|0.837000	0.47467|0.47467	6.629000|6.629000	0.74267|0.74267	2.104000|2.104000	0.64026|0.64026	0.561000|0.561000	0.74099|0.74099	CCC|CCT	G|0.898;A|0.102	0.102	strong		0.632	IQSEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339865.2	NM_014869	
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 GAIIx	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_ENST00000554173.1_Missense_Mutation_p.M410R|SERPINA10_ENST00000554723.1_Missense_Mutation_p.M450R|SERPINA10_ENST00000261994.4_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	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	86	42	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	
CRMP1	1400	hgsc.bcm.edu	37	4	5841350	5841350	+	Silent	SNP	A	A	G	rs16837723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:5841350A>G	ENST00000397890.2	-	9	1081	c.867T>C	c.(865-867)caT>caC	p.H289H	CRMP1_ENST00000512574.1_Silent_p.H287H|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000324989.7_Silent_p.H403H	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	289					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|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)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TGCTCCAGTAATGGGTGCCAT	0.587													A|||	1494	0.298323	0.4531	0.1628	5008	,	,		17453	0.4762		0.1163	False		,,,				2504	0.1892				p.H403H		Atlas-SNP	.											.	CRMP1	118	.	0			c.T1209C						PASS	.	A	,	1797,2609	512.4+/-368.1	352,1093,758	32.0	34.0	34.0		1209,867	0.6	1.0	4	dbSNP_123	34	1133,7467	226.9+/-262.5	69,995,3236	no	coding-synonymous,coding-synonymous	CRMP1	NM_001014809.1,NM_001313.3	,	421,2088,3994	GG,GA,AA		13.1744,40.7853,22.5281	,	403/687,289/573	5841350	2930,10076	2203	4300	6503	SO:0001819	synonymous_variant	1400	exon9			CCAGTAATGGGTG	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.867T>C	4.37:g.5841350A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	33	11	0.333333	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																			A|0.731;G|0.269	0.269	strong		0.587	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
PSMA6	5687	hgsc.bcm.edu	37	14	35783656	35783656	+	Silent	SNP	A	A	G	rs13393	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:35783656A>G	ENST00000261479.4	+	6	798	c.678A>G	c.(676-678)aaA>aaG	p.K226K	PSMA6_ENST00000540871.1_Silent_p.K207K|PSMA6_ENST00000555764.1_Silent_p.K147K|PSMA6_ENST00000553809.1_Silent_p.K232K|PSMA6_ENST00000556506.1_Intron|KIAA0391_ENST00000557565.1_3'UTR	NM_002791.1	NP_002782.1	P60900	PSA6_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 6	226					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)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of inflammatory response (GO:0050727)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|myofibril (GO:0030016)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysome (GO:0005844)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)|sarcomere (GO:0030017)	endopeptidase activity (GO:0004175)|NF-kappaB binding (GO:0051059)|purine ribonucleoside triphosphate binding (GO:0035639)|RNA binding (GO:0003723)|threonine-type endopeptidase activity (GO:0004298)			kidney(2)|large_intestine(1)|lung(5)|prostate(1)|urinary_tract(1)	10	Breast(36;0.0519)|Hepatocellular(127;0.158)		Lung(238;3.81e-05)|LUAD - Lung adenocarcinoma(48;5.59e-05)|Epithelial(34;0.00342)|all cancers(34;0.00973)	GBM - Glioblastoma multiforme(112;0.0234)		AAAATCCTAAATTCAGGTGAG	0.393													A|||	210	0.0419329	0.0847	0.0144	5008	,	,		17374	0.001		0.0258	False		,,,				2504	0.0624				p.K226K		Atlas-SNP	.											.	PSMA6	18	.	0			c.A678G						PASS	.	A		419,3987	201.8+/-224.7	26,367,1810	56.0	51.0	53.0		678	1.9	1.0	14	dbSNP_52	53	242,8358	96.3+/-158.1	1,240,4059	no	coding-synonymous	PSMA6	NM_002791.1		27,607,5869	GG,GA,AA		2.814,9.5098,5.0823		226/247	35783656	661,12345	2203	4300	6503	SO:0001819	synonymous_variant	5687	exon6			TCCTAAATTCAGG	X59417	CCDS9655.1, CCDS61437.1, CCDS61438.1	14q13	2003-03-12			ENSG00000100902	ENSG00000100902		"""Proteasome (prosome, macropain) subunits"""	9535	protein-coding gene	gene with protein product		602855				1888762, 8811196	Standard	NM_002791		Approved	IOTA, PROS27, p27K, MGC22756, MGC2333, MGC23846	uc001wtd.3	P60900	OTTHUMG00000140221	ENST00000261479.4:c.678A>G	14.37:g.35783656A>G		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	222	101	0.454955	NM_002791	B2R7J9|B4DQR4|B4DXJ9|P34062|Q6IB60	Silent	SNP	ENST00000261479.4	37	CCDS9655.1	65	0.02976190476190476	42	0.08536585365853659	6	0.016574585635359115	0	0.0	17	0.022427440633245383	A	9.601	1.128795	0.21041	0.095098	0.02814	ENSG00000100902	ENST00000556221	.	.	.	5.55	1.88	0.25563	.	.	.	.	.	T	0.02888	0.0086	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00822	-1.1552	4	.	.	.	-11.0995	9.9144	0.41425	0.7254:0.0:0.2746:0.0	rs13393;rs17586;rs28600041	.	.	.	S	65	.	.	N	+	2	0	PSMA6	34853407	0.978000	0.34361	1.000000	0.80357	0.994000	0.84299	0.408000	0.21065	0.480000	0.27534	0.528000	0.53228	AAT	A|0.955;G|0.045	0.045	strong		0.393	PSMA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276684.1		
FAM131C	348487	hgsc.bcm.edu	37	1	16385131	16385131	+	Missense_Mutation	SNP	C	C	A	rs1832151	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:16385131C>A	ENST00000375662.4	-	7	827	c.644G>T	c.(643-645)aGc>aTc	p.S215I	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	215	Pro-rich.		S -> I (in dbSNP:rs1832151).							large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		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;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGGAGGGGCTGGGCGAGGA	0.677																																					p.S215I		Atlas-SNP	.											.	FAM131C	21	.	0			c.G644T						PASS	.						25.0	24.0	25.0					1																	16385131		2030	4181	6211	SO:0001583	missense	348487	exon7			GAGGGGCTGGGCG		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.644G>T	1.37:g.16385131C>A	ENSP00000364814:p.Ser215Ile	Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	452	236	0.522124	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	376	0.17216117216117216	179	0.3638211382113821	57	0.1574585635359116	3	0.005244755244755245	137	0.18073878627968337	C	8.925	0.962089	0.18583	.	.	ENSG00000185519	ENST00000375662	T	0.13901	2.55	4.45	3.53	0.40419	.	0.518857	0.19640	N	0.109468	T	0.00012	0.0000	N	0.22421	0.69	0.45295	P	0.0017059999999999853	B	0.22983	0.078	B	0.19391	0.025	T	0.44772	-0.9306	9	0.52906	T	0.07	-7.2114	7.4371	0.27162	0.0:0.8818:0.0:0.1182	rs1832151;rs3961587	215	Q96AQ9	F131C_HUMAN	I	215	ENSP00000364814:S215I	ENSP00000364814:S215I	S	-	2	0	FAM131C	16257718	0.771000	0.28555	0.979000	0.43373	0.031000	0.12232	1.588000	0.36633	2.054000	0.61138	0.479000	0.44913	AGC	C|0.837;A|0.163	0.163	strong		0.677	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
HMCN1	83872	hgsc.bcm.edu	37	1	186031041	186031041	+	Silent	SNP	C	C	T	rs7522627	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186031041C>T	ENST00000271588.4	+	47	7600	c.7371C>T	c.(7369-7371)tgC>tgT	p.C2457C	HMCN1_ENST00000367492.2_Silent_p.C2457C	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2457	Ig-like C2-type 22.				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						AATATACTTGCGTTGTAAGGA	0.378													T|||	3277	0.654353	0.8495	0.647	5008	,	,		16476	0.5903		0.5348	False		,,,				2504	0.5849				p.C2457C		Atlas-SNP	.											.	HMCN1	797	.	0			c.C7371T						PASS	.	T		3571,835	333.6+/-303.0	1454,663,86	124.0	136.0	132.0		7371	1.9	0.9	1	dbSNP_116	132	4602,3998	553.3+/-386.3	1252,2098,950	no	coding-synonymous	HMCN1	NM_031935.2		2706,2761,1036	TT,TC,CC		46.4884,18.9514,37.1598		2457/5636	186031041	8173,4833	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon47			TACTTGCGTTGTA	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.7371C>T	1.37:g.186031041C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	87	30	0.344828	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			C|0.372;T|0.628	0.628	strong		0.378	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
OR52E8	390079	hgsc.bcm.edu	37	11	5877979	5877979	+	Nonstop_Mutation	SNP	T	T	A	rs12419602	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5877979T>A	ENST00000537935.1	-	1	985	c.954A>T	c.(952-954)taA>taT	p.*318Y	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	0						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(3)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCCAACTGGTTAGTGATTGG	0.428													T|||	1877	0.3748	0.3737	0.4135	5008	,	,		14340	0.373		0.4085	False		,,,				2504	0.316				p.X318Y		Atlas-SNP	.											.	OR52E8	54	.	0			c.A954T						PASS	.	T	TYR/stop	1647,2629		463,721,954	62.0	75.0	71.0		954	-1.1	0.0	11	dbSNP_120	71	3637,4955		789,2059,1448	yes	stop-lost	OR52E8	NM_001005168.1		1252,2780,2402	AA,AT,TT		42.3301,38.5173,41.0631		318/318	5877979	5284,7584	2138	4296	6434	SO:0001578	stop_lost	390079	exon1			AACTGGTTAGTGA	BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269		"""GPCR / Class A : Olfactory receptors"""	15217	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily E, member 8 pseudogene"""				Standard	NM_001005168		Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.954A>T	11.37:g.5877979T>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	99	40	0.40404	NM_001005168	B9EH38	Missense_Mutation	SNP	ENST00000537935.1	37	CCDS31400.1	842	0.38553113553113555	157	0.31910569105691056	156	0.430939226519337	213	0.3723776223776224	316	0.41688654353562005	T	2.130	-0.399348	0.04865	0.385173	0.423301	ENSG00000183269	ENST00000537935	.	.	.	3.16	-1.13	0.09775	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.9181	0.09231	0.2033:0.4983:0.0:0.2984	rs12419602;rs52797402;rs12419602	.	.	.	Y	318	.	.	X	-	3	2	OR52E8	5834555	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.134000	0.10436	-0.300000	0.08895	-0.398000	0.06409	TAA	T|0.599;A|0.401	0.401	strong		0.428	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401145.1	NM_001005168	
SALL1	6299	hgsc.bcm.edu	37	16	51172677	51172677	+	Silent	SNP	G	G	A	rs11645288	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:51172677G>A	ENST00000251020.4	-	2	3489	c.3456C>T	c.(3454-3456)caC>caT	p.H1152H	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Silent_p.H1055H	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1152					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|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 (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GAGTTCTCTCGTGAATCTGCA	0.512													G|||	707	0.141174	0.1868	0.147	5008	,	,		24279	0.0248		0.2247	False		,,,				2504	0.1094				p.H1152H	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C3456T						PASS	.	G	,	722,3674	300.7+/-286.5	66,590,1542	100.0	90.0	94.0		3165,3456	1.8	1.0	16	dbSNP_120	94	1862,6738	333.3+/-320.5	189,1484,2627	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	255,2074,4169	AA,AG,GG		21.6512,16.424,19.883	,	1055/1228,1152/1325	51172677	2584,10412	2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			TCTCTCGTGAATC	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3456C>T	16.37:g.51172677G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			G|0.822;A|0.178	0.178	strong		0.512	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
RABEP1	9135	hgsc.bcm.edu	37	17	5284698	5284698	+	Silent	SNP	A	A	G	rs1143206	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5284698A>G	ENST00000546142.2	+	17	2572	c.2385A>G	c.(2383-2385)caA>caG	p.Q795Q	RABEP1_ENST00000262477.6_Silent_p.Q795Q|RABEP1_ENST00000408982.2_Silent_p.Q762Q|RABEP1_ENST00000537505.1_Silent_p.Q752Q|RABEP1_ENST00000341923.6_Silent_p.Q762Q|NUP88_ENST00000573169.1_Intron			Q15276	RABE1_HUMAN	rabaptin, RAB GTPase binding effector protein 1	795					apoptotic process (GO:0006915)|endocytosis (GO:0006897)|membrane fusion (GO:0061025)|protein transport (GO:0015031)	early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	8						CCGTTGAACAACTAATGTTTG	0.368													A|||	2765	0.552117	0.3964	0.4251	5008	,	,		22136	0.8254		0.4394	False		,,,				2504	0.6871				p.Q795Q		Atlas-SNP	.											.	RABEP1	59	.	0			c.A2385G						PASS	.	A	,	1519,2169		324,871,649	77.0	76.0	76.0		2286,2385	-2.4	1.0	17	dbSNP_86	76	3199,4981		620,1959,1511	no	coding-synonymous,coding-synonymous	RABEP1	NM_001083585.1,NM_004703.4	,	944,2830,2160	GG,GA,AA		39.1076,41.1876,39.754	,	762/830,795/863	5284698	4718,7150	1844	4090	5934	SO:0001819	synonymous_variant	9135	exon17			TGAACAACTAATG	AF098638	CCDS42243.1, CCDS45592.1	17p13.2	2008-02-05				ENSG00000029725			17677	protein-coding gene	gene with protein product		603616				8521472	Standard	NM_001291582		Approved	neurocrescin, RAB5EP, RABPT5, rabaptin-5	uc002gbm.4	Q15276		ENST00000546142.2:c.2385A>G	17.37:g.5284698A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	32	0.463768	NM_004703	B2RAG7|O95369|Q8IVX3	Silent	SNP	ENST00000546142.2	37	CCDS45592.1																																																																																			A|0.519;G|0.481	0.481	strong		0.368	RABEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439349.1	NM_004703	
HDX	139324	hgsc.bcm.edu	37	X	83723541	83723541	+	Missense_Mutation	SNP	A	A	G	rs35161124	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:83723541A>G	ENST00000297977.5	-	3	1301	c.1190T>C	c.(1189-1191)tTt>tCt	p.F397S	HDX_ENST00000373177.2_Missense_Mutation_p.F397S|HDX_ENST00000506585.2_Missense_Mutation_p.F339S	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	397			F -> S (in dbSNP:rs35161124). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						ATGAGGAGAAAAATTACTCCG	0.318													A|||	317	0.0839735	0.0045	0.0634	3775	,	,		14176	0.0357		0.1769	False		,,,				2504	0.0542				p.F397S	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.T1190C						PASS	.	A	SER/PHE,SER/PHE,SER/PHE	107,3726		1,86,19,1544,552	122.0	103.0	109.0		1016,1190,1190	4.0	1.0	X	dbSNP_126	109	1295,5433		85,752,373,1591,1499	yes	missense,missense,missense	HDX	NM_001177478.1,NM_001177479.1,NM_144657.4	155,155,155	86,838,392,3135,2051	GG,GA,G,AA,A		19.2479,2.7915,13.2753	possibly-damaging,possibly-damaging,possibly-damaging	339/633,397/691,397/691	83723541	1402,9159	2202	4300	6502	SO:0001583	missense	139324	exon3			GGAGAAAAATTAC	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"""Homeoboxes / POU class"""	26411	protein-coding gene	gene with protein product			"""chromosome X open reading frame 43"""	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1190T>C	X.37:g.83723541A>G	ENSP00000297977:p.Phe397Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	142	104	0.732394	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	173	0.10427968655816756	3	0.006097560975609756	18	0.05202312138728324	16	0.02867383512544803	90	0.12931034482758622	A	11.29	1.595385	0.28445	0.027915	0.192479	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.38887	1.17;1.11;1.17	5.19	4.0	0.46444	.	0.188641	0.47093	D	0.000258	T	0.00073	0.0002	L	0.56769	1.78	0.30517	P	0.768818	P	0.37466	0.596	B	0.34722	0.188	T	0.04333	-1.0959	9	0.87932	D	0	-9.4178	10.5637	0.45161	0.8532:0.0:0.0:0.1468	rs35161124	397	Q7Z353	HDX_HUMAN	S	397;339;397	ENSP00000297977:F397S;ENSP00000362272:F339S;ENSP00000423670:F397S	ENSP00000297977:F397S	F	-	2	0	HDX	83610197	1.000000	0.71417	1.000000	0.80357	0.647000	0.38526	6.139000	0.71728	0.602000	0.29896	0.339000	0.21740	TTT	A|0.879;G|0.121	0.121	strong		0.318	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657	
MATN4	8785	hgsc.bcm.edu	37	20	43926573	43926573	+	Missense_Mutation	SNP	C	C	T	rs2227275	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:43926573C>T	ENST00000372754.1	-	8	1695	c.1687G>A	c.(1687-1689)Ggc>Agc	p.G563S	MATN4_ENST00000537548.1_Missense_Mutation_p.G522S|MATN4_ENST00000372751.4_Missense_Mutation_p.G373S|MATN4_ENST00000342716.4_Missense_Mutation_p.G522S|MATN4_ENST00000360607.6_Missense_Mutation_p.G481S|MATN4_ENST00000353917.5_Missense_Mutation_p.G440S|MATN4_ENST00000372756.1_Missense_Mutation_p.G522S			O95460	MATN4_HUMAN	matrilin 4	563				G -> S (in Ref. 2; BAC11083). {ECO:0000305}.	extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CAGATGCTGCCTCTGAGGTTC	0.622													C|||	1095	0.21865	0.261	0.3415	5008	,	,		17973	0.1121		0.2773	False		,,,				2504	0.1237				p.G522S		Atlas-SNP	.											.	MATN4	57	.	0			c.G1564A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	1121,3285	398.3+/-330.8	136,849,1218	76.0	78.0	78.0		1564,1441,1318	4.6	1.0	20	dbSNP_98	78	2126,6474	366.3+/-334.3	262,1602,2436	yes	missense,missense,missense	MATN4	NM_003833.3,NM_030590.2,NM_030592.2	56,56,56	398,2451,3654	TT,TC,CC		24.7209,25.4426,24.9654	benign,benign,benign	522/582,481/541,440/500	43926573	3247,9759	2203	4300	6503	SO:0001583	missense	8785	exon8			TGCTGCCTCTGAG	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.1687G>A	20.37:g.43926573C>T	ENSP00000361840:p.Gly563Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_003833	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Missense_Mutation	SNP	ENST00000372754.1	37		542	0.24816849816849818	138	0.2804878048780488	114	0.3149171270718232	78	0.13636363636363635	212	0.2796833773087071	C	11.07	1.530132	0.27387	0.254426	0.247209	ENSG00000124159	ENST00000372753;ENST00000372754;ENST00000372756;ENST00000353917;ENST00000360607;ENST00000342716;ENST00000537548;ENST00000255132;ENST00000372751	T;T;T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	5.64	4.64	0.57946	.	0.164448	0.29002	N	0.013458	T	0.00012	0.0000	N	0.11427	0.14	0.32213	P	0.576256	B;B;B	0.20550	0.002;0.045;0.046	B;B;B	0.23574	0.024;0.047;0.041	T	0.02282	-1.1183	9	0.11182	T	0.66	.	13.0781	0.59099	0.0:0.6907:0.3093:0.0	rs2227275;rs17426884;rs52795698;rs56588055;rs59660933;rs2227275	440;481;522	A6NNA4;O95460-4;O95460-2	.;.;.	S	373;563;522;440;481;522;522;563;373	ENSP00000361839:G373S;ENSP00000361840:G563S;ENSP00000361842:G522S;ENSP00000243983:G440S;ENSP00000353819:G481S;ENSP00000343164:G522S;ENSP00000440328:G522S;ENSP00000361837:G373S	ENSP00000255132:G563S	G	-	1	0	MATN4	43359987	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	1.529000	0.35996	2.661000	0.90470	0.644000	0.83932	GGC	C|0.757;T|0.243	0.243	strong		0.622	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		
CYP2D6	1565	hgsc.bcm.edu	37	22	42523558	42523558	+	Missense_Mutation	SNP	T	T	C	rs202102799		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:42523558T>C	ENST00000360608.5	-	7	1178	c.1064A>G	c.(1063-1065)tAc>tGc	p.Y355C	NDUFA6-AS1_ENST00000417327.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.Y355C|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.Y304C|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000451451.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA|NDUFA6-AS1_ENST00000610250.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	355					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	GGCAGTGGTGTAGGGCATGTG	0.607																																					p.Y355C		Atlas-SNP	.											CYP2D6_ENST00000360608,NS,carcinoma,0,2	CYP2D6	104	2	0			c.A1064G						scavenged	.						106.0	82.0	90.0					22																	42523558		2202	4300	6502	SO:0001583	missense	1565	exon7			GTGGTGTAGGGCA	M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.1064A>G	22.37:g.42523558T>C	ENSP00000353820:p.Tyr355Cys	Somatic	224	4	0.0178571		WXS	Illumina HiSeq	Phase_I	193	7	0.0362694	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.884011	0.51908	.	.	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640;ENST00000359033;ENST00000542856	T;T;T	0.76186	-1.0;-1.0;-1.0	4.93	-8.43	0.00953	.	0.656947	0.15234	N	0.273223	D	0.88265	0.6390	H	0.96518	3.835	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.81914	0.995;0.976;0.995	D	0.91542	0.5250	10	0.87932	D	0	.	18.217	0.89889	0.1595:0.0:0.0:0.8405	.	355;304;355	C1ID54;Q6NXU8;Q6NWU0	.;.;.	C	355;355;301;304;304	ENSP00000353820:Y355C;ENSP00000374620:Y355C;ENSP00000351927:Y304C	ENSP00000351927:Y304C	Y	-	2	0	CYP2D6	40853502	0.995000	0.38212	0.872000	0.34217	0.407000	0.30961	0.270000	0.18607	-1.565000	0.01676	-0.509000	0.04479	TAC	T|0.999;C|0.001	0.001	weak		0.607	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
CABP5	56344	hgsc.bcm.edu	37	19	48537585	48537585	+	Missense_Mutation	SNP	A	A	G	rs3745746	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:48537585A>G	ENST00000293255.2	-	5	513	c.383T>C	c.(382-384)gTg>gCg	p.V128A		NM_019855.4	NP_062829.1	Q9NP86	CABP5_HUMAN	calcium binding protein 5	128	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.		V -> A (in dbSNP:rs3745746).		signal transduction (GO:0007165)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(3)|prostate(2)|skin(2)	11		all_cancers(25;1.86e-08)|all_lung(116;1.14e-06)|all_epithelial(76;1.16e-06)|Lung NSC(112;2.54e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;4.09e-05)|all cancers(93;0.000322)|Epithelial(262;0.01)|GBM - Glioblastoma multiforme(486;0.058)		CTGTAGCTCCACCAGGGTGAT	0.522													g|||	1113	0.222244	0.1399	0.281	5008	,	,		16208	0.0645		0.3569	False		,,,				2504	0.316				p.V128A		Atlas-SNP	.											.	CABP5	28	.	0			c.T383C						PASS	.	G	ALA/VAL	756,3650	754.6+/-412.5	68,620,1515	59.0	56.0	57.0		383	-5.2	0.3	19	dbSNP_107	57	3333,5267	644.2+/-400.0	647,2039,1614	yes	missense	CABP5	NM_019855.4	64	715,2659,3129	GG,GA,AA		38.7558,17.1584,31.4393	benign	128/174	48537585	4089,8917	2203	4300	6503	SO:0001583	missense	56344	exon5			AGCTCCACCAGGG	AF169159	CCDS12709.1	19q13.33	2014-08-12			ENSG00000105507	ENSG00000105507		"""EF-hand domain containing"""	13714	protein-coding gene	gene with protein product		607315	"""calcium binding protein 3"""	CABP3		10625670	Standard	NM_019855		Approved	CaBP3	uc002phu.2	Q9NP86	OTTHUMG00000183139	ENST00000293255.2:c.383T>C	19.37:g.48537585A>G	ENSP00000293255:p.Val128Ala	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_019855	A0AUY4	Missense_Mutation	SNP	ENST00000293255.2	37	CCDS12709.1	508	0.2326007326007326	70	0.14227642276422764	120	0.3314917127071823	52	0.09090909090909091	266	0.35092348284960423	G	0.023	-1.402989	0.01165	0.171584	0.387558	ENSG00000105507	ENST00000293255	T	0.68765	-0.35	5.01	-5.16	0.02857	EF-hand-like domain (1);	0.442432	0.23732	N	0.045101	T	0.00012	0.0000	N	0.00300	-1.685	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.17258	-1.0375	9	0.02654	T	1	-9.6053	8.8389	0.35129	0.3967:0.2939:0.3094:0.0	rs3745746;rs17663756;rs52805288;rs60664550;rs3745746	128	Q9NP86	CABP5_HUMAN	A	128	ENSP00000293255:V128A	ENSP00000293255:V128A	V	-	2	0	CABP5	53229397	0.000000	0.05858	0.314000	0.25224	0.351000	0.29236	-2.822000	0.00748	-0.593000	0.05844	-0.930000	0.02707	GTG	G|0.275;N|0.000	0.275	strong		0.522	CABP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465212.1	NM_019855	
BDKRB2	624	hgsc.bcm.edu	37	14	96707457	96707457	+	Silent	SNP	A	A	G	rs5224	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:96707457A>G	ENST00000306005.3	+	3	988	c.792A>G	c.(790-792)acA>acG	p.T264T	RP11-404P21.8_ENST00000553811.1_Intron|BDKRB2_ENST00000539359.1_Silent_p.T237T|BDKRB2_ENST00000554311.1_Silent_p.T264T|BDKRB2_ENST00000542454.2_Silent_p.T237T	NM_000623.3	NP_000614.1	P30411	BKRB2_HUMAN	bradykinin receptor B2	264					arachidonic acid secretion (GO:0050482)|blood circulation (GO:0008015)|cell surface receptor signaling pathway (GO:0007166)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|metabolic process (GO:0008152)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator (GO:1902239)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of vascular permeability (GO:0043114)|regulation of vasoconstriction (GO:0019229)|response to salt stress (GO:0009651)|smooth muscle contraction (GO:0006939)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bradykinin receptor activity (GO:0004947)|phosphatidylinositol phospholipase C activity (GO:0004435)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(5)|lung(7)|ovary(3)|skin(1)	24		all_cancers(154;0.0678)|Melanoma(154;0.155)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.226)	Icatibant(DB06196)	AGATCCAGACAGAGAGGAGGG	0.567													G|||	4302	0.859026	0.9947	0.9063	5008	,	,		23569	0.8194		0.832	False		,,,				2504	0.7106				p.T264T		Atlas-SNP	.											BDKRB2,NS,carcinoma,+1,1	BDKRB2	56	1	0			c.A792G						PASS	.	G		4276,130	94.8+/-133.5	2074,128,1	80.0	76.0	77.0		792	-5.6	0.7	14	dbSNP_52	77	7202,1398	270.2+/-288.9	3011,1180,109	no	coding-synonymous	BDKRB2	NM_000623.3		5085,1308,110	GG,GA,AA		16.2558,2.9505,11.7484		264/392	96707457	11478,1528	2203	4300	6503	SO:0001819	synonymous_variant	624	exon3			CCAGACAGAGAGG	S56772	CCDS9942.1	14q32.1-q32.2	2012-08-08				ENSG00000168398		"""GPCR / Class A : Bradykinin receptors"""	1030	protein-coding gene	gene with protein product		113503				7916737	Standard	NM_000623		Approved	BK-2	uc010avm.1	P30411		ENST00000306005.3:c.792A>G	14.37:g.96707457A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_000623		Silent	SNP	ENST00000306005.3	37	CCDS9942.1																																																																																			A|0.123;G|0.877	0.877	strong		0.567	BDKRB2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413294.1		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067063	79067063	+	Silent	SNP	A	A	G	rs117662146	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:79067063A>G	ENST00000388820.4	-	12	1989	c.1779T>C	c.(1777-1779)ccT>ccC	p.P593P	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	593	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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 chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.P593P(2)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GGCGGCCAGCAGGGCAGGCCT	0.642																																					p.P593P		Atlas-SNP	.											ADAMTS7,NS,carcinoma,0,2	ADAMTS7	142	2	2	Substitution - coding silent(2)	prostate(2)	c.T1779C						scavenged	.						51.0	58.0	55.0					15																	79067063		2196	4293	6489	SO:0001819	synonymous_variant	11173	exon12			GCCAGCAGGGCAG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.1779T>C	15.37:g.79067063A>G		Somatic	96	2	0.0208333		WXS	Illumina HiSeq	Phase_I	72	10	0.138889	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			A|0.998;G|0.002	0.002	strong		0.642	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
SUN2	25777	hgsc.bcm.edu	37	22	39134207	39134207	+	Missense_Mutation	SNP	C	C	T	rs2072797	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39134207C>T	ENST00000405510.1	-	18	2369	c.2011G>A	c.(2011-2013)Ggc>Agc	p.G671S	SUN2_ENST00000411587.2_Missense_Mutation_p.G660S|SUN2_ENST00000216064.4_Missense_Mutation_p.G671S|RP3-508I15.14_ENST00000416406.1_RNA|RP3-508I15.20_ENST00000609428.1_RNA|RP3-508I15.18_ENST00000420118.1_RNA|SUN2_ENST00000406622.1_Missense_Mutation_p.G671S|SUN2_ENST00000405018.1_Missense_Mutation_p.G692S|RP3-508I15.19_ENST00000418803.1_RNA	NM_001199580.1	NP_001186509.1	Q9UH99	SUN2_HUMAN	Sad1 and UNC84 domain containing 2	671	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.		G -> S (in dbSNP:rs2072797). {ECO:0000269|PubMed:15489334}.		centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|mitotic spindle organization (GO:0007052)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)	condensed nuclear chromosome (GO:0000794)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|nuclear chromosome, telomeric region (GO:0000784)|nuclear envelope (GO:0005635)|nuclear inner membrane (GO:0005637)|nuclear membrane (GO:0031965)|SUN-KASH complex (GO:0034993)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|microtubule binding (GO:0008017)	p.G671S(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)|stomach(1)	15						ATAGGCTCGCCGTCCTGATCG	0.597													C|||	476	0.0950479	0.0068	0.0519	5008	,	,		21248	0.1677		0.1312	False		,,,				2504	0.1329				p.G692S		Atlas-SNP	.											SUN2,NS,carcinoma,0,1	SUN2	59	1	1	Substitution - Missense(1)	stomach(1)	c.G2074A	GRCh37	CM076582	SUN2	M	rs2072797	scavenged	.	C	SER/GLY,SER/GLY,SER/GLY	94,4312	75.7+/-113.9	2,90,2111	152.0	114.0	127.0		2074,2011,2011	4.9	1.0	22	dbSNP_96	127	977,7623	213.4+/-253.3	56,865,3379	yes	missense,missense,missense	SUN2	NM_001199579.1,NM_001199580.1,NM_015374.2	56,56,56	58,955,5490	TT,TC,CC		11.3605,2.1335,8.2347	probably-damaging,probably-damaging,probably-damaging	692/739,671/718,671/718	39134207	1071,11935	2203	4300	6503	SO:0001583	missense	25777	exon17			GCTCGCCGTCCTG	AF202723	CCDS13978.1, CCDS56231.1	22q12-q13	2010-05-18	2010-05-18	2010-01-27	ENSG00000100242	ENSG00000100242			14210	protein-coding gene	gene with protein product		613569	"""unc-84 homolog B (C. elegans)"""	UNC84B		10508607, 10375507	Standard	NM_015374		Approved		uc010gxq.2	Q9UH99	OTTHUMG00000151031	ENST00000405510.1:c.2011G>A	22.37:g.39134207C>T	ENSP00000385740:p.Gly671Ser	Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001199579	B0QY62|O75156|Q2NKN8|Q2T9F7|Q504T5|Q6B4H1|Q7Z3E3	Missense_Mutation	SNP	ENST00000405510.1	37	CCDS13978.1	248	0.11355311355311355	5	0.01016260162601626	24	0.06629834254143646	111	0.19405594405594406	108	0.1424802110817942	C	24.8	4.573738	0.86542	0.021335	0.113605	ENSG00000100242	ENST00000405510;ENST00000216064;ENST00000405018;ENST00000406622;ENST00000411587;ENST00000455125	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	4.89	4.89	0.63831	Sad1/UNC-like, C-terminal (2);	0.219873	0.37437	N	0.002081	T	0.00178	0.0005	M	0.76433	2.335	0.09310	P	0.999999627684	P;P;P;D;B	0.54964	0.846;0.666;0.666;0.969;0.355	B;B;B;P;B	0.59595	0.359;0.257;0.257;0.86;0.171	T	0.00166	-1.1965	9	0.48119	T	0.1	-22.721	17.7536	0.88442	0.0:1.0:0.0:0.0	rs2072797;rs59334882;rs2072797	660;706;671;692;671	B4DIU6;B4E2A6;Q2T9F7;B0QY62;Q9UH99	.;.;.;.;SUN2_HUMAN	S	671;671;692;671;660;144	ENSP00000385740:G671S;ENSP00000216064:G671S;ENSP00000385616:G692S;ENSP00000383992:G671S;ENSP00000395601:G660S;ENSP00000390154:G144S	ENSP00000216064:G671S	G	-	1	0	SUN2	37464153	1.000000	0.71417	0.990000	0.47175	0.928000	0.56348	5.529000	0.67135	2.284000	0.76573	0.597000	0.82753	GGC	C|0.906;T|0.094	0.094	strong		0.597	SUN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321057.1	XM_039332	
COG5	10466	hgsc.bcm.edu	37	7	106897237	106897237	+	Intron	SNP	A	A	C	rs17349904	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:106897237A>C	ENST00000347053.3	-	15	1830				COG5_ENST00000393603.2_Silent_p.V594V|COG5_ENST00000297135.3_Silent_p.V594V	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5						intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						GACTGGAAACAACCTAGAACA	0.338													A|||	650	0.129792	0.0136	0.121	5008	,	,		16049	0.1587		0.2028	False		,,,				2504	0.1881				p.V594V		Atlas-SNP	.											.	COG5	78	.	0			c.T1782G						PASS	.	A	,,	220,4186	131.0+/-167.6	6,208,1989	78.0	78.0	78.0		1782,1782,	-3.4	1.0	7	dbSNP_123	78	1847,6753	326.9+/-317.6	207,1433,2660	no	coding-synonymous,coding-synonymous,intron	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	,,	213,1641,4649	CC,CA,AA		21.4767,4.9932,15.8927	,,	594/824,594/861,	106897237	2067,10939	2203	4300	6503	SO:0001627	intron_variant	10466	exon16			GGAAACAACCTAG	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1779+1480T>G	7.37:g.106897237A>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	47	32	0.680851	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Silent	SNP	ENST00000347053.3	37	CCDS5743.1																																																																																			A|0.851;C|0.149	0.149	strong		0.338	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
MUC16	94025	hgsc.bcm.edu	37	19	9066874	9066874	+	Missense_Mutation	SNP	G	G	T	rs12609150	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9066874G>T	ENST00000397910.4	-	3	20775	c.20572C>A	c.(20572-20574)Cca>Aca	p.P6858T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6860	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCAAATTTGGAGGTGAACTG	0.493													g|||	1007	0.201078	0.0946	0.2824	5008	,	,		23077	0.3254		0.167	False		,,,				2504	0.1943				p.P6858T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C20572A						PASS	.	G	THR/PRO	425,3671		18,389,1641	163.0	154.0	157.0		20572	-3.0	0.0	19	dbSNP_120	157	1520,6886		138,1244,2821	yes	missense	MUC16	NM_024690.2	38	156,1633,4462	TT,TG,GG		18.0823,10.376,15.5575	probably-damaging	6858/14508	9066874	1945,10557	2048	4203	6251	SO:0001583	missense	94025	exon3			AATTTGGAGGTGA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20572C>A	19.37:g.9066874G>T	ENSP00000381008:p.Pro6858Thr	Somatic	321	1	0.00311526		WXS	Illumina HiSeq	Phase_I	322	159	0.493789	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	479	0.21932234432234432	56	0.11382113821138211	92	0.2541436464088398	205	0.3583916083916084	126	0.1662269129287599	g	2.557	-0.302824	0.05495	0.10376	0.180823	ENSG00000181143	ENST00000397910	T	0.26067	1.76	2.12	-2.96	0.05547	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	.	.	.	B	0.27351	0.176	B	0.19946	0.027	T	0.45381	-0.9265	8	0.87932	D	0	.	2.1735	0.03856	0.4264:0.0:0.3309:0.2427	rs12609150;rs52836809;rs12609150	6858	B5ME49	.	T	6858	ENSP00000381008:P6858T	ENSP00000381008:P6858T	P	-	1	0	MUC16	8927874	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.960000	0.03849	-0.553000	0.06158	-0.513000	0.04457	CCA	G|0.786;T|0.214	0.214	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ACAT2	39	hgsc.bcm.edu	37	6	160196343	160196343	+	Missense_Mutation	SNP	A	A	G	rs25683	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:160196343A>G	ENST00000367048.4	+	5	2392	c.632A>G	c.(631-633)aAa>aGa	p.K211R	ACAT2_ENST00000472052.1_3'UTR|ACAT2_ENST00000541436.1_Missense_Mutation_p.K240R	NM_005891.2	NP_005882.2	Q9BWD1	THIC_HUMAN	acetyl-CoA acetyltransferase 2	211			K -> R (in dbSNP:rs25683). {ECO:0000269|PubMed:15489334}.		lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acetyl-CoA C-acetyltransferase activity (GO:0003985)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(1)	9		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.51e-18)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		TCAACTAGAAAAGGTGAGTAT	0.358													A|||	1829	0.365216	0.1679	0.5965	5008	,	,		22141	0.1637		0.5457	False		,,,				2504	0.4898				p.K211R		Atlas-SNP	.											.	ACAT2	32	.	0			c.A632G						PASS	.	A	ARG/LYS	969,3437	358.9+/-314.6	112,745,1346	95.0	86.0	89.0		632	5.7	1.0	6	dbSNP_72	89	4940,3660	620.1+/-397.0	1451,2038,811	yes	missense	ACAT2	NM_005891.2	26	1563,2783,2157	GG,GA,AA		42.5581,21.9927,45.4329	possibly-damaging	211/398	160196343	5909,7097	2203	4300	6503	SO:0001583	missense	39	exon5			CTAGAAAAGGTGA	AF356877	CCDS5268.1	6q25.3	2014-05-19	2010-04-30		ENSG00000120437	ENSG00000120437	2.3.1.9		94	protein-coding gene	gene with protein product	"""acetoacetyl Coenzyme A thiolase"""	100678	"""acetyl-Coenzyme A acetyltransferase 2 (acetoacetyl Coenzyme A thiolase)"", ""acetyl-Coenzyme A acetyltransferase 2"""			2475872	Standard	NM_005891		Approved		uc010kjy.3	Q9BWD1	OTTHUMG00000015935	ENST00000367048.4:c.632A>G	6.37:g.160196343A>G	ENSP00000356015:p.Lys211Arg	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_005891	B7Z233|E1P5B1|Q16146|Q5TCL7|Q8TDM4	Missense_Mutation	SNP	ENST00000367048.4	37	CCDS5268.1	798	0.36538461538461536	83	0.16869918699186992	207	0.5718232044198895	85	0.1486013986013986	423	0.558047493403694	A	29.2	4.986498	0.93044	0.219927	0.574419	ENSG00000120437	ENST00000367048;ENST00000541436	D;D	0.91407	-2.84;-2.84	5.65	5.65	0.86999	Thiolase-like, subgroup (1);Thiolase, N-terminal (1);Thiolase-like (1);	0.089722	0.85682	D	0.000000	D	0.88941	0.6574	L	0.53617	1.68	0.09310	P	0.9999999753599	D;P	0.54964	0.969;0.916	P;P	0.49752	0.621;0.621	D	0.90299	0.4328	9	0.56958	D	0.05	0.3009	15.8801	0.79197	1.0:0.0:0.0:0.0	rs25683;rs1127093;rs2070083;rs2273829;rs11540136;rs11759570;rs17398832;rs17849305;rs41318625;rs52807819;rs57687231;rs25683	240;211	B7Z233;Q9BWD1	.;THIC_HUMAN	R	211;240	ENSP00000356015:K211R;ENSP00000437850:K240R	ENSP00000356015:K211R	K	+	2	0	ACAT2	160116333	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.691000	0.91279	2.166000	0.68216	0.460000	0.39030	AAA	A|0.593;G|0.407	0.407	strong		0.358	ACAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042912.1	NM_005891	
ZNF639	51193	hgsc.bcm.edu	37	3	179051472	179051472	+	Silent	SNP	A	A	G	rs35983049	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:179051472A>G	ENST00000326361.3	+	7	1165	c.720A>G	c.(718-720)gaA>gaG	p.E240E	ZNF639_ENST00000484866.1_Silent_p.E240E|ZNF639_ENST00000496856.1_Silent_p.E240E|ZNF639_ENST00000466663.1_3'UTR	NM_016331.1	NP_057415.1	Q9UID6	ZN639_HUMAN	zinc finger protein 639	240					negative regulation by host of viral transcription (GO:0043922)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of cell growth (GO:0030307)|transcription, DNA-templated (GO:0006351)|viral entry into host cell (GO:0046718)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein self-association (GO:0043621)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(10)|urinary_tract(1)	16	all_cancers(143;7.9e-17)|Ovarian(172;0.0172)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;5.78e-26)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0923)			TATGCAAGGAAAGTTTCTCTA	0.343													A|||	441	0.0880591	0.0643	0.0879	5008	,	,		25760	0.0714		0.165	False		,,,				2504	0.0583				p.E240E		Atlas-SNP	.											.	ZNF639	45	.	0			c.A720G						PASS	.	A		355,4051	180.8+/-209.0	11,333,1859	79.0	73.0	75.0		720	1.8	1.0	3	dbSNP_126	75	1398,7202	270.8+/-289.2	111,1176,3013	no	coding-synonymous	ZNF639	NM_016331.1		122,1509,4872	GG,GA,AA		16.2558,8.0572,13.4784		240/486	179051472	1753,11253	2203	4300	6503	SO:0001819	synonymous_variant	51193	exon7			CAAGGAAAGTTTC	BC020500	CCDS3227.1	3q27.1	2010-03-26			ENSG00000121864	ENSG00000121864		"""Zinc fingers, C2H2-type"""	30950	protein-coding gene	gene with protein product	"""zinc finger amplified in esophageal squamous cell carcinomas 1"""					14522885	Standard	NM_016331		Approved	ANC-2H01, ZASC1	uc003fjr.1	Q9UID6	OTTHUMG00000157439	ENST00000326361.3:c.720A>G	3.37:g.179051472A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_016331	A9X3Z9|D3DNR3	Silent	SNP	ENST00000326361.3	37	CCDS3227.1																																																																																			A|0.877;G|0.123	0.123	strong		0.343	ZNF639-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348855.1	NM_016331	
GALNT4	8693	hgsc.bcm.edu	37	12	89917037	89917037	+	Silent	SNP	G	G	A	rs2230282	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:89917037G>A	ENST00000529983.2	-	1	1546	c.1290C>T	c.(1288-1290)aaC>aaT	p.N430N	POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000393179.4_Intron|GALNT4_ENST00000413530.1_Silent_p.N258N|POC1B-GALNT4_ENST00000548729.1_Silent_p.N427N	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	430					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						TAGGAAAAACGTTTTTCAAAT	0.408													G|||	358	0.0714856	0.0408	0.0821	5008	,	,		19584	0.0228		0.1282	False		,,,				2504	0.0971				p.N430N		Atlas-SNP	.											.	GALNT4	38	.	0			c.C1290T						PASS	.	G	,,,,	170,3510		1,168,1671	87.0	84.0	85.0		,1281,774,1290,	-10.7	0.1	12	dbSNP_98	85	924,7268		45,834,3217	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,,,,	46,1002,4888	AA,AG,GG		11.2793,4.6196,9.215	,,,,	,427/576,258/407,430/579,	89917037	1094,10778	1840	4096	5936	SO:0001819	synonymous_variant	8693	exon1			AAAAACGTTTTTC	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1290C>T	12.37:g.89917037G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_003774	B2R775|B4DMX6|O00208	Silent	SNP	ENST00000529983.2	37	CCDS53817.1																																																																																			G|0.924;A|0.076	0.076	strong		0.408	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
FDFT1	2222	hgsc.bcm.edu	37	8	11689119	11689119	+	Silent	SNP	G	G	C	rs9205	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11689119G>C	ENST00000220584.4	+	7	1194	c.972G>C	c.(970-972)ctG>ctC	p.L324L	FDFT1_ENST00000525777.1_Silent_p.L239L|FDFT1_ENST00000528643.1_Silent_p.L239L|FDFT1_ENST00000528812.1_Silent_p.L260L|FDFT1_ENST00000525900.1_Silent_p.L317L|FDFT1_ENST00000530664.1_Silent_p.L260L|FDFT1_ENST00000443614.2_Silent_p.L281L|FDFT1_ENST00000446331.2_3'UTR|FDFT1_ENST00000538689.1_Silent_p.L213L	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	324					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		CAGTGACCCTGATGATGGATG	0.443													G|||	1537	0.306909	0.084	0.2824	5008	,	,		19543	0.7252		0.2097	False		,,,				2504	0.2945				p.L324L		Atlas-SNP	.											.	FDFT1	25	.	0			c.G972C						PASS	.	G		506,3900	234.2+/-247.1	20,466,1717	212.0	198.0	203.0		972	-9.1	0.2	8	dbSNP_52	203	1801,6799	324.6+/-316.5	208,1385,2707	no	coding-synonymous	FDFT1	NM_004462.3		228,1851,4424	CC,CG,GG		20.9419,11.4843,17.738		324/418	11689119	2307,10699	2203	4300	6503	SO:0001819	synonymous_variant	2222	exon7			GACCCTGATGATG	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.972G>C	8.37:g.11689119G>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Silent	SNP	ENST00000220584.4	37	CCDS5985.1																																																																																			G|0.773;C|0.227	0.227	strong		0.443	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
SFSWAP	6433	hgsc.bcm.edu	37	12	132241162	132241162	+	Missense_Mutation	SNP	A	A	G	rs145713017	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132241162A>G	ENST00000261674.4	+	11	1834	c.1693A>G	c.(1693-1695)Acc>Gcc	p.T565A	SFSWAP_ENST00000541286.1_Missense_Mutation_p.T565A|RP11-495K9.5_ENST00000537032.1_lincRNA	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	565					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						GTCCAGTAAGACCGTCCCGGA	0.607													A|||	33	0.00658946	0.0	0.0029	5008	,	,		18321	0.0		0.007	False		,,,				2504	0.0245				p.T565A		Atlas-SNP	.											.	SFSWAP	69	.	0			c.A1693G						PASS	.	A	ALA/THR	3,4403	8.1+/-20.4	0,3,2200	83.0	59.0	67.0		1693	-3.7	0.0	12	dbSNP_134	67	44,8556	29.0+/-79.6	0,44,4256	yes	missense	SFSWAP	NM_004592.2	58	0,47,6456	GG,GA,AA		0.5116,0.0681,0.3614	benign	565/952	132241162	47,12959	2203	4300	6503	SO:0001583	missense	6433	exon11			AGTAAGACCGTCC	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.1693A>G	12.37:g.132241162A>G	ENSP00000261674:p.Thr565Ala	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	CCDS9273.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	5.631	0.301084	0.10678	6.81E-4	0.005116	ENSG00000061936	ENST00000261674;ENST00000544623;ENST00000535236;ENST00000541286	T;T;T	0.22539	2.98;1.95;2.99	5.34	-3.66	0.04489	.	1.222960	0.05418	N	0.543757	T	0.07188	0.0182	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.32798	-0.9893	10	0.06236	T	0.91	-4.829	5.5618	0.17148	0.2274:0.0973:0.5789:0.0964	.	565;565	F5H6B8;Q12872	.;SFSWA_HUMAN	A	565;502;358;565	ENSP00000261674:T565A;ENSP00000443045:T358A;ENSP00000437738:T565A	ENSP00000261674:T565A	T	+	1	0	SFSWAP	130807115	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.389000	0.07342	-1.039000	0.03275	-0.444000	0.05651	ACC	A|0.997;G|0.003	0.003	strong		0.607	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
IFNB1	3456	hgsc.bcm.edu	37	9	21077716	21077716	+	Silent	SNP	G	G	A	rs1051922	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:21077716G>A	ENST00000380232.2	-	1	227	c.153C>T	c.(151-153)taC>taT	p.Y51Y		NM_002176.2	NP_002167.1	P01574	IFNB_HUMAN	interferon, beta 1, fibroblast	51					adaptive immune response (GO:0002250)|B cell activation involved in immune response (GO:0002312)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of viral genome replication (GO:0045071)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	12				GBM - Glioblastoma multiforme(5;7.45e-142)|Lung(24;2.42e-17)|LUSC - Lung squamous cell carcinoma(38;7.17e-11)		CCTTGAGGCAGTATTCAAGCC	0.483													A|||	1644	0.328275	0.3979	0.2608	5008	,	,		20472	0.3204		0.3579	False		,,,				2504	0.2597				p.Y51Y		Atlas-SNP	.											.	IFNB1	33	.	0			c.C153T						PASS	.	A		1651,2755	657.8+/-400.3	300,1051,852	69.0	68.0	68.0		153	-8.9	0.0	9	dbSNP_86	68	2819,5781	674.9+/-403.2	472,1875,1953	no	coding-synonymous	IFNB1	NM_002176.2		772,2926,2805	AA,AG,GG		32.7791,37.4716,34.3688		51/188	21077716	4470,8536	2203	4300	6503	SO:0001819	synonymous_variant	3456	exon1			GAGGCAGTATTCA		CCDS6495.1	9p22	2008-07-21			ENSG00000171855	ENSG00000171855		"""Interferons"""	5434	protein-coding gene	gene with protein product		147640		IFNB			Standard	NM_002176		Approved	IFB, IFF	uc003zok.3	P01574	OTTHUMG00000019652	ENST00000380232.2:c.153C>T	9.37:g.21077716G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	113	60	0.530973	NM_002176	Q5VWC9	Silent	SNP	ENST00000380232.2	37	CCDS6495.1																																																																																			G|0.656;N|0.000	.	strong		0.483	IFNB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051881.1	NM_002176	
ARHGEF28	64283	hgsc.bcm.edu	37	5	73144845	73144845	+	Silent	SNP	A	A	G	rs2973568	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:73144845A>G	ENST00000426542.2	+	12	1700	c.1680A>G	c.(1678-1680)tcA>tcG	p.S560S	ARHGEF28_ENST00000296799.4_Silent_p.S247S|ARHGEF28_ENST00000513841.1_3'UTR|ARHGEF28_ENST00000287898.5_Silent_p.S560S|ARHGEF28_ENST00000545377.1_Silent_p.S560S|ARHGEF28_ENST00000437974.1_Silent_p.S560S|ARHGEF28_ENST00000296794.6_Silent_p.S560S|ARHGEF28_ENST00000513042.2_Silent_p.S560S			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	560					central nervous system neuron axonogenesis (GO:0021955)|intracellular signal transduction (GO:0035556)|neurofilament cytoskeleton organization (GO:0060052)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|RNA binding (GO:0003723)										ATTCTTGCTCATCACCCAAAA	0.323													a|||	3387	0.676318	0.9531	0.5937	5008	,	,		17198	0.5109		0.5577	False		,,,				2504	0.6534				p.S560S		Atlas-SNP	.											NP_001073948_1,NS,carcinoma,+1,2	.	.	2	0			c.A1680G						PASS	.	G	,	3265,383		1465,335,24	62.0	58.0	59.0		1680,1680	-1.1	1.0	5	dbSNP_101	59	4669,3519		1357,1955,782	no	coding-synonymous,coding-synonymous	RGNEF	NM_001080479.2,NM_001177693.1	,	2822,2290,806	GG,GA,AA		42.9775,10.4989,32.9672	,	560/1732,560/1706	73144845	7934,3902	1824	4094	5918	SO:0001819	synonymous_variant	64283	exon13			TTGCTCATCACCC		CCDS47231.1, CCDS47231.2, CCDS54870.1, CCDS58957.1	5q13.2	2012-08-08			ENSG00000214944	ENSG00000214944			30322	protein-coding gene	gene with protein product		612790				9199174, 11058585	Standard	NM_001177693		Approved	RGNEF, p190RhoGEF, RIP2	uc010izf.3	Q8N1W1	OTTHUMG00000162454	ENST00000426542.2:c.1680A>G	5.37:g.73144845A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Silent	SNP	ENST00000426542.2	37	CCDS54870.1																																																																																			A|0.346;G|0.654	0.654	strong		0.323	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1		
STK32A	202374	hgsc.bcm.edu	37	5	146619206	146619206	+	Silent	SNP	G	G	C	rs4705132	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:146619206G>C	ENST00000397936.3	+	2	342	c.9G>C	c.(7-9)gcG>gcC	p.A3A	STK32A_ENST00000541094.1_Silent_p.A3A|STK32A_ENST00000398521.3_Silent_p.A3A|STK32A_ENST00000398523.3_Silent_p.A3A	NM_001112724.1	NP_001106195.1	Q8WU08	ST32A_HUMAN	serine/threonine kinase 32A	3							ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCATGGGAGCGAACACTTCAA	0.403													C|||	2606	0.520367	0.6384	0.732	5008	,	,		18521	0.3135		0.5646	False		,,,				2504	0.3783				p.A3A		Atlas-SNP	.											.	STK32A	54	.	0			c.G9C						PASS	.	C	,	2305,1373		726,853,260	61.0	58.0	59.0		9,9	3.0	1.0	5	dbSNP_111	59	4583,3611		1275,2033,789	no	coding-synonymous,coding-synonymous	STK32A	NM_001112724.1,NM_145001.3	,	2001,2886,1049	CC,CG,GG		44.0688,37.3301,41.9811	,	3/397,3/167	146619206	6888,4984	1839	4097	5936	SO:0001819	synonymous_variant	202374	exon2			GGGAGCGAACACT		CCDS47299.1, CCDS75351.1	5q32	2008-02-05			ENSG00000169302	ENSG00000169302			28317	protein-coding gene	gene with protein product						12477932	Standard	NM_001112724		Approved	MGC22688, YANK1	uc010jgn.1	Q8WU08	OTTHUMG00000163411	ENST00000397936.3:c.9G>C	5.37:g.146619206G>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	102	53	0.519608	NM_145001	B3KSY0	Silent	SNP	ENST00000397936.3	37	CCDS47299.1																																																																																			G|0.476;C|0.523	0.523	strong		0.403	STK32A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373306.1	NM_145001	
SERPINA1	5265	hgsc.bcm.edu	37	14	94849201	94849201	+	Missense_Mutation	SNP	C	C	T	rs709932	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94849201C>T	ENST00000448921.1	-	4	946	c.374G>A	c.(373-375)cGt>cAt	p.R125H	SERPINA1_ENST00000393088.4_Missense_Mutation_p.R125H|SERPINA1_ENST00000437397.1_Missense_Mutation_p.R125H|SERPINA1_ENST00000555289.1_5'Flank|SERPINA1_ENST00000440909.1_Missense_Mutation_p.R125H|SERPINA1_ENST00000404814.4_Missense_Mutation_p.R125H|SERPINA1_ENST00000402629.1_Missense_Mutation_p.R125H|SERPINA1_ENST00000449399.3_Missense_Mutation_p.R125H|SERPINA1_ENST00000355814.4_Missense_Mutation_p.R125H|SERPINA1_ENST00000393087.4_Missense_Mutation_p.R125H	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	125			R -> H (in M2; associated with D-400; dbSNP:rs709932).		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		GTTGAGGGTACGGAGGAGTTC	0.552													C|||	804	0.160543	0.0197	0.1138	5008	,	,		17932	0.2282		0.1561	False		,,,				2504	0.319				p.R125H		Atlas-SNP	.											.	SERPINA1	51	.	0			c.G374A	GRCh37	CM900182	SERPINA1	M	rs709932	PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	160,4246	109.1+/-147.4	1,158,2044	58.0	57.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	374,374,374,374,374,374,374,374,374,374,374	-2.8	0.0	14	dbSNP_86	57	1421,7179	273.7+/-290.8	117,1187,2996	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	SERPINA1	NM_000295.4,NM_001002235.2,NM_001002236.2,NM_001127700.1,NM_001127701.1,NM_001127702.1,NM_001127703.1,NM_001127704.1,NM_001127705.1,NM_001127706.1,NM_001127707.1	29,29,29,29,29,29,29,29,29,29,29	118,1345,5040	TT,TC,CC		16.5233,3.6314,12.1559	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	125/419,125/419,125/419,125/419,125/419,125/419,125/419,125/419,125/419,125/419,125/419	94849201	1581,11425	2203	4300	6503	SO:0001583	missense	5265	exon4			AGGGTACGGAGGA	X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"""Serine (or cysteine) peptidase inhibitors"""	8941	protein-coding gene	gene with protein product	"""protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"""	107400	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"""	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.374G>A	14.37:g.94849201C>T	ENSP00000416066:p.Arg125His	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	22	0.360656	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Missense_Mutation	SNP	ENST00000448921.1	37	CCDS9925.1	285	0.1304945054945055	9	0.018292682926829267	48	0.13259668508287292	124	0.21678321678321677	104	0.13720316622691292	C	1.988	-0.432510	0.04669	0.036314	0.165233	ENSG00000197249	ENST00000440909;ENST00000448921;ENST00000437397;ENST00000355814;ENST00000393087;ENST00000393088;ENST00000404814;ENST00000449399;ENST00000402629;ENST00000554720;ENST00000556091;ENST00000557492	D;D;D;D;D;D;D;D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77;-1.77	5.62	-2.82	0.05787	Serpin domain (3);	1.216040	0.05869	N	0.624379	T	0.00039	0.0001	N	0.02674	-0.535	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.07424	-1.0773	9	0.05525	T	0.97	.	7.3598	0.26739	0.0:0.2499:0.1816:0.5685	rs709932;rs3189606;rs52795514;rs57636922;rs709932	125;125	P01009-2;P01009	.;A1AT_HUMAN	H	125;125;125;125;125;125;125;125;125;39;125;125	ENSP00000390299:R125H;ENSP00000416066:R125H;ENSP00000408474:R125H;ENSP00000348068:R125H;ENSP00000376802:R125H;ENSP00000376803:R125H;ENSP00000385960:R125H;ENSP00000416354:R125H;ENSP00000386094:R125H;ENSP00000450561:R39H;ENSP00000452169:R125H;ENSP00000452452:R125H	ENSP00000348068:R125H	R	-	2	0	SERPINA1	93918954	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-0.755000	0.04782	-0.129000	0.11620	-1.199000	0.01669	CGT	T|0.129;G|0.004	0.129	strong		0.552	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235	
TTC21A	199223	hgsc.bcm.edu	37	3	39161456	39161456	+	Missense_Mutation	SNP	G	G	A	rs1274972	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:39161456G>A	ENST00000431162.2	+	8	1003	c.869G>A	c.(868-870)aGg>aAg	p.R290K	TTC21A_ENST00000301819.6_Missense_Mutation_p.R290K|TTC21A_ENST00000440121.1_Missense_Mutation_p.R241K			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	290			R -> K (in dbSNP:rs1274972).							NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		CTAGAGACAAGGGAACCCGAA	0.458													G|||	2282	0.455671	0.8495	0.3429	5008	,	,		18365	0.2738		0.334	False		,,,				2504	0.316				p.R290K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G869A						PASS	.	G	LYS/ARG,LYS/ARG	2803,953		1044,715,119	114.0	123.0	120.0		722,869	1.8	0.4	3	dbSNP_87	120	2777,5435		486,1805,1815	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	26,26	1530,2520,1934	AA,AG,GG		33.8164,25.3727,46.6243	benign,benign	241/1273,290/1321	39161456	5580,6388	1878	4106	5984	SO:0001583	missense	199223	exon8			AGACAAGGGAACC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.869G>A	3.37:g.39161456G>A	ENSP00000398211:p.Arg290Lys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	150	60	0.4	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	959	0.4391025641025641	410	0.8333333333333334	133	0.3674033149171271	166	0.2902097902097902	250	0.32981530343007914	G	3.931	-0.016256	0.07681	0.746273	0.338164	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.34472	1.36;1.36;2.31	5.67	1.76	0.24704	.	0.359920	0.28989	N	0.013481	T	0.00012	0.0000	L	0.33485	1.01	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.002	B;B;B	0.14578	0.006;0.011;0.005	T	0.13872	-1.0493	9	0.27785	T	0.31	-0.8765	6.5884	0.22634	0.2034:0.2446:0.552:0.0	rs1274972;rs61530584;rs1274972	241;290;290	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	290;282;290;241	ENSP00000301819:R290K;ENSP00000398211:R290K;ENSP00000410882:R241K	ENSP00000301819:R290K	R	+	2	0	TTC21A	39136460	0.007000	0.16637	0.354000	0.25760	0.288000	0.27193	0.778000	0.26732	0.315000	0.23110	-0.175000	0.13238	AGG	G|0.555;A|0.445	0.445	strong		0.458	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
SCG2	7857	hgsc.bcm.edu	37	2	224463164	224463164	+	Silent	SNP	G	G	A	rs16864975	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:224463164G>A	ENST00000305409.2	-	2	1069	c.837C>T	c.(835-837)aaC>aaT	p.N279N		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0	Interaction with FANCD2.		E -> A (in parathyroid tumor). {ECO:0000269|PubMed:11034102}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		TCATCTCATCGTTGATTTGTT	0.438													g|||	106	0.0211661	0.0	0.0432	5008	,	,		20891	0.0		0.0577	False		,,,				2504	0.0184				p.N279N		Atlas-SNP	.											.	SCG2	99	.	0			c.C837T						PASS	.	A		44,4362	48.2+/-83.0	0,44,2159	173.0	176.0	175.0		837	-2.9	0.1	2	dbSNP_123	175	585,8015	156.0+/-209.9	28,529,3743	no	coding-synonymous	SCG2	NM_003469.4		28,573,5902	AA,AG,GG		6.8023,0.9986,4.8362		279/618	224463164	629,12377	2203	4300	6503	SO:0001819	synonymous_variant	7857	exon2			CTCATCGTTGATT	M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"""secretoneurin"", ""chromogranin C"""	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.837C>T	2.37:g.224463164G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	219	105	0.479452	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000305409.2	37	CCDS2457.1																																																																																			G|0.956;A|0.044	0.044	strong		0.438	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469	
WT1	7490	hgsc.bcm.edu	37	11	32417945	32417945	+	Silent	SNP	T	T	C	rs16754	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:32417945T>C	ENST00000379079.2	-	7	744	c.471A>G	c.(469-471)cgA>cgG	p.R157R	WT1_ENST00000530998.1_Silent_p.R140R|WT1_ENST00000448076.3_Silent_p.R369R|WT1_ENST00000332351.3_Silent_p.R369R	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	301					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.?(2)|p.R301fs*16(2)|p.R302fs*15(2)|p.R301fs*3(1)|p.R301fs*11(1)|p.R302fs*11(1)|p.R301fs*17(1)|p.R301fs*6(1)|p.V300fs*6(1)|p.R301fs*19(1)|p.D299fs*15(1)|p.R301fs*73(1)|p.R302fs*12(1)|p.R302fs*5(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			CAGGCACACGTCGCACATCCT	0.522			"""D, Mis, N, F, S"""	EWSR1	"""Wilms, desmoplastic small round cell tumor"""	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome				C|||	1660	0.33147	0.121	0.3156	5008	,	,		20951	0.6984		0.172	False		,,,				2504	0.4131				p.R369R		Atlas-SNP	.	yes	Rec	yes	"""Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"""	11	11p13	7490	Wilms tumour 1 gene		O	WT1_ENST00000379079,colon,carcinoma,0,7	WT1	744	7	17	Complex - frameshift(9)|Deletion - Frameshift(3)|Insertion - Frameshift(3)|Unknown(2)	haematopoietic_and_lymphoid_tissue(15)|kidney(2)	c.A1107G						PASS	.	C	,,,,	497,3907	780.4+/-414.4	29,439,1734	87.0	77.0	80.0		1056,471,420,1107,1107	-2.8	0.9	11	dbSNP_60	80	1197,7401	763.6+/-407.6	84,1029,3186	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WT1	NM_000378.4,NM_001198551.1,NM_001198552.1,NM_024424.3,NM_024426.4	,,,,	113,1468,4920	CC,CT,TT		13.9218,11.2852,13.0288	,,,,	352/498,157/303,140/289,369/515,369/518	32417945	1694,11308	2202	4299	6501	SO:0001819	synonymous_variant	7490	exon7	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	CACACGTCGCACA		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"""Zinc fingers, C2H2-type"""	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.471A>G	11.37:g.32417945T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Silent	SNP	ENST00000379079.2	37	CCDS55751.1	703	0.3218864468864469	57	0.11585365853658537	104	0.287292817679558	407	0.7115384615384616	135	0.17810026385224276	C	9.160	1.018548	0.19355	0.112852	0.139218	ENSG00000184937	ENST00000527882	.	.	.	6.17	-2.75	0.05914	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.35500	-0.9786	3	.	.	.	.	7.3485	0.26676	0.0:0.3562:0.2657:0.3781	rs16754;rs5030275;rs17846027;rs17859011;rs59880152;rs16754	.	.	.	A	60	.	.	T	-	1	0	WT1	32374521	0.001000	0.12720	0.854000	0.33618	0.876000	0.50452	-1.287000	0.02785	-0.854000	0.04131	-0.119000	0.15052	ACG	T|0.782;C|0.218	0.218	strong		0.522	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378	
OR1S1	219959	hgsc.bcm.edu	37	11	57982763	57982763	+	Missense_Mutation	SNP	A	A	G	rs1993088	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57982763A>G	ENST00000309433.6	+	1	547	c.547A>G	c.(547-549)Aac>Gac	p.N183D		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	183			N -> D (in dbSNP:rs1993088).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.N183D(1)		breast(1)|central_nervous_system(1)|endometrium(24)|kidney(1)|large_intestine(1)|liver(1)|lung(10)|prostate(1)|skin(2)|stomach(3)|urinary_tract(3)	48		Breast(21;0.0589)				GCTCTTCTGTAACCACAACAC	0.463																																					p.N183D		Atlas-SNP	.											OR1S1,NS,carcinoma,0,2	OR1S1	139	2	1	Substitution - Missense(1)	stomach(1)	c.A547G						PASS	.	A	ASP/ASN	839,3563		197,445,1559	211.0	172.0	185.0		547	-1.1	0.0	11	dbSNP_92	185	2540,6040		772,996,2522	no	missense	OR1S1	NM_001004458.1	23	969,1441,4081	GG,GA,AA		29.6037,19.0595,26.0283	benign	183/326	57982763	3379,9603	2201	4290	6491	SO:0001583	missense	219959	exon1			TTCTGTAACCACA	BK004299	CCDS31546.1	11q12.1	2012-08-09			ENSG00000172774	ENSG00000172774		"""GPCR / Class A : Olfactory receptors"""	8227	protein-coding gene	gene with protein product							Standard	NM_001004458		Approved	OST034	uc010rkc.2	Q8NH92	OTTHUMG00000167463	ENST00000309433.6:c.547A>G	11.37:g.57982763A>G	ENSP00000311688:p.Asn183Asp	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	962	0.44047619047619047	111	0.22560975609756098	174	0.48066298342541436	408	0.7132867132867133	269	0.3548812664907652	A	0.009	-1.849961	0.00563	0.190595	0.296037	ENSG00000172774	ENST00000309433	T	0.00241	8.46	3.45	-1.1	0.09872	GPCR, rhodopsin-like superfamily (1);	0.551977	0.16162	N	0.226699	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38286	-0.9668	9	0.37606	T	0.19	.	5.0446	0.14477	0.2795:0.278:0.4425:0.0	rs1993088	183	Q8NH92	OR1S1_HUMAN	D	183	ENSP00000311688:N183D	ENSP00000311688:N183D	N	+	1	0	OR1S1	57739339	0.000000	0.05858	0.017000	0.16124	0.033000	0.12548	0.105000	0.15333	-0.506000	0.06558	-1.305000	0.01319	AAC	A|0.671;G|0.329	0.329	strong		0.463	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
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 GAIIx	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	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	80	36	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	
GLOD4	51031	hgsc.bcm.edu	37	17	685640	685640	+	5'Flank	SNP	G	G	T	rs2273454|rs11546732	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:685640G>T	ENST00000301328.5	-	0	0				GLOD4_ENST00000301329.6_5'Flank|GLOD4_ENST00000536578.1_5'Flank|RNMTL1_ENST00000304478.4_Missense_Mutation_p.A8S			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GGTGAGACCCGCGAGGTTTGT	0.701													G|||	1323	0.264177	0.0809	0.3314	5008	,	,		15716	0.505		0.1988	False		,,,				2504	0.2832				p.A8S		Atlas-SNP	.											RNMTL1,NS,carcinoma,-1,1	RNMTL1	25	1	0			c.G22T						PASS	.	G	SER/ALA	487,3919	217.1+/-235.6	28,431,1744	27.0	31.0	29.0		22	-8.4	0.0	17	dbSNP_100	29	1717,6881	299.0+/-304.2	171,1375,2753	yes	missense	RNMTL1	NM_018146.2	99	199,1806,4497	TT,TG,GG		19.9698,11.0531,16.9486	benign	8/421	685640	2204,10800	2203	4299	6502	SO:0001631	upstream_gene_variant	55178	exon1			AGACCCGCGAGGT	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38			17.37:g.685640G>T	Exception_encountered	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	NM_018146	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	37		565	0.2586996336996337	46	0.09349593495934959	107	0.2955801104972376	254	0.44405594405594406	158	0.20844327176781002	G	12.65	2.002514	0.35320	0.110531	0.199698	ENSG00000171861	ENST00000304478	T	0.17854	2.25	4.97	-8.41	0.00961	.	1.317790	0.04892	N	0.449707	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43327	-0.9398	9	0.07325	T	0.83	.	1.9843	0.03433	0.4602:0.0985:0.1421:0.2992	rs2273454;rs17845293;rs17858127;rs17859517;rs52816295;rs58876583	8	Q9HC36	RMTL1_HUMAN	S	8	ENSP00000306080:A8S	ENSP00000306080:A8S	A	+	1	0	RNMTL1	632390	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.782000	0.04643	-1.851000	0.01168	-0.217000	0.12591	GCG	G|0.803;T|0.197	0.197	strong		0.701	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
MTHFR	4524	hgsc.bcm.edu	37	1	11854476	11854476	+	Missense_Mutation	SNP	T	T	G	rs1801131	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11854476T>G	ENST00000376592.1	-	7	1414	c.1286A>C	c.(1285-1287)gAa>gCa	p.E429A	MTHFR_ENST00000376585.1_Missense_Mutation_p.E470A|MTHFR_ENST00000376583.3_Missense_Mutation_p.E470A|MTHFR_ENST00000376590.3_Missense_Mutation_p.E429A			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	429			E -> A (common polymorphism; thermolabile; decreased activity; decreased risk for adult acute leukemia; dbSNP:rs1801131). {ECO:0000269|PubMed:10536004, ECO:0000269|PubMed:9545395, ECO:0000269|PubMed:9719624, ECO:0000269|Ref.5}.		blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	AAAGACACTTTCTTCACTGGT	0.537													T|||	1249	0.249401	0.1513	0.1513	5008	,	,		21917	0.2192		0.3131	False		,,,				2504	0.4172				p.E429A		Atlas-SNP	.											.	MTHFR	65	.	0			c.A1286C	GRCh37	CM981315	MTHFR	M	rs1801131	PASS	.	T	ALA/GLU	683,3723	289.8+/-280.6	65,553,1585	103.0	111.0	109.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1286	4.7	0.5	1	dbSNP_89	109	2693,5907	432.0+/-357.0	428,1837,2035	yes	missense	MTHFR	NM_005957.4	107	493,2390,3620	GG,GT,TT		31.314,15.5016,25.9573	benign	429/657	11854476	3376,9630	2203	4300	6503	SO:0001583	missense	4524	exon8			ACACTTTCTTCAC	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"""5,10-methylenetetrahydrofolate reductase (NADPH)"""			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.1286A>C	1.37:g.11854476T>G	ENSP00000365777:p.Glu429Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	501	0.22939560439560439	83	0.16869918699186992	65	0.17955801104972377	109	0.19055944055944055	244	0.32189973614775724	T	15.29	2.790872	0.50102	0.155016	0.31314	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78	4.74	4.74	0.60224	.	0.095160	0.64402	D	0.000001	T	0.00012	0.0000	L	0.43701	1.375	0.09310	P	0.99999834978	B;P	0.34662	0.021;0.462	B;B	0.25987	0.009;0.065	T	0.07693	-1.0759	9	0.38643	T	0.18	.	13.7416	0.62852	0.0:0.0:0.0:1.0	rs1801131;rs4134712;rs17367365;rs17857426;rs1801131	429;470	P42898;Q5SNW6	MTHR_HUMAN;.	A	429;470;429;470	ENSP00000365777:E429A;ENSP00000365767:E470A;ENSP00000365775:E429A;ENSP00000365770:E470A	ENSP00000365767:E470A	E	-	2	0	MTHFR	11777063	0.968000	0.33430	0.496000	0.27539	0.772000	0.43724	3.792000	0.55476	1.898000	0.54952	0.374000	0.22700	GAA	T|0.722;G|0.238	0.238	strong		0.537	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957	
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 GAIIx	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	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	29	16	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 GAIIx	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_ENST00000292309.5_Silent_p.Y1922Y|NBEAL2_ENST00000383740.2_Silent_p.Y385Y	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		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	39	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	
NEUROG3	50674	hgsc.bcm.edu	37	10	71332204	71332204	+	Missense_Mutation	SNP	A	A	G	rs4536103	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:71332204A>G	ENST00000242462.4	-	2	625	c.596T>C	c.(595-597)tTt>tCt	p.F199S		NM_020999.3	NP_066279.2	Q9Y4Z2	NGN3_HUMAN	neurogenin 3	199			F -> S (in dbSNP:rs4536103). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		central nervous system development (GO:0007417)|endocrine pancreas development (GO:0031018)|epithelial cell differentiation (GO:0030855)|forebrain development (GO:0030900)|hindbrain development (GO:0030902)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|peripheral nervous system development (GO:0007422)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of dendrite morphogenesis (GO:0048814)|spinal cord development (GO:0021510)|transdifferentiation (GO:0060290)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription coactivator activity (GO:0003713)			endometrium(4)|large_intestine(2)|lung(6)|prostate(1)	13						GCAGGCGGAAAAGGTGGCCCC	0.657													G|||	2153	0.429912	0.2572	0.611	5008	,	,		14845	0.3125		0.666	False		,,,				2504	0.4131				p.F199S		Atlas-SNP	.											.	NEUROG3	33	.	0			c.T596C	GRCh37	CM068025	NEUROG3	M	rs4536103	PASS	.	G	SER/PHE	1453,2229		343,767,731	5.0	5.0	5.0		596	2.9	0.2	10	dbSNP_111	5	5305,2511		1897,1511,500	yes	missense	NEUROG3	NM_020999.3	155	2240,2278,1231	GG,GA,AA		32.1264,39.4622,41.2246	benign	199/215	71332204	6758,4740	1841	3908	5749	SO:0001583	missense	50674	exon2			GCGGAAAAGGTGG	AJ133776	CCDS31212.1	10q21.3	2013-05-21			ENSG00000122859	ENSG00000122859		"""Basic helix-loop-helix proteins"""	13806	protein-coding gene	gene with protein product		604882				9000438, 10677506	Standard	NM_020999		Approved	Atoh5, Math4B, ngn3, bHLHa7	uc001jpp.3	Q9Y4Z2	OTTHUMG00000018391	ENST00000242462.4:c.596T>C	10.37:g.71332204A>G	ENSP00000242462:p.Phe199Ser	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_020999	Q5VVI0|Q6DJX6|Q9BY24	Missense_Mutation	SNP	ENST00000242462.4	37	CCDS31212.1	990	0.4532967032967033	121	0.2459349593495935	212	0.585635359116022	158	0.2762237762237762	499	0.658311345646438	G	3.112	-0.182485	0.06340	0.394622	0.678736	ENSG00000122859	ENST00000242462	D	0.92965	-3.14	4.83	2.94	0.34122	.	0.183574	0.26620	N	0.023369	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41787	-0.9489	9	0.06757	T	0.87	-13.4227	9.496	0.38989	0.2399:0.0:0.7601:0.0	rs4536103;rs4536103	199	Q9Y4Z2	NGN3_HUMAN	S	199	ENSP00000242462:F199S	ENSP00000242462:F199S	F	-	2	0	NEUROG3	71002210	0.013000	0.17824	0.179000	0.23059	0.003000	0.03518	1.496000	0.35638	0.643000	0.30638	-0.119000	0.15052	TTT	A|0.573;G|0.427	0.427	strong		0.657	NEUROG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048464.1	NM_020999	
AP4B1	10717	hgsc.bcm.edu	37	1	114438951	114438951	+	Missense_Mutation	SNP	A	A	G	rs1217401	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:114438951A>G	ENST00000369569.1	-	8	1719	c.1439T>C	c.(1438-1440)tTg>tCg	p.L480S	AP4B1_ENST00000462591.1_5'UTR|AP4B1_ENST00000369567.1_Missense_Mutation_p.L312S|AP4B1-AS1_ENST00000419536.1_RNA|AP4B1_ENST00000256658.4_Missense_Mutation_p.L480S	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	480			L -> S (in dbSNP:rs1217401). {ECO:0000269|PubMed:10066790, ECO:0000269|Ref.3}.		intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAGGCGCAGCAAAGCAGTGAG	0.453													A|||	1888	0.376997	0.8003	0.2536	5008	,	,		20016	0.0794		0.2694	False		,,,				2504	0.3098				p.L480S		Atlas-SNP	.											.	AP4B1	72	.	0			c.T1439C						PASS	.	A	SER/LEU	3017,1389	689.6+/-405.1	1046,925,232	158.0	154.0	155.0		1439	6.0	0.9	1	dbSNP_87	155	2679,5921	430.6+/-356.6	424,1831,2045	yes	missense	AP4B1	NM_006594.2	145	1470,2756,2277	GG,GA,AA		31.1512,31.5252,43.7952	possibly-damaging	480/740	114438951	5696,7310	2203	4300	6503	SO:0001583	missense	10717	exon9			CGCAGCAAAGCAG	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"""beta 4 subunit of AP-4"""	607245	"""spastic paraplegia 47"""	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.1439T>C	1.37:g.114438951A>G	ENSP00000358582:p.Leu480Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Missense_Mutation	SNP	ENST00000369569.1	37	CCDS865.1	756	0.34615384615384615	390	0.7926829268292683	103	0.2845303867403315	54	0.0944055944055944	209	0.2757255936675462	A	15.36	2.810246	0.50421	0.684748	0.311512	ENSG00000134262	ENST00000369567;ENST00000369569;ENST00000256658	T;T;T	0.24538	1.85;1.85;1.85	6.04	6.04	0.98038	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.389021	0.27996	N	0.017016	T	0.09598	0.0236	N	0.10809	0.05	0.09310	P	1.0	B;B;B;B	0.22541	0.071;0.008;0.033;0.001	B;B;B;B	0.30105	0.111;0.02;0.111;0.007	T	0.13442	-1.0509	9	0.52906	T	0.07	-2.4422	16.5885	0.84745	1.0:0.0:0.0:0.0	rs1217401;rs3170575;rs58628725;rs1217401	480;312;480;381	B2RBF6;B1ALD0;Q9Y6B7;B4DTG3	.;.;AP4B1_HUMAN;.	S	312;480;480	ENSP00000358580:L312S;ENSP00000358582:L480S;ENSP00000256658:L480S	ENSP00000256658:L480S	L	-	2	0	AP4B1	114240474	1.000000	0.71417	0.868000	0.34077	0.986000	0.74619	6.230000	0.72301	2.317000	0.78254	0.460000	0.39030	TTG	A|0.589;G|0.411	0.411	strong		0.453	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594	
TTLL2	83887	hgsc.bcm.edu	37	6	167754702	167754702	+	Silent	SNP	C	C	T	rs909546	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:167754702C>T	ENST00000239587.5	+	3	1402	c.1314C>T	c.(1312-1314)gaC>gaT	p.D438D		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	438					cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CCAACATCGACGCTGCAAAAA	0.428													C|||	2571	0.513379	0.6437	0.4265	5008	,	,		23083	0.6181		0.3966	False		,,,				2504	0.411				p.D438D		Atlas-SNP	.											TTLL2,NS,carcinoma,0,1	TTLL2	82	1	0			c.C1314T						PASS	.	C		2691,1715	650.3+/-399.0	823,1045,335	102.0	95.0	98.0		1314	-0.3	0.0	6	dbSNP_86	98	3605,4995	521.5+/-379.9	736,2133,1431	no	coding-synonymous	TTLL2	NM_031949.4		1559,3178,1766	TT,TC,CC		41.9186,38.9242,48.4084		438/593	167754702	6296,6710	2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			CATCGACGCTGCA	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1314C>T	6.37:g.167754702C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	37	CCDS5301.1																																																																																			C|0.503;A|0.003	.	strong		0.428	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
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 GAIIx	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	AC005523.3_ENST00000598782.1_lincRNA|AC005523.2_ENST00000601192.1_RNA|AC005523.2_ENST00000596170.1_RNA	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	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	52	20	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		
FAM186A	121006	hgsc.bcm.edu	37	12	50727706	50727706	+	Missense_Mutation	SNP	G	G	C	rs6580741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:50727706G>C	ENST00000327337.5	-	5	6683	c.6684C>G	c.(6682-6684)caC>caG	p.H2228Q	FAM186A_ENST00000543096.1_Missense_Mutation_p.H239Q|FAM186A_ENST00000543111.1_Missense_Mutation_p.H2228Q	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2228			H -> Q (in dbSNP:rs6580741). {ECO:0000269|Ref.3}.														GGTTGAATACGTGTATCATTT	0.448													g|||	1739	0.347244	0.3434	0.2565	5008	,	,		21530	0.2569		0.339	False		,,,				2504	0.5184				p.H2228Q	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.C6684G						PASS	.						217.0	171.0	185.0					12																	50727706		692	1591	2283	SO:0001583	missense	121006	exon5			GAATACGTGTATC		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6684C>G	12.37:g.50727706G>C	ENSP00000329995:p.His2228Gln	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	216	102	0.472222	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	685	0.31364468864468864	180	0.36585365853658536	94	0.2596685082872928	160	0.27972027972027974	251	0.3311345646437995	g	2.650	-0.282130	0.05642	.	.	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.40225	1.04;1.04;1.04	4.27	-0.179	0.13299	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.19583	0.037;0.037	B;B	0.20384	0.029;0.029	T	0.45948	-0.9226	8	0.33141	T	0.24	.	7.0351	0.24989	0.2306:0.1377:0.6317:0.0	rs6580741;rs52828511;rs60724480;rs6580741	2228;2228	F5GYN0;A6NE01	.;F186A_HUMAN	Q	2228;239;2228	ENSP00000441337:H2228Q;ENSP00000443703:H239Q;ENSP00000329995:H2228Q	ENSP00000329995:H2228Q	H	-	3	2	FAM186A	49013973	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.315000	0.19451	-0.245000	0.09625	-2.620000	0.00156	CAC	G|0.688;C|0.312	0.312	strong		0.448	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
HSP90B1	7184	hgsc.bcm.edu	37	12	104341103	104341103	+	Silent	SNP	C	C	T	rs7645	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:104341103C>T	ENST00000299767.5	+	17	2459	c.2277C>T	c.(2275-2277)ccC>ccT	p.P759P	C12orf73_ENST00000543740.2_5'Flank	NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	759					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	aagaagagcccgaagaagaac	0.383													C|||	2285	0.45627	0.6362	0.4582	5008	,	,		19219	0.4692		0.336	False		,,,				2504	0.3221				p.P759P		Atlas-SNP	.											.	HSP90B1	72	.	0			c.C2277T						PASS	.	C		2585,1821	637.6+/-396.8	766,1053,384	124.0	131.0	129.0		2277	-5.9	0.9	12	dbSNP_52	129	2771,5829	437.2+/-358.5	446,1879,1975	no	coding-synonymous	HSP90B1	NM_003299.1		1212,2932,2359	TT,TC,CC		32.2209,41.33,41.181		759/804	104341103	5356,7650	2203	4300	6503	SO:0001819	synonymous_variant	7184	exon17			AGAGCCCGAAGAA	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"""Heat shock proteins / HSPC"""	12028	protein-coding gene	gene with protein product		191175	"""tumor rejection antigen (gp96) 1"""	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.2277C>T	12.37:g.104341103C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	184	183	0.994565	NM_003299	Q96A97	Silent	SNP	ENST00000299767.5	37	CCDS9094.1	981	0.4491758241758242	311	0.6321138211382114	154	0.425414364640884	266	0.46503496503496505	250	0.32981530343007914	C	8.541	0.873248	0.17322	0.5867	0.322209	ENSG00000166598	ENST00000550595	T	0.09445	2.98	4.5	-5.92	0.02261	.	0.123738	0.56097	D	0.000037	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999378523	.	.	.	.	.	.	T	0.32348	-0.9910	6	0.51188	T	0.08	.	5.3475	0.16018	0.3908:0.1407:0.0:0.4685	rs7645;rs1131448;rs1185171;rs17161899;rs7645	.	.	.	L	110	ENSP00000450215:P110L	ENSP00000450215:P110L	P	+	2	0	HSP90B1	102865233	0.011000	0.17503	0.888000	0.34837	0.890000	0.51754	-2.780000	0.00773	-1.182000	0.02727	-0.150000	0.13652	CCG	C|0.550;T|0.450	0.450	strong		0.383	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
OR1S2	219958	hgsc.bcm.edu	37	11	57971195	57971195	+	Silent	SNP	G	G	A	rs11229279	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57971195G>A	ENST00000302592.6	-	1	458	c.459C>T	c.(457-459)ttC>ttT	p.F153F		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F153F(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				GCAAAGTGCCGAACCTGGCCC	0.483													G|||	2137	0.426717	0.2239	0.3876	5008	,	,		21853	0.752		0.3161	False		,,,				2504	0.5072				p.F153F		Atlas-SNP	.											OR1S2,caecum,carcinoma,-2,2	OR1S2	119	2	1	Substitution - coding silent(1)	stomach(1)	c.C459T						PASS	.	G		1096,3306	396.5+/-330.1	131,834,1236	175.0	164.0	168.0		459	1.5	0.0	11	dbSNP_120	168	2804,5788	443.7+/-360.5	477,1850,1969	no	coding-synonymous	OR1S2	NM_001004459.1		608,2684,3205	AA,AG,GG		32.635,24.8978,30.0139		153/326	57971195	3900,9094	2201	4296	6497	SO:0001819	synonymous_variant	219958	exon1			AGTGCCGAACCTG	BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.459C>T	11.37:g.57971195G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	147	130	0.884354	NM_001004459	Q6IFG5|Q96R85	Silent	SNP	ENST00000302592.6	37	CCDS31545.1																																																																																			G|0.677;A|0.323	0.323	strong		0.483	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
KMT2B	9757	hgsc.bcm.edu	37	19	36224161	36224161	+	Silent	SNP	C	C	A	rs112013670	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:36224161C>A	ENST00000222270.7	+	28	6711	c.6711C>A	c.(6709-6711)ggC>ggA	p.G2237G	KMT2B_ENST00000420124.1_Silent_p.G2237G|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2237					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGCCCCCAGGCCCCCTCCTCG	0.731													C|||	523	0.104433	0.087	0.1037	5008	,	,		6096	0.0883		0.1223	False		,,,				2504	0.1268				p.G2237G		Atlas-SNP	.											.	MLL4	229	.	0			c.C6711A						PASS	.	C		236,3094		5,226,1434	17.0	18.0	18.0		6711	0.7	1.0	19	dbSNP_132	18	641,6845		21,599,3123	no	coding-synonymous	MLL4	NM_014727.1		26,825,4557	AA,AC,CC		8.5627,7.0871,8.1084		2237/2716	36224161	877,9939	1665	3743	5408	SO:0001819	synonymous_variant	8085	exon28			CCCAGGCCCCCTC	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.6711C>A	19.37:g.36224161C>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	37	CCDS46055.1																																																																																			C|0.894;A|0.106	0.106	strong		0.731	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
VWF	7450	hgsc.bcm.edu	37	12	6138595	6138595	+	Silent	SNP	C	C	T	rs1800380	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6138595C>T	ENST00000261405.5	-	22	3134	c.2880G>A	c.(2878-2880)cgG>cgA	p.R960R		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	960	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GAATGATGTACCGGCCAGACT	0.557													C|||	897	0.179113	0.3079	0.1902	5008	,	,		20208	0.004		0.2555	False		,,,				2504	0.0992				p.R960R		Atlas-SNP	.											.	VWF	338	.	0			c.G2880A						PASS	.	C		1373,3033	456.9+/-351.5	210,953,1040	131.0	116.0	121.0		2880	-5.1	0.1	12	dbSNP_89	121	2162,6438	370.9+/-336.0	264,1634,2402	no	coding-synonymous	VWF	NM_000552.3		474,2587,3442	TT,TC,CC		25.1395,31.1621,27.1798		960/2814	6138595	3535,9471	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon22			GATGTACCGGCCA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2880G>A	12.37:g.6138595C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			C|0.766;T|0.234	0.234	strong		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
TCEB3C	162699	hgsc.bcm.edu	37	18	44555232	44555232	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:44555232G>C	ENST00000330682.2	-	1	1217	c.982C>G	c.(982-984)Cct>Gct	p.P328A	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron	NM_145653.3	NP_663628.2	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide 3C (elongin A3)	328	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(16)|skin(2)	30						TGGCAGGCAGGCCTGGAGCCC	0.667																																					p.P328A		Atlas-SNP	.											TCEB3C,NS,carcinoma,+1,1	TCEB3C	49	1	0			c.C982G						scavenged	.						47.0	50.0	49.0					18																	44555232		1643	3252	4895	SO:0001583	missense	162699	exon1			AGGCAGGCCTGGA	AB076840	CCDS11931.1	18q21.1	2008-08-13			ENSG00000183791	ENSG00000183791			24617	protein-coding gene	gene with protein product	"""elongin A3"""					11932239, 11994304	Standard	NM_145653		Approved	HsT829, TCEB3L2	uc010xdb.2	Q8NG57	OTTHUMG00000132651	ENST00000330682.2:c.982C>G	18.37:g.44555232G>C	ENSP00000328232:p.Pro328Ala	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	222	6	0.027027	NM_145653		Missense_Mutation	SNP	ENST00000330682.2	37	CCDS11931.1	.	.	.	.	.	.	.	.	.	.	g	3.159	-0.172460	0.06421	.	.	ENSG00000183791	ENST00000330682	T	0.10960	2.82	1.34	-2.68	0.06041	.	1.893950	0.03068	N	0.156781	T	0.07863	0.0197	L	0.47716	1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42172	-0.9467	10	0.07990	T	0.79	-0.1368	0.1824	0.00125	0.2463:0.1948:0.1744:0.3845	.	328	Q8NG57	ELOA3_HUMAN	A	328	ENSP00000328232:P328A	ENSP00000328232:P328A	P	-	1	0	TCEB3C	42809230	0.006000	0.16342	0.000000	0.03702	0.001000	0.01503	-0.186000	0.09670	-2.618000	0.00441	-1.572000	0.00871	CCT	.	.	none		0.667	TCEB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255902.1	NM_145653	
HEATR5B	54497	hgsc.bcm.edu	37	2	37241050	37241050	+	Silent	SNP	G	G	A	rs17020125	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:37241050G>A	ENST00000233099.5	-	27	4313	c.4218C>T	c.(4216-4218)tcC>tcT	p.S1406S	HEATR5B_ENST00000354531.2_Silent_p.S1406S	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1406						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				ACAGCTGGCTGGAAGATCCTT	0.463													G|||	1304	0.260383	0.0484	0.2651	5008	,	,		14467	0.5288		0.1948	False		,,,				2504	0.3344				p.S1406S		Atlas-SNP	.											.	HEATR5B	185	.	0			c.C4218T						PASS	.	G		336,4070	176.2+/-205.4	11,314,1878	131.0	125.0	127.0		4218	-0.9	1.0	2	dbSNP_123	127	1590,7010	297.9+/-303.7	164,1262,2874	no	coding-synonymous	HEATR5B	NM_019024.1		175,1576,4752	AA,AG,GG		18.4884,7.626,14.8085		1406/2072	37241050	1926,11080	2203	4300	6503	SO:0001819	synonymous_variant	54497	exon27			CTGGCTGGAAGAT	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4218C>T	2.37:g.37241050G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	113	62	0.548673	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			G|0.798;A|0.202	0.202	strong		0.463	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
AAK1	22848	hgsc.bcm.edu	37	2	69741609	69741609	+	Silent	SNP	C	C	T	rs2276689	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:69741609C>T	ENST00000409085.4	-	13	2146	c.1770G>A	c.(1768-1770)gaG>gaA	p.E590E	AAK1_ENST00000406297.3_Silent_p.E590E|AAK1_ENST00000409068.1_Silent_p.E590E|RN7SL604P_ENST00000492589.2_RNA	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	590	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						TTACCGCTGGCTCCTgggcag	0.607													C|||	1609	0.321286	0.0628	0.4524	5008	,	,		17194	0.5079		0.3867	False		,,,				2504	0.318				p.E590E		Atlas-SNP	.											.	AAK1	121	.	0			c.G1770A						PASS	.	C		407,3515		31,345,1585	10.0	11.0	11.0		1770	2.8	1.0	2	dbSNP_100	11	2665,4979		458,1749,1615	no	coding-synonymous	AAK1	NM_014911.3		489,2094,3200	TT,TC,CC		34.8639,10.3774,26.5606		590/962	69741609	3072,8494	1961	3822	5783	SO:0001819	synonymous_variant	22848	exon13			CGCTGGCTCCTGG	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1770G>A	2.37:g.69741609C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	8	0.153846	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																			C|0.642;T|0.358	0.358	strong		0.607	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
HDAC10	83933	hgsc.bcm.edu	37	22	50684747	50684747	+	Missense_Mutation	SNP	C	C	T	rs76578729	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50684747C>T	ENST00000216271.5	-	17	1982	c.1630G>A	c.(1630-1632)Gtc>Atc	p.V544I	TUBGCP6_ENST00000248846.5_5'Flank|MAPK12_ENST00000497036.1_5'UTR|HDAC10_ENST00000448072.1_Missense_Mutation_p.V494I|TUBGCP6_ENST00000439308.2_5'Flank|HDAC10_ENST00000349505.4_Missense_Mutation_p.V524I|HDAC10_ENST00000498366.1_5'UTR	NM_001159286.1|NM_032019.5	NP_001152758.1|NP_114408.3	Q969S8	HDA10_HUMAN	histone deacetylase 10	544					chromatin modification (GO:0016568)|histone deacetylation (GO:0016575)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|oligodendrocyte development (GO:0014003)|protein deacetylation (GO:0006476)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)			endometrium(2)|kidney(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	8		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GGCGTGGAGACATGGAACATG	0.592													C|||	211	0.0421326	0.0008	0.0245	5008	,	,		20552	0.129		0.0099	False		,,,				2504	0.0542				p.V544I		Atlas-SNP	.											.	HDAC10	29	.	0			c.G1630A						PASS	.	C	ILE/VAL,ILE/VAL	10,4396	15.5+/-35.6	0,10,2193	145.0	120.0	128.0		1570,1630	-3.3	0.0	22	dbSNP_131	128	104,8496	56.0+/-117.1	0,104,4196	yes	missense,missense	HDAC10	NM_001159286.1,NM_032019.5	29,29	0,114,6389	TT,TC,CC		1.2093,0.227,0.8765	benign,benign	524/650,544/670	50684747	114,12892	2203	4300	6503	SO:0001583	missense	83933	exon17			TGGAGACATGGAA	AF393962	CCDS14088.1, CCDS54545.1	22q13.31	2008-06-10			ENSG00000100429	ENSG00000100429			18128	protein-coding gene	gene with protein product		608544				11677242, 11726666	Standard	NM_032019		Approved	DKFZP761B039	uc003bkg.3	Q969S8	OTTHUMG00000044647	ENST00000216271.5:c.1630G>A	22.37:g.50684747C>T	ENSP00000216271:p.Val544Ile	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_032019	Q08AP4|Q6STF9|Q96P77|Q96P78|Q9H028|Q9UGX1|Q9UGX2	Missense_Mutation	SNP	ENST00000216271.5	37	CCDS14088.1	95	0.043498168498168496	0	0.0	8	0.022099447513812154	78	0.13636363636363635	9	0.011873350923482849	C	1.550	-0.539573	0.04053	0.00227	0.012093	ENSG00000100429	ENST00000216271;ENST00000448072;ENST00000349505	T;T;T	0.32515	1.45;1.45;1.45	4.64	-3.28	0.05033	Histone deacetylase domain (1);	0.481266	0.15997	N	0.234515	T	0.00178	0.0005	M	0.71581	2.175	0.09310	N	0.999997	B;B;B;B	0.10296	0.002;0.003;0.002;0.003	B;B;B;B	0.14578	0.004;0.004;0.011;0.002	T	0.26087	-1.0113	10	0.15499	T	0.54	-16.7152	4.6822	0.12741	0.1592:0.3231:0.0:0.5178	.	524;494;544;544	Q969S8-2;C9J8B8;Q969S8-4;Q969S8	.;.;.;HDA10_HUMAN	I	544;494;524	ENSP00000216271:V544I;ENSP00000397542:V494I;ENSP00000343540:V524I	ENSP00000216271:V544I	V	-	1	0	HDAC10	49026874	0.006000	0.16342	0.001000	0.08648	0.012000	0.07955	-0.271000	0.08572	-0.613000	0.05694	0.561000	0.74099	GTC	C|0.981;G|0.000;T|0.019	0.019	strong		0.592	HDAC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104141.4	NM_032019	
MED16	10025	hgsc.bcm.edu	37	19	872089	872089	+	Silent	SNP	A	A	G	rs72984031	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:872089A>G	ENST00000589119.1	-	11	1934	c.1935T>C	c.(1933-1935)ttT>ttC	p.F645F	MED16_ENST00000269814.4_Intron|MED16_ENST00000312090.6_Silent_p.F645F|MED16_ENST00000325464.1_Silent_p.F645F|MED16_ENST00000395808.3_Silent_p.F645F|MED16_ENST00000606828.1_5'Flank			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	645					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|receptor activity (GO:0004872)|thyroid hormone receptor binding (GO:0046966)|thyroid hormone receptor coactivator activity (GO:0030375)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|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)		CGTCCCGCAGAAAGCTGTGGC	0.657													-|||	885	0.176717	0.2133	0.1412	5008	,	,		9195	0.0089		0.2793	False		,,,				2504	0.2198				p.F645F		Atlas-SNP	.											.	MED16	61	.	0			c.T1935C						PASS	.			1029,3309	361.4+/-315.7	131,767,1271	35.0	33.0	33.0		1935	-0.2	1.0	19	dbSNP_130	33	2337,6219	368.3+/-335.0	331,1675,2272	no	coding-synonymous	MED16	NM_005481.2		462,2442,3543	GG,GA,AA		27.3142,23.7206,26.1052		645/878	872089	3366,9528	2169	4278	6447	SO:0001819	synonymous_variant	10025	exon12			CCGCAGAAAGCTG	AF121228	CCDS12047.1	19p13.3	2013-01-10	2007-07-30	2007-07-30		ENSG00000175221		"""WD repeat domain containing"""	17556	protein-coding gene	gene with protein product		604062	"""thyroid hormone receptor associated protein 5"""	THRAP5		10235266, 10198638	Standard	NM_005481		Approved	DRIP92, TRAP95	uc002lqd.1	Q9Y2X0		ENST00000589119.1:c.1935T>C	19.37:g.872089A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			A|0.775;G|0.225	0.225	strong		0.657	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
ZNF239	8187	hgsc.bcm.edu	37	10	44052903	44052903	+	Missense_Mutation	SNP	A	A	C	rs2230661	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:44052903A>C	ENST00000306006.6	-	2	1277	c.625T>G	c.(625-627)Tgt>Ggt	p.C209G	ZNF239_ENST00000491188.1_5'Flank|ZNF239_ENST00000535642.1_Missense_Mutation_p.C209G|ZNF239_ENST00000426961.1_Missense_Mutation_p.C209G|ZNF239_ENST00000374446.2_Missense_Mutation_p.C209G	NM_005674.2	NP_005665.2	Q16600	ZN239_HUMAN	zinc finger protein 239	209			C -> G (in dbSNP:rs2230661). {ECO:0000269|PubMed:8587123}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CACTGACTACATTCGTATTGT	0.423													A|||	2729	0.544928	0.4917	0.513	5008	,	,		23891	0.5506		0.5308	False		,,,				2504	0.6483				p.C209G		Atlas-SNP	.											.	ZNF239	45	.	0			c.T625G						PASS	.	A	GLY/CYS,GLY/CYS,GLY/CYS,GLY/CYS	2162,1898		604,954,472	115.0	109.0	111.0		625,625,625,625	2.9	0.2	10	dbSNP_98	111	4483,3903		1205,2073,915	yes	missense,missense,missense,missense	ZNF239	NM_001099282.1,NM_001099283.1,NM_001099284.1,NM_005674.2	159,159,159,159	1809,3027,1387	CC,CA,AA		46.5419,46.7488,46.6094	probably-damaging,probably-damaging,probably-damaging,probably-damaging	209/459,209/459,209/459,209/459	44052903	6645,5801	2030	4193	6223	SO:0001583	missense	8187	exon2			GACTACATTCGTA	X82125	CCDS41502.1	10q11.22-q11.23	2013-01-08			ENSG00000196793	ENSG00000196793		"""Zinc fingers, C2H2-type"""	13031	protein-coding gene	gene with protein product		601069				8903737, 8587123	Standard	NM_005674		Approved	MOK2, HOK-2	uc009xmk.3	Q16600	OTTHUMG00000018033	ENST00000306006.6:c.625T>G	10.37:g.44052903A>C	ENSP00000307774:p.Cys209Gly	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_001099283	Q5T1G9|Q8TAS5	Missense_Mutation	SNP	ENST00000306006.6	37	CCDS41502.1	1136	0.5201465201465202	221	0.4491869918699187	173	0.47790055248618785	327	0.5716783216783217	415	0.5474934036939314	A	12.38	1.920041	0.33908	0.532512	0.534581	ENSG00000196793	ENST00000306006;ENST00000374446;ENST00000426961;ENST00000535642;ENST00000339962	T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97	4.01	2.88	0.33553	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	H	0.96861	3.895	0.29663	P	0.843084	D	0.71674	0.998	D	0.78314	0.991	T	0.39440	-0.9614	8	0.72032	D	0.01	-3.9059	7.2808	0.26310	0.8888:0.0:0.1112:0.0	rs2230661;rs3750891;rs17153871;rs17843211;rs52799106;rs60450561;rs2230661	209	Q16600	ZN239_HUMAN	G	209	ENSP00000307774:C209G;ENSP00000363569:C209G;ENSP00000398202:C209G;ENSP00000443907:C209G	ENSP00000307774:C209G	C	-	1	0	ZNF239	43372909	0.998000	0.40836	0.152000	0.22495	0.008000	0.06430	4.452000	0.60054	0.900000	0.36469	0.533000	0.62120	TGT	A|0.480;C|0.520	0.520	strong		0.423	ZNF239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047710.1		
IL7R	3575	hgsc.bcm.edu	37	5	35871273	35871273	+	Silent	SNP	C	C	T	rs2228141	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:35871273C>T	ENST00000303115.3	+	4	624	c.495C>T	c.(493-495)caC>caT	p.H165H	IL7R_ENST00000343305.4_Silent_p.H165H|IL7R_ENST00000506850.1_Silent_p.H165H	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	165	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			TTTTAATGCACGATGTAGCTT	0.348			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						C|||	644	0.128594	0.1278	0.1657	5008	,	,		17496	0.1528		0.1441	False		,,,				2504	0.0624				p.H165H		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	.	IL7R	200	.	0			c.C495T						PASS	.	C		534,3872	242.5+/-252.5	36,462,1705	73.0	72.0	73.0		495	-2.7	0.4	5	dbSNP_98	73	1223,7377	246.4+/-274.8	92,1039,3169	no	coding-synonymous	IL7R	NM_002185.2		128,1501,4874	TT,TC,CC		14.2209,12.1198,13.5091		165/460	35871273	1757,11249	2203	4300	6503	SO:0001819	synonymous_variant	3575	exon4			AATGCACGATGTA	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.495C>T	5.37:g.35871273C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	22	0.34375	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Silent	SNP	ENST00000303115.3	37	CCDS3911.1																																																																																			C|0.867;G|0.000;T|0.133	0.133	strong		0.348	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
NPY4R	5540	hgsc.bcm.edu	37	10	47087501	47087501	+	Missense_Mutation	SNP	C	C	T	rs3824733	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:47087501C>T	ENST00000395716.1	+	2	803	c.718C>T	c.(718-720)Cgc>Tgc	p.R240C	NPY4R_ENST00000374312.1_Missense_Mutation_p.R240C			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	240			R -> C (in dbSNP:rs3824733). {ECO:0000269|Ref.6}.		blood circulation (GO:0008015)|digestion (GO:0007586)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|pancreatic polypeptide receptor activity (GO:0001602)|peptide binding (GO:0042277)|peptide YY receptor activity (GO:0001601)										CATCTACCGGCGCCTGCAGAG	0.602																																					p.R240C		Atlas-SNP	.											PPYR1,rectum,carcinoma,-1,1	PPYR1	54	1	0			c.C718T						PASS	.	C	CYS/ARG	529,3877		0,529,1674	155.0	130.0	139.0		718	4.2	1.0	10	dbSNP_107	139	2450,6150		2,2446,1852	yes	missense	PPYR1	NM_005972.4	180	2,2975,3526	TT,TC,CC		28.4884,12.0064,22.9048	possibly-damaging	240/376	47087501	2979,10027	2203	4300	6503	SO:0001583	missense	5540	exon3			TACCGGCGCCTGC		CCDS73100.1	10q11.2	2013-03-26	2013-03-26	2013-03-26	ENSG00000204174	ENSG00000204174		"""GPCR / Class A : Neuropeptide receptors : Y"""	9329	protein-coding gene	gene with protein product		601790	"""pancreatic polypeptide receptor 1"""	PPYR1		9417917	Standard	NM_005972		Approved	Y4, PP1	uc001jee.3	P50391	OTTHUMG00000018108	ENST00000395716.1:c.718C>T	10.37:g.47087501C>T	ENSP00000379066:p.Arg240Cys	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	37	CCDS31193.1	648	0.2967032967032967	45	0.09146341463414634	116	0.32044198895027626	269	0.47027972027972026	218	0.287598944591029	C	11.53	1.666627	0.29604	0.120064	0.284884	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.38240	1.15;1.15	5.12	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.116071	0.64402	D	0.000009	T	0.00012	0.0000	L	0.51422	1.61	0.80722	D	1	B	0.22346	0.068	B	0.28385	0.089	T	0.54153	-0.8336	10	0.37606	T	0.19	.	11.5752	0.50858	0.0:0.9121:0.0:0.0879	rs3824733	240	P50391	NPY4R_HUMAN	C	240	ENSP00000363431:R240C;ENSP00000379066:R240C	ENSP00000363431:R240C	R	+	1	0	PPYR1	46507507	1.000000	0.71417	0.967000	0.41034	0.627000	0.37826	4.530000	0.60595	1.307000	0.44944	0.609000	0.83330	CGC	C|0.702;T|0.298	0.298	strong		0.602	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1		
ZNF672	79894	hgsc.bcm.edu	37	1	249142169	249142169	+	Silent	SNP	C	C	T	rs58906520	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:249142169C>T	ENST00000306562.3	+	4	1442	c.696C>T	c.(694-696)tgC>tgT	p.C232C		NM_024836.1	NP_079112.1	Q499Z4	ZN672_HUMAN	zinc finger protein 672	232					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(1)	5	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			GCCCGGAGTGCGGCAAGGGCT	0.652													C|||	603	0.120407	0.0628	0.1239	5008	,	,		14270	0.1915		0.0388	False		,,,				2504	0.2065				p.C232C		Atlas-SNP	.											.	ZNF672	32	.	0			c.C696T						PASS	.	C		244,4142		3,238,1952	10.0	10.0	10.0		696	-7.9	0.1	1	dbSNP_129	10	306,8250		5,296,3977	no	coding-synonymous	ZNF672	NM_024836.1		8,534,5929	TT,TC,CC		3.5764,5.5632,4.2497		232/453	249142169	550,12392	2193	4278	6471	SO:0001819	synonymous_variant	79894	exon4			GGAGTGCGGCAAG	AK027476	CCDS1638.1	1q44	2013-01-08			ENSG00000171161	ENSG00000171161		"""Zinc fingers, C2H2-type"""	26179	protein-coding gene	gene with protein product	"""hypothetical protein FLJ22301"""					12477932	Standard	NM_024836		Approved	FLJ22301	uc001iex.3	Q499Z4	OTTHUMG00000040377	ENST00000306562.3:c.696C>T	1.37:g.249142169C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_024836	Q96H65|Q96IM3|Q9H6G5	Silent	SNP	ENST00000306562.3	37	CCDS1638.1																																																																																			C|0.902;T|0.098	0.098	strong		0.652	ZNF672-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097125.2	NM_024836	
ELAC2	60528	hgsc.bcm.edu	37	17	12898295	12898295	+	Silent	SNP	T	T	C	rs17552022	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:12898295T>C	ENST00000338034.4	-	20	2132	c.1893A>G	c.(1891-1893)acA>acG	p.T631T	ELAC2_ENST00000395962.2_Silent_p.T612T|ELAC2_ENST00000426905.3_Silent_p.T591T	NM_018127.6|NM_173717.1	NP_060597.4|NP_776065.1	Q9BQ52	RNZ2_HUMAN	elaC ribonuclease Z 2	631					mitochondrial tRNA 3'-trailer cleavage, endonucleolytic (GO:0072684)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|skin(1)	23						CCAAATCACATGTTCGCAACA	0.532													T|||	252	0.0503195	0.0053	0.0793	5008	,	,		19149	0.001		0.1203	False		,,,				2504	0.0695				p.T631T		Atlas-SNP	.											.	ELAC2	48	.	0			c.A1893G						PASS	.	T	,,	99,4307	78.8+/-117.2	3,93,2107	178.0	185.0	183.0		1773,1893,1890	-10.6	0.0	17	dbSNP_123	183	1095,7505	228.6+/-263.6	76,943,3281	no	coding-synonymous,coding-synonymous,coding-synonymous	ELAC2	NM_001165962.1,NM_018127.6,NM_173717.1	,,	79,1036,5388	CC,CT,TT		12.7326,2.2469,9.1804	,,	591/787,631/827,630/826	12898295	1194,11812	2203	4300	6503	SO:0001819	synonymous_variant	60528	exon20			ATCACATGTTCGC	AF304370	CCDS11164.1, CCDS54093.1	17p11.2	2013-05-24	2013-05-24		ENSG00000006744	ENSG00000006744	3.1.26.11		14198	protein-coding gene	gene with protein product	"""tRNase Z (long form)"""	605367	"""elaC (E. coli) homolog 2"", ""elaC homolog 2 (E. coli)"""			10986046, 16636667, 21559454	Standard	NM_018127		Approved	FLJ10530, HPC2	uc010vvr.2	Q9BQ52	OTTHUMG00000058764	ENST00000338034.4:c.1893A>G	17.37:g.12898295T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_018127	B4DPL9|Q6IA94|Q9HAS8|Q9HAS9|Q9NVT1	Silent	SNP	ENST00000338034.4	37	CCDS11164.1																																																																																			T|0.921;C|0.079	0.079	strong		0.532	ELAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129934.5		
TLCD1	116238	hgsc.bcm.edu	37	17	27052358	27052358	+	Silent	SNP	C	C	T	rs2288595	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27052358C>T	ENST00000292090.3	-	3	434	c.324G>A	c.(322-324)acG>acA	p.T108T	AC010761.14_ENST00000587898.1_RNA|AC010761.8_ENST00000582718.1_RNA|SNORD4A_ENST00000459174.1_RNA|SNORD4B_ENST00000459083.1_RNA|SNORD42A_ENST00000459584.1_RNA|TLCD1_ENST00000394933.3_Silent_p.T61T	NM_138463.3	NP_612472.1	Q96CP7	TLCD1_HUMAN	TLC domain containing 1	108	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(2)|lung(2)	7	Lung NSC(42;0.00431)					AAGAGGCTCGCGTCTGTCCGC	0.512													C|||	562	0.11222	0.1377	0.062	5008	,	,		14496	0.121		0.0726	False		,,,				2504	0.1452				p.T108T		Atlas-SNP	.											.	TLCD1	15	.	0			c.G324A						PASS	.	C	,	568,3838	253.0+/-259.1	41,486,1676	81.0	70.0	74.0		183,324	-11.2	0.0	17	dbSNP_100	74	768,7832	181.5+/-230.2	32,704,3564	no	coding-synonymous,coding-synonymous	TLCD1	NM_001160407.1,NM_138463.3	,	73,1190,5240	TT,TC,CC		8.9302,12.8915,10.2722	,	61/201,108/248	27052358	1336,11670	2203	4300	6503	SO:0001819	synonymous_variant	116238	exon3			GGCTCGCGTCTGT	BC014072	CCDS11242.1, CCDS54102.1	17q11.2	2007-03-23			ENSG00000160606	ENSG00000160606			25177	protein-coding gene	gene with protein product						12151215	Standard	NM_138463		Approved		uc002hco.3	Q96CP7	OTTHUMG00000132683	ENST00000292090.3:c.324G>A	17.37:g.27052358C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	46	0.38983	NM_138463	A8MYP9	Silent	SNP	ENST00000292090.3	37	CCDS11242.1																																																																																			C|0.894;T|0.106	0.106	strong		0.512	TLCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255973.1	NM_138463	
RTN4IP1	84816	hgsc.bcm.edu	37	6	107019880	107019880	+	Silent	SNP	A	A	G	rs9486410	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:107019880A>G	ENST00000369063.3	-	9	1647	c.1182T>C	c.(1180-1182)aaT>aaC	p.N394N	RTN4IP1_ENST00000498091.1_5'UTR|RTN4IP1_ENST00000539449.1_3'UTR	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	394						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;9.45e-05)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0144)	Epithelial(6;0.000873)|all cancers(7;0.00363)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0394)	all cancers(137;0.113)|BRCA - Breast invasive adenocarcinoma(108;0.127)|Epithelial(106;0.144)		TTTAAACAACATTAATTACAG	0.383													G|||	929	0.185503	0.3011	0.1081	5008	,	,		19931	0.1696		0.1561	False		,,,				2504	0.1309				p.N394N		Atlas-SNP	.											RTN4IP1,NS,carcinoma,-2,1	RTN4IP1	31	1	0			c.T1182C						PASS	.	G		1228,3178	706.5+/-407.4	171,886,1146	111.0	105.0	107.0		1182	-0.6	0.0	6	dbSNP_119	107	981,7619	773.9+/-407.7	54,873,3373	no	coding-synonymous	RTN4IP1	NM_032730.4		225,1759,4519	GG,GA,AA		11.407,27.8711,16.9845		394/397	107019880	2209,10797	2203	4300	6503	SO:0001819	synonymous_variant	84816	exon9			AACAACATTAATT	AF336861	CCDS5056.1	6q21	2008-02-05			ENSG00000130347	ENSG00000130347			18647	protein-coding gene	gene with protein product		610502					Standard	NM_032730		Approved	NIMP	uc003prj.3	Q8WWV3	OTTHUMG00000015304	ENST00000369063.3:c.1182T>C	6.37:g.107019880A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Silent	SNP	ENST00000369063.3	37	CCDS5056.1																																																																																			A|0.834;G|0.166	0.166	strong		0.383	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1		
ECE2	9718	hgsc.bcm.edu	37	3	183976108	183976108	+	Intron	SNP	T	T	C	rs902415	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:183976108T>C	ENST00000402825.3	+	2	480				EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000324557.4_Silent_p.F171F	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2						brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GAGGCCGGTTTATCTCAATGA	0.552													C|||	1629	0.32528	0.4818	0.2536	5008	,	,		19663	0.3393		0.2455	False		,,,				2504	0.2321				p.F171F		Atlas-SNP	.											.	ECE2	303	.	0			c.T513C						PASS	.	C	,	1812,2594	639.0+/-397.0	394,1024,785	146.0	138.0	141.0		,513	3.2	1.0	3	dbSNP_86	141	1974,6626	723.8+/-406.5	226,1522,2552	no	intron,coding-synonymous	ECE2	NM_014693.3,NM_032331.3	,	620,2546,3337	CC,CT,TT		22.9535,41.1257,29.1096	,	,171/256	183976108	3786,9220	2203	4300	6503	SO:0001627	intron_variant	9718	exon3			CCGGTTTATCTCA	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.480+564T>C	3.37:g.183976108T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	56	0.523364	NM_032331	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																			T|0.697;C|0.303	0.303	strong		0.552	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
ELMOD3	84173	hgsc.bcm.edu	37	2	85617579	85617579	+	Intron	SNP	C	C	T	rs17851663	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:85617579C>T	ENST00000409890.2	+	13	1610				ELMOD3_ENST00000315658.7_Silent_p.V378V|ELMOD3_ENST00000409344.3_Intron|ELMOD3_ENST00000409013.3_Intron|ELMOD3_ENST00000490508.1_Intron|ELMOD3_ENST00000393852.4_Intron			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3						phagocytosis (GO:0006909)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	12						CCCTGACTGTCGCCCTTTTCT	0.448													C|||	214	0.0427316	0.0439	0.0432	5008	,	,		20875	0.006		0.0656	False		,,,				2504	0.0552				p.V378V		Atlas-SNP	.											.	ELMOD3	53	.	0			c.C1134T						PASS	.	C	,,,	206,4200	126.1+/-163.2	5,196,2002	90.0	97.0	95.0		,,,1134	-0.3	0.0	2	dbSNP_123	95	583,8017	155.8+/-209.8	17,549,3734	no	intron,intron,intron,coding-synonymous	ELMOD3	NM_001135021.1,NM_001135022.1,NM_001135023.1,NM_032213.4	,,,	22,745,5736	TT,TC,CC		6.7791,4.6754,6.0664	,,,	,,,378/392	85617579	789,12217	2203	4300	6503	SO:0001627	intron_variant	84173	exon11			GACTGTCGCCCTT	AF258573	CCDS1973.1, CCDS46352.1	2p11.2	2014-01-28	2008-08-14	2008-08-14	ENSG00000115459	ENSG00000115459		"""RNA binding motif (RRM) containing"""	26158	protein-coding gene	gene with protein product		615427	"""RNA binding motif protein 29"", ""RNA binding motif and ELMO/CED-12 domain 1"", ""deafness, autosomal recessive 88"""	RBM29, RBED1, DFNB88		24039609	Standard	NM_032213		Approved	FLJ21977	uc010ysn.2	Q96FG2	OTTHUMG00000130170	ENST00000409890.2:c.943+191C>T	2.37:g.85617579C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	92	70	0.76087	NM_032213	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Silent	SNP	ENST00000409890.2	37	CCDS46352.1																																																																																			C|0.951;T|0.049	0.049	strong		0.448	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213	
INPP5B	3633	hgsc.bcm.edu	37	1	38329999	38329999	+	Missense_Mutation	SNP	C	C	G	rs41311191	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:38329999C>G	ENST00000373026.1	-	22	2851	c.2851G>C	c.(2851-2853)Gat>Cat	p.D951H	INPP5B_ENST00000373023.2_Missense_Mutation_p.D951H|INPP5B_ENST00000373024.3_Missense_Mutation_p.D871H|INPP5B_ENST00000373027.1_Missense_Mutation_p.D707H|RP11-109P14.10_ENST00000419993.1_RNA			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	951	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)				ATATTCTCATCCAAATGATTT	0.413													C|||	395	0.0788738	0.0189	0.0908	5008	,	,		19962	0.003		0.164	False		,,,				2504	0.1421				p.D871H		Atlas-SNP	.											.	INPP5B	76	.	0			c.G2611C						PASS	.	C	HIS/ASP	129,3511		2,125,1693	76.0	66.0	69.0		2611	5.5	1.0	1	dbSNP_127	69	1177,6997		76,1025,2986	yes	missense	INPP5B	NM_005540.2	81	78,1150,4679	GG,GC,CC		14.3993,3.544,11.0547	probably-damaging	871/914	38329999	1306,10508	1820	4087	5907	SO:0001583	missense	3633	exon23			TCTCATCCAAATG	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.2851G>C	1.37:g.38329999C>G	ENSP00000362117:p.Asp951His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		161	0.07371794871794872	12	0.024390243902439025	39	0.10773480662983426	0	0.0	110	0.14511873350923482	C	18.74	3.687909	0.68271	0.03544	0.143993	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373026;ENST00000373024	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.00875	0.0029	M	0.79123	2.44	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.05386	-1.0888	9	0.72032	D	0.01	.	19.7445	0.96247	0.0:1.0:0.0:0.0	rs41311191;rs61736709	871	P32019-2	.	H	707;951;951;871	ENSP00000362118:D707H;ENSP00000362114:D951H;ENSP00000362117:D951H;ENSP00000362115:D871H	ENSP00000362114:D951H	D	-	1	0	INPP5B	38102586	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.156000	0.58138	2.739000	0.93911	0.655000	0.94253	GAT	C|0.887;G|0.113	0.113	strong		0.413	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
RAB6C	84084	hgsc.bcm.edu	37	2	130738183	130738183	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:130738183G>A	ENST00000410061.2	+	1	949	c.495G>A	c.(493-495)caG>caA	p.Q165Q	AC079776.7_ENST00000412425.1_RNA	NM_032144.2	NP_115520.2	Q9H0N0	RAB6C_HUMAN	RAB6C, member RAS oncogene family	165	Required for centrosome localization.				cell cycle process (GO:0022402)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|regulation of centrosome duplication (GO:0010824)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(2)|lung(1)|skin(1)|urinary_tract(1)	5	Colorectal(110;0.1)					ATGTAAAGCAGCTCTTTCGAC	0.478																																					p.Q165Q		Atlas-SNP	.											RAB6C,NS,carcinoma,+1,1	RAB6C	28	1	0			c.G495A						scavenged	.						84.0	71.0	76.0					2																	130738183		2202	4280	6482	SO:0001819	synonymous_variant	84084	exon1			AAAGCAGCTCTTT	AF124200	CCDS46408.1	2q21.1	2012-07-02			ENSG00000222014	ENSG00000222014		"""RAB, member RAS oncogene"""	16525	protein-coding gene	gene with protein product		612909				11054569, 17426708	Standard	NM_032144		Approved	WTH3	uc002tpx.1	Q9H0N0	OTTHUMG00000153487	ENST00000410061.2:c.495G>A	2.37:g.130738183G>A		Somatic	479	0	0		WXS	Illumina HiSeq	Phase_I	365	7	0.0191781	NM_032144	Q53RU3|Q6FIF7|Q9P128	Silent	SNP	ENST00000410061.2	37	CCDS46408.1																																																																																			.	.	none		0.478	RAB6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331384.1	NM_032144	
NR5A2	2494	hgsc.bcm.edu	37	1	200143281	200143281	+	Silent	SNP	C	C	T	rs1060060	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:200143281C>T	ENST00000367362.3	+	8	1815	c.1569C>T	c.(1567-1569)aaC>aaT	p.N523N	NR5A2_ENST00000236914.3_Silent_p.N477N|NR5A2_ENST00000544748.1_Silent_p.N451N	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	523					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					AGCACCTGAACGGGGATGTGC	0.448													C|||	1775	0.354433	0.3669	0.3213	5008	,	,		17133	0.5179		0.2913	False		,,,				2504	0.2577				p.C523C	Melanoma(179;1138 2773 15678 26136)	Atlas-SNP	.											NR5A2,NS,carcinoma,+1,1	NR5A2	83	1	0			c.C1569T						PASS	.	C	,	1499,2907	478.1+/-358.1	267,965,971	60.0	55.0	56.0		1431,1569	-0.3	1.0	1	dbSNP_86	56	2522,6078	413.5+/-351.2	386,1750,2164	no	coding-synonymous,coding-synonymous	NR5A2	NM_003822.3,NM_205860.1	,	653,2715,3135	TT,TC,CC		29.3256,34.0218,30.9165	,	477/496,523/542	200143281	4021,8985	2203	4300	6503	SO:0001819	synonymous_variant	2494	exon8			CCTGAACGGGGAT	U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"""Nuclear hormone receptors"""	7984	protein-coding gene	gene with protein product	"""liver receptor homolog-1"""	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.1569C>T	1.37:g.200143281C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	47	0.602564	NM_205860	B4E2P3|O95642|Q147U3	Silent	SNP	ENST00000367362.3	37	CCDS1401.1																																																																																			T|0.348;G|0.007	0.348	strong		0.448	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2		
RBBP6	5930	hgsc.bcm.edu	37	16	24582299	24582299	+	Silent	SNP	C	C	G	rs7196736	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:24582299C>G	ENST00000319715.4	+	18	4344	c.3912C>G	c.(3910-3912)acC>acG	p.T1304T	RBBP6_ENST00000348022.2_Silent_p.T1270T|RBBP6_ENST00000381039.3_Silent_p.T464T	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1304					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		ATGACAATACCGCGCCAGCTG	0.393													G|||	641	0.127995	0.149	0.1585	5008	,	,		16201	0.0149		0.1402	False		,,,				2504	0.182				p.T1304T		Atlas-SNP	.											RBBP6,NS,adenocarcinoma,+2,1	RBBP6	158	1	0			c.C3912G						PASS	.	G	,	712,3682	755.0+/-412.5	57,598,1542	55.0	53.0	54.0		3912,3810	-3.1	0.5	16	dbSNP_116	54	1472,7128	747.2+/-407.3	128,1216,2956	no	coding-synonymous,coding-synonymous	RBBP6	NM_006910.4,NM_018703.3	,	185,1814,4498	GG,GC,CC		17.1163,16.2039,16.8078	,	1304/1793,1270/1759	24582299	2184,10810	2197	4300	6497	SO:0001819	synonymous_variant	5930	exon18			CAATACCGCGCCA		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.3912C>G	16.37:g.24582299C>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	146	64	0.438356	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Silent	SNP	ENST00000319715.4	37	CCDS10621.1																																																																																			C|0.848;G|0.152	0.152	strong		0.393	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
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 GAIIx	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	PIEZO1_ENST00000327397.7_Silent_p.D215D|RP5-1142A6.9_ENST00000564984.1_RNA|MIR4722_ENST00000578292.1_RNA	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		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	24	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	
TAAR5	9038	hgsc.bcm.edu	37	6	132910612	132910612	+	Silent	SNP	G	G	A	rs3813355	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:132910612G>A	ENST00000258034.2	-	1	265	c.214C>T	c.(214-216)Ctg>Ttg	p.L72L		NM_003967.2	NP_003958.2	O14804	TAAR5_HUMAN	trace amine associated receptor 5	72					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|trimethylamine receptor activity (GO:1990081)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	32	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		GAGAGCAGCAGGAAGTTGGTG	0.567													A|||	3370	0.672923	0.7277	0.683	5008	,	,		19607	0.5595		0.665	False		,,,				2504	0.7168				p.L72L		Atlas-SNP	.											TAAR5,colon,carcinoma,0,1	TAAR5	53	1	0			c.C214T						PASS	.	A		2936,1470	472.4+/-356.4	963,1010,230	175.0	178.0	177.0		214	-9.5	0.1	6	dbSNP_107	177	5608,2992	463.7+/-366.0	1835,1938,527	no	coding-synonymous	TAAR5	NM_003967.2		2798,2948,757	AA,AG,GG		34.7907,33.3636,34.3072		72/338	132910612	8544,4462	2203	4300	6503	SO:0001819	synonymous_variant	9038	exon1			GCAGCAGGAAGTT	AF021818	CCDS5156.1	6q23.2	2012-08-08			ENSG00000135569	ENSG00000135569		"""GPCR / Class A : Trace amine associated receptors"""	30236	protein-coding gene	gene with protein product		607405				9464258, 15718104	Standard	NM_003967		Approved	PNR	uc003qdk.2	O14804	OTTHUMG00000015581	ENST00000258034.2:c.214C>T	6.37:g.132910612G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_003967	D8KZS1|Q2M1V1|Q4VBL1|Q5VUQ3|Q6NTA8	Silent	SNP	ENST00000258034.2	37	CCDS5156.1																																																																																			G|0.343;A|0.657	0.657	strong		0.567	TAAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042257.1	NM_003967	
MAGEB10	139422	hgsc.bcm.edu	37	X	27839617	27839617	+	Missense_Mutation	SNP	G	G	A	rs12557898	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:27839617G>A	ENST00000356790.2	+	3	439	c.194G>A	c.(193-195)cGg>cAg	p.R65Q		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	65			R -> Q (in dbSNP:rs12557898). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						CATGGACTTCGGGAAGCCCAA	0.498													G|||	792	0.209801	0.1112	0.1873	3775	,	,		13898	0.0357		0.3559	False		,,,				2504	0.1237				p.R65Q		Atlas-SNP	.											.	MAGEB10	107	.	0			c.G194A						PASS	.	G	GLN/ARG	678,3155		54,465,105,1112,466	58.0	45.0	49.0		194	-5.0	0.0	X	dbSNP_120	49	3376,3351		620,1200,936,608,935	yes	missense	MAGEB10	NM_182506.3	43	674,1665,1041,1720,1401	AA,AG,A,GG,G		49.8142,17.6885,38.3902	benign	65/348	27839617	4054,6506	2202	4299	6501	SO:0001583	missense	139422	exon3			GACTTCGGGAAGC		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.194G>A	X.37:g.27839617G>A	ENSP00000368304:p.Arg65Gln	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Missense_Mutation	SNP	ENST00000356790.2	37	CCDS35221.1	407	0.24532851115129597	35	0.07608695652173914	52	0.16666666666666666	13	0.022887323943661973	184	0.3076923076923077	g	0.010	-1.757108	0.00657	0.176885	0.501858	ENSG00000177689	ENST00000356790	T	0.02737	4.18	2.52	-5.04	0.02964	Melanoma associated antigen, MAGE, N-terminal (1);	14.954800	0.00166	N	0.000004	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.15141	0.012	B	0.09377	0.004	T	0.43940	-0.9360	9	0.02654	T	1	.	4.2766	0.10811	0.4058:0.3297:0.2645:0.0	rs12557898;rs52801205;rs58263199;rs12557898	65	Q96LZ2	MAGBA_HUMAN	Q	65	ENSP00000368304:R65Q	ENSP00000368304:R65Q	R	+	2	0	MAGEB10	27749538	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.569000	0.05902	-1.585000	0.01634	-2.735000	0.00129	CGG	0|0.012;A|0.299	0.299	strong		0.498	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506	
NIN	51199	hgsc.bcm.edu	37	14	51202311	51202311	+	Missense_Mutation	SNP	G	G	C	rs2295847	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:51202311G>C	ENST00000382041.3	-	28	5990	c.5800C>G	c.(5800-5802)Caa>Gaa	p.Q1934E	NIN_ENST00000389868.3_Missense_Mutation_p.Q1221E|NIN_ENST00000530997.2_Missense_Mutation_p.Q1934E|NIN_ENST00000453196.1_Missense_Mutation_p.Q1934E|NIN_ENST00000245441.5_Missense_Mutation_p.Q1934E|NIN_ENST00000382043.4_Missense_Mutation_p.Q1221E|NIN_ENST00000324330.9_Missense_Mutation_p.Q1934E	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1934			Q -> E (in dbSNP:rs2295847).		centrosome localization (GO:0051642)|centrosome-templated microtubule nucleation (GO:0090222)|microtubule anchoring at centrosome (GO:0034454)	centriole (GO:0005814)|centrosome (GO:0005813)|microtubule (GO:0005874)|nucleolus (GO:0005730)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|GTP binding (GO:0005525)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(13)|lung(16)|ovary(1)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	71	all_epithelial(31;0.00244)|Breast(41;0.127)					TCTAATTCTTGTTCAAGGGAA	0.338			T	PDGFRB	MPD								G|||	968	0.193291	0.0076	0.2305	5008	,	,		18869	0.5228		0.1153	False		,,,				2504	0.1585				p.Q1934E		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C5800G						PASS	.	G	GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN	119,4285	87.8+/-126.4	3,113,2086	113.0	98.0	103.0		3661,5800,5800,5800	3.5	1.0	14	dbSNP_100	103	913,7685	203.1+/-246.2	47,819,3433	yes	missense,missense,missense,missense	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	29,29,29,29	50,932,5519	CC,CG,GG		10.6187,2.7021,7.9372	benign,benign,benign,benign	1221/1378,1934/2134,1934/2047,1934/2091	51202311	1032,11970	2202	4299	6501	SO:0001583	missense	51199	exon28			ATTCTTGTTCAAG	AF212162	CCDS32078.1, CCDS32079.1, CCDS32078.2	14q21-q22	2013-01-10			ENSG00000100503	ENSG00000100503		"""EF-hand domain containing"""	14906	protein-coding gene	gene with protein product		608684				11004522, 11162463	Standard	NM_020921		Approved		uc001wyi.3	Q8N4C6	OTTHUMG00000029569	ENST00000382041.3:c.5800C>G	14.37:g.51202311G>C	ENSP00000371472:p.Gln1934Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	470|470	0.21520146520146521|0.21520146520146521	4|4	0.008130081300813009|0.008130081300813009	75|75	0.20718232044198895|0.20718232044198895	295|295	0.5157342657342657|0.5157342657342657	96|96	0.1266490765171504|0.1266490765171504	G|G	15.18|15.18	2.756350|2.756350	0.49362|0.49362	0.027021|0.027021	0.106187|0.106187	ENSG00000100503|ENSG00000100503	ENST00000245441;ENST00000311149;ENST00000389868;ENST00000382043;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196|ENST00000530997;ENST00000389869;ENST00000530853	T;T;T;T;T;T|.	0.10668|.	3.65;2.85;2.89;3.41;3.37;3.38|.	5.45|5.45	3.55|3.55	0.40652|0.40652	.|.	0.674545|.	0.14169|.	N|.	0.336878|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.49915|0.49915	P|P	1.6499999999997073E-4|1.6499999999997073E-4	B;B;B;B;B|.	0.28378|.	0.094;0.047;0.072;0.209;0.033|.	B;B;B;B;B|.	0.30646|.	0.034;0.031;0.054;0.118;0.025|.	T|T	0.48747|0.48747	-0.9008|-0.9008	9|4	0.20046|.	T|.	0.44|.	-0.0051|-0.0051	11.9354|11.9354	0.52870|0.52870	0.0:0.1274:0.728:0.1446|0.0:0.1274:0.728:0.1446	rs2295847;rs52793228;rs58858000|rs2295847;rs52793228;rs58858000	1940;1934;1934;1221;1934|.	Q8N4C6-5;C9J066;Q8N4C6;Q5BKU3;Q8N4C6-7|.	.;.;NIN_HUMAN;.;.|.	E|R	1934;1917;1221;1221;1940;1934;1934;1934|1424	ENSP00000245441:Q1934E;ENSP00000374518:Q1221E;ENSP00000371474:Q1221E;ENSP00000371472:Q1934E;ENSP00000324210:Q1934E;ENSP00000412391:Q1934E|.	ENSP00000245441:Q1934E|.	Q|T	-|-	1|2	0|0	NIN|NIN	50272061|50272061	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.986000|0.986000	0.74619|0.74619	2.766000|2.766000	0.47629|0.47629	0.873000|0.873000	0.35799|0.35799	0.655000|0.655000	0.94253|0.94253	CAA|ACA	G|0.873;C|0.127	0.127	strong		0.338	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
MUC6	4588	hgsc.bcm.edu	37	11	1017773	1017773	+	Silent	SNP	G	G	A	rs57384288	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1017773G>A	ENST00000421673.2	-	31	5078	c.5028C>T	c.(5026-5028)agC>agT	p.S1676S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1676	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.S1676S(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|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;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGCTGGTCCCGCTGGTGGTCA	0.557													A|||	1486	0.296725	0.3298	0.1542	5008	,	,		31162	0.3165		0.2505	False		,,,				2504	0.3804				p.S1676S		Atlas-SNP	.											MUC6,NS,carcinoma,0,1	MUC6	408	1	1	Substitution - coding silent(1)	ovary(1)	c.C5028T						scavenged	.						688.0	686.0	687.0					11																	1017773		2198	4294	6492	SO:0001819	synonymous_variant	4588	exon31			GGTCCCGCTGGTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5028C>T	11.37:g.1017773G>A		Somatic	538	28	0.0520446		WXS	Illumina HiSeq	Phase_I	678	99	0.146018	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			G|0.500;A|0.500	0.500	strong		0.557	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
PGLYRP3	114771	hgsc.bcm.edu	37	1	153277423	153277423	+	Splice_Site	SNP	C	C	T	rs843971	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153277423C>T	ENST00000290722.1	-	3	428	c.376G>A	c.(376-378)Ggc>Agc	p.G126S		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	126			G -> S (in dbSNP:rs843971). {ECO:0000269|PubMed:15489334}.		defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGACCCTTACCTATCTTATTG	0.512													C|||	2353	0.469848	0.385	0.4553	5008	,	,		20058	0.5833		0.3996	False		,,,				2504	0.5501				p.G126S		Atlas-SNP	.											.	PGLYRP3	55	.	0			c.G376A						PASS	.	C	SER/GLY	1690,2716	509.9+/-367.4	337,1016,850	130.0	113.0	119.0		376	4.5	1.0	1	dbSNP_86	119	3316,5284	494.4+/-373.8	657,2002,1641	yes	missense-near-splice	PGLYRP3	NM_052891.1	56	994,3018,2491	TT,TC,CC		38.5581,38.3568,38.4899	probably-damaging	126/342	153277423	5006,8000	2203	4300	6503	SO:0001630	splice_region_variant	114771	exon3			CCTTACCTATCTT	AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I alpha precursor"""	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.376+1G>A	1.37:g.153277423C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_052891	A1A4U8|Q5SY65	Missense_Mutation	SNP	ENST00000290722.1	37	CCDS1035.1	983	0.4500915750915751	215	0.4369918699186992	164	0.4530386740331492	317	0.5541958041958042	287	0.3786279683377309	C	15.97	2.988634	0.53934	0.383568	0.385581	ENSG00000159527	ENST00000290722	T	0.13307	2.6	4.48	4.48	0.54585	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.000000	0.49916	D	0.000123	T	0.08758	0.0217	L	0.37507	1.11	0.32243	P	0.572436	P	0.48503	0.911	P	0.49085	0.6	T	0.11494	-1.0585	8	.	.	.	-8.6536	12.509	0.55997	0.0:1.0:0.0:0.0	rs843971;rs1655321;rs16835150;rs59808458;rs843971	126	Q96LB9	PGRP3_HUMAN	S	126	ENSP00000290722:G126S	.	G	-	1	0	PGLYRP3	151544047	0.977000	0.34250	0.991000	0.47740	0.269000	0.26545	2.539000	0.45718	2.307000	0.77673	0.557000	0.71058	GGC	C|0.580;T|0.420	0.420	strong		0.512	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1	NM_052891	Missense_Mutation
SLC9C1	285335	hgsc.bcm.edu	37	3	111918215	111918215	+	Missense_Mutation	SNP	C	C	T	rs386664658|rs28516377	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:111918215C>T	ENST00000305815.5	-	20	2728	c.2476G>A	c.(2476-2478)Ggc>Agc	p.G826S	SLC9C1_ENST00000487372.1_Missense_Mutation_p.G778S	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	826			G -> S (in dbSNP:rs28516377). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|ion transmembrane transport (GO:0034220)|multicellular organismal development (GO:0007275)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	solute:proton antiporter activity (GO:0015299)										CCTTTTAAGCCAAAAGCCTTA	0.308													T|||	1682	0.335863	0.3699	0.4049	5008	,	,		17248	0.3393		0.2376	False		,,,				2504	0.3384				p.G826S		Atlas-SNP	.											SLC9A10,NS,carcinoma,0,1	.	.	1	0			c.G2476A						PASS	.	T	SER/GLY	1595,2807	650.4+/-399.0	307,981,913	75.0	82.0	80.0		2476	-3.0	0.0	3	dbSNP_125	80	2317,6279	697.4+/-404.9	321,1675,2302	yes	missense	SLC9A10	NM_183061.1	56	628,2656,3215	TT,TC,CC		26.9544,36.2335,30.0969	benign	826/1178	111918215	3912,9086	2201	4298	6499	SO:0001583	missense	285335	exon20			TTAAGCCAAAAGC	AK128084	CCDS33817.1	3q13	2013-05-22	2012-03-22	2012-03-22	ENSG00000172139	ENSG00000172139		"""Solute carriers"""	31401	protein-coding gene	gene with protein product	"""sperm-NHE"""	612738	"""solute carrier family 9, isoform 10"", ""solute carrier family 9, member 10"""	SLC9A10		12783626	Standard	NM_183061		Approved	NHE	uc003dyu.3	Q4G0N8	OTTHUMG00000159245	ENST00000305815.5:c.2476G>A	3.37:g.111918215C>T	ENSP00000306627:p.Gly826Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	23	0.383333	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	540	0.24725274725274726	114	0.23170731707317074	121	0.3342541436464088	160	0.27972027972027974	145	0.19129287598944592	T	0.024	-1.394455	0.01175	0.362335	0.269544	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.76060	-0.98;-0.99	5.55	-3.0	0.05480	.	1.049680	0.07428	N	0.895123	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.29716	0.004;0.255	B;B	0.24394	0.006;0.053	T	0.05683	-1.0870	9	0.15952	T	0.53	.	8.7266	0.34474	0.0:0.4304:0.1116:0.458	rs28516377	778;826	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	S	826;778	ENSP00000306627:G826S;ENSP00000420688:G778S	ENSP00000306627:G826S	G	-	1	0	SLC9A10	113400905	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.009000	0.13219	-0.760000	0.04677	-3.067000	0.00067	GGC	C|0.725;T|0.275	0.275	strong		0.308	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
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 GAIIx	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		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	153	10	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
PIWIL4	143689	hgsc.bcm.edu	37	11	94322353	94322353	+	Silent	SNP	G	G	A	rs11020846|rs386756343	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:94322353G>A	ENST00000299001.6	+	8	1192	c.981G>A	c.(979-981)caG>caA	p.Q327Q	RP11-867G2.8_ENST00000537874.1_RNA|RP11-867G2.8_ENST00000536540.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	327	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.		Q -> L (in dbSNP:rs11020845). {ECO:0000269|PubMed:14702039}.		cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				ACACCTTTCAGAAGCGGGATG	0.398													G|||	942	0.188099	0.0598	0.1873	5008	,	,		18396	0.2817		0.2813	False		,,,				2504	0.1697				p.Q327Q		Atlas-SNP	.											.	PIWIL4	70	.	0			c.G981A						PASS	.	G		21,4381		7,7,2187	178.0	161.0	167.0		981	4.0	0.8	11	dbSNP_120	167	308,8288		118,72,4108	no	coding-synonymous	PIWIL4	NM_152431.2		125,79,6295	AA,AG,GG		3.5831,0.4771,2.5312		327/853	94322353	329,12669	2201	4298	6499	SO:0001819	synonymous_variant	143689	exon8			CTTTCAGAAGCGG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.981G>A	11.37:g.94322353G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	176	30	0.170455	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			G|0.793;A|0.207	0.207	strong		0.398	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
TEX14	56155	hgsc.bcm.edu	37	17	56690848	56690848	+	Silent	SNP	T	T	C	rs8077548	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:56690848T>C	ENST00000240361.8	-	9	1042	c.957A>G	c.(955-957)ctA>ctG	p.L319L	TEX14_ENST00000349033.5_Silent_p.L313L|TEX14_ENST00000389934.3_Silent_p.L313L			Q8IWB6	TEX14_HUMAN	testis expressed 14	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.L313L(1)|p.L319L(1)		breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GGGTTTTCTCTAGGTCCTGGG	0.502													T|||	1169	0.233427	0.3328	0.0663	5008	,	,		17596	0.3036		0.0726	False		,,,				2504	0.3108				p.L319L		Atlas-SNP	.											TEX14_ENST00000240361,NS,carcinoma,0,2	TEX14	343	2	2	Substitution - coding silent(2)	stomach(2)	c.A957G						PASS	.	T	,,	1205,3201	421.5+/-339.4	161,883,1159	162.0	139.0	147.0		957,939,939	2.5	1.0	17	dbSNP_116	147	564,8036	152.7+/-207.2	19,526,3755	no	coding-synonymous,coding-synonymous,coding-synonymous	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	,,	180,1409,4914	CC,CT,TT		6.5581,27.3491,13.6014	,,	319/1498,313/1452,313/1492	56690848	1769,11237	2203	4300	6503	SO:0001819	synonymous_variant	56155	exon9			TTTCTCTAGGTCC	AF285601	CCDS32692.1, CCDS32693.1, CCDS56042.1	17q22	2013-09-20	2007-03-13		ENSG00000121101	ENSG00000121101			11737	protein-coding gene	gene with protein product	"""cancer/testis antigen 113"""	605792	"""testis expressed sequence 14"""			11279525, 12711554	Standard	NM_031272		Approved	CT113	uc010dcz.2	Q8IWB6	OTTHUMG00000179245	ENST00000240361.8:c.957A>G	17.37:g.56690848T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																			T|0.835;C|0.165	0.165	strong		0.502	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		
SDK2	54549	hgsc.bcm.edu	37	17	71503636	71503636	+	Silent	SNP	T	T	C	rs9895895	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:71503636T>C	ENST00000392650.3	-	2	165	c.165A>G	c.(163-165)ccA>ccG	p.P55P	SDK2_ENST00000388726.3_Silent_p.P55P	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	55	Ig-like C2-type 1.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						TGAACTCCAGTGGCCAGCTGC	0.582													t|||	2849	0.56889	0.5113	0.4827	5008	,	,		21470	0.5		0.6899	False		,,,				2504	0.6544				p.P55P		Atlas-SNP	.											.	SDK2	219	.	0			c.A165G						PASS	.	T		752,632		207,338,147	95.0	94.0	94.0		165	-2.4	1.0	17	dbSNP_119	94	2117,1065		705,707,179	yes	coding-synonymous	SDK2	NM_001144952.1		912,1045,326	CC,CT,TT		33.4695,45.6647,37.166		55/2173	71503636	2869,1697	692	1591	2283	SO:0001819	synonymous_variant	54549	exon2			CTCCAGTGGCCAG	AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.165A>G	17.37:g.71503636T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	106	41	0.386792	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1																																																																																			T|0.439;C|0.561	0.561	strong		0.582	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
FGF18	8817	hgsc.bcm.edu	37	5	170883734	170883734	+	Silent	SNP	G	G	A	rs34347344	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:170883734G>A	ENST00000274625.5	+	5	1093	c.549G>A	c.(547-549)ccG>ccA	p.P183P		NM_003862.2	NP_003853.1	O76093	FGF18_HUMAN	fibroblast growth factor 18	183					anatomical structure morphogenesis (GO:0009653)|angiogenesis (GO:0001525)|cell-cell signaling (GO:0007267)|chondrocyte development (GO:0002063)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intramembranous ossification (GO:0001957)|lung development (GO:0030324)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleolus (GO:0005730)	growth factor activity (GO:0008083)|type 1 fibroblast growth factor receptor binding (GO:0005105)|type 2 fibroblast growth factor receptor binding (GO:0005111)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	9	Renal(175;0.000159)|Lung NSC(126;0.011)|all_lung(126;0.0175)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGGGGCAGCCGGAGCTTCAGA	0.667													G|||	279	0.0557109	0.003	0.1196	5008	,	,		14303	0.123		0.0288	False		,,,				2504	0.0399				p.P183P		Atlas-SNP	.											.	FGF18	33	.	0			c.G549A						PASS	.	G		49,4357	46.0+/-80.4	1,47,2155	41.0	51.0	48.0		549	-11.1	0.0	5	dbSNP_126	48	408,8192	126.8+/-185.2	9,390,3901	no	coding-synonymous	FGF18	NM_003862.2		10,437,6056	AA,AG,GG		4.7442,1.1121,3.5138		183/208	170883734	457,12549	2203	4300	6503	SO:0001819	synonymous_variant	8817	exon5			GCAGCCGGAGCTT	AB007422	CCDS4378.1	5q34	2008-02-05			ENSG00000156427	ENSG00000156427			3674	protein-coding gene	gene with protein product		603726				9660775, 9742123	Standard	NM_003862		Approved	FGF-18, ZFGF5	uc003mbk.3	O76093	OTTHUMG00000130464	ENST00000274625.5:c.549G>A	5.37:g.170883734G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	NM_003862	D3DQL7|Q6UWF1	Silent	SNP	ENST00000274625.5	37	CCDS4378.1																																																																																			G|0.958;A|0.042	0.042	strong		0.667	FGF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252857.2	NM_033649, NM_003862	
UBE2Q2	92912	hgsc.bcm.edu	37	15	76136768	76136768	+	Intron	SNP	C	C	T	rs72734531	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:76136768C>T	ENST00000267938.4	+	1	562				UBE2Q2_ENST00000569423.1_Intron|UBE2Q2_ENST00000562635.1_3'UTR|UBE2Q2_ENST00000338677.4_Intron|UBE2Q2_ENST00000561851.1_Missense_Mutation_p.P25L	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2						protein K48-linked ubiquitination (GO:0070936)	cytoplasm (GO:0005737)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	12						CCCTCTCCCCCGGGCCTGGCT	0.547													.|||	988	0.197284	0.0106	0.1729	5008	,	,		15457	0.3631		0.1392	False		,,,				2504	0.3558				p.P25L		Atlas-SNP	.											.	UBE2Q2	26	.	0			c.C74T						PASS	.	C	LEU/PRO,	41,1331		0,41,645	155.0	142.0	146.0		74,	2.5	0.0	15	dbSNP_130	146	415,2755		28,359,1198	no	missense,intron	UBE2Q2	NM_001145335.1,NM_173469.2	98,	28,400,1843	TT,TC,CC		13.0915,2.9883,10.0396	,	25/360,	76136768	456,4086	686	1585	2271	SO:0001627	intron_variant	92912	exon1			CTCCCCCGGGCCT	BC017708	CCDS10286.1, CCDS45309.1, CCDS66839.1	15q24.2	2010-05-12	2008-05-02		ENSG00000140367	ENSG00000140367		"""Ubiquitin-conjugating enzymes E2"""	19248	protein-coding gene	gene with protein product		612501	"""ubiquitin-conjugating enzyme E2Q (putative) 2"""			16300736	Standard	NM_001145335		Approved	DKFZp762C143	uc002bbg.2	Q8WVN8	OTTHUMG00000142839	ENST00000267938.4:c.180+581C>T	15.37:g.76136768C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_001145335	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	Missense_Mutation	SNP	ENST00000267938.4	37	CCDS10286.1	394	0.1804029304029304	10	0.02032520325203252	63	0.17403314917127072	206	0.36013986013986016	115	0.1517150395778364	c	0.796	-0.757115	0.03019	0.029883	0.130915	ENSG00000140367	ENST00000426727	.	.	.	2.46	2.46	0.29980	.	.	.	.	.	T	0.00012	0.0000	L	0.59436	1.845	0.38578	P	0.049892999999999965	B	0.22851	0.076	B	0.16722	0.016	T	0.26780	-1.0093	7	0.45353	T	0.12	.	8.5404	0.33388	0.0:1.0:0.0:0.0	.	25	E9PHD0	.	L	25	.	ENSP00000400960:P25L	P	+	2	0	UBE2Q2	73923823	0.000000	0.05858	0.003000	0.11579	0.010000	0.07245	0.031000	0.13710	1.681000	0.50988	0.460000	0.39030	CCG	C|0.812;T|0.188	0.188	strong		0.547	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286475.1	NM_173469	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98411293	98411293	+	Silent	SNP	G	G	A	rs35668691	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:98411293G>A	ENST00000339364.5	-	5	947	c.828C>T	c.(826-828)gcC>gcT	p.A276A	PIK3AP1_ENST00000468783.1_5'UTR|PIK3AP1_ENST00000371110.2_Silent_p.A98A	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	276	DBB. {ECO:0000255|PROSITE- ProRule:PRU00707}.				negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		CAGGATTCGCGGCATTGGACA	0.393													G|||	77	0.0153754	0.003	0.0303	5008	,	,		21313	0.0		0.0427	False		,,,				2504	0.0092				p.A276A		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.C828T						PASS	.	G		18,4388	25.3+/-52.1	0,18,2185	97.0	95.0	96.0		828	-4.5	1.0	10	dbSNP_126	96	307,8293	110.6+/-171.0	7,293,4000	yes	coding-synonymous	PIK3AP1	NM_152309.2		7,311,6185	AA,AG,GG		3.5698,0.4085,2.4988		276/806	98411293	325,12681	2203	4300	6503	SO:0001819	synonymous_variant	118788	exon5			ATTCGCGGCATTG	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.828C>T	10.37:g.98411293G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Silent	SNP	ENST00000339364.5	37	CCDS31259.1																																																																																			G|0.975;A|0.025	0.025	strong		0.393	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
RHBG	57127	hgsc.bcm.edu	37	1	156347131	156347131	+	Missense_Mutation	SNP	G	G	A	rs2245623	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156347131G>A	ENST00000368249.1	+	2	265	c.227G>A	c.(226-228)gGc>gAc	p.G76D	RHBG_ENST00000451864.2_Missense_Mutation_p.G7D|RHBG_ENST00000537040.1_Intron|RHBG_ENST00000255013.3_Missense_Mutation_p.G7D|RHBG_ENST00000368246.2_Missense_Mutation_p.G76D|RHBG_ENST00000400992.2_Missense_Mutation_p.G7D	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	76			G -> D (in dbSNP:rs2245623). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					GTGGGCTTTGGCTTCCTCATG	0.637													G|||	1355	0.270567	0.1936	0.2781	5008	,	,		21225	0.1012		0.4563	False		,,,				2504	0.3528				p.G76D		Atlas-SNP	.											.	RHBG	133	.	0			c.G227A						PASS	.	G	ASP/GLY	993,3413	365.9+/-317.6	106,781,1316	142.0	144.0	143.0		227	4.9	1.0	1	dbSNP_100	143	3847,4753	537.9+/-383.3	886,2075,1339	yes	missense	RHBG	NM_020407.3	94	992,2856,2655	AA,AG,GG		44.7326,22.5374,37.2136	probably-damaging	76/459	156347131	4840,8166	2203	4300	6503	SO:0001583	missense	57127	exon2			GCTTTGGCTTCCT	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"""Solute carriers"""	14572	protein-coding gene	gene with protein product		607079	"""Rhesus blood group, B glycoprotein"""			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.227G>A	1.37:g.156347131G>A	ENSP00000357232:p.Gly76Asp	Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	188	184	0.978723	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Missense_Mutation	SNP	ENST00000368249.1	37		608	0.2783882783882784	95	0.19308943089430894	109	0.3011049723756906	58	0.10139860139860139	346	0.45646437994722955	G	34	5.389342	0.95988	0.225374	0.447326	ENSG00000132677	ENST00000368249;ENST00000368246;ENST00000400992;ENST00000255013;ENST00000451864	D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51	4.86	4.86	0.63082	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	D	0.91744	0.7389	H	0.94582	3.555	0.09310	P	0.9999999999972279	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.93736	0.7046	9	0.87932	D	0	-6.6399	16.7188	0.85405	0.0:0.0:1.0:0.0	rs2245623;rs17387461;rs2245623	76;7;113	Q9H310;Q9H310-3;Q5SZW5	RHBG_HUMAN;.;.	D	76;76;7;7;7	ENSP00000357232:G76D;ENSP00000357229:G76D;ENSP00000383777:G7D;ENSP00000255013:G7D;ENSP00000389836:G7D	ENSP00000255013:G7D	G	+	2	0	RHBG	154613755	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.395000	0.97266	2.512000	0.84698	0.561000	0.74099	GGC	G|0.713;A|0.287	0.287	strong		0.637	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395	
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75785100	75785100	+	Silent	SNP	C	C	T	rs11180483	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:75785100C>T	ENST00000550916.1	+	1	251	c.204C>T	c.(202-204)gtC>gtT	p.V68V	GLIPR1L2_ENST00000547164.1_Silent_p.V68V|CAPS2_ENST00000442339.2_5'Flank|GLIPR1L2_ENST00000378689.2_Silent_p.V68V|GLIPR1L2_ENST00000320460.4_Silent_p.V68V|GLIPR1L2_ENST00000435775.1_Silent_p.V68V|GLIPR1L2_ENST00000378692.3_5'UTR|GLIPR1L2_ENST00000441218.1_5'Flank	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	68	SCP.					integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						GGGGCGACGTCATTCCCCGAG	0.562											OREG0021999	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1614	0.322284	0.2254	0.2608	5008	,	,		16266	0.4673		0.3767	False		,,,				2504	0.2914				p.V68V		Atlas-SNP	.											.	GLIPR1L2	54	.	0			c.C204T						PASS	.	C		1207,3199	421.3+/-339.3	159,889,1155	108.0	82.0	91.0		204	0.8	0.0	12	dbSNP_120	91	3405,5195	503.3+/-375.9	686,2033,1581	no	coding-synonymous	GLIPR1L2	NM_152436.1		845,2922,2736	TT,TC,CC		39.593,27.3945,35.4606		68/254	75785100	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	144321	exon1			CGACGTCATTCCC	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.204C>T	12.37:g.75785100C>T		Somatic	127	0	0	1163	WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Silent	SNP	ENST00000550916.1	37	CCDS58258.1																																																																																			C|0.653;T|0.347	0.347	strong		0.562	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
TMEM132B	114795	hgsc.bcm.edu	37	12	125834095	125834095	+	Silent	SNP	C	C	A	rs1491893	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:125834095C>A	ENST00000299308.3	+	2	158	c.150C>A	c.(148-150)tcC>tcA	p.S50S	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	50						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CAGAGGAGTCCTTTTTCCTTA	0.532													C|||	1374	0.274361	0.1838	0.3458	5008	,	,		17454	0.2728		0.3012	False		,,,				2504	0.32				p.S50S		Atlas-SNP	.											.	TMEM132B	207	.	0			c.C150A						PASS	.	C		793,3097		79,635,1231	132.0	133.0	132.0		150	2.0	0.4	12	dbSNP_88	132	2441,5849		364,1713,2068	no	coding-synonymous	TMEM132B	NM_052907.2		443,2348,3299	AA,AC,CC		29.4451,20.3856,26.5517		50/1079	125834095	3234,8946	1945	4145	6090	SO:0001819	synonymous_variant	114795	exon2			GGAGTCCTTTTTC	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.150C>A	12.37:g.125834095C>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			C|0.737;A|0.262	0.262	strong		0.532	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
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 GAIIx	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_ENST00000360802.1_Missense_Mutation_p.M39V|UBAP2_ENST00000418786.2_Missense_Mutation_p.M39V|UBAP2_ENST00000449054.1_Missense_Mutation_p.M39V|UBAP2_ENST00000379239.4_5'UTR|UBAP2_ENST00000480885.1_5'UTR|UBAP2_ENST00000539807.1_Start_Codon_SNP_p.M1V					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	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	16	11	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	
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 GAIIx	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	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	132	62	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		
UNC5C	8633	hgsc.bcm.edu	37	4	96166270	96166270	+	Silent	SNP	C	C	T	rs35120448	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:96166270C>T	ENST00000453304.1	-	6	1149	c.801G>A	c.(799-801)acG>acA	p.T267T	UNC5C_ENST00000506749.1_Silent_p.T267T	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	267	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CAGACCACTCCGTCCAGGTGG	0.512													C|||	116	0.0231629	0.0159	0.0346	5008	,	,		17093	0.0		0.0537	False		,,,				2504	0.0174				p.T267T		Atlas-SNP	.											UNC5C,NS,carcinoma,-1,1	UNC5C	141	1	0			c.G801A						PASS	.	C		97,4309	78.3+/-116.7	3,91,2109	64.0	55.0	58.0		801	-5.9	1.0	4	dbSNP_126	58	444,8156	133.1+/-190.7	8,428,3864	no	coding-synonymous	UNC5C	NM_003728.3		11,519,5973	TT,TC,CC		5.1628,2.2015,4.1596		267/932	96166270	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon6			CCACTCCGTCCAG	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.801G>A	4.37:g.96166270C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.961;T|0.039	0.039	strong		0.512	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
TIMM10B	26515	hgsc.bcm.edu	37	11	6502780	6502780	+	Silent	SNP	C	C	A	rs11555935	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6502780C>A	ENST00000254616.6	+	1	104	c.34C>A	c.(34-36)Cga>Aga	p.R12R	TIMM10B_ENST00000472836.1_Silent_p.R12R|ARFIP2_ENST00000525235.1_5'Flank|TIMM10B_ENST00000530751.1_Silent_p.R12R|ARFIP2_ENST00000445086.2_5'Flank|ARFIP2_ENST00000423813.2_5'Flank|ARFIP2_ENST00000254584.2_5'Flank|ARFIP2_ENST00000396777.3_5'Flank	NM_012192.3	NP_036324.1	Q9Y5J6	T10B_HUMAN	translocase of inner mitochondrial membrane 10 homolog B (yeast)	12					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial intermembrane space protein transporter complex (GO:0042719)	metal ion binding (GO:0046872)										acagcaACTGCGAAACGTAAG	0.607													A|||	837	0.167133	0.2118	0.1686	5008	,	,		17547	0.0327		0.1839	False		,,,				2504	0.227				p.R12R		Atlas-SNP	.											.	.	.	.	0			c.C34A						PASS	.	A		910,3492	721.9+/-409.2	93,724,1384	98.0	67.0	78.0		34	2.9	0.9	11	dbSNP_120	78	1667,6925	727.2+/-406.6	170,1327,2799	no	coding-synonymous	FXC1	NM_012192.3		263,2051,4183	AA,AC,CC		19.4018,20.6724,19.8322		12/104	6502780	2577,10417	2201	4296	6497	SO:0001819	synonymous_variant	26515	exon1			CAACTGCGAAACG	AF150105	CCDS7766.1	11p15.4	2012-12-07	2012-12-07	2012-12-07	ENSG00000132286	ENSG00000132286			4022	protein-coding gene	gene with protein product		607388	"""fracture callus 1 (rat) homolog"", ""fracture callus 1 homolog (rat)"""	FXC1		10552927	Standard	NM_012192		Approved	Tim9b, TIM10B	uc001mdn.4	Q9Y5J6	OTTHUMG00000133400	ENST00000254616.6:c.34C>A	11.37:g.6502780C>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_012192	Q96FF3	Silent	SNP	ENST00000254616.6	37	CCDS7766.1																																																																																			A|0.180;C|0.820;G|0.000;T|0.000	0.180	strong		0.607	TIMM10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257257.2	NM_012192	
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 GAIIx	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		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	11	5	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	
GET4	51608	hgsc.bcm.edu	37	7	930608	930608	+	Silent	SNP	G	G	A	rs11543223	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:930608G>A	ENST00000265857.3	+	5	604	c.510G>A	c.(508-510)gcG>gcA	p.A170A	GET4_ENST00000407192.1_Silent_p.A117A	NM_015949.2	NP_057033.2	Q7L5D6	GET4_HUMAN	golgi to ER traffic protein 4 homolog (S. cerevisiae)	170					tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)				breast(1)|large_intestine(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TGCACTCAGCGGACGGGGAGG	0.502													G|||	291	0.058107	0.1172	0.0346	5008	,	,		22241	0.0		0.0765	False		,,,				2504	0.0358				p.A170A		Atlas-SNP	.											.	GET4	17	.	0			c.G510A						PASS	.	G		569,3837	252.7+/-259.0	35,499,1669	136.0	124.0	128.0		510	-10.2	0.0	7	dbSNP_120	128	577,8023	155.5+/-209.5	21,535,3744	no	coding-synonymous	GET4	NM_015949.2		56,1034,5413	AA,AG,GG		6.7093,12.9142,8.8113		170/328	930608	1146,11860	2203	4300	6503	SO:0001819	synonymous_variant	51608	exon5			CTCAGCGGACGGG	AK023560	CCDS5317.1	7p22.3	2010-08-05	2010-03-24	2010-03-24	ENSG00000239857	ENSG00000239857			21690	protein-coding gene	gene with protein product	"""CGI-20 protein"", ""conserved edge protein"", ""transmembrane domain recognition complex, 35kDa"""	612056	"""chromosome 7 open reading frame 20"""	C7orf20		10810093, 20106980, 20676083	Standard	NM_015949		Approved	CGI-20, H_NH1244M04.5, CEE, TRC35	uc003sjl.1	Q7L5D6	OTTHUMG00000112459	ENST00000265857.3:c.510G>A	7.37:g.930608G>A		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	264	104	0.393939	NM_015949	A4D2Q1|B3KNC7|Q9UFC9|Q9Y309	Silent	SNP	ENST00000265857.3	37	CCDS5317.1																																																																																			G|0.921;A|0.079	0.079	strong		0.502	GET4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000231930.1	NM_015949	
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 GAIIx	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	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	61	29	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	
OR10H3	26532	hgsc.bcm.edu	37	19	15853080	15853080	+	Missense_Mutation	SNP	G	G	A	rs2240229	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15853080G>A	ENST00000305892.1	+	1	878	c.878G>A	c.(877-879)aGt>aAt	p.S293N		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	293			S -> N (in dbSNP:rs2240229).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						ATCATTTTCAGTCTAAGGAAC	0.443													g|||	788	0.157348	0.1505	0.111	5008	,	,		21377	0.122		0.169	False		,,,				2504	0.2239				p.S293N		Atlas-SNP	.											.	OR10H3	53	.	0			c.G878A						PASS	.	G	ASN/SER	766,3640		64,638,1501	154.0	148.0	150.0		878	2.4	1.0	19	dbSNP_98	150	1623,6977		169,1285,2846	yes	missense	OR10H3	NM_013938.1	46	233,1923,4347	AA,AG,GG		18.8721,17.3854,18.3684	probably-damaging	293/317	15853080	2389,10617	2203	4300	6503	SO:0001583	missense	26532	exon1			TTTTCAGTCTAAG		CCDS12334.1	19p13.1	2012-08-09				ENSG00000171936		"""GPCR / Class A : Olfactory receptors"""	8174	protein-coding gene	gene with protein product							Standard	NM_013938		Approved		uc010xoq.2	O60404		ENST00000305892.1:c.878G>A	19.37:g.15853080G>A	ENSP00000307130:p.Ser293Asn	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_013938	Q2HIZ3|Q6IFQ0	Missense_Mutation	SNP	ENST00000305892.1	37	CCDS12334.1	323	0.1478937728937729	79	0.16056910569105692	36	0.09944751381215469	79	0.1381118881118881	129	0.17018469656992086	.	11.25	1.582703	0.28180	0.173854	0.188721	ENSG00000171936	ENST00000305892	T	0.39056	1.1	2.37	2.37	0.29283	.	0.274240	0.25439	U	0.030667	T	0.00241	0.0007	M	0.93197	3.39	0.38547	P	0.050629000000000035	D	0.89917	1.0	D	0.91635	0.999	T	0.32214	-0.9915	9	0.72032	D	0.01	.	10.3915	0.44171	0.0:0.0:1.0:0.0	rs2240229;rs17682603;rs60748494;rs2240229	293	O60404	O10H3_HUMAN	N	293	ENSP00000307130:S293N	ENSP00000307130:S293N	S	+	2	0	OR10H3	15714080	0.017000	0.18338	0.996000	0.52242	0.017000	0.09413	0.941000	0.29005	1.330000	0.45394	0.205000	0.17691	AGT	G|0.833;A|0.167	0.167	strong		0.443	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
CEP72	55722	hgsc.bcm.edu	37	5	640705	640705	+	Missense_Mutation	SNP	A	A	G	rs868649|rs386684282	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:640705A>G	ENST00000264935.5	+	9	1615	c.1525A>G	c.(1525-1527)Aca>Gca	p.T509A	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	509			T -> A (in dbSNP:rs868649). {ECO:0000269|PubMed:10819331}.		G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			GCTGCACCACACACACAAGGA	0.627													A|||	1346	0.26877	0.2579	0.2507	5008	,	,		17932	0.4683		0.2286	False		,,,				2504	0.1319				p.T509A		Atlas-SNP	.											.	CEP72	53	.	0			c.A1525G						PASS	.	A	ALA/THR	878,3528		149,580,1474	43.0	46.0	45.0		1525	-2.3	0.0	5	dbSNP_89	45	1946,6654		238,1470,2592	yes	missense	CEP72	NM_018140.3	58	387,2050,4066	GG,GA,AA		22.6279,19.9274,21.7131	benign	509/648	640705	2824,10182	2203	4300	6503	SO:0001583	missense	55722	exon9			CACCACACACACA	BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.1525A>G	5.37:g.640705A>G	ENSP00000264935:p.Thr509Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_018140	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	622	0.2847985347985348	117	0.23780487804878048	90	0.24861878453038674	243	0.42482517482517484	172	0.22691292875989447	A	3.791	-0.043731	0.07452	0.199274	0.226279	ENSG00000112877	ENST00000264935	T	0.33865	1.39	5.02	-2.31	0.06765	.	0.317210	0.32444	N	0.006085	T	0.00012	0.0000	N	0.25201	0.72	0.58432	P	1.0000000000287557E-6	B	0.09022	0.002	B	0.08055	0.003	T	0.48234	-0.9053	9	0.15066	T	0.55	-1.275	10.9594	0.47376	0.3702:0.0:0.6298:0.0	rs868649;rs58588705;rs868649	509	Q9P209	CEP72_HUMAN	A	509	ENSP00000264935:T509A	ENSP00000264935:T509A	T	+	1	0	CEP72	693705	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.852000	0.00731	-0.271000	0.09272	0.459000	0.35465	ACA	T|0.001;G|0.251	0.251	strong		0.627	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140	
TPM1	7168	hgsc.bcm.edu	37	15	63351873	63351873	+	Silent	SNP	T	T	C	rs11558747	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:63351873T>C	ENST00000403994.3	+	4	566	c.486T>C	c.(484-486)taT>taC	p.Y162Y	TPM1_ENST00000560445.1_Intron|TPM1_ENST00000559281.1_Silent_p.Y126Y|TPM1_ENST00000560959.1_Silent_p.Y126Y|TPM1_ENST00000334895.5_Silent_p.Y126Y|TPM1_ENST00000559556.1_Silent_p.Y162Y|TPM1_ENST00000357980.4_Silent_p.Y204Y|TPM1_ENST00000559397.1_Silent_p.Y162Y|TPM1_ENST00000288398.6_Silent_p.Y162Y|TPM1_ENST00000358278.3_Silent_p.Y162Y|TPM1_ENST00000267996.7_Silent_p.Y162Y|TPM1_ENST00000317516.7_Silent_p.Y126Y|TPM1_ENST00000404484.4_Silent_p.Y126Y	NM_001018005.1	NP_001018005.1	P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	162					cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						ACCGCAAATATGAAGAGGTCA	0.502													T|||	121	0.0241613	0.0015	0.0447	5008	,	,		19741	0.0		0.0676	False		,,,				2504	0.0204				p.Y162Y		Atlas-SNP	.											.	TPM1	59	.	0			c.T486C						PASS	.	T	,,,,,,	49,4357	50.2+/-85.5	1,47,2155	60.0	59.0	59.0		486,486,486,486,486,378,486	4.7	1.0	15	dbSNP_120	59	613,7987	161.1+/-214.1	26,561,3713	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPM1	NM_000366.5,NM_001018004.1,NM_001018005.1,NM_001018006.1,NM_001018007.1,NM_001018008.1,NM_001018020.1	,,,,,,	27,608,5868	CC,CT,TT		7.1279,1.1121,5.09	,,,,,,	162/285,162/285,162/285,162/285,162/285,126/246,162/285	63351873	662,12344	2203	4300	6503	SO:0001819	synonymous_variant	7168	exon4			CAAATATGAAGAG	AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"""Tropomyosins"""	12010	protein-coding gene	gene with protein product		191010	"""chromosome 15 open reading frame 13"", ""cardiomyopathy, hypertrophic 3"""	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000403994.3:c.486T>C	15.37:g.63351873T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_001018007	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Silent	SNP	ENST00000403994.3	37	CCDS45273.1																																																																																			T|0.951;C|0.049	0.049	strong		0.502	TPM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417083.2	NM_001018004	
GAREM	64762	hgsc.bcm.edu	37	18	29867091	29867091	+	Missense_Mutation	SNP	G	G	A	rs16962974	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:29867091G>A	ENST00000269209.6	-	4	1472	c.1469C>T	c.(1468-1470)gCg>gTg	p.A490V	GAREM_ENST00000578619.1_5'Flank|RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000399218.4_Missense_Mutation_p.A490V			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	490			A -> V (in dbSNP:rs16962974).		cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)										AGGAGAAGTCGCACATTTGGA	0.547													G|||	307	0.0613019	0.174	0.0346	5008	,	,		19219	0.0		0.0388	False		,,,				2504	0.0143				p.A490V		Atlas-SNP	.											.	.	.	.	0			c.C1469T						PASS	.	G	VAL/ALA,VAL/ALA	716,3690	296.7+/-284.4	61,594,1548	141.0	132.0	135.0		1469,1469	4.4	0.4	18	dbSNP_123	135	189,8411	84.2+/-146.7	0,189,4111	yes	missense,missense	FAM59A	NM_001242409.1,NM_022751.2	64,64	61,783,5659	AA,AG,GG		2.1977,16.2506,6.9583	benign,benign	490/877,490/876	29867091	905,12101	2203	4300	6503	SO:0001583	missense	64762	exon4			GAAGTCGCACATT	AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.1469C>T	18.37:g.29867091G>A	ENSP00000269209:p.Ala490Val	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	37	CCDS56057.1	120	0.054945054945054944	80	0.16260162601626016	12	0.03314917127071823	0	0.0	28	0.036939313984168866	G	9.516	1.106909	0.20714	0.162506	0.021977	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.14766	2.48;2.48	5.26	4.38	0.52667	.	0.820590	0.11537	N	0.554161	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;P	0.37573	0.357;0.6	B;B	0.32289	0.033;0.143	T	0.37709	-0.9694	9	0.48119	T	0.1	-2.4914	13.1388	0.59423	0.0:0.5019:0.4981:0.0	rs16962974;rs52790984;rs61472108;rs16962974	490;490	Q9H706;Q9H706-3	FA59A_HUMAN;.	V	490	ENSP00000382165:A490V;ENSP00000269209:A490V	ENSP00000269209:A490V	A	-	2	0	FAM59A	28121089	0.941000	0.31946	0.362000	0.25862	0.495000	0.33615	2.077000	0.41557	1.585000	0.49928	0.655000	0.94253	GCG	G|0.936;A|0.064	0.064	strong		0.547	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751	
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 GAIIx	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	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	108	47	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 GAIIx	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		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	183	12	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	
DCANP1	140947	hgsc.bcm.edu	37	5	134782510	134782510	+	Missense_Mutation	SNP	T	T	C	rs12520809	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134782510T>C	ENST00000503143.2	-	1	528	c.289A>G	c.(289-291)Aat>Gat	p.N97D	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		97			N -> D (in dbSNP:rs12520809).			nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTCGAAAGATTGGAGTTGCAG	0.597													C|||	3231	0.645168	0.9312	0.5533	5008	,	,		19045	0.5645		0.5149	False		,,,				2504	0.5409				p.N97D		Atlas-SNP	.											.	C5orf20	16	.	0			c.A289G						PASS	.	C	ASP/ASN	3800,606	264.4+/-266.0	1647,506,50	60.0	64.0	62.0		289	-1.4	0.0	5	dbSNP_120	62	3987,4613	599.4+/-394.1	907,2173,1220	yes	missense	C5orf20	NM_130848.2	23	2554,2679,1270	CC,CT,TT		46.3605,13.754,40.1276	benign	97/245	134782510	7787,5219	2203	4300	6503	SO:0001583	missense	140947	exon1			AAAGATTGGAGTT																												ENST00000503143.2:c.289A>G	5.37:g.134782510T>C	ENSP00000421871:p.Asn97Asp	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	1332	0.6098901098901099	452	0.9186991869918699	184	0.5082872928176796	316	0.5524475524475524	380	0.5013192612137203	C	3.765	-0.048825	0.07407	0.86246	0.463605	ENSG00000251380	ENST00000503143	T	0.36699	1.24	1.85	-1.38	0.09027	.	.	.	.	.	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	0.17501	-1.0367	8	0.87932	D	0	.	6.7317	0.23387	0.0:0.3181:0.0:0.6819	rs12520809;rs17733329;rs56639907;rs60343948;rs12520809	97	Q8TF63	DCNP1_HUMAN	D	97	ENSP00000421871:N97D	ENSP00000421871:N97D	N	-	1	0	C5orf20	134810409	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.320000	0.02700	-0.932000	0.03742	-1.295000	0.01343	AAT	C|0.631;N|0.000	0.631	strong		0.597	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
ZNF804A	91752	hgsc.bcm.edu	37	2	185801559	185801559	+	Missense_Mutation	SNP	A	A	G	rs35676856	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:185801559A>G	ENST00000302277.6	+	4	2030	c.1436A>G	c.(1435-1437)gAc>gGc	p.D479G		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	479			D -> G (in dbSNP:rs35676856). {ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)			NS(5)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(22)|liver(2)|lung(79)|ovary(7)|pancreas(1)|prostate(2)|skin(12)|urinary_tract(1)	146						AATAAGCCAGACTTAAAAGAT	0.338													A|||	177	0.0353435	0.0159	0.0331	5008	,	,		17452	0.0159		0.0666	False		,,,				2504	0.0511				p.D479G		Atlas-SNP	.											ZNF804A,NS,carcinoma,+1,1	ZNF804A	322	1	0			c.A1436G						PASS	.	A	GLY/ASP	115,4289	81.9+/-120.4	1,113,2088	76.0	80.0	79.0		1436	1.5	0.0	2	dbSNP_126	79	669,7931	162.9+/-215.5	33,603,3664	yes	missense	ZNF804A	NM_194250.1	94	34,716,5752	GG,GA,AA		7.7791,2.6113,6.0289	benign	479/1210	185801559	784,12220	2202	4300	6502	SO:0001583	missense	91752	exon4			AGCCAGACTTAAA	AF052145	CCDS2291.1	2q32.1	2012-10-05	2006-10-27	2006-10-27	ENSG00000170396	ENSG00000170396			21711	protein-coding gene	gene with protein product		612282		C2orf10		12970790	Standard	NM_194250		Approved		uc002uph.3	Q7Z570	OTTHUMG00000132625	ENST00000302277.6:c.1436A>G	2.37:g.185801559A>G	ENSP00000303252:p.Asp479Gly	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	126	63	0.5	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	72	0.03296703296703297	3	0.006097560975609756	12	0.03314917127071823	9	0.015734265734265736	48	0.0633245382585752	A	0.808	-0.753030	0.03041	0.026113	0.077791	ENSG00000170396	ENST00000302277	T	0.05996	3.36	5.69	1.48	0.22813	.	1.391250	0.04406	N	0.365125	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42849	-0.9427	10	0.22706	T	0.39	0.1455	2.8485	0.05550	0.4077:0.37:0.1275:0.0948	rs35676856	479	Q7Z570	Z804A_HUMAN	G	479	ENSP00000303252:D479G	ENSP00000303252:D479G	D	+	2	0	ZNF804A	185509804	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.058000	0.14301	0.713000	0.32060	-0.144000	0.13903	GAC	A|0.947;G|0.053	0.053	strong		0.338	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
JAG1	182	hgsc.bcm.edu	37	20	10637057	10637057	+	Silent	SNP	T	T	C	rs10485741|rs34271232	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:10637057T>C	ENST00000254958.5	-	5	1259	c.744A>G	c.(742-744)ccA>ccG	p.P248P	JAG1_ENST00000423891.2_Silent_p.P89P	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	248	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						TGCAGTCACCTGGGAGTTTGC	0.433									Alagille Syndrome				C|||	294	0.0587061	0.0461	0.121	5008	,	,		17762	0.0198		0.0825	False		,,,				2504	0.047				p.P248P		Atlas-SNP	.											.	JAG1	213	.	0			c.A744G						PASS	.	C		243,4163	804.0+/-415.7	4,235,1964	78.0	74.0	75.0		744	-8.9	0.8	20	dbSNP_119	75	608,7992	791.8+/-407.5	17,574,3709	no	coding-synonymous	JAG1	NM_000214.2		21,809,5673	CC,CT,TT		7.0698,5.5152,6.5431		248/1219	10637057	851,12155	2203	4300	6503	SO:0001819	synonymous_variant	182	exon5	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GTCACCTGGGAGT	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.744A>G	20.37:g.10637057T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			T|0.940;C|0.060	0.060	strong		0.433	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
APBB3	10307	hgsc.bcm.edu	37	5	139940233	139940233	+	Silent	SNP	G	G	A	rs250431	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:139940233G>A	ENST00000357560.4	-	11	1466	c.1023C>T	c.(1021-1023)caC>caT	p.H341H	SRA1_ENST00000520427.1_5'Flank|APBB3_ENST00000358580.5_Intron|APBB3_ENST00000412920.3_Silent_p.H339H|APBB3_ENST00000511201.2_Intron|APBB3_ENST00000356738.2_Silent_p.H346H|APBB3_ENST00000508496.2_Silent_p.H118H|SRA1_ENST00000336283.6_5'Flank|APBB3_ENST00000354402.5_Silent_p.H348H|APBB3_ENST00000507279.1_5'Flank	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	341	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGAATGGGGTGTGCAGTCA	0.582													G|||	3162	0.63139	0.292	0.7248	5008	,	,		19374	0.8254		0.7137	False		,,,				2504	0.7393				p.H348H		Atlas-SNP	.											APBB3,NS,carcinoma,-1,1	APBB3	34	1	0			c.C1044T						scavenged	.	G	,,,	1633,2773	501.7+/-365.1	297,1039,867	62.0	53.0	56.0		1044,1038,1023,1017	-0.3	1.0	5	dbSNP_79	56	6011,2589	689.2+/-404.3	2102,1807,391	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	APBB3	NM_006051.3,NM_133172.2,NM_133173.2,NM_133174.2	,,,	2399,2846,1258	AA,AG,GG		30.1047,37.0631,41.2271	,,,	348/494,346/492,341/487,339/485	139940233	7644,5362	2203	4300	6503	SO:0001819	synonymous_variant	10307	exon10			AATGGGGTGTGCA	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.1023C>T	5.37:g.139940233G>A		Somatic	69	1	0.0144928		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_006051	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Silent	SNP	ENST00000357560.4	37	CCDS4229.1																																																																																			G|0.389;A|0.611	0.611	strong		0.582	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251677.2	NM_006051	
MACROD1	28992	hgsc.bcm.edu	37	11	63885287	63885287	+	Intron	SNP	C	C	T	rs947939	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:63885287C>T	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Silent_p.Y516Y	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|large_intestine(3)|lung(6)|skin(1)	11						GCAATGCCTACGTAGCTGATG	0.592													C|||	347	0.0692891	0.0121	0.0821	5008	,	,		21394	0.0675		0.1392	False		,,,				2504	0.0675				p.Y516Y		Atlas-SNP	.											.	FLRT1	46	.	0			c.C1548T						PASS	.	C	,	160,4242	109.5+/-147.8	2,156,2043	103.0	75.0	85.0		1548,	-2.8	0.1	11	dbSNP_86	85	1320,7274	259.7+/-282.8	106,1108,3083	no	coding-synonymous,intron	FLRT1,MACROD1	NM_013280.4,NM_014067.3	,	108,1264,5126	TT,TC,CC		15.3596,3.6347,11.3881	,	516/675,	63885287	1480,11516	2201	4297	6498	SO:0001627	intron_variant	23769	exon2			TGCCTACGTAGCT	AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+33423G>A	11.37:g.63885287C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	158	88	0.556962	NM_013280	Q9UH96	Silent	SNP	ENST00000255681.6	37	CCDS8056.1																																																																																			C|0.896;T|0.104	0.104	strong		0.592	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
CSF1	1435	hgsc.bcm.edu	37	1	110466466	110466466	+	Missense_Mutation	SNP	T	T	C	rs1058885	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:110466466T>C	ENST00000329608.6	+	6	1614	c.1223T>C	c.(1222-1224)cTg>cCg	p.L408P	CSF1_ENST00000369801.1_Intron|CSF1_ENST00000369802.3_Missense_Mutation_p.L408P|CSF1_ENST00000420111.2_Intron|CSF1_ENST00000344188.5_Intron	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	408	O-glycosylated at one site.		L -> P (in dbSNP:rs1058885). {ECO:0000269|PubMed:2660794}.		branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|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 cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		ATCTCATCACTGCGCCCCCAG	0.657													C|||	2111	0.421526	0.4554	0.3271	5008	,	,		15689	0.5972		0.336	False		,,,				2504	0.3497				p.L408P		Atlas-SNP	.											.	CSF1	40	.	0			c.T1223C	GRCh37	CM066774	CSF1	M	rs1058885	PASS	.	C	PRO/LEU,,,PRO/LEU	1940,2466	604.3+/-390.3	432,1076,695	42.0	52.0	48.0		1223,,,1223	-9.1	0.0	1	dbSNP_86	48	3204,5396	633.4+/-398.7	603,1998,1699	yes	missense,intron,intron,missense	CSF1	NM_000757.5,NM_172210.2,NM_172211.2,NM_172212.2	98,,,98	1035,3074,2394	CC,CT,TT		37.2558,44.0309,39.551	benign,,,benign	408/555,,,408/555	110466466	5144,7862	2203	4300	6503	SO:0001583	missense	1435	exon6			CATCACTGCGCCC	BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.1223T>C	1.37:g.110466466T>C	ENSP00000327513:p.Leu408Pro	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_000757	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Missense_Mutation	SNP	ENST00000329608.6	37	CCDS816.1	930	0.4258241758241758	201	0.40853658536585363	127	0.35082872928176795	347	0.6066433566433567	255	0.33641160949868076	C	8.471	0.857555	0.17106	0.440309	0.372558	ENSG00000184371	ENST00000329608;ENST00000369802	T;T	0.15139	2.45;2.45	4.98	-9.14	0.00701	.	1.321200	0.05647	N	0.584474	T	0.01353	0.0044	N	0.04508	-0.205	0.58432	P	1.999999999946489E-6	B	0.09022	0.002	B	0.12156	0.007	T	0.36720	-0.9736	9	0.26408	T	0.33	.	3.9327	0.09293	0.0867:0.3667:0.1863:0.3603	rs1058885;rs3093042;rs3738762;rs60942435;rs1058885	408	P09603	CSF1_HUMAN	P	408	ENSP00000327513:L408P;ENSP00000358817:L408P	ENSP00000327513:L408P	L	+	2	0	CSF1	110267989	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.105000	0.03323	-2.705000	0.00396	-2.386000	0.00229	CTG	T|0.587;C|0.413	0.413	strong		0.657	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757	
TMEM173	340061	hgsc.bcm.edu	37	5	138857925	138857925	+	Missense_Mutation	SNP	C	C	G	rs78233829	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:138857925C>G	ENST00000330794.4	-	6	1022	c.689G>C	c.(688-690)gGt>gCt	p.G230A	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	230	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGCATGGTCACCGGTCTGCTG	0.557													G|||	1342	0.267971	0.2368	0.2983	5008	,	,		19260	0.4058		0.1541	False		,,,				2504	0.2638				p.G230A		Atlas-SNP	.											.	TMEM173	19	.	0			c.G689C						PASS	.	G	ALA/GLY	1046,3360	725.9+/-409.7	118,810,1275	114.0	106.0	109.0		689	1.0	0.0	5	dbSNP_131	109	1218,7382	762.7+/-407.6	91,1036,3173	yes	missense	TMEM173	NM_198282.2	60	209,1846,4448	GG,GC,CC		14.1628,23.7404,17.4074	benign	230/380	138857925	2264,10742	2203	4300	6503	SO:0001583	missense	340061	exon6			TGGTCACCGGTCT		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.689G>C	5.37:g.138857925C>G	ENSP00000331288:p.Gly230Ala	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	551	0.2522893772893773	108	0.21951219512195122	91	0.2513812154696133	238	0.4160839160839161	114	0.1503957783641161	G	5.562	0.288555	0.10513	0.237404	0.141628	ENSG00000184584	ENST00000330794;ENST00000510817	T;T	0.20598	2.06;2.06	5.79	0.964	0.19655	.	1.017410	0.07828	N	0.960847	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45731	-0.9241	9	0.22109	T	0.4	0.8351	5.5191	0.16923	0.4359:0.1359:0.4282:0.0	.	230	Q86WV6	TM173_HUMAN	A	230	ENSP00000331288:G230A;ENSP00000427455:G230A	ENSP00000331288:G230A	G	-	2	0	TMEM173	138838109	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.501000	0.22578	-0.103000	0.12175	-0.998000	0.02512	GGT	C|0.807;G|0.193	0.193	strong		0.557	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
SLC4A1AP	22950	hgsc.bcm.edu	37	2	27887034	27887034	+	Missense_Mutation	SNP	C	C	A	rs9678851	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27887034C>A	ENST00000326019.6	+	1	697	c.415C>A	c.(415-417)Ccg>Acg	p.P139T	SUPT7L_ENST00000405491.1_5'Flank|SUPT7L_ENST00000464789.2_5'Flank|SUPT7L_ENST00000406540.1_5'Flank|SUPT7L_ENST00000337768.5_5'Flank|SUPT7L_ENST00000404798.2_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	139			P -> T (in dbSNP:rs9678851). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19690332}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					GTCGCGCCCCCCGACAGCGGT	0.652													C|||	1698	0.339058	0.2534	0.3501	5008	,	,		15682	0.0794		0.5388	False		,,,				2504	0.5092				p.P139T		Atlas-SNP	.											.	SLC4A1AP	63	.	0			c.C415A						PASS	.	C	THR/PRO	1376,3028	437.8+/-345.1	201,974,1027	44.0	51.0	49.0		415	-1.9	0.0	2	dbSNP_119	49	4827,3773	594.4+/-393.3	1360,2107,833	yes	missense	SLC4A1AP	NM_018158.2	38	1561,3081,1860	AA,AC,CC		43.8721,31.2443,47.7007	benign	139/797	27887034	6203,6801	2202	4300	6502	SO:0001583	missense	22950	exon1			CGCCCCCCGACAG		CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"""lung cancer oncogene 3"""	602655	"""solute carrier family 4 (anion exchanger), member 1, adapter protein"""			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.415C>A	2.37:g.27887034C>A	ENSP00000323837:p.Pro139Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_018158	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Missense_Mutation	SNP	ENST00000326019.6	37	CCDS33166.1	744	0.34065934065934067	130	0.26422764227642276	153	0.42265193370165743	45	0.07867132867132867	416	0.5488126649076517	C	11.78	1.740201	0.30865	0.312443	0.561279	ENSG00000163798	ENST00000326019	T	0.35973	1.28	4.7	-1.94	0.07571	.	1.031550	0.07703	N	0.940809	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.18166	0.026	B	0.15870	0.014	T	0.48163	-0.9059	9	0.10902	T	0.67	-0.0166	7.7146	0.28698	0.0:0.3641:0.4132:0.2226	rs9678851;rs17757122;rs9678851	139	Q9BWU0	NADAP_HUMAN	T	139	ENSP00000323837:P139T	ENSP00000323837:P139T	P	+	1	0	SLC4A1AP	27740538	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.550000	0.06034	-0.042000	0.13535	-0.266000	0.10368	CCG	C|0.590;A|0.410	0.410	strong		0.652	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158	
NEIL3	55247	hgsc.bcm.edu	37	4	178256913	178256913	+	Missense_Mutation	SNP	C	C	G	rs7689099	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:178256913C>G	ENST00000264596.3	+	3	468	c.350C>G	c.(349-351)cCt>cGt	p.P117R		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	117			P -> R (in dbSNP:rs7689099). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		GGAGCTTCTCCTGTTTTGGAA	0.323								Base excision repair (BER), DNA glycosylases					C|||	360	0.071885	0.0408	0.1182	5008	,	,		15048	0.0258		0.1183	False		,,,				2504	0.0808				p.P117R		Atlas-SNP	.											.	NEIL3	89	.	0			c.C350G						PASS	.	C	ARG/PRO	268,4134	142.7+/-177.9	6,256,1939	59.0	66.0	64.0		350	5.1	1.0	4	dbSNP_116	64	1013,7587	214.8+/-254.3	49,915,3336	yes	missense	NEIL3	NM_018248.2	103	55,1171,5275	GG,GC,CC		11.7791,6.0881,9.8523	probably-damaging	117/606	178256913	1281,11721	2201	4300	6501	SO:0001583	missense	55247	exon3			CTTCTCCTGTTTT	AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.350C>G	4.37:g.178256913C>G	ENSP00000264596:p.Pro117Arg	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	238	113	0.47479	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	153	0.07005494505494506	20	0.04065040650406504	37	0.10220994475138122	19	0.033216783216783216	77	0.10158311345646438	C	13.06	2.125028	0.37533	0.060881	0.117791	ENSG00000109674	ENST00000264596	T	0.28454	1.61	5.14	5.14	0.70334	DNA glycosylase/AP lyase, catalytic domain (2);	0.173062	0.52532	N	0.000075	T	0.00524	0.0017	M	0.75264	2.295	0.09310	P	0.999999880221	P	0.44344	0.833	B	0.35655	0.207	T	0.14337	-1.0476	9	0.62326	D	0.03	-2.4229	17.7745	0.88503	0.0:1.0:0.0:0.0	rs7689099;rs17727101;rs17845788;rs17858749;rs52806877;rs7689099	117	Q8TAT5	NEIL3_HUMAN	R	117	ENSP00000264596:P117R	ENSP00000264596:P117R	P	+	2	0	NEIL3	178493907	0.995000	0.38212	1.000000	0.80357	0.602000	0.36980	5.205000	0.65186	2.666000	0.90696	0.561000	0.74099	CCT	C|0.910;G|0.090	0.090	strong		0.323	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
TPBG	7162	hgsc.bcm.edu	37	6	83075914	83075914	+	Silent	SNP	G	G	A	rs700494	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:83075914G>A	ENST00000369750.3	+	2	1853	c.1236G>A	c.(1234-1236)acG>acA	p.T412T	TPBG_ENST00000535040.1_Silent_p.T412T|TPBG_ENST00000543496.1_Silent_p.T412T			Q13641	TPBG_HUMAN	trophoblast glycoprotein	412					cell adhesion (GO:0007155)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	15		all_cancers(76;0.000805)|Acute lymphoblastic leukemia(125;3.85e-06)|all_hematologic(105;0.0017)|all_epithelial(107;0.0897)		BRCA - Breast invasive adenocarcinoma(397;0.107)		CCAGATTAACGAACCTCAGTT	0.433													A|||	3434	0.685703	0.733	0.7161	5008	,	,		19959	0.5774		0.6889	False		,,,				2504	0.7086				p.T412T		Atlas-SNP	.											.	TPBG	37	.	0			c.G1236A						PASS	.	A	,	3216,1190	408.6+/-334.7	1174,868,161	56.0	58.0	57.0		1236,1236	-0.3	1.0	6	dbSNP_86	57	5833,2767	439.2+/-359.1	1962,1909,429	no	coding-synonymous,coding-synonymous	TPBG	NM_001166392.1,NM_006670.4	,	3136,2777,590	AA,AG,GG		32.1744,27.0086,30.4244	,	412/421,412/421	83075914	9049,3957	2203	4300	6503	SO:0001819	synonymous_variant	7162	exon2			ATTAACGAACCTC	AJ012159	CCDS4995.1	6q14-q15	2008-07-29			ENSG00000146242	ENSG00000146242			12004	protein-coding gene	gene with protein product		190920				8132670	Standard	NM_006670		Approved	5T4-AG, 5T4	uc003pjo.3	Q13641	OTTHUMG00000015103	ENST00000369750.3:c.1236G>A	6.37:g.83075914G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	48	0.6	NM_001166392	A8K555	Silent	SNP	ENST00000369750.3	37	CCDS4995.1																																																																																			G|0.316;A|0.684	0.684	strong		0.433	TPBG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041340.1		
MED11	400569	hgsc.bcm.edu	37	17	4638563	4638563	+	IGR	SNP	G	G	A	rs2277680	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:4638563G>A	ENST00000293777.5	+	0	833				CXCL16_ENST00000293778.6_Missense_Mutation_p.A200V|CXCL16_ENST00000576153.1_5'UTR|CXCL16_ENST00000574412.1_Missense_Mutation_p.A200V|RP11-314A20.5_ENST00000570493.2_RNA	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			lung(2)|ovary(2)	4						CTCAGGCCCAGCTGCCAGACT	0.602													A|||	2311	0.461462	0.2958	0.4813	5008	,	,		17949	0.5804		0.4394	False		,,,				2504	0.5716				p.A200V		Atlas-SNP	.											.	CXCL16	30	.	0			c.C599T	GRCh37	CM057933	CXCL16	M	rs2277680	PASS	.	A	VAL/ALA,VAL/ALA	1377,3029	689.7+/-405.2	217,943,1043	63.0	58.0	59.0		599,599	-2.6	0.0	17	dbSNP_100	59	3756,4844	616.2+/-396.5	835,2086,1379	yes	missense,missense	CXCL16	NM_001100812.1,NM_022059.2	64,64	1052,3029,2422	AA,AG,GG		43.6744,31.2528,39.4664	possibly-damaging,possibly-damaging	200/274,200/274	4638563	5133,7873	2203	4300	6503	SO:0001628	intergenic_variant	58191	exon4			GGCCCAGCTGCCA	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"""mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"""			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086			17.37:g.4638563G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	180	101	0.561111	NM_022059	Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	CCDS32533.1	986	0.45146520146520147	149	0.30284552845528456	162	0.44751381215469616	340	0.5944055944055944	335	0.4419525065963061	A	7.358	0.624211	0.14193	0.312528	0.436744	ENSG00000161921	ENST00000293778	T	0.37058	1.22	5.31	-2.64	0.06114	.	1.206380	0.05967	N	0.641717	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.45205	-0.9277	9	0.19147	T	0.46	-0.9058	13.3114	0.60382	0.2755:0.0:0.7245:0.0	rs2277680;rs17824095;rs17857293;rs52830669;rs58179207;rs2277680	181	Q9H2A7	CXL16_HUMAN	V	200	ENSP00000293778:A200V	ENSP00000293778:A200V	A	-	2	0	CXCL16	4585312	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.819000	0.04462	-0.477000	0.06832	-1.214000	0.01621	GCT	G|0.576;A|0.424	0.424	strong		0.602	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683	
DHX58	79132	hgsc.bcm.edu	37	17	40263400	40263400	+	Missense_Mutation	SNP	C	C	T	rs35118457	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40263400C>T	ENST00000251642.3	-	4	506	c.284G>A	c.(283-285)cGg>cAg	p.R95Q		NM_024119.2	NP_077024.2	Q96C10	DHX58_HUMAN	DEXH (Asp-Glu-X-His) box polypeptide 58	95	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		R -> Q (in dbSNP:rs35118457).		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of innate immune response (GO:0045824)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of type I interferon production (GO:0032481)|regulation of innate immune response (GO:0045088)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(22;9.73e-07)|all_epithelial(22;3.58e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GTCATGGCACCGGGCCAGGTG	0.632													C|||	144	0.028754	0.0136	0.0303	5008	,	,		20040	0.0		0.0557	False		,,,				2504	0.0501				p.R95Q		Atlas-SNP	.											.	DHX58	39	.	0			c.G284A						PASS	.	C	GLN/ARG	71,4335	63.5+/-100.7	0,71,2132	58.0	52.0	54.0		284	3.5	0.2	17	dbSNP_126	54	514,8086	144.5+/-200.4	26,462,3812	yes	missense	DHX58	NM_024119.2	43	26,533,5944	TT,TC,CC		5.9767,1.6114,4.4979	possibly-damaging	95/679	40263400	585,12421	2203	4300	6503	SO:0001583	missense	79132	exon4			TGGCACCGGGCCA	BC014949	CCDS11416.1	17q21.2	2008-02-05			ENSG00000108771	ENSG00000108771			29517	protein-coding gene	gene with protein product	"""RNA helicase LGP2"""	608588				11735219	Standard	NM_024119		Approved	LGP2, D11LGP2	uc002hyw.3	Q96C10	OTTHUMG00000133493	ENST00000251642.3:c.284G>A	17.37:g.40263400C>T	ENSP00000251642:p.Arg95Gln	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_024119	Q9HAM6	Missense_Mutation	SNP	ENST00000251642.3	37	CCDS11416.1	67	0.030677655677655676	12	0.024390243902439025	13	0.03591160220994475	0	0.0	42	0.055408970976253295	C	16.73	3.202963	0.58234	0.016114	0.059767	ENSG00000108771	ENST00000251642;ENST00000423748;ENST00000413196;ENST00000430773	T;T;T	0.35973	3.53;1.28;1.28	5.54	3.53	0.40419	DEAD-like helicase (2);Helicase/UvrB domain (1);	0.205917	0.41396	D	0.000892	T	0.02119	0.0066	N	0.13003	0.285	0.09310	N	1	P;D	0.54772	0.934;0.968	B;P	0.45310	0.28;0.476	T	0.04165	-1.0972	10	0.10377	T	0.69	.	8.9573	0.35825	0.0:0.7656:0.0:0.2344	rs35118457	88;95	B7Z455;Q96C10	.;DHX58_HUMAN	Q	95	ENSP00000251642:R95Q;ENSP00000416389:R95Q;ENSP00000404639:R95Q	ENSP00000251642:R95Q	R	-	2	0	DHX58	37516926	0.157000	0.22836	0.179000	0.23059	0.984000	0.73092	0.835000	0.27531	1.362000	0.46000	0.555000	0.69702	CGG	C|0.957;T|0.043	0.043	strong		0.632	DHX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257396.1	NM_024119	
SETMAR	6419	hgsc.bcm.edu	37	3	4358210	4358210	+	Silent	SNP	A	A	G	rs7647539	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:4358210A>G	ENST00000358065.4	+	3	1402	c.1335A>G	c.(1333-1335)cgA>cgG	p.R445R	SETMAR_ENST00000425863.1_Silent_p.R306R|SUMF1_ENST00000534863.1_Intron	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	445	Mariner transposase Hsmar1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		cggtcgttcgacatttgaagc	0.423								Chromatin Structure					G|||	2081	0.415535	0.8865	0.2954	5008	,	,		14865	0.1062		0.3559	False		,,,				2504	0.2444				p.R445R		Atlas-SNP	.											.	SETMAR	30	.	0			c.A1335G						PASS	.	G		3505,895		1406,693,101	13.0	15.0	14.0		1335	0.2	0.7	3	dbSNP_116	14	2843,5743		487,1869,1937	no	coding-synonymous	SETMAR	NM_006515.3		1893,2562,2038	GG,GA,AA		33.112,20.3409,48.8834		445/685	4358210	6348,6638	2200	4293	6493	SO:0001819	synonymous_variant	6419	exon3			CGTTCGACATTTG	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.1335A>G	3.37:g.4358210A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Silent	SNP	ENST00000358065.4	37	CCDS2563.2																																																																																			A|0.558;G|0.442	0.442	strong		0.423	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515	
URGCP	55665	hgsc.bcm.edu	37	7	43917013	43917013	+	Silent	SNP	G	G	A	rs2232105	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:43917013G>A	ENST00000453200.1	-	6	2542	c.2049C>T	c.(2047-2049)caC>caT	p.H683H	URGCP_ENST00000336086.6_Silent_p.H640H|URGCP-MRPS24_ENST00000603700.1_Intron|URGCP_ENST00000443736.1_Silent_p.H640H|URGCP_ENST00000447717.3_Silent_p.H640H|URGCP_ENST00000223341.7_Silent_p.H640H|URGCP_ENST00000402306.3_Silent_p.H674H|URGCP_ENST00000497914.1_5'UTR			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	683					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCAGTCGGACGTGCAGCTCCT	0.637													G|||	2466	0.492412	0.326	0.5173	5008	,	,		19545	0.5764		0.4602	False		,,,				2504	0.6462				p.H683H		Atlas-SNP	.											.	URGCP	170	.	0			c.C2049T						PASS	.	G	,,,	1341,2899		221,899,1000	31.0	34.0	33.0		2049,1920,,2022	-6.7	0.0	7	dbSNP_98	33	4003,4463		973,2057,1203	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	,,,	1194,2956,2203	AA,AG,GG		47.2833,31.6274,42.0589	,,,	683/932,640/889,,674/923	43917013	5344,7362	2120	4233	6353	SO:0001819	synonymous_variant	55665	exon6			TCGGACGTGCAGC		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.2049C>T	7.37:g.43917013G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	34	8	0.235294	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Silent	SNP	ENST00000453200.1	37	CCDS47578.1																																																																																			G|0.529;A|0.471	0.471	strong		0.637	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
TMEM132E	124842	hgsc.bcm.edu	37	17	32953258	32953258	+	Silent	SNP	G	G	A	rs4795954	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:32953258G>A	ENST00000321639.5	+	2	508	c.180G>A	c.(178-180)gaG>gaA	p.E60E		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	60						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TCCTGCGGGAGGCGCGGCCCC	0.731													G|||	893	0.178315	0.0318	0.1657	5008	,	,		13279	0.3403		0.1382	False		,,,				2504	0.2597				p.E60E		Atlas-SNP	.											.	TMEM132E	122	.	0			c.G180A						PASS	.	G		187,4153		6,175,1989	10.0	10.0	10.0		180	1.7	0.8	17	dbSNP_111	10	1127,7357		85,957,3200	no	coding-synonymous	TMEM132E	NM_207313.1		91,1132,5189	AA,AG,GG		13.2838,4.3088,10.2464		60/985	32953258	1314,11510	2170	4242	6412	SO:0001819	synonymous_variant	124842	exon2			GCGGGAGGCGCGG	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.180G>A	17.37:g.32953258G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_207313	Q8WUF4|Q8WVA5	Silent	SNP	ENST00000321639.5	37	CCDS11283.1																																																																																			G|0.870;A|0.130	0.130	strong		0.731	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
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 GAIIx	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_ENST00000297798.7_Missense_Mutation_p.G297R|HGSNAT_ENST00000521576.1_Missense_Mutation_p.G282R|HGSNAT_ENST00000379644.4_Missense_Mutation_p.G565R			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	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	236	123	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	
CD40LG	959	hgsc.bcm.edu	37	X	135730555	135730555	+	Silent	SNP	T	T	C	rs1126535	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:135730555T>C	ENST00000370629.2	+	1	204	c.148T>C	c.(148-150)Ttg>Ctg	p.L50L	CD40LG_ENST00000370628.2_Silent_p.L50L	NM_000074.2	NP_000065.1	P29965	CD40L_HUMAN	CD40 ligand	50					B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|immunoglobulin secretion (GO:0048305)|inflammatory response (GO:0006954)|isotype switching (GO:0045190)|leukocyte cell-cell adhesion (GO:0007159)|negative regulation of apoptotic process (GO:0043066)|platelet activation (GO:0030168)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of interleukin-12 production (GO:0032735)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CD40 receptor binding (GO:0005174)			endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|skin(1)|stomach(1)	26	Acute lymphoblastic leukemia(192;0.000127)					TCATAGAAGGTTGGACAAGGT	0.368									Immune Deficiency with Hyper-IgM				t|||	849	0.224901	0.121	0.3372	3775	,	,		16072	0.0565		0.1322	False		,,,				2504	0.271				p.L50L		Atlas-SNP	.											.	CD40LG	46	.	0			c.T148C						PASS	.			602,3233		44,414,100,1174,471	137.0	129.0	131.0		148	1.2	1.0	X	dbSNP_86	131	1221,5507		62,739,358,1627,1514	no	coding-synonymous	CD40LG	NM_000074.2		106,1153,458,2801,1985	CC,CT,C,TT,T		18.148,15.6975,17.2584		50/262	135730555	1823,8740	2203	4300	6503	SO:0001819	synonymous_variant	959	exon1	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	AGAAGGTTGGACA	X67878	CCDS14659.1	Xq26	2014-09-17	2008-08-01	2005-01-14	ENSG00000102245	ENSG00000102245		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"", ""Endogenous ligands"""	11935	protein-coding gene	gene with protein product	"""CD40 antigen ligand"", ""tumor necrosis factor (ligand) superfamily member 5"", ""T-B cell-activating molecule"", ""TNF-related activation protein"", ""hyper-IgM syndrome"""	300386	"""tumor necrosis factor (ligand) superfamily, member 5 (hyper-IgM syndrome)"""	HIGM1, IMD3, TNFSF5		1427881, 7678782	Standard	NM_000074		Approved	CD40L, TRAP, gp39, hCD40L, CD154	uc004faa.3	P29965	OTTHUMG00000022512	ENST00000370629.2:c.148T>C	X.37:g.135730555T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	NM_000074		Silent	SNP	ENST00000370629.2	37	CCDS14659.1																																																																																			0|0.032;C|0.165	0.165	strong		0.368	CD40LG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058501.1	NM_000074	
SGPL1	8879	hgsc.bcm.edu	37	10	72631626	72631626	+	Silent	SNP	C	C	T	rs865832	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72631626C>T	ENST00000373202.3	+	11	1142	c.942C>T	c.(940-942)gtC>gtT	p.V314V		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	314					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117)			large_intestine(4)	4						CCCTTCATGTCGACGCTTGTC	0.418													C|||	804	0.160543	0.0779	0.1758	5008	,	,		16876	0.2163		0.2316	False		,,,				2504	0.1309				p.V314V	Colon(151;1054 2458 6676 40971)	Atlas-SNP	.											.	SGPL1	37	.	0			c.C942T						PASS	.	C		400,4006	199.1+/-222.7	13,374,1816	143.0	134.0	137.0		942	-6.0	0.8	10	dbSNP_86	137	1739,6861	316.7+/-312.9	170,1399,2731	no	coding-synonymous	SGPL1	NM_003901.3		183,1773,4547	TT,TC,CC		20.2209,9.0785,16.4463		314/569	72631626	2139,10867	2203	4300	6503	SO:0001819	synonymous_variant	8879	exon11			TCATGTCGACGCT	AI128825	CCDS31216.1	10q21	2008-08-01			ENSG00000166224	ENSG00000166224			10817	protein-coding gene	gene with protein product		603729				9464245, 17090686	Standard	NM_003901		Approved	SPL	uc001jrm.3	O95470	OTTHUMG00000018421	ENST00000373202.3:c.942C>T	10.37:g.72631626C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	47	30	0.638298	NM_003901	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	Silent	SNP	ENST00000373202.3	37	CCDS31216.1																																																																																			C|0.828;T|0.172	0.172	strong		0.418	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048533.1	NM_003901	
LCTL	197021	hgsc.bcm.edu	37	15	66850204	66850204	+	Silent	SNP	A	A	G	rs16953566	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:66850204A>G	ENST00000341509.5	-	8	909	c.778T>C	c.(778-780)Ttg>Ctg	p.L260L	LCTL_ENST00000537670.1_Silent_p.L87L	NM_207338.2	NP_997221.2	Q6UWM7	LCTL_HUMAN	lactase-like	260					carbohydrate metabolic process (GO:0005975)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TCACAGTTCAATGAAATTCCC	0.527													A|||	290	0.0579073	0.034	0.1167	5008	,	,		17508	0.0883		0.0229	False		,,,				2504	0.0532				p.L260L		Atlas-SNP	.											.	LCTL	73	.	0			c.T778C						PASS	.	A		126,4276	91.1+/-129.8	3,120,2078	83.0	91.0	88.0		778	-10.6	0.0	15	dbSNP_123	88	116,8482	59.8+/-121.6	0,116,4183	no	coding-synonymous	LCTL	NM_207338.2		3,236,6261	GG,GA,AA		1.3492,2.8623,1.8615		260/568	66850204	242,12758	2201	4299	6500	SO:0001819	synonymous_variant	197021	exon8			AGTTCAATGAAAT	AY358729	CCDS10220.1, CCDS61678.1	15q21.3	2008-02-05			ENSG00000188501	ENSG00000188501			15583	protein-coding gene	gene with protein product	"""klotho gamma"", ""KL lactase phlorizin hydrolase"""					12084582	Standard	NM_207338		Approved	KLPH, FLJ33279, KLG	uc002aqc.3	Q6UWM7	OTTHUMG00000133207	ENST00000341509.5:c.778T>C	15.37:g.66850204A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_207338	B3KQY0	Silent	SNP	ENST00000341509.5	37	CCDS10220.1																																																																																			A|0.965;G|0.035	0.035	strong		0.527	LCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256921.2	NM_207338	
C6orf15	29113	hgsc.bcm.edu	37	6	31079894	31079894	+	Missense_Mutation	SNP	A	A	G	rs2233977	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31079894A>G	ENST00000259870.3	-	2	245	c.242T>C	c.(241-243)gTg>gCg	p.V81A	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	81			V -> A (in dbSNP:rs2233977).		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						TGATGCAGGCACGCTGAGCTT	0.607													G|||	1071	0.213858	0.087	0.1974	5008	,	,		16805	0.3899		0.169	False		,,,				2504	0.2618				p.V81A		Atlas-SNP	.											C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	0			c.T242C						PASS	.	G	ALA/VAL	464,3942	764.3+/-413.3	21,422,1760	61.0	67.0	65.0		242	-8.4	0.0	6	dbSNP_98	65	1456,7144	744.7+/-407.2	131,1194,2975	yes	missense	C6orf15	NM_014070.2	64	152,1616,4735	GG,GA,AA		16.9302,10.5311,14.7624	benign	81/326	31079894	1920,11086	2203	4300	6503	SO:0001583	missense	29113	exon2			GCAGGCACGCTGA	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.242T>C	6.37:g.31079894A>G	ENSP00000259870:p.Val81Ala	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	99	14	0.141414	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	458	0.2097069597069597	53	0.10772357723577236	54	0.14917127071823205	222	0.3881118881118881	129	0.17018469656992086	G	1.094	-0.663129	0.03428	0.105311	0.169302	ENSG00000204542	ENST00000259870	T	0.05025	3.51	4.61	-8.37	0.00976	.	1.975560	0.02836	N	0.127304	T	0.00412	0.0013	N	0.01267	-0.92	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40515	-0.9559	9	0.07644	T	0.81	-15.0007	5.3978	0.16278	0.3695:0.0:0.2882:0.3423	rs2233977;rs2233977	81	Q6UXA7	CF015_HUMAN	A	81	ENSP00000259870:V81A	ENSP00000259870:V81A	V	-	2	0	C6orf15	31187873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.201000	0.01236	-2.546000	0.00482	-1.841000	0.00585	GTG	A|0.825;G|0.175	0.175	strong		0.607	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
NT5E	4907	hgsc.bcm.edu	37	6	86199243	86199243	+	Missense_Mutation	SNP	T	T	C	rs2229524	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:86199243T>C	ENST00000257770.3	+	6	1185	c.1136T>C	c.(1135-1137)aTg>aCg	p.M379T	NT5E_ENST00000369651.3_Missense_Mutation_p.M379T	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	379			M -> T (in dbSNP:rs2229524).		adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	ACGGATGAAATGTTCTGGAAC	0.473													T|||	780	0.155751	0.407	0.0576	5008	,	,		21001	0.0516		0.0537	False		,,,				2504	0.0982				p.M379T	Melanoma(140;797 1765 2035 2752 18208)	Atlas-SNP	.											.	NT5E	56	.	0			c.T1136C						PASS	.	T	THR/MET,THR/MET	1603,2803	498.6+/-364.2	294,1015,894	143.0	120.0	128.0		1136,1136	-0.3	0.9	6	dbSNP_98	128	589,8011	156.1+/-210.0	20,549,3731	yes	missense,missense	NT5E	NM_001204813.1,NM_002526.3	81,81	314,1564,4625	CC,CT,TT		6.8488,36.3822,16.8538	benign,benign	379/525,379/575	86199243	2192,10814	2203	4300	6503	SO:0001583	missense	4907	exon6			ATGAAATGTTCTG	X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"""CD molecules"""	8021	protein-coding gene	gene with protein product		129190	"""5' nucleotidase (CD73)"""	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.1136T>C	6.37:g.86199243T>C	ENSP00000257770:p.Met379Thr	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_001204813	B3KQI8|O75520|Q5W116	Missense_Mutation	SNP	ENST00000257770.3	37	CCDS5002.1	282|282	0.12912087912087913|0.12912087912087913	187|187	0.3800813008130081|0.3800813008130081	21|21	0.058011049723756904|0.058011049723756904	32|32	0.055944055944055944|0.055944055944055944	42|42	0.055408970976253295|0.055408970976253295	T|T	2.618|2.618	-0.289306|-0.289306	0.05605|0.05605	0.363822|0.363822	0.068488|0.068488	ENSG00000135318|ENSG00000135318	ENST00000416334;ENST00000437581|ENST00000369647;ENST00000257770;ENST00000369651	.|T;T	.|0.54071	.|0.59;0.59	5.21|5.21	-0.33|-0.33	0.12683|0.12683	.|5&apos (3);-Nucleotidase, C-terminal (3);	.|0.825447	.|0.11656	.|N	.|0.542338	T|T	0.04907|0.04907	0.0132|0.0132	N|N	0.01352|0.01352	-0.895|-0.895	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.10450	.|0.005;0.005	T|T	0.29274|0.29274	-1.0017|-1.0017	4|9	.|0.12430	.|T	.|0.62	-2.4118|-2.4118	0.9741|0.9741	0.01422|0.01422	0.2381:0.2036:0.0989:0.4594|0.2381:0.2036:0.0989:0.4594	rs2229524;rs10081139;rs52794129;rs10081139|rs2229524;rs10081139;rs52794129;rs10081139	.|379;379	.|B3KQI8;P21589	.|.;5NTD_HUMAN	R|T	144;75|155;379;379	.|ENSP00000257770:M379T;ENSP00000358665:M379T	.|ENSP00000257770:M379T	C|M	+|+	1|2	0|0	NT5E|NT5E	86255962|86255962	0.005000|0.005000	0.15991|0.15991	0.886000|0.886000	0.34754|0.34754	0.800000|0.800000	0.45204|0.45204	0.677000|0.677000	0.25262|0.25262	0.017000|0.017000	0.15025|0.15025	0.379000|0.379000	0.24179|0.24179	TGT|ATG	A|0.000;C|0.157;G|0.000;T|0.843	0.157	strong		0.473	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1		
CD276	80381	hgsc.bcm.edu	37	15	73996101	73996101	+	Missense_Mutation	SNP	G	G	A	rs10083681	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:73996101G>A	ENST00000318443.5	+	5	1137	c.835G>A	c.(835-837)Gca>Aca	p.A279T	CD276_ENST00000537340.2_Missense_Mutation_p.A133T|CD276_ENST00000318424.5_Intron|CD276_ENST00000561213.1_Missense_Mutation_p.A279T|CD276_ENST00000564751.1_Intron	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	279	Ig-like V-type 2.		A -> T (in dbSNP:rs10083681).		cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						CTTCAGCCTGGCACAGCTCAA	0.662													G|||	991	0.197883	0.4281	0.0965	5008	,	,		16216	0.127		0.0964	False		,,,				2504	0.136				p.A279T		Atlas-SNP	.											.	CD276	29	.	0			c.G835A						PASS	.	G	THR/ALA,	1700,2696	503.9+/-365.7	353,994,851	41.0	38.0	39.0		835,	3.9	0.9	15	dbSNP_119	39	840,7754	192.3+/-238.3	33,774,3490	no	missense,intron	CD276	NM_001024736.1,NM_025240.2	58,	386,1768,4341	AA,AG,GG		9.7743,38.6715,19.5535	possibly-damaging,	279/535,	73996101	2540,10450	2198	4297	6495	SO:0001583	missense	80381	exon5			AGCCTGGCACAGC	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.835G>A	15.37:g.73996101G>A	ENSP00000320084:p.Ala279Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	137	79	0.576642	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	387	0.1771978021978022	207	0.42073170731707316	41	0.1132596685082873	66	0.11538461538461539	73	0.09630606860158311	G	11.70	1.717707	0.30413	0.386715	0.097743	ENSG00000103855	ENST00000318443;ENST00000379823;ENST00000537340	T;T	0.65549	-0.16;-0.16	4.84	3.92	0.45320	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.642372	0.16272	N	0.221732	T	0.00012	0.0000	N	0.05031	-0.125	0.09310	P	0.9999999999802466	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.10450	0.003;0.005;0.004	T	0.39035	-0.9633	9	0.33940	T	0.23	-28.4616	9.0187	0.36186	0.1775:0.0:0.8225:0.0	rs10083681	225;279;279	B4DK26;Q5ZPR3;Q5ZPR3-4	.;CD276_HUMAN;.	T	279;279;133	ENSP00000320084:A279T;ENSP00000441087:A133T	ENSP00000320084:A279T	A	+	1	0	CD276	71783154	0.983000	0.35010	0.947000	0.38551	0.957000	0.61999	1.835000	0.39181	1.164000	0.42652	0.561000	0.74099	GCA	G|0.813;A|0.187	0.187	strong		0.662	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
HSPG2	3339	hgsc.bcm.edu	37	1	22157545	22157545	+	Silent	SNP	G	G	A	rs112494360	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:22157545G>A	ENST00000374695.3	-	85	11680	c.11601C>T	c.(11599-11601)taC>taT	p.Y3867Y	HSPG2_ENST00000486901.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3867	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	AGACGCACACGTAGCTGCTGC	0.632													g|||	145	0.0289537	0.0015	0.0231	5008	,	,		14817	0.0		0.0398	False		,,,				2504	0.089				p.Y3867Y		Atlas-SNP	.											HSPG2,NS,carcinoma,0,1	HSPG2	311	1	0			c.C11601T						PASS	.			34,4364		0,34,2165	24.0	26.0	25.0		11601	2.3	0.8	1	dbSNP_132	25	409,8179		10,389,3895	no	coding-synonymous	HSPG2	NM_005529.5		10,423,6060	AA,AG,GG		4.7625,0.7731,3.4114		3867/4392	22157545	443,12543	2199	4294	6493	SO:0001819	synonymous_variant	3339	exon85			GCACACGTAGCTG	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.11601C>T	1.37:g.22157545G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	96	46	0.479167	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			A|0.024;C|0.000;G|0.976	0.024	strong		0.632	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
NRIP1	8204	hgsc.bcm.edu	37	21	16340289	16340289	+	Silent	SNP	C	C	T	rs2229741	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:16340289C>T	ENST00000400202.1	-	3	937	c.225G>A	c.(223-225)ggG>ggA	p.G75G	NRIP1_ENST00000400199.1_Silent_p.G75G|NRIP1_ENST00000318948.4_Silent_p.G75G			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	75	Interaction with ZNF366.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.G75G(1)		cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		GCATGCCAGACCCCTGATATG	0.443													T|||	3002	0.599441	0.7829	0.549	5008	,	,		22522	0.7738		0.4026	False		,,,				2504	0.41				p.G75G		Atlas-SNP	.											NRIP1,NS,carcinoma,0,1	NRIP1	103	1	1	Substitution - coding silent(1)	prostate(1)	c.G225A						PASS	.	T		3170,1236	426.6+/-341.2	1153,864,186	62.0	56.0	58.0	http://www.ncbi.nlm.nih.gov/pubmed?term	225	3.3	1.0	21	dbSNP_98	58	3594,5006	626.6+/-397.9	736,2122,1442	yes	coding-synonymous	NRIP1	NM_003489.3		1889,2986,1628	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	41.7907,28.0527,47.9932		75/1159	16340289	6764,6242	2203	4300	6503	SO:0001819	synonymous_variant	8204	exon4			GCCAGACCCCTGA	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"""receptor interacting protein 140"", ""nuclear factor RIP140"""	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.225G>A	21.37:g.16340289C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	131	83	0.633588	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			C|0.443;T|0.557	0.557	strong		0.443	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
CUBN	8029	hgsc.bcm.edu	37	10	16979661	16979661	+	Silent	SNP	T	T	C	rs1801234	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:16979661T>C	ENST00000377833.4	-	39	5921	c.5856A>G	c.(5854-5856)tcA>tcG	p.S1952S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1952	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATCCCTTCCCTGAGATTGAAG	0.438													C|||	2711	0.541334	0.7542	0.5548	5008	,	,		14518	0.4911		0.4175	False		,,,				2504	0.4233				p.S1952S		Atlas-SNP	.											.	CUBN	515	.	0			c.A5856G						PASS	.	C		3022,1384	454.4+/-350.6	1029,964,210	62.0	66.0	65.0		5856	-4.0	0.2	10	dbSNP_89	65	3622,4978	625.2+/-397.7	782,2058,1460	no	coding-synonymous	CUBN	NM_001081.3		1811,3022,1670	CC,CT,TT		42.1163,31.4117,48.9159		1952/3624	16979661	6644,6362	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon39			CTTCCCTGAGATT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.5856A>G	10.37:g.16979661T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	62	39	0.629032	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			T|0.475;C|0.525	0.525	strong		0.438	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
KRT9	3857	hgsc.bcm.edu	37	17	39723990	39723990	+	Silent	SNP	T	T	A	rs3890472	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39723990T>A	ENST00000246662.4	-	7	1472	c.1407A>T	c.(1405-1407)ggA>ggT	p.G469G	KRT9_ENST00000588431.1_Silent_p.G236G	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	469	Tail.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TTTTTCCAGCTCCGGAGGATT	0.507													T|||	3242	0.647364	0.385	0.7147	5008	,	,		21027	0.9444		0.5616	False		,,,				2504	0.7362				p.G469G		Atlas-SNP	.											KRT9,NS,adenoma,0,1	KRT9	78	1	0			c.A1407T						PASS	.	T		1752,2654	521.7+/-370.6	345,1062,796	74.0	72.0	72.0		1407	2.5	0.8	17	dbSNP_108	72	4737,3863	608.8+/-395.4	1280,2177,843	no	coding-synonymous	KRT9	NM_000226.3		1625,3239,1639	AA,AT,TT		44.9186,39.764,49.8924		469/624	39723990	6489,6517	2203	4300	6503	SO:0001819	synonymous_variant	3857	exon7			TCCAGCTCCGGAG		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.1407A>T	17.37:g.39723990T>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	26	15	0.576923	NM_000226	O00109|Q0IJ47|Q14665	Silent	SNP	ENST00000246662.4	37	CCDS32654.1																																																																																			T|0.457;A|0.543	0.543	strong		0.507	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226	
ZNF853	54753	hgsc.bcm.edu	37	7	6656830	6656830	+	Missense_Mutation	SNP	G	G	A	rs2243563	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6656830G>A	ENST00000457543.3	+	2	580	c.22G>A	c.(22-24)Ggg>Agg	p.G8R		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	8			G -> R (in dbSNP:rs2243563).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						GCCGACTCCCGGGAATCGGGG	0.637													G|||	3712	0.741214	0.823	0.683	5008	,	,		18907	0.753		0.5427	False		,,,				2504	0.864				p.G8R		Atlas-SNP	.											ZNF853_ENST00000457543,rectum,carcinoma,0,2	ZNF853	32	2	0			c.G22A						PASS	.	G	ARG/GLY	1085,299		429,227,36	24.0	31.0	29.0		22	-7.7	0.0	7	dbSNP_100	29	1749,1433		478,793,320	yes	missense	ZNF853	NM_017560.1	125	907,1020,356	AA,AG,GG		45.0346,21.604,37.9325	benign	8/660	6656830	2834,1732	692	1591	2283	SO:0001583	missense	54753	exon2			ACTCCCGGGAATC	AL133055	CCDS59048.1	7p22.1	2013-01-08				ENSG00000236609		"""Zinc fingers, C2H2-type"""	21767	protein-coding gene	gene with protein product							Standard	NM_017560		Approved	DKFZp434J1015	uc011jwz.2	P0CG23		ENST00000457543.3:c.22G>A	7.37:g.6656830G>A	ENSP00000455585:p.Gly8Arg	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_017560		Missense_Mutation	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			G|0.313;A|0.687	0.687	strong		0.637	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
LRRK2	120892	hgsc.bcm.edu	37	12	40742254	40742254	+	Silent	SNP	G	G	A	rs10878405	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:40742254G>A	ENST00000298910.7	+	43	6382	c.6324G>A	c.(6322-6324)gaG>gaA	p.E2108E		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2108	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)			NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CTATGGTTGAGAAATTAATTA	0.308													G|||	1371	0.273762	0.1241	0.2349	5008	,	,		14989	0.3383		0.3231	False		,,,				2504	0.3865				p.E2108E		Atlas-SNP	.											.	LRRK2	763	.	0			c.G6324A						PASS	.	G		646,3760	272.8+/-271.0	46,554,1603	87.0	86.0	86.0		6324	3.2	1.0	12	dbSNP_120	86	2684,5914	427.6+/-355.6	408,1868,2023	no	coding-synonymous	LRRK2	NM_198578.3		454,2422,3626	AA,AG,GG		31.2166,14.6618,25.6075		2108/2528	40742254	3330,9674	2203	4299	6502	SO:0001819	synonymous_variant	120892	exon43			GGTTGAGAAATTA	AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.6324G>A	12.37:g.40742254G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Silent	SNP	ENST00000298910.7	37	CCDS31774.1																																																																																			G|0.735;A|0.265	0.265	strong		0.308	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
SSTR4	6754	hgsc.bcm.edu	37	20	23017044	23017044	+	Silent	SNP	C	C	T	rs3746728	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:23017044C>T	ENST00000255008.3	+	1	988	c.924C>T	c.(922-924)ccC>ccT	p.P308P	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	308					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GCGCCAACCCCATTCTCTATG	0.587													C|||	1548	0.309105	0.2315	0.2824	5008	,	,		18308	0.2351		0.3698	False		,,,				2504	0.4468				p.P308P	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,colon,carcinoma,0,2	SSTR4	83	2	0			c.C924T						PASS	.	C		1076,3328	370.0+/-319.4	145,786,1271	151.0	151.0	151.0		924	2.4	0.9	20	dbSNP_107	151	3312,5286	482.4+/-370.9	670,1972,1657	no	coding-synonymous	SSTR4	NM_001052.2		815,2758,2928	TT,TC,CC		38.5206,24.4323,33.7487		308/389	23017044	4388,8614	2202	4299	6501	SO:0001819	synonymous_variant	6754	exon1			CAACCCCATTCTC		CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.924C>T	20.37:g.23017044C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Silent	SNP	ENST00000255008.3	37	CCDS42856.1																																																																																			C|0.669;T|0.331	0.331	strong		0.587	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
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 GAIIx	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		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	23	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	
PROP1	5626	hgsc.bcm.edu	37	5	177422908	177422908	+	Silent	SNP	A	A	G	rs1135320	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:177422908A>G	ENST00000308304.2	-	1	335	c.27T>C	c.(25-27)gcT>gcC	p.A9A		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	9					blood vessel development (GO:0001568)|canonical Wnt signaling pathway (GO:0060070)|cell migration (GO:0016477)|central nervous system development (GO:0007417)|dorsal/ventral pattern formation (GO:0009953)|hypophysis morphogenesis (GO:0048850)|hypothalamus cell differentiation (GO:0021979)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatotropin secreting cell differentiation (GO:0060126)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(9)|stomach(1)	13	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	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)			TTGGCTTCTCAGCCTGGCGCC	0.622													G|||	2242	0.447684	0.2481	0.4942	5008	,	,		14630	0.5595		0.4712	False		,,,				2504	0.545				p.A9A		Atlas-SNP	.											.	PROP1	28	.	0			c.T27C						PASS	.	G		1262,3144		181,900,1122	75.0	67.0	70.0		27	-0.8	0.0	5	dbSNP_86	70	3850,4750		887,2076,1337	no	coding-synonymous	PROP1	NM_006261.4		1068,2976,2459	GG,GA,AA		44.7674,28.6428,39.3049		9/227	177422908	5112,7894	2203	4300	6503	SO:0001819	synonymous_variant	5626	exon1			CTTCTCAGCCTGG	AF076215	CCDS4430.1	5q35.3	2011-06-20	2007-07-12		ENSG00000175325	ENSG00000175325		"""Homeoboxes / PRD class"""	9455	protein-coding gene	gene with protein product		601538	"""prophet of Pit1, paired-like homeodomain transcription factor"""			9462743	Standard	NM_006261		Approved		uc003mif.1	O75360	OTTHUMG00000130887	ENST00000308304.2:c.27T>C	5.37:g.177422908A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_006261		Silent	SNP	ENST00000308304.2	37	CCDS4430.1																																																																																			A|0.580;G|0.420	0.420	strong		0.622	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261	
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 GAIIx	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	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	34	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		
HTR2C	3358	hgsc.bcm.edu	37	X	113965735	113965735	+	Missense_Mutation	SNP	G	G	C	rs6318	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:113965735G>C	ENST00000276198.1	+	4	796	c.68G>C	c.(67-69)tGt>tCt	p.C23S	HTR2C_ENST00000371951.1_Missense_Mutation_p.C23S|HTR2C_ENST00000371950.3_Missense_Mutation_p.C23S	NM_000868.2	NP_000859.1	P28335	5HT2C_HUMAN	5-hydroxytryptamine (serotonin) receptor 2C, G protein-coupled	23			C -> S (in dbSNP:rs6318). {ECO:0000269|PubMed:10206230, ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10581480, ECO:0000269|PubMed:22497996, ECO:0000269|PubMed:7557992}.		behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|cGMP biosynthetic process (GO:0006182)|feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipase C-activating serotonin receptor signaling pathway (GO:0007208)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|regulation of appetite (GO:0032098)|regulation of corticotropin-releasing hormone secretion (GO:0043397)|regulation of neurological system process (GO:0031644)|release of sequestered calcium ion into cytosol (GO:0051209)|response to drug (GO:0042493)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding (GO:0071886)|drug binding (GO:0008144)|Gq/11-coupled serotonin receptor activity (GO:0001587)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50					Agomelatine(DB06594)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Clomipramine(DB01242)|Clozapine(DB00363)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Dexfenfluramine(DB01191)|Doxepin(DB01142)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Lorcaserin(DB04871)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methysergide(DB00247)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Pramipexole(DB00413)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Sertindole(DB06144)|Tramadol(DB00193)|Trazodone(DB00656)|Trimipramine(DB00726)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GTTTGGCAATGTGATATTTCT	0.383													G|||	626	0.165828	0.2995	0.0663	3775	,	,		13781	0.0119		0.1173	False		,,,				2504	0.0552				p.C23S		Atlas-SNP	.											.	HTR2C	117	.	0			c.G68C	GRCh37	CM981007	HTR2C	M	rs6318	PASS	.	G	SER/CYS	1306,2529		196,703,211,733,360	101.0	96.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	68	2.7	0.6	X	dbSNP_52	98	1179,5549		73,716,317,1639,1555	yes	missense	HTR2C	NM_000868.2	112	269,1419,528,2372,1915	CC,CG,C,GG,G		17.5238,34.0548,23.5255	benign	23/459	113965735	2485,8078	2203	4300	6503	SO:0001583	missense	3358	exon4			GGCAATGTGATAT		CCDS14564.1, CCDS59174.1	Xq23	2013-12-19	2012-02-03		ENSG00000147246	ENSG00000147246		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5295	protein-coding gene	gene with protein product		312861	"""5-hydroxytryptamine (serotonin) receptor 2C"""	HTR1C		7895773	Standard	NM_000868		Approved	5-HT2C, 5HTR2C	uc004epu.1	P28335	OTTHUMG00000022226	ENST00000276198.1:c.68G>C	X.37:g.113965735G>C	ENSP00000276198:p.Cys23Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	181	55	0.303867	NM_000868	B1AMW4|Q5VUF8|Q9NP28	Missense_Mutation	SNP	ENST00000276198.1	37	CCDS14564.1	276	0.16636528028933092	103	0.2654639175257732	22	0.0625	3	0.00528169014084507	59	0.08501440922190202	G	9.655	1.142518	0.21205	0.340548	0.175238	ENSG00000147246	ENST00000276198;ENST00000371951;ENST00000371950	T;T;T	0.56611	0.45;0.45;0.65	4.57	2.7	0.31948	.	0.426952	0.23319	N	0.049465	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B	0.29909	0.261;0.009	B;B	0.26416	0.069;0.008	T	0.40608	-0.9554	9	0.21540	T	0.41	.	4.5956	0.12327	0.115:0.0:0.4223:0.4627	rs6318;rs6318	23;23	B1AMW4;P28335	.;5HT2C_HUMAN	S	23	ENSP00000276198:C23S;ENSP00000361019:C23S;ENSP00000361018:C23S	ENSP00000276198:C23S	C	+	2	0	HTR2C	113871991	0.750000	0.28316	0.586000	0.28679	0.777000	0.43975	0.924000	0.28777	0.586000	0.29626	0.594000	0.82650	TGT	0|0.015;C|0.215	0.215	strong		0.383	HTR2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057962.1	NM_000868	
KIAA0753	9851	hgsc.bcm.edu	37	17	6531648	6531648	+	Silent	SNP	A	A	G	rs2072149	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6531648A>G	ENST00000361413.3	-	3	865	c.507T>C	c.(505-507)tcT>tcC	p.S169S	KIAA0753_ENST00000572370.1_5'UTR|KIAA0753_ENST00000542606.1_5'UTR	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	169						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		CTTTGGCACCAGAGCTGGAGA	0.498													G|||	3491	0.697085	0.8563	0.6801	5008	,	,		17862	0.7103		0.5457	False		,,,				2504	0.636				p.S169S		Atlas-SNP	.											.	KIAA0753	63	.	0			c.T507C						PASS	.	G		3411,805		1390,631,87	100.0	110.0	106.0		507	-6.3	0.9	17	dbSNP_96	106	4870,3570		1416,2038,766	no	coding-synonymous	KIAA0753	NM_014804.2		2806,2669,853	GG,GA,AA		42.2986,19.0939,34.5686		169/968	6531648	8281,4375	2108	4220	6328	SO:0001819	synonymous_variant	9851	exon3			GGCACCAGAGCTG		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.507T>C	17.37:g.6531648A>G		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	221	111	0.502262	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Silent	SNP	ENST00000361413.3	37	CCDS42247.1																																																																																			A|0.332;G|0.668	0.668	strong		0.498	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
SIX4	51804	hgsc.bcm.edu	37	14	61180657	61180657	+	Missense_Mutation	SNP	T	T	G	rs3742636	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:61180657T>G	ENST00000216513.4	-	3	1873	c.1814A>C	c.(1813-1815)cAt>cCt	p.H605P		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	605			H -> P (in dbSNP:rs3742636). {ECO:0000269|PubMed:10640827, ECO:0000269|PubMed:15489334}.		anatomical structure morphogenesis (GO:0009653)|embryonic cranial skeleton morphogenesis (GO:0048701)|generation of neurons (GO:0048699)|inner ear morphogenesis (GO:0042472)|metanephric mesenchyme development (GO:0072075)|myoblast migration (GO:0051451)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of protein localization (GO:0032880)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|skeletal muscle tissue development (GO:0007519)|thymus development (GO:0048538)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|large_intestine(11)|liver(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28				OV - Ovarian serous cystadenocarcinoma(108;0.0275)		GGCCAGTGGATGCAGGCCACT	0.453													T|||	3231	0.645168	0.5567	0.732	5008	,	,		20840	0.6558		0.7177	False		,,,				2504	0.6176				p.H605P		Atlas-SNP	.											.	SIX4	69	.	0			c.A1814C						PASS	.	T	PRO/HIS	2475,1931	624.3+/-394.3	695,1085,423	70.0	68.0	68.0		1814	5.4	1.0	14	dbSNP_107	68	6062,2538	691.9+/-404.5	2116,1830,354	yes	missense	SIX4	NM_017420.4	77	2811,2915,777	GG,GT,TT		29.5116,43.8266,34.3611	possibly-damaging	605/782	61180657	8537,4469	2203	4300	6503	SO:0001583	missense	51804	exon3			AGTGGATGCAGGC	AB024687	CCDS9749.2	14q23.1	2012-10-02	2007-07-13		ENSG00000100625	ENSG00000100625		"""Homeoboxes / SINE class"""	10890	protein-coding gene	gene with protein product		606342	"""sine oculis homeobox (Drosophila) homolog 4"", ""sine oculis homeobox homolog 4 (Drosophila)"""			10512683, 10640827	Standard	NM_017420		Approved	AREC3	uc001xfc.3	Q9UIU6	OTTHUMG00000028996	ENST00000216513.4:c.1814A>C	14.37:g.61180657T>G	ENSP00000216513:p.His605Pro	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	1455	0.6662087912087912	276	0.5609756097560976	260	0.7182320441988951	357	0.6241258741258742	562	0.741424802110818	T	12.42	1.932798	0.34096	0.561734	0.704884	ENSG00000100625	ENST00000216513;ENST00000554079	D;T	0.91295	-2.82;0.8	5.44	5.44	0.79542	.	0.575750	0.19231	N	0.119417	T	0.00012	0.0000	N	0.19112	0.55	0.09310	P	1.0	P	0.44578	0.838	B	0.41813	0.367	T	0.48536	-0.9027	9	0.46703	T	0.11	.	15.5141	0.75809	0.0:0.0:0.0:1.0	rs3742636;rs52821006;rs3742636	605	Q9UIU6	SIX4_HUMAN	P	605;278	ENSP00000216513:H605P;ENSP00000451537:H278P	ENSP00000216513:H605P	H	-	2	0	SIX4	60250410	1.000000	0.71417	0.987000	0.45799	0.583000	0.36354	3.674000	0.54598	2.071000	0.62044	0.533000	0.62120	CAT	T|0.345;G|0.655	0.655	strong		0.453	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2		
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25258035	25258035	+	Silent	SNP	A	A	G	rs11649280	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:25258035A>G	ENST00000328086.7	-	5	2285	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	494					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		TACCACTGAGATTCTGAAACA	0.463													G|||	1682	0.335863	0.4758	0.3026	5008	,	,		23355	0.3294		0.2107	False		,,,				2504	0.3057				p.N494N		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.T1482C						PASS	.	G		1988,2406	614.6+/-392.4	454,1080,663	110.0	108.0	109.0		1482	2.5	1.0	16	dbSNP_120	109	1787,6813	733.2+/-406.9	181,1425,2694	no	coding-synonymous	ZKSCAN2	NM_001012981.4		635,2505,3357	GG,GA,AA		20.7791,45.2435,29.0519		494/968	25258035	3775,9219	2197	4300	6497	SO:0001819	synonymous_variant	342357	exon5			ACTGAGATTCTGA	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.1482T>C	16.37:g.25258035A>G		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	176	90	0.511364	NM_001012981	A1L3B4|Q6ZN77	Silent	SNP	ENST00000328086.7	37	CCDS32410.1																																																																																			A|0.696;G|0.304	0.304	strong		0.463	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
TG	7038	hgsc.bcm.edu	37	8	133881996	133881996	+	Missense_Mutation	SNP	G	G	A	rs116340633	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:133881996G>A	ENST00000220616.4	+	3	239	c.199G>A	c.(199-201)Ggc>Agc	p.G67S	TG_ENST00000377869.1_Missense_Mutation_p.G67S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	67	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CCAGAACGACGGCCGCTCCTG	0.642													G|||	26	0.00519169	0.0106	0.0	5008	,	,		15975	0.0		0.0119	False		,,,				2504	0.0				p.G67S		Atlas-SNP	.											.	TG	416	.	0			c.G199A						PASS	.	G	SER/GLY	51,4355	52.3+/-87.9	0,51,2152	59.0	55.0	57.0		199	4.5	0.1	8	dbSNP_132	57	82,8518	47.2+/-106.3	0,82,4218	yes	missense	TG	NM_003235.4	56	0,133,6370	AA,AG,GG		0.9535,1.1575,1.0226	probably-damaging	67/2769	133881996	133,12873	2203	4300	6503	SO:0001583	missense	7038	exon3			AACGACGGCCGCT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.199G>A	8.37:g.133881996G>A	ENSP00000220616:p.Gly67Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	16	0.007326007326007326	4	0.008130081300813009	0	0.0	0	0.0	12	0.0158311345646438	G	27.6	4.849775	0.91277	0.011575	0.009535	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.62232	0.04;0.04	5.44	4.51	0.55191	Thyroglobulin type-1 (6);	0.205829	0.34314	N	0.004066	T	0.52092	0.1713	L	0.39245	1.2	0.32812	D	0.501558	D	0.76494	0.999	P	0.62435	0.902	T	0.69243	-0.5196	10	0.46703	T	0.11	.	13.1275	0.59364	0.0:0.1603:0.8397:0.0	.	67	P01266	THYG_HUMAN	S	67	ENSP00000367100:G67S;ENSP00000220616:G67S	ENSP00000220616:G67S	G	+	1	0	TG	133951178	0.998000	0.40836	0.098000	0.21074	0.191000	0.23601	2.801000	0.47908	2.550000	0.86006	0.462000	0.41574	GGC	G|0.992;A|0.008	0.008	strong		0.642	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
DHX9	1660	hgsc.bcm.edu	37	1	182845346	182845346	+	Silent	SNP	C	C	T	rs35533583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:182845346C>T	ENST00000367549.3	+	17	2087	c.1977C>T	c.(1975-1977)ggC>ggT	p.G659G		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	659	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						TTTTGCCTGGCTGGAATCTGA	0.358													C|||	91	0.0181709	0.0204	0.0461	5008	,	,		18919	0.0		0.0219	False		,,,				2504	0.0102				p.G659G	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.C1977T						PASS	.	C		87,3629		0,87,1771	165.0	151.0	155.0		1977	4.7	1.0	1	dbSNP_126	155	258,7926		2,254,3836	no	coding-synonymous	DHX9	NM_001357.4		2,341,5607	TT,TC,CC		3.1525,2.3412,2.8992		659/1271	182845346	345,11555	1858	4092	5950	SO:0001819	synonymous_variant	1660	exon17			GCCTGGCTGGAAT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.1977C>T	1.37:g.182845346C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	143	72	0.503497	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																			C|0.976;T|0.024	0.024	strong		0.358	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
TMEM169	92691	hgsc.bcm.edu	37	2	216964944	216964944	+	Silent	SNP	C	C	T	rs61732367	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:216964944C>T	ENST00000295658.4	+	3	780	c.573C>T	c.(571-573)ttC>ttT	p.F191F	TMEM169_ENST00000454545.1_Silent_p.F191F|TMEM169_ENST00000437356.2_Silent_p.F191F|TMEM169_ENST00000406027.2_Silent_p.F191F	NM_001142311.1|NM_001142312.1|NM_138390.3	NP_001135783.1|NP_001135784.1|NP_612399.1	Q96HH4	TM169_HUMAN	transmembrane protein 169	191						integral component of membrane (GO:0016021)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)	13		Renal(323;0.0651)		Epithelial(149;6.44e-06)|all cancers(144;0.000398)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACAACATCTTCCTCGTGTATA	0.493													C|||	38	0.00758786	0.0045	0.0173	5008	,	,		23573	0.0		0.0189	False		,,,				2504	0.001				p.F191F		Atlas-SNP	.											TMEM169,caecum,carcinoma,+1,1	TMEM169	46	1	0			c.C573T						scavenged	.	C	,,,	26,4380	33.5+/-64.1	0,26,2177	314.0	256.0	275.0		573,573,573,573	2.9	1.0	2	dbSNP_129	275	141,8459	70.0+/-132.6	1,139,4160	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TMEM169	NM_001142310.1,NM_001142311.1,NM_001142312.1,NM_138390.3	,,,	1,165,6337	TT,TC,CC		1.6395,0.5901,1.284	,,,	191/298,191/298,191/298,191/298	216964944	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	92691	exon4			CATCTTCCTCGTG	AK091582	CCDS2401.1	2q35	2008-02-05			ENSG00000163449	ENSG00000163449			25130	protein-coding gene	gene with protein product						12477932	Standard	NM_001142310		Approved	FLJ34263	uc002vfv.4	Q96HH4	OTTHUMG00000133053	ENST00000295658.4:c.573C>T	2.37:g.216964944C>T		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	153	78	0.509804	NM_001142310	B2R8W6	Silent	SNP	ENST00000295658.4	37	CCDS2401.1																																																																																			C|0.987;T|0.013	0.013	strong		0.493	TMEM169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256666.2	NM_138390	
RIPK2	8767	hgsc.bcm.edu	37	8	90784979	90784979	+	Missense_Mutation	SNP	T	T	C	rs2230801	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:90784979T>C	ENST00000220751.4	+	6	1090	c.776T>C	c.(775-777)aTa>aCa	p.I259T	RIPK2_ENST00000540020.1_Missense_Mutation_p.I122T	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	259	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> T (in dbSNP:rs2230801). {ECO:0000269|PubMed:17344846}.		activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|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 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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			CCATATGATATACCTCACCGA	0.368													T|||	322	0.0642971	0.0998	0.0548	5008	,	,		17728	0.0129		0.1233	False		,,,				2504	0.0153				p.I259T		Atlas-SNP	.											.	RIPK2	37	.	0			c.T776C						PASS	.	T	THR/ILE	354,4052	185.0+/-212.2	15,324,1864	115.0	110.0	111.0		776	4.7	1.0	8	dbSNP_98	111	680,7920	169.7+/-221.0	31,618,3651	yes	missense	RIPK2	NM_003821.5	89	46,942,5515	CC,CT,TT		7.907,8.0345,7.9502	probably-damaging	259/541	90784979	1034,11972	2203	4300	6503	SO:0001583	missense	8767	exon6			ATGATATACCTCA	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.776T>C	8.37:g.90784979T>C	ENSP00000220751:p.Ile259Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_003821	B7Z748|Q6UWF0	Missense_Mutation	SNP	ENST00000220751.4	37	CCDS6247.1	164	0.07509157509157509	49	0.09959349593495935	17	0.04696132596685083	12	0.02097902097902098	86	0.11345646437994723	T	18.22	3.576466	0.65878	0.080345	0.07907	ENSG00000104312	ENST00000220751;ENST00000540020	T;T	0.64438	-0.1;-0.05	5.86	4.71	0.59529	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.47093	D	0.000245	T	0.01558	0.0050	L	0.39020	1.185	0.09310	P	0.99999601492	P	0.38300	0.626	B	0.39876	0.312	T	0.29518	-1.0009	9	0.41790	T	0.15	-13.3255	11.8421	0.52361	0.0:0.0681:0.0:0.9319	rs2230801	259	O43353	RIPK2_HUMAN	T	259;122	ENSP00000220751:I259T;ENSP00000441623:I122T	ENSP00000220751:I259T	I	+	2	0	RIPK2	90854116	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.731000	0.62022	1.047000	0.40274	0.533000	0.62120	ATA	T|0.922;C|0.078	0.078	strong		0.368	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1		
OR2L2	26246	hgsc.bcm.edu	37	1	248202412	248202412	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248202412C>T	ENST00000366479.2	+	1	939	c.843C>T	c.(841-843)acC>acT	p.T281T	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	281						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)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	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)			CCATCCTCACCCCAATGCTCA	0.468																																					p.T281T		Atlas-SNP	.											OR2L2,NS,carcinoma,0,1	OR2L2	115	1	0			c.C843T						scavenged	.						98.0	93.0	95.0					1																	248202412		2203	4300	6503	SO:0001819	synonymous_variant	26246	exon1			CCTCACCCCAATG	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"""GPCR / Class A : Olfactory receptors"""	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.843C>T	1.37:g.248202412C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	126	7	0.0555556	NM_001004686	Q2M3T5	Silent	SNP	ENST00000366479.2	37	CCDS31103.1																																																																																			.	.	none		0.468	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686	
SLC11A1	6556	hgsc.bcm.edu	37	2	219249013	219249013	+	Silent	SNP	C	C	T	rs2276631	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:219249013C>T	ENST00000233202.6	+	3	538	c.198C>T	c.(196-198)ttC>ttT	p.F66F	SLC11A1_ENST00000473367.1_Intron|SLC11A1_ENST00000539932.1_5'UTR	NM_000578.3	NP_000569.3	P49279	NRAM1_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 1	66	Pro/Ser-rich.				activation of protein kinase activity (GO:0032147)|antigen processing and presentation of peptide antigen (GO:0048002)|cadmium ion transmembrane transport (GO:0070574)|cellular cadmium ion homeostasis (GO:0006876)|cellular iron ion homeostasis (GO:0006879)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|divalent metal ion export (GO:0070839)|inflammatory response (GO:0006954)|interaction with host (GO:0051701)|interleukin-2 production (GO:0032623)|interleukin-3 production (GO:0032632)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|L-arginine import (GO:0043091)|macrophage activation (GO:0042116)|manganese ion transport (GO:0006828)|MHC class II biosynthetic process (GO:0045342)|mRNA stabilization (GO:0048255)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of cytokine production (GO:0001818)|nitrite transport (GO:0015707)|phagocytosis (GO:0006909)|phagosome maturation (GO:0090382)|positive regulation of cytokine production (GO:0001819)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of gene expression (GO:0010628)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein import into nucleus, translocation (GO:0000060)|respiratory burst (GO:0045730)|response to bacterium (GO:0009617)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|T cell cytokine production (GO:0002369)|T cell proliferation involved in immune response (GO:0002309)|transmembrane transport (GO:0055085)|vacuolar acidification (GO:0007035)|wound healing (GO:0042060)	cell outer membrane (GO:0009279)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|tertiary granule membrane (GO:0070821)	manganese ion transmembrane transporter activity (GO:0005384)|metal ion:proton antiporter activity (GO:0051139)|protein homodimerization activity (GO:0042803)|transition metal ion transmembrane transporter activity (GO:0046915)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.0474)		Epithelial(149;1.16e-06)|all cancers(144;0.000195)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GGCCTGGCTTCCTCATGAGCA	0.597													C|||	841	0.167931	0.1452	0.2695	5008	,	,		14695	0.0982		0.2505	False		,,,				2504	0.1135				p.F66F		Atlas-SNP	.											.	SLC11A1	41	.	0			c.C198T	GRCh37	CM057841	SLC11A1	M	rs2276631	PASS	.	C		758,3648	311.1+/-291.9	69,620,1514	110.0	105.0	107.0		198	2.0	1.0	2	dbSNP_100	107	2313,6287	389.5+/-342.9	323,1667,2310	no	coding-synonymous	SLC11A1	NM_000578.3		392,2287,3824	TT,TC,CC		26.8953,17.2038,23.6122		66/551	219249013	3071,9935	2203	4300	6503	SO:0001819	synonymous_variant	6556	exon3			TGGCTTCCTCATG	D38171	CCDS2415.1	2q35	2013-07-18	2013-07-18		ENSG00000018280	ENSG00000018280		"""Solute carriers"""	10907	protein-coding gene	gene with protein product	"""natural resistance-associated macrophage protein 1"""	600266		LSH, NRAMP, NRAMP1		7964458, 7980580	Standard	NM_000578		Approved		uc002vhv.3	P49279	OTTHUMG00000086747	ENST00000233202.6:c.198C>T	2.37:g.219249013C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	101	53	0.524752	NM_000578	C0H5Y3	Silent	SNP	ENST00000233202.6	37	CCDS2415.1																																																																																			C|0.789;T|0.211	0.211	strong		0.597	SLC11A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195076.2	NM_000578	
LDLRAP1	26119	hgsc.bcm.edu	37	1	25890189	25890189	+	Silent	SNP	A	A	G	rs386629679|rs28969504	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:25890189A>G	ENST00000374338.4	+	7	773	c.654A>G	c.(652-654)acA>acG	p.T218T	LDLRAP1_ENST00000488127.1_3'UTR	NM_015627.2	NP_056442.2	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein 1	218					amyloid precursor protein metabolic process (GO:0042982)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|positive regulation of cholesterol metabolic process (GO:0090205)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of signal transduction (GO:0009967)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein binding (GO:0043393)|transport (GO:0006810)	axon (GO:0030424)|basal plasma membrane (GO:0009925)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|neurofilament (GO:0005883)|recycling endosome (GO:0055037)	AP-2 adaptor complex binding (GO:0035612)|beta-amyloid binding (GO:0001540)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphotyrosine binding (GO:0001784)|receptor signaling complex scaffold activity (GO:0030159)|signaling adaptor activity (GO:0035591)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)		TAGAGGAGACAGCTAAGGCCC	0.622													a|||	2936	0.586262	0.829	0.5951	5008	,	,		18937	0.4435		0.5338	False		,,,				2504	0.453				p.T218T		Atlas-SNP	.											.	LDLRAP1	28	.	0			c.A654G						PASS	.	A		3448,958	730.8+/-410.2	1354,740,109	75.0	61.0	65.0		654	-6.3	0.0	1	dbSNP_125	65	4774,3826	610.4+/-395.7	1299,2176,825	no	coding-synonymous	LDLRAP1	NM_015627.2		2653,2916,934	GG,GA,AA		44.4884,21.7431,36.783		218/309	25890189	8222,4784	2203	4300	6503	SO:0001819	synonymous_variant	26119	exon7			GGAGACAGCTAAG	BC029770	CCDS30639.1	1p36-p35	2014-09-17			ENSG00000157978	ENSG00000157978			18640	protein-coding gene	gene with protein product		605747					Standard	NM_015627		Approved	ARH, ARH2, FHCB1, FHCB2, MGC34705, DKFZp586D0624	uc001bkl.4	Q5SW96	OTTHUMG00000007386	ENST00000374338.4:c.654A>G	1.37:g.25890189A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	37	19	0.513514	NM_015627	A2BHI5|Q6TQS9|Q8N2Y0|Q9UFI9	Silent	SNP	ENST00000374338.4	37	CCDS30639.1																																																																																			A|0.383;G|0.617	0.617	strong		0.622	LDLRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019350.3	NM_015627	
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 GAIIx	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	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	209	58	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	
SGK223	157285	hgsc.bcm.edu	37	8	8234077	8234077	+	Silent	SNP	G	G	C	rs4840952|rs386721946	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:8234077G>C	ENST00000520004.1	-	3	2106	c.1842C>G	c.(1840-1842)gcC>gcG	p.A614A	SGK223_ENST00000330777.4_Silent_p.A614A			Q86YV5	SG223_HUMAN		616							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CTGACGAGGCGGCAGGCTGGG	0.647													C|||	2132	0.425719	0.3064	0.4222	5008	,	,		17439	0.6409		0.2783	False		,,,				2504	0.5194				p.A614A	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1842G						PASS	.	C		1125,2761		166,793,984	37.0	42.0	41.0		1842	-3.7	0.0	8	dbSNP_111	41	2275,6009		318,1639,2185	no	coding-synonymous	SGK223	NM_001080826.1		484,2432,3169	CC,CG,GG		27.4626,28.9501,27.9376		614/1403	8234077	3400,8770	1943	4142	6085	SO:0001819	synonymous_variant	0	exon2			CGAGGCGGCAGGC																												ENST00000520004.1:c.1842C>G	8.37:g.8234077G>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			G|0.632;C|0.368	0.368	strong		0.647	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
ENGASE	64772	hgsc.bcm.edu	37	17	77075673	77075673	+	Silent	SNP	A	A	G	rs3744185	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77075673A>G	ENST00000579016.1	+	4	519	c.519A>G	c.(517-519)ccA>ccG	p.P173P	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	173						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						CCATTCCCCCAGTGGGCTGGA	0.587													G|||	2085	0.416334	0.6316	0.4063	5008	,	,		19809	0.38		0.173	False		,,,				2504	0.4202				p.P173P		Atlas-SNP	.											ENGASE,caecum,adenoma,0,1	ENGASE	55	1	0			c.A519G						PASS	.						94.0	121.0	112.0					17																	77075673		2109	4219	6328	SO:0001819	synonymous_variant	64772	exon4			TCCCCCAGTGGGC	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.519A>G	17.37:g.77075673A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	46	17	0.369565	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			A|0.715;G|0.285	0.285	strong		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
AASDH	132949	hgsc.bcm.edu	37	4	57219613	57219613	+	Silent	SNP	C	C	T	rs17086696	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:57219613C>T	ENST00000205214.6	-	9	1713	c.1533G>A	c.(1531-1533)ccG>ccA	p.P511P	AASDH_ENST00000510762.1_5'Flank|AASDH_ENST00000434343.2_Silent_p.P26P|AASDH_ENST00000602986.1_Silent_p.P358P|AASDH_ENST00000502617.1_Silent_p.P511P|AASDH_ENST00000451613.1_Silent_p.P511P|AASDH_ENST00000513376.1_Silent_p.P411P	NM_181806.2	NP_861522.2	Q4L235	ACSF4_HUMAN	aminoadipate-semialdehyde dehydrogenase	511					fatty acid metabolic process (GO:0006631)		acid-thiol ligase activity (GO:0016878)|ATP binding (GO:0005524)			endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	40	Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.0017)				CAAGCTCATCCGGGACTGCAT	0.338													C|||	1138	0.227236	0.2224	0.3804	5008	,	,		17420	0.2192		0.1302	False		,,,				2504	0.2331				p.P511P		Atlas-SNP	.											.	AASDH	101	.	0			c.G1533A						PASS	.	C		950,3456	359.9+/-315.0	103,744,1356	83.0	82.0	82.0		1533	-11.4	0.2	4	dbSNP_123	82	1096,7504	227.8+/-263.0	70,956,3274	no	coding-synonymous	AASDH	NM_181806.2		173,1700,4630	TT,TC,CC		12.7442,21.5615,15.7312		511/1099	57219613	2046,10960	2203	4300	6503	SO:0001819	synonymous_variant	132949	exon9			CTCATCCGGGACT	AF516672	CCDS3504.1, CCDS68705.1, CCDS68706.1, CCDS75126.1, CCDS75127.1	4q12	2010-12-14			ENSG00000157426	ENSG00000157426	1.2.1.31	"""Acyl-CoA synthetase family"""	23993	protein-coding gene	gene with protein product	"""acyl-CoA synthetase family member 4"""	614365				15865210, 12712191, 17762044	Standard	XM_005265721		Approved	NRPS998, LYS2, ACSF4	uc003hbn.3	Q4L235	OTTHUMG00000128841	ENST00000205214.6:c.1533G>A	4.37:g.57219613C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_181806	A5D8V3|A5PL22|Q63HK2|Q63HR7|Q6IPP8|Q6TFZ6|Q7Z5Y3|Q96BW4|Q9P064	Silent	SNP	ENST00000205214.6	37	CCDS3504.1																																																																																			C|0.825;T|0.175	0.175	strong		0.338	AASDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250780.1	NM_181806	
CEP85	64793	hgsc.bcm.edu	37	1	26582091	26582091	+	Missense_Mutation	SNP	G	G	A	rs3795686	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26582091G>A	ENST00000252992.4	+	4	769	c.638G>A	c.(637-639)aGc>aAc	p.S213N	CEP85_ENST00000451429.2_Missense_Mutation_p.S162N	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	213			S -> N (in dbSNP:rs3795686).			centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						CCAAGAACCAGCACAAGTAAG	0.517													G|||	933	0.186302	0.0575	0.2363	5008	,	,		21145	0.2599		0.3022	False		,,,				2504	0.1299				p.S213N		Atlas-SNP	.											.	CEP85	61	.	0			c.G638A						PASS	.	G	ASN/SER	418,3988	203.8+/-226.2	23,372,1808	94.0	87.0	89.0		638	4.2	0.2	1	dbSNP_107	89	2645,5955	428.0+/-355.8	406,1833,2061	yes	missense	CEP85	NM_022778.2	46	429,2205,3869	AA,AG,GG		30.7558,9.4871,23.5507	benign	213/763	26582091	3063,9943	2203	4300	6503	SO:0001583	missense	64793	exon4			GAACCAGCACAAG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"""coiled-coil domain containing 21"""	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.638G>A	1.37:g.26582091G>A	ENSP00000252992:p.Ser213Asn	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	495	0.22664835164835165	36	0.07317073170731707	86	0.23756906077348067	142	0.24825174825174826	231	0.30474934036939316	G	0.115	-1.133765	0.01756	0.094871	0.307558	ENSG00000130695	ENST00000451429;ENST00000252992	T;T	0.11385	2.78;2.78	5.43	4.24	0.50183	.	0.254552	0.46145	D	0.000320	T	0.00012	0.0000	N	0.04508	-0.205	0.43351	P	0.004585999999999979	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.44360	-0.9333	9	0.02654	T	1	-6.4603	9.9193	0.41455	0.9227:0.0:0.0773:0.0	rs3795686;rs52795730;rs58466682;rs3795686	162;213;213	F8W7K4;Q6P2H3;Q6P2H3-2	.;CEP85_HUMAN;.	N	162;213	ENSP00000417002:S162N;ENSP00000252992:S213N	ENSP00000252992:S213N	S	+	2	0	CEP85	26454678	0.005000	0.15991	0.241000	0.24154	0.019000	0.09904	1.327000	0.33746	1.069000	0.40788	-0.290000	0.09829	AGC	G|0.777;A|0.223	0.223	strong		0.517	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778	
MUC16	94025	hgsc.bcm.edu	37	19	9085004	9085004	+	Missense_Mutation	SNP	T	T	C	rs11085805	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9085004T>C	ENST00000397910.4	-	1	7014	c.6811A>G	c.(6811-6813)Act>Gct	p.T2271A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2271	Ser-rich.|Thr-rich.		T -> A (in dbSNP:rs11085805).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AATGAATGAGTTGTCTTTTCT	0.448													T|||	952	0.190096	0.0711	0.2709	5008	,	,		21748	0.3036		0.172	False		,,,				2504	0.1953				p.T2271A		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+1,2	MUC16	4315	2	0			c.A6811G						PASS	.	T	ALA/THR	277,3563		5,267,1648	66.0	63.0	64.0		6811	-0.4	0.0	19	dbSNP_120	64	1482,6780		126,1230,2775	yes	missense	MUC16	NM_024690.2	58	131,1497,4423	CC,CT,TT		17.9375,7.2135,14.5348	benign	2271/14508	9085004	1759,10343	1920	4131	6051	SO:0001583	missense	94025	exon1			AATGAGTTGTCTT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.6811A>G	19.37:g.9085004T>C	ENSP00000381008:p.Thr2271Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	t	0.055	-1.238975	0.01493	0.072135	0.179375	ENSG00000181143	ENST00000397910	T	0.02301	4.35	0.225	-0.451	0.12214	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.46247	-0.9205	7	0.87932	D	0	.	.	.	.	rs11085805;rs52821244;rs59875884;rs11085805	2271	B5ME49	.	A	2271	ENSP00000381008:T2271A	ENSP00000381008:T2271A	T	-	1	0	MUC16	8946004	0.003000	0.15002	0.016000	0.15963	0.016000	0.09150	-0.705000	0.05052	-0.874000	0.04027	-0.902000	0.02854	ACT	T|0.812;C|0.188	0.188	strong		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GK	2710	hgsc.bcm.edu	37	X	30686141	30686141	+	Silent	SNP	G	G	A	rs34795481	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:30686141G>A	ENST00000378941.3	+	3	165	c.165G>A	c.(163-165)caG>caA	p.Q55Q	GK_ENST00000427190.1_5'UTR|GK_ENST00000378945.3_Silent_p.Q55Q|GK_ENST00000378946.3_Silent_p.Q55Q|GK_ENST00000378943.3_Silent_p.Q55Q			P32189	GLPK_HUMAN	glycerol kinase	55					cellular lipid metabolic process (GO:0044255)|glucose homeostasis (GO:0042593)|glycerol catabolic process (GO:0019563)|glycerol metabolic process (GO:0006071)|glycerol-3-phosphate biosynthetic process (GO:0046167)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|glycerol kinase activity (GO:0004370)			central_nervous_system(1)|large_intestine(3)	4						GGGTGGAACAGGACCCTAAGG	0.338													G|||	118	0.0312583	0.0008	0.0403	3775	,	,		12612	0.001		0.0726	False		,,,				2504	0.0153				p.Q55Q		Atlas-SNP	.											.	GK	95	.	0			c.G165A						PASS	.	G	,,,	48,3785		1,38,8,1592,563	63.0	53.0	57.0		165,165,165,165	1.5	1.0	X	dbSNP_126	57	511,6214		15,346,135,2067,1734	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GK	NM_000167.5,NM_001128127.2,NM_001205019.1,NM_203391.3	,,,	16,384,143,3659,2297	AA,AG,A,GG,G		7.5985,1.2523,5.2946	,,,	55/525,55/554,55/560,55/531	30686141	559,9999	2202	4297	6499	SO:0001819	synonymous_variant	2710	exon3			GGAACAGGACCCT	X78711	CCDS14225.1, CCDS35224.1, CCDS48090.1, CCDS75963.1	Xp21.3	2014-09-17			ENSG00000198814	ENSG00000198814	2.7.1.30	"""Glycerol kinases"""	4289	protein-coding gene	gene with protein product		300474				7987308	Standard	NM_203391		Approved	GK1, GKD	uc022buj.1	P32189	OTTHUMG00000021328	ENST00000378941.3:c.165G>A	X.37:g.30686141G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	224	152	0.678571	NM_203391	A6NJP5|B2R833|Q6IQ27|Q8IVR5|Q9UMP0|Q9UMP1	Silent	SNP	ENST00000378941.3	37																																																																																				G|0.953;A|0.047	0.047	strong		0.338	GK-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000056171.1	NM_000167	
CELSR1	9620	hgsc.bcm.edu	37	22	46930107	46930107	+	Silent	SNP	C	C	T	rs8141744	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:46930107C>T	ENST00000262738.3	-	1	2960	c.2961G>A	c.(2959-2961)gtG>gtA	p.V987V	CELSR1_ENST00000395964.1_Silent_p.V987V|CELSR1_ENST00000497509.1_5'Flank	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	987	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)		CCAAGATGGTCACCTGGATTT	0.567													C|||	882	0.176118	0.2708	0.1225	5008	,	,		19808	0.0585		0.2276	False		,,,				2504	0.1544				p.V987V		Atlas-SNP	.											.	CELSR1	242	.	0			c.G2961A						PASS	.	C		1044,3360	382.3+/-324.4	109,826,1267	97.0	95.0	96.0		2961	4.4	0.9	22	dbSNP_116	96	2111,6489	363.2+/-333.1	263,1585,2452	no	coding-synonymous	CELSR1	NM_014246.1		372,2411,3719	TT,TC,CC		24.5465,23.7057,24.2618		987/3015	46930107	3155,9849	2202	4300	6502	SO:0001819	synonymous_variant	9620	exon1			GATGGTCACCTGG	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.2961G>A	22.37:g.46930107C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	174	87	0.5	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			C|0.794;T|0.206	0.206	strong		0.567	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
RBMXL3	139804	hgsc.bcm.edu	37	X	114424941	114424941	+	Missense_Mutation	SNP	G	G	A	rs62601530		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:114424941G>A	ENST00000424776.3	+	1	979	c.937G>A	c.(937-939)Gct>Act	p.A313T	LRCH2_ENST00000538422.1_Intron|LRCH2_ENST00000317135.8_Intron	NM_001145346.1	NP_001138818.1	Q8N7X1	RMXL3_HUMAN	RNA binding motif protein, X-linked-like 3	313							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(13)|kidney(2)|skin(1)	16						CCCATGCGGCGCTGCCCCTGT	0.622													G|||	225	0.0596026	0.0053	0.0533	3775	,	,		11134	0.002		0.1133	False		,,,				2504	0.0665				p.A313T		Atlas-SNP	.											.	RBMXL3	83	.	0			c.G937A						PASS	.	G	THR/ALA,	34,1175		1,25,7,491,168	30.0	34.0	33.0		937,	-0.3	0.0	X	dbSNP_129	33	392,1999		18,215,141,567,650	yes	missense,intron	LRCH2,RBMXL3	NM_001145346.1,NM_020871.3	58,	19,240,148,1058,818	AA,AG,A,GG,G		16.3948,2.8122,11.8333	benign,	313/1068,	114424941	426,3174	692	1591	2283	SO:0001583	missense	139804	exon1			TGCGGCGCTGCCC	AK097568	CCDS55478.1	Xq23	2013-02-12	2009-03-24	2009-03-24	ENSG00000175718	ENSG00000175718		"""RNA binding motif (RRM) containing"""	26859	protein-coding gene	gene with protein product			"""chromosome X open reading frame 55"""	CXorf55			Standard	NM_001145346		Approved	FLJ40249	uc011mte.1	Q8N7X1	OTTHUMG00000022230	ENST00000424776.3:c.937G>A	X.37:g.114424941G>A	ENSP00000417451:p.Ala313Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	149	41	0.275168	NM_001145346	B4DXC0	Missense_Mutation	SNP	ENST00000424776.3	37	CCDS55478.1	117	0.0705244122965642	3	0.006122448979591836	20	0.056179775280898875	2	0.0034965034965034965	53	0.07703488372093023	G	11.07	1.531256	0.27387	0.028122	0.163948	ENSG00000175718	ENST00000424776	T	0.05513	3.43	0.682	-0.276	0.12902	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.36837	0.571	B	0.17098	0.017	T	0.48352	-0.9043	7	0.87932	D	0	.	.	.	.	rs62601530	313	Q8N7X1	RMXL3_HUMAN	T	313	ENSP00000417451:A313T	ENSP00000417451:A313T	A	+	1	0	RBMXL3	114331197	0.026000	0.19158	0.000000	0.03702	0.000000	0.00434	1.366000	0.34193	-0.218000	0.10018	-0.494000	0.04653	GCT	G|0.929;A|0.071	0.071	strong		0.622	RBMXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057968.3	NM_001145346	
BPIFB1	92747	hgsc.bcm.edu	37	20	31894766	31894766	+	Silent	SNP	C	C	T	rs41311304	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:31894766C>T	ENST00000253354.1	+	15	1529	c.1368C>T	c.(1366-1368)ttC>ttT	p.F456F	BPIFB1_ENST00000464032.1_3'UTR	NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	456					innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										CCTTGGGATTCGAGGCAGCTG	0.577													C|||	73	0.0145767	0.0	0.0331	5008	,	,		19893	0.0		0.0447	False		,,,				2504	0.0051				p.F456F		Atlas-SNP	.											.	.	.	.	0			c.C1368T						PASS	.	C		46,4360	50.2+/-85.5	0,46,2157	141.0	120.0	127.0		1368	-7.1	0.0	20	dbSNP_127	127	433,8167	132.8+/-190.4	17,399,3884	no	coding-synonymous	BPIFB1	NM_033197.2		17,445,6041	TT,TC,CC		5.0349,1.044,3.6829		456/485	31894766	479,12527	2203	4300	6503	SO:0001819	synonymous_variant	92747	exon15			GGGATTCGAGGCA	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"""BPI fold containing"""	16108	protein-coding gene	gene with protein product	"""von Ebner minor salivary gland protein"""		"""chromosome 20 open reading frame 114"""	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.1368C>T	20.37:g.31894766C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Silent	SNP	ENST00000253354.1	37	CCDS13218.1																																																																																			C|0.965;T|0.035	0.035	strong		0.577	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	
PON3	5446	hgsc.bcm.edu	37	7	95025600	95025600	+	Silent	SNP	G	G	A	rs13226149	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:95025600G>A	ENST00000265627.5	-	1	73	c.63C>T	c.(61-63)ttC>ttT	p.F21F	PON1_ENST00000542556.1_Silent_p.F21F|PON3_ENST00000427422.1_Silent_p.F21F|PON3_ENST00000475439.1_5'Flank|PON3_ENST00000451904.1_Silent_p.F21F	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	21					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	TAAACGCCAGGAACATCTCCC	0.657													G|||	1526	0.304712	0.4024	0.245	5008	,	,		13487	0.1667		0.2555	False		,,,				2504	0.408				p.F21F		Atlas-SNP	.											.	PON3	59	.	0			c.C63T						PASS	.	G		1480,2926	474.1+/-356.9	236,1008,959	133.0	118.0	123.0		63	-8.7	0.0	7	dbSNP_121	123	2187,6413	373.5+/-337.0	283,1621,2396	no	coding-synonymous	PON3	NM_000940.2		519,2629,3355	AA,AG,GG		25.4302,33.5906,28.1947		21/355	95025600	3667,9339	2203	4300	6503	SO:0001819	synonymous_variant	5446	exon1			CGCCAGGAACATC	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.63C>T	7.37:g.95025600G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																			G|0.723;A|0.277	0.277	strong		0.657	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
MRPL28	10573	hgsc.bcm.edu	37	16	420179	420179	+	Silent	SNP	G	G	A	rs11557300	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:420179G>A	ENST00000199706.8	-	2	75	c.40C>T	c.(40-42)Ctg>Ttg	p.L14L	MRPL28_ENST00000389675.2_Silent_p.L14L|MRPL28_ENST00000429738.1_5'Flank	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	14					translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				CGCAGCTGCAGCCGCTTCCAG	0.697													G|||	369	0.0736821	0.0068	0.0476	5008	,	,		9303	0.128		0.1193	False		,,,				2504	0.0798				p.L14L		Atlas-SNP	.											.	MRPL28	15	.	0			c.C40T						PASS	.	G		118,4228		5,108,2060	15.0	16.0	16.0		40	-0.4	0.0	16	dbSNP_120	16	1111,7467		64,983,3242	no	coding-synonymous	MRPL28	NM_006428.4		69,1091,5302	AA,AG,GG		12.9517,2.7151,9.5094		14/257	420179	1229,11695	2173	4289	6462	SO:0001819	synonymous_variant	10573	exon2			GCTGCAGCCGCTT	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.40C>T	16.37:g.420179G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Silent	SNP	ENST00000199706.8	37	CCDS32349.1																																																																																			G|0.916;C|0.000;A|0.083	0.083	strong		0.697	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
CAMK1G	57172	hgsc.bcm.edu	37	1	209782343	209782343	+	Silent	SNP	A	A	G	rs11119314	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:209782343A>G	ENST00000009105.1	+	8	899	c.654A>G	c.(652-654)ccA>ccG	p.P218P	CAMK1G_ENST00000494990.1_3'UTR|CAMK1G_ENST00000361322.2_Silent_p.P218P			Q96NX5	KCC1G_HUMAN	calcium/calmodulin-dependent protein kinase IG	218	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.P218P(1)		breast(2)|central_nervous_system(1)|large_intestine(8)|lung(8)|stomach(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.0475)		GATACCCCCCATTCTATGAAG	0.517													A|||	2732	0.545527	0.7073	0.5476	5008	,	,		20101	0.5714		0.3867	False		,,,				2504	0.4622				p.P218P	Ovarian(163;530 1939 9680 28669 48710)	Atlas-SNP	.											CAMK1G,NS,adenoma,0,2	CAMK1G	49	2	1	Substitution - coding silent(1)	stomach(1)	c.A654G						PASS	.	A		2909,1497	675.5+/-403.1	957,995,251	117.0	112.0	114.0		654	-10.2	0.5	1	dbSNP_120	114	3346,5254	497.4+/-374.5	643,2060,1597	no	coding-synonymous	CAMK1G	NM_020439.2		1600,3055,1848	GG,GA,AA		38.907,33.9764,48.0932		218/477	209782343	6255,6751	2203	4300	6503	SO:0001819	synonymous_variant	57172	exon8			CCCCCCATTCTAT		CCDS1486.1	1q32.2	2012-09-20			ENSG00000008118	ENSG00000008118			14585	protein-coding gene	gene with protein product		614994				12637513	Standard	NM_020439		Approved	VWS1, CLICKIII, dJ272L16.1	uc001hhd.3	Q96NX5	OTTHUMG00000036361	ENST00000009105.1:c.654A>G	1.37:g.209782343A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	111	41	0.369369	NM_020439	Q86UH5|Q9Y3J7	Silent	SNP	ENST00000009105.1	37	CCDS1486.1	1134	0.5192307692307693	350	0.7113821138211383	179	0.494475138121547	327	0.5716783216783217	278	0.36675461741424803	A	6.373	0.436872	0.12104	0.660236	0.38907	ENSG00000008118	ENST00000423146	T	0.64085	-0.08	5.48	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.38308	-0.9667	5	0.87932	D	0	.	0.8075	0.01086	0.336:0.2448:0.2567:0.1625	rs11119314;rs17846018;rs17859002;rs60747756;rs11119314	.	.	.	R	193	ENSP00000392173:H193R	ENSP00000392173:H193R	H	+	2	0	CAMK1G	207848966	0.000000	0.05858	0.481000	0.27354	0.191000	0.23601	-3.434000	0.00472	-1.907000	0.01087	-2.614000	0.00158	CAT	A|0.485;G|0.515	0.515	strong		0.517	CAMK1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088526.1	NM_020439	
UGDH	7358	hgsc.bcm.edu	37	4	39512347	39512347	+	Silent	SNP	T	T	C	rs11544855	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:39512347T>C	ENST00000316423.6	-	4	741	c.399A>G	c.(397-399)ccA>ccG	p.P133P	UGDH_ENST00000507089.1_Silent_p.P36P|UGDH_ENST00000501493.2_Intron|UGDH_ENST00000506179.1_Silent_p.P133P|UGDH_ENST00000515398.1_5'Flank	NM_001184701.1|NM_003359.3	NP_001171630.1|NP_003350.1	O60701	UGDH_HUMAN	UDP-glucose 6-dehydrogenase	133					cellular glucuronidation (GO:0052695)|gastrulation with mouth forming second (GO:0001702)|glycosaminoglycan biosynthetic process (GO:0006024)|small molecule metabolic process (GO:0044281)|UDP-glucose metabolic process (GO:0006011)|UDP-glucuronate biosynthetic process (GO:0006065)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|NAD binding (GO:0051287)|UDP-glucose 6-dehydrogenase activity (GO:0003979)			breast(1)|central_nervous_system(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(2)	27						CTGCCCGCACTGGAACTGTGC	0.408													T|||	311	0.0621006	0.0121	0.0735	5008	,	,		18962	0.0268		0.1551	False		,,,				2504	0.0624				p.P133P		Atlas-SNP	.											UGDH,caecum,carcinoma,-2,1	UGDH	52	1	0			c.A399G						scavenged	.	T	,,	149,4257	102.1+/-140.7	5,139,2059	182.0	174.0	176.0		,108,399	-8.9	0.7	4	dbSNP_120	176	1222,7378	246.4+/-274.8	83,1056,3161	no	intron,coding-synonymous,coding-synonymous	UGDH	NM_001184700.1,NM_001184701.1,NM_003359.3	,,	88,1195,5220	CC,CT,TT		14.2093,3.3818,10.5413	,,	,36/398,133/495	39512347	1371,11635	2203	4300	6503	SO:0001819	synonymous_variant	7358	exon4			CCGCACTGGAACT	AF061016	CCDS3455.1, CCDS54757.1, CCDS54758.1	4p14	2011-11-16	2010-04-28		ENSG00000109814	ENSG00000109814	1.1.1.22		12525	protein-coding gene	gene with protein product		603370	"""UDP-glucose dehydrogenase"""			9737970, 10575217	Standard	NM_003359		Approved		uc003guk.2	O60701	OTTHUMG00000099371	ENST00000316423.6:c.399A>G	4.37:g.39512347T>C		Somatic	218	3	0.0137615		WXS	Illumina HiSeq	Phase_I	246	117	0.47561	NM_003359	B3KUU2|B4DN25|O60589	Silent	SNP	ENST00000316423.6	37	CCDS3455.1																																																																																			T|0.904;C|0.096	0.096	strong		0.408	UGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216818.3	NM_003359	
TEX38	374973	hgsc.bcm.edu	37	1	47138819	47138819	+	Missense_Mutation	SNP	T	T	G	rs614486	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:47138819T>G	ENST00000334122.4	+	2	419	c.312T>G	c.(310-312)gaT>gaG	p.D104E	ATPAF1_ENST00000525633.1_Intron|TEX38_ENST00000569393.1_Missense_Mutation_p.D158E|EFCAB14-AS1_ENST00000442839.1_RNA|TEX38_ENST00000564373.1_Missense_Mutation_p.D50E|EFCAB14-AS1_ENST00000418985.1_RNA|TEX38_ENST00000415500.1_Missense_Mutation_p.D28E|EFCAB14_ENST00000544071.1_Intron	NM_001145474.2	NP_001138946.1	Q6PEX7	TEX38_HUMAN	testis expressed 38	104			D -> E (in dbSNP:rs614486). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)											TTCTGTGGGATTTGGACATCC	0.612													G|||	2701	0.539337	0.6513	0.4625	5008	,	,		19138	0.7996		0.3121	False		,,,				2504	0.408				p.D104E		Atlas-SNP	.											.	.	.	.	0			c.T312G						PASS	.	G	GLU/ASP	817,567		235,347,110	69.0	70.0	70.0		312	1.4	0.1	1	dbSNP_83	70	868,2314		102,664,825	yes	missense	ATPAF1-AS1	NM_001145474.2	45	337,1011,935	GG,GT,TT		27.2784,40.9682,36.9032	benign	104/207	47138819	1685,2881	692	1591	2283	SO:0001583	missense	374973	exon2			GTGGGATTTGGAC		CCDS57999.1, CCDS72780.1, CCDS72781.1	1p33	2012-10-12	2012-10-12	2012-10-12	ENSG00000186118	ENSG00000186118			29589	protein-coding gene	gene with protein product	"""testis highly expressed protein 4"""		"""chromosome 1 open reading frame 223"", ""ATPAF1 antisense RNA 1 (non-protein coding)"", ""ATPAF1 antisense RNA 1"""	C1orf223, ATPAF1-AS1		12477932	Standard	XM_005270845		Approved	LOC374973, THEG4	uc001cqj.3	Q6PEX7	OTTHUMG00000007991	ENST00000334122.4:c.312T>G	1.37:g.47138819T>G	ENSP00000455854:p.Asp104Glu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001145474	A1A4F8	Missense_Mutation	SNP	ENST00000334122.4	37	CCDS57999.1																																																																																			T|0.461;G|0.539	0.539	strong		0.612	TEX38-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000021929.2	NM_001145474	
AP3B1	8546	hgsc.bcm.edu	37	5	77412011	77412011	+	Silent	SNP	A	A	G	rs42360	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:77412011A>G	ENST00000255194.6	-	18	2191	c.2016T>C	c.(2014-2016)gcT>gcC	p.A672A	AP3B1_ENST00000519295.1_Silent_p.A623A	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	672					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		AAAACTTCTTAGCAGAATTCT	0.338									Hermansky-Pudlak syndrome				A|||	946	0.188898	0.2383	0.3271	5008	,	,		16072	0.0754		0.2127	False		,,,				2504	0.1166				p.A672A		Atlas-SNP	.											AP3B1,NS,carcinoma,0,1	AP3B1	94	1	0			c.T2016C						PASS	.	A		1135,3271	401.5+/-332.0	163,809,1231	87.0	91.0	89.0		2016	3.6	0.8	5	dbSNP_76	89	2013,6587	351.2+/-328.2	249,1515,2536	no	coding-synonymous	AP3B1	NM_003664.3		412,2324,3767	GG,GA,AA		23.407,25.7603,24.2042		672/1095	77412011	3148,9858	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon18	Familial Cancer Database	HPS, HPS1-8	CTTCTTAGCAGAA	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2016T>C	5.37:g.77412011A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.776;C|0.001	.	strong		0.338	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
CILP2	148113	hgsc.bcm.edu	37	19	19656615	19656615	+	Silent	SNP	C	C	T	rs61744761	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:19656615C>T	ENST00000291495.5	+	8	3346	c.3261C>T	c.(3259-3261)ggC>ggT	p.G1087G	CILP2_ENST00000586018.1_Silent_p.G1093G	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	1087						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCTCTGACGGCTTCTCCAGAG	0.622													C|||	582	0.116214	0.174	0.1167	5008	,	,		14302	0.0		0.166	False		,,,				2504	0.1063				p.G1087G		Atlas-SNP	.											.	CILP2	84	.	0			c.C3261T						PASS	.	C		761,3643	284.3+/-277.5	57,647,1498	31.0	24.0	26.0		3261	3.5	1.0	19	dbSNP_129	26	1411,7189	252.2+/-278.4	111,1189,3000	no	coding-synonymous	CILP2	NM_153221.2		168,1836,4498	TT,TC,CC		16.407,17.2797,16.7026		1087/1157	19656615	2172,10832	2202	4300	6502	SO:0001819	synonymous_variant	148113	exon8			TGACGGCTTCTCC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.3261C>T	19.37:g.19656615C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	195	101	0.517949	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			C|0.845;T|0.155	0.155	strong		0.622	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
ENGASE	64772	hgsc.bcm.edu	37	17	77079576	77079576	+	Silent	SNP	A	A	G	rs61756761	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77079576A>G	ENST00000579016.1	+	9	1155	c.1155A>G	c.(1153-1155)cgA>cgG	p.R385R	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	385						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						TCTGGGGCCGACTGGAGCGTT	0.612													G|||	682	0.136182	0.357	0.0677	5008	,	,		20375	0.0476		0.0577	False		,,,				2504	0.0583				p.R385R		Atlas-SNP	.											ENGASE,NS,carcinoma,+1,1	ENGASE	55	1	0			c.A1155G						PASS	.	G		1152,3078		150,852,1113	92.0	102.0	99.0		1155	5.5	0.9	17	dbSNP_129	99	481,7973		9,463,3755	no	coding-synonymous	ENGASE	NM_001042573.1		159,1315,4868	GG,GA,AA		5.6896,27.234,12.8745		385/744	77079576	1633,11051	2115	4227	6342	SO:0001819	synonymous_variant	64772	exon9			GGGCCGACTGGAG	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.1155A>G	17.37:g.77079576A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			A|0.902;G|0.098	0.098	strong		0.612	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
SLC35G5	83650	hgsc.bcm.edu	37	8	11189616	11189616	+	Missense_Mutation	SNP	G	G	A	rs200495954		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:11189616G>A	ENST00000382435.4	+	1	1220	c.1001G>A	c.(1000-1002)gGg>gAg	p.G334E		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	334						integral component of membrane (GO:0016021)											GAGAGGACAGGGAAGGTGGAG	0.498																																					p.G334E		Atlas-SNP	.											AMAC1L2,right_upper_lobe,carcinoma,+1,1	.	.	1	0			c.G1001A						scavenged	.						55.0	58.0	57.0					8																	11189616		2203	4300	6503	SO:0001583	missense	83650	exon1			GGACAGGGAAGGT	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.1001G>A	8.37:g.11189616G>A	ENSP00000371872:p.Gly334Glu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	55	6	0.109091	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	g	5.777	0.327688	0.10956	.	.	ENSG00000177710	ENST00000382435	T	0.38560	1.13	.	.	.	.	0.350088	0.20838	N	0.084754	T	0.26484	0.0647	L	0.50333	1.59	0.28172	N	0.928524	B	0.06786	0.001	B	0.04013	0.001	T	0.35574	-0.9783	8	0.02654	T	1	-1.4658	.	.	.	.	334	Q96KT7	S35G5_HUMAN	E	334	ENSP00000371872:G334E	ENSP00000371872:G334E	G	+	2	0	SLC35G5	11227026	0.086000	0.21541	0.277000	0.24703	0.278000	0.26855	-0.233000	0.09041	0.064000	0.16427	0.064000	0.15345	GGG	G|0.999;A|0.001	0.001	weak		0.498	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
PITX3	5309	hgsc.bcm.edu	37	10	103991381	103991381	+	Silent	SNP	G	G	A	rs2281983	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:103991381G>A	ENST00000370002.3	-	3	438	c.285C>T	c.(283-285)atC>atT	p.I95I	PITX3_ENST00000539804.1_Silent_p.I95I	NM_005029.3	NP_005020.1	O75364	PITX3_HUMAN	paired-like homeodomain 3	95					dopaminergic neuron differentiation (GO:0071542)|lens development in camera-type eye (GO:0002088)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|locomotory behavior (GO:0007626)|midbrain development (GO:0030901)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)	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)			endometrium(1)|large_intestine(2)|lung(2)	5		Colorectal(252;0.00957)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		TCCACACGGCGATCTCCTCGC	0.701													G|||	3326	0.664137	0.7753	0.6254	5008	,	,		10795	0.7718		0.5974	False		,,,				2504	0.499				p.I95I		Atlas-SNP	.											.	PITX3	9	.	0			c.C285T						PASS	.	G		3325,1081	692.8+/-405.6	1260,805,138	49.0	46.0	47.0		285	2.5	1.0	10	dbSNP_100	47	5301,3299	623.3+/-397.4	1613,2075,612	no	coding-synonymous	PITX3	NM_005029.3		2873,2880,750	AA,AG,GG		38.3605,24.5347,33.6768		95/303	103991381	8626,4380	2203	4300	6503	SO:0001819	synonymous_variant	5309	exon3			CACGGCGATCTCC		CCDS7532.1	10q24.32	2013-11-14	2007-07-12		ENSG00000107859	ENSG00000107859		"""Homeoboxes / PRD class"""	9006	protein-coding gene	gene with protein product		602669	"""paired-like homeodomain transcription factor 3"", ""anterior segment mesenchymal dysgenesis"""	ASMD		9620774	Standard	NM_005029		Approved		uc001kuu.1	O75364	OTTHUMG00000018952	ENST00000370002.3:c.285C>T	10.37:g.103991381G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	94	0.979167	NM_005029	Q5VZL2	Silent	SNP	ENST00000370002.3	37	CCDS7532.1																																																																																			G|0.327;A|0.673	0.673	strong		0.701	PITX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050031.1		
ZCWPW2	152098	hgsc.bcm.edu	37	3	28520417	28520417	+	Missense_Mutation	SNP	T	T	A	rs1563656	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:28520417T>A	ENST00000383768.2	+	5	793	c.605T>A	c.(604-606)cTa>cAa	p.L202Q	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.L202Q			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	202			L -> Q (in dbSNP:rs1563656).				zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						CTATCAAAACTACAAGGTGTA	0.303													A|||	2277	0.454673	0.323	0.4654	5008	,	,		12654	0.6171		0.4304	False		,,,				2504	0.4826				p.L202Q		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.T605A						PASS	.	A	GLN/LEU	1561,2845	664.3+/-401.3	279,1003,921	68.0	71.0	70.0		605	0.2	0.0	3	dbSNP_88	70	3658,4938	619.7+/-397.0	768,2122,1408	yes	missense	ZCWPW2	NM_001040432.1	113	1047,3125,2329	AA,AT,TT		42.5547,35.429,40.14	benign	202/357	28520417	5219,7783	2203	4298	6501	SO:0001583	missense	152098	exon4			CAAAACTACAAGG	BC065764	CCDS33723.1	3p23	2005-08-22			ENSG00000206559	ENSG00000206559			23574	protein-coding gene	gene with protein product						14607086	Standard	XM_005264892		Approved	ZCW2	uc003cei.3	Q504Y3	OTTHUMG00000155705	ENST00000383768.2:c.605T>A	3.37:g.28520417T>A	ENSP00000373278:p.Leu202Gln	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	155	75	0.483871	NM_001040432		Missense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	1006	0.4606227106227106	173	0.3516260162601626	163	0.45027624309392267	343	0.5996503496503497	327	0.4313984168865435	A	0.016	-1.524785	0.00959	0.35429	0.425547	ENSG00000206559	ENST00000383768;ENST00000421010	T;T	0.33438	1.41;1.41	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39702	-0.9601	7	0.12430	T	0.62	2.2514	.	.	.	rs1563656;rs4493386;rs17357234;rs52813176;rs56536652;rs60931131;rs1563656	202	Q504Y3	ZCPW2_HUMAN	Q	202	ENSP00000373278:L202Q;ENSP00000412386:L202Q	ENSP00000373278:L202Q	L	+	2	0	ZCWPW2	28495421	0.002000	0.14202	0.004000	0.12327	0.092000	0.18411	-0.562000	0.05950	-0.843000	0.04189	-0.868000	0.02995	CTA	T|0.574;A|0.426	0.426	strong		0.303	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384	
FLT4	2324	hgsc.bcm.edu	37	5	180043388	180043388	+	Silent	SNP	G	G	A	rs1130378	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:180043388G>A	ENST00000261937.6	-	23	3276	c.3198C>T	c.(3196-3198)ccC>ccT	p.P1066P	FLT4_ENST00000393347.3_Silent_p.P1066P|FLT4_ENST00000502649.1_Silent_p.P1066P	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1066	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GGACGTAGTCGGGGTCTTTGT	0.597													A|||	1204	0.240415	0.1566	0.1888	5008	,	,		20056	0.2619		0.2823	False		,,,				2504	0.3252				p.P1066P	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C3198T						PASS	.	A	,	749,3657	753.7+/-412.4	64,621,1518	114.0	104.0	108.0		3198,3198	0.6	1.0	5	dbSNP_86	108	2536,6064	691.9+/-404.5	393,1750,2157	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	457,2371,3675	AA,AG,GG		29.4884,16.9995,25.2576	,	1066/1299,1066/1364	180043388	3285,9721	2203	4300	6503	SO:0001819	synonymous_variant	2324	exon23			GTAGTCGGGGTCT	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3198C>T	5.37:g.180043388G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	128	125	0.976562	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			G|0.751;A|0.249	0.249	strong		0.597	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
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 GAIIx	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_ENST00000413996.3_Missense_Mutation_p.Q54E|SGK1_ENST00000367857.5_Missense_Mutation_p.Q30E|SGK1_ENST00000475719.2_Missense_Mutation_p.Q40E|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367858.5_Missense_Mutation_p.Q135E|SGK1_ENST00000528577.1_Missense_Mutation_p.Q68E	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	Somatic	70	0	0	1611	WXS	Illumina HiSeq	Phase_I	46	16	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		
TAS1R1	80835	hgsc.bcm.edu	37	1	6635306	6635306	+	Missense_Mutation	SNP	G	G	A	rs34160967	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:6635306G>A	ENST00000333172.6	+	3	1307	c.1114G>A	c.(1114-1116)Gca>Aca	p.A372T	TAS1R1_ENST00000351136.3_Intron|TAS1R1_ENST00000328191.4_Missense_Mutation_p.A372T	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	372			A -> T (in dbSNP:rs34160967).		detection of chemical stimulus involved in sensory perception of taste (GO:0050912)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(13)|ovary(1)|skin(1)|urinary_tract(2)	29	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;8.73e-34)|all_epithelial(116;9.26e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Breast(487;0.000353)|Renal(390;0.0007)|Colorectal(325;0.00104)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0443)		Colorectal(212;1.29e-07)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0642)		AGCTTTCATGGCACACACGAT	0.592													G|||	678	0.135383	0.0582	0.0648	5008	,	,		20875	0.3204		0.1223	False		,,,				2504	0.1125				p.A372T		Atlas-SNP	.											TAS1R1,caecum,carcinoma,0,1	TAS1R1	76	1	0			c.G1114A						PASS	.	G	THR/ALA,	304,4102	154.8+/-188.1	17,270,1916	65.0	53.0	57.0		1114,	-0.6	0.0	1	dbSNP_126	57	1080,7520	217.7+/-256.3	69,942,3289	yes	missense,intron	TAS1R1	NM_138697.3,NM_177540.2	58,	86,1212,5205	AA,AG,GG		12.5581,6.8997,10.6412	benign,	372/842,	6635306	1384,11622	2203	4300	6503	SO:0001583	missense	80835	exon3			TTCATGGCACACA		CCDS81.1, CCDS82.1	1p36.23	2012-08-22	2003-03-24		ENSG00000173662	ENSG00000173662		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14448	protein-coding gene	gene with protein product		606225	"""G protein-coupled receptor 70"""	GPR70			Standard	NM_138697		Approved	T1R1, TR1	uc001ant.3	Q7RTX1	OTTHUMG00000001441	ENST00000333172.6:c.1114G>A	1.37:g.6635306G>A	ENSP00000331867:p.Ala372Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	37	CCDS81.1	334|334	0.15293040293040294|0.15293040293040294	23|23	0.046747967479674794|0.046747967479674794	26|26	0.0718232044198895|0.0718232044198895	197|197	0.34440559440559443|0.34440559440559443	88|88	0.11609498680738786|0.11609498680738786	G|G	1.258|1.258	-0.616607|-0.616607	0.03663|0.03663	0.068997|0.068997	0.125581|0.125581	ENSG00000173662|ENSG00000173662	ENST00000333172;ENST00000328191|ENST00000411823	D;D|.	0.91237|.	-2.43;-2.81|.	5.24|5.24	-0.638|-0.638	0.11500|0.11500	Extracellular ligand-binding receptor (1);|.	1.364240|.	0.04390|.	N|.	0.362231|.	T|.	0.00012|.	0.0000|.	L|L	0.33753|0.33753	1.03|1.03	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.32467|.	0.372;0.158|.	B;B|.	0.28784|.	0.076;0.094|.	T|.	0.43114|.	-0.9411|.	9|.	0.09338|.	T|.	0.73|.	.|.	4.9085|4.9085	0.13811|0.13811	0.3505:0.3088:0.3407:0.0|0.3505:0.3088:0.3407:0.0	rs34160967;rs57648522|rs34160967;rs57648522	372;372|.	Q7RTX1-3;Q7RTX1|.	.;TS1R1_HUMAN|.	T|X	372|297	ENSP00000331867:A372T;ENSP00000327705:A372T|.	ENSP00000327705:A372T|.	A|W	+|+	1|3	0|0	TAS1R1|TAS1R1	6557893|6557893	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	-0.147000|-0.147000	0.10234|0.10234	0.160000|0.160000	0.19432|0.19432	-0.218000|-0.218000	0.12543|0.12543	GCA|TGG	G|0.871;A|0.129	0.129	strong		0.592	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1		
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 GAIIx	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_ENST00000369976.1_Intron|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000369970.3_Silent_p.K464K|CLCC1_ENST00000302500.4_Silent_p.K393K|CLCC1_ENST00000369968.2_Silent_p.K329K|CLCC1_ENST00000415331.1_Silent_p.K464K|CLCC1_ENST00000356970.2_Silent_p.K514K|CLCC1_ENST00000369969.2_Silent_p.K393K|CLCC1_ENST00000348264.2_Silent_p.K329K	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		Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	203	102	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	
SPHKAP	80309	hgsc.bcm.edu	37	2	228883029	228883029	+	Missense_Mutation	SNP	A	A	C	rs3811515	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:228883029A>C	ENST00000392056.3	-	7	2587	c.2541T>G	c.(2539-2541)caT>caG	p.H847Q	SPHKAP_ENST00000344657.5_Missense_Mutation_p.H847Q	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	847			H -> Q (in dbSNP:rs3811515). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.H847Q(1)		NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		TCTCACTGTGATGAGGGCTTT	0.493													A|||	1115	0.222644	0.0318	0.2464	5008	,	,		21416	0.2242		0.2406	False		,,,				2504	0.4438				p.H847Q		Atlas-SNP	.											SPHKAP,NS,carcinoma,0,1	SPHKAP	750	1	1	Substitution - Missense(1)	stomach(1)	c.T2541G						scavenged	.	A	GLN/HIS,GLN/HIS	282,4124	156.3+/-189.4	13,256,1934	745.0	703.0	717.0		2541,2541	1.0	0.0	2	dbSNP_107	717	2167,6433	371.6+/-336.3	287,1593,2420	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	24,24	300,1849,4354	CC,CA,AA		25.1977,6.4004,18.8298	possibly-damaging,possibly-damaging	847/1701,847/1672	228883029	2449,10557	2203	4300	6503	SO:0001583	missense	80309	exon7			ACTGTGATGAGGG		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2541T>G	2.37:g.228883029A>C	ENSP00000375909:p.His847Gln	Somatic	290	2	0.00689655		WXS	Illumina HiSeq	Phase_I	256	110	0.429688	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	469	0.21474358974358973	26	0.052845528455284556	96	0.26519337016574585	156	0.2727272727272727	191	0.2519788918205805	A	5.226	0.227206	0.09916	0.064004	0.251977	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.11169	2.8;2.8	5.97	0.984	0.19773	.	1.321610	0.04419	N	0.367345	T	0.00012	0.0000	M	0.65975	2.015	0.80722	P	0.0	B;B	0.16802	0.011;0.019	B;B	0.15052	0.003;0.012	T	0.39742	-0.9599	9	0.59425	D	0.04	.	6.0637	0.19852	0.5854:0.2766:0.138:0.0	rs3811515;rs17266858;rs52816852;rs56487013;rs57755256;rs3811515	847;847	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	Q	847	ENSP00000375909:H847Q;ENSP00000339886:H847Q	ENSP00000339886:H847Q	H	-	3	2	SPHKAP	228591273	0.031000	0.19500	0.000000	0.03702	0.414000	0.31173	0.219000	0.17641	0.148000	0.19059	0.533000	0.62120	CAT	A|0.784;C|0.216	0.216	strong		0.493	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
TRIM22	10346	hgsc.bcm.edu	37	11	5717762	5717762	+	Silent	SNP	T	T	C	rs10838543	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5717762T>C	ENST00000379965.3	+	2	577	c.300T>C	c.(298-300)caT>caC	p.H100H	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	100					defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		GTGAGCACCATGGAAAAAAAC	0.478													T|||	1975	0.394369	0.3714	0.415	5008	,	,		21250	0.1766		0.5209	False		,,,				2504	0.5051				p.H100H	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.T300C						PASS	.	T	,	1594,2616		316,962,827	63.0	70.0	68.0		300,300	0.7	1.0	11	dbSNP_120	68	4227,4297		1072,2083,1107	no	coding-synonymous,coding-synonymous	TRIM22	NM_001199573.1,NM_006074.4	,	1388,3045,1934	CC,CT,TT		49.5894,37.8622,45.7123	,	100/495,100/499	5717762	5821,6913	2105	4262	6367	SO:0001819	synonymous_variant	10346	exon2			GCACCATGGAAAA	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16379	protein-coding gene	gene with protein product		606559	"""tripartite motif-containing 22"""			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.300T>C	11.37:g.5717762T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_001199573	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			T|0.595;C|0.405	0.405	strong		0.478	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
PKD1L1	168507	hgsc.bcm.edu	37	7	47879049	47879049	+	Missense_Mutation	SNP	G	G	A	rs76100363	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:47879049G>A	ENST00000289672.2	-	36	5814	c.5764C>T	c.(5764-5766)Cgg>Tgg	p.R1922W		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1922					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CCTACCTTCCGGAAGCCGAGT	0.642													G|||	816	0.162939	0.0174	0.2291	5008	,	,		16788	0.2321		0.2078	False		,,,				2504	0.1953				p.R1922W		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	0			c.C5764T						PASS	.	G	TRP/ARG	211,4195		3,205,1995	29.0	24.0	26.0		5764	-9.7	0.1	7	dbSNP_131	26	1513,7087		124,1265,2911	yes	missense	PKD1L1	NM_138295.3	101	127,1470,4906	AA,AG,GG		17.593,4.7889,13.2554	benign	1922/2850	47879049	1724,11282	2203	4300	6503	SO:0001583	missense	168507	exon36			CCTTCCGGAAGCC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5764C>T	7.37:g.47879049G>A	ENSP00000289672:p.Arg1922Trp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	67	46	0.686567	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	376	0.17216117216117216	11	0.022357723577235773	91	0.2513812154696133	120	0.2097902097902098	154	0.20316622691292877	G	6.846	0.525413	0.13066	0.047889	0.17593	ENSG00000158683	ENST00000289672	T	0.20738	2.05	4.87	-9.73	0.00512	.	1.518000	0.04159	N	0.322748	T	0.00012	0.0000	N	0.11064	0.09	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.28776	-1.0033	9	0.48119	T	0.1	0.0923	8.3591	0.32348	0.6412:0.0:0.1727:0.1862	.	1922	Q8TDX9	PK1L1_HUMAN	W	1922	ENSP00000289672:R1922W	ENSP00000289672:R1922W	R	-	1	2	PKD1L1	47845574	0.000000	0.05858	0.055000	0.19348	0.255000	0.26057	-2.918000	0.00695	-2.336000	0.00628	-0.749000	0.03505	CGG	G|0.859;A|0.141	0.141	strong		0.642	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
LILRB3	11025	hgsc.bcm.edu	37	19	54721320	54721320	+	Missense_Mutation	SNP	C	C	G	rs1053002	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54721320C>G	ENST00000391750.1	-	13	1753	c.1617G>C	c.(1615-1617)caG>caC	p.Q539H	LILRB3_ENST00000407860.2_Missense_Mutation_p.Q556H|LILRA6_ENST00000440558.2_Missense_Mutation_p.Q539H|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000245620.9_Missense_Mutation_p.Q540H|LILRA6_ENST00000270464.5_Missense_Mutation_p.Q540H|LILRB3_ENST00000346401.6_Missense_Mutation_p.Q551H|LILRB3_ENST00000424807.1_Missense_Mutation_p.Q539H|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.Q540H			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	539			Q -> H (in dbSNP:rs1053002). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACGTCACTGCCTGGGGGTCTT	0.577																																					p.Q540H		Atlas-SNP	.											LILRB3,NS,carcinoma,-2,1	LILRB3	67	1	0			c.G1620C						PASS	.						97.0	102.0	100.0					19																	54721320		2202	4300	6502	SO:0001583	missense	11025	exon12			CACTGCCTGGGGG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1617G>C	19.37:g.54721320C>G	ENSP00000375630:p.Gln539His	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	213	115	0.539906	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	256	0.11721611721611722	140	0.2845528455284553	37	0.10220994475138122	3	0.005244755244755245	76	0.10026385224274406	C	6.747	0.506690	0.12883	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00531	6.77;6.77;6.79;6.78;6.84;6.76;6.77;6.79	2.47	-2.73	0.05950	.	.	.	.	.	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	B;D;B;B;D;D;D	0.76494	0.095;0.988;0.226;0.004;0.967;0.999;0.994	B;P;B;B;P;P;D	0.68765	0.028;0.816;0.068;0.007;0.77;0.894;0.96	T	0.51403	-0.8710	8	0.59425	D	0.04	.	2.8244	0.05481	0.2046:0.4038:0.0:0.3916	rs1053002;rs3193491	556;539;540;551;556;539;540	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	H	539;539;551;540;556;539;540;540	ENSP00000375630:Q539H;ENSP00000412771:Q539H;ENSP00000345184:Q551H;ENSP00000245620:Q540H;ENSP00000384274:Q556H;ENSP00000390120:Q539H;ENSP00000270464:Q540H;ENSP00000411227:Q540H	ENSP00000270464:Q540H	Q	-	3	2	LILRB3;LILRA6	59413132	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.903000	0.04084	-0.478000	0.06823	0.413000	0.27773	CAG	C|0.891;G|0.109	0.109	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
C6orf15	29113	hgsc.bcm.edu	37	6	31079264	31079264	+	Missense_Mutation	SNP	C	C	T	rs2233984	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31079264C>T	ENST00000259870.3	-	2	875	c.872G>A	c.(871-873)gGt>gAt	p.G291D		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	291	Pro-rich.		G -> D (in dbSNP:rs2233984).		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GTTATTGATACCTGGGTATAG	0.532													C|||	521	0.104034	0.0068	0.0994	5008	,	,		15975	0.2361		0.0785	False		,,,				2504	0.1288				p.G291D		Atlas-SNP	.											C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	0			c.G872A						scavenged	.	C	ASP/GLY	54,3498		0,54,1722	55.0	57.0	56.0		872	0.1	0.0	6	dbSNP_98	56	463,6601		21,421,3090	yes	missense	C6orf15	NM_014070.2	94	21,475,4812	TT,TC,CC		6.5544,1.5203,4.87	probably-damaging	291/326	31079264	517,10099	1776	3532	5308	SO:0001583	missense	29113	exon2			TTGATACCTGGGT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.872G>A	6.37:g.31079264C>T	ENSP00000259870:p.Gly291Asp	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	90	12	0.133333	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	213	0.09752747252747253	8	0.016260162601626018	29	0.08011049723756906	122	0.21328671328671328	54	0.0712401055408971	C	12.76	2.035246	0.35893	0.015203	0.065544	ENSG00000204542	ENST00000259870	T	0.09163	3.01	4.21	0.0657	0.14358	.	0.132959	0.34411	N	0.003986	T	0.13756	0.0333	M	0.69823	2.125	0.48395	P	3.570000000000517E-4	D	0.89917	1.0	D	0.70935	0.971	T	0.02294	-1.1181	9	0.52906	T	0.07	-11.2596	8.2102	0.31479	0.4442:0.4117:0.1441:0.0	rs2233984;rs3823389;rs59556962;rs2233984	291	Q6UXA7	CF015_HUMAN	D	291	ENSP00000259870:G291D	ENSP00000259870:G291D	G	-	2	0	C6orf15	31187243	0.276000	0.24211	0.014000	0.15608	0.045000	0.14185	0.536000	0.23129	-0.212000	0.10109	-0.195000	0.12781	GGT	C|0.921;T|0.079	0.079	strong		0.532	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
ATP12A	479	hgsc.bcm.edu	37	13	25266932	25266932	+	Silent	SNP	C	C	A	rs963984	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25266932C>A	ENST00000381946.3	+	10	1442	c.1275C>A	c.(1273-1275)gtC>gtA	p.V425V	ATP12A_ENST00000218548.6_Silent_p.V431V			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	425					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		CAGACCAAGTCTTTGACCAAA	0.512													C|||	1165	0.232628	0.1263	0.2983	5008	,	,		21097	0.4593		0.0805	False		,,,				2504	0.2526				p.V431V	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C1293A						PASS	.	C	,	499,3907	232.6+/-246.1	32,435,1736	213.0	211.0	212.0		1293,1275	0.4	0.2	13	dbSNP_86	212	809,7791	188.6+/-235.5	47,715,3538	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	79,1150,5274	AA,AC,CC		9.407,11.3255,10.0569	,	431/1046,425/1040	25266932	1308,11698	2203	4300	6503	SO:0001819	synonymous_variant	479	exon10			CCAAGTCTTTGAC	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1275C>A	13.37:g.25266932C>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.845;A|0.155	0.155	strong		0.512	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:14542654C>A	ENST00000358970.5	-	1	491	c.492G>T	c.(490-492)acG>acT	p.T164T	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	164								p.T164T(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TGTTCATGTCCGTGTCCCTGA	0.592																																					p.T164T		Atlas-SNP	.											POTEC,NS,carcinoma,-1,5	POTEC	129	5	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G492T						scavenged	.						260.0	241.0	247.0					18																	14542654		692	1591	2283	SO:0001819	synonymous_variant	388468	exon1			CATGTCCGTGTCC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.492G>T	18.37:g.14542654C>A		Somatic	346	2	0.00578035		WXS	Illumina HiSeq	Phase_I	380	7	0.0184211	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	none		0.592	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
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 GAIIx	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_ENST00000424408.2_Missense_Mutation_p.E483D|LAMA4_ENST00000522006.1_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	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	100	41	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	
ACOT2	10965	hgsc.bcm.edu	37	14	74036370	74036370	+	Silent	SNP	G	G	T	rs60568739	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74036370G>T	ENST00000238651.5	+	1	608	c.426G>T	c.(424-426)ctG>ctT	p.L142L	ACOT2_ENST00000538782.1_Intron	NM_006821.5	NP_006812.3	P49753	ACOT2_HUMAN	acyl-CoA thioesterase 2	142					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)			breast(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	13				BRCA - Breast invasive adenocarcinoma(234;0.0033)|OV - Ovarian serous cystadenocarcinoma(108;0.0639)		CCATGGGGCTGCTCTGGGCCT	0.716													G|||	317	0.0632987	0.0772	0.0778	5008	,	,		13128	0.0625		0.0547	False		,,,				2504	0.044				p.L142L		Atlas-SNP	.											.	ACOT2	24	.	0			c.G426T						PASS	.	G		172,3824		5,162,1831	9.0	9.0	9.0		426	0.3	0.7	14	dbSNP_129	9	331,7633		3,325,3654	no	coding-synonymous	ACOT2	NM_006821.4		8,487,5485	TT,TG,GG		4.1562,4.3043,4.2057		142/484	74036370	503,11457	1998	3982	5980	SO:0001819	synonymous_variant	10965	exon1			GGGGCTGCTCTGG	AY005822, AK001939	CCDS9816.1	14q24.3	2013-09-20			ENSG00000119673	ENSG00000119673		"""Acyl CoA thioesterases"""	18431	protein-coding gene	gene with protein product	"""mitochondrial acyl-CoA thioesterase 1"""	609972				16103133, 16940157	Standard	NM_006821		Approved	Mte1, ZAP128	uc001xon.5	P49753	OTTHUMG00000171608	ENST00000238651.5:c.426G>T	14.37:g.74036370G>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_006821	Q3I5F8|Q53EK4|Q9NUX4	Silent	SNP	ENST00000238651.5	37	CCDS9816.1																																																																																			G|0.940;T|0.060	0.060	strong		0.716	ACOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414435.1	NM_006821	
FRA10AC1	118924	hgsc.bcm.edu	37	10	95441272	95441272	+	Missense_Mutation	SNP	G	G	A	rs11187583	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:95441272G>A	ENST00000359204.4	-	11	949	c.752C>T	c.(751-753)tCt>tTt	p.S251F	FRA10AC1_ENST00000371430.2_Missense_Mutation_p.S251F|FRA10AC1_ENST00000394100.2_Missense_Mutation_p.S251F|FRA10AC1_ENST00000536233.1_Missense_Mutation_p.S251F	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1	251	Lys-rich.		S -> F (in dbSNP:rs11187583).			nucleus (GO:0005634)				NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						TTCTGCAGAAGATAATCTGGA	0.303													G|||	409	0.0816693	0.093	0.0965	5008	,	,		15209	0.0337		0.1193	False		,,,				2504	0.0665				p.S251F		Atlas-SNP	.											FRA10AC1_ENST00000371426,colon,carcinoma,-1,2	FRA10AC1	68	2	0			c.C752T						scavenged	.	G	PHE/SER	385,4019	194.0+/-219.0	18,349,1835	177.0	156.0	163.0		752	5.2	0.9	10	dbSNP_120	163	974,7624	211.0+/-251.7	65,844,3390	yes	missense	FRA10AC1	NM_145246.4	155	83,1193,5225	AA,AG,GG		11.3282,8.7421,10.4522	possibly-damaging	251/316	95441272	1359,11643	2202	4299	6501	SO:0001583	missense	118924	exon11			GCAGAAGATAATC	AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"""chromosome 10 open reading frame 4"""	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.752C>T	10.37:g.95441272G>A	ENSP00000360488:p.Ser251Phe	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_145246	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Missense_Mutation	SNP	ENST00000359204.4	37	CCDS7430.1	188	0.08608058608058608	42	0.08536585365853659	46	0.1270718232044199	14	0.024475524475524476	86	0.11345646437994723	G	15.10	2.734050	0.48939	0.087421	0.113282	ENSG00000148690	ENST00000359204;ENST00000536233;ENST00000371426;ENST00000371430;ENST00000394100	T;T;T;T	0.25579	1.81;1.8;1.79;1.8	5.17	5.17	0.71159	.	0.293421	0.37857	N	0.001919	T	0.00328	0.0010	L	0.59436	1.845	0.38708	P	0.04685600000000001	P	0.48407	0.91	B	0.43575	0.424	T	0.03139	-1.1068	9	0.66056	D	0.02	-3.4566	15.7456	0.77939	0.0:0.0:1.0:0.0	rs11187583;rs52826468;rs11187583	251	Q70Z53	F10C1_HUMAN	F	251	ENSP00000360488:S251F;ENSP00000438405:S251F;ENSP00000360484:S251F;ENSP00000377660:S251F	ENSP00000360488:S251F	S	-	2	0	FRA10AC1	95431262	1.000000	0.71417	0.890000	0.34922	0.831000	0.47069	4.748000	0.62148	2.572000	0.86782	0.655000	0.94253	TCT	G|0.902;A|0.098	0.098	strong		0.303	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246	
STK33	65975	hgsc.bcm.edu	37	11	8486310	8486310	+	Silent	SNP	C	C	A	rs1446464	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:8486310C>A	ENST00000447869.1	-	3	1317	c.399G>T	c.(397-399)gcG>gcT	p.A133A	STK33_ENST00000358872.3_5'UTR|STK33_ENST00000315204.1_Silent_p.A133A|STK33_ENST00000534493.1_Silent_p.A92A|STK33_ENST00000396673.1_Silent_p.A133A|STK33_ENST00000396672.1_Silent_p.A133A			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.A133A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		CCTTGTCTGTCGCTTCAATGA	0.393													C|||	2229	0.445088	0.3411	0.3703	5008	,	,		16305	0.4871		0.4245	False		,,,				2504	0.6166				p.A133A		Atlas-SNP	.											STK33_ENST00000447869,NS,adenoma,0,2	STK33	147	2	1	Substitution - coding silent(1)	stomach(1)	c.G399T						PASS	.	C		1449,2953	467.0+/-354.7	248,953,1000	295.0	247.0	263.0		399	-5.1	0.1	11	dbSNP_88	263	3518,5074	512.9+/-378.0	721,2076,1499	no	coding-synonymous	STK33	NM_030906.2		969,3029,2499	AA,AC,CC		40.9451,32.9169,38.2253		133/515	8486310	4967,8027	2201	4296	6497	SO:0001819	synonymous_variant	65975	exon5			GTCTGTCGCTTCA	AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.399G>T	11.37:g.8486310C>A		Somatic	308	1	0.00324675		WXS	Illumina HiSeq	Phase_I	290	151	0.52069	NM_030906	Q658S6|Q8NEF5	Silent	SNP	ENST00000447869.1	37	CCDS7789.1																																																																																			C|0.587;A|0.413	0.413	strong		0.393	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906	
ZNF683	257101	hgsc.bcm.edu	37	1	26691174	26691174	+	Missense_Mutation	SNP	C	C	A	rs11247933	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26691174C>A	ENST00000436292.1	-	4	983	c.863G>T	c.(862-864)cGt>cTt	p.R288L	ZNF683_ENST00000349618.3_Missense_Mutation_p.R288L|ZNF683_ENST00000403843.1_Missense_Mutation_p.R288L|ZNF683_ENST00000374204.1_Missense_Mutation_p.R288L			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	288			R -> L (in dbSNP:rs11247933).		natural killer cell differentiation (GO:0001779)|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)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		CATGCCACCACGCTCCAGGCC	0.617													C|||	1319	0.263379	0.1233	0.4193	5008	,	,		16688	0.2778		0.341	False		,,,				2504	0.2474				p.R288L		Atlas-SNP	.											.	ZNF683	51	.	0			c.G863T						PASS	.	C	LEU/ARG,LEU/ARG	720,3686	295.9+/-283.9	58,604,1541	75.0	77.0	76.0		863,863	-7.0	0.0	1	dbSNP_120	76	3089,5511	470.5+/-367.8	547,1995,1758	yes	missense,missense	ZNF683	NM_001114759.1,NM_173574.2	102,102	605,2599,3299	AA,AC,CC		35.9186,16.3414,29.2865	benign,benign	288/505,288/505	26691174	3809,9197	2203	4300	6503	SO:0001583	missense	257101	exon4			CCACCACGCTCCA	BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"""Zinc fingers, C2H2-type"""	28495	protein-coding gene	gene with protein product	"""hypothetical protein MGC33414"""					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.863G>T	1.37:g.26691174C>A	ENSP00000388792:p.Arg288Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Missense_Mutation	SNP	ENST00000436292.1	37		620	0.2838827838827839	64	0.13008130081300814	144	0.39779005524861877	147	0.256993006993007	265	0.3496042216358839	C	7.602	0.672902	0.14776	0.163414	0.359186	ENSG00000176083	ENST00000403843;ENST00000436292;ENST00000374204;ENST00000349618	T;T;T;T	0.09630	3.01;3.01;2.96;2.96	3.52	-7.04	0.01578	.	2.010380	0.02183	N	0.060622	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.12630	0.006;0.003	B;B	0.17098	0.017;0.008	T	0.44467	-0.9326	9	0.10377	T	0.69	3.2031	3.8651	0.09013	0.1064:0.2623:0.1055:0.5259	rs11247933;rs52829071;rs59372706;rs11247933	288;288	Q8IZ20-2;Q8IZ20	.;ZN683_HUMAN	L	288	ENSP00000384782:R288L;ENSP00000388792:R288L;ENSP00000363320:R288L;ENSP00000344095:R288L	ENSP00000344095:R288L	R	-	2	0	ZNF683	26563761	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.192000	0.01245	-2.439000	0.00551	-1.134000	0.01955	CGT	C|0.728;A|0.272	0.272	strong		0.617	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574	
GOLGA5	9950	hgsc.bcm.edu	37	14	93276654	93276654	+	Missense_Mutation	SNP	T	T	C	rs1040835	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:93276654T>C	ENST00000163416.2	+	5	1304	c.1048T>C	c.(1048-1050)Ttt>Ctt	p.F350L	GOLGA5_ENST00000355976.2_Missense_Mutation_p.F350L	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	350				F -> L (in Ref. 1; AAD09753, 2; AAV85456, 4; EAW81502, 5; AAH23021, 6; CAA33787 and 8; CAB36967). {ECO:0000305}.	Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		TCTGCAGACTTTTCAGGAGAG	0.423			T	RET	papillary thyroid								C|||	4305	0.859625	0.9697	0.8602	5008	,	,		18409	0.8323		0.7465	False		,,,				2504	0.8548				p.F350L		Atlas-SNP	.		Dom	yes		14	14q	9950	"""golgi autoantigen, golgin subfamily a, 5  (PTC5)"""		E	.	GOLGA5	84	.	0			c.T1048C						PASS	.	C	LEU/PHE	4110,296	159.6+/-192.1	1917,276,10	71.0	76.0	74.0		1048	4.8	0.8	14	dbSNP_86	74	6246,2354	392.7+/-344.1	2277,1692,331	yes	missense	GOLGA5	NM_005113.2	22	4194,1968,341	CC,CT,TT		27.3721,6.7181,20.3752	benign	350/732	93276654	10356,2650	2203	4300	6503	SO:0001583	missense	9950	exon5			CAGACTTTTCAGG	AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"""golgi integral membrane protein 5"""	606918	"""golgi autoantigen, golgin subfamily a, 5"""			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.1048T>C	14.37:g.93276654T>C	ENSP00000163416:p.Phe350Leu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	142	142	1	NM_005113	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Missense_Mutation	SNP	ENST00000163416.2	37	CCDS9905.1	1784	0.8168498168498168	475	0.9654471544715447	299	0.8259668508287292	465	0.8129370629370629	545	0.7189973614775725	C	6.273	0.418430	0.11870	0.932819	0.726279	ENSG00000066455	ENST00000163416;ENST00000355976;ENST00000439315	T;T	0.11930	2.73;2.73	5.63	4.75	0.60458	.	0.000000	0.43747	N	0.000526	T	0.00012	0.0000	N	0.00128	-2.045	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.32903	-0.9889	9	0.02654	T	1	-8.1937	7.4259	0.27098	0.1351:0.7268:0.0:0.1381	rs1040835;rs17747858;rs17856683;rs57721927;rs1040835	350	Q8TBA6	GOGA5_HUMAN	L	350;350;259	ENSP00000163416:F350L;ENSP00000348252:F350L	ENSP00000163416:F350L	F	+	1	0	GOLGA5	92346407	0.857000	0.29778	0.759000	0.31340	0.931000	0.56810	1.657000	0.37366	0.870000	0.35726	-0.186000	0.12905	TTT	T|0.201;C|0.799	0.799	strong		0.423	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1		
ISG20L2	81875	hgsc.bcm.edu	37	1	156697056	156697056	+	Missense_Mutation	SNP	T	T	C	rs3795737	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156697056T>C	ENST00000313146.6	-	1	1171	c.389A>G	c.(388-390)aAt>aGt	p.N130S	ISG20L2_ENST00000472824.2_5'Flank|RRNAD1_ENST00000368218.4_5'Flank|RRNAD1_ENST00000524343.1_5'Flank|RRNAD1_ENST00000368216.4_5'Flank|ISG20L2_ENST00000368219.1_Missense_Mutation_p.N130S	NM_030980.1	NP_112242.1	Q9H9L3	I20L2_HUMAN	interferon stimulated exonuclease gene 20kDa-like 2	130			N -> S (in dbSNP:rs3795737).		ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)	exonuclease activity (GO:0004527)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	16	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TGGGTGGCTATTGATCTTTGG	0.498											OREG0013885	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	828	0.165335	0.2201	0.2824	5008	,	,		17577	0.1687		0.0577	False		,,,				2504	0.1155				p.N130S		Atlas-SNP	.											.	ISG20L2	43	.	0			c.A389G						PASS	.	T	SER/ASN	766,3640	308.6+/-290.6	70,626,1507	92.0	97.0	95.0		389	0.7	0.1	1	dbSNP_107	95	506,8094	143.7+/-199.7	16,474,3810	yes	missense	ISG20L2	NM_030980.1	46	86,1100,5317	CC,CT,TT		5.8837,17.3854,9.7801	benign	130/354	156697056	1272,11734	2203	4300	6503	SO:0001583	missense	81875	exon1			TGGCTATTGATCT	AK095697	CCDS1153.1	1q23.1	2013-10-11			ENSG00000143319	ENSG00000143319			25745	protein-coding gene	gene with protein product		611930				18065403	Standard	NM_030980		Approved	FLJ12671	uc001fps.1	Q9H9L3	OTTHUMG00000041301	ENST00000313146.6:c.389A>G	1.37:g.156697056T>C	ENSP00000323424:p.Asn130Ser	Somatic	126	0	0	1780	WXS	Illumina HiSeq	Phase_I	135	62	0.459259	NM_030980	D3DVC6|Q64KA2	Missense_Mutation	SNP	ENST00000313146.6	37	CCDS1153.1	351	0.16071428571428573	124	0.25203252032520324	87	0.24033149171270718	99	0.17307692307692307	41	0.05408970976253298	T	0.015	-1.555116	0.00918	0.173854	0.058837	ENSG00000143319	ENST00000313146;ENST00000368219	T;T	0.21734	1.99;1.99	4.31	0.673	0.17941	.	3.951200	0.01206	N	0.007706	T	0.02688	0.0081	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28073	-1.0055	9	0.10636	T	0.68	-4.0536	6.6611	0.23014	0.0:0.276:0.0:0.724	rs3795737;rs56513381;rs59810365;rs3795737	130	Q9H9L3	I20L2_HUMAN	S	130	ENSP00000323424:N130S;ENSP00000357202:N130S	ENSP00000323424:N130S	N	-	2	0	ISG20L2	154963680	0.011000	0.17503	0.062000	0.19696	0.005000	0.04900	0.383000	0.20651	0.094000	0.17404	-1.140000	0.01884	AAT	T|0.877;C|0.123	0.123	strong		0.498	ISG20L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098969.1	NM_030980	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389007	1389007	+	Silent	SNP	C	C	T	rs78871723	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:1389007C>T	ENST00000324803.4	+	1	3668	c.708C>T	c.(706-708)tgC>tgT	p.C236C		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	236					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCGATGCGGAGTGCCCG	0.677													t|||	434	0.0866613	0.1702	0.0605	5008	,	,		14541	0.002		0.0805	False		,,,				2504	0.0859				p.C236C		Atlas-SNP	.											CRIPAK,rectum,NS,+2,1	CRIPAK	185	1	0			c.C708T						scavenged	.						160.0	133.0	142.0					4																	1389007		2188	4293	6481	SO:0001819	synonymous_variant	285464	exon1			CCGATGCGGAGTG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.708C>T	4.37:g.1389007C>T		Somatic	7	1	0.142857		WXS	Illumina HiSeq	Phase_I	39	2	0.0512821	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																			C|0.918;T|0.082	0.082	strong		0.677	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
PRSS1	5644	hgsc.bcm.edu	37	7	142460339	142460339	+	Missense_Mutation	SNP	G	G	A	rs200973660		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:142460339G>A	ENST00000311737.7	+	4	518	c.512G>A	c.(511-513)tGt>tAt	p.C171Y	PRSS1_ENST00000486171.1_Missense_Mutation_p.C185Y	NM_002769.4	NP_002760.1	P07477	TRY1_HUMAN	protease, serine, 1 (trypsin 1)	171	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(24)|prostate(2)	38	Melanoma(164;0.047)	all_cancers(3;2.14e-49)|Acute lymphoblastic leukemia(3;7.3e-185)|all_hematologic(3;1.1e-165)	all cancers(2;0.000126)|Colorectal(2;0.000157)|Epithelial(2;0.000191)|COAD - Colon adenocarcinoma(2;0.00189)		Aprotinin(DB06692)	CAGGCTAAGTGTGAAGCCTCC	0.527																																					p.C171Y		Atlas-SNP	.											.	PRSS1	68	.	0			c.G512A						PASS	.						293.0	285.0	288.0					7																	142460339		2203	4300	6503	SO:0001583	missense	5644	exon4			CTAAGTGTGAAGC	M22612	CCDS5872.1	7q34	2012-10-02			ENSG00000204983	ENSG00000204983	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9475	protein-coding gene	gene with protein product		276000		TRY1			Standard	NM_002769		Approved		uc003wak.2	P07477	OTTHUMG00000158923	ENST00000311737.7:c.512G>A	7.37:g.142460339G>A	ENSP00000308720:p.Cys171Tyr	Somatic	377	0	0		WXS	Illumina HiSeq	Phase_I	286	35	0.122378	NM_002769	A1A509|A6NJ71|B2R5I5|Q5NV57|Q7M4N3|Q7M4N4|Q92955|Q9HAN4|Q9HAN5|Q9HAN6|Q9HAN7	Missense_Mutation	SNP	ENST00000311737.7	37	CCDS5872.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.153199	0.38021	.	.	ENSG00000204983	ENST00000486171;ENST00000311737;ENST00000529243;ENST00000492062	D;D;D	0.96992	-4.2;-4.2;-2.52	3.28	3.28	0.37604	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.98918	0.9633	H	0.99104	4.43	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98703	1.0701	10	0.87932	D	0	.	14.0086	0.64481	0.0:0.0:1.0:0.0	.	185;171	E7EQ64;P07477	.;TRY1_HUMAN	Y	185;171;161;121	ENSP00000417854:C185Y;ENSP00000308720:C171Y;ENSP00000419912:C121Y	ENSP00000308720:C171Y	C	+	2	0	PRSS1	142139913	1.000000	0.71417	0.080000	0.20451	0.020000	0.10135	9.762000	0.98944	1.789000	0.52484	0.398000	0.26397	TGT	.	.	weak		0.527	PRSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352538.2		
CD300E	342510	hgsc.bcm.edu	37	17	72608834	72608834	+	Silent	SNP	G	G	A	rs579238	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72608834G>A	ENST00000328630.3	-	4	616	c.576C>T	c.(574-576)gtC>gtT	p.V192V	CD300E_ENST00000426295.2_Silent_p.V233V|CD300E_ENST00000392619.1_Silent_p.V219V			Q496F6	CLM2_HUMAN	CD300e molecule	192					innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						TCACCCAGAAGACAGCACCCA	0.627													G|||	1319	0.263379	0.3525	0.2133	5008	,	,		16911	0.1042		0.3022	False		,,,				2504	0.3027				p.V192V		Atlas-SNP	.											.	CD300E	70	.	0			c.C576T						PASS	.	G		1474,2932	474.8+/-357.1	246,982,975	76.0	74.0	75.0		576	4.0	1.0	17	dbSNP_83	75	2492,6108	408.9+/-349.7	372,1748,2180	no	coding-synonymous	CD300E	NM_181449.2		618,2730,3155	AA,AG,GG		28.9767,33.4544,30.4936		192/206	72608834	3966,9040	2203	4300	6503	SO:0001819	synonymous_variant	342510	exon4			CCAGAAGACAGCA	BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	28874	protein-coding gene	gene with protein product		609801	"""CD300 antigen like family member E"", ""CD300e antigen"""	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.576C>T	17.37:g.72608834G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	24	15	0.625	NM_181449	B4DNS1|Q7Z7I3	Silent	SNP	ENST00000328630.3	37	CCDS11702.1																																																																																			G|0.713;A|0.287	0.287	strong		0.627	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449	
GZMM	3004	hgsc.bcm.edu	37	19	549728	549728	+	Silent	SNP	C	C	G	rs58601458	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:549728C>G	ENST00000264553.3	+	5	749	c.711C>G	c.(709-711)ccC>ccG	p.P237P		NM_001258351.1|NM_005317.3	NP_001245280.1|NP_005308	P51124	GRAM_HUMAN	granzyme M (lymphocyte met-ase 1)	237	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|large_intestine(1)|prostate(1)	3		all_cancers(10;1.94e-35)|all_epithelial(18;5.94e-23)|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)		TCAAGCCTCCCGTGGCCACCG	0.662													c|||	507	0.101238	0.0756	0.0447	5008	,	,		13835	0.2083		0.0398	False		,,,				2504	0.1288				p.P237P		Atlas-SNP	.											.	GZMM	11	.	0			c.C711G						PASS	.			45,4361	41.6+/-74.8	5,35,2163	94.0	77.0	83.0		711	-7.7	0.0	19	dbSNP_129	83	3,8597		0,3,4297	no	coding-synonymous	GZMM	NM_005317.2		5,38,6460	GG,GC,CC		0.0349,1.0213,0.3691		237/258	549728	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	3004	exon5			GCCTCCCGTGGCC		CCDS12031.1, CCDS74240.1	19p13.3	2008-07-16				ENSG00000197540			4712	protein-coding gene	gene with protein product	"""lymphocyte met-ase 1"""	600311				8119738	Standard	NM_005317		Approved	MET1, LMET1	uc002low.2	P51124		ENST00000264553.3:c.711C>G	19.37:g.549728C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_005317		Silent	SNP	ENST00000264553.3	37	CCDS12031.1																																																																																			C|0.931;G|0.069	0.069	strong		0.662	GZMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451895.2	NM_005317	
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 GAIIx	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_ENST00000391754.1_Silent_p.S148S|MBOAT7_ENST00000338624.6_Silent_p.S75S|MBOAT7_ENST00000431666.2_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		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	40	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 GAIIx	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	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	122	49	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		
SUSD5	26032	hgsc.bcm.edu	37	3	33195284	33195284	+	Silent	SNP	G	G	A	rs61743511	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:33195284G>A	ENST00000309558.3	-	5	1257	c.840C>T	c.(838-840)ccC>ccT	p.P280P		NM_015551.1	NP_056366.1	O60279	SUSD5_HUMAN	sushi domain containing 5	280					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	hyaluronic acid binding (GO:0005540)	p.P280P(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						GTGAATCTGCGGGGACACTGC	0.547													G|||	810	0.161741	0.0862	0.1758	5008	,	,		18901	0.1905		0.1541	False		,,,				2504	0.2321				p.P280P		Atlas-SNP	.											SUSD5,NS,carcinoma,0,1	SUSD5	53	1	1	Substitution - coding silent(1)	stomach(1)	c.C840T						PASS	.	G		346,3490		21,304,1593	47.0	48.0	48.0		840	3.0	0.0	3	dbSNP_129	48	1323,6933		106,1111,2911	no	coding-synonymous	SUSD5	NM_015551.1		127,1415,4504	AA,AG,GG		16.0247,9.0198,13.8025		280/630	33195284	1669,10423	1918	4128	6046	SO:0001819	synonymous_variant	26032	exon5			ATCTGCGGGGACA	AB011099	CCDS46787.1	3p23	2014-02-12	2006-01-13		ENSG00000173705	ENSG00000173705			29061	protein-coding gene	gene with protein product							Standard	NM_015551		Approved	KIAA0527	uc003cfo.1	O60279	OTTHUMG00000155829	ENST00000309558.3:c.840C>T	3.37:g.33195284G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_015551		Silent	SNP	ENST00000309558.3	37	CCDS46787.1	338	0.15476190476190477	43	0.08739837398373984	64	0.17679558011049723	117	0.20454545454545456	114	0.1503957783641161	G	0.009	-1.842924	0.00568	0.090198	0.160247	ENSG00000173705	ENST00000412539	T	0.11063	2.81	5.9	2.99	0.34606	.	0.323106	0.32852	N	0.005575	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.45542	-0.9254	6	0.16420	T	0.52	-6.8588	4.4684	0.11700	0.1477:0.1153:0.6059:0.131	.	.	.	.	L	216	ENSP00000406475:P216L	ENSP00000406475:P216L	P	-	2	0	SUSD5	33170288	1.000000	0.71417	0.002000	0.10522	0.000000	0.00434	1.206000	0.32321	0.418000	0.25898	-0.797000	0.03246	CCG	G|0.848;A|0.152	0.152	strong		0.547	SUSD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341902.1	XM_171054	
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 GAIIx	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_ENST00000428982.2_Nonsense_Mutation_p.W598*|SYNGAP1_ENST00000496374.1_3'UTR|MIR5004_ENST00000579078.1_RNA|SYNGAP1_ENST00000293748.5_Nonsense_Mutation_p.W657*	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*	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	118	11	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	
GEMIN4	50628	hgsc.bcm.edu	37	17	649505	649505	+	Missense_Mutation	SNP	T	T	A	rs4968104	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:649505T>A	ENST00000319004.5	-	2	1896	c.1778A>T	c.(1777-1779)gAg>gTg	p.E593V	GEMIN4_ENST00000576778.1_Missense_Mutation_p.E582V	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	593				E -> V (in Ref. 1; AAF35283 and 3; CAB45743). {ECO:0000305}.	gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GGGACCCTGCTCTTCCACAAA	0.498													T|||	795	0.158746	0.0545	0.1772	5008	,	,		19029	0.122		0.2465	False		,,,				2504	0.2342				p.E593V		Atlas-SNP	.											GEMIN4_ENST00000319004,NS,carcinoma,0,4	GEMIN4	116	4	0			c.A1778T						PASS	.	T	VAL/GLU	361,3573		17,327,1623	98.0	102.0	101.0		1778	5.5	0.9	17	dbSNP_111	101	2103,6257		286,1531,2363	yes	missense	GEMIN4	NM_015721.2	121	303,1858,3986	AA,AT,TT		25.1555,9.1764,20.0423	possibly-damaging	593/1059	649505	2464,9830	1967	4180	6147	SO:0001583	missense	50628	exon2			CCCTGCTCTTCCA	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.1778A>T	17.37:g.649505T>A	ENSP00000321706:p.Glu593Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	41	0.585714	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	358	0.16391941391941392	26	0.052845528455284556	72	0.19889502762430938	75	0.13111888111888112	185	0.24406332453825857	T	2.280	-0.364930	0.05103	0.091764	0.251555	ENSG00000179409	ENST00000319004	T	0.16597	2.33	5.46	5.46	0.80206	.	0.885835	0.09880	N	0.743765	T	0.00012	0.0000	L	0.57536	1.79	0.09310	P	0.9999999547019	B	0.30439	0.279	B	0.28139	0.086	T	0.34850	-0.9812	9	0.36615	T	0.2	-13.2991	5.9152	0.19052	0.0:0.0844:0.168:0.7476	rs4968104;rs52822209;rs4968104	593	P57678	GEMI4_HUMAN	V	593	ENSP00000321706:E593V	ENSP00000321706:E593V	E	-	2	0	GEMIN4	596255	0.000000	0.05858	0.900000	0.35374	0.022000	0.10575	0.530000	0.23036	2.079000	0.62486	0.482000	0.46254	GAG	T|0.816;A|0.184	0.184	strong		0.498	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
IL17RC	84818	hgsc.bcm.edu	37	3	9974809	9974809	+	Silent	SNP	G	G	A	rs76999397	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9974809G>A	ENST00000295981.3	+	19	2126	c.1908G>A	c.(1906-1908)gcG>gcA	p.A636A	IL17RC_ENST00000416074.2_Silent_p.A391A|IL17RC_ENST00000413608.1_Silent_p.A552A|CRELD1_ENST00000383811.3_5'Flank|RP11-1020A11.1_ENST00000602411.1_RNA|IL17RC_ENST00000403601.3_Silent_p.A565A|IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000455057.1_Silent_p.A533A|CRELD1_ENST00000326434.5_5'Flank|CRELD1_ENST00000452070.1_5'Flank|CRELD1_ENST00000397170.3_5'Flank|IL17RC_ENST00000383812.4_Silent_p.A550A	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	636	SEFIR. {ECO:0000255|PROSITE- ProRule:PRU00867}.				cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGTTTCACGCGCAGCGGCGCC	0.711											OREG0015383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	154	0.0307508	0.0	0.0216	5008	,	,		12731	0.0417		0.0378	False		,,,				2504	0.0603				p.A636A		Atlas-SNP	.											IL17RC,NS,carcinoma,0,1	IL17RC	55	1	0			c.G1908A						PASS	.	G	,,,,,	51,4341		1,49,2146	17.0	17.0	17.0		1656,1605,1599,1650,1695,1908	-7.9	0.8	3	dbSNP_132	17	417,8165		9,399,3883	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	,,,,,	10,448,6029	AA,AG,GG		4.859,1.1612,3.6072	,,,,,	552/708,535/691,533/689,550/706,565/721,636/792	9974809	468,12506	2196	4291	6487	SO:0001819	synonymous_variant	84818	exon19			TCACGCGCAGCGG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1908G>A	3.37:g.9974809G>A		Somatic	57	0	0	661	WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			G|0.968;A|0.032	0.032	strong		0.711	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
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 GAIIx	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_ENST00000532959.1_Missense_Mutation_p.F169V|TMEM135_ENST00000535167.1_Missense_Mutation_p.F159V	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	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	20	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	
C6orf15	29113	hgsc.bcm.edu	37	6	31079644	31079644	+	Silent	SNP	G	G	A	rs2233980	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31079644G>A	ENST00000259870.3	-	2	495	c.492C>T	c.(490-492)ccC>ccT	p.P164P	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	164					extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GTGAAGCCTTGGGTGAGAGGC	0.617													G|||	119	0.023762	0.0083	0.0317	5008	,	,		16520	0.0		0.0855	False		,,,				2504	0.0				p.P164P		Atlas-SNP	.											.	C6orf15	29	.	0			c.C492T						PASS	.	G		103,3523		2,99,1712	32.0	36.0	34.0		492	-9.1	0.0	6	dbSNP_98	34	726,6374		42,642,2866	no	coding-synonymous	C6orf15	NM_014070.2		44,741,4578	AA,AG,GG		10.2254,2.8406,7.7289		164/326	31079644	829,9897	1813	3550	5363	SO:0001819	synonymous_variant	29113	exon2			AGCCTTGGGTGAG	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.492C>T	6.37:g.31079644G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	83	71	0.855422	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			G|0.926;A|0.074	0.074	strong		0.617	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
ASPM	259266	hgsc.bcm.edu	37	1	197070707	197070707	+	Silent	SNP	G	G	A	rs41308365	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:197070707G>A	ENST00000367409.4	-	18	7930	c.7674C>T	c.(7672-7674)atC>atT	p.I2558I	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2558	IQ 27. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTTGTATTACGATAGAAGCTT	0.333													G|||	1073	0.214257	0.0431	0.2277	5008	,	,		18864	0.1637		0.4105	False		,,,				2504	0.2863				p.I2558I		Atlas-SNP	.											.	ASPM	444	.	0			c.C7674T						PASS	.	G	,	462,3944	214.1+/-233.5	27,408,1768	68.0	60.0	63.0		,7674	3.3	0.0	1	dbSNP_127	63	3721,4875	521.6+/-379.9	811,2099,1388	no	intron,coding-synonymous	ASPM	NM_001206846.1,NM_018136.4	,	838,2507,3156	AA,AG,GG		43.2876,10.4857,32.172	,	,2558/3478	197070707	4183,8819	2203	4298	6501	SO:0001819	synonymous_variant	259266	exon18			TATTACGATAGAA	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.7674C>T	1.37:g.197070707G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	40	39	0.975	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Silent	SNP	ENST00000367409.4	37	CCDS1389.1																																																																																			A|0.300;G|0.700;T|0.000	0.300	strong		0.333	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
CHRM3	1131	hgsc.bcm.edu	37	1	240070944	240070944	+	Missense_Mutation	SNP	G	G	A	rs2067481	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:240070944G>A	ENST00000255380.4	+	5	972	c.193G>A	c.(193-195)Gtc>Atc	p.V65I		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	65			V -> I (in dbSNP:rs2067481).		cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)			breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	AGGTCATACCGTCTGGCAAGT	0.517													G|||	63	0.0125799	0.0008	0.0072	5008	,	,		19664	0.0089		0.0179	False		,,,				2504	0.0307				p.V65I		Atlas-SNP	.											.	CHRM3	118	.	0			c.G193A						PASS	.	G	ILE/VAL	12,4394	19.1+/-41.9	0,12,2191	132.0	117.0	122.0		193	-10.5	0.0	1	dbSNP_96	122	109,8491	59.1+/-120.7	1,107,4192	yes	missense	CHRM3	NM_000740.2	29	1,119,6383	AA,AG,GG		1.2674,0.2724,0.9303	benign	65/591	240070944	121,12885	2203	4300	6503	SO:0001583	missense	1131	exon5			CATACCGTCTGGC	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.193G>A	1.37:g.240070944G>A	ENSP00000255380:p.Val65Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	131	72	0.549618	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	24	0.01098901098901099	1	0.0020325203252032522	2	0.0055248618784530384	4	0.006993006993006993	17	0.022427440633245383	G	3.777	-0.046335	0.07407	0.002724	0.012674	ENSG00000133019	ENST00000255380;ENST00000448020	T;T	0.37058	1.22;1.22	5.6	-10.5	0.00291	.	0.592340	0.16364	N	0.217648	T	0.12646	0.0307	L	0.54323	1.7	0.22648	N	0.998894	B	0.09022	0.002	B	0.06405	0.002	T	0.08391	-1.0724	10	0.19147	T	0.46	-6.6566	14.2355	0.65925	0.1836:0.1711:0.6453:0.0	rs2067481;rs2067481	65	P20309	ACM3_HUMAN	I	65	ENSP00000255380:V65I;ENSP00000404764:V65I	ENSP00000255380:V65I	V	+	1	0	CHRM3	238137567	0.003000	0.15002	0.017000	0.16124	0.503000	0.33858	0.005000	0.13129	-2.245000	0.00705	-0.806000	0.03193	GTC	G|0.990;A|0.010	0.010	strong		0.517	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
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 GAIIx	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_ENST00000476376.1_Missense_Mutation_p.V361M|WDR49_ENST00000453925.2_Intron|WDR49_ENST00000479765.1_Intron	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	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	72	39	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	
NOP56	10528	hgsc.bcm.edu	37	20	2638579	2638579	+	Missense_Mutation	SNP	T	T	C	rs6753	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:2638579T>C	ENST00000329276.5	+	12	1940	c.1424T>C	c.(1423-1425)aTg>aCg	p.M475T	SNORD56_ENST00000413522.1_RNA|NOP56_ENST00000492135.1_3'UTR|SNORD86_ENST00000391196.1_RNA|SNORA51_ENST00000606420.1_RNA|SNORD57_ENST00000448188.1_RNA|IDH3B_ENST00000488299.1_5'Flank	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	475	Lys-rich.		M -> T (in dbSNP:rs6753). {ECO:0000269|PubMed:9372940}.		cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						CTTTAGGAGATGAGTGAAAAA	0.458													C|||	1888	0.376997	0.6188	0.379	5008	,	,		17492	0.254		0.2654	False		,,,				2504	0.2904				p.M475T		Atlas-SNP	.											NOP56,caecum,carcinoma,-1,1	NOP56	73	1	0			c.T1424C						PASS	.	C	THR/MET	2294,2012		620,1054,479	139.0	155.0	150.0		1424	-3.1	0.0	20	dbSNP_52	150	2312,6232		339,1634,2299	no	missense	NOP56	NM_006392.3	81	959,2688,2778	CC,CT,TT		27.0599,46.7255,35.8444	benign	475/595	2638579	4606,8244	2153	4272	6425	SO:0001583	missense	10528	exon12			AGGAGATGAGTGA	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.1424T>C	20.37:g.2638579T>C	ENSP00000370589:p.Met475Thr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_006392	Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	800	0.3663003663003663	330	0.6707317073170732	130	0.35911602209944754	136	0.23776223776223776	204	0.2691292875989446	C	0.012	-1.685592	0.00745	0.532745	0.270599	ENSG00000101361	ENST00000329276	T	0.39997	1.05	4.64	-3.07	0.05363	.	1.567430	0.03170	N	0.170662	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38929	-0.9638	9	0.11485	T	0.65	1.0538	11.6995	0.51562	0.0:0.3003:0.0:0.6997	rs6753;rs1071606;rs2273136;rs3177051;rs3182722;rs3182969;rs16907603;rs17419589;rs52816246;rs60600923;rs6753	475	O00567	NOP56_HUMAN	T	475	ENSP00000370589:M475T	ENSP00000370589:M475T	M	+	2	0	NOP56	2586579	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.138000	0.01303	-0.892000	0.03935	-0.748000	0.03510	ATG	T|0.637;C|0.363	0.363	strong		0.458	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
PRMT6	55170	hgsc.bcm.edu	37	1	107599918	107599918	+	Missense_Mutation	SNP	C	C	T	rs2232016	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:107599918C>T	ENST00000370078.1	+	1	618	c.581C>T	c.(580-582)gCc>gTc	p.A194V	PRMT6_ENST00000361318.5_Missense_Mutation_p.A135V			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	194	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.		A -> V (in dbSNP:rs2232016). {ECO:0000269|PubMed:15489334}.		base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		CTCTTCATAGCCCCCATCAGC	0.642													C|||	627	0.1252	0.0098	0.0865	5008	,	,		17486	0.1448		0.1918	False		,,,				2504	0.2198				p.A194V		Atlas-SNP	.											.	PRMT6	55	.	0			c.C581T						PASS	.	C	VAL/ALA	175,3777		2,171,1803	35.0	37.0	37.0		581	5.5	1.0	1	dbSNP_98	37	1727,6597		160,1407,2595	yes	missense	PRMT6	NM_018137.2	64	162,1578,4398	TT,TC,CC		20.7472,4.4281,15.4936	probably-damaging	194/376	107599918	1902,10374	1976	4162	6138	SO:0001583	missense	55170	exon1			TCATAGCCCCCAT	AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"""Protein arginine methyltransferases"""	18241	protein-coding gene	gene with protein product		608274	"""HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"""	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.581C>T	1.37:g.107599918C>T	ENSP00000359095:p.Ala194Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	95	32	0.336842	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Missense_Mutation	SNP	ENST00000370078.1	37	CCDS41360.2	280	0.1282051282051282	8	0.016260162601626018	30	0.08287292817679558	89	0.1555944055944056	153	0.20184696569920843	C	31	5.100072	0.94197	0.044281	0.207472	ENSG00000198890	ENST00000361318;ENST00000370078	T;T	0.22336	1.96;1.96	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.16471	0.0396	M	0.62723	1.935	0.09310	P	0.99999585951	P	0.37997	0.614	B	0.39379	0.298	T	0.03148	-1.1067	9	0.33940	T	0.23	-17.7437	16.9117	0.86142	0.0:1.0:0.0:0.0	rs2232016;rs3748839;rs52822166;rs59101028;rs2232016	194	Q96LA8	ANM6_HUMAN	V	135;194	ENSP00000355145:A135V;ENSP00000359095:A194V	ENSP00000355145:A135V	A	+	2	0	PRMT6	107401441	0.952000	0.32445	0.991000	0.47740	0.981000	0.71138	3.666000	0.54540	2.584000	0.87258	0.442000	0.29010	GCC	C|0.849;T|0.151	0.151	strong		0.642	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137	
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 GAIIx	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	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	16	6	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	
TULP4	56995	hgsc.bcm.edu	37	6	158870081	158870081	+	Silent	SNP	A	A	G	rs705956	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:158870081A>G	ENST00000367097.3	+	4	1954	c.597A>G	c.(595-597)agA>agG	p.R199R	TULP4_ENST00000367094.2_Silent_p.R199R	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	199			R -> S (in dbSNP:rs705956).		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)		GCCACGGCAGAATGCTGGCCC	0.612													G|||	3032	0.605431	0.7844	0.5288	5008	,	,		20217	0.3968		0.5895	False		,,,				2504	0.6493				p.R199R		Atlas-SNP	.											TULP4,NS,carcinoma,+1,1	TULP4	137	1	0			c.A597G						scavenged	.	G	,	3371,1035	381.6+/-324.1	1305,761,137	166.0	121.0	136.0		597,597	3.5	1.0	6	dbSNP_86	136	5009,3591	519.7+/-379.5	1469,2071,760	no	coding-synonymous,coding-synonymous	TULP4	NM_001007466.1,NM_020245.3	,	2774,2832,897	GG,GA,AA		41.7558,23.4907,35.5682	,	199/679,199/1544	158870081	8380,4626	2203	4300	6503	SO:0001819	synonymous_variant	56995	exon4			CGGCAGAATGCTG		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.597A>G	6.37:g.158870081A>G		Somatic	50	2	0.04		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Silent	SNP	ENST00000367097.3	37	CCDS34561.1																																																																																			A|0.374;G|0.626	0.626	strong		0.612	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
SERPINB10	5273	hgsc.bcm.edu	37	18	61585260	61585260	+	Missense_Mutation	SNP	T	T	C	rs724558	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61585260T>C	ENST00000238508.3	+	4	355	c.296T>C	c.(295-297)aTc>aCc	p.I99T		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	99			I -> T (in dbSNP:rs724558).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.I99T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				ATCTCAGAAATCCTCAAGCCC	0.343													T|||	1241	0.247804	0.3003	0.2954	5008	,	,		19842	0.25		0.1968	False		,,,				2504	0.1933				p.I99T		Atlas-SNP	.											SERPINB10,NS,carcinoma,0,1	SERPINB10	53	1	1	Substitution - Missense(1)	stomach(1)	c.T296C						PASS	.	T	THR/ILE	1379,3025	453.4+/-350.3	219,941,1042	94.0	88.0	90.0		296	5.8	0.9	18	dbSNP_86	90	1609,6991	297.1+/-303.3	146,1317,2837	yes	missense	SERPINB10	NM_005024.1	89	365,2258,3879	CC,CT,TT		18.7093,31.3124,22.9775		99/398	61585260	2988,10016	2202	4300	6502	SO:0001583	missense	5273	exon3			CAGAAATCCTCAA	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.296T>C	18.37:g.61585260T>C	ENSP00000238508:p.Ile99Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	497	0.22756410256410256	140	0.2845528455284553	100	0.27624309392265195	117	0.20454545454545456	140	0.18469656992084432	T	16.54	3.150615	0.57151	0.313124	0.187093	ENSG00000242550	ENST00000238508	D	0.85339	-1.97	5.82	5.82	0.92795	Serpin domain (3);	0.118518	0.64402	D	0.000017	T	0.00039	0.0001	M	0.74546	2.27	0.26773	P	0.9697622	D	0.89917	1.0	D	0.87578	0.998	T	0.00000	-1.3326	9	0.56958	D	0.05	.	14.1425	0.65329	0.0:0.0:0.0:1.0	rs724558;rs52793058;rs57025225;rs724558	99	P48595	SPB10_HUMAN	T	99	ENSP00000238508:I99T	ENSP00000238508:I99T	I	+	2	0	SERPINB10	59736240	1.000000	0.71417	0.904000	0.35570	0.404000	0.30871	4.786000	0.62425	2.231000	0.72958	0.528000	0.53228	ATC	A|0.020;C|0.224	0.224	strong		0.343	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
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 GAIIx	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	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	66	18	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	
KCNB1	3745	hgsc.bcm.edu	37	20	47990250	47990250	+	Missense_Mutation	SNP	G	G	C	rs2229006	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47990250G>C	ENST00000371741.4	-	2	2013	c.1847C>G	c.(1846-1848)aCt>aGt	p.T616S		NM_004975.2	NP_004966.1	Q14721	KCNB1_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 1	616			T -> N (in dbSNP:rs2229006).|T -> S (in dbSNP:rs2229006).		energy reserve metabolic process (GO:0006112)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|dendrite membrane (GO:0032590)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(22)|pancreas(2)|prostate(7)|skin(4)|stomach(1)|urinary_tract(1)	53			BRCA - Breast invasive adenocarcinoma(12;0.000405)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Dalfampridine(DB06637)	GCTGCCCCCAGTCTTGCTGGG	0.592													G|||	48	0.00958466	0.0	0.0159	5008	,	,		17190	0.0		0.0219	False		,,,				2504	0.0153				p.T616S		Atlas-SNP	.											.	KCNB1	142	.	0			c.C1847G						PASS	.	G	SER/THR	17,4389	24.3+/-50.5	0,17,2186	37.0	36.0	36.0		1847	5.0	0.1	20	dbSNP_98	36	169,8431	75.7+/-138.4	1,167,4132	yes	missense	KCNB1	NM_004975.2	58	1,184,6318	CC,CG,GG		1.9651,0.3858,1.4301	benign	616/859	47990250	186,12820	2203	4300	6503	SO:0001583	missense	3745	exon2			CCCCCAGTCTTGC	AF026005	CCDS13418.1	20q13.2	2012-07-05			ENSG00000158445	ENSG00000158445		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6231	protein-coding gene	gene with protein product		600397				7774931, 16382104	Standard	NM_004975		Approved	Kv2.1	uc002xur.1	Q14721	OTTHUMG00000033051	ENST00000371741.4:c.1847C>G	20.37:g.47990250G>C	ENSP00000360806:p.Thr616Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_004975	Q14193	Missense_Mutation	SNP	ENST00000371741.4	37	CCDS13418.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	0	0.0	11	0.014511873350923483	G	0.013	-1.610031	0.00835	0.003858	0.019651	ENSG00000158445	ENST00000371741;ENST00000538812	T	0.21191	2.02	5.97	5.01	0.66863	.	1.439320	0.04002	N	0.296646	T	0.05731	0.0150	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23691	-1.0181	10	0.17369	T	0.5	.	9.4193	0.38541	0.0747:0.3447:0.5807:0.0	rs2229006	616	Q14721	KCNB1_HUMAN	S	616;571	ENSP00000360806:T616S	ENSP00000360806:T616S	T	-	2	0	KCNB1	47423657	0.124000	0.22315	0.119000	0.21687	0.820000	0.46376	3.191000	0.50981	1.497000	0.48584	0.655000	0.94253	ACT	G|0.986;C|0.014	0.014	strong		0.592	KCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080374.3	NM_004975	
Unknown	0	hgsc.bcm.edu	37	11	124096277	124096277	+	IGR	SNP	G	G	A	rs2466612	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124096277G>A								OR10D3 (39325 upstream) : OR8G1 (24145 downstream)																							TTATACTATTGTTGTGCCCAT	0.438													g|||	494	0.0986422	0.0174	0.1527	5008	,	,		20206	0.13		0.1412	False		,,,				2504	0.0941				p.V294I		Atlas-SNP	.											.	.	.	.	0			c.G880A						PASS	.						73.0	67.0	69.0					11																	124096277		1925	4152	6077	SO:0001628	intergenic_variant	26492	exon1			ACTATTGTTGTGC																													11.37:g.124096277G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	195	143	0.733333	NM_001007249		Missense_Mutation	SNP		37																																																																																				G|0.888;A|0.112	0.112	strong	0	0.438								
SCRIB	23513	hgsc.bcm.edu	37	8	144895669	144895669	+	Silent	SNP	G	G	A	rs56748182	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144895669G>A	ENST00000320476.3	-	5	480	c.474C>T	c.(472-474)ctC>ctT	p.L158L	MIR937_ENST00000401271.1_RNA|SCRIB_ENST00000377533.3_Silent_p.L77L|SCRIB_ENST00000356994.2_Silent_p.L158L	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	158	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-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;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GGTTCTCCCGGAGCTCCAGGG	0.652													G|||	206	0.0411342	0.0106	0.0504	5008	,	,		18796	0.0248		0.0994	False		,,,				2504	0.0327				p.L158L	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C474T						PASS	.	G	,	103,4303	79.3+/-117.8	3,97,2103	40.0	38.0	39.0		474,474	-3.9	1.0	8	dbSNP_129	39	783,7817	183.7+/-231.9	44,695,3561	no	coding-synonymous,coding-synonymous	SCRIB	NM_015356.3,NM_182706.3	,	47,792,5664	AA,AG,GG		9.1047,2.3377,6.8122	,	158/1631,158/1656	144895669	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	23513	exon5			CTCCCGGAGCTCC	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.474C>T	8.37:g.144895669G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1																																																																																			G|0.941;A|0.059	0.059	strong		0.652	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
NFATC3	4775	hgsc.bcm.edu	37	16	68225515	68225515	+	Silent	SNP	G	G	A	rs12598	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:68225515G>A	ENST00000346183.3	+	9	2967	c.2943G>A	c.(2941-2943)acG>acA	p.T981T	NFATC3_ENST00000575270.1_Silent_p.T981T|NFATC3_ENST00000329524.4_Silent_p.T981T|NFATC3_ENST00000349223.5_Silent_p.T981T|NFATC3_ENST00000535127.2_3'UTR|SNORA48_ENST00000391143.1_RNA	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	981					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|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)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		CACAAAGTACGGGCCAGGGGG	0.507													G|||	173	0.0345447	0.0038	0.0187	5008	,	,		20869	0.0		0.0825	False		,,,				2504	0.0736				p.T981T		Atlas-SNP	.											.	NFATC3	190	.	0			c.G2943A						PASS	.	G	,,	75,4321	67.0+/-104.6	1,73,2124	150.0	145.0	146.0		2943,2943,2943	0.3	1.0	16	dbSNP_52	146	780,7820	185.3+/-233.1	34,712,3554	no	coding-synonymous,coding-synonymous,coding-synonymous	NFATC3	NM_004555.3,NM_173163.2,NM_173165.2	,,	35,785,5678	AA,AG,GG		9.0698,1.7061,6.5789	,,	981/1069,981/1066,981/1076	68225515	855,12141	2198	4300	6498	SO:0001819	synonymous_variant	4775	exon9			AAGTACGGGCCAG	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2943G>A	16.37:g.68225515G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Silent	SNP	ENST00000346183.3	37	CCDS10860.1																																																																																			G|0.945;A|0.055	0.055	strong		0.507	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
C3	718	hgsc.bcm.edu	37	19	6713262	6713262	+	Missense_Mutation	SNP	G	G	A	rs1047286	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:6713262G>A	ENST00000245907.6	-	9	1033	c.941C>T	c.(940-942)cCc>cTc	p.P314L		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	314			P -> L (in dbSNP:rs1047286). {ECO:0000269|PubMed:1976733, ECO:0000269|PubMed:2579379, ECO:0000269|Ref.2}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TTCTGCTCGGGGGTTCTGCAC	0.617													G|||	350	0.0698882	0.0091	0.0865	5008	,	,		15986	0.003		0.2048	False		,,,				2504	0.0706				p.P314L		Atlas-SNP	.											.	C3	192	.	0			c.C941T						PASS	.	G	LEU/PRO	177,4229	112.1+/-150.2	1,175,2027	53.0	47.0	49.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	941	2.8	0.0	19	dbSNP_86	49	1760,6840	316.2+/-312.6	162,1436,2702	yes	missense	C3	NM_000064.2	98	163,1611,4729	AA,AG,GG		20.4651,4.0172,14.8931	benign	314/1664	6713262	1937,11069	2203	4300	6503	SO:0001583	missense	718	exon9			GCTCGGGGGTTCT	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.941C>T	19.37:g.6713262G>A	ENSP00000245907:p.Pro314Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	187	0.08562271062271062	6	0.012195121951219513	33	0.09116022099447514	2	0.0034965034965034965	146	0.19261213720316622	G	12.86	2.063821	0.36373	0.040172	0.204651	ENSG00000125730	ENST00000245907	T	0.33654	1.4	5.04	2.84	0.33178	.	0.889887	0.09345	N	0.814950	T	0.00039	0.0001	L	0.53249	1.67	0.80722	P	0.0	B	0.28900	0.227	B	0.31946	0.138	T	0.18999	-1.0319	9	0.18276	T	0.48	.	7.2662	0.26232	0.0939:0.1741:0.732:0.0	rs1047286;rs2230202;rs11085198	314	P01024	CO3_HUMAN	L	314	ENSP00000245907:P314L	ENSP00000245907:P314L	P	-	2	0	C3	6664262	0.000000	0.05858	0.004000	0.12327	0.007000	0.05969	0.635000	0.24629	1.071000	0.40834	0.484000	0.47621	CCC	G|0.864;A|0.136	0.136	strong		0.617	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
KIAA1755	85449	hgsc.bcm.edu	37	20	36850988	36850988	+	Silent	SNP	C	C	T	rs35524973	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:36850988C>T	ENST00000279024.4	-	10	2551	c.2280G>A	c.(2278-2280)agG>agA	p.R760R		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	760										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				TGCTCAGGCACCTGGTAGCCT	0.657											OREG0025921	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	113	0.0225639	0.0507	0.013	5008	,	,		17572	0.002		0.0159	False		,,,				2504	0.0194				p.R760R		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G2280A						PASS	.	C		274,4132	150.7+/-184.7	12,250,1941	39.0	35.0	37.0		2280	3.0	1.0	20	dbSNP_126	37	143,8457	68.4+/-130.8	3,137,4160	no	coding-synonymous	KIAA1755	NM_001029864.1		15,387,6101	TT,TC,CC		1.6628,6.2188,3.2062		760/1201	36850988	417,12589	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon10			CAGGCACCTGGTA	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2280G>A	20.37:g.36850988C>T		Somatic	25	0	0	866	WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			A|0.000;C|0.971;T|0.029	0.029	strong		0.657	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
ZNF211	10520	hgsc.bcm.edu	37	19	58152795	58152795	+	Missense_Mutation	SNP	C	C	T	rs11879465	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58152795C>T	ENST00000347302.3	+	3	1120	c.941C>T	c.(940-942)gCg>gTg	p.A314V	ZNF211_ENST00000299871.5_Missense_Mutation_p.A379V|ZNF211_ENST00000254182.7_Missense_Mutation_p.A305V|ZNF211_ENST00000420680.1_Missense_Mutation_p.A318V|ZNF211_ENST00000240731.4_Missense_Mutation_p.A327V|ZNF211_ENST00000544273.1_Missense_Mutation_p.A326V|ZNF211_ENST00000541801.1_Missense_Mutation_p.A305V|ZNF211_ENST00000391703.3_Missense_Mutation_p.A253V	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	314			A -> V (in dbSNP:rs11879465). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		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(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		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;0.026)		AGGCCTTATGCGTGCCCTGAA	0.418													A|||	1072	0.214058	0.2352	0.1297	5008	,	,		22359	0.3214		0.159	False		,,,				2504	0.1912				p.A379V		Atlas-SNP	.											.	ZNF211	78	.	0			c.C1136T						PASS	.	A	VAL/ALA,VAL/ALA	980,3426		117,746,1340	73.0	73.0	73.0		980,941	-2.3	0.0	19	dbSNP_120	73	1345,7255		97,1151,3052	yes	missense,missense	ZNF211	NM_006385.3,NM_198855.2	64,64	214,1897,4392	TT,TC,CC		15.6395,22.2424,17.8764	benign,benign	327/578,314/565	58152795	2325,10681	2203	4300	6503	SO:0001583	missense	10520	exon5			CTTATGCGTGCCC	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.941C>T	19.37:g.58152795C>T	ENSP00000339562:p.Ala314Val	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	485	0.22206959706959706	135	0.27439024390243905	52	0.143646408839779	180	0.3146853146853147	118	0.15567282321899736	A	10.08	1.251787	0.22880	0.222424	0.156395	ENSG00000121417	ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731	T;T;T;T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29;2.29;2.29;2.29	3.21	-2.34	0.06704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.11651	0.15	0.80722	P	0.0	B;B;B;B;B;B	0.22146	0.065;0.027;0.004;0.027;0.033;0.033	B;B;B;B;B;B	0.10450	0.003;0.002;0.001;0.003;0.005;0.005	T	0.45948	-0.9226	8	0.44086	T	0.13	.	4.3681	0.11233	0.3986:0.4122:0.0837:0.1056	rs11879465;rs52794337;rs59585398;rs11879465	318;326;379;305;314;327	Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1	.;.;.;.;ZN211_HUMAN;.	V	318;314;305;253;305;379;326;327	ENSP00000399193:A318V;ENSP00000339562:A314V;ENSP00000254182:A305V;ENSP00000375584:A253V;ENSP00000442601:A305V;ENSP00000299871:A379V;ENSP00000441386:A326V;ENSP00000240731:A327V	ENSP00000240731:A327V	A	+	2	0	ZNF211	62844607	0.000000	0.05858	0.000000	0.03702	0.533000	0.34776	-2.055000	0.01397	-1.230000	0.02561	-4.775000	0.00003	GCG	C|0.792;T|0.208	0.208	strong		0.418	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720540	135720540	+	Missense_Mutation	SNP	A	A	G	rs9814557	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:135720540A>G	ENST00000264977.3	+	2	817	c.200A>G	c.(199-201)gAt>gGt	p.D67G	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	67			D -> G (in dbSNP:rs9814557).|D -> N (in dbSNP:rs57374999).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAAGATGCAGATCTGAACTCT	0.488													A|||	713	0.142372	0.0567	0.1369	5008	,	,		20072	0.0268		0.2773	False		,,,				2504	0.2423				p.D67G		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A200G						PASS	.	A	,GLY/ASP	448,3958	214.5+/-233.7	22,404,1777	111.0	91.0	98.0		,200	3.3	0.5	3	dbSNP_119	98	2694,5906	431.6+/-356.9	412,1870,2018	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,94	434,2274,3795	GG,GA,AA		31.3256,10.168,24.1581	,benign	,67/1151	135720540	3142,9864	2203	4300	6503	SO:0001583	missense	5523	exon2			ATGCAGATCTGAA	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.200A>G	3.37:g.135720540A>G	ENSP00000264977:p.Asp67Gly	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	165	77	0.466667	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	299	0.13690476190476192	29	0.05894308943089431	56	0.15469613259668508	11	0.019230769230769232	203	0.2678100263852243	A	9.131	1.011458	0.19277	0.10168	0.313256	ENSG00000073711	ENST00000264977	T	0.14391	2.51	5.79	3.3	0.37823	.	0.350012	0.31461	N	0.007608	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	1.999999999946489E-6	B	0.23442	0.085	B	0.19666	0.026	T	0.41875	-0.9484	9	0.56958	D	0.05	.	8.4145	0.32664	0.7085:0.2165:0.0751:0.0	rs9814557;rs52807842;rs57498404;rs9814557	67	Q06190	P2R3A_HUMAN	G	67	ENSP00000264977:D67G	ENSP00000264977:D67G	D	+	2	0	PPP2R3A	137203230	1.000000	0.71417	0.534000	0.28014	0.980000	0.70556	3.716000	0.54904	1.032000	0.39892	0.523000	0.50628	GAT	A|0.801;G|0.199	0.199	strong		0.488	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
TIAM1	7074	hgsc.bcm.edu	37	21	32567589	32567589	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:32567589G>C	ENST00000286827.3	-	14	2997	c.2526C>G	c.(2524-2526)gtC>gtG	p.V842V	TIAM1_ENST00000541036.1_Silent_p.V782V	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	842					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						TGCTCTGAGTGACTTTTGGAC	0.303																																					p.V842V		Atlas-SNP	.											.	TIAM1	522	.	0			c.C2526G						PASS	.						129.0	118.0	121.0					21																	32567589		2203	4300	6503	SO:0001819	synonymous_variant	7074	exon14			CTGAGTGACTTTT		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.2526C>G	21.37:g.32567589G>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																			.	.	none		0.303	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
ZBTB41	360023	hgsc.bcm.edu	37	1	197168690	197168690	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:197168690T>G	ENST00000367405.4	-	1	982	c.914A>C	c.(913-915)gAa>gCa	p.E305A	CRB1_ENST00000535699.1_5'Flank|ZBTB41_ENST00000467322.1_5'UTR	NM_194314.2	NP_919290.2	Q5SVQ8	ZBT41_HUMAN	zinc finger and BTB domain containing 41	305					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(2)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(11)|lung(11)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)	40						CTCATCTTCTTCAGCATTATA	0.388																																					p.E305A		Atlas-SNP	.											ZBTB41,NS,carcinoma,0,1	ZBTB41	116	1	0			c.A914C						scavenged	.						115.0	115.0	115.0					1																	197168690		2202	4300	6502	SO:0001583	missense	360023	exon1			TCTTCTTCAGCAT		CCDS30960.1	1q31.3	2013-01-08			ENSG00000177888	ENSG00000177888		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	24819	protein-coding gene	gene with protein product							Standard	NM_194314		Approved	FRBZ1, FLJ36199, DKFZp686C06120, ZNF924	uc001gtx.1	Q5SVQ8	OTTHUMG00000036275	ENST00000367405.4:c.914A>C	1.37:g.197168690T>G	ENSP00000356375:p.Glu305Ala	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	189	6	0.031746	NM_194314	A2RUA8|Q6MZT8|Q6ZR25|Q7Z4T1|Q8IZ99	Missense_Mutation	SNP	ENST00000367405.4	37	CCDS30960.1	.	.	.	.	.	.	.	.	.	.	T	11.37	1.617337	0.28801	.	.	ENSG00000177888	ENST00000367405	T	0.06294	3.32	4.65	4.65	0.58169	.	0.362026	0.19680	N	0.108532	T	0.05868	0.0153	N	0.19112	0.55	0.45205	D	0.998213	B	0.16166	0.016	B	0.14578	0.011	T	0.30534	-0.9975	10	0.72032	D	0.01	.	14.0718	0.64865	0.0:0.0:0.0:1.0	.	305	Q5SVQ8	ZBT41_HUMAN	A	305	ENSP00000356375:E305A	ENSP00000356375:E305A	E	-	2	0	ZBTB41	195435313	1.000000	0.71417	0.998000	0.56505	0.854000	0.48673	5.628000	0.67791	1.703000	0.51240	0.254000	0.18369	GAA	.	.	none		0.388	ZBTB41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088249.2	NM_194314	
COX4I2	84701	hgsc.bcm.edu	37	20	30232673	30232673	+	Missense_Mutation	SNP	G	G	A	rs11907253	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:30232673G>A	ENST00000376075.3	+	5	557	c.482G>A	c.(481-483)cGc>cAc	p.R161H		NM_032609.2	NP_115998.2	Q96KJ9	COX42_HUMAN	cytochrome c oxidase subunit IV isoform 2 (lung)	161			R -> H (in dbSNP:rs11907253). {ECO:0000269|PubMed:11311561}.		cellular respiration (GO:0045333)|generation of precursor metabolites and energy (GO:0006091)|hydrogen ion transmembrane transport (GO:1902600)|oxidation-reduction process (GO:0055114)	mitochondrial respiratory chain complex IV (GO:0005751)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	11	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.01e-05)|all cancers(5;9.46e-05)|OV - Ovarian serous cystadenocarcinoma(3;0.00121)|Colorectal(19;0.0055)|COAD - Colon adenocarcinoma(19;0.0264)			CTGGCCTCCCGCTGGGACTAT	0.627													G|||	287	0.0573083	0.0961	0.0764	5008	,	,		16625	0.001		0.0815	False		,,,				2504	0.0245				p.R161H		Atlas-SNP	.											.	COX4I2	18	.	0			c.G482A						PASS	.	G	HIS/ARG	411,3995	201.1+/-224.2	12,387,1804	73.0	64.0	67.0		482	-1.1	0.6	20	dbSNP_120	67	702,7898	172.9+/-223.5	33,636,3631	yes	missense	COX4I2	NM_032609.2	29	45,1023,5435	AA,AG,GG		8.1628,9.3282,8.5576	benign	161/172	30232673	1113,11893	2203	4300	6503	SO:0001583	missense	84701	exon5			CCTCCCGCTGGGA	AF257180	CCDS13187.1	20q11.21	2011-07-04	2004-08-11		ENSG00000131055	ENSG00000131055		"""Mitochondrial respiratory chain complex / Complex IV"""	16232	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit IV-like 2"""	607976	"""cytochrome c oxidase subunit IV isoform 2"""	COX4L2		11311561, 17937768	Standard	NM_032609		Approved	COXIV-2, COX4B, dJ857M17.2, COX4-2	uc002wwj.1	Q96KJ9	OTTHUMG00000032180	ENST00000376075.3:c.482G>A	20.37:g.30232673G>A	ENSP00000365243:p.Arg161His	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	118	59	0.5	NM_032609	Q6GTF4|Q9H0Z4	Missense_Mutation	SNP	ENST00000376075.3	37	CCDS13187.1	164	0.07509157509157509	55	0.11178861788617886	41	0.1132596685082873	1	0.0017482517482517483	67	0.08839050131926121	G	11.36	1.615359	0.28801	0.093282	0.081628	ENSG00000131055	ENST00000376075	T	0.55930	0.49	4.38	-1.06	0.10002	.	0.324544	0.28442	N	0.015337	T	0.00412	0.0013	N	0.02916	-0.46	0.39291	P	0.035267999999999966	B	0.06786	0.001	B	0.04013	0.001	T	0.06127	-1.0844	9	0.35671	T	0.21	-17.387	7.746	0.28869	0.4725:0.0:0.5275:0.0	rs11907253;rs57114915;rs11907253	161	Q96KJ9	COX42_HUMAN	H	161	ENSP00000365243:R161H	ENSP00000365243:R161H	R	+	2	0	COX4I2	29696334	0.997000	0.39634	0.583000	0.28640	0.836000	0.47400	1.246000	0.32803	-0.361000	0.08125	-1.305000	0.01319	CGC	G|0.919;A|0.081	0.081	strong		0.627	COX4I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078548.1	NM_032609	
SUPT6H	6830	hgsc.bcm.edu	37	17	27014396	27014396	+	Silent	SNP	C	C	T	rs28753762	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:27014396C>T	ENST00000314616.6	+	23	3196	c.2913C>T	c.(2911-2913)gtC>gtT	p.V971V	SUPT6H_ENST00000347486.4_Silent_p.V971V	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	971	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AGGTCGGGGTCGATGTCAACC	0.542													C|||	547	0.109225	0.1369	0.062	5008	,	,		17780	0.1062		0.0726	False		,,,				2504	0.1462				p.V971V		Atlas-SNP	.											.	SUPT6H	165	.	0			c.C2913T						PASS	.	C		566,3840	254.0+/-259.7	40,486,1677	106.0	87.0	93.0		2913	-11.2	0.5	17	dbSNP_125	93	766,7834	182.2+/-230.7	32,702,3566	no	coding-synonymous	SUPT6H	NM_003170.3		72,1188,5243	TT,TC,CC		8.907,12.8461,10.2414		971/1727	27014396	1332,11674	2203	4300	6503	SO:0001819	synonymous_variant	6830	exon23			CGGGGTCGATGTC	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.2913C>T	17.37:g.27014396C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Silent	SNP	ENST00000314616.6	37	CCDS32596.1																																																																																			C|0.898;T|0.102	0.102	strong		0.542	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
TNR	7143	hgsc.bcm.edu	37	1	175293629	175293629	+	Missense_Mutation	SNP	G	G	A	rs570797805		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:175293629G>A	ENST00000367674.2	-	22	4528	c.3820C>T	c.(3820-3822)Cgc>Tgc	p.R1274C	TNR_ENST00000263525.2_Missense_Mutation_p.R1274C|RP3-518E13.2_ENST00000569593.1_RNA			Q92752	TENR_HUMAN	tenascin R	1274	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					GAGAAAGGGCGTCCTTGATGA	0.473													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19222	0.0		0.0	False		,,,				2504	0.0				p.R1274C		Atlas-SNP	.											TNR,colon,carcinoma,0,3	TNR	399	3	0			c.C3820T						scavenged	.						229.0	193.0	205.0					1																	175293629		2203	4300	6503	SO:0001583	missense	7143	exon22			AAGGGCGTCCTTG	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3820C>T	1.37:g.175293629G>A	ENSP00000356646:p.Arg1274Cys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	163	2	0.0122699	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	33	5.199215	0.94997	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.78364	-1.17;-1.17	5.66	5.66	0.87406	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.85682	D	0.000000	D	0.88127	0.6353	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88530	0.3102	10	0.72032	D	0.01	.	19.3551	0.94408	0.0:0.0:1.0:0.0	.	1274	Q92752	TENR_HUMAN	C	1274;1274;1184	ENSP00000356646:R1274C;ENSP00000263525:R1274C	ENSP00000263525:R1274C	R	-	1	0	TNR	173560252	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.865000	0.87049	2.666000	0.90696	0.655000	0.94253	CGC	.	.	none		0.473	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
MUC16	94025	hgsc.bcm.edu	37	19	9059232	9059232	+	Missense_Mutation	SNP	T	T	C	rs12710265	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9059232T>C	ENST00000397910.4	-	3	28417	c.28214A>G	c.(28213-28215)cAg>cGg	p.Q9405R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9407	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CACCACTGACTGTGGAAATCT	0.537													T|||	907	0.18111	0.149	0.2075	5008	,	,		20338	0.0099		0.3121	False		,,,				2504	0.2474				p.Q9405R		Atlas-SNP	.											.	MUC16	4315	.	0			c.A28214G						PASS	.	T	ARG/GLN	633,3363		46,541,1411	121.0	118.0	119.0		28214	-0.0	0.0	19	dbSNP_121	119	2825,5559		498,1829,1865	yes	missense	MUC16	NM_024690.2	43	544,2370,3276	CC,CT,TT		33.6951,15.8408,27.9321	benign	9405/14508	9059232	3458,8922	1998	4192	6190	SO:0001583	missense	94025	exon3			ACTGACTGTGGAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.28214A>G	19.37:g.9059232T>C	ENSP00000381008:p.Gln9405Arg	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	149	84	0.563758	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	390	0.17857142857142858	68	0.13821138211382114	78	0.2154696132596685	5	0.008741258741258742	239	0.3153034300791557	t	4.217	0.039079	0.08148	0.158408	0.336951	ENSG00000181143	ENST00000397910	T	0.21932	1.98	2.14	-0.0415	0.13867	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	.	.	.	B	0.16603	0.018	B	0.17722	0.019	T	0.44636	-0.9315	8	0.87932	D	0	.	4.3999	0.11381	0.0:0.3505:0.0:0.6495	rs12710265;rs12710265	9405	B5ME49	.	R	9405	ENSP00000381008:Q9405R	ENSP00000381008:Q9405R	Q	-	2	0	MUC16	8920232	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-0.483000	0.06536	-0.076000	0.12775	0.255000	0.18592	CAG	T|0.786;C|0.214	0.214	strong		0.537	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
GLOD4	51031	hgsc.bcm.edu	37	17	685752	685752	+	5'Flank	SNP	G	G	A	rs2249542	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:685752G>A	ENST00000301328.5	-	0	0				GLOD4_ENST00000301329.6_5'Flank|GLOD4_ENST00000536578.1_5'Flank|RNMTL1_ENST00000304478.4_Missense_Mutation_p.G45E			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TTTCCTTCCGGAGAGGTGGTG	0.657													G|||	763	0.152356	0.0469	0.1787	5008	,	,		16019	0.0923		0.2525	False		,,,				2504	0.2352				p.G45E		Atlas-SNP	.											.	RNMTL1	25	.	0			c.G134A						PASS	.	G	GLU/GLY	377,4029	186.7+/-213.5	21,335,1847	35.0	38.0	37.0		134	5.5	0.6	17	dbSNP_100	37	2255,6345	371.1+/-336.1	316,1623,2361	yes	missense	RNMTL1	NM_018146.2	98	337,1958,4208	AA,AG,GG		26.2209,8.5565,20.2368	benign	45/421	685752	2632,10374	2203	4300	6503	SO:0001631	upstream_gene_variant	55178	exon1			CTTCCGGAGAGGT	AF177342	CCDS32520.1	17p13.3	2008-02-05	2007-03-14	2007-03-14		ENSG00000167699			14111	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 25"""	C17orf25		11642406, 12528892	Standard	NM_016080		Approved	CGI-150, HC71	uc002fru.3	Q9HC38			17.37:g.685752G>A	Exception_encountered	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_018146	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Missense_Mutation	SNP	ENST00000301328.5	37		349|349	0.15979853479853479|0.15979853479853479	30|30	0.06097560975609756|0.06097560975609756	72|72	0.19889502762430938|0.19889502762430938	54|54	0.0944055944055944|0.0944055944055944	193|193	0.2546174142480211|0.2546174142480211	G|G	21.0|21.0	4.081462|4.081462	0.76528|0.76528	0.085565|0.085565	0.262209|0.262209	ENSG00000171861|ENSG00000167699	ENST00000304478|ENST00000397393	T|.	0.17370|.	2.28|.	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	0.624563|.	0.16419|.	N|.	0.215225|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.42245|0.42245	1.32|1.32	0.27102|0.27102	P|P	0.9625959|0.9625959	B|.	0.29909|.	0.261|.	B|.	0.22880|.	0.042|.	T|T	0.09684|0.09684	-1.0663|-1.0663	9|5	0.02654|0.87932	T|D	1|0	.|.	11.7682|11.7682	0.51943|0.51943	0.0814:0.0:0.9186:0.0|0.0814:0.0:0.9186:0.0	rs2249542;rs17617499;rs28969601;rs52825357;rs2249542|rs2249542;rs17617499;rs28969601;rs52825357;rs2249542	45|.	Q9HC36|.	RMTL1_HUMAN|.	E|S	45|121	ENSP00000306080:G45E|.	ENSP00000306080:G45E|ENSP00000380548:P121S	G|P	+|-	2|1	0|0	RNMTL1|GLOD4	632502|632502	0.433000|0.433000	0.25562|0.25562	0.592000|0.592000	0.28758|0.28758	0.600000|0.600000	0.36913|0.36913	1.415000|1.415000	0.34748|0.34748	2.737000|2.737000	0.93849|0.93849	0.563000|0.563000	0.77884|0.77884	GGA|CCG	G|0.824;A|0.175	0.175	strong		0.657	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080	
LLGL2	3993	hgsc.bcm.edu	37	17	73565171	73565171	+	Missense_Mutation	SNP	T	T	C	rs1671021	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73565171T>C	ENST00000392550.3	+	13	1552	c.1435T>C	c.(1435-1437)Ttc>Ctc	p.F479L	LLGL2_ENST00000577200.1_Missense_Mutation_p.F479L|LLGL2_ENST00000167462.5_Missense_Mutation_p.F479L	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	479			F -> L (in dbSNP:rs1671021). {ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CAACGAGAACTTCAGTGCCCA	0.667													C|||	2328	0.464856	0.907	0.3372	5008	,	,		17795	0.2639		0.3738	False		,,,				2504	0.2587				p.F479L		Atlas-SNP	.											.	LLGL2	155	.	0			c.T1435C						PASS	.	C	LEU/PHE,LEU/PHE	3630,776	303.5+/-288.0	1501,628,74	45.0	44.0	45.0		1435,1435	4.3	0.9	17	dbSNP_89	45	3320,5280	632.4+/-398.6	673,1974,1653	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	22,22	2174,2602,1727	CC,CT,TT		38.6047,17.6123,46.5631	benign,benign	479/1021,479/1016	73565171	6950,6056	2203	4300	6503	SO:0001583	missense	3993	exon13			GAGAACTTCAGTG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1435T>C	17.37:g.73565171T>C	ENSP00000376333:p.Phe479Leu	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	982	0.44963369963369965	442	0.8983739837398373	128	0.35359116022099446	125	0.21853146853146854	287	0.3786279683377309	C	10.65	1.409361	0.25378	0.823877	0.386047	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.09538	2.97;2.97	5.29	4.33	0.51752	WD40 repeat-like-containing domain (1);	0.192645	0.49916	N	0.000140	T	0.00012	0.0000	N	0.01267	-0.92	0.46542	P	9.050000000000447E-4	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.23476	-1.0187	9	0.18710	T	0.47	-3.4459	2.7305	0.05226	0.1772:0.5462:0.1184:0.1582	rs1671021;rs17492156;rs17855940;rs61228063;rs1671021	468;468;479;479	B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;L2GL2_HUMAN	L	479;479;468	ENSP00000167462:F479L;ENSP00000376333:F479L	ENSP00000167462:F479L	F	+	1	0	LLGL2	71076766	1.000000	0.71417	0.896000	0.35187	0.404000	0.30871	2.038000	0.41184	0.637000	0.30526	-0.222000	0.12452	TTC	T|0.486;C|0.514	0.514	strong		0.667	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
ICAM1	3383	hgsc.bcm.edu	37	19	10395683	10395683	+	Missense_Mutation	SNP	A	A	G	rs5498	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10395683A>G	ENST00000264832.3	+	6	1730	c.1405A>G	c.(1405-1407)Aag>Gag	p.K469E	ICAM4_ENST00000393717.2_5'Flank|ICAM1_ENST00000423829.2_Missense_Mutation_p.K247E|CTD-2369P2.8_ENST00000589379.1_RNA|ICAM4_ENST00000340992.4_5'Flank|ICAM4_ENST00000380770.3_5'Flank|CTD-2369P2.5_ENST00000592893.1_RNA	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	469			K -> E (in dbSNP:rs5498). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15572059, ECO:0000269|PubMed:1680919, ECO:0000269|PubMed:3340213, ECO:0000269|PubMed:3349522, ECO:0000269|PubMed:7525451}.		adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	GGTCACCCGCAAGGTGACCGT	0.612													a|||	1797	0.358826	0.1354	0.5548	5008	,	,		17106	0.2788		0.4662	False		,,,				2504	0.4939				p.K469E		Atlas-SNP	.											.	ICAM1	32	.	0			c.A1405G	GRCh37	CM003891	ICAM1	M	rs5498	PASS	.	A	GLU/LYS	849,3557	332.3+/-302.4	78,693,1432	58.0	57.0	57.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1405	-2.6	0.0	19	dbSNP_52	57	3708,4892	529.2+/-381.5	825,2058,1417	yes	missense	ICAM1	NM_000201.2	56	903,2751,2849	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	43.1163,19.2692,35.0377	benign	469/533	10395683	4557,8449	2203	4300	6503	SO:0001583	missense	3383	exon6			ACCCGCAAGGTGA		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	5344	protein-coding gene	gene with protein product	"""human rhinovirus receptor"""	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.1405A>G	19.37:g.10395683A>G	ENSP00000264832:p.Lys469Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	86	44	0.511628	NM_000201	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	37	CCDS12231.1	763	0.34935897435897434	59	0.11991869918699187	185	0.511049723756906	174	0.3041958041958042	345	0.4551451187335092	a	0.754	-0.771911	0.02951	0.192692	0.431163	ENSG00000090339	ENST00000264832;ENST00000423829	T;T	0.12039	2.72;2.72	4.61	-2.57	0.06248	Immunoglobulin-like fold (1);	1.925990	0.02941	N	0.140416	T	0.00012	0.0000	N	0.00525	-1.395	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46133	-0.9213	9	0.02654	T	1	-1.9773	5.4083	0.16335	0.3754:0.1751:0.4495:0.0	rs5498;rs1135683;rs1801713;rs2228118;rs3198540;rs5030382;rs17000453;rs58198099;rs5498	247;469	E7ESS4;P05362	.;ICAM1_HUMAN	E	469;247	ENSP00000264832:K469E;ENSP00000413124:K247E	ENSP00000264832:K469E	K	+	1	0	ICAM1	10256683	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.132000	0.15891	-0.217000	0.10033	-0.244000	0.11960	AAG	A|0.656;G|0.344	0.344	strong		0.612	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1		
CPB2	1361	hgsc.bcm.edu	37	13	46638826	46638826	+	Silent	SNP	G	G	A	rs2277440	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:46638826G>A	ENST00000181383.4	-	8	769	c.753C>T	c.(751-753)atC>atT	p.I251I	CPB2_ENST00000439329.3_Silent_p.I214I|CPB2-AS1_ENST00000606991.1_RNA|CPB2-AS1_ENST00000606351.1_RNA|CPB2-AS1_ENST00000415033.2_RNA|CPB2-AS1_ENST00000606243.1_RNA	NM_001872.3	NP_001863.3	Q96IY4	CBPB2_HUMAN	carboxypeptidase B2 (plasma)	251					blood coagulation (GO:0007596)|cellular response to glucose stimulus (GO:0071333)|fibrinolysis (GO:0042730)|liver regeneration (GO:0097421)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of plasminogen activation (GO:0010757)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to heat (GO:0009408)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.I251I(1)		NS(1)|cervix(1)|large_intestine(3)|liver(1)|lung(9)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(96;4.21e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)|all_neural(104;0.235)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.44e-05)		GGTCTGTTCCGATGCAATGAT	0.423													G|||	718	0.143371	0.1112	0.1556	5008	,	,		20854	0.2917		0.0626	False		,,,				2504	0.1084				p.I251I		Atlas-SNP	.											CPB2,NS,carcinoma,0,1	CPB2	60	1	1	Substitution - coding silent(1)	stomach(1)	c.C753T						PASS	.	G	,	546,3860	247.2+/-255.5	39,468,1696	188.0	156.0	167.0		753,642	-11.3	0.0	13	dbSNP_100	167	544,8056	149.2+/-204.3	10,524,3766	no	coding-synonymous,coding-synonymous	CPB2	NM_001872.3,NM_016413.3	,	49,992,5462	AA,AG,GG		6.3256,12.3922,8.3807	,	251/424,214/361	46638826	1090,11916	2203	4300	6503	SO:0001819	synonymous_variant	1361	exon8			TGTTCCGATGCAA	M75106	CCDS9401.1, CCDS73568.1	13q14.11	2012-02-10	2007-02-21		ENSG00000080618	ENSG00000080618			2300	protein-coding gene	gene with protein product	"""thrombin-activatable fibrinolysis inhibitor"", ""carboxypeptidase U"", ""plasma carboxypeptidase B"", ""carboxypeptidase R"""	603101	"""carboxypeptidase B2 (plasma, carboxypeptidase U)"""			1939207, 1427879	Standard	NM_001278541		Approved	CPU, PCPB, TAFI	uc001vaw.3	Q96IY4	OTTHUMG00000016867	ENST00000181383.4:c.753C>T	13.37:g.46638826G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	116	41	0.353448	NM_001872	A8K464|Q15114|Q5T9K1|Q5T9K2|Q9P2Y6	Silent	SNP	ENST00000181383.4	37	CCDS9401.1																																																																																			G|0.890;A|0.110	0.110	strong		0.423	CPB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044803.2	NM_001872	
SLCO4A1	28231	hgsc.bcm.edu	37	20	61288355	61288355	+	Silent	SNP	G	G	T	rs3195701	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61288355G>T	ENST00000370507.1	+	1	645	c.549G>T	c.(547-549)ggG>ggT	p.G183G	SLCO4A1_ENST00000217159.1_Silent_p.G183G			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	183					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TGGGCACGGGGTCGCTGGTGT	0.687													G|||	771	0.153954	0.0159	0.1599	5008	,	,		16750	0.1706		0.2913	False		,,,				2504	0.1779				p.G183G	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											SLCO4A1,caecum,carcinoma,0,1	SLCO4A1	65	1	0			c.G549T						PASS	.	G		254,4150	142.3+/-177.5	9,236,1957	44.0	41.0	42.0		549	2.5	0.7	20	dbSNP_105	42	2311,6285	379.5+/-339.3	308,1695,2295	no	coding-synonymous	SLCO4A1	NM_016354.3		317,1931,4252	TT,TG,GG		26.8846,5.7675,19.7308		183/723	61288355	2565,10435	2202	4298	6500	SO:0001819	synonymous_variant	28231	exon2			CACGGGGTCGCTG	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"""Solute carriers"""	10953	protein-coding gene	gene with protein product		612436	"""solute carrier family 21 (organic anion transporter), member 12"""	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.549G>T	20.37:g.61288355G>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Silent	SNP	ENST00000370507.1	37	CCDS13501.1																																																																																			G|0.820;T|0.180	0.180	strong		0.687	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	
DYSF	8291	hgsc.bcm.edu	37	2	71838597	71838597	+	Silent	SNP	C	C	A	rs2303606	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71838597C>A	ENST00000258104.3	+	38	4285	c.4008C>A	c.(4006-4008)atC>atA	p.I1336I	DYSF_ENST00000394120.2_Silent_p.I1337I|DYSF_ENST00000409366.1_Silent_p.I1337I|DYSF_ENST00000409762.1_Silent_p.I1353I|DYSF_ENST00000409651.1_Silent_p.I1368I|DYSF_ENST00000409744.1_Silent_p.I1323I|DYSF_ENST00000410041.1_Silent_p.I1354I|DYSF_ENST00000410020.3_Silent_p.I1354I|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409582.3_Silent_p.I1353I|DYSF_ENST00000413539.2_Silent_p.I1367I|DYSF_ENST00000429174.2_Silent_p.I1336I	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1336	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GTGCTTAGATCCTGGCATGGG	0.647													C|||	2251	0.449481	0.3585	0.5331	5008	,	,		17324	0.4792		0.5378	False		,,,				2504	0.3916				p.I1368I		Atlas-SNP	.											.	DYSF	536	.	0			c.C4104A						PASS	.	C	,,,,,,,,,,,,,	1741,2665	514.2+/-368.6	338,1065,800	53.0	51.0	52.0		4011,3966,3966,4008,4101,4059,4059,4104,4011,3969,4062,3969,4062,4008	2.8	1.0	2	dbSNP_100	52	4392,4208	577.1+/-390.5	1120,2152,1028	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	1458,3217,1828	AA,AC,CC		48.9302,39.5143,47.1552	,,,,,,,,,,,,,	1337/2082,1322/2067,1322/2088,1336/2102,1367/2112,1353/2098,1353/2119,1368/2113,1337/2103,1323/2089,1354/2099,1323/2068,1354/2120,1336/2081	71838597	6133,6873	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon39			TTAGATCCTGGCA	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4008C>A	2.37:g.71838597C>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	38	26	0.684211	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			C|0.529;A|0.471	0.471	strong		0.647	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
ZNF385C	201181	hgsc.bcm.edu	37	17	40189847	40189847	+	Missense_Mutation	SNP	G	G	A	rs145907332	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40189847G>A	ENST00000436535.3	-	2	307	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W	CTD-2132N18.2_ENST00000587304.1_RNA|CTD-2132N18.4_ENST00000602842.1_RNA			Q66K41	Z385C_HUMAN	zinc finger protein 385C	22						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				TGCAGAGGCCGGGTGGGCAGG	0.677													G|||	19	0.00379393	0.0023	0.0029	5008	,	,		12004	0.0		0.0129	False		,,,				2504	0.001				p.R24W		Atlas-SNP	.											.	ZNF385C	7	.	0			c.C70T						PASS	.																																			SO:0001583	missense	201181	exon2			GAGGCCGGGTGGG	BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595			33722	protein-coding gene	gene with protein product							Standard	NM_001242704		Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.307C>T	17.37:g.40189847G>A	ENSP00000411514:p.Arg103Trp	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_001242704	Q4G0J1	Missense_Mutation	SNP	ENST00000436535.3	37		14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	G	16.02	3.003963	0.54254	.	.	ENSG00000187595	ENST00000436535;ENST00000453355	T	0.37915	1.17	4.9	1.7	0.24286	.	0.355889	0.24373	U	0.039093	T	0.35364	0.0929	M	0.63428	1.95	0.53688	D	0.999971	.	.	.	.	.	.	T	0.18967	-1.0320	8	0.62326	D	0.03	-4.0258	8.0948	0.30822	0.0784:0.0:0.5739:0.3477	.	.	.	.	W	103	ENSP00000411514:R103W	ENSP00000411514:R103W	R	-	1	2	ZNF385C	37443373	1.000000	0.71417	0.353000	0.25747	0.973000	0.67179	3.523000	0.53488	0.149000	0.19098	-0.219000	0.12488	CGG	G|0.994;A|0.006	0.006	strong		0.677	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000347740.3	NM_001013624	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50657008	50657008	+	Silent	SNP	C	C	T	rs111335098		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50657008C>T	ENST00000248846.5	-	22	4967	c.4863G>A	c.(4861-4863)gtG>gtA	p.V1621V	TUBGCP6_ENST00000439308.2_3'UTR|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1621			V -> L (in dbSNP:rs4838864). {ECO:0000269|PubMed:15489334}.		G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-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)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TGTACTTGCTCACGCAGCCCT	0.632													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17146	0.0		0.0	False		,,,				2504	0.0				p.V1621V		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.G4863A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	52.0	48.0	49.0		4863	5.2	1.0	22	dbSNP_132	49	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	TUBGCP6	NM_020461.3		0,10,6493	TT,TC,CC		0.093,0.0454,0.0769		1621/1820	50657008	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	85378	exon22			CTTGCTCACGCAG	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.4863G>A	22.37:g.50657008C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			C|0.999;T|0.001	0.001	strong		0.632	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
USH2A	7399	hgsc.bcm.edu	37	1	216258194	216258194	+	Silent	SNP	G	G	T	rs56110889	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:216258194G>T	ENST00000307340.3	-	25	5399	c.5013C>A	c.(5011-5013)ggC>ggA	p.G1671G	RP11-22M7.2_ENST00000446411.1_RNA|USH2A_ENST00000366943.2_Silent_p.G1671G|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000430890.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1671	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CCTTGAGACAGCCCACAAAAC	0.328										HNSCC(13;0.011)			G|||	530	0.105831	0.1906	0.0951	5008	,	,		17135	0.0		0.163	False		,,,				2504	0.0491				p.G1671G		Atlas-SNP	.											.	USH2A	1168	.	0			c.C5013A						PASS	.	G		844,3562	331.2+/-301.9	100,644,1459	83.0	85.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5013	2.9	1.0	1	dbSNP_129	85	1481,7119	280.2+/-294.4	139,1203,2958	no	coding-synonymous	USH2A	NM_206933.2		239,1847,4417	TT,TG,GG		17.2209,19.1557,17.8764		1671/5203	216258194	2325,10681	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon25			GAGACAGCCCACA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.5013C>A	1.37:g.216258194G>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			G|0.844;T|0.156	0.156	strong		0.328	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
RNF213	57674	hgsc.bcm.edu	37	17	78319380	78319380	+	Silent	SNP	G	G	C	rs4890012	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78319380G>C	ENST00000582970.1	+	29	7388	c.7245G>C	c.(7243-7245)ccG>ccC	p.P2415P	RNF213_ENST00000336301.6_Silent_p.P488P|RNF213_ENST00000508628.2_Silent_p.P2464P	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	2415					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			GTGGGATCCCGGTTATCATCA	0.527													G|||	2370	0.473243	0.407	0.3948	5008	,	,		22033	0.378		0.668	False		,,,				2504	0.5164				p.P2415P		Atlas-SNP	.											.	RNF213	766	.	0			c.G7245C						PASS	.	G		1946,2460	551.4+/-378.3	452,1042,709	82.0	80.0	81.0		7392	-10.2	0.0	17	dbSNP_111	81	5500,3100	658.6+/-401.6	1772,1956,572	no	coding-synonymous	RNF213	NM_020914.4		2224,2998,1281	CC,CG,GG		36.0465,44.167,42.7495		2464/5257	78319380	7446,5560	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon29			GATCCCGGTTATC	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.7245G>C	17.37:g.78319380G>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	117	116	0.991453	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			G|0.447;C|0.553	0.553	strong		0.527	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
TMEM17	200728	hgsc.bcm.edu	37	2	62733201	62733201	+	Missense_Mutation	SNP	A	A	T	rs78110679	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:62733201A>T	ENST00000335390.5	-	1	275	c.64T>A	c.(64-66)Tcc>Acc	p.S22T		NM_198276.2	NP_938017.2	Q86X19	TMM17_HUMAN	transmembrane protein 17	22					cilium assembly (GO:0042384)|smoothened signaling pathway (GO:0007224)	ciliary membrane (GO:0060170)|ciliary transition zone (GO:0035869)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)	9	Lung NSC(7;0.0274)|all_lung(7;0.0568)		LUSC - Lung squamous cell carcinoma(7;1.31e-05)|Epithelial(17;0.169)			GTCCGATTGGAATCACTGAAC	0.662													A|||	335	0.066893	0.1233	0.0403	5008	,	,		12266	0.0069		0.0656	False		,,,				2504	0.0726				p.S22T		Atlas-SNP	.											.	TMEM17	19	.	0			c.T64A						PASS	.	A	THR/SER	524,3882	226.9+/-242.2	35,454,1714	34.0	36.0	35.0		64	3.6	1.0	2	dbSNP_131	35	650,7950	159.1+/-212.4	24,602,3674	yes	missense	TMEM17	NM_198276.2	58	59,1056,5388	TT,TA,AA		7.5581,11.8929,9.0266	benign	22/199	62733201	1174,11832	2203	4300	6503	SO:0001583	missense	200728	exon1			GATTGGAATCACT		CCDS1871.1	2p15	2008-02-05			ENSG00000186889	ENSG00000186889			26623	protein-coding gene	gene with protein product		614950				12477932	Standard	NM_198276		Approved	FLJ34583	uc002sbt.2	Q86X19	OTTHUMG00000129455	ENST00000335390.5:c.64T>A	2.37:g.62733201A>T	ENSP00000335094:p.Ser22Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_198276	Q53QP7|Q53R98	Missense_Mutation	SNP	ENST00000335390.5	37	CCDS1871.1	122	0.055860805860805864	56	0.11382113821138211	12	0.03314917127071823	2	0.0034965034965034965	52	0.06860158311345646	A	3.916	-0.019007	0.07681	0.118929	0.075581	ENSG00000186889	ENST00000335390	T	0.42900	0.96	4.82	3.59	0.41128	.	0.548588	0.18807	N	0.130637	T	0.00271	0.0008	N	0.12182	0.205	0.25286	N	0.989391	B	0.11235	0.004	B	0.06405	0.002	T	0.12268	-1.0554	10	0.11182	T	0.66	-5.5351	7.1569	0.25643	0.7408:0.0:0.0:0.2592	.	22	Q86X19	TMM17_HUMAN	T	22	ENSP00000335094:S22T	ENSP00000335094:S22T	S	-	1	0	TMEM17	62586705	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	2.292000	0.43549	2.043000	0.60533	0.374000	0.22700	TCC	A|0.925;T|0.075	0.075	strong		0.662	TMEM17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251618.3	NM_198276	
CARD9	64170	hgsc.bcm.edu	37	9	139265088	139265088	+	Silent	SNP	C	C	T	rs59902911	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139265088C>T	ENST00000371732.5	-	5	858	c.693G>A	c.(691-693)acG>acA	p.T231T	CARD9_ENST00000371734.3_Silent_p.T231T|CARD9_ENST00000315908.7_Silent_p.T231T	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	231					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		TGAGCTTCAGCGTGTGCTTGC	0.657													C|||	317	0.0632987	0.0598	0.0101	5008	,	,		18469	0.1181		0.0378	False		,,,				2504	0.0757				p.T231T		Atlas-SNP	.											.	CARD9	47	.	0			c.G693A						PASS	.	C	,	223,4179	133.3+/-169.7	10,203,1988	77.0	59.0	65.0		693,693	-1.9	1.0	9	dbSNP_129	65	268,8328	103.1+/-164.3	2,264,4032	no	coding-synonymous,coding-synonymous	CARD9	NM_052813.4,NM_052814.3	,	12,467,6020	TT,TC,CC		3.1177,5.0659,3.7775	,	231/537,231/493	139265088	491,12507	2201	4298	6499	SO:0001819	synonymous_variant	64170	exon5			CTTCAGCGTGTGC	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.693G>A	9.37:g.139265088C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			C|0.955;T|0.045	0.045	strong		0.657	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
SERPINB3	6317	hgsc.bcm.edu	37	18	61323012	61323012	+	Missense_Mutation	SNP	C	C	G	rs3180227|rs386804125|rs72132327	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:61323012C>G	ENST00000283752.5	-	8	1195	c.1052G>C	c.(1051-1053)gGa>gCa	p.G351A	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.G299A	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	351			G -> A (increased antiprotease activity and increased MAPK8 inhibition activity; dbSNP:rs3180227). {ECO:0000269|PubMed:12975381, ECO:0000269|PubMed:14970861, ECO:0000269|PubMed:21383048, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TGATCCGAATCCTACTACAGC	0.488														623	0.124401	0.0514	0.1945	5008	,	,		20109	0.1141		0.1561	False		,,,				2504	0.1513				p.G351A		Atlas-SNP	.											.	SERPINB3	90	.	0			c.G1052C						PASS	.	G	ALA/GLY	354,4052		62,230,1911	120.0	129.0	126.0		1052	-6.0	0.0	18	dbSNP_105	126	1407,7193		127,1153,3020	yes	missense	SERPINB3	NM_006919.2	60	189,1383,4931	GG,GC,CC		16.3605,8.0345,13.5399	benign	351/391	61323012	1761,11245	2203	4300	6503	SO:0001583	missense	6317	exon8			CCGAATCCTACTA	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1052G>C	18.37:g.61323012C>G	ENSP00000283752:p.Gly351Ala	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	169	85	0.502959	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	305	0.13965201465201466	47	0.09552845528455285	68	0.1878453038674033	70	0.12237762237762238	120	0.158311345646438	G	0.814	-0.750872	0.03041	0.080345	0.163605	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.81996	-1.56;-1.56	2.99	-5.99	0.02213	Serpin domain (3);	46.123900	0.00357	N	0.000038	T	0.00144	0.0004	N	0.02420	-0.555	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40232	-0.9574	9	0.20046	T	0.44	.	3.9015	0.09164	0.5397:0.1843:0.0748:0.2012	rs3180227;rs58542861;rs3180227	299;351	P29508-2;P29508	.;SPB3_HUMAN	A	351;299	ENSP00000283752:G351A;ENSP00000329498:G299A	ENSP00000283752:G351A	G	-	2	0	SERPINB3	59473992	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.636000	0.02016	-7.648000	0.00000	-2.790000	0.00116	GGA	C|0.858;G|0.142	0.142	strong		0.488	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
LILRB4	11006	hgsc.bcm.edu	37	19	55179377	55179377	+	Missense_Mutation	SNP	T	T	G	rs149600113		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:55179377T>G	ENST00000391736.1	+	14	1569	c.1254T>G	c.(1252-1254)ttT>ttG	p.F418L	LILRB4_ENST00000391733.3_Missense_Mutation_p.F419L|LILRB4_ENST00000270452.2_Missense_Mutation_p.F418L|LILRB4_ENST00000430952.2_Missense_Mutation_p.F417L|LILRB4_ENST00000391734.3_Missense_Mutation_p.F365L	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	418					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		TGCACAGCTTTACCCTCAGAC	0.627													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16015	0.0		0.0	False		,,,				2504	0.0				p.F418L		Atlas-SNP	.											LILRB4,NS,carcinoma,0,1	LILRB4	86	1	0			c.T1254G						scavenged	.						93.0	97.0	95.0					19																	55179377		2203	4300	6503	SO:0001583	missense	11006	exon12			CAGCTTTACCCTC	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1254T>G	19.37:g.55179377T>G	ENSP00000375616:p.Phe418Leu	Somatic	215	4	0.0186047		WXS	Illumina HiSeq	Phase_I	167	7	0.0419162	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	G	0.039	-1.292496	0.01375	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733	T;T;T;T;T	0.00460	7.32;7.32;7.31;7.27;7.33	2.07	-0.638	0.11500	.	.	.	.	.	T	0.00073	0.0002	N	0.00251	-1.775	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.06405	0.0;0.0;0.002;0.0	T	0.42849	-0.9427	9	0.02654	T	1	.	0.6834	0.00878	0.1703:0.2396:0.3472:0.2428	.	365;419;417;418	A8MUE1;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	L	418;418;417;365;419	ENSP00000375616:F418L;ENSP00000270452:F418L;ENSP00000408995:F417L;ENSP00000375614:F365L;ENSP00000375613:F419L	ENSP00000270452:F418L	F	+	3	2	LILRB4	59871189	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.085000	0.14912	-0.134000	0.11516	-0.484000	0.04775	TTT	.	.	weak		0.627	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
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 GAIIx	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	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	117	59	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	
ZFPM1	161882	hgsc.bcm.edu	37	16	88594567	88594567	+	Silent	SNP	C	C	T	rs35121729	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:88594567C>T	ENST00000319555.3	+	6	955	c.633C>T	c.(631-633)tgC>tgT	p.C211C	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	211					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	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)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		AGCCCACGTGCCCGGCCCCTG	0.697													c|||	633	0.126398	0.0098	0.1326	5008	,	,		14718	0.3591		0.0905	False		,,,				2504	0.0767				p.C211C	Pancreas(49;850 1106 29641 32847 38344)	Atlas-SNP	.											ZFPM1,NS,carcinoma,0,1	ZFPM1	32	1	0			c.C633T						PASS	.	C		84,4268		1,82,2093	18.0	21.0	20.0		633	4.1	0.0	16	dbSNP_126	20	684,7898		23,638,3630	no	coding-synonymous	ZFPM1	NM_153813.2		24,720,5723	TT,TC,CC		7.9702,1.9301,5.9378		211/1007	88594567	768,12166	2176	4291	6467	SO:0001819	synonymous_variant	161882	exon6			CACGTGCCCGGCC	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.633C>T	16.37:g.88594567C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_153813		Silent	SNP	ENST00000319555.3	37	CCDS32502.1																																																																																			C|0.911;T|0.089	0.089	strong		0.697	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		
MYOM1	8736	hgsc.bcm.edu	37	18	3176040	3176040	+	Splice_Site	SNP	C	C	G	rs8099021	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:3176040C>G	ENST00000356443.4	-	6	1355	c.1022G>C	c.(1021-1023)gGa>gCa	p.G341A	MYOM1_ENST00000261606.7_Splice_Site_p.G341A|MYOM1_ENST00000400569.3_Splice_Site_p.G341A	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	341	Ig-like C2-type 1.		G -> A (in dbSNP:rs8099021). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505783, ECO:0000269|Ref.1}.		muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GTTCTCTTACCCATTAATCTC	0.448													G|||	3792	0.757188	0.7829	0.7579	5008	,	,		21009	0.7421		0.7097	False		,,,				2504	0.7863				p.G341A		Atlas-SNP	.											.	MYOM1	192	.	0			c.G1022C						PASS	.	G	ALA/GLY,ALA/GLY	3239,769		1315,609,80	92.0	91.0	91.0		1022,1022	2.0	0.0	18	dbSNP_116	91	5968,2372		2123,1722,325	yes	missense-near-splice,missense-near-splice	MYOM1	NM_003803.3,NM_019856.1	60,60	3438,2331,405	GG,GC,CC		28.4412,19.1866,25.4373	benign,benign	341/1686,341/1590	3176040	9207,3141	2004	4170	6174	SO:0001630	splice_region_variant	8736	exon6			TCTTACCCATTAA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1022+1G>C	18.37:g.3176040C>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	1642	0.7518315018315018	406	0.8252032520325203	274	0.7569060773480663	425	0.743006993006993	537	0.7084432717678101	G	0.030	-1.340284	0.01277	0.808134	0.715588	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.73789	-0.78;-0.78;-0.78	6.17	1.97	0.26223	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.977805	0.08458	N	0.942917	T	0.00012	0.0000	N	0.05574	-0.02	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46911	-0.9157	8	.	.	.	.	14.7465	0.69492	0.0:0.0786:0.2483:0.6731	rs8099021;rs52789327;rs57236833;rs8099021	341;341	P52179-2;P52179	.;MYOM1_HUMAN	A	341	ENSP00000348821:G341A;ENSP00000383413:G341A;ENSP00000261606:G341A	.	G	-	2	0	MYOM1	3166040	0.637000	0.27216	0.048000	0.18961	0.600000	0.36913	0.158000	0.16422	-0.160000	0.11002	-0.120000	0.15030	GGA	C|0.250;G|0.750	0.750	strong		0.448	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	Missense_Mutation
RNF19B	127544	hgsc.bcm.edu	37	1	33402542	33402542	+	Silent	SNP	G	G	C	rs35756506	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:33402542G>C	ENST00000373456.7	-	9	2063	c.2064C>G	c.(2062-2064)ccC>ccG	p.P688P	RNF19B_ENST00000356990.5_3'UTR|RNF19B_ENST00000235150.4_Silent_p.P687P	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	688					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				TATGGGAGCGGGGGGAGCCAC	0.607													G|||	279	0.0557109	0.0151	0.1585	5008	,	,		17587	0.0		0.0765	False		,,,				2504	0.0736				p.P688P		Atlas-SNP	.											.	RNF19B	43	.	0			c.C2064G						PASS	.	G	,	111,4295	85.8+/-124.5	0,111,2092	86.0	88.0	87.0		,2064	3.0	1.0	1	dbSNP_126	87	595,8005	158.2+/-211.7	13,569,3718	no	utr-3,coding-synonymous	RNF19B	NM_001127361.1,NM_153341.2	,	13,680,5810	CC,CG,GG		6.9186,2.5193,5.4283	,	,688/733	33402542	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	127544	exon9			GGAGCGGGGGGAG	AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"""RING-type (C3HC4) zinc fingers"""	26886	protein-coding gene	gene with protein product		610872	"""IBR domain containing 3"""	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.2064C>G	1.37:g.33402542G>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_153341	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Silent	SNP	ENST00000373456.7	37	CCDS372.2																																																																																			G|0.947;C|0.053	0.053	strong		0.607	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341	
NUP210	23225	hgsc.bcm.edu	37	3	13379400	13379400	+	Silent	SNP	C	C	T	rs3773302	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:13379400C>T	ENST00000254508.5	-	26	3571	c.3489G>A	c.(3487-3489)gaG>gaA	p.E1163E	NUP210_ENST00000485755.1_Intron	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1163					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					GCAGCAGCACCTCCACCTGCA	0.642													C|||	2561	0.511382	0.8026	0.4207	5008	,	,		20915	0.3333		0.5239	False		,,,				2504	0.3528				p.E1163E		Atlas-SNP	.											.	NUP210	182	.	0			c.G3489A						PASS	.	C		3285,1121	705.3+/-407.2	1226,833,144	54.0	47.0	50.0		3489	4.0	1.0	3	dbSNP_107	50	4673,3927	595.6+/-393.5	1278,2117,905	no	coding-synonymous	NUP210	NM_024923.2		2504,2950,1049	TT,TC,CC		45.6628,25.4426,38.8129		1163/1888	13379400	7958,5048	2203	4300	6503	SO:0001819	synonymous_variant	23225	exon26			CAGCACCTCCACC	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.3489G>A	3.37:g.13379400C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1																																																																																			C|0.416;T|0.584	0.584	strong		0.642	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
MUC16	94025	hgsc.bcm.edu	37	19	9083457	9083457	+	Missense_Mutation	SNP	C	C	T	rs17000886	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9083457C>T	ENST00000397910.4	-	1	8561	c.8358G>A	c.(8356-8358)atG>atA	p.M2786I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2786	Ser-rich.|Thr-rich.		M -> I (in dbSNP:rs17000886).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGGTTAGTGGCATCACAGATG	0.498													C|||	953	0.190296	0.0711	0.2709	5008	,	,		21275	0.3036		0.173	False		,,,				2504	0.1953				p.M2786I		Atlas-SNP	.											.	MUC16	4315	.	0			c.G8358A						PASS	.	C	ILE/MET	288,3560		7,274,1643	63.0	61.0	61.0		8358	0.2	0.4	19	dbSNP_123	61	1491,6793		126,1239,2777	yes	missense	MUC16	NM_024690.2	10	133,1513,4420	TT,TC,CC		17.9986,7.4844,14.6637	benign	2786/14508	9083457	1779,10353	1924	4142	6066	SO:0001583	missense	94025	exon1			TAGTGGCATCACA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.8358G>A	19.37:g.9083457C>T	ENSP00000381008:p.Met2786Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	c	5.769	0.326198	0.10900	0.074844	0.179986	ENSG00000181143	ENST00000397910	T	0.02085	4.46	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.33000	0.393	B	0.36030	0.216	T	0.47381	-0.9122	7	0.87932	D	0	.	.	.	.	rs17000886;rs52829317;rs17000886	2786	B5ME49	.	I	2786	ENSP00000381008:M2786I	ENSP00000381008:M2786I	M	-	3	0	MUC16	8944457	0.116000	0.22171	0.407000	0.26434	0.417000	0.31264	0.500000	0.22562	0.308000	0.22923	0.313000	0.20887	ATG	C|0.797;T|0.203	0.203	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TRIM16	10626	hgsc.bcm.edu	37	17	15554504	15554504	+	Silent	SNP	G	G	A	rs4792642	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:15554504G>A	ENST00000578237.1	-	6	1275	c.420C>T	c.(418-420)gcC>gcT	p.A140A	RP11-385D13.1_ENST00000455584.2_Silent_p.A140A|TRIM16_ENST00000336708.7_Silent_p.A140A|TRIM16_ENST00000416464.2_Intron|TRIM16_ENST00000581224.1_Intron|RP11-640I15.1_ENST00000584540.1_RNA			O95361	TRI16_HUMAN	tripartite motif containing 16	140					histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		GGCAGCAGAAGGCAGACAGTG	0.602													G|||	1384	0.276358	0.2829	0.281	5008	,	,		21480	0.3125		0.2107	False		,,,				2504	0.2945				p.A140A		Atlas-SNP	.											.	TRIM16	45	.	0			c.C420T						PASS	.	G		1318,3088	443.3+/-347.0	205,908,1090	147.0	137.0	140.0		420	4.4	1.0	17	dbSNP_111	140	1949,6651	343.2+/-324.8	214,1521,2565	no	coding-synonymous	TRIM16	NM_006470.3		419,2429,3655	AA,AG,GG		22.6628,29.9138,25.1192		140/565	15554504	3267,9739	2203	4300	6503	SO:0001819	synonymous_variant	10626	exon4			GCAGAAGGCAGAC	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.420C>T	17.37:g.15554504G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Silent	SNP	ENST00000578237.1	37	CCDS11171.1	541	0.24771062271062272	134	0.27235772357723576	90	0.24861878453038674	159	0.27797202797202797	158	0.20844327176781002	g	10.27	1.304808	0.23736	0.299138	0.226628	ENSG00000251537	ENST00000455584	.	.	.	5.47	4.44	0.53790	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999375809	.	.	.	.	.	.	T	0.07462	-1.0771	3	.	.	.	.	13.5372	0.61653	0.0:0.2408:0.7592:0.0	rs4792642;rs4792642	.	.	.	L	155	.	.	P	-	2	0	RP11-385D13.1	15495229	0.844000	0.29557	0.998000	0.56505	0.842000	0.47809	0.296000	0.19083	2.563000	0.86464	0.563000	0.77884	CCT	G|0.746;A|0.254	0.254	strong		0.602	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	
CLHC1	130162	hgsc.bcm.edu	37	2	55436934	55436934	+	Missense_Mutation	SNP	G	G	A	rs9677948	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:55436934G>A	ENST00000401408.1	-	6	878	c.533C>T	c.(532-534)gCt>gTt	p.A178V	CLHC1_ENST00000406076.1_Missense_Mutation_p.A56V|CLHC1_ENST00000406437.2_Intron|CLHC1_ENST00000494539.1_Intron|CLHC1_ENST00000407122.1_Missense_Mutation_p.A178V	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	178			A -> V (in dbSNP:rs9677948). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.														TTTAGTGAGAGCATCTAGATT	0.393													G|||	1053	0.210264	0.3699	0.1715	5008	,	,		16962	0.0853		0.2137	False		,,,				2504	0.1472				p.A178V		Atlas-SNP	.											.	.	.	.	0			c.C533T						PASS	.	G	VAL/ALA,VAL/ALA	1585,2821	484.4+/-360.0	288,1009,906	48.0	46.0	46.0		167,533	3.3	0.9	2	dbSNP_119	46	1885,6709	321.3+/-315.0	224,1437,2636	yes	missense,missense	C2orf63	NM_001135598.1,NM_152385.2	64,64	512,2446,3542	AA,AG,GG		21.9339,35.9737,26.6923	benign,benign	56/465,178/587	55436934	3470,9530	2203	4297	6500	SO:0001583	missense	130162	exon6			GTGAGAGCATCTA		CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.533C>T	2.37:g.55436934G>A	ENSP00000384869:p.Ala178Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	57	37	0.649123	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	37	CCDS33201.1	463	0.211996336996337	199	0.40447154471544716	60	0.16574585635359115	43	0.07517482517482517	161	0.21240105540897097	G	19.13	3.767599	0.69878	0.359737	0.219339	ENSG00000162994	ENST00000407122;ENST00000401408;ENST00000406076	T;T;T	0.19669	2.13;2.13;2.15	5.21	3.33	0.38152	.	0.382481	0.23098	N	0.051951	T	0.00012	0.0000	M	0.62723	1.935	0.19300	P	0.9999714307	P	0.52463	0.953	P	0.47744	0.556	T	0.47446	-0.9117	9	0.33141	T	0.24	-5.2384	5.1184	0.14847	0.0801:0.1438:0.6276:0.1485	rs9677948;rs17846200;rs17859215;rs52789690;rs59173455;rs9677948	178	Q8NHS4	CB063_HUMAN	V	178;178;56	ENSP00000385778:A178V;ENSP00000384869:A178V;ENSP00000385512:A56V	ENSP00000384869:A178V	A	-	2	0	C2orf63	55290438	0.991000	0.36638	0.892000	0.35008	0.942000	0.58702	2.381000	0.44336	1.195000	0.43115	0.655000	0.94253	GCT	G|0.762;A|0.238	0.238	strong		0.393	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
CSE1L	1434	hgsc.bcm.edu	37	20	47685320	47685320	+	Silent	SNP	G	G	C	rs2227946	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:47685320G>C	ENST00000262982.2	+	7	759	c.636G>C	c.(634-636)ctG>ctC	p.L212L	CSE1L_ENST00000396192.3_Silent_p.L212L|CSE1L_ENST00000542325.1_Intron	NM_001256135.1|NM_001316.3	NP_001243064.1|NP_001307.2	P55060	XPO2_HUMAN	CSE1 chromosome segregation 1-like (yeast)	212					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	importin-alpha export receptor activity (GO:0008262)			breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	35			BRCA - Breast invasive adenocarcinoma(12;0.000491)|Colorectal(8;0.198)			TTTCTTCCCTGATCCTGATCT	0.358													G|||	746	0.148962	0.2186	0.1844	5008	,	,		17604	0.0407		0.2107	False		,,,				2504	0.0777				p.L212L		Atlas-SNP	.											.	CSE1L	83	.	0			c.G636C						PASS	.	G		938,3468	357.4+/-313.9	99,740,1364	181.0	153.0	162.0		636	2.4	1.0	20	dbSNP_98	162	2133,6467	367.5+/-334.7	250,1633,2417	yes	coding-synonymous	CSE1L	NM_001316.2		349,2373,3781	CC,CG,GG		24.8023,21.2892,23.6122		212/972	47685320	3071,9935	2203	4300	6503	SO:0001819	synonymous_variant	1434	exon7			TTCCCTGATCCTG	U33286	CCDS13412.1, CCDS58773.1	20q13	2013-05-01	2001-11-28		ENSG00000124207	ENSG00000124207		"""Exportins"""	2431	protein-coding gene	gene with protein product	"""cellular apoptosis susceptibility"""	601342	"""chromosome segregation 1 (yeast homolog)-like"""			8963895, 7479798	Standard	NM_001316		Approved	CAS, XPO2, CSE1	uc002xty.4	P55060	OTTHUMG00000033046	ENST00000262982.2:c.636G>C	20.37:g.47685320G>C		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	206	98	0.475728	NM_001256135	A3RLL6|B2R5T4|E1P5Y0|F8W904|O75432|Q32M40|Q9H5B7|Q9NTS0|Q9UP98|Q9UP99|Q9UPA0	Silent	SNP	ENST00000262982.2	37	CCDS13412.1																																																																																			G|0.784;C|0.216	0.216	strong		0.358	CSE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080345.2	NM_001316	
PATE4	399968	hgsc.bcm.edu	37	11	125708293	125708293	+	Missense_Mutation	SNP	T	T	G	rs12224646	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:125708293T>G	ENST00000457514.2	+	3	312	c.268T>G	c.(268-270)Tgt>Ggt	p.C90G	PATE4_ENST00000534411.1_Missense_Mutation_p.C51G	NM_001144874.1	NP_001138346.1	P0C8F1	PATE4_HUMAN	prostate and testis expressed 4	90					regulation of synaptic transmission (GO:0050804)|response to wounding (GO:0009611)	acrosomal vesicle (GO:0001669)|extracellular space (GO:0005615)				breast(1)	1						GACACTGTGCTGTGACAGAAA	0.418													T|||	695	0.138778	0.0242	0.2709	5008	,	,		19377	0.1647		0.1123	False		,,,				2504	0.2004				p.C90G		Atlas-SNP	.											.	PATE4	10	.	0			c.T268G						PASS	.	T	GLY/CYS	50,1334		1,48,643	118.0	105.0	109.0		268	1.1	0.1	11	dbSNP_120	109	344,2838		17,310,1264	yes	missense	PATE4	NM_001144874.1	159	18,358,1907	GG,GT,TT		10.8108,3.6127,8.629	benign	90/99	125708293	394,4172	692	1591	2283	SO:0001583	missense	399968	exon3			CTGTGCTGTGACA	AK123042	CCDS44765.1	11q24.2	2010-07-14			ENSG00000237353	ENSG00000237353		"""PATE family"""	35427	protein-coding gene	gene with protein product						18390568	Standard	NM_001144874		Approved	FLJ41047, PATE-B	uc001qcv.3	P0C8F1	OTTHUMG00000165235	ENST00000457514.2:c.268T>G	11.37:g.125708293T>G	ENSP00000411439:p.Cys90Gly	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	108	90	0.833333	NM_001144874		Missense_Mutation	SNP	ENST00000457514.2	37	CCDS44765.1	302	0.1382783882783883	15	0.03048780487804878	90	0.24861878453038674	107	0.18706293706293706	90	0.11873350923482849	T	4.083	0.013419	0.07912	0.036127	0.108108	ENSG00000237353	ENST00000534411;ENST00000457514	D	0.96136	-3.92	1.11	1.11	0.20524	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	P	0.39131	0.661	B	0.33750	0.169	T	0.49890	-0.8891	7	0.07813	T	0.8	.	4.4187	0.11470	0.0:0.0:0.0:1.0	rs12224646;rs52801203;rs12224646	90	P0C8F1	PATE4_HUMAN	G	51;90	ENSP00000411439:C90G	ENSP00000411439:C90G	C	+	1	0	PATE4	125213503	0.262000	0.24073	0.095000	0.20976	0.484000	0.33280	1.054000	0.30455	0.759000	0.33084	0.383000	0.25322	TGT	T|0.874;G|0.126	0.126	strong		0.418	PATE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382865.1	NM_001144874	
MYOM3	127294	hgsc.bcm.edu	37	1	24406535	24406535	+	Missense_Mutation	SNP	G	G	A	rs35446243	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:24406535G>A	ENST00000374434.3	-	20	2719	c.2557C>T	c.(2557-2559)Cca>Tca	p.P853S	MYOM3_ENST00000330966.7_Missense_Mutation_p.P854S|MYOM3_ENST00000329601.7_Missense_Mutation_p.P853S|RP11-293P20.4_ENST00000429191.1_RNA|RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000475306.1_5'Flank	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	853	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.		P -> S (in dbSNP:rs35446243). {ECO:0000269|PubMed:17974005}.			M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		ATGGGGCCTGGGGTGACCGGC	0.587													G|||	445	0.0888578	0.0091	0.2363	5008	,	,		19087	0.002		0.1859	False		,,,				2504	0.0818				p.P853S		Atlas-SNP	.											.	MYOM3	131	.	0			c.C2557T						PASS	.	G	SER/PRO	161,3759		6,149,1805	68.0	77.0	74.0		2557	1.2	0.4	1	dbSNP_126	74	1653,6647		172,1309,2669	yes	missense	MYOM3	NM_152372.3	74	178,1458,4474	AA,AG,GG		19.9157,4.1071,14.8445	possibly-damaging	853/1438	24406535	1814,10406	1960	4150	6110	SO:0001583	missense	127294	exon20			GGCCTGGGGTGAC	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.2557C>T	1.37:g.24406535G>A	ENSP00000363557:p.Pro853Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	240	0.10989010989010989	10	0.02032520325203252	88	0.2430939226519337	2	0.0034965034965034965	140	0.18469656992084432	G	7.875	0.729060	0.15507	0.041071	0.199157	ENSG00000142661	ENST00000374434;ENST00000330966;ENST00000329601	T;T;T	0.52526	0.66;0.66;0.66	5.51	1.21	0.21127	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.543085	0.20338	N	0.094300	T	0.00012	0.0000	N	0.05534	-0.03	0.80722	P	0.0	B;B	0.17667	0.004;0.023	B;B	0.15052	0.012;0.012	T	0.25572	-1.0128	9	0.19590	T	0.45	.	1.5761	0.02624	0.1609:0.2173:0.4062:0.2155	rs35446243;rs61773553	853;853	Q5VTT5-2;Q5VTT5	.;MYOM3_HUMAN	S	853;854;853	ENSP00000363557:P853S;ENSP00000332670:P854S;ENSP00000328415:P853S	ENSP00000328415:P853S	P	-	1	0	MYOM3	24279122	0.164000	0.22935	0.357000	0.25798	0.376000	0.30014	0.246000	0.18160	0.691000	0.31592	-0.140000	0.14226	CCA	G|0.869;A|0.131	0.131	strong		0.587	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
ENTPD7	57089	hgsc.bcm.edu	37	10	101451259	101451259	+	Missense_Mutation	SNP	T	T	C	rs11190245	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:101451259T>C	ENST00000370489.4	+	8	1005	c.827T>C	c.(826-828)gTc>gCc	p.V276A		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	276			V -> A (in dbSNP:rs11190245). {ECO:0000269|PubMed:14702039}.			cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;4.72e-10)|all cancers(201;3.75e-08)		TCAACCTCTGTCCTTCCTGCA	0.463													T|||	1155	0.230631	0.1785	0.2118	5008	,	,		17738	0.2956		0.3022	False		,,,				2504	0.1738				p.V276A		Atlas-SNP	.											.	ENTPD7	44	.	0			c.T827C						PASS	.	T	ALA/VAL	840,3566	332.8+/-302.6	77,686,1440	111.0	101.0	104.0		827	-1.6	0.9	10	dbSNP_120	104	2540,6060	416.0+/-352.0	380,1780,2140	yes	missense	ENTPD7	NM_020354.3	64	457,2466,3580	CC,CT,TT		29.5349,19.0649,25.988	benign	276/605	101451259	3380,9626	2203	4300	6503	SO:0001583	missense	57089	exon8			CCTCTGTCCTTCC	AF269255	CCDS7480.1	10q23-q24	2004-07-01			ENSG00000198018	ENSG00000198018			19745	protein-coding gene	gene with protein product						11278936	Standard	NM_020354		Approved	LALP1, FLJ30978	uc001kqa.4	Q9NQZ7	OTTHUMG00000018888	ENST00000370489.4:c.827T>C	10.37:g.101451259T>C	ENSP00000359520:p.Val276Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	88	52	0.590909	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	571	0.26144688644688646	93	0.18902439024390244	78	0.2154696132596685	163	0.28496503496503495	237	0.31266490765171506	T	10.00	1.233309	0.22626	0.190649	0.295349	ENSG00000198018	ENST00000370489	T	0.11277	2.79	5.05	-1.58	0.08479	.	0.421504	0.25352	N	0.031284	T	0.00012	0.0000	N	0.04508	-0.205	0.48040	P	4.290000000000127E-4	B	0.09022	0.002	B	0.08055	0.003	T	0.37979	-0.9682	9	0.07325	T	0.83	-0.0184	0.8258	0.01120	0.3396:0.1366:0.128:0.3958	rs11190245;rs57104982;rs11190245	276	Q9NQZ7	ENTP7_HUMAN	A	276	ENSP00000359520:V276A	ENSP00000359520:V276A	V	+	2	0	ENTPD7	101441249	0.918000	0.31147	0.880000	0.34516	0.918000	0.54935	0.223000	0.17719	-0.462000	0.06984	-1.054000	0.02325	GTC	T|0.752;C|0.248	0.248	strong		0.463	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354	
NOTCH4	4855	hgsc.bcm.edu	37	6	32190390	32190390	+	Missense_Mutation	SNP	T	T	G	rs915894	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:32190390T>G	ENST00000375023.3	-	3	487	c.349A>C	c.(349-351)Aag>Cag	p.K117Q		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	117			K -> Q (in dbSNP:rs915894). {ECO:0000269|PubMed:14574404, ECO:0000269|Ref.4}.		cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						TCTTCAAGCTTGGCCTGGCAT	0.627													G|||	1997	0.398762	0.3714	0.3285	5008	,	,		18522	0.5109		0.3519	False		,,,				2504	0.4182				p.K117Q		Atlas-SNP	.											.	NOTCH4	201	.	0			c.A349C						PASS	.	G	GLN/LYS	1664,2742	646.3+/-398.3	324,1016,863	66.0	70.0	69.0		349	2.4	0.0	6	dbSNP_86	69	3177,5423	645.4+/-400.2	590,1997,1713	yes	missense	NOTCH4	NM_004557.3	53	914,3013,2576	GG,GT,TT		36.9419,37.7667,37.2213	benign	117/2004	32190390	4841,8165	2203	4300	6503	SO:0001583	missense	4855	exon3			CAAGCTTGGCCTG		CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.349A>C	6.37:g.32190390T>G	ENSP00000364163:p.Lys117Gln	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	156	155	0.99359	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	836	0.38278388278388276	159	0.3231707317073171	120	0.3314917127071823	286	0.5	271	0.3575197889182058	G	3.312	-0.140568	0.06669	0.377667	0.369419	ENSG00000204301	ENST00000375023	D	0.91843	-2.92	3.28	2.36	0.29203	.	2.488560	0.01877	N	0.037616	T	0.74291	0.3697	N	0.12853	0.265	0.09310	P	0.99999858293	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.58752	-0.7581	9	0.38643	T	0.18	.	9.6611	0.39956	0.0:0.0:0.6258:0.3742	rs915894;rs17604639;rs915894	117;117	Q6P3V5;Q99466	.;NOTC4_HUMAN	Q	117	ENSP00000364163:K117Q	ENSP00000364163:K117Q	K	-	1	0	NOTCH4	32298368	0.008000	0.16893	0.025000	0.17156	0.073000	0.16967	1.331000	0.33793	0.361000	0.24292	-0.217000	0.12591	AAG	T|0.623;G|0.377	0.377	strong		0.627	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
ZFHX3	463	hgsc.bcm.edu	37	16	72993706	72993706	+	Silent	SNP	G	G	A	rs62053191	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:72993706G>A	ENST00000268489.5	-	2	1011	c.339C>T	c.(337-339)gcC>gcT	p.A113A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	113					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				CGGTGTCGCTGGCGCTCTCCT	0.672													G|||	137	0.0273562	0.0061	0.0303	5008	,	,		12816	0.002		0.0596	False		,,,				2504	0.047				p.A113A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C339T						PASS	.	G	,	72,4324		1,70,2127	22.0	23.0	23.0		,339	-0.8	1.0	16	dbSNP_129	23	584,8000		21,542,3729	no	intron,coding-synonymous	ZFHX3	NM_001164766.1,NM_006885.3	,	22,612,5856	AA,AG,GG		6.8034,1.6379,5.0539	,	,113/3704	72993706	656,12324	2198	4292	6490	SO:0001819	synonymous_variant	463	exon2			GTCGCTGGCGCTC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.339C>T	16.37:g.72993706G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			G|0.958;A|0.042	0.042	strong		0.672	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
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 GAIIx	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	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	129	31	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	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57081146	57081146	+	Missense_Mutation	SNP	G	G	C	rs12364724	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57081146G>C	ENST00000532437.1	-	4	1327	c.1016C>G	c.(1015-1017)cCa>cGa	p.P339R	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P339R			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	339	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				GGCTGCACTTGGAGCTGATGG	0.682													G|||	196	0.0391374	0.0113	0.0576	5008	,	,		11229	0.0179		0.0885	False		,,,				2504	0.0348				p.P339R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.C1016G						PASS	.	G	ARG/PRO	78,4226		2,74,2076	13.0	17.0	16.0		1016	0.8	0.0	11	dbSNP_120	16	818,7726		34,750,3488	yes	missense	TNKS1BP1	NM_033396.2	103	36,824,5564	CC,CG,GG		9.574,1.8123,6.9738	probably-damaging	339/1730	57081146	896,11952	2152	4272	6424	SO:0001583	missense	85456	exon5			GCACTTGGAGCTG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1016C>G	11.37:g.57081146G>C	ENSP00000437271:p.Pro339Arg	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	98	39	0.397959	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	107	0.04899267399267399	10	0.02032520325203252	24	0.06629834254143646	10	0.017482517482517484	63	0.08311345646437995	G	14.30	2.492988	0.44352	0.018123	0.09574	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.38560	1.13;1.13	4.11	0.747	0.18371	.	0.558107	0.13607	N	0.375363	T	0.00998	0.0033	L	0.34521	1.04	0.09310	N	1	P	0.49635	0.926	P	0.52481	0.7	T	0.03268	-1.1054	10	0.72032	D	0.01	-0.2204	0.6374	0.00804	0.2568:0.184:0.371:0.1881	rs12364724	339	Q9C0C2	TB182_HUMAN	R	339	ENSP00000350990:P339R;ENSP00000437271:P339R	ENSP00000350990:P339R	P	-	2	0	TNKS1BP1	56837722	0.010000	0.17322	0.006000	0.13384	0.104000	0.19210	0.291000	0.18994	0.301000	0.22738	0.462000	0.41574	CCA	G|0.949;C|0.051	0.051	strong		0.682	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
IL10RB	3588	hgsc.bcm.edu	37	21	34640788	34640788	+	Missense_Mutation	SNP	A	A	G	rs2834167	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:34640788A>G	ENST00000290200.2	+	2	247	c.139A>G	c.(139-141)Aaa>Gaa	p.K47E	IL10RB-AS1_ENST00000411998.1_RNA|AP000295.9_ENST00000433395.2_Silent_p.P174P	NM_000628.4	NP_000619.3	Q08334	I10R2_HUMAN	interleukin 10 receptor, beta	47	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		K -> E (associated with susceptibility to HBV infection; higher cell surface levels; dbSNP:rs2834167). {ECO:0000269|PubMed:16757563, ECO:0000269|Ref.4}.		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	14						TGCTTTTGCCAAAGGGAACCT	0.493													A|||	1700	0.339457	0.0855	0.5014	5008	,	,		20653	0.5635		0.2684	False		,,,				2504	0.41				p.K47E	Melanoma(67;315 1275 21667 21943 44564)	Atlas-SNP	.											.	IL10RB	37	.	0			c.A139G	GRCh37	CM066574	IL10RB	M	rs2834167	PASS	.	A	GLU/LYS	576,3830	257.4+/-261.8	23,530,1650	96.0	88.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	139	2.6	1.0	21	dbSNP_100	91	2214,6386	376.3+/-338.1	290,1634,2376	yes	missense	IL10RB	NM_000628.3	56	313,2164,4026	GG,GA,AA		25.7442,13.0731,21.4516		47/326	34640788	2790,10216	2203	4300	6503	SO:0001583	missense	3588	exon2			TTTGCCAAAGGGA	U08988	CCDS13623.1	21q22.11	2014-09-17			ENSG00000243646	ENSG00000243646		"""Interleukins and interleukin receptors"", ""CD molecules"""	5965	protein-coding gene	gene with protein product		123889		CRFB4, D21S58, D21S66		8314576, 9312047	Standard	NM_000628		Approved	CRF2-4, CDW210B, IL-10R2		Q08334	OTTHUMG00000065128	ENST00000290200.2:c.139A>G	21.37:g.34640788A>G	ENSP00000290200:p.Lys47Glu	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	148	98	0.662162	NM_000628	Q9BUU4	Missense_Mutation	SNP	ENST00000290200.2	37	CCDS13623.1	755	0.3456959706959707	47	0.09552845528455285	172	0.47513812154696133	323	0.5646853146853147	213	0.28100263852242746	A	15.76	2.927466	0.52759	0.130731	0.257442	ENSG00000243646	ENST00000290200;ENST00000539894	T	0.72835	-0.69	5.35	2.61	0.31194	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.428243	0.24405	N	0.038805	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	P;B	0.37122	0.583;0.392	B;B	0.38880	0.284;0.109	T	0.51779	-0.8662	9	0.25751	T	0.34	-16.1558	5.6759	0.17747	0.6598:0.1733:0.0:0.1669	rs2834167;rs52815411;rs61161628;rs2834167	47;47	Q08334;F5H766	I10R2_HUMAN;.	E	47	ENSP00000290200:K47E	ENSP00000290200:K47E	K	+	1	0	IL10RB	33562658	0.741000	0.28217	0.992000	0.48379	0.968000	0.65278	0.790000	0.26900	2.021000	0.59480	0.533000	0.62120	AAA	A|0.728;G|0.272	0.272	strong		0.493	IL10RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139831.3		
MRTO4	51154	hgsc.bcm.edu	37	1	19583636	19583636	+	Silent	SNP	C	C	T	rs1126682	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19583636C>T	ENST00000330263.4	+	4	567	c.270C>T	c.(268-270)caC>caT	p.H90H		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	90					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		ACAACCTGCACCAGGTAAGTC	0.557													C|||	681	0.135982	0.1293	0.1311	5008	,	,		20981	0.0238		0.2008	False		,,,				2504	0.1973				p.H90H	GBM(192;2418 3032 7540 48714)	Atlas-SNP	.											MRTO4,NS,carcinoma,0,1	MRTO4	17	1	0			c.C270T						PASS	.	C		595,3811	261.0+/-264.0	43,509,1651	184.0	174.0	178.0		270	0.2	1.0	1	dbSNP_86	178	1553,7047	292.8+/-301.0	141,1271,2888	no	coding-synonymous	MRTO4	NM_016183.3		184,1780,4539	TT,TC,CC		18.0581,13.5043,16.5155		90/240	19583636	2148,10858	2203	4300	6503	SO:0001819	synonymous_variant	51154	exon4			CCTGCACCAGGTA	AK027569	CCDS191.1	1p36.13	2008-02-05	2006-12-21	2007-01-05	ENSG00000053372	ENSG00000053372			18477	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 33"", ""MRT4, mRNA turnover 4, homolog (S. cerevisiae)"""	C1orf33			Standard	NM_016183		Approved	dJ657E11.4, MRT4	uc001bbs.3	Q9UKD2	OTTHUMG00000002496	ENST00000330263.4:c.270C>T	1.37:g.19583636C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	94	39	0.414894	NM_016183	B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	CCDS191.1																																																																																			C|0.842;T|0.158	0.158	strong		0.557	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
CCDC6	8030	hgsc.bcm.edu	37	10	61552692	61552692	+	Missense_Mutation	SNP	G	G	T	rs1053266	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:61552692G>T	ENST00000263102.6	-	9	1639	c.1408C>A	c.(1408-1410)Ccc>Acc	p.P470T		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	470			P -> T (in dbSNP:rs1053266). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8058316, ECO:0000269|Ref.4}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)	p.P470T(1)	CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		TGGGAGGAGGGGTGCGCCGAA	0.597			T	RET	NSCLC								G|||	2180	0.435304	0.1989	0.598	5008	,	,		16944	0.6121		0.4503	False		,,,				2504	0.4417				p.P470T		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	CCDC6,NS,carcinoma,0,1	CCDC6	44	1	1	Substitution - Missense(1)	stomach(1)	c.C1408A						PASS	.	G	THR/PRO	1164,3242	411.7+/-335.8	177,810,1216	146.0	139.0	142.0		1408	5.6	1.0	10	dbSNP_86	142	4329,4271	579.5+/-390.9	1098,2133,1069	yes	missense	CCDC6	NM_005436.4	38	1275,2943,2285	TT,TG,GG		49.6628,26.4185,42.2344	probably-damaging	470/475	61552692	5493,7513	2203	4300	6503	SO:0001583	missense	8030	exon9			AGGAGGGGTGCGC	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.1408C>A	10.37:g.61552692G>T	ENSP00000263102:p.Pro470Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_005436	Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	37	CCDS7257.1	1001	0.4583333333333333	109	0.22154471544715448	211	0.5828729281767956	328	0.5734265734265734	353	0.4656992084432718	G	17.13	3.311702	0.60414	0.264185	0.503372	ENSG00000108091	ENST00000263102	T	0.55052	0.54	5.6	5.6	0.85130	.	0.410909	0.25467	N	0.030472	T	0.00012	0.0000	L	0.44542	1.39	0.09310	P	0.999999823558	D	0.71674	0.998	D	0.76071	0.987	T	0.51482	-0.8700	9	0.66056	D	0.02	1.6527	19.9854	0.97342	0.0:0.0:1.0:0.0	rs1053266;rs3193780;rs3750802;rs57560743;rs1053266	470	Q16204	CCDC6_HUMAN	T	470	ENSP00000263102:P470T	ENSP00000263102:P470T	P	-	1	0	CCDC6	61222698	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.852000	0.92215	2.786000	0.95864	0.563000	0.77884	CCC	G|0.577;T|0.423	0.423	strong		0.597	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
MICAL2	9645	hgsc.bcm.edu	37	11	12183846	12183846	+	Silent	SNP	C	C	T	rs28625145|rs111445151	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:12183846C>T	ENST00000256194.4	+	3	432	c.144C>T	c.(142-144)aaC>aaT	p.N48N	MICAL2_ENST00000342902.5_Silent_p.N48N|MICAL2_ENST00000527546.1_Silent_p.N48N|MICAL2_ENST00000537344.1_Silent_p.N48N|MICAL2_ENST00000379612.3_Silent_p.N48N	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	48	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|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)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		ACCACAGAAACTTTTATTCCA	0.493													C|||	885	0.176717	0.1702	0.2118	5008	,	,		19646	0.1528		0.2107	False		,,,				2504	0.1503				p.N48N		Atlas-SNP	.											.	MICAL2	114	.	0			c.C144T						PASS	.	C		756,3646	307.7+/-290.2	71,614,1516	66.0	65.0	66.0		144	2.7	1.0	11	dbSNP_125	66	1693,6895	311.4+/-310.3	160,1373,2761	no	coding-synonymous	MICAL2	NM_014632.2		231,1987,4277	TT,TC,CC		19.7136,17.174,18.853		48/1125	12183846	2449,10541	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon3			CAGAAACTTTTAT	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.144C>T	11.37:g.12183846C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			C|0.813;T|0.187	0.187	strong		0.493	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16842991	16842991	+	Missense_Mutation	SNP	G	G	A	rs34562254	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:16842991G>A	ENST00000261652.2	-	5	764	c.752C>T	c.(751-753)cCc>cTc	p.P251L	TNFRSF13B_ENST00000579315.1_Intron|TNFRSF13B_ENST00000437538.2_Missense_Mutation_p.P205L|TNFRSF13B_ENST00000581616.2_5'Flank|TNFRSF13B_ENST00000583789.1_Missense_Mutation_p.P205L	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	251			P -> L (in dbSNP:rs34562254). {ECO:0000269|PubMed:14702039}.		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						AGTGGGGTCGGGGGTCCCAGG	0.652									IgA Deficiency, Selective				.|||	955	0.190695	0.1399	0.1182	5008	,	,		15407	0.4236		0.1064	False		,,,				2504	0.1575				p.P251L		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.C752T						PASS	.	G	LEU/PRO	589,3817	253.7+/-259.5	41,507,1655	37.0	34.0	35.0		752	0.9	0.0	17	dbSNP_126	35	945,7655	203.0+/-246.1	51,843,3406	yes	missense	TNFRSF13B	NM_012452.2	98	92,1350,5061	AA,AG,GG		10.9884,13.3681,11.7946	probably-damaging	251/294	16842991	1534,11472	2203	4300	6503	SO:0001583	missense	23495	exon5	Familial Cancer Database	IGAD1, IGAD2	GGGTCGGGGGTCC	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.752C>T	17.37:g.16842991G>A	ENSP00000261652:p.Pro251Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Missense_Mutation	SNP	ENST00000261652.2	37	CCDS11181.1	395	0.18086080586080586	59	0.11991869918699187	35	0.09668508287292818	222	0.3881118881118881	79	0.10422163588390501	G	5.925	0.354776	0.11239	0.133681	0.109884	ENSG00000240505	ENST00000437538;ENST00000261652	D;D	0.92647	-3.03;-3.08	3.12	0.879	0.19155	.	0.652988	0.14091	N	0.342023	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	P;P	0.40731	0.698;0.728	P;B	0.45310	0.476;0.284	T	0.46965	-0.9153	9	0.02654	T	1	-1.6478	2.8954	0.05689	0.1597:0.0:0.5137:0.3266	rs34562254	205;251	O14836-2;O14836	.;TR13B_HUMAN	L	205;251	ENSP00000413453:P205L;ENSP00000261652:P251L	ENSP00000261652:P251L	P	-	2	0	TNFRSF13B	16783716	0.001000	0.12720	0.003000	0.11579	0.013000	0.08279	-0.051000	0.11885	0.505000	0.28104	0.448000	0.29417	CCC	G|0.865;A|0.135	0.135	strong		0.652	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2		
NLRC5	84166	hgsc.bcm.edu	37	16	57060340	57060340	+	Silent	SNP	T	T	C	rs34531240	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57060340T>C	ENST00000262510.6	+	6	1710	c.1485T>C	c.(1483-1485)acT>acC	p.T495T	NLRC5_ENST00000539144.1_Silent_p.T495T|NLRC5_ENST00000308149.7_Silent_p.T495T|NLRC5_ENST00000436936.1_Silent_p.T495T	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	495	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				GCCTGCTGACTTCCTTCTGCG	0.572													T|||	1408	0.28115	0.1589	0.1988	5008	,	,		21819	0.5933		0.1272	False		,,,				2504	0.3415				p.T495T		Atlas-SNP	.											.	NLRC5	186	.	0			c.T1485C						PASS	.	T		773,3623	310.8+/-291.8	76,621,1501	53.0	52.0	52.0		1485	2.2	1.0	16	dbSNP_126	52	907,7693	200.0+/-243.9	53,801,3446	no	coding-synonymous	NLRC5	NM_032206.3		129,1422,4947	CC,CT,TT		10.5465,17.5842,12.9271		495/1867	57060340	1680,11316	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon5			GCTGACTTCCTTC	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1485T>C	16.37:g.57060340T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	98	34	0.346939	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	559	0.25595238095238093	75	0.1524390243902439	54	0.14917127071823205	335	0.5856643356643356	95	0.12532981530343007	T	3.065	-0.192349	0.06259	0.175842	0.105465	ENSG00000140853	ENST00000538805	.	.	.	5.4	2.19	0.27852	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999720056	.	.	.	.	.	.	T	0.46830	-0.9163	3	.	.	.	.	7.4693	0.27340	0.0:0.5093:0.0:0.4907	rs34531240	.	.	.	L	248	.	.	F	+	1	0	NLRC5	55617841	0.941000	0.31946	1.000000	0.80357	0.374000	0.29953	-0.077000	0.11394	0.190000	0.20209	-0.232000	0.12228	TTC	T|0.837;C|0.163	0.163	strong		0.572	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
BIN1	274	hgsc.bcm.edu	37	2	127816632	127816632	+	Silent	SNP	G	G	A	rs2276579	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:127816632G>A	ENST00000316724.5	-	11	1368	c.957C>T	c.(955-957)gcC>gcT	p.A319A	BIN1_ENST00000346226.3_Silent_p.A288A|BIN1_ENST00000351659.3_Silent_p.A319A|BIN1_ENST00000409400.1_Silent_p.A288A|BIN1_ENST00000393041.3_Silent_p.A288A|BIN1_ENST00000352848.3_Silent_p.A303A|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000376113.2_Silent_p.A303A|BIN1_ENST00000259238.4_Silent_p.A303A|BIN1_ENST00000393040.3_Silent_p.A288A|BIN1_ENST00000348750.4_Silent_p.A288A|BIN1_ENST00000357970.3_Silent_p.A319A	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	319					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		tggccccgccggccggcTCTG	0.672													G|||	474	0.0946486	0.0129	0.1859	5008	,	,		10779	0.0486		0.1889	False		,,,				2504	0.091				p.A319A		Atlas-SNP	.											.	BIN1	85	.	0			c.C957T						PASS	.	G	,,,,,,,,,	159,4203		4,151,2026	15.0	19.0	17.0		909,957,957,957,909,864,864,864,864,864	0.0	0.0	2	dbSNP_100	17	1632,6900		159,1314,2793	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	163,1465,4819	AA,AG,GG		19.128,3.6451,13.8902	,,,,,,,,,	303/455,319/594,319/551,319/507,303/498,288/519,288/483,288/476,288/440,288/410	127816632	1791,11103	2181	4266	6447	SO:0001819	synonymous_variant	274	exon11			CCCGCCGGCCGGC	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.957C>T	2.37:g.127816632G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	33	25	0.757576	NM_139345	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			G|0.886;A|0.114	0.114	strong		0.672	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
PTGS1	5742	hgsc.bcm.edu	37	9	125143973	125143973	+	Missense_Mutation	SNP	C	C	A	rs5789	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:125143973C>A	ENST00000362012.2	+	7	714	c.709C>A	c.(709-711)Ctg>Atg	p.L237M	PTGS1_ENST00000540753.1_Missense_Mutation_p.L212M|PTGS1_ENST00000223423.4_Missense_Mutation_p.L237M|PTGS1_ENST00000373698.5_Missense_Mutation_p.L128M	NM_000962.3|NM_001271164.1|NM_001271367.1|NM_080591.2	NP_000953.2|NP_001258093.1|NP_001258296.1|NP_542158.1	P23219	PGH1_HUMAN	prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)	237			L -> M (in dbSNP:rs5789). {ECO:0000269|PubMed:15308583, ECO:0000269|Ref.8}.		arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|prostaglandin biosynthetic process (GO:0001516)|regulation of blood pressure (GO:0008217)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|photoreceptor outer segment (GO:0001750)	dioxygenase activity (GO:0051213)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)			large_intestine(3)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	8					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bortezomib(DB00188)|Bromfenac(DB00963)|Candesartan(DB00796)|Carprofen(DB00821)|Carvedilol(DB01136)|Chlorpropamide(DB00672)|Dapsone(DB00250)|Desmopressin(DB00035)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Diphenhydramine(DB01075)|Dronabinol(DB00470)|Eletriptan(DB00216)|Eszopiclone(DB00402)|Etodolac(DB00749)|Etoposide(DB00773)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Hexobarbital(DB01355)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Icosapent(DB00159)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indomethacin(DB00328)|Irbesartan(DB01029)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Minoxidil(DB00350)|Montelukast(DB00471)|Nabumetone(DB00461)|Naproxen(DB00788)|Nateglinide(DB00731)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nortriptyline(DB00540)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Rosiglitazone(DB00412)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfamethoxazole(DB01015)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Torasemide(DB00214)|Trabectedin(DB05109)|Triflusal(DB08814)|Trisalicylate-choline(DB01401)|Valproic Acid(DB00313)|Voriconazole(DB00582)|Zafirlukast(DB00549)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TGGAGACAATCTGGAGCGTCA	0.582													C|||	65	0.0129792	0.0008	0.0274	5008	,	,		17236	0.0		0.0348	False		,,,				2504	0.0102				p.L237M		Atlas-SNP	.											.	PTGS1	84	.	0			c.C709A	GRCh37	CM071954	PTGS1	M	rs5789	PASS	.	C	MET/LEU,MET/LEU	21,4385	29.0+/-57.7	0,21,2182	52.0	51.0	52.0		709,709	4.8	1.0	9	dbSNP_52	52	242,8358	97.5+/-159.1	4,234,4062	yes	missense,missense	PTGS1	NM_000962.2,NM_080591.1	15,15	4,255,6244	AA,AC,CC		2.814,0.4766,2.0221	benign,benign	237/600,237/563	125143973	263,12743	2203	4300	6503	SO:0001583	missense	5742	exon7			GACAATCTGGAGC	M59979	CCDS6842.1, CCDS6843.1, CCDS59520.1, CCDS59521.1, CCDS75895.1	9q32-q33.3	2008-02-05			ENSG00000095303	ENSG00000095303	1.14.99.1		9604	protein-coding gene	gene with protein product		176805				2512924, 1907252	Standard	NM_000962		Approved	COX1, PGHS-1, PTGHS	uc004bmg.2	P23219	OTTHUMG00000020605	ENST00000362012.2:c.709C>A	9.37:g.125143973C>A	ENSP00000354612:p.Leu237Met	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_000962	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Missense_Mutation	SNP	ENST00000362012.2	37	CCDS6842.1	39	0.017857142857142856	0	0.0	14	0.03867403314917127	0	0.0	25	0.032981530343007916	C	15.52	2.858868	0.51376	0.004766	0.02814	ENSG00000095303	ENST00000540753;ENST00000362012;ENST00000223423;ENST00000426608;ENST00000373698	T;T;T;T;T	0.69306	-0.39;-0.39;-0.39;-0.39;-0.39	4.82	4.82	0.62117	.	0.067485	0.64402	D	0.000009	T	0.56187	0.1968	M	0.86420	2.815	0.58432	D	0.999999	D;B;B	0.76494	0.999;0.37;0.338	D;B;B	0.79108	0.992;0.177;0.26	T	0.75233	-0.3390	10	0.56958	D	0.05	-15.6693	10.6416	0.45596	0.0:0.9131:0.0:0.0869	rs5789;rs3842796;rs4987007;rs57008519;rs5789	212;237;237	B4DHQ2;P23219;P23219-2	.;PGH1_HUMAN;.	M	212;237;237;131;128	ENSP00000437709:L212M;ENSP00000354612:L237M;ENSP00000223423:L237M;ENSP00000411606:L131M;ENSP00000362802:L128M	ENSP00000223423:L237M	L	+	1	2	PTGS1	124183794	0.981000	0.34729	0.968000	0.41197	0.909000	0.53808	2.567000	0.45956	2.505000	0.84491	0.555000	0.69702	CTG	C|0.979;A|0.021	0.021	strong		0.582	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1		
OR4N2	390429	hgsc.bcm.edu	37	14	20296226	20296226	+	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20296226A>G	ENST00000315947.1	+	1	619	c.619A>G	c.(619-621)Aca>Gca	p.T207A	OR4N2_ENST00000568211.1_3'UTR	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	207						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(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGGCCTGATGACACTCCTGTG	0.522																																					p.T207A		Atlas-SNP	.											OR4N2,right_upper_lobe,carcinoma,-1,2	OR4N2	125	2	0			c.A619G						scavenged	.						138.0	137.0	137.0					14																	20296226		2203	4300	6503	SO:0001583	missense	390429	exon1			CTGATGACACTCC		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.619A>G	14.37:g.20296226A>G	ENSP00000319601:p.Thr207Ala	Somatic	369	3	0.00813008		WXS	Illumina HiSeq	Phase_I	426	7	0.0164319	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	5.907	0.351367	0.11182	.	.	ENSG00000176294	ENST00000315947	T	0.36878	1.23	4.52	0.84	0.18912	GPCR, rhodopsin-like superfamily (1);	0.126220	0.36200	N	0.002736	T	0.17534	0.0421	N	0.20685	0.6	0.09310	N	1	B	0.30605	0.287	B	0.32149	0.141	T	0.08700	-1.0709	10	0.27082	T	0.32	-16.7831	2.5862	0.04831	0.5054:0.0:0.2951:0.1995	.	207	Q8NGD1	OR4N2_HUMAN	A	207	ENSP00000319601:T207A	ENSP00000319601:T207A	T	+	1	0	OR4N2	19366066	0.000000	0.05858	0.028000	0.17463	0.558000	0.35554	-0.237000	0.08990	0.310000	0.22990	0.477000	0.44152	ACA	.	.	none		0.522	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
MUC2	4583	hgsc.bcm.edu	37	11	1083293	1083293	+	Silent	SNP	T	T	C	rs7394853	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 GAIIx	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1083293T>C	ENST00000441003.2	+	16	2220	c.2193T>C	c.(2191-2193)gaT>gaC	p.D731D	MUC2_ENST00000359061.5_Silent_p.D731D	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	731					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)	AGGCGGGGGATGTGGTCGTCA	0.672													C|||	1860	0.371406	0.444	0.366	5008	,	,		14043	0.3919		0.2167	False		,,,				2504	0.4151				p.D731D		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.T2193C						PASS	.			1636,2364		342,952,706	25.0	30.0	28.0		2193	-8.5	0.0	11	dbSNP_116	28	1685,6627		181,1323,2652	no	coding-synonymous	MUC2	NM_002457.2		523,2275,3358	CC,CT,TT		20.2719,40.9,26.9737		731/2813	1083293	3321,8991	2000	4156	6156	SO:0001819	synonymous_variant	4583	exon16			GGGGGATGTGGTC	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.2193T>C	11.37:g.1083293T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.705;C|0.295	0.295	strong		0.672	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
